diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 164bc05d60..7d1f1a417b 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -29,6 +29,7 @@ src/USER-MEAMC/* @martok src/USER-MOFFF/* @hheenen src/USER-MOLFILE/* @akohlmey src/USER-NETCDF/* @pastewka +src/USER-PLUMED/* @gtribello src/USER-PHONON/* @lingtikong src/USER-PTM/* @pmla src/USER-OMP/* @akohlmey @@ -125,3 +126,6 @@ python/* @rbberger doc/utils/*/* @rbberger doc/Makefile @rbberger doc/README @rbberger + +# for releases +src/version.h @sjplimp diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md new file mode 100644 index 0000000000..0e681c280d --- /dev/null +++ b/.github/CODE_OF_CONDUCT.md @@ -0,0 +1,67 @@ +# Code of Conduct for the LAMMPS Project on GitHub + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as LAMMPS +developers, contributors, and maintainers pledge to making participation in +our project a harassment-free experience for everyone. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment +include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of explicit language or imagery +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic + address, without explicit permission + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, issues, and other contributions that are not +aligned to this Code of Conduct, or to ban temporarily or permanently any +developer, maintainer, or contributor for this or other behaviors that they +deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies to all public exchanges in the LAMMPS project +on GitHub and in submitted code. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at developer@lammps.org. All +complaints will be reviewed and investigated and will result in a response +that is deemed necessary and appropriate to the circumstances. The project +team is obligated to maintain confidentiality with regard to the reporter +of an incident. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, +available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see +https://www.contributor-covenant.org/faq + diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 1631fd618c..5a67c547df 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -2,10 +2,10 @@ Thank your for considering to contribute to the LAMMPS software project. -The following is a set of guidelines as well as explanations of policies and workflows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project. +The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project. Thus please also have a look at: -* [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15) +* [The Section on submitting new features for inclusion in LAMMPS of the Manual](https://lammps.sandia.gov/doc/Modify_contribute.html) * [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html) ## Table of Contents @@ -18,7 +18,7 @@ Thus please also have a look at: * [Suggesting Enhancements](#suggesting-enhancements) * [Contributing Code](#contributing-code) -[GitHub Workflows](#github-workflows) +[GitHub Work flows](#github-workflows) * [Issues](#issues) * [Pull Requests](#pull-requests) @@ -26,17 +26,17 @@ __ ## I don't want to read this whole thing I just have a question! -> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](http://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. +> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. ## How Can I Contribute? There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code -to one of the [LAMMPS core developers](http://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers. +to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers. ### Discussing How To Use LAMMPS The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours. -You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response. +You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response. Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better. @@ -44,7 +44,7 @@ If you post a message and you are a subscriber, your message will appear immedia ### Reporting Bugs -While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](http://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version. +While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version. When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions. You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly). @@ -62,13 +62,13 @@ To be able to submit an issue on GitHub, you have to register for an account (fo We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others. -How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/Howto_github.html) +How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](https://lammps.sandia.gov/doc/Howto_github.html) for instructions on how to submit your changes or new files through a GitHub pull request Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list. * All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI. -* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, class header files should not import any system headers outside , STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. Header files must not import namespaces with using. This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. +* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, style class header files should not import any system headers outside of , STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included ( instead of , or instead of ). This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. * If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `.cpp` and `.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. * If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. * Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. @@ -102,10 +102,10 @@ For bug reports, the next step is that one of the core LAMMPS developers will se ### Pull Requests -For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers. +For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers. Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub. -Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. -You may also receive comments and suggestions on the overall submission or specific details. If permitted, additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes. +Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). +You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes. The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer. If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork. Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted. diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md deleted file mode 100644 index 53a17a1476..0000000000 --- a/.github/ISSUE_TEMPLATE.md +++ /dev/null @@ -1,31 +0,0 @@ -## Summary - -_Please provide a brief description of the issue_ - -## Type of Issue - -_Is this a 'Bug Report' or a 'Suggestion for an Enhancement'?_ - -## Detailed Description (Enhancement Suggestion) - -_Explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, provide references to relevant background information, and whether you are willing to implement the enhancement yourself or would like to participate in the implementation_ - -## LAMMPS Version (Bug Report) - -_Please specify which LAMMPS version this issue was detected with. If this is not the latest development version, please stop and test that version, too, and report it here if the bug persists_ - -## Expected Behavior (Bug Report) - -_Describe the expected behavior. Quote from the LAMMPS manual where needed or explain why the expected behavior is meaningful, especially when it differs from the manual_ - -## Actual Behavior (Bug Report) - -_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. Try to be specific and do **not* use vague terms like "doesn't work" or "wrong result". Do not assume that the person reading this has any experience with or knowledge of your specific research._ - -## Steps to Reproduce (Bug Report) - -_Describe the steps required to quickly reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create input that are as small as possible and run as fast as possible. NOTE: the less effort and time it takes to reproduce your issue, the more likely, that somebody will look into it._ - -## Further Information, Files, and Links - -_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_ diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000000..91b7e2bf48 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,32 @@ +--- +name: Bug report +about: Create a bug report to help us eliminate issues and improve LAMMPS +title: "[BUG] _Replace With Suitable Title_" +labels: bug +assignees: '' + +--- + +**Summary** + +_Please provide a clear and concise description of what the bug is._ + +**LAMMPS Version and Platform** + +_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_ + +**Expected Behavior** + +_Describe the expected behavior. Quote from the LAMMPS manual where needed, or explain why the expected behavior is meaningful, especially when it differs from the manual_ + +**Actual Behavior** + +_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. Try to be specific and do **not** use vague terms like "doesn't work" or "wrong result". Do not assume that the person reading this has any experience with or knowledge of your specific area of research._ + +**Steps to Reproduce** + +_Describe the steps required to (quickly) reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem._ + +**Further Information, Files, and Links** + +_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_ diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000000..a3a70c0d5a --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Make a suggestion for a new feature or a change to LAMMPS +title: "[Feature Request] _Replace with Title_" +labels: enhancement +assignees: '' + +--- + +**Summary** + +_Please provide a brief and concise description of the suggested feature or change_ + +**Detailed Description** + +_Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address._ + +**Further Information, Files, and Links** + +_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_ diff --git a/.github/ISSUE_TEMPLATE/generic.md b/.github/ISSUE_TEMPLATE/generic.md new file mode 100644 index 0000000000..15d2763919 --- /dev/null +++ b/.github/ISSUE_TEMPLATE/generic.md @@ -0,0 +1,21 @@ +--- +name: Generic Issue +about: For issues that do not fit any of the other categories +title: "_Replace With a Descriptive Title_" +labels: +assignees: '' + +--- + +**Summary** + +_Please provide a clear and concise description of what this issue report is about._ + +**LAMMPS Version and Platform** + +_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_ + +**Details** + +_Please explain the issue in detail here_ + diff --git a/.github/ISSUE_TEMPLATE/help_request.md b/.github/ISSUE_TEMPLATE/help_request.md new file mode 100644 index 0000000000..5e5b3ebffd --- /dev/null +++ b/.github/ISSUE_TEMPLATE/help_request.md @@ -0,0 +1,15 @@ +--- +name: Request for Help +about: "Don't post help requests here, email the lammps-users mailing list" +title: "" +labels: invalid +assignees: '' + +--- + +Please **do not** post requests for help (e.g. with installing or using LAMMPS) here. +Instead send an e-mail to the lammps-users mailing list. + +This issue tracker is for tracking LAMMPS development related issues only. + +Thanks for your cooperation. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 77c81ea69d..9e43aa0244 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,28 +1,43 @@ -## Purpose +**Summary** -_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request. If this addresses an open GitHub Issue, mention the issue number, e.g. with `fixes #221` or `closes #135`, so that issue will be automatically closed when the pull request is merged_ +_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request._ -## Author(s) +**Related Issues** -_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_ +_If this addresses an open GitHub issue for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_ -## Backward Compatibility +**Author(s)** -_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_ +_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (ideally something that can outlive your institution's e-mail, in case you change jobs) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this contributed code._ -## Implementation Notes +**Licensing** + +By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1). + +**Backward Compatibility** + +_Please state whether any changes in the pull request will break backward compatibility for inputs, and - if yes - explain what has been changed and why_ + +**Implementation Notes** _Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_ -## Post Submission Checklist +**Post Submission Checklist** + +_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_ -_Please check the fields below as they are completed_ - [ ] The feature or features in this pull request is complete -- [ ] Suitable new documentation files and/or updates to the existing docs are included -- [ ] One or more example input decks are included +- [ ] Licensing information is complete +- [ ] Corresponding author information is complete - [ ] The source code follows the LAMMPS formatting guidelines +- [ ] Suitable new documentation files and/or updates to the existing docs are included +- [ ] The added/updated documentation is integrated and tested with the documentation build system +- [ ] The feature has been verified to work with the conventional build system +- [ ] The feature has been verified to work with the CMake based build system +- [ ] A package specific README file has been included or updated +- [ ] One or more example input decks are included -## Further Information, Files, and Links +**Further Information, Files, and Links** _Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_ diff --git a/.github/PULL_REQUEST_TEMPLATE/bug_fix.md b/.github/PULL_REQUEST_TEMPLATE/bug_fix.md new file mode 100644 index 0000000000..cea04c6873 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/bug_fix.md @@ -0,0 +1,42 @@ +--- +name: Bug fix +about: Submit a pull request that fixes one or more bugs +title: "[BUGFIX] _Replace With Suitable Title_" +labels: bugfix +assignees: '' + +--- + +**Summary** + +_Briefly describe the bug or bugs, that are eliminated by this pull request._ + +**Related Issue(s)** + +_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`._ + +**Author(s)** + +_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_ + +**Licensing** + +By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified. + +**Backward Compatibility** + +_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_ + +**Detailed Description** + +_Provide any relevant details about how the fixed bug can be reproduced, how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_ + +## Post Submission Checklist + +_Please check the fields below as they are completed *after* the pull request is submitted_ +- [ ] The code in this pull request is complete +- [ ] The source code follows the LAMMPS formatting guidelines + +## Further Information, Files, and Links + +_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. to download input decks for testing)_ diff --git a/.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md b/.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md new file mode 100644 index 0000000000..b3599cb36d --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md @@ -0,0 +1,35 @@ +--- +name: Maintenance or Refactoring +about: Submit a pull request that does code refactoring or other maintenance changes +title: "[MAINTENANCE] _Replace With Suitable Title_" +labels: maintenance +assignees: '' + +--- + +**Summary** + +_Briefly describe the included changes._ + +**Related Issue(s)** + +_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`. + +**Author(s)** + +_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_ + +**Licensing** + +By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified. + +**Detailed Description** + +_Provide any relevant details about the included changes._ + +## Post Submission Checklist + +_Please check the fields below as they are completed *after* the pull request is submitted_ +- [ ] The pull request is complete +- [ ] The source code follows the LAMMPS formatting guidelines + diff --git a/.github/PULL_REQUEST_TEMPLATE/new_feature.md b/.github/PULL_REQUEST_TEMPLATE/new_feature.md new file mode 100644 index 0000000000..e9d16a0fc7 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/new_feature.md @@ -0,0 +1,56 @@ +--- +name: New Feature +about: Submit a pull request that adds new Features (complete files) to LAMMPS +title: "[New Feature] _Replace With Suitable Title_" +labels: enhancement +assignees: '' + +--- + +**Summary** + +_Briefly describe the new feature(s) included in this pull request._ + +**Related Issues** + +_If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`._ + +**Author(s)** + +_Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_ + +**Licensing** + +_Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)_ + +My contribution may be licensed as GPL v2 (default LAMMPS license): +My contribution may be licensed as LGPL (for use as a library with proprietary software): + +**Backward Compatibility** + +_Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why_ + +**Implementation Notes** + +_Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on_ + +## Post Submission Checklist + +_Please check the fields below as they are completed *after* the pull request has been submitted_ + +- [ ] The feature or features in this pull request is complete +- [ ] Licensing information is complete +- [ ] Corresponding author information is complete +- [ ] The source code follows the LAMMPS formatting guidelines +- [ ] Suitable new documentation files and/or updates to the existing docs are included +- [ ] The added/updated documentation is integrated and tested with the documentation build system +- [ ] The feature has been verified to work with the conventional build system +- [ ] The feature has been verified to work with the CMake based build system +- [ ] A package specific README file has been included or updated +- [ ] One or more example input decks are included + +## Further Information, Files, and Links + +_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_ + + diff --git a/.github/PULL_REQUEST_TEMPLATE/update_enhancement.md b/.github/PULL_REQUEST_TEMPLATE/update_enhancement.md new file mode 100644 index 0000000000..52ef91e6c1 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/update_enhancement.md @@ -0,0 +1,42 @@ +--- +name: Update or Enhancement +about: Submit a pull request that provides update or enhancements for a package or feature in LAMMPS +title: "[UPDATE] _Replace With Suitable Title_" +labels: enhancement +assignees: '' + +--- + +**Summary** + +_Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author._ + +**Author(s)** + +_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_ + +**Licensing** + +By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the original package or feature(s) that are updated or amended by this pull request. + +**Backward Compatibility** + +_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_ + +**Implementation Notes** + +_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_ + +**Post Submission Checklist** + +_Please check the fields below as they are completed_ +- [ ] The feature or features in this pull request is complete +- [ ] Suitable updates to the existing docs are included +- [ ] One or more example input decks are included +- [ ] The source code follows the LAMMPS formatting guidelines + +**Further Information, Files, and Links** + +_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_ + + diff --git a/.gitignore b/.gitignore index 1ce415678e..f9dda49da6 100644 --- a/.gitignore +++ b/.gitignore @@ -22,6 +22,7 @@ log.cite .*.swp *.orig *.rej +vgcore.* .vagrant \#*# .#* diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 418bdd0dba..e189aa291e 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -11,6 +11,12 @@ get_filename_component(LAMMPS_LIB_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../lib get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE) get_filename_component(LAMMPS_DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../doc ABSOLUTE) +find_package(Git) + +# by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed +if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE ) +endif() # To avoid conflicts with the conventional Makefile build system, we build everything here file(GLOB LIB_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp) @@ -75,12 +81,13 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) #release comes with -O3 by default set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE) endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS) +string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) # check for files auto-generated by make-based buildsystem # this is fast, so check for it all the time message(STATUS "Running check for auto-generated files from make-based build system") file(GLOB SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/style_*.h) -list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h) +list(APPEND SRC_AUTOGEN_FILES ${LAMMPS_SOURCE_DIR}/lmpinstalledpkgs.h ${LAMMPS_SOURCE_DIR}/lmpgitversion.h) foreach(_SRC ${SRC_AUTOGEN_FILES}) get_filename_component(FILENAME "${_SRC}" NAME) if(EXISTS ${LAMMPS_SOURCE_DIR}/${FILENAME}) @@ -166,13 +173,14 @@ set(LAMMPS_DEPS) set(LAMMPS_API_DEFINES) set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR - KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK + KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF - USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ - USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM) + USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS + USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK + USER-QUIP USER-QMMM USER-YAFF USER-ADIOS) set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU) set(OTHER_PACKAGES CORESHELL QEQ) foreach(PKG ${DEFAULT_PACKAGES}) @@ -185,16 +193,27 @@ endforeach() ###################################################### # packages with special compiler needs or external libs ###################################################### -if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS) +if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS) enable_language(Fortran) endif() -if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS) +if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS) enable_language(C) endif() include_directories(${LAMMPS_SOURCE_DIR}) + +if(PKG_USER-ADIOS) + # The search for ADIOS2 must come before MPI because + # it includes its own MPI search with the latest FindMPI.cmake + # script that defines the MPI::MPI_C target + enable_language(C) + find_package(ADIOS2 REQUIRED) + list(APPEND LAMMPS_LINK_LIBS adios2::adios2) +endif() + + # do MPI detection after language activation, if MPI for these language is required find_package(MPI QUIET) option(BUILD_MPI "Build MPI version" ${MPI_FOUND}) @@ -215,7 +234,7 @@ else() endif() -set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit") +set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)") set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall) set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES}) validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES) @@ -303,7 +322,7 @@ pkg_depends(USER-SCAFACOS MPI) find_package(OpenMP QUIET) option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND}) -if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL) +if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL) find_package(OpenMP REQUIRED) set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}") set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}") @@ -421,19 +440,33 @@ if(WITH_FFMPEG) add_definitions(-DLAMMPS_FFMPEG) endif() +if(BUILD_SHARED_LIBS) + set(CONFIGURE_REQUEST_PIC "--with-pic") + set(CMAKE_REQUEST_PIC "-DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE}") + set(CUDA_REQUEST_PIC "-Xcompiler ${CMAKE_SHARED_LIBRARY_CXX_FLAGS}") +else() + set(CONFIGURE_REQUEST_PIC) + set(CMAKE_REQUEST_PIC) + set(CUDA_REQUEST_PIC) +endif() + + if(PKG_VORONOI) - option(DOWNLOAD_VORO "Download voro++ (instead of using the system's one)" OFF) + option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" OFF) if(DOWNLOAD_VORO) + message(STATUS "Voro++ download requested - we will build our own") include(ExternalProject) if(BUILD_SHARED_LIBS) - set(VORO_BUILD_OPTIONS "CFLAGS=-fPIC") + set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}") else() - set(VORO_BUILD_OPTIONS) + set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}") endif() + string(APPEND VORO_BUILD_CFLAGS ${CMAKE_CXX_FLAGS}) + set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS}) ExternalProject_Add(voro_build - URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz + URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz URL_MD5 2338b824c3b7b25590e18e8df5d68af9 CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND "" ) @@ -444,7 +477,7 @@ if(PKG_VORONOI) else() find_package(VORO) if(NOT VORO_FOUND) - message(FATAL_ERROR "VORO not found, help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it") + message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it") endif() endif() include_directories(${VORO_INCLUDE_DIRS}) @@ -452,26 +485,26 @@ if(PKG_VORONOI) endif() if(PKG_LATTE) - option(DOWNLOAD_LATTE "Download latte (instead of using the system's one)" OFF) + option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" OFF) if(DOWNLOAD_LATTE) - if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR + if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7") endif() - message(STATUS "LATTE not found - we will build our own") + message(STATUS "LATTE download requested - we will build our own") include(ExternalProject) ExternalProject_Add(latte_build URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz URL_MD5 85ac414fdada2d04619c8f936344df14 SOURCE_SUBDIR cmake - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} - ) + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} + ) ExternalProject_get_property(latte_build INSTALL_DIR) set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a) list(APPEND LAMMPS_DEPS latte_build) else() find_package(LATTE) if(NOT LATTE_FOUND) - message(FATAL_ERROR "LATTE not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it") + message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it") endif() endif() list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES}) @@ -479,24 +512,22 @@ endif() if(PKG_USER-SCAFACOS) find_package(GSL REQUIRED) - option(DOWNLOAD_SCAFACOS "Download ScaFaCoS (instead of using the system's one)" OFF) + option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" OFF) if(DOWNLOAD_SCAFACOS) + message(STATUS "ScaFaCoS download requested - we will build our own") include(ExternalProject) ExternalProject_Add(scafacos_build URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz URL_MD5 bd46d74e3296bd8a444d731bb10c1738 - CONFIGURE_COMMAND /configure --prefix= - --disable-doc + CONFIGURE_COMMAND /configure --prefix= --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m - --with-internal-fftw - --with-internal-pfft - --with-internal-pnfft - $<$:--with-pic> - FC=${CMAKE_MPI_Fortran_COMPILER} - CXX=${CMAKE_MPI_CXX_COMPILER} + --with-internal-fftw --with-internal-pfft + --with-internal-pnfft ${CONFIGURE_REQUEST_PIC} + FC=${CMAKE_MPI_Fortran_COMPILER} + CXX=${CMAKE_MPI_CXX_COMPILER} CC=${CMAKE_MPI_C_COMPILER} F77= - ) + ) ExternalProject_get_property(scafacos_build INSTALL_DIR) set(SCAFACOS_BUILD_DIR ${INSTALL_DIR}) set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include) @@ -528,9 +559,63 @@ if(PKG_USER-SCAFACOS) include_directories(${SCAFACOS_INCLUDE_DIRS}) endif() +if(PKG_USER-PLUMED) + find_package(GSL REQUIRED) + set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library") + set(PLUMED_MODE_VALUES static shared runtime) + set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES}) + validate_option(PLUMED_MODE PLUMED_MODE_VALUES) + string(TOUPPER ${PLUMED_MODE} PLUMED_MODE) + + option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" OFF) + if(DOWNLOAD_PLUMED) + message(STATUS "PLUMED download requested - we will build our own") + include(ExternalProject) + ExternalProject_Add(plumed_build + URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz + URL_MD5 71ed465bdc7c2059e282dbda8d564e71 + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND /configure --prefix= + ${CONFIGURE_REQUEST_PIC} + --enable-modules=all + CXX=${CMAKE_MPI_CXX_COMPILER} + CC=${CMAKE_MPI_C_COMPILER} + ) + ExternalProject_get_property(plumed_build INSTALL_DIR) + set(PLUMED_INSTALL_DIR ${INSTALL_DIR}) + list(APPEND LAMMPS_DEPS plumed_build) + if(PLUMED_MODE STREQUAL "STATIC") + add_definitions(-D__PLUMED_WRAPPER_CXX=1) + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/plumed/obj/kernel.o + "${PLUMED_INSTALL_DIR}/lib/plumed/obj/PlumedStatic.o" ${GSL_LIBRARIES} ${CMAKE_DL_LIBS}) + elseif(PLUMED_MODE STREQUAL "SHARED") + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.so ${CMAKE_DL_LIBS}) + elseif(PLUMED_MODE STREQUAL "RUNTIME") + add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel.so) + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS}) + endif() + set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include") + else() + find_package(PkgConfig REQUIRED) + pkg_check_modules(PLUMED plumed REQUIRED) + if(PLUMED_MODE STREQUAL "STATIC") + add_definitions(-D__PLUMED_WRAPPER_CXX=1) + include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static) + elseif(PLUMED_MODE STREQUAL "SHARED") + include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared) + elseif(PLUMED_MODE STREQUAL "RUNTIME") + add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel.so) + include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime) + endif() + list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD}) + endif() + include_directories(${PLUMED_INCLUDE_DIRS}) +endif() + if(PKG_USER-MOLFILE) + set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers") add_library(molfile INTERFACE) - target_include_directories(molfile INTERFACE ${LAMMPS_LIB_SOURCE_DIR}/molfile) + target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS}) target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS}) list(APPEND LAMMPS_LINK_LIBS molfile) endif() @@ -543,12 +628,13 @@ if(PKG_USER-NETCDF) endif() if(PKG_USER-SMD) - option(DOWNLOAD_EIGEN3 "Download Eigen3 (instead of using the system's one)" OFF) + option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF) if(DOWNLOAD_EIGEN3) + message(STATUS "Eigen3 download requested - we will build our own") include(ExternalProject) ExternalProject_Add(Eigen3_build - URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz - URL_MD5 1a47e78efe365a97de0c022d127607c3 + URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz + URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07 CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" ) ExternalProject_get_property(Eigen3_build SOURCE_DIR) @@ -584,27 +670,40 @@ if(PKG_USER-VTK) endif() if(PKG_KIM) - option(DOWNLOAD_KIM "Download kim-api (instead of using the system's one)" OFF) + find_package(CURL) + if(CURL_FOUND) + include_directories(${CURL_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES}) + add_definitions(-DLMP_KIM_CURL) + endif() + option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF) if(DOWNLOAD_KIM) + message(STATUS "KIM-API v2 download requested - we will build our own") + enable_language(C) + enable_language(Fortran) include(ExternalProject) ExternalProject_Add(kim_build - URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz - URL_MD5 9f66efc128da33039e30659f36fc6d00 - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND /configure --prefix= + URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz + URL_MD5 289c57f0c3bc2a549662283cac1c4ef1 + BINARY_DIR build + CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} + -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} + -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} + -DCMAKE_INSTALL_PREFIX= + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} ) ExternalProject_get_property(kim_build INSTALL_DIR) - set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1) - set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so) + set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2) + set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX}) list(APPEND LAMMPS_DEPS kim_build) else() - find_package(KIM) - if(NOT KIM_FOUND) - message(FATAL_ERROR "KIM not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it") + find_package(KIM-API-V2) + if(NOT KIM-API-V2_FOUND) + message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it") endif() endif() - list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES}) - include_directories(${KIM_INCLUDE_DIRS}) + list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}") + include_directories(${KIM-API-V2_INCLUDE_DIRS}) endif() if(PKG_MESSAGE) @@ -613,12 +712,7 @@ if(PKG_MESSAGE) ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp) - if(BUILD_SHARED_LIBS) - add_library(cslib SHARED ${cslib_SOURCES}) - else() - add_library(cslib STATIC ${cslib_SOURCES}) - endif() - + add_library(cslib STATIC ${cslib_SOURCES}) if(BUILD_MPI) target_compile_definitions(cslib PRIVATE -DMPI_YES) set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi") @@ -643,10 +737,10 @@ endif() if(PKG_MSCG) find_package(GSL REQUIRED) - option(DOWNLOAD_MSCG "Download latte (instead of using the system's one)" OFF) + option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" OFF) if(DOWNLOAD_MSCG) - if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR - message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7") + if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR + message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7") endif() include(ExternalProject) if(NOT LAPACK_FOUND) @@ -656,7 +750,7 @@ if(PKG_MSCG) URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz URL_MD5 8c45e269ee13f60b303edd7823866a91 SOURCE_SUBDIR src/CMake - CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= -DCMAKE_POSITION_INDEPENDENT_CODE=${CMAKE_POSITION_INDEPENDENT_CODE} ${EXTRA_MSCG_OPTS} + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX= ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS} BUILD_COMMAND make mscg INSTALL_COMMAND "" ) ExternalProject_get_property(mscg_build BINARY_DIR) @@ -693,7 +787,7 @@ endif() # Basic system tests (standard libraries, headers, functions, types) # ######################################################################## include(CheckIncludeFileCXX) -foreach(HEADER math.h) +foreach(HEADER cmath) check_include_file_cxx(${HEADER} FOUND_${HEADER}) if(NOT FOUND_${HEADER}) message(FATAL_ERROR "Could not find needed header - ${HEADER}") @@ -704,7 +798,7 @@ set(MATH_LIBRARIES "m" CACHE STRING "math library") mark_as_advanced( MATH_LIBRARIES ) include(CheckLibraryExists) if (CMAKE_VERSION VERSION_LESS "3.4") - enable_language(C) # check_library_exists isn't supported without a c compiler before v3.4 + enable_language(C) # check_library_exists isn't supported without a C compiler before v3.4 endif() # RB: disabled this check because it breaks with KOKKOS CUDA enabled #foreach(FUNC sin cos) @@ -742,6 +836,13 @@ foreach(PKG ${DEFAULT_PACKAGES}) endif() endforeach() +# packages that need defines set +foreach(PKG MPIIO) + if(PKG_${PKG}) + add_definitions(-DLMP_${PKG}) + endif() +endforeach() + # dedicated check for entire contents of accelerator packages foreach(PKG ${ACCEL_PACKAGES}) set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG}) @@ -756,7 +857,7 @@ endforeach() ############################################## # add lib sources of (simple) enabled packages ############################################ -foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD +foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-QMMM) if(PKG_${SIMPLE_LIB}) string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}") @@ -770,7 +871,7 @@ foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD if(PKG_LIB STREQUAL awpmd) target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include) elseif(PKG_LIB STREQUAL h5md) - target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include) + target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS}) elseif(PKG_LIB STREQUAL colvars) target_compile_options(colvars PRIVATE -DLEPTON) target_include_directories(colvars PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton/include) @@ -786,6 +887,9 @@ if(PKG_USER-AWPMD) endif() if(PKG_USER-ATC) + if(LAMMPS_SIZES STREQUAL BIGBIG) + message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG") + endif() target_link_libraries(atc ${LAPACK_LIBRARIES}) endif() @@ -793,6 +897,7 @@ if(PKG_USER-H5MD) find_package(HDF5 REQUIRED) target_link_libraries(h5md ${HDF5_LIBRARIES}) target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS}) + include_directories(${HDF5_INCLUDE_DIRS}) endif() @@ -878,6 +983,20 @@ if(PKG_USER-OMP) include_directories(${USER-OMP_SOURCES_DIR}) endif() +# Fix rigid/meso requires RIGID to be installed +if(PKG_USER-SDPD) + set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD) + + get_property(hlist GLOBAL PROPERTY FIX) + if(NOT PKG_RIGID) + list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h) + list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp) + endif() + set_property(GLOBAL PROPERTY FIX "${hlist}") + + include_directories(${USER-SDPD_SOURCES_DIR}) +endif() + if(PKG_KOKKOS) set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos) @@ -955,7 +1074,7 @@ if(PKG_USER-INTEL) endif() if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16) - message(FATAL_ERROR "USER-INTEL is needed at least 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") + message(FATAL_ERROR "USER-INTEL needs at least a 2016 intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}") endif() if(NOT BUILD_OMP) @@ -1020,7 +1139,7 @@ if(PKG_USER-INTEL) endif() if(PKG_GPU) - if (CMAKE_VERSION VERSION_LESS "3.1") + if (CMAKE_VERSION VERSION_LESS "3.1") message(FATAL_ERROR "For the GPU package you need at least cmake-3.1") endif() set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU) @@ -1055,11 +1174,11 @@ if(PKG_GPU) find_package(CUDA REQUIRED) find_program(BIN2C bin2c) if(NOT BIN2C) - message(FATAL_ERROR "Couldn't find bin2c, use -DBIN2C helping cmake to find it.") + message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.") endif() option(CUDPP_OPT "Enable CUDPP_OPT" ON) - set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM architecture (e.g. sm_60)") + set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)") file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu) list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu) @@ -1072,11 +1191,39 @@ if(PKG_GPU) file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu) endif() - cuda_compile_cubin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS - -DUNIX -O3 -Xptxas -v --use_fast_math -DNV_KERNEL -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING}) + # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice + # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture + set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ") + # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0 + if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0")) + string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ") + endif() + # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later + if(CUDA_VERSION VERSION_GREATER "4.9") + string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ") + endif() + # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later + if(CUDA_VERSION VERSION_GREATER "5.9") + string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ") + endif() + # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later + if(CUDA_VERSION VERSION_GREATER "7.9") + string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ") + endif() + # Volta (GPU Arch 7.0) is supported by CUDA 9 and later + if(CUDA_VERSION VERSION_GREATER "8.9") + string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ") + endif() + # Turing (GPU Arch 7.5) is supported by CUDA 10 and later + if(CUDA_VERSION VERSION_GREATER "9.9") + string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ") + endif() - cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS $<$:-Xcompiler=-fPIC> - -DUNIX -O3 -Xptxas -v --use_fast_math -DUCL_CUDADR -arch=${GPU_ARCH} -D_${GPU_PREC_SETTING}) + cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS + -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) + + cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC} + -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING}) foreach(CU_OBJ ${GPU_GEN_OBJS}) get_filename_component(CU_NAME ${CU_OBJ} NAME_WE) @@ -1187,6 +1334,18 @@ message(STATUS "Generating lmpinstalledpkgs.h...") file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${temp}" ) execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpinstalledpkgs.h") +###################################### +# Generate lmpgitversion.h +###################################### +add_custom_target(gitversion COMMAND ${CMAKE_COMMAND} + -DCMAKE_CURRENT_SOURCE_DIR="${CMAKE_CURRENT_SOURCE_DIR}" + -DGIT_EXECUTABLE="${GIT_EXECUTABLE}" + -DGIT_FOUND="${GIT_FOUND}" + -DLAMMPS_STYLE_HEADERS_DIR="${LAMMPS_STYLE_HEADERS_DIR}" + -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/generate_lmpgitversion.cmake) +set_property(DIRECTORY APPEND PROPERTY ADDITIONAL_MAKE_CLEAN_FILES ${LAMMPS_STYLE_HEADERS_DIR}/gitversion.h) +list(APPEND LAMMPS_DEPS gitversion) + ########################################### # Actually add executable and lib to build ############################################ @@ -1209,7 +1368,7 @@ if(BUILD_LIB) configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY) install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig) configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY) - install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module) + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules) else() list(APPEND LMP_SOURCES ${LIB_SOURCES}) endif() @@ -1224,7 +1383,7 @@ if(BUILD_EXE) add_dependencies(lmp ${LAMMPS_DEPS}) endif() endif() - + set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY}) install(TARGETS lmp DESTINATION ${CMAKE_INSTALL_BINDIR}) install(FILES ${LAMMPS_DOC_DIR}/lammps.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1 RENAME ${LAMMPS_BINARY}.1) @@ -1233,6 +1392,7 @@ if(BUILD_EXE) endif() endif() + ############################################################################### # Build documentation ############################################################################### @@ -1345,7 +1505,6 @@ foreach(PKG ${DEFAULT_PACKAGES} ${ACCEL_PACKAGES} ${OTHER_PACKAGES}) endif() endforeach() -string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE) get_directory_property(CPPFLAGS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS) include(FeatureSummary) feature_summary(DESCRIPTION "The following packages have been found:" WHAT PACKAGES_FOUND) @@ -1361,14 +1520,14 @@ message(STATUS "<<< Build configuration >>> get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES) list (FIND LANGUAGES "Fortran" _index) if (${_index} GREATER -1) - message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} + message(STATUS "Fortran Compiler ${CMAKE_Fortran_COMPILER} Type ${CMAKE_Fortran_COMPILER_ID} Version ${CMAKE_Fortran_COMPILER_VERSION} Fortran Flags ${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}") endif() list (FIND LANGUAGES "C" _index) if (${_index} GREATER -1) - message(STATUS "C Compiler ${CMAKE_C_COMPILER} + message(STATUS "C Compiler ${CMAKE_C_COMPILER} Type ${CMAKE_C_COMPILER_ID} Version ${CMAKE_C_COMPILER_VERSION} C Flags ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}") @@ -1376,7 +1535,7 @@ endif() if(CMAKE_EXE_LINKER_FLAGS) message(STATUS "Linker flags: Executable ${CMAKE_EXE_LINKER_FLAGS}") - endif() +endif() if(BUILD_SHARED_LIBS) message(STATUS "Shared libraries ${CMAKE_SHARED_LINKER_FLAGS}") else() diff --git a/cmake/Modules/FindKIM-API-V2.cmake b/cmake/Modules/FindKIM-API-V2.cmake new file mode 100644 index 0000000000..6ca6e068df --- /dev/null +++ b/cmake/Modules/FindKIM-API-V2.cmake @@ -0,0 +1,50 @@ +# +# CDDL HEADER START +# +# The contents of this file are subject to the terms of the Common Development +# and Distribution License Version 1.0 (the "License"). +# +# You can obtain a copy of the license at +# http://www.opensource.org/licenses/CDDL-1.0. See the License for the +# specific language governing permissions and limitations under the License. +# +# When distributing Covered Code, include this CDDL HEADER in each file and +# include the License file in a prominent location with the name LICENSE.CDDL. +# If applicable, add the following below this CDDL HEADER, with the fields +# enclosed by brackets "[]" replaced with your own identifying information: +# +# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved. +# +# CDDL HEADER END +# + +# +# Copyright (c) 2013--2018, Regents of the University of Minnesota. +# All rights reserved. +# +# Contributors: +# Richard Berger +# Christoph Junghans +# Ryan S. Elliott +# + +# - Find KIM-API-V2 +# +# sets standard pkg_check_modules variables plus: +# +# KIM-API-V2-CMAKE_C_COMPILER +# KIM-API-V2-CMAKE_CXX_COMPILER +# KIM-API-V2-CMAKE_Fortran_COMPILER +# +find_package(PkgConfig REQUIRED) +include(FindPackageHandleStandardArgs) + +pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0) + +pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER) +pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER) +pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER) + +# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE +# if all listed variables are TRUE +find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES) diff --git a/cmake/Modules/FindKIM.cmake b/cmake/Modules/FindKIM.cmake deleted file mode 100644 index a01f817cf6..0000000000 --- a/cmake/Modules/FindKIM.cmake +++ /dev/null @@ -1,22 +0,0 @@ -# - Find kim -# Find the native KIM headers and libraries. -# -# KIM_INCLUDE_DIRS - where to find kim.h, etc. -# KIM_LIBRARIES - List of libraries when using kim. -# KIM_FOUND - True if kim found. -# - -find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1) - -find_library(KIM_LIBRARY NAMES kim-api-v1) - -set(KIM_LIBRARIES ${KIM_LIBRARY}) -set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR}) - -include(FindPackageHandleStandardArgs) -# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE -# if all listed variables are TRUE - -find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR) - -mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY ) diff --git a/cmake/Modules/StyleHeaderUtils.cmake b/cmake/Modules/StyleHeaderUtils.cmake index a89d098dd0..a7b23b4cf1 100644 --- a/cmake/Modules/StyleHeaderUtils.cmake +++ b/cmake/Modules/StyleHeaderUtils.cmake @@ -50,6 +50,7 @@ function(CreateStyleHeader path filename) list(REMOVE_AT ARGV 0 1) set(header_list) foreach(FNAME ${ARGV}) + set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}") get_filename_component(FNAME ${FNAME} NAME) list(APPEND header_list ${FNAME}) endforeach() @@ -61,6 +62,7 @@ function(CreateStyleHeader path filename) message(STATUS "Generating ${filename}...") file(WRITE "${path}/${filename}.tmp" "${temp}" ) execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}") + set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}") endfunction(CreateStyleHeader) function(GenerateStyleHeader path property style) diff --git a/cmake/Modules/generate_lmpgitversion.cmake b/cmake/Modules/generate_lmpgitversion.cmake new file mode 100644 index 0000000000..8aead88f5f --- /dev/null +++ b/cmake/Modules/generate_lmpgitversion.cmake @@ -0,0 +1,30 @@ +set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n") +set(temp_git_commit "(unknown)") +set(temp_git_branch "(unknown)") +set(temp_git_describe "(unknown)") +set(temp_git_info "false") +if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git) + set(temp_git_info "true") + execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse HEAD + OUTPUT_VARIABLE temp_git_commit + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git rev-parse --abbrev-ref HEAD + OUTPUT_VARIABLE temp_git_branch + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) + execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/../.git describe --dirty=-modified + OUTPUT_VARIABLE temp_git_describe + ERROR_QUIET + OUTPUT_STRIP_TRAILING_WHITESPACE) +endif() + +set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n") +set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n") +set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n") +set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n") +set(temp "${temp}#endif\n\n") + +message(STATUS "Generating lmpgitversion.h...") +file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" ) +execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h") diff --git a/cmake/README.md b/cmake/README.md index 21e728c1f0..ce3b4502af 100644 --- a/cmake/README.md +++ b/cmake/README.md @@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases. * [Build directory vs. Source Directory](#build-directory-vs-source-directory) * [Defining and using presets](#defining-and-using-presets) * [Reference](#reference) - * [Common CMAKE Configuration Options](#common-cmake-configuration-options) + * [Common CMake Configuration Options](#common-cmake-configuration-options) * [LAMMPS Configuration Options](#lammps-configuration-options) * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages) * [Default Packages](#default-packages) @@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake # Reference -## Common CMAKE Configuration Options +## Common CMake Configuration Options @@ -195,6 +195,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake @@ -207,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake + + + + +
CMAKE_INSTALL_PREFIX Install location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do. + Default setting is $HOME/.local.
Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call. +
+
off (default)
+
on
+
+
@@ -1492,6 +1503,11 @@ target API. + + BIN2C (CUDA only) + Path to bin2c executable, will automatically pick up the first one in your $PATH. + (automatic) + @@ -1647,9 +1663,8 @@ requires `gzip` to be in your `PATH` GZIP_EXECUTABLE - - - + Path to gzip executable, will automatically pick up the first one in your $PATH. + (automatic) @@ -1679,9 +1694,8 @@ requires `ffmpeg` to be in your `PATH` FFMPEG_EXECUTABLE - - - + Path to ffmpeg executable, will automatically pick up the first one in your $PATH. + (automatic) @@ -1725,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, value of `FC` environment variable at first `cmake` run + + CXX_COMPILER_LAUNCHER + CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache. + + (empty) + + diff --git a/cmake/pkgconfig/liblammps.pc.in b/cmake/pkgconfig/liblammps.pc.in index 7850972f3b..a8710ca224 100644 --- a/cmake/pkgconfig/liblammps.pc.in +++ b/cmake/pkgconfig/liblammps.pc.in @@ -1,9 +1,29 @@ # pkg-config file for lammps # https://people.freedesktop.org/~dbn/pkg-config-guide.html -# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c -# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH, + +# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig +# Use this on commandline with: +# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp + +# Use this in a Makefile: +# myapp: myapp.cpp +# $(CC) `pkg-config --cflags --libs lammps` -o $@ $< + +# Use this in autotools: +# configure.ac: +# PKG_CHECK_MODULES([LAMMPS], [lammps]) +# Makefile.am: +# myapp_CFLAGS = $(LAMMPS_CFLAGS) +# myapp_LDADD = $(LAMMPS_LIBS) + +# Use this in CMake: +# CMakeLists.txt: +# find_package(PkgConfig) +# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps) +# target_link_libraries( PkgConfig::LAMMPS) + prefix=@CMAKE_INSTALL_PREFIX@ libdir=@CMAKE_INSTALL_FULL_LIBDIR@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@ diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index f7e90ddbb4..b434796d7c 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK) set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 2c6f67904e..3a1100f337 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK) set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) diff --git a/cmake/presets/manual_selection.cmake b/cmake/presets/manual_selection.cmake index 6c03d983f6..6db41b708c 100644 --- a/cmake/presets/manual_selection.cmake +++ b/cmake/presets/manual_selection.cmake @@ -56,11 +56,13 @@ set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE) set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE) set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE) set(PKG_USER-OMP OFF CACHE BOOL "" FORCE) -set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE) +set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE) +set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE) set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE) set(PKG_USER-QTB OFF CACHE BOOL "" FORCE) set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE) set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE) +set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE) set(PKG_USER-SMD OFF CACHE BOOL "" FORCE) set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE) set(PKG_USER-SPH OFF CACHE BOOL "" FORCE) diff --git a/cmake/presets/nolib.cmake b/cmake/presets/nolib.cmake index cd603aa804..4c02fb6210 100644 --- a/cmake/presets/nolib.cmake +++ b/cmake/presets/nolib.cmake @@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK) set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) diff --git a/cmake/presets/std.cmake b/cmake/presets/std.cmake index 36da897957..4176aba44e 100644 --- a/cmake/presets/std.cmake +++ b/cmake/presets/std.cmake @@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK) set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI diff --git a/cmake/presets/std_nolib.cmake b/cmake/presets/std_nolib.cmake index 9bffefcbe0..aa067f2ba0 100644 --- a/cmake/presets/std_nolib.cmake +++ b/cmake/presets/std_nolib.cmake @@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK) set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI diff --git a/cmake/presets/user.cmake b/cmake/presets/user.cmake index cb81b67558..af606203e9 100644 --- a/cmake/presets/user.cmake +++ b/cmake/presets/user.cmake @@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB - USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY + USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK) set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE - USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK) + USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK) set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES}) diff --git a/doc/.gitignore b/doc/.gitignore index 7d30949237..88679898a8 100644 --- a/doc/.gitignore +++ b/doc/.gitignore @@ -1,4 +1,6 @@ +/old /html +/latex /spelling /LAMMPS.epub /LAMMPS.mobi diff --git a/doc/Makefile b/doc/Makefile index cf649eb37b..044e358bd5 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -1,7 +1,7 @@ # Makefile for LAMMPS documentation -SHELL = /bin/bash -SHA1 = $(shell echo $USER-$PWD | python utils/sha1sum.py) +SHELL = /bin/bash +SHA1 = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py) BUILDDIR = /tmp/lammps-docs-$(SHA1) RSTDIR = $(BUILDDIR)/rst VENV = $(BUILDDIR)/docenv @@ -39,7 +39,7 @@ help: @echo "Please use \`make ' where is one of" @echo " html create HTML doc pages in html dir" @echo " pdf create Developer.pdf and Manual.pdf in this dir" - @echo " old create old-style HTML doc pages in old dir" + @echo " old create old-style HTML doc pages and Manual.pdf in old dir" @echo " fetch fetch HTML and PDF files from LAMMPS web site" @echo " epub create ePUB format manual for e-book readers" @echo " mobi convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)" @@ -48,6 +48,7 @@ help: @echo " clean-all reset the entire build environment" @echo " txt2html build txt2html tool" @echo " anchor_check scan for duplicate anchor labels" + @echo " spelling spell-check the manual" # ------------------------------------------ @@ -55,7 +56,7 @@ clean-all: clean rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe clean: - rm -rf $(RSTDIR) html old epub + rm -rf $(RSTDIR) html old epub latex rm -rf spelling clean-spelling: @@ -114,21 +115,44 @@ mobi: epub @ebook-convert LAMMPS.epub LAMMPS.mobi @echo "Conversion finished. The MOBI manual file is created." -pdf: utils/txt2html/txt2html.exe +pdf: $(OBJECTS) $(ANCHORCHECK) + @(\ + . $(VENV)/bin/activate ;\ + cp -r src/* $(RSTDIR)/ ;\ + sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\ + echo "############################################" ;\ + doc_anchor_check src/*.txt ;\ + echo "############################################" ;\ + deactivate ;\ + ) + @cd latex && \ + sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \ + mv temp Makefile && \ + sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \ + mv tmp.tex LAMMPS.tex && \ + sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \ + mv tmp.tex LAMMPS.tex && \ + make && \ + make && \ + mv LAMMPS.pdf ../Manual.pdf && \ + cd ../; @(\ - set -e; \ cd src/Developer; \ pdflatex developer; \ pdflatex developer; \ mv developer.pdf ../../Developer.pdf; \ - cd ..; \ - ../utils/txt2html/txt2html.exe -b *.txt; \ - htmldoc --batch lammps.book; \ - for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \ - do grep -q ^$$s lammps.book || \ - echo WARNING: doc file $$s missing in src/lammps.book; done; \ - rm *.html; \ + cd ../../; \ ) + @rm -rf latex/_sources + @rm -rf latex/PDF + @rm -rf latex/USER + @cp -r src/PDF latex/PDF + @cp -r src/USER latex/USER + @rm -rf latex/PDF/.[sg]* + @rm -rf latex/USER/.[sg]* + @rm -rf latex/USER/*/.[sg]* + @rm -rf latex/USER/*/*.[sg]* + @echo "Build finished. Manual.pdf and Developer.pdf are in this directory." old: utils/txt2html/txt2html.exe @rm -rf old @@ -138,6 +162,18 @@ old: utils/txt2html/txt2html.exe cp Eqs/*.jpg ../old/Eqs; \ cp JPG/* ../old/JPG; \ cp PDF/* ../old/PDF; + @( set -e;\ + cd src/Developer; \ + pdflatex developer; \ + pdflatex developer; \ + mv developer.pdf ../../old/Developer.pdf; \ + cd ../../old; \ + for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \ + do grep -q ^$$s ../src/lammps.book || \ + echo WARNING: doc file $$s missing in src/lammps.book; done; \ + htmldoc --batch ../src/lammps.book; \ + ) + fetch: @rm -rf html_www Manual_www.pdf Developer_www.pdf @@ -176,7 +212,6 @@ $(VENV): $(VIRTUALENV) -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ pip install Sphinx; \ - pip install sphinxcontrib-images; \ deactivate;\ ) diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md new file mode 100644 index 0000000000..ee64703707 --- /dev/null +++ b/doc/github-development-workflow.md @@ -0,0 +1,196 @@ +# Outline of the GitHub Development Workflow + +This purpose of this document is to provide a point of reference for the +core LAMMPS developers and other LAMMPS contributors to understand the +choices the LAMMPS developers have agreed on. Git and GitHub provide the +tools, but do not set policies, so it is up to the developers to come to +an agreement as to how to define and interpret policies. This document +is likely to change as our experiences and needs change and we try to +adapt accordingly. Last change 2018-12-19. + +## Table of Contents + + * [GitHub Merge Management](#github-merge-management) + * [Pull Requests](#pull-requests) + * [Pull Request Assignments](#pull-request-assignments) + * [Pull Request Reviews](#pull-request-reviews) + * [Pull Request Discussions](#pull-request-discussions) + * [Checklist for Pull Requests](#checklist-for-pull-requests) + * [GitHub Issues](#github-issues) + * [Milestones and Release Planning](#milestones-and-release-planning) + +## GitHub Merge Management + +In the interest of consistency, ONLY ONE of the core LAMMPS developers +should doing the merging itself. This is currently +[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer). +If this assignment needs to be changed, it shall be done right after a +stable release. If the currently assigned developer cannot merge outstanding pull +requests in a timely manner, or in other extenuating circumstances, +other core LAMMPS developers with merge rights can merge pull requests, +when necessary. + +## Pull Requests + +ALL changes to the LAMMPS code and documentation, however trivial, MUST +be submitted as a pull request to GitHub. All changes to the "master" +branch must be made exclusively through merging pull requests. The +"unstable" and "stable" branches, respectively are only to be updated +upon patch or stable releases with fast-forward merges based on the +associated tags. Pull requests may also be submitted to (long-running) +feature branches created by LAMMPS developers inside the LAMMPS project, +if needed. Those are not subject to the merge and review restrictions +discussed in this document, though, but get managed as needed on a +case-by-case basis. + +### Pull Request Assignments + +Pull requests can be "chaperoned" by one of the LAMMPS core developers. +This is indicated by who the pull request is assigned to. LAMMPS core +developers can self-assign or they can decide to assign a pull request +to a different LAMMPS developer. Being assigned to a pull request means, +that this pull request may need some work and the assignee is tasked to +determine whether this might be needed or not, and may either implement +the required changes or ask the submitter of the pull request to implement +them. Even though, all LAMMPS developers may have write access to pull +requests (if enabled by the submitter, which is the default), only the +submitter or the assignee of a pull request may do so. During this +period the `work_in_progress` label shall be applied to the pull +request. The assignee gets to decide what happens to the pull request +next, e.g. whether it should be assigned to a different developer for +additional checks and changes, or is recommended to be merged. Removing +the `work_in_progress` label and assigning the pull request to the +developer tasked with merging signals that a pull request is ready to be +merged. + +### Pull Request Reviews + +People can be assigned to review a pull request in two ways: + + * They can be assigned manually to review a pull request + by the submitter or a LAMMPS developer + * They can be automatically assigned, because a developers matches + a file pattern in the `.github/CODEOWNERS` file, which associates + developers with the code they contributed and maintain. + +Reviewers are requested to state their appraisal of the proposed changes +and either approve or request changes. People may unassign themselves +from review, if they feel not competent about the changes proposed. At +least two approvals from LAMMPS developers with write access are required +before merging in addition to the automated compilation tests. +Merging counts as implicit approval, so does submission of a pull request +(by a LAMMPS developer). So the person doing the merge may not also submit +an approving review. The feature, that reviews from code owners are "hard" +reviews (i.e. they must all be approved before merging is allowed), is +currently disabled and it is in the discretion of the merge maintainer to +assess when a sufficient degree of approval, especially from external +contributors, has been reached in these cases. Reviews may be +(automatically) dismissed, when the reviewed code has been changed, +and then approval is required a second time. + +### Pull Request Discussions + +All discussions about a pull request should be kept as much as possible +on the pull request discussion page on GitHub, so that other developers +can later review the entire discussion after the fact and understand the +rationale behind choices made. Exceptions to this policy are technical +discussions, that are centered on tools or policies themselves +(git, github, c++) rather than on the content of the pull request. + +### Checklist for Pull Requests + +Here are some items to check: + * source and text files should not have CR/LF line endings (use dos2unix to remove) + * every new command or style should have documentation. The names of + source files (c++ and manual) should follow the name of the style. + (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command, + implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`) + * all new style names should be lower case, the must be no dashes, + blanks, or underscores separating words, only forward slashes. + * new style docs should be added to the "overview" files in + `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt` + and `doc/src/lammps.book` + * check whether manual cleanly translates with `make html` and `make pdf` + * check spelling of manual with `make spelling` in doc folder + * new source files in packages should be added to `src/.gitignore` + * removed or renamed files in packages should be added to `src/Purge.list` + * C++ source files should use C++ style include files for accessing + C-library APIs, e.g. `#include ` instead of `#include `. + And they should use angular brackets instead of double quotes. Full list: + * assert.h -> cassert + * ctype.h -> cctype + * errno.h -> cerrno + * float.h -> cfloat + * limits.h -> climits + * math.h -> cmath + * complex.h -> complex + * setjmp.h -> csetjmp + * signal.h -> csignal + * stddef.h -> cstddef + * stdint.h -> cstdint + * stdio.h -> cstdio + * stdlib.h -> cstdlib + * string.h -> cstring + * time.h -> ctime + * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`. + * Code should follow the C++-98 standard. C++-11 is only accepted + in individual special purpose packages + * indentation is 2 spaces per level + * there should be NO tabs and no trailing whitespace + * header files, especially of new styles, should not include any + other headers, except the header with the base class or cstdio. + Forward declarations should be used instead when possible. + * iostreams should be avoided. LAMMPS uses stdio from the C-library. + * use of STL in headers and class definitions should be avoided. + * there MUST NOT be any "using namespace XXX;" statements in headers. + * static class members should be avoided at all cost. + * anything storing atom IDs should be using `tagint` and not `int`. + This can be flagged by the compiler only for pointers and only when + compiling LAMMPS with `-DLAMMPS_BIGBIG`. + * when including both `lmptype.h` (and using defines or macros from it) + and `mpi.h`, `lmptype.h` must be included first. + * when pair styles are added, check if settings for flags like + `single_enable`, `writedata`, `reinitflag`, `manybody_flag` + and others are correctly set and supported. + +## GitHub Issues + +The GitHub issue tracker is the location where the LAMMPS developers +and other contributors or LAMMPS users can report issues or bugs with +the LAMMPS code or request new features to be added. Feature requests +are usually indicated by a `[Feature Request]` marker in the subject. +Issues are assigned to a person, if this person is working on this +feature or working to resolve an issue. Issues that have nobody working +on them at the moment, have the label `volunteer needed` attached. + +When an issue, say `#125` is resolved by a specific pull request, +the comment for the pull request shall contain the text `closes #125` +or `fixes #125`, so that the issue is automatically deleted when +the pull request is merged. + +## Milestones and Release Planning + +LAMMPS uses a continuous release development model with incremental +changes, i.e. significant effort is made - including automated pre-merge +testing - that the code in the branch "master" does not get broken. +More extensive testing (including regression testing) is performed after +code is merged to the "master" branch. There are patch releases of +LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that +a sufficient amount of changes have happened, and the post-merge testing +has been successful. These patch releases are marked with a +`patch_` tag and the "unstable" branch follows only these +versions (and thus is always supposed to be of production quality, +unlike "master", which may be temporary broken, in the case of larger +change sets or unexpected incompatibilities or side effects. + +About 3-4 times each year, there are going to be "stable" releases +of LAMMPS. These have seen additional, manual testing and review of +results from testing with instrumented code and static code analysis. +Also, in the last 2-3 patch releases before a stable release are +"release candidate" versions which only contain bugfixes and +documentation updates. For release planning and the information of +code contributors, issues and pull requests being actively worked on +are assigned a "milestone", which corresponds to the next stable +release or the stable release after that, with a tentative release +date. + diff --git a/doc/src/Build_basics.txt b/doc/src/Build_basics.txt index 4b3a347bf1..fa4ef12586 100644 --- a/doc/src/Build_basics.txt +++ b/doc/src/Build_basics.txt @@ -49,7 +49,7 @@ make mybox :pre # uses Makefile.mybox to produce lmp_mybox :pre Serial build (see src/MAKE/Makefile.serial): -MPI_INC = -I../STUBS +MPI_INC = -I../STUBS MPI_PATH = -L../STUBS MPI_LIB = -lmpi_stubs :pre @@ -116,6 +116,18 @@ enables OpenMP. For GNU compilers it is -fopenmp. For (recent) Intel compilers it is -qopenmp. If you are using a different compiler, please refer to its documentation. +[OpenMP Compiler compatibility info]: :link(default-none-issues) + +Some compilers do not fully support the 'default(none)' directive +and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0 +semantics, which are incompatible with the OpenMP 3.1 directives used +in LAMMPS (for maximal compatibility with compiler versions in use). +In those case, all 'default(none)' directives (which aid in detecting +incorrect and unwanted sharing) can be replaced with 'default(shared)' +while dropping all 'shared()' directives. The script +'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate +this conversion. + :line Choice of compiler and compile/link options :h4,link(compile) @@ -137,9 +149,9 @@ simply loading the appropriate module before building LAMMPS. -D CMAKE_C_COMPILER=name # name of C compiler -D CMAKE_Fortran_COMPILER=name # name of Fortran compiler :pre --D CMAKE_CXX_FlAGS=string # flags to use with C++ compiler --D CMAKE_C_FlAGS=string # flags to use with C compiler --D CMAKE_Fortran_FlAGS=string # flags to use with Fortran compiler :pre +-D CMAKE_CXX_FLAGS=string # flags to use with C++ compiler +-D CMAKE_C_FLAGS=string # flags to use with C compiler +-D CMAKE_Fortran_FLAGS=string # flags to use with Fortran compiler :pre By default CMake will use a compiler it finds and it will add optimization flags appropriate to that compiler and any "accelerator @@ -172,7 +184,7 @@ want. Parallel build (see src/MAKE/Makefile.mpi): CC = mpicxx -CCFLAGS = -g -O3 +CCFLAGS = -g -O3 LINK = mpicxx LINKFLAGS = -g -O :pre @@ -292,7 +304,7 @@ This will create a lammps/doc/html dir with the HTML doc pages so that you can browse them locally on your system. Type "make" from the lammps/doc dir to see other options. -NOTE: You can also download a tarball of the documention for the +NOTE: You can also download a tarball of the documentation for the current LAMMPS version (HTML and PDF files), from the website "download page"_http://lammps.sandia.gov/download.html. diff --git a/doc/src/Build_cmake.txt b/doc/src/Build_cmake.txt index f8b52056fc..5c29e11280 100644 --- a/doc/src/Build_cmake.txt +++ b/doc/src/Build_cmake.txt @@ -27,7 +27,7 @@ make command to build LAMMPS, which uses the created Makefile(s). Example: cd lammps # change to the LAMMPS distribution directory -mkdir build; cd build # create a new directory (folder) for build +mkdir build; cd build # create a new directory (folder) for build cmake ../cmake \[options ...\] # configuration with (command-line) cmake make # compilation :pre @@ -44,7 +44,7 @@ LAMMPS or need to re-compile LAMMPS repeatedly, installation of the ccache (= Compiler Cache) software may speed up compilation even more. After compilation, you can optionally copy the LAMMPS executable and -library into your system folders (by default under /usr/local) with: +library into your system folders (by default under $HOME/.local) with: make install # optional, copy LAMMPS executable & library elsewhere :pre diff --git a/doc/src/Build_extras.txt b/doc/src/Build_extras.txt index d256a1afc8..65a05c267e 100644 --- a/doc/src/Build_extras.txt +++ b/doc/src/Build_extras.txt @@ -36,8 +36,8 @@ This is the list of packages that may require additional steps. "OPT"_#opt, "POEMS"_#poems, "PYTHON"_#python, -"REAX"_#reax, "VORONOI"_#voronoi, +"USER-ADIOS"_#user-adios, "USER-ATC"_#user-atc, "USER-AWPMD"_#user-awpmd, "USER-COLVARS"_#user-colvars, @@ -45,6 +45,7 @@ This is the list of packages that may require additional steps. "USER-INTEL"_#user-intel, "USER-MOLFILE"_#user-molfile, "USER-NETCDF"_#user-netcdf, +"USER-PLUMED"_#user-plumed, "USER-OMP"_#user-omp, "USER-QMMM"_#user-qmmm, "USER-QUIP"_#user-quip, @@ -63,7 +64,7 @@ available on your system. If CMake cannot find the library, you can set these variables: --D ZLIB_INCLUDE_DIR=path # path to zlib.h header file +-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file -D ZLIB_LIBRARIES=path # path to libz.a (.so) file :pre [Traditional make]: @@ -86,22 +87,31 @@ which GPU hardware to build for. # value = double or mixed (default) or single -D OCL_TUNE=value # hardware choice for GPU_API=opencl # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA) --D GPU_ARCH=value # hardware choice for GPU_API=cuda +-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda # value = sm_XX, see below # default is Cuda-compiler dependent, but typically sm_20 --D CUDPP_OPT=value # optimization setting for GPU_API=cudea +-D CUDPP_OPT=value # optimization setting for GPU_API=cuda # enables CUDA Performance Primitives Optimizations # yes (default) or no :pre GPU_ARCH settings for different GPU hardware is as follows: -sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar -sm_30 for Kepler (K10) -sm_35 for Kepler (K40) or GeForce GTX Titan or similar -sm_37 for Kepler (dual K80) -sm_50 for Maxwell -sm_60 for Pascal (P100) -sm_70 for Volta :ul +sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5) +sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5) +sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5) +sm_50 or sm_52 for Maxwell (supported since CUDA 6) +sm_60 or sm_61 for Pascal (supported since CUDA 8) +sm_70 for Volta (supported since CUDA 9) +sm_75 for Turing (supported since CUDA 10) :ul + +A more detailed list can be found, for example, +at "Wikipedia's CUDA article"_https://en.wikipedia.org/wiki/CUDA#GPUs_supported + +CMake can detect which version of the CUDA toolkit is used and thus can +include support for [all] major GPU architectures supported by this toolkit. +Thus the GPU_ARCH setting is merely an optimization, to have code for +the preferred GPU architecture directly included rather than having to wait +for the JIT compiler of the CUDA driver to translate it. [Traditional make]: @@ -127,7 +137,7 @@ specified by the "-m" switch. For your convenience, machine makefiles for "mpi" and "serial" are provided, which have the same settings as the corresponding machine makefiles in the main LAMMPS source folder. In addition you can alter 4 important settings in the -Makefile.machine you start from via the corresponding -h, -a, -p, -e +Makefile.machine you start from via the corresponding -c, -a, -p, -e switches (as in the examples above), and also save a copy of the new Makefile if desired: @@ -136,6 +146,11 @@ CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above CUDA_PRECISION = precision (double, mixed, single) EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul +The file Makefile.linux_multi is set up to include support for multiple +GPU architectures as supported by the CUDA toolkit in use. This is done +through using the "--gencode " flag, which can be used multiple times and +thus support all GPU architectures supported by your CUDA compiler. + If the library build is successful, 3 files should be created: lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps. The latter has settings that enable LAMMPS @@ -149,43 +164,38 @@ re-build LAMMPS. This is because the compilation of files in the GPU package uses the library settings from the lib/gpu/Makefile.machine used to build the GPU library. + :line - + KIM package :h4,link(kim) -To build with this package, the KIM library must be downloaded and -built on your system. It must include the KIM models that you want to -use with LAMMPS. +To build with this package, the KIM library with API v2 must be downloaded +and built on your system. It must include the KIM models that you want to +use with LAMMPS. If you want to use the "kim_query"_kim_query.html +command, you also need to have libcurl installed with the matching +development headers and the curl-config tool. Note that in LAMMPS lingo, a KIM model driver is a pair style (e.g. EAM or Tersoff). A KIM model is a pair style for a particular element or alloy and set of parameters, e.g. EAM for Cu with a -specific EAM potential file. Also note that installing the KIM API -library with all its models, may take around 30 min to build. Of -course you only need to do that once. +specific EAM potential file. Also note that downloading and installing +the KIM API library with all its models, may take a long time (10s of +minutes to hours) to build. Of course you only need to do that once. See the list of KIM model drivers here: -https://openkim.org/kim-items/model-drivers/alphabetical +https://openkim.org/browse/model-drivers/alphabetical See the list of all KIM models here: -https://openkim.org/kim-items/models/by-model-drivers - -See the list of example KIM models included by default here: -https://openkim.org/kim-api on the "What is in the KIM API source -package?" page. +https://openkim.org/browse/models/by-model-drivers [CMake build]: --D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes --D KIM_LIBRARY=path # KIM library file (only needed if a custom location) --D KIM_INCLUDE_DIR=path # KIM include directory (only needed if a custom location) :pre +-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes :pre If DOWNLOAD_KIM is set, the KIM library will be downloaded and built inside the CMake build directory. If the KIM library is already on -your system (in a location CMake cannot find it), KIM_LIBRARY is the -filename (plus path) of the KIM library file, not the directory the -library file is in. KIM_INCLUDE_DIR is the directory the KIM include -file is in. +your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH +environment variable so that libkim-api-v2 can be found. [Traditional make]: @@ -199,8 +209,8 @@ make lib-kim args="-b " # (re-)install KIM API lib with only example models make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model make lib-kim args="-b -a everything" # install KIM API lib with all models make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver -make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location -make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre +make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location +make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre :line @@ -254,7 +264,7 @@ For NVIDIA GPUs using CUDA, set these 4 variables: -D KOKKOS_ARCH="archCPU;archGPU" # archCPU = CPU from list above that is hosting the GPU # archGPU = GPU from list above -D KOKKOS_ENABLE_CUDA=yes --D KOKKOS_ENABLE_OPENMP=yes +-D KOKKOS_ENABLE_OPENMP=yes -D CMAKE_CXX_COMPILER=wrapper # wrapper = full path to Cuda nvcc wrapper :pre The wrapper value is the Cuda nvcc compiler wrapper provided in the @@ -296,7 +306,7 @@ export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper CC = mpicxx :pre :line - + LATTE package :h4,link(latte) To build with this package, you must download and build the LATTE @@ -324,7 +334,7 @@ args: make lib-latte # print help message make lib-latte args="-b" # download and build in lib/latte/LATTE-master make lib-latte args="-p $HOME/latte" # use existing LATTE installation in $HOME/latte -make lib-latte args="-b -m gfortran" # download and build in lib/latte and +make lib-latte args="-b -m gfortran" # download and build in lib/latte and # copy Makefile.lammps.gfortran to Makefile.lammps :pre @@ -335,7 +345,7 @@ also check that the Makefile.lammps file you create is appropriate for the compiler you use on your system to build LATTE. :line - + MEAM package :h4,link(meam) NOTE: the use of the MEAM package is discouraged, as it has been @@ -378,7 +388,7 @@ EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. :line - + MESSAGE package :h4,link(message) This package can optionally include support for messaging via sockets, @@ -407,7 +417,7 @@ existing Makefile.lammps.* and has settings to link with the ZeroMQ library if requested in the build. :line - + MSCG package :h4,link(mscg) To build with this package, you must download and build the MS-CG @@ -419,7 +429,7 @@ lib/mscg/README and MSCG/Install files for more details. [CMake build]: -D DOWNLOAD_MSCG=value # download MSCG for build, value = no (default) or yes --D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) +-D MSCG_LIBRARY=path # MSCG library file (only needed if a custom location) -D MSCG_INCLUDE_DIR=path # MSCG include directory (only needed if a custom location) :pre If DOWNLOAD_MSCG is set, the MSCG library will be downloaded and built @@ -464,7 +474,7 @@ line of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.opt for an example. :line - + POEMS package :h4,link(poems) [CMake build]: @@ -493,7 +503,7 @@ for your system, which should define an EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. :line - + PYTHON package :h4,link(python) Building with the PYTHON package requires you have a Python shared @@ -519,45 +529,6 @@ process to find Python. You should only need to create a new Makefile.lammps.* file (and copy it to Makefile.lammps) if the LAMMPS build fails. -:line - -REAX package :h4,link(reax) - -NOTE: the use of the REAX package and its "pair_style -reax"_pair_reax.html command is discouraged, as it is no longer -maintained. Please use the USER-REAXC package and its "pair_style -reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS -enabled variant (pair_style reax/c/kk), which has a more robust memory -management. See the "pair_style reax/c"_pair_reaxc.html doc page for -details. - -[CMake build]: - -No additional settings are needed besides "-D PKG_REAX=yes". - -[Traditional make]: - -Before building LAMMPS, you must build the REAX library in lib/reax. -You can do this manually if you prefer; follow the instructions in -lib/reax/README. You can also do it in one step from the lammps/src -dir, using a command like these, which simply invoke the -lib/reax/Install.py script with the specified args: - -make lib-reax # print help message -make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") -make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") -make lib-reax args="-m ifort" # build with Intel ifort compiler :pre - -The build should produce two files: lib/reax/libreax.a and -lib/reax/Makefile.lammps. The latter is copied from an existing -Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with -Fortran (REAX library). Typically the two compilers used for LAMMPS -and the REAX library need to be consistent (e.g. both Intel or both -GNU compilers). If necessary, you can edit/create a new -lib/reax/Makefile.machine file for your system, which should define an -EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine -file. - :line VORONOI package :h4,link(voronoi) @@ -570,7 +541,7 @@ library"_voro-home. [CMake build]: -D DOWNLOAD_VORO=value # download Voro++ for build, value = no (default) or yes --D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) +-D VORO_LIBRARY=path # Voro++ library file (only needed if at custom location) -D VORO_INCLUDE_DIR=path # Voro++ include directory (only needed if at custom location) :pre If DOWNLOAD_VORO is set, the Voro++ library will be downloaded and @@ -600,14 +571,40 @@ the lib/voronoi/Makefile.lammps file. :line +USER-ADIOS package :h4,link(user-adios) + +The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2, +version 2.3.1 or newer. Make sure that you have ADIOS built either with or +without MPI to match if you build LAMMPS with or without MPI. +ADIOS compilation settings for LAMMPS are automatically detected, if the PATH +and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS +installation and the instructions below are followed for the respective build systems. + +[CMake build]: + +-D ADIOS2_DIR=path # path is where ADIOS 2.x is installed +-D PKG_USER-ADIOS=yes :pre + +[Traditional make]: + +Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do: + +make yes-user-adios :pre + +otherwise, set ADIOS2_DIR environment variable when turning on the package: + +ADIOS2_DIR=path make yes-user-adios # path is where ADIOS 2.x is installed :pre + +:line + USER-ATC package :h4,link(user-atc) The USER-ATC package requires the MANYBODY package also be installed. [CMake build]: -No additional settings are needed besides "-D PKG_REAX=yes" and "-D -PKG_MANYBODY=yes". +No additional settings are needed besides "-D PKG_USER-ATC=yes" +and "-D PKG_MANYBODY=yes". [Traditional make]: @@ -712,6 +709,114 @@ a corresponding Makefile.lammps.machine file. :line +USER-PLUMED package :h4,link(user-plumed) + +Before building LAMMPS with this package, you must first build PLUMED. +PLUMED can be built as part of the LAMMPS build or installed separately +from LAMMPS using the generic "plumed installation instructions"_plumedinstall. +:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html) + +PLUMED can be linked into MD codes in three different modes: static, +shared, and runtime. With the "static" mode, all the code that PLUMED +requires is linked statically into LAMMPS. LAMMPS is then fully +independent from the PLUMED installation, but you have to rebuild/relink +it in order to update the PLUMED code inside it. With the "shared" +linkage mode, LAMMPS is linked to a shared library that contains the +PLUMED code. This library should preferably be installed in a globally +accessible location. When PLUMED is linked in this way the same library +can be used by multiple MD packages. Furthermore, the PLUMED library +LAMMPS uses can be updated without the need for a recompile of LAMMPS +for as long as the shared PLUMED library is ABI-compatible. + +The third linkage mode is "runtime" which allows the user to specify +which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL +environment variable. This variable should point to the location of the +libplumedKernel.so dynamical shared object, which is then loaded at +runtime. This mode of linking is particularly convenient for doing +PLUMED development and comparing multiple PLUMED versions as these sorts +of comparisons can be done without recompiling the hosting MD code. All +three linkage modes are supported by LAMMPS on selected operating +systems (e.g. Linux) and using either CMake or traditional make +build. The "static" mode should be the most portable, while the +"runtime" mode support in LAMMPS makes the most assumptions about +operating system and compiler environment. If one mode does not work, +try a different one, switch to a different build system, consider a +global PLUMED installation or consider downloading PLUMED during the +LAMMPS build. + +[CMake build]: + +When the "-D PKG_USER-PLUMED" flag is included in the cmake command you +must ensure that GSL is installed in locations that are specified in +your environment. There are then two additional commands that control +the manner in which PLUMED is obtained and linked into LAMMPS. + +-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes +-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre + +If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be +downloaded (the version of PLUMED that will be downloaded is hard-coded +to a vetted version of PLUMED, usually a recent stable release version) +and built inside the CMake build directory. If DOWNLOAD_PLUMED is set +to "no" (the default), CMake will try to detect and link to an installed +version of PLUMED. For this to work, the PLUMED library has to be +installed into a location where the pkg-config tool can find it or the +PKG_CONFIG_PATH environment variable has to be set up accordingly. +PLUMED should be installed in such a location if you compile it using +the default make; make install commands. + +The PLUMED_MODE setting determines the linkage mode for the PLUMED +library. The allowed values for this flag are "static" (default), +"shared", or "runtime". For a discussion of PLUMED linkage modes, +please see above. When DOWNLOAD_PLUMED is enabled the static linkage +mode is recommended. + +[Traditional make]: + +PLUMED needs to be installed before the USER-PLUMED package is installed +so that LAMMPS can find the right settings when compiling and linking +the LAMMPS executable. You can either download and build PLUMED inside +the LAMMPS plumed library folder or use a previously installed PLUMED +library and point LAMMPS to its location. You also have to choose the +linkage mode: "static" (default), "shared" or "runtime". For a +discussion of PLUMED linkage modes, please see above. + +Download/compilation/configuration of the plumed library can be done +from the src folder through the following make args: + +make lib-plumed # print help message +make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2 +make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local +make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in + # /usr/local and use shared linkage mode +:pre + +Note that 2 symbolic (soft) links, "includelink" and "liblink" are +created in lib/plumed that point to the location of the PLUMED build to +use. A new file lib/plumed/Makefile.lammps is also created with settings +suitable for LAMMPS to compile and link PLUMED using the desired linkage +mode. After this step is completed, you can install the USER-PLUMED +package and compile LAMMPS in the usual manner: + +make yes-user-plumed +make machine :pre + +Once this compilation completes you should be able to run LAMMPS in the +usual way. For shared linkage mode, libplumed.so must be found by the +LAMMPS executable, which on many operating systems means, you have to +set the LD_LIBRARY_PATH environment variable accordingly. + +Support for the different linkage modes in LAMMPS varies for different +operating systems, using the static linkage is expected to be the most +portable, and thus set to be the default. + +If you want to change the linkage mode, you have to re-run "make +lib-plumed" with the desired settings [and] do a re-install if the +USER-PLUMED package with "make yes-user-plumed" to update the required +makefile settings with the changes in the lib/plumed folder. + +:line + USER-H5MD package :h4,link(user-h5md) To build with this package you must have the HDF5 software package @@ -790,7 +895,17 @@ USER-MOLFILE package :h4,link(user-molfile) [CMake build]: -No additional settings are needed besides "-D PKG_USER-MOLFILE=yes". +-D MOLFILE_INCLUDE_DIRS=path # (optional) path where VMD molfile plugin headers are installed +-D PKG_USER-MOLFILE=yes :pre + + +Using "-D PKG_USER-MOLFILE=yes" enables the package, and setting +"-D MOLFILE_INCLUDE DIRS" allows to provide a custom location for +the molfile plugin header files. These should match the ABI of the +plugin files used, and thus one typically sets them to include +folder of the local VMD installation in use. LAMMPS ships with a +couple of default header files that correspond to a popular VMD +version, usually the latest release. [Traditional make]: @@ -799,7 +914,11 @@ loading library libdl.a that is typically present on all systems. It is required for LAMMPS to link with this package. If the setting is not valid for your system, you will need to edit the Makefile.lammps file. See lib/molfile/README and lib/molfile/Makefile.lammps for -details. +details. It is also possible to configure a different folder with +the VMD molfile plugin header files. LAMMPS ships with a couple of +default headers, but these are not compatible with all VMD versions, +so it is often best to change this setting to the location of the +same include files of the local VMD installation in use. :line @@ -848,7 +967,9 @@ LINKFLAGS: -fopenmp # for GNU Compilers LINKFLAGS: -qopenmp # for Intel compilers on Linux :pre For other platforms and compilers, please consult the documentation -about OpenMP support for your compiler. +about OpenMP support for your compiler. Please see the note about +how to address compatibility "issues with the 'default(none)' +directive"_Build_basics.html#default-none-issues of some compilers. :line @@ -869,7 +990,7 @@ Quantum ESPRESSO known to work with this QM/MM interface was version [CMake build]: The CMake build system currently does not support building the full -QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. +QM/MM-capable hybrid executable of LAMMPS and QE called pwqmmm.x. You must use the traditional make build for this package. [Traditional make]: @@ -939,7 +1060,7 @@ Coulomb solver library"_scafacos-home [CMake build]: -D DOWNLOAD_SCAFACOS=value # download ScaFaCoS for build, value = no (default) or yes --D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) +-D SCAFACOS_LIBRARY=path # ScaFaCos library file (only needed if at custom location) -D SCAFACOS_INCLUDE_DIR=path # ScaFaCoS include directory (only needed if at custom location) :pre If DOWNLOAD_SCAFACOS is set, the ScaFaCoS library will be downloaded diff --git a/doc/src/Build_link.txt b/doc/src/Build_link.txt index 1a1b387f3f..706c51d6bc 100644 --- a/doc/src/Build_link.txt +++ b/doc/src/Build_link.txt @@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style interface. See the sample codes in examples/COUPLE/simple for examples of C++ and -C and Fortran codes that invoke LAMMPS thru its library interface. +C and Fortran codes that invoke LAMMPS through its library interface. Other examples in the COUPLE directory use coupling ideas discussed on the "Howto couple"_Howto_couple.html doc page. diff --git a/doc/src/Build_package.txt b/doc/src/Build_package.txt index f1aa4bb671..c5eca96edb 100644 --- a/doc/src/Build_package.txt +++ b/doc/src/Build_package.txt @@ -47,8 +47,8 @@ packages: "OPT"_Build_extras.html#opt, "POEMS"_Build_extras.html#poems, "PYTHON"_Build_extras.html#python, -"REAX"_Build_extras.html#reax, "VORONOI"_Build_extras.html#voronoi, +"USER-ADIOS"_Build_extras.html#user-adios, "USER-ATC"_Build_extras.html#user-atc, "USER-AWPMD"_Build_extras.html#user-awpmd, "USER-COLVARS"_Build_extras.html#user-colvars, @@ -56,6 +56,7 @@ packages: "USER-INTEL"_Build_extras.html#user-intel, "USER-MOLFILE"_Build_extras.html#user-molfile, "USER-NETCDF"_Build_extras.html#user-netcdf, +"USER-PLUMED"_Build_extras.html#user-plumed, "USER-OMP"_Build_extras.html#user-omp, "USER-QMMM"_Build_extras.html#user-qmmm, "USER-QUIP"_Build_extras.html#user-quip, diff --git a/doc/src/Build_settings.txt b/doc/src/Build_settings.txt index 500130ecee..f1db9f0130 100644 --- a/doc/src/Build_settings.txt +++ b/doc/src/Build_settings.txt @@ -22,7 +22,7 @@ explain how to do this for building both with CMake and make. "Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b) :line - + FFT library :h4,link(fft) When the KSPACE package is included in a LAMMPS build, the @@ -73,7 +73,7 @@ FFT_LIB with the appropriate FFT libraries to include in the link. The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS distribution. It is portable across all platforms. Depending on the size of the FFTs and the number of processors used, the other -libraries listed here can be faster. +libraries listed here can be faster. However, note that long-range Coulombics are only a portion of the per-timestep CPU cost, FFTs are only a portion of long-range @@ -92,7 +92,7 @@ Building FFTW for your box should be as simple as ./configure; make; make install. The install command typically requires root privileges (e.g. invoke it via sudo), unless you specify a local directory with the "--prefix" option of configure. Type "./configure --help" to see -various options. +various options. The Intel MKL math library is part of the Intel compiler suite. It can be used with the Intel or GNU compiler (see FFT_LIB setting above). @@ -139,16 +139,16 @@ adequate. [Makefile.machine setting]: LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre - # default is LAMMMPS_SMALLBIG if not specified + # default is LAMMPS_SMALLBIG if not specified [CMake and make info]: The default "smallbig" setting allows for simulations with: - + total atom count = 2^63 atoms (about 9e18) total timesteps = 2^63 (about 9e18) atom IDs = 2^31 (about 2 billion) image flags = roll over at 512 :ul - + The "bigbig" setting increases the latter two limits. It allows for: total atom count = 2^63 atoms (about 9e18) @@ -209,12 +209,12 @@ Usually these settings are all that is needed. If CMake cannot find the graphics header, library, executable files, you can set these variables: --D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file --D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file --D PNG_INCLUDE_DIR=path # path to png.h header file --D PNG_LIBRARIES=path # path to libpng.a (.so) file --D ZLIB_INCLUDE_DIR=path # path to zlib.h header file --D ZLIB_LIBRARIES=path # path to libz.a (.so) file +-D JPEG_INCLUDE_DIR=path # path to jpeglib.h header file +-D JPEG_LIBRARIES=path # path to libjpeg.a (.so) file +-D PNG_INCLUDE_DIR=path # path to png.h header file +-D PNG_LIBRARIES=path # path to libpng.a (.so) file +-D ZLIB_INCLUDE_DIR=path # path to zlib.h header file +-D ZLIB_LIBRARIES=path # path to libz.a (.so) file -D FFMPEG_EXECUTABLE=path # path to ffmpeg executable :pre [Makefile.machine settings]: diff --git a/doc/src/Build_windows.txt b/doc/src/Build_windows.txt index 0caad589fb..bf1ec265a1 100644 --- a/doc/src/Build_windows.txt +++ b/doc/src/Build_windows.txt @@ -53,20 +53,20 @@ are included, but may not always up-to-date for recently added functionality and the corresponding new code. A machine makefile for using cygwin for the old build system is provided. The CMake build system is untested for this; you will have to request that makefiles are generated and -manually set the compiler. +manually set the compiler. When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker -flags in LIB makefile variable. Try adding -static-libgcc or -static or +flags in LIB makefile variable. Try adding -static-libgcc or -static or both to the linker flags when your resulting LAMMPS Windows executable complains about missing .dll files. The CMake configuration should set -this up automatically, but is untested. +this up automatically, but is untested. In case of problems, you are recommended to contact somebody with experience in using cygwin. If you do come across portability problems requiring changes to the LAMMPS source code, or figure out corrections yourself, please report them on the lammps-users mailing list, or file -them as an issue or pull request on the LAMMPS github project. +them as an issue or pull request on the LAMMPS GitHub project. Using a cross-compiler :h4,link(cross) diff --git a/doc/src/Commands.txt b/doc/src/Commands.txt index a1a94c6d29..bb3fab3683 100644 --- a/doc/src/Commands.txt +++ b/doc/src/Commands.txt @@ -42,10 +42,10 @@ END_RST --> "Input script structure"_Commands_structure.html "Commands by category"_Commands_category.html :all(b) -"All commands"_Commands_all.html -"Fix commands"_Commands_fix.html -"Compute commands"_Commands_compute.html -"Pair commands"_Commands_pair.html +"General commands"_Commands_all.html +"Fix commands"_Commands_fix.html +"Compute commands"_Commands_compute.html +"Pair commands"_Commands_pair.html "Bond, angle, dihedral, improper commands"_Commands_bond.html "KSpace solvers"_Commands_kspace.html :all(b) diff --git a/doc/src/Commands_all.txt b/doc/src/Commands_all.txt index 6f54681342..66c348ee30 100644 --- a/doc/src/Commands_all.txt +++ b/doc/src/Commands_all.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, @@ -17,9 +17,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c "Improper styles"_Commands_bond.html#improper, "KSpace styles"_Commands_kspace.html :tb(c=3,ea=c) -All commands :h3 +General commands :h3 -An alphabetic list of all LAMMPS commands. +An alphabetic list of all general LAMMPS commands. "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, @@ -48,23 +48,27 @@ An alphabetic list of all LAMMPS commands. "dimension"_dimension.html, "displace_atoms"_displace_atoms.html, "dump"_dump.html, +"dump adios"_dump_adios.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html, "dump movie"_dump_image.html, "dump netcdf"_dump_netcdf.html, "dump netcdf/mpiio"_dump_netcdf.html, "dump vtk"_dump_vtk.html, +"dynamical_matrix"_dynamical_matrix.html, "echo"_echo.html, "fix"_fix.html, "fix_modify"_fix_modify.html, "group"_group.html, "group2ndx"_group2ndx.html, +"hyper"_hyper.html, "if"_if.html, "info"_info.html, "improper_coeff"_improper_coeff.html, "improper_style"_improper_style.html, "include"_include.html, "jump"_jump.html, +"kim_query"_kim_query.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "label"_label.html, @@ -75,6 +79,7 @@ An alphabetic list of all LAMMPS commands. "minimize"_minimize.html, "min_modify"_min_modify.html, "min_style"_min_style.html, +"min_style spin"_min_spin.html, "molecule"_molecule.html, "ndx2group"_group2ndx.html, "neb"_neb.html, diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt index d4d48924a7..3d889ac08e 100644 --- a/doc/src/Commands_bond.txt +++ b/doc/src/Commands_bond.txt @@ -5,7 +5,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :link(ld,Manual.html) :link(lc,Commands_all.html) -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, @@ -37,6 +37,7 @@ OPT. "harmonic (iko)"_bond_harmonic.html, "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, +"mm3"_bond_mm3.html, "morse (o)"_bond_morse.html, "nonlinear (o)"_bond_nonlinear.html, "oxdna/fene"_bond_oxdna.html, @@ -60,17 +61,19 @@ OPT. "charmm (iko)"_angle_charmm.html, "class2 (ko)"_angle_class2.html, "class2/p6"_angle_class2.html, -"cosine (o)"_angle_cosine.html, +"cosine (ko)"_angle_cosine.html, "cosine/buck6d"_angle_cosine_buck6d.html, "cosine/delta (o)"_angle_cosine_delta.html, "cosine/periodic (o)"_angle_cosine_periodic.html, "cosine/shift (o)"_angle_cosine_shift.html, "cosine/shift/exp (o)"_angle_cosine_shift_exp.html, "cosine/squared (o)"_angle_cosine_squared.html, +"cross"_angle_cross.html, "dipole (o)"_angle_dipole.html, "fourier (o)"_angle_fourier.html, "fourier/simple (o)"_angle_fourier_simple.html, "harmonic (iko)"_angle_harmonic.html, +"mm3"_angle_mm3.html, "quartic (o)"_angle_quartic.html, "sdk (o)"_angle_sdk.html, "table (o)"_angle_table.html :tb(c=4,ea=c) @@ -120,8 +123,10 @@ OPT. "cossq (o)"_improper_cossq.html, "cvff (io)"_improper_cvff.html, "distance"_improper_distance.html, +"distharm"_improper_distharm.html, "fourier (o)"_improper_fourier.html, "harmonic (iko)"_improper_harmonic.html, "inversion/harmonic"_improper_inversion_harmonic.html, "ring (o)"_improper_ring.html, +"sqdistharm"_improper_sqdistharm.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) diff --git a/doc/src/Commands_category.txt b/doc/src/Commands_category.txt index 5d047c6727..134dae82bb 100644 --- a/doc/src/Commands_category.txt +++ b/doc/src/Commands_category.txt @@ -10,10 +10,9 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Commands by category :h3 This page lists most of the LAMMPS commands, grouped by category. The -"Commands all"_Commands_all.html doc page lists all commands -alphabetically. It also includes long lists of style options for -entries that appear in the following categories as a single command -(fix, compute, pair, etc). +"General commands"_Commands_all.html doc page lists all general commands +alphabetically. Style options for entries like fix, compute, pair etc. +have their own pages where they are listed alphabetically. Initialization: diff --git a/doc/src/Commands_compute.txt b/doc/src/Commands_compute.txt index eb802030e2..f566702609 100644 --- a/doc/src/Commands_compute.txt +++ b/doc/src/Commands_compute.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, diff --git a/doc/src/Commands_fix.txt b/doc/src/Commands_fix.txt index 4144c7eb90..678cc9ba0d 100644 --- a/doc/src/Commands_fix.txt +++ b/doc/src/Commands_fix.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, @@ -78,6 +78,8 @@ OPT. "grem"_fix_grem.html, "halt"_fix_halt.html, "heat"_fix_heat.html, +"hyper/global"_fix_hyper_global.html, +"hyper/local"_fix_hyper_local.html, "imd"_fix_imd.html, "indent"_fix_indent.html, "ipi"_fix_ipi.html, @@ -94,6 +96,7 @@ OPT. "lineforce"_fix_lineforce.html, "manifoldforce"_fix_manifoldforce.html, "meso"_fix_meso.html, +"meso/move"_fix_meso_move.html, "meso/stationary"_fix_meso_stationary.html, "momentum (k)"_fix_momentum.html, "move"_fix_move.html, @@ -107,7 +110,7 @@ OPT. "nph/asphere (o)"_fix_nph_asphere.html, "nph/body"_fix_nph_body.html, "nph/eff"_fix_nh_eff.html, -"nph/sphere (ko)"_fix_nph_sphere.html, +"nph/sphere (o)"_fix_nph_sphere.html, "nphug (o)"_fix_nphug.html, "npt (iko)"_fix_nh.html, "npt/asphere (o)"_fix_npt_asphere.html, @@ -127,7 +130,7 @@ OPT. "nve/line"_fix_nve_line.html, "nve/manifold/rattle"_fix_nve_manifold_rattle.html, "nve/noforce"_fix_nve_noforce.html, -"nve/sphere (o)"_fix_nve_sphere.html, +"nve/sphere (ko)"_fix_nve_sphere.html, "nve/spin"_fix_nve_spin.html, "nve/tri"_fix_nve_tri.html, "nvk"_fix_nvk.html, @@ -146,6 +149,7 @@ OPT. "phonon"_fix_phonon.html, "pimd"_fix_pimd.html, "planeforce"_fix_planeforce.html, +"plumed"_fix_plumed.html, "poems"_fix_poems.html, "pour"_fix_pour.html, "precession/spin"_fix_precession_spin.html, @@ -165,13 +169,13 @@ OPT. "qmmm"_fix_qmmm.html, "qtb"_fix_qtb.html, "rattle"_fix_shake.html, -"reax/bonds"_fix_reax_bonds.html, -"reax/c/bonds (k)"_fix_reax_bonds.html, +"reax/c/bonds (k)"_fix_reaxc_bonds.html, "reax/c/species (k)"_fix_reaxc_species.html, "recenter"_fix_recenter.html, "restrain"_fix_restrain.html, "rhok"_fix_rhok.html, "rigid (o)"_fix_rigid.html, +"rigid/meso"_fix_rigid_meso.html, "rigid/nph (o)"_fix_rigid.html, "rigid/nph/small"_fix_rigid.html, "rigid/npt (o)"_fix_rigid.html, @@ -230,4 +234,4 @@ OPT. "wall/reflect (k)"_fix_wall_reflect.html, "wall/region"_fix_wall_region.html, "wall/region/ees"_fix_wall_ees.html, -"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) +"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c) diff --git a/doc/src/Commands_kspace.txt b/doc/src/Commands_kspace.txt index d56b7fa767..02b41b9d67 100644 --- a/doc/src/Commands_kspace.txt +++ b/doc/src/Commands_kspace.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt index a74574367c..b18d852c09 100644 --- a/doc/src/Commands_pair.txt +++ b/doc/src/Commands_pair.txt @@ -7,7 +7,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c :line -"All commands"_Commands_all.html, +"General commands"_Commands_all.html, "Fix styles"_Commands_fix.html, "Compute styles"_Commands_compute.html, "Pair styles"_Commands_pair.html, @@ -63,13 +63,13 @@ OPT. "comb (o)"_pair_comb.html, "comb3"_pair_comb.html, "coul/cut (gko)"_pair_coul.html, -"coul/cut/soft (o)"_pair_lj_soft.html, +"coul/cut/soft (o)"_pair_fep_soft.html, "coul/debye (gko)"_pair_coul.html, "coul/diel (o)"_pair_coul_diel.html, "coul/dsf (gko)"_pair_coul.html, "coul/long (gko)"_pair_coul.html, "coul/long/cs (g)"_pair_cs.html, -"coul/long/soft (o)"_pair_lj_soft.html, +"coul/long/soft (o)"_pair_fep_soft.html, "coul/msm (o)"_pair_coul.html, "coul/shield"_pair_coul_shield.html, "coul/streitz"_pair_coul.html, @@ -107,38 +107,42 @@ OPT. "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "lcbop"_pair_lcbop.html, +"lebedeva/z"_pair_lebedeva_z.html, "lennard/mdf"_pair_mdf.html, "line/lj"_pair_line_lj.html, "list"_pair_list.html, "lj/charmm/coul/charmm (iko)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, "lj/charmm/coul/long (gikot)"_pair_charmm.html, -"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html, +"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html, "lj/charmm/coul/msm (o)"_pair_charmm.html, "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, "lj/charmmfsw/coul/long"_pair_charmm.html, "lj/class2 (gko)"_pair_class2.html, "lj/class2/coul/cut (ko)"_pair_class2.html, +"lj/class2/coul/cut/soft"_pair_fep_soft.html, "lj/class2/coul/long (gko)"_pair_class2.html, +"lj/class2/coul/long/soft"_pair_fep_soft.html, +"lj/class2/soft"_pair_fep_soft.html, "lj/cubic (go)"_pair_lj_cubic.html, "lj/cut (gikot)"_pair_lj.html, "lj/cut/coul/cut (gko)"_pair_lj.html, -"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html, "lj/cut/coul/debye (gko)"_pair_lj.html, "lj/cut/coul/dsf (gko)"_pair_lj.html, "lj/cut/coul/long (gikot)"_pair_lj.html, "lj/cut/coul/long/cs"_pair_cs.html, -"lj/cut/coul/long/soft (o)"_pair_lj_soft.html, +"lj/cut/coul/long/soft (o)"_pair_fep_soft.html, "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/coul/wolf (o)"_pair_lj.html, "lj/cut/dipole/cut (go)"_pair_dipole.html, "lj/cut/dipole/long (g)"_pair_dipole.html, "lj/cut/dipole/sf (go)"_pair_dipole.html, -"lj/cut/soft (o)"_pair_lj_soft.html, +"lj/cut/soft (o)"_pair_fep_soft.html, "lj/cut/thole/long (o)"_pair_thole.html, "lj/cut/tip4p/cut (o)"_pair_lj.html, "lj/cut/tip4p/long (ot)"_pair_lj.html, -"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, +"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html, "lj/expand (gko)"_pair_lj_expand.html, "lj/expand/coul/long (g)"_pair_lj_expand.html, "lj/gromacs (gko)"_pair_gromacs.html, @@ -153,6 +157,7 @@ OPT. "lj/sf/dipole/sf (go)"_pair_dipole.html, "lj/smooth (o)"_pair_lj_smooth.html, "lj/smooth/linear (o)"_pair_lj_smooth_linear.html, +"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html, "lj96/cut (go)"_pair_lj96.html, "lubricate (o)"_pair_lubricate.html, "lubricate/poly (o)"_pair_lubricate.html, @@ -160,8 +165,7 @@ OPT. "lubricateU/poly"_pair_lubricateU.html, "mdpd"_pair_meso.html, "mdpd/rhosum"_pair_meso.html, -"meam"_pair_meam.html, -"meam/c"_pair_meam.html, +"meam/c"_pair_meamc.html, "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, @@ -169,7 +173,7 @@ OPT. "momb"_pair_momb.html, "morse (gkot)"_pair_morse.html, "morse/smooth/linear (o)"_pair_morse.html, -"morse/soft"_pair_morse.html, +"morse/soft"_pair_fep_soft.html, "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx (k)"_pair_multi_lucy_rx.html, "nb3b/harmonic"_pair_nb3b_harmonic.html, @@ -194,10 +198,10 @@ OPT. "polymorphic"_pair_polymorphic.html, "python"_pair_python.html, "quip"_pair_quip.html, -"reax"_pair_reax.html, "reax/c (ko)"_pair_reaxc.html, "rebo (io)"_pair_airebo.html, "resquared (go)"_pair_resquared.html, +"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, "smd/tri_surface"_pair_smd_triangulated_surface.html, @@ -229,7 +233,7 @@ OPT. "thole"_pair_thole.html, "tip4p/cut (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html, -"tip4p/long/soft (o)"_pair_lj_soft.html, +"tip4p/long/soft (o)"_pair_fep_soft.html, "tri/lj"_pair_tri_lj.html, "ufm (got)"_pair_ufm.html, "vashishta (gko)"_pair_vashishta.html, diff --git a/doc/src/Commands_parse.txt b/doc/src/Commands_parse.txt index 1d7c754fa7..13a4c2699d 100644 --- a/doc/src/Commands_parse.txt +++ b/doc/src/Commands_parse.txt @@ -91,7 +91,7 @@ See the "variable"_variable.html command for more details of how strings are assigned to variables and evaluated, and how they can be used in input script commands. -(4) The line is broken into "words" separated by whitespace (tabs, +(4) The line is broken into "words" separated by white-space (tabs, spaces). Note that words can thus contain letters, digits, underscores, or punctuation characters. diff --git a/doc/src/Developer/.gitignore b/doc/src/Developer/.gitignore new file mode 100644 index 0000000000..38f7323f7b --- /dev/null +++ b/doc/src/Developer/.gitignore @@ -0,0 +1,3 @@ +/developer.aux +/developer.log +/developer.toc diff --git a/doc/src/Eqs/angle_cross.jpg b/doc/src/Eqs/angle_cross.jpg new file mode 100644 index 0000000000..b0f3fcf83a Binary files /dev/null and b/doc/src/Eqs/angle_cross.jpg differ diff --git a/doc/src/Eqs/angle_cross.tex b/doc/src/Eqs/angle_cross.tex new file mode 100644 index 0000000000..9d1fdcb7f8 --- /dev/null +++ b/doc/src/Eqs/angle_cross.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} +$$ + E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right) +$$ + +\end{document} diff --git a/doc/src/Eqs/angle_mm3.jpg b/doc/src/Eqs/angle_mm3.jpg new file mode 100644 index 0000000000..5b9f3e34f0 Binary files /dev/null and b/doc/src/Eqs/angle_mm3.jpg differ diff --git a/doc/src/Eqs/angle_mm3.tex b/doc/src/Eqs/angle_mm3.tex new file mode 100644 index 0000000000..e2d96f2d69 --- /dev/null +++ b/doc/src/Eqs/angle_mm3.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} +$$ + E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right] +$$ + +\end{document} diff --git a/doc/src/Eqs/bond_mm3.jpg b/doc/src/Eqs/bond_mm3.jpg new file mode 100644 index 0000000000..2c17739db5 Binary files /dev/null and b/doc/src/Eqs/bond_mm3.jpg differ diff --git a/doc/src/Eqs/bond_mm3.tex b/doc/src/Eqs/bond_mm3.tex new file mode 100644 index 0000000000..549500ebac --- /dev/null +++ b/doc/src/Eqs/bond_mm3.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} +$$ + E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right] +$$ + +\end{document} diff --git a/doc/src/Eqs/improper_distharm.jpg b/doc/src/Eqs/improper_distharm.jpg new file mode 100644 index 0000000000..e55036b5bf Binary files /dev/null and b/doc/src/Eqs/improper_distharm.jpg differ diff --git a/doc/src/Eqs/improper_distharm.tex b/doc/src/Eqs/improper_distharm.tex new file mode 100644 index 0000000000..218de6a0dd --- /dev/null +++ b/doc/src/Eqs/improper_distharm.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} +$$ + E = K (d - d_0)^2 +$$ + +\end{document} diff --git a/doc/src/Eqs/improper_sqdistharm.jpg b/doc/src/Eqs/improper_sqdistharm.jpg new file mode 100644 index 0000000000..b1a84e995e Binary files /dev/null and b/doc/src/Eqs/improper_sqdistharm.jpg differ diff --git a/doc/src/Eqs/improper_sqdistharm.tex b/doc/src/Eqs/improper_sqdistharm.tex new file mode 100644 index 0000000000..1b50a309a0 --- /dev/null +++ b/doc/src/Eqs/improper_sqdistharm.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} +$$ + E = K (d^2 - d_0^2)^2 +$$ + +\end{document} diff --git a/doc/src/Eqs/min_spin_damping.jpg b/doc/src/Eqs/min_spin_damping.jpg new file mode 100644 index 0000000000..0c700cc678 Binary files /dev/null and b/doc/src/Eqs/min_spin_damping.jpg differ diff --git a/doc/src/Eqs/min_spin_damping.tex b/doc/src/Eqs/min_spin_damping.tex new file mode 100644 index 0000000000..88b05447d3 --- /dev/null +++ b/doc/src/Eqs/min_spin_damping.tex @@ -0,0 +1,13 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + \frac{d \vec{s}_{i}}{dt} = \lambda\, \vec{s}_{i} \times\left( \vec{\omega}_{i} \times\vec{s}_{i} \right) + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/min_spin_timestep.jpg b/doc/src/Eqs/min_spin_timestep.jpg new file mode 100644 index 0000000000..0d8f8d07f9 Binary files /dev/null and b/doc/src/Eqs/min_spin_timestep.jpg differ diff --git a/doc/src/Eqs/min_spin_timestep.tex b/doc/src/Eqs/min_spin_timestep.tex new file mode 100644 index 0000000000..b0f6e68e4d --- /dev/null +++ b/doc/src/Eqs/min_spin_timestep.tex @@ -0,0 +1,14 @@ +\documentclass[preview]{standalone} +\usepackage{varwidth} +\usepackage[utf8x]{inputenc} +\usepackage{amsmath, amssymb, graphics, setspace} + +\begin{document} +\begin{varwidth}{50in} + \begin{equation} + {\Delta t}_{\rm max} = \frac{2\pi}{\kappa + \left|\vec{\omega}_{\rm max} \right|} + \nonumber + \end{equation} +\end{varwidth} +\end{document} diff --git a/doc/src/Eqs/pair_coulgauss.jpg b/doc/src/Eqs/pair_coulgauss.jpg new file mode 100644 index 0000000000..bf84d90c4a Binary files /dev/null and b/doc/src/Eqs/pair_coulgauss.jpg differ diff --git a/doc/src/Eqs/pair_coulgauss.tex b/doc/src/Eqs/pair_coulgauss.tex new file mode 100644 index 0000000000..216d3b3360 --- /dev/null +++ b/doc/src/Eqs/pair_coulgauss.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + \thispagestyle{empty} +\begin{eqnarray*} + E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}} +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/pair_lebedeva.png b/doc/src/Eqs/pair_lebedeva.png new file mode 100644 index 0000000000..af2ac87653 Binary files /dev/null and b/doc/src/Eqs/pair_lebedeva.png differ diff --git a/doc/src/Eqs/pair_lj_switch3.jpg b/doc/src/Eqs/pair_lj_switch3.jpg new file mode 100644 index 0000000000..a1f98ea2c2 Binary files /dev/null and b/doc/src/Eqs/pair_lj_switch3.jpg differ diff --git a/doc/src/Eqs/pair_lj_switch3.tex b/doc/src/Eqs/pair_lj_switch3.tex new file mode 100644 index 0000000000..29161fb2ef --- /dev/null +++ b/doc/src/Eqs/pair_lj_switch3.tex @@ -0,0 +1,11 @@ +\documentclass[12pt]{article} + +\begin{document} + \thispagestyle{empty} + +\begin{eqnarray*} + E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right] +% \qquad r < r_c \\ +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/pair_mm3_switch3.jpg b/doc/src/Eqs/pair_mm3_switch3.jpg new file mode 100644 index 0000000000..5d662584a7 Binary files /dev/null and b/doc/src/Eqs/pair_mm3_switch3.jpg differ diff --git a/doc/src/Eqs/pair_mm3_switch3.tex b/doc/src/Eqs/pair_mm3_switch3.tex new file mode 100644 index 0000000000..a80278cce2 --- /dev/null +++ b/doc/src/Eqs/pair_mm3_switch3.tex @@ -0,0 +1,11 @@ +\documentclass[12pt]{article} + +\begin{document} + \thispagestyle{empty} +\begin{eqnarray*} + E &=& \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\ + r_{v,ij} &=& r_{v,i} + r_{v,j} \\ + \epsilon_{ij} &=& \sqrt{\epsilon_i \epsilon_j} +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/pair_switch3.jpg b/doc/src/Eqs/pair_switch3.jpg new file mode 100644 index 0000000000..e6327ee5ff Binary files /dev/null and b/doc/src/Eqs/pair_switch3.jpg differ diff --git a/doc/src/Eqs/pair_switch3.tex b/doc/src/Eqs/pair_switch3.tex new file mode 100644 index 0000000000..7ae67a5e65 --- /dev/null +++ b/doc/src/Eqs/pair_switch3.tex @@ -0,0 +1,14 @@ +\documentclass[12pt]{article} + +\begin{document} +\thispagestyle{empty} + +\begin{eqnarray*} + S_3(r) = \left\lbrace \begin{array}{ll} + 1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\ + 3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\ + 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c} + \end{array} \right. +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Errors.txt b/doc/src/Errors.txt index 10f84874a3..0489d228bd 100644 --- a/doc/src/Errors.txt +++ b/doc/src/Errors.txt @@ -32,7 +32,7 @@ END_RST --> "Common problems"_Errors_common.html "Reporting bugs"_Errors_bugs.html -"Error messages"_Errors_messages.html +"Error messages"_Errors_messages.html "Warning messages"_Errors_warnings.html :all(b) diff --git a/doc/src/Errors_common.txt b/doc/src/Errors_common.txt index 651040ebc9..da90aad64b 100644 --- a/doc/src/Errors_common.txt +++ b/doc/src/Errors_common.txt @@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the input with an error message (for instance, when an integer is required, but a floating-point number 1.0 is provided): -ERROR: Expected integer parameter in input script or data file :pre +ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre Some commands allow for using variable references in place of numeric constants so that the value can be evaluated and may change over the @@ -85,6 +85,9 @@ reading the input and before parsing commands, NOTE: Using a variable reference (i.e. {v_name}) is only allowed if the documentation of the corresponding command explicitly says it is. +Otherwise, you will receive an error message of this kind: + +ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre Generally, LAMMPS will print a message to the screen and logfile and exit gracefully when it encounters a fatal error. Sometimes it will diff --git a/doc/src/Errors_messages.txt b/doc/src/Errors_messages.txt index 695b949f7e..fb5003e602 100644 --- a/doc/src/Errors_messages.txt +++ b/doc/src/Errors_messages.txt @@ -279,12 +279,6 @@ multibody joint). The bodies you have defined exceed this limit. :dd This is an internal LAMMPS error. Please report it to the developers. :dd -{Atom sorting has bin size = 0.0} :dt - -The neighbor cutoff is being used as the bin size, but it is zero. -Thus you must explicitly list a bin size in the atom_modify sort -command or turn off sorting. :dd - {Atom style hybrid cannot have hybrid as an argument} :dt Self-explanatory. :dd @@ -421,9 +415,9 @@ This is an internal error. It should normally not occur. :dd This is an internal error. It should normally not occur. :dd -{Bad real space Coulomb cutoff in fix tune/kspace} :dt +{Bad real space Coulombic cutoff in fix tune/kspace} :dt -Fix tune/kspace tried to find the optimal real space Coulomb cutoff using +Fix tune/kspace tried to find the optimal real space Coulombic cutoff using the Newton-Rhaphson method, but found a non-positive or NaN cutoff :dd {Balance command before simulation box is defined} :dt @@ -460,7 +454,7 @@ compute. :dd {Big particle in fix srd cannot be point particle} :dt -Big particles must be extended spheriods or ellipsoids. :dd +Big particles must be extended spheroids or ellipsoids. :dd {Bigint setting in lmptype.h is invalid} :dt @@ -780,7 +774,7 @@ Cannot use tilt factors unless the simulation box is non-orthogonal. :dd Self-explanatory. :dd -{Cannot change box z boundary to nonperiodic for a 2d simulation} :dt +{Cannot change box z boundary to non-periodic for a 2d simulation} :dt Self-explanatory. :dd @@ -1288,7 +1282,7 @@ are defined. :dd You cannot reset the timestep when a fix that keeps track of elapsed time is in place. :dd -{Cannot run 2d simulation with nonperiodic Z dimension} :dt +{Cannot run 2d simulation with non-periodic Z dimension} :dt Use the boundary command to make the z dimension periodic in order to run a 2d simulation. :dd @@ -2116,29 +2110,29 @@ Self-explanatory. :dd Fix setforce cannot be used in this manner. Use fix addforce instead. :dd -{Cannot use nonperiodic boundares with fix ttm} :dt +{Cannot use non-periodic boundares with fix ttm} :dt This fix requires a fully periodic simulation box. :dd -{Cannot use nonperiodic boundaries with Ewald} :dt +{Cannot use non-periodic boundaries with Ewald} :dt For kspace style ewald, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with EwaldDisp} :dt +{Cannot use non-periodic boundaries with EwaldDisp} :dt For kspace style ewald/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with PPPM} :dt +{Cannot use non-periodic boundaries with PPPM} :dt For kspace style pppm, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a non-periodic z dimension. :dd -{Cannot use nonperiodic boundaries with PPPMDisp} :dt +{Cannot use non-periodic boundaries with PPPMDisp} :dt For kspace style pppm/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d @@ -3351,21 +3345,21 @@ probably due to errors in the Python code. :dd The default minimum order is 2. This can be reset by the kspace_modify minorder command. :dd -{Coulomb cut not supported in pair_style buck/long/coul/coul} :dt +{Coulombic cutoff not supported in pair_style buck/long/coul/coul} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cut not supported in pair_style lj/long/coul/long} :dt +{Coulombic cutoff not supported in pair_style lj/long/coul/long} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cut not supported in pair_style lj/long/tip4p/long} :dt +{Coulombic cutoff not supported in pair_style lj/long/tip4p/long} :dt Must use long-range Coulombic interactions. :dd -{Coulomb cutoffs of pair hybrid sub-styles do not match} :dt +{Coulombic cutoffs of pair hybrid sub-styles do not match} :dt -If using a Kspace solver, all Coulomb cutoffs of long pair styles must +If using a Kspace solver, all Coulombic cutoffs of long pair styles must be the same. :dd {Coulombic cut not supported in pair_style lj/long/dipole/long} :dt @@ -5938,9 +5932,9 @@ map command will force an atom map to be created. :dd Self-explanatory. :dd -{Input line quote not followed by whitespace} :dt +{Input line quote not followed by white-space} :dt -An end quote must be followed by whitespace. :dd +An end quote must be followed by white-space. :dd {Insertion region extends outside simulation box} :dt @@ -6923,7 +6917,7 @@ types. :dd {Invalid use of library file() function} :dt -This function is called thru the library interface. This +This function is called through the library interface. This error should not occur. Contact the developers if it does. :dd {Invalid value in set command} :dt @@ -6994,12 +6988,6 @@ The atom style defined does not have this attribute. :dd The atom style defined does not have these attributes. :dd -{KIM neighbor iterator exceeded range} :dt - -This should not happen. It likely indicates a bug -in the KIM implementation of the interatomic potential -where it is requesting neighbors incorrectly. :dd - {KOKKOS package does not yet support comm_style tiled} :dt Self-explanatory. :dd @@ -7014,7 +7002,7 @@ The kspace accuracy designated in the input must be greater than zero. :dd {KSpace accuracy too large to estimate G vector} :dt -Reduce the accuracy request or specify gwald explicitly +Reduce the accuracy request or specify gewald explicitly via the kspace_modify command. :dd {KSpace accuracy too low} :dt @@ -8014,7 +8002,7 @@ Self-explanatory. :dd {Package command after simulation box is defined} :dt -The package command cannot be used afer a read_data, read_restart, or +The package command cannot be used after a read_data, read_restart, or create_box command. :dd {Package gpu command without GPU package installed} :dt @@ -9198,7 +9186,7 @@ creates one large file for all processors. :dd {Restart file byte ordering is not recognized} :dt The file does not appear to be a LAMMPS restart file since it doesn't -contain a recognized byte-orderomg flag at the beginning. :dd +contain a recognized byte-ordering flag at the beginning. :dd {Restart file byte ordering is swapped} :dt @@ -9410,7 +9398,7 @@ You may also want to boost the page size. :dd {Small to big integers are not sized correctly} :dt -This error occurs whenthe sizes of smallint, imageint, tagint, bigint, +This error occurs when the sizes of smallint, imageint, tagint, bigint, as defined in src/lmptype.h are not what is expected. Contact the developers if this occurs. :dd @@ -10191,10 +10179,6 @@ valid. :dd Self-explanatory. :dd -{Unrecognized virial argument in pair_style command} :dt - -Only two options are supported: LAMMPSvirial and KIMvirial :dd - {Unsupported mixing rule in kspace_style ewald/disp} :dt Only geometric mixing is supported. :dd diff --git a/doc/src/Errors_warnings.txt b/doc/src/Errors_warnings.txt index 0980120a10..47dd597af8 100644 --- a/doc/src/Errors_warnings.txt +++ b/doc/src/Errors_warnings.txt @@ -178,12 +178,6 @@ When using fixes like box/relax, the potential energy used by the minimizer is augmented by an additional energy provided by the fix. Thus the printed converged energy may be different from the total potential energy. :dd -{Energy tally does not account for 'zero yes'} :dt - -The energy removed by using the 'zero yes' flag is not accounted -for in the energy tally and thus energy conservation cannot be -monitored in this case. :dd - {Estimated error in splitting of dispersion coeffs is %g} :dt Error is greater than 0.0001 percent. :dd @@ -757,7 +751,7 @@ Self-explanatory. :dd This may indicate the shell command did not operate as expected. :dd -{Should not allow rigid bodies to bounce off relecting walls} :dt +{Should not allow rigid bodies to bounce off reflecting walls} :dt LAMMPS allows this, but their dynamics are not computed correctly. :dd @@ -850,10 +844,10 @@ Most FENE models need this setting for the special_bonds command. :dd Most FENE models need this setting for the special_bonds command. :dd -{Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions} :dt +{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt This is likely not what you want to do. The exclusion settings will -eliminate neighbors in the neighbor list, which the manybody potential +eliminate neighbors in the neighbor list, which the many-body potential needs to calculated its terms correctly. :dd {Using compute temp/deform with inconsistent fix deform remap option} :dt diff --git a/doc/src/Examples.txt b/doc/src/Examples.txt index 4b6db8a047..e26e6abd99 100644 --- a/doc/src/Examples.txt +++ b/doc/src/Examples.txt @@ -78,7 +78,7 @@ micelle: self-assembly of small lipid-like molecules into 2d bilayers min: energy minimization of 2d LJ melt mscg: parameterize a multi-scale coarse-graining (MSCG) model msst: MSST shock dynamics -nb3b: use of nonbonded 3-body harmonic pair style +nb3b: use of non-bonded 3-body harmonic pair style neb: nudged elastic band (NEB) calculation for barrier finding nemd: non-equilibrium MD of 2d sheared system obstacle: flow around two voids in a 2d channel diff --git a/doc/src/Howto.txt b/doc/src/Howto.txt index 730b492699..36f6be7194 100644 --- a/doc/src/Howto.txt +++ b/doc/src/Howto.txt @@ -45,7 +45,7 @@ General howto :h3 LAMMPS Users Manual - + @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 -24 Oct 2018 version :c,h2 +28 Feb 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html @@ -37,27 +37,21 @@ LAMMPS is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The "LAMMPS website"_lws has a variety of information about the code. -It includes links to an on-line version of this manual, a "mail +It includes links to an on-line version of this manual, a "mailing list"_http://lammps.sandia.gov/mail.html where users can post -questions, and a "GitHub site"https://github.com/lammps/lammps where +questions, and a "GitHub site"_https://github.com/lammps/lammps where all LAMMPS development is coordinated. :line -"PDF file"_Manual.pdf of the entire manual, generated by -"htmldoc"_http://freecode.com/projects/htmldoc - The content for this manual is part of the LAMMPS distribution. You can build a local copy of the Manual as HTML pages or a PDF file, by following the steps on the "Manual build"_Manual_build.html doc page. - There is also a "Developer.pdf"_Developer.pdf document which gives a brief description of the basic code structure of LAMMPS. :line -This manual is organized into the following sections. - Once you are familiar with LAMMPS, you may want to bookmark "this page"_Commands.html since it gives quick access to a doc page for every LAMMPS command. diff --git a/doc/src/Manual_build.txt b/doc/src/Manual_build.txt index ac12dd7b2e..e9df0d2cfc 100644 --- a/doc/src/Manual_build.txt +++ b/doc/src/Manual_build.txt @@ -61,10 +61,12 @@ make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf) make old # generate old-style HTML pages in old dir via txt2html make fetch # fetch HTML doc pages and 2 PDF files from web site # as a tarball and unpack into html dir and 2 PDFs -make epub # generate LAMMPS.epub in ePUB format using Sphinx +make epub # generate LAMMPS.epub in ePUB format using Sphinx make mobi # generate LAMMPS.mobi in MOBI format using ebook-convert make clean # remove intermediate RST files created by HTML build make clean-all # remove entire build folder and any cached data :pre +make anchor_check # check for duplicate anchor labels +make spelling # spell-check the manual :line @@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index. Installing prerequisites for PDF build -[TBA] +Building the PDF manual requires a working C++ compiler (to +compile the txt2html tool and a working installation of +"HTMLDOC"_https://www.msweet.org/htmldoc/ +HTMLDOC has its own list of prerequisites, but in most cases +you can install a binary package of it either through your +Linux package manager or MacOS (dmg) and Windows installer +(msi) packages from its +"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases :line diff --git a/doc/src/Modify_contribute.txt b/doc/src/Modify_contribute.txt index 8cbea8bb31..31d459de1a 100644 --- a/doc/src/Modify_contribute.txt +++ b/doc/src/Modify_contribute.txt @@ -33,11 +33,11 @@ how much effort it will cause to integrate and test it, how much it requires changes to the core codebase, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see the -"Howto github"_Howto_github.html doc page for instructions on how to +"Using GitHub with LAMMPS Howto"_Howto_github.html doc page for instructions on how to submit your changes or new files through a GitHub pull request. If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of -LAMMPS and contains all bugfixes from it. Then create a gzipped tar +LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms. @@ -108,9 +108,13 @@ your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, [no tabs], no lines over 80 characters. I/O is done via -the C-style stdio library, class header files should not import any -system headers outside , STL containers should be avoided -in headers, and forward declarations used where possible or needed. +the C-style stdio library (mixing of stdio and iostreams is generally +discouraged), class header files should not import any system headers +outside of , STL containers should be avoided in headers, +system header from the C library should use the C++-style names +(, , or ) instead of the C-style names +, , or ), and forward declarations +used where possible or needed to avoid including headers. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. diff --git a/doc/src/Modify_pair.txt b/doc/src/Modify_pair.txt index 0ebf2daa30..40806937d6 100644 --- a/doc/src/Modify_pair.txt +++ b/doc/src/Modify_pair.txt @@ -10,7 +10,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c Pair styles :h3 Classes that compute pairwise interactions are derived from the Pair -class. In LAMMPS, pairwise calculation include manybody potentials +class. In LAMMPS, pairwise calculation include many-body potentials such as EAM or Tersoff where particles interact without a static bond topology. New styles can be created to add new pair potentials to LAMMPS. diff --git a/doc/src/Modify_region.txt b/doc/src/Modify_region.txt index cdf192323a..c7a56bd32a 100644 --- a/doc/src/Modify_region.txt +++ b/doc/src/Modify_region.txt @@ -20,6 +20,6 @@ Here is a brief description of methods you define in your new derived class. See region.h for details. inside: determine whether a point is in the region -surface_interior: determine if a point is within a cutoff distance inside of surc -surface_exterior: determine if a point is within a cutoff distance outside of surf +surface_interior: determine if a point is within a cutoff distance inside of surface +surface_exterior: determine if a point is within a cutoff distance outside of surface shape_update : change region shape if set by time-dependent variable :tb(s=:) diff --git a/doc/src/PDF/SPH_LAMMPS_userguide.pdf b/doc/src/PDF/SPH_LAMMPS_userguide.pdf old mode 100755 new mode 100644 diff --git a/doc/src/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf index 843bba00d5..7fcf366015 100644 Binary files a/doc/src/PDF/USER-CGDNA.pdf and b/doc/src/PDF/USER-CGDNA.pdf differ diff --git a/doc/src/PDF/colvars-refman-lammps.pdf b/doc/src/PDF/colvars-refman-lammps.pdf index 4afeedccc8..07d8254475 100644 Binary files a/doc/src/PDF/colvars-refman-lammps.pdf and b/doc/src/PDF/colvars-refman-lammps.pdf differ diff --git a/doc/src/PDF/kspace.pdf b/doc/src/PDF/kspace.pdf old mode 100755 new mode 100644 diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt index 031858e846..0ab1b5e4fd 100644 --- a/doc/src/Packages_details.txt +++ b/doc/src/Packages_details.txt @@ -45,7 +45,6 @@ as contained in the file name. "LATTE"_#PKG-LATTE, "MANYBODY"_#PKG-MANYBODY, "MC"_#PKG-MC, -"MEAM"_#PKG-MEAM, "MESSAGE"_#PKG-MESSAGE, "MISC"_#PKG-MISC, "MOLECULE"_#PKG-MOLECULE, @@ -56,7 +55,6 @@ as contained in the file name. "POEMS"_#PKG-POEMS, "PYTHON"_#PKG-PYTHON, "QEQ"_#PKG-QEQ, -"REAX"_#PKG-REAX, "REPLICA"_#PKG-REPLICA2, "RIGID"_#PKG-RIGID, "SHOCK"_#PKG-SHOCK, @@ -65,6 +63,7 @@ as contained in the file name. "SRD"_#PKG-SRD, "VORONOI"_#PKG-VORONOI :tb(c=6,ea=c) +"USER-ADIOS"_#PKG-USER-ADIOS, "USER-ATC"_#PKG-USER-ATC, "USER-AWPMD"_#PKG-USER-AWPMD, "USER-BOCS"_#PKG-USER-BOCS, @@ -89,18 +88,21 @@ as contained in the file name. "USER-NETCDF"_#PKG-USER-NETCDF, "USER-OMP"_#PKG-USER-OMP, "USER-PHONON"_#PKG-USER-PHONON, +"USER-PLUMED"_#PKG-USER-PLUMED, "USER-PTM"_#PKG-USER-PTM, "USER-QMMM"_#PKG-USER-QMMM, "USER-QTB"_#PKG-USER-QTB, "USER-QUIP"_#PKG-USER-QUIP, "USER-REAXC"_#PKG-USER-REAXC, "USER-SCAFACOS"_#PKG-USER-SCAFACOS, +"USER-SDPD"_#PKG-USER-SDPD, "USER-SMD"_#PKG-USER-SMD, "USER-SMTBQ"_#PKG-USER-SMTBQ, "USER-SPH"_#PKG-USER-SPH, "USER-TALLY"_#PKG-USER-TALLY, "USER-UEF"_#PKG-USER-UEF, -"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c) +"USER-VTK"_#PKG-USER-VTK, +"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c) :line @@ -203,7 +205,7 @@ available on your system. [Author:] Axel Kohlmeyer (Temple U). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -284,7 +286,7 @@ also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles. [Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen (Northwestern U) while at ORNL. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -339,20 +341,21 @@ KIM package :link(PKG-KIM),h4 A "pair_style kim"_pair_kim.html command which is a wrapper on the Knowledge Base for Interatomic Models (KIM) repository of interatomic potentials, enabling any of them to be used in LAMMPS simulations. +Also a "kim_query"_kim_query.html command, which allows to query +the OpenKIM database for stored properties. To use this package you must have the KIM library available on your system. Information about the KIM project can be found at its website: https://openkim.org. The KIM project is led by Ellad Tadmor and Ryan -Elliott (U Minnesota) and James Sethna (Cornell U). +Elliott (U Minnesota). [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM API which the "pair_style kim"_pair_kim.html command uses. He -developed the pair style in collaboration with Valeriu Smirichinski (U -Minnesota). +developed the pair style. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -398,7 +401,7 @@ which was developed by Carter Edwards, Christian Trott, and others at Sandia, and which is included in the LAMMPS distribution in lib/kokkos. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -492,7 +495,7 @@ MANYBODY package :link(PKG-MANYBODY),h4 [Contents:] -A variety of manybody and bond-order potentials. These include +A variety of many-body and bond-order potentials. These include (AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials. [Supporting info:] @@ -516,7 +519,7 @@ MC package :link(PKG-MC),h4 Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjuction with dynamics. +(GCMC) in conjunction with dynamics. [Supporting info:] @@ -531,37 +534,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul :line -MEAM package :link(PKG-MEAM),h4 - -[Contents:] - -A pair style for the modified embedded atom (MEAM) potential. - -Please note that the use of the MEAM package is discouraged as -it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package, -which is a direct translation of the MEAM package to C++. -USER-MEAMC contains additional optimizations making it run faster -than MEAM on most machines, while providing the identical features -and user interface. - -[Author:] Greg Wagner (Northwestern U) while at Sandia. - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#gpu on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/MEAM: filenames -> commands -src/meam/README -lib/meam/README -"pair_style meam"_pair_meam.html -examples/meam :ul - -:line - MESSAGE package :link(PKG-MESSAGE),h4 [Contents:] @@ -679,7 +651,7 @@ system. library was developed by Jacob Wagner in Greg Voth's group at the University of Chicago. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -711,7 +683,7 @@ have styles optimized for CPU performance. [Authors:] James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge Technolgy). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -768,7 +740,7 @@ connections at hinge points. [Author:] Rudra Mukherjee (JPL) while at RPI. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -800,7 +772,7 @@ shared library available on your system, which needs to be a Python 2 version, 2.6 or later. Python 3 is not yet supported. See the lib/python/README for more details. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -832,38 +804,6 @@ examples/streitz :ul :line -REAX package :link(PKG-REAX),h4 - -[Contents:] - -NOTE: the use of the REAX package is discouraged, as it is no longer -maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead, -and possibly the KOKKOS enabled variant of that, which has a more robust -memory management. - -A pair style which wraps a Fortran library which implements the ReaxFF -potential, which is a universal reactive force field. Also included is -a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules -as bonds are created and destroyed. - -[Author:] Aidan Thompson (Sandia). - -[Install:] - -This package has "specific installation -instructions"_Build_extras.html#gpu on the "Build -extras"_Build_extras.html doc page. - -[Supporting info:] - -src/REAX: filenames -> commands -lib/reax/README -"pair_style reax"_pair_reax.html -"fix reax/bonds"_fix_reax_bonds.html -examples/reax :ul - -:line - REPLICA package :link(PKG-REPLICA2),h4 [Contents:] @@ -1021,7 +961,7 @@ system. library was written by Chris Rycroft (Harvard U) while at UC Berkeley and LBNL. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1037,6 +977,31 @@ examples/voronoi :ul :line +USER-ADIOS package :link(PKG-USER-ADIOS),h4 + +[Contents:] + +ADIOS is a high-performance I/O library. This package implements the +dump "atom/adios" and dump "custom/adios" commands to write data using +the ADIOS library. + +[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team. + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#user-adios on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-ADIOS: filenames -> commands +src/USER-ADIOS/README +examples/USER/adios +https://github.com/ornladios/ADIOS2 :ul + +:line + USER-ATC package :link(PKG-USER-ATC),h4 [Contents:] @@ -1048,7 +1013,7 @@ atomic information to continuum fields. [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1075,7 +1040,7 @@ model. [Author:] Ilya Valuev (JIHT, Russia). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1098,7 +1063,7 @@ This package provides "fix bocs"_fix_bocs.html, a modified version of "fix npt"_fix_nh.html which includes the pressure correction to the barostat as outlined in: -N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that +N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids," J. Chem. Phys. 143, 243148 (2015). @@ -1183,10 +1148,10 @@ and Jerome Henin (LISM, CNRS, Marseille, France), originally for the NAMD MD code, but with portability in mind. Axel Kohlmeyer (Temple U) provided the interface to LAMMPS. -[Install:] +[Install:] This package has "specific installation -instructions"_Build_extras.html#gpu on the "Build +instructions"_Build_extras.html#user-colvars on the "Build extras"_Build_extras.html doc page. [Supporting info:] @@ -1200,6 +1165,36 @@ examples/USER/colvars :ul :line +USER-PLUMED package :link(PKG-USER-PLUMED),h4 + +[Contents:] + +The fix plumed command allows you to use the PLUMED free energy plugin +for molecular dynamics to analyze and bias your LAMMPS trajectory on +the fly. The PLUMED library is called from within the LAMMPS input +script by using the "fix plumed _fix_plumed.html command. + +[Authors:] The "PLUMED library"_#PLUMED is written and maintained by +Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth +Tribello. + +:link(PLUMED,http://www.plumed.org) + +[Install:] + +This package has "specific installation +instructions"_Build_extras.html#gpu on the "Build +extras"_Build_extras.html doc page. + +[Supporting info:] + +src/USER-PLUMED/README +lib/plumed/README +"fix plumed"_fix_plumed.html +examples/USER/plumed :ul + +:line + USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4 [Contents:] @@ -1338,7 +1333,7 @@ src/USER-FEP: filenames -> commands src/USER-FEP/README "fix adapt/fep"_fix_adapt_fep.html "compute fep"_compute_fep.html -"pair_style */soft"_pair_lj_soft.html +"pair_style */soft"_pair_fep_soft.html examples/USER/fep tools/fep/README tools/fep :ul @@ -1363,7 +1358,7 @@ system. [Author:] Pierre de Buyl (KU Leuven) created both the package and the H5MD format. -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1401,7 +1396,7 @@ NOTE: the USER-INTEL package contains styles that require using the [Author:] Mike Brown (Intel). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1520,10 +1515,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4 [Contents:] A pair style for the modified embedded atom (MEAM) potential -translated from the Fortran version in the "MEAM"_#PKG-MEAM package -to plain C++. In contrast to the MEAM package, no library -needs to be compiled and the pair style can be instantiated -multiple times. +translated from the Fortran version in the (obsolete) "MEAM" package +to plain C++. The USER-MEAMC fully replaces the MEAM package, which +has been removed from LAMMPS after the 12 December 2018 version. [Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg) based on the Fortran version of Greg Wagner (Northwestern U) while at @@ -1533,8 +1527,8 @@ Sandia. src/USER-MEAMC: filenames -> commands src/USER-MEAMC/README -"pair_style meam/c"_pair_meam.html -examples/meam :ul +"pair_style meam/c"_pair_meamc.html +examples/meamc :ul :line @@ -1571,17 +1565,17 @@ USER-MOFFF package :link(PKG-USER-MOFFF),h4 [Contents:] Pair, angle and improper styles needed to employ the MOF-FF -force field by Schmid and coworkers with LAMMPS. +force field by Schmid and coworkers with LAMMPS. MOF-FF is a first principles derived force field with the primary aim -to simulate MOFs and related porous framework materials, using spherical +to simulate MOFs and related porous framework materials, using spherical Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B 2013, 250, 1128-1141. -For the usage of MOF-FF see the example in the example directory as +For the usage of MOF-FF see the example in the example directory as well as the "MOF+"_MOFplus website. :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) -[Author:] Hendrik Heenen (Technical U of Munich), +[Author:] Hendrik Heenen (Technical U of Munich), Rochus Schmid (Ruhr-University Bochum). [Supporting info:] @@ -1622,7 +1616,7 @@ at [Author:] Axel Kohlmeyer (Temple U). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1662,7 +1656,7 @@ tools: [Author:] Lars Pastewka (Karlsruhe Institute of Technology). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1706,7 +1700,7 @@ See src/MAKE/OPTIONS/Makefile.omp for an example. Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner: -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1733,14 +1727,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4 A "fix phonon"_fix_phonon.html command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. +And a "dynamical_matrix" command to compute the dynamical matrix +from finite differences. + +[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon" +and Charlie Sievers (UC Davis) for "dynamical_matrix" -[Author:] Ling-Ti Kong (Shanghai Jiao Tong University). [Supporting info:] src/USER-PHONON: filenames -> commands src/USER-PHONON/README "fix phonon"_fix_phonon.html +"dynamical_matrix"_dynamical_matrix.html examples/USER/phonon :ul :line @@ -1785,7 +1784,7 @@ without changes to LAMMPS itself. [Author:] Axel Kohlmeyer (Temple U). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1843,7 +1842,7 @@ on your system. [Author:] Albert Bartok (Cambridge University) -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -1862,9 +1861,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4 [Contents:] -A pair style which implements the ReaxFF potential in C/C++ (in -contrast to the "REAX package"_#PKG-REAX and its Fortran library). ReaxFF -is universal reactive force field. See the src/USER-REAXC/README file +A pair style which implements the ReaxFF potential in C/C++. ReaxFF +is a universal reactive force field. See the src/USER-REAXC/README file for more info on differences between the two packages. Also two fixes for monitoring molecules as bonds are created and destroyed. @@ -1875,7 +1873,7 @@ for monitoring molecules as bonds are created and destroyed. src/USER-REAXC: filenames -> commands src/USER-REAXC/README "pair_style reax/c"_pair_reaxc.html -"fix reax/c/bonds"_fix_reax_bonds.html +"fix reax/c/bonds"_fix_reaxc_bonds.html "fix reax/c/species"_fix_reaxc_species.html examples/reax :ul @@ -1916,6 +1914,31 @@ examples/USER/scafacos :ul :line +USER-SDPD package :link(PKG-USER-SDPD),h4 + +[Contents:] + +A pair style for smoothed dissipative particle dynamics (SDPD), which +is an extension of smoothed particle hydrodynamics (SPH) to mesoscale +where thermal fluctuations are important (see the +"USER-SPH package"_#PKG-USER-SPH). +Also two fixes for moving and rigid body integration of SPH/SDPD particles +(particles of atom_style meso). + +[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic +Sciences, Iran). + +[Supporting info:] + +src/USER-SDPD: filenames -> commands +src/USER-SDPD/README +"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html +"fix meso/move"_fix_meso_move.html +"fix rigid/meso"_fix_rigid_meso.html +examples/USER/sdpd :ul + +:line + USER-SMD package :link(PKG-USER-SMD),h4 [Contents:] @@ -1937,7 +1960,7 @@ specified as surface geometries from *.STL files. [Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute, Germany). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -2063,7 +2086,7 @@ system. [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). -[Install:] +[Install:] This package has "specific installation instructions"_Build_extras.html#gpu on the "Build @@ -2077,3 +2100,37 @@ lib/vtk/README "dump vtk"_dump_vtk.html :ul +:line + +USER-YAFF package :link(PKG-USER-YAFF),h4 + +[Contents:] + +Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code. +The expressions and their use are discussed in the following papers + +Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015 +Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul + +which discuss the "QuickFF"_quickff methodology. + + +:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877) +:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173) +:link(quickff,http://molmod.github.io/QuickFF) +:link(yaff,https://github.com/molmod/yaff) + + +[Author:] Steven Vandenbrande. + +[Supporting info:] + +src/USER-YAFF/README +"angle_style cross"_angle_cross.html +"angle_style mm3"_angle_mm3.html +"bond_style mm3"_bond_mm3.html +"improper_style distharm"_improper_distharm.html +"improper_style sqdistharm"_improper_sqdistharm.html +"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html +"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html +examples/USER/yaff :ul diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt index 583ecf39fe..7fb1d99174 100644 --- a/doc/src/Packages_standard.txt +++ b/doc/src/Packages_standard.txt @@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no -"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int "MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int "MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no @@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys "QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no -"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int "REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no "RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no "SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt index 9bb3fbd18c..4210f617ef 100644 --- a/doc/src/Packages_user.txt +++ b/doc/src/Packages_user.txt @@ -38,8 +38,9 @@ int = internal library: provided with LAMMPS, but you may need to build it ext = external library: you will need to download and install it on your machine :ul Package, Description, Doc page, Example, Library -"USER-ATC"_Packages_details.html#PKG-USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int -"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int +"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext +"USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int +"USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no "USER-CGDNA"_Packages_details.html#PKG-USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, no "USER-CGSDK"_Packages_details.html#PKG-USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, no @@ -53,7 +54,7 @@ Package, Description, Doc page, Example, Library "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no -"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no +"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no @@ -62,16 +63,21 @@ Package, Description, Doc page, Example, Library "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no +"USER-PLUMED"_Packages_details.html#PKG-USER-PLUMED, "PLUMED"_#PLUMED free energy library,"fix plumed"_fix_plumed.html, USER/plumed, ext "USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext "USER-REAXC"_Packages_details.html#PKG-USER-REAXC, ReaxFF potential (C/C++) ,"pair_style reaxc"_pair_reaxc.html, reax, no "USER-SCAFACOS"_Packages_details.html#PKG-USER-SCAFACOS, wrapper on ScaFaCoS solver,"kspace_style scafacos"_kspace_style.html, USER/scafacos, ext +"USER-SDPD"_Packages_details.html#PKG-USER-SDPD, smoothed dissipative particle dynamics,"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html, USER/sdpd, no "USER-SMD"_Packages_details.html#PKG-USER-SMD, smoothed Mach dynamics,"SMD User Guide"_PDF/SMD_LAMMPS_userguide.pdf, USER/smd, ext "USER-SMTBQ"_Packages_details.html#PKG-USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, no "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no -"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l) +"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext +"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l) + :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF) +:link(PLUMED,http://www.plumed.org) diff --git a/doc/src/Python_call.txt b/doc/src/Python_call.txt index 3c382de1ba..34b04679d5 100644 --- a/doc/src/Python_call.txt +++ b/doc/src/Python_call.txt @@ -79,7 +79,7 @@ of Python and your machine to successfully build LAMMPS. See the lib/python/README file for more info. If you want to write Python code with callbacks to LAMMPS, then you -must also follow the steps overviewed in the "Python +must also follow the steps summarized in the "Python run"_Python_run.html doc page. I.e. you must build LAMMPS as a shared library and insure that Python can find the python/lammps.py file and the shared library. diff --git a/doc/src/Python_examples.txt b/doc/src/Python_examples.txt index f4b2197464..181181dfb2 100644 --- a/doc/src/Python_examples.txt +++ b/doc/src/Python_examples.txt @@ -15,7 +15,7 @@ things that are possible when Python wraps LAMMPS. If you create your own scripts, send them to us and we can include them in the LAMMPS distribution. -trivial.py, read/run a LAMMPS input script thru Python, +trivial.py, read/run a LAMMPS input script through Python, demo.py, invoke various LAMMPS library interface routines, simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp, split.py, same as simple.py but running in parallel on a subset of procs, @@ -46,7 +46,7 @@ http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html :pre :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) :link(atomeye3,http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html) -The latter link is to AtomEye 3 which has the scriping +The latter link is to AtomEye 3 which has the scripting capability needed by these Python scripts. Note that for PyMol, you need to have built and installed the diff --git a/doc/src/Python_run.txt b/doc/src/Python_run.txt index 963248efce..8974d1469a 100644 --- a/doc/src/Python_run.txt +++ b/doc/src/Python_run.txt @@ -31,7 +31,7 @@ language is, and that it can be run interactively, enabling rapid development and debugging. If you use it to mostly invoke costly operations within LAMMPS, such as running a simulation for a reasonable number of timesteps, then the overhead cost of invoking -LAMMPS thru Python will be negligible. +LAMMPS through Python will be negligible. The Python wrapper for LAMMPS uses the "ctypes" package in Python, which auto-generates the interface code needed between Python and a diff --git a/doc/src/Python_test.txt b/doc/src/Python_test.txt index 2bfec91bd6..3909ea9979 100644 --- a/doc/src/Python_test.txt +++ b/doc/src/Python_test.txt @@ -32,7 +32,7 @@ first importing from the lammps.py file: >>> from ctypes import CDLL >>> CDLL("liblammps.so") :pre -If an error occurs, carefully go thru the steps on the +If an error occurs, carefully go through the steps on the "Build_basics"_Build_basics.html doc page about building a shared library and the "Python_install"_Python_install.html doc page about insuring Python can find the necessary two files it needs. diff --git a/doc/src/Run_options.txt b/doc/src/Run_options.txt index db5a7baa6e..9c12b3ff24 100644 --- a/doc/src/Run_options.txt +++ b/doc/src/Run_options.txt @@ -354,29 +354,31 @@ the LAMMPS simulation domain. :line -[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data) +[-restart2data restartfile \[remap\] datafile keyword value ...] +:link(restart2data) Convert the restart file into a data file and immediately exit. This is the same operation as if the following 2-line input script were run: -read_restart restartfile (remap) +read_restart restartfile \[remap\] write_data datafile keyword value ... :pre -Note that the specified restartfile and/or datafile can have the -wild-card character "*". The restartfile can also have the wild-card +The specified restartfile and/or datafile name may contain the wild-card +character "*". The restartfile name may also contain the wild-card character "%". The meaning of these characters is explained on the "read_restart"_read_restart.html and "write_data"_write_data.html doc pages. The use of "%" means that a parallel restart file can be read. -Note that a filename such as file.* will need to be enclosed in quotes -to avoid shell expansion of the "*" character. +Note that a filename such as file.* may need to be enclosed in quotes or +the "*" character prefixed with a backslash ("\") to avoid shell +expansion of the "*" character. -Note that following restartfile, the optional word "remap" can be -used. This has the effect of adding it to the -"read_restart"_read_restart.html command, as explained on its doc -page. This is useful if reading the restart file triggers an error -that atoms have been lost. In that case, use of the remap flag should -allow the data file to still be produced. +Following restartfile argument, the optional word "remap" may be used. +This has the same effect like adding it to a +"read_restart"_read_restart.html command, and operates as explained on +its doc page. This is useful if reading the restart file triggers an +error that atoms have been lost. In that case, use of the remap flag +should allow the data file to still be produced. The syntax following restartfile (or remap), namely @@ -388,29 +390,30 @@ optional keyword/value settings. :line -[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump) +[-restart2dump restartfile \[remap\] group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump) Convert the restart file into a dump file and immediately exit. This is the same operation as if the following 2-line input script were run: -read_restart restartfile (remap) +read_restart restartfile \[remap\] write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre -Note that the specified restartfile and dumpfile can have wild-card -characters ("*","%") as explained on the +Note that the specified restartfile and dumpfile names may contain +wild-card characters ("*","%") as explained on the "read_restart"_read_restart.html and "write_dump"_write_dump.html doc pages. The use of "%" means that a parallel restart file and/or parallel dump file can be read and/or written. Note that a filename -such as file.* will need to be enclosed in quotes to avoid shell -expansion of the "*" character. +such as file.* may need to be enclosed in quotes or the "*" character +prefixed with a backslash ("\") to avoid shell expansion of the "*" +character. -Note that following restartfile, the optional word "remap" can be -used. This has the effect as adding it to the -"read_restart"_read_restart.html command, as explained on its doc -page. This is useful if reading the restart file triggers an error -that atoms have been lost. In that case, use of the remap flag should -allow the dump file to still be produced. +Note that following the restartfile argument, the optional word "remap" +can be used. This has the effect as adding it to the +"read_restart"_read_restart.html command, as explained on its doc page. +This is useful if reading the restart file triggers an error that atoms +have been lost. In that case, use of the remap flag should allow the +dump file to still be produced. The syntax following restartfile (or remap), namely @@ -524,7 +527,7 @@ option is equivalent to putting the line "variable name index value1 value2 ..." at the beginning of the input script. Defining an index variable as a command-line argument overrides any setting for the same index variable in the input script, since index variables cannot be -re-defined. +re-defined. See the "variable"_variable.html command for more info on defining index and other kinds of variables and the "Commands diff --git a/doc/src/Run_windows.txt b/doc/src/Run_windows.txt index 85c9a6550d..e9c3b60dbe 100644 --- a/doc/src/Run_windows.txt +++ b/doc/src/Run_windows.txt @@ -41,7 +41,7 @@ path for the default location of this MPI package. After the installation of the MPICH2 software, it needs to be integrated into the system. For this you need to start a Command Prompt in {Administrator Mode} (right click on the icon and select it). Change -into the MPICH2 installation directory, then into the subdirectory +into the MPICH2 installation directory, then into the sub-directory [bin] and execute [smpd.exe -install]. Exit the command window. Get a new, regular command prompt by going to Start->Run... , diff --git a/doc/src/Speed.txt b/doc/src/Speed.txt index dd2052bac1..28aef26a5d 100644 --- a/doc/src/Speed.txt +++ b/doc/src/Speed.txt @@ -19,7 +19,7 @@ using code options that implement alternate algorithms that can speed-up a simulation. The second is to use one of the several accelerator packages provided with LAMMPS that contain code optimized for certain kinds of hardware, including multi-core CPUs, GPUs, and -Intel Xeon Phi coprocessors. +Intel Xeon Phi co-processors. The "Benchmark page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives performance results for the various accelerator diff --git a/doc/src/Speed_intel.txt b/doc/src/Speed_intel.txt index d35a311f46..da772f29fd 100644 --- a/doc/src/Speed_intel.txt +++ b/doc/src/Speed_intel.txt @@ -14,11 +14,11 @@ Corporation. It provides two methods for accelerating simulations, depending on the hardware you have. The first is acceleration on Intel CPUs by running in single, mixed, or double precision with vectorization. The second is acceleration on Intel Xeon Phi -coprocessors via offloading neighbor list and non-bonded force +co-processors via offloading neighbor list and non-bonded force calculations to the Phi. The same C++ code is used in both cases. -When offloading to a coprocessor from a CPU, the same routine is run +When offloading to a co-processor from a CPU, the same routine is run twice, once on the CPU and once with an offload flag. This allows -LAMMPS to run on the CPU cores and coprocessor cores simultaneously. +LAMMPS to run on the CPU cores and co-processor cores simultaneously. [Currently Available USER-INTEL Styles:] @@ -27,9 +27,9 @@ Bond Styles: fene, fourier, harmonic :l Dihedral Styles: charmm, harmonic, opls :l Fixes: nve, npt, nvt, nvt/sllod, nve/asphere :l Improper Styles: cvff, harmonic :l -Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, -buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, -lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, +Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, +buck, dpd, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, +lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo, sw, tersoff :l K-Space Styles: pppm, pppm/disp :l :ule @@ -47,7 +47,7 @@ These are scalable in size; the results given are with 512K particles (524K for Liquid Crystal). Most of the simulations are standard LAMMPS benchmarks (indicated by the filename extension in parenthesis) with modifications to the run length and to add a -warmup run (for use with offload benchmarks). +warm-up run (for use with offload benchmarks). :c,image(JPG/user_intel.png) @@ -134,19 +134,19 @@ Do not use thread affinity (set KMP_AFFINITY=none) :l The "newton off" setting may provide better scalability :l :ule -For Intel Xeon Phi coprocessors (Offload): +For Intel Xeon Phi co-processors (Offload): -Edit src/MAKE/OPTIONS/Makefile.intel_coprocessor as necessary :ulb,l +Edit src/MAKE/OPTIONS/Makefile.intel_co-processor as necessary :ulb,l "-pk intel N omp 1" added to command-line where N is the number of -coprocessors per node. :l +co-processors per node. :l :ule :line [Required hardware/software:] -In order to use offload to coprocessors, an Intel Xeon Phi -coprocessor and an Intel compiler are required. For this, the +In order to use offload to co-processors, an Intel Xeon Phi +co-processor and an Intel compiler are required. For this, the recommended version of the Intel compiler is 14.0.1.106 or versions 15.0.2.044 and higher. @@ -214,7 +214,7 @@ Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload Makefile.knl # Intel Compiler, Intel MPI, No Offload Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload -Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload :pre +Makefile.intel_co-processor # Intel Compiler, Intel MPI, Offload :pre Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that it explicitly specifies that vectorization should be for Intel Xeon @@ -227,18 +227,18 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi :pre -Note that if you build with support for a Phi coprocessor, the same -binary can be used on nodes with or without coprocessors installed. -However, if you do not have coprocessors on your system, building +Note that if you build with support for a Phi co-processor, the same +binary can be used on nodes with or without co-processors installed. +However, if you do not have co-processors on your system, building without offload support will produce a smaller binary. The general requirements for Makefiles with the USER-INTEL package -are as follows. When using Intel compilers, "-restrict" is required -and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. +are as follows. When using Intel compilers, "-restrict" is required +and "-qopenmp" is highly recommended for CCFLAGS and LINKFLAGS. CCFLAGS should include "-DLMP_INTEL_USELRT" (unless POSIX Threads are not supported in the build environment) and "-DLMP_USE_MKL_RNG" (unless Intel Math Kernel Library (MKL) is not available in the build -environment). For Intel compilers, LIB should include "-ltbbmalloc" +environment). For Intel compilers, LIB should include "-ltbbmalloc" or if the library is not available, "-DLMP_INTEL_NO_TBB" can be added to CCFLAGS. For builds supporting offload, "-DLMP_INTEL_OFFLOAD" is required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other @@ -272,7 +272,7 @@ Advanced performance tuning options are also described below to get the best performance. When running on a single node (including runs using offload to a -coprocessor), best performance is normally obtained by using 1 MPI +co-processor), best performance is normally obtained by using 1 MPI task per physical core and additional OpenMP threads with SMT. For Intel Xeon processors, 2 OpenMP threads should be used for SMT. For Intel Xeon Phi CPUs, 2 or 4 OpenMP threads should be used @@ -290,7 +290,7 @@ NOTE: Setting core affinity is often used to pin MPI tasks and OpenMP threads to a core or group of cores so that memory access can be uniform. Unless disabled at build time, affinity for MPI tasks and OpenMP threads on the host (CPU) will be set by default on the host -{when using offload to a coprocessor}. In this case, it is unnecessary +{when using offload to a co-processor}. In this case, it is unnecessary to use other methods to control affinity (e.g. taskset, numactl, I_MPI_PIN_DOMAIN, etc.). This can be disabled with the {no_affinity} option to the "package intel"_package.html command or by disabling the @@ -310,15 +310,15 @@ editing the input script. This switch will automatically append options for the USER-INTEL package. The default package command will specify that USER-INTEL calculations are performed in mixed precision, that the number of OpenMP threads is specified by the OMP_NUM_THREADS -environment variable, and that if coprocessors are present and the -binary was built with offload support, that 1 coprocessor per node +environment variable, and that if co-processors are present and the +binary was built with offload support, that 1 co-processor per node will be used with automatic balancing of work between the CPU and the -coprocessor. +co-processor. You can specify different options for the USER-INTEL package by using the "-pk intel Nphi" "command-line switch"_Run_options.html with keyword/value pairs as specified in the documentation. Here, Nphi = # -of Xeon Phi coprocessors/node (ignored without offload +of Xeon Phi co-processors/node (ignored without offload support). Common options to the USER-INTEL package include {omp} to override any OMP_NUM_THREADS setting and specify the number of OpenMP threads, {mode} to set the floating-point precision mode, and {lrt} to @@ -332,7 +332,7 @@ Examples (see documentation for your MPI/Machine for differences in launching MPI applications): mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads -mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision :pre +mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any co-processors that might be available, use 2 OpenMP threads for each task, use double precision :pre [Or run with the USER-INTEL package by editing an input script:] @@ -364,7 +364,7 @@ intel"_package.html command that can improve performance when using "PPPM"_kspace_style.html for long-range electrostatics on processors with SMT. It generates an extra pthread for each MPI task. The thread is dedicated to performing some of the PPPM calculations and MPI -communications. This feature requires setting the preprocessor flag +communications. This feature requires setting the pre-processor flag -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. It is unset in the default makefiles ({Makefile.mpi} and {Makefile.serial}) but it is set in all makefiles tuned for the USER-INTEL package. On Intel @@ -399,7 +399,7 @@ the "suffix hybrid intel omp"_suffix.html command can also be used within the input script to automatically append the "omp" suffix to styles when USER-INTEL styles are not available. -NOTE: For simulations on higher node counts, add "processors * * * +NOTE: For simulations on higher node counts, add "processors * * * grid numa"_processors.html to the beginning of the input script for better scalability. @@ -422,29 +422,29 @@ that MPI runs are performed in MCDRAM. The default settings for offload should give good performance. -When using LAMMPS with offload to Intel coprocessors, best performance +When using LAMMPS with offload to Intel co-processors, best performance will typically be achieved with concurrent calculations performed on -both the CPU and the coprocessor. This is achieved by offloading only -a fraction of the neighbor and pair computations to the coprocessor or +both the CPU and the co-processor. This is achieved by offloading only +a fraction of the neighbor and pair computations to the co-processor or using "hybrid"_pair_hybrid.html pair styles where only one style uses the "intel" suffix. For simulations with long-range electrostatics or bond, angle, dihedral, improper calculations, computation and data -transfer to the coprocessor will run concurrently with computations +transfer to the co-processor will run concurrently with computations and MPI communications for these calculations on the host CPU. This is illustrated in the figure below for the rhodopsin protein benchmark running on E5-2697v2 processors with a Intel Xeon Phi 7120p -coprocessor. In this plot, the vertical access is time and routines +co-processor. In this plot, the vertical access is time and routines running at the same time are running concurrently on both the host and -the coprocessor. +the co-processor. :c,image(JPG/offload_knc.png) The fraction of the offloaded work is controlled by the {balance} keyword in the "package intel"_package.html command. A balance of 0 runs all calculations on the CPU. A balance of 1 runs all -supported calculations on the coprocessor. A balance of 0.5 runs half -of the calculations on the coprocessor. Setting the balance to -1 -(the default) will enable dynamic load balancing that continously +supported calculations on the co-processor. A balance of 0.5 runs half +of the calculations on the co-processor. Setting the balance to -1 +(the default) will enable dynamic load balancing that continuously adjusts the fraction of offloaded work throughout the simulation. Because data transfer cannot be timed, this option typically produces results within 5 to 10 percent of the optimal fixed balance. @@ -455,23 +455,23 @@ near-optimal setting that will carry over to additional runs. The default for the "package intel"_package.html command is to have all the MPI tasks on a given compute node use a single Xeon Phi -coprocessor. In general, running with a large number of MPI tasks on +co-processor. In general, running with a large number of MPI tasks on each node will perform best with offload. Each MPI task will automatically get affinity to a subset of the hardware threads -available on the coprocessor. For example, if your card has 61 cores, +available on the co-processor. For example, if your card has 61 cores, with 60 cores available for offload and 4 hardware threads per core (240 total threads), running with 24 MPI tasks per node will cause -each MPI task to use a subset of 10 threads on the coprocessor. Fine +each MPI task to use a subset of 10 threads on the co-processor. Fine tuning of the number of threads to use per MPI task or the number of threads to use per core can be accomplished with keyword settings of the "package intel"_package.html command. The USER-INTEL package has two modes for deciding which atoms will be -handled by the coprocessor. This choice is controlled with the {ghost} +handled by the co-processor. This choice is controlled with the {ghost} keyword of the "package intel"_package.html command. When set to 0, ghost atoms (atoms at the borders between MPI tasks) are not offloaded to the card. This allows for overlap of MPI communication of forces -with computation on the coprocessor when the "newton"_newton.html +with computation on the co-processor when the "newton"_newton.html setting is "on". The default is dependent on the style being used, however, better performance may be achieved by setting this option explicitly. @@ -482,21 +482,21 @@ cores. This is due to the fact that additional threads are generated internally to handle the asynchronous offload tasks. If pair computations are being offloaded to an Intel Xeon Phi -coprocessor, a diagnostic line is printed to the screen (not to the +co-processor, a diagnostic line is printed to the screen (not to the log file), during the setup phase of a run, indicating that offload -mode is being used and indicating the number of coprocessor threads +mode is being used and indicating the number of co-processor threads per MPI task. Additionally, an offload timing summary is printed at the end of each run. When offloading, the frequency for "atom sorting"_atom_modify.html is changed to 1 so that the per-atom data is effectively sorted at every rebuild of the neighbor lists. All the -available coprocessor threads on each Phi will be divided among MPI +available co-processor threads on each Phi will be divided among MPI tasks, unless the {tptask} option of the "-pk intel" "command-line -switch"_Run_options.html is used to limit the coprocessor threads per +switch"_Run_options.html is used to limit the co-processor threads per MPI task. [Restrictions:] -When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles +When offloading to a co-processor, "hybrid"_pair_hybrid.html styles that require skip lists for neighbor builds cannot be offloaded. Using "hybrid/overlay"_pair_hybrid.html is allowed. Only one intel accelerated style may be used with hybrid styles when offloading. @@ -510,7 +510,7 @@ supported. [References:] -Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l +Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l diff --git a/doc/src/Speed_kokkos.txt b/doc/src/Speed_kokkos.txt index f74c9c9ed7..ef193d7401 100644 --- a/doc/src/Speed_kokkos.txt +++ b/doc/src/Speed_kokkos.txt @@ -13,11 +13,11 @@ Kokkos is a templated C++ library that provides abstractions to allow a single implementation of an application kernel (e.g. a pair style) to run efficiently on different kinds of hardware, such as GPUs, Intel Xeon Phis, or many-core CPUs. Kokkos maps the C++ kernel onto -different backend languages such as CUDA, OpenMP, or Pthreads. The +different back end languages such as CUDA, OpenMP, or Pthreads. The Kokkos library also provides data abstractions to adjust (at compile time) the memory layout of data structures like 2d and 3d arrays to optimize performance on different hardware. For more information on -Kokkos, see "Github"_https://github.com/kokkos/kokkos. Kokkos is part +Kokkos, see "GitHub"_https://github.com/kokkos/kokkos. Kokkos is part of "Trilinos"_http://trilinos.sandia.gov/packages/kokkos. The Kokkos library was written primarily by Carter Edwards, Christian Trott, and Dan Sunderland (all Sandia). @@ -106,10 +106,10 @@ modification to the input script is needed. Alternatively, one can run with the KOKKOS package by editing the input script as described below. -NOTE: When using a single OpenMP thread, the Kokkos Serial backend (i.e. -Makefile.kokkos_mpi_only) will give better performance than the OpenMP -backend (i.e. Makefile.kokkos_omp) because some of the overhead to make -the code thread-safe is removed. +NOTE: When using a single OpenMP thread, the Kokkos Serial back end (i.e. +Makefile.kokkos_mpi_only) will give better performance than the OpenMP +back end (i.e. Makefile.kokkos_omp) because some of the overhead to make +the code thread-safe is removed. NOTE: The default for the "package kokkos"_package.html command is to use "full" neighbor lists and set the Newton flag to "off" for both @@ -127,21 +127,21 @@ mpirun -np 16 lmp_kokkos_mpi_only -k on -sf kk -pk kokkos newton on neigh half c If the "newton"_newton.html command is used in the input script, it can also override the Newton flag defaults. -For half neighbor lists and OpenMP, the KOKKOS package uses data -duplication (i.e. thread-private arrays) by default to avoid -thread-level write conflicts in the force arrays (and other data -structures as necessary). Data duplication is typically fastest for -small numbers of threads (i.e. 8 or less) but does increase memory -footprint and is not scalable to large numbers of threads. An -alternative to data duplication is to use thread-level atomics, which -don't require duplication. The use of atomics can be forced by compiling -with the "-DLMP_KOKKOS_USE_ATOMICS" compile switch. Most but not all -Kokkos-enabled pair_styles support data duplication. Alternatively, full -neighbor lists avoid the need for duplication or atomics but require -more compute operations per atom. When using the Kokkos Serial backend -or the OpenMP backend with a single thread, no duplication or atomics are -used. For CUDA and half neighbor lists, the KOKKOS package always uses -atomics. +For half neighbor lists and OpenMP, the KOKKOS package uses data +duplication (i.e. thread-private arrays) by default to avoid +thread-level write conflicts in the force arrays (and other data +structures as necessary). Data duplication is typically fastest for +small numbers of threads (i.e. 8 or less) but does increase memory +footprint and is not scalable to large numbers of threads. An +alternative to data duplication is to use thread-level atomic operations +which do not require data duplication. The use of atomic operations can +be enforced by compiling LAMMPS with the "-DLMP_KOKKOS_USE_ATOMICS" +pre-processor flag. Most but not all Kokkos-enabled pair_styles support +data duplication. Alternatively, full neighbor lists avoid the need for +duplication or atomic operations but require more compute operations per +atom. When using the Kokkos Serial back end or the OpenMP back end with +a single thread, no duplication or atomic operations are used. For CUDA +and half neighbor lists, the KOKKOS package always uses atomic operations. [Core and Thread Affinity:] @@ -193,7 +193,7 @@ threads/task as Nt. The product of these two values should be N, i.e. NOTE: The default for the "package kokkos"_package.html command is to use "full" neighbor lists and set the Newton flag to "off" for both pairwise and bonded interactions. When running on KNL, this will -typically be best for pair-wise potentials. For manybody potentials, +typically be best for pair-wise potentials. For many-body potentials, using "half" neighbor lists and setting the Newton flag to "on" may be faster. It can also be faster to use non-threaded communication. Use the "-pk kokkos" "command-line switch"_Run_options.html to change the @@ -207,7 +207,7 @@ mpirun -np 64 lmp_kokkos_phi -k on t 4 -sf kk -pk kokkos newton on neigh half co NOTE: MPI tasks and threads should be bound to cores as described above for CPUs. -NOTE: To build with Kokkos support for Intel Xeon Phi coprocessors +NOTE: To build with Kokkos support for Intel Xeon Phi co-processors such as Knight's Corner (KNC), your system must be configured to use them in "native" mode, not "offload" mode like the USER-INTEL package supports. diff --git a/doc/src/Speed_omp.txt b/doc/src/Speed_omp.txt index 238909d1b4..97aa251e9e 100644 --- a/doc/src/Speed_omp.txt +++ b/doc/src/Speed_omp.txt @@ -131,7 +131,7 @@ effect worsens when using an increasing number of nodes. :l The system has a spatially inhomogeneous particle density which does not map well to the "domain decomposition scheme"_processors.html or "load-balancing"_balance.html options that LAMMPS provides. This is -because multi-threading achives parallelism over the number of +because multi-threading achieves parallelism over the number of particles, not via their distribution in space. :l A machine is being used in "capability mode", i.e. near the point @@ -143,7 +143,7 @@ the performance-limiting factor. Using multi-threading allows less MPI tasks to be invoked and can speed-up the long-range solver, while increasing overall performance by parallelizing the pairwise and bonded calculations via OpenMP. Likewise additional speedup can be -sometimes be achived by increasing the length of the Coulombic cutoff +sometimes be achieved by increasing the length of the Coulombic cutoff and thus reducing the work done by the long-range solver. Using the "run_style verlet/split"_run_style.html command, which is compatible with the USER-OMP package, is an alternative way to reduce the number diff --git a/doc/src/Speed_packages.txt b/doc/src/Speed_packages.txt index 4c87091e7e..2f72a46b3a 100644 --- a/doc/src/Speed_packages.txt +++ b/doc/src/Speed_packages.txt @@ -14,7 +14,7 @@ Accelerated versions of various "pair_style"_pair_style.html, been added to LAMMPS, which will typically run faster than the standard non-accelerated versions. Some require appropriate hardware to be present on your system, e.g. GPUs or Intel Xeon Phi -coprocessors. +co-processors. All of these commands are in packages provided with LAMMPS. An overview of packages is give on the "Packages"_Packages.html doc @@ -161,7 +161,7 @@ package. These styles support vectorized single and mixed precision calculations, in addition to full double precision. In extreme cases, this can provide speedups over 3.5x on CPUs. The package also supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM) -coprocessors. This can result in additional speedup over 2x depending +co-processors. This can result in additional speedup over 2x depending on the hardware configuration. :l Styles with a "kk" suffix are part of the KOKKOS package, and can be diff --git a/doc/src/Tools.txt b/doc/src/Tools.txt index a9ad5032ce..af9fd4298c 100644 --- a/doc/src/Tools.txt +++ b/doc/src/Tools.txt @@ -163,7 +163,7 @@ for the "chain benchmark"_Speed_bench.html. colvars tools :h4,link(colvars) -The colvars directory contains a collection of tools for postprocessing +The colvars directory contains a collection of tools for post-processing data produced by the colvars collective variable library. To compile the tools, edit the makefile for your system and run "make". @@ -263,7 +263,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech emacs tool :h4,link(emacs) -The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs +The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs that enables a lammps-mode for editing input scripts when using GNU Emacs, with various highlighting options set up. @@ -391,30 +391,31 @@ definition file. This tool was used to create the system for the moltemplate tool :h4,link(moltemplate) -The moltemplate sub-directory contains a Python-based tool for -building molecular systems based on a text-file description, and -creating LAMMPS data files that encode their molecular topology as -lists of bonds, angles, dihedrals, etc. See the README.TXT file for -more information. +The moltemplate sub-directory contains instructions for installing +moltemplate, a Python-based tool for building molecular systems based +on a text-file description, and creating LAMMPS data files that encode +their molecular topology as lists of bonds, angles, dihedrals, etc. +See the README.txt file for more information. This tool was written by Andrew Jewett (jewett.aij at gmail.com), who supports it. It has its own WWW page at "http://moltemplate.org"_http://moltemplate.org. +The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases :line msi2lmp tool :h4,link(msi) The msi2lmp sub-directory contains a tool for creating LAMMPS template -input and data files from BIOVIA's Materias Studio files (formerly Accelrys' -Insight MD code, formerly MSI/Biosym and its Discover MD code). +input and data files from BIOVIA's Materias Studio files (formerly +Accelrys' Insight MD code, formerly MSI/Biosym and its Discover MD code). This tool was written by John Carpenter (Cray), Michael Peachey (Cray), and Steve Lustig (Dupont). Several people contributed changes to remove bugs and adapt its output to changes in LAMMPS. This tool has several known limitations and is no longer under active -development, so there are no changes except for the occasional bugfix. +development, so there are no changes except for the occasional bug fix. See the README file in the tools/msi2lmp folder for more information. @@ -485,9 +486,9 @@ README for more info on Pizza.py and how to use these scripts. reax tool :h4,link(reax_tool) -The reax sub-directory contains stand-alond codes that can -post-process the output of the "fix reax/bonds"_fix_reax_bonds.html -command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See +The reax sub-directory contains stand-alone codes that can +post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html +command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html. See the README.txt file for more info. These tools were written by Aidan Thompson at Sandia. diff --git a/doc/src/angle_coeff.txt b/doc/src/angle_coeff.txt index 4c217bae7d..5dc9c13381 100644 --- a/doc/src/angle_coeff.txt +++ b/doc/src/angle_coeff.txt @@ -60,26 +60,14 @@ doc page for details. :line -Here is an alphabetic list of angle styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "angle_coeff"_angle_coeff.html command. - -Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The full list of all -angle styles is on the "Commands bond"_Commands_bond.html#angle doc +The list of all angle styles defined in LAMMPS is given on the +"angle_style"_angle_style.html doc page. They are also listed in more +compact form on the "Commands angle"_Commands_bond.html#angle doc page. -"angle_style none"_angle_none.html - turn off angle interactions -"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul - -"angle_style charmm"_angle_charmm.html - CHARMM angle -"angle_style class2"_angle_class2.html - COMPASS (class 2) angle -"angle_style cosine"_angle_cosine.html - cosine angle potential -"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential -"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle -"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential -"angle_style harmonic"_angle_harmonic.html - harmonic angle -"angle_style table"_angle_table.html - tabulated by angle :ul +On either of those pages, click on the style to display the formula it +computes and its coefficients as specified by the associated +angle_coeff command. :line diff --git a/doc/src/angle_cosine.txt b/doc/src/angle_cosine.txt index 80cf8ae8f1..93fed32c38 100644 --- a/doc/src/angle_cosine.txt +++ b/doc/src/angle_cosine.txt @@ -8,6 +8,7 @@ angle_style cosine command :h3 angle_style cosine/omp command :h3 +angle_style cosine/kk command :h3 [Syntax:] diff --git a/doc/src/angle_cosine_buck6d.txt b/doc/src/angle_cosine_buck6d.txt index 686e123ca0..1ce3556ea6 100644 --- a/doc/src/angle_cosine_buck6d.txt +++ b/doc/src/angle_cosine_buck6d.txt @@ -23,19 +23,19 @@ The {cosine/buck6d} angle style uses the potential :c,image(Eqs/angle_cosine_buck6d.jpg) -where K is the energy constant, n is the periodic multiplicity and +where K is the energy constant, n is the periodic multiplicity and Theta0 is the equilibrium angle. -The coefficients must be defined for each angle type via the +The coefficients must be defined for each angle type via the "angle_coeff"_angle_coeff.html command as in the example above, or in the data file or restart files read by the "read_data"_read_data.html or "read_restart"_read_restart.html commands in the following order: K (energy) -n +n Theta0 (degrees) :ul -Theta0 is specified in degrees, but LAMMPS converts it to radians +Theta0 is specified in degrees, but LAMMPS converts it to radians internally. Additional to the cosine term the {cosine/buck6d} angle style computes @@ -51,8 +51,8 @@ the "special_bonds"_special_bonds.html 1-3 interactions to be weighted [Restrictions:] {cosine/buck6d} can only be used in combination with the -"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a -"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions. +"pair_buck6d"_pair_buck6d_coul_gauss.html style and with a +"special_bonds"_special_bonds.html 0.0 weighting of 1-3 interactions. This angle style can only be used if LAMMPS was built with the USER-MOFFF package. See the "Build package"_Build_package.html doc diff --git a/doc/src/angle_cosine_shift.txt b/doc/src/angle_cosine_shift.txt index 3a4efad218..65dc0924e5 100644 --- a/doc/src/angle_cosine_shift.txt +++ b/doc/src/angle_cosine_shift.txt @@ -63,7 +63,7 @@ instructions on how to use the accelerated styles effectively. [Restrictions:] This angle style can only be used if LAMMPS was built with the -USER-MISC package. +USER-MISC package. [Related commands:] diff --git a/doc/src/angle_cross.txt b/doc/src/angle_cross.txt new file mode 100644 index 0000000000..d9d83ed4b6 --- /dev/null +++ b/doc/src/angle_cross.txt @@ -0,0 +1,62 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +angle_style cross command :h3 + +[Syntax:] + +angle_style cross :pre + +[Examples:] + +angle_style cross +angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre + +[Description:] + +The {cross} angle style uses a potential that couples the bond stretches of +a bend with the angle stretch of that bend: + +:c,image(Eqs/angle_cross.jpg) + +where r12,0 is the rest value of the bond length between atom 1 and 2, +r32,0 is the rest value of the bond length between atom 2 and 2, +and theta0 is the rest value of the angle. KSS is the force constant of +the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants +of the bond stretch-angle stretch terms. + +The following coefficients must be defined for each angle type via the +"angle_coeff"_angle_coeff.html command as in the example above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +KSS (energy/distance^2) +KBS0 (energy/distance/rad) +KBS1 (energy/distance/rad) +r12,0 (distance) +r32,0 (distance) +theta0 (degrees) :ul + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of KBS0 and KBS1 are in energy/distance/radian. + +[Restrictions:] + +This angle style can only be used if LAMMPS was built with the +USER_YAFF package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"angle_coeff"_angle_coeff.html + +[Default:] none + +:line + + diff --git a/doc/src/angle_mm3.txt b/doc/src/angle_mm3.txt new file mode 100644 index 0000000000..9ae032c4ff --- /dev/null +++ b/doc/src/angle_mm3.txt @@ -0,0 +1,55 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +angle_style mm3 command :h3 + +[Syntax:] + +angle_style mm3 :pre + +[Examples:] + +angle_style mm3 +angle_coeff 1 100.0 107.0 :pre + +[Description:] + +The {mm3} angle style uses the potential that is anharmonic in the angle +as defined in "(Allinger)"_#mm3-allinger1989 + +:c,image(Eqs/angle_mm3.jpg) + +where theta0 is the equilibrium value of the angle, and K is a +prefactor. The anharmonic prefactors have units deg^(-n), for example +-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ... + +The following coefficients must be defined for each angle type via the +"angle_coeff"_angle_coeff.html command as in the example above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +K (energy/radian^2) +theta0 (degrees) :ul + +Theta0 is specified in degrees, but LAMMPS converts it to radians +internally; hence the units of K are in energy/radian^2. + +[Restrictions:] + +This angle style can only be used if LAMMPS was built with the +USER_YAFF package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"angle_coeff"_angle_coeff.html + +[Default:] none + +:line + diff --git a/doc/src/angle_sdk.txt b/doc/src/angle_sdk.txt index 22238880fe..9382d560d3 100644 --- a/doc/src/angle_sdk.txt +++ b/doc/src/angle_sdk.txt @@ -28,7 +28,7 @@ The {sdk} angle style is a combination of the harmonic angle potential, where theta0 is the equilibrium value of the angle and K a prefactor, with the {repulsive} part of the non-bonded {lj/sdk} pair style between the atoms 1 and 3. This angle potential is intended for -coarse grained MD simulations with the CMM parametrization using the +coarse grained MD simulations with the CMM parameterization using the "pair_style lj/sdk"_pair_sdk.html. Relative to the pair_style {lj/sdk}, however, the energy is shifted by {epsilon}, to avoid sudden jumps. Note that the usual 1/2 factor is included in K. diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt index a0bc47ba4c..2f2da678d8 100644 --- a/doc/src/angle_style.txt +++ b/doc/src/angle_style.txt @@ -57,10 +57,15 @@ Here is an alphabetic list of angle styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated "angle_coeff"_angle_coeff.html command. -Note that there are also additional angle styles submitted by users -which are included in the LAMMPS distribution. The full list of all -angle styles are is on the "Commands bond"_Commands_bond.html#angle -doc page. +Click on the style to display the formula it computes, any additional +arguments specified in the angle_style command, and coefficients +specified by the associated "angle_coeff"_angle_coeff.html command. + +There are also additional accelerated pair styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands +angle"_Commands_bond.html#angle doc page are followed by one or more +of (g,i,k,o,t) to indicate which accelerated styles exist. "none"_angle_none.html - turn off angle interactions "zero"_angle_zero.html - topology but no interactions @@ -76,10 +81,12 @@ doc page. "cosine/shift"_angle_cosine_shift.html - angle cosine with a shift "cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant "cosine/squared"_angle_cosine_squared.html - angle with cosine squared term +"cross"_angle_cross.html - cross term coupling angle and bond lengths "dipole"_angle_dipole.html - angle that controls orientation of a point dipole "fourier"_angle_fourier.html - angle with multiple cosine terms "fourier/simple"_angle_fourier_simple.html - angle with a single cosine term "harmonic"_angle_harmonic.html - harmonic angle +"mm3"_angle_mm3.html - anharmonic angle "quartic"_angle_quartic.html - angle with cubic and quartic terms "sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms "table"_angle_table.html - tabulated by angle :ul diff --git a/doc/src/angles.txt b/doc/src/angles.txt index 3e91ba9917..3d8a47b2eb 100644 --- a/doc/src/angles.txt +++ b/doc/src/angles.txt @@ -14,11 +14,13 @@ Angle Styles :h1 angle_cosine_shift angle_cosine_shift_exp angle_cosine_squared + angle_cross angle_dipole angle_fourier angle_fourier_simple angle_harmonic angle_hybrid + angle_mm3 angle_none angle_quartic angle_sdk diff --git a/doc/src/atom_modify.txt b/doc/src/atom_modify.txt index 0f0b241b76..d598b4697c 100644 --- a/doc/src/atom_modify.txt +++ b/doc/src/atom_modify.txt @@ -166,7 +166,8 @@ info), a map is used. The default map style is array if no atom ID is larger than 1 million, otherwise the default is hash. By default, a "first" group is not defined. By default, sorting is enabled with a frequency of 1000 and a binsize of 0.0, which means the neighbor -cutoff will be used to set the bin size. +cutoff will be used to set the bin size. If no neighbor cutoff is +defined, sorting will be turned off. :line diff --git a/doc/src/atom_style.txt b/doc/src/atom_style.txt index db2e285dc4..ff96fedab9 100644 --- a/doc/src/atom_style.txt +++ b/doc/src/atom_style.txt @@ -39,7 +39,7 @@ atom_style body nparticle 2 10 atom_style hybrid charge bond atom_style hybrid charge body nparticle 2 5 atom_style spin -atom_style template myMols +atom_style template myMols atom_style tdpd 2 :pre [Description:] @@ -87,7 +87,7 @@ quantities. {line} | end points, angular velocity | rigid bodies | {meso} | rho, e, cv | SPH particles | {molecular} | bonds, angles, dihedrals, impropers | uncharged molecules | -{peri} | mass, volume | mesocopic Peridynamic models | +{peri} | mass, volume | mesoscopic Peridynamic models | {smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles | {sphere} | diameter, mass, angular velocity | granular models | {spin} | magnetic moment | system with magnetic particles | @@ -309,9 +309,9 @@ force fields"_pair_eff.html. The {dpd} style is part of the USER-DPD package for dissipative particle dynamics (DPD). -The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package -for energy-conserving dissipative particle dynamics (eDPD), many-body -dissipative particle dynamics (mDPD), and transport dissipative particle +The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package +for energy-conserving dissipative particle dynamics (eDPD), many-body +dissipative particle dynamics (mDPD), and transport dissipative particle dynamics (tDPD), respectively. The {meso} style is part of the USER-SPH package for smoothed particle diff --git a/doc/src/balance.txt b/doc/src/balance.txt index 49202b0149..2ca44203f6 100644 --- a/doc/src/balance.txt +++ b/doc/src/balance.txt @@ -247,7 +247,7 @@ to {Niter} times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the {stopthresh} criterion is met. -A rebalance operation in a single dimension is performed using a +A re-balance operation in a single dimension is performed using a recursive multisectioning algorithm, where the position of each cutting plane (line in 2d) in the dimension is adjusted independently. This is similar to a recursive bisectioning for a single value, except @@ -261,11 +261,11 @@ information, so that they become closer together over time. Thus as the recursion progresses, the count of particles on either side of the plane gets closer to the target value. -Once the rebalancing is complete and final processor sub-domains +Once the re-balancing is complete and final processor sub-domains assigned, particles are migrated to their new owning processor, and the balance procedure ends. -NOTE: At each rebalance operation, the bisectioning for each cutting +NOTE: At each re-balance operation, the bisectioning for each cutting plane (line in 2d) typically starts with low and high bounds separated by the extent of a processor's sub-domain in one dimension. The size of this bracketing region shrinks by 1/2 every iteration. Thus if @@ -348,7 +348,7 @@ specified groups, its weight is not changed. If it belongs to multiple groups, its weight is the product of the weight factors. This weight style is useful in combination with pair style -"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody +"hybrid"_pair_hybrid.html, e.g. when combining a more costly many-body potential with a fast pair-wise potential. It is also useful when using "run_style respa"_run_style.html where some portions of the system have many bonded interactions and others none. It assumes that @@ -510,10 +510,13 @@ each processor, instead of 4, and "SQUARES" replaced by "CUBES". For 2d simulations, the {z} style cannot be used. Nor can a "z" appear in {dimstr} for the {shift} style. +Balancing through recursive bisectioning ({rcb} style) requires +"comm_style tiled"_comm_style.html + [Related commands:] "group"_group.html, "processors"_processors.html, -"fix balance"_fix_balance.html +"fix balance"_fix_balance.html, "comm_style"_comm_style.html [Default:] none :link(pizza,http://pizza.sandia.gov) diff --git a/doc/src/bond_coeff.txt b/doc/src/bond_coeff.txt index 7485fa3d8d..1280ae3fb0 100644 --- a/doc/src/bond_coeff.txt +++ b/doc/src/bond_coeff.txt @@ -56,25 +56,13 @@ corresponds to the 1st example above would be listed as :line -Here is an alphabetic list of bond styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "bond_coeff"_bond_coeff.html command. +The list of all bond styles defined in LAMMPS is given on the +"bond_style"_bond_style.html doc page. They are also listed in more +compact form on the "Commands bond"_Commands_bond.html doc page. -Note that here are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The full list of all -bond styles is on the "Commands bond"_Commands_bond.html doc page. - -"bond_style none"_bond_none.html - turn off bonded interactions -"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul - -"bond_style class2"_bond_class2.html - COMPASS (class 2) bond -"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond -"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles -"bond_style harmonic"_bond_harmonic.html - harmonic bond -"bond_style morse"_bond_morse.html - Morse bond -"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond -"bond_style quartic"_bond_quartic.html - breakable quartic bond -"bond_style table"_bond_table.html - tabulated by bond length :ul +On either of those pages, click on the style to display the formula it +computes and its coefficients as specified by the associated +bond_coeff command. :line diff --git a/doc/src/bond_mm3.txt b/doc/src/bond_mm3.txt new file mode 100644 index 0000000000..c3d0e39f52 --- /dev/null +++ b/doc/src/bond_mm3.txt @@ -0,0 +1,58 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +bond_style mm3 command :h3 + +[Syntax:] + +bond_style mm3 :pre + +[Examples:] + +bond_style mm3 +bond_coeff 1 100.0 107.0 :pre + +[Description:] + +The {mm3} bond style uses the potential that is anharmonic in the bond +as defined in "(Allinger)"_#mm3-allinger1989 + +:c,image(Eqs/bond_mm3.jpg) + +where r0 is the equilibrium value of the bond, and K is a +prefactor. The anharmonic prefactors have units angstrom^(-n): +-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes +care of the necessary unit conversion for these factors internally. +Note that the MM3 papers contains an error in Eq (1): +(7/12)2.55 should be replaced with (7/12)2.55^2 + +The following coefficients must be defined for each bond type via the +"bond_coeff"_bond_coeff.html command as in the example above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +K (energy/distance^2) +r0 (distance) :ul + +[Restrictions:] + +This bond style can only be used if LAMMPS was built with the +USER_YAFF package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"bond_coeff"_bond_coeff.html + +[Default:] none + +:line + +:link(mm3-allinger1989) +[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 +(1989), diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index 724951f961..88afe435e6 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -52,7 +52,7 @@ hydrogen-bonding interaction {oxdna/hbond} (see also documentation of "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot -be changed without reparametrizing the entire model. +be changed without reparameterizing the entire model. Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt index 197a4fb1b6..aba6d3a778 100644 --- a/doc/src/bond_style.txt +++ b/doc/src/bond_style.txt @@ -65,9 +65,15 @@ Here is an alphabetic list of bond styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated "bond_coeff"_bond_coeff.html command. -Note that there are also additional bond styles submitted by users -which are included in the LAMMPS distribution. The full list of all -bond styles is on the "Commands bond"_Commands_bond.html doc page. +Click on the style to display the formula it computes, any additional +arguments specified in the bond_style command, and coefficients +specified by the associated "bond_coeff"_bond_coeff.html command. + +There are also additional accelerated pair styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands bond"_Commands_bond.html +doc page are followed by one or more of (g,i,k,o,t) to indicate which +accelerated styles exist. "none"_bond_none.html - turn off bonded interactions "zero"_bond_zero.html - topology but no interactions @@ -80,10 +86,11 @@ bond styles is on the "Commands bond"_Commands_bond.html doc page. "harmonic"_bond_harmonic.html - harmonic bond "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff +"mm3"_bond_mm3.html - MM3 anharmonic bond "morse"_bond_morse.html - Morse bond "nonlinear"_bond_nonlinear.html - nonlinear bond "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling -"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles +"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles "quartic"_bond_quartic.html - breakable quartic bond "table"_bond_table.html - tabulated by bond length :ul diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt index d33515eb88..48896e711c 100644 --- a/doc/src/bonds.txt +++ b/doc/src/bonds.txt @@ -13,6 +13,7 @@ Bond Styles :h1 bond_harmonic_shift bond_harmonic_shift_cut bond_hybrid + bond_mm3 bond_morse bond_none bond_nonlinear diff --git a/doc/src/comm_modify.txt b/doc/src/comm_modify.txt index 489278523b..482259142b 100644 --- a/doc/src/comm_modify.txt +++ b/doc/src/comm_modify.txt @@ -154,6 +154,6 @@ Communication mode {multi} is currently only available for [Default:] -The option defauls are mode = single, group = all, cutoff = 0.0, vel = +The option defaults are mode = single, group = all, cutoff = 0.0, vel = no. The cutoff default of 0.0 means that ghost cutoff = neighbor cutoff = pairwise force cutoff + neighbor skin. diff --git a/doc/src/comm_style.txt b/doc/src/comm_style.txt index 39eb1d4ef5..cd9631dd88 100644 --- a/doc/src/comm_style.txt +++ b/doc/src/comm_style.txt @@ -51,7 +51,10 @@ decomposition will be the same, as described by commands. The decomposition can be changed via the "balance"_balance.html or "fix balance"_fix_balance.html commands. -[Restrictions:] none +[Restrictions:] + +Communication style {tiled} cannot be used with {triclinic} simulation +cells. [Related commands:] diff --git a/doc/src/commands_list.txt b/doc/src/commands_list.txt index db3ef36ddf..6f90d9c93a 100644 --- a/doc/src/commands_list.txt +++ b/doc/src/commands_list.txt @@ -32,6 +32,7 @@ Commands :h1 dimension displace_atoms dump + dump_adios dump_cfg_uef dump_h5md dump_image @@ -39,17 +40,20 @@ Commands :h1 dump_molfile dump_netcdf dump_vtk + dynamical_matrix echo fix fix_modify group group2ndx + hyper if improper_coeff improper_style include info jump + kim_query kspace_modify kspace_style label @@ -58,6 +62,7 @@ Commands :h1 mass message min_modify + min_spin min_style minimize molecule diff --git a/doc/src/compute.txt b/doc/src/compute.txt index 676c00d7a5..c8456fb342 100644 --- a/doc/src/compute.txt +++ b/doc/src/compute.txt @@ -54,9 +54,10 @@ local quantities have the word "local" in their style, e.g. {bond/local}. Styles with neither "atom" or "local" in their style produce global quantities. -Note that a single compute produces either global or per-atom or local -quantities, but never more than one of these (with only a few -exceptions, as documented by individual compute commands). +Note that a single compute can produce either global or per-atom or +local quantities, but not both global and per-atom. It can produce +local quantities in tandem with global or per-atom quantities. The +compute doc page will explain. Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The @@ -164,20 +165,20 @@ and what it does. Here is an alphabetic list of compute styles available in LAMMPS. They are also listed in more compact form on the "Commands compute"_Commands_compute.html doc page. -There are also additional compute styles (not listed here) submitted -by users which are included in the LAMMPS distribution. The full list -of all compute styles is on the "Commands -compute"_Commands_compute.html doc page. - There are also additional accelerated compute styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands compute"_Commands_compute.html doc page are followed by one or more of (g,i,k,o,t) to indicate which accerlerated styles exist. +"ackland/atom"_compute_ackland_atom.html - +"adf"_compute_adf.html - angular distribution function of triples of atoms "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom +"angle"_compute_angle.html - +"angle/local"_compute_angle_local.html - "angle/local"_compute_bond_local.html - theta and energy of each angle "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk +"basal/atom"_compute_basal_atom.html - "body/local"_compute_body_local.html - attributes of body sub-particles "bond"_compute_bond.html - values computed by a bond style "bond/local"_compute_bond_local.html - distance and energy of each bond @@ -185,31 +186,43 @@ compute"_Commands_compute.html doc page are followed by one or more of "chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom +"cnp/atom"_compute_cnp_atom.html - "com"_compute_com.html - center-of-mass of group of atoms "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk "contact/atom"_compute_contact_atom.html - contact count for each spherical particle "coord/atom"_compute_coord_atom.html - coordination number for each atom "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom +"dihedral"_compute_dihedral.html - "dihedral/local"_compute_dihedral_local.html - angle of each dihedral "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom +"dipole/chunk"_compute_dipole_chunk.html - "displace/atom"_compute_displace_atom.html - displacement of each atom +"dpd"_compute_dpd.html - +"dpd/atom"_compute_dpd_atom.html - +"edpd/temp/atom"_compute_edpd_temp_atom.html - +"entropy/atom"_compute_entropy_atom.html - "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle +"erotate/sphere/atom"_compute_erotate_sphere_atom.html - "event/displace"_compute_event_displace.html - detect event on atom displacement +"fep"_compute_fep.html - +"force/tally"_compute_tally.html - "fragment/atom"_compute_cluster_atom.html - fragment ID for each atom +"global/atom"_compute_global_atom.html - "group/group"_compute_group_group.html - energy/force between two groups of atoms "gyration"_compute_gyration.html - radius of gyration of group of atoms "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms +"heat/flux/tally"_compute_tally.html - "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6 "hma"_compute_hma.html - harmonically mapped averaging for atomic crystals +"improper"_compute_improper.html - "improper/local"_compute_improper_local.html - angle of each improper "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk "ke"_compute_ke.html - translational kinetic energy "ke/atom"_compute_ke_atom.html - kinetic energy for each atom -"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies "msd"_compute_msd.html - mean-squared displacement of group of atoms "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms @@ -219,34 +232,72 @@ compute"_Commands_compute.html doc page are followed by one or more of "pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction "pe"_compute_pe.html - potential energy "pe/atom"_compute_pe_atom.html - potential energy for each atom +"pe/mol/tally"_compute_tally.html - +"pe/tally"_compute_tally.html - "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom "pressure"_compute_pressure.html - total pressure and pressure tensor +"pressure/cylinder"_compute_pressure_cylinder.html - +"pressure/uef"_compute_pressure_uef.html - "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays "property/local"_compute_property_local.html - convert local attributes to localvectors/arrays -"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes +"ptm/atom"_compute_ptm_atom.html - "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms "reduce"_compute_reduce.html - combine per-atom quantities into a single global value "reduce/region"_compute_reduce.html - same as compute reduce, within a region "rigid/local"_compute_rigid_local.html - extract rigid body attributes +"saed"_compute_saed.html - "slice"_compute_slice.html - extract values from global vector or array +"smd/contact/radius"_compute_smd_contact_radius.html - +"smd/damage"_compute_smd_damage.html - +"smd/hourglass/error"_compute_smd_hourglass_error.html - +"smd/internal/energy"_compute_smd_internal_energy.html - +"smd/plastic/strain"_compute_smd_plastic_strain.html - +"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - +"smd/rho"_compute_smd_rho.html - +"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - +"smd/tlsph/dt"_compute_smd_tlsph_dt.html - +"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - +"smd/tlsph/shape"_compute_smd_tlsph_shape.html - +"smd/tlsph/strain"_compute_smd_tlsph_strain.html - +"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - +"smd/tlsph/stress"_compute_smd_tlsph_stress.html - +"smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/triangle/vertices"_compute_smd_triangle_vertices.html - +"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - +"smd/ulsph/strain"_compute_smd_ulsph_strain.html - +"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - +"smd/ulsph/stress"_compute_smd_ulsph_stress.html - +"smd/vol"_compute_smd_vol.html - "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom +"spin"_compute_spin.html - "stress/atom"_compute_stress_atom.html - stress tensor for each atom +"stress/mop"_compute_stress_mop.html - +"stress/mop/profile"_compute_stress_mop.html - +"stress/tally"_compute_tally.html - +"tdpd/cc/atom"_compute_tdpd_cc_atom.html - "temp"_compute_temp.html - temperature of group of atoms "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles "temp/body"_compute_temp_body.html - temperature of body particles "temp/chunk"_compute_temp_chunk.html - temperature of each chunk "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity +"temp/cs"_compute_temp_cs.html - "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity +"temp/deform/eff"_compute_temp_deform_eff.html - +"temp/drude"_compute_temp_drude.html - +"temp/eff"_compute_temp_eff.html - "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component "temp/region"_compute_temp_region.html - temperature of a region of atoms +"temp/region/eff"_compute_temp_region_eff.html - +"temp/rotate"_compute_temp_rotate.html - "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles +"temp/uef"_compute_temp_uef.html - "ti"_compute_ti.html - thermodynamic integration free energy values "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk -"vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms +"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk "voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul diff --git a/doc/src/compute_adf.txt b/doc/src/compute_adf.txt index 3d0646e294..20b9fad3f6 100644 --- a/doc/src/compute_adf.txt +++ b/doc/src/compute_adf.txt @@ -33,22 +33,22 @@ keyword = {ordinate} :l compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 & 1 1 2 0.0 1.2 0.0 1.5 & - 1 2 2 0.0 1.5 0.0 1.5 & + 1 2 2 0.0 1.5 0.0 1.5 & 2 1 1 0.0 1.2 0.0 1.2 & 2 1 2 0.0 1.5 2.0 3.5 & - 2 2 2 2.0 3.5 2.0 3.5 + 2 2 2 2.0 3.5 2.0 3.5 compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5 compute 1 fluid adf 32 :pre [Description:] Define a computation that calculates one or more angular distribution functions -(ADF) for a group of particles. Each ADF is calculated in histogram form +(ADF) for a group of particles. Each ADF is calculated in histogram form by measuring the angle formed by a central atom and two neighbor atoms and binning these angles into {Nbin} bins. Only neighbors for which {Rinner} < {R} < {Router} are counted, where {Rinner} and {Router} are specified separately for the first and second -neighbor atom in each requested ADF. +neighbor atom in each requested ADF. NOTE: If you have a bonded system, then the settings of "special_bonds"_special_bonds.html command can remove pairwise @@ -66,18 +66,18 @@ the dump file. The rerun script can use a "special_bonds"_special_bonds.html command that includes all pairs in the neighbor list. -NOTE: If you request any outer cutoff {Router} > force cutoff, or if no +NOTE: If you request any outer cutoff {Router} > force cutoff, or if no pair style is defined, e.g. the "rerun"_rerun.html command is being used to -post-process a dump file of snapshots you must insure ghost atom information -out to the largest value of {Router} + {skin} is communicated, via the -"comm_modify cutoff"_comm_modify.html command, else the ADF computation -cannot be performed, and LAMMPS will give an error message. The {skin} value -is what is specified with the "neighbor"_neighbor.html command. +post-process a dump file of snapshots you must insure ghost atom information +out to the largest value of {Router} + {skin} is communicated, via the +"comm_modify cutoff"_comm_modify.html command, else the ADF computation +cannot be performed, and LAMMPS will give an error message. The {skin} value +is what is specified with the "neighbor"_neighbor.html command. The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two ways. An explicit numeric value can be used, as in the 1st example above. Or a wild-card asterisk can be used to specify a range of atom -types as in the 2nd example above. +types as in the 2nd example above. This takes the form "*" or "*n" or "n*" or "m*n". If N = the number of atom types, then an asterisk with no numeric values means all types from 1 to N. A leading asterisk means all types from 1 to n @@ -88,13 +88,13 @@ all types from 1 to N. A leading asterisk means all types from 1 to n If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example above, this means that the ADF is computed where atoms of type {itypeN} are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN} -are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN} +are forming the angle. If any of {itypeN}, {jtypeN}, or {ktypeN} represent a range of values via the wild-card asterisk, as in the 2nd example above, this means that the ADF is computed where atoms of any of the range of types represented by {itypeN} are the central atom, and the angle is formed by two neighbors, -one neighbor in the range of types represented by {jtypeN} and another neighbor -in the range of types represented by {ktypeN}. +one neighbor in the range of types represented by {jtypeN} and another neighbor +in the range of types represented by {ktypeN}. If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then LAMMPS will generate a single ADF for all atoms in the group. @@ -106,13 +106,13 @@ Such an ADF is both uninformative and extremely expensive to compute. For example, with liquid water with a 10 A force cutoff, there are 80,000 angles per atom. In addition, most of the interesting angular structure occurs for -neighbors that are the closest to the central atom, involving +neighbors that are the closest to the central atom, involving just a few dozen angles. -Angles for each ADF are generated by double-looping over the list of -neighbors of each central atom I, -just as they would be in the force calculation for -a threebody potential such as "Stillinger-Weber"_pair_sw.html. +Angles for each ADF are generated by double-looping over the list of +neighbors of each central atom I, +just as they would be in the force calculation for +a three-body potential such as "Stillinger-Weber"_pair_sw.html. The angle formed by central atom I and neighbor atoms J and K is included in an ADF if the following criteria are met: @@ -121,12 +121,12 @@ the distance between atoms I,J is between Rjinner and Rjouter the distance between atoms I,K is between Rkinner and Rkouter the type of the I atom matches itypeN (one or a range of types) atoms I,J,K are distinct -the type of the J atom matches jtypeN (one or a range of types) +the type of the J atom matches jtypeN (one or a range of types) the type of the K atom matches ktypeN (one or a range of types) :ul Each unique angle satisfying the above criteria is counted only once, regardless of whether either or both of the neighbor atoms making up the -angle appear in both the J and K lists. +angle appear in both the J and K lists. It is OK if a particular angle is included in more than one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN} arguments are specified. @@ -146,15 +146,15 @@ number radial distribution function. The {ordinate} optional keyword determines whether the bins are of uniform angular size from zero -to 180 ({degree}), zero to Pi ({radian}), or the +to 180 ({degree}), zero to Pi ({radian}), or the cosine of the angle uniform in the range \[-1,1\] ({cosine}). {cosine} has the advantage of eliminating the {acos()} function call, which speeds up the compute by 2-3x, and it is also preferred -on physical grounds, because the for uniformly distributed particles +on physical grounds, because the for uniformly distributed particles in 3D, the angular probability density w.r.t dtheta is -sin(theta)/2, while for d(cos(theta)), it is 1/2, -Regardless of which ordinate is chosen, the first column of ADF -values is normalized w.r.t. the range of that ordinate, so that +sin(theta)/2, while for d(cos(theta)), it is 1/2, +Regardless of which ordinate is chosen, the first column of ADF +values is normalized w.r.t. the range of that ordinate, so that the integral is 1. The simplest way to output the results of the compute adf calculation @@ -170,7 +170,7 @@ This compute calculates a global array with the number of rows = {Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the number of I,J,K triples specified. The first column has the bin coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has -the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) +the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) interactions, as described above. These values can be used by any command that uses a global values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of @@ -181,15 +181,15 @@ The array values calculated by this compute are all "intensive". The first column of array values is the angle-related ordinate, either the angle in degrees or radians, or the cosine of the angle. Each subsequent pair of columns gives the first and second kinds of ADF -for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values +for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values in the first ADF column are normalized numbers >= 0.0, whose integral w.r.t. the ordinate is 1, -i.e. the first ADF is a normalized probability distribution. +i.e. the first ADF is a normalized probability distribution. The values in the second ADF column are also numbers >= 0.0. They are the cumulative density distribution of angles per atom. By definition, this ADF is monotonically increasing from zero to a maximum value equal to the average total number of -angles per atom satisfying the ADF criteria. +angles per atom satisfying the ADF criteria. [Restrictions:] @@ -200,7 +200,7 @@ distances, you can use the "rerun"_rerun.html command to post-process a dump file and set the cutoff for the potential to be longer in the rerun script. Note that in the rerun context, the force cutoff is arbitrary, since you aren't running dynamics and thus are not changing -your model. +your model. [Related commands:] diff --git a/doc/src/compute_angle_local.txt b/doc/src/compute_angle_local.txt index 8acaec94d5..332a7a07af 100644 --- a/doc/src/compute_angle_local.txt +++ b/doc/src/compute_angle_local.txt @@ -29,7 +29,7 @@ keyword = {set} :l [Examples:] compute 1 all angle/local theta -compute 1 all angle/local eng theta +compute 1 all angle/local eng theta compute 1 all angle/local theta v_cos set theta t :pre [Description:] diff --git a/doc/src/compute_angmom_chunk.txt b/doc/src/compute_angmom_chunk.txt index 7e49ff3024..f542ab51ab 100644 --- a/doc/src/compute_angmom_chunk.txt +++ b/doc/src/compute_angmom_chunk.txt @@ -37,7 +37,7 @@ they can be used to measure properties of a system. This compute calculates the 3 components of the angular momentum vector for each chunk, due to the velocity/momentum of the individual atoms in the chunk around the center-of-mass of the chunk. The -calculation includes all effects due to atoms passing thru periodic +calculation includes all effects due to atoms passing through periodic boundaries. Note that only atoms in the specified group contribute to the diff --git a/doc/src/compute_basal_atom.txt b/doc/src/compute_basal_atom.txt index 5c28b8e378..c74bd4342e 100644 --- a/doc/src/compute_basal_atom.txt +++ b/doc/src/compute_basal_atom.txt @@ -28,7 +28,7 @@ The results enable efficient identification and characterization of twins and grains in hexagonal close-packed structures. The output of the compute is thus the 3 components of a unit vector -associdate with each atom. The components are set to 0.0 for +associated with each atom. The components are set to 0.0 for atoms not in the group. Details of the calculation are given in "(Barrett)"_#Barrett. diff --git a/doc/src/compute_bond_local.txt b/doc/src/compute_bond_local.txt index 4afd1aec40..6055d28770 100644 --- a/doc/src/compute_bond_local.txt +++ b/doc/src/compute_bond_local.txt @@ -68,7 +68,7 @@ in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and v2 are the magnitude of the velocity of the 2 atoms along the bond direction, after the COM velocity has been subtracted from each. -The value {engrot} is the rotationsl kinetic energy of the two atoms +The value {engrot} is the rotational kinetic energy of the two atoms in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and v2 are the magnitude of the velocity of the 2 atoms perpendicular to the bond direction, after the COM velocity has been subtracted from diff --git a/doc/src/compute_chunk_atom.txt b/doc/src/compute_chunk_atom.txt index c29a5600a9..b924f90da8 100644 --- a/doc/src/compute_chunk_atom.txt +++ b/doc/src/compute_chunk_atom.txt @@ -210,7 +210,7 @@ between {crmin} and {crmax}. For example, if {crmin} = 1.0 and {crmax} = 10.0 and {ncbin} = 9, then the first bin spans 1.0 < r < 2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in the radial dimensions is the same whether the simulation box is -orthogonal or triclinic; i.e. the concetric circles are not tilted or +orthogonal or triclinic; i.e. the concentric circles are not tilted or scaled differently in the two different dimensions to transform them into ellipses. diff --git a/doc/src/compute_chunk_spread_atom.txt b/doc/src/compute_chunk_spread_atom.txt index f84ef67974..5f65900a49 100644 --- a/doc/src/compute_chunk_spread_atom.txt +++ b/doc/src/compute_chunk_spread_atom.txt @@ -74,7 +74,7 @@ produces a global vector or array. :line -Each listed input is operated on independently. +Each listed input is operated on independently. If a bracketed index I is used, it can be specified using a wildcard asterisk with the index to effectively specify multiple values. This @@ -134,16 +134,16 @@ compute gyr all gyration/chunk cmol variable ave equal ave(c_gyr) thermo_style custom step etotal press v_ave :pre - 0 22.394765 4.6721833 5.128278 - 100 22.445002 4.8166709 5.0348372 - 200 22.500128 4.8790392 4.9364875 - 300 22.534686 4.9183766 4.8590693 - 400 22.557196 4.9492211 4.7937849 - 500 22.571017 4.9161853 4.7412008 - 600 22.573944 5.0229708 4.6931243 - 700 22.581804 5.0541301 4.6440647 - 800 22.584683 4.9691734 4.6000016 - 900 22.59128 5.0247538 4.5611513 + 0 22.394765 4.6721833 5.128278 + 100 22.445002 4.8166709 5.0348372 + 200 22.500128 4.8790392 4.9364875 + 300 22.534686 4.9183766 4.8590693 + 400 22.557196 4.9492211 4.7937849 + 500 22.571017 4.9161853 4.7412008 + 600 22.573944 5.0229708 4.6931243 + 700 22.581804 5.0541301 4.6440647 + 800 22.584683 4.9691734 4.6000016 + 900 22.59128 5.0247538 4.5611513 1000 22.586832 4.94697 4.5238362 :pre :line diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index d69c5e9c46..56ad7dd715 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -33,7 +33,7 @@ Currently, there are five kinds of CNA patterns LAMMPS recognizes: fcc = 1 hcp = 2 bcc = 3 -icosohedral = 4 +icosahedral = 4 unknown = 5 :ul The value of the CNA pattern will be 0 for atoms not in the specified diff --git a/doc/src/compute_com.txt b/doc/src/compute_com.txt index fdc631a263..35cdd37c4d 100644 --- a/doc/src/compute_com.txt +++ b/doc/src/compute_com.txt @@ -22,7 +22,7 @@ compute 1 all com :pre [Description:] Define a computation that calculates the center-of-mass of the group -of atoms, including all effects due to atoms passing thru periodic +of atoms, including all effects due to atoms passing through periodic boundaries. A vector of three quantities is calculated by this compute, which diff --git a/doc/src/compute_com_chunk.txt b/doc/src/compute_com_chunk.txt index b982f0d901..9c14a554d7 100644 --- a/doc/src/compute_com_chunk.txt +++ b/doc/src/compute_com_chunk.txt @@ -35,7 +35,7 @@ doc pages for details of how chunks can be defined and examples of how they can be used to measure properties of a system. This compute calculates the x,y,z coordinates of the center-of-mass -for each chunk, which includes all effects due to atoms passing thru +for each chunk, which includes all effects due to atoms passing through periodic boundaries. Note that only atoms in the specified group contribute to the diff --git a/doc/src/compute_damage_atom.txt b/doc/src/compute_damage_atom.txt index 2594dfe356..c3e822d79f 100644 --- a/doc/src/compute_damage_atom.txt +++ b/doc/src/compute_damage_atom.txt @@ -26,7 +26,7 @@ in a group. This is a quantity relevant for "Peridynamics models"_pair_peri.html. See "this document"_PDF/PDLammps_overview.pdf for an overview of LAMMPS commands for Peridynamics modeling. -The "damage" of a Peridymaics particles is based on the bond breakage +The "damage" of a Peridynamics particles is based on the bond breakage between the particle and its neighbors. If all the bonds are broken the particle is considered to be fully damaged. diff --git a/doc/src/compute_dipole_chunk.txt b/doc/src/compute_dipole_chunk.txt index d45fde9af2..2a3d1d9b56 100644 --- a/doc/src/compute_dipole_chunk.txt +++ b/doc/src/compute_dipole_chunk.txt @@ -38,7 +38,7 @@ they can be used to measure properties of a system. This compute calculates the x,y,z coordinates of the dipole vector and the total dipole moment for each chunk, which includes all effects -due to atoms passing thru periodic boundaries. For chunks with a net +due to atoms passing through periodic boundaries. For chunks with a net charge the resulting dipole is made position independent by subtracting the position vector of the center of mass or geometric center times the net charge from the computed dipole vector. diff --git a/doc/src/compute_displace_atom.txt b/doc/src/compute_displace_atom.txt index 7cea62c7b3..27111b2c67 100644 --- a/doc/src/compute_displace_atom.txt +++ b/doc/src/compute_displace_atom.txt @@ -29,7 +29,7 @@ compute 1 all displace/atom refresh myVar :pre Define a computation that calculates the current displacement of each atom in the group from its original (reference) coordinates, including -all effects due to atoms passing thru periodic boundaries. +all effects due to atoms passing through periodic boundaries. A vector of four quantities per atom is calculated by this compute. The first 3 elements of the vector are the dx,dy,dz displacements. @@ -57,7 +57,7 @@ correctly with time=0 atom coordinates from the restart file. :line -The {refresh} option can be used in conjuction with the "dump_modify +The {refresh} option can be used in conjunction with the "dump_modify refresh" command to generate incremental dump files. The definition and motivation of an incremental dump file is as diff --git a/doc/src/compute_edpd_temp_atom.txt b/doc/src/compute_edpd_temp_atom.txt index f3c1418d44..ac3fb5e277 100644 --- a/doc/src/compute_edpd_temp_atom.txt +++ b/doc/src/compute_edpd_temp_atom.txt @@ -24,7 +24,7 @@ compute 1 all edpd/temp/atom :pre Define a computation that calculates the per-atom temperature for each eDPD particle in a group. -The temperature is a local temperature derived from the internal energy +The temperature is a local temperature derived from the internal energy of each eDPD particle based on the local equilibrium hypothesis. For more details please see "(Espanol1997)"_#Espanol1997 and "(Li2014)"_#Li2014a. diff --git a/doc/src/compute_entropy_atom.txt b/doc/src/compute_entropy_atom.txt index 04f0fd0b82..cd90a9b590 100644 --- a/doc/src/compute_entropy_atom.txt +++ b/doc/src/compute_entropy_atom.txt @@ -35,11 +35,11 @@ compute 1 all entropy/atom 0.125 7.3 avg yes 5.1 local yes :pre Define a computation that calculates the pair entropy fingerprint for each atom in the group. The fingerprint is useful to distinguish between -ordered and disordered environments, for instance liquid and solid-like -environments, or glassy and crystalline-like environments. Some -applications could be the identification of grain boundaries, a -melt-solid interface, or a solid cluster emerging from the melt. -The advantage of this parameter over others is that no a priori +ordered and disordered environments, for instance liquid and solid-like +environments, or glassy and crystalline-like environments. Some +applications could be the identification of grain boundaries, a +melt-solid interface, or a solid cluster emerging from the melt. +The advantage of this parameter over others is that no a priori information about the solid structure is required. This parameter for atom i is computed using the following formula from @@ -47,8 +47,8 @@ This parameter for atom i is computed using the following formula from :c,image(Eqs/pair_entropy.jpg) -where r is a distance, g(r) is the radial distribution function of atom -i and rho is the density of the system. The g(r) computed for each +where r is a distance, g(r) is the radial distribution function of atom +i and rho is the density of the system. The g(r) computed for each atom i can be noisy and therefore it is smoothed using: :c,image(Eqs/pair_entropy2.jpg) @@ -57,7 +57,7 @@ where the sum in j goes through the neighbors of atom i, and sigma is a parameter to control the smoothing. The input parameters are {sigma} the smoothing parameter, and the -{cutoff} for the calculation of g(r). +{cutoff} for the calculation of g(r). If the keyword {avg} has the setting {yes}, then this compute also averages the parameter over the neighbors of atom i according to: @@ -66,25 +66,25 @@ averages the parameter over the neighbors of atom i according to: where the sum j goes over the neighbors of atom i and N is the number of neighbors. This procedure provides a sharper distinction between -order and disorder environments. In this case the input parameter -{cutoff2} is the cutoff for the averaging over the neighbors and +order and disorder environments. In this case the input parameter +{cutoff2} is the cutoff for the averaging over the neighbors and must also be specified. If the {avg yes} option is used, the effective cutoff of the neighbor -list should be {cutoff}+{cutoff2} and therefore it might be necessary +list should be {cutoff}+{cutoff2} and therefore it might be necessary to increase the skin of the neighbor list with: neighbor skin bin :pre See "neighbor"_neighbor.html for details. -If the {local yes} option is used, the g(r) is normalized by the -local density around each atom, that is to say the density around each -atom is the number of neighbors within the neighbor list cutoff divided -by the corresponding volume. This option can be useful when dealing with +If the {local yes} option is used, the g(r) is normalized by the +local density around each atom, that is to say the density around each +atom is the number of neighbors within the neighbor list cutoff divided +by the corresponding volume. This option can be useful when dealing with inhomogeneous systems such as those that have surfaces. -Here are typical input parameters for fcc aluminum (lattice +Here are typical input parameters for fcc aluminum (lattice constant 4.05 Angstroms), compute 1 all entropy/atom 0.25 5.7 avg yes 3.7 :pre @@ -102,7 +102,7 @@ uses per-atom values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. -The pair entropy values have units of the Boltzmann constant. They are +The pair entropy values have units of the Boltzmann constant. They are always negative, and lower values (lower entropy) correspond to more ordered environments. diff --git a/doc/src/compute_fep.txt b/doc/src/compute_fep.txt index 5b3a6915dd..a46ab5b8d3 100644 --- a/doc/src/compute_fep.txt +++ b/doc/src/compute_fep.txt @@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it. The {pstyle} argument is the name of the pair style. For example, {pstyle} could be specified as "lj/cut". The {pparam} argument is the -name of the parameter to change. This is a (non-exclusive) list of +name of the parameter to change. This is a list of pair styles and parameters that can be used with this compute. See the doc pages for individual pair styles and their energy formulas for the meaning of these parameters: -"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs: -"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs: -"coul/long/soft"_pair_lj_soft.html: lambda: type pairs: -"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: -"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs: -"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs: "born"_pair_born.html: a,b,c: type pairs: -"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:) +"buck"_pair_buck.html: a,c: type pairs: +"buck/mdf"_pair_mdf.html: a,c: type pairs: +"coul/cut"_pair_coul.html: scale: type pairs: +"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs: +"coul/long, coul/msm"_pair_coul.html: scale: type pairs: +"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs: +"eam"_pair_eam.html: scale: type pairs: +"gauss"_pair_gauss.html: a: type pairs: +"lennard/mdf"_pair_mdf.html: a,b: type pairs: +"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: +"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs: +"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: +"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: +"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: +"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: +"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: +"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs: +"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs: +"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs: +"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs: +"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs: +"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs: +"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) Note that it is easy to add new potentials and their parameters to this list. All it typically takes is adding an extract() method to @@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info. [Related commands:] "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html, -"pair_style lj/soft/coul/soft"_pair_lj_soft.html +"pair_fep_soft"_pair_fep_soft.html [Default:] diff --git a/doc/src/compute_group_group.txt b/doc/src/compute_group_group.txt index cff3687354..5dfd8cf60b 100644 --- a/doc/src/compute_group_group.txt +++ b/doc/src/compute_group_group.txt @@ -137,11 +137,12 @@ Not all pair styles can be evaluated in a pairwise mode as required by this compute. For example, 3-body and other many-body potentials, such as "Tersoff"_pair_tersoff.html and "Stillinger-Weber"_pair_sw.html cannot be used. "EAM"_pair_eam.html -potentials only include the pair potential portion of the EAM -interaction when used by this compute, not the embedding term. +potentials will re-use previously computed embedding term contributions, +so the computed pairwise forces and energies are based on the whole +system and not valid if particles have been moved since. -Not all Kspace styles support calculation of group/group interactions. -The {ewald} and {pppm} styles do. +Not all "Kspace styles"_kspace_style.html support the calculation of +group/group interactions. The regular {ewald} and {pppm} styles do. [Related commands:] none diff --git a/doc/src/compute_gyration.txt b/doc/src/compute_gyration.txt index 4dc883ad0b..8deeddf585 100644 --- a/doc/src/compute_gyration.txt +++ b/doc/src/compute_gyration.txt @@ -22,7 +22,7 @@ compute 1 molecule gyration :pre [Description:] Define a computation that calculates the radius of gyration Rg of the -group of atoms, including all effects due to atoms passing thru +group of atoms, including all effects due to atoms passing through periodic boundaries. Rg is a measure of the size of the group of atoms, and is computed as diff --git a/doc/src/compute_gyration_chunk.txt b/doc/src/compute_gyration_chunk.txt index dcbfc65393..4d2c30d9c7 100644 --- a/doc/src/compute_gyration_chunk.txt +++ b/doc/src/compute_gyration_chunk.txt @@ -40,7 +40,7 @@ doc pages for details of how chunks can be defined and examples of how they can be used to measure properties of a system. This compute calculates the radius of gyration Rg for each chunk, -which includes all effects due to atoms passing thru periodic +which includes all effects due to atoms passing through periodic boundaries. Rg is a measure of the size of a chunk, and is computed by this diff --git a/doc/src/compute_heat_flux.txt b/doc/src/compute_heat_flux.txt index 81a2a3f517..edd46f7587 100644 --- a/doc/src/compute_heat_flux.txt +++ b/doc/src/compute_heat_flux.txt @@ -82,11 +82,11 @@ first term in the equation for J above. The heat flux can be output every so many timesteps (e.g. via the "thermo_style custom"_thermo_style.html command). Then as a -post-processing operation, an autocorrelation can be performed, its +post-processing operation, an auto-correlation can be performed, its integral estimated, and the Green-Kubo formula above evaluated. The "fix ave/correlate"_fix_ave_correlate.html command can calculate -the autocorrelation. The trap() function in the +the auto-correlation. The trap() function in the "variable"_variable.html command can calculate the integral. An example LAMMPS input script for solid Ar is appended below. The diff --git a/doc/src/compute_inertia_chunk.txt b/doc/src/compute_inertia_chunk.txt index d6cdb3fe79..6ded3312c5 100644 --- a/doc/src/compute_inertia_chunk.txt +++ b/doc/src/compute_inertia_chunk.txt @@ -36,7 +36,7 @@ they can be used to measure properties of a system. This compute calculates the 6 components of the symmetric inertia tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz. The -calculation includes all effects due to atoms passing thru periodic +calculation includes all effects due to atoms passing through periodic boundaries. Note that only atoms in the specified group contribute to the diff --git a/doc/src/compute_msd.txt b/doc/src/compute_msd.txt index b54e05bc64..dbbe0d637d 100644 --- a/doc/src/compute_msd.txt +++ b/doc/src/compute_msd.txt @@ -29,7 +29,7 @@ compute 1 upper msd com yes average yes :pre Define a computation that calculates the mean-squared displacement (MSD) of the group of atoms, including all effects due to atoms -passing thru periodic boundaries. For computation of the non-Gaussian +passing through periodic boundaries. For computation of the non-Gaussian parameter of mean-squared displacement, see the "compute msd/nongauss"_compute_msd_nongauss.html command. @@ -50,7 +50,7 @@ The value of the displacement will be If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calculated. +displacement of each atom is calculated. If the {average} option is set to {yes} then the reference position of an atom is based on the average position of that atom, corrected for diff --git a/doc/src/compute_msd_chunk.txt b/doc/src/compute_msd_chunk.txt index 7ff57c9844..12f54408d1 100644 --- a/doc/src/compute_msd_chunk.txt +++ b/doc/src/compute_msd_chunk.txt @@ -38,7 +38,7 @@ Four quantities are calculated by this compute for each chunk. The first 3 quantities are the squared dx,dy,dz displacements of the center-of-mass. The 4th component is the total squared displacement, i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. These -calculations include all effects due to atoms passing thru periodic +calculations include all effects due to atoms passing through periodic boundaries. Note that only atoms in the specified group contribute to the diff --git a/doc/src/compute_msd_nongauss.txt b/doc/src/compute_msd_nongauss.txt index c6e89a1061..b745cf5a5b 100644 --- a/doc/src/compute_msd_nongauss.txt +++ b/doc/src/compute_msd_nongauss.txt @@ -28,7 +28,7 @@ compute 1 upper msd/nongauss com yes :pre Define a computation that calculates the mean-squared displacement (MSD) and non-Gaussian parameter (NGP) of the group of atoms, -including all effects due to atoms passing thru periodic boundaries. +including all effects due to atoms passing through periodic boundaries. A vector of three quantities is calculated by this compute. The first element of the vector is the total squared dx,dy,dz displacements @@ -48,7 +48,7 @@ others. If the {com} option is set to {yes} then the effect of any drift in the center-of-mass of the group of atoms is subtracted out before the -displacment of each atom is calculated. +displacement of each atom is calculated. See the "compute msd"_compute_msd.html doc page for further important NOTEs, which also apply to this compute. diff --git a/doc/src/compute_omega_chunk.txt b/doc/src/compute_omega_chunk.txt index 84b25ac6f2..393440759c 100644 --- a/doc/src/compute_omega_chunk.txt +++ b/doc/src/compute_omega_chunk.txt @@ -38,7 +38,7 @@ This compute calculates the 3 components of the angular velocity vector for each chunk, via the formula L = Iw where L is the angular momentum vector of the chunk, I is its moment of inertia tensor, and w is omega = angular velocity of the chunk. The calculation includes -all effects due to atoms passing thru periodic boundaries. +all effects due to atoms passing through periodic boundaries. Note that only atoms in the specified group contribute to the calculation. The "compute chunk/atom"_compute_chunk_atom.html command diff --git a/doc/src/compute_pair.txt b/doc/src/compute_pair.txt index b36d61f71c..c1bd4f74d9 100644 --- a/doc/src/compute_pair.txt +++ b/doc/src/compute_pair.txt @@ -15,7 +15,7 @@ compute ID group-ID pair pstyle \[nstyle\] \[evalue\] :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l pair = style name of this compute command :l pstyle = style name of a pair style that calculates additional values :l -nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l +nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a hybrid style :l {evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l :ule @@ -24,7 +24,7 @@ nsub = {n}-instance of a substyle, if a pair style is used multiple times in a h compute 1 all pair gauss compute 1 all pair lj/cut/coul/cut ecoul compute 1 all pair tersoff 2 epair -compute 1 all pair reax :pre +compute 1 all pair reax/c :pre [Description:] @@ -60,8 +60,8 @@ corrections, even if they are enabled via the "pair_modify"_pair_modify.html command. Some pair styles tally additional quantities, e.g. a breakdown of -potential energy into a dozen or so components is tallied by the -"pair_style reax"_pair_reax.html command. These values (1 or more) +potential energy into 14 components is tallied by the "pair_style +reax/c"_pair_reaxc.html command. These values (1 or more) are stored as a global vector by this compute. See the doc page for "individual pair styles"_pair_style.html for info on these values. diff --git a/doc/src/compute_plasticity_atom.txt b/doc/src/compute_plasticity_atom.txt index b82179712a..6c21cecd6c 100644 --- a/doc/src/compute_plasticity_atom.txt +++ b/doc/src/compute_plasticity_atom.txt @@ -30,7 +30,7 @@ The plasticity for a Peridynamic particle is the so-called consistency parameter (lambda). For elastic deformation lambda = 0, otherwise lambda > 0 for plastic deformation. For details, see "(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS -distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. +distribution in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. This command can be invoked for one of the Peridynamic "pair styles"_pair_peri.html: peri/eps. diff --git a/doc/src/compute_pressure.txt b/doc/src/compute_pressure.txt index 6acbaf7d3d..bd6e38e392 100644 --- a/doc/src/compute_pressure.txt +++ b/doc/src/compute_pressure.txt @@ -40,7 +40,7 @@ below), Kb is the Boltzmann constant, T is the temperature, d is the dimensionality of the system (2 or 3 for 2d/3d), and V is the system volume (or area in 2d). The second term is the virial, equal to -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body, -manybody, and long-range interactions, where r_i and f_i are the +many-body, and long-range interactions, where r_i and f_i are the position and force vector of atom i, and the black dot indicates a dot product. When periodic boundary conditions are used, N' necessarily includes periodic image (ghost) atoms outside the central box, and the @@ -68,7 +68,7 @@ compute temperature or ke and/or the virial. The {virial} keyword means include all terms except the kinetic energy {ke}. Details of how LAMMPS computes the virial efficiently for the entire -system, including for manybody potentials and accounting for the +system, including for many-body potentials and accounting for the effects of periodic boundary conditions are discussed in "(Thompson)"_#Thompson1. diff --git a/doc/src/compute_pressure_cylinder.txt b/doc/src/compute_pressure_cylinder.txt index 4865fe8a79..5cca9ea3a5 100644 --- a/doc/src/compute_pressure_cylinder.txt +++ b/doc/src/compute_pressure_cylinder.txt @@ -42,14 +42,14 @@ output in pressure units. [Output info:] This compute calculates a global array with 5 columns and Rmax/bin_width -rows. The output columns are: R (distance units), number density (inverse -volume units), configurational radial pressure (pressure units), +rows. The output columns are: R (distance units), number density (inverse +volume units), configurational radial pressure (pressure units), configurational azimuthal pressure (pressure units), and configurational axial pressure (pressure units). The values calculated by this compute are "intensive". The pressure values will be in pressure -"units"_units.html. The number density values will be in +"units"_units.html. The number density values will be in inverse volume "units"_units.html. [Restrictions:] @@ -58,7 +58,7 @@ This compute currently calculates the pressure tensor contributions for pair styles only (i.e. no bond, angle, dihedral, etc. contributions and in the presence of bonded interactions, the result will be incorrect due to exclusions for special bonds) and requires pair-wise force -calculations not available for most manybody pair styles. K-space +calculations not available for most many-body pair styles. K-space calculations are also excluded. Note that this pressure compute outputs the configurational terms only; the kinetic contribution is not included and may be calculated from the number density output by P_kin=density*k*T. diff --git a/doc/src/compute_property_atom.txt b/doc/src/compute_property_atom.txt index bc1e3049fa..a0c8579283 100644 --- a/doc/src/compute_property_atom.txt +++ b/doc/src/compute_property_atom.txt @@ -19,7 +19,7 @@ input = one or more atom attributes :l x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, vx, vy, vz, fx, fy, fz, q, mux, muy, muz, mu, - sp, spx, spy, spz, fmx, fmy, fmz, + sp, spx, spy, spz, fmx, fmy, fmz, radius, diameter, omegax, omegay, omegaz, angmomx, angmomy, angmomz, shapex,shapey, shapez, @@ -86,7 +86,7 @@ input = one or more atom attributes :l compute 1 all property/atom xs vx fx mux compute 2 all property/atom type -compute 1 all property/atom ix iy iz +compute 1 all property/atom ix iy iz compute 3 all property/atom sp spx spy spz :pre [Description:] @@ -158,8 +158,8 @@ corresponding attribute is in, e.g. velocity units for vx, charge units for q, etc. For the spin quantities, sp is in the units of the Bohr magneton, spx, -spy, and spz are adimensional quantities, and fmx, fmy and fmz are -given in rad.THz. +spy, and spz are unitless quantities, and fmx, fmy and fmz are given +in rad/THz. [Restrictions:] none diff --git a/doc/src/compute_ptm_atom.txt b/doc/src/compute_ptm_atom.txt index 2e22e4e9fb..dfe3afe970 100644 --- a/doc/src/compute_ptm_atom.txt +++ b/doc/src/compute_ptm_atom.txt @@ -38,20 +38,20 @@ ico (icosahedral) = 4 sc (simple cubic) = 5 dcub (diamond cubic) = 6 dhex (diamond hexagonal) = 7 -other = 8 :ul +graphene = 8 :ul -The value of the PTM structure will be 0 for atoms not in the specified +The value of the PTM structure will be 0 for unknown types and -1 for atoms not in the specified compute group. The choice of structures to search for can be specified using the "structures" argument, which is a hyphen-separated list of structure keywords. Two convenient pre-set options are provided: default: fcc-hcp-bcc-ico -all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul +all: fcc-hcp-bcc-ico-sc-dcub-dhex-graphene :ul The 'default' setting detects the same structures as the Common Neighbor Analysis method. -The 'all' setting searches for all structure types. A small performance penalty is -incurred for the diamond structures, so it is not recommended to use this option if -it is known that the simulation does not contain diamond structures. +The 'all' setting searches for all structure types. A performance penalty is +incurred for the diamond and graphene structures, so it is not recommended to use this option if +it is known that the simulation does not contain these structures. PTM identifies structures using two steps. First, a graph isomorphism test is used @@ -80,7 +80,7 @@ too frequently or to have multiple compute/dump commands, each with a [Output info:] -This compute calculates a per-atom arry, which can be accessed by +This compute calculates a per-atom array, which can be accessed by any command that uses per-atom values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. @@ -93,9 +93,9 @@ interatomic distance qw qx qy -qw :ul +qz :ul -The type is a number from 0 to 8. The rmsd is a positive real number. +The type is a number from -1 to 8. The rmsd is a positive real number. The interatomic distance is computed from the scale factor in the RMSD equation. The (qw,qx,qy,qz) parameters represent the orientation of the local structure in quaternion form. The reference coordinates for each template (from which the @@ -117,5 +117,5 @@ package"_Build_package.html doc page for more info. :line :link(Larsen) -[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016). +[(Larsen)] Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016). diff --git a/doc/src/compute_reduce.txt b/doc/src/compute_reduce.txt index 0bd2accf3c..1e9cc651e1 100644 --- a/doc/src/compute_reduce.txt +++ b/doc/src/compute_reduce.txt @@ -61,7 +61,7 @@ or {max} options find the minimum or maximum value across all vector values. The {ave} setting adds the vector values into a global total, then divides by the number of values in the vector. The {sumsq} option sums the square of the values in the vector into a global -total. The {avesq} setting does the same as {sumsq}, then divdes the +total. The {avesq} setting does the same as {sumsq}, then divides the sum of squares by the number of values. The last two options can be useful for calculating the variance of some quantity, e.g. variance = sumsq - ave^2. diff --git a/doc/src/compute_reduce_chunk.txt b/doc/src/compute_reduce_chunk.txt index 3628c0f1ad..f19ed00c6a 100644 --- a/doc/src/compute_reduce_chunk.txt +++ b/doc/src/compute_reduce_chunk.txt @@ -137,7 +137,7 @@ compute micelle all chunk/atom c_spread compress yes :pre Further analysis on a per-micelle basis can now be performed using any of the per-chunk computes listed on the "Howto chunk"_Howto_chunk.html doc page. E.g. count the number of atoms in each micelle, calculate -its center or mass, shape (moments of intertia), radius of gyration, +its center or mass, shape (moments of inertia), radius of gyration, etc. compute prop all property/chunk micelle count diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 67c6209bdf..73e9e4a609 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -106,8 +106,8 @@ There are two options for outputting the coordinates of the center of mass (COM) of the body. The {x}, {y}, {z} attributes write the COM "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by -the image flags for each atobody. Unwrapped means that if the body -COM has passed thru a periodic boundary one or more times, the value +the image flags for each body. Unwrapped means that if the body +COM has passed through a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box. diff --git a/doc/src/compute_smd_hourglass_error.txt b/doc/src/compute_smd_hourglass_error.txt index 5bc3e3a2de..28f1f351a8 100644 --- a/doc/src/compute_smd_hourglass_error.txt +++ b/doc/src/compute_smd_hourglass_error.txt @@ -29,7 +29,7 @@ within the neighborhood of the central node and the deformation gradient, the approximated relative separation will coincide with the actual relative separation of the particles i and j in the deformed configuration. This compute is only really useful for debugging the -hourglass control mechanim which is part of the Total-Lagrangian SPH +hourglass control mechanism which is part of the Total-Lagrangian SPH pair style. See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth diff --git a/doc/src/compute_smd_tlsph_defgrad.txt b/doc/src/compute_smd_tlsph_defgrad.txt index a733a3d6a7..bdd3a26a8f 100644 --- a/doc/src/compute_smd_tlsph_defgrad.txt +++ b/doc/src/compute_smd_tlsph_defgrad.txt @@ -30,7 +30,7 @@ Mach Dynamics in LAMMPS. [Output info:] -This compute outputss a per-particle vector of vectors (tensors), +This compute outputs a per-particle vector of vectors (tensors), which can be accessed by any command that uses per-particle values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. diff --git a/doc/src/compute_smd_tlsph_shape.txt b/doc/src/compute_smd_tlsph_shape.txt index 9c17194ec1..0ecfec0187 100644 --- a/doc/src/compute_smd_tlsph_shape.txt +++ b/doc/src/compute_smd_tlsph_shape.txt @@ -38,7 +38,7 @@ overview of LAMMPS output options. The per-particle vector has 7 entries. The first three entries correspond to the lengths of the ellipsoid's axes and have units of -length. These axis valus are computed as the contact radius times the +length. These axis values are computed as the contact radius times the xx, yy, or zz components of the Green-Lagrange strain tensor associated with the particle. The next 4 values are quaternions (order: q, x, y, z) which describe the spatial rotation of the diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index 95d183937f..efbf2e9ea3 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l w_1, w_2,... = list of neighbor weights, one for each type :l zero or more keyword/value pairs may be appended :l -keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l +keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l {diagonal} value = {0} or {1} or {2} or {3} {0} = all j1, j2, j <= twojmax, j2 <= j1 {1} = subset satisfying j1 == j2 @@ -161,7 +161,7 @@ function. The keyword {bzeroflag} determines whether or not {B0}, the bispectrum components of an atom with no neighbors, are subtracted from -the calculated bispectrum components. This optional keyword +the calculated bispectrum components. This optional keyword normally only affects compute {sna/atom}. However, when {quadraticflag} is on, it also affects {snad/atom} and {snav/atom}. diff --git a/doc/src/compute_spin.txt b/doc/src/compute_spin.txt index 4edecc2408..d27e402972 100644 --- a/doc/src/compute_spin.txt +++ b/doc/src/compute_spin.txt @@ -21,7 +21,7 @@ compute out_mag all spin :pre [Description:] -Define a computation that calculates magnetic quantities for a system +Define a computation that calculates magnetic quantities for a system of atoms having spins. This compute calculates 6 magnetic quantities. @@ -31,11 +31,11 @@ magnetization. The fourth quantity is the norm of the total magnetization. -The fifth quantity is the magnetic energy. +The fifth quantity is the magnetic energy. The sixth one is referred to as the spin temperature, according -to the work of "(Nurdin)"_#Nurdin1. - +to the work of "(Nurdin)"_#Nurdin1. + The simplest way to output the results of the compute spin calculation is to define some of the quantities as variables, and to use the thermo and thermo_style commands, for example: @@ -49,9 +49,9 @@ variable temp_mag equal c_out_mag\[6\] :pre thermo 10 thermo_style custom step v_mag_z v_mag_norm v_temp_mag :pre -This series of commands evaluates the total magnetization along z, the norm of -the total magnetization, and the magnetic temperature. Three variables are -assigned to those quantities. The thermo and thermo_style commands print them +This series of commands evaluates the total magnetization along z, the norm of +the total magnetization, and the magnetic temperature. Three variables are +assigned to those quantities. The thermo and thermo_style commands print them every 10 timesteps. [Output info:] @@ -59,7 +59,7 @@ every 10 timesteps. The array values are "intensive". The array values will be in metal units ("units"_units.html). -[Restrictions:] +[Restrictions:] The {spin} compute is part of the SPIN package. This compute is only enabled if LAMMPS was built with this package. See the "Build diff --git a/doc/src/compute_stress_atom.txt b/doc/src/compute_stress_atom.txt index 222513da61..d81d97061c 100644 --- a/doc/src/compute_stress_atom.txt +++ b/doc/src/compute_stress_atom.txt @@ -73,9 +73,9 @@ Note that the stress for each atom is due to its interaction with all other atoms in the simulation, not just with other atoms in the group. Details of how LAMMPS computes the virial for individual atoms for -either pairwise or manybody potentials, and including the effects of +either pairwise or many-body potentials, and including the effects of periodic boundary conditions is discussed in "(Thompson)"_#Thompson2. -The basic idea for manybody potentials is to treat each component of +The basic idea for many-body potentials is to treat each component of the force computation between a small cluster of atoms in the same manner as in the formula above for bond, angle, dihedral, etc interactions. Namely the quantity R dot F is summed over the atoms in diff --git a/doc/src/compute_stress_mop.txt b/doc/src/compute_stress_mop.txt index 1006463179..d97581afd5 100644 --- a/doc/src/compute_stress_mop.txt +++ b/doc/src/compute_stress_mop.txt @@ -60,7 +60,7 @@ Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total). -NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. +NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. NOTE 2: The local stress does not include any Lennard-Jones tail corrections to the pressure added by the "pair_modify tail @@ -80,11 +80,11 @@ keywords have been declared). For each keyword, the profiles of stress tensor components are ordered as follows: stress_dir,x; stress_dir,y; and stress_dir,z. -The values are in pressure "units"_units.html. +The values are in pressure "units"_units.html. The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder. -[Restrictions:] +[Restrictions:] These styles are part of the USER-MISC package. They are only enabled if LAMMPS is built with that package. See the "Build package"_Build_package.html @@ -107,5 +107,5 @@ intra-molecular interactions, and long range (kspace) interactions. :line :link(mop-todd) -[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", +[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995). diff --git a/doc/src/compute_tally.txt b/doc/src/compute_tally.txt index a4a8441f9e..6401be54e9 100644 --- a/doc/src/compute_tally.txt +++ b/doc/src/compute_tally.txt @@ -47,7 +47,7 @@ the based classes of LAMMPS. The pairwise contributions are computing via a callback that the compute registers with the non-bonded pairwise force computation. This limits the use to systems that have no bonds, no Kspace, and no -manybody interactions. On the other hand, the computation does not +many-body interactions. On the other hand, the computation does not have to compute forces or energies a second time and thus can be much more efficient. The callback mechanism allows to write more complex pairwise property computations. diff --git a/doc/src/compute_tdpd_cc_atom.txt b/doc/src/compute_tdpd_cc_atom.txt index a385bef10b..d1f9c38319 100644 --- a/doc/src/compute_tdpd_cc_atom.txt +++ b/doc/src/compute_tdpd_cc_atom.txt @@ -13,7 +13,7 @@ compute tdpd/cc/atom command :h3 compute ID group-ID tdpd/cc/atom index :pre ID, group-ID are documented in "compute"_compute.html command -tdpd/cc/atom = style name of this compute command +tdpd/cc/atom = style name of this compute command index = index of chemical species (1 to Nspecies) :ul [Examples:] @@ -37,7 +37,7 @@ any command that uses per-atom values from a compute as input. See the "Howto output"_Howto_output.html doc page for an overview of LAMMPS output options. -The per-atom vector values will be in the units of chemical species +The per-atom vector values will be in the units of chemical species per unit mass. [Restrictions:] diff --git a/doc/src/compute_temp_asphere.txt b/doc/src/compute_temp_asphere.txt index eb73891e82..0b06ae0b48 100644 --- a/doc/src/compute_temp_asphere.txt +++ b/doc/src/compute_temp_asphere.txt @@ -60,7 +60,7 @@ same. If it does not rotate around the axis perpendicular to its circular cross section, then it should have 5 dof instead of 6 in 3d. The latter is the case for uniaxial ellipsoids in a "GayBerne model"_pair_gayberne.html since there is no induced torque around the -optical axis. It will also be the case for biaxial ellipsoids when +optical axis. It will also be the case for bi-axial ellipsoids when exactly two of the semiaxes have the same length and the corresponding relative well depths are equal. diff --git a/doc/src/compute_temp_chunk.txt b/doc/src/compute_temp_chunk.txt index de8c850a70..30dda79caf 100644 --- a/doc/src/compute_temp_chunk.txt +++ b/doc/src/compute_temp_chunk.txt @@ -118,7 +118,7 @@ or "fix rigid"_fix_rigid.html. This is because those degrees of freedom (e.g. a constrained bond) could apply to sets of atoms that are both included and excluded from a specific chunk, and hence the concept is somewhat ill-defined. In some cases, you can use the -{adof} and {cdof} keywords to adjust the calculated degress of freedom +{adof} and {cdof} keywords to adjust the calculated degrees of freedom appropriately, as explained below. Note that the per-chunk temperature calculated by this compute and the diff --git a/doc/src/compute_temp_cs.txt b/doc/src/compute_temp_cs.txt index 0236319f54..5fc939e375 100644 --- a/doc/src/compute_temp_cs.txt +++ b/doc/src/compute_temp_cs.txt @@ -74,7 +74,7 @@ relative to the COM velocity of the core/shell pair. If this compute is used with a fix command that performs thermostatting then this bias will be subtracted from each atom, thermostatting of the remaining COM velocity will be performed, and the bias will be added back in. This -means the thermostating will effectively be performed on the +means the thermostatting will effectively be performed on the core/shell pairs, instead of on the individual core and shell atoms. Thermostatting fixes that work in this way include "fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix diff --git a/doc/src/compute_temp_uef.txt b/doc/src/compute_temp_uef.txt index 97e1d6e1ae..b9e6187533 100644 --- a/doc/src/compute_temp_uef.txt +++ b/doc/src/compute_temp_uef.txt @@ -17,17 +17,17 @@ temp/uef = style name of this compute command :ul [Examples:] -compute 1 all temp/uef +compute 1 all temp/uef compute 2 sel temp/uef :pre [Description:] -This command is used to compute the kinetic energy tensor in +This command is used to compute the kinetic energy tensor in the reference frame of the applied flow field when "fix nvt/uef"_fix_nh_uef.html or "fix npt/uef"_fix_nh_uef.html is used. It is not necessary to use this command to compute the scalar -value of the temperature. A "compute temp"_compute_temp.html +value of the temperature. A "compute temp"_compute_temp.html may be used for that purpose. Output information for this command can be found in the @@ -39,7 +39,7 @@ This fix is part of the USER-UEF package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. -This command can only be used when "fix nvt/uef"_fix_nh_uef.html +This command can only be used when "fix nvt/uef"_fix_nh_uef.html or "fix npt/uef"_fix_nh_uef.html is active. [Related commands:] diff --git a/doc/src/compute_ti.txt b/doc/src/compute_ti.txt index 9057cab476..0dec297183 100644 --- a/doc/src/compute_ti.txt +++ b/doc/src/compute_ti.txt @@ -45,7 +45,7 @@ described in "Eike"_#Eike. Typically this compute will be used in conjunction with the "fix adapt"_fix_adapt.html command which can perform alchemical -transformations by adusting the strength of an interaction potential +transformations by adjusting the strength of an interaction potential as a simulation runs, as defined by one or more "pair_style"_pair_style.html or "kspace_style"_kspace_style.html commands. This scaling is done via a prefactor on the energy, forces, diff --git a/doc/src/compute_torque_chunk.txt b/doc/src/compute_torque_chunk.txt index 6484076b37..8121c42781 100644 --- a/doc/src/compute_torque_chunk.txt +++ b/doc/src/compute_torque_chunk.txt @@ -37,7 +37,7 @@ they can be used to measure properties of a system. This compute calculates the 3 components of the torque vector for eqch chunk, due to the forces on the individual atoms in the chunk around the center-of-mass of the chunk. The calculation includes all effects -due to atoms passing thru periodic boundaries. +due to atoms passing through periodic boundaries. Note that only atoms in the specified group contribute to the calculation. The "compute chunk/atom"_compute_chunk_atom.html command diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index fbf741d914..abd1959e81 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -90,7 +90,7 @@ The {many} style will create bonds between pairs of atoms I,J where I is in one of the two specified groups, and J is in the other. The two groups can be the same, e.g. group "all". The created bonds will be of bond type {btype}, where {btype} must be a value between 1 and the -number of bond types defined. +number of bond types defined. For a bond to be created, an I,J pair of atoms must be a distance D apart such that {rmin} <= D <= {rmax}. diff --git a/doc/src/create_box.txt b/doc/src/create_box.txt index 0993b4f927..cc57c96f93 100644 --- a/doc/src/create_box.txt +++ b/doc/src/create_box.txt @@ -58,7 +58,7 @@ edge vectors starting from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values and are called "tilt factors" because they are the amount of displacement applied to faces of an originally -orthogonal box to transform it into the parallelipiped. +orthogonal box to transform it into the parallelepiped. By default, a {prism} region used with the create_box command must have tilt factors (xy,xz,yz) that do not skew the box more than half diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 637a10102d..043188466a 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -41,7 +41,7 @@ field. NOTE: The newer {charmmfsw} style was released in March 2017. We recommend it be used instead of the older {charmm} style when running a simulation with the CHARMM force field, either with long-range -Coulombics or a Coulomb cutoff, via the "pair_style +Coulombics or a Coulombic cutoff, via the "pair_style lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively. Otherwise the older {charmm} style is fine to use. See the discussion @@ -87,7 +87,7 @@ special_bonds 1-4 scaling factor to 0.0 (which is the default). Otherwise 1-4 non-bonded interactions in dihedrals will be computed twice. -For simulations using the CHARMM force field with a Coulomb cutoff, +For simulations using the CHARMM force field with a Coulombic cutoff, the difference between the {charmm} and {charmmfsw} styles is in the computation of the 1-4 non-bond interactions, though only if the distance between the two atoms is within the switching region of the diff --git a/doc/src/dihedral_coeff.txt b/doc/src/dihedral_coeff.txt index 1db69e40d5..718a73144e 100644 --- a/doc/src/dihedral_coeff.txt +++ b/doc/src/dihedral_coeff.txt @@ -69,24 +69,14 @@ necessary. :line -Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "dihedral_coeff"_dihedral_coeff.html command. +The list of all dihedral styles defined in LAMMPS is given on the +"dihedral_style"_dihedral_style.html doc page. They are also listed +in more compact form on the "Commands +dihedral"_Commands_bond.html#dihedral doc page. -Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The full list of all -dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral -doc page. - -"dihedral_style none"_dihedral_none.html - turn off dihedral interactions -"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul - -"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral -"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral -"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral -"dihedral_style helix"_dihedral_helix.html - helix dihedral -"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral -"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul +On either of those pages, click on the style to display the formula it +computes and its coefficients as specified by the associated +dihedral_coeff command. :line diff --git a/doc/src/dihedral_style.txt b/doc/src/dihedral_style.txt index d45d9b488d..2a5b9baf52 100644 --- a/doc/src/dihedral_style.txt +++ b/doc/src/dihedral_style.txt @@ -80,10 +80,16 @@ Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on the style to display the formula it computes and coefficients specified by the associated "dihedral_coeff"_dihedral_coeff.html command. -Note that there are also additional dihedral styles submitted by users -which are included in the LAMMPS distribution. The full list of all -dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral -doc page. +Click on the style to display the formula it computes, any additional +arguments specified in the dihedral_style command, and coefficients +specified by the associated "dihedral_coeff"_dihedral_coeff.html +command. + +There are also additional accelerated pair styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands +dihedral"_Commands_bond.html#dihedral doc page are followed by one or +more of (g,i,k,o,t) to indicate which accelerated styles exist. "none"_dihedral_none.html - turn off dihedral interactions "zero"_dihedral_zero.html - topology but no interactions diff --git a/doc/src/dihedral_table_cut.txt b/doc/src/dihedral_table_cut.txt index b8e0ec64c8..6f3f6edbcc 100644 --- a/doc/src/dihedral_table_cut.txt +++ b/doc/src/dihedral_table_cut.txt @@ -59,7 +59,7 @@ cutoff angle2 filename keyword :ul -The cutoff dihedral style uses a tabulated dihedral interaction with a +The cutoff dihedral style uses a tabulated dihedral interaction with a cutoff function: :c,image(Eqs/dihedral_table_cut.jpg) diff --git a/doc/src/displace_atoms.txt b/doc/src/displace_atoms.txt index b4afd5c3a9..b0fa2d3bc4 100644 --- a/doc/src/displace_atoms.txt +++ b/doc/src/displace_atoms.txt @@ -83,7 +83,7 @@ used in such a way that the displacement of a particular atom is the same, regardless of how many processors are being used. The {rotate} style rotates each atom in the group by the angle {theta} -around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} = +around a rotation axis {R} = (Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your right-hand thumb points along {R}, then your fingers wrap around the diff --git a/doc/src/dump.txt b/doc/src/dump.txt index 8b630cc706..a776ff70fc 100644 --- a/doc/src/dump.txt +++ b/doc/src/dump.txt @@ -13,6 +13,7 @@ dump command :h3 "dump netcdf"_dump_netcdf.html command :h3 "dump image"_dump_image.html command :h3 "dump movie"_dump_image.html command :h3 +"dump adios"_dump_adios.html command :h3 [Syntax:] @@ -27,10 +28,12 @@ args = list of arguments for a particular style :l {atom} args = none {atom/gz} args = none {atom/mpiio} args = none + {atom/adios} args = none, discussed on "dump adios"_dump_adios.html doc page {cfg} args = same as {custom} args, see below {cfg/gz} args = same as {custom} args, see below {cfg/mpiio} args = same as {custom} args, see below {custom}, {custom/gz}, {custom/mpiio} args = see below + {custom/adios} args = same as {custom} args, discussed on "dump adios"_dump_adios.html doc page {dcd} args = none {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page {image} args = discussed on "dump image"_dump_image.html doc page @@ -312,7 +315,7 @@ so that any machine which supports XDR should be able to read them. The number of atoms per snapshot cannot change with the {xtc} style. The {unwrap} option of the "dump_modify"_dump_modify.html command allows XTC coordinates to be written "unwrapped" by the image flags for each -atom. Unwrapped means that if the atom has passed thru a periodic +atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the box size @@ -534,7 +537,7 @@ on the "Howto triclinic"_Howto_triclinic.html doc page. Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the image flags for each atom. Unwrapped means that if the atom has -passed thru a periodic boundary one or more times, the value is +passed through a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the periodic box. Note that using {xu}, {yu}, {zu} means that the coordinate values may be far outside the box bounds printed @@ -653,7 +656,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"dump h5md"_dump_h5md.html, "dump image"_dump_image.html, +"dump adios"_dump_adios.html "dump h5md"_dump_h5md.html, "dump image"_dump_image.html, "dump molfile"_dump_molfile.html, "dump_modify"_dump_modify.html, "undump"_undump.html diff --git a/doc/src/dump_adios.txt b/doc/src/dump_adios.txt new file mode 100644 index 0000000000..e3c919db5a --- /dev/null +++ b/doc/src/dump_adios.txt @@ -0,0 +1,73 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +dump atoms/adios command :h3 +dump custom/adios command :h3 + +[Syntax:] + +dump ID group-ID atoms/adios N file.bp :pre +dump ID group-ID custom/adios N file.bp args :pre + +ID = user-assigned name for the dump :ulb,l +group-ID = ID of the group of atoms to be imaged :l +adios = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l +N = dump every this many timesteps :l +file.bp = name of file/stream to write to :l +args = same options as in "{dump custom}"_dump.html command :l +:ule + + +[Examples:] + +dump adios1 all atom/adios 100 atoms.bp +dump 4a all custom/adios 100 dump_adios.bp id v_p x y z +dump 2 subgroup custom/adios 100 dump_adios.bp mass type xs ys zs vx vy vz :pre + +[Description:] + +Dump a snapshot of atom coordinates every N timesteps in the +"ADIOS"_adios based "BP" file format, or using different I/O solutions in ADIOS, +to a stream that can be read on-line by another program. +ADIOS-BP files are binary, portable and self-describing. + +:link(adios,https://github.com/ornladios/ADIOS2) + + +[Use from write_dump:] + +It is possible to use these dump styles with the +"write_dump"_write_dump.html command. In this case, the sub-intervals +must not be set at all. The write_dump command can be used to +create a new file at each individual dump. + +dump 4 all atom/adios 100 dump.bp +write_dump all atom/adios singledump.bp :pre + +:line + +[Restrictions:] + +The number of atoms per snapshot CAN change with the adios style. +When using the ADIOS tool 'bpls' to list the content of a .bp file, +bpls will print {__} for the size of the output table indicating that +its size is changing every step. + +The {atom/adios} and {custom/adios} dump styles are part of the USER-ADIOS +package. They are only enabled if LAMMPS was built with that package. +See the "Build package"_Build_package.html doc page for more info. + + +:line + +[Related commands:] + +"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html + +:line + diff --git a/doc/src/dump_cfg_uef.txt b/doc/src/dump_cfg_uef.txt index 16e4aba4c0..ca43b0b6ea 100644 --- a/doc/src/dump_cfg_uef.txt +++ b/doc/src/dump_cfg_uef.txt @@ -28,10 +28,10 @@ dump 2 all cfg/uef 100 dump.*.cfg mass type xs ys zs id c_stress :pre [Description:] This command is used to dump atomic coordinates in the -reference frame of the applied flow field when +reference frame of the applied flow field when "fix nvt/uef"_fix_nh_uef.html or -"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic -coordinates and frame-invariant scalar quantities +"fix npt/uef"_fix_nh_uef.html or is used. Only the atomic +coordinates and frame-invariant scalar quantities will be in the flow frame. If velocities are selected as output, for example, they will not be in the same reference frame as the atomic positions. diff --git a/doc/src/dump_h5md.txt b/doc/src/dump_h5md.txt index a3849f103c..6e9e7284df 100644 --- a/doc/src/dump_h5md.txt +++ b/doc/src/dump_h5md.txt @@ -17,7 +17,7 @@ group-ID = ID of the group of atoms to be imaged :l h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l N = dump every this many timesteps :l file.h5 = name of file to write to :l -args = list of data elements to dump, with their dump "subintervals" +args = list of data elements to dump, with their dump "sub-intervals" position options image velocity options @@ -63,7 +63,7 @@ another particle group must specify {create_group yes}. :link(h5md,http://nongnu.org/h5md/) Each data element is written every N*N_element steps. For {image}, no -subinterval is needed as it must be present at the same interval as +sub-interval is needed as it must be present at the same interval as {position}. {image} must be given after {position} in any case. The box information (edges in each dimension) is stored at the same interval than the {position} element, if present. Else it is stored @@ -76,7 +76,7 @@ written to a dump file may be slightly outside the simulation box. [Use from write_dump:] It is possible to use this dump style with the -"write_dump"_write_dump.html command. In this case, the subintervals +"write_dump"_write_dump.html command. In this case, the sub-intervals must not be set at all. The write_dump command can be used either to create a new file or to add current data to an existing dump file by using the {file_from} keyword. diff --git a/doc/src/dump_image.txt b/doc/src/dump_image.txt index df1ff324c1..2b10e9f230 100644 --- a/doc/src/dump_image.txt +++ b/doc/src/dump_image.txt @@ -541,10 +541,11 @@ a) Use the ImageMagick convert program. :ulb,l % convert *.jpg foo.gif % convert -loop 1 *.ppm foo.mpg :pre -Animated GIF files from ImageMagick are unoptimized. You can use a -program like gifsicle to optimize and massively shrink them. -MPEG files created by ImageMagick are in MPEG-1 format with rather -inefficient compression and low quality. +Animated GIF files from ImageMagick are not optimized. You can use +a program like gifsicle to optimize and thus massively shrink them. +MPEG files created by ImageMagick are in MPEG-1 format with a rather +inefficient compression and low quality compared to more modern +compression styles like MPEG-4, H.264, VP8, VP9, H.265 and so on. b) Use QuickTime. :l @@ -564,7 +565,7 @@ allows extremely flexible encoding and decoding of movies. cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre -Frontends for FFmpeg exist for multiple platforms. For more +Front ends for FFmpeg exist for multiple platforms. For more information see the "FFmpeg homepage"_http://www.ffmpeg.org/ :ule diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index 72f4935916..9a35956055 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -201,7 +201,7 @@ atom type (1 to Ntype) in the simulation. The same element name can be given to multiple atom types. In the case of {xyz} format dumps, there are no restrictions to what -label can be used as an element name. Any whitespace separated text +label can be used as an element name. Any white-space separated text will be accepted. :link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A) @@ -344,7 +344,7 @@ The {image} keyword applies only to the dump {atom} style. If the image value is {yes}, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For example, an x image flag of -2 with a normalized coord of 0.5 means -the atom is in the center of the box, but has passed thru the box +the atom is in the center of the box, but has passed through the box boundary 2 times and is really 2 box lengths to the left of its current coordinate. Note that for dump style {custom} these various values can be printed in the dump file by using the appropriate atom @@ -461,10 +461,10 @@ last snapshot. This can be accomplished with something the following commands: variable Dhop equal 0.6 -variable check atom "c_dsp[4] > v_Dhop" +variable check atom "c_dsp\[4\] > v_Dhop" compute dsp all displace/atom refresh check dump 1 all custom 20 tmp.dump id type x y z -dump_modify 1 append yes thresh c_dsp[4] > ${Dhop} refresh c_dsp :pre +dump_modify 1 append yes thresh c_dsp\[4\] > $\{Dhop\} refresh c_dsp :pre The "compute displace/atom"_compute_displace_atom.html command calculates the displacement of each atom from its reference position. @@ -622,7 +622,7 @@ threshold criterion is met. Otherwise it is not met. The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles. If set to {yes}, coordinates will be written "unwrapped" by the image -flags for each atom. Unwrapped means that if the atom has passed thru +flags for each atom. Unwrapped means that if the atom has passed through a periodic boundary one or more times, the value is printed for what the coordinate would be if it had not been wrapped back into the periodic box. Note that these coordinates may thus be far outside the @@ -667,7 +667,7 @@ command, when its atom diameter setting is {type}, to set the size that atoms of each type will be drawn in the image. The specified {type} should be an integer from 1 to Ntypes. As with the {acolor} keyword, a wildcard asterisk can be used as part of the {type} -argument to specify a range of atomt types. The specified {diam} is +argument to specify a range of atom types. The specified {diam} is the size in whatever distance "units"_units.html the input script is using, e.g. Angstroms. diff --git a/doc/src/dynamical_matrix.txt b/doc/src/dynamical_matrix.txt new file mode 100644 index 0000000000..a7dc4e442e --- /dev/null +++ b/doc/src/dynamical_matrix.txt @@ -0,0 +1,52 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +dynamical_matrix command :h3 + +[Syntax:] + +dynamical_matrix group-ID style gamma args keyword value ... :pre + +group-ID = ID of group of atoms to displace :ulb,l +style = {regular} or {eskm} :l +gamma = finite different displacement length (distance units) :l +one or more keyword/arg pairs may be appended :l + keyword = {file} or {binary} + {file} name = name of output file for the dynamical matrix + {binary} arg = {yes} or {no} or {gzip} :pre +:ule + +[Examples:] + +dynamical_matrix 1 regular 0.000001 +dynamical_matrix 1 eskm 0.000001 +dynamical_matrix 3 regular 0.00004 file dynmat.dat +dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes :pre + +[Description:] + +Calculate the dynamical matrix of the selected group. + +[Restrictions:] + +The command collects the entire dynamical matrix a single MPI rank, +so the memory requirements can be very significant for large systems. + +This command assumes a periodic system. + +This command is part of the USER-PHONON package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"fix phonon"_fix_phonon.html + +[Default:] + +The default settings are file = "dynmat.dyn", binary = no diff --git a/doc/src/fix.txt b/doc/src/fix.txt index 27cc0467e2..9b48ee13bf 100644 --- a/doc/src/fix.txt +++ b/doc/src/fix.txt @@ -83,8 +83,10 @@ not in the specified fix group. Local quantities are calculated by each processor based on the atoms it owns, but there may be zero or more per atoms. -Note that a single fix may produces either global or per-atom or local -quantities (or none at all), but never more than one of these. +Note that a single fix can produce either global or per-atom or local +quantities (or none at all), but not both global and per-atom. It can +produce local quantities in tandem with global or per-atom quantities. +The fix doc page will explain. Global, per-atom, and local quantities each come in three kinds: a single scalar value, a vector of values, or a 2d array of values. The @@ -156,10 +158,6 @@ what it does, as listed below. Here is an alphabetic list of fix styles available in LAMMPS. They are also listed in more compact form on the "Commands fix"_Commands_fix.html doc page. -There are also additional fix styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The full list of -all fix styles is on the "Commands fix"_Commands_fix.html doc page. - There are also additional accelerated fix styles included in the LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. The individual style names on the "Commands fix"_Commands_fix.html doc @@ -167,182 +165,187 @@ page are followed by one or more of (g,i,k,o,t) to indicate which accelerated styles exist. "adapt"_fix_adapt.html - change a simulation parameter over time -"adapt/fep"_fix_adapt_fep.html - +"adapt/fep"_fix_adapt_fep.html - "addforce"_fix_addforce.html - add a force to each atom -"addtorque"_fix_addtorque.html - +"addtorque"_fix_addtorque.html - "append/atoms"_fix_append_atoms.html - append atoms to a running simulation -"atc"_fix_atc.html - +"atc"_fix_atc.html - "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities "ave/correlate"_fix_ave_correlate.html - compute/output time correlations -"ave/correlate/long"_fix_ave_correlate_long.html - +"ave/correlate/long"_fix_ave_correlate_long.html - "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms -"ave/histo/weight"_fix_ave_histo.html - +"ave/histo/weight"_fix_ave_histo.html - "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities "aveforce"_fix_aveforce.html - add an averaged force to each atom "balance"_fix_balance.html - perform dynamic load-balancing -"bocs"_fix_bocs.html - +"bocs"_fix_bocs.html - "bond/break"_fix_bond_break.html - break bonds on the fly "bond/create"_fix_bond_create.html - create bonds on the fly -"bond/react"_fix_bond_react.html - +"bond/react"_fix_bond_react.html - "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "box/relax"_fix_box_relax.html - relax box size during energy minimization -"client/md"_fix_client_md.html - -"cmap"_fix_cmap.html - -"colvars"_fix_colvars.html - -"controller"_fix_controller.html - +"client/md"_fix_client_md.html - +"cmap"_fix_cmap.html - +"colvars"_fix_colvars.html - +"controller"_fix_controller.html - "deform"_fix_deform.html - change the simulation box size/shape "deposit"_fix_deposit.html - add new atoms above a surface -"dpd/energy"_fix_dpd_energy.html - +"dpd/energy"_fix_dpd_energy.html - "drag"_fix_drag.html - drag atoms towards a defined coordinate -"drude"_fix_drude.html - -"drude/transform/direct"_fix_drude_transform.html - -"drude/transform/inverse"_fix_drude_transform.html - +"drude"_fix_drude.html - +"drude/transform/direct"_fix_drude_transform.html - +"drude/transform/inverse"_fix_drude_transform.html - "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces -"edpd/source"_fix_dpd_source.html - +"edpd/source"_fix_dpd_source.html - "efield"_fix_efield.html - impose electric field on system -"ehex"_fix_ehex.html - ehanced heat exchange algorithm +"ehex"_fix_ehex.html - enhanced heat exchange algorithm "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force -"eos/cv"_fix_eos_cv.html - -"eos/table"_fix_eos_table.html - -"eos/table/rx"_fix_eos_table_rx.html - +"eos/cv"_fix_eos_cv.html - +"eos/table"_fix_eos_table.html - +"eos/table/rx"_fix_eos_table_rx.html - "evaporate"_fix_evaporate.html - remove atoms from simulation periodically "external"_fix_external.html - callback to an external driver program -"ffl"_fix_ffl.html - -"filter/corotate"_fix_filter_corotate.html - -"flow/gauss"_fix_flow_gauss.html - +"ffl"_fix_ffl.html - +"filter/corotate"_fix_filter_corotate.html - +"flow/gauss"_fix_flow_gauss.html - "freeze"_fix_freeze.html - freeze atoms in a granular simulation "gcmc"_fix_gcmc.html - grand canonical insertions/deletions "gld"_fix_gcmc.html - generalized Langevin dynamics integrator -"gld"_fix_gld.html - -"gle"_fix_gle.html - +"gld"_fix_gld.html - +"gle"_fix_gle.html - "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation -"grem"_fix_grem.html - +"grem"_fix_grem.html - "halt"_fix_halt.html - terminate a dynamics run or minimization "heat"_fix_heat.html - add/subtract momentum-conserving heat -"imd"_fix_imd.html - +"hyper/global"_fix_hyper_global.html - global hyperdynamics +"hyper/local"_fix_hyper_local.html - local hyperdynamics +"imd"_fix_imd.html - "indent"_fix_indent.html - impose force due to an indenter -"ipi"_fix_ipi.html - +"ipi"_fix_ipi.html - "langevin"_fix_langevin.html - Langevin temperature control -"langevin/drude"_fix_langevin_drude.html - -"langevin/eff"_fix_langevin_eff.html - -"langevin/spin"_fix_langevin_spin.html - +"langevin/drude"_fix_langevin_drude.html - +"langevin/eff"_fix_langevin_eff.html - +"langevin/spin"_fix_langevin_spin.html - "latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code -"lb/fluid"_fix_lb_fluid.html - -"lb/momentum"_fix_lb_momentum.html - -"lb/pc"_fix_lb_pc.html - -"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - -"lb/viscous"_fix_lb_viscous.html - +"lb/fluid"_fix_lb_fluid.html - +"lb/momentum"_fix_lb_momentum.html - +"lb/pc"_fix_lb_pc.html - +"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - +"lb/viscous"_fix_lb_viscous.html - "lineforce"_fix_lineforce.html - constrain atoms to move in a line -"manifoldforce"_fix_manifoldforce.html - -"meso"_fix_meso.html - -"meso/stationary"_fix_meso_stationary.html - +"manifoldforce"_fix_manifoldforce.html - +"meso"_fix_meso.html - +"meso"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion +"meso/move"_fix_meso_move.html - +"meso/stationary"_fix_meso_stationary.html - "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms "move"_fix_move.html - move atoms in a prescribed fashion -"mscg"_fix_mscg.html - +"mscg"_fix_mscg.html - "msst"_fix_msst.html - multi-scale shock technique (MSST) integration -"mvv/dpd"_fix_mvv_dpd.html - -"mvv/edpd"_fix_mvv_dpd.html - -"mvv/tdpd"_fix_mvv_dpd.html - +"mvv/dpd"_fix_mvv_dpd.html - +"mvv/edpd"_fix_mvv_dpd.html - +"mvv/tdpd"_fix_mvv_dpd.html - "neb"_fix_neb.html - nudged elastic band (NEB) spring forces "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles -"nph/body"_fix_nph_body.html - +"nph/body"_fix_nph_body.html - "nph/body"_fix_nve_body.html - NPH for body particles -"nph/eff"_fix_nh_eff.html - +"nph/eff"_fix_nh_eff.html - "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles "nphug"_fix_nphug.html - constant-stress Hugoniostat integration "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles -"npt/body"_fix_npt_body.html - +"npt/body"_fix_npt_body.html - "npt/body"_fix_nve_body.html - NPT for body particles -"npt/eff"_fix_nh_eff.html - +"npt/eff"_fix_nh_eff.html - "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles -"npt/uef"_fix_nh_uef.html - +"npt/uef"_fix_nh_uef.html - "nve"_fix_nve.html - constant NVE time integration "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles "nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces" -"nve/awpmd"_fix_nve_awpmd.html - +"nve/awpmd"_fix_nve_awpmd.html - "nve/body"_fix_nve_body.html - NVE for body particles -"nve/dot"_fix_nve_dot.html - -"nve/dotc/langevin"_fix_nve_dotc_langevin.html - -"nve/eff"_fix_nve_eff.html - +"nve/dot"_fix_nve_dot.html - +"nve/dotc/langevin"_fix_nve_dotc_langevin.html - +"nve/eff"_fix_nve_eff.html - "nve/limit"_fix_nve_limit.html - NVE with limited step length "nve/line"_fix_nve_line.html - NVE for line segments -"nve/manifold/rattle"_fix_nve_manifold_rattle.html - +"nve/manifold/rattle"_fix_nve_manifold_rattle.html - "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only) "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles -"nve/spin"_fix_nve_spin.html - +"nve/spin"_fix_nve_spin.html - "nve/tri"_fix_nve_tri.html - NVE for triangles -"nvk"_fix_nvk.html - +"nvk"_fix_nvk.html - "nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles "nvt/body"_fix_nve_body.html - NVT for body particles -"nvt/body"_fix_nvt_body.html - -"nvt/eff"_fix_nh_eff.html - -"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - +"nvt/body"_fix_nvt_body.html - +"nvt/eff"_fix_nh_eff.html - +"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations -"nvt/sllod/eff"_fix_nvt_sllod_eff.html - +"nvt/sllod/eff"_fix_nvt_sllod_eff.html - "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles -"nvt/uef"_fix_nh_uef.html - +"nvt/uef"_fix_nh_uef.html - "oneway"_fix_oneway.html - constrain particles on move in one direction "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC -"phonon"_fix_phonon.html - -"pimd"_fix_pimd.html - +"phonon"_fix_phonon.html - +"pimd"_fix_pimd.html - "planeforce"_fix_planeforce.html - constrain atoms to move in a plane +"plumed"_fix_plumed.html - wrapper on PLUMED free energy library "poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies "pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain -"precession/spin"_fix_precession_spin.html - +"precession/spin"_fix_precession_spin.html - "press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat "print"_fix_print.html - print text and variables during a simulation "property/atom"_fix_property_atom.html - add customized per-atom values -"python/invoke"_fix_python_invoke.html - -"python/move"_fix_python_move.html - -"qbmsst"_fix_qbmsst.html - +"python/invoke"_fix_python_invoke.html - +"python/move"_fix_python_move.html - +"qbmsst"_fix_qbmsst.html - "qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential "qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method "qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer "qeq/point"_fix_qeq.html - charge equilibration via point method -"qeq/reax"_fix_qeq_reax.html - +"qeq/reax"_fix_qeq_reax.html - "qeq/shielded"_fix_qeq.html - charge equilibration via shielded method "qeq/slater"_fix_qeq.html - charge equilibration via Slater method -"qmmm"_fix_qmmm.html - -"qtb"_fix_qtb.html - +"qmmm"_fix_qmmm.html - +"qtb"_fix_qtb.html - "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles -"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information -"reax/c/bonds"_fix_reax_bonds.html - -"reax/c/species"_fix_reaxc_species.html - +"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information +"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information "recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms "restrain"_fix_restrain.html - constrain a bond, angle, dihedral -"rhok"_fix_rhok.html - +"rhok"_fix_rhok.html - "rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration "rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration -"rigid/nph/small"_fix_rigid.html - +"rigid/nph/small"_fix_rigid.html - "rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration -"rigid/npt/small"_fix_rigid.html - +"rigid/npt/small"_fix_rigid.html - "rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration -"rigid/nve/small"_fix_rigid.html - +"rigid/nve/small"_fix_rigid.html - "rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration -"rigid/nvt/small"_fix_rigid.html - +"rigid/nvt/small"_fix_rigid.html - "rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration "rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration "rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration "rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration "rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration -"rx"_fix_rx.html - -"saed/vtk"_fix_saed_vtk.html - +"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body +"rx"_fix_rx.html - +"saed/vtk"_fix_saed_vtk.html - "setforce"_fix_setforce.html - set the force on each atom "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles -"shardlow"_fix_shardlow.html - -"smd"_fix_smd.html - -"smd/adjust_dt"_fix_smd_adjust_dt.html - -"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - -"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - -"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html - -"smd/setvel"_fix_smd_setvel.html - -"smd/wall_surface"_fix_smd_wall_surface.html - +"shardlow"_fix_shardlow.html - +"smd"_fix_smd.html - +"smd/adjust_dt"_fix_smd_adjust_dt.html - +"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - +"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - +"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html - +"smd/setvel"_fix_smd_setvel.html - +"smd/wall_surface"_fix_smd_wall_surface.html - "spring"_fix_spring.html - apply harmonic spring force to group of atoms "spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms "spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms @@ -350,28 +353,28 @@ accelerated styles exist. "srd"_fix_srd.html - stochastic rotation dynamics (SRD) "store/force"_fix_store_force.html - store force on each atom "store/state"_fix_store_state.html - store attributes for each atom -"tdpd/source"_fix_dpd_source.html - +"tdpd/source"_fix_dpd_source.html - "temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics "temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling -"temp/rescale/eff"_fix_temp_rescale_eff.html - +"temp/rescale/eff"_fix_temp_rescale_eff.html - "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method "thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation -"ti/spring"_fix_ti_spring.html - +"ti/spring"_fix_ti_spring.html - "tmd"_fix_tmd.html - guide a group of atoms to a new configuration "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling -"ttm/mod"_fix_ttm.html - +"ttm/mod"_fix_ttm.html - "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters "vector"_fix_vector.html - accumulate a global vector every N timesteps "viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation "viscous"_fix_viscous.html - viscous damping for granular simulations -"wall/body/polygon"_fix_wall_body_polygon.html - -"wall/body/polyhedron"_fix_wall_body_polyhedron.html - +"wall/body/polygon"_fix_wall_body_polygon.html - +"wall/body/polyhedron"_fix_wall_body_polyhedron.html - "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles -"wall/ees"_fix_wall_ees.html - +"wall/ees"_fix_wall_ees.html - "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations -"wall/gran/region"_fix_wall_gran_region.html - +"wall/gran/region"_fix_wall_gran_region.html - "wall/harmonic"_fix_wall.html - harmonic spring wall "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall @@ -379,7 +382,7 @@ accelerated styles exist. "wall/piston"_fix_wall_piston.html - moving reflective piston wall "wall/reflect"_fix_wall_reflect.html - reflecting wall(s) "wall/region"_fix_wall_region.html - use region surface as wall -"wall/region/ees"_fix_wall_ees.html - +"wall/region/ees"_fix_wall_ees.html - "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul [Restrictions:] diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index 0ca28fb869..0d862a890d 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -112,17 +112,43 @@ pages for individual pair styles and their energy formulas for the meaning of these parameters: "born"_pair_born.html: a,b,c: type pairs: +"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global: "buck"_pair_buck.html: a,c: type pairs: +"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global: +"buck/mdf"_pair_mdf.html: a,c: type pairs: "coul/cut"_pair_coul.html: scale: type pairs: +"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs: "coul/debye"_pair_coul.html: scale: type pairs: -"coul/long"_pair_coul.html: scale: type pairs: +"coul/dsf"_pair_coul.html: coulombic_cutoff: type global: +"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs: +"coul/long/soft"_pair_fep_soft.html: scale, lambda, coulombic_cutoff: type pairs: "eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs: +"gauss"_pair_gauss.html: a: type pairs: +"lennard/mdf"_pair_mdf.html: A,B: type pairs: +"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: +"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs: "lj/cut"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs: +"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global: +"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs: +"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: "lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: "lubricate"_pair_lubricate.html: mu: global: -"gauss"_pair_gauss.html: a: type pairs: -"morse"_pair_morse.html: d0,r0,alpha: type pairs: +"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs: +"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs: +"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs: +"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs: +"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs: +"reax/c"_pair_reaxc.html: chi, eta, gamma: type global: +"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global: +"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global: +"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global: +"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global: +"table"_pair_table.html: table_cutoff: type pairs: +"ufm"_pair_ufm.html: epsilon,sigma: type pairs: "soft"_pair_soft.html: a: type pairs: "kim"_pair_kim.html: PARAM_FREE_*:i,j,...: global :tb(c=3,s=:) @@ -132,12 +158,6 @@ the pair_*.cpp file associated with the potential. Some parameters are global settings for the pair style, e.g. the viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html. -For "pair_kim"_pair_kim.html, all free parameters supported by the -KIM Model are available (e.g., PARAM_FREE_sigmas provided by the -LennardJones612_Universal__MO_826355984548_001 Model). If the free -parameter corresponds to an array, then the particular array element -to be adapted must be specified (e.g., "PARAM_FREE_sigmas:10", to -adapt the tenth entry of the sigmas array). Other parameters apply to atom type pairs within the pair style, e.g. the prefactor "a" for "pair_style soft"_pair_soft.html. @@ -217,6 +237,7 @@ Currently {bond} does not support bond_style hybrid nor bond_style hybrid/overlay as bond styles. The only bonds that currently are working with fix_adapt are +"gromos"_bond_gromos.html: k, r0: type bonds: "harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:) :line diff --git a/doc/src/fix_adapt_fep.txt b/doc/src/fix_adapt_fep.txt index 7e30a1d29d..9a9255db06 100644 --- a/doc/src/fix_adapt_fep.txt +++ b/doc/src/fix_adapt_fep.txt @@ -114,24 +114,37 @@ styles and their energy formulas for the meaning of these parameters: "born"_pair_born.html: a,b,c: type pairs: "buck"_pair_buck.html: a,c: type pairs: +"buck/mdf"_pair_mdf.html: a,c: type pairs: "coul/cut"_pair_coul.html: scale: type pairs: -"coul/debye"_pair_coul.html: scale: type pairs: -"coul/long"_pair_coul.html: scale: type pairs: -"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: -"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: -"lubricate"_pair_lubricate.html: mu: global: +"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs: +"coul/long, coul/msm"_pair_coul.html: scale: type pairs: +"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs: +"eam"_pair_eam.html: scale: type pairs: "gauss"_pair_gauss.html: a: type pairs: +"lennard/mdf"_pair_mdf.html: a,b: type pairs: +"lj/class2"_pair_class2.html: epsilon,sigma: type pairs: +"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs: +"lj/cut"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: +"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: +"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs: +"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs: +"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs: +"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs: +"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs: +"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs: +"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs: +"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs: +"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs: +"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs: +"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs: "soft"_pair_soft.html: a: type pairs :tb(c=3,s=:) NOTE: It is easy to add new potentials and their parameters to this list. All it typically takes is adding an extract() method to the pair_*.cpp file associated with the potential. -Some parameters are global settings for the pair style, e.g. the -viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html. -Other parameters apply to atom type pairs within the pair style, -e.g. the prefactor "a" for "pair_style soft"_pair_soft.html. - Note that for many of the potentials, the parameter that can be varied is effectively a prefactor on the entire energy expression for the potential, e.g. the lj/cut epsilon. The parameters listed as "scale" @@ -253,7 +266,7 @@ minimization"_minimize.html. [Related commands:] "compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute -ti"_compute_ti.html +ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html [Default:] diff --git a/doc/src/fix_append_atoms.txt b/doc/src/fix_append_atoms.txt index d83f265982..860be9c9fa 100644 --- a/doc/src/fix_append_atoms.txt +++ b/doc/src/fix_append_atoms.txt @@ -28,7 +28,7 @@ keyword = {basis} or {size} or {freq} or {temp} or {random} or {units} :l target = target temperature for the region between zhi-extent and zhi (temperature units) damp = damping parameter (time units) seed = random number seed for langevin kicks - extent = extent of thermostated region (distance units) + extent = extent of thermostatted region (distance units) {random} args = xmax ymax zmax seed {xmax}, {ymax}, {zmax} = maximum displacement in particular direction (distance units) {seed} = random number seed for random displacement @@ -68,7 +68,7 @@ be added. The {random} keyword will give the atoms random displacements around their lattice points to simulate some initial temperature. -The {temp} keyword will cause a region to be thermostated with a +The {temp} keyword will cause a region to be thermostatted with a Langevin thermostat on the zhi boundary. The size of the region is measured from zhi and is set with the {extent} argument. diff --git a/doc/src/fix_ave_chunk.txt b/doc/src/fix_ave_chunk.txt index d331e51295..4e036367e2 100644 --- a/doc/src/fix_ave_chunk.txt +++ b/doc/src/fix_ave_chunk.txt @@ -240,7 +240,7 @@ shake"_fix_shake.html or "fix rigid"_fix_rigid.html. This is because those degrees of freedom (e.g. a constrained bond) could apply to sets of atoms that are both included and excluded from a specific chunk, and hence the concept is somewhat ill-defined. In some cases, you can -use the {adof} and {cdof} keywords to adjust the calculated degress of +use the {adof} and {cdof} keywords to adjust the calculated degrees of freedom appropriately, as explained below. Also note that a bias can be subtracted from atom velocities before diff --git a/doc/src/fix_ave_histo.txt b/doc/src/fix_ave_histo.txt index f1da130ff7..0a17813d21 100644 --- a/doc/src/fix_ave_histo.txt +++ b/doc/src/fix_ave_histo.txt @@ -35,6 +35,7 @@ keyword = {mode} or {file} or {ave} or {start} or {beyond} or {overwrite} or {ti {mode} arg = {scalar} or {vector} scalar = all input values are scalars vector = all input values are vectors + {kind} arg = {global} or {peratom} or {local} {file} arg = filename filename = name of file to output histogram(s) to {ave} args = {one} or {running} or {window} @@ -92,7 +93,8 @@ either all global, all per-atom, or all local quantities. Inputs of different kinds (e.g. global and per-atom) cannot be mixed. Atom attributes are per-atom vector values. See the doc page for individual "compute" and "fix" commands to see what kinds of -quantities they generate. +quantities they generate. See the optional {kind} keyword below for +how to force the fix ave/histo command to disambiguate if necessary. Note that the output of this command is a single histogram for all input values combined together, not one histogram per input value. @@ -231,6 +233,14 @@ keyword is set to {vector}, then all input values must be global or per-atom or local vectors, or columns of global or per-atom or local arrays. +The {kind} keyword only needs to be set if a compute or fix produces +more than one kind of output (global, per-atom, local). If this is +not the case, then LAMMPS will determine what kind of input is +provided and whether all the input arguments are consistent. If a +compute or fix produces more than one kind of output, the {kind} +keyword should be used to specify which output will be used. The +remaining input arguments must still be consistent. + The {beyond} keyword determines how input values that fall outside the {lo} to {hi} bounds are treated. Values such that {lo} <= value <= {hi} are assigned to one bin. Values on a bin boundary are assigned @@ -240,8 +250,8 @@ If {beyond} is set to {end} then values < {lo} are counted in the first bin and values > {hi} are counted in the last bin. If {beyond} is set to {extend} then two extra bins are created, so that there are Nbins+2 total bins. Values < {lo} are counted in the first bin and -values > {hi} are counted in the last bin (Nbins+1). Values between -{lo} and {hi} (inclusive) are counted in bins 2 thru Nbins+1. The +values > {hi} are counted in the last bin (Nbins+2). Values between +{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1. The "coordinate" stored and printed for these two extra bins is {lo} and {hi}. @@ -354,5 +364,6 @@ ave/chunk"_fix_ave_chunk.html, "fix ave/time"_fix_ave_time.html, [Default:] none -The option defaults are mode = scalar, ave = one, start = 0, no file -output, beyond = ignore, and title 1,2,3 = strings as described above. +The option defaults are mode = scalar, kind = figured out from input +arguments, ave = one, start = 0, no file output, beyond = ignore, and +title 1,2,3 = strings as described above. diff --git a/doc/src/fix_ave_time.txt b/doc/src/fix_ave_time.txt index a53e318d3f..cca881f2f8 100644 --- a/doc/src/fix_ave_time.txt +++ b/doc/src/fix_ave_time.txt @@ -133,7 +133,7 @@ fix 2 all ave/time 100 1 100 c_myRDF\[1\] c_myRDF\[2\] c_myRDF\[3\] file tmp2.rd The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what timesteps the input values will be used in order to contribute to the average. The final averaged quantities are generated on timesteps -that are a mlutiple of {Nfreq}. The average is over {Nrepeat} +that are a multiple of {Nfreq}. The average is over {Nrepeat} quantities, computed in the preceding portion of the simulation every {Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps diff --git a/doc/src/fix_balance.txt b/doc/src/fix_balance.txt index 77ad13033e..0f77fd4ecd 100644 --- a/doc/src/fix_balance.txt +++ b/doc/src/fix_balance.txt @@ -57,7 +57,7 @@ This command adjusts the size and shape of processor sub-domains within the simulation box, to attempt to balance the number of particles and thus the computational cost (load) evenly across processors. The load balancing is "dynamic" in the sense that -rebalancing is performed periodically during the simulation. To +re-balancing is performed periodically during the simulation. To perform "static" balancing, before or between runs, see the "balance"_balance.html command. @@ -178,15 +178,15 @@ The {group-ID} is ignored. However the impact of balancing on different groups of atoms can be affected by using the {group} weight style as described below. -The {Nfreq} setting determines how often a rebalance is performed. If -{Nfreq} > 0, then rebalancing will occur every {Nfreq} steps. Each -time a rebalance occurs, a reneighboring is triggered, so {Nfreq} -should not be too small. If {Nfreq} = 0, then rebalancing will be +The {Nfreq} setting determines how often a re-balance is performed. If +{Nfreq} > 0, then re-balancing will occur every {Nfreq} steps. Each +time a re-balance occurs, a reneighboring is triggered, so {Nfreq} +should not be too small. If {Nfreq} = 0, then re-balancing will be done every time reneighboring normally occurs, as determined by the the "neighbor"_neighbor.html and "neigh_modify"_neigh_modify.html command settings. -On rebalance steps, rebalancing will only be attempted if the current +On re-balance steps, re-balancing will only be attempted if the current imbalance factor, as defined above, exceeds the {thresh} setting. :line @@ -208,7 +208,7 @@ to {Niter} times. After each dimension finishes, the imbalance factor is re-computed, and the balancing operation halts if the {stopthresh} criterion is met. -A rebalance operation in a single dimension is performed using a +A re-balance operation in a single dimension is performed using a density-dependent recursive multisectioning algorithm, where the position of each cutting plane (line in 2d) in the dimension is adjusted independently. This is similar to a recursive bisectioning @@ -226,19 +226,19 @@ the recursion progresses, the count of particles on either side of the plane gets closer to the target value. The density-dependent part of this algorithm is often an advantage -when you rebalance a system that is already nearly balanced. It +when you re-balance a system that is already nearly balanced. It typically converges more quickly than the geometric bisectioning algorithm used by the "balance"_balance.html command. However, if can -be a disadvantage if you attempt to rebalance a system that is far +be a disadvantage if you attempt to re-balance a system that is far from balanced, and converge more slowly. In this case you probably want to use the "balance"_balance.html command before starting a run, so that you begin the run with a balanced system. -Once the rebalancing is complete and final processor sub-domains +Once the re-balancing is complete and final processor sub-domains assigned, particles migrate to their new owning processor as part of the normal reneighboring procedure. -NOTE: At each rebalance operation, the bisectioning for each cutting +NOTE: At each re-balance operation, the bisectioning for each cutting plane (line in 2d) typically starts with low and high bounds separated by the extent of a processor's sub-domain in one dimension. The size of this bracketing region shrinks based on the local density, as @@ -248,7 +248,7 @@ typically be positioned to better than 1 part in 1000 accuracy (relative to the perfect target position). For {Niter} = 20, it will be accurate to better than 1 part in a million. Thus there is no need to set {Niter} to a large value. This is especially true if you are -rebalancing often enough that each time you expect only an incremental +re-balancing often enough that each time you expect only an incremental adjustment in the cutting planes is necessary. LAMMPS will check if the threshold accuracy is reached (in a dimension) is less iterations than {Niter} and exit early. @@ -283,7 +283,7 @@ in that sub-box. :line The {out} keyword writes text to the specified {filename} with the -results of each rebalancing operation. The file contains the bounds +results of each re-balancing operation. The file contains the bounds of the sub-domain for each processor after the balancing operation completes. The format of the file is compatible with the "Pizza.py"_pizza {mdump} tool which has support for manipulating and @@ -344,13 +344,13 @@ files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes a global scalar which is the imbalance factor -after the most recent rebalance and a global vector of length 3 with -additional information about the most recent rebalancing. The 3 +after the most recent re-balance and a global vector of length 3 with +additional information about the most recent re-balancing. The 3 values in the vector are as follows: 1 = max # of particles per processor -2 = total # iterations performed in last rebalance -3 = imbalance factor right before the last rebalance was performed :ul +2 = total # iterations performed in last re-balance +3 = imbalance factor right before the last re-balance was performed :ul As explained above, the imbalance factor is the ratio of the maximum number of particles (or total weight) on any processor to the average @@ -371,9 +371,13 @@ minimization"_minimize.html. For 2d simulations, the {z} style cannot be used. Nor can a "z" appear in {dimstr} for the {shift} style. +Balancing through recursive bisectioning ({rcb} style) requires +"comm_style tiled"_comm_style.html + [Related commands:] -"group"_group.html, "processors"_processors.html, "balance"_balance.html +"group"_group.html, "processors"_processors.html, "balance"_balance.html, +"comm_style"_comm_style.html [Default:] none :link(pizza,http://pizza.sandia.gov) diff --git a/doc/src/fix_bocs.txt b/doc/src/fix_bocs.txt index b7d4e7badf..db9c35069c 100644 --- a/doc/src/fix_bocs.txt +++ b/doc/src/fix_bocs.txt @@ -24,7 +24,7 @@ keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline} [Examples:] fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 :pre - + fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre thermo_modify press 1_press :pre @@ -32,55 +32,55 @@ thermo_modify press 1_press :pre [Description:] -These commands incorporate a pressure correction as described by +These commands incorporate a pressure correction as described by Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna . The first half of the command mimics a standard fix npt command: fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre -The two differences are replacing {npt} with {bocs}, and replacing +The two differences are replacing {npt} with {bocs}, and replacing {iso}/{aniso}/{etc} with {cgiso}. -The rest of the command details what form you would like to use for -the pressure correction equation. The choices are: {analytic}, {linear_spline}, -or {cubic_spline}. +The rest of the command details what form you would like to use for +the pressure correction equation. The choices are: {analytic}, {linear_spline}, +or {cubic_spline}. -With either spline method, the only argument that needs to follow it -is the name of a file that contains the desired pressure correction +With either spline method, the only argument that needs to follow it +is the name of a file that contains the desired pressure correction as a function of volume. The file should be formatted so each line has: Volume_i, PressureCorrection_i :pre -Note both the COMMA and the SPACE separating the volume's -value and its corresponding pressure correction. The volumes in the file -should be uniformly spaced. Both the volumes and the pressure corrections -should be provided in the proper units, e.g. if you are using {units real}, -the volumes should all be in cubic angstroms, and the pressure corrections -should all be in atmospheres. Furthermore, the table should start/end at a -volume considerably smaller/larger than you expect your system to sample -during the simulation. If the system ever reaches a volume outside of the +Note both the COMMA and the SPACE separating the volume's +value and its corresponding pressure correction. The volumes in the file +should be uniformly spaced. Both the volumes and the pressure corrections +should be provided in the proper units, e.g. if you are using {units real}, +the volumes should all be in cubic angstroms, and the pressure corrections +should all be in atmospheres. Furthermore, the table should start/end at a +volume considerably smaller/larger than you expect your system to sample +during the simulation. If the system ever reaches a volume outside of the range provided, the simulation will stop. With the {analytic} option, the arguments are as follows: ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre -Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you -are using {units real}, {V_avg} should be in cubic angstroms, and the +Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you +are using {units real}, {V_avg} should be in cubic angstroms, and the coefficients should all be in atmospheres * cubic angstroms. [Restrictions:] As this is computing a (modified) pressure, group-ID should be {all}. -The pressure correction has only been tested for use with an isotropic -pressure coupling in 3 dimensions. +The pressure correction has only been tested for use with an isotropic +pressure coupling in 3 dimensions. By default, LAMMPS will still report the normal value for the pressure if the pressure is printed via a {thermo} command, or if the pressures are written to a file every so often. In order to have LAMMPS report the -modified pressure, you must include the {thermo_modify} command given in -the examples. For the last argument in the command, you should put +modified pressure, you must include the {thermo_modify} command given in +the examples. For the last argument in the command, you should put XXXX_press, where XXXX is the ID given to the fix bocs command (in the example, the ID of the fix bocs command is 1 ). @@ -90,8 +90,8 @@ package"_Build_package.html doc page for more info. [Related:] -For more details about the pressure correction and the entire BOCS software -package, visit the "BOCS package on github"_bocsgithub and read the release +For more details about the pressure correction and the entire BOCS software +package, visit the "BOCS package on GitHub"_bocsgithub and read the release paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 . diff --git a/doc/src/fix_bond_break.txt b/doc/src/fix_bond_break.txt index 5927ceb4e5..bde0beae02 100644 --- a/doc/src/fix_bond_break.txt +++ b/doc/src/fix_bond_break.txt @@ -101,7 +101,7 @@ NOTE: Breaking a bond typically alters the energy of a system. You should be careful not to choose bond breaking criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and break it when 2 atoms are separated by a distance -far from the equilibribum bond length, then the 2 atoms will be +far from the equilibrium bond length, then the 2 atoms will be dramatically released when the bond is broken. More generally, you may need to thermostat your system to compensate for energy changes resulting from broken bonds (and angles, dihedrals, impropers). diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt index de1a9f93f1..e78a283ece 100644 --- a/doc/src/fix_bond_create.txt +++ b/doc/src/fix_bond_create.txt @@ -139,8 +139,8 @@ for "extra angle per atom", "extra dihedral per atom", and "extra improper per atom" if angles, dihedrals, or impropers are being added when bonds are created. See the "read_data"_read_data.html or "create_box"_create_box.html command for more details. Note that a -data file with no atoms can be used if you wish to add unbonded atoms -via the "create atoms"_create_atoms.html command, e.g. for a +data file with no atoms can be used if you wish to add non-bonded +atoms via the "create atoms"_create_atoms.html command, e.g. for a percolation simulation. NOTE: LAMMPS stores and maintains a data structure with a list of the @@ -196,7 +196,7 @@ NOTE: Creating a bond typically alters the energy of a system. You should be careful not to choose bond creation criteria that induce a dramatic change in energy. For example, if you define a very stiff harmonic bond and create it when 2 atoms are separated by a distance -far from the equilibribum bond length, then the 2 atoms will oscillate +far from the equilibrium bond length, then the 2 atoms will oscillate dramatically when the bond is formed. More generally, you may need to thermostat your system to compensate for energy changes resulting from created bonds (and angles, dihedrals, impropers). diff --git a/doc/src/fix_bond_react.txt b/doc/src/fix_bond_react.txt index fc08a9b14e..af443ede92 100644 --- a/doc/src/fix_bond_react.txt +++ b/doc/src/fix_bond_react.txt @@ -25,7 +25,7 @@ common_keyword = {stabilization} :l {no} = no reaction site stabilization {yes} = perform reaction site stabilization {group-ID} = user-assigned prefix for the dynamic group of non-reacting atoms - {xmax} = xmax value that is used by an internally created "nve/limit"_fix_nve_limit.html integrator :pre + {xmax} = xmax value that is used by an internally-created "nve/limit"_fix_nve_limit.html integrator :pre react = mandatory argument indicating new reaction specification :l react-ID = user-assigned name for the reaction :l react-group-ID = only atoms in this group are considered for the reaction :l @@ -36,15 +36,18 @@ react = mandatory argument indicating new reaction specification :l template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l zero or more individual keyword/value pairs may be appended to each react argument :l - individual_keyword = {prob} or {stabilize_steps} :l + individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l {prob} values = fraction seed fraction = initiate reaction with this probability if otherwise eligible seed = random number seed (positive integer) + {max_rxn} value = N + N = maximum number of reactions allowed to occur {stabilize_steps} value = timesteps - timesteps = number of timesteps to apply internally created nve/limit.html - {update_edges} value = {none} or {charges} :l + timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms + {update_edges} value = {none} or {charges} or {custom} none = do not update topology near the edges of reaction templates - charges = update atomic charges of all atoms in reaction templates :pre + charges = update atomic charges of all atoms in reaction templates + custom = force the update of user-specified atomic charges :pre :ule [Examples:] @@ -68,8 +71,9 @@ Initiate complex covalent bonding (topology) changes. These topology changes will be referred to as 'reactions' throughout this documentation. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, -angles, dihedrals, impropers, bond-types, angle-types, dihedral-types, -atom-types, or atomic charges. +angles, dihedrals, impropers, bond types, angle types, dihedral types, +atom types, or atomic charges. In addition, reaction by-products or +other molecules can be identified and deleted. Fix bond/react does not use quantum mechanical (eg. fix qmmm) or pairwise bond-order potential (eg. Tersoff or AIREBO) methods to @@ -78,7 +82,7 @@ probabilistic criteria to effect predetermined topology changes in simulations using standard force fields. This fix was created to facilitate the dynamic creation of polymeric, -amorphous or highly-crosslinked systems. A suggested workflow for +amorphous or highly cross-linked systems. A suggested workflow for using this fix is: 1) identify a reaction to be simulated 2) build a molecule template of the reaction site before the reaction has occurred 3) build a molecule template of the reaction site after the @@ -94,7 +98,7 @@ necessary because the 'common keywords' are applied to all reactions. The {stabilization} keyword enables reaction site stabilization. Reaction site stabilization is performed by including reacting atoms -in an internally created fix "nve/limit"_fix_nve_limit.html time +in an internally-created fix "nve/limit"_fix_nve_limit.html time integrator for a set number of timesteps given by the {stabilize_steps} keyword. While reacting atoms are being time integrated by the internal nve/limit, they are prevented from being @@ -121,12 +125,13 @@ due to the internal dynamic grouping performed by fix bond/react. NOTE: If the group-ID is an existing static group, react-group-IDs should also be specified as this static group, or a subset. -NOTE: If the group-ID is previously unused, the internally created +NOTE: If the group-ID is previously unused, the internally-created group applies to all atoms in the system, i.e. you should generally not have a separate thermostat which acts on the 'all' group, or any other group. -The following comments pertain to each {react} argument: +The following comments pertain to each {react} argument (in other +words, can be customized for each reaction, or reaction step): A check for possible new reaction sites is performed every {Nevery} timesteps. @@ -139,20 +144,20 @@ modified to match the post-reaction template. A bonding atom pair will be identified if several conditions are met. First, a pair of atoms I,J within the specified react-group-ID of type -itype and jtype must separated by a distance between {Rmin} and +itype and jtype must be separated by a distance between {Rmin} and {Rmax}. It is possible that multiple bonding atom pairs are -identified: if the bonding atoms in the pre-reacted template are not -1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as -its bonding partner; otherwise, the farthest potential partner is -chosen. Then, if both an atom I and atom J have each other as their -nearest bonding partners, these two atoms are identified as the -bonding atom pair of the reaction site. Once this unique bonding atom -pair is identified for each reaction, there could two or more -reactions that involve a given atom on the same timestep. If this is -the case, only one such reaction is permitted to occur. This reaction -is chosen randomly from all potential reactions. This capability -allows e.g. for different reaction pathways to proceed from identical -reaction sites with user-specified probabilities. +identified: if the bonding atoms in the pre-reacted template are 1-2 +neighbors, i.e. directly bonded, the farthest bonding atom partner is +set as its bonding partner; otherwise, the closest potential partner +is chosen. Then, if both an atom I and atom J have each other as their +bonding partners, these two atoms are identified as the bonding atom +pair of the reaction site. Once this unique bonding atom pair is +identified for each reaction, there could two or more reactions that +involve a given atom on the same timestep. If this is the case, only +one such reaction is permitted to occur. This reaction is chosen +randomly from all potential reactions. This capability allows e.g. for +different reaction pathways to proceed from identical reaction sites +with user-specified probabilities. The pre-reacted molecule template is specified by a molecule command. This molecule template file contains a sample reaction site and its @@ -201,23 +206,37 @@ A discussion of correctly handling this is also provided on the The map file is a text document with the following format: A map file has a header and a body. The header of map file the -contains one mandatory keyword and one optional keyword. The mandatory -keyword is 'equivalences' and the optional keyword is 'edgeIDs': +contains one mandatory keyword and three optional keywords. The +mandatory keyword is 'equivalences' and the optional keywords are +'edgeIDs' and 'deleteIDs' and 'customIDs': N {equivalences} = # of atoms N in the reaction molecule templates -N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template :pre +N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template +N {deleteIDs} = # of atoms N that are specified for deletion +N {customIDs} = # of atoms N that are specified for a custom update +N {constraints} = # of specified reaction constraints N :pre -The body of the map file contains two mandatory sections and one -optional section. The first mandatory section begins with the keyword +The body of the map file contains two mandatory sections and four +optional sections. The first mandatory section begins with the keyword 'BondingIDs' and lists the atom IDs of the bonding atom pair in the pre-reacted molecule template. The second mandatory section begins with the keyword 'Equivalences' and lists a one-to-one correspondence between atom IDs of the pre- and post-reacted templates. The first column is an atom ID of the pre-reacted molecule template, and the second column is the corresponding atom ID of the post-reacted -molecule template. The optional section begins with the keyword +molecule template. The first optional section begins with the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted -molecule template. +molecule template. The second optional section begins with the keyword +'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to +delete. The third optional section begins with the keyword 'Custom +Edges' and allows for forcing the update of a specific atom's atomic +charge. The first column is the ID of an atom near the edge of the +pre-reacted molecule template, and the value of the second column is +either 'none' or 'charges.' Further details are provided in the +discussion of the 'update_edges' keyword. The fourth optional section +begins with the keyword 'Constraints' and lists additional criteria +that must be satisfied in order for the reaction to occur. Currently, +there is one type of constraint available, as discussed below. A sample map file is given below: @@ -250,6 +269,18 @@ Equivalences :pre :line +Any number of additional constraints may be specified in the +Constraints section of the map file. Currently there is one type of +additional constraint, of type 'distance', whose syntax is as follows: + +distance {ID1} {ID2} {rmin} {rmax} :pre + +where 'distance' is the required keyword, {ID1} and {ID2} are +pre-reaction atom IDs, and these two atoms must be separated by a +distance between {rmin} and {rmax} for the reaction to occur. This +constraint can be used to enforce a certain orientation between +reacting molecules. + Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the post-reacted molecule template. All force fields with fixed bonds, @@ -272,18 +303,13 @@ The {prob} keyword can affect whether an eligible reaction actually occurs. The fraction setting must be a value between 0.0 and 1.0. A uniform random number between 0.0 and 1.0 is generated and the eligible reaction only occurs if the random number is less than the -fraction. +fraction. Up to N reactions are permitted to occur, as optionally +specified by the {max_rxn} keyword. The {stabilize_steps} keyword allows for the specification of how many timesteps a reaction site is stabilized before being returned to the overall system thermostat. -The {update_edges} keyword can increase the number of atoms whose -atomic charges are updated, when the pre-reaction template contains -edge atoms. When the value is set to 'charges,' all atoms' atomic -charges are updated to those specified by the post-reaction template, -including atoms near the edge of reaction templates. - In order to produce the most physical behavior, this 'reaction site equilibration time' should be tuned to be as small as possible while retaining stability for a given system or reaction step. After a @@ -292,9 +318,30 @@ of 60 timesteps. Ideally, it should be individually tuned for each fix reaction step. Note that in some situations, decreasing rather than increasing this parameter will result in an increase in stability. +The {update_edges} keyword can increase the number of atoms whose +atomic charges are updated, when the pre-reaction template contains +edge atoms. When the value is set to 'charges,' all atoms' atomic +charges are updated to those specified by the post-reaction template, +including atoms near the edge of reaction templates. When the value is +set to 'custom,' an additional section must be included in the map +file that specifies whether to update charges, on a per-atom basis. +The format of this section is detailed above. Listing a pre-reaction +atom ID with a value of 'charges' will force the update of the atom's +charge, even if it is near a template edge. Atoms not near a template +edge are unaffected by this setting. + A few other considerations: -It may be beneficial to ensure reacting atoms are at a certain +Many reactions result in one or more atoms that are considered +unwanted by-products. Therefore, bond/react provides the option to +delete a user-specified set of atoms. These pre-reaction atoms are +identified in the map file. A deleted atom must still be included in +the post-reaction molecule template, in which it cannot be bonded to +an atom that is not deleted. In addition to deleting unwanted reaction +by-products, this feature can be used to remove specific topologies, +such as small rings, that may be otherwise indistinguishable. + +Also, it may be beneficial to ensure reacting atoms are at a certain temperature before being released to the overall thermostat. For this, you can use the internally-created dynamic group named "bond_react_MASTER_group." For example, adding the following command @@ -338,6 +385,10 @@ No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. +When fix bond/react is 'unfixed,' all internally-created groups are +deleted. Therefore, fix bond/react can only be unfixed after unfixing +all other fixes that use any group created by fix bond/react. + [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if diff --git a/doc/src/fix_bond_swap.txt b/doc/src/fix_bond_swap.txt index 3c90bb53f6..9a4e7c2b55 100644 --- a/doc/src/fix_bond_swap.txt +++ b/doc/src/fix_bond_swap.txt @@ -84,7 +84,7 @@ the molecule IDs for your polymer chains in a certain way, typically in the data file, read by the "read_data"_read_data.html command. Consider a system of 6-mer chains. You have 2 choices. If the molecule IDs for monomers on each chain are set to 1,2,3,4,5,6 then -swaps will conserve chain length. For a particular momoner there will +swaps will conserve chain length. For a particular monomer there will be only one other monomer on another chain which is a potential swap partner. If the molecule IDs for monomers on each chain are set to 1,2,3,3,2,1 then swaps will conserve chain length but swaps will be diff --git a/doc/src/fix_client_md.txt b/doc/src/fix_client_md.txt index 77f6b82c5e..5fee8511fe 100644 --- a/doc/src/fix_client_md.txt +++ b/doc/src/fix_client_md.txt @@ -51,7 +51,7 @@ md"_server_md.html doc page. Note that when using LAMMPS as an MD client, your LAMMPS input script should not normally contain force field commands, like a "pair_style"_pair_style.html, "bond_style"_bond_style.html, or -"kspace_style"_kspace_style.html commmand. However it is possible for +"kspace_style"_kspace_style.html command. However it is possible for a server code to only compute a portion of the full force-field, while LAMMPS computes the remaining part. Your LAMMPS script can also specify boundary conditions or force constraints in the usual way, @@ -68,7 +68,7 @@ LAMMPS and another code in tandem to perform a coupled simulation. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart -files"_restart.html. +files"_restart.html. The "fix_modify"_fix_modify.html {energy} option is supported by this fix to add the potential energy computed by the server application to diff --git a/doc/src/fix_cmap.txt b/doc/src/fix_cmap.txt index ef48e8b51c..aef565e89e 100644 --- a/doc/src/fix_cmap.txt +++ b/doc/src/fix_cmap.txt @@ -24,12 +24,12 @@ fix_modify myCMAP energy yes :pre [Description:] -This command enables CMAP crossterms to be added to simulations which +This command enables CMAP cross-terms to be added to simulations which use the CHARMM force field. These are relevant for any CHARMM model of a peptide or protein sequences that is 3 or more amino-acid residues long; see "(Buck)"_#Buck and "(Brooks)"_#Brooks2 for details, including the analytic energy expressions for CMAP interactions. The -CMAP crossterms add additional potential energy contributions to pairs +CMAP cross-terms add additional potential energy contributions to pairs of overlapping phi-psi dihedrals of amino-acids, which are important to properly represent their conformational behavior. @@ -49,7 +49,7 @@ in its header section: N crossterms :pre -where N is the number of CMAP crossterms. It should also have a section +where N is the number of CMAP cross-terms. It should also have a section in the body of the data file like this with N lines: CMAP :pre @@ -69,7 +69,7 @@ sections match those specified in the read_data command following the data file name; see the "read_data"_read_data.html doc page for more details. -A data file containing CMAP crossterms can be generated from a PDB +A data file containing CMAP cross-terms can be generated from a PDB file using the charmm2lammps.pl script in the tools/ch2lmp directory of the LAMMPS distribution. The script must be invoked with the optional "-cmap" flag to do this; see the tools/ch2lmp/README file for @@ -87,7 +87,7 @@ the note below about how to include the CMAP energy when performing an [Restart, fix_modify, output, run start/stop, minimize info:] -This fix writes the list of CMAP crossterms to "binary restart +This fix writes the list of CMAP cross-terms to "binary restart files"_restart.html. See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an diff --git a/doc/src/fix_colvars.txt b/doc/src/fix_colvars.txt index 3a64840bdc..d9eb9ac5aa 100644 --- a/doc/src/fix_colvars.txt +++ b/doc/src/fix_colvars.txt @@ -81,7 +81,7 @@ the image flags to reconstruct the absolute atom positions. Setting this to {no} will use the current local coordinates that are wrapped back into the simulation cell at each re-neighboring instead. -The {tstat} keyword can be either NULL or the label of a thermostating +The {tstat} keyword can be either NULL or the label of a thermostatting fix that thermostats all atoms in the fix colvars group. This will be used to provide the colvars module with the current thermostat target temperature. @@ -116,7 +116,8 @@ not a limitation of functionality. [Related commands:] -"fix smd"_fix_smd.html +"fix smd"_fix_smd.html, "fix spring"_fix_spring.html, +"fix plumed"_fix_plumed.html [Default:] @@ -126,4 +127,4 @@ and tstat = NULL. :line :link(Fiorin) -[(Fiorin)] Fiorin , Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 +[(Fiorin)] Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594 diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index d35c3065a2..3259f79497 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -86,7 +86,7 @@ Change the volume and/or shape of the simulation box during a dynamics run. Orthogonal simulation boxes have 3 adjustable parameters (x,y,z). Triclinic (non-orthogonal) simulation boxes have 6 adjustable parameters (x,y,z,xy,xz,yz). Any or all of them can be -adjusted independently and simultaneously by this command. +adjusted independently and simultaneously by this command. This fix can be used to perform non-equilibrium MD (NEMD) simulations of a continuously strained system. See the "fix diff --git a/doc/src/fix_deposit.txt b/doc/src/fix_deposit.txt index 265f43bd4b..fd12d4bb45 100644 --- a/doc/src/fix_deposit.txt +++ b/doc/src/fix_deposit.txt @@ -255,7 +255,7 @@ temperature compute you are using. This fix writes the state of the deposition to "binary restart files"_restart.html. This includes information about how many -particles have been depositied, the random number generator seed, the +particles have been deposited, the random number generator seed, the next timestep for deposition, etc. See the "read_restart"_read_restart.html command for info on how to re-specify a fix in an input script that reads a restart file, so that the diff --git a/doc/src/fix_drude_transform.txt b/doc/src/fix_drude_transform.txt index 8864cc4eb6..a102368b5c 100644 --- a/doc/src/fix_drude_transform.txt +++ b/doc/src/fix_drude_transform.txt @@ -91,8 +91,8 @@ different temperatures, two Nose-Hoover thermostats must be defined, acting on two distinct groups. NOTE: The {fix drude/transform/direct} command must appear before any -Nose-Hoover thermostating fixes. The {fix drude/transform/inverse} -command must appear after any Nose-Hoover thermostating fixes. +Nose-Hoover thermostatting fixes. The {fix drude/transform/inverse} +command must appear after any Nose-Hoover thermostatting fixes. Example: @@ -106,8 +106,8 @@ thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDR In this example, {gCORES} is the group of the atom cores and {gDRUDES} is the group of the Drude particles (electrons). The centers of mass -of the Drude oscillators will be thermostated at 300.0 and the -internal degrees of freedom will be thermostated at 1.0. The +of the Drude oscillators will be thermostatted at 300.0 and the +internal degrees of freedom will be thermostatted at 1.0. The temperatures of cores and Drude particles, in center-of-mass and relative coordinates, are calculated using "compute temp/drude"_compute_temp_drude.html @@ -130,9 +130,9 @@ fix fINVERSE all drude/transform/inverse :pre In this example, {gCORES} is the group of the atom cores and {gDRUDES} is the group of the Drude particles. The centers of mass of the Drude -oscillators will be thermostated at 298.0 and the internal degrees of -freedom will be thermostated at 5.0. The whole system will be -barostated at 1.0. +oscillators will be thermostatted at 298.0 and the internal degrees of +freedom will be thermostatted at 5.0. The whole system will be +barostatted at 1.0. In order to avoid the flying ice cube problem (irreversible transfer of linear momentum to the center of mass of the system), you may need diff --git a/doc/src/fix_dt_reset.txt b/doc/src/fix_dt_reset.txt index 0c5a4493ae..adca2c3072 100644 --- a/doc/src/fix_dt_reset.txt +++ b/doc/src/fix_dt_reset.txt @@ -55,7 +55,7 @@ current velocity and force. Since performing this calculation exactly would require the solution to a quartic equation, a cheaper estimate is generated. The estimate is conservative in that the atom's displacement is guaranteed not to exceed {Xmax}, though it may be -smaller. +smaller. In addition if the {emax} keyword is used, the specified {Emax} value is enforced as a limit on how much an atom's kinetic energy can diff --git a/doc/src/fix_ehex.txt b/doc/src/fix_ehex.txt index 75651e21a4..79cfce4b01 100644 --- a/doc/src/fix_ehex.txt +++ b/doc/src/fix_ehex.txt @@ -80,9 +80,9 @@ position to the respective reservoir. The quantity \(F_\{\Gamma_\{k(\mathbf r_i)\}\}\) corresponds to the input parameter {F}, which is the energy flux into the reservoir. Furthermore, \(K_\{\Gamma_\{k(\mathbf r_i)\}\}\) and \(v_\{\Gamma_\{k(\mathbf r_i)\}\}\) -denote the non-translational kinetic energy and the centre of mass +denote the non-translational kinetic energy and the center of mass velocity of that reservoir. The thermostatting force does not affect -the centre of mass velocities of the individual reservoirs and the +the center of mass velocities of the individual reservoirs and the entire simulation box. A derivation of the equations and details on the numerical implementation with velocity Verlet in LAMMPS can be found in reference "(Wirnsberger)"#_Wirnsberger. @@ -116,10 +116,10 @@ specified in the input script and the keyword {constrain} is set, the bond distances will be corrected a second time at the end of the integration step. It is recommended to specify the keyword {com} in addition to the keyword {constrain}. With this option all sites of a -constrained cluster are rescaled, if its centre of mass is located +constrained cluster are rescaled, if its center of mass is located inside the region. Rescaling all sites of a cluster by the same factor does not introduce any velocity components along fixed bonds. No -rescaling takes place if the centre of mass lies outside the region. +rescaling takes place if the center of mass lies outside the region. NOTE: You can only use the keyword {com} along with {constrain}. diff --git a/doc/src/fix_eos_table.txt b/doc/src/fix_eos_table.txt index 53b3204372..72c8523662 100644 --- a/doc/src/fix_eos_table.txt +++ b/doc/src/fix_eos_table.txt @@ -35,13 +35,13 @@ temperature. The interpolation tables are created by fitting cubic splines to the file values and interpolating energy values at each of {N} internal -temperatures, and vice-versa. During a simulation, these tables are +temperatures, and vice versa. During a simulation, these tables are used to interpolate internal energy or temperature values as needed. The interpolation is done with the {linear} style. For the {linear} style, the internal temperature is used to find 2 surrounding table values from which an internal energy is computed by -linear interpolation, and vice-versa. +linear interpolation, and vice versa. The filename specifies a file containing tabulated internal temperature and internal energy values. The keyword specifies a diff --git a/doc/src/fix_evaporate.txt b/doc/src/fix_evaporate.txt index 59dab43d9a..69572b96cf 100644 --- a/doc/src/fix_evaporate.txt +++ b/doc/src/fix_evaporate.txt @@ -54,8 +54,8 @@ just the single atom is deleted. As an example, if you wish to delete 10 water molecules every {N} steps, you should set {M} to 30. If only the water's oxygen atoms were in the fix group, then two hydrogen atoms would be deleted when -an oxygen atom is selected for deletion, whether the hydrogens are -inside the evaporation region or not. +an oxygen atom is selected for deletion, whether the hydrogen atoms +are inside the evaporation region or not. Note that neighbor lists are re-built on timesteps that atoms are removed. Thus you should not remove atoms too frequently or you will diff --git a/doc/src/fix_ffl.txt b/doc/src/fix_ffl.txt index ea33dc432f..a5d3f80a62 100644 --- a/doc/src/fix_ffl.txt +++ b/doc/src/fix_ffl.txt @@ -82,7 +82,7 @@ sense, a restarted simulation should produce the same behavior. Note however that you should use a different seed each time you restart, otherwise the same sequence of random numbers will be used each time, which might lead to stochastic synchronization and -subtle artefacts in the sampling. +subtle artifacts in the sampling. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 6b9a02eeca..8a66a007a3 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -74,7 +74,7 @@ materials, or computing vapor-liquid coexistence curves. Every N timesteps the fix attempts both GCMC exchanges (insertions or deletions) and MC moves of gas atoms or molecules. On those timesteps, the average number of attempted GCMC exchanges is X, -while the average number of attempted MC moves is M. +while the average number of attempted MC moves is M. For GCMC exchanges of either molecular or atomic gasses, these exchanges can be either deletions or insertions, with equal probability. @@ -203,7 +203,7 @@ atom translations, molecule translations, and molecule rotations, respectively. The values must be non-negative integers or real numbers, with at least one non-zero value. For example, (10,30,0) would result in 25% of the MC moves being atomic translations, 75% -molecular translations, and no molecular rotations. +molecular translations, and no molecular rotations. Optionally, users may specify the maximum rotation angle for molecular rotations using the {maxangle} keyword and specifying the angle in diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index 70a8e7f342..a8026256b0 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -104,7 +104,7 @@ sense, a restarted simulation should produce the same behavior. Note however that you should use a different seed each time you restart, otherwise the same sequence of random numbers will be used each time, which might lead to stochastic synchronization and -subtle artefacts in the sampling. +subtle artifacts in the sampling. This fix can ramp its target temperature over multiple runs, using the {start} and {stop} keywords of the "run"_run.html command. See the diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index e096d4bd3c..edf11b337c 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -53,7 +53,7 @@ particles as usual. Either constant volume or constant pressure algorithms can be used. The fix enforces a generalized ensemble in a single replica -only. Typically, this ideaology is combined with replica exchange with +only. Typically, this ideology is combined with replica exchange with replicas differing by {lambda} only for simplicity, but this is not required. A multi-replica simulation can be run within the LAMMPS environment using the "temper/grem"_temper_grem.html command. This diff --git a/doc/src/fix_heat.txt b/doc/src/fix_heat.txt index 6db7592609..640b211f99 100644 --- a/doc/src/fix_heat.txt +++ b/doc/src/fix_heat.txt @@ -109,7 +109,7 @@ are relevant to this fix. This fix computes a global scalar which can be accessed by various "output commands"_Howto_output.html. This scalar is the most recent -value by which velocites were scaled. The scalar value calculated by +value by which velocities were scaled. The scalar value calculated by this fix is "intensive". If {eflux} is specified as an atom-style variable, this fix computes the average value by which the velocities were scaled for all of the atoms that had their velocities scaled. diff --git a/doc/src/fix_hyper_global.txt b/doc/src/fix_hyper_global.txt new file mode 100644 index 0000000000..81404ac6a2 --- /dev/null +++ b/doc/src/fix_hyper_global.txt @@ -0,0 +1,263 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix hyper/global command :h3 + +[Syntax:] + +fix ID group-ID hyper/global cutbond qfactor Vmax Tequil :pre + +ID, group-ID are documented in "fix"_fix.html command +hyper/global = style name of this fix command +cutbond = max distance at which a pair of atoms is considered bonded (distance units) +qfactor = max strain at which bias potential goes to 0.0 (unitless) +Vmax = height of bias potential (energy units) +Tequil = equilibration temperature (temperature units) :ul + +[Examples:] + +fix 1 all hyper/global 1.0 0.3 0.8 300.0 :pre + +[Description:] + +This fix is meant to be used with the "hyper"_hyper.html command to +perform a bond-boost global hyperdynamics (GHD) simulation. The role +of this fix is to a select a single pair of atoms in the system at +each timestep to add a global bias potential to, which will alter the +dynamics of the system in a manner that effectively accelerates time. +This is in contrast to the "fix hyper/local"_fix_hyper_local.html +command, which can be user to perform a local hyperdynamics (LHD) +simulation, by adding a local bias potential to multiple pairs of +atoms at each timestep. GHD can time accelerate a small simulation +with up to a few 100 atoms. For larger systems, LHD is needed to +achieve good time acceleration. + +For a system that undergoes rare transition events, where one or more +atoms move over an energy barrier to a new potential energy basin, the +effect of the bias potential is to induce more rapid transitions. +This can lead to a dramatic speed-up in the rate at which events +occurs, without altering their relative frequencies, thus leading to +an overall increase in the elapsed real time of the simulation as +compared to running for the same number of timesteps with normal MD. +See the "hyper"_hyper.html doc page for a more general discussion of +hyperdynamics and citations that explain both GHD and LHD. + +The equations and logic used by this fix and described here to perform +GHD follow the description given in "(Voter2013)"_#Voter2013ghd. The +bond-boost form of a bias potential for HD is due to Miron and +Fichthorn as described in "(Miron)"_#Mironghd. In LAMMPS we use a +simplified version of bond-boost GHD where a single bond in the system +is biased at any one timestep. + +Bonds are defined between each pair of I,J atoms whose R0ij distance +is less than {cutbond}, when the system is in a quenched state +(minimum) energy. Note that these are not "bonds" in a covalent +sense. A bond is simply any pair of atoms that meet the distance +criterion. {Cutbond} is an argument to this fix; it is discussed +below. A bond is only formed if one or both of the I.J atoms are in +the specified group. + +The current strain of bond IJ (when running dynamics) is defined as + +Eij = (Rij - R0ij) / R0ij :pre + +where Rij is the current distance between atoms I,J, and R0ij is the +equilibrium distance in the quenched state. + +The bias energy Vij of any bond IJ is defined as + +Vij = Vmax * (1 - (Eij/q)^2) for abs(Eij) < qfactor + = 0 otherwise :pre + +where the prefactor {Vmax} and the cutoff {qfactor} are arguments to +this fix; they are discussed below. This functional form is an +inverse parabola centered at 0.0 with height Vmax and which goes to +0.0 at +/- qfactor. + +Let Emax = the maximum of abs(Eij) for all IJ bonds in the system on a +given timestep. On that step, Vij is added as a bias potential to +only the single bond with strain Emax, call it Vij(max). Note that +Vij(max) will be 0.0 if Emax >= qfactor on that timestep. Also note +that Vij(max) is added to the normal interatomic potential that is +computed between all atoms in the system at every step. + +The derivative of Vij(max) with respect to the position of each atom +in the Emax bond gives a bias force Fij(max) acting on the bond as + +Fij(max) = - dVij(max)/dEij = 2 Vmax Eij / qfactor^2 for abs(Eij) < qfactor + = 0 otherwise :pre + +which can be decomposed into an equal and opposite force acting on +only the two I,J atoms in the Emax bond. + +The time boost factor for the system is given each timestep I by + +Bi = exp(beta * Vij(max)) :pre + +where beta = 1/kTequil, and {Tequil} is the temperature of the system +and an argument to this fix. Note that Bi >= 1 at every step. + +NOTE: To run a GHD simulation, the input script must also use the "fix +langevin"_fix_langevin.html command to thermostat the atoms at the +same {Tequil} as specified by this fix, so that the system is running +constant-temperature (NVT) dynamics. LAMMPS does not check that this +is done. + +The elapsed time t_hyper for a GHD simulation running for {N} +timesteps is simply + +t_hyper = Sum (i = 1 to N) Bi * dt :pre + +where dt is the timestep size defined by the "timestep"_timestep.html +command. The effective time acceleration due to GHD is thus t_hyper / +N*dt, where N*dt is elapsed time for a normal MD run of N timesteps. + +Note that in GHD, the boost factor varies from timestep to timestep. +Likewise, which bond has Emax strain and thus which pair of atoms the +bias potential is added to, will also vary from timestep to timestep. +This is in contrast to local hyperdynamics (LHD) where the boost +factor is an input parameter; see the "fix +hyper/local"_fix_hyper_local.html doc page for details. + +:line + +Here is additional information on the input parameters for GHD. + +The {cutbond} argument is the cutoff distance for defining bonds +between pairs of nearby atoms. A pair of I,J atoms in their +equilibrium, minimum-energy configuration, which are separated by a +distance Rij < {cutbond}, are flagged as a bonded pair. Setting +{cubond} to be ~25% larger than the nearest-neighbor distance in a +crystalline lattice is a typical choice for solids, so that bonds +exist only between nearest neighbor pairs. + +The {qfactor} argument is the limiting strain at which the bias +potential goes to 0.0. It is dimensionless, so a value of 0.3 means a +bond distance can be up to 30% larger or 30% smaller than the +equilibrium (quenched) R0ij distance and the two atoms in the bond +could still experience a non-zero bias force. + +If {qfactor} is set too large, then transitions from one energy basin +to another are affected because the bias potential is non-zero at the +transition state (e.g. saddle point). If {qfactor} is set too small +than little boost is achieved because the Eij strain of some bond in +the system will (nearly) always exceed {qfactor}. A value of 0.3 for +{qfactor} is typically reasonable. + +The {Vmax} argument is the prefactor on the bias potential. Ideally, +tt should be set to a value slightly less than the smallest barrier +height for an event to occur. Otherwise the applied bias potential +may be large enough (when added to the interatomic potential) to +produce a local energy basin with a maxima in the center. This can +produce artificial energy minima in the same basin that trap an atom. +Or if {Vmax} is even larger, it may induce an atom(s) to rapidly +transition to another energy basin. Both cases are "bad dynamics" +which violate the assumptions of GHD that guarantee an accelerated +time-accurate trajectory of the system. + +Note that if {Vmax} is set too small, the GHD simulation will run +correctly. There will just be fewer events because the hyper time +(t_hyper equation above) will be shorter. + +NOTE: If you have no physical intuition as to the smallest barrier +height in your system, a reasonable strategy to determine the largest +{Vmax} you can use for a GHD model, is to run a sequence of +simulations with smaller and smaller {Vmax} values, until the event +rate does not change (as a function of hyper time). + +The {Tequil} argument is the temperature at which the system is +simulated; see the comment above about the "fix +langevin"_fix_langevin.html thermostatting. It is also part of the +beta term in the exponential factor that determines how much boost is +achieved as a function of the bias potential. + +In general, the lower the value of {Tequil} and the higher the value +of {Vmax}, the more time boost will be achievable by the GHD +algorithm. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy of the bias potential to the the system's +potential energy as part of "thermodynamic output"_thermo_style.html. + +This fix computes a global scalar and global vector of length 12, which +can be accessed by various "output commands"_Howto_output.html. The +scalar is the magnitude of the bias potential (energy units) applied on +the current timestep. The vector stores the following quantities: + +1 = boost factor on this step (unitless) +2 = max strain Eij of any bond on this step (absolute value, unitless) +3 = ID of first atom in the max-strain bond +4 = ID of second atom in the max-strain bond +5 = average # of bonds/atom on this step :ul + +6 = fraction of timesteps where the biased bond has bias = 0.0 during this run +7 = fraction of timesteps where the biased bond has negative strain during this run +8 = max drift distance of any atom during this run (distance units) +9 = max bond length during this run (distance units) :ul + +10 = cumulative hyper time since fix was defined (time units) +11 = cumulative count of event timesteps since fix was defined +12 = cumulative count of atoms in events since fix was defined :ul + +The first 5 quantities are for the current timestep. Quantities 6-9 +are for the current hyper run. They are reset each time a new hyper +run is performed. Quantities 19-12 are cumulative across multiple +runs (since the point in the input script the fix was defined). + +For value 8, drift is the distance an atom moves between two quenched +states when the second quench determines an event has occurred. Atoms +involved in an event will typically move the greatest distance since +others typically remain near their original quenched position. + +For value 11, events are checked for by the "hyper"_hyper.html command +once every {Nevent} timesteps. This value is the count of those +timesteps on which one (or more) events was detected. It is NOT the +number of distinct events, since more than one event may occur in the +same {Nevent} time window. + +For value 12, each time the "hyper"_hyper.html command checks for an +event, it invokes a compute to flag zero or more atoms as +participating in one or more events. E.g. atoms that have displaced +more than some distance from the previous quench state. Value 11 is +the cumulative count of the number of atoms participating in any of +the events that were found. + +The scalar and vector values calculated by this fix are all +"intensive". + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This command can only be used if LAMMPS was built with the REPLICA +package. See the "Build package"_Build_package.html doc page for more +info. + +[Related commands:] + +"hyper"_hyper.html, "fix hyper/local"_fix_hyper_local.html + +[Default:] None + +:line + +:link(Voter2013ghd) +[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, +144110 (2013). + +:link(Mironghd) +[(Miron)] R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). diff --git a/doc/src/fix_hyper_local.txt b/doc/src/fix_hyper_local.txt new file mode 100644 index 0000000000..185fa8f20b --- /dev/null +++ b/doc/src/fix_hyper_local.txt @@ -0,0 +1,463 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +fix hyper/local command :h3 + +[Syntax:] + +fix ID group-ID hyper/local cutbond qfactor Vmax Tequil Dcut alpha Btarget :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +hyper/local = style name of this fix command :l +cutbond = max distance at which a pair of atoms is considered bonded (distance units) :l +qfactor = max strain at which bias potential goes to 0.0 (unitless) :l +Vmax = estimated height of bias potential (energy units) :l +Tequil = equilibration temperature (temperature units) :l +Dcut = minimum distance between boosted bonds (distance units) :l +alpha = boostostat relaxation time (time units) :l +Btarget = desired time boost factor (unitless) :l +zero or more keyword/value pairs may be appended :l +keyword = {check/ghost} or {check/bias} :l + {check/ghost} values = none + {check/bias} values = Nevery error/warn/ignore :pre +:ule + +[Examples:] + +fix 1 all hyper/local 1.0 0.3 0.8 300.0 :pre + +[Description:] + +This fix is meant to be used with the "hyper"_hyper.html command to +perform a bond-boost local hyperdynamics (LHD) simulation. The role +of this fix is to a select multiple pairs of atoms in the system at +each timestep to add a local bias potential to, which will alter the +dynamics of the system in a manner that effectively accelerates time. +This is in contrast to the "fix hyper/global"_fix_hyper_global.html +command, which can be user to perform a global hyperdynamics (GHD) +simulation, by adding a global bias potential to a single pair of +atoms at each timestep. GHD can time accelerate a small simulation +with up to a few 100 atoms. For larger systems, LHD is needed to +achieve good time acceleration. + +For a system that undergoes rare transition events, where one or more +atoms move over an energy barrier to a new potential energy basin, the +effect of the bias potential is to induce more rapid transitions. +This can lead to a dramatic speed-up in the rate at which events +occurs, without altering their relative frequencies, thus leading to +an overall increase in the elapsed real time of the simulation as +compared to running for the same number of timesteps with normal MD. +See the "hyper"_hyper.html doc page for a more general discussion of +hyperdynamics and citations that explain both GHD and LHD. + +The equations and logic used by this fix and described here to perform +LHD follow the description given in "(Voter2013)"_#Voter2013lhd. The +bond-boost form of a bias potential for HD is due to Miron and +Fichthorn as described in "(Miron)"_#Mironlhd. + +To understand this description, you should first read the description +of the GHD algorithm on the "fix hyper/global"_fix_hyper_global.html +doc page. This description of LHD builds on the GHD description. + +The definition of bonds and Eij are the same for GHD and LHD. The +formulas for Vij(max) and Fij(max) are also the same except for a +pre-factor Cij, explained below. + +The bias energy Vij applied to a bond IJ with maximum strain is + +Vij(max) = Cij * Vmax * (1 - (Eij/q)^2) for abs(Eij) < qfactor + = 0 otherwise :pre + +The derivative of Vij(max) with respect to the position of each atom +in the IJ bond gives a bias force Fij(max) acting on the bond as + +Fij(max) = - dVij(max)/dEij = 2 Cij Vmax Eij / qfactor^2 for abs(Eij) < qfactor + = 0 otherwise :pre + +which can be decomposed into an equal and opposite force acting on +only the two I,J atoms in the IJ bond. + +The key difference is that in GHD a bias energy and force is added (on +a particular timestep) to only one bond (pair of atoms) in the system, +which is the bond with maximum strain Emax. + +In LHD, a bias energy and force can be added to multiple bonds +separated by the specified {Dcut} distance or more. A bond IJ is +biased if it is the maximum strain bond within its local +"neighborhood", which is defined as the bond IJ plus any neighbor +bonds within a distance {Dcut} from IJ. The "distance" between bond +IJ and bond KL is the minimum distance between any of the IK, IL, JK, +JL pairs of atoms. + +For a large system, multiple bonds will typically meet this +requirement, and thus a bias potential Vij(max) will be applied to +many bonds on the same timestep. + +In LHD, all bonds store a Cij prefactor which appears in the Vij(max) +and Fij(max) equations above. Note that the Cij factor scales the +strength of the bias energy and forces whenever bond IJ is the maximum +strain bond in its neighborhood. + +Cij is initialized to 1.0 when a bond between the I,J atoms is first +defined. The specified {Btarget} factor is then used to adjust the +Cij prefactors for each bond every timestep in the following manner. + +An instantaneous boost factor Bij is computed each timestep +for each bond, as + +Bij = exp(beta * Vkl(max)) :pre + +where Vkl(max) is the bias energy of the maxstrain bond KL within bond +IJ's neighborhood, beta = 1/kTequil, and {Tequil} is the temperature +of the system and an argument to this fix. + +NOTE: To run an LHD simulation, the input script must also use the +"fix langevin"_fix_langevin.html command to thermostat the atoms at +the same {Tequil} as specified by this fix, so that the system is +running constant-temperature (NVT) dynamics. LAMMPS does not check +that this is done. + +Note that if IJ = KL, then bond IJ is a biased bond on that timestep, +otherwise it is not. But regardless, the boost factor Bij can be +thought of an estimate of time boost currently being applied within a +local region centered on bond IJ. For LHD, we want this to be the +specified {Btarget} value everywhere in the simulation domain. + +To accomplish this, if Bij < Btarget, the Cij prefactor for bond IJ is +incremented on the current timestep by an amount proportional to the +inverse of the specified {alpha} and the difference (Bij - Btarget). +Conversely if Bij > Btarget, Cij is decremented by the same amount. +This procedure is termed "boostostatting" in +"(Voter2013)"_#Voter2013lhd. It drives all of the individual Cij to +values such that when Vij{max} is applied as a bias to bond IJ, the +resulting boost factor Bij will be close to {Btarget} on average. +Thus the LHD time acceleration factor for the overall system is +effectively {Btarget}. + +Note that in LHD, the boost factor {Btarget} is specified by the user. +This is in contrast to global hyperdynamics (GHD) where the boost +factor varies each timestep and is computed as a function of {Vmax}, +Emax, and {Tequil}; see the "fix hyper/global"_fix_hyper_global.html +doc page for details. + +:line + +Here is additional information on the input parameters for LHD. + +Note that the {cutbond}, {qfactor}, and {Tequil} arguments have the +same meaning as for GHD. The {Vmax} argument is slightly different. +The {Dcut}, {alpha}, and {Btarget} parameters are unique to LHD. + +The {cutbond} argument is the cutoff distance for defining bonds +between pairs of nearby atoms. A pair of I,J atoms in their +equilibrium, minimum-energy configuration, which are separated by a +distance Rij < {cutbond}, are flagged as a bonded pair. Setting +{cubond} to be ~25% larger than the nearest-neighbor distance in a +crystalline lattice is a typical choice for solids, so that bonds +exist only between nearest neighbor pairs. + +The {qfactor} argument is the limiting strain at which the bias +potential goes to 0.0. It is dimensionless, so a value of 0.3 means a +bond distance can be up to 30% larger or 30% smaller than the +equilibrium (quenched) R0ij distance and the two atoms in the bond +could still experience a non-zero bias force. + +If {qfactor} is set too large, then transitions from one energy basin +to another are affected because the bias potential is non-zero at the +transition state (e.g. saddle point). If {qfactor} is set too small +than little boost can be achieved because the Eij strain of some bond in +the system will (nearly) always exceed {qfactor}. A value of 0.3 for +{qfactor} is typically a reasonable value. + +The {Vmax} argument is a fixed prefactor on the bias potential. There +is a also a dynamic prefactor Cij, driven by the choice of {Btarget} +as discussed above. The product of these should be a value less than +the smallest barrier height for an event to occur. Otherwise the +applied bias potential may be large enough (when added to the +interatomic potential) to produce a local energy basin with a maxima +in the center. This can produce artificial energy minima in the same +basin that trap an atom. Or if Cij*{Vmax} is even larger, it may +induce an atom(s) to rapidly transition to another energy basin. Both +cases are "bad dynamics" which violate the assumptions of LHD that +guarantee an accelerated time-accurate trajectory of the system. + +NOTE: It may seem that {Vmax} can be set to any value, and Cij will +compensate to reduce the overall prefactor if necessary. However the +Cij are initialized to 1.0 and the boostostatting procedure typically +operates slowly enough that there can be a time period of bad dynamics +if {Vmax} is set too large. A better strategy is to set {Vmax} to the +smallest barrier height for an event (the same as for GHD), so that +the Cij remain near unity. + +The {Tequil} argument is the temperature at which the system is +simulated; see the comment above about the "fix +langevin"_fix_langevin.html thermostatting. It is also part of the +beta term in the exponential factor that determines how much boost is +achieved as a function of the bias potential. See the discussion of +the {Btarget} argument below. + +As discussed above, the {Dcut} argument is the distance required +between two locally maxstrain bonds for them to both be selected as +biased bonds on the same timestep. Computationally, the larger {Dcut} +is, the more work (computation and communication) must be done each +timestep within the LHD algorithm. And the fewer bonds can be +simultaneously biased, which may mean the specified {Btarget} time +acceleration cannot be achieved. + +Physically {Dcut} should be a long enough distance that biasing two +pairs of atoms that close together will not influence the dynamics of +each pair. E.g. something like 2x the cutoff of the interatomic +potential. In practice a {Dcut} value of ~10 Angstroms seems to work +well for many solid-state systems. + +NOTE: You should insure that ghost atom communication is performed for +a distance of at least {Dcut} + {cutevent} = the distance one or more +atoms move (between quenched states) to be considered an "event". It +is an argument to the "compute event/displace" command used to detect +events. By default the ghost communication distance is set by the +pair_style cutoff, which will typically be < {Dcut}. The "comm_modify +cutoff"_comm_modify.html command should be used to override the ghost +cutoff explicitly, e.g. + +comm_modify cutoff 12.0 :pre + +Note that this fix does not know the {cutevent} parameter, but uses +half the {cutbond} parameter as an estimate to warn if the ghost +cutoff is not long enough. + +As described above the {alpha} argument is a pre-factor in the +boostostat update equation for each bond's Cij prefactor. {Alpha} is +specified in time units, similar to other thermostat or barostat +damping parameters. It is roughly the physical time it will take the +boostostat to adjust a Cij value from a too high (or too low) value to +a correct one. An {alpha} setting of a few ps is typically good for +solid-state systems. Note that the {alpha} argument here is the +inverse of the alpha parameter discussed in +"(Voter2013)"_#Voter2013lhd. + +The {Btarget} argument is the desired time boost factor (a value > 1) +that all the atoms in the system will experience. The elapsed time +t_hyper for an LHD simulation running for {N} timesteps is simply + +t_hyper = Btarget * N*dt :pre + +where dt is the timestep size defined by the "timestep"_timestep.html +command. The effective time acceleration due to LHD is thus t_hyper / +N*dt = Btarget, where N*dt is elapsed time for a normal MD run +of N timesteps. + +You cannot choose an arbitrarily large setting for {Btarget}. The +maximum value you should choose is + +Btarget = exp(beta * Vsmall) :pre + +where Vsmall is the smallest event barrier height in your system, beta += 1/kTequil, and {Tequil} is the specified temperature of the system +(both by this fix and the Langevin thermostat). + +Note that if {Btarget} is set smaller than this, the LHD simulation +will run correctly. There will just be fewer events because the hyper +time (t_hyper equation above) will be shorter. + +NOTE: If you have no physical intuition as to the smallest barrier +height in your system, a reasonable strategy to determine the largest +{Btarget} you can use for an LHD model, is to run a sequence of +simulations with smaller and smaller {Btarget} values, until the event +rate does not change (as a function of hyper time). + +:line + +Here is additional information on the optional keywords for this fix. + +The {check/ghost} keyword turns on extra computation each timestep to +compute statistics about ghost atoms used to determine which bonds to +bias. The output of these stats are the vector values 14 and 15, +described below. If this keyword is not enabled, the output +of the stats will be zero. + +The {check/bias} keyword turns on extra computation and communication +to check if any biased bonds are closer than {Dcut} to each other, +which should not be the case if LHD is operating correctly. Thus it +is a debugging check. The {Nevery} setting determines how often the +check is made. The {error}, {warn}, or {ignore} setting determines +what is done if the count of too-close bonds is not zero. Either the +code will exit, or issue a warning, or silently tally the count. The +count can be output as vector value 17, as described below. If this +keyword is not enabled, the output of that statistic will be 0. + +Note that both of these computations are costly, hence they are only +enabled by these keywords. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information about this fix is written to "binary restart +files"_restart.html. + +The "fix_modify"_fix_modify.html {energy} option is supported by this +fix to add the energy of the bias potential to the the system's +potential energy as part of "thermodynamic output"_thermo_style.html. + +This fix computes a global scalar and global vector of length 21, +which can be accessed by various "output commands"_Howto_output.html. +The scalar is the magnitude of the bias potential (energy units) +applied on the current timestep, summed over all biased bonds. The +vector stores the following quantities: + +1 = # of biased bonds on this step +2 = max strain Eij of any bond on this step (absolute value, unitless) +3 = average bias coeff for all bonds on this step (unitless) +4 = average # of bonds/atom on this step +5 = average neighbor bonds/bond on this step within {Dcut} :ul + +6 = max bond length during this run (distance units) +7 = average # of biased bonds/step during this run +8 = fraction of biased bonds with no bias during this run +9 = fraction of biased bonds with negative strain during this run +10 = average bias coeff for all bonds during this run (unitless) +11 = min bias coeff for any bond during this run (unitless) +12 = max bias coeff for any bond during this run (unitless) + +13 = max drift distance of any bond atom during this run (distance units) +14 = max distance from proc subbox of any ghost atom with maxstrain < qfactor during this run (distance units) +15 = max distance outside my box of any ghost atom with any maxstrain during this run (distance units) +16 = count of ghost atoms that could not be found on reneighbor steps during this run +17 = count of bias overlaps (< Dcut) found during this run + +18 = cumulative hyper time since fix created (time units) +19 = cumulative count of event timesteps since fix created +20 = cumulative count of atoms in events since fix created +21 = cumulative # of new bonds formed since fix created :ul + +The first quantities (1-5) are for the current timestep. Quantities +6-17 are for the current hyper run. They are reset each time a new +hyper run is performed. Quantities 18-21 are cumulative across +multiple runs (since the point in the input script the fix was +defined). + +For value 8, the numerator is a count of all biased bonds on each +timestep whose bias energy = 0.0 due to Eij >= {qfactor}. The +denominator is the count of all biased bonds on all timesteps. + +For value 9, the numerator is a count of all biased bonds on each +timestep with negative strain. The denominator is the count of all +biased bonds on all timesteps. + +Values 13-17 are mostly useful for debugging and diagnostic purposes. + +For value 13, drift is the distance an atom moves between two quenched +states when the second quench determines an event has occurred. Atoms +involved in an event will typically move the greatest distance since +others typically remain near their original quenched position. + +For values 14-16, neighbor atoms in the full neighbor list with cutoff +{Dcut} may be ghost atoms outside a processor's sub-box. Before the +next event occurs they may move further than {Dcut} away from the +sub-box boundary. Value 14 is the furthest (from the sub-box) any +ghost atom in the neighbor list with maxstrain < {qfactor} was +accessed during the run. Value 15 is the same except that the ghost +atom's maxstrain may be >= {qfactor}, which may mean it is about to +participate in an event. Value 16 is a count of how many ghost atoms +could not be found on reneighbor steps, presumably because they moved +too far away due to their participation in an event (which will likely +be detected at the next quench). + +Typical values for 14 and 15 should be slightly larger than {Dcut}, +which accounts for ghost atoms initially at a {Dcut} distance moving +thermally before the next event takes place. + +Note that for values 14 and 15 to be computed, the optional keyword +{check/ghost} must be specified. Otherwise these values will be zero. +This is because computing them incurs overhead, so the values are only +computed if requested. + +Value 16 should be zero or small. As explained above a small count +likely means some ghost atoms were participating in their own events +and moved a longer distance. If the value is large, it likely means +the communication cutoff for ghosts is too close to {Dcut} leading to +many not-found ghost atoms before the next event. This may lead to a +reduced number of bonds being selected for biasing, since the code +assumes those atoms are part of highly strained bonds. As explained +above, the "comm_modify cutoff"_comm_modify.html command can be used +to set a longer cutoff. + +For value 17, no two bonds should be biased if they are within a +{Dcut} distance of each other. This value should be zero, indicating +that no pair of biased bonds are closer than {Dcut} from each other. + +Note that for values 17 to be computed, the optional keyword +{check/bias} must be specified and it determines how often this check +is performed. This is because performing the check incurs overhead, +so if only computed as often as requested. + +The result at the end of the run is the cumulative total from every +timestep the check was made. Note that the value is a count of atoms +in bonds which found other atoms in bonds too close, so it is almost +always an over-count of the number of too-close bonds. + +Value 18 is simply the specified {boost} factor times the number of +timesteps times the timestep size. + +For value 19, events are checked for by the "hyper"_hyper.html command +once every {Nevent} timesteps. This value is the count of those +timesteps on which one (or more) events was detected. It is NOT the +number of distinct events, since more than one event may occur in the +same {Nevent} time window. + +For value 20, each time the "hyper"_hyper.html command checks for an +event, it invokes a compute to flag zero or more atoms as +participating in one or more events. E.g. atoms that have displaced +more than some distance from the previous quench state. Value 20 is +the cumulative count of the number of atoms participating in any of +the events that were found. + +Value 21 tallies the number of new bonds created by the bond reset +operation. Bonds between a specific I,J pair of atoms may persist for +the entire hyperdynamics simulation if neither I or J are involved in +an event. + +The scalar and vector values calculated by this fix are all +"intensive". + +This fix also computes a local vector of length the number of bonds +currently in the system. The value for each bond is its Cij prefactor +(bias coefficient). These values can be can be accessed by various +"output commands"_Howto_output.html. A particularly useful one is the +"fix ave/histo"_fix_ave_histo.html command which can be used to +histogram the Cij values to see if they are distributed reasonably +close to 1.0, which indicates a good choice of {Vmax}. + +The local values calculated by this fix are unitless. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. This fix is not invoked during "energy +minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the REPLICA package. It is only enabled if LAMMPS +was built with that package. See the "Build package"_Build_package.html +doc page for more info. + +[Related commands:] + +"hyper"_hyper.html, "fix hyper/global"_fix_hyper_global.html + +[Default:] + +The check/ghost and check/bias keywords are not enabled by default. + +:line + +:link(Voter2013lhd) +[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, +144110 (2013). + +:link(Mironlhd) +[(Miron)] R. A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003). diff --git a/doc/src/fix_imd.txt b/doc/src/fix_imd.txt index a58cfdb3d3..3e7792d51a 100644 --- a/doc/src/fix_imd.txt +++ b/doc/src/fix_imd.txt @@ -41,7 +41,7 @@ it allows LAMMPS to connect an IMD client, for example the "VMD visualization program"_VMD, so that it can monitor the progress of the simulation and interactively apply forces to selected atoms. -If LAMMPS is compiled with the preprocessor flag -DLAMMPS_ASYNC_IMD +If LAMMPS is compiled with the pre-processor flag -DLAMMPS_ASYNC_IMD then fix imd will use POSIX threads to spawn a IMD communication thread on MPI rank 0 in order to offload data reading and writing from the main execution thread and potentially lower the inferred diff --git a/doc/src/fix_indent.txt b/doc/src/fix_indent.txt index 9931793c0b..ca93c78c79 100644 --- a/doc/src/fix_indent.txt +++ b/doc/src/fix_indent.txt @@ -129,7 +129,7 @@ variable rate equal 1.0 variable r equal "v_r0 + step*dt*v_rate" :pre If the {side} keyword is specified as {out}, which is the default, -then particles outside the indenter are pushded away from its outer +then particles outside the indenter are pushed away from its outer surface, as described above. This only applies to spherical or cylindrical indenters. If the {side} keyword is specified as {in}, the action of the indenter is reversed. Particles inside the indenter diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt index e97c7c3c37..861eed4a6f 100644 --- a/doc/src/fix_langevin.txt +++ b/doc/src/fix_langevin.txt @@ -179,7 +179,7 @@ options. For the {omega} keyword there is also a scale factor of 10.0/3.0 that is applied as a multiplier on the Ff (damping) term in the equation above and of sqrt(10.0/3.0) as a multiplier on the Fr term. This does -not affect the thermostatting behaviour of the Langevin formalism but +not affect the thermostatting behavior of the Langevin formalism but insures that the randomized rotational diffusivity of spherical particles is correct. @@ -217,10 +217,6 @@ the particles. As described below, this energy can then be printed out or added to the potential energy of the system to monitor energy conservation. -NOTE: this accumulated energy does NOT include kinetic energy removed -by the {zero} flag. LAMMPS will print a warning when both options are -active. - The keyword {zero} can be used to eliminate drift due to the thermostat. Because the random forces on different atoms are independent, they do not sum exactly to zero. As a result, this fix @@ -255,7 +251,7 @@ bonds, configurational properties generated with dt = 2.5 fs and tdamp = 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity distribution systematically decreases with increasing timestep, the method should not be used to generate properties that depend on the -velocity distribution, such as the velocity autocorrelation function +velocity distribution, such as the velocity auto-correlation function (VACF). In this example, the velocity distribution at dt = 2.5fs generates an average temperature of 220 K, instead of 300 K. diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index 19a3f87ffc..dae12fb156 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -78,22 +78,22 @@ transform: \begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\} \begin\{equation\} f = \frac m \{M'\}\, F' + f' \end\{equation\} -This fix also thermostates non-polarizable atoms in the group at +This fix also thermostats non-polarizable atoms in the group at temperature {Tcom}, as if they had a massless Drude partner. The Drude particles themselves need not be in the group. The center of -mass and the dipole are thermostated iff the core atom is in the +mass and the dipole are thermostatted iff the core atom is in the group. Note that the thermostat effect of this fix is applied to only the translational degrees of freedom of the particles, which is an important consideration if finite-size particles, which have -rotational degrees of freedom, are being thermostated. The +rotational degrees of freedom, are being thermostatted. The translational degrees of freedom can also have a bias velocity removed -from them before thermostating takes place; see the description below. +from them before thermostatting takes place; see the description below. NOTE: Like the "fix langevin"_fix_langevin.html command, this fix does NOT perform time integration. It only modifies forces to effect -thermostating. Thus you must use a separate time integration fix, like +thermostatting. Thus you must use a separate time integration fix, like "fix nve"_fix_nve.html or "fix nph"_fix_nh.html to actually update the velocities and positions of atoms using the modified forces. Likewise, this fix should not normally be used on atoms that also have @@ -102,7 +102,7 @@ nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html commands. See the "Howto thermostat"_Howto_thermostat.html doc page for a discussion of different ways to compute temperature and perform -thermostating. +thermostatting. :line @@ -126,7 +126,7 @@ comm_modify vel yes :pre :line {Tcom} is the target temperature of the centers of mass, which would -be used to thermostate the non-polarizable atoms. {Tdrude} is the +be used to thermostat the non-polarizable atoms. {Tdrude} is the (normally low) target temperature of the core-Drude particle pairs (dipoles). {Tcom} and {Tdrude} can be specified as an equal-style "variable"_variable.html. If the value is a variable, it should be @@ -139,7 +139,7 @@ functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed time. Thus it is easy to specify a time-dependent temperature. -Like other fixes that perform thermostating, this fix can be used with +Like other fixes that perform thermostatting, this fix can be used with "compute commands"_compute.html that remove a "bias" from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms. This is not done by default, but only if the @@ -147,11 +147,11 @@ atoms. This is not done by default, but only if the compute to this fix that includes such a bias term. See the doc pages for individual "compute commands"_compute.html to determine which ones include a bias. In this case, the thermostat works in the following -manner: bias is removed from each atom, thermostating is performed on +manner: bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in. NOTE: this feature has not been tested. -Note: The temperature thermostating the core-Drude particle pairs +Note: The temperature thermostatting the core-Drude particle pairs should be chosen low enough, so as to mimic as closely as possible the self-consistent minimization. It must however be high enough, so that the dipoles can follow the local electric field exerted by the @@ -213,7 +213,7 @@ the system, but is a bit slower. :l Use two different random seeds to avoid unphysical correlations. :l Temperature is controlled by the fix {langevin/drude}, so the -time-integration fixes do not thermostate. Don't forget to +time-integration fixes do not thermostat. Don't forget to time-integrate both cores and Drude particles. :l Pressure is time-integrated only once by using {nve} for Drude @@ -223,11 +223,11 @@ for both. :l The temperatures of cores and Drude particles are calculated by "compute temp/drude"_compute_temp_drude.html :l -Contrary to the alternative thermostating using Nose-Hoover thermostat +Contrary to the alternative thermostatting using Nose-Hoover thermostat fix {npt} and "fix drude/transform"_fix_drude_transform.html, the {fix_modify} command is not required here, because the fix {nph} computes the global pressure even if its group is {ATOMS}. This is -what we want. If we thermostated {ATOMS} using {npt}, the pressure +what we want. If we thermostatted {ATOMS} using {npt}, the pressure should be the global one, but the temperature should be only that of the cores. That's why the command {fix_modify} should be called in that case. :l @@ -247,7 +247,7 @@ restarted simulation should produce the same behavior. The "fix_modify"_fix_modify.html {temp} option is supported by this fix. You can use it to assign a temperature "compute"_compute.html -you have defined to this fix which will be used in its thermostating +you have defined to this fix which will be used in its thermostatting procedure, as described above. For consistency, the group used by the compute should include the group of this fix and the Drude particles. diff --git a/doc/src/fix_langevin_spin.txt b/doc/src/fix_langevin_spin.txt index d4836706e2..ddd3a0319b 100644 --- a/doc/src/fix_langevin_spin.txt +++ b/doc/src/fix_langevin_spin.txt @@ -25,35 +25,35 @@ fix 2 all langevin/spin 300.0 0.01 21 :pre [Description:] -Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the -magnetic spins associated to the atoms. -Used with "fix nve/spin"_fix_nve_spin.html, this command performs -Brownian dynamics (BD). +Apply a Langevin thermostat as described in "(Mayergoyz)"_#Mayergoyz1 to the +magnetic spins associated to the atoms. +Used with "fix nve/spin"_fix_nve_spin.html, this command performs +Brownian dynamics (BD). A random torque and a transverse dissipation are applied to each spin i according to the following stochastic differential equation: :c,image(Eqs/fix_langevin_spin_sLLG.jpg) with lambda the transverse damping, and eta a random vector. -This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) +This equation is referred to as the stochastic Landau-Lifshitz-Gilbert (sLLG) equation. -The components of eta are drawn from a Gaussian probability law. Their amplitude -is defined as a proportion of the temperature of the external thermostat T (in K +The components of eta are drawn from a Gaussian probability law. Their amplitude +is defined as a proportion of the temperature of the external thermostat T (in K in metal units). More details about this implementation are reported in "(Tranchida)"_#Tranchida2. Note: due to the form of the sLLG equation, this fix has to be defined just -before the nve/spin fix (and after all other magnetic fixes). +before the nve/spin fix (and after all other magnetic fixes). As an example: fix 1 all precession/spin zeeman 0.01 0.0 0.0 1.0 -fix 2 all langevin/spin 300.0 0.01 21 +fix 2 all langevin/spin 300.0 0.01 21 fix 3 all nve/spin lattice yes :pre is correct, but defining a force/spin command after the langevin/spin command -would give an error message. +would give an error message. Note: The random # {seed} must be a positive integer. A Marsaglia random number generator is used. Each processor uses the input seed to @@ -81,10 +81,10 @@ only enabled if LAMMPS was built with this package. See the "Build package"_Build_package.html doc page for more info. The numerical integration has to be performed with {fix nve/spin} -when {fix langevin/spin} is enabled. +when {fix langevin/spin} is enabled. This fix has to be the last defined magnetic fix before the time -integration fix (e.g. {fix nve/spin}). +integration fix (e.g. {fix nve/spin}). [Related commands:] diff --git a/doc/src/fix_latte.txt b/doc/src/fix_latte.txt index c97095bcfc..e6edf6ac8a 100644 --- a/doc/src/fix_latte.txt +++ b/doc/src/fix_latte.txt @@ -58,7 +58,7 @@ LATTE is a code for performing self-consistent charge transfer tight-binding (SC-TB) calculations of total energies and the forces acting on atoms in molecules and solids. This tight-binding method is becoming more and more popular and widely used in chemistry, -biochemistry, material science, etc. +biochemistry, material science, etc. The SC-TB formalism is derived from an expansion of the Kohn-Sham density functional to second order in charge fluctuations about a @@ -66,7 +66,7 @@ reference charge of overlapping atom-centered densities and bond integrals are parameterized using a Slater-Koster tight-binding approach. This procedure, which usually is referred to as the DFTB method has been described in detail by ("Elstner"_#Elstner) and -("Finnis"_#Finnis2) and coworkers. +("Finnis"_#Finnis2) and coworkers. The work of the LATTE developers follows that of Elstner closely with respect to the physical model. However, the development of LATTE is diff --git a/doc/src/fix_meso_move.txt b/doc/src/fix_meso_move.txt new file mode 100644 index 0000000000..abd6e0cca1 --- /dev/null +++ b/doc/src/fix_meso_move.txt @@ -0,0 +1,233 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix meso/move command :h3 + +[Syntax:] + +fix ID group-ID meso/move style args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +meso/move = style name of this fix command :l +style = {linear} or {wiggle} or {rotate} or {variable} :l + {linear} args = Vx Vy Vz + Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL + {wiggle} args = Ax Ay Az period + Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL + period = period of oscillation (time units) + {rotate} args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) + {variable} args = v_dx v_dy v_dz v_vx v_vy v_vz + v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL + v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre + +zero or more keyword/value pairs may be appended :l +keyword = {units} :l + {units} value = {box} or {lattice} :pre +:ule + +[Examples:] + +fix 1 boundary meso/move wiggle 3.0 0.0 0.0 1.0 units box +fix 2 boundary meso/move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0 +fix 2 boundary meso/move variable v_myx v_myy NULL v_VX v_VY NULL :pre + +[Description:] + +Perform updates of position, velocity, internal energy and local +density for mesoscopic particles in the group each timestep using the +specified settings or formulas, without regard to forces on the +particles. This can be useful for boundary, solid bodies or other +particles, whose movement can influence nearby particles. + +The operation of this fix is exactly like that described by the +"fix move"_fix_move.html command, except that particles' density, +internal energy and extrapolated velocity are also updated. + +NOTE: The particles affected by this fix should not be time integrated +by other fixes (e.g. "fix meso"_fix_meso.html, "fix +meso/stationary"_fix_meso_stationary.html), since that will change their +positions and velocities twice. + +NOTE: As particles move due to this fix, they will pass through periodic +boundaries and be remapped to the other side of the simulation box, +just as they would during normal time integration (e.g. via the "fix +meso"_fix_meso.html command). It is up to you to decide whether periodic +boundaries are appropriate with the kind of particle motion you are +prescribing with this fix. + +NOTE: As discussed below, particles are moved relative to their initial +position at the time the fix is specified. These initial coordinates +are stored by the fix in "unwrapped" form, by using the image flags +associated with each particle. See the "dump custom"_dump.html command +for a discussion of "unwrapped" coordinates. See the Atoms section of +the "read_data"_read_data.html command for a discussion of image flags +and how they are set for each particle. You can reset the image flags +(e.g. to 0) before invoking this fix by using the "set image"_set.html +command. + +:line + +The {linear} style moves particles at a constant velocity, so that their +position {X} = (x,y,z) as a function of time is given in vector +notation as + +X(t) = X0 + V * delta :pre + +where {X0} = (x0,y0,z0) is their position at the time the fix is +specified, {V} is the specified velocity vector with components +(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was +specified. This style also sets the velocity of each particle to V = +(Vx,Vy,Vz). If any of the velocity components is specified as NULL, +then the position and velocity of that component is time integrated +the same as the "fix meso"_fix_meso.html command would perform, using +the corresponding force component on the particle. + +Note that the {linear} style is identical to using the {variable} +style with an "equal-style variable"_variable.html that uses the +vdisplace() function. E.g. + +variable V equal 10.0 +variable x equal vdisplace(0.0,$V) +fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre + +The {wiggle} style moves particles in an oscillatory fashion, so that +their position {X} = (x,y,z) as a function of time is given in vector +notation as + +X(t) = X0 + A sin(omega*delta) :pre + +where {X0} = (x0,y0,z0) is their position at the time the fix is +specified, {A} is the specified amplitude vector with components +(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the fix was specified. This style also sets the +velocity of each particle to the time derivative of this expression. +If any of the amplitude components is specified as NULL, then the +position and velocity of that component is time integrated the same as +the "fix meso"_fix_meso.html command would perform, using the +corresponding force component on the particle. + +Note that the {wiggle} style is identical to using the {variable} +style with "equal-style variables"_variable.html that use the +swiggle() and cwiggle() functions. E.g. + +variable A equal 10.0 +variable T equal 5.0 +variable omega equal 2.0*PI/$T +variable x equal swiggle(0.0,$A,$T) +variable v equal v_omega*($A-cwiggle(0.0,$A,$T)) +fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre + +The {rotate} style rotates particles around a rotation axis {R} = +(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The {period} of +the rotation is also specified. The direction of rotation for the +particles around the rotation axis is consistent with the right-hand +rule: if your right-hand thumb points along {R}, then your fingers wrap +around the axis in the direction of rotation. + +This style also sets the velocity of each particle to (omega cross +Rperp) where omega is its angular velocity around the rotation axis and +Rperp is a perpendicular vector from the rotation axis to the particle. + +The {variable} style allows the position and velocity components of +each particle to be set by formulas specified via the +"variable"_variable.html command. Each of the 6 variables is +specified as an argument to the fix as v_name, where name is the +variable name that is defined elsewhere in the input script. + +Each variable must be of either the {equal} or {atom} style. +{Equal}-style variables compute a single numeric quantity, that can be +a function of the timestep as well as of other simulation values. +{Atom}-style variables compute a numeric quantity for each particle, that +can be a function per-atom quantities, such as the particle's position, as +well as of the timestep and other simulation values. Note that this +fix stores the original coordinates of each particle (see note below) so +that per-atom quantity can be used in an atom-style variable formula. +See the "variable"_variable.html command for details. + +The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable} +style are used to calculate a displacement from the particle's original +position at the time the fix was specified. The second 3 variables +(v_vx,v_vy,v_vz) specified are used to compute a velocity for each +particle. + +Any of the 6 variables can be specified as NULL. If both the +displacement and velocity variables for a particular x,y,z component +are specified as NULL, then the position and velocity of that +component is time integrated the same as the "fix meso"_fix_meso.html +command would perform, using the corresponding force component on the +particle. If only the velocity variable for a component is specified as +NULL, then the displacement variable will be used to set the position +of the particle, and its velocity component will not be changed. If only +the displacement variable for a component is specified as NULL, then +the velocity variable will be used to set the velocity of the particle, +and the position of the particle will be time integrated using that +velocity. + +The {units} keyword determines the meaning of the distance units used +to define the {linear} velocity and {wiggle} amplitude and {rotate} +origin. This setting is ignored for the {variable} style. A {box} +value selects standard units as defined by the "units"_units.html +command, e.g. velocity in Angstroms/fmsec and amplitude and position +in Angstroms for units = real. A {lattice} value means the velocity +units are in lattice spacings per time and the amplitude and position +are in lattice spacings. The "lattice"_lattice.html command must have +been previously used to define the lattice spacing. Each of these 3 +quantities may be dependent on the x,y,z dimension, since the lattice +spacings can be different in x,y,z. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +This fix writes the original coordinates of moving particles to "binary +restart files"_restart.html, as well as the initial timestep, so that +the motion can be continuous in a restarted simulation. See the +"read_restart"_read_restart.html command for info on how to re-specify +a fix in an input script that reads a restart file, so that the +operation of the fix continues in an uninterrupted fashion. + +NOTE: Because the move positions are a function of the current +timestep and the initial timestep, you cannot reset the timestep to a +different value after reading a restart file, if you expect a fix move +command to work in an uninterrupted fashion. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. + +This fix produces a per-atom array which can be accessed by various +"output commands"_Howto_output.html. The number of columns for each +atom is 3, and the columns store the original unwrapped x,y,z coords +of each particle. The per-atom values can be accessed on any timestep. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +This fix is not invoked during "energy minimization"_minimize.html. + +[Restrictions:] + +This fix is part of the USER-SDPD package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +This fix requires that atoms store density and internal energy as +defined by the "atom_style meso"_atom_style.html command. + +All particles in the group must be mesoscopic SPH/SDPD particles. + +[Related commands:] + +"fix move"_fix_move.html, "fix meso"_fix_meso.html, +"displace_atoms"_displace_atoms.html + +[Default:] + +The option default is units = lattice. diff --git a/doc/src/fix_modify.txt b/doc/src/fix_modify.txt index f50747948a..f7882c58f7 100644 --- a/doc/src/fix_modify.txt +++ b/doc/src/fix_modify.txt @@ -78,7 +78,7 @@ virial is included in the calculation performed by the "compute pressure"_compute_pressure.html or "compute stress/atom"_compute_stress_atom.html commands. See the "thermo_style"_thermo_style.html command for info -on how pressure is output. +on how pressure is output. NOTE: You must specify the {virial yes} setting for a fix if you are doing "box relaxation"_fix_box_relax.html and diff --git a/doc/src/fix_move.txt b/doc/src/fix_move.txt index 08f38d0ed6..b8ccfbebfe 100644 --- a/doc/src/fix_move.txt +++ b/doc/src/fix_move.txt @@ -51,7 +51,7 @@ integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix nvt"_fix_nh.html), since that will change their positions and velocities twice. -NOTE: As atoms move due to this fix, they will pass thru periodic +NOTE: As atoms move due to this fix, they will pass through periodic boundaries and be remapped to the other side of the simulation box, just as they would during normal time integration (e.g. via the "fix nve"_fix_nve.html command). It is up to you to decide whether @@ -121,7 +121,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T)) fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre The {rotate} style rotates atoms around a rotation axis {R} = -(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of +(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The {period} of the rotation is also specified. The direction of rotation for the atoms around the rotation axis is consistent with the right-hand rule: if your right-hand thumb points along {R}, then your fingers wrap diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index 7f0e5512ae..a46e79c5b0 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -23,7 +23,7 @@ keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l {p0} value = initial pressure in the shock equations (pressure units) {v0} value = initial simulation cell volume in the shock equations (distance^3 units) {e0} value = initial total energy (energy units) - {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) + {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+ {beta} value = scale factor for improved energy conservation :pre :ule @@ -74,7 +74,7 @@ equations, but is used in calculating the deviation from the Hugoniot. The keyword {beta} is a scaling term that can be added to the MSST ionic equations of motion to account for drift in the conserved -quantity during long timescale simulations, similar to a Berendson +quantity during long timescale simulations, similar to a Berendsen thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman2 for more details. The value of {beta} must be between 0.0 and 1.0 inclusive. A value of 0.0 means no contribution, a value of 1.0 means a full diff --git a/doc/src/fix_nh.txt b/doc/src/fix_nh.txt index 644ced4bdc..a07d4e7965 100644 --- a/doc/src/fix_nh.txt +++ b/doc/src/fix_nh.txt @@ -123,7 +123,12 @@ of {Tdamp}. If {Tdamp} is too small, the temperature can fluctuate wildly; if it is too large, the temperature will take a very long time to equilibrate. A good choice for many models is a {Tdamp} of around 100 timesteps. Note that this is NOT the same as 100 time units for -most "units"_units.html settings. +most "units"_units.html settings. A simple way to ensure this, is +via using an "immediate variable"_variable.html expression accessing +the thermo property 'dt', which is the length of the time step. Example: + +fix 1 all nvt temp 300.0 300.0 $(100.0*dt) :pre + :line @@ -281,7 +286,7 @@ negligible. The keyword {tloop} can be used to improve the accuracy of integration scheme at little extra cost. The initial and final updates of the -thermostat variables are broken up into {tloop} substeps, each of +thermostat variables are broken up into {tloop} sub-steps, each of length {dt}/{tloop}. This corresponds to using a first-order Suzuki-Yoshida scheme "(Tuckerman)"_#nh-Tuckerman. The keyword {ploop} does the same thing for the barostat thermostat. @@ -357,7 +362,7 @@ The flip operation is described in more detail in the doc page for "fix deform"_fix_deform.html. Both the barostat dynamics and the atom trajectories are unaffected by this operation. However, if a tilt factor is incremented by a large amount (1.5 times the box length) on -a single timestep, LAMMPS can not accomodate this event and will +a single timestep, LAMMPS can not accommodate this event and will terminate the simulation with an error. This error typically indicates that there is something badly wrong with how the simulation was constructed, such as specifying values of {Pstart} that are too far @@ -621,10 +626,10 @@ over time or the atom count becomes very small. [Default:] -The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = +The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1, ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none, -scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and -not coupled to barostat, otherwise no. +flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd +dimension and not coupled to barostat, otherwise no. :line diff --git a/doc/src/fix_nh_uef.txt b/doc/src/fix_nh_uef.txt index dc05948de3..4d58ee7c49 100644 --- a/doc/src/fix_nh_uef.txt +++ b/doc/src/fix_nh_uef.txt @@ -37,7 +37,7 @@ fix biax_npt all npt/uef temp 400 400 100 erate -0.00001 0.000005 x 1 1 3000 :pr [Description:] This fix can be used to simulate non-equilibrium molecular dynamics -(NEMD) under diagonal flow fields, including uniaxial and biaxial +(NEMD) under diagonal flow fields, including uniaxial and bi-axial flow. Simulations under continuous extensional flow may be carried out for an indefinite amount of time. It is an implementation of the boundary conditions from "(Dobson)"_#Dobson, and also uses numerical diff --git a/doc/src/fix_nve_awpmd.txt b/doc/src/fix_nve_awpmd.txt index c266d46eee..11951c2fe1 100644 --- a/doc/src/fix_nve_awpmd.txt +++ b/doc/src/fix_nve_awpmd.txt @@ -29,7 +29,7 @@ ensemble. The operation of this fix is exactly like that described by the "fix nve"_fix_nve.html command, except that the width and width-velocity of -the electron wavefunctions are also updated. +the electron wave functions are also updated. :line diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index 3112b586d1..fcd8926c13 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -36,7 +36,7 @@ The command is equivalent to the "fix nve"_fix_nve.html. The particles are always considered to have a finite size. An example input file can be found in /examples/USER/cgdna/examples/duplex1/. -Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3. +Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index bb59a8423c..898ca5132b 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -24,7 +24,7 @@ keyword = {angmom} :l [Examples:] -fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 +fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre [Description:] @@ -79,9 +79,9 @@ a Gaussian random number) for speed. :line {Tstart} and {Tstop} have to be constant values, i.e. they cannot -be variables. If used together with the oxDNA force field for +be variables. If used together with the oxDNA force field for coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units -corresponds to T = 300 K. +corresponds to T = 300 K. The {damp} parameter is specified in time units and determines how rapidly the temperature is relaxed. For example, a value of 0.03 @@ -92,10 +92,10 @@ viscosity of the solvent, i.e. a small relaxation time implies a hi-viscosity solvent and vice versa. See the discussion about gamma and viscosity in the documentation for the "fix viscous"_fix_viscous.html command for more details. -Note that the value 78.9375 in the second example above corresponds -to a diffusion constant, which is about an order of magnitude larger +Note that the value 78.9375 in the second example above corresponds +to a diffusion constant, which is about an order of magnitude larger than realistic ones. This has been used to sample configurations faster -in Brownian dynamics simulations. +in Brownian dynamics simulations. The random # {seed} must be a positive integer. A Marsaglia random number generator is used. Each processor uses the input seed to @@ -114,7 +114,7 @@ The scale factor after the {angmom} keyword gives the ratio of the rotational to the translational friction coefficient. An example input file can be found in /examples/USER/cgdna/examples/duplex2/. -Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4. +Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. :line diff --git a/doc/src/fix_nve_spin.txt b/doc/src/fix_nve_spin.txt index 08f0eab61d..af435dc730 100644 --- a/doc/src/fix_nve_spin.txt +++ b/doc/src/fix_nve_spin.txt @@ -27,20 +27,20 @@ fix 1 all nve/spin lattice no :pre Perform a symplectic integration for the spin or spin-lattice system. -The {lattice} keyword defines if the spins are integrated on a lattice +The {lattice} keyword defines if the spins are integrated on a lattice of fixed atoms (lattice = no), or if atoms are moving (lattice = yes). By default (lattice = yes), a spin-lattice integration is performed. -The {nve/spin} fix applies a Suzuki-Trotter decomposition to +The {nve/spin} fix applies a Suzuki-Trotter decomposition to the equations of motion of the spin lattice system, following the scheme: :c,image(Eqs/fix_integration_spin_stdecomposition.jpg) according to the implementation reported in "(Omelyan)"_#Omelyan1. -A sectoring method enables this scheme for parallel calculations. -The implementation of this sectoring algorithm is reported +A sectoring method enables this scheme for parallel calculations. +The implementation of this sectoring algorithm is reported in "(Tranchida)"_#Tranchida1. :line @@ -51,7 +51,7 @@ This fix style can only be used if LAMMPS was built with the SPIN package. See the "Build package"_Build_package.html doc page for more info. -To use the spin algorithm, it is necessary to define a map with +To use the spin algorithm, it is necessary to define a map with the atom_modify command. Typically, by adding the command: atom_modify map array :pre @@ -68,7 +68,7 @@ instead of "array" is also valid. :line :link(Omelyan1) -[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. +[(Omelyan)] Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001). :link(Tranchida1) diff --git a/doc/src/fix_nvt_sllod.txt b/doc/src/fix_nvt_sllod.txt index 7a350e48b5..7050be58b3 100644 --- a/doc/src/fix_nvt_sllod.txt +++ b/doc/src/fix_nvt_sllod.txt @@ -184,5 +184,5 @@ Same as "fix nvt"_fix_nh.html, except tchain = 1. [(Daivis and Todd)] Daivis and Todd, J Chem Phys, 124, 194103 (2006). :link(Daivis-sllod) -[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dyanmics (book), +[(Daivis and Todd)] Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017). diff --git a/doc/src/fix_phonon.txt b/doc/src/fix_phonon.txt index 0c449899df..73f2f4600b 100644 --- a/doc/src/fix_phonon.txt +++ b/doc/src/fix_phonon.txt @@ -46,7 +46,7 @@ based on fluctuation-dissipation theory for a group of atoms. Consider a crystal with \(N\) unit cells in three dimensions labeled \(l = (l_1, l_2, l_3)\) where \(l_i\) are integers. Each unit cell is defined by three linearly independent vectors \(\mathbf\{a\}_1\), -\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelipiped, +\(\mathbf\{a\}_2\), \(\mathbf\{a\}_3\) forming a parallelepiped, containing \(K\) basis atoms labeled \(k\). Based on fluctuation-dissipation theory, the force constant @@ -103,7 +103,7 @@ computation is then done. After every {Noutput} measurements, the matrix \(\mathbf\{G\}(\mathbf\{q\})\) is calculated and inverted to obtain the elastic stiffness coefficients. The dynamical matrices are then constructed and written to {prefix}.bin.timestep files in binary -format and to the file {prefix}.log for each wavevector +format and to the file {prefix}.log for each wave-vector \(\mathbf\{q\}\). A detailed description of this method can be found in @@ -127,7 +127,7 @@ which lattice point; the lattice indices start from 0. An auxiliary code, "latgen"_http://code.google.com/p/latgen, can be employed to generate the compatible map file for various crystals. -In case one simulates an aperiodic system, where the whole simulation +In case one simulates a non-periodic system, where the whole simulation box is treated as a unit cell, one can set {map_file} as {GAMMA}, so that the mapping info will be generated internally and a file is not needed. In this case, the dynamical matrix at only the gamma-point @@ -179,7 +179,8 @@ settings"_Build_settings.html doc page for details. [Related commands:] -"compute msd"_compute_msd.html +"compute msd"_compute_msd.html, +"dynamical_matrix"_dynamical_matrix.html [Default:] diff --git a/doc/src/fix_plumed.txt b/doc/src/fix_plumed.txt new file mode 100644 index 0000000000..97b3150a0b --- /dev/null +++ b/doc/src/fix_plumed.txt @@ -0,0 +1,118 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix plumed command :h3 + +[Syntax:] + +fix ID group-ID plumed keyword value ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +plumed = style name of this fix command :l +keyword = {plumedfile} or {outfile} :l + {plumedfile} arg = name of PLUMED input file to use (default: NULL) + {outfile} arg = name of file on which to write the PLUMED log (default: NULL) :pre +:ule + +[Examples:] + +fix pl all plumed all plumed plumedfile plumed.dat outfile p.log + +[Description:] + +This fix instructs LAMMPS to call the "PLUMED"_plumedhome library, which +allows one to perform various forms of trajectory analysis on the fly +and to also use methods such as umbrella sampling and metadynamics to +enhance the sampling of phase space. + +The documentation included here only describes the fix plumed command +itself. This command is LAMMPS specific, whereas most of the +functionality implemented in PLUMED will work with a range of MD codes, +and when PLUMED is used as a stand alone code for analysis. The full +"documentation for PLUMED"_plumeddocs is available online and included +in the PLUMED source code. The PLUMED library development is hosted at +"https://github.com/plumed/plumed2"_https://github.com/plumed/plumed2 +A detailed discussion of the code can be found in "(PLUMED)"_#PLUMED. + +There is an example input for using this package with LAMMPS in the +examples/USER/plumed directory. + +:line + +The command to make LAMMPS call PLUMED during a run requires two keyword +value pairs pointing to the PLUMED input file and an output file for the +PLUMED log. The user must specify these arguments every time PLUMED is +to be used. Furthermore, the fix plumed command should appear in the +LAMMPS input file [after] relevant input parameters (e.g. the timestep) +have been set. + +The {group-ID} entry is ignored. LAMMPS will always pass all the atoms +to PLUMED and there can only be one instance of the plumed fix at a +time. The way the plumed fix is implemented ensures that the minimum +amount of information required is communicated. Furthermore, PLUMED +supports multiple, completely independent collective variables, multiple +independent biases and multiple independent forms of analysis. There is +thus really no restriction in functionality by only allowing only one +plumed fix in the LAMMPS input. + +The {plumedfile} keyword allows the user to specify the name of the +PLUMED input file. Instructions as to what should be included in a +plumed input file can be found in the "documentation for +PLUMED"_plumeddocs + +The {outfile} keyword allows the user to specify the name of a file in +which to output the PLUMED log. This log file normally just repeats the +information that is contained in the input file to confirm it was +correctly read and parsed. The names of the files in which the results +are stored from the various analysis options performed by PLUMED will +be specified by the user in the PLUMED input file. + +[Restart, fix_modify, output, run start/stop, minimize info:] + +When performing a restart of a calculation that involves PLUMED you must +include a RESTART command in the PLUMED input file as detailed in the +"PLUMED documentation"_plumeddocs. When the restart command is found in +the PLUMED input PLUMED will append to the files that were generated in +the run that was performed previously. No part of the PLUMED restart +data is included in the LAMMPS restart files. Furthermore, any history +dependent bias potentials that were accumulated in previous calculations +will be read in when the RESTART command is included in the PLUMED +input. + +The "fix_modify"_fix_modify.html {energy} option is not supported by +this fix. + +Nothing is computed by this fix that can be accessed by any of the +"output commands"_Howto_output.html within LAMMPS. All the quantities +of interest can be output by commands that are native to PLUMED, +however. + +[Restrictions:] + +This fix is part of the USER-PLUMED package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +There can only be one plumed fix active at a time. + +[Related commands:] + +"fix smd"_fix_smd.html +"fix colvars"_fix_colvars.html + +[Default:] + +The default options are plumedfile = NULL and outfile = NULL + +:line + +:link(PLUMED) +[(PLUMED)] G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014) + +:link(plumeddocs,http://www.plumed.org/documentation) +:link(plumedhome,http://www.plumed.org/) diff --git a/doc/src/fix_poems.txt b/doc/src/fix_poems.txt index 8fe793ce7f..027a15a5ff 100644 --- a/doc/src/fix_poems.txt +++ b/doc/src/fix_poems.txt @@ -106,7 +106,7 @@ off, and there is only a single fix poems defined. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart -files"_restart.html. +files"_restart.html. The "fix_modify"_fix_modify.html {bodyforces} option is supported by this fix style to set whether per-body forces and torques are computed diff --git a/doc/src/fix_precession_spin.txt b/doc/src/fix_precession_spin.txt index d58cd622b0..f16522c7b6 100644 --- a/doc/src/fix_precession_spin.txt +++ b/doc/src/fix_precession_spin.txt @@ -15,7 +15,7 @@ fix ID group precession/spin style args :pre ID, group are documented in "fix"_fix.html command :ulb,l precession/spin = style name of this fix command :l style = {zeeman} or {anisotropy} :l - {zeeman} args = H x y z + {zeeman} args = H x y z H = intensity of the magnetic field (in Tesla) x y z = vector direction of the field {anisotropy} args = K x y z @@ -26,43 +26,43 @@ style = {zeeman} or {anisotropy} :l [Examples:] fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 -fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 +fix 1 all precession/spin anisotropy 0.001 0.0 0.0 1.0 fix 1 all precession/spin zeeman 0.1 0.0 0.0 1.0 anisotropy 0.001 0.0 0.0 1.0 :pre [Description:] Impose a force torque to each magnetic spin in the group. -Style {zeeman} is used for the simulation of the interaction -between the magnetic spins in the defined group and an external +Style {zeeman} is used for the simulation of the interaction +between the magnetic spins in the defined group and an external magnetic field: :c,image(Eqs/force_spin_zeeman.jpg) -with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T -in metal units). +with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T +in metal units). -Style {anisotropy} is used to simulate an easy axis or an easy plane -for the magnetic spins in the defined group: +Style {anisotropy} is used to simulate an easy axis or an easy plane +for the magnetic spins in the defined group: :c,image(Eqs/force_spin_aniso.jpg) -with n defining the direction of the anisotropy, and K (in eV) its intensity. +with n defining the direction of the anisotropy, and K (in eV) its intensity. If K>0, an easy axis is defined, and if K<0, an easy plane is defined. -In both cases, the choice of (x y z) imposes the vector direction for the force. -Only the direction of the vector is important; it's length is ignored. +In both cases, the choice of (x y z) imposes the vector direction for the force. +Only the direction of the vector is important; it's length is ignored. -Both styles can be combined within one single command line. +Both styles can be combined within one single command line. :line [Restart, fix_modify, output, run start/stop, minimize info:] -By default, the energy associated to this fix is not added to the potential -energy of the system. -The "fix_modify"_fix_modify.html {energy} option is supported by this fix -to add this magnetic potential energy to the potential energy of the system, +By default, the energy associated to this fix is not added to the potential +energy of the system. +The "fix_modify"_fix_modify.html {energy} option is supported by this fix +to add this magnetic potential energy to the potential energy of the system, fix 1 all precession/spin zeeman 1.0 0.0 0.0 1.0 fix_modify 1 energy yes :pre diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt index 19e3b0ca40..a62f523c5d 100644 --- a/doc/src/fix_property_atom.txt +++ b/doc/src/fix_property_atom.txt @@ -100,7 +100,7 @@ then you most likely want to set {ghost} yes, since these properties are stored with ghost atoms if you use an "atom_style"_atom_style.html that defines them, and many LAMMPS operations that use molecule IDs or charge, such as neighbor lists and pair styles, will expect ghost -atoms to have these valuse. LAMMPS will issue a warning it you define +atoms to have these values. LAMMPS will issue a warning it you define those vectors but do not set {ghost} yes. NOTE: The properties for ghost atoms are not updated every timestep, @@ -170,7 +170,7 @@ assigned a molecule ID of 4. Note that "atomfile-style variables"_variable.html can also be used in place of atom-style variables, which means in this case that the -molecule IDs could be read-in from a separate file and assinged by the +molecule IDs could be read-in from a separate file and assigned by the "set"_set.html command. This allows you to initialize new per-atom properties in a completely general fashion. diff --git a/doc/src/fix_qeq.txt b/doc/src/fix_qeq.txt index 46d2dd918c..2e3872de60 100644 --- a/doc/src/fix_qeq.txt +++ b/doc/src/fix_qeq.txt @@ -22,7 +22,7 @@ Nevery = perform charge equilibration every this many steps :l cutoff = global cutoff for charge-charge interactions (distance unit) :l tolerance = precision to which charges will be equilibrated :l maxiter = maximum iterations to perform charge equilibration :l -qfile = a filename with QEq parameters :l +qfile = a filename with QEq parameters or {coul/streitz} or {reax/c} :l zero or more keyword/value pairs may be appended :l keyword = {alpha} or {qdamp} or {qstep} :l @@ -122,7 +122,9 @@ field"_#vanDuin paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style reax/c"_pair_reaxc.html. Only the {chi}, {eta}, and {gamma} -parameters from the {qfile} file are used. This style solves partial +parameters from the {qfile} file are used. When using the string +{reax/c} as filename, these parameters are extracted directly from +an active {reax/c} pair style. This style solves partial charges on atoms via the matrix inversion method. A tolerance of 1.0e-6 is usually a good number. @@ -132,7 +134,9 @@ that the interaction between a pair of charged particles is the product of two Slater 1{s} orbitals. The expression for the Slater 1{s} orbital is given under equation (6) of the "Streitz-Mintmire"_#Streitz1 paper. Only the {chi}, {eta}, {zeta}, and -{qcore} parameters from the {qfile} file are used. This style solves +{qcore} parameters from the {qfile} file are used. When using the string +{coul/streitz} as filename, these parameters are extracted directly from +an active {coul/streitz} pair style. This style solves partial charges on atoms via the matrix inversion method. A tolerance of 1.0e-6 is usually a good number. Keyword {alpha} can be used to change the Slater type orbital exponent. diff --git a/doc/src/fix_qmmm.txt b/doc/src/fix_qmmm.txt index 2dbf935f93..c39a58ed86 100644 --- a/doc/src/fix_qmmm.txt +++ b/doc/src/fix_qmmm.txt @@ -22,7 +22,7 @@ fix 1 qmol qmmm [Description:] This fix provides functionality to enable a quantum -mechanics/molecular mechanice (QM/MM) coupling of LAMMPS to a quantum +mechanics/molecular mechanics (QM/MM) coupling of LAMMPS to a quantum mechanical code. The current implementation only supports an ONIOM style mechanical coupling to the "Quantum ESPRESSO"_espresso plane wave DFT package. Electrostatic coupling is in preparation and the @@ -58,7 +58,7 @@ library provided with LAMMPS. See the "Build package"_Build_package.html doc page for more info. The fix is only functional when LAMMPS is built as a library and -linked with a compatible QM program and a QM/MM frontend into a QM/MM +linked with a compatible QM program and a QM/MM front end into a QM/MM executable. See the lib/qmmm/README file for details. [Related commands:] none diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reaxc_bonds.txt similarity index 78% rename from doc/src/fix_reax_bonds.txt rename to doc/src/fix_reaxc_bonds.txt index 06d30d871a..9cd4ed7610 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reaxc_bonds.txt @@ -6,13 +6,12 @@ :line -fix reax/bonds command :h3 fix reax/c/bonds command :h3 fix reax/c/bonds/kk command :h3 [Syntax:] -fix ID group-ID reax/bonds Nevery filename :pre +fix ID group-ID reaxc/bonds Nevery filename :pre ID, group-ID are documented in "fix"_fix.html command reax/bonds = style name of this fix command @@ -21,16 +20,14 @@ filename = name of output file :ul [Examples:] -fix 1 all reax/bonds 100 bonds.tatb fix 1 all reax/c/bonds 100 bonds.reaxc :pre [Description:] -Write out the bond information computed by the ReaxFF potential -specified by "pair_style reax"_pair_reax.html or "pair_style -reax/c"_pair_reaxc.html in the exact same format as the original -stand-alone ReaxFF code of Adri van Duin. The bond information is -written to {filename} on timesteps that are multiples of {Nevery}, +Write out the bond information computed by the ReaxFF potential specified +by "pair_style reax/c"_pair_reaxc.html in the exact same format as the +original stand-alone ReaxFF code of Adri van Duin. The bond information +is written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. @@ -94,12 +91,8 @@ more instructions on how to use the accelerated styles effectively. [Restrictions:] -The fix reax/bonds command requires that the "pair_style -reax"_pair_reax.html be invoked. This fix is part of the REAX -package. It is only enabled if LAMMPS was built with that package, -which also requires the REAX library be built and linked with LAMMPS. The fix reax/c/bonds command requires that the "pair_style -reax/c"_pair_reaxc.html be invoked. This fix is part of the +reax/c"_pair_reaxc.html is invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. @@ -109,7 +102,6 @@ To write gzipped bond files, you must compile LAMMPS with the [Related commands:] -"pair_style reax"_pair_reax.html, "pair_style -reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html +"pair_style reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html [Default:] none diff --git a/doc/src/fix_reaxc_species.txt b/doc/src/fix_reaxc_species.txt index 980384ff34..60fa3a1d70 100644 --- a/doc/src/fix_reaxc_species.txt +++ b/doc/src/fix_reaxc_species.txt @@ -161,7 +161,7 @@ more instructions on how to use the accelerated styles effectively. [Restrictions:] -The fix species currently only works with "pair_style +The "fix reax/c/species" currently only works with "pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style reax/c"_pair_reaxc.html be invoked. This fix is part of the USER-REAXC package. It is only enabled if LAMMPS was built with that @@ -177,8 +177,7 @@ It should be possible to extend it to other reactive pair_styles (such as [Related commands:] -"pair_style reax/c"_pair_reaxc.html, "fix -reax/bonds"_fix_reax_bonds.html +"pair_style reax/c"_pair_reaxc.html, "fix reax/c/bonds"_fix_reaxc_bonds.html [Default:] diff --git a/doc/src/fix_recenter.txt b/doc/src/fix_recenter.txt index cfac756cd1..05c93c3e2f 100644 --- a/doc/src/fix_recenter.txt +++ b/doc/src/fix_recenter.txt @@ -79,10 +79,10 @@ in solvent) without using the {shift} keyword to adjust the positions of all atoms in the system, then the results can be unpredictable. For example, if the molecule is pushed consistently in one direction by a flowing solvent, its velocity will increase. But its coordinates -will be recentered, meaning it is moved back towards the force. Thus +will be re-centered, meaning it is moved back towards the force. Thus over time, the velocity and effective temperature of the molecule could become very large, though it won't actually be moving due to the -recentering. If you are thermostatting the entire system, then the +re-centering. If you are thermostatting the entire system, then the solvent would be cooled to compensate. A better solution for this simulation scenario is to use the "fix spring"_fix_spring.html command to tether the molecule in place. diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 2edc7e3296..8e962f4cc9 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -49,7 +49,7 @@ file, as specified by the "read_data"_read_data.html command, albeit with a time-varying pre-factor coefficient, and except for exclusion rules, as explained below. -For the purpose of forcefield parameter-fitting or mapping a molecular +For the purpose of force field parameter-fitting or mapping a molecular potential energy surface, this fix reduces the hassle and risk associated with modifying data files. In other words, use this fix to temporarily force a molecule to adopt a particular conformation. To @@ -82,7 +82,7 @@ self-consistent minimization problem (see below). In order for a restraint to be effective, the restraint force must typically be significantly larger than the forces associated with -conventional forcefield terms. If the restraint is applied during a +conventional force field terms. If the restraint is applied during a dynamics run (as opposed to during an energy minimization), a large restraint coefficient can significantly reduce the stable timestep size, especially if the atoms are initially far from the preferred @@ -90,7 +90,7 @@ conformation. You may need to experiment to determine what value of K works best for a given application. For the case of finding a minimum energy structure for a single -molecule with particular restraints (e.g. for fitting forcefield +molecule with particular restraints (e.g. for fitting force field parameters or constructing a potential energy surface), commands such as the following may be useful: diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 5d65856735..d45705b2b2 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -247,7 +247,7 @@ of atoms that form rigid bodies. An integer vector defined by the "fix property/atom"_fix_property_atom.html command can be used. Or an "atom-style or atomfile-style variable"_variable.html can be used; the floating-point value produced by the variable is rounded to an -integer. As with bondstyle {molecule}, each set of atoms in the fix +integer. As with bodystyle {molecule}, each set of atoms in the fix groups with the same integer value is treated as a different rigid body. Since fix property/atom vectors and atom-style variables produce values for all atoms, you should be careful to use a fix group diff --git a/doc/src/fix_rigid_meso.txt b/doc/src/fix_rigid_meso.txt new file mode 100644 index 0000000000..0819fdb2fb --- /dev/null +++ b/doc/src/fix_rigid_meso.txt @@ -0,0 +1,350 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +fix rigid/meso command :h3 + +[Syntax:] + +fix ID group-ID rigid/meso bodystyle args keyword values ... :pre + +ID, group-ID are documented in "fix"_fix.html command :ulb,l +rigid/meso = style name of this fix command :l +bodystyle = {single} or {molecule} or {group} :l + {single} args = none + {molecule} args = none + {custom} args = {i_propname} or {v_varname} + i_propname = an integer property defined via fix property/atom + v_varname = an atom-style or atomfile-style variable + {group} args = N groupID1 groupID2 ... + N = # of groups + groupID1, groupID2, ... = list of N group IDs :pre + +zero or more keyword/value pairs may be appended :l +keyword = {reinit} or {force} or {torque} or {infile} :l + {reinit} = {yes} or {no} + {force} values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass force is active + {torque} values = M xflag yflag zflag + M = which rigid body from 1-Nbody (see asterisk form below) + xflag,yflag,zflag = off/on if component of center-of-mass torque is active + {infile} filename + filename = file with per-body values of mass, center-of-mass, moments of inertia :pre +:ule + +[Examples:] + +fix 1 ellipsoid rigid/meso single +fix 1 rods rigid/meso molecule +fix 1 spheres rigid/meso single force 1 off off on +fix 1 particles rigid/meso molecule force 1*5 off off off force 6*10 off off on +fix 2 spheres rigid/meso group 3 sphere1 sphere2 sphere3 torque * off off off :pre + +[Description:] + +Treat one or more sets of mesoscopic SPH/SDPD particles as independent +rigid bodies. This means that each timestep the total force and torque +on each rigid body is computed as the sum of the forces and torques on +its constituent particles. The coordinates and velocities of the +particles in each body are then updated so that the body moves and +rotates as a single entity using the methods described in the paper by +"(Miller)"_#Miller. Density and internal energy of the particles will +also be updated. This is implemented by creating internal data structures +for each rigid body and performing time integration on these data +structures. Positions and velocities of the constituent particles are +regenerated from the rigid body data structures in every time step. This +restricts which operations and fixes can be applied to rigid bodies. See +below for a detailed discussion. + +The operation of this fix is exactly like that described by the +"fix rigid/nve"_fix_rigid.html command, except that particles' density, +internal energy and extrapolated velocity are also updated. + +NOTE: You should not update the particles in rigid bodies via other +time-integration fixes (e.g. "fix meso"_fix_meso.html, +"fix meso/stationary"_fix_meso_stationary.html), or you will have conflicting +updates to positions and velocities resulting in unphysical behavior in most +cases. When performing a hybrid simulation with some atoms in rigid bodies, +and some not, a separate time integration fix like "fix meso"_fix_meso.html +should be used for the non-rigid particles. + +NOTE: These fixes are overkill if you simply want to hold a collection +of particles stationary or have them move with a constant velocity. To +hold particles stationary use "fix +meso/stationary"_fix_meso_stationary.html instead. If you would like to +move particles with a constant velocity use "fix +meso/move"_fix_meso_move.html. + +IMPORTANT NOTE: The aggregate properties of each rigid body are +calculated at the start of a simulation run and are maintained in +internal data structures. The properties include the position and +velocity of the center-of-mass of the body, its moments of inertia, and +its angular momentum. This is done using the properties of the +constituent particles of the body at that point in time (or see the {infile} +keyword option). Thereafter, changing these properties of individual +particles in the body will have no effect on a rigid body's dynamics, unless +they effect any computation of per-particle forces or torques. If the +keyword {reinit} is set to {yes} (the default), the rigid body data +structures will be recreated at the beginning of each {run} command; +if the keyword {reinit} is set to {no}, the rigid body data structures +will be built only at the very first {run} command and maintained for +as long as the rigid fix is defined. For example, you might think you +could displace the particles in a body or add a large velocity to each particle +in a body to make it move in a desired direction before a 2nd run is +performed, using the "set"_set.html or +"displace_atoms"_displace_atoms.html or "velocity"_velocity.html +commands. But these commands will not affect the internal attributes +of the body unless {reinit} is set to {yes}. With {reinit} set to {no} +(or using the {infile} option, which implies {reinit} {no}) the position +and velocity of individual particles in the body will be reset when time +integration starts again. + +:line + +Each rigid body must have two or more particles. A particle can belong +to at most one rigid body. Which particles are in which bodies can be +defined via several options. + +For bodystyle {single} the entire fix group of particles is treated as +one rigid body. + +For bodystyle {molecule}, particles are grouped into rigid bodies by their +respective molecule IDs: each set of particles in the fix group with the +same molecule ID is treated as a different rigid body. Note that particles +with a molecule ID = 0 will be treated as a single rigid body. For a +system with solvent (typically this is particles with molecule ID = 0) +surrounding rigid bodies, this may not be what you want. Thus you +should be careful to use a fix group that only includes particles you +want to be part of rigid bodies. + +Bodystyle {custom} is similar to bodystyle {molecule} except that it +is more flexible in using other per-atom properties to define the sets +of particles that form rigid bodies. An integer vector defined by the +"fix property/atom"_fix_property_atom.html command can be used. Or an +"atom-style or atomfile-style variable"_variable.html can be used; the +floating-point value produced by the variable is rounded to an +integer. As with bodystyle {molecule}, each set of particles in the fix +groups with the same integer value is treated as a different rigid +body. Since fix property/atom vectors and atom-style variables +produce values for all particles, you should be careful to use a fix group +that only includes particles you want to be part of rigid bodies. + +For bodystyle {group}, each of the listed groups is treated as a +separate rigid body. Only particles that are also in the fix group are +included in each rigid body. + +NOTE: To compute the initial center-of-mass position and other +properties of each rigid body, the image flags for each particle in the +body are used to "unwrap" the particle coordinates. Thus you must +insure that these image flags are consistent so that the unwrapping +creates a valid rigid body (one where the particles are close together) +, particularly if the particles in a single rigid body straddle a +periodic boundary. This means the input data file or restart file must +define the image flags for each particle consistently or that you have +used the "set"_set.html command to specify them correctly. If a +dimension is non-periodic then the image flag of each particle must be +0 in that dimension, else an error is generated. + +By default, each rigid body is acted on by other particles which induce +an external force and torque on its center of mass, causing it to +translate and rotate. Components of the external center-of-mass force +and torque can be turned off by the {force} and {torque} keywords. +This may be useful if you wish a body to rotate but not translate, or +vice versa, or if you wish it to rotate or translate continuously +unaffected by interactions with other particles. Note that if you +expect a rigid body not to move or rotate by using these keywords, you +must insure its initial center-of-mass translational or angular +velocity is 0.0. Otherwise the initial translational or angular +momentum, the body has, will persist. + +An xflag, yflag, or zflag set to {off} means turn off the component of +force or torque in that dimension. A setting of {on} means turn on +the component, which is the default. Which rigid body(s) the settings +apply to is determined by the first argument of the {force} and +{torque} keywords. It can be an integer M from 1 to Nbody, where +Nbody is the number of rigid bodies defined. A wild-card asterisk can +be used in place of, or in conjunction with, the M argument to set the +flags for multiple rigid bodies. This takes the form "*" or "*n" or +"n*" or "m*n". If N = the number of rigid bodies, then an asterisk +with no numeric values means all bodies from 1 to N. A leading +asterisk means all bodies from 1 to n (inclusive). A trailing +asterisk means all bodies from n to N (inclusive). A middle asterisk +means all bodies from m to n (inclusive). Note that you can use the +{force} or {torque} keywords as many times as you like. If a +particular rigid body has its component flags set multiple times, the +settings from the final keyword are used. + +For computational efficiency, you should typically define one fix +rigid/meso command which includes all the desired rigid bodies. LAMMPS +will allow multiple rigid/meso fixes to be defined, but it is more +expensive. + +:line + +The keyword/value option pairs are used in the following ways. + +The {reinit} keyword determines, whether the rigid body properties +are re-initialized between run commands. With the option {yes} (the +default) this is done, with the option {no} this is not done. Turning +off the re-initialization can be helpful to protect rigid bodies against +unphysical manipulations between runs or when properties cannot be +easily re-computed (e.g. when read from a file). When using the {infile} +keyword, the {reinit} option is automatically set to {no}. + +:line + +The {infile} keyword allows a file of rigid body attributes to be read +in from a file, rather then having LAMMPS compute them. There are 5 +such attributes: the total mass of the rigid body, its center-of-mass +position, its 6 moments of inertia, its center-of-mass velocity, and +the 3 image flags of the center-of-mass position. For rigid bodies +consisting of point particles or non-overlapping finite-size +particles, LAMMPS can compute these values accurately. However, for +rigid bodies consisting of finite-size particles which overlap each +other, LAMMPS will ignore the overlaps when computing these 4 +attributes. The amount of error this induces depends on the amount of +overlap. To avoid this issue, the values can be pre-computed +(e.g. using Monte Carlo integration). + +The format of the file is as follows. Note that the file does not +have to list attributes for every rigid body integrated by fix rigid. +Only bodies which the file specifies will have their computed +attributes overridden. The file can contain initial blank lines or +comment lines starting with "#" which are ignored. The first +non-blank, non-comment line should list N = the number of lines to +follow. The N successive lines contain the following information: + +ID1 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm +ID2 masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm +... +IDN masstotal xcm ycm zcm ixx iyy izz ixy ixz iyz vxcm vycm vzcm lx ly lz ixcm iycm izcm :pre + +The rigid body IDs are all positive integers. For the {single} +bodystyle, only an ID of 1 can be used. For the {group} bodystyle, +IDs from 1 to Ng can be used where Ng is the number of specified +groups. For the {molecule} bodystyle, use the molecule ID for the +atoms in a specific rigid body as the rigid body ID. + +The masstotal and center-of-mass coordinates (xcm,ycm,zcm) are +self-explanatory. The center-of-mass should be consistent with what +is calculated for the position of the rigid body with all its atoms +unwrapped by their respective image flags. If this produces a +center-of-mass that is outside the simulation box, LAMMPS wraps it +back into the box. + +The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the +values consistent with the current orientation of the rigid body +around its center of mass. The values are with respect to the +simulation box XYZ axes, not with respect to the principal axes of the +rigid body itself. LAMMPS performs the latter calculation internally. + +The (vxcm,vycm,vzcm) values are the velocity of the center of mass. +The (lx,ly,lz) values are the angular momentum of the body. The +(vxcm,vycm,vzcm) and (lx,ly,lz) values can simply be set to 0 if you +wish the body to have no initial motion. + +The (ixcm,iycm,izcm) values are the image flags of the center of mass +of the body. For periodic dimensions, they specify which image of the +simulation box the body is considered to be in. An image of 0 means +it is inside the box as defined. A value of 2 means add 2 box lengths +to get the true value. A value of -1 means subtract 1 box length to +get the true value. LAMMPS updates these flags as the rigid bodies +cross periodic boundaries during the simulation. + +NOTE: If you use the {infile} keyword and write restart +files during a simulation, then each time a restart file is written, +the fix also write an auxiliary restart file with the name +rfile.rigid, where "rfile" is the name of the restart file, +e.g. tmp.restart.10000 and tmp.restart.10000.rigid. This auxiliary +file is in the same format described above. Thus it can be used in a +new input script that restarts the run and re-specifies a rigid fix +using an {infile} keyword and the appropriate filename. Note that the +auxiliary file will contain one line for every rigid body, even if the +original file only listed a subset of the rigid bodies. + +:line + +[Restart, fix_modify, output, run start/stop, minimize info:] + +No information is written to "binary restart files"_restart.html. +If the {infile} keyword is used, an auxiliary file is written out +with rigid body information each time a restart file is written, as +explained above for the {infile} keyword. + +None of the "fix_modify"_fix_modify.html options are relevant to this +fix. + +This fix computes a global array of values which can be accessed by +various "output commands"_Howto_output.html. + +The number of rows in the array is equal to the number of rigid +bodies. The number of columns is 28. Thus for each rigid body, 28 +values are stored: the xyz coords of the center of mass (COM), the xyz +components of the COM velocity, the xyz components of the force acting +on the COM, the components of the 4-vector quaternion representing the +orientation of the rigid body, the xyz components of the angular velocity +of the body around its COM, the xyz components of the torque acting on the +COM, the 3 principal components of the moment of inertia, the xyz components +of the angular momentum of the body around its COM, and the xyz image +flags of the COM. + +The center of mass (COM) for each body is similar to unwrapped +coordinates written to a dump file. It will always be inside (or +slightly outside) the simulation box. The image flags have the same +meaning as image flags for particle positions (see the "dump" command). +This means you can calculate the unwrapped COM by applying the image +flags to the COM, the same as when unwrapped coordinates are written +to a dump file. + +The force and torque values in the array are not affected by the +{force} and {torque} keywords in the fix rigid command; they reflect +values before any changes are made by those keywords. + +The ordering of the rigid bodies (by row in the array) is as follows. +For the {single} keyword there is just one rigid body. For the +{molecule} keyword, the bodies are ordered by ascending molecule ID. +For the {group} keyword, the list of group IDs determines the ordering +of bodies. + +The array values calculated by this fix are "intensive", meaning they +are independent of the number of particles in the simulation. + +No parameter of this fix can be used with the {start/stop} keywords of +the "run"_run.html command. + +This fix is not invoked during "energy minimization"_minimize.html. + +:line + +[Restrictions:] + +This fix is part of the USER-SDPD package and also depends on the RIGID +package. It is only enabled if LAMMPS was built with both packages. See +the "Build package"_Build_package.html doc page for more info. + +This fix requires that atoms store density and internal energy as +defined by the "atom_style meso"_atom_style.html command. + +All particles in the group must be mesoscopic SPH/SDPD particles. + +[Related commands:] + +"fix meso/move"_fix_meso_move.html, "fix rigid"_fix_rigid.html, +"neigh_modify exclude"_neigh_modify.html + +[Default:] + +The option defaults are force * on on on and torque * on on on, +meaning all rigid bodies are acted on by center-of-mass force and +torque. Also reinit = yes. + +:line + +:link(Miller) +[(Miller)] Miller, Eleftheriou, Pattnaik, Ndirango, and Newns, +J Chem Phys, 116, 8649 (2002). diff --git a/doc/src/fix_smd.txt b/doc/src/fix_smd.txt index 774842c7cf..907df7ab1f 100644 --- a/doc/src/fix_smd.txt +++ b/doc/src/fix_smd.txt @@ -137,7 +137,8 @@ package"_Build_package.html doc page for more info. "fix drag"_fix_drag.html, "fix spring"_fix_spring.html, "fix spring/self"_fix_spring_self.html, -"fix spring/rg"_fix_spring_rg.html +"fix spring/rg"_fix_spring_rg.html, +"fix colvars"_fix_colvars.html, "fix plumed"_fix_plumed.html [Default:] none diff --git a/doc/src/fix_srd.txt b/doc/src/fix_srd.txt index 557eee1cfc..018813c361 100644 --- a/doc/src/fix_srd.txt +++ b/doc/src/fix_srd.txt @@ -61,7 +61,7 @@ in "(Hecht)"_#Hecht. The key idea behind using SRD particles as a cheap coarse-grained solvent is that SRD particles do not interact with each other, but only with the solute particles, which in LAMMPS can be spheroids, ellipsoids, or line segments, or triangles, or rigid -bodies containing multiple spheriods or ellipsoids or line segments +bodies containing multiple spheroids or ellipsoids or line segments or triangles. The collision and rotation properties of the model imbue the SRD particles with fluid-like properties, including an effective viscosity. Thus simulations with large solute particles can @@ -117,7 +117,7 @@ Lamda cannot be smaller than 0.6 * hgrid, else an error is generated SRD particles are bounded by Vmax, which is set so that an SRD particle will not advect further than Dmax = 4*lamda in dt_SRD. This means that roughly speaking, Dmax should not be larger than a big -particle diameter, else SRDs may pass thru big particles without +particle diameter, else SRDs may pass through big particles without colliding. A warning is generated if this is the case. Collisions between SRD particles and big particles or walls are diff --git a/doc/src/fix_tfmc.txt b/doc/src/fix_tfmc.txt index 2d4f003607..e14663bebd 100644 --- a/doc/src/fix_tfmc.txt +++ b/doc/src/fix_tfmc.txt @@ -54,7 +54,7 @@ estimation of the effective time scale of such a simulation, but it was later shown that the speed-up one can gain from a tfMC simulation is system- and process-dependent, ranging from none to several orders of magnitude. In general, solid-state processes such as -(re)crystallisation or growth can be accelerated by up to two or three +(re)crystallization or growth can be accelerated by up to two or three orders of magnitude, whereas diffusion in the liquid phase is not accelerated at all. The observed pseudodynamics when using the tfMC method is not the actual dynamics one would obtain using MD, but the diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index 290ee95b9a..d212579510 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -35,7 +35,7 @@ solid of interest and an Einstein crystal. A detailed explanation of how to use this command and choose its parameters for optimal performance and accuracy is given in the paper by "Freitas"_#Freitas1. The paper also presents a short summary of the -theory of nonequilibrium thermodynamic integrations. +theory of nonequilibrium thermodynamic integration. The thermodynamic integration procedure is performed by rescaling the force on each atom. Given an atomic configuration the force (F) on diff --git a/doc/src/fix_tune_kspace.txt b/doc/src/fix_tune_kspace.txt index 147bb1eb3d..f5173b4cae 100644 --- a/doc/src/fix_tune_kspace.txt +++ b/doc/src/fix_tune_kspace.txt @@ -26,7 +26,7 @@ fix 2 all tune/kspace 100 :pre This fix tests each kspace style (Ewald, PPPM, and MSM), and automatically selects the fastest style to use for the remainder of the run. If the fastest style is Ewald or PPPM, the fix also -adjusts the coulomb cutoff towards optimal speed. Future versions +adjusts the Coulombic cutoff towards optimal speed. Future versions of this fix will automatically select other kspace parameters to use for maximum simulation speed. The kspace parameters may include the style, cutoff, grid points in each direction, order, @@ -55,7 +55,7 @@ inordinate amount of wall time to complete. An N of 100 for most problems seems reasonable. Once an optimal parameter set is found, that set is used for the remainder of the run. -This fix uses heristics to guide it's selection of parameter sets to test, +This fix uses heuristics to guide it's selection of parameter sets to test, but the actual timed results will be used to decide which set to use in the simulation. @@ -86,6 +86,9 @@ package"_Build_package.html doc page for more info. Do not set "neigh_modify once yes" or else this fix will never be called. Reneighboring is required. +This fix is not compatible with a hybrid pair style, long-range dispersion, +TIP4P water support, or long-range point dipole support. + [Related commands:] "kspace_style"_kspace_style.html, "boundary"_boundary.html diff --git a/doc/src/fix_wall_gran_region.txt b/doc/src/fix_wall_gran_region.txt index 50d744b305..e4145c003e 100644 --- a/doc/src/fix_wall_gran_region.txt +++ b/doc/src/fix_wall_gran_region.txt @@ -71,12 +71,13 @@ exterior surfaces of regions. Regions can either be primitive shapes (block, sphere, cylinder, etc) or combinations of primitive shapes specified via the {union} or {intersect} region styles. These latter styles can be used to -construct particle containers with complex shapes. Regions can also -move dynamically via the "region"_region.html command keywords (move) -and {rotate}, or change their shape by use of variables as inputs to -the "region"_region.html command. If such a region is used with this -fix, then the region surface will move in time in the corresponding -manner. +construct particle containers with complex shapes. + +Regions can also move dynamically via the "region"_region.html command +keywords (move) and {rotate}, or change their shape by use of variables +as inputs to the "region"_region.html command. If such a region is used +with this fix, then the region surface will move in time in the +corresponding manner. NOTE: As discussed on the "region"_region.html command doc page, regions in LAMMPS do not get wrapped across periodic boundaries. It diff --git a/doc/src/fix_wall_piston.txt b/doc/src/fix_wall_piston.txt index b1968e0d49..475517ed66 100644 --- a/doc/src/fix_wall_piston.txt +++ b/doc/src/fix_wall_piston.txt @@ -26,7 +26,7 @@ keyword = {pos} or {vel} or {ramp} or {units} :l target = target velocity for region immediately ahead of the piston damp = damping parameter (time units) seed = random number seed for langevin kicks - extent = extent of thermostated region (distance units) + extent = extent of thermostatted region (distance units) {units} value = {lattice} or {box} {lattice} = the wall position is defined in lattice units {box} = the wall position is defined in simulation box units :pre @@ -69,7 +69,7 @@ the {ramp} keyword is omitted then the wall/piston moves at a constant velocity defined by {vel}. The {temp} keyword will cause the region immediately in front of the -wall/piston to be thermostated with a Langevin thermostat. This +wall/piston to be thermostatted with a Langevin thermostat. This region moves with the piston. The damping and kicking are measured in the reference frame of the piston. So, a temperature of zero would mean all particles were moving at exactly the speed of the diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt index d43cafbf09..9f787c721f 100644 --- a/doc/src/fix_wall_reflect.txt +++ b/doc/src/fix_wall_reflect.txt @@ -41,7 +41,7 @@ fix top all wall/reflect zhi v_pressdown :pre [Description:] Bound the simulation with one or more walls which reflect particles -in the specified group when they attempt to move thru them. +in the specified group when they attempt to move through them. Reflection means that if an atom moves outside the wall on a timestep by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index 66f6633124..3853bb77a9 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -57,6 +57,8 @@ Fixes :h1 fix_grem fix_halt fix_heat + fix_hyper_global + fix_hyper_local fix_imd fix_indent fix_ipi @@ -73,6 +75,7 @@ Fixes :h1 fix_lineforce fix_manifoldforce fix_meso + fix_meso_move fix_meso_stationary fix_momentum fix_move @@ -117,6 +120,7 @@ Fixes :h1 fix_phonon fix_pimd fix_planeforce + fix_plumed fix_poems fix_pour fix_precession_spin @@ -131,12 +135,13 @@ Fixes :h1 fix_qeq_reax fix_qmmm fix_qtb - fix_reax_bonds + fix_reaxc_bonds fix_reaxc_species fix_recenter fix_restrain fix_rhok fix_rigid + fix_rigid_meso fix_rx fix_saed_vtk fix_setforce diff --git a/doc/src/hyper.txt b/doc/src/hyper.txt new file mode 100644 index 0000000000..b0428a7a3e --- /dev/null +++ b/doc/src/hyper.txt @@ -0,0 +1,192 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +hyper command :h3 + +[Syntax:] + +hyper N Nevent fix-ID compute-ID keyword values ... :pre + +N = # of timesteps to run :ulb,l +Nevent = check for events every this many steps :l +fix-ID = ID of a fix that applies a global or local bias potential, can be NULL :l +compute-ID = ID of a compute that identifies when an event has occurred :l +zero or more keyword/value pairs may be appended :l +keyword = {min} or {dump} or {rebond} :l + {min} values = etol ftol maxiter maxeval + etol = stopping tolerance for energy, used in quenching + ftol = stopping tolerance for force, used in quenching + maxiter = max iterations of minimize, used in quenching + maxeval = max number of force/energy evaluations, used in quenching + {dump} value = dump-ID + dump-ID = ID of dump to trigger whenever an event takes place + {rebond} value = Nrebond + Nrebond = frequency at which to reset bonds, even if no event has occurred + :pre +:ule + +[Examples:] + +compute event all event/displace 1.0 +fix HG mobile hyper/global 3.0 0.3 0.4 800.0 +hyper 5000 100 HG event min 1.0e-6 1.0e-6 100 100 dump 1 dump 5 :pre + +[Description:] + +Run a bond-boost hyperdynamics (HD) simulation where time is +accelerated by application of a bias potential to one or more pairs of +nearby atoms in the system. This command can be used to run both +global and local hyperdynamics. In global HD a single bond within the +system is biased on each timestep. In local HD multiple bonds +(separated by a sufficient distance) can be biased simultaneously at +each timestep. In the bond-boost hyperdynamics context, a "bond" is +not a covalent bond between a pair of atoms in a molecule. Rather it +is simply a pair of nearby atoms as discussed below. + +Both global and local HD are described in "(Voter2013)"_#Voter2013 by +Art Voter and collaborators. Similar to parallel replica dynamics +(PRD), global and local HD are methods for performing accelerated +dynamics that are suitable for infrequent-event systems that obey +first-order kinetics. A good overview of accelerated dynamics methods +for such systems in given in "(Voter2002)"_#Voter2002hd from the same +group. To quote from the review paper: "The dynamical evolution is +characterized by vibrational excursions within a potential basin, +punctuated by occasional transitions between basins." The transition +probability is characterized by p(t) = k*exp(-kt) where k is the rate +constant. Running multiple replicas gives an effective enhancement in +the timescale spanned by the multiple simulations, while waiting for +an event to occur. + +Both HD and PRD produce a time-accurate trajectory that effectively +extends the timescale over which a system can be simulated, but they +do it differently. HD uses a single replica of the system and +accelerates time by biasing the interaction potential in a manner such +that each timestep is effectively longer. PRD creates Nr replicas of +the system and runs dynamics on each independently with a normal +unbiased potential until an event occurs in one of the replicas. The +time between events is reduced by a factor of Nr replicas. For both +methods, per CPU second, more physical time elapses and more events +occur. See the "prd"_prd.html doc page for more info about PRD. + +An HD run has several stages, which are repeated each time an event +occurs, as explained below. The logic for an HD run is as follows: + +quench +create initial list of bonds :pre + +while (time remains): + run dynamics for Nevent steps + quench + check for an event + if event occurred: reset list of bonds + restore pre-quench state :pre + +The list of bonds is the list of atom pairs of atoms that are within a +short cutoff distance of each other after the system energy is +minimized (quenched). This list is created and reset by a "fix +hyper/global"_fix_hyper_global.html or "fix +hyper/local"_fix_hyper_local.html command specified as {fix-ID}. At +every dynamics timestep, the same fix selects one of more bonds to +apply a bias potential to. + +NOTE: The style of fix associated with the specified {fix-ID} +determines whether you are running the global versus local +hyperdynamics algorithm. + +Dynamics (with the bias potential) is run continuously, stopping every +{Nevent} steps to check if a transition event has occurred. The +specified {N} for total steps must be a multiple of {Nevent}. check +is performed by quenching the system and comparing the resulting atom +coordinates to the coordinates from the previous basin. + +A quench is an energy minimization and is performed by whichever +algorithm has been defined by the "min_style"_min_style.html command. +Minimization parameters may be set via the +"min_modify"_min_modify.html command and by the {min} keyword of the +hyper command. The latter are the settings that would be used with +the "minimize"_minimize.html command. Note that typically, you do not +need to perform a highly-converged minimization to detect a transition +event, though you may need to in order to prevent a set of atoms in +the system from relaxing to a saddle point. + +The event check is performed by a compute with the specified +{compute-ID}. Currently there is only one compute that works with the +hyper command, which is the "compute +event/displace"_compute_event_displace.html command. Other +event-checking computes may be added. "Compute +event/displace"_compute_event_displace.html checks whether any atom in +the compute group has moved further than a specified threshold +distance. If so, an event has occurred. + +If this happens, the list of bonds is reset, since some bond pairs +are likely now too far apart, and new pairs are likely close enough +to be considered a bond. The pre-quenched state of the +system (coordinates and velocities) is restored, and dynamics continue. + +At the end of the hyper run, a variety of statistics are output to the +screen and logfile. These include info relevant to both global and +local hyperdynamics, such as the number of events and the elapsed +hyper time (accelerated time), And it includes info specific to one or +the other, depending on which style of fix was specified by {fix-ID}. + +:line + +The optional keywords operate as follows. + +As explained above, the {min} keyword can be used to specify +parameters for the quench. Their meaning is the same +as for the "minimize"_minimize.html command + +The {dump} keyword can be used to trigger a specific dump command with +the specified {dump-ID} to output a snapshot each time an event is +detected. It can be specified multiple times with different {dump-ID} +values, as in the example above. These snapshots will be for the +quenched state of the system on a timestep that is a multiple of +{Nevent}, i.e. a timestep after the event has occurred. Note that any +dump command in the input script will also output snapshots at +whatever timestep interval it defines via its {N} argument; see the +"dump"_dump.html command for details. This means if you only want a +particular dump to output snapshots when events are detected, you +should specify its {N} as a value larger than the length of the +hyperdynamics run. + +As in the code logic above, the bond list is normally only reset when +an event occurs. The {rebond} keyword will force a reset of the bond +list every {Nrebond} steps, even if an event has not occurred. +{Nrebond} must be a multiple of {Nevent}. This can be useful to check +if more frequent resets alter event statistics, perhaps because the +parameters chosen for defining what is a bond and what is an event are +producing bad dynamics in the presence of the bias potential. + +:line + +[Restrictions:] + +This command can only be used if LAMMPS was built with the REPLICA +package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"fix hyper/global"_fix_hyper_global.html, "fix +hyper/local"_fix_hyper_local.html, "compute +event/displace"_compute_event_displace.html, "prd"_prd.html + +[Default:] + +The option defaults are min = 0.1 0.1 40 50 and time = steps. + +:line + +:link(Voter2013) +[(Voter2013)] S. Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, +144110 (2013). + +:link(Voter2002hd) +[(Voter2002)] Voter, Montalenti, Germann, Annual Review of Materials +Research 32, 321 (2002). diff --git a/doc/src/if.txt b/doc/src/if.txt index 513e451034..20caf1a1ef 100644 --- a/doc/src/if.txt +++ b/doc/src/if.txt @@ -107,7 +107,7 @@ print "ALL DONE" :pre Here is an example of a double loop which uses the if and "jump"_jump.html commands to break out of the inner loop when a -condition is met, then continues iterating thru the outer loop. +condition is met, then continues iterating through the outer loop. label loopa variable a loop 5 diff --git a/doc/src/improper_coeff.txt b/doc/src/improper_coeff.txt index 8ed65f9535..1d2083d7ad 100644 --- a/doc/src/improper_coeff.txt +++ b/doc/src/improper_coeff.txt @@ -62,22 +62,14 @@ page for details. :line -Here is an alphabetic list of improper styles defined in LAMMPS. Click on -the style to display the formula it computes and coefficients -specified by the associated "improper_coeff"_improper_coeff.html command. +The list of all improper styles defined in LAMMPS is given on the +"improper_style"_improper_style.html doc page. They are also listed +in more compact form on the "Commands +improper"_Commands_bond.html#improper doc page. -Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The full list of all -improper styles is on the "Commands bond"_Commands_bond.html#improper -doc page. - -"improper_style none"_improper_none.html - turn off improper interactions -"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul - -"improper_style class2"_improper_class2.html - COMPASS (class 2) improper -"improper_style cvff"_improper_cvff.html - CVFF improper -"improper_style harmonic"_improper_harmonic.html - harmonic improper -"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul +On either of those pages, click on the style to display the formula it +computes and its coefficients as specified by the associated +improper_coeff command. :line diff --git a/doc/src/improper_distharm.txt b/doc/src/improper_distharm.txt new file mode 100644 index 0000000000..52815e76aa --- /dev/null +++ b/doc/src/improper_distharm.txt @@ -0,0 +1,53 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +improper_style distharm command :h3 + +[Syntax:] + +improper_style distharm + +[Examples:] + +improper_style distharm +improper_coeff 1 25.0 0.5 :pre + +[Description:] + +The {distharm} improper style uses the potential + +:c,image(Eqs/improper_distharm.jpg) + +where d is the oriented distance between the central atom and the plane formed +by the other three atoms. If the 4 atoms in an improper quadruplet +(listed in the data file read by the "read_data"_read_data.html +command) are ordered I,J,K,L then the L-atom is assumed to be the +central atom. Note that this is different from the convention used +in the improper_style distance. The distance d is oriented and can take +on negative values. This may lead to unwanted behavior if d0 is not equal to zero. + +The following coefficients must be defined for each improper type via +the improper_coeff command as in the example above, or in the data +file or restart files read by the read_data or read_restart commands: + +K (energy/distance^2) +d0 (distance) :ul + +:line + +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +USER-YAFF package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"improper_coeff"_improper_coeff.html + +[Default:] none diff --git a/doc/src/improper_inversion_harmonic.txt b/doc/src/improper_inversion_harmonic.txt index 43ffdeb8e9..857eaecc5f 100644 --- a/doc/src/improper_inversion_harmonic.txt +++ b/doc/src/improper_inversion_harmonic.txt @@ -15,7 +15,7 @@ improper_style inversion/harmonic :pre [Examples:] improper_style inversion/harmonic -improper_coeff 1 18.776340 0.000000 :pre +improper_coeff 1 18.776340 0.000000 :pre [Description:] @@ -24,15 +24,15 @@ out-of-plane angle definition and uses an harmonic potential: :c,image(Eqs/improper_inversion_harmonic.jpg) -where K is the force constant and omega is the angle evaluated for +where K is the force constant and omega is the angle evaluated for all three axis-plane combinations centered around the atom I. For the IL axis and the IJK plane omega looks as follows: :c,image(Eqs/umbrella.jpg) -Note that the {inversion/harmonic} angle term evaluation differs to -the "improper_umbrella"_improper_umbrella.html due to the cyclic -evaluation of all possible angles omega. +Note that the {inversion/harmonic} angle term evaluation differs to +the "improper_umbrella"_improper_umbrella.html due to the cyclic +evaluation of all possible angles omega. The following coefficients must be defined for each improper type via the "improper_coeff"_improper_coeff.html command as in the example @@ -45,7 +45,7 @@ omega0 (degrees) :ul If omega0 = 0 the potential term has a minimum for the planar structure. Otherwise it has two minima at +/- omega0, with a barrier -in between. +in between. :line diff --git a/doc/src/improper_none.txt b/doc/src/improper_none.txt index f97af101fc..78a7489837 100644 --- a/doc/src/improper_none.txt +++ b/doc/src/improper_none.txt @@ -18,7 +18,7 @@ improper_style none :pre [Description:] -Using an improper style of none means imroper forces and energies are +Using an improper style of none means improper forces and energies are not computed, even if quadruplets of improper atoms were listed in the data file read by the "read_data"_read_data.html command. diff --git a/doc/src/improper_sqdistharm.txt b/doc/src/improper_sqdistharm.txt new file mode 100644 index 0000000000..7473fd8c5d --- /dev/null +++ b/doc/src/improper_sqdistharm.txt @@ -0,0 +1,54 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +improper_style sqdistharm command :h3 + +[Syntax:] + +improper_style sqdistharm + +[Examples:] + +improper_style sqdistharm +improper_coeff 1 50.0 0.1 :pre + +[Description:] + +The {sqdistharm} improper style uses the potential + +:c,image(Eqs/improper_sqdistharm.jpg) + +where d is the distance between the central atom and the plane formed +by the other three atoms. If the 4 atoms in an improper quadruplet +(listed in the data file read by the "read_data"_read_data.html +command) are ordered I,J,K,L then the L-atom is assumed to be the +central atom. Note that this is different from the convention used +in the improper_style distance. + +The following coefficients must be defined for each improper type via +the improper_coeff command as in the example above, or in the data +file or restart files read by the read_data or read_restart commands: + +K (energy/distance^4) +d0^2 (distance^2) :ul + +Note that d0^2 (in units distance^2) has be provided and not d0. + +:line + +[Restrictions:] + +This improper style can only be used if LAMMPS was built with the +USER-MISC package. See the "Build package"_Build_package.html doc +page for more info. + +[Related commands:] + +"improper_coeff"_improper_coeff.html + +[Default:] none diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt index f315509fe4..cd72da4d07 100644 --- a/doc/src/improper_style.txt +++ b/doc/src/improper_style.txt @@ -59,10 +59,16 @@ Click on the style to display the formula it computes and coefficients specified by the associated "improper_coeff"_improper_coeff.html command. -Note that there are also additional improper styles submitted by users -which are included in the LAMMPS distribution. The full list of all -improper styles is on the "Commands bond"_Commands_bond.html#improper -doc page. +Click on the style to display the formula it computes, any additional +arguments specified in the improper_style command, and coefficients +specified by the associated "improper_coeff"_improper_coeff.html +command. + +There are also additional accelerated pair styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands +improper"_Commands_bond.html#improper doc page are followed by one or +more of (g,i,k,o,t) to indicate which accelerated styles exist. "none"_improper_none.html - turn off improper interactions "zero"_improper_zero.html - topology but no interactions @@ -72,11 +78,13 @@ doc page. "cossq"_improper_cossq.html - improper with a cosine squared term "cvff"_improper_cvff.html - CVFF improper "distance"_improper_distance.html - improper based on distance between atom planes +"distharm"_improper_distharm.html - improper that is harmonic in the out-of-plane distance "fourier"_improper_fourier.html - improper with multiple cosine terms "harmonic"_improper_harmonic.html - harmonic improper "inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition "ring"_improper_ring.html - improper which prevents planar conformations "umbrella"_improper_umbrella.html - DREIDING improper :ul +"sqdistharm"_improper_sqdistharm.html - improper that is harmonic in the square of the out-of-plane distance :line diff --git a/doc/src/impropers.txt b/doc/src/impropers.txt index ca6c839c95..ce829197fe 100644 --- a/doc/src/impropers.txt +++ b/doc/src/impropers.txt @@ -9,6 +9,7 @@ Improper Styles :h1 improper_cossq improper_cvff improper_distance + improper_distharm improper_fourier improper_harmonic improper_hybrid @@ -16,6 +17,7 @@ Improper Styles :h1 improper_none improper_ring improper_umbrella + improper_sqdistharm improper_zero END_RST --> diff --git a/doc/src/jump.txt b/doc/src/jump.txt index 2e26d32c40..5bda178515 100644 --- a/doc/src/jump.txt +++ b/doc/src/jump.txt @@ -100,7 +100,7 @@ print "ALL DONE" :pre Here is an example of a double loop which uses the if and "jump"_jump.html commands to break out of the inner loop when a -condition is met, then continues iterating thru the outer loop. +condition is met, then continues iterating through the outer loop. label loopa variable a loop 5 diff --git a/doc/src/kim_query.txt b/doc/src/kim_query.txt new file mode 100644 index 0000000000..be46783d82 --- /dev/null +++ b/doc/src/kim_query.txt @@ -0,0 +1,45 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +kim_query command :h3 + +[Syntax:] + +kim_query variable query_function web_query_flags :pre + +variable = name of a (string style) variable where the result of the query is stored +query_function = name of the OpenKIM web API query function to be used +web_query_flags = a series of keyword=value pairs that represent the web query; supported keywords depend on query function :ul + +[Examples:] + +kim_query latconst get_test_result test=TE_156715955670 model=MO_800509458712 & + prop=structure-cubic-crystal-npt species=\["Al"\] keys=\["a"\] units=\["angstrom"\] :pre + +[Description:] + +The kim_query command allows to retrieve properties from the OpenKIM +through a web query. The result is stored in a string style +"variable"_variable.html, the name of which must be given as the first +argument of the kim_query command. The second required argument is the +name of the actual query function (e.g. {get_test_result}). All following +arguments are parameters handed over to the web query in the format +{keyword=value}. This list of supported keywords and the type of how +the value has to be encoded depends on the query function used. +For more details on this, please refer to the OpenKIM homepage. + +[Restrictions:] + +This command is part of the KIM package. It is only enabled if +LAMMPS was built with that package. Furthermore, its correct +functioning depends on compiling LAMMPS with libcurl support. +See the "Build package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_style kim"_pair_kim.html, "variable"_variable.html diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index 41973601d7..65b2174334 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -58,7 +58,7 @@ keyword = {collective} or {compute} or {cutoff/adjust} or {diff} or {disp/auto} [Examples:] kspace_modify mesh 24 24 30 order 6 -kspace_modify slab 3.0 +kspace_modify slab 3.0 kspace_modify scafacos tolerance energy :pre [Description:] @@ -317,19 +317,19 @@ The {tolerance} option affects how the {accuracy} specified with the "kspace_style"_kspace_style.html command is interpreted by ScaFaCoS. The following values may be used: -energy = absolute accuracy in total Coulomic energy -energy_rel = relative accuracy in total Coulomic energy -potential = absolute accuracy in total Coulomic potential -potential_rel = relative accuracy in total Coulomic potential +energy = absolute accuracy in total Coulombic energy +energy_rel = relative accuracy in total Coulombic energy +potential = absolute accuracy in total Coulombic potential +potential_rel = relative accuracy in total Coulombic potential field = absolute accuracy in electric field field_rel = relative accuracy in electric field :ul The values with suffix _rel indicate the tolerance is a relative tolerance; the other values impose an absolute tolerance on the given -quantity. Absoulte tolerance in this case means, that for a given +quantity. Absolute tolerance in this case means, that for a given quantity q and a given absolute tolerance of t_a the result should -be between q-t_a and q+t_a. For a relative tolerance t_r the relative -error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. +be between q-t_a and q+t_a. For a relative tolerance t_r the relative +error should not be greater than t_r, i.e. abs(1 - (result/q)) < t_r. As a consequence of this, the tolerance type should be checked, when performing computations with a high absolute field / energy. E.g. if the total energy in the system is 1000000.0 an absolute tolerance @@ -338,12 +338,12 @@ of 1e-3 would mean that the result has to be between 999999.999 and 1e-9. The energy and energy_rel values, set a tolerance based on the total -Coulomic energy of the system. The potential and potential_rel set a -tolerance based on the per-atom Coulomic energy. The field and +Coulombic energy of the system. The potential and potential_rel set a +tolerance based on the per-atom Coulombic energy. The field and field_rel tolerance types set a tolerance based on the electric field values computed by ScaFaCoS. Since per-atom forces are derived from the per-atom electric field, this effectively sets a tolerance on the -forces, simimlar to other LAMMPS KSpace styles, as explained on the +forces, similar to other LAMMPS KSpace styles, as explained on the "kspace_style"_kspace_style.html doc page. Note that not all ScaFaCoS solvers support all tolerance types. @@ -363,7 +363,7 @@ The {fmm_tuning} option is only relevant when using the FMM method. It activates (value=1) or deactivates (value=0) an internal tuning mechanism for the FMM solver. The tuning operation runs sequentially and can be very time-consuming. Usually it is not needed for systems -with a homogenous charge distribution. The default for this option is +with a homogeneous charge distribution. The default for this option is therefore {0}. The FMM internal tuning is performed once, when the solver is set up. diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 6d8a289470..e1f799a6c9 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -58,7 +58,7 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces smallq = cutoff for charges to be considered (optional) (charge units) {scafacos} values = method accuracy - method = fmm or p2nfft or ewald or direct + method = fmm or p2nfft or p3m or ewald or direct accuracy = desired relative error in forces :pre :ule @@ -193,7 +193,7 @@ the -DFFT_SINGLE compiler switch. The {msm} style invokes a multi-level summation method MSM solver, "(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser -meshes on which direct coulomb solves are done. This method does not +meshes on which direct Coulomb solvers are done. This method does not use FFTs and scales as N. It may therefore be faster than the other K-space solvers for relatively large problems when running on large core counts. MSM can also be used for non-periodic boundary conditions @@ -201,7 +201,7 @@ and for mixed periodic and non-periodic boundaries. MSM is most competitive versus Ewald and PPPM when only relatively low accuracy forces, about 1e-4 relative error or less accurate, -are needed. Note that use of a larger coulomb cutoff (i.e. 15 +are needed. Note that use of a larger Coulombic cutoff (i.e. 15 angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces. @@ -237,7 +237,7 @@ See details on "this page"_Section_packages.html#USER-SCAFACOS. NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all Coulombic interactions, both short- and long-range. Thus you should -NOT use a Coulmbic pair style when using kspace_style scafacos. This +NOT use a Coulombic pair style when using kspace_style scafacos. This also means the total Coulombic energy (short- and long-range) will be tallied for "thermodynamic output"_thermo_style.html command as part of the {elong} keyword; the {ecoul} keyword will be zero. @@ -370,8 +370,7 @@ of these styles. All of the kspace styles are part of the KSPACE package. They are only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. Note that the -KSPACE package is installed by default. +package"_Build_package.html doc page for more info. For MSM, a simulation must be 3d and one can use any combination of periodic, non-periodic, or shrink-wrapped boundaries (specified using @@ -392,6 +391,8 @@ the same bond/angle/dihedral are weighted by the "special_bonds"_special_bonds.html command. Likewise it does not support the "TIP4P water style" where a fictitious charge site is introduced in each water molecule. +Finally, the methods {p3m} and {ewald} do not support computing the +virial, so this contribution is not included. [Related commands:] diff --git a/doc/src/lammps.book b/doc/src/lammps.book index f739712f08..eb8aa16968 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -1,5 +1,5 @@ #HTMLDOC 1.8.28 --t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow +-t pdf14 -f "Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow Manual.html Intro.html Intro_overview.html @@ -150,6 +150,7 @@ dielectric.html dimension.html displace_atoms.html dump.html +dump_adios.html dump_h5md.html dump_image.html dump_modify.html @@ -157,13 +158,16 @@ dump_molfile.html dump_netcdf.html dump_vtk.html dump_cfg_uef.html +dynamical_matrix.html echo.html group.html group2ndx.html +hyper.html if.html include.html info.html jump.html +kim_query.html label.html lattice.html log.html @@ -171,6 +175,7 @@ mass.html message.html min_modify.html min_style.html +min_spin.html minimize.html molecule.html neb.html @@ -277,6 +282,8 @@ fix_gravity.html fix_grem.html fix_halt.html fix_heat.html +fix_hyper_global.html +fix_hyper_local.html fix_imd.html fix_indent.html fix_ipi.html @@ -293,6 +300,7 @@ fix_lb_viscous.html fix_lineforce.html fix_manifoldforce.html fix_meso.html +fix_meso_move.html fix_meso_stationary.html fix_momentum.html fix_move.html @@ -337,6 +345,7 @@ fix_orient.html fix_phonon.html fix_pimd.html fix_planeforce.html +fix_plumed.html fix_poems.html fix_pour.html fix_precession_spin.html @@ -351,11 +360,12 @@ fix_qeq_comb.html fix_qeq_reax.html fix_qmmm.html fix_qtb.html -fix_reax_bonds.html +fix_reaxc_bonds.html fix_reaxc_species.html fix_recenter.html fix_restrain.html fix_rigid.html +fix_rigid_meso.html fix_rhok.html fix_rx.html fix_saed_vtk.html @@ -579,6 +589,7 @@ pair_kim.html pair_kolmogorov_crespi_full.html pair_kolmogorov_crespi_z.html pair_lcbop.html +pair_lebedeva_z.html pair_line_lj.html pair_list.html pair_lj.html @@ -588,16 +599,18 @@ pair_lj_expand.html pair_lj_long.html pair_lj_smooth.html pair_lj_smooth_linear.html -pair_lj_soft.html +pair_fep_soft.html +pair_lj_switch3_coulgauss.html pair_lubricate.html pair_lubricateU.html pair_mdf.html -pair_meam.html +pair_meamc.html pair_meam_spline.html pair_meam_sw_spline.html pair_meso.html pair_mgpt.html pair_mie.html +pair_mm3_switch3_coulgauss.html pair_momb.html pair_morse.html pair_multi_lucy.html @@ -611,10 +624,10 @@ pair_peri.html pair_polymorphic.html pair_python.html pair_quip.html -pair_reax.html pair_reaxc.html pair_resquared.html pair_sdk.html +pair_sdpd_taitwater_isothermal.html pair_smd_hertz.html pair_smd_tlsph.html pair_smd_triangulated_surface.html @@ -661,6 +674,7 @@ bond_harmonic_shift.html bond_harmonic_shift_cut.html bond_hybrid.html bond_morse.html +bond_mm3.html bond_none.html bond_nonlinear.html bond_oxdna.html @@ -680,11 +694,13 @@ angle_cosine_periodic.html angle_cosine_shift.html angle_cosine_shift_exp.html angle_cosine_squared.html +angle_cross.html angle_dipole.html angle_fourier.html angle_fourier_simple.html angle_harmonic.html angle_hybrid.html +angle_mm3.html angle_none.html angle_quartic.html angle_sdk.html @@ -718,6 +734,7 @@ improper_class2.html improper_cossq.html improper_cvff.html improper_distance.html +improper_distharm.html improper_fourier.html improper_harmonic.html improper_hybrid.html @@ -725,6 +742,7 @@ improper_inversion_harmonic.html improper_none.html improper_ring.html improper_umbrella.html +improper_sqdistharm.html improper_zero.html lammps_commands_kspace.html diff --git a/doc/src/message.txt b/doc/src/message.txt index 6ceb62a3e6..0c10af4ac6 100644 --- a/doc/src/message.txt +++ b/doc/src/message.txt @@ -22,11 +22,11 @@ mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l socket-ID for server = *:5555, see description below {mpi/one} arg = none {mpi/two} arg = filename - filename = file used to establish communication bewteen 2 MPI jobs :pre + filename = file used to establish communication between 2 MPI jobs :pre :ule [Examples:] - + message client md file tmp.couple message server md file tmp.couple :pre @@ -93,7 +93,7 @@ localhost:5555 # client and server running on same machine 192.168.1.1:5555 # server is 192.168.1.1 deptbox.uni.edu:5555 # server is deptbox.uni.edu :pre -The server specifes "*:5555" where "*" represents all available +The server specifies "*:5555" where "*" represents all available interfaces on the server's machine, and the port ID must match what the client specifies. diff --git a/doc/src/min_modify.txt b/doc/src/min_modify.txt index 9408eea167..d342e8bf01 100644 --- a/doc/src/min_modify.txt +++ b/doc/src/min_modify.txt @@ -13,11 +13,15 @@ min_modify command :h3 min_modify keyword values ... :pre one or more keyword/value pairs may be listed :ulb,l -keyword = {dmax} or {line} +keyword = {dmax} or {line} or {alpha_damp} or {discrete_factor} {dmax} value = max max = maximum distance for line search to move (distance units) {line} value = {backtrack} or {quadratic} or {forcezero} - backtrack,quadratic,forcezero = style of linesearch to use :pre + backtrack,quadratic,forcezero = style of linesearch to use + {alpha_damp} value = damping + damping = fictitious Gilbert damping for spin minimization (adim) + {discrete_factor} value = factor + factor = discretization factor for adaptive spin timestep (adim) :pre :ule [Examples:] @@ -65,6 +69,17 @@ difference of two large values (energy before and energy after) and that difference may be smaller than machine epsilon even if atoms could move in the gradient direction to reduce forces further. +Keywords {alpha_damp} and {discrete_factor} only make sense when +a "min_spin"_min_spin.html command is declared. +Keyword {alpha_damp} defines an analog of a magnetic Gilbert +damping. It defines a relaxation rate toward an equilibrium for +a given magnetic system. +Keyword {discrete_factor} defines a discretization factor for the +adaptive timestep used in the {spin} minimization. +See "min_spin"_min_spin.html for more information about those +quantities. +Default values are {alpha_damp} = 1.0 and {discrete_factor} = 10.0. + [Restrictions:] none [Related commands:] diff --git a/doc/src/min_spin.txt b/doc/src/min_spin.txt new file mode 100644 index 0000000000..890e324aca --- /dev/null +++ b/doc/src/min_spin.txt @@ -0,0 +1,65 @@ +"LAMMPS WWW Page"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) +:line + +min_style spin command :h3 + +[Syntax:] + +min_style spin :pre + +[Examples:] + +min_style spin :pre + +[Description:] + +Apply a minimization algorithm to use when a "minimize"_minimize.html +command is performed. + +Style {spin} defines a damped spin dynamics with an adaptive +timestep, according to: + +:c,image(Eqs/min_spin_damping.jpg) + +with lambda a damping coefficient (similar to a Gilbert +damping). +Lambda can be defined by setting the {alpha_damp} keyword with the +"min_modify"_min_modify.html command. + +The minimization procedure solves this equation using an +adaptive timestep. The value of this timestep is defined +by the largest precession frequency that has to be solved in the +system: + +:c,image(Eqs/min_spin_timestep.jpg) + +with {|omega|_{max}} the norm of the largest precession frequency +in the system (across all processes, and across all replicas if a +spin/neb calculation is performed). + +Kappa defines a discretization factor {discrete_factor} for the +definition of this timestep. +{discrete_factor} can be defined with the "min_modify"_min_modify.html +command. + +NOTE: The {spin} style replaces the force tolerance by a torque +tolerance. See "minimize"_minimize.html for more explanation. + +[Restrictions:] + +This minimization procedure is only applied to spin degrees of +freedom for a frozen lattice configuration. + +[Related commands:] + +"min_style"_min_style.html, "minimize"_minimize.html, +"min_modify"_min_modify.html + +[Default:] + +The option defaults are {alpha_damp} = 1.0 and {discrete_factor} = +10.0. diff --git a/doc/src/min_style.txt b/doc/src/min_style.txt index 4948a34864..c46c1492b4 100644 --- a/doc/src/min_style.txt +++ b/doc/src/min_style.txt @@ -11,11 +11,12 @@ min_style command :h3 min_style style :pre -style = {cg} or {hftn} or {sd} or {quickmin} or {fire} :ul +style = {cg} or {hftn} or {sd} or {quickmin} or {fire} or {spin} :ul [Examples:] min_style cg +min_style spin min_style fire :pre [Description:] @@ -61,6 +62,10 @@ the velocity non-parallel to the current force vector. The velocity of each atom is initialized to 0.0 by this style, at the beginning of a minimization. +Style {spin} is a damped spin dynamics with an adaptive +timestep. +See the "min/spin"_min_spin.html doc page for more information. + Either the {quickmin} and {fire} styles are useful in the context of nudged elastic band (NEB) calculations via the "neb"_neb.html command. diff --git a/doc/src/minimize.txt b/doc/src/minimize.txt index 73858fc249..ecf1ad0fcf 100644 --- a/doc/src/minimize.txt +++ b/doc/src/minimize.txt @@ -82,12 +82,12 @@ coordinates: where the first term is the sum of all non-bonded "pairwise interactions"_pair_style.html including "long-range Coulombic -interactions"_kspace_style.html, the 2nd thru 5th terms are +interactions"_kspace_style.html, the 2nd through 5th terms are "bond"_bond_style.html, "angle"_angle_style.html, "dihedral"_dihedral_style.html, and "improper"_improper_style.html interactions respectively, and the last term is energy due to "fixes"_fix.html which can act as constraints or apply force to atoms, -such as thru interaction with a wall. See the discussion below about +such as through interaction with a wall. See the discussion below about how fix commands affect minimization. The starting point for the minimization is the current configuration @@ -103,6 +103,13 @@ the line search fails because the step distance backtracks to 0.0 the number of outer iterations or timesteps exceeds {maxiter} the number of total force evaluations exceeds {maxeval} :ul +NOTE: the "minimization style"_min_style.html {spin} replaces +the force tolerance {ftol} by a torque tolerance. +The minimization procedure stops if the 2-norm (length) of the +global torque vector (defined as the cross product between the +spins and their precession vectors omega) is less than {ftol}, +or if any of the other criteria are met. + NOTE: You can also use the "fix halt"_fix_halt.html command to specify a general criterion for exiting a minimization, that is a calculation performed on the state of the current system, as defined by an @@ -190,7 +197,7 @@ it when running dynamics). If you do not do this, the total energy of the system will have discontinuities when the relative distance between any pair of atoms changes from cutoff+epsilon to cutoff-epsilon and the minimizer may behave poorly. Some of the -manybody potentials use splines and other internal cutoffs that +many-body potentials use splines and other internal cutoffs that inherently have this problem. The "long-range Coulombic styles"_kspace_style.html (PPPM, Ewald) are approximate to within the user-specified tolerance, which means their energy and forces may not diff --git a/doc/src/molecule.txt b/doc/src/molecule.txt index 88c6292d8b..4c066b5e2e 100644 --- a/doc/src/molecule.txt +++ b/doc/src/molecule.txt @@ -96,7 +96,7 @@ the molecule (header keyword = com), and the moments of inertia of the molecule (header keyword = inertia). NOTE: The molecule command can be used to define molecules with bonds, -angles, dihedrals, imporopers, or special bond lists of neighbors +angles, dihedrals, impropers, or special bond lists of neighbors within a molecular topology, so that you can later add the molecules to your simulation, via one or more of the commands listed above. Since this topology-related information requires that suitable storage @@ -117,7 +117,7 @@ A molecule file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the -line is blank (only whitespace after comment is deleted), it is +line is blank (only white-space after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn't contain a header keyword, the line begins the body of the file. diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 75d199e0b4..fbe06d3d3d 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -59,7 +59,7 @@ performance speed-up you would see with one or more physical processors per replica. See the "Howto replica"_Howto_replica.html doc page for further discussion. -NOTE: As explained below, a NEB calculation perfoms a damped dynamics +NOTE: As explained below, a NEB calculation performs a damped dynamics minimization across all the replicas. The minimizer uses whatever timestep you have defined in your input script, via the "timestep"_timestep.html command. Often NEB will converge more @@ -211,7 +211,7 @@ over a barrier. The MEP for a transition is defined as a sequence of 3N-dimensional states, each of which has a potential energy gradient parallel to the MEP itself. The configuration of highest energy along a MEP corresponds to a saddle point. The replica states will also be -roughly equally spaced along the MEP due to the inter-replica nugding +roughly equally spaced along the MEP due to the inter-replica nudging force added by the "fix neb"_fix_neb.html command. In the second stage of NEB, the replica with the highest energy is @@ -340,7 +340,7 @@ MaxAtomForce is the maximum force component of any atom in replica i. When a NEB calculation does not converge properly, the supplementary information can help understanding what is going wrong. For instance -when the path angle becomes accute, the definition of tangent used in +when the path angle becomes acute, the definition of tangent used in the NEB calculation is questionable and the NEB cannot may diverge "(Maras)"_#Maras2. diff --git a/doc/src/next.txt b/doc/src/next.txt index aefb2ca594..3f43b1b752 100644 --- a/doc/src/next.txt +++ b/doc/src/next.txt @@ -79,7 +79,7 @@ and after such a LAMMPS run. Here is an example of running a series of simulations using the next command with an {index}-style variable. If this input script is named in.polymer, 8 simulations would be run using data files from -directories run1 thru run8. +directories run1 through run8. variable d index run1 run2 run3 run4 run5 run6 run7 run8 shell cd $d @@ -114,7 +114,7 @@ jump in.script :pre Here is an example of a double loop which uses the "if"_if.html and "jump"_jump.html commands to break out of the inner loop when a -condition is met, then continues iterating thru the outer loop. +condition is met, then continues iterating through the outer loop. label loopa variable a loop 5 diff --git a/doc/src/package.txt b/doc/src/package.txt index 65117ba3c3..c226d7942f 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -40,7 +40,7 @@ args = arguments specific to the style :l {blocksize} value = size size = thread block size for pair force computation {intel} args = NPhi keyword value ... - Nphi = # of coprocessors per node + Nphi = # of co-processors per node zero or more keyword/value pairs may be appended keywords = {mode} or {omp} or {lrt} or {balance} or {ghost} or {tpc} or {tptask} or {no_affinity} {mode} value = {single} or {mixed} or {double} @@ -53,14 +53,14 @@ args = arguments specific to the style :l yes = use additional thread dedicated for some PPPM calculations no = do not dedicate an extra thread for some PPPM calculations {balance} value = split - split = fraction of work to offload to coprocessor, -1 for dynamic + split = fraction of work to offload to co-processor, -1 for dynamic {ghost} value = {yes} or {no} yes = include ghost atoms for offload no = do not include ghost atoms for offload {tpc} value = Ntpc - Ntpc = max number of coprocessor threads per coprocessor core (default = 4) + Ntpc = max number of co-processor threads per co-processor core (default = 4) {tptask} value = Ntptask - Ntptask = max number of coprocessor threads per MPI task (default = 240) + Ntptask = max number of co-processor threads per MPI task (default = 240) {no_affinity} values = none {kokkos} args = keyword value ... zero or more keyword/value pairs may be appended @@ -289,7 +289,7 @@ MAX_BIO_SHARED_TYPES :ul The {blocksize} keyword allows you to tweak the number of threads used per thread block. This number should be a multiple of 32 (for GPUs) and its maximum depends on the specific GPU hardware. Typical choices -are 64, 128, or 256. A larger blocksize increases occupancy of +are 64, 128, or 256. A larger block size increases occupancy of individual GPU cores, but reduces the total number of thread blocks, thus may lead to load imbalance. @@ -298,13 +298,13 @@ thus may lead to load imbalance. The {intel} style invokes settings associated with the use of the USER-INTEL package. All of its settings, except the {omp} and {mode} keywords, are ignored if LAMMPS was not built with Xeon Phi -coprocessor support. All of its settings, including the {omp} and -{mode} keyword are applicable if LAMMPS was built with coprocessor +co-processor support. All of its settings, including the {omp} and +{mode} keyword are applicable if LAMMPS was built with co-processor support. -The {Nphi} argument sets the number of coprocessors per node. +The {Nphi} argument sets the number of co-processors per node. This can be set to any value, including 0, if LAMMPS was not -built with coprocessor support. +built with co-processor support. Optional keyword/value pairs can also be specified. Each has a default value as listed below. @@ -312,14 +312,14 @@ default value as listed below. The {omp} keyword determines the number of OpenMP threads allocated for each MPI task when any portion of the interactions computed by a USER-INTEL pair style are run on the CPU. This can be the case even -if LAMMPS was built with coprocessor support; see the {balance} +if LAMMPS was built with co-processor support; see the {balance} keyword discussion below. If you are running with less MPI tasks/node than there are CPUs, it can be advantageous to use OpenMP threading on the CPUs. -NOTE: The {omp} keyword has nothing to do with coprocessor threads on +NOTE: The {omp} keyword has nothing to do with co-processor threads on the Xeon Phi; see the {tpc} and {tptask} keywords below for a -discussion of coprocessor threads. +discussion of co-processor threads. The {Nthread} value for the {omp} keyword sets the number of OpenMP threads allocated for each MPI task. Setting {Nthread} = 0 (the @@ -346,7 +346,7 @@ command, followed by a "package omp" command, both with a setting of {Nthreads} = 0. The {mode} keyword determines the precision mode to use for -computing pair style forces, either on the CPU or on the coprocessor, +computing pair style forces, either on the CPU or on the co-processor, when using a USER-INTEL supported "pair style"_pair_style.html. It can take a value of {single}, {mixed} which is the default, or {double}. {Single} means single precision is used for the entire @@ -371,13 +371,13 @@ from the USER-INTEL package is not used, then the LRT setting is ignored and no extra threads are generated. Enabling LRT will replace the "run_style"_run_style.html with the {verlet/lrt/intel} style that is identical to the default {verlet} style aside from supporting the -LRT feature. This feature requires setting the preprocessor flag +LRT feature. This feature requires setting the pre-processor flag -DLMP_INTEL_USELRT in the makefile when compiling LAMMPS. The {balance} keyword sets the fraction of "pair -style"_pair_style.html work offloaded to the coprocessor for split +style"_pair_style.html work offloaded to the co-processor for split values between 0.0 and 1.0 inclusive. While this fraction of work is -running on the coprocessor, other calculations will run on the host, +running on the co-processor, other calculations will run on the host, including neighbor and pair calculations that are not offloaded, as well as angle, bond, dihedral, kspace, and some MPI communications. If {split} is set to -1, the fraction of work is dynamically adjusted @@ -388,18 +388,18 @@ The {ghost} keyword determines whether or not ghost atoms, i.e. atoms at the boundaries of processor sub-domains, are offloaded for neighbor and force calculations. When the value = "no", ghost atoms are not offloaded. This option can reduce the amount of data transfer with -the coprocessor and can also overlap MPI communication of forces with -computation on the coprocessor when the "newton pair"_newton.html +the co-processor and can also overlap MPI communication of forces with +computation on the co-processor when the "newton pair"_newton.html setting is "on". When the value = "yes", ghost atoms are offloaded. In some cases this can provide better performance, especially if the {balance} fraction is high. -The {tpc} keyword sets the max # of coprocessor threads {Ntpc} that -will run on each core of the coprocessor. The default value = 4, +The {tpc} keyword sets the max # of co-processor threads {Ntpc} that +will run on each core of the co-processor. The default value = 4, which is the number of hardware threads per core supported by the current generation Xeon Phi chips. -The {tptask} keyword sets the max # of coprocessor threads (Ntptask} +The {tptask} keyword sets the max # of co-processor threads (Ntptask} assigned to each MPI task. The default value = 240, which is the total # of threads an entire current generation Xeon Phi chip can run (240 = 60 cores * 4 threads/core). This means each MPI task assigned @@ -415,7 +415,7 @@ most problems, regardless of how many MPI tasks you assign to a Phi. The {no_affinity} keyword will turn off automatic setting of core affinity for MPI tasks and OpenMP threads on the host when using -offload to a coprocessor. Affinity settings are used when possible +offload to a co-processor. Affinity settings are used when possible to prevent MPI tasks and OpenMP threads from being on separate NUMA domains and to prevent offload threads from interfering with other processes/threads used for LAMMPS. @@ -488,7 +488,7 @@ packing/unpacking operation. The optimal choice for these keywords depends on the input script and the hardware used. The {no} value is useful for verifying that the -Kokkos-based {host} and {device} values are working correctly. +Kokkos-based {host} and {device} values are working correctly. It may also be the fastest choice when using Kokkos styles in MPI-only mode (i.e. with a thread count of 1). @@ -617,7 +617,7 @@ tptask = 240. The default ghost option is determined by the pair style being used. This value is output to the screen in the offload report at the end of each run. Note that all of these settings, except "omp" and "mode", are ignored if LAMMPS was not built with Xeon -Phi coprocessor support. These settings are made automatically if the +Phi co-processor support. These settings are made automatically if the "-sf intel" "command-line switch"_Run_options.html is used. If it is not used, you must invoke the package intel command in your input script or or via the "-pk intel" "command-line diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 74aef41255..8cb1bf34e4 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -19,7 +19,7 @@ pair_coeff * * Al.agni Al [Description:] -Style {agni} style computes the manybody vectorial force components for +Style {agni} style computes the many-body vectorial force components for an atom as :c,image(Eqs/pair_agni.jpg) diff --git a/doc/src/pair_airebo.txt b/doc/src/pair_airebo.txt index c090a39af7..3708fb287d 100644 --- a/doc/src/pair_airebo.txt +++ b/doc/src/pair_airebo.txt @@ -103,7 +103,7 @@ would be 10.2 Angstroms. By default, the longer-ranged interaction is smoothly switched off between 2.16 and 3.0 sigma. By specifying {cutoff_min} in addition -to {cutoff}, the switching can be configured to take place between +to {cutoff}, the switching can be configured to take place between {cutoff_min} and {cutoff}. {cutoff_min} can only be specified if all optional arguments are given. diff --git a/doc/src/pair_atm.txt b/doc/src/pair_atm.txt index 63a450c51a..adbc6b6f3b 100644 --- a/doc/src/pair_atm.txt +++ b/doc/src/pair_atm.txt @@ -118,7 +118,7 @@ pair_coeff 3 3 3 nu10 :pre By default the nu value for all triplets is set to 0.0. Thus it is not required to provide pair_coeff commands that enumerate triplet interactions for all K types. If some I,J,K combination is not -speficied, then there will be no 3-body ATM interactions for that +specified, then there will be no 3-body ATM interactions for that combination and all its permutations. However, as with all pair styles, it is required to specify a pair_coeff command for all I,J combinations, else an error will result. diff --git a/doc/src/pair_awpmd.txt b/doc/src/pair_awpmd.txt index ec87101d0d..4401f5b706 100644 --- a/doc/src/pair_awpmd.txt +++ b/doc/src/pair_awpmd.txt @@ -58,7 +58,7 @@ keyword is used, then an unrestricted Hartree-Fock trial wave function is used. The {free}, {pbc}, and {fix} keywords specify a width constraint on -the electron wavepackets. If the {free} keyword is specified, then there is no +the electron wave packets. If the {free} keyword is specified, then there is no constraint. If the {pbc} keyword is used and {Plen} is specified as -1, then the maximum width is half the shortest box length. If {Plen} is a positive value, then the value is the maximum width. If the @@ -68,7 +68,7 @@ positive value, then the constant width for all electrons is set to {Flen}. The {harm} keyword allow oscillations in the width of the -electron wavepackets. More details are needed. +electron wave packets. More details are needed. The {ermscale} keyword specifies a unitless scaling factor between the electron masses and the width variable mass. More @@ -119,5 +119,5 @@ This pair style can only be used via the {pair} keyword of the [Default:] These are the defaults for the pair_style keywords: {hartree} for the -initial wavefunction, {free} for the wavepacket width. +initial wave function, {free} for the wave packet width. diff --git a/doc/src/pair_bop.txt b/doc/src/pair_bop.txt index f9b4262f0c..ef6fff2963 100644 --- a/doc/src/pair_bop.txt +++ b/doc/src/pair_bop.txt @@ -28,7 +28,7 @@ comm_modify cutoff 14.70 :pre [Description:] The {bop} pair style computes Bond-Order Potentials (BOP) based on -quantum mechanical theory incorporating both sigma and pi bondings. +quantum mechanical theory incorporating both sigma and pi bonding. By analytically deriving the BOP from quantum mechanical theory its transferability to different phases can approach that of quantum mechanical methods. This potential is similar to the original BOP diff --git a/doc/src/pair_buck6d_coul_gauss.txt b/doc/src/pair_buck6d_coul_gauss.txt index 21de3330f4..1f013e91ef 100644 --- a/doc/src/pair_buck6d_coul_gauss.txt +++ b/doc/src/pair_buck6d_coul_gauss.txt @@ -37,55 +37,55 @@ pair_coeff 1 1 1030. 3.061 457.179 4.521 0.608 :pre The {buck6d/coul/gauss} styles evaluate vdW and Coulomb interactions following the MOF-FF force field after -"(Schmid)"_#Schmid. The vdW term of the {buck6d} styles +"(Schmid)"_#Schmid. The vdW term of the {buck6d} styles computes a dispersion damped Buckingham potential: :c,image(Eqs/pair_buck6d.jpg) -where A and C are a force constant, kappa is an ionic-pair dependent -reciprocal length parameter, D is a dispersion correction parameter, +where A and C are a force constant, kappa is an ionic-pair dependent +reciprocal length parameter, D is a dispersion correction parameter, and the cutoff Rc truncates the interaction distance. -The first term in the potential corresponds to the Buckingham -repulsion term and the second term to the dispersion attraction with -a damping correction analog to the Grimme correction used in DFT. -The latter corrects for artifacts occurring at short distances which -become an issue for soft vdW potentials. +The first term in the potential corresponds to the Buckingham +repulsion term and the second term to the dispersion attraction with +a damping correction analog to the Grimme correction used in DFT. +The latter corrects for artifacts occurring at short distances which +become an issue for soft vdW potentials. -The {buck6d} styles include a smoothing function which is invoked -according to the global smoothing parameter within the specified -cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing +The {buck6d} styles include a smoothing function which is invoked +according to the global smoothing parameter within the specified +cutoff. Hereby a parameter of i.e. 0.9 invokes the smoothing within 90% of the cutoff. No smoothing is applied at a value -of 1.0. For the {gauss/dsf} style this smoothing is only applicable +of 1.0. For the {gauss/dsf} style this smoothing is only applicable for the dispersion damped Buckingham potential. For the {gauss/long} styles the smoothing function can also be invoked for the real -space coulomb interactions which enforce continuous energies and +space coulomb interactions which enforce continuous energies and forces at the cutoff. -Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long} -evaluate a Coulomb potential using spherical Gaussian type charge -distributions which effectively dampen electrostatic interactions +Both styles {buck6d/coul/gauss/dsf} and {buck6d/coul/gauss/long} +evaluate a Coulomb potential using spherical Gaussian type charge +distributions which effectively dampen electrostatic interactions for high charges at close distances. The electrostatic potential is thus evaluated as: :c,image(Eqs/pair_coul_gauss.jpg) -where C is an energy-conversion constant, Qi and Qj are the -charges on the 2 atoms, epsilon is the dielectric constant which -can be set by the "dielectric"_dielectric.html command, alpha is -ion pair dependent damping parameter and erf() is the error-function. +where C is an energy-conversion constant, Qi and Qj are the +charges on the 2 atoms, epsilon is the dielectric constant which +can be set by the "dielectric"_dielectric.html command, alpha is +ion pair dependent damping parameter and erf() is the error-function. The cutoff Rc truncates the interaction distance. The style {buck6d/coul/gauss/dsf} computes the Coulomb interaction -via the damped shifted force model described in "(Fennell)"_#Fennell +via the damped shifted force model described in "(Fennell)"_#Fennell approximating an Ewald sum similar to the "pair coul/dsf"_pair_coul.html -styles. In {buck6d/coul/gauss/long} an additional damping factor is -applied to the Coulombic term so it can be used in conjunction with the -"kspace_style"_kspace_style.html command and its {ewald} or {pppm} -options. The Coulombic cutoff in this case separates the real and +styles. In {buck6d/coul/gauss/long} an additional damping factor is +applied to the Coulombic term so it can be used in conjunction with the +"kspace_style"_kspace_style.html command and its {ewald} or {pppm} +options. The Coulombic cutoff in this case separates the real and reciprocal space evaluation of the Ewald sum. If one cutoff is specified it is used for both the vdW and Coulomb -terms. If two cutoffs are specified, the first is used as the cutoff +terms. If two cutoffs are specified, the first is used as the cutoff for the vdW terms, and the second is the cutoff for the Coulombic term. The following coefficients must be defined for each pair of atoms @@ -101,9 +101,9 @@ D (distance^14 units) alpha (distance^-1 units) cutoff (distance units) :ul -The second coefficient, rho, must be greater than zero. The latter -coefficient is optional. If not specified, the global vdW cutoff -is used. +The second coefficient, rho, must be greater than zero. The latter +coefficient is optional. If not specified, the global vdW cutoff +is used. :line diff --git a/doc/src/pair_buck_long.txt b/doc/src/pair_buck_long.txt index 7f3a959ad6..ff27f6b005 100644 --- a/doc/src/pair_buck_long.txt +++ b/doc/src/pair_buck_long.txt @@ -154,8 +154,7 @@ details. This style is part of the KSPACE package. It is only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. Note that the -KSPACE package is installed by default. +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 131e289227..f5344b752f 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -131,7 +131,7 @@ same for both formulas or different depending on whether 2 or 4 arguments are used in the pair_style command. For the {lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an inner and outer cutoff, while the Coulombic term requires only one -cutoff. If the Coulomb cutoff is not specified (2 instead of 3 +cutoff. If the Coulombic cutoff is not specified (2 instead of 3 arguments), the LJ outer cutoff is used for the Coulombic cutoff. In all cases where an inner and outer cutoff are specified, the inner cutoff distance must be less than the outer cutoff. It is typical to @@ -249,8 +249,7 @@ All the styles with {coul/charmm} or {coul/charmmfsh} styles are part of the MOLECULE package. All the styles with {coul/long} style are part of the KSPACE package. They are only enabled if LAMMPS was built with those packages. See the "Build package"_Build_package.html doc -page for more info. Note that the MOLECULE and KSPACE packages are -installed by default. +page for more info. [Related commands:] diff --git a/doc/src/pair_class2.txt b/doc/src/pair_class2.txt index 5fc42e78f9..8d4aa48602 100644 --- a/doc/src/pair_class2.txt +++ b/doc/src/pair_class2.txt @@ -99,6 +99,14 @@ cutoff distance. :line +A version of these styles with a soft core, {lj/cut/soft}, suitable for use in +free energy calculations, is part of the USER-FEP package and is documented with +the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is +only available if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +:line + Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -159,7 +167,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"pair_coeff"_pair_coeff.html +"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html [Default:] none diff --git a/doc/src/pair_coeff.txt b/doc/src/pair_coeff.txt index 88f95b5b2c..a1bbf94e83 100644 --- a/doc/src/pair_coeff.txt +++ b/doc/src/pair_coeff.txt @@ -90,7 +90,7 @@ is looked for in the current working directory. If it is specified as directory, assuming it is a sister directory of the current working directory. If the file is not found, it is then looked for in the directory specified by the LAMMPS_POTENTIALS environment variable. -Thus if this is set to the potentials directory in the LAMMPS distro, +Thus if this is set to the potentials directory in the LAMMPS distribution, then you can use those files from anywhere on your system, without copying them into your working directory. Environment variables are set in different ways for different shells. Here are example settings @@ -114,21 +114,8 @@ The alphabetic list of pair styles defined in LAMMPS is given on the "pair_style"_pair_style.html doc page. They are also listed in more compact form on the "Commands pair"_Commands_pair.html doc page. -Click on the style to display the formula it computes, arguments -specified in the pair_style command, and coefficients specified by the -associated "pair_coeff"_pair_coeff.html command. - -Note that there are also additional pair styles (not listed on the -"pair_style"_pair_style.html doc page) submitted by users which are -included in the LAMMPS distribution. The full list of all pair styles -is on the "Commands pair"_Commands_pair.html doc page. - -There are also additional accelerated pair styles (not listed on the -"pair_style"_pair_style.html doc page) included in the LAMMPS -distribution for faster performance on CPUs, GPUs, and KNLs. The -individual style names on the "Commands pair"_Commands_pair.html doc -page are followed by one or more of (g,i,k,o,t) to indicate which -accelerated styles exist. +Click on the style to display the formula it computes and its +coefficients as specified by the associated pair_coeff command. :line diff --git a/doc/src/pair_coul.txt b/doc/src/pair_coul.txt index cf66c711c8..06838a97e6 100644 --- a/doc/src/pair_coul.txt +++ b/doc/src/pair_coul.txt @@ -197,7 +197,7 @@ option. The Coulombic cutoff specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of +Styles {tip4p/cut} and {tip4p/long} implement the Coulomb part of the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces a massless site located a short distance away from the oxygen atom along the bisector of the HOH angle. The atomic types of the oxygen and @@ -219,7 +219,7 @@ Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is typically best in an -efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. diff --git a/doc/src/pair_cs.txt b/doc/src/pair_cs.txt index 830e0586d2..5fce65d6f7 100644 --- a/doc/src/pair_cs.txt +++ b/doc/src/pair_cs.txt @@ -95,7 +95,7 @@ the "/cs" in the name: except that they correctly treat the special case where the distance between two charged core and shell atoms in the same core/shell pair -approach r = 0.0. +approach r = 0.0. Styles with a "/long" in the name are used with a long-range solver for Coulombic interactions via the "kspace_style"_kspace_style.html diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index bdf37983b6..c695601061 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -82,7 +82,7 @@ styles. Style {lj/sf/dipole/sf} computes "shifted-force" interactions between pairs of particles that each have a charge and/or a point dipole -moment. In general, a shifted-force potential is a (sligthly) modified +moment. In general, a shifted-force potential is a (slightly) modified potential containing extra terms that make both the energy and its derivative go to zero at the cutoff distance; this removes (cutoff-related) problems in energy conservation and any numerical @@ -103,8 +103,8 @@ the two particles. Note that Eqq and Fqq are simply Coulombic energy and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the torques do not act symmetrically. The shifted-force formula for the Lennard-Jones potential is reported in "(Stoddard)"_#Stoddard. The -original (unshifted) formulas for the electrostatic potentials, forces -and torques can be found in "(Price)"_#Price2. The shifted-force +original (non-shifted) formulas for the electrostatic potentials, +forces and torques can be found in "(Price)"_#Price2. The shifted-force electrostatic potentials have been obtained by applying equation 5.13 of "(Allen)"_#Allen2. The formulas for the corresponding forces and torques have been obtained by applying the 'chain rule' as in appendix diff --git a/doc/src/pair_dpd.txt b/doc/src/pair_dpd.txt index 55ae298682..db6fc174d4 100644 --- a/doc/src/pair_dpd.txt +++ b/doc/src/pair_dpd.txt @@ -97,7 +97,7 @@ The GPU-accelerated versions of these styles are implemented based on the work of "(Afshar)"_#Afshar and "(Phillips)"_#Phillips. NOTE: If you are modeling DPD polymer chains, you may want to use the -"pair_style srp"_pair_srp.html command in conjuction with these pair +"pair_style srp"_pair_srp.html command in conjunction with these pair styles. It is a soft segmental repulsive potential (SRP) that can prevent DPD polymer chains from crossing each other. @@ -178,7 +178,7 @@ simulation), you should experiment with forcing reneighboring more often and see if system energies/trajectories change. These pair styles requires you to use the "comm_modify vel -yes"_comm_modify.html command so that velocites are stored by ghost +yes"_comm_modify.html command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the diff --git a/doc/src/pair_dpd_fdt.txt b/doc/src/pair_dpd_fdt.txt index 4f2459588a..52605aef39 100644 --- a/doc/src/pair_dpd_fdt.txt +++ b/doc/src/pair_dpd_fdt.txt @@ -155,7 +155,7 @@ enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. Pair styles {dpd/fdt} and {dpd/fdt/energy} require use of the -"comm_modify vel yes"_comm_modify.html option so that velocites are +"comm_modify vel yes"_comm_modify.html option so that velocities are stored by ghost atoms. Pair style {dpd/fdt/energy} requires "atom_style dpd"_atom_style.html diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index e0e8fbb27e..09eb6ee63a 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -99,7 +99,7 @@ specify EDIP parameters for all permutations of the two elements interacting in three-body configurations. Thus for 3 elements, 27 entries would be required, etc. -At the moment, only a single element parametrization is +At the moment, only a single element parameterization is implemented. However, the author is not aware of other multi-element EDIP parameterization. If you know any and you are interest in that, please contact the author of diff --git a/doc/src/pair_eff.txt b/doc/src/pair_eff.txt index a665654af0..1df94ebecc 100644 --- a/doc/src/pair_eff.txt +++ b/doc/src/pair_eff.txt @@ -48,21 +48,21 @@ structure methods to describe atomic structure, bonding, and chemistry in materials, and of plasma methods to describe nonequilibrium dynamics of large systems with a large number of highly excited electrons. Yet, eFF relies on a simplification of the electronic -wavefunction in which electrons are described as floating Gaussian +wave function in which electrons are described as floating Gaussian wave packets whose position and size respond to the various dynamic forces between interacting classical nuclear particles and spherical -Gaussian electron wavepackets. The wavefunction is taken to be a +Gaussian electron wave packets. The wave function is taken to be a Hartree product of the wave packets. To compensate for the lack of -explicit antisymmetry in the resulting wavefunction, a spin-dependent +explicit antisymmetry in the resulting wave function, a spin-dependent Pauli potential is included in the Hamiltonian. Substituting this -wavefunction into the time-dependent Schrodinger equation produces +wave function into the time-dependent Schrodinger equation produces equations of motion that correspond - to second order - to classical Hamiltonian relations between electron position and size, and their -conjugate momenta. The N-electron wavefunction is described as a +conjugate momenta. The N-electron wave function is described as a product of one-electron Gaussian functions, whose size is a dynamical variable and whose position is not constrained to a nuclear center. This form allows for straightforward propagation of the -wavefunction, with time, using a simple formulation from which the +wave function, with time, using a simple formulation from which the equations of motion are then integrated with conventional MD algorithms. In addition to this spin-dependent Pauli repulsion potential term between Gaussians, eFF includes the electron kinetic @@ -229,7 +229,7 @@ system. The charge for a pseudo-core atom should be given by the number of outer shell electrons. In general, eFF excels at computing the properties of materials in -extreme conditions and tracing the system dynamics over multi-picosend +extreme conditions and tracing the system dynamics over multi-picosecond timescales; this is particularly relevant where electron excitations can change significantly the nature of bonding in the system. It can capture with surprising accuracy the behavior of such systems because @@ -289,7 +289,7 @@ such as radius, radial velocity, and radial force, as defined by the this. Thes pair styles require you to use the "comm_modify vel -yes"_comm_modify.html command so that velocites are stored by ghost +yes"_comm_modify.html command so that velocities are stored by ghost atoms. [Related commands:] diff --git a/doc/src/pair_extep.txt b/doc/src/pair_extep.txt index 3acad1132d..5d69df69e9 100644 --- a/doc/src/pair_extep.txt +++ b/doc/src/pair_extep.txt @@ -35,6 +35,6 @@ interactions as described in "(Los2017)"_#Los2017. :line :link(Los2017) -[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride: -Energetics and elastic properties of pristine and defective h-BN", +[(Los2017)] J. H. Los et al. "Extended Tersoff potential for boron nitride: +Energetics and elastic properties of pristine and defective h-BN", Phys. Rev. B 96 (184108), 2017. diff --git a/doc/src/pair_lj_soft.txt b/doc/src/pair_fep_soft.txt similarity index 50% rename from doc/src/pair_lj_soft.txt rename to doc/src/pair_fep_soft.txt index 9bcc83fa66..d5e848cd1e 100644 --- a/doc/src/pair_lj_soft.txt +++ b/doc/src/pair_fep_soft.txt @@ -16,18 +16,21 @@ pair_style lj/cut/tip4p/long/soft command :h3 pair_style lj/cut/tip4p/long/soft/omp command :h3 pair_style lj/charmm/coul/long/soft command :h3 pair_style lj/charmm/coul/long/soft/omp command :h3 -pair_style coul/cut/soft command :h3 +pair_style lj/class2/soft command :h3 +pair_style lj/class2/coul/cut/soft command :h3 +pair_style lj/class2/coul/long/soft command :h3 + pair_style coul/cut/soft command :h3 pair_style coul/cut/soft/omp command :h3 pair_style coul/long/soft command :h3 pair_style coul/long/soft/omp command :h3 pair_style tip4p/long/soft command :h3 pair_style tip4p/long/soft/omp command :h3 - +pair_style morse/soft command :h3 [Syntax:] pair_style style args :pre -style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft} +style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {lj/class2/soft} or {lj/class2/coul/cut/soft} or {lj/class2/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft} or {morse/soft} args = list of arguments for a particular style :ul {lj/cut/soft} args = n alpha_lj cutoff n, alpha_LJ = parameters of soft-core potential @@ -51,6 +54,17 @@ args = list of arguments for a particular style :ul n, alpha_LJ, alpha_C = parameters of the soft-core potential inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args) cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args) + {lj/class2/soft} args = n alpha_lj cutoff + n, alpha_LJ = parameters of soft-core potential + cutoff = global cutoff for Lennard-Jones interactions (distance units) + {lj/class2/coul/cut/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) + n, alpha_LJ, alpha_C = parameters of soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + {lj/class2/coul/long/soft} args = n alpha_LJ alpha_C cutoff (cutoff2) + n, alpha_LJ, alpha_C = parameters of soft-core potential + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) {coul/cut/soft} args = n alpha_C cutoff n, alpha_C = parameters of the soft-core potential cutoff = global cutoff for Coulomb interactions (distance units) @@ -63,6 +77,10 @@ args = list of arguments for a particular style :ul qdist = distance from O atom to massless charge (distance units) n, alpha_C = parameters of the soft-core potential cutoff = global cutoff for Coulomb interactions (distance units) + {morse/soft} args = n lf cutoff + n = soft-core parameter + lf = transformation range is lf < lambda < 1 + cutoff = global cutoff for Morse interactions (distance units) :pre [Examples:] @@ -93,6 +111,12 @@ pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 pair_coeff * * 0.28 3.1 1.0 pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 :pre +pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 +pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 0.0 10.0 +pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 :pre + pair_style coul/long/soft 1.0 10.0 9.5 pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 :pre @@ -101,17 +125,31 @@ pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 pair_coeff * * 1.0 pair_coeff 1 1 1.0 9.5 :pre +pair_style morse/soft 4 0.9 10.0 +pair_coeff * * 100.0 2.0 1.5 1.0 +pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre + [Description:] -The {lj/cut/soft} style and substyles compute the 12/6 Lennard-Jones -and Coulomb potential modified by a soft core, in order to avoid -singularities during free energy calculations when sites are created -or annihilated "(Beutler)"_#Beutler, +These pair styles have a soft repulsive core, tunable by a parameter lambda, +in order to avoid singularities during free energy calculations when sites are +created or annihilated "(Beutler)"_#Beutler. When lambda tends to 0 the pair +interaction vanishes with a soft repulsive core. When lambda tends to 1, the pair +interaction approaches the normal, non-soft potential. These pair styles +are suited for "alchemical" free energy calculations using the "fix +adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html commands. + +The {lj/cut/soft} style and related sub-styles compute the 12-6 Lennard-Jones +and Coulomb potentials modified by a soft core, with the functional form :c,image(Eqs/pair_lj_soft.jpg) -Coulomb interactions are also damped with a soft core at short -distance, +The {lj/class2/soft} style is a 9-6 potential with the exponent of the +denominator of the first term in brackets taking the value 1.5 instead of 2 +(other details differ, see the form of the potential in +"pair_class2"_pair_class2.html). + +Coulomb interactions can also be damped with a soft core at short distance, :c,image(Eqs/pair_coul_soft.jpg) @@ -119,34 +157,32 @@ In the Coulomb part C is an energy-conversion constant, q_i and q_j are the charges on the 2 atoms, and epsilon is the dielectric constant which can be set by the "dielectric"_dielectric.html command. -The coefficient lambda is an activation parameter. When lambda = 1 the -pair potential is identical to a Lennard-Jones term or a Coulomb term -or a combination of both. When lambda = 0 the interactions are -deactivated. The transition between these two extrema is smoothed by a -soft repulsive core in order to avoid singularities in potential -energy and forces when sites are created or annihilated and can overlap -"(Beutler)"_#Beutler. +The coefficient lambda is an activation parameter. When lambda = 1 the pair +potential is identical to a Lennard-Jones term or a Coulomb term or a +combination of both. When lambda = 0 the interactions are deactivated. The +transition between these two extrema is smoothed by a soft repulsive core in +order to avoid singularities in potential energy and forces when sites are +created or annihilated and can overlap "(Beutler)"_#Beutler. The parameters n, alpha_LJ and alpha_C are set in the -"pair_style"_pair_style.html command, before the cutoffs. Usual -choices for the exponent are n = 2 or n = 1. For the remaining -coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are -appropriate choices. Plots of the LJ and Coulomb terms are shown -below, for lambda ranging from 1 to 0 every 0.1. +"pair_style"_pair_style.html command, before the cutoffs. Usual choices for the +exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and +alpha_C = 10 Angstrom^2 are appropriate choices. Plots of the 12/6 LJ and +Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1. :image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg) :c -For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, -the following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: +For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, as well +as for the equivalent {class2} versions, the following coefficients must be +defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html +command as in the examples above, or in the data file or restart files read by +the "read_data"_read_data.html or "read_restart"_read_restart.html commands, or +by mixing as described below: epsilon (energy units) sigma (distance units) -lambda (activation parameter between 0 and 1) +lambda (activation parameter, between 0 and 1) cutoff1 (distance units) cutoff2 (distance units) :ul @@ -160,36 +196,41 @@ since it has no Coulombic terms. For the {coul/cut/soft} and {coul/long/soft} only lambda and the optional cutoff2 are to be specified. -Style {lj/cut/tip4p/long/soft} implements a soft-core version of the -TIP4P water model. The usage of this pair style is documented in the -"pair_lj"_pair_lj.html styles. The soft-core version introduces the -lambda parameter to the list of arguments, after epsilon and sigma in -the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ -and alpha_C are set in the "pair_style"_pair_style.html command, -before the cutoffs. +Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water +model. The usage of the TIP4P pair style is documented in the +"pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ +and alpha_C are set in the "pair_style"_pair_style.html command, after the +specific parameters of the TIP4P water model and before the cutoffs. The +activation parameter lambda is supplied as an argument of the the +"pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the +optional cutoffs. -Style {lj/charmm/coul/long/soft} implements a soft-core version of the -CHARMM version of LJ interactions with an additional switching -function S(r) that ramps the energy and force smoothly to zero between -an inner and outer cutoff. The usage of this pair style is documented -in the "pair_charmm"_pair_charmm.html styles. The soft-core version -introduces the lambda parameter to the list of arguments, after -epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and -before the optional eps14 and sigma14). The parameters n, -alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html -command, before the cutoffs. +Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified +12-6 LJ potential used in CHARMM and documented in the +"pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n, +alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before +the global cutoffs. The activation parameter lambda is introduced as an argument +of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and +before the optional eps14 and sigma14. -The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} substyles +Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in +"pair_class2"_pair_class2.html. In the soft version the parameters n, alpha_LJ +and alpha_C are set in the "pair_style"_pair_style.html command, before the +global cutoffs. The activation parameter lambda is introduced as an argument of +the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before +the optional cutoffs. + +The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles are designed to be combined with other pair potentials via the "pair_style hybrid/overlay"_pair_hybrid.html command. This is because they have no repulsive core. Hence, if used by themselves, there will be no repulsion to keep two oppositely charged particles from overlapping each other. In this case, if lambda = 1, a singularity may -occur. These substyles are suitable to represent charges embedded in +occur. These sub-styles are suitable to represent charges embedded in the Lennard-Jones radius of another site (for example hydrogen atoms in several water models). -NOTES: When using the core-softed Coulomb potentials with long-range +NOTE: When using the soft-core Coulomb potentials with long-range solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.) in a free energy calculation in which sites holding electrostatic charges are being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html @@ -197,11 +238,36 @@ and "compute fep"_compute_fep.html) it is important to adapt both the lambda activation parameter (from 0 to 1, or the reverse) and the value of the charge (from 0 to its final value, or the reverse). This ensures that long-range electrostatic terms (kspace) are correct. It -is not necessary to use core-softed Coulomb potentials if the van der +is not necessary to use soft-core Coulomb potentials if the van der Waals site is present during the free-energy route, thus avoiding overlap of the charges. Examples are provided in the LAMMPS source directory tree, under examples/USER/fep. +NOTE: To avoid division by zero do not set sigma = 0 in the {lj/cut/soft} and +related styles; use the lambda parameter instead to activate/deactivate +interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not +interact though the Lennard-Jones term the {coul/long/soft} or similar sub-style +can be used via the "pair_style hybrid/overlay"_pair_hybrid.html command. + +:line + +The {morse/soft} variant modifies the "pair_morse"_pair_morse.html style at +short range to have a soft core. The functional form differs from that of the +{lj/soft} styles, and is instead given by: + +:c,image(Eqs/pair_morse_soft.jpg) + +The {morse/soft} style requires the following pair coefficients: + +D0 (energy units) +alpha (1/distance units) +r0 (distance units) +lambda (unitless, between 0.0 and 1.0) +cutoff (distance units) :ul + +The last coefficient is optional. If not specified, the global morse cutoff is +used. + :line Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are @@ -228,40 +294,57 @@ instructions on how to use the accelerated styles effectively. [Mixing, shift, tail correction, restart info]: -For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for this pair style can be mixed. -The default mix value is {geometric}. See the "pair_modify" command -for details. +The different versions of the {lj/cut/soft} pair styles support mixing. For atom +type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff +distance for these pair style can be mixed. The default mix value is +{geometric} for 12-6 styles. -These pair styles support the "pair_modify"_pair_modify.html shift -option for the energy of the Lennard-Jones portion of the pair +The mixing rule for epsilon and sigma for {lj/class2/soft} 9-6 potentials is to use the +{sixthpower} formulas. The "pair_modify mix"_pair_modify.html setting is thus +ignored for class2 potentials for epsilon and sigma. However it is still +followed for mixing the cutoff distance. See the "pair_modify"_pair_modify.html +command for details. + +The {morse/soft} pair style does not support mixing. Thus, coefficients for all +LJ pairs must be specified explicitly. + +All of the pair styles with soft core support the "pair_modify"_pair_modify.html +shift option for the energy of the Lennard-Jones portion of the pair interaction. -These pair styles support the "pair_modify"_pair_modify.html tail -option for adding a long-range tail correction to the energy and -pressure for the Lennard-Jones portion of the pair interaction. +The different versions of the {lj/cut/soft} pair styles support the +"pair_modify"_pair_modify.html tail option for adding a long-range tail +correction to the energy and pressure for the Lennard-Jones portion of the pair +interaction. -These pair styles write information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. +NOTE: The analytical form of the tail corrections for energy and pressure used +in the {lj/cut/soft} potentials are approximate, being identical to that of the +corresponding non-soft potentials scaled by a factor lambda^n. The errors due to +this approximation should be negligible. For example, for a cutoff of 2.5 sigma +this approximation leads to maximum relative errors in tail corrections of the +order of 1e-4 for energy and virial (alpha_LJ = 0.5, n = 2). The error vanishes +when lambda approaches 0 or 1. Note that these are the errors affecting the +long-range tail (itself a correction to the interaction energy) which includes +other approximations, namely that the system is homogeneous (local density equal +the average density) beyond the cutoff. + +The {morse/soft} pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and pressure. + +All of these pair styles write information to "binary restart +files"_restart.html, so pair_style and pair_coeff commands do not need to be +specified in an input script that reads a restart file. :line [Restrictions:] -To avoid division by zero do not set sigma = 0; use the lambda -parameter instead to activate/deactivate interactions, or use -epsilon = 0 and sigma = 1. Alternatively, when sites do not -interact though the Lennard-Jones term the {coul/long/soft} or -similar substyle can be used via the -"pair_style hybrid/overlay"_pair_hybrid.html command. - -:line - -All of the plain {soft} pair styles are part of the USER-FEP package. -The {long} styles also requires the KSPACE package to be installed. -They are only enabled if LAMMPS was built with those packages. See -the "Build package"_Build_package.html doc page for more info. +The pair styles with soft core are only enabled if LAMMPS was built with the +USER-FEP package. The {long} versions also require the KSPACE package to be +installed. The soft {tip4p} versions also require the MOLECULE package to be +installed. These styles are only enabled if LAMMPS was built with those +packages. See the "Build package"_Build_package.html doc page for more +info. [Related commands:] diff --git a/doc/src/pair_gran.txt b/doc/src/pair_gran.txt index e322f8da15..f747d15ec4 100644 --- a/doc/src/pair_gran.txt +++ b/doc/src/pair_gran.txt @@ -242,7 +242,7 @@ require a per-particle radius is stored. The {sphere} atom style does all of this. This pair style requires you to use the "comm_modify vel -yes"_comm_modify.html command so that velocites are stored by ghost +yes"_comm_modify.html command so that velocities are stored by ghost atoms. These pair styles will not restart exactly when using the diff --git a/doc/src/pair_hbond_dreiding.txt b/doc/src/pair_hbond_dreiding.txt index d4bdcd9258..9dd0bed87f 100644 --- a/doc/src/pair_hbond_dreiding.txt +++ b/doc/src/pair_hbond_dreiding.txt @@ -66,7 +66,7 @@ that the Morse form gives improved results for Dendrimer simulations, when n = 2. See the "Howto bioFF"_Howto_bioFF.html doc page for more information -on the DREIDING forcefield. +on the DREIDING force field. NOTE: Because the Dreiding hydrogen bond potential is only one portion of an overall force field which typically includes other pairwise @@ -135,9 +135,9 @@ distance cutoff Rin (distance units) distance cutoff Rout (distance units) angle cutoff (degrees) :ul -A single hydrogen atom type K can be specified, or a wild-card -asterisk can be used in place of or in conjunction with the K -arguments to select multiple types as hydrogens. This takes the form +A single hydrogen atom type K can be specified, or a wild-card asterisk +can be used in place of or in conjunction with the K arguments to +select multiple types as hydrogen atoms. This takes the form "*" or "*n" or "n*" or "m*n". See the "pair_coeff"_pair_coeff.html command doc page for details. diff --git a/doc/src/pair_hybrid.txt b/doc/src/pair_hybrid.txt index 97a5972bfb..4467ac1d51 100644 --- a/doc/src/pair_hybrid.txt +++ b/doc/src/pair_hybrid.txt @@ -70,15 +70,10 @@ other pairwise potential for several different atom type pairs in your model, then you should just list the sub-style once and use the pair_coeff command to assign parameters for the different type pairs. -NOTE: There are two exceptions to this option to list an individual -pair style multiple times. The first is for pair styles implemented -as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style -reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK). -This is because unlike a C++ class, they can not be instantiated -multiple times, due to the manner in which they were coded in Fortran. -The second is for GPU-enabled pair styles in the GPU package. This is -b/c the GPU package also currently assumes that only one instance of a -pair style is being used. +NOTE: There is one exception to this option to list an individual +pair style multiple times: GPU-enabled pair styles in the GPU package. +This is because the GPU package currently assumes that only one +instance of a pair style is being used. In the pair_coeff commands, the name of a pair style must be added after the I,J type specification, with the remaining coefficients @@ -229,7 +224,7 @@ For use with the various "compute */tally"_compute_tally.html computes, the "pair_modify compute/tally"_pair_modify.html command can be used to selectively turn off processing of the compute tally styles, for example, if those pair styles -(e.g. manybody styles) do not support this feature. +(e.g. many-body styles) do not support this feature. See the "pair_modify"_pair_modify.html doc page for details on the specific syntax, requirements and restrictions. @@ -270,7 +265,7 @@ atoms when the potential computes 3-body or 4-body interactions. However, you can still use the pair_coeff none setting or the "neigh_modify exclude"_neigh_modify.html command to exclude certain -type pairs from the neighbor list that will be passed to a manybody +type pairs from the neighbor list that will be passed to a many-body sub-style. This will alter the calculations made by a many-body potential, since it builds its list of 3-body, 4-body, etc interactions from the pair list. You will need to think carefully as diff --git a/doc/src/pair_ilp_graphene_hbn.txt b/doc/src/pair_ilp_graphene_hbn.txt index f048b16ccf..76dda14ec6 100644 --- a/doc/src/pair_ilp_graphene_hbn.txt +++ b/doc/src/pair_ilp_graphene_hbn.txt @@ -10,10 +10,10 @@ pair_style ilp/graphene/hbn command :h3 [Syntax:] -pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre +pair_style \[hybrid/overlay ...\] ilp/graphene/hbn cutoff tap_flag :pre cutoff = global cutoff (distance units) -tap_flag = 0/1 to turn off/on the taper function +tap_flag = 0/1 to turn off/on the taper function [Examples:] @@ -40,7 +40,7 @@ in "(Kolmogorov)"_#Kolmogorov2. Where Tap(r_ij) is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations larger than -r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above +r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2. @@ -110,6 +110,7 @@ units, if your simulation does not use {metal} units. "pair_style hybrid/overlay"_pair_hybrid.html, "pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html, "pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html, +"pair_style pair_lebedeva_z"_pair_lebedeva_z.html, "pair_style pair_coul_shield"_pair_coul_shield.html. [Default:] tap_flag = 1 diff --git a/doc/src/pair_kim.txt b/doc/src/pair_kim.txt index e1bde4f10e..a415ac606b 100644 --- a/doc/src/pair_kim.txt +++ b/doc/src/pair_kim.txt @@ -10,18 +10,13 @@ pair_style kim command :h3 [Syntax:] -pair_style kim virialmode model printflag :pre +pair_style kim model :pre -virialmode = KIMvirial or LAMMPSvirial model = name of KIM model (potential) -printflag = 1/0 do or do not print KIM descriptor file, optional :ul [Examples:] -pair_style kim KIMvirial model_Ar_P_Morse -pair_coeff * * Ar Ar :pre - -pair_style kim KIMvirial model_Ar_P_Morse 1 +pair_style kim ex_model_Ar_P_LJ pair_coeff * * Ar Ar :pre [Description:] @@ -36,14 +31,10 @@ element or alloy and set of parameters, e.g. EAM for Cu with a specific EAM potential file. See the current list of "KIM model -drivers"_https://openkim.org/kim-items/model-drivers/alphabetical. +drivers"_https://openkim.org/browse/model-drivers/alphabetical. See the current list of all "KIM -models"_https://openkim.org/kim-items/models/by-model-drivers - -See the list of "example KIM models"_https://openkim.org/kim-api which -are included in the KIM library by default, in the "What is in the KIM -API source package?" section. +models"_https://openkim.org/browse/models/by-model-drivers To use this pair style, you must first download and install the KIM API library from the "OpenKIM website"_https://openkim.org. The KIM @@ -53,23 +44,14 @@ building LAMMPS. See the examples/kim dir for an input script that uses a KIM model (potential) for Lennard-Jones. - + :line -The argument {virialmode} determines how the global virial is -calculated. If {KIMvirial} is specified, the KIM model performs the -global virial calculation (if it knows how). If {LAMMPSvirial} is -specified, LAMMPS computes the global virial using its fdotr mechanism. - The argument {model} is the name of the KIM model for a specific potential as KIM defines it. In principle, LAMMPS can invoke any KIM model. You should get an error or warning message from either LAMMPS or KIM if there is an incompatibility. -The argument {printflag} is optional. If it is set to a non-zero -value then a KIM descriptor file is printed when KIM is invoked. This -can be useful for debugging. The default is to not print this file. - Only a single pair_coeff command is used with the {kim} style which specifies the mapping of LAMMPS atom types to KIM elements. This is done by specifying N additional arguments after the * * in the @@ -86,18 +68,14 @@ pair_coeff * * Si Si Si C :pre The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to Si as defined within KIM. The final C argument maps LAMMPS atom type 4 to C -as defined within KIM. If a mapping value is specified as NULL, the -mapping is not performed. This can only be used when a {kim} -potential is used as part of the {hybrid} pair style. The NULL values -are placeholders for atom types that will be used with other -potentials. +as defined within KIM. :line In addition to the usual LAMMPS error messages, the KIM library itself may generate errors, which should be printed to the screen. In this case it is also useful to check the kim.log file for additional error -information. This file kim.log should be generated in the same +information. The file kim.log should be generated in the same directory where LAMMPS is running. To download, build, and install the KIM library on your system, see @@ -130,7 +108,7 @@ LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. This current version of pair_style kim is compatible with the -kim-api package version 1.6.0 and higher. +kim-api package version 2.0.0 and higher. [Related commands:] diff --git a/doc/src/pair_kolmogorov_crespi_full.txt b/doc/src/pair_kolmogorov_crespi_full.txt index df9a9696be..6d76a24bdb 100644 --- a/doc/src/pair_kolmogorov_crespi_full.txt +++ b/doc/src/pair_kolmogorov_crespi_full.txt @@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3 pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre cutoff = global cutoff (distance units) -tap_flag = 0/1 to turn off/on the taper function +tap_flag = 0/1 to turn off/on the taper function [Examples:] @@ -100,6 +100,7 @@ units. "pair_coeff"_pair_coeff.html, "pair_none"_pair_none.html, "pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style pair_lebedeva_z"_pair_lebedeva_z.html, "pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 912fca1657..aabb3460e7 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -10,7 +10,7 @@ pair_style kolmogorov/crespi/z command :h3 [Syntax:] -pair_style hybrid/overlay kolmogorov/crespi/z cutoff :pre +pair_style \[hybrid/overlay ...\] kolmogorov/crespi/z cutoff :pre [Examples:] @@ -31,7 +31,7 @@ which is to take all normals along the z-axis. :c,image(Eqs/pair_kolmogorov_crespi_z.jpg) It is important to have a sufficiently large cutoff to ensure smooth forces. -Energies are shifted so that they go continously to zero at the cutoff assuming +Energies are shifted so that they go continuously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by the last term in the equation for {Vij} above. @@ -56,9 +56,12 @@ package"_Build_package.html doc page for more info. [Related commands:] -"pair_coeff"_pair_coeff.html -"pair_none"_pair_none.html -"pair_style hybrid/overlay"_pair_hybrid.html +"pair_coeff"_pair_coeff.html, +"pair_none"_pair_none.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html. +"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html, +"pair_style lebedeva/z"_pair_lebedeva_z.html [Default:] none diff --git a/doc/src/pair_lebedeva_z.txt b/doc/src/pair_lebedeva_z.txt new file mode 100644 index 0000000000..9eab56d0d9 --- /dev/null +++ b/doc/src/pair_lebedeva_z.txt @@ -0,0 +1,66 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style lebedeva/z command :h3 + +[Syntax:] + +pair_style \[hybrid/overlay ...\] lebedeva/z cutoff :pre + +[Examples:] + +pair_style hybrid/overlay lebedeva/z 20.0 +pair_coeff * * none +pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre + +pair_style hybrid/overlay rebo lebedeva/z 14.0 +pair_coeff * * rebo CH.airebo C C +pair_coeff 1 2 lebedeva/z CC.Lebedeva C C :pre + +[Description:] + +The {lebedeva/z} style computes the Lebedeva interaction +potential as described in "(Lebedeva et al.)"_#Leb01. An important simplification is made, +which is to take all normals along the z-axis. + +:c,image(Eqs/pair_lebedeva.png) + +It is important to have a sufficiently large cutoff to ensure smooth forces. +Energies are shifted so that they go continuously to zero at the cutoff assuming +that the exponential part of {Vij} (first term) decays sufficiently fast. +This shift is achieved by the last term in the equation for {Vij} above. + +The parameter file (e.g. CC.Lebedeva), is intended for use with metal +"units"_units.html, with energies in meV. An additional parameter, {S}, +is available to facilitate scaling of energies. + +This potential must be used in combination with hybrid/overlay. +Other interactions can be set to zero using pair_style {none}. + +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, +"pair_style none"_pair_none.html, +"pair_style hybrid/overlay"_pair_hybrid.html, +"pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html, +"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, +"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html. + +[Default:] none + +:line + +:link(Leb01) +[(Lebedeva et al.)] I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011) + diff --git a/doc/src/pair_lj.txt b/doc/src/pair_lj.txt index 9c61e0bf25..8dce8383e5 100644 --- a/doc/src/pair_lj.txt +++ b/doc/src/pair_lj.txt @@ -223,7 +223,7 @@ Note that the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is typically best in an -efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2*qdist, to +efficiency sense to use a LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. @@ -260,6 +260,14 @@ pair_style command. :line +A version of these styles with a soft core, {lj/cut/soft}, suitable for use in +free energy calculations, is part of the USER-FEP package and is documented with +the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is +only available if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +:line + Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -321,8 +329,7 @@ The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE package. These styles are only enabled if LAMMPS was built with those packages. See the "Build package"_Build_package.html doc page for -more info. Note that the KSPACE and MOLECULE packages are installed -by default. +more info. [Related commands:] diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index 47a554ef4f..4e8410d062 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -97,7 +97,7 @@ neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2*qdist when using the TIP4P pair style, to account for the offset distance of the fictitious charges on O atoms in water molecules. Thus it is typically best in an efficiency sense to use a -LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the +LJ cutoff >= Coulombic cutoff + 2*qdist, to shrink the size of the neighbor list. This leads to slightly larger cost for the long-range calculation, so you can test the trade-off for your model. @@ -154,6 +154,14 @@ specified in the pair_style command. :line +A version of these styles with a soft core, {lj/cut/soft}, suitable for use in +free energy calculations, is part of the USER-FEP package and is documented with +the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is +only available if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +:line + Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -211,8 +219,7 @@ different levels of the rRESPA hierarchy. See the These styles are part of the KSPACE package. They are only enabled if LAMMPS was built with that package. See the "Build -package"_Build_package.html doc page for more info. Note that the -KSPACE package is installed by default. +package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_lj_smooth.txt b/doc/src/pair_lj_smooth.txt index 0c66dd0f66..d320cb83ff 100644 --- a/doc/src/pair_lj_smooth.txt +++ b/doc/src/pair_lj_smooth.txt @@ -34,7 +34,7 @@ cause the force to vary smoothly from the inner cutoff Rin to the outer cutoff Rc. At the inner cutoff the force and its 1st derivative -will match the unsmoothed LJ formula. At the outer cutoff the force +will match the non-smoothed LJ formula. At the outer cutoff the force and its 1st derivative will be 0.0. The inner cutoff cannot be 0.0. NOTE: this force smoothing causes the energy to be discontinuous both diff --git a/doc/src/pair_lj_switch3_coulgauss.txt b/doc/src/pair_lj_switch3_coulgauss.txt new file mode 100644 index 0000000000..1277cff9aa --- /dev/null +++ b/doc/src/pair_lj_switch3_coulgauss.txt @@ -0,0 +1,86 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style lj/switch3/coulgauss/long command :h3 + +[Syntax:] + +pair_style style args :pre + +style = {lj/switch3/coulgauss/long} +args = list of arguments for a particular style :ul + {lj/switch3/coulgauss/long} args = cutoff (cutoff2) width + cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + width = width parameter of the smoothing function (distance units) :pre + +[Examples:] + +pair_style lj/switch3/coulgauss/long 12.0 3.0 +pair_coeff 1 0.2 2.5 1.2 :pre + +pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0 +pair_coeff 1 0.2 2.5 1.2 :pre + +[Description:] + +The {lj/switch3/coulgauss} style evaluates the LJ +vdW potential + +:c,image(Eqs/pair_lj_switch3.jpg) + +, which goes smoothly to zero at the cutoff r_c as defined +by the switching function + +:c,image(Eqs/pair_switch3.jpg) + +where w is the width defined in the arguments. This potential +is combined with Coulomb interaction between Gaussian charge densities: + +:c,image(Eqs/pair_coulgauss.jpg) + +where qi and qj are the +charges on the 2 atoms, epsilon is the dielectric constant which +can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j +are the widths of the Gaussian charge distribution and erf() is the error-function. +This style has to be used in conjunction with the "kspace_style"_kspace_style.html command + +If one cutoff is specified it is used for both the vdW and Coulomb +terms. If two cutoffs are specified, the first is used as the cutoff +for the vdW terms, and the second is the cutoff for the Coulombic term. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands: + +epsilon (energy) +sigma (distance) +gamma (distance) :ul + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +Shifting the potential energy is not necessary because the switching +function ensures that the potential is zero at the cut-off. + + +[Restrictions:] + +These styles are part of the USER-YAFF package. They are only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index 74adba2432..7a185b4d55 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -152,7 +152,7 @@ info. [Related commands:] -"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html +"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html [Default:] none diff --git a/doc/src/pair_meam_sw_spline.txt b/doc/src/pair_meam_sw_spline.txt index 77322953cf..a9ad3484d3 100644 --- a/doc/src/pair_meam_sw_spline.txt +++ b/doc/src/pair_meam_sw_spline.txt @@ -116,7 +116,7 @@ info. [Related commands:] -"pair_coeff"_pair_coeff.html, "pair_style meam"_pair_meam.html, +"pair_coeff"_pair_coeff.html, "pair_style meam/c"_pair_meamc.html, "pair_style meam/spline"_pair_meam_spline.html [Default:] none diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meamc.txt similarity index 95% rename from doc/src/pair_meam.txt rename to doc/src/pair_meamc.txt index 0b1c1ac767..b57339b180 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meamc.txt @@ -6,18 +6,17 @@ :line -pair_style meam command :h3 pair_style meam/c command :h3 [Syntax:] pair_style style :pre -style = {meam} or {meam/c} +style = {meam/c} [Examples:] -pair_style meam +pair_style meam/c pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre @@ -27,14 +26,16 @@ NOTE: The behavior of the MEAM potential for alloy systems has changed as of November 2010; see description below of the mixture_ref_t parameter -Style {meam} computes pairwise interactions for a variety of materials +Style {meam/c} computes pairwise interactions for a variety of materials using modified embedded-atom method (MEAM) potentials "(Baskes)"_#Baskes. Conceptually, it is an extension to the original "EAM potentials"_pair_eam.html which adds angular forces. It is thus suitable for modeling metals and alloys with fcc, bcc, hcp and diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. Style {meam/c} is a translation of the {meam} code -from (mostly) Fortran to C++. It is functionally equivalent to {meam}. +silicon and carbon. Style {meam/c} is a translation of the (now obsolete) +{meam} code from Fortran to C++. It is functionally equivalent to {meam} +but more efficient, and thus {meam} has been removed from LAMMPS after +the 12 December 2018 release. In the MEAM formulation, the total energy E of a system of atoms is given by: @@ -179,7 +180,7 @@ selected starting from 1. Thus for the example given below pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre -an index of 1 would refer to Si and an index of 2 to C. +an index of 1 would refer to Si and an index of 2 to C. The recognized keywords for the parameter file are as follows: @@ -352,13 +353,8 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -The {meam} style is part of the MEAM package. It is only enabled if -LAMMPS was built with that package, which also requires the MEAM -library be built and linked with LAMMPS. The {meam/c} style is -provided in the USER-MEAMC package. It is only enabled if LAMMPS was -built with that package. In contrast to the {meam} style, {meam/c} -does not require a separate library to be compiled and it can be -instantiated multiple times in a "hybrid"_pair_hybrid.html pair style. +The {meam/c} style is provided in the USER-MEAMC package. It is +only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. [Related commands:] diff --git a/doc/src/pair_meso.txt b/doc/src/pair_meso.txt index 005498d8bf..54186a0e75 100644 --- a/doc/src/pair_meso.txt +++ b/doc/src/pair_meso.txt @@ -24,7 +24,7 @@ args = list of arguments for a particular style :l T = temperature (temperature units) cutoff = global cutoff for mDPD interactions (distance units) seed = random # seed (integer) (if <= 0, mDPD will use current time as the seed) - {mdpd/rhosum} args = + {mdpd/rhosum} args = {tdpd} args = T cutoff seed T = temperature (temperature units) cutoff = global cutoff for tDPD interactions (distance units) @@ -43,7 +43,7 @@ pair_coeff 1 1 mdpd/rhosum 0.75 pair_coeff 1 1 mdpd -40.0 25.0 18.0 1.0 0.75 :pre pair_style tdpd 1.0 1.58 935662 -pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 +pair_coeff * * 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0 :pre [Description:] @@ -73,7 +73,7 @@ heat flux qV, and random heat flux :c,image(Eqs/pair_edpd_heat.jpg) -where the mesoscopic heat friction κ is given by +where the mesoscopic heat friction κ is given by :c,image(Eqs/pair_edpd_kappa.jpg) @@ -84,7 +84,7 @@ The following coefficients must be defined in eDPD system for each pair of atom types via the "pair_coeff"_pair_coeff.html command as in the examples above. -A (force units) +A (force units) gamma (force/velocity units) power_f (positive real) cutoff (distance units) @@ -172,7 +172,7 @@ size="4">ms is much smaller than the mass of a tDPD particle m. For more details, see "(Li2015_JCP)"_#Li2015_JCP. -The following coefficients must be defined for each pair of atom types via the +The following coefficients must be defined for each pair of atom types via the "pair_coeff"_pair_coeff.html command as in the examples above. A (force units) @@ -250,10 +250,10 @@ more info. [Related commands:] -"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html, +"pair_coeff"_pair_coeff.html, "fix mvv/dpd"_fix_mvv_dpd.html, "fix mvv/edpd"_fix_mvv_dpd.html, "fix mvv/tdpd"_fix_mvv_dpd.html, -"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html, -"compute edpd/temp/atom"_compute_edpd_temp_atom.html, +"fix edpd/source"_fix_dpd_source.html, "fix tdpd/source"_fix_dpd_source.html, +"compute edpd/temp/atom"_compute_edpd_temp_atom.html, "compute tdpd/cc/atom"_compute_tdpd_cc_atom.html [Default:] none diff --git a/doc/src/pair_mm3_switch3_coulgauss.txt b/doc/src/pair_mm3_switch3_coulgauss.txt new file mode 100644 index 0000000000..3e0e24150e --- /dev/null +++ b/doc/src/pair_mm3_switch3_coulgauss.txt @@ -0,0 +1,88 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style mm3/switch3/coulgauss/long command :h3 + +[Syntax:] + +pair_style style args :pre + +style = {mm3/switch3/coulgauss/long} +args = list of arguments for a particular style :ul + {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width + cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units) + cutoff2 = global cutoff for Coulombic (optional) (distance units) + width = width parameter of the smoothing function (distance units) :pre + +[Examples:] + +pair_style mm3/switch3/coulgauss/long 12.0 3.0 +pair_coeff 1 0.2 2.5 1.2 :pre + +pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0 +pair_coeff 1 0.2 2.5 1.2 :pre + +[Description:] + +The {mm3/switch3/coulgauss} style evaluates the MM3 +vdW potential "(Allinger)"_#mm3-allinger1989 + +:c,image(Eqs/pair_mm3_switch3.jpg) + +, which goes smoothly to zero at the cutoff r_c as defined +by the switching function + +:c,image(Eqs/pair_switch3.jpg) + +where w is the width defined in the arguments. This potential +is combined with Coulomb interaction between Gaussian charge densities: + +:c,image(Eqs/pair_coulgauss.jpg) + +where qi and qj are the +charges on the 2 atoms, epsilon is the dielectric constant which +can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j +are the widths of the Gaussian charge distribution and erf() is the error-function. +This style has to be used in conjunction with the "kspace_style"_kspace_style.html command + +If one cutoff is specified it is used for both the vdW and Coulomb +terms. If two cutoffs are specified, the first is used as the cutoff +for the vdW terms, and the second is the cutoff for the Coulombic term. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands: + +epsilon (energy) +r_v (distance) +gamma (distance) :ul + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +Mixing rules are fixed for this style as defined above. + +Shifting the potential energy is not necessary because the switching +function ensures that the potential is zero at the cut-off. + + +[Restrictions:] + +These styles are part of the USER-YAFF package. They are only +enabled if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index c043fde5a7..4824a3d83e 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -183,7 +183,7 @@ an approximation. :l The tail corrections are computed at the beginning of each simulation run. If the number of atoms changes during the run, e.g. due to atoms leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html -command, then the corrections are not updates to relect the changed +command, then the corrections are not updated to reflect the changed atom count. If this is a large effect in your simulation, you should break the long run into several short runs, so that the correction factors are re-computed multiple times. diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index 68894f6913..7faa6ab785 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -12,7 +12,6 @@ pair_style morse/omp command :h3 pair_style morse/opt command :h3 pair_style morse/smooth/linear command :h3 pair_style morse/smooth/linear/omp command :h3 -pair_style morse/soft command :h3 pair_style morse/kk command :h3 [Syntax:] @@ -25,10 +24,6 @@ args = list of arguments for a particular style :ul cutoff = global cutoff for Morse interactions (distance units) {morse/smooth/linear} args = cutoff cutoff = global cutoff for Morse interactions (distance units) - {morse/soft} args = n lf cutoff - n = soft-core parameter - lf = transformation range is lf < lambda < 1 - cutoff = global cutoff for Morse interactions (distance units) :pre [Examples:] @@ -38,10 +33,6 @@ pair_style morse/smooth/linear 2.5 pair_coeff * * 100.0 2.0 1.5 pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre -pair_style morse/soft 4 0.9 10.0 -pair_coeff * * 100.0 2.0 1.5 1.0 -pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre - [Description:] Style {morse} computes pairwise interactions with the formula @@ -77,24 +68,11 @@ the {morse} and {morse/smooth/linear} styles. :line -The {morse/soft} variant is similar to the {lj/cut/soft} pair style -in that it modifies the potential at short range to have a soft core. -This helps to avoid singularities during free energy calculation in -which sites are created or annihilated. The formula differs from that -of {lj/cut/soft}, and is instead given by: - -:c,image(Eqs/pair_morse_soft.jpg) - -The {morse/soft} style requires the following pair coefficients: - -D0 (energy units) -alpha (1/distance units) -r0 (distance units) -lamda (unitless, between 0.0 and 1.0) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global morse -cutoff is used. +A version of the {morse} style with a soft core, {morse/soft}, suitable for use in +free energy calculations, is part of the USER-FEP package and is documented with +the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is only +available if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. :line @@ -151,12 +129,8 @@ The {morse/smooth/linear} pair style is only enabled if LAMMPS was built with the USER-MISC package. See the "Build package"_Build_package.html doc page for more info. -The {morse/soft} pair style is only enabled if LAMMPS was built with -the USER-FEP package. See the "Build package"_Build_package.html doc -page for more info. - [Related commands:] -"pair_coeff"_pair_coeff.html +"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html [Default:] none diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 2b2152a873..3a6d1026ed 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -19,7 +19,7 @@ pair_coeff * * MgOH.nb3bharmonic Mg O H :pre [Description:] -This pair style computes a nonbonded 3-body harmonic potential for the +This pair style computes a non-bonded 3-body harmonic potential for the energy E of a system of atoms as :c,image(Eqs/pair_nb3b_harmonic.jpg) @@ -60,7 +60,7 @@ other potentials. An example of a pair_coeff command for use with the pair_coeff * * nb3b/harmonic MgOH.nb3b.harmonic Mg O H -Three-body nonbonded harmonic files in the {potentials} directory of +Three-body non-bonded harmonic files in the {potentials} directory of the LAMMPS distribution have a ".nb3b.harmonic" suffix. Lines that are not blank or comments (starting with #) define parameters for a triplet of elements. diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index b24e3c07df..b63b5371cf 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -25,10 +25,10 @@ args = list of arguments for these particular styles :ul {oxdna/stk} args = seq T 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength) - T = temperature (oxDNA units, 0.1 = 300 K) + T = temperature (oxDNA units, 0.1 = 300 K) {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength) - eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre + eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre [Examples:] @@ -61,7 +61,7 @@ for a detailed description of the oxDNA force field. NOTE: These pair styles have to be used together with the related oxDNA bond style {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients -in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. +in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first and second coefficient after {oxdna/stk} (seq=seqdep and T=0.1 in the above example) and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example). When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html @@ -72,8 +72,8 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool +Please cite "(Henrich)"_#Henrich1 and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index c5662abdeb..f2963f7b17 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -67,9 +67,9 @@ and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force fi NOTE: These pair styles have to be used together with the related oxDNA2 bond style {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients -in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. +in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model. Exceptions are the first and the second coefficient after {oxdna2/stk} (seq=seqdep and T=0.1 in the above example), -the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients +the first coefficient after {oxdna/hbond} (seq=seqdep in the above example) and the three coefficients after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. @@ -78,8 +78,8 @@ Example input and data files for DNA duplexes can be found in examples/USER/cgdn A simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/. -Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. -The article contains more information on the model, the structure of the input file, the setup tool +Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation. +The article contains more information on the model, the structure of the input file, the setup tool and the performance of the LAMMPS-implementation of oxDNA. The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf. diff --git a/doc/src/pair_peri.txt b/doc/src/pair_peri.txt index b6baa4edc5..5c5a41ca6c 100644 --- a/doc/src/pair_peri.txt +++ b/doc/src/pair_peri.txt @@ -36,7 +36,7 @@ pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43 :pre [Description:] The peridynamic pair styles implement material models that can be used -at the mescscopic and macroscopic scales. See "this +at the mesoscopic and macroscopic scales. See "this document"_PDF/PDLammps_overview.pdf for an overview of LAMMPS commands for Peridynamics modeling. @@ -63,7 +63,7 @@ R. Rahman and J. T. Foster at University of Texas at San Antonio. The original VES formulation is described in "(Mitchell2011)" and the original EPS formulation is in "(Mitchell2011a)". Additional PDF docs that describe the VES and EPS implementations are include in the -LAMMPS distro in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf and +LAMMPS distribution in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf and "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. For questions regarding the VES and EPS models in LAMMPS you can contact R. Rahman (rezwanur.rahman at utsa.edu). diff --git a/doc/src/pair_polymorphic.txt b/doc/src/pair_polymorphic.txt index 7460044043..d9e73d8492 100644 --- a/doc/src/pair_polymorphic.txt +++ b/doc/src/pair_polymorphic.txt @@ -95,7 +95,7 @@ N element names = mapping of Tersoff elements to atom types :ul See the pair_coeff doc page for alternate ways to specify the path for the potential file. Several files for polymorphic potentials are -included in the potentials dir of the LAMMPS distro. They have a +included in the potentials dir of the LAMMPS distribution. They have a "poly" suffix. As an example, imagine the SiC_tersoff.polymorphic file has tabulated diff --git a/doc/src/pair_quip.txt b/doc/src/pair_quip.txt index 1f794d0c84..30f1d80450 100644 --- a/doc/src/pair_quip.txt +++ b/doc/src/pair_quip.txt @@ -77,7 +77,7 @@ This pair style is part of the USER-QUIP package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. -QUIP potentials are parametrized in electron-volts and Angstroms and +QUIP potentials are parameterized in electron-volts and Angstroms and therefore should be used with LAMMPS metal "units"_units.html. QUIP potentials are generally not designed to work with the scaling @@ -93,7 +93,7 @@ because it may remove pairs from the neighbor list that are still required. Pair style {quip} cannot be used with pair style {hybrid}, only -with {hybrid/overlay} and only the {quip} substyle is applied to +with {hybrid/overlay} and only the {quip} sub-style is applied to all atom types. [Related commands:] diff --git a/doc/src/pair_reax.txt b/doc/src/pair_reax.txt deleted file mode 100644 index a3b84955cd..0000000000 --- a/doc/src/pair_reax.txt +++ /dev/null @@ -1,216 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style reax command :h3 - -[Syntax:] - -pair_style reax hbcut hbnewflag tripflag precision :pre - -hbcut = hydrogen-bond cutoff (optional) (distance units) -hbnewflag = use old or new hbond function style (0 or 1) (optional) -tripflag = apply stabilization to all triple bonds (0 or 1) (optional) -precision = precision for charge equilibration (optional) :ul - -[Examples:] - -pair_style reax -pair_style reax 10.0 0 1 1.0e-5 -pair_coeff * * ffield.reax 3 1 2 2 -pair_coeff * * ffield.reax 3 NULL NULL 3 :pre - -[Description:] - -Style {reax} computes the ReaxFF potential of van Duin, Goddard and -co-workers. ReaxFF uses distance-dependent bond-order functions to -represent the contributions of chemical bonding to the potential -energy. There is more than one version of ReaxFF. The version -implemented in LAMMPS uses the functional forms documented in the -supplemental information of the following paper: -"(Chenoweth)"_#Chenoweth_20081. The version integrated into LAMMPS matches -the most up-to-date version of ReaxFF as of summer 2010. - -WARNING: pair style reax is now deprecated and will soon be retired. Users -should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style -differs from the {reax/c} style in the lo-level implementation details. -The {reax} style is a -Fortran library, linked to LAMMPS. The {reax/c} style was initially -implemented as stand-alone C code and is now integrated into LAMMPS as -a package. - -LAMMPS requires that a file called ffield.reax be provided, containing -the ReaxFF parameters for each atom type, bond type, etc. The format -is identical to the ffield file used by van Duin and co-workers. The -filename is required as an argument in the pair_coeff command. Any -value other than "ffield.reax" will be rejected (see below). - -LAMMPS provides several different versions of ffield.reax in its -potentials dir, each called potentials/ffield.reax.label. These are -documented in potentials/README.reax. The default ffield.reax -contains parameterizations for the following elements: C, H, O, N. - -NOTE: We do not distribute a wide variety of ReaxFF force field files -with LAMMPS. Adri van Duin's group at PSU is the central repository -for this kind of data as they are continuously deriving and updating -parameterizations for different classes of materials. You can submit -a contact request at the Materials Computation Center (MCC) website -"https://www.mri.psu.edu/materials-computation-center/connect-mcc"_https://www.mri.psu.edu/materials-computation-center/connect-mcc, -describing the material(s) you are interested in modeling with ReaxFF. -They can tell -you what is currently available or what it would take to create a -suitable ReaxFF parameterization. - -The format of these files is identical to that used originally by van -Duin. We have tested the accuracy of {pair_style reax} potential -against the original ReaxFF code for the systems mentioned above. You -can use other ffield files for specific chemical systems that may be -available elsewhere (but note that their accuracy may not have been -tested). - -The {hbcut}, {hbnewflag}, {tripflag}, and {precision} settings are -optional arguments. If none are provided, default settings are used: -{hbcut} = 6 (which is Angstroms in real units), {hbnewflag} = 1 (use -new hbond function style), {tripflag} = 1 (apply stabilization to all -triple bonds), and {precision} = 1.0e-6 (one part in 10^6). If you -wish to override any of these defaults, then all of the settings must -be specified. - -Two examples using {pair_style reax} are provided in the examples/reax -sub-directory, along with corresponding examples for -"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force -calculated by both of these pair styles match very closely, the -contributions due to the valence angles differ slightly due to -the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq} -is 0.00001, while for {pair_style reax} it is hard-coded to be 0.001. - -Use of this pair style requires that a charge be defined for every -atom since the {reax} pair style performs a charge equilibration (QEq) -calculation. See the "atom_style"_atom_style.html and -"read_data"_read_data.html commands for details on how to specify -charges. - -The thermo variable {evdwl} stores the sum of all the ReaxFF potential -energy contributions, with the exception of the Coulombic and charge -equilibration contributions which are stored in the thermo variable -{ecoul}. The output of these quantities is controlled by the -"thermo"_thermo.html command. - -This pair style tallies a breakdown of the total ReaxFF potential -energy into sub-categories, which can be accessed via the "compute -pair"_compute_pair.html command as a vector of values of length 14. -The 14 values correspond to the following sub-categories (the variable -names in italics match those used in the ReaxFF FORTRAN library): - -{eb} = bond energy -{ea} = atom energy -{elp} = lone-pair energy -{emol} = molecule energy (always 0.0) -{ev} = valence angle energy -{epen} = double-bond valence angle penalty -{ecoa} = valence angle conjugation energy -{ehb} = hydrogen bond energy -{et} = torsion energy -{eco} = conjugation energy -{ew} = van der Waals energy -{ep} = Coulomb energy -{efi} = electric field energy (always 0.0) -{eqeq} = charge equilibration energy :ol - -To print these quantities to the log file (with descriptive column -headings) the following commands could be included in an input script: - -compute reax all pair reax -variable eb equal c_reax\[1\] -variable ea equal c_reax\[2\] -... -variable eqeq equal c_reax\[14\] -thermo_style custom step temp epair v_eb v_ea ... v_eqeq :pre - -Only a single pair_coeff command is used with the {reax} style which -specifies a ReaxFF potential file with parameters for all needed -elements. These are mapped to LAMMPS atom types by specifying N -additional arguments after the filename in the pair_coeff command, -where N is the number of LAMMPS atom types: - -filename -N indices = mapping of ReaxFF elements to atom types :ul - -The specification of the filename and the mapping of LAMMPS atom types -recognized by the ReaxFF is done differently than for other LAMMPS -potentials, due to the non-portable difficulty of passing character -strings (e.g. filename, element names) between C++ and Fortran. - -The filename has to be "ffield.reax" and it has to exist in the -directory you are running LAMMPS in. This means you cannot prepend a -path to the file in the potentials dir. Rather, you should copy that -file into the directory you are running from. If you wish to use -another ReaxFF potential file, then name it "ffield.reax" and put it -in the directory you run from. - -In the ReaxFF potential file, near the top, after the general -parameters, is the atomic parameters section that contains element -names, each with a couple dozen numeric parameters. If there are M -elements specified in the {ffield} file, think of these as numbered 1 -to M. Each of the N indices you specify for the N atom types of LAMMPS -atoms must be an integer from 1 to M. Atoms with LAMMPS type 1 will -be mapped to whatever element you specify as the first index value, -etc. If a mapping value is specified as NULL, the mapping is not -performed. This can be used when a ReaxFF potential is used as part -of the {hybrid} pair style. The NULL values are placeholders for atom -types that will be used with other potentials. - -NOTE: Currently the reax pair style cannot be used as part of the -{hybrid} pair style. Some additional changes still need to be made to -enable this. - -As an example, say your LAMMPS simulation has 4 atom types and the -elements are ordered as C, H, O, N in the {ffield} file. If you want -the LAMMPS atom type 1 and 2 to be C, type 3 to be N, and type 4 to be -H, you would use the following pair_coeff command: - -pair_coeff * * ffield.reax 1 1 4 2 :pre - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -This pair style does not support the "pair_modify"_pair_modify.html -mix, shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, since it is stored in potential files. Thus, you -need to re-specify the pair_style and pair_coeff commands in an input -script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -[Restrictions:] - -The ReaxFF potential files provided with LAMMPS in the potentials -directory are parameterized for real "units"_units.html. You can use -the ReaxFF potential with any LAMMPS units, but you would need to -create your own potential file with coefficients listed in the -appropriate units if your simulation doesn't use "real" units. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html, -"fix_reax_bonds"_fix_reax_bonds.html - -[Default:] - -The keyword defaults are {hbcut} = 6, {hbnewflag} = 1, {tripflag} = 1, -{precision} = 1.0e-6. - -:line - -:link(Chenoweth_20081) -[(Chenoweth_2008)] Chenoweth, van Duin and Goddard, -Journal of Physical Chemistry A, 112, 1040-1053 (2008). diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index e63f4a90ee..37482beacf 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -37,7 +37,7 @@ pair_coeff * * ffield.reax C H O N :pre Style {reax/c} computes the ReaxFF potential of van Duin, Goddard and co-workers. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential -energy. There is more than one version of ReaxFF. The version +energy. There is more than one version of ReaxFF. The version implemented in LAMMPS uses the functional forms documented in the supplemental information of the following paper: "(Chenoweth et al., 2008)"_#Chenoweth_20082. The version integrated into LAMMPS matches @@ -56,11 +56,10 @@ consideration when using the {reax/c/kk} style is the choice of either half or full neighbor lists. This setting can be changed using the Kokkos "package"_package.html command. -The {reax/c} style differs from the "pair_style reax"_pair_reax.html -command in the lo-level implementation details. The {reax} style is a -Fortran library, linked to LAMMPS. The {reax/c} style was initially -implemented as stand-alone C code and is now integrated into LAMMPS as -a package. +The {reax/c} style differs from the (obsolete) "pair_style reax" +command in the implementation details. The {reax} style was a +Fortran library, linked to LAMMPS. The {reax} style has been removed +from LAMMPS after the 12 December 2018 version. LAMMPS provides several different versions of ffield.reax in its potentials dir, each called potentials/ffield.reax.label. These are @@ -98,9 +97,8 @@ correspond to those used by Adri van Duin's stand-alone serial code. If these are changed by setting control variables in the control file, the results from LAMMPS and the serial code will not agree. -Two examples using {pair_style reax/c} are provided in the examples/reax -sub-directory, along with corresponding examples for -"pair_style reax"_pair_reax.html. +Examples using {pair_style reax/c} are provided in the examples/reax +sub-directory. Use of this pair style requires that a charge be defined for every atom. See the "atom_style"_atom_style.html and @@ -193,8 +191,7 @@ where N is the number of LAMMPS atom types: filename N indices = ReaxFF elements :ul -The filename is the ReaxFF potential file. Unlike for the {reax} -pair style, any filename can be used. +The filename is the ReaxFF potential file. In the ReaxFF potential file, near the top, after the general parameters, is the atomic parameters section that contains element @@ -337,9 +334,8 @@ appropriate units if your simulation doesn't use "real" units. [Related commands:] "pair_coeff"_pair_coeff.html, "fix qeq/reax"_fix_qeq_reax.html, "fix -reax/c/bonds"_fix_reax_bonds.html, "fix -reax/c/species"_fix_reaxc_species.html, "pair_style -reax"_pair_reax.html +reax/c/bonds"_fix_reaxc_bonds.html, "fix +reax/c/species"_fix_reaxc_species.html [Default:] diff --git a/doc/src/pair_sdk.txt b/doc/src/pair_sdk.txt index 06a0a42d5a..7c596ed1d8 100644 --- a/doc/src/pair_sdk.txt +++ b/doc/src/pair_sdk.txt @@ -48,7 +48,7 @@ given by :c,image(Eqs/pair_cmm.jpg) -as required for the SDK Coarse-grained MD parametrization discussed in +as required for the SDK Coarse-grained MD parameterization discussed in "(Shinoda)"_#Shinoda3 and "(DeVane)"_#DeVane. Rc is the cutoff. Style {lj/sdk/coul/long} computes the adds Coulombic interactions diff --git a/doc/src/pair_sdpd_taitwater_isothermal.txt b/doc/src/pair_sdpd_taitwater_isothermal.txt new file mode 100644 index 0000000000..fba97e1bc2 --- /dev/null +++ b/doc/src/pair_sdpd_taitwater_isothermal.txt @@ -0,0 +1,108 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Commands_all.html) + +:line + +pair_style sdpd/taitwater/isothermal command :h3 + +[Syntax:] + +pair_style sdpd/taitwater/isothermal temperature viscosity seed +:pre + +temperature = temperature of the fluid (temperature units) +viscosity = dynamic viscosity of the fluid (mass*distance/time units) +seed = random number generator seed (positive integer, optional) :ul + +[Examples:] + +pair_style sdpd/taitwater/isothermal 300. 1. 28681 +pair_coeff * * 1000.0 1430.0 2.4 :pre + +[Description:] + +The sdpd/taitwater/isothermal style computes forces between mesoscopic +particles according to the Smoothed Dissipative Particle Dynamics model +described in this paper by "(Espanol and Revenga)"_#Espanol_Revenga under +the following assumptions: + +:olb +The temperature is constant and uniform. :l +The shear viscosity is constant and uniform. :l +The volume viscosity is negligible before the shear viscosity. :l +The Boltzmann constant is negligible before the heat capacity of a +single mesoscopic particle of fluid. :ole,l + +The third assumption is true for water in nearly incompressible flows. +The fourth holds true for water for any reasonable size one can +imagine for a mesoscopic particle. + +The pressure forces between particles will be computed according to +Tait's equation of state: + +:c,image(Eqs/pair_sph_tait.jpg) + +where gamma = 7 and B = c_0^2 rho_0 / gamma, with rho_0 being the +reference density and c_0 the reference speed of sound. + +The laminar viscosity and the random forces will be computed according +to formulas described in "(Espanol and Revenga)"_#Espanol_Revenga. + +IMPORTANT NOTE: Similar to "brownian"_pair_brownian.html and +"dpd"_pair_dpd.html styles, the "newton"_newton.html setting for +pairwise interactions needs to be on when running LAMMPS in parallel +if you want to ensure linear momentum conservation. Otherwise random +forces generated for pairs straddling processor boundary will not be +equal and opposite. + +NOTE: The actual random seed used will be a mix of what you specify +and other parameters like the MPI ranks. This is to ensure that +different MPI tasks have distinct seeds. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above. + +rho0 reference density (mass/volume units) +c0 reference soundspeed (distance/time units) +h kernel function cutoff (distance units) :ul + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +This style does not support mixing. Thus, coefficients for all +I,J pairs must be specified explicitly. + +This style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This style does not write information to "binary restart +files"_restart.html. Thus, you need to re-specify the pair_style and +pair_coeff commands in an input script that reads a restart file. + +This style can only be used via the {pair} keyword of the "run_style +respa"_run_style.html command. It does not support the {inner}, +{middle}, {outer} keywords. + +[Restrictions:] + +This pair style is part of the USER-SDPD package. It is only enabled +if LAMMPS was built with that package. See the "Build +package"_Build_package.html doc page for more info. + +[Related commands:] + +"pair coeff"_pair_coeff.html, "pair sph/rhosum"_pair_sph_rhosum.html + +[Default:] + +The default seed is 0 (before mixing). + +:line + +:link(Espanol_Revenga) +[(Espanol and Revenga)] Espanol, Revenga, Physical Review E, 67, 026705 (2003). diff --git a/doc/src/pair_smd_tlsph.txt b/doc/src/pair_smd_tlsph.txt index 44b0c6cae8..13ffbbabc1 100644 --- a/doc/src/pair_smd_tlsph.txt +++ b/doc/src/pair_smd_tlsph.txt @@ -33,7 +33,7 @@ pair style is defined. Note that {i} and {j} must be equal, i.e., no {tlsph} cross interactions between different particle types are allowed. In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a number of floats and integers, the {tlsph} -{pair coeff} definition is organised using keywords. These keywords +{pair coeff} definition is organized using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The {pair coeff} line must be terminated with the {*END} keyword. The use the diff --git a/doc/src/pair_smd_ulsph.txt b/doc/src/pair_smd_ulsph.txt index f28dd9043c..39e9c76841 100644 --- a/doc/src/pair_smd_ulsph.txt +++ b/doc/src/pair_smd_ulsph.txt @@ -37,7 +37,7 @@ pair style is defined. Note that {i} and {j} can be different, i.e., allowed. However, {i}--{i} respectively {j}--{j} pair_coeff lines have to precede a cross interaction. In contrast to the usual {LAMMPS} {pair coeff} definitions, which are given solely a number of floats -and integers, the {ulsph} {pair coeff} definition is organised using +and integers, the {ulsph} {pair coeff} definition is organized using keywords. These keywords mark the beginning of different sets of parameters for particle properties, material constitutive models, and damage models. The {pair coeff} line must be terminated with the diff --git a/doc/src/pair_smtbq.txt b/doc/src/pair_smtbq.txt index e81411678a..41e124a94f 100644 --- a/doc/src/pair_smtbq.txt +++ b/doc/src/pair_smtbq.txt @@ -19,7 +19,7 @@ pair_coeff * * ffield.smtbq.Al2O3 O Al :pre [Description:] -This pair stylecomputes a variable charge SMTB-Q (Second-Moment +This pair style computes a variable charge SMTB-Q (Second-Moment tight-Binding QEq) potential as described in "SMTB-Q_1"_#SMTB-Q_1 and "SMTB-Q_2"_#SMTB-Q_2. Briefly, the energy of metallic-oxygen systems is given by three contributions: @@ -28,7 +28,7 @@ is given by three contributions: where {Etot} is the total potential energy of the system, {EES} is the electrostatic part of the total energy, -{EOO} is the interaction between oxygens and +{EOO} is the interaction between oxygen atoms and {EMO} is a short-range interaction between metal and oxygen atoms. This interactions depend on interatomic distance {rij} and/or the charge {Qi} of atoms @@ -107,7 +107,7 @@ Thus parameter μ, indicated above, is given by : μ = (√n The potential offers the possibility to consider the polarizability of the electron clouds of oxygen by changing the slater radius of the -charge density around the oxygens through the parameters {rBB, rB and +charge density around the oxygen atoms through the parameters {rBB, rB and rS} in the ffield.SMTBQ.Syst. This change in radius is performed according to the method developed by E. Maras "SMTB-Q_2"_#SMTB-Q_2. This method needs to determine the number of @@ -142,7 +142,7 @@ For the anion (oxygen) : Name of element (char) and stoichiometry in oxide Formal charge and mass of element -Principal quantic number of outer orbital ({n}), electronegativity ({χ0i}) and hardness ({J0i}) +Principal quantum number of outer orbital ({n}), electronegativity ({χ0i}) and hardness ({J0i}) Ionic radius parameters : max coordination number ({coordBB} = 6 by default), bulk coordination number {(coordB)}, surface coordination number {(coordS)} and {rBB, rB and rS} the slater radius for each coordination number. (note : If you don't want to change the slater radius, use three identical radius values) Number of orbital shared by the element in the oxide ({di}) Divided line :ul diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index 6f8cc3d8a8..a796cfdeba 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -16,7 +16,7 @@ pair_style snap :pre [Examples:] pair_style snap -pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre +pair_coeff * * InP.snapcoeff InP.snapparam In In P P :pre [Description:] @@ -48,14 +48,12 @@ not set in the pair_style or pair_coeff command; they are specified in the SNAP potential files themselves. Only a single pair_coeff command is used with the {snap} style which -specifies two SNAP files and the list SNAP element(s) to be -extracted. -The SNAP elements are mapped to LAMMPS atom types by specifying -N additional arguments after the 2nd filename in the pair_coeff -command, where N is the number of LAMMPS atom types: +specifies a SNAP coefficient file followed by a SNAP parameter file +and then N additional arguments specifying the mapping of SNAP +elements to LAMMPS atom types, where N is the number of +LAMMPS atom types: -SNAP element file -Elem1, Elem2, ... +SNAP coefficient file SNAP parameter file N element names = mapping of SNAP elements to atom types :ul @@ -63,13 +61,11 @@ As an example, if a LAMMPS indium phosphide simulation has 4 atoms types, with the first two being indium and the 3rd and 4th being phophorous, the pair_coeff command would look like this: -pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P :pre +pair_coeff * * snap InP.snapcoeff InP.snapparam In In P P :pre The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The two filenames are for the element and parameter files, respectively. -The 'In' and 'P' arguments (between the file names) are the two elements -which will be extracted from the element file. The -two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the +The two filenames are for the coefficient and parameter files, respectively. +The two trailing 'In' arguments map LAMMPS atom types 1 and 2 to the SNAP 'In' element. The two trailing 'P' arguments map LAMMPS atom types 3 and 4 to the SNAP 'P' element. @@ -79,10 +75,11 @@ This can be used when a {snap} potential is used as part of the {hybrid} pair style. The NULL values are placeholders for atom types that will be used with other potentials. -The name of the SNAP element file usually ends in the +The name of the SNAP coefficient file usually ends in the ".snapcoeff" extension. It may contain coefficients -for many SNAP elements. -Only those elements listed in the pair_coeff command are extracted. +for many SNAP elements. The only requirement is that it +contain at least those element names appearing in the +LAMMPS mapping list. The name of the SNAP parameter file usually ends in the ".snapparam" extension. It contains a small number of parameters that define the overall form of the SNAP potential. @@ -103,15 +100,13 @@ by the following commands: zbl $\{zblcutinner\} $\{zblcutouter\} snap pair_coeff * * zbl 0.0 pair_coeff 1 1 zbl $\{zblz\} - pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta & - ../potentials/Ta06A.snapparam Ta :pre + pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta :pre It is convenient to keep these commands in a separate file that can be inserted in any LAMMPS input script using the "include"_include.html command. -The top of the SNAP element file can contain any number of blank and comment -lines (start with #), but follows a strict +The top of the SNAP coefficient file can contain any number of blank and comment lines (start with #), but follows a strict format after that. The first non-blank non-comment line must contain two integers: diff --git a/doc/src/pair_spin_dmi.txt b/doc/src/pair_spin_dmi.txt index bd605bd064..bc67e43ecd 100644 --- a/doc/src/pair_spin_dmi.txt +++ b/doc/src/pair_spin_dmi.txt @@ -25,44 +25,44 @@ pair_coeff 1 2 dmi 4.0 0.00109 0.0 0.0 1.0 :pre [Description:] Style {spin/dmi} computes the Dzyaloshinskii-Moriya (DM) interaction -between pairs of magnetic spins. +between pairs of magnetic spins. According to the expression reported in "(Rohart)"_#Rohart, one has the following DM energy: :c,image(Eqs/pair_spin_dmi_interaction.jpg) -where si and sj are two neighboring magnetic spins of two particles, +where si and sj are two neighboring magnetic spins of two particles, eij = (ri - rj)/|ri-rj| is the unit vector between sites i and j, -and D is the DM vector defining the intensity (in eV) and the direction +and D is the DM vector defining the intensity (in eV) and the direction of the interaction. -In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented -from the high spin-orbit layer to the magnetic ultrathin film. +In "(Rohart)"_#Rohart, D is defined as the direction normal to the film oriented +from the high spin-orbit layer to the magnetic ultra-thin film. The application of a spin-lattice Poisson bracket to this energy (as described in "(Tranchida)"_#Tranchida5) allows to derive a magnetic torque omega, and a -mechanical force F (for spin-lattice calculations only) for each magnetic -particle i: +mechanical force F (for spin-lattice calculations only) for each magnetic +particle i: :c,image(Eqs/pair_spin_dmi_forces.jpg) More details about the derivation of these torques/forces are reported in "(Tranchida)"_#Tranchida5. -For the {spin/dmi} pair style, the following coefficients must be defined for -each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in -the examples above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html commands, and -set in the following order: +For the {spin/dmi} pair style, the following coefficients must be defined for +each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: rc (distance units) |D| (energy units) Dx, Dy, Dz (direction of D) :ul -Note that rc is the radius cutoff of the considered DM interaction, |D| is -the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. +Note that rc is the radius cutoff of the considered DM interaction, |D| is +the norm of the DM vector (in eV), and Dx, Dy and Dz define its direction. -None of those coefficients is optional. If not specified, the {spin/dmi} +None of those coefficients is optional. If not specified, the {spin/dmi} pair style cannot be used. :line @@ -76,7 +76,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, "pair_eam"_pair_eam.html, [Default:] none diff --git a/doc/src/pair_spin_exchange.txt b/doc/src/pair_spin_exchange.txt index 2f158704a9..10d65a55a1 100644 --- a/doc/src/pair_spin_exchange.txt +++ b/doc/src/pair_spin_exchange.txt @@ -24,14 +24,14 @@ pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre [Description:] -Style {spin/exchange} computes the exchange interaction between +Style {spin/exchange} computes the exchange interaction between pairs of magnetic spins: :c,image(Eqs/pair_spin_exchange_interaction.jpg) -where si and sj are two neighboring magnetic spins of two particles, +where si and sj are two neighboring magnetic spins of two particles, rij = ri - rj is the inter-atomic distance between the two particles, -and J(rij) is a function defining the intensity and the sign of the exchange +and J(rij) is a function defining the intensity and the sign of the exchange interaction for different neighboring shells. This function is defined as: :c,image(Eqs/pair_spin_exchange_function.jpg) @@ -41,38 +41,38 @@ where a, b and d are the three constant coefficients defined in the associated The coefficients a, b, and d need to be fitted so that the function above matches with the value of the exchange interaction for the N neighbor shells taken into account. -Examples and more explanations about this function and its parametrization are reported +Examples and more explanations about this function and its parameterization are reported in "(Tranchida)"_#Tranchida3. -From this exchange interaction, each spin i will be submitted +From this exchange interaction, each spin i will be submitted to a magnetic torque omega, and its associated atom can be submitted to a force F for spin-lattice calculations (see "fix_nve_spin"_fix_nve_spin.html), such as: :c,image(Eqs/pair_spin_exchange_forces.jpg) -with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit +with h the Planck constant (in metal units), and eij = (ri - rj)/|ri-rj| the unit vector between sites i and j. More details about the derivation of these torques/forces are reported in "(Tranchida)"_#Tranchida3. -For the {spin/exchange} pair style, the following coefficients must be defined -for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in -the examples above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html commands, and -set in the following order: +For the {spin/exchange} pair style, the following coefficients must be defined +for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in +the examples above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html commands, and +set in the following order: rc (distance units) a (energy units) -b (adim parameter) +b (adim parameter) d (distance units) :ul Note that rc is the radius cutoff of the considered exchange interaction, -and a, b and d are the three coefficients performing the parametrization +and a, b and d are the three coefficients performing the parameterization of the function J(rij) defined above. -None of those coefficients is optional. If not specified, the +None of those coefficients is optional. If not specified, the {spin/exchange} pair style cannot be used. :line @@ -86,7 +86,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, "pair_eam"_pair_eam.html, [Default:] none diff --git a/doc/src/pair_spin_magelec.txt b/doc/src/pair_spin_magelec.txt index 360f440792..151ecdec3d 100644 --- a/doc/src/pair_spin_magelec.txt +++ b/doc/src/pair_spin_magelec.txt @@ -25,7 +25,7 @@ pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre Style {spin/me} computes a magneto-electric interaction between pairs of magnetic spins. According to the derivation reported in -"(Katsura)"_#Katsura1, this interaction is defined as: +"(Katsura)"_#Katsura1, this interaction is defined as: :c,image(Eqs/pair_spin_me_interaction.jpg) @@ -69,5 +69,5 @@ package"_Build_package.html doc page for more info. [(Katsura)] H. Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005) :link(Tranchida4) -[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, +[(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, Journal of Computational Physics, (2018). diff --git a/doc/src/pair_spin_neel.txt b/doc/src/pair_spin_neel.txt index 7af71021a0..8e2242f013 100644 --- a/doc/src/pair_spin_neel.txt +++ b/doc/src/pair_spin_neel.txt @@ -24,8 +24,8 @@ pair_coeff 1 2 neel 4.0 0.0048 0.234 1.168 0.0 0.0 1.0 :pre [Description:] -Style {spin/neel} computes the Neel pair anisotropy model -between pairs of magnetic spins: +Style {spin/neel} computes the Neel pair anisotropy model +between pairs of magnetic spins: :c,image(Eqs/pair_spin_neel_interaction.jpg) @@ -50,8 +50,8 @@ above matches with the values of the magneto-elastic constant of the materials at stake. Examples and more explanations about this function and its -parametrization are reported in "(Tranchida)"_#Tranchida6. More -examples of parametrization will be provided in future work. +parameterization are reported in "(Tranchida)"_#Tranchida6. More +examples of parameterization will be provided in future work. From this DM interaction, each spin i will be submitted to a magnetic torque omega and its associated atom to a force F (for spin-lattice @@ -71,7 +71,7 @@ package"_Build_package.html doc page for more info. [Related commands:] -"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, +"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, "pair_eam"_pair_eam.html, [Default:] none diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt index 14e3f79215..f6fcd110d8 100644 --- a/doc/src/pair_style.txt +++ b/doc/src/pair_style.txt @@ -81,19 +81,15 @@ Here is an alphabetic list of pair styles defined in LAMMPS. They are also listed in more compact form on the "Commands pair"_Commands_pair.html doc page. -Click on the style to display the formula it computes, arguments -specified in the pair_style command, and coefficients specified by the -associated "pair_coeff"_pair_coeff.html command. +Click on the style to display the formula it computes, any additional +arguments specified in the pair_style command, and coefficients +specified by the associated "pair_coeff"_pair_coeff.html command. -There are also additional pair styles (not listed here) submitted by -users which are included in the LAMMPS distribution. The full list of -all pair styles is on the "Commands pair"_Commands_pair.html doc page. - -There are also additional accelerated pair styles (not listed here) -included in the LAMMPS distribution for faster performance on CPUs, -GPUs, and KNLs. The individual style names on the "Commands -pair"_Commands_pair.html doc page are followed by one or more of -(g,i,k,o,t) to indicate which accelerated styles exist. +There are also additional accelerated pair styles included in the +LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs. +The individual style names on the "Commands pair"_Commands_pair.html +doc page are followed by one or more of (g,i,k,o,t) to indicate which +accelerated styles exist. "none"_pair_none.html - turn off pairwise interactions "hybrid"_pair_hybrid.html - multiple styles of pairwise interactions @@ -134,13 +130,13 @@ pair"_Commands_pair.html doc page are followed by one or more of "comb"_pair_comb.html - charge-optimized many-body (COMB) potential "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential "coul/cut"_pair_coul.html - cutoff Coulombic potential -"coul/cut/soft"_pair_lj_soft.html - Coulombic potential with a soft core +"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening "coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity "coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model "coul/long"_pair_coul.html - long-range Coulombic potential "coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell -"coul/long/soft"_pair_lj_soft.html - long-range Coulombic potential with a soft core +"coul/long/soft"_pair_fep_soft.html - long-range Coulombic potential with a soft core "coul/msm"_pair_coul.html - long-range MSM Coulombics "coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential "coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals @@ -178,37 +174,41 @@ pair"_Commands_pair.html doc page are followed by one or more of "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP) +"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis "lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function "line/lj"_pair_line_lj.html - LJ potential between line segments "list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb -"lj/charmm/coul/long/soft"_pair_lj_soft.html - CHARMM with long-range Coulomb and a soft core +"lj/charmm/coul/long/soft"_pair_fep_soft.html - CHARMM with long-range Coulomb and a soft core "lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting "lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics "lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb "lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb +"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core "lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb +"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core +"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core "lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point "lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb "lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb -"lj/cut/coul/cut/soft"_pair_lj_soft.html - LJ with cutoff Coulomb with a soft core +"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core "lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb "lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces "lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics "lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments -"lj/cut/coul/long/soft"_pair_lj_soft.html - LJ with long-range Coulombics with a soft core +"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core "lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics "lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential "lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff "lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald -"lj/cut/soft"_pair_lj_soft.html - LJ with a soft core -"lj/cut/thole/long"_pair_thole.html - LJ with Coulomibics with thole damping +"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core +"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping "lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water "lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water -"lj/cut/tip4p/long/soft"_pair_lj_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core +"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core "lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles "lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics "lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential @@ -223,6 +223,7 @@ pair"_Commands_pair.html doc page are followed by one or more of "lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces "lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential "lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential +"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential "lubricate"_pair_lubricate.html - hydrodynamic lubrication forces "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity @@ -230,79 +231,79 @@ pair"_Commands_pair.html doc page are followed by one or more of "lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity "mdpd"_pair_meso.html - mDPD particle interactions "mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density -"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran -"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C +"meam/c"_pair_meamc.html - modified embedded atom method (MEAM) in C "meam/spline"_pair_meam_spline.html - splined version of MEAM "meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term "mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential "mie/cut"_pair_mie.html - Mie potential -"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field +"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics +"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field "morse"_pair_morse.html - Morse potential "morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential "morse/soft"_pair_morse.html - Morse potential with a soft core "multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force "multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force -"nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential +"nb3b/harmonic"_pair_nb3b_harmonic.html - non-bonded 3-body harmonic potential "nm/cut"_pair_nm.html - N-M potential "nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb "nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics -"oxdna/coaxstk"_pair_oxdna.html - -"oxdna/excv"_pair_oxdna.html - -"oxdna/hbond"_pair_oxdna.html - -"oxdna/stk"_pair_oxdna.html - -"oxdna/xstk"_pair_oxdna.html - -"oxdna2/coaxstk"_pair_oxdna2.html - -"oxdna2/dh"_pair_oxdna2.html - -"oxdna2/excv"_pair_oxdna2.html - -"oxdna2/hbond"_pair_oxdna2.html - -"oxdna2/stk"_pair_oxdna2.html - -"oxdna2/xstk"_pair_oxdna2.html - +"oxdna/coaxstk"_pair_oxdna.html - +"oxdna/excv"_pair_oxdna.html - +"oxdna/hbond"_pair_oxdna.html - +"oxdna/stk"_pair_oxdna.html - +"oxdna/xstk"_pair_oxdna.html - +"oxdna2/coaxstk"_pair_oxdna2.html - +"oxdna2/dh"_pair_oxdna2.html - +"oxdna2/excv"_pair_oxdna2.html - +"oxdna2/hbond"_pair_oxdna2.html - +"oxdna2/stk"_pair_oxdna2.html - +"oxdna2/xstk"_pair_oxdna2.html - "peri/eps"_pair_peri.html - peridynamic EPS potential "peri/lps"_pair_peri.html - peridynamic LPS potential "peri/pmb"_pair_peri.html - peridynamic PMB potential "peri/ves"_pair_peri.html - peridynamic VES potential "polymorphic"_pair_polymorphic.html - polymorphic 3-body potential -"python"_pair_python.html - -"quip"_pair_quip.html - -"reax"_pair_reax.html - ReaxFF potential in Fortran +"python"_pair_python.html - +"quip"_pair_quip.html - "reax/c"_pair_reaxc.html - ReaxFF potential in C "rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner "resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential -"smd/hertz"_pair_smd_hertz.html - -"smd/tlsph"_pair_smd_tlsph.html - -"smd/tri_surface"_pair_smd_triangulated_surface.html - -"smd/ulsph"_pair_smd_ulsph.html - -"smtbq"_pair_smtbq.html - +"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions +"smd/hertz"_pair_smd_hertz.html - +"smd/tlsph"_pair_smd_tlsph.html - +"smd/tri_surface"_pair_smd_triangulated_surface.html - +"smd/ulsph"_pair_smd_ulsph.html - +"smtbq"_pair_smtbq.html - "snap"_pair_snap.html - SNAP quantum-accurate potential "soft"_pair_soft.html - Soft (cosine) potential -"sph/heatconduction"_pair_sph_heatconduction.html - -"sph/idealgas"_pair_sph_idealgas.html - -"sph/lj"_pair_sph_lj.html - -"sph/rhosum"_pair_sph_rhosum.html - -"sph/taitwater"_pair_sph_taitwater.html - -"sph/taitwater/morris"_pair_sph_taitwater_morris.html - -"spin/dmi"_pair_spin_dmi.html - -"spin/exchange"_pair_spin_exchange.html - -"spin/magelec"_pair_spin_magelec.html - -"spin/neel"_pair_spin_neel.html - -"srp"_pair_srp.html - +"sph/heatconduction"_pair_sph_heatconduction.html - +"sph/idealgas"_pair_sph_idealgas.html - +"sph/lj"_pair_sph_lj.html - +"sph/rhosum"_pair_sph_rhosum.html - +"sph/taitwater"_pair_sph_taitwater.html - +"sph/taitwater/morris"_pair_sph_taitwater_morris.html - +"spin/dmi"_pair_spin_dmi.html - +"spin/exchange"_pair_spin_exchange.html - +"spin/magelec"_pair_spin_magelec.html - +"spin/neel"_pair_spin_neel.html - +"srp"_pair_srp.html - "sw"_pair_sw.html - Stillinger-Weber 3-body potential "table"_pair_table.html - tabulated pair potential -"table/rx"_pair_table_rx.html - +"table/rx"_pair_table_rx.html - "tdpd"_pair_meso.html - tDPD particle interactions "tersoff"_pair_tersoff.html - Tersoff 3-body potential "tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential -"tersoff/mod/c"_pair_tersoff_mod.html - -"tersoff/table"_pair_tersoff.html - +"tersoff/mod/c"_pair_tersoff_mod.html - +"tersoff/table"_pair_tersoff.html - "tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential "thole"_pair_thole.html - Coulomb interactions with thole damping "tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ "tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ -"tip4p/long/soft"_pair_lj_soft.html - +"tip4p/long/soft"_pair_fep_soft.html - "tri/lj"_pair_tri_lj.html - LJ potential between triangles -"ufm"_pair_ufm.html - +"ufm"_pair_ufm.html - "vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential -"vashishta/table"_pair_vashishta.html - +"vashishta/table"_pair_vashishta.html - "yukawa"_pair_yukawa.html - Yukawa potential "yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles "zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul diff --git a/doc/src/pair_sw.txt b/doc/src/pair_sw.txt index ff83316419..33c3892c62 100644 --- a/doc/src/pair_sw.txt +++ b/doc/src/pair_sw.txt @@ -124,13 +124,13 @@ configuration. In the literature, however, the three-body parameters are usually defined by simple formulas involving two sets of pair-wise parameters, corresponding to the ij and ik pairs, where i is the center atom. The user must ensure that the correct combining rule is -used to calculate the values of the threebody parameters for +used to calculate the values of the three-body parameters for alloys. Note also that the function phi3 contains two exponential screening factors with parameter values from the ij pair and ik pairs. So phi3 for a C atom bonded to a Si atom and a second C atom will depend on the three-body parameters for the CSiC entry, and also on the two-body parameters for the CCC and CSiSi entries. Since the -order of the two neighbors is arbitrary, the threebody parameters for +order of the two neighbors is arbitrary, the three-body parameters for entries CSiC and CCSi should be the same. Similarly, the two-body parameters for entries SiCC and CSiSi should also be the same. The parameters used only for two-body interactions (A, B, p, and q) in diff --git a/doc/src/pair_tri_lj.txt b/doc/src/pair_tri_lj.txt index 98bb4e284e..75108c0743 100644 --- a/doc/src/pair_tri_lj.txt +++ b/doc/src/pair_tri_lj.txt @@ -52,7 +52,7 @@ spheres. It the diameter is larger than sigma_II, then split the triangle into 2 triangles by bisecting its longest side. Repeat the process on each sub-triangle, recursing as far as needed to generate a set of covering spheres. When finished, the original criteria are -met, and the set of covering spheres shoule be near minimal in number +met, and the set of covering spheres should be near minimal in number and overlap, at least for input triangles with a reasonable aspect-ratio. diff --git a/doc/src/pair_ufm.txt b/doc/src/pair_ufm.txt index 787c60a1bd..f0efcfbf19 100644 --- a/doc/src/pair_ufm.txt +++ b/doc/src/pair_ufm.txt @@ -37,7 +37,7 @@ Style {ufm} computes pairwise interactions using the Uhlenbeck-Ford model (UFM) where rc is the cutoff, sigma is a distance-scale and epsilon is an energy-scale, i.e., a product of Boltzmann constant kB, temperature T and the Uhlenbeck-Ford p-parameter which is responsible to control the softness of the interactions "(Paula Leite2017)"_#PL1. -This model is useful as a reference system for fluid-phase free-energy calculations "(Paula Leite2016)"_#PL2. +This model is useful as a reference system for fluid-phase free-energy calculations "(Paula Leite2016)"_#PL2. The following coefficients must be defined for each pair of atom types via the "pair_coeff"_pair_coeff.html command as in the examples above, diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index d535798482..09c310a110 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -38,6 +38,7 @@ Pair Styles :h1 pair_eim pair_exp6_rx pair_extep + pair_fep_soft pair_gauss pair_gayberne pair_gran @@ -50,6 +51,7 @@ Pair Styles :h1 pair_kolmogorov_crespi_full pair_kolmogorov_crespi_z pair_lcbop + pair_lebedeva_z pair_line_lj pair_list pair_lj @@ -59,16 +61,17 @@ Pair Styles :h1 pair_lj_long pair_lj_smooth pair_lj_smooth_linear - pair_lj_soft + pair_lj_switch3_coulgauss pair_lubricate pair_lubricateU pair_mdf - pair_meam + pair_meamc pair_meam_spline pair_meam_sw_spline pair_meso pair_mgpt pair_mie + pair_mm3_switch3_coulgauss pair_momb pair_morse pair_multi_lucy @@ -82,10 +85,10 @@ Pair Styles :h1 pair_polymorphic pair_python pair_quip - pair_reax pair_reaxc pair_resquared pair_sdk + pair_sdpd_taitwater_isothermal pair_smd_hertz pair_smd_tlsph pair_smd_triangulated_surface diff --git a/doc/src/prd.txt b/doc/src/prd.txt index f71f285336..e1d6fc1b4e 100644 --- a/doc/src/prd.txt +++ b/doc/src/prd.txt @@ -48,11 +48,12 @@ replicas of a system. One or more replicas can be used. The total number of steps {N} to run can be interpreted in one of two ways; see discussion of the {time} keyword below. -PRD is described in "this paper"_#Voter1998 by Art Voter. It is a method -for performing accelerated dynamics that is suitable for -infrequent-event systems that obey first-order kinetics. A good -overview of accelerated dynamics methods for such systems in given in -"this review paper"_#Voter2002prd from the same group. To quote from the +PRD is described in "(Voter1998)"_#Voter1998 by Art Voter. Similar to +global or local hyperdynamics (HD), PRD is a method for performing +accelerated dynamics that is suitable for infrequent-event systems +that obey first-order kinetics. A good overview of accelerated +dynamics methods for such systems in given in this review paper +"(Voter2002)"_#Voter2002prd from Art's group. To quote from the paper: "The dynamical evolution is characterized by vibrational excursions within a potential basin, punctuated by occasional transitions between basins." The transition probability is @@ -61,15 +62,26 @@ Running multiple replicas gives an effective enhancement in the timescale spanned by the multiple simulations, while waiting for an event to occur. -Each replica runs on a partition of one or more processors. Processor -partitions are defined at run-time using the "-partition command-line -switch"_Run_options.html. Note that if you have MPI installed, you -can run a multi-replica simulation with more replicas (partitions) -than you have physical processors, e.g you can run a 10-replica -simulation on one or two processors. However for PRD, this makes -little sense, since running a replica on virtual instead of physical -processors,offers no effective parallel speed-up in searching for -infrequent events. See the "Howto replica"_Howto_replica.html doc +Both PRD and HD produce a time-accurate trajectory that effectively +extends the timescale over which a system can be simulated, but they +do it differently. PRD creates Nr replicas of the system and runs +dynamics on each independently with a normal unbiased potential until +an event occurs in one of the replicas. The time between events is +reduced by a factor of Nr replicas. HD uses a single replica of the +system and accelerates time by biasing the interaction potential in a +manner such that each timestep is effectively longer. For both +methods, per CPU second, more physical time elapses and more events +occur. See the "hyper"_hyper.html doc page for more info about HD. + +In PRD, each replica runs on a partition of one or more processors. +Processor partitions are defined at run-time using the "-partition +command-line switch"_Run_options.html. Note that if you have MPI +installed, you can run a multi-replica simulation with more replicas +(partitions) than you have physical processors, e.g you can run a +10-replica simulation on one or two processors. However for PRD, this +makes little sense, since running a replica on virtual instead of +physical processors,offers no effective parallel speed-up in searching +for infrequent events. See the "Howto replica"_Howto_replica.html doc page for further discussion. When a PRD simulation is performed, it is assumed that each replica is @@ -78,8 +90,8 @@ I.e. the simulation domain, the number of atoms, the interaction potentials, etc should be the same for every replica. A PRD run has several stages, which are repeated each time an "event" -occurs in one of the replicas, as defined below. The logic for a PRD -run is as follows: +occurs in one of the replicas, as explained below. The logic for a +PRD run is as follows: while (time remains): dephase for n_dephase*t_dephase steps @@ -129,7 +141,8 @@ Minimization parameters may be set via the PRD command. The latter are the settings that would be used with the "minimize"_minimize.html command. Note that typically, you do not need to perform a highly-converged minimization to detect a transition -event. +event, though you may need to in order to prevent a set of atoms in +the system from relaxing to a saddle point. The event check is performed by a compute with the specified {compute-ID}. Currently there is only one compute that works with the @@ -307,7 +320,7 @@ deposit"_fix_deposit.html. "min_modify"_min_modify.html, "min_style"_min_style.html, "run_style"_run_style.html, "minimize"_minimize.html, "velocity"_velocity.html, "temper"_temper.html, "neb"_neb.html, -"tad"_tad.html +"tad"_tad.html, "hyper"_hyper.html [Default:] diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index 6aa30d9e63..30ee1201d9 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -220,7 +220,7 @@ A data file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Then lines are read one at a time. Lines can have a trailing comment starting with '#' that is ignored. If the -line is blank (only whitespace after comment is deleted), it is +line is blank (only white-space after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn't contain a header keyword, the line begins the body of the file. @@ -249,7 +249,7 @@ standard header settings, such as the number of atoms. The formatting of individual lines in the data file (indentation, spacing between words and numbers) is not important except that header and section keywords (e.g. atoms, xlo xhi, Masses, Bond Coeffs) must -be capitalized as shown and can't have extra white space between their +be capitalized as shown and can't have extra white-space between their words - e.g. two spaces or a tab between the 2 words in "xlo xhi" or the 2 words in "Bond Coeffs", is not valid. @@ -553,7 +553,7 @@ bond: atom-ID molecule-ID atom-type x y z charge: atom-ID atom-type q x y z dipole: atom-ID atom-type q x y z mux muy muz dpd: atom-ID atom-type theta x y z -edpd: atom-ID atom-type edpd_temp edpd_cv x y z +edpd: atom-ID atom-type edpd_temp edpd_cv x y z mdpd: atom-ID atom-type rho x y z tdpd: atom-ID atom-type x y z cc1 cc2 ... ccNspecies electron: atom-ID atom-type q spin eradius x y z @@ -577,7 +577,7 @@ atom-type = type of atom (1-Ntype) bodyflag = 1 for body particles, 0 for point particles cc = chemical concentration for tDPD particles for each species (mole/volume units) contact-radius = ??? (distance units) -cs_re,cs_im = real/imaginary parts of wavepacket coefficients +cs_re,cs_im = real/imaginary parts of wave packet coefficients cv = heat capacity (need units) for SPH particles density = density of particle (mass/distance^3 or mass/distance^2 or mass/distance units, depending on dimensionality of particle) diameter = diameter of spherical atom (distance units) @@ -586,7 +586,7 @@ edpd_temp = temperature for eDPD particles (temperature units) edpd_cv = volumetric heat capacity for eDPD particles (energy/temperature/volume units) ellipsoidflag = 1 for ellipsoidal particles, 0 for point particles eradius = electron radius (or fixed-core radius) -etag = integer ID of electron that each wavepacket belongs to +etag = integer ID of electron that each wave packet belongs to kernel-radius = ??? (distance units) lineflag = 1 for line segment particles, 0 for point or spherical particles mass = mass of particle (mass units) @@ -620,7 +620,7 @@ to 0. The molecule ID is a 2nd identifier attached to an atom. Normally, it is a number from 1 to N, identifying which molecule the atom belongs -to. It can be 0 if it is an unbonded atom or if you don't care to +to. It can be 0 if it is a non-bonded atom or if you don't care to keep track of molecule assignments. The diameter specifies the size of a finite-size spherical particle. @@ -682,7 +682,7 @@ were used in the input script, each atom line would have these fields: atom-ID atom-type x y z q diameter density :pre Note that if a non-standard value is defined by multiple sub-styles, -it must appear mutliple times in the atom line. E.g. the atom line +it must appear multiple times in the atom line. E.g. the atom line for atom_style hybrid dipole full would list "q" twice: atom-ID atom-type x y z q mux muy myz molecule-ID q :pre diff --git a/doc/src/read_dump.txt b/doc/src/read_dump.txt index db9cfca825..df357a5018 100644 --- a/doc/src/read_dump.txt +++ b/doc/src/read_dump.txt @@ -22,7 +22,8 @@ field = {x} or {y} or {z} or {vx} or {vy} or {vz} or {q} or {ix} or {iy} or {iz} {ix},{iy},{iz} = image flags in each dimension {fx},{fy},{fz} = force components :pre zero or more keyword/value pairs may be appended :l -keyword = {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l +keyword = {nfile} or {box} or {replace} or {purge} or {trim} or {add} or {label} or {scaled} or {wrapped} or {format} :l + {nfile} value = Nfiles = how many parallel dump files exist {box} value = {yes} or {no} = replace simulation box with dump box {replace} value = {yes} or {no} = overwrite atoms with dump atoms {purge} value = {yes} or {no} = delete all atoms before adding dump atoms @@ -85,9 +86,18 @@ command, after the dump snapshot is read. If the dump filename specified as {file} ends with ".gz", the dump file is read in gzipped format. You cannot (yet) read a dump file -that was written in binary format with a ".bin" suffix, or to multiple -files via the "%" option in the dump file name. See the -"dump"_dump.html command for details. +that was written in binary format with a ".bin" suffix. + +You can read dump files that were written (in parallel) to multiple +files via the "%" wild-card character in the dump file name. If any +specified dump file name contains a "%", they must all contain it. +See the "dump"_dump.html command for details. +The "%" wild-card character is only supported by the {native} format +for dump files, described next. + +If reading parallel dump files, you must also use the {nfile} keyword +to tell LAMMPS how many parallel files exist, via its specified +{Nfiles} value. The format of the dump file is selected through the {format} keyword. If specified, it must be the last keyword used, since all remaining @@ -119,7 +129,7 @@ Support for other dump format readers may be added in the future. Global information is first read from the dump file, namely timestep and box information. -The dump file is scanned for a snapshot with a time stamp that matches +The dump file is scanned for a snapshot with a timestamp that matches the specified {Nstep}. This means the LAMMPS timestep the dump file snapshot was written on for the {native} format. Note that the {xyz} and {molfile} formats do not store the timestep. For these formats, diff --git a/doc/src/region.txt b/doc/src/region.txt index acc85dcebb..d163f62dcb 100644 --- a/doc/src/region.txt +++ b/doc/src/region.txt @@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp dim = {x} or {y} or {z} = axis of cylinder c1,c2 = coords of cylinder axis in other 2 dimensions (distance units) radius = cylinder radius (distance units) - radius can be a variable (see below) + c1,c2, and radius can be a variable (see below) lo,hi = bounds of cylinder in dim (distance units) {plane} args = px py pz nx ny nz px,py,pz = point on the plane (distance units) @@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp {sphere} args = x y z radius x,y,z = center of sphere (distance units) radius = radius of sphere (distance units) - radius can be a variable (see below) + x,y,z, and radius can be a variable (see below) {union} args = N reg-ID1 reg-ID2 ... N = # of regions to follow, must be 2 or greater reg-ID1,reg-ID2, ... = IDs of regions to join together @@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified as an equal-style "variable"_variable.html. If the value is a variable, it should be specified as v_name, where name is the variable name. In this case, the variable will be evaluated each timestep, and -its value used to determine the radius of the region. +its value used to determine the radius of the region. For style {sphere} +also the x-, y-, and z- coordinate of the center of the sphere and for +style {cylinder} the two center positions c1 and c2 for the location of +the cylinder axes can be a variable with the same kind of effect and +requirements than for the radius. Equal-style variables can specify formulas with various mathematical functions, and include "thermo_style"_thermo_style.html command keywords for the simulation box parameters and timestep and elapsed -time. Thus it is easy to specify a time-dependent radius. +time. Thus it is easy to specify a time-dependent radius or have +a time dependent position of the sphere or cylinder region. See the "Howto tricilinc"_Howto_triclinic.html doc page for a geometric description of triclinic boxes, as defined by LAMMPS, and @@ -293,7 +298,7 @@ variable dysame equal 5*sin(2*PI*elaplong*dt/100) region 2 sphere 10.0 10.0 0.0 5 move NULL v_dy NULL :pre The {rotate} keyword rotates the region around a rotation axis {R} = -(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The rotation +(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz). The rotation angle is calculated, presumably as a function of time, by a variable specified as v_theta, where theta is the variable name. The variable should generate its result in radians. The direction of rotation for diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index 71ad464bb0..3d5cdfff3c 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -89,12 +89,31 @@ this auxiliary information should be defined in the usual way, e.g. in a data file read in by a "read_data"_read_data.html command, before using the rerun command. +Also note that the frequency of thermodynamic or dump output from the +rerun simulation will depend on settings made in the rerun script, the +same as for output from any LAMMPS simulation. See further info below +as to what that means if the timesteps for snapshots read from dump +files do not match the specified output frequency. + :line If more than one dump file is specified, the dump files are read one after the other. It is assumed that snapshot timesteps will be in ascending order. If a snapshot is encountered that is not in -ascending order, it will cause the rerun command to complete. +ascending order, it will skip the snapshot until it reads one that is. +This allows skipping of a duplicate snapshot (same timestep), +e.g. that appeared at the end of one file and beginning of the next. +However if you specify a series of dump files in an incorrect order +(with respect to the timesteps they contain), you may skip large +numbers of snapshots + +Note that the dump files specified as part of the {dump} keyword can +be parallel files, i.e. written as multiple files either per processor +and/or per snapshot. If that is the case they will also be read in +parallel which can make the rerun command operate dramatically faster +for large systems. See the doc page for the "read_dump"_read_dump and +"dump"_dump.html commands which describe how to read and write +parallel dump files. The {first}, {last}, {every}, {skip} keywords determine which snapshots are read from the dump file(s). Snapshots are skipped until @@ -150,8 +169,8 @@ indent"_fix_indent.html and "fix langevin"_fix_langevin.html. So you should think carefully as to whether that makes sense for the manner in which you are reprocessing the dump snapshots. -If you only want the rerun script to perform analyses that do not -involve pair interactions, such as use compute msd to calculated +If you only want the rerun script to perform an analysis that does +not involve pair interactions, such as use compute msd to calculated displacements over time, you do not need to define a "pair style"_pair_style.html, which may also mean neighbor lists will not need to be calculated which saves time. The "comm_modify @@ -177,12 +196,12 @@ a timestep it expects to be, LAMMPS will flag an error. The various forms of LAMMPS output, as defined by the "thermo_style"_thermo_style.html, "thermo"_thermo.html, -"dump"_dump.html, and "restart"_restart.html commands occur on -specific timesteps. If successive dump snapshots skip those -timesteps, then no output will be produced. E.g. if you request -thermodynamic output every 100 steps, but the dump file snapshots are -every 1000 steps, then you will only see thermodynamic output every -1000 steps. +"dump"_dump.html, and "restart"_restart.html commands occur with +specified frequency, e.g. every N steps. If the timestep for a dump +snapshot is not a multiple of N, then it will be read and processed, +but no output will be produced. If you want output for every dump +snapshot, you can simply use N=1 for an output frequency, e.g. for +thermodynamic output or new dump file output. :line diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 9defd1314e..bf13d20439 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -191,7 +191,7 @@ hybrid/overlay"_pair_hybrid.html command. In this scenario, different sub-styles of the hybrid pair style are evaluated at different rRESPA levels. This can be useful, for example, to set different timesteps for hybrid coarse-grained/all-atom models. The {hybrid} keyword -requires as many level assignments as there are hybrid substyles, +requires as many level assignments as there are hybrid sub-styles, which assigns each sub-style to a rRESPA level, following their order of definition in the pair_style command. Since the {hybrid} keyword operates on pair style computations, it is mutually exclusive with diff --git a/doc/src/server.txt b/doc/src/server.txt index 86fb68d012..8f87b5c76b 100644 --- a/doc/src/server.txt +++ b/doc/src/server.txt @@ -15,7 +15,7 @@ server protocol :pre protocol = {md} or {mc} :ul [Examples:] - + server md :pre [Description:] diff --git a/doc/src/server_mc.txt b/doc/src/server_mc.txt index 58ca415be3..ef3c56f886 100644 --- a/doc/src/server_mc.txt +++ b/doc/src/server_mc.txt @@ -15,7 +15,7 @@ server mc :pre mc = the protocol argument to the "server"_server.html command [Examples:] - + server mc :pre [Description:] @@ -46,7 +46,7 @@ examples/COUPLE/lammps_mc/in.server. When using this command, LAMMPS (as the server code) receives instructions from a Monte Carlo (MC) driver to displace random atoms, compute the energy before and after displacement, and run dynamics to -equilibrate the system. +equilibrate the system. The MC driver performs the random displacements on random atoms, accepts or rejects the move in an MC sense, and orchestrates the MD @@ -60,7 +60,7 @@ pages for more details on the actual library syntax. The "cs" object in this pseudo code is a pointer to an instance of the CSlib. See the src/MESSAGE/server_mc.cpp file for details on how LAMMPS uses -these messages. See the examples/COUPLE/lammmps_mc/mc.cpp file for an +these messages. See the examples/COUPLE/lammps_mc/mc.cpp file for an example of how an MC driver code can use these messages. Define NATOMS=1, EINIT=2, DISPLACE=3, ACCEPT=4, RUN=5. @@ -83,7 +83,7 @@ cs->pack_int(1,nsteps) # 1st field = # of timesteps to run MD :pre [Server replies]: -cs->send(NATOMS,1) # msgID = 1 with 1 field +cs->send(NATOMS,1) # msgID = 1 with 1 field cs->pack_int(1,natoms) # 1st field = number of atoms :pre cs->send(EINIT,2) # msgID = 2 with 2 fields diff --git a/doc/src/server_md.txt b/doc/src/server_md.txt index 753542dc75..03f3db7e19 100644 --- a/doc/src/server_md.txt +++ b/doc/src/server_md.txt @@ -15,7 +15,7 @@ server md :pre md = the protocol argument to the "server"_server.html command [Examples:] - + server md :pre [Description:] @@ -119,7 +119,7 @@ The units for various quantities that are sent and received iva messages are defined for atomic-scale simulations in the table below. The client and server codes (including LAMMPS) can use internal units different than these (e.g. "real units"_units.html in LAMMPS), so long -as they convert to these units for meesaging. +as they convert to these units for messaging. COORDS, ORIGIN, BOX = Angstroms CHARGE = multiple of electron charge (1.0 is a proton) diff --git a/doc/src/set.txt b/doc/src/set.txt index b83ad54f4e..15c96071ae 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -245,13 +245,13 @@ many processors are being used. This keyword does not allow use of an atom-style variable. Keyword {spin} uses the specified g value to set the magnitude of the -magnetic spin vectors, and the x,y,z values as components of a vector -to set as the orientation of the magnetic spin vectors of the selected -atoms. +magnetic spin vectors, and the x,y,z values as components of a vector +to set as the orientation of the magnetic spin vectors of the selected +atoms. Keyword {spin/random} randomizes the orientation of the magnetic spin -vectors for the selected atoms and sets the magnitude of each to the -specified {Dlen} value. +vectors for the selected atoms and sets the magnitude of each to the +specified {Dlen} value. Keyword {quat} uses the specified values to create a quaternion (4-vector) that represents the orientation of the selected atoms. The diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index e90535e65f..f8316a9bfb 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -61,9 +61,9 @@ Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, e.g. when using the "pair_style hybrid"_pair_hybrid.html command. -Thus LAMMPS ignores special_bonds settings when manybody potentials +Thus LAMMPS ignores special_bonds settings when many-body potentials are calculated. Please note, that the existence of explicit bonds -for atoms that are described by a manybody potential will alter the +for atoms that are described by a many-body potential will alter the neighbor list and thus can render the computation of those interactions invalid, since those pairs are not only used to determine direct pairwise interactions but also neighbors of neighbors and more. @@ -196,19 +196,25 @@ the options you need each time. This command cannot be used a 2nd time incrementally. E.g. these two commands: special_bonds lj 0.0 1.0 1.0 -special_bonds coul 0.0 0.0 1.0 +special_bonds coul 0.0 0.0 1.0 :pre are not the same as -special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0 +special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0 :pre In the first case you end up with (after the 2nd command): LJ: 0.0 0.0 0.0 -Coul: coul 0.0 0.0 1.0 +Coul: 0.0 0.0 1.0 :pre -because the LJ settings are reset to their default values -each time the command is issued. +while only in the second case, you get the desired settings of: + +LJ: 0.0 1.0 1.0 +Coul: 0.0 0.0 1.0 :pre + +This happens because the LJ (and Coul) settings are reset to +their default values before modifying them, each time the +{special_bonds} command is issued. [Restrictions:] none diff --git a/doc/src/suffix.txt b/doc/src/suffix.txt index 62e41ed29a..e9fae44088 100644 --- a/doc/src/suffix.txt +++ b/doc/src/suffix.txt @@ -46,7 +46,7 @@ run on one or more GPUs or multicore CPU/GPU nodes :ulb,l USER-INTEL = a collection of pair styles and neighbor routines optimized to run in single, mixed, or double precision on CPUs and -Intel(R) Xeon Phi(TM) coprocessors. :l +Intel(R) Xeon Phi(TM) co-processors. :l KOKKOS = a collection of atom, pair, and fix styles optimized to run using the Kokkos library on various kinds of hardware, including GPUs diff --git a/doc/src/tad.txt b/doc/src/tad.txt index 9b34a68636..effb998f94 100644 --- a/doc/src/tad.txt +++ b/doc/src/tad.txt @@ -18,7 +18,7 @@ t_event = timestep interval between event checks :l T_lo = temperature at which event times are desired :l T_hi = temperature at which MD simulation is performed :l delta = desired confidence level for stopping criterion :l -tmax = reciprocal of lowest expected preexponential factor (time units) :l +tmax = reciprocal of lowest expected pre-exponential factor (time units) :l compute-ID = ID of the compute used for event detection :l zero or more keyword/value pairs may be appended :l keyword = {min} or {neb} or {min_style} or {neb_style} or {neb_log} :l diff --git a/doc/src/temper_npt.txt b/doc/src/temper_npt.txt index 50ac5615f6..00a3e35ec3 100644 --- a/doc/src/temper_npt.txt +++ b/doc/src/temper_npt.txt @@ -23,7 +23,7 @@ index = which temperature (0 to N-1) I am simulating (optional) :ul [Examples:] temper/npt 100000 100 $t nptfix 0 58728 1 -temper/npt 2500000 1000 300 nptfix 0 32285 $p +temper/npt 2500000 1000 300 nptfix 0 32285 $p temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre [Description:] @@ -43,7 +43,7 @@ of pressure, this command works much like the "temper"_temper.html command. See the documentation on "temper"_temper.html for information on how the parallel tempering is handled in general. -:line +:line [Restrictions:] diff --git a/doc/src/timer.txt b/doc/src/timer.txt index 4025af9ea6..6da74ca153 100644 --- a/doc/src/timer.txt +++ b/doc/src/timer.txt @@ -19,7 +19,7 @@ timer args :pre {full} = like {normal} but also include CPU and thread utilization {sync} = explicitly synchronize MPI tasks between sections {nosync} = do not synchronize MPI tasks between sections (default) - {timeout} elapse = set walltime limit to {elapse} + {timeout} elapse = set wall time limit to {elapse} {every} Ncheck = perform timeout check every {Ncheck} steps :pre [Examples:] @@ -57,13 +57,13 @@ though it can also slow down the simulation by prohibiting overlapping independent computations on different MPI ranks Using the {nosync} setting (which is the default) turns this synchronization off. -With the {timeout} keyword a walltime limit can be imposed, that +With the {timeout} keyword a wall time limit can be imposed, that affects the "run"_run.html and "minimize"_minimize.html commands. This can be convenient when calculations have to comply with execution time limits, e.g. when running under a batch system when you want to maximize the utilization of the batch time slot, especially for runs where the time per timestep varies much and thus it becomes difficult -to predict how many steps a simulation can perform for a given walltime +to predict how many steps a simulation can perform for a given wall time limit. This also applies for difficult to converge minimizations. The timeout {elapse} value should be somewhat smaller than the maximum wall time requested from the batch system, as there is usually diff --git a/doc/src/units.txt b/doc/src/units.txt index 8df8fe6810..844504d977 100644 --- a/doc/src/units.txt +++ b/doc/src/units.txt @@ -201,13 +201,13 @@ The units command also sets the timestep size and neighbor skin distance to default values for each style: For style {lj} these are dt = 0.005 tau and skin = 0.3 sigma. -For style {real} these are dt = 1.0 fmsec and skin = 2.0 Angstroms. -For style {metal} these are dt = 0.001 psec and skin = 2.0 Angstroms. -For style {si} these are dt = 1.0e-8 sec and skin = 0.001 meters. -For style {cgs} these are dt = 1.0e-8 sec and skin = 0.1 cm. -For style {electron} these are dt = 0.001 fmsec and skin = 2.0 Bohr. -For style {micro} these are dt = 2.0 microsec and skin = 0.1 micrometers. -For style {nano} these are dt = 0.00045 nanosec and skin = 0.1 nanometers. :ul +For style {real} these are dt = 1.0 femtoseconds and skin = 2.0 Angstroms. +For style {metal} these are dt = 0.001 picoseconds and skin = 2.0 Angstroms. +For style {si} these are dt = 1.0e-8 seconds and skin = 0.001 meters. +For style {cgs} these are dt = 1.0e-8 seconds and skin = 0.1 centimeters. +For style {electron} these are dt = 0.001 femtoseconds and skin = 2.0 Bohr. +For style {micro} these are dt = 2.0 microseconds and skin = 0.1 micrometers. +For style {nano} these are dt = 0.00045 nanoseconds and skin = 0.1 nanometers. :ul [Restrictions:] diff --git a/doc/src/variable.txt b/doc/src/variable.txt index a8d50503ac..77c1f6eeb0 100644 --- a/doc/src/variable.txt +++ b/doc/src/variable.txt @@ -339,7 +339,7 @@ below. The rules for formatting the file are as follows. A comment character "#" can be used anywhere on a line; text starting with the comment character is stripped. Blank lines are skipped. The first "word" of -a non-blank line, delimited by white space, is the "string" assigned +a non-blank line, delimited by white-space, is the "string" assigned to the variable. For the {atomfile} style, a filename is provided which contains one or @@ -358,7 +358,7 @@ The rules for formatting the file are as follows. Each time a set of per-atom values is read, a non-blank line is searched for in the file. A comment character "#" can be used anywhere on a line; text starting with the comment character is stripped. Blank lines are skipped. The -first "word" of a non-blank line, delimited by white space, is read as +first "word" of a non-blank line, delimited by white-space, is read as the count N of per-atom lines to immediately follow. N can be be the total number of atoms in the system, or only a subset. The next N lines have the following format diff --git a/doc/src/write_data.txt b/doc/src/write_data.txt index b6002b5252..a8168b70a0 100644 --- a/doc/src/write_data.txt +++ b/doc/src/write_data.txt @@ -87,7 +87,7 @@ are read in separately anyway, e.g. from an include file. The {nofix} keyword requests that no extra sections read by fixes should be written to the data file (see the {fix} option of the "read_data"_read_data.html command for details). For example, this -option excludes sections for user-created per-atom properties +option excludes sections for user-created per-atom properties from "fix property/atom"_fix_property_atom.html. The {pair} keyword lets you specify in what format the pair diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py index 6c70cf9804..29de3af156 100644 --- a/doc/utils/sphinx-config/conf.py +++ b/doc/utils/sphinx-config/conf.py @@ -211,7 +211,9 @@ latex_elements = { #'pointsize': '10pt', # Additional stuff for the LaTeX preamble. -#'preamble': '', +'preamble': r''' +\setcounter{tocdepth}{2} +''' } # Grouping the document tree into LaTeX files. List of tuples @@ -219,7 +221,7 @@ latex_elements = { # author, documentclass [howto, manual, or own class]). latex_documents = [ ('Manual', 'LAMMPS.tex', 'LAMMPS Documentation', - 'Steve Plimpton', 'manual'), + 'The LAMMPS Developers', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of @@ -229,7 +231,7 @@ latex_documents = [ # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False - +latex_toplevel_sectioning = 'part' # If true, show page references after internal links. #latex_show_pagerefs = False @@ -248,7 +250,7 @@ latex_documents = [ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ - ('Manual', 'liggghts', 'LAMMPS Documentation', + ('Manual', 'lammps', 'LAMMPS Documentation', ['Steve Plimpton'], 1) ] diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index febd5c20a0..6eb158396f 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -2,37 +2,38 @@ aa aat abc abf +ABI +abo +Abramyan absTol Acc +Accelerys Accelrys acceptor Acceptor acceptors -accomodate accuracies ach -achived -achives ackland Ackland acolor acos Acta actinide -adaptation addforce +Addington addtorque +adf Adhikari adiam +adim Adjiman adof adp Adri -adusting advect advection advects -afer affine Afshar agilio @@ -49,6 +50,7 @@ Aktulga al alain Alain +Alamos alat Albe alchemical @@ -58,18 +60,24 @@ Alejandre alessandro Alessandro aliceblue +Allinger allocaters allosws AlO -alond Alonso amap Amatrix +amino +Amirjalayer Amit amu Amzallag +analytical +Anders Andzelm Ang +anglegrad +angletangrad angmom angmomx angmomy @@ -79,12 +87,13 @@ anharmonic anharmonicity aniso anisotropic +anisotropy ansi antiquewhite Antisymmetrized antisymmetry +anton Antonelli -aperiodic api Appl Apu @@ -92,8 +101,8 @@ arccos arcsin arg args -artefacts Arun +arXiv asin Askari askoose @@ -101,8 +110,7 @@ asphere ASPHERE aspherical Asq -assinged -associdate +assignee Asta Astart Astop @@ -114,12 +122,11 @@ atc AtC ATC athomps -atobody +atm atomeye atomfile atomID atomistic -atomt attogram attograms attrac @@ -128,7 +135,6 @@ Atwater atwt augt AuO -autocorrelation automagically Avalos avalue @@ -139,33 +145,36 @@ AVX awpmd AWPMD Axel +Axilrod Ay Ayton Az +Azevedo azimuthal +Azuri ba Babadi backcolor -backend Baczewski Bal balancer +Balankura Balasubramanian +Balatsky Ballenegger Bammann Barashev barostat -barostated -barostating +Barostats barostatted barostatting Barostatting -barosttating Barrat Bartels barycenter barye Bashford +bashrc Baskes Batra Bayly @@ -173,6 +182,7 @@ bb bcc bcolor bdiam +bdw Beckman behaviour Belak @@ -187,12 +197,14 @@ berger Berkowitz berlin Berne +Bertotti Beutler bgq Bh -biaxial Biersack +bigbig bigint +Bij bilayer bilayers binsize @@ -205,6 +217,7 @@ Biosym bisectioning bispectrum Bispectrum +bitbucket bitmapped bitrate bitrates @@ -215,53 +228,72 @@ blocksize blueviolet bn bni +bo +Bochum +bocs bodyflag +bodyforce bodystyle Bogaerts Bogusz Bohrs +Boltzman bondchk -bondings bondmax bondtype Bonet +Bonomi boolean +boostostat +boostostatting Boresch Botero Botu Bouguet -bount boxcolor +bp +bpls bpclermont br +Branduardi Branicio brennan Brilliantov Broadwell +Broglie brownian brownw Bryantsev +Btarget btype buckPlusAttr -bugfixes Bulatov +Bureekaew burlywood Bussi +Buturigakkwaishi Buyl Bybee bz cadetblue +calibre caltech Caltech +Camilloni +Camiloni Campana Cao Capolungo Caro cartesian +Caswell Cates +Cavium +Cawkwell cbecker ccache ccmake +ccNspecies CCu cd cdeam @@ -269,7 +301,6 @@ cdennist cdof ceil Ceil -centre centro centroid Centroid @@ -285,20 +316,26 @@ CFL cgdna CGDNA cgs +cgsdk +CGSDK Chalopin Champaign charmm -charmmfsw -charmmfsh -charmm CHARMM +charmmfsh +charmmfsw +Chaudhuri +checkbox checkmark checkqeq +chemistries +Chemnitz Cheng Chenoweth chiral chirality Cho +chris Christoph Chu chunkID @@ -310,6 +347,7 @@ cis civ clearstore Clebsch +clemson Clermont clo Clovertown @@ -325,6 +363,7 @@ cn cN Cn cna +cnp cnr coaxstk codebase @@ -333,51 +372,51 @@ Coeff CoefficientN coeffs Coeffs +Coker Colberg coleman Colliex collinear +collisional +Columic colvars Colvars COLVARS comID Commun -complier compressibility compressive Comput computable compute -concetric +concat cond Condens +conf config configfile configurational conformational -conjuction -consiting -continously Contrib coord Coord CoordN coords -coprocessor -coprocessors coreshell cornflowerblue cornsilk +corotate +corotational correlator cosineshifted cossq costheta Couette coul +coulgauss coulombic Coulombic Coulombics -Coulommbic Courant covalent covalently @@ -386,17 +425,23 @@ cpp cpu createatoms createAtoms +crespi +Crespi Critchley crossterm -crossterms +Crowson Crozier -crystallisation Crystallogr Csanyi csh cshrc CSiC csld +cslib +CSlib +cstdio +cstdlib +cstring cstyle csvr Ctypes @@ -404,6 +449,9 @@ cuda Cuda CUDA CuH +Curk +customIDs +cutbond cuthi cutinner cutlo @@ -444,52 +492,61 @@ darkturquoise darkviolet Das Dasgupta +dat datafile datums Davidchack Daw dcd +dcub +Dcut de dE De debye Debye +Decius decompositions +decrementing deeppink deepskyblue -defauls defgrad deformable -degress del +deleteIDs Dellago delocalization delocalized delr deltaHf Dendrimer -dendtritic +dendritic Denniston dephase dephasing -depositied dequidt Dequidt der +derekt Derjagin Derlet Deserno Destree detils Devanathan +devel Devemy deviatoric Devine df dfftw DFT +dftb +dh +dhex dia diag +diagonalization diagonalized Diallo diel @@ -511,24 +568,28 @@ discoverable discretization discretized disp -displacment dissipative Dissipative -distro -divdes +distharm dl dlambda DLAMMPS +dll dlopen dm dmax Dmax +dmg +dmi +dnf +Dobson Dodds dodgerblue dof Donadio dotc Doty +doxygen Doye dpd DPD @@ -549,11 +610,13 @@ DRUDE dsf dsmc dt +dtheta du dU Dudarev Duin Dullweber +dumpfile Dunbrack Dunweg Dupont @@ -564,9 +627,12 @@ dVx dW dx dy +dyn dyne dynes +dynmat Dyre +Dzyaloshinskii Eaa Eaat Eacn @@ -575,26 +641,35 @@ eangle eatom Eba ebond +ebook ebt +ec Ec ecoul ecp +edgeIDs edihed edim edip +edpd +eDPD edu ee Eebt +ees eFF efield eflux +eg Eggebrecht -ehanced ehex eHEX Ei Eigen Eigensolve +eij +Eij +Eijnden Eike eim eimp @@ -612,8 +687,13 @@ Elj Ellad ellipsoidflag elong +Elsevier +Elsner +Elstner elt emacs +emax +Emax Embt emi emol @@ -626,16 +706,22 @@ engilitycorp engrot engtrans engvib +enobonds enthalpy +enums envoke eos epair epcc +epl Epp Epq eps Epton +epub +ePUB eq +eqal eqch Eqp Eqq @@ -647,11 +733,11 @@ equilibrated equilibrating equilibration Equilibria -equilibribum equilization eradius erate erc +erf erfc Erhart erorate @@ -659,11 +745,14 @@ erose erotate Ertas ervel +Espanol esu esub +esw et etag etap +ETarget ethernet etol etot @@ -682,14 +771,18 @@ excitations excv exe executables +extep extrema +exy ey ez factorizable factorizations +Fahrenberger Faken Farago Fasolino +Fath Fava fbMC Fc @@ -712,6 +805,7 @@ Ferrand fexternal Fexternal ffield +ffl ffmpeg FFmpeg ffplay @@ -720,13 +814,17 @@ fftbench fftw fhg Fi +Fichthorn +Fickian figshare Fij +filelink filename -filenames Filename +filenames Filenames fileper +filesystem Fincham Finchham Finnis @@ -741,24 +839,31 @@ flagN flagVF fld floralwhite +Florez flv fmackay fmag fmass +fmm fmsec +fmx +fmy +fmz fN Fn fname fno +Fnudge foces Fock Fogarty Foiles fopenmp -forcefield forestgreen formulae +Forschungszentrum Fortran +Fosado fourier fp fphi @@ -767,19 +872,21 @@ fplo Fqq Fraige framerate +Frauenheim Fraunhofer Freitas Frenkel Friedrichs -frontend -Frontends fs +fsh fstyle +fsw ftol fugacity Fumi func funcs +functionalities functionals funroll fx @@ -788,6 +895,8 @@ fz Gahler gainsboro Galindo +gamA +gamR gammaA gammaFactor gammaR @@ -797,8 +906,10 @@ ganzenmueller Ganzenmuller Gao Gathert +Gaus gauss gaussian +gaussians Gaussians Gavhane gayberne @@ -806,6 +917,7 @@ gcc gcmc gdot GeC +gencode georg Georg Germann @@ -823,11 +935,13 @@ gif gifsicle Gillan Gingold +Gissinger github -Github gjf gjwagne gl +gladky +Gladky gld gle globbing @@ -837,11 +951,13 @@ gmail gmake gmask Gmask +googlemail Gordan GPa gpu gpuID gpus +gradV graining Graining Grama @@ -855,30 +971,36 @@ grem gREM Grest Grigera +Grimme grmask Grmask gromacs Gromacs +gromos Gronbech Groot groupbig +grp Grueneisen gsmooth gstyle GTL +Gubbins +Guericke gui -guidline Gumbsch Gunsteren Gunzenmuller Guo -gwald +gw gz gzipped Haak Hafskjold Halperin +Halver Hamaker +Hamel haptic Hara Harpertown @@ -886,9 +1008,12 @@ Harting Hartree Hartrees Hasan +Haswell +Haugk Hayoun Hayre hbcut +hbn hbnewflag hbond hcp @@ -901,7 +1026,6 @@ Henin Henkelman henrich Henrich -heristics Herrmann Hertizian hertzian @@ -914,12 +1038,14 @@ HfO hgrid Hibbs Higdon +Hijazi Hilger histo histogrammed histogramming hmaktulga hoc +Hochbruck Hofling Holian Holm @@ -934,27 +1060,32 @@ Hoyt hstyle html hTST +https hu +Hueckel +Huetter +Hugonio hugoniostat Hugoniostat Hugoniot Hura +hux hwloc -hydrogens +hydrophobicity hydrostatic hydrostatically Hynninen Hyoungki +hyperdynamics hyperradius hyperspherical -hyperthreaded -Hyperthreading +Ibanez ibar ibm icc -icosohedral +ico +icosahedral idealgas -ideaology IDR ielement ieni @@ -969,6 +1100,7 @@ ik Ikeshoji ilmenau Ilmenau +ilp Ilya im Im @@ -977,10 +1109,8 @@ Imageint Imagemagick imd Impey -imporopers impropers Impropers -imroper includelink incompressible incrementing @@ -997,7 +1127,6 @@ init initializations InP inregion -integrations integrators Integrators intel @@ -1006,10 +1135,11 @@ interal interatomic Interatomic interconvert -intergation interial +interlayer intermolecular interstitials +Intr intra intramolecular ints @@ -1017,12 +1147,15 @@ inv invariants inversed ionocovalent +iostreams iparam ipi ipp +IPv IPython Isele isenthalpic +ish iso isodemic isoenergetic @@ -1038,6 +1171,7 @@ Ith Itsets itype itypeN +iva Ivector Iw ixcm @@ -1063,11 +1197,13 @@ izz Izz Jacobsen jagreat +Jalalvand james Janssens Jaramillo Jarzynski jatempl +jcp jea jec Jeffers @@ -1079,10 +1215,12 @@ Jiao jik JIK jku +jN Joannopoulos Jochim Jonsson Jorgensen +jp jparam jpeg jpeglib @@ -1092,7 +1230,11 @@ jpl Jth jtype jtypeN +Juelich Julien +junghans +Junghans +Jungnickel Jupyter Justo Jusufi @@ -1105,17 +1247,23 @@ Kalia Kamberaj Kapfer Karlsruhe +Karniadakis Karplus Karttunen kate +Katsnelson +Katsura Kaufmann +Kawata Kayser kb kB kbit kbits kcal +kcl Kd +KDevelop ke KE Keblinski @@ -1126,6 +1274,7 @@ Kelkar Kemper Keyes Khersonskii +Khrapak Khvostov Ki kim @@ -1136,29 +1285,38 @@ Klapp Kloss kmax Kmax +Knizhnik knl Kohlmeyer +Kohn kokkos Kolafa Kollman +kolmogorov +Kolmogorov Kondor konglt Koning Kooser Koskinen +Koster Kosztin Kp Kraker Kraus Kremer Kress +Kronik kspace Kspace KSpace Kspring kT +kTequil kth Kth +kTln +ktypeN Kub Kubo Kumagai @@ -1181,11 +1339,14 @@ Landron langevin Langevin Langston +lanl larentzos Larentzos Laroche lars latencies +Latour +latourr lattce Laupretre lavenderblush @@ -1197,9 +1358,13 @@ lcbop ld ldfftw ldg +Lebedeva +lebedeva +Lebold Lechman Lehoucq Leimkuhler +Leite leiu lemonchiffon Lenart @@ -1208,24 +1373,39 @@ Lennard Lenosky Lett Leuven +Leven Lewy lgvdw Liang +libatc libAtoms +libawpmd +libch +libcolvars +libcurl libdir +libdl +libfftw +libgcc libgpu libjpeg +libkim liblammps Liblammps liblink libmeam +libmessage libmpi libmpich +libplumed +libplumedKernel libpng libpoems +libqmmm librar libreax libs +Lifshitz ligand lightblue lightcoral @@ -1242,6 +1422,7 @@ lightsteelblue lightyellow Likhtman limegreen +linalg Lindahl lineflag lineforce @@ -1254,6 +1435,7 @@ Littmark Liu Livermore lj +llammps lm lmp lmpptr @@ -1272,8 +1454,12 @@ lookups Lookups LoopVar Lorant +lorenz +lossless lossy +Lozovik lps +lpsapi lrt lsfftw ltbbmalloc @@ -1281,17 +1467,23 @@ lubricateU lucy Lussetti Lustig +lwsock lx ly Lybrand Lyulin lz +Maaravi Mackay Mackrodt macroparticle Madura Magda +Magdeburg +magelec Maginn +magneton +mainboard mainboards makefile Makefile @@ -1303,6 +1495,7 @@ malloc Malolepsza Manby Mandadapu +Mandelli Manh manifoldforce Manolopoulos @@ -1313,10 +1506,14 @@ Marrink Marsaglia Marseille Martyna +Masaglia Mashayak +Massimilliano massless masstotal +Masuhiro Matchett +Materias matlab matplotlib Mattox @@ -1324,24 +1521,32 @@ Mattson maxangle maxbond maxeval +maxfiles Maxfoo +maxima maxit maxiter maxsize maxspecial maxSteps +maxstrain maxX +Mayergoyz mbt Mbytes MBytes +mc McLachlan md mdf +mdpd +mDPD meam +meamc +MEAMC meamf +meanDist mech -mechanice -mechanim Mecke mediumaquamarine mediumblue @@ -1364,24 +1569,26 @@ membered Mendelev mer Meremianin +Mersenne Merz -mescscopic meshless meso -mesocopic mesoparticle mesoscale mesoscopic metadynamics Metadynamics +Methfessel methine Metin +meV Mezei mgpt MGPT mgptfast mh micelle +micelles michael michele Mickel @@ -1389,7 +1596,6 @@ microcanonical microelastic microporous Microscale -microsec midnightblue mie Mie @@ -1406,6 +1612,7 @@ minorder minSteps mintcream Mintmire +Miron mis Mises Mishin @@ -1417,19 +1624,24 @@ mK mkdir mkv mlparks -mlutiple +Mniszewski +mnt +mobi modc Modell modelled modelling Modelling Modine +mofff +MOFFF +Mohd mol Mol molfile Molfile moltemplate -momoner +momb Monaghan Monaghans monodisperse @@ -1438,22 +1650,29 @@ monovalent Montalenti Montero Morefoo +Morfill +Mori +Moriya morris Morriss morse +Morteza +Mosayebi Moseler Moskalev mov mpi -Mpi MPI mpicc +mpiCC mpich +mpicolor mpicxx mpiexec mpiio mpirun mplayer +Mryglod mscg MSCG msd @@ -1466,6 +1685,7 @@ Mtchell Mth mtk Mtotal +muB Muccioli Mukherjee Mulders @@ -1474,6 +1694,7 @@ multibody Multibody multicenter multicmd +multicomponent multicore multielectron multinode @@ -1487,8 +1708,7 @@ Murdick Murtola Murty Muser -mutli -mutliple +Muto muVT mux muy @@ -1496,6 +1716,7 @@ muz mv mV Mvapich +mvv MxN myCompute myIndex @@ -1503,11 +1724,15 @@ mylammps mysocket myTemp myVec +na nabla +Nagaosa Nakano namespace namespaces +nan NaN +Nandor Nangletype nangletypes Nangletypes @@ -1517,10 +1742,11 @@ Nanoletters nanometer nanometers nanoparticles -nanosec +nanotubes Narulkar nasa nasr +natively Natoli natoms Natoms @@ -1554,20 +1780,25 @@ Ndof Ndouble ndx neb +neel +Neel Neelov -neighbouring +Negre nelem Nelement Nelements nemd netcdf +Nettleton Neumann +Nevent nevery Nevery Newns newtype Neyts Nf +nfft nfile Nfile Nfreq @@ -1576,15 +1807,18 @@ Ng nghost Nghost Ngpu +Ngyuen nh nharmonic nhc NiAlH Nicklas +Niklasson Nimpropertype Ninteger Nissila nist +nitride nitrides niu Nk @@ -1594,6 +1828,7 @@ Nlines nlocal Nlocal Nlog +nlp nm Nm Nmax @@ -1606,8 +1841,7 @@ nocoeff nodeless noforce Noid -Nonbond -nonbonded +nolib nonequilibrium nongauss nonGaussian @@ -1650,29 +1884,33 @@ Ns Nsample nsec Nskip +Nspecies nsq Nstart nstats Nstep Nsteplast Nstop +nsub Nswap Nt Ntable ntheta nthreads Ntptask +Ntriples Ntype ntypes Ntypes nucleotides -nulcear num numa numactl +numericalfreedom numerics numpy Numpy +Nurdin Nvalue Nvaluelast Nvalues @@ -1691,13 +1929,15 @@ ny Ny nz Nz +ocl octahedral octants ohenrich ok -OKeefe -OKeefe +Okabe +Okamoto O'Keefe +OKeefe oldlace Oleinik Olfason @@ -1707,6 +1947,7 @@ omegaDD omegax omegay omegaz +Omelyan omp OMP onelevel @@ -1716,12 +1957,11 @@ ons OO openKIM OpenMP +openmp +openmpi opls Oppelstrup -optionns orangered -orderomg -organised organometallic orientational orientorder @@ -1729,20 +1969,20 @@ Orlikowski ornl Ornstein Orsi +ortho orthonormal orthorhombic ot Ouldridge +outfile outmost outpur outputss -outut +Ouyang overlayed -overviewed Ovito oxdna oxDNA -oxygens padua Padua palegoldenrod @@ -1756,7 +1996,6 @@ papayawhip paquay Paquay parallelepiped -parallelipiped Parallelizable parallelization parallelized @@ -1766,19 +2005,18 @@ parameterization parameterizations parameterize parameterized -parametrization -parametrized params -Parinello parmin Parrinello Partay -partices Particuology pastewka Pastewka +pathangle +Patomtrans Pattnaik Pavese +Paxton pbc pc pchain @@ -1786,23 +2024,26 @@ Pchain Pdamp pdb pdf +pdfs pdim pe Peachey peachpuff Pearlman Pedersen +peID Peng +peptide peratom -perfoms Pergamon peri -Peridymaics peridynamic Peridynamic peridynamics Peridynamics +perl permittivity +perp Perram persp Persp @@ -1810,20 +2051,23 @@ peru Peskin Pettifor pfactor +pgi ph Phillpot +phiphi phonon phophorous phosphide +Phs Physica physik +Piaggi picocoulomb picocoulombs picogram picograms picosecond picoseconds -picosend pid Pieter pimd @@ -1839,9 +2083,13 @@ plog ploop PloS plt +plumedfile pmb +Pmolrotate +Pmoltrans pN png +Podhorszki Poiseuille Polak polarizabilities @@ -1849,18 +2097,22 @@ polarizability polarizable Polarizable polarizables +polarizer Politano polyA polybond polydisperse polydispersity +polyhedra popen +Popov popstore +Poresag pos Poschel posix Postma -postprocessing +Potapkin potin Pourtois powderblue @@ -1870,14 +2122,16 @@ prd pre Pre prec -preexponential +preceed +preceeded +precession prefactor prefactors prepend preprint -preprocessor printf printflag +priori Priya proc Proc @@ -1896,13 +2150,15 @@ pstyle Ptarget pthread pthreads +ptm +PTM ptr pu purdue -pushded pushstore pvar pw +pwqmmm px Px pxx @@ -1913,6 +2169,7 @@ Py pydir pylammps PyLammps +pymodule pymol pypar Pyy @@ -1923,9 +2180,11 @@ qbmsst qcore qdist qE +qeff qeq QeQ QEq +qfactor qfile qi Qi @@ -1940,8 +2199,8 @@ qoffload qopenmp qoverride qtb +quadrupolar Quant -quantic quartic quaternion quaternions @@ -1950,6 +2209,10 @@ quatj quatk quatw Queteschiner +qw +qx +qy +qz radian radians Rafferty @@ -1957,7 +2220,9 @@ rahman Rahman Raman ramped +ramping Ramprasad +Randisi randomizations Raphson Rappe @@ -1971,32 +2236,32 @@ Rcut rcutfac rdc rdf +RDideal README realtime reamin reax +REAXC ReaxFF -rebalance -rebalancing rebo -recentered -recentering recursing Ree +refactored regoin Reinders -relect -relesed +reinit +relink relTol remappings -remediate Ren Rendon +reneighbor reneighboring Reneighboring reneighborings Rensselaer -reparametrizing +reparameterizing +repo representable repuls rescale @@ -2011,7 +2276,9 @@ responder resquared REsquared restartfile +restartinfo rethrowing +Revenga rewrap rezwanur rfac @@ -2023,15 +2290,20 @@ rheological rhodo Rhodo rhodopsin +rhok +rhorho rhosum +ri Ri Ribiere richard rigidID rigidify rij +rIJ Rij RIj +Rik Rin Rino RiRj @@ -2040,10 +2312,18 @@ Rix Riy rj Rj +Rjinner +RjinnerN Rjk rjones +Rjouter +RjouterN rk rkf +Rkinner +RkinnerN +Rkouter +RkouterN rmask Rmask rmax @@ -2052,24 +2332,32 @@ rmdir rmin Rmin RMS +rmsd +rnage rNEMD ro +Rochus Rockett +Rohart Ronchetti Rosati Rossky rosybrown rotationally -rotationsl +Rovigatti royalblue rozero Rperp +Rr rRESPA Rspace +rsq +Rubensson Rubia Rudd Rudra Rudranarayan +Rudzinski Runge runtime Rutuparna @@ -2084,11 +2372,14 @@ saed safezone Safran Sagui +Saidi Salles sandia Sandia sandybrown sc +scafacos +SCAFACOS scalability scalable Scalable @@ -2096,32 +2387,43 @@ scalexy scalexz scaleyz Schaik +Schilfgarde +Schiotz Schlitter Schmid Schoen +Schotte Schulten Schunk +Schuring Schwen -scriping Scripta sdk +sdpd +SDPD seagreen Secor +sectoring sed segmental +Seifert sellerio Sellerio +Semaev semiaxes semimetals Semin Sensable +Sep +seqdep +Serpico setfl setforce +Sethna setmask Setmask setpoint setvel -severeal sfftw Sg Shan @@ -2137,16 +2439,16 @@ Shenderova Shiga Shinoda shockvel -shoule si SiC Siepmann +Sievers Sij Sikandar Silbert Silling +Sim Simul -simulataneous simulations Sinnott sinusoid @@ -2157,18 +2459,23 @@ Sival sizeI sizeJ sizex +sj sjplimp sjtu skyblue +Skylake slateblue slategray slater Slepoy -sligthly Sliozberg +sLLG sllod +sm +smallbig smallint Smallint +smallsmall smd SMD smi @@ -2181,9 +2488,9 @@ snapcoeff snaphots snapparam snav +Snodin Sodani Soderlind -softed solvated Sorensen soundspeed @@ -2194,18 +2501,24 @@ Spearot Spellmeyer sph SPH -spheriods +Spickermann +splined spparks Springer springgreen +spx +spz +sqdistharm sqrt src srd +Srinivasan Srolovitz srp srun ss ssao +stamoor stamoore stanford Starikov @@ -2214,9 +2527,12 @@ Startstep statcoul statcoulombs statvolt +stdlib stdin +stdio steelblue Stegailov +Steinbach Steinhardt Steinhauser Stepaniants @@ -2234,6 +2550,7 @@ stopstep Stouch Straatsma Stratford +Strathclyde Straub strcmp streitz @@ -2242,29 +2559,25 @@ Streiz strided strietz Stukowski -stylecomputes Su subbox subcutoff -subdirectory -subdomains -subinterval -subintervals Subramaniyan subscripted subscripting -substeps -substyle -substyles sudo +Sugaku +Suhai Sukumaran +Sulc sumsq Sunderland superset supersphere Supinski -surc surfactants +Sutmann +svn sw Swegat swiggle @@ -2278,72 +2591,77 @@ symplectic Synechococcus sys sysdim -sysmte Syst Sz Tabbernor tabinner Tadmor +Tafipolsky +tagID tagint Tait taitwater Tajkhorshid +Tamaskovics tanh +Tartakovsky taskset taubi +tb tchain Tchain Tcom tcsh tdamp +tdpd +tDPD Tdrude Technolgy Telsa tempCorrCoeff templated Templeton +Tequil ters tersoff Tersoff tesselation -tesselations Tetot tex +tfac tfmc tfMC th Thakkar -Thakker thb thei Theor thermalization thermalize thermalized +Thermalized thermalizing +Thermalizing thermo thermochemical thermochemistry -thermodynamic thermodynamically Thermophysical -thermostate -thermostated -thermostates -thermostating -Thermostating thermostatted thermostatting Thermostatting Thes Thess Thexe +Thiaville +Thibaudeau Thijsse Thirumalai -threebody thrid +ThunderX thylakoid THz +Tigran Tij Tildesley timespan @@ -2368,7 +2686,9 @@ Tmin tmp tN Tobias +tokyo tol +toolchain topologies Torder torsions @@ -2381,25 +2701,32 @@ tptask tqx tqy tqz +traceless tradeoff traj +Tranchida transferability translational +Translational trate Tref Tretyakov tri triangleflag +Tribello triclinic +Triclinic triflag trigonal trilinear +Trinkle tripflag tris trj trott Trott Trung +Trushin tscale Tschopp Tsige @@ -2408,14 +2735,17 @@ Tstart tstat Tstop Tsuzuki +tt Tt TThis ttm tu Tuckerman tue +tunable Turkand Tutein +tweakable twobody twojmax Tx @@ -2429,10 +2759,14 @@ ub Uberuaga uChem uCond +uef +UEF +ufm Uhlenbeck Ui uk ul +ulb uloop ulsph uMech @@ -2440,7 +2774,6 @@ umin Umin un unary -unbonded uncomment uncompute underprediction @@ -2457,7 +2790,6 @@ unphysical unphysically unscaled unsets -unshifted unsmoothed unsolvated unsplit @@ -2466,9 +2798,11 @@ untar untilted upenn upto +Urbakh Urbana usec userguide +username usr util utils @@ -2483,23 +2817,26 @@ valgrind Valone valuev Valuev -valus -valuse +Vanden +Vandenbrande +Vanduyfhuys +varavg Varshalovich Varshney vashishta Vashishta +vasp vcm Vcm vdim vdisplace +vdW vec vectorial vectorization +Vectorization vectorized -Vectorized vel -velocites Verlag verlet Verlet @@ -2514,13 +2851,13 @@ Virial virialmode virials virtualenv -virutal viscoelastic viscoelasticity viscosities viscously vizplotgui Vj +Vkl vlo vmax vmd @@ -2529,6 +2866,7 @@ VMDHOME vn Voigt volfactor +Volpe volpress volumetric von @@ -2542,6 +2880,7 @@ Voth vpz vratio Vries +Vsmall Vstream vtarget vtk @@ -2564,31 +2903,33 @@ Waals Wadley wallstyle walltime -warmup -wavefunction +Waltham wavepacket -wavepackets -wavevector wB Wbody +webpage Weckner +WeinenE Wennberg Westview +wget Whelan -whenthe whitesmoke -whitespace Wi Wicaksono wih +Wijk wildcard +Wildcard Wirnsberger wirtes witin wn Wolde +workflow Worley Wriggers +Wuppertal Wurtzite www wx @@ -2603,11 +2944,13 @@ xb Xc xcm Xcm +Xcode xCORE Xeon xflag xhi xHost +Xiaohu Xiaowang xk xlat @@ -2621,6 +2964,7 @@ Xmovie xmu Xmu XP +xplane XPlor xrd xs @@ -2633,7 +2977,10 @@ xy xyz xz xzhou +YAFF +yaff Yamada +Yazdani Ybar ybox Yc @@ -2650,8 +2997,10 @@ ys ysu yu Yu +Yuh yukawa Yukawa +Yusof yx yy yz @@ -2660,9 +3009,11 @@ zbl ZBL Zc zcm +Zeeman Zepeda zflag Zhang +Zhen zhi Zhou Zhu @@ -2673,6 +3024,7 @@ Ziegenhain Zj zlim zlo +zmq zN zs zsu diff --git a/examples/README b/examples/README index 3c9c299819..e03dacec82 100644 --- a/examples/README +++ b/examples/README @@ -78,6 +78,7 @@ friction: frictional contact of spherical asperities between 2d surfaces gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command granregion: use of fix wall/region/gran as boundary on granular particles hugoniostat: Hugoniostat shock dynamics +hyper: global and local hyperdynamics of diffusion on Pt surface indent: spherical indenter into a 2d solid kim: use of potentials in Knowledge Base for Interatomic Models (KIM) latte: use of LATTE density-functional tight-binding quantum code diff --git a/examples/SPIN/spinmin/in.spinmin.bfo b/examples/SPIN/spinmin/in.spinmin.bfo new file mode 100644 index 0000000000..5ebc9e0afe --- /dev/null +++ b/examples/SPIN/spinmin/in.spinmin.bfo @@ -0,0 +1,55 @@ +# bfo in a 3d periodic box + +units metal +dimension 3 +boundary p p f +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice sc 3.96 +region box block 0.0 34.0 0.0 34.0 0.0 1.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 1.0 +set group all spin/random 11 2.50 + +pair_style hybrid/overlay spin/exchange 6.0 spin/magelec 4.5 spin/dmi 4.5 +pair_coeff * * spin/exchange exchange 6.0 -0.01575 0.0 1.965 +#pair_coeff * * spin/magelec magelec 4.5 0.000109 1.0 1.0 1.0 +pair_coeff * * spin/magelec magelec 4.5 0.00109 1.0 1.0 1.0 +pair_coeff * * spin/dmi dmi 4.5 0.00005 1.0 1.0 1.0 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 +fix 1 all precession/spin anisotropy 0.0000033 0.0 0.0 1.0 +fix_modify 1 energy yes + +timestep 0.0001 + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 50 +thermo_style custom step time v_magnorm v_emag v_tmag temp etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 50 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +min_style spin +min_modify alpha_damp 1.0 discrete_factor 10.0 +minimize 1.0e-10 0.0 1000 100 diff --git a/examples/SPIN/spinmin/in.spinmin.iron b/examples/SPIN/spinmin/in.spinmin.iron new file mode 100644 index 0000000000..ebbd229b89 --- /dev/null +++ b/examples/SPIN/spinmin/in.spinmin.iron @@ -0,0 +1,55 @@ +# bcc iron in a 3d periodic box + +units metal +dimension 3 +boundary p p f +atom_style spin + +# necessary for the serial algorithm (sametag) +atom_modify map array + +lattice bcc 2.8665 +region box block 0.0 4.0 0.0 4.0 0.0 4.0 +create_box 1 box +create_atoms 1 box + +# setting mass, mag. moments, and interactions for bcc iron + +mass 1 55.845 +set group all spin/random 31 2.2 +#set group all spin 2.2 1.0 1.0 -1.0 + +pair_style spin/exchange 3.5 +pair_coeff * * exchange 3.4 0.02726 0.2171 1.841 + +neighbor 0.1 bin +neigh_modify every 10 check yes delay 20 + +#fix 1 all precession/spin zeeman 0.001 0.0 0.0 1.0 anisotropy 0.01 1.0 0.0 0.0 +fix 1 all precession/spin anisotropy 0.0001 0.0 0.0 1.0 +fix_modify 1 energy yes + +timestep 0.0001 + +compute out_mag all spin +compute out_pe all pe +compute out_ke all ke +compute out_temp all temp + +variable magx equal c_out_mag[1] +variable magy equal c_out_mag[2] +variable magz equal c_out_mag[3] +variable magnorm equal c_out_mag[4] +variable emag equal c_out_mag[5] +variable tmag equal c_out_mag[6] + +thermo 100 +thermo_style custom step time v_magx v_magz v_magnorm v_tmag etotal +thermo_modify format float %20.15g + +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 100 dump.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] c_outsp[4] c_outsp[5] c_outsp[6] c_outsp[7] + +min_style spin +min_modify alpha_damp 1.0 discrete_factor 10.0 +minimize 1.0e-10 1.0e-10 100000 1000 diff --git a/examples/USER/adios/adios2_config.xml b/examples/USER/adios/adios2_config.xml new file mode 100644 index 0000000000..4b9cd9b9b5 --- /dev/null +++ b/examples/USER/adios/adios2_config.xml @@ -0,0 +1,41 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/examples/USER/adios/in.adios_balance b/examples/USER/adios/in.adios_balance new file mode 100644 index 0000000000..d89ae52b41 --- /dev/null +++ b/examples/USER/adios/in.adios_balance @@ -0,0 +1,57 @@ +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 +variable v index 5 +variable w index 2 + +units lj +dimension 2 +atom_style atomic +boundary f f p + +lattice hex 0.85 +region box block 0 $x 0 $y -0.5 0.5 +create_box 1 box +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +create_atoms 1 region circle +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 + +comm_style tiled +fix 10 all balance 50 0.9 rcb + +compute 1 all property/atom proc +variable p atom c_1%10 +dump 2 all custom 50 balance.dump id v_p x y z +dump 3 all custom/adios 50 balance_custom.bp id v_p x y z +dump 4 all atom/adios 50 balance_atom.bp + +#dump 3 all image 50 image.*.jpg v_p type & +# adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string & +# "red green blue yellow white & +# purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 200 +write_dump all atom/adios balance_atom_final.bp diff --git a/examples/USER/adios/log.balance b/examples/USER/adios/log.balance new file mode 100644 index 0000000000..162ecf7741 --- /dev/null +++ b/examples/USER/adios/log.balance @@ -0,0 +1,114 @@ +LAMMPS (4 Jan 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 +variable v index 5 +variable w index 2 + +units lj +dimension 2 +atom_style atomic +boundary f f p + +lattice hex 0.85 +Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 +region box block 0 $x 0 $y -0.5 0.5 +region box block 0 50 0 $y -0.5 0.5 +region box block 0 50 0 20 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) + 2 by 2 by 1 MPI processor grid +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 10 +create_atoms 1 region circle +Created 361 atoms + Time spent = 0.00171804 secs +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes +velocity all set 5 $w 0 sum yes +velocity all set 5 2 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 + +comm_style tiled +fix 10 all balance 50 0.9 rcb + +compute 1 all property/atom proc +variable p atom c_1%10 +dump 2 all custom 50 balance.dump id v_p x y z +dump 3 all custom/adios 50 balance_custom.bp id v_p x y z +dump 4 all atom/adios 50 balance_atom.bp + +#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string # "red green blue yellow white # purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 200 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.926 | 4.933 | 4.944 Mbytes +Step Temp E_pair Press f_10[3] f_10 + 0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316 + 100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709 + 200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102 +Loop time of 0.0992351 on 4 procs for 200 steps with 361 atoms + +Performance: 870660.046 tau/day, 2015.417 timesteps/s +32.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0078368 | 0.0081607 | 0.0085468 | 0.3 | 8.22 +Neigh | 0.002804 | 0.0045915 | 0.0092173 | 3.9 | 4.63 +Comm | 0.044407 | 0.05352 | 0.062051 | 3.0 | 53.93 +Output | 0.011406 | 0.012025 | 0.01342 | 0.7 | 12.12 +Modify | 0.006305 | 0.0064294 | 0.0066617 | 0.2 | 6.48 +Other | | 0.01451 | | | 14.62 + +Nlocal: 90.25 ave 91 max 90 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 58.25 ave 64 max 51 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 730.75 ave 801 max 671 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 2923 +Ave neighs/atom = 8.09695 +Neighbor list builds = 60 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/atc/cauchy_born/Au_u3.eam b/examples/USER/atc/cauchy_born/Au_u3.eam new file mode 120000 index 0000000000..2ace8a4162 --- /dev/null +++ b/examples/USER/atc/cauchy_born/Au_u3.eam @@ -0,0 +1 @@ +../../../../potentials/Au_u3.eam \ No newline at end of file diff --git a/examples/USER/atc/cauchy_born/ftcb_constV_setup.init b/examples/USER/atc/cauchy_born/ftcb_constV_setup.init new file mode 100644 index 0000000000..c8ab629267 --- /dev/null +++ b/examples/USER/atc/cauchy_born/ftcb_constV_setup.init @@ -0,0 +1,1751 @@ +LAMMPS data file from restart file: timestep = 0, procs = 1 + +864 atoms + +1 atom types + +0.0000000000000000e+00 3.1537364922000002e+01 xlo xhi +0.0000000000000000e+00 3.1537364922000002e+01 ylo yhi +0.0000000000000000e+00 3.1537364922000002e+01 zlo zhi + +Masses + +1 39.95 + +Pair Coeffs + +1 0.238 3.405 + +Atoms + +1 1 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 +2 1 2.6281137435000002e+00 2.6281137435000002e+00 0.0000000000000000e+00 0 0 0 +3 1 2.6281137435000002e+00 0.0000000000000000e+00 2.6281137435000002e+00 0 0 0 +4 1 0.0000000000000000e+00 2.6281137435000002e+00 2.6281137435000002e+00 0 0 0 +5 1 5.2562274870000003e+00 0.0000000000000000e+00 0.0000000000000000e+00 0 0 0 +6 1 7.8843412305000005e+00 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diff --git a/examples/USER/awpmd/H/README b/examples/USER/awpmd/README similarity index 100% rename from examples/USER/awpmd/H/README rename to examples/USER/awpmd/README diff --git a/examples/USER/awpmd/H/data.h_atom b/examples/USER/awpmd/data.h_atom similarity index 100% rename from examples/USER/awpmd/H/data.h_atom rename to examples/USER/awpmd/data.h_atom diff --git a/examples/USER/awpmd/H/data.h_molecule b/examples/USER/awpmd/data.h_molecule similarity index 100% rename from examples/USER/awpmd/H/data.h_molecule rename to examples/USER/awpmd/data.h_molecule diff --git a/examples/USER/awpmd/H/in.h_atom b/examples/USER/awpmd/in.h_atom similarity index 96% rename from examples/USER/awpmd/H/in.h_atom rename to examples/USER/awpmd/in.h_atom index 6eb78ba4c2..60b7a07da4 100644 --- a/examples/USER/awpmd/H/in.h_atom +++ b/examples/USER/awpmd/in.h_atom @@ -1,5 +1,4 @@ variable sname index h_atom -log ${sname}.spe.log units real newton on @@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press -run 0 +run 10 diff --git a/examples/USER/awpmd/H/in.h_molecule b/examples/USER/awpmd/in.h_molecule similarity index 96% rename from examples/USER/awpmd/H/in.h_molecule rename to examples/USER/awpmd/in.h_molecule index 78df85d185..2f02aa7038 100644 --- a/examples/USER/awpmd/H/in.h_molecule +++ b/examples/USER/awpmd/in.h_molecule @@ -1,5 +1,4 @@ variable sname index h_molecule -log ${sname}.spe.log units real newton on @@ -37,4 +36,4 @@ variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) thermo 1 thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press -run 0 +run 10 diff --git a/examples/USER/awpmd/log.27Nov18.h_atom.g++.1 b/examples/USER/awpmd/log.27Nov18.h_atom.g++.1 new file mode 100644 index 0000000000..2ee048f3c9 --- /dev/null +++ b/examples/USER/awpmd/log.27Nov18.h_atom.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable sname index h_atom + +units real +newton on +boundary p p p +processors 1 * * + + +atom_style wavepacket + +read_data data.${sname} +read_data data.h_atom + orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + +#neighbor 2.0 nsq + +pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press +pair_coeff * * + + + +timestep 0.001 + +fix 1 all nve/awpmd + +comm_modify vel yes + +compute energies all pair awpmd/cut +variable eke equal c_energies[1] +variable epauli equal c_energies[2] +variable estatics equal c_energies[3] +variable errestrain equal c_energies[4] + +compute peratom all stress/atom NULL +compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] +variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) + +thermo 1 +thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press + +run 10 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.52918 + ghost atom cutoff = 2.52918 + binsize = 1.26459, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair awpmd/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933) +Per MPI rank memory allocation (min/avg/max) = 5.111 | 5.111 | 5.111 Mbytes +Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press + 0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0 + 1 -266.3192 -266.3192 0 266.32746 0 -532.64666 0 0 159.30733 -0 + 2 -266.3192 -266.3192 1.7273458e-17 266.32797 0 -532.64718 0 5.7948873e-15 169.14686 6.6606909e-13 + 3 -266.3192 -266.3192 4.6899813e-15 266.32927 0 -532.64847 0 1.5733915e-12 194.06892 1.8084691e-10 + 4 -266.3192 -266.3192 1.4824973e-13 266.33199 0 -532.6512 0 4.9734712e-11 246.65762 5.7165485e-09 + 5 -266.3192 -266.3192 1.9298888e-12 266.33712 0 -532.65632 0 6.4743771e-10 345.53056 7.441702e-08 + 6 -266.3192 -266.3192 1.5343223e-11 266.34601 0 -532.66521 0 5.1473332e-09 516.91949 5.9163869e-07 + 7 -266.3192 -266.3192 8.8661674e-11 266.36051 0 -532.6797 0 2.9744154e-08 796.4357 3.4188175e-06 + 8 -266.31919 -266.31919 4.0865149e-10 266.38304 0 -532.70223 0 1.3709411e-07 1231.0302 1.5757709e-05 + 9 -266.31918 -266.31918 1.5889509e-09 266.41674 0 -532.73592 0 5.3306012e-07 1881.1652 6.1270366e-05 + 10 -266.31916 -266.31916 5.4070747e-09 266.46554 0 -532.7847 0 1.8139615e-06 2823.2238 0.00020849822 +Loop time of 0.000725031 on 1 procs for 10 steps with 2 atoms + +Performance: 1.192 ns/day, 20.140 hours/ns, 13792.516 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00030851 | 0.00030851 | 0.00030851 | 0.0 | 42.55 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0001204 | 0.0001204 | 0.0001204 | 0.0 | 16.61 +Output | 0.00028038 | 0.00028038 | 0.00028038 | 0.0 | 38.67 +Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.85 +Other | | 9.537e-06 | | | 1.32 + +Nlocal: 2 ave 2 max 2 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 248 ave 248 max 248 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 225 ave 225 max 225 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 225 +Ave neighs/atom = 112.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/awpmd/log.27Nov18.h_atom.g++.4 b/examples/USER/awpmd/log.27Nov18.h_atom.g++.4 new file mode 100644 index 0000000000..2ab2177279 --- /dev/null +++ b/examples/USER/awpmd/log.27Nov18.h_atom.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable sname index h_atom + +units real +newton on +boundary p p p +processors 1 * * + + +atom_style wavepacket + +read_data data.${sname} +read_data data.h_atom + orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2 atoms + +#neighbor 2.0 nsq + +pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press +pair_coeff * * + + + +timestep 0.001 + +fix 1 all nve/awpmd + +comm_modify vel yes + +compute energies all pair awpmd/cut +variable eke equal c_energies[1] +variable epauli equal c_energies[2] +variable estatics equal c_energies[3] +variable errestrain equal c_energies[4] + +compute peratom all stress/atom NULL +compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] +variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) + +thermo 1 +thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press + +run 10 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.52918 + ghost atom cutoff = 2.52918 + binsize = 1.26459, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair awpmd/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933) +Per MPI rank memory allocation (min/avg/max) = 5.391 | 5.391 | 5.391 Mbytes +Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press + 0 -266.3192 -266.3192 0 266.32732 0 -532.64652 0 0 156.59865 -0 + 1 -266.3192 -266.3192 0 266.32789 0 -532.64709 0 0 167.49891 -0 + 2 -266.3192 -266.3192 1.219316e-15 266.3314 0 -532.6506 0 4.0905525e-13 235.2267 4.7017146e-11 + 3 -266.3192 -266.3192 8.3179871e-14 266.34548 0 -532.66468 0 2.7905123e-11 506.68594 3.2074377e-09 + 4 -266.3192 -266.3192 4.4091748e-12 266.39036 0 -532.70955 0 1.4791868e-09 1372.0565 1.7001894e-07 + 5 -266.31916 -266.31916 9.8904198e-11 266.51357 0 -532.83273 0 3.3180309e-08 3748.6725 3.8137718e-06 + 6 -266.31893 -266.31893 1.3132578e-09 266.81733 0 -533.13626 0 4.4057077e-07 9611.8807 5.0639565e-05 + 7 -266.31762 -266.31762 1.2317167e-08 267.50719 0 -533.82481 0 4.1321544e-06 22950.26 0.00047495321 + 8 -266.31123 -266.31123 9.0048883e-08 268.97689 0 -535.28812 0 3.0209534e-05 51470.197 0.0034723086 + 9 -266.28324 -266.28324 5.4612621e-07 271.95757 0 -538.24082 0 0.00018321403 109735.25 0.02105877 + 10 -266.17113 -266.17114 2.8729529e-06 277.79384 0 -543.96498 0 0.00096381615 225424.02 0.11078182 +Loop time of 0.00176561 on 4 procs for 10 steps with 2 atoms + +Performance: 0.489 ns/day, 49.045 hours/ns, 5663.769 timesteps/s +87.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.3419e-05 | 0.00012642 | 0.00030923 | 0.0 | 7.16 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00073171 | 0.00086534 | 0.001025 | 0.0 | 49.01 +Output | 0.00063562 | 0.00075388 | 0.00094962 | 0.0 | 42.70 +Modify | 3.8147e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.25 +Other | | 1.55e-05 | | | 0.88 + +Nlocal: 0.5 ave 2 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 249.5 ave 250 max 248 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 56.25 ave 225 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 225 +Ave neighs/atom = 112.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/awpmd/log.27Nov18.h_molecule.g++.1 b/examples/USER/awpmd/log.27Nov18.h_molecule.g++.1 new file mode 100644 index 0000000000..a4c201abf2 --- /dev/null +++ b/examples/USER/awpmd/log.27Nov18.h_molecule.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable sname index h_molecule + +units real +newton on +boundary p p p +processors 1 * * + + +atom_style wavepacket + +read_data data.${sname} +read_data data.h_molecule + orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4 atoms + +#neighbor 2.0 nsq + +pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press +pair_coeff * * + + + +timestep 0.001 + +fix 1 all nve/awpmd + +comm_modify vel yes + +compute energies all pair awpmd/cut +variable eke equal c_energies[1] +variable epauli equal c_energies[2] +variable estatics equal c_energies[3] +variable errestrain equal c_energies[4] + +compute peratom all stress/atom NULL +compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] +variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) + +thermo 1 +thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press + +run 10 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.52918 + ghost atom cutoff = 2.52918 + binsize = 1.26459, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair awpmd/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933) +Per MPI rank memory allocation (min/avg/max) = 5.142 | 5.142 | 5.142 Mbytes +Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press + 0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0 + 1 30360.49 30360.489 0.0009272222 39540.081 2.0463631e-12 -9179.5926 0 0.10368794 1.3476061e+09 35.753932 + 2 67447.779 67447.776 0.00370884 80547.07 -1.1368684e-12 -13099.294 0 0.41474633 2.8529839e+09 143.01385 + 3 3713046.5 3713046.5 0.0041850026 3803060.3 -1.29603e-10 -90013.788 0 0.46799388 1.4486958e+11 161.3748 + 4 2445632.1 2445620 12.171486 2452194.4 -9.777068e-11 -6574.4062 0 1361.0937 -6.5572589e+08 469335.68 + 5 2434860.1 2434845.9 14.215419 2433638.8 -1.0663825e-10 1207.1541 0 1589.6595 -359380.29 548150.31 + 6 2444984.1 2444969.8 14.215428 2451100 5.1841198e-11 -6130.1373 0 1589.6605 -5.6327282e+08 548150.63 + 7 2436128.7 2436110.9 17.793789 2434903.7 2.0190782e-10 1207.154 0 1989.8158 -221406.77 686133.18 + 8 2444786.5 2444768.7 17.793798 2450583.8 -1.1027623e-10 -5815.0651 0 1989.8169 -5.0227031e+08 686133.54 + 9 2437198.9 2437175.9 22.942086 2435968.8 2.2600943e-10 1207.1538 0 2565.5315 -22903.736 884652.88 + 10 2444787.1 2444764.2 22.942097 2450333.1 -3.1832315e-11 -5568.9214 0 2565.5327 -4.5741803e+08 884653.3 +Loop time of 0.00158453 on 1 procs for 10 steps with 4 atoms + +Performance: 0.545 ns/day, 44.015 hours/ns, 6311.020 timesteps/s +85.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00088882 | 0.00088882 | 0.00088882 | 0.0 | 56.09 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00031352 | 0.00031352 | 0.00031352 | 0.0 | 19.79 +Output | 0.00036216 | 0.00036216 | 0.00036216 | 0.0 | 22.86 +Modify | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.38 +Other | | 1.407e-05 | | | 0.89 + +Nlocal: 4 ave 4 max 4 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 596 ave 596 max 596 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 966 ave 966 max 966 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 966 +Ave neighs/atom = 241.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/awpmd/log.27Nov18.h_molecule.g++.4 b/examples/USER/awpmd/log.27Nov18.h_molecule.g++.4 new file mode 100644 index 0000000000..39531640e1 --- /dev/null +++ b/examples/USER/awpmd/log.27Nov18.h_molecule.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable sname index h_molecule + +units real +newton on +boundary p p p +processors 1 * * + + +atom_style wavepacket + +read_data data.${sname} +read_data data.h_molecule + orthogonal box = (-0.529177 -0.529177 -0.529177) to (0.529177 0.529177 0.529177) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 4 atoms + +#neighbor 2.0 nsq + +pair_style awpmd/cut -1. hartree ermscale 0.99 free flex_press +pair_coeff * * + + + +timestep 0.001 + +fix 1 all nve/awpmd + +comm_modify vel yes + +compute energies all pair awpmd/cut +variable eke equal c_energies[1] +variable epauli equal c_energies[2] +variable estatics equal c_energies[3] +variable errestrain equal c_energies[4] + +compute peratom all stress/atom NULL +compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] +variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) + +thermo 1 +thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press + +run 10 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.52918 + ghost atom cutoff = 2.52918 + binsize = 1.26459, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair awpmd/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (src/domain.cpp:933) +Per MPI rank memory allocation (min/avg/max) = 5.172 | 5.234 | 5.422 Mbytes +Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press + 0 30358.159 30358.159 0 39537.73 -1.5916157e-12 -9179.5713 0 0 1.3475994e+09 -0 + 1 30360.982 30360.981 0.0009272222 39540.638 -1.1368684e-12 -9179.6571 0 0.10368794 1.3476263e+09 35.753932 + 2 67459.392 67459.388 0.0037086548 80559.71 6.5938366e-12 -13100.322 0 0.41472561 2.8534514e+09 143.0067 + 3 3732209.2 3732209.2 0.0041861902 3822452.2 -3.1604941e-11 -90242.984 0 0.46812669 1.4561246e+11 161.42059 + 4 2482974.7 2482961.9 12.860712 2489531.2 -2.2896529e-10 -6569.2968 0 1438.1675 -6.5458119e+08 495912.44 + 5 2472238.2 2472223.2 14.933049 2471015.7 -1.6120794e-10 1207.5188 0 1669.9095 -324992.65 575822.3 + 6 2482233.1 2482218.1 14.933057 2488321.7 -2.0691004e-11 -6103.5677 0 1669.9104 -5.5786438e+08 575822.62 + 7 2473498.5 2473479.8 18.61401 2472272.3 1.459739e-10 1207.5167 0 2081.5382 -183348.11 717761.12 + 8 2481621.3 2481602.6 18.614019 2487299.1 7.0258466e-11 -5696.4589 0 2081.5393 -4.7962801e+08 717761.48 + 9 2474506.2 2474482.2 24.021181 2473274.7 2.1395863e-10 1207.508 0 2686.2029 24318.554 926263.07 + 10 2480376.3 2480352.2 24.021192 2485505 -8.5719876e-11 -5152.7478 0 2686.2041 -3.8355089e+08 926263.48 +Loop time of 0.00267726 on 4 procs for 10 steps with 4 atoms + +Performance: 0.323 ns/day, 74.368 hours/ns, 3735.160 timesteps/s +91.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00011826 | 0.00027376 | 0.00073862 | 0.0 | 10.23 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00080514 | 0.0011864 | 0.001574 | 0.9 | 44.31 +Output | 0.00094914 | 0.0011944 | 0.0017326 | 0.9 | 44.61 +Modify | 3.3379e-06 | 4.4703e-06 | 6.1989e-06 | 0.0 | 0.17 +Other | | 1.824e-05 | | | 0.68 + +Nlocal: 1 ave 4 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 599 ave 600 max 596 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 241.5 ave 966 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 966 +Ave neighs/atom = 241.5 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.1 b/examples/USER/bocs/log.27Nov18.methanol.g++.1 similarity index 60% rename from examples/USER/bocs/log.20Apr18.methanol.g++.1 rename to examples/USER/bocs/log.27Nov18.methanol.g++.1 index a94bd959c8..21bbc0c823 100644 --- a/examples/USER/bocs/log.20Apr18.methanol.g++.1 +++ b/examples/USER/bocs/log.27Nov18.methanol.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 @@ -21,7 +20,7 @@ pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:481) + Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin @@ -90,54 +89,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 - 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 - 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 - 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 - 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 - 2500 301.18564 1033.9214 1902.0719 40.48255 66607.667 - 3000 301.06632 1022.0381 1889.8447 47.582344 66341.947 - 3500 297.98361 989.80983 1848.7307 -204.69879 67462.078 - 4000 299.03493 1034.6571 1896.6083 89.188888 66457.385 - 4500 306.03351 985.4121 1867.5363 -51.102407 67519.446 - 5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467 - 5500 292.23444 1029.5558 1871.905 20.764579 66683.876 - 6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031 - 6500 305.26461 960.08118 1839.9891 -352.42596 67612.317 - 7000 300.34449 1055.0664 1920.7923 22.04027 66187.27 - 7500 305.48612 1038.6651 1919.2115 17.807254 66324.168 - 8000 316.03232 1034.6809 1945.6262 27.482857 66502.198 - 8500 294.28636 1038.8213 1887.085 -72.840559 66851.661 - 9000 316.69029 1065.7481 1978.5899 245.61677 65678.385 - 9500 297.46127 1034.5547 1891.97 54.23428 66892.627 - 10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506 -Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms + 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 + 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 + 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 + 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 + 2500 305.51905 1051.59 1932.2314 -34.076658 66487.327 + 3000 291.76224 1053.524 1894.5121 45.522865 65879.535 + 3500 297.65795 1017.1028 1875.085 -79.41965 67185.19 + 4000 285.98779 1042.3622 1866.7058 88.549172 66357.051 + 4500 295.35 1071.4505 1922.7801 -16.75965 65378.949 + 5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38 + 5500 292.40422 1085.3901 1928.2287 161.88502 65677.644 + 6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05 + 6500 308.03807 1046.1413 1934.0436 249.70237 66052.045 + 7000 289.33716 1037.9657 1871.9636 47.662734 66782.578 + 7500 297.3092 1032.356 1889.3329 -24.049617 66129.95 + 8000 298.27827 1044.118 1903.8882 -26.61809 66720.381 + 8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559 + 9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4 + 9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848 + 10000 309.9256 1043.5321 1936.875 -103.81403 66222.21 +Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms -Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 timesteps/s +Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 33.324 | 33.324 | 33.324 | 0.0 | 96.80 -Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35 -Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25 -Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00 -Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24 -Other | | 0.1252 | | | 0.36 +Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39 +Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44 +Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68 +Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00 +Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25 +Other | | 0.1042 | | | 0.25 Nlocal: 968 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 9112 ave 9112 max 9112 min +Nghost: 9215 ave 9215 max 9215 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 404392 ave 404392 max 404392 min +Neighs: 411837 ave 411837 max 411837 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 404392 -Ave neighs/atom = 417.76 +Total # of neighbors = 411837 +Ave neighs/atom = 425.451 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:34 +Total wall time: 0:00:42 diff --git a/examples/USER/bocs/log.20Apr18.methanol.g++.4 b/examples/USER/bocs/log.27Nov18.methanol.g++.4 similarity index 57% rename from examples/USER/bocs/log.20Apr18.methanol.g++.4 rename to examples/USER/bocs/log.27Nov18.methanol.g++.4 index cf5891f97c..7dcf61d32c 100644 --- a/examples/USER/bocs/log.20Apr18.methanol.g++.4 +++ b/examples/USER/bocs/log.27Nov18.methanol.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 @@ -21,7 +20,7 @@ pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:481) + Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin @@ -90,54 +89,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.37 | 3.37 | 3.371 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 - 500 314.54728 1034.1091 1940.7738 194.42689 65660.282 - 1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543 - 1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605 - 2000 294.78476 1046.8207 1896.521 50.592942 66316.735 - 2500 301.18564 1033.9214 1902.0719 40.482557 66607.667 - 3000 301.06631 1022.0381 1889.8447 47.582403 66341.947 - 3500 297.98353 989.81011 1848.7308 -204.69823 67462.076 - 4000 299.03465 1034.6603 1896.6108 89.196235 66457.338 - 4500 306.04532 985.37017 1867.5285 -51.094929 67519.735 - 5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517 - 5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551 - 6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611 - 6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898 - 7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674 - 7500 292.45089 1068.2863 1911.2595 103.23295 65778.08 - 8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038 - 8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305 - 9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344 - 9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361 - 10000 296.3083 1004.126 1858.2178 -28.293045 66862.576 -Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms + 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 + 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 + 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 + 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 + 2500 305.51905 1051.59 1932.2314 -34.076657 66487.327 + 3000 291.76224 1053.524 1894.5121 45.522919 65879.535 + 3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183 + 4000 285.99141 1042.379 1866.733 88.735986 66356.756 + 4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597 + 5000 292.47 1012.3769 1855.405 -255.07433 67527.215 + 5500 294.04431 1080.4547 1928.0208 192.6588 65811.742 + 6000 300.45893 986.16669 1852.2225 -167.3405 67858.175 + 6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704 + 7000 312.11968 1032.7392 1932.4065 152.17956 66016.299 + 7500 306.80585 1032.1157 1916.4662 51.07705 66875.727 + 8000 292.30957 1048.9003 1891.4661 61.280503 65894.103 + 8500 297.79592 1013.4061 1871.786 -133.01136 66842.574 + 9000 290.36753 1043.7732 1880.7412 65.208248 66010.86 + 9500 288.92211 1077.8835 1910.6851 46.291982 65674.639 + 10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692 +Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms -Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s -95.2% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 19.929 | 21.765 | 23.391 | 27.8 | 75.56 -Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25 -Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16 -Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01 -Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95 -Other | | 0.3112 | | | 1.08 +Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35 +Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33 +Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42 +Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02 +Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28 +Other | | 0.08323 | | | 0.60 -Nlocal: 242 ave 244 max 239 min +Nlocal: 242 ave 248 max 232 min Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 5718.5 ave 5736 max 5702 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 100703 ave 108064 max 93454 min -Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 5845.75 ave 5877 max 5808 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Neighs: 104313 ave 113860 max 95507 min +Histogram: 1 1 0 0 0 0 0 1 0 1 -Total # of neighbors = 402813 -Ave neighs/atom = 416.129 -Neighbor list builds = 14 +Total # of neighbors = 417252 +Ave neighs/atom = 431.045 +Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:28 +Total wall time: 0:00:14 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1 b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1 rename to examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 index af0f965336..6485312731 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/input.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/in.duplex1 @@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 1000000 +run 10000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1 deleted file mode 100644 index 3afed6b6ce..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.1 +++ /dev/null @@ -1,1161 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05 -1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.0173888111295073 | erot = 0.0643039804300224 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136619 | erot = 0.0987844033142069 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948556079 | erot = 0.139336571052566 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.04839505571915 | erot = 0.185086295692081 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336920643 | erot = 0.235071307523532 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406440561 | erot = 0.288273694501538 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563085878 | erot = 0.343654369293473 | epot = -15.0710491710418 | etot = -14.6424332454398 -11000 ekin = 0.0965486715045649 | erot = 0.400187932108223 | epot = -15.1391698491357 | etot = -14.6424332455229 -12000 ekin = 0.10722146628289 | erot = 0.456896095459165 | epot = -15.20655080734 | etot = -14.642433245598 -13000 ekin = 0.116672809719548 | erot = 0.512877765427643 | epot = -15.2719838208099 | etot = -14.6424332456627 -14000 ekin = 0.12465407373104 | erot = 0.567333962045116 | epot = -15.3344212814913 | etot = -14.6424332457151 -15000 ekin = 0.13098393968427 | erot = 0.619586028256667 | epot = -15.3930032136954 | etot = -14.6424332457544 -16000 ekin = 0.135553354544872 | erot = 0.669086028489761 | epot = -15.447072628815 | etot = -14.6424332457804 -17000 ekin = 0.138326263958247 | erot = 0.715418858085449 | epot = -15.4961783678372 | etot = -14.6424332457935 -18000 ekin = 0.139336096664052 | erot = 0.758296324627745 | epot = -15.5400656670872 | etot = -14.6424332457954 -19000 ekin = 0.138678360045177 | erot = 0.797544234275864 | epot = -15.5786558401088 | etot = -14.6424332457878 -20000 ekin = 0.136500074655373 | erot = 0.83308420441103 | epot = -15.6120175248394 | etot = -14.642433245773 -21000 ekin = 0.132987065285671 | erot = 0.864912408452581 | epot = -15.6403327194916 | etot = -14.6424332457533 -22000 ekin = 0.128350288213556 | erot = 0.893077649557994 | epot = -15.6638611835027 | etot = -14.6424332457311 -23000 ekin = 0.122812385135508 | erot = 0.917661024683964 | epot = -15.6829066555277 | etot = -14.6424332457083 -24000 ekin = 0.116595521408284 | erot = 0.938759014332096 | epot = -15.6977877814267 | etot = -14.6424332456863 -25000 ekin = 0.109911323474816 | erot = 0.956471207347236 | epot = -15.7088157764882 | etot = -14.6424332456662 -26000 ekin = 0.102953426207644 | erot = 0.970893163953198 | epot = -15.7162798358091 | etot = -14.6424332456483 -27000 ekin = 0.0958928250746637 | erot = 0.982114250194049 | epot = -15.7204403209013 | etot = -14.6424332456326 -28000 ekin = 0.0888759410950343 | erot = 0.990219731539835 | epot = -15.7215289182535 | etot = -14.6424332456186 -29000 ekin = 0.0820250748773376 | erot = 0.995296041202909 | epot = -15.719754361686 | etot = -14.6424332456058 -30000 ekin = 0.0754407616839748 | erot = 0.997437949320991 | epot = -15.7153119565981 | etot = -14.6424332455932 -31000 ekin = 0.0692054432610605 | erot = 0.996756332762285 | epot = -15.7083950216035 | etot = -14.6424332455802 -32000 ekin = 0.0633878377978472 | erot = 0.993385345349211 | epot = -15.699206428713 | etot = -14.6424332455659 -33000 ekin = 0.0580474070871663 | erot = 0.987487973309961 | epot = -15.6879686259471 | etot = -14.64243324555 -34000 ekin = 0.0532383791888181 | erot = 0.979259192921736 | epot = -15.6749308176426 | etot = -14.642433245532 -35000 ekin = 0.0490128758307997 | erot = 0.968926197407215 | epot = -15.66037231875 | etot = -14.642433245512 -36000 ekin = 0.0454228081410747 | erot = 0.95674540962595 | epot = -15.6446014632576 | etot = -14.6424332454906 -37000 ekin = 0.0425203357176436 | erot = 0.942996238000708 | epot = -15.6279498191869 | etot = -14.6424332454685 -38000 ekin = 0.0403568280949567 | erot = 0.92797176661665 | epot = -15.6107618401582 | etot = -14.6424332454466 -39000 ekin = 0.0389804214212708 | erot = 0.911966804110001 | epot = -15.5933804709572 | etot = -14.642433245426 -40000 ekin = 0.0384324238856422 | erot = 0.8952639595629 | epot = -15.5761296288567 | etot = -14.6424332454081 -41000 ekin = 0.0387429860408521 | erot = 0.878118672838247 | epot = -15.5592949042733 | etot = -14.6424332453942 -42000 ekin = 0.0399266053637504 | erot = 0.860744395135471 | epot = -15.5431042458848 | etot = -14.6424332453856 -43000 ekin = 0.0419781561011205 | erot = 0.843299365355946 | epot = -15.52771076684 | etot = -14.6424332453829 -44000 ekin = 0.0448701894086706 | erot = 0.825876603312506 | epot = -15.5131800381079 | etot = -14.6424332453867 -45000 ekin = 0.0485521857411509 | erot = 0.808498758184836 | epot = -15.4994841893228 | etot = -14.6424332453969 -46000 ekin = 0.0529522094031963 | erot = 0.791119212186772 | epot = -15.4865046670025 | etot = -14.6424332454125 -47000 ekin = 0.0579809824236739 | erot = 0.773630265882115 | epot = -15.4740444937379 | etot = -14.6424332454321 -48000 ekin = 0.063537784649307 | erot = 0.755878310836066 | epot = -15.4618493409392 | etot = -14.6424332454538 -49000 ekin = 0.0695169124457283 | erot = 0.737684732482629 | epot = -15.4496348904038 | etot = -14.6424332454754 -50000 ekin = 0.0758129058454745 | erot = 0.718870126218063 | epot = -15.4371162775588 | etot = -14.6424332454952 -51000 ekin = 0.082322663864191 | erot = 0.69927859951883 | epot = -15.4240345088949 | etot = -14.6424332455119 -52000 ekin = 0.0889431481334984 | erot = 0.67879880709845 | epot = -15.4101752007568 | etot = -14.6424332455248 -53000 ekin = 0.0955646689255781 | erot = 0.657379086769954 | epot = -15.3953770012299 | etot = -14.6424332455344 -54000 ekin = 0.102061477509349 | erot = 0.635035489168609 | epot = -15.3795302122192 | etot = -14.6424332455412 -55000 ekin = 0.108282960174 | erot = 0.611853171347129 | epot = -15.3625693770671 | etot = -14.6424332455459 -56000 ekin = 0.114049426281782 | erot = 0.58798294592476 | epot = -15.3444656177551 | etot = -14.6424332455485 -57000 ekin = 0.119155806186856 | erot = 0.563635255923989 | epot = -15.3252243076595 | etot = -14.6424332455486 -58000 ekin = 0.123384552305436 | erot = 0.539073355224011 | epot = -15.3048911530747 | etot = -14.6424332455453 -59000 ekin = 0.126526300954942 | erot = 0.514606324860975 | epot = -15.2835658713528 | etot = -14.6424332455369 -60000 ekin = 0.128404399836505 | erot = 0.490581338842491 | epot = -15.2614189842015 | etot = -14.6424332455225 -61000 ekin = 0.128898142362338 | erot = 0.46737389240369 | epot = -15.2387052802676 | etot = -14.6424332455016 -62000 ekin = 0.127959880290304 | erot = 0.445374820089083 | epot = -15.2157679458544 | etot = -14.642433245475 -63000 ekin = 0.125622870624957 | erot = 0.424973765390021 | epot = -15.1930298814589 | etot = -14.6424332454439 -64000 ekin = 0.121999044843205 | erot = 0.406539918574829 | epot = -15.1709722088285 | etot = -14.6424332454105 -65000 ekin = 0.117268056619305 | erot = 0.390401831022814 | epot = -15.1501031330194 | etot = -14.6424332453773 -66000 ekin = 0.111660385257246 | erot = 0.376828594080988 | epot = -15.1309222246848 | etot = -14.6424332453465 -67000 ekin = 0.105437746905138 | erot = 0.366014539812675 | epot = -15.1138855320384 | etot = -14.6424332453205 -68000 ekin = 0.0988737375607886 | erot = 0.3580690141562 | epot = -15.0993759970177 | etot = -14.6424332453007 -69000 ekin = 0.0922368286502271 | erot = 0.353011948772473 | epot = -15.0876820227105 | etot = -14.6424332452878 -70000 ekin = 0.085776901527448 | erot = 0.350775174164851 | epot = -15.0789853209745 | etot = -14.6424332452822 -71000 ekin = 0.0797156921642142 | erot = 0.351208844244805 | epot = -15.0733577816926 | etot = -14.6424332452835 -72000 ekin = 0.0742409440406418 | erot = 0.354092037745935 | epot = -15.0707662270776 | etot = -14.6424332452911 -73000 ekin = 0.0695037498701448 | erot = 0.359146526959505 | epot = -15.0710835221334 | etot = -14.6424332453038 -74000 ekin = 0.0656184497423043 | erot = 0.366052769876549 | epot = -15.0741044649392 | etot = -14.6424332453204 -75000 ekin = 0.0626644690389266 | erot = 0.374467290031506 | epot = -15.07956500441 | etot = -14.6424332453396 -76000 ekin = 0.0606895535086054 | erot = 0.384040683400738 | epot = -15.0871634822693 | etot = -14.64243324536 -77000 ekin = 0.0597139401235012 | erot = 0.394435495890075 | epot = -15.0965826813934 | etot = -14.6424332453798 -78000 ekin = 0.059735062986913 | erot = 0.405343151479082 | epot = -15.1075114598642 | etot = -14.6424332453982 -79000 ekin = 0.0607324264355555 | erot = 0.416499017639937 | epot = -15.1196646894892 | etot = -14.6424332454137 -80000 ekin = 0.06267229049498 | erot = 0.427694630236126 | epot = -15.1328001661568 | etot = -14.6424332454257 -81000 ekin = 0.0655118235328765 | erot = 0.438786127846728 | epot = -15.1467311968131 | etot = -14.6424332454335 -82000 ekin = 0.0692024020835893 | erot = 0.449698113828473 | epot = -15.1613337613493 | etot = -14.6424332454372 -83000 ekin = 0.0736917936906618 | erot = 0.460422490738957 | epot = -15.1765475298665 | etot = -14.6424332454369 -84000 ekin = 0.0789250526546722 | erot = 0.471012272293582 | epot = -15.1923705703818 | etot = -14.6424332454336 -85000 ekin = 0.0848440878750035 | erot = 0.481570908649162 | epot = -15.2088482419522 | etot = -14.642433245428 -86000 ekin = 0.0913860133254624 | erot = 0.492238169205216 | epot = -15.2260574279521 | etot = -14.6424332454214 -87000 ekin = 0.0984805441200046 | erot = 0.503174014616525 | epot = -15.2440878041518 | etot = -14.6424332454153 -88000 ekin = 0.106046830304297 | erot = 0.514542076496056 | epot = -15.263022152211 | etot = -14.6424332454106 -89000 ekin = 0.113990204127984 | erot = 0.526494309539207 | epot = -15.2829177590758 | etot = -14.6424332454087 -90000 ekin = 0.122199339151894 | erot = 0.539158097285698 | epot = -15.3037906818477 | etot = -14.6424332454101 -91000 ekin = 0.130544275971403 | erot = 0.552626637865723 | epot = -15.3256041592524 | etot = -14.6424332454152 -92000 ekin = 0.138875666148815 | erot = 0.566952900962156 | epot = -15.3482618125355 | etot = -14.6424332454245 -93000 ekin = 0.147025440614642 | erot = 0.582146933737432 | epot = -15.3716056197897 | etot = -14.6424332454376 -94000 ekin = 0.154808946847822 | erot = 0.598175891801207 | epot = -15.3954180841032 | etot = -14.6424332454542 -95000 ekin = 0.162028449602152 | erot = 0.614965942453837 | epot = -15.4194276375299 | etot = -14.6424332454739 -96000 ekin = 0.168477779667818 | erot = 0.632405154082029 | epot = -15.4433161792459 | etot = -14.642433245496 -97000 ekin = 0.17394786302672 | erot = 0.650346631628325 | epot = -15.4667277401752 | etot = -14.6424332455201 -98000 ekin = 0.178232875004242 | erot = 0.668611435745948 | epot = -15.4892775562957 | etot = -14.6424332455455 -99000 ekin = 0.181136831926353 | erot = 0.686991165056211 | epot = -15.5105612425543 | etot = -14.6424332455718 -100000 ekin = 0.182480533643598 | erot = 0.705250413407778 | epot = -15.5301641926495 | etot = -14.6424332455981 -101000 ekin = 0.182108871451935 | erot = 0.723129571003179 | epot = -15.547671688079 | etot = -14.6424332456239 -102000 ekin = 0.179898581170268 | erot = 0.740348571090314 | epot = -15.5626803979088 | etot = -14.6424332456482 -103000 ekin = 0.175766517608084 | erot = 0.756612167825837 | epot = -15.5748119311039 | etot = -14.64243324567 -104000 ekin = 0.169678431535445 | erot = 0.771617166851602 | epot = -15.5837288440751 | etot = -14.6424332456881 -105000 ekin = 0.161658036036865 | erot = 0.785061742962005 | epot = -15.5891530247 | etot = -14.6424332457012 -106000 ekin = 0.151795867650478 | erot = 0.796656613424597 | epot = -15.5908857267829 | etot = -14.6424332457078 -107000 ekin = 0.140257112952727 | erot = 0.806137449197231 | epot = -15.5888278078568 | etot = -14.6424332457068 -108000 ekin = 0.127287240201241 | erot = 0.813277564481104 | epot = -15.5829980503796 | etot = -14.6424332456973 -109000 ekin = 0.113214025490917 | erot = 0.817899691734432 | epot = -15.573546962904 | etot = -14.6424332456787 -110000 ekin = 0.0984444823805213 | erot = 0.819885578053921 | epot = -15.5607633060856 | etot = -14.6424332456512 -111000 ekin = 0.0834553769364569 | erot = 0.819182262545785 | epot = -15.545070885098 | etot = -14.6424332456157 -112000 ekin = 0.0687764915871027 | erot = 0.815804215094415 | epot = -15.5270139522555 | etot = -14.642433245574 -113000 ekin = 0.0549665904028903 | erot = 0.809830999844441 | epot = -15.5072308357759 | etot = -14.6424332455285 -114000 ekin = 0.0425830583120619 | erot = 0.801400700350953 | epot = -15.4864170041452 | etot = -14.6424332454821 -115000 ekin = 0.032147280213263 | erot = 0.790699910049051 | epot = -15.4652804357003 | etot = -14.642433245438 -116000 ekin = 0.024108778034577 | erot = 0.777951546674724 | epot = -15.4444935701085 | etot = -14.6424332453992 -117000 ekin = 0.0188117102728931 | erot = 0.763402004774069 | epot = -15.4246469604154 | etot = -14.6424332453684 -118000 ekin = 0.0164673894159043 | erot = 0.747309167856945 | epot = -15.4062098026203 | etot = -14.6424332453474 -119000 ekin = 0.0171359296532898 | erot = 0.729932564575393 | epot = -15.3895017395657 | etot = -14.642433245337 -120000 ekin = 0.0207190822430497 | erot = 0.711526526250247 | epot = -15.3746788538305 | etot = -14.6424332453372 -121000 ekin = 0.0269649552319816 | erot = 0.692336677373422 | epot = -15.3617348779522 | etot = -14.6424332453468 -122000 ekin = 0.0354839220297736 | erot = 0.672599570214091 | epot = -15.3505167376079 | etot = -14.642433245364 -123000 ekin = 0.0457738626451366 | erot = 0.652544850165416 | epot = -15.3407519581971 | etot = -14.6424332453865 -124000 ekin = 0.0572521324296466 | erot = 0.632399068066114 | epot = -15.3320844459074 | etot = -14.6424332454117 -125000 ekin = 0.0692913736002564 | erot = 0.612390156186006 | epot = -15.324114775223 | etot = -14.6424332454368 -126000 ekin = 0.0812564128172846 | erot = 0.592751635109578 | epot = -15.3164412933862 | etot = -14.6424332454593 -127000 ekin = 0.0925398817823717 | erot = 0.573725774407888 | epot = -15.3086989016675 | etot = -14.6424332454772 -128000 ekin = 0.102594692018529 | erot = 0.55556513894369 | epot = -15.3005930764509 | etot = -14.6424332454887 -129000 ekin = 0.110961953873462 | erot = 0.538532171478003 | epot = -15.291927370844 | etot = -14.6424332454925 -130000 ekin = 0.117293279472125 | erot = 0.52289666445339 | epot = -15.2826231894136 | etot = -14.642433245488 -131000 ekin = 0.121366644774014 | erot = 0.508931150171021 | epot = -15.2727310404203 | etot = -14.6424332454752 -132000 ekin = 0.123095155538848 | erot = 0.49690439090507 | epot = -15.2624327918984 | etot = -14.6424332454545 -133000 ekin = 0.122528239670491 | erot = 0.487073282996463 | epot = -15.2520347680938 | etot = -14.6424332454268 -134000 ekin = 0.119845042600695 | erot = 0.47967360116923 | epot = -15.2419518891638 | etot = -14.6424332453939 -135000 ekin = 0.115340171966309 | erot = 0.474910093714588 | epot = -15.2326835110385 | etot = -14.6424332453576 -136000 ekin = 0.10940241928465 | erot = 0.472946484072521 | epot = -15.2247821486777 | etot = -14.6424332453205 -137000 ekin = 0.102487634021818 | erot = 0.473895929917005 | epot = -15.2188168092237 | etot = -14.6424332452849 -138000 ekin = 0.0950874634047233 | erot = 0.477812435582745 | epot = -15.2153331442409 | etot = -14.6424332452534 -139000 ekin = 0.0876961121512815 | erot = 0.484683617748011 | epot = -15.2148129751279 | etot = -14.6424332452286 -140000 ekin = 0.0807775418431626 | erot = 0.494425108537478 | epot = -15.2176358955931 | etot = -14.6424332452125 -141000 ekin = 0.0747355681577817 | erot = 0.50687677080795 | epot = -15.2240455841725 | etot = -14.6424332452068 -142000 ekin = 0.0698891098450116 | erot = 0.521800821238808 | epot = -15.2341231762965 | etot = -14.6424332452127 -143000 ekin = 0.0664544171866063 | erot = 0.538881922424094 | epot = -15.2477695848413 | etot = -14.6424332452306 -144000 ekin = 0.0645355104692083 | erot = 0.557729316020225 | epot = -15.2646980717496 | etot = -14.6424332452602 -145000 ekin = 0.0641233595162911 | erot = 0.577881111412627 | epot = -15.2844377162297 | etot = -14.6424332453008 -146000 ekin = 0.0651036077515188 | erot = 0.598810893851628 | epot = -15.3063477469538 | etot = -14.6424332453507 -147000 ekin = 0.0672719578973601 | erot = 0.619936843681753 | epot = -15.3296420469868 | etot = -14.6424332454077 -148000 ekin = 0.0703557492692045 | erot = 0.640633538190902 | epot = -15.3534225329294 | etot = -14.6424332454693 -149000 ekin = 0.0740398128642427 | erot = 0.660246523237691 | epot = -15.3767195816347 | etot = -14.6424332455328 -150000 ekin = 0.0779944201058678 | erot = 0.678109590376156 | epot = -15.398537256077 | etot = -14.642433245595 -151000 ekin = 0.0819030604172323 | erot = 0.693564488648094 | epot = -15.4179007947185 | etot = -14.6424332456531 -152000 ekin = 0.0854878938552624 | erot = 0.705982563003889 | epot = -15.4339037025634 | etot = -14.6424332457043 -153000 ekin = 0.0885310147328532 | erot = 0.714787575382088 | epot = -15.4457518358609 | etot = -14.6424332457459 -154000 ekin = 0.0908901012887555 | erot = 0.719478762727528 | epot = -15.4528021097924 | etot = -14.6424332457761 -155000 ekin = 0.092507570371455 | erot = 0.719653046097721 | epot = -15.4545938622626 | etot = -14.6424332457934 -156000 ekin = 0.0934129479728847 | erot = 0.715025243753982 | epot = -15.4508714375239 | etot = -14.642433245797 -157000 ekin = 0.0937187435779626 | erot = 0.705445163946324 | epot = -15.4415971533109 | etot = -14.6424332457866 -158000 ekin = 0.0936106185393401 | erot = 0.690910554325706 | epot = -15.4269544186278 | etot = -14.6424332457627 -159000 ekin = 0.0933330174010987 | erot = 0.671575051659785 | epot = -15.4073413147871 | etot = -14.6424332457262 -160000 ekin = 0.0931716565242322 | erot = 0.647750492120645 | epot = -15.3833553943234 | etot = -14.6424332456785 -161000 ekin = 0.0934343296231438 | erot = 0.619903194016586 | epot = -15.3557707692612 | etot = -14.6424332456215 -162000 ekin = 0.0944314104804186 | erot = 0.588644098979611 | epot = -15.3255087550173 | etot = -14.6424332455572 -163000 ekin = 0.0964572425739502 | erot = 0.55471294345392 | epot = -15.2936034315161 | etot = -14.6424332454882 -164000 ekin = 0.0997733472806136 | erot = 0.518956918561936 | epot = -15.2611635112594 | etot = -14.6424332454169 -165000 ekin = 0.104594102019911 | erot = 0.482304549422426 | epot = -15.2293318967882 | etot = -14.6424332453459 -166000 ekin = 0.11107527651625 | erot = 0.445735768512381 | epot = -15.1992442903065 | etot = -14.6424332452778 -167000 ekin = 0.11930559751358 | erot = 0.410249354728318 | epot = -15.1719881974571 | etot = -14.6424332452152 -168000 ekin = 0.129301354725086 | erot = 0.37682904617874 | epot = -15.1485636460642 | etot = -14.6424332451604 -169000 ekin = 0.14100396578975 | erot = 0.346409702527097 | epot = -15.1298469134321 | etot = -14.6424332451152 -170000 ekin = 0.154280377439942 | erot = 0.319844892417961 | epot = -15.1165585149394 | etot = -14.6424332450815 -171000 ekin = 0.168926178621544 | erot = 0.297877221606916 | epot = -15.109236645289 | etot = -14.6424332450606 -172000 ekin = 0.184671319364511 | erot = 0.281112611137243 | epot = -15.108217175555 | etot = -14.6424332450532 -173000 ekin = 0.201188345437118 | erot = 0.269999595570268 | epot = -15.1136211860672 | etot = -14.6424332450598 -174000 ekin = 0.218103052207035 | erot = 0.264814547402982 | epot = -15.12535084469 | etot = -14.6424332450799 -175000 ekin = 0.235007413035623 | erot = 0.265653545950115 | epot = -15.1430942040986 | etot = -14.6424332451129 -176000 ekin = 0.251474534267915 | erot = 0.272431389432266 | epot = -15.1663391688573 | etot = -14.6424332451571 -177000 ekin = 0.267075225143436 | erot = 0.284887984978803 | epot = -15.1943964553329 | etot = -14.6424332452107 -178000 ekin = 0.281395553895287 | erot = 0.302602030915412 | epot = -15.2264308300819 | etot = -14.6424332452712 -179000 ekin = 0.294054514411866 | erot = 0.325011526057904 | epot = -15.2614992858055 | etot = -14.6424332453358 -180000 ekin = 0.304720692896942 | erot = 0.351440214935852 | epot = -15.2985941532343 | etot = -14.6424332454015 -181000 ekin = 0.313126658918426 | erot = 0.381128639602688 | epot = -15.3366885439866 | etot = -14.6424332454655 -182000 ekin = 0.319079775823621 | erot = 0.413268071114152 | epot = -15.374781092463 | etot = -14.6424332455252 -183000 ekin = 0.322468290005762 | erot = 0.447035301736728 | epot = -15.4119368373208 | etot = -14.6424332455783 -184000 ekin = 0.323261947554671 | erot = 0.48162615508044 | epot = -15.4473213482583 | etot = -14.6424332456231 -185000 ekin = 0.321506983530827 | erot = 0.516285658867815 | epot = -15.4802258880574 | etot = -14.6424332456588 -186000 ekin = 0.317316057633682 | erot = 0.550333132629112 | epot = -15.5100824359478 | etot = -14.642433245685 -187000 ekin = 0.310854440590084 | erot = 0.583180936761968 | epot = -15.5364686230541 | etot = -14.642433245702 -188000 ekin = 0.302324329763947 | erot = 0.614346238385429 | epot = -15.55910381386 | etot = -14.6424332457106 -189000 ekin = 0.291949445197116 | erot = 0.64345577901281 | epot = -15.5778384699217 | etot = -14.6424332457118 -190000 ekin = 0.279961942768254 | erot = 0.67024418570442 | epot = -15.5926393741794 | etot = -14.6424332457067 -191000 ekin = 0.266593185653664 | erot = 0.694546781233348 | epot = -15.6035732125832 | etot = -14.6424332456962 -192000 ekin = 0.252069141623363 | erot = 0.716288088786984 | epot = -15.6107904760917 | etot = -14.6424332456814 -193000 ekin = 0.236610293254145 | erot = 0.735467302242536 | epot = -15.6145108411597 | etot = -14.642433245663 -194000 ekin = 0.22043514940511 | erot = 0.75214194302714 | epot = -15.615010338074 | etot = -14.6424332456418 -195000 ekin = 0.20376588009334 | erot = 0.76641079902996 | epot = -15.6126099247417 | etot = -14.6424332456184 -196000 ekin = 0.186834339037366 | erot = 0.778397083250806 | epot = -15.6076646678817 | etot = -14.6424332455935 -197000 ekin = 0.169886782294183 | erot = 0.788232586070618 | epot = -15.6005526139326 | etot = -14.6424332455678 -198000 ekin = 0.153185871077985 | erot = 0.796043434538987 | epot = -15.5916625511591 | etot = -14.6424332455421 -199000 ekin = 0.137008972987403 | erot = 0.801937915798979 | epot = -15.581380134304 | etot = -14.6424332455176 -200000 ekin = 0.121642272364804 | erot = 0.805996673261661 | epot = -15.5700721911217 | etot = -14.6424332454953 -201000 ekin = 0.107370722656483 | erot = 0.808265456806726 | epot = -15.5580694249396 | etot = -14.6424332454764 -202000 ekin = 0.0944644042392164 | erot = 0.808750524310001 | epot = -15.5456481740113 | etot = -14.6424332454621 -203000 ekin = 0.0831623790893979 | erot = 0.807416772443554 | epot = -15.5330123969865 | etot = -14.6424332454535 -204000 ekin = 0.0736556272335549 | erot = 0.80418872541979 | epot = -15.5202775981049 | etot = -14.6424332454516 -205000 ekin = 0.0660710401675949 | erot = 0.79895460735586 | epot = -15.50745889298 | etot = -14.6424332454565 -206000 ekin = 0.0604586317681684 | erot = 0.791573809424189 | epot = -15.4944656866607 | etot = -14.6424332454683 -207000 ekin = 0.0567840026883034 | erot = 0.781888054798422 | epot = -15.4811053029728 | etot = -14.642433245486 -208000 ekin = 0.0549275971601569 | erot = 0.769736381379661 | epot = -15.4670972240478 | etot = -14.642433245508 -209000 ekin = 0.054691444753805 | erot = 0.754973659533912 | epot = -15.4520983498196 | etot = -14.6424332455319 -210000 ekin = 0.055813012677523 | erot = 0.737491764374765 | epot = -15.4357380226072 | etot = -14.6424332455549 -211000 ekin = 0.0579847210238433 | erot = 0.717241838880031 | epot = -15.417659805478 | etot = -14.6424332455742 -212000 ekin = 0.0608768356205362 | erot = 0.694255492639193 | epot = -15.3975655738466 | etot = -14.6424332455869 -213000 ekin = 0.06416104270831 | erot = 0.668662476163316 | epot = -15.3752567644624 | etot = -14.6424332455907 -214000 ekin = 0.0675321043587428 | erot = 0.64070249551798 | epot = -15.3506678454611 | etot = -14.6424332455844 -215000 ekin = 0.070725533636788 | erot = 0.610729417267909 | epot = -15.3238881964721 | etot = -14.6424332455674 -216000 ekin = 0.0735300437834057 | erot = 0.579207054837054 | epot = -15.2951703441606 | etot = -14.6424332455401 -217000 ekin = 0.0757943994895767 | erot = 0.546696813208958 | epot = -15.2649244582023 | etot = -14.6424332455037 -218000 ekin = 0.0774290394184473 | erot = 0.513838451215592 | epot = -15.2337007360942 | etot = -14.6424332454601 -219000 ekin = 0.0784033323161932 | erot = 0.481325894960063 | epot = -15.2021624726878 | etot = -14.6424332454116 -220000 ekin = 0.0787395495628362 | erot = 0.449880299616975 | epot = -15.1710530945401 | etot = -14.6424332453603 -221000 ekin = 0.0785046319692606 | erot = 0.420222425154575 | epot = -15.1411603024325 | etot = -14.6424332453087 -222000 ekin = 0.0778006814288784 | erot = 0.393045972165179 | epot = -15.1132798988531 | etot = -14.642433245259 -223000 ekin = 0.0767549035403029 | erot = 0.368992968905302 | epot = -15.0881811176588 | etot = -14.6424332452132 -224000 ekin = 0.0755095293719489 | erot = 0.348631757026569 | epot = -15.0665745315716 | etot = -14.6424332451731 -225000 ekin = 0.0742120885680923 | erot = 0.332437700423116 | epot = -15.0490830341315 | etot = -14.6424332451403 -226000 ekin = 0.0730063028703669 | erot = 0.320776497496383 | epot = -15.0362160454828 | etot = -14.6424332451161 -227000 ekin = 0.072023814088989 | erot = 0.313889923623787 | epot = -15.0283469828147 | etot = -14.642433245102 -228000 ekin = 0.0713769419944175 | erot = 0.31188394524302 | epot = -15.025694132336 | etot = -14.6424332450985 -229000 ekin = 0.0711526728859894 | erot = 0.314719386436074 | epot = -15.0283053044287 | etot = -14.6424332451066 -230000 ekin = 0.0714080974064438 | erot = 0.322205638587393 | epot = -15.0360469811206 | etot = -14.6424332451268 -231000 ekin = 0.0721675361185073 | erot = 0.333998222200335 | epot = -15.0485990034776 | etot = -14.6424332451588 -232000 ekin = 0.073421602289788 | erot = 0.349601270465542 | epot = -15.0654561179573 | etot = -14.6424332452019 -233000 ekin = 0.0751284397495051 | erot = 0.368376135876568 | epot = -15.0859378208814 | etot = -14.6424332452553 -234000 ekin = 0.0772173235430231 | erot = 0.389557254435346 | epot = -15.1092078232955 | etot = -14.6424332453172 -235000 ekin = 0.0795947059788063 | erot = 0.412276079792834 | epot = -15.1343040311561 | etot = -14.6424332453845 -236000 ekin = 0.0821526186131156 | erot = 0.435593295650787 | epot = -15.1601791597182 | etot = -14.6424332454543 -237000 ekin = 0.084779101422344 | erot = 0.458538653868273 | epot = -15.1857510008135 | etot = -14.6424332455229 -238000 ekin = 0.0873700423841441 | erot = 0.480156759890549 | epot = -15.2099600478608 | etot = -14.6424332455861 -239000 ekin = 0.0898415153120331 | erot = 0.499556095556538 | epot = -15.2318308565087 | etot = -14.6424332456401 -240000 ekin = 0.0921414623518645 | erot = 0.515957735404849 | epot = -15.2505324434381 | etot = -14.6424332456814 -241000 ekin = 0.0942594490127862 | erot = 0.528739776890127 | epot = -15.2654324716098 | etot = -14.6424332457069 -242000 ekin = 0.0962332805866192 | erot = 0.537473606139427 | epot = -15.276140132441 | etot = -14.6424332457149 -243000 ekin = 0.0981515319325858 | erot = 0.541948785982857 | epot = -15.2825335636204 | etot = -14.642433245705 -244000 ekin = 0.100151482350114 | erot = 0.542184479376275 | epot = -15.2847692074041 | etot = -14.6424332456777 -245000 ekin = 0.102412491094951 | erot = 0.538426702319034 | epot = -15.2832724390489 | etot = -14.642433245635 -246000 ekin = 0.105145395544293 | erot = 0.531132085866979 | epot = -15.2787107269906 | etot = -14.6424332455793 -247000 ekin = 0.108578961411821 | erot = 0.52093999420686 | epot = -15.271952201133 | etot = -14.6424332455143 -248000 ekin = 0.112944688754725 | erot = 0.50863565229471 | epot = -15.2640135864931 | etot = -14.6424332454436 -249000 ekin = 0.118461348905719 | erot = 0.495107336752391 | epot = -15.2560019310293 | etot = -14.6424332453712 -250000 ekin = 0.125320510714173 | erot = 0.481300713195434 | epot = -15.2490544692103 | etot = -14.6424332453007 -251000 ekin = 0.133674056956427 | erot = 0.468173145421896 | epot = -15.2442804476139 | etot = -14.6424332452356 -252000 ekin = 0.143624355874461 | erot = 0.456650355971834 | epot = -15.2427079570251 | etot = -14.6424332451788 -253000 ekin = 0.155217400156353 | erot = 0.447587277163379 | epot = -15.2452379224523 | etot = -14.6424332451326 -254000 ekin = 0.168438906846637 | erot = 0.441734376015244 | epot = -15.2526065279605 | etot = -14.6424332450987 -255000 ekin = 0.183213121646734 | erot = 0.439710227351439 | epot = -15.2653565940763 | etot = -14.6424332450781 -256000 ekin = 0.199403908834921 | erot = 0.441980689731424 | epot = -15.283817843638 | etot = -14.6424332450717 -257000 ekin = 0.216817638464824 | erot = 0.448844730303074 | epot = -15.3080956138475 | etot = -14.6424332450796 -258000 ekin = 0.235207399038843 | erot = 0.460426746273175 | epot = -15.3380673904137 | etot = -14.6424332451017 -259000 ekin = 0.254278151369354 | erot = 0.476675120646266 | epot = -15.3733865171527 | etot = -14.6424332451371 -260000 ekin = 0.273692576680278 | erot = 0.497366691704049 | epot = -15.4134925135692 | etot = -14.6424332451849 -261000 ekin = 0.293077534076593 | erot = 0.522116767902341 | epot = -15.4576275472227 | etot = -14.6424332452438 -262000 ekin = 0.312031202024041 | erot = 0.550394247117889 | epot = -15.5048586944538 | etot = -14.6424332453119 -263000 ekin = 0.330131107619666 | erot = 0.58154128199589 | epot = -15.5541056350029 | etot = -14.6424332453873 -264000 ekin = 0.346943319973835 | erot = 0.614796773442864 | epot = -15.6041733388843 | etot = -14.6424332454676 -265000 ekin = 0.36203307825833 | erot = 0.649322794992431 | epot = -15.6537891188012 | etot = -14.6424332455505 -266000 ekin = 0.374977027500473 | erot = 0.684232889055386 | epot = -15.7016431621889 | etot = -14.6424332456331 -267000 ekin = 0.385377045185273 | erot = 0.718621072058621 | epot = -15.7464313629566 | etot = -14.6424332457127 -268000 ekin = 0.392875374680177 | erot = 0.751590369461549 | epot = -15.7868989899282 | etot = -14.6424332457865 -269000 ekin = 0.397170471139152 | erot = 0.782279784272065 | epot = -15.8218835012632 | etot = -14.6424332458519 -270000 ekin = 0.398032662028036 | erot = 0.809888771673587 | epot = -15.8503546796086 | etot = -14.642433245907 -271000 ekin = 0.395318487598681 | erot = 0.833698516709737 | epot = -15.8714502502579 | etot = -14.6424332459495 -272000 ekin = 0.388982474352113 | erot = 0.853089551908481 | epot = -15.8845052722386 | etot = -14.642433245978 -273000 ekin = 0.379085147931406 | erot = 0.867555470405084 | epot = -15.8890738643282 | etot = -14.6424332459917 -274000 ekin = 0.36579632219322 | erot = 0.876712662629334 | epot = -15.8849422308128 | etot = -14.6424332459903 -275000 ekin = 0.349393082921511 | erot = 0.880306121913819 | epot = -15.8721324508092 | etot = -14.6424332459739 -276000 ekin = 0.330252358905648 | erot = 0.878211432148985 | epot = -15.8508970369982 | etot = -14.6424332459435 -277000 ekin = 0.308838461220188 | erot = 0.870433084876957 | epot = -15.8217047919976 | etot = -14.6424332459005 -278000 ekin = 0.285686394604086 | erot = 0.857099294885159 | epot = -15.7852189353358 | etot = -14.6424332458466 -279000 ekin = 0.261382042766412 | erot = 0.838453513181032 | epot = -15.7422688017312 | etot = -14.6424332457837 -280000 ekin = 0.23654047332595 | erot = 0.814842890587961 | epot = -15.6938166096284 | etot = -14.6424332457145 -281000 ekin = 0.211783602608016 | erot = 0.78670403285839 | epot = -15.6409208811076 | etot = -14.6424332456411 -282000 ekin = 0.187718337271894 | erot = 0.754546508157669 | epot = -15.5846980909958 | etot = -14.6424332455662 -283000 ekin = 0.164916115090795 | erot = 0.718934708845181 | epot = -15.5262840694281 | etot = -14.6424332454921 -284000 ekin = 0.143894549221715 | erot = 0.680468811939352 | epot = -15.4667966065823 | etot = -14.6424332454213 -285000 ekin = 0.125101678372295 | erot = 0.639765701847641 | epot = -15.4073006255757 | etot = -14.6424332453557 -286000 ekin = 0.108903164107394 | erot = 0.597440790010453 | epot = -15.3487771994148 | etot = -14.6424332452969 -287000 ekin = 0.0955726645551815 | erot = 0.554091668604978 | epot = -15.2920975784066 | etot = -14.6424332452464 -288000 ekin = 0.0852855448006968 | erot = 0.510284456822097 | epot = -15.2380032468277 | etot = -14.6424332452049 -289000 ekin = 0.07811604131029 | erot = 0.466543535623142 | epot = -15.1870928221065 | etot = -14.6424332451731 -290000 ekin = 0.0740379578618433 | erot = 0.423345127589082 | epot = -15.1398163306018 | etot = -14.6424332451509 -291000 ekin = 0.072928910063375 | erot = 0.381114879437431 | epot = -15.0964770346385 | etot = -14.6424332451377 -292000 ekin = 0.0745780357927571 | erot = 0.340229271737873 | epot = -15.0572405526631 | etot = -14.6424332451325 -293000 ekin = 0.0786969407539254 | erot = 0.301020346548472 | epot = -15.0221505324365 | etot = -14.6424332451341 -294000 ekin = 0.0849334564702411 | erot = 0.263782947588667 | epot = -14.9911496491996 | etot = -14.6424332451407 -295000 ekin = 0.0928875723607584 | erot = 0.228783448806939 | epot = -14.9641042663184 | etot = -14.6424332451507 -296000 ekin = 0.102128697507195 | erot = 0.19626884038738 | epot = -14.9408307830571 | etot = -14.6424332451625 -297000 ekin = 0.112213252496717 | erot = 0.166475068218863 | epot = -14.9211215658901 | etot = -14.6424332451745 -298000 ekin = 0.122701527066801 | erot = 0.139633685446912 | epot = -14.9047684576991 | etot = -14.6424332451854 -299000 ekin = 0.13317279291057 | erot = 0.115976150690173 | epot = -14.8915821887951 | etot = -14.6424332451943 -300000 ekin = 0.143237839707087 | erot = 0.0957354521215326 | epot = -14.8814065370293 | etot = -14.6424332452007 -301000 ekin = 0.152548387988438 | erot = 0.0791450908732747 | epot = -14.8741267240661 | etot = -14.6424332452044 -302000 ekin = 0.160803184299453 | erot = 0.0664357608561943 | epot = -14.8696721903613 | etot = -14.6424332452057 -303000 ekin = 0.167750948486611 | erot = 0.0578302677257495 | epot = -14.868014461417 | etot = -14.6424332452046 -304000 ekin = 0.173190665587053 | erot = 0.0535373136372916 | epot = -14.8691612244265 | etot = -14.6424332452022 -305000 ekin = 0.176969952948865 | erot = 0.0537447402909072 | epot = -14.8731479384385 | etot = -14.6424332451988 -306000 ekin = 0.178982363290529 | erot = 0.0586126977876584 | epot = -14.8800283062732 | etot = -14.642433245195 -307000 ekin = 0.179164502944002 | erot = 0.0682670321056827 | epot = -14.8898647802413 | etot = -14.6424332451916 -308000 ekin = 0.177493763288021 | erot = 0.0827930029186529 | epot = -14.9027200113955 | etot = -14.6424332451889 -309000 ekin = 0.173987301150961 | erot = 0.102229291870645 | epot = -14.9186498382089 | etot = -14.6424332451873 -310000 ekin = 0.168702678647172 | erot = 0.126562162216051 | epot = -14.9376980860502 | etot = -14.642433245187 -311000 ekin = 0.16174029700891 | erot = 0.155719593406526 | epot = -14.9598931356034 | etot = -14.642433245188 -312000 ekin = 0.15324744012492 | erot = 0.189565237977728 | epot = -14.985245923293 | etot = -14.6424332451904 -313000 ekin = 0.14342338999696 | erot = 0.227892126760383 | epot = -15.0137487619518 | etot = -14.6424332451944 -314000 ekin = 0.132524706018464 | erot = 0.270416174780403 | epot = -15.0453741259986 | etot = -14.6424332451998 -315000 ekin = 0.120869409552541 | erot = 0.31676970828902 | epot = -15.0800723630488 | etot = -14.6424332452072 -316000 ekin = 0.108838546104728 | erot = 0.366495437994318 | epot = -15.1177672293161 | etot = -14.642433245217 -317000 ekin = 0.0968734934277246 | erot = 0.419041536809129 | epot = -15.1583482754668 | etot = -14.6424332452299 -318000 ekin = 0.0854675378549793 | erot = 0.47375872576408 | epot = -15.2016595088657 | etot = -14.6424332452467 -319000 ekin = 0.0751507271451901 | erot = 0.529900497448216 | epot = -15.247484469862 | etot = -14.6424332452686 -320000 ekin = 0.0664678443364345 | erot = 0.586627760739854 | epot = -15.2955288503729 | etot = -14.6424332452966 -321000 ekin = 0.0599504590563252 | erot = 0.643019202691537 | epot = -15.3454029070798 | etot = -14.6424332453319 -322000 ekin = 0.0560852142800011 | erot = 0.698088453267024 | epot = -15.3966069129217 | etot = -14.6424332453747 -323000 ekin = 0.0552815181248971 | erot = 0.750808639916102 | epot = -15.4485234034659 | etot = -14.6424332454249 -324000 ekin = 0.057842325520568 | erot = 0.800144112657426 | epot = -15.5004196836595 | etot = -14.6424332454815 -325000 ekin = 0.0639414864634492 | erot = 0.845088070114938 | epot = -15.5514628021208 | etot = -14.6424332455424 -326000 ekin = 0.0736101694210054 | erot = 0.884703689967212 | epot = -15.6007471049934 | etot = -14.6424332456052 -327000 ekin = 0.0867333560896964 | erot = 0.91816541981297 | epot = -15.6473320215697 | etot = -14.642433245667 -328000 ekin = 0.103055779603987 | erot = 0.944796600223873 | epot = -15.6902856255527 | etot = -14.6424332457249 -329000 ekin = 0.12219544617078 | erot = 0.964099781594463 | epot = -15.7287284735416 | etot = -14.6424332457764 -330000 ekin = 0.143662406710238 | erot = 0.975776996237359 | epot = -15.7618726487672 | etot = -14.6424332458196 -331000 ekin = 0.166880785133575 | erot = 0.979738667517989 | epot = -15.7890526985047 | etot = -14.6424332458532 -332000 ekin = 0.191212923969923 | erot = 0.976101405902871 | epot = -15.8097475757491 | etot = -14.6424332458763 -333000 ekin = 0.215985355319577 | erot = 0.965176233539036 | epot = -15.8235948347474 | etot = -14.6424332458887 -334000 ekin = 0.240516656831147 | erot = 0.947449485112495 | epot = -15.8303993878336 | etot = -14.64243324589 -335000 ekin = 0.264146896086235 | erot = 0.923558676868035 | epot = -15.8301388188342 | etot = -14.6424332458799 -336000 ekin = 0.286267467754231 | erot = 0.894265184760612 | epot = -15.8229658983734 | etot = -14.6424332458586 -337000 ekin = 0.306349134750088 | erot = 0.860424939336672 | epot = -15.809207319913 | etot = -14.6424332458262 -338000 ekin = 0.323965497674696 | erot = 0.822957838322753 | epot = -15.7893565817813 | etot = -14.6424332457838 -339000 ekin = 0.338809250788985 | erot = 0.782816380150479 | epot = -15.7640588766724 | etot = -14.6424332457329 -340000 ekin = 0.35069944423374 | erot = 0.740954141303117 | epot = -15.7340868312125 | etot = -14.6424332456757 -341000 ekin = 0.359579293536495 | erot = 0.698295027831847 | epot = -15.700307566983 | etot = -14.6424332456147 -342000 ekin = 0.365505462154926 | erot = 0.655704542034982 | epot = -15.6636432497426 | etot = -14.6424332455527 -343000 ekin = 0.368630832661383 | erot = 0.613964463465552 | epot = -15.6250285416195 | etot = -14.6424332454926 -344000 ekin = 0.369183369589215 | erot = 0.573752273080787 | epot = -15.5853688881069 | etot = -14.6424332454369 -345000 ekin = 0.367443732824289 | erot = 0.535626361233146 | epot = -15.5455033394448 | etot = -14.6424332453874 -346000 ekin = 0.36372393313177 | erot = 0.500017626276193 | epot = -15.5061748047535 | etot = -14.6424332453455 -347000 ekin = 0.358348705277679 | erot = 0.467227585427262 | epot = -15.4680095360169 | etot = -14.642433245312 -348000 ekin = 0.351640582954838 | erot = 0.437432666908102 | epot = -15.4315064951499 | etot = -14.642433245287 -349000 ekin = 0.343909024694815 | erot = 0.410693986169929 | epot = -15.3970362561344 | etot = -14.6424332452696 -350000 ekin = 0.335443435968793 | erot = 0.386971649880727 | epot = -15.3648483311092 | etot = -14.6424332452597 -351000 ekin = 0.326509584093778 | erot = 0.366142474251511 | epot = -15.3350853036005 | etot = -14.6424332452552 -352000 ekin = 0.317348699022207 | erot = 0.34801993040111 | epot = -15.3078018746784 | etot = -14.6424332452551 -353000 ekin = 0.30817846664876 | erot = 0.332375117501944 | epot = -15.2829868294085 | etot = -14.6424332452578 -354000 ekin = 0.299195119854399 | erot = 0.318957598139001 | epot = -15.2605859632553 | etot = -14.6424332452619 -355000 ekin = 0.290575888248862 | erot = 0.307515001370356 | epot = -15.2405241348854 | etot = -14.6424332452662 -356000 ekin = 0.282481160312497 | erot = 0.29781040621721 | epot = -15.2227248117992 | etot = -14.6424332452695 -357000 ekin = 0.275055828993789 | erot = 0.289636664277857 | epot = -15.2071257385429 | etot = -14.6424332452713 -358000 ekin = 0.26842942725494 | erot = 0.282827006912222 | epot = -15.1936896794383 | etot = -14.6424332452711 -359000 ekin = 0.262714810201762 | erot = 0.277261507858003 | epot = -15.1824095633288 | etot = -14.642433245269 -360000 ekin = 0.258005302569436 | erot = 0.272869227748658 | epot = -15.1733077755836 | etot = -14.6424332452655 -361000 ekin = 0.254370400621781 | erot = 0.269626137802017 | epot = -15.1664297836851 | etot = -14.6424332452613 -362000 ekin = 0.251850290178651 | erot = 0.267549186087959 | epot = -15.1618327215239 | etot = -14.6424332452573 -363000 ekin = 0.250449609862751 | erot = 0.266687109597485 | epot = -15.159569964715 | etot = -14.6424332452548 -364000 ekin = 0.250131041863336 | erot = 0.267108788857729 | epot = -15.1596730759762 | etot = -14.6424332452551 -365000 ekin = 0.250809442162066 | erot = 0.268890073928026 | epot = -15.1621327613494 | etot = -14.6424332452593 -366000 ekin = 0.25234731876335 | erot = 0.272100073006091 | epot = -15.1668806370379 | etot = -14.6424332452684 -367000 ekin = 0.254552520178511 | erot = 0.276787886819413 | epot = -15.1737736522811 | etot = -14.6424332452832 -368000 ekin = 0.257178996153298 | erot = 0.282970699523766 | epot = -15.1825829409812 | etot = -14.6424332453042 -369000 ekin = 0.259931424908708 | erot = 0.29062401114344 | epot = -15.1929886813832 | etot = -14.642433245331 -370000 ekin = 0.262474349326632 | erot = 0.299674631814998 | epot = -15.2045822265049 | etot = -14.6424332453633 -371000 ekin = 0.264446209428301 | erot = 0.309996869297344 | epot = -15.2168763241253 | etot = -14.6424332453996 -372000 ekin = 0.265478281861433 | erot = 0.321412142686654 | epot = -15.2293236699864 | etot = -14.6424332454383 -373000 ekin = 0.265218028290041 | erot = 0.333692059448718 | epot = -15.2413433332161 | etot = -14.6424332454774 -374000 ekin = 0.26335572124772 | erot = 0.346564809671271 | epot = -15.2523537764331 | etot = -14.6424332455141 -375000 ekin = 0.259652497500777 | erot = 0.359724567998165 | epot = -15.2618103110451 | etot = -14.6424332455462 -376000 ekin = 0.253967268934319 | erot = 0.372843454384699 | epot = -15.2692439688902 | etot = -14.6424332455711 -377000 ekin = 0.246279333497663 | erot = 0.385585491299193 | epot = -15.2742980703837 | etot = -14.6424332455868 -378000 ekin = 0.236703249874173 | erot = 0.397621906702965 | epot = -15.2767584021691 | etot = -14.642433245592 -379000 ekin = 0.22549275694072 | erot = 0.408647066936832 | epot = -15.2765730694637 | etot = -14.6424332455862 -380000 ekin = 0.213031377534934 | erot = 0.418394279001949 | epot = -15.2738589021069 | etot = -14.64243324557 -381000 ekin = 0.19980887731166 | erot = 0.426650676217107 | epot = -15.2688927990735 | etot = -14.6424332455448 -382000 ekin = 0.186384809014969 | erot = 0.433270396060972 | epot = -15.2620884505889 | etot = -14.642433245513 -383000 ekin = 0.173342616140343 | erot = 0.4381852790555 | epot = -15.2539611406731 | etot = -14.6424332454773 -384000 ekin = 0.161239700828087 | erot = 0.441412371407271 | epot = -15.2450853176757 | etot = -14.6424332454403 -385000 ekin = 0.15055995464474 | erot = 0.443057612556821 | epot = -15.2360508126064 | etot = -14.6424332454049 -386000 ekin = 0.141675129696877 | erot = 0.443315241526503 | epot = -15.2274236165962 | etot = -14.6424332453728 -387000 ekin = 0.134820015696259 | erot = 0.442462667351556 | epot = -15.2197159283931 | etot = -14.6424332453452 -388000 ekin = 0.130083976412379 | erot = 0.44085081351593 | epot = -15.2133680352507 | etot = -14.6424332453224 -389000 ekin = 0.12741857023722 | erot = 0.43889024628032 | epot = -15.2087420618216 | etot = -14.6424332453041 -390000 ekin = 0.126658423092956 | erot = 0.43703370208669 | epot = -15.2061253704692 | etot = -14.6424332452895 -391000 ekin = 0.127550804261056 | erot = 0.435755902066133 | epot = -15.2057399516053 | etot = -14.6424332452781 -392000 ekin = 0.129788752936039 | erot = 0.435531744058152 | epot = -15.2077537422634 | etot = -14.6424332452692 -393000 ekin = 0.133043055316541 | erot = 0.43681406507717 | epot = -15.2122903656559 | etot = -14.6424332452622 -394000 ekin = 0.136989561466299 | erot = 0.440012156509965 | epot = -15.2194349632336 | etot = -14.6424332452574 -395000 ekin = 0.141329833042564 | erot = 0.445472096884898 | epot = -15.2292351751821 | etot = -14.6424332452547 -396000 ekin = 0.145804542777373 | erot = 0.45345976764831 | epot = -15.2416975556805 | etot = -14.6424332452548 -397000 ekin = 0.150200153188676 | erot = 0.464147173461378 | epot = -15.2567805719085 | etot = -14.6424332452585 -398000 ekin = 0.154350089766152 | erot = 0.477602441558481 | epot = -15.2743857765906 | etot = -14.642433245266 -399000 ekin = 0.158131920622366 | erot = 0.493783661155649 | epot = -15.2943488270562 | etot = -14.6424332452782 -400000 ekin = 0.161462056173796 | erot = 0.512536568006325 | epot = -15.3164318694755 | etot = -14.6424332452953 -401000 ekin = 0.164289301181072 | erot = 0.533595989002473 | epot = -15.3403185355012 | etot = -14.6424332453177 -402000 ekin = 0.166588323050693 | erot = 0.556590928839834 | epot = -15.3656124972355 | etot = -14.642433245345 -403000 ekin = 0.168353810379696 | erot = 0.581053183644485 | epot = -15.3918402394011 | etot = -14.6424332453769 -404000 ekin = 0.169595821301193 | erot = 0.606429376023291 | epot = -15.4184584427372 | etot = -14.6424332454127 -405000 ekin = 0.170336578562018 | erot = 0.63209629254071 | epot = -15.444866116554 | etot = -14.6424332454513 -406000 ekin = 0.170608761978812 | erot = 0.65737934451496 | epot = -15.4704213519851 | etot = -14.6424332454913 -407000 ekin = 0.170455178567329 | erot = 0.681573854094723 | epot = -15.4944622781935 | etot = -14.6424332455315 -408000 ekin = 0.169929554809759 | erot = 0.703968692151394 | epot = -15.5163314925311 | etot = -14.64243324557 -409000 ekin = 0.169098093451394 | erot = 0.723871579521683 | epot = -15.5354029185781 | etot = -14.6424332456051 -410000 ekin = 0.168041369040759 | erot = 0.740635137248624 | epot = -15.5511097519242 | etot = -14.6424332456348 -411000 ekin = 0.166856102809036 | erot = 0.753682569971393 | epot = -15.5629719184382 | etot = -14.6424332456577 -412000 ekin = 0.165656359033239 | erot = 0.762531725093238 | epot = -15.5706213297988 | etot = -14.6424332456724 -413000 ekin = 0.164573741711749 | erot = 0.766816218739624 | epot = -15.5738232061291 | etot = -14.6424332456777 -414000 ekin = 0.163756240957875 | erot = 0.766302377571564 | epot = -15.5724918642026 | etot = -14.6424332456732 -415000 ekin = 0.163365479945837 | erot = 0.76090092022446 | epot = -15.5666996458289 | etot = -14.6424332456586 -416000 ekin = 0.16357224009456 | erot = 0.750672586698944 | epot = -15.556678072428 | etot = -14.6424332456345 -417000 ekin = 0.164550286199954 | erot = 0.7358272978906 | epot = -15.5428108296923 | etot = -14.6424332456018 -418000 ekin = 0.166468663393413 | erot = 0.716716857299939 | epot = -15.5256187662552 | etot = -14.6424332455618 -419000 ekin = 0.169482781127082 | erot = 0.693821649098591 | epot = -15.5057376757421 | etot = -14.6424332455164 -420000 ekin = 0.173724722667737 | erot = 0.66773219168281 | epot = -15.4838901598182 | etot = -14.6424332454677 -421000 ekin = 0.179293310761201 | erot = 0.639126725581016 | epot = -15.4608532817598 | etot = -14.6424332454176 -422000 ekin = 0.18624451452154 | erot = 0.608746211198834 | epot = -15.437423971089 | etot = -14.6424332453687 -423000 ekin = 0.194582798147166 | erot = 0.577368165576623 | epot = -15.4143842090466 | etot = -14.6424332453228 -424000 ekin = 0.204253993032127 | erot = 0.545780680985215 | epot = -15.3924679192995 | etot = -14.6424332452822 -425000 ekin = 0.215140228919709 | erot = 0.514757766830984 | epot = -15.3723312409989 | etot = -14.6424332452482 -426000 ekin = 0.227057395200028 | erot = 0.485036881514174 | epot = -15.354527521936 | etot = -14.6424332452218 -427000 ekin = 0.239755526228602 | erot = 0.457299221560653 | epot = -15.3394879929934 | etot = -14.6424332452042 -428000 ekin = 0.252922416271923 | erot = 0.432153058134052 | epot = -15.3275087196016 | etot = -14.6424332451956 -429000 ekin = 0.266190667181531 | erot = 0.410120192007372 | epot = -15.3187441043849 | etot = -14.642433245196 -430000 ekin = 0.279148248287616 | erot = 0.391625457761957 | epot = -15.3132069512549 | etot = -14.6424332452053 -431000 ekin = 0.291352495295092 | erot = 0.376989149810484 | epot = -15.3107748903279 | etot = -14.6424332452223 -432000 ekin = 0.302347287571197 | erot = 0.366422254466197 | epot = -15.311202787284 | etot = -14.6424332452466 -433000 ekin = 0.311682921771834 | erot = 0.360024429012416 | epot = -15.3141405960599 | etot = -14.6424332452756 -434000 ekin = 0.318937954387398 | erot = 0.357784738270779 | epot = -15.3191559379664 | etot = -14.6424332453082 -435000 ekin = 0.323742037714837 | erot = 0.359585207272863 | epot = -15.3257604903308 | etot = -14.6424332453431 -436000 ekin = 0.325798554031316 | erot = 0.365207245305789 | epot = -15.3334390447156 | etot = -14.6424332453785 -437000 ekin = 0.324905697097303 | erot = 0.374340922349983 | epot = -15.3416798648586 | etot = -14.6424332454113 -438000 ekin = 0.320974589858357 | erot = 0.386596930160468 | epot = -15.3500047654588 | etot = -14.64243324544 -439000 ekin = 0.314043077746361 | erot = 0.401520852185505 | epot = -15.3579971753956 | etot = -14.6424332454637 -440000 ekin = 0.304283988020539 | erot = 0.41860913221399 | epot = -15.3653263657148 | etot = -14.6424332454802 -441000 ekin = 0.292006859111611 | erot = 0.437325916193047 | epot = -15.3717660207934 | etot = -14.6424332454888 -442000 ekin = 0.277652365815072 | erot = 0.457119792518877 | epot = -15.3772054038232 | etot = -14.6424332454893 -443000 ekin = 0.261778853590747 | erot = 0.477439412175799 | epot = -15.3816515112488 | etot = -14.6424332454822 -444000 ekin = 0.245040553434245 | erot = 0.497747053376455 | epot = -15.3852208522799 | etot = -14.6424332454692 -445000 ekin = 0.22815726042029 | erot = 0.517529408202492 | epot = -15.3881199140742 | etot = -14.6424332454515 -446000 ekin = 0.211875681729375 | erot = 0.536305196856599 | epot = -15.3906141240179 | etot = -14.6424332454319 -447000 ekin = 0.196923472681452 | erot = 0.553629632753462 | epot = -15.3929863508487 | etot = -14.6424332454138 -448000 ekin = 0.183958277880794 | erot = 0.569096233370998 | epot = -15.3954877566523 | etot = -14.6424332454005 -449000 ekin = 0.173515771313212 | erot = 0.582336947151654 | epot = -15.3982859638601 | etot = -14.6424332453953 -450000 ekin = 0.16596236119942 | erot = 0.593021970145928 | epot = -15.4014175767459 | etot = -14.6424332454006 -451000 ekin = 0.161459280835239 | erot = 0.600860851249478 | epot = -15.4047533775022 | etot = -14.6424332454175 -452000 ekin = 0.159944578253891 | erot = 0.605606408076375 | epot = -15.4079842317757 | etot = -14.6424332454454 -453000 ekin = 0.161137653115343 | erot = 0.607062496368088 | epot = -15.410633394965 | etot = -14.6424332454816 -454000 ekin = 0.164567591513362 | erot = 0.605095779306127 | epot = -15.4120966163413 | etot = -14.6424332455218 -455000 ekin = 0.169622334209561 | erot = 0.599650455421312 | epot = -15.4117060351916 | etot = -14.6424332455607 -456000 ekin = 0.175611802350684 | erot = 0.59076370289457 | epot = -15.4088087508384 | etot = -14.6424332455932 -457000 ekin = 0.181835621982265 | erot = 0.578578749363215 | epot = -15.4028476169601 | etot = -14.6424332456146 -458000 ekin = 0.187645727030889 | erot = 0.563352302649359 | epot = -15.3934312753016 | etot = -14.6424332456214 -459000 ekin = 0.192495880384906 | erot = 0.545453717149624 | epot = -15.380382843147 | etot = -14.6424332456124 -460000 ekin = 0.195973381637233 | erot = 0.52535459771201 | epot = -15.3637612249374 | etot = -14.6424332455881 -461000 ekin = 0.197811920991221 | erot = 0.503609203464267 | epot = -15.3438543700064 | etot = -14.642433245551 -462000 ekin = 0.197887724919133 | erot = 0.480827560284759 | epot = -15.3211485307077 | etot = -14.6424332455038 -463000 ekin = 0.196203198485173 | erot = 0.457644248439117 | epot = -15.2962806923751 | etot = -14.6424332454508 -464000 ekin = 0.192863034125905 | erot = 0.434686220431875 | epot = -15.2699824999537 | etot = -14.6424332453959 -465000 ekin = 0.188047435822221 | erot = 0.412542760093999 | epot = -15.2430234412586 | etot = -14.6424332453424 -466000 ekin = 0.181986107552774 | erot = 0.391740010674855 | epot = -15.2161593635207 | etot = -14.6424332452931 -467000 ekin = 0.174935400197985 | erot = 0.372721626737699 | epot = -15.1900902721857 | etot = -14.64243324525 -468000 ekin = 0.167159826102144 | erot = 0.355836258353897 | epot = -15.1654293296704 | etot = -14.6424332452144 -469000 ekin = 0.15891821802259 | erot = 0.341331890767446 | epot = -15.1426833539768 | etot = -14.6424332451868 -470000 ekin = 0.150454185653208 | erot = 0.329356584635644 | epot = -15.1222440154559 | etot = -14.642433245167 -471000 ekin = 0.141990180749418 | erot = 0.319964871778395 | epot = -15.1043882976824 | etot = -14.6424332451546 -472000 ekin = 0.133724353868212 | erot = 0.313128906246322 | epot = -15.089286505263 | etot = -14.6424332451484 -473000 ekin = 0.125829398101873 | erot = 0.308753392325049 | epot = -15.0770160355744 | etot = -14.6424332451474 -474000 ekin = 0.11845266636319 | erot = 0.306693264414359 | epot = -15.0675791759278 | etot = -14.6424332451502 -475000 ekin = 0.111716976218895 | erot = 0.306773053291037 | epot = -15.0609232746653 | etot = -14.6424332451553 -476000 ekin = 0.105721655633226 | erot = 0.308806833537935 | epot = -15.0569617343327 | etot = -14.6424332451616 -477000 ekin = 0.100543523675716 | erot = 0.31261761713068 | epot = -15.055594385974 | etot = -14.6424332451676 -478000 ekin = 0.0962376398644556 | erot = 0.318055055635918 | epot = -15.056725940673 | etot = -14.6424332451726 -479000 ekin = 0.0928377950023828 | erot = 0.32501035703107 | epot = -15.0602813972092 | etot = -14.6424332451757 -480000 ekin = 0.0903568546344153 | erot = 0.333427427764655 | epot = -15.0662175275757 | etot = -14.6424332451766 -481000 ekin = 0.0887871989354853 | erot = 0.343309423711623 | epot = -15.0745298678221 | etot = -14.642433245175 -482000 ekin = 0.0881016191313906 | erot = 0.354720133059459 | epot = -15.085254997362 | etot = -14.6424332451712 -483000 ekin = 0.0882551127429689 | erot = 0.367779908275294 | epot = -15.0984682661837 | etot = -14.6424332451655 -484000 ekin = 0.0891880440123854 | erot = 0.382656193510864 | epot = -15.1142774826819 | etot = -14.6424332451586 -485000 ekin = 0.0908310739090707 | erot = 0.399549033149909 | epot = -15.1328133522102 | etot = -14.6424332451512 -486000 ekin = 0.0931120890965817 | erot = 0.418672269926991 | epot = -15.1542176041678 | etot = -14.6424332451442 -487000 ekin = 0.0959650526362288 | erot = 0.440231422324977 | epot = -15.1786297200997 | etot = -14.6424332451385 -488000 ekin = 0.0993402613831306 | erot = 0.464399451388421 | epot = -15.2061729579064 | etot = -14.6424332451348 -489000 ekin = 0.103214957393528 | erot = 0.491291775407019 | epot = -15.2369399779349 | etot = -14.6424332451343 -490000 ekin = 0.107602676592561 | erot = 0.52094196550166 | epot = -15.2709778872321 | etot = -14.6424332451379 -491000 ekin = 0.112559247659633 | erot = 0.553279563919969 | epot = -15.3082720567263 | etot = -14.6424332451467 -492000 ekin = 0.118183136718381 | erot = 0.58811142531092 | epot = -15.3487278071915 | etot = -14.6424332451622 -493000 ekin = 0.124608040121107 | erot = 0.625107908280808 | epot = -15.3921491935878 | etot = -14.6424332451859 -494000 ekin = 0.131986393307422 | erot = 0.663795156036242 | epot = -15.4382147945631 | etot = -14.6424332452194 -495000 ekin = 0.140463823895352 | erot = 0.703554605722129 | epot = -15.4864516748821 | etot = -14.6424332452647 -496000 ekin = 0.150146408031556 | erot = 0.743630741562838 | epot = -15.5362103949171 | etot = -14.6424332453227 -497000 ekin = 0.16106457906773 | erot = 0.783147917316532 | epot = -15.5866457417786 | etot = -14.6424332453944 -498000 ekin = 0.173139219154639 | erot = 0.82113675497104 | epot = -15.6367092196045 | etot = -14.6424332454788 -499000 ekin = 0.186156317831581 | erot = 0.856570103854347 | epot = -15.6851596672597 | etot = -14.6424332455737 -500000 ekin = 0.19975619506813 | erot = 0.88840775827112 | epot = -15.7305971990145 | etot = -14.6424332456752 -501000 ekin = 0.213441517837533 | erot = 0.915648078729441 | epot = -15.7715228423447 | etot = -14.6424332457777 -502000 ekin = 0.226605416599146 | erot = 0.937383433645324 | epot = -15.8064220961188 | etot = -14.6424332458743 -503000 ekin = 0.238577508979602 | erot = 0.952855183120694 | epot = -15.833865938058 | etot = -14.6424332459577 -504000 ekin = 0.248682347019085 | erot = 0.961503066783805 | epot = -15.852618659824 | etot = -14.6424332460211 -505000 ekin = 0.256302488972944 | erot = 0.963003656361843 | epot = -15.8617393913939 | etot = -14.6424332460591 -506000 ekin = 0.260937583147995 | erot = 0.957293217915528 | epot = -15.8606640471316 | etot = -14.6424332460681 -507000 ekin = 0.262251679303344 | erot = 0.944571918253377 | epot = -15.8492568436041 | etot = -14.6424332460473 -508000 ekin = 0.260103184115665 | erot = 0.925288564929115 | epot = -15.8278249950432 | etot = -14.6424332459984 -509000 ekin = 0.254554875284736 | erot = 0.900107536932479 | epot = -15.7970956581425 | etot = -14.6424332459253 -510000 ekin = 0.245864483352384 | erot = 0.869861717980019 | epot = -15.7581594471659 | etot = -14.6424332458335 -511000 ekin = 0.234458914530909 | erot = 0.835496660121179 | epot = -15.7123888203816 | etot = -14.6424332457295 -512000 ekin = 0.220896820243757 | erot = 0.798011684060737 | epot = -15.6613417499247 | etot = -14.6424332456202 -513000 ekin = 0.205824805091359 | erot = 0.758403224573371 | epot = -15.6066612751765 | etot = -14.6424332455118 -514000 ekin = 0.189932244119314 | erot = 0.717614706855598 | epot = -15.5499801963845 | etot = -14.6424332454096 -515000 ekin = 0.17390874820256 | erot = 0.676495918868179 | epot = -15.4928379123889 | etot = -14.6424332453181 -516000 ekin = 0.158407108511413 | erot = 0.635773516021293 | epot = -15.4366138697731 | etot = -14.6424332452404 -517000 ekin = 0.144013350185935 | erot = 0.596033149114501 | epot = -15.3824797444789 | etot = -14.6424332451784 -518000 ekin = 0.131224514119671 | erot = 0.557712825685801 | epot = -15.3313705849381 | etot = -14.6424332451327 -519000 ekin = 0.120434042407119 | erot = 0.521106495595061 | epot = -15.283973783105 | etot = -14.6424332451028 -520000 ekin = 0.111924165177638 | erot = 0.486376443197605 | epot = -15.2407338534629 | etot = -14.6424332450877 -521000 ekin = 0.10586442481646 | erot = 0.45357280605877 | epot = -15.2018704759605 | etot = -14.6424332450853 -522000 ekin = 0.102315362067637 | erot = 0.422658367130315 | epot = -15.1674069742913 | etot = -14.6424332450933 -523000 ekin = 0.101236366465097 | erot = 0.393536647096217 | epot = -15.1372062586706 | etot = -14.6424332451092 -524000 ekin = 0.102496717236361 | erot = 0.366081244307775 | epot = -15.1110112066744 | etot = -14.6424332451302 -525000 ekin = 0.105888887335359 | erot = 0.340164343214466 | epot = -15.0884864757035 | etot = -14.6424332451537 -526000 ekin = 0.111143247849972 | erot = 0.315682368378565 | epot = -15.0692588614059 | etot = -14.6424332451774 -527000 ekin = 0.117943398961211 | erot = 0.292576937806859 | epot = -15.0529535819675 | etot = -14.6424332451994 -528000 ekin = 0.125941474254374 | erot = 0.270849598243548 | epot = -15.0392243177162 | etot = -14.6424332452183 -529000 ekin = 0.134772916008759 | erot = 0.25056931723892 | epot = -15.0277754784807 | etot = -14.642433245233 -530000 ekin = 0.144070383401968 | erot = 0.23187234065126 | epot = -15.0183759692966 | etot = -14.6424332452434 -531000 ekin = 0.153476601968784 | erot = 0.214954741433899 | epot = -15.0108645886522 | etot = -14.6424332452495 -532000 ekin = 0.162656054076994 | erot = 0.200058697647296 | epot = -15.0051479969762 | etot = -14.6424332452519 -533000 ekin = 0.171305419079581 | erot = 0.187454143182374 | epot = -15.0011928075132 | etot = -14.6424332452513 -534000 ekin = 0.179162595538561 | erot = 0.177417842692276 | epot = -14.9990136834796 | etot = -14.6424332452488 -535000 ekin = 0.186014006484957 | erot = 0.17021209444073 | epot = -14.9986593461707 | etot = -14.642433245245 -536000 ekin = 0.1916997592389 | erot = 0.166065149224443 | epot = -15.0001981537043 | etot = -14.642433245241 -537000 ekin = 0.196116169930245 | erot = 0.165155084977448 | epot = -15.003704500145 | etot = -14.6424332452373 -538000 ekin = 0.199215220532697 | erot = 0.167598364569289 | epot = -15.0092468303365 | etot = -14.6424332452345 -539000 ekin = 0.201000709668931 | erot = 0.173443713615177 | epot = -15.0168776685174 | etot = -14.6424332452333 -540000 ekin = 0.201521164037736 | erot = 0.182671367030118 | epot = -15.0266257763017 | etot = -14.6424332452339 -541000 ekin = 0.200859940141596 | erot = 0.19519721144006 | epot = -15.0384903968184 | etot = -14.6424332452367 -542000 ekin = 0.199123298889486 | erot = 0.210880936221535 | epot = -15.0524374803529 | etot = -14.6424332452418 -543000 ekin = 0.196427519384799 | erot = 0.229537017788173 | epot = -15.0683977824221 | etot = -14.6424332452491 -544000 ekin = 0.192886294946266 | erot = 0.250947202002022 | epot = -15.0862667422075 | etot = -14.6424332452592 -545000 ekin = 0.188599710888658 | erot = 0.274873110236026 | epot = -15.1059060663961 | etot = -14.6424332452714 -546000 ekin = 0.183646045244012 | erot = 0.301067663120912 | epot = -15.1271469536507 | etot = -14.6424332452858 -547000 ekin = 0.178077473819966 | erot = 0.329284179376574 | epot = -15.1497948984983 | etot = -14.6424332453018 -548000 ekin = 0.171920510268459 | erot = 0.359282253787704 | epot = -15.1736360093752 | etot = -14.6424332453191 -549000 ekin = 0.16518167057886 | erot = 0.390829837836036 | epot = -15.1984447537517 | etot = -14.6424332453368 -550000 ekin = 0.157858408655944 | erot = 0.423701326923133 | epot = -15.2239929809336 | etot = -14.6424332453545 -551000 ekin = 0.14995480900584 | erot = 0.457671882722303 | epot = -15.2500599370996 | etot = -14.6424332453714 -552000 ekin = 0.141500835822425 | erot = 0.492508662666516 | epot = -15.2764427438757 | etot = -14.6424332453867 -553000 ekin = 0.132573145480455 | erot = 0.527960055130333 | epot = -15.3029664460106 | etot = -14.6424332453998 -554000 ekin = 0.123314645146755 | erot = 0.563744383275445 | epot = -15.3294922738324 | etot = -14.6424332454102 -555000 ekin = 0.113949270900201 | erot = 0.599539792629047 | epot = -15.3559223089471 | etot = -14.6424332454179 -556000 ekin = 0.104788088804124 | erot = 0.634977129568493 | epot = -15.3821984637957 | etot = -14.6424332454231 -557000 ekin = 0.0962230654738455 | erot = 0.669637513728679 | epot = -15.4082938246296 | etot = -14.642433245427 -558000 ekin = 0.088705961438158 | erot = 0.703055990484119 | epot = -15.4341951973534 | etot = -14.6424332454312 -559000 ekin = 0.0827118847692418 | erot = 0.734732129426884 | epot = -15.4598772596337 | etot = -14.6424332454376 -560000 ekin = 0.0786899547209703 | erot = 0.764147748401053 | epot = -15.4852709485705 | etot = -14.6424332454484 -561000 ekin = 0.0770067720584858 | erot = 0.790791153077639 | epot = -15.5102311706015 | etot = -14.6424332454654 -562000 ekin = 0.0778911706718927 | erot = 0.814186471630364 | epot = -15.5345108877916 | etot = -14.6424332454893 -563000 ekin = 0.0813901113631772 | erot = 0.833925925484042 | epot = -15.5577492823671 | etot = -14.6424332455199 -564000 ekin = 0.0873448530183822 | erot = 0.849702302566594 | epot = -15.5794804011401 | etot = -14.6424332455551 -565000 ekin = 0.0953935152513702 | erot = 0.861338569498078 | epot = -15.5991653303408 | etot = -14.6424332455914 -566000 ekin = 0.105001366117373 | erot = 0.868811531658348 | epot = -15.6162461434002 | etot = -14.6424332456244 -567000 ekin = 0.115514789209081 | erot = 0.872266750929459 | epot = -15.6302147857878 | etot = -14.6424332456493 -568000 ekin = 0.12623032098928 | erot = 0.872022546762645 | epot = -15.6406861134138 | etot = -14.6424332456618 -569000 ekin = 0.136467575204533 | erot = 0.868561781939923 | epot = -15.6474626028035 | etot = -14.642433245659 -570000 ekin = 0.145634823228531 | erot = 0.862511177265096 | epot = -15.6505792461335 | etot = -14.6424332456399 -571000 ekin = 0.153278250259458 | erot = 0.854608991358708 | epot = -15.6503204872235 | etot = -14.6424332456053 -572000 ekin = 0.159109636953243 | erot = 0.845662918619347 | epot = -15.6472058011307 | etot = -14.6424332455581 -573000 ekin = 0.163011362016527 | erot = 0.836500892322521 | epot = -15.6419454998419 | etot = -14.6424332455028 -574000 ekin = 0.165021239079052 | erot = 0.827918058207678 | epot = -15.6353725427317 | etot = -14.6424332454449 -575000 ekin = 0.165302195907203 | erot = 0.820623479706266 | epot = -15.6283589210035 | etot = -14.6424332453901 -576000 ekin = 0.164102988099449 | erot = 0.815190165400521 | epot = -15.6217263988437 | etot = -14.6424332453438 -577000 ekin = 0.161716152385045 | erot = 0.81201181794545 | epot = -15.6161612156414 | etot = -14.6424332453109 -578000 ekin = 0.158438569369355 | erot = 0.811269345694715 | epot = -15.6121411603589 | etot = -14.6424332452948 -579000 ekin = 0.154538688866594 | erot = 0.812909695779921 | epot = -15.609881629944 | etot = -14.6424332452975 -580000 ekin = 0.150232988451468 | erot = 0.816638977240042 | epot = -15.6093052110108 | etot = -14.6424332453193 -581000 ekin = 0.14567280981178 | erot = 0.821931135408262 | epot = -15.610037190579 | etot = -14.6424332453589 -582000 ekin = 0.140941476788232 | erot = 0.828052590347223 | epot = -15.6114273125488 | etot = -14.6424332454134 -583000 ekin = 0.136060602595893 | erot = 0.83410224689192 | epot = -15.6125960949662 | etot = -14.6424332454784 -584000 ekin = 0.131003759893424 | erot = 0.839065139153169 | epot = -15.6125021445953 | etot = -14.6424332455487 -585000 ekin = 0.125715216480054 | erot = 0.841876757443394 | epot = -15.6100252195419 | etot = -14.6424332456185 -586000 ekin = 0.120131224766288 | erot = 0.841493945660771 | epot = -15.6040584161087 | etot = -14.6424332456817 -587000 ekin = 0.114201380569865 | erot = 0.836967317747604 | epot = -15.5936019440502 | etot = -14.6424332457327 -588000 ekin = 0.107907808224942 | erot = 0.827509595977129 | epot = -15.5778506499689 | etot = -14.6424332457668 -589000 ekin = 0.101280337908464 | erot = 0.812554260667739 | epot = -15.5562678443567 | etot = -14.6424332457805 -590000 ekin = 0.0944063548781473 | erot = 0.791799488415124 | epot = -15.5286390890653 | etot = -14.642433245772 -591000 ekin = 0.0874345511051118 | erot = 0.765233519218442 | epot = -15.4951013160646 | etot = -14.6424332457411 -592000 ekin = 0.0805723392090093 | erot = 0.733139214281049 | epot = -15.4561447991793 | etot = -14.6424332456893 -593000 ekin = 0.074077159409156 | erot = 0.696077455345262 | epot = -15.4125878603743 | etot = -14.6424332456198 -594000 ekin = 0.068242308961577 | erot = 0.65485096335545 | epot = -15.3655265178543 | etot = -14.6424332455373 -595000 ekin = 0.0633782539035074 | erot = 0.610451848321685 | epot = -15.3162633476722 | etot = -14.642433245447 -596000 ekin = 0.059790654067382 | erot = 0.563997548399928 | epot = -15.2662214478224 | etot = -14.6424332453551 -597000 ekin = 0.0577565493651041 | erot = 0.516660644083728 | epot = -15.2168504387162 | etot = -14.6424332452674 -598000 ekin = 0.0575003158564816 | erot = 0.469598294353669 | epot = -15.1695318553997 | etot = -14.6424332451895 -599000 ekin = 0.0591710965315296 | erot = 0.423886769451575 | epot = -15.1254911111095 | etot = -14.6424332451264 -600000 ekin = 0.0628234356919141 | erot = 0.380465849282312 | epot = -15.0857225300557 | etot = -14.6424332450815 -601000 ekin = 0.0684027903404326 | erot = 0.340096852290174 | epot = -15.0509328876876 | etot = -14.642433245057 -602000 ekin = 0.0757374499151583 | erot = 0.303336891510099 | epot = -15.0215075864787 | etot = -14.6424332450534 -603000 ekin = 0.0845381560125233 | erot = 0.270530726253805 | epot = -14.9975021273362 | etot = -14.6424332450699 -604000 ekin = 0.0944063594091485 | erot = 0.24182034796485 | epot = -14.9786599524776 | etot = -14.6424332451036 -605000 ekin = 0.104851562461312 | erot = 0.21717122479241 | epot = -14.964456032404 | etot = -14.6424332451503 -606000 ekin = 0.115317556389988 | erot = 0.196412930357425 | epot = -14.9541637319519 | etot = -14.6424332452045 -607000 ekin = 0.125216580352841 | erot = 0.179290709848654 | epot = -14.9469405354616 | etot = -14.6424332452601 -608000 ekin = 0.133969542489582 | erot = 0.165523445158815 | epot = -14.9419262329591 | etot = -14.6424332453107 -609000 ekin = 0.141049537027062 | erot = 0.154862582266164 | epot = -14.9383453646429 | etot = -14.6424332453497 -610000 ekin = 0.14602509517412 | erot = 0.147146040889398 | epot = -14.9356043814356 | etot = -14.642433245372 -611000 ekin = 0.148599079333681 | erot = 0.142341118194548 | epot = -14.9333734429023 | etot = -14.6424332453741 -612000 ekin = 0.148639027540064 | erot = 0.140571068728133 | epot = -14.9316433416223 | etot = -14.6424332453541 -613000 ekin = 0.146195193891214 | erot = 0.142121441396099 | epot = -14.9307498806002 | etot = -14.6424332453129 -614000 ekin = 0.141503544703139 | erot = 0.14742429365942 | epot = -14.9313610836163 | etot = -14.6424332452537 -615000 ekin = 0.134972482668015 | erot = 0.157020849768272 | epot = -14.934426577618 | etot = -14.6424332451817 -616000 ekin = 0.127153892886365 | erot = 0.171505679771465 | epot = -14.941092817762 | etot = -14.6424332451042 -617000 ekin = 0.118700960496657 | erot = 0.191457667913342 | epot = -14.9525918734391 | etot = -14.6424332450291 -618000 ekin = 0.110316794781996 | erot = 0.217364584488773 | epot = -14.9701146242354 | etot = -14.6424332449646 -619000 ekin = 0.102698942666763 | erot = 0.249548776229937 | epot = -14.9946809638152 | etot = -14.6424332449185 -620000 ekin = 0.0964852203328184 | erot = 0.288101317488974 | epot = -15.0270197827188 | etot = -14.642433244897 -621000 ekin = 0.0922059091543981 | erot = 0.332831044361854 | epot = -15.0674701984207 | etot = -14.6424332449044 -622000 ekin = 0.0902463647122994 | erot = 0.383233451857257 | epot = -15.1159130615124 | etot = -14.6424332449428 -623000 ekin = 0.0908226920728218 | erot = 0.438482716260173 | epot = -15.1717386533448 | etot = -14.6424332450118 -624000 ekin = 0.0939716062548917 | erot = 0.497448307332085 | epot = -15.2338531586955 | etot = -14.6424332451085 -625000 ekin = 0.099554161125272 | erot = 0.558735886776433 | epot = -15.3007232931297 | etot = -14.642433245228 -626000 ekin = 0.107271859328493 | erot = 0.620750477448093 | epot = -15.37045558214 | etot = -14.6424332453634 -627000 ekin = 0.116692826740208 | erot = 0.681778220892823 | epot = -15.4409042931397 | etot = -14.6424332455067 -628000 ekin = 0.127285245275883 | erot = 0.740081431761517 | epot = -15.5097999226863 | etot = -14.6424332456489 -629000 ekin = 0.138455039155814 | erot = 0.794000196763232 | epot = -15.5748884817003 | etot = -14.6424332457813 -630000 ekin = 0.14958484293868 | erot = 0.84205264023402 | epot = -15.6340707290682 | etot = -14.6424332458955 -631000 ekin = 0.160071499854196 | erot = 0.883025442873215 | epot = -15.6855301887124 | etot = -14.642433245985 -632000 ekin = 0.169359720293525 | erot = 0.916046503423099 | epot = -15.7278394697615 | etot = -14.6424332460449 -633000 ekin = 0.176970053692886 | erot = 0.940632922938969 | epot = -15.7600362227044 | etot = -14.6424332460726 -634000 ekin = 0.182519961289899 | erot = 0.956709735133559 | epot = -15.7816629424915 | etot = -14.642433246068 -635000 ekin = 0.185737466035222 | erot = 0.96459776020741 | epot = -15.7927684722762 | etot = -14.6424332460336 -636000 ekin = 0.186467519302543 | erot = 0.964972204258758 | epot = -15.7938729695347 | etot = -14.6424332459734 -637000 ekin = 0.184671774603421 | erot = 0.95879666038002 | epot = -15.7859016808768 | etot = -14.6424332458934 -638000 ekin = 0.180422825776731 | erot = 0.947239527077254 | epot = -15.770095598654 | etot = -14.6424332458 -639000 ekin = 0.173894119063323 | erot = 0.931581224200984 | epot = -15.7479085889646 | etot = -14.6424332457002 -640000 ekin = 0.165346701826108 | erot = 0.913120838758361 | epot = -15.720900786185 | etot = -14.6424332456005 -641000 ekin = 0.155113786101913 | erot = 0.893090060094541 | epot = -15.6906370917029 | etot = -14.6424332455064 -642000 ekin = 0.14358386924239 | erot = 0.872580710310639 | epot = -15.6585978249755 | etot = -14.6424332454225 -643000 ekin = 0.131182953687752 | erot = 0.852490168058137 | epot = -15.6261063670979 | etot = -14.642433245352 -644000 ekin = 0.118356305759434 | erot = 0.833486853993186 | epot = -15.5942764050496 | etot = -14.642433245297 -645000 ekin = 0.105550209083476 | erot = 0.815995971214683 | epot = -15.5639794255563 | etot = -14.6424332452581 -646000 ekin = 0.0931942744180483 | erot = 0.800204061932059 | epot = -15.5358315815852 | etot = -14.6424332452351 -647000 ekin = 0.0816850001789074 | erot = 0.786079744440671 | epot = -15.5101979898462 | etot = -14.6424332452266 -648000 ekin = 0.0713713598429194 | erot = 0.773407243191889 | epot = -15.4872118482656 | etot = -14.6424332452308 -649000 ekin = 0.0625431628711588 | erot = 0.761828976528596 | epot = -15.4668053846449 | etot = -14.6424332452451 -650000 ekin = 0.0554227735501149 | erot = 0.750893453411355 | epot = -15.4487494722281 | etot = -14.6424332452667 -651000 ekin = 0.0501605027659971 | erot = 0.740104978445364 | epot = -15.4326987265038 | etot = -14.6424332452925 -652000 ekin = 0.0468336713668983 | erot = 0.728972100417351 | epot = -15.418239017104 | etot = -14.6424332453198 -653000 ekin = 0.0454490492583018 | erot = 0.717052285941663 | epot = -15.4049345805457 | etot = -14.6424332453457 -654000 ekin = 0.0459481524955995 | erot = 0.703990869780714 | epot = -15.3923722676442 | etot = -14.6424332453679 -655000 ekin = 0.0482147495301528 | erot = 0.68955283510374 | epot = -15.3802008300183 | etot = -14.6424332453844 -656000 ekin = 0.0520838761279946 | erot = 0.67364633274675 | epot = -15.3681634542684 | etot = -14.6424332453937 -657000 ekin = 0.0573516620867051 | erot = 0.656337023113083 | epot = -15.3561219305946 | etot = -14.6424332453948 -658000 ekin = 0.0637853134946618 | erot = 0.63785234821795 | epot = -15.3440709071001 | etot = -14.6424332453875 -659000 ekin = 0.0711326702887102 | erot = 0.618574815847016 | epot = -15.332140731508 | etot = -14.6424332453723 -660000 ekin = 0.0791308828116018 | erot = 0.599023454708778 | epot = -15.3205875828711 | etot = -14.6424332453507 -661000 ekin = 0.0875139366244703 | erot = 0.579822939748203 | epot = -15.3097701216976 | etot = -14.6424332453249 -662000 ekin = 0.096019000420537 | erot = 0.561660610348982 | epot = -15.3001128560675 | etot = -14.642433245298 -663000 ekin = 0.104391848885278 | erot = 0.545232746056464 | epot = -15.2920578402152 | etot = -14.6424332452734 -664000 ekin = 0.112391863389549 | erot = 0.531182949320099 | epot = -15.2860080579647 | etot = -14.6424332452551 -665000 ekin = 0.119797262719822 | erot = 0.520037124798772 | epot = -15.2822676327651 | etot = -14.6424332452465 -666000 ekin = 0.12641119006126 | erot = 0.512141060962442 | epot = -15.2809854962746 | etot = -14.6424332452509 -667000 ekin = 0.132069035722124 | erot = 0.507607681730339 | epot = -15.2821099627223 | etot = -14.6424332452698 -668000 ekin = 0.136646914538571 | erot = 0.506281315754969 | epot = -15.2853614755973 | etot = -14.6424332453038 -669000 ekin = 0.140070616008918 | erot = 0.507725566171611 | epot = -15.2902294275316 | etot = -14.6424332453511 -670000 ekin = 0.142323740902303 | erot = 0.511239425097838 | epot = -15.2959964114084 | etot = -14.6424332454083 -671000 ekin = 0.143453306298645 | erot = 0.515903234043348 | epot = -15.3017897858128 | etot = -14.6424332454708 -672000 ekin = 0.143571012728205 | erot = 0.520652256715801 | epot = -15.3066565149767 | etot = -14.6424332455327 -673000 ekin = 0.142848733833195 | erot = 0.524371563354086 | epot = -15.309653542775 | etot = -14.6424332455877 -674000 ekin = 0.141507613274639 | erot = 0.52600236292734 | epot = -15.3099432218318 | etot = -14.6424332456299 -675000 ekin = 0.139801302823377 | erot = 0.524647629020981 | epot = -15.306882177499 | etot = -14.6424332456547 -676000 ekin = 0.137995095209425 | erot = 0.519664439037895 | epot = -15.3000927799066 | etot = -14.6424332456593 -677000 ekin = 0.136343677285032 | erot = 0.510732098514586 | epot = -15.2895090214423 | etot = -14.6424332456427 -678000 ekin = 0.135070664123505 | erot = 0.497888575253489 | epot = -15.2753924849828 | etot = -14.6424332456058 -679000 ekin = 0.134352810446744 | erot = 0.481532294130089 | epot = -15.2583183501281 | etot = -14.6424332455513 -680000 ekin = 0.134310862658471 | erot = 0.462390968603499 | epot = -15.2391350767451 | etot = -14.6424332454831 -681000 ekin = 0.135007638926492 | erot = 0.441462941783694 | epot = -15.2189038261163 | etot = -14.6424332454061 -682000 ekin = 0.136452461528385 | erot = 0.419938865037324 | epot = -15.198824571891 | etot = -14.6424332453253 -683000 ekin = 0.138609887401928 | erot = 0.399112293315509 | epot = -15.1801554259633 | etot = -14.6424332452459 -684000 ekin = 0.141410065652186 | erot = 0.380287181762815 | epot = -15.1641304925878 | etot = -14.6424332451728 -685000 ekin = 0.144758102725877 | erot = 0.364688846300047 | epot = -15.1518801941366 | etot = -14.6424332451107 -686000 ekin = 0.148540467122571 | erot = 0.353383275615104 | epot = -15.1443569878014 | etot = -14.6424332450637 -687000 ekin = 0.152627512101204 | erot = 0.347208212231211 | epot = -15.1422689693677 | etot = -14.6424332450353 -688000 ekin = 0.156872371009938 | erot = 0.346718408271002 | epot = -15.1460240243092 | etot = -14.6424332450283 -689000 ekin = 0.161107527975608 | erot = 0.352146941114583 | epot = -15.1556877141345 | etot = -14.6424332450443 -690000 ekin = 0.165141087380569 | erot = 0.363384304940391 | epot = -15.1709586374048 | etot = -14.6424332450838 -691000 ekin = 0.168755042648096 | erot = 0.379976931153895 | epot = -15.1911652189474 | etot = -14.6424332451454 -692000 ekin = 0.171707649701853 | erot = 0.401146558394068 | epot = -15.2152874533221 | etot = -14.6424332452262 -693000 ekin = 0.173741393440484 | erot = 0.425831232783826 | epot = -15.2420058715458 | etot = -14.6424332453215 -694000 ekin = 0.174597110621515 | erot = 0.452747528134271 | epot = -15.2697778841807 | etot = -14.642433245425 -695000 ekin = 0.174033757468476 | erot = 0.480471830915694 | epot = -15.2969388339131 | etot = -14.6424332455289 -696000 ekin = 0.171852263360651 | erot = 0.50753639815094 | epot = -15.3218219071367 | etot = -14.6424332456251 -697000 ekin = 0.167921065286663 | erot = 0.532533688685253 | epot = -15.3428879996771 | etot = -14.6424332457052 -698000 ekin = 0.162200409472774 | erot = 0.554220619917019 | epot = -15.3588542751517 | etot = -14.6424332457619 -699000 ekin = 0.154762415711575 | erot = 0.571613361019907 | epot = -15.368809022521 | etot = -14.6424332457895 -700000 ekin = 0.145804230005083 | erot = 0.584063387080077 | epot = -15.3723008628696 | etot = -14.6424332457845 -701000 ekin = 0.135652269555388 | erot = 0.591306922713827 | epot = -15.3693924380153 | etot = -14.6424332457461 -702000 ekin = 0.124756460204868 | erot = 0.593482464342007 | epot = -15.3606721702233 | etot = -14.6424332456764 -703000 ekin = 0.113674325949345 | erot = 0.591114401850601 | epot = -15.3472219733802 | etot = -14.6424332455803 -704000 ekin = 0.103045675944418 | erot = 0.585064323190893 | epot = -15.3305432445999 | etot = -14.6424332454646 -705000 ekin = 0.0935593581959002 | erot = 0.576454826529687 | epot = -15.3124474300636 | etot = -14.6424332453381 -706000 ekin = 0.0859140824288037 | erot = 0.566573150252357 | epot = -15.2949204778913 | etot = -14.6424332452102 -707000 ekin = 0.0807756759567911 | erot = 0.55676342760568 | epot = -15.2799723486533 | etot = -14.6424332450908 -708000 ekin = 0.0787333622616226 | erot = 0.548316855287879 | epot = -15.2694834625385 | etot = -14.642433244989 -709000 ekin = 0.0802577669172481 | erot = 0.542368667950794 | epot = -15.2650596797808 | etot = -14.6424332449128 -710000 ekin = 0.0856633545554356 | erot = 0.539809747046207 | epot = -15.2679063464701 | etot = -14.6424332448684 -711000 ekin = 0.0950778519056364 | erot = 0.541219180888258 | epot = -15.2787302776538 | etot = -14.6424332448599 -712000 ekin = 0.108420876625278 | erot = 0.546822307908264 | epot = -15.2976764294222 | etot = -14.6424332448887 -713000 ekin = 0.125393451698083 | erot = 0.556476834654375 | epot = -15.3243035313063 | etot = -14.6424332449538 -714000 ekin = 0.145479367624718 | erot = 0.569687600115898 | epot = -15.3576002127924 | etot = -14.6424332450518 -715000 ekin = 0.167958541120058 | erot = 0.585648522299604 | epot = -15.3960403085967 | etot = -14.642433245177 -716000 ekin = 0.191931735854316 | erot = 0.603308292527971 | epot = -15.4376732737042 | etot = -14.642433245322 -717000 ekin = 0.216355400179798 | erot = 0.621454592033853 | epot = -15.4802432376916 | etot = -14.642433245478 -718000 ekin = 0.240085056513101 | erot = 0.638810139728773 | epot = -15.5213284418773 | etot = -14.6424332456354 -719000 ekin = 0.2619256985777 | erot = 0.654132895983971 | epot = -15.5584918403466 | etot = -14.6424332457849 -720000 ekin = 0.28068796931356 | erot = 0.666312379865739 | epot = -15.5894335950965 | etot = -14.6424332459173 -721000 ekin = 0.29524934559066 | erot = 0.67445438592732 | epot = -15.6121369775421 | etot = -14.6424332460241 -722000 ekin = 0.304619886334692 | erot = 0.677947410255783 | epot = -15.6250005426889 | etot = -14.6424332460984 -723000 ekin = 0.308011983728305 | erot = 0.676505724572205 | epot = -15.6269509544349 | etot = -14.6424332461343 -724000 ekin = 0.304912667283982 | erot = 0.670186105902464 | epot = -15.6175320193144 | etot = -14.6424332461279 -725000 ekin = 0.295155116710403 | erot = 0.659377522493332 | epot = -15.5969658852807 | etot = -14.642433246077 -726000 ekin = 0.278983134898141 | erot = 0.64476536316321 | epot = -15.566181744043 | etot = -14.6424332459817 -727000 ekin = 0.257098790791632 | erot = 0.627273860368463 | epot = -15.5268058970053 | etot = -14.6424332458452 -728000 ekin = 0.230680158271491 | erot = 0.607992016186509 | epot = -15.481105420132 | etot = -14.642433245674 -729000 ekin = 0.201354496272656 | erot = 0.588089464040682 | epot = -15.431877205792 | etot = -14.6424332454786 -730000 ekin = 0.171114103974891 | erot = 0.568729214721915 | epot = -15.3822765639702 | etot = -14.6424332452734 -731000 ekin = 0.142168923907701 | erot = 0.550984135076555 | epot = -15.3355863040604 | etot = -14.6424332450762 -732000 ekin = 0.116742007096137 | erot = 0.53576334904922 | epot = -15.2949386010513 | etot = -14.642433244906 -733000 ekin = 0.0968293027534553 | erot = 0.523753647326354 | epot = -15.263016194861 | etot = -14.6424332447811 -734000 ekin = 0.0839596135584523 | erot = 0.515379592342376 | epot = -15.2417724506166 | etot = -14.6424332447158 -735000 ekin = 0.0789983701763479 | erot = 0.510784464198715 | epot = -15.2322160790922 | etot = -14.6424332447172 -736000 ekin = 0.0820355551921709 | erot = 0.50983264226798 | epot = -15.2343014422443 | etot = -14.6424332447842 -737000 ekin = 0.0923827123855584 | erot = 0.512132550856096 | epot = -15.2469485081487 | etot = -14.6424332449071 -738000 ekin = 0.108680448513224 | erot = 0.517077971027258 | epot = -15.2681916646102 | etot = -14.6424332450697 -739000 ekin = 0.129093715682814 | erot = 0.523904364925766 | epot = -15.2954313258602 | etot = -14.6424332452517 -740000 ekin = 0.15155527779348 | erot = 0.531755895778197 | epot = -15.3257444190044 | etot = -14.6424332454328 -741000 ekin = 0.174012721806218 | erot = 0.539758083451595 | epot = -15.3562040508525 | etot = -14.6424332455947 -742000 ekin = 0.194640916831006 | erot = 0.547090549697286 | epot = -15.3841647122521 | etot = -14.6424332457238 -743000 ekin = 0.211995737398214 | erot = 0.553054125335325 | epot = -15.4074831085448 | etot = -14.6424332458113 -744000 ekin = 0.225100508722262 | erot = 0.557126762307569 | epot = -15.4246605168834 | etot = -14.6424332458535 -745000 ekin = 0.233469424486088 | erot = 0.559003260237168 | epot = -15.4349059305748 | etot = -14.6424332458516 -746000 ekin = 0.237079913464344 | erot = 0.558614810498451 | epot = -15.4381279697727 | etot = -14.6424332458099 -747000 ekin = 0.236308652984203 | erot = 0.556125790081759 | epot = -15.4348676888019 | etot = -14.6424332457359 -748000 ekin = 0.231845097887216 | erot = 0.551907079329399 | epot = -15.4261854228557 | etot = -14.6424332456391 -749000 ekin = 0.224593843483544 | erot = 0.546487360029099 | epot = -15.4135144490426 | etot = -14.64243324553 -750000 ekin = 0.215574369391573 | erot = 0.540486233484455 | epot = -15.3984938482957 | etot = -14.6424332454197 -751000 ekin = 0.205824583426189 | erot = 0.534535356763915 | epot = -15.382793185509 | etot = -14.6424332453189 -752000 ekin = 0.196313335741652 | erot = 0.529195815217452 | epot = -15.3679423961962 | etot = -14.6424332452371 -753000 ekin = 0.18786647578713 | erot = 0.524881252730246 | epot = -15.3551809736993 | etot = -14.6424332451819 -754000 ekin = 0.181110613625679 | erot = 0.521796491095261 | epot = -15.3453403498786 | etot = -14.6424332451577 -755000 ekin = 0.176438042203775 | erot = 0.519900210803555 | epot = -15.338771498173 | etot = -14.6424332451657 -756000 ekin = 0.173994962646467 | erot = 0.518897676280472 | epot = -15.3353258841305 | etot = -14.6424332452036 -757000 ekin = 0.17369319027005 | erot = 0.518265706176924 | epot = -15.3343921417126 | etot = -14.6424332452657 -758000 ekin = 0.175243155014308 | erot = 0.517307659815071 | epot = -15.3349840601729 | etot = -14.6424332453435 -759000 ekin = 0.178203703092603 | erot = 0.515231902157245 | epot = -15.3358688506773 | etot = -14.6424332454274 -760000 ekin = 0.182042463548514 | erot = 0.511243837941253 | epot = -15.3357195469971 | etot = -14.6424332455073 -761000 ekin = 0.186199747761112 | erot = 0.504639825539833 | epot = -15.3332728188749 | etot = -14.642433245574 -762000 ekin = 0.190149235945201 | erot = 0.494891409026379 | epot = -15.3274738905916 | etot = -14.64243324562 -763000 ekin = 0.19344992109476 | erot = 0.481710238280289 | epot = -15.3175934050153 | etot = -14.6424332456403 -764000 ekin = 0.195785552426666 | erot = 0.465087294345553 | epot = -15.3033060924049 | etot = -14.6424332456327 -765000 ekin = 0.196989678185073 | erot = 0.445303873487137 | epot = -15.2847267972699 | etot = -14.6424332455977 -766000 ekin = 0.197055919183212 | erot = 0.42291544028835 | epot = -15.2624046050097 | etot = -14.6424332455381 -767000 ekin = 0.196134076494303 | erot = 0.398712320920496 | epot = -15.2372796428733 | etot = -14.6424332454585 -768000 ekin = 0.194513096653068 | erot = 0.373662938956883 | epot = -15.2106092809751 | etot = -14.6424332453652 -769000 ekin = 0.192592017627892 | erot = 0.348845887484768 | epot = -15.1838711503777 | etot = -14.6424332452651 -770000 ekin = 0.190840163687176 | erot = 0.325376840212375 | epot = -15.1586502490656 | etot = -14.642433245166 -771000 ekin = 0.18974839722849 | erot = 0.304335529900748 | epot = -15.1365171722051 | etot = -14.6424332450758 -772000 ekin = 0.189774341851785 | erot = 0.286697153922276 | epot = -15.1189047407762 | etot = -14.6424332450021 -773000 ekin = 0.191286034501687 | erot = 0.273271857837846 | epot = -15.1069911372907 | etot = -14.6424332449512 -774000 ekin = 0.194510000609648 | erot = 0.264655458971537 | epot = -15.1015987045095 | etot = -14.6424332449283 -775000 ekin = 0.199490639679984 | erot = 0.26119419315712 | epot = -15.1031180777729 | etot = -14.6424332449358 -776000 ekin = 0.206067477066117 | erot = 0.262965803936521 | epot = -15.1114665259767 | etot = -14.642433244974 -777000 ekin = 0.213875019086253 | erot = 0.26977856841343 | epot = -15.1260868325399 | etot = -14.6424332450402 -778000 ekin = 0.222366868965248 | erot = 0.28118879067645 | epot = -15.1459889047707 | etot = -14.642433245129 -779000 ekin = 0.230862102269003 | erot = 0.296535944175655 | epot = -15.1698312916776 | etot = -14.642433245233 -780000 ekin = 0.238608567019459 | erot = 0.314993169090484 | epot = -15.1960349814533 | etot = -14.6424332453433 -781000 ekin = 0.244855557741724 | erot = 0.335629445234017 | epot = -15.2229182484265 | etot = -14.6424332454508 -782000 ekin = 0.248927612478539 | erot = 0.357478674283243 | epot = -15.2488395323083 | etot = -14.6424332455465 -783000 ekin = 0.250291897529527 | erot = 0.379610269023874 | epot = -15.2723354121762 | etot = -14.6424332456228 -784000 ekin = 0.248613283253061 | erot = 0.401195731117841 | epot = -15.2922422600443 | etot = -14.6424332456734 -785000 ekin = 0.243793133450601 | erot = 0.421566090461024 | epot = -15.307792469606 | etot = -14.6424332456943 -786000 ekin = 0.235989501852303 | erot = 0.440255905201143 | epot = -15.3186786527374 | etot = -14.6424332456839 -787000 ekin = 0.225617610784108 | erot = 0.457030673426751 | epot = -15.3250815298537 | etot = -14.6424332456428 -788000 ekin = 0.213330260901183 | erot = 0.471895861690619 | epot = -15.3276593681661 | etot = -14.6424332455743 -789000 ekin = 0.199978499676554 | erot = 0.485087183878154 | epot = -15.3274989290383 | etot = -14.6424332454836 -790000 ekin = 0.186553834702685 | erot = 0.49704314123859 | epot = -15.3260302213197 | etot = -14.6424332453784 -791000 ekin = 0.1741147667921 | erot = 0.50836204856622 | epot = -15.3249100606257 | etot = -14.6424332452674 -792000 ekin = 0.163702420431701 | erot = 0.51974673917794 | epot = -15.3258824047698 | etot = -14.6424332451602 -793000 ekin = 0.156252224966457 | erot = 0.531940822987137 | epot = -15.3306262930203 | etot = -14.6424332450667 -794000 ekin = 0.152510350035464 | erot = 0.545660777313288 | epot = -15.3406043723442 | etot = -14.6424332449954 -795000 ekin = 0.152964251159109 | erot = 0.561528326979684 | epot = -15.3569258230922 | etot = -14.6424332449534 -796000 ekin = 0.157795747358515 | erot = 0.580007578776928 | epot = -15.3802365710806 | etot = -14.6424332449452 -797000 ekin = 0.166862457859355 | erot = 0.601351255568643 | epot = -15.4106469584005 | etot = -14.6424332449725 -798000 ekin = 0.179709603433533 | erot = 0.625560121844511 | epot = -15.4477029703124 | etot = -14.6424332450343 -799000 ekin = 0.195609966062582 | erot = 0.652359247175382 | epot = -15.4904024583648 | etot = -14.6424332451268 -800000 ekin = 0.21362615879192 | erot = 0.681194021872161 | epot = -15.5372534259079 | etot = -14.6424332452438 -801000 ekin = 0.232687040194013 | erot = 0.711247726384676 | epot = -15.5863680119565 | etot = -14.6424332453778 -802000 ekin = 0.251669429106418 | erot = 0.741480919833798 | epot = -15.6355835944601 | etot = -14.6424332455199 -803000 ekin = 0.269477067858474 | erot = 0.770691008418421 | epot = -15.6826013219377 | etot = -14.6424332456608 -804000 ekin = 0.285110541457613 | erot = 0.797588259155307 | epot = -15.7251320464044 | etot = -14.6424332457915 -805000 ekin = 0.297723982505881 | erot = 0.820882528796191 | epot = -15.7610397572058 | etot = -14.6424332459037 -806000 ekin = 0.306666387686681 | erot = 0.839373432909927 | epot = -15.7884730665872 | etot = -14.6424332459906 -807000 ekin = 0.31150697555513 | erot = 0.852035914442321 | epot = -15.8059761360442 | etot = -14.6424332460468 -808000 ekin = 0.312045176252278 | erot = 0.858093398524838 | epot = -15.8125718208465 | etot = -14.6424332460693 -809000 ekin = 0.308306642386273 | erot = 0.857071970755581 | epot = -15.8078118591994 | etot = -14.6424332460575 -810000 ekin = 0.300527220558769 | erot = 0.848831113926185 | epot = -15.7917915804976 | etot = -14.6424332460127 -811000 ekin = 0.289127204418015 | erot = 0.833569138620148 | epot = -15.7651295889766 | etot = -14.6424332459384 -812000 ekin = 0.274678427598496 | erot = 0.811804116491607 | epot = -15.7289157899298 | etot = -14.6424332458397 -813000 ekin = 0.257866835579426 | erot = 0.784333459541846 | epot = -15.684633540844 | etot = -14.6424332457228 -814000 ekin = 0.23945308058931 | erot = 0.752176980196106 | epot = -15.63406330638 | etot = -14.6424332455946 -815000 ekin = 0.220233415146519 | erot = 0.716509170266752 | epot = -15.5791758308753 | etot = -14.642433245462 -816000 ekin = 0.201002751041399 | erot = 0.678586569748396 | epot = -15.5220225661216 | etot = -14.6424332453318 -817000 ekin = 0.18252126107505 | erot = 0.639675603865343 | epot = -15.4646301101503 | etot = -14.6424332452099 -818000 ekin = 0.165485401522846 | erot = 0.600985363831713 | epot = -15.4089040104561 | etot = -14.6424332451015 -819000 ekin = 0.150503789775747 | erot = 0.563608719249245 | epot = -15.3565457540357 | etot = -14.6424332450107 -820000 ekin = 0.138078032174272 | erot = 0.528474068971833 | epot = -15.3089853460868 | etot = -14.6424332449407 -821000 ekin = 0.128588386726511 | erot = 0.496309093116561 | epot = -15.2673307247364 | etot = -14.6424332448933 -822000 ekin = 0.122284066133867 | erot = 0.467617125513717 | epot = -15.2323344365172 | etot = -14.6424332448696 -823000 ekin = 0.119278020922156 | erot = 0.442666228475767 | epot = -15.2043774942676 | etot = -14.6424332448697 -824000 ekin = 0.11954615860232 | erot = 0.421490682734675 | epot = -15.1834700862293 | etot = -14.6424332448923 -825000 ekin = 0.122931110514063 | erot = 0.403904342218782 | epot = -15.1692686976681 | etot = -14.6424332449353 -826000 ekin = 0.129150803764736 | erot = 0.389525074994087 | epot = -15.1611091237546 | etot = -14.6424332449958 -827000 ekin = 0.13781217640048 | erot = 0.377809252263739 | epot = -15.1580546737341 | etot = -14.6424332450699 -828000 ekin = 0.148430331610552 | erot = 0.368094906955303 | epot = -15.1589584837189 | etot = -14.642433245153 -829000 ekin = 0.160453205764678 | erot = 0.359651737503965 | epot = -15.1625381885083 | etot = -14.6424332452397 -830000 ekin = 0.173291382900488 | erot = 0.351735589536941 | epot = -15.1674602177616 | etot = -14.6424332453242 -831000 ekin = 0.186352012967306 | erot = 0.343644456321439 | epot = -15.1724297146895 | etot = -14.6424332454008 -832000 ekin = 0.199074924610257 | erot = 0.334772487912775 | epot = -15.1762806579872 | etot = -14.6424332454642 -833000 ekin = 0.21096808488557 | erot = 0.324658115180945 | epot = -15.1780594455761 | etot = -14.6424332455096 -834000 ekin = 0.221638757262048 | erot = 0.313022323435154 | epot = -15.1770943262313 | etot = -14.6424332455341 -835000 ekin = 0.230816330006817 | erot = 0.299793483320239 | epot = -15.1730430588632 | etot = -14.6424332455362 -836000 ekin = 0.238363132178598 | erot = 0.285116039955304 | epot = -15.1659124176506 | etot = -14.6424332455167 -837000 ekin = 0.244270841534601 | erot = 0.269341751255032 | epot = -15.1560458382682 | etot = -14.6424332454786 -838000 ekin = 0.248642320238311 | erot = 0.253003904100191 | epot = -15.1440794697648 | etot = -14.6424332454263 -839000 ekin = 0.251661569329026 | erot = 0.236776758984402 | epot = -15.1308715736792 | etot = -14.6424332453657 -840000 ekin = 0.253557306828186 | erot = 0.221424057159563 | epot = -15.1174146092908 | etot = -14.6424332453031 -841000 ekin = 0.254567562695226 | erot = 0.207741475742368 | epot = -15.1047422836813 | etot = -14.6424332452437 -842000 ekin = 0.254912814680658 | erot = 0.196498262353642 | epot = -15.0938443222261 | etot = -14.6424332451918 -843000 ekin = 0.254783130761356 | erot = 0.188382921786835 | epot = -15.0855992976984 | etot = -14.6424332451502 -844000 ekin = 0.254340789692271 | erot = 0.183956927272144 | epot = -15.0807309620841 | etot = -14.6424332451197 -845000 ekin = 0.253734932885291 | erot = 0.183619247980767 | epot = -15.0797874259665 | etot = -14.6424332451004 -846000 ekin = 0.253120504189352 | erot = 0.187583282240028 | epot = -15.083137031521 | etot = -14.6424332450917 -847000 ekin = 0.252671650081555 | erot = 0.195866742639204 | epot = -15.0909716378138 | etot = -14.6424332450931 -848000 ekin = 0.252580915304149 | erot = 0.20829422246311 | epot = -15.1033083828722 | etot = -14.6424332451049 -849000 ekin = 0.253039966843155 | erot = 0.224511555531671 | epot = -15.1199847675026 | etot = -14.6424332451278 -850000 ekin = 0.254204001794827 | erot = 0.244010590097553 | epot = -15.1406478370548 | etot = -14.6424332451625 -851000 ekin = 0.256148339024765 | erot = 0.266162563602365 | epot = -15.1647441478362 | etot = -14.6424332452091 -852000 ekin = 0.258829686440353 | erot = 0.290257858698016 | epot = -15.1915207904047 | etot = -14.6424332452664 -853000 ekin = 0.262064657830116 | erot = 0.315549558167712 | epot = -15.2200474613291 | etot = -14.6424332453313 -854000 ekin = 0.265534116125784 | erot = 0.341297947736661 | epot = -15.2492653092617 | etot = -14.6424332453992 -855000 ekin = 0.268815174658043 | erot = 0.366813004431579 | epot = -15.2780614245539 | etot = -14.6424332454642 -856000 ekin = 0.271435486960036 | erot = 0.391492007902628 | epot = -15.3053607403828 | etot = -14.6424332455201 -857000 ekin = 0.272939108069001 | erot = 0.414849750475152 | epot = -15.3302221041057 | etot = -14.6424332455615 -858000 ekin = 0.272951155045922 | erot = 0.43653939069034 | epot = -15.3519237913207 | etot = -14.6424332455845 -859000 ekin = 0.271229880682349 | erot = 0.45636275006221 | epot = -15.3700258763315 | etot = -14.6424332455869 -860000 ekin = 0.267698633839169 | erot = 0.474269718464024 | epot = -15.3844015978727 | etot = -14.6424332455695 -861000 ekin = 0.262455001757241 | erot = 0.49034731601152 | epot = -15.3952355633029 | etot = -14.6424332455341 -862000 ekin = 0.25575879717988 | erot = 0.504799761302853 | epot = -15.4029918039674 | etot = -14.6424332454846 -863000 ekin = 0.248003564343274 | erot = 0.51792153281644 | epot = -15.4083583425854 | etot = -14.6424332454256 -864000 ekin = 0.239677655585274 | erot = 0.530065823507129 | epot = -15.4121767244547 | etot = -14.6424332453623 -865000 ekin = 0.231320889444316 | erot = 0.541610953537655 | epot = -15.4153650882814 | etot = -14.6424332452994 -866000 ekin = 0.223481813673762 | erot = 0.552927233334676 | epot = -15.4188422922498 | etot = -14.6424332452414 -867000 ekin = 0.216679174488042 | erot = 0.564346499434233 | epot = -15.4234589191143 | etot = -14.642433245192 -868000 ekin = 0.211369750013041 | erot = 0.576136138939756 | epot = -15.4299391341068 | etot = -14.642433245154 -869000 ekin = 0.207923502302012 | erot = 0.588478941151288 | epot = -15.4388356885826 | etot = -14.6424332451293 -870000 ekin = 0.206606152993218 | erot = 0.601459626889061 | epot = -15.4504990250012 | etot = -14.6424332451189 -871000 ekin = 0.207568796750693 | erot = 0.615058451103092 | epot = -15.4650604929769 | etot = -14.6424332451232 -872000 ekin = 0.210843969893697 | erot = 0.629151875755849 | epot = -15.4824290907908 | etot = -14.6424332451412 -873000 ekin = 0.216347593110921 | erot = 0.643519970828816 | epot = -15.5023008091116 | etot = -14.6424332451719 -874000 ekin = 0.223886305135079 | erot = 0.657859909724887 | epot = -15.5241794600731 | etot = -14.6424332452131 -875000 ekin = 0.233169807545165 | erot = 0.671804662204345 | epot = -15.5474077150121 | etot = -14.6424332452626 -876000 ekin = 0.243827877956283 | erot = 0.684945735792735 | epot = -15.5712068590662 | etot = -14.6424332453172 -877000 ekin = 0.255431632539533 | erot = 0.69685856734687 | epot = -15.59472344526 | etot = -14.6424332453736 -878000 ekin = 0.267518408507977 | erot = 0.707128927380794 | epot = -15.6170805813173 | etot = -14.6424332454285 -879000 ekin = 0.279619300255103 | erot = 0.715378495713086 | epot = -15.6374310414467 | etot = -14.6424332454785 -880000 ekin = 0.291287955018077 | erot = 0.721287639191124 | epot = -15.6550088397298 | etot = -14.6424332455206 -881000 ekin = 0.302128778463813 | erot = 0.724613422802814 | epot = -15.6691754468188 | etot = -14.6424332455522 -882000 ekin = 0.311822304069663 | erot = 0.725201068169202 | epot = -15.6794566178107 | etot = -14.6424332455718 -883000 ekin = 0.320145243790182 | erot = 0.722987481096826 | epot = -15.6855659704656 | etot = -14.6424332455786 -884000 ekin = 0.326982762202934 | erot = 0.717996120152177 | epot = -15.6874121279285 | etot = -14.6424332455734 -885000 ekin = 0.332330882217903 | erot = 0.710323349665429 | epot = -15.6850874774411 | etot = -14.6424332455577 -886000 ekin = 0.3362876733376 | erot = 0.700117442969925 | epot = -15.6788383618422 | etot = -14.6424332455347 -887000 ekin = 0.339032964159152 | erot = 0.687552454430956 | epot = -15.669018664098 | etot = -14.6424332455079 -888000 ekin = 0.340797654552513 | erot = 0.672800100939676 | epot = -15.6560310009738 | etot = -14.6424332454816 -889000 ekin = 0.34182510616745 | erot = 0.656003407096659 | epot = -15.6402617587242 | etot = -14.6424332454601 -890000 ekin = 0.342328347583626 | erot = 0.637256013160498 | epot = -15.6220176061908 | etot = -14.6424332454466 -891000 ekin = 0.342447730500156 | erot = 0.616590618565209 | epot = -15.6014715945095 | etot = -14.6424332454441 -892000 ekin = 0.342214057419173 | erot = 0.593979026501716 | epot = -15.5786263293744 | etot = -14.6424332454535 -893000 ekin = 0.341522004916655 | erot = 0.569344767729282 | epot = -15.5533000181202 | etot = -14.6424332454743 -894000 ekin = 0.340117934122973 | erot = 0.542587519912699 | epot = -15.5251386995399 | etot = -14.6424332455043 -895000 ekin = 0.337605044786591 | erot = 0.513616778977829 | epot = -15.4936550693041 | etot = -14.6424332455397 -896000 ekin = 0.333467462875004 | erot = 0.482390775172149 | epot = -15.4582914836226 | etot = -14.6424332455754 -897000 ekin = 0.327113397523287 | erot = 0.448955709001752 | epot = -15.4185023521305 | etot = -14.6424332456055 -898000 ekin = 0.317936017621248 | erot = 0.413480165458506 | epot = -15.3738494287033 | etot = -14.6424332456235 -899000 ekin = 0.305389123795995 | erot = 0.376280077469328 | epot = -15.3241024468887 | etot = -14.6424332456234 -900000 ekin = 0.289072881395205 | erot = 0.33783075231933 | epot = -15.2693368793137 | etot = -14.6424332455992 -901000 ekin = 0.268822686259722 | erot = 0.298764046957525 | epot = -15.210019978764 | etot = -14.6424332455467 -902000 ekin = 0.244791653969059 | erot = 0.259850521118117 | epot = -15.1470754205508 | etot = -14.6424332454636 -903000 ekin = 0.217514571462647 | erot = 0.221968047210559 | epot = -15.0819158640231 | etot = -14.6424332453499 -904000 ekin = 0.187939204411547 | erot = 0.186059692012671 | epot = -15.0164321416336 | etot = -14.6424332452094 -905000 ekin = 0.157410847731421 | erot = 0.153084564883885 | epot = -14.9529286576649 | etot = -14.6424332450496 -906000 ekin = 0.127599356271486 | erot = 0.123965703545322 | epot = -14.8939983046986 | etot = -14.6424332448818 -907000 ekin = 0.100365589130874 | erot = 0.0995389863896986 | epot = -14.8423378202417 | etot = -14.6424332447211 -908000 ekin = 0.0775759855947723 | erot = 0.0805066337401136 | epot = -14.8005158639184 | etot = -14.6424332445836 -909000 ekin = 0.0608876950035596 | erot = 0.0673982354566904 | epot = -14.7707191749448 | etot = -14.6424332444846 -910000 ekin = 0.0515382922990323 | erot = 0.0605415547705503 | epot = -14.754513091506 | etot = -14.6424332444364 -911000 ekin = 0.0501789452912214 | erot = 0.0600446989619074 | epot = -14.7526568886984 | etot = -14.6424332444452 -912000 ekin = 0.0567846925756438 | erot = 0.0657906450220636 | epot = -14.7650085821077 | etot = -14.64243324451 -913000 ekin = 0.0706603747975919 | erot = 0.0774445361854764 | epot = -14.7905381556062 | etot = -14.6424332446231 -914000 ekin = 0.0905398584143928 | erot = 0.09447356942817 | epot = -14.8274466726137 | etot = -14.6424332447712 -915000 ekin = 0.114756144633922 | erot = 0.116178630204486 | epot = -14.8733680197766 | etot = -14.6424332449382 -916000 ekin = 0.1414470434077 | erot = 0.141736093135148 | epot = -14.9256163816507 | etot = -14.6424332451079 -917000 ekin = 0.168758535424857 | erot = 0.170247440483861 | epot = -14.9814392211747 | etot = -14.642433245266 -918000 ekin = 0.195014913443985 | erot = 0.200793639362916 | epot = -15.0382417982087 | etot = -14.6424332454018 -919000 ekin = 0.218837422087163 | erot = 0.232490666329869 | epot = -15.0937613339254 | etot = -14.6424332455083 -920000 ekin = 0.239206641026251 | erot = 0.264542267085451 | epot = -15.1461821536942 | etot = -14.6424332455825 -921000 ekin = 0.255474577150147 | erot = 0.296286050795695 | epot = -15.1941938735699 | etot = -14.6424332456241 -922000 ekin = 0.267338631216215 | erot = 0.3272293631989 | epot = -15.2370012400505 | etot = -14.6424332456354 -923000 ekin = 0.274791412213643 | erot = 0.357072039931594 | epot = -15.2742966977653 | etot = -14.6424332456201 -924000 ekin = 0.278059017514867 | erot = 0.385714059427163 | epot = -15.3062063225251 | etot = -14.642433245583 -925000 ekin = 0.277537405166003 | erot = 0.413247220090432 | epot = -15.3332178707861 | etot = -14.6424332455297 -926000 ekin = 0.273733135235186 | erot = 0.439931173656859 | epot = -15.3560975543577 | etot = -14.6424332454656 -927000 ekin = 0.2672118596377 | erot = 0.466155363878069 | epot = -15.3758004689124 | etot = -14.6424332453966 -928000 ekin = 0.258555847531663 | erot = 0.492389553498773 | epot = -15.3933786463588 | etot = -14.6424332453284 -929000 ekin = 0.24833056788698 | erot = 0.519126582978183 | epot = -15.4098903961313 | etot = -14.6424332452661 -930000 ekin = 0.237059747160854 | erot = 0.546821711628368 | epot = -15.4263147040038 | etot = -14.6424332452146 -931000 ekin = 0.225208144800208 | erot = 0.575833282920124 | epot = -15.443474672898 | etot = -14.6424332451776 -932000 ekin = 0.213171319360021 | erot = 0.606369490848263 | epot = -15.4619740553664 | etot = -14.6424332451581 -933000 ekin = 0.201271722990002 | erot = 0.638445690375275 | epot = -15.4821506585228 | etot = -14.6424332451576 -934000 ekin = 0.1897604601043 | erot = 0.671856006695392 | epot = -15.5040497119758 | etot = -14.6424332451761 -935000 ekin = 0.178823941832683 | erot = 0.706161996583481 | epot = -15.5274191836287 | etot = -14.6424332452125 -936000 ekin = 0.168594479109542 | erot = 0.740699865833205 | epot = -15.5517275902069 | etot = -14.6424332452642 -937000 ekin = 0.159163635629853 | erot = 0.774606336201985 | epot = -15.5762032171592 | etot = -14.6424332453274 -938000 ekin = 0.150596971910365 | erot = 0.806861786792148 | epot = -15.5998920040998 | etot = -14.6424332453973 -939000 ekin = 0.142948711628503 | erot = 0.836347883522741 | epot = -15.6217298406201 | etot = -14.6424332454689 -940000 ekin = 0.136274889167954 | erot = 0.861915676025228 | epot = -15.6406238107298 | etot = -14.6424332455366 -941000 ekin = 0.130643703196503 | erot = 0.882459199117352 | epot = -15.6555361479093 | etot = -14.6424332455954 -942000 ekin = 0.126142088159133 | erot = 0.896989065169588 | epot = -15.6655643989696 | etot = -14.6424332456409 -943000 ekin = 0.122877886109422 | erot = 0.904700444356994 | epot = -15.6700115761358 | etot = -14.6424332456694 -944000 ekin = 0.120977407412092 | erot = 0.905030230235766 | epot = -15.6684408833268 | etot = -14.6424332456789 -945000 ekin = 0.120578563691415 | erot = 0.897699054745272 | epot = -15.6607108641053 | etot = -14.6424332456687 -946000 ekin = 0.121820103594848 | erot = 0.882735070928782 | epot = -15.6469884201628 | etot = -14.6424332456392 -947000 ekin = 0.12482776113095 | erot = 0.860477935597256 | epot = -15.6277389423208 | etot = -14.6424332455926 -948000 ekin = 0.129698334170892 | erot = 0.831563037039252 | epot = -15.6036946167425 | etot = -14.6424332455323 -949000 ekin = 0.136482857560577 | erot = 0.79688755472377 | epot = -15.575803657747 | etot = -14.6424332454626 -950000 ekin = 0.145170138933631 | erot = 0.757561255989922 | epot = -15.5451646403118 | etot = -14.6424332453883 -951000 ekin = 0.155672002997439 | erot = 0.714845916095212 | epot = -15.5129511644071 | etot = -14.6424332453145 -952000 ekin = 0.167811650838207 | erot = 0.670087833251298 | epot = -15.4803327293357 | etot = -14.6424332452462 -953000 ekin = 0.181316579472716 | erot = 0.624648095212403 | epot = -15.448397919873 | etot = -14.6424332451879 -954000 ekin = 0.195817500701975 | erot = 0.579835080695394 | epot = -15.4180858265403 | etot = -14.642433245143 -955000 ekin = 0.210854606876723 | erot = 0.536843219767467 | epot = -15.3901310717581 | etot = -14.6424332451139 -956000 ekin = 0.225892299836499 | erot = 0.496701376789209 | epot = -15.3650269217274 | etot = -14.6424332451017 -957000 ekin = 0.240343066496853 | erot = 0.460233438090621 | epot = -15.3430097496933 | etot = -14.6424332451058 -958000 ekin = 0.253600493836736 | erot = 0.42803284988996 | epot = -15.3240665888511 | etot = -14.6424332451244 -959000 ekin = 0.26508043374485 | erot = 0.400452005454048 | epot = -15.3079656843528 | etot = -14.6424332451539 -960000 ekin = 0.274268068126471 | erot = 0.377606549444118 | epot = -15.2943078627606 | etot = -14.6424332451901 -961000 ekin = 0.280767177999 | erot = 0.359393861243669 | epot = -15.2825942844703 | etot = -14.6424332452277 -962000 ekin = 0.284346484058602 | erot = 0.345524198810441 | epot = -15.2723039281306 | etot = -14.6424332452616 -963000 ekin = 0.284976816085034 | erot = 0.335562232323024 | epot = -15.2629722936952 | etot = -14.6424332452871 -964000 ekin = 0.282852494243522 | erot = 0.32897598649096 | epot = -15.2542617260352 | etot = -14.6424332453007 -965000 ekin = 0.278391086611738 | erot = 0.325189577593378 | epot = -15.2460139095058 | etot = -14.6424332453007 -966000 ekin = 0.272207924676691 | erot = 0.323635640146036 | epot = -15.2382768101097 | etot = -14.642433245287 -967000 ekin = 0.265065367869027 | erot = 0.323803079983457 | epot = -15.2313016931143 | etot = -14.6424332452618 -968000 ekin = 0.257801293713719 | erot = 0.325275872287662 | epot = -15.2255104112302 | etot = -14.6424332452289 -969000 ekin = 0.251245661475449 | erot = 0.327759142574007 | epot = -15.2214380492423 | etot = -14.6424332451928 -970000 ekin = 0.246137008995739 | erot = 0.331089781179757 | epot = -15.2196600353342 | etot = -14.6424332451587 -971000 ekin = 0.243051319619966 | erot = 0.33523032566459 | epot = -15.2207148904156 | etot = -14.642433245131 -972000 ekin = 0.242353409643608 | erot = 0.340246678804723 | epot = -15.2250333335617 | etot = -14.6424332451134 -973000 ekin = 0.244176338168007 | erot = 0.346272190711145 | epot = -15.2328817739873 | etot = -14.6424332451082 -974000 ekin = 0.248428661663755 | erot = 0.353462430362483 | epot = -15.2443243371428 | etot = -14.6424332451165 -975000 ekin = 0.254824314808551 | erot = 0.361946299431228 | epot = -15.2592038593783 | etot = -14.6424332451385 -976000 ekin = 0.262926848825407 | erot = 0.371779749930384 | epot = -15.2771398439293 | etot = -14.6424332451735 -977000 ekin = 0.272199235334814 | erot = 0.382908123264365 | epot = -15.297540603819 | etot = -14.6424332452198 -978000 ekin = 0.282052066854459 | erot = 0.395142048097357 | epot = -15.3196273602271 | etot = -14.6424332452753 -979000 ekin = 0.291885751915387 | erot = 0.408150081470895 | epot = -15.3424690787234 | etot = -14.6424332453371 -980000 ekin = 0.30112508378997 | erot = 0.421469125221684 | epot = -15.3650274544136 | etot = -14.642433245402 -981000 ekin = 0.309246535916074 | erot = 0.434531423654951 | epot = -15.3862112050371 | etot = -14.642433245466 -982000 ekin = 0.315799497488349 | erot = 0.44670496561477 | epot = -15.4049377086282 | etot = -14.6424332455251 -983000 ekin = 0.320422573217601 | erot = 0.457342632741541 | epot = -15.4201984515344 | etot = -14.6424332455753 -984000 ekin = 0.322855465254285 | erot = 0.465834622596771 | epot = -15.4311233334638 | etot = -14.6424332456128 -985000 ekin = 0.32294630247049 | erot = 0.471658590971291 | epot = -15.4370381390766 | etot = -14.6424332456348 -986000 ekin = 0.320653917800856 | erot = 0.474422556587777 | epot = -15.4375097200284 | etot = -14.6424332456398 -987000 ekin = 0.316044627357359 | erot = 0.47389675551299 | epot = -15.4323746284975 | etot = -14.6424332456271 -988000 ekin = 0.309283477264266 | erot = 0.470032116942702 | epot = -15.4217488398045 | etot = -14.6424332455975 -989000 ekin = 0.300620522165247 | erot = 0.462964620619614 | epot = -15.4060183883377 | etot = -14.6424332455528 -990000 ekin = 0.290373280687973 | erot = 0.453006262992725 | epot = -15.3858127891764 | etot = -14.6424332454957 -991000 ekin = 0.278906915703279 | erot = 0.440624526217148 | epot = -15.3619646873498 | etot = -14.6424332454294 -992000 ekin = 0.266613826413674 | erot = 0.42641300688918 | epot = -15.3354600786602 | etot = -14.6424332453573 -993000 ekin = 0.253894212446015 | erot = 0.411056197522459 | epot = -15.3073836552517 | etot = -14.6424332452832 -994000 ekin = 0.241138837000525 | erot = 0.395291372386185 | epot = -15.2788634545968 | etot = -14.6424332452101 -995000 ekin = 0.228714768908315 | erot = 0.37987020785268 | epot = -15.2510182219022 | etot = -14.6424332451412 -996000 ekin = 0.216954417472588 | erot = 0.365522282704471 | epot = -15.224909945256 | etot = -14.6424332450789 -997000 ekin = 0.206147766458975 | erot = 0.352922066135133 | epot = -15.2015030776194 | etot = -14.6424332450253 -998000 ekin = 0.196537413161466 | erot = 0.342660495987147 | epot = -15.1816311541304 | etot = -14.6424332449818 -999000 ekin = 0.188315843917223 | erot = 0.335221830000783 | epot = -15.1659709188674 | etot = -14.6424332449494 -1000000 ekin = 0.181624323072292 | erot = 0.330966139643599 | epot = -15.155023707645 | etot = -14.6424332449291 - 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -0.00017938261 -Loop time of 20.6222 on 1 procs for 1000000 steps with 10 atoms - -Performance: 41896.597 tau/day, 48491.432 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 16.511 | 16.511 | 16.511 | 0.0 | 80.07 -Bond | 0.67362 | 0.67362 | 0.67362 | 0.0 | 3.27 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.28264 | 0.28264 | 0.28264 | 0.0 | 1.37 -Output | 6.9141e-06 | 6.9141e-06 | 6.9141e-06 | 0.0 | 0.00 -Modify | 2.735 | 2.735 | 2.735 | 0.0 | 13.26 -Other | | 0.4197 | | | 2.04 - -Nlocal: 10 ave 10 max 10 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 43 ave 43 max 43 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 43 -Ave neighs/atom = 4.3 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:20 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4 deleted file mode 100644 index ba8d099913..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex1/log.24Mar17.duplex1.g++.4 +++ /dev/null @@ -1,1161 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05 -1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 -2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 -3000 ekin = 0.00997964450840756 | erot = 0.0366523356056466 | epot = -14.6890652250033 | etot = -14.6424332448892 -4000 ekin = 0.017388811129498 | erot = 0.0643039804300251 | epot = -14.7241260365031 | etot = -14.6424332449436 -5000 ekin = 0.0264744514136422 | erot = 0.0987844033142134 | epot = -14.7676920997383 | etot = -14.6424332450104 -6000 ekin = 0.0369277948555727 | erot = 0.13933657105258 | epot = -14.8186976109956 | etot = -14.6424332450875 -7000 ekin = 0.0483950557190949 | erot = 0.18508629569211 | epot = -14.8759145965832 | etot = -14.642433245172 -8000 ekin = 0.0604909336919856 | erot = 0.235071307523581 | epot = -14.9379954864767 | etot = -14.6424332452611 -9000 ekin = 0.0728137406439518 | erot = 0.288273694501614 | epot = -15.003520680497 | etot = -14.6424332453514 -10000 ekin = 0.0849615563084574 | erot = 0.343654369293588 | epot = -15.0710491710418 | etot = -14.6424332454398 -11000 ekin = 0.0965486715044103 | erot = 0.400187932108392 | epot = -15.1391698491357 | etot = -14.6424332455229 -12000 ekin = 0.107221466282716 | erot = 0.456896095459393 | epot = -15.2065508073401 | etot = -14.642433245598 -13000 ekin = 0.116672809719361 | erot = 0.512877765427946 | epot = -15.27198382081 | etot = -14.6424332456627 -14000 ekin = 0.124654073730849 | erot = 0.567333962045503 | epot = -15.3344212814915 | etot = -14.6424332457151 -15000 ekin = 0.130983939684084 | erot = 0.619586028257146 | epot = -15.3930032136957 | etot = -14.6424332457544 -16000 ekin = 0.135553354544703 | erot = 0.66908602849033 | epot = -15.4470726288154 | etot = -14.6424332457804 -17000 ekin = 0.138326263958104 | erot = 0.715418858086103 | epot = -15.4961783678378 | etot = -14.6424332457936 -18000 ekin = 0.139336096663942 | erot = 0.758296324628468 | epot = -15.5400656670878 | etot = -14.6424332457954 -19000 ekin = 0.138678360045107 | erot = 0.797544234276629 | epot = -15.5786558401095 | etot = -14.6424332457878 -20000 ekin = 0.136500074655344 | erot = 0.83308420441182 | epot = -15.6120175248401 | etot = -14.642433245773 -21000 ekin = 0.13298706528568 | erot = 0.864912408453368 | epot = -15.6403327194924 | etot = -14.6424332457533 -22000 ekin = 0.128350288213599 | erot = 0.893077649558725 | epot = -15.6638611835035 | etot = -14.6424332457311 -23000 ekin = 0.122812385135574 | erot = 0.917661024684598 | epot = -15.6829066555285 | etot = -14.6424332457083 -24000 ekin = 0.116595521408358 | erot = 0.938759014332585 | epot = -15.6977877814273 | etot = -14.6424332456863 -25000 ekin = 0.109911323474882 | erot = 0.95647120734756 | epot = -15.7088157764886 | etot = -14.6424332456662 -26000 ekin = 0.102953426207684 | erot = 0.970893163953299 | epot = -15.7162798358093 | etot = -14.6424332456483 -27000 ekin = 0.0958928250746602 | erot = 0.982114250193902 | epot = -15.7204403209011 | etot = -14.6424332456326 -28000 ekin = 0.08887594109497 | erot = 0.990219731539409 | epot = -15.721528918253 | etot = -14.6424332456186 -29000 ekin = 0.0820250748771992 | erot = 0.995296041202176 | epot = -15.7197543616852 | etot = -14.6424332456058 -30000 ekin = 0.0754407616837525 | erot = 0.997437949319921 | epot = -15.7153119565969 | etot = -14.6424332455933 -31000 ekin = 0.0692054432607511 | erot = 0.996756332760935 | epot = -15.708395021602 | etot = -14.6424332455803 -32000 ekin = 0.0633878377974532 | erot = 0.993385345347625 | epot = -15.6992064287111 | etot = -14.6424332455661 -33000 ekin = 0.0580474070866977 | erot = 0.987487973308193 | epot = -15.6879686259451 | etot = -14.6424332455502 -34000 ekin = 0.0532383791882916 | erot = 0.979259192919847 | epot = -15.6749308176403 | etot = -14.6424332455322 -35000 ekin = 0.0490128758302373 | erot = 0.96892619740531 | epot = -15.6603723187477 | etot = -14.6424332455122 -36000 ekin = 0.0454228081405034 | erot = 0.956745409624112 | epot = -15.6446014632554 | etot = -14.6424332454908 -37000 ekin = 0.0425203357170931 | erot = 0.942996237999014 | epot = -15.6279498191848 | etot = -14.6424332454687 -38000 ekin = 0.0403568280944582 | erot = 0.927971766615185 | epot = -15.6107618401563 | etot = -14.6424332454467 -39000 ekin = 0.0389804214208553 | erot = 0.911966804108842 | epot = -15.5933804709559 | etot = -14.6424332454262 -40000 ekin = 0.0384324238853386 | erot = 0.89526395956212 | epot = -15.5761296288558 | etot = -14.6424332454083 -41000 ekin = 0.0387429860406854 | erot = 0.878118672837898 | epot = -15.559294904273 | etot = -14.6424332453944 -42000 ekin = 0.0399266053637397 | erot = 0.860744395135588 | epot = -15.543104245885 | etot = -14.6424332453857 -43000 ekin = 0.041978156101278 | erot = 0.84329936535652 | epot = -15.5277107668409 | etot = -14.6424332453831 -44000 ekin = 0.044870189409001 | erot = 0.825876603313516 | epot = -15.5131800381094 | etot = -14.6424332453868 -45000 ekin = 0.0485521857416513 | erot = 0.808498758186241 | epot = -15.4994841893249 | etot = -14.642433245397 -46000 ekin = 0.0529522094038552 | erot = 0.791119212188506 | epot = -15.486504667005 | etot = -14.6424332454127 -47000 ekin = 0.0579809824244721 | erot = 0.773630265884098 | epot = -15.4740444937409 | etot = -14.6424332454323 -48000 ekin = 0.0635377846502182 | erot = 0.755878310838203 | epot = -15.4618493409424 | etot = -14.6424332454539 -49000 ekin = 0.0695169124467202 | erot = 0.737684732484798 | epot = -15.4496348904071 | etot = -14.6424332454756 -50000 ekin = 0.0758129058465097 | erot = 0.718870126220151 | epot = -15.437116277562 | etot = -14.6424332454953 -51000 ekin = 0.0823226638652294 | erot = 0.699278599520714 | epot = -15.424034508898 | etot = -14.642433245512 -52000 ekin = 0.0889431481344998 | erot = 0.67879880710002 | epot = -15.4101752007595 | etot = -14.642433245525 -53000 ekin = 0.0955646689265025 | erot = 0.657379086771117 | epot = -15.3953770012321 | etot = -14.6424332455345 -54000 ekin = 0.10206147751016 | erot = 0.635035489169276 | epot = -15.3795302122208 | etot = -14.6424332455414 -55000 ekin = 0.108282960174665 | erot = 0.611853171347244 | epot = -15.362569377068 | etot = -14.6424332455461 -56000 ekin = 0.114049426282277 | erot = 0.587982945924297 | epot = -15.3444656177552 | etot = -14.6424332455486 -57000 ekin = 0.119155806187163 | erot = 0.563635255922951 | epot = -15.3252243076589 | etot = -14.6424332455488 -58000 ekin = 0.123384552305545 | erot = 0.539073355222428 | epot = -15.3048911530734 | etot = -14.6424332455454 -59000 ekin = 0.126526300954853 | erot = 0.514606324858911 | epot = -15.2835658713509 | etot = -14.6424332455371 -60000 ekin = 0.128404399836229 | erot = 0.490581338840044 | epot = -15.261418984199 | etot = -14.6424332455227 -61000 ekin = 0.128898142361897 | erot = 0.467373892400972 | epot = -15.2387052802646 | etot = -14.6424332455018 -62000 ekin = 0.127959880289726 | erot = 0.445374820086222 | epot = -15.2157679458511 | etot = -14.6424332454752 -63000 ekin = 0.125622870624277 | erot = 0.424973765387148 | epot = -15.1930298814554 | etot = -14.642433245444 -64000 ekin = 0.121999044842466 | erot = 0.406539918572074 | epot = -15.1709722088251 | etot = -14.6424332454105 -65000 ekin = 0.117268056618551 | erot = 0.390401831020312 | epot = -15.1501031330161 | etot = -14.6424332453772 -66000 ekin = 0.11166038525652 | erot = 0.376828594078856 | epot = -15.1309222246818 | etot = -14.6424332453464 -67000 ekin = 0.105437746904482 | erot = 0.366014539811009 | epot = -15.1138855320359 | etot = -14.6424332453204 -68000 ekin = 0.0988737375602389 | erot = 0.358069014155077 | epot = -15.0993759970158 | etot = -14.6424332453005 -69000 ekin = 0.0922368286498126 | erot = 0.353011948771943 | epot = -15.0876820227093 | etot = -14.6424332452876 -70000 ekin = 0.0857769015271899 | erot = 0.350775174164931 | epot = -15.078985320974 | etot = -14.6424332452819 -71000 ekin = 0.0797156921641249 | erot = 0.351208844245481 | epot = -15.0733577816927 | etot = -14.6424332452831 -72000 ekin = 0.0742409440407228 | erot = 0.354092037747166 | epot = -15.0707662270784 | etot = -14.6424332452906 -73000 ekin = 0.069503749870388 | erot = 0.359146526961232 | epot = -15.0710835221349 | etot = -14.6424332453033 -74000 ekin = 0.065618449742691 | erot = 0.366052769878692 | epot = -15.0741044649412 | etot = -14.6424332453199 -75000 ekin = 0.0626644690394284 | erot = 0.374467290033975 | epot = -15.0795650044124 | etot = -14.642433245339 -76000 ekin = 0.0606895535091863 | erot = 0.384040683403432 | epot = -15.087163482272 | etot = -14.6424332453594 -77000 ekin = 0.0597139401241188 | erot = 0.394435495892894 | epot = -15.0965826813962 | etot = -14.6424332453792 -78000 ekin = 0.0597350629875199 | erot = 0.405343151481916 | epot = -15.107511459867 | etot = -14.6424332453975 -79000 ekin = 0.0607324264361021 | erot = 0.4164990176427 | epot = -15.1196646894919 | etot = -14.6424332454131 -80000 ekin = 0.0626722904954161 | erot = 0.427694630238743 | epot = -15.1328001661592 | etot = -14.6424332454251 -81000 ekin = 0.0655118235331528 | erot = 0.438786127849131 | epot = -15.1467311968152 | etot = -14.6424332454329 -82000 ekin = 0.0692024020836604 | erot = 0.449698113830624 | epot = -15.1613337613509 | etot = -14.6424332454366 -83000 ekin = 0.0736917936904884 | erot = 0.460422490740831 | epot = -15.1765475298676 | etot = -14.6424332454363 -84000 ekin = 0.0789250526542207 | erot = 0.471012272295187 | epot = -15.1923705703823 | etot = -14.6424332454329 -85000 ekin = 0.0848440878742484 | erot = 0.481570908650517 | epot = -15.2088482419521 | etot = -14.6424332454273 -86000 ekin = 0.0913860133243867 | erot = 0.492238169206351 | epot = -15.2260574279515 | etot = -14.6424332454207 -87000 ekin = 0.0984805441186007 | erot = 0.503174014617495 | epot = -15.2440878041506 | etot = -14.6424332454146 -88000 ekin = 0.106046830302566 | erot = 0.514542076496893 | epot = -15.2630221522094 | etot = -14.6424332454099 -89000 ekin = 0.113990204125935 | erot = 0.526494309539958 | epot = -15.2829177590739 | etot = -14.642433245408 -90000 ekin = 0.122199339149549 | erot = 0.539158097286396 | epot = -15.3037906818453 | etot = -14.6424332454094 -91000 ekin = 0.130544275968789 | erot = 0.552626637866402 | epot = -15.3256041592497 | etot = -14.6424332454146 -92000 ekin = 0.138875666145969 | erot = 0.566952900962838 | epot = -15.3482618125326 | etot = -14.6424332454238 -93000 ekin = 0.14702544061161 | erot = 0.582146933738122 | epot = -15.3716056197866 | etot = -14.6424332454369 -94000 ekin = 0.154808946844654 | erot = 0.598175891801918 | epot = -15.3954180841001 | etot = -14.6424332454535 -95000 ekin = 0.162028449598908 | erot = 0.614965942454569 | epot = -15.4194276375267 | etot = -14.6424332454732 -96000 ekin = 0.168477779664562 | erot = 0.632405154082769 | epot = -15.4433161792427 | etot = -14.6424332454953 -97000 ekin = 0.173947863023519 | erot = 0.650346631629065 | epot = -15.466727740172 | etot = -14.6424332455194 -98000 ekin = 0.178232875001165 | erot = 0.668611435746703 | epot = -15.4892775562927 | etot = -14.6424332455449 -99000 ekin = 0.181136831923469 | erot = 0.686991165056991 | epot = -15.5105612425515 | etot = -14.6424332455711 -100000 ekin = 0.182480533640974 | erot = 0.705250413408614 | epot = -15.530164192647 | etot = -14.6424332455974 -101000 ekin = 0.182108871449632 | erot = 0.723129571004103 | epot = -15.5476716880769 | etot = -14.6424332456232 -102000 ekin = 0.179898581168339 | erot = 0.740348571091352 | epot = -15.5626803979071 | etot = -14.6424332456474 -103000 ekin = 0.17576651760657 | erot = 0.756612167827034 | epot = -15.5748119311029 | etot = -14.6424332456693 -104000 ekin = 0.169678431534372 | erot = 0.771617166852996 | epot = -15.5837288440748 | etot = -14.6424332456874 -105000 ekin = 0.161658036036246 | erot = 0.785061742963598 | epot = -15.5891530247003 | etot = -14.6424332457005 -106000 ekin = 0.151795867650305 | erot = 0.796656613426427 | epot = -15.5908857267839 | etot = -14.6424332457071 -107000 ekin = 0.140257112952978 | erot = 0.806137449199291 | epot = -15.5888278078584 | etot = -14.6424332457061 -108000 ekin = 0.127287240201874 | erot = 0.813277564483374 | epot = -15.5829980503819 | etot = -14.6424332456966 -109000 ekin = 0.113214025491877 | erot = 0.817899691736857 | epot = -15.5735469629067 | etot = -14.642433245678 -110000 ekin = 0.0984444823817425 | erot = 0.819885578056442 | epot = -15.5607633060887 | etot = -14.6424332456505 -111000 ekin = 0.0834553769378644 | erot = 0.819182262548316 | epot = -15.5450708851012 | etot = -14.6424332456151 -112000 ekin = 0.0687764915886182 | erot = 0.815804215096852 | epot = -15.5270139522588 | etot = -14.6424332455734 -113000 ekin = 0.0549665904044371 | erot = 0.809830999846678 | epot = -15.507230835779 | etot = -14.6424332455279 -114000 ekin = 0.04258305831357 | erot = 0.801400700352889 | epot = -15.486417004148 | etot = -14.6424332454815 -115000 ekin = 0.0321472802146729 | erot = 0.790699910050576 | epot = -15.4652804357026 | etot = -14.6424332454374 -116000 ekin = 0.0241087780358441 | erot = 0.77795154667576 | epot = -15.4444935701102 | etot = -14.6424332453986 -117000 ekin = 0.0188117102739907 | erot = 0.763402004774545 | epot = -15.4246469604164 | etot = -14.6424332453678 -118000 ekin = 0.0164673894168237 | erot = 0.747309167856841 | epot = -15.4062098026205 | etot = -14.6424332453468 -119000 ekin = 0.0171359296540399 | erot = 0.72993256457469 | epot = -15.3895017395652 | etot = -14.6424332453364 -120000 ekin = 0.0207190822436548 | erot = 0.711526526248979 | epot = -15.3746788538292 | etot = -14.6424332453366 -121000 ekin = 0.0269649552324778 | erot = 0.692336677371657 | epot = -15.3617348779503 | etot = -14.6424332453462 -122000 ekin = 0.0354839220302051 | erot = 0.672599570211917 | epot = -15.3505167376055 | etot = -14.6424332453634 -123000 ekin = 0.0457738626455503 | erot = 0.652544850162978 | epot = -15.3407519581944 | etot = -14.6424332453859 -124000 ekin = 0.0572521324300892 | erot = 0.632399068063538 | epot = -15.3320844459047 | etot = -14.6424332454111 -125000 ekin = 0.0692913736007693 | erot = 0.612390156183436 | epot = -15.3241147752204 | etot = -14.6424332454362 -126000 ekin = 0.0812564128179015 | erot = 0.592751635107163 | epot = -15.3164412933838 | etot = -14.6424332454587 -127000 ekin = 0.0925398817831139 | erot = 0.573725774405781 | epot = -15.3086989016655 | etot = -14.6424332454766 -128000 ekin = 0.102594692019405 | erot = 0.555565138942023 | epot = -15.3005930764495 | etot = -14.6424332454881 -129000 ekin = 0.110961953874467 | erot = 0.538532171476875 | epot = -15.2919273708433 | etot = -14.6424332454919 -130000 ekin = 0.117293279473242 | erot = 0.52289666445288 | epot = -15.2826231894136 | etot = -14.6424332454874 -131000 ekin = 0.121366644775211 | erot = 0.508931150171171 | epot = -15.272731040421 | etot = -14.6424332454746 -132000 ekin = 0.123095155540088 | erot = 0.496904390905875 | epot = -15.2624327918998 | etot = -14.6424332454539 -133000 ekin = 0.122528239671731 | erot = 0.487073282997897 | epot = -15.2520347680959 | etot = -14.6424332454262 -134000 ekin = 0.119845042601891 | erot = 0.47967360117123 | epot = -15.2419518891664 | etot = -14.6424332453933 -135000 ekin = 0.115340171967418 | erot = 0.474910093717058 | epot = -15.2326835110415 | etot = -14.642433245357 -136000 ekin = 0.109402419285639 | erot = 0.472946484075354 | epot = -15.2247821486809 | etot = -14.6424332453199 -137000 ekin = 0.102487634022662 | erot = 0.473895929920083 | epot = -15.218816809227 | etot = -14.6424332452843 -138000 ekin = 0.0950874634054098 | erot = 0.477812435585943 | epot = -15.2153331442442 | etot = -14.6424332452528 -139000 ekin = 0.0876961121518108 | erot = 0.484683617751208 | epot = -15.2148129751311 | etot = -14.6424332452281 -140000 ekin = 0.0807775418435451 | erot = 0.494425108540545 | epot = -15.217635895596 | etot = -14.6424332452119 -141000 ekin = 0.0747355681580393 | erot = 0.506876770810791 | epot = -15.2240455841751 | etot = -14.6424332452063 -142000 ekin = 0.0698891098451726 | erot = 0.521800821241339 | epot = -15.2341231762987 | etot = -14.6424332452121 -143000 ekin = 0.0664544171867034 | erot = 0.538881922426252 | epot = -15.247769584843 | etot = -14.64243324523 -144000 ekin = 0.064535510469277 | erot = 0.557729316021967 | epot = -15.2646980717509 | etot = -14.6424332452596 -145000 ekin = 0.0641233595163659 | erot = 0.577881111413926 | epot = -15.2844377162305 | etot = -14.6424332453002 -146000 ekin = 0.065103607751629 | erot = 0.598810893852487 | epot = -15.3063477469542 | etot = -14.6424332453501 -147000 ekin = 0.0672719578975296 | erot = 0.619936843682188 | epot = -15.3296420469869 | etot = -14.6424332454072 -148000 ekin = 0.0703557492694474 | erot = 0.64063353819095 | epot = -15.3534225329292 | etot = -14.6424332454688 -149000 ekin = 0.0740398128645644 | erot = 0.660246523237392 | epot = -15.3767195816342 | etot = -14.6424332455323 -150000 ekin = 0.0779944201062649 | erot = 0.67810959037558 | epot = -15.3985372560763 | etot = -14.6424332455945 -151000 ekin = 0.0819030604176924 | erot = 0.693564488647308 | epot = -15.4179007947176 | etot = -14.6424332456526 -152000 ekin = 0.0854878938557652 | erot = 0.705982563002958 | epot = -15.4339037025624 | etot = -14.6424332457037 -153000 ekin = 0.0885310147333713 | erot = 0.714787575381071 | epot = -15.4457518358598 | etot = -14.6424332457454 -154000 ekin = 0.0908901012892559 | erot = 0.719478762726488 | epot = -15.4528021097913 | etot = -14.6424332457756 -155000 ekin = 0.0925075703719017 | erot = 0.719653046096719 | epot = -15.4545938622615 | etot = -14.6424332457929 -156000 ekin = 0.0934129479732407 | erot = 0.715025243753081 | epot = -15.4508714375228 | etot = -14.6424332457965 -157000 ekin = 0.0937187435781918 | erot = 0.70544516394557 | epot = -15.4415971533099 | etot = -14.6424332457861 -158000 ekin = 0.093610618539412 | erot = 0.690910554325135 | epot = -15.4269544186267 | etot = -14.6424332457622 -159000 ekin = 0.093333017400989 | erot = 0.671575051659432 | epot = -15.4073413147861 | etot = -14.6424332457257 -160000 ekin = 0.0931716565239226 | erot = 0.647750492120542 | epot = -15.3833553943224 | etot = -14.642433245678 -161000 ekin = 0.0934343296226242 | erot = 0.619903194016743 | epot = -15.3557707692603 | etot = -14.6424332456209 -162000 ekin = 0.0944314104796886 | erot = 0.588644098980031 | epot = -15.3255087550164 | etot = -14.6424332455567 -163000 ekin = 0.0964572425730171 | erot = 0.554712943454593 | epot = -15.2936034315153 | etot = -14.6424332454877 -164000 ekin = 0.0997733472794941 | erot = 0.518956918562839 | epot = -15.2611635112587 | etot = -14.6424332454164 -165000 ekin = 0.10459410201863 | erot = 0.482304549423526 | epot = -15.2293318967876 | etot = -14.6424332453454 -166000 ekin = 0.111075276514836 | erot = 0.445735768513645 | epot = -15.1992442903058 | etot = -14.6424332452774 -167000 ekin = 0.119305597512064 | erot = 0.410249354729672 | epot = -15.1719881974565 | etot = -14.6424332452148 -168000 ekin = 0.129301354723501 | erot = 0.376829046180125 | epot = -15.1485636460635 | etot = -14.6424332451599 -169000 ekin = 0.141003965788129 | erot = 0.346409702528434 | epot = -15.1298469134313 | etot = -14.6424332451147 -170000 ekin = 0.154280377438315 | erot = 0.319844892419163 | epot = -15.1165585149384 | etot = -14.642433245081 -171000 ekin = 0.168926178619937 | erot = 0.297877221607912 | epot = -15.1092366452878 | etot = -14.64243324506 -172000 ekin = 0.184671319362945 | erot = 0.281112611137957 | epot = -15.1082171755535 | etot = -14.6424332450526 -173000 ekin = 0.201188345435608 | erot = 0.269999595570643 | epot = -15.1136211860654 | etot = -14.6424332450591 -174000 ekin = 0.218103052205593 | erot = 0.264814547402958 | epot = -15.1253508446879 | etot = -14.6424332450793 -175000 ekin = 0.235007413034248 | erot = 0.26565354594967 | epot = -15.1430942040961 | etot = -14.6424332451122 -176000 ekin = 0.251474534266605 | erot = 0.272431389431399 | epot = -15.1663391688545 | etot = -14.6424332451565 -177000 ekin = 0.267075225142185 | erot = 0.284887984977542 | epot = -15.1943964553297 | etot = -14.64243324521 -178000 ekin = 0.281395553894086 | erot = 0.302602030913814 | epot = -15.2264308300784 | etot = -14.6424332452705 -179000 ekin = 0.294054514410706 | erot = 0.325011526056047 | epot = -15.2614992858018 | etot = -14.642433245335 -180000 ekin = 0.304720692895809 | erot = 0.351440214933843 | epot = -15.2985941532305 | etot = -14.6424332454008 -181000 ekin = 0.31312665891731 | erot = 0.381128639600658 | epot = -15.3366885439828 | etot = -14.6424332454648 -182000 ekin = 0.319079775822511 | erot = 0.413268071112237 | epot = -15.3747810924591 | etot = -14.6424332455244 -183000 ekin = 0.322468290004652 | erot = 0.447035301735071 | epot = -15.4119368373172 | etot = -14.6424332455774 -184000 ekin = 0.323261947553553 | erot = 0.481626155079182 | epot = -15.447321348255 | etot = -14.6424332456223 -185000 ekin = 0.321506983529694 | erot = 0.516285658867092 | epot = -15.4802258880547 | etot = -14.6424332456579 -186000 ekin = 0.317316057632528 | erot = 0.55033313262905 | epot = -15.5100824359457 | etot = -14.6424332456841 -187000 ekin = 0.310854440588901 | erot = 0.583180936762646 | epot = -15.5364686230527 | etot = -14.6424332457011 -188000 ekin = 0.302324329762727 | erot = 0.614346238386904 | epot = -15.5591038138593 | etot = -14.6424332457097 -189000 ekin = 0.291949445195851 | erot = 0.643455779015123 | epot = -15.5778384699218 | etot = -14.6424332457108 -190000 ekin = 0.279961942766932 | erot = 0.670244185707557 | epot = -15.5926393741802 | etot = -14.6424332457057 -191000 ekin = 0.266593185652274 | erot = 0.694546781237238 | epot = -15.6035732125847 | etot = -14.6424332456952 -192000 ekin = 0.252069141621898 | erot = 0.716288088791539 | epot = -15.6107904760939 | etot = -14.6424332456804 -193000 ekin = 0.236610293252604 | erot = 0.735467302247627 | epot = -15.6145108411624 | etot = -14.6424332456621 -194000 ekin = 0.220435149403497 | erot = 0.752141943032621 | epot = -15.615010338077 | etot = -14.6424332456409 -195000 ekin = 0.203765880091669 | erot = 0.766410799035668 | epot = -15.6126099247448 | etot = -14.6424332456175 -196000 ekin = 0.18683433903566 | erot = 0.778397083256566 | epot = -15.6076646678848 | etot = -14.6424332455926 -197000 ekin = 0.169886782292475 | erot = 0.788232586076231 | epot = -15.6005526139356 | etot = -14.6424332455669 -198000 ekin = 0.153185871076313 | erot = 0.796043434544288 | epot = -15.5916625511618 | etot = -14.6424332455412 -199000 ekin = 0.137008972985806 | erot = 0.801937915803797 | epot = -15.5813801343063 | etot = -14.6424332455167 -200000 ekin = 0.121642272363325 | erot = 0.805996673265862 | epot = -15.5700721911235 | etot = -14.6424332454943 -201000 ekin = 0.107370722655158 | erot = 0.80826545681021 | epot = -15.5580694249408 | etot = -14.6424332454755 -202000 ekin = 0.0944644042380686 | erot = 0.808750524312687 | epot = -15.5456481740119 | etot = -14.6424332454612 -203000 ekin = 0.0831623790884404 | erot = 0.807416772445398 | epot = -15.5330123969864 | etot = -14.6424332454526 -204000 ekin = 0.0736556272327849 | erot = 0.80418872542083 | epot = -15.5202775981042 | etot = -14.6424332454506 -205000 ekin = 0.066071040166992 | erot = 0.798954607356127 | epot = -15.5074588929787 | etot = -14.6424332454556 -206000 ekin = 0.0604586317676969 | erot = 0.791573809423779 | epot = -15.4944656866589 | etot = -14.6424332454674 -207000 ekin = 0.0567840026879154 | erot = 0.781888054797448 | epot = -15.4811053029705 | etot = -14.6424332454851 -208000 ekin = 0.0549275971597956 | erot = 0.769736381378278 | epot = -15.4670972240452 | etot = -14.6424332455071 -209000 ekin = 0.0546914447534107 | erot = 0.754973659532307 | epot = -15.4520983498168 | etot = -14.642433245531 -210000 ekin = 0.0558130126770382 | erot = 0.737491764373139 | epot = -15.4357380226042 | etot = -14.642433245554 -211000 ekin = 0.0579847210232175 | erot = 0.717241838878594 | epot = -15.4176598054751 | etot = -14.6424332455733 -212000 ekin = 0.0608768356197291 | erot = 0.694255492638144 | epot = -15.3975655738438 | etot = -14.642433245586 -213000 ekin = 0.0641610427072956 | erot = 0.668662476162839 | epot = -15.37525676446 | etot = -14.6424332455898 -214000 ekin = 0.06753210435751 | erot = 0.640702495518234 | epot = -15.3506678454592 | etot = -14.6424332455835 -215000 ekin = 0.0707255336353407 | erot = 0.610729417269012 | epot = -15.3238881964708 | etot = -14.6424332455665 -216000 ekin = 0.0735300437817614 | erot = 0.579207054839078 | epot = -15.2951703441601 | etot = -14.6424332455392 -217000 ekin = 0.0757943994877656 | erot = 0.546696813211925 | epot = -15.2649244582025 | etot = -14.6424332455028 -218000 ekin = 0.0774290394165114 | erot = 0.51383845121948 | epot = -15.2337007360952 | etot = -14.6424332454592 -219000 ekin = 0.0784033323141814 | erot = 0.481325894964792 | epot = -15.2021624726897 | etot = -14.6424332454107 -220000 ekin = 0.0787395495608023 | erot = 0.449880299622429 | epot = -15.1710530945426 | etot = -14.6424332453594 -221000 ekin = 0.0785046319672615 | erot = 0.420222425160601 | epot = -15.1411603024356 | etot = -14.6424332453078 -222000 ekin = 0.0778006814269721 | erot = 0.39304597217159 | epot = -15.1132798988567 | etot = -14.6424332452581 -223000 ekin = 0.0767549035385447 | erot = 0.368992968911897 | epot = -15.0881811176628 | etot = -14.6424332452123 -224000 ekin = 0.0755095293703893 | erot = 0.348631757033145 | epot = -15.0665745315757 | etot = -14.6424332451722 -225000 ekin = 0.0742120885667742 | erot = 0.332437700429458 | epot = -15.0490830341357 | etot = -14.6424332451395 -226000 ekin = 0.073006302869323 | erot = 0.320776497502283 | epot = -15.0362160454868 | etot = -14.6424332451152 -227000 ekin = 0.0720238140882433 | erot = 0.313889923629061 | epot = -15.0283469828184 | etot = -14.6424332451011 -228000 ekin = 0.0713769419939847 | erot = 0.311883945247506 | epot = -15.0256941323392 | etot = -14.6424332450977 -229000 ekin = 0.0711526728858743 | erot = 0.314719386439641 | epot = -15.0283053044313 | etot = -14.6424332451058 -230000 ekin = 0.0714080974066408 | erot = 0.322205638589943 | epot = -15.0360469811226 | etot = -14.642433245126 -231000 ekin = 0.0721675361190023 | erot = 0.333998222201819 | epot = -15.0485990034788 | etot = -14.642433245158 -232000 ekin = 0.0734216022905603 | erot = 0.349601270465958 | epot = -15.0654561179576 | etot = -14.6424332452011 -233000 ekin = 0.0751284397505271 | erot = 0.368376135875951 | epot = -15.085937820881 | etot = -14.6424332452545 -234000 ekin = 0.0772173235442621 | erot = 0.389557254433776 | epot = -15.1092078232944 | etot = -14.6424332453164 -235000 ekin = 0.0795947059802265 | erot = 0.412276079790441 | epot = -15.1343040311543 | etot = -14.6424332453836 -236000 ekin = 0.0821526186146775 | erot = 0.43559329564772 | epot = -15.160179159716 | etot = -14.6424332454536 -237000 ekin = 0.0847791014240061 | erot = 0.458538653864716 | epot = -15.1857510008108 | etot = -14.6424332455221 -238000 ekin = 0.0873700423858637 | erot = 0.480156759886701 | epot = -15.2099600478579 | etot = -14.6424332455853 -239000 ekin = 0.0898415153137649 | erot = 0.499556095552604 | epot = -15.2318308565057 | etot = -14.6424332456393 -240000 ekin = 0.0921414623535621 | erot = 0.515957735401017 | epot = -15.2505324434351 | etot = -14.6424332456806 -241000 ekin = 0.0942594490144011 | erot = 0.528739776886579 | epot = -15.2654324716071 | etot = -14.6424332457061 -242000 ekin = 0.0962332805881029 | erot = 0.537473606136305 | epot = -15.2761401324386 | etot = -14.6424332457142 -243000 ekin = 0.0981515319338902 | erot = 0.541948785980292 | epot = -15.2825335636184 | etot = -14.6424332457042 -244000 ekin = 0.100151482351193 | erot = 0.542184479374338 | epot = -15.2847692074024 | etot = -14.6424332456769 -245000 ekin = 0.102412491095761 | erot = 0.538426702317763 | epot = -15.2832724390477 | etot = -14.6424332456342 -246000 ekin = 0.105145395544795 | erot = 0.531132085866374 | epot = -15.2787107269897 | etot = -14.6424332455785 -247000 ekin = 0.108578961411983 | erot = 0.520939994206881 | epot = -15.2719522011324 | etot = -14.6424332455135 -248000 ekin = 0.112944688754523 | erot = 0.508635652295277 | epot = -15.2640135864926 | etot = -14.6424332454428 -249000 ekin = 0.11846134890514 | erot = 0.495107336753422 | epot = -15.2560019310289 | etot = -14.6424332453704 -250000 ekin = 0.125320510713214 | erot = 0.48130071319683 | epot = -15.2490544692099 | etot = -14.6424332452999 -251000 ekin = 0.133674056955099 | erot = 0.468173145423569 | epot = -15.2442804476134 | etot = -14.6424332452347 -252000 ekin = 0.143624355872782 | erot = 0.456650355973676 | epot = -15.2427079570244 | etot = -14.6424332451779 -253000 ekin = 0.155217400154351 | erot = 0.447587277165331 | epot = -15.2452379224514 | etot = -14.6424332451318 -254000 ekin = 0.168438906844348 | erot = 0.441734376017242 | epot = -15.2526065279594 | etot = -14.6424332450978 -255000 ekin = 0.183213121644194 | erot = 0.43971022735347 | epot = -15.2653565940749 | etot = -14.6424332450772 -256000 ekin = 0.199403908832166 | erot = 0.441980689733479 | epot = -15.2838178436365 | etot = -14.6424332450708 -257000 ekin = 0.216817638461889 | erot = 0.448844730305189 | epot = -15.3080956138459 | etot = -14.6424332450788 -258000 ekin = 0.235207399035754 | erot = 0.460426746275392 | epot = -15.338067390412 | etot = -14.6424332451008 -259000 ekin = 0.254278151366129 | erot = 0.476675120648644 | epot = -15.373386517151 | etot = -14.6424332451362 -260000 ekin = 0.273692576676924 | erot = 0.49736669170667 | epot = -15.4134925135676 | etot = -14.642433245184 -261000 ekin = 0.293077534073102 | erot = 0.522116767905281 | epot = -15.4576275472213 | etot = -14.6424332452429 -262000 ekin = 0.312031202020399 | erot = 0.550394247121215 | epot = -15.5048586944527 | etot = -14.642433245311 -263000 ekin = 0.330131107615849 | erot = 0.581541281999657 | epot = -15.554105635002 | etot = -14.6424332453865 -264000 ekin = 0.346943319969814 | erot = 0.614796773447099 | epot = -15.6041733388837 | etot = -14.6424332454667 -265000 ekin = 0.362033078254078 | erot = 0.64932279499714 | epot = -15.6537891188008 | etot = -14.6424332455496 -266000 ekin = 0.374977027495969 | erot = 0.684232889060528 | epot = -15.7016431621888 | etot = -14.6424332456323 -267000 ekin = 0.385377045180505 | erot = 0.718621072064159 | epot = -15.7464313629565 | etot = -14.6424332457118 -268000 ekin = 0.392875374675151 | erot = 0.75159036946739 | epot = -15.7868989899282 | etot = -14.6424332457857 -269000 ekin = 0.397170471133891 | erot = 0.782279784278107 | epot = -15.8218835012631 | etot = -14.6424332458511 -270000 ekin = 0.398032662022584 | erot = 0.809888771679725 | epot = -15.8503546796085 | etot = -14.6424332459062 -271000 ekin = 0.395318487593106 | erot = 0.833698516715849 | epot = -15.8714502502576 | etot = -14.6424332459487 -272000 ekin = 0.3889824743465 | erot = 0.853089551914417 | epot = -15.8845052722381 | etot = -14.6424332459772 -273000 ekin = 0.379085147925856 | erot = 0.867555470410714 | epot = -15.8890738643275 | etot = -14.6424332459909 -274000 ekin = 0.365796322187845 | erot = 0.876712662634537 | epot = -15.8849422308118 | etot = -14.6424332459894 -275000 ekin = 0.349393082916426 | erot = 0.880306121918472 | epot = -15.872132450808 | etot = -14.6424332459731 -276000 ekin = 0.330252358900968 | erot = 0.878211432153003 | epot = -15.8508970369967 | etot = -14.6424332459427 -277000 ekin = 0.308838461216024 | erot = 0.870433084880285 | epot = -15.821704791996 | etot = -14.6424332458996 -278000 ekin = 0.285686394600537 | erot = 0.857099294887754 | epot = -15.785218935334 | etot = -14.6424332458457 -279000 ekin = 0.261382042763559 | erot = 0.838453513182875 | epot = -15.7422688017293 | etot = -14.6424332457829 -280000 ekin = 0.236540473323853 | erot = 0.814842890589049 | epot = -15.6938166096265 | etot = -14.6424332457136 -281000 ekin = 0.211783602606715 | erot = 0.786704032858738 | epot = -15.6409208811057 | etot = -14.6424332456403 -282000 ekin = 0.187718337271409 | erot = 0.754546508157302 | epot = -15.5846980909941 | etot = -14.6424332455654 -283000 ekin = 0.16491611509112 | erot = 0.718934708844168 | epot = -15.5262840694266 | etot = -14.6424332454913 -284000 ekin = 0.143894549222822 | erot = 0.680468811937736 | epot = -15.466796606581 | etot = -14.6424332454204 -285000 ekin = 0.125101678374138 | erot = 0.639765701845489 | epot = -15.4073006255745 | etot = -14.6424332453549 -286000 ekin = 0.108903164109909 | erot = 0.597440790007828 | epot = -15.3487771994138 | etot = -14.6424332452961 -287000 ekin = 0.0955726645582895 | erot = 0.554091668601936 | epot = -15.2920975784057 | etot = -14.6424332452455 -288000 ekin = 0.0852855448043095 | erot = 0.510284456818714 | epot = -15.2380032468271 | etot = -14.6424332452041 -289000 ekin = 0.0781160413143099 | erot = 0.466543535619487 | epot = -15.187092822106 | etot = -14.6424332451722 -290000 ekin = 0.0740379578661698 | erot = 0.423345127585219 | epot = -15.1398163306013 | etot = -14.6424332451499 -291000 ekin = 0.0729289100679055 | erot = 0.38111487943343 | epot = -15.0964770346381 | etot = -14.6424332451368 -292000 ekin = 0.07457803579739 | erot = 0.340229271733799 | epot = -15.0572405526628 | etot = -14.6424332451316 -293000 ekin = 0.0786969407585632 | erot = 0.301020346544403 | epot = -15.0221505324361 | etot = -14.6424332451332 -294000 ekin = 0.0849334564747931 | erot = 0.263782947584683 | epot = -14.9911496491992 | etot = -14.6424332451397 -295000 ekin = 0.0928875723651433 | erot = 0.228783448803118 | epot = -14.964104266318 | etot = -14.6424332451498 -296000 ekin = 0.102128697511344 | erot = 0.196268840383812 | epot = -14.9408307830567 | etot = -14.6424332451616 -297000 ekin = 0.112213252500573 | erot = 0.166475068215632 | epot = -14.9211215658898 | etot = -14.6424332451736 -298000 ekin = 0.122701527070322 | erot = 0.139633685444096 | epot = -14.9047684576989 | etot = -14.6424332451845 -299000 ekin = 0.133172792913731 | erot = 0.115976150687847 | epot = -14.891582188795 | etot = -14.6424332451934 -300000 ekin = 0.143237839709879 | erot = 0.0957354521197614 | epot = -14.8814065370294 | etot = -14.6424332451998 -301000 ekin = 0.152548387990868 | erot = 0.079145090872109 | epot = -14.8741267240665 | etot = -14.6424332452036 -302000 ekin = 0.160803184301541 | erot = 0.0664357608556664 | epot = -14.869672190362 | etot = -14.6424332452048 -303000 ekin = 0.167750948488392 | erot = 0.0578302677258683 | epot = -14.8680144614181 | etot = -14.6424332452038 -304000 ekin = 0.173190665588574 | erot = 0.053537313638039 | epot = -14.869161224428 | etot = -14.6424332452014 -305000 ekin = 0.17696995295018 | erot = 0.0537447402922378 | epot = -14.8731479384404 | etot = -14.642433245198 -306000 ekin = 0.178982363291699 | erot = 0.0586126977894969 | epot = -14.8800283062755 | etot = -14.6424332451943 -307000 ekin = 0.179164502945091 | erot = 0.0682670321079287 | epot = -14.8898647802439 | etot = -14.6424332451908 -308000 ekin = 0.177493763289092 | erot = 0.0827930029211812 | epot = -14.9027200113984 | etot = -14.6424332451881 -309000 ekin = 0.173987301152073 | erot = 0.102229291873313 | epot = -14.9186498382119 | etot = -14.6424332451865 -310000 ekin = 0.168702678648375 | erot = 0.126562162218708 | epot = -14.9376980860533 | etot = -14.6424332451862 -311000 ekin = 0.161740297010248 | erot = 0.155719593409014 | epot = -14.9598931356065 | etot = -14.6424332451872 -312000 ekin = 0.153247440126422 | erot = 0.189565237979898 | epot = -14.985245923296 | etot = -14.6424332451897 -313000 ekin = 0.143423389998644 | erot = 0.227892126762103 | epot = -15.0137487619544 | etot = -14.6424332451937 -314000 ekin = 0.132524706020331 | erot = 0.270416174781572 | epot = -15.0453741260009 | etot = -14.642433245199 -315000 ekin = 0.120869409554577 | erot = 0.316769708289568 | epot = -15.0800723630506 | etot = -14.6424332452064 -316000 ekin = 0.1088385461069 | erot = 0.366495437994217 | epot = -15.1177672293174 | etot = -14.6424332452163 -317000 ekin = 0.0968734934299855 | erot = 0.419041536808397 | epot = -15.1583482754675 | etot = -14.6424332452291 -318000 ekin = 0.0854675378572644 | erot = 0.473758725762784 | epot = -15.2016595088659 | etot = -14.6424332452459 -319000 ekin = 0.075150727147421 | erot = 0.529900497446475 | epot = -15.2474844698617 | etot = -14.6424332452678 -320000 ekin = 0.0664678443385232 | erot = 0.586627760737823 | epot = -15.2955288503722 | etot = -14.6424332452959 -321000 ekin = 0.059950459058179 | erot = 0.643019202689393 | epot = -15.3454029070786 | etot = -14.6424332453311 -322000 ekin = 0.0560852142815268 | erot = 0.698088453264993 | epot = -15.3966069129204 | etot = -14.6424332453739 -323000 ekin = 0.0552815181260069 | erot = 0.750808639914419 | epot = -15.4485234034645 | etot = -14.6424332454241 -324000 ekin = 0.0578423255211866 | erot = 0.800144112656301 | epot = -15.5004196836582 | etot = -14.6424332454807 -325000 ekin = 0.0639414864635146 | erot = 0.845088070114596 | epot = -15.5514628021197 | etot = -14.6424332455416 -326000 ekin = 0.0736101694204752 | erot = 0.884703689967817 | epot = -15.6007471049927 | etot = -14.6424332456044 -327000 ekin = 0.0867333560885487 | erot = 0.918165419814667 | epot = -15.6473320215694 | etot = -14.6424332456662 -328000 ekin = 0.103055779602217 | erot = 0.944796600226744 | epot = -15.690285625553 | etot = -14.642433245724 -329000 ekin = 0.1221954461684 | erot = 0.96409978159851 | epot = -15.7287284735425 | etot = -14.6424332457755 -330000 ekin = 0.143662406707273 | erot = 0.975776996242528 | epot = -15.7618726487686 | etot = -14.6424332458188 -331000 ekin = 0.166880785130064 | erot = 0.979738667524189 | epot = -15.7890526985066 | etot = -14.6424332458523 -332000 ekin = 0.191212923965915 | erot = 0.976101405909937 | epot = -15.8097475757514 | etot = -14.6424332458755 -333000 ekin = 0.215985355315125 | erot = 0.965176233546748 | epot = -15.8235948347498 | etot = -14.6424332458879 -334000 ekin = 0.24051665682631 | erot = 0.947449485120597 | epot = -15.8303993878361 | etot = -14.6424332458892 -335000 ekin = 0.26414689608108 | erot = 0.923558676876283 | epot = -15.8301388188364 | etot = -14.6424332458791 -336000 ekin = 0.286267467748829 | erot = 0.894265184768752 | epot = -15.8229658983753 | etot = -14.6424332458577 -337000 ekin = 0.306349134744513 | erot = 0.860424939344407 | epot = -15.8092073199143 | etot = -14.6424332458254 -338000 ekin = 0.323965497669025 | erot = 0.822957838329877 | epot = -15.7893565817819 | etot = -14.642433245783 -339000 ekin = 0.338809250783304 | erot = 0.782816380156787 | epot = -15.7640588766722 | etot = -14.6424332457321 -340000 ekin = 0.350699444228141 | erot = 0.740954141308451 | epot = -15.7340868312115 | etot = -14.6424332456749 -341000 ekin = 0.359579293531071 | erot = 0.698295027836097 | epot = -15.700307566981 | etot = -14.6424332456138 -342000 ekin = 0.365505462149765 | erot = 0.655704542038121 | epot = -15.6636432497398 | etot = -14.6424332455519 -343000 ekin = 0.368630832656567 | erot = 0.613964463467572 | epot = -15.6250285416159 | etot = -14.6424332454918 -344000 ekin = 0.369183369584817 | erot = 0.573752273081738 | epot = -15.5853688881026 | etot = -14.642433245436 -345000 ekin = 0.367443732820373 | erot = 0.535626361233109 | epot = -15.54550333944 | etot = -14.6424332453865 -346000 ekin = 0.363723933128383 | erot = 0.500017626275288 | epot = -15.5061748047483 | etot = -14.6424332453446 -347000 ekin = 0.358348705274846 | erot = 0.467227585425628 | epot = -15.4680095360116 | etot = -14.6424332453111 -348000 ekin = 0.351640582952566 | erot = 0.4374326669059 | epot = -15.4315064951446 | etot = -14.6424332452861 -349000 ekin = 0.343909024693087 | erot = 0.410693986167346 | epot = -15.3970362561292 | etot = -14.6424332452687 -350000 ekin = 0.335443435967581 | erot = 0.386971649877954 | epot = -15.3648483311043 | etot = -14.6424332452588 -351000 ekin = 0.326509584093039 | erot = 0.366142474248718 | epot = -15.335085303596 | etot = -14.6424332452543 -352000 ekin = 0.317348699021883 | erot = 0.348019930398466 | epot = -15.3078018746745 | etot = -14.6424332452541 -353000 ekin = 0.308178466648788 | erot = 0.332375117499591 | epot = -15.2829868294052 | etot = -14.6424332452568 -354000 ekin = 0.299195119854707 | erot = 0.318957598137064 | epot = -15.2605859632527 | etot = -14.6424332452609 -355000 ekin = 0.290575888249379 | erot = 0.307515001368934 | epot = -15.2405241348835 | etot = -14.6424332452652 -356000 ekin = 0.282481160313156 | erot = 0.297810406216369 | epot = -15.222724811798 | etot = -14.6424332452685 -357000 ekin = 0.275055828994531 | erot = 0.289636664277624 | epot = -15.2071257385424 | etot = -14.6424332452703 -358000 ekin = 0.268429427255711 | erot = 0.282827006912599 | epot = -15.1936896794384 | etot = -14.6424332452701 -359000 ekin = 0.262714810202522 | erot = 0.27726150785896 | epot = -15.1824095633295 | etot = -14.642433245268 -360000 ekin = 0.258005302570153 | erot = 0.27286922775014 | epot = -15.1733077755847 | etot = -14.6424332452644 -361000 ekin = 0.254370400622442 | erot = 0.269626137803928 | epot = -15.1664297836866 | etot = -14.6424332452602 -362000 ekin = 0.251850290179253 | erot = 0.267549186090195 | epot = -15.1618327215257 | etot = -14.6424332452562 -363000 ekin = 0.250449609863304 | erot = 0.266687109599918 | epot = -15.159569964717 | etot = -14.6424332452538 -364000 ekin = 0.250131041863865 | erot = 0.267108788860229 | epot = -15.1596730759782 | etot = -14.6424332452541 -365000 ekin = 0.250809442162603 | erot = 0.268890073930453 | epot = -15.1621327613513 | etot = -14.6424332452583 -366000 ekin = 0.252347318763936 | erot = 0.272100073008305 | epot = -15.1668806370397 | etot = -14.6424332452674 -367000 ekin = 0.254552520179196 | erot = 0.276787886821285 | epot = -15.1737736522827 | etot = -14.6424332452822 -368000 ekin = 0.257178996154131 | erot = 0.282970699525181 | epot = -15.1825829409825 | etot = -14.6424332453031 -369000 ekin = 0.259931424909745 | erot = 0.290624011144299 | epot = -15.192988681384 | etot = -14.64243324533 -370000 ekin = 0.262474349327928 | erot = 0.299674631815222 | epot = -15.2045822265054 | etot = -14.6424332453623 -371000 ekin = 0.264446209429907 | erot = 0.309996869296871 | epot = -15.2168763241254 | etot = -14.6424332453986 -372000 ekin = 0.265478281863389 | erot = 0.321412142685457 | epot = -15.2293236699861 | etot = -14.6424332454373 -373000 ekin = 0.265218028292376 | erot = 0.333692059446785 | epot = -15.2413433332155 | etot = -14.6424332454763 -374000 ekin = 0.263355721250448 | erot = 0.346564809668627 | epot = -15.2523537764321 | etot = -14.642433245513 -375000 ekin = 0.259652497503897 | erot = 0.359724567994853 | epot = -15.2618103110439 | etot = -14.6424332455451 -376000 ekin = 0.253967268937808 | erot = 0.372843454380789 | epot = -15.2692439688887 | etot = -14.6424332455701 -377000 ekin = 0.246279333501477 | erot = 0.385585491294775 | epot = -15.274298070382 | etot = -14.6424332455858 -378000 ekin = 0.236703249878247 | erot = 0.397621906698149 | epot = -15.2767584021673 | etot = -14.6424332455909 -379000 ekin = 0.225492756944964 | erot = 0.408647066931745 | epot = -15.2765730694618 | etot = -14.6424332455851 -380000 ekin = 0.213031377539245 | erot = 0.418394278996723 | epot = -15.2738589021049 | etot = -14.642433245569 -381000 ekin = 0.199808877315916 | erot = 0.426650676211877 | epot = -15.2688927990715 | etot = -14.6424332455437 -382000 ekin = 0.186384809019047 | erot = 0.433270396055878 | epot = -15.2620884505868 | etot = -14.6424332455119 -383000 ekin = 0.17334261614412 | erot = 0.43818527905067 | epot = -15.253961140671 | etot = -14.6424332454763 -384000 ekin = 0.161239700831456 | erot = 0.441412371402826 | epot = -15.2450853176736 | etot = -14.6424332454393 -385000 ekin = 0.150559954647611 | erot = 0.44305761255287 | epot = -15.2360508126044 | etot = -14.6424332454039 -386000 ekin = 0.141675129699194 | erot = 0.443315241523142 | epot = -15.2274236165942 | etot = -14.6424332453719 -387000 ekin = 0.134820015697999 | erot = 0.442462667348848 | epot = -15.2197159283911 | etot = -14.6424332453443 -388000 ekin = 0.13008397641356 | erot = 0.440850813513913 | epot = -15.2133680352489 | etot = -14.6424332453214 -389000 ekin = 0.127418570237893 | erot = 0.438890246279018 | epot = -15.2087420618201 | etot = -14.6424332453031 -390000 ekin = 0.126658423093208 | erot = 0.43703370208609 | epot = -15.2061253704679 | etot = -14.6424332452886 -391000 ekin = 0.127550804261 | erot = 0.435755902066193 | epot = -15.2057399516044 | etot = -14.6424332452772 -392000 ekin = 0.129788752935804 | erot = 0.435531744058787 | epot = -15.2077537422628 | etot = -14.6424332452682 -393000 ekin = 0.13304305531626 | erot = 0.436814065078293 | epot = -15.2122903656558 | etot = -14.6424332452612 -394000 ekin = 0.136989561466103 | erot = 0.440012156511466 | epot = -15.2194349632339 | etot = -14.6424332452564 -395000 ekin = 0.14132983304257 | erot = 0.445472096886654 | epot = -15.2292351751829 | etot = -14.6424332452536 -396000 ekin = 0.145804542777681 | erot = 0.453459767650199 | epot = -15.2416975556816 | etot = -14.6424332452538 -397000 ekin = 0.150200153189366 | erot = 0.464147173463272 | epot = -15.25678057191 | etot = -14.6424332452573 -398000 ekin = 0.15435008976728 | erot = 0.477602441560255 | epot = -15.2743857765924 | etot = -14.6424332452649 -399000 ekin = 0.158131920623959 | erot = 0.493783661157207 | epot = -15.2943488270583 | etot = -14.6424332452771 -400000 ekin = 0.161462056175853 | erot = 0.512536568007593 | epot = -15.3164318694778 | etot = -14.6424332452943 -401000 ekin = 0.164289301183567 | erot = 0.533595989003385 | epot = -15.3403185355036 | etot = -14.6424332453166 -402000 ekin = 0.166588323053572 | erot = 0.55659092884037 | epot = -15.3656124972378 | etot = -14.6424332453439 -403000 ekin = 0.16835381038289 | erot = 0.58105318364463 | epot = -15.3918402394033 | etot = -14.6424332453758 -404000 ekin = 0.169595821304614 | erot = 0.606429376023061 | epot = -15.4184584427392 | etot = -14.6424332454115 -405000 ekin = 0.170336578565564 | erot = 0.632096292540154 | epot = -15.4448661165559 | etot = -14.6424332454501 -406000 ekin = 0.170608761982374 | erot = 0.657379344514133 | epot = -15.4704213519868 | etot = -14.6424332454903 -407000 ekin = 0.170455178570794 | erot = 0.681573854093717 | epot = -15.494462278195 | etot = -14.6424332455305 -408000 ekin = 0.169929554813016 | erot = 0.703968692150293 | epot = -15.5163314925322 | etot = -14.6424332455689 -409000 ekin = 0.169098093454333 | erot = 0.723871579520596 | epot = -15.5354029185788 | etot = -14.6424332456039 -410000 ekin = 0.168041369043282 | erot = 0.740635137247647 | epot = -15.5511097519246 | etot = -14.6424332456336 -411000 ekin = 0.166856102811057 | erot = 0.753682569970613 | epot = -15.5629719184382 | etot = -14.6424332456565 -412000 ekin = 0.165656359034687 | erot = 0.76253172509273 | epot = -15.5706213297985 | etot = -14.6424332456711 -413000 ekin = 0.164573741712574 | erot = 0.766816218739474 | epot = -15.5738232061285 | etot = -14.6424332456765 -414000 ekin = 0.163756240958045 | erot = 0.766302377571816 | epot = -15.5724918642017 | etot = -14.6424332456719 -415000 ekin = 0.163365479945339 | erot = 0.760900920225148 | epot = -15.5666996458277 | etot = -14.6424332456572 -416000 ekin = 0.163572240093402 | erot = 0.750672586700066 | epot = -15.5566780724265 | etot = -14.642433245633 -417000 ekin = 0.164550286198168 | erot = 0.735827297892153 | epot = -15.5428108296905 | etot = -14.6424332456002 -418000 ekin = 0.166468663391044 | erot = 0.716716857301884 | epot = -15.5256187662531 | etot = -14.6424332455602 -419000 ekin = 0.169482781124195 | erot = 0.693821649100888 | epot = -15.5057376757398 | etot = -14.6424332455147 -420000 ekin = 0.173724722664409 | erot = 0.667732191685395 | epot = -15.4838901598156 | etot = -14.6424332454658 -421000 ekin = 0.179293310757521 | erot = 0.6391267255838 | epot = -15.4608532817571 | etot = -14.6424332454157 -422000 ekin = 0.186244514517606 | erot = 0.608746211201722 | epot = -15.437423971086 | etot = -14.6424332453667 -423000 ekin = 0.19458279814308 | erot = 0.577368165579534 | epot = -15.4143842090434 | etot = -14.6424332453208 -424000 ekin = 0.204253993027993 | erot = 0.545780680988055 | epot = -15.3924679192961 | etot = -14.64243324528 -425000 ekin = 0.215140228915628 | erot = 0.514757766833693 | epot = -15.3723312409952 | etot = -14.6424332452459 -426000 ekin = 0.227057395196094 | erot = 0.485036881516685 | epot = -15.3545275219322 | etot = -14.6424332452194 -427000 ekin = 0.2397555262249 | erot = 0.457299221562917 | epot = -15.3394879929896 | etot = -14.6424332452018 -428000 ekin = 0.252922416268525 | erot = 0.432153058136034 | epot = -15.3275087195978 | etot = -14.6424332451932 -429000 ekin = 0.266190667178493 | erot = 0.410120192009067 | epot = -15.3187441043812 | etot = -14.6424332451936 -430000 ekin = 0.279148248284974 | erot = 0.391625457763382 | epot = -15.3132069512513 | etot = -14.6424332452029 -431000 ekin = 0.29135249529286 | erot = 0.376989149811693 | epot = -15.3107748903245 | etot = -14.64243324522 -432000 ekin = 0.302347287569365 | erot = 0.366422254467258 | epot = -15.3112027872808 | etot = -14.6424332452442 -433000 ekin = 0.311682921770367 | erot = 0.360024429013421 | epot = -15.3141405960571 | etot = -14.6424332452733 -434000 ekin = 0.318937954386236 | erot = 0.357784738271833 | epot = -15.3191559379639 | etot = -14.6424332453059 -435000 ekin = 0.323742037713895 | erot = 0.359585207274089 | epot = -15.3257604903287 | etot = -14.6424332453407 -436000 ekin = 0.325798554030487 | erot = 0.365207245307322 | epot = -15.3334390447139 | etot = -14.6424332453761 -437000 ekin = 0.324905697096463 | erot = 0.374340922351957 | epot = -15.3416798648574 | etot = -14.6424332454089 -438000 ekin = 0.320974589857369 | erot = 0.386596930163013 | epot = -15.3500047654581 | etot = -14.6424332454377 -439000 ekin = 0.314043077745089 | erot = 0.401520852188733 | epot = -15.3579971753951 | etot = -14.6424332454613 -440000 ekin = 0.304283988018853 | erot = 0.418609132217991 | epot = -15.3653263657148 | etot = -14.6424332454779 -441000 ekin = 0.292006859109404 | erot = 0.437325916197886 | epot = -15.3717660207937 | etot = -14.6424332454864 -442000 ekin = 0.277652365812269 | erot = 0.457119792524577 | epot = -15.3772054038238 | etot = -14.6424332454869 -443000 ekin = 0.261778853587318 | erot = 0.477439412182355 | epot = -15.3816515112496 | etot = -14.6424332454799 -444000 ekin = 0.245040553430214 | erot = 0.497747053383824 | epot = -15.3852208522809 | etot = -14.6424332454669 -445000 ekin = 0.228157260415731 | erot = 0.517529408210585 | epot = -15.3881199140755 | etot = -14.6424332454491 -446000 ekin = 0.211875681724412 | erot = 0.536305196865295 | epot = -15.3906141240194 | etot = -14.6424332454297 -447000 ekin = 0.196923472676251 | erot = 0.55362963276261 | epot = -15.3929863508503 | etot = -14.6424332454115 -448000 ekin = 0.183958277875551 | erot = 0.569096233380425 | epot = -15.3954877566541 | etot = -14.6424332453982 -449000 ekin = 0.173515771308133 | erot = 0.58233694716115 | epot = -15.3982859638622 | etot = -14.642433245393 -450000 ekin = 0.165962361194704 | erot = 0.593021970155263 | epot = -15.4014175767483 | etot = -14.6424332453983 -451000 ekin = 0.161459280831059 | erot = 0.600860851258439 | epot = -15.4047533775047 | etot = -14.6424332454152 -452000 ekin = 0.159944578250382 | erot = 0.605606408084731 | epot = -15.4079842317782 | etot = -14.6424332454431 -453000 ekin = 0.161137653112592 | erot = 0.60706249637563 | epot = -15.4106333949674 | etot = -14.6424332454792 -454000 ekin = 0.164567591511406 | erot = 0.60509577931268 | epot = -15.4120966163435 | etot = -14.6424332455195 -455000 ekin = 0.169622334208391 | erot = 0.599650455426718 | epot = -15.4117060351935 | etot = -14.6424332455584 -456000 ekin = 0.17561180235025 | erot = 0.590763702898742 | epot = -15.4088087508399 | etot = -14.6424332455909 -457000 ekin = 0.181835621982482 | erot = 0.578578749366101 | epot = -15.4028476169608 | etot = -14.6424332456122 -458000 ekin = 0.187645727031656 | erot = 0.563352302650951 | epot = -15.3934312753017 | etot = -14.6424332456191 -459000 ekin = 0.192495880386114 | erot = 0.54545371714998 | epot = -15.3803828431462 | etot = -14.6424332456101 -460000 ekin = 0.195973381638774 | erot = 0.525354597711239 | epot = -15.3637612249358 | etot = -14.6424332455858 -461000 ekin = 0.197811920992994 | erot = 0.503609203462524 | epot = -15.3438543700041 | etot = -14.6424332455486 -462000 ekin = 0.197887724921045 | erot = 0.480827560282241 | epot = -15.3211485307047 | etot = -14.6424332455014 -463000 ekin = 0.196203198487146 | erot = 0.457644248436018 | epot = -15.2962806923716 | etot = -14.6424332454485 -464000 ekin = 0.192863034127871 | erot = 0.4346862204284 | epot = -15.2699824999498 | etot = -14.6424332453935 -465000 ekin = 0.188047435824124 | erot = 0.412542760090356 | epot = -15.2430234412545 | etot = -14.64243324534 -466000 ekin = 0.18198610755457 | erot = 0.391740010671241 | epot = -15.2161593635165 | etot = -14.6424332452907 -467000 ekin = 0.174935400199639 | erot = 0.372721626734284 | epot = -15.1900902721815 | etot = -14.6424332452476 -468000 ekin = 0.167159826103632 | erot = 0.35583625835081 | epot = -15.1654293296664 | etot = -14.642433245212 -469000 ekin = 0.158918218023896 | erot = 0.341331890764782 | epot = -15.142683353973 | etot = -14.6424332451844 -470000 ekin = 0.150454185654319 | erot = 0.329356584633462 | epot = -15.1222440154524 | etot = -14.6424332451646 -471000 ekin = 0.141990180750332 | erot = 0.319964871776705 | epot = -15.1043882976792 | etot = -14.6424332451522 -472000 ekin = 0.133724353868932 | erot = 0.313128906245091 | epot = -15.08928650526 | etot = -14.642433245146 -473000 ekin = 0.125829398102408 | erot = 0.308753392324225 | epot = -15.0770160355716 | etot = -14.642433245145 -474000 ekin = 0.118452666363557 | erot = 0.306693264413833 | epot = -15.0675791759251 | etot = -14.6424332451477 -475000 ekin = 0.111716976219119 | erot = 0.306773053290691 | epot = -15.0609232746627 | etot = -14.6424332451529 -476000 ekin = 0.105721655633339 | erot = 0.308806833537639 | epot = -15.0569617343301 | etot = -14.6424332451591 -477000 ekin = 0.10054352367576 | erot = 0.312617617130302 | epot = -15.0555943859713 | etot = -14.6424332451652 -478000 ekin = 0.0962376398644811 | erot = 0.318055055635326 | epot = -15.0567259406699 | etot = -14.6424332451701 -479000 ekin = 0.0928377950024513 | erot = 0.325010357030152 | epot = -15.0602813972059 | etot = -14.6424332451733 -480000 ekin = 0.0903568546345963 | erot = 0.333427427763319 | epot = -15.066217527572 | etot = -14.6424332451741 -481000 ekin = 0.088787198935855 | erot = 0.343309423709807 | epot = -15.0745298678182 | etot = -14.6424332451725 -482000 ekin = 0.0881016191320308 | erot = 0.354720133057142 | epot = -15.0852549973579 | etot = -14.6424332451687 -483000 ekin = 0.0882551127439617 | erot = 0.367779908272486 | epot = -15.0984682661795 | etot = -14.642433245163 -484000 ekin = 0.0891880440138072 | erot = 0.382656193507619 | epot = -15.1142774826776 | etot = -14.6424332451562 -485000 ekin = 0.0908310739109877 | erot = 0.399549033146302 | epot = -15.1328133522061 | etot = -14.6424332451488 -486000 ekin = 0.0931120890990441 | erot = 0.418672269923144 | epot = -15.154217604164 | etot = -14.6424332451418 -487000 ekin = 0.0959650526392659 | erot = 0.440231422321023 | epot = -15.1786297200963 | etot = -14.642433245136 -488000 ekin = 0.0993402613867423 | erot = 0.464399451384504 | epot = -15.2061729579036 | etot = -14.6424332451324 -489000 ekin = 0.103214957397683 | erot = 0.491291775403278 | epot = -15.2369399779328 | etot = -14.6424332451318 -490000 ekin = 0.107602676597188 | erot = 0.520941965498224 | epot = -15.2709778872309 | etot = -14.6424332451355 -491000 ekin = 0.112559247664625 | erot = 0.553279563916973 | epot = -15.3082720567259 | etot = -14.6424332451443 -492000 ekin = 0.118183136723599 | erot = 0.588111425308464 | epot = -15.3487278071918 | etot = -14.6424332451598 -493000 ekin = 0.12460804012638 | erot = 0.625107908278983 | epot = -15.3921491935888 | etot = -14.6424332451835 -494000 ekin = 0.131986393312559 | erot = 0.663795156035105 | epot = -15.4382147945647 | etot = -14.642433245217 -495000 ekin = 0.140463823900155 | erot = 0.703554605721716 | epot = -15.4864516748841 | etot = -14.6424332452623 -496000 ekin = 0.150146408035833 | erot = 0.743630741563153 | epot = -15.5362103949194 | etot = -14.6424332453204 -497000 ekin = 0.161064579071306 | erot = 0.783147917317561 | epot = -15.5866457417809 | etot = -14.642433245392 -498000 ekin = 0.173139219157371 | erot = 0.821136754972764 | epot = -15.6367092196066 | etot = -14.6424332454764 -499000 ekin = 0.186156317833367 | erot = 0.856570103856702 | epot = -15.6851596672615 | etot = -14.6424332455714 -500000 ekin = 0.199756195068917 | erot = 0.888407758274046 | epot = -15.7305971990159 | etot = -14.642433245673 -501000 ekin = 0.21344151783732 | erot = 0.915648078732857 | epot = -15.7715228423457 | etot = -14.6424332457755 -502000 ekin = 0.226605416597982 | erot = 0.937383433649182 | epot = -15.8064220961193 | etot = -14.6424332458721 -503000 ekin = 0.238577508977576 | erot = 0.952855183124931 | epot = -15.833865938058 | etot = -14.6424332459555 -504000 ekin = 0.248682347016318 | erot = 0.961503066788369 | epot = -15.8526186598236 | etot = -14.6424332460189 -505000 ekin = 0.256302488969577 | erot = 0.963003656366666 | epot = -15.8617393913931 | etot = -14.6424332460568 -506000 ekin = 0.260937583144178 | erot = 0.957293217920571 | epot = -15.8606640471306 | etot = -14.6424332460659 -507000 ekin = 0.262251679299231 | erot = 0.944571918258594 | epot = -15.8492568436029 | etot = -14.6424332460451 -508000 ekin = 0.260103184111397 | erot = 0.925288564934429 | epot = -15.827824995042 | etot = -14.6424332459962 -509000 ekin = 0.254554875280442 | erot = 0.900107536937821 | epot = -15.7970956581413 | etot = -14.6424332459231 -510000 ekin = 0.245864483348175 | erot = 0.86986171798534 | epot = -15.7581594471648 | etot = -14.6424332458313 -511000 ekin = 0.234458914526877 | erot = 0.835496660126416 | epot = -15.7123888203806 | etot = -14.6424332457274 -512000 ekin = 0.220896820239971 | erot = 0.798011684065844 | epot = -15.6613417499238 | etot = -14.642433245618 -513000 ekin = 0.205824805087871 | erot = 0.758403224578284 | epot = -15.6066612751758 | etot = -14.6424332455096 -514000 ekin = 0.189932244116161 | erot = 0.717614706860263 | epot = -15.5499801963839 | etot = -14.6424332454075 -515000 ekin = 0.173908748199765 | erot = 0.676495918872529 | epot = -15.4928379123883 | etot = -14.642433245316 -516000 ekin = 0.158407108508989 | erot = 0.635773516025286 | epot = -15.4366138697725 | etot = -14.6424332452382 -517000 ekin = 0.144013350183886 | erot = 0.596033149118079 | epot = -15.3824797444782 | etot = -14.6424332451762 -518000 ekin = 0.131224514117994 | erot = 0.557712825688904 | epot = -15.3313705849374 | etot = -14.6424332451305 -519000 ekin = 0.120434042405807 | erot = 0.521106495597668 | epot = -15.2839737831041 | etot = -14.6424332451006 -520000 ekin = 0.111924165176683 | erot = 0.486376443199705 | epot = -15.2407338534619 | etot = -14.6424332450855 -521000 ekin = 0.105864424815849 | erot = 0.453572806060381 | epot = -15.2018704759593 | etot = -14.6424332450831 -522000 ekin = 0.102315362067358 | erot = 0.422658367131465 | epot = -15.1674069742899 | etot = -14.6424332450911 -523000 ekin = 0.101236366465137 | erot = 0.393536647096961 | epot = -15.1372062586691 | etot = -14.642433245107 -524000 ekin = 0.102496717236706 | erot = 0.366081244308194 | epot = -15.1110112066729 | etot = -14.642433245128 -525000 ekin = 0.105888887335992 | erot = 0.34016434321467 | epot = -15.0884864757021 | etot = -14.6424332451514 -526000 ekin = 0.111143247850877 | erot = 0.315682368378667 | epot = -15.0692588614047 | etot = -14.6424332451752 -527000 ekin = 0.117943398962365 | erot = 0.292576937806993 | epot = -15.0529535819666 | etot = -14.6424332451972 -528000 ekin = 0.125941474255752 | erot = 0.270849598243849 | epot = -15.0392243177156 | etot = -14.642433245216 -529000 ekin = 0.134772916010328 | erot = 0.250569317239513 | epot = -15.0277754784806 | etot = -14.6424332452307 -530000 ekin = 0.144070383403691 | erot = 0.231872340652251 | epot = -15.018375969297 | etot = -14.6424332452411 -531000 ekin = 0.153476601970616 | erot = 0.21495474143537 | epot = -15.0108645886531 | etot = -14.6424332452472 -532000 ekin = 0.162656054078885 | erot = 0.200058697649297 | epot = -15.0051479969778 | etot = -14.6424332452496 -533000 ekin = 0.171305419081474 | erot = 0.187454143184918 | epot = -15.0011928075154 | etot = -14.642433245249 -534000 ekin = 0.179162595540396 | erot = 0.177417842695335 | epot = -14.9990136834823 | etot = -14.6424332452466 -535000 ekin = 0.186014006486671 | erot = 0.170212094444235 | epot = -14.9986593461737 | etot = -14.6424332452428 -536000 ekin = 0.191699759240431 | erot = 0.166065149228291 | epot = -15.0001981537075 | etot = -14.6424332452388 -537000 ekin = 0.196116169931534 | erot = 0.165155084981491 | epot = -15.0037045001481 | etot = -14.642433245235 -538000 ekin = 0.199215220533694 | erot = 0.167598364573351 | epot = -15.0092468303393 | etot = -14.6424332452323 -539000 ekin = 0.201000709669595 | erot = 0.173443713619053 | epot = -15.0168776685196 | etot = -14.6424332452309 -540000 ekin = 0.201521164038038 | erot = 0.182671367033605 | epot = -15.0266257763031 | etot = -14.6424332452315 -541000 ekin = 0.200859940141528 | erot = 0.195197211442955 | epot = -15.0384903968187 | etot = -14.6424332452342 -542000 ekin = 0.199123298889056 | erot = 0.210880936223658 | epot = -15.052437480352 | etot = -14.6424332452393 -543000 ekin = 0.19642751938404 | erot = 0.22953701778937 | epot = -15.0683977824199 | etot = -14.6424332452465 -544000 ekin = 0.192886294945236 | erot = 0.250947202002185 | epot = -15.086266742204 | etot = -14.6424332452566 -545000 ekin = 0.188599710887435 | erot = 0.274873110235089 | epot = -15.1059060663913 | etot = -14.6424332452688 -546000 ekin = 0.183646045242698 | erot = 0.301067663118868 | epot = -15.1271469536447 | etot = -14.6424332452831 -547000 ekin = 0.178077473818678 | erot = 0.329284179373465 | epot = -15.1497948984913 | etot = -14.6424332452992 -548000 ekin = 0.171920510267324 | erot = 0.359282253783629 | epot = -15.1736360093673 | etot = -14.6424332453164 -549000 ekin = 0.165181670578013 | erot = 0.390829837831145 | epot = -15.1984447537432 | etot = -14.6424332453341 -550000 ekin = 0.157858408655518 | erot = 0.423701326917604 | epot = -15.2239929809249 | etot = -14.6424332453518 -551000 ekin = 0.149954809005955 | erot = 0.457671882716344 | epot = -15.2500599370909 | etot = -14.6424332453686 -552000 ekin = 0.141500835823186 | erot = 0.492508662660355 | epot = -15.2764427438674 | etot = -14.6424332453839 -553000 ekin = 0.132573145481932 | erot = 0.527960055124183 | epot = -15.3029664460032 | etot = -14.6424332453971 -554000 ekin = 0.123314645148981 | erot = 0.563744383269515 | epot = -15.329492273826 | etot = -14.6424332454075 -555000 ekin = 0.113949270903167 | erot = 0.599539792623517 | epot = -15.3559223089418 | etot = -14.6424332454152 -556000 ekin = 0.104788088807775 | erot = 0.634977129563511 | epot = -15.3821984637917 | etot = -14.6424332454204 -557000 ekin = 0.0962230654780801 | erot = 0.669637513724341 | epot = -15.4082938246267 | etot = -14.6424332454242 -558000 ekin = 0.0887059614428306 | erot = 0.703055990480491 | epot = -15.4341951973517 | etot = -14.6424332454284 -559000 ekin = 0.0827118847741739 | erot = 0.734732129423963 | epot = -15.4598772596329 | etot = -14.6424332454348 -560000 ekin = 0.0786899547259678 | erot = 0.764147748398776 | epot = -15.4852709485703 | etot = -14.6424332454456 -561000 ekin = 0.077006772063353 | erot = 0.790791153075906 | epot = -15.5102311706018 | etot = -14.6424332454625 -562000 ekin = 0.0778911706764506 | erot = 0.814186471629049 | epot = -15.534510887792 | etot = -14.6424332454865 -563000 ekin = 0.0813901113672784 | erot = 0.833925925482987 | epot = -15.5577492823675 | etot = -14.6424332455173 -564000 ekin = 0.0873448530219235 | erot = 0.849702302565643 | epot = -15.57948040114 | etot = -14.6424332455524 -565000 ekin = 0.0953935152542986 | erot = 0.861338569497109 | epot = -15.5991653303401 | etot = -14.6424332455887 -566000 ekin = 0.105001366119689 | erot = 0.868811531657212 | epot = -15.6162461433986 | etot = -14.6424332456216 -567000 ekin = 0.115514789210836 | erot = 0.872266750928061 | epot = -15.6302147857854 | etot = -14.6424332456465 -568000 ekin = 0.126230320990563 | erot = 0.87202254676091 | epot = -15.6406861134105 | etot = -14.642433245659 -569000 ekin = 0.136467575205463 | erot = 0.868561781937853 | epot = -15.6474626027996 | etot = -14.6424332456563 -570000 ekin = 0.145634823229245 | erot = 0.862511177262726 | epot = -15.6505792461291 | etot = -14.6424332456371 -571000 ekin = 0.153278250260091 | erot = 0.854608991356116 | epot = -15.6503204872188 | etot = -14.6424332456026 -572000 ekin = 0.159109636953922 | erot = 0.845662918616649 | epot = -15.6472058011259 | etot = -14.6424332455553 -573000 ekin = 0.163011362017366 | erot = 0.83650089231986 | epot = -15.6419454998373 | etot = -14.6424332455001 -574000 ekin = 0.165021239080139 | erot = 0.827918058205197 | epot = -15.6353725427275 | etot = -14.6424332454422 -575000 ekin = 0.165302195908603 | erot = 0.82062347970414 | epot = -15.6283589210001 | etot = -14.6424332453874 -576000 ekin = 0.164102988101199 | erot = 0.815190165398918 | epot = -15.6217263988412 | etot = -14.6424332453411 -577000 ekin = 0.161716152387156 | erot = 0.812011817944536 | epot = -15.6161612156399 | etot = -14.6424332453082 -578000 ekin = 0.158438569371811 | erot = 0.81126934569462 | epot = -15.6121411603585 | etot = -14.6424332452921 -579000 ekin = 0.154538688869358 | erot = 0.812909695780722 | epot = -15.6098816299449 | etot = -14.6424332452948 -580000 ekin = 0.150232988454481 | erot = 0.816638977241796 | epot = -15.6093052110129 | etot = -14.6424332453166 -581000 ekin = 0.145672809814969 | erot = 0.821931135410972 | epot = -15.6100371905821 | etot = -14.6424332453562 -582000 ekin = 0.140941476791511 | erot = 0.828052590350848 | epot = -15.611427312553 | etot = -14.6424332454106 -583000 ekin = 0.136060602599167 | erot = 0.834102246896349 | epot = -15.6125960949712 | etot = -14.6424332454757 -584000 ekin = 0.131003759896591 | erot = 0.839065139158288 | epot = -15.6125021446008 | etot = -14.642433245546 -585000 ekin = 0.125715216483012 | erot = 0.841876757449037 | epot = -15.6100252195478 | etot = -14.6424332456157 -586000 ekin = 0.120131224768942 | erot = 0.841493945666758 | epot = -15.6040584161146 | etot = -14.6424332456789 -587000 ekin = 0.114201380572126 | erot = 0.836967317753738 | epot = -15.5936019440558 | etot = -14.6424332457299 -588000 ekin = 0.107907808226734 | erot = 0.827509595983212 | epot = -15.577850649974 | etot = -14.642433245764 -589000 ekin = 0.101280337909725 | erot = 0.812554260673577 | epot = -15.556267844361 | etot = -14.6424332457777 -590000 ekin = 0.0944063548788355 | erot = 0.79179948842053 | epot = -15.5286390890686 | etot = -14.6424332457692 -591000 ekin = 0.0874345511052061 | erot = 0.765233519223278 | epot = -15.4951013160667 | etot = -14.6424332457382 -592000 ekin = 0.0805723392085111 | erot = 0.733139214285209 | epot = -15.4561447991801 | etot = -14.6424332456864 -593000 ekin = 0.0740771594080883 | erot = 0.696077455348681 | epot = -15.4125878603738 | etot = -14.642433245617 -594000 ekin = 0.0682423089599854 | erot = 0.654850963358098 | epot = -15.3655265178525 | etot = -14.6424332455344 -595000 ekin = 0.0633782539014572 | erot = 0.610451848323546 | epot = -15.3162633476691 | etot = -14.6424332454441 -596000 ekin = 0.0597906540649578 | erot = 0.563997548401054 | epot = -15.2662214478181 | etot = -14.6424332453521 -597000 ekin = 0.0577565493624065 | erot = 0.516660644084201 | epot = -15.216850438711 | etot = -14.6424332452644 -598000 ekin = 0.0575003158536251 | erot = 0.46959829435358 | epot = -15.1695318553938 | etot = -14.6424332451866 -599000 ekin = 0.0591710965286367 | erot = 0.423886769451031 | epot = -15.1254911111031 | etot = -14.6424332451235 -600000 ekin = 0.0628234356891102 | erot = 0.380465849281421 | epot = -15.0857225300491 | etot = -14.6424332450786 -601000 ekin = 0.0684027903378405 | erot = 0.340096852289037 | epot = -15.0509328876809 | etot = -14.6424332450541 -602000 ekin = 0.0757374499128925 | erot = 0.303336891508809 | epot = -15.0215075864722 | etot = -14.6424332450505 -603000 ekin = 0.0845381560106828 | erot = 0.270530726252434 | epot = -14.99750212733 | etot = -14.6424332450669 -604000 ekin = 0.0944063594078121 | erot = 0.241820347963461 | epot = -14.9786599524719 | etot = -14.6424332451006 -605000 ekin = 0.104851562460535 | erot = 0.217171224791041 | epot = -14.9644560323989 | etot = -14.6424332451473 -606000 ekin = 0.115317556389795 | erot = 0.196412930356109 | epot = -14.9541637319474 | etot = -14.6424332452015 -607000 ekin = 0.125216580353228 | erot = 0.179290709847405 | epot = -14.9469405354578 | etot = -14.6424332452571 -608000 ekin = 0.133969542490509 | erot = 0.165523445157638 | epot = -14.9419262329558 | etot = -14.6424332453076 -609000 ekin = 0.141049537028455 | erot = 0.154862582265071 | epot = -14.9383453646402 | etot = -14.6424332453467 -610000 ekin = 0.146025095175882 | erot = 0.147146040888404 | epot = -14.9356043814333 | etot = -14.6424332453691 -611000 ekin = 0.148599079335686 | erot = 0.14234111819369 | epot = -14.9333734429005 | etot = -14.6424332453711 -612000 ekin = 0.148639027542167 | erot = 0.140571068727464 | epot = -14.9316433416208 | etot = -14.6424332453511 -613000 ekin = 0.146195193893263 | erot = 0.142121441395694 | epot = -14.9307498805989 | etot = -14.6424332453099 -614000 ekin = 0.141503544704983 | erot = 0.147424293659382 | epot = -14.9313610836151 | etot = -14.6424332452507 -615000 ekin = 0.134972482669517 | erot = 0.157020849768724 | epot = -14.934426577617 | etot = -14.6424332451788 -616000 ekin = 0.127153892887408 | erot = 0.171505679772539 | epot = -14.9410928177611 | etot = -14.6424332451012 -617000 ekin = 0.118700960497153 | erot = 0.191457667915174 | epot = -14.9525918734384 | etot = -14.6424332450261 -618000 ekin = 0.110316794781893 | erot = 0.217364584491491 | epot = -14.970114624235 | etot = -14.6424332449616 -619000 ekin = 0.10269894266605 | erot = 0.24954877623364 | epot = -14.9946809638152 | etot = -14.6424332449155 -620000 ekin = 0.0964852203315238 | erot = 0.288101317493722 | epot = -15.0270197827192 | etot = -14.642433244894 -621000 ekin = 0.0922059091525849 | erot = 0.332831044367661 | epot = -15.0674701984217 | etot = -14.6424332449015 -622000 ekin = 0.0902463647100601 | erot = 0.383233451864067 | epot = -15.115913061514 | etot = -14.6424332449399 -623000 ekin = 0.0908226920702702 | erot = 0.438482716267865 | epot = -15.171738653347 | etot = -14.6424332450089 -624000 ekin = 0.0939716062521546 | erot = 0.497448307340481 | epot = -15.2338531586982 | etot = -14.6424332451056 -625000 ekin = 0.0995541611224779 | erot = 0.558735886785281 | epot = -15.3007232931328 | etot = -14.6424332452251 -626000 ekin = 0.107271859325763 | erot = 0.620750477457113 | epot = -15.3704555821434 | etot = -14.6424332453605 -627000 ekin = 0.11669282673765 | erot = 0.681778220901699 | epot = -15.4409042931431 | etot = -14.6424332455038 -628000 ekin = 0.127285245273588 | erot = 0.740081431769906 | epot = -15.5097999226895 | etot = -14.642433245646 -629000 ekin = 0.138455039153851 | erot = 0.794000196770826 | epot = -15.574888481703 | etot = -14.6424332457784 -630000 ekin = 0.149584842937095 | erot = 0.842052640240528 | epot = -15.6340707290702 | etot = -14.6424332458926 -631000 ekin = 0.160071499853017 | erot = 0.883025442878399 | epot = -15.6855301887135 | etot = -14.6424332459821 -632000 ekin = 0.169359720292761 | erot = 0.916046503426791 | epot = -15.7278394697615 | etot = -14.642433246042 -633000 ekin = 0.176970053692532 | erot = 0.940632922941054 | epot = -15.7600362227033 | etot = -14.6424332460697 -634000 ekin = 0.182519961289937 | erot = 0.956709735134042 | epot = -15.7816629424891 | etot = -14.6424332460651 -635000 ekin = 0.185737466035627 | erot = 0.964597760206376 | epot = -15.7927684722726 | etot = -14.6424332460306 -636000 ekin = 0.186467519303283 | erot = 0.964972204256364 | epot = -15.7938729695302 | etot = -14.6424332459705 -637000 ekin = 0.184671774604459 | erot = 0.958796660376478 | epot = -15.7859016808714 | etot = -14.6424332458905 -638000 ekin = 0.180422825778025 | erot = 0.947239527072856 | epot = -15.770095598648 | etot = -14.6424332457971 -639000 ekin = 0.173894119064824 | erot = 0.931581224196041 | epot = -15.7479085889582 | etot = -14.6424332456973 -640000 ekin = 0.165346701827766 | erot = 0.913120838753206 | epot = -15.7209007861785 | etot = -14.6424332455976 -641000 ekin = 0.155113786103673 | erot = 0.893090060089469 | epot = -15.6906370916966 | etot = -14.6424332455035 -642000 ekin = 0.143583869244195 | erot = 0.872580710305971 | epot = -15.6585978249697 | etot = -14.6424332454196 -643000 ekin = 0.131182953689543 | erot = 0.852490168054141 | epot = -15.6261063670928 | etot = -14.6424332453491 -644000 ekin = 0.118356305761149 | erot = 0.833486853990058 | epot = -15.5942764050452 | etot = -14.642433245294 -645000 ekin = 0.105550209085058 | erot = 0.815995971212585 | epot = -15.5639794255528 | etot = -14.6424332452552 -646000 ekin = 0.0931942744194403 | erot = 0.800204061931068 | epot = -15.5358315815827 | etot = -14.6424332452322 -647000 ekin = 0.0816850001800569 | erot = 0.786079744440791 | epot = -15.5101979898446 | etot = -14.6424332452237 -648000 ekin = 0.0713713598437807 | erot = 0.773407243193091 | epot = -15.4872118482647 | etot = -14.6424332452279 -649000 ekin = 0.0625431628716936 | erot = 0.761828976530777 | epot = -15.4668053846446 | etot = -14.6424332452421 -650000 ekin = 0.0554227735502947 | erot = 0.750893453414337 | epot = -15.4487494722283 | etot = -14.6424332452637 -651000 ekin = 0.0501605027658048 | erot = 0.740104978448961 | epot = -15.4326987265043 | etot = -14.6424332452896 -652000 ekin = 0.0468336713663306 | erot = 0.728972100421323 | epot = -15.4182390171045 | etot = -14.6424332453168 -653000 ekin = 0.0454490492573717 | erot = 0.717052285945757 | epot = -15.4049345805459 | etot = -14.6424332453428 -654000 ekin = 0.0459481524943393 | erot = 0.703990869784694 | epot = -15.3923722676441 | etot = -14.6424332453651 -655000 ekin = 0.0482147495286144 | erot = 0.689552835107378 | epot = -15.3802008300176 | etot = -14.6424332453816 -656000 ekin = 0.0520838761262489 | erot = 0.673646332749853 | epot = -15.368163454267 | etot = -14.6424332453909 -657000 ekin = 0.057351662084844 | erot = 0.656337023115504 | epot = -15.3561219305924 | etot = -14.6424332453921 -658000 ekin = 0.0637853134927951 | erot = 0.637852348219592 | epot = -15.3440709070972 | etot = -14.6424332453848 -659000 ekin = 0.0711326702869636 | erot = 0.618574815847833 | epot = -15.3321407315044 | etot = -14.6424332453696 -660000 ekin = 0.0791308828101084 | erot = 0.599023454708773 | epot = -15.3205875828669 | etot = -14.642433245348 -661000 ekin = 0.0875139366233652 | erot = 0.579822939747469 | epot = -15.3097701216932 | etot = -14.6424332453223 -662000 ekin = 0.0960190004199466 | erot = 0.561660610347632 | epot = -15.300112856063 | etot = -14.6424332452954 -663000 ekin = 0.104391848885314 | erot = 0.545232746054679 | epot = -15.2920578402109 | etot = -14.6424332452709 -664000 ekin = 0.112391863390296 | erot = 0.531182949318074 | epot = -15.286008057961 | etot = -14.6424332452526 -665000 ekin = 0.119797262721329 | erot = 0.520037124796732 | epot = -15.2822676327621 | etot = -14.6424332452441 -666000 ekin = 0.126411190063532 | erot = 0.512141060960607 | epot = -15.2809854962726 | etot = -14.6424332452485 -667000 ekin = 0.132069035725113 | erot = 0.507607681728921 | epot = -15.2821099627213 | etot = -14.6424332452672 -668000 ekin = 0.136646914542181 | erot = 0.506281315754145 | epot = -15.2853614755973 | etot = -14.6424332453009 -669000 ekin = 0.140070616012996 | erot = 0.507725566171501 | epot = -15.2902294275325 | etot = -14.642433245348 -670000 ekin = 0.142323740906653 | erot = 0.511239425098507 | epot = -15.2959964114102 | etot = -14.642433245405 -671000 ekin = 0.143453306303039 | erot = 0.515903234044805 | epot = -15.3017897858151 | etot = -14.6424332454672 -672000 ekin = 0.143571012732396 | erot = 0.520652256717971 | epot = -15.3066565149792 | etot = -14.6424332455288 -673000 ekin = 0.142848733836934 | erot = 0.524371563356863 | epot = -15.3096535427773 | etot = -14.6424332455835 -674000 ekin = 0.141507613277702 | erot = 0.526002362930559 | epot = -15.3099432218337 | etot = -14.6424332456255 -675000 ekin = 0.139801302825577 | erot = 0.524647629024427 | epot = -15.3068821775002 | etot = -14.6424332456502 -676000 ekin = 0.137995095210629 | erot = 0.519664439041358 | epot = -15.3000927799067 | etot = -14.6424332456547 -677000 ekin = 0.136343677285176 | erot = 0.510732098517846 | epot = -15.2895090214411 | etot = -14.642433245638 -678000 ekin = 0.135070664122595 | erot = 0.497888575256361 | epot = -15.27539248498 | etot = -14.6424332456011 -679000 ekin = 0.134352810444857 | erot = 0.481532294132433 | epot = -15.2583183501238 | etot = -14.6424332455465 -680000 ekin = 0.134310862655746 | erot = 0.462390968605226 | epot = -15.2391350767392 | etot = -14.6424332454783 -681000 ekin = 0.135007638923116 | erot = 0.441462941784772 | epot = -15.2189038261091 | etot = -14.6424332454012 -682000 ekin = 0.13645246152458 | erot = 0.419938865037781 | epot = -15.1988245718827 | etot = -14.6424332453204 -683000 ekin = 0.138609887397935 | erot = 0.399112293315445 | epot = -15.1801554259542 | etot = -14.6424332452409 -684000 ekin = 0.141410065648248 | erot = 0.380287181762368 | epot = -15.1641304925783 | etot = -14.6424332451677 -685000 ekin = 0.144758102722225 | erot = 0.364688846299406 | epot = -15.1518801941271 | etot = -14.6424332451055 -686000 ekin = 0.148540467119406 | erot = 0.353383275614485 | epot = -15.1443569877923 | etot = -14.6424332450585 -687000 ekin = 0.152627512098693 | erot = 0.347208212230851 | epot = -15.1422689693595 | etot = -14.64243324503 -688000 ekin = 0.156872371008209 | erot = 0.346718408271121 | epot = -15.1460240243023 | etot = -14.642433245023 -689000 ekin = 0.161107527974744 | erot = 0.352146941115391 | epot = -15.1556877141291 | etot = -14.642433245039 -690000 ekin = 0.165141087380609 | erot = 0.363384304942047 | epot = -15.1709586374011 | etot = -14.6424332450784 -691000 ekin = 0.168755042649038 | erot = 0.379976931156532 | epot = -15.1911652189456 | etot = -14.64243324514 -692000 ekin = 0.171707649703648 | erot = 0.40114655839773 | epot = -15.2152874533222 | etot = -14.6424332452208 -693000 ekin = 0.173741393443047 | erot = 0.425831232788526 | epot = -15.2420058715477 | etot = -14.6424332453161 -694000 ekin = 0.17459711062473 | erot = 0.452747528139949 | epot = -15.2697778841842 | etot = -14.6424332454195 -695000 ekin = 0.174033757472198 | erot = 0.480471830922223 | epot = -15.2969388339179 | etot = -14.6424332455235 -696000 ekin = 0.171852263364718 | erot = 0.507536398158151 | epot = -15.3218219071426 | etot = -14.6424332456197 -697000 ekin = 0.167921065290898 | erot = 0.532533688692959 | epot = -15.3428879996838 | etot = -14.6424332456999 -698000 ekin = 0.162200409476997 | erot = 0.554220619924979 | epot = -15.3588542751587 | etot = -14.6424332457567 -699000 ekin = 0.154762415715614 | erot = 0.571613361027875 | epot = -15.3688090225278 | etot = -14.6424332457844 -700000 ekin = 0.145804230008778 | erot = 0.584063387087836 | epot = -15.372300862876 | etot = -14.6424332457794 -701000 ekin = 0.135652269558596 | erot = 0.59130692272119 | epot = -15.3693924380208 | etot = -14.6424332457411 -702000 ekin = 0.124756460207472 | erot = 0.593482464348829 | epot = -15.3606721702278 | etot = -14.6424332456715 -703000 ekin = 0.113674325951261 | erot = 0.591114401856776 | epot = -15.3472219733834 | etot = -14.6424332455753 -704000 ekin = 0.103045675945596 | erot = 0.585064323196386 | epot = -15.3305432446017 | etot = -14.6424332454597 -705000 ekin = 0.0935593581963268 | erot = 0.576454826534503 | epot = -15.312447430064 | etot = -14.6424332453332 -706000 ekin = 0.0859140824284977 | erot = 0.566573150256555 | epot = -15.2949204778904 | etot = -14.6424332452053 -707000 ekin = 0.0807756759558007 | erot = 0.556763427609362 | epot = -15.2799723486511 | etot = -14.642433245086 -708000 ekin = 0.0787333622600193 | erot = 0.548316855291188 | epot = -15.2694834625354 | etot = -14.6424332449842 -709000 ekin = 0.0802577669151192 | erot = 0.542368667953882 | epot = -15.265059679777 | etot = -14.642433244908 -710000 ekin = 0.0856633545528786 | erot = 0.539809747049216 | epot = -15.2679063464658 | etot = -14.6424332448637 -711000 ekin = 0.0950778519027538 | erot = 0.541219180891322 | epot = -15.2787302776492 | etot = -14.6424332448551 -712000 ekin = 0.108420876622172 | erot = 0.546822307911462 | epot = -15.2976764294175 | etot = -14.6424332448839 -713000 ekin = 0.125393451694849 | erot = 0.556476834657724 | epot = -15.3243035313016 | etot = -14.6424332449491 -714000 ekin = 0.145479367621443 | erot = 0.569687600119355 | epot = -15.3576002127879 | etot = -14.6424332450471 -715000 ekin = 0.167958541116821 | erot = 0.585648522303096 | epot = -15.3960403085922 | etot = -14.6424332451723 -716000 ekin = 0.191931735851186 | erot = 0.603308292531368 | epot = -15.4376732736998 | etot = -14.6424332453172 -717000 ekin = 0.216355400176841 | erot = 0.621454592037002 | epot = -15.4802432376871 | etot = -14.6424332454732 -718000 ekin = 0.240085056510385 | erot = 0.638810139731497 | epot = -15.5213284418726 | etot = -14.6424332456307 -719000 ekin = 0.261925698575292 | erot = 0.65413289598608 | epot = -15.5584918403416 | etot = -14.6424332457802 -720000 ekin = 0.280687969311534 | erot = 0.666312379867044 | epot = -15.5894335950911 | etot = -14.6424332459125 -721000 ekin = 0.295249345589098 | erot = 0.674454385927666 | epot = -15.6121369775362 | etot = -14.6424332460194 -722000 ekin = 0.304619886333681 | erot = 0.677947410255072 | epot = -15.6250005426824 | etot = -14.6424332460937 -723000 ekin = 0.30801198372793 | erot = 0.676505724570388 | epot = -15.626950954428 | etot = -14.6424332461296 -724000 ekin = 0.304912667284322 | erot = 0.670186105899534 | epot = -15.6175320193071 | etot = -14.6424332461232 -725000 ekin = 0.295155116711518 | erot = 0.659377522489357 | epot = -15.5969658852731 | etot = -14.6424332460723 -726000 ekin = 0.27898313490006 | erot = 0.644765363158316 | epot = -15.5661817440354 | etot = -14.642433245977 -727000 ekin = 0.257098790794337 | erot = 0.62727386036282 | epot = -15.5268058969977 | etot = -14.6424332458405 -728000 ekin = 0.230680158274908 | erot = 0.607992016180347 | epot = -15.4811054201246 | etot = -14.6424332456694 -729000 ekin = 0.201354496276652 | erot = 0.588089464034279 | epot = -15.4318772057849 | etot = -14.642433245474 -730000 ekin = 0.171114103979276 | erot = 0.568729214715524 | epot = -15.3822765639636 | etot = -14.6424332452688 -731000 ekin = 0.142168923912243 | erot = 0.550984135070421 | epot = -15.3355863040542 | etot = -14.6424332450715 -732000 ekin = 0.116742007100586 | erot = 0.535763349043612 | epot = -15.2949386010455 | etot = -14.6424332449013 -733000 ekin = 0.0968293027575733 | erot = 0.523753647321484 | epot = -15.2630161948554 | etot = -14.6424332447764 -734000 ekin = 0.0839596135620446 | erot = 0.51537959233841 | epot = -15.2417724506114 | etot = -14.642433244711 -735000 ekin = 0.0789983701792907 | erot = 0.510784464195777 | epot = -15.2322160790874 | etot = -14.6424332447124 -736000 ekin = 0.0820355551944224 | erot = 0.509832642266136 | epot = -15.23430144224 | etot = -14.6424332447794 -737000 ekin = 0.0923827123871587 | erot = 0.51213255085533 | epot = -15.2469485081448 | etot = -14.6424332449023 -738000 ekin = 0.108680448514282 | erot = 0.517077971027511 | epot = -15.2681916646066 | etot = -14.6424332450648 -739000 ekin = 0.12909371568348 | erot = 0.523904364926912 | epot = -15.2954313258572 | etot = -14.6424332452468 -740000 ekin = 0.151555277793917 | erot = 0.53175589578008 | epot = -15.325744419002 | etot = -14.642433245428 -741000 ekin = 0.174012721806586 | erot = 0.539758083454025 | epot = -15.3562040508505 | etot = -14.6424332455899 -742000 ekin = 0.194640916831425 | erot = 0.547090549700052 | epot = -15.3841647122504 | etot = -14.642433245719 -743000 ekin = 0.211995737398774 | erot = 0.55305412533823 | epot = -15.4074831085434 | etot = -14.6424332458064 -744000 ekin = 0.225100508723011 | erot = 0.55712676231043 | epot = -15.4246605168821 | etot = -14.6424332458487 -745000 ekin = 0.233469424487037 | erot = 0.559003260239848 | epot = -15.4349059305736 | etot = -14.6424332458467 -746000 ekin = 0.237079913465485 | erot = 0.558614810500861 | epot = -15.4381279697714 | etot = -14.642433245805 -747000 ekin = 0.236308652985516 | erot = 0.556125790083883 | epot = -15.4348676888006 | etot = -14.6424332457312 -748000 ekin = 0.231845097888681 | erot = 0.551907079331287 | epot = -15.4261854228543 | etot = -14.6424332456343 -749000 ekin = 0.224593843485155 | erot = 0.546487360030866 | epot = -15.4135144490412 | etot = -14.6424332455252 -750000 ekin = 0.215574369393343 | erot = 0.54048623348627 | epot = -15.3984938482945 | etot = -14.6424332454149 -751000 ekin = 0.205824583428144 | erot = 0.53453535676598 | epot = -15.3827931855082 | etot = -14.642433245314 -752000 ekin = 0.196313335743836 | erot = 0.529195815219999 | epot = -15.3679423961962 | etot = -14.6424332452323 -753000 ekin = 0.187866475789588 | erot = 0.524881252733496 | epot = -15.3551809737002 | etot = -14.6424332451771 -754000 ekin = 0.181110613628451 | erot = 0.521796491099419 | epot = -15.3453403498808 | etot = -14.6424332451529 -755000 ekin = 0.176438042206882 | erot = 0.519900210808722 | epot = -15.3387714981766 | etot = -14.642433245161 -756000 ekin = 0.173994962649905 | erot = 0.51889767628673 | epot = -15.3353258841354 | etot = -14.6424332451988 -757000 ekin = 0.17369319027378 | erot = 0.518265706184262 | epot = -15.3343921417188 | etot = -14.6424332452608 -758000 ekin = 0.175243155018255 | erot = 0.517307659823357 | epot = -15.3349840601802 | etot = -14.6424332453386 -759000 ekin = 0.178203703096654 | erot = 0.515231902166286 | epot = -15.3358688506855 | etot = -14.6424332454225 -760000 ekin = 0.182042463552526 | erot = 0.511243837950772 | epot = -15.3357195470057 | etot = -14.6424332455024 -761000 ekin = 0.186199747764921 | erot = 0.504639825549507 | epot = -15.3332728188834 | etot = -14.642433245569 -762000 ekin = 0.190149235948631 | erot = 0.494891409035836 | epot = -15.3274738905994 | etot = -14.6424332456149 -763000 ekin = 0.193449921097639 | erot = 0.481710238289171 | epot = -15.3175934050221 | etot = -14.6424332456353 -764000 ekin = 0.19578555242884 | erot = 0.465087294353515 | epot = -15.30330609241 | etot = -14.6424332456277 -765000 ekin = 0.196989678186415 | erot = 0.445303873493914 | epot = -15.284726797273 | etot = -14.6424332455926 -766000 ekin = 0.197055919183636 | erot = 0.422915440293736 | epot = -15.2624046050104 | etot = -14.642433245533 -767000 ekin = 0.196134076493768 | erot = 0.398712320924378 | epot = -15.2372796428716 | etot = -14.6424332454534 -768000 ekin = 0.194513096651584 | erot = 0.373662938959247 | epot = -15.2106092809709 | etot = -14.6424332453601 -769000 ekin = 0.192592017625517 | erot = 0.348845887485673 | epot = -15.1838711503712 | etot = -14.64243324526 -770000 ekin = 0.190840163684011 | erot = 0.325376840211974 | epot = -15.1586502490569 | etot = -14.6424332451609 -771000 ekin = 0.189748397224672 | erot = 0.304335529899268 | epot = -15.1365171721947 | etot = -14.6424332450707 -772000 ekin = 0.189774341847475 | erot = 0.28669715391999 | epot = -15.1189047407645 | etot = -14.642433244997 -773000 ekin = 0.191286034497063 | erot = 0.273271857835071 | epot = -15.1069911372783 | etot = -14.6424332449461 -774000 ekin = 0.194510000604886 | erot = 0.264655458968603 | epot = -15.1015987044967 | etot = -14.6424332449232 -775000 ekin = 0.199490639675254 | erot = 0.261194193154345 | epot = -15.1031180777603 | etot = -14.6424332449307 -776000 ekin = 0.20606747706157 | erot = 0.262965803934196 | epot = -15.1114665259647 | etot = -14.642433244969 -777000 ekin = 0.213875019082022 | erot = 0.269778568411809 | epot = -15.126086832529 | etot = -14.6424332450352 -778000 ekin = 0.222366868961445 | erot = 0.281188790675727 | epot = -15.1459889047611 | etot = -14.6424332451239 -779000 ekin = 0.230862102265721 | erot = 0.296535944175963 | epot = -15.1698312916696 | etot = -14.6424332452279 -780000 ekin = 0.238608567016769 | erot = 0.314993169091884 | epot = -15.1960349814469 | etot = -14.6424332453382 -781000 ekin = 0.244855557739683 | erot = 0.335629445236496 | epot = -15.2229182484219 | etot = -14.6424332454457 -782000 ekin = 0.248927612477182 | erot = 0.357478674286721 | epot = -15.2488395323054 | etot = -14.6424332455415 -783000 ekin = 0.250291897528864 | erot = 0.379610269028215 | epot = -15.2723354121748 | etot = -14.6424332456177 -784000 ekin = 0.248613283253074 | erot = 0.401195731122854 | epot = -15.2922422600443 | etot = -14.6424332456684 -785000 ekin = 0.243793133451241 | erot = 0.421566090466491 | epot = -15.3077924696071 | etot = -14.6424332456894 -786000 ekin = 0.235989501853483 | erot = 0.440255905206823 | epot = -15.3186786527393 | etot = -14.6424332456789 -787000 ekin = 0.225617610785701 | erot = 0.457030673432402 | epot = -15.325081529856 | etot = -14.6424332456379 -788000 ekin = 0.213330260903022 | erot = 0.471895861696016 | epot = -15.3276593681683 | etot = -14.6424332455693 -789000 ekin = 0.199978499678437 | erot = 0.485087183883112 | epot = -15.3274989290403 | etot = -14.6424332454787 -790000 ekin = 0.186553834704387 | erot = 0.497043141242962 | epot = -15.3260302213208 | etot = -14.6424332453735 -791000 ekin = 0.174114766793386 | erot = 0.508362048569917 | epot = -15.3249100606257 | etot = -14.6424332452624 -792000 ekin = 0.16370242043235 | erot = 0.51974673918094 | epot = -15.3258824047686 | etot = -14.6424332451553 -793000 ekin = 0.156252224966279 | erot = 0.531940822989476 | epot = -15.3306262930175 | etot = -14.6424332450617 -794000 ekin = 0.152510350034319 | erot = 0.545660777315051 | epot = -15.3406043723398 | etot = -14.6424332449904 -795000 ekin = 0.152964251156929 | erot = 0.561528326980994 | epot = -15.3569258230863 | etot = -14.6424332449484 -796000 ekin = 0.157795747355314 | erot = 0.580007578777949 | epot = -15.3802365710734 | etot = -14.6424332449401 -797000 ekin = 0.166862457855228 | erot = 0.601351255569557 | epot = -15.4106469583922 | etot = -14.6424332449674 -798000 ekin = 0.179709603428652 | erot = 0.625560121845491 | epot = -15.4477029703033 | etot = -14.6424332450292 -799000 ekin = 0.195609966057178 | erot = 0.652359247176569 | epot = -15.4904024583554 | etot = -14.6424332451217 -800000 ekin = 0.213626158786268 | erot = 0.681194021873679 | epot = -15.5372534258987 | etot = -14.6424332452387 -801000 ekin = 0.2326870401884 | erot = 0.711247726386626 | epot = -15.5863680119477 | etot = -14.6424332453727 -802000 ekin = 0.251669429101128 | erot = 0.741480919836206 | epot = -15.6355835944521 | etot = -14.6424332455148 -803000 ekin = 0.269477067853758 | erot = 0.770691008421269 | epot = -15.6826013219307 | etot = -14.6424332456557 -804000 ekin = 0.285110541453684 | erot = 0.797588259158539 | epot = -15.7251320463986 | etot = -14.6424332457864 -805000 ekin = 0.297723982502899 | erot = 0.8208825287997 | epot = -15.7610397572013 | etot = -14.6424332458987 -806000 ekin = 0.30666638768475 | erot = 0.839373432913578 | epot = -15.7884730665839 | etot = -14.6424332459855 -807000 ekin = 0.311506975554297 | erot = 0.852035914445945 | epot = -15.805976136042 | etot = -14.6424332460417 -808000 ekin = 0.312045176252541 | erot = 0.858093398528272 | epot = -15.8125718208451 | etot = -14.6424332460643 -809000 ekin = 0.308306642387587 | erot = 0.857071970758693 | epot = -15.8078118591987 | etot = -14.6424332460525 -810000 ekin = 0.300527220561047 | erot = 0.848831113928854 | epot = -15.7917915804975 | etot = -14.6424332460076 -811000 ekin = 0.289127204421145 | erot = 0.833569138622277 | epot = -15.7651295889768 | etot = -14.6424332459334 -812000 ekin = 0.274678427602345 | erot = 0.811804116493158 | epot = -15.7289157899301 | etot = -14.6424332458346 -813000 ekin = 0.257866835583845 | erot = 0.784333459542837 | epot = -15.6846335408444 | etot = -14.6424332457177 -814000 ekin = 0.239453080594144 | erot = 0.752176980196583 | epot = -15.6340633063802 | etot = -14.6424332455895 -815000 ekin = 0.220233415151612 | erot = 0.716509170266826 | epot = -15.5791758308755 | etot = -14.642433245457 -816000 ekin = 0.201002751046596 | erot = 0.678586569748228 | epot = -15.5220225661217 | etot = -14.6424332453268 -817000 ekin = 0.182521261080197 | erot = 0.639675603865118 | epot = -15.4646301101502 | etot = -14.6424332452049 -818000 ekin = 0.165485401527799 | erot = 0.600985363831631 | epot = -15.4089040104559 | etot = -14.6424332450965 -819000 ekin = 0.150503789780369 | erot = 0.563608719249515 | epot = -15.3565457540356 | etot = -14.6424332450057 -820000 ekin = 0.138078032178435 | erot = 0.528474068972645 | epot = -15.3089853460867 | etot = -14.6424332449356 -821000 ekin = 0.1285883867301 | erot = 0.496309093118099 | epot = -15.2673307247365 | etot = -14.6424332448883 -822000 ekin = 0.122284066136782 | erot = 0.467617125516122 | epot = -15.2323344365175 | etot = -14.6424332448646 -823000 ekin = 0.119278020924313 | erot = 0.442666228479138 | epot = -15.2043774942681 | etot = -14.6424332448646 -824000 ekin = 0.119546158603652 | erot = 0.421490682739058 | epot = -15.1834700862299 | etot = -14.6424332448872 -825000 ekin = 0.122931110514523 | erot = 0.40390434222418 | epot = -15.1692686976689 | etot = -14.6424332449302 -826000 ekin = 0.129150803764299 | erot = 0.389525075000447 | epot = -15.1611091237554 | etot = -14.6424332449907 -827000 ekin = 0.137812176399144 | erot = 0.377809252270954 | epot = -15.158054673735 | etot = -14.6424332450649 -828000 ekin = 0.14843033160834 | erot = 0.368094906963214 | epot = -15.1589584837195 | etot = -14.6424332451479 -829000 ekin = 0.160453205761645 | erot = 0.359651737512377 | epot = -15.1625381885086 | etot = -14.6424332452346 -830000 ekin = 0.173291382896719 | erot = 0.351735589545628 | epot = -15.1674602177614 | etot = -14.6424332453191 -831000 ekin = 0.186352012962919 | erot = 0.343644456330166 | epot = -15.1724297146887 | etot = -14.6424332453957 -832000 ekin = 0.199074924605406 | erot = 0.334772487921297 | epot = -15.1762806579857 | etot = -14.642433245459 -833000 ekin = 0.210968084880445 | erot = 0.324658115189039 | epot = -15.1780594455739 | etot = -14.6424332455044 -834000 ekin = 0.221638757256876 | erot = 0.31302232344262 | epot = -15.1770943262284 | etot = -14.6424332455289 -835000 ekin = 0.230816330001854 | erot = 0.299793483326917 | epot = -15.1730430588598 | etot = -14.642433245531 -836000 ekin = 0.238363132174117 | erot = 0.285116039961078 | epot = -15.1659124176467 | etot = -14.6424332455115 -837000 ekin = 0.244270841530878 | erot = 0.269341751259836 | epot = -15.1560458382641 | etot = -14.6424332454734 -838000 ekin = 0.248642320235611 | erot = 0.253003904104012 | epot = -15.1440794697608 | etot = -14.6424332454211 -839000 ekin = 0.251661569327577 | erot = 0.236776758987282 | epot = -15.1308715736755 | etot = -14.6424332453606 -840000 ekin = 0.253557306828159 | erot = 0.221424057161585 | epot = -15.1174146092877 | etot = -14.6424332452979 -841000 ekin = 0.254567562696711 | erot = 0.20774147574365 | epot = -15.1047422836789 | etot = -14.6424332452386 -842000 ekin = 0.254912814683647 | erot = 0.196498262354328 | epot = -15.0938443222247 | etot = -14.6424332451867 -843000 ekin = 0.254783130765731 | erot = 0.188382921787082 | epot = -15.0855992976979 | etot = -14.6424332451451 -844000 ekin = 0.254340789697796 | erot = 0.183956927272106 | epot = -15.0807309620845 | etot = -14.6424332451146 -845000 ekin = 0.253734932891626 | erot = 0.183619247980584 | epot = -15.0797874259675 | etot = -14.6424332450953 -846000 ekin = 0.253120504196072 | erot = 0.187583282239813 | epot = -15.0831370315223 | etot = -14.6424332450865 -847000 ekin = 0.252671650088183 | erot = 0.195866742639043 | epot = -15.0909716378151 | etot = -14.6424332450879 -848000 ekin = 0.252580915310197 | erot = 0.208294222463049 | epot = -15.103308382873 | etot = -14.6424332450997 -849000 ekin = 0.253039966848168 | erot = 0.224511555531714 | epot = -15.1199847675025 | etot = -14.6424332451226 -850000 ekin = 0.254204001798429 | erot = 0.244010590097668 | epot = -15.1406478370534 | etot = -14.6424332451573 -851000 ekin = 0.256148339026697 | erot = 0.266162563602488 | epot = -15.1647441478331 | etot = -14.6424332452039 -852000 ekin = 0.258829686440493 | erot = 0.290257858698055 | epot = -15.1915207903997 | etot = -14.6424332452612 -853000 ekin = 0.262064657828486 | erot = 0.315549558167563 | epot = -15.2200474613222 | etot = -14.6424332453261 -854000 ekin = 0.265534116122544 | erot = 0.3412979477362 | epot = -15.2492653092528 | etot = -14.642433245394 -855000 ekin = 0.268815174653471 | erot = 0.366813004430713 | epot = -15.2780614245432 | etot = -14.642433245459 -856000 ekin = 0.271435486954491 | erot = 0.391492007901263 | epot = -15.3053607403707 | etot = -14.6424332455149 -857000 ekin = 0.272939108062895 | erot = 0.414849750473244 | epot = -15.3302221040925 | etot = -14.6424332455563 -858000 ekin = 0.272951155039673 | erot = 0.436539390687867 | epot = -15.3519237913068 | etot = -14.6424332455792 -859000 ekin = 0.271229880676363 | erot = 0.456362750059196 | epot = -15.3700258763173 | etot = -14.6424332455817 -860000 ekin = 0.267698633833807 | erot = 0.474269718460551 | epot = -15.3844015978586 | etot = -14.6424332455643 -861000 ekin = 0.262455001752809 | erot = 0.490347316007701 | epot = -15.3952355632894 | etot = -14.6424332455289 -862000 ekin = 0.255758797176621 | erot = 0.504799761298855 | epot = -15.4029918039549 | etot = -14.6424332454794 -863000 ekin = 0.24800356434136 | erot = 0.517921532812456 | epot = -15.4083583425742 | etot = -14.6424332454204 -864000 ekin = 0.239677655584812 | erot = 0.530065823503365 | epot = -15.4121767244452 | etot = -14.642433245357 -865000 ekin = 0.231320889445349 | erot = 0.541610953534325 | epot = -15.4153650882738 | etot = -14.6424332452942 -866000 ekin = 0.223481813676273 | erot = 0.552927233331992 | epot = -15.4188422922445 | etot = -14.6424332452362 -867000 ekin = 0.216679174491962 | erot = 0.56434649943238 | epot = -15.4234589191111 | etot = -14.6424332451867 -868000 ekin = 0.211369750018252 | erot = 0.576136138938899 | epot = -15.4299391341059 | etot = -14.6424332451488 -869000 ekin = 0.207923502308352 | erot = 0.588478941151549 | epot = -15.438835688584 | etot = -14.6424332451241 -870000 ekin = 0.206606153000488 | erot = 0.601459626890518 | epot = -15.4504990250047 | etot = -14.6424332451137 -871000 ekin = 0.207568796758665 | erot = 0.615058451105769 | epot = -15.4650604929824 | etot = -14.6424332451179 -872000 ekin = 0.210843969902117 | erot = 0.629151875759721 | epot = -15.4824290907979 | etot = -14.642433245136 -873000 ekin = 0.216347593119518 | erot = 0.643519970833803 | epot = -15.50230080912 | etot = -14.6424332451667 -874000 ekin = 0.223886305143568 | erot = 0.657859909730861 | epot = -15.5241794600824 | etot = -14.642433245208 -875000 ekin = 0.233169807553262 | erot = 0.671804662211148 | epot = -15.5474077150218 | etot = -14.6424332452574 -876000 ekin = 0.243827877963711 | erot = 0.684945735800201 | epot = -15.571206859076 | etot = -14.642433245312 -877000 ekin = 0.255431632546027 | erot = 0.696858567354813 | epot = -15.5947234452694 | etot = -14.6424332453685 -878000 ekin = 0.267518408513302 | erot = 0.707128927389039 | epot = -15.6170805813258 | etot = -14.6424332454235 -879000 ekin = 0.279619300259058 | erot = 0.715378495721438 | epot = -15.637431041454 | etot = -14.6424332454735 -880000 ekin = 0.291287955020503 | erot = 0.721287639199418 | epot = -15.6550088397355 | etot = -14.6424332455156 -881000 ekin = 0.302128778464605 | erot = 0.724613422810924 | epot = -15.6691754468228 | etot = -14.6424332455472 -882000 ekin = 0.31182230406878 | erot = 0.725201068177037 | epot = -15.6794566178127 | etot = -14.6424332455669 -883000 ekin = 0.320145243787645 | erot = 0.722987481104317 | epot = -15.6855659704657 | etot = -14.6424332455737 -884000 ekin = 0.326982762198833 | erot = 0.717996120159309 | epot = -15.6874121279266 | etot = -14.6424332455685 -885000 ekin = 0.332330882212394 | erot = 0.710323349672191 | epot = -15.6850874774375 | etot = -14.6424332455529 -886000 ekin = 0.336287673330895 | erot = 0.700117442976369 | epot = -15.6788383618372 | etot = -14.6424332455299 -887000 ekin = 0.339032964151514 | erot = 0.687552454437141 | epot = -15.6690186640918 | etot = -14.6424332455032 -888000 ekin = 0.340797654544245 | erot = 0.672800100945642 | epot = -15.6560310009668 | etot = -14.642433245477 -889000 ekin = 0.341825106158877 | erot = 0.65600340710247 | epot = -15.6402617587168 | etot = -14.6424332454555 -890000 ekin = 0.342328347575086 | erot = 0.637256013166159 | epot = -15.6220176061834 | etot = -14.6424332454421 -891000 ekin = 0.342447730491975 | erot = 0.616590618570723 | epot = -15.6014715945023 | etot = -14.6424332454396 -892000 ekin = 0.342214057411655 | erot = 0.593979026507039 | epot = -15.5786263293678 | etot = -14.6424332454491 -893000 ekin = 0.341522004910065 | erot = 0.569344767734354 | epot = -15.5533000181144 | etot = -14.6424332454699 -894000 ekin = 0.340117934117532 | erot = 0.542587519917411 | epot = -15.5251386995349 | etot = -14.6424332454999 -895000 ekin = 0.337605044782463 | erot = 0.513616778982068 | epot = -15.4936550692998 | etot = -14.6424332455353 -896000 ekin = 0.333467462872296 | erot = 0.482390775175794 | epot = -15.458291483619 | etot = -14.6424332455709 -897000 ekin = 0.327113397522047 | erot = 0.448955709004676 | epot = -15.4185023521276 | etot = -14.6424332456009 -898000 ekin = 0.317936017621463 | erot = 0.413480165460617 | epot = -15.3738494287011 | etot = -14.642433245619 -899000 ekin = 0.305389123797586 | erot = 0.37628007747055 | epot = -15.3241024468869 | etot = -14.6424332456188 -900000 ekin = 0.289072881398034 | erot = 0.337830752319645 | epot = -15.2693368793123 | etot = -14.6424332455946 -901000 ekin = 0.268822686263592 | erot = 0.298764046956938 | epot = -15.2100199787627 | etot = -14.6424332455422 -902000 ekin = 0.24479165397371 | erot = 0.259850521116705 | epot = -15.1470754205494 | etot = -14.642433245459 -903000 ekin = 0.217514571467766 | erot = 0.221968047208425 | epot = -15.0819158640215 | etot = -14.6424332453453 -904000 ekin = 0.187939204416785 | erot = 0.186059692009975 | epot = -15.0164321416314 | etot = -14.6424332452047 -905000 ekin = 0.157410847736408 | erot = 0.153084564880817 | epot = -14.9529286576619 | etot = -14.6424332450446 -906000 ekin = 0.127599356275853 | erot = 0.123965703542096 | epot = -14.8939983046948 | etot = -14.6424332448769 -907000 ekin = 0.100365589134282 | erot = 0.0995389863865378 | epot = -14.8423378202369 | etot = -14.6424332447161 -908000 ekin = 0.077575985596938 | erot = 0.0805066337372383 | epot = -14.8005158639127 | etot = -14.6424332445785 -909000 ekin = 0.0608876950042913 | erot = 0.067398235454302 | epot = -14.770719174938 | etot = -14.6424332444794 -910000 ekin = 0.0515382922982553 | erot = 0.0605415547688289 | epot = -14.7545130914983 | etot = -14.6424332444312 -911000 ekin = 0.0501789452889865 | erot = 0.0600446989609947 | epot = -14.7526568886899 | etot = -14.64243324444 -912000 ekin = 0.0567846925721246 | erot = 0.0657906450220629 | epot = -14.7650085820989 | etot = -14.6424332445047 -913000 ekin = 0.0706603747930615 | erot = 0.0774445361864401 | epot = -14.7905381555972 | etot = -14.6424332446177 -914000 ekin = 0.0905398584091933 | erot = 0.0944735694301048 | epot = -14.8274466726051 | etot = -14.6424332447658 -915000 ekin = 0.114756144628423 | erot = 0.116178630207352 | epot = -14.8733680197685 | etot = -14.6424332449327 -916000 ekin = 0.141447043402261 | erot = 0.141736093138861 | epot = -14.9256163816435 | etot = -14.6424332451024 -917000 ekin = 0.168758535419804 | erot = 0.170247440488293 | epot = -14.9814392211687 | etot = -14.6424332452606 -918000 ekin = 0.195014913439577 | erot = 0.200793639367908 | epot = -15.0382417982038 | etot = -14.6424332453963 -919000 ekin = 0.218837422083594 | erot = 0.232490666335247 | epot = -15.0937613339217 | etot = -14.6424332455029 -920000 ekin = 0.239206641023645 | erot = 0.264542267091037 | epot = -15.1461821536917 | etot = -14.642433245577 -921000 ekin = 0.255474577148561 | erot = 0.296286050801315 | epot = -15.1941938735685 | etot = -14.6424332456186 -922000 ekin = 0.267338631215656 | erot = 0.327229363204391 | epot = -15.2370012400499 | etot = -14.6424332456299 -923000 ekin = 0.274791412214081 | erot = 0.357072039936817 | epot = -15.2742966977655 | etot = -14.6424332456146 -924000 ekin = 0.278059017516243 | erot = 0.385714059432018 | epot = -15.3062063225258 | etot = -14.6424332455775 -925000 ekin = 0.277537405168241 | erot = 0.41324722009486 | epot = -15.3332178707873 | etot = -14.6424332455242 -926000 ekin = 0.273733135238203 | erot = 0.439931173660845 | epot = -15.3560975543592 | etot = -14.6424332454601 -927000 ekin = 0.267211859641411 | erot = 0.46615536388163 | epot = -15.3758004689142 | etot = -14.6424332453911 -928000 ekin = 0.258555847535982 | erot = 0.492389553501975 | epot = -15.3933786463608 | etot = -14.6424332453229 -929000 ekin = 0.248330567891816 | erot = 0.519126582981108 | epot = -15.4098903961335 | etot = -14.6424332452606 -930000 ekin = 0.237059747166114 | erot = 0.546821711631127 | epot = -15.4263147040064 | etot = -14.6424332452091 -931000 ekin = 0.225208144805798 | erot = 0.57583328292282 | epot = -15.4434746729008 | etot = -14.6424332451722 -932000 ekin = 0.213171319365834 | erot = 0.606369490850999 | epot = -15.4619740553695 | etot = -14.6424332451527 -933000 ekin = 0.201271722995926 | erot = 0.638445690378123 | epot = -15.4821506585261 | etot = -14.6424332451521 -934000 ekin = 0.189760460110219 | erot = 0.671856006698404 | epot = -15.5040497119793 | etot = -14.6424332451707 -935000 ekin = 0.178823941838474 | erot = 0.706161996586672 | epot = -15.5274191836322 | etot = -14.6424332452071 -936000 ekin = 0.168594479115077 | erot = 0.740699865836542 | epot = -15.5517275902104 | etot = -14.6424332452587 -937000 ekin = 0.159163635635008 | erot = 0.774606336205393 | epot = -15.5762032171623 | etot = -14.6424332453219 -938000 ekin = 0.150596971915019 | erot = 0.806861786795504 | epot = -15.5998920041024 | etot = -14.6424332453919 -939000 ekin = 0.14294871163255 | erot = 0.836347883525934 | epot = -15.6217298406219 | etot = -14.6424332454634 -940000 ekin = 0.136274889171307 | erot = 0.861915676028113 | epot = -15.6406238107306 | etot = -14.6424332455312 -941000 ekin = 0.130643703199096 | erot = 0.882459199119799 | epot = -15.6555361479089 | etot = -14.64243324559 -942000 ekin = 0.126142088160929 | erot = 0.896989065171445 | epot = -15.6655643989678 | etot = -14.6424332456355 -943000 ekin = 0.122877886110413 | erot = 0.904700444358206 | epot = -15.6700115761326 | etot = -14.642433245664 -944000 ekin = 0.120977407412306 | erot = 0.905030230236292 | epot = -15.6684408833221 | etot = -14.6424332456735 -945000 ekin = 0.120578563690912 | erot = 0.897699054745102 | epot = -15.6607108640992 | etot = -14.6424332456632 -946000 ekin = 0.121820103593719 | erot = 0.882735070927983 | epot = -15.6469884201554 | etot = -14.6424332456337 -947000 ekin = 0.124827761129314 | erot = 0.860477935595928 | epot = -15.6277389423123 | etot = -14.6424332455871 -948000 ekin = 0.129698334168894 | erot = 0.831563037037535 | epot = -15.6036946167333 | etot = -14.6424332455268 -949000 ekin = 0.136482857558376 | erot = 0.796887554721867 | epot = -15.5758036577374 | etot = -14.6424332454571 -950000 ekin = 0.145170138931399 | erot = 0.757561255988068 | epot = -15.5451646403023 | etot = -14.6424332453828 -951000 ekin = 0.155672002995351 | erot = 0.714845916093614 | epot = -15.512951164398 | etot = -14.642433245309 -952000 ekin = 0.167811650836438 | erot = 0.670087833250183 | epot = -15.4803327293273 | etot = -14.6424332452407 -953000 ekin = 0.181316579471426 | erot = 0.624648095211963 | epot = -15.4483979198658 | etot = -14.6424332451824 -954000 ekin = 0.195817500701304 | erot = 0.579835080695791 | epot = -15.4180858265346 | etot = -14.6424332451375 -955000 ekin = 0.210854606876787 | erot = 0.536843219768805 | epot = -15.390131071754 | etot = -14.6424332451084 -956000 ekin = 0.225892299837379 | erot = 0.496701376791544 | epot = -15.3650269217251 | etot = -14.6424332450962 -957000 ekin = 0.240343066498589 | erot = 0.460233438093954 | epot = -15.3430097496929 | etot = -14.6424332451004 -958000 ekin = 0.25360049383932 | erot = 0.428032849894234 | epot = -15.3240665888525 | etot = -14.6424332451189 -959000 ekin = 0.265080433748221 | erot = 0.400452005459141 | epot = -15.3079656843558 | etot = -14.6424332451485 -960000 ekin = 0.274268068130506 | erot = 0.37760654944986 | epot = -15.294307862765 | etot = -14.6424332451846 -961000 ekin = 0.280767178003527 | erot = 0.359393861249854 | epot = -15.2825942844756 | etot = -14.6424332452222 -962000 ekin = 0.284346484063387 | erot = 0.345524198816839 | epot = -15.2723039281363 | etot = -14.6424332452561 -963000 ekin = 0.284976816089799 | erot = 0.335562232329375 | epot = -15.2629722937007 | etot = -14.6424332452816 -964000 ekin = 0.282852494247959 | erot = 0.328975986497034 | epot = -15.2542617260401 | etot = -14.6424332452952 -965000 ekin = 0.278391086615529 | erot = 0.325189577598941 | epot = -15.2460139095095 | etot = -14.6424332452951 -966000 ekin = 0.272207924679531 | erot = 0.323635640150906 | epot = -15.2382768101118 | etot = -14.6424332452814 -967000 ekin = 0.265065367870656 | erot = 0.323803079987486 | epot = -15.2313016931143 | etot = -14.6424332452561 -968000 ekin = 0.257801293713953 | erot = 0.325275872290767 | epot = -15.2255104112278 | etot = -14.6424332452231 -969000 ekin = 0.251245661474204 | erot = 0.327759142576171 | epot = -15.2214380492373 | etot = -14.642433245187 -970000 ekin = 0.246137008993053 | erot = 0.331089781181015 | epot = -15.2196600353269 | etot = -14.6424332451528 -971000 ekin = 0.243051319616002 | erot = 0.335230325665042 | epot = -15.2207148904062 | etot = -14.6424332451251 -972000 ekin = 0.242353409638639 | erot = 0.340246678804514 | epot = -15.2250333335506 | etot = -14.6424332451075 -973000 ekin = 0.244176338162395 | erot = 0.34627219071044 | epot = -15.2328817739751 | etot = -14.6424332451022 -974000 ekin = 0.248428661657912 | erot = 0.353462430361481 | epot = -15.24432433713 | etot = -14.6424332451106 -975000 ekin = 0.254824314802904 | erot = 0.361946299430119 | epot = -15.2592038593657 | etot = -14.6424332451327 -976000 ekin = 0.262926848820355 | erot = 0.371779749929349 | epot = -15.2771398439173 | etot = -14.6424332451676 -977000 ekin = 0.272199235330701 | erot = 0.38290812326356 | epot = -15.2975406038081 | etot = -14.6424332452139 -978000 ekin = 0.282052066851546 | erot = 0.395142048096898 | epot = -15.3196273602178 | etot = -14.6424332452693 -979000 ekin = 0.291885751913825 | erot = 0.408150081470842 | epot = -15.3424690787159 | etot = -14.6424332453312 -980000 ekin = 0.301125083789806 | erot = 0.421469125222054 | epot = -15.365027454408 | etot = -14.6424332453961 -981000 ekin = 0.309246535917258 | erot = 0.434531423655728 | epot = -15.3862112050331 | etot = -14.6424332454601 -982000 ekin = 0.315799497490744 | erot = 0.446704965615888 | epot = -15.4049377086259 | etot = -14.6424332455192 -983000 ekin = 0.320422573221004 | erot = 0.457342632742922 | epot = -15.4201984515333 | etot = -14.6424332455694 -984000 ekin = 0.322855465258447 | erot = 0.465834622598312 | epot = -15.4311233334637 | etot = -14.6424332456069 -985000 ekin = 0.322946302475138 | erot = 0.471658590972897 | epot = -15.437038139077 | etot = -14.642433245629 -986000 ekin = 0.320653917805709 | erot = 0.474422556589351 | epot = -15.437509720029 | etot = -14.6424332456339 -987000 ekin = 0.316044627362148 | erot = 0.47389675551445 | epot = -15.4323746284979 | etot = -14.6424332456213 -988000 ekin = 0.309283477268748 | erot = 0.470032116944019 | epot = -15.4217488398044 | etot = -14.6424332455917 -989000 ekin = 0.30062052216921 | erot = 0.462964620620772 | epot = -15.406018388337 | etot = -14.642433245547 -990000 ekin = 0.290373280691244 | erot = 0.45300626299374 | epot = -15.3858127891748 | etot = -14.6424332454898 -991000 ekin = 0.278906915705727 | erot = 0.440624526218079 | epot = -15.3619646873473 | etot = -14.6424332454235 -992000 ekin = 0.266613826415212 | erot = 0.426413006890097 | epot = -15.3354600786568 | etot = -14.6424332453515 -993000 ekin = 0.253894212446597 | erot = 0.411056197523472 | epot = -15.3073836552474 | etot = -14.6424332452773 -994000 ekin = 0.241138837000143 | erot = 0.395291372387429 | epot = -15.2788634545919 | etot = -14.6424332452043 -995000 ekin = 0.228714768906998 | erot = 0.379870207854295 | epot = -15.2510182218967 | etot = -14.6424332451354 -996000 ekin = 0.216954417470394 | erot = 0.365522282706593 | epot = -15.2249099452501 | etot = -14.6424332450731 -997000 ekin = 0.20614776645599 | erot = 0.35292206613789 | epot = -15.2015030776133 | etot = -14.6424332450194 -998000 ekin = 0.196537413157798 | erot = 0.342660495990661 | epot = -15.1816311541244 | etot = -14.6424332449759 -999000 ekin = 0.188315843913 | erot = 0.335221830005141 | epot = -15.1659709188617 | etot = -14.6424332449435 -1000000 ekin = 0.181624323067651 | erot = 0.330966139648843 | epot = -15.1550237076396 | etot = -14.6424332449231 - 1000000 0.013453654 -1.5270261 0.011523695 -1.4973399 -0.00016850969 -Loop time of 18.8945 on 4 procs for 1000000 steps with 10 atoms - -Performance: 45727.664 tau/day, 52925.537 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.58931 | 7.2806 | 13.001 | 192.7 | 38.53 -Bond | 0.08158 | 0.3024 | 0.49236 | 29.7 | 1.60 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.6616 | 1.8619 | 2.1581 | 13.8 | 9.85 -Output | 2.2173e-05 | 2.4319e-05 | 2.5034e-05 | 0.0 | 0.00 -Modify | 0.20928 | 0.94821 | 1.6085 | 58.7 | 5.02 -Other | | 8.501 | | | 44.99 - -Nlocal: 2.5 ave 5 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10 max 5 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 17.5 ave 33 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 70 -Ave neighs/atom = 7 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:18 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 new file mode 100644 index 0000000000..abbd917f05 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.1 @@ -0,0 +1,172 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.859 | 2.859 | 2.859 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05 +1000 ekin = 0.00113448721737003 | erot = 0.00413455947734281 | epot = -14.6477022915193 | etot = -14.6424332448246 +2000 ekin = 0.00449927223902336 | erot = 0.0164446434455805 | epot = -14.6633771605337 | etot = -14.6424332448491 +3000 ekin = 0.00997964450841065 | erot = 0.0366523356056461 | epot = -14.6890652250033 | etot = -14.6424332448892 +4000 ekin = 0.0173888111295073 | erot = 0.0643039804300221 | epot = -14.7241260365031 | etot = -14.6424332449436 +5000 ekin = 0.0264744514136619 | erot = 0.0987844033142066 | epot = -14.7676920997383 | etot = -14.6424332450104 +6000 ekin = 0.0369277948556079 | erot = 0.139336571052565 | epot = -14.8186976109956 | etot = -14.6424332450875 +7000 ekin = 0.04839505571915 | erot = 0.18508629569208 | epot = -14.8759145965832 | etot = -14.642433245172 +8000 ekin = 0.0604909336920643 | erot = 0.23507130752353 | epot = -14.9379954864767 | etot = -14.6424332452611 +9000 ekin = 0.0728137406440561 | erot = 0.288273694501537 | epot = -15.003520680497 | etot = -14.6424332453514 +10000 ekin = 0.0849615563085879 | erot = 0.343654369293472 | epot = -15.0710491710418 | etot = -14.6424332454398 + 10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -9.9021593e-05 +Loop time of 0.141929 on 1 procs for 10000 steps with 10 atoms + +Performance: 60875.649 tau/day, 70457.927 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11467 | 0.11467 | 0.11467 | 0.0 | 80.79 +Bond | 0.0050094 | 0.0050094 | 0.0050094 | 0.0 | 3.53 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0013616 | 0.0013616 | 0.0013616 | 0.0 | 0.96 +Output | 4.0531e-06 | 4.0531e-06 | 4.0531e-06 | 0.0 | 0.00 +Modify | 0.017901 | 0.017901 | 0.017901 | 0.0 | 12.61 +Other | | 0.002982 | | | 2.10 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 43 ave 43 max 43 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43 +Ave neighs/atom = 4.3 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 new file mode 100644 index 0000000000..78712bf913 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex1/log.27Nov18.duplex1.g++.4 @@ -0,0 +1,172 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.341 | 7.523 | 7.705 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4711818 0.0069384985 -1.4642433 -6.2745089e-05 +1000 ekin = 0.00113448721737009 | erot = 0.0041345594773427 | epot = -14.6477022915193 | etot = -14.6424332448246 +2000 ekin = 0.00449927223902292 | erot = 0.0164446434455803 | epot = -14.6633771605337 | etot = -14.6424332448491 +3000 ekin = 0.00997964450840756 | erot = 0.0366523356056465 | epot = -14.6890652250033 | etot = -14.6424332448892 +4000 ekin = 0.017388811129498 | erot = 0.0643039804300254 | epot = -14.7241260365031 | etot = -14.6424332449436 +5000 ekin = 0.0264744514136422 | erot = 0.098784403314214 | epot = -14.7676920997383 | etot = -14.6424332450104 +6000 ekin = 0.0369277948555727 | erot = 0.139336571052581 | epot = -14.8186976109956 | etot = -14.6424332450875 +7000 ekin = 0.0483950557190949 | erot = 0.185086295692111 | epot = -14.8759145965832 | etot = -14.642433245172 +8000 ekin = 0.0604909336919856 | erot = 0.235071307523583 | epot = -14.9379954864767 | etot = -14.6424332452611 +9000 ekin = 0.0728137406439517 | erot = 0.288273694501617 | epot = -15.003520680497 | etot = -14.6424332453514 +10000 ekin = 0.0849615563084573 | erot = 0.34365436929359 | epot = -15.0710491710418 | etot = -14.6424332454398 + 10000 0.0062934486 -1.5138305 0.0067255788 -1.4986088 -0.00010196899 +Loop time of 0.134536 on 4 procs for 10000 steps with 10 atoms + +Performance: 64220.659 tau/day, 74329.466 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0030077 | 0.052212 | 0.093066 | 17.4 | 38.81 +Bond | 0.00061846 | 0.00234 | 0.0039451 | 2.8 | 1.74 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013431 | 0.014091 | 0.014596 | 0.4 | 10.47 +Output | 5.0783e-05 | 5.1141e-05 | 5.1498e-05 | 0.0 | 0.04 +Modify | 0.0011578 | 0.0059478 | 0.010331 | 4.8 | 4.42 +Other | | 0.05989 | | | 44.52 + +Nlocal: 2.5 ave 5 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 7.5 ave 10 max 5 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 17.5 ave 33 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 70 +Ave neighs/atom = 7 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2 b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2 rename to examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 index dd14c3ae11..a5a09af9f4 100644 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/input.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/in.duplex2 @@ -72,6 +72,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 1000000 +run 10000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1 deleted file mode 100644 index f59e6bd016..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.1 +++ /dev/null @@ -1,1161 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05 -1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287 -2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165 -3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165 -4000 ekin = 2.04461800191989 | erot = 1.49015219763161 | epot = -24.2959428773347 | etot = -20.7611726777832 -5000 ekin = 1.76794859210155 | erot = 2.54289684465819 | epot = -24.2337587736863 | etot = -19.9229133369266 -6000 ekin = 3.1106424806079 | erot = 2.04409805200893 | epot = -24.1585729744133 | etot = -19.0038324417964 -7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107 -8000 ekin = 2.82489935901743 | erot = 2.66790555575695 | epot = -24.0194805097633 | etot = -18.526675594989 -9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972 -10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334 -11000 ekin = 2.33860420545645 | erot = 2.067780391377 | epot = -23.6589739475584 | etot = -19.2525893507249 -12000 ekin = 2.71377849618258 | erot = 2.08757199120023 | epot = -23.5483571834756 | etot = -18.7470066960928 -13000 ekin = 2.62930153930326 | erot = 2.36926332727578 | epot = -23.4509629615768 | etot = -18.4523980949977 -14000 ekin = 3.08200416316113 | erot = 2.52340746291244 | epot = -23.3378147651053 | etot = -17.7324031390317 -15000 ekin = 2.98008664779269 | erot = 1.871644860882 | epot = -23.1940665570191 | etot = -18.3423350483444 -16000 ekin = 2.18422481774796 | erot = 2.13029325858584 | epot = -23.0709946755646 | etot = -18.7564765992308 -17000 ekin = 1.86029951221073 | erot = 2.30856215831156 | epot = -22.9148241979648 | etot = -18.7459625274425 -18000 ekin = 2.26757205264074 | erot = 1.23282183419698 | epot = -22.7667657090377 | etot = -19.2663718222 -19000 ekin = 2.39717301992408 | erot = 2.43814713185077 | epot = -22.6249045514987 | etot = -17.7895843997239 -20000 ekin = 2.4972090427325 | erot = 2.14695469209109 | epot = -22.4687873897505 | etot = -17.824623654927 -21000 ekin = 2.97591775854817 | erot = 2.40996811711195 | epot = -22.580475447988 | etot = -17.1945895723278 -22000 ekin = 3.04727168578733 | erot = 1.83825256427932 | epot = -22.6695853833015 | etot = -17.7840611332348 -23000 ekin = 2.64835731773193 | erot = 2.22162785501705 | epot = -22.6565689169972 | etot = -17.7865837442483 -24000 ekin = 2.64866576787001 | erot = 2.80157082833922 | epot = -22.6222797420052 | etot = -17.172043145796 -25000 ekin = 2.29527970143855 | erot = 2.22049811939069 | epot = -22.6228421013006 | etot = -18.1070642804714 -26000 ekin = 1.6242512251805 | erot = 2.52390475262917 | epot = -22.6746055892862 | etot = -18.5264496114765 -27000 ekin = 1.74746467550781 | erot = 3.7138606202505 | epot = -22.7150312690973 | etot = -17.253705973339 -28000 ekin = 2.26500128280479 | erot = 2.34791343563183 | epot = -22.7926648585827 | etot = -18.179750140146 -29000 ekin = 2.04774074424512 | erot = 1.86347261547111 | epot = -22.8081204933408 | etot = -18.8969071336246 -30000 ekin = 2.41140146125466 | erot = 1.86296915421469 | epot = -22.7764612164305 | etot = -18.5020906009612 -31000 ekin = 2.76447800297261 | erot = 2.7393253404681 | epot = -22.7808698156252 | etot = -17.2770664721845 -32000 ekin = 2.08103539953574 | erot = 2.81216171106146 | epot = -22.8081908465747 | etot = -17.9149937359775 -33000 ekin = 2.08672340074227 | erot = 3.65510023442519 | epot = -22.7575363468642 | etot = -17.0157127116967 -34000 ekin = 2.34180742039869 | erot = 3.10027175201874 | epot = -22.6657421559553 | etot = -17.2236629835378 -35000 ekin = 2.32430602395272 | erot = 2.01607522370048 | epot = -22.5813705492547 | etot = -18.2409893016015 -36000 ekin = 1.91917507775106 | erot = 1.97289747304336 | epot = -22.481118994336 | etot = -18.5890464435416 -37000 ekin = 1.57560528527468 | erot = 2.63029511887642 | epot = -22.4456699464305 | etot = -18.2397695422794 -38000 ekin = 2.20652731867584 | erot = 2.89671984141264 | epot = -22.3965902387972 | etot = -17.2933430787087 -39000 ekin = 2.54765822667968 | erot = 2.47352619735437 | epot = -22.3525131983352 | etot = -17.3313287743012 -40000 ekin = 2.24172560748699 | erot = 1.87314319107769 | epot = -22.3791956830638 | etot = -18.2643268844991 -41000 ekin = 2.45176361826215 | erot = 2.49992612251747 | epot = -22.4441192111887 | etot = -17.492429470409 -42000 ekin = 2.68254780786499 | erot = 2.04382131696989 | epot = -22.4352265851614 | etot = -17.7088574603266 -43000 ekin = 2.39383336858508 | erot = 1.66587291396325 | epot = -22.4337243898148 | etot = -18.3740181072664 -44000 ekin = 2.30758870966958 | erot = 2.39381816537748 | epot = -22.4636201484766 | etot = -17.7622132734295 -45000 ekin = 1.84308929771583 | erot = 2.25880380151546 | epot = -22.5697712917435 | etot = -18.4678781925122 -46000 ekin = 1.98608215049724 | erot = 3.02136983211363 | epot = -22.5606085774834 | etot = -17.5531565948725 -47000 ekin = 1.31457586857024 | erot = 1.99780932836913 | epot = -22.5522289127255 | etot = -19.2398437157862 -48000 ekin = 2.59855199680394 | erot = 1.90772345027383 | epot = -22.5972680906756 | etot = -18.0909926435978 -49000 ekin = 2.32140483916261 | erot = 2.72932938830521 | epot = -22.6070371995253 | etot = -17.5563029720575 -50000 ekin = 2.48248035385828 | erot = 3.42713570109107 | epot = -22.5294064222472 | etot = -16.6197903672979 -51000 ekin = 2.73677705777971 | erot = 1.43285265191038 | epot = -22.4272695862992 | etot = -18.2576398766091 -52000 ekin = 3.03746109762767 | erot = 1.97878223690383 | epot = -22.4105817052324 | etot = -17.3943383707009 -53000 ekin = 2.4689045601064 | erot = 4.26434186327668 | epot = -22.4059567857723 | etot = -15.6727103623892 -54000 ekin = 2.48025904071626 | erot = 2.36957879662632 | epot = -22.4049729842648 | etot = -17.5551351469222 -55000 ekin = 2.28269445417385 | erot = 1.92149293107792 | epot = -22.4643082993723 | etot = -18.2601209141205 -56000 ekin = 2.36225428889468 | erot = 2.21818002425493 | epot = -22.5516502452859 | etot = -17.9712159321363 -57000 ekin = 2.5222034650231 | erot = 2.87044520913643 | epot = -22.6517599833465 | etot = -17.259111309187 -58000 ekin = 2.50677816066749 | erot = 2.80087142998998 | epot = -22.7046490897181 | etot = -17.3969994990606 -59000 ekin = 2.7442153349817 | erot = 2.17375311266844 | epot = -22.7630968852437 | etot = -17.8451284375935 -60000 ekin = 3.28881699963202 | erot = 1.98491245229834 | epot = -22.7493813857704 | etot = -17.47565193384 -61000 ekin = 2.42749732003947 | erot = 1.80500042748845 | epot = -22.6954080097403 | etot = -18.4629102622124 -62000 ekin = 2.82051548232979 | erot = 1.69220614985812 | epot = -22.5840860651657 | etot = -18.0713644329778 -63000 ekin = 3.66818847100113 | erot = 1.91510536540651 | epot = -22.4235299160084 | etot = -16.8402360796008 -64000 ekin = 3.60192162647095 | erot = 3.02302140162941 | epot = -22.4028966408394 | etot = -15.777953612739 -65000 ekin = 3.37797300912952 | erot = 3.90646944425564 | epot = -22.3508227873685 | etot = -15.0663803339833 -66000 ekin = 2.90796062513305 | erot = 2.46538835419998 | epot = -22.2656130116827 | etot = -16.8922640323497 -67000 ekin = 2.57641483706472 | erot = 2.1063925708314 | epot = -22.1586423836372 | etot = -17.4758349757411 -68000 ekin = 2.5516902727465 | erot = 2.46870040285813 | epot = -22.1454741588102 | etot = -17.1250834832056 -69000 ekin = 2.42897294997603 | erot = 2.86774435615082 | epot = -22.1788582092806 | etot = -16.8821409031537 -70000 ekin = 3.08406596014674 | erot = 2.51171720098584 | epot = -22.2680651617951 | etot = -16.6722820006626 -71000 ekin = 2.55052721315253 | erot = 2.49486492124423 | epot = -22.3940848075589 | etot = -17.3486926731621 -72000 ekin = 1.77666138705941 | erot = 2.52301579845699 | epot = -22.4956655989824 | etot = -18.195988413466 -73000 ekin = 1.86857924146303 | erot = 2.33110810852355 | epot = -22.5401005215029 | etot = -18.3404131715163 -74000 ekin = 3.14875320805144 | erot = 2.12002807961601 | epot = -22.5354282257998 | etot = -17.2666469381323 -75000 ekin = 2.60566180511119 | erot = 2.16421143606062 | epot = -22.5109742574449 | etot = -17.7411010162731 -76000 ekin = 1.94500512300058 | erot = 1.94681992806367 | epot = -22.5134561384461 | etot = -18.6216310873819 -77000 ekin = 2.09005510206219 | erot = 2.13354294429721 | epot = -22.5157248384152 | etot = -18.2921267920558 -78000 ekin = 2.48381695181472 | erot = 2.49598603867482 | epot = -22.449809286019 | etot = -17.4700062955295 -79000 ekin = 3.09582217320064 | erot = 2.46630074007712 | epot = -22.3464652405845 | etot = -16.7843423273068 -80000 ekin = 2.51380629427529 | erot = 1.89207626467031 | epot = -22.2775752521275 | etot = -17.8716926931819 -81000 ekin = 2.32322780911516 | erot = 2.24954513249787 | epot = -22.2655235360186 | etot = -17.6927505944055 -82000 ekin = 1.54779729878415 | erot = 2.01487148845307 | epot = -22.2126473128098 | etot = -18.6499785255726 -83000 ekin = 2.24267653112482 | erot = 3.34721522119025 | epot = -22.2063282117648 | etot = -16.6164364594498 -84000 ekin = 2.86948852339533 | erot = 2.11915315181827 | epot = -22.2055386975617 | etot = -17.2168970223481 -85000 ekin = 3.13802387827786 | erot = 2.93900498543376 | epot = -22.2240733080824 | etot = -16.1470444443708 -86000 ekin = 3.46160079449538 | erot = 2.80798287444336 | epot = -22.2732645073155 | etot = -16.0036808383767 -87000 ekin = 3.63139446909085 | erot = 2.3166794204513 | epot = -22.2567856660101 | etot = -16.308711776468 -88000 ekin = 3.15348314879937 | erot = 2.2785763709033 | epot = -22.2154422326699 | etot = -16.7833827129672 -89000 ekin = 3.30271147105659 | erot = 1.80791256125564 | epot = -22.1564153597823 | etot = -17.04579132747 -90000 ekin = 2.42655906518194 | erot = 2.24507038389518 | epot = -21.9481188512569 | etot = -17.2764894021798 -91000 ekin = 1.89051217909395 | erot = 2.51049066719493 | epot = -21.7877769537306 | etot = -17.3867741074417 -92000 ekin = 2.07833668466679 | erot = 2.218324246302 | epot = -21.6997103074282 | etot = -17.4030493764594 -93000 ekin = 1.94321435585196 | erot = 2.99473985773914 | epot = -21.6748650469777 | etot = -16.7369108333866 -94000 ekin = 2.07878576812463 | erot = 3.37631892101902 | epot = -21.7659932416399 | etot = -16.3108885524963 -95000 ekin = 2.10517721407769 | erot = 2.08345895044788 | epot = -21.8951718799354 | etot = -17.7065357154098 -96000 ekin = 2.68821593238919 | erot = 1.86988637992409 | epot = -21.9622848400866 | etot = -17.4041825277733 -97000 ekin = 1.95061152706206 | erot = 2.81054215683073 | epot = -22.0229813258884 | etot = -17.2618276419957 -98000 ekin = 1.98463063611221 | erot = 2.05732763357977 | epot = -22.0930102039112 | etot = -18.0510519342192 -99000 ekin = 2.51292852217217 | erot = 3.54194472638845 | epot = -22.199088757298 | etot = -16.1442155087374 -100000 ekin = 1.8757570387949 | erot = 2.3690785580876 | epot = -22.348409587438 | etot = -18.1035739905555 -101000 ekin = 1.66160772204006 | erot = 3.59766032223856 | epot = -22.3604908173889 | etot = -17.1012227731103 -102000 ekin = 1.62075182718474 | erot = 3.3442006848817 | epot = -22.3063629504087 | etot = -17.3414104383422 -103000 ekin = 2.00871148652538 | erot = 2.33677124900284 | epot = -22.275557852692 | etot = -17.9300751171637 -104000 ekin = 2.04513709976292 | erot = 2.74664593650967 | epot = -22.2818713634637 | etot = -17.4900883271911 -105000 ekin = 1.87027868596139 | erot = 1.98922389218239 | epot = -22.223503909299 | etot = -18.3640013311552 -106000 ekin = 1.71540784443942 | erot = 1.9177953110688 | epot = -22.2562839843324 | etot = -18.6230808288242 -107000 ekin = 2.61024905591622 | erot = 1.57446439985464 | epot = -22.3171357124015 | etot = -18.1324222566306 -108000 ekin = 2.13751756724178 | erot = 2.18822458113098 | epot = -22.2268794585969 | etot = -17.9011373102241 -109000 ekin = 2.24408198608307 | erot = 2.11438299352724 | epot = -22.076564108576 | etot = -17.7180991289657 -110000 ekin = 1.66706562020821 | erot = 2.50986066169373 | epot = -22.0833343008135 | etot = -17.9064080189116 -111000 ekin = 2.30463895640872 | erot = 2.24982560856989 | epot = -22.0940837732696 | etot = -17.539619208291 -112000 ekin = 2.63019524472749 | erot = 2.43696110420532 | epot = -22.0953344558745 | etot = -17.0281781069417 -113000 ekin = 2.42282638113981 | erot = 3.06190927482913 | epot = -22.1061661458173 | etot = -16.6214304898484 -114000 ekin = 2.34214572325658 | erot = 2.31899235523686 | epot = -22.0941430549288 | etot = -17.4330049764353 -115000 ekin = 1.70336449422736 | erot = 3.10166879044198 | epot = -22.1252095896431 | etot = -17.3201763049738 -116000 ekin = 1.51705870113214 | erot = 2.21425252709695 | epot = -22.1823772627204 | etot = -18.4510660344913 -117000 ekin = 1.70129809180508 | erot = 2.34142425076372 | epot = -22.2067668262467 | etot = -18.1640444836779 -118000 ekin = 2.20482827236051 | erot = 2.3179714809504 | epot = -22.1855414590757 | etot = -17.6627417057647 -119000 ekin = 2.54272629601484 | erot = 2.46528921750297 | epot = -22.2113175246519 | etot = -17.2033020111341 -120000 ekin = 1.76640390552554 | erot = 2.16116304616032 | epot = -22.1536331723646 | etot = -18.2260662206787 -121000 ekin = 2.81281157959688 | erot = 2.31761005518346 | epot = -22.1492969323239 | etot = -17.0188752975435 -122000 ekin = 3.25156823587966 | erot = 3.31679050874322 | epot = -22.2050361016166 | etot = -15.6366773569938 -123000 ekin = 2.87462309654081 | erot = 3.25604816714397 | epot = -22.1785374359393 | etot = -16.0478661722546 -124000 ekin = 2.18213410260632 | erot = 2.77182209342785 | epot = -22.0161464482698 | etot = -17.0621902522356 -125000 ekin = 1.85317252616068 | erot = 1.36623599567638 | epot = -21.8721650279344 | etot = -18.6527565060973 -126000 ekin = 2.47747071965844 | erot = 3.09909384826334 | epot = -21.8840309142636 | etot = -16.3074663463419 -127000 ekin = 2.42177426273027 | erot = 2.35209644429656 | epot = -21.8861939604609 | etot = -17.1123232534341 -128000 ekin = 2.76000040231245 | erot = 1.8231678837239 | epot = -21.8538456680958 | etot = -17.2706773820595 -129000 ekin = 2.78355536315491 | erot = 2.88851981621501 | epot = -21.9251039267855 | etot = -16.2530287474156 -130000 ekin = 3.26834278926799 | erot = 2.56228354573336 | epot = -22.0546105678549 | etot = -16.2239842328536 -131000 ekin = 2.64714688907849 | erot = 2.51107513446137 | epot = -22.0961160192681 | etot = -16.9378939957282 -132000 ekin = 2.61847248883524 | erot = 3.38899164334156 | epot = -22.1218916777659 | etot = -16.1144275455891 -133000 ekin = 2.03408861514006 | erot = 2.87401070790187 | epot = -22.0785989417621 | etot = -17.1704996187202 -134000 ekin = 1.64140897264888 | erot = 1.66986416585675 | epot = -22.0323643102285 | etot = -18.7210911717228 -135000 ekin = 2.46650096367446 | erot = 2.111120611107 | epot = -21.9976572593399 | etot = -17.4200356845585 -136000 ekin = 2.32880805911731 | erot = 3.05940125193231 | epot = -21.8983392007847 | etot = -16.5101298897351 -137000 ekin = 2.7601019905106 | erot = 2.47443779429795 | epot = -21.752125264204 | etot = -16.5175854793954 -138000 ekin = 3.30162084678948 | erot = 1.73084735415554 | epot = -21.7423849642075 | etot = -16.7099167632625 -139000 ekin = 2.76669064053124 | erot = 1.72642745910431 | epot = -21.8898577306654 | etot = -17.3967396310298 -140000 ekin = 2.73595287215366 | erot = 2.46891829250481 | epot = -21.9884857831833 | etot = -16.7836146185249 -141000 ekin = 2.79316289615844 | erot = 2.46753088695597 | epot = -22.0064855648443 | etot = -16.7457917817299 -142000 ekin = 3.51694745558129 | erot = 3.49862438784827 | epot = -21.9623193335451 | etot = -14.9467474901156 -143000 ekin = 2.58689934548697 | erot = 2.04008576044027 | epot = -21.9563338194557 | etot = -17.3293487135285 -144000 ekin = 3.72611917000993 | erot = 3.04855733322793 | epot = -21.9536376487796 | etot = -15.1789611455417 -145000 ekin = 3.61191106831147 | erot = 2.71915407989904 | epot = -21.870542665333 | etot = -15.5394775171225 -146000 ekin = 3.85060594912677 | erot = 2.47210219931339 | epot = -21.8285858153921 | etot = -15.505877666952 -147000 ekin = 3.26481933196161 | erot = 2.06864347299802 | epot = -21.6752809049183 | etot = -16.3418180999587 -148000 ekin = 2.47977997895053 | erot = 1.65169267241014 | epot = -21.4172781734276 | etot = -17.2858055220669 -149000 ekin = 2.70771685463074 | erot = 2.28028425953227 | epot = -21.2324293178539 | etot = -16.2444282036909 -150000 ekin = 2.60726181496431 | erot = 2.88955230103659 | epot = -21.126549406853 | etot = -15.6297352908521 -151000 ekin = 2.06865005733849 | erot = 2.13537039813292 | epot = -21.0304193709383 | etot = -16.8263989154669 -152000 ekin = 2.41210154812787 | erot = 2.60104053370075 | epot = -20.8967777045302 | etot = -15.8836356227016 -153000 ekin = 2.12406231442824 | erot = 2.25444655142795 | epot = -20.9199278716094 | etot = -16.5414190057532 -154000 ekin = 2.34622678455546 | erot = 2.58439374093403 | epot = -21.0040588663533 | etot = -16.0734383408638 -155000 ekin = 2.08240965570452 | erot = 3.02621505767145 | epot = -21.0204738431416 | etot = -15.9118491297656 -156000 ekin = 2.04576145796301 | erot = 3.17151405834467 | epot = -20.8558463949479 | etot = -15.6385708786402 -157000 ekin = 2.36459548410747 | erot = 1.89207417055424 | epot = -20.8025485082277 | etot = -16.545878853566 -158000 ekin = 2.16996178916575 | erot = 2.46547727482113 | epot = -20.8673070433024 | etot = -16.2318679793155 -159000 ekin = 2.86272730849306 | erot = 2.27590841865057 | epot = -20.9710387207245 | etot = -15.8324029935809 -160000 ekin = 2.19288173853782 | erot = 2.36312829884111 | epot = -21.0403123366075 | etot = -16.4843022992286 -161000 ekin = 2.14059248149909 | erot = 2.4287283799048 | epot = -21.1333683100403 | etot = -16.5640474486365 -162000 ekin = 1.76077466564934 | erot = 2.66561836368342 | epot = -21.1782130850259 | etot = -16.7518200556931 -163000 ekin = 2.23068698955417 | erot = 2.02664945757243 | epot = -21.3281780197228 | etot = -17.0708415725963 -164000 ekin = 2.75358320318999 | erot = 1.43717365990088 | epot = -21.4675480212853 | etot = -17.2767911581945 -165000 ekin = 2.65171600986478 | erot = 2.29632253260765 | epot = -21.493178025826 | etot = -16.5451394833536 -166000 ekin = 3.27298673277591 | erot = 2.41252396730596 | epot = -21.4477711984927 | etot = -15.7622604984108 -167000 ekin = 3.02574105268454 | erot = 2.02770436019795 | epot = -21.5236773217566 | etot = -16.4702319088741 -168000 ekin = 3.14659813654158 | erot = 1.8374607941321 | epot = -21.5547269116736 | etot = -16.5706679809999 -169000 ekin = 2.22493755697302 | erot = 2.67175500860652 | epot = -21.4662206077311 | etot = -16.5695280421515 -170000 ekin = 2.41921977325643 | erot = 2.49142716001801 | epot = -21.3123035293873 | etot = -16.4016565961128 -171000 ekin = 1.89798915040775 | erot = 2.39492100285877 | epot = -21.2153991969519 | etot = -16.9224890436853 -172000 ekin = 2.86894215563086 | erot = 3.22914449693158 | epot = -21.1827352206441 | etot = -15.0846485680816 -173000 ekin = 2.74888252418688 | erot = 2.13556434483052 | epot = -21.2166792789418 | etot = -16.3322324099244 -174000 ekin = 2.45887587066864 | erot = 2.23682521338056 | epot = -21.2633056658561 | etot = -16.5676045818069 -175000 ekin = 2.84703517745999 | erot = 2.39381254916381 | epot = -21.2430876358358 | etot = -16.002239909212 -176000 ekin = 2.14025231000119 | erot = 1.89894722702466 | epot = -21.3238321496633 | etot = -17.2846326126375 -177000 ekin = 2.5795061901144 | erot = 2.75365074391219 | epot = -21.3022195274207 | etot = -15.9690625933941 -178000 ekin = 1.83122028490793 | erot = 2.59468068841507 | epot = -21.2483113201278 | etot = -16.8224103468048 -179000 ekin = 2.50706581632049 | erot = 2.3918046623687 | epot = -21.3152464598324 | etot = -16.4163759811432 -180000 ekin = 1.88211034410738 | erot = 2.47063835849692 | epot = -21.4741119346399 | etot = -17.1213632320356 -181000 ekin = 1.74209654097779 | erot = 3.05723824722444 | epot = -21.4808621715442 | etot = -16.681527383342 -182000 ekin = 1.55789914013104 | erot = 2.05767448814763 | epot = -21.423526482018 | etot = -17.8079528537394 -183000 ekin = 2.00937540548925 | erot = 2.80898978674436 | epot = -21.491360735728 | etot = -16.6729955434944 -184000 ekin = 2.69285960778353 | erot = 2.42969439668747 | epot = -21.6024209898208 | etot = -16.4798669853498 -185000 ekin = 3.01326925127938 | erot = 3.19083239326424 | epot = -21.6730258967931 | etot = -15.4689242522495 -186000 ekin = 3.2083067153638 | erot = 2.42899016869201 | epot = -21.7143665695974 | etot = -16.0770696855416 -187000 ekin = 2.672906100919 | erot = 3.41560404715603 | epot = -21.6726605039613 | etot = -15.5841503558862 -188000 ekin = 2.89349337388582 | erot = 3.06258669113775 | epot = -21.6216664732832 | etot = -15.6655864082597 -189000 ekin = 2.65435973176118 | erot = 1.82043381700644 | epot = -21.5604872976485 | etot = -17.0856937488809 -190000 ekin = 2.21855159698309 | erot = 1.84826944038784 | epot = -21.5263477340278 | etot = -17.4595266966569 -191000 ekin = 2.26980616064111 | erot = 2.05944589507645 | epot = -21.4543005141097 | etot = -17.1250484583921 -192000 ekin = 2.27219103053707 | erot = 3.11210788791052 | epot = -21.4899273087562 | etot = -16.1056283903086 -193000 ekin = 1.95008147026928 | erot = 1.89648921534019 | epot = -21.4843079374128 | etot = -17.6377372518033 -194000 ekin = 2.45477671526091 | erot = 2.0272304242676 | epot = -21.3709228769337 | etot = -16.8889157374052 -195000 ekin = 3.09567411006595 | erot = 2.10081767143638 | epot = -21.3012041149762 | etot = -16.1047123334739 -196000 ekin = 2.67423122149492 | erot = 2.50738189755519 | epot = -21.2164124023053 | etot = -16.0347992832552 -197000 ekin = 2.50338730962556 | erot = 2.07349764616723 | epot = -21.041867486922 | etot = -16.4649825311292 -198000 ekin = 2.66945928982616 | erot = 1.79012921820209 | epot = -21.0169215356766 | etot = -16.5573330276483 -199000 ekin = 2.53947964790256 | erot = 2.33176467953655 | epot = -21.0171165577067 | etot = -16.1458722302676 -200000 ekin = 2.90451062704866 | erot = 1.42170066957004 | epot = -21.0113804229743 | etot = -16.6851691263556 -201000 ekin = 2.68927776239674 | erot = 1.56650335894554 | epot = -21.0245916399581 | etot = -16.7688105186158 -202000 ekin = 2.2601329351618 | erot = 2.25401443373177 | epot = -20.9769308007641 | etot = -16.4627834318706 -203000 ekin = 2.12073487355488 | erot = 2.03553028991747 | epot = -20.919035946492 | etot = -16.7627707830197 -204000 ekin = 2.11829086582788 | erot = 1.89731962488617 | epot = -20.9376264283538 | etot = -16.9220159376397 -205000 ekin = 1.30964171332167 | erot = 2.12770406224885 | epot = -20.9991335630718 | etot = -17.5617877875013 -206000 ekin = 1.39940057572522 | erot = 2.24496791209126 | epot = -20.963919219062 | etot = -17.3195507312455 -207000 ekin = 1.8871608804017 | erot = 1.79849326266382 | epot = -21.0552898160204 | etot = -17.3696356729549 -208000 ekin = 1.81558541079753 | erot = 3.24210836817276 | epot = -21.3060144768834 | etot = -16.2483206979131 -209000 ekin = 2.79588064252181 | erot = 2.3467149173832 | epot = -21.4301997554495 | etot = -16.2876041955445 -210000 ekin = 3.17544887511567 | erot = 3.12704516116654 | epot = -21.5100449360932 | etot = -15.2075508998109 -211000 ekin = 2.47442327377226 | erot = 2.0990867711376 | epot = -21.6455723047062 | etot = -17.0720622597963 -212000 ekin = 2.36672302145397 | erot = 1.93445871446419 | epot = -21.7283038297487 | etot = -17.4271220938306 -213000 ekin = 1.91045426241161 | erot = 2.52535628540462 | epot = -21.8158508544504 | etot = -17.3800403066341 -214000 ekin = 1.99794025866061 | erot = 2.49896939492127 | epot = -21.8606548137084 | etot = -17.3637451601266 -215000 ekin = 1.97741561009525 | erot = 3.17667494473254 | epot = -21.8701701582032 | etot = -16.7160796033754 -216000 ekin = 1.88829990821377 | erot = 1.87402623825167 | epot = -21.8343889393413 | etot = -18.0720627928759 -217000 ekin = 2.10000293878932 | erot = 1.95052404495887 | epot = -21.8965404786646 | etot = -17.8460134949164 -218000 ekin = 2.34753598782339 | erot = 1.69695019504401 | epot = -21.8560027679962 | etot = -17.8115165851288 -219000 ekin = 2.497223564463 | erot = 2.20999914485705 | epot = -21.8797649478059 | etot = -17.1725422384859 -220000 ekin = 1.75274593087921 | erot = 3.03992746556406 | epot = -21.8491595252171 | etot = -17.0564861287739 -221000 ekin = 1.78874686645809 | erot = 2.79359542964647 | epot = -21.869798634642 | etot = -17.2874563385375 -222000 ekin = 2.63608430516661 | erot = 2.86817933637385 | epot = -21.8351218383832 | etot = -16.3308581968427 -223000 ekin = 3.02706758581511 | erot = 1.93888641555348 | epot = -21.8582453001765 | etot = -16.8922912988079 -224000 ekin = 2.71704451339112 | erot = 2.42079327531441 | epot = -21.8188420875657 | etot = -16.6810042988601 -225000 ekin = 2.04245190508395 | erot = 3.38216222891907 | epot = -21.8232190868647 | etot = -16.3986049528616 -226000 ekin = 2.37968015829255 | erot = 2.38384696857065 | epot = -21.8913549487127 | etot = -17.1278278218495 -227000 ekin = 2.73883397024414 | erot = 2.62491632372019 | epot = -21.9496900700867 | etot = -16.5859397761223 -228000 ekin = 2.06833362780412 | erot = 2.25049628751225 | epot = -21.9946760345141 | etot = -17.6758461191977 -229000 ekin = 1.78618617304217 | erot = 1.80509591500329 | epot = -22.0671964085329 | etot = -18.4759143204874 -230000 ekin = 2.76967283780387 | erot = 2.22492545317995 | epot = -22.0913590121729 | etot = -17.0967607211891 -231000 ekin = 3.15653922952316 | erot = 2.77099247609325 | epot = -22.0635255129442 | etot = -16.1359938073278 -232000 ekin = 1.86633326635991 | erot = 1.70672288688982 | epot = -22.0959715052869 | etot = -18.5229153520371 -233000 ekin = 1.75856846080021 | erot = 1.55694263125625 | epot = -22.0729289884755 | etot = -18.7574178964191 -234000 ekin = 2.32322575892498 | erot = 2.05793864740336 | epot = -21.9849429433607 | etot = -17.6037785370324 -235000 ekin = 1.95327191686568 | erot = 2.52519338885861 | epot = -21.9357201856672 | etot = -17.4572548799429 -236000 ekin = 2.25952484966859 | erot = 1.90005304846995 | epot = -21.9422471368741 | etot = -17.7826692387355 -237000 ekin = 2.49082301609303 | erot = 2.65327564887437 | epot = -22.0049130762794 | etot = -16.860814411312 -238000 ekin = 2.21076048871751 | erot = 2.74154862479023 | epot = -22.0553236426831 | etot = -17.1030145291754 -239000 ekin = 2.71464884454142 | erot = 2.48739530580561 | epot = -22.0661894571024 | etot = -16.8641453067554 -240000 ekin = 3.08961933821573 | erot = 2.17857064931927 | epot = -21.9596599475175 | etot = -16.6914699599825 -241000 ekin = 3.04172562407922 | erot = 2.64442433974962 | epot = -21.872950064824 | etot = -16.1868001009951 -242000 ekin = 2.21355627539455 | erot = 2.33429157450905 | epot = -21.7850463200938 | etot = -17.2371984701902 -243000 ekin = 1.52065138183895 | erot = 2.81375224845254 | epot = -21.724672004357 | etot = -17.3902683740655 -244000 ekin = 1.90352576583831 | erot = 2.43821138840079 | epot = -21.6320468184555 | etot = -17.2903096642164 -245000 ekin = 1.96342069667742 | erot = 2.61760141174562 | epot = -21.509789944958 | etot = -16.928767836535 -246000 ekin = 2.05478829283868 | erot = 2.42643933263093 | epot = -21.4781109635143 | etot = -16.9968833380447 -247000 ekin = 1.54618395739204 | erot = 2.28537401295509 | epot = -21.4411828355572 | etot = -17.6096248652101 -248000 ekin = 1.83924983769609 | erot = 2.55904554412921 | epot = -21.4587985205918 | etot = -17.0605031387665 -249000 ekin = 1.78703007063825 | erot = 2.03411349475431 | epot = -21.516607560139 | etot = -17.6954639947464 -250000 ekin = 1.69317901626952 | erot = 3.382620023581 | epot = -21.5380480709889 | etot = -16.4622490311384 -251000 ekin = 2.13799462687096 | erot = 3.25868442484789 | epot = -21.5254595658408 | etot = -16.1287805141219 -252000 ekin = 2.04357045453396 | erot = 2.53079336098227 | epot = -21.5456931883614 | etot = -16.9713293728452 -253000 ekin = 1.63287738205387 | erot = 3.20992823373492 | epot = -21.5622010587548 | etot = -16.719395442966 -254000 ekin = 2.31269246359595 | erot = 3.10766702207071 | epot = -21.5505863172024 | etot = -16.1302268315358 -255000 ekin = 2.50767926641465 | erot = 2.76631276495167 | epot = -21.5288449153183 | etot = -16.254852883952 -256000 ekin = 1.97163698305487 | erot = 2.61682132599931 | epot = -21.5273539828767 | etot = -16.9388956738225 -257000 ekin = 2.21091422886157 | erot = 3.2624387389365 | epot = -21.5385504601779 | etot = -16.0651974923798 -258000 ekin = 2.0351730783025 | erot = 1.84693461512361 | epot = -21.6544556001779 | etot = -17.7723479067518 -259000 ekin = 2.85718947138204 | erot = 2.78701165242275 | epot = -21.7587237542941 | etot = -16.1145226304893 -260000 ekin = 2.90387286634678 | erot = 2.18817434737477 | epot = -21.8080383126913 | etot = -16.7159910989698 -261000 ekin = 2.76190440948559 | erot = 2.33968169215532 | epot = -21.8592909726424 | etot = -16.7577048710015 -262000 ekin = 3.50919242681178 | erot = 1.76925994550144 | epot = -21.8779228441577 | etot = -16.5994704718445 -263000 ekin = 3.07696270254058 | erot = 2.41477320555763 | epot = -21.8078566004281 | etot = -16.3161206923299 -264000 ekin = 2.26633389925754 | erot = 2.04161743361595 | epot = -21.8372928128571 | etot = -17.5293414799836 -265000 ekin = 1.95747124461577 | erot = 2.5081300879884 | epot = -21.8490876266416 | etot = -17.3834862940375 -266000 ekin = 2.34517905801099 | erot = 3.31486209922478 | epot = -21.8287737874741 | etot = -16.1687326302383 -267000 ekin = 1.74030193361906 | erot = 2.23366459528059 | epot = -21.699850097441 | etot = -17.7258835685413 -268000 ekin = 2.04858677018814 | erot = 3.28744422098426 | epot = -21.6459408923623 | etot = -16.3099099011899 -269000 ekin = 1.93146929709294 | erot = 2.79280735598121 | epot = -21.549773802712 | etot = -16.8254971496378 -270000 ekin = 2.19788894271016 | erot = 2.64563279687103 | epot = -21.4165389672397 | etot = -16.5730172276585 -271000 ekin = 2.21923220579694 | erot = 3.10768708967444 | epot = -21.2197121954353 | etot = -15.8927928999639 -272000 ekin = 2.54992061853163 | erot = 2.29721880581853 | epot = -21.0816515756819 | etot = -16.2345121513317 -273000 ekin = 1.914618407838 | erot = 2.01420401968473 | epot = -21.0503637141725 | etot = -17.1215412866498 -274000 ekin = 1.89671513770876 | erot = 2.24334386161735 | epot = -21.0967103438301 | etot = -16.9566513445039 -275000 ekin = 1.78930707116537 | erot = 3.09754687865994 | epot = -21.1385700371941 | etot = -16.2517160873688 -276000 ekin = 3.37110328153971 | erot = 2.41957324257529 | epot = -21.0908388312033 | etot = -15.3001623070883 -277000 ekin = 2.38921825148496 | erot = 1.50604988822737 | epot = -21.034620883997 | etot = -17.1393527442847 -278000 ekin = 2.51997301930638 | erot = 2.14026171776896 | epot = -21.0117379332914 | etot = -16.351503196216 -279000 ekin = 1.88315206280857 | erot = 2.37342905263994 | epot = -20.9993757709145 | etot = -16.742794655466 -280000 ekin = 2.33534713190787 | erot = 3.58626468287222 | epot = -20.8573252930133 | etot = -14.9357134782332 -281000 ekin = 1.75252641954511 | erot = 1.7907930540809 | epot = -20.9036528826792 | etot = -17.3603334090531 -282000 ekin = 2.26373977259215 | erot = 3.04032073608633 | epot = -20.8497513702237 | etot = -15.5456908615452 -283000 ekin = 2.1783387139443 | erot = 2.20833158301333 | epot = -20.8002776734785 | etot = -16.4136073765209 -284000 ekin = 1.9148667268656 | erot = 2.21521993135969 | epot = -20.8277491648056 | etot = -16.6976625065804 -285000 ekin = 3.15634443167765 | erot = 1.80033231604849 | epot = -21.0046435881196 | etot = -16.0479668403934 -286000 ekin = 3.84877574957331 | erot = 1.82969969667577 | epot = -21.1628555811447 | etot = -15.4843801348956 -287000 ekin = 3.60615742824732 | erot = 2.91608688151215 | epot = -21.2126952882302 | etot = -14.6904509784708 -288000 ekin = 3.19613259393802 | erot = 1.67736393077137 | epot = -21.1713552834963 | etot = -16.297858758787 -289000 ekin = 2.45584885114799 | erot = 2.77781979747336 | epot = -21.1669115721543 | etot = -15.9332429235329 -290000 ekin = 2.74570408981357 | erot = 2.40443247852242 | epot = -21.1874427766533 | etot = -16.0373062083173 -291000 ekin = 2.10295274468233 | erot = 2.37092484671539 | epot = -21.2419107014544 | etot = -16.7680331100567 -292000 ekin = 2.36118713930732 | erot = 2.05558127949017 | epot = -21.3137361602548 | etot = -16.8969677414573 -293000 ekin = 2.2786196308825 | erot = 2.35874555054765 | epot = -21.4302415460533 | etot = -16.7928763646231 -294000 ekin = 2.93315982813019 | erot = 2.90313008187785 | epot = -21.5210917917479 | etot = -15.6848018817399 -295000 ekin = 2.66360761710434 | erot = 2.28100565751945 | epot = -21.6885021477336 | etot = -16.7438888731098 -296000 ekin = 2.18767827164471 | erot = 2.90589885547353 | epot = -21.7355037190159 | etot = -16.6419265918977 -297000 ekin = 2.15987738107365 | erot = 3.29819575592636 | epot = -21.7177655658756 | etot = -16.2596924288756 -298000 ekin = 2.92956976611296 | erot = 2.36377210613469 | epot = -21.6748271071566 | etot = -16.3814852349089 -299000 ekin = 3.19167138064488 | erot = 2.23480811780853 | epot = -21.8042612344918 | etot = -16.3777817360384 -300000 ekin = 3.3133572846982 | erot = 1.38932157247169 | epot = -21.8799906137235 | etot = -17.1773117565536 -301000 ekin = 2.39061971962408 | erot = 3.30110260608963 | epot = -21.8919200817915 | etot = -16.2001977560778 -302000 ekin = 2.954460706029 | erot = 3.2304815881765 | epot = -21.8557645140423 | etot = -15.6708222198368 -303000 ekin = 2.44700205353933 | erot = 2.60676303242282 | epot = -21.8414046718167 | etot = -16.7876395858546 -304000 ekin = 2.23578509140697 | erot = 2.68770420047938 | epot = -21.7680601199659 | etot = -16.8445708280796 -305000 ekin = 2.35505207220215 | erot = 2.3823003115585 | epot = -21.7344089784493 | etot = -16.9970565946887 -306000 ekin = 1.91790567526689 | erot = 2.90107494003232 | epot = -21.7170004822351 | etot = -16.8980198669359 -307000 ekin = 2.48241777758708 | erot = 2.0836708009946 | epot = -21.6510481218459 | etot = -17.0849595432642 -308000 ekin = 2.77531620706104 | erot = 2.63103510715158 | epot = -21.6349123878086 | etot = -16.2285610735959 -309000 ekin = 2.30440955942791 | erot = 2.1249829765834 | epot = -21.5927938975113 | etot = -17.1634013615 -310000 ekin = 2.50879527040005 | erot = 3.21338829421535 | epot = -21.6043932917725 | etot = -15.8822097271571 -311000 ekin = 2.31939145866558 | erot = 3.03649241514151 | epot = -21.6247503351754 | etot = -16.2688664613683 -312000 ekin = 1.78383134659847 | erot = 3.26262247889992 | epot = -21.4948144284683 | etot = -16.4483606029699 -313000 ekin = 1.6465994694839 | erot = 2.08133087588833 | epot = -21.4920309735611 | etot = -17.7641006281889 -314000 ekin = 2.2552391830868 | erot = 2.55077633299239 | epot = -21.5103692936944 | etot = -16.7043537776152 -315000 ekin = 2.5352734391515 | erot = 2.13089997124613 | epot = -21.5923709217299 | etot = -16.9261975113323 -316000 ekin = 1.99944427781285 | erot = 1.80072924409704 | epot = -21.6039893771529 | etot = -17.803815855243 -317000 ekin = 2.11848744585804 | erot = 2.01459693810075 | epot = -21.5948976630665 | etot = -17.4618132791077 -318000 ekin = 2.29013024301854 | erot = 1.92405818620914 | epot = -21.5643695946921 | etot = -17.3501811654644 -319000 ekin = 1.97314693278018 | erot = 1.67996578959134 | epot = -21.4554808400841 | etot = -17.8023681177126 -320000 ekin = 2.45681719546631 | erot = 3.07835144499744 | epot = -21.3924125538101 | etot = -15.8572439133463 -321000 ekin = 1.85729238455498 | erot = 2.67083565671245 | epot = -21.433818829251 | etot = -16.9056907879836 -322000 ekin = 1.96132292396412 | erot = 3.36792274118279 | epot = -21.3663490830085 | etot = -16.0371034178616 -323000 ekin = 1.94437285233567 | erot = 2.09558156605687 | epot = -21.4151250968679 | etot = -17.3751706784754 -324000 ekin = 2.229181524904 | erot = 2.4674418745061 | epot = -21.532385908563 | etot = -16.8357625091529 -325000 ekin = 2.74582842770392 | erot = 2.36717454305098 | epot = -21.6443544237971 | etot = -16.5313514530422 -326000 ekin = 1.91124551133375 | erot = 1.93084217743114 | epot = -21.7077957426602 | etot = -17.8657080538953 -327000 ekin = 3.05627483509655 | erot = 1.67325209460963 | epot = -21.7948818019128 | etot = -17.0653548722066 -328000 ekin = 2.73933273476856 | erot = 1.92380912803777 | epot = -21.8364014823586 | etot = -17.1732596195523 -329000 ekin = 2.95907896099514 | erot = 3.15654168356681 | epot = -21.898199971646 | etot = -15.7825793270841 -330000 ekin = 2.90795110595274 | erot = 2.01765890034968 | epot = -21.9037795505258 | etot = -16.9781695442234 -331000 ekin = 2.27446048340228 | erot = 2.03754878634056 | epot = -21.8760842049291 | etot = -17.5640749351863 -332000 ekin = 2.43262938612094 | erot = 3.19219171897213 | epot = -21.9305186945662 | etot = -16.3056975894732 -333000 ekin = 2.47357651298171 | erot = 2.70061045814697 | epot = -22.0416691323271 | etot = -16.8674821611985 -334000 ekin = 2.38171387374892 | erot = 3.00424927873366 | epot = -22.0746318522988 | etot = -16.6886686998162 -335000 ekin = 2.10465470910016 | erot = 3.57382014016833 | epot = -22.1175420615632 | etot = -16.4390672122947 -336000 ekin = 2.61374577374183 | erot = 2.13386927281299 | epot = -22.08988251196 | etot = -17.3422674654052 -337000 ekin = 2.72124526751511 | erot = 2.74800480481403 | epot = -22.0768537131621 | etot = -16.607603640833 -338000 ekin = 1.83524121485421 | erot = 2.24338894827196 | epot = -22.1591955034455 | etot = -18.0805653403194 -339000 ekin = 1.54928432997334 | erot = 2.49812246084905 | epot = -22.202239883467 | etot = -18.1548330926446 -340000 ekin = 1.44405714940632 | erot = 4.0451327092417 | epot = -22.1149458734013 | etot = -16.6257560147533 -341000 ekin = 1.67447392575555 | erot = 2.77749751745982 | epot = -22.0760831546714 | etot = -17.624111711456 -342000 ekin = 1.9825676117275 | erot = 2.71655566521084 | epot = -22.1563522566984 | etot = -17.45722897976 -343000 ekin = 2.68213676683887 | erot = 3.16686462846914 | epot = -22.2498477633288 | etot = -16.4008463680208 -344000 ekin = 1.77905771753907 | erot = 2.19153667254074 | epot = -22.2907212723871 | etot = -18.3201268823073 -345000 ekin = 1.5460499615042 | erot = 1.85960255696712 | epot = -22.3447003428977 | etot = -18.9390478244264 -346000 ekin = 1.71554664484034 | erot = 1.79880968736714 | epot = -22.3117022609055 | etot = -18.797345928698 -347000 ekin = 1.38672912049481 | erot = 2.61484473767931 | epot = -22.332503239512 | etot = -18.3309293813379 -348000 ekin = 2.15015924850684 | erot = 2.86300326453563 | epot = -22.3337312775957 | etot = -17.3205687645532 -349000 ekin = 1.83066085453602 | erot = 1.9844132649487 | epot = -22.3967822584585 | etot = -18.5817081389738 -350000 ekin = 1.83318738252649 | erot = 2.56907029661254 | epot = -22.4577827539416 | etot = -18.0555250748026 -351000 ekin = 1.72790505260219 | erot = 2.87456274671834 | epot = -22.5159555107051 | etot = -17.9134877113846 -352000 ekin = 2.80786740016944 | erot = 2.08750448125769 | epot = -22.6549834386892 | etot = -17.7596115572621 -353000 ekin = 3.5492801472091 | erot = 1.42584537334883 | epot = -22.6849212734238 | etot = -17.7097957528659 -354000 ekin = 3.49129244374804 | erot = 2.25156548638802 | epot = -22.604182620693 | etot = -16.861324690557 -355000 ekin = 2.06248783371663 | erot = 2.92733565233054 | epot = -22.5494488364627 | etot = -17.5596253504155 -356000 ekin = 2.13415426306312 | erot = 3.32668319049641 | epot = -22.6122425286523 | etot = -17.1514050750927 -357000 ekin = 2.75897049849731 | erot = 2.51843165594436 | epot = -22.6042888591885 | etot = -17.3268867047468 -358000 ekin = 2.51778220496547 | erot = 2.28374144764325 | epot = -22.5654155469984 | etot = -17.7638918943897 -359000 ekin = 3.2037278512604 | erot = 2.5552016027623 | epot = -22.6749569097326 | etot = -16.91602745571 -360000 ekin = 2.52669169359923 | erot = 1.97563796824025 | epot = -22.7314557612254 | etot = -18.229126099386 -361000 ekin = 2.60424632123629 | erot = 2.51068088850826 | epot = -22.7715023743751 | etot = -17.6565751646306 -362000 ekin = 2.43350156723209 | erot = 3.84566788758402 | epot = -22.7352151098034 | etot = -16.4560456549873 -363000 ekin = 2.91069717970492 | erot = 1.99710098714122 | epot = -22.6302259934474 | etot = -17.7224278266013 -364000 ekin = 2.2553832868325 | erot = 1.87832387363455 | epot = -22.5083625296191 | etot = -18.374655369152 -365000 ekin = 2.04575884197224 | erot = 2.797742068412 | epot = -22.332262738426 | etot = -17.4887618280417 -366000 ekin = 2.26894187965217 | erot = 1.94379382552235 | epot = -22.2788727984906 | etot = -18.0661370933161 -367000 ekin = 2.82509630766737 | erot = 2.50361468767084 | epot = -22.3209381619452 | etot = -16.992227166607 -368000 ekin = 2.81542036602322 | erot = 2.18733627644489 | epot = -22.4297259451244 | etot = -17.4269693026563 -369000 ekin = 2.30426035796382 | erot = 2.85653411706989 | epot = -22.4923286665588 | etot = -17.3315341915251 -370000 ekin = 2.67871033327547 | erot = 2.11464921695177 | epot = -22.578069860797 | etot = -17.7847103105697 -371000 ekin = 2.19281044135007 | erot = 3.60165960664287 | epot = -22.6424730832337 | etot = -16.8480030352407 -372000 ekin = 1.77481259468411 | erot = 3.406547444381 | epot = -22.7147683829008 | etot = -17.5334083438357 -373000 ekin = 2.15551547517191 | erot = 2.7877825236183 | epot = -22.7559497214321 | etot = -17.8126517226419 -374000 ekin = 2.71938368055486 | erot = 3.58127823243842 | epot = -22.9084433694729 | etot = -16.6077814564796 -375000 ekin = 2.42759321485976 | erot = 2.9742127178716 | epot = -22.9740378563778 | etot = -17.5722319236464 -376000 ekin = 3.39126830110572 | erot = 3.24733797625004 | epot = -22.9874015798135 | etot = -16.3487953024578 -377000 ekin = 3.20966733323472 | erot = 2.65934060364476 | epot = -22.9452111216365 | etot = -17.076203184757 -378000 ekin = 1.56095946168131 | erot = 2.66159033944991 | epot = -22.9575870308253 | etot = -18.7350372296941 -379000 ekin = 1.9498568748538 | erot = 2.54085216255828 | epot = -22.9834751642939 | etot = -18.4927661268818 -380000 ekin = 2.65820438237073 | erot = 2.88045867212573 | epot = -22.9984703542083 | etot = -17.4598072997118 -381000 ekin = 2.97084599252829 | erot = 2.18892549461574 | epot = -23.0341895570111 | etot = -17.8744180698671 -382000 ekin = 2.61355176942653 | erot = 2.02938704043227 | epot = -23.00841197151 | etot = -18.3654731616512 -383000 ekin = 2.03830671072154 | erot = 2.50516194855525 | epot = -23.0393965606452 | etot = -18.4959279013684 -384000 ekin = 2.1060608733416 | erot = 2.2184025045895 | epot = -23.0602182522593 | etot = -18.7357548743282 -385000 ekin = 1.89114918519107 | erot = 1.63701051320103 | epot = -23.0834434146806 | etot = -19.5552837162885 -386000 ekin = 1.55124380123707 | erot = 1.36147797265396 | epot = -23.1300518396949 | etot = -20.2173300658039 -387000 ekin = 2.19627825752355 | erot = 1.75751396098972 | epot = -23.1280875332419 | etot = -19.1742953147287 -388000 ekin = 1.96387084539616 | erot = 1.95852585326804 | epot = -23.0327752892415 | etot = -19.1103785905773 -389000 ekin = 2.50801560941705 | erot = 2.32519825784836 | epot = -23.0011464671235 | etot = -18.1679325998581 -390000 ekin = 2.03596866068489 | erot = 1.88295618907177 | epot = -22.8810338311575 | etot = -18.9621089814009 -391000 ekin = 1.8098591016452 | erot = 2.39622167162874 | epot = -22.81955664632 | etot = -18.613475873046 -392000 ekin = 2.17725370142733 | erot = 2.87094426544089 | epot = -22.7839731045438 | etot = -17.7357751376756 -393000 ekin = 2.14224634181997 | erot = 3.17242974303658 | epot = -22.8435025538357 | etot = -17.5288264689792 -394000 ekin = 1.97769550804367 | erot = 2.16375300420729 | epot = -22.8342667825711 | etot = -18.6928182703201 -395000 ekin = 2.03687268736298 | erot = 2.49567469731651 | epot = -22.8892034986303 | etot = -18.3566561139508 -396000 ekin = 2.16189109047463 | erot = 1.95308746486161 | epot = -22.9781386034885 | etot = -18.8631600481523 -397000 ekin = 2.41744222422408 | erot = 1.65310699287476 | epot = -23.0900453292844 | etot = -19.0194961121856 -398000 ekin = 3.58905654436294 | erot = 2.51930256503331 | epot = -23.2070733343384 | etot = -17.0987142249422 -399000 ekin = 2.65051654249497 | erot = 1.78138450529865 | epot = -23.3040478764215 | etot = -18.8721468286279 -400000 ekin = 2.49402752614129 | erot = 2.10290777432183 | epot = -23.3608759462318 | etot = -18.7639406457687 -401000 ekin = 2.04176177605462 | erot = 2.154995213856 | epot = -23.4039603394011 | etot = -19.2072033494905 -402000 ekin = 2.44505875861459 | erot = 2.11318097973378 | epot = -23.3975262709888 | etot = -18.8392865326404 -403000 ekin = 2.54858079745147 | erot = 2.81138206601919 | epot = -23.476064698677 | etot = -18.1161018352063 -404000 ekin = 2.21063952462117 | erot = 2.64710865829565 | epot = -23.574696037266 | etot = -18.7169478543492 -405000 ekin = 2.47328118101332 | erot = 2.40933750599425 | epot = -23.5927917139469 | etot = -18.7101730269393 -406000 ekin = 2.24891173527799 | erot = 2.23777884116047 | epot = -23.6086191890417 | etot = -19.1219286126032 -407000 ekin = 2.0107940045037 | erot = 2.78642832526904 | epot = -23.5246032469978 | etot = -18.727380917225 -408000 ekin = 2.59464051790823 | erot = 2.59123578102097 | epot = -23.4198302602656 | etot = -18.2339539613364 -409000 ekin = 2.37170880608734 | erot = 2.26136902851213 | epot = -23.317258193724 | etot = -18.6841803591245 -410000 ekin = 1.99754661347185 | erot = 1.95523998485755 | epot = -23.2950402043273 | etot = -19.3422536059979 -411000 ekin = 1.8693657058423 | erot = 2.63899492681176 | epot = -23.2490367633041 | etot = -18.74067613065 -412000 ekin = 1.98214047746227 | erot = 2.68315820775202 | epot = -23.1987357483281 | etot = -18.5334370631139 -413000 ekin = 2.39078873487373 | erot = 2.65589562872907 | epot = -23.1435198518627 | etot = -18.0968354882599 -414000 ekin = 2.40821090859775 | erot = 1.75574324408225 | epot = -23.0725048141377 | etot = -18.9085506614577 -415000 ekin = 2.74601981183015 | erot = 2.43675176686816 | epot = -23.1211711904486 | etot = -17.9383996117503 -416000 ekin = 2.08828454200993 | erot = 2.76783506526218 | epot = -23.1383119239965 | etot = -18.2821923167244 -417000 ekin = 2.01455344430628 | erot = 1.95306265456051 | epot = -23.1433633505287 | etot = -19.1757472516619 -418000 ekin = 2.42716528853985 | erot = 2.57642821145486 | epot = -23.127531797131 | etot = -18.1239382971363 -419000 ekin = 3.04095103685797 | erot = 2.58427576972734 | epot = -23.0602279332617 | etot = -17.4350011266764 -420000 ekin = 2.6360746280152 | erot = 2.44478111019393 | epot = -22.982092315172 | etot = -17.9012365769629 -421000 ekin = 2.53019765722915 | erot = 1.78389585255477 | epot = -22.9707435541329 | etot = -18.6566500443489 -422000 ekin = 2.72457425772367 | erot = 1.67768634886349 | epot = -22.9542997027495 | etot = -18.5520390961623 -423000 ekin = 2.11402997037893 | erot = 2.55034580375608 | epot = -22.8263851956497 | etot = -18.1620094215147 -424000 ekin = 1.8895880210325 | erot = 2.31332431343561 | epot = -22.772666888172 | etot = -18.5697545537039 -425000 ekin = 2.3595116370971 | erot = 1.95762380637298 | epot = -22.7752082759346 | etot = -18.4580728324645 -426000 ekin = 2.23706657164627 | erot = 2.60016134755148 | epot = -22.7844114251539 | etot = -17.9471835059562 -427000 ekin = 1.88801598248841 | erot = 2.12415782350886 | epot = -22.9416586386639 | etot = -18.9294848326666 -428000 ekin = 1.92849031333042 | erot = 2.44097902588716 | epot = -23.0611368174399 | etot = -18.6916674782223 -429000 ekin = 1.70536802258415 | erot = 2.14916257389792 | epot = -23.0556586745393 | etot = -19.2011280780572 -430000 ekin = 2.30226095973205 | erot = 2.14689932813604 | epot = -23.0606502516208 | etot = -18.6114899637527 -431000 ekin = 2.45988288454318 | erot = 2.42278380298657 | epot = -23.0729777223881 | etot = -18.1903110348583 -432000 ekin = 2.80869332724974 | erot = 2.19954129490925 | epot = -23.0939746542044 | etot = -18.0857400320454 -433000 ekin = 2.21130556188282 | erot = 1.62882156110628 | epot = -23.1534080352157 | etot = -19.3132809122266 -434000 ekin = 2.60574953870752 | erot = 2.36088790768803 | epot = -23.1901717047879 | etot = -18.2235342583923 -435000 ekin = 2.30377529593091 | erot = 2.53917715731259 | epot = -23.1716983948432 | etot = -18.3287459415997 -436000 ekin = 2.42707603554825 | erot = 2.75234181061924 | epot = -23.2197996577197 | etot = -18.0403818115522 -437000 ekin = 1.65090540276074 | erot = 3.25345231298367 | epot = -23.2216366145388 | etot = -18.3172788987944 -438000 ekin = 1.56145302974407 | erot = 2.60950810563796 | epot = -23.1303770792279 | etot = -18.9594159438458 -439000 ekin = 2.30955439722234 | erot = 1.94011743371103 | epot = -23.1353170794497 | etot = -18.8856452485163 -440000 ekin = 2.53037674867674 | erot = 3.0652704286103 | epot = -23.196858945292 | etot = -17.601211768005 -441000 ekin = 2.80107707952534 | erot = 2.53664155736544 | epot = -23.1712373428919 | etot = -17.8335187060011 -442000 ekin = 2.92536323090713 | erot = 2.88384500930016 | epot = -23.1123001627208 | etot = -17.3030919225135 -443000 ekin = 1.96543935969482 | erot = 1.753449631552 | epot = -23.0380529084378 | etot = -19.3191639171909 -444000 ekin = 2.00309477401363 | erot = 2.23897509587738 | epot = -22.9472103119533 | etot = -18.7051404420623 -445000 ekin = 2.20302071819722 | erot = 2.06928381371827 | epot = -22.7775434364172 | etot = -18.5052389045017 -446000 ekin = 2.43487889302299 | erot = 2.37751556007799 | epot = -22.6838190597697 | etot = -17.8714246066687 -447000 ekin = 2.2620819636031 | erot = 2.41400188145198 | epot = -22.7082516636546 | etot = -18.0321678185995 -448000 ekin = 2.16184472791984 | erot = 1.93539407204278 | epot = -22.8144859493263 | etot = -18.7172471493637 -449000 ekin = 2.21107967973114 | erot = 2.34659682978741 | epot = -22.9059503054159 | etot = -18.3482737958974 -450000 ekin = 2.7467774000444 | erot = 1.97222921372039 | epot = -22.8607559267161 | etot = -18.1417493129513 -451000 ekin = 2.2050889378155 | erot = 2.13042736119386 | epot = -22.8862608894796 | etot = -18.5507445904703 -452000 ekin = 2.52760608607095 | erot = 2.340068156366 | epot = -22.9138111972133 | etot = -18.0461369547764 -453000 ekin = 2.23448825172916 | erot = 1.77834418215733 | epot = -22.8879238301791 | etot = -18.8750913962927 -454000 ekin = 2.4343851915949 | erot = 2.59700848533281 | epot = -22.8184361849036 | etot = -17.7870425079759 -455000 ekin = 2.04195793930991 | erot = 2.7963904374768 | epot = -22.6032980500354 | etot = -17.7649496732487 -456000 ekin = 2.00799933710202 | erot = 2.53653815407519 | epot = -22.4355596266522 | etot = -17.891022135475 -457000 ekin = 2.60426208759883 | erot = 2.46609612876191 | epot = -22.3409120082078 | etot = -17.270553791847 -458000 ekin = 2.01368468059038 | erot = 1.99613816245311 | epot = -22.2549400327206 | etot = -18.2451171896771 -459000 ekin = 1.73688781588865 | erot = 2.48572034306893 | epot = -22.2282088298767 | etot = -18.0056006709191 -460000 ekin = 1.91682575775988 | erot = 2.08308677023945 | epot = -22.2211874714416 | etot = -18.2212749434423 -461000 ekin = 1.54933673126938 | erot = 1.29454502815254 | epot = -22.1945151049368 | etot = -19.3506333455149 -462000 ekin = 2.44160489340629 | erot = 1.34721473707675 | epot = -22.2846713076971 | etot = -18.495851677214 -463000 ekin = 2.63165365707667 | erot = 2.0814376012804 | epot = -22.4004513395625 | etot = -17.6873600812054 -464000 ekin = 2.67929276186416 | erot = 3.7256379306109 | epot = -22.5200042545289 | etot = -16.1150735620538 -465000 ekin = 1.94880111369479 | erot = 2.23148844819349 | epot = -22.685554296329 | etot = -18.5052647344407 -466000 ekin = 2.13853049638891 | erot = 2.95056624305957 | epot = -22.7822881705531 | etot = -17.6931914311047 -467000 ekin = 2.46452767169615 | erot = 2.1077848077008 | epot = -22.9485753844866 | etot = -18.3762629050897 -468000 ekin = 1.98589158006998 | erot = 1.62816092182055 | epot = -23.0180008829524 | etot = -19.4039483810619 -469000 ekin = 2.498810820967 | erot = 2.63615462725918 | epot = -23.0547833968841 | etot = -17.9198179486579 -470000 ekin = 2.91491361681313 | erot = 3.19115611298995 | epot = -23.0448741101699 | etot = -16.9388043803669 -471000 ekin = 2.37554627514204 | erot = 1.71739792236247 | epot = -22.9932329645513 | etot = -18.9002887670468 -472000 ekin = 2.18486807923518 | erot = 2.00687069908098 | epot = -22.9563182572702 | etot = -18.764579478954 -473000 ekin = 2.36185345820899 | erot = 2.86259041401025 | epot = -22.9161024426125 | etot = -17.6916585703933 -474000 ekin = 2.17077693495272 | erot = 2.59376596740918 | epot = -22.7894018760353 | etot = -18.0248589736733 -475000 ekin = 2.37844153079293 | erot = 2.01112751381906 | epot = -22.6793191497969 | etot = -18.2897501051849 -476000 ekin = 2.08763676439641 | erot = 2.59647624455221 | epot = -22.6700039875052 | etot = -17.9858909785566 -477000 ekin = 2.52249432714936 | erot = 3.55251934739865 | epot = -22.6424099194917 | etot = -16.5673962449437 -478000 ekin = 2.40424947791157 | erot = 2.73239117258611 | epot = -22.544776325228 | etot = -17.4081356747303 -479000 ekin = 1.27637524434413 | erot = 2.99749792697945 | epot = -22.4994949498981 | etot = -18.2256217785745 -480000 ekin = 1.81374950293817 | erot = 2.14389317135941 | epot = -22.4678405170785 | etot = -18.5101978427809 -481000 ekin = 2.394967741862 | erot = 3.1829944182452 | epot = -22.4930736763178 | etot = -16.9151115162106 -482000 ekin = 3.21051763720184 | erot = 2.40962326270834 | epot = -22.4479376181304 | etot = -16.8277967182202 -483000 ekin = 3.06081116762377 | erot = 2.49856996934407 | epot = -22.4288948733282 | etot = -16.8695137363604 -484000 ekin = 2.7452293328759 | erot = 2.530126299931 | epot = -22.4837563329191 | etot = -17.2084007001122 -485000 ekin = 3.33103095180521 | erot = 2.42091818181916 | epot = -22.4922555047182 | etot = -16.7403063710938 -486000 ekin = 1.99323479363108 | erot = 1.76127718142275 | epot = -22.5432098594132 | etot = -18.7886978843593 -487000 ekin = 2.64825718911653 | erot = 2.50204426232019 | epot = -22.6407366935242 | etot = -17.4904352420874 -488000 ekin = 1.7638589171947 | erot = 2.642665551735 | epot = -22.6990728058786 | etot = -18.2925483369489 -489000 ekin = 2.10357630534276 | erot = 2.95613916443127 | epot = -22.7877124402073 | etot = -17.7279969704332 -490000 ekin = 2.33515649128314 | erot = 2.32995416999057 | epot = -22.7920703811403 | etot = -18.1269597198666 -491000 ekin = 2.48752587426647 | erot = 2.58310949760555 | epot = -22.7834811495388 | etot = -17.7128457776668 -492000 ekin = 3.29820665204488 | erot = 2.18682924183923 | epot = -22.7674519489923 | etot = -17.2824160551082 -493000 ekin = 3.40238156707505 | erot = 2.35717041222451 | epot = -22.7149408840448 | etot = -16.9553889047453 -494000 ekin = 3.59348050162499 | erot = 2.23182460532058 | epot = -22.7081682295491 | etot = -16.8828631226035 -495000 ekin = 2.52030309238562 | erot = 2.16229430067424 | epot = -22.6973031832711 | etot = -18.0147057902113 -496000 ekin = 1.96100991422337 | erot = 3.58581695215168 | epot = -22.7342002900883 | etot = -17.1873734237132 -497000 ekin = 2.2228647925968 | erot = 2.49495319949133 | epot = -22.752706201593 | etot = -18.0348882095049 -498000 ekin = 1.71033952564695 | erot = 2.41331591511584 | epot = -22.7131621100868 | etot = -18.589506669324 -499000 ekin = 2.41919864300729 | erot = 2.82349519531823 | epot = -22.7304918052927 | etot = -17.4877979669671 -500000 ekin = 2.76271068346558 | erot = 2.22796445937144 | epot = -22.810945568044 | etot = -17.820270425207 -501000 ekin = 2.97642553987186 | erot = 1.97769778889399 | epot = -22.8306304048616 | etot = -17.8765070760957 -502000 ekin = 2.96175345860855 | erot = 1.80859086419487 | epot = -22.8525538190094 | etot = -18.082209496206 -503000 ekin = 2.51126831088417 | erot = 2.88572311841925 | epot = -22.8673362278446 | etot = -17.4703447985412 -504000 ekin = 2.84611165351303 | erot = 2.67626783872457 | epot = -22.7848919576011 | etot = -17.2625124653635 -505000 ekin = 2.96124584448914 | erot = 2.59100575301934 | epot = -22.8251284225259 | etot = -17.2728768250174 -506000 ekin = 2.19858217910528 | erot = 1.97142936872075 | epot = -22.8530995461461 | etot = -18.6830879983201 -507000 ekin = 2.27398115142402 | erot = 2.68837996151516 | epot = -22.8141163798141 | etot = -17.8517552668749 -508000 ekin = 2.64439339973837 | erot = 2.0475646786945 | epot = -22.8146247157346 | etot = -18.1226666373017 -509000 ekin = 2.96023637315629 | erot = 2.90549934754532 | epot = -22.8719625385966 | etot = -17.006226817895 -510000 ekin = 2.26067558634545 | erot = 2.8086491851952 | epot = -22.9774448292236 | etot = -17.9081200576829 -511000 ekin = 2.88512738978599 | erot = 2.15263877534436 | epot = -23.086672848248 | etot = -18.0489066831176 -512000 ekin = 2.17783748155516 | erot = 2.31389139764187 | epot = -23.1520181882638 | etot = -18.6602893090668 -513000 ekin = 1.69717952556151 | erot = 2.88265468656802 | epot = -23.1640284548406 | etot = -18.5841942427111 -514000 ekin = 1.72432024724117 | erot = 2.32742209152174 | epot = -23.1602225830814 | etot = -19.1084802443185 -515000 ekin = 2.00525337522086 | erot = 1.80102864435033 | epot = -23.1548763180746 | etot = -19.3485942985034 -516000 ekin = 3.04706172157038 | erot = 1.54171785431327 | epot = -23.1202751246552 | etot = -18.5314955487716 -517000 ekin = 2.47323892251936 | erot = 2.10799615007355 | epot = -23.0942246440307 | etot = -18.5129895714378 -518000 ekin = 2.03556879740597 | erot = 2.51531294708502 | epot = -23.01998934344 | etot = -18.469107598949 -519000 ekin = 1.59255614728459 | erot = 1.63520468579905 | epot = -22.9787913166931 | etot = -19.7510304836094 -520000 ekin = 2.17210761761845 | erot = 1.89753667353918 | epot = -22.9877149955356 | etot = -18.918070704378 -521000 ekin = 1.98466680078867 | erot = 2.09219045542651 | epot = -23.0348541858322 | etot = -18.9579969296171 -522000 ekin = 2.72098469914433 | erot = 2.19565658619461 | epot = -23.1001210576502 | etot = -18.1834797723112 -523000 ekin = 2.26033454380754 | erot = 1.67112114369623 | epot = -23.1475509854345 | etot = -19.2160952979307 -524000 ekin = 2.34603831546138 | erot = 2.10546610119491 | epot = -23.1746761633772 | etot = -18.723171746721 -525000 ekin = 2.13671314300235 | erot = 2.07172081705865 | epot = -23.241177743004 | etot = -19.032743782943 -526000 ekin = 2.50849953901566 | erot = 2.27662230434506 | epot = -23.3179050583979 | etot = -18.5327832150372 -527000 ekin = 3.04322527932213 | erot = 1.81280570832388 | epot = -23.3977373118239 | etot = -18.5417063241779 -528000 ekin = 2.572303182379 | erot = 2.54386055260816 | epot = -23.4208428708383 | etot = -18.3046791358511 -529000 ekin = 2.39361269633634 | erot = 1.91637577362226 | epot = -23.3966015599491 | etot = -19.0866130899905 -530000 ekin = 3.3562937907424 | erot = 3.4168381587646 | epot = -23.2977853851851 | etot = -16.5246534356781 -531000 ekin = 2.52741741752381 | erot = 2.34075342407641 | epot = -23.1721175623278 | etot = -18.3039467207276 -532000 ekin = 2.78397051305127 | erot = 1.78575123294094 | epot = -23.2171711834401 | etot = -18.6474494374478 -533000 ekin = 2.27408274334043 | erot = 2.01427501035042 | epot = -23.2885684059727 | etot = -19.0002106522818 -534000 ekin = 2.54998010491125 | erot = 2.01645453645072 | epot = -23.340767920006 | etot = -18.7743332786441 -535000 ekin = 2.49595662250557 | erot = 2.09586427439366 | epot = -23.3878755759449 | etot = -18.7960546790457 -536000 ekin = 2.47717157546008 | erot = 1.92116873587363 | epot = -23.3847675210096 | etot = -18.9864272096758 -537000 ekin = 1.75235621440218 | erot = 2.11852052216091 | epot = -23.4590860280326 | etot = -19.5882092914695 -538000 ekin = 2.19317209186627 | erot = 2.75191518419657 | epot = -23.5517834707225 | etot = -18.6066961946597 -539000 ekin = 2.16135327665112 | erot = 2.25935011393787 | epot = -23.5718250119029 | etot = -19.1511216213139 -540000 ekin = 2.35701554620646 | erot = 1.6449529057333 | epot = -23.5490867129451 | etot = -19.5471182610053 -541000 ekin = 2.61451212811978 | erot = 2.52550284426681 | epot = -23.5334576350385 | etot = -18.3934426626519 -542000 ekin = 2.78909215024063 | erot = 2.09346850400965 | epot = -23.5754619290989 | etot = -18.6929012748486 -543000 ekin = 2.77024528778678 | erot = 1.84116991183092 | epot = -23.4849560716084 | etot = -18.8735408719907 -544000 ekin = 2.15807529188369 | erot = 1.50139575300257 | epot = -23.4530822422947 | etot = -19.7936111974084 -545000 ekin = 1.72860204886328 | erot = 2.56468335549414 | epot = -23.4524953434144 | etot = -19.159209939057 -546000 ekin = 2.38494138419347 | erot = 1.87772638427254 | epot = -23.4950389557032 | etot = -19.2323711872372 -547000 ekin = 2.44871634556834 | erot = 2.44464466893214 | epot = -23.544915775382 | etot = -18.6515547608815 -548000 ekin = 2.36962922994878 | erot = 2.40235228488721 | epot = -23.5548428056052 | etot = -18.7828612907692 -549000 ekin = 2.57958168249613 | erot = 2.04930779813673 | epot = -23.5565149978684 | etot = -18.9276255172355 -550000 ekin = 1.9793136647427 | erot = 1.85207468704396 | epot = -23.5614067919063 | etot = -19.7300184401196 -551000 ekin = 2.41217743270811 | erot = 2.03489368862993 | epot = -23.5115216908382 | etot = -19.0644505695002 -552000 ekin = 2.6621149390197 | erot = 1.41279265378133 | epot = -23.3450678435402 | etot = -19.2701602507392 -553000 ekin = 1.76359346131444 | erot = 2.63019210822712 | epot = -23.1435570943958 | etot = -18.7497715248543 -554000 ekin = 2.29840754300073 | erot = 2.34424452982824 | epot = -23.1114395278817 | etot = -18.4687874550528 -555000 ekin = 3.29672420152566 | erot = 1.64146930698359 | epot = -23.0891292168918 | etot = -18.1509357083826 -556000 ekin = 2.92076699655596 | erot = 2.59602967895818 | epot = -23.0268314200473 | etot = -17.5100347445331 -557000 ekin = 2.90322014804994 | erot = 3.16052668894917 | epot = -23.0146480567182 | etot = -16.9509012197191 -558000 ekin = 2.78018761002223 | erot = 2.59826947006757 | epot = -22.7877399275349 | etot = -17.4092828474451 -559000 ekin = 2.48661596771863 | erot = 3.22596665511861 | epot = -22.8226574327834 | etot = -17.1100748099462 -560000 ekin = 2.34942852601698 | erot = 2.32773162877397 | epot = -22.8255608134696 | etot = -18.1484006586787 -561000 ekin = 2.0520192544917 | erot = 2.90306975046937 | epot = -22.848851605114 | etot = -17.8937626001529 -562000 ekin = 2.18821919117372 | erot = 3.66499439159819 | epot = -22.7618817506902 | etot = -16.9086681679183 -563000 ekin = 3.11505518852414 | erot = 2.28057725990562 | epot = -22.7914306402871 | etot = -17.3957981918573 -564000 ekin = 2.45343120006931 | erot = 2.36321638506708 | epot = -22.75807077839 | etot = -17.9414231932536 -565000 ekin = 2.7783583550222 | erot = 2.07073547186411 | epot = -22.7486053888412 | etot = -17.8995115619549 -566000 ekin = 2.43655641927934 | erot = 2.19832280178868 | epot = -22.7227654505167 | etot = -18.0878862294486 -567000 ekin = 2.71233133108495 | erot = 2.01281091173406 | epot = -22.8839744455115 | etot = -18.1588322026925 -568000 ekin = 3.12450796157709 | erot = 1.93520150351058 | epot = -22.9625972279254 | etot = -17.9028877628378 -569000 ekin = 3.72714267701978 | erot = 2.06562452789051 | epot = -22.9814174117752 | etot = -17.188650206865 -570000 ekin = 2.68808623045676 | erot = 2.36042122391806 | epot = -22.9989590266921 | etot = -17.9504515723173 -571000 ekin = 1.97223467321357 | erot = 2.85558181274649 | epot = -22.9369001315648 | etot = -18.1090836456048 -572000 ekin = 2.41820497321229 | erot = 2.40910077907643 | epot = -22.934930836907 | etot = -18.1076250846183 -573000 ekin = 1.76702714285012 | erot = 2.31739567602695 | epot = -22.9768902017483 | etot = -18.8924673828712 -574000 ekin = 2.0874025921411 | erot = 2.59288012722137 | epot = -23.0518321557917 | etot = -18.3715494364293 -575000 ekin = 2.34020490338786 | erot = 2.78500973557003 | epot = -23.106579446946 | etot = -17.9813648079881 -576000 ekin = 2.15506609467458 | erot = 3.30452875380292 | epot = -23.1521162771299 | etot = -17.6925214286524 -577000 ekin = 2.45698150895878 | erot = 2.31876672704205 | epot = -23.1781917242716 | etot = -18.4024434882707 -578000 ekin = 2.59353106592521 | erot = 2.33790294336518 | epot = -23.2101395643707 | etot = -18.2787055550803 -579000 ekin = 2.58102015460711 | erot = 1.71748063175119 | epot = -23.1865014452815 | etot = -18.8880006589232 -580000 ekin = 2.30361750578347 | erot = 2.87410564379617 | epot = -23.2045008793077 | etot = -18.0267777297281 -581000 ekin = 2.45915247103344 | erot = 2.59640238490727 | epot = -23.1882783600354 | etot = -18.1327235040947 -582000 ekin = 2.33801590725494 | erot = 3.19256035650614 | epot = -23.2501410058056 | etot = -17.7195647420445 -583000 ekin = 1.95982078382855 | erot = 2.8194405158621 | epot = -23.4085593869414 | etot = -18.6292980872508 -584000 ekin = 2.00358327245437 | erot = 1.71267270263011 | epot = -23.4960310960901 | etot = -19.7797751210056 -585000 ekin = 2.28859150562676 | erot = 2.06309046911261 | epot = -23.5306230166998 | etot = -19.1789410419605 -586000 ekin = 2.21858454582016 | erot = 1.97776854350185 | epot = -23.4873397268817 | etot = -19.2909866375596 -587000 ekin = 3.70065233550663 | erot = 1.82187748311298 | epot = -23.4652388428899 | etot = -17.9427090242703 -588000 ekin = 3.49447328534893 | erot = 2.31981981591506 | epot = -23.3985567739262 | etot = -17.5842636726622 -589000 ekin = 2.66144502802388 | erot = 3.02756546370717 | epot = -23.2783756079917 | etot = -17.5893651162607 -590000 ekin = 1.52141257336428 | erot = 2.09874614600561 | epot = -23.1290158071881 | etot = -19.5088570878182 -591000 ekin = 1.82897193042273 | erot = 1.75592223095376 | epot = -23.0622736076074 | etot = -19.4773794462309 -592000 ekin = 2.49491276892191 | erot = 2.54829881978519 | epot = -23.054885494985 | etot = -18.0116739062779 -593000 ekin = 2.36845716276159 | erot = 1.78503341410575 | epot = -23.0052643101941 | etot = -18.8517737333267 -594000 ekin = 2.07907010887474 | erot = 2.14563658430187 | epot = -22.9611396232755 | etot = -18.7364329300989 -595000 ekin = 2.62736231723873 | erot = 2.0397582574453 | epot = -22.9495489717352 | etot = -18.2824283970512 -596000 ekin = 2.58985967531624 | erot = 2.12449830164849 | epot = -22.9908505579803 | etot = -18.2764925810155 -597000 ekin = 3.02540042664855 | erot = 3.14256707367048 | epot = -22.9740991012936 | etot = -16.8061316009746 -598000 ekin = 3.44397104083287 | erot = 2.86057908398566 | epot = -23.0035411551227 | etot = -16.6989910303042 -599000 ekin = 2.13932500926497 | erot = 3.49187029024977 | epot = -22.9657391359988 | etot = -17.334543836484 -600000 ekin = 2.19758597945325 | erot = 2.49610822362375 | epot = -22.9452235009931 | etot = -18.2515292979161 -601000 ekin = 2.80918982916751 | erot = 2.81768433603376 | epot = -22.8970508934525 | etot = -17.2701767282513 -602000 ekin = 2.30031523379462 | erot = 2.40907304500535 | epot = -22.8523950981498 | etot = -18.1430068193498 -603000 ekin = 1.9133550139642 | erot = 1.99518053980754 | epot = -22.7884152302357 | etot = -18.879879676464 -604000 ekin = 2.59767150954919 | erot = 3.14351403383689 | epot = -22.7430641975849 | etot = -17.0018786541988 -605000 ekin = 2.63203298717972 | erot = 2.07906613894388 | epot = -22.7307949909782 | etot = -18.0196958648546 -606000 ekin = 2.94678399289781 | erot = 2.03982213630798 | epot = -22.6555302524726 | etot = -17.6689241232668 -607000 ekin = 2.85272606479019 | erot = 2.3669346725768 | epot = -22.6318548820143 | etot = -17.4121941446474 -608000 ekin = 3.6642968125636 | erot = 2.46706737589233 | epot = -22.5724662590778 | etot = -16.4411020706218 -609000 ekin = 2.69343886620625 | erot = 2.25873504143678 | epot = -22.6007364465804 | etot = -17.6485625389374 -610000 ekin = 2.99904616523658 | erot = 2.13621966615343 | epot = -22.5973658485054 | etot = -17.4621000171154 -611000 ekin = 3.86832985948943 | erot = 2.1209664457764 | epot = -22.5702925425382 | etot = -16.5809962372724 -612000 ekin = 2.88515301824618 | erot = 2.45910554524355 | epot = -22.4848584522585 | etot = -17.1405998887688 -613000 ekin = 2.9367425327116 | erot = 2.14436169371534 | epot = -22.465526703267 | etot = -17.38442247684 -614000 ekin = 2.79116462876301 | erot = 2.024409539648 | epot = -22.5207406301148 | etot = -17.7051664617038 -615000 ekin = 2.29338048298908 | erot = 2.38828872470981 | epot = -22.6082782403584 | etot = -17.9266090326595 -616000 ekin = 1.78195169789474 | erot = 2.45334803626967 | epot = -22.6887534547644 | etot = -18.4534537206 -617000 ekin = 2.57505808534158 | erot = 2.55345758187856 | epot = -22.7014638394959 | etot = -17.5729481722758 -618000 ekin = 2.29561379442387 | erot = 2.68043259355499 | epot = -22.629958627306 | etot = -17.6539122393272 -619000 ekin = 1.94323313590202 | erot = 2.00964911157701 | epot = -22.5681911047399 | etot = -18.6153088572609 -620000 ekin = 2.92263589097657 | erot = 2.15657756066214 | epot = -22.6264664894927 | etot = -17.547253037854 -621000 ekin = 2.90437881656455 | erot = 1.70649555848315 | epot = -22.6654194475729 | etot = -18.0545450725253 -622000 ekin = 2.03426149564846 | erot = 2.51826459248401 | epot = -22.6086250578043 | etot = -18.0560989696718 -623000 ekin = 1.98348786592097 | erot = 3.08484972830225 | epot = -22.6234743341759 | etot = -17.5551367399527 -624000 ekin = 2.08463083558978 | erot = 2.64004606903046 | epot = -22.6266529328942 | etot = -17.901976028274 -625000 ekin = 2.52963490334089 | erot = 2.37033264022622 | epot = -22.6750436783155 | etot = -17.7750761347484 -626000 ekin = 2.73147680333727 | erot = 2.07051651598002 | epot = -22.7272383647964 | etot = -17.9252450454791 -627000 ekin = 2.23447399123207 | erot = 2.35288557052271 | epot = -22.7136740507756 | etot = -18.1263144890208 -628000 ekin = 2.28933754695898 | erot = 2.29676268895052 | epot = -22.6176528573237 | etot = -18.0315526214142 -629000 ekin = 2.5355466362136 | erot = 1.9208254303353 | epot = -22.5693331526924 | etot = -18.1129610861435 -630000 ekin = 3.11700824717166 | erot = 2.51611049765933 | epot = -22.5144695759915 | etot = -16.8813508311605 -631000 ekin = 2.38844807455605 | erot = 3.31601650504462 | epot = -22.5190998334878 | etot = -16.8146352538871 -632000 ekin = 2.59939587493746 | erot = 2.51496212358954 | epot = -22.4711049664696 | etot = -17.3567469679426 -633000 ekin = 2.45338619933597 | erot = 1.89874016257143 | epot = -22.4394257686937 | etot = -18.0872994067863 -634000 ekin = 2.23819111967046 | erot = 1.98305652730465 | epot = -22.3433365860708 | etot = -18.1220889390957 -635000 ekin = 2.22438000857701 | erot = 1.95893208021228 | epot = -22.2877959440852 | etot = -18.1044838552959 -636000 ekin = 2.26938644192167 | erot = 2.77816773779857 | epot = -22.304696935737 | etot = -17.2571427560168 -637000 ekin = 1.97799147515644 | erot = 2.59610837639354 | epot = -22.3353238115757 | etot = -17.7612239600257 -638000 ekin = 2.54901279963355 | erot = 3.14232301833368 | epot = -22.3113570318406 | etot = -16.6200212138734 -639000 ekin = 2.38194254982011 | erot = 2.49468098011846 | epot = -22.2696251856513 | etot = -17.3930016557128 -640000 ekin = 2.07438054408915 | erot = 2.20336226777045 | epot = -22.1673693230787 | etot = -17.8896265112191 -641000 ekin = 2.49150296422893 | erot = 3.53882164550032 | epot = -22.0473233874349 | etot = -16.0169987777057 -642000 ekin = 3.37964058409635 | erot = 2.18458831029804 | epot = -21.9324522713975 | etot = -16.3682233770031 -643000 ekin = 2.80862431007863 | erot = 2.40815089193717 | epot = -21.8726014240441 | etot = -16.6558262220283 -644000 ekin = 2.952235016065 | erot = 1.92776262379329 | epot = -21.8260574231829 | etot = -16.9460597833247 -645000 ekin = 4.10488984334312 | erot = 1.89062109330211 | epot = -21.7981661301139 | etot = -15.8026551934687 -646000 ekin = 2.50234872105284 | erot = 2.00205075040523 | epot = -21.7221642434957 | etot = -17.2177647720376 -647000 ekin = 2.52267281239589 | erot = 2.19481558810103 | epot = -21.7438885460027 | etot = -17.0264001455058 -648000 ekin = 2.99344241657583 | erot = 2.11139263207284 | epot = -21.7373240000025 | etot = -16.6324889513538 -649000 ekin = 2.55027365085817 | erot = 3.20350991793737 | epot = -21.7192481424448 | etot = -15.9654645736493 -650000 ekin = 3.75163896052814 | erot = 2.44189212282279 | epot = -21.6756681314986 | etot = -15.4821370481477 -651000 ekin = 3.29740056237165 | erot = 2.36780448747273 | epot = -21.5372361691657 | etot = -15.8720311193214 -652000 ekin = 2.54645886055823 | erot = 2.99097829596978 | epot = -21.4549655298412 | etot = -15.9175283733131 -653000 ekin = 2.88682688109756 | erot = 2.53633970608343 | epot = -21.4696471597398 | etot = -16.0464805725588 -654000 ekin = 2.28614085804932 | erot = 2.12026601708473 | epot = -21.5642684321318 | etot = -17.1578615569977 -655000 ekin = 2.20709609517086 | erot = 2.10729950549552 | epot = -21.5349466292622 | etot = -17.2205510285958 -656000 ekin = 2.40310876229412 | erot = 2.09663823500904 | epot = -21.5631924595208 | etot = -17.0634454622177 -657000 ekin = 2.78865513467509 | erot = 2.19608839827217 | epot = -21.794507747247 | etot = -16.8097642142997 -658000 ekin = 3.10257138071619 | erot = 2.59154293692776 | epot = -21.9667559942099 | etot = -16.272641676566 -659000 ekin = 2.88891106020275 | erot = 3.47010878893494 | epot = -22.0542552611187 | etot = -15.695235411981 -660000 ekin = 2.90074521854052 | erot = 1.62850743298557 | epot = -22.1003034196589 | etot = -17.5710507681328 -661000 ekin = 3.26666543815737 | erot = 1.86223225384177 | epot = -22.202664217118 | etot = -17.0737665251188 -662000 ekin = 3.1558491019044 | erot = 2.16868634291728 | epot = -22.3049478747804 | etot = -16.9804124299587 -663000 ekin = 1.94349853674084 | erot = 2.45687952722593 | epot = -22.3908978754177 | etot = -17.990519811451 -664000 ekin = 1.45445820960401 | erot = 1.37641815749116 | epot = -22.5088813854798 | etot = -19.6780050183846 -665000 ekin = 1.57568561901953 | erot = 2.30379312359824 | epot = -22.5957949572926 | etot = -18.7163162146748 -666000 ekin = 2.46162449261636 | erot = 1.76978614573264 | epot = -22.7431602236663 | etot = -18.5117495853173 -667000 ekin = 2.82410423268351 | erot = 2.3383666365949 | epot = -22.9350563238978 | etot = -17.7725854546193 -668000 ekin = 2.73717686116191 | erot = 3.18779777915034 | epot = -23.0188768131827 | etot = -17.0939021728704 -669000 ekin = 3.41035672635339 | erot = 2.4547960177761 | epot = -23.0718232403885 | etot = -17.206670496259 -670000 ekin = 2.54649164859505 | erot = 1.9952097916917 | epot = -23.0246775830826 | etot = -18.4829761427958 -671000 ekin = 2.3802025684166 | erot = 3.00742736998539 | epot = -23.0023479116088 | etot = -17.6147179732068 -672000 ekin = 3.0126952152146 | erot = 2.55297219144565 | epot = -22.9947723733501 | etot = -17.4291049666898 -673000 ekin = 3.39486270740071 | erot = 2.38087002620332 | epot = -22.9033457919094 | etot = -17.1276130583054 -674000 ekin = 3.13698489626098 | erot = 2.10609113054064 | epot = -22.8089270617647 | etot = -17.565851034963 -675000 ekin = 2.32294130821675 | erot = 1.52858514820731 | epot = -22.6840603385672 | etot = -18.8325338821432 -676000 ekin = 2.43564726401376 | erot = 2.26860623636409 | epot = -22.6133446272028 | etot = -17.9090911268249 -677000 ekin = 2.75162757613842 | erot = 1.94219014743456 | epot = -22.7039380847023 | etot = -18.0101203611293 -678000 ekin = 2.86321973687601 | erot = 1.66387788364136 | epot = -22.7223510604726 | etot = -18.1952534399552 -679000 ekin = 2.3507920877287 | erot = 2.70386328048644 | epot = -22.7977445343494 | etot = -17.7430891661343 -680000 ekin = 2.48449675729004 | erot = 2.90645575582477 | epot = -22.8559375688936 | etot = -17.4649850557788 -681000 ekin = 1.91581136662334 | erot = 2.58179603882022 | epot = -22.7891325966099 | etot = -18.2915251911664 -682000 ekin = 2.10466427353706 | erot = 2.69470735868805 | epot = -22.6959043279182 | etot = -17.896532695693 -683000 ekin = 2.34504535409022 | erot = 2.1159203570079 | epot = -22.5718670441909 | etot = -18.1109013330928 -684000 ekin = 2.87198876498959 | erot = 2.65732173958705 | epot = -22.4986977268025 | etot = -16.9693872222258 -685000 ekin = 3.03375238110976 | erot = 2.18190577381517 | epot = -22.4634189289575 | etot = -17.2477607740326 -686000 ekin = 2.46248931777657 | erot = 2.43025710170918 | epot = -22.4079029677658 | etot = -17.5151565482801 -687000 ekin = 2.74662486817896 | erot = 1.79609152562409 | epot = -22.3360381567114 | etot = -17.7933217629083 -688000 ekin = 1.81703718003042 | erot = 2.06511603415634 | epot = -22.3083758541197 | etot = -18.426222639933 -689000 ekin = 2.84202633430563 | erot = 1.92033962884778 | epot = -22.3752571185822 | etot = -17.6128911554288 -690000 ekin = 2.07525448405017 | erot = 2.46342632176817 | epot = -22.4633535431152 | etot = -17.9246727372969 -691000 ekin = 2.12558517800138 | erot = 2.52961097164 | epot = -22.483426266766 | etot = -17.8282301171246 -692000 ekin = 2.86720433292881 | erot = 2.65102150657025 | epot = -22.4003374064863 | etot = -16.8821115669872 -693000 ekin = 2.30143055084864 | erot = 2.5229094638336 | epot = -22.2859681228791 | etot = -17.4616281081969 -694000 ekin = 2.88400701080874 | erot = 2.34320802755438 | epot = -22.2063185842819 | etot = -16.9791035459188 -695000 ekin = 2.93184722112895 | erot = 2.22933507376833 | epot = -22.2348177906806 | etot = -17.0736354957833 -696000 ekin = 2.63173546326796 | erot = 2.34275369570834 | epot = -22.274597219839 | etot = -17.3001080608627 -697000 ekin = 1.87084079501972 | erot = 1.78050094908736 | epot = -22.2730387150935 | etot = -18.6216969709864 -698000 ekin = 2.19791428580687 | erot = 2.8288358175635 | epot = -22.2819378523404 | etot = -17.2551877489701 -699000 ekin = 2.34279295545267 | erot = 2.07514436344563 | epot = -22.2061425261575 | etot = -17.7882052072592 -700000 ekin = 2.576803119019 | erot = 2.32167543064962 | epot = -22.1658685747825 | etot = -17.2673900251139 -701000 ekin = 2.99438658075389 | erot = 1.89982533986207 | epot = -22.2191193266439 | etot = -17.3249074060279 -702000 ekin = 2.68548464757459 | erot = 2.65050744453206 | epot = -22.2547415922756 | etot = -16.918749500169 -703000 ekin = 2.01996957402024 | erot = 2.04032822241736 | epot = -22.3253693056515 | etot = -18.2650715092139 -704000 ekin = 1.58871069317829 | erot = 1.64014270467761 | epot = -22.3617232281452 | etot = -19.1328698302893 -705000 ekin = 2.3089415754982 | erot = 1.90252913035993 | epot = -22.4307958564623 | etot = -18.2193251506042 -706000 ekin = 2.61729186445575 | erot = 3.21879868039103 | epot = -22.5603358780911 | etot = -16.7242453332443 -707000 ekin = 2.60797107906866 | erot = 2.31455039977394 | epot = -22.7102471053997 | etot = -17.7877256265571 -708000 ekin = 1.81633850341999 | erot = 2.34822575669419 | epot = -22.841408787855 | etot = -18.6768445277408 -709000 ekin = 1.83541322105378 | erot = 2.51792380003796 | epot = -23.0137235815795 | etot = -18.6603865604877 -710000 ekin = 2.21420583262459 | erot = 1.92378721690472 | epot = -23.1433453130908 | etot = -19.0053522635615 -711000 ekin = 2.06744054454462 | erot = 2.39811709353194 | epot = -23.1532717948854 | etot = -18.6877141568089 -712000 ekin = 2.17279472706345 | erot = 1.75362175342097 | epot = -23.0479262273955 | etot = -19.121509746911 -713000 ekin = 2.87118830138473 | erot = 1.54943993787556 | epot = -22.8430575230906 | etot = -18.4224292838303 -714000 ekin = 2.01079466743971 | erot = 1.87510988392749 | epot = -22.9212969433222 | etot = -19.035392391955 -715000 ekin = 2.49921829589269 | erot = 1.91934008289237 | epot = -22.9679126658062 | etot = -18.5493542870212 -716000 ekin = 2.94666510633352 | erot = 2.18714442405523 | epot = -23.0339970974289 | etot = -17.9001875670402 -717000 ekin = 3.07404079722084 | erot = 2.46628262765134 | epot = -23.1869721551174 | etot = -17.6466487302452 -718000 ekin = 3.47060078371108 | erot = 2.28206620506098 | epot = -23.2524492340768 | etot = -17.4997822453048 -719000 ekin = 4.08343792096551 | erot = 3.10429377075216 | epot = -23.2448292181926 | etot = -16.0570975264749 -720000 ekin = 2.52774819763971 | erot = 1.92867508904585 | epot = -23.1435084559681 | etot = -18.6870851692826 -721000 ekin = 2.58294244811584 | erot = 2.0383053178033 | epot = -23.0601633758883 | etot = -18.4389156099691 -722000 ekin = 1.94458885450861 | erot = 2.32008660802526 | epot = -22.9811929404572 | etot = -18.7165174779233 -723000 ekin = 2.4199834057626 | erot = 2.12369728979368 | epot = -23.0570939793876 | etot = -18.5134132838313 -724000 ekin = 1.90406371300862 | erot = 1.97533505769877 | epot = -23.1267629042383 | etot = -19.2473641335309 -725000 ekin = 2.14287056473423 | erot = 2.79289687450021 | epot = -23.1695632046138 | etot = -18.2337957653793 -726000 ekin = 2.26423317099721 | erot = 2.55343019202652 | epot = -23.2432909083709 | etot = -18.4256275453472 -727000 ekin = 1.69816397656716 | erot = 2.64011919415554 | epot = -23.2988376893209 | etot = -18.9605545185982 -728000 ekin = 2.23000862561934 | erot = 3.5852147057867 | epot = -23.3528245832468 | etot = -17.5376012518407 -729000 ekin = 2.70076566380343 | erot = 1.73367306410751 | epot = -23.3971276122796 | etot = -18.9626888843686 -730000 ekin = 2.54818673802759 | erot = 2.77394958410254 | epot = -23.3988686964744 | etot = -18.0767323743443 -731000 ekin = 2.69782550956093 | erot = 2.04855826523075 | epot = -23.4310969813891 | etot = -18.6847132065974 -732000 ekin = 2.79613002753751 | erot = 1.87867430486714 | epot = -23.4885161441653 | etot = -18.8137118117607 -733000 ekin = 2.20346728125046 | erot = 2.64365594749976 | epot = -23.5261309431819 | etot = -18.6790077144316 -734000 ekin = 1.69780111261444 | erot = 2.30917909560789 | epot = -23.5188046470474 | etot = -19.5118244388251 -735000 ekin = 2.18402736165936 | erot = 2.72051620230872 | epot = -23.4712689506937 | etot = -18.5667253867257 -736000 ekin = 2.26138696009405 | erot = 1.17083930058802 | epot = -23.4348107178754 | etot = -20.0025844571933 -737000 ekin = 2.22219419044796 | erot = 3.14114682990359 | epot = -23.3869288757725 | etot = -18.0235878554209 -738000 ekin = 1.75464981631085 | erot = 2.28485941478059 | epot = -23.2709893028052 | etot = -19.2314800717138 -739000 ekin = 1.41806378584362 | erot = 2.1671403411282 | epot = -23.2213775300888 | etot = -19.636173403117 -740000 ekin = 1.90901017596351 | erot = 2.27102763422489 | epot = -23.1829198366046 | etot = -19.0028820264162 -741000 ekin = 1.9930994487751 | erot = 2.73523269523397 | epot = -23.1169670577823 | etot = -18.3886349137733 -742000 ekin = 1.99876411117685 | erot = 1.89882876917752 | epot = -23.030082580085 | etot = -19.1324896997307 -743000 ekin = 1.96472814667687 | erot = 2.79504722629176 | epot = -22.8990488521609 | etot = -18.1392734791923 -744000 ekin = 2.02442646092311 | erot = 2.35044838626025 | epot = -22.8186526150799 | etot = -18.4437777678966 -745000 ekin = 1.65344231988822 | erot = 1.87919095141019 | epot = -22.7624827109091 | etot = -19.2298494396107 -746000 ekin = 2.1034668185472 | erot = 2.03078530569664 | epot = -22.743454277698 | etot = -18.6092021534541 -747000 ekin = 3.06690414848489 | erot = 1.67540297869492 | epot = -22.7625979159322 | etot = -18.0202907887524 -748000 ekin = 3.06965414483401 | erot = 1.86014593098646 | epot = -22.8118567150739 | etot = -17.8820566392534 -749000 ekin = 2.53718696167216 | erot = 2.02710579059033 | epot = -22.8431046011969 | etot = -18.2788118489344 -750000 ekin = 2.756573548081 | erot = 2.34953156046293 | epot = -22.9548205390759 | etot = -17.8487154305319 -751000 ekin = 2.52290020835147 | erot = 2.34873763599979 | epot = -23.0238691402084 | etot = -18.1522312958572 -752000 ekin = 2.47222247869325 | erot = 1.68679846444685 | epot = -22.9958559112491 | etot = -18.836834968109 -753000 ekin = 2.48263277172423 | erot = 1.54669382815741 | epot = -23.0858212396418 | etot = -19.0564946397602 -754000 ekin = 2.54806257410878 | erot = 2.26636466676166 | epot = -23.1896472696843 | etot = -18.3752200288138 -755000 ekin = 1.53168409517921 | erot = 2.22665478278013 | epot = -23.2059118234918 | etot = -19.4475729455324 -756000 ekin = 2.10751715527953 | erot = 2.40525774326678 | epot = -23.114150245375 | etot = -18.6013753468287 -757000 ekin = 2.93395895491028 | erot = 2.05821177584912 | epot = -23.0783355599275 | etot = -18.0861648291681 -758000 ekin = 2.38307945406233 | erot = 2.50598165375059 | epot = -22.9691152621287 | etot = -18.0800541543158 -759000 ekin = 2.60292884338835 | erot = 2.36916677072546 | epot = -22.7987274767845 | etot = -17.8266318626707 -760000 ekin = 3.2284318196987 | erot = 2.73822716520639 | epot = -22.6756147646272 | etot = -16.7089557797221 -761000 ekin = 3.41868727786494 | erot = 1.68975765213406 | epot = -22.5638952547581 | etot = -17.4554503247591 -762000 ekin = 3.43033946346107 | erot = 2.5283975140253 | epot = -22.3549032489322 | etot = -16.3961662714458 -763000 ekin = 2.65773094814485 | erot = 1.8397513397556 | epot = -22.234833339183 | etot = -17.7373510512825 -764000 ekin = 2.3815484472129 | erot = 2.70684992442146 | epot = -22.0890752688231 | etot = -17.0006768971887 -765000 ekin = 2.23212803588897 | erot = 1.94868597739427 | epot = -21.9918715237933 | etot = -17.81105751051 -766000 ekin = 2.49097891886065 | erot = 1.96764603993155 | epot = -21.8443436680801 | etot = -17.3857187092879 -767000 ekin = 2.34579214976749 | erot = 2.64636009163515 | epot = -21.7634962034012 | etot = -16.7713439619986 -768000 ekin = 1.87671147825105 | erot = 2.05549869178485 | epot = -21.7324638416527 | etot = -17.8002536716168 -769000 ekin = 3.05058687860238 | erot = 2.66104171022372 | epot = -21.6679219598699 | etot = -15.9562933710438 -770000 ekin = 2.44115683640632 | erot = 1.9755493247975 | epot = -21.644882066475 | etot = -17.2281759052712 -771000 ekin = 2.23687464004429 | erot = 2.5504097070879 | epot = -21.5811924169691 | etot = -16.793908069837 -772000 ekin = 2.76529680592008 | erot = 1.97873499811186 | epot = -21.6543448952384 | etot = -16.9103130912064 -773000 ekin = 2.14632888240094 | erot = 2.41330587525516 | epot = -21.7728828090227 | etot = -17.2132480513667 -774000 ekin = 2.19848545803079 | erot = 1.9765131024719 | epot = -21.8398858604883 | etot = -17.6648872999856 -775000 ekin = 2.52300137989083 | erot = 2.80935365273516 | epot = -22.0219985274259 | etot = -16.6896434947999 -776000 ekin = 3.15842485269273 | erot = 2.47066157093646 | epot = -22.183029096161 | etot = -16.5539426725318 -777000 ekin = 1.91784338934576 | erot = 1.76045300517084 | epot = -22.2259652888115 | etot = -18.5476688942949 -778000 ekin = 2.93738066043323 | erot = 2.2945784249029 | epot = -22.2339481852393 | etot = -17.0019890999032 -779000 ekin = 3.09847206114319 | erot = 2.0455771700605 | epot = -22.240438366259 | etot = -17.0963891350553 -780000 ekin = 2.86127568397807 | erot = 3.12055135138657 | epot = -22.1865692766137 | etot = -16.2047422412491 -781000 ekin = 2.36069914420785 | erot = 3.53186431088488 | epot = -22.1210563364352 | etot = -16.2284928813425 -782000 ekin = 2.31592690319261 | erot = 2.85730598644035 | epot = -22.0302855151548 | etot = -16.8570526255218 -783000 ekin = 1.86647729944746 | erot = 3.03450246093096 | epot = -21.8860143679489 | etot = -16.9850346075705 -784000 ekin = 2.04055627573201 | erot = 2.26047908607292 | epot = -21.7534271639393 | etot = -17.4523918021343 -785000 ekin = 2.02248469828703 | erot = 2.13950421850547 | epot = -21.6318967501918 | etot = -17.4699078333993 -786000 ekin = 2.34211746551601 | erot = 2.34838133643264 | epot = -21.5890308210084 | etot = -16.8985320190598 -787000 ekin = 2.74971447554938 | erot = 2.24123553296042 | epot = -21.5192132515563 | etot = -16.5282632430465 -788000 ekin = 2.14142056672039 | erot = 2.27008574684963 | epot = -21.4982362621713 | etot = -17.0867299486013 -789000 ekin = 1.98580913341303 | erot = 2.00702444041792 | epot = -21.5235331659838 | etot = -17.5306995921528 -790000 ekin = 1.68578263083924 | erot = 1.43485602862152 | epot = -21.64400815936 | etot = -18.5233694998993 -791000 ekin = 2.13583938840528 | erot = 2.53730095458942 | epot = -21.7916440698418 | etot = -17.1185037268471 -792000 ekin = 1.71937483898028 | erot = 2.1956380421601 | epot = -21.8794946709408 | etot = -17.9644817898004 -793000 ekin = 3.15868943755338 | erot = 1.94575875708421 | epot = -22.0398145404618 | etot = -16.9353663458242 -794000 ekin = 2.45478602538953 | erot = 3.00825554959564 | epot = -22.0843165283013 | etot = -16.6212749533161 -795000 ekin = 2.87760320917193 | erot = 3.06920266633565 | epot = -22.1595628991904 | etot = -16.2127570236828 -796000 ekin = 2.29816690595058 | erot = 1.61510864654314 | epot = -22.1869705548184 | etot = -18.2736950023247 -797000 ekin = 2.1901525606721 | erot = 3.65734446008351 | epot = -22.1432608090644 | etot = -16.2957637883088 -798000 ekin = 2.12018787925578 | erot = 2.92822258455554 | epot = -22.1311312789224 | etot = -17.0827208151111 -799000 ekin = 2.49416140154829 | erot = 2.73328283280217 | epot = -22.0825726051882 | etot = -16.8551283708377 -800000 ekin = 2.18932007838552 | erot = 2.97640731559392 | epot = -21.9793621521909 | etot = -16.8136347582115 -801000 ekin = 2.58827112124839 | erot = 2.7440442483726 | epot = -21.9108490336924 | etot = -16.5785336640714 -802000 ekin = 3.07870342348167 | erot = 2.87961505564285 | epot = -21.822560433681 | etot = -15.8642419545565 -803000 ekin = 2.2398624368064 | erot = 2.50525058807594 | epot = -21.72759408181 | etot = -16.9824810569277 -804000 ekin = 2.91885860068427 | erot = 1.57889040451429 | epot = -21.6896376725624 | etot = -17.1918886673638 -805000 ekin = 2.68277363980194 | erot = 3.0552786891574 | epot = -21.6710764398127 | etot = -15.9330241108533 -806000 ekin = 2.77769607049014 | erot = 2.18887276909081 | epot = -21.6314833902336 | etot = -16.6649145506527 -807000 ekin = 2.12673239079668 | erot = 2.86003407600807 | epot = -21.7295924017744 | etot = -16.7428259349697 -808000 ekin = 1.89599614774678 | erot = 2.29237053227661 | epot = -21.7511361510417 | etot = -17.5627694710183 -809000 ekin = 1.96405066221971 | erot = 1.92110393348367 | epot = -21.7075506883706 | etot = -17.8223960926672 -810000 ekin = 2.01518137594275 | erot = 2.60119247286596 | epot = -21.6788385874729 | etot = -17.0624647386642 -811000 ekin = 2.31084800889289 | erot = 1.75270367309064 | epot = -21.6837819033718 | etot = -17.6202302213883 -812000 ekin = 2.57701031002089 | erot = 2.34932304073588 | epot = -21.7246716033188 | etot = -16.798338252562 -813000 ekin = 2.87706904926076 | erot = 2.35686610624156 | epot = -21.8375922236049 | etot = -16.6036570681026 -814000 ekin = 2.89908405023865 | erot = 2.31423299883227 | epot = -21.8379261473901 | etot = -16.6246090983192 -815000 ekin = 2.54050064212256 | erot = 2.82732568868832 | epot = -21.6068952707049 | etot = -16.239068939894 -816000 ekin = 2.17040404256386 | erot = 2.53711088209171 | epot = -21.5560322071982 | etot = -16.8485172825427 -817000 ekin = 1.7842696071831 | erot = 2.67810959410575 | epot = -21.8738878035325 | etot = -17.4115086022436 -818000 ekin = 2.29659398017837 | erot = 2.63718862373661 | epot = -22.164277271391 | etot = -17.230494667476 -819000 ekin = 2.15801167884061 | erot = 2.62095572928876 | epot = -22.1816109590115 | etot = -17.4026435508821 -820000 ekin = 1.94384548213955 | erot = 2.28597987799276 | epot = -22.0986187375021 | etot = -17.8687933773698 -821000 ekin = 2.10513194007576 | erot = 2.3869817556922 | epot = -22.1146754444784 | etot = -17.6225617487105 -822000 ekin = 2.2481971678644 | erot = 2.15258805680876 | epot = -22.0539472940485 | etot = -17.6531620693753 -823000 ekin = 2.26584952085582 | erot = 2.60619852526611 | epot = -22.0924201800579 | etot = -17.2203721339359 -824000 ekin = 1.65187935478514 | erot = 1.48703119037229 | epot = -22.1682955997985 | etot = -19.0293850546411 -825000 ekin = 1.60213094818649 | erot = 1.98592524368393 | epot = -22.1687104063708 | etot = -18.5806542145004 -826000 ekin = 1.97430720107255 | erot = 2.19175014677162 | epot = -22.1061881978654 | etot = -17.9401308500212 -827000 ekin = 2.1793755983405 | erot = 2.44975419075935 | epot = -21.9704586607304 | etot = -17.3413288716305 -828000 ekin = 1.90399088418587 | erot = 2.72532994798818 | epot = -21.9585923270582 | etot = -17.3292714948841 -829000 ekin = 2.06478103068884 | erot = 2.96583035402589 | epot = -21.9849402038681 | etot = -16.9543288191534 -830000 ekin = 1.98920675238979 | erot = 2.15331250444998 | epot = -22.0339146439702 | etot = -17.8913953871304 -831000 ekin = 2.33567462674689 | erot = 2.36888807413497 | epot = -22.1271573756461 | etot = -17.4225946747642 -832000 ekin = 2.01194709991921 | erot = 1.94769143293624 | epot = -22.2038482709588 | etot = -18.2442097381033 -833000 ekin = 2.26025933495882 | erot = 2.16012558191462 | epot = -22.2882501045414 | etot = -17.867865187668 -834000 ekin = 2.11529426445865 | erot = 1.52405523315359 | epot = -22.3075608649825 | etot = -18.6682113673703 -835000 ekin = 2.89920750905511 | erot = 2.7380108175103 | epot = -22.3942491248321 | etot = -16.7570307982667 -836000 ekin = 3.33069528982658 | erot = 2.42771267807862 | epot = -22.4321737300743 | etot = -16.6737657621691 -837000 ekin = 2.74831774333782 | erot = 2.31991750378627 | epot = -22.4290234552872 | etot = -17.3607882081631 -838000 ekin = 3.13714871682188 | erot = 3.21601751721778 | epot = -22.464238390645 | etot = -16.1110721566054 -839000 ekin = 2.73358272751807 | erot = 2.60144488190506 | epot = -22.4062682687367 | etot = -17.0712406593136 -840000 ekin = 2.96121930874636 | erot = 1.42725942278117 | epot = -22.3293755621293 | etot = -17.9408968306018 -841000 ekin = 2.95134811170866 | erot = 2.67666861874609 | epot = -22.2936348151224 | etot = -16.6656180846676 -842000 ekin = 2.15783928636402 | erot = 2.30287195796691 | epot = -22.2978011147172 | etot = -17.8370898703863 -843000 ekin = 2.84565152669617 | erot = 2.05108014775139 | epot = -22.3162908719778 | etot = -17.4195591975303 -844000 ekin = 2.99645803669157 | erot = 1.50433298006521 | epot = -22.3768320579304 | etot = -17.8760410411736 -845000 ekin = 3.20248025697125 | erot = 2.27246140825564 | epot = -22.3985708422076 | etot = -16.9236291769807 -846000 ekin = 3.35773945734322 | erot = 2.54074745551552 | epot = -22.4144833015876 | etot = -16.5159963887288 -847000 ekin = 2.17779203733109 | erot = 2.7381758118846 | epot = -22.3524825149514 | etot = -17.4365146657357 -848000 ekin = 2.51627348417144 | erot = 2.81170686694718 | epot = -22.2066307862469 | etot = -16.8786504351283 -849000 ekin = 1.99679455190557 | erot = 2.5685584677309 | epot = -22.0763062134929 | etot = -17.5109531938564 -850000 ekin = 2.05799123916877 | erot = 1.80888056240785 | epot = -22.0665032506705 | etot = -18.1996314490939 -851000 ekin = 2.08889793767921 | erot = 1.86172181790291 | epot = -22.0629711763889 | etot = -18.1123514208068 -852000 ekin = 1.68990805178902 | erot = 1.42763535981882 | epot = -22.002100112701 | etot = -18.8845567010931 -853000 ekin = 1.99310886654811 | erot = 3.05226969048294 | epot = -22.0306903552277 | etot = -16.9853117981967 -854000 ekin = 2.98378700534986 | erot = 2.23102745240542 | epot = -22.1115820238811 | etot = -16.8967675661258 -855000 ekin = 2.17087415585277 | erot = 2.83781472268791 | epot = -22.111510639597 | etot = -17.1028217610564 -856000 ekin = 2.42228475387308 | erot = 1.53328604594476 | epot = -22.0841888628208 | etot = -18.128618063003 -857000 ekin = 2.50431566526893 | erot = 2.80498769176513 | epot = -21.9881235267533 | etot = -16.6788201697193 -858000 ekin = 2.17333686672378 | erot = 2.8259111550717 | epot = -21.9093201368614 | etot = -16.9100721150659 -859000 ekin = 2.29930070497242 | erot = 2.32417368939059 | epot = -21.8849849636103 | etot = -17.2615105692473 -860000 ekin = 1.99153024057672 | erot = 1.9467463860015 | epot = -21.8998709373216 | etot = -17.9615943107434 -861000 ekin = 2.69177523559624 | erot = 2.23997750036371 | epot = -21.8915522194994 | etot = -16.9597994835394 -862000 ekin = 2.86117050047985 | erot = 2.41530060322761 | epot = -21.876687883023 | etot = -16.6002167793155 -863000 ekin = 2.59841547044276 | erot = 3.35017050085432 | epot = -21.8162649771436 | etot = -15.8676790058466 -864000 ekin = 2.92496272611018 | erot = 2.30350236144452 | epot = -21.7820358973268 | etot = -16.5535708097721 -865000 ekin = 1.94718216128952 | erot = 2.16572180916633 | epot = -21.7000823492195 | etot = -17.5871783787636 -866000 ekin = 1.9900612787169 | erot = 1.65011901234952 | epot = -21.6190182409267 | etot = -17.9788379498603 -867000 ekin = 1.76250718110787 | erot = 3.37958608370307 | epot = -21.5401486584561 | etot = -16.3980553936451 -868000 ekin = 1.845623450314 | erot = 2.78812196028613 | epot = -21.5771917352235 | etot = -16.9434463246233 -869000 ekin = 2.39300849969204 | erot = 2.38301618173174 | epot = -21.6710790825578 | etot = -16.895054401134 -870000 ekin = 1.91899243212541 | erot = 3.22222440717391 | epot = -21.6734733803871 | etot = -16.5322565410878 -871000 ekin = 3.10255827845531 | erot = 2.95454268850897 | epot = -21.5913249106744 | etot = -15.5342239437101 -872000 ekin = 2.94582883077842 | erot = 1.38261935263093 | epot = -21.4597055547832 | etot = -17.1312573713739 -873000 ekin = 2.72830997927423 | erot = 2.23223699637276 | epot = -21.3657566950046 | etot = -16.4052097193576 -874000 ekin = 2.41464704842014 | erot = 2.10351476791497 | epot = -21.2635161734954 | etot = -16.7453543571603 -875000 ekin = 2.99468455803481 | erot = 2.72761242382523 | epot = -21.248888128938 | etot = -15.526591147078 -876000 ekin = 2.13382009818493 | erot = 2.23152059294678 | epot = -21.2388603913311 | etot = -16.8735197001994 -877000 ekin = 1.839391763993 | erot = 1.60727997722602 | epot = -21.2015948102408 | etot = -17.7549230690217 -878000 ekin = 2.01267175782178 | erot = 2.73109796378376 | epot = -21.2125253160263 | etot = -16.4687555944207 -879000 ekin = 1.42911941081343 | erot = 2.17371661448624 | epot = -21.1345316334464 | etot = -17.5316956081467 -880000 ekin = 2.10605339224632 | erot = 2.58847517789128 | epot = -21.0787246891645 | etot = -16.3841961190269 -881000 ekin = 1.54924791070118 | erot = 2.00685139154178 | epot = -21.1356465207066 | etot = -17.5795472184636 -882000 ekin = 2.199643157135 | erot = 2.65509097106009 | epot = -21.2389026935677 | etot = -16.3841685653726 -883000 ekin = 2.20850404171077 | erot = 2.22833605977577 | epot = -21.3067394383395 | etot = -16.8698993368529 -884000 ekin = 2.76978562647275 | erot = 2.10395845939753 | epot = -21.3429618615584 | etot = -16.4692177756882 -885000 ekin = 1.93339807672781 | erot = 1.77156241344965 | epot = -21.3858074096933 | etot = -17.6808469195158 -886000 ekin = 2.00408769971894 | erot = 3.10736267931433 | epot = -21.3935346347812 | etot = -16.2820842557479 -887000 ekin = 1.96987943750801 | erot = 2.82035886899742 | epot = -21.3967073105592 | etot = -16.6064690040538 -888000 ekin = 1.91464371566412 | erot = 2.33371232948869 | epot = -21.4767119016419 | etot = -17.2283558564891 -889000 ekin = 1.88227414130201 | erot = 2.45915914930409 | epot = -21.5790392436829 | etot = -17.2376059530768 -890000 ekin = 1.84515176532447 | erot = 2.24992378831496 | epot = -21.6747594004542 | etot = -17.5796838468148 -891000 ekin = 2.6016566869706 | erot = 2.34500453305756 | epot = -21.8016735536793 | etot = -16.8550123336512 -892000 ekin = 2.71287751886859 | erot = 2.69544224573132 | epot = -21.9063749565584 | etot = -16.4980551919585 -893000 ekin = 2.17862714611329 | erot = 2.98452123742221 | epot = -21.9155556335136 | etot = -16.7524072499781 -894000 ekin = 2.52079948361477 | erot = 2.46355933674926 | epot = -21.9151100794549 | etot = -16.9307512590909 -895000 ekin = 2.53566097944338 | erot = 2.45130454442939 | epot = -21.9477860878339 | etot = -16.9608205639611 -896000 ekin = 1.84455393639213 | erot = 2.77499090684944 | epot = -21.9167554809878 | etot = -17.2972106377462 -897000 ekin = 2.38519326880694 | erot = 2.019802873173 | epot = -21.8644918203992 | etot = -17.4594956784193 -898000 ekin = 2.14354914407572 | erot = 1.89196669459414 | epot = -21.7953104274974 | etot = -17.7597945888275 -899000 ekin = 2.65485657727374 | erot = 2.32374560038191 | epot = -21.6964754705568 | etot = -16.7178732929011 -900000 ekin = 2.1437154528087 | erot = 2.28119066740276 | epot = -21.6934954112434 | etot = -17.2685892910319 -901000 ekin = 1.9396581494688 | erot = 1.81495571440908 | epot = -21.7369092433376 | etot = -17.9822953794597 -902000 ekin = 2.60993957981555 | erot = 2.50321386623392 | epot = -21.6842517568354 | etot = -16.5710983107859 -903000 ekin = 1.87484955546756 | erot = 2.17008893987963 | epot = -21.6383913984978 | etot = -17.5934529031506 -904000 ekin = 1.87454064845764 | erot = 2.32484081519397 | epot = -21.5866637125315 | etot = -17.3872822488799 -905000 ekin = 2.31407473814843 | erot = 2.15094868542393 | epot = -21.5154415841816 | etot = -17.0504181606092 -906000 ekin = 2.49583383758853 | erot = 2.25091096848465 | epot = -21.5170853902294 | etot = -16.7703405841562 -907000 ekin = 4.19798796104343 | erot = 2.50305323228071 | epot = -21.5976736513859 | etot = -14.8966324580617 -908000 ekin = 3.26730891548756 | erot = 2.11222217905481 | epot = -21.7526644402475 | etot = -16.3731333457052 -909000 ekin = 2.64106561110374 | erot = 1.92197432194202 | epot = -21.8748043207924 | etot = -17.3117643877466 -910000 ekin = 2.61805562731904 | erot = 2.90737422678698 | epot = -21.9709470207745 | etot = -16.4455171666685 -911000 ekin = 2.62012718860141 | erot = 4.35318528241845 | epot = -22.0282478750366 | etot = -15.0549354040167 -912000 ekin = 3.07628909273119 | erot = 3.69371809788395 | epot = -22.0511180009901 | etot = -15.2811108103749 -913000 ekin = 2.82956898268832 | erot = 2.17078429141201 | epot = -22.0149543706266 | etot = -17.0146010965263 -914000 ekin = 2.16386655780066 | erot = 1.22303673036132 | epot = -21.9243495493208 | etot = -18.5374462611588 -915000 ekin = 1.59447095066509 | erot = 2.95966391292003 | epot = -21.8264580452026 | etot = -17.2723231816175 -916000 ekin = 2.58365539107524 | erot = 3.75147270955028 | epot = -21.8922962938607 | etot = -15.5571681932352 -917000 ekin = 3.01643029206973 | erot = 2.88035639021002 | epot = -21.9150526568514 | etot = -16.0182659745717 -918000 ekin = 2.89929776900147 | erot = 2.64137394041291 | epot = -21.9078998623094 | etot = -16.367228152895 -919000 ekin = 3.20476671865013 | erot = 2.76036957969153 | epot = -21.8878055443404 | etot = -15.9226692459987 -920000 ekin = 2.28949350558684 | erot = 2.38558870046817 | epot = -21.8659406759967 | etot = -17.1908584699417 -921000 ekin = 2.39158312157106 | erot = 2.44959700788171 | epot = -21.8638974869224 | etot = -17.0227173574696 -922000 ekin = 2.30678787768013 | erot = 2.42145678067296 | epot = -21.8218369909645 | etot = -17.0935923326114 -923000 ekin = 2.49697778842282 | erot = 2.66565493744118 | epot = -21.8078634464732 | etot = -16.6452307206092 -924000 ekin = 1.55676047489502 | erot = 2.97115254541009 | epot = -21.7829722234117 | etot = -17.2550592031066 -925000 ekin = 1.86603413909288 | erot = 1.96274861601778 | epot = -21.7288604040748 | etot = -17.9000776489642 -926000 ekin = 1.36993364395821 | erot = 2.11749584641399 | epot = -21.7083442855147 | etot = -18.2209147951426 -927000 ekin = 2.55718977538496 | erot = 2.08109095048878 | epot = -21.7242353526192 | etot = -17.0859546267455 -928000 ekin = 2.0974272910786 | erot = 2.73922911267238 | epot = -21.7673808868818 | etot = -16.9307244831309 -929000 ekin = 1.85550591174835 | erot = 1.84990976935039 | epot = -21.8639426090856 | etot = -18.1585269279869 -930000 ekin = 1.99594723517184 | erot = 2.09151231016389 | epot = -21.8461015073052 | etot = -17.7586419619695 -931000 ekin = 2.45331651079282 | erot = 1.86703658018612 | epot = -21.7382799817761 | etot = -17.4179268907972 -932000 ekin = 2.76909250526758 | erot = 2.34990175754267 | epot = -21.7639792890093 | etot = -16.6449850261991 -933000 ekin = 3.0474736633548 | erot = 2.52740756503517 | epot = -21.6783727845496 | etot = -16.1034915561596 -934000 ekin = 2.93463275640818 | erot = 2.48893095891024 | epot = -21.5784996926913 | etot = -16.1549359773729 -935000 ekin = 2.77799347567549 | erot = 2.13929358412251 | epot = -21.5334239467005 | etot = -16.6161368869025 -936000 ekin = 2.96529953690397 | erot = 2.07095365726712 | epot = -21.5249249864243 | etot = -16.4886717922532 -937000 ekin = 3.04850537701749 | erot = 2.32432162998049 | epot = -21.4386642161072 | etot = -16.0658372091092 -938000 ekin = 2.99262628505359 | erot = 2.35224559307842 | epot = -21.3457080466207 | etot = -16.0008361684887 -939000 ekin = 2.61238181353702 | erot = 2.2678035683729 | epot = -21.3079422537804 | etot = -16.4277568718705 -940000 ekin = 2.65930112044941 | erot = 2.75497479722395 | epot = -21.2170493356503 | etot = -15.8027734179769 -941000 ekin = 2.27574261339217 | erot = 2.61419196501686 | epot = -21.1297657597672 | etot = -16.2398311813582 -942000 ekin = 1.89172011891054 | erot = 2.82029488513786 | epot = -21.0410099256113 | etot = -16.3289949215629 -943000 ekin = 2.47643464476757 | erot = 2.34737109151874 | epot = -21.0466687727979 | etot = -16.2228630365116 -944000 ekin = 2.13883995897326 | erot = 1.92577316206135 | epot = -21.0114219746513 | etot = -16.9468088536167 -945000 ekin = 2.57768697869113 | erot = 2.21470136124071 | epot = -21.0634624131724 | etot = -16.2710740732406 -946000 ekin = 2.36420709243626 | erot = 2.89647330776423 | epot = -21.088814693033 | etot = -15.8281342928325 -947000 ekin = 2.07104171538468 | erot = 1.86575631327233 | epot = -21.1004860950451 | etot = -17.1636880663881 -948000 ekin = 1.85532958802996 | erot = 1.36952834086551 | epot = -21.1364231315615 | etot = -17.911565202666 -949000 ekin = 1.76206591178366 | erot = 2.3173732855863 | epot = -21.1463744779337 | etot = -17.0669352805637 -950000 ekin = 1.72021033353108 | erot = 2.24191394295309 | epot = -21.1376324866855 | etot = -17.1755082102013 -951000 ekin = 1.96140007830504 | erot = 2.32248863487758 | epot = -21.1955927656813 | etot = -16.9117040524986 -952000 ekin = 2.93256201500607 | erot = 2.74550490827502 | epot = -21.234781024541 | etot = -15.5567141012599 -953000 ekin = 2.95031285986316 | erot = 2.39822873263992 | epot = -21.252609183133 | etot = -15.9040675906299 -954000 ekin = 3.09579074538113 | erot = 1.98159252445734 | epot = -21.1641538136741 | etot = -16.0867705438357 -955000 ekin = 3.59360323486037 | erot = 2.06789679071824 | epot = -21.0522880782497 | etot = -15.3907880526711 -956000 ekin = 2.97416074498495 | erot = 3.66953591785754 | epot = -20.9097603766373 | etot = -14.2660637137948 -957000 ekin = 3.03140562067951 | erot = 2.6607808376071 | epot = -20.741905867784 | etot = -15.0497194094974 -958000 ekin = 2.68913434704071 | erot = 2.94057112873837 | epot = -20.5488384129042 | etot = -14.9191329371251 -959000 ekin = 1.93264217407773 | erot = 2.45198406257091 | epot = -20.468781161493 | etot = -16.0841549248444 -960000 ekin = 1.49632279167951 | erot = 3.13346348599985 | epot = -20.4844974178568 | etot = -15.8547111401775 -961000 ekin = 1.96353429663481 | erot = 2.07553358516997 | epot = -20.4805590123498 | etot = -16.441491130545 -962000 ekin = 2.02830196392006 | erot = 1.88908496389356 | epot = -20.5374211599972 | etot = -16.6200342321836 -963000 ekin = 1.80829526034561 | erot = 2.46258345726266 | epot = -20.5841835730968 | etot = -16.3133048554885 -964000 ekin = 2.79449124937198 | erot = 2.42527551362847 | epot = -20.6238805444481 | etot = -15.4041137814477 -965000 ekin = 2.53493670506137 | erot = 2.27804362684502 | epot = -20.6549300812152 | etot = -15.8419497493088 -966000 ekin = 2.0920817650402 | erot = 2.27478990703181 | epot = -20.7044739042411 | etot = -16.3376022321691 -967000 ekin = 1.55562260797661 | erot = 3.55543363172461 | epot = -20.739375276301 | etot = -15.6283190365998 -968000 ekin = 1.93439891222236 | erot = 2.37295903815892 | epot = -20.7189229543386 | etot = -16.4115650039573 -969000 ekin = 2.16199728898304 | erot = 2.4601205252494 | epot = -20.6747113173024 | etot = -16.05259350307 -970000 ekin = 1.84926216722517 | erot = 2.96951777569265 | epot = -20.601159998151 | etot = -15.7823800552332 -971000 ekin = 1.93656411083027 | erot = 3.08724923997924 | epot = -20.5835250734813 | etot = -15.5597117226718 -972000 ekin = 1.90452783927712 | erot = 2.58230766783159 | epot = -20.578290598021 | etot = -16.0914550909123 -973000 ekin = 2.1922712122506 | erot = 2.92686386394504 | epot = -20.586817370265 | etot = -15.4676822940694 -974000 ekin = 2.53094641465528 | erot = 2.69271305556799 | epot = -20.5382547781502 | etot = -15.314595307927 -975000 ekin = 3.41187201669924 | erot = 2.32917219553093 | epot = -20.5109803919918 | etot = -14.7699361797616 -976000 ekin = 2.88156114272554 | erot = 3.10474521611249 | epot = -20.5158119249461 | etot = -14.5295055661081 -977000 ekin = 2.73962881168093 | erot = 2.50884169958543 | epot = -20.4964590298 | etot = -15.2479885185336 -978000 ekin = 1.79682802545478 | erot = 2.06924041504343 | epot = -20.4730821934977 | etot = -16.6070137529995 -979000 ekin = 1.86521389998383 | erot = 2.22151626929011 | epot = -20.4069392895634 | etot = -16.3202091202895 -980000 ekin = 1.92383169177415 | erot = 1.56425965548878 | epot = -20.3533353734709 | etot = -16.8652440262079 -981000 ekin = 1.5511019928294 | erot = 2.05381225133937 | epot = -20.3970890782077 | etot = -16.7921748340389 -982000 ekin = 1.85559395816059 | erot = 1.96991369841494 | epot = -20.499354149896 | etot = -16.6738464933205 -983000 ekin = 2.75061857015335 | erot = 1.7944840218308 | epot = -20.5241519929379 | etot = -15.9790494009537 -984000 ekin = 3.65069712553538 | erot = 2.64237329124735 | epot = -20.6374699142713 | etot = -14.3443994974885 -985000 ekin = 2.95637321931061 | erot = 2.18846412126771 | epot = -20.8122975273334 | etot = -15.6674601867551 -986000 ekin = 2.87072902054599 | erot = 2.18810434250117 | epot = -20.9390290724606 | etot = -15.8801957094134 -987000 ekin = 3.37463328642758 | erot = 2.53713666674669 | epot = -21.0098323012659 | etot = -15.0980623480916 -988000 ekin = 3.45107854450337 | erot = 3.23625536313168 | epot = -21.0554260480417 | etot = -14.3680921404067 -989000 ekin = 2.83591404363755 | erot = 2.20564156324815 | epot = -21.19499265416 | etot = -16.1534370472743 -990000 ekin = 2.79864389348437 | erot = 1.8317842666354 | epot = -21.1880268304373 | etot = -16.5575986703175 -991000 ekin = 3.14781925181036 | erot = 3.20782471808907 | epot = -21.1115234865128 | etot = -14.7558795166134 -992000 ekin = 3.30033725309946 | erot = 2.62749912694386 | epot = -21.0030296251663 | etot = -15.0751932451229 -993000 ekin = 3.07374297249948 | erot = 2.22697230616357 | epot = -20.9385586572609 | etot = -15.6378433785979 -994000 ekin = 3.21461776403449 | erot = 2.80599707993708 | epot = -20.8790524582442 | etot = -14.8584376142727 -995000 ekin = 3.25071478747346 | erot = 1.73415439498321 | epot = -20.8037804714003 | etot = -15.8189112889436 -996000 ekin = 3.07999632962569 | erot = 3.18107550500821 | epot = -20.7805295335828 | etot = -14.5194576989489 -997000 ekin = 2.97118118001025 | erot = 3.14046656474895 | epot = -20.7334885248756 | etot = -14.6218407801164 -998000 ekin = 3.09169861594907 | erot = 1.99060706981745 | epot = -20.6553134096535 | etot = -15.573007723887 -999000 ekin = 2.0749813057658 | erot = 2.75045972766915 | epot = -20.6160915262949 | etot = -15.79065049286 -1000000 ekin = 2.07851119592056 | erot = 2.11869313853033 | epot = -20.4539417072874 | etot = -16.2567373728365 - 1000000 0.092378275 -1.3359709 0.057599499 -1.1484644 -5.0252938e-05 -Loop time of 41.7341 on 1 procs for 1000000 steps with 16 atoms - -Performance: 20702.495 tau/day, 23961.221 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 29.954 | 29.954 | 29.954 | 0.0 | 71.77 -Bond | 1.0147 | 1.0147 | 1.0147 | 0.0 | 2.43 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.32043 | 0.32043 | 0.32043 | 0.0 | 0.77 -Output | 6.9141e-06 | 6.9141e-06 | 6.9141e-06 | 0.0 | 0.00 -Modify | 10.025 | 10.025 | 10.025 | 0.0 | 24.02 -Other | | 0.4203 | | | 1.01 - -Nlocal: 16 ave 16 max 16 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 88 ave 88 max 88 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 88 -Ave neighs/atom = 5.5 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:41 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4 deleted file mode 100644 index 54ec267735..0000000000 --- a/examples/USER/cgdna/examples/oxDNA/duplex2/log.24Mar17.duplex2.g++.4 +++ /dev/null @@ -1,1161 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna/fene -bond_coeff * 2.0 0.25 0.7525 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk -pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.92828 - ghost atom cutoff = 1.92828 - binsize = 0.964142, bins = 42 42 42 - 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair oxdna/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05 -1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 -2000 ekin = 2.15911766687235 | erot = 2.16031365874706 | epot = -24.4723177103698 | etot = -20.1528863847504 -3000 ekin = 3.26561948796015 | erot = 2.75651822936605 | epot = -24.412573068346 | etot = -18.3904353510198 -4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038505 -5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 -6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 -7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 -8000 ekin = 2.51333548501169 | erot = 2.34649854571052 | epot = -24.0812769481836 | etot = -19.2214429174614 -9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 -10000 ekin = 2.36632635249862 | erot = 1.79592471761529 | epot = -23.9002627850602 | etot = -19.7380117149463 -11000 ekin = 2.03296432220126 | erot = 1.687070009478 | epot = -23.8527188138995 | etot = -20.1326844822202 -12000 ekin = 2.65352743446956 | erot = 2.50226345616878 | epot = -23.8480805937578 | etot = -18.6922897031194 -13000 ekin = 1.89067421214403 | erot = 2.35043092595414 | epot = -23.7714712440931 | etot = -19.5303661059949 -14000 ekin = 1.90680463918722 | erot = 2.127459870274 | epot = -23.7545354032947 | etot = -19.7202708938335 -15000 ekin = 2.40428667481004 | erot = 2.06172433796653 | epot = -23.6726347642127 | etot = -19.2066237514361 -16000 ekin = 2.7510166356243 | erot = 1.18896277635345 | epot = -23.5745121257654 | etot = -19.6345327137876 -17000 ekin = 2.44090826892662 | erot = 2.38166706806442 | epot = -23.5888433865641 | etot = -18.766268049573 -18000 ekin = 2.16977970545217 | erot = 2.46915729098831 | epot = -23.6023194416344 | etot = -18.9633824451939 -19000 ekin = 2.19378610033861 | erot = 2.45183819484608 | epot = -23.5449084745393 | etot = -18.8992841793546 -20000 ekin = 2.07734013817241 | erot = 1.81448496219961 | epot = -23.5782673056894 | etot = -19.6864422053173 -21000 ekin = 2.27781532351243 | erot = 2.76369118136087 | epot = -23.5986545956161 | etot = -18.5571480907428 -22000 ekin = 2.69375785791379 | erot = 1.86436952967315 | epot = -23.5521083325077 | etot = -18.9939809449208 -23000 ekin = 1.99952884103097 | erot = 2.28032953163858 | epot = -23.4448504933921 | etot = -19.1649921207226 -24000 ekin = 2.19993258930349 | erot = 2.97916455146846 | epot = -23.365299008021 | etot = -18.1862018672491 -25000 ekin = 2.28089469652686 | erot = 2.97627567077201 | epot = -23.2873526827526 | etot = -18.0301823154537 -26000 ekin = 1.99390998801618 | erot = 2.79250495479073 | epot = -23.1859723519608 | etot = -18.3995574091539 -27000 ekin = 2.00992865272585 | erot = 2.66533768693446 | epot = -23.0781687640813 | etot = -18.402902424421 -28000 ekin = 2.00322172723407 | erot = 2.36418499091004 | epot = -23.0032647032354 | etot = -18.6358579850913 -29000 ekin = 2.52361436071784 | erot = 2.06140753694879 | epot = -22.9685706338047 | etot = -18.383548736138 -30000 ekin = 1.94969919616482 | erot = 2.13601590002587 | epot = -22.8657664932105 | etot = -18.7800513970198 -31000 ekin = 1.81286761012387 | erot = 2.31717861791922 | epot = -22.8372197907213 | etot = -18.7071735626782 -32000 ekin = 1.88389491638451 | erot = 2.00512246825909 | epot = -22.9321024454487 | etot = -19.0430850608051 -33000 ekin = 1.78524470387102 | erot = 1.83154598239148 | epot = -22.9538943248059 | etot = -19.3371036385434 -34000 ekin = 2.28023843988047 | erot = 3.11357086039976 | epot = -23.0617618407572 | etot = -17.6679525404769 -35000 ekin = 2.88795920533174 | erot = 1.81662227096288 | epot = -23.1342233361349 | etot = -18.4296418598403 -36000 ekin = 2.40018487148211 | erot = 2.59182059399979 | epot = -23.2153198761915 | etot = -18.2233144107096 -37000 ekin = 2.22699211630433 | erot = 1.73889017332476 | epot = -23.2291614908027 | etot = -19.2632792011736 -38000 ekin = 2.13593461964592 | erot = 3.07590136326317 | epot = -23.1607724763685 | etot = -17.9489364934594 -39000 ekin = 2.08839393640823 | erot = 2.80471150509565 | epot = -23.1352878747759 | etot = -18.242182433272 -40000 ekin = 2.94982054413846 | erot = 2.19484102372242 | epot = -23.1842229043853 | etot = -18.0395613365244 -41000 ekin = 2.47855373480178 | erot = 3.46795094832273 | epot = -23.1698888629099 | etot = -17.2233841797854 -42000 ekin = 2.57225931171306 | erot = 3.11160980977123 | epot = -23.0914425999525 | etot = -17.4075734784682 -43000 ekin = 2.16695829201326 | erot = 2.67063324875933 | epot = -22.9841690345739 | etot = -18.1465774938013 -44000 ekin = 2.3251045436594 | erot = 3.31069456451417 | epot = -22.9099977707014 | etot = -17.2741986625278 -45000 ekin = 1.8593572517472 | erot = 3.48256913429863 | epot = -22.7853293556222 | etot = -17.4434029695763 -46000 ekin = 2.59906260222482 | erot = 2.2320785378511 | epot = -22.67184319375 | etot = -17.8407020536741 -47000 ekin = 1.9041935097682 | erot = 3.39352467596442 | epot = -22.5624536061979 | etot = -17.2647354204653 -48000 ekin = 2.46191536162938 | erot = 2.50024189038396 | epot = -22.5888330081063 | etot = -17.626675756093 -49000 ekin = 3.18008619674965 | erot = 2.18329398142911 | epot = -22.6110647388653 | etot = -17.2476845606865 -50000 ekin = 2.92380640638808 | erot = 1.5483538313346 | epot = -22.6682279672282 | etot = -18.1960677295055 -51000 ekin = 2.86729503225236 | erot = 2.67529217516738 | epot = -22.6748886664557 | etot = -17.132301459036 -52000 ekin = 2.30283827457731 | erot = 1.82645474029553 | epot = -22.6607030819086 | etot = -18.5314100670358 -53000 ekin = 3.18697616339313 | erot = 1.67211265049679 | epot = -22.7158951183044 | etot = -17.8568063044145 -54000 ekin = 2.63274995193146 | erot = 1.96664130685844 | epot = -22.7877787224364 | etot = -18.1883874636465 -55000 ekin = 3.18311630681888 | erot = 2.85127254864952 | epot = -22.8390589862477 | etot = -16.8046701307793 -56000 ekin = 2.55275960671527 | erot = 3.05720384772627 | epot = -22.8187750450683 | etot = -17.2088115906267 -57000 ekin = 2.43682051944963 | erot = 3.45782031837861 | epot = -22.7770565571277 | etot = -16.8824157192995 -58000 ekin = 1.93888380963701 | erot = 2.51321017005842 | epot = -22.7135987564736 | etot = -18.2615047767781 -59000 ekin = 2.5584899615086 | erot = 3.52166542523796 | epot = -22.6623202639297 | etot = -16.5821648771831 -60000 ekin = 2.80661395039301 | erot = 2.89055248290059 | epot = -22.5801959967487 | etot = -16.8830295634551 -61000 ekin = 2.68598657973729 | erot = 2.54741083070049 | epot = -22.4806361765055 | etot = -17.2472387660677 -62000 ekin = 2.74493324548126 | erot = 2.23648307303268 | epot = -22.4129547813458 | etot = -17.4315384628319 -63000 ekin = 2.65627195091608 | erot = 2.46107949280746 | epot = -22.3986334001314 | etot = -17.2812819564079 -64000 ekin = 2.12379240032878 | erot = 2.79203441675508 | epot = -22.3495990435982 | etot = -17.4337722265143 -65000 ekin = 1.86782238979936 | erot = 2.70277079938775 | epot = -22.3710220966341 | etot = -17.800428907447 -66000 ekin = 2.74983103317414 | erot = 1.93532287297328 | epot = -22.3642892005435 | etot = -17.6791352943961 -67000 ekin = 2.51092055125345 | erot = 2.46618624666164 | epot = -22.3997780561407 | etot = -17.4226712582257 -68000 ekin = 2.95469759114172 | erot = 1.97026833535316 | epot = -22.465077041847 | etot = -17.5401111153521 -69000 ekin = 2.60179538487173 | erot = 2.27022574694886 | epot = -22.4013876082186 | etot = -17.529366476398 -70000 ekin = 2.38624525335423 | erot = 2.82124637267728 | epot = -22.3329612644329 | etot = -17.1254696384013 -71000 ekin = 2.62641919853461 | erot = 2.89332429923839 | epot = -22.3324946257813 | etot = -16.8127511280083 -72000 ekin = 2.93199679301318 | erot = 2.83600213853038 | epot = -22.4418753486332 | etot = -16.6738764170897 -73000 ekin = 2.20521324648382 | erot = 3.0506384171445 | epot = -22.5078076718832 | etot = -17.2519560082549 -74000 ekin = 2.16594519672766 | erot = 2.82993872672918 | epot = -22.5187768617569 | etot = -17.5228929383001 -75000 ekin = 1.52753824412461 | erot = 1.91758574309003 | epot = -22.6434864113427 | etot = -19.198362424128 -76000 ekin = 1.89477517532868 | erot = 2.83145375092217 | epot = -22.7507099037207 | etot = -18.0244809774699 -77000 ekin = 2.84722966394523 | erot = 3.20523918524771 | epot = -22.8263123696514 | etot = -16.7738435204585 -78000 ekin = 2.44900478430451 | erot = 2.80964787966682 | epot = -22.8119237303111 | etot = -17.5532710663397 -79000 ekin = 2.16549328835506 | erot = 1.67531288307153 | epot = -22.8278994273521 | etot = -18.9870932559255 -80000 ekin = 2.38929173610466 | erot = 2.58355997375491 | epot = -22.7453472674483 | etot = -17.7724955575887 -81000 ekin = 2.74182188148999 | erot = 1.92580771183151 | epot = -22.6872721828913 | etot = -18.0196425895698 -82000 ekin = 1.90254633515813 | erot = 1.70958501101745 | epot = -22.5904815431895 | etot = -18.9783501970139 -83000 ekin = 1.63862423461032 | erot = 1.87668722448406 | epot = -22.5030898166236 | etot = -18.9877783575292 -84000 ekin = 1.65768128899531 | erot = 2.10186039233844 | epot = -22.4199436013011 | etot = -18.6604019199674 -85000 ekin = 2.40787065796921 | erot = 2.04965431830703 | epot = -22.3401854879212 | etot = -17.882660511645 -86000 ekin = 2.51073542405177 | erot = 1.79768841940749 | epot = -22.3948638623201 | etot = -18.0864400188608 -87000 ekin = 2.13729284484532 | erot = 1.97886338867606 | epot = -22.4457225556767 | etot = -18.3295663221553 -88000 ekin = 1.7511616822056 | erot = 2.36434608342924 | epot = -22.4232555875236 | etot = -18.3077478218887 -89000 ekin = 1.85498863251071 | erot = 3.29466014836527 | epot = -22.4615925106509 | etot = -17.3119437297749 -90000 ekin = 2.22730928223451 | erot = 2.36761183779185 | epot = -22.5498488806969 | etot = -17.9549277606706 -91000 ekin = 2.40026068010467 | erot = 3.1312454261103 | epot = -22.5445138059197 | etot = -17.0130076997047 -92000 ekin = 2.69184894487886 | erot = 3.01111638487596 | epot = -22.5488335054242 | etot = -16.8458681756693 -93000 ekin = 3.04452081584098 | erot = 3.0289315825034 | epot = -22.4857514998612 | etot = -16.4122991015169 -94000 ekin = 3.21054020599498 | erot = 1.87554208928457 | epot = -22.58235617796 | etot = -17.4962738826805 -95000 ekin = 3.49164555041805 | erot = 2.89107259754101 | epot = -22.651746211573 | etot = -16.2690280636139 -96000 ekin = 2.8961145983777 | erot = 2.38403691628048 | epot = -22.6376886129393 | etot = -17.3575370982811 -97000 ekin = 1.94001816357315 | erot = 2.09603205774619 | epot = -22.6212143095229 | etot = -18.5851640882036 -98000 ekin = 2.21812472183551 | erot = 3.66512951907029 | epot = -22.5400207863669 | etot = -16.6567665454611 -99000 ekin = 1.96304801418099 | erot = 2.78092002528644 | epot = -22.4500077741119 | etot = -17.7060397346444 -100000 ekin = 1.78146596589238 | erot = 2.66087063973067 | epot = -22.3806285021859 | etot = -17.9382918965629 -101000 ekin = 2.13576431486591 | erot = 2.39189697670582 | epot = -22.3671198416411 | etot = -17.8394585500694 -102000 ekin = 1.54265458925823 | erot = 2.31301627489861 | epot = -22.3596033820568 | etot = -18.5039325179 -103000 ekin = 1.6493299781162 | erot = 2.82700146777614 | epot = -22.4044472055819 | etot = -17.9281157596895 -104000 ekin = 1.88425130865015 | erot = 3.36695629589132 | epot = -22.4614117565727 | etot = -17.2102041520312 -105000 ekin = 2.0873628063424 | erot = 1.99902589912497 | epot = -22.4857870795246 | etot = -18.3993983740572 -106000 ekin = 2.85192200005481 | erot = 1.96124421177818 | epot = -22.4885148263279 | etot = -17.6753486144949 -107000 ekin = 2.27699301124082 | erot = 1.54572940373457 | epot = -22.4328687856414 | etot = -18.610146370666 -108000 ekin = 2.43341212242248 | erot = 1.7101452395327 | epot = -22.4750159709763 | etot = -18.3314586090212 -109000 ekin = 2.3240302459673 | erot = 2.92730273400661 | epot = -22.4544447404649 | etot = -17.203111760491 -110000 ekin = 2.75939007795593 | erot = 2.3726124845783 | epot = -22.4066316113363 | etot = -17.2746290488021 -111000 ekin = 2.30202775259985 | erot = 2.09098171366697 | epot = -22.340628179725 | etot = -17.9476187134581 -112000 ekin = 2.89672803093986 | erot = 1.84536318388285 | epot = -22.189229344937 | etot = -17.4471381301143 -113000 ekin = 2.802868120203 | erot = 1.68317583122193 | epot = -22.1739192926257 | etot = -17.6878753412008 -114000 ekin = 3.41134331362353 | erot = 2.66279011393036 | epot = -22.2993892060878 | etot = -16.2252557785339 -115000 ekin = 3.04096848543598 | erot = 1.72164164793761 | epot = -22.3101669297006 | etot = -17.547556796327 -116000 ekin = 3.18249263106367 | erot = 3.21872780579631 | epot = -22.3766120310369 | etot = -15.975391594177 -117000 ekin = 3.04033644338918 | erot = 2.4163277414929 | epot = -22.3406101341932 | etot = -16.8839459493111 -118000 ekin = 3.2297663279461 | erot = 1.46870208555873 | epot = -22.262910646297 | etot = -17.5644422327922 -119000 ekin = 2.35815331598994 | erot = 3.07464675916892 | epot = -22.21629705762 | etot = -16.7834969824611 -120000 ekin = 1.93901604028919 | erot = 2.21087803685818 | epot = -22.1596747789505 | etot = -18.0097807018031 -121000 ekin = 1.94791988346889 | erot = 3.06697908719322 | epot = -22.1473490758084 | etot = -17.1324501051462 -122000 ekin = 1.69642311218451 | erot = 1.71065948591522 | epot = -22.235021693017 | etot = -18.8279390949172 -123000 ekin = 1.74537927001903 | erot = 2.31042772730644 | epot = -22.3250546948603 | etot = -18.2692476975348 -124000 ekin = 2.74229806685692 | erot = 1.94346011848795 | epot = -22.3376426377462 | etot = -17.6518844524013 -125000 ekin = 2.77628031613761 | erot = 1.95737420539167 | epot = -22.3561899601979 | etot = -17.6225354386686 -126000 ekin = 2.05898577806786 | erot = 1.47493157618749 | epot = -22.3918669376121 | etot = -18.8579495833568 -127000 ekin = 1.88620727578863 | erot = 1.58698481884328 | epot = -22.3753405588623 | etot = -18.9021484642304 -128000 ekin = 1.65027256647601 | erot = 1.87589048163674 | epot = -22.3576574967822 | etot = -18.8314944486694 -129000 ekin = 2.51771860981078 | erot = 2.38745668871875 | epot = -22.3622404512641 | etot = -17.4570651527346 -130000 ekin = 1.60778116741171 | erot = 2.81983062254802 | epot = -22.3043401463426 | etot = -17.8767283563829 -131000 ekin = 2.27966529707091 | erot = 2.29465997580789 | epot = -22.1860056729234 | etot = -17.6116804000446 -132000 ekin = 2.94605151024306 | erot = 2.34727265039698 | epot = -22.1004107829512 | etot = -16.8070866223112 -133000 ekin = 2.00184520718143 | erot = 2.13597622566089 | epot = -22.0860804435183 | etot = -17.948259010676 -134000 ekin = 1.54536260297594 | erot = 2.86019181856985 | epot = -22.0324797134652 | etot = -17.6269252919194 -135000 ekin = 1.7899169229158 | erot = 2.40585579784188 | epot = -22.0564792277569 | etot = -17.8607065069992 -136000 ekin = 1.63315069688348 | erot = 2.13968964990471 | epot = -22.0645410751455 | etot = -18.2917007283573 -137000 ekin = 2.36475220491125 | erot = 1.93075105476848 | epot = -22.101884847306 | etot = -17.8063815876262 -138000 ekin = 2.9554682114977 | erot = 1.58329215843879 | epot = -22.158920719349 | etot = -17.6201603494125 -139000 ekin = 3.18559985564368 | erot = 2.24978247982886 | epot = -22.2766713145625 | etot = -16.84128897909 -140000 ekin = 2.25331500051846 | erot = 3.04264261269698 | epot = -22.4413209794807 | etot = -17.1453633662653 -141000 ekin = 1.8939664036255 | erot = 3.12730191483887 | epot = -22.6943708703895 | etot = -17.6731025519251 -142000 ekin = 2.48698722341786 | erot = 2.50204475841097 | epot = -22.8022645411412 | etot = -17.8132325593124 -143000 ekin = 2.39031114354901 | erot = 2.72027514737474 | epot = -22.7789363640121 | etot = -17.6683500730884 -144000 ekin = 1.93009742932803 | erot = 2.68112648713777 | epot = -22.6600942975092 | etot = -18.0488703810434 -145000 ekin = 1.81543048110687 | erot = 1.73927524532866 | epot = -22.6290694904769 | etot = -19.0743637640413 -146000 ekin = 2.4125202126428 | erot = 2.0856902293417 | epot = -22.560764077018 | etot = -18.0625536350335 -147000 ekin = 1.44642974398304 | erot = 1.86921415702345 | epot = -22.4437745695725 | etot = -19.128130668566 -148000 ekin = 1.94224767107089 | erot = 2.57935525538892 | epot = -22.4110987100046 | etot = -17.8894957835448 -149000 ekin = 2.03195649040454 | erot = 3.31786202502786 | epot = -22.312227106758 | etot = -16.9624085913256 -150000 ekin = 2.47792894576431 | erot = 2.68612874200302 | epot = -22.1392843642772 | etot = -16.9752266765099 -151000 ekin = 2.75692645092955 | erot = 1.88122565848133 | epot = -21.9329416416722 | etot = -17.2947895322613 -152000 ekin = 2.7753834344323 | erot = 1.78115734250796 | epot = -21.745072490984 | etot = -17.1885317140438 -153000 ekin = 3.09316888168833 | erot = 1.80744228044955 | epot = -21.6451473427313 | etot = -16.7445361805934 -154000 ekin = 2.31433640945477 | erot = 2.19304386678896 | epot = -21.5946356595636 | etot = -17.0872553833199 -155000 ekin = 1.94169881401553 | erot = 2.67959698479411 | epot = -21.6941053409436 | etot = -17.0728095421339 -156000 ekin = 2.69151609119638 | erot = 2.25048211983205 | epot = -21.7610571974251 | etot = -16.8190589863966 -157000 ekin = 3.89507004263776 | erot = 2.74501587672577 | epot = -21.8157728797742 | etot = -15.1756869604107 -158000 ekin = 2.88173407476086 | erot = 2.69702262693026 | epot = -21.8854957137509 | etot = -16.3067390120597 -159000 ekin = 3.15173323195919 | erot = 2.61743473710129 | epot = -21.8245251626835 | etot = -16.055357193623 -160000 ekin = 2.54983562435716 | erot = 3.26037467643908 | epot = -21.8527884226329 | etot = -16.0425781218366 -161000 ekin = 2.47569624391789 | erot = 2.44418416527208 | epot = -21.7973550812186 | etot = -16.8774746720287 -162000 ekin = 2.9422872213738 | erot = 2.59784970938383 | epot = -21.7813251561028 | etot = -16.2411882253452 -163000 ekin = 3.25812805712343 | erot = 2.2523933100784 | epot = -21.820089307521 | etot = -16.3095679403192 -164000 ekin = 3.52786799143084 | erot = 2.22392713421413 | epot = -21.7646946348872 | etot = -16.0128995092422 -165000 ekin = 2.47839548873417 | erot = 2.58744140761171 | epot = -21.679095294504 | etot = -16.6132583981582 -166000 ekin = 2.14435847552791 | erot = 3.04732688845808 | epot = -21.6219995979976 | etot = -16.4303142340116 -167000 ekin = 2.77664659649902 | erot = 2.89037999868329 | epot = -21.5339928834654 | etot = -15.8669662882831 -168000 ekin = 1.74464407802389 | erot = 2.78052653338967 | epot = -21.4288999288374 | etot = -16.9037293174239 -169000 ekin = 1.80689129093329 | erot = 2.46391033708927 | epot = -21.4128285618694 | etot = -17.1420269338468 -170000 ekin = 1.6949814594151 | erot = 2.88911238881154 | epot = -21.4319269866203 | etot = -16.8478331383937 -171000 ekin = 2.15326316196645 | erot = 1.61346547801869 | epot = -21.2861470779283 | etot = -17.5194184379432 -172000 ekin = 1.67904916339532 | erot = 2.36509147316375 | epot = -21.1250864759441 | etot = -17.080945839385 -173000 ekin = 2.05349972960735 | erot = 2.1886466510775 | epot = -21.0744450592631 | etot = -16.8322986785782 -174000 ekin = 2.49402795941962 | erot = 3.10392317000879 | epot = -20.9332609664624 | etot = -15.335309837034 -175000 ekin = 2.60611029063986 | erot = 2.90993176119182 | epot = -20.8533230180668 | etot = -15.3372809662352 -176000 ekin = 2.14535974511637 | erot = 2.67710511021539 | epot = -20.8508037764829 | etot = -16.0283389211511 -177000 ekin = 2.82654664242577 | erot = 2.80647819657321 | epot = -20.9303681620826 | etot = -15.2973433230836 -178000 ekin = 3.17006270723388 | erot = 1.88204403688962 | epot = -21.0665744865168 | etot = -16.0144677423933 -179000 ekin = 2.33834827123178 | erot = 2.84870047825869 | epot = -21.1082901606943 | etot = -15.9212414112039 -180000 ekin = 2.39362550925045 | erot = 2.94575326168227 | epot = -21.1089731290028 | etot = -15.7695943580701 -181000 ekin = 2.78703231260152 | erot = 3.29998898392537 | epot = -21.0761138110654 | etot = -14.9890925145385 -182000 ekin = 3.02338391239199 | erot = 2.32533107462881 | epot = -21.0444377426861 | etot = -15.6957227556653 -183000 ekin = 2.44126401356994 | erot = 2.19853056632819 | epot = -20.8846280234405 | etot = -16.2448334435424 -184000 ekin = 2.56448211253962 | erot = 2.77267067014066 | epot = -20.6657911214549 | etot = -15.3286383387746 -185000 ekin = 2.16427057092672 | erot = 1.95880146934286 | epot = -20.5647658775173 | etot = -16.4416938372477 -186000 ekin = 2.06536030915311 | erot = 3.14593463137772 | epot = -20.4537584304771 | etot = -15.2424634899463 -187000 ekin = 2.43846121057803 | erot = 1.93593042270703 | epot = -20.4775765627296 | etot = -16.1031849294445 -188000 ekin = 2.28827356508696 | erot = 2.89699235589217 | epot = -20.6028880527163 | etot = -15.4176221317372 -189000 ekin = 1.67206333515898 | erot = 3.05807378739729 | epot = -20.6184572736204 | etot = -15.8883201510642 -190000 ekin = 1.96995062226968 | erot = 2.94301967439401 | epot = -20.6150380630742 | etot = -15.7020677664105 -191000 ekin = 2.31558303301195 | erot = 2.65062200614568 | epot = -20.5845049099943 | etot = -15.6182998708367 -192000 ekin = 3.58105122568799 | erot = 2.89866835149675 | epot = -20.555036456006 | etot = -14.0753168788213 -193000 ekin = 2.69738971383614 | erot = 3.08390984677749 | epot = -20.5718609412494 | etot = -14.7905613806358 -194000 ekin = 2.65963556416735 | erot = 2.28486501061268 | epot = -20.4488832942326 | etot = -15.5043827194526 -195000 ekin = 1.85289053427901 | erot = 2.65318671222087 | epot = -20.3816844231208 | etot = -15.8756071766209 -196000 ekin = 2.28257181147918 | erot = 2.31175601065462 | epot = -20.4051132325268 | etot = -15.810785410393 -197000 ekin = 2.49770460330585 | erot = 2.55587879440511 | epot = -20.4716020539923 | etot = -15.4180186562814 -198000 ekin = 2.01700960777427 | erot = 1.51922008609382 | epot = -20.4907970823156 | etot = -16.9545673884475 -199000 ekin = 1.50027537520987 | erot = 2.19604462463446 | epot = -20.5138434458212 | etot = -16.8175234459769 -200000 ekin = 1.64850512926723 | erot = 2.4596633548257 | epot = -20.4934420686449 | etot = -16.385273584552 -201000 ekin = 2.62997533994907 | erot = 2.61637339049483 | epot = -20.5569645618355 | etot = -15.3106158313916 -202000 ekin = 2.3089517547524 | erot = 2.5565329388766 | epot = -20.6262537118088 | etot = -15.7607690181798 -203000 ekin = 1.64768887888551 | erot = 2.11556417528285 | epot = -20.6617888215465 | etot = -16.8985357673782 -204000 ekin = 2.01924097320136 | erot = 1.97748949636931 | epot = -20.7002685556682 | etot = -16.7035380860975 -205000 ekin = 2.97656554045711 | erot = 3.25408007971553 | epot = -20.9425038008424 | etot = -14.7118581806698 -206000 ekin = 2.56613069661945 | erot = 2.21624244224461 | epot = -21.0621833598182 | etot = -16.2798102209542 -207000 ekin = 3.44850636848559 | erot = 2.48816050856267 | epot = -21.2038849430867 | etot = -15.2672180660384 -208000 ekin = 2.54208934028226 | erot = 2.22605232144502 | epot = -21.3476404533667 | etot = -16.5794987916394 -209000 ekin = 3.84151461096732 | erot = 2.16534559513903 | epot = -21.4932373455843 | etot = -15.486377139478 -210000 ekin = 3.06873591712904 | erot = 2.24760815652574 | epot = -21.6427793540355 | etot = -16.3264352803807 -211000 ekin = 1.64176280869923 | erot = 2.17721976802011 | epot = -21.8130439048272 | etot = -17.9940613281078 -212000 ekin = 2.5985934050661 | erot = 2.41520703335869 | epot = -21.9964648294563 | etot = -16.9826643910315 -213000 ekin = 2.51136104390039 | erot = 1.99503544560738 | epot = -22.161492842604 | etot = -17.6550963530962 -214000 ekin = 2.77089845962619 | erot = 3.17247228684199 | epot = -22.208715104286 | etot = -16.2653443578179 -215000 ekin = 2.53408528186206 | erot = 1.84963848601798 | epot = -22.1148567901871 | etot = -17.7311330223071 -216000 ekin = 2.52671619876928 | erot = 2.77873014449688 | epot = -22.1370884570131 | etot = -16.8316421137469 -217000 ekin = 2.50171921508545 | erot = 1.89238935467003 | epot = -22.226079201001 | etot = -17.8319706312455 -218000 ekin = 2.43936294263937 | erot = 2.41974828067303 | epot = -22.2447049583244 | etot = -17.385593735012 -219000 ekin = 2.30221269367205 | erot = 2.65120674162376 | epot = -22.2807164841742 | etot = -17.3272970488784 -220000 ekin = 1.70065256620687 | erot = 2.34758543213915 | epot = -22.2809933538228 | etot = -18.2327553554768 -221000 ekin = 2.09298237125575 | erot = 2.47886481595909 | epot = -22.267957001012 | etot = -17.6961098137972 -222000 ekin = 1.58469709510937 | erot = 2.14490786301286 | epot = -22.1867412404881 | etot = -18.4571362823659 -223000 ekin = 1.83926923346352 | erot = 1.89456034969536 | epot = -22.131893392038 | etot = -18.3980638088791 -224000 ekin = 2.59583657132575 | erot = 2.93869915115497 | epot = -22.1425986650605 | etot = -16.6080629425798 -225000 ekin = 3.29351563254165 | erot = 2.8433953581414 | epot = -22.12757310355 | etot = -15.9906621128669 -226000 ekin = 3.03135339447922 | erot = 2.08293143143602 | epot = -22.15283624886 | etot = -17.0385514229448 -227000 ekin = 2.50176282992082 | erot = 3.15084128846395 | epot = -22.2250438959744 | etot = -16.5724397775897 -228000 ekin = 2.32013498351673 | erot = 2.67554406359438 | epot = -22.3177515383563 | etot = -17.3220724912452 -229000 ekin = 2.89545450975319 | erot = 2.90735055857068 | epot = -22.4361496683348 | etot = -16.6333446000109 -230000 ekin = 2.28321229485933 | erot = 3.48420465632866 | epot = -22.548785995051 | etot = -16.781369043863 -231000 ekin = 2.0778632375453 | erot = 3.10673973696435 | epot = -22.5896609633152 | etot = -17.4050579888055 -232000 ekin = 2.1202374109541 | erot = 1.98747810033066 | epot = -22.5738924334392 | etot = -18.4661769221544 -233000 ekin = 2.33571877855589 | erot = 2.83585090202738 | epot = -22.5402065195541 | etot = -17.3686368389708 -234000 ekin = 2.10578223747154 | erot = 2.07381218733636 | epot = -22.5507693150833 | etot = -18.3711748902754 -235000 ekin = 2.44321041214394 | erot = 2.80846352304319 | epot = -22.5606929563186 | etot = -17.3090190211315 -236000 ekin = 2.93630791731799 | erot = 3.0631591853173 | epot = -22.4860653874721 | etot = -16.4865982848369 -237000 ekin = 3.21264879506079 | erot = 3.268665084783 | epot = -22.3683553437861 | etot = -15.8870414639424 -238000 ekin = 2.46595539123277 | erot = 2.32502019506661 | epot = -22.3144456769666 | etot = -17.5234700906672 -239000 ekin = 2.10325864915823 | erot = 2.47631139904043 | epot = -22.3011392921811 | etot = -17.7215692439824 -240000 ekin = 1.77270999777839 | erot = 2.60141429112665 | epot = -22.2344206081543 | etot = -17.8602963192493 -241000 ekin = 1.94952922244078 | erot = 1.39715216866764 | epot = -22.2207225048761 | etot = -18.8740411137677 -242000 ekin = 3.05687991591411 | erot = 2.00862394928707 | epot = -22.2213200390944 | etot = -17.1558161738932 -243000 ekin = 2.86735711945299 | erot = 1.79948118674679 | epot = -22.2697610280427 | etot = -17.6029227218429 -244000 ekin = 2.00525854269389 | erot = 2.36445341214555 | epot = -22.2726788994494 | etot = -17.90296694461 -245000 ekin = 2.28011102404837 | erot = 2.78700520532799 | epot = -22.2995433574618 | etot = -17.2324271280854 -246000 ekin = 2.06819738789813 | erot = 2.24624952782285 | epot = -22.2551680110138 | etot = -17.9407210952928 -247000 ekin = 1.69964711256213 | erot = 3.22260619239828 | epot = -22.1916408256116 | etot = -17.2693875206512 -248000 ekin = 1.92997585194759 | erot = 3.61155944514372 | epot = -22.0096484177853 | etot = -16.468113120694 -249000 ekin = 2.16278530892653 | erot = 3.27771891456707 | epot = -21.8856058980727 | etot = -16.4451016745791 -250000 ekin = 2.32204054211024 | erot = 2.46317574116846 | epot = -21.8028762710591 | etot = -17.0176599877804 -251000 ekin = 1.23768964067254 | erot = 2.241505337621 | epot = -21.7630657074039 | etot = -18.2838707291104 -252000 ekin = 1.79818833522214 | erot = 2.12556386664126 | epot = -21.7586349357284 | etot = -17.8348827338651 -253000 ekin = 2.12809689846393 | erot = 2.59685639208402 | epot = -21.7226495687758 | etot = -16.9976962782278 -254000 ekin = 2.46813261968532 | erot = 2.0039181266287 | epot = -21.7113918037362 | etot = -17.2393410574222 -255000 ekin = 2.3156672908729 | erot = 2.03619058028115 | epot = -21.7265453183256 | etot = -17.3746874471716 -256000 ekin = 2.87223929491326 | erot = 2.61790933826623 | epot = -21.659332511914 | etot = -16.1691838787345 -257000 ekin = 2.85756762932927 | erot = 2.081746739162 | epot = -21.6161821054731 | etot = -16.6768677369818 -258000 ekin = 2.06111021157734 | erot = 2.32748664972428 | epot = -21.5132485706726 | etot = -17.124651709371 -259000 ekin = 2.23305784057759 | erot = 2.88843859953734 | epot = -21.5040039667854 | etot = -16.3825075266705 -260000 ekin = 2.49862397932476 | erot = 2.38336885848388 | epot = -21.488210637319 | etot = -16.6062177995103 -261000 ekin = 2.09280296934734 | erot = 2.39632540029207 | epot = -21.4325331777953 | etot = -16.9434048081559 -262000 ekin = 2.33576913564289 | erot = 2.67273419354396 | epot = -21.3832241450035 | etot = -16.3747208158166 -263000 ekin = 2.20536189489354 | erot = 2.71530627040564 | epot = -21.4329409070981 | etot = -16.5122727417989 -264000 ekin = 2.2858247573423 | erot = 2.76839346219664 | epot = -21.3931084431599 | etot = -16.338890223621 -265000 ekin = 1.70928536820409 | erot = 1.79395423442894 | epot = -21.2682341921474 | etot = -17.7649945895143 -266000 ekin = 2.48721735474525 | erot = 2.08745460533224 | epot = -21.1746995817337 | etot = -16.6000276216562 -267000 ekin = 2.69283567987774 | erot = 2.10301910407212 | epot = -21.1705161290062 | etot = -16.3746613450563 -268000 ekin = 3.00000233743719 | erot = 2.80954585635721 | epot = -21.164752112651 | etot = -15.3552039188566 -269000 ekin = 3.50713810468527 | erot = 2.35763817348001 | epot = -21.1537110688984 | etot = -15.2889347907331 -270000 ekin = 3.50686942248863 | erot = 1.86462765875889 | epot = -21.1925508822801 | etot = -15.8210538010326 -271000 ekin = 3.57026082273992 | erot = 2.08172467795386 | epot = -21.2775817182941 | etot = -15.6255962176003 -272000 ekin = 2.4484752533773 | erot = 3.08466485039761 | epot = -21.3619851902072 | etot = -15.8288450864323 -273000 ekin = 2.39748176307242 | erot = 3.13355050446718 | epot = -21.4386234252579 | etot = -15.9075911577183 -274000 ekin = 2.48208144431864 | erot = 2.00552494041966 | epot = -21.4476232953882 | etot = -16.9600169106499 -275000 ekin = 2.48721081149369 | erot = 3.05413598233601 | epot = -21.4713984309063 | etot = -15.9300516370766 -276000 ekin = 2.82709589676966 | erot = 2.88384306577856 | epot = -21.4434590118161 | etot = -15.7325200492679 -277000 ekin = 2.23479555963312 | erot = 2.20310851955638 | epot = -21.3883073251199 | etot = -16.9504032459304 -278000 ekin = 2.81418916407429 | erot = 3.24537052192614 | epot = -21.3155364074003 | etot = -15.2559767213999 -279000 ekin = 2.57366525203698 | erot = 1.81705578305927 | epot = -21.2862101233851 | etot = -16.8954890882888 -280000 ekin = 2.41063464320149 | erot = 1.76282693004731 | epot = -21.254962528096 | etot = -17.0815009548472 -281000 ekin = 2.58126226070486 | erot = 2.29258221702166 | epot = -21.306394928225 | etot = -16.4325504504985 -282000 ekin = 3.02016903398222 | erot = 2.43094523890342 | epot = -21.4340900724633 | etot = -15.9829757995777 -283000 ekin = 2.59269149790331 | erot = 2.11330689541034 | epot = -21.6296517079942 | etot = -16.9236533146805 -284000 ekin = 2.51704243107537 | erot = 3.13156683036761 | epot = -21.7452694753527 | etot = -16.0966602139097 -285000 ekin = 2.4236537221525 | erot = 1.77228258125504 | epot = -21.8557019037769 | etot = -17.6597656003694 -286000 ekin = 1.9446719552166 | erot = 2.0366097411672 | epot = -21.901435736722 | etot = -17.9201540403382 -287000 ekin = 2.56319670376172 | erot = 2.60867050510164 | epot = -21.90675099349 | etot = -16.7348837846266 -288000 ekin = 2.19574207425737 | erot = 1.69805542160022 | epot = -21.8143855675961 | etot = -17.9205880717385 -289000 ekin = 2.35326278833026 | erot = 1.65840109676147 | epot = -21.6976038565284 | etot = -17.6859399714367 -290000 ekin = 2.35194561775049 | erot = 1.99444238353746 | epot = -21.6551012116075 | etot = -17.3087132103195 -291000 ekin = 1.48585281531715 | erot = 2.66475825861553 | epot = -21.56036793472 | etot = -17.4097568607873 -292000 ekin = 2.10739944756451 | erot = 2.42809824662637 | epot = -21.4451596117638 | etot = -16.9096619175729 -293000 ekin = 2.11618090223715 | erot = 1.86694554151197 | epot = -21.3593625692767 | etot = -17.3762361255276 -294000 ekin = 2.06078090566331 | erot = 2.13941873359477 | epot = -21.232623310094 | etot = -17.032423670836 -295000 ekin = 2.11467178034793 | erot = 2.32673436675181 | epot = -21.1123588667461 | etot = -16.6709527196463 -296000 ekin = 1.53087058859332 | erot = 2.94008409149155 | epot = -21.2112197533847 | etot = -16.7402650732999 -297000 ekin = 2.52732986791198 | erot = 2.18380855337859 | epot = -21.1955190508786 | etot = -16.484380629588 -298000 ekin = 1.89033945823198 | erot = 2.02521913176 | epot = -21.2593750718295 | etot = -17.3438164818375 -299000 ekin = 1.87142873048437 | erot = 1.66404563221549 | epot = -21.2919162310488 | etot = -17.7564418683489 -300000 ekin = 2.23872615546787 | erot = 1.50807257618897 | epot = -21.3339204593826 | etot = -17.5871217277257 -301000 ekin = 1.99965506724557 | erot = 2.00145094516844 | epot = -21.4707589194324 | etot = -17.4696529070184 -302000 ekin = 1.76370349732521 | erot = 2.23787708901489 | epot = -21.5675275978257 | etot = -17.5659470114856 -303000 ekin = 2.69610887251788 | erot = 1.69957221429741 | epot = -21.5563765448092 | etot = -17.1606954579939 -304000 ekin = 2.55447143501921 | erot = 2.0206081309035 | epot = -21.5692327321341 | etot = -16.9941531662114 -305000 ekin = 2.38230604232717 | erot = 2.31489374428113 | epot = -21.5335950166329 | etot = -16.8363952300246 -306000 ekin = 2.07785475765118 | erot = 2.4523066068597 | epot = -21.4550895345846 | etot = -16.9249281700737 -307000 ekin = 3.17130424567277 | erot = 3.29574614566805 | epot = -21.4151535289882 | etot = -14.9481031376474 -308000 ekin = 3.40959217051674 | erot = 2.68389483402973 | epot = -21.4778643688409 | etot = -15.3843773642944 -309000 ekin = 2.36068264180092 | erot = 2.91715332823342 | epot = -21.5794336507741 | etot = -16.3015976807397 -310000 ekin = 2.4995235722922 | erot = 2.36028950896138 | epot = -21.5982142524176 | etot = -16.738401171164 -311000 ekin = 2.53288726180906 | erot = 2.29596940545853 | epot = -21.6418553661546 | etot = -16.8129986988871 -312000 ekin = 2.05123272208704 | erot = 2.92023923411837 | epot = -21.7377547517075 | etot = -16.7662827955021 -313000 ekin = 1.80834719374888 | erot = 2.29357283142129 | epot = -21.7993116362532 | etot = -17.697391611083 -314000 ekin = 2.30684015099018 | erot = 2.20859462712274 | epot = -21.8029398081388 | etot = -17.2875050300258 -315000 ekin = 1.86413924486173 | erot = 2.14748794238474 | epot = -21.8550418960799 | etot = -17.8434147088334 -316000 ekin = 2.20558056533517 | erot = 3.03447287931583 | epot = -21.8868412075708 | etot = -16.6467877629198 -317000 ekin = 2.4782093112548 | erot = 3.56870099099488 | epot = -21.9902146748518 | etot = -15.9433043726021 -318000 ekin = 2.3658234380168 | erot = 3.01887804681554 | epot = -22.1178732891163 | etot = -16.7331718042839 -319000 ekin = 2.40464629760757 | erot = 3.15910789488742 | epot = -22.2289401281564 | etot = -16.6651859356614 -320000 ekin = 1.80206494109346 | erot = 2.83527990295434 | epot = -22.3120263401861 | etot = -17.6746814961383 -321000 ekin = 2.91146951948762 | erot = 2.25772268449839 | epot = -22.3029455835946 | etot = -17.1337533796086 -322000 ekin = 2.8226351296685 | erot = 2.67950826833978 | epot = -22.3041650189947 | etot = -16.8020216209864 -323000 ekin = 2.067323568424 | erot = 2.31975284775299 | epot = -22.3338840353559 | etot = -17.9468076191789 -324000 ekin = 2.6012747278288 | erot = 2.58351861537748 | epot = -22.3215168526944 | etot = -17.1367235094881 -325000 ekin = 3.45560055552843 | erot = 2.50162515355503 | epot = -22.1825527777624 | etot = -16.225327068679 -326000 ekin = 3.51422890604519 | erot = 2.84426061018009 | epot = -22.0201095272525 | etot = -15.6616200110272 -327000 ekin = 2.63551490316293 | erot = 2.20570805472231 | epot = -21.9384479867006 | etot = -17.0972250288154 -328000 ekin = 1.8043914440792 | erot = 2.37599512200968 | epot = -21.8619803976419 | etot = -17.681593831553 -329000 ekin = 2.15766181563134 | erot = 2.45286496267963 | epot = -21.8518523862112 | etot = -17.2413256079002 -330000 ekin = 1.8483425992464 | erot = 2.03367429366602 | epot = -21.7684095252419 | etot = -17.8863926323295 -331000 ekin = 2.3531484336258 | erot = 1.80165819621477 | epot = -21.7197009414848 | etot = -17.5648943116443 -332000 ekin = 1.67855936307207 | erot = 2.53341219651313 | epot = -21.7336434355881 | etot = -17.5216718760029 -333000 ekin = 1.60376334688456 | erot = 2.14058675025446 | epot = -21.835637958395 | etot = -18.091287861256 -334000 ekin = 2.26551990081779 | erot = 2.62486254825419 | epot = -21.879497107847 | etot = -16.989114658775 -335000 ekin = 2.91208137486082 | erot = 3.1105287045201 | epot = -21.9161692767172 | etot = -15.8935591973362 -336000 ekin = 2.73132973682385 | erot = 2.56213100489406 | epot = -21.8312488568505 | etot = -16.5377881151326 -337000 ekin = 3.15411918141902 | erot = 3.87512819831196 | epot = -21.9061152574783 | etot = -14.8768678777473 -338000 ekin = 2.33141760424507 | erot = 2.1321194508968 | epot = -21.9137461112381 | etot = -17.4502090560962 -339000 ekin = 1.71915361945719 | erot = 2.31270220754043 | epot = -21.904207477372 | etot = -17.8723516503744 -340000 ekin = 1.62199393011805 | erot = 3.16990972384469 | epot = -21.8898233676232 | etot = -17.0979197136605 -341000 ekin = 1.71588704296646 | erot = 3.17642860992461 | epot = -21.834555812815 | etot = -16.9422401599239 -342000 ekin = 1.82178091247658 | erot = 2.58875985611026 | epot = -21.7161502950573 | etot = -17.3056095264705 -343000 ekin = 3.08559255942693 | erot = 2.94813449265469 | epot = -21.7030445300997 | etot = -15.6693174780181 -344000 ekin = 2.95985387154985 | erot = 3.11547515850353 | epot = -21.6815483295521 | etot = -15.6062192994987 -345000 ekin = 2.33428072266865 | erot = 2.88044431283022 | epot = -21.6567075042344 | etot = -16.4419824687355 -346000 ekin = 2.02077664062698 | erot = 3.45936833964703 | epot = -21.5877268821218 | etot = -16.1075819018478 -347000 ekin = 2.34924784800441 | erot = 1.93056350805623 | epot = -21.4896151766055 | etot = -17.2098038205449 -348000 ekin = 2.79839267202794 | erot = 2.79408776517964 | epot = -21.4682057474678 | etot = -15.8757253102603 -349000 ekin = 2.33820470114614 | erot = 3.1296631867051 | epot = -21.5603039389199 | etot = -16.0924360510686 -350000 ekin = 2.22383234890832 | erot = 2.38886870388012 | epot = -21.5375784703118 | etot = -16.9248774175233 -351000 ekin = 2.33329735253339 | erot = 2.84447430695178 | epot = -21.5078106306152 | etot = -16.3300389711301 -352000 ekin = 2.74923373919408 | erot = 2.76796181793624 | epot = -21.5537134920816 | etot = -16.0365179349513 -353000 ekin = 1.76111836153717 | erot = 2.12255592617519 | epot = -21.5037017999956 | etot = -17.6200275122832 -354000 ekin = 2.29967358188085 | erot = 2.37615363620184 | epot = -21.5592579778191 | etot = -16.8834307597364 -355000 ekin = 2.32956787601564 | erot = 2.41406261152026 | epot = -21.5311925684017 | etot = -16.7875620808658 -356000 ekin = 2.99536507165417 | erot = 3.01337867890171 | epot = -21.4612138261641 | etot = -15.4524700756082 -357000 ekin = 1.79487551861703 | erot = 2.14781775756833 | epot = -21.4425100027869 | etot = -17.4998167266016 -358000 ekin = 2.06856992699964 | erot = 1.9158505155371 | epot = -21.4597512525558 | etot = -17.475330810019 -359000 ekin = 2.03457633089973 | erot = 2.13725650388115 | epot = -21.434584367242 | etot = -17.2627515324611 -360000 ekin = 2.64289898809605 | erot = 2.45722294398597 | epot = -21.3798303659973 | etot = -16.2797084339153 -361000 ekin = 2.44681633772951 | erot = 2.40323525392196 | epot = -21.4535746870958 | etot = -16.6035230954443 -362000 ekin = 2.27284400709389 | erot = 2.04866562998476 | epot = -21.4444048899962 | etot = -17.1228952529175 -363000 ekin = 3.23945885057605 | erot = 1.79247859381386 | epot = -21.4992698914106 | etot = -16.4673324470207 -364000 ekin = 3.01124200487831 | erot = 2.1649586732171 | epot = -21.5330648567406 | etot = -16.3568641786452 -365000 ekin = 2.51472285580868 | erot = 2.29864111879033 | epot = -21.6252096459669 | etot = -16.8118456713679 -366000 ekin = 2.59356655410023 | erot = 2.21031948632572 | epot = -21.6397726115724 | etot = -16.8358865711464 -367000 ekin = 2.23422490605625 | erot = 1.85375489374335 | epot = -21.7036464131407 | etot = -17.6156666133411 -368000 ekin = 2.47747707853681 | erot = 2.36511710555107 | epot = -21.7442459693683 | etot = -16.9016517852804 -369000 ekin = 2.03854183495619 | erot = 2.80790943599038 | epot = -21.829546112742 | etot = -16.9830948417954 -370000 ekin = 2.08495509326204 | erot = 2.15717784784085 | epot = -21.8579547558589 | etot = -17.615821814756 -371000 ekin = 2.1649158804987 | erot = 2.10731342711638 | epot = -21.750730287247 | etot = -17.4785009796319 -372000 ekin = 1.83416420958724 | erot = 1.90082367490456 | epot = -21.678422472552 | etot = -17.9434345880602 -373000 ekin = 1.97176482573297 | erot = 1.77796007890949 | epot = -21.6393712386779 | etot = -17.8896463340354 -374000 ekin = 2.89940710658304 | erot = 1.91194262525379 | epot = -21.5337545453636 | etot = -16.7224048135268 -375000 ekin = 2.32339676163341 | erot = 1.92362318361283 | epot = -21.4217091025191 | etot = -17.1746891572729 -376000 ekin = 2.59047552311153 | erot = 2.32394149083979 | epot = -21.4139727856535 | etot = -16.4995557717022 -377000 ekin = 2.24598863840517 | erot = 1.65770205797294 | epot = -21.3405339068233 | etot = -17.4368432104452 -378000 ekin = 2.38351514056703 | erot = 2.54156262207209 | epot = -21.312238058745 | etot = -16.3871602961058 -379000 ekin = 2.08457212928957 | erot = 2.11819645676888 | epot = -21.2663127721438 | etot = -17.0635441860853 -380000 ekin = 2.62168026009058 | erot = 2.36576073073355 | epot = -21.2469701231192 | etot = -16.2595291322951 -381000 ekin = 2.42554871977308 | erot = 2.21588725182519 | epot = -21.2594018196932 | etot = -16.6179658480949 -382000 ekin = 2.04454090532124 | erot = 3.35199327879852 | epot = -21.3507561156205 | etot = -15.9542219315007 -383000 ekin = 2.57756769789844 | erot = 1.58356833947094 | epot = -21.4206473136968 | etot = -17.2595112763274 -384000 ekin = 2.32411392435713 | erot = 2.07034159075994 | epot = -21.4254017003271 | etot = -17.0309461852101 -385000 ekin = 1.93815279071873 | erot = 3.2997037447625 | epot = -21.4993838182002 | etot = -16.261527282719 -386000 ekin = 2.10645704249443 | erot = 2.94380940917573 | epot = -21.5050572923383 | etot = -16.4547908406682 -387000 ekin = 2.28625118399722 | erot = 2.404880226949 | epot = -21.4350466670763 | etot = -16.7439152561301 -388000 ekin = 2.84183807689895 | erot = 2.72440789072403 | epot = -21.4487672968481 | etot = -15.8825213292251 -389000 ekin = 3.39750799106374 | erot = 3.08194517695387 | epot = -21.6559630447604 | etot = -15.1765098767428 -390000 ekin = 2.82211920760116 | erot = 2.04880343622588 | epot = -21.7229608878359 | etot = -16.8520382440089 -391000 ekin = 2.25113345866117 | erot = 2.45876014532078 | epot = -21.7793475672489 | etot = -17.0694539632669 -392000 ekin = 2.67779739921769 | erot = 2.75278604715789 | epot = -21.9200377033299 | etot = -16.4894542569543 -393000 ekin = 2.07336639249413 | erot = 1.66102921524043 | epot = -22.0500496423094 | etot = -18.3156540345749 -394000 ekin = 2.1138614951422 | erot = 2.40654905841557 | epot = -22.0647062581753 | etot = -17.5442957046175 -395000 ekin = 2.46967791557608 | erot = 2.46187607744979 | epot = -22.0113006362932 | etot = -17.0797466432673 -396000 ekin = 3.17858061422169 | erot = 1.60030928107609 | epot = -21.9570022338793 | etot = -17.1781123385815 -397000 ekin = 2.37483507726777 | erot = 2.17387816921976 | epot = -21.8769234701935 | etot = -17.328210223706 -398000 ekin = 2.29815779154462 | erot = 2.20148627030488 | epot = -21.829364101453 | etot = -17.3297200396035 -399000 ekin = 2.66620669497936 | erot = 2.78316441348842 | epot = -21.7420307764658 | etot = -16.292659667998 -400000 ekin = 1.8196142363994 | erot = 2.77573291920479 | epot = -21.7225828560708 | etot = -17.1272357004667 -401000 ekin = 2.39347596566752 | erot = 3.11237720134101 | epot = -21.7632198127752 | etot = -16.2573666457667 -402000 ekin = 4.0137909252526 | erot = 3.58756310879364 | epot = -21.6952307126457 | etot = -14.0938766785994 -403000 ekin = 3.6423872335827 | erot = 3.44210139074533 | epot = -21.6932224157204 | etot = -14.6087337913923 -404000 ekin = 2.52116102522202 | erot = 2.99286839639892 | epot = -21.7395466120139 | etot = -16.225517190393 -405000 ekin = 2.80514548558626 | erot = 3.0980722844015 | epot = -21.8096811205532 | etot = -15.9064633505654 -406000 ekin = 2.32696376764903 | erot = 2.03572639782902 | epot = -21.9111381639249 | etot = -17.5484479984469 -407000 ekin = 2.33504128016395 | erot = 1.91320949168965 | epot = -21.9359478399848 | etot = -17.6876970681312 -408000 ekin = 1.90942025822265 | erot = 2.20375631379573 | epot = -21.9849314014528 | etot = -17.8717548294345 -409000 ekin = 1.98818542800297 | erot = 1.95540808206523 | epot = -22.0378349759701 | etot = -18.0942414659019 -410000 ekin = 1.59823476401333 | erot = 1.9127296785249 | epot = -22.0830507565097 | etot = -18.5720863139715 -411000 ekin = 1.87320182179615 | erot = 2.46575148951075 | epot = -22.1911106440468 | etot = -17.8521573327399 -412000 ekin = 2.51909186028136 | erot = 2.65534868642724 | epot = -22.2816800676061 | etot = -17.1072395208975 -413000 ekin = 2.80929435327117 | erot = 3.19888285052217 | epot = -22.1907679968742 | etot = -16.1825907930808 -414000 ekin = 2.79014519733558 | erot = 2.72515195410934 | epot = -22.144863024243 | etot = -16.6295658727981 -415000 ekin = 2.46789019087319 | erot = 2.24891720770209 | epot = -22.1977268949426 | etot = -17.4809194963673 -416000 ekin = 3.30766536008866 | erot = 1.55878918639506 | epot = -22.169487821356 | etot = -17.3030332748722 -417000 ekin = 3.95074944679108 | erot = 2.44780201516575 | epot = -22.1018895242095 | etot = -15.7033380622527 -418000 ekin = 2.77340936693415 | erot = 2.68993840817535 | epot = -21.9773275627671 | etot = -16.5139797876576 -419000 ekin = 2.38275203991916 | erot = 2.97769109273477 | epot = -21.9010102007429 | etot = -16.540567068089 -420000 ekin = 1.80397709765343 | erot = 1.82715488758969 | epot = -21.8849019003166 | etot = -18.2537699150735 -421000 ekin = 1.35294173647285 | erot = 1.77463275951321 | epot = -21.8324727162455 | etot = -18.7048982202595 -422000 ekin = 1.39101035408781 | erot = 2.74626781088313 | epot = -21.8922044238521 | etot = -17.7549262588812 -423000 ekin = 1.58313118355036 | erot = 3.07988587276089 | epot = -21.9303489156376 | etot = -17.2673318593264 -424000 ekin = 2.38308976422852 | erot = 2.0290563283423 | epot = -22.0003513420112 | etot = -17.5882052494404 -425000 ekin = 2.32292982636641 | erot = 2.54472792699356 | epot = -22.0461884305753 | etot = -17.1785306772154 -426000 ekin = 2.07274921207621 | erot = 3.12068562025982 | epot = -21.9899604929779 | etot = -16.7965256606419 -427000 ekin = 2.16499158921497 | erot = 2.43609860560846 | epot = -21.883756502818 | etot = -17.2826663079946 -428000 ekin = 1.81001230881453 | erot = 1.65184910311941 | epot = -21.8651168729134 | etot = -18.4032554609795 -429000 ekin = 1.67080799563552 | erot = 2.5582900403394 | epot = -21.8232038220611 | etot = -17.5941057860861 -430000 ekin = 2.68658781224626 | erot = 2.85919253371561 | epot = -21.8545360487503 | etot = -16.3087557027885 -431000 ekin = 2.77334901985547 | erot = 1.57746917070685 | epot = -21.8360353910944 | etot = -17.485217200532 -432000 ekin = 2.50244674166433 | erot = 1.60779258881598 | epot = -21.7381087453319 | etot = -17.6278694148516 -433000 ekin = 1.85649371322471 | erot = 2.49173358917941 | epot = -21.7919912827364 | etot = -17.4437639803323 -434000 ekin = 2.89302367450633 | erot = 2.79890045602689 | epot = -21.923157505168 | etot = -16.2312333746348 -435000 ekin = 3.67647442700573 | erot = 1.38588132381276 | epot = -22.1019777057281 | etot = -17.0396219549096 -436000 ekin = 3.05510329104704 | erot = 2.00142902882894 | epot = -22.1034257027066 | etot = -17.0468933828306 -437000 ekin = 3.2334117289381 | erot = 1.78346855436479 | epot = -22.113702088725 | etot = -17.0968218054222 -438000 ekin = 2.86378458795302 | erot = 1.84588842157478 | epot = -22.072414124752 | etot = -17.3627411152242 -439000 ekin = 2.41407153953135 | erot = 2.70066632790347 | epot = -22.0535011599236 | etot = -16.9387632924888 -440000 ekin = 2.22110309163133 | erot = 3.01674685818989 | epot = -22.0773629228072 | etot = -16.8395129729859 -441000 ekin = 2.8952003347941 | erot = 2.87911130379515 | epot = -22.209849236351 | etot = -16.4355375977618 -442000 ekin = 2.05598301233623 | erot = 1.73562369066665 | epot = -22.2689079268812 | etot = -18.4773012238783 -443000 ekin = 1.86650631344267 | erot = 2.0081617804031 | epot = -22.3072964279924 | etot = -18.4326283341466 -444000 ekin = 2.06088560705618 | erot = 2.15265011198711 | epot = -22.3186686701218 | etot = -18.1051329510785 -445000 ekin = 2.10029110633058 | erot = 2.28003314051319 | epot = -22.3739249314238 | etot = -17.99360068458 -446000 ekin = 2.42121462246176 | erot = 2.85365097104761 | epot = -22.4030820729313 | etot = -17.1282164794219 -447000 ekin = 2.19905370994783 | erot = 2.98216231903377 | epot = -22.4760062523441 | etot = -17.2947902233625 -448000 ekin = 2.35344530580997 | erot = 2.94496431571714 | epot = -22.4927466941726 | etot = -17.1943370726455 -449000 ekin = 2.39032460069844 | erot = 2.92889137252359 | epot = -22.5027878081879 | etot = -17.1835718349658 -450000 ekin = 1.87543018481826 | erot = 1.69603328668916 | epot = -22.4562462785528 | etot = -18.8847828070454 -451000 ekin = 2.01850498861612 | erot = 1.92812989993405 | epot = -22.4817672986218 | etot = -18.5351324100716 -452000 ekin = 1.36652609658347 | erot = 1.87105620810406 | epot = -22.4501755877893 | etot = -19.2125932831018 -453000 ekin = 2.0599225820261 | erot = 2.56027964608565 | epot = -22.2765869721545 | etot = -17.6563847440428 -454000 ekin = 1.47421749728914 | erot = 2.19120144206327 | epot = -22.1381671023588 | etot = -18.4727481630064 -455000 ekin = 1.65550022307771 | erot = 2.72165814308169 | epot = -21.9904394751434 | etot = -17.613281108984 -456000 ekin = 2.34827062603187 | erot = 2.00722438151076 | epot = -21.9105114729145 | etot = -17.5550164653719 -457000 ekin = 2.01338249991754 | erot = 2.37170378033694 | epot = -21.8819790372449 | etot = -17.4968927569905 -458000 ekin = 1.72815421955305 | erot = 2.26329746701053 | epot = -21.9116044050661 | etot = -17.9201527185025 -459000 ekin = 2.48347398227003 | erot = 2.3237619692994 | epot = -21.9949404038569 | etot = -17.1877044522874 -460000 ekin = 2.18770854699575 | erot = 2.0008166291832 | epot = -21.9585322440376 | etot = -17.7700070678586 -461000 ekin = 2.27716435663744 | erot = 2.90195656269069 | epot = -21.887768217766 | etot = -16.7086472984378 -462000 ekin = 2.61244889701714 | erot = 1.79757533309513 | epot = -21.9143949779913 | etot = -17.504370747879 -463000 ekin = 2.55684814656524 | erot = 3.31200610027657 | epot = -21.8497749242034 | etot = -15.9809206773616 -464000 ekin = 2.15312235839157 | erot = 2.38947690136821 | epot = -21.7825241097984 | etot = -17.2399248500386 -465000 ekin = 2.5257577253008 | erot = 3.61331808321477 | epot = -21.70727052519 | etot = -15.5681947166744 -466000 ekin = 1.97943618964772 | erot = 2.8868852833762 | epot = -21.7222514097775 | etot = -16.8559299367535 -467000 ekin = 1.62882257493983 | erot = 2.60892282315519 | epot = -21.8080861041928 | etot = -17.5703407060978 -468000 ekin = 1.09823854644375 | erot = 3.35073251937297 | epot = -21.852381101233 | etot = -17.4034100354163 -469000 ekin = 1.70229597385131 | erot = 2.75889840726388 | epot = -21.8665756757502 | etot = -17.4053812946351 -470000 ekin = 1.85844768422772 | erot = 2.87065462176252 | epot = -21.9036130079377 | etot = -17.1745107019474 -471000 ekin = 2.74399539924327 | erot = 2.3494335495508 | epot = -21.954398971724 | etot = -16.8609700229299 -472000 ekin = 2.7182617922689 | erot = 2.13581917182001 | epot = -22.0449294707038 | etot = -17.1908485066149 -473000 ekin = 2.29380642077303 | erot = 2.07595163501545 | epot = -22.0706135180041 | etot = -17.7008554622156 -474000 ekin = 2.22690782122655 | erot = 2.16470599013947 | epot = -22.0704871162387 | etot = -17.6788733048726 -475000 ekin = 2.49786795333289 | erot = 2.09510196885222 | epot = -22.0509742163569 | etot = -17.4580042941718 -476000 ekin = 2.20264299239668 | erot = 1.76757923556401 | epot = -21.9427521555982 | etot = -17.9725299276376 -477000 ekin = 2.45872237399503 | erot = 2.38426997478538 | epot = -21.9051474088983 | etot = -17.0621550601179 -478000 ekin = 1.8990596403089 | erot = 2.04864356713722 | epot = -21.9114508304737 | etot = -17.9637476230276 -479000 ekin = 2.27133902137491 | erot = 3.08755197682257 | epot = -21.8872829373266 | etot = -16.5283919391291 -480000 ekin = 1.67015605151468 | erot = 2.76560365045836 | epot = -21.8968158425889 | etot = -17.4610561406159 -481000 ekin = 1.81882995680353 | erot = 2.94136105971067 | epot = -21.8571304925408 | etot = -17.0969394760266 -482000 ekin = 2.15305069632652 | erot = 2.07327897823919 | epot = -21.8152992914386 | etot = -17.5889696168728 -483000 ekin = 1.50004535981758 | erot = 1.99364343935403 | epot = -21.7843644990947 | etot = -18.2906756999231 -484000 ekin = 1.85234844255529 | erot = 2.34000231202781 | epot = -21.8614293841666 | etot = -17.6690786295835 -485000 ekin = 1.64682178328831 | erot = 2.50437862576679 | epot = -21.8969405008956 | etot = -17.7457400918405 -486000 ekin = 1.86104257115938 | erot = 2.15995925522772 | epot = -21.8879397421696 | etot = -17.8669379157825 -487000 ekin = 2.34639026339217 | erot = 3.11622773972822 | epot = -21.9707194220383 | etot = -16.5081014189179 -488000 ekin = 2.27484994031488 | erot = 3.28147617368226 | epot = -21.9426475486812 | etot = -16.3863214346841 -489000 ekin = 2.38811933287365 | erot = 2.56070014238266 | epot = -21.860086116809 | etot = -16.9112666415526 -490000 ekin = 2.12976254880773 | erot = 3.54525746010285 | epot = -21.7617637919249 | etot = -16.0867437830143 -491000 ekin = 2.20850764560417 | erot = 2.48919239454316 | epot = -21.6468680069132 | etot = -16.9491679667659 -492000 ekin = 2.43957739853024 | erot = 2.76323186690379 | epot = -21.6230951653169 | etot = -16.4202858998828 -493000 ekin = 1.79391622496105 | erot = 2.29052518470038 | epot = -21.6945975278841 | etot = -17.6101561182227 -494000 ekin = 2.11542949642227 | erot = 3.0131386587248 | epot = -21.763700447204 | etot = -16.6351322920569 -495000 ekin = 2.1568591957283 | erot = 2.49005677705244 | epot = -21.8783556810054 | etot = -17.2314397082246 -496000 ekin = 2.06037552826019 | erot = 2.60698629104701 | epot = -21.9276220332962 | etot = -17.260260213989 -497000 ekin = 2.52228141248763 | erot = 1.71013019276801 | epot = -21.8769629373864 | etot = -17.6445513321308 -498000 ekin = 2.1539450080541 | erot = 1.78777085700021 | epot = -21.8243748366057 | etot = -17.8826589715514 -499000 ekin = 3.01296343053107 | erot = 1.73934813146709 | epot = -21.839263268044 | etot = -17.0869517060458 -500000 ekin = 2.76642119718551 | erot = 2.50182215373005 | epot = -21.830671988603 | etot = -16.5624286376875 -501000 ekin = 2.69367571720338 | erot = 2.99042817784737 | epot = -21.7039103667138 | etot = -16.0198064716631 -502000 ekin = 1.91666556639458 | erot = 3.89815239299715 | epot = -21.5845300715443 | etot = -15.7697121121526 -503000 ekin = 1.80513448090425 | erot = 2.94463129244924 | epot = -21.408846856306 | etot = -16.6590810829525 -504000 ekin = 1.70082883689617 | erot = 3.04312463877849 | epot = -21.3315058298564 | etot = -16.5875523541817 -505000 ekin = 2.75953000022913 | erot = 2.14635942194521 | epot = -21.3525103549444 | etot = -16.4466209327701 -506000 ekin = 2.29728093923375 | erot = 2.04403144683578 | epot = -21.3794572010067 | etot = -17.0381448149372 -507000 ekin = 3.17636857959624 | erot = 2.42164349794528 | epot = -21.4731108320935 | etot = -15.875098754552 -508000 ekin = 2.53590109429522 | erot = 2.52790695399207 | epot = -21.6300410847597 | etot = -16.5662330364724 -509000 ekin = 2.12748393236721 | erot = 2.83071060777934 | epot = -21.7781347526393 | etot = -16.8199402124928 -510000 ekin = 2.16138023827908 | erot = 1.44739524871433 | epot = -21.8661383228762 | etot = -18.2573628358828 -511000 ekin = 2.5432337386743 | erot = 2.77108674378181 | epot = -21.9670096484362 | etot = -16.6526891659801 -512000 ekin = 2.32820226144234 | erot = 2.80424931634042 | epot = -22.0177071813426 | etot = -16.8852556035598 -513000 ekin = 2.47700215188742 | erot = 2.17127792631491 | epot = -22.0110285387344 | etot = -17.362748460532 -514000 ekin = 2.76651136580705 | erot = 2.55680467976048 | epot = -22.0909970005814 | etot = -16.7676809550139 -515000 ekin = 2.52023319653878 | erot = 1.82499891391155 | epot = -22.1712715169566 | etot = -17.8260394065063 -516000 ekin = 2.81741012640847 | erot = 2.22255273815334 | epot = -22.2621950124767 | etot = -17.2222321479149 -517000 ekin = 2.03287831599843 | erot = 2.04932227860396 | epot = -22.2794486174447 | etot = -18.1972480228424 -518000 ekin = 2.18753527424292 | erot = 2.76011341951325 | epot = -22.2667176836094 | etot = -17.3190689898532 -519000 ekin = 2.23127004412532 | erot = 2.23036422155451 | epot = -22.3641437250362 | etot = -17.9025094593563 -520000 ekin = 1.88835704965194 | erot = 2.20137678015022 | epot = -22.4547788180202 | etot = -18.365044988218 -521000 ekin = 2.57911594310158 | erot = 1.87216207270883 | epot = -22.6071563154982 | etot = -18.1558782996878 -522000 ekin = 3.47551915105823 | erot = 1.7762374523623 | epot = -22.6852629490162 | etot = -17.4335063455957 -523000 ekin = 2.84545293485784 | erot = 2.47507537559666 | epot = -22.727728352182 | etot = -17.4072000417275 -524000 ekin = 2.40278895519472 | erot = 2.37529684497555 | epot = -22.6643160930412 | etot = -17.8862302928709 -525000 ekin = 1.5950703357501 | erot = 2.61508341973267 | epot = -22.5633164974796 | etot = -18.3531627419969 -526000 ekin = 1.67007684014044 | erot = 1.59545284095806 | epot = -22.5113199784161 | etot = -19.2457902973176 -527000 ekin = 2.19667533945248 | erot = 1.93330231246751 | epot = -22.4181345854018 | etot = -18.2881569334818 -528000 ekin = 2.6386695788743 | erot = 2.84200507572114 | epot = -22.4271496272375 | etot = -16.9464749726421 -529000 ekin = 2.71685924097596 | erot = 3.01195511036349 | epot = -22.4607209136928 | etot = -16.7319065623534 -530000 ekin = 2.59646038482582 | erot = 2.13176928192349 | epot = -22.3209630404852 | etot = -17.5927333737359 -531000 ekin = 2.96818211550215 | erot = 2.3583690601903 | epot = -22.2240561584029 | etot = -16.8975049827104 -532000 ekin = 2.54400448114086 | erot = 2.3226642368829 | epot = -22.2383323718679 | etot = -17.3716636538441 -533000 ekin = 2.47235456553947 | erot = 2.96337386592411 | epot = -22.2434312615742 | etot = -16.8077028301106 -534000 ekin = 2.104894788263 | erot = 2.0389464069744 | epot = -22.2624131617689 | etot = -18.1185719665315 -535000 ekin = 3.76811893478762 | erot = 2.64694643296528 | epot = -22.2342741399369 | etot = -15.819208772184 -536000 ekin = 2.78932048770647 | erot = 1.95046774407585 | epot = -22.1710588414063 | etot = -17.4312706096239 -537000 ekin = 2.84547413963847 | erot = 2.6235440651257 | epot = -22.0792539675812 | etot = -16.6102357628171 -538000 ekin = 2.67615418297319 | erot = 2.08962546790894 | epot = -21.9560559397442 | etot = -17.1902762888621 -539000 ekin = 2.73041224389434 | erot = 2.35761678189143 | epot = -22.0360310245606 | etot = -16.9480019987748 -540000 ekin = 2.45513520817503 | erot = 2.49807124796168 | epot = -22.1997448500024 | etot = -17.2465383938656 -541000 ekin = 3.48268229748521 | erot = 2.77797330372247 | epot = -22.2939060084685 | etot = -16.0332504072608 -542000 ekin = 2.48960436886327 | erot = 2.87332479229811 | epot = -22.3004887690915 | etot = -16.9375596079301 -543000 ekin = 2.34699181381528 | erot = 2.86167842257192 | epot = -22.3027783678197 | etot = -17.0941081314325 -544000 ekin = 2.22918134297117 | erot = 1.46827924617161 | epot = -22.2757921511235 | etot = -18.5783315619807 -545000 ekin = 2.45393652663684 | erot = 2.14178562937396 | epot = -22.2696521197313 | etot = -17.6739299637205 -546000 ekin = 1.98434977645848 | erot = 2.2414409311316 | epot = -22.232171992891 | etot = -18.0063812853009 -547000 ekin = 2.5623035019647 | erot = 1.89574625912019 | epot = -22.2013923967025 | etot = -17.7433426356176 -548000 ekin = 1.72907614338158 | erot = 1.64127030305736 | epot = -22.1897325934373 | etot = -18.8193861469984 -549000 ekin = 1.95696682165778 | erot = 2.6453998894305 | epot = -22.3281210018679 | etot = -17.7257542907796 -550000 ekin = 1.80672944936439 | erot = 1.58554489058936 | epot = -22.4379557312283 | etot = -19.0456813912745 -551000 ekin = 2.19785864069662 | erot = 2.26344341600384 | epot = -22.4944444264338 | etot = -18.0331423697333 -552000 ekin = 2.07444252867401 | erot = 2.49246441473271 | epot = -22.5313734934249 | etot = -17.9644665500182 -553000 ekin = 2.94841939583914 | erot = 2.12309786300738 | epot = -22.5870982488507 | etot = -17.5155809900042 -554000 ekin = 2.86687820100223 | erot = 1.94287298381727 | epot = -22.755332978123 | etot = -17.9455817933035 -555000 ekin = 2.43102414091851 | erot = 2.28708167460998 | epot = -22.8409516497234 | etot = -18.1228458341949 -556000 ekin = 2.31020008885682 | erot = 2.55815314755914 | epot = -22.8777743355339 | etot = -18.0094210991179 -557000 ekin = 2.81359485404958 | erot = 1.42586137655668 | epot = -22.93912738 | etot = -18.6996711493937 -558000 ekin = 2.79709708533549 | erot = 1.99545051650403 | epot = -22.9823826800611 | etot = -18.1898350782216 -559000 ekin = 3.34842854089642 | erot = 2.30939572175804 | epot = -23.0558646505447 | etot = -17.3980403878903 -560000 ekin = 3.12583165184862 | erot = 2.33613566970362 | epot = -23.0537007225862 | etot = -17.591733401034 -561000 ekin = 2.91276096736789 | erot = 2.07459481236914 | epot = -22.9822607654341 | etot = -17.994904985697 -562000 ekin = 3.33017095598493 | erot = 2.52215992853225 | epot = -22.8889363116258 | etot = -17.0366054271086 -563000 ekin = 2.70200701416854 | erot = 1.64770113379201 | epot = -22.8712722594835 | etot = -18.521564111523 -564000 ekin = 2.82953631474814 | erot = 2.52900560163794 | epot = -22.8387855460795 | etot = -17.4802436296934 -565000 ekin = 2.6799988891771 | erot = 2.05091800967452 | epot = -22.7937507048715 | etot = -18.0628338060199 -566000 ekin = 2.32986557500305 | erot = 2.16379904557211 | epot = -22.8028233873669 | etot = -18.3091587667918 -567000 ekin = 1.92319601586312 | erot = 2.83258522428556 | epot = -22.7588270107034 | etot = -18.0030457705547 -568000 ekin = 2.1767237164987 | erot = 2.23391201707385 | epot = -22.7857243432792 | etot = -18.3750886097067 -569000 ekin = 2.44197408396629 | erot = 2.65159536305571 | epot = -22.7197314796375 | etot = -17.6261620326155 -570000 ekin = 2.4317740620905 | erot = 1.89764945519459 | epot = -22.6963472615905 | etot = -18.3669237443054 -571000 ekin = 2.86160521289846 | erot = 2.96804382024775 | epot = -22.6961835038032 | etot = -16.866534470657 -572000 ekin = 1.92662919536386 | erot = 3.79135909534691 | epot = -22.6587081618988 | etot = -16.9407198711881 -573000 ekin = 2.40137439242945 | erot = 2.29982613356341 | epot = -22.6365074046859 | etot = -17.9353068786931 -574000 ekin = 1.68882589350908 | erot = 2.32097404492489 | epot = -22.6783832960446 | etot = -18.6685833576106 -575000 ekin = 1.85490665091732 | erot = 1.85640808911424 | epot = -22.7444448136904 | etot = -19.0331300736589 -576000 ekin = 3.24775679594035 | erot = 2.95569268214308 | epot = -22.6991990620438 | etot = -16.4957495839604 -577000 ekin = 2.89423151645282 | erot = 2.87486712706735 | epot = -22.6284365608021 | etot = -16.8593379172819 -578000 ekin = 2.40460916677569 | erot = 2.78216711024699 | epot = -22.4348874817266 | etot = -17.2481112047039 -579000 ekin = 2.40580528046575 | erot = 1.99557814482531 | epot = -22.2889136736671 | etot = -17.887530248376 -580000 ekin = 2.69817090358905 | erot = 1.94741864170503 | epot = -22.1754486864787 | etot = -17.5298591411846 -581000 ekin = 2.06309668646281 | erot = 2.97621367011722 | epot = -22.0670098600828 | etot = -17.0276995035028 -582000 ekin = 2.33869527454826 | erot = 3.07898324506954 | epot = -21.9478320300714 | etot = -16.5301535104536 -583000 ekin = 2.23428959741492 | erot = 2.6847669308886 | epot = -21.837983720672 | etot = -16.9189271923685 -584000 ekin = 2.94321016295283 | erot = 2.59995039730547 | epot = -21.7517635625832 | etot = -16.2086030023249 -585000 ekin = 2.36063475490837 | erot = 2.49112677628936 | epot = -21.7173359488816 | etot = -16.8655744176839 -586000 ekin = 3.56583702163526 | erot = 2.02487858259688 | epot = -21.7707868137139 | etot = -16.1800712094817 -587000 ekin = 3.53727585853246 | erot = 1.97258932652023 | epot = -21.7665121756112 | etot = -16.2566469905585 -588000 ekin = 2.82339556293759 | erot = 1.59340504807045 | epot = -21.7545319340973 | etot = -17.3377313230892 -589000 ekin = 2.31627310139819 | erot = 2.20582604523296 | epot = -21.8199173705564 | etot = -17.2978182239252 -590000 ekin = 2.57616671531331 | erot = 1.72768273328209 | epot = -21.8427138199643 | etot = -17.5388643713689 -591000 ekin = 1.91473306171853 | erot = 3.80604384238378 | epot = -21.9351393124188 | etot = -16.2143624083165 -592000 ekin = 2.11222958764659 | erot = 2.84208333850203 | epot = -21.9639458839076 | etot = -17.009632957759 -593000 ekin = 1.66462149590471 | erot = 2.46217253451013 | epot = -21.9921445323972 | etot = -17.8653505019823 -594000 ekin = 1.86314045588477 | erot = 2.37275936142266 | epot = -22.1149191228505 | etot = -17.8790193055431 -595000 ekin = 1.6397125755004 | erot = 2.1497024679856 | epot = -22.2960530768755 | etot = -18.5066380333895 -596000 ekin = 1.86247376576131 | erot = 1.56938095427868 | epot = -22.4014957466218 | etot = -18.9696410265818 -597000 ekin = 2.21073901406701 | erot = 2.3087175693751 | epot = -22.4599242604733 | etot = -17.9404676770312 -598000 ekin = 1.8660134932493 | erot = 3.0231172739981 | epot = -22.5165298316334 | etot = -17.627399064386 -599000 ekin = 2.86271635930755 | erot = 2.19928854437227 | epot = -22.536599708025 | etot = -17.4745948043452 -600000 ekin = 2.65062163067179 | erot = 2.14533898812783 | epot = -22.4620537969304 | etot = -17.6660931781308 -601000 ekin = 2.97018864875202 | erot = 3.19824090103877 | epot = -22.3271949752462 | etot = -16.1587654254554 -602000 ekin = 2.93416893709002 | erot = 2.68627449040959 | epot = -22.2245183728174 | etot = -16.6040749453178 -603000 ekin = 2.5987545006459 | erot = 2.71301833029982 | epot = -22.1705323477201 | etot = -16.8587595167744 -604000 ekin = 1.79059859762798 | erot = 2.11515305424794 | epot = -22.1931056020218 | etot = -18.2873539501458 -605000 ekin = 1.82914051863723 | erot = 2.27656979248767 | epot = -22.2183915784731 | etot = -18.1126812673482 -606000 ekin = 2.33864125390346 | erot = 2.20416493777799 | epot = -22.1617656383863 | etot = -17.6189594467049 -607000 ekin = 2.72666217259877 | erot = 2.97710334336214 | epot = -22.1572786906588 | etot = -16.4535131746979 -608000 ekin = 2.45226937954678 | erot = 2.41232790919958 | epot = -22.1263051367365 | etot = -17.2617078479901 -609000 ekin = 1.91032127854288 | erot = 2.62712516529569 | epot = -22.0127581830193 | etot = -17.4753117391808 -610000 ekin = 3.01319055031108 | erot = 2.17098104720966 | epot = -21.9304996298691 | etot = -16.7463280323483 -611000 ekin = 2.44410994437292 | erot = 2.75159061185423 | epot = -21.9258193850469 | etot = -16.7301188288197 -612000 ekin = 2.50271115837173 | erot = 2.1681764069217 | epot = -21.9676183236646 | etot = -17.2967307583711 -613000 ekin = 3.01842230632867 | erot = 2.12784419676568 | epot = -22.0277467117808 | etot = -16.8814802086865 -614000 ekin = 2.25331711369829 | erot = 2.99334048390158 | epot = -22.0701464667308 | etot = -16.8234888691309 -615000 ekin = 1.66376443031995 | erot = 2.63613776051568 | epot = -21.9985978951917 | etot = -17.6986957043561 -616000 ekin = 1.89454248699047 | erot = 2.8731835516953 | epot = -22.0041678369047 | etot = -17.2364417982189 -617000 ekin = 2.14789714287838 | erot = 2.51249074123956 | epot = -22.0251474680605 | etot = -17.3647595839426 -618000 ekin = 3.11174934178843 | erot = 2.74374306269143 | epot = -21.980284295602 | etot = -16.1247918911222 -619000 ekin = 3.41036213968179 | erot = 2.1061679415973 | epot = -21.9557959924962 | etot = -16.4392659112171 -620000 ekin = 4.28430989238204 | erot = 2.19572475327592 | epot = -21.9033881020935 | etot = -15.4233534564355 -621000 ekin = 3.095687767491 | erot = 2.55794040804606 | epot = -21.8286763731364 | etot = -16.1750481975993 -622000 ekin = 2.76030419206698 | erot = 2.60754397958252 | epot = -21.7459002641758 | etot = -16.3780520925263 -623000 ekin = 2.87269212022169 | erot = 2.9040131195019 | epot = -21.5853226709315 | etot = -15.8086174312079 -624000 ekin = 2.01889500087931 | erot = 3.41825755609796 | epot = -21.4095311686243 | etot = -15.972378611647 -625000 ekin = 2.87966631754696 | erot = 2.69115421564282 | epot = -21.2859406043045 | etot = -15.7151200711148 -626000 ekin = 2.56087279949319 | erot = 2.15801254335176 | epot = -21.2329175358056 | etot = -16.5140321929606 -627000 ekin = 2.30197939613517 | erot = 2.40176668957967 | epot = -21.2932794652839 | etot = -16.589533379569 -628000 ekin = 2.23988628353727 | erot = 2.75332535542197 | epot = -21.4558642198861 | etot = -16.4626525809268 -629000 ekin = 2.20891060851903 | erot = 1.97036896055006 | epot = -21.6109313731644 | etot = -17.4316518040953 -630000 ekin = 2.48711004105953 | erot = 2.14055508379567 | epot = -21.6286281269545 | etot = -17.0009630020993 -631000 ekin = 2.05035510102044 | erot = 1.7851913104256 | epot = -21.633635046353 | etot = -17.798088634907 -632000 ekin = 1.65439924450982 | erot = 3.28310987077495 | epot = -21.6999899301469 | etot = -16.7624808148621 -633000 ekin = 2.3465798853121 | erot = 2.34109631044867 | epot = -21.8317647703271 | etot = -17.1440885745664 -634000 ekin = 2.31570267703931 | erot = 2.47129317382499 | epot = -21.8814211467029 | etot = -17.0944252958386 -635000 ekin = 1.99068848818427 | erot = 3.35493927676214 | epot = -21.9111632351734 | etot = -16.565535470227 -636000 ekin = 2.50156763858618 | erot = 2.48847742334417 | epot = -21.8752689055208 | etot = -16.8852238435905 -637000 ekin = 2.76558055064046 | erot = 2.80410341825292 | epot = -21.7874464522771 | etot = -16.2177624833838 -638000 ekin = 2.45488734924466 | erot = 2.81516363335623 | epot = -21.8973623385979 | etot = -16.627311355997 -639000 ekin = 1.89221088715375 | erot = 2.13319565970053 | epot = -21.932098303477 | etot = -17.9066917566227 -640000 ekin = 2.12173400886946 | erot = 3.32302167857402 | epot = -21.8808288554835 | etot = -16.4360731680401 -641000 ekin = 2.09554541112561 | erot = 2.23098450754964 | epot = -21.9203390995502 | etot = -17.5938091808749 -642000 ekin = 2.28696138506763 | erot = 2.67378976619349 | epot = -21.9723604262128 | etot = -17.0116092749516 -643000 ekin = 2.74450005384909 | erot = 2.20403941809546 | epot = -21.9235240791533 | etot = -16.9749846072088 -644000 ekin = 2.87909523138454 | erot = 3.40688779630213 | epot = -21.9417833997401 | etot = -15.6558003720534 -645000 ekin = 2.38284095628021 | erot = 2.10846397463902 | epot = -21.8306349073152 | etot = -17.3393299763959 -646000 ekin = 2.68568471833194 | erot = 1.8085210536706 | epot = -21.6853054888873 | etot = -17.1910997168848 -647000 ekin = 2.44462012552757 | erot = 2.00446720103469 | epot = -21.497463529291 | etot = -17.0483762027288 -648000 ekin = 2.2215075315945 | erot = 1.69679185313771 | epot = -21.5947311257684 | etot = -17.6764317410362 -649000 ekin = 2.55943952639506 | erot = 1.77203724563613 | epot = -22.016770390185 | etot = -17.6852936181538 -650000 ekin = 2.7234725572106 | erot = 2.20418229003753 | epot = -22.1594214535889 | etot = -17.2317666063407 -651000 ekin = 2.25383373914402 | erot = 3.26326768595797 | epot = -22.2274805933885 | etot = -16.7103791682865 -652000 ekin = 2.35810253390822 | erot = 2.29591208392315 | epot = -22.233219519731 | etot = -17.5792049018997 -653000 ekin = 2.06421004499471 | erot = 2.14171845474572 | epot = -22.2265612208312 | etot = -18.0206327210908 -654000 ekin = 2.30460304373657 | erot = 1.85567946278893 | epot = -22.2521914868227 | etot = -18.0919089802972 -655000 ekin = 2.1118882401511 | erot = 1.79072614414006 | epot = -22.2262193909715 | etot = -18.3236050066803 -656000 ekin = 2.44561836830366 | erot = 2.32567811025773 | epot = -22.1872376286341 | etot = -17.4159411500727 -657000 ekin = 2.45751083141107 | erot = 2.86439216413735 | epot = -22.1805503246548 | etot = -16.8586473291064 -658000 ekin = 2.49955432693123 | erot = 2.85472680235228 | epot = -22.1390040132353 | etot = -16.7847228839518 -659000 ekin = 3.37980090980362 | erot = 2.77552992994232 | epot = -21.9898923341708 | etot = -15.8345614944249 -660000 ekin = 2.69414626219179 | erot = 1.99094454704573 | epot = -21.839770569098 | etot = -17.1546797598605 -661000 ekin = 2.21049176877593 | erot = 2.52393650500607 | epot = -21.6857326790216 | etot = -16.9513044052396 -662000 ekin = 2.06962867519899 | erot = 2.53976085175021 | epot = -21.6239147287107 | etot = -17.0145252017615 -663000 ekin = 2.27770295544224 | erot = 2.30124717941156 | epot = -21.5870186127932 | etot = -17.0080684779394 -664000 ekin = 2.39061717453215 | erot = 1.87616423363737 | epot = -21.4930500427881 | etot = -17.2262686346186 -665000 ekin = 2.6692440512318 | erot = 2.29240983153228 | epot = -21.4402310096657 | etot = -16.4785771269016 -666000 ekin = 1.66318176263893 | erot = 2.30827907651665 | epot = -21.3477804932103 | etot = -17.3763196540547 -667000 ekin = 1.65573830146343 | erot = 2.82613611933529 | epot = -21.2651811028886 | etot = -16.7833066820899 -668000 ekin = 2.50126196238916 | erot = 3.29062396521938 | epot = -21.1310768281354 | etot = -15.3391909005268 -669000 ekin = 1.61008562219097 | erot = 2.65727107854379 | epot = -21.0513800034041 | etot = -16.7840233026694 -670000 ekin = 2.21851826153845 | erot = 2.60770568109394 | epot = -20.9727942140714 | etot = -16.146570271439 -671000 ekin = 2.25905318343359 | erot = 2.1596549557503 | epot = -20.920836534986 | etot = -16.5021283958021 -672000 ekin = 1.93426342346647 | erot = 1.6536504766844 | epot = -20.8333028169839 | etot = -17.245388916833 -673000 ekin = 1.880896686753 | erot = 2.07483128120026 | epot = -20.79952620348 | etot = -16.8437982355267 -674000 ekin = 2.067834680573 | erot = 2.16234064938725 | epot = -20.8176950919606 | etot = -16.5875197620003 -675000 ekin = 2.03952283590142 | erot = 2.48129689359269 | epot = -20.8297865902612 | etot = -16.3089668607671 -676000 ekin = 2.44687523374789 | erot = 2.7793299573525 | epot = -20.8513819036484 | etot = -15.625176712548 -677000 ekin = 2.18851088067448 | erot = 2.6192892566419 | epot = -20.8589021998564 | etot = -16.0511020625401 -678000 ekin = 2.13451298865477 | erot = 2.78742961560772 | epot = -20.7380850837789 | etot = -15.8161424795164 -679000 ekin = 2.15556981522704 | erot = 2.17593910434841 | epot = -20.629255081746 | etot = -16.2977461621705 -680000 ekin = 2.0771745141444 | erot = 2.6843689719881 | epot = -20.6512705044544 | etot = -15.8897270183219 -681000 ekin = 2.16836766753576 | erot = 1.82666294843077 | epot = -20.7392652191905 | etot = -16.744234603224 -682000 ekin = 3.01810965188602 | erot = 2.39774897550359 | epot = -20.7185667085479 | etot = -15.3027080811583 -683000 ekin = 2.84169666492798 | erot = 2.09885122074905 | epot = -20.7261705834807 | etot = -15.7856226978037 -684000 ekin = 1.9625035286937 | erot = 2.99543980855399 | epot = -20.769704567373 | etot = -15.8117612301253 -685000 ekin = 1.50086016290167 | erot = 2.0447864872958 | epot = -20.778895252848 | etot = -17.2332486026506 -686000 ekin = 2.3009298353038 | erot = 2.55442118756325 | epot = -20.7673358731011 | etot = -15.911984850234 -687000 ekin = 1.86053862979302 | erot = 2.84846934037481 | epot = -20.7009117540897 | etot = -15.9919037839219 -688000 ekin = 2.56859020075851 | erot = 2.23263295871677 | epot = -20.6563366249256 | etot = -15.8551134654503 -689000 ekin = 2.74930141700633 | erot = 2.68327386026118 | epot = -20.8092642099637 | etot = -15.3766889326962 -690000 ekin = 2.674773108413 | erot = 2.52397256899153 | epot = -21.073030341665 | etot = -15.8742846642604 -691000 ekin = 2.28465281003007 | erot = 2.52273866559282 | epot = -21.2401157605126 | etot = -16.4327242848898 -692000 ekin = 2.42087744380445 | erot = 3.24812320332688 | epot = -21.2665776826931 | etot = -15.5975770355618 -693000 ekin = 2.37642605279042 | erot = 2.99546830568891 | epot = -21.3330277418611 | etot = -15.9611333833818 -694000 ekin = 2.69750178365982 | erot = 2.53085866970818 | epot = -21.521485598392 | etot = -16.293125145024 -695000 ekin = 2.49230316198816 | erot = 1.1810586448532 | epot = -21.6959912399269 | etot = -18.0226294330855 -696000 ekin = 1.86075498586632 | erot = 1.46501529683134 | epot = -21.6808441671222 | etot = -18.3550738844245 -697000 ekin = 2.40460770445907 | erot = 2.10461647488794 | epot = -21.7143559347048 | etot = -17.2051317553578 -698000 ekin = 2.32098148261584 | erot = 1.91506962097516 | epot = -21.7787361369849 | etot = -17.5426850333939 -699000 ekin = 2.44943497732061 | erot = 2.56143482106644 | epot = -21.7638026578475 | etot = -16.7529328594605 -700000 ekin = 2.13119890669415 | erot = 2.28802336161954 | epot = -21.6714710604343 | etot = -17.2522487921206 -701000 ekin = 2.15013169314239 | erot = 2.18565847708909 | epot = -21.5488216255628 | etot = -17.2130314553313 -702000 ekin = 1.57482438035702 | erot = 1.99931097090509 | epot = -21.5047640382371 | etot = -17.930628686975 -703000 ekin = 2.08829522236785 | erot = 2.17557396869524 | epot = -21.5242713758433 | etot = -17.2604021847802 -704000 ekin = 2.82144699483838 | erot = 1.94479401958833 | epot = -21.5462466947694 | etot = -16.7800056803427 -705000 ekin = 2.8101978674582 | erot = 2.16662483548887 | epot = -21.497690476826 | etot = -16.520867773879 -706000 ekin = 1.97639068263159 | erot = 2.31468002405234 | epot = -21.494117475981 | etot = -17.2030467692971 -707000 ekin = 1.90740387464487 | erot = 2.04436544372039 | epot = -21.5505486138141 | etot = -17.5987792954489 -708000 ekin = 2.4927128838246 | erot = 2.15829540621564 | epot = -21.5728746117359 | etot = -16.9218663216956 -709000 ekin = 2.89296518644075 | erot = 2.58120965850486 | epot = -21.6152997801577 | etot = -16.1411249352121 -710000 ekin = 2.18515172086139 | erot = 2.27924743097099 | epot = -21.5865916502443 | etot = -17.122192498412 -711000 ekin = 2.31589231212299 | erot = 1.40143925977899 | epot = -21.6089597508521 | etot = -17.8916281789502 -712000 ekin = 2.55835611026778 | erot = 2.27281573655802 | epot = -21.7227687229586 | etot = -16.8915968761328 -713000 ekin = 1.95615391137192 | erot = 2.31806852238961 | epot = -21.8059432402922 | etot = -17.5317208065307 -714000 ekin = 2.5623858309981 | erot = 2.10850361056242 | epot = -21.8681675013087 | etot = -17.1972780597482 -715000 ekin = 2.42321114653449 | erot = 3.74023135295617 | epot = -21.8498336266088 | etot = -15.6863911271181 -716000 ekin = 2.83316600532177 | erot = 2.84850242081136 | epot = -21.7640231598545 | etot = -16.0823547337214 -717000 ekin = 3.45113934412558 | erot = 3.20598462177205 | epot = -21.667790662391 | etot = -15.0106666964934 -718000 ekin = 3.10736232683018 | erot = 3.94031338601796 | epot = -21.5629179727886 | etot = -14.5152422599405 -719000 ekin = 2.38564322644682 | erot = 2.9508981175584 | epot = -21.5481188237003 | etot = -16.2115774796951 -720000 ekin = 2.22543420991222 | erot = 3.14305432696275 | epot = -21.5381615962024 | etot = -16.1696730593275 -721000 ekin = 1.71709109813907 | erot = 2.23939430363992 | epot = -21.4645851946692 | etot = -17.5080997928902 -722000 ekin = 1.93213958129581 | erot = 2.8157321827673 | epot = -21.4896847080113 | etot = -16.7418129439482 -723000 ekin = 2.38145345346889 | erot = 2.55666957995949 | epot = -21.4374887927968 | etot = -16.4993657593684 -724000 ekin = 1.74740284448188 | erot = 2.4555617568904 | epot = -21.4125175551609 | etot = -17.2095529537886 -725000 ekin = 2.29233638352031 | erot = 2.95267014777738 | epot = -21.4751392844086 | etot = -16.2301327531109 -726000 ekin = 1.63503646092183 | erot = 2.30649262262119 | epot = -21.5156851039583 | etot = -17.5741560204153 -727000 ekin = 2.46705454176009 | erot = 3.19802987014478 | epot = -21.5382715508197 | etot = -15.8731871389148 -728000 ekin = 2.21709576272191 | erot = 2.16616227421246 | epot = -21.5244744557247 | etot = -17.1412164187904 -729000 ekin = 1.89396537247993 | erot = 1.66596987620967 | epot = -21.5644109232526 | etot = -18.004475674563 -730000 ekin = 1.78155182892059 | erot = 2.15399661961712 | epot = -21.5594738957829 | etot = -17.6239254472452 -731000 ekin = 2.16713092512296 | erot = 2.96875570154116 | epot = -21.4952326145864 | etot = -16.3593459879223 -732000 ekin = 2.40927355189018 | erot = 2.27189990077001 | epot = -21.3831563581627 | etot = -16.7019829055025 -733000 ekin = 3.04824198143783 | erot = 2.57289903054808 | epot = -21.429005165309 | etot = -15.8078641533231 -734000 ekin = 2.36703883022854 | erot = 2.04468815017471 | epot = -21.4926214065431 | etot = -17.0808944261399 -735000 ekin = 2.13292788677937 | erot = 1.55097035487251 | epot = -21.5455592190822 | etot = -17.8616609774303 -736000 ekin = 2.13562110082197 | erot = 3.45795834862289 | epot = -21.6515763333194 | etot = -16.0579968838745 -737000 ekin = 1.73550703692746 | erot = 3.58781244645388 | epot = -21.6785680654269 | etot = -16.3552485820456 -738000 ekin = 2.0113668076702 | erot = 2.50533140705366 | epot = -21.7068415263434 | etot = -17.1901433116195 -739000 ekin = 1.85122466968334 | erot = 2.19323904324287 | epot = -21.7211705032462 | etot = -17.67670679032 -740000 ekin = 2.84677298867338 | erot = 2.79086338446698 | epot = -21.7460997683893 | etot = -16.1084633952489 -741000 ekin = 2.47281769013275 | erot = 2.90867674862124 | epot = -21.8038806031311 | etot = -16.4223861643772 -742000 ekin = 2.74212748781965 | erot = 3.26601844940295 | epot = -21.9417105639309 | etot = -15.9335646267083 -743000 ekin = 2.23337436613033 | erot = 3.20752099935253 | epot = -22.076993886109 | etot = -16.6360985206262 -744000 ekin = 2.0100758296396 | erot = 3.79208398827072 | epot = -22.1581491314472 | etot = -16.3559893135369 -745000 ekin = 3.14168435406401 | erot = 2.32756039064277 | epot = -22.1552791709709 | etot = -16.6860344262641 -746000 ekin = 2.96147960587595 | erot = 2.64919778641528 | epot = -22.131657657659 | etot = -16.5209802653677 -747000 ekin = 2.31713973406908 | erot = 2.05388385027238 | epot = -22.1362115743711 | etot = -17.7651879900297 -748000 ekin = 2.36228107661837 | erot = 2.41530550223615 | epot = -22.1703943251346 | etot = -17.3928077462801 -749000 ekin = 2.07006713072585 | erot = 2.7743291960411 | epot = -22.1708421357977 | etot = -17.3264458090308 -750000 ekin = 1.65834656870048 | erot = 2.38415657369845 | epot = -22.2465520170919 | etot = -18.2040488746929 -751000 ekin = 1.79302728344389 | erot = 2.82710216006101 | epot = -22.3488339479635 | etot = -17.7287045044586 -752000 ekin = 1.35555517803007 | erot = 1.46019783589211 | epot = -22.4342877547318 | etot = -19.6185347408096 -753000 ekin = 1.88586262445723 | erot = 2.44014879801272 | epot = -22.3837690917336 | etot = -18.0577576692636 -754000 ekin = 1.74745498380874 | erot = 2.736120118542 | epot = -22.2852965474798 | etot = -17.8017214451291 -755000 ekin = 2.39590781949903 | erot = 2.41019902787153 | epot = -22.2066358684386 | etot = -17.400529021068 -756000 ekin = 1.83745653598818 | erot = 2.79024351605604 | epot = -22.133592240187 | etot = -17.5058921881428 -757000 ekin = 1.97281200687049 | erot = 2.57792722235946 | epot = -22.0604464398181 | etot = -17.5097072105881 -758000 ekin = 1.18945619136922 | erot = 2.72372183682492 | epot = -21.9899494795137 | etot = -18.0767714513196 -759000 ekin = 2.16230453116658 | erot = 1.39722896511083 | epot = -22.0003304659983 | etot = -18.4407969697208 -760000 ekin = 2.57253050230034 | erot = 2.33269711137818 | epot = -22.0357457302398 | etot = -17.1305181165613 -761000 ekin = 2.08545216810509 | erot = 2.24940559703296 | epot = -22.1132097744113 | etot = -17.7783520092732 -762000 ekin = 2.13509249172209 | erot = 1.66078369856518 | epot = -22.1380840935026 | etot = -18.3422079032154 -763000 ekin = 2.42851727622128 | erot = 3.36016749294484 | epot = -22.2079173436287 | etot = -16.4192325744626 -764000 ekin = 2.84703530894743 | erot = 2.79172375883347 | epot = -22.2143624032421 | etot = -16.5756033354612 -765000 ekin = 1.81325658345262 | erot = 2.77448180912352 | epot = -22.1194010453623 | etot = -17.5316626527862 -766000 ekin = 2.64831101430988 | erot = 2.3138164970859 | epot = -21.9919179324216 | etot = -17.0297904210258 -767000 ekin = 2.58949745571041 | erot = 2.86718473216886 | epot = -21.9087370669525 | etot = -16.4520548790732 -768000 ekin = 1.86313167956692 | erot = 2.78552244417216 | epot = -21.9381577980074 | etot = -17.2895036742684 -769000 ekin = 2.40162376419982 | erot = 2.31402374045873 | epot = -22.0373843590673 | etot = -17.3217368544087 -770000 ekin = 2.49146487205158 | erot = 3.23101926076329 | epot = -22.1439576198693 | etot = -16.4214734870544 -771000 ekin = 2.33226337742861 | erot = 2.27787220200642 | epot = -22.1812213688413 | etot = -17.5710857894063 -772000 ekin = 2.28990016215835 | erot = 2.99389364569331 | epot = -22.2765115340955 | etot = -16.9927177262439 -773000 ekin = 2.23002457595115 | erot = 1.82240115552768 | epot = -22.3379686916384 | etot = -18.2855429601596 -774000 ekin = 2.82350297312971 | erot = 2.21054815770296 | epot = -22.331524297742 | etot = -17.2974731669094 -775000 ekin = 1.82305982105504 | erot = 1.8710033654222 | epot = -22.2729891281483 | etot = -18.578925941671 -776000 ekin = 1.39169167990076 | erot = 3.16027505319298 | epot = -22.2459295451277 | etot = -17.6939628120339 -777000 ekin = 1.6265637770548 | erot = 2.80881827044757 | epot = -22.1611617112313 | etot = -17.7257796637289 -778000 ekin = 1.49436478903863 | erot = 2.2416123685623 | epot = -22.1732646444852 | etot = -18.4372874868843 -779000 ekin = 1.88107404119767 | erot = 1.90732846459753 | epot = -22.2125828989308 | etot = -18.4241803931357 -780000 ekin = 1.70209634464212 | erot = 2.3051529921035 | epot = -22.2800747799124 | etot = -18.2728254431668 -781000 ekin = 2.12615575710869 | erot = 2.56065358398066 | epot = -22.3657963731658 | etot = -17.6789870320765 -782000 ekin = 2.60319344794517 | erot = 1.95716880667361 | epot = -22.2788895886639 | etot = -17.7185273340451 -783000 ekin = 2.19489638548848 | erot = 2.90033506167529 | epot = -22.2004563501245 | etot = -17.1052249029607 -784000 ekin = 2.84914111009348 | erot = 2.24051018422877 | epot = -22.2093010900996 | etot = -17.1196497957773 -785000 ekin = 3.14240765153577 | erot = 2.92860772919916 | epot = -22.2500274240077 | etot = -16.1790120432728 -786000 ekin = 2.83372300736035 | erot = 3.44593690351847 | epot = -22.2923595270367 | etot = -16.0126996161579 -787000 ekin = 2.41074903520556 | erot = 3.01381650302091 | epot = -22.2329745868673 | etot = -16.8084090486408 -788000 ekin = 1.99557665602945 | erot = 2.01600225895996 | epot = -22.1996915458458 | etot = -18.1881126308564 -789000 ekin = 2.46258971641133 | erot = 2.27406771625315 | epot = -22.1314921413931 | etot = -17.3948347087286 -790000 ekin = 3.5794195002921 | erot = 2.8244086481244 | epot = -22.0691321886934 | etot = -15.6653040402769 -791000 ekin = 3.1240271028451 | erot = 2.42401718962738 | epot = -22.0808685046086 | etot = -16.5328242121361 -792000 ekin = 3.95429056548242 | erot = 1.97241939137158 | epot = -22.0156932891881 | etot = -16.0889833323341 -793000 ekin = 2.26828416500901 | erot = 2.58677202552918 | epot = -21.9219598803777 | etot = -17.0669036898395 -794000 ekin = 2.16106559150924 | erot = 2.44310931274124 | epot = -21.7619518452423 | etot = -17.1577769409918 -795000 ekin = 1.62519700428841 | erot = 2.41826691867446 | epot = -21.6012749849542 | etot = -17.5578110619913 -796000 ekin = 2.18377144801669 | erot = 2.13093440679002 | epot = -21.4820337714693 | etot = -17.1673279166625 -797000 ekin = 1.81427862345353 | erot = 1.99534051513422 | epot = -21.4739195915569 | etot = -17.6643004529692 -798000 ekin = 2.22012195132989 | erot = 2.51363796316555 | epot = -21.5008270155092 | etot = -16.7670671010137 -799000 ekin = 1.88984581553595 | erot = 2.87047971528298 | epot = -21.4708608053325 | etot = -16.7105352745135 -800000 ekin = 2.14235800297794 | erot = 2.35196377273804 | epot = -21.3792596865245 | etot = -16.8849379108085 -801000 ekin = 1.84302686949433 | erot = 1.65480855802627 | epot = -21.2211741734437 | etot = -17.7233387459231 -802000 ekin = 2.20305615004888 | erot = 2.22355768328245 | epot = -21.1073599995259 | etot = -16.6807461661946 -803000 ekin = 2.64836814873033 | erot = 1.9076187180486 | epot = -21.075204188547 | etot = -16.5192173217681 -804000 ekin = 2.34495845479318 | erot = 2.89112045330491 | epot = -21.0176734836814 | etot = -15.7815945755833 -805000 ekin = 1.79915640284781 | erot = 2.71685844764876 | epot = -20.8858433761952 | etot = -16.3698285256986 -806000 ekin = 1.74992507845556 | erot = 2.08517047523251 | epot = -20.8503301901418 | etot = -17.0152346364538 -807000 ekin = 1.57172452594495 | erot = 1.70422569898767 | epot = -20.9092333967052 | etot = -17.6332831717726 -808000 ekin = 2.08106901002531 | erot = 2.40367065218828 | epot = -20.985869179598 | etot = -16.5011295173844 -809000 ekin = 2.61736488835992 | erot = 1.51251405170843 | epot = -20.9790910298502 | etot = -16.8492120897818 -810000 ekin = 3.07344763503492 | erot = 2.65428122600395 | epot = -20.8962978903169 | etot = -15.1685690292781 -811000 ekin = 3.02889983101699 | erot = 3.61686315729186 | epot = -20.9396616028789 | etot = -14.2938986145701 -812000 ekin = 2.13832655324419 | erot = 2.7919099294265 | epot = -21.0260005012596 | etot = -16.0957640185889 -813000 ekin = 2.19077235410927 | erot = 3.16158040032407 | epot = -21.2169108164963 | etot = -15.864558062063 -814000 ekin = 1.70775111413747 | erot = 2.98436840501864 | epot = -21.308951189013 | etot = -16.6168316698569 -815000 ekin = 2.14630779714624 | erot = 2.27335416843264 | epot = -21.3099230783926 | etot = -16.8902611128138 -816000 ekin = 2.70331501775258 | erot = 1.53093796189124 | epot = -21.3384418834225 | etot = -17.1041889037787 -817000 ekin = 2.55738086811903 | erot = 2.58558173150041 | epot = -21.4691891608916 | etot = -16.3262265612721 -818000 ekin = 2.27829786328906 | erot = 2.26089725682101 | epot = -21.5162183667694 | etot = -16.9770232466593 -819000 ekin = 2.10478260130361 | erot = 3.02380855832961 | epot = -21.5292309310152 | etot = -16.400639771382 -820000 ekin = 2.50608188233135 | erot = 2.71783485224718 | epot = -21.5036816055507 | etot = -16.2797648709722 -821000 ekin = 2.62609848062628 | erot = 2.55164634943843 | epot = -21.478766185164 | etot = -16.3010213550993 -822000 ekin = 3.63941681915299 | erot = 2.20246894917129 | epot = -21.4688230156577 | etot = -15.6269372473334 -823000 ekin = 3.58953515450024 | erot = 2.7355620654562 | epot = -21.4650227341942 | etot = -15.1399255142378 -824000 ekin = 4.11304720722591 | erot = 3.29174595135481 | epot = -21.4062011377905 | etot = -14.0014079792098 -825000 ekin = 2.90620097853795 | erot = 3.46409084826254 | epot = -21.2436944546109 | etot = -14.8734026278104 -826000 ekin = 1.72188438195169 | erot = 1.97028277378149 | epot = -21.0473904580338 | etot = -17.3552233023006 -827000 ekin = 1.9124069409458 | erot = 2.55760488338655 | epot = -20.9206700763424 | etot = -16.4506582520101 -828000 ekin = 2.38145056979363 | erot = 2.55544957149183 | epot = -20.8204865756543 | etot = -15.8835864343688 -829000 ekin = 2.24733826946604 | erot = 1.78474837345229 | epot = -20.7084449579388 | etot = -16.6763583150204 -830000 ekin = 2.52795893691035 | erot = 2.34146724282711 | epot = -20.5883731027638 | etot = -15.7189469230264 -831000 ekin = 2.68310001004752 | erot = 2.07407005901145 | epot = -20.4364451382899 | etot = -15.6792750692309 -832000 ekin = 2.6732342426401 | erot = 2.02167788192501 | epot = -20.3691783993746 | etot = -15.6742662748095 -833000 ekin = 2.55071664949192 | erot = 2.59972899624767 | epot = -20.3036213925319 | etot = -15.1531757467923 -834000 ekin = 2.87089088359562 | erot = 2.32463192225235 | epot = -20.2984653371648 | etot = -15.1029425313169 -835000 ekin = 2.77558903596269 | erot = 2.73757154391999 | epot = -20.4022293845421 | etot = -14.8890688046595 -836000 ekin = 2.57713146919653 | erot = 2.85322310545496 | epot = -20.5403137141641 | etot = -15.1099591395126 -837000 ekin = 1.78075406754283 | erot = 1.97503243561097 | epot = -20.5889142070484 | etot = -16.8331277038946 -838000 ekin = 1.98032617531702 | erot = 2.79829467073936 | epot = -20.6049667376349 | etot = -15.8263458915785 -839000 ekin = 2.0003179521848 | erot = 2.70198331564818 | epot = -20.5921495833285 | etot = -15.8898483154955 -840000 ekin = 1.70031236242703 | erot = 2.9568568949057 | epot = -20.6678372916037 | etot = -16.010668034271 -841000 ekin = 2.77705100359315 | erot = 2.84742847205068 | epot = -20.7929304121764 | etot = -15.1684509365325 -842000 ekin = 2.54393458307436 | erot = 2.87172695192626 | epot = -20.8173418291016 | etot = -15.401680294101 -843000 ekin = 2.00273625390939 | erot = 2.63437491598433 | epot = -20.8053999188197 | etot = -16.1682887489259 -844000 ekin = 1.5290074956935 | erot = 1.92882434140973 | epot = -20.8427655387949 | etot = -17.3849337016917 -845000 ekin = 2.27176799938834 | erot = 2.30843636540598 | epot = -20.9384881501645 | etot = -16.3582837853702 -846000 ekin = 2.06718804989496 | erot = 2.3310866232498 | epot = -21.008503215967 | etot = -16.6102285428222 -847000 ekin = 2.457310325364 | erot = 2.64112097293886 | epot = -20.9624761048838 | etot = -15.8640448065809 -848000 ekin = 2.13894899278458 | erot = 1.46487099434191 | epot = -20.9909626022983 | etot = -17.3871426151718 -849000 ekin = 2.0007946308419 | erot = 2.48568109050424 | epot = -20.9995492646628 | etot = -16.5130735433167 -850000 ekin = 2.54186297995285 | erot = 2.66929613872207 | epot = -20.9906717645297 | etot = -15.7795126458548 -851000 ekin = 2.16443404123471 | erot = 2.92830981454153 | epot = -20.9932718794596 | etot = -15.9005280236834 -852000 ekin = 2.48255398040851 | erot = 2.46238001266592 | epot = -21.0187491181079 | etot = -16.0738151250335 -853000 ekin = 2.4154146701692 | erot = 2.97520224443386 | epot = -20.9598722543997 | etot = -15.5692553397966 -854000 ekin = 2.35150751079563 | erot = 2.85453387569364 | epot = -20.8693696367608 | etot = -15.6633282502715 -855000 ekin = 2.36749640703667 | erot = 2.0675340835823 | epot = -20.8980197782033 | etot = -16.4629892875844 -856000 ekin = 2.52164598863741 | erot = 2.75265020302047 | epot = -20.800830948998 | etot = -15.5265347573401 -857000 ekin = 2.55862872070476 | erot = 3.03030828592916 | epot = -20.6910887919773 | etot = -15.1021517853433 -858000 ekin = 3.12628251408762 | erot = 2.14554604261068 | epot = -20.6394579492303 | etot = -15.367629392532 -859000 ekin = 2.91259413572113 | erot = 2.23773675238285 | epot = -20.6611486479508 | etot = -15.5108177598468 -860000 ekin = 2.88318377110753 | erot = 1.51972062646445 | epot = -20.6828066069552 | etot = -16.2799022093833 -861000 ekin = 2.33529167415754 | erot = 2.85116617791257 | epot = -20.6796212139896 | etot = -15.4931633619195 -862000 ekin = 3.06091745354044 | erot = 1.86960550588564 | epot = -20.7257485328209 | etot = -15.7952255733949 -863000 ekin = 2.88295223464283 | erot = 1.77743902656173 | epot = -20.8340328987095 | etot = -16.1736416375049 -864000 ekin = 2.95602292127633 | erot = 2.6505641071531 | epot = -21.016295456145 | etot = -15.4097084277156 -865000 ekin = 3.3172549369506 | erot = 2.24347319046511 | epot = -21.1441095096619 | etot = -15.5833813822461 -866000 ekin = 2.8446879555804 | erot = 3.16802464112882 | epot = -21.2275167371632 | etot = -15.214804140454 -867000 ekin = 2.74149808612436 | erot = 3.09628634794252 | epot = -21.2140642048229 | etot = -15.376279770756 -868000 ekin = 2.1914148486481 | erot = 2.23765996064102 | epot = -21.1661691183494 | etot = -16.7370943090603 -869000 ekin = 2.92726848075923 | erot = 2.49663936074753 | epot = -21.1109612585256 | etot = -15.6870534170188 -870000 ekin = 2.47986538741065 | erot = 2.11907230969517 | epot = -21.0900293946685 | etot = -16.4910916975627 -871000 ekin = 2.18342640526418 | erot = 2.37474045896628 | epot = -20.9804914418025 | etot = -16.422324577572 -872000 ekin = 1.52873571215979 | erot = 2.08908078804674 | epot = -20.9343176993392 | etot = -17.3165011991327 -873000 ekin = 1.39281578471524 | erot = 2.29034780878959 | epot = -21.0007866828842 | etot = -17.3176230893794 -874000 ekin = 1.40786554880768 | erot = 2.77007970032351 | epot = -21.1600842742429 | etot = -16.9821390251117 -875000 ekin = 1.18320018517441 | erot = 2.73058842883514 | epot = -21.2959059488291 | etot = -17.3821173348196 -876000 ekin = 1.8300189393038 | erot = 2.99586941144888 | epot = -21.3298635968753 | etot = -16.5039752461226 -877000 ekin = 2.38032906471077 | erot = 2.03722695211229 | epot = -21.4152790752831 | etot = -16.99772305846 -878000 ekin = 2.1293851684127 | erot = 1.75666654131943 | epot = -21.412657760354 | etot = -17.5266060506219 -879000 ekin = 2.23837299177367 | erot = 2.71307243504656 | epot = -21.4006541150457 | etot = -16.4492086882254 -880000 ekin = 2.68032631557358 | erot = 2.78439945590095 | epot = -21.4462782448912 | etot = -15.9815524734167 -881000 ekin = 2.86810525851389 | erot = 2.35959915589951 | epot = -21.4314549447334 | etot = -16.20375053032 -882000 ekin = 2.33172283615115 | erot = 2.17176020371466 | epot = -21.369535469283 | etot = -16.8660524294172 -883000 ekin = 2.36331150998289 | erot = 1.97634374053965 | epot = -21.1748990104138 | etot = -16.8352437598913 -884000 ekin = 2.53782271833829 | erot = 2.25243670168425 | epot = -21.0795767771653 | etot = -16.2893173571428 -885000 ekin = 2.86057103069745 | erot = 2.27462544190305 | epot = -21.0782171958267 | etot = -15.9430207232262 -886000 ekin = 3.17034195996096 | erot = 1.7483264672941 | epot = -21.1280719510454 | etot = -16.2094035237903 -887000 ekin = 2.66023408534638 | erot = 2.49426802108019 | epot = -21.1909579488463 | etot = -16.0364558424197 -888000 ekin = 2.14156056158802 | erot = 2.8306592029555 | epot = -21.2749898508176 | etot = -16.3027700862741 -889000 ekin = 2.13776380125426 | erot = 2.19994227158625 | epot = -21.1902576201104 | etot = -16.8525515472699 -890000 ekin = 1.76446650263826 | erot = 2.97354753014622 | epot = -21.2518724314555 | etot = -16.513858398671 -891000 ekin = 1.64433607192947 | erot = 2.28044235221045 | epot = -21.3759471910581 | etot = -17.4511687669181 -892000 ekin = 1.97381907006141 | erot = 2.35969977765341 | epot = -21.5200869372681 | etot = -17.1865680895533 -893000 ekin = 1.77998159671209 | erot = 1.83959134574388 | epot = -21.5960425863495 | etot = -17.9764696438936 -894000 ekin = 2.8098996128374 | erot = 2.80337844303783 | epot = -21.6896955865519 | etot = -16.0764175306767 -895000 ekin = 2.03570642281182 | erot = 2.73641442629082 | epot = -21.7763280754101 | etot = -17.0042072263074 -896000 ekin = 1.6670401968188 | erot = 2.55842313387757 | epot = -21.9079691828366 | etot = -17.6825058521403 -897000 ekin = 1.79364820755772 | erot = 2.35937074837064 | epot = -22.0466195733302 | etot = -17.8936006174019 -898000 ekin = 1.84103348909591 | erot = 2.41596980112089 | epot = -22.0792153246985 | etot = -17.8222120344817 -899000 ekin = 1.6644807831865 | erot = 3.06295573986189 | epot = -22.0050930291629 | etot = -17.2776565061145 -900000 ekin = 2.15301263014261 | erot = 2.62503812958041 | epot = -21.9769631774149 | etot = -17.1989124176919 -901000 ekin = 2.43323525076021 | erot = 2.69661561775584 | epot = -22.0455467285607 | etot = -16.9156958600446 -902000 ekin = 2.57983518470479 | erot = 2.40634661051269 | epot = -22.0504126836938 | etot = -17.0642308884763 -903000 ekin = 2.38804084084236 | erot = 2.40369143268286 | epot = -22.0548572254258 | etot = -17.2631249519006 -904000 ekin = 1.99756799382411 | erot = 3.1573673373966 | epot = -22.0783783499621 | etot = -16.9234430187413 -905000 ekin = 2.2804213599578 | erot = 2.20746001153528 | epot = -22.092475444409 | etot = -17.6045940729159 -906000 ekin = 2.49914497220395 | erot = 1.67106173041059 | epot = -22.0649292741971 | etot = -17.8947225715826 -907000 ekin = 2.3417075346135 | erot = 2.1683018981558 | epot = -21.9182395193391 | etot = -17.4082300865698 -908000 ekin = 2.83101675354561 | erot = 2.39226452568031 | epot = -21.9393923471479 | etot = -16.716111067922 -909000 ekin = 3.13519044247879 | erot = 2.07053636961478 | epot = -22.044039894957 | etot = -16.8383130828635 -910000 ekin = 2.91492350277448 | erot = 3.54269221448407 | epot = -22.1774209001616 | etot = -15.7198051829031 -911000 ekin = 1.86299522014884 | erot = 2.75425299355672 | epot = -22.2318842654016 | etot = -17.6146360516961 -912000 ekin = 2.64270620869814 | erot = 1.86916034984858 | epot = -22.2816929482531 | etot = -17.7698263897064 -913000 ekin = 2.45835259040075 | erot = 2.03343540339215 | epot = -22.4051980318983 | etot = -17.9134100381055 -914000 ekin = 2.01630257583653 | erot = 3.01931541129967 | epot = -22.505580829989 | etot = -17.4699628428528 -915000 ekin = 2.73550820750708 | erot = 2.14051989379168 | epot = -22.5067223019055 | etot = -17.6306942006067 -916000 ekin = 2.38833694849903 | erot = 3.26236542376324 | epot = -22.5299732656691 | etot = -16.8792708934069 -917000 ekin = 2.21211072529667 | erot = 2.24425221182158 | epot = -22.5175498112378 | etot = -18.0611868741196 -918000 ekin = 2.11721632678553 | erot = 2.05681940825278 | epot = -22.4485798442659 | etot = -18.2745441092276 -919000 ekin = 2.66065401645241 | erot = 2.41853759346264 | epot = -22.4819256778217 | etot = -17.4027340679067 -920000 ekin = 3.26471044916533 | erot = 2.75531911342506 | epot = -22.5858600689149 | etot = -16.5658305063245 -921000 ekin = 2.72028388628927 | erot = 1.96960596371279 | epot = -22.6394402751861 | etot = -17.949550425184 -922000 ekin = 1.43428549123067 | erot = 1.52428475569852 | epot = -22.6914991306333 | etot = -19.7329288837041 -923000 ekin = 1.67603986848274 | erot = 1.86522020655462 | epot = -22.7510571233686 | etot = -19.2097970483313 -924000 ekin = 2.15000311118185 | erot = 1.53327070095754 | epot = -22.7223413241931 | etot = -19.0390675120537 -925000 ekin = 2.27769316315994 | erot = 1.3558291477729 | epot = -22.6317669747038 | etot = -18.998244663771 -926000 ekin = 2.00370753803371 | erot = 2.07123237010034 | epot = -22.5811533157097 | etot = -18.5062134075757 -927000 ekin = 2.51631428248841 | erot = 1.98711239136865 | epot = -22.6957752134475 | etot = -18.1923485395904 -928000 ekin = 2.57502157703452 | erot = 2.51449316644153 | epot = -22.8486668477059 | etot = -17.7591521042298 -929000 ekin = 2.66015175923782 | erot = 1.82991995656988 | epot = -22.8894816710892 | etot = -18.3994099552814 -930000 ekin = 2.41758548277495 | erot = 2.009770197394 | epot = -22.9023129289068 | etot = -18.4749572487379 -931000 ekin = 3.01936517399358 | erot = 2.11115283295647 | epot = -22.8598478032753 | etot = -17.7293297963252 -932000 ekin = 2.34904883629148 | erot = 1.87134929534041 | epot = -22.900230384769 | etot = -18.6798322531371 -933000 ekin = 2.16775611540092 | erot = 2.83796264813669 | epot = -22.9075292968865 | etot = -17.9018105333489 -934000 ekin = 2.17428610858913 | erot = 2.11891276299499 | epot = -22.9275911153102 | etot = -18.6343922437261 -935000 ekin = 2.35380058127247 | erot = 2.22719757040086 | epot = -22.9178791070039 | etot = -18.3368809553306 -936000 ekin = 2.29398857252167 | erot = 2.52122883801967 | epot = -23.0254587453496 | etot = -18.2102413348083 -937000 ekin = 2.32405492839276 | erot = 2.82571975062453 | epot = -23.1134869099967 | etot = -17.9637122309794 -938000 ekin = 2.46190818228192 | erot = 1.99586541720566 | epot = -23.1690855883854 | etot = -18.7113119888978 -939000 ekin = 2.99494633358444 | erot = 2.11200579979091 | epot = -23.1621265982256 | etot = -18.0551744648502 -940000 ekin = 3.76773061527755 | erot = 2.67954167018356 | epot = -23.1020260319689 | etot = -16.6547537465078 -941000 ekin = 3.15108874053801 | erot = 2.26610050109568 | epot = -23.0042404655517 | etot = -17.587051223918 -942000 ekin = 3.50311245643908 | erot = 1.8837360214302 | epot = -22.9671180112669 | etot = -17.5802695333976 -943000 ekin = 3.82043792465856 | erot = 2.71285823250348 | epot = -22.9404059827705 | etot = -16.4071098256085 -944000 ekin = 2.68278476017665 | erot = 2.75585489458161 | epot = -22.9190580774811 | etot = -17.4804184227228 -945000 ekin = 2.55880828345199 | erot = 2.02741981318914 | epot = -22.8232630911495 | etot = -18.2370349945083 -946000 ekin = 2.47548691870273 | erot = 1.6686405936174 | epot = -22.6586979544826 | etot = -18.5145704421625 -947000 ekin = 2.41867478100658 | erot = 1.99274780926994 | epot = -22.5542133657001 | etot = -18.1427907754236 -948000 ekin = 3.54970439277899 | erot = 2.57756240201337 | epot = -22.4104376157297 | etot = -16.2831708209373 -949000 ekin = 2.98589976166071 | erot = 2.44208964275301 | epot = -22.1971411230011 | etot = -16.7691517185874 -950000 ekin = 1.82147308870196 | erot = 3.05083899379336 | epot = -22.0435130221228 | etot = -17.1712009396274 -951000 ekin = 2.20031505253436 | erot = 2.38004890424643 | epot = -22.0174402075992 | etot = -17.4370762508184 -952000 ekin = 2.14165422682636 | erot = 1.67045420750586 | epot = -21.9875031647928 | etot = -18.1753947304605 -953000 ekin = 2.2983346942831 | erot = 1.97349532600852 | epot = -21.9532851584682 | etot = -17.6814551381766 -954000 ekin = 1.48835290094507 | erot = 3.3569245199183 | epot = -21.8812774176255 | etot = -17.0359999967622 -955000 ekin = 1.87513794155827 | erot = 2.65898918540886 | epot = -21.7919528937349 | etot = -17.2578257667678 -956000 ekin = 1.6947359470094 | erot = 2.15427252360417 | epot = -21.7268035908356 | etot = -17.877795120222 -957000 ekin = 1.75579814865835 | erot = 1.63901039608816 | epot = -21.7007270322021 | etot = -18.3059184874556 -958000 ekin = 1.59869777656518 | erot = 2.20104985114387 | epot = -21.7023937250484 | etot = -17.9026460973393 -959000 ekin = 2.58438881562723 | erot = 2.4897790743314 | epot = -21.7153511733982 | etot = -16.6411832834396 -960000 ekin = 2.53916903929275 | erot = 2.05995138561217 | epot = -21.7134163297426 | etot = -17.1142959048376 -961000 ekin = 2.28282707786747 | erot = 2.18347157951508 | epot = -21.7152390799839 | etot = -17.2489404226013 -962000 ekin = 1.65520100959905 | erot = 3.51416445242778 | epot = -21.7329558565077 | etot = -16.5635903944808 -963000 ekin = 1.99568689924178 | erot = 1.50126173817714 | epot = -21.6847527677603 | etot = -18.1878041303414 -964000 ekin = 2.18616111169191 | erot = 2.27601428306195 | epot = -21.6212716735791 | etot = -17.1590962788252 -965000 ekin = 2.12688674785305 | erot = 2.31141713690627 | epot = -21.6018715374843 | etot = -17.163567652725 -966000 ekin = 3.18043989665768 | erot = 3.42455452205085 | epot = -21.638305203769 | etot = -15.0333107850605 -967000 ekin = 3.07300409154252 | erot = 2.17511749698304 | epot = -21.5951488445701 | etot = -16.3470272560445 -968000 ekin = 2.0866315065553 | erot = 2.13997027735021 | epot = -21.5232721871232 | etot = -17.2966704032177 -969000 ekin = 2.26951411936363 | erot = 2.21822796004341 | epot = -21.4611553284776 | etot = -16.9734132490706 -970000 ekin = 2.4916739659978 | erot = 2.62083774678042 | epot = -21.4077353682587 | etot = -16.2952236554805 -971000 ekin = 2.49745059610599 | erot = 2.64553775005006 | epot = -21.3712924820093 | etot = -16.2283041358532 -972000 ekin = 3.2069302084461 | erot = 2.4701129448845 | epot = -21.3144344371103 | etot = -15.6373912837797 -973000 ekin = 3.3593544808794 | erot = 2.62917582888825 | epot = -21.2433830591837 | etot = -15.2548527494161 -974000 ekin = 2.71069552226069 | erot = 2.13944446989064 | epot = -21.1404268855179 | etot = -16.2902868933666 -975000 ekin = 1.81165819781674 | erot = 2.10218924092727 | epot = -21.0499905566304 | etot = -17.1361431178864 -976000 ekin = 2.36984742020937 | erot = 1.38488988265326 | epot = -20.9803229653516 | etot = -17.2255856624889 -977000 ekin = 2.83728662155799 | erot = 3.02976542728586 | epot = -21.086860961914 | etot = -15.2198089130701 -978000 ekin = 3.14169266917129 | erot = 3.02799812032621 | epot = -21.1408187166748 | etot = -14.9711279271773 -979000 ekin = 3.63725915757345 | erot = 2.47075910077982 | epot = -21.0348329782418 | etot = -14.9268147198885 -980000 ekin = 3.42622785415583 | erot = 3.24164435781271 | epot = -20.9604411583363 | etot = -14.2925689463677 -981000 ekin = 2.9282364939793 | erot = 2.44516658563953 | epot = -20.999389015838 | etot = -15.6259859362192 -982000 ekin = 2.04558911070081 | erot = 2.21302288881358 | epot = -21.0172581853275 | etot = -16.7586461858131 -983000 ekin = 2.56053983213181 | erot = 1.98406283304104 | epot = -21.0054554868711 | etot = -16.4608528216982 -984000 ekin = 2.31455025377677 | erot = 2.58584391470351 | epot = -21.0528748947299 | etot = -16.1524807262496 -985000 ekin = 2.31703817263369 | erot = 2.99965025262556 | epot = -21.1270579315131 | etot = -15.8103695062538 -986000 ekin = 2.05103854432386 | erot = 2.15351550911371 | epot = -21.2182405597612 | etot = -17.0136865063236 -987000 ekin = 2.41899263793245 | erot = 1.58416150281503 | epot = -21.1906087726859 | etot = -17.1874546319384 -988000 ekin = 2.75135283132848 | erot = 2.70498731016258 | epot = -21.09026978368 | etot = -15.6339296421889 -989000 ekin = 2.29408577956131 | erot = 2.8565620534449 | epot = -21.0178170251465 | etot = -15.8671691921403 -990000 ekin = 2.23414139649767 | erot = 2.58987928207186 | epot = -20.9412338597721 | etot = -16.1172131812026 -991000 ekin = 2.20140095465642 | erot = 2.53421928109187 | epot = -20.8284298905317 | etot = -16.0928096547834 -992000 ekin = 1.73516341340694 | erot = 2.49726908126815 | epot = -20.8981414535471 | etot = -16.665708958872 -993000 ekin = 1.38883779880923 | erot = 1.96818984395136 | epot = -20.9939445972526 | etot = -17.6369169544921 -994000 ekin = 1.48978908674572 | erot = 2.95636513336705 | epot = -21.0608370227911 | etot = -16.6146828026783 -995000 ekin = 2.31404204513712 | erot = 1.67482961392507 | epot = -21.1264761824825 | etot = -17.1376045234203 -996000 ekin = 2.8977650484701 | erot = 2.85063328331352 | epot = -21.0879631716189 | etot = -15.3395648398352 -997000 ekin = 3.12980664910276 | erot = 2.14994147346884 | epot = -21.0789162715404 | etot = -15.7991681489688 -998000 ekin = 2.21592279552963 | erot = 3.03017611615787 | epot = -20.9989402817529 | etot = -15.7528413700654 -999000 ekin = 2.60947995309596 | erot = 1.73829419308785 | epot = -20.9136108602423 | etot = -16.5658367140585 -1000000 ekin = 2.32269547490305 | erot = 2.87794942105203 | epot = -20.9071852604882 | etot = -15.7065403645331 - 1000000 0.10323091 -1.356822 0.050122912 -1.1615306 -8.852818e-05 -Loop time of 33.1901 on 4 procs for 1000000 steps with 16 atoms - -Performance: 26031.848 tau/day, 30129.454 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.5594 | 12.197 | 22.984 | 287.1 | 36.75 -Bond | 0.088184 | 0.40908 | 0.68101 | 42.5 | 1.23 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.0155 | 2.194 | 2.4681 | 11.3 | 6.61 -Output | 1.6928e-05 | 2.3246e-05 | 2.5988e-05 | 0.0 | 0.00 -Modify | 0.2003 | 2.7296 | 5.1641 | 131.4 | 8.22 -Other | | 15.66 | | | 47.19 - -Nlocal: 4 ave 8 max 0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 9 ave 10 max 8 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 34.5 ave 67 max 0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 138 -Ave neighs/atom = 8.625 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:33 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 new file mode 100644 index 0000000000..56f1b72277 --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.1 @@ -0,0 +1,172 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.861 | 2.861 | 2.861 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05 +1000 ekin = 1.54234964773389 | erot = 1.71563526070267 | epot = -24.5477045187653 | etot = -21.2897196103287 +2000 ekin = 1.85988866919215 | erot = 1.9424302796508 | epot = -24.4843044999595 | etot = -20.6819855511165 +3000 ekin = 2.68354339452998 | erot = 2.14216528317607 | epot = -24.4019350693561 | etot = -19.57622639165 +4000 ekin = 2.04461800191989 | erot = 1.49015219763162 | epot = -24.2959428773347 | etot = -20.7611726777832 +5000 ekin = 1.76794859210155 | erot = 2.54289684465818 | epot = -24.2337587736863 | etot = -19.9229133369266 +6000 ekin = 3.1106424806079 | erot = 2.04409805200892 | epot = -24.1585729744133 | etot = -19.0038324417964 +7000 ekin = 3.21360097519306 | erot = 2.71941303605722 | epot = -24.0566262531609 | etot = -18.1236122419107 +8000 ekin = 2.82489935901743 | erot = 2.66790555575696 | epot = -24.0194805097633 | etot = -18.526675594989 +9000 ekin = 2.69381302856378 | erot = 2.59107820129446 | epot = -23.9216126050554 | etot = -18.6367213751972 +10000 ekin = 2.65765007662471 | erot = 1.95562671446597 | epot = -23.7978334881241 | etot = -19.1845566970334 + 10000 0.11811778 -1.4992295 0.011864944 -1.3212615 -0.00013416809 +Loop time of 0.295538 on 1 procs for 10000 steps with 16 atoms + +Performance: 29234.801 tau/day, 33836.575 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.20959 | 0.20959 | 0.20959 | 0.0 | 70.92 +Bond | 0.0073669 | 0.0073669 | 0.0073669 | 0.0 | 2.49 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0016472 | 0.0016472 | 0.0016472 | 0.0 | 0.56 +Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00 +Modify | 0.073117 | 0.073117 | 0.073117 | 0.0 | 24.74 +Other | | 0.003813 | | | 1.29 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 88 ave 88 max 88 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 88 +Ave neighs/atom = 5.5 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 new file mode 100644 index 0000000000..5cb953cd8c --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA/duplex2/log.27Nov18.duplex2.g++.4 @@ -0,0 +1,172 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna/fene +bond_coeff * 2.0 0.25 0.7525 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk +pair_coeff * * oxdna/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna/hbond seqav 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.92828 + ghost atom cutoff = 1.92828 + binsize = 0.964142, bins = 42 42 42 + 5 neighbor lists, perpetual/occasional/extra = 5 0 0 + (1) pair oxdna/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.466 | 7.648 | 7.83 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5402493 0.0070469125 -1.5332024 -8.5641987e-05 +1000 ekin = 1.34565986428024 | erot = 2.31051421234078 | epot = -24.5061991591502 | etot = -20.8500250825292 +2000 ekin = 2.15911766687235 | erot = 2.16031365874707 | epot = -24.4723177103698 | etot = -20.1528863847504 +3000 ekin = 3.26561948796015 | erot = 2.75651822936604 | epot = -24.412573068346 | etot = -18.3904353510198 +4000 ekin = 1.92438809241066 | erot = 2.12016940074985 | epot = -24.3496233970111 | etot = -20.3050659038506 +5000 ekin = 1.35986357015476 | erot = 1.99413493074226 | epot = -24.2789445616949 | etot = -20.9249460607979 +6000 ekin = 2.19432475124593 | erot = 1.74281260409078 | epot = -24.2128064295788 | etot = -20.2756690742421 +7000 ekin = 2.65619274477635 | erot = 1.74094257048458 | epot = -24.1673462333493 | etot = -19.7702109180883 +8000 ekin = 2.51333548501168 | erot = 2.34649854571051 | epot = -24.0812769481836 | etot = -19.2214429174614 +9000 ekin = 2.24506493169711 | erot = 2.0652555461504 | epot = -23.9906736063989 | etot = -19.6803531285514 +10000 ekin = 2.36632635249862 | erot = 1.7959247176153 | epot = -23.9002627850602 | etot = -19.7380117149463 + 10000 0.10517006 -1.5057137 0.011947302 -1.345871 -9.5924016e-05 +Loop time of 0.251867 on 4 procs for 10000 steps with 16 atoms + +Performance: 34303.820 tau/day, 39703.495 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0035377 | 0.092047 | 0.17435 | 26.0 | 36.55 +Bond | 0.00065637 | 0.0031857 | 0.0053554 | 3.8 | 1.26 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.013929 | 0.01497 | 0.015733 | 0.6 | 5.94 +Output | 5.0783e-05 | 5.2691e-05 | 5.3883e-05 | 0.0 | 0.02 +Modify | 0.0013576 | 0.020825 | 0.040231 | 11.8 | 8.27 +Other | | 0.1208 | | | 47.96 + +Nlocal: 4 ave 8 max 0 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 9 ave 10 max 8 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 34.5 ave 67 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 138 +Ave neighs/atom = 8.625 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1 rename to examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 index 366e5db67a..5260e51330 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/input.duplex1 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/in.duplex1 @@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 1000000 +run 10000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1 deleted file mode 100644 index 25c705daf8..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.1 +++ /dev/null @@ -1,1167 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05 -1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342 -2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675 -3000 ekin = 0.00995035259649285 | erot = 0.0381961780846484 | epot = -14.6656605650904 | etot = -14.6175140344093 -4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659 -5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355 -6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157 -7000 ekin = 0.0483200640564843 | erot = 0.192565862515508 | epot = -14.8583999612756 | etot = -14.6175140347036 -8000 ekin = 0.0604312317605998 | erot = 0.244417870131508 | epot = -14.9223631366883 | etot = -14.6175140347962 -9000 ekin = 0.0727907119671751 | erot = 0.299521949931839 | epot = -14.989826696789 | etot = -14.6175140348899 -10000 ekin = 0.0850022498875221 | erot = 0.356777997217902 | epot = -15.0592942820869 | etot = -14.6175140349815 -11000 ekin = 0.0966857134041704 | erot = 0.415102860829614 | epot = -15.1293026093013 | etot = -14.6175140350675 -12000 ekin = 0.107492790688446 | erot = 0.473466334178045 | epot = -15.1984731600115 | etot = -14.617514035145 -13000 ekin = 0.117121180381715 | erot = 0.530923485009724 | epot = -15.2655587006029 | etot = -14.6175140352115 -14000 ekin = 0.125326348459166 | erot = 0.586641324447693 | epot = -15.329481708172 | etot = -14.6175140352651 -15000 ekin = 0.131930017119452 | erot = 0.639918104234695 | epot = -15.389362156659 | etot = -14.6175140353048 -16000 ekin = 0.136824741331535 | erot = 0.690194029501056 | epot = -15.4445328061632 | etot = -14.6175140353306 -17000 ekin = 0.139974218116303 | erot = 0.73705286614779 | epot = -15.4945411196072 | etot = -14.6175140353432 -18000 ekin = 0.141409342139924 | erot = 0.780214750583505 | epot = -15.5391381280674 | etot = -14.617514035344 -19000 ekin = 0.14122042490348 | erot = 0.819521373491594 | epot = -15.5782558337303 | etot = -14.6175140353352 -20000 ekin = 0.139546371890615 | erot = 0.854915474127934 | epot = -15.6119758813378 | etot = -14.6175140353193 -21000 ekin = 0.136561897558623 | erot = 0.886417110947779 | epot = -15.6404930438051 | etot = -14.6175140352987 -22000 ekin = 0.132464002543739 | erot = 0.914099368829953 | epot = -15.6640774066495 | etot = -14.6175140352758 -23000 ekin = 0.127458921012922 | erot = 0.938065991541773 | epot = -15.6830389478072 | etot = -14.6175140352525 -24000 ekin = 0.121750582423385 | erot = 0.958432936326242 | epot = -15.6976975539802 | etot = -14.6175140352305 -25000 ekin = 0.115531361418989 | erot = 0.97531514293118 | epot = -15.7083605395609 | etot = -14.6175140352107 -26000 ekin = 0.108975565586104 | erot = 0.988819027952036 | epot = -15.7153086287315 | etot = -14.6175140351934 -27000 ekin = 0.102235785319049 | erot = 0.999040485514132 | epot = -15.7187903060115 | etot = -14.6175140351783 -28000 ekin = 0.095441943431881 | erot = 1.00606759140964 | epot = -15.7190235700066 | etot = -14.6175140351651 -29000 ekin = 0.0887026587343887 | erot = 1.00998681843601 | epot = -15.7162035123233 | etot = -14.6175140351529 -30000 ekin = 0.0821083868014372 | erot = 1.01089138149893 | epot = -15.7105138034411 | etot = -14.6175140351407 -31000 ekin = 0.0757357206087773 | erot = 1.00889031641317 | epot = -15.7021400721498 | etot = -14.6175140351278 -32000 ekin = 0.0696522149388972 | erot = 1.00411701389994 | epot = -15.691283263952 | etot = -14.6175140351132 -33000 ekin = 0.0639211300028632 | erot = 0.996736133735177 | epot = -15.6781712988344 | etot = -14.6175140350964 -34000 ekin = 0.0586055597939536 | erot = 0.986948071943124 | epot = -15.6630676668141 | etot = -14.617514035077 -35000 ekin = 0.0537715085519321 | erot = 0.97499041461744 | epot = -15.6462759582244 | etot = -14.617514035055 -36000 ekin = 0.0494895953264297 | erot = 0.961136064967259 | epot = -15.6281396953245 | etot = -14.6175140350308 -37000 ekin = 0.0458351949405726 | erot = 0.945687966086967 | epot = -15.6090371960325 | etot = -14.617514035005 -38000 ekin = 0.0428869588016531 | erot = 0.928970560852795 | epot = -15.5893715546332 | etot = -14.6175140349787 -39000 ekin = 0.0407237982122988 | erot = 0.9113183396798 | epot = -15.5695561728451 | etot = -14.617514034953 -40000 ekin = 0.0394205547754457 | erot = 0.893062038097747 | epot = -15.5499966278026 | etot = -14.6175140349294 -41000 ekin = 0.0390427256107104 | erot = 0.874513269990878 | epot = -15.5310700305109 | etot = -14.6175140349093 -42000 ekin = 0.0396407506458402 | erot = 0.855948622306271 | epot = -15.5131034078461 | etot = -14.617514034894 -43000 ekin = 0.0412444930542154 | erot = 0.837594480923697 | epot = -15.4963530088628 | etot = -14.6175140348849 -44000 ekin = 0.0438586280730372 | erot = 0.819614069272971 | epot = -15.4809867322287 | etot = -14.6175140348826 -45000 ekin = 0.0474596621516281 | erot = 0.802098297010783 | epot = -15.4670719940501 | etot = -14.6175140348877 -46000 ekin = 0.0519951857192148 | erot = 0.785061947877571 | epot = -15.4545711684965 | etot = -14.6175140348997 -47000 ekin = 0.0573856747191636 | erot = 0.76844639238657 | epot = -15.4433461020232 | etot = -14.6175140349174 -48000 ekin = 0.0635286843632004 | erot = 0.75212933501618 | epot = -15.433172054319 | etot = -14.6175140349396 -49000 ekin = 0.070304673538874 | erot = 0.735941123250837 | epot = -15.4237598317539 | etot = -14.6175140349642 -50000 ekin = 0.0775831019857076 | erot = 0.719686007781425 | epot = -15.4147831447563 | etot = -14.6175140349892 -51000 ekin = 0.0852270843845694 | erot = 0.703165726695028 | epot = -15.4059068460928 | etot = -14.6175140350132 -52000 ekin = 0.0930950223451647 | erot = 0.686202231166125 | epot = -15.396811288546 | etot = -14.6175140350347 -53000 ekin = 0.101038429252995 | erot = 0.668656546988927 | epot = -15.3872090112954 | etot = -14.6175140350535 -54000 ekin = 0.10889654098061 | erot = 0.650441726174306 | epot = -15.3768523022246 | etot = -14.6175140350697 -55000 ekin = 0.116489881626234 | erot = 0.631529329348001 | epot = -15.3655332460579 | etot = -14.6175140350836 -56000 ekin = 0.12361610349192 | erot = 0.611950383382611 | epot = -15.35308052197 | etot = -14.6175140350954 -57000 ekin = 0.130051530401153 | erot = 0.591792721317295 | epot = -15.3393582868232 | etot = -14.6175140351048 -58000 ekin = 0.135560625193501 | erot = 0.571196690673292 | epot = -15.3242713509773 | etot = -14.6175140351105 -59000 ekin = 0.139913350827135 | erot = 0.550350463180279 | epot = -15.307777849119 | etot = -14.6175140351115 -60000 ekin = 0.142907875045794 | erot = 0.529485019662529 | epot = -15.2899069298147 | etot = -14.6175140351063 -61000 ekin = 0.144394224777542 | erot = 0.508867904998907 | epot = -15.2707761648706 | etot = -14.6175140350941 -62000 ekin = 0.144294003785763 | erot = 0.488794507592477 | epot = -15.2506025464531 | etot = -14.6175140350748 -63000 ekin = 0.142612256998146 | erot = 0.469576039421557 | epot = -15.2297023314688 | etot = -14.6175140350491 -64000 ekin = 0.139439544726902 | erot = 0.45152434495459 | epot = -15.2084779247003 | etot = -14.6175140350188 -65000 ekin = 0.134944526553566 | erot = 0.434934714913839 | epot = -15.1873932764535 | etot = -14.6175140349861 -66000 ekin = 0.129359146358223 | erot = 0.420068607767106 | epot = -15.1669417890788 | etot = -14.6175140349535 -67000 ekin = 0.122959458764236 | erot = 0.407138362059705 | epot = -15.1476118557469 | etot = -14.617514034923 -68000 ekin = 0.116045210525559 | erot = 0.396295631876262 | epot = -15.1298548772986 | etot = -14.6175140348968 -69000 ekin = 0.108920722072365 | erot = 0.38762458997195 | epot = -15.1140593469202 | etot = -14.6175140348758 -70000 ekin = 0.101878740729572 | erot = 0.381140173640836 | epot = -15.1005329492313 | etot = -14.6175140348609 -71000 ekin = 0.0951880561484016 | erot = 0.376791007701538 | epot = -15.0894930987019 | etot = -14.617514034852 -72000 ekin = 0.0890849677261927 | erot = 0.374466237250371 | epot = -15.0810652398255 | etot = -14.6175140348489 -73000 ekin = 0.0837682427021612 | erot = 0.374005347599889 | epot = -15.0752876251531 | etot = -14.617514034851 -74000 ekin = 0.0793969849744096 | erot = 0.375210076750601 | epot = -15.0721210965825 | etot = -14.6175140348575 -75000 ekin = 0.0760907865069267 | erot = 0.377857644572265 | epot = -15.0714624659463 | etot = -14.6175140348671 -76000 ekin = 0.0739315834908328 | erot = 0.381714646755152 | epot = -15.0731602651247 | etot = -14.6175140348788 -77000 ekin = 0.0729667273608161 | erot = 0.386551032956121 | epot = -15.0770317952083 | etot = -14.6175140348914 -78000 ekin = 0.073212865507933 | erot = 0.392153586683229 | epot = -15.0828804870951 | etot = -14.617514034904 -79000 ekin = 0.074660287835072 | erot = 0.398338263929461 | epot = -15.09051258668 | etot = -14.6175140349155 -80000 ekin = 0.0772774298944847 | erot = 0.404960669863083 | epot = -15.0997521346826 | etot = -14.6175140349251 -81000 ekin = 0.0810152396746107 | erot = 0.411923913359048 | epot = -15.1104531879657 | etot = -14.617514034932 -82000 ekin = 0.0858111278279411 | erot = 0.419183131304986 | epot = -15.1225082940691 | etot = -14.6175140349362 -83000 ekin = 0.0915922459205373 | erot = 0.426746154030553 | epot = -15.1358524348887 | etot = -14.6175140349376 -84000 ekin = 0.0982778862653023 | erot = 0.434670094582779 | epot = -15.1504620157846 | etot = -14.6175140349365 -85000 ekin = 0.105780875252123 | erot = 0.443054055542032 | epot = -15.1663489657278 | etot = -14.6175140349337 -86000 ekin = 0.114007936320491 | erot = 0.452028591870552 | epot = -15.183550563121 | etot = -14.6175140349299 -87000 ekin = 0.122859117093021 | erot = 0.461742961599068 | epot = -15.2021161136185 | etot = -14.6175140349264 -88000 ekin = 0.132226490250365 | erot = 0.472351454260961 | epot = -15.2220919794351 | etot = -14.6175140349238 -89000 ekin = 0.14199243043518 | erot = 0.484000150228927 | epot = -15.2435066155872 | etot = -14.6175140349231 -90000 ekin = 0.152027823848745 | erot = 0.49681531383988 | epot = -15.2663571726137 | etot = -14.6175140349251 -91000 ekin = 0.162190574344125 | erot = 0.510894287760631 | epot = -15.2905988970349 | etot = -14.6175140349302 -92000 ekin = 0.172324730223241 | erot = 0.526299304076712 | epot = -15.3161380692387 | etot = -14.6175140349387 -93000 ekin = 0.182260479602514 | erot = 0.543054150883983 | epot = -15.342828665437 | etot = -14.6175140349505 -94000 ekin = 0.191815166424497 | erot = 0.561143224560487 | epot = -15.3704724259505 | etot = -14.6175140349655 -95000 ekin = 0.200795384589871 | erot = 0.580512230413669 | epot = -15.398821649987 | etot = -14.6175140349834 -96000 ekin = 0.209000133284301 | erot = 0.601069706845445 | epot = -15.4275838751336 | etot = -14.6175140350039 -97000 ekin = 0.216224974983076 | erot = 0.622688639933065 | epot = -15.4564276499427 | etot = -14.6175140350266 -98000 ekin = 0.222267131485452 | erot = 0.645207670246426 | epot = -15.4849888367829 | etot = -14.617514035051 -99000 ekin = 0.226931474008822 | erot = 0.668431711040234 | epot = -15.5128772201258 | etot = -14.6175140350768 -100000 ekin = 0.230037392185194 | erot = 0.692132125756912 | epot = -15.5396835530455 | etot = -14.6175140351034 -101000 ekin = 0.231426538774339 | erot = 0.716046886549487 | epot = -15.5649874604541 | etot = -14.6175140351302 -102000 ekin = 0.230971416186116 | erot = 0.739881303910906 | epot = -15.5883667552535 | etot = -14.6175140351565 -103000 ekin = 0.228584676860968 | erot = 0.763309953365433 | epot = -15.6094086654079 | etot = -14.6175140351815 -104000 ekin = 0.224228843046698 | erot = 0.785980326921886 | epot = -15.6277232051725 | etot = -14.6175140352039 -105000 ekin = 0.217925953180593 | erot = 0.807518535460022 | epot = -15.6429585238635 | etot = -14.6175140352229 -106000 ekin = 0.209766205881976 | erot = 0.827537066837565 | epot = -15.6548173079567 | etot = -14.6175140352372 -107000 ekin = 0.19991466311948 | erot = 0.845644346598459 | epot = -15.6630730449638 | etot = -14.6175140352459 -108000 ekin = 0.188614735691129 | erot = 0.861455562303715 | epot = -15.6675843332431 | etot = -14.6175140352483 -109000 ekin = 0.176187061061687 | erot = 0.874603999194433 | epot = -15.6683050955002 | etot = -14.6175140352441 -110000 ekin = 0.163022626611995 | erot = 0.88475208463374 | epot = -15.6652887464792 | etot = -14.6175140352335 -111000 ekin = 0.14956938211077 | erot = 0.89160140093568 | epot = -15.6586848182637 | etot = -14.6175140352173 -112000 ekin = 0.136312261124986 | erot = 0.8949011206007 | epot = -15.6487274169225 | etot = -14.6175140351968 -113000 ekin = 0.123747404857758 | erot = 0.894454602033368 | epot = -15.6357160420648 | etot = -14.6175140351736 -114000 ekin = 0.112352324429831 | erot = 0.890124196452667 | epot = -15.6199905560322 | etot = -14.6175140351497 -115000 ekin = 0.102554569787556 | erot = 0.881834585426713 | epot = -15.6019031903412 | etot = -14.6175140351269 -116000 ekin = 0.0947020047096738 | erot = 0.869575126614186 | epot = -15.5817911664307 | etot = -14.6175140351068 -117000 ekin = 0.0890378681937318 | erot = 0.853401690493949 | epot = -15.559953593778 | etot = -14.6175140350903 -118000 ekin = 0.0856833736308548 | erot = 0.833438318818926 | epot = -15.5366357275277 | etot = -14.6175140350779 -119000 ekin = 0.0846297171118248 | erot = 0.809878764032089 | epot = -15.5120225162133 | etot = -14.6175140350694 -120000 ekin = 0.0857402026936468 | erot = 0.782987649501416 | epot = -15.4862418872589 | etot = -14.6175140350638 -121000 ekin = 0.088761978164944 | erot = 0.753100709615785 | epot = -15.4593767228408 | etot = -14.61751403506 -122000 ekin = 0.0933458418336512 | erot = 0.720623403982127 | epot = -15.4314832808722 | etot = -14.6175140350564 -123000 ekin = 0.0990718975139699 | erot = 0.68602719834959 | epot = -15.4026131309152 | etot = -14.6175140350516 -124000 ekin = 0.105478567535099 | erot = 0.649842971567299 | epot = -15.3728355741467 | etot = -14.6175140350443 -125000 ekin = 0.112092583657528 | erot = 0.61265130691034 | epot = -15.3422579256011 | etot = -14.6175140350332 -126000 ekin = 0.118457948670349 | erot = 0.575069793125981 | epot = -15.3110417768144 | etot = -14.617514035018 -127000 ekin = 0.124162352097832 | erot = 0.537737821903371 | epot = -15.2794142089993 | etot = -14.6175140349981 -128000 ekin = 0.128860000475183 | erot = 0.501299660072983 | epot = -15.2476736955218 | etot = -14.6175140349736 -129000 ekin = 0.132290197681538 | erot = 0.466386755141783 | epot = -15.2161909877681 | etot = -14.6175140349448 -130000 ekin = 0.134291248323408 | erot = 0.433600287194685 | epot = -15.1854055704302 | etot = -14.6175140349121 -131000 ekin = 0.134809368079367 | erot = 0.403494917851113 | epot = -15.1558183208069 | etot = -14.6175140348764 -132000 ekin = 0.133902311413259 | erot = 0.376564532721602 | epot = -15.1279808789733 | etot = -14.6175140348385 -133000 ekin = 0.131737425950174 | erot = 0.353230559449875 | epot = -15.1024820201993 | etot = -14.6175140347993 -134000 ekin = 0.128583872250139 | erot = 0.333833200745338 | epot = -15.0799311077557 | etot = -14.6175140347602 -135000 ekin = 0.124798858319487 | erot = 0.31862567876175 | epot = -15.0609385718037 | etot = -14.6175140347224 -136000 ekin = 0.12080796695122 | erot = 0.307771366705934 | epot = -15.0460933683448 | etot = -14.6175140346877 -137000 ekin = 0.117080018573556 | erot = 0.301343503849859 | epot = -15.0359375570811 | etot = -14.6175140346577 -138000 ekin = 0.114097404451637 | erot = 0.299327064918768 | epot = -15.0309385040046 | etot = -14.6175140346342 -139000 ekin = 0.112323403877397 | erot = 0.301622293047273 | epot = -15.0314597315437 | etot = -14.6175140346191 -140000 ekin = 0.112168587317134 | erot = 0.308049410073558 | epot = -15.0377320320047 | etot = -14.617514034614 -141000 ekin = 0.113958896787483 | erot = 0.318354084563277 | epot = -15.0498270159712 | etot = -14.6175140346204 -142000 ekin = 0.117908250110044 | erot = 0.332213334114174 | epot = -15.0676356188633 | etot = -14.6175140346391 -143000 ekin = 0.124098500240116 | erot = 0.349241744868859 | epot = -15.0908542797794 | etot = -14.6175140346704 -144000 ekin = 0.132469049162244 | erot = 0.36899804234383 | epot = -15.1189811262199 | etot = -14.6175140347138 -145000 ekin = 0.142817534773294 | erot = 0.390992018433025 | epot = -15.1513235879745 | etot = -14.6175140347682 -146000 ekin = 0.154812002594044 | erot = 0.414692148538822 | epot = -15.1870181859643 | etot = -14.6175140348315 -147000 ekin = 0.168013608208165 | erot = 0.43953414756317 | epot = -15.2250617906724 | etot = -14.6175140349011 -148000 ekin = 0.181907755044192 | erot = 0.46493071599216 | epot = -15.2643525060103 | etot = -14.617514034974 -149000 ekin = 0.195940689918404 | erot = 0.490282644230507 | epot = -15.3037373691959 | etot = -14.6175140350469 -150000 ekin = 0.209558115498161 | erot = 0.514991307802203 | epot = -15.3420634584171 | etot = -14.6175140351168 -151000 ekin = 0.222242375358722 | erot = 0.538472447669863 | epot = -15.3782288582089 | etot = -14.6175140351803 -152000 ekin = 0.233545181100895 | erot = 0.560170967504241 | epot = -15.4112301838403 | etot = -14.6175140352351 -153000 ekin = 0.243113638171897 | erot = 0.579575715963473 | epot = -15.4402033894145 | etot = -14.6175140352791 -154000 ekin = 0.250708030719563 | erot = 0.596234520730074 | epot = -15.4644565867606 | etot = -14.617514035311 -155000 ekin = 0.256210874594961 | erot = 0.609768185048496 | epot = -15.4834930949732 | etot = -14.6175140353298 -156000 ekin = 0.259627463842806 | erot = 0.619882772314079 | epot = -15.4970242714923 | etot = -14.6175140353354 -157000 ekin = 0.26107875673392 | erot = 0.626379517381585 | epot = -15.5049723094438 | etot = -14.6175140353283 -158000 ekin = 0.260787877594978 | erot = 0.629161788909624 | epot = -15.5074637018139 | etot = -14.6175140353093 -159000 ekin = 0.259061752299553 | erot = 0.628238692725195 | epot = -15.5048144803046 | etot = -14.6175140352799 -160000 ekin = 0.256269476948141 | erot = 0.623725097357881 | epot = -15.4975086095477 | etot = -14.6175140352417 -161000 ekin = 0.252818974262866 | erot = 0.615838055765116 | epot = -15.4861710652245 | etot = -14.6175140351965 -162000 ekin = 0.249133354781009 | erot = 0.604889772114047 | epot = -15.4715371620415 | etot = -14.6175140351465 -163000 ekin = 0.245628201594233 | erot = 0.591277407066157 | epot = -15.4544196437542 | etot = -14.6175140350938 -164000 ekin = 0.242690765770646 | erot = 0.5754701254003 | epot = -15.4356749262112 | etot = -14.6175140350402 -165000 ekin = 0.240661818237773 | erot = 0.557993868664013 | epot = -15.4161697218898 | etot = -14.617514034988 -166000 ekin = 0.239820672159938 | erot = 0.539414388849556 | epot = -15.3967490959484 | etot = -14.6175140349389 -167000 ekin = 0.24037368261711 | erot = 0.520319112884873 | epot = -15.3782068303964 | etot = -14.6175140348944 -168000 ekin = 0.24244635767351 | erot = 0.501298426047331 | epot = -15.3612588185771 | etot = -14.6175140348562 -169000 ekin = 0.246079081489649 | erot = 0.482926967022199 | epot = -15.3465200833372 | etot = -14.6175140348253 -170000 ekin = 0.2512263556708 | erot = 0.465745518941327 | epot = -15.334485909415 | etot = -14.6175140348028 -171000 ekin = 0.257759407502687 | erot = 0.450244072412507 | epot = -15.3255175147045 | etot = -14.6175140347893 -172000 ekin = 0.265471962315305 | erot = 0.436846557572436 | epot = -15.3198325546728 | etot = -14.617514034785 -173000 ekin = 0.274088992052948 | erot = 0.425897760801831 | epot = -15.3175007876449 | etot = -14.6175140347901 -174000 ekin = 0.283278228108448 | erot = 0.417652965987037 | epot = -15.3184452288997 | etot = -14.6175140348042 -175000 ekin = 0.292664164217591 | erot = 0.412270652066437 | epot = -15.3224488511105 | etot = -14.6175140348264 -176000 ekin = 0.301844276744599 | erot = 0.409808663992694 | epot = -15.3291669755931 | etot = -14.6175140348558 -177000 ekin = 0.310407103278429 | erot = 0.410224178772685 | epot = -15.3381453169418 | etot = -14.6175140348907 -178000 ekin = 0.317951707449239 | erot = 0.413377690532346 | epot = -15.3488434329111 | etot = -14.6175140349295 -179000 ekin = 0.324107901132174 | erot = 0.419041092198358 | epot = -15.3606630283006 | etot = -14.6175140349701 -180000 ekin = 0.328556397749118 | erot = 0.426909726006353 | epot = -15.3729801587658 | etot = -14.6175140350103 -181000 ekin = 0.331047834154798 | erot = 0.436618006901549 | epot = -15.3851798761042 | etot = -14.6175140350478 -182000 ekin = 0.331419420115411 | erot = 0.447757936313848 | epot = -15.3966913915096 | etot = -14.6175140350804 -183000 ekin = 0.329607792338432 | erot = 0.459899520064776 | epot = -15.4070213475094 | etot = -14.6175140351062 -184000 ekin = 0.325656516855951 | erot = 0.472611792132538 | epot = -15.4157823441122 | etot = -14.6175140351237 -185000 ekin = 0.319716934488103 | erot = 0.485483030926984 | epot = -15.4227140005474 | etot = -14.6175140351323 -186000 ekin = 0.312041347783061 | erot = 0.498138700397667 | epot = -15.4276940833127 | etot = -14.6175140351319 -187000 ekin = 0.302968200961952 | erot = 0.510255791848641 | epot = -15.4307380279341 | etot = -14.6175140351235 -188000 ekin = 0.292899787357099 | erot = 0.521572552051206 | epot = -15.4319863745165 | etot = -14.6175140351082 -189000 ekin = 0.282274048056294 | erot = 0.531893031493142 | epot = -15.4316811146379 | etot = -14.6175140350885 -190000 ekin = 0.271533034589587 | erot = 0.541086413296707 | epot = -15.4301334829529 | etot = -14.6175140350666 -191000 ekin = 0.261091384545769 | erot = 0.54908161018572 | epot = -15.4276870297764 | etot = -14.6175140350449 -192000 ekin = 0.251308489708551 | erot = 0.555858063434352 | epot = -15.4246805881686 | etot = -14.6175140350257 -193000 ekin = 0.242467771120031 | erot = 0.561433978654736 | epot = -15.4214157847852 | etot = -14.6175140350104 -194000 ekin = 0.2347655816246 | erot = 0.565853352187793 | epot = -15.4181329688123 | etot = -14.6175140349999 -195000 ekin = 0.228310848061445 | erot = 0.569173077812631 | epot = -15.4149979608682 | etot = -14.6175140349941 -196000 ekin = 0.223134890550306 | erot = 0.57145120860725 | epot = -15.4121001341502 | etot = -14.6175140349926 -197000 ekin = 0.219209242156003 | erot = 0.572737138233763 | epot = -15.409460415384 | etot = -14.6175140349943 -198000 ekin = 0.216468062809104 | erot = 0.573064123808166 | epot = -15.4070462216152 | etot = -14.6175140349979 -199000 ekin = 0.214831137522652 | erot = 0.572444258403913 | epot = -15.4047894309289 | etot = -14.6175140350023 -200000 ekin = 0.214223573902254 | erot = 0.57086576066316 | epot = -15.4026033695722 | etot = -14.6175140350067 -201000 ekin = 0.214589119166907 | erot = 0.568292309386801 | epot = -15.4003954635645 | etot = -14.6175140350107 -202000 ekin = 0.215895325602457 | erot = 0.564664121433424 | epot = -15.3980734820503 | etot = -14.6175140350145 -203000 ekin = 0.218130347570136 | erot = 0.559900543318492 | epot = -15.395544925907 | etot = -14.6175140350184 -204000 ekin = 0.221292667473869 | erot = 0.553904074217835 | epot = -15.3927107767149 | etot = -14.6175140350232 -205000 ekin = 0.225376258610798 | erot = 0.546565915588112 | epot = -15.3894562092286 | etot = -14.6175140350297 -206000 ekin = 0.230354397529151 | erot = 0.537773288683187 | epot = -15.3856417212507 | etot = -14.6175140350384 -207000 ekin = 0.236165428414771 | erot = 0.527418806929786 | epot = -15.3810982703936 | etot = -14.617514035049 -208000 ekin = 0.242703261860427 | erot = 0.515412077175151 | epot = -15.3756293740966 | etot = -14.617514035061 -209000 ekin = 0.249814382550021 | erot = 0.501693407691568 | epot = -15.3690218253148 | etot = -14.6175140350732 -210000 ekin = 0.257301864855649 | erot = 0.486249049965564 | epot = -15.361064949905 | etot = -14.6175140350838 -211000 ekin = 0.264935635394273 | erot = 0.469126912720557 | epot = -15.3515765832057 | etot = -14.6175140350909 -212000 ekin = 0.272467183646406 | erot = 0.450451153648061 | epot = -15.3404323723872 | etot = -14.6175140350927 -213000 ekin = 0.279646306736793 | erot = 0.430433702677846 | epot = -15.3275940445023 | etot = -14.6175140350876 -214000 ekin = 0.286237611276688 | erot = 0.409381288017783 | epot = -15.3131329343691 | etot = -14.6175140350746 -215000 ekin = 0.292034643872632 | erot = 0.387696263734527 | epot = -15.2972449426606 | etot = -14.6175140350534 -216000 ekin = 0.296870258152624 | erot = 0.365870567411729 | epot = -15.2802548605889 | etot = -14.6175140350245 -217000 ekin = 0.300622666324868 | erot = 0.344472695102956 | epot = -15.2626093964168 | etot = -14.617514034989 -218000 ekin = 0.303217269541043 | erot = 0.324128407398458 | epot = -15.2448597118882 | etot = -14.6175140349487 -219000 ekin = 0.304624843911682 | erot = 0.305496496152239 | epot = -15.2276353749694 | etot = -14.6175140349055 -220000 ekin = 0.304856982073792 | erot = 0.289241221676068 | epot = -15.2116122386118 | etot = -14.6175140348619 -221000 ekin = 0.303959749544065 | erot = 0.276003133762455 | epot = -15.1974769181266 | etot = -14.61751403482 -222000 ekin = 0.302006434070655 | erot = 0.266369862265548 | epot = -15.1858903311184 | etot = -14.6175140347822 -223000 ekin = 0.299090105490396 | erot = 0.260848208954625 | epot = -15.1774523491954 | etot = -14.6175140347503 -224000 ekin = 0.29531650374511 | erot = 0.259838588557332 | epot = -15.1726691270288 | etot = -14.6175140347264 -225000 ekin = 0.290797600317434 | erot = 0.263612591735795 | epot = -15.1719242267649 | etot = -14.6175140347117 -226000 ekin = 0.285646103232653 | erot = 0.272294318080247 | epot = -15.1754544560203 | etot = -14.6175140347074 -227000 ekin = 0.279971018689074 | erot = 0.285846075011501 | epot = -15.1833311284151 | etot = -14.6175140347145 -228000 ekin = 0.273874374727583 | erot = 0.304059069119542 | epot = -15.1954474785804 | etot = -14.6175140347333 -229000 ekin = 0.267449174159942 | erot = 0.326549807965912 | epot = -15.2115130168895 | etot = -14.6175140347636 -230000 ekin = 0.260778614118952 | erot = 0.352763004039877 | epot = -15.2310556529637 | etot = -14.6175140348048 -231000 ekin = 0.253936564976955 | erot = 0.381981763344646 | epot = -15.2534323631772 | etot = -14.6175140348556 -232000 ekin = 0.24698923084228 | erot = 0.413345683736504 | epot = -15.2778489494931 | etot = -14.6175140349143 -233000 ekin = 0.239997814735683 | erot = 0.445877135783545 | epot = -15.3033889854978 | etot = -14.6175140349785 -234000 ekin = 0.233021891669698 | erot = 0.478515439398703 | epot = -15.3290513661138 | etot = -14.6175140350454 -235000 ekin = 0.226123071286244 | erot = 0.510157919201248 | epot = -15.3537950255994 | etot = -14.6175140351119 -236000 ekin = 0.219368436952614 | erot = 0.539706010633753 | epot = -15.3765884827609 | etot = -14.6175140351745 -237000 ekin = 0.212833212708479 | erot = 0.566113832023268 | epot = -15.3964610799618 | etot = -14.6175140352301 -238000 ekin = 0.206602165162757 | erot = 0.588436180449468 | epot = -15.412552380888 | etot = -14.6175140352757 -239000 ekin = 0.200769360307635 | erot = 0.605872583258753 | epot = -15.4241559788757 | etot = -14.6175140353093 -240000 ekin = 0.195436190928488 | erot = 0.617803458378408 | epot = -15.4307536846362 | etot = -14.6175140353293 -241000 ekin = 0.190707920284559 | erot = 0.623817360381655 | epot = -15.4320393160013 | etot = -14.6175140353351 -242000 ekin = 0.186689132523883 | erot = 0.623726737660644 | epot = -15.4279299055112 | etot = -14.6175140353267 -243000 ekin = 0.18347888087463 | erot = 0.61757185737741 | epot = -15.418564773557 | etot = -14.617514035305 -244000 ekin = 0.181166166759762 | erot = 0.60561292371356 | epot = -15.4042931257446 | etot = -14.6175140352713 -245000 ekin = 0.179826690515581 | erot = 0.588311983398978 | epot = -15.3856527091421 | etot = -14.6175140352276 -246000 ekin = 0.179521473344392 | erot = 0.566306329740652 | epot = -15.3633418382609 | etot = -14.6175140351758 -247000 ekin = 0.180297726608685 | erot = 0.54037552872489 | epot = -15.3381872904519 | etot = -14.6175140351184 -248000 ekin = 0.182192022180427 | erot = 0.511404282992934 | epot = -15.3111103402306 | etot = -14.6175140350572 -249000 ekin = 0.185235475058219 | erot = 0.480343275338998 | epot = -15.2830927853917 | etot = -14.6175140349945 -250000 ekin = 0.18946032457762 | erot = 0.448169956263045 | epot = -15.2551443157728 | etot = -14.6175140349321 -251000 ekin = 0.194907020011059 | erot = 0.415851007133659 | epot = -15.2282720620165 | etot = -14.6175140348718 -252000 ekin = 0.201630699422451 | erot = 0.384307951122869 | epot = -15.2034526853603 | etot = -14.617514034815 -253000 ekin = 0.209705815254746 | erot = 0.354387113740477 | epot = -15.1816069637584 | etot = -14.6175140347632 -254000 ekin = 0.219227629545986 | erot = 0.326834860919931 | epot = -15.1635765251836 | etot = -14.6175140347177 -255000 ekin = 0.230309407956005 | erot = 0.302278768995696 | epot = -15.1501022116313 | etot = -14.6175140346796 -256000 ekin = 0.243074422920893 | erot = 0.281215109558497 | epot = -15.1418035671295 | etot = -14.6175140346501 -257000 ekin = 0.257642364628865 | erot = 0.264002762945737 | epot = -15.139159162205 | etot = -14.6175140346304 -258000 ekin = 0.274110461102935 | erot = 0.250863404057276 | epot = -15.1424878997817 | etot = -14.6175140346215 -259000 ekin = 0.292530483428745 | erot = 0.241887528332562 | epot = -15.1519320463858 | etot = -14.6175140346245 -260000 ekin = 0.312883750214262 | erot = 0.237045600990929 | epot = -15.167443385845 | etot = -14.6175140346398 -261000 ekin = 0.335057071665646 | erot = 0.23620332462488 | epot = -15.1887744309582 | etot = -14.6175140346677 -262000 ekin = 0.358823075932977 | erot = 0.239139750883904 | epot = -15.2154768615246 | etot = -14.6175140347077 -263000 ekin = 0.383828346058697 | erot = 0.24556675356939 | epot = -15.2469091343868 | etot = -14.6175140347588 -264000 ekin = 0.409592161639846 | erot = 0.25514829095879 | epot = -15.2822544874178 | etot = -14.6175140348192 -265000 ekin = 0.435517425641053 | erot = 0.267517972446926 | epot = -15.3205494329745 | etot = -14.6175140348865 -266000 ekin = 0.460913759434934 | erot = 0.28229374222826 | epot = -15.3607215366211 | etot = -14.6175140349579 -267000 ekin = 0.485031075314244 | erot = 0.299088986461549 | epot = -15.4016340968062 | etot = -14.6175140350304 -268000 ekin = 0.507100517474285 | erot = 0.317519986657596 | epot = -15.4421345392328 | etot = -14.6175140351009 -269000 ekin = 0.526378761164296 | erot = 0.337210258004039 | epot = -15.4811030543346 | etot = -14.6175140351662 -270000 ekin = 0.542191399558024 | erot = 0.357792786171182 | epot = -15.5174982209533 | etot = -14.6175140352241 -271000 ekin = 0.55397150127625 | erot = 0.378911394713957 | epot = -15.5503969312626 | etot = -14.6175140352724 -272000 ekin = 0.561290243477908 | erot = 0.400222387434508 | epot = -15.579026666222 | etot = -14.6175140353095 -273000 ekin = 0.563877614618957 | erot = 0.421397250044594 | epot = -15.6027888999983 | etot = -14.6175140353347 -274000 ekin = 0.561632338448697 | erot = 0.442126671656052 | epot = -15.6212730454525 | etot = -14.6175140353478 -275000 ekin = 0.554621238225524 | erot = 0.462125606775959 | epot = -15.6342608803503 | etot = -14.6175140353488 -276000 ekin = 0.543069132888247 | erot = 0.481138682332307 | epot = -15.6417218505594 | etot = -14.6175140353389 -277000 ekin = 0.527340979966703 | erot = 0.498945052082944 | epot = -15.6438000673687 | etot = -14.617514035319 -278000 ekin = 0.507918337218215 | erot = 0.515361832412993 | epot = -15.6407942049222 | etot = -14.617514035291 -279000 ekin = 0.485372319602766 | erot = 0.53024547360125 | epot = -15.6331318284605 | etot = -14.6175140352565 -280000 ekin = 0.460335116507262 | erot = 0.543490744710295 | epot = -15.6213398964351 | etot = -14.6175140352175 -281000 ekin = 0.433471859961099 | erot = 0.555027349455695 | epot = -15.606013244593 | etot = -14.6175140351762 -282000 ekin = 0.405454262481042 | erot = 0.564814480005611 | epot = -15.5877827776215 | etot = -14.6175140351348 -283000 ekin = 0.376937038993841 | erot = 0.572833827991569 | epot = -15.56728490208 | etot = -14.6175140350946 -284000 ekin = 0.348537747962758 | erot = 0.579081711929156 | epot = -15.5451334949486 | etot = -14.6175140350567 -285000 ekin = 0.320820372083395 | erot = 0.583561068644996 | epot = -15.5218954757513 | etot = -14.6175140350229 -286000 ekin = 0.294282726921591 | erot = 0.586274110944376 | epot = -15.49807087286 | etot = -14.617514034994 -287000 ekin = 0.269347634013421 | erot = 0.58721647590847 | epot = -15.4740781448926 | etot = -14.6175140349707 -288000 ekin = 0.246357704467551 | erot = 0.586373659771232 | epot = -15.450245399192 | etot = -14.6175140349532 -289000 ekin = 0.22557352214567 | erot = 0.583720426230562 | epot = -15.4268079833179 | etot = -14.6175140349417 -290000 ekin = 0.207174962818393 | erot = 0.57922365744791 | epot = -15.4039126552014 | etot = -14.6175140349351 -291000 ekin = 0.191265313940187 | erot = 0.572848780862473 | epot = -15.3816281297352 | etot = -14.6175140349326 -292000 ekin = 0.177877757396419 | erot = 0.564569470031942 | epot = -15.3599612623613 | etot = -14.617514034933 -293000 ekin = 0.166983649288418 | erot = 0.554379837681261 | epot = -15.3388775219044 | etot = -14.6175140349348 -294000 ekin = 0.158501898150678 | erot = 0.542307895558042 | epot = -15.3183238286452 | etot = -14.6175140349364 -295000 ekin = 0.152308641379645 | erot = 0.528428741575596 | epot = -15.298251417892 | etot = -14.6175140349367 -296000 ekin = 0.148246390134139 | erot = 0.512875830575803 | epot = -15.2786362556445 | etot = -14.6175140349346 -297000 ekin = 0.146131889948737 | erot = 0.495848833634457 | epot = -15.2594947585125 | etot = -14.6175140349293 -298000 ekin = 0.145762142540829 | erot = 0.477616979344766 | epot = -15.2408931568064 | etot = -14.6175140349208 -299000 ekin = 0.146918339842591 | erot = 0.458517327975552 | epot = -15.2229497027275 | etot = -14.6175140349094 -300000 ekin = 0.149367830717969 | erot = 0.438948042713275 | epot = -15.205829908327 | etot = -14.6175140348958 -301000 ekin = 0.152864610233931 | erot = 0.419357266834875 | epot = -15.1897359119496 | etot = -14.6175140348808 -302000 ekin = 0.157149122640062 | erot = 0.400228590599294 | epot = -15.1748917481051 | etot = -14.6175140348658 -303000 ekin = 0.16194834771892 | erot = 0.382064246008704 | epot = -15.1615266285792 | etot = -14.6175140348516 -304000 ekin = 0.166977167327322 | erot = 0.365367110080369 | epot = -15.1498583122469 | etot = -14.6175140348392 -305000 ekin = 0.171941885875759 | erot = 0.350622387002877 | epot = -15.1400783077083 | etot = -14.6175140348297 -306000 ekin = 0.176546522696758 | erot = 0.338279561365245 | epot = -15.1323401188853 | etot = -14.6175140348233 -307000 ekin = 0.180502080572099 | erot = 0.328734935092634 | epot = -15.1267510504853 | etot = -14.6175140348206 -308000 ekin = 0.183539117579173 | erot = 0.32231506851894 | epot = -15.1233682209196 | etot = -14.6175140348214 -309000 ekin = 0.185422589168761 | erot = 0.31926113518105 | epot = -15.1221977591756 | etot = -14.6175140348258 -310000 ekin = 0.18596838252546 | erot = 0.319714556778101 | epot = -15.1231969741369 | etot = -14.6175140348333 -311000 ekin = 0.185060444471766 | erot = 0.323704474533048 | epot = -15.1262789538485 | etot = -14.6175140348436 -312000 ekin = 0.18266705569995 | erot = 0.331137883754578 | epot = -15.1313189743107 | etot = -14.6175140348562 -313000 ekin = 0.178854671448202 | erot = 0.341793554574001 | epot = -15.1381622608926 | etot = -14.6175140348704 -314000 ekin = 0.173797674113419 | erot = 0.355321045101389 | epot = -15.1466327541005 | etot = -14.6175140348857 -315000 ekin = 0.167782440686126 | erot = 0.371246117949507 | epot = -15.1565425935371 | etot = -14.6175140349014 -316000 ekin = 0.161204347699483 | erot = 0.388983636697569 | epot = -15.1677020193138 | etot = -14.6175140349167 -317000 ekin = 0.154556738723145 | erot = 0.407858516720337 | epot = -15.1799292903744 | etot = -14.6175140349309 -318000 ekin = 0.148411457828143 | erot = 0.427134549770667 | epot = -15.1930600425422 | etot = -14.6175140349434 -319000 ekin = 0.143391260343367 | erot = 0.446049980955804 | epot = -15.2069552762529 | etot = -14.6175140349537 -320000 ekin = 0.140135163879429 | erot = 0.463857713006082 | epot = -15.2215069118471 | etot = -14.6175140349616 -321000 ekin = 0.139258496830789 | erot = 0.479867117343116 | epot = -15.2366396491412 | etot = -14.6175140349673 -322000 ekin = 0.141309963686665 | erot = 0.493483840953484 | epot = -15.2523078396112 | etot = -14.6175140349711 -323000 ekin = 0.146728465401823 | erot = 0.504243890594755 | epot = -15.2684863909706 | etot = -14.6175140349741 -324000 ekin = 0.155802740978128 | erot = 0.511838753068286 | epot = -15.285155529024 | etot = -14.6175140349776 -325000 ekin = 0.168637192339279 | erot = 0.516129344219886 | epot = -15.3022805715426 | etot = -14.6175140349834 -326000 ekin = 0.185127492740314 | erot = 0.517147991937071 | epot = -15.31978951967 | etot = -14.6175140349926 -327000 ekin = 0.204949583924698 | erot = 0.515089155112464 | epot = -15.3375527740434 | etot = -14.6175140350062 -328000 ekin = 0.227565145375698 | erot = 0.510290835145397 | epot = -15.3553700155455 | etot = -14.6175140350244 -329000 ekin = 0.252245305620947 | erot = 0.503209396461946 | epot = -15.3729687371292 | etot = -14.6175140350463 -330000 ekin = 0.278112223737838 | erot = 0.494390678508285 | epot = -15.3900169373164 | etot = -14.6175140350703 -331000 ekin = 0.304195517643728 | erot = 0.484439927615862 | epot = -15.4061494803532 | etot = -14.6175140350936 -332000 ekin = 0.329497983391289 | erot = 0.473992405220338 | epot = -15.4210044237253 | etot = -14.6175140351137 -333000 ekin = 0.353063353197021 | erot = 0.463685785197061 | epot = -15.4342631735221 | etot = -14.617514035128 -334000 ekin = 0.374038491014966 | erot = 0.454134842084351 | epot = -15.4456873682339 | etot = -14.6175140351346 -335000 ekin = 0.391723520498624 | erot = 0.44590856262641 | epot = -15.4551461182577 | etot = -14.6175140351327 -336000 ekin = 0.405605581596876 | erot = 0.439509690041266 | epot = -15.4626293067607 | etot = -14.6175140351225 -337000 ekin = 0.415374601836511 | erot = 0.435356764652945 | epot = -15.4682454015947 | etot = -14.6175140351053 -338000 ekin = 0.420921997008494 | erot = 0.4337688621957 | epot = -15.4722048942871 | etot = -14.6175140350829 -339000 ekin = 0.422325110445994 | erot = 0.434953376212245 | epot = -15.4747925217162 | etot = -14.6175140350579 -340000 ekin = 0.419821259879065 | erot = 0.438997304560045 | epot = -15.4763325994719 | etot = -14.6175140350328 -341000 ekin = 0.413775534579932 | erot = 0.445862573585468 | epot = -15.4771521431752 | etot = -14.6175140350098 -342000 ekin = 0.404646174019828 | erot = 0.455385967573506 | epot = -15.4775461765844 | etot = -14.617514034991 -343000 ekin = 0.392950705832007 | erot = 0.467284215126369 | epot = -15.4777489559361 | etot = -14.6175140349777 -344000 ekin = 0.379235231728315 | erot = 0.481164689425287 | epot = -15.4779139561242 | etot = -14.6175140349706 -345000 ekin = 0.364048459932831 | erot = 0.49654196729344 | epot = -15.4781044621959 | etot = -14.6175140349696 -346000 ekin = 0.347921358320248 | erot = 0.512860132814242 | epot = -15.4782955261082 | etot = -14.6175140349738 -347000 ekin = 0.331352665808313 | erot = 0.529520204052381 | epot = -15.4783869048424 | etot = -14.6175140349817 -348000 ekin = 0.314799955037007 | erot = 0.545911447468509 | epot = -15.478225437497 | etot = -14.6175140349915 -349000 ekin = 0.298675493175969 | erot = 0.561444708833552 | epot = -15.4776342370106 | etot = -14.6175140350011 -350000 ekin = 0.28334581552179 | erot = 0.575585348315622 | epot = -15.4764451988457 | etot = -14.6175140350083 -351000 ekin = 0.269133730328657 | erot = 0.587883045338955 | epot = -15.474530810679 | etot = -14.6175140350114 -352000 ekin = 0.256321431306528 | erot = 0.597995738138102 | epot = -15.4718312044538 | etot = -14.6175140350092 -353000 ekin = 0.245153509655857 | erot = 0.605705335206491 | epot = -15.4683728798634 | etot = -14.617514035001 -354000 ekin = 0.235838910987786 | erot = 0.610923562934953 | epot = -15.4642765089099 | etot = -14.6175140349872 -355000 ekin = 0.228551231301984 | erot = 0.613687305426088 | epot = -15.4597525716969 | etot = -14.6175140349688 -356000 ekin = 0.223427131308619 | erot = 0.61414390282533 | epot = -15.4550850690815 | etot = -14.6175140349475 -357000 ekin = 0.220563006919496 | erot = 0.612527933402533 | epot = -15.4506049752473 | etot = -14.6175140349253 -358000 ekin = 0.220010333199303 | erot = 0.609131855544879 | epot = -15.4466562236489 | etot = -14.6175140349047 -359000 ekin = 0.221770268741646 | erot = 0.604273418958276 | epot = -15.443557722588 | etot = -14.6175140348881 -360000 ekin = 0.225788163654918 | erot = 0.598262925571842 | epot = -15.4415651241044 | etot = -14.6175140348777 -361000 ekin = 0.231948578438913 | erot = 0.59137325198523 | epot = -15.4408358652996 | etot = -14.6175140348754 -362000 ekin = 0.240071331019464 | erot = 0.583815109039738 | epot = -15.4414004749418 | etot = -14.6175140348826 -363000 ekin = 0.249908988059078 | erot = 0.575719406612622 | epot = -15.4431424295716 | etot = -14.6175140348999 -364000 ekin = 0.261146140583132 | erot = 0.56712790648618 | epot = -15.4457880819966 | etot = -14.6175140349273 -365000 ekin = 0.273400773646818 | erot = 0.557992653604894 | epot = -15.4489074622159 | etot = -14.6175140349642 -366000 ekin = 0.286228056504663 | erot = 0.548184015757871 | epot = -15.4519261072718 | etot = -14.6175140350093 -367000 ekin = 0.299126926926786 | erot = 0.537506547610907 | epot = -15.4541475095983 | etot = -14.6175140350606 -368000 ekin = 0.311549892639084 | erot = 0.525721330951755 | epot = -15.4547852587065 | etot = -14.6175140351156 -369000 ekin = 0.322916493342769 | erot = 0.512572942753926 | epot = -15.4530034712682 | etot = -14.6175140351715 -370000 ekin = 0.332630833324557 | erot = 0.497818805481132 | epot = -15.4479636740308 | etot = -14.6175140352251 -371000 ekin = 0.340103492446634 | erot = 0.481258447415918 | epot = -15.4388759751356 | etot = -14.6175140352731 -372000 ekin = 0.344777943664193 | erot = 0.462760223983496 | epot = -15.4250522029596 | etot = -14.6175140353119 -373000 ekin = 0.346161332162081 | erot = 0.442283380417406 | epot = -15.405958747918 | etot = -14.6175140353385 -374000 ekin = 0.343859062980667 | erot = 0.419893962766177 | epot = -15.3812670610967 | etot = -14.6175140353498 -375000 ekin = 0.337612023151491 | erot = 0.395773904235502 | epot = -15.35089996273 | etot = -14.617514035343 -376000 ekin = 0.327334336193659 | erot = 0.370223433835828 | epot = -15.3150718053453 | etot = -14.6175140353159 -377000 ekin = 0.313148263712968 | erot = 0.3436575453366 | epot = -15.2743198443167 | etot = -14.6175140352671 -378000 ekin = 0.295411338277735 | erot = 0.316597454537734 | epot = -15.2295228280119 | etot = -14.6175140351964 -379000 ekin = 0.274729408510529 | erot = 0.289657740939432 | epot = -15.1819011845551 | etot = -14.6175140351051 -380000 ekin = 0.251948675267414 | erot = 0.263529414055011 | epot = -15.1329921243187 | etot = -14.6175140349963 -381000 ekin = 0.228120837035203 | erot = 0.238958749468097 | epot = -15.0845936213794 | etot = -14.6175140348761 -382000 ekin = 0.204438854506746 | erot = 0.216721270519329 | epot = -15.0386741597779 | etot = -14.6175140347518 -383000 ekin = 0.182146263755385 | erot = 0.19759188098445 | epot = -14.9972521793722 | etot = -14.6175140346323 -384000 ekin = 0.162429780679522 | erot = 0.182311896924387 | epot = -14.9622557121308 | etot = -14.6175140345269 -385000 ekin = 0.146310622123822 | erot = 0.171555128911536 | epot = -14.9353797854792 | etot = -14.6175140344439 -386000 ekin = 0.134552389652403 | erot = 0.165895597224741 | epot = -14.9179620212657 | etot = -14.6175140343886 -387000 ekin = 0.127600986328395 | erot = 0.165779213534325 | epot = -14.9108942342266 | etot = -14.6175140343639 -388000 ekin = 0.125565151523028 | erot = 0.171500950984996 | epot = -14.9145801368772 | etot = -14.6175140343691 -389000 ekin = 0.128237001096973 | erot = 0.183188026636525 | epot = -14.9289390621349 | etot = -14.6175140344014 -390000 ekin = 0.135143637923168 | erot = 0.200788930663413 | epot = -14.9534466030433 | etot = -14.6175140344567 -391000 ekin = 0.145616156499953 | erot = 0.224068074688611 | epot = -14.9871982657191 | etot = -14.6175140345306 -392000 ekin = 0.158862235246809 | erot = 0.252606362171908 | epot = -15.0289826320371 | etot = -14.6175140346184 -393000 ekin = 0.174032087603698 | erot = 0.285808726839658 | epot = -15.0773548491589 | etot = -14.6175140347155 -394000 ekin = 0.190272707003915 | erot = 0.322920107512839 | epot = -15.1307068493349 | etot = -14.6175140348181 -395000 ekin = 0.206769905102427 | erot = 0.363051013228117 | epot = -15.1873349532527 | etot = -14.6175140349221 -396000 ekin = 0.222780272470673 | erot = 0.405212687947374 | epot = -15.2455069954414 | etot = -14.6175140350234 -397000 ekin = 0.23765569871957 | erot = 0.448360183482314 | epot = -15.3035299173199 | etot = -14.6175140351181 -398000 ekin = 0.250862154070767 | erot = 0.491439914329226 | epot = -15.3598161036022 | etot = -14.6175140352022 -399000 ekin = 0.261993055954332 | erot = 0.533437059170117 | epot = -15.4129441503972 | etot = -14.6175140352727 -400000 ekin = 0.270776550507805 | erot = 0.573417887949047 | epot = -15.4617084737844 | etot = -14.6175140353276 -401000 ekin = 0.277075831016468 | erot = 0.610562842823497 | epot = -15.505152709206 | etot = -14.6175140353661 -402000 ekin = 0.280882158892238 | erot = 0.644187798759039 | epot = -15.5425839930397 | etot = -14.6175140353884 -403000 ekin = 0.282301228579434 | erot = 0.67375296864169 | epot = -15.5735682326173 | etot = -14.6175140353962 -404000 ekin = 0.281534519812515 | erot = 0.698860907481897 | epot = -15.5979094626858 | etot = -14.6175140353913 -405000 ekin = 0.278857975737129 | erot = 0.719246574878127 | epot = -15.6156185859915 | etot = -14.6175140353763 -406000 ekin = 0.274600555759476 | erot = 0.734763157396773 | epot = -15.6268777485094 | etot = -14.6175140353531 -407000 ekin = 0.269124923358509 | erot = 0.745367259285043 | epot = -15.6320062179672 | etot = -14.6175140353237 -408000 ekin = 0.26281185316572 | erot = 0.751106276665205 | epot = -15.63143216512 | etot = -14.6175140352891 -409000 ekin = 0.256049112192118 | erot = 0.752109968276165 | epot = -15.6256731157185 | etot = -14.6175140352503 -410000 ekin = 0.249224269809733 | erot = 0.748584332259637 | epot = -15.6153226372768 | etot = -14.6175140352074 -411000 ekin = 0.242720888553438 | erot = 0.740809103918405 | epot = -15.6010440276326 | etot = -14.6175140351607 -412000 ekin = 0.236916379506096 | erot = 0.729136085380813 | epot = -15.5835664999974 | etot = -14.6175140351105 -413000 ekin = 0.232179735243654 | erot = 0.713985498456962 | epot = -15.5636792687578 | etot = -14.6175140350572 -414000 ekin = 0.228867632642245 | erot = 0.695838652585844 | epot = -15.5422203202303 | etot = -14.6175140350022 -415000 ekin = 0.227317772307857 | erot = 0.67522569539618 | epot = -15.520057502651 | etot = -14.6175140349469 -416000 ekin = 0.227838940777609 | erot = 0.652708261105125 | epot = -15.4980612367764 | etot = -14.6175140348937 -417000 ekin = 0.230697970866892 | erot = 0.628857925336008 | epot = -15.477069931048 | etot = -14.6175140348451 -418000 ekin = 0.236104416120682 | erot = 0.604232291329717 | epot = -15.4578507422538 | etot = -14.6175140348034 -419000 ekin = 0.244194252200402 | erot = 0.579351108945084 | epot = -15.4410593959167 | etot = -14.6175140347712 -420000 ekin = 0.255014214168465 | erot = 0.554674986841137 | epot = -15.4272032357599 | etot = -14.6175140347503 -421000 ekin = 0.268508458340296 | erot = 0.530589008736319 | epot = -15.4166115018185 | etot = -14.6175140347419 -422000 ekin = 0.284509119560497 | erot = 0.507392982380563 | epot = -15.4094161366875 | etot = -14.6175140347464 -423000 ekin = 0.302732060426935 | erot = 0.485299248118974 | epot = -15.4055453433094 | etot = -14.6175140347635 -424000 ekin = 0.322778728051397 | erot = 0.464438075670481 | epot = -15.4047308385137 | etot = -14.6175140347918 -425000 ekin = 0.344144594922636 | erot = 0.444869796712133 | epot = -15.4065284264641 | etot = -14.6175140348294 -426000 ekin = 0.366234204300036 | erot = 0.42660205298371 | epot = -15.4103502921573 | etot = -14.6175140348736 -427000 ekin = 0.388382398339813 | erot = 0.409609962240046 | epot = -15.4155063955013 | etot = -14.6175140349215 -428000 ekin = 0.409880900047521 | erot = 0.393856678091914 | epot = -15.4212516131094 | etot = -14.61751403497 -429000 ekin = 0.430009061106474 | erot = 0.379311788381608 | epot = -15.4268348845041 | etot = -14.617514035016 -430000 ekin = 0.448067283636569 | erot = 0.365965282400515 | epot = -15.4315466010941 | etot = -14.617514035057 -431000 ekin = 0.463411378723581 | erot = 0.353835411175173 | epot = -15.4347608249895 | etot = -14.6175140350908 -432000 ekin = 0.475485941535261 | erot = 0.342969616703679 | epot = -15.4359695933546 | etot = -14.6175140351157 -433000 ekin = 0.483854704021325 | erot = 0.333438714396286 | epot = -15.4348074535484 | etot = -14.6175140351308 -434000 ekin = 0.488225698519512 | erot = 0.325325491782385 | epot = -15.4310652254377 | etot = -14.6175140351358 -435000 ekin = 0.48846961521867 | erot = 0.318709988965961 | epot = -15.4246936393158 | etot = -14.6175140351311 -436000 ekin = 0.484629100798387 | erot = 0.313653867974887 | epot = -15.4157970038909 | etot = -14.6175140351177 -437000 ekin = 0.476917712285183 | erot = 0.310186654191005 | epot = -15.4046184015729 | etot = -14.6175140350967 -438000 ekin = 0.465707830236418 | erot = 0.308296241623084 | epot = -15.3915181069294 | etot = -14.6175140350699 -439000 ekin = 0.451507536801451 | erot = 0.307925153770687 | epot = -15.3769467256113 | etot = -14.6175140350392 -440000 ekin = 0.43492765901413 | erot = 0.308973010492867 | epot = -15.3614147045135 | etot = -14.6175140350065 -441000 ekin = 0.41664165734993 | erot = 0.311304747383586 | epot = -15.3454604397074 | etot = -14.6175140349739 -442000 ekin = 0.397341542601565 | erot = 0.314762618736299 | epot = -15.3296181962812 | etot = -14.6175140349433 -443000 ekin = 0.377694362715541 | erot = 0.319179725729324 | epot = -15.314388123361 | etot = -14.6175140349161 -444000 ekin = 0.358304425136815 | erot = 0.324393298190027 | epot = -15.3002117582203 | etot = -14.6175140348934 -445000 ekin = 0.339684383335157 | erot = 0.330254911559458 | epot = -15.2874533297707 | etot = -14.6175140348761 -446000 ekin = 0.322237701351825 | erot = 0.336636009507997 | epot = -15.2763877457241 | etot = -14.6175140348643 -447000 ekin = 0.306253086583715 | erot = 0.343428242757654 | epot = -15.2671953641993 | etot = -14.6175140348579 -448000 ekin = 0.291909091343981 | erot = 0.350538602019956 | epot = -15.2599617282208 | etot = -14.6175140348568 -449000 ekin = 0.279285717664383 | erot = 0.357880263087869 | epot = -15.254680015613 | etot = -14.6175140348608 -450000 ekin = 0.268379332693761 | erot = 0.365360767815961 | epot = -15.2512541353793 | etot = -14.6175140348696 -451000 ekin = 0.259117719163038 | erot = 0.372869677558774 | epot = -15.2495014316051 | etot = -14.6175140348833 -452000 ekin = 0.251373384973841 | erot = 0.380268095669017 | epot = -15.2491555155445 | etot = -14.6175140349017 -453000 ekin = 0.244974824127976 | erot = 0.387382402362654 | epot = -15.2498712614149 | etot = -14.6175140349243 -454000 ekin = 0.239716691076602 | erot = 0.394004131859282 | epot = -15.251234857886 | etot = -14.6175140349502 -455000 ekin = 0.235370413814525 | erot = 0.399897145639886 | epot = -15.252781594432 | etot = -14.6175140349776 -456000 ekin = 0.231696513790873 | erot = 0.404812188422494 | epot = -15.254022737218 | etot = -14.6175140350046 -457000 ekin = 0.22845901443235 | erot = 0.408507709512941 | epot = -15.2544807589739 | etot = -14.6175140350286 -458000 ekin = 0.225441196082655 | erot = 0.410774705621955 | epot = -15.2537299367515 | etot = -14.6175140350469 -459000 ekin = 0.222461018940778 | erot = 0.411462514810065 | epot = -15.251437568808 | etot = -14.6175140350572 -460000 ekin = 0.219384094438711 | erot = 0.410502136527464 | epot = -15.2474002660241 | etot = -14.6175140350579 -461000 ekin = 0.216132245240217 | erot = 0.407923844131223 | epot = -15.2415701244196 | etot = -14.6175140350481 -462000 ekin = 0.212686361973379 | erot = 0.403866554422698 | epot = -15.2340669514243 | etot = -14.6175140350282 -463000 ekin = 0.20908321848285 | erot = 0.398577486489113 | epot = -15.2251747399712 | etot = -14.6175140349992 -464000 ekin = 0.205406888263726 | erot = 0.392401883856584 | epot = -15.2153228070836 | etot = -14.6175140349633 -465000 ekin = 0.201776197881064 | erot = 0.385763783461888 | epot = -15.205054016266 | etot = -14.617514034923 -466000 ekin = 0.198330130961176 | erot = 0.379139817336958 | epot = -15.1949839831793 | etot = -14.6175140348812 -467000 ekin = 0.195213224017119 | erot = 0.373028711257446 | epot = -15.1857559701151 | etot = -14.6175140348405 -468000 ekin = 0.192562810062153 | erot = 0.367919448414883 | epot = -15.1779962932808 | etot = -14.6175140348038 -469000 ekin = 0.190499545154762 | erot = 0.364261004085585 | epot = -15.1722745840131 | etot = -14.6175140347728 -470000 ekin = 0.189122086032732 | erot = 0.362436180586967 | epot = -15.1690723013685 | etot = -14.6175140347488 -471000 ekin = 0.188506156938858 | erot = 0.362741456207262 | epot = -15.1687616478786 | etot = -14.6175140347325 -472000 ekin = 0.188707621222383 | erot = 0.365373993438327 | epot = -15.1715956493846 | etot = -14.6175140347239 -473000 ekin = 0.189768618622269 | erot = 0.370426120543873 | epot = -15.1777087738884 | etot = -14.6175140347222 -474000 ekin = 0.191725397341757 | erot = 0.377886798112627 | epot = -15.1871262301808 | etot = -14.6175140347264 -475000 ekin = 0.194616213071354 | erot = 0.387648901412458 | epot = -15.1997791492193 | etot = -14.6175140347355 -476000 ekin = 0.198487636161311 | erot = 0.39952067815555 | epot = -15.2155223490652 | etot = -14.6175140347483 -477000 ekin = 0.203397790430554 | erot = 0.413239540254437 | epot = -15.2341513654491 | etot = -14.6175140347641 -478000 ekin = 0.209415519783972 | erot = 0.42848646692651 | epot = -15.2554160214928 | etot = -14.6175140347823 -479000 ekin = 0.216615156595466 | erot = 0.444899686771501 | epot = -15.2790288781697 | etot = -14.6175140348028 -480000 ekin = 0.225067223158473 | erot = 0.462086880017466 | epot = -15.3046681380015 | etot = -14.6175140348255 -481000 ekin = 0.234826185148504 | erot = 0.479635803738671 | epot = -15.3319760237382 | etot = -14.617514034851 -482000 ekin = 0.24591693935591 | erot = 0.497123799837159 | epot = -15.3605547740724 | etot = -14.6175140348793 -483000 ekin = 0.258322039581452 | erot = 0.514126984880453 | epot = -15.3899630593723 | etot = -14.6175140349104 -484000 ekin = 0.27197166705544 | erot = 0.530229960568061 | epot = -15.4197156625675 | etot = -14.617514034944 -485000 ekin = 0.28673803081022 | erot = 0.545036619609118 | epot = -15.4492886853988 | etot = -14.6175140349795 -486000 ekin = 0.302435294442587 | erot = 0.558182125190107 | epot = -15.4781314546481 | etot = -14.6175140350154 -487000 ekin = 0.318825369858622 | erot = 0.569345540302361 | epot = -15.5056849452114 | etot = -14.6175140350504 -488000 ekin = 0.335629120856587 | erot = 0.578262027782387 | epot = -15.5314051837218 | etot = -14.6175140350828 -489000 ekin = 0.352541803825709 | erot = 0.584733173542209 | epot = -15.5547890124787 | etot = -14.6175140351108 -490000 ekin = 0.369251041133789 | erot = 0.588633902376135 | epot = -15.5753989786432 | etot = -14.6175140351333 -491000 ekin = 0.385455339944 | erot = 0.589914693970006 | epot = -15.5928840690632 | etot = -14.6175140351492 -492000 ekin = 0.400881156478982 | erot = 0.588598334680707 | epot = -15.6069935263179 | etot = -14.6175140351582 -493000 ekin = 0.415296746377544 | erot = 0.584771169137607 | epot = -15.6175819506758 | etot = -14.6175140351607 -494000 ekin = 0.428521503102922 | erot = 0.578569614095767 | epot = -15.6246051523561 | etot = -14.6175140351574 -495000 ekin = 0.440430011858761 | erot = 0.570163426568541 | epot = -15.6281074735769 | etot = -14.6175140351496 -496000 ekin = 0.450950706316723 | erot = 0.559737766477561 | epot = -15.628202507933 | etot = -14.6175140351387 -497000 ekin = 0.460059581798179 | erot = 0.547476355485722 | epot = -15.6250499724103 | etot = -14.6175140351264 -498000 ekin = 0.467769906492305 | erot = 0.533547985555255 | epot = -15.6188319271617 | etot = -14.6175140351141 -499000 ekin = 0.474119221073068 | erot = 0.518098277332677 | epot = -15.6097315335085 | etot = -14.6175140351028 -500000 ekin = 0.479155106635165 | erot = 0.50124797893749 | epot = -15.5979171206657 | etot = -14.617514035093 -501000 ekin = 0.482921233338954 | erot = 0.483098304082639 | epot = -15.5835335725064 | etot = -14.6175140350848 -502000 ekin = 0.485445093649074 | erot = 0.463742920559534 | epot = -15.5667020492864 | etot = -14.6175140350778 -503000 ekin = 0.486728599209635 | erot = 0.443285305605599 | epot = -15.5475279398862 | etot = -14.617514035071 -504000 ekin = 0.486742408087914 | erot = 0.42185937463177 | epot = -15.5261158177829 | etot = -14.6175140350632 -505000 ekin = 0.485424480827684 | erot = 0.399650657768078 | epot = -15.5025891736488 | etot = -14.6175140350531 -506000 ekin = 0.482682973411861 | erot = 0.376914939267211 | epot = -15.4771119477183 | etot = -14.6175140350393 -507000 ekin = 0.478403198154604 | erot = 0.353991273961022 | epot = -15.4499085071364 | etot = -14.6175140350208 -508000 ekin = 0.472458052935435 | erot = 0.33130671013391 | epot = -15.4212787980667 | etot = -14.6175140349973 -509000 ekin = 0.464721062855385 | erot = 0.309370883447746 | epot = -15.3916059812719 | etot = -14.6175140349688 -510000 ekin = 0.455081004104092 | erot = 0.288759823578743 | epot = -15.3613548626187 | etot = -14.6175140349359 -511000 ekin = 0.443456979180403 | erot = 0.270089690707412 | epot = -15.3310607047875 | etot = -14.6175140348997 -512000 ekin = 0.429812848219576 | erot = 0.253982534898693 | epot = -15.3013094179802 | etot = -14.617514034862 -513000 ekin = 0.414169942618991 | erot = 0.241027258547331 | epot = -15.2727112359909 | etot = -14.6175140348246 -514000 ekin = 0.396617122319463 | erot = 0.231739657368321 | epot = -15.2458708144771 | etot = -14.6175140347893 -515000 ekin = 0.377317407138792 | erot = 0.2265255487572 | epot = -15.221356990654 | etot = -14.617514034758 -516000 ekin = 0.356510629533619 | erot = 0.225650587239691 | epot = -15.1996752515051 | etot = -14.6175140347318 -517000 ekin = 0.334511811731562 | erot = 0.229219509886498 | epot = -15.18124535633 | etot = -14.6175140347119 -518000 ekin = 0.311705249160027 | erot = 0.237166415926756 | epot = -15.1663856997855 | etot = -14.6175140346987 -519000 ekin = 0.288534562405514 | erot = 0.24925645619383 | epot = -15.1553050532917 | etot = -14.6175140346924 -520000 ekin = 0.265489234982409 | erot = 0.265098165451265 | epot = -15.1481014351262 | etot = -14.6175140346926 -521000 ekin = 0.243088358087734 | erot = 0.28416474516013 | epot = -15.1447671379465 | etot = -14.6175140346986 -522000 ekin = 0.221862437060796 | erot = 0.305821970140485 | epot = -15.1451984419112 | etot = -14.6175140347099 -523000 ekin = 0.202334169776219 | erot = 0.329360070797331 | epot = -15.1492082752991 | etot = -14.6175140347255 -524000 ekin = 0.184999091076192 | erot = 0.354026911471077 | epot = -15.1565400372919 | etot = -14.6175140347446 -525000 ekin = 0.170306912739357 | erot = 0.379059948771681 | epot = -15.1668808962775 | etot = -14.6175140347665 -526000 ekin = 0.158644243148446 | erot = 0.403715126925617 | epot = -15.1798734048646 | etot = -14.6175140347905 -527000 ekin = 0.150319367666608 | erot = 0.42729102581269 | epot = -15.1951244282959 | etot = -14.6175140348166 -528000 ekin = 0.145549592055317 | erot = 0.449147424933789 | epot = -15.2122110518333 | etot = -14.6175140348442 -529000 ekin = 0.144451603984813 | erot = 0.468718121850924 | epot = -15.2306837607091 | etot = -14.6175140348734 -530000 ekin = 0.147035267138347 | erot = 0.485518371011576 | epot = -15.2500676730542 | etot = -14.6175140349043 -531000 ekin = 0.153201203684288 | erot = 0.49914783549727 | epot = -15.2698630741182 | etot = -14.6175140349366 -532000 ekin = 0.162742448479711 | erot = 0.509290301682675 | epot = -15.2895467851327 | etot = -14.6175140349703 -533000 ekin = 0.17535035488191 | erot = 0.515711587206687 | epot = -15.3085759770934 | etot = -14.6175140350048 -534000 ekin = 0.190624856013511 | erot = 0.518257146630579 | epot = -15.3263960376834 | etot = -14.6175140350393 -535000 ekin = 0.208088493536815 | erot = 0.516850140104718 | epot = -15.3424526687142 | etot = -14.6175140350727 -536000 ekin = 0.227204325842678 | erot = 0.511491240065689 | epot = -15.3562096010119 | etot = -14.6175140351036 -537000 ekin = 0.247396768812971 | erot = 0.502260311074144 | epot = -15.3671711150173 | etot = -14.6175140351302 -538000 ekin = 0.268074342413378 | erot = 0.489319600961445 | epot = -15.3749079785256 | etot = -14.6175140351508 -539000 ekin = 0.288653182933434 | erot = 0.472917679672164 | epot = -15.3790848977693 | etot = -14.6175140351637 -540000 ekin = 0.308579985825766 | erot = 0.453392904739558 | epot = -15.3794869257329 | etot = -14.6175140351676 -541000 ekin = 0.327353008191228 | erot = 0.431174973010935 | epot = -15.3760420163632 | etot = -14.6175140351611 -542000 ekin = 0.344539853506947 | erot = 0.406783142888998 | epot = -15.3688370315398 | etot = -14.6175140351439 -543000 ekin = 0.359790986513975 | erot = 0.380819988063775 | epot = -15.3581250096939 | etot = -14.6175140351162 -544000 ekin = 0.372848263090832 | erot = 0.35396003067243 | epot = -15.344322328842 | etot = -14.6175140350787 -545000 ekin = 0.383548167009797 | erot = 0.32693321248176 | epot = -15.3279954145248 | etot = -14.6175140350332 -546000 ekin = 0.39181986738573 | erot = 0.300503784237963 | epot = -15.3098376866052 | etot = -14.6175140349816 -547000 ekin = 0.397678590182378 | erot = 0.27544571388707 | epot = -15.2906383389957 | etot = -14.6175140349263 -548000 ekin = 0.401215088504814 | erot = 0.25251605036599 | epot = -15.2712451737407 | etot = -14.6175140348699 -549000 ekin = 0.402582175512773 | erot = 0.232427794767611 | epot = -15.2525240050959 | etot = -14.6175140348155 -550000 ekin = 0.401979352687952 | erot = 0.21582374083298 | epot = -15.2353171282862 | etot = -14.6175140347652 -551000 ekin = 0.399636550193979 | erot = 0.203252510909713 | epot = -15.220403095825 | etot = -14.6175140347213 -552000 ekin = 0.395797934840878 | erot = 0.195147714573752 | epot = -15.2084596841006 | etot = -14.617514034686 -553000 ekin = 0.390706676476181 | erot = 0.191810879117309 | epot = -15.2000315902546 | etot = -14.6175140346611 -554000 ekin = 0.384591526958083 | erot = 0.193398609454344 | epot = -15.1955041710601 | etot = -14.6175140346477 -555000 ekin = 0.377656068332665 | erot = 0.199914362893988 | epot = -15.1950844658734 | etot = -14.6175140346468 -556000 ekin = 0.370071512615674 | erot = 0.211205266307097 | epot = -15.1987908135806 | etot = -14.6175140346578 -557000 ekin = 0.361973939272807 | erot = 0.226964515102961 | epot = -15.2064524890562 | etot = -14.6175140346805 -558000 ekin = 0.353466765020814 | erot = 0.246739996102198 | epot = -15.2177207958362 | etot = -14.6175140347132 -559000 ekin = 0.344628961765223 | erot = 0.26994976567065 | epot = -15.2320927621895 | etot = -14.6175140347536 -560000 ekin = 0.335528980568069 | erot = 0.295904778796301 | epot = -15.2489477941631 | etot = -14.6175140347987 -561000 ekin = 0.326243446081701 | erot = 0.323838714909082 | epot = -15.2675961958353 | etot = -14.6175140348445 -562000 ekin = 0.316878486813716 | erot = 0.352943857553535 | epot = -15.2873363792543 | etot = -14.617514034887 -563000 ekin = 0.307590234582006 | erot = 0.382410843957942 | epot = -15.3075151134627 | etot = -14.6175140349228 -564000 ekin = 0.298599911427738 | erot = 0.411468934029839 | epot = -15.3275828804064 | etot = -14.6175140349488 -565000 ekin = 0.290198521501629 | erot = 0.439422606477971 | epot = -15.3471351629437 | etot = -14.6175140349641 -566000 ekin = 0.282736992095932 | erot = 0.465680158920132 | epot = -15.3659311859852 | etot = -14.6175140349691 -567000 ekin = 0.276599956454254 | erot = 0.489770841523124 | epot = -15.3838848329439 | etot = -14.6175140349665 -568000 ekin = 0.272165052790864 | erot = 0.511348887820875 | epot = -15.401027975572 | etot = -14.6175140349602 -569000 ekin = 0.269753809413365 | erot = 0.530185258477411 | epot = -15.4174531028455 | etot = -14.6175140349548 -570000 ekin = 0.269583567607375 | erot = 0.546150320474818 | epot = -15.4332479230362 | etot = -14.617514034954 -571000 ekin = 0.271731068577883 | erot = 0.559192265325737 | epot = -15.4484373688642 | etot = -14.6175140349606 -572000 ekin = 0.276116495687097 | erot = 0.5693163216341 | epot = -15.4629468522959 | etot = -14.6175140349747 -573000 ekin = 0.282512256444537 | erot = 0.576569321998212 | epot = -15.4765956134374 | etot = -14.6175140349947 -574000 ekin = 0.290574483947443 | erot = 0.581030490761516 | epot = -15.4891190097262 | etot = -14.6175140350173 -575000 ekin = 0.299890113326591 | erot = 0.582808418137568 | epot = -15.5002125665028 | etot = -14.6175140350386 -576000 ekin = 0.310029076130856 | erot = 0.582041678954806 | epot = -15.5095847901412 | etot = -14.6175140350555 -577000 ekin = 0.320591144135671 | erot = 0.578899817193345 | epot = -15.5170049963946 | etot = -14.6175140350656 -578000 ekin = 0.33123968081773 | erot = 0.573581904321356 | epot = -15.5223356202072 | etot = -14.6175140350681 -579000 ekin = 0.341718767395709 | erot = 0.566311213814785 | epot = -15.5255440162742 | etot = -14.6175140350637 -580000 ekin = 0.351854361646189 | erot = 0.557326170820722 | epot = -15.526694567521 | etot = -14.617514035054 -581000 ekin = 0.361543170719957 | erot = 0.546869043111496 | epot = -15.5259262488727 | etot = -14.6175140350413 -582000 ekin = 0.370734291431731 | erot = 0.535174473618109 | epot = -15.5234228000774 | etot = -14.6175140350276 -583000 ekin = 0.379408545146361 | erot = 0.522459863754298 | epot = -15.5193824439152 | etot = -14.6175140350145 -584000 ekin = 0.387559338332067 | erot = 0.508918999939668 | epot = -15.5139923732753 | etot = -14.6175140350036 -585000 ekin = 0.395177418309442 | erot = 0.494719483694806 | epot = -15.5074109369995 | etot = -14.6175140349952 -586000 ekin = 0.402240533516603 | erot = 0.480003760424766 | epot = -15.4997583289309 | etot = -14.6175140349896 -587000 ekin = 0.408707997145274 | erot = 0.464893014294149 | epot = -15.4911150464257 | etot = -14.6175140349863 -588000 ekin = 0.414519545772962 | erot = 0.449492951760492 | epot = -15.4815265325182 | etot = -14.6175140349848 -589000 ekin = 0.419597612555348 | erot = 0.433900487905301 | epot = -15.4710121354448 | etot = -14.6175140349842 -590000 ekin = 0.423852083806582 | erot = 0.418210489542943 | epot = -15.4595766083332 | etot = -14.6175140349837 -591000 ekin = 0.427186671517495 | erot = 0.402521929657886 | epot = -15.447222636158 | etot = -14.6175140349827 -592000 ekin = 0.429506137373701 | erot = 0.386943005728732 | epot = -15.4339631780827 | etot = -14.6175140349803 -593000 ekin = 0.430723706116628 | erot = 0.371594936609101 | epot = -15.4198326777017 | etot = -14.617514034976 -594000 ekin = 0.430768094953851 | erot = 0.356614269836485 | epot = -15.4048963997596 | etot = -14.6175140349693 -595000 ekin = 0.429589664830371 | erot = 0.342153609169837 | epot = -15.3892573089603 | etot = -14.6175140349601 -596000 ekin = 0.427165296133683 | erot = 0.328380718540713 | epot = -15.3730600496226 | etot = -14.6175140349482 -597000 ekin = 0.423501658500194 | erot = 0.315475989401854 | epot = -15.3564916828361 | etot = -14.6175140349341 -598000 ekin = 0.418636501255828 | erot = 0.303628359580228 | epot = -15.3397788957539 | etot = -14.6175140349179 -599000 ekin = 0.412638207582772 | erot = 0.293029673722308 | epot = -15.3231819162053 | etot = -14.6175140349002 -600000 ekin = 0.405603414753991 | erot = 0.283867637225042 | epot = -15.306985086861 | etot = -14.617514034882 -601000 ekin = 0.397652939448921 | erot = 0.276317573359969 | epot = -15.2914845476729 | etot = -14.617514034864 -602000 ekin = 0.388926339151973 | erot = 0.270533300127964 | epot = -15.2769736741272 | etot = -14.6175140348473 -603000 ekin = 0.379575547711316 | erot = 0.266637582798161 | epot = -15.2637271653423 | etot = -14.6175140348328 -604000 ekin = 0.36975811222467 | erot = 0.264712769809215 | epot = -15.2519849168554 | etot = -14.6175140348215 -605000 ekin = 0.359630614964768 | erot = 0.264792359550132 | epot = -15.241937009329 | etot = -14.6175140348141 -606000 ekin = 0.349342882571473 | erot = 0.266854337886995 | epot = -15.2337112552696 | etot = -14.6175140348112 -607000 ekin = 0.339033558751712 | erot = 0.270817131627804 | epot = -15.2273647251924 | etot = -14.6175140348129 -608000 ekin = 0.328827538259548 | erot = 0.276538908097638 | epot = -15.2228804811762 | etot = -14.617514034819 -609000 ekin = 0.31883562108778 | erot = 0.283820700144897 | epot = -15.2201703560617 | etot = -14.6175140348291 -610000 ekin = 0.30915654256846 | erot = 0.292413461056469 | epot = -15.219084038467 | etot = -14.617514034842 -611000 ekin = 0.299881272108338 | erot = 0.302028697870661 | epot = -15.2194240048357 | etot = -14.6175140348567 -612000 ekin = 0.291099167856369 | erot = 0.312351863790414 | epot = -15.2209650665183 | etot = -14.6175140348715 -613000 ekin = 0.282905257831717 | erot = 0.323057294042809 | epot = -15.2234765867597 | etot = -14.6175140348852 -614000 ekin = 0.275407632339979 | erot = 0.333823223653552 | epot = -15.2267448908899 | etot = -14.6175140348964 -615000 ekin = 0.268733725567263 | erot = 0.344345386321353 | epot = -15.2305931467927 | etot = -14.6175140349041 -616000 ekin = 0.26303418113654 | erot = 0.354347879927357 | epot = -15.2348960959719 | etot = -14.617514034908 -617000 ekin = 0.258483071857804 | erot = 0.363590372787407 | epot = -15.2395874795532 | etot = -14.617514034908 -618000 ekin = 0.255273496413556 | erot = 0.37187125453879 | epot = -15.2446587858571 | etot = -14.6175140349048 -619000 ekin = 0.253608004174612 | erot = 0.379026921287115 | epot = -15.2501489603613 | etot = -14.6175140348996 -620000 ekin = 0.253683881421971 | erot = 0.38492793451358 | epot = -15.2561258508295 | etot = -14.6175140348939 -621000 ekin = 0.255674023709782 | erot = 0.389473226071952 | epot = -15.2626612846714 | etot = -14.6175140348897 -622000 ekin = 0.259704853367547 | erot = 0.392583779639718 | epot = -15.2698026678959 | etot = -14.6175140348886 -623000 ekin = 0.26583342999938 | erot = 0.394197274405698 | epot = -15.2775447392974 | etot = -14.6175140348924 -624000 ekin = 0.274026439188205 | erot = 0.394265031624513 | epot = -15.2858055057147 | etot = -14.617514034902 -625000 ekin = 0.284144015738361 | erot = 0.392752285176072 | epot = -15.2944103358322 | etot = -14.6175140349178 -626000 ekin = 0.295931256226117 | erot = 0.3896423443803 | epot = -15.3030876355457 | etot = -14.6175140349393 -627000 ekin = 0.309019727829642 | erot = 0.384944676504115 | epot = -15.3114784392987 | etot = -14.6175140349649 -628000 ekin = 0.322940275279045 | erot = 0.378706350959298 | epot = -15.3191606612307 | etot = -14.6175140349924 -629000 ekin = 0.33714704369826 | erot = 0.371025698974093 | epot = -15.3256867776909 | etot = -14.6175140350185 -630000 ekin = 0.351051052994966 | erot = 0.362066500826319 | epot = -15.3306315888613 | etot = -14.61751403504 -631000 ekin = 0.364060148819084 | erot = 0.352070586245444 | epot = -15.333644770118 | etot = -14.6175140350535 -632000 ekin = 0.375621025661728 | erot = 0.341366514680726 | epot = -15.3345015753988 | etot = -14.6175140350564 -633000 ekin = 0.38525854122481 | erot = 0.330372092305293 | epot = -15.3331446685769 | etot = -14.6175140350468 -634000 ekin = 0.39260786561676 | erot = 0.319588956493476 | epot = -15.3297108571345 | etot = -14.6175140350243 -635000 ekin = 0.39743609727868 | erot = 0.309588318033233 | epot = -15.3245384503017 | etot = -14.6175140349898 -636000 ekin = 0.399651602685356 | erot = 0.300988094378316 | epot = -15.318153732009 | etot = -14.6175140349453 -637000 ekin = 0.399301141333133 | erot = 0.294422893568946 | epot = -15.3112380697961 | etot = -14.6175140348941 -638000 ekin = 0.396556439147412 | erot = 0.290509369489622 | epot = -15.3045798434768 | etot = -14.6175140348397 -639000 ekin = 0.391692975514002 | erot = 0.289810143797406 | epot = -15.2990171540975 | etot = -14.6175140347861 -640000 ekin = 0.385064212934167 | erot = 0.292799653113662 | epot = -15.2953779007848 | etot = -14.617514034737 -641000 ekin = 0.377074355551307 | erot = 0.299834934663043 | epot = -15.2944233249095 | etot = -14.6175140346952 -642000 ekin = 0.368152133961519 | erot = 0.311133625026294 | epot = -15.296799793651 | etot = -14.6175140346632 -643000 ekin = 0.358727298275115 | erot = 0.326760494743852 | epot = -15.3030018276615 | etot = -14.6175140346425 -644000 ekin = 0.349210670243501 | erot = 0.346622862554313 | epot = -15.3133475674318 | etot = -14.617514034634 -645000 ekin = 0.339977915474887 | erot = 0.370474376280179 | epot = -15.3279663263927 | etot = -14.6175140346377 -646000 ekin = 0.331356734049285 | erot = 0.397926004729584 | epot = -15.346796773432 | etot = -14.6175140346531 -647000 ekin = 0.323616951062017 | erot = 0.428462692622329 | epot = -15.3695936783638 | etot = -14.6175140346795 -648000 ekin = 0.316962984679742 | erot = 0.461463981264509 | epot = -15.39594100066 | etot = -14.6175140347157 -649000 ekin = 0.311528303721762 | erot = 0.496226945506592 | epot = -15.4252692839889 | etot = -14.6175140347606 -650000 ekin = 0.307371814502042 | erot = 0.531990113312007 | epot = -15.4568759626268 | etot = -14.6175140348128 -651000 ekin = 0.304476169211518 | erot = 0.567957247023611 | epot = -15.4899474511058 | etot = -14.6175140348706 -652000 ekin = 0.302748327843053 | erot = 0.603320352539316 | epot = -15.523582715315 | etot = -14.6175140349326 -653000 ekin = 0.302022769689551 | erot = 0.637281675063945 | epot = -15.5568184797506 | etot = -14.6175140349971 -654000 ekin = 0.302067723594143 | erot = 0.669074745116215 | epot = -15.5886565037724 | etot = -14.617514035062 -655000 ekin = 0.302594671774764 | erot = 0.697984728110322 | epot = -15.6180934350104 | etot = -14.6175140351253 -656000 ekin = 0.30327116127365 | erot = 0.723368330432018 | epot = -15.6441535268902 | etot = -14.6175140351846 -657000 ekin = 0.303736663270782 | erot = 0.744673311812384 | epot = -15.6659240103206 | etot = -14.6175140352374 -658000 ekin = 0.303620889262373 | erot = 0.761457272710321 | epot = -15.6825921972542 | etot = -14.6175140352815 -659000 ekin = 0.302563666907973 | erot = 0.773404945480973 | epot = -15.6934826477033 | etot = -14.6175140353143 -660000 ekin = 0.30023539569508 | erot = 0.780343280385769 | epot = -15.698092711415 | etot = -14.6175140353342 -661000 ekin = 0.296355710531891 | erot = 0.782250083093068 | epot = -15.6961198289648 | etot = -14.6175140353398 -662000 ekin = 0.290710478297174 | erot = 0.779257959177616 | epot = -15.6874824728051 | etot = -14.6175140353303 -663000 ekin = 0.283165147463628 | erot = 0.771650651991629 | epot = -15.6723298347615 | etot = -14.6175140353062 -664000 ekin = 0.273673427176436 | erot = 0.759850562455816 | epot = -15.6510380249007 | etot = -14.6175140352684 -665000 ekin = 0.262280913452373 | erot = 0.744397727319011 | epot = -15.6241926759904 | etot = -14.617514035219 -666000 ekin = 0.249123647022469 | erot = 0.725921231744643 | epot = -15.5925589139278 | etot = -14.6175140351607 -667000 ekin = 0.234422061210132 | erot = 0.705104954964981 | epot = -15.5570410512716 | etot = -14.6175140350965 -668000 ekin = 0.218471158369307 | erot = 0.682650243124726 | epot = -15.5186354365237 | etot = -14.6175140350297 -669000 ekin = 0.201627981911825 | erot = 0.659238455806499 | epot = -15.4783804726816 | etot = -14.6175140349633 -670000 ekin = 0.184297501939045 | erot = 0.635496303880848 | epot = -15.4373078407201 | etot = -14.6175140349002 -671000 ekin = 0.166917915804983 | erot = 0.61196652574798 | epot = -15.3963984763957 | etot = -14.6175140348427 -672000 ekin = 0.149946120674174 | erot = 0.589085832361449 | epot = -15.3565459878283 | etot = -14.6175140347927 -673000 ekin = 0.13384380190456 | erot = 0.56717130681257 | epot = -15.3185291434681 | etot = -14.617514034751 -674000 ekin = 0.119064262674554 | erot = 0.546415679820826 | epot = -15.2829939772136 | etot = -14.6175140347183 -675000 ekin = 0.106039855017063 | erot = 0.526891195482464 | epot = -15.2504450851941 | etot = -14.6175140346945 -676000 ekin = 0.0951697078773662 | erot = 0.508561175678426 | epot = -15.2212449182352 | etot = -14.6175140346794 -677000 ekin = 0.0868074519861716 | erot = 0.491297978909916 | epot = -15.1956194655684 | etot = -14.6175140346723 -678000 ekin = 0.0812485969712638 | erot = 0.474905301099129 | epot = -15.1736679327428 | etot = -14.6175140346724 -679000 ekin = 0.078717761980004 | erot = 0.459143233464715 | epot = -15.1553750301235 | etot = -14.6175140346788 -680000 ekin = 0.0793562024648403 | erot = 0.443753980649279 | epot = -15.140624217805 | etot = -14.6175140346909 -681000 ekin = 0.083210490078987 | erot = 0.428486254341738 | epot = -15.1292107791286 | etot = -14.6175140347079 -682000 ekin = 0.0902236865225082 | erot = 0.413116880933255 | epot = -15.1208546021848 | etot = -14.617514034729 -683000 ekin = 0.1002305434624 | erot = 0.397468585264337 | epot = -15.1152131634801 | etot = -14.6175140347534 -684000 ekin = 0.112958164258862 | erot = 0.381423459018558 | epot = -15.1118956580575 | etot = -14.61751403478 -685000 ekin = 0.128033094046143 | erot = 0.364932120277273 | epot = -15.1104792491312 | etot = -14.6175140348077 -686000 ekin = 0.144995008361598 | erot = 0.348018922992613 | epot = -15.1105279661894 | etot = -14.6175140348352 -687000 ekin = 0.163316207854765 | erot = 0.330783730220992 | epot = -15.1116139729366 | etot = -14.6175140348609 -688000 ekin = 0.182425234215549 | erot = 0.313400732953834 | epot = -15.1133400020526 | etot = -14.6175140348832 -689000 ekin = 0.201732335852576 | erot = 0.296114640201427 | epot = -15.1153610109552 | etot = -14.6175140349012 -690000 ekin = 0.220654383891153 | erot = 0.279234374240419 | epot = -15.1174027930454 | etot = -14.6175140349138 -691000 ekin = 0.23863718992453 | erot = 0.263124260136845 | epot = -15.119275484982 | etot = -14.6175140349206 -692000 ekin = 0.255173895596428 | erot = 0.248192653897456 | epot = -15.1208805844157 | etot = -14.6175140349218 -693000 ekin = 0.269818995118043 | erot = 0.234878024009094 | epot = -15.1222110540447 | etot = -14.6175140349176 -694000 ekin = 0.282198402189112 | erot = 0.223632668706412 | epot = -15.1233451058045 | etot = -14.617514034909 -695000 ekin = 0.292016609393229 | erot = 0.214904477348979 | epot = -15.1244351216391 | etot = -14.6175140348969 -696000 ekin = 0.299062308191109 | erot = 0.209117382947929 | epot = -15.1256937260213 | etot = -14.6175140348822 -697000 ekin = 0.303213809972136 | erot = 0.206651361568472 | epot = -15.1273792064065 | etot = -14.6175140348659 -698000 ekin = 0.304445256192184 | erot = 0.207822979229852 | epot = -15.1297822702706 | etot = -14.6175140348485 -699000 ekin = 0.30283398390494 | erot = 0.212867544425252 | epot = -15.1332155631608 | etot = -14.6175140348306 -700000 ekin = 0.298568596343312 | erot = 0.221923881123307 | epot = -15.1380065122785 | etot = -14.6175140348119 -701000 ekin = 0.291956369738233 | erot = 0.235022588976802 | epot = -15.1444929935075 | etot = -14.6175140347925 -702000 ekin = 0.283427734153824 | erot = 0.252078414121441 | epot = -15.153020183048 | etot = -14.6175140347727 -703000 ekin = 0.273534855576733 | erot = 0.272887068861325 | epot = -15.163935959191 | etot = -14.6175140347529 -704000 ekin = 0.26294104616422 | erot = 0.297126498876385 | epot = -15.1775815797744 | etot = -14.6175140347338 -705000 ekin = 0.252398060444351 | erot = 0.324362359960341 | epot = -15.1942744551221 | etot = -14.6175140347174 -706000 ekin = 0.242709489752058 | erot = 0.354057349893431 | epot = -15.2142808743514 | etot = -14.6175140347059 -707000 ekin = 0.234680465258621 | erot = 0.385584073394173 | epot = -15.2377785733552 | etot = -14.6175140347024 -708000 ekin = 0.229056562326141 | erot = 0.418241319394794 | epot = -15.264811916431 | etot = -14.6175140347101 -709000 ekin = 0.226457657533242 | erot = 0.451273895783572 | epot = -15.2952455880485 | etot = -14.6175140347317 -710000 ekin = 0.227314828595294 | erot = 0.483896330830862 | epot = -15.328725194195 | etot = -14.6175140347688 -711000 ekin = 0.23181947949711 | erot = 0.515320742171119 | epot = -15.3646542564899 | etot = -14.6175140348216 -712000 ekin = 0.239893150548946 | erot = 0.544788749312626 | epot = -15.4021959347498 | etot = -14.6175140348882 -713000 ekin = 0.25118375882327 | erot = 0.571606341188741 | epot = -15.4403041349767 | etot = -14.6175140349647 -714000 ekin = 0.265090036185506 | erot = 0.5951798863727 | epot = -15.4777839576035 | etot = -14.6175140350453 -715000 ekin = 0.280811306968538 | erot = 0.615050345044185 | epot = -15.5133756871366 | etot = -14.6175140351239 -716000 ekin = 0.297415784950386 | erot = 0.63092216570354 | epot = -15.5458519858478 | etot = -14.6175140351939 -717000 ekin = 0.313918116237893 | erot = 0.642683345316623 | epot = -15.5741154968041 | etot = -14.6175140352496 -718000 ekin = 0.329356373327087 | erot = 0.650413757300117 | epot = -15.597284165914 | etot = -14.6175140352868 -719000 ekin = 0.34286009348443 | erot = 0.654380316354403 | epot = -15.6147544451422 | etot = -14.6175140353033 -720000 ekin = 0.35370349740302 | erot = 0.655019233384483 | epot = -15.6262367660863 | etot = -14.6175140352988 -721000 ekin = 0.361340844905818 | erot = 0.652906431496234 | epot = -15.6317613116767 | etot = -14.6175140352747 -722000 ekin = 0.365423978941542 | erot = 0.648719378780847 | epot = -15.6316573929562 | etot = -14.6175140352338 -723000 ekin = 0.365803989072271 | erot = 0.643193727890392 | epot = -15.6265117521426 | etot = -14.6175140351799 -724000 ekin = 0.362520178745276 | erot = 0.637078359572933 | epot = -15.6171125734355 | etot = -14.6175140351173 -725000 ekin = 0.355779938480328 | erot = 0.631092082280429 | epot = -15.604386055811 | etot = -14.6175140350503 -726000 ekin = 0.345932952941784 | erot = 0.625884613514165 | epot = -15.5893316014386 | etot = -14.6175140349826 -727000 ekin = 0.333442641405631 | erot = 0.622003743386354 | epot = -15.5729604197102 | etot = -14.6175140349182 -728000 ekin = 0.318857050497206 | erot = 0.619869891937827 | epot = -15.5562409772948 | etot = -14.6175140348598 -729000 ekin = 0.302780724957336 | erot = 0.619758691690166 | epot = -15.5400534514572 | etot = -14.6175140348097 -730000 ekin = 0.285848455041273 | erot = 0.621791770570761 | epot = -15.5251542603814 | etot = -14.6175140347694 -731000 ekin = 0.268701272205121 | erot = 0.625935552811619 | epot = -15.5121508597567 | etot = -14.6175140347399 -732000 ekin = 0.251964649664111 | erot = 0.632007594592137 | epot = -15.5014862789778 | etot = -14.6175140347216 -733000 ekin = 0.236228569496749 | erot = 0.639689689353067 | epot = -15.493432293564 | etot = -14.6175140347142 -734000 ekin = 0.222028960746785 | erot = 0.648546698715147 | epot = -15.4880896941795 | etot = -14.6175140347175 -735000 ekin = 0.209830023527889 | erot = 0.658049804517642 | epot = -15.4853938627762 | etot = -14.6175140347306 -736000 ekin = 0.200007166761123 | erot = 0.667602683399471 | epot = -15.4851238849136 | etot = -14.617514034753 -737000 ekin = 0.19283071962502 | erot = 0.676569044421092 | epot = -15.4869137988299 | etot = -14.6175140347838 -738000 ekin = 0.188451200585513 | erot = 0.684300102137722 | epot = -15.4902653375454 | etot = -14.6175140348222 -739000 ekin = 0.186887639936557 | erot = 0.690160900651572 | epot = -15.4945625754553 | etot = -14.6175140348671 -740000 ekin = 0.188021068410415 | erot = 0.693554915034912 | epot = -15.4990900183627 | etot = -14.6175140349173 -741000 ekin = 0.19159556899499 | erot = 0.69394692273054 | epot = -15.503056526696 | etot = -14.6175140349705 -742000 ekin = 0.197228843628155 | erot = 0.690884208638677 | epot = -15.5056270872913 | etot = -14.6175140350244 -743000 ekin = 0.204433503637525 | erot = 0.684016821527742 | epot = -15.5059643602409 | etot = -14.6175140350756 -744000 ekin = 0.212648433381485 | erot = 0.673116668202851 | epot = -15.503279136705 | etot = -14.6175140351207 -745000 ekin = 0.221277722248097 | erot = 0.658094727365381 | epot = -15.4968864847691 | etot = -14.6175140351556 -746000 ekin = 0.229733012317463 | erot = 0.63901458378143 | epot = -15.4862616312764 | etot = -14.6175140351775 -747000 ekin = 0.237474044144344 | erot = 0.616100096672917 | epot = -15.4710881760012 | etot = -14.6175140351839 -748000 ekin = 0.244042266762894 | erot = 0.589734872787402 | epot = -15.4512911747244 | etot = -14.6175140351741 -749000 ekin = 0.249083597953193 | erot = 0.560451518403377 | epot = -15.4270491515054 | etot = -14.6175140351488 -750000 ekin = 0.252358330147156 | erot = 0.528910066811303 | epot = -15.3987824320686 | etot = -14.6175140351102 -751000 ekin = 0.253738423481677 | erot = 0.495866496254572 | epot = -15.367118954798 | etot = -14.6175140350618 -752000 ekin = 0.253194394015732 | erot = 0.46213378533314 | epot = -15.3328422143564 | etot = -14.6175140350075 -753000 ekin = 0.250775308155814 | erot = 0.428539072350427 | epot = -15.2968284154581 | etot = -14.6175140349519 -754000 ekin = 0.246585878546982 | erot = 0.395880964578682 | epot = -15.2599808780245 | etot = -14.6175140348988 -755000 ekin = 0.240764398113247 | erot = 0.364890850085507 | epot = -15.2231692830502 | etot = -14.6175140348515 -756000 ekin = 0.233464471043397 | erot = 0.336201330030416 | epot = -15.1871798358858 | etot = -14.6175140348119 -757000 ekin = 0.22484246715835 | erot = 0.310323830730206 | epot = -15.15268033267 | etot = -14.6175140347814 -758000 ekin = 0.215051562421395 | erot = 0.287636293952656 | epot = -15.1202018911341 | etot = -14.61751403476 -759000 ekin = 0.204242275876241 | erot = 0.26838075350982 | epot = -15.0901370641326 | etot = -14.6175140347466 -760000 ekin = 0.192568636065448 | erot = 0.252669695562805 | epot = -15.062752366368 | etot = -14.6175140347397 -761000 ekin = 0.180198520175862 | erot = 0.240499428911612 | epot = -15.0382119838248 | etot = -14.6175140347373 -762000 ekin = 0.167326299029169 | erot = 0.231768292967749 | epot = -15.016608626734 | etot = -14.6175140347371 -763000 ekin = 0.154185685901938 | erot = 0.226297425416151 | epot = -14.997997146055 | etot = -14.6175140347369 -764000 ekin = 0.14106063274887 | erot = 0.22385200334861 | epot = -14.9824266708324 | etot = -14.6175140347349 -765000 ekin = 0.128292252296672 | erot = 0.224161332818099 | epot = -14.9699676198448 | etot = -14.6175140347301 -766000 ekin = 0.116280064488082 | erot = 0.226936813023217 | epot = -14.9607309122327 | etot = -14.6175140347214 -767000 ekin = 0.105476340626952 | erot = 0.231887507270348 | epot = -14.9548778826068 | etot = -14.6175140347095 -768000 ekin = 0.0963728909459186 | erot = 0.238733641345068 | epot = -14.9526205669854 | etot = -14.6175140346944 -769000 ekin = 0.0894802427431469 | erot = 0.247218655408997 | epot = -14.9542129328296 | etot = -14.6175140346774 -770000 ekin = 0.0852997361092876 | erot = 0.257120353608144 | epot = -14.9599341243774 | etot = -14.61751403466 -771000 ekin = 0.0842896183570361 | erot = 0.268261228608818 | epot = -14.9700648816097 | etot = -14.6175140346439 -772000 ekin = 0.0868267987477087 | erot = 0.280517313419977 | epot = -14.984858146799 | etot = -14.6175140346314 -773000 ekin = 0.0931666172479923 | erot = 0.29382416266008 | epot = -15.004504814533 | etot = -14.6175140346249 -774000 ekin = 0.103403843826641 | erot = 0.308178073397097 | epot = -15.0290959518507 | etot = -14.6175140346269 -775000 ekin = 0.117439110045724 | erot = 0.323630675217774 | epot = -15.0585838199035 | etot = -14.61751403464 -776000 ekin = 0.134955835365939 | erot = 0.340275613675428 | epot = -15.0927454837075 | etot = -14.6175140346662 -777000 ekin = 0.155413263635942 | erot = 0.358227842745886 | epot = -15.1311551410881 | etot = -14.6175140347063 -778000 ekin = 0.178060391221854 | erot = 0.377596905889472 | epot = -15.1731713318715 | etot = -14.6175140347601 -779000 ekin = 0.201973803865606 | erot = 0.398457850158034 | epot = -15.217945688849 | etot = -14.6175140348253 -780000 ekin = 0.226119091214232 | erot = 0.420824480238242 | epot = -15.2644576063504 | etot = -14.6175140348979 -781000 ekin = 0.24943115662658 | erot = 0.444629585314812 | epot = -15.311574776914 | etot = -14.6175140349726 -782000 ekin = 0.270904470269597 | erot = 0.469715692367534 | epot = -15.3581341976802 | etot = -14.617514035043 -783000 ekin = 0.28968127378351 | erot = 0.495837747641239 | epot = -15.4030330565279 | etot = -14.6175140351032 -784000 ekin = 0.305125009986887 | erot = 0.522676532161855 | epot = -15.4453155772971 | etot = -14.6175140351484 -785000 ekin = 0.316868262923396 | erot = 0.54985935370727 | epot = -15.4842416518065 | etot = -14.6175140351758 -786000 ekin = 0.324828845889219 | erot = 0.576983310022926 | epot = -15.5193261910972 | etot = -14.6175140351851 -787000 ekin = 0.329193233879357 | erot = 0.603636505801434 | epot = -15.550343774859 | etot = -14.6175140351782 -788000 ekin = 0.330371864852122 | erot = 0.629413875563613 | epot = -15.5772997755747 | etot = -14.617514035159 -789000 ekin = 0.328934711355469 | erot = 0.653926193132238 | epot = -15.6003749396201 | etot = -14.6175140351324 -790000 ekin = 0.325537319473758 | erot = 0.676802790006183 | epot = -15.6198541445837 | etot = -14.6175140351038 -791000 ekin = 0.32084726793344 | erot = 0.69768994321138 | epot = -15.6360512462227 | etot = -14.6175140350779 -792000 ekin = 0.315479253539376 | erot = 0.716247584423856 | epot = -15.6492408730215 | etot = -14.6175140350583 -793000 ekin = 0.309944490982093 | erot = 0.732146955921931 | epot = -15.6596054819516 | etot = -14.6175140350476 -794000 ekin = 0.304617480925228 | erot = 0.745071299199299 | epot = -15.6672028151708 | etot = -14.6175140350463 -795000 ekin = 0.299720880976412 | erot = 0.754720862084488 | epot = -15.6719557781149 | etot = -14.617514035054 -796000 ekin = 0.29532739618015 | erot = 0.760822658787176 | epot = -15.6736640900359 | etot = -14.6175140350686 -797000 ekin = 0.291376296851662 | erot = 0.763144639344813 | epot = -15.6720349712838 | etot = -14.6175140350874 -798000 ekin = 0.287701294703692 | erot = 0.761513269131305 | epot = -15.6667285989415 | etot = -14.6175140351065 -799000 ekin = 0.284065979572203 | erot = 0.755832991336525 | epot = -15.6574130060308 | etot = -14.617514035122 -800000 ekin = 0.280202790631629 | erot = 0.746105645863904 | epot = -15.643822471626 | etot = -14.6175140351305 -801000 ekin = 0.275851560112625 | erot = 0.732447665813198 | epot = -15.6258132610544 | etot = -14.6175140351285 -802000 ekin = 0.27079403443356 | erot = 0.715102809072512 | epot = -15.6034108786199 | etot = -14.6175140351138 -803000 ekin = 0.264881442636428 | erot = 0.694448356025774 | epot = -15.5768438337476 | etot = -14.6175140350854 -804000 ekin = 0.258053167891064 | erot = 0.670993199746582 | epot = -15.5465604026809 | etot = -14.6175140350432 -805000 ekin = 0.250345604728439 | erot = 0.64536694143664 | epot = -15.5132265811537 | etot = -14.6175140349886 -806000 ekin = 0.241890533712057 | erot = 0.618299214644394 | epot = -15.4777037832804 | etot = -14.6175140349239 -807000 ekin = 0.232905655207338 | erot = 0.590591287736413 | epot = -15.4410109777962 | etot = -14.6175140348525 -808000 ekin = 0.223678061733332 | erot = 0.563080896688416 | epot = -15.4042729931999 | etot = -14.6175140347781 -809000 ekin = 0.214543035230941 | erot = 0.536602758842007 | epot = -15.3686598287782 | etot = -14.6175140347053 -810000 ekin = 0.20586048831352 | erot = 0.511947500023869 | epot = -15.3353220229752 | etot = -14.6175140346378 -811000 ekin = 0.197991117805961 | erot = 0.489821758278059 | epot = -15.3053269106636 | etot = -14.6175140345796 -812000 ekin = 0.191273941671482 | erot = 0.470812030934247 | epot = -15.2796000071394 | etot = -14.6175140345337 -813000 ekin = 0.186006404369946 | erot = 0.455354451062637 | epot = -15.2588748899354 | etot = -14.6175140345029 -814000 ekin = 0.182427753712325 | erot = 0.443712201374086 | epot = -15.243653989575 | etot = -14.6175140344886 -815000 ekin = 0.18070598633538 | erot = 0.435961774091637 | epot = -15.2341817949191 | etot = -14.617514034492 -816000 ekin = 0.180928373605466 | erot = 0.43198881411332 | epot = -15.2304312222318 | etot = -14.617514034513 -817000 ekin = 0.183095431234163 | erot = 0.431493858263641 | epot = -15.2321033240487 | etot = -14.6175140345509 -818000 ekin = 0.187118173911448 | erot = 0.434007895069537 | epot = -15.2386401035849 | etot = -14.617514034604 -819000 ekin = 0.19281856805337 | erot = 0.438917286806818 | epot = -15.24924988953 | etot = -14.6175140346698 -820000 ekin = 0.199933211814762 | erot = 0.445497181488378 | epot = -15.2629444280487 | etot = -14.6175140347455 -821000 ekin = 0.208120374081947 | erot = 0.45295206948383 | epot = -15.2785864783932 | etot = -14.6175140348274 -822000 ekin = 0.216970558498262 | erot = 0.460461605795687 | epot = -15.2949461992055 | etot = -14.6175140349115 -823000 ekin = 0.226020685629107 | erot = 0.467229260922838 | epot = -15.3107639815453 | etot = -14.6175140349933 -824000 ekin = 0.234771793851542 | erot = 0.472530858216688 | epot = -15.324816687137 | etot = -14.6175140350687 -825000 ekin = 0.242709867661977 | erot = 0.475759712130444 | epot = -15.3359836149261 | etot = -14.6175140351336 -826000 ekin = 0.24932906085789 | erot = 0.476465014357235 | epot = -15.3433081103995 | etot = -14.6175140351844 -827000 ekin = 0.254156259485729 | erot = 0.474380409602746 | epot = -15.3460507043068 | etot = -14.6175140352183 -828000 ekin = 0.256775693170751 | erot = 0.469440383344517 | epot = -15.3437301117489 | etot = -14.6175140352337 -829000 ekin = 0.256852201216646 | erot = 0.461783092102062 | epot = -15.3361493285486 | etot = -14.6175140352299 -830000 ekin = 0.254151805816703 | erot = 0.45173946704119 | epot = -15.3234053080652 | etot = -14.6175140352073 -831000 ekin = 0.248558416433715 | erot = 0.439809632306566 | epot = -15.3058820839078 | etot = -14.6175140351675 -832000 ekin = 0.240085737091028 | erot = 0.426628719076058 | epot = -15.2842284912798 | etot = -14.6175140351127 -833000 ekin = 0.228883712687663 | erot = 0.412924890624256 | epot = -15.2593226383578 | etot = -14.6175140350459 -834000 ekin = 0.215239082681816 | erot = 0.399472764056069 | epot = -15.2322258817084 | etot = -14.6175140349706 -835000 ekin = 0.199569787294636 | erot = 0.38704544051957 | epot = -15.2041292627046 | etot = -14.6175140348904 -836000 ekin = 0.182413100763742 | erot = 0.376368114580784 | epot = -15.176295250154 | etot = -14.6175140348094 -837000 ekin = 0.164407483062677 | erot = 0.368075825931377 | epot = -15.1499973437255 | etot = -14.6175140347315 -838000 ekin = 0.146268295773427 | erot = 0.362677435797702 | epot = -15.1264597662312 | etot = -14.6175140346601 -839000 ekin = 0.128757768426377 | erot = 0.360527421580394 | epot = -15.1067992246057 | etot = -14.6175140345989 -840000 ekin = 0.112649960717962 | erot = 0.361806618656276 | epot = -15.0919706139251 | etot = -14.6175140345508 -841000 ekin = 0.0986919456676882 | erot = 0.366512603929065 | epot = -15.0827185841154 | etot = -14.6175140345186 -842000 ekin = 0.0875630029234267 | erot = 0.374460003555766 | epot = -15.0795370409834 | etot = -14.6175140345042 -843000 ekin = 0.0798341847686289 | erot = 0.385290606532755 | epot = -15.08263882581 | etot = -14.6175140345086 -844000 ekin = 0.0759310929907371 | erot = 0.398492769729592 | epot = -15.0919378972526 | etot = -14.6175140345323 -845000 ekin = 0.0761029610203549 | erot = 0.413429207168603 | epot = -15.1070462027631 | etot = -14.6175140345741 -846000 ekin = 0.0804010613290312 | erot = 0.429371869322519 | epot = -15.1272869652842 | etot = -14.6175140346326 -847000 ekin = 0.0886689809240991 | erot = 0.445542241998012 | epot = -15.1517252576266 | etot = -14.6175140347045 -848000 ekin = 0.10054642145979 | erot = 0.461155038711596 | epot = -15.1792154949571 | etot = -14.6175140347857 -849000 ekin = 0.115486960010843 | erot = 0.475462945351667 | epot = -15.2084639402341 | etot = -14.6175140348716 -850000 ekin = 0.132788806695687 | erot = 0.487799837752767 | epot = -15.2381026794056 | etot = -14.6175140349572 -851000 ekin = 0.151636227786327 | erot = 0.497619785576575 | epot = -15.2667700484 | etot = -14.6175140350371 -852000 ekin = 0.171148194576108 | erot = 0.504529242627505 | epot = -15.2931914723103 | etot = -14.6175140351066 -853000 ekin = 0.19043015939565 | erot = 0.508310157461236 | epot = -15.3162543520186 | etot = -14.6175140351617 -854000 ekin = 0.208624756899518 | erot = 0.508932337650936 | epot = -15.3350711297498 | etot = -14.6175140351993 -855000 ekin = 0.224957674812131 | erot = 0.506554231539352 | epot = -15.3490259415693 | etot = -14.6175140352178 -856000 ekin = 0.238775816538927 | erot = 0.501512259960049 | epot = -15.3578021117157 | etot = -14.6175140352167 -857000 ekin = 0.249575992233873 | erot = 0.494299801981698 | epot = -15.3613898294123 | etot = -14.6175140351968 -858000 ekin = 0.257023502073655 | erot = 0.485537766821928 | epot = -15.3600753040554 | etot = -14.6175140351598 -859000 ekin = 0.260960921285528 | erot = 0.475939247615908 | epot = -15.3544142040099 | etot = -14.6175140351085 -860000 ekin = 0.261408037072217 | erot = 0.46627098460475 | epot = -15.3451930567228 | etot = -14.6175140350458 -861000 ekin = 0.258554187538184 | erot = 0.457314264403307 | epot = -15.3333824869164 | etot = -14.6175140349749 -862000 ekin = 0.252744258032984 | erot = 0.449827506886398 | epot = -15.3200857998187 | etot = -14.6175140348993 -863000 ekin = 0.244459417796508 | erot = 0.44451214183432 | epot = -15.3064855944533 | etot = -14.6175140348225 -864000 ekin = 0.234293368840137 | erot = 0.441983030939926 | epot = -15.2937904345275 | etot = -14.6175140347475 -865000 ekin = 0.222924696623973 | erot = 0.442744308395109 | epot = -15.2831830396966 | etot = -14.6175140346776 -866000 ekin = 0.211086026109098 | erot = 0.447169652381157 | epot = -15.275769713106 | etot = -14.6175140346158 -867000 ekin = 0.199530465892687 | erot = 0.455487658924226 | epot = -15.2725321593816 | etot = -14.6175140345647 -868000 ekin = 0.188996288427053 | erot = 0.467771811643752 | epot = -15.2742821345979 | etot = -14.6175140345271 -869000 ekin = 0.180171161859058 | erot = 0.4839348556269 | epot = -15.2816200519912 | etot = -14.6175140345052 -870000 ekin = 0.173657413868177 | erot = 0.503727420429686 | epot = -15.2948988687985 | etot = -14.6175140345006 -871000 ekin = 0.169940429081807 | erot = 0.526741193132036 | epot = -15.3141956567285 | etot = -14.6175140345146 -872000 ekin = 0.16936227417812 | erot = 0.552417088945945 | epot = -15.3392933976716 | etot = -14.6175140345475 -873000 ekin = 0.172102391201256 | erot = 0.580058846014348 | epot = -15.3696752718142 | etot = -14.6175140345986 -874000 ekin = 0.178167002901486 | erot = 0.608852557307869 | epot = -15.4045335948759 | etot = -14.6175140346666 -875000 ekin = 0.187388233890387 | erot = 0.637892396630056 | epot = -15.4427946652691 | etot = -14.6175140347487 -876000 ekin = 0.199433181367003 | erot = 0.666212376945488 | epot = -15.4831595931541 | etot = -14.6175140348416 -877000 ekin = 0.213822249050295 | erot = 0.69282332523819 | epot = -15.5241596092293 | etot = -14.6175140349408 -878000 ekin = 0.229955728385689 | erot = 0.716754212645022 | epot = -15.5642239760723 | etot = -14.6175140350416 -879000 ekin = 0.247146104644683 | erot = 0.737095186135023 | epot = -15.6017553259188 | etot = -14.6175140351391 -880000 ekin = 0.264653797001979 | erot = 0.753040153406023 | epot = -15.6352079856363 | etot = -14.6175140352283 -881000 ekin = 0.281723784261018 | erot = 0.76392624159128 | epot = -15.6631640611574 | etot = -14.6175140353051 -882000 ekin = 0.29762064160649 | erot = 0.769267373447792 | epot = -15.68440205042 | etot = -14.6175140353658 -883000 ekin = 0.311659967165901 | erot = 0.768779581882543 | epot = -15.6979535844562 | etot = -14.6175140354077 -884000 ekin = 0.323234773767649 | erot = 0.762396270684338 | epot = -15.7031450798815 | etot = -14.6175140354295 -885000 ekin = 0.331836099624964 | erot = 0.750272396067583 | epot = -15.6996225311231 | etot = -14.6175140354306 -886000 ekin = 0.337067751563746 | erot = 0.732777385265791 | epot = -15.6873591722412 | etot = -14.6175140354117 -887000 ekin = 0.338655649766074 | erot = 0.710477420750299 | epot = -15.6666471058906 | etot = -14.6175140353742 -888000 ekin = 0.336452632420706 | erot = 0.684108417156166 | epot = -15.6380750848972 | etot = -14.6175140353204 -889000 ekin = 0.330439768515544 | erot = 0.654541548240117 | epot = -15.6024953520084 | etot = -14.6175140352528 -890000 ekin = 0.320725208484752 | erot = 0.622743520027164 | epot = -15.5609827636863 | etot = -14.6175140351744 -891000 ekin = 0.307541386208986 | erot = 0.589733936087572 | epot = -15.5147893573846 | etot = -14.6175140350881 -892000 ekin = 0.2912409981298 | erot = 0.556542080398037 | epot = -15.4652971135247 | etot = -14.6175140349969 -893000 ekin = 0.272291667891316 | erot = 0.524165278720867 | epot = -15.413970981516 | etot = -14.6175140349038 -894000 ekin = 0.251268620703445 | erot = 0.493530718297755 | epot = -15.3623133738123 | etot = -14.6175140348111 -895000 ekin = 0.228844131843626 | erot = 0.465462234286617 | epot = -15.3118204008516 | etot = -14.6175140347214 -896000 ekin = 0.205772103521913 | erot = 0.440653137307236 | epot = -15.2639392754666 | etot = -14.6175140346375 -897000 ekin = 0.182866017803022 | erot = 0.419645693758353 | epot = -15.2200257461231 | etot = -14.6175140345618 -898000 ekin = 0.16096887000853 | erot = 0.402817425242944 | epot = -15.1813003297485 | etot = -14.617514034497 -899000 ekin = 0.1409146251284 | erot = 0.39037402416295 | epot = -15.1488026837377 | etot = -14.6175140344464 -900000 ekin = 0.123482269337589 | erot = 0.38234845168916 | epot = -15.1233447554394 | etot = -14.6175140344126 -901000 ekin = 0.109345484385139 | erot = 0.37860573755432 | epot = -15.1054652563377 | etot = -14.6175140343982 -902000 ekin = 0.0990229789068497 | erot = 0.378853140166106 | epot = -15.0953901534782 | etot = -14.6175140344052 -903000 ekin = 0.0928360184564096 | erot = 0.382655585825617 | epot = -15.0930056387162 | etot = -14.6175140344341 -904000 ekin = 0.090880112387998 | erot = 0.389456554773451 | epot = -15.0978507016453 | etot = -14.6175140344838 -905000 ekin = 0.0930167096525896 | erot = 0.39860464884997 | epot = -15.1091353930541 | etot = -14.6175140345515 -906000 ekin = 0.0988880708462436 | erot = 0.409385812369162 | epot = -15.1257879178478 | etot = -14.6175140346324 -907000 ekin = 0.107954659147334 | erot = 0.421060528764045 | epot = -15.1465292226318 | etot = -14.6175140347204 -908000 ekin = 0.119550305154274 | erot = 0.432904367174429 | epot = -15.1699687071372 | etot = -14.6175140348085 -909000 ekin = 0.132947118364179 | erot = 0.444249232158146 | epot = -15.1947103854125 | etot = -14.6175140348901 -910000 ekin = 0.147420543333259 | erot = 0.454521879656393 | epot = -15.2194564579492 | etot = -14.6175140349596 -911000 ekin = 0.162305506309105 | erot = 0.463275978359197 | epot = -15.243095519681 | etot = -14.6175140350127 -912000 ekin = 0.177037050912772 | erot = 0.470214361754794 | epot = -15.2647654477151 | etot = -14.6175140350475 -913000 ekin = 0.191172462463139 | erot = 0.47519909256644 | epot = -15.2838855900937 | etot = -14.6175140350642 -914000 ekin = 0.204395616840708 | erot = 0.478248345048065 | epot = -15.300157996953 | etot = -14.6175140350642 -915000 ekin = 0.21650723869536 | erot = 0.479520616572313 | epot = -15.3135418903184 | etot = -14.6175140350508 -916000 ekin = 0.227406352399341 | erot = 0.479288139236201 | epot = -15.3242085266631 | etot = -14.6175140350275 -917000 ekin = 0.237068358848407 | erot = 0.477902392723181 | epot = -15.33248478657 | etot = -14.6175140349984 -918000 ekin = 0.245524170399248 | erot = 0.475755244752233 | epot = -15.3387934501184 | etot = -14.6175140349669 -919000 ekin = 0.252843202023962 | erot = 0.473239468155714 | epot = -15.3435967051161 | etot = -14.6175140349364 -920000 ekin = 0.259121284815245 | erot = 0.470712244290019 | epot = -15.3473475640143 | etot = -14.6175140349091 -921000 ekin = 0.264473144076567 | erot = 0.468464808092164 | epot = -15.3504519870555 | etot = -14.6175140348867 -922000 ekin = 0.269028180853978 | erot = 0.466700668341743 | epot = -15.3532428840659 | etot = -14.6175140348702 -923000 ekin = 0.272927944745733 | erot = 0.465523908452111 | epot = -15.3559658880574 | etot = -14.6175140348595 -924000 ekin = 0.276323793829006 | erot = 0.464938026324776 | epot = -15.3587758550082 | etot = -14.6175140348544 -925000 ekin = 0.279373649323261 | erot = 0.464854721380715 | epot = -15.361742405558 | etot = -14.617514034854 -926000 ekin = 0.282237300897746 | erot = 0.465111106681012 | epot = -15.3648624424358 | etot = -14.617514034857 -927000 ekin = 0.285070250341514 | erot = 0.465493135293291 | epot = -15.368077420497 | etot = -14.6175140348622 -928000 ekin = 0.288016501944524 | erot = 0.465762600718085 | epot = -15.3712931375312 | etot = -14.6175140348686 -929000 ekin = 0.291201026098177 | erot = 0.465684740678902 | epot = -15.3743998016517 | etot = -14.6175140348746 -930000 ekin = 0.294722459178862 | erot = 0.465054261989064 | epot = -15.3772907560474 | etot = -14.6175140348795 -931000 ekin = 0.298646764015084 | erot = 0.463717248452556 | epot = -15.37987804735 | etot = -14.6175140348824 -932000 ekin = 0.303002304639533 | erot = 0.461587311532279 | epot = -15.3821036510548 | etot = -14.617514034883 -933000 ekin = 0.307776651094719 | erot = 0.45865494559038 | epot = -15.3839456315665 | etot = -14.6175140348814 -934000 ekin = 0.312915338271965 | erot = 0.454989722654165 | epot = -15.3854190958038 | etot = -14.6175140348777 -935000 ekin = 0.318322768321313 | erot = 0.450735625549507 | epot = -15.3865724287433 | etot = -14.6175140348725 -936000 ekin = 0.323865441581091 | erot = 0.446100385693733 | epot = -15.3874798621412 | etot = -14.6175140348664 -937000 ekin = 0.329377658420717 | erot = 0.441340069469407 | epot = -15.3882317627502 | etot = -14.6175140348601 -938000 ekin = 0.334669609401427 | erot = 0.436740154637041 | epot = -15.3889237988926 | etot = -14.6175140348541 -939000 ekin = 0.339538182698642 | erot = 0.432595723626032 | epot = -15.3896479411737 | etot = -14.617514034849 -940000 ekin = 0.343779460435288 | erot = 0.429190561371735 | epot = -15.3904840566522 | etot = -14.6175140348451 -941000 ekin = 0.347202304174036 | erot = 0.42677706535814 | epot = -15.391493404375 | etot = -14.6175140348428 -942000 ekin = 0.349642062607919 | erot = 0.425558062624862 | epot = -15.3927141600748 | etot = -14.617514034842 -943000 ekin = 0.350973206935886 | erot = 0.425671371650738 | epot = -15.3941586134297 | etot = -14.6175140348431 -944000 ekin = 0.351119786154907 | erot = 0.427178062459248 | epot = -15.3958118834598 | etot = -14.6175140348457 -945000 ekin = 0.35006281650887 | erot = 0.430055404933682 | epot = -15.3976322562924 | etot = -14.6175140348499 -946000 ekin = 0.347844068536815 | erot = 0.434195447789962 | epot = -15.3995535511821 | etot = -14.6175140348553 -947000 ekin = 0.344566017441613 | erot = 0.439410327984511 | epot = -15.4014903802876 | etot = -14.6175140348614 -948000 ekin = 0.340388212507457 | erot = 0.445444378277369 | epot = -15.4033466256523 | etot = -14.6175140348675 -949000 ekin = 0.335520427168566 | erot = 0.451992965714887 | epot = -15.405027427756 | etot = -14.6175140348726 -950000 ekin = 0.330213181196298 | erot = 0.458727107975925 | epot = -15.4064543240478 | etot = -14.6175140348755 -951000 ekin = 0.324745816556508 | erot = 0.465321341197559 | epot = -15.4075811926297 | etot = -14.6175140348756 -952000 ekin = 0.319412679962217 | erot = 0.471482169177577 | epot = -15.4084088840117 | etot = -14.6175140348719 -953000 ekin = 0.314508037100193 | erot = 0.476974139327336 | epot = -15.4089962112918 | etot = -14.6175140348643 -954000 ekin = 0.310309685024347 | erot = 0.48163943141791 | epot = -15.4094631512954 | etot = -14.6175140348532 -955000 ekin = 0.307061947765186 | erot = 0.485408201613806 | epot = -15.4099841842186 | etot = -14.6175140348396 -956000 ekin = 0.304958921288862 | erot = 0.488297803841355 | epot = -15.4107707599557 | etot = -14.6175140348255 -957000 ekin = 0.304129209168565 | erot = 0.490400499132381 | epot = -15.412043743114 | etot = -14.6175140348131 -958000 ekin = 0.304623714619813 | erot = 0.491860923621326 | epot = -15.4139986730459 | etot = -14.6175140348048 -959000 ekin = 0.306408207891363 | erot = 0.492846142548816 | epot = -15.416768385243 | etot = -14.6175140348028 -960000 ekin = 0.309362278813016 | erot = 0.493512316198131 | epot = -15.4203886298201 | etot = -14.617514034809 -961000 ekin = 0.313285873784613 | erot = 0.493972653387225 | epot = -15.4247725619958 | etot = -14.6175140348239 -962000 ekin = 0.317913924784037 | erot = 0.49427132476265 | epot = -15.4296992843941 | etot = -14.6175140348474 -963000 ekin = 0.322938673952701 | erot = 0.494367337737219 | epot = -15.4348200465675 | etot = -14.6175140348776 -964000 ekin = 0.328038281530663 | erot = 0.494131108238372 | epot = -15.4396834246808 | etot = -14.6175140349117 -965000 ekin = 0.332909295682717 | erot = 0.49335475067624 | epot = -15.4437780813052 | etot = -14.6175140349462 -966000 ekin = 0.337299689762522 | erot = 0.491775167781797 | epot = -15.4465888925212 | etot = -14.6175140349769 -967000 ekin = 0.34103857432651 | erot = 0.489107134739221 | epot = -15.4476597440656 | etot = -14.6175140349998 -968000 ekin = 0.344058508086205 | erot = 0.485082040988229 | epot = -15.4466545840861 | etot = -14.6175140350116 -969000 ekin = 0.346406687226285 | erot = 0.479487053292109 | epot = -15.4434077755287 | etot = -14.6175140350103 -970000 ekin = 0.34824225995059 | erot = 0.472199376075301 | epot = -15.4379556710211 | etot = -14.6175140349952 -971000 ekin = 0.349818577908303 | erot = 0.463211040207767 | epot = -15.4305436530838 | etot = -14.6175140349677 -972000 ekin = 0.351451221504232 | erot = 0.452641107454375 | epot = -15.4216063638894 | etot = -14.6175140349308 -973000 ekin = 0.353474851841729 | erot = 0.440734047140837 | epot = -15.4117229338711 | etot = -14.6175140348885 -974000 ekin = 0.356193968986766 | erot = 0.427844962323539 | epot = -15.4015529661561 | etot = -14.6175140348458 -975000 ekin = 0.359834072253365 | erot = 0.414413971021917 | epot = -15.3917620780827 | etot = -14.6175140348075 -976000 ekin = 0.364500158165173 | erot = 0.400933139115753 | epot = -15.3829473320587 | etot = -14.6175140347778 -977000 ekin = 0.370148756532453 | erot = 0.387909813696966 | epot = -15.3755726049891 | etot = -14.6175140347597 -978000 ekin = 0.376577842833186 | erot = 0.375830059082977 | epot = -15.3699219366708 | etot = -14.6175140347546 -979000 ekin = 0.383436289100162 | erot = 0.365125297246737 | epot = -15.3660756211092 | etot = -14.6175140347623 -980000 ekin = 0.390251542223268 | erot = 0.356144397459458 | epot = -15.3639099744644 | etot = -14.6175140347817 -981000 ekin = 0.396471539317057 | erot = 0.349132547197909 | epot = -15.3631181213249 | etot = -14.61751403481 -982000 ekin = 0.401514997592997 | erot = 0.34421743579967 | epot = -15.3632464682369 | etot = -14.6175140348443 -983000 ekin = 0.404823458771299 | erot = 0.341402706416171 | epot = -15.363740200069 | etot = -14.6175140348815 -984000 ekin = 0.40590886668649 | erot = 0.340568324597754 | epot = -15.363991226203 | etot = -14.6175140349188 -985000 ekin = 0.404391803061251 | erot = 0.341477444720376 | epot = -15.3633832827353 | etot = -14.6175140349537 -986000 ekin = 0.400027422801557 | erot = 0.343789434461309 | epot = -15.3613308922472 | etot = -14.6175140349843 -987000 ekin = 0.39271818074518 | erot = 0.347078806738243 | epot = -15.3573110224926 | etot = -14.6175140350092 -988000 ekin = 0.382514239214593 | erot = 0.350859769146629 | epot = -15.3508880433885 | etot = -14.6175140350273 -989000 ekin = 0.369603726654222 | erot = 0.35461583718875 | epot = -15.3417335988805 | etot = -14.6175140350376 -990000 ekin = 0.354295674461627 | erot = 0.357833454087969 | epot = -15.3296431635889 | etot = -14.6175140350393 -991000 ekin = 0.336998529351739 | erot = 0.360037895318097 | epot = -15.3145504597016 | etot = -14.6175140350318 -992000 ekin = 0.318196763890777 | erot = 0.36082906519084 | epot = -15.2965398640959 | etot = -14.6175140350143 -993000 ekin = 0.298427479538935 | erot = 0.35991430308946 | epot = -15.2758558176151 | etot = -14.6175140349867 -994000 ekin = 0.278258203580379 | erot = 0.357135170965394 | epot = -15.2529074094949 | etot = -14.6175140349491 -995000 ekin = 0.258266471895333 | erot = 0.3524854802127 | epot = -15.2282659870102 | etot = -14.6175140349022 -996000 ekin = 0.239021351636219 | erot = 0.346118523027928 | epot = -15.2026539095113 | etot = -14.6175140348472 -997000 ekin = 0.221066818081282 | erot = 0.338342492442889 | epot = -15.1769233453103 | etot = -14.6175140347861 -998000 ekin = 0.204906835818327 | erot = 0.329604233509051 | epot = -15.1520251040489 | etot = -14.6175140347215 -999000 ekin = 0.190992053959175 | erot = 0.320462575794979 | epot = -15.1289686644105 | etot = -14.6175140346564 -1000000 ekin = 0.179708146665515 | erot = 0.311553394429263 | epot = -15.1087755756886 | etot = -14.6175140345938 - 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -0.00013590491 -Loop time of 22.0853 on 1 procs for 1000000 steps with 10 atoms - -Performance: 39120.988 tau/day, 45278.921 timesteps/s -99.6% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 17.818 | 17.818 | 17.818 | 0.0 | 80.68 -Bond | 0.67599 | 0.67599 | 0.67599 | 0.0 | 3.06 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.29087 | 0.29087 | 0.29087 | 0.0 | 1.32 -Output | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.00 -Modify | 2.8906 | 2.8906 | 2.8906 | 0.0 | 13.09 -Other | | 0.41 | | | 1.86 - -Nlocal: 10 ave 10 max 10 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 45 ave 45 max 45 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 45 -Ave neighs/atom = 4.5 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:22 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4 deleted file mode 100644 index 6ee77cb005..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.24Mar17.duplex1.g++.4 +++ /dev/null @@ -1,1167 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 1 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex1 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 10 atoms - reading velocities ... - 10 velocities - 10 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 8 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 2 = max # of 1-4 neighbors - 4 = max # of special neighbors - -set atom * mass 3.1575 - 10 settings made for mass - -group all type 1 4 -10 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -fix 1 all nve/dot -#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05 -1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342 -2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675 -3000 ekin = 0.0099503525964896 | erot = 0.0381961780846439 | epot = -14.6656605650904 | etot = -14.6175140344093 -4000 ekin = 0.0173418024861991 | erot = 0.0669935184860482 | epot = -14.7018493554381 | etot = -14.6175140344659 -5000 ekin = 0.0264109356285965 | erot = 0.102878288094483 | epot = -14.7468032582586 | etot = -14.6175140345355 -6000 ekin = 0.0368533113591267 | erot = 0.14504542056981 | epot = -14.7994127665446 | etot = -14.6175140346157 -7000 ekin = 0.0483200640564583 | erot = 0.192565862515414 | epot = -14.8583999612755 | etot = -14.6175140347036 -8000 ekin = 0.0604312317605635 | erot = 0.244417870131371 | epot = -14.9223631366881 | etot = -14.6175140347962 -9000 ekin = 0.072790711967127 | erot = 0.299521949931656 | epot = -14.9898266967887 | etot = -14.6175140348899 -10000 ekin = 0.0850022498874609 | erot = 0.356777997217668 | epot = -15.0592942820866 | etot = -14.6175140349815 -11000 ekin = 0.0966857134040954 | erot = 0.415102860829322 | epot = -15.1293026093009 | etot = -14.6175140350675 -12000 ekin = 0.107492790688356 | erot = 0.473466334177699 | epot = -15.1984731600111 | etot = -14.617514035145 -13000 ekin = 0.117121180381612 | erot = 0.530923485009329 | epot = -15.2655587006024 | etot = -14.6175140352115 -14000 ekin = 0.125326348459051 | erot = 0.586641324447251 | epot = -15.3294817081714 | etot = -14.6175140352651 -15000 ekin = 0.131930017119328 | erot = 0.63991810423422 | epot = -15.3893621566583 | etot = -14.6175140353048 -16000 ekin = 0.136824741331405 | erot = 0.690194029500566 | epot = -15.4445328061626 | etot = -14.6175140353306 -17000 ekin = 0.139974218116171 | erot = 0.737052866147306 | epot = -15.4945411196066 | etot = -14.6175140353432 -18000 ekin = 0.141409342139797 | erot = 0.780214750583043 | epot = -15.5391381280668 | etot = -14.617514035344 -19000 ekin = 0.141220424903361 | erot = 0.819521373491177 | epot = -15.5782558337298 | etot = -14.6175140353352 -20000 ekin = 0.139546371890511 | erot = 0.854915474127585 | epot = -15.6119758813374 | etot = -14.6175140353193 -21000 ekin = 0.136561897558541 | erot = 0.886417110947522 | epot = -15.6404930438047 | etot = -14.6175140352986 -22000 ekin = 0.132464002543684 | erot = 0.914099368829796 | epot = -15.6640774066492 | etot = -14.6175140352758 -23000 ekin = 0.127458921012898 | erot = 0.938065991541741 | epot = -15.6830389478072 | etot = -14.6175140352525 -24000 ekin = 0.121750582423396 | erot = 0.958432936326346 | epot = -15.6976975539803 | etot = -14.6175140352306 -25000 ekin = 0.115531361419039 | erot = 0.975315142931434 | epot = -15.7083605395612 | etot = -14.6175140352107 -26000 ekin = 0.108975565586195 | erot = 0.988819027952452 | epot = -15.715308628732 | etot = -14.6175140351934 -27000 ekin = 0.102235785319183 | erot = 0.999040485514706 | epot = -15.7187903060122 | etot = -14.6175140351783 -28000 ekin = 0.0954419434320554 | erot = 1.00606759141037 | epot = -15.7190235700075 | etot = -14.6175140351651 -29000 ekin = 0.0887026587346012 | erot = 1.00998681843686 | epot = -15.7162035123244 | etot = -14.6175140351529 -30000 ekin = 0.0821083868016836 | erot = 1.01089138149989 | epot = -15.7105138034423 | etot = -14.6175140351407 -31000 ekin = 0.0757357206090521 | erot = 1.00889031641421 | epot = -15.702140072151 | etot = -14.6175140351278 -32000 ekin = 0.0696522149391935 | erot = 1.00411701390103 | epot = -15.6912832639534 | etot = -14.6175140351132 -33000 ekin = 0.0639211300031737 | erot = 0.996736133736263 | epot = -15.6781712988358 | etot = -14.6175140350964 -34000 ekin = 0.0586055597942697 | erot = 0.986948071944207 | epot = -15.6630676668155 | etot = -14.617514035077 -35000 ekin = 0.0537715085522448 | erot = 0.974990414618501 | epot = -15.6462759582258 | etot = -14.617514035055 -36000 ekin = 0.0494895953267295 | erot = 0.961136064968264 | epot = -15.6281396953257 | etot = -14.6175140350307 -37000 ekin = 0.0458351949408502 | erot = 0.945687966087874 | epot = -15.6090371960337 | etot = -14.617514035005 -38000 ekin = 0.0428869588018996 | erot = 0.928970560853581 | epot = -15.5893715546342 | etot = -14.6175140349787 -39000 ekin = 0.0407237982125063 | erot = 0.911318339680438 | epot = -15.5695561728459 | etot = -14.617514034953 -40000 ekin = 0.0394205547756063 | erot = 0.893062038098217 | epot = -15.5499966278032 | etot = -14.6175140349294 -41000 ekin = 0.0390427256108178 | erot = 0.874513269991183 | epot = -15.5310700305113 | etot = -14.6175140349092 -42000 ekin = 0.0396407506458889 | erot = 0.855948622306388 | epot = -15.5131034078463 | etot = -14.617514034894 -43000 ekin = 0.0412444930542012 | erot = 0.837594480923648 | epot = -15.4963530088627 | etot = -14.6175140348848 -44000 ekin = 0.0438586280729573 | erot = 0.819614069272763 | epot = -15.4809867322283 | etot = -14.6175140348826 -45000 ekin = 0.0474596621514809 | erot = 0.802098297010425 | epot = -15.4670719940496 | etot = -14.6175140348876 -46000 ekin = 0.0519951857190001 | erot = 0.785061947877089 | epot = -15.4545711684958 | etot = -14.6175140348997 -47000 ekin = 0.0573856747188828 | erot = 0.768446392385995 | epot = -15.4433461020223 | etot = -14.6175140349174 -48000 ekin = 0.0635286843628562 | erot = 0.752129335015535 | epot = -15.433172054318 | etot = -14.6175140349396 -49000 ekin = 0.0703046735384702 | erot = 0.735941123250163 | epot = -15.4237598317528 | etot = -14.6175140349642 -50000 ekin = 0.0775831019852491 | erot = 0.719686007780774 | epot = -15.4147831447551 | etot = -14.6175140349891 -51000 ekin = 0.0852270843840623 | erot = 0.703165726694424 | epot = -15.4059068460916 | etot = -14.6175140350132 -52000 ekin = 0.0930950223446157 | erot = 0.686202231165621 | epot = -15.3968112885448 | etot = -14.6175140350346 -53000 ekin = 0.101038429252411 | erot = 0.668656546988554 | epot = -15.3872090112944 | etot = -14.6175140350534 -54000 ekin = 0.108896540979999 | erot = 0.65044172617409 | epot = -15.3768523022237 | etot = -14.6175140350696 -55000 ekin = 0.116489881625605 | erot = 0.631529329347953 | epot = -15.3655332460571 | etot = -14.6175140350836 -56000 ekin = 0.12361610349128 | erot = 0.611950383382754 | epot = -15.3530805219694 | etot = -14.6175140350954 -57000 ekin = 0.130051530400511 | erot = 0.591792721317636 | epot = -15.3393582868229 | etot = -14.6175140351047 -58000 ekin = 0.135560625192868 | erot = 0.571196690673809 | epot = -15.3242713509772 | etot = -14.6175140351105 -59000 ekin = 0.13991335082652 | erot = 0.550350463180971 | epot = -15.307777849119 | etot = -14.6175140351115 -60000 ekin = 0.142907875045205 | erot = 0.529485019663366 | epot = -15.2899069298149 | etot = -14.6175140351063 -61000 ekin = 0.144394224776987 | erot = 0.508867904999859 | epot = -15.2707761648709 | etot = -14.6175140350941 -62000 ekin = 0.14429400378525 | erot = 0.488794507593493 | epot = -15.2506025464535 | etot = -14.6175140350748 -63000 ekin = 0.142612256997681 | erot = 0.469576039422599 | epot = -15.2297023314693 | etot = -14.617514035049 -64000 ekin = 0.139439544726489 | erot = 0.451524344955609 | epot = -15.2084779247008 | etot = -14.6175140350187 -65000 ekin = 0.134944526553205 | erot = 0.434934714914789 | epot = -15.1873932764541 | etot = -14.6175140349861 -66000 ekin = 0.129359146357915 | erot = 0.42006860776795 | epot = -15.1669417890793 | etot = -14.6175140349534 -67000 ekin = 0.122959458763979 | erot = 0.407138362060406 | epot = -15.1476118557473 | etot = -14.6175140349229 -68000 ekin = 0.116045210525348 | erot = 0.396295631876791 | epot = -15.1298548772989 | etot = -14.6175140348967 -69000 ekin = 0.108920722072196 | erot = 0.387624589972286 | epot = -15.1140593469203 | etot = -14.6175140348758 -70000 ekin = 0.10187874072944 | erot = 0.381140173640969 | epot = -15.1005329492312 | etot = -14.6175140348608 -71000 ekin = 0.0951880561483024 | erot = 0.376791007701474 | epot = -15.0894930987017 | etot = -14.6175140348519 -72000 ekin = 0.0890849677261225 | erot = 0.374466237250124 | epot = -15.0810652398251 | etot = -14.6175140348489 -73000 ekin = 0.0837682427021172 | erot = 0.37400534759948 | epot = -15.0752876251526 | etot = -14.617514034851 -74000 ekin = 0.0793969849743902 | erot = 0.375210076750066 | epot = -15.0721210965819 | etot = -14.6175140348574 -75000 ekin = 0.0760907865069309 | erot = 0.377857644571635 | epot = -15.0714624659456 | etot = -14.617514034867 -76000 ekin = 0.073931583490861 | erot = 0.381714646754472 | epot = -15.073160265124 | etot = -14.6175140348787 -77000 ekin = 0.0729667273608691 | erot = 0.386551032955436 | epot = -15.0770317952076 | etot = -14.6175140348913 -78000 ekin = 0.0732128655080132 | erot = 0.392153586682573 | epot = -15.0828804870945 | etot = -14.6175140349039 -79000 ekin = 0.0746602878351816 | erot = 0.398338263928879 | epot = -15.0905125866795 | etot = -14.6175140349154 -80000 ekin = 0.0772774298946258 | erot = 0.404960669862598 | epot = -15.0997521346822 | etot = -14.617514034925 -81000 ekin = 0.0810152396747851 | erot = 0.411923913358685 | epot = -15.1104531879654 | etot = -14.617514034932 -82000 ekin = 0.0858111278281503 | erot = 0.419183131304765 | epot = -15.122508294069 | etot = -14.6175140349361 -83000 ekin = 0.0915922459207823 | erot = 0.426746154030485 | epot = -15.1358524348888 | etot = -14.6175140349375 -84000 ekin = 0.0982778862655832 | erot = 0.434670094582864 | epot = -15.1504620157849 | etot = -14.6175140349364 -85000 ekin = 0.105780875252437 | erot = 0.443054055542249 | epot = -15.1663489657283 | etot = -14.6175140349336 -86000 ekin = 0.114007936320836 | erot = 0.452028591870875 | epot = -15.1835505631216 | etot = -14.6175140349299 -87000 ekin = 0.122859117093393 | erot = 0.461742961599463 | epot = -15.2021161136192 | etot = -14.6175140349264 -88000 ekin = 0.132226490250757 | erot = 0.472351454261397 | epot = -15.2220919794359 | etot = -14.6175140349237 -89000 ekin = 0.141992430435586 | erot = 0.48400015022936 | epot = -15.243506615588 | etot = -14.6175140349231 -90000 ekin = 0.152027823849156 | erot = 0.496815313840275 | epot = -15.2663571726144 | etot = -14.617514034925 -91000 ekin = 0.162190574344531 | erot = 0.510894287760946 | epot = -15.2905988970356 | etot = -14.6175140349301 -92000 ekin = 0.172324730223634 | erot = 0.526299304076921 | epot = -15.3161380692392 | etot = -14.6175140349387 -93000 ekin = 0.182260479602882 | erot = 0.543054150884053 | epot = -15.3428286654374 | etot = -14.6175140349505 -94000 ekin = 0.19181516642483 | erot = 0.561143224560411 | epot = -15.3704724259507 | etot = -14.6175140349654 -95000 ekin = 0.200795384590157 | erot = 0.580512230413436 | epot = -15.398821649987 | etot = -14.6175140349834 -96000 ekin = 0.209000133284529 | erot = 0.601069706845066 | epot = -15.4275838751334 | etot = -14.6175140350038 -97000 ekin = 0.216224974983237 | erot = 0.62268863993255 | epot = -15.4564276499423 | etot = -14.6175140350265 -98000 ekin = 0.222267131485539 | erot = 0.6452076702458 | epot = -15.4849888367823 | etot = -14.617514035051 -99000 ekin = 0.226931474008825 | erot = 0.668431711039527 | epot = -15.5128772201251 | etot = -14.6175140350767 -100000 ekin = 0.230037392185109 | erot = 0.692132125756159 | epot = -15.5396835530446 | etot = -14.6175140351033 -101000 ekin = 0.231426538774162 | erot = 0.716046886548711 | epot = -15.5649874604531 | etot = -14.6175140351302 -102000 ekin = 0.230971416185847 | erot = 0.739881303910146 | epot = -15.5883667552525 | etot = -14.6175140351565 -103000 ekin = 0.228584676860608 | erot = 0.763309953364731 | epot = -15.6094086654068 | etot = -14.6175140351814 -104000 ekin = 0.224228843046253 | erot = 0.78598032692129 | epot = -15.6277232051714 | etot = -14.6175140352039 -105000 ekin = 0.217925953180068 | erot = 0.807518535459536 | epot = -15.6429585238624 | etot = -14.6175140352228 -106000 ekin = 0.209766205881383 | erot = 0.827537066837229 | epot = -15.6548173079557 | etot = -14.6175140352371 -107000 ekin = 0.199914663118832 | erot = 0.845644346598305 | epot = -15.6630730449629 | etot = -14.6175140352458 -108000 ekin = 0.188614735690438 | erot = 0.86145556230374 | epot = -15.6675843332424 | etot = -14.6175140352482 -109000 ekin = 0.176187061060969 | erot = 0.874603999194657 | epot = -15.6683050954996 | etot = -14.617514035244 -110000 ekin = 0.163022626611269 | erot = 0.884752084634178 | epot = -15.6652887464788 | etot = -14.6175140352334 -111000 ekin = 0.149569382110055 | erot = 0.891601400936344 | epot = -15.6586848182636 | etot = -14.6175140352172 -112000 ekin = 0.136312261124298 | erot = 0.894901120601569 | epot = -15.6487274169225 | etot = -14.6175140351967 -113000 ekin = 0.123747404857111 | erot = 0.894454602034433 | epot = -15.635716042065 | etot = -14.6175140351735 -114000 ekin = 0.112352324429236 | erot = 0.89012419645392 | epot = -15.6199905560327 | etot = -14.6175140351496 -115000 ekin = 0.102554569787019 | erot = 0.881834585428133 | epot = -15.601903190342 | etot = -14.6175140351268 -116000 ekin = 0.094702004709198 | erot = 0.869575126615747 | epot = -15.5817911664316 | etot = -14.6175140351067 -117000 ekin = 0.0890378681933156 | erot = 0.853401690495617 | epot = -15.5599535937792 | etot = -14.6175140350902 -118000 ekin = 0.0856833736304911 | erot = 0.833438318820653 | epot = -15.536635727529 | etot = -14.6175140350778 -119000 ekin = 0.0846297171115028 | erot = 0.809878764033866 | epot = -15.5120225162146 | etot = -14.6175140350693 -120000 ekin = 0.0857402026933537 | erot = 0.782987649503194 | epot = -15.4862418872603 | etot = -14.6175140350638 -121000 ekin = 0.0887619781646647 | erot = 0.753100709617513 | epot = -15.4593767228421 | etot = -14.61751403506 -122000 ekin = 0.0933458418333701 | erot = 0.720623403983765 | epot = -15.4314832808735 | etot = -14.6175140350564 -123000 ekin = 0.0990718975136712 | erot = 0.686027198351099 | epot = -15.4026131309163 | etot = -14.6175140350515 -124000 ekin = 0.10547856753477 | erot = 0.649842971568616 | epot = -15.3728355741476 | etot = -14.6175140350442 -125000 ekin = 0.112092583657157 | erot = 0.612651306911466 | epot = -15.3422579256018 | etot = -14.6175140350331 -126000 ekin = 0.118457948669929 | erot = 0.575069793126885 | epot = -15.3110417768148 | etot = -14.6175140350179 -127000 ekin = 0.12416235209736 | erot = 0.537737821904032 | epot = -15.2794142089994 | etot = -14.617514034998 -128000 ekin = 0.12886000047466 | erot = 0.50129966007338 | epot = -15.2476736955216 | etot = -14.6175140349735 -129000 ekin = 0.132290197680968 | erot = 0.466386755141928 | epot = -15.2161909877676 | etot = -14.6175140349447 -130000 ekin = 0.134291248322799 | erot = 0.433600287194598 | epot = -15.1854055704295 | etot = -14.6175140349121 -131000 ekin = 0.134809368078731 | erot = 0.403494917850824 | epot = -15.1558183208059 | etot = -14.6175140348763 -132000 ekin = 0.133902311412609 | erot = 0.376564532721137 | epot = -15.1279808789722 | etot = -14.6175140348384 -133000 ekin = 0.131737425949523 | erot = 0.35323055944927 | epot = -15.102482020198 | etot = -14.6175140347992 -134000 ekin = 0.128583872249503 | erot = 0.333833200744645 | epot = -15.0799311077543 | etot = -14.6175140347601 -135000 ekin = 0.124798858318881 | erot = 0.318625678761018 | epot = -15.0609385718023 | etot = -14.6175140347224 -136000 ekin = 0.120807966950657 | erot = 0.307771366705204 | epot = -15.0460933683435 | etot = -14.6175140346876 -137000 ekin = 0.117080018573046 | erot = 0.301343503849178 | epot = -15.0359375570798 | etot = -14.6175140346576 -138000 ekin = 0.11409740445119 | erot = 0.299327064918184 | epot = -15.0309385040035 | etot = -14.6175140346342 -139000 ekin = 0.112323403877017 | erot = 0.30162229304682 | epot = -15.0314597315429 | etot = -14.6175140346191 -140000 ekin = 0.112168587316825 | erot = 0.308049410073269 | epot = -15.0377320320041 | etot = -14.617514034614 -141000 ekin = 0.113958896787242 | erot = 0.318354084563179 | epot = -15.0498270159708 | etot = -14.6175140346204 -142000 ekin = 0.117908250109871 | erot = 0.332213334114279 | epot = -15.0676356188632 | etot = -14.6175140346391 -143000 ekin = 0.124098500240005 | erot = 0.349241744869171 | epot = -15.0908542797795 | etot = -14.6175140346704 -144000 ekin = 0.132469049162189 | erot = 0.368998042344344 | epot = -15.1189811262203 | etot = -14.6175140347138 -145000 ekin = 0.142817534773286 | erot = 0.390992018433719 | epot = -15.1513235879751 | etot = -14.6175140347681 -146000 ekin = 0.154812002594074 | erot = 0.414692148539669 | epot = -15.1870181859652 | etot = -14.6175140348314 -147000 ekin = 0.168013608208222 | erot = 0.439534147564146 | epot = -15.2250617906734 | etot = -14.617514034901 -148000 ekin = 0.181907755044263 | erot = 0.464930715993231 | epot = -15.2643525060114 | etot = -14.617514034974 -149000 ekin = 0.195940689918476 | erot = 0.490282644231627 | epot = -15.303737369197 | etot = -14.6175140350469 -150000 ekin = 0.209558115498224 | erot = 0.514991307803342 | epot = -15.3420634584183 | etot = -14.6175140351167 -151000 ekin = 0.222242375358764 | erot = 0.538472447670959 | epot = -15.37822885821 | etot = -14.6175140351803 -152000 ekin = 0.233545181100908 | erot = 0.560170967505261 | epot = -15.4112301838413 | etot = -14.6175140352351 -153000 ekin = 0.243113638171877 | erot = 0.579575715964384 | epot = -15.4402033894153 | etot = -14.6175140352791 -154000 ekin = 0.250708030719506 | erot = 0.596234520730852 | epot = -15.4644565867613 | etot = -14.617514035311 -155000 ekin = 0.256210874594867 | erot = 0.60976818504912 | epot = -15.4834930949737 | etot = -14.6175140353297 -156000 ekin = 0.259627463842678 | erot = 0.619882772314523 | epot = -15.4970242714926 | etot = -14.6175140353354 -157000 ekin = 0.261078756733762 | erot = 0.626379517381851 | epot = -15.5049723094439 | etot = -14.6175140353283 -158000 ekin = 0.260787877594799 | erot = 0.629161788909728 | epot = -15.5074637018138 | etot = -14.6175140353093 -159000 ekin = 0.259061752299363 | erot = 0.628238692725143 | epot = -15.5048144803044 | etot = -14.6175140352799 -160000 ekin = 0.256269476947947 | erot = 0.623725097357694 | epot = -15.4975086095473 | etot = -14.6175140352416 -161000 ekin = 0.252818974262676 | erot = 0.615838055764808 | epot = -15.486171065224 | etot = -14.6175140351965 -162000 ekin = 0.249133354780831 | erot = 0.604889772113657 | epot = -15.471537162041 | etot = -14.6175140351465 -163000 ekin = 0.245628201594069 | erot = 0.591277407065719 | epot = -15.4544196437535 | etot = -14.6175140350937 -164000 ekin = 0.242690765770497 | erot = 0.575470125399849 | epot = -15.4356749262106 | etot = -14.6175140350402 -165000 ekin = 0.240661818237638 | erot = 0.557993868663582 | epot = -15.4161697218892 | etot = -14.617514034988 -166000 ekin = 0.239820672159809 | erot = 0.53941438884916 | epot = -15.3967490959478 | etot = -14.6175140349388 -167000 ekin = 0.240373682616981 | erot = 0.520319112884548 | epot = -15.3782068303959 | etot = -14.6175140348944 -168000 ekin = 0.24244635767337 | erot = 0.501298426047094 | epot = -15.3612588185766 | etot = -14.6175140348562 -169000 ekin = 0.246079081489486 | erot = 0.482926967022081 | epot = -15.3465200833369 | etot = -14.6175140348253 -170000 ekin = 0.251226355670601 | erot = 0.465745518941346 | epot = -15.3344859094148 | etot = -14.6175140348028 -171000 ekin = 0.257759407502439 | erot = 0.450244072412675 | epot = -15.3255175147044 | etot = -14.6175140347893 -172000 ekin = 0.265471962314995 | erot = 0.43684655757276 | epot = -15.3198325546728 | etot = -14.617514034785 -173000 ekin = 0.274088992052566 | erot = 0.425897760802307 | epot = -15.317500787645 | etot = -14.6175140347901 -174000 ekin = 0.283278228107989 | erot = 0.417652965987653 | epot = -15.3184452288998 | etot = -14.6175140348041 -175000 ekin = 0.292664164217049 | erot = 0.41227065206718 | epot = -15.3224488511106 | etot = -14.6175140348264 -176000 ekin = 0.301844276743974 | erot = 0.409808663993543 | epot = -15.3291669755933 | etot = -14.6175140348558 -177000 ekin = 0.310407103277722 | erot = 0.410224178773613 | epot = -15.338145316942 | etot = -14.6175140348907 -178000 ekin = 0.317951707448459 | erot = 0.413377690533319 | epot = -15.3488434329112 | etot = -14.6175140349295 -179000 ekin = 0.324107901131331 | erot = 0.419041092199345 | epot = -15.3606630283007 | etot = -14.61751403497 -180000 ekin = 0.328556397748226 | erot = 0.426909726007329 | epot = -15.3729801587658 | etot = -14.6175140350103 -181000 ekin = 0.331047834153872 | erot = 0.436618006902467 | epot = -15.3851798761041 | etot = -14.6175140350478 -182000 ekin = 0.331419420114469 | erot = 0.447757936314679 | epot = -15.3966913915095 | etot = -14.6175140350803 -183000 ekin = 0.32960779233749 | erot = 0.459899520065503 | epot = -15.4070213475091 | etot = -14.6175140351061 -184000 ekin = 0.325656516855028 | erot = 0.472611792133139 | epot = -15.4157823441118 | etot = -14.6175140351236 -185000 ekin = 0.319716934487211 | erot = 0.485483030927449 | epot = -15.4227140005469 | etot = -14.6175140351322 -186000 ekin = 0.312041347782212 | erot = 0.498138700398001 | epot = -15.4276940833121 | etot = -14.6175140351319 -187000 ekin = 0.302968200961153 | erot = 0.510255791848845 | epot = -15.4307380279334 | etot = -14.6175140351234 -188000 ekin = 0.292899787356355 | erot = 0.5215725520513 | epot = -15.4319863745157 | etot = -14.6175140351081 -189000 ekin = 0.282274048055605 | erot = 0.531893031493143 | epot = -15.4316811146372 | etot = -14.6175140350884 -190000 ekin = 0.271533034588949 | erot = 0.541086413296656 | epot = -15.4301334829521 | etot = -14.6175140350665 -191000 ekin = 0.261091384545176 | erot = 0.549081610185661 | epot = -15.4276870297757 | etot = -14.6175140350448 -192000 ekin = 0.251308489707993 | erot = 0.555858063434326 | epot = -15.4246805881679 | etot = -14.6175140350256 -193000 ekin = 0.242467771119499 | erot = 0.561433978654792 | epot = -15.4214157847846 | etot = -14.6175140350103 -194000 ekin = 0.234765581624083 | erot = 0.565853352187983 | epot = -15.4181329688119 | etot = -14.6175140349998 -195000 ekin = 0.228310848060933 | erot = 0.569173077812972 | epot = -15.414997960868 | etot = -14.6175140349941 -196000 ekin = 0.223134890549791 | erot = 0.571451208607789 | epot = -15.4121001341501 | etot = -14.6175140349925 -197000 ekin = 0.219209242155479 | erot = 0.572737138234515 | epot = -15.4094604153842 | etot = -14.6175140349942 -198000 ekin = 0.216468062808567 | erot = 0.573064123809139 | epot = -15.4070462216157 | etot = -14.6175140349979 -199000 ekin = 0.214831137522102 | erot = 0.572444258405115 | epot = -15.4047894309295 | etot = -14.6175140350023 -200000 ekin = 0.214223573901692 | erot = 0.570865760664587 | epot = -15.402603369573 | etot = -14.6175140350067 -201000 ekin = 0.214589119166338 | erot = 0.568292309388425 | epot = -15.4003954635655 | etot = -14.6175140350107 -202000 ekin = 0.215895325601886 | erot = 0.564664121435213 | epot = -15.3980734820515 | etot = -14.6175140350144 -203000 ekin = 0.218130347569574 | erot = 0.559900543320399 | epot = -15.3955449259083 | etot = -14.6175140350184 -204000 ekin = 0.221292667473328 | erot = 0.553904074219809 | epot = -15.3927107767163 | etot = -14.6175140350232 -205000 ekin = 0.225376258610291 | erot = 0.546565915590086 | epot = -15.3894562092301 | etot = -14.6175140350297 -206000 ekin = 0.230354397528691 | erot = 0.537773288685104 | epot = -15.3856417212522 | etot = -14.6175140350384 -207000 ekin = 0.236165428414371 | erot = 0.527418806931578 | epot = -15.381098270395 | etot = -14.617514035049 -208000 ekin = 0.242703261860097 | erot = 0.515412077176742 | epot = -15.3756293740978 | etot = -14.617514035061 -209000 ekin = 0.249814382549771 | erot = 0.501693407692904 | epot = -15.3690218253158 | etot = -14.6175140350732 -210000 ekin = 0.257301864855487 | erot = 0.486249049966601 | epot = -15.3610649499058 | etot = -14.6175140350838 -211000 ekin = 0.264935635394205 | erot = 0.469126912721255 | epot = -15.3515765832064 | etot = -14.6175140350909 -212000 ekin = 0.272467183646432 | erot = 0.450451153648385 | epot = -15.3404323723875 | etot = -14.6175140350927 -213000 ekin = 0.279646306736913 | erot = 0.43043370267778 | epot = -15.3275940445023 | etot = -14.6175140350876 -214000 ekin = 0.2862376112769 | erot = 0.409381288017335 | epot = -15.3131329343688 | etot = -14.6175140350746 -215000 ekin = 0.292034643872931 | erot = 0.387696263733716 | epot = -15.29724494266 | etot = -14.6175140350534 -216000 ekin = 0.296870258153004 | erot = 0.365870567410597 | epot = -15.2802548605881 | etot = -14.6175140350245 -217000 ekin = 0.300622666325324 | erot = 0.344472695101548 | epot = -15.2626093964159 | etot = -14.617514034989 -218000 ekin = 0.303217269541565 | erot = 0.324128407396833 | epot = -15.2448597118871 | etot = -14.6175140349487 -219000 ekin = 0.30462484391226 | erot = 0.305496496150472 | epot = -15.2276353749682 | etot = -14.6175140349055 -220000 ekin = 0.304856982074418 | erot = 0.28924122167423 | epot = -15.2116122386105 | etot = -14.6175140348619 -221000 ekin = 0.303959749544728 | erot = 0.276003133760621 | epot = -15.1974769181254 | etot = -14.61751403482 -222000 ekin = 0.302006434071344 | erot = 0.266369862263784 | epot = -15.1858903311172 | etot = -14.6175140347821 -223000 ekin = 0.299090105491097 | erot = 0.260848208952983 | epot = -15.1774523491944 | etot = -14.6175140347503 -224000 ekin = 0.295316503745814 | erot = 0.259838588555869 | epot = -15.172669127028 | etot = -14.6175140347263 -225000 ekin = 0.290797600318129 | erot = 0.263612591734552 | epot = -15.1719242267643 | etot = -14.6175140347116 -226000 ekin = 0.285646103233329 | erot = 0.272294318079252 | epot = -15.1754544560199 | etot = -14.6175140347073 -227000 ekin = 0.27997101868972 | erot = 0.285846075010759 | epot = -15.1833311284149 | etot = -14.6175140347144 -228000 ekin = 0.273874374728189 | erot = 0.30405906911905 | epot = -15.1954474785805 | etot = -14.6175140347332 -229000 ekin = 0.267449174160499 | erot = 0.326549807965651 | epot = -15.2115130168897 | etot = -14.6175140347636 -230000 ekin = 0.260778614119454 | erot = 0.352763004039823 | epot = -15.2310556529641 | etot = -14.6175140348048 -231000 ekin = 0.253936564977397 | erot = 0.381981763344756 | epot = -15.2534323631777 | etot = -14.6175140348555 -232000 ekin = 0.246989230842658 | erot = 0.413345683736729 | epot = -15.2778489494936 | etot = -14.6175140349142 -233000 ekin = 0.239997814735999 | erot = 0.445877135783826 | epot = -15.3033889854983 | etot = -14.6175140349785 -234000 ekin = 0.233021891669954 | erot = 0.478515439398985 | epot = -15.3290513661143 | etot = -14.6175140350454 -235000 ekin = 0.226123071286447 | erot = 0.510157919201476 | epot = -15.3537950255997 | etot = -14.6175140351118 -236000 ekin = 0.219368436952772 | erot = 0.539706010633882 | epot = -15.3765884827611 | etot = -14.6175140351745 -237000 ekin = 0.212833212708605 | erot = 0.566113832023257 | epot = -15.3964610799619 | etot = -14.61751403523 -238000 ekin = 0.206602165162868 | erot = 0.588436180449293 | epot = -15.4125523808878 | etot = -14.6175140352756 -239000 ekin = 0.200769360307751 | erot = 0.605872583258375 | epot = -15.4241559788754 | etot = -14.6175140353093 -240000 ekin = 0.195436190928629 | erot = 0.617803458377821 | epot = -15.4307536846357 | etot = -14.6175140353292 -241000 ekin = 0.190707920284747 | erot = 0.623817360380854 | epot = -15.4320393160006 | etot = -14.617514035335 -242000 ekin = 0.186689132524139 | erot = 0.623726737659663 | epot = -15.4279299055104 | etot = -14.6175140353266 -243000 ekin = 0.183478880874974 | erot = 0.617571857376276 | epot = -15.4185647735561 | etot = -14.6175140353049 -244000 ekin = 0.18116616676021 | erot = 0.605612923712308 | epot = -15.4042931257437 | etot = -14.6175140352712 -245000 ekin = 0.179826690516149 | erot = 0.588311983397651 | epot = -15.3856527091413 | etot = -14.6175140352275 -246000 ekin = 0.17952147334509 | erot = 0.566306329739293 | epot = -15.3633418382601 | etot = -14.6175140351757 -247000 ekin = 0.180297726609518 | erot = 0.540375528723556 | epot = -15.3381872904514 | etot = -14.6175140351183 -248000 ekin = 0.182192022181396 | erot = 0.511404282991674 | epot = -15.3111103402302 | etot = -14.6175140350572 -249000 ekin = 0.185235475059317 | erot = 0.480343275337862 | epot = -15.2830927853916 | etot = -14.6175140349945 -250000 ekin = 0.189460324578836 | erot = 0.448169956262068 | epot = -15.255144315773 | etot = -14.6175140349321 -251000 ekin = 0.194907020012373 | erot = 0.415851007132876 | epot = -15.228272062017 | etot = -14.6175140348717 -252000 ekin = 0.201630699423839 | erot = 0.384307951122292 | epot = -15.2034526853611 | etot = -14.617514034815 -253000 ekin = 0.20970581525618 | erot = 0.354387113740114 | epot = -15.1816069637594 | etot = -14.6175140347631 -254000 ekin = 0.219227629547435 | erot = 0.326834860919777 | epot = -15.1635765251848 | etot = -14.6175140347176 -255000 ekin = 0.230309407957435 | erot = 0.302278768995732 | epot = -15.1501022116327 | etot = -14.6175140346795 -256000 ekin = 0.243074422922269 | erot = 0.281215109558699 | epot = -15.141803567131 | etot = -14.61751403465 -257000 ekin = 0.257642364630155 | erot = 0.264002762946071 | epot = -15.1391591622066 | etot = -14.6175140346303 -258000 ekin = 0.27411046110411 | erot = 0.250863404057696 | epot = -15.1424878997833 | etot = -14.6175140346215 -259000 ekin = 0.292530483429778 | erot = 0.241887528333028 | epot = -15.1519320463872 | etot = -14.6175140346244 -260000 ekin = 0.312883750215132 | erot = 0.23704560099139 | epot = -15.1674433858462 | etot = -14.6175140346397 -261000 ekin = 0.335057071666337 | erot = 0.236203324625287 | epot = -15.1887744309592 | etot = -14.6175140346676 -262000 ekin = 0.358823075933478 | erot = 0.239139750884219 | epot = -15.2154768615253 | etot = -14.6175140347076 -263000 ekin = 0.383828346059002 | erot = 0.245566753569579 | epot = -15.2469091343872 | etot = -14.6175140347586 -264000 ekin = 0.409592161639953 | erot = 0.255148290958821 | epot = -15.2822544874178 | etot = -14.617514034819 -265000 ekin = 0.435517425640971 | erot = 0.267517972446788 | epot = -15.3205494329742 | etot = -14.6175140348864 -266000 ekin = 0.460913759434669 | erot = 0.282293742227945 | epot = -15.3607215366204 | etot = -14.6175140349578 -267000 ekin = 0.485031075313803 | erot = 0.299088986461064 | epot = -15.4016340968052 | etot = -14.6175140350303 -268000 ekin = 0.50710051747369 | erot = 0.317519986656959 | epot = -15.4421345392314 | etot = -14.6175140351007 -269000 ekin = 0.526378761163567 | erot = 0.337210258003277 | epot = -15.481103054333 | etot = -14.6175140351661 -270000 ekin = 0.542191399557179 | erot = 0.357792786170331 | epot = -15.5174982209515 | etot = -14.617514035224 -271000 ekin = 0.55397150127531 | erot = 0.37891139471306 | epot = -15.5503969312606 | etot = -14.6175140352722 -272000 ekin = 0.561290243476898 | erot = 0.40022238743361 | epot = -15.5790266662199 | etot = -14.6175140353094 -273000 ekin = 0.563877614617904 | erot = 0.42139725004376 | epot = -15.6027888999963 | etot = -14.6175140353346 -274000 ekin = 0.561632338447624 | erot = 0.44212667165534 | epot = -15.6212730454506 | etot = -14.6175140353476 -275000 ekin = 0.554621238224451 | erot = 0.462125606775406 | epot = -15.6342608803486 | etot = -14.6175140353487 -276000 ekin = 0.543069132887202 | erot = 0.481138682331976 | epot = -15.6417218505579 | etot = -14.6175140353387 -277000 ekin = 0.527340979965708 | erot = 0.498945052082867 | epot = -15.6438000673675 | etot = -14.6175140353189 -278000 ekin = 0.50791833721729 | erot = 0.515361832413215 | epot = -15.6407942049214 | etot = -14.6175140352909 -279000 ekin = 0.485372319601928 | erot = 0.530245473601801 | epot = -15.6331318284601 | etot = -14.6175140352564 -280000 ekin = 0.460335116506523 | erot = 0.543490744711177 | epot = -15.6213398964351 | etot = -14.6175140352174 -281000 ekin = 0.433471859960465 | erot = 0.555027349456908 | epot = -15.6060132445935 | etot = -14.6175140351761 -282000 ekin = 0.405454262480516 | erot = 0.56481448000714 | epot = -15.5877827776223 | etot = -14.6175140351346 -283000 ekin = 0.376937038993425 | erot = 0.572833827993367 | epot = -15.5672849020813 | etot = -14.6175140350945 -284000 ekin = 0.34853774796245 | erot = 0.57908171193117 | epot = -15.5451334949501 | etot = -14.6175140350565 -285000 ekin = 0.320820372083186 | erot = 0.583561068647179 | epot = -15.5218954757531 | etot = -14.6175140350227 -286000 ekin = 0.294282726921471 | erot = 0.586274110946644 | epot = -15.4980708728619 | etot = -14.6175140349938 -287000 ekin = 0.269347634013377 | erot = 0.587216475910743 | epot = -15.4740781448946 | etot = -14.6175140349705 -288000 ekin = 0.24635770446757 | erot = 0.586373659773426 | epot = -15.450245399194 | etot = -14.6175140349531 -289000 ekin = 0.22557352214574 | erot = 0.583720426232605 | epot = -15.4268079833199 | etot = -14.6175140349415 -290000 ekin = 0.2071749628185 | erot = 0.579223657449731 | epot = -15.4039126552032 | etot = -14.6175140349349 -291000 ekin = 0.191265313940318 | erot = 0.572848780864004 | epot = -15.3816281297367 | etot = -14.6175140349324 -292000 ekin = 0.177877757396561 | erot = 0.564569470033125 | epot = -15.3599612623625 | etot = -14.6175140349328 -293000 ekin = 0.166983649288562 | erot = 0.554379837682064 | epot = -15.3388775219052 | etot = -14.6175140349346 -294000 ekin = 0.158501898150816 | erot = 0.542307895558441 | epot = -15.3183238286455 | etot = -14.6175140349363 -295000 ekin = 0.152308641379775 | erot = 0.528428741575586 | epot = -15.2982514178919 | etot = -14.6175140349366 -296000 ekin = 0.148246390134261 | erot = 0.512875830575391 | epot = -15.278636255644 | etot = -14.6175140349344 -297000 ekin = 0.146131889948849 | erot = 0.495848833633677 | epot = -15.2594947585116 | etot = -14.6175140349291 -298000 ekin = 0.145762142540935 | erot = 0.477616979343651 | epot = -15.2408931568052 | etot = -14.6175140349206 -299000 ekin = 0.146918339842694 | erot = 0.45851732797416 | epot = -15.2229497027261 | etot = -14.6175140349092 -300000 ekin = 0.149367830718072 | erot = 0.438948042711665 | epot = -15.2058299083253 | etot = -14.6175140348956 -301000 ekin = 0.152864610234037 | erot = 0.419357266833116 | epot = -15.1897359119478 | etot = -14.6175140348806 -302000 ekin = 0.157149122640173 | erot = 0.400228590597456 | epot = -15.1748917481032 | etot = -14.6175140348656 -303000 ekin = 0.161948347719037 | erot = 0.382064246006854 | epot = -15.1615266285773 | etot = -14.6175140348514 -304000 ekin = 0.166977167327442 | erot = 0.365367110078576 | epot = -15.1498583122451 | etot = -14.617514034839 -305000 ekin = 0.171941885875878 | erot = 0.350622387001197 | epot = -15.1400783077066 | etot = -14.6175140348295 -306000 ekin = 0.17654652269687 | erot = 0.338279561363739 | epot = -15.1323401188837 | etot = -14.6175140348231 -307000 ekin = 0.180502080572199 | erot = 0.328734935091342 | epot = -15.126751050484 | etot = -14.6175140348204 -308000 ekin = 0.183539117579255 | erot = 0.322315068517902 | epot = -15.1233682209184 | etot = -14.6175140348212 -309000 ekin = 0.185422589168818 | erot = 0.319261135180292 | epot = -15.1221977591747 | etot = -14.6175140348256 -310000 ekin = 0.185968382525486 | erot = 0.319714556777639 | epot = -15.1231969741363 | etot = -14.6175140348331 -311000 ekin = 0.185060444471757 | erot = 0.323704474532877 | epot = -15.1262789538481 | etot = -14.6175140348434 -312000 ekin = 0.182667055699906 | erot = 0.331137883754682 | epot = -15.1313189743106 | etot = -14.617514034856 -313000 ekin = 0.178854671448125 | erot = 0.341793554574352 | epot = -15.1381622608927 | etot = -14.6175140348702 -314000 ekin = 0.173797674113312 | erot = 0.355321045101953 | epot = -15.1466327541008 | etot = -14.6175140348856 -315000 ekin = 0.167782440685997 | erot = 0.371246117950235 | epot = -15.1565425935375 | etot = -14.6175140349012 -316000 ekin = 0.161204347699341 | erot = 0.388983636698412 | epot = -15.1677020193143 | etot = -14.6175140349165 -317000 ekin = 0.154556738723005 | erot = 0.407858516721223 | epot = -15.179929290375 | etot = -14.6175140349308 -318000 ekin = 0.148411457828021 | erot = 0.427134549771537 | epot = -15.1930600425428 | etot = -14.6175140349433 -319000 ekin = 0.143391260343281 | erot = 0.446049980956607 | epot = -15.2069552762534 | etot = -14.6175140349535 -320000 ekin = 0.140135163879396 | erot = 0.463857713006752 | epot = -15.2215069118476 | etot = -14.6175140349615 -321000 ekin = 0.139258496830827 | erot = 0.479867117343613 | epot = -15.2366396491415 | etot = -14.6175140349671 -322000 ekin = 0.141309963686793 | erot = 0.493483840953768 | epot = -15.2523078396114 | etot = -14.6175140349709 -323000 ekin = 0.146728465402056 | erot = 0.504243890594794 | epot = -15.2684863909708 | etot = -14.6175140349739 -324000 ekin = 0.155802740978481 | erot = 0.511838753068078 | epot = -15.285155529024 | etot = -14.6175140349775 -325000 ekin = 0.168637192339767 | erot = 0.516129344219425 | epot = -15.3022805715425 | etot = -14.6175140349833 -326000 ekin = 0.185127492740946 | erot = 0.517147991936385 | epot = -15.3197895196698 | etot = -14.6175140349924 -327000 ekin = 0.204949583925484 | erot = 0.51508915511157 | epot = -15.3375527740431 | etot = -14.6175140350061 -328000 ekin = 0.227565145376643 | erot = 0.510290835144336 | epot = -15.3553700155452 | etot = -14.6175140350242 -329000 ekin = 0.252245305622049 | erot = 0.503209396460757 | epot = -15.372968737129 | etot = -14.6175140350462 -330000 ekin = 0.278112223739094 | erot = 0.494390678507019 | epot = -15.3900169373162 | etot = -14.6175140350701 -331000 ekin = 0.304195517645128 | erot = 0.48443992761456 | epot = -15.4061494803532 | etot = -14.6175140350935 -332000 ekin = 0.329497983392816 | erot = 0.473992405219049 | epot = -15.4210044237254 | etot = -14.6175140351136 -333000 ekin = 0.353063353198652 | erot = 0.463685785195841 | epot = -15.4342631735224 | etot = -14.6175140351279 -334000 ekin = 0.374038491016672 | erot = 0.454134842083235 | epot = -15.4456873682343 | etot = -14.6175140351344 -335000 ekin = 0.391723520500374 | erot = 0.445908562625435 | epot = -15.4551461182583 | etot = -14.6175140351325 -336000 ekin = 0.405605581598632 | erot = 0.439509690040463 | epot = -15.4626293067615 | etot = -14.6175140351224 -337000 ekin = 0.415374601838237 | erot = 0.435356764652333 | epot = -15.4682454015957 | etot = -14.6175140351051 -338000 ekin = 0.420921997010151 | erot = 0.433768862195292 | epot = -15.4722048942882 | etot = -14.6175140350828 -339000 ekin = 0.422325110447546 | erot = 0.43495337621205 | epot = -15.4747925217174 | etot = -14.6175140350578 -340000 ekin = 0.419821259880477 | erot = 0.438997304560058 | epot = -15.4763325994731 | etot = -14.6175140350326 -341000 ekin = 0.413775534581175 | erot = 0.44586257358568 | epot = -15.4771521431765 | etot = -14.6175140350096 -342000 ekin = 0.404646174020876 | erot = 0.455385967573906 | epot = -15.4775461765857 | etot = -14.6175140349909 -343000 ekin = 0.392950705832838 | erot = 0.467284215126923 | epot = -15.4777489559374 | etot = -14.6175140349776 -344000 ekin = 0.379235231728912 | erot = 0.481164689425971 | epot = -15.4779139561254 | etot = -14.6175140349705 -345000 ekin = 0.364048459933183 | erot = 0.496541967294209 | epot = -15.4781044621969 | etot = -14.6175140349695 -346000 ekin = 0.347921358320347 | erot = 0.512860132815035 | epot = -15.478295526109 | etot = -14.6175140349736 -347000 ekin = 0.331352665808157 | erot = 0.529520204053152 | epot = -15.4783869048429 | etot = -14.6175140349816 -348000 ekin = 0.314799955036598 | erot = 0.545911447469195 | epot = -15.4782254374972 | etot = -14.6175140349914 -349000 ekin = 0.298675493175313 | erot = 0.561444708834118 | epot = -15.4776342370104 | etot = -14.617514035001 -350000 ekin = 0.283345815520902 | erot = 0.575585348316022 | epot = -15.4764451988451 | etot = -14.6175140350082 -351000 ekin = 0.269133730327555 | erot = 0.587883045339148 | epot = -15.474530810678 | etot = -14.6175140350113 -352000 ekin = 0.256321431305235 | erot = 0.597995738138075 | epot = -15.4718312044524 | etot = -14.6175140350091 -353000 ekin = 0.245153509654402 | erot = 0.605705335206248 | epot = -15.4683728798615 | etot = -14.6175140350009 -354000 ekin = 0.235838910986199 | erot = 0.610923562934513 | epot = -15.4642765089078 | etot = -14.6175140349871 -355000 ekin = 0.228551231300299 | erot = 0.613687305425488 | epot = -15.4597525716945 | etot = -14.6175140349687 -356000 ekin = 0.223427131306872 | erot = 0.614143902824619 | epot = -15.4550850690789 | etot = -14.6175140349474 -357000 ekin = 0.220563006917723 | erot = 0.612527933401769 | epot = -15.4506049752447 | etot = -14.6175140349252 -358000 ekin = 0.220010333197538 | erot = 0.60913185554413 | epot = -15.4466562236462 | etot = -14.6175140349045 -359000 ekin = 0.221770268739923 | erot = 0.604273418957614 | epot = -15.4435577225855 | etot = -14.6175140348879 -360000 ekin = 0.225788163653265 | erot = 0.59826292557133 | epot = -15.4415651241022 | etot = -14.6175140348776 -361000 ekin = 0.231948578437353 | erot = 0.591373251984939 | epot = -15.4408358652976 | etot = -14.6175140348753 -362000 ekin = 0.240071331018014 | erot = 0.583815109039721 | epot = -15.4414004749402 | etot = -14.6175140348825 -363000 ekin = 0.249908988057748 | erot = 0.575719406612921 | epot = -15.4431424295704 | etot = -14.6175140348997 -364000 ekin = 0.261146140581928 | erot = 0.567127906486825 | epot = -15.4457880819959 | etot = -14.6175140349271 -365000 ekin = 0.273400773645737 | erot = 0.557992653605887 | epot = -15.4489074622157 | etot = -14.6175140349641 -366000 ekin = 0.286228056503698 | erot = 0.548184015759201 | epot = -15.451926107272 | etot = -14.6175140350091 -367000 ekin = 0.299126926925929 | erot = 0.537506547612545 | epot = -15.4541475095989 | etot = -14.6175140350605 -368000 ekin = 0.311549892638321 | erot = 0.525721330953661 | epot = -15.4547852587075 | etot = -14.6175140351155 -369000 ekin = 0.322916493342089 | erot = 0.512572942756051 | epot = -15.4530034712696 | etot = -14.6175140351714 -370000 ekin = 0.332630833323947 | erot = 0.497818805483414 | epot = -15.4479636740324 | etot = -14.617514035225 -371000 ekin = 0.340103492446085 | erot = 0.481258447418289 | epot = -15.4388759751373 | etot = -14.6175140352729 -372000 ekin = 0.344777943663694 | erot = 0.462760223985889 | epot = -15.4250522029613 | etot = -14.6175140353117 -373000 ekin = 0.346161332161625 | erot = 0.442283380419747 | epot = -15.4059587479197 | etot = -14.6175140353383 -374000 ekin = 0.34385906298025 | erot = 0.419893962768399 | epot = -15.3812670610983 | etot = -14.6175140353497 -375000 ekin = 0.337612023151115 | erot = 0.395773904237539 | epot = -15.3508999627315 | etot = -14.6175140353429 -376000 ekin = 0.327334336193325 | erot = 0.370223433837622 | epot = -15.3150718053467 | etot = -14.6175140353157 -377000 ekin = 0.313148263712678 | erot = 0.343657545338106 | epot = -15.2743198443178 | etot = -14.617514035267 -378000 ekin = 0.295411338277493 | erot = 0.31659745453892 | epot = -15.2295228280126 | etot = -14.6175140351962 -379000 ekin = 0.274729408510339 | erot = 0.289657740940279 | epot = -15.1819011845556 | etot = -14.617514035105 -380000 ekin = 0.251948675267282 | erot = 0.26352941405552 | epot = -15.132992124319 | etot = -14.6175140349962 -381000 ekin = 0.228120837035132 | erot = 0.238958749468289 | epot = -15.0845936213795 | etot = -14.617514034876 -382000 ekin = 0.204438854506735 | erot = 0.216721270519236 | epot = -15.0386741597777 | etot = -14.6175140347517 -383000 ekin = 0.18214626375543 | erot = 0.197591880984119 | epot = -14.9972521793718 | etot = -14.6175140346322 -384000 ekin = 0.162429780679613 | erot = 0.182311896923878 | epot = -14.9622557121303 | etot = -14.6175140345268 -385000 ekin = 0.14631062212394 | erot = 0.171555128910918 | epot = -14.9353797854786 | etot = -14.6175140344437 -386000 ekin = 0.134552389652524 | erot = 0.165895597224088 | epot = -14.9179620212651 | etot = -14.6175140343885 -387000 ekin = 0.127600986328493 | erot = 0.165779213533709 | epot = -14.910894234226 | etot = -14.6175140343638 -388000 ekin = 0.125565151523076 | erot = 0.171500950984482 | epot = -14.9145801368766 | etot = -14.617514034369 -389000 ekin = 0.128237001096944 | erot = 0.183188026636168 | epot = -14.9289390621344 | etot = -14.6175140344012 -390000 ekin = 0.135143637923039 | erot = 0.200788930663258 | epot = -14.9534466030429 | etot = -14.6175140344566 -391000 ekin = 0.145616156499708 | erot = 0.224068074688681 | epot = -14.9871982657188 | etot = -14.6175140345305 -392000 ekin = 0.158862235246441 | erot = 0.252606362172211 | epot = -15.0289826320369 | etot = -14.6175140346182 -393000 ekin = 0.174032087603203 | erot = 0.285808726840186 | epot = -15.0773548491587 | etot = -14.6175140347154 -394000 ekin = 0.190272707003301 | erot = 0.322920107513567 | epot = -15.1307068493349 | etot = -14.617514034818 -395000 ekin = 0.206769905101704 | erot = 0.363051013229015 | epot = -15.1873349532528 | etot = -14.617514034922 -396000 ekin = 0.222780272469859 | erot = 0.405212687948395 | epot = -15.2455069954415 | etot = -14.6175140350232 -397000 ekin = 0.237655698718688 | erot = 0.448360183483404 | epot = -15.30352991732 | etot = -14.6175140351179 -398000 ekin = 0.250862154069842 | erot = 0.491439914330344 | epot = -15.3598161036022 | etot = -14.617514035202 -399000 ekin = 0.26199305595339 | erot = 0.533437059171214 | epot = -15.4129441503972 | etot = -14.6175140352726 -400000 ekin = 0.270776550506873 | erot = 0.573417887950088 | epot = -15.4617084737844 | etot = -14.6175140353274 -401000 ekin = 0.277075831015576 | erot = 0.610562842824445 | epot = -15.505152709206 | etot = -14.6175140353659 -402000 ekin = 0.280882158891411 | erot = 0.644187798759867 | epot = -15.5425839930396 | etot = -14.6175140353883 -403000 ekin = 0.282301228578692 | erot = 0.673752968642393 | epot = -15.5735682326171 | etot = -14.6175140353961 -404000 ekin = 0.281534519811875 | erot = 0.698860907482472 | epot = -15.5979094626856 | etot = -14.6175140353912 -405000 ekin = 0.278857975736601 | erot = 0.719246574878549 | epot = -15.6156185859913 | etot = -14.6175140353761 -406000 ekin = 0.274600555759064 | erot = 0.734763157397056 | epot = -15.6268777485091 | etot = -14.617514035353 -407000 ekin = 0.269124923358215 | erot = 0.745367259285198 | epot = -15.632006217967 | etot = -14.6175140353236 -408000 ekin = 0.262811853165536 | erot = 0.751106276665246 | epot = -15.6314321651198 | etot = -14.617514035289 -409000 ekin = 0.256049112192036 | erot = 0.752109968276093 | epot = -15.6256731157183 | etot = -14.6175140352501 -410000 ekin = 0.249224269809745 | erot = 0.748584332259483 | epot = -15.6153226372765 | etot = -14.6175140352073 -411000 ekin = 0.242720888553536 | erot = 0.740809103918216 | epot = -15.6010440276323 | etot = -14.6175140351606 -412000 ekin = 0.236916379506269 | erot = 0.729136085380601 | epot = -15.5835664999972 | etot = -14.6175140351103 -413000 ekin = 0.232179735243895 | erot = 0.713985498456758 | epot = -15.5636792687577 | etot = -14.6175140350571 -414000 ekin = 0.228867632642548 | erot = 0.69583865258568 | epot = -15.5422203202302 | etot = -14.617514035002 -415000 ekin = 0.227317772308217 | erot = 0.675225695396091 | epot = -15.5200575026511 | etot = -14.6175140349468 -416000 ekin = 0.227838940778023 | erot = 0.652708261105137 | epot = -15.4980612367767 | etot = -14.6175140348936 -417000 ekin = 0.230697970867357 | erot = 0.628857925336153 | epot = -15.4770699310484 | etot = -14.6175140348449 -418000 ekin = 0.236104416121193 | erot = 0.604232291330004 | epot = -15.4578507422545 | etot = -14.6175140348033 -419000 ekin = 0.244194252200952 | erot = 0.579351108945525 | epot = -15.4410593959175 | etot = -14.617514034771 -420000 ekin = 0.255014214169041 | erot = 0.554674986841728 | epot = -15.4272032357609 | etot = -14.6175140347501 -421000 ekin = 0.268508458340882 | erot = 0.530589008737048 | epot = -15.4166115018197 | etot = -14.6175140347417 -422000 ekin = 0.284509119561071 | erot = 0.507392982381401 | epot = -15.4094161366887 | etot = -14.6175140347463 -423000 ekin = 0.302732060427469 | erot = 0.485299248119889 | epot = -15.4055453433107 | etot = -14.6175140347633 -424000 ekin = 0.322778728051863 | erot = 0.464438075671437 | epot = -15.404730838515 | etot = -14.6175140347917 -425000 ekin = 0.344144594922996 | erot = 0.444869796713076 | epot = -15.4065284264653 | etot = -14.6175140348292 -426000 ekin = 0.366234204300256 | erot = 0.426602052984605 | epot = -15.4103502921583 | etot = -14.6175140348734 -427000 ekin = 0.38838239833986 | erot = 0.409609962240836 | epot = -15.415506395502 | etot = -14.6175140349213 -428000 ekin = 0.40988090004737 | erot = 0.393856678092568 | epot = -15.4212516131098 | etot = -14.6175140349698 -429000 ekin = 0.430009061106105 | erot = 0.3793117883821 | epot = -15.4268348845041 | etot = -14.6175140350159 -430000 ekin = 0.448067283635965 | erot = 0.365965282400821 | epot = -15.4315466010937 | etot = -14.6175140350569 -431000 ekin = 0.463411378722737 | erot = 0.353835411175292 | epot = -15.4347608249886 | etot = -14.6175140350906 -432000 ekin = 0.47548594153418 | erot = 0.342969616703626 | epot = -15.4359695933533 | etot = -14.6175140351155 -433000 ekin = 0.483854704020027 | erot = 0.333438714396081 | epot = -15.4348074535467 | etot = -14.6175140351306 -434000 ekin = 0.488225698518024 | erot = 0.325325491782049 | epot = -15.4310652254357 | etot = -14.6175140351357 -435000 ekin = 0.488469615217025 | erot = 0.318709988965525 | epot = -15.4246936393136 | etot = -14.617514035131 -436000 ekin = 0.484629100796627 | erot = 0.313653867974387 | epot = -15.4157970038885 | etot = -14.6175140351175 -437000 ekin = 0.476917712283352 | erot = 0.31018665419048 | epot = -15.4046184015704 | etot = -14.6175140350966 -438000 ekin = 0.465707830234562 | erot = 0.308296241622574 | epot = -15.3915181069269 | etot = -14.6175140350697 -439000 ekin = 0.451507536799618 | erot = 0.307925153770233 | epot = -15.3769467256089 | etot = -14.617514035039 -440000 ekin = 0.434927659012361 | erot = 0.308973010492508 | epot = -15.3614147045112 | etot = -14.6175140350063 -441000 ekin = 0.416641657348261 | erot = 0.311304747383359 | epot = -15.3454604397054 | etot = -14.6175140349738 -442000 ekin = 0.397341542600016 | erot = 0.314762618736227 | epot = -15.3296181962794 | etot = -14.6175140349432 -443000 ekin = 0.377694362714129 | erot = 0.319179725729442 | epot = -15.3143881233595 | etot = -14.617514034916 -444000 ekin = 0.358304425135544 | erot = 0.324393298190371 | epot = -15.3002117582192 | etot = -14.6175140348933 -445000 ekin = 0.339684383334022 | erot = 0.330254911560055 | epot = -15.2874533297701 | etot = -14.617514034876 -446000 ekin = 0.322237701350815 | erot = 0.336636009508868 | epot = -15.2763877457239 | etot = -14.6175140348642 -447000 ekin = 0.306253086582814 | erot = 0.343428242758809 | epot = -15.2671953641995 | etot = -14.6175140348578 -448000 ekin = 0.291909091343174 | erot = 0.350538602021399 | epot = -15.2599617282213 | etot = -14.6175140348568 -449000 ekin = 0.279285717663651 | erot = 0.357880263089595 | epot = -15.254680015614 | etot = -14.6175140348607 -450000 ekin = 0.268379332693091 | erot = 0.365360767817947 | epot = -15.2512541353806 | etot = -14.6175140348695 -451000 ekin = 0.259117719162419 | erot = 0.37286967756099 | epot = -15.2495014316066 | etot = -14.6175140348832 -452000 ekin = 0.251373384973268 | erot = 0.380268095671416 | epot = -15.2491555155463 | etot = -14.6175140349016 -453000 ekin = 0.244974824127447 | erot = 0.38738240236518 | epot = -15.2498712614169 | etot = -14.6175140349242 -454000 ekin = 0.239716691076118 | erot = 0.394004131861865 | epot = -15.2512348578881 | etot = -14.6175140349501 -455000 ekin = 0.235370413814089 | erot = 0.39989714564245 | epot = -15.2527815944341 | etot = -14.6175140349775 -456000 ekin = 0.231696513790491 | erot = 0.404812188424975 | epot = -15.25402273722 | etot = -14.6175140350045 -457000 ekin = 0.228459014432025 | erot = 0.408507709515261 | epot = -15.2544807589758 | etot = -14.6175140350285 -458000 ekin = 0.225441196082393 | erot = 0.410774705624056 | epot = -15.2537299367532 | etot = -14.6175140350468 -459000 ekin = 0.222461018940579 | erot = 0.411462514811907 | epot = -15.2514375688096 | etot = -14.6175140350571 -460000 ekin = 0.219384094438575 | erot = 0.410502136529012 | epot = -15.2474002660254 | etot = -14.6175140350578 -461000 ekin = 0.216132245240139 | erot = 0.407923844132457 | epot = -15.2415701244206 | etot = -14.6175140350481 -462000 ekin = 0.212686361973351 | erot = 0.403866554423602 | epot = -15.2340669514251 | etot = -14.6175140350282 -463000 ekin = 0.209083218482862 | erot = 0.39857748648972 | epot = -15.2251747399718 | etot = -14.6175140349992 -464000 ekin = 0.205406888263765 | erot = 0.392401883856923 | epot = -15.2153228070839 | etot = -14.6175140349632 -465000 ekin = 0.201776197881114 | erot = 0.385763783462 | epot = -15.205054016266 | etot = -14.6175140349229 -466000 ekin = 0.19833013096122 | erot = 0.379139817336891 | epot = -15.1949839831792 | etot = -14.6175140348811 -467000 ekin = 0.19521322401714 | erot = 0.373028711257264 | epot = -15.1857559701149 | etot = -14.6175140348405 -468000 ekin = 0.192562810062132 | erot = 0.367919448414635 | epot = -15.1779962932805 | etot = -14.6175140348037 -469000 ekin = 0.190499545154684 | erot = 0.364261004085321 | epot = -15.1722745840127 | etot = -14.6175140347727 -470000 ekin = 0.189122086032584 | erot = 0.36243618058674 | epot = -15.169072301368 | etot = -14.6175140347487 -471000 ekin = 0.188506156938628 | erot = 0.36274145620712 | epot = -15.1687616478782 | etot = -14.6175140347324 -472000 ekin = 0.188707621222064 | erot = 0.365373993438309 | epot = -15.1715956493842 | etot = -14.6175140347238 -473000 ekin = 0.189768618621859 | erot = 0.370426120543988 | epot = -15.177708773888 | etot = -14.6175140347222 -474000 ekin = 0.19172539734126 | erot = 0.377886798112904 | epot = -15.1871262301805 | etot = -14.6175140347263 -475000 ekin = 0.194616213070776 | erot = 0.387648901412899 | epot = -15.1997791492191 | etot = -14.6175140347354 -476000 ekin = 0.198487636160664 | erot = 0.399520678156148 | epot = -15.215522349065 | etot = -14.6175140347482 -477000 ekin = 0.203397790429852 | erot = 0.413239540255191 | epot = -15.234151365449 | etot = -14.617514034764 -478000 ekin = 0.209415519783228 | erot = 0.428486466927386 | epot = -15.2554160214929 | etot = -14.6175140347822 -479000 ekin = 0.216615156594694 | erot = 0.444899686772485 | epot = -15.2790288781698 | etot = -14.6175140348026 -480000 ekin = 0.225067223157684 | erot = 0.462086880018517 | epot = -15.3046681380016 | etot = -14.6175140348254 -481000 ekin = 0.234826185147705 | erot = 0.479635803739747 | epot = -15.3319760237383 | etot = -14.6175140348509 -482000 ekin = 0.245916939355105 | erot = 0.497123799838217 | epot = -15.3605547740725 | etot = -14.6175140348792 -483000 ekin = 0.258322039580641 | erot = 0.514126984881453 | epot = -15.3899630593724 | etot = -14.6175140349103 -484000 ekin = 0.271971667054619 | erot = 0.530229960568958 | epot = -15.4197156625675 | etot = -14.617514034944 -485000 ekin = 0.286738030809382 | erot = 0.545036619609882 | epot = -15.4492886853986 | etot = -14.6175140349794 -486000 ekin = 0.302435294441725 | erot = 0.558182125190716 | epot = -15.4781314546478 | etot = -14.6175140350153 -487000 ekin = 0.318825369857728 | erot = 0.569345540302787 | epot = -15.5056849452108 | etot = -14.6175140350503 -488000 ekin = 0.335629120855656 | erot = 0.578262027782619 | epot = -15.531405183721 | etot = -14.6175140350827 -489000 ekin = 0.352541803824741 | erot = 0.584733173542245 | epot = -15.5547890124777 | etot = -14.6175140351107 -490000 ekin = 0.369251041132792 | erot = 0.588633902375989 | epot = -15.5753989786419 | etot = -14.6175140351332 -491000 ekin = 0.385455339942983 | erot = 0.589914693969693 | epot = -15.5928840690617 | etot = -14.6175140351491 -492000 ekin = 0.400881156477967 | erot = 0.588598334680247 | epot = -15.6069935263163 | etot = -14.6175140351581 -493000 ekin = 0.415296746376553 | erot = 0.584771169137042 | epot = -15.6175819506742 | etot = -14.6175140351606 -494000 ekin = 0.428521503101982 | erot = 0.578569614095138 | epot = -15.6246051523544 | etot = -14.6175140351573 -495000 ekin = 0.440430011857908 | erot = 0.570163426567876 | epot = -15.6281074735752 | etot = -14.6175140351495 -496000 ekin = 0.450950706315982 | erot = 0.559737766476903 | epot = -15.6282025079315 | etot = -14.6175140351386 -497000 ekin = 0.460059581797582 | erot = 0.547476355485087 | epot = -15.625049972409 | etot = -14.6175140351264 -498000 ekin = 0.467769906491875 | erot = 0.533547985554663 | epot = -15.6188319271606 | etot = -14.617514035114 -499000 ekin = 0.474119221072824 | erot = 0.518098277332154 | epot = -15.6097315335076 | etot = -14.6175140351027 -500000 ekin = 0.479155106635124 | erot = 0.501247978937035 | epot = -15.5979171206651 | etot = -14.6175140350929 -501000 ekin = 0.482921233339119 | erot = 0.483098304082253 | epot = -15.5835335725061 | etot = -14.6175140350847 -502000 ekin = 0.485445093649443 | erot = 0.463742920559215 | epot = -15.5667020492863 | etot = -14.6175140350777 -503000 ekin = 0.486728599210195 | erot = 0.443285305605345 | epot = -15.5475279398864 | etot = -14.6175140350709 -504000 ekin = 0.486742408088644 | erot = 0.421859374631577 | epot = -15.5261158177833 | etot = -14.6175140350631 -505000 ekin = 0.485424480828556 | erot = 0.399650657767951 | epot = -15.5025891736495 | etot = -14.617514035053 -506000 ekin = 0.482682973412845 | erot = 0.376914939267146 | epot = -15.4771119477192 | etot = -14.6175140350392 -507000 ekin = 0.478403198155664 | erot = 0.353991273961026 | epot = -15.4499085071374 | etot = -14.6175140350207 -508000 ekin = 0.472458052936533 | erot = 0.331306710133979 | epot = -15.4212787980677 | etot = -14.6175140349972 -509000 ekin = 0.464721062856486 | erot = 0.309370883447877 | epot = -15.391605981273 | etot = -14.6175140349687 -510000 ekin = 0.455081004105158 | erot = 0.288759823578934 | epot = -15.3613548626199 | etot = -14.6175140349358 -511000 ekin = 0.443456979181397 | erot = 0.270089690707654 | epot = -15.3310607047886 | etot = -14.6175140348996 -512000 ekin = 0.42981284822047 | erot = 0.253982534898966 | epot = -15.3013094179813 | etot = -14.6175140348619 -513000 ekin = 0.414169942619758 | erot = 0.241027258547605 | epot = -15.2727112359918 | etot = -14.6175140348245 -514000 ekin = 0.396617122320082 | erot = 0.231739657368568 | epot = -15.2458708144779 | etot = -14.6175140347892 -515000 ekin = 0.377317407139249 | erot = 0.226525548757382 | epot = -15.2213569906545 | etot = -14.6175140347578 -516000 ekin = 0.35651062953391 | erot = 0.225650587239776 | epot = -15.1996752515054 | etot = -14.6175140347317 -517000 ekin = 0.334511811731694 | erot = 0.229219509886453 | epot = -15.1812453563299 | etot = -14.6175140347118 -518000 ekin = 0.31170524916001 | erot = 0.237166415926557 | epot = -15.1663856997852 | etot = -14.6175140346986 -519000 ekin = 0.288534562405369 | erot = 0.249256456193465 | epot = -15.1553050532911 | etot = -14.6175140346923 -520000 ekin = 0.265489234982165 | erot = 0.26509816545072 | epot = -15.1481014351253 | etot = -14.6175140346925 -521000 ekin = 0.243088358087426 | erot = 0.28416474515941 | epot = -15.1447671379453 | etot = -14.6175140346985 -522000 ekin = 0.221862437060459 | erot = 0.305821970139614 | epot = -15.1451984419099 | etot = -14.6175140347098 -523000 ekin = 0.202334169775895 | erot = 0.329360070796339 | epot = -15.1492082752977 | etot = -14.6175140347254 -524000 ekin = 0.184999091075918 | erot = 0.354026911469998 | epot = -15.1565400372904 | etot = -14.6175140347445 -525000 ekin = 0.170306912739171 | erot = 0.379059948770565 | epot = -15.1668808962761 | etot = -14.6175140347663 -526000 ekin = 0.158644243148381 | erot = 0.403715126924508 | epot = -15.1798734048633 | etot = -14.6175140347904 -527000 ekin = 0.150319367666692 | erot = 0.427291025811637 | epot = -15.1951244282948 | etot = -14.6175140348165 -528000 ekin = 0.145549592055572 | erot = 0.449147424932832 | epot = -15.2122110518325 | etot = -14.6175140348441 -529000 ekin = 0.144451603985253 | erot = 0.468718121850102 | epot = -15.2306837607087 | etot = -14.6175140348733 -530000 ekin = 0.147035267138977 | erot = 0.485518371010921 | epot = -15.2500676730541 | etot = -14.6175140349042 -531000 ekin = 0.153201203685106 | erot = 0.499147835496811 | epot = -15.2698630741185 | etot = -14.6175140349365 -532000 ekin = 0.162742448480708 | erot = 0.509290301682427 | epot = -15.2895467851333 | etot = -14.6175140349702 -533000 ekin = 0.175350354883068 | erot = 0.515711587206655 | epot = -15.3085759770944 | etot = -14.6175140350047 -534000 ekin = 0.190624856014803 | erot = 0.518257146630764 | epot = -15.3263960376848 | etot = -14.6175140350392 -535000 ekin = 0.20808849353821 | erot = 0.516850140105114 | epot = -15.3424526687159 | etot = -14.6175140350726 -536000 ekin = 0.227204325844138 | erot = 0.511491240066273 | epot = -15.3562096010139 | etot = -14.6175140351035 -537000 ekin = 0.247396768814454 | erot = 0.502260311074903 | epot = -15.3671711150195 | etot = -14.6175140351301 -538000 ekin = 0.268074342414838 | erot = 0.48931960096235 | epot = -15.3749079785279 | etot = -14.6175140351507 -539000 ekin = 0.288653182934825 | erot = 0.472917679673195 | epot = -15.3790848977717 | etot = -14.6175140351636 -540000 ekin = 0.308579985827042 | erot = 0.453392904740686 | epot = -15.3794869257352 | etot = -14.6175140351675 -541000 ekin = 0.327353008192347 | erot = 0.431174973012141 | epot = -15.3760420163655 | etot = -14.617514035161 -542000 ekin = 0.34453985350787 | erot = 0.406783142890255 | epot = -15.3688370315419 | etot = -14.6175140351438 -543000 ekin = 0.359790986514668 | erot = 0.380819988065056 | epot = -15.3581250096958 | etot = -14.6175140351161 -544000 ekin = 0.372848263091271 | erot = 0.353960030673709 | epot = -15.3443223288436 | etot = -14.6175140350786 -545000 ekin = 0.383548167009962 | erot = 0.326933212483004 | epot = -15.3279954145261 | etot = -14.6175140350331 -546000 ekin = 0.391819867385613 | erot = 0.300503784239149 | epot = -15.3098376866062 | etot = -14.6175140349815 -547000 ekin = 0.397678590181979 | erot = 0.275445713888173 | epot = -15.2906383389964 | etot = -14.6175140349262 -548000 ekin = 0.401215088504143 | erot = 0.252516050366992 | epot = -15.271245173741 | etot = -14.6175140348699 -549000 ekin = 0.402582175511846 | erot = 0.2324277947685 | epot = -15.2525240050957 | etot = -14.6175140348154 -550000 ekin = 0.401979352686794 | erot = 0.215823740833745 | epot = -15.2353171282857 | etot = -14.6175140347651 -551000 ekin = 0.399636550192623 | erot = 0.203252510910342 | epot = -15.2204030958242 | etot = -14.6175140347212 -552000 ekin = 0.395797934839361 | erot = 0.195147714574245 | epot = -15.2084596840995 | etot = -14.6175140346859 -553000 ekin = 0.390706676474544 | erot = 0.191810879117663 | epot = -15.2000315902532 | etot = -14.617514034661 -554000 ekin = 0.384591526956369 | erot = 0.193398609454551 | epot = -15.1955041710585 | etot = -14.6175140346476 -555000 ekin = 0.377656068330916 | erot = 0.19991436289405 | epot = -15.1950844658716 | etot = -14.6175140346467 -556000 ekin = 0.370071512613931 | erot = 0.211205266307017 | epot = -15.1987908135787 | etot = -14.6175140346577 -557000 ekin = 0.36197393927111 | erot = 0.226964515102746 | epot = -15.2064524890542 | etot = -14.6175140346804 -558000 ekin = 0.353466765019197 | erot = 0.246739996101858 | epot = -15.2177207958342 | etot = -14.6175140347131 -559000 ekin = 0.344628961763717 | erot = 0.269949765670202 | epot = -15.2320927621874 | etot = -14.6175140347535 -560000 ekin = 0.335528980566697 | erot = 0.295904778795752 | epot = -15.248947794161 | etot = -14.6175140347986 -561000 ekin = 0.326243446080483 | erot = 0.323838714908449 | epot = -15.2675961958333 | etot = -14.6175140348444 -562000 ekin = 0.316878486812668 | erot = 0.352943857552838 | epot = -15.2873363792524 | etot = -14.6175140348869 -563000 ekin = 0.307590234581136 | erot = 0.382410843957192 | epot = -15.307515113461 | etot = -14.6175140349227 -564000 ekin = 0.298599911427049 | erot = 0.411468934029058 | epot = -15.3275828804048 | etot = -14.6175140349487 -565000 ekin = 0.29019852150112 | erot = 0.439422606477175 | epot = -15.3471351629423 | etot = -14.617514034964 -566000 ekin = 0.282736992095597 | erot = 0.465680158919343 | epot = -15.365931185984 | etot = -14.617514034969 -567000 ekin = 0.276599956454081 | erot = 0.489770841522359 | epot = -15.3838848329429 | etot = -14.6175140349664 -568000 ekin = 0.27216505279084 | erot = 0.511348887820148 | epot = -15.4010279755711 | etot = -14.6175140349601 -569000 ekin = 0.269753809413471 | erot = 0.530185258476735 | epot = -15.4174531028449 | etot = -14.6175140349547 -570000 ekin = 0.269583567607588 | erot = 0.546150320474201 | epot = -15.4332479230357 | etot = -14.6175140349539 -571000 ekin = 0.271731068578172 | erot = 0.559192265325177 | epot = -15.4484373688639 | etot = -14.6175140349605 -572000 ekin = 0.276116495687432 | erot = 0.569316321633614 | epot = -15.4629468522957 | etot = -14.6175140349746 -573000 ekin = 0.282512256444886 | erot = 0.576569321997795 | epot = -15.4765956134373 | etot = -14.6175140349946 -574000 ekin = 0.290574483947776 | erot = 0.581030490761164 | epot = -15.4891190097261 | etot = -14.6175140350172 -575000 ekin = 0.29989011332688 | erot = 0.582808418137279 | epot = -15.5002125665027 | etot = -14.6175140350386 -576000 ekin = 0.310029076131083 | erot = 0.58204167895457 | epot = -15.5095847901411 | etot = -14.6175140350554 -577000 ekin = 0.32059114413582 | erot = 0.578899817193175 | epot = -15.5170049963945 | etot = -14.6175140350655 -578000 ekin = 0.331239680817797 | erot = 0.57358190432124 | epot = -15.5223356202071 | etot = -14.617514035068 -579000 ekin = 0.341718767395696 | erot = 0.56631121381473 | epot = -15.525544016274 | etot = -14.6175140350636 -580000 ekin = 0.351854361646102 | erot = 0.557326170820742 | epot = -15.5266945675208 | etot = -14.6175140350539 -581000 ekin = 0.361543170719809 | erot = 0.546869043111593 | epot = -15.5259262488726 | etot = -14.6175140350412 -582000 ekin = 0.370734291431534 | erot = 0.535174473618308 | epot = -15.5234228000773 | etot = -14.6175140350275 -583000 ekin = 0.379408545146128 | erot = 0.522459863754616 | epot = -15.5193824439152 | etot = -14.6175140350144 -584000 ekin = 0.387559338331809 | erot = 0.508918999940124 | epot = -15.5139923732754 | etot = -14.6175140350035 -585000 ekin = 0.395177418309166 | erot = 0.494719483695415 | epot = -15.5074109369997 | etot = -14.6175140349952 -586000 ekin = 0.40224053351631 | erot = 0.480003760425538 | epot = -15.4997583289313 | etot = -14.6175140349895 -587000 ekin = 0.408707997144967 | erot = 0.46489301429509 | epot = -15.4911150464262 | etot = -14.6175140349862 -588000 ekin = 0.41451954577264 | erot = 0.449492951761598 | epot = -15.4815265325189 | etot = -14.6175140349847 -589000 ekin = 0.419597612555005 | erot = 0.433900487906577 | epot = -15.4710121354457 | etot = -14.6175140349841 -590000 ekin = 0.423852083806215 | erot = 0.418210489544372 | epot = -15.4595766083342 | etot = -14.6175140349836 -591000 ekin = 0.427186671517101 | erot = 0.402521929659454 | epot = -15.4472226361592 | etot = -14.6175140349826 -592000 ekin = 0.429506137373277 | erot = 0.386943005730419 | epot = -15.4339631780839 | etot = -14.6175140349802 -593000 ekin = 0.430723706116176 | erot = 0.371594936610879 | epot = -15.4198326777029 | etot = -14.6175140349759 -594000 ekin = 0.430768094953374 | erot = 0.356614269838323 | epot = -15.4048963997609 | etot = -14.6175140349692 -595000 ekin = 0.429589664829875 | erot = 0.342153609171697 | epot = -15.3892573089615 | etot = -14.61751403496 -596000 ekin = 0.427165296133174 | erot = 0.328380718542556 | epot = -15.3730600496239 | etot = -14.6175140349482 -597000 ekin = 0.423501658499685 | erot = 0.315475989403645 | epot = -15.3564916828373 | etot = -14.617514034934 -598000 ekin = 0.418636501255329 | erot = 0.303628359581922 | epot = -15.339778895755 | etot = -14.6175140349178 -599000 ekin = 0.412638207582293 | erot = 0.293029673723861 | epot = -15.3231819162063 | etot = -14.6175140349001 -600000 ekin = 0.405603414753543 | erot = 0.283867637226416 | epot = -15.3069850868619 | etot = -14.6175140348819 -601000 ekin = 0.397652939448511 | erot = 0.276317573361135 | epot = -15.2914845476735 | etot = -14.6175140348639 -602000 ekin = 0.388926339151605 | erot = 0.270533300128888 | epot = -15.2769736741277 | etot = -14.6175140348472 -603000 ekin = 0.379575547710993 | erot = 0.266637582798826 | epot = -15.2637271653425 | etot = -14.6175140348327 -604000 ekin = 0.369758112224389 | erot = 0.264712769809609 | epot = -15.2519849168554 | etot = -14.6175140348214 -605000 ekin = 0.359630614964524 | erot = 0.264792359550254 | epot = -15.2419370093288 | etot = -14.617514034814 -606000 ekin = 0.349342882571262 | erot = 0.266854337886864 | epot = -15.2337112552692 | etot = -14.617514034811 -607000 ekin = 0.339033558751527 | erot = 0.270817131627439 | epot = -15.2273647251917 | etot = -14.6175140348127 -608000 ekin = 0.328827538259385 | erot = 0.276538908097079 | epot = -15.2228804811754 | etot = -14.6175140348189 -609000 ekin = 0.318835621087638 | erot = 0.283820700144191 | epot = -15.2201703560608 | etot = -14.6175140348289 -610000 ekin = 0.309156542568334 | erot = 0.292413461055663 | epot = -15.2190840384659 | etot = -14.6175140348419 -611000 ekin = 0.299881272108232 | erot = 0.302028697869809 | epot = -15.2194240048346 | etot = -14.6175140348565 -612000 ekin = 0.291099167856286 | erot = 0.312351863789578 | epot = -15.2209650665173 | etot = -14.6175140348714 -613000 ekin = 0.282905257831661 | erot = 0.323057294042041 | epot = -15.2234765867588 | etot = -14.6175140348851 -614000 ekin = 0.275407632339961 | erot = 0.333823223652894 | epot = -15.2267448908891 | etot = -14.6175140348962 -615000 ekin = 0.26873372556729 | erot = 0.344345386320852 | epot = -15.2305931467921 | etot = -14.617514034904 -616000 ekin = 0.263034181136622 | erot = 0.354347879927032 | epot = -15.2348960959715 | etot = -14.6175140349079 -617000 ekin = 0.258483071857947 | erot = 0.363590372787281 | epot = -15.2395874795531 | etot = -14.6175140349079 -618000 ekin = 0.255273496413766 | erot = 0.371871254538862 | epot = -15.2446587858573 | etot = -14.6175140349047 -619000 ekin = 0.253608004174891 | erot = 0.37902692128738 | epot = -15.2501489603617 | etot = -14.6175140348994 -620000 ekin = 0.253683881422316 | erot = 0.384927934514025 | epot = -15.2561258508301 | etot = -14.6175140348938 -621000 ekin = 0.255674023710186 | erot = 0.38947322607256 | epot = -15.2626612846723 | etot = -14.6175140348895 -622000 ekin = 0.259704853368001 | erot = 0.392583779640456 | epot = -15.2698026678969 | etot = -14.6175140348885 -623000 ekin = 0.265833429999869 | erot = 0.394197274406528 | epot = -15.2775447392986 | etot = -14.6175140348922 -624000 ekin = 0.274026439188712 | erot = 0.39426503162541 | epot = -15.2858055057159 | etot = -14.6175140349018 -625000 ekin = 0.28414401573886 | erot = 0.392752285177006 | epot = -15.2944103358335 | etot = -14.6175140349177 -626000 ekin = 0.295931256226584 | erot = 0.389642344381237 | epot = -15.3030876355469 | etot = -14.6175140349391 -627000 ekin = 0.309019727830048 | erot = 0.38494467650503 | epot = -15.3114784392999 | etot = -14.6175140349648 -628000 ekin = 0.322940275279362 | erot = 0.378706350960167 | epot = -15.3191606612317 | etot = -14.6175140349922 -629000 ekin = 0.33714704369846 | erot = 0.371025698974889 | epot = -15.3256867776917 | etot = -14.6175140350184 -630000 ekin = 0.351051052995026 | erot = 0.362066500827023 | epot = -15.3306315888619 | etot = -14.6175140350398 -631000 ekin = 0.364060148818982 | erot = 0.352070586246042 | epot = -15.3336447701184 | etot = -14.6175140350534 -632000 ekin = 0.375621025661451 | erot = 0.341366514681197 | epot = -15.3345015753989 | etot = -14.6175140350562 -633000 ekin = 0.385258541224348 | erot = 0.330372092305628 | epot = -15.3331446685766 | etot = -14.6175140350467 -634000 ekin = 0.392607865616114 | erot = 0.319588956493675 | epot = -15.3297108571339 | etot = -14.6175140350242 -635000 ekin = 0.397436097277863 | erot = 0.309588318033291 | epot = -15.3245384503008 | etot = -14.6175140349896 -636000 ekin = 0.399651602684384 | erot = 0.300988094378239 | epot = -15.3181537320078 | etot = -14.6175140349452 -637000 ekin = 0.399301141332031 | erot = 0.294422893568743 | epot = -15.3112380697947 | etot = -14.6175140348939 -638000 ekin = 0.396556439146212 | erot = 0.290509369489303 | epot = -15.3045798434751 | etot = -14.6175140348396 -639000 ekin = 0.391692975512742 | erot = 0.289810143796987 | epot = -15.2990171540957 | etot = -14.617514034786 -640000 ekin = 0.385064212932884 | erot = 0.292799653113167 | epot = -15.2953779007829 | etot = -14.6175140347368 -641000 ekin = 0.377074355550043 | erot = 0.299834934662484 | epot = -15.2944233249075 | etot = -14.617514034695 -642000 ekin = 0.36815213396031 | erot = 0.311133625025692 | epot = -15.296799793649 | etot = -14.617514034663 -643000 ekin = 0.358727298273998 | erot = 0.326760494743229 | epot = -15.3030018276596 | etot = -14.6175140346424 -644000 ekin = 0.34921067024251 | erot = 0.346622862553685 | epot = -15.31334756743 | etot = -14.6175140346338 -645000 ekin = 0.339977915474048 | erot = 0.37047437627955 | epot = -15.3279663263911 | etot = -14.6175140346375 -646000 ekin = 0.331356734048622 | erot = 0.397926004728971 | epot = -15.3467967734305 | etot = -14.6175140346529 -647000 ekin = 0.323616951061544 | erot = 0.428462692621732 | epot = -15.3695936783625 | etot = -14.6175140346793 -648000 ekin = 0.316962984679468 | erot = 0.461463981263932 | epot = -15.395941000659 | etot = -14.6175140347156 -649000 ekin = 0.311528303721688 | erot = 0.496226945506027 | epot = -15.4252692839881 | etot = -14.6175140347604 -650000 ekin = 0.307371814502165 | erot = 0.531990113311448 | epot = -15.4568759626262 | etot = -14.6175140348126 -651000 ekin = 0.304476169211829 | erot = 0.567957247023059 | epot = -15.4899474511054 | etot = -14.6175140348705 -652000 ekin = 0.302748327843535 | erot = 0.60332035253876 | epot = -15.5235827153148 | etot = -14.6175140349325 -653000 ekin = 0.302022769690184 | erot = 0.637281675063402 | epot = -15.5568184797505 | etot = -14.6175140349969 -654000 ekin = 0.302067723594906 | erot = 0.669074745115681 | epot = -15.5886565037724 | etot = -14.6175140350619 -655000 ekin = 0.302594671775626 | erot = 0.697984728109799 | epot = -15.6180934350106 | etot = -14.6175140351251 -656000 ekin = 0.303271161274583 | erot = 0.723368330431512 | epot = -15.6441535268905 | etot = -14.6175140351844 -657000 ekin = 0.303736663271753 | erot = 0.744673311811916 | epot = -15.665924010321 | etot = -14.6175140352373 -658000 ekin = 0.303620889263351 | erot = 0.761457272709908 | epot = -15.6825921972546 | etot = -14.6175140352814 -659000 ekin = 0.302563666908925 | erot = 0.773404945480632 | epot = -15.6934826477037 | etot = -14.6175140353142 -660000 ekin = 0.300235395695972 | erot = 0.780343280385513 | epot = -15.6980927114155 | etot = -14.617514035334 -661000 ekin = 0.296355710532695 | erot = 0.782250083092907 | epot = -15.6961198289653 | etot = -14.6175140353397 -662000 ekin = 0.290710478297866 | erot = 0.779257959177568 | epot = -15.6874824728056 | etot = -14.6175140353302 -663000 ekin = 0.283165147464187 | erot = 0.771650651991695 | epot = -15.6723298347619 | etot = -14.6175140353061 -664000 ekin = 0.27367342717685 | erot = 0.759850562456021 | epot = -15.6510380249011 | etot = -14.6175140352683 -665000 ekin = 0.262280913452634 | erot = 0.744397727319339 | epot = -15.6241926759908 | etot = -14.6175140352189 -666000 ekin = 0.249123647022579 | erot = 0.725921231745118 | epot = -15.5925589139283 | etot = -14.6175140351606 -667000 ekin = 0.234422061210101 | erot = 0.705104954965606 | epot = -15.5570410512721 | etot = -14.6175140350964 -668000 ekin = 0.21847115836915 | erot = 0.682650243125486 | epot = -15.5186354365242 | etot = -14.6175140350295 -669000 ekin = 0.201627981911564 | erot = 0.659238455807376 | epot = -15.4783804726821 | etot = -14.6175140349631 -670000 ekin = 0.184297501938707 | erot = 0.635496303881828 | epot = -15.4373078407206 | etot = -14.6175140349 -671000 ekin = 0.166917915804601 | erot = 0.611966525749056 | epot = -15.3963984763962 | etot = -14.6175140348426 -672000 ekin = 0.14994612067378 | erot = 0.589085832362602 | epot = -15.3565459878289 | etot = -14.6175140347925 -673000 ekin = 0.133843801904186 | erot = 0.567171306813788 | epot = -15.3185291434687 | etot = -14.6175140347508 -674000 ekin = 0.11906426267423 | erot = 0.546415679822096 | epot = -15.2829939772144 | etot = -14.6175140347181 -675000 ekin = 0.106039855016816 | erot = 0.526891195483755 | epot = -15.250445085195 | etot = -14.6175140346944 -676000 ekin = 0.0951697078772152 | erot = 0.50856117567973 | epot = -15.2212449182362 | etot = -14.6175140346792 -677000 ekin = 0.0868074519861288 | erot = 0.491297978911212 | epot = -15.1956194655695 | etot = -14.6175140346721 -678000 ekin = 0.0812485969713333 | erot = 0.474905301100386 | epot = -15.1736679327439 | etot = -14.6175140346722 -679000 ekin = 0.0787177619801802 | erot = 0.459143233465912 | epot = -15.1553750301247 | etot = -14.6175140346786 -680000 ekin = 0.0793562024651087 | erot = 0.443753980650389 | epot = -15.1406242178062 | etot = -14.6175140346907 -681000 ekin = 0.0832104900793269 | erot = 0.428486254342735 | epot = -15.1292107791297 | etot = -14.6175140347077 -682000 ekin = 0.0902236865228919 | erot = 0.413116880934118 | epot = -15.1208546021858 | etot = -14.6175140347288 -683000 ekin = 0.100230543462796 | erot = 0.397468585265044 | epot = -15.115213163481 | etot = -14.6175140347532 -684000 ekin = 0.112958164259237 | erot = 0.381423459019101 | epot = -15.1118956580582 | etot = -14.6175140347798 -685000 ekin = 0.128033094046463 | erot = 0.364932120277628 | epot = -15.1104792491316 | etot = -14.6175140348076 -686000 ekin = 0.144995008361833 | erot = 0.348018922992772 | epot = -15.1105279661896 | etot = -14.617514034835 -687000 ekin = 0.163316207854889 | erot = 0.330783730220943 | epot = -15.1116139729365 | etot = -14.6175140348607 -688000 ekin = 0.182425234215544 | erot = 0.313400732953569 | epot = -15.1133400020522 | etot = -14.617514034883 -689000 ekin = 0.201732335852432 | erot = 0.296114640200949 | epot = -15.1153610109544 | etot = -14.617514034901 -690000 ekin = 0.220654383890869 | erot = 0.279234374239734 | epot = -15.1174027930442 | etot = -14.6175140349136 -691000 ekin = 0.238637189924115 | erot = 0.263124260135964 | epot = -15.1192754849805 | etot = -14.6175140349204 -692000 ekin = 0.255173895595901 | erot = 0.248192653896393 | epot = -15.1208805844139 | etot = -14.6175140349216 -693000 ekin = 0.269818995117429 | erot = 0.234878024007872 | epot = -15.1222110540427 | etot = -14.6175140349174 -694000 ekin = 0.282198402188447 | erot = 0.223632668705063 | epot = -15.1233451058023 | etot = -14.6175140349088 -695000 ekin = 0.292016609392549 | erot = 0.214904477347542 | epot = -15.1244351216368 | etot = -14.6175140348967 -696000 ekin = 0.299062308190453 | erot = 0.20911738294645 | epot = -15.1256937260189 | etot = -14.617514034882 -697000 ekin = 0.303213809971544 | erot = 0.206651361566997 | epot = -15.1273792064042 | etot = -14.6175140348657 -698000 ekin = 0.304445256191692 | erot = 0.207822979228434 | epot = -15.1297822702684 | etot = -14.6175140348483 -699000 ekin = 0.302833983904582 | erot = 0.212867544423939 | epot = -15.1332155631589 | etot = -14.6175140348303 -700000 ekin = 0.298568596343111 | erot = 0.221923881122147 | epot = -15.1380065122769 | etot = -14.6175140348117 -701000 ekin = 0.291956369738205 | erot = 0.235022588975841 | epot = -15.1444929935063 | etot = -14.6175140347923 -702000 ekin = 0.283427734153978 | erot = 0.252078414120717 | epot = -15.1530201830472 | etot = -14.6175140347725 -703000 ekin = 0.273534855577064 | erot = 0.272887068860867 | epot = -15.1639359591906 | etot = -14.6175140347527 -704000 ekin = 0.262941046164713 | erot = 0.297126498876207 | epot = -15.1775815797745 | etot = -14.6175140347336 -705000 ekin = 0.252398060444981 | erot = 0.324362359960446 | epot = -15.1942744551226 | etot = -14.6175140347171 -706000 ekin = 0.242709489752792 | erot = 0.354057349893809 | epot = -15.2142808743523 | etot = -14.6175140347057 -707000 ekin = 0.23468046525942 | erot = 0.385584073394808 | epot = -15.2377785733565 | etot = -14.6175140347022 -708000 ekin = 0.229056562326963 | erot = 0.418241319395649 | epot = -15.2648119164325 | etot = -14.6175140347099 -709000 ekin = 0.226457657534039 | erot = 0.451273895784603 | epot = -15.2952455880501 | etot = -14.6175140347315 -710000 ekin = 0.227314828596025 | erot = 0.483896330832019 | epot = -15.3287251941967 | etot = -14.6175140347686 -711000 ekin = 0.231819479497738 | erot = 0.515320742172354 | epot = -15.3646542564915 | etot = -14.6175140348214 -712000 ekin = 0.239893150549438 | erot = 0.544788749313879 | epot = -15.4021959347513 | etot = -14.617514034888 -713000 ekin = 0.251183758823603 | erot = 0.571606341189959 | epot = -15.4403041349781 | etot = -14.6175140349645 -714000 ekin = 0.265090036185668 | erot = 0.595179886373849 | epot = -15.4777839576047 | etot = -14.6175140350452 -715000 ekin = 0.28081130696852 | erot = 0.615050345045233 | epot = -15.5133756871375 | etot = -14.6175140351237 -716000 ekin = 0.297415784950189 | erot = 0.630922165704455 | epot = -15.5458519858483 | etot = -14.6175140351937 -717000 ekin = 0.313918116237523 | erot = 0.642683345317396 | epot = -15.5741154968043 | etot = -14.6175140352494 -718000 ekin = 0.329356373326552 | erot = 0.650413757300739 | epot = -15.5972841659139 | etot = -14.6175140352866 -719000 ekin = 0.342860093483745 | erot = 0.654380316354885 | epot = -15.6147544451418 | etot = -14.6175140353032 -720000 ekin = 0.353703497402202 | erot = 0.655019233384843 | epot = -15.6262367660857 | etot = -14.6175140352986 -721000 ekin = 0.361340844904886 | erot = 0.65290643149649 | epot = -15.6317613116759 | etot = -14.6175140352745 -722000 ekin = 0.365423978940517 | erot = 0.648719378781022 | epot = -15.6316573929551 | etot = -14.6175140352336 -723000 ekin = 0.365803989071178 | erot = 0.643193727890515 | epot = -15.6265117521415 | etot = -14.6175140351798 -724000 ekin = 0.362520178744139 | erot = 0.637078359573047 | epot = -15.6171125734343 | etot = -14.6175140351171 -725000 ekin = 0.355779938479173 | erot = 0.631092082280536 | epot = -15.6043860558098 | etot = -14.6175140350501 -726000 ekin = 0.345932952940639 | erot = 0.625884613514309 | epot = -15.5893316014374 | etot = -14.6175140349825 -727000 ekin = 0.333442641404524 | erot = 0.622003743386552 | epot = -15.5729604197091 | etot = -14.617514034918 -728000 ekin = 0.318857050496168 | erot = 0.619869891938089 | epot = -15.5562409772939 | etot = -14.6175140348596 -729000 ekin = 0.302780724956394 | erot = 0.619758691690499 | epot = -15.5400534514564 | etot = -14.6175140348095 -730000 ekin = 0.285848455040455 | erot = 0.621791770571174 | epot = -15.5251542603809 | etot = -14.6175140347692 -731000 ekin = 0.26870127220445 | erot = 0.625935552812111 | epot = -15.5121508597563 | etot = -14.6175140347397 -732000 ekin = 0.251964649663605 | erot = 0.632007594592718 | epot = -15.5014862789777 | etot = -14.6175140347214 -733000 ekin = 0.23622856949642 | erot = 0.639689689353724 | epot = -15.4934322935641 | etot = -14.617514034714 -734000 ekin = 0.22202896074664 | erot = 0.648546698715862 | epot = -15.4880896941799 | etot = -14.6175140347174 -735000 ekin = 0.209830023527923 | erot = 0.658049804518407 | epot = -15.4853938627768 | etot = -14.6175140347305 -736000 ekin = 0.200007166761325 | erot = 0.667602683400252 | epot = -15.4851238849144 | etot = -14.6175140347528 -737000 ekin = 0.192830719625369 | erot = 0.676569044421863 | epot = -15.4869137988308 | etot = -14.6175140347836 -738000 ekin = 0.188451200585979 | erot = 0.684300102138454 | epot = -15.4902653375465 | etot = -14.617514034822 -739000 ekin = 0.186887639937102 | erot = 0.690160900652221 | epot = -15.4945625754563 | etot = -14.617514034867 -740000 ekin = 0.188021068410999 | erot = 0.693554915035455 | epot = -15.4990900183636 | etot = -14.6175140349171 -741000 ekin = 0.191595568995565 | erot = 0.69394692273094 | epot = -15.5030565266968 | etot = -14.6175140349703 -742000 ekin = 0.197228843628675 | erot = 0.690884208638915 | epot = -15.5056270872918 | etot = -14.6175140350242 -743000 ekin = 0.204433503637947 | erot = 0.684016821527801 | epot = -15.5059643602412 | etot = -14.6175140350754 -744000 ekin = 0.212648433381768 | erot = 0.673116668202712 | epot = -15.503279136705 | etot = -14.6175140351205 -745000 ekin = 0.221277722248209 | erot = 0.658094727365056 | epot = -15.4968864847687 | etot = -14.6175140351555 -746000 ekin = 0.229733012317386 | erot = 0.639014583780922 | epot = -15.4862616312757 | etot = -14.6175140351773 -747000 ekin = 0.237474044144066 | erot = 0.616100096672262 | epot = -15.4710881760001 | etot = -14.6175140351838 -748000 ekin = 0.24404226676242 | erot = 0.589734872786629 | epot = -15.451291174723 | etot = -14.617514035174 -749000 ekin = 0.249083597952536 | erot = 0.56045151840253 | epot = -15.4270491515038 | etot = -14.6175140351487 -750000 ekin = 0.252358330146342 | erot = 0.528910066810434 | epot = -15.3987824320668 | etot = -14.61751403511 -751000 ekin = 0.253738423480739 | erot = 0.495866496253741 | epot = -15.3671189547961 | etot = -14.6175140350616 -752000 ekin = 0.253194394014706 | erot = 0.462133785332398 | epot = -15.3328422143544 | etot = -14.6175140350073 -753000 ekin = 0.250775308154742 | erot = 0.428539072349833 | epot = -15.2968284154563 | etot = -14.6175140349517 -754000 ekin = 0.246585878545906 | erot = 0.39588096457829 | epot = -15.2599808780228 | etot = -14.6175140348986 -755000 ekin = 0.240764398112206 | erot = 0.364890850085353 | epot = -15.2231692830488 | etot = -14.6175140348513 -756000 ekin = 0.233464471042429 | erot = 0.336201330030534 | epot = -15.1871798358847 | etot = -14.6175140348117 -757000 ekin = 0.224842467157488 | erot = 0.310323830730611 | epot = -15.1526803326693 | etot = -14.6175140347812 -758000 ekin = 0.215051562420665 | erot = 0.28763629395336 | epot = -15.1202018911339 | etot = -14.6175140347598 -759000 ekin = 0.204242275875669 | erot = 0.268380753510823 | epot = -15.0901370641329 | etot = -14.6175140347464 -760000 ekin = 0.192568636065047 | erot = 0.252669695564096 | epot = -15.0627523663687 | etot = -14.6175140347396 -761000 ekin = 0.180198520175642 | erot = 0.240499428913165 | epot = -15.0382119838259 | etot = -14.6175140347371 -762000 ekin = 0.167326299029133 | erot = 0.231768292969525 | epot = -15.0166086267356 | etot = -14.6175140347369 -763000 ekin = 0.154185685902082 | erot = 0.226297425418103 | epot = -14.9979971460569 | etot = -14.6175140347367 -764000 ekin = 0.141060632749181 | erot = 0.223852003350681 | epot = -14.9824266708346 | etot = -14.6175140347347 -765000 ekin = 0.12829225229713 | erot = 0.224161332820225 | epot = -14.9699676198472 | etot = -14.6175140347299 -766000 ekin = 0.116280064488657 | erot = 0.226936813025332 | epot = -14.9607309122353 | etot = -14.6175140347213 -767000 ekin = 0.105476340627603 | erot = 0.231887507272391 | epot = -14.9548778826093 | etot = -14.6175140347093 -768000 ekin = 0.0963728909465996 | erot = 0.238733641346968 | epot = -14.9526205669878 | etot = -14.6175140346942 -769000 ekin = 0.0894802427438036 | erot = 0.2472186554107 | epot = -14.9542129328318 | etot = -14.6175140346773 -770000 ekin = 0.08529973610986 | erot = 0.2571203536096 | epot = -14.9599341243793 | etot = -14.6175140346598 -771000 ekin = 0.0842896183574619 | erot = 0.268261228609979 | epot = -14.9700648816111 | etot = -14.6175140346437 -772000 ekin = 0.0868267987479274 | erot = 0.280517313420821 | epot = -14.9848581468 | etot = -14.6175140346312 -773000 ekin = 0.0931666172479489 | erot = 0.293824162660612 | epot = -15.0045048145333 | etot = -14.6175140346247 -774000 ekin = 0.10340384382629 | erot = 0.308178073397322 | epot = -15.0290959518504 | etot = -14.6175140346268 -775000 ekin = 0.117439110045037 | erot = 0.323630675217712 | epot = -15.0585838199026 | etot = -14.6175140346399 -776000 ekin = 0.134955835364906 | erot = 0.340275613675123 | epot = -15.092745483706 | etot = -14.617514034666 -777000 ekin = 0.155413263634573 | erot = 0.35822784274539 | epot = -15.1311551410861 | etot = -14.6175140347062 -778000 ekin = 0.178060391220184 | erot = 0.377596905888857 | epot = -15.173171331869 | etot = -14.6175140347599 -779000 ekin = 0.201973803863688 | erot = 0.398457850157365 | epot = -15.2179456888462 | etot = -14.6175140348252 -780000 ekin = 0.226119091212137 | erot = 0.420824480237588 | epot = -15.2644576063475 | etot = -14.6175140348978 -781000 ekin = 0.249431156624394 | erot = 0.44462958531423 | epot = -15.311574776911 | etot = -14.6175140349724 -782000 ekin = 0.270904470267411 | erot = 0.469715692367093 | epot = -15.3581341976773 | etot = -14.6175140350428 -783000 ekin = 0.28968127378142 | erot = 0.495837747640981 | epot = -15.4030330565254 | etot = -14.617514035103 -784000 ekin = 0.305125009984979 | erot = 0.522676532161812 | epot = -15.4453155772949 | etot = -14.6175140351481 -785000 ekin = 0.316868262921746 | erot = 0.549859353707455 | epot = -15.4842416518048 | etot = -14.6175140351756 -786000 ekin = 0.324828845887884 | erot = 0.576983310023367 | epot = -15.5193261910961 | etot = -14.6175140351849 -787000 ekin = 0.329193233878375 | erot = 0.603636505802115 | epot = -15.5503437748585 | etot = -14.617514035178 -788000 ekin = 0.330371864851512 | erot = 0.62941387556452 | epot = -15.5772997755748 | etot = -14.6175140351588 -789000 ekin = 0.328934711355232 | erot = 0.653926193133343 | epot = -15.6003749396208 | etot = -14.6175140351322 -790000 ekin = 0.325537319473875 | erot = 0.676802790007464 | epot = -15.6198541445849 | etot = -14.6175140351035 -791000 ekin = 0.32084726793388 | erot = 0.697689943212792 | epot = -15.6360512462243 | etot = -14.6175140350777 -792000 ekin = 0.315479253540088 | erot = 0.716247584425374 | epot = -15.6492408730235 | etot = -14.6175140350581 -793000 ekin = 0.309944490983019 | erot = 0.732146955923502 | epot = -15.6596054819539 | etot = -14.6175140350473 -794000 ekin = 0.304617480926299 | erot = 0.745071299200878 | epot = -15.6672028151732 | etot = -14.617514035046 -795000 ekin = 0.299720880977559 | erot = 0.754720862086029 | epot = -15.6719557781173 | etot = -14.6175140350537 -796000 ekin = 0.295327396181303 | erot = 0.76082265878866 | epot = -15.6736640900384 | etot = -14.6175140350684 -797000 ekin = 0.29137629685275 | erot = 0.763144639346192 | epot = -15.6720349712861 | etot = -14.6175140350872 -798000 ekin = 0.287701294704656 | erot = 0.761513269132569 | epot = -15.6667285989435 | etot = -14.6175140351063 -799000 ekin = 0.284065979572991 | erot = 0.755832991337627 | epot = -15.6574130060325 | etot = -14.6175140351218 -800000 ekin = 0.2802027906322 | erot = 0.746105645864821 | epot = -15.6438224716273 | etot = -14.6175140351303 -801000 ekin = 0.275851560112955 | erot = 0.732447665813925 | epot = -15.6258132610552 | etot = -14.6175140351283 -802000 ekin = 0.270794034433638 | erot = 0.715102809073011 | epot = -15.6034108786203 | etot = -14.6175140351136 -803000 ekin = 0.264881442636258 | erot = 0.694448356026044 | epot = -15.5768438337475 | etot = -14.6175140350852 -804000 ekin = 0.258053167890663 | erot = 0.670993199746617 | epot = -15.5465604026803 | etot = -14.617514035043 -805000 ekin = 0.250345604727835 | erot = 0.645366941436453 | epot = -15.5132265811527 | etot = -14.6175140349884 -806000 ekin = 0.241890533711289 | erot = 0.618299214643985 | epot = -15.477703783279 | etot = -14.6175140349237 -807000 ekin = 0.232905655206452 | erot = 0.590591287735814 | epot = -15.4410109777946 | etot = -14.6175140348523 -808000 ekin = 0.223678061732375 | erot = 0.563080896687659 | epot = -15.404272993198 | etot = -14.617514034778 -809000 ekin = 0.21454303522996 | erot = 0.536602758841135 | epot = -15.3686598287762 | etot = -14.6175140347051 -810000 ekin = 0.205860488312556 | erot = 0.511947500022913 | epot = -15.3353220229731 | etot = -14.6175140346377 -811000 ekin = 0.197991117805052 | erot = 0.489821758277054 | epot = -15.3053269106615 | etot = -14.6175140345794 -812000 ekin = 0.191273941670663 | erot = 0.470812030933229 | epot = -15.2796000071375 | etot = -14.6175140345336 -813000 ekin = 0.18600640436924 | erot = 0.45535445106164 | epot = -15.2588748899336 | etot = -14.6175140345027 -814000 ekin = 0.182427753711751 | erot = 0.443712201373144 | epot = -15.2436539895734 | etot = -14.6175140344885 -815000 ekin = 0.180705986334949 | erot = 0.435961774090769 | epot = -15.2341817949177 | etot = -14.6175140344919 -816000 ekin = 0.180928373605182 | erot = 0.431988814112557 | epot = -15.2304312222307 | etot = -14.6175140345129 -817000 ekin = 0.183095431234026 | erot = 0.431493858262996 | epot = -15.2321033240478 | etot = -14.6175140345508 -818000 ekin = 0.187118173911453 | erot = 0.434007895069015 | epot = -15.2386401035843 | etot = -14.6175140346039 -819000 ekin = 0.192818568053509 | erot = 0.438917286806428 | epot = -15.2492498895297 | etot = -14.6175140346697 -820000 ekin = 0.199933211815025 | erot = 0.445497181488113 | epot = -15.2629444280486 | etot = -14.6175140347454 -821000 ekin = 0.20812037408232 | erot = 0.452952069483673 | epot = -15.2785864783934 | etot = -14.6175140348274 -822000 ekin = 0.216970558498732 | erot = 0.460461605795622 | epot = -15.2949461992058 | etot = -14.6175140349114 -823000 ekin = 0.226020685629658 | erot = 0.467229260922841 | epot = -15.3107639815457 | etot = -14.6175140349932 -824000 ekin = 0.234771793852156 | erot = 0.472530858216735 | epot = -15.3248166871376 | etot = -14.6175140350687 -825000 ekin = 0.242709867662636 | erot = 0.475759712130497 | epot = -15.3359836149267 | etot = -14.6175140351335 -826000 ekin = 0.249329060858576 | erot = 0.476465014357267 | epot = -15.3433081104001 | etot = -14.6175140351843 -827000 ekin = 0.254156259486422 | erot = 0.474380409602728 | epot = -15.3460507043074 | etot = -14.6175140352182 -828000 ekin = 0.256775693171427 | erot = 0.469440383344433 | epot = -15.3437301117495 | etot = -14.6175140352336 -829000 ekin = 0.25685220121729 | erot = 0.46178309210189 | epot = -15.336149328549 | etot = -14.6175140352298 -830000 ekin = 0.254151805817293 | erot = 0.45173946704091 | epot = -15.3234053080654 | etot = -14.6175140352072 -831000 ekin = 0.248558416434232 | erot = 0.439809632306185 | epot = -15.3058820839078 | etot = -14.6175140351674 -832000 ekin = 0.240085737091458 | erot = 0.426628719075598 | epot = -15.2842284912796 | etot = -14.6175140351126 -833000 ekin = 0.228883712687993 | erot = 0.41292489062373 | epot = -15.2593226383575 | etot = -14.6175140350458 -834000 ekin = 0.21523908268204 | erot = 0.399472764055511 | epot = -15.232225881708 | etot = -14.6175140349705 -835000 ekin = 0.19956978729475 | erot = 0.38704544051902 | epot = -15.2041292627042 | etot = -14.6175140348904 -836000 ekin = 0.182413100763752 | erot = 0.376368114580287 | epot = -15.1762952501534 | etot = -14.6175140348094 -837000 ekin = 0.164407483062593 | erot = 0.368075825930974 | epot = -15.149997343725 | etot = -14.6175140347314 -838000 ekin = 0.146268295773265 | erot = 0.362677435797434 | epot = -15.1264597662307 | etot = -14.61751403466 -839000 ekin = 0.128757768426159 | erot = 0.360527421580297 | epot = -15.1067992246053 | etot = -14.6175140345988 -840000 ekin = 0.112649960717713 | erot = 0.361806618656372 | epot = -15.0919706139248 | etot = -14.6175140345507 -841000 ekin = 0.0986919456674347 | erot = 0.366512603929372 | epot = -15.0827185841153 | etot = -14.6175140345185 -842000 ekin = 0.0875630029231966 | erot = 0.374460003556287 | epot = -15.0795370409836 | etot = -14.6175140345041 -843000 ekin = 0.0798341847684494 | erot = 0.385290606533481 | epot = -15.0826388258105 | etot = -14.6175140345086 -844000 ekin = 0.0759310929906315 | erot = 0.3984927697305 | epot = -15.0919378972533 | etot = -14.6175140345322 -845000 ekin = 0.0761029610203411 | erot = 0.413429207169668 | epot = -15.1070462027641 | etot = -14.6175140345741 -846000 ekin = 0.0804010613291213 | erot = 0.429371869323703 | epot = -15.1272869652854 | etot = -14.6175140346325 -847000 ekin = 0.0886689809242991 | erot = 0.44554224199926 | epot = -15.151725257628 | etot = -14.6175140347044 -848000 ekin = 0.100546421460098 | erot = 0.461155038712865 | epot = -15.1792154949586 | etot = -14.6175140347856 -849000 ekin = 0.11548696001125 | erot = 0.4754629453529 | epot = -15.2084639402357 | etot = -14.6175140348715 -850000 ekin = 0.132788806696176 | erot = 0.487799837753922 | epot = -15.2381026794072 | etot = -14.6175140349571 -851000 ekin = 0.151636227786878 | erot = 0.497619785577613 | epot = -15.2667700484016 | etot = -14.6175140350371 -852000 ekin = 0.171148194576695 | erot = 0.50452924262839 | epot = -15.2931914723117 | etot = -14.6175140351066 -853000 ekin = 0.190430159396249 | erot = 0.50831015746194 | epot = -15.3162543520199 | etot = -14.6175140351617 -854000 ekin = 0.208624756900102 | erot = 0.508932337651427 | epot = -15.3350711297508 | etot = -14.6175140351993 -855000 ekin = 0.224957674812677 | erot = 0.506554231539623 | epot = -15.3490259415701 | etot = -14.6175140352178 -856000 ekin = 0.238775816539417 | erot = 0.501512259960098 | epot = -15.3578021117162 | etot = -14.6175140352166 -857000 ekin = 0.249575992234296 | erot = 0.494299801981519 | epot = -15.3613898294125 | etot = -14.6175140351967 -858000 ekin = 0.25702350207401 | erot = 0.485537766821524 | epot = -15.3600753040553 | etot = -14.6175140351598 -859000 ekin = 0.260960921285819 | erot = 0.475939247615288 | epot = -15.3544142040096 | etot = -14.6175140351085 -860000 ekin = 0.261408037072455 | erot = 0.466270984603919 | epot = -15.3451930567221 | etot = -14.6175140350458 -861000 ekin = 0.258554187538387 | erot = 0.457314264402285 | epot = -15.3333824869156 | etot = -14.6175140349749 -862000 ekin = 0.252744258033177 | erot = 0.449827506885211 | epot = -15.3200857998177 | etot = -14.6175140348993 -863000 ekin = 0.24445941779672 | erot = 0.444512141833 | epot = -15.3064855944522 | etot = -14.6175140348224 -864000 ekin = 0.234293368840396 | erot = 0.441983030938497 | epot = -15.2937904345264 | etot = -14.6175140347475 -865000 ekin = 0.222924696624307 | erot = 0.442744308393614 | epot = -15.2831830396955 | etot = -14.6175140346775 -866000 ekin = 0.211086026109529 | erot = 0.447169652379615 | epot = -15.2757697131049 | etot = -14.6175140346158 -867000 ekin = 0.199530465893234 | erot = 0.455487658922665 | epot = -15.2725321593806 | etot = -14.6175140345647 -868000 ekin = 0.188996288427726 | erot = 0.467771811642194 | epot = -15.274282134597 | etot = -14.6175140345271 -869000 ekin = 0.180171161859857 | erot = 0.483934855625369 | epot = -15.2816200519904 | etot = -14.6175140345052 -870000 ekin = 0.173657413869096 | erot = 0.503727420428206 | epot = -15.2948988687979 | etot = -14.6175140345006 -871000 ekin = 0.169940429082833 | erot = 0.526741193130623 | epot = -15.3141956567281 | etot = -14.6175140345146 -872000 ekin = 0.169362274179232 | erot = 0.552417088944611 | epot = -15.3392933976713 | etot = -14.6175140345475 -873000 ekin = 0.172102391202427 | erot = 0.580058846013093 | epot = -15.3696752718142 | etot = -14.6175140345987 -874000 ekin = 0.178167002902688 | erot = 0.608852557306719 | epot = -15.404533594876 | etot = -14.6175140346666 -875000 ekin = 0.187388233891592 | erot = 0.637892396629009 | epot = -15.4427946652693 | etot = -14.6175140347487 -876000 ekin = 0.199433181368184 | erot = 0.666212376944545 | epot = -15.4831595931543 | etot = -14.6175140348416 -877000 ekin = 0.213822249051427 | erot = 0.692823325237341 | epot = -15.5241596092295 | etot = -14.6175140349408 -878000 ekin = 0.229955728386756 | erot = 0.716754212644264 | epot = -15.5642239760726 | etot = -14.6175140350416 -879000 ekin = 0.24714610464567 | erot = 0.737095186134359 | epot = -15.601755325919 | etot = -14.617514035139 -880000 ekin = 0.26465379700288 | erot = 0.753040153405439 | epot = -15.6352079856366 | etot = -14.6175140352283 -881000 ekin = 0.281723784261826 | erot = 0.763926241590759 | epot = -15.6631640611576 | etot = -14.617514035305 -882000 ekin = 0.297620641607206 | erot = 0.769267373447322 | epot = -15.6844020504202 | etot = -14.6175140353657 -883000 ekin = 0.311659967166528 | erot = 0.768779581882121 | epot = -15.6979535844563 | etot = -14.6175140354077 -884000 ekin = 0.323234773768187 | erot = 0.762396270683934 | epot = -15.7031450798816 | etot = -14.6175140354295 -885000 ekin = 0.331836099625414 | erot = 0.750272396067172 | epot = -15.6996225311231 | etot = -14.6175140354306 -886000 ekin = 0.33706775156411 | erot = 0.732777385265372 | epot = -15.6873591722412 | etot = -14.6175140354117 -887000 ekin = 0.338655649766352 | erot = 0.710477420749861 | epot = -15.6666471058904 | etot = -14.6175140353742 -888000 ekin = 0.336452632420901 | erot = 0.6841084171557 | epot = -15.6380750848969 | etot = -14.6175140353203 -889000 ekin = 0.330439768515659 | erot = 0.654541548239618 | epot = -15.6024953520081 | etot = -14.6175140352528 -890000 ekin = 0.320725208484789 | erot = 0.622743520026649 | epot = -15.5609827636858 | etot = -14.6175140351743 -891000 ekin = 0.307541386208951 | erot = 0.589733936087058 | epot = -15.5147893573841 | etot = -14.6175140350881 -892000 ekin = 0.291240998129697 | erot = 0.556542080397536 | epot = -15.4652971135242 | etot = -14.6175140349969 -893000 ekin = 0.272291667891157 | erot = 0.524165278720401 | epot = -15.4139709815154 | etot = -14.6175140349038 -894000 ekin = 0.251268620703245 | erot = 0.493530718297354 | epot = -15.3623133738117 | etot = -14.6175140348111 -895000 ekin = 0.228844131843401 | erot = 0.465462234286291 | epot = -15.3118204008511 | etot = -14.6175140347214 -896000 ekin = 0.205772103521686 | erot = 0.440653137307012 | epot = -15.2639392754662 | etot = -14.6175140346375 -897000 ekin = 0.182866017802818 | erot = 0.41964569375824 | epot = -15.2200257461228 | etot = -14.6175140345617 -898000 ekin = 0.160968870008375 | erot = 0.402817425242945 | epot = -15.1813003297484 | etot = -14.6175140344971 -899000 ekin = 0.140914625128323 | erot = 0.390374024163074 | epot = -15.1488026837378 | etot = -14.6175140344464 -900000 ekin = 0.123482269337613 | erot = 0.382348451689397 | epot = -15.1233447554396 | etot = -14.6175140344126 -901000 ekin = 0.109345484385286 | erot = 0.378605737554656 | epot = -15.1054652563382 | etot = -14.6175140343982 -902000 ekin = 0.0990229789071331 | erot = 0.378853140166514 | epot = -15.0953901534789 | etot = -14.6175140344052 -903000 ekin = 0.0928360184568331 | erot = 0.382655585826067 | epot = -15.0930056387171 | etot = -14.6175140344342 -904000 ekin = 0.090880112388556 | erot = 0.389456554773916 | epot = -15.0978507016463 | etot = -14.6175140344839 -905000 ekin = 0.0930167096532645 | erot = 0.398604648850404 | epot = -15.1091353930552 | etot = -14.6175140345515 -906000 ekin = 0.0988880708470082 | erot = 0.409385812369539 | epot = -15.125787917849 | etot = -14.6175140346324 -907000 ekin = 0.107954659148151 | erot = 0.421060528764331 | epot = -15.1465292226329 | etot = -14.6175140347204 -908000 ekin = 0.119550305155103 | erot = 0.432904367174592 | epot = -15.1699687071382 | etot = -14.6175140348085 -909000 ekin = 0.132947118364974 | erot = 0.444249232158161 | epot = -15.1947103854133 | etot = -14.6175140348901 -910000 ekin = 0.147420543333974 | erot = 0.454521879656246 | epot = -15.2194564579498 | etot = -14.6175140349596 -911000 ekin = 0.1623055063097 | erot = 0.463275978358893 | epot = -15.2430955196813 | etot = -14.6175140350127 -912000 ekin = 0.177037050913212 | erot = 0.470214361754332 | epot = -15.2647654477151 | etot = -14.6175140350476 -913000 ekin = 0.191172462463397 | erot = 0.475199092565833 | epot = -15.2838855900934 | etot = -14.6175140350642 -914000 ekin = 0.204395616840769 | erot = 0.478248345047336 | epot = -15.3001579969523 | etot = -14.6175140350642 -915000 ekin = 0.216507238695221 | erot = 0.479520616571487 | epot = -15.3135418903175 | etot = -14.6175140350508 -916000 ekin = 0.22740635239901 | erot = 0.479288139235317 | epot = -15.3242085266619 | etot = -14.6175140350275 -917000 ekin = 0.237068358847904 | erot = 0.47790239272228 | epot = -15.3324847865685 | etot = -14.6175140349984 -918000 ekin = 0.245524170398601 | erot = 0.475755244751353 | epot = -15.3387934501169 | etot = -14.6175140349669 -919000 ekin = 0.252843202023208 | erot = 0.473239468154888 | epot = -15.3435967051145 | etot = -14.6175140349364 -920000 ekin = 0.259121284814425 | erot = 0.470712244289296 | epot = -15.3473475640128 | etot = -14.6175140349091 -921000 ekin = 0.264473144075726 | erot = 0.468464808091583 | epot = -15.350451987054 | etot = -14.6175140348867 -922000 ekin = 0.269028180853159 | erot = 0.466700668341345 | epot = -15.3532428840647 | etot = -14.6175140348702 -923000 ekin = 0.272927944744977 | erot = 0.465523908451933 | epot = -15.3559658880565 | etot = -14.6175140348596 -924000 ekin = 0.27632379382835 | erot = 0.464938026324847 | epot = -15.3587758550076 | etot = -14.6175140348544 -925000 ekin = 0.279373649322731 | erot = 0.464854721381053 | epot = -15.3617424055578 | etot = -14.617514034854 -926000 ekin = 0.282237300897359 | erot = 0.465111106681621 | epot = -15.364862442436 | etot = -14.6175140348571 -927000 ekin = 0.285070250341276 | erot = 0.465493135294172 | epot = -15.3680774204977 | etot = -14.6175140348622 -928000 ekin = 0.288016501944431 | erot = 0.465762600719218 | epot = -15.3712931375322 | etot = -14.6175140348686 -929000 ekin = 0.291201026098216 | erot = 0.465684740680258 | epot = -15.3743998016531 | etot = -14.6175140348746 -930000 ekin = 0.294722459179011 | erot = 0.46505426199062 | epot = -15.3772907560491 | etot = -14.6175140348795 -931000 ekin = 0.298646764015314 | erot = 0.46371724845426 | epot = -15.379878047352 | etot = -14.6175140348824 -932000 ekin = 0.30300230463981 | erot = 0.461587311534084 | epot = -15.3821036510569 | etot = -14.617514034883 -933000 ekin = 0.307776651095006 | erot = 0.458654945592231 | epot = -15.3839456315686 | etot = -14.6175140348814 -934000 ekin = 0.312915338272225 | erot = 0.454989722656003 | epot = -15.3854190958059 | etot = -14.6175140348777 -935000 ekin = 0.318322768321516 | erot = 0.450735625551274 | epot = -15.3865724287453 | etot = -14.6175140348725 -936000 ekin = 0.323865441581208 | erot = 0.446100385695376 | epot = -15.387479862143 | etot = -14.6175140348664 -937000 ekin = 0.329377658420725 | erot = 0.441340069470882 | epot = -15.3882317627517 | etot = -14.6175140348601 -938000 ekin = 0.334669609401316 | erot = 0.436740154638295 | epot = -15.3889237988937 | etot = -14.6175140348541 -939000 ekin = 0.339538182698404 | erot = 0.432595723627046 | epot = -15.3896479411745 | etot = -14.617514034849 -940000 ekin = 0.343779460434926 | erot = 0.429190561372464 | epot = -15.3904840566525 | etot = -14.6175140348451 -941000 ekin = 0.347202304173565 | erot = 0.426777065358581 | epot = -15.3914934043749 | etot = -14.6175140348428 -942000 ekin = 0.349642062607354 | erot = 0.425558062625005 | epot = -15.3927141600744 | etot = -14.617514034842 -943000 ekin = 0.350973206935252 | erot = 0.425671371650571 | epot = -15.3941586134289 | etot = -14.617514034843 -944000 ekin = 0.351119786154226 | erot = 0.427178062458784 | epot = -15.3958118834587 | etot = -14.6175140348457 -945000 ekin = 0.350062816508175 | erot = 0.430055404932934 | epot = -15.397632256291 | etot = -14.6175140348498 -946000 ekin = 0.347844068536132 | erot = 0.434195447788954 | epot = -15.3995535511804 | etot = -14.6175140348553 -947000 ekin = 0.344566017440973 | erot = 0.439410327983287 | epot = -15.4014903802857 | etot = -14.6175140348614 -948000 ekin = 0.340388212506886 | erot = 0.445444378275965 | epot = -15.4033466256503 | etot = -14.6175140348675 -949000 ekin = 0.335520427168089 | erot = 0.451992965713356 | epot = -15.405027427754 | etot = -14.6175140348726 -950000 ekin = 0.330213181195942 | erot = 0.458727107974317 | epot = -15.4064543240458 | etot = -14.6175140348755 -951000 ekin = 0.324745816556292 | erot = 0.465321341195928 | epot = -15.4075811926278 | etot = -14.6175140348756 -952000 ekin = 0.319412679962154 | erot = 0.471482169175981 | epot = -15.40840888401 | etot = -14.6175140348719 -953000 ekin = 0.314508037100295 | erot = 0.476974139325829 | epot = -15.4089962112904 | etot = -14.6175140348643 -954000 ekin = 0.310309685024622 | erot = 0.481639431416537 | epot = -15.4094631512943 | etot = -14.6175140348532 -955000 ekin = 0.307061947765635 | erot = 0.485408201612612 | epot = -15.4099841842179 | etot = -14.6175140348396 -956000 ekin = 0.304958921289484 | erot = 0.488297803840366 | epot = -15.4107707599553 | etot = -14.6175140348255 -957000 ekin = 0.304129209169354 | erot = 0.490400499131608 | epot = -15.4120437431141 | etot = -14.6175140348131 -958000 ekin = 0.304623714620758 | erot = 0.491860923620771 | epot = -15.4139986730463 | etot = -14.6175140348048 -959000 ekin = 0.306408207892448 | erot = 0.492846142548464 | epot = -15.4167683852437 | etot = -14.6175140348028 -960000 ekin = 0.309362278814217 | erot = 0.493512316197957 | epot = -15.4203886298212 | etot = -14.617514034809 -961000 ekin = 0.313285873785905 | erot = 0.493972653387197 | epot = -15.4247725619971 | etot = -14.617514034824 -962000 ekin = 0.317913924785389 | erot = 0.494271324762711 | epot = -15.4296992843955 | etot = -14.6175140348474 -963000 ekin = 0.322938673954078 | erot = 0.494367337737335 | epot = -15.434820046569 | etot = -14.6175140348776 -964000 ekin = 0.328038281532033 | erot = 0.494131108238473 | epot = -15.4396834246822 | etot = -14.6175140349117 -965000 ekin = 0.332909295684048 | erot = 0.493354750676282 | epot = -15.4437780813066 | etot = -14.6175140349462 -966000 ekin = 0.337299689763782 | erot = 0.491775167781756 | epot = -15.4465888925225 | etot = -14.6175140349769 -967000 ekin = 0.341038574327672 | erot = 0.489107134739068 | epot = -15.4476597440666 | etot = -14.6175140349999 -968000 ekin = 0.344058508087241 | erot = 0.485082040987962 | epot = -15.4466545840869 | etot = -14.6175140350117 -969000 ekin = 0.346406687227172 | erot = 0.479487053291733 | epot = -15.4434077755292 | etot = -14.6175140350103 -970000 ekin = 0.348242259951303 | erot = 0.472199376074833 | epot = -15.4379556710214 | etot = -14.6175140349953 -971000 ekin = 0.349818577908824 | erot = 0.46321104020724 | epot = -15.4305436530838 | etot = -14.6175140349678 -972000 ekin = 0.351451221504542 | erot = 0.452641107453832 | epot = -15.4216063638892 | etot = -14.6175140349308 -973000 ekin = 0.353474851841814 | erot = 0.440734047140308 | epot = -15.4117229338706 | etot = -14.6175140348885 -974000 ekin = 0.356193968986615 | erot = 0.427844962323066 | epot = -15.4015529661555 | etot = -14.6175140348458 -975000 ekin = 0.359834072252972 | erot = 0.41441397102154 | epot = -15.391762078082 | etot = -14.6175140348075 -976000 ekin = 0.364500158164539 | erot = 0.400933139115516 | epot = -15.3829473320579 | etot = -14.6175140347778 -977000 ekin = 0.370148756531585 | erot = 0.387909813696897 | epot = -15.3755726049882 | etot = -14.6175140347597 -978000 ekin = 0.376577842832097 | erot = 0.375830059083101 | epot = -15.3699219366698 | etot = -14.6175140347546 -979000 ekin = 0.383436289098875 | erot = 0.365125297247076 | epot = -15.3660756211083 | etot = -14.6175140347623 -980000 ekin = 0.39025154222181 | erot = 0.356144397460029 | epot = -15.3639099744636 | etot = -14.6175140347817 -981000 ekin = 0.396471539315466 | erot = 0.34913254719872 | epot = -15.3631181213242 | etot = -14.61751403481 -982000 ekin = 0.401514997591316 | erot = 0.344217435800717 | epot = -15.3632464682363 | etot = -14.6175140348443 -983000 ekin = 0.404823458769572 | erot = 0.341402706417443 | epot = -15.3637402000685 | etot = -14.6175140348815 -984000 ekin = 0.405908866684762 | erot = 0.340568324599231 | epot = -15.3639912262028 | etot = -14.6175140349188 -985000 ekin = 0.404391803059563 | erot = 0.341477444722043 | epot = -15.3633832827353 | etot = -14.6175140349537 -986000 ekin = 0.400027422799949 | erot = 0.343789434463128 | epot = -15.3613308922474 | etot = -14.6175140349843 -987000 ekin = 0.392718180743682 | erot = 0.347078806740175 | epot = -15.357311022493 | etot = -14.6175140350092 -988000 ekin = 0.38251423921323 | erot = 0.350859769148633 | epot = -15.3508880433891 | etot = -14.6175140350273 -989000 ekin = 0.36960372665301 | erot = 0.354615837190772 | epot = -15.3417335988814 | etot = -14.6175140350376 -990000 ekin = 0.354295674460579 | erot = 0.357833454089954 | epot = -15.3296431635899 | etot = -14.6175140350393 -991000 ekin = 0.336998529350858 | erot = 0.360037895319985 | epot = -15.3145504597026 | etot = -14.6175140350317 -992000 ekin = 0.318196763890059 | erot = 0.360829065192577 | epot = -15.2965398640969 | etot = -14.6175140350143 -993000 ekin = 0.298427479538372 | erot = 0.359914303090989 | epot = -15.2758558176161 | etot = -14.6175140349867 -994000 ekin = 0.278258203579959 | erot = 0.35713517096667 | epot = -15.2529074094957 | etot = -14.6175140349491 -995000 ekin = 0.25826647189504 | erot = 0.352485480213687 | epot = -15.2282659870109 | etot = -14.6175140349021 -996000 ekin = 0.239021351636035 | erot = 0.346118523028601 | epot = -15.2026539095118 | etot = -14.6175140348471 -997000 ekin = 0.221066818081189 | erot = 0.33834249244324 | epot = -15.1769233453105 | etot = -14.6175140347861 -998000 ekin = 0.204906835818305 | erot = 0.32960423350908 | epot = -15.1520251040489 | etot = -14.6175140347215 -999000 ekin = 0.190992053959206 | erot = 0.320462575794709 | epot = -15.1289686644102 | etot = -14.6175140346563 -1000000 ekin = 0.179708146665582 | erot = 0.311553394428723 | epot = -15.1087755756881 | etot = -14.6175140345938 - 1000000 0.013311715 -1.5443684 0.033490821 -1.4929067 -0.00013590491 -Loop time of 20.562 on 4 procs for 1000000 steps with 10 atoms - -Performance: 42019.279 tau/day, 48633.425 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.64919 | 7.8156 | 14.197 | 201.2 | 38.01 -Bond | 0.087187 | 0.29612 | 0.4961 | 30.3 | 1.44 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 1.7094 | 2.016 | 2.3707 | 16.8 | 9.80 -Output | 1.6928e-05 | 2.0683e-05 | 2.2888e-05 | 0.0 | 0.00 -Modify | 0.23071 | 0.97353 | 1.6748 | 60.0 | 4.73 -Other | | 9.461 | | | 46.01 - -Nlocal: 2.5 ave 5 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Nghost: 7.5 ave 10 max 5 min -Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 18.5 ave 35 max 0 min -Histogram: 1 0 1 0 0 0 0 0 1 1 - -Total # of neighbors = 74 -Ave neighs/atom = 7.4 -Ave special neighs/atom = 3.6 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:20 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 new file mode 100644 index 0000000000..2c09a4f99d --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.1 @@ -0,0 +1,178 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.023 | 3.023 | 3.023 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05 +1000 ekin = 0.00113086229080528 | erot = 0.0043101016040658 | epot = -14.6229549982368 | etot = -14.617514034342 +2000 ekin = 0.0044853322434243 | erot = 0.0171407706505008 | epot = -14.6391401372615 | etot = -14.6175140343675 +3000 ekin = 0.00995035259649284 | erot = 0.0381961780846485 | epot = -14.6656605650904 | etot = -14.6175140344093 +4000 ekin = 0.0173418024862054 | erot = 0.0669935184860634 | epot = -14.7018493554381 | etot = -14.6175140344659 +5000 ekin = 0.0264109356286075 | erot = 0.102878288094517 | epot = -14.7468032582586 | etot = -14.6175140345355 +6000 ekin = 0.0368533113591442 | erot = 0.14504542056987 | epot = -14.7994127665447 | etot = -14.6175140346157 +7000 ekin = 0.0483200640564843 | erot = 0.19256586251551 | epot = -14.8583999612756 | etot = -14.6175140347036 +8000 ekin = 0.0604312317605998 | erot = 0.24441787013151 | epot = -14.9223631366883 | etot = -14.6175140347962 +9000 ekin = 0.0727907119671751 | erot = 0.299521949931843 | epot = -14.989826696789 | etot = -14.6175140348899 +10000 ekin = 0.0850022498875221 | erot = 0.356777997217908 | epot = -15.0592942820869 | etot = -14.6175140349815 + 10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792 +Loop time of 0.149406 on 1 procs for 10000 steps with 10 atoms + +Performance: 57828.835 tau/day, 66931.522 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11971 | 0.11971 | 0.11971 | 0.0 | 80.12 +Bond | 0.0051196 | 0.0051196 | 0.0051196 | 0.0 | 3.43 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0013614 | 0.0013614 | 0.0013614 | 0.0 | 0.91 +Output | 5.0068e-06 | 5.0068e-06 | 5.0068e-06 | 0.0 | 0.00 +Modify | 0.018941 | 0.018941 | 0.018941 | 0.0 | 12.68 +Other | | 0.004268 | | | 2.86 + +Nlocal: 10 ave 10 max 10 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 45 ave 45 max 45 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 45 +Ave neighs/atom = 4.5 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 new file mode 100644 index 0000000000..a326248cdb --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex1/log.27Nov18.duplex1.g++.4 @@ -0,0 +1,178 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 1 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex1 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 10 atoms + reading velocities ... + 10 velocities + 10 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 8 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 2 = max # of 1-4 neighbors + 4 = max # of special neighbors + +set atom * mass 3.1575 + 10 settings made for mass + +group all type 1 4 +10 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +fix 1 all nve/dot +#fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.652 | 7.834 | 8.016 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.4712768 0.009525411 -1.4617514 -5.8922361e-05 +1000 ekin = 0.00113086229080478 | erot = 0.00431010160406708 | epot = -14.6229549982368 | etot = -14.617514034342 +2000 ekin = 0.00448533224342286 | erot = 0.0171407706505013 | epot = -14.6391401372615 | etot = -14.6175140343675 +3000 ekin = 0.0099503525964896 | erot = 0.0381961780846438 | epot = -14.6656605650904 | etot = -14.6175140344093 +4000 ekin = 0.0173418024861991 | erot = 0.0669935184860479 | epot = -14.7018493554381 | etot = -14.6175140344659 +5000 ekin = 0.0264109356285965 | erot = 0.102878288094482 | epot = -14.7468032582586 | etot = -14.6175140345355 +6000 ekin = 0.0368533113591268 | erot = 0.145045420569809 | epot = -14.7994127665446 | etot = -14.6175140346156 +7000 ekin = 0.0483200640564584 | erot = 0.192565862515413 | epot = -14.8583999612755 | etot = -14.6175140347036 +8000 ekin = 0.0604312317605635 | erot = 0.24441787013137 | epot = -14.9223631366881 | etot = -14.6175140347962 +9000 ekin = 0.072790711967127 | erot = 0.299521949931654 | epot = -14.9898266967887 | etot = -14.6175140348899 +10000 ekin = 0.0850022498874609 | erot = 0.356777997217666 | epot = -15.0592942820866 | etot = -14.6175140349815 + 10000 0.006296463 -1.5144685 0.0085391004 -1.4974292 -0.00010794792 +Loop time of 0.14583 on 4 procs for 10000 steps with 10 atoms + +Performance: 59247.054 tau/day, 68572.979 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0034175 | 0.055587 | 0.10059 | 17.9 | 38.12 +Bond | 0.00064635 | 0.002131 | 0.0035357 | 2.5 | 1.46 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.014538 | 0.014932 | 0.015271 | 0.2 | 10.24 +Output | 5.7459e-05 | 5.7697e-05 | 5.7936e-05 | 0.0 | 0.04 +Modify | 0.0012829 | 0.0063873 | 0.011321 | 5.2 | 4.38 +Other | | 0.06674 | | | 45.76 + +Nlocal: 2.5 ave 5 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 7.5 ave 10 max 5 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 18.5 ave 35 max 0 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 74 +Ave neighs/atom = 7.4 +Ave special neighs/atom = 3.6 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2 b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 similarity index 99% rename from examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2 rename to examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 index 451fe62e3c..3d4393e09b 100644 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/input.duplex2 +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/in.duplex2 @@ -73,6 +73,6 @@ fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${e #dump_modify out sort id #dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" -run 1000000 +run 10000 #write_restart config.${number}.* diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1 deleted file mode 100644 index 386fbd7579..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.1 +++ /dev/null @@ -1,1167 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05 -1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817 -2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591 -3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324 -4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247 -5000 ekin = 1.77654023802719 | erot = 2.53418650522101 | epot = -24.1246365663843 | etot = -19.8139098231361 -6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.8863108281781 -7000 ekin = 3.22418765752177 | erot = 2.72037570174022 | epot = -23.9458569915548 | etot = -18.0012936322928 -8000 ekin = 2.83204202112963 | erot = 2.67060276413776 | epot = -23.9211291529766 | etot = -18.4184843677092 -9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833 -10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884567 -11000 ekin = 2.34346978235591 | erot = 2.0608750207871 | epot = -23.5779637301072 | etot = -19.1736189269642 -12000 ekin = 2.71430148816282 | erot = 2.08352509995717 | epot = -23.4639027443831 | etot = -18.6660761562631 -13000 ekin = 2.61978682102879 | erot = 2.37135270083347 | epot = -23.3602247027812 | etot = -18.3690851809189 -14000 ekin = 3.07648218347461 | erot = 2.513719767243 | epot = -23.2345584968309 | etot = -17.6443565461133 -15000 ekin = 2.98155804409324 | erot = 1.87766202539412 | epot = -23.0833749664029 | etot = -18.2241548969156 -16000 ekin = 2.18215330648447 | erot = 2.12621179836828 | epot = -22.9601160092383 | etot = -18.6517509043856 -17000 ekin = 1.85636180329758 | erot = 2.31208745603367 | epot = -22.8022922969143 | etot = -18.633843037583 -18000 ekin = 2.26768559168017 | erot = 1.2389450409061 | epot = -22.668242963885 | etot = -19.1616123312987 -19000 ekin = 2.41605854545852 | erot = 2.44791952321404 | epot = -22.5387095337131 | etot = -17.6747314650405 -20000 ekin = 2.51175765558337 | erot = 2.15047735899709 | epot = -22.3909493829452 | etot = -17.7287143683647 -21000 ekin = 2.9915110961596 | erot = 2.41132105778464 | epot = -22.5047205397251 | etot = -17.1018883857809 -22000 ekin = 3.06067007914886 | erot = 1.83986675392832 | epot = -22.6049739626141 | etot = -17.7044371295369 -23000 ekin = 2.66061083480474 | erot = 2.22251362834379 | epot = -22.5979829967718 | etot = -17.7148585336233 -24000 ekin = 2.65745533322327 | erot = 2.79344397300952 | epot = -22.5688422615674 | etot = -17.1179429553346 -25000 ekin = 2.30064465907917 | erot = 2.20975367009042 | epot = -22.5633453862602 | etot = -18.0529470570906 -26000 ekin = 1.6282588103248 | erot = 2.51914272742421 | epot = -22.6015006270016 | etot = -18.4540990892526 -27000 ekin = 1.76021840072103 | erot = 3.70719293889859 | epot = -22.6409357152274 | etot = -17.1735243756077 -28000 ekin = 2.28064774169505 | erot = 2.34192414128161 | epot = -22.7124772012735 | etot = -18.0899053182968 -29000 ekin = 2.05883865245349 | erot = 1.85387249117169 | epot = -22.7242388348361 | etot = -18.811527691211 -30000 ekin = 2.41090888362676 | erot = 1.86304539977924 | epot = -22.6876650006964 | etot = -18.4137107172904 -31000 ekin = 2.76955959719985 | erot = 2.74117025737249 | epot = -22.6962463526981 | etot = -17.1855164981257 -32000 ekin = 2.08562644954365 | erot = 2.81609166367558 | epot = -22.7309387973059 | etot = -17.8292206840867 -33000 ekin = 2.08306771838837 | erot = 3.6412168312574 | epot = -22.671701882331 | etot = -16.9474173326852 -34000 ekin = 2.32648544880974 | erot = 3.09480128654123 | epot = -22.5637155764017 | etot = -17.1424288410507 -35000 ekin = 2.32492461599899 | erot = 2.02549181832456 | epot = -22.4811871522455 | etot = -18.1307707179219 -36000 ekin = 1.9160219633488 | erot = 1.97655634076097 | epot = -22.3849871062612 | etot = -18.4924088021514 -37000 ekin = 1.57338784336504 | erot = 2.62872199467344 | epot = -22.3528406869297 | etot = -18.1507308488912 -38000 ekin = 2.21547906806797 | erot = 2.89630123965964 | epot = -22.3056616105138 | etot = -17.1938813027862 -39000 ekin = 2.55049061085212 | erot = 2.46486573403212 | epot = -22.2602280028032 | etot = -17.244871657919 -40000 ekin = 2.25628181110086 | erot = 1.87515483835113 | epot = -22.2878959489406 | etot = -18.1564592994886 -41000 ekin = 2.46478791133629 | erot = 2.50742704532316 | epot = -22.3614598606398 | etot = -17.3892449039804 -42000 ekin = 2.69217693496336 | erot = 2.04021031621289 | epot = -22.3505245167544 | etot = -17.6181372655782 -43000 ekin = 2.40211339309477 | erot = 1.6668978842528 | epot = -22.353509525279 | etot = -18.2844982479314 -44000 ekin = 2.30891568897327 | erot = 2.40213237626172 | epot = -22.3871831090405 | etot = -17.6761350438055 -45000 ekin = 1.83275065976638 | erot = 2.26068140262528 | epot = -22.4994702091406 | etot = -18.406038146749 -46000 ekin = 1.97585087518641 | erot = 3.0186371421683 | epot = -22.4902643909032 | etot = -17.4957763735485 -47000 ekin = 1.30702141485601 | erot = 1.99592830992523 | epot = -22.4679405795691 | etot = -19.1649908547879 -48000 ekin = 2.58893650014613 | erot = 1.90050780837457 | epot = -22.5072015009757 | etot = -18.017757192455 -49000 ekin = 2.30293607053961 | erot = 2.71885537559561 | epot = -22.5026363414396 | etot = -17.4808448953044 -50000 ekin = 2.47053682632632 | erot = 3.4216531112208 | epot = -22.415032340787 | etot = -16.5228424032399 -51000 ekin = 2.70972992123879 | erot = 1.4301791663753 | epot = -22.3056750708571 | etot = -18.165765983243 -52000 ekin = 3.01390456844682 | erot = 1.97787470370191 | epot = -22.2827481318966 | etot = -17.2909688597479 -53000 ekin = 2.43796472406694 | erot = 4.25598325759163 | epot = -22.2611961774508 | etot = -15.5672481957922 -54000 ekin = 2.47286167616923 | erot = 2.3677730007818 | epot = -22.243519577301 | etot = -17.40288490035 -55000 ekin = 2.25994505035907 | erot = 1.91872181759988 | epot = -22.2996523252175 | etot = -18.1209854572585 -56000 ekin = 2.3461223108806 | erot = 2.20461695689782 | epot = -22.370356062429 | etot = -17.8196167946505 -57000 ekin = 2.51587877543148 | erot = 2.87451767129977 | epot = -22.4723343857415 | etot = -17.0819379390103 -58000 ekin = 2.49925674722554 | erot = 2.80569508565646 | epot = -22.5303780310556 | etot = -17.2254261981736 -59000 ekin = 2.75080755995156 | erot = 2.17181245800364 | epot = -22.5861118023788 | etot = -17.6634917844236 -60000 ekin = 3.2849676836621 | erot = 1.98487748777051 | epot = -22.5789662701264 | etot = -17.3091210986938 -61000 ekin = 2.4147550327795 | erot = 1.80972454908232 | epot = -22.5207352876114 | etot = -18.2962557057495 -62000 ekin = 2.82665653061546 | erot = 1.68517769072779 | epot = -22.4078181490349 | etot = -17.8959839276917 -63000 ekin = 3.70002607874218 | erot = 1.92704686824234 | epot = -22.2626867402007 | etot = -16.6356137932161 -64000 ekin = 3.61736288982706 | erot = 3.03600982585025 | epot = -22.2659045523542 | etot = -15.6125318366769 -65000 ekin = 3.40363639902008 | erot = 3.89044870099903 | epot = -22.2274777177663 | etot = -14.9333926177472 -66000 ekin = 2.94418257190202 | erot = 2.45963190668857 | epot = -22.1363667635561 | etot = -16.7325522849655 -67000 ekin = 2.60477940218663 | erot = 2.10479080523513 | epot = -22.038362895265 | etot = -17.3287926878432 -68000 ekin = 2.57158327795866 | erot = 2.46431755410219 | epot = -22.0244560205645 | etot = -16.9885551885036 -69000 ekin = 2.43845102321476 | erot = 2.85996177461682 | epot = -22.0620804569545 | etot = -16.7636676591229 -70000 ekin = 3.08348233524936 | erot = 2.49640850205841 | epot = -22.1433186271748 | etot = -16.563427789867 -71000 ekin = 2.5576093427884 | erot = 2.50957641127969 | epot = -22.2697187660694 | etot = -17.2025330120013 -72000 ekin = 1.7831483145096 | erot = 2.52806261120156 | epot = -22.3815818044114 | etot = -18.0703708787002 -73000 ekin = 1.86053585113659 | erot = 2.3350857968737 | epot = -22.4387359493251 | etot = -18.2431143013148 -74000 ekin = 3.14016175467449 | erot = 2.13186507521504 | epot = -22.447062887188 | etot = -17.1750360572984 -75000 ekin = 2.60368665360454 | erot = 2.18680067560206 | epot = -22.4438479629936 | etot = -17.653360633787 -76000 ekin = 1.9633244939079 | erot = 1.96057322365503 | epot = -22.4704022140376 | etot = -18.5465044964747 -77000 ekin = 2.09841107775422 | erot = 2.1471460143176 | epot = -22.4970899098551 | etot = -18.2515328177832 -78000 ekin = 2.49484391610508 | erot = 2.50538853212234 | epot = -22.4472882748805 | etot = -17.4470558266531 -79000 ekin = 3.10058476014063 | erot = 2.47637061915656 | epot = -22.3558276087081 | etot = -16.7788722294109 -80000 ekin = 2.52610159631253 | erot = 1.89085194000216 | epot = -22.2951000287249 | etot = -17.8781464924102 -81000 ekin = 2.34286765202483 | erot = 2.2376810918426 | epot = -22.2933034850974 | etot = -17.71275474123 -82000 ekin = 1.55517061572748 | erot = 2.02195112736337 | epot = -22.2470532436032 | etot = -18.6699315005123 -83000 ekin = 2.27421747802727 | erot = 3.34135950792192 | epot = -22.2406089881454 | etot = -16.6250320021963 -84000 ekin = 2.91603956429582 | erot = 2.09861057599124 | epot = -22.2305865946953 | etot = -17.2159364544083 -85000 ekin = 3.17172070756641 | erot = 2.91883241347319 | epot = -22.2381339647476 | etot = -16.147580843708 -86000 ekin = 3.48918734688943 | erot = 2.79711547316344 | epot = -22.2890012778608 | etot = -16.0026984578079 -87000 ekin = 3.648834525211 | erot = 2.30637362835037 | epot = -22.2817018896603 | etot = -16.3264937360989 -88000 ekin = 3.16156585935194 | erot = 2.24503314085539 | epot = -22.2225172277202 | etot = -16.8159182275129 -89000 ekin = 3.32092350591891 | erot = 1.79966969251215 | epot = -22.1549711261911 | etot = -17.03437792776 -90000 ekin = 2.41383485147934 | erot = 2.22694238351369 | epot = -21.9352492588881 | etot = -17.294472023895 -91000 ekin = 1.87769980964557 | erot = 2.50898156232204 | epot = -21.766796868726 | etot = -17.3801154967584 -92000 ekin = 2.06420930396832 | erot = 2.23853979300919 | epot = -21.6902828653619 | etot = -17.3875337683844 -93000 ekin = 1.94960374605101 | erot = 3.00245663654886 | epot = -21.6771969695753 | etot = -16.7251365869754 -94000 ekin = 2.07633340602167 | erot = 3.38669471112637 | epot = -21.7794316475531 | etot = -16.3164035304051 -95000 ekin = 2.09307446139111 | erot = 2.0811295310408 | epot = -21.9165143849258 | etot = -17.7423103924939 -96000 ekin = 2.66782345206074 | erot = 1.87453507536254 | epot = -21.9748225431664 | etot = -17.4324640157432 -97000 ekin = 1.93962158410337 | erot = 2.81228342262069 | epot = -22.0301811391172 | etot = -17.2782761323932 -98000 ekin = 1.98651083318125 | erot = 2.05358325550364 | epot = -22.1050988415859 | etot = -18.065004752901 -99000 ekin = 2.50729461715162 | erot = 3.55227490812968 | epot = -22.2148658268239 | etot = -16.1552963015426 -100000 ekin = 1.87954195221303 | erot = 2.38994009743578 | epot = -22.3826768493088 | etot = -18.11319479966 -101000 ekin = 1.66917867676911 | erot = 3.61296864361924 | epot = -22.4122779848186 | etot = -17.1301306644303 -102000 ekin = 1.63707836649616 | erot = 3.33958463197985 | epot = -22.3664797586262 | etot = -17.3898167601502 -103000 ekin = 2.00216132457488 | erot = 2.34409134088738 | epot = -22.338100531932 | etot = -17.9918478664698 -104000 ekin = 2.03704734920245 | erot = 2.74903331701925 | epot = -22.3478074938274 | etot = -17.5617268276057 -105000 ekin = 1.85601249652044 | erot = 2.00020228548217 | epot = -22.2937670136133 | etot = -18.4375522316107 -106000 ekin = 1.70582694215149 | erot = 1.90992656339968 | epot = -22.3252996603125 | etot = -18.7095461547614 -107000 ekin = 2.61183521416777 | erot = 1.56756438600251 | epot = -22.3815585845482 | etot = -18.2021589843779 -108000 ekin = 2.13345133147477 | erot = 2.1967764492834 | epot = -22.2873637709221 | etot = -17.9571359901639 -109000 ekin = 2.23517703897427 | erot = 2.12289589403282 | epot = -22.1519605830327 | etot = -17.7938876500256 -110000 ekin = 1.66340581480182 | erot = 2.52573727214601 | epot = -22.1681066766204 | etot = -17.9789635896725 -111000 ekin = 2.28529122032929 | erot = 2.24044883756493 | epot = -22.1711980210611 | etot = -17.6454579631669 -112000 ekin = 2.60405127944181 | erot = 2.43646974545776 | epot = -22.1582164438795 | etot = -17.11769541898 -113000 ekin = 2.40208651796091 | erot = 3.06270264515793 | epot = -22.1587051510952 | etot = -16.6939159879764 -114000 ekin = 2.34302229470158 | erot = 2.30426477746864 | epot = -22.1439772736805 | etot = -17.4966902015103 -115000 ekin = 1.69616053999229 | erot = 3.11049212247371 | epot = -22.1736739038021 | etot = -17.3670212413361 -116000 ekin = 1.51961045217859 | erot = 2.22203808801726 | epot = -22.2355447345615 | etot = -18.4938961943657 -117000 ekin = 1.69355164638512 | erot = 2.33913072714747 | epot = -22.2671845473364 | etot = -18.2345021738038 -118000 ekin = 2.1960991163694 | erot = 2.33815079858085 | epot = -22.2453229868293 | etot = -17.7110730718791 -119000 ekin = 2.55982892523823 | erot = 2.47378749563683 | epot = -22.2824155531543 | etot = -17.2487991322793 -120000 ekin = 1.76091001620491 | erot = 2.1741296357231 | epot = -22.2369948282136 | etot = -18.3019551762855 -121000 ekin = 2.80671234452976 | erot = 2.30128219469303 | epot = -22.2260257995407 | etot = -17.1180312603179 -122000 ekin = 3.23136903340218 | erot = 3.30036165167127 | epot = -22.2515019863338 | etot = -15.7197713012603 -123000 ekin = 2.8561114897291 | erot = 3.24294818442618 | epot = -22.2018342366988 | etot = -16.1027745625435 -124000 ekin = 2.14842162472016 | erot = 2.7693802805091 | epot = -22.0303368839078 | etot = -17.1125349786785 -125000 ekin = 1.83317468651689 | erot = 1.37271219749613 | epot = -21.8885764971633 | etot = -18.6826896131502 -126000 ekin = 2.45181092117661 | erot = 3.08753876167365 | epot = -21.8912653158441 | etot = -16.3519156329938 -127000 ekin = 2.39800706812202 | erot = 2.35255982488708 | epot = -21.8786845575463 | etot = -17.1281176645372 -128000 ekin = 2.72073389273301 | erot = 1.81206134758344 | epot = -21.8246886433981 | etot = -17.2918934030816 -129000 ekin = 2.76648233159587 | erot = 2.90133130407443 | epot = -21.9103698595755 | etot = -16.2425562239052 -130000 ekin = 3.26919771496399 | erot = 2.56804213542044 | epot = -22.0468205769693 | etot = -16.2095807265849 -131000 ekin = 2.65797021501453 | erot = 2.51912811588696 | epot = -22.1046945041584 | etot = -16.9275961732569 -132000 ekin = 2.60615175826329 | erot = 3.39821871959342 | epot = -22.1393658191679 | etot = -16.1349953413112 -133000 ekin = 2.01702653257964 | erot = 2.88164356754679 | epot = -22.1083395633022 | etot = -17.2096694631758 -134000 ekin = 1.62732528940444 | erot = 1.66916296573806 | epot = -22.0617984863721 | etot = -18.7653102312296 -135000 ekin = 2.44472224525446 | erot = 2.12100291286044 | epot = -22.0290071826116 | etot = -17.4632820244967 -136000 ekin = 2.29361895961086 | erot = 3.04813516280966 | epot = -21.9240579822781 | etot = -16.5823038598575 -137000 ekin = 2.71943103843212 | erot = 2.46250134466529 | epot = -21.759346222065 | etot = -16.5774138389676 -138000 ekin = 3.29026615453928 | erot = 1.74005246857097 | epot = -21.7424803627639 | etot = -16.7121617396537 -139000 ekin = 2.76078280183931 | erot = 1.72093988964439 | epot = -21.8915740702781 | etot = -17.4098513787944 -140000 ekin = 2.72717929836212 | erot = 2.46093572161851 | epot = -21.9730696792527 | etot = -16.784954659272 -141000 ekin = 2.79178566984556 | erot = 2.45152416051809 | epot = -21.9760531770405 | etot = -16.7327433466769 -142000 ekin = 3.51808959230238 | erot = 3.47662361887462 | epot = -21.9144706671159 | etot = -14.9197574559389 -143000 ekin = 2.56674276565954 | erot = 2.02320192154355 | epot = -21.887847774869 | etot = -17.2979030876659 -144000 ekin = 3.71876753045239 | erot = 3.03518010984555 | epot = -21.8693810552709 | etot = -15.115433414973 -145000 ekin = 3.61067898932004 | erot = 2.70461629179152 | epot = -21.7768865247848 | etot = -15.4615912436733 -146000 ekin = 3.85672431702576 | erot = 2.48360222237068 | epot = -21.7383083831155 | etot = -15.3979818437191 -147000 ekin = 3.26264642879795 | erot = 2.07790943830875 | epot = -21.612808589745 | etot = -16.2722527226383 -148000 ekin = 2.49411629896921 | erot = 1.64570933977901 | epot = -21.3601881264357 | etot = -17.2203624876875 -149000 ekin = 2.73353556199719 | erot = 2.27529903215971 | epot = -21.180923940444 | etot = -16.1720893462871 -150000 ekin = 2.6282457385967 | erot = 2.90058901460194 | epot = -21.0864924194498 | etot = -15.5576576662512 -151000 ekin = 2.07954165316093 | erot = 2.1164125590575 | epot = -20.9951076802445 | etot = -16.7991534680261 -152000 ekin = 2.41868973763601 | erot = 2.60413735099777 | epot = -20.8520585412647 | etot = -15.8292314526309 -153000 ekin = 2.12569822788918 | erot = 2.25674944787518 | epot = -20.8874716791535 | etot = -16.5050240033891 -154000 ekin = 2.34486280100484 | erot = 2.61050919353092 | epot = -20.9924730886396 | etot = -16.0371010941038 -155000 ekin = 2.06912274657395 | erot = 3.0299583491991 | epot = -21.0207700832301 | etot = -15.921688987457 -156000 ekin = 2.03235057930374 | erot = 3.18386486882217 | epot = -20.8574059636368 | etot = -15.6411905155109 -157000 ekin = 2.3579061324469 | erot = 1.91132393217369 | epot = -20.8256173876826 | etot = -16.556387323062 -158000 ekin = 2.17332819176356 | erot = 2.47832446500284 | epot = -20.9206749462161 | etot = -16.2690222894497 -159000 ekin = 2.87139796431922 | erot = 2.29125458595932 | epot = -21.0425793637301 | etot = -15.8799268134516 -160000 ekin = 2.19495281512895 | erot = 2.37206762182712 | epot = -21.12868212155 | etot = -16.5616616845939 -161000 ekin = 2.13209841436583 | erot = 2.44149028746738 | epot = -21.2267263358883 | etot = -16.6531376340551 -162000 ekin = 1.75046056470489 | erot = 2.66847316377717 | epot = -21.2792984888785 | etot = -16.8603647603965 -163000 ekin = 2.22203312194875 | erot = 2.03600602857084 | epot = -21.4244626156303 | etot = -17.1664234651107 -164000 ekin = 2.74926161019501 | erot = 1.42936965542836 | epot = -21.5631783920293 | etot = -17.384547126406 -165000 ekin = 2.66465183950737 | erot = 2.28908630196103 | epot = -21.572272285795 | etot = -16.6185341443266 -166000 ekin = 3.29267065001881 | erot = 2.38564084157004 | epot = -21.5039232020267 | etot = -15.8256117104378 -167000 ekin = 3.03664818915841 | erot = 2.03669674074452 | epot = -21.5747204885882 | etot = -16.5013755586853 -168000 ekin = 3.16556842965113 | erot = 1.85206282714724 | epot = -21.6223493129218 | etot = -16.6047180561234 -169000 ekin = 2.24511985727904 | erot = 2.66889068764969 | epot = -21.5368970033532 | etot = -16.6228864584245 -170000 ekin = 2.43734116474603 | erot = 2.49716986363814 | epot = -21.3912465276853 | etot = -16.4567354993011 -171000 ekin = 1.90620260936893 | erot = 2.39687883544744 | epot = -21.3008997539566 | etot = -16.9978183091402 -172000 ekin = 2.87444998880216 | erot = 3.21713663160875 | epot = -21.2616188758685 | etot = -15.1700322554576 -173000 ekin = 2.74942738368889 | erot = 2.14120450530294 | epot = -21.2850360200821 | etot = -16.3944041310903 -174000 ekin = 2.4529377396394 | erot = 2.23261644076142 | epot = -21.3299047479428 | etot = -16.644350567542 -175000 ekin = 2.84864650053625 | erot = 2.37733794803682 | epot = -21.2943230039461 | etot = -16.068338555373 -176000 ekin = 2.13647755199109 | erot = 1.89602819204849 | epot = -21.3605335602015 | etot = -17.3280278161619 -177000 ekin = 2.57740970525463 | erot = 2.74252419383388 | epot = -21.3306809364134 | etot = -16.0107470373249 -178000 ekin = 1.83680522170069 | erot = 2.5856914127028 | epot = -21.2632846497336 | etot = -16.8407880153301 -179000 ekin = 2.51484018139121 | erot = 2.38459479892641 | epot = -21.325303559771 | etot = -16.4258685794534 -180000 ekin = 1.88523508330591 | erot = 2.46381998482447 | epot = -21.4811020579528 | etot = -17.1320469898224 -181000 ekin = 1.75689043588625 | erot = 3.04324017089631 | epot = -21.474228259015 | etot = -16.6740976522324 -182000 ekin = 1.56534231241504 | erot = 2.04864866727399 | epot = -21.4129540971941 | etot = -17.798963117505 -183000 ekin = 2.00287899563344 | erot = 2.82515065812734 | epot = -21.49258719815 | etot = -16.6645575443892 -184000 ekin = 2.68544625765532 | erot = 2.43626281495748 | epot = -21.6103862218356 | etot = -16.4886771492228 -185000 ekin = 2.99891111533195 | erot = 3.19602779235331 | epot = -21.6822175762628 | etot = -15.4872786685775 -186000 ekin = 3.18195376963592 | erot = 2.43765957688182 | epot = -21.7117512273523 | etot = -16.0921378808346 -187000 ekin = 2.64722090162018 | erot = 3.43145857630564 | epot = -21.6694156065006 | etot = -15.5907361285748 -188000 ekin = 2.8593721905413 | erot = 3.05764002667605 | epot = -21.6129263142805 | etot = -15.6959140970631 -189000 ekin = 2.64258352431382 | erot = 1.81957536948003 | epot = -21.5503774009301 | etot = -17.0882185071363 -190000 ekin = 2.2190608435254 | erot = 1.84740673329965 | epot = -21.5105703637082 | etot = -17.4441027868831 -191000 ekin = 2.27442549063464 | erot = 2.06581774328105 | epot = -21.4485511972947 | etot = -17.108307963379 -192000 ekin = 2.27419285809427 | erot = 3.10822480468651 | epot = -21.4844439428341 | etot = -16.1020262800533 -193000 ekin = 1.95256612457884 | erot = 1.88944690058107 | epot = -21.4719648319093 | etot = -17.6299518067494 -194000 ekin = 2.46290863552507 | erot = 2.02714246570739 | epot = -21.3483686370757 | etot = -16.8583175358433 -195000 ekin = 3.12615833704228 | erot = 2.09882827884293 | epot = -21.2854694780647 | etot = -16.0604828621794 -196000 ekin = 2.70126861243405 | erot = 2.51307250710585 | epot = -21.2052184052664 | etot = -15.9908772857265 -197000 ekin = 2.55113347479427 | erot = 2.07490331769114 | epot = -21.0379488001649 | etot = -16.4119120076795 -198000 ekin = 2.7091171175815 | erot = 1.79542986755821 | epot = -21.0311079948236 | etot = -16.5265610096839 -199000 ekin = 2.57086088527333 | erot = 2.33194065149168 | epot = -21.0448935828999 | etot = -16.1420920461349 -200000 ekin = 2.89149033048946 | erot = 1.42165157230865 | epot = -21.03770919399 | etot = -16.7245672911919 -201000 ekin = 2.68304721320748 | erot = 1.55647352804279 | epot = -21.0368254418007 | etot = -16.7973047005504 -202000 ekin = 2.2656487707054 | erot = 2.24246330836477 | epot = -20.9783437689148 | etot = -16.4702316898446 -203000 ekin = 2.11263799464235 | erot = 2.0311722239375 | epot = -20.9045528293636 | etot = -16.7607426107837 -204000 ekin = 2.10289033168206 | erot = 1.89431766090034 | epot = -20.917707897003 | etot = -16.9204999044206 -205000 ekin = 1.32594040742044 | erot = 2.12787440210413 | epot = -20.9650467335179 | etot = -17.5112319239933 -206000 ekin = 1.37942510627947 | erot = 2.255876437166 | epot = -20.9344799697865 | etot = -17.299178426341 -207000 ekin = 1.89707208497052 | erot = 1.80792832329628 | epot = -21.0372131039119 | etot = -17.3322126956451 -208000 ekin = 1.82394216235567 | erot = 3.24636401083921 | epot = -21.2905133091558 | etot = -16.2202071359609 -209000 ekin = 2.80235035495642 | erot = 2.34817422826193 | epot = -21.4119988544966 | etot = -16.2614742712782 -210000 ekin = 3.17268831077415 | erot = 3.11920168004874 | epot = -21.4880486169942 | etot = -15.1961586261713 -211000 ekin = 2.46911290485391 | erot = 2.09583435351186 | epot = -21.6131156278285 | etot = -17.0481683694628 -212000 ekin = 2.36983963899524 | erot = 1.93490727968814 | epot = -21.6916906588951 | etot = -17.3869437402117 -213000 ekin = 1.90089387455099 | erot = 2.5187405361218 | epot = -21.7688631446424 | etot = -17.3492287339696 -214000 ekin = 1.97453946438608 | erot = 2.49804990679736 | epot = -21.7968032544022 | etot = -17.3242138832188 -215000 ekin = 1.97170537707849 | erot = 3.1720109210939 | epot = -21.7980499435109 | etot = -16.6543336453385 -216000 ekin = 1.89064429395263 | erot = 1.88113651267029 | epot = -21.7625464985643 | etot = -17.9907656919414 -217000 ekin = 2.0626433286583 | erot = 1.95286476791462 | epot = -21.8181895344454 | etot = -17.8026814378725 -218000 ekin = 2.31967181974704 | erot = 1.6896622434335 | epot = -21.7699992955268 | etot = -17.7606652323462 -219000 ekin = 2.46739391618502 | erot = 2.20775453602831 | epot = -21.776978875084 | etot = -17.1018304228706 -220000 ekin = 1.73785505731585 | erot = 3.0372433480804 | epot = -21.7321393101048 | etot = -16.9570409047086 -221000 ekin = 1.778697043089 | erot = 2.7846909329313 | epot = -21.7425830987872 | etot = -17.1791951227669 -222000 ekin = 2.62634865011186 | erot = 2.86077326472522 | epot = -21.7007933593054 | etot = -16.2136714444683 -223000 ekin = 3.04431297723215 | erot = 1.94008328047868 | epot = -21.7188465939138 | etot = -16.734450336203 -224000 ekin = 2.71939424183677 | erot = 2.42480251627533 | epot = -21.6866518782312 | etot = -16.5424551201191 -225000 ekin = 2.02593449761365 | erot = 3.37613250979673 | epot = -21.6919775986917 | etot = -16.2899105912813 -226000 ekin = 2.36496088602628 | erot = 2.39060577783945 | epot = -21.7612411053054 | etot = -17.0056744414397 -227000 ekin = 2.73527371921374 | erot = 2.63040468048003 | epot = -21.8235720454426 | etot = -16.4578936457488 -228000 ekin = 2.09009153610323 | erot = 2.26861924367323 | epot = -21.8859446312141 | etot = -17.5272338514377 -229000 ekin = 1.80131280326501 | erot = 1.7963110804324 | epot = -21.9677974652423 | etot = -18.3701735815449 -230000 ekin = 2.77436270232913 | erot = 2.22792046726092 | epot = -21.9902739646399 | etot = -16.9879907950498 -231000 ekin = 3.15789416871844 | erot = 2.77494856675301 | epot = -21.9771750398138 | etot = -16.0443323043424 -232000 ekin = 1.86920525086143 | erot = 1.70617009970185 | epot = -22.0127465263534 | etot = -18.4373711757901 -233000 ekin = 1.75915660001321 | erot = 1.56505378532405 | epot = -21.9936912811375 | etot = -18.6694808958002 -234000 ekin = 2.33631680564953 | erot = 2.05523369254154 | epot = -21.9151391633044 | etot = -17.5235886651133 -235000 ekin = 1.95729755108493 | erot = 2.52297007842176 | epot = -21.8622583087295 | etot = -17.3819906792228 -236000 ekin = 2.26174488772854 | erot = 1.90926942275389 | epot = -21.8776848863915 | etot = -17.7066705759091 -237000 ekin = 2.48859859508474 | erot = 2.6489237604941 | epot = -21.9479801146397 | etot = -16.8104577590608 -238000 ekin = 2.21074117955686 | erot = 2.74245988956904 | epot = -22.0027094279364 | etot = -17.0495083588105 -239000 ekin = 2.72897236706913 | erot = 2.49153579775713 | epot = -22.0211522435864 | etot = -16.8006440787602 -240000 ekin = 3.10410575629688 | erot = 2.19185039149975 | epot = -21.9285399490843 | etot = -16.6325838012877 -241000 ekin = 3.04659381738443 | erot = 2.65407823399251 | epot = -21.8553999209703 | etot = -16.1547278695933 -242000 ekin = 2.22634814860329 | erot = 2.33710119371497 | epot = -21.778295180705 | etot = -17.2148458383868 -243000 ekin = 1.53739989500925 | erot = 2.804422651144 | epot = -21.7210994015014 | etot = -17.3792768553481 -244000 ekin = 1.91594160283678 | erot = 2.43897673315061 | epot = -21.6239948430905 | etot = -17.2690765071031 -245000 ekin = 1.9573212108497 | erot = 2.60792757585164 | epot = -21.4969890421964 | etot = -16.931740255495 -246000 ekin = 2.07155268659352 | erot = 2.40712847472271 | epot = -21.4555802858827 | etot = -16.9768991245664 -247000 ekin = 1.55687592357629 | erot = 2.27937051296287 | epot = -21.415801560854 | etot = -17.5795551243148 -248000 ekin = 1.83815644169539 | erot = 2.56757546633135 | epot = -21.4396063392852 | etot = -17.0338744312585 -249000 ekin = 1.79880701831597 | erot = 2.0439839568354 | epot = -21.5116552123395 | etot = -17.6688642371882 -250000 ekin = 1.6819474109243 | erot = 3.39458382990459 | epot = -21.5432862054069 | etot = -16.466754964578 -251000 ekin = 2.13148829031636 | erot = 3.25959517865089 | epot = -21.5335137503413 | etot = -16.142430281374 -252000 ekin = 2.05395839402013 | erot = 2.53819950912971 | epot = -21.5603119938518 | etot = -16.9681540907019 -253000 ekin = 1.65837982841157 | erot = 3.21084156386521 | epot = -21.5856483774528 | etot = -16.716426985176 -254000 ekin = 2.32607189562296 | erot = 3.10904441141191 | epot = -21.5835562113995 | etot = -16.1484399043647 -255000 ekin = 2.50516183463011 | erot = 2.76806754476897 | epot = -21.5622650070292 | etot = -16.2890356276301 -256000 ekin = 1.97348594928106 | erot = 2.62554900973971 | epot = -21.5549569513865 | etot = -16.9559219923657 -257000 ekin = 2.23010268129159 | erot = 3.26394503338319 | epot = -21.5756937773404 | etot = -16.0816460626656 -258000 ekin = 2.0447966409083 | erot = 1.84671550533958 | epot = -21.6926265414806 | etot = -17.8011143952327 -259000 ekin = 2.87403716266236 | erot = 2.7890686554313 | epot = -21.799948240906 | etot = -16.1368424228124 -260000 ekin = 2.90780294403218 | erot = 2.19263097772001 | epot = -21.8560884935551 | etot = -16.7556545718029 -261000 ekin = 2.76828016335186 | erot = 2.34066383431491 | epot = -21.904753347489 | etot = -16.7958093498223 -262000 ekin = 3.52268021990509 | erot = 1.77075610541266 | epot = -21.923252751046 | etot = -16.6298164257282 -263000 ekin = 3.08420493567484 | erot = 2.42539400967894 | epot = -21.8573813915989 | etot = -16.3477824462451 -264000 ekin = 2.24745015945595 | erot = 2.03541588430139 | epot = -21.8692313889178 | etot = -17.5863653451605 -265000 ekin = 1.92522220276231 | erot = 2.5003676829468 | epot = -21.7418152763709 | etot = -17.3162253906618 -266000 ekin = 2.39641107663208 | erot = 3.25288398956727 | epot = -21.6961161037834 | etot = -16.046821037584 -267000 ekin = 1.71111784450077 | erot = 2.23671058890166 | epot = -21.6618183077995 | etot = -17.7139898743971 -268000 ekin = 2.10089423119538 | erot = 3.22434301936133 | epot = -21.6199098144813 | etot = -16.2946725639246 -269000 ekin = 1.9625053447265 | erot = 2.78709438989466 | epot = -21.512378343547 | etot = -16.7627786089258 -270000 ekin = 2.11347862898579 | erot = 2.66955708081142 | epot = -21.4131997021519 | etot = -16.6301639923547 -271000 ekin = 2.18755627878071 | erot = 3.10635949745237 | epot = -21.231195119641 | etot = -15.9372793434079 -272000 ekin = 2.53142755489725 | erot = 2.28018838604503 | epot = -21.0716416692008 | etot = -16.2600257282585 -273000 ekin = 1.9364743445402 | erot = 1.99261296885892 | epot = -21.007557675667 | etot = -17.0784703622679 -274000 ekin = 1.91013630831847 | erot = 2.2120127665723 | epot = -21.0477834541013 | etot = -16.9256343792105 -275000 ekin = 1.79273258693701 | erot = 3.10050032804429 | epot = -21.0858519409205 | etot = -16.1926190259392 -276000 ekin = 3.35719138398128 | erot = 2.41111345420191 | epot = -21.0304226706007 | etot = -15.2621178324176 -277000 ekin = 2.41774397151369 | erot = 1.50719443697989 | epot = -20.9759671563228 | etot = -17.0510287478292 -278000 ekin = 2.53951758510302 | erot = 2.14756601555722 | epot = -20.9653070148297 | etot = -16.2782234141694 -279000 ekin = 1.90856122527452 | erot = 2.38982437581387 | epot = -20.9745429336076 | etot = -16.6761573325192 -280000 ekin = 2.37131544290542 | erot = 3.59489996493466 | epot = -20.85613421052 | etot = -14.8899188026799 -281000 ekin = 1.76889591811704 | erot = 1.7951894912658 | epot = -20.9289254822807 | etot = -17.3648400728979 -282000 ekin = 2.27070827347114 | erot = 3.05009551199377 | epot = -20.8916515658568 | etot = -15.5708477803919 -283000 ekin = 2.18685960365006 | erot = 2.20812220616949 | epot = -20.8474969045899 | etot = -16.4525150947704 -284000 ekin = 1.91940159973892 | erot = 2.20890146173499 | epot = -20.8751887573221 | etot = -16.7468856958482 -285000 ekin = 3.15509933694634 | erot = 1.80738796351619 | epot = -21.0554892608396 | etot = -16.0930019603771 -286000 ekin = 3.87415003559708 | erot = 1.83530883692693 | epot = -21.2366462656484 | etot = -15.5271873931244 -287000 ekin = 3.65191681280166 | erot = 2.913547855761 | epot = -21.3085830740657 | etot = -14.7431184055031 -288000 ekin = 3.25566521528532 | erot = 1.61409275051713 | epot = -21.3016538192157 | etot = -16.4318958534132 -289000 ekin = 2.57277357969492 | erot = 2.7865509468974 | epot = -21.2753452951968 | etot = -15.9160207686044 -290000 ekin = 2.70842209282674 | erot = 2.41918512811132 | epot = -21.2877903800065 | etot = -16.1601831590685 -291000 ekin = 2.06014704473036 | erot = 2.36104758138505 | epot = -21.2845199368975 | etot = -16.8633253107821 -292000 ekin = 2.28556270655109 | erot = 2.04929815389926 | epot = -21.3435089189608 | etot = -17.0086480585104 -293000 ekin = 2.24999256733429 | erot = 2.35234276421049 | epot = -21.4532864362272 | etot = -16.8509511046824 -294000 ekin = 2.93128079968628 | erot = 2.88901294012339 | epot = -21.5344832077337 | etot = -15.7141894679241 -295000 ekin = 2.66786158124138 | erot = 2.29144551421467 | epot = -21.6972562684637 | etot = -16.7379491730076 -296000 ekin = 2.20703931624838 | erot = 2.91798090137806 | epot = -21.7499994740518 | etot = -16.6249792564254 -297000 ekin = 2.17711857895463 | erot = 3.3139407196584 | epot = -21.7438418246471 | etot = -16.2527825260341 -298000 ekin = 2.91263821701566 | erot = 2.35687557807243 | epot = -21.7003108484957 | etot = -16.4307970534076 -299000 ekin = 3.16765240032233 | erot = 2.23927360570976 | epot = -21.8111744518828 | etot = -16.4042484458507 -300000 ekin = 3.29571242152463 | erot = 1.38932168050636 | epot = -21.8854995787115 | etot = -17.2004654766805 -301000 ekin = 2.38336849338668 | erot = 3.30873138065989 | epot = -21.9040100279112 | etot = -16.2119101538647 -302000 ekin = 2.92546415072637 | erot = 3.247691767578 | epot = -21.8700812142841 | etot = -15.6969252959798 -303000 ekin = 2.4103373416559 | erot = 2.62018947425678 | epot = -21.8591741279587 | etot = -16.828647312046 -304000 ekin = 2.22974120288231 | erot = 2.69525972032883 | epot = -21.7977946057185 | etot = -16.8727936825074 -305000 ekin = 2.37900884029014 | erot = 2.39016080950149 | epot = -21.7722637572341 | etot = -17.0030941074424 -306000 ekin = 1.9446171443063 | erot = 2.89927908625624 | epot = -21.772518921465 | etot = -16.9286226909024 -307000 ekin = 2.51296678773709 | erot = 2.07871985749639 | epot = -21.7145354205816 | etot = -17.1228487753482 -308000 ekin = 2.81300442192371 | erot = 2.63068774502107 | epot = -21.7059595575782 | etot = -16.2622673906334 -309000 ekin = 2.33295752921531 | erot = 2.12114847477695 | epot = -21.6789859227475 | etot = -17.2248799187552 -310000 ekin = 2.52283407385729 | erot = 3.21577684610766 | epot = -21.6977338722704 | etot = -15.9591229523054 -311000 ekin = 2.34905401714491 | erot = 3.03961744974846 | epot = -21.7112095513776 | etot = -16.3225380844842 -312000 ekin = 1.82668239636477 | erot = 3.25882975871633 | epot = -21.5839087054203 | etot = -16.4983965503392 -313000 ekin = 1.63596397844578 | erot = 2.08106491982899 | epot = -21.6088054377576 | etot = -17.8917765394829 -314000 ekin = 2.27268061655198 | erot = 2.56861774872119 | epot = -21.622333325343 | etot = -16.7810349600698 -315000 ekin = 2.53123691731374 | erot = 2.1324731770604 | epot = -21.7018350864597 | etot = -17.0381249920856 -316000 ekin = 1.99511026234591 | erot = 1.80085053236165 | epot = -21.7165753862862 | etot = -17.9206145915787 -317000 ekin = 2.11342130166581 | erot = 2.00931752224566 | epot = -21.7049091699378 | etot = -17.5821703460263 -318000 ekin = 2.29657040201996 | erot = 1.9218952520588 | epot = -21.6732020643863 | etot = -17.4547364103076 -319000 ekin = 1.98100978177984 | erot = 1.68241530251755 | epot = -21.5700337503682 | etot = -17.9066086660708 -320000 ekin = 2.46277902525288 | erot = 3.0707129249839 | epot = -21.5118277867106 | etot = -15.9783358364738 -321000 ekin = 1.8533722862421 | erot = 2.67441728470359 | epot = -21.5413634192757 | etot = -17.01357384833 -322000 ekin = 1.94543884879318 | erot = 3.3613066315754 | epot = -21.4649757180038 | etot = -16.1582302376352 -323000 ekin = 1.92582236335168 | erot = 2.08582462630249 | epot = -21.5020070864549 | etot = -17.4903600968007 -324000 ekin = 2.21385975174577 | erot = 2.45972054558752 | epot = -21.6040339423077 | etot = -16.9304536449744 -325000 ekin = 2.71973574551436 | erot = 2.37172075216282 | epot = -21.7154750081878 | etot = -16.6240185105106 -326000 ekin = 1.88834012476607 | erot = 1.92160793718507 | epot = -21.7697066104337 | etot = -17.9597585484825 -327000 ekin = 3.03100650626309 | erot = 1.66914039489952 | epot = -21.8474776692767 | etot = -17.1473307681141 -328000 ekin = 2.74123304387623 | erot = 1.9170666048058 | epot = -21.8856206551572 | etot = -17.2273210064752 -329000 ekin = 2.94158338898171 | erot = 3.13997083102765 | epot = -21.9406516192959 | etot = -15.8590973992865 -330000 ekin = 2.91669398329971 | erot = 2.01301123001111 | epot = -21.9369752911326 | etot = -17.0072700778218 -331000 ekin = 2.28417665381006 | erot = 2.04960167200569 | epot = -21.927160006304 | etot = -17.5933816804883 -332000 ekin = 2.4148148688836 | erot = 3.18178691603942 | epot = -21.9797962539673 | etot = -16.3831944690443 -333000 ekin = 2.45630818257634 | erot = 2.70954264697347 | epot = -22.0834375892948 | etot = -16.917586759745 -334000 ekin = 2.37347521855933 | erot = 2.99534828037212 | epot = -22.119902754337 | etot = -16.7510792554055 -335000 ekin = 2.11274250313861 | erot = 3.56585847378427 | epot = -22.1620352555629 | etot = -16.48343427864 -336000 ekin = 2.63429420241716 | erot = 2.12841745309053 | epot = -22.1384285356293 | etot = -17.3757168801216 -337000 ekin = 2.74014146566976 | erot = 2.73588205536329 | epot = -22.1194416289215 | etot = -16.6434181078884 -338000 ekin = 1.84480508690214 | erot = 2.23455733552335 | epot = -22.1965093971539 | etot = -18.1171469747284 -339000 ekin = 1.56183988387053 | erot = 2.489100411134 | epot = -22.2396203002948 | etot = -18.1886800052903 -340000 ekin = 1.46409027371678 | erot = 4.0512372950447 | epot = -22.1584645354502 | etot = -16.6431369666887 -341000 ekin = 1.68589245970878 | erot = 2.79353148184118 | epot = -22.1393063295445 | etot = -17.6598823879945 -342000 ekin = 1.9632055547669 | erot = 2.74455536956775 | epot = -22.2008946996018 | etot = -17.4931337752671 -343000 ekin = 2.66782090058793 | erot = 3.18156117072004 | epot = -22.2922370675599 | etot = -16.4428549962519 -344000 ekin = 1.78878469299216 | erot = 2.18063379585249 | epot = -22.3229742728833 | etot = -18.3535557840387 -345000 ekin = 1.540972096623 | erot = 1.85836807653953 | epot = -22.3669594635967 | etot = -18.9676192904341 -346000 ekin = 1.69306131915114 | erot = 1.80797582028411 | epot = -22.3312791976866 | etot = -18.8302420582514 -347000 ekin = 1.37617258934979 | erot = 2.61616357123582 | epot = -22.3534264320593 | etot = -18.3610902714737 -348000 ekin = 2.13829045790164 | erot = 2.85908731375532 | epot = -22.3464198630052 | etot = -17.3490420913483 -349000 ekin = 1.82945196641201 | erot = 1.97678849263654 | epot = -22.3619223728943 | etot = -18.5556819138458 -350000 ekin = 1.78944470920989 | erot = 2.50950790539659 | epot = -22.3467767277336 | etot = -18.0478241131271 -351000 ekin = 1.68749587286921 | erot = 2.81742906170281 | epot = -22.4171372510498 | etot = -17.9122123164778 -352000 ekin = 2.77021178817643 | erot = 2.15256178979697 | epot = -22.5877268787862 | etot = -17.6649533008128 -353000 ekin = 3.5651579503159 | erot = 1.46627940614144 | epot = -22.6396840781933 | etot = -17.608246721736 -354000 ekin = 3.44763260550689 | erot = 2.25092776011915 | epot = -22.5553143373262 | etot = -16.8567539717001 -355000 ekin = 2.03402845200418 | erot = 2.90906782343746 | epot = -22.5137132330461 | etot = -17.5706169576044 -356000 ekin = 2.10644486273696 | erot = 3.31938387624324 | epot = -22.5442634045104 | etot = -17.1184346655302 -357000 ekin = 2.76535001946383 | erot = 2.50873330135166 | epot = -22.52215971412 | etot = -17.2480763933045 -358000 ekin = 2.53751054023787 | erot = 2.26477084741189 | epot = -22.5103746530379 | etot = -17.7080932653881 -359000 ekin = 3.23570364771486 | erot = 2.52813698122051 | epot = -22.6019986378314 | etot = -16.838158008896 -360000 ekin = 2.59175576606819 | erot = 1.97223576668381 | epot = -22.6470028729806 | etot = -18.0830113402286 -361000 ekin = 2.61182361704566 | erot = 2.50385714239847 | epot = -22.6927829246934 | etot = -17.5771021652493 -362000 ekin = 2.38475515872101 | erot = 3.84233912950958 | epot = -22.6454854809905 | etot = -16.4183911927599 -363000 ekin = 2.88487115582968 | erot = 1.98709532428838 | epot = -22.5316518293815 | etot = -17.6596853492635 -364000 ekin = 2.24456282663807 | erot = 1.87857741688963 | epot = -22.4065988337859 | etot = -18.2834585902582 -365000 ekin = 2.04295690198209 | erot = 2.81008642631349 | epot = -22.2314366274422 | etot = -17.3783932991466 -366000 ekin = 2.266544192376 | erot = 1.95642386899595 | epot = -22.1933765521819 | etot = -17.97040849081 -367000 ekin = 2.81580114465084 | erot = 2.51878026336671 | epot = -22.2503978612043 | etot = -16.9158164531867 -368000 ekin = 2.81616947616975 | erot = 2.18673959088794 | epot = -22.3700662776457 | etot = -17.367157210588 -369000 ekin = 2.31685128708704 | erot = 2.8485166214536 | epot = -22.4347113127671 | etot = -17.2693434042264 -370000 ekin = 2.66633369096824 | erot = 2.10373843245294 | epot = -22.5097473869516 | etot = -17.7396752635304 -371000 ekin = 2.19554700980946 | erot = 3.61136788339347 | epot = -22.5751109079912 | etot = -16.7681960147883 -372000 ekin = 1.77355024694411 | erot = 3.42422008956619 | epot = -22.6682235461143 | etot = -17.470453209604 -373000 ekin = 2.14882393689494 | erot = 2.79102164241389 | epot = -22.7183823639386 | etot = -17.7785367846297 -374000 ekin = 2.69471790401649 | erot = 3.57888941010137 | epot = -22.8644350080836 | etot = -16.5908276939657 -375000 ekin = 2.40588229328688 | erot = 2.98559431132055 | epot = -22.9231560989464 | etot = -17.5316794943389 -376000 ekin = 3.36525975858234 | erot = 3.24749522030667 | epot = -22.9448546765658 | etot = -16.3320996976767 -377000 ekin = 3.1898535090454 | erot = 2.65440981370779 | epot = -22.8890189773608 | etot = -17.0447556546076 -378000 ekin = 1.54661929765086 | erot = 2.66304115784623 | epot = -22.8894135140088 | etot = -18.6797530585117 -379000 ekin = 1.93848939303329 | erot = 2.54534330055222 | epot = -22.9081180555037 | etot = -18.4242853619182 -380000 ekin = 2.66258042260528 | erot = 2.88895789126712 | epot = -22.9376621442708 | etot = -17.3861238303984 -381000 ekin = 2.95374671041029 | erot = 2.1769850563328 | epot = -22.9816080577256 | etot = -17.8508762909825 -382000 ekin = 2.58850292280408 | erot = 2.01885613358327 | epot = -22.9279053853416 | etot = -18.3205463289542 -383000 ekin = 2.01542491830335 | erot = 2.50444856286716 | epot = -22.9509700194999 | etot = -18.4310965383294 -384000 ekin = 2.10088918623931 | erot = 2.19861971638621 | epot = -22.9637245689725 | etot = -18.664215666347 -385000 ekin = 1.91381637067085 | erot = 1.63023926713733 | epot = -22.9798616984434 | etot = -19.4358060606352 -386000 ekin = 1.55997375471681 | erot = 1.35864886272388 | epot = -23.026401230456 | etot = -20.1077786130153 -387000 ekin = 2.21265030198491 | erot = 1.7501227932087 | epot = -23.0266356759123 | etot = -19.0638625807187 -388000 ekin = 1.98732621523102 | erot = 1.96003045102707 | epot = -22.9343684877508 | etot = -18.9870118214927 -389000 ekin = 2.5418388293764 | erot = 2.33933777400626 | epot = -22.9288764120935 | etot = -18.0476998087109 -390000 ekin = 2.07840415144685 | erot = 1.88714080084969 | epot = -22.8368099519711 | etot = -18.8712649996745 -391000 ekin = 1.85201287716429 | erot = 2.41309749069991 | epot = -22.8035614550317 | etot = -18.5384510871675 -392000 ekin = 2.19897450334475 | erot = 2.90002030847564 | epot = -22.8026053664846 | etot = -17.7036105546642 -393000 ekin = 2.15250422129825 | erot = 3.1954140871906 | epot = -22.8935871868038 | etot = -17.5456688783149 -394000 ekin = 1.99220043003136 | erot = 2.14720550675182 | epot = -22.8839525821639 | etot = -18.7445466453807 -395000 ekin = 2.03384825587122 | erot = 2.5026704188622 | epot = -22.9355340107645 | etot = -18.3990153360311 -396000 ekin = 2.14388612805494 | erot = 1.95887569078926 | epot = -23.0314147787906 | etot = -18.9286529599464 -397000 ekin = 2.39817268086959 | erot = 1.65198489715495 | epot = -23.1381610188687 | etot = -19.0880034408442 -398000 ekin = 3.5848529329223 | erot = 2.5137795193631 | epot = -23.2493671328086 | etot = -17.1507346805232 -399000 ekin = 2.65690410152896 | erot = 1.78815540583896 | epot = -23.3551071826471 | etot = -18.9100476752792 -400000 ekin = 2.5116972230557 | erot = 2.10904464709597 | epot = -23.4242760069967 | etot = -18.803534136845 -401000 ekin = 2.05111703519218 | erot = 2.15375363886755 | epot = -23.4796569613041 | etot = -19.2747862872443 -402000 ekin = 2.43372934314587 | erot = 2.11260100954187 | epot = -23.4682554876931 | etot = -18.9219251350053 -403000 ekin = 2.53598880596584 | erot = 2.81278076880176 | epot = -23.5378775828587 | etot = -18.1891080080911 -404000 ekin = 2.18194702425602 | erot = 2.63711249102604 | epot = -23.6244518702206 | etot = -18.8053923549385 -405000 ekin = 2.45121967393562 | erot = 2.40500763090291 | epot = -23.6357713162683 | etot = -18.7795440114298 -406000 ekin = 2.21958671378093 | erot = 2.24922226746756 | epot = -23.6553601287 | etot = -19.1865511474515 -407000 ekin = 1.98564574231222 | erot = 2.77863717556005 | epot = -23.5607032705187 | etot = -18.7964203526464 -408000 ekin = 2.57646591315375 | erot = 2.58095218000659 | epot = -23.4398366413677 | etot = -18.2824185482073 -409000 ekin = 2.36945583486912 | erot = 2.25935935813466 | epot = -23.3294611001761 | etot = -18.7006459071724 -410000 ekin = 2.02254604345491 | erot = 1.96483214055515 | epot = -23.3122760741247 | etot = -19.3248978901146 -411000 ekin = 1.87895167522371 | erot = 2.65152784802951 | epot = -23.2919254735047 | etot = -18.7614459502515 -412000 ekin = 1.99369299492691 | erot = 2.68971636909523 | epot = -23.2559513781021 | etot = -18.57254201408 -413000 ekin = 2.38900558877156 | erot = 2.64564764432049 | epot = -23.2013938450539 | etot = -18.1667406119618 -414000 ekin = 2.42764300748033 | erot = 1.75174590229272 | epot = -23.1266922276306 | etot = -18.9473033178576 -415000 ekin = 2.76414124953308 | erot = 2.44215852210494 | epot = -23.1817305186064 | etot = -17.9754307469683 -416000 ekin = 2.08280868301927 | erot = 2.76578542751831 | epot = -23.1905832299196 | etot = -18.341989119382 -417000 ekin = 1.99968890800012 | erot = 1.95787693284286 | epot = -23.194417716001 | etot = -19.236851875158 -418000 ekin = 2.38298881868294 | erot = 2.55898711987873 | epot = -23.1586352965619 | etot = -18.2166593580002 -419000 ekin = 2.9839633883085 | erot = 2.57065203496089 | epot = -23.0544780894577 | etot = -17.4998626661883 -420000 ekin = 2.60178854557762 | erot = 2.46052060802045 | epot = -22.9622762729971 | etot = -17.899967119399 -421000 ekin = 2.51720276737396 | erot = 1.77804167911051 | epot = -22.9515897224038 | etot = -18.6563452759193 -422000 ekin = 2.7320348139792 | erot = 1.67298118116889 | epot = -22.9404137463627 | etot = -18.5353977512146 -423000 ekin = 2.13282380031375 | erot = 2.54987675813572 | epot = -22.8157706530705 | etot = -18.133070094621 -424000 ekin = 1.90610672595356 | erot = 2.31894231724673 | epot = -22.7787002443962 | etot = -18.553651201196 -425000 ekin = 2.37366400687573 | erot = 1.95578603620107 | epot = -22.7873996262579 | etot = -18.4579495831811 -426000 ekin = 2.23502410344739 | erot = 2.60951465135819 | epot = -22.8069525247999 | etot = -17.9624137699943 -427000 ekin = 1.88572309905852 | erot = 2.12675775194484 | epot = -22.973782602072 | etot = -18.9613017510686 -428000 ekin = 1.93180562731872 | erot = 2.45432362930894 | epot = -23.1062681387344 | etot = -18.7201388821067 -429000 ekin = 1.72618205037519 | erot = 2.1638575670951 | epot = -23.1203764425356 | etot = -19.2303368250654 -430000 ekin = 2.31236502680075 | erot = 2.14057167953237 | epot = -23.127316365141 | etot = -18.6743796588079 -431000 ekin = 2.45859340033276 | erot = 2.41557475448707 | epot = -23.137683007962 | etot = -18.2635148531422 -432000 ekin = 2.80043339920945 | erot = 2.19140888866301 | epot = -23.1459051340744 | etot = -18.1540628462019 -433000 ekin = 2.2038223816989 | erot = 1.62239062651454 | epot = -23.1902054552061 | etot = -19.3639924469927 -434000 ekin = 2.59117398719482 | erot = 2.35262979682601 | epot = -23.2174180769097 | etot = -18.2736142928889 -435000 ekin = 2.29283868462832 | erot = 2.54026007379789 | epot = -23.1968654207439 | etot = -18.3637666623176 -436000 ekin = 2.43256920688117 | erot = 2.74968424233253 | epot = -23.2466230085986 | etot = -18.0643695593849 -437000 ekin = 1.64425125112848 | erot = 3.23329270267647 | epot = -23.2380191669749 | etot = -18.3604752131699 -438000 ekin = 1.56124620606823 | erot = 2.60252333491232 | epot = -23.1341667906033 | etot = -18.9703972496228 -439000 ekin = 2.30501653948793 | erot = 1.93890022921162 | epot = -23.14170715719 | etot = -18.8977903884904 -440000 ekin = 2.52023257151789 | erot = 3.04669715760005 | epot = -23.2021590525686 | etot = -17.6352293234507 -441000 ekin = 2.79903748157629 | erot = 2.54578114158762 | epot = -23.1760357267403 | etot = -17.8312171035764 -442000 ekin = 2.93503932875119 | erot = 2.87674150367343 | epot = -23.1192988997858 | etot = -17.3075180673612 -443000 ekin = 1.96853850230447 | erot = 1.76444304280728 | epot = -23.0474504745021 | etot = -19.3144689293904 -444000 ekin = 2.00740903163919 | erot = 2.25338146232896 | epot = -22.9768126386128 | etot = -18.7160221446446 -445000 ekin = 2.22543241532629 | erot = 2.06325853122729 | epot = -22.8128736901554 | etot = -18.5241827436018 -446000 ekin = 2.44497213168066 | erot = 2.37296472072563 | epot = -22.7182187420116 | etot = -17.9002818896053 -447000 ekin = 2.27682912672612 | erot = 2.40590062157627 | epot = -22.73821768508 | etot = -18.0554879367776 -448000 ekin = 2.17717815648414 | erot = 1.94002353369628 | epot = -22.8515885285926 | etot = -18.7343868384122 -449000 ekin = 2.21957974285234 | erot = 2.34288028472299 | epot = -22.9413256171992 | etot = -18.3788655896239 -450000 ekin = 2.75054329798646 | erot = 1.97942707751151 | epot = -22.8960066852305 | etot = -18.1660363097325 -451000 ekin = 2.21127283509867 | erot = 2.13383865709095 | epot = -22.93012845553 | etot = -18.5850169633403 -452000 ekin = 2.54342208027875 | erot = 2.35725031977164 | epot = -22.9678192920236 | etot = -18.0671468919732 -453000 ekin = 2.22826691368246 | erot = 1.78505555998555 | epot = -22.9525856519538 | etot = -18.9392631782858 -454000 ekin = 2.43963081757063 | erot = 2.59545869820689 | epot = -22.8816014548474 | etot = -17.8465119390699 -455000 ekin = 2.04579285921012 | erot = 2.79600798010941 | epot = -22.6671256943706 | etot = -17.8253248550511 -456000 ekin = 2.02054568037702 | erot = 2.5142933737518 | epot = -22.4807651427491 | etot = -17.9459260886202 -457000 ekin = 2.62427297855768 | erot = 2.43881475758852 | epot = -22.3628471473124 | etot = -17.2997594111662 -458000 ekin = 2.00982157063058 | erot = 1.99237218757745 | epot = -22.2563036448067 | etot = -18.2541098865987 -459000 ekin = 1.75248702434071 | erot = 2.49686008961238 | epot = -22.2467888503062 | etot = -17.9974417363531 -460000 ekin = 1.91910131837566 | erot = 2.07619395094217 | epot = -22.2400567481829 | etot = -18.2447614788651 -461000 ekin = 1.56844353839394 | erot = 1.28973659789019 | epot = -22.2093526564538 | etot = -19.3511725201697 -462000 ekin = 2.45174884293064 | erot = 1.36031689293857 | epot = -22.3089787954009 | etot = -18.4969130595317 -463000 ekin = 2.64349839520108 | erot = 2.07831354185085 | epot = -22.4300376076151 | etot = -17.7082256705631 -464000 ekin = 2.67299819724031 | erot = 3.73615881795558 | epot = -22.554470130186 | etot = -16.1453131149901 -465000 ekin = 1.95390361110071 | erot = 2.23920710641231 | epot = -22.7384686297881 | etot = -18.545357912275 -466000 ekin = 2.13348556167989 | erot = 2.96280610170109 | epot = -22.8443072066537 | etot = -17.7480155432727 -467000 ekin = 2.46613760277875 | erot = 2.11616591175904 | epot = -23.0265043956358 | etot = -18.444200881098 -468000 ekin = 1.99036864211387 | erot = 1.62858187482038 | epot = -23.0961237334908 | etot = -19.4771732165565 -469000 ekin = 2.49659836745282 | erot = 2.63661728128629 | epot = -23.1411267023576 | etot = -18.0079110536185 -470000 ekin = 2.92199371715687 | erot = 3.21712399422296 | epot = -23.1457817109815 | etot = -17.0066639996017 -471000 ekin = 2.36477645073574 | erot = 1.72314859686431 | epot = -23.1045733261495 | etot = -19.0166482785494 -472000 ekin = 2.18519498855062 | erot = 2.00240720258206 | epot = -23.072627104452 | etot = -18.8850249133193 -473000 ekin = 2.3714321613692 | erot = 2.86124663404655 | epot = -23.0328429128019 | etot = -17.8001641173862 -474000 ekin = 2.1857949588469 | erot = 2.60051446256873 | epot = -22.9136735669303 | etot = -18.1273641455147 -475000 ekin = 2.39661135768768 | erot = 2.01358694537797 | epot = -22.813046501162 | etot = -18.4028481980963 -476000 ekin = 2.10676579065005 | erot = 2.60327856915634 | epot = -22.8119267991277 | etot = -18.1018824393213 -477000 ekin = 2.53295314095718 | erot = 3.55510942450984 | epot = -22.7955031957515 | etot = -16.7074406302845 -478000 ekin = 2.40630114318287 | erot = 2.73236241457618 | epot = -22.7034337758127 | etot = -17.5647702180536 -479000 ekin = 1.27745698905519 | erot = 2.99245403250463 | epot = -22.6605920931777 | etot = -18.3906810716179 -480000 ekin = 1.82390564518045 | erot = 2.13920354248295 | epot = -22.6299626931083 | etot = -18.6668535054449 -481000 ekin = 2.3880478628611 | erot = 3.18399864702822 | epot = -22.6553769169915 | etot = -17.0833304071022 -482000 ekin = 3.20116727691415 | erot = 2.41976760575225 | epot = -22.6125762236254 | etot = -16.991641340959 -483000 ekin = 3.03846588981692 | erot = 2.48627946336888 | epot = -22.5774232520165 | etot = -17.0526778988307 -484000 ekin = 2.70181776439228 | erot = 2.52677846233176 | epot = -22.6070502809988 | etot = -17.3784540542748 -485000 ekin = 3.27224317472663 | erot = 2.42431335826243 | epot = -22.5997277235211 | etot = -16.9031711905321 -486000 ekin = 1.96596043103987 | erot = 1.75891125021975 | epot = -22.642547970919 | etot = -18.9176762896594 -487000 ekin = 2.6234378417876 | erot = 2.50755895035553 | epot = -22.7339556642929 | etot = -17.6029588721497 -488000 ekin = 1.75208074499658 | erot = 2.6448687233026 | epot = -22.7917400975639 | etot = -18.3947906292648 -489000 ekin = 2.08733298303259 | erot = 2.9523180967106 | epot = -22.881879447047 | etot = -17.8422283673038 -490000 ekin = 2.30760030156363 | erot = 2.33161319100248 | epot = -22.8847649865187 | etot = -18.2455514939526 -491000 ekin = 2.48196214295004 | erot = 2.59523958504393 | epot = -22.8776771178079 | etot = -17.800475389814 -492000 ekin = 3.28209206383218 | erot = 2.1852502939697 | epot = -22.8577625078557 | etot = -17.3904201500538 -493000 ekin = 3.37967323337949 | erot = 2.35355143859173 | epot = -22.8047552632571 | etot = -17.0715305912858 -494000 ekin = 3.57464120696614 | erot = 2.24853455202993 | epot = -22.8042956353342 | etot = -16.9811198763381 -495000 ekin = 2.5052992174061 | erot = 2.15850924694968 | epot = -22.7996067752132 | etot = -18.1357983108574 -496000 ekin = 1.95429188426678 | erot = 3.5825937389492 | epot = -22.837298805698 | etot = -17.3004131824821 -497000 ekin = 2.22186292996358 | erot = 2.46502235984734 | epot = -22.8432554612651 | etot = -18.1563701714542 -498000 ekin = 1.72648192614392 | erot = 2.39641281876546 | epot = -22.7792810810776 | etot = -18.6563863361682 -499000 ekin = 2.44591165293457 | erot = 2.82720242160824 | epot = -22.7953427712295 | etot = -17.5222286966867 -500000 ekin = 2.7851302139546 | erot = 2.23270136622152 | epot = -22.8991185931508 | etot = -17.8812870129746 -501000 ekin = 2.99439211318652 | erot = 1.97783069072832 | epot = -22.9279475016441 | etot = -17.9557246977292 -502000 ekin = 2.9862206030979 | erot = 1.79973926744011 | epot = -22.956155459855 | etot = -18.170195589317 -503000 ekin = 2.51500932637374 | erot = 2.88863666961797 | epot = -22.9858023469845 | etot = -17.5821563509928 -504000 ekin = 2.84387999289216 | erot = 2.69340549636984 | epot = -22.9170131486245 | etot = -17.3797276593625 -505000 ekin = 2.95569075243612 | erot = 2.602585876956 | epot = -22.9907249028698 | etot = -17.4324482734777 -506000 ekin = 2.19812159740513 | erot = 1.96718410179931 | epot = -23.0318373952185 | etot = -18.8665316960141 -507000 ekin = 2.26250501037088 | erot = 2.70461320689487 | epot = -22.9974394720575 | etot = -18.0303212547917 -508000 ekin = 2.63634784309456 | erot = 2.05036585895923 | epot = -23.0090804345496 | etot = -18.3223667324958 -509000 ekin = 2.94151668821484 | erot = 2.91160221114196 | epot = -23.0621014211554 | etot = -17.2089825217986 -510000 ekin = 2.26258273420884 | erot = 2.8155823326395 | epot = -23.1767418648115 | etot = -18.0985767979631 -511000 ekin = 2.89871784417207 | erot = 2.15651428734314 | epot = -23.2992796007865 | etot = -18.2440474692713 -512000 ekin = 2.18241701331153 | erot = 2.32471024525139 | epot = -23.3744961479659 | etot = -18.867368889403 -513000 ekin = 1.69086971293502 | erot = 2.8783745660792 | epot = -23.3843289700052 | etot = -18.8150846909909 -514000 ekin = 1.72546832120935 | erot = 2.33325616873572 | epot = -23.3798363194193 | etot = -19.3211118294743 -515000 ekin = 1.99840202228396 | erot = 1.80255577214453 | epot = -23.3747953532199 | etot = -19.5738375587914 -516000 ekin = 3.02853898966319 | erot = 1.54004582498168 | epot = -23.3386782444955 | etot = -18.7700934298506 -517000 ekin = 2.46344499126943 | erot = 2.11388687673044 | epot = -23.3135548350045 | etot = -18.7362229670046 -518000 ekin = 2.0362169291028 | erot = 2.51796163147274 | epot = -23.2504637438686 | etot = -18.6962851832931 -519000 ekin = 1.58660977959654 | erot = 1.63211831489779 | epot = -23.2081782818072 | etot = -19.9894501873129 -520000 ekin = 2.16318611090781 | erot = 1.89658879288914 | epot = -23.2096974204855 | etot = -19.1499225166885 -521000 ekin = 1.97684804456375 | erot = 2.08731550434085 | epot = -23.2527315496486 | etot = -19.188568000744 -522000 ekin = 2.69827007409924 | erot = 2.19560826391663 | epot = -23.3133573112007 | etot = -18.4194789731848 -523000 ekin = 2.2478363305578 | erot = 1.67442261891177 | epot = -23.3604551637841 | etot = -19.4381962143146 -524000 ekin = 2.34895041229461 | erot = 2.10078601700867 | epot = -23.381233923661 | etot = -18.9314974943577 -525000 ekin = 2.13155817393156 | erot = 2.07239357304026 | epot = -23.4395046885398 | etot = -19.235552941568 -526000 ekin = 2.50234900291801 | erot = 2.25431525777582 | epot = -23.4988198653879 | etot = -18.7421556046941 -527000 ekin = 3.03511403104629 | erot = 1.80504692374136 | epot = -23.5562539149297 | etot = -18.7160929601421 -528000 ekin = 2.56074044727573 | erot = 2.54331285469023 | epot = -23.5735936308822 | etot = -18.4695403289162 -529000 ekin = 2.37500349152887 | erot = 1.93006279746846 | epot = -23.5580125050353 | etot = -19.252946216038 -530000 ekin = 3.34194424343389 | erot = 3.41373524710891 | epot = -23.4507267657596 | etot = -16.6950472752168 -531000 ekin = 2.42341072166937 | erot = 2.35978455298084 | epot = -23.1501712562452 | etot = -18.366975981595 -532000 ekin = 2.58886764526949 | erot = 1.86996947608086 | epot = -23.1663546344342 | etot = -18.7075175130839 -533000 ekin = 2.18022742299593 | erot = 2.16045486833456 | epot = -23.380637574335 | etot = -19.0399552830045 -534000 ekin = 2.34791679374047 | erot = 2.03855517230123 | epot = -23.463831563993 | etot = -19.0773595979513 -535000 ekin = 2.37817813408508 | erot = 2.07397219148902 | epot = -23.4832900392636 | etot = -19.0311397136895 -536000 ekin = 2.46210672665338 | erot = 1.8947790016655 | epot = -23.4672059982835 | etot = -19.1103202699646 -537000 ekin = 1.71186030024847 | erot = 2.1344462698512 | epot = -23.5555571897054 | etot = -19.7092506196057 -538000 ekin = 2.16671541009104 | erot = 2.76559932728314 | epot = -23.6609154290595 | etot = -18.7286006916853 -539000 ekin = 2.16621132370208 | erot = 2.29104148484627 | epot = -23.7377569804062 | etot = -19.2805041718579 -540000 ekin = 2.37610335621453 | erot = 1.63780764528448 | epot = -23.7325177726622 | etot = -19.7186067711632 -541000 ekin = 2.61201541528826 | erot = 2.52498155703037 | epot = -23.6623419839272 | etot = -18.5253450116085 -542000 ekin = 2.72898292667725 | erot = 2.10989431729706 | epot = -23.7000798212983 | etot = -18.861202577324 -543000 ekin = 2.72070152721044 | erot = 1.85641764017256 | epot = -23.6069628280622 | etot = -19.0298436606792 -544000 ekin = 2.11779438939827 | erot = 1.50576740930398 | epot = -23.5826778503359 | etot = -19.9591160516337 -545000 ekin = 1.70778076743634 | erot = 2.56995673058895 | epot = -23.583343914622 | etot = -19.3056064165967 -546000 ekin = 2.3805758278215 | erot = 1.86648142267507 | epot = -23.6114100683877 | etot = -19.3643528178911 -547000 ekin = 2.45245186799104 | erot = 2.45758854207408 | epot = -23.6611856045782 | etot = -18.7511451945131 -548000 ekin = 2.39042546399151 | erot = 2.39603897463391 | epot = -23.6735607421256 | etot = -18.8870963035002 -549000 ekin = 2.59234094316699 | erot = 2.03286284306236 | epot = -23.6646331709071 | etot = -19.0394293846778 -550000 ekin = 1.99320521419403 | erot = 1.84894458030441 | epot = -23.6669378249973 | etot = -19.8247880304988 -551000 ekin = 2.44898809443739 | erot = 2.0219242208942 | epot = -23.6235443659669 | etot = -19.1526320506353 -552000 ekin = 2.69502802037877 | erot = 1.40870700355959 | epot = -23.4610294466586 | etot = -19.3572944227202 -553000 ekin = 1.76133393557171 | erot = 2.61023484195893 | epot = -23.254624102607 | etot = -18.8830553250764 -554000 ekin = 2.30411800065654 | erot = 2.33064249173903 | epot = -23.2181242479504 | etot = -18.5833637555548 -555000 ekin = 3.27047384641377 | erot = 1.6422371773255 | epot = -23.1973795659522 | etot = -18.2846685422129 -556000 ekin = 2.90314776795354 | erot = 2.59897046564306 | epot = -23.1460736374982 | etot = -17.6439554039016 -557000 ekin = 2.91673821282758 | erot = 3.16411852075219 | epot = -23.1459806883625 | etot = -17.0651239547827 -558000 ekin = 2.82902946234823 | erot = 2.71147602500681 | epot = -23.1195640745749 | etot = -17.5790585872199 -559000 ekin = 2.44501247164481 | erot = 3.2946921444891 | epot = -23.1638653139107 | etot = -17.4241606977768 -560000 ekin = 2.31903153876872 | erot = 2.34794389762528 | epot = -23.1221343768987 | etot = -18.4551589405047 -561000 ekin = 2.04778211145284 | erot = 2.88230317636058 | epot = -23.0254469759625 | etot = -18.0953616881491 -562000 ekin = 2.23097749779459 | erot = 3.71637560430596 | epot = -22.8954878936692 | etot = -16.9481347915687 -563000 ekin = 3.13589796296721 | erot = 2.30360204009239 | epot = -22.9672461823823 | etot = -17.5277461793227 -564000 ekin = 2.43468506100309 | erot = 2.37780089042927 | epot = -22.9400399192094 | etot = -18.127553967777 -565000 ekin = 2.74707381978168 | erot = 2.07635638038451 | epot = -22.9404100305402 | etot = -18.116979830374 -566000 ekin = 2.4222424655432 | erot = 2.23675573588529 | epot = -22.964317030412 | etot = -18.3053188289835 -567000 ekin = 2.66075150820169 | erot = 2.00813116398473 | epot = -23.0598382212572 | etot = -18.3909555490708 -568000 ekin = 3.04180913535304 | erot = 1.98452490185762 | epot = -23.1129541055894 | etot = -18.0866200683787 -569000 ekin = 3.57499094364799 | erot = 2.06992850387417 | epot = -23.117960007112 | etot = -17.4730405595898 -570000 ekin = 2.66020768003306 | erot = 2.34012507933247 | epot = -23.1339632056245 | etot = -18.133630446259 -571000 ekin = 1.94924082891001 | erot = 2.84220462440654 | epot = -23.0609933320748 | etot = -18.2695478787583 -572000 ekin = 2.41536650984725 | erot = 2.40871845587551 | epot = -23.0560879925718 | etot = -18.232003026849 -573000 ekin = 1.75696177901838 | erot = 2.31680084915611 | epot = -23.107424588529 | etot = -19.0336619603545 -574000 ekin = 2.1071071848933 | erot = 2.59270710144433 | epot = -23.1966129698341 | etot = -18.4967986834965 -575000 ekin = 2.37668274547159 | erot = 2.79832262601946 | epot = -23.2697902014998 | etot = -18.0947848300088 -576000 ekin = 2.17648663043414 | erot = 3.28534323951364 | epot = -23.3035961850707 | etot = -17.8417663151229 -577000 ekin = 2.48653402473871 | erot = 2.29382004189646 | epot = -23.3348256872303 | etot = -18.5544716205951 -578000 ekin = 2.63497646120015 | erot = 2.38541222697017 | epot = -23.3938829535157 | etot = -18.3734942653454 -579000 ekin = 2.68807604490538 | erot = 1.70832449354964 | epot = -23.3711370904455 | etot = -18.9747365519905 -580000 ekin = 2.35405412912148 | erot = 2.8553242408976 | epot = -23.3804498064804 | etot = -18.1710714364613 -581000 ekin = 2.45622900796811 | erot = 2.60461398742566 | epot = -23.3507481421638 | etot = -18.28990514677 -582000 ekin = 2.33821855888559 | erot = 3.20610340688907 | epot = -23.4193095100182 | etot = -17.8749875442436 -583000 ekin = 1.96183085357235 | erot = 2.81826367270291 | epot = -23.5872275727996 | etot = -18.8071330465243 -584000 ekin = 2.00096559581716 | erot = 1.71662185522173 | epot = -23.6766993596687 | etot = -19.9591119086298 -585000 ekin = 2.2650842350347 | erot = 2.08204874292297 | epot = -23.7234738719865 | etot = -19.3763408940288 -586000 ekin = 2.20207640113325 | erot = 1.96861811478536 | epot = -23.6859240119471 | etot = -19.5152294960285 -587000 ekin = 3.67938790357027 | erot = 1.82484412869377 | epot = -23.6634672548209 | etot = -18.1592352225569 -588000 ekin = 3.48089636122829 | erot = 2.30691916064612 | epot = -23.5643712718911 | etot = -17.7765557500167 -589000 ekin = 2.63030533099327 | erot = 2.9702466869305 | epot = -23.3767694123201 | etot = -17.7762173943963 -590000 ekin = 1.60813837628253 | erot = 2.03263132264272 | epot = -23.1946522249358 | etot = -19.5538825260106 -591000 ekin = 1.81653381805571 | erot = 1.75591263591366 | epot = -23.1302877005862 | etot = -19.5578412466168 -592000 ekin = 2.57247249135485 | erot = 2.59257155085885 | epot = -23.1533569826366 | etot = -17.9883129404229 -593000 ekin = 2.43678836763256 | erot = 1.78797409267748 | epot = -23.1035527853187 | etot = -18.8787903250087 -594000 ekin = 2.12126425466624 | erot = 2.16319102375819 | epot = -23.0537965790237 | etot = -18.7693413005993 -595000 ekin = 2.61494655403376 | erot = 2.04015446622256 | epot = -23.041588630948 | etot = -18.3864876106917 -596000 ekin = 2.58385979830463 | erot = 2.125984026295 | epot = -23.0987578414776 | etot = -18.388914016878 -597000 ekin = 3.0356528884646 | erot = 3.13920569000609 | epot = -23.0959220060406 | etot = -16.92106342757 -598000 ekin = 3.448018111133 | erot = 2.86438132305443 | epot = -23.1524961324829 | etot = -16.8400966982954 -599000 ekin = 2.14568317629689 | erot = 3.49762367929462 | epot = -23.1236320419091 | etot = -17.4803251863176 -600000 ekin = 2.20856388598401 | erot = 2.50873295237986 | epot = -23.1229244675557 | etot = -18.4056276291918 -601000 ekin = 2.82305805419651 | erot = 2.82785171484619 | epot = -23.093817009667 | etot = -17.4429072406243 -602000 ekin = 2.33756515640057 | erot = 2.3814563165261 | epot = -23.0592036595801 | etot = -18.3401821866535 -603000 ekin = 1.93163217766375 | erot = 1.95544716703194 | epot = -22.941151667404 | etot = -19.0540723227083 -604000 ekin = 2.67918576808855 | erot = 3.14415640026539 | epot = -22.9119901406973 | etot = -17.0886479723434 -605000 ekin = 2.72017891571417 | erot = 2.06410352610178 | epot = -22.9250944568005 | etot = -18.1408120149845 -606000 ekin = 2.99653903957879 | erot = 2.03201724640129 | epot = -22.8426486789921 | etot = -17.814092393012 -607000 ekin = 2.88290327274547 | erot = 2.37629823895312 | epot = -22.8265624505584 | etot = -17.5673609388598 -608000 ekin = 3.6564890765792 | erot = 2.46096427245297 | epot = -22.7637531347954 | etot = -16.6462997857633 -609000 ekin = 2.67772613172483 | erot = 2.28052588350936 | epot = -22.784032519386 | etot = -17.8257805041518 -610000 ekin = 2.96660977711584 | erot = 2.13935236193287 | epot = -22.7753012812081 | etot = -17.6693391421594 -611000 ekin = 3.84936812341098 | erot = 2.13515328821562 | epot = -22.7555358965927 | etot = -16.7710144849661 -612000 ekin = 2.85991416578252 | erot = 2.46799936153364 | epot = -22.6670923038619 | etot = -17.3391787765458 -613000 ekin = 2.93458428860956 | erot = 2.15612272200133 | epot = -22.6620509726505 | etot = -17.5713439620396 -614000 ekin = 2.80109550846435 | erot = 2.03413630963325 | epot = -22.735929073337 | etot = -17.9006972552394 -615000 ekin = 2.29275572188425 | erot = 2.37295436060996 | epot = -22.8265717932651 | etot = -18.1608617107709 -616000 ekin = 1.78880182339297 | erot = 2.46512387757483 | epot = -22.9181914142038 | etot = -18.664265713236 -617000 ekin = 2.58548247747108 | erot = 2.53734413400793 | epot = -22.9371325341202 | etot = -17.8143059226412 -618000 ekin = 2.31891017470357 | erot = 2.68587322473765 | epot = -22.8737927646705 | etot = -17.8690093652293 -619000 ekin = 1.95260275466613 | erot = 2.00546202293513 | epot = -22.8346556656307 | etot = -18.8765908880295 -620000 ekin = 2.9312355259843 | erot = 2.17154966265513 | epot = -22.9093263040915 | etot = -17.806541115452 -621000 ekin = 2.92251791603671 | erot = 1.69365790820559 | epot = -22.9491849521548 | etot = -18.3330091279125 -622000 ekin = 2.04583493083921 | erot = 2.52347309118728 | epot = -22.8885087146283 | etot = -18.3192006926018 -623000 ekin = 1.97949309574552 | erot = 3.07796024634624 | epot = -22.899088756596 | etot = -17.8416354145043 -624000 ekin = 2.09648243468335 | erot = 2.65430331108241 | epot = -22.914733999871 | etot = -18.1639482541052 -625000 ekin = 2.53179488470072 | erot = 2.36095144458489 | epot = -22.9722766139489 | etot = -18.0795302846633 -626000 ekin = 2.71471201325311 | erot = 2.038002303651 | epot = -23.0006194176227 | etot = -18.2479051007186 -627000 ekin = 2.22374294193216 | erot = 2.35282114621755 | epot = -22.9588355159151 | etot = -18.3822714277654 -628000 ekin = 2.28003968408293 | erot = 2.28859673286464 | epot = -22.8537881524811 | etot = -18.2851517355335 -629000 ekin = 2.52123014813329 | erot = 1.89624895610832 | epot = -22.7908976494591 | etot = -18.3734185452175 -630000 ekin = 3.09551469183927 | erot = 2.51634259883875 | epot = -22.7156574639271 | etot = -17.1038001732491 -631000 ekin = 2.38491234780997 | erot = 3.31746706623938 | epot = -22.7274824388449 | etot = -17.0251030247955 -632000 ekin = 2.58509546960735 | erot = 2.52764681234154 | epot = -22.6801845001954 | etot = -17.5674422182465 -633000 ekin = 2.43450196234921 | erot = 1.9074646477535 | epot = -22.6545806388637 | etot = -18.312614028761 -634000 ekin = 2.22577935817066 | erot = 2.00781737526926 | epot = -22.5723806994747 | etot = -18.3387839660348 -635000 ekin = 2.21833116743445 | erot = 1.98256884900851 | epot = -22.5422908112103 | etot = -18.3413907947673 -636000 ekin = 2.25207449335774 | erot = 2.77890466668274 | epot = -22.5736742647701 | etot = -17.5426951047296 -637000 ekin = 1.94359576469155 | erot = 2.6121109986752 | epot = -22.6035657643129 | etot = -18.0478590009461 -638000 ekin = 2.53947002676468 | erot = 3.14006412371943 | epot = -22.5826147275244 | etot = -16.9030805770402 -639000 ekin = 2.37745481188141 | erot = 2.49540365345358 | epot = -22.5449630195302 | etot = -17.6721045541952 -640000 ekin = 2.08212454926531 | erot = 2.21940536991445 | epot = -22.453303862966 | etot = -18.1517739437862 -641000 ekin = 2.47971433110368 | erot = 3.55852071727848 | epot = -22.3500233136602 | etot = -16.3117882652781 -642000 ekin = 3.38958957156561 | erot = 2.18184701440171 | epot = -22.2389727056174 | etot = -16.6675361196501 -643000 ekin = 2.84881174665207 | erot = 2.413254877821 | epot = -22.1927147648616 | etot = -16.9306481403886 -644000 ekin = 2.9788163296922 | erot = 1.93799042516405 | epot = -22.1764728944767 | etot = -17.2596661396204 -645000 ekin = 4.12550859701587 | erot = 1.89960014649319 | epot = -22.1706973334318 | etot = -16.1455885899228 -646000 ekin = 2.52696357860359 | erot = 2.00637360005821 | epot = -22.1102258356952 | etot = -17.5768886570333 -647000 ekin = 2.55512268942677 | erot = 2.20922204555245 | epot = -22.1538572894812 | etot = -17.389512554502 -648000 ekin = 3.02957533574521 | erot = 2.11325139659861 | epot = -22.1575349215939 | etot = -17.0147081892501 -649000 ekin = 2.58453912449214 | erot = 3.20631221677863 | epot = -22.1339073532352 | etot = -16.3430560119644 -650000 ekin = 3.77204744414227 | erot = 2.43066777037188 | epot = -22.0837500061792 | etot = -15.8810347916651 -651000 ekin = 3.31369677202991 | erot = 2.36221103045568 | epot = -21.9243902112032 | etot = -16.2484824087176 -652000 ekin = 2.49262898649827 | erot = 3.02155153905954 | epot = -21.7253342697997 | etot = -16.2111537442419 -653000 ekin = 2.82559687485827 | erot = 2.53899564631137 | epot = -21.7211782659414 | etot = -16.3565857447718 -654000 ekin = 2.35170683287638 | erot = 2.15925543988734 | epot = -21.9219546077978 | etot = -17.4109923350341 -655000 ekin = 2.2746913368331 | erot = 2.12498780379593 | epot = -21.9020101665877 | etot = -17.5023310259586 -656000 ekin = 2.33856358324454 | erot = 2.10525554685067 | epot = -21.9227166217961 | etot = -17.4788974917008 -657000 ekin = 2.74434355807405 | erot = 2.19006149870653 | epot = -22.1368388094875 | etot = -17.2024337527069 -658000 ekin = 3.04721032533817 | erot = 2.59752520159664 | epot = -22.2936626687419 | etot = -16.6489271418071 -659000 ekin = 2.86427564828999 | erot = 3.42151988715138 | epot = -22.2986314842237 | etot = -16.0128359487823 -660000 ekin = 2.92506899234012 | erot = 1.63381738879488 | epot = -22.3375917964994 | etot = -17.7787054153644 -661000 ekin = 3.22051797741487 | erot = 1.86658559874782 | epot = -22.4692759662967 | etot = -17.382172390134 -662000 ekin = 3.06008561550976 | erot = 2.20194497946945 | epot = -22.5616874184536 | etot = -17.2996568234744 -663000 ekin = 1.91383924631387 | erot = 2.47155788641765 | epot = -22.6270449564058 | etot = -18.2416478236743 -664000 ekin = 1.43175220258741 | erot = 1.36481827202384 | epot = -22.714938601816 | etot = -19.9183681272047 -665000 ekin = 1.55751729325324 | erot = 2.30904543593978 | epot = -22.7903483651339 | etot = -18.9237856359409 -666000 ekin = 2.44554812999981 | erot = 1.7728381640758 | epot = -22.9292683336281 | etot = -18.7108820395525 -667000 ekin = 2.81292959120154 | erot = 2.33182461186713 | epot = -23.1152300896738 | etot = -17.9704758866051 -668000 ekin = 2.71701517852366 | erot = 3.1927510370022 | epot = -23.1898047541379 | etot = -17.2800385386121 -669000 ekin = 3.4211844979108 | erot = 2.4483988547294 | epot = -23.2367567149657 | etot = -17.3671733623255 -670000 ekin = 2.540272537006 | erot = 1.98108817711494 | epot = -23.1773017073799 | etot = -18.655940993259 -671000 ekin = 2.38054183576284 | erot = 2.98341127846263 | epot = -23.1403357669317 | etot = -17.7763826527062 -672000 ekin = 3.02714775234025 | erot = 2.54429912094893 | epot = -23.1240813931427 | etot = -17.5526345198536 -673000 ekin = 3.42342714962536 | erot = 2.36764796314287 | epot = -23.0365834633316 | etot = -17.2455083505634 -674000 ekin = 3.1787369792725 | erot = 2.10003598211897 | epot = -22.9565366380298 | etot = -17.6777636766383 -675000 ekin = 2.35379506516488 | erot = 1.53509045481238 | epot = -22.8504434741329 | etot = -18.9615579541557 -676000 ekin = 2.44888744246419 | erot = 2.24653163842729 | epot = -22.7725645250621 | etot = -18.0771454441706 -677000 ekin = 2.75831894151647 | erot = 1.93124166774781 | epot = -22.8527844251281 | etot = -18.1632238158638 -678000 ekin = 2.86751481243524 | erot = 1.65310315497864 | epot = -22.8648869805436 | etot = -18.3442690131297 -679000 ekin = 2.34238342331609 | erot = 2.69036620616395 | epot = -22.9330609670147 | etot = -17.9003113375347 -680000 ekin = 2.47092831167294 | erot = 2.90821987338148 | epot = -22.9893989293305 | etot = -17.610250744276 -681000 ekin = 1.90592213851373 | erot = 2.57738203916981 | epot = -22.9226803153478 | etot = -18.4393761376642 -682000 ekin = 2.11776015116235 | erot = 2.69956516894844 | epot = -22.8385618600593 | etot = -18.0212365399485 -683000 ekin = 2.36569744411279 | erot = 2.12377742206911 | epot = -22.7248964050232 | etot = -18.2354215388413 -684000 ekin = 2.87481829504096 | erot = 2.65568540935019 | epot = -22.6557781340276 | etot = -17.1252744296364 -685000 ekin = 3.04590812681261 | erot = 2.17384411148381 | epot = -22.6239841629455 | etot = -17.4042319246491 -686000 ekin = 2.45732454887051 | erot = 2.42727693460545 | epot = -22.5554269158738 | etot = -17.6708254323979 -687000 ekin = 2.74615797772517 | erot = 1.80419114366277 | epot = -22.4906419692597 | etot = -17.9402928478718 -688000 ekin = 1.7920739822545 | erot = 2.04572898801195 | epot = -22.4080555397627 | etot = -18.5702525694962 -689000 ekin = 2.87658871003945 | erot = 1.89509928788519 | epot = -22.4597913998897 | etot = -17.6881034019651 -690000 ekin = 2.12362847773645 | erot = 2.42433705189552 | epot = -22.5737079170673 | etot = -18.0257423874353 -691000 ekin = 2.15963929746743 | erot = 2.52975117929537 | epot = -22.5896382204305 | etot = -17.9002477436677 -692000 ekin = 2.88714768351631 | erot = 2.65189982514091 | epot = -22.4796475018852 | etot = -16.9405999932279 -693000 ekin = 2.30934205113368 | erot = 2.51896960835911 | epot = -22.3454093965687 | etot = -17.5170977370759 -694000 ekin = 2.90083400146798 | erot = 2.34214046553658 | epot = -22.2620689836397 | etot = -17.0190945166351 -695000 ekin = 2.9577943585455 | erot = 2.23887088042094 | epot = -22.303054593607 | etot = -17.1063893546405 -696000 ekin = 2.65803880066321 | erot = 2.33953886943022 | epot = -22.3444459486844 | etot = -17.3468682785909 -697000 ekin = 1.89104688866877 | erot = 1.78290264315477 | epot = -22.3519476787994 | etot = -18.6779981469758 -698000 ekin = 2.22763370474282 | erot = 2.82521193129044 | epot = -22.374966668557 | etot = -17.3221210325237 -699000 ekin = 2.35357258316915 | erot = 2.06864522211151 | epot = -22.302995332199 | etot = -17.8807775269184 -700000 ekin = 2.58206368687336 | erot = 2.33093601350411 | epot = -22.2613878464485 | etot = -17.3483881460711 -701000 ekin = 2.99704307093403 | erot = 1.89954183386767 | epot = -22.3232249760621 | etot = -17.4266400712604 -702000 ekin = 2.67512006336489 | erot = 2.64729282748452 | epot = -22.3604874692709 | etot = -17.0380745784215 -703000 ekin = 2.02348242287829 | erot = 2.03755058248806 | epot = -22.4348344343157 | etot = -18.3738014289493 -704000 ekin = 1.59657624705204 | erot = 1.63613322855987 | epot = -22.4674717825454 | etot = -19.2347623069335 -705000 ekin = 2.34019771505867 | erot = 1.91006554831154 | epot = -22.5441024225864 | etot = -18.2938391592161 -706000 ekin = 2.47926998793354 | erot = 3.26999075651193 | epot = -22.5117539612542 | etot = -16.7624932168087 -707000 ekin = 2.38604341038216 | erot = 2.41699636933021 | epot = -22.604009927914 | etot = -17.8009701482016 -708000 ekin = 1.68115636633466 | erot = 2.34002138995268 | epot = -22.7466665621618 | etot = -18.7254888058744 -709000 ekin = 1.80992626994918 | erot = 2.57911114058356 | epot = -23.0637398035031 | etot = -18.6747023929704 -710000 ekin = 2.07665974484992 | erot = 1.83617776589231 | epot = -23.1977961917903 | etot = -19.2849586810481 -711000 ekin = 1.95352231029107 | erot = 2.41454578486037 | epot = -23.2358193849337 | etot = -18.8677512897822 -712000 ekin = 2.13370686414587 | erot = 1.78661700982467 | epot = -23.2645434465923 | etot = -19.3442195726217 -713000 ekin = 2.90695161716251 | erot = 1.55091931636559 | epot = -23.1835772351912 | etot = -18.7257063016631 -714000 ekin = 2.06629801094757 | erot = 1.86611085535956 | epot = -23.2239032864041 | etot = -19.2914944200969 -715000 ekin = 2.52903922778277 | erot = 1.94261958015835 | epot = -23.1658397986034 | etot = -18.6941809906622 -716000 ekin = 3.03498992772823 | erot = 2.21064066235538 | epot = -23.2216970852983 | etot = -17.9760664952147 -717000 ekin = 3.07971375394894 | erot = 2.47094593918087 | epot = -23.3639588975855 | etot = -17.8132992044557 -718000 ekin = 3.49703192209654 | erot = 2.27170758510088 | epot = -23.4199184473786 | etot = -17.6511789401811 -719000 ekin = 4.06139770605771 | erot = 3.10418818480813 | epot = -23.4072026156126 | etot = -16.2416167247468 -720000 ekin = 2.49828440590245 | erot = 1.90909738802778 | epot = -23.262316602338 | etot = -18.8549348084078 -721000 ekin = 2.57931762358207 | erot = 1.98570897250437 | epot = -23.1440560046385 | etot = -18.579029408552 -722000 ekin = 2.01081836336836 | erot = 2.2747167647488 | epot = -23.1040519922181 | etot = -18.8185168641009 -723000 ekin = 2.44097316114449 | erot = 2.07630856281912 | epot = -23.1828606158314 | etot = -18.6655788918678 -724000 ekin = 1.90797367222605 | erot = 1.93592443836535 | epot = -23.2376437089983 | etot = -19.3937455984069 -725000 ekin = 2.19373210936071 | erot = 2.80513028222362 | epot = -23.2888134461385 | etot = -18.2899510545542 -726000 ekin = 2.2764864004673 | erot = 2.54378150467671 | epot = -23.3354979947709 | etot = -18.5152300896268 -727000 ekin = 1.72219216954142 | erot = 2.62563304726333 | epot = -23.3703740298761 | etot = -19.0225488130713 -728000 ekin = 2.25087046178847 | erot = 3.59486012962608 | epot = -23.435416924773 | etot = -17.5896863333584 -729000 ekin = 2.68839033328484 | erot = 1.72111131116557 | epot = -23.4784810452544 | etot = -19.0689794008039 -730000 ekin = 2.5329756962683 | erot = 2.7666773813211 | epot = -23.4899025882625 | etot = -18.1902495106731 -731000 ekin = 2.6760609901083 | erot = 2.04579712240261 | epot = -23.5241973416199 | etot = -18.802339229109 -732000 ekin = 2.77848516459028 | erot = 1.88432734797838 | epot = -23.5774208145874 | etot = -18.9146083020187 -733000 ekin = 2.18895381088671 | erot = 2.63471719118119 | epot = -23.6107634586383 | etot = -18.7870924565704 -734000 ekin = 1.69467760927658 | erot = 2.30338410687055 | epot = -23.5936446347431 | etot = -19.595582918596 -735000 ekin = 2.17749689272956 | erot = 2.71618098412724 | epot = -23.5330417303215 | etot = -18.6393638534647 -736000 ekin = 2.29375858428166 | erot = 1.1740900723812 | epot = -23.503450790287 | etot = -20.0356021336242 -737000 ekin = 2.20827752624533 | erot = 3.11531250945766 | epot = -23.4552023795231 | etot = -18.1316123438201 -738000 ekin = 1.72303720787712 | erot = 2.28747842674015 | epot = -23.3309270174989 | etot = -19.3204113828816 -739000 ekin = 1.39492824364512 | erot = 2.17488386602882 | epot = -23.28548996576 | etot = -19.7156778560861 -740000 ekin = 1.90426261774289 | erot = 2.27825159935278 | epot = -23.2514184467463 | etot = -19.0689042296506 -741000 ekin = 2.02024508457136 | erot = 2.72073546284876 | epot = -23.1876217096301 | etot = -18.4466411622099 -742000 ekin = 1.97487019042321 | erot = 1.87541960482772 | epot = -23.0929182320365 | etot = -19.2426284367856 -743000 ekin = 1.96486238454688 | erot = 2.76982785281128 | epot = -22.9318899502109 | etot = -18.1971997128528 -744000 ekin = 2.04909521933131 | erot = 2.34373814592941 | epot = -22.8510525613065 | etot = -18.4582191960458 -745000 ekin = 1.66771130319646 | erot = 1.87270341329448 | epot = -22.7977076876185 | etot = -19.2572929711276 -746000 ekin = 2.11650515037838 | erot = 2.03542197982564 | epot = -22.7785820280378 | etot = -18.6266548978338 -747000 ekin = 3.07964448387158 | erot = 1.66910106460583 | epot = -22.8037757029139 | etot = -18.0550301544365 -748000 ekin = 3.03811477337698 | erot = 1.85631102018694 | epot = -22.8436239146773 | etot = -17.9491981211133 -749000 ekin = 2.53753852426481 | erot = 2.01199117356573 | epot = -22.860297041716 | etot = -18.3107673438855 -750000 ekin = 2.77210902960465 | erot = 2.32628560304478 | epot = -22.9528220918576 | etot = -17.8544274592082 -751000 ekin = 2.52040431872467 | erot = 2.34903725042469 | epot = -23.0127359055533 | etot = -18.1432943364039 -752000 ekin = 2.46408285580806 | erot = 1.68868786663082 | epot = -22.9901282704654 | etot = -18.8373575480265 -753000 ekin = 2.47364326188914 | erot = 1.55776271670366 | epot = -23.1135680684223 | etot = -19.0821620898295 -754000 ekin = 2.5278916038673 | erot = 2.29496804643662 | epot = -23.2403939606523 | etot = -18.4175343103483 -755000 ekin = 1.52934303772527 | erot = 2.21322404979637 | epot = -23.262110017443 | etot = -19.5195429299214 -756000 ekin = 2.10423967353423 | erot = 2.40303050505255 | epot = -23.1685739957517 | etot = -18.6613038171649 -757000 ekin = 2.92559629660516 | erot = 2.0691293568206 | epot = -23.1502917576405 | etot = -18.1555661042147 -758000 ekin = 2.37300490719645 | erot = 2.51363215153151 | epot = -23.0495756460038 | etot = -18.1629385872758 -759000 ekin = 2.6014595730178 | erot = 2.39657042348208 | epot = -22.9025259489071 | etot = -17.9044959524072 -760000 ekin = 3.23086874355225 | erot = 2.77072134903012 | epot = -22.8089299952235 | etot = -16.8073399026412 -761000 ekin = 3.41475369307092 | erot = 1.70180532416599 | epot = -22.7404708369396 | etot = -17.6239118197027 -762000 ekin = 3.40874473404401 | erot = 2.52147443954634 | epot = -22.5276669204419 | etot = -16.5974477468515 -763000 ekin = 2.64281892112082 | erot = 1.82464895439093 | epot = -22.3890167593186 | etot = -17.9215488838069 -764000 ekin = 2.38098664175603 | erot = 2.71455563654527 | epot = -22.2309521785191 | etot = -17.1354099002178 -765000 ekin = 2.24221473762586 | erot = 1.94826539133556 | epot = -22.122583392123 | etot = -17.9321032631616 -766000 ekin = 2.50645584526003 | erot = 1.96129579948818 | epot = -21.9857907119498 | etot = -17.5180390672015 -767000 ekin = 2.34028568638226 | erot = 2.64592471376141 | epot = -21.9051815399867 | etot = -16.918971139843 -768000 ekin = 1.86752761821211 | erot = 2.06138447840236 | epot = -21.8874171216963 | etot = -17.9585050250818 -769000 ekin = 3.03590459157853 | erot = 2.66440802561784 | epot = -21.8247140853503 | etot = -16.124401468154 -770000 ekin = 2.42567220683552 | erot = 1.97830158892933 | epot = -21.8110526122117 | etot = -17.4070788164468 -771000 ekin = 2.20056711884501 | erot = 2.53255190976195 | epot = -21.7341162461991 | etot = -17.0009972175921 -772000 ekin = 2.75016173617492 | erot = 1.98403019503999 | epot = -21.8164316952287 | etot = -17.0822397640138 -773000 ekin = 2.14723076845117 | erot = 2.41512334908793 | epot = -21.9576017041203 | etot = -17.3952475865812 -774000 ekin = 2.20536023895281 | erot = 1.98379412617599 | epot = -22.043759647449 | etot = -17.8546052823202 -775000 ekin = 2.53158393271132 | erot = 2.8225938280108 | epot = -22.2469056379858 | etot = -16.8927278772637 -776000 ekin = 3.15988726149912 | erot = 2.46223044860468 | epot = -22.4204382258798 | etot = -16.798320515776 -777000 ekin = 1.91542872566335 | erot = 1.75408058586262 | epot = -22.4517075164596 | etot = -18.7821982049336 -778000 ekin = 2.94665474162607 | erot = 2.31805831302194 | epot = -22.4632153304498 | etot = -17.1985022758018 -779000 ekin = 3.10970934270731 | erot = 2.04446179405629 | epot = -22.4851490287702 | etot = -17.3309778920066 -780000 ekin = 2.85215832341045 | erot = 3.13312086675091 | epot = -22.4501531708741 | etot = -16.4648739807127 -781000 ekin = 2.36733074493229 | erot = 3.56399648845806 | epot = -22.4171363625471 | etot = -16.4858091291567 -782000 ekin = 2.32796510372074 | erot = 2.86343667143255 | epot = -22.3438054250098 | etot = -17.1524036498565 -783000 ekin = 1.86439500745061 | erot = 3.05233385447291 | epot = -22.2079509833896 | etot = -17.2912221214661 -784000 ekin = 2.05476588420882 | erot = 2.29789997988689 | epot = -22.1006364427793 | etot = -17.7479705786836 -785000 ekin = 2.03879516593738 | erot = 2.15052527915338 | epot = -22.0056061371158 | etot = -17.816285692025 -786000 ekin = 2.3752160296601 | erot = 2.32156698168742 | epot = -21.9727988200248 | etot = -17.2760158086773 -787000 ekin = 2.76686314352376 | erot = 2.23625261993099 | epot = -21.8969600931556 | etot = -16.8938443297008 -788000 ekin = 2.13318993659091 | erot = 2.25162748275281 | epot = -21.8604178455632 | etot = -17.4756004262194 -789000 ekin = 1.98216852118508 | erot = 1.98058785261598 | epot = -21.844134033761 | etot = -17.8813776599599 -790000 ekin = 1.67847851427146 | erot = 1.42560334440858 | epot = -21.941301490604 | etot = -18.837219631924 -791000 ekin = 2.12689982203095 | erot = 2.53200907087448 | epot = -22.0864434478656 | etot = -17.4275345549602 -792000 ekin = 1.72797703494859 | erot = 2.22448376175168 | epot = -22.1854190028922 | etot = -18.2329582061919 -793000 ekin = 3.18409314211953 | erot = 1.94056710411296 | epot = -22.3760603901177 | etot = -17.2514001438852 -794000 ekin = 2.49071782059139 | erot = 3.01186430180266 | epot = -22.4315505782774 | etot = -16.9289684558833 -795000 ekin = 2.89844296027926 | erot = 3.07659510288655 | epot = -22.5164404652995 | etot = -16.5414024021337 -796000 ekin = 2.32845268798927 | erot = 1.62708270564126 | epot = -22.5660647482766 | etot = -18.6105293546461 -797000 ekin = 2.20766900620157 | erot = 3.6597733457204 | epot = -22.5351911425215 | etot = -16.6677487905995 -798000 ekin = 2.12139450500735 | erot = 2.94419809776829 | epot = -22.53586560158 | etot = -17.4702729988044 -799000 ekin = 2.48452434226029 | erot = 2.7415786036137 | epot = -22.4941328101442 | etot = -17.2680298642702 -800000 ekin = 2.17521613585505 | erot = 2.96480330538541 | epot = -22.3818079549674 | etot = -17.2417885137269 -801000 ekin = 2.54690065539559 | erot = 2.74966931670846 | epot = -22.3008594124712 | etot = -17.0042894403671 -802000 ekin = 3.02823775407486 | erot = 2.8915936784506 | epot = -22.2024149184001 | etot = -16.2825834858746 -803000 ekin = 2.21042161290743 | erot = 2.51594019231142 | epot = -22.1069208353333 | etot = -17.3805590301145 -804000 ekin = 2.91061289296152 | erot = 1.5830418961718 | epot = -22.0839512655924 | etot = -17.5902964764591 -805000 ekin = 2.67762522194669 | erot = 3.06970455948968 | epot = -22.0793101970619 | etot = -16.3319804156255 -806000 ekin = 2.75979804034939 | erot = 2.2176860954027 | epot = -22.0549669082474 | etot = -17.0774827724953 -807000 ekin = 2.11041519443391 | erot = 2.83915265443807 | epot = -22.1073292774231 | etot = -17.1577614285511 -808000 ekin = 1.84392510139081 | erot = 2.29797054411878 | epot = -22.0753255923415 | etot = -17.9334299468319 -809000 ekin = 1.93171652686567 | erot = 1.94021167949754 | epot = -22.0668297694372 | etot = -18.194901563074 -810000 ekin = 1.97774334424761 | erot = 2.6472977913531 | epot = -22.1020544833021 | etot = -17.4770133477014 -811000 ekin = 2.2417092413671 | erot = 1.75505259459069 | epot = -22.1062654329495 | etot = -18.1095035969917 -812000 ekin = 2.49053159164605 | erot = 2.33986799245713 | epot = -22.124141511127 | etot = -17.2937419270238 -813000 ekin = 3.01755249739549 | erot = 2.24004680047387 | epot = -22.1167722656682 | etot = -16.8591729677989 -814000 ekin = 2.86045886242639 | erot = 2.24119269343823 | epot = -22.1084535534804 | etot = -17.0068019976158 -815000 ekin = 2.57503557502156 | erot = 2.76212054641368 | epot = -21.9950519676046 | etot = -16.6578958461694 -816000 ekin = 2.19961906931023 | erot = 2.59194277056134 | epot = -22.0843443380244 | etot = -17.2927824981528 -817000 ekin = 1.75062364873707 | erot = 2.66165019507354 | epot = -22.3739862599355 | etot = -17.9617124161249 -818000 ekin = 2.24809257416679 | erot = 2.59026399650675 | epot = -22.5610524731389 | etot = -17.7226959024654 -819000 ekin = 2.12537334404071 | erot = 2.59618311382673 | epot = -22.5606510650104 | etot = -17.839094607143 -820000 ekin = 1.93414650390356 | erot = 2.29085663493509 | epot = -22.4839314706954 | etot = -18.2589283318568 -821000 ekin = 2.11382182469737 | erot = 2.38685226676536 | epot = -22.47627897247 | etot = -17.9756048810073 -822000 ekin = 2.2613431095799 | erot = 2.12056938305333 | epot = -22.370909843474 | etot = -17.9889973508408 -823000 ekin = 2.31560863750917 | erot = 2.60350436456086 | epot = -22.4988996092736 | etot = -17.5797866072036 -824000 ekin = 1.73697879038959 | erot = 1.5185057021212 | epot = -22.6200401147494 | etot = -19.3645556222386 -825000 ekin = 1.63614248894086 | erot = 1.97731468932685 | epot = -22.6198150724223 | etot = -19.0063578941546 -826000 ekin = 2.00841233147246 | erot = 2.17850248200248 | epot = -22.5466518143203 | etot = -18.3597370008454 -827000 ekin = 2.18457105279113 | erot = 2.44711764942285 | epot = -22.4005870169979 | etot = -17.7688983147839 -828000 ekin = 1.91039404464085 | erot = 2.73449242191012 | epot = -22.3948651441296 | etot = -17.7499786775786 -829000 ekin = 2.07228257188588 | erot = 2.97134747466499 | epot = -22.4347910090961 | etot = -17.3911609625452 -830000 ekin = 1.99293621346915 | erot = 2.15765133255911 | epot = -22.4843800017124 | etot = -18.3337924556842 -831000 ekin = 2.33241187954984 | erot = 2.37634533076884 | epot = -22.5757045912718 | etot = -17.8669473809531 -832000 ekin = 2.02856108052035 | erot = 1.94729581180225 | epot = -22.6670251626246 | etot = -18.691168270302 -833000 ekin = 2.28623411522758 | erot = 2.15108044390973 | epot = -22.7566850878713 | etot = -18.319370528734 -834000 ekin = 2.12105013529711 | erot = 1.5116778668129 | epot = -22.7735851481702 | etot = -19.1408571460602 -835000 ekin = 2.88531776933573 | erot = 2.74027641398136 | epot = -22.8585330533172 | etot = -17.2329388700001 -836000 ekin = 3.32070208623905 | erot = 2.42231134749978 | epot = -22.8959107751695 | etot = -17.1528973414306 -837000 ekin = 2.74149226799164 | erot = 2.32127198719276 | epot = -22.8906677110002 | etot = -17.8279034558158 -838000 ekin = 3.13302338440878 | erot = 3.19829232559053 | epot = -22.9166668544453 | etot = -16.585351144446 -839000 ekin = 2.73522885875602 | erot = 2.61100294075548 | epot = -22.8499426413711 | etot = -17.5037108418596 -840000 ekin = 2.97139629828009 | erot = 1.43157972743722 | epot = -22.7763904271576 | etot = -18.3734144014403 -841000 ekin = 2.9571795545775 | erot = 2.67280681737836 | epot = -22.7408850128302 | etot = -17.1108986408743 -842000 ekin = 2.17222575948606 | erot = 2.30478646820068 | epot = -22.7382440804492 | etot = -18.2612318527624 -843000 ekin = 2.83292824269634 | erot = 2.04165126380544 | epot = -22.7426687858571 | etot = -17.8680892793554 -844000 ekin = 2.95938970875204 | erot = 1.50198210425589 | epot = -22.783719790782 | etot = -18.3223479777741 -845000 ekin = 3.16076837184522 | erot = 2.28216144351779 | epot = -22.7913524647186 | etot = -17.3484226493555 -846000 ekin = 3.3398977708405 | erot = 2.53602189023877 | epot = -22.7943227793905 | etot = -16.9184031183113 -847000 ekin = 2.14145435242079 | erot = 2.75036267291773 | epot = -22.7255800042885 | etot = -17.83376297895 -848000 ekin = 2.48912550447967 | erot = 2.81875176956459 | epot = -22.5834297802211 | etot = -17.2755525061768 -849000 ekin = 1.98023552181666 | erot = 2.5692134285068 | epot = -22.4587431120173 | etot = -17.9092941616939 -850000 ekin = 2.0475383789703 | erot = 1.80627608629883 | epot = -22.442868440532 | etot = -18.5890539752628 -851000 ekin = 2.09704360250612 | erot = 1.85768640504848 | epot = -22.4344168330881 | etot = -18.4796868255335 -852000 ekin = 1.70813487206096 | erot = 1.42387059402563 | epot = -22.3764553852037 | etot = -19.2444499191171 -853000 ekin = 2.00140314580349 | erot = 3.04689599134399 | epot = -22.4103147041128 | etot = -17.3620155669653 -854000 ekin = 3.02149896921022 | erot = 2.22990677084323 | epot = -22.4965128093929 | etot = -17.2451070693394 -855000 ekin = 2.19607047478225 | erot = 2.83672007906388 | epot = -22.5083573431917 | etot = -17.4755667893456 -856000 ekin = 2.44947669543341 | erot = 1.52884872890501 | epot = -22.4898047833717 | etot = -18.5114793590332 -857000 ekin = 2.53345481305323 | erot = 2.80399799726174 | epot = -22.39864736443 | etot = -17.061194554115 -858000 ekin = 2.20266598505728 | erot = 2.82477658278041 | epot = -22.322749893257 | etot = -17.2953073254193 -859000 ekin = 2.30655855498922 | erot = 2.31428920065484 | epot = -22.299458676259 | etot = -17.6786109206149 -860000 ekin = 1.99697183524065 | erot = 1.95028062775308 | epot = -22.3156691349687 | etot = -18.3684166719749 -861000 ekin = 2.69687116915107 | erot = 2.24433771449493 | epot = -22.3086232893581 | etot = -17.3674144057121 -862000 ekin = 2.86022987586877 | erot = 2.41684736135787 | epot = -22.2874375572893 | etot = -17.0103603200626 -863000 ekin = 2.60871204568914 | erot = 3.3557366458487 | epot = -22.2313024399491 | etot = -16.2668537484113 -864000 ekin = 2.90978326967391 | erot = 2.29745178043259 | epot = -22.1985713670251 | etot = -16.9913363169186 -865000 ekin = 1.92892881804686 | erot = 2.15731715168145 | epot = -22.0984656787339 | etot = -18.0122197090056 -866000 ekin = 1.96990768776308 | erot = 1.64764578107637 | epot = -21.9980087709689 | etot = -18.3804553021294 -867000 ekin = 1.75218832670564 | erot = 3.37220276943672 | epot = -21.9060579112704 | etot = -16.781666815128 -868000 ekin = 1.82818126605702 | erot = 2.79449094294287 | epot = -21.9401796601767 | etot = -17.3175074511768 -869000 ekin = 2.38095838431442 | erot = 2.38587739965205 | epot = -22.0329803939138 | etot = -17.2661446099473 -870000 ekin = 1.91334960398162 | erot = 3.22058637313173 | epot = -22.0372634175766 | etot = -16.9033274404632 -871000 ekin = 3.11762256076551 | erot = 2.95337521110721 | epot = -21.9585521021423 | etot = -15.8875543302696 -872000 ekin = 2.97995457097216 | erot = 1.38589789821627 | epot = -21.8388140547637 | etot = -17.4729615855753 -873000 ekin = 2.75063242740213 | erot = 2.24384409185972 | epot = -21.7621446383558 | etot = -16.767668119094 -874000 ekin = 2.42548187796032 | erot = 2.11160399589529 | epot = -21.6726796153781 | etot = -17.1355937415225 -875000 ekin = 2.99029080863986 | erot = 2.74119845235593 | epot = -21.6681717382462 | etot = -15.9366824772504 -876000 ekin = 2.13275197859305 | erot = 2.233203194222 | epot = -21.6687594523732 | etot = -17.3028042795581 -877000 ekin = 1.83070162423874 | erot = 1.6010526911626 | epot = -21.6263742280813 | etot = -18.19461991268 -878000 ekin = 2.01997494895548 | erot = 2.72070409004295 | epot = -21.632105565574 | etot = -16.8914265265756 -879000 ekin = 1.43444833027133 | erot = 2.17422677437648 | epot = -21.5501867528963 | etot = -17.9415116482485 -880000 ekin = 2.09181862571921 | erot = 2.57771231025419 | epot = -21.4847603093162 | etot = -16.8152293733428 -881000 ekin = 1.54081572899847 | erot = 1.98591498012594 | epot = -21.5197472943257 | etot = -17.9930165852013 -882000 ekin = 2.2061903789583 | erot = 2.64808794630213 | epot = -21.6149395754995 | etot = -16.760661250239 -883000 ekin = 2.22398786469444 | erot = 2.23146516226547 | epot = -21.6814015671086 | etot = -17.2259485401487 -884000 ekin = 2.78668802039765 | erot = 2.10130089852047 | epot = -21.7272273228039 | etot = -16.8392384038858 -885000 ekin = 1.92361997638943 | erot = 1.77572378933155 | epot = -21.7696517903878 | etot = -18.0703080246668 -886000 ekin = 1.99836032534883 | erot = 3.11596676947403 | epot = -21.7879382713548 | etot = -16.673611176532 -887000 ekin = 1.98879909318866 | erot = 2.81589132946027 | epot = -21.7923091863043 | etot = -16.9876187636554 -888000 ekin = 1.92041141945741 | erot = 2.3252911526479 | epot = -21.8607011941373 | etot = -17.614998622032 -889000 ekin = 1.8806357075667 | erot = 2.46119753007268 | epot = -21.9506056361693 | etot = -17.6087723985299 -890000 ekin = 1.86005551534237 | erot = 2.25705356539098 | epot = -22.0523870894554 | etot = -17.9352780087221 -891000 ekin = 2.60384568426052 | erot = 2.35330960558484 | epot = -22.1900620535717 | etot = -17.2329067637263 -892000 ekin = 2.68682478776143 | erot = 2.69192226449536 | epot = -22.2913421142228 | etot = -16.9125950619661 -893000 ekin = 2.17360632388892 | erot = 2.98553431183659 | epot = -22.2913111245685 | etot = -17.132170488843 -894000 ekin = 2.52600330506545 | erot = 2.45861329518365 | epot = -22.2813523194117 | etot = -17.2967357191626 -895000 ekin = 2.51964265942842 | erot = 2.458508768977 | epot = -22.3090530666537 | etot = -17.3309016382482 -896000 ekin = 1.83970949418621 | erot = 2.7876698428861 | epot = -22.2816769795447 | etot = -17.6542976424724 -897000 ekin = 2.36177466310812 | erot = 2.0208895092276 | epot = -22.2244555724411 | etot = -17.8417914001054 -898000 ekin = 2.11475930620727 | erot = 1.90142689771282 | epot = -22.1399515435435 | etot = -18.1237653396234 -899000 ekin = 2.62628238826603 | erot = 2.33607509693707 | epot = -22.040854543184 | etot = -17.0784970579809 -900000 ekin = 2.1134311489616 | erot = 2.28923041198217 | epot = -22.042922147544 | etot = -17.6402605866003 -901000 ekin = 1.9156742929676 | erot = 1.81441237665855 | epot = -22.0776682049659 | etot = -18.3475815353397 -902000 ekin = 2.56902181313363 | erot = 2.49856756454338 | epot = -22.0065137105888 | etot = -16.9389243329118 -903000 ekin = 1.85774740371253 | erot = 2.17490444163848 | epot = -21.9440961512363 | etot = -17.9114443058853 -904000 ekin = 1.86493397406833 | erot = 2.32873873815716 | epot = -21.8931358584844 | etot = -17.6994631462589 -905000 ekin = 2.31979070947169 | erot = 2.14360558294755 | epot = -21.824385320242 | etot = -17.3609890278228 -906000 ekin = 2.49844805906095 | erot = 2.24842339845928 | epot = -21.8343155675942 | etot = -17.087444110074 -907000 ekin = 4.2050069684007 | erot = 2.50213003512293 | epot = -21.926981437738 | etot = -15.2198444342144 -908000 ekin = 3.27384188266606 | erot = 2.113986364986 | epot = -22.0851390841283 | etot = -16.6973108364762 -909000 ekin = 2.63126156907554 | erot = 1.92589592890071 | epot = -22.2067426627273 | etot = -17.649585164751 -910000 ekin = 2.59247391196527 | erot = 2.91530974700789 | epot = -22.3083595488238 | etot = -16.8005758898507 -911000 ekin = 2.58542931349158 | erot = 4.35273181589072 | epot = -22.3703725466068 | etot = -15.4322114172245 -912000 ekin = 3.05788115941417 | erot = 3.70629270837706 | epot = -22.3924331468687 | etot = -15.6282592790774 -913000 ekin = 2.82179099955174 | erot = 2.17271040546975 | epot = -22.3592523787226 | etot = -17.3647509737011 -914000 ekin = 2.15502438011904 | erot = 1.21668409626845 | epot = -22.2678100512732 | etot = -18.8961015748857 -915000 ekin = 1.59606663662058 | erot = 2.96270026674799 | epot = -22.1740650061606 | etot = -17.615298102792 -916000 ekin = 2.59113116114426 | erot = 3.74925276784446 | epot = -22.2376802645764 | etot = -15.8972963355877 -917000 ekin = 3.04931771481537 | erot = 2.87183708314021 | epot = -22.2631766381559 | etot = -16.3420218402004 -918000 ekin = 2.92188996322642 | erot = 2.63336986904281 | epot = -22.2586011448583 | etot = -16.7033413125891 -919000 ekin = 3.21078589975638 | erot = 2.75946192406924 | epot = -22.2354679015341 | etot = -16.2652200777085 -920000 ekin = 2.28588196467068 | erot = 2.37332214874002 | epot = -22.2033589800159 | etot = -17.5441548666052 -921000 ekin = 2.38962275209347 | erot = 2.43661594631483 | epot = -22.1850468087942 | etot = -17.3588081103859 -922000 ekin = 2.30444121290069 | erot = 2.41446680487179 | epot = -22.1364838134968 | etot = -17.4175757957243 -923000 ekin = 2.49328668364371 | erot = 2.66692739305866 | epot = -22.1214525565084 | etot = -16.961238479806 -924000 ekin = 1.53749552443357 | erot = 2.96826070169594 | epot = -22.0894201538095 | etot = -17.58366392768 -925000 ekin = 1.85840160112661 | erot = 1.96300614534087 | epot = -22.0261080308484 | etot = -18.2047002843809 -926000 ekin = 1.36444139420093 | erot = 2.1171911056521 | epot = -22.0105169062661 | etot = -18.5288844064131 -927000 ekin = 2.55080456695379 | erot = 2.08771192494034 | epot = -22.0296775970306 | etot = -17.3911611051365 -928000 ekin = 2.08687563155734 | erot = 2.73937352627042 | epot = -22.0655254209395 | etot = -17.2392762631117 -929000 ekin = 1.85842465674464 | erot = 1.85229951899858 | epot = -22.161879510768 | etot = -18.4511553350248 -930000 ekin = 1.98312460976539 | erot = 2.1107410982594 | epot = -22.14836282055 | etot = -18.0544971125252 -931000 ekin = 2.44403538776918 | erot = 1.87099700190232 | epot = -22.0455015122594 | etot = -17.7304691225879 -932000 ekin = 2.7450847259232 | erot = 2.34428750425033 | epot = -22.0610452671158 | etot = -16.9716730369423 -933000 ekin = 3.03611053551161 | erot = 2.51768120120295 | epot = -21.9625013660046 | etot = -16.4087096292901 -934000 ekin = 2.94656859108538 | erot = 2.48807299457996 | epot = -21.861427363924 | etot = -16.4267857782587 -935000 ekin = 2.79276097099932 | erot = 2.14683659927043 | epot = -21.8273092000012 | etot = -16.8877116297315 -936000 ekin = 2.97178317336133 | erot = 2.07585468409967 | epot = -21.8285263420326 | etot = -16.7808884845716 -937000 ekin = 3.04678623330025 | erot = 2.3469475727902 | epot = -21.7540111620946 | etot = -16.3602773560041 -938000 ekin = 2.98751343731959 | erot = 2.36094469095133 | epot = -21.6698990656412 | etot = -16.3214409373703 -939000 ekin = 2.58148991378899 | erot = 2.28540307033942 | epot = -21.641624391377 | etot = -16.7747314072486 -940000 ekin = 2.64449140269543 | erot = 2.76444805229845 | epot = -21.5519193090555 | etot = -16.1429798540616 -941000 ekin = 2.27119597888968 | erot = 2.6047011226429 | epot = -21.4613787017959 | etot = -16.5854816002633 -942000 ekin = 1.87372343217533 | erot = 2.80846718394805 | epot = -21.3627475231486 | etot = -16.6805569070252 -943000 ekin = 2.47144243861285 | erot = 2.33780411758964 | epot = -21.3635196463293 | etot = -16.5542730901269 -944000 ekin = 2.13395812695593 | erot = 1.92152946754219 | epot = -21.3250397924826 | etot = -17.2695521979844 -945000 ekin = 2.55906013749132 | erot = 2.2064112111687 | epot = -21.3688330068161 | etot = -16.6033616581561 -946000 ekin = 2.36057360323902 | erot = 2.87561909021941 | epot = -21.3642087487724 | etot = -16.128016055314 -947000 ekin = 2.0664007802554 | erot = 1.8712733843037 | epot = -21.3615863875836 | etot = -17.4239122230245 -948000 ekin = 1.84827298766581 | erot = 1.37746869479931 | epot = -21.4042186851624 | etot = -18.1784770026972 -949000 ekin = 1.76268582715986 | erot = 2.31704980534492 | epot = -21.4240851264671 | etot = -17.3443494939624 -950000 ekin = 1.71596526195605 | erot = 2.24238613701562 | epot = -21.4136184248624 | etot = -17.4552670258908 -951000 ekin = 1.97739431794919 | erot = 2.32356723589743 | epot = -21.4746626443703 | etot = -17.1737010905236 -952000 ekin = 2.93969915889367 | erot = 2.72641565709973 | epot = -21.5183559681327 | etot = -15.8522411521393 -953000 ekin = 2.94576770934606 | erot = 2.38856498634115 | epot = -21.5141407104899 | etot = -16.1798080148027 -954000 ekin = 3.09120782928501 | erot = 1.98547863545544 | epot = -21.4220978424351 | etot = -16.3454113776947 -955000 ekin = 3.57635302907509 | erot = 2.07344226252239 | epot = -21.3055276294275 | etot = -15.65573233783 -956000 ekin = 2.96199697760255 | erot = 3.68176573533001 | epot = -21.1569123839441 | etot = -14.5131496710115 -957000 ekin = 2.99343140156395 | erot = 2.6641673976979 | epot = -20.9767503534011 | etot = -15.3191515541393 -958000 ekin = 2.66519710291016 | erot = 2.94296730915348 | epot = -20.778322783175 | etot = -15.1701583711114 -959000 ekin = 1.92859078964251 | erot = 2.44737003089627 | epot = -20.7022563699757 | etot = -16.3262955494369 -960000 ekin = 1.49451727360012 | erot = 3.13583888779427 | epot = -20.7118848436939 | etot = -16.0815286822995 -961000 ekin = 1.95030797402212 | erot = 2.08601754519332 | epot = -20.7116280307748 | etot = -16.6753025115593 -962000 ekin = 2.02519672504697 | erot = 1.8993614904036 | epot = -20.7772856698007 | etot = -16.8527274543501 -963000 ekin = 1.81866098250674 | erot = 2.47413067985077 | epot = -20.8446590259958 | etot = -16.5518673636383 -964000 ekin = 2.82274927013719 | erot = 2.43518028535965 | epot = -20.9038261011269 | etot = -15.64589654563 -965000 ekin = 2.55107687208175 | erot = 2.29878175210651 | epot = -20.9717669792334 | etot = -16.1219083550452 -966000 ekin = 2.1200913755337 | erot = 2.2846988725502 | epot = -21.0606259488472 | etot = -16.6558357007633 -967000 ekin = 1.58229605946639 | erot = 3.55757301639252 | epot = -21.1224849810159 | etot = -15.982615905157 -968000 ekin = 1.95011274740584 | erot = 2.3752003899703 | epot = -21.1147445818894 | etot = -16.7894314445132 -969000 ekin = 2.19259033480515 | erot = 2.45911844664679 | epot = -21.0841141670188 | etot = -16.4324053855669 -970000 ekin = 1.87048608890169 | erot = 2.95646346755995 | epot = -21.0142741201673 | etot = -16.1873245637056 -971000 ekin = 1.950153162929 | erot = 3.0717285905854 | epot = -20.9854323440231 | etot = -15.9635505905087 -972000 ekin = 1.93197938125398 | erot = 2.56232300543577 | epot = -20.9700672251306 | etot = -16.4757648384409 -973000 ekin = 2.21536036218028 | erot = 2.92680374210101 | epot = -20.9735070987956 | etot = -15.8313429945143 -974000 ekin = 2.53787477442507 | erot = 2.68950390909793 | epot = -20.9249780227203 | etot = -15.6975993391973 -975000 ekin = 3.3832404833891 | erot = 2.33888514036507 | epot = -20.8975294326534 | etot = -15.1754038088992 -976000 ekin = 2.84644457799265 | erot = 3.11578234174529 | epot = -20.8919958508098 | etot = -14.9297689310719 -977000 ekin = 2.71728271399263 | erot = 2.50842582300821 | epot = -20.8689034899506 | etot = -15.6431949529497 -978000 ekin = 1.79447160570111 | erot = 2.0736426807417 | epot = -20.8420102217514 | etot = -16.9738959353086 -979000 ekin = 1.87121723303036 | erot = 2.21930404593537 | epot = -20.7748213462523 | etot = -16.6843000672865 -980000 ekin = 1.92329753072694 | erot = 1.58075512357095 | epot = -20.7449893755876 | etot = -17.2409367212897 -981000 ekin = 1.54378956643562 | erot = 2.05667260838343 | epot = -20.8055475552994 | etot = -17.2050853804803 -982000 ekin = 1.84106018589786 | erot = 1.96434982363189 | epot = -20.9115392638984 | etot = -17.1061292543687 -983000 ekin = 2.72419781781661 | erot = 1.79041192395563 | epot = -20.935370561762 | etot = -16.4207608199898 -984000 ekin = 3.62592878226169 | erot = 2.63360520982709 | epot = -21.0391300854773 | etot = -14.7795960933885 -985000 ekin = 2.94852029277516 | erot = 2.17123324675229 | epot = -21.210668025134 | etot = -16.0909144856065 -986000 ekin = 2.87308205004233 | erot = 2.17802315487852 | epot = -21.3375937115616 | etot = -16.2864885066408 -987000 ekin = 3.37012638403781 | erot = 2.51985184465596 | epot = -21.4043627880157 | etot = -15.514384559322 -988000 ekin = 3.46870329025365 | erot = 3.24288958557111 | epot = -21.4574256625201 | etot = -14.7458327866953 -989000 ekin = 2.84167714920458 | erot = 2.20794124486355 | epot = -21.6063889534189 | etot = -16.5567705593508 -990000 ekin = 2.79616762915596 | erot = 1.83962543905575 | epot = -21.6049428673847 | etot = -16.969149799173 -991000 ekin = 3.12376374867622 | erot = 3.19217780569165 | epot = -21.5124272449002 | etot = -15.1964856905324 -992000 ekin = 3.28266282243327 | erot = 2.63435990952508 | epot = -21.3973672594977 | etot = -15.4803445275393 -993000 ekin = 3.03845590773447 | erot = 2.22451011589011 | epot = -21.3214832241627 | etot = -16.0585172005382 -994000 ekin = 3.17417330085466 | erot = 2.79358287085479 | epot = -21.2400043434466 | etot = -15.2722481717371 -995000 ekin = 3.20646780888655 | erot = 1.72565517852613 | epot = -21.1372155372729 | etot = -16.2050925498602 -996000 ekin = 3.05109485375234 | erot = 3.18000631651671 | epot = -21.0952864235923 | etot = -14.8641852533233 -997000 ekin = 2.95625677593347 | erot = 3.15916554858247 | epot = -21.058148007987 | etot = -14.942725683471 -998000 ekin = 3.06605914614908 | erot = 1.97682176881012 | epot = -20.9834240684974 | etot = -15.9405431535382 -999000 ekin = 2.08919327368179 | erot = 2.76364485800616 | epot = -20.9705413117635 | etot = -16.1177031800756 -1000000 ekin = 2.11761701334905 | erot = 2.1409630347026 | epot = -20.9096627221725 | etot = -16.6510826741208 - 1000000 0.094116312 -1.3659956 0.059141691 -1.1745029 -0.0001320501 -Loop time of 47.7342 on 1 procs for 1000000 steps with 16 atoms - -Performance: 18100.242 tau/day, 20949.354 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 35.978 | 35.978 | 35.978 | 0.0 | 75.37 -Bond | 1.0053 | 1.0053 | 1.0053 | 0.0 | 2.11 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.28221 | 0.28221 | 0.28221 | 0.0 | 0.59 -Output | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.00 -Modify | 10.039 | 10.039 | 10.039 | 0.0 | 21.03 -Other | | 0.4294 | | | 0.90 - -Nlocal: 16 ave 16 max 16 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 116 ave 116 max 116 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 116 -Ave neighs/atom = 7.25 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:47 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4 deleted file mode 100644 index 320d186f80..0000000000 --- a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.24Mar17.duplex2.g++.4 +++ /dev/null @@ -1,1167 +0,0 @@ -LAMMPS (24 Mar 2017) -variable number equal 2 -variable ofreq equal 1000 -variable efreq equal 1000 - -units lj - -dimension 3 - -newton off - -boundary p p p - -atom_style hybrid bond ellipsoid -atom_modify sort 0 1.0 - -# Pair interactions require lists of neighbours to be calculated -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -read_data data.duplex2 - orthogonal box = (-20 -20 -20) to (20 20 20) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 16 atoms - reading velocities ... - 16 velocities - 16 ellipsoids - scanning bonds ... - 2 = max bonds/atom - reading bonds ... - 13 bonds - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - -set atom * mass 3.1575 - 16 settings made for mass - -group all type 1 4 -16 atoms in group all - -# oxDNA bond interactions - FENE backbone -bond_style oxdna2/fene -bond_coeff * 2.0 0.25 0.7564 - -# oxDNA pair interactions -pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh -pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 -pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 -pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 -pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 -pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 -pair_coeff * * oxdna2/dh 0.1 1.0 0.815 - -# NVE ensemble -#fix 1 all nve/dot -fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 -#fix 1 all nve/asphere -#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 - -timestep 1e-5 - -#comm_style tiled -#fix 3 all balance 10000 1.1 rcb - -#compute mol all chunk/atom molecule -#compute mychunk all vcm/chunk mol -#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector - -#dump pos all xyz ${ofreq} traj.${number}.xyz - -#compute quat all property/atom quatw quati quatj quatk -#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] -#dump_modify quat sort id -#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" - -compute erot all erotate/asphere -compute ekin all ke -compute epot all pe -variable erot equal c_erot -variable ekin equal c_ekin -variable epot equal c_epot -variable etot equal c_erot+c_ekin+c_epot -fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes -fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes - -#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz -#dump_modify out sort id -#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" - -run 1000000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.6274 - ghost atom cutoff = 2.6274 - binsize = 1.3137, bins = 31 31 31 - 6 neighbor lists, perpetual/occasional/extra = 6 0 0 - (1) pair oxdna2/excv, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard - (2) pair oxdna2/stk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (3) pair oxdna2/hbond, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (4) pair oxdna2/xstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (5) pair oxdna2/coaxstk, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none - (6) pair oxdna2/dh, perpetual, copy from (1) - attributes: half, newton off - pair build: copy - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.141 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05 -1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698 -2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481 -3000 ekin = 3.26433550542939 | erot = 2.76107866472087 | epot = -24.2947953202752 | etot = -18.269381150125 -4000 ekin = 1.9203212531997 | erot = 2.133394384253 | epot = -24.234098584123 | etot = -20.1803829466703 -5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963 -6000 ekin = 2.18974627635306 | erot = 1.73271671162436 | epot = -24.1096616118305 | etot = -20.1871986238531 -7000 ekin = 2.65472853187395 | erot = 1.73258720631297 | epot = -24.0561118130561 | etot = -19.6687960748691 -8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058 -9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658 -10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535 -11000 ekin = 2.03264234985168 | erot = 1.68707706801736 | epot = -23.7396221351636 | etot = -20.0199027172945 -12000 ekin = 2.66329111303325 | erot = 2.49804687909781 | epot = -23.7366995564469 | etot = -18.5753615643158 -13000 ekin = 1.89677055811531 | erot = 2.34624821263612 | epot = -23.6591067615901 | etot = -19.4160879908387 -14000 ekin = 1.91279445145792 | erot = 2.13129118502405 | epot = -23.6468743458148 | etot = -19.6027887093328 -15000 ekin = 2.41876331112169 | erot = 2.07362128417238 | epot = -23.5767792498568 | etot = -19.0843946545628 -16000 ekin = 2.76615310647131 | erot = 1.19495009524763 | epot = -23.4862363509196 | etot = -19.5251331492006 -17000 ekin = 2.45632569069911 | erot = 2.37627186077148 | epot = -23.500787861849 | etot = -18.6681903103784 -18000 ekin = 2.18348858414473 | erot = 2.46933014500077 | epot = -23.5223047738331 | etot = -18.8694860446876 -19000 ekin = 2.2074746303434 | erot = 2.45349372324724 | epot = -23.4618353655003 | etot = -18.8008670119096 -20000 ekin = 2.06964129991908 | erot = 1.80832666230414 | epot = -23.4930879797962 | etot = -19.615120017573 -21000 ekin = 2.26572194434983 | erot = 2.76680470094409 | epot = -23.5023070260553 | etot = -18.4697803807614 -22000 ekin = 2.69295306575102 | erot = 1.86984875574017 | epot = -23.4463493063166 | etot = -18.8835474848254 -23000 ekin = 1.99930153068661 | erot = 2.27735339437466 | epot = -23.3493214662276 | etot = -19.0726665411663 -24000 ekin = 2.20679650752062 | erot = 2.98147599881873 | epot = -23.273517698415 | etot = -18.0852451920757 -25000 ekin = 2.28085541692287 | erot = 2.99165466281124 | epot = -23.2072100929465 | etot = -17.9347000132124 -26000 ekin = 1.9530124305314 | erot = 2.81680126246586 | epot = -23.0636678500934 | etot = -18.2938541570962 -27000 ekin = 1.96948983508855 | erot = 2.69266617300682 | epot = -22.9870601707012 | etot = -18.3249041626058 -28000 ekin = 2.02061868464074 | erot = 2.37038530969117 | epot = -22.9383598315964 | etot = -18.5473558372645 -29000 ekin = 2.51387846128098 | erot = 2.0265039132053 | epot = -22.888959880923 | etot = -18.3485775064367 -30000 ekin = 1.95889729807242 | erot = 2.1170713545074 | epot = -22.7896312662562 | etot = -18.7136626136764 -31000 ekin = 1.81775203419098 | erot = 2.326796842935 | epot = -22.7561124537192 | etot = -18.6115635765932 -32000 ekin = 1.87947265787065 | erot = 2.0009346769358 | epot = -22.8533570528062 | etot = -18.9729497179997 -33000 ekin = 1.77435214491107 | erot = 1.82826131933673 | epot = -22.8632647352802 | etot = -19.2606512710324 -34000 ekin = 2.27098719472917 | erot = 3.11275511420439 | epot = -22.9527052663856 | etot = -17.5689629574521 -35000 ekin = 2.88921171289845 | erot = 1.82538384737236 | epot = -23.0316569923336 | etot = -18.3170614320628 -36000 ekin = 2.40471013682393 | erot = 2.59817148723643 | epot = -23.1277697887139 | etot = -18.1248881646536 -37000 ekin = 2.23499312928139 | erot = 1.74662115184433 | epot = -23.1542126827759 | etot = -19.1725984016501 -38000 ekin = 2.13875747252781 | erot = 3.07733571118648 | epot = -23.0916051545794 | etot = -17.8755119708651 -39000 ekin = 2.08901196654187 | erot = 2.81975762995374 | epot = -23.0796147800379 | etot = -18.1708451835423 -40000 ekin = 2.95155149177527 | erot = 2.19459039829335 | epot = -23.141500571363 | etot = -17.9953586812944 -41000 ekin = 2.49235596566196 | erot = 3.45295839915509 | epot = -23.115526015811 | etot = -17.1702116509939 -42000 ekin = 2.58401591894786 | erot = 3.0976076851145 | epot = -23.0181097727229 | etot = -17.3364861686605 -43000 ekin = 2.17593293893362 | erot = 2.65403748718844 | epot = -22.8962504257564 | etot = -18.0662799996343 -44000 ekin = 2.34068034665607 | erot = 3.294882771572 | epot = -22.8143844644656 | etot = -17.1788213462375 -45000 ekin = 1.87200112415306 | erot = 3.49863859200052 | epot = -22.6989374637074 | etot = -17.3282977475538 -46000 ekin = 2.60943921333194 | erot = 2.23170007842725 | epot = -22.5884035122493 | etot = -17.7472642204901 -47000 ekin = 1.89594756436345 | erot = 3.4002587629387 | epot = -22.4938472923117 | etot = -17.1976409650096 -48000 ekin = 2.49339593279701 | erot = 2.5104785556399 | epot = -22.5372062210456 | etot = -17.5333317326087 -49000 ekin = 3.2041407554348 | erot = 2.17669016194865 | epot = -22.5688036423094 | etot = -17.1879727249259 -50000 ekin = 2.93024070185999 | erot = 1.55416219951966 | epot = -22.6087903765995 | etot = -18.1243874752199 -51000 ekin = 2.8585759501124 | erot = 2.69193261792584 | epot = -22.6228353253324 | etot = -17.0723267572942 -52000 ekin = 2.3079418078843 | erot = 1.84260643306147 | epot = -22.6230480697441 | etot = -18.4724998287983 -53000 ekin = 3.1803685919024 | erot = 1.67451273370508 | epot = -22.6834814309773 | etot = -17.8286001053698 -54000 ekin = 2.6151376953128 | erot = 1.96091197875017 | epot = -22.7484551927013 | etot = -18.1724055186384 -55000 ekin = 3.1639577845443 | erot = 2.86286196426802 | epot = -22.7917236196438 | etot = -16.7649038708315 -56000 ekin = 2.52994034294643 | erot = 3.05544364249365 | epot = -22.7651844773103 | etot = -17.1798004918702 -57000 ekin = 2.40889871674401 | erot = 3.4525690879514 | epot = -22.7113139496974 | etot = -16.849846145002 -58000 ekin = 1.9363727739706 | erot = 2.52762778976703 | epot = -22.6468058892224 | etot = -18.1828053254848 -59000 ekin = 2.55505415922972 | erot = 3.52385701835933 | epot = -22.6037443858311 | etot = -16.5248332082421 -60000 ekin = 2.80945252332612 | erot = 2.88606183204889 | epot = -22.5227874119079 | etot = -16.8272730565329 -61000 ekin = 2.69750183117722 | erot = 2.55373633146433 | epot = -22.4306469225965 | etot = -17.1794087599549 -62000 ekin = 2.74494354639602 | erot = 2.23074517653766 | epot = -22.3675792436719 | etot = -17.3918905207383 -63000 ekin = 2.66335513293138 | erot = 2.46159865380861 | epot = -22.3527707145482 | etot = -17.2278169278082 -64000 ekin = 2.12832019835147 | erot = 2.78772793164811 | epot = -22.3048690294469 | etot = -17.3888208994473 -65000 ekin = 1.88429801911228 | erot = 2.70719871478483 | epot = -22.3342736701749 | etot = -17.7427769362778 -66000 ekin = 2.77106091929282 | erot = 1.94126620531915 | epot = -22.338257942783 | etot = -17.625930818171 -67000 ekin = 2.53561386235746 | erot = 2.45901054739082 | epot = -22.3780784743028 | etot = -17.3834540645545 -68000 ekin = 2.9678648663671 | erot = 1.95502711706149 | epot = -22.4420512915713 | etot = -17.5191593081427 -69000 ekin = 2.61501630036274 | erot = 2.2429513448561 | epot = -22.3607835407198 | etot = -17.502815895501 -70000 ekin = 2.41492598760663 | erot = 2.80885610657203 | epot = -22.2905725083407 | etot = -17.066790414162 -71000 ekin = 2.65062529541957 | erot = 2.88868401392431 | epot = -22.2951070257787 | etot = -16.7557977164349 -72000 ekin = 2.93273744051009 | erot = 2.82552508252073 | epot = -22.4016757930526 | etot = -16.6434132700218 -73000 ekin = 2.18922665452238 | erot = 3.03559183860538 | epot = -22.4509770394845 | etot = -17.2261585463568 -74000 ekin = 2.16074843540078 | erot = 2.83668185121384 | epot = -22.4374624006144 | etot = -17.4400321139998 -75000 ekin = 1.52329638473031 | erot = 1.91520672578907 | epot = -22.5623153080324 | etot = -19.123812197513 -76000 ekin = 1.89250964827726 | erot = 2.83358650938892 | epot = -22.6698326202442 | etot = -17.943736462578 -77000 ekin = 2.82066630152179 | erot = 3.19779433197964 | epot = -22.7402096770599 | etot = -16.7217490435584 -78000 ekin = 2.42603824235662 | erot = 2.82319136688957 | epot = -22.7334053911689 | etot = -17.4841757819227 -79000 ekin = 2.1571494738421 | erot = 1.67722302323495 | epot = -22.7616861631187 | etot = -18.9273136660417 -80000 ekin = 2.3760789053548 | erot = 2.58372913427157 | epot = -22.6889139769023 | etot = -17.729105937276 -81000 ekin = 2.73468961033338 | erot = 1.92748741387075 | epot = -22.6388260929897 | etot = -17.9766490687856 -82000 ekin = 1.90565370838817 | erot = 1.71715050303634 | epot = -22.5547415381056 | etot = -18.9319373266811 -83000 ekin = 1.63698443616271 | erot = 1.88092293220519 | epot = -22.4792739412377 | etot = -18.9613665728698 -84000 ekin = 1.65571812906993 | erot = 2.10290321918187 | epot = -22.4031972735297 | etot = -18.6445759252779 -85000 ekin = 2.40863681830855 | erot = 2.04741059095057 | epot = -22.321221903585 | etot = -17.8651744943259 -86000 ekin = 2.50560893716733 | erot = 1.80624308622105 | epot = -22.3789065133115 | etot = -18.0670544899231 -87000 ekin = 2.13576456371582 | erot = 1.97115993651017 | epot = -22.4335511413526 | etot = -18.3266266411266 -88000 ekin = 1.74897318407528 | erot = 2.37233945814529 | epot = -22.4142028246849 | etot = -18.2928901824643 -89000 ekin = 1.85559683216276 | erot = 3.29559734355419 | epot = -22.4519626048678 | etot = -17.3007684291509 -90000 ekin = 2.22181579992018 | erot = 2.33948779846394 | epot = -22.5289826258985 | etot = -17.9676790275144 -91000 ekin = 2.40596540834273 | erot = 3.11545124680293 | epot = -22.4975752624166 | etot = -16.9761586072709 -92000 ekin = 2.6773157744569 | erot = 3.00279439655287 | epot = -22.4834827179575 | etot = -16.8033725469477 -93000 ekin = 3.0427813598525 | erot = 3.03722776158512 | epot = -22.4121259471479 | etot = -16.3321168257103 -94000 ekin = 3.20507830840023 | erot = 1.86440047317737 | epot = -22.5079833350679 | etot = -17.4385045534903 -95000 ekin = 3.4839955648833 | erot = 2.87934575393031 | epot = -22.5675869456428 | etot = -16.2042456268292 -96000 ekin = 2.8873631080951 | erot = 2.38554372248299 | epot = -22.5453635283434 | etot = -17.2724566977653 -97000 ekin = 1.92899149350272 | erot = 2.09886479790579 | epot = -22.5208382020819 | etot = -18.4929819106733 -98000 ekin = 2.21420868967462 | erot = 3.66528252896999 | epot = -22.4426781355708 | etot = -16.5631869169262 -99000 ekin = 1.98238051924192 | erot = 2.77358159119584 | epot = -22.3579409961467 | etot = -17.6019788857089 -100000 ekin = 1.80278462349605 | erot = 2.65457154995031 | epot = -22.2926900475079 | etot = -17.8353338740616 -101000 ekin = 2.14042196591663 | erot = 2.38610603254675 | epot = -22.2789462117326 | etot = -17.7524182132692 -102000 ekin = 1.54923043145398 | erot = 2.30485616158943 | epot = -22.27519637673 | etot = -18.4211097836866 -103000 ekin = 1.66618004359352 | erot = 2.82192794888076 | epot = -22.3284746660305 | etot = -17.8403666735562 -104000 ekin = 1.8840390723585 | erot = 3.37607054348826 | epot = -22.4068162519772 | etot = -17.1467066361304 -105000 ekin = 2.08970806137592 | erot = 2.01278733908098 | epot = -22.450865561264 | etot = -18.3483701608071 -106000 ekin = 2.87186619049714 | erot = 1.95029477179727 | epot = -22.46479383237 | etot = -17.6426328700756 -107000 ekin = 2.28516102595382 | erot = 1.55115426482474 | epot = -22.420448971169 | etot = -18.5841336803904 -108000 ekin = 2.4440862469061 | erot = 1.71323205815914 | epot = -22.4934628688132 | etot = -18.336144563748 -109000 ekin = 2.33376449416318 | erot = 2.92962175925398 | epot = -22.4792154966925 | etot = -17.2158292432753 -110000 ekin = 2.7815613020599 | erot = 2.36483486971455 | epot = -22.4384263756783 | etot = -17.2920302039039 -111000 ekin = 2.32472851347632 | erot = 2.09554567134106 | epot = -22.3756448055424 | etot = -17.955370620725 -112000 ekin = 2.91126509700492 | erot = 1.82787812400381 | epot = -22.2278235937356 | etot = -17.4886803727269 -113000 ekin = 2.82522334536064 | erot = 1.67936756938672 | epot = -22.2030639545535 | etot = -17.6984730398062 -114000 ekin = 3.42964629994365 | erot = 2.67287683722422 | epot = -22.3274259722919 | etot = -16.224902835124 -115000 ekin = 3.0542495603856 | erot = 1.72370226125567 | epot = -22.3530732875163 | etot = -17.575121465875 -116000 ekin = 3.19934505541307 | erot = 3.20304074939431 | epot = -22.4112422200445 | etot = -16.0088564152371 -117000 ekin = 3.03942349360439 | erot = 2.40720645224432 | epot = -22.3646852618703 | etot = -16.9180553160216 -118000 ekin = 3.21704225120818 | erot = 1.46425401673932 | epot = -22.2864155249032 | etot = -17.6051192569557 -119000 ekin = 2.33989996826882 | erot = 3.07668030790319 | epot = -22.2283862990246 | etot = -16.8118060228526 -120000 ekin = 1.93772242476321 | erot = 2.20130457047854 | epot = -22.1620199969907 | etot = -18.022993001749 -121000 ekin = 1.94013950333198 | erot = 3.08987281123524 | epot = -22.1565667857742 | etot = -17.126554471207 -122000 ekin = 1.68663003450368 | erot = 1.73461876453175 | epot = -22.2565715090021 | etot = -18.8353227099667 -123000 ekin = 1.72841976989173 | erot = 2.32750063038672 | epot = -22.3665160016578 | etot = -18.3105956013793 -124000 ekin = 2.73468934475335 | erot = 1.93313584543738 | epot = -22.378088078826 | etot = -17.7102628886353 -125000 ekin = 2.77507735763211 | erot = 1.95244582221335 | epot = -22.3863676939847 | etot = -17.6588445141392 -126000 ekin = 2.04549959008918 | erot = 1.485897173428 | epot = -22.4226219879524 | etot = -18.8912252244352 -127000 ekin = 1.86410777734907 | erot = 1.58829497411524 | epot = -22.4027380289015 | etot = -18.9503352774372 -128000 ekin = 1.63329448006254 | erot = 1.88032753965974 | epot = -22.3918784566533 | etot = -18.878256436931 -129000 ekin = 2.51522192674941 | erot = 2.38822614049101 | epot = -22.396225517968 | etot = -17.4927774507275 -130000 ekin = 1.61191166117177 | erot = 2.81688343133434 | epot = -22.341565060394 | etot = -17.9127699678879 -131000 ekin = 2.29569747740708 | erot = 2.28868769760912 | epot = -22.2184139794107 | etot = -17.6340288043945 -132000 ekin = 2.97393694467802 | erot = 2.36135254406015 | epot = -22.1410658382525 | etot = -16.8057763495143 -133000 ekin = 2.01357676743256 | erot = 2.125828419273 | epot = -22.1312019600638 | etot = -17.9917967733582 -134000 ekin = 1.56048037412857 | erot = 2.84208065022547 | epot = -22.0682869067536 | etot = -17.6657258823995 -135000 ekin = 1.79811942319758 | erot = 2.40075843487508 | epot = -22.0853555614258 | etot = -17.8864777033531 -136000 ekin = 1.63631696233012 | erot = 2.13166656554855 | epot = -22.0879615470249 | etot = -18.3199780191462 -137000 ekin = 2.36040439516093 | erot = 1.937854866329 | epot = -22.1234845924018 | etot = -17.8252253309118 -138000 ekin = 2.94591421775872 | erot = 1.58866111192914 | epot = -22.1783168558241 | etot = -17.6437415261363 -139000 ekin = 3.17560544591524 | erot = 2.24933296614108 | epot = -22.2966418842012 | etot = -16.8717034721449 -140000 ekin = 2.24781162873235 | erot = 3.05934139328613 | epot = -22.4681108223249 | etot = -17.1609578003064 -141000 ekin = 1.89078628042285 | erot = 3.13246933186327 | epot = -22.730922227649 | etot = -17.7076666153629 -142000 ekin = 2.51033894675651 | erot = 2.49428943091232 | epot = -22.8404165502847 | etot = -17.8357881726159 -143000 ekin = 2.40438807844298 | erot = 2.71461817456284 | epot = -22.8207220890737 | etot = -17.7017158360679 -144000 ekin = 1.93074254879639 | erot = 2.67760329085926 | epot = -22.6973757396236 | etot = -18.0890298999679 -145000 ekin = 1.82681171280412 | erot = 1.73674169257735 | epot = -22.6628534675149 | etot = -19.0993000621335 -146000 ekin = 2.42423538163981 | erot = 2.09087762946581 | epot = -22.6072904345337 | etot = -18.0921774234281 -147000 ekin = 1.44607209743073 | erot = 1.88012639062509 | epot = -22.5001275476876 | etot = -19.1739290596318 -148000 ekin = 1.9349809420382 | erot = 2.57774390934156 | epot = -22.4721664357448 | etot = -17.959441584365 -149000 ekin = 2.023702656427 | erot = 3.31795764580129 | epot = -22.3745153112138 | etot = -17.0328550089855 -150000 ekin = 2.48124469844233 | erot = 2.68185291250581 | epot = -22.1950329772129 | etot = -17.0319353662648 -151000 ekin = 2.76319440452883 | erot = 1.87355938382631 | epot = -21.986630645846 | etot = -17.3498768574909 -152000 ekin = 2.77453107952051 | erot = 1.77016628972892 | epot = -21.7977108098427 | etot = -17.2530134405933 -153000 ekin = 3.08827014622555 | erot = 1.80976617511255 | epot = -21.6910123469877 | etot = -16.7929760256496 -154000 ekin = 2.32051051770812 | erot = 2.18004857730092 | epot = -21.6406733490633 | etot = -17.1401142540543 -155000 ekin = 1.95766873014157 | erot = 2.67064554154833 | epot = -21.7315745360126 | etot = -17.1032602643227 -156000 ekin = 2.69830438989808 | erot = 2.24987636164773 | epot = -21.7962907570244 | etot = -16.8481100054785 -157000 ekin = 3.89340900899948 | erot = 2.7373331532516 | epot = -21.8437967078712 | etot = -15.2130545456202 -158000 ekin = 2.84737207100032 | erot = 2.70157958556584 | epot = -21.878244439129 | etot = -16.3292927825628 -159000 ekin = 3.1312088996125 | erot = 2.65375527842549 | epot = -21.8350703791794 | etot = -16.0501062011414 -160000 ekin = 2.54316260055465 | erot = 3.27950281054044 | epot = -21.8888467298127 | etot = -16.0661813187176 -161000 ekin = 2.49549109190182 | erot = 2.45028506429479 | epot = -21.8585593359585 | etot = -16.9127831797619 -162000 ekin = 3.05200272259996 | erot = 2.59164651185652 | epot = -21.8439750046483 | etot = -16.2003257701918 -163000 ekin = 3.30374280597554 | erot = 2.2419396021266 | epot = -21.8717863279577 | etot = -16.3261039198555 -164000 ekin = 3.53081155329031 | erot = 2.22419322011391 | epot = -21.8162094860939 | etot = -16.0612047126897 -165000 ekin = 2.48919804649028 | erot = 2.59105984700638 | epot = -21.7395563276218 | etot = -16.6592984341251 -166000 ekin = 2.14880495285182 | erot = 3.05770380831397 | epot = -21.6850566092694 | etot = -16.4785478481036 -167000 ekin = 2.78181890034675 | erot = 2.90402826001926 | epot = -21.5971987360122 | etot = -15.9113515756462 -168000 ekin = 1.74726050172142 | erot = 2.76898886506122 | epot = -21.490566893224 | etot = -16.9743175264413 -169000 ekin = 1.8134289785439 | erot = 2.45780601602371 | epot = -21.4680710936728 | etot = -17.1968360991052 -170000 ekin = 1.69364478039988 | erot = 2.87928997590298 | epot = -21.4668806356843 | etot = -16.8939458793814 -171000 ekin = 2.14879448642638 | erot = 1.61442218455816 | epot = -21.3172106430715 | etot = -17.5539939720869 -172000 ekin = 1.68431962963431 | erot = 2.36087816720613 | epot = -21.1539793618528 | etot = -17.1087815650124 -173000 ekin = 2.05784071815669 | erot = 2.17142592689102 | epot = -21.0926393885011 | etot = -16.8633727434534 -174000 ekin = 2.49611606122761 | erot = 3.09665692560808 | epot = -20.9460348670979 | etot = -15.3532618802622 -175000 ekin = 2.61673440848865 | erot = 2.88720331620429 | epot = -20.8525764091519 | etot = -15.348638684459 -176000 ekin = 2.16190213742438 | erot = 2.672518464664 | epot = -20.8442274508468 | etot = -16.0098068487584 -177000 ekin = 2.83236394902012 | erot = 2.81489135382761 | epot = -20.925759607446 | etot = -15.2785043045983 -178000 ekin = 3.17804494293424 | erot = 1.88346790512582 | epot = -21.0677853312893 | etot = -16.0062724832292 -179000 ekin = 2.33267448424064 | erot = 2.85731052069526 | epot = -21.1181390109479 | etot = -15.9281540060119 -180000 ekin = 2.39061531304011 | erot = 2.93791308775999 | epot = -21.1146449531392 | etot = -15.7861165523391 -181000 ekin = 2.79990361156737 | erot = 3.2889152028739 | epot = -21.0834365456108 | etot = -14.9946177311695 -182000 ekin = 3.02616507870526 | erot = 2.33414327030088 | epot = -21.0600545808658 | etot = -15.6997462318597 -183000 ekin = 2.45290144562467 | erot = 2.21141617846261 | epot = -20.911866387917 | etot = -16.2475487638297 -184000 ekin = 2.56560515060991 | erot = 2.7739810551646 | epot = -20.6989716212004 | etot = -15.3593854154259 -185000 ekin = 2.17586139274635 | erot = 1.95913868179524 | epot = -20.5985322435751 | etot = -16.4635321690335 -186000 ekin = 2.07303044902321 | erot = 3.15122816264526 | epot = -20.4965070011281 | etot = -15.2722483894597 -187000 ekin = 2.44319481307615 | erot = 1.92784212082445 | epot = -20.5124982035642 | etot = -16.1414612696636 -188000 ekin = 2.28870879542405 | erot = 2.8871121346017 | epot = -20.6323506293031 | etot = -15.4565296992773 -189000 ekin = 1.6804728023783 | erot = 3.05535775765803 | epot = -20.6378101864803 | etot = -15.901979626444 -190000 ekin = 1.97184665786398 | erot = 2.95271452778011 | epot = -20.6376534135265 | etot = -15.7130922278824 -191000 ekin = 2.30626539196432 | erot = 2.64854814117513 | epot = -20.6037323569657 | etot = -15.6489188238262 -192000 ekin = 3.54976671698923 | erot = 2.91090725702116 | epot = -20.552550883251 | etot = -14.0918769092406 -193000 ekin = 2.63938438600417 | erot = 3.14409581682355 | epot = -20.5892132844066 | etot = -14.8057330815789 -194000 ekin = 2.67903757365036 | erot = 2.30768318132376 | epot = -20.4753987179502 | etot = -15.488677962976 -195000 ekin = 1.89257615363316 | erot = 2.64508051866103 | epot = -20.4197880125066 | etot = -15.8821313402124 -196000 ekin = 2.29151017050608 | erot = 2.32636787964873 | epot = -20.4440761857987 | etot = -15.8261981356439 -197000 ekin = 2.48344018982904 | erot = 2.56544009419632 | epot = -20.516126938087 | etot = -15.4672466540617 -198000 ekin = 2.01386156849612 | erot = 1.52779840514975 | epot = -20.537160292649 | etot = -16.9955003190031 -199000 ekin = 1.50729232131931 | erot = 2.19878124720505 | epot = -20.5584754599869 | etot = -16.8524018914625 -200000 ekin = 1.64236235330806 | erot = 2.46736341802313 | epot = -20.5387924113649 | etot = -16.4290666400337 -201000 ekin = 2.627066472214 | erot = 2.61321940355395 | epot = -20.6089911163939 | etot = -15.368705240626 -202000 ekin = 2.3129503751722 | erot = 2.54874856259559 | epot = -20.6732219111123 | etot = -15.8115229733446 -203000 ekin = 1.63961009223968 | erot = 2.10835750593015 | epot = -20.7002051999768 | etot = -16.9522376018069 -204000 ekin = 2.0558049009161 | erot = 1.9161072834091 | epot = -20.8154459612946 | etot = -16.8435337769694 -205000 ekin = 3.0460386009419 | erot = 3.24233043438683 | epot = -20.9297600758299 | etot = -14.6413910405012 -206000 ekin = 2.56775422508359 | erot = 2.20992928465511 | epot = -21.0192669133083 | etot = -16.2415834035696 -207000 ekin = 3.46597997409567 | erot = 2.48427015330086 | epot = -21.1513990264881 | etot = -15.2011488990916 -208000 ekin = 2.51159742060494 | erot = 2.22948191756654 | epot = -21.2942477400986 | etot = -16.5531684019271 -209000 ekin = 3.78908644724162 | erot = 2.17660742759512 | epot = -21.4499700336111 | etot = -15.4842761587744 -210000 ekin = 3.03133642129733 | erot = 2.21595982730354 | epot = -21.5648709610245 | etot = -16.3175747124237 -211000 ekin = 1.63075564056512 | erot = 2.12650387194817 | epot = -21.6099552204253 | etot = -17.852695707912 -212000 ekin = 2.67694215598975 | erot = 2.47186432110288 | epot = -21.8481434074352 | etot = -16.6993369303426 -213000 ekin = 2.70688282449408 | erot = 1.96666534072977 | epot = -22.1170796448084 | etot = -17.4435314795845 -214000 ekin = 2.88993887341391 | erot = 3.16392577542177 | epot = -22.1689844550676 | etot = -16.1151198062319 -215000 ekin = 2.59587305508912 | erot = 1.84775314628516 | epot = -22.0799472955548 | etot = -17.6363210941805 -216000 ekin = 2.59710486720184 | erot = 2.7917023259487 | epot = -22.123050002636 | etot = -16.7342428094855 -217000 ekin = 2.50043297628753 | erot = 1.89569946865143 | epot = -22.2232445790842 | etot = -17.8271121341452 -218000 ekin = 2.42608117861514 | erot = 2.42380011003406 | epot = -22.2442965405807 | etot = -17.3944152519315 -219000 ekin = 2.31038806457502 | erot = 2.64910389607573 | epot = -22.2862511100887 | etot = -17.326759149438 -220000 ekin = 1.69989575631519 | erot = 2.34717348369245 | epot = -22.293625326138 | etot = -18.2465560861304 -221000 ekin = 2.0597604328414 | erot = 2.46172578709591 | epot = -22.2693428350923 | etot = -17.747856615155 -222000 ekin = 1.56778478035701 | erot = 2.12765432596981 | epot = -22.1639011265164 | etot = -18.4684620201895 -223000 ekin = 1.84761048251748 | erot = 1.88006246465219 | epot = -22.0932628941084 | etot = -18.3655899469387 -224000 ekin = 2.59436846043989 | erot = 2.94714248251078 | epot = -22.1101977210218 | etot = -16.5686867780712 -225000 ekin = 3.30446830369106 | erot = 2.86069163428056 | epot = -22.113033571733 | etot = -15.9478736337614 -226000 ekin = 3.03148439961004 | erot = 2.08577158411852 | epot = -22.1515480756286 | etot = -17.0342920919 -227000 ekin = 2.52473737037051 | erot = 3.15152330374791 | epot = -22.2272979755787 | etot = -16.5510373014602 -228000 ekin = 2.32773029487821 | erot = 2.67887550863526 | epot = -22.328984615758 | etot = -17.3223788122445 -229000 ekin = 2.908632187774 | erot = 2.89972099244785 | epot = -22.4590990625922 | etot = -16.6507458823704 -230000 ekin = 2.30901008738396 | erot = 3.48892218468537 | epot = -22.5811133380348 | etot = -16.7831810659655 -231000 ekin = 2.09445974553367 | erot = 3.10137653837904 | epot = -22.6273628788263 | etot = -17.4315265949136 -232000 ekin = 2.11347252785341 | erot = 1.99214840222577 | epot = -22.6148559367411 | etot = -18.509235006662 -233000 ekin = 2.31469131808301 | erot = 2.82702779723523 | epot = -22.5734680782721 | etot = -17.4317489629539 -234000 ekin = 2.08691986790862 | erot = 2.09006771152618 | epot = -22.5768924885421 | etot = -18.3999049091073 -235000 ekin = 2.43602788311011 | erot = 2.79756094595937 | epot = -22.5841308018507 | etot = -17.3505419727812 -236000 ekin = 2.93232983655882 | erot = 3.05945149934942 | epot = -22.501128172066 | etot = -16.5093468361577 -237000 ekin = 3.2236915032749 | erot = 3.26810349425041 | epot = -22.3869936414795 | etot = -15.8951986439542 -238000 ekin = 2.46749959233529 | erot = 2.31630563795609 | epot = -22.3210409459326 | etot = -17.5372357156412 -239000 ekin = 2.10887317283391 | erot = 2.47562990634414 | epot = -22.3008221039948 | etot = -17.7163190248167 -240000 ekin = 1.76092230208337 | erot = 2.62077674301801 | epot = -22.2503883436817 | etot = -17.8686892985803 -241000 ekin = 1.93966929781469 | erot = 1.41063904300122 | epot = -22.2367099354245 | etot = -18.8864015946086 -242000 ekin = 3.03220831764684 | erot = 2.02809667614525 | epot = -22.2529237351146 | etot = -17.1926187413225 -243000 ekin = 2.84396619393303 | erot = 1.7910064306681 | epot = -22.276868026587 | etot = -17.6418954019859 -244000 ekin = 1.94630661585722 | erot = 2.3722540427007 | epot = -22.2272698315536 | etot = -17.9087091729957 -245000 ekin = 2.21268964174709 | erot = 2.75899365563148 | epot = -22.1926413343767 | etot = -17.2209580369981 -246000 ekin = 2.07547606015104 | erot = 2.22089229769684 | epot = -22.1194718227511 | etot = -17.8231034649033 -247000 ekin = 1.58341517009487 | erot = 3.06778333448389 | epot = -22.0033087190278 | etot = -17.352110214449 -248000 ekin = 2.13651389755269 | erot = 3.53502738921422 | epot = -21.8495423719647 | etot = -16.1780010851978 -249000 ekin = 2.17149547481658 | erot = 3.29316066315612 | epot = -21.8139336708841 | etot = -16.3492775329114 -250000 ekin = 2.39365756609178 | erot = 2.39580124119371 | epot = -21.7677335444041 | etot = -16.9782747371186 -251000 ekin = 1.2828204065042 | erot = 2.24293125468608 | epot = -21.720961335271 | etot = -18.1952096740807 -252000 ekin = 1.76792385357404 | erot = 2.13774913157991 | epot = -21.7157436468391 | etot = -17.8100706616851 -253000 ekin = 2.15844787240193 | erot = 2.599108391401 | epot = -21.6939194867274 | etot = -16.9363632229245 -254000 ekin = 2.46988601582316 | erot = 1.99393049965303 | epot = -21.6738244724958 | etot = -17.2100079570196 -255000 ekin = 2.31014544453096 | erot = 2.03140480982291 | epot = -21.6888108217888 | etot = -17.3472605674349 -256000 ekin = 2.90570988017011 | erot = 2.61779108741194 | epot = -21.6304219101589 | etot = -16.1069209425768 -257000 ekin = 2.87227426842453 | erot = 2.08598550349755 | epot = -21.5998306482427 | etot = -16.6415708763207 -258000 ekin = 2.06365418401471 | erot = 2.33103720962374 | epot = -21.5019981919812 | etot = -17.1073067983428 -259000 ekin = 2.23106413601667 | erot = 2.88992031738565 | epot = -21.4929751490586 | etot = -16.3719906956563 -260000 ekin = 2.49064109684832 | erot = 2.38083177290805 | epot = -21.4659963710748 | etot = -16.5945235013184 -261000 ekin = 2.09140199827798 | erot = 2.40209752473159 | epot = -21.4076397934529 | etot = -16.9141402704434 -262000 ekin = 2.36091906713391 | erot = 2.66652490187928 | epot = -21.3599371255921 | etot = -16.3324931565789 -263000 ekin = 2.21121697961579 | erot = 2.73059503173093 | epot = -21.4187723839514 | etot = -16.4769603726047 -264000 ekin = 2.28961718487932 | erot = 2.75455515229635 | epot = -21.370776058554 | etot = -16.3266037213784 -265000 ekin = 1.71596203334806 | erot = 1.76104932073226 | epot = -21.2034176623528 | etot = -17.7264063082725 -266000 ekin = 2.51424635704546 | erot = 2.09488481391075 | epot = -21.081865694267 | etot = -16.4727345233107 -267000 ekin = 2.813938959256 | erot = 2.1423270532825 | epot = -21.1259701200623 | etot = -16.1697041075238 -268000 ekin = 3.10191854871685 | erot = 2.80451383793942 | epot = -21.0933882633303 | etot = -15.186955876674 -269000 ekin = 3.52550118014124 | erot = 2.35973600910592 | epot = -21.0585255577117 | etot = -15.1732883684646 -270000 ekin = 3.50731584216641 | erot = 1.86855463358786 | epot = -21.0937109465411 | etot = -15.7178404707868 -271000 ekin = 3.56753314536821 | erot = 2.08234599715571 | epot = -21.171785030296 | etot = -15.5219058877721 -272000 ekin = 2.43382567191708 | erot = 3.09591378837426 | epot = -21.2584464912719 | etot = -15.7287070309805 -273000 ekin = 2.38177594135517 | erot = 3.14028416008422 | epot = -21.3418702267284 | etot = -15.819810125289 -274000 ekin = 2.46408091312733 | erot = 2.01407385193325 | epot = -21.3513679347442 | etot = -16.8732131696836 -275000 ekin = 2.45653813926169 | erot = 3.0678001028164 | epot = -21.3769507768007 | etot = -15.8526125347226 -276000 ekin = 2.79508720985829 | erot = 2.87011619931109 | epot = -21.3368600634474 | etot = -15.671656654278 -277000 ekin = 2.21394865880381 | erot = 2.19504097967887 | epot = -21.2606836087454 | etot = -16.8516939702627 -278000 ekin = 2.75723780567064 | erot = 3.25107227641374 | epot = -21.1755556732392 | etot = -15.1672455911548 -279000 ekin = 2.50738352588257 | erot = 1.80312795092015 | epot = -21.119949297869 | etot = -16.8094378210663 -280000 ekin = 2.35419479075042 | erot = 1.75661043515291 | epot = -21.0612865360218 | etot = -16.9504813101184 -281000 ekin = 2.54091624756361 | erot = 2.29354970120308 | epot = -21.0950091005498 | etot = -16.2605431517831 -282000 ekin = 2.99712896075656 | erot = 2.42094408338315 | epot = -21.2220089565005 | etot = -15.8039359123608 -283000 ekin = 2.56696810638689 | erot = 2.10068113035835 | epot = -21.4031615768381 | etot = -16.7355123400928 -284000 ekin = 2.50149529685552 | erot = 3.1289485057255 | epot = -21.5256946024496 | etot = -15.8952507998685 -285000 ekin = 2.42104861452631 | erot = 1.77738842506871 | epot = -21.6343236201922 | etot = -17.4358865805972 -286000 ekin = 1.95703367775988 | erot = 2.02947038358404 | epot = -21.6777606373855 | etot = -17.6912565760416 -287000 ekin = 2.563069553437 | erot = 2.57822888294094 | epot = -21.709678841217 | etot = -16.5683804048391 -288000 ekin = 2.18408141161779 | erot = 1.69724000161795 | epot = -21.6059228036046 | etot = -17.7246013903688 -289000 ekin = 2.32975723406078 | erot = 1.67288237726622 | epot = -21.4690249265466 | etot = -17.4663853152196 -290000 ekin = 2.22773933829103 | erot = 2.00568808096403 | epot = -21.3936416309444 | etot = -17.1602142116893 -291000 ekin = 1.46140048209222 | erot = 2.68187349132486 | epot = -21.3203096611521 | etot = -17.1770356877351 -292000 ekin = 2.07752653885401 | erot = 2.42042811850752 | epot = -21.222571015269 | etot = -16.7246163579075 -293000 ekin = 2.14598735312316 | erot = 1.87232699516306 | epot = -21.150311210566 | etot = -17.1319968622798 -294000 ekin = 2.15249843510191 | erot = 2.17548638187735 | epot = -21.1209057143322 | etot = -16.7929208973529 -295000 ekin = 2.1341724680407 | erot = 2.31578295657372 | epot = -21.023273761855 | etot = -16.5733183372406 -296000 ekin = 1.52381700282725 | erot = 2.92433462308731 | epot = -21.0839283123443 | etot = -16.6357766864297 -297000 ekin = 2.45165869902148 | erot = 2.17953392904489 | epot = -21.0491333291916 | etot = -16.4179407011253 -298000 ekin = 1.77920935759372 | erot = 2.01251348063453 | epot = -21.0971977522748 | etot = -17.3054749140466 -299000 ekin = 1.87538650376615 | erot = 1.65135039658662 | epot = -21.119277949862 | etot = -17.5925410495092 -300000 ekin = 2.31670567519938 | erot = 1.51090264865399 | epot = -21.1789130994511 | etot = -17.3513047755977 -301000 ekin = 2.00567209290794 | erot = 2.01270349508403 | epot = -21.2857234594099 | etot = -17.2673478714179 -302000 ekin = 1.78598592595272 | erot = 2.23540554928791 | epot = -21.3905601140029 | etot = -17.3691686387623 -303000 ekin = 2.73278841880506 | erot = 1.64856089415774 | epot = -21.3608973804115 | etot = -16.9795480674487 -304000 ekin = 2.5809493598196 | erot = 2.00558555026354 | epot = -21.400198286629 | etot = -16.8136633765459 -305000 ekin = 2.43647384348742 | erot = 2.28275438290433 | epot = -21.3863075230184 | etot = -16.6670792966266 -306000 ekin = 2.14332823539982 | erot = 2.43384616344108 | epot = -21.3233075109442 | etot = -16.7461331121033 -307000 ekin = 3.21424191196813 | erot = 3.27591538479567 | epot = -21.289790084126 | etot = -14.7996327873622 -308000 ekin = 3.45838026839177 | erot = 2.68116130354005 | epot = -21.3419403426811 | etot = -15.2023987707493 -309000 ekin = 2.38041738433959 | erot = 2.92081370932153 | epot = -21.4463399141034 | etot = -16.1451088204423 -310000 ekin = 2.50977269558789 | erot = 2.34824464102404 | epot = -21.4648074532888 | etot = -16.6067901166769 -311000 ekin = 2.5748862881926 | erot = 2.29375467353798 | epot = -21.5151382155269 | etot = -16.6464972537963 -312000 ekin = 2.09623150906876 | erot = 2.93795890592973 | epot = -21.6260240426366 | etot = -16.5918336276381 -313000 ekin = 1.81844997291941 | erot = 2.28463898505894 | epot = -21.6999003790643 | etot = -17.596811421086 -314000 ekin = 2.32283241742321 | erot = 2.19580475273395 | epot = -21.6870491287185 | etot = -17.1684119585614 -315000 ekin = 1.84546653836013 | erot = 2.13886071139629 | epot = -21.7312132691438 | etot = -17.7468860193874 -316000 ekin = 2.1657114199577 | erot = 3.03124199276296 | epot = -21.7430929234306 | etot = -16.54613951071 -317000 ekin = 2.42793755919909 | erot = 3.57187833839243 | epot = -21.8303487369249 | etot = -15.8305328393334 -318000 ekin = 2.31418145055206 | erot = 3.02858542885927 | epot = -21.9347898317926 | etot = -16.5920229523813 -319000 ekin = 2.35032973997068 | erot = 3.16078759112676 | epot = -22.0387665246751 | etot = -16.5276491935776 -320000 ekin = 1.78202525445684 | erot = 2.83297321443626 | epot = -22.1187616541783 | etot = -17.5037631852852 -321000 ekin = 2.87441941784728 | erot = 2.26223197636946 | epot = -22.1065455913123 | etot = -16.9698941970956 -322000 ekin = 2.79013397204362 | erot = 2.68769432639937 | epot = -22.1121405540936 | etot = -16.6343122556507 -323000 ekin = 2.070121980457 | erot = 2.31830584817614 | epot = -22.1539458855415 | etot = -17.7655180569083 -324000 ekin = 2.58383941134684 | erot = 2.58296807603305 | epot = -22.1539753505052 | etot = -16.9871678631253 -325000 ekin = 3.43451304817783 | erot = 2.45405386180799 | epot = -21.938960387404 | etot = -16.0503934774182 -326000 ekin = 3.49680929786584 | erot = 2.85196633398114 | epot = -21.8204400999953 | etot = -15.4716644681484 -327000 ekin = 2.68799300805475 | erot = 2.21805195956658 | epot = -21.7892073548558 | etot = -16.8831623872344 -328000 ekin = 1.81477491971657 | erot = 2.35891534842887 | epot = -21.7275637950057 | etot = -17.5538735268603 -329000 ekin = 2.19319322627005 | erot = 2.40717958919079 | epot = -21.6826095784948 | etot = -17.0822367630339 -330000 ekin = 1.87131927244382 | erot = 2.03694340108432 | epot = -21.5934239674848 | etot = -17.6851612939566 -331000 ekin = 2.37197683084607 | erot = 1.80087022346347 | epot = -21.5641185835514 | etot = -17.3912715292419 -332000 ekin = 1.69601394569049 | erot = 2.54947032294377 | epot = -21.5986464339748 | etot = -17.3531621653406 -333000 ekin = 1.59867443991714 | erot = 2.14911483871163 | epot = -21.7162173059518 | etot = -17.968428027323 -334000 ekin = 2.25811733625553 | erot = 2.62323988136569 | epot = -21.7749416190679 | etot = -16.8935844014467 -335000 ekin = 2.93433632601273 | erot = 3.10350297573265 | epot = -21.7966831809595 | etot = -15.7588438792141 -336000 ekin = 2.76337640462581 | erot = 2.54930710489016 | epot = -21.7180312833467 | etot = -16.4053477738307 -337000 ekin = 3.19235531401951 | erot = 3.871461468741 | epot = -21.8022396262892 | etot = -14.7384228435286 -338000 ekin = 2.33305125173567 | erot = 2.13094194678888 | epot = -21.8068682042896 | etot = -17.3428750057651 -339000 ekin = 1.71673308889604 | erot = 2.30964121170971 | epot = -21.7941224580796 | etot = -17.7677481574738 -340000 ekin = 1.59424151294027 | erot = 3.16324993863714 | epot = -21.7679173396748 | etot = -17.0104258880974 -341000 ekin = 1.69465464335694 | erot = 3.18694861883741 | epot = -21.7067352043109 | etot = -16.8251319421166 -342000 ekin = 1.81243763026219 | erot = 2.60448215582795 | epot = -21.5993126794634 | etot = -17.1823928933732 -343000 ekin = 3.08243814047349 | erot = 2.92174663333229 | epot = -21.5855979229594 | etot = -15.5814131491537 -344000 ekin = 2.94964594107349 | erot = 3.10231272046814 | epot = -21.5506154266351 | etot = -15.4986567650935 -345000 ekin = 2.34525111670595 | erot = 2.88045261854214 | epot = -21.530734043011 | etot = -16.3050303077629 -346000 ekin = 2.03136740406842 | erot = 3.44352096435561 | epot = -21.4703041890966 | etot = -15.9954158206726 -347000 ekin = 2.34515762081498 | erot = 1.91414074840887 | epot = -21.3488386855954 | etot = -17.0895403163716 -348000 ekin = 2.76763212340836 | erot = 2.78035348102326 | epot = -21.3102796687364 | etot = -15.7622940643048 -349000 ekin = 2.29342234253801 | erot = 3.14526664575919 | epot = -21.3922932631024 | etot = -15.9536042748052 -350000 ekin = 2.17828641691343 | erot = 2.38211689163937 | epot = -21.3570978647003 | etot = -16.7966945561475 -351000 ekin = 2.2787342054874 | erot = 2.85568682453816 | epot = -21.3165609660186 | etot = -16.182139935993 -352000 ekin = 2.70894563927919 | erot = 2.77656375044279 | epot = -21.3565059314145 | etot = -15.8709965416925 -353000 ekin = 1.74748047732916 | erot = 2.14191122851258 | epot = -21.3195625770357 | etot = -17.430170871194 -354000 ekin = 2.30492780756569 | erot = 2.37159952583724 | epot = -21.3742968901642 | etot = -16.6977695567613 -355000 ekin = 2.32493886573113 | erot = 2.38411746089986 | epot = -21.339340741587 | etot = -16.630284414956 -356000 ekin = 2.97496495432681 | erot = 2.99166555175531 | epot = -21.2468948072712 | etot = -15.2802643011891 -357000 ekin = 1.79541671946026 | erot = 2.13971792108731 | epot = -21.2216819829681 | etot = -17.2865473424205 -358000 ekin = 2.06637919290965 | erot = 1.90765307155781 | epot = -21.2447441674953 | etot = -17.2707119030279 -359000 ekin = 2.02344077580052 | erot = 2.11726163321539 | epot = -21.2183688961264 | etot = -17.0776664871105 -360000 ekin = 2.64012587839158 | erot = 2.43776362828977 | epot = -21.1472477161847 | etot = -16.0693582095034 -361000 ekin = 2.41850555983883 | erot = 2.39054736245268 | epot = -21.2133787743639 | etot = -16.4043258520724 -362000 ekin = 2.2486199222758 | erot = 2.04489136793498 | epot = -21.2088914287919 | etot = -16.9153801385811 -363000 ekin = 3.21904252076973 | erot = 1.79717950163014 | epot = -21.2620537293498 | etot = -16.24583170695 -364000 ekin = 2.98456974484978 | erot = 2.18316673460244 | epot = -21.2883338312843 | etot = -16.120597351832 -365000 ekin = 2.49427392981408 | erot = 2.31205455481899 | epot = -21.4001153296815 | etot = -16.5937868450484 -366000 ekin = 2.61706523565787 | erot = 2.20229130507576 | epot = -21.4506718008963 | etot = -16.6313152601626 -367000 ekin = 2.24650816549397 | erot = 1.87906237362997 | epot = -21.5207044850599 | etot = -17.395133945936 -368000 ekin = 2.46672276241561 | erot = 2.37638546053105 | epot = -21.5628581383217 | etot = -16.719749915375 -369000 ekin = 2.0361463514985 | erot = 2.85426887707092 | epot = -21.6803034764487 | etot = -16.7898882478793 -370000 ekin = 2.13410724028003 | erot = 2.17304603842011 | epot = -21.7343761700059 | etot = -17.4272228913057 -371000 ekin = 2.21722409826113 | erot = 2.11058746733931 | epot = -21.6422617131999 | etot = -17.3144501475994 -372000 ekin = 1.88083333566672 | erot = 1.90617172826128 | epot = -21.6005499693119 | etot = -17.8135449053839 -373000 ekin = 1.98298204516521 | erot = 1.7826768212841 | epot = -21.5708808628646 | etot = -17.8052219964153 -374000 ekin = 2.88981201933267 | erot = 1.90326894499807 | epot = -21.4624711307906 | etot = -16.6693901664599 -375000 ekin = 2.31951869092548 | erot = 1.92779670517485 | epot = -21.3521768069862 | etot = -17.1048614108859 -376000 ekin = 2.60113015271721 | erot = 2.31181306588443 | epot = -21.34681055463 | etot = -16.4338673360284 -377000 ekin = 2.23867315344603 | erot = 1.65923992926405 | epot = -21.2611852709132 | etot = -17.3632721882031 -378000 ekin = 2.38125181613767 | erot = 2.54002618279123 | epot = -21.2390275318703 | etot = -16.3177495329414 -379000 ekin = 2.06952281308678 | erot = 2.11888196225294 | epot = -21.1940256065771 | etot = -17.0056208312374 -380000 ekin = 2.59961269461524 | erot = 2.37512007885032 | epot = -21.1885781090515 | etot = -16.213845335586 -381000 ekin = 2.42019573552876 | erot = 2.20667402504615 | epot = -21.1989968748535 | etot = -16.5721271142786 -382000 ekin = 2.04746564398744 | erot = 3.34439482672214 | epot = -21.2903574441546 | etot = -15.898496973445 -383000 ekin = 2.65699216362738 | erot = 1.56546061375907 | epot = -21.3572338418187 | etot = -17.1347810644323 -384000 ekin = 2.43156675693925 | erot = 2.00097327452754 | epot = -21.3434156392383 | etot = -16.9108756077715 -385000 ekin = 1.95152101616516 | erot = 3.28345377140316 | epot = -21.4173973675699 | etot = -16.1824225800016 -386000 ekin = 2.10919215730741 | erot = 2.90700736383438 | epot = -21.3963452767616 | etot = -16.3801457556198 -387000 ekin = 2.34448447096483 | erot = 2.50155013212482 | epot = -21.3487258248085 | etot = -16.5026912217188 -388000 ekin = 2.71771591111728 | erot = 2.76803950274557 | epot = -21.3515918112167 | etot = -15.8658363973538 -389000 ekin = 3.06825183100774 | erot = 3.06148533146043 | epot = -21.4826430036712 | etot = -15.352905841203 -390000 ekin = 2.56997560639923 | erot = 2.05646161654306 | epot = -21.5623801506969 | etot = -16.9359429277546 -391000 ekin = 2.1110114400687 | erot = 2.44612603817532 | epot = -21.6052888202632 | etot = -17.0481513420192 -392000 ekin = 2.58328475785099 | erot = 2.75249392862467 | epot = -21.7336094646939 | etot = -16.3978307782182 -393000 ekin = 2.03977041996533 | erot = 1.67448219405537 | epot = -21.8740604202475 | etot = -18.1598078062268 -394000 ekin = 2.1229408356241 | erot = 2.43410977254956 | epot = -21.9094739378951 | etot = -17.3524233297215 -395000 ekin = 2.48696003315341 | erot = 2.48225062557349 | epot = -21.8799685903484 | etot = -16.9107579316215 -396000 ekin = 3.18909661029635 | erot = 1.62675064803774 | epot = -21.852000027704 | etot = -17.0361527693699 -397000 ekin = 2.39161566907255 | erot = 2.17052346752456 | epot = -21.7939512244376 | etot = -17.2318120878405 -398000 ekin = 2.29946433742665 | erot = 2.18115834594541 | epot = -21.7285069861956 | etot = -17.2478843028235 -399000 ekin = 2.65449075133045 | erot = 2.80318185995815 | epot = -21.6503181327212 | etot = -16.1926455214326 -400000 ekin = 1.800915604111 | erot = 2.76596769548035 | epot = -21.6418619272709 | etot = -17.0749786276796 -401000 ekin = 2.35073130822393 | erot = 3.12299222057742 | epot = -21.6675586342212 | etot = -16.1938351054199 -402000 ekin = 3.95550191914708 | erot = 3.58855023837879 | epot = -21.5840051268209 | etot = -14.039952969295 -403000 ekin = 3.59615502379622 | erot = 3.44558176696766 | epot = -21.5781150073618 | etot = -14.5363782165979 -404000 ekin = 2.50360365952137 | erot = 3.01285184176069 | epot = -21.6258060641304 | etot = -16.1093505628483 -405000 ekin = 2.77241560720114 | erot = 3.10596549510785 | epot = -21.7046789178921 | etot = -15.8262978155831 -406000 ekin = 2.33934923007339 | erot = 2.04671975867732 | epot = -21.8191042863881 | etot = -17.4330352976373 -407000 ekin = 2.34277955096233 | erot = 1.89301717692528 | epot = -21.8450916691373 | etot = -17.6092949412497 -408000 ekin = 1.91561948833426 | erot = 2.1955160435361 | epot = -21.874404183535 | etot = -17.7632686516646 -409000 ekin = 1.98819074442449 | erot = 1.93870533007335 | epot = -21.9219030266971 | etot = -17.9950069521992 -410000 ekin = 1.59047218684375 | erot = 1.93259851333215 | epot = -21.9698907875581 | etot = -18.4468200873822 -411000 ekin = 1.88305362601542 | erot = 2.47249081001964 | epot = -22.0985208042932 | etot = -17.7429763682581 -412000 ekin = 2.51301623282815 | erot = 2.67550740966368 | epot = -22.2078537029906 | etot = -17.0193300604988 -413000 ekin = 2.81407439938451 | erot = 3.21402559358061 | epot = -22.1310120840188 | etot = -16.1029120910537 -414000 ekin = 2.79247479268938 | erot = 2.73425265524032 | epot = -22.0977113063587 | etot = -16.570983858429 -415000 ekin = 2.47916660937973 | erot = 2.25382914436718 | epot = -22.1646477745645 | etot = -17.4316520208176 -416000 ekin = 3.33232223339091 | erot = 1.56386062957 | epot = -22.1461937000839 | etot = -17.250010837123 -417000 ekin = 3.95877285814837 | erot = 2.43917045295872 | epot = -22.0789469190763 | etot = -15.6810036079692 -418000 ekin = 2.77978041892218 | erot = 2.67961998913592 | epot = -21.9429456651674 | etot = -16.4835452571093 -419000 ekin = 2.38024484823695 | erot = 2.99229133054454 | epot = -21.8677152868897 | etot = -16.4951791081082 -420000 ekin = 1.8087119495316 | erot = 1.84151089264677 | epot = -21.8596865313186 | etot = -18.2094636891402 -421000 ekin = 1.25971024821534 | erot = 1.84154088985395 | epot = -21.8144945739243 | etot = -18.713243435855 -422000 ekin = 1.38801644153196 | erot = 2.76287955544761 | epot = -21.9448046693443 | etot = -17.7939086723647 -423000 ekin = 1.61378102360037 | erot = 3.08643589903682 | epot = -21.9876910184368 | etot = -17.2874740957996 -424000 ekin = 2.38187559636675 | erot = 2.03497345340564 | epot = -22.0529622043823 | etot = -17.6361131546099 -425000 ekin = 2.30172600419956 | erot = 2.56124787306542 | epot = -22.0909144547264 | etot = -17.2279405774614 -426000 ekin = 2.08135734353847 | erot = 3.11029155110105 | epot = -22.0318884881516 | etot = -16.840239593512 -427000 ekin = 2.14905284759742 | erot = 2.44063059706749 | epot = -21.9221859408585 | etot = -17.3325024961936 -428000 ekin = 1.77884336055357 | erot = 1.65616500997461 | epot = -21.9003025672496 | etot = -18.4652941967215 -429000 ekin = 1.6463484323549 | erot = 2.54977814749913 | epot = -21.8505053104909 | etot = -17.6543787306369 -430000 ekin = 2.66566369380164 | erot = 2.85826638798746 | epot = -21.8749831872768 | etot = -16.3510531054877 -431000 ekin = 2.77262842672212 | erot = 1.57008239418361 | epot = -21.8682859290024 | etot = -17.5255751080967 -432000 ekin = 2.55459213758159 | erot = 1.62943387255927 | epot = -21.8357562133881 | etot = -17.6517302032473 -433000 ekin = 1.99645419170626 | erot = 2.46386731011039 | epot = -21.9426115259013 | etot = -17.4822900240846 -434000 ekin = 3.03855037499723 | erot = 2.70114732868001 | epot = -22.0521183162707 | etot = -16.3124206125934 -435000 ekin = 3.56249359412514 | erot = 1.3916907800745 | epot = -22.1907087359577 | etot = -17.236524361758 -436000 ekin = 2.9919519436941 | erot = 2.00780906096745 | epot = -22.1944569501236 | etot = -17.194695945462 -437000 ekin = 3.22983002449305 | erot = 1.78457838368284 | epot = -22.2079862630257 | etot = -17.1935778548498 -438000 ekin = 2.89357954274282 | erot = 1.84712438388029 | epot = -22.1640149633625 | etot = -17.4233110367394 -439000 ekin = 2.43548109922482 | erot = 2.6972566722099 | epot = -22.15552566419 | etot = -17.0227878927553 -440000 ekin = 2.2623759777343 | erot = 3.00532913929839 | epot = -22.1911581748161 | etot = -16.9234530577835 -441000 ekin = 2.91169601545459 | erot = 2.87109172357539 | epot = -22.3349024428918 | etot = -16.5521147038619 -442000 ekin = 2.09099397022228 | erot = 1.73520313922451 | epot = -22.4051258365299 | etot = -18.5789287270832 -443000 ekin = 1.89190436364779 | erot = 2.0033880577304 | epot = -22.4571595679749 | etot = -18.5618671465967 -444000 ekin = 2.07260612589383 | erot = 2.15261859961606 | epot = -22.4762155543905 | etot = -18.2509908288806 -445000 ekin = 2.10794043544075 | erot = 2.27849500108989 | epot = -22.528911365565 | etot = -18.1424759290343 -446000 ekin = 2.43249129570082 | erot = 2.857987858417 | epot = -22.5578450371516 | etot = -17.2673658830337 -447000 ekin = 2.18427449291498 | erot = 2.9948705870288 | epot = -22.6332096652429 | etot = -17.4540645852991 -448000 ekin = 2.33125251154889 | erot = 2.9537271150568 | epot = -22.6544934614541 | etot = -17.3695138348484 -449000 ekin = 2.34830834177128 | erot = 2.93433423081579 | epot = -22.6524261630772 | etot = -17.3697835904901 -450000 ekin = 1.83059864091627 | erot = 1.69583085832557 | epot = -22.5959718193006 | etot = -19.0695423200588 -451000 ekin = 1.97008420530445 | erot = 1.93005789483907 | epot = -22.6042016377466 | etot = -18.7040595376031 -452000 ekin = 1.36031716300771 | erot = 1.88416646481666 | epot = -22.5654500281941 | etot = -19.3209664003697 -453000 ekin = 2.08394677326601 | erot = 2.55637003071466 | epot = -22.3996731437446 | etot = -17.759356339764 -454000 ekin = 1.46122132979163 | erot = 2.19325045587991 | epot = -22.2559783518549 | etot = -18.6015065661833 -455000 ekin = 1.66159562683808 | erot = 2.72214658377913 | epot = -22.1100881227337 | etot = -17.7263459121165 -456000 ekin = 2.35139002285136 | erot = 1.99736695780608 | epot = -22.0265180206658 | etot = -17.6777610400084 -457000 ekin = 2.02337666353787 | erot = 2.36288174917836 | epot = -21.987041986587 | etot = -17.6007835738707 -458000 ekin = 1.74388716034854 | erot = 2.25704341258626 | epot = -22.0124765184275 | etot = -18.0115459454927 -459000 ekin = 2.51302694941203 | erot = 2.31610812350976 | epot = -22.0905335599533 | etot = -17.2613984870315 -460000 ekin = 2.20235980851235 | erot = 2.00073208070751 | epot = -22.0624281815267 | etot = -17.8593362923069 -461000 ekin = 2.27697813860511 | erot = 2.92153186175594 | epot = -22.0043780203814 | etot = -16.8058680200203 -462000 ekin = 2.61751250591993 | erot = 1.79446367088041 | epot = -22.034566251344 | etot = -17.6225900745436 -463000 ekin = 2.59076396942114 | erot = 3.29959067151567 | epot = -21.9680597931617 | etot = -16.0777051522249 -464000 ekin = 2.18897688760923 | erot = 2.37342380725931 | epot = -21.9014176363545 | etot = -17.3390169414859 -465000 ekin = 2.55336811292171 | erot = 3.60208553232435 | epot = -21.8218243406516 | etot = -15.6663706954055 -466000 ekin = 1.98087073364118 | erot = 2.88377492118972 | epot = -21.8240279062597 | etot = -16.9593822514288 -467000 ekin = 1.63963444033068 | erot = 2.61720118783827 | epot = -21.9072568806945 | etot = -17.6504212525255 -468000 ekin = 1.11353612829142 | erot = 3.36362638075103 | epot = -21.9675488944805 | etot = -17.490386385438 -469000 ekin = 1.72228182007046 | erot = 2.77659856111655 | epot = -21.9967286251287 | etot = -17.4978482439417 -470000 ekin = 1.86957223270987 | erot = 2.88200736733018 | epot = -22.0532435258198 | etot = -17.3016639257798 -471000 ekin = 2.73889257490363 | erot = 2.33805868565126 | epot = -22.1018048913227 | etot = -17.0248536307678 -472000 ekin = 2.69336835751318 | erot = 2.14497398823592 | epot = -22.1783319655624 | etot = -17.3399896198133 -473000 ekin = 2.2834012228809 | erot = 2.08779065134066 | epot = -22.2062566289287 | etot = -17.8350647547071 -474000 ekin = 2.2375339334342 | erot = 2.18021358366906 | epot = -22.2186470965394 | etot = -17.8008995794361 -475000 ekin = 2.52144972759887 | erot = 2.10742888877791 | epot = -22.2200376200674 | etot = -17.5911590036907 -476000 ekin = 2.21750839437398 | erot = 1.76993465858265 | epot = -22.122840778158 | etot = -18.1353977252014 -477000 ekin = 2.49639604606981 | erot = 2.38997154938616 | epot = -22.0914213950017 | etot = -17.2050537995458 -478000 ekin = 1.92476411077776 | erot = 2.05068061613982 | epot = -22.1165013146126 | etot = -18.141056587695 -479000 ekin = 2.27814065534965 | erot = 3.09902158675162 | epot = -22.1039609371193 | etot = -16.726798695018 -480000 ekin = 1.67684718675217 | erot = 2.75298455656159 | epot = -22.107572084908 | etot = -17.6777403415942 -481000 ekin = 1.82004035403442 | erot = 2.94243611851483 | epot = -22.0570042571709 | etot = -17.2945277846216 -482000 ekin = 2.15620792762657 | erot = 2.07225318674483 | epot = -22.0195504604851 | etot = -17.7910893461137 -483000 ekin = 1.49597937205779 | erot = 1.99748154603234 | epot = -21.9846691787552 | etot = -18.4912082606651 -484000 ekin = 1.84801031899853 | erot = 2.33839306142132 | epot = -22.057622803598 | etot = -17.8712194231781 -485000 ekin = 1.63994449952444 | erot = 2.49474020960605 | epot = -22.0873319631203 | etot = -17.9526472539898 -486000 ekin = 1.86878710017944 | erot = 2.15121977781066 | epot = -22.0738722433192 | etot = -18.0538653653291 -487000 ekin = 2.36575535267026 | erot = 3.1012540127672 | epot = -22.144928398152 | etot = -16.6779190327145 -488000 ekin = 2.28442246943195 | erot = 3.25683393002514 | epot = -22.0988506325681 | etot = -16.557594233111 -489000 ekin = 2.42271484675 | erot = 2.545421459121 | epot = -22.0089541135478 | etot = -17.0408178076768 -490000 ekin = 2.15700463004959 | erot = 3.54046810332718 | epot = -21.9046622319151 | etot = -16.2071894985384 -491000 ekin = 2.21877065503535 | erot = 2.48745097433186 | epot = -21.7908019627883 | etot = -17.0845803334211 -492000 ekin = 2.42517437413503 | erot = 2.76311171529556 | epot = -21.7601749752715 | etot = -16.5718888858409 -493000 ekin = 1.78704503482098 | erot = 2.27560531894263 | epot = -21.8193757259442 | etot = -17.7567253721806 -494000 ekin = 2.08676036701357 | erot = 2.99995787427429 | epot = -21.8611051542237 | etot = -16.7743869129359 -495000 ekin = 2.13526814465422 | erot = 2.49327519100041 | epot = -21.9512664264056 | etot = -17.322723090751 -496000 ekin = 2.04396376951351 | erot = 2.616205394925 | epot = -21.9926597066747 | etot = -17.3324905422362 -497000 ekin = 2.51384009922531 | erot = 1.7082513952147 | epot = -21.9316573881385 | etot = -17.7095658936985 -498000 ekin = 2.15599563393455 | erot = 1.79545847566161 | epot = -21.8684844569259 | etot = -17.9170303473297 -499000 ekin = 3.01748439271979 | erot = 1.75754764004203 | epot = -21.8933218662966 | etot = -17.1182898335348 -500000 ekin = 2.75260982901106 | erot = 2.51842805388797 | epot = -21.8943946135574 | etot = -16.6233567306584 -501000 ekin = 2.67931288903133 | erot = 3.01160406637169 | epot = -21.7750232065095 | etot = -16.0841062511065 -502000 ekin = 1.89360306182664 | erot = 3.89791941021244 | epot = -21.6573468922303 | etot = -15.8658244201912 -503000 ekin = 1.79321931974652 | erot = 2.94204976962203 | epot = -21.4684952360274 | etot = -16.7332261466588 -504000 ekin = 1.67757593959819 | erot = 3.03667519772549 | epot = -21.3740498051044 | etot = -16.6597986677807 -505000 ekin = 2.71879314198246 | erot = 2.13553052885652 | epot = -21.3748517524097 | etot = -16.5205280815708 -506000 ekin = 2.26416011641767 | erot = 2.03983903573872 | epot = -21.3744734731022 | etot = -17.0704743209458 -507000 ekin = 3.1361217829786 | erot = 2.43598082432094 | epot = -21.4637546760327 | etot = -15.8916520687332 -508000 ekin = 2.50986106907072 | erot = 2.54739392181408 | epot = -21.6231060681634 | etot = -16.5658510772786 -509000 ekin = 2.11468804004737 | erot = 2.82565642150502 | epot = -21.7737120459513 | etot = -16.833367584399 -510000 ekin = 2.15001055304937 | erot = 1.42727017491936 | epot = -21.8417870574446 | etot = -18.2645063294759 -511000 ekin = 2.52545394756595 | erot = 2.75161712587396 | epot = -21.9086876613652 | etot = -16.6316165879253 -512000 ekin = 2.30866784309731 | erot = 2.74554976662382 | epot = -21.9096028664776 | etot = -16.8553852567565 -513000 ekin = 2.48902345599679 | erot = 2.14823762928073 | epot = -21.8729373600799 | etot = -17.2356762748023 -514000 ekin = 2.80071109914889 | erot = 2.54489890263222 | epot = -22.0260959105663 | etot = -16.6804859087852 -515000 ekin = 2.54951114466541 | erot = 1.81830545608794 | epot = -22.1182236024142 | etot = -17.7504070016608 -516000 ekin = 2.82429114749714 | erot = 2.22223190254032 | epot = -22.2027443448739 | etot = -17.1562212948364 -517000 ekin = 2.0440652856654 | erot = 2.05268379810237 | epot = -22.2270328001489 | etot = -18.1302837163812 -518000 ekin = 2.19098614618396 | erot = 2.75233490105158 | epot = -22.2209877154937 | etot = -17.2776666682582 -519000 ekin = 2.24036502705843 | erot = 2.22532553600965 | epot = -22.3180679614818 | etot = -17.8523773984137 -520000 ekin = 1.89058003919379 | erot = 2.20041260684314 | epot = -22.4024099853452 | etot = -18.3114173393083 -521000 ekin = 2.59235690452871 | erot = 1.87867658572833 | epot = -22.562076955749 | etot = -18.091043465492 -522000 ekin = 3.47612340255834 | erot = 1.77091315262669 | epot = -22.6560013672146 | etot = -17.4089648120296 -523000 ekin = 2.86973311568959 | erot = 2.45931135481362 | epot = -22.7015468187878 | etot = -17.3725023482846 -524000 ekin = 2.43256318748705 | erot = 2.35726786724123 | epot = -22.6382055947879 | etot = -17.8483745400596 -525000 ekin = 1.5862220801759 | erot = 2.67712917770356 | epot = -22.6016118927227 | etot = -18.3382606348432 -526000 ekin = 1.68941966580457 | erot = 1.56387338489763 | epot = -22.5489288531346 | etot = -19.2956358024324 -527000 ekin = 2.25322718958956 | erot = 1.91908592764601 | epot = -22.4417549635527 | etot = -18.2694418463172 -528000 ekin = 2.66412422381676 | erot = 2.81704928468167 | epot = -22.424921723381 | etot = -16.9437482148826 -529000 ekin = 2.68379060052796 | erot = 3.01205280488719 | epot = -22.4295574265689 | etot = -16.7337140211538 -530000 ekin = 2.58073227215728 | erot = 2.12870295195895 | epot = -22.2883086480465 | etot = -17.5788734239303 -531000 ekin = 2.96770457160388 | erot = 2.3539174245284 | epot = -22.185671173874 | etot = -16.8640491777417 -532000 ekin = 2.56038964370912 | erot = 2.30878740571671 | epot = -22.1997799918586 | etot = -17.3306029424328 -533000 ekin = 2.47143825522097 | erot = 2.96338918263316 | epot = -22.2065233272062 | etot = -16.771695889352 -534000 ekin = 2.10112886915673 | erot = 2.0617073534125 | epot = -22.2366529232831 | etot = -18.0738167007138 -535000 ekin = 3.76894732289842 | erot = 2.64646203076615 | epot = -22.2276744548844 | etot = -15.8122651012198 -536000 ekin = 2.7696162230836 | erot = 1.9580523477121 | epot = -22.165452917338 | etot = -17.4377843465423 -537000 ekin = 2.84154244437418 | erot = 2.62704512023092 | epot = -22.0849688339384 | etot = -16.6163812693333 -538000 ekin = 2.6844256357838 | erot = 2.11441739965432 | epot = -22.0125688846838 | etot = -17.2137258492457 -539000 ekin = 2.71421145807768 | erot = 2.40915133591279 | epot = -22.1313332530724 | etot = -17.0079704590819 -540000 ekin = 2.43518407250594 | erot = 2.49363815768249 | epot = -22.2749632551309 | etot = -17.3461410249425 -541000 ekin = 3.40444579850307 | erot = 2.79359613706623 | epot = -22.3466180642399 | etot = -16.1485761286706 -542000 ekin = 2.43275262454038 | erot = 2.89267129498909 | epot = -22.3556133688797 | etot = -17.0301894493503 -543000 ekin = 2.33375802900843 | erot = 2.8782226670354 | epot = -22.3545030310921 | etot = -17.1425223350483 -544000 ekin = 2.20372430185483 | erot = 1.45976141003991 | epot = -22.3227611685587 | etot = -18.659275456664 -545000 ekin = 2.44172510086273 | erot = 2.14426798374486 | epot = -22.3064237448697 | etot = -17.7204306602621 -546000 ekin = 1.97339115566055 | erot = 2.22847557914697 | epot = -22.2636677476265 | etot = -18.061801012819 -547000 ekin = 2.54002001617726 | erot = 1.88945501268907 | epot = -22.2158143598029 | etot = -17.7863393309366 -548000 ekin = 1.68526456618957 | erot = 1.65049155866195 | epot = -22.1214578510427 | etot = -18.7857017261912 -549000 ekin = 1.87014690614357 | erot = 2.68376307045223 | epot = -22.3040985050479 | etot = -17.7501885284521 -550000 ekin = 1.8122987774087 | erot = 1.59166644509218 | epot = -22.4560870327804 | etot = -19.0521218102795 -551000 ekin = 2.18773128797503 | erot = 2.27087388044657 | epot = -22.5158361799814 | etot = -18.0572310115598 -552000 ekin = 2.05249497087455 | erot = 2.50761265901317 | epot = -22.5719393540104 | etot = -18.0118317241227 -553000 ekin = 2.95454924363312 | erot = 2.14558063826842 | epot = -22.6616695566089 | etot = -17.5615396747074 -554000 ekin = 2.82907288726942 | erot = 1.93583607418193 | epot = -22.8114472173087 | etot = -18.0465382558574 -555000 ekin = 2.39144194814064 | erot = 2.26903467149231 | epot = -22.8607776699893 | etot = -18.2003010503564 -556000 ekin = 2.29377130416531 | erot = 2.58082229477441 | epot = -22.912355957237 | etot = -18.0377623582973 -557000 ekin = 2.83942594504113 | erot = 1.46630323732686 | epot = -22.995524783667 | etot = -18.689795601299 -558000 ekin = 2.74466783679159 | erot = 2.01704787654692 | epot = -23.0269943374554 | etot = -18.2652786241169 -559000 ekin = 3.32013685758138 | erot = 2.33070588278053 | epot = -23.0724440783112 | etot = -17.4216013379493 -560000 ekin = 3.06575014862304 | erot = 2.32407723614369 | epot = -23.0584521203812 | etot = -17.6686247356144 -561000 ekin = 2.86678914129225 | erot = 2.08494050984237 | epot = -22.9757329649368 | etot = -18.0240033138022 -562000 ekin = 3.27279507804288 | erot = 2.51484206553919 | epot = -22.876340054703 | etot = -17.0887029111209 -563000 ekin = 2.66038070150058 | erot = 1.6411653076616 | epot = -22.8496252506976 | etot = -18.5480792415354 -564000 ekin = 2.80463843262515 | erot = 2.52666063138349 | epot = -22.8040898690868 | etot = -17.4727908050782 -565000 ekin = 2.64623234011006 | erot = 2.04560086917497 | epot = -22.7528472206812 | etot = -18.0610140113961 -566000 ekin = 2.31861442156789 | erot = 2.17941765713977 | epot = -22.7559143900142 | etot = -18.2578823113065 -567000 ekin = 1.93226018038665 | erot = 2.82020539323093 | epot = -22.7113049006744 | etot = -17.9588393270568 -568000 ekin = 2.20139908423164 | erot = 2.21734716414422 | epot = -22.7309883250973 | etot = -18.3122420767214 -569000 ekin = 2.47190977966691 | erot = 2.65968832242272 | epot = -22.6724326928843 | etot = -17.5408345907946 -570000 ekin = 2.43697670060318 | erot = 1.88669477532771 | epot = -22.6652860601546 | etot = -18.3416145842237 -571000 ekin = 2.89014026085716 | erot = 2.95617526869998 | epot = -22.6585089246085 | etot = -16.8121933950514 -572000 ekin = 1.93596118948627 | erot = 3.77290573984752 | epot = -22.6179860492832 | etot = -16.9091191199494 -573000 ekin = 2.40454634711712 | erot = 2.31316721466244 | epot = -22.5941857447927 | etot = -17.8764721830132 -574000 ekin = 1.69171540489496 | erot = 2.32939319863946 | epot = -22.6485181547003 | etot = -18.6274095511659 -575000 ekin = 1.84147438222145 | erot = 1.86451086977538 | epot = -22.7257563443533 | etot = -19.0197710923564 -576000 ekin = 3.22125710715105 | erot = 2.95826776175098 | epot = -22.6735851458117 | etot = -16.4940602769097 -577000 ekin = 2.86653117003728 | erot = 2.88010628292142 | epot = -22.6061554079342 | etot = -16.8595179549755 -578000 ekin = 2.38032268318988 | erot = 2.7671019602175 | epot = -22.4015577816724 | etot = -17.254133138265 -579000 ekin = 2.40088404436445 | erot = 1.99411758494037 | epot = -22.2441807849415 | etot = -17.8491791556366 -580000 ekin = 2.62022193893446 | erot = 1.97772953708398 | epot = -22.0981459564787 | etot = -17.5001944804603 -581000 ekin = 2.04609920382364 | erot = 3.02021971917519 | epot = -21.9713515823038 | etot = -16.9050326593049 -582000 ekin = 2.17556767215607 | erot = 3.10885810822425 | epot = -21.8451828402322 | etot = -16.5607570598519 -583000 ekin = 2.12792577884129 | erot = 2.7142175246668 | epot = -21.8090540348 | etot = -16.9669107312919 -584000 ekin = 2.99197492146327 | erot = 2.6185428756741 | epot = -21.801471166218 | etot = -16.1909533690806 -585000 ekin = 2.41600413666428 | erot = 2.49968403996097 | epot = -21.758207975142 | etot = -16.8425197985167 -586000 ekin = 3.57880609498066 | erot = 1.99026777936242 | epot = -21.7793800190222 | etot = -16.2103061446791 -587000 ekin = 3.5356931879588 | erot = 1.96660845702857 | epot = -21.7574182658134 | etot = -16.255116620826 -588000 ekin = 2.80385841316336 | erot = 1.58927534150912 | epot = -21.7290695763864 | etot = -17.3359358217139 -589000 ekin = 2.31178332958481 | erot = 2.19605556561578 | epot = -21.7771889269559 | etot = -17.2693500317554 -590000 ekin = 2.57159955455666 | erot = 1.71441305781987 | epot = -21.7801644206484 | etot = -17.4941518082719 -591000 ekin = 1.90027597697965 | erot = 3.807942925131 | epot = -21.8693595444135 | etot = -16.1611406423029 -592000 ekin = 2.10287592275467 | erot = 2.85572724854608 | epot = -21.9132458203291 | etot = -16.9546426490283 -593000 ekin = 1.6630679389305 | erot = 2.4593797067513 | epot = -21.9499391362603 | etot = -17.8274914905785 -594000 ekin = 1.85147249869391 | erot = 2.37596539021725 | epot = -22.0748010854883 | etot = -17.8473631965771 -595000 ekin = 1.62801913987931 | erot = 2.13760745860406 | epot = -22.2650343535208 | etot = -18.4994077550374 -596000 ekin = 1.8507787756783 | erot = 1.55277904845735 | epot = -22.3618759263936 | etot = -18.958318102258 -597000 ekin = 2.21873580046472 | erot = 2.31247364510899 | epot = -22.4218283315558 | etot = -17.8906188859821 -598000 ekin = 1.87152940931079 | erot = 3.02770945247866 | epot = -22.4928956008977 | etot = -17.5936567391083 -599000 ekin = 2.84160333456022 | erot = 2.19202304201413 | epot = -22.5210806388342 | etot = -17.4874542622599 -600000 ekin = 2.63824255094171 | erot = 2.13280883838529 | epot = -22.4361553764614 | etot = -17.6651039871344 -601000 ekin = 2.95991744971104 | erot = 3.20891387142302 | epot = -22.3089419175364 | etot = -16.1401105964023 -602000 ekin = 2.94287171911394 | erot = 2.68015446943143 | epot = -22.2205146380183 | etot = -16.5974884494729 -603000 ekin = 2.59651768027527 | erot = 2.70994674634415 | epot = -22.1626040385702 | etot = -16.8561396119508 -604000 ekin = 1.79237423166218 | erot = 2.11638057359598 | epot = -22.1934477586593 | etot = -18.2846929534011 -605000 ekin = 1.83068473031178 | erot = 2.27957438186889 | epot = -22.2254684973409 | etot = -18.1152093851602 -606000 ekin = 2.3318585405123 | erot = 2.19626289047849 | epot = -22.1692552740622 | etot = -17.6411338430714 -607000 ekin = 2.71184010988539 | erot = 2.97108975720826 | epot = -22.1536579122904 | etot = -16.4707280451968 -608000 ekin = 2.42009843612053 | erot = 2.4160965003039 | epot = -22.110570505977 | etot = -17.2743755695526 -609000 ekin = 1.88829617874732 | erot = 2.63290748875971 | epot = -21.9999822454274 | etot = -17.4787785779204 -610000 ekin = 3.00361337450474 | erot = 2.1770990927646 | epot = -21.9226199750059 | etot = -16.7419075077366 -611000 ekin = 2.45804405292799 | erot = 2.74756316868512 | epot = -21.9190479764513 | etot = -16.7134407548382 -612000 ekin = 2.52217588638914 | erot = 2.13391253924555 | epot = -21.9544188877756 | etot = -17.2983304621409 -613000 ekin = 3.03676008822022 | erot = 2.11841016157454 | epot = -22.0017416346015 | etot = -16.8465713848068 -614000 ekin = 2.28555718180927 | erot = 3.00540928021108 | epot = -22.076196502849 | etot = -16.7852300408287 -615000 ekin = 1.68510287809686 | erot = 2.62386193001631 | epot = -22.0327006368424 | etot = -17.7237358287293 -616000 ekin = 1.93880828018172 | erot = 2.84237691352499 | epot = -22.0612297066235 | etot = -17.2800445129167 -617000 ekin = 2.16704933019324 | erot = 2.51662857724104 | epot = -22.0595683849495 | etot = -17.3758904775152 -618000 ekin = 3.09933970351516 | erot = 2.74545743402537 | epot = -22.0170483082271 | etot = -16.1722511706866 -619000 ekin = 3.43176670397203 | erot = 2.12195823326367 | epot = -21.9875785418916 | etot = -16.4338536046559 -620000 ekin = 4.28780554984769 | erot = 2.22709196760531 | epot = -21.9605251543895 | etot = -15.4456276369365 -621000 ekin = 3.0817124482252 | erot = 2.57159564010566 | epot = -21.9025163812385 | etot = -16.2492082929077 -622000 ekin = 2.7316886075754 | erot = 2.62820058118157 | epot = -21.8412338594045 | etot = -16.4813446706475 -623000 ekin = 2.85452079274903 | erot = 2.89943500147418 | epot = -21.6852443941174 | etot = -15.9312885998942 -624000 ekin = 2.03273271064348 | erot = 3.41737453659277 | epot = -21.5180611078538 | etot = -16.0679538606176 -625000 ekin = 2.93860287466087 | erot = 2.67773023023639 | epot = -21.3855450802948 | etot = -15.7692119753975 -626000 ekin = 2.62772208534214 | erot = 2.18165419852426 | epot = -21.3747765229082 | etot = -16.5654002390418 -627000 ekin = 2.31977818310487 | erot = 2.39484209061114 | epot = -21.4372090577008 | etot = -16.7225887839848 -628000 ekin = 2.22183190227213 | erot = 2.76412054255637 | epot = -21.5969078027882 | etot = -16.6109553579597 -629000 ekin = 2.21761787409423 | erot = 1.98066149405243 | epot = -21.7578561859452 | etot = -17.5595768177986 -630000 ekin = 2.47350494176362 | erot = 2.13931642231379 | epot = -21.7773766650218 | etot = -17.1645553009444 -631000 ekin = 2.05047278007875 | erot = 1.79296462014617 | epot = -21.7869475538217 | etot = -17.9435101535968 -632000 ekin = 1.64845667747476 | erot = 3.28396465847895 | epot = -21.8333012025328 | etot = -16.9008798665791 -633000 ekin = 2.3500132343185 | erot = 2.33909753328782 | epot = -21.9539301797825 | etot = -17.2648194121761 -634000 ekin = 2.35704893279045 | erot = 2.4648325451317 | epot = -22.0204072629832 | etot = -17.1985257850611 -635000 ekin = 1.98907577162677 | erot = 3.37071781675286 | epot = -22.0690924871448 | etot = -16.7092988987652 -636000 ekin = 2.50984196335063 | erot = 2.4868899453394 | epot = -22.0714906026257 | etot = -17.0747586939356 -637000 ekin = 2.77501317112848 | erot = 2.80709332215511 | epot = -21.9923972278243 | etot = -16.4102907345407 -638000 ekin = 2.43799129572064 | erot = 2.79007198504632 | epot = -22.0591413868447 | etot = -16.8310781060777 -639000 ekin = 1.88073995546173 | erot = 2.09679843998315 | epot = -22.0499554202514 | etot = -18.0724170248065 -640000 ekin = 2.08188045172847 | erot = 3.35894090591921 | epot = -21.9976614802368 | etot = -16.5568401225891 -641000 ekin = 2.09182367506332 | erot = 2.24091541077085 | epot = -22.0969663672431 | etot = -17.764227281409 -642000 ekin = 2.29630816296813 | erot = 2.69496533496292 | epot = -22.1529742829376 | etot = -17.1617007850066 -643000 ekin = 2.73580847855275 | erot = 2.20074971448877 | epot = -22.0965451673466 | etot = -17.1599869743051 -644000 ekin = 2.87754738253099 | erot = 3.41752705378108 | epot = -22.1314614085222 | etot = -15.8363869722101 -645000 ekin = 2.42917363330758 | erot = 2.10617126422417 | epot = -22.0684179655268 | etot = -17.5330730679951 -646000 ekin = 2.69471397724187 | erot = 1.80009045225373 | epot = -21.899080412774 | etot = -17.4042759832784 -647000 ekin = 2.47700110999563 | erot = 1.99221351689818 | epot = -21.6986646197609 | etot = -17.2294499928671 -648000 ekin = 2.27330015032657 | erot = 1.67398094476719 | epot = -21.7984825454865 | etot = -17.8512014503928 -649000 ekin = 2.56285740395647 | erot = 1.7492398457574 | epot = -22.193749898698 | etot = -17.8816526489841 -650000 ekin = 2.76035969172864 | erot = 2.20984080080436 | epot = -22.3536470081185 | etot = -17.3834465155855 -651000 ekin = 2.26255154523698 | erot = 3.27496991661066 | epot = -22.4274148303115 | etot = -16.8898933684638 -652000 ekin = 2.37279828196649 | erot = 2.29630046443082 | epot = -22.4456643066012 | etot = -17.7765655602039 -653000 ekin = 2.07651844100825 | erot = 2.14699861111495 | epot = -22.4487464586909 | etot = -18.2252294065677 -654000 ekin = 2.31499263290336 | erot = 1.84798657187727 | epot = -22.4715481148371 | etot = -18.3085689100565 -655000 ekin = 2.12344600536595 | erot = 1.79742316518917 | epot = -22.4407504825062 | etot = -18.5198813119511 -656000 ekin = 2.44238672537433 | erot = 2.33314467296102 | epot = -22.4050518721078 | etot = -17.6295204737724 -657000 ekin = 2.44684720738066 | erot = 2.8701090435522 | epot = -22.3954429054341 | etot = -17.0784866545012 -658000 ekin = 2.49369435044193 | erot = 2.86933833355584 | epot = -22.3577847118899 | etot = -16.9947520278921 -659000 ekin = 3.38707666874149 | erot = 2.79117377884123 | epot = -22.223368870827 | etot = -16.0451184232443 -660000 ekin = 2.69464750718904 | erot = 1.98877163007961 | epot = -22.0868371976708 | etot = -17.4034180604021 -661000 ekin = 2.21484386108131 | erot = 2.52686187560577 | epot = -21.9324475602906 | etot = -17.1907418236035 -662000 ekin = 2.04483468145689 | erot = 2.52786214958085 | epot = -21.8656118118387 | etot = -17.2929149808009 -663000 ekin = 2.25554994547888 | erot = 2.29981193022508 | epot = -21.8121151333291 | etot = -17.2567532576251 -664000 ekin = 2.38378154392877 | erot = 1.87242521142839 | epot = -21.7163692740767 | etot = -17.4601625187196 -665000 ekin = 2.64936843119576 | erot = 2.29899861147532 | epot = -21.6597356727188 | etot = -16.7113686300477 -666000 ekin = 1.64494457505825 | erot = 2.30638161556459 | epot = -21.5641898301394 | etot = -17.6128636395165 -667000 ekin = 1.65735220589392 | erot = 2.82614341732318 | epot = -21.4751653585362 | etot = -16.9916697353191 -668000 ekin = 2.4984482511387 | erot = 3.27950898400316 | epot = -21.3387145475146 | etot = -15.5607573123728 -669000 ekin = 1.61611201967415 | erot = 2.67203522811057 | epot = -21.2655442255719 | etot = -16.9773969777871 -670000 ekin = 2.23077474650819 | erot = 2.61363425835143 | epot = -21.200889249368 | etot = -16.3564802445084 -671000 ekin = 2.26765830930916 | erot = 2.16388121545908 | epot = -21.1515274648836 | etot = -16.7199879401153 -672000 ekin = 1.94916146819699 | erot = 1.65479713709718 | epot = -21.0650678898705 | etot = -17.4611092845763 -673000 ekin = 1.92556066199439 | erot = 2.07900172108798 | epot = -21.0394363569889 | etot = -17.0348739739065 -674000 ekin = 2.12432357869026 | erot = 2.16781085660272 | epot = -21.0725830613714 | etot = -16.7804486260784 -675000 ekin = 2.06851819258985 | erot = 2.48317287761026 | epot = -21.1036073609478 | etot = -16.5519162907477 -676000 ekin = 2.45484997181755 | erot = 2.79183078710856 | epot = -21.1301283632783 | etot = -15.8834476043522 -677000 ekin = 2.20334154136532 | erot = 2.62444584525115 | epot = -21.1495626618895 | etot = -16.321775275273 -678000 ekin = 2.1472401432145 | erot = 2.79545747432264 | epot = -21.0405241444795 | etot = -16.0978265269423 -679000 ekin = 2.17033413623503 | erot = 2.18513653140294 | epot = -20.9421185444834 | etot = -16.5866478768454 -680000 ekin = 2.0995303513191 | erot = 2.68744418062156 | epot = -20.96987060062 | etot = -16.1828960686794 -681000 ekin = 2.18304447310098 | erot = 1.84812119436562 | epot = -21.0743862151371 | etot = -17.0432205476705 -682000 ekin = 3.04278123794938 | erot = 2.40409586716962 | epot = -21.0797568548334 | etot = -15.6328797497144 -683000 ekin = 2.86269023881705 | erot = 2.09728443896194 | epot = -21.0991655055584 | etot = -16.1391908277794 -684000 ekin = 1.98767037715953 | erot = 2.9959196882898 | epot = -21.1362036730577 | etot = -16.1526136076084 -685000 ekin = 1.57295457528713 | erot = 2.03034771002016 | epot = -21.146987158564 | etot = -17.5436848732567 -686000 ekin = 2.37743960028747 | erot = 2.54064910359147 | epot = -21.1479154694211 | etot = -16.2298267655422 -687000 ekin = 1.90905424981707 | erot = 2.87649471802562 | epot = -21.1390488337729 | etot = -16.3534998659303 -688000 ekin = 2.62740557427769 | erot = 2.25087525520175 | epot = -21.1259808926564 | etot = -16.247700063177 -689000 ekin = 2.68026630351849 | erot = 2.6526429118304 | epot = -21.2405393346747 | etot = -15.9076301193258 -690000 ekin = 2.56393304559924 | erot = 2.48495065222977 | epot = -21.4016015121778 | etot = -16.3527178143488 -691000 ekin = 2.19270435018289 | erot = 2.52704457861404 | epot = -21.5068265566119 | etot = -16.787077627815 -692000 ekin = 2.34077396593207 | erot = 3.24867065054241 | epot = -21.5176021816803 | etot = -15.9281575652058 -693000 ekin = 2.29029075483227 | erot = 3.0057489559252 | epot = -21.5358866889498 | etot = -16.2398469781924 -694000 ekin = 2.65674046511194 | erot = 2.58629868712488 | epot = -21.7490636357026 | etot = -16.5060244834658 -695000 ekin = 2.43126197328693 | erot = 1.19706323700545 | epot = -21.9401398969725 | etot = -18.3118146866802 -696000 ekin = 1.81474808623755 | erot = 1.46920096781106 | epot = -21.9089223337524 | etot = -18.6249732797038 -697000 ekin = 2.39476771383887 | erot = 2.11183502257124 | epot = -21.9420332766104 | etot = -17.4354305402003 -698000 ekin = 2.35926337724267 | erot = 1.92783320549515 | epot = -22.0277191263436 | etot = -17.7406225436057 -699000 ekin = 2.48176872675363 | erot = 2.56000644090341 | epot = -22.0212596021869 | etot = -16.9794844345299 -700000 ekin = 2.14129959772679 | erot = 2.29861037684921 | epot = -21.9318234409146 | etot = -17.4919134663386 -701000 ekin = 2.17049668499625 | erot = 2.20225192400486 | epot = -21.8245513288874 | etot = -17.4518027198863 -702000 ekin = 1.56275271552921 | erot = 2.01171151000642 | epot = -21.7865003044462 | etot = -18.2120360789105 -703000 ekin = 2.06065227779357 | erot = 2.17329473717682 | epot = -21.8026608939335 | etot = -17.5687138789631 -704000 ekin = 2.81952809577903 | erot = 1.94266087393332 | epot = -21.8212186788769 | etot = -17.0590297091646 -705000 ekin = 2.82050127519938 | erot = 2.18154028834386 | epot = -21.7752102636878 | etot = -16.7731687001446 -706000 ekin = 1.98267828238497 | erot = 2.32706466032388 | epot = -21.7893242385512 | etot = -17.4795812958423 -707000 ekin = 1.9119199256382 | erot = 2.05897787647104 | epot = -21.8430722730707 | etot = -17.8721744709615 -708000 ekin = 2.5016490217549 | erot = 2.18383615173375 | epot = -21.8544847432184 | etot = -17.1689995697297 -709000 ekin = 2.87304116461984 | erot = 2.56843564623619 | epot = -21.904442472254 | etot = -16.462965661398 -710000 ekin = 2.19867234802447 | erot = 2.26714812026437 | epot = -21.8819798989583 | etot = -17.4161594306695 -711000 ekin = 2.3389229861775 | erot = 1.44633862250318 | epot = -21.9197827259336 | etot = -18.1345211172529 -712000 ekin = 2.57005480809075 | erot = 2.2870655996051 | epot = -22.0346026838636 | etot = -17.1774822761678 -713000 ekin = 1.98393390580316 | erot = 2.33525788511066 | epot = -22.1280127822608 | etot = -17.808820991347 -714000 ekin = 2.59844561627729 | erot = 2.10769412707777 | epot = -22.1916311346269 | etot = -17.4854913912719 -715000 ekin = 2.41851974197057 | erot = 3.74888525577189 | epot = -22.1607861798611 | etot = -15.9933811821186 -716000 ekin = 2.84180231325819 | erot = 2.85971600497619 | epot = -22.0686589684412 | etot = -16.3671406502068 -717000 ekin = 3.44841444935858 | erot = 3.22605040091162 | epot = -21.9727882885698 | etot = -15.2983234382996 -718000 ekin = 3.10436184228426 | erot = 3.94950630255786 | epot = -21.8709253031511 | etot = -14.817057158309 -719000 ekin = 2.37806574336788 | erot = 2.95502686702169 | epot = -21.8563367317645 | etot = -16.523244121375 -720000 ekin = 2.2124258408194 | erot = 3.13473166149202 | epot = -21.8329644507669 | etot = -16.4858069484555 -721000 ekin = 1.6946894391771 | erot = 2.2319374275637 | epot = -21.7424084526643 | etot = -17.8157815859235 -722000 ekin = 1.90287140868432 | erot = 2.80483524098529 | epot = -21.7497487144859 | etot = -17.0420420648163 -723000 ekin = 2.36731223380046 | erot = 2.56327951769446 | epot = -21.6831418267135 | etot = -16.7525500752186 -724000 ekin = 1.73555921199202 | erot = 2.45238016332292 | epot = -21.6581802464112 | etot = -17.4702408710963 -725000 ekin = 2.29059437023039 | erot = 2.94575894857245 | epot = -21.7174261464808 | etot = -16.481072827678 -726000 ekin = 1.6348314779852 | erot = 2.30383185500796 | epot = -21.7564933587679 | etot = -17.8178300257747 -727000 ekin = 2.48240653489463 | erot = 3.20354227059191 | epot = -21.7912108634862 | etot = -16.1052620579997 -728000 ekin = 2.22769215153325 | erot = 2.16489072994622 | epot = -21.7890771091799 | etot = -17.3964942277004 -729000 ekin = 1.89768095869013 | erot = 1.6572167258809 | epot = -21.828690265207 | etot = -18.273792580636 -730000 ekin = 1.81050835100381 | erot = 2.15777747975244 | epot = -21.8264469741817 | etot = -17.8581611434255 -731000 ekin = 2.19898236908282 | erot = 2.98408098832206 | epot = -21.78613179764 | etot = -16.6030684402351 -732000 ekin = 2.43355047343304 | erot = 2.27170844305627 | epot = -21.6883863408735 | etot = -16.9831274243842 -733000 ekin = 3.07212273972684 | erot = 2.56783751855607 | epot = -21.7364921079321 | etot = -16.0965318496492 -734000 ekin = 2.38307322516835 | erot = 2.02726646964742 | epot = -21.7939757502944 | etot = -17.3836360554786 -735000 ekin = 2.14195880954703 | erot = 1.5562480724188 | epot = -21.8426856981853 | etot = -18.1444788162194 -736000 ekin = 2.14667447582535 | erot = 3.43698049451813 | epot = -21.9502105525335 | etot = -16.36655558219 -737000 ekin = 1.74866123585724 | erot = 3.58266975404538 | epot = -21.9688156583779 | etot = -16.6374846684753 -738000 ekin = 2.03996249374858 | erot = 2.50844136963081 | epot = -22.0013918784185 | etot = -17.4529880150391 -739000 ekin = 1.85238190118676 | erot = 2.20010970404148 | epot = -22.0186271684577 | etot = -17.9661355632294 -740000 ekin = 2.83862945300649 | erot = 2.79090377324796 | epot = -22.0338814904878 | etot = -16.4043482642334 -741000 ekin = 2.46678702773207 | erot = 2.91050038280045 | epot = -22.0853235069126 | etot = -16.7080360963801 -742000 ekin = 2.71529029375188 | erot = 3.27395653072503 | epot = -22.2140748190892 | etot = -16.2248279946123 -743000 ekin = 2.22536600879676 | erot = 3.21179247126421 | epot = -22.3431375024118 | etot = -16.9059790223508 -744000 ekin = 2.01371736615449 | erot = 3.77601393842181 | epot = -22.4261509869247 | etot = -16.6364196823484 -745000 ekin = 3.15730296333415 | erot = 2.31558796250714 | epot = -22.4108926873302 | etot = -16.9380017614889 -746000 ekin = 2.9774013013854 | erot = 2.63107362961468 | epot = -22.3694265664285 | etot = -16.7609516354285 -747000 ekin = 2.34209064832564 | erot = 2.04683419375201 | epot = -22.362862794452 | etot = -17.9739379523744 -748000 ekin = 2.37156256463876 | erot = 2.40538773919507 | epot = -22.3979208424336 | etot = -17.6209705385998 -749000 ekin = 2.06136855553992 | erot = 2.76585915349198 | epot = -22.3831536512816 | etot = -17.5559259422497 -750000 ekin = 1.6465677500269 | erot = 2.38368935068673 | epot = -22.444703911786 | etot = -18.4144468110724 -751000 ekin = 1.78122844885827 | erot = 2.81833836133589 | epot = -22.533438976529 | etot = -17.9338721663348 -752000 ekin = 1.34730592473949 | erot = 1.45838401317446 | epot = -22.6090848823224 | etot = -19.8033949444084 -753000 ekin = 1.87571626319839 | erot = 2.45354665197219 | epot = -22.5588053116254 | etot = -18.2295423964549 -754000 ekin = 1.7497031355263 | erot = 2.74314075044426 | epot = -22.4698920344377 | etot = -17.9770481484671 -755000 ekin = 2.42081076696332 | erot = 2.41217357398057 | epot = -22.3964223120254 | etot = -17.5634379710815 -756000 ekin = 1.85475003398 | erot = 2.78259891044769 | epot = -22.320596272712 | etot = -17.6832473282843 -757000 ekin = 1.97578050121355 | erot = 2.51781218539579 | epot = -22.1263927786385 | etot = -17.6328000920292 -758000 ekin = 1.22826853890878 | erot = 2.60763168332871 | epot = -21.9863700054333 | etot = -18.1504697831958 -759000 ekin = 2.21637457917738 | erot = 1.43949125248239 | epot = -22.1514665432947 | etot = -18.4956007116349 -760000 ekin = 2.68033406797328 | erot = 2.41719679588396 | epot = -22.2590376675296 | etot = -17.1615068036723 -761000 ekin = 2.17537440635552 | erot = 2.27171718649739 | epot = -22.3344047362676 | etot = -17.8873131434147 -762000 ekin = 2.18577068124738 | erot = 1.66829735822053 | epot = -22.3621686129861 | etot = -18.5081005735182 -763000 ekin = 2.45478818575914 | erot = 3.35299551820635 | epot = -22.4281249366375 | etot = -16.620341232672 -764000 ekin = 2.82872579097198 | erot = 2.78775814269904 | epot = -22.4216595904293 | etot = -16.8051756567583 -765000 ekin = 1.82575545759012 | erot = 2.76238969739238 | epot = -22.3222506299712 | etot = -17.7341054749887 -766000 ekin = 2.64667028577446 | erot = 2.30816231818548 | epot = -22.178450499249 | etot = -17.2236178952891 -767000 ekin = 2.57518863120179 | erot = 2.85636091304187 | epot = -22.0829371218307 | etot = -16.651387577587 -768000 ekin = 1.86419535586237 | erot = 2.77038508826208 | epot = -22.1032134089885 | etot = -17.4686329648641 -769000 ekin = 2.3968210365344 | erot = 2.30725355924691 | epot = -22.1808553751715 | etot = -17.4767807793902 -770000 ekin = 2.47007838986713 | erot = 3.2324442599133 | epot = -22.2845706013469 | etot = -16.5820479515665 -771000 ekin = 2.32978280625416 | erot = 2.29082247939233 | epot = -22.3223780040389 | etot = -17.7017727183924 -772000 ekin = 2.26109456847871 | erot = 3.00930315380543 | epot = -22.420252339108 | etot = -17.1498546168239 -773000 ekin = 2.23291379974971 | erot = 1.81993150945886 | epot = -22.4876821856977 | etot = -18.4348368764892 -774000 ekin = 2.82112723374611 | erot = 2.20399964233336 | epot = -22.478004597296 | etot = -17.4528777212165 -775000 ekin = 1.80765894464448 | erot = 1.85918506821 | epot = -22.4072882679054 | etot = -18.7404442550509 -776000 ekin = 1.4002136736383 | erot = 3.15411215412015 | epot = -22.3650958887673 | etot = -17.8107700610088 -777000 ekin = 1.64184304615234 | erot = 2.80565056199557 | epot = -22.2758630382017 | etot = -17.8283694300538 -778000 ekin = 1.48552010960747 | erot = 2.23385655322066 | epot = -22.280627961357 | etot = -18.5612512985289 -779000 ekin = 1.8612416844269 | erot = 1.89467011122748 | epot = -22.3098169150752 | etot = -18.5539051194208 -780000 ekin = 1.69992943470698 | erot = 2.31253245346999 | epot = -22.3678364729485 | etot = -18.3553745847716 -781000 ekin = 2.09952906112346 | erot = 2.56012058482574 | epot = -22.4462778123775 | etot = -17.7866281664283 -782000 ekin = 2.5656681981454 | erot = 1.9584872929859 | epot = -22.3478635193415 | etot = -17.8237080282102 -783000 ekin = 2.16529384416182 | erot = 2.88344914114143 | epot = -22.2446053910143 | etot = -17.1958624057111 -784000 ekin = 2.82003342353257 | erot = 2.22795791523757 | epot = -22.2211041777196 | etot = -17.1731128389495 -785000 ekin = 3.1175846654813 | erot = 2.90935771938994 | epot = -22.2344563156641 | etot = -16.2075139307929 -786000 ekin = 2.80016717549673 | erot = 3.42867564957488 | epot = -22.249645155972 | etot = -16.0208023309004 -787000 ekin = 2.38498105317564 | erot = 3.01080705704522 | epot = -22.1644901078413 | etot = -16.7687019976204 -788000 ekin = 1.98689482841944 | erot = 2.00265266168407 | epot = -22.1102205855985 | etot = -18.120673095495 -789000 ekin = 2.4429381578802 | erot = 2.28303571912851 | epot = -22.0438356575627 | etot = -17.317861780554 -790000 ekin = 3.54942607073523 | erot = 2.80791853998026 | epot = -21.9672470303852 | etot = -15.6099024196697 -791000 ekin = 3.07978044254695 | erot = 2.41844793702322 | epot = -21.9558944305006 | etot = -16.4576660509305 -792000 ekin = 3.91878473045569 | erot = 1.97318255021653 | epot = -21.8851857762129 | etot = -15.9932184955406 -793000 ekin = 2.24379464034279 | erot = 2.58359475602036 | epot = -21.774610681239 | etot = -16.9472212848758 -794000 ekin = 2.14799943871595 | erot = 2.45378042225318 | epot = -21.6055963838422 | etot = -17.0038165228731 -795000 ekin = 1.62858645550717 | erot = 2.41208539626205 | epot = -21.4428264365968 | etot = -17.4021545848276 -796000 ekin = 2.20626767900772 | erot = 2.13905661758329 | epot = -21.3317362060421 | etot = -16.9864119094511 -797000 ekin = 1.82996184067328 | erot = 1.99906119944912 | epot = -21.3393574083459 | etot = -17.5103343682235 -798000 ekin = 2.25667499558209 | erot = 2.51245793530998 | epot = -21.3768565865698 | etot = -16.6077236556778 -799000 ekin = 1.90911035219009 | erot = 2.87369878279889 | epot = -21.3617435253193 | etot = -16.5789343903304 -800000 ekin = 2.1677625897713 | erot = 2.3474017295601 | epot = -21.2761013083254 | etot = -16.760936988994 -801000 ekin = 1.87638787205728 | erot = 1.64434088909027 | epot = -21.119685062831 | etot = -17.5989563016835 -802000 ekin = 2.22686790237102 | erot = 2.21112245128269 | epot = -21.0065136937552 | etot = -16.5685233401015 -803000 ekin = 2.68797844582698 | erot = 1.9055042783616 | epot = -20.977533512373 | etot = -16.3840507881845 -804000 ekin = 2.34860603481644 | erot = 2.89571698053519 | epot = -20.9203141084123 | etot = -15.6759910930607 -805000 ekin = 1.76197291834029 | erot = 2.71253740465393 | epot = -20.7889998983483 | etot = -16.3144895753541 -806000 ekin = 1.74735080203811 | erot = 2.06758975379032 | epot = -20.7361939926422 | etot = -16.9212534368137 -807000 ekin = 1.56935370454675 | erot = 1.70438269927345 | epot = -20.7922156879383 | etot = -17.5184792841181 -808000 ekin = 2.10918656723178 | erot = 2.39856508826458 | epot = -20.8730295437323 | etot = -16.3652778882359 -809000 ekin = 2.6421817829379 | erot = 1.51718119689586 | epot = -20.8620425969582 | etot = -16.7026796171244 -810000 ekin = 3.0961523233869 | erot = 2.66382304688042 | epot = -20.7945446198551 | etot = -15.0345692495878 -811000 ekin = 3.044772851549 | erot = 3.63336291459448 | epot = -20.8540215443024 | etot = -14.1758857781589 -812000 ekin = 2.15160716251187 | erot = 2.79673763715996 | epot = -20.9409883926875 | etot = -15.9926435930156 -813000 ekin = 2.18680935122609 | erot = 3.17362835755789 | epot = -21.1408022790473 | etot = -15.7803645702634 -814000 ekin = 1.72092572696808 | erot = 2.99575126024499 | epot = -21.2437075371712 | etot = -16.5270305499581 -815000 ekin = 2.15299829462666 | erot = 2.27035656487164 | epot = -21.2458654890398 | etot = -16.8225106295415 -816000 ekin = 2.70812245065399 | erot = 1.52125307187337 | epot = -21.2616781989935 | etot = -17.0323026764661 -817000 ekin = 2.58901717437677 | erot = 2.58536627670114 | epot = -21.3956545078513 | etot = -16.2212710567734 -818000 ekin = 2.27875756856436 | erot = 2.24624264725762 | epot = -21.4318935062254 | etot = -16.9068932904034 -819000 ekin = 2.10656184615864 | erot = 3.01130039050671 | epot = -21.4327594058407 | etot = -16.3148971691754 -820000 ekin = 2.45661353119087 | erot = 2.70775294944127 | epot = -21.3798106611916 | etot = -16.2154441805595 -821000 ekin = 2.56789243532195 | erot = 2.54922758508946 | epot = -21.3170915318809 | etot = -16.1999715114695 -822000 ekin = 3.57333066089329 | erot = 2.21054956102183 | epot = -21.2861057645662 | etot = -15.5022255426511 -823000 ekin = 3.55383413213107 | erot = 2.72435850620162 | epot = -21.2727846567926 | etot = -14.9945920184599 -824000 ekin = 4.1160622349429 | erot = 3.29139599112172 | epot = -21.2039659493682 | etot = -13.7965077233036 -825000 ekin = 2.91568774544338 | erot = 3.47057612959321 | epot = -21.0618933558847 | etot = -14.6756294808481 -826000 ekin = 1.71667097443836 | erot = 1.97830555981832 | epot = -20.877676668146 | etot = -17.1827001338893 -827000 ekin = 1.87676981471837 | erot = 2.56467088925009 | epot = -20.7862250182708 | etot = -16.3447843143024 -828000 ekin = 2.38071607948713 | erot = 2.54624446499465 | epot = -20.7057379171107 | etot = -15.778777372629 -829000 ekin = 2.23087866970086 | erot = 1.78456567522681 | epot = -20.6078136299298 | etot = -16.5923692850021 -830000 ekin = 2.54758016482261 | erot = 2.32440405635603 | epot = -20.4881081818274 | etot = -15.6161239606487 -831000 ekin = 2.68445862644274 | erot = 2.08263260479753 | epot = -20.3542193485844 | etot = -15.5871281173442 -832000 ekin = 2.63412360308727 | erot = 2.01244922883236 | epot = -20.215817212176 | etot = -15.5692443802563 -833000 ekin = 2.52816532834198 | erot = 2.59604450500369 | epot = -20.1546011863618 | etot = -15.0303913530161 -834000 ekin = 2.89178882882708 | erot = 2.32656568068784 | epot = -20.1544579940429 | etot = -14.936103484528 -835000 ekin = 2.77377023733644 | erot = 2.76167763911259 | epot = -20.2925945781537 | etot = -14.7571467017047 -836000 ekin = 2.5461758373878 | erot = 2.86272526489881 | epot = -20.4572179712234 | etot = -15.0483168689368 -837000 ekin = 1.73852270651189 | erot = 1.97943492340463 | epot = -20.5100877279362 | etot = -16.7921300980197 -838000 ekin = 1.97190789156808 | erot = 2.79058337256638 | epot = -20.5305299708183 | etot = -15.7680387066838 -839000 ekin = 1.97773711155226 | erot = 2.72413991034569 | epot = -20.5265807034223 | etot = -15.8247036815244 -840000 ekin = 1.72329638748709 | erot = 2.96738113282628 | epot = -20.6321231069653 | etot = -15.9414455866519 -841000 ekin = 2.83071457484448 | erot = 2.84941397463212 | epot = -20.7926258530585 | etot = -15.1124973035819 -842000 ekin = 2.59731855411368 | erot = 2.84178819703383 | epot = -20.8313063579288 | etot = -15.3921996067813 -843000 ekin = 2.04928376150595 | erot = 2.61288435498261 | epot = -20.8099267672998 | etot = -16.1477586508113 -844000 ekin = 1.54583411960153 | erot = 1.93893729147582 | epot = -20.8613105352917 | etot = -17.3765391242144 -845000 ekin = 2.31382540600799 | erot = 2.32466241883301 | epot = -20.9823282893205 | etot = -16.3438404644795 -846000 ekin = 2.08903634512997 | erot = 2.31578856009953 | epot = -21.0646153757684 | etot = -16.6597904705389 -847000 ekin = 2.48001373621179 | erot = 2.63006614696695 | epot = -21.0262265568771 | etot = -15.9161466736983 -848000 ekin = 2.15184282735255 | erot = 1.47311006297177 | epot = -21.0583979355085 | etot = -17.4334450451842 -849000 ekin = 2.01842760273387 | erot = 2.48110730715335 | epot = -21.0805165806606 | etot = -16.5809816707734 -850000 ekin = 2.55741512224125 | erot = 2.68263416508461 | epot = -21.0773082596903 | etot = -15.8372589723644 -851000 ekin = 2.18005669935449 | erot = 2.93569398882538 | epot = -21.0924777064981 | etot = -15.9767270183182 -852000 ekin = 2.4696261459638 | erot = 2.47026576605629 | epot = -21.121182921383 | etot = -16.1812910093629 -853000 ekin = 2.39950550338299 | erot = 2.98750142132014 | epot = -21.0612995182631 | etot = -15.67429259356 -854000 ekin = 2.33465924490094 | erot = 2.85274307519462 | epot = -20.968723969517 | etot = -15.7813216494214 -855000 ekin = 2.3422738818298 | erot = 2.06894784165372 | epot = -20.9841257021182 | etot = -16.5729039786347 -856000 ekin = 2.50117711580693 | erot = 2.74791206324423 | epot = -20.8738269143243 | etot = -15.6247377352732 -857000 ekin = 2.54090672086302 | erot = 3.01990349760069 | epot = -20.7453092144205 | etot = -15.1844989959568 -858000 ekin = 3.06946696795817 | erot = 2.15496603972172 | epot = -20.6851307548641 | etot = -15.4606977471842 -859000 ekin = 2.85023303418271 | erot = 2.24419946408454 | epot = -20.6787263175177 | etot = -15.5842938192505 -860000 ekin = 2.81341243833326 | erot = 1.51974619370821 | epot = -20.6783502445099 | etot = -16.3451916124685 -861000 ekin = 2.27419936469319 | erot = 2.84736568193219 | epot = -20.6476685348769 | etot = -15.5261034882515 -862000 ekin = 2.99814535919907 | erot = 1.87200304458179 | epot = -20.6714218686896 | etot = -15.8012734649087 -863000 ekin = 2.82320132781551 | erot = 1.77959785908835 | epot = -20.7642045825074 | etot = -16.1614053956035 -864000 ekin = 2.91892607599649 | erot = 2.64325528924267 | epot = -20.9317153856013 | etot = -15.3695340203621 -865000 ekin = 3.32989545880504 | erot = 2.25510784979563 | epot = -21.0557741374338 | etot = -15.4707708288331 -866000 ekin = 2.85710406140164 | erot = 3.16185395635699 | epot = -21.1425088224093 | etot = -15.1235508046507 -867000 ekin = 2.74742982523498 | erot = 3.06773761977148 | epot = -21.134531707449 | etot = -15.3193642624426 -868000 ekin = 2.1948650568198 | erot = 2.22458860510737 | epot = -21.0697126630059 | etot = -16.6502590010787 -869000 ekin = 2.92239964068214 | erot = 2.50065925324413 | epot = -21.0149378764857 | etot = -15.5918789825595 -870000 ekin = 2.48931117933877 | erot = 2.13038554226927 | epot = -20.9976655364142 | etot = -16.3779688148061 -871000 ekin = 2.19107246828585 | erot = 2.37839051284132 | epot = -20.8765191273408 | etot = -16.3070561462136 -872000 ekin = 1.55081886521515 | erot = 2.09762459684261 | epot = -20.8521940121747 | etot = -17.203750550117 -873000 ekin = 1.3896067615701 | erot = 2.27757856660906 | epot = -20.9255865429236 | etot = -17.2584012147445 -874000 ekin = 1.41282979514325 | erot = 2.76881886831622 | epot = -21.0901483490344 | etot = -16.9084996855749 -875000 ekin = 1.18979270807644 | erot = 2.71872907877546 | epot = -21.2270266717577 | etot = -17.3185048849058 -876000 ekin = 1.81100671707876 | erot = 2.98963277694411 | epot = -21.2472610575188 | etot = -16.446621563496 -877000 ekin = 2.36243541111364 | erot = 2.03609143795482 | epot = -21.3277863705839 | etot = -16.9292595215155 -878000 ekin = 2.12451961824681 | erot = 1.75451707226955 | epot = -21.3222506595257 | etot = -17.4432139690093 -879000 ekin = 2.2716997631568 | erot = 2.70191568133045 | epot = -21.3119311913779 | etot = -16.3383157468906 -880000 ekin = 2.68326313012635 | erot = 2.77340532358103 | epot = -21.3535728447366 | etot = -15.8969043910293 -881000 ekin = 2.87483307600209 | erot = 2.33652901733378 | epot = -21.3292700652532 | etot = -16.1179079719173 -882000 ekin = 2.32758906799515 | erot = 2.16795489269515 | epot = -21.2584233833351 | etot = -16.7628794226448 -883000 ekin = 2.35908631800799 | erot = 1.97904048991531 | epot = -21.0655746410777 | etot = -16.7274478331544 -884000 ekin = 2.52269362644082 | erot = 2.25025361307444 | epot = -20.9641879640376 | etot = -16.1912407245223 -885000 ekin = 2.84711898438829 | erot = 2.26506458535076 | epot = -20.9641383727442 | etot = -15.8519548030051 -886000 ekin = 3.18322288605135 | erot = 1.73470875511279 | epot = -21.0012427194847 | etot = -16.0833110783206 -887000 ekin = 2.68813414464724 | erot = 2.50204216522369 | epot = -21.067976555709 | etot = -15.8778002458381 -888000 ekin = 2.15187544250472 | erot = 2.83221089603917 | epot = -21.1763900792301 | etot = -16.1923037406862 -889000 ekin = 2.16956995574787 | erot = 2.20198656261183 | epot = -21.1017572530619 | etot = -16.7302007347022 -890000 ekin = 1.78556825977743 | erot = 2.98410700070924 | epot = -21.186208638226 | etot = -16.4165333777394 -891000 ekin = 1.64917016933854 | erot = 2.2775040392346 | epot = -21.3189640243097 | etot = -17.3922898157365 -892000 ekin = 1.96583947510742 | erot = 2.36271973263346 | epot = -21.4596361006042 | etot = -17.1310768928634 -893000 ekin = 1.79314340564254 | erot = 1.84111074899918 | epot = -21.5470179462123 | etot = -17.9127637915706 -894000 ekin = 2.81442382935654 | erot = 2.80759818283315 | epot = -21.6538835081476 | etot = -16.031861495958 -895000 ekin = 2.0070369904664 | erot = 2.75374249882318 | epot = -21.7499760057857 | etot = -16.9891965164962 -896000 ekin = 1.6507008342202 | erot = 2.56296228195541 | epot = -21.8927812332096 | etot = -17.679118117034 -897000 ekin = 1.78139405234358 | erot = 2.35356223356247 | epot = -22.0286409132692 | etot = -17.8936846273632 -898000 ekin = 1.85207490030025 | erot = 2.39285557286479 | epot = -22.0495390022753 | etot = -17.8046085291103 -899000 ekin = 1.66216066819287 | erot = 3.04222938639383 | epot = -21.9579747350568 | etot = -17.2535846804701 -900000 ekin = 2.15165827067079 | erot = 2.62356927804176 | epot = -21.9156104880733 | etot = -17.1403829393607 -901000 ekin = 2.41248642142908 | erot = 2.69714418093218 | epot = -21.9837417963999 | etot = -16.8741111940386 -902000 ekin = 2.57545214239909 | erot = 2.40635843208184 | epot = -21.996436412966 | etot = -17.0146258384851 -903000 ekin = 2.40335601179058 | erot = 2.40575417529011 | epot = -22.0230111828253 | etot = -17.2139009957446 -904000 ekin = 1.99365997109403 | erot = 3.12264199705155 | epot = -22.0954468558153 | etot = -16.9791448876697 -905000 ekin = 2.45160047861299 | erot = 2.11889478277437 | epot = -22.0620083174753 | etot = -17.491513056088 -906000 ekin = 2.69446662881179 | erot = 1.66991631401457 | epot = -22.0555442490735 | etot = -17.6911613062472 -907000 ekin = 2.57344988637111 | erot = 2.16877319112329 | epot = -22.0376984236082 | etot = -17.2954753461138 -908000 ekin = 2.96467760769891 | erot = 2.40252252045293 | epot = -22.0191047803794 | etot = -16.6519046522276 -909000 ekin = 3.12793409264581 | erot = 2.12009742665766 | epot = -22.0610667288554 | etot = -16.813035209552 -910000 ekin = 2.92206025021313 | erot = 3.50302372345589 | epot = -22.1277774480558 | etot = -15.7026934743868 -911000 ekin = 1.85381948048669 | erot = 2.73401011795405 | epot = -22.1683975531304 | etot = -17.5805679546896 -912000 ekin = 2.64405242900444 | erot = 1.86324838607163 | epot = -22.2002570143971 | etot = -17.6929561993211 -913000 ekin = 2.46824283660222 | erot = 2.03086335466052 | epot = -22.3203806242275 | etot = -17.8212744329648 -914000 ekin = 2.01871966356281 | erot = 2.94283156821208 | epot = -22.3513452914152 | etot = -17.3897940596404 -915000 ekin = 2.82676643872102 | erot = 2.11643553756711 | epot = -22.3640471312087 | etot = -17.4208451549205 -916000 ekin = 2.54227707175729 | erot = 3.23335822897872 | epot = -22.4652663102875 | etot = -16.6896310095515 -917000 ekin = 2.31676859881433 | erot = 2.24272005825761 | epot = -22.4635852813361 | etot = -17.9040966242641 -918000 ekin = 2.08681780124232 | erot = 2.05685815910104 | epot = -22.3748058531194 | etot = -18.231129892776 -919000 ekin = 2.60282015977208 | erot = 2.38968293687317 | epot = -22.3822670579485 | etot = -17.3897639613033 -920000 ekin = 3.21847224306531 | erot = 2.75010700480467 | epot = -22.4646189595793 | etot = -16.4960397117093 -921000 ekin = 2.67829101318105 | erot = 1.98386933580364 | epot = -22.5250186592845 | etot = -17.8628583102998 -922000 ekin = 1.43283799739774 | erot = 1.5210967069851 | epot = -22.5925015236451 | etot = -19.6385668192623 -923000 ekin = 1.69052063428542 | erot = 1.88300391650268 | epot = -22.66377714455 | etot = -19.0902525937619 -924000 ekin = 2.14340021014736 | erot = 1.52248843908133 | epot = -22.6402388027506 | etot = -18.9743501535219 -925000 ekin = 2.26091939109784 | erot = 1.33050454776919 | epot = -22.5227280014395 | etot = -18.9313040625724 -926000 ekin = 2.00930540350536 | erot = 2.07372939007629 | epot = -22.4428200376094 | etot = -18.3597852440277 -927000 ekin = 2.5328908262125 | erot = 1.99783542507571 | epot = -22.5727269691716 | etot = -18.0420007178834 -928000 ekin = 2.57275295957812 | erot = 2.50503787417692 | epot = -22.7397714760282 | etot = -17.6619806422732 -929000 ekin = 2.66131598383108 | erot = 1.82871097568714 | epot = -22.7889092091996 | etot = -18.2988822496813 -930000 ekin = 2.41369096322635 | erot = 2.00598415451169 | epot = -22.802343205586 | etot = -18.3826680878479 -931000 ekin = 3.02636364754007 | erot = 2.11596225016102 | epot = -22.7562575819635 | etot = -17.6139316842624 -932000 ekin = 2.34573343934799 | erot = 1.88269819474442 | epot = -22.8028018252265 | etot = -18.5743701911341 -933000 ekin = 2.16951834533283 | erot = 2.85677231086966 | epot = -22.8240172791918 | etot = -17.7977266229894 -934000 ekin = 2.17177152489559 | erot = 2.1194660688678 | epot = -22.8652321779361 | etot = -18.5739945841727 -935000 ekin = 2.34485090948927 | erot = 2.23417606918542 | epot = -22.85888707632 | etot = -18.2798600976453 -936000 ekin = 2.28188124919414 | erot = 2.53015822921571 | epot = -22.9782518612072 | etot = -18.1662123827973 -937000 ekin = 2.30619254942948 | erot = 2.82857457174385 | epot = -23.071665648819 | etot = -17.9368985276457 -938000 ekin = 2.44229226509269 | erot = 2.00737414808354 | epot = -23.1363676072135 | etot = -18.6867011940373 -939000 ekin = 2.97744015155648 | erot = 2.10212870842129 | epot = -23.1206613400026 | etot = -18.0410924800248 -940000 ekin = 3.7421966126526 | erot = 2.68184060115532 | epot = -23.0494489680041 | etot = -16.6254117541962 -941000 ekin = 3.11307007541058 | erot = 2.28700344636989 | epot = -22.9451834918749 | etot = -17.5451099700944 -942000 ekin = 3.46654816859627 | erot = 1.87509182259239 | epot = -22.9048558084883 | etot = -17.5632158172997 -943000 ekin = 3.79224818385642 | erot = 2.70927084823341 | epot = -22.8698482349085 | etot = -16.3683292028187 -944000 ekin = 2.65995525590795 | erot = 2.74912726816421 | epot = -22.8317889960132 | etot = -17.422706471941 -945000 ekin = 2.54659137616624 | erot = 2.02239421261016 | epot = -22.725938832337 | etot = -18.1569532435606 -946000 ekin = 2.46388617435412 | erot = 1.67037983156325 | epot = -22.5545307163886 | etot = -18.4202647104712 -947000 ekin = 2.40803821488281 | erot = 1.99424876436282 | epot = -22.4581247656852 | etot = -18.0558377864396 -948000 ekin = 3.53604042034896 | erot = 2.5799787743484 | epot = -22.3226574127032 | etot = -16.2066382180059 -949000 ekin = 2.9885427180707 | erot = 2.43476486608199 | epot = -22.1081978358245 | etot = -16.6848902516719 -950000 ekin = 1.85098760333696 | erot = 3.01138499180169 | epot = -21.9481390655564 | etot = -17.0857664704178 -951000 ekin = 2.24140231384639 | erot = 2.36101456496683 | epot = -21.9054305662226 | etot = -17.3030136874094 -952000 ekin = 2.17674596142229 | erot = 1.66164476273624 | epot = -21.8857446244282 | etot = -18.0473539002697 -953000 ekin = 2.32434436644842 | erot = 1.96780923551529 | epot = -21.8640893071839 | etot = -17.5719357052202 -954000 ekin = 1.49071594272053 | erot = 3.34931219540536 | epot = -21.7966718941877 | etot = -16.9566437560618 -955000 ekin = 1.88457697665867 | erot = 2.69006961792184 | epot = -21.7221575712774 | etot = -17.1475109766969 -956000 ekin = 1.69307087749047 | erot = 2.16469646035311 | epot = -21.6721199805375 | etot = -17.8143526426939 -957000 ekin = 1.73487330688787 | erot = 1.64307450157791 | epot = -21.6559256952542 | etot = -18.2779778867884 -958000 ekin = 1.60385894866933 | erot = 2.19168737006629 | epot = -21.6476897105174 | etot = -17.8521433917818 -959000 ekin = 2.59262245343361 | erot = 2.48219361032085 | epot = -21.6596277279705 | etot = -16.584811664216 -960000 ekin = 2.55386671368679 | erot = 2.05771846301768 | epot = -21.6626200672137 | etot = -17.0510348905092 -961000 ekin = 2.27765806186204 | erot = 2.17958354193564 | epot = -21.6544957188757 | etot = -17.1972541150781 -962000 ekin = 1.66004639932187 | erot = 3.51004740828815 | epot = -21.6650529510448 | etot = -16.4949591434348 -963000 ekin = 1.98935936955203 | erot = 1.50490949194663 | epot = -21.6088711497268 | etot = -18.1146022882282 -964000 ekin = 2.17983717879189 | erot = 2.29031074234418 | epot = -21.5586262428097 | etot = -17.0884783216737 -965000 ekin = 2.10787439045543 | erot = 2.32210778851089 | epot = -21.5497920382512 | etot = -17.1198098592848 -966000 ekin = 3.1408040905672 | erot = 3.41823133718859 | epot = -21.5836404263087 | etot = -15.0246049985529 -967000 ekin = 3.0568623124503 | erot = 2.17332066321312 | epot = -21.5260931467357 | etot = -16.2959101710723 -968000 ekin = 2.05064192877793 | erot = 2.14124924922395 | epot = -21.4479972163208 | etot = -17.2561060383189 -969000 ekin = 2.21517858837653 | erot = 2.21735686304379 | epot = -21.3822587820383 | etot = -16.9497233306179 -970000 ekin = 2.44665062708038 | erot = 2.63919176763313 | epot = -21.3192840477867 | etot = -16.2334416530732 -971000 ekin = 2.47241679333996 | erot = 2.68621090896416 | epot = -21.3036698600043 | etot = -16.1450421577002 -972000 ekin = 3.18976408247807 | erot = 2.45901954667695 | epot = -21.2523934460447 | etot = -15.6036098168897 -973000 ekin = 3.35475115149159 | erot = 2.61012752320777 | epot = -21.183068859057 | etot = -15.2181901843576 -974000 ekin = 2.71127807449815 | erot = 2.1297435585203 | epot = -21.0816906098712 | etot = -16.2406689768527 -975000 ekin = 1.81295894463494 | erot = 2.07595649769211 | epot = -20.9964165264668 | etot = -17.1075010841398 -976000 ekin = 2.3761992679076 | erot = 1.37981441384236 | epot = -20.8930101654835 | etot = -17.1369964837335 -977000 ekin = 2.85555210767403 | erot = 3.03619369635209 | epot = -21.0095574945916 | etot = -15.1178116905655 -978000 ekin = 3.13849116757389 | erot = 3.01118356119965 | epot = -21.0732326779662 | etot = -14.9235579491927 -979000 ekin = 3.64170438280054 | erot = 2.46121267957824 | epot = -20.9593695826043 | etot = -14.8564525202255 -980000 ekin = 3.43680535726821 | erot = 3.27333588575054 | epot = -20.9004670674902 | etot = -14.1903258244714 -981000 ekin = 2.95806185202903 | erot = 2.46811293942084 | epot = -20.98680384597 | etot = -15.5606290545201 -982000 ekin = 2.05823037945997 | erot = 2.23573651589998 | epot = -21.0420814071853 | etot = -16.7481145118254 -983000 ekin = 2.5553610304344 | erot = 1.97272050888113 | epot = -21.0434200461187 | etot = -16.5153385068031 -984000 ekin = 2.32140326985734 | erot = 2.58284655378619 | epot = -21.0826601835728 | etot = -16.1784103599293 -985000 ekin = 2.30327577152247 | erot = 3.01569210622986 | epot = -21.1731422974946 | etot = -15.8541744197423 -986000 ekin = 2.0247579133688 | erot = 2.17885674714072 | epot = -21.2745593334951 | etot = -17.0709446729856 -987000 ekin = 2.38610984160001 | erot = 1.60437579739601 | epot = -21.2569575649581 | etot = -17.2664719259621 -988000 ekin = 2.73926231299059 | erot = 2.71146350841209 | epot = -21.1552791211024 | etot = -15.7045532996998 -989000 ekin = 2.26697151561908 | erot = 2.87750604798637 | epot = -21.0937789068057 | etot = -15.9493013432003 -990000 ekin = 2.20943106152859 | erot = 2.59684886899362 | epot = -21.0203331776817 | etot = -16.2140532471594 -991000 ekin = 2.18249266283081 | erot = 2.5464965741117 | epot = -20.9130337682104 | etot = -16.1840445312678 -992000 ekin = 1.6979885228163 | erot = 2.49592807829765 | epot = -20.9758495875099 | etot = -16.7819329863959 -993000 ekin = 1.37413745875443 | erot = 1.97736806672933 | epot = -21.0653195519546 | etot = -17.7138140264709 -994000 ekin = 1.46489942286098 | erot = 2.9578292103502 | epot = -21.1261867461739 | etot = -16.7034581129628 -995000 ekin = 2.313206084368 | erot = 1.68064795849454 | epot = -21.1907262676308 | etot = -17.1968722247682 -996000 ekin = 2.91635623044139 | erot = 2.86817278212845 | epot = -21.1749728841881 | etot = -15.3904438716183 -997000 ekin = 3.14117227050211 | erot = 2.13892951607982 | epot = -21.1714996184257 | etot = -15.8913978318438 -998000 ekin = 2.24297046385175 | erot = 3.02327291553882 | epot = -21.1032039558863 | etot = -15.8369605764957 -999000 ekin = 2.61553981530106 | erot = 1.73872891845711 | epot = -21.0217257279765 | etot = -16.6674569942184 -1000000 ekin = 2.34012577497833 | erot = 2.86436388995813 | epot = -21.020156604404 | etot = -15.8156669394675 - 1000000 0.10400559 -1.3746133 0.060853481 -1.1675019 -8.3808461e-05 -Loop time of 39.3636 on 4 procs for 1000000 steps with 16 atoms - -Performance: 21949.237 tau/day, 25404.210 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.71602 | 15.145 | 28.607 | 317.4 | 38.47 -Bond | 0.090624 | 0.44555 | 0.74546 | 44.3 | 1.13 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.0699 | 2.2587 | 2.5059 | 10.9 | 5.74 -Output | 3.0994e-05 | 4.0352e-05 | 4.5061e-05 | 0.0 | 0.00 -Modify | 0.21689 | 2.7926 | 5.2575 | 132.2 | 7.09 -Other | | 18.72 | | | 47.56 - -Nlocal: 4 ave 8 max 0 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 11 ave 14 max 8 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 46 ave 89 max 0 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 184 -Ave neighs/atom = 11.5 -Ave special neighs/atom = 3.75 -Neighbor list builds = 0 -Dangerous builds = 0 - -#write_restart config.${number}.* -Total wall time: 0:00:39 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 new file mode 100644 index 0000000000..ba36d696fb --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.1 @@ -0,0 +1,178 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.025 | 3.025 | 3.025 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05 +1000 ekin = 1.54282272464468 | erot = 1.71757897250772 | epot = -24.4403527731341 | etot = -21.1799510759817 +2000 ekin = 1.86109566690716 | erot = 1.93804145796026 | epot = -24.3759816748265 | etot = -20.5768445499591 +3000 ekin = 2.68769182431188 | erot = 2.14559269500086 | epot = -24.2916556822451 | etot = -19.4583711629324 +4000 ekin = 2.04710303757243 | erot = 1.48774072590987 | epot = -24.190371461807 | etot = -20.6555276983247 +5000 ekin = 1.77654023802719 | erot = 2.534186505221 | epot = -24.1246365663843 | etot = -19.8139098231361 +6000 ekin = 3.12253137872527 | erot = 2.04028266818831 | epot = -24.0491248750916 | etot = -18.886310828178 +7000 ekin = 3.22418765752177 | erot = 2.72037570174023 | epot = -23.9458569915548 | etot = -18.0012936322928 +8000 ekin = 2.83204202112963 | erot = 2.67060276413777 | epot = -23.9211291529766 | etot = -18.4184843677092 +9000 ekin = 2.69585642754481 | erot = 2.59559820250212 | epot = -23.8340823338302 | etot = -18.5426277037833 +10000 ekin = 2.66058119525512 | erot = 1.95965933336077 | epot = -23.7132443170725 | etot = -19.0930037884566 + 10000 0.11824805 -1.4953627 0.013284973 -1.3157914 -0.00012999454 +Loop time of 0.32781 on 1 procs for 10000 steps with 16 atoms + +Performance: 26356.746 tau/day, 30505.493 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24211 | 0.24211 | 0.24211 | 0.0 | 73.86 +Bond | 0.0075173 | 0.0075173 | 0.0075173 | 0.0 | 2.29 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0014515 | 0.0014515 | 0.0014515 | 0.0 | 0.44 +Output | 5.4836e-06 | 5.4836e-06 | 5.4836e-06 | 0.0 | 0.00 +Modify | 0.073331 | 0.073331 | 0.073331 | 0.0 | 22.37 +Other | | 0.003398 | | | 1.04 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 116 ave 116 max 116 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 116 +Ave neighs/atom = 7.25 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 new file mode 100644 index 0000000000..3237d4849e --- /dev/null +++ b/examples/USER/cgdna/examples/oxDNA2/duplex2/log.27Nov18.duplex2.g++.4 @@ -0,0 +1,178 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable number equal 2 +variable ofreq equal 1000 +variable efreq equal 1000 + +units lj + +dimension 3 + +newton off + +boundary p p p + +atom_style hybrid bond ellipsoid +atom_modify sort 0 1.0 + +# Pair interactions require lists of neighbours to be calculated +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +read_data data.duplex2 + orthogonal box = (-20 -20 -20) to (20 20 20) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 16 atoms + reading velocities ... + 16 velocities + 16 ellipsoids + scanning bonds ... + 2 = max bonds/atom + reading bonds ... + 13 bonds + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + +set atom * mass 3.1575 + 16 settings made for mass + +group all type 1 4 +16 atoms in group all + +# oxDNA bond interactions - FENE backbone +bond_style oxdna2/fene +bond_coeff * 2.0 0.25 0.7564 + +# oxDNA pair interactions +pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh +pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32 +pair_coeff * * oxdna2/stk seqav 0.1 6.0 0.4 0.9 0.32 0.6 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65 +pair_coeff * * oxdna2/hbond seqav 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 1 4 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff 2 3 oxdna2/hbond seqav 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45 +pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68 +pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793 +pair_coeff * * oxdna2/dh 0.1 1.0 0.815 + +# NVE ensemble +#fix 1 all nve/dot +fix 1 all nve/dotc/langevin 0.1 0.1 0.03 457145 angmom 10 +#fix 1 all nve/asphere +#fix 2 all langevin 0.1 0.1 0.03 457145 angmom 10 + +timestep 1e-5 + +#comm_style tiled +#fix 3 all balance 10000 1.1 rcb + +#compute mol all chunk/atom molecule +#compute mychunk all vcm/chunk mol +#fix 4 all ave/time 10000 1 10000 c_mychunk[1] c_mychunk[2] c_mychunk[3] file vcm.txt mode vector + +#dump pos all xyz ${ofreq} traj.${number}.xyz + +#compute quat all property/atom quatw quati quatj quatk +#dump quat all custom ${ofreq} quat.${number}.txt id c_quat[1] c_quat[2] c_quat[3] c_quat[4] +#dump_modify quat sort id +#dump_modify quat format line "%d %13.6le %13.6le %13.6le %13.6le" + +compute erot all erotate/asphere +compute ekin all ke +compute epot all pe +variable erot equal c_erot +variable ekin equal c_ekin +variable epot equal c_epot +variable etot equal c_erot+c_ekin+c_epot +fix 5 all print ${efreq} "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes +fix 5 all print 1000 "$(step) ekin = ${ekin} | erot = ${erot} | epot = ${epot} | etot = ${etot}" screen yes + +#dump out all custom ${ofreq} out.${number}.txt id x y z vx vy vz fx fy fz tqx tqy tqz +#dump_modify out sort id +#dump_modify out format line "%d %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le %13.6le" + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.6274 + ghost atom cutoff = 2.6274 + binsize = 1.3137, bins = 31 31 31 + 6 neighbor lists, perpetual/occasional/extra = 6 0 0 + (1) pair oxdna2/excv, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard + (2) pair oxdna2/stk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (3) pair oxdna2/hbond, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (4) pair oxdna2/xstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (5) pair oxdna2/coaxstk, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none + (6) pair oxdna2/dh, perpetual, copy from (1) + attributes: half, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 7.777 | 7.959 | 8.142 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -1.5358787 0.0096742456 -1.5262045 -7.9568629e-05 +1000 ekin = 1.34554291364716 | erot = 2.30525041754444 | epot = -24.3924150888896 | etot = -20.741621757698 +2000 ekin = 2.15972469811184 | erot = 2.1628675965276 | epot = -24.3548203354875 | etot = -20.0322280408481 +3000 ekin = 3.26433550542939 | erot = 2.76107866472085 | epot = -24.2947953202752 | etot = -18.269381150125 +4000 ekin = 1.9203212531997 | erot = 2.13339438425299 | epot = -24.234098584123 | etot = -20.1803829466703 +5000 ekin = 1.35481075814721 | erot = 2.00854026688447 | epot = -24.1768963201279 | etot = -20.8135452950963 +6000 ekin = 2.18974627635306 | erot = 1.73271671162435 | epot = -24.1096616118305 | etot = -20.1871986238531 +7000 ekin = 2.65472853187395 | erot = 1.73258720631296 | epot = -24.0561118130561 | etot = -19.6687960748691 +8000 ekin = 2.51192327964357 | erot = 2.34132844779952 | epot = -23.9708695663488 | etot = -19.1176178389058 +9000 ekin = 2.24554900802464 | erot = 2.0522939078286 | epot = -23.874757758319 | etot = -19.5769148424658 +10000 ekin = 2.36227360512089 | erot = 1.80185994066737 | epot = -23.7793375260418 | etot = -19.6152039802535 + 10000 0.10498994 -1.5020657 0.015857071 -1.3385665 -8.8930899e-05 +Loop time of 0.291642 on 4 procs for 10000 steps with 16 atoms + +Performance: 29625.313 tau/day, 34288.557 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0035026 | 0.1107 | 0.20674 | 28.3 | 37.96 +Bond | 0.00062203 | 0.0029532 | 0.0049176 | 3.6 | 1.01 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.016712 | 0.018041 | 0.01914 | 0.7 | 6.19 +Output | 5.0306e-05 | 5.424e-05 | 5.579e-05 | 0.0 | 0.02 +Modify | 0.0013862 | 0.020914 | 0.039594 | 11.7 | 7.17 +Other | | 0.139 | | | 47.65 + +Nlocal: 4 ave 8 max 0 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 11 ave 14 max 8 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 46 ave 89 max 0 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 184 +Ave neighs/atom = 11.5 +Ave special neighs/atom = 3.75 +Neighbor list builds = 0 +Dangerous builds = 0 + +#write_restart config.${number}.* +Total wall time: 0:00:00 diff --git a/examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 similarity index 66% rename from examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle rename to examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 index c57ca24963..0650210418 100644 --- a/examples/USER/cgsdk/peg-verlet/log.pegc12e8-angle +++ b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide @@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) - 2 by 1 by 1 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... @@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 -Memory usage per processor = 12.4188 Mbytes +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 15 15 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/sdk, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ----------------- Step 200 ----- CPU = 8.7547 (sec) ---------------- +---------------- Step 200 ----- CPU = 11.2079 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ----------------- Step 400 ----- CPU = 17.7479 (sec) ---------------- +---------------- Step 400 ----- CPU = 22.6137 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ----------------- Step 600 ----- CPU = 26.7299 (sec) ---------------- +---------------- Step 600 ----- CPU = 33.9441 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ----------------- Step 800 ----- CPU = 35.8941 (sec) ---------------- +---------------- Step 800 ----- CPU = 45.4291 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ----------------- Step 1000 ----- CPU = 45.1542 (sec) ---------------- +---------------- Step 1000 ----- CPU = 56.9328 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 +Loop time of 56.9329 on 1 procs for 1000 steps with 40140 atoms -Loop time of 45.1542 on 2 procs for 1000 steps with 40140 atoms -99.5% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 9.567 ns/day 2.509 hours/ns 22.146 timesteps/s +Performance: 7.588 ns/day, 3.163 hours/ns, 17.565 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 38.906 | 38.953 | 39.001 | 0.8 | 86.27 -Bond | 0.90927 | 0.96844 | 1.0276 | 6.0 | 2.14 -Neigh | 3.7623 | 3.7641 | 3.766 | 0.1 | 8.34 -Comm | 0.56974 | 0.67309 | 0.77643 | 12.6 | 1.49 -Output | 0.00067949 | 0.00072169 | 0.00076389 | 0.2 | 0.00 -Modify | 0.52627 | 0.53756 | 0.54885 | 1.5 | 1.19 -Other | | 0.2571 | | | 0.57 +Pair | 50.734 | 50.734 | 50.734 | 0.0 | 89.11 +Bond | 0.94032 | 0.94032 | 0.94032 | 0.0 | 1.65 +Neigh | 4.5195 | 4.5195 | 4.5195 | 0.0 | 7.94 +Comm | 0.15045 | 0.15045 | 0.15045 | 0.0 | 0.26 +Output | 0.00056767 | 0.00056767 | 0.00056767 | 0.0 | 0.00 +Modify | 0.47228 | 0.47228 | 0.47228 | 0.0 | 0.83 +Other | | 0.1154 | | | 0.20 -Nlocal: 20070 ave 20100 max 20040 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 20230.5 ave 20241 max 20220 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 2.84338e+06 ave 2.85198e+06 max 2.83477e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 40140 ave 40140 max 40140 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 25966 ave 25966 max 25966 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5.68676e+06 ave 5.68676e+06 max 5.68676e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5686756 Ave neighs/atom = 141.673 @@ -113,3 +124,4 @@ Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart +Total wall time: 0:00:57 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 new file mode 100644 index 0000000000..bebab0e390 --- /dev/null +++ b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 @@ -0,0 +1,127 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +dimension 3 +atom_style angle + +# enforce that in z-direction there is only one +# processor (could be two) for optimal performance +processors * * 1 + +# read topology and force field +pair_style lj/sdk 15.0 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.pegc12e8.gz + orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 40140 atoms + reading velocities ... + 40140 velocities + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 13284 bonds + reading angles ... + 12177 angles + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of special neighbors + +neighbor 3.0 bin +neigh_modify delay 5 + +timestep 5.0 +#dump 1 all xtc 200 pegc12e8-1.xtc +#dump_modify 1 unwrap yes +#dump 2 all dcd 200 pegc12e8-1.dcd unwrap +#dump_modify 2 unwrap yes + +velocity all create 303.0 46659 mom yes rot yes dist gaussian + +fix 1 all nvt temp 303.0 303.0 100.0 + +thermo_style multi +thermo 200 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 15 15 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/sdk, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 +PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 +E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 +---------------- Step 200 ----- CPU = 3.0597 (sec) ---------------- +TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 +PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 +E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 +---------------- Step 400 ----- CPU = 6.2514 (sec) ---------------- +TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 +PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 +E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 +---------------- Step 600 ----- CPU = 9.4073 (sec) ---------------- +TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 +PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 +E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 +---------------- Step 800 ----- CPU = 12.6096 (sec) ---------------- +TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 +PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 +E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 +---------------- Step 1000 ----- CPU = 15.9134 (sec) ---------------- +TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 +PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 +E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 +Loop time of 15.9135 on 4 procs for 1000 steps with 40140 atoms + +Performance: 27.147 ns/day, 0.884 hours/ns, 62.840 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.325 | 13.6 | 13.755 | 4.7 | 85.46 +Bond | 0.2432 | 0.25007 | 0.25671 | 1.0 | 1.57 +Neigh | 1.2394 | 1.2399 | 1.2402 | 0.0 | 7.79 +Comm | 0.41026 | 0.5737 | 0.85471 | 23.4 | 3.61 +Output | 0.00025368 | 0.0004195 | 0.00091338 | 0.0 | 0.00 +Modify | 0.17159 | 0.17316 | 0.17459 | 0.3 | 1.09 +Other | | 0.0768 | | | 0.48 + +Nlocal: 10035 ave 10084 max 9971 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 14548.8 ave 14610 max 14509 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 1.42169e+06 ave 1.42961e+06 max 1.40922e+06 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 5686756 +Ave neighs/atom = 141.673 +Ave special neighs/atom = 1.26861 +Neighbor list builds = 38 +Dangerous builds = 0 +#write_restart pegc12e8-1.restart + +Total wall time: 0:00:16 diff --git a/examples/USER/cgsdk/peg-verlet/log.pegc12e8 b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 similarity index 66% rename from examples/USER/cgsdk/peg-verlet/log.pegc12e8 rename to examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 index 13f7a0cf18..3c85fcfb54 100644 --- a/examples/USER/cgsdk/peg-verlet/log.pegc12e8 +++ b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide @@ -19,7 +18,7 @@ special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) - 2 by 1 by 1 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... @@ -52,59 +51,71 @@ fix 1 all nvt temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 -Memory usage per processor = 12.4188 Mbytes +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 15 15 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/sdk, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 ----------------- Step 200 ----- CPU = 8.6552 (sec) ---------------- +---------------- Step 200 ----- CPU = 11.2074 (sec) ---------------- TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 ----------------- Step 400 ----- CPU = 17.5807 (sec) ---------------- +---------------- Step 400 ----- CPU = 22.6113 (sec) ---------------- TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 ----------------- Step 600 ----- CPU = 28.1043 (sec) ---------------- +---------------- Step 600 ----- CPU = 34.0551 (sec) ---------------- TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 ----------------- Step 800 ----- CPU = 40.5132 (sec) ---------------- +---------------- Step 800 ----- CPU = 45.5316 (sec) ---------------- TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 ----------------- Step 1000 ----- CPU = 52.8166 (sec) ---------------- +---------------- Step 1000 ----- CPU = 56.9111 (sec) ---------------- TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 +Loop time of 56.9112 on 1 procs for 1000 steps with 40140 atoms -Loop time of 52.8166 on 2 procs for 1000 steps with 40140 atoms -99.6% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 8.179 ns/day 2.934 hours/ns 18.933 timesteps/s +Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 45.657 | 45.84 | 46.022 | 2.7 | 86.79 -Bond | 0.98427 | 0.99283 | 1.0014 | 0.9 | 1.88 -Neigh | 4.4454 | 4.4458 | 4.4462 | 0.0 | 8.42 -Comm | 0.49872 | 0.6719 | 0.84508 | 21.1 | 1.27 -Output | 0.00076818 | 0.00083113 | 0.00089407 | 0.2 | 0.00 -Modify | 0.59218 | 0.59264 | 0.5931 | 0.1 | 1.12 -Other | | 0.2731 | | | 0.52 +Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22 +Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55 +Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94 +Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26 +Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00 +Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83 +Other | | 0.1127 | | | 0.20 -Nlocal: 20070 ave 20109 max 20031 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 20234 ave 20281 max 20187 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 2.84584e+06 ave 2.85375e+06 max 2.83793e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 40140 ave 40140 max 40140 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 25968 ave 25968 max 25968 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 5691680 Ave neighs/atom = 141.796 @@ -113,3 +124,4 @@ Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart +Total wall time: 0:00:57 diff --git a/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 new file mode 100644 index 0000000000..b214e0d6bc --- /dev/null +++ b/examples/USER/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 @@ -0,0 +1,127 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +dimension 3 +atom_style angle + +# enforce that in z-direction there is only one +# processor (could be two) for optimal performance +processors * * 1 + +# read topology and force field +pair_style lj/sdk 15.0 +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.pegc12e8.gz + orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 40140 atoms + reading velocities ... + 40140 velocities + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 13284 bonds + reading angles ... + 12177 angles + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of special neighbors + +neighbor 3.0 bin +neigh_modify delay 5 + +timestep 5.0 +#dump 1 all xtc 200 pegc12e8-1.xtc +#dump_modify 1 unwrap yes +#dump 2 all dcd 200 pegc12e8-1.dcd unwrap +#dump_modify 2 unwrap yes + +velocity all create 303.0 46659 mom yes rot yes dist gaussian + +fix 1 all nvt temp 303.0 303.0 100.0 + +thermo_style multi +thermo 200 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 18 + ghost atom cutoff = 18 + binsize = 9, bins = 15 15 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/sdk, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.87 | 15.87 | 15.87 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 +PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 +E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 +---------------- Step 200 ----- CPU = 3.0107 (sec) ---------------- +TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 +PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 +E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 +---------------- Step 400 ----- CPU = 6.1324 (sec) ---------------- +TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 +PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 +E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 +---------------- Step 600 ----- CPU = 9.3443 (sec) ---------------- +TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 +PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 +E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 +---------------- Step 800 ----- CPU = 12.5388 (sec) ---------------- +TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 +PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 +E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 +---------------- Step 1000 ----- CPU = 15.7416 (sec) ---------------- +TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 +PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 +E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 +E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 +Loop time of 15.7417 on 4 procs for 1000 steps with 40140 atoms + +Performance: 27.443 ns/day, 0.875 hours/ns, 63.525 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 13.591 | 13.612 | 13.626 | 0.4 | 86.47 +Bond | 0.22508 | 0.23213 | 0.23791 | 1.0 | 1.47 +Neigh | 1.2257 | 1.2261 | 1.2266 | 0.0 | 7.79 +Comm | 0.39628 | 0.41769 | 0.44666 | 2.9 | 2.65 +Output | 0.000247 | 0.00041109 | 0.00090098 | 0.0 | 0.00 +Modify | 0.17674 | 0.17803 | 0.17952 | 0.2 | 1.13 +Other | | 0.07576 | | | 0.48 + +Nlocal: 10035 ave 10098 max 10004 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Nghost: 14546.5 ave 14564 max 14503 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Neighs: 1.42292e+06 ave 1.43408e+06 max 1.41615e+06 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 5691680 +Ave neighs/atom = 141.796 +Ave special neighs/atom = 1.26861 +Neighbor list builds = 38 +Dangerous builds = 0 +#write_restart pegc12e8-1.restart + +Total wall time: 0:00:15 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 new file mode 100644 index 0000000000..65ad480bdd --- /dev/null +++ b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 @@ -0,0 +1,145 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# coarse grained SDS surfactant monolayer + +units real +dimension 3 +atom_style full +processors * * 1 + +pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.sds.gz + orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 31280 atoms + reading velocities ... + 31280 velocities + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4096 bonds + reading angles ... + 3072 angles + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of special neighbors + +pair_coeff 1 4 coul/long # SO4 SOD +pair_coeff 4 4 coul/long # SOD SOD +pair_coeff 1 1 lj/sdk lj9_6 0.7000 4.3210 # SO4 SO4 +pair_coeff 1 2 lj/sdk lj9_6 0.3830 4.4135 # SO4 CM +pair_coeff 1 3 lj/sdk lj9_6 0.4050 4.4530 # SO4 CT +pair_coeff 1 4 lj/sdk lj12_4 1.1000 4.1000 # SO4 SOD +pair_coeff 1 5 lj/sdk lj12_4 1.1000 4.1000 # SO4 W +pair_coeff 2 2 lj/sdk lj9_6 0.4200 4.5060 # CM CM +pair_coeff 2 3 lj/sdk lj9_6 0.4440 4.5455 # CT CM +pair_coeff 2 4 lj/sdk lj12_4 0.3400 4.4385 # SOD CM +pair_coeff 2 5 lj/sdk lj12_4 0.3400 4.4385 # W CM +pair_coeff 3 3 lj/sdk lj9_6 0.4690 4.5850 # CT CT +pair_coeff 3 4 lj/sdk lj12_4 0.3600 4.4780 # SOD CT +pair_coeff 3 5 lj/sdk lj12_4 0.3600 4.4780 # W CT +pair_coeff 4 4 lj/sdk lj12_4 0.3500 4.3710 # SOD SOD +pair_coeff 4 5 lj/sdk lj12_4 0.8950 4.3710 # SOD W +pair_coeff 5 5 lj/sdk lj12_4 0.8950 4.3710 # W W + + +group charged type 1 4 +2048 atoms in group charged +atom_modify first charged + +kspace_style pppm/cg 0.00001 +kspace_modify order 3 + +comm_modify mode multi +neighbor 2.0 multi +neigh_modify delay 4 every 2 check yes + +timestep 10.0 + +fix 1 all nvt temp 310.0 310.0 100.0 + +thermo 10 + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.0416781 + grid = 8 4 12 + stencil order = 3 + estimated absolute RMS force accuracy = 0.00248777 + estimated relative force accuracy = 7.49185e-06 + using double precision FFTs + 3d grid and FFT values/proc = 1155 384 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 28.5 + ghost atom cutoff = 28.5 + binsize = 8.5, bins = 27 14 48 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/sdk, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/3d/newton + bin: standard + (2) pair coul/long, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + PPPM/cg optimization cutoff: 1e-05 + Total charged atoms: 6.5% + Min/max charged atoms/proc: 6.5% 6.5% +Per MPI rank memory allocation (min/avg/max) = 35.49 | 35.49 | 35.49 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516 + 10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262 + 20 310.33025 -249325.09 2543.0138 -217847.89 -30.069751 + 30 308.24273 -249331.54 2604.3227 -217987.66 -28.033129 + 40 309.41339 -249363.5 2560.6727 -217954.13 -25.802838 + 50 309.16857 -249071.94 2571.9117 -217674.15 -17.946457 + 60 312.67237 -249288.77 2621.0185 -217515.19 -25.723545 + 70 310.13623 -249262.32 2595.874 -217750.35 -26.276067 + 80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924 + 90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575 + 100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823 +Loop time of 9.61984 on 1 procs for 100 steps with 31280 atoms + +Performance: 8.981 ns/day, 2.672 hours/ns, 10.395 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.2928 | 7.2928 | 7.2928 | 0.0 | 75.81 +Bond | 0.036198 | 0.036198 | 0.036198 | 0.0 | 0.38 +Kspace | 0.053125 | 0.053125 | 0.053125 | 0.0 | 0.55 +Neigh | 2.117 | 2.117 | 2.117 | 0.0 | 22.01 +Comm | 0.029731 | 0.029731 | 0.029731 | 0.0 | 0.31 +Output | 0.0014369 | 0.0014369 | 0.0014369 | 0.0 | 0.01 +Modify | 0.079014 | 0.079014 | 0.079014 | 0.0 | 0.82 +Other | | 0.01051 | | | 0.11 + +Nlocal: 31280 ave 31280 max 31280 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 16629 ave 16629 max 16629 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3.40168e+06 ave 3.40168e+06 max 3.40168e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3401676 +Ave neighs/atom = 108.749 +Ave special neighs/atom = 0.458312 +Neighbor list builds = 10 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/USER/cgsdk/sds-monolayer/log.sds-hybrid b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 similarity index 72% rename from examples/USER/cgsdk/sds-monolayer/log.sds-hybrid rename to examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 index 1a8e3b65f3..247f553ecc 100644 --- a/examples/USER/cgsdk/sds-monolayer/log.sds-hybrid +++ b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # coarse grained SDS surfactant monolayer @@ -58,7 +57,7 @@ atom_modify first charged kspace_style pppm/cg 0.00001 kspace_modify order 3 -communicate multi +comm_modify mode multi neighbor 2.0 multi neigh_modify delay 4 every 2 check yes @@ -70,6 +69,7 @@ thermo 10 run 100 PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.0416781 grid = 8 4 12 stencil order = 3 @@ -77,10 +77,27 @@ PPPM initialization ... estimated relative force accuracy = 7.49185e-06 using double precision FFTs 3d grid and FFT values/proc = 525 96 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 28.5 + ghost atom cutoff = 28.5 + binsize = 8.5, bins = 27 14 48 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/sdk, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/3d/newton + bin: standard + (2) pair coul/long, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none PPPM/cg optimization cutoff: 1e-05 Total charged atoms: 6.5% Min/max charged atoms/proc: 6.4% 6.7% -Memory usage per processor = 7.66668 Mbytes +Per MPI rank memory allocation (min/avg/max) = 17.48 | 17.48 | 17.48 Mbytes Step Temp E_pair E_mol TotEng Press 0 310.0934 -249339.72 2566.2036 -217861.41 -25.664516 10 310.88051 -249369.1 2549.1166 -217834.49 -29.095262 @@ -93,22 +110,22 @@ Step Temp E_pair E_mol TotEng Press 80 310.60448 -249415.99 2596.6752 -217859.56 -27.942924 90 309.63209 -249403.14 2606.3186 -217927.73 -24.456575 100 309.40793 -249341.62 2599.6402 -217893.79 -22.554823 +Loop time of 2.54454 on 4 procs for 100 steps with 31280 atoms -Loop time of 4.07239 on 4 procs for 100 steps with 31280 atoms -98.6% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 21.216 ns/day 1.131 hours/ns 24.556 timesteps/s +Performance: 33.955 ns/day, 0.707 hours/ns, 39.300 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.082 | 3.0928 | 3.1091 | 0.6 | 75.95 -Bond | 0.021077 | 0.021421 | 0.021823 | 0.2 | 0.53 -Kspace | 0.042646 | 0.058859 | 0.069797 | 4.1 | 1.45 -Neigh | 0.79689 | 0.79696 | 0.79711 | 0.0 | 19.57 -Comm | 0.048668 | 0.049552 | 0.050446 | 0.3 | 1.22 -Output | 0.00072145 | 0.00095147 | 0.0016341 | 1.3 | 0.02 -Modify | 0.034767 | 0.035175 | 0.035714 | 0.2 | 0.86 -Other | | 0.01665 | | | 0.41 +Pair | 1.8639 | 1.8913 | 1.9283 | 1.8 | 74.33 +Bond | 0.0092797 | 0.0094567 | 0.0095828 | 0.1 | 0.37 +Kspace | 0.018389 | 0.056616 | 0.084424 | 10.7 | 2.23 +Neigh | 0.53553 | 0.53569 | 0.53605 | 0.0 | 21.05 +Comm | 0.023819 | 0.02433 | 0.02506 | 0.3 | 0.96 +Output | 0.00058866 | 0.00084978 | 0.0016243 | 0.0 | 0.03 +Modify | 0.021841 | 0.022059 | 0.022308 | 0.1 | 0.87 +Other | | 0.004233 | | | 0.17 Nlocal: 7820 ave 7866 max 7774 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -125,3 +142,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation +Total wall time: 0:00:02 diff --git a/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 new file mode 100644 index 0000000000..ab0a9a33e9 --- /dev/null +++ b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 @@ -0,0 +1,129 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# coarse grained SDS surfactant monolayer + +units real +dimension 3 +atom_style full +processors * * 1 + +pair_style lj/sdk/coul/long 15.0 +bond_style harmonic +angle_style sdk +special_bonds lj/coul 0.0 0.0 1.0 + +read_data data.sds.gz + orthogonal box = (-27.713 -27.713 -200) to (193.991 83.139 200) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 31280 atoms + reading velocities ... + 31280 velocities + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 4096 bonds + reading angles ... + 3072 angles + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 lj9_6 0.7000 4.3210 # SO4 SO4 +pair_coeff 1 2 lj9_6 0.3830 4.4135 # SO4 CM +pair_coeff 1 3 lj9_6 0.4050 4.4530 # SO4 CT +pair_coeff 1 4 lj12_4 1.1000 4.1000 # SO4 SOD +pair_coeff 1 5 lj12_4 1.1000 4.1000 # SO4 W +pair_coeff 2 2 lj9_6 0.4200 4.5060 # CM CM +pair_coeff 2 3 lj9_6 0.4440 4.5455 # CT CM +pair_coeff 2 4 lj12_4 0.3400 4.4385 # SOD CM +pair_coeff 2 5 lj12_4 0.3400 4.4385 # W CM +pair_coeff 3 3 lj9_6 0.4690 4.5850 # CT CT +pair_coeff 3 4 lj12_4 0.3600 4.4780 # SOD CT +pair_coeff 3 5 lj12_4 0.3600 4.4780 # W CT +pair_coeff 4 4 lj12_4 0.3500 4.3710 # SOD SOD +pair_coeff 4 5 lj12_4 0.8950 4.3710 # SOD W +pair_coeff 5 5 lj12_4 0.8950 4.3710 # W W + +kspace_style pppm/cg 0.00001 +kspace_modify order 3 + +neighbor 2.0 bin +neigh_modify delay 4 every 2 check yes + +timestep 10.0 + +fix 1 all nvt temp 310.0 310.0 100.0 + +thermo 10 + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.0789325 + grid = 15 8 25 + stencil order = 3 + estimated absolute RMS force accuracy = 0.00275556 + estimated relative force accuracy = 8.29828e-06 + using double precision FFTs + 3d grid and FFT values/proc = 5544 3000 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 27 14 48 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/sdk/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + PPPM/cg optimization cutoff: 1e-05 + Total charged atoms: 6.5% + Min/max charged atoms/proc: 6.5% 6.5% +Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393 + 10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512 + 20 310.29287 -247017.8 2542.4491 -215544.65 -19.148631 + 30 308.13371 -247024.82 2602.1061 -215693.32 -17.390902 + 40 309.40426 -247058.41 2558.7402 -215651.82 -15.445066 + 50 309.11317 -246753.92 2570.8603 -215362.36 -7.4232007 + 60 312.52974 -246964.73 2618.8108 -215206.66 -15.23965 + 70 310.11675 -246941.68 2591.8668 -215435.53 -16.153691 + 80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368 + 90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764 + 100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624 +Loop time of 9.23618 on 1 procs for 100 steps with 31280 atoms + +Performance: 9.355 ns/day, 2.566 hours/ns, 10.827 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7363 | 7.7363 | 7.7363 | 0.0 | 83.76 +Bond | 0.032901 | 0.032901 | 0.032901 | 0.0 | 0.36 +Kspace | 0.078907 | 0.078907 | 0.078907 | 0.0 | 0.85 +Neigh | 1.2706 | 1.2706 | 1.2706 | 0.0 | 13.76 +Comm | 0.026005 | 0.026005 | 0.026005 | 0.0 | 0.28 +Output | 0.0014131 | 0.0014131 | 0.0014131 | 0.0 | 0.02 +Modify | 0.079446 | 0.079446 | 0.079446 | 0.0 | 0.86 +Other | | 0.01055 | | | 0.11 + +Nlocal: 31280 ave 31280 max 31280 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 15812 ave 15812 max 15812 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3.3521e+06 ave 3.3521e+06 max 3.3521e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3352103 +Ave neighs/atom = 107.164 +Ave special neighs/atom = 0.458312 +Neighbor list builds = 10 +Dangerous builds = 0 +Total wall time: 0:00:09 diff --git a/examples/USER/cgsdk/sds-monolayer/log.sds-regular b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 similarity index 72% rename from examples/USER/cgsdk/sds-monolayer/log.sds-regular rename to examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 index 7ab9d1a760..934b0ae0f2 100644 --- a/examples/USER/cgsdk/sds-monolayer/log.sds-regular +++ b/examples/USER/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # coarse grained SDS surfactant monolayer @@ -62,6 +61,7 @@ thermo 10 run 100 PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.0789325 grid = 15 8 25 stencil order = 3 @@ -69,10 +69,22 @@ PPPM initialization ... estimated relative force accuracy = 8.29828e-06 using double precision FFTs 3d grid and FFT values/proc = 2156 840 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 17 + ghost atom cutoff = 17 + binsize = 8.5, bins = 27 14 48 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/sdk/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard PPPM/cg optimization cutoff: 1e-05 Total charged atoms: 6.5% Min/max charged atoms/proc: 6.4% 6.7% -Memory usage per processor = 8.05923 Mbytes +Per MPI rank memory allocation (min/avg/max) = 17.32 | 17.32 | 17.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 310.0934 -247030.21 2566.2036 -215551.9 -14.547393 10 310.89138 -247061.61 2549.4854 -215525.62 -18.043512 @@ -85,22 +97,22 @@ Step Temp E_pair E_mol TotEng Press 80 310.48262 -247090.02 2595.0493 -215546.58 -18.080368 90 309.60017 -247067.1 2604.6545 -215596.33 -14.583764 100 309.7356 -247004.05 2604.8729 -215520.43 -12.78624 +Loop time of 2.45408 on 4 procs for 100 steps with 31280 atoms -Loop time of 3.44972 on 4 procs for 100 steps with 31280 atoms -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 25.046 ns/day 0.958 hours/ns 28.988 timesteps/s +Performance: 35.207 ns/day, 0.682 hours/ns, 40.748 timesteps/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.7883 | 2.817 | 2.8415 | 1.1 | 81.66 -Bond | 0.017868 | 0.018973 | 0.020636 | 0.7 | 0.55 -Kspace | 0.063881 | 0.088012 | 0.11571 | 6.2 | 2.55 -Neigh | 0.42765 | 0.42828 | 0.42882 | 0.1 | 12.41 -Comm | 0.043887 | 0.044575 | 0.045079 | 0.2 | 1.29 -Output | 0.00072694 | 0.00096422 | 0.0016718 | 1.3 | 0.03 -Modify | 0.035513 | 0.035955 | 0.036887 | 0.3 | 1.04 -Other | | 0.01597 | | | 0.46 +Pair | 2.0065 | 2.0143 | 2.0326 | 0.8 | 82.08 +Bond | 0.0084255 | 0.0086145 | 0.0088007 | 0.1 | 0.35 +Kspace | 0.033373 | 0.052041 | 0.060933 | 4.8 | 2.12 +Neigh | 0.32741 | 0.32748 | 0.32754 | 0.0 | 13.34 +Comm | 0.022403 | 0.023025 | 0.023735 | 0.4 | 0.94 +Output | 0.00060058 | 0.00086623 | 0.0016549 | 0.0 | 0.04 +Modify | 0.022533 | 0.022723 | 0.022876 | 0.1 | 0.93 +Other | | 0.005038 | | | 0.21 Nlocal: 7820 ave 7866 max 7775 min Histogram: 1 1 0 0 0 0 0 1 0 1 @@ -114,3 +126,4 @@ Ave neighs/atom = 107.164 Ave special neighs/atom = 0.458312 Neighbor list builds = 10 Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/colvars/log.peptide-colvars b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 similarity index 52% rename from examples/USER/colvars/log.peptide-colvars rename to examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 index 6fb85fddc0..3b5203ba6f 100644 --- a/examples/USER/colvars/log.peptide-colvars +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide @@ -15,7 +14,7 @@ kspace_style pppm 0.0001 read_data data.peptide orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 2004 atoms reading velocities ... @@ -78,134 +77,179 @@ thermo 10 run 100 PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0228209 estimated relative force accuracy = 6.87243e-05 using double precision FFTs - 3d grid and FFT values/proc = 6776 1800 + 3d grid and FFT values/proc = 10648 3375 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2013-10-22. -colvars: # indexFile = "" [default] -colvars: # analysis = off [default] +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. +colvars: Using LAMMPS interface, version 2018-08-29. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "peptide.colvars": +colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out.colvars.state". -colvars: Writing to colvar trajectory file "out.colvars.traj". +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = one +colvars: # name = "one" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = two +colvars: # name = "two" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot +colvars: # name = "h_pot" colvars: # colvars = { one, two } colvars: # outputEnergy = off [default] -colvars: # forceConstant = 100 +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 10, 10 } colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # outputAccumulatedWork = off [default] +colvars: # forceConstant = 100 +colvars: # targetForceConstant = -1 [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. +colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "out.colvars.state". +colvars: Writing to colvar trajectory file "out.colvars.traj". colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. +colvars: Performing analysis. SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 @@ -215,51 +259,52 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 -Memory usage per processor = 10.4104 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 - 10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344 - 20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706 - 30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914 - 40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396 - 50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.818 55.459511 0.20679816 - 60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527 - 70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.62715 11.433633 - 80 267.51476 -5206.4041 -6282.6428 1076.2386 -6456.6352 31.611841 6.3553235 - 90 278.15512 -5245.383 -6364.4288 1119.0458 -6499.8036 28.849902 0.36938817 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97185e-05 - 6 0.996996 1.00569e-05 - 8 1.08 6.02346e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 + 4 1.11098 8.97155e-05 + 6 0.996996 1.00568e-05 + 8 1.08 6.02345e-06 + 10 1.111 1.84253e-05 + 12 1.08 7.2713e-06 14 0.959996 0 - 18 0.957198 3.36078e-05 - 31 104.52 0.00306008 - 100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866 + 18 0.957198 3.36079e-05 + 31 104.52 0.0030599 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +colvars: Saving collective variables state to "out.colvars.state". +Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms -Loop time of 1.04673 on 2 procs for 100 steps with 2004 atoms -99.3% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 16.509 ns/day 1.454 hours/ns 95.536 timesteps/s +Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.76537 | 0.76832 | 0.77127 | 0.3 | 73.40 -Bond | 0.0024452 | 0.0025067 | 0.0025682 | 0.1 | 0.24 -Kspace | 0.088877 | 0.092861 | 0.096845 | 1.3 | 8.87 -Neigh | 0.13657 | 0.13657 | 0.13658 | 0.0 | 13.05 -Comm | 0.0172 | 0.018169 | 0.019137 | 0.7 | 1.74 -Output | 0.0002296 | 0.00031686 | 0.00040412 | 0.5 | 0.03 -Modify | 0.025518 | 0.025554 | 0.025591 | 0.0 | 2.44 -Other | | 0.002431 | | | 0.23 +Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79 +Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14 +Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99 +Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19 +Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63 +Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01 +Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17 +Other | | 0.001615 | | | 0.07 -Nlocal: 1002 ave 1013 max 991 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 8629.5 ave 8641 max 8618 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 354118 ave 356534 max 351703 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11124 ave 11124 max 11124 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708237 ave 708237 max 708237 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 708237 Ave neighs/atom = 353.412 @@ -269,279 +314,316 @@ Dangerous builds = 2 run 100 PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0228209 estimated relative force accuracy = 6.87243e-05 using double precision FFTs - 3d grid and FFT values/proc = 6776 1800 + 3d grid and FFT values/proc = 10648 3375 colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97185e-05 - 6 0.996996 1.00569e-05 - 8 1.08 6.02346e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 + 4 1.11098 8.97155e-05 + 6 0.996996 1.00568e-05 + 8 1.08 6.02345e-06 + 10 1.111 1.84253e-05 + 12 1.08 7.2713e-06 14 0.959996 0 - 18 0.957198 3.36078e-05 - 31 104.52 0.00306008 -Memory usage per processor = 10.4104 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 100 260.10505 -5292.689 -6339.1177 1046.4286 -6471.6693 25.361881 0.21986866 - 110 266.26279 -5341.2085 -6412.4103 1071.2018 -6552.7566 33.572973 1.9229795 - 120 262.66439 -5386.2495 -6442.9746 1056.7251 -6587.5499 29.859549 2.712489 - 130 252.83437 -5422.5446 -6439.7226 1017.1779 -6580.4751 25.979056 1.2031649 - 140 253.85101 -5452.1904 -6473.4584 1021.268 -6609.4883 26.071526 0.30586448 - 150 261.31821 -5490.4808 -6541.7901 1051.3093 -6646.615 16.258546 6.904992 - 160 255.73714 -5521.6048 -6550.4609 1028.8561 -6658.1531 19.717543 12.339834 - 170 253.42881 -5540.0985 -6559.668 1019.5695 -6656.6862 23.293616 10.289885 - 180 248.51049 -5550.3254 -6550.1079 999.78252 -6661.4178 26.200082 3.4339077 - 190 250.80375 -5555.2616 -6564.2702 1009.0086 -6666.1496 25.536628 3.3495235 + 18 0.957198 3.36079e-05 + 31 104.52 0.0030599 +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 + 110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657 + 120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812 + 130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592 + 140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517 + 150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008 + 160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679 + 170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217 + 180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038 + 190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288 SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.81287e-06 - 6 0.997 7.79626e-07 - 8 1.08 1.08933e-06 - 10 1.111 2.96498e-07 - 12 1.08 4.69169e-07 + 4 1.111 1.81266e-06 + 6 0.997 7.79424e-07 + 8 1.08 1.08903e-06 + 10 1.111 2.96503e-07 + 12 1.08 4.69038e-07 14 0.960001 0 - 18 0.957201 3.76617e-06 - 31 104.52 0.000411076 - 200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891 + 18 0.957201 3.76471e-06 + 31 104.52 0.000411055 + 200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574 +colvars: Saving collective variables state to "out.colvars.state". +Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms -Loop time of 1.00434 on 2 procs for 100 steps with 2004 atoms -99.1% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 17.205 ns/day 1.395 hours/ns 99.568 timesteps/s +Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.78001 | 0.78091 | 0.78181 | 0.1 | 77.75 -Bond | 0.0025158 | 0.0025688 | 0.0026219 | 0.1 | 0.26 -Kspace | 0.093375 | 0.094821 | 0.096266 | 0.5 | 9.44 -Neigh | 0.080238 | 0.08025 | 0.080261 | 0.0 | 7.99 -Comm | 0.01671 | 0.017204 | 0.017699 | 0.4 | 1.71 -Output | 0.0002296 | 0.00031531 | 0.00040102 | 0.5 | 0.03 -Modify | 0.025788 | 0.025804 | 0.02582 | 0.0 | 2.57 -Other | | 0.002469 | | | 0.25 +Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58 +Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16 +Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53 +Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81 +Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59 +Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01 +Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23 +Other | | 0.001596 | | | 0.08 -Nlocal: 1002 ave 1014 max 990 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 8654 ave 8667 max 8641 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 354044 ave 355332 max 352756 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11159 ave 11159 max 11159 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708083 ave 708083 max 708083 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 708088 -Ave neighs/atom = 353.337 +Total # of neighbors = 708083 +Ave neighs/atom = 353.335 Ave special neighs/atom = 2.34032 Neighbor list builds = 7 Dangerous builds = 0 fix 2 all colvars peptide.colvars input out.colvars.state output out2 -colvars: Saving collective variables state to "out.colvars.state". +colvars: Resetting the Collective Variables module. run 100 PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0228209 estimated relative force accuracy = 6.87243e-05 using double precision FFTs - 3d grid and FFT values/proc = 6776 1800 + 3d grid and FFT values/proc = 10648 3375 colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2013-10-22. -colvars: # indexFile = "" [default] -colvars: # analysis = off [default] +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. +colvars: Using LAMMPS interface, version 2018-08-29. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "peptide.colvars": +colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out2.colvars.state". -colvars: Writing to colvar trajectory file "out2.colvars.traj". +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = one +colvars: # name = "one" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = two +colvars: # name = "two" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 2 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot +colvars: # name = "h_pot" colvars: # colvars = { one, two } colvars: # outputEnergy = off [default] -colvars: # forceConstant = 100 +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 10, 10 } colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # outputAccumulatedWork = off [default] +colvars: # forceConstant = 100 +colvars: # targetForceConstant = -1 [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. +colvars: ---------------------------------------------------------------------- colvars: Restarting from file "out.colvars.state". colvars: Restarting collective variable "one" from value: 10.0128 colvars: Restarting collective variable "two" from value: 9.62236 -colvars: Restarting harmonic bias "h_pot". colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -colvars: Initializing step number as firstTimestep. +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "out2.colvars.state". +colvars: Writing to colvar trajectory file "out2.colvars.traj". +colvars: Setting initial step number from LAMMPS: 200 colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. +colvars: Performing analysis. SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.81287e-06 - 6 0.997 7.79626e-07 - 8 1.08 1.08933e-06 - 10 1.111 2.96498e-07 - 12 1.08 4.69169e-07 + 4 1.111 1.81266e-06 + 6 0.997 7.79424e-07 + 8 1.08 1.08903e-06 + 10 1.111 2.96503e-07 + 12 1.08 4.69038e-07 14 0.960001 0 - 18 0.957201 3.76617e-06 - 31 104.52 0.000411076 -Memory usage per processor = 10.4104 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 200 251.50646 -5557.4204 -6569.256 1011.8356 -6674.0889 24.805155 7.13891 - 210 253.15173 -5538.5647 -6557.0194 1018.4547 -6672.044 37.671405 0.61299805 - 220 245.19832 -5522.5253 -6508.9826 986.45735 -6628.2043 36.656213 0.04862311 - 230 258.65093 -5495.7204 -6536.2989 1040.5785 -6658.0891 34.855426 0.22044707 - 240 260.80348 -5469.8527 -6519.0912 1049.2385 -6624.1806 31.576284 3.7570152 - 250 269.06517 -5438.3941 -6520.8701 1082.4761 -6616.3835 25.443998 8.6642401 - 260 266.10873 -5397.3229 -6467.905 1070.582 -6580.6583 26.873845 8.3331291 - 270 272.81399 -5350.8435 -6448.4015 1097.5579 -6563.7941 23.11303 10.972811 - 280 279.52614 -5307.9857 -6432.5473 1124.5616 -6557.7474 33.640052 8.5474491 - 290 286.8015 -5260.87 -6414.7011 1153.8311 -6515.4961 28.571844 5.9093384 + 18 0.957201 3.76471e-06 + 31 104.52 0.000411055 +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574 + 210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496 + 220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338 + 230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547 + 240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816 + 250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014 + 260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097 + 270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131 + 280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492 + 290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133 SHAKE stats (type/ave/delta) on step 300 - 4 1.111 1.79747e-05 - 6 0.997005 1.02624e-05 - 8 1.08 1.84986e-05 - 10 1.111 9.9852e-06 - 12 1.08 8.8315e-06 + 4 1.111 1.79792e-05 + 6 0.997005 1.02512e-05 + 8 1.08 1.85102e-05 + 10 1.111 9.98839e-06 + 12 1.08 8.84111e-06 14 0.960008 0 - 18 0.957203 1.84856e-05 - 31 104.52 0.00169095 - 300 291.51723 -5216.3366 -6389.1396 1172.803 -6503.1168 27.877108 2.2481775 + 18 0.957203 1.8445e-05 + 31 104.52 0.00168383 + 300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459 +colvars: Saving collective variables state to "out2.colvars.state". +Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms -Loop time of 1.0092 on 2 procs for 100 steps with 2004 atoms -99.1% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 17.123 ns/day 1.402 hours/ns 99.089 timesteps/s +Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.77015 | 0.77511 | 0.78007 | 0.6 | 76.80 -Bond | 0.0022984 | 0.0024998 | 0.0027013 | 0.4 | 0.25 -Kspace | 0.088884 | 0.093076 | 0.097267 | 1.4 | 9.22 -Neigh | 0.092871 | 0.092888 | 0.092905 | 0.0 | 9.20 -Comm | 0.016476 | 0.017 | 0.017524 | 0.4 | 1.68 -Output | 0.00022602 | 0.00031459 | 0.00040317 | 0.5 | 0.03 -Modify | 0.025814 | 0.025818 | 0.025823 | 0.0 | 2.56 -Other | | 0.002488 | | | 0.25 +Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46 +Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15 +Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36 +Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12 +Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59 +Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01 +Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22 +Other | | 0.001731 | | | 0.08 -Nlocal: 1002 ave 1024 max 980 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 8717.5 ave 8755 max 8680 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 354073 ave 358151 max 349995 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11296 ave 11296 max 11296 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708152 ave 708152 max 708152 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 708146 -Ave neighs/atom = 353.366 +Total # of neighbors = 708152 +Ave neighs/atom = 353.369 Ave special neighs/atom = 2.34032 Neighbor list builds = 8 Dangerous builds = 0 -colvars: Saving collective variables state to "out2.colvars.state". +colvars: Resetting the Collective Variables module. Please see the log.cite file for references relevant to this simulation +Total wall time: 0:00:06 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 new file mode 100644 index 0000000000..586ebbc5c5 --- /dev/null +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars.g++.4 @@ -0,0 +1,629 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +shell "rm -f out*.colvars.*" +fix 2 all colvars peptide.colvars +fix 2a ref setforce 0.0 0.0 0.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_2 +thermo 10 + + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +colvars: Creating proxy instance +colvars: ---------------------------------------------------------------------- +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. +colvars: Using LAMMPS interface, version 2018-08-29. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "peptide.colvars": +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 1000 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 1 [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "two" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 1 [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 2 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: # name = "h_pot" +colvars: # colvars = { one, two } +colvars: # outputEnergy = off [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { 10, 10 } +colvars: # targetCenters = { 10, 10 } [default] +colvars: # outputCenters = off [default] +colvars: # forceConstant = 100 +colvars: # targetForceConstant = -1 [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "out.colvars.state". +colvars: Writing to colvar trajectory file "out.colvars.traj". +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. +colvars: Performing analysis. +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta) on step 100 + 4 1.11098 8.97155e-05 + 6 0.996996 1.00568e-05 + 8 1.08 6.02345e-06 + 10 1.111 1.84253e-05 + 12 1.08 7.2713e-06 + 14 0.959996 0 + 18 0.957198 3.36079e-05 + 31 104.52 0.0030599 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +colvars: Saving collective variables state to "out.colvars.state". +Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms + +Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52 +Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19 +Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83 +Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48 +Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58 +Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06 +Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16 +Other | | 0.001141 | | | 0.19 + +Nlocal: 501 ave 513 max 489 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 6563.25 ave 6596 max 6519 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177059 ave 181742 max 172942 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.412 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 12 +Dangerous builds = 2 + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. +SHAKE stats (type/ave/delta) on step 100 + 4 1.11098 8.97155e-05 + 6 0.996996 1.00568e-05 + 8 1.08 6.02345e-06 + 10 1.111 1.84253e-05 + 12 1.08 7.2713e-06 + 14 0.959996 0 + 18 0.957198 3.36079e-05 + 31 104.52 0.0030599 +Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 + 110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657 + 120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812 + 130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592 + 140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517 + 150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008 + 160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679 + 170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217 + 180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037 + 190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287 +SHAKE stats (type/ave/delta) on step 200 + 4 1.111 1.81266e-06 + 6 0.997 7.79424e-07 + 8 1.08 1.08903e-06 + 10 1.111 2.96503e-07 + 12 1.08 4.69038e-07 + 14 0.960001 0 + 18 0.957201 3.76471e-06 + 31 104.52 0.000411055 + 200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572 +colvars: Saving collective variables state to "out.colvars.state". +Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms + +Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50 +Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20 +Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23 +Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84 +Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48 +Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08 +Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38 +Other | | 0.001623 | | | 0.28 + +Nlocal: 501 ave 513 max 481 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 6556.5 ave 6608 max 6514 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 177021 ave 182259 max 172089 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 708083 +Ave neighs/atom = 353.335 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 7 +Dangerous builds = 0 + +fix 2 all colvars peptide.colvars input out.colvars.state output out2 +colvars: Resetting the Collective Variables module. + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +colvars: Creating proxy instance +colvars: ---------------------------------------------------------------------- +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. +colvars: Using LAMMPS interface, version 2018-08-29. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "peptide.colvars": +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 1000 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 1 [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "two" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 1 [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 2 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: # name = "h_pot" +colvars: # colvars = { one, two } +colvars: # outputEnergy = off [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { 10, 10 } +colvars: # targetCenters = { 10, 10 } [default] +colvars: # outputCenters = off [default] +colvars: # forceConstant = 100 +colvars: # targetForceConstant = -1 [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1. +colvars: ---------------------------------------------------------------------- +colvars: Restarting from file "out.colvars.state". +colvars: Restarting collective variable "one" from value: 10.0128 +colvars: Restarting collective variable "two" from value: 9.62236 +colvars: ---------------------------------------------------------------------- +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "out2.colvars.state". +colvars: Writing to colvar trajectory file "out2.colvars.traj". +colvars: Setting initial step number from LAMMPS: 200 +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011. +colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011. +colvars: Performing analysis. +SHAKE stats (type/ave/delta) on step 200 + 4 1.111 1.81266e-06 + 6 0.997 7.79424e-07 + 8 1.08 1.08903e-06 + 10 1.111 2.96503e-07 + 12 1.08 4.69038e-07 + 14 0.960001 0 + 18 0.957201 3.76471e-06 + 31 104.52 0.000411055 +Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572 + 210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486 + 220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368 + 230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541 + 240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818 + 250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013 + 260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096 + 270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131 + 280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488 + 290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135 +SHAKE stats (type/ave/delta) on step 300 + 4 1.111 1.79792e-05 + 6 0.997005 1.02512e-05 + 8 1.08 1.85102e-05 + 10 1.111 9.98838e-06 + 12 1.08 8.84113e-06 + 14 0.960008 0 + 18 0.957203 1.8445e-05 + 31 104.52 0.00168382 + 300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246 +colvars: Saving collective variables state to "out2.colvars.state". +Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms + +Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60 +Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20 +Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99 +Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05 +Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39 +Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09 +Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40 +Other | | 0.001705 | | | 0.29 + +Nlocal: 501 ave 513 max 472 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 6612.75 ave 6681 max 6561 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 177038 ave 180136 max 170218 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 708152 +Ave neighs/atom = 353.369 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 8 +Dangerous builds = 0 + +colvars: Resetting the Collective Variables module. + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/USER/colvars/log.peptide-colvars2 b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 similarity index 56% rename from examples/USER/colvars/log.peptide-colvars2 rename to examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 index 9966f34a3a..8e5c990f40 100644 --- a/examples/USER/colvars/log.peptide-colvars2 +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide @@ -15,7 +14,7 @@ kspace_style pppm 0.0001 read_data data.peptide orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 2004 atoms reading velocities ... @@ -77,88 +76,122 @@ thermo 10 run 100 PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0228209 estimated relative force accuracy = 6.87243e-05 using double precision FFTs - 3d grid and FFT values/proc = 6776 1800 + 3d grid and FFT values/proc = 10648 3375 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard colvars: Creating proxy instance colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2013-10-22. -colvars: # indexFile = "" [default] -colvars: # analysis = off [default] +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. +colvars: Using LAMMPS interface, version 2018-08-29. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "peptide.colvars2": +colvars: # smp = on [default] colvars: # colvarsTrajFrequency = 1 colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "peptide2.colvars.state". -colvars: Writing to colvar trajectory file "peptide2.colvars.traj". +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] colvars: ---------------------------------------------------------------------- colvars: Initializing a new collective variable. -colvars: # name = one +colvars: # name = "one" colvars: Initializing a new "distance" component. +colvars: # name = "" [default] colvars: # componentCoeff = 1 [default] colvars: # componentExp = 1 [default] colvars: # period = 0 [default] colvars: # wrapAround = 0 [default] colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] +colvars: # scalable = on [default] colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] colvars: # indexGroup = "" [default] colvars: # psfSegID = [default] colvars: # atomsFile = "" [default] colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] colvars: # enableForces = on [default] -colvars: # disableForces = off [default] -colvars: # centerReference = off [default] -colvars: # rotateReference = off [default] colvars: # enableFitGradients = on [default] -colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 0. +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] colvars: # width = 1 [default] colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] colvars: # expandBoundaries = off [default] colvars: # extendedLagrangian = off [default] colvars: # outputValue = on [default] colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] +colvars: # outputTotalForce = off [default] colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables initialized, 1 in total. colvars: ---------------------------------------------------------------------- colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot +colvars: # name = "h_pot" colvars: # colvars = { one } colvars: # outputEnergy = off [default] -colvars: # forceConstant = 100 +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] colvars: # centers = { 10 } colvars: # targetCenters = { 10 } [default] -colvars: # targetForceConstant = 0 [default] colvars: # outputCenters = off [default] -colvars: # outputAccumulatedWork = off [default] +colvars: # forceConstant = 100 +colvars: # targetForceConstant = -1 [default] colvars: ---------------------------------------------------------------------- colvars: Collective variables biases initialized, 1 in total. colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. +colvars: Collective variables module (re)initialized. colvars: ---------------------------------------------------------------------- +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4. +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "peptide2.colvars.state". +colvars: Writing to colvar trajectory file "peptide2.colvars.traj". colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035. +colvars: Performing analysis. SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 @@ -168,58 +201,60 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 -Memory usage per processor = 10.4103 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 - 10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269 - 20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393 - 30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862 - 40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154 - 50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302 - 60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8833 26.28765 20.573958 - 70 277.26045 -5224.8416 -6340.2881 1115.4465 -6447.8495 27.742889 0.69414895 - 80 268.01458 -5281.8501 -6360.0996 1078.2495 -6496.6062 20.300729 5.260642 - 90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249 + 10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263 + 20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314 + 30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585 + 40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024 + 50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863 + 60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037 + 70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283 + 80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186 + 90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272 SHAKE stats (type/ave/delta) on step 100 - 4 1.11096 0.000191466 - 6 0.996989 3.5552e-05 - 8 1.08 9.10001e-06 - 10 1.111 1.58547e-05 - 12 1.08 5.80613e-06 + 4 1.11096 0.000191462 + 6 0.996989 3.55508e-05 + 8 1.08 9.0997e-06 + 10 1.111 1.58544e-05 + 12 1.08 5.80604e-06 14 0.959997 0 - 18 0.957198 2.92454e-05 - 31 104.52 0.00239929 - 100 260.35617 -5387.2298 -6434.6687 1047.4389 -6534.1957 20.246734 0.075048991 + 18 0.957198 2.92445e-05 + 31 104.52 0.00239923 + 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 +colvars: Saving collective variables state to "peptide2.colvars.state". +Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms -Loop time of 1.07439 on 2 procs for 100 steps with 2004 atoms -98.2% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 16.084 ns/day 1.492 hours/ns 93.076 timesteps/s +Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.77154 | 0.77308 | 0.77462 | 0.2 | 71.96 -Bond | 0.0023637 | 0.0025266 | 0.0026896 | 0.3 | 0.24 -Kspace | 0.095779 | 0.097411 | 0.099043 | 0.5 | 9.07 -Neigh | 0.15521 | 0.15521 | 0.15522 | 0.0 | 14.45 -Comm | 0.018134 | 0.018364 | 0.018594 | 0.2 | 1.71 -Output | 0.00024295 | 0.00032854 | 0.00041413 | 0.5 | 0.03 -Modify | 0.024936 | 0.024973 | 0.02501 | 0.0 | 2.32 -Other | | 0.002498 | | | 0.23 +Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46 +Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14 +Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72 +Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90 +Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62 +Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01 +Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08 +Other | | 0.001465 | | | 0.06 -Nlocal: 1002 ave 1010 max 994 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 8645 ave 8652 max 8638 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 354116 ave 356373 max 351860 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11143 ave 11143 max 11143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708234 ave 708234 max 708234 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 708233 +Total # of neighbors = 708234 Ave neighs/atom = 353.41 Ave special neighs/atom = 2.34032 Neighbor list builds = 13 Dangerous builds = 1 -colvars: Saving collective variables state to "peptide2.colvars.state". +colvars: Resetting the Collective Variables module. Please see the log.cite file for references relevant to this simulation +Total wall time: 0:00:02 diff --git a/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 new file mode 100644 index 0000000000..47f1b672df --- /dev/null +++ b/examples/USER/colvars/log.27Nov18.peptide-colvars2.g++.4 @@ -0,0 +1,260 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +shell "rm -f peptide2.colvars.*" +fix 2 all colvars peptide.colvars2 output peptide2 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_2 +thermo 10 + + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +colvars: Creating proxy instance +colvars: ---------------------------------------------------------------------- +colvars: Initializing the collective variables module, version 2018-11-16. +colvars: Please cite Fiorin et al, Mol Phys 2013: +colvars: http://dx.doi.org/10.1080/00268976.2013.813594 +colvars: in any publication based on this calculation. +colvars: SMP parallelism is available. +colvars: Using LAMMPS interface, version 2018-08-29. +colvars: ---------------------------------------------------------------------- +colvars: Reading new configuration from file "peptide.colvars2": +colvars: # smp = on [default] +colvars: # colvarsTrajFrequency = 1 +colvars: # colvarsRestartFrequency = 1000 +colvars: # scriptedColvarForces = off [default] +colvars: # scriptingAfterBiases = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new collective variable. +colvars: # name = "one" +colvars: Initializing a new "distance" component. +colvars: # name = "" [default] +colvars: # componentCoeff = 1 [default] +colvars: # componentExp = 1 [default] +colvars: # period = 0 [default] +colvars: # wrapAround = 0 [default] +colvars: # forceNoPBC = off [default] +colvars: # scalable = on [default] +colvars: Initializing atom group "group1". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: Initializing atom group "group2". +colvars: # name = "" [default] +colvars: # centerReference = off [default] +colvars: # rotateReference = off [default] +colvars: # atomsOfGroup = "" [default] +colvars: # indexGroup = "" [default] +colvars: # psfSegID = [default] +colvars: # atomsFile = "" [default] +colvars: # dummyAtom = ( 0 , 0 , 0 ) [default] +colvars: # enableForces = on [default] +colvars: # enableFitGradients = on [default] +colvars: # printAtomIDs = off [default] +colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0. +colvars: # oneSiteSystemForce = off [default] +colvars: # oneSiteTotalForce = off [default] +colvars: All components initialized. +colvars: # timeStepFactor = 1 [default] +colvars: # width = 1 [default] +colvars: # lowerBoundary = 0 [default] +colvars: # upperBoundary = 0 [default] +colvars: # expandBoundaries = off [default] +colvars: # extendedLagrangian = off [default] +colvars: # outputValue = on [default] +colvars: # outputVelocity = off [default] +colvars: # outputTotalForce = off [default] +colvars: # outputAppliedForce = off [default] +colvars: # subtractAppliedForce = off [default] +colvars: # runAve = off [default] +colvars: # corrFunc = off [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Initializing a new "harmonic" instance. +colvars: # name = "h_pot" +colvars: # colvars = { one } +colvars: # outputEnergy = off [default] +colvars: # timeStepFactor = 1 [default] +colvars: # writeTISamples = off [default] +colvars: # writeTIPMF = off [default] +colvars: # centers = { 10 } +colvars: # targetCenters = { 10 } [default] +colvars: # outputCenters = off [default] +colvars: # forceConstant = 100 +colvars: # targetForceConstant = -1 [default] +colvars: ---------------------------------------------------------------------- +colvars: Collective variables biases initialized, 1 in total. +colvars: ---------------------------------------------------------------------- +colvars: Collective variables module (re)initialized. +colvars: ---------------------------------------------------------------------- +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4. +colvars: The restart output state file will be "rest.colvars.state". +colvars: The final output state file will be "peptide2.colvars.state". +colvars: Writing to colvar trajectory file "peptide2.colvars.traj". +colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035. +colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035. +colvars: Performing analysis. +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 + 10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263 + 20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314 + 30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585 + 40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024 + 50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863 + 60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037 + 70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283 + 80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186 + 90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272 +SHAKE stats (type/ave/delta) on step 100 + 4 1.11096 0.000191462 + 6 0.996989 3.55508e-05 + 8 1.08 9.0997e-06 + 10 1.111 1.58544e-05 + 12 1.08 5.80604e-06 + 14 0.959997 0 + 18 0.957198 2.92445e-05 + 31 104.52 0.00239923 + 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 +colvars: Saving collective variables state to "peptide2.colvars.state". +Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms + +Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99 +Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18 +Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33 +Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56 +Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64 +Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05 +Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04 +Other | | 0.001264 | | | 0.20 + +Nlocal: 501 ave 513 max 494 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 6572.5 ave 6593 max 6548 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177058 ave 181778 max 174301 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 708234 +Ave neighs/atom = 353.41 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 13 +Dangerous builds = 1 +colvars: Resetting the Collective Variables module. + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 b/examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 new file mode 100644 index 0000000000..a6801fe306 --- /dev/null +++ b/examples/USER/colvars/log.27Nov18.peptide-spring.g++.1 @@ -0,0 +1,163 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 +fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 + +fix 2a ref setforce 0.0 0.0 0.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +variable sp equal f_3a+f_3b + +thermo_style custom step temp etotal pe ke epair ebond v_sp +thermo 10 + + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 10648 3375 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond v_sp + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta) on step 100 + 4 1.11098 8.97155e-05 + 6 0.996996 1.00568e-05 + 8 1.08 6.02345e-06 + 10 1.111 1.84253e-05 + 12 1.08 7.2713e-06 + 14 0.959996 0 + 18 0.957198 3.36079e-05 + 31 104.52 0.0030599 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms + +Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23 +Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15 +Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90 +Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88 +Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63 +Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02 +Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12 +Other | | 0.001613 | | | 0.07 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11124 ave 11124 max 11124 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708237 ave 708237 max 708237 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.412 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 12 +Dangerous builds = 2 +Total wall time: 0:00:02 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 b/examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 new file mode 100644 index 0000000000..025c371640 --- /dev/null +++ b/examples/USER/colvars/log.27Nov18.peptide-spring.g++.4 @@ -0,0 +1,163 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 +fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 + +fix 2a ref setforce 0.0 0.0 0.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +variable sp equal f_3a+f_3b + +thermo_style custom step temp etotal pe ke epair ebond v_sp +thermo 10 + + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond v_sp + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 + 10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345 + 20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695 + 30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933 + 40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517 + 50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217 + 60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945 + 70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603 + 80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178 + 90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576 +SHAKE stats (type/ave/delta) on step 100 + 4 1.11098 8.97155e-05 + 6 0.996996 1.00568e-05 + 8 1.08 6.02345e-06 + 10 1.111 1.84253e-05 + 12 1.08 7.2713e-06 + 14 0.959996 0 + 18 0.957198 3.36079e-05 + 31 104.52 0.0030599 + 100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323 +Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms + +Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27 +Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19 +Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25 +Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57 +Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58 +Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09 +Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85 +Other | | 0.001274 | | | 0.21 + +Nlocal: 501 ave 513 max 489 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 6563.25 ave 6596 max 6519 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177059 ave 181742 max 172942 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 708237 +Ave neighs/atom = 353.412 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 12 +Dangerous builds = 2 +Total wall time: 0:00:00 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 b/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 new file mode 100644 index 0000000000..7397c5475d --- /dev/null +++ b/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.1 @@ -0,0 +1,158 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_3 +thermo 10 + + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 10648 3375 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_3 + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 + 10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263 + 20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314 + 30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585 + 40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024 + 50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863 + 60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037 + 70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283 + 80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186 + 90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272 +SHAKE stats (type/ave/delta) on step 100 + 4 1.11096 0.000191462 + 6 0.996989 3.55508e-05 + 8 1.08 9.0997e-06 + 10 1.111 1.58544e-05 + 12 1.08 5.80604e-06 + 14 0.959997 0 + 18 0.957198 2.92445e-05 + 31 104.52 0.00239923 + 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 +Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms + +Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93 +Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15 +Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85 +Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27 +Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64 +Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01 +Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07 +Other | | 0.001546 | | | 0.07 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11143 ave 11143 max 11143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708234 ave 708234 max 708234 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708234 +Ave neighs/atom = 353.41 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 13 +Dangerous builds = 1 +Total wall time: 0:00:02 diff --git a/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 b/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 new file mode 100644 index 0000000000..0e3f0d3b6b --- /dev/null +++ b/examples/USER/colvars/log.27Nov18.peptide-spring2.g++.4 @@ -0,0 +1,158 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_3 +thermo 10 + + +run 100 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_3 + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 + 10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263 + 20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314 + 30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585 + 40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024 + 50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863 + 60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037 + 70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283 + 80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186 + 90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272 +SHAKE stats (type/ave/delta) on step 100 + 4 1.11096 0.000191462 + 6 0.996989 3.55508e-05 + 8 1.08 9.0997e-06 + 10 1.111 1.58544e-05 + 12 1.08 5.80604e-06 + 14 0.959997 0 + 18 0.957198 2.92445e-05 + 31 104.52 0.00239923 + 100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487 +Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms + +Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95 +Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18 +Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39 +Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80 +Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67 +Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05 +Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75 +Other | | 0.001239 | | | 0.20 + +Nlocal: 501 ave 513 max 494 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 6572.5 ave 6593 max 6548 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 177058 ave 181778 max 174301 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 708234 +Ave neighs/atom = 353.41 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 13 +Dangerous builds = 1 +Total wall time: 0:00:00 diff --git a/examples/USER/colvars/log.peptide-colvars-1 b/examples/USER/colvars/log.peptide-colvars-1 deleted file mode 100644 index 515480efe5..0000000000 --- a/examples/USER/colvars/log.peptide-colvars-1 +++ /dev/null @@ -1,516 +0,0 @@ -LAMMPS (21 May 2012-ICMS) -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - 3 = max bonds/atom - 6 = max angles/atom - 14 = max dihedrals/atom - 1 = max impropers/atom - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 1 MPI processor grid - 2004 atoms - 2004 velocities - 1365 bonds - 786 angles - 207 dihedrals - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -84 atoms in group peptide -group one id 2 4 5 6 -4 atoms in group one -group two id 80 82 83 84 -4 atoms in group two -group ref id 37 -1 atoms in group ref -group colvar union one two ref -9 atoms in group colvar - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -shell "rm -f out*.colvars.*" -fix 2 all colvars peptide.colvars -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 - - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 10648 3375 5808 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out.colvars.state". -colvars: The trajectory file will be "out.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = two -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one, two } -colvars: # forceConstant = 100 -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 22.5866 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604 - 10 305.06198 -5058.8899 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344 - 20 311.00592 -4999.0544 -6250.2623 1251.2079 -6417.0984 47.695274 36.699706 - 30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344163 10.563914 - 40 297.87524 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.723201 3.8354392 - 50 304.02086 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459508 0.20679801 - 60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.76729 0.69356508 - 70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7015 39.627148 11.433632 - 80 267.51473 -5206.4042 -6282.6427 1076.2385 -6456.6352 31.611843 6.3553235 - 90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938867 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97184e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 - 14 0.959996 0 - 18 0.957198 3.36077e-05 - 31 104.52 0.00306008 - 100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms - - Pair time (%) = 1.86583 (78.0347) - Bond time (%) = 0.00628591 (0.262896) -Kspace time (%) = 0.165128 (6.90614) -Neigh time (%) = 0.314792 (13.1656) - Comm time (%) = 0.0111108 (0.464687) -Output time (%) = 0.000252724 (0.0105697) -Modify time (%) = 0.0253747 (1.06125) -Other time (%) = 0.0022521 (0.0941899) - -FFT time (% of Kspce) = 0.0274372 (16.6158) -FFT Gflps 3d (1d only) = 1.99867 2.86506 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11124 ave 11124 max 11124 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708237 ave 708237 max 708237 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 10648 3375 5808 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out.colvars.state". -colvars: The trajectory file will be "out.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = two -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one, two } -colvars: # forceConstant = 100 -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "out.colvars.state". -colvars: Restarting collective variable "one" from value: 10.0137 -colvars: Restarting collective variable "two" from value: 10.0649 -colvars: Restarting harmonic bias "h_pot". -colvars: Reading current stage from the restart. -colvars: # stage = 3900175693153042431 -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -colvars: Initializing step number as firstTimestep. -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97184e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 - 14 0.959996 0 - 18 0.957198 3.36077e-05 - 31 104.52 0.00306008 -Memory usage per processor = 22.5866 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687 - 110 266.26278 -5341.2103 -6412.412 1071.2018 -6552.7583 33.572968 1.9229782 - 120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859553 2.7124877 - 130 252.8344 -5422.5446 -6439.7226 1017.1781 -6580.4752 25.979049 1.2031628 - 140 253.85115 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071514 0.30586247 - 150 261.31825 -5490.48 -6541.7895 1051.3095 -6646.6144 16.258548 6.9049974 - 160 255.7368 -5521.6048 -6550.4596 1028.8547 -6658.1517 19.717533 12.339821 - 170 253.42877 -5540.1003 -6559.6695 1019.5693 -6656.6878 23.293662 10.289878 - 180 248.51086 -5550.3244 -6550.1084 999.78404 -6661.4182 26.200056 3.4339065 - 190 250.8039 -5555.2614 -6564.2706 1009.0092 -6666.15 25.536594 3.3495152 -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.8129e-06 - 6 0.997 7.7964e-07 - 8 1.08 1.08934e-06 - 10 1.111 2.96501e-07 - 12 1.08 4.69174e-07 - 14 0.960001 0 - 18 0.957201 3.76571e-06 - 31 104.52 0.000411068 - 200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms - - Pair time (%) = 1.84544 (82.572) - Bond time (%) = 0.00609159 (0.27256) -Kspace time (%) = 0.163201 (7.30223) -Neigh time (%) = 0.183405 (8.20622) - Comm time (%) = 0.00959301 (0.429227) -Output time (%) = 0.000245094 (0.0109664) -Modify time (%) = 0.0247326 (1.10663) -Other time (%) = 0.00223875 (0.10017) - -FFT time (% of Kspce) = 0.0272989 (16.7271) -FFT Gflps 3d (1d only) = 2.0088 2.93901 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11159 ave 11159 max 11159 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708088 ave 708088 max 708088 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708088 -Ave neighs/atom = 353.337 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 7 -Dangerous builds = 0 - -fix 2 all colvars peptide.colvars input out.colvars.state output out2 - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 10648 3375 5808 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out2.colvars.state". -colvars: The trajectory file will be "out2.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = two -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one, two } -colvars: # forceConstant = 100 -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "out.colvars.state". -colvars: Restarting collective variable "one" from value: 10.0128 -colvars: Restarting collective variable "two" from value: 9.62236 -colvars: Restarting harmonic bias "h_pot". -colvars: Reading current stage from the restart. -colvars: # stage = 3900175693153042431 -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -colvars: Initializing step number as firstTimestep. -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.8129e-06 - 6 0.997 7.7964e-07 - 8 1.08 1.08934e-06 - 10 1.111 2.96501e-07 - 12 1.08 4.69174e-07 - 14 0.960001 0 - 18 0.957201 3.76571e-06 - 31 104.52 0.000411068 -Memory usage per processor = 22.5866 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858 - 210 253.15043 -5538.5668 -6557.0163 1018.4495 -6672.041 37.67158 0.61296982 - 220 245.19746 -5522.5242 -6508.9781 986.4539 -6628.1999 36.656356 0.048624555 - 230 258.65299 -5495.7177 -6536.3046 1040.5868 -6658.0952 34.855726 0.22046598 - 240 260.80143 -5469.8517 -6519.0819 1049.2302 -6624.1723 31.576409 3.7570726 - 250 269.06507 -5438.3971 -6520.8727 1082.4757 -6616.3871 25.444125 8.6640978 - 260 266.10282 -5397.3162 -6467.8744 1070.5583 -6580.628 26.873936 8.3330854 - 270 272.81993 -5350.8393 -6448.4211 1097.5819 -6563.8139 23.113421 10.972906 - 280 279.52079 -5307.9855 -6432.5256 1124.5401 -6557.7274 33.641095 8.5474821 - 290 286.81184 -5260.8728 -6414.7455 1153.8727 -6515.5418 28.572468 5.9092648 -SHAKE stats (type/ave/delta) on step 300 - 4 1.111 1.79733e-05 - 6 0.997005 1.02622e-05 - 8 1.08 1.84996e-05 - 10 1.111 9.98595e-06 - 12 1.08 8.83195e-06 - 14 0.960008 0 - 18 0.957203 1.84801e-05 - 31 104.52 0.00169221 - 300 291.51842 -5216.3285 -6389.1362 1172.8077 -6503.1141 27.877464 2.2482411 -colvars: Saving collective variables state to "out2.colvars.state". -Loop time of 2.25031 on 1 procs for 100 steps with 2004 atoms - - Pair time (%) = 1.83745 (81.6533) - Bond time (%) = 0.00609803 (0.270987) -Kspace time (%) = 0.162178 (7.20694) -Neigh time (%) = 0.207886 (9.23812) - Comm time (%) = 0.00977254 (0.434276) -Output time (%) = 0.000240803 (0.0107009) -Modify time (%) = 0.024461 (1.08701) -Other time (%) = 0.00221944 (0.0986283) - -FFT time (% of Kspce) = 0.0273609 (16.8709) -FFT Gflps 3d (1d only) = 2.00425 2.94806 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11292 ave 11292 max 11292 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708145 ave 708145 max 708145 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708145 -Ave neighs/atom = 353.366 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 8 -Dangerous builds = 0 - diff --git a/examples/USER/colvars/log.peptide-colvars-4 b/examples/USER/colvars/log.peptide-colvars-4 deleted file mode 100644 index 4b7c045c4c..0000000000 --- a/examples/USER/colvars/log.peptide-colvars-4 +++ /dev/null @@ -1,516 +0,0 @@ -LAMMPS (21 May 2012-ICMS) -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - 3 = max bonds/atom - 6 = max angles/atom - 14 = max dihedrals/atom - 1 = max impropers/atom - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 MPI processor grid - 2004 atoms - 2004 velocities - 1365 bonds - 786 angles - 207 dihedrals - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -84 atoms in group peptide -group one id 2 4 5 6 -4 atoms in group one -group two id 80 82 83 84 -4 atoms in group two -group ref id 37 -1 atoms in group ref -group colvar union one two ref -9 atoms in group colvar - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -shell "rm -f out*.colvars.*" -fix 2 all colvars peptide.colvars -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 - - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 4312 960 3696 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out.colvars.state". -colvars: The trajectory file will be "out.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = two -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one, two } -colvars: # forceConstant = 100 -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 10.1924 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604 - 10 305.06198 -5058.8898 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344 - 20 311.00592 -4999.0545 -6250.2624 1251.2079 -6417.0984 47.695274 36.699706 - 30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344162 10.563914 - 40 297.87524 -5020.8339 -6219.2157 1198.3819 -6389.85 27.723201 3.8354392 - 50 304.02086 -5056.254 -6279.3603 1223.1063 -6456.8182 55.459508 0.206798 - 60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.767289 0.69356507 - 70 277.835 -5163.9751 -6281.7331 1117.758 -6447.7014 39.627147 11.433632 - 80 267.51474 -5206.4042 -6282.6428 1076.2385 -6456.6352 31.611843 6.3553237 - 90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8036 28.849898 0.36938879 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97184e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 - 14 0.959996 0 - 18 0.957198 3.36077e-05 - 31 104.52 0.00306008 - 100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 0.686681 on 4 procs for 100 steps with 2004 atoms - - Pair time (%) = 0.47104 (68.5966) - Bond time (%) = 0.00184608 (0.26884) -Kspace time (%) = 0.0808357 (11.7719) -Neigh time (%) = 0.0772016 (11.2427) - Comm time (%) = 0.0293136 (4.26888) -Output time (%) = 0.000323951 (0.0471764) -Modify time (%) = 0.0247293 (3.60128) -Other time (%) = 0.00139064 (0.202516) - -FFT time (% of Kspce) = 0.0117171 (14.4949) -FFT Gflps 3d (1d only) = 4.68018 10.009 - -Nlocal: 501 ave 513 max 489 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 6563.25 ave 6596 max 6519 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 177059 ave 181741 max 172943 min -Histogram: 1 0 1 0 0 0 1 0 0 1 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 4312 960 3696 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out.colvars.state". -colvars: The trajectory file will be "out.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = two -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one, two } -colvars: # forceConstant = 100 -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "out.colvars.state". -colvars: Restarting collective variable "one" from value: 10.0137 -colvars: Restarting collective variable "two" from value: 10.0649 -colvars: Restarting harmonic bias "h_pot". -colvars: Reading current stage from the restart. -colvars: # stage = 8103505641670189088 -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -colvars: Initializing step number as firstTimestep. -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97184e-05 - 6 0.996996 1.00568e-05 - 8 1.08 6.02345e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 - 14 0.959996 0 - 18 0.957198 3.36077e-05 - 31 104.52 0.00306008 -Memory usage per processor = 10.1967 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866 - 110 266.26278 -5341.2101 -6412.4119 1071.2018 -6552.7582 33.572969 1.9229778 - 120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859555 2.7124877 - 130 252.83442 -5422.5444 -6439.7226 1017.1781 -6580.4752 25.979048 1.2031628 - 140 253.85116 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071518 0.30586252 - 150 261.31828 -5490.48 -6541.7895 1051.3096 -6646.6145 16.25855 6.9049978 - 160 255.73681 -5521.6048 -6550.4596 1028.8548 -6658.1518 19.717536 12.339819 - 170 253.42879 -5540.1004 -6559.6697 1019.5694 -6656.688 23.293657 10.289879 - 180 248.51083 -5550.3244 -6550.1084 999.78393 -6661.4181 26.200057 3.433906 - 190 250.80387 -5555.2613 -6564.2703 1009.009 -6666.1497 25.536596 3.3495164 -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.8129e-06 - 6 0.997 7.79639e-07 - 8 1.08 1.08934e-06 - 10 1.111 2.96501e-07 - 12 1.08 4.69175e-07 - 14 0.960001 0 - 18 0.957201 3.76571e-06 - 31 104.52 0.000411069 - 200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874 -colvars: Saving collective variables state to "out.colvars.state". -Loop time of 0.653275 on 4 procs for 100 steps with 2004 atoms - - Pair time (%) = 0.47279 (72.3723) - Bond time (%) = 0.00182116 (0.278774) -Kspace time (%) = 0.079544 (12.1762) -Neigh time (%) = 0.0451868 (6.91696) - Comm time (%) = 0.027427 (4.19838) -Output time (%) = 0.000316501 (0.0484483) -Modify time (%) = 0.0247022 (3.78129) -Other time (%) = 0.00148731 (0.227671) - -FFT time (% of Kspce) = 0.0109947 (13.8221) -FFT Gflps 3d (1d only) = 4.98769 10.1728 - -Nlocal: 501 ave 513 max 481 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 6556.5 ave 6608 max 6514 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 177022 ave 182261 max 172093 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 708086 -Ave neighs/atom = 353.336 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 7 -Dangerous builds = 0 - -fix 2 all colvars peptide.colvars input out.colvars.state output out2 - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 4312 960 3696 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "out2.colvars.state". -colvars: The trajectory file will be "out2.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = two -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 2 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one, two } -colvars: # forceConstant = 100 -colvars: # centers = { 10, 10 } -colvars: # targetCenters = { 10, 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Restarting from file "out.colvars.state". -colvars: Restarting collective variable "one" from value: 10.0128 -colvars: Restarting collective variable "two" from value: 9.62236 -colvars: Restarting harmonic bias "h_pot". -colvars: Reading current stage from the restart. -colvars: # stage = 8103505641670189088 -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -colvars: Initializing step number as firstTimestep. -SHAKE stats (type/ave/delta) on step 200 - 4 1.111 1.8129e-06 - 6 0.997 7.79639e-07 - 8 1.08 1.08934e-06 - 10 1.111 2.96501e-07 - 12 1.08 4.69175e-07 - 14 0.960001 0 - 18 0.957201 3.76571e-06 - 31 104.52 0.000411069 -Memory usage per processor = 10.201 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874 - 210 253.15047 -5538.5669 -6557.0165 1018.4497 -6672.0412 37.671574 0.61297094 - 220 245.19752 -5522.5242 -6508.9784 986.45412 -6628.2001 36.656348 0.048624447 - 230 258.65297 -5495.7177 -6536.3044 1040.5868 -6658.0951 34.855726 0.22046446 - 240 260.8016 -5469.8518 -6519.0827 1049.2309 -6624.173 31.576408 3.757081 - 250 269.06524 -5438.3971 -6520.8735 1082.4764 -6616.3878 25.444134 8.6641098 - 260 266.10241 -5397.317 -6467.8736 1070.5566 -6580.6272 26.87393 8.333095 - 270 272.82004 -5350.8402 -6448.4225 1097.5823 -6563.8152 23.113398 10.972914 - 280 279.52006 -5307.9867 -6432.5238 1124.5371 -6557.7256 33.641067 8.5474809 - 290 286.81221 -5260.8707 -6414.7449 1153.8742 -6515.5413 28.572449 5.9092582 -SHAKE stats (type/ave/delta) on step 300 - 4 1.111 1.79733e-05 - 6 0.997005 1.02621e-05 - 8 1.08 1.84996e-05 - 10 1.111 9.98591e-06 - 12 1.08 8.83192e-06 - 14 0.960008 0 - 18 0.957203 1.84805e-05 - 31 104.52 0.00169223 - 300 291.51901 -5216.3298 -6389.1399 1172.8101 -6503.1178 27.877408 2.2482392 -colvars: Saving collective variables state to "out2.colvars.state". -Loop time of 0.662081 on 4 procs for 100 steps with 2004 atoms - - Pair time (%) = 0.47307 (71.452) - Bond time (%) = 0.00178617 (0.269781) -Kspace time (%) = 0.0802494 (12.1208) -Neigh time (%) = 0.0528576 (7.98355) - Comm time (%) = 0.0277618 (4.19311) -Output time (%) = 0.000293612 (0.0443469) -Modify time (%) = 0.0245907 (3.71416) -Other time (%) = 0.00147164 (0.222275) - -FFT time (% of Kspce) = 0.011487 (14.3141) -FFT Gflps 3d (1d only) = 4.77392 9.91625 - -Nlocal: 501 ave 514 max 471 min -Histogram: 1 0 0 0 0 0 0 0 1 2 -Nghost: 6609.75 ave 6681 max 6555 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 177036 ave 180240 max 169752 min -Histogram: 1 0 0 0 0 0 0 0 1 2 - -Total # of neighbors = 708146 -Ave neighs/atom = 353.366 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 8 -Dangerous builds = 0 - diff --git a/examples/USER/colvars/log.peptide-colvars2-1 b/examples/USER/colvars/log.peptide-colvars2-1 deleted file mode 100644 index 21b4ce5f27..0000000000 --- a/examples/USER/colvars/log.peptide-colvars2-1 +++ /dev/null @@ -1,182 +0,0 @@ -LAMMPS (21 May 2012-ICMS) -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - 3 = max bonds/atom - 6 = max angles/atom - 14 = max dihedrals/atom - 1 = max impropers/atom - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 1 MPI processor grid - 2004 atoms - 2004 velocities - 1365 bonds - 786 angles - 207 dihedrals - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -84 atoms in group peptide -group one id 2 4 5 6 -4 atoms in group one -group two id 80 82 83 84 -4 atoms in group two -group ref id 37 -1 atoms in group ref -group colvar union one two ref -9 atoms in group colvar - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -shell "rm -f peptide2.colvars.*" -fix 2 all colvars peptide.colvars2 output peptide2 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 - - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 10648 3375 5808 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "peptide2.colvars.state". -colvars: The trajectory file will be "peptide2.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one } -colvars: # forceConstant = 100 -colvars: # centers = { 10 } -colvars: # targetCenters = { 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 22.5865 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323 - 10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.4169 21.367753 12.393269 - 20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392 - 30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862 - 40 297.5581 -5088.2156 -6285.3215 1197.106 -6395.3714 13.676872 25.625156 - 50 296.80003 -5117.2926 -6311.3488 1194.0562 -6451.8274 30.631279 5.3320296 - 60 281.72797 -5188.4941 -6321.9139 1133.4198 -6427.8834 26.287652 20.573958 - 70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742888 0.69414894 - 80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606438 - 90 270.43386 -5334.0846 -6422.067 1087.9824 -6563.2486 39.845993 1.1832496 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11096 0.000191466 - 6 0.996989 3.5552e-05 - 8 1.08 9.1e-06 - 10 1.111 1.58547e-05 - 12 1.08 5.80613e-06 - 14 0.959997 0 - 18 0.957198 2.92453e-05 - 31 104.52 0.00239929 - 100 260.3562 -5387.2263 -6434.6653 1047.439 -6534.1923 20.24674 0.075048834 -colvars: Saving collective variables state to "peptide2.colvars.state". -Loop time of 2.37975 on 1 procs for 100 steps with 2004 atoms - - Pair time (%) = 1.83713 (77.1984) - Bond time (%) = 0.00636029 (0.267267) -Kspace time (%) = 0.162295 (6.81981) -Neigh time (%) = 0.336338 (14.1333) - Comm time (%) = 0.0106671 (0.448243) -Output time (%) = 0.000264168 (0.0111006) -Modify time (%) = 0.024472 (1.02834) -Other time (%) = 0.00222516 (0.0935038) - -FFT time (% of Kspce) = 0.028162 (17.3524) -FFT Gflps 3d (1d only) = 1.94723 2.85015 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11143 ave 11143 max 11143 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708233 ave 708233 max 708233 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 708233 -Ave neighs/atom = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 diff --git a/examples/USER/colvars/log.peptide-colvars2-4 b/examples/USER/colvars/log.peptide-colvars2-4 deleted file mode 100644 index 38e6cc9384..0000000000 --- a/examples/USER/colvars/log.peptide-colvars2-4 +++ /dev/null @@ -1,182 +0,0 @@ -LAMMPS (21 May 2012-ICMS) -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - 3 = max bonds/atom - 6 = max angles/atom - 14 = max dihedrals/atom - 1 = max impropers/atom - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 MPI processor grid - 2004 atoms - 2004 velocities - 1365 bonds - 786 angles - 207 dihedrals - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -84 atoms in group peptide -group one id 2 4 5 6 -4 atoms in group one -group two id 80 82 83 84 -4 atoms in group two -group ref id 37 -1 atoms in group ref -group colvar union one two ref -9 atoms in group colvar - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -shell "rm -f peptide2.colvars.*" -fix 2 all colvars peptide.colvars2 output peptide2 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz -#dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_2 -thermo 10 - - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268721 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.01614 - estimated relative force accuracy = 4.86052e-05 - using single precision FFTs - brick FFT buffer size/proc = 4312 960 3696 -colvars: ---------------------------------------------------------------------- -colvars: Initializing the collective variables module, version 2012-03-23. -colvars: # analysis = off [default] -colvars: # colvarsTrajFrequency = 1 -colvars: # colvarsRestartFrequency = 1000 -colvars: # colvarsTrajAppend = off [default] -colvars: The restart output state file will be "rest.colvars.state". -colvars: The final output state file will be "peptide2.colvars.state". -colvars: The trajectory file will be "peptide2.colvars.traj". -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new collective variable. -colvars: # name = one -colvars: Initializing a new "distance" component. -colvars: # componentCoeff = 1 [default] -colvars: # componentExp = 1 [default] -colvars: # period = 0 [default] -colvars: # wrapAround = 0 [default] -colvars: # forceNoPBC = off [default] -colvars: # oneSiteSystemForce = off [default] -colvars: Initializing atom group "group1". -colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035. -colvars: Initializing atom group "group2". -colvars: Atom group "group2" defined, 4 initialized: total mass = 15.035. -colvars: All components initialized. -colvars: # width = 1 [default] -colvars: # lowerBoundary = 0 [default] -colvars: # lowerWallConstant = 0 [default] -colvars: # upperBoundary = 0 [default] -colvars: # upperWallConstant = 0 [default] -colvars: # expandBoundaries = off [default] -colvars: # extendedLagrangian = off [default] -colvars: # outputValue = on [default] -colvars: # outputVelocity = off [default] -colvars: # outputSystemForce = off [default] -colvars: # outputAppliedForce = off [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Initializing a new "harmonic" instance. -colvars: # name = h_pot -colvars: # colvars = { one } -colvars: # forceConstant = 100 -colvars: # centers = { 10 } -colvars: # targetCenters = { 10 } [default] -colvars: # targetForceConstant = 0 [default] -colvars: ---------------------------------------------------------------------- -colvars: Collective variables biases initialized, 1 in total. -colvars: ---------------------------------------------------------------------- -colvars: Collective variables module initialized. -colvars: ---------------------------------------------------------------------- -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 10.1924 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 2 - 0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323 - 10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269 - 20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392 - 30 316.97689 -5025.5598 -6300.7896 1275.2297 -6422.5336 27.323113 6.7588863 - 40 297.5581 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676872 25.625156 - 50 296.80003 -5117.2927 -6311.3488 1194.0562 -6451.8275 30.631279 5.3320297 - 60 281.72797 -5188.494 -6321.9138 1133.4198 -6427.8833 26.287652 20.573959 - 70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742889 0.69414888 - 80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606437 - 90 270.43386 -5334.0846 -6422.067 1087.9825 -6563.2486 39.845992 1.1832495 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11096 0.000191466 - 6 0.996989 3.5552e-05 - 8 1.08 9.10001e-06 - 10 1.111 1.58547e-05 - 12 1.08 5.80613e-06 - 14 0.959997 0 - 18 0.957198 2.92453e-05 - 31 104.52 0.00239929 - 100 260.35619 -5387.2298 -6434.6688 1047.439 -6534.1958 20.24674 0.07504876 -colvars: Saving collective variables state to "peptide2.colvars.state". -Loop time of 0.650999 on 4 procs for 100 steps with 2004 atoms - - Pair time (%) = 0.466917 (71.7232) - Bond time (%) = 0.00176847 (0.271655) -Kspace time (%) = 0.0588512 (9.04015) -Neigh time (%) = 0.0832494 (12.788) - Comm time (%) = 0.0190871 (2.93197) -Output time (%) = 0.000295341 (0.0453674) -Modify time (%) = 0.0194815 (2.99255) -Other time (%) = 0.00134867 (0.20717) - -FFT time (% of Kspce) = 0.010457 (17.7686) -FFT Gflps 3d (1d only) = 5.24412 9.93123 - -Nlocal: 501 ave 513 max 494 min -Histogram: 1 1 0 1 0 0 0 0 0 1 -Nghost: 6572.5 ave 6593 max 6548 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 177058 ave 181777 max 174301 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 708233 -Ave neighs/atom = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 diff --git a/examples/USER/colvars/log.peptide-spring b/examples/USER/colvars/log.peptide-spring deleted file mode 100644 index f88eb4a6ba..0000000000 --- a/examples/USER/colvars/log.peptide-spring +++ /dev/null @@ -1,150 +0,0 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) - using 1 OpenMP thread(s) per MPI task -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 2004 atoms - reading velocities ... - 2004 velocities - scanning bonds ... - 3 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 14 = max dihedrals/atom - scanning impropers ... - 1 = max impropers/atom - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -84 atoms in group peptide -group one id 2 4 5 6 -4 atoms in group one -group two id 80 82 83 84 -4 atoms in group two -group ref id 37 -1 atoms in group ref -group colvar union one two ref -9 atoms in group colvar - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 -fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 - -fix 2a ref setforce 0.0 0.0 0.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz -dump_modify 1 sort id - -variable sp equal f_3a+f_3b - -thermo_style custom step temp etotal pe ke epair ebond v_sp -thermo 10 - - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268725 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0228209 - estimated relative force accuracy = 6.87243e-05 - using double precision FFTs - 3d grid and FFT values/proc = 6776 1800 -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 11.5952 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond sp - 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 - 10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344 - 20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706 - 30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914 - 40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396 - 50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816 - 60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527 - 70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633 - 80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235 - 90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11098 8.97185e-05 - 6 0.996996 1.00569e-05 - 8 1.08 6.02346e-06 - 10 1.111 1.84257e-05 - 12 1.08 7.27136e-06 - 14 0.959996 0 - 18 0.957198 3.36078e-05 - 31 104.52 0.00306008 - 100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866 - -Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms -98.1% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 16.126 ns/day 1.488 hours/ns 93.325 timesteps/s - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45 -Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24 -Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70 -Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62 -Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77 -Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62 -Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36 -Other | | 0.002651 | | | 0.25 - -Nlocal: 1002 ave 1013 max 991 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 8629.5 ave 8641 max 8618 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 354118 ave 356534 max 351703 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 708237 -Ave neighs/atom = 353.412 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 12 -Dangerous builds = 2 diff --git a/examples/USER/colvars/log.peptide-spring2 b/examples/USER/colvars/log.peptide-spring2 deleted file mode 100644 index e32506b6cd..0000000000 --- a/examples/USER/colvars/log.peptide-spring2 +++ /dev/null @@ -1,145 +0,0 @@ -LAMMPS (20 Mar 2014-ICMS) -WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) - using 1 OpenMP thread(s) per MPI task -# Solvated 5-mer peptide - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 2004 atoms - reading velocities ... - 2004 velocities - scanning bonds ... - 3 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 14 = max dihedrals/atom - scanning impropers ... - 1 = max impropers/atom - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -timestep 2.0 - -group peptide type <= 12 -84 atoms in group peptide -group one id 2 4 5 6 -4 atoms in group one -group two id 80 82 83 84 -4 atoms in group two -group ref id 37 -1 atoms in group ref -group colvar union one two ref -9 atoms in group colvar - -fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 - -fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 - -fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 - 19 = # of size 2 clusters - 6 = # of size 3 clusters - 3 = # of size 4 clusters - 640 = # of frozen angles - -dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz -dump_modify 1 sort id - -thermo_style custom step temp etotal pe ke epair ebond f_3 -thermo 10 - - -run 100 -PPPM initialization ... - G vector (1/distance) = 0.268725 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0228209 - estimated relative force accuracy = 6.87243e-05 - using double precision FFTs - 3d grid and FFT values/proc = 6776 1800 -SHAKE stats (type/ave/delta) on step 0 - 4 1.111 1.44264e-05 - 6 0.996998 7.26967e-06 - 8 1.08 1.32536e-05 - 10 1.111 1.22749e-05 - 12 1.08 1.11767e-05 - 14 0.96 0 - 18 0.957206 4.37979e-05 - 31 104.519 0.00396029 -Memory usage per processor = 11.5952 Mbytes -Step Temp TotEng PotEng KinEng E_pair E_bond 3 - 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 - 10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269 - 20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393 - 30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862 - 40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154 - 50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302 - 60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958 - 70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895 - 80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642 - 90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249 -SHAKE stats (type/ave/delta) on step 100 - 4 1.11096 0.000191466 - 6 0.996989 3.5552e-05 - 8 1.08 9.10001e-06 - 10 1.111 1.58547e-05 - 12 1.08 5.80613e-06 - 14 0.959997 0 - 18 0.957198 2.92454e-05 - 31 104.52 0.00239929 - 100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996 - -Loop time of 1.07264 on 2 procs for 100 steps with 2004 atoms -98.6% CPU use with 2 MPI tasks x 1 OpenMP threads -Performance: 16.110 ns/day 1.490 hours/ns 93.228 timesteps/s - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.76647 | 0.77219 | 0.77792 | 0.7 | 71.99 -Bond | 0.0024974 | 0.0025403 | 0.0025833 | 0.1 | 0.24 -Kspace | 0.091998 | 0.096921 | 0.10184 | 1.6 | 9.04 -Neigh | 0.14764 | 0.14765 | 0.14767 | 0.0 | 13.77 -Comm | 0.018904 | 0.01937 | 0.019835 | 0.3 | 1.81 -Output | 0.005985 | 0.0067209 | 0.0074568 | 0.9 | 0.63 -Modify | 0.024529 | 0.024536 | 0.024542 | 0.0 | 2.29 -Other | | 0.002705 | | | 0.25 - -Nlocal: 1002 ave 1010 max 994 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 8645 ave 8652 max 8638 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 354116 ave 356373 max 351860 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 708233 -Ave neighs/atom = 353.41 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 13 -Dangerous builds = 1 diff --git a/examples/USER/colvars/out.colvars.state b/examples/USER/colvars/out.colvars.state index 3c0b4752e8..e5c6e98ef5 100644 --- a/examples/USER/colvars/out.colvars.state +++ b/examples/USER/colvars/out.colvars.state @@ -1,22 +1,23 @@ configuration { step 200 dt 2.000000e+00 + version 2018-11-16 } colvar { name one - x 1.00127641579482e+01 + x 1.00127732034965e+01 } colvar { name two - x 9.62235621950587e+00 + x 9.62235997490241e+00 } -harmonic { +restraint { configuration { + step 200 name h_pot - stage 8103505641670189088 } } diff --git a/examples/USER/colvars/out.colvars.state.old b/examples/USER/colvars/out.colvars.state.old new file mode 100644 index 0000000000..ea33a8b1b1 --- /dev/null +++ b/examples/USER/colvars/out.colvars.state.old @@ -0,0 +1,23 @@ +configuration { + step 100 + dt 2.000000e+00 + version 2018-11-16 +} + +colvar { + name one + x 1.00136989326255e+01 +} + +colvar { + name two + x 1.00648830006091e+01 +} + +restraint { + configuration { + step 100 + name h_pot + } +} + diff --git a/examples/USER/colvars/out.colvars.traj b/examples/USER/colvars/out.colvars.traj index 4d835cadcd..15aa912846 100644 --- a/examples/USER/colvars/out.colvars.traj +++ b/examples/USER/colvars/out.colvars.traj @@ -1,102 +1,203 @@ -# step one two - 100 1.00136999784453e+01 1.00648820764882e+01 - 101 1.00137686830422e+01 1.00611307186442e+01 - 102 1.00135851804620e+01 1.00551774768670e+01 - 103 1.00127019172615e+01 1.00448609599088e+01 - 104 1.00107148677220e+01 1.00279880647254e+01 - 105 1.00073753998706e+01 1.00031566249892e+01 - 106 1.00026887490897e+01 9.97035299845099e+00 - 107 9.99696380204809e+00 9.93114513453873e+00 - 108 9.99079173947846e+00 9.88834426761621e+00 - 109 9.98495634348822e+00 9.84525182069547e+00 - 110 9.98029608653331e+00 9.80488128973958e+00 - 111 9.97755063903513e+00 9.76956423088248e+00 - 112 9.97722827031026e+00 9.74089978578719e+00 - 113 9.97952719395978e+00 9.71964890219001e+00 - 114 9.98433213818614e+00 9.70572160189541e+00 - 115 9.99128820986690e+00 9.69882648932897e+00 - 116 9.99993078708906e+00 9.69906675982844e+00 - 117 1.00098268026590e+01 9.70676032193502e+00 - 118 1.00206800068605e+01 9.72193925284532e+00 - 119 1.00323638324515e+01 9.74392975114862e+00 - 120 1.00448758513666e+01 9.77144823009299e+00 - 121 1.00582368252610e+01 9.80293582393448e+00 - 122 1.00723784561855e+01 9.83653845611926e+00 - 123 1.00870571871815e+01 9.86996653086528e+00 - 124 1.01018149909563e+01 9.90067054070927e+00 - 125 1.01159957146856e+01 9.92637090832991e+00 - 126 1.01288197202732e+01 9.94568593115900e+00 - 127 1.01395051017779e+01 9.95858909349258e+00 - 128 1.01474031546764e+01 9.96651060978132e+00 - 129 1.01521102583250e+01 9.97197886676780e+00 - 130 1.01535305336566e+01 9.97782726175993e+00 - 131 1.01518703644018e+01 9.98617108245763e+00 - 132 1.01475651582407e+01 9.99754271679455e+00 - 133 1.01411660808109e+01 1.00106700599276e+01 - 134 1.01332313643590e+01 1.00230219318765e+01 - 135 1.01242577071328e+01 1.00317168123542e+01 - 136 1.01146539200964e+01 1.00343611311947e+01 - 137 1.01047327535065e+01 1.00296410219261e+01 - 138 1.00947009258946e+01 1.00175740354601e+01 - 139 1.00846525340704e+01 9.99930113951843e+00 - 140 1.00745850435896e+01 9.97645596333061e+00 - 141 1.00644392647413e+01 9.95041162930873e+00 - 142 1.00541491709691e+01 9.92180111647481e+00 - 143 1.00436823424749e+01 9.89050169056719e+00 - 144 1.00330636529660e+01 9.85603208426972e+00 - 145 1.00223839228086e+01 9.81818334237853e+00 - 146 1.00118047065649e+01 9.77758921505729e+00 - 147 1.00015612314349e+01 9.73590349870836e+00 - 148 9.99195527218088e+00 9.69551788236989e+00 - 149 9.98332631801527e+00 9.65911749675800e+00 - 150 9.97599491711484e+00 9.62915810268995e+00 - 151 9.97018870425343e+00 9.60717358806770e+00 - 152 9.96597676149386e+00 9.59319263515552e+00 - 153 9.96323912038658e+00 9.58560496094010e+00 - 154 9.96168472712778e+00 9.58154384221214e+00 - 155 9.96091708239459e+00 9.57764409185937e+00 - 156 9.96053284836430e+00 9.57094226701891e+00 - 157 9.96022340231744e+00 9.55966218699141e+00 - 158 9.95984104841431e+00 9.54367921177888e+00 - 159 9.95941115970323e+00 9.52452532866834e+00 - 160 9.95909775592352e+00 9.50490062318069e+00 - 161 9.95913472197875e+00 9.48781177595095e+00 - 162 9.95973716567135e+00 9.47562216260840e+00 - 163 9.96102283681378e+00 9.46939618474568e+00 - 164 9.96297512061468e+00 9.46883909503368e+00 - 165 9.96545450087319e+00 9.47284744786104e+00 - 166 9.96824446676367e+00 9.48032505757766e+00 - 167 9.97111490093449e+00 9.49080999053287e+00 - 168 9.97388723087919e+00 9.50468382474366e+00 - 169 9.97648454853684e+00 9.52297944488190e+00 - 170 9.97895120221314e+00 9.54683939172159e+00 - 171 9.98143439573287e+00 9.57673744631037e+00 - 172 9.98412851702981e+00 9.61177677879831e+00 - 173 9.98719912546727e+00 9.64941646139346e+00 - 174 9.99071466036109e+00 9.68581516318204e+00 - 175 9.99461255041478e+00 9.71674194992540e+00 - 176 9.99871362276481e+00 9.73875618365856e+00 - 177 1.00027752607551e+01 9.75023319932384e+00 - 178 1.00065593228689e+01 9.75187374895997e+00 - 179 1.00098932819698e+01 9.74651102922357e+00 - 180 1.00127089751067e+01 9.73824323715410e+00 - 181 1.00150539578018e+01 9.73118937807432e+00 - 182 1.00170703552922e+01 9.72834303011533e+00 - 183 1.00189424568686e+01 9.73087964994846e+00 - 184 1.00208211796404e+01 9.73798531353725e+00 - 185 1.00227525196798e+01 9.74722518450810e+00 - 186 1.00246411639883e+01 9.75544038568881e+00 - 187 1.00262714680409e+01 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1.00213474465750e+01 9.70762043885231e+00 + 194 1.00187805230869e+01 9.69773175124558e+00 + 195 1.00164016154513e+01 9.68784935173366e+00 + 196 1.00144402674219e+01 9.67667427007303e+00 + 197 1.00130444574495e+01 9.66343938720852e+00 + 198 1.00122912607270e+01 9.64854739476250e+00 + 199 1.00122066750836e+01 9.63383866331536e+00 + 200 1.00127732034965e+01 9.62235997490241e+00 diff --git a/examples/USER/colvars/out2.colvars.state b/examples/USER/colvars/out2.colvars.state index 8917077caf..e923862831 100644 --- a/examples/USER/colvars/out2.colvars.state +++ b/examples/USER/colvars/out2.colvars.state @@ -1,22 +1,23 @@ configuration { step 300 dt 2.000000e+00 + version 2018-11-16 } colvar { name one - x 9.95354148699614e+00 + x 9.95315918568411e+00 } colvar { name two - x 9.79310294857288e+00 + x 9.79318883680258e+00 } -harmonic { +restraint { configuration { + step 300 name h_pot - stage 8103505641670189088 } } diff --git a/examples/USER/colvars/out2.colvars.traj b/examples/USER/colvars/out2.colvars.traj index 5130ca99f1..365f9b8306 100644 --- a/examples/USER/colvars/out2.colvars.traj +++ b/examples/USER/colvars/out2.colvars.traj @@ -1,102 +1,102 @@ -# step one two - 200 1.00127641579482e+01 9.62235621950587e+00 - 201 1.00139098397954e+01 9.61766067322651e+00 - 202 1.00154895322849e+01 9.62284260846102e+00 - 203 1.00172625720562e+01 9.63964717046032e+00 - 204 1.00188930177704e+01 9.66786064733448e+00 - 205 1.00199761813056e+01 9.70519780219794e+00 - 206 1.00200944106384e+01 9.74779969655747e+00 - 207 1.00188963572281e+01 9.79111374012340e+00 - 208 1.00161883604793e+01 9.83086787098858e+00 - 209 1.00120201470551e+01 9.86403984083060e+00 - 210 1.00067290723642e+01 9.88948240692241e+00 - 211 1.00009114042457e+01 9.90790280320401e+00 - 212 9.99530858712775e+00 9.92119319076851e+00 - 213 9.99063126799011e+00 9.93149262690681e+00 - 214 9.98737350983788e+00 9.94043951053174e+00 - 215 9.98567811211086e+00 9.94878566374960e+00 - 216 9.98529977833156e+00 9.95640488686023e+00 - 217 9.98567740511041e+00 9.96270367197379e+00 - 218 9.98609281741416e+00 9.96726160094494e+00 - 219 9.98586784093273e+00 9.97033437532426e+00 - 220 9.98454831898211e+00 9.97291246609646e+00 - 221 9.98202887687821e+00 9.97627400695988e+00 - 222 9.97858776161328e+00 9.98128372296812e+00 - 223 9.97481791063232e+00 9.98787692577356e+00 - 224 9.97146915301902e+00 9.99495319867179e+00 - 225 9.96924741695340e+00 1.00005781312739e+01 - 226 9.96863280571612e+00 1.00023562928510e+01 - 227 9.96977462939505e+00 9.99793468396390e+00 - 228 9.97249206995624e+00 9.98558877312050e+00 - 229 9.97637419760570e+00 9.96476526430303e+00 - 230 9.98093600414111e+00 9.93639297716863e+00 - 231 9.98577334632368e+00 9.90279138444459e+00 - 232 9.99066901099700e+00 9.86714667869485e+00 - 233 9.99562704815141e+00 9.83274230148512e+00 - 234 1.00008356809073e+01 9.80226834521352e+00 - 235 1.00065772362800e+01 9.77744581513232e+00 - 236 1.00131097048912e+01 9.75894408214992e+00 - 237 1.00205553485494e+01 9.74639403983496e+00 - 238 1.00288314258010e+01 9.73851464709533e+00 - 239 1.00376482262668e+01 9.73355843502651e+00 - 240 1.00465718867162e+01 9.72986544373201e+00 - 241 1.00551241447104e+01 9.72616365347388e+00 - 242 1.00628799016098e+01 9.72156081057173e+00 - 243 1.00695359569141e+01 9.71533506969961e+00 - 244 1.00749394351078e+01 9.70669135454371e+00 - 245 1.00790729024702e+01 9.69470862769774e+00 - 246 1.00820010382698e+01 9.67869454326621e+00 - 247 1.00837917095021e+01 9.65894101136318e+00 - 248 1.00844414119874e+01 9.63696223650643e+00 - 249 1.00838441989246e+01 9.61423476365400e+00 - 250 1.00818306797879e+01 9.59185059543549e+00 - 251 1.00782686429397e+01 9.57154356576350e+00 - 252 1.00731806695096e+01 9.55550278600070e+00 - 253 1.00668200834919e+01 9.54554307033366e+00 - 254 1.00596730176507e+01 9.54248962932697e+00 - 255 1.00523895763009e+01 9.54590976255577e+00 - 256 1.00456784264533e+01 9.55421544253452e+00 - 257 1.00402005024002e+01 9.56513899116782e+00 - 258 1.00364831006552e+01 9.57640458000444e+00 - 259 1.00348576492106e+01 9.58619146455749e+00 - 260 1.00354210621162e+01 9.59329709957898e+00 - 261 1.00380245202744e+01 9.59728096353517e+00 - 262 1.00422960600822e+01 9.59832037848005e+00 - 263 1.00476990763950e+01 9.59672497993560e+00 - 264 1.00536104533027e+01 9.59261911381189e+00 - 265 1.00594002482137e+01 9.58602304006163e+00 - 266 1.00644981793165e+01 9.57714719542419e+00 - 267 1.00684482704210e+01 9.56662135439055e+00 - 268 1.00709580655557e+01 9.55551489305294e+00 - 269 1.00719418900228e+01 9.54518226195314e+00 - 270 1.00715463773733e+01 9.53703197862875e+00 - 271 1.00701345227997e+01 9.53228911010047e+00 - 272 1.00682184887617e+01 9.53176321322706e+00 - 273 1.00663378629920e+01 9.53558933249131e+00 - 274 1.00649132448630e+01 9.54304329234477e+00 - 275 1.00641243212406e+01 9.55266696753925e+00 - 276 1.00638595454980e+01 9.56275901409309e+00 - 277 1.00637587244679e+01 9.57196213233751e+00 - 278 1.00633313189549e+01 9.57961568108488e+00 - 279 1.00621123193119e+01 9.58575692732997e+00 - 280 1.00598117112007e+01 9.59088855190189e+00 - 281 1.00564177173993e+01 9.59570566223894e+00 - 282 1.00522270044392e+01 9.60088836897012e+00 - 283 1.00477888199161e+01 9.60693590561625e+00 - 284 1.00437690523107e+01 9.61400570555926e+00 - 285 1.00407622307256e+01 9.62182265962647e+00 - 286 1.00391028258991e+01 9.62979902243492e+00 - 287 1.00387366035163e+01 9.63738040674711e+00 - 288 1.00391979793082e+01 9.64439605217689e+00 - 289 1.00397008587343e+01 9.65118231683256e+00 - 290 1.00393154139857e+01 9.65847479887268e+00 - 291 1.00371856971467e+01 9.66716430247627e+00 - 292 1.00327325013742e+01 9.67799413246555e+00 - 293 1.00257889436952e+01 9.69130066948859e+00 - 294 1.00166284740574e+01 9.70687426338097e+00 - 295 1.00058767991341e+01 9.72395332252100e+00 - 296 9.99433972822595e+00 9.74134088397850e+00 - 297 9.98281255441855e+00 9.75768650006539e+00 - 298 9.97193339524040e+00 9.77194269576588e+00 - 299 9.96211387496966e+00 9.78370254738211e+00 - 300 9.95354148699614e+00 9.79310294857288e+00 +# step one two + 200 1.00127732034965e+01 9.62235997490241e+00 + 201 1.00139198864982e+01 9.61766167925624e+00 + 202 1.00155004339120e+01 9.62284272858813e+00 + 203 1.00172741972246e+01 9.63964899323068e+00 + 204 1.00189052021826e+01 9.66786718571673e+00 + 205 1.00199887119842e+01 9.70521202056400e+00 + 206 1.00201070660155e+01 9.74782380666112e+00 + 207 1.00189089093749e+01 9.79114913038349e+00 + 208 1.00162005540278e+01 9.83091553260188e+00 + 209 1.00120316562035e+01 9.86409994884863e+00 + 210 1.00067394529596e+01 9.88955328455197e+00 + 211 1.00009200584653e+01 9.90798080826055e+00 + 212 9.99531475905311e+00 9.92127385542524e+00 + 213 9.99063400342297e+00 9.93157198661852e+00 + 214 9.98737188807678e+00 9.94051482696048e+00 + 215 9.98567127567181e+00 9.94885527957784e+00 + 216 9.98528704043382e+00 9.95646746111755e+00 + 217 9.98565832937415e+00 9.96275739929720e+00 + 218 9.98606724184677e+00 9.96730423246689e+00 + 219 9.98583582550472e+00 9.97036378703713e+00 + 220 9.98451001643477e+00 9.97292736129215e+00 + 221 9.98198434901656e+00 9.97627439806637e+00 + 222 9.97853678731273e+00 9.98127100659218e+00 + 223 9.97475984191141e+00 9.98785371236258e+00 + 224 9.97140286510626e+00 9.99492286335624e+00 + 225 9.96917137580259e+00 1.00005443231922e+01 + 226 9.96854523900174e+00 1.00023222923235e+01 + 227 9.96967375964547e+00 9.99790273206806e+00 + 228 9.97237636771905e+00 9.98555960216881e+00 + 229 9.97624253505807e+00 9.96473792067690e+00 + 230 9.98078777310055e+00 9.93636511602182e+00 + 231 9.98560846780419e+00 9.90275990393703e+00 + 232 9.99048787217569e+00 9.86710855077386e+00 + 233 9.99543040822038e+00 9.83269539984149e+00 + 234 1.00006246021103e+01 9.80221208335553e+00 + 235 1.00063530848982e+01 9.77738136586701e+00 + 236 1.00128741709083e+01 9.75887400813685e+00 + 237 1.00203106975850e+01 9.74632163179798e+00 + 238 1.00285805371730e+01 9.73844350416337e+00 + 239 1.00373945897865e+01 9.73349215182819e+00 + 240 1.00463194539327e+01 9.72980720779576e+00 + 241 1.00548770491533e+01 9.72611599020063e+00 + 242 1.00626421174965e+01 9.72152572108181e+00 + 243 1.00693109823863e+01 9.71531423107737e+00 + 244 1.00747300690509e+01 9.70668632474813e+00 + 245 1.00788811512303e+01 9.69472082245661e+00 + 246 1.00818281591535e+01 9.67872530149764e+00 + 247 1.00836382918008e+01 9.65899116363609e+00 + 248 1.00843077585461e+01 9.63702967428387e+00 + 249 1.00837304601058e+01 9.61431312359133e+00 + 250 1.00817369874724e+01 9.59193249256670e+00 + 251 1.00781951382998e+01 9.57162234547176e+00 + 252 1.00731274409141e+01 9.55557274350384e+00 + 253 1.00667870632608e+01 9.54560001126946e+00 + 254 1.00596598859158e+01 9.54253147668434e+00 + 255 1.00523956909045e+01 9.54593692832520e+00 + 256 1.00457028282132e+01 9.55423082330650e+00 + 257 1.00402418669526e+01 9.56514761944992e+00 + 258 1.00365397691695e+01 9.57641296971103e+00 + 259 1.00349276270394e+01 9.58620624196598e+00 + 260 1.00355019919770e+01 9.59332346959128e+00 + 261 1.00381137097146e+01 9.59732188686984e+00 + 262 1.00423905760179e+01 9.59837618250971e+00 + 263 1.00477959188736e+01 9.59679324477687e+00 + 264 1.00537068007149e+01 9.59269523141530e+00 + 265 1.00594937260641e+01 9.58610120816249e+00 + 266 1.00645870781682e+01 9.57722117048002e+00 + 267 1.00685316571224e+01 9.56668493985151e+00 + 268 1.00710357823615e+01 9.55556251047062e+00 + 269 1.00720144042107e+01 9.54520978473172e+00 + 270 1.00716144493745e+01 9.53703781183182e+00 + 271 1.00701992199135e+01 9.53227489206590e+00 + 272 1.00682808706064e+01 9.53173333554826e+00 + 273 1.00663988075209e+01 9.53554943194497e+00 + 274 1.00649733063520e+01 9.54299862049767e+00 + 275 1.00641836485840e+01 9.55262143610080e+00 + 276 1.00639178664285e+01 9.56271517955029e+00 + 277 1.00638153921535e+01 9.57192148747872e+00 + 278 1.00633853985923e+01 9.57957875475062e+00 + 279 1.00621626720543e+01 9.58572327394556e+00 + 280 1.00598570838615e+01 9.59085686511578e+00 + 281 1.00564566071967e+01 9.59567423393283e+00 + 282 1.00522576614697e+01 9.60085550637412e+00 + 283 1.00478091897332e+01 9.60690040068280e+00 + 284 1.00437767664032e+01 9.61396708331890e+00 + 285 1.00407546813490e+01 9.62178118810825e+00 + 286 1.00390773261870e+01 9.62975547860500e+00 + 287 1.00386906040191e+01 9.63733595704590e+00 + 288 1.00391292740982e+01 9.64435229335154e+00 + 289 1.00396077171765e+01 9.65114124926381e+00 + 290 1.00391967746350e+01 9.65843904962787e+00 + 291 1.00370409303829e+01 9.66713735495098e+00 + 292 1.00325613495850e+01 9.67798035621834e+00 + 293 1.00255913568518e+01 9.69130440474672e+00 + 294 1.00164044158125e+01 9.70689841022156e+00 + 295 1.00056261321876e+01 9.72399810930261e+00 + 296 9.99406221883501e+00 9.74140402524052e+00 + 297 9.98250803362175e+00 9.75776438941627e+00 + 298 9.97160202027972e+00 9.77203069297329e+00 + 299 9.96175637151037e+00 9.78379375044905e+00 + 300 9.95315918568411e+00 9.79318883680258e+00 diff --git a/examples/USER/colvars/peptide2.colvars.state b/examples/USER/colvars/peptide2.colvars.state index cfb7c49930..5272bb7c4a 100644 --- a/examples/USER/colvars/peptide2.colvars.state +++ b/examples/USER/colvars/peptide2.colvars.state @@ -1,17 +1,18 @@ configuration { step 100 dt 2.000000e+00 + version 2018-11-16 } colvar { name one - x 1.00387424212228e+01 + x 1.00387423506482e+01 } -harmonic { +restraint { configuration { + step 100 name h_pot - stage 4044288781530052640 } } diff --git a/examples/USER/colvars/peptide2.colvars.traj b/examples/USER/colvars/peptide2.colvars.traj index 2c4bf7ad54..0d8931bda7 100644 --- a/examples/USER/colvars/peptide2.colvars.traj +++ b/examples/USER/colvars/peptide2.colvars.traj @@ -1,102 +1,102 @@ -# step one - 0 1.23398428397332e+01 - 1 1.23379000531837e+01 - 2 1.22833752132682e+01 - 3 1.21783464524822e+01 - 4 1.20268109152646e+01 - 5 1.18342676552027e+01 - 6 1.16071240696111e+01 - 7 1.13522568477758e+01 - 8 1.10769760454451e+01 - 9 1.07892333501017e+01 - 10 1.04978607983300e+01 - 11 1.02148368912480e+01 - 12 9.95820967758655e+00 - 13 9.74528082635713e+00 - 14 9.59065550809125e+00 - 15 9.49025917553263e+00 - 16 9.43254360388750e+00 - 17 9.41011962734900e+00 - 18 9.41602364253240e+00 - 19 9.44413444723206e+00 - 20 9.49001191595699e+00 - 21 9.55036186844267e+00 - 22 9.62258413071055e+00 - 23 9.70460340526413e+00 - 24 9.79475248209609e+00 - 25 9.89135077720185e+00 - 26 9.99213105078110e+00 - 27 1.00938499722663e+01 - 28 1.01925349210626e+01 - 29 1.02845107805173e+01 - 30 1.03676652352347e+01 - 31 1.04416367894860e+01 - 32 1.05071334937552e+01 - 33 1.05650452299048e+01 - 34 1.06158824214188e+01 - 35 1.06595186275218e+01 - 36 1.06948928511102e+01 - 37 1.07202580715959e+01 - 38 1.07337399401028e+01 - 39 1.07331885445159e+01 - 40 1.07158932314825e+01 - 41 1.06789136129953e+01 - 42 1.06198862520319e+01 - 43 1.05380120055201e+01 - 44 1.04346603936480e+01 - 45 1.03132931131809e+01 - 46 1.01792839195940e+01 - 47 1.00398967921774e+01 - 48 9.90373826474332e+00 - 49 9.77934819842326e+00 - 50 9.67344128626180e+00 - 51 9.58957431460176e+00 - 52 9.52771755964755e+00 - 53 9.48463676001684e+00 - 54 9.45495927636316e+00 - 55 9.43277262066999e+00 - 56 9.41329687195946e+00 - 57 9.39418023785890e+00 - 58 9.37608079167942e+00 - 59 9.36244026161597e+00 - 60 9.35853356967195e+00 - 61 9.36993825765332e+00 - 62 9.40084295384763e+00 - 63 9.45286334548428e+00 - 64 9.52464492798022e+00 - 65 9.61230778865749e+00 - 66 9.71074173620872e+00 - 67 9.81506921139973e+00 - 68 9.92117599348263e+00 - 69 1.00244217575122e+01 - 70 1.01178260477346e+01 - 71 1.01986938379172e+01 - 72 1.02670956368544e+01 - 73 1.03213051063305e+01 - 74 1.03597191337854e+01 - 75 1.03817745676591e+01 - 76 1.03880610583944e+01 - 77 1.03809103738027e+01 - 78 1.03645558156884e+01 - 79 1.03441497701913e+01 - 80 1.03243653409000e+01 - 81 1.03082112818858e+01 - 82 1.02961296917318e+01 - 83 1.02862106580352e+01 - 84 1.02756069146933e+01 - 85 1.02618115908758e+01 - 86 1.02435132305408e+01 - 87 1.02212121470422e+01 - 88 1.01972799936680e+01 - 89 1.01743931780361e+01 - 90 1.01538342930689e+01 - 91 1.01363020288600e+01 - 92 1.01223080393853e+01 - 93 1.01118050646187e+01 - 94 1.01038513159042e+01 - 95 1.00967020139234e+01 - 96 1.00885782989097e+01 - 97 1.00784257293241e+01 - 98 1.00661428832570e+01 - 99 1.00524912515310e+01 - 100 1.00387424212228e+01 +# step one + 0 1.23398428397332e+01 + 1 1.23379000532662e+01 + 2 1.22833752135957e+01 + 3 1.21783464514507e+01 + 4 1.20268109095184e+01 + 5 1.18342676394048e+01 + 6 1.16071240372003e+01 + 7 1.13522567926249e+01 + 8 1.10769759646337e+01 + 9 1.07892332454600e+01 + 10 1.04978606745989e+01 + 11 1.02148367517604e+01 + 12 9.95820954052204e+00 + 13 9.74528077043305e+00 + 14 9.59065564952749e+00 + 15 9.49025959957862e+00 + 16 9.43254431868731e+00 + 17 9.41012058917623e+00 + 18 9.41602481112176e+00 + 19 9.44413580740584e+00 + 20 9.49001346044027e+00 + 21 9.55036359015270e+00 + 22 9.62258602486444e+00 + 23 9.70460545744668e+00 + 24 9.79475465622561e+00 + 25 9.89135302429916e+00 + 26 9.99213332770717e+00 + 27 1.00938522423366e+01 + 28 1.01925371414626e+01 + 29 1.02845129002944e+01 + 30 1.03676671987640e+01 + 31 1.04416385355998e+01 + 32 1.05071349561950e+01 + 33 1.05650463398331e+01 + 34 1.06158831174766e+01 + 35 1.06595188661313e+01 + 36 1.06948926085038e+01 + 37 1.07202573517647e+01 + 38 1.07337387802787e+01 + 39 1.07331870068021e+01 + 40 1.07158913924701e+01 + 41 1.06789115566470e+01 + 42 1.06198840652253e+01 + 43 1.05380097743725e+01 + 44 1.04346581978275e+01 + 45 1.03132910149185e+01 + 46 1.01792819503691e+01 + 47 1.00398949454818e+01 + 48 9.90373650268307e+00 + 49 9.77934647164350e+00 + 50 9.67343955381284e+00 + 51 9.58957255517495e+00 + 52 9.52771577288560e+00 + 53 9.48463495848957e+00 + 54 9.45495747488851e+00 + 55 9.43277083061229e+00 + 56 9.41329510571902e+00 + 57 9.39417852043035e+00 + 58 9.37607916767444e+00 + 59 9.36243879601093e+00 + 60 9.35853234890725e+00 + 61 9.36993739187210e+00 + 62 9.40084256925489e+00 + 63 9.45286356660258e+00 + 64 9.52464585631223e+00 + 65 9.61230948096192e+00 + 66 9.71074418990813e+00 + 67 9.81507236552599e+00 + 68 9.92117974657176e+00 + 69 1.00244259961919e+01 + 70 1.01178306268727e+01 + 71 1.01986985644537e+01 + 72 1.02671003889995e+01 + 73 1.03213098011429e+01 + 74 1.03597236984298e+01 + 75 1.03817789163109e+01 + 76 1.03880650963390e+01 + 77 1.03809140245635e+01 + 78 1.03645590344102e+01 + 79 1.03441525373194e+01 + 80 1.03243676495902e+01 + 81 1.03082131278348e+01 + 82 1.02961310659179e+01 + 83 1.02862115513553e+01 + 84 1.02756073299153e+01 + 85 1.02618115461408e+01 + 86 1.02435127550163e+01 + 87 1.02212112849545e+01 + 88 1.01972788307491e+01 + 89 1.01743918261207e+01 + 90 1.01538328424605e+01 + 91 1.01363005552771e+01 + 92 1.01223066231827e+01 + 93 1.01118037967830e+01 + 94 1.01038502876980e+01 + 95 1.00967012947728e+01 + 96 1.00885779123137e+01 + 97 1.00784256309007e+01 + 98 1.00661429612272e+01 + 99 1.00524913461711e+01 + 100 1.00387423506482e+01 diff --git a/examples/USER/diffraction/BulkNi.in b/examples/USER/diffraction/in.BulkNi similarity index 92% rename from examples/USER/diffraction/BulkNi.in rename to examples/USER/diffraction/in.BulkNi index 8315e57750..ab82986f50 100644 --- a/examples/USER/diffraction/BulkNi.in +++ b/examples/USER/diffraction/in.BulkNi @@ -1,5 +1,4 @@ variable A string bulkNi -log $A.log boundary p p p @@ -26,7 +25,7 @@ fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] & fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed -dump 1 all custom 1 $A.dump id x y z +#dump 1 all custom 1 $A.dump id x y z run 0 unfix 1 diff --git a/examples/USER/diffraction/log.27Nov18.BulkNi.g++.1 b/examples/USER/diffraction/log.27Nov18.BulkNi.g++.1 new file mode 100644 index 0000000000..d716f827e0 --- /dev/null +++ b/examples/USER/diffraction/log.27Nov18.BulkNi.g++.1 @@ -0,0 +1,72 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable A string bulkNi + +boundary p p p + +units metal +timestep 0.001 + +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (70.4 70.4 70.4) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 32000 atoms + Time spent = 0.0037179 secs + +pair_style none +mass * 58.71 +atom_modify sort 0 0 + +compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo + +compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 0 0 0 c 0.025 0.025 0.025 dR_Ewald 0.01 echo manual + +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file $A.hist.xrd +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file bulkNi.hist.xrd + +fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed +fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed + +#dump 1 all custom 1 $A.dump id x y z +run 0 +Per MPI rank memory allocation (min/avg/max) = 21.91 | 21.91 | 21.91 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 9.53674e-07 on 1 procs for 0 steps with 32000 atoms + +314.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 9.537e-07 | | |100.00 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2461 ave 2461 max 2461 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +unfix 2 +uncompute XRD +uncompute SAED + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:03:30 diff --git a/examples/USER/diffraction/log.27Nov18.BulkNi.g++.4 b/examples/USER/diffraction/log.27Nov18.BulkNi.g++.4 new file mode 100644 index 0000000000..04761a1e06 --- /dev/null +++ b/examples/USER/diffraction/log.27Nov18.BulkNi.g++.4 @@ -0,0 +1,72 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +variable A string bulkNi + +boundary p p p + +units metal +timestep 0.001 + +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 20 0 20 0 20 +create_box 1 box +Created orthogonal box = (0 0 0) to (70.4 70.4 70.4) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 32000 atoms + Time spent = 0.0010488 secs + +pair_style none +mass * 58.71 +atom_modify sort 0 0 + +compute XRD all xrd 1.541838 Ni 2Theta 40 80 c 2 2 2 LP 1 echo + +compute SAED all saed 0.0251 Ni Kmax 0.85 Zone 0 0 0 c 0.025 0.025 0.025 dR_Ewald 0.01 echo manual + +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file $A.hist.xrd +fix 1 all ave/histo/weight 1 1 1 40 80 200 c_XRD[1] c_XRD[2] mode vector file bulkNi.hist.xrd + +fix 2 all saed/vtk 1 1 1 c_SAED file $A_001.saed +fix 2 all saed/vtk 1 1 1 c_SAED file bulkNi_001.saed + +#dump 1 all custom 1 $A.dump id x y z +run 0 +Per MPI rank memory allocation (min/avg/max) = 16.08 | 16.08 | 16.08 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 1.84774e-06 on 4 procs for 0 steps with 32000 atoms + +162.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.848e-06 | | |100.00 + +Nlocal: 8000 ave 8000 max 8000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 1041 ave 1041 max 1041 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + +unfix 1 +unfix 2 +uncompute XRD +uncompute SAED + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:54 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 new file mode 100644 index 0000000000..0302966447 --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.1 @@ -0,0 +1,193 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +comm_modify vel yes + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nve + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 79507 46656 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 1.8285224 3442.9216 2047.8425 187.41713 1395.0792 844.61103 802.43438 114.10967 0 -765.532 595242.44 -594842.98 3027.409 55742.797 200.4343 152.51723 + 100 3.7075663 2949.9137 1973.6229 180.62461 976.29073 358.0742 923.62856 174.43734 0 -919.88297 595306.76 -594866.72 2009.106 55742.797 229.49986 50.10998 + 150 5.5383921 2885.0697 1951.4547 178.59578 933.61499 234.26452 991.10197 194.44106 0 -910.03339 595293.22 -594869.38 4963.8801 55742.797 240.13548 14.311317 + 200 7.4217758 2890.343 1901.2801 174.00384 989.06297 227.57533 1077.5605 200.01467 0 -943.83325 595298.11 -594870.36 2977.5804 55742.797 237.27186 5.1150968 + 250 9.2994335 2922.348 1945.2702 178.02978 977.07781 212.26144 1127.8726 194.65284 0 -984.2934 595297.59 -594871.01 1592.2372 55742.797 243.81864 2.4147813 + 300 11.125204 2986.575 2013.159 184.24291 973.41608 212.85963 1130.6272 194.90599 0 -992.98724 595299.3 -594871.29 2816.8628 55742.797 252.63444 1.681279 + 350 12.99769 3051.4916 1978.4541 181.06675 1073.0375 228.43411 1195.4688 205.43169 0 -982.55178 595297.25 -594871 1408.7973 55742.797 248.34887 1.4666749 + 400 14.865399 3011.3983 1995.0047 182.58145 1016.3936 237.79955 1167.8185 197.49857 0 -1014.9362 595298.99 -594870.78 1456.5007 55742.797 250.45674 1.3981189 + 450 16.681866 3010.262 1976.9744 180.93133 1033.2876 216.3478 1196.7189 197.65964 0 -1005.6015 595298.72 -594870.56 1296.528 55742.797 248.1869 1.4022273 + 500 18.553431 3051.4554 2022.049 185.05652 1029.4064 220.84993 1196.1502 199.57249 0 -1014.3775 595298.27 -594871.05 2481.7571 55742.797 253.85835 1.3999256 + 550 20.416665 3086.0021 2018.9226 184.7704 1067.0796 221.95877 1215.9767 213.3405 0 -1012.5564 595299.48 -594871.12 1694.9376 55742.797 253.47686 1.3683935 + 600 22.27849 3110.9928 2030.8992 185.86649 1080.0935 220.35725 1253.9571 208.13083 0 -1030.4314 595298.96 -594870.88 -76.102661 55742.797 254.95682 1.4397403 + 650 24.087152 3154.373 2024.8469 185.31258 1129.5261 221.85968 1283.352 210.69451 0 -1015.2311 595299.67 -594870.82 1280.5683 55742.797 254.20302 1.4194509 + 700 25.941822 3133.85 2054.2045 187.99938 1079.6454 225.19338 1242.7819 192.54094 0 -1010.8971 595301.2 -594871.18 696.8538 55742.797 257.8878 1.4422435 + 750 27.79477 3189.0815 2103.7507 192.53381 1085.3308 219.46949 1243.7676 203.10695 0 -1010.2442 595299.93 -594870.7 483.46393 55742.797 264.14441 1.3796789 + 800 29.64589 3173.663 2053.4832 187.93336 1120.1799 219.59931 1256.2721 218.76191 0 -1003.0067 595299.37 -594870.81 543.09774 55742.797 257.81268 1.4005681 + 850 31.44585 3221.2873 2083.5215 190.68244 1137.7658 224.0492 1276.9143 219.91997 0 -1011.193 595298.47 -594870.4 143.54962 55742.797 261.60038 1.3772624 + 900 33.293605 3214.96 2053.8414 187.96614 1161.1187 222.21434 1296.0291 226.57612 0 -1013.6289 595300.61 -594870.68 473.39553 55742.797 257.85596 1.4053153 + 950 35.166863 3213.1086 2123.777 194.3666 1089.3317 221.79126 1251.6851 200.63798 0 -1014.0889 595300.01 -594870.7 1206.8497 55742.797 266.62111 1.4935247 + 1000 36.983663 3211.3103 2079.738 190.33618 1131.5723 225.4767 1260.2162 204.61245 0 -986.95685 595298.7 -594870.48 787.31501 55742.797 261.0928 1.4615275 + 1050 38.806926 3199.3221 2095.9148 191.81667 1103.4073 212.62976 1255.417 208.36886 0 -1001.9237 595299.13 -594870.21 239.45594 55742.797 263.14173 1.4246893 + 1100 40.634771 3199.8694 2067.6467 189.2296 1132.2227 235.50505 1264.2214 198.42446 0 -994.78564 595299.12 -594870.26 830.67515 55742.797 259.58627 1.4225726 + 1150 42.427903 3172.4663 2083.0988 190.64376 1089.3675 209.20043 1236.7213 204.50261 0 -990.26027 595299.43 -594870.22 1355.1408 55742.797 261.54264 1.389433 + 1200 44.302469 3178.2153 2055.1801 188.08866 1123.0351 230.76616 1258.2175 205.04893 0 -999.28826 595298.25 -594869.96 819.5423 55742.797 258.01926 1.4189827 + 1250 46.164956 3224.5367 2108.1449 192.93596 1116.3918 235.56939 1247.0387 212.74774 0 -1007.3896 595298.16 -594869.74 -146.38102 55742.797 264.67477 1.4395372 + 1300 48.015128 3286.0631 2125.3364 194.50931 1160.7267 236.69229 1272.7247 218.49151 0 -995.46842 595298.38 -594870.1 434.46496 55742.797 266.83295 1.451771 + 1350 49.79655 3247.1808 2087.4518 191.04214 1159.7291 215.07571 1301.219 211.43766 0 -995.15128 595297.24 -594870.09 1501.3496 55742.797 262.07016 1.44305 + 1400 51.624074 3194.7716 2041.9251 186.87557 1152.8466 236.94802 1261.0635 209.14663 0 -982.03995 595297.35 -594869.63 346.64925 55742.797 256.31352 1.5208162 + 1450 53.450535 3229.6083 2087.4545 191.04239 1142.1538 246.85361 1264.077 205.22437 0 -1003.5382 595299.44 -594869.9 278.1536 55742.797 262.08335 1.4087832 + 1500 55.288627 3249.6608 2089.8541 191.262 1159.8067 238.99337 1274.9502 206.61799 0 -988.99015 595297.98 -594869.75 636.34142 55742.797 262.36618 1.4595924 + 1550 57.093174 3273.2213 2122.5463 194.25397 1150.675 230.16428 1274.9965 195.7686 0 -979.24728 595298.84 -594869.85 528.01943 55742.797 266.47594 1.4678006 + 1600 58.978489 3288.6787 2120.7284 194.0876 1167.9503 229.10278 1274.2494 205.30619 0 -969.94195 595298.85 -594869.62 1126.6579 55742.797 266.23416 1.5026913 + 1650 60.803467 3286.3327 2148.1031 196.59291 1138.2295 234.18582 1256.2009 214.69184 0 -995.41699 595298.38 -594869.81 -457.07393 55742.797 269.67989 1.4977223 + 1700 62.624963 3296.9487 2092.8432 191.53556 1204.1055 238.05554 1313.8592 213.47968 0 -989.09874 595297.16 -594869.35 981.42569 55742.797 262.7423 1.4593707 + 1750 64.39829 3310.3958 2097.6547 191.97591 1212.7411 243.56621 1309.681 210.07115 0 -978.63733 595297.78 -594869.72 -41.877565 55742.797 263.31945 1.5344885 + 1800 66.216881 3229.7417 2079.7567 190.33789 1149.985 226.57585 1276.3941 202.60118 0 -984.26122 595298.62 -594869.94 515.97995 55742.797 261.07174 1.5239416 + 1850 68.038292 3199.6375 2033.1459 186.0721 1166.4916 242.84458 1267.7768 212.87764 0 -984.52187 595296.72 -594869.21 440.77319 55742.797 255.22287 1.4839954 + 1900 69.841965 3155.3872 2019.0731 184.78417 1136.3141 213.38104 1263.0105 213.0042 0 -980.43253 595296.92 -594869.57 469.76979 55742.797 253.48524 1.3965366 + 1950 71.702563 3191.9366 2051.5475 187.75621 1140.3891 211.61608 1278.9441 206.1048 0 -984.04544 595297.56 -594869.79 758.07165 55742.797 257.54478 1.4655839 + 2000 73.520102 3214.3938 2041.9357 186.87654 1172.4582 237.13198 1275.4194 218.0467 0 -985.25597 595296.76 -594869.64 375.81502 55742.797 256.33161 1.4761528 +Loop time of 73.5201 on 1 procs for 2000 steps with 4500 atoms + +Performance: 1.175 ns/day, 20.422 hours/ns, 27.203 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 50.346 | 50.346 | 50.346 | 0.0 | 68.48 +Bond | 3.3227 | 3.3227 | 3.3227 | 0.0 | 4.52 +Kspace | 16.003 | 16.003 | 16.003 | 0.0 | 21.77 +Neigh | 1.3495 | 1.3495 | 1.3495 | 0.0 | 1.84 +Comm | 0.33013 | 0.33013 | 0.33013 | 0.0 | 0.45 +Output | 0.0044131 | 0.0044131 | 0.0044131 | 0.0 | 0.01 +Modify | 2.1068 | 2.1068 | 2.1068 | 0.0 | 2.87 +Other | | 0.05755 | | | 0.08 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8703 ave 8703 max 8703 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 860806 ave 860806 max 860806 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 860806 +Ave neighs/atom = 191.29 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 28 +Dangerous builds = 0 +Total wall time: 0:01:13 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 new file mode 100644 index 0000000000..3a0f60f3cb --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.lang.g++.4 @@ -0,0 +1,193 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +comm_modify vel yes + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nve + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 26875 11664 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 0.60067916 3418.0026 2021.3092 184.98882 1396.6934 835.43668 808.1357 113.8069 0 -759.89265 595242.48 -594843.28 3040.8412 55742.797 197.07838 152.67751 + 100 1.1808443 2892.8432 1932.7674 176.88554 960.07578 363.31823 924.84568 164.52097 0 -931.84989 595306.29 -594867.05 1694.4336 55742.797 224.44681 49.87859 + 150 1.7504072 2833.9225 1947.7257 178.2545 886.19681 243.64601 972.03324 186.73658 0 -941.85405 595295.47 -594869.83 4603.775 55742.797 239.63159 14.40403 + 200 2.3280952 2870.6299 1920.2424 175.73925 950.38759 226.3737 1061.7175 186.27763 0 -950.17253 595296.43 -594870.24 2606.5041 55742.797 239.64552 5.1468097 + 250 2.9009523 2894.0913 1933.574 176.95936 960.51728 215.18824 1118.0957 195.43563 0 -993.95102 595296.54 -594870.8 1812.6379 55742.797 242.26101 2.6446653 + 300 3.4866827 2959.1219 1970.1936 180.31075 988.92834 209.63552 1155.4811 193.64322 0 -996.9511 595297.92 -594870.8 3371.5528 55742.797 247.17325 1.8304564 + 350 4.1206505 2988.7765 1988.8664 182.01968 999.91007 217.65998 1148.4029 204.96757 0 -996.5586 595296.05 -594870.61 3021.4005 55742.797 249.63956 1.5179762 + 400 4.7467482 3014.5638 1983.6589 181.54309 1030.9049 225.81008 1174.5083 214.70193 0 -1012.492 595298.89 -594870.51 668.28879 55742.797 249.02834 1.40089 + 450 5.3385043 3065.528 2028.5299 185.64965 1036.9981 206.85828 1232.536 204.7453 0 -1034.5447 595297.52 -594870.12 1276.895 55742.797 254.65283 1.4568976 + 500 5.8841732 3087.3359 1998.9143 182.93925 1088.4216 209.84037 1244.2781 211.45124 0 -1004.5214 595297.9 -594870.53 1811.1357 55742.797 250.95893 1.3696214 + 550 6.495003 3082.7524 2000.662 183.0992 1082.0904 218.46927 1229.7948 204.12764 0 -997.16039 595297.23 -594870.37 2005.0512 55742.797 251.16775 1.399994 + 600 7.0529547 3089.1148 2008.9702 183.85957 1080.1445 215.63956 1239.6501 205.6559 0 -1008.3414 595297.61 -594870.07 1579.3906 55742.797 252.19307 1.453043 + 650 7.6147993 3094.7607 1984.215 181.59398 1110.5457 217.2587 1270.5436 217.11567 0 -1021.7236 595297.37 -594870.02 922.17911 55742.797 249.09972 1.3970954 + 700 8.1847589 3085.7974 1977.7443 181.00179 1108.0531 226.89107 1263.0937 209.93619 0 -1019.8382 595298.21 -594870.24 1358.6744 55742.797 248.27153 1.4348071 + 750 8.7551639 3098.7075 1990.5214 182.17114 1108.186 210.53964 1263.8112 208.67005 0 -1002.6807 595298.31 -594870.47 1389.4827 55742.797 249.86686 1.4670711 + 800 9.3312614 3106.7743 2001.1286 183.14191 1105.6457 223.39008 1267.3688 200.94765 0 -1014.1025 595298.4 -594870.36 498.96153 55742.797 251.20537 1.4561965 + 850 9.9120548 3162.1905 2015.7594 184.4809 1146.4311 238.91403 1296.3319 216.49567 0 -1033.2993 595298.07 -594870.08 -146.24973 55742.797 253.06241 1.4124079 + 900 10.506582 3151.6622 2017.7351 184.66172 1133.9272 225.66798 1259.6857 214.41352 0 -993.82625 595298.42 -594870.44 855.52595 55742.797 253.32946 1.3630807 + 950 11.073148 3108.5571 1984.4638 181.61676 1124.0933 219.09683 1258.9728 215.5009 0 -998.11162 595299.1 -594870.46 742.29532 55742.797 249.13228 1.3937456 + 1000 11.712476 3151.1431 2010.1073 183.96363 1141.0358 234.62673 1262.3296 218.152 0 -1001.9319 595297.94 -594870.08 -15.429859 55742.797 252.31702 1.5039719 + 1050 12.416933 3154.9906 2025.2409 185.34864 1129.7498 240.28475 1245.2732 211.12104 0 -994.07995 595297.56 -594870.41 220.34341 55742.797 254.21036 1.5313366 + 1100 13.000971 3146.7058 2015.0512 184.41609 1131.6546 217.69098 1255.773 216.52818 0 -985.5434 595297.52 -594870.32 245.54987 55742.797 252.9731 1.4117211 + 1150 13.566174 3184.3315 2097.0388 191.91954 1087.2926 210.06417 1226.6616 216.15719 0 -994.73562 595299.65 -594870.51 960.8241 55742.797 263.29333 1.3975188 + 1200 14.098352 3181.1191 2062.3454 188.74443 1118.7737 228.90526 1255.3357 202.92363 0 -997.73355 595299.52 -594870.18 341.31357 55742.797 258.91222 1.4415835 + 1250 14.653097 3174.3638 2030.9146 185.8679 1143.4492 239.32477 1267.7689 201.40964 0 -992.67835 595297.78 -594870.16 399.69023 55742.797 254.97189 1.4037218 + 1300 15.198202 3181.4157 2020.4604 184.91114 1160.9553 213.94195 1283.8134 212.79399 0 -977.52401 595298.12 -594870.19 141.81633 55742.797 253.64065 1.447907 + 1350 15.763844 3221.4526 2077.8786 190.16601 1143.574 237.97099 1261.8854 206.43835 0 -991.01514 595298.43 -594870.14 293.86155 55742.797 260.85797 1.4643006 + 1400 16.36341 3273.4082 2117.3713 193.78035 1156.0369 241.63847 1257.3077 215.03947 0 -986.42491 595298.6 -594870.13 881.28305 55742.797 265.82788 1.4598428 + 1450 16.907335 3277.2159 2086.1619 190.92409 1191.054 245.42292 1289.0177 220.33432 0 -991.71405 595297.92 -594869.93 24.577369 55742.797 261.91752 1.4173689 + 1500 17.461373 3277.8652 2139.2814 195.78556 1138.5838 230.79453 1253.5268 210.7018 0 -984.94169 595298.66 -594870.16 612.24618 55742.797 268.59444 1.432741 + 1550 17.996041 3247.9903 2120.4397 194.06118 1127.5505 237.85251 1244.2413 207.38138 0 -989.02975 595297.17 -594870.07 908.40409 55742.797 266.20105 1.4941148 + 1600 18.546506 3263.2065 2095.2604 191.75678 1167.9461 222.27478 1287.0828 217.80256 0 -988.01164 595299.17 -594870.37 372.09439 55742.797 263.06244 1.4165997 + 1650 19.087156 3279.007 2102.6708 192.43497 1176.3363 228.35925 1287.432 218.78886 0 -987.87117 595299.94 -594870.32 -277.43091 55742.797 263.9961 1.4129192 + 1700 19.665064 3297.4084 2103.7436 192.53316 1193.6648 248.40926 1304.8649 202.53258 0 -989.5236 595297.12 -594869.74 1158.9952 55742.797 264.11122 1.4655993 + 1750 20.367483 3280.0391 2075.6964 189.9663 1204.3427 240.06411 1311.9499 213.18798 0 -987.79028 595296.5 -594869.56 437.83034 55742.797 260.60055 1.4183112 + 1800 20.942509 3272.2429 2082.8406 190.62013 1189.4023 235.68331 1306.7318 216.11438 0 -997.06553 595297.79 -594869.86 1293.8956 55742.797 261.49937 1.4181999 + 1850 21.546463 3288.8649 2088.0429 191.09624 1200.822 239.22801 1297.8732 214.15066 0 -979.04152 595298.01 -594869.39 217.43385 55742.797 262.15237 1.4245994 + 1900 22.118972 3213.0018 2032.382 186.00219 1180.6198 222.35796 1278.9261 222.52754 0 -969.8068 595296.01 -594869.39 563.16684 55742.797 255.16077 1.393322 + 1950 22.701752 3228.1804 2084.1556 190.74048 1144.0248 232.43889 1247.3333 216.54358 0 -981.18306 595298.59 -594869.7 -309.06733 55742.797 261.65433 1.4460719 + 2000 23.402514 3297.5065 2091.6171 191.42335 1205.8894 238.75396 1287.293 220.47084 0 -968.78447 595297.97 -594869.81 128.84944 55742.797 262.59803 1.4363623 +Loop time of 23.4026 on 4 procs for 2000 steps with 4500 atoms + +Performance: 3.692 ns/day, 6.501 hours/ns, 85.461 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.545 | 13.094 | 13.896 | 14.0 | 55.95 +Bond | 0.83177 | 0.90776 | 0.96459 | 5.1 | 3.88 +Kspace | 6.3904 | 7.1918 | 7.7297 | 18.8 | 30.73 +Neigh | 0.38941 | 0.38974 | 0.38988 | 0.0 | 1.67 +Comm | 0.65148 | 0.70795 | 0.7821 | 5.6 | 3.03 +Output | 0.0028274 | 0.0036304 | 0.0057163 | 2.0 | 0.02 +Modify | 1.0483 | 1.0571 | 1.0693 | 0.9 | 4.52 +Other | | 0.05109 | | | 0.22 + +Nlocal: 1125 ave 1207 max 1003 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 5763 ave 5904 max 5656 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 214633 ave 220347 max 204542 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 858532 +Ave neighs/atom = 190.785 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 28 +Dangerous builds = 0 +Total wall time: 0:00:23 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 new file mode 100644 index 0000000000..fbbe14192e --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.1 @@ -0,0 +1,199 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_CORE gCORES temp/com +compute cTEMP all temp/drude + +fix fDIRECT all drude/transform/direct +fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 260 100.0 +fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 1 20.0 +fix fINVERSE all drude/transform/inverse + +fix fMOMENTUM all momentum 100 linear 1 1 1 + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 79507 46656 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 26.29 | 26.29 | 26.29 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 1.9199426 2090.3465 1466.1274 134.17896 624.21909 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015 + 100 3.8672287 2131.9775 1633.3979 149.48744 498.57958 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587 + 150 5.7598403 2177.6381 1711.4959 156.63492 466.14214 134.74039 700.59918 168.27759 0 -965.58407 595300.38 -594872.27 4413.0226 55742.797 215.26856 0.12192183 + 200 7.7044377 2233.5218 1730.4556 158.3701 503.06611 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5946 55742.797 217.61368 0.22886584 + 250 9.6830325 2297.301 1773.2292 162.28471 524.07183 151.53589 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0574 55742.797 222.691 1.0389647 + 300 11.612487 2368.3956 1891.828 173.13879 476.56753 142.49028 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9226 55742.797 236.85673 3.051144 + 350 13.534112 2414.4805 1843.9331 168.75548 570.54737 181.42276 808.67959 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5958 55742.797 231.57282 1.0738202 + 400 15.432559 2466.7093 1924.3089 176.11142 542.40037 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79722 55742.797 241.94266 0.38534823 + 450 17.325742 2522.7871 1875.8855 171.67974 646.90166 133.40905 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.401476 55742.797 235.86638 0.34369113 + 500 19.162983 2580.277 1955.7507 178.98895 624.52624 185.08446 827.39298 175.04156 0 -984.94513 595290.88 -594868.93 3484.9214 55742.797 245.79119 0.67067789 + 550 21.070935 2640.6835 1866.0349 170.77823 774.64852 176.89611 988.92025 176.49761 0 -991.07213 595292.32 -594868.91 1773.3487 55742.797 234.10561 1.7344182 + 600 22.994624 2690.8564 1876.0664 171.6963 814.79004 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72494 55742.797 235.38014 1.7010295 + 650 24.877667 2732.1824 1963.5421 179.70202 768.64029 165.39218 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9019 55742.797 246.76774 0.68037803 + 700 26.759878 2775.7295 1921.9362 175.89427 853.7933 175.21242 987.66711 186.48684 0 -918.75412 595291.36 -594868.18 670.06325 55742.797 241.62283 0.44222016 + 750 28.615888 2820.0743 2038.1503 186.53011 781.92393 168.58533 929.80575 193.62705 0 -939.93789 595298.09 -594868.25 398.72744 55742.797 256.20117 0.55407341 + 800 30.410775 2865.9592 1943.5754 177.87467 922.38383 197.16018 1009.2236 201.50387 0 -914.81706 595297.54 -594868.23 -717.10982 55742.797 244.0452 1.2420646 + 850 32.248099 2909.1134 2101.5572 192.33306 807.55624 195.1889 876.12791 184.47417 0 -876.31499 595296.17 -594868.09 -1403.423 55742.797 263.69793 1.8344087 + 900 34.102496 2938.1375 2038.9241 186.60092 899.21338 183.32678 989.0166 184.31256 0 -889.86015 595300.05 -594867.63 -1087.2756 55742.797 256.12731 1.0106116 + 950 35.940632 2965.6943 2007.942 183.76546 957.75234 227.45507 972.71509 206.37948 0 -880.42319 595299.46 -594867.83 -1848.76 55742.797 252.40652 0.53885795 + 1000 37.768527 2994.2318 2058.0187 188.34845 936.2131 170.68954 965.88084 205.36587 0 -833.14442 595294.86 -594867.44 327.63778 55742.797 258.71295 0.52143526 + 1050 39.603905 3022.9502 2095.3849 191.76817 927.56532 203.90713 935.91395 205.082 0 -845.07245 595294.32 -594866.59 -355.70498 55742.797 263.25608 0.94199109 + 1100 41.345196 3051.1765 2047.7198 187.4059 1003.4567 212.39896 989.65688 227.20813 0 -856.11279 595297.04 -594866.74 -1402.0226 55742.797 256.98382 1.677375 + 1150 43.126233 3071.8156 2127.8628 194.74053 943.95283 188.38429 926.24314 223.28057 0 -821.63214 595294.06 -594866.38 550.31162 55742.797 267.19152 1.343134 + 1200 44.919531 3087.7694 2015.2957 184.43847 1072.4737 199.90941 1034.9531 215.15479 0 -804.43316 595293.38 -594866.49 -333.57889 55742.797 253.2678 0.70913779 + 1250 46.708812 3102.5825 2176.9514 199.23308 925.63109 155.81514 956.83605 230.07299 0 -847.4765 595296.65 -594866.26 -932.66378 55742.797 273.66546 0.54750847 + 1300 48.515239 3116.8403 2087.6042 191.05609 1029.2361 209.96221 974.81036 241.13636 0 -823.38395 595292.74 -594866.03 -825.75374 55742.797 262.34482 0.76176534 + 1350 50.311301 3131.0791 2089.6528 191.24358 1041.4264 186.48162 998.11153 233.70979 0 -801.36955 595290.06 -594865.57 684.79541 55742.797 262.36803 1.3871258 + 1400 52.135502 3138.996 2186.2583 200.08485 952.73772 168.60362 957.20176 227.71916 0 -826.52254 595291.08 -594865.34 1796.7314 55742.797 274.47405 1.5135697 + 1450 53.920154 3139.5791 2010.7381 184.02136 1128.841 192.80138 1074.5202 245.37245 0 -807.31625 595288.01 -594864.55 -16.506503 55742.797 252.6314 0.8772328 + 1500 55.713369 3143.899 2099.4529 192.14047 1044.4461 186.04036 980.83507 242.01351 0 -784.81179 595285 -594864.63 2343.8872 55742.797 263.89144 0.6124176 + 1550 57.492258 3149.7317 2086.0668 190.91539 1063.6649 165.80538 1056.0892 230.89557 0 -813.37736 595289.09 -594864.84 2260.7336 55742.797 262.17651 0.69483863 + 1600 59.30172 3156.5347 2013.4253 184.26729 1143.1093 210.65899 1098.2888 243.95147 0 -835.61974 595290.47 -594864.64 -838.56538 55742.797 252.86557 1.1543025 + 1650 61.139585 3160.0034 2081.0689 190.45799 1078.9345 212.2197 1005.7495 250.37949 0 -813.72039 595289.15 -594864.85 796.20008 55742.797 261.22489 1.5557795 + 1700 62.942445 3155.5695 2113.3768 193.41478 1042.1927 146.0358 1019.0909 249.77844 0 -798.16322 595290.59 -594865.14 359.703 55742.797 265.47004 1.0739924 + 1750 64.762126 3151.7963 2063.5473 188.85442 1088.249 224.89092 997.01992 247.37169 0 -807.87664 595291.82 -594864.98 -1081.2896 55742.797 259.34344 0.69485895 + 1800 66.592646 3150.4284 2097.9263 192.00076 1052.5021 202.22769 974.42253 248.58755 0 -799.53819 595291.61 -594864.8 94.59915 55742.797 263.68436 0.65251966 + 1850 68.418504 3153.4497 2106.6304 192.79735 1046.8193 177.57201 971.73173 249.90467 0 -777.13268 595289.76 -594865.02 881.42667 55742.797 264.65056 0.99601086 + 1900 70.216536 3159.2067 2092.2719 191.48328 1066.9348 198.78887 969.41481 260.03017 0 -787.26086 595290.41 -594864.45 606.42691 55742.797 262.6612 1.4839999 + 1950 72.044671 3164.5166 2059.5681 188.49025 1104.9485 214.12266 1000.4479 263.39571 0 -799.45144 595291.13 -594864.69 -1248.7635 55742.797 258.62997 1.2624764 + 2000 73.841754 3171.2996 2080.1586 190.37468 1091.1409 179.21893 996.41501 248.41662 0 -760.00915 595292.04 -594864.94 940.6962 55742.797 261.39988 0.78376244 +Loop time of 73.8418 on 1 procs for 2000 steps with 4500 atoms + +Performance: 1.170 ns/day, 20.512 hours/ns, 27.085 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 48.171 | 48.171 | 48.171 | 0.0 | 65.23 +Bond | 3.3962 | 3.3962 | 3.3962 | 0.0 | 4.60 +Kspace | 16.344 | 16.344 | 16.344 | 0.0 | 22.13 +Neigh | 1.6599 | 1.6599 | 1.6599 | 0.0 | 2.25 +Comm | 0.35976 | 0.35976 | 0.35976 | 0.0 | 0.49 +Output | 0.0045705 | 0.0045705 | 0.0045705 | 0.0 | 0.01 +Modify | 3.8475 | 3.8475 | 3.8475 | 0.0 | 5.21 +Other | | 0.05927 | | | 0.08 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10103 ave 10103 max 10103 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 774433 ave 774433 max 774433 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 774433 +Ave neighs/atom = 172.096 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 35 +Dangerous builds = 0 +Total wall time: 0:01:14 diff --git a/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 new file mode 100644 index 0000000000..d91bba57b1 --- /dev/null +++ b/examples/USER/drude/butane/log.27Nov18.butane.nh.g++.4 @@ -0,0 +1,199 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 butane system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 +pair_modify mix geometric tail yes +kspace_style pppm 1.0e-4 + +read_data data.butane + orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 4250 bonds + reading angles ... + 6000 angles + reading dihedrals ... + 6750 dihedrals + 5 = max # of 1-2 neighbors + 8 = max # of 1-3 neighbors + 12 = max # of 1-4 neighbors + 17 = max # of special neighbors + +group gBUTANE molecule 1:250 +4500 atoms in group gBUTANE +group gCORES type 1 2 3 +3500 atoms in group gCORES +group gDRUDES type 4 5 +1000 atoms in group gDRUDES + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 * thole 1.368000 +pair_coeff 2 * thole 1.368000 +pair_coeff 4 * thole 1.368000 +pair_coeff 5 * thole 1.368000 + +neighbor 2.0 bin + +variable vTEMP equal 260.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gCORES create ${vTEMP} 12345 +velocity gCORES create 260 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N D D + +fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 + 0 = # of size 2 clusters + 500 = # of size 3 clusters + 500 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_CORE gCORES temp/com +compute cTEMP all temp/drude + +fix fDIRECT all drude/transform/direct +fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 +fix fNVT1 gCORES nvt temp 260 260 100.0 +fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 +fix fNVT2 gDRUDES nvt temp 1 1 20.0 +fix fINVERSE all drude/transform/inverse + +fix fMOMENTUM all momentum 100 linear 1 1 1 + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 50 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.367867 + grid = 36 36 36 + stencil order = 5 + estimated absolute RMS force accuracy = 0.031354 + estimated relative force accuracy = 9.44215e-05 + using double precision FFTs + 3d grid and FFT values/proc = 26875 11664 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 17 +New max number of 1-2 to 1-4 neighbors: 17 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 8 8 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 16.75 | 17.03 | 17.13 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 4439.7916 55742.797 334.61375 18.435655 + 50 0.63524747 2090.3465 1466.1274 134.17896 624.2191 190.60044 660.09649 113.3603 0 -768.0633 595300.82 -594872.6 2826.2298 55742.797 184.22006 0.60185015 + 100 1.2804167 2131.9774 1633.3979 149.48744 498.57955 179.65934 694.88741 164.06284 0 -972.81644 595305.26 -594872.47 1226.789 55742.797 205.4291 0.16019587 + 150 1.9264774 2177.6381 1711.4959 156.63492 466.14218 134.74039 700.59917 168.27759 0 -965.58407 595300.38 -594872.27 4413.0227 55742.797 215.26856 0.12192187 + 200 2.5798194 2233.5217 1730.4557 158.3701 503.06601 188.43014 712.9189 165.88668 0 -988.5136 595295.4 -594871.06 2113.5944 55742.797 217.61368 0.22886584 + 250 3.234822 2297.3011 1773.2292 162.28471 524.07191 151.5359 821.1354 166.81416 0 -1042.1458 595297.16 -594870.43 1173.0577 55742.797 222.691 1.0389643 + 300 3.9885037 2368.3956 1891.828 173.13879 476.56759 142.49027 789.96852 154.5939 0 -1037.1885 595297.25 -594870.54 2520.9227 55742.797 236.85673 3.0511439 + 350 4.7276039 2414.4804 1843.9331 168.75548 570.54727 181.42277 808.6796 163.12794 0 -1005.9572 595293.4 -594870.13 2879.5954 55742.797 231.57282 1.0738212 + 400 5.3416793 2466.7094 1924.3089 176.11142 542.40044 167.48008 817.71904 181.25315 0 -1050.6473 595296.37 -594869.77 494.79737 55742.797 241.94266 0.38534799 + 450 6.0018888 2522.7872 1875.8855 171.67974 646.90169 133.40906 944.20903 180.31147 0 -1037.0957 595295.5 -594869.43 63.40141 55742.797 235.86638 0.34369111 + 500 6.6298664 2580.2771 1955.7507 178.98895 624.52635 185.08445 827.39297 175.04156 0 -984.94513 595290.88 -594868.93 3484.9216 55742.797 245.79119 0.67067791 + 550 7.2369561 2640.6835 1866.035 170.77823 774.64858 176.89609 988.92025 176.49761 0 -991.07212 595292.32 -594868.91 1773.3486 55742.797 234.10561 1.7344207 + 600 7.8453741 2690.8569 1876.0664 171.6963 814.7905 186.23916 1032.0131 182.3033 0 -1010.7649 595293.3 -594868.3 919.72487 55742.797 235.38014 1.7010285 + 650 8.4387105 2732.1825 1963.5421 179.70202 768.64035 165.39219 949.23884 183.81872 0 -951.98446 595290.3 -594868.13 2658.9017 55742.797 246.76774 0.68037827 + 700 9.0765064 2775.7294 1921.9362 175.89427 853.79318 175.21242 987.66712 186.48684 0 -918.75413 595291.36 -594868.18 670.06264 55742.797 241.62283 0.44222019 + 750 9.6925657 2820.0741 2038.1504 186.53011 781.92376 168.58531 929.80574 193.62706 0 -939.9379 595298.09 -594868.25 398.72752 55742.797 256.20117 0.55407442 + 800 10.302839 2865.959 1943.5754 177.87467 922.38359 197.16019 1009.2236 201.50386 0 -914.81706 595297.54 -594868.23 -717.10975 55742.797 244.0452 1.2420644 + 850 10.916842 2909.1138 2101.5572 192.33306 807.55656 195.18897 876.12792 184.47417 0 -876.31499 595296.17 -594868.09 -1403.4232 55742.797 263.69793 1.8344028 + 900 11.513051 2938.1376 2038.9242 186.60093 899.21343 183.32681 989.01659 184.31258 0 -889.86018 595300.05 -594867.63 -1087.2761 55742.797 256.12732 1.0106144 + 950 12.11419 2965.6942 2007.942 183.76546 957.75216 227.45503 972.71506 206.37949 0 -880.4232 595299.46 -594867.83 -1848.7603 55742.797 252.40653 0.53885876 + 1000 12.740639 2994.2317 2058.0187 188.34845 936.21302 170.68957 965.88085 205.36589 0 -833.14441 595294.86 -594867.44 327.6391 55742.797 258.71295 0.52143283 + 1050 13.346812 3022.9501 2095.3848 191.76817 927.56526 203.90712 935.91396 205.08197 0 -845.07232 595294.32 -594866.59 -355.70418 55742.797 263.25608 0.94198602 + 1100 13.938097 3051.1769 2047.7199 187.4059 1003.457 212.39892 989.65684 227.20812 0 -856.11277 595297.04 -594866.74 -1402.022 55742.797 256.98383 1.6773742 + 1150 14.508841 3071.8157 2127.8626 194.74051 943.95311 188.38445 926.24309 223.28071 0 -821.63207 595294.06 -594866.38 550.31236 55742.797 267.1915 1.3431353 + 1200 15.110682 3087.7694 2015.2955 184.43845 1072.4739 199.90932 1034.9531 215.15511 0 -804.43314 595293.38 -594866.49 -333.57793 55742.797 253.26777 0.70913778 + 1250 15.728746 3102.5825 2176.9518 199.23312 925.63076 155.81519 956.83624 230.0728 0 -847.47674 595296.65 -594866.26 -932.66685 55742.797 273.66551 0.54750805 + 1300 16.365541 3116.8403 2087.6045 191.05612 1029.2357 209.96201 974.81053 241.13608 0 -823.38398 595292.74 -594866.03 -825.75383 55742.797 262.34486 0.76175709 + 1350 16.943579 3131.0787 2089.6524 191.24354 1041.4264 186.48189 998.11168 233.71019 0 -801.37003 595290.06 -594865.57 684.79151 55742.797 262.36797 1.3871293 + 1400 17.542898 3138.996 2186.2582 200.08483 952.73785 168.60338 957.20178 227.71944 0 -826.52269 595291.08 -594865.34 1796.7295 55742.797 274.47403 1.5135537 + 1450 18.144658 3139.5791 2010.7377 184.02132 1128.8414 192.8015 1074.5205 245.37206 0 -807.3159 595288.01 -594864.55 -16.504608 55742.797 252.63135 0.87723467 + 1500 18.759382 3143.8991 2099.4529 192.14048 1044.4462 186.04014 980.83524 242.01309 0 -784.81131 595285 -594864.63 2343.8986 55742.797 263.89145 0.61241549 + 1550 19.331644 3149.7316 2086.068 190.9155 1063.6635 165.80546 1056.0893 230.89463 0 -813.37768 595289.09 -594864.84 2260.7364 55742.797 262.17666 0.69483626 + 1600 19.91757 3156.535 2013.4276 184.2675 1143.1073 210.65881 1098.2892 243.94955 0 -835.62037 595290.47 -594864.64 -838.57356 55742.797 252.86585 1.1542996 + 1650 20.503137 3160.0031 2081.0656 190.45768 1078.9375 212.2197 1005.7509 250.38023 0 -813.71955 595289.15 -594864.85 796.21731 55742.797 261.22447 1.5557945 + 1700 21.130273 3155.5677 2113.3761 193.41472 1042.1916 146.036 1019.0909 249.77802 0 -798.16357 595290.59 -594865.14 359.69262 55742.797 265.46995 1.074008 + 1750 21.735444 3151.796 2063.5487 188.85455 1088.2472 224.89093 997.02075 247.36817 0 -807.87592 595291.82 -594864.98 -1081.2667 55742.797 259.34362 0.69484916 + 1800 22.302735 3150.4232 2097.9294 192.00105 1052.4938 202.22751 974.42358 248.58229 0 -799.53722 595291.6 -594864.8 94.58692 55742.797 263.68474 0.65252808 + 1850 22.902581 3153.4477 2106.6272 192.79706 1046.8205 177.57166 971.73469 249.90348 0 -777.13298 595289.76 -594865.02 881.42516 55742.797 264.65016 0.99601444 + 1900 23.480426 3159.2037 2092.2693 191.48304 1066.9343 198.78895 969.41309 260.03288 0 -787.26163 595290.41 -594864.45 606.40366 55742.797 262.66088 1.4839893 + 1950 24.086136 3164.5139 2059.5653 188.48999 1104.9485 214.12027 1000.4493 263.39543 0 -799.45067 595291.13 -594864.69 -1248.7209 55742.797 258.62963 1.2624825 + 2000 24.655188 3171.2963 2080.1555 190.37439 1091.1408 179.21892 996.41486 248.41626 0 -760.00877 595292.04 -594864.94 940.70366 55742.797 261.39948 0.7837686 +Loop time of 24.6553 on 4 procs for 2000 steps with 4500 atoms + +Performance: 3.504 ns/day, 6.849 hours/ns, 81.119 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.825 | 12.439 | 13.012 | 12.2 | 50.45 +Bond | 0.82239 | 0.89713 | 0.95859 | 5.7 | 3.64 +Kspace | 6.6353 | 7.2001 | 7.8139 | 15.7 | 29.20 +Neigh | 0.44976 | 0.44994 | 0.45003 | 0.0 | 1.82 +Comm | 0.55452 | 0.62432 | 0.70013 | 6.6 | 2.53 +Output | 0.003664 | 0.0043042 | 0.0061252 | 1.6 | 0.02 +Modify | 2.9457 | 2.959 | 2.9736 | 0.7 | 12.00 +Other | | 0.08099 | | | 0.33 + +Nlocal: 1125 ave 1166 max 1096 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 5867.25 ave 5956 max 5793 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 193608 ave 200510 max 186198 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 774433 +Ave neighs/atom = 172.096 +Ave special neighs/atom = 13.3333 +Neighbor list builds = 35 +Dangerous builds = 0 +Total wall time: 0:00:24 diff --git a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 b/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 deleted file mode 100644 index a46d9b7cd5..0000000000 --- a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.1 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -comm_modify vel yes - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 79507 46656 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 20.1567 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 2.8944459 3475.1575 2067.5082 189.21692 1407.6493 846.00752 810.92425 115.58516 0 -764.28457 595242.38 -594842.96 3029.5187 55742.797 202.89871 152.54291 - 100 5.6009829 2975.2938 1988.4777 181.98411 986.81605 358.65377 931.63831 175.54125 0 -919.10691 595306.8 -594866.71 2010.6143 55742.797 231.36532 50.118891 - 150 8.2652578 2904.7202 1962.6821 179.62331 942.03808 234.91712 997.34884 195.22618 0 -909.31364 595293.23 -594869.37 4956.5664 55742.797 241.54715 14.313437 - 200 10.97319 2905.616 1909.813 174.78477 995.80302 228.33514 1082.3513 200.51771 0 -943.19777 595298.16 -594870.37 2973.6338 55742.797 238.34584 5.1137785 - 250 13.676164 2934.0626 1952.0155 178.6471 982.0471 212.76463 1131.5055 194.94566 0 -983.79846 595297.63 -594871 1591.8677 55742.797 244.66672 2.4161409 - 300 16.381759 2995.4781 2017.7772 184.66557 977.70088 213.25867 1133.9492 195.13329 0 -992.6543 595299.31 -594871.29 2817.7518 55742.797 253.21545 1.6812532 - 350 19.14905 3058.4882 1982.338 181.4222 1076.1502 228.54692 1197.9766 205.68279 0 -982.30502 595297.25 -594871 1408.2609 55742.797 248.83728 1.4672371 - 400 21.914272 3016.5895 1998.3531 182.8879 1018.2363 238.06518 1169.309 197.52924 0 -1014.8678 595298.98 -594870.78 1454.1926 55742.797 250.8778 1.3985907 - 450 24.629148 3014.232 1979.0496 181.12125 1035.1824 216.45567 1198.2831 197.81853 0 -1005.5029 595298.68 -594870.56 1296.2887 55742.797 248.44786 1.4025051 - 500 27.390589 3054.4694 2023.8824 185.22432 1030.587 220.97548 1197.2137 199.51957 0 -1014.3543 595298.28 -594871.05 2481.3102 55742.797 254.08894 1.4000969 - 550 30.147365 3088.0877 2020.1967 184.887 1067.8909 221.93439 1216.8427 213.27263 0 -1012.4867 595299.44 -594871.11 1697.8283 55742.797 253.63701 1.3687703 - 600 32.854639 3112.7966 2031.7038 185.94013 1081.0928 220.37419 1254.8806 208.09272 0 -1030.3329 595298.95 -594870.87 -75.358619 55742.797 255.05809 1.439614 - 650 35.725004 3155.4753 2025.6962 185.39031 1129.7792 221.82928 1284.1281 210.16702 0 -1015.1565 595299.63 -594870.82 1286.1601 55742.797 254.30974 1.4197689 - 700 38.70379 3134.5524 2054.9292 188.0657 1079.6232 225.36387 1243.5643 191.53984 0 -1010.9148 595301.25 -594871.18 700.78109 55742.797 257.97902 1.4421042 - 750 41.679769 3189.6098 2103.3042 192.49294 1086.3056 219.5641 1243.9772 203.81533 0 -1010.2161 595299.86 -594870.7 482.90086 55742.797 264.08828 1.3795515 - 800 44.637671 3173.7718 2053.4131 187.92694 1120.3587 219.52183 1256.8457 218.62858 0 -1003.175 595299.34 -594870.81 538.9293 55742.797 257.80398 1.4002525 - 850 47.531367 3221.5884 2084.0326 190.72922 1137.5559 224.32279 1277.7167 218.74781 0 -1011.3685 595298.54 -594870.4 145.40179 55742.797 261.66451 1.3777132 - 900 50.379314 3214.7916 2054.2398 188.00261 1160.5518 222.07439 1296.738 225.4151 0 -1013.6054 595300.61 -594870.68 490.09072 55742.797 257.90629 1.4047863 - 950 53.038527 3213.4974 2122.2134 194.2235 1091.284 221.85551 1252.3002 201.89089 0 -1014.1089 595300.04 -594870.69 1203.4321 55742.797 266.42418 1.4941572 - 1000 55.653448 3212.7244 2079.8287 190.34449 1132.8956 225.42816 1261.5078 204.71764 0 -986.95829 595298.68 -594870.48 790.47665 55742.797 261.10437 1.4611106 - 1050 58.290098 3216.1124 2106.2454 192.76212 1109.8669 213.54607 1261.1068 207.93437 0 -1001.5715 595299.05 -594870.2 69.145866 55742.797 264.43815 1.4332898 - 1100 60.921228 3218.0797 2082.4185 190.5815 1135.6611 236.95827 1266.8625 198.25038 0 -995.08857 595298.88 -594870.2 694.35787 55742.797 261.43907 1.4374087 - 1150 63.510285 3208.3968 2119.1968 193.94742 1089.2 210.20908 1236.1825 202.19163 0 -988.56762 595299.35 -594870.17 1528.4475 55742.797 266.08185 1.3950176 - 1200 66.140576 3219.1289 2078.071 190.18362 1141.0579 234.57015 1268.2146 206.93186 0 -997.01686 595298.32 -594869.97 939.70203 55742.797 260.89628 1.4263352 - 1250 68.774998 3268.5006 2115.3231 193.5929 1153.1775 241.50662 1262.3711 220.71001 0 -1000.1626 595298.37 -594869.62 -187.61926 55742.797 265.57695 1.4418423 - 1300 71.409732 3324.099 2138.7146 195.73368 1185.3844 242.3031 1279.7915 223.94399 0 -989.04901 595298.47 -594870.08 258.69655 55742.797 268.51674 1.4497832 - 1350 73.990336 3290.8471 2103.0993 192.47419 1187.7477 219.60844 1312.8653 221.57552 0 -993.69832 595297.61 -594870.21 1651.4259 55742.797 264.03877 1.4428477 - 1400 76.620059 3227.0141 2052.6998 187.86167 1174.3143 236.01325 1272.4804 217.65692 0 -979.6779 595297.5 -594869.66 595.11702 55742.797 257.67276 1.5108922 - 1450 79.249466 3253.5975 2107.984 192.92124 1145.6135 248.51645 1261.8304 208.79164 0 -1002.8333 595299.15 -594869.84 170.12671 55742.797 264.66781 1.4041436 - 1500 81.830899 3276.1976 2101.6206 192.33886 1174.577 242.38394 1288.61 204.9722 0 -989.7383 595298.02 -594869.67 619.26135 55742.797 263.84288 1.4691362 - 1550 84.449908 3271.9376 2117.6914 193.80965 1154.2463 234.62432 1268.5368 202.02117 0 -979.66071 595298.65 -594869.92 568.43047 55742.797 265.86458 1.4693675 - 1600 87.073373 3281.1387 2105.1447 192.66139 1175.994 219.69265 1288.3244 205.52796 0 -966.68015 595298.79 -594869.67 1351.6273 55742.797 264.27256 1.5056051 - 1650 89.695136 3287.675 2131.7955 195.10045 1155.8795 235.54527 1262.9178 220.26583 0 -991.68887 595298.56 -594869.72 -750.34342 55742.797 267.63101 1.4905169 - 1700 92.342235 3295.9626 2079.4982 190.31424 1216.4644 232.74928 1329.4691 218.51323 0 -992.04439 595297.16 -594869.38 589.94184 55742.797 261.06357 1.4590401 - 1750 94.911541 3315.2639 2097.2605 191.93983 1218.0035 241.24927 1312.3575 214.88139 0 -978.98823 595298.34 -594869.84 -92.971422 55742.797 263.26817 1.5389785 - 1800 97.525025 3241.5219 2086.8653 190.98847 1154.6566 221.03432 1282.1774 209.03793 0 -986.54668 595299 -594870.05 456.17335 55742.797 261.96332 1.5311996 - 1850 100.13804 3222.7069 2040.0335 186.70245 1182.6734 242.74754 1272.8794 221.80974 0 -982.51665 595296.99 -594869.24 279.00233 55742.797 256.09213 1.4766233 - 1900 102.70693 3190.3766 2032.3946 186.00335 1157.9819 213.06329 1268.187 220.21025 0 -971.50314 595297.54 -594869.51 499.15225 55742.797 255.16226 1.3935863 - 1950 105.30868 3208.3096 2053.9844 187.97923 1154.3252 212.46296 1277.2726 210.16078 0 -974.19087 595298.44 -594869.82 807.22906 55742.797 257.85261 1.4622515 - 2000 107.9105 3231.8811 2053.6913 187.9524 1178.1899 229.11239 1280.6492 220.1084 0 -979.25259 595297.02 -594869.45 474.05197 55742.797 257.80782 1.4833297 -Loop time of 107.911 on 1 procs for 2000 steps with 4500 atoms - -Pair time (%) = 65.8442 (61.0173) -Bond time (%) = 16.6061 (15.3887) -Kspce time (%) = 20.7451 (19.2244) -Neigh time (%) = 1.24307 (1.15195) -Comm time (%) = 0.386346 (0.358024) -Outpt time (%) = 0.00603366 (0.00559135) -Other time (%) = 3.07976 (2.854) - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 8739 ave 8739 max 8739 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 860638 ave 860638 max 860638 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 860638 -Ave neighs/atom = 191.253 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 28 -Dangerous builds = 0 diff --git a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 b/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 deleted file mode 100644 index 18e16e4975..0000000000 --- a/examples/USER/drude/butane/log.butane.lang.18Jul15.linux.4 +++ /dev/null @@ -1,171 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -comm_modify vel yes - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 26875 11664 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 14.7792 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 0.91017509 3449.6475 2040.7698 186.76984 1408.8777 836.85155 816.32124 115.24642 0 -758.7276 595242.44 -594843.26 3042.2937 55742.797 199.51659 152.7045 - 100 1.829694 2917.9137 1947.102 178.19743 970.81176 363.96553 932.94225 165.60761 0 -931.00296 595306.34 -594867.04 1697.0127 55742.797 226.24749 49.885738 - 150 2.6620312 2853.3142 1959.0731 179.29301 894.24108 244.19792 978.17893 187.28366 0 -941.03478 595295.44 -594869.82 4597.2005 55742.797 241.05848 14.405808 - 200 3.4969041 2885.6715 1928.6381 176.50762 957.03347 227.09245 1066.5297 186.6858 0 -949.52603 595296.49 -594870.24 2602.8275 55742.797 240.70211 5.1458056 - 250 4.621171 2905.8961 1939.7876 177.52802 966.10847 215.77945 1122.1238 195.98218 0 -993.52132 595296.54 -594870.79 1808.1681 55742.797 243.04306 2.643716 - 300 5.5216351 2968.5517 1974.9277 180.74402 993.624 210.11413 1158.7871 194.142 0 -996.53154 595297.91 -594870.79 3371.8618 55742.797 247.7682 1.8321312 - 350 6.3789251 2996.151 1992.9982 182.39782 1003.1527 217.80518 1150.726 205.32316 0 -996.14478 595296.05 -594870.61 3022.9945 55742.797 250.15947 1.5176819 - 400 7.208317 2991.7201 1975.3852 180.78589 1016.3349 221.46133 1169.8254 213.90874 0 -1016.9906 595298.44 -594870.31 753.59124 55742.797 247.99744 1.3743032 - 450 8.0359671 3061.6051 2009.1302 183.87421 1052.4749 212.54169 1234.7697 205.71762 0 -1028.2259 595297.95 -594870.28 996.71341 55742.797 252.23801 1.3870863 - 500 8.8456361 3127.3783 2009.8033 183.93581 1117.5749 222.16507 1246.5854 215.82607 0 -994.66665 595298.3 -594870.63 2537.6157 55742.797 252.32947 1.367397 - 550 9.6647151 3181.037 2069.9836 189.44346 1111.0534 218.00575 1246.961 212.55852 0 -992.83597 595296.16 -594869.79 1333.8768 55742.797 259.86467 1.4641506 - 600 10.484356 3194.2009 2007.5349 183.7282 1186.666 228.93838 1309.4718 215.93595 0 -995.70641 595297.81 -594869.79 1336.7994 55742.797 252.00698 1.4677515 - 650 11.30116 3145.4387 2028.2544 185.62444 1117.1843 209.73722 1277.9793 217.12799 0 -1015.2398 595297.88 -594870.3 1442.6875 55742.797 254.61499 1.4639962 - 700 12.106719 3163.3345 2053.2645 187.91335 1110.07 209.45249 1257.3108 216.7541 0 -1000.1505 595296.63 -594869.92 1093.9724 55742.797 257.76091 1.4652884 - 750 12.924665 3145.6215 2010.7195 184.01966 1134.902 224.53065 1248.3301 222.25374 0 -988.4479 595298.83 -594870.59 470.73988 55742.797 252.39115 1.5116555 - 800 13.736913 3191.2614 2043.4195 187.01234 1147.842 225.71717 1239.3564 234.89539 0 -980.97352 595299.07 -594870.22 1472.0305 55742.797 256.53524 1.4309304 - 850 14.550736 3157.6279 2004.8472 183.48223 1152.7806 217.72587 1269.3398 224.40554 0 -987.51794 595299.15 -594870.32 293.76575 55742.797 251.69397 1.4007963 - 900 15.344895 3188.5027 2077.065 190.09155 1111.4377 216.92608 1251.4141 213.7672 0 -1000.1269 595299.5 -594870.05 702.56821 55742.797 260.7853 1.3847905 - 950 16.157597 3205.6761 2090.9807 191.3651 1114.6954 223.7729 1252.7887 225.91029 0 -1016.3682 595299.15 -594870.56 -19.492925 55742.797 262.50762 1.4603579 - 1000 16.969809 3231.5931 2078.7058 190.24172 1152.8873 228.77504 1273.1611 219.28923 0 -995.58473 595296.82 -594869.57 1292.4071 55742.797 260.98775 1.3954023 - 1050 17.771785 3264.2837 2106.0113 192.7407 1158.2724 224.16481 1278.5557 212.91309 0 -985.93386 595298.71 -594870.14 1357.1588 55742.797 264.40381 1.4463397 - 1100 18.572331 3243.3355 2125.1664 194.49376 1118.1691 227.38559 1247.5134 210.61488 0 -996.85878 595299.68 -594870.17 650.53225 55742.797 266.82195 1.4240918 - 1150 19.40463 3255.4144 2096.5982 191.87922 1158.8162 234.11389 1267.4257 217.02225 0 -989.70892 595299.81 -594869.84 688.78475 55742.797 263.2133 1.4631154 - 1200 20.321045 3266.2609 2088.3727 191.12642 1177.8882 225.40174 1284.1097 225.77008 0 -985.63518 595297.81 -594869.57 182.80287 55742.797 262.21901 1.3550749 - 1250 21.233994 3277.4365 2093.1481 191.56346 1184.2884 250.33569 1267.9985 235.70102 0 -999.80819 595299.96 -594869.9 780.87528 55742.797 262.80001 1.4077597 - 1300 22.113268 3280.4141 2121.4996 194.15818 1158.9145 228.23585 1259.7304 230.65174 0 -989.06345 595298.99 -594869.63 932.19341 55742.797 266.34543 1.4646736 - 1350 23.007421 3272.2214 2088.047 191.09662 1184.1744 224.66504 1284.656 217.03214 0 -970.5252 595297.72 -594869.37 63.097535 55742.797 262.16781 1.3823451 - 1400 23.903494 3239.3096 2099.1837 192.11584 1140.1259 221.3215 1252.8691 215.64014 0 -978.70393 595298.89 -594869.89 1125.3057 55742.797 263.59141 1.3221979 - 1450 24.833224 3226.293 2042.7354 186.94973 1183.5576 241.40449 1273.025 233.66813 0 -994.70934 595299.55 -594869.38 -412.31857 55742.797 256.45155 1.4245996 - 1500 25.736203 3245.4596 2097.0431 191.91994 1148.4164 250.3854 1248.1507 212.36871 0 -990.48467 595297.36 -594869.36 245.49743 55742.797 263.28349 1.4252034 - 1550 26.633033 3308.5518 2113.8467 193.45778 1194.7051 234.5293 1286.7563 233.20552 0 -987.36764 595297.06 -594869.48 1324.7098 55742.797 265.37419 1.4864431 - 1600 27.530123 3319.786 2130.8949 195.01803 1188.8911 234.06508 1292.3987 225.94876 0 -992.81161 595299.1 -594869.81 343.14209 55742.797 267.51024 1.5104547 - 1650 28.41116 3239.0425 2066.8485 189.15654 1172.194 219.46922 1303.0071 210.00869 0 -989.28577 595298.63 -594869.64 -505.97551 55742.797 259.48305 1.4300292 - 1700 29.313339 3281.3023 2054.581 188.03383 1226.7213 224.72686 1339.1948 208.65914 0 -974.24634 595297.79 -594869.4 331.11846 55742.797 257.92342 1.4735531 - 1750 30.216241 3237.8348 2043.3835 187.00904 1194.4513 238.16066 1281.9383 221.74494 0 -976.72731 595299.4 -594870.06 612.69867 55742.797 256.53793 1.4116726 - 1800 31.113153 3242.1274 2087.94 191.08683 1154.1873 240.53142 1256.6966 210.49591 0 -983.16111 595299.34 -594869.72 -8.1277769 55742.797 262.14149 1.4166426 - 1850 31.993161 3249.8016 2079.8947 190.35052 1169.9069 233.21641 1269.4077 215.23716 0 -975.12835 595296.5 -594869.33 1156.1724 55742.797 261.13101 1.4122227 - 1900 32.891621 3251.9579 2097.6037 191.97124 1154.3541 243.13703 1228.3357 235.37914 0 -983.06313 595300.37 -594869.8 293.60486 55742.797 263.33664 1.4715416 - 1950 33.791255 3202.0703 2076.0894 190.00227 1125.9809 233.71337 1217.6976 227.58496 0 -981.8352 595298.07 -594869.25 -544.65606 55742.797 260.61868 1.5018224 - 2000 34.690323 3215.7987 2015.5993 184.46625 1200.1994 242.43605 1281.6846 227.48326 0 -980.70325 595298.82 -594869.52 248.82508 55742.797 253.04055 1.4169879 -Loop time of 34.6904 on 4 procs for 2000 steps with 4500 atoms - -Pair time (%) = 16.514 (47.6038) -Bond time (%) = 4.35555 (12.5555) -Kspce time (%) = 10.6198 (30.613) -Neigh time (%) = 0.393407 (1.13405) -Comm time (%) = 1.18699 (3.42165) -Outpt time (%) = 0.00467861 (0.0134867) -Other time (%) = 1.6161 (4.65863) - -Nlocal: 1125 ave 1219 max 1009 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Nghost: 5768 ave 5890 max 5664 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 215002 ave 223956 max 206872 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 860008 -Ave neighs/atom = 191.113 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 29 -Dangerous builds = 0 diff --git a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 b/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 deleted file mode 100644 index 26ef8dad2c..0000000000 --- a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.3 +++ /dev/null @@ -1,177 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 79507 46656 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 20.1567 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 2.8816051 2130.0808 1490.8248 136.43926 639.25601 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137 - 100 5.569447 2172.0554 1656.5476 151.60609 515.50773 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117 - 150 8.2248161 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6234 55742.797 218.02975 0.12336382 - 200 10.911476 2271.1314 1750.9955 160.2499 520.13587 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.4949 55742.797 220.19714 0.23035017 - 250 13.588019 2333.7822 1793.0252 164.09642 540.75705 153.18169 833.95287 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339004 - 300 16.26521 2403.6147 1909.3441 174.74185 494.27059 144.27299 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3721 55742.797 239.06243 3.0455686 - 350 18.937858 2448.2389 1862.67 170.47027 585.56885 181.70523 821.7917 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806435 - 400 21.590191 2498.6994 1942.5496 177.7808 556.14976 168.5792 828.99117 182.0756 0 -1050.149 595296.43 -594869.77 485.86761 55742.797 244.23632 0.3882729 - 450 24.247025 2552.9641 1890.0917 172.97989 662.87241 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452669 55742.797 237.65323 0.34464588 - 500 26.850275 2608.55 1970.0729 180.29971 638.4771 187.01392 838.62129 176.10775 0 -985.23355 595290.89 -594868.93 3471.1633 55742.797 247.59402 0.66791252 - 550 29.482354 2667.002 1875.8227 171.67399 791.17931 178.48765 1003.6885 176.78989 0 -991.21705 595292.35 -594868.92 1767.0543 55742.797 235.34039 1.7252619 - 600 32.10773 2715.2399 1883.279 172.35639 831.96094 186.79504 1047.6877 183.04311 0 -1010.5423 595293.27 -594868.29 931.85523 55742.797 236.28437 1.7094253 - 650 34.715398 2754.4497 1970.794 180.3657 783.65568 166.02823 963.09399 184.8464 0 -952.45217 595290.25 -594868.11 2640.017 55742.797 247.67755 0.68709275 - 700 37.337317 2795.9461 1928.2674 176.4737 867.67874 176.09641 1002.4636 186.11483 0 -920.14356 595291.32 -594868.18 664.78904 55742.797 242.41897 0.44316381 - 750 39.927419 2838.2052 2043.2258 186.99461 794.97945 170.34991 941.73148 193.53082 0 -940.49604 595298.1 -594868.23 410.24758 55742.797 256.84035 0.55229077 - 800 42.469991 2881.9788 1945.9722 178.09402 936.00667 197.5203 1021.5571 202.83524 0 -915.18511 595297.49 -594868.21 -716.81442 55742.797 244.35112 1.2303511 - 850 45.05362 2923.3858 2106.5752 192.79231 816.81052 195.94987 886.41681 184.36064 0 -878.10485 595296.29 -594868.1 -1407.5711 55742.797 264.3276 1.8387296 - 900 47.651245 2950.6673 2039.6221 186.6648 911.04515 183.79618 1000.7954 184.49766 0 -890.38965 595299.97 -594867.63 -1085.794 55742.797 256.21167 1.0198208 - 950 50.451391 2976.6436 2006.5932 183.64202 970.05039 228.60059 985.21322 206.18529 0 -881.65815 595299.54 -594867.83 -1851.9703 55742.797 252.23637 0.54012241 - 1000 53.018937 3003.743 2056.8471 188.24122 946.89587 171.73287 976.85675 207.05097 0 -836.24563 595294.95 -594867.45 282.61914 55742.797 258.5658 0.52076804 - 1050 55.532595 3031.3535 2095.4846 191.7773 935.86887 203.54188 945.75569 204.8504 0 -846.10969 595294.45 -594866.62 -376.91112 55742.797 263.27093 0.93584407 - 1100 58.115412 3058.5347 2047.3098 187.36838 1011.2249 211.94076 1001.093 223.66214 0 -855.82424 595297.13 -594866.78 -1381.6531 55742.797 256.93409 1.6724456 - 1150 60.799698 3078.3996 2123.1811 194.31206 955.21855 189.50189 937.18685 224.21465 0 -823.63222 595294.38 -594866.43 524.70113 55742.797 266.5974 1.3568376 - 1200 63.295243 3093.556 2005.8939 183.57802 1087.6621 201.3428 1044.9909 219.39202 0 -805.37122 595293.83 -594866.52 -370.32492 55742.797 252.0829 0.71475597 - 1250 65.797931 3108.5155 2175.8972 199.13661 932.61826 156.6571 969.72254 225.30586 0 -850.00503 595297.25 -594866.31 -1015.3093 55742.797 273.53154 0.55100418 - 1300 68.300441 3122.9792 2090.3719 191.30939 1032.6073 209.92015 984.36624 236.75408 0 -825.27583 595292.92 -594866.08 -798.51816 55742.797 262.69421 0.75855207 - 1350 70.793202 3136.8213 2084.47 190.76925 1052.3513 186.49827 1004.7564 234.55362 0 -798.08335 595290.25 -594865.63 702.53782 55742.797 261.71553 1.3884089 - 1400 73.326733 3144.9028 2180.3659 199.54558 964.53687 170.02484 962.43948 235.07761 0 -829.27156 595291.77 -594865.51 1682.2488 55742.797 273.7286 1.5246324 - 1450 75.821906 3146.3365 2013.3816 184.26329 1132.9549 193.77936 1084.1403 252.3227 0 -821.23045 595288.54 -594864.6 -160.21484 55742.797 252.96375 0.87780357 - 1500 78.325264 3150.6861 2107.4863 192.87569 1043.1998 185.11752 988.72532 245.47682 0 -796.86739 595285.46 -594864.71 2242.3101 55742.797 264.90216 0.61222547 - 1550 80.779931 3156.3483 2074.5953 189.86552 1081.7531 166.52863 1062.4971 238.93518 0 -810.65247 595289.34 -594864.9 2224.9015 55742.797 260.73559 0.68881715 - 1600 83.275807 3163.8714 2000.6756 183.10045 1163.1958 210.70823 1110.4519 256.16493 0 -840.1463 595290.73 -594864.71 -830.17884 55742.797 251.26533 1.1443116 - 1650 85.768304 3169.3489 2056.4309 188.20313 1112.918 214.6419 1021.762 268.00157 0 -815.69477 595289 -594864.8 813.12089 55742.797 258.12835 1.5476743 - 1700 88.261463 3168.7666 2119.4079 193.96675 1049.3587 147.25006 1027.6415 246.49221 0 -797.55007 595290.74 -594865.22 412.59618 55742.797 266.23017 1.0703149 - 1750 90.746918 3168.2304 2066.7675 189.14913 1101.463 224.44009 1005.0052 243.56874 0 -797.83359 595291.25 -594864.96 -858.91314 55742.797 259.74684 0.69942293 - 1800 93.246077 3169.7579 2109.6017 193.06929 1060.1562 204.57678 981.05867 249.37843 0 -801.42006 595291.51 -594864.95 137.05559 55742.797 265.15197 0.65571606 - 1850 95.734661 3174.8532 2133.5052 195.25692 1041.348 175.87566 982.18775 244.55231 0 -786.49546 595290.43 -594865.21 882.03323 55742.797 268.02768 1.006296 - 1900 98.221874 3180.3842 2106.4808 192.78367 1073.9034 207.8879 977.47746 250.68948 0 -788.04039 595290.55 -594864.66 574.40162 55742.797 264.45175 1.4759897 - 1950 100.72148 3182.921 2084.8893 190.80763 1098.0317 207.26976 1007.5583 256.52302 0 -800.37789 595291.76 -594864.71 -981.75066 55742.797 261.81202 1.271779 - 2000 103.20588 3185.2881 2079.8136 190.3431 1105.4745 185.44441 1008.6997 251.0561 0 -766.97142 595292.22 -594864.97 661.65951 55742.797 261.35563 0.78600155 -Loop time of 103.206 on 1 procs for 2000 steps with 4500 atoms - -Pair time (%) = 60.3651 (58.49) -Bond time (%) = 16.8315 (16.3087) -Kspce time (%) = 20.1106 (19.4859) -Neigh time (%) = 1.52801 (1.48054) -Comm time (%) = 0.328804 (0.318591) -Outpt time (%) = 0.00495553 (0.00480159) -Other time (%) = 4.03695 (3.91155) - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 10060 ave 10060 max 10060 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 774908 ave 774908 max 774908 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 774908 -Ave neighs/atom = 172.202 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 35 -Dangerous builds = 0 diff --git a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 b/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 deleted file mode 100644 index 6a310d08dc..0000000000 --- a/examples/USER/drude/butane/log.butane.nh.18Jul15.linux.4 +++ /dev/null @@ -1,177 +0,0 @@ -LAMMPS (18 Jul 2015) -# 250 butane system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.089 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.butane - orthogonal box = (-19.1 -19.0999 -19.1) to (19.1 19.1 19.1) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 4250 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6750 dihedrals - 5 = max # of 1-2 neighbors - 8 = max # of 1-3 neighbors - 12 = max # of 1-4 neighbors - 17 = max # of special neighbors - -group gBUTANE molecule 1:250 -4500 atoms in group gBUTANE -group gCORES type 1 2 3 -3500 atoms in group gCORES -group gDRUDES type 4 5 -1000 atoms in group gDRUDES - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H C2H -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # C2H C2H -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # C2H H -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff * 4*5 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 * thole 1.368000 -pair_coeff 2 * thole 1.368000 -pair_coeff 4 * thole 1.368000 -pair_coeff 5 * thole 1.368000 - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 2 4 - 0 = # of size 2 clusters - 500 = # of size 3 clusters - 500 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.367867 - grid = 36 36 36 - stencil order = 5 - estimated absolute RMS force accuracy = 0.031354 - estimated relative force accuracy = 9.44215e-05 - using double precision FFTs - 3d grid and FFT values/proc = 26875 11664 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 17 -New max number of 1-2 to 1-4 neighbors: 17 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 - ghost atom cutoff = 10 -Memory usage per processor = 14.7792 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 6535.5187 2714.74 248.45112 3820.7787 3724.3278 140.75328 1.4735401 0 -518.77975 595169.42 -594696.41 -353319.1 55742.797 334.61375 18.435655 - 50 1.019057 2130.0808 1490.8248 136.43926 639.25599 192.16834 670.26518 115.15685 0 -766.5636 595300.83 -594872.6 2829.5958 55742.797 187.32686 0.60253137 - 100 2.043848 2172.0553 1656.5476 151.60609 515.50769 180.41449 708.03397 165.80788 0 -971.62525 595305.35 -594872.47 1231.388 55742.797 208.34096 0.16151117 - 150 3.0405529 2216.471 1733.4485 158.644 483.02256 136.16281 713.34485 169.62608 0 -964.30363 595300.47 -594872.27 4400.6233 55742.797 218.02975 0.12336381 - 200 4.0440719 2271.1314 1750.9955 160.2499 520.13584 190.12953 725.63606 167.04635 0 -987.11203 595295.5 -594871.06 2107.495 55742.797 220.19714 0.23035002 - 250 5.0482569 2333.7821 1793.0252 164.09642 540.75694 153.18169 833.95288 168.1507 0 -1041.2955 595297.2 -594870.43 1165.6922 55742.797 225.18334 1.0339003 - 300 6.044857 2403.6147 1909.3441 174.74185 494.27053 144.273 803.8452 155.85505 0 -1036.4615 595297.31 -594870.55 2511.3723 55742.797 239.06243 3.0455683 - 350 7.0382209 2448.239 1862.67 170.47027 585.56896 181.70522 821.79171 164.10713 0 -1005.4167 595293.5 -594870.12 2874.0826 55742.797 233.92745 1.0806438 - 400 8.025661 2498.6992 1942.5496 177.78079 556.14963 168.5792 828.99116 182.0756 0 -1050.149 595296.43 -594869.77 485.86784 55742.797 244.23632 0.38827289 - 450 9.010309 2552.9639 1890.0917 172.97988 662.87225 134.42613 957.3361 181.42951 0 -1036.4237 595295.53 -594869.43 66.452466 55742.797 237.65323 0.34464586 - 500 9.979717 2608.5501 1970.0729 180.29971 638.47718 187.01392 838.62128 176.10774 0 -985.23355 595290.89 -594868.93 3471.1636 55742.797 247.59402 0.66791289 - 550 10.965174 2667.002 1875.8227 171.674 791.17932 178.48766 1003.6885 176.78987 0 -991.21707 595292.35 -594868.92 1767.0547 55742.797 235.34039 1.7252612 - 600 11.944224 2715.2397 1883.279 172.35639 831.96067 186.79504 1047.6877 183.0431 0 -1010.5423 595293.27 -594868.29 931.85415 55742.797 236.28437 1.7094243 - 650 12.916431 2754.4495 1970.794 180.36571 783.65547 166.02823 963.09393 184.84638 0 -952.45216 595290.25 -594868.11 2640.0169 55742.797 247.67755 0.68709272 - 700 13.889729 2795.9463 1928.2674 176.47369 867.67893 176.09642 1002.4636 186.11482 0 -920.14357 595291.32 -594868.18 664.78857 55742.797 242.41896 0.44316458 - 750 14.849284 2838.2051 2043.2257 186.9946 794.97938 170.34989 941.73149 193.53082 0 -940.49605 595298.1 -594868.23 410.24692 55742.797 256.84034 0.55228895 - 800 15.765569 2881.9786 1945.9721 178.09402 936.00653 197.52035 1021.5571 202.83523 0 -915.18508 595297.49 -594868.21 -716.8133 55742.797 244.35111 1.2303486 - 850 16.62147 2923.386 2106.5752 192.79231 816.81079 195.9499 886.4168 184.36063 0 -878.10486 595296.29 -594868.1 -1407.5716 55742.797 264.3276 1.8387295 - 900 17.476931 2950.6672 2039.6221 186.6648 911.04508 183.7962 1000.7955 184.49765 0 -890.38971 595299.97 -594867.63 -1085.795 55742.797 256.21167 1.0198179 - 950 18.332394 2976.6435 2006.5931 183.64202 970.05037 228.60059 985.21322 206.18531 0 -881.65816 595299.54 -594867.83 -1851.9704 55742.797 252.23636 0.54012295 - 1000 19.192022 3003.7432 2056.8471 188.24122 946.89612 171.73291 976.85679 207.05089 0 -836.24565 595294.95 -594867.45 282.61893 55742.797 258.5658 0.52076763 - 1050 20.070536 3031.3535 2095.4845 191.77729 935.86893 203.54188 945.75571 204.85039 0 -846.10968 595294.45 -594866.62 -376.91144 55742.797 263.27092 0.93584075 - 1100 20.978902 3058.5346 2047.3099 187.36839 1011.2247 211.94079 1001.093 223.66207 0 -855.82432 595297.13 -594866.78 -1381.6546 55742.797 256.93411 1.6724371 - 1150 21.886788 3078.3992 2123.1811 194.31206 955.21814 189.50191 937.18689 224.21463 0 -823.63239 595294.38 -594866.43 524.69914 55742.797 266.59741 1.3568273 - 1200 22.731807 3093.5558 2005.8937 183.57801 1087.6621 201.34278 1044.991 219.39206 0 -805.37129 595293.83 -594866.52 -370.32731 55742.797 252.08289 0.71475598 - 1250 23.577332 3108.5154 2175.8971 199.1366 932.61825 156.65715 969.72264 225.30585 0 -850.00508 595297.25 -594866.31 -1015.3099 55742.797 273.53152 0.55101046 - 1300 24.41954 3122.979 2090.3725 191.30944 1032.6065 209.92008 984.36627 236.75348 0 -825.27575 595292.92 -594866.08 -798.51517 55742.797 262.69428 0.75855174 - 1350 25.260247 3136.8213 2084.4701 190.76926 1052.3512 186.49846 1004.7564 234.55382 0 -798.08358 595290.25 -594865.63 702.53502 55742.797 261.71554 1.3884097 - 1400 26.111855 3144.9027 2180.3656 199.54555 964.53705 170.02479 962.43949 235.07796 0 -829.2718 595291.77 -594865.51 1682.2458 55742.797 273.72857 1.5246347 - 1450 26.950639 3146.3362 2013.3813 184.26326 1132.955 193.77936 1084.1402 252.32287 0 -821.23025 595288.54 -594864.6 -160.21134 55742.797 252.96371 0.87779957 - 1500 27.790502 3150.6919 2107.4861 192.87567 1043.2058 185.11758 988.72513 245.47693 0 -796.86696 595285.47 -594864.71 2242.3607 55742.797 264.90213 0.61222945 - 1550 28.619789 3156.3482 2074.5978 189.86575 1081.7504 166.52858 1062.4966 238.93331 0 -810.65249 595289.34 -594864.9 2224.9023 55742.797 260.7359 0.68881915 - 1600 29.460929 3163.8714 2000.6737 183.10027 1163.1978 210.70797 1110.4522 256.16659 0 -840.14623 595290.73 -594864.71 -830.17835 55742.797 251.26509 1.1443132 - 1650 30.299437 3169.3484 2056.4317 188.20321 1112.9167 214.64223 1021.7623 268.00145 0 -815.6963 595289 -594864.8 813.10459 55742.797 258.12846 1.5476742 - 1700 31.139599 3168.7665 2119.4084 193.96679 1049.3581 147.25025 1027.6419 246.49323 0 -797.55219 595290.74 -594865.22 412.56019 55742.797 266.23023 1.0703144 - 1750 31.982883 3168.2311 2066.7649 189.14889 1101.4662 224.43981 1005.0038 243.56888 0 -797.82899 595291.25 -594864.96 -858.8853 55742.797 259.74652 0.69941609 - 1800 32.826623 3169.7582 2109.6043 193.06952 1060.154 204.57671 981.05578 249.38028 0 -801.42264 595291.51 -594864.95 137.07377 55742.797 265.1523 0.65571522 - 1850 33.670608 3174.8602 2133.4946 195.25594 1041.3657 175.87741 982.18471 244.56078 0 -786.49062 595290.44 -594865.21 882.07943 55742.797 268.02634 1.0063027 - 1900 34.515605 3180.392 2106.493 192.78478 1073.8991 207.88481 977.47602 250.68433 0 -788.04013 595290.55 -594864.66 574.47687 55742.797 264.45328 1.4759962 - 1950 35.361549 3182.9198 2084.8984 190.80846 1098.0214 207.26715 1007.5534 256.52264 0 -800.37486 595291.76 -594864.71 -981.72234 55742.797 261.81317 1.2717649 - 2000 36.208456 3185.292 2079.8093 190.34271 1105.4827 185.44479 1008.7001 251.06381 0 -766.97114 595292.22 -594864.97 661.65731 55742.797 261.3551 0.78598984 -Loop time of 36.2086 on 4 procs for 2000 steps with 4500 atoms - -Pair time (%) = 15.6569 (43.2408) -Bond time (%) = 4.33273 (11.966) -Kspce time (%) = 10.271 (28.3662) -Neigh time (%) = 0.435532 (1.20284) -Comm time (%) = 0.83936 (2.31813) -Outpt time (%) = 0.00456434 (0.0126057) -Other time (%) = 4.66849 (12.8933) - -Nlocal: 1125 ave 1165 max 1096 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Nghost: 5854.5 ave 5931 max 5788 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 193727 ave 200966 max 187020 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 774908 -Ave neighs/atom = 172.202 -Ave special neighs/atom = 13.3333 -Neighbor list builds = 35 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 new file mode 100644 index 0000000000..127d859702 --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.1 @@ -0,0 +1,277 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +comm_modify vel yes +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 +fix fNPH all nph iso 1 ${vPRESS} 500.0 +fix fNPH all nph iso 1 1 500.0 + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 50653 27000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.48 | 22.48 | 22.48 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.81254506 10970.11 5646.659 758.03805 5323.451 2059.6082 2216.9981 125.92585 0 1728.656 514096.92 -514904.66 75437.598 22442.383 899.52209 426.89792 + 40 1.7067263 8946.2741 5328.0351 715.26425 3618.239 1462.1404 1696.2927 256.70344 0 1227.0694 513938.28 -514962.25 46636.214 23048.268 913.15414 252.56747 + 60 2.5404506 7510.8082 4723.1172 634.0568 2787.6909 1200.8053 1745.3972 301.30817 0 557.80687 513950.19 -514967.82 37794.247 23517.363 840.69812 151.04831 + 80 3.3801596 6348.9157 4602.0926 617.80981 1746.8231 881.76663 1380.8166 300.54007 0 204.03797 513929.56 -514949.9 33851.301 23924.559 841.20021 95.741792 + 100 4.2437606 5485.1689 4144.6876 556.40528 1340.4814 784.82013 1301.8493 289.61476 0 -77.16227 514016.31 -514974.95 23853.877 24319.093 768.90717 59.825643 + 120 5.0577445 4861.8148 3777.2483 507.07825 1084.5665 621.85238 1297.2272 283.15722 0 -165.13412 514030.3 -514982.83 17461.708 24661.819 708.89192 35.503576 + 140 5.8777206 4340.7393 3447.4973 462.81068 893.24198 643.1178 1248.6088 275.35463 0 -264.6674 513962.95 -514972.12 14977.074 24942.76 650.90916 23.297159 + 160 6.688663 3926.6789 3280.6852 440.41693 645.99367 590.74309 1125.6956 275.31466 0 -402.41978 514040.08 -514983.42 17550.63 25183.539 623.01495 13.767656 + 180 7.4729645 3510.0638 3034.3628 407.34927 475.70103 580.84695 1065.6783 271.61808 0 -478.33275 514008.17 -514972.28 9895.4157 25410.444 577.92533 8.7953368 + 200 8.2036176 3232.9542 2804.7026 376.51845 428.25158 560.53426 1096.7584 268.56297 0 -524.94297 514009.86 -514982.53 8536.536 25604.126 535.28025 5.5722323 + 220 8.9682925 3019.8368 2679.2202 359.67301 340.61655 534.32413 1086.0764 252.71411 0 -554.59208 514001.04 -514978.94 7625.0406 25766.134 511.84268 4.1308947 + 240 9.730809 2817.4084 2557.6953 343.35885 259.71311 533.47006 1096.7331 235.22275 0 -594.9152 513968.32 -514979.12 6062.2975 25913.841 489.03736 2.9845074 + 260 10.499042 2630.9155 2460.3336 330.28849 170.58193 520.16741 1043.8106 228.53526 0 -637.28205 514004.22 -514988.87 5628.429 26050.517 470.64131 2.358198 + 280 11.217016 2462.5369 2379.2296 319.40065 83.307285 525.29091 971.98774 226.2588 0 -624.49241 513966.97 -514982.71 4755.8332 26171.267 455.29613 1.8853352 + 300 11.964113 2313.8618 2233.2275 299.80054 80.634294 520.99642 985.55834 216.66019 0 -623.05887 513969.74 -514989.27 3495.3603 26275.734 427.3819 1.7109763 + 320 12.723562 2171.4928 2215.8464 297.4672 -44.353519 513.03114 926.86216 206.3972 0 -647.51178 513946.73 -514989.86 3549.145 26372.81 424.12312 1.5400892 + 340 13.426266 2048.6698 2102.88 282.30198 -54.210215 517.14417 972.13286 198.86927 0 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586.50951 1587.5928 213.12705 -1001.0833 727.94474 823.60521 129.12956 0 -460.11816 512780.21 -515001.85 1024.9885 26777.699 303.8049 1.2612311 + 1860 65.909234 575.80278 1557.8819 209.13849 -982.07909 727.5608 800.91998 138.66389 0 -454.06531 512808.05 -515003.21 -696.69404 26772.219 298.09238 1.3005467 + 1880 66.632258 611.28789 1604.6616 215.41846 -993.37373 737.40385 802.26484 139.2269 0 -450.63031 512780.24 -515001.88 -40.643962 26765.841 307.08153 1.2507275 + 1900 67.314627 606.24473 1611.9641 216.39878 -1005.7194 718.10757 783.64683 141.16739 0 -478.54415 512835.51 -515005.61 564.61472 26761.053 308.45922 1.3025385 + 1920 67.997687 622.32128 1652.1009 221.78697 -1029.7797 709.21175 808.86628 140.79666 0 -489.67469 512806.75 -515005.73 -2045.2966 26762.21 316.16296 1.280607 + 1940 68.720055 585.91734 1580.5482 212.18134 -994.63085 701.86656 823.41307 141.76963 0 -476.56128 512820.97 -515006.09 -1477.9457 26758.847 302.44297 1.2879495 + 1960 69.400974 599.23183 1573.8307 211.27954 -974.59884 703.80549 834.20676 141.74855 0 -473.96154 512825.62 -515006.02 -555.31861 26748.97 301.16698 1.2604779 + 1980 70.082469 604.67649 1570.9488 210.89266 -966.27229 709.67328 842.22196 142.29376 0 -479.29842 512823.2 -515004.37 220.13578 26738.567 300.59944 1.2956585 + 2000 70.804962 610.11958 1559.2324 209.31979 -949.11278 723.21777 823.79015 145.64191 0 -461.27302 512827.63 -515008.12 -226.50414 26731.515 298.36269 1.2739114 +Loop time of 70.805 on 1 procs for 2000 steps with 3000 atoms + +Performance: 1.220 ns/day, 19.668 hours/ns, 28.247 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 46.358 | 46.358 | 46.358 | 0.0 | 65.47 +Bond | 1.8097 | 1.8097 | 1.8097 | 0.0 | 2.56 +Kspace | 10.643 | 10.643 | 10.643 | 0.0 | 15.03 +Neigh | 1.8814 | 1.8814 | 1.8814 | 0.0 | 2.66 +Comm | 0.38412 | 0.38412 | 0.38412 | 0.0 | 0.54 +Output | 0.008601 | 0.008601 | 0.008601 | 0.0 | 0.01 +Modify | 9.6728 | 9.6728 | 9.6728 | 0.0 | 13.66 +Other | | 0.04689 | | | 0.07 + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10022 ave 10022 max 10022 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 721937 ave 721937 max 721937 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 721937 +Ave neighs/atom = 240.646 +Ave special neighs/atom = 10.5 +Neighbor list builds = 49 +Dangerous builds = 0 +Total wall time: 0:01:10 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 new file mode 100644 index 0000000000..a0f886795b --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.lang.g++.4 @@ -0,0 +1,277 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +comm_modify vel yes +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes +fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes +fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 +fix fNPH all nph iso 1 ${vPRESS} 500.0 +fix fNPH all nph iso 1 1 500.0 + +compute cTEMP all temp/drude + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 17908 7200 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 15.7 | 15.72 | 15.75 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.24885726 10977.523 5649.4234 758.40916 5328.0995 2062.3542 2228.2406 127.20787 0 1716.2655 514097.62 -514903.59 75540.788 22441.711 900.66455 425.71754 + 40 0.52037597 8971.222 5307.0197 712.44303 3664.2023 1468.3101 1727.552 263.87374 0 1220.3688 513944.03 -514959.93 46704.125 23047.094 909.55742 251.59686 + 60 0.7807281 7598.3479 4774.3053 640.92856 2824.0427 1194.6424 1771.6653 314.85756 0 553.7151 513952.94 -514963.78 37329.2 23513.994 850.78607 150.29302 + 80 1.1572349 6500.0058 4632.0732 621.83456 1867.9325 914.32396 1444.2432 317.24546 0 213.11185 513930.12 -514951.11 33256.762 23919.646 847.27963 94.966975 + 100 1.4178512 5591.472 4319.1968 579.83234 1272.2752 772.47756 1235.8385 306.35435 0 -56.189361 513990.32 -514976.52 21842.59 24315.598 802.33641 59.89227 + 120 1.6625795 4952.7621 3881.7096 521.1017 1071.0525 630.88446 1260.1912 299.84296 0 -147.16305 514014.9 -514987.6 17191.638 24657.729 728.78527 35.811873 + 140 1.8984792 4373.9331 3440.7548 461.90553 933.1783 670.28429 1238.1308 300.44834 0 -260.57044 513963.56 -514978.68 17252.83 24939.26 649.60264 23.329745 + 160 2.1378865 3923.229 3251.2581 436.46647 671.97091 632.15143 1144.4146 307.32283 0 -436.68046 514014.07 -514989.31 17845.825 25185.451 617.37678 13.751529 + 180 2.3720722 3558.1557 3060.4382 410.84977 497.71755 621.70998 1085.8204 297.1556 0 -495.34468 513968.54 -514980.16 9885.361 25415.428 582.93783 8.7536435 + 200 2.6049569 3228.4936 2864.4301 384.53659 364.06344 591.33636 1077.5366 257.50944 0 -521.78289 513950.34 -514990.87 5925.7217 25605.563 546.61818 5.8335105 + 220 2.8426785 2922.7424 2668.2075 358.19461 254.5349 552.38924 1045.2135 238.94168 0 -548.4004 513955.45 -514989.06 7136.0052 25761.984 509.82785 3.9098309 + 240 3.1155882 2721.0612 2574.2915 345.58681 146.76969 547.99652 1035.0606 226.51837 0 -609.21222 513928.45 -514982.05 6971.5001 25907.597 492.18737 3.0535008 + 260 3.3265111 2525.7518 2460.9077 330.36557 64.844061 536.78625 1022.3311 211.32544 0 -633.92783 513919.8 -514991.47 4534.5804 26040.845 470.74694 2.3688839 + 280 3.5478129 2338.039 2324.3983 312.03981 13.640708 519.09042 970.16233 197.76897 0 -621.27548 513937.32 -514989.43 2909.3322 26151.714 444.74626 1.9753672 + 300 3.7687361 2194.851 2189.0474 293.86956 5.8036062 530.74509 982.33557 190.99311 0 -652.24555 513946.83 -514992.86 4224.0345 26246.212 418.93917 1.6487718 + 320 3.9801922 2045.4487 2132.0617 286.21949 -86.613049 531.53518 935.90803 188.46605 0 -683.41226 513935.36 -514994.47 1710.734 26338.321 408.05555 1.5540687 + 340 4.1992741 1929.4058 2083.452 279.69387 -154.04619 509.02677 906.15126 186.62933 0 -668.19644 513908.44 -514996.09 2736.2098 26423.379 398.77795 1.4580758 + 360 4.4171088 1853.7062 1992.5995 267.49733 -138.89334 525.34864 891.90355 178.21101 0 -654.64078 513920.99 -515000.71 3816.7092 26502.12 381.4127 1.3381612 + 380 4.6217661 1760.9358 1947.0158 261.37793 -186.07997 516.89889 919.58404 172.53796 0 -676.7004 513879.46 -514997.86 2960.1316 26580.115 372.6985 1.2814406 + 400 4.8376818 1687.8988 1905.9227 255.86137 -218.0239 535.53769 922.01769 176.20545 0 -684.03744 513833.88 -515001.63 1297.7806 26648.895 364.81828 1.2874209 + 420 5.0580292 1605.7787 1889.0825 253.60065 -283.30381 517.08427 857.72563 180.14818 0 -663.15367 513826.27 -515001.38 2609.7387 26710.911 361.58795 1.2934789 + 440 5.2613502 1518.1412 1794.5719 240.91304 -276.43077 531.12246 893.04683 188.1283 0 -667.41934 513778.75 -515000.06 1448.9344 26771.955 343.49864 1.2323194 + 460 5.474973 1455.6369 1796.1847 241.12955 -340.54775 527.17043 846.65061 188.73693 0 -650.46422 513749.2 -515001.84 161.63078 26825.587 343.80003 1.2432983 + 480 5.6766918 1423.3951 1780.4686 239.01974 -357.07349 555.37302 861.62016 179.25213 0 -642.3686 513685.22 -514996.17 1728.4109 26870.018 340.77367 1.2753301 + 500 5.8963647 1414.5107 1792.5124 240.63656 -378.00171 562.06965 865.1732 172.51081 0 -638.43613 513657.38 -514996.7 2852.5688 26914.25 343.08652 1.2642269 + 520 6.1024427 1359.8646 1801.0839 241.78725 -441.21931 573.29268 804.68005 169.59419 0 -635.98014 513644.06 -514996.86 917.97283 26965.499 344.72952 1.264948 + 540 6.3182905 1320.129 1763.768 236.77776 -443.63898 564.54015 851.18104 169.65891 0 -632.69528 513601.13 -514997.45 393.78094 27008.775 337.59196 1.2311182 + 560 6.5340965 1288.8769 1741.0597 233.72927 -452.18283 588.80641 843.7906 164.29947 0 -639.61003 513594.25 -515003.72 2022.6586 27046.802 333.24957 1.2004945 + 580 6.738924 1250.8612 1701.7462 228.45162 -450.88502 575.95012 877.76059 153.10544 0 -632.21312 513575.06 -515000.54 319.43567 27087.59 325.68988 1.258461 + 600 6.9839265 1237.7875 1721.861 231.15193 -484.0735 586.2774 851.82884 147.45104 0 -635.34134 513566.1 -515000.39 -1495.8007 27125.397 329.56435 1.2147693 + 620 7.1886187 1255.6883 1741.6598 233.80983 -485.97147 593.81316 838.06474 152.61844 0 -618.48814 513546.09 -514998.07 -239.76675 27153.275 333.35756 1.2207133 + 640 7.403686 1231.453 1734.6085 232.86323 -503.15553 592.94732 847.14537 157.31902 0 -622.72191 513517.06 -514994.9 1262.739 27174.105 331.96914 1.3100227 + 660 7.6087363 1205.9453 1720.7921 231.00844 -514.84686 605.97637 844.61854 156.72343 0 -608.38182 513480.7 -514994.48 541.26917 27199.495 329.34901 1.2412012 + 680 7.8241618 1168.82 1693.3809 227.32862 -524.5609 610.91696 859.82389 152.3176 0 -616.40743 513464.95 -514996.17 -529.37821 27221.433 324.05587 1.3283313 + 700 8.0318077 1139.7968 1686.9214 226.46146 -547.12461 600.49589 835.94756 154.05863 0 -606.7429 513467.63 -514998.52 679.06473 27236.703 322.81056 1.3423643 + 720 8.2363923 1092.9537 1676.7232 225.09239 -583.76953 599.79941 810.70949 154.32485 0 -586.40642 513433.08 -514995.27 -585.69662 27255.925 320.84689 1.3625931 + 740 8.4505181 1128.5561 1686.198 226.36434 -557.64189 608.39888 814.40376 148.31341 0 -576.35219 513440.47 -514992.87 1244.5446 27274.826 322.70284 1.2739521 + 760 8.6553326 1117.7278 1739.2464 233.48585 -621.51863 612.4462 767.55338 143.8046 0 -557.71655 513408.23 -514995.84 1093.5729 27295.505 332.85864 1.3081834 + 780 8.8741109 1106.8963 1694.5955 227.49166 -587.69917 621.94129 814.60472 148.54444 0 -544.5269 513368.24 -514996.5 1020.894 27319.829 324.31438 1.2670368 + 800 9.0792463 1119.8416 1718.8899 230.75307 -599.04828 615.79521 822.09893 150.20192 0 -544.21016 513354.51 -514997.44 -145.29684 27346.503 328.96744 1.27833 + 820 9.2923503 1100.7099 1661.8207 223.0918 -561.11086 634.74953 843.11877 146.78045 0 -554.19608 513367.17 -514998.73 1869.737 27372.705 318.03624 1.2563109 + 840 9.4957469 1050.0874 1692.7796 227.24789 -642.69222 601.30056 816.98683 139.43809 0 -553.50651 513352.19 -514999.1 1348.2664 27400.511 323.96534 1.2729707 + 860 9.7094629 1042.7553 1659.2043 222.74056 -616.44901 621.75625 821.47309 138.21191 0 -555.05691 513354.19 -514997.03 -727.5674 27429.255 317.50236 1.3339135 + 880 9.9195423 1033.8676 1659.2249 222.74333 -625.35739 603.51906 847.42057 149.36712 0 -565.95565 513337.79 -514997.5 -313.44149 27451.297 317.53888 1.2570577 + 900 10.142613 1033.7624 1637.6339 219.84483 -603.87149 622.06547 811.88787 155.52952 0 -542.52312 513343.54 -514994.37 1047.3137 27471.84 313.40683 1.2403795 + 920 10.345829 1008.6446 1641.2497 220.33024 -632.60508 603.07732 856.65655 154.41458 0 -548.68151 513295.17 -514993.24 103.24221 27494.927 314.0879 1.2685922 + 940 10.547752 1014.9632 1643.6054 220.64648 -628.64224 651.79962 816.08408 149.02041 0 -527.85081 513276.54 -514994.23 -364.67163 27515.823 314.56245 1.2150283 + 960 10.760628 1032.4206 1694.3296 227.45598 -661.90901 631.32636 826.29861 143.25116 0 -525.82257 513258.93 -514995.89 1416.1446 27534.39 324.25519 1.2878583 + 980 10.96867 997.2143 1637.471 219.82297 -640.25673 649.17389 840.91105 145.10691 0 -527.22384 513248.84 -514997.07 1027.4324 27556.624 313.33467 1.3359011 + 1000 11.181152 980.70328 1679.6252 225.48198 -698.92196 616.29851 808.49173 143.96963 0 -518.492 513246.09 -514995.28 328.95214 27580.508 321.45785 1.23763 + 1020 11.385127 964.62633 1655.3416 222.22201 -690.71527 637.09502 844.75137 135.25445 0 -525.02956 513212.27 -514995.06 80.148272 27602.021 316.79063 1.2656102 + 1040 11.594135 956.01316 1683.0451 225.94108 -727.03194 631.81212 818.33077 128.9891 0 -520.68359 513210.27 -514995.75 470.78306 27620.292 322.12502 1.2135338 + 1060 11.787688 933.22039 1693.9231 227.4014 -760.70274 646.39135 803.29817 130.04881 0 -528.24124 513182.71 -514994.91 239.4629 27638.164 324.20286 1.2314242 + 1080 12.019302 924.08701 1655.3855 222.2279 -731.29849 657.61421 824.59227 129.04796 0 -511.96678 513168.73 -514999.31 303.67371 27653.716 316.81728 1.223067 + 1100 12.213108 898.91261 1623.3761 217.93078 -724.46344 664.01917 828.5969 133.99752 0 -516.0614 513164.69 -514999.71 -222.62542 27666.941 310.68427 1.2153994 + 1120 12.41604 853.75082 1604.1305 215.34715 -750.37966 641.42123 819.9451 135.53827 0 -522.84677 513174.17 -514998.61 -712.60931 27680.156 306.99082 1.2247886 + 1140 12.609285 856.11685 1597.8188 214.49984 -741.70197 667.36627 802.82977 138.4139 0 -519.32453 513168.41 -514999.4 -102.39627 27691.615 305.78084 1.224836 + 1160 12.804644 841.06502 1588.8444 213.29507 -747.7794 639.48731 820.18846 145.23411 0 -514.61341 513163.68 -515001.76 -1183.509 27699.206 304.05355 1.2408942 + 1180 13.054664 860.51613 1621.2063 217.6395 -760.69016 641.94901 812.05607 135.63519 0 -518.65348 513173.02 -515004.7 281.47746 27701.81 310.24087 1.2817118 + 1200 13.250304 837.02718 1605.8013 215.57145 -768.77412 647.08878 819.62137 134.70383 0 -535.25329 513169.92 -515004.85 -741.61789 27704.108 307.27044 1.3202509 + 1220 13.454972 847.88424 1630.4606 218.88185 -782.57635 632.73877 814.55949 134.45986 0 -543.58866 513187.28 -515008.03 301.16905 27705.337 312.02884 1.2480776 + 1240 13.650697 847.8463 1613.1526 216.55833 -765.3063 657.26308 817.09263 131.44411 0 -533.77746 513168.85 -515006.17 -1738.246 27705.837 308.69599 1.2825009 + 1260 13.848417 864.10938 1604.3359 215.37473 -740.22655 654.64386 830.80471 136.50167 0 -518.80899 513162.82 -515006.19 -457.58037 27701.516 306.99469 1.3056189 + 1280 14.058141 892.58539 1622.354 217.79358 -729.76865 654.56025 853.72132 146.37045 0 -502.50853 513124.64 -515006.56 1617.9621 27698.218 310.47185 1.2538957 + 1300 14.25655 910.15714 1649.6144 221.45317 -739.4573 669.55948 824.60696 152.88156 0 -495.91044 513118.29 -515008.89 -947.37179 27701.819 315.68715 1.2786016 + 1320 14.462712 881.86464 1653.5515 221.98169 -771.68682 667.15825 811.67934 146.31009 0 -501.83979 513113.06 -515008.06 -836.07194 27703.296 316.44487 1.2716419 + 1340 14.66221 870.89257 1685.0409 226.20901 -814.14836 639.83879 820.7611 137.05399 0 -502.59799 513100.73 -515009.93 1322.9199 27705.806 322.51431 1.1950205 + 1360 14.876581 853.37228 1650.3504 221.55197 -796.97814 646.59807 828.89771 128.53685 0 -518.68585 513127.01 -515009.33 -685.77178 27711.07 315.84173 1.2552323 + 1380 15.07645 846.05537 1652.3957 221.82654 -806.34037 655.80177 845.42057 123.99858 0 -508.17399 513084.95 -515008.34 -1611.4393 27715.739 316.20591 1.3081133 + 1400 15.290876 845.61911 1643.3419 220.6111 -797.72277 681.7704 794.40988 122.51167 0 -491.96431 513103.8 -515008.25 1340.3832 27715.764 314.49703 1.249787 + 1420 15.489104 803.39863 1630.1296 218.83742 -826.73099 671.35628 807.63619 122.01003 0 -484.93762 513065.22 -515008.01 1599.9415 27715.83 311.97673 1.2205741 + 1440 15.695448 798.11794 1586.2583 212.94789 -788.14035 691.5246 832.65594 120.76201 0 -465.82995 513043.17 -515010.42 693.27083 27722.616 303.53977 1.2829192 + 1460 15.91282 786.25408 1614.9027 216.79327 -828.64859 657.62541 813.69119 123.75957 0 -476.8708 513064.69 -515011.54 411.32225 27731.39 309.03286 1.2785029 + 1480 16.12012 763.25782 1608.2178 215.89585 -844.95995 668.25992 798.0135 125.60791 0 -501.0795 513074.18 -515009.94 -210.6788 27739.429 307.75344 1.2722038 + 1500 16.31711 742.2781 1642.6489 220.51807 -900.3708 642.57755 747.85628 128.7751 0 -506.59888 513093.85 -515006.83 657.03263 27745.692 314.34071 1.3056262 + 1520 16.523088 729.1993 1560.7352 209.52153 -831.53586 684.2385 779.3475 135.75119 0 -498.45899 513072.79 -515005.21 64.426284 27753.859 298.64905 1.276366 + 1540 16.719949 744.18971 1581.6321 212.32685 -837.44244 684.68705 806.72314 139.08406 0 -507.07664 513045.21 -515006.07 -1592.594 27760.726 302.65236 1.2826649 + 1560 16.955894 732.25034 1589.2114 213.34434 -856.96111 671.90468 790.0602 135.77523 0 -516.63197 513069.7 -515007.77 -483.90212 27760.814 304.08818 1.324249 + 1580 17.152081 767.01867 1612.3153 216.44593 -845.29663 682.6108 787.28261 132.5621 0 -507.32097 513069.61 -515010.04 -555.1036 27759.537 308.50615 1.3501402 + 1600 17.357651 765.40129 1608.2406 215.89892 -842.8393 685.49537 792.49876 133.14916 0 -503.66586 513056.44 -515006.76 205.34219 27753.467 307.76245 1.2628065 + 1620 17.55409 772.17408 1631.4594 219.01594 -859.28536 668.94991 789.22477 139.7312 0 -488.80931 513038.28 -515006.66 869.15057 27745.263 312.19213 1.312809 + 1640 17.750204 790.00313 1585.8898 212.89842 -795.88666 698.581 834.90324 141.30234 0 -480.2032 513014.32 -515004.79 425.63098 27741.564 303.48802 1.2388328 + 1660 17.9655 747.54165 1583.9657 212.64013 -836.4241 681.84949 818.22116 144.32659 0 -480.9488 513005 -515004.87 393.07342 27741.508 303.09446 1.2953283 + 1680 18.160659 733.30069 1561.2237 209.58711 -827.92298 700.21145 825.04894 140.46392 0 -471.32136 512986.07 -515008.4 358.86819 27742.435 298.74386 1.2734665 + 1700 18.356133 711.44468 1578.4996 211.90632 -867.05487 695.93174 805.45219 136.97231 0 -472.62368 512976.67 -515009.46 536.5943 27744.152 302.06506 1.2553362 + 1720 18.560144 721.96636 1575.331 211.48095 -853.36463 702.17681 830.22534 135.88637 0 -477.83518 512966.99 -515010.81 -645.91282 27748.165 301.45254 1.2652763 + 1740 18.756074 711.63956 1586.0957 212.92606 -874.45612 689.4748 798.79974 136.08847 0 -473.58719 512984.43 -515009.66 -1624.8445 27748.356 303.52048 1.2551975 + 1760 18.958437 724.24881 1594.573 214.0641 -870.32418 693.92297 821.07919 134.86949 0 -499.044 512991.53 -515012.68 -67.704697 27743.489 305.14895 1.2473787 + 1780 19.161341 715.10685 1646.5039 221.03559 -931.39709 696.96446 758.9442 137.66678 0 -506.22154 512995.87 -515014.62 -40.253747 27743.38 315.10841 1.2414332 + 1800 19.355029 729.61134 1620.3158 217.51995 -890.70444 705.93766 795.61246 140.68696 0 -489.30347 512967.54 -515011.18 -766.11724 27742.605 310.0618 1.2972844 + 1820 19.55902 729.31305 1608.8589 215.98192 -879.54588 679.10327 811.20714 148.4305 0 -487.995 512981.33 -515011.62 -171.78807 27733.221 307.90957 1.1975335 + 1840 19.753109 755.00585 1604.0683 215.33881 -849.06248 704.5529 836.72831 145.47772 0 -486.71807 512964.36 -515013.46 214.63499 27724.953 306.97134 1.2429474 + 1860 19.967638 750.425 1611.9697 216.39953 -861.54467 681.08979 817.41958 140.85922 0 -481.23461 512994.18 -515013.86 458.39691 27723.378 308.4884 1.2369562 + 1880 20.162438 731.26375 1599.4322 214.71642 -868.16842 699.34308 809.01864 139.89206 0 -501.58244 512999.06 -515013.9 -1549.9632 27725.425 306.09592 1.211311 + 1900 20.356956 708.62541 1610.6874 216.22739 -902.06199 683.06943 810.51769 134.55613 0 -508.02851 512990.33 -515012.5 675.39868 27720.583 308.23181 1.2620963 + 1920 20.560648 703.81181 1586.8847 213.03199 -883.0729 690.93049 825.78591 131.84894 0 -498.42445 512977.68 -515010.9 367.15667 27713.888 303.69961 1.1917227 + 1940 20.754765 701.93422 1590.5107 213.51875 -888.57645 687.55932 818.62417 128.12087 0 -485.00453 512971.02 -515008.9 1457.2723 27711.175 304.3668 1.2586653 + 1960 20.966151 702.58467 1615.2174 216.83553 -912.63277 695.227 811.79161 131.25635 0 -468.08028 512925.61 -515008.44 812.93978 27708.617 309.10899 1.2402714 + 1980 21.169778 704.12312 1614.6957 216.76549 -910.5726 710.51045 811.95687 140.34792 0 -452.87904 512887.51 -515008.02 -604.37886 27705.003 309.00871 1.242271 + 2000 21.363046 700.52702 1604.4991 215.39664 -903.9721 726.08016 810.67383 139.90807 0 -443.00664 512870.59 -515008.22 148.09738 27699.21 307.02152 1.3180547 +Loop time of 21.3631 on 4 procs for 2000 steps with 3000 atoms + +Performance: 4.044 ns/day, 5.934 hours/ns, 93.619 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.835 | 11.289 | 12.258 | 17.2 | 52.85 +Bond | 0.4537 | 0.48285 | 0.50792 | 3.1 | 2.26 +Kspace | 4.2572 | 5.2354 | 5.6853 | 25.4 | 24.51 +Neigh | 0.54701 | 0.5472 | 0.54747 | 0.0 | 2.56 +Comm | 0.60596 | 0.64067 | 0.67884 | 3.8 | 3.00 +Output | 0.0058618 | 0.0073152 | 0.011671 | 2.9 | 0.03 +Modify | 2.769 | 2.9549 | 3.1306 | 8.9 | 13.83 +Other | | 0.2055 | | | 0.96 + +Nlocal: 750 ave 757 max 742 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 5838 ave 5894 max 5784 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 175398 ave 186533 max 165750 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 701594 +Ave neighs/atom = 233.865 +Ave special neighs/atom = 10.5 +Neighbor list builds = 53 +Dangerous builds = 0 +Total wall time: 0:00:21 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 new file mode 100644 index 0000000000..f6d4d7452e --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.1 @@ -0,0 +1,286 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_ATOM gATOMS temp +compute cTEMP all temp/drude + +fix fDTDIR all drude/transform/direct +fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 +fix_modify fNPT temp cTEMP_ATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) +fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 1 100.0 +fix fDTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 50653 27000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 22.48 | 22.48 | 22.48 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.82186079 11385.283 5995.2608 804.83624 5390.0219 2039.7455 2312.5467 131.6964 0 1710.3725 514098.33 -514902.67 75869.034 22408.215 975.27381 406.07545 + 40 1.7293625 9812.345 6009.1868 806.70574 3803.1582 1442.3552 1826.1503 275.19417 0 1288.22 513934.99 -514963.75 48672.13 22980.211 1057.0198 221.56388 + 60 2.5726278 8857.8006 5779.5918 775.88366 3078.2088 1190.8886 1938.5953 328.68401 0 619.17987 513971 -514970.14 39706.347 23441.277 1050.8999 133.14459 + 80 3.4535189 8115.6222 5997.8743 805.18709 2117.7479 901.83124 1587.5299 325.40736 0 288.22238 513957.46 -514942.7 37586.493 23835.221 1111.6406 89.055348 + 100 4.2757752 7496.057 5770.3042 774.63685 1725.7528 829.61731 1420.6409 325.39973 0 62.226626 514051.66 -514963.79 27290.384 24226.433 1080.2534 60.498681 + 120 5.1343639 6986.3331 5396.8054 724.49634 1589.5277 678.23213 1535.5139 325.88286 0 -9.8121501 514027.1 -514967.39 21714.378 24578.965 1016.2738 42.716174 + 140 5.9375162 6548.6966 5126.4765 688.20593 1422.2201 724.92776 1477.7366 315.11557 0 -99.615083 513960.65 -514956.6 19741.549 24878.09 969.48208 30.977308 + 160 6.7352271 6130.9708 5000.2242 671.25714 1130.7466 703.21482 1302.0806 314.9338 0 -258.62211 514042.38 -514973.24 23045.182 25144.056 948.68855 23.022183 + 180 7.5256455 5749.5567 4700.6896 631.046 1048.867 674.90328 1301.3631 310.04329 0 -326.92492 514044.37 -514954.88 14218.695 25401.78 893.70987 17.322259 + 200 8.3062081 5429.1755 4392.2849 589.64408 1036.8906 611.96666 1296.169 303.15486 0 -300.5535 514093.83 -514967.68 10827.179 25624.937 836.11247 13.764989 + 220 9.0794528 5133.41 4290.3608 575.96124 843.04924 572.47213 1261.7692 289.97557 0 -383.86544 514078.49 -514975.79 12503.3 25816.637 817.71346 11.104784 + 240 9.8436809 4849.9512 4119.9044 553.07825 730.04677 553.72774 1263.639 278.92306 0 -487.89901 514091.57 -514969.91 10886.302 25998.932 785.78404 9.3606461 + 260 10.605034 4583.5435 3910.7331 524.99797 672.81042 541.41982 1175.0582 273.43969 0 -475.41044 514139.92 -514981.62 8078.6171 26172.119 746.49788 7.4648407 + 280 11.362397 4348.81 3691.9428 495.62637 656.86725 598.7722 1148.0372 278.86509 0 -444.28194 514045.6 -514970.12 5115.8688 26326.635 704.97777 6.4789284 + 300 12.115575 4128.489 3579.1998 480.49114 549.2892 583.98038 1089.487 267.65383 0 -457.0616 514043.78 -514978.55 8341.4597 26460.833 683.88483 5.2652332 + 320 12.823282 3913.3823 3456.6176 464.03504 456.76476 556.22095 1103.3421 263.7791 0 -485.68641 514000.55 -514981.44 9109.6369 26597.284 660.68384 4.5691163 + 340 13.570274 3712.2734 3258.0793 437.38219 454.19409 533.60879 1068.9434 271.82635 0 -454.64507 514002.17 -514967.71 7179.0605 26741.746 622.91874 3.8804069 + 360 14.315206 3532.9579 3023.6802 405.91518 509.27768 522.48836 1104.2686 276.28278 0 -456.22486 514036.79 -514974.33 4545.215 26882.126 578.23151 3.3025371 + 380 15.055002 3366.746 2970.7631 398.8113 395.98299 508.12217 1059.1562 257.91185 0 -499.79406 514032.85 -514962.26 5636.5329 27008.105 568.28965 2.830075 + 400 15.75335 3204.5091 2873.415 385.74277 331.09416 543.77882 1018.7946 231.10838 0 -519.43553 514029.65 -514972.81 7243.9791 27130.53 549.73386 2.5825543 + 420 16.480976 3050.3022 2775.7673 372.63402 274.53487 517.37336 953.14854 225.86836 0 -505.67105 514057.58 -514973.77 4018.2502 27257.578 531.12039 2.3356262 + 440 17.20372 2915.9612 2639.1922 354.29944 276.76899 507.07374 983.90795 236.07195 0 -534.71742 514060.31 -514975.87 1699.7076 27372.134 505.04906 2.0779128 + 460 17.925103 2787.2795 2609.7668 350.34921 177.51264 485.49348 933.6558 234.43516 0 -560.63202 514070.07 -514985.51 3390.2752 27466.686 499.52337 1.8090485 + 480 18.647898 2662.2222 2514.1136 337.50821 148.10854 464.53566 928.19247 239.15967 0 -570.39028 514071.12 -514984.5 5075.4159 27556.806 481.25552 1.6478036 + 500 19.332267 2540.2584 2432.8576 326.59997 107.40071 473.20947 888.84623 239.12328 0 -565.53809 514057.83 -514986.07 3129.6192 27653.186 465.74774 1.486379 + 520 20.047809 2431.9884 2374.7243 318.79583 57.264134 460.05267 838.76564 228.73042 0 -579.0486 514094.39 -514985.63 462.28535 27743.092 454.64978 1.3782218 + 540 20.762916 2328.6134 2274.6313 305.35881 53.982075 473.12149 875.45698 220.60795 0 -604.15461 514076.11 -514987.16 2622.3468 27815.745 435.47546 1.3461692 + 560 21.477821 2228.4408 2278.1084 305.82559 -49.667558 455.45537 820.96545 214.46954 0 -604.66916 514053.07 -514988.96 3774.7454 27887.17 436.23203 1.136117 + 580 22.156966 2134.2145 2127.7975 285.64705 6.4169804 480.53632 836.99951 218.25579 0 -563.43994 514020.11 -514986.04 1347.9073 27963.805 407.4267 1.1136558 + 600 22.868461 2048.3341 2102.8549 282.29862 -54.520854 486.1799 795.85772 224.19443 0 -574.58492 514004 -514990.16 -100.5692 28031.415 402.6784 1.0360651 + 620 23.582384 1967.2649 2050.2745 275.23994 -83.009549 477.31366 785.52916 222.26776 0 -570.5843 513998.54 -514996.08 1809.6235 28084.448 392.60381 1.0239108 + 640 24.25969 1887.8882 1984.0464 266.34912 -96.158235 482.78351 800.40092 220.19212 0 -557.48535 513952.64 -514994.69 3804.7495 28138.319 379.94961 0.92618662 + 660 24.968904 1812.5853 1960.7266 263.21855 -148.1413 497.47994 750.65798 215.15703 0 -556.35598 513938.64 -514993.72 1173.0953 28202.964 375.50038 0.8766551 + 680 25.642951 1744.2287 1912.3074 256.71848 -168.07864 497.12304 725.28297 210.74936 0 -554.7656 513943.75 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34.650169 1076.5361 1629.6248 218.76965 -553.08868 510.90659 619.76241 167.78799 0 -557.43468 513695.73 -514989.85 296.76427 28751.218 312.16525 0.55489087 + 960 35.315701 1040.3478 1609.1044 216.01487 -568.7566 511.15544 602.92746 166.01646 0 -548.67061 513692.97 -514993.15 742.32048 28759.401 308.22081 0.57967815 + 980 36.013822 1006.0783 1560.5473 209.49631 -554.46902 516.03243 629.22012 171.82488 0 -544.97376 513663.64 -514990.21 -1243.6962 28769.845 298.9291 0.54046046 + 1000 36.709116 974.24875 1558.0215 209.15723 -583.77273 506.6472 601.9316 165.11551 0 -553.06573 513688.1 -514992.5 -1282.1536 28770.759 298.43904 0.55412832 + 1020 37.34906 943.47684 1567.4776 210.42667 -624.00074 507.7679 618.07297 152.13649 0 -569.64661 513661.22 -514993.55 -186.03132 28762.516 300.24615 0.56731507 + 1040 38.021245 913.48747 1599.9646 214.7879 -686.47709 487.43669 574.25818 153.42118 0 -593.34764 513684.82 -514993.06 479.26449 28754.262 306.47982 0.55368609 + 1060 38.667195 884.53789 1558.1773 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532.34349 570.6807 154.35233 0 -512.26701 513492.93 -514980.09 926.11765 28566.848 285.74878 0.73922998 + 1200 43.293101 735.32682 1504.5521 201.97921 -769.22524 536.2319 594.47464 155.80234 0 -515.01641 513442.47 -514983.19 33.948973 28534.509 288.11106 0.73558261 + 1220 43.977824 720.73905 1495.8029 200.80467 -775.06381 558.11107 561.07651 159.20703 0 -503.03817 513434.59 -514985.01 -986.07615 28506.699 286.43244 0.73880049 + 1240 44.630923 707.60909 1486.697 199.58224 -779.08789 564.73341 574.9815 160.19665 0 -467.65622 513371.76 -514983.1 39.386144 28476.751 284.65743 0.8073656 + 1260 45.316338 696.90935 1495.2634 200.73224 -798.35401 576.91144 565.71232 154.53813 0 -455.98096 513344.03 -514983.57 859.74504 28450.875 286.27774 0.85844048 + 1280 45.972141 687.90416 1485.152 199.37484 -797.24786 581.1043 593.28449 150.90626 0 -447.852 513310.83 -514985.52 746.2051 28434.182 284.33627 0.86567683 + 1300 46.659596 680.05111 1479.108 198.56346 -799.05687 585.50039 589.75255 148.14575 0 -422.7668 513283.23 -514982.92 -524.66474 28424.119 283.14576 0.93998516 + 1320 47.315349 673.52979 1476.4577 198.20767 -802.9279 572.81659 595.26192 147.37054 0 -424.83034 513287.53 -514981.08 106.77633 28412.923 282.64612 0.92033657 + 1340 48.004338 668.69073 1484.7214 199.31704 -816.03069 582.3039 588.40727 153.74406 0 -434.27973 513271.16 -514977.36 731.28971 28403.842 284.19266 1.0081579 + 1360 48.666622 665.51033 1519.3878 203.97084 -853.87752 575.99453 554.12668 159.19953 0 -458.43153 513293.36 -514978.13 422.98973 28400.634 290.81807 1.0553453 + 1380 49.357293 663.82821 1467.8065 197.04629 -803.97832 578.21925 592.65789 156.17923 0 -458.90398 513308.34 -514980.47 -203.04754 28400.637 280.90634 1.1101023 + 1400 50.048356 663.49309 1516.9007 203.63695 -853.40759 571.04838 580.61589 146.23345 0 -462.76173 513293.95 -514982.5 -448.98731 28399.279 290.29749 1.1575012 + 1420 50.708454 664.15896 1499.9167 201.35693 -835.75773 566.58488 603.52748 148.50712 0 -471.56553 513299.67 -514982.48 260.66933 28395.449 287.02615 1.1936028 + 1440 51.401936 665.7749 1505.3913 202.09187 -839.61636 568.31696 588.02115 157.51085 0 -462.77296 513294.54 -514985.23 686.32226 28393.937 288.0844 1.1731726 + 1460 52.062043 668.60203 1501.3101 201.54398 -832.70805 581.33476 579.96642 157.99886 0 -456.96282 513291.57 -514986.61 -271.294 28396.763 287.25414 1.2848928 + 1480 52.756437 672.78069 1509.7227 202.67334 -836.94203 577.59283 567.71153 162.7344 0 -467.11093 513309.03 -514986.9 -936.72661 28397.351 288.85976 1.3014708 + 1500 53.420877 678.15981 1516.2442 203.54882 -838.08436 568.973 592.07243 169.01021 0 -495.80017 513315.7 -514988.04 88.20689 28392.187 290.08472 1.3603151 + 1520 54.114697 684.70508 1526.4386 204.91738 -841.73356 557.42832 581.42465 168.54996 0 -496.59211 513336.95 -514989.5 515.33669 28387.812 292.03285 1.3747328 + 1540 54.776816 692.26725 1535.4798 206.13111 -843.21253 551.89278 584.81969 156.31938 0 -472.91843 513327.8 -514991.12 -260.08916 28386.831 293.74312 1.4282442 + 1560 55.471466 700.38373 1542.1981 207.03301 -841.81433 551.6024 611.83194 152.66068 0 -499.25336 513334.3 -514992.96 -881.89875 28383.701 295.04052 1.4061086 + 1580 56.134557 708.58784 1550.4384 208.13924 -841.85055 556.69767 582.39421 162.30767 0 -515.06887 513365.13 -514993.31 317.46976 28375.679 296.61441 1.4196493 + 1600 56.831572 717.16972 1560.1894 209.44826 -843.01966 549.14904 592.56757 172.02873 0 -494.96769 513331.32 -514993.12 268.64262 28369.888 298.46813 1.4559812 + 1620 57.496371 726.01824 1544.6646 207.36413 -818.64636 564.25447 620.2534 171.6366 0 -481.33955 513299.03 -514992.48 -928.98251 28365.608 295.50693 1.4211187 + 1640 58.192956 734.97748 1599.5833 214.73672 -864.60585 559.51067 584.21101 166.15126 0 -484.99381 513300.49 -514989.98 -395.19323 28356.094 306.02332 1.448322 + 1660 58.859821 743.85098 1568.6598 210.58537 -824.80879 567.20594 620.40617 159.81333 0 -485.47565 513302.38 -514989.14 275.6277 28344.463 300.08676 1.4680092 + 1680 59.556888 752.397 1614.4574 216.7335 -862.06044 567.74587 617.24576 156.34105 0 -474.64789 513259.55 -514988.29 153.36452 28335.561 308.89368 1.4040884 + 1700 60.222487 760.11363 1574.8766 211.41996 -814.76301 589.13636 635.26767 165.24375 0 -441.39255 513225.54 -514988.56 -449.5961 28328.169 301.30175 1.4138952 + 1720 60.92238 767.32908 1633.2653 219.25837 -865.93623 593.92768 614.12149 168.83762 0 -435.93625 513180.07 -514986.96 625.88498 28319.407 312.50976 1.3794422 + 1740 61.588997 773.58335 1604.1264 215.34661 -830.5431 611.54553 634.6288 170.13873 0 -425.1955 513161.11 -514982.77 1258.1591 28315.688 306.93109 1.3623528 + 1760 62.288118 778.46232 1604.1065 215.34394 -825.64421 601.28947 635.92844 169.10255 0 -409.79824 513164.39 -514986.55 923.97553 28321.077 306.93241 1.3503708 + 1780 62.95488 782.68573 1585.9867 212.91143 -803.30098 634.82805 637.66853 173.52039 0 -396.05083 513134.96 -514988.23 308.41322 28332.765 303.45213 1.3659282 + 1800 63.656662 786.45168 1632.4834 219.1534 -846.0317 626.46808 612.859 170.73849 0 -389.28328 513124.73 -514991.55 434.99541 28346.181 312.38153 1.3288883 + 1820 64.322505 789.07103 1622.34 217.7917 -833.26902 631.84388 628.97419 164.08777 0 -403.37081 513135.19 -514989.99 1423.3137 28362.768 310.45751 1.2810964 + 1840 65.020631 790.43307 1598.2845 214.56235 -807.85142 593.52496 652.49021 167.51591 0 -408.69698 513177.63 -514990.32 862.95994 28387.747 305.87197 1.2204936 + 1860 65.687176 791.36821 1585.9825 212.91087 -794.61429 619.37616 661.00216 170.47785 0 -410.28902 513156.18 -514991.36 -22.140042 28417.059 303.51149 1.2255437 + 1880 66.353485 791.94788 1630.1749 218.8435 -838.22706 591.52981 652.79092 178.67552 0 -433.7293 513160.08 -514987.57 -35.653011 28444.349 312.01504 1.151451 + 1900 67.051143 791.5025 1611.2186 216.2987 -819.71613 604.66631 614.52658 185.27138 0 -426.58089 513192.07 -514989.67 1492.9051 28470.603 308.39205 1.1258287 + 1920 67.749766 789.33745 1638.8687 220.0106 -849.53124 604.75057 634.21383 186.54046 0 -427.33715 513139.73 -514987.43 863.10157 28504.605 313.697 1.1156351 + 1940 68.417711 786.91982 1566.7995 210.33564 -779.87972 606.00187 648.68271 182.72186 0 -430.75201 513205.37 -514991.9 -1132.9713 28541.397 299.9167 1.0327394 + 1960 69.114583 784.25672 1592.2094 213.7468 -807.95267 595.81907 669.03472 172.75782 0 -436.10776 513181.4 -514990.86 78.431195 28569.12 304.79729 1.0106551 + 1980 69.778898 780.04995 1637.1409 219.77865 -857.09092 606.44426 629.01991 163.80784 0 -440.75819 513180.63 -514996.23 1330.6593 28595.247 313.42473 0.97808647 + 2000 70.476083 774.653 1633.3807 219.27386 -858.72771 607.3352 611.62149 162.37854 0 -449.5387 513203.88 -514994.4 -192.50999 28627.445 312.71969 0.94122657 +Loop time of 70.4761 on 1 procs for 2000 steps with 3000 atoms + +Performance: 1.226 ns/day, 19.577 hours/ns, 28.378 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 43.881 | 43.881 | 43.881 | 0.0 | 62.26 +Bond | 1.8093 | 1.8093 | 1.8093 | 0.0 | 2.57 +Kspace | 10.585 | 10.585 | 10.585 | 0.0 | 15.02 +Neigh | 2.3196 | 2.3196 | 2.3196 | 0.0 | 3.29 +Comm | 0.38965 | 0.38965 | 0.38965 | 0.0 | 0.55 +Output | 0.0086887 | 0.0086887 | 0.0086887 | 0.0 | 0.01 +Modify | 11.438 | 11.438 | 11.438 | 0.0 | 16.23 +Other | | 0.04561 | | | 0.06 + +Nlocal: 3000 ave 3000 max 3000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 10476 ave 10476 max 10476 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 658684 ave 658684 max 658684 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 658684 +Ave neighs/atom = 219.561 +Ave special neighs/atom = 10.5 +Neighbor list builds = 65 +Dangerous builds = 0 +Total wall time: 0:01:10 diff --git a/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 new file mode 100644 index 0000000000..593ed8c982 --- /dev/null +++ b/examples/USER/drude/ethanol/log.27Nov18.ethanol.nh.g++.4 @@ -0,0 +1,286 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 +kspace_style pppm 1.0e-4 + +read_data data.ethanol + orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 3000 atoms + scanning bonds ... + 5 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + reading bonds ... + 2750 bonds + reading angles ... + 3250 angles + reading dihedrals ... + 3000 dihedrals + 5 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of 1-4 neighbors + 11 = max # of special neighbors + + +pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H +pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO +pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H +pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH +pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO +pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO +pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H +pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH +pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO +pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H +pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH +pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO +pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH +pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO +pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO +pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes +pair_coeff 1 1 thole 2.051000 +pair_coeff 1 2 thole 1.580265 +pair_coeff 1 4 thole 1.416087 +pair_coeff 1 6 thole 2.051000 +pair_coeff 1 7 thole 1.580265 +pair_coeff 1 8 thole 1.416087 +pair_coeff 2 2 thole 1.217570 +pair_coeff 2 4 thole 1.091074 +pair_coeff 2 6 thole 1.580265 +pair_coeff 2 7 thole 1.217570 +pair_coeff 2 8 thole 1.091074 +pair_coeff 4 4 thole 0.977720 +pair_coeff 4 6 thole 1.416087 +pair_coeff 4 7 thole 1.091074 +pair_coeff 4 8 thole 0.977720 +pair_coeff 6 6 thole 2.051000 +pair_coeff 6 7 thole 1.580265 +pair_coeff 6 8 thole 1.416087 +pair_coeff 7 7 thole 1.217570 +pair_coeff 7 8 thole 1.091074 +pair_coeff 8 8 thole 0.977720 + +group gETHANOL molecule 1:250 +3000 atoms in group gETHANOL +group gATOMS type 1 2 3 4 5 +2250 atoms in group gATOMS +group gDRUDES type 6 7 8 +750 atoms in group gDRUDES + + +neighbor 2.0 bin + +variable vTEMP equal 300.0 +variable vTEMP_D equal 1.0 +variable vPRESS equal 1.0 + +velocity gATOMS create ${vTEMP} 12345 +velocity gATOMS create 300 12345 +velocity gDRUDES create ${vTEMP_D} 12345 +velocity gDRUDES create 1 12345 + +fix fDRUDE all drude C C N C N D D D + +fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 + 250 = # of size 2 clusters + 250 = # of size 3 clusters + 250 = # of size 4 clusters + 0 = # of frozen angles + +comm_modify vel yes +compute cTEMP_ATOM gATOMS temp +compute cTEMP all temp/drude + +fix fDTDIR all drude/transform/direct +fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 +fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 +fix_modify fNPT temp cTEMP_ATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/fix_nh.cpp:1404) +fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 +fix fNVT gDRUDES nvt temp 1 1 100.0 +fix fDTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] +thermo 20 + +timestep 0.5 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.379738 + grid = 30 30 30 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0289979 + estimated relative force accuracy = 8.73262e-05 + using double precision FFTs + 3d grid and FFT values/proc = 17908 7200 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 11 +New max number of 1-2 to 1-4 neighbors: 11 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 10 + ghost atom cutoff = 10 + binsize = 5, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair thole, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 15.7 | 15.72 | 15.75 Mbytes +Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] + 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170210.19 22094.109 381.62759 10.134301 + 20 0.26940155 11385.283 5995.2608 804.83624 5390.0219 2039.7455 2312.5467 131.6964 0 1710.3725 514098.33 -514902.67 75869.034 22408.215 975.27381 406.07545 + 40 0.56039548 9812.345 6009.1868 806.70574 3803.1582 1442.3552 1826.1503 275.19417 0 1288.22 513934.99 -514963.75 48672.13 22980.211 1057.0198 221.56388 + 60 0.88414049 8857.8007 5779.5918 775.88366 3078.2089 1190.8886 1938.5954 328.68401 0 619.17987 513971 -514970.14 39706.347 23441.277 1050.8999 133.14459 + 80 1.1696272 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28383.721 294.92477 1.4055318 + 1580 17.929113 708.77379 1550.3407 208.12612 -841.56691 556.60852 582.39053 162.12325 0 -515.10224 513365.77 -514993.35 322.32831 28375.626 296.59534 1.4204419 + 1600 18.144745 717.39964 1559.9665 209.41835 -842.56689 549.07216 592.74611 171.9088 0 -494.99998 513331.85 -514993.14 267.08424 28369.799 298.42556 1.4556193 + 1620 18.363554 726.25369 1544.67 207.36486 -818.41631 564.24547 620.11593 171.47239 0 -481.42668 513299.67 -514992.5 -929.2129 28365.483 295.50817 1.4206365 + 1640 18.578192 735.20307 1599.669 214.74822 -864.46597 559.44554 584.31101 166.36248 0 -485.25281 513300.68 -514990.01 -400.32794 28355.927 306.03975 1.4483397 + 1660 18.788682 744.13508 1567.4804 210.42705 -823.34534 567.22939 620.98009 160.76689 0 -485.86239 513302.82 -514989.28 275.23727 28344.229 299.86144 1.466234 + 1680 19.002967 752.73626 1613.0757 216.548 -860.33939 567.6576 617.82475 157.94412 0 -474.89518 513259.71 -514988.58 145.60417 28335.257 308.62904 1.4035192 + 1700 19.208987 760.45858 1575.0294 211.44047 -814.57086 588.97206 634.68664 166.27782 0 -441.79702 513226.22 -514988.93 -455.69419 28327.746 301.33081 1.4144311 + 1720 19.424031 767.76378 1634.9553 219.48525 -867.19156 594.28118 613.97792 169.57851 0 -435.89528 513178.39 -514987.52 624.6147 28318.833 312.83371 1.3795127 + 1740 19.630425 774.0707 1607.3304 215.77673 -833.25975 612.27366 635.89702 170.90768 0 -425.06946 513156.42 -514983.69 1245.2476 28314.962 307.54418 1.3649994 + 1760 19.88556 778.94063 1606.5499 215.67195 -827.60929 602.10334 636.54708 169.93908 0 -409.46967 513160.13 -514986.86 900.23197 28320.117 307.40099 1.3499664 + 1780 20.156405 783.13015 1582.8925 212.49605 -799.76233 635.8022 637.81662 173.60641 0 -395.27083 513136.4 -514988.12 303.67422 28331.437 302.86049 1.3623691 + 1800 20.394003 786.8472 1629.8795 218.80383 -843.03226 626.87797 613.50519 171.66383 0 -388.22631 513124.5 -514991.35 452.45767 28344.488 311.88054 1.3331104 + 1820 20.604631 789.49317 1623.8201 217.99039 -834.32693 632.3375 629.50791 165.54164 0 -402.81199 513130.95 -514989.85 1435.9558 28360.845 310.74273 1.2776203 + 1840 20.882926 790.84026 1595.8459 214.23498 -805.0056 593.44998 654.04584 168.32988 0 -408.05005 513177.2 -514989.98 869.17595 28385.701 305.40649 1.2158021 + 1860 21.104003 791.82787 1587.2175 213.07667 -795.38968 618.69585 660.77302 168.60246 0 -408.77525 513157.18 -514991.87 14.63364 28414.975 303.75155 1.217843 + 1880 21.318712 792.39264 1628.8097 218.66022 -836.41704 590.23683 653.83304 177.71688 0 -432.28625 513162.12 -514988.04 -17.001449 28442.457 311.75357 1.1508692 + 1900 21.52406 792.00166 1611.7686 216.37254 -819.76695 604.55866 613.59005 183.84763 0 -425.02508 513192.41 -514989.15 1501.7473 28469.05 308.49923 1.1217532 + 1920 21.740008 789.87504 1640.0559 220.16997 -850.18086 603.67271 634.84308 183.31253 0 -426.75252 513142.08 -514987.34 889.51113 28503.487 313.92438 1.1161317 + 1940 21.949681 787.46267 1570.9429 210.89187 -783.48022 605.27114 651.32573 181.65051 0 -435.56723 513206.5 -514992.66 -1213.4071 28540.767 300.71188 1.0306517 + 1960 22.16336 784.79852 1591.8755 213.70197 -807.07695 594.43439 669.69922 174.81078 0 -440.94269 513185.58 -514990.66 -9.1610879 28568.421 304.73308 1.0111234 + 1980 22.368034 780.57674 1632.8138 219.19775 -852.23704 605.41038 630.06225 169.19473 0 -441.49651 513181.33 -514996.74 1265.2908 28593.818 312.59942 0.96826781 + 2000 22.581326 775.20404 1636.2577 219.66008 -861.05366 609.0993 612.37884 163.97498 0 -448.27188 513197.01 -514995.24 -167.85231 28624.885 313.26825 0.94815628 +Loop time of 22.5814 on 4 procs for 2000 steps with 3000 atoms + +Performance: 3.826 ns/day, 6.273 hours/ns, 88.568 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.479 | 10.867 | 11.348 | 9.5 | 48.12 +Bond | 0.47013 | 0.48392 | 0.50035 | 1.7 | 2.14 +Kspace | 4.4559 | 4.9538 | 5.3493 | 14.5 | 21.94 +Neigh | 0.65502 | 0.65523 | 0.65539 | 0.0 | 2.90 +Comm | 0.47358 | 0.47448 | 0.47606 | 0.1 | 2.10 +Output | 0.0062618 | 0.0089129 | 0.014062 | 3.2 | 0.04 +Modify | 5.0877 | 5.0948 | 5.1016 | 0.3 | 22.56 +Other | | 0.04382 | | | 0.19 + +Nlocal: 750 ave 769 max 722 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Nghost: 5829.25 ave 5873 max 5791 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 164687 ave 168810 max 157995 min +Histogram: 1 0 0 0 0 0 1 0 1 1 + +Total # of neighbors = 658749 +Ave neighs/atom = 219.583 +Ave special neighs/atom = 10.5 +Neighbor list builds = 65 +Dangerous builds = 0 +Total wall time: 0:00:22 diff --git a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 b/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 deleted file mode 100644 index 5509458f14..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.1 +++ /dev/null @@ -1,254 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -comm_modify vel yes -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 -fix fNPH all nph iso 1 ${vPRESS} 500.0 -fix fNPH all nph iso 1 1 500.0 - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 50653 27000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 17.0416 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 1.385576 10970.012 5646.6301 758.03417 5323.3819 2059.5936 2216.9884 125.92554 0 1728.6053 514096.92 -514904.65 75436.064 22442.45 899.51659 426.89782 - 40 2.8551838 8946.3004 5328.0205 715.26229 3618.2799 1462.1369 1696.2859 256.70292 0 1227.1291 513938.28 -514962.25 46638.926 23048.183 913.15135 252.56746 - 60 4.256644 7510.9138 4723.1153 634.05655 2787.7985 1200.8153 1745.4103 301.30777 0 557.91727 513950.17 -514967.82 37797.472 23517.111 840.69781 151.04819 - 80 5.6700039 6349.0396 4602.1226 617.81383 1746.917 881.77472 1380.8268 300.54011 0 204.13917 513929.54 -514949.9 33853.354 23924.249 841.20585 95.742025 - 100 7.1165569 5485.3222 4144.7402 556.41234 1340.582 784.84009 1301.8671 289.61557 0 -77.062714 514016.28 -514974.95 23857.465 24318.637 768.91722 59.825738 - 120 8.510273 4862.0053 3777.3363 507.09006 1084.669 621.87069 1297.2363 283.15963 0 -165.00092 514030.24 -514982.84 17467.301 24661.1 708.90876 35.503627 - 140 9.89271 4340.9652 3447.5936 462.82361 893.3716 643.1449 1248.6314 275.36087 0 -264.51028 513962.87 -514972.13 14982.178 24941.74 650.92753 23.297372 - 160 11.266981 3926.9368 3280.8104 440.43373 646.12637 590.77624 1125.7232 275.3221 0 -402.26335 514039.99 -514983.43 17555.529 25182.215 623.03896 13.767615 - 180 12.636709 3510.3411 3034.5182 407.37013 475.82289 580.88726 1065.7063 271.62555 0 -478.17514 514008.07 -514972.29 9901.7384 25408.806 577.95511 8.7953435 - 200 13.951961 3233.2057 2804.8754 376.54165 428.33026 560.57334 1096.7788 268.56938 0 -524.79217 514009.74 -514982.54 8543.4492 25602.16 535.31334 5.5723047 - 220 15.315 3020.0557 2679.3857 359.69523 340.66996 534.37676 1086.1078 252.72365 0 -554.44877 514000.87 -514978.96 7630.6161 25763.835 511.8744 4.1309201 - 240 16.66608 2817.6362 2557.8968 343.3859 259.73947 533.53125 1096.7513 235.23483 0 -594.78212 513968.14 -514979.14 6067.9397 25911.192 489.07601 2.9844639 - 260 18.020921 2631.1316 2460.4934 330.30994 170.63824 520.23801 1043.849 228.55335 0 -637.15729 514004.04 -514988.88 5635.1903 26047.493 470.67196 2.358136 - 280 19.327414 2462.7215 2379.403 319.42393 83.318543 525.36331 972.01762 226.26993 0 -624.36335 513966.76 -514982.73 4763.2439 26167.845 455.32938 1.8853017 - 300 20.664073 2314.007 2233.3945 299.82295 80.612529 521.07514 985.58156 216.6623 0 -622.92535 513969.51 -514989.29 3501.9257 26271.903 427.41388 1.7110326 - 320 21.998284 2171.6005 2216.0458 297.49398 -44.445373 513.1225 926.87268 206.39293 0 -647.39127 513946.45 -514989.89 3556.0249 26368.557 424.16134 1.5401544 - 340 23.295565 2048.7645 2103.0412 282.32362 -54.276671 517.24017 972.17593 198.86832 0 -648.49462 513890.61 -514984.68 3723.4258 26461.822 402.56097 1.3933654 - 360 24.639426 1940.255 2045.2119 274.5603 -104.95688 499.1817 932.32957 187.5616 0 -652.16846 513915.39 -514987.25 2301.433 26551.361 391.50737 1.3177372 - 380 25.919177 1826.4337 1933.9251 259.62057 -107.49138 518.5733 919.38362 182.08763 0 -651.72644 513909.35 -514985.16 2618.7931 26632.025 370.16974 1.3263382 - 400 27.23436 1760.0079 1974.3468 265.04699 -214.33884 494.88766 905.27809 184.94874 0 -673.15814 513861.2 -514987.5 2096.731 26707.742 377.93896 1.2790015 - 420 28.50932 1674.2459 1875.0429 251.7159 -200.79701 494.32791 919.1307 191.42967 0 -660.09631 513843.82 -514989.41 358.06627 26778.924 358.8831 1.3234648 - 440 29.823068 1636.3668 1886.8736 253.30412 -250.50682 501.37304 885.96911 179.94725 0 -646.55634 513813.44 -514984.68 465.97294 26842.197 361.1633 1.2949713 - 460 31.092765 1593.0934 1860.7484 249.79693 -267.65503 491.39115 906.9344 174.33035 0 -666.38274 513814.92 -514988.85 126.16052 26894.743 356.1632 1.2759204 - 480 32.406062 1505.0407 1837.1657 246.63106 -332.12503 509.85902 860.16645 173.43061 0 -651.2259 513765.85 -514990.2 1646.3283 26939.521 351.6473 1.2643358 - 500 33.677199 1442.2558 1798.394 241.42613 -356.13819 522.53768 861.77071 168.42903 0 -655.02572 513738.55 -514992.4 1526.9168 26984.71 344.22043 1.2508825 - 520 34.98888 1429.2148 1796.9298 241.22958 -367.71495 524.55666 871.69773 162.68814 0 -664.81406 513731.94 -514993.79 -680.86121 27027.519 343.9346 1.2628675 - 540 36.290854 1386.5466 1788.8853 240.14964 -402.33868 549.35219 874.93475 154.34652 0 -656.82759 513667.79 -514991.93 -112.10182 27063.585 342.37563 1.3021222 - 560 37.52542 1344.4167 1829.4102 245.58992 -484.99349 543.86102 827.43025 144.96524 0 -643.51447 513638.79 -514996.53 701.10406 27094.487 350.14354 1.3040182 - 580 38.796225 1286.7629 1718.567 230.70973 -431.80414 561.04865 874.04358 152.41827 0 -615.40981 513590.72 -514994.62 826.08615 27125.818 328.91939 1.2462575 - 600 40.032106 1275.3861 1701.9169 228.47454 -426.53082 558.07219 895.26591 163.23964 0 -608.79386 513561.43 -514995.74 284.53547 27152.441 325.68878 1.3366627 - 620 41.297358 1273.8918 1712.1906 229.85372 -438.29876 558.54787 859.08268 175.40704 0 -603.76978 513568.36 -514995.92 -799.98388 27171.09 327.70761 1.2215062 - 640 42.526453 1217.1518 1736.1072 233.06442 -518.95534 572.52862 823.16123 163.5653 0 -606.82177 513521.07 -514992.46 -528.59646 27187.499 332.28172 1.2466277 - 660 43.751388 1139.8934 1675.8281 224.97222 -535.93471 572.5104 829.99341 152.69698 0 -620.77477 513527.1 -514997.46 127.63393 27203.689 320.71564 1.270961 - 680 44.951294 1132.7801 1684.9691 226.19937 -552.18903 579.17897 824.9868 153.95243 0 -613.89121 513497.59 -514994 -375.69988 27217.538 322.46995 1.266406 - 700 46.114508 1123.7259 1689.7673 226.8435 -566.04141 579.34852 817.35591 160.76324 0 -604.95952 513473.67 -514992.22 539.9968 27228.562 323.38291 1.2824201 - 720 47.311101 1109.2452 1679.3944 225.45099 -570.14919 580.49864 815.37954 166.39557 0 -599.53737 513460.9 -514993.78 1379.628 27240.51 321.38269 1.3097525 - 740 48.482072 1103.9038 1664.1003 223.39782 -560.19651 598.28549 826.45607 162.40108 0 -577.67737 513419.55 -514989.21 -688.06905 27252.803 318.47888 1.2441535 - 760 49.66032 1069.6322 1656.8299 222.42181 -587.19776 602.32252 832.89566 153.82032 0 -575.90234 513395.07 -514995.41 40.843646 27264.248 317.07409 1.2699292 - 780 50.861186 1034.9853 1655.3151 222.21845 -620.3298 585.98097 809.14501 152.10567 0 -574.09092 513399.41 -514992.88 -542.13898 27275.872 316.80217 1.2268067 - 800 52.028532 1040.3169 1665.5678 223.59483 -625.25085 605.03042 803.57295 148.68705 0 -581.69335 513396.32 -514997.16 535.8591 27285.478 318.74392 1.2821524 - 820 53.219595 1058.9481 1736.3976 233.1034 -677.4495 598.69968 784.98413 145.24433 0 -598.32684 513390.35 -514998.4 661.30446 27295.669 332.34879 1.2200226 - 840 54.41621 1045.3784 1676.8277 225.10642 -631.4493 612.87881 813.63091 148.70121 0 -579.94856 513372.94 -514999.65 -709.36037 27305.36 320.91078 1.2627849 - 860 55.601647 1020.7309 1672.697 224.55189 -651.96607 601.90752 814.84165 150.80576 0 -580.50172 513365.58 -515004.6 -495.61008 27311.4 320.12878 1.239739 - 880 56.769503 989.87899 1623.5853 217.95888 -633.70636 614.6379 850.57766 146.023 0 -574.97001 513330.69 -515000.67 642.87966 27315.764 310.68993 1.2958041 - 900 57.983504 951.29928 1656.7713 222.41394 -705.47199 612.66694 803.70933 146.11306 0 -578.97014 513313.84 -515002.83 -24.66438 27323.702 317.06441 1.2662666 - 920 59.146542 990.23712 1682.9256 225.92504 -692.68849 625.49291 805.11902 145.39781 0 -566.50947 513298.1 -515000.28 -197.4677 27331.656 322.09842 1.2192545 - 940 60.311439 975.32007 1655.1496 222.19623 -679.82952 644.56888 830.44185 142.39994 0 -571.05582 513274.28 -515000.46 -57.36251 27336.591 316.75027 1.2738836 - 960 61.537265 970.70957 1646.9748 221.0988 -676.26523 621.55653 860.81553 137.50196 0 -570.35847 513277.66 -515003.44 356.66027 27339.657 315.18748 1.2637636 - 980 62.841358 922.60821 1622.7907 217.8522 -700.18247 618.71597 851.23286 133.07652 0 -567.79027 513264.96 -515000.37 5.1281321 27344.467 310.55109 1.2643077 - 1000 64.061049 903.52078 1692.943 227.26982 -789.4222 615.63909 786.17473 136.0751 0 -548.92889 513225.82 -515004.21 -1215.8274 27349.08 323.99743 1.2690479 - 1020 65.198298 880.82937 1611.9406 216.39562 -731.11119 641.95133 825.78985 138.47494 0 -548.19881 513212.76 -515001.89 -120.47994 27348.478 308.46852 1.2703282 - 1040 66.338573 859.35882 1637.2347 219.79124 -777.87584 642.91383 781.96671 129.07882 0 -535.68978 513205.22 -515001.36 -128.41699 27349.25 313.3121 1.2828435 - 1060 67.506762 843.6634 1588.9732 213.31236 -745.30982 645.93104 848.24527 128.71177 0 -531.00457 513167.02 -515004.21 111.3449 27352.063 304.04699 1.3138151 - 1080 68.625545 819.34273 1604.5527 215.40383 -785.20997 653.64454 797.74835 132.82208 0 -520.03981 513152.36 -515001.74 -705.09278 27353.042 307.03668 1.306641 - 1100 69.741567 799.10089 1574.7957 211.40909 -775.69478 654.13763 825.37479 142.68152 0 -514.52184 513120.3 -515003.67 1350.915 27353.287 301.3473 1.2713755 - 1120 70.887971 807.77511 1606.5291 215.66916 -798.75403 677.02 802.76738 138.71115 0 -519.19695 513103.61 -515001.67 551.01047 27358.309 307.4238 1.2874498 - 1140 72.009922 822.40019 1605.593 215.54349 -783.19283 664.08656 825.14971 139.5036 0 -525.0726 513119.2 -515006.06 -1500.6927 27365.732 307.25006 1.2741015 - 1160 73.11993 799.60355 1627.1824 218.44176 -827.57881 660.53797 810.61642 135.99659 0 -549.15929 513120.99 -515006.56 -463.83247 27365.87 311.39885 1.2506312 - 1180 74.237157 808.71869 1627.4862 218.48255 -818.76747 671.07453 814.08104 132.68184 0 -536.0374 513101.27 -515001.83 -1497.9686 27360.344 311.48219 1.1920705 - 1200 75.389495 800.76402 1602.0973 215.0742 -801.33325 661.27319 818.56681 137.56688 0 -528.29009 513116.11 -515006.56 727.09082 27352.249 306.62538 1.1680129 - 1220 76.512266 786.90424 1625.6159 218.23148 -838.7117 654.42667 808.06282 144.23638 0 -544.37793 513103.11 -515004.17 -1016.333 27347.251 311.10383 1.2383451 - 1240 77.618425 784.43915 1618.0202 217.21178 -833.58101 652.75565 810.84854 144.21786 0 -538.55907 513104.01 -515006.86 -1688.0609 27338.945 309.66351 1.2014646 - 1260 78.767789 792.64493 1616.6996 217.03449 -824.05464 659.33158 832.96211 136.95679 0 -535.25333 513087.8 -515005.85 -240.86746 27324.585 309.38787 1.2538953 - 1280 79.890153 772.02964 1579.0067 211.9744 -806.97707 680.62465 825.10068 128.65485 0 -522.39638 513085.1 -515004.06 1026.3484 27308.077 302.15133 1.2789362 - 1300 81.045542 794.71268 1640.9493 220.28991 -846.23661 653.48559 809.8286 126.57126 0 -529.35975 513101 -515007.77 -222.24259 27295.577 314.02093 1.2904787 - 1320 82.165808 784.00371 1619.7825 217.44836 -835.77876 666.10367 843.1839 129.04786 0 -537.48412 513064.75 -515001.38 -904.29245 27284.448 309.98624 1.2367093 - 1340 83.287128 768.52183 1621.7783 217.71629 -853.25649 658.65554 797.98287 135.92558 0 -517.31157 513072.35 -515000.86 556.43774 27269.699 310.3284 1.3310985 - 1360 84.450531 750.55548 1561.8653 209.67325 -811.30983 659.33682 849.22159 146.12076 0 -514.99584 513050.84 -515001.83 156.64838 27254.169 298.83628 1.3466087 - 1380 85.572197 744.55824 1600.9118 214.91506 -856.35357 669.28688 822.92318 135.57716 0 -509.75984 513027.33 -515001.71 395.88113 27246.862 306.32946 1.3282506 - 1400 86.727889 740.37698 1618.0191 217.21163 -877.6421 680.34192 804.16104 122.37614 0 -510.05578 513028.7 -515003.17 -1778.0909 27242.463 309.60983 1.3262175 - 1420 87.853329 707.95242 1606.2301 215.62901 -898.27766 681.75825 834.81666 117.56052 0 -511.14444 512980.84 -515002.11 132.87977 27231.78 307.36642 1.2875563 - 1440 88.999557 701.0459 1631.5857 219.03289 -930.53982 689.29026 778.55166 121.13791 0 -503.03703 512986.74 -515003.22 502.08629 27220.348 312.26072 1.2092436 - 1460 90.173845 691.9965 1611.7145 216.36527 -919.71797 691.89285 800.91685 123.97376 0 -504.76462 512970.72 -515002.46 530.64797 27214.26 308.41315 1.2983911 - 1480 91.318457 691.7249 1594.0369 213.99213 -902.31197 688.47809 838.61898 125.21502 0 -504.16566 512953.09 -515003.55 -1094.2326 27210.327 305.01536 1.3192889 - 1500 92.483926 665.64633 1571.5229 210.96973 -905.87653 681.91529 823.02708 127.30163 0 -506.25486 512973.62 -515005.48 -1022.5661 27200.233 300.72872 1.2507982 - 1520 93.612424 675.29951 1631.0635 218.96279 -955.76401 670.77264 825.29942 133.56984 0 -531.08736 512951.49 -515005.81 -389.61365 27187.165 312.13799 1.2620465 - 1540 94.741199 653.89323 1632.9694 219.21864 -979.07615 678.96106 792.69599 132.07987 0 -515.25022 512939.14 -515006.7 -1030.2457 27174.091 312.51532 1.234099 - 1560 95.9062 636.91726 1590.0999 213.46361 -953.18262 687.04134 809.44011 127.54619 0 -523.45302 512956.52 -515010.28 -951.93121 27155.942 304.27362 1.288966 - 1580 97.028125 627.56968 1601.8646 215.04297 -974.29496 686.96797 803.53231 128.08068 0 -517.28126 512935.11 -515010.71 -1043.2395 27131.362 306.54052 1.2619672 - 1600 98.159189 639.59673 1591.5973 213.66464 -952.00062 695.73225 820.03411 126.92265 0 -523.57295 512936.97 -515008.08 -516.36154 27101.901 304.53745 1.3431812 - 1620 99.322595 631.83759 1582.6681 212.46592 -950.83047 708.36138 817.50888 123.99588 0 -518.92537 512930.72 -515012.49 -2198.9765 27071.135 302.85679 1.2706043 - 1640 100.45901 621.88183 1569.4451 210.6908 -947.56326 703.57599 823.87187 132.80048 0 -497.70649 512900.32 -515010.43 -1335.78 27038.969 300.32548 1.2622751 - 1660 101.60839 642.07332 1595.5476 214.19493 -953.47423 705.46998 794.82235 141.09052 0 -484.29874 512898.11 -515008.66 -403.23344 27004.83 305.30235 1.3253687 - 1680 102.77636 620.05889 1604.721 215.42642 -984.66208 704.63874 808.2235 139.26176 0 -475.937 512849.25 -515010.1 -336.0674 26974.635 307.06907 1.3063348 - 1700 103.9216 625.14905 1627.936 218.54293 -1002.7869 700.41444 790.63143 141.47429 0 -472.95296 512847.83 -515010.18 432.43074 26948.842 311.5388 1.2611748 - 1720 105.07527 635.67026 1585.5068 212.84701 -949.83654 711.22133 826.38676 138.90157 0 -470.74615 512857.96 -515013.56 -927.08791 26927.403 303.39054 1.2949652 - 1740 106.19526 622.55036 1629.9419 218.81221 -1007.3915 701.72972 807.03841 133.88234 0 -462.62233 512821.73 -515009.15 60.724835 26906.734 311.91698 1.2759906 - 1760 107.3157 601.07861 1563.031 209.82973 -961.95237 721.05163 813.03641 135.83107 0 -472.1521 512852.13 -515011.85 1071.0762 26889.11 299.11764 1.211508 - 1780 108.47195 615.76689 1612.7311 216.50175 -996.96425 712.00335 812.2101 135.93651 0 -469.54632 512821.55 -515009.11 -1171.9908 26876.291 308.62781 1.2522701 - 1800 109.60652 590.39061 1576.6095 211.65259 -986.21891 706.7567 822.39219 137.15671 0 -470.15251 512825.84 -515008.21 -1051.5297 26860.1 301.6752 1.3176335 - 1820 110.78553 603.65994 1596.51 214.32414 -992.85007 711.49043 808.94991 132.38543 0 -461.89866 512827.37 -515011.15 180.50052 26844.34 305.50815 1.2756752 - 1840 111.93685 591.93917 1596.2013 214.2827 -1004.2621 720.41618 814.51338 137.96161 0 -460.4745 512793.12 -515009.8 605.10058 26833.73 305.47844 1.2069138 - 1860 113.12134 609.8248 1577.7772 211.80934 -967.95236 716.21723 808.30329 144.61624 0 -461.04538 512833.46 -515009.51 -1143.3982 26826.019 301.93343 1.2373879 - 1880 114.2602 614.25513 1599.756 214.7599 -985.50088 748.39555 792.89735 140.36606 0 -460.16996 512800.85 -515007.84 -261.10141 26816.306 306.15319 1.2225442 - 1900 115.40316 615.77501 1599.1853 214.68329 -983.41029 729.35936 798.81735 146.34452 0 -492.16069 512844.21 -515009.98 493.95161 26806.893 306.01603 1.2873103 - 1920 116.55442 628.99417 1652.3184 221.81616 -1023.3242 715.08536 813.8821 147.49091 0 -508.7856 512818.33 -515009.33 -2250.9701 26803.895 316.19125 1.3118467 - 1940 117.73809 613.28705 1595.717 214.21768 -982.42996 719.54904 821.80704 150.0739 0 -493.66309 512828.25 -515008.45 -2187.7221 26796.819 305.33907 1.3154875 - 1960 118.91834 594.22322 1584.9306 212.76966 -990.7074 717.75467 820.27772 151.35897 0 -491.90915 512819.49 -515007.68 -736.31063 26780.283 303.29276 1.2654066 - 1980 120.06148 614.4096 1572.4353 211.09222 -958.02568 732.31342 826.01815 154.79578 0 -487.35165 512824.93 -515008.73 39.731855 26764.092 300.89417 1.2728833 - 2000 121.20194 604.51985 1580.7247 212.20504 -976.20489 716.50209 820.59198 155.66948 0 -482.48478 512823.08 -515009.56 -465.82593 26752.509 302.47674 1.2881296 -Loop time of 121.202 on 1 procs for 2000 steps with 3000 atoms - -Pair time (%) = 58.9106 (48.6053) -Bond time (%) = 7.9266 (6.53999) -Kspce time (%) = 14.2366 (11.7462) -Neigh time (%) = 1.79608 (1.48189) -Comm time (%) = 0.562635 (0.464213) -Outpt time (%) = 0.0137095 (0.0113113) -Other time (%) = 37.7558 (31.1511) - -Nlocal: 3000 ave 3000 max 3000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 10007 ave 10007 max 10007 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 720894 ave 720894 max 720894 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 720894 -Ave neighs/atom = 240.298 -Ave special neighs/atom = 10.5 -Neighbor list builds = 49 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 b/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 deleted file mode 100644 index 245a37c6d0..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.lang.8Jul15.linux.4 +++ /dev/null @@ -1,254 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -comm_modify vel yes -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 300 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nph iso ${vPRESS} ${vPRESS} 500.0 -fix fNPH all nph iso 1 ${vPRESS} 500.0 -fix fNPH all nph iso 1 1 500.0 - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 17908 7200 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 13.7041 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 0.44569397 10977.424 5649.3945 758.40528 5328.0296 2062.3394 2228.2308 127.20754 0 1716.2152 514097.63 -514903.59 75539.256 22441.778 900.65907 425.71739 - 40 0.90527296 8971.2482 5307.0059 712.44118 3664.2423 1468.3059 1727.5451 263.87315 0 1220.4282 513944.02 -514959.93 46706.836 23047.009 909.55477 251.59684 - 60 1.361037 7598.4556 4774.303 640.92826 2824.1526 1194.6529 1771.6791 314.85714 0 553.82536 513952.92 -514963.78 37332.483 23513.741 850.78562 150.29304 - 80 1.7987111 6500.1249 4632.1069 621.83909 1868.0179 914.33309 1444.251 317.2453 0 213.21366 513930.08 -514951.11 33258.709 23919.334 847.28599 94.967207 - 100 2.243571 5591.6251 4319.2496 579.83942 1272.3755 772.49711 1235.8559 306.35507 0 -56.084846 513990.28 -514976.52 21846.137 24315.14 802.34652 59.892261 - 120 2.672169 4952.948 3881.7989 521.11369 1071.1491 630.90018 1260.1994 299.84546 0 -147.02839 514014.84 -514987.6 17197.209 24657.008 728.80233 35.812029 - 140 3.0969729 4374.1711 3440.8515 461.91852 933.31957 670.31509 1238.1527 300.45294 0 -260.41129 513963.49 -514978.68 17258.201 24938.237 649.62114 23.329848 - 160 3.522228 3923.495 3251.4038 436.48603 672.0912 632.18705 1144.4394 307.33026 0 -436.52375 514013.97 -514989.32 17850.515 25184.125 617.40474 13.751472 - 180 3.939676 3558.426 3060.6065 410.87237 497.81946 621.75343 1085.8467 297.16091 0 -495.18434 513968.41 -514980.17 9891.4148 25413.786 582.97006 8.7537197 - 200 4.3550711 3228.7597 2864.5929 384.55845 364.16674 591.37767 1077.5669 257.51603 0 -521.62174 513950.21 -514990.89 5932.7994 25603.593 546.64932 5.8336845 - 220 4.781127 2922.9928 2668.3732 358.21686 254.61956 552.45115 1045.2477 238.95571 0 -548.2597 513955.3 -514989.07 7141.8585 25759.687 509.85961 3.9098706 - 240 5.195529 2721.2831 2574.4897 345.61343 146.79339 548.06208 1035.0795 226.53387 0 -609.08183 513928.26 -514982.06 6976.8028 25904.957 492.22535 3.0535597 - 260 5.5978601 2525.9513 2461.0955 330.39077 64.855761 536.85769 1022.3488 211.33422 0 -633.79065 513919.59 -514991.49 4541.0707 26037.832 470.78293 2.3688827 - 280 6.0106721 2338.1989 2324.5678 312.06255 13.63115 519.14801 970.18634 197.76634 0 -621.14257 513937.12 -514989.44 2916.5572 26148.311 444.7787 1.975451 - 300 6.4294651 2194.9975 2189.2141 293.89194 5.7833943 530.82824 982.37216 190.98549 0 -652.12498 513946.6 -514992.88 4231.0047 26242.419 418.97109 1.6488796 - 320 6.825505 2045.5803 2132.2428 286.24381 -86.66256 531.61575 935.95137 188.46723 0 -683.29899 513935.09 -514994.49 1717.7425 26334.126 408.09021 1.554221 - 340 7.23614 1929.4862 2083.5954 279.71312 -154.10925 509.11673 906.18183 186.63991 0 -668.08147 513908.15 -514996.11 2743.5013 26418.758 398.8054 1.4581893 - 360 7.6401701 1853.7734 1992.7639 267.5194 -138.99054 525.44894 891.90785 178.2228 0 -654.5178 513920.68 -515000.73 3824.9512 26497.054 381.4442 1.3381947 - 380 8.035013 1760.9758 1947.1807 261.40007 -186.20493 517.02356 919.61194 172.55666 0 -676.58938 513879.08 -514997.89 2968.2379 26574.581 372.73009 1.2814975 - 400 8.439594 1687.9145 1906.019 255.8743 -218.10451 535.676 922.06535 176.24936 0 -683.92633 513833.49 -515001.66 1305.3348 26642.871 364.83666 1.2876267 - 420 8.849108 1605.8081 1889.1783 253.61351 -283.37015 517.23187 857.77943 180.22369 0 -663.03698 513825.85 -515001.41 2618.2332 26704.387 361.60626 1.2936035 - 440 9.2419581 1518.1322 1794.7348 240.93491 -276.60265 531.28729 893.06522 188.20612 0 -667.29018 513778.24 -515000.11 1458.8151 26764.917 343.52984 1.2323667 - 460 9.6461852 1455.546 1796.4 241.15845 -340.85398 527.34366 846.65226 188.77031 0 -650.31889 513748.59 -515001.89 169.77154 26818.027 343.8413 1.2433195 - 480 10.037471 1423.2564 1780.6643 239.04601 -357.40797 555.56132 861.65053 179.25353 0 -642.23744 513684.59 -514996.23 1737.2169 26861.945 340.81112 1.2754844 - 500 10.442603 1414.4159 1792.7736 240.67163 -378.35771 562.25347 865.25285 172.51254 0 -638.36916 513656.76 -514996.77 2862.5086 26905.68 343.13664 1.264128 - 520 10.840656 1359.8057 1801.5592 241.85105 -441.75349 573.49082 804.76936 169.51784 0 -635.89324 513643.32 -514996.96 927.77773 26956.407 344.82065 1.2649106 - 540 11.24422 1319.969 1763.9685 236.80467 -443.9995 564.76203 851.23442 169.85422 0 -632.66442 513600.38 -514997.57 402.68456 26999.135 337.63034 1.2312338 - 560 11.656965 1288.5175 1741.1847 233.74605 -452.66718 589.0843 843.68941 164.33111 0 -639.59483 513593.61 -515003.78 2031.8562 27036.616 333.27376 1.1999696 - 580 12.050085 1250.4981 1701.8135 228.46065 -451.3154 576.17535 877.82925 152.94556 0 -632.24298 513574.54 -515000.56 328.36451 27076.846 325.70282 1.2583556 - 600 12.463133 1212.0751 1699.8202 228.19306 -487.74513 586.11242 850.6289 146.9891 0 -635.87543 513564.76 -515000.36 -593.07635 27114.131 325.34702 1.1966401 - 620 12.857609 1202.6969 1724.5891 231.51816 -521.8922 586.546 815.3615 149.33058 0 -627.92161 513553.83 -514999.04 -16.881985 27141.295 330.08328 1.2224592 - 640 13.267988 1180.7392 1717.1928 230.52525 -536.45363 595.45079 837.47314 150.14341 0 -635.92342 513512.84 -514996.44 1253.4658 27161.366 328.61164 1.3535393 - 660 13.661833 1146.6245 1693.9969 227.4113 -547.37231 603.66965 823.99031 147.75109 0 -616.07296 513489.44 -514996.15 -632.85642 27186.187 324.23124 1.1905446 - 680 14.057714 1112.6845 1649.8772 221.48844 -537.19275 594.76928 869.75332 148.3474 0 -610.67856 513459.02 -514998.41 -656.86895 27208.556 315.75904 1.2280206 - 700 14.46045 1080.853 1662.6225 223.19944 -581.76952 607.13692 800.72097 155.37025 0 -590.53466 513444.43 -514998.9 1478.4986 27230.38 318.17518 1.2929123 - 720 14.858115 1074.1453 1681.4035 225.7207 -607.2582 602.55649 804.73664 155.69335 0 -578.62035 513406.54 -514998.16 -312.12065 27255.88 321.76305 1.3178416 - 740 15.262165 1057.2173 1626.1913 218.30872 -568.97405 614.54113 851.40449 158.65878 0 -585.61227 513391.12 -514999.09 -252.45558 27276.192 311.20516 1.2592718 - 760 15.664885 1062.4809 1661.9166 223.10468 -599.4357 613.01783 805.30824 157.10102 0 -572.92999 513401.46 -515003.4 8.2424603 27294.015 318.05423 1.2582564 - 780 16.067218 1054.4338 1611.1036 216.28327 -556.66986 619.88711 869.25572 154.03862 0 -563.00792 513365.76 -515002.61 -325.5131 27313.202 308.30577 1.2766112 - 800 16.469454 1045.3661 1667.4808 223.85165 -622.11476 607.72536 819.84304 154.6324 0 -551.0017 513351.46 -515004.78 -711.73517 27333.225 319.1255 1.2459692 - 820 16.874566 1025.6074 1655.4437 222.23572 -629.83638 617.12876 822.09062 147.69173 0 -566.57998 513354.87 -515005.04 399.28085 27347.385 316.79906 1.2953686 - 840 17.272044 995.37917 1669.6204 224.13888 -674.24128 600.79611 821.7655 140.46192 0 -568.05887 513337.46 -515006.66 583.69527 27361.364 319.5132 1.2991152 - 860 17.673279 971.05977 1639.0518 220.03518 -667.99202 608.93496 824.23202 133.94234 0 -564.33929 513334.29 -515005.05 -413.73876 27378.37 313.69629 1.2004828 - 880 18.080302 944.37506 1628.7217 218.64842 -684.34669 617.46083 825.05882 135.40531 0 -569.6048 513312.82 -515005.49 512.87669 27389.533 311.69643 1.2448601 - 900 18.477336 949.5982 1677.4393 225.18853 -727.84115 624.49844 772.75351 136.94704 0 -549.4139 513292.05 -515004.67 271.20937 27400.579 321.05001 1.211493 - 920 18.873705 932.25995 1610.381 216.18626 -678.12109 623.29028 843.94403 144.55915 0 -557.17786 513270.07 -515002.81 1097.4299 27412.447 308.17027 1.2686712 - 940 19.284093 916.57919 1640.5258 220.23305 -723.94658 619.65583 814.76133 144.02609 0 -552.83588 513253.39 -515002.95 -342.60513 27424.209 313.98093 1.1943711 - 960 19.678839 941.9627 1630.8148 218.9294 -688.85213 647.73279 836.44195 147.48183 0 -533.27218 513217.4 -515004.64 -291.64501 27431.009 312.08648 1.2709839 - 980 20.091488 888.07492 1615.6407 216.89235 -727.56578 644.39061 818.66717 151.18945 0 -530.05167 513198.49 -515010.26 835.04931 27433.771 309.19916 1.2205907 - 1000 20.484026 903.45687 1626.7477 218.38341 -723.29085 660.33039 814.13089 154.52432 0 -517.32081 513174.16 -515009.12 -597.08083 27441.855 311.29984 1.2872278 - 1020 20.884939 884.61313 1628.0576 218.55926 -743.44446 659.18164 792.2445 148.42138 0 -501.95147 513167.72 -515009.06 -227.27612 27447.478 311.54441 1.3024911 - 1040 21.279846 852.14085 1593.0292 213.85686 -740.88834 648.79571 822.31823 141.59479 0 -492.90372 513148.22 -515008.91 1544.7468 27454.311 304.83469 1.2878493 - 1060 21.655111 848.20594 1615.8134 216.91553 -767.60742 629.3671 795.01871 137.79728 0 -487.7332 513167.91 -515009.96 818.90975 27467.219 309.21127 1.2684583 - 1080 22.037992 831.86637 1618.7361 217.30789 -786.86971 636.48473 828.1039 138.80398 0 -531.02117 513152.33 -515011.57 -796.09024 27482.281 309.76171 1.2933978 - 1100 22.412974 796.80267 1592.7483 213.81915 -795.94567 625.90981 798.78644 146.80857 0 -536.96836 513184.36 -515014.85 -84.200922 27491.353 304.78282 1.2860228 - 1120 22.801171 772.10069 1567.5834 210.44088 -795.48274 658.82509 788.14264 148.88807 0 -539.176 513162.6 -515014.76 867.66407 27496.215 299.95125 1.3027473 - 1140 23.17888 770.63813 1565.9379 210.21998 -795.2998 640.7064 799.36864 147.80124 0 -535.9357 513166.65 -515013.89 -1183.537 27499.574 299.64709 1.2856405 - 1160 23.563832 764.75496 1564.5598 210.03497 -799.80482 647.22053 811.27899 146.29888 0 -543.29534 513150.92 -515012.23 -1228.125 27500.914 299.39235 1.2526237 - 1180 23.941609 764.17598 1617.4255 217.13195 -853.24954 659.94837 768.65464 144.94873 0 -529.07191 513110.91 -515008.64 107.09246 27498.487 309.51287 1.287252 - 1200 24.317012 762.98696 1589.6792 213.40714 -826.69227 651.88091 816.19739 145.19502 0 -517.91574 513088.48 -515010.53 -1052.4085 27492.624 304.22381 1.2172354 - 1220 24.706198 764.88104 1566.9504 210.3559 -802.06936 679.17803 822.8538 134.80594 0 -509.18914 513076.83 -515006.55 694.03102 27483.433 299.85098 1.253554 - 1240 25.083107 767.93518 1615.6009 216.887 -847.66571 671.38696 801.01511 123.2586 0 -498.24308 513061.33 -515006.42 -367.46541 27476.952 309.13859 1.3441052 - 1260 25.461219 769.84629 1597.441 214.44912 -827.59471 670.93506 820.00134 122.64096 0 -489.27375 513053.94 -515005.84 -58.54717 27470.667 305.70834 1.2250043 - 1280 25.850924 761.02257 1637.0908 219.77192 -876.06819 685.99978 801.7347 121.99508 0 -498.90642 513022.12 -515009.01 667.72097 27460.84 313.30874 1.2269128 - 1300 26.230407 725.15653 1614.5991 216.75252 -889.44257 676.06266 795.73111 129.44616 0 -500.04123 513019.86 -515010.51 346.28961 27453.003 309.01166 1.1958813 - 1320 26.616651 690.04147 1555.4057 208.80608 -865.36428 674.77824 814.17441 138.30234 0 -503.84683 513024.03 -515012.8 -953.72011 27450.174 297.64076 1.2471902 - 1340 26.997168 731.37012 1629.8044 218.79375 -898.43423 672.50861 814.71248 139.58285 0 -509.67436 512995.22 -515010.78 -1831.2948 27443.855 311.896 1.2621742 - 1360 27.377617 745.65434 1610.5181 216.20467 -864.8638 691.11602 810.45797 140.60405 0 -508.77522 513011.95 -515010.21 -479.36536 27427.931 308.19958 1.2616878 - 1380 27.768431 746.41678 1674.6182 224.8098 -928.2014 661.11056 795.29365 134.53957 0 -512.17435 513003.03 -515010 726.71849 27412.674 320.49072 1.2545772 - 1400 28.151466 706.81871 1607.416 215.78822 -900.5973 709.47611 804.4224 129.7539 0 -509.52634 512973.57 -515008.29 -712.21584 27401.879 307.61219 1.2445794 - 1420 28.544365 667.95202 1582.3831 212.42766 -914.43103 664.88892 801.83372 136.47795 0 -514.32654 513008.75 -515012.06 -674.60825 27385.407 302.81863 1.2330197 - 1440 28.92417 662.21363 1572.2132 211.0624 -909.99957 695.6883 812.01519 141.73013 0 -511.80853 512960.55 -515008.18 -73.453766 27362.02 300.86905 1.233181 - 1460 29.303746 673.3058 1590.356 213.49799 -917.05016 660.8122 809.16185 137.34151 0 -506.78651 512991.4 -515008.98 487.20204 27337.657 304.34864 1.2293292 - 1480 29.683979 690.74904 1599.4915 214.72439 -908.74246 688.89665 819.23241 129.49598 0 -495.16925 512954.44 -515005.64 487.60757 27316.061 306.12959 1.159563 - 1500 30.073856 696.13426 1627.5685 218.49359 -931.4342 677.25983 808.26514 125.60011 0 -489.59764 512955.4 -515008.36 519.17541 27293.341 311.4741 1.2480919 - 1520 30.451939 716.4485 1613.3483 216.5846 -896.89978 696.36687 820.98027 134.70464 0 -469.43851 512929.25 -515008.76 544.98379 27271.903 308.73614 1.2765559 - 1540 30.839949 711.84578 1602.4823 215.1259 -890.63656 708.76314 793.80104 146.48285 0 -451.73842 512918.02 -515005.96 454.52189 27257.543 306.63893 1.3081885 - 1560 31.255883 702.95447 1604.1384 215.34821 -901.1839 701.09472 795.80519 150.09855 0 -450.00841 512908.1 -515006.27 -175.16964 27248.208 306.99599 1.217717 - 1580 31.634972 666.16399 1593.9574 213.98146 -927.79341 709.48317 798.22341 141.85062 0 -483.91855 512915.54 -515008.98 -174.37068 27241.403 305.02798 1.2549165 - 1600 32.013681 688.42678 1613.6536 216.62559 -925.22683 708.7011 810.24587 137.18807 0 -474.54073 512902.73 -515009.55 175.74764 27236.695 308.81599 1.2269417 - 1620 32.377997 686.38631 1599.6555 214.7464 -913.26914 723.55612 796.07516 144.8931 0 -474.73319 512907.37 -515010.43 33.582792 27234.316 306.09396 1.3145429 - 1640 32.739099 705.79223 1615.3667 216.85556 -909.57442 705.06325 806.35123 150.08668 0 -479.53397 512919.18 -515010.72 -276.47112 27230.877 309.12408 1.2740414 - 1660 33.111364 701.27726 1607.2688 215.76845 -905.99149 721.97907 787.92231 144.01692 0 -463.68107 512916.64 -515012.87 929.51954 27224.725 307.57382 1.2682264 - 1680 33.474256 700.51394 1604.7821 215.43463 -904.2682 712.18636 816.32021 135.23856 0 -471.34583 512915.88 -515012.55 169.46579 27223.825 307.07661 1.316103 - 1700 33.847599 653.51775 1574.3177 211.34492 -920.79992 708.22805 829.01689 135.77013 0 -456.72703 512872.35 -515009.44 -1331.9277 27225.869 301.24451 1.2944188 - 1720 34.210801 646.19978 1583.018 212.5129 -936.81823 721.83771 788.24431 140.19453 0 -469.87575 512893.23 -515010.45 722.29697 27224.305 302.91185 1.3016769 - 1740 34.57351 650.08331 1600.9298 214.91747 -950.84647 709.99119 789.79721 138.23225 0 -460.97413 512880.98 -515008.87 1102.6045 27225.414 306.34618 1.3045986 - 1760 34.947762 647.44786 1591.6127 213.6667 -944.16484 703.25888 831.27698 133.1631 0 -463.47718 512860.59 -515008.98 1152.8885 27230.97 304.56068 1.2966664 - 1780 35.311829 634.92036 1581.508 212.31019 -946.58767 707.7771 807.97758 140.70709 0 -473.2579 512882.95 -515012.74 229.64632 27235.632 302.63254 1.2770484 - 1800 35.686407 609.58199 1563.2412 209.85795 -953.65919 706.83652 811.29431 136.56443 0 -482.58705 512887.2 -515012.97 -1428.3239 27239.537 299.14762 1.235579 - 1820 36.050632 615.78755 1553.6653 208.57243 -937.87771 721.32849 827.06658 126.75248 0 -476.19143 512873.72 -515010.55 -1558.7353 27240.307 297.30295 1.2564383 - 1840 36.425851 595.24691 1623.2931 217.91965 -1028.0462 715.62813 759.44377 125.14223 0 -486.38933 512873.86 -515015.73 -393.40048 27233.914 310.63049 1.3037899 - 1860 36.791862 584.14833 1580.8506 212.22194 -996.70229 725.49209 786.41557 129.34385 0 -497.01606 512871.73 -515012.67 -445.7964 27227.234 302.53512 1.2082224 - 1880 37.159068 571.94192 1587.3128 213.08945 -1015.3709 727.21492 776.53831 128.97058 0 -472.95741 512835.25 -515010.39 -2430.0222 27217.82 303.74009 1.2871788 - 1900 37.534434 588.18296 1575.532 211.50794 -987.34908 735.18962 822.01431 121.27343 0 -474.15326 512820.83 -515012.5 -1004.9937 27200.966 301.48221 1.2875721 - 1920 37.899018 595.6429 1593.2862 213.89136 -997.64331 728.16052 813.67464 116.25522 0 -474.41478 512829.4 -515010.72 56.20061 27185.033 304.87735 1.3063391 - 1940 38.263855 552.10655 1586.7384 213.01234 -1034.6318 727.69915 794.08444 116.66262 0 -474.42985 512811.77 -515010.42 229.42949 27173.976 303.61874 1.3140118 - 1960 38.637106 571.50083 1614.8554 216.78693 -1043.3546 729.51741 761.23804 128.23909 0 -464.44507 512811.41 -515009.31 -496.32744 27162.867 309.02606 1.2732453 - 1980 38.999486 554.31018 1603.5237 215.26569 -1049.2135 738.87358 785.7371 126.13553 0 -468.044 512779.36 -515011.27 467.45037 27149.813 306.82565 1.3387674 - 2000 39.362048 570.16479 1585.0529 212.78608 -1014.8882 754.53304 813.00379 125.06015 0 -448.86583 512751.21 -515009.83 -257.98779 27141.691 303.29539 1.313977 -Loop time of 39.3621 on 4 procs for 2000 steps with 3000 atoms - -Pair time (%) = 15.1636 (38.5233) -Bond time (%) = 2.04281 (5.18978) -Kspce time (%) = 8.76608 (22.2704) -Neigh time (%) = 0.513343 (1.30415) -Comm time (%) = 1.60174 (4.06924) -Outpt time (%) = 0.00888807 (0.0225803) -Other time (%) = 11.2657 (28.6206) - -Nlocal: 750 ave 771 max 713 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 5881.75 ave 5954 max 5826 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 178004 ave 198102 max 168052 min -Histogram: 1 2 0 0 0 0 0 0 0 1 - -Total # of neighbors = 712018 -Ave neighs/atom = 237.339 -Ave special neighs/atom = 10.5 -Neighbor list builds = 50 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 b/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 deleted file mode 100644 index d8b8fb07f7..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.1 +++ /dev/null @@ -1,263 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_ATOM gATOMS temp -compute cTEMP all temp/drude - -fix fDTDIR all drude/transform/direct -fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 -fix_modify fNPT temp cTEMP_ATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349) -fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 1 100.0 -fix fDTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 50653 27000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 17.0416 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 1.485518 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565 - 40 2.9579411 9812.3728 6009.1747 806.70411 3803.1981 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0176 221.56359 - 60 4.3728549 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.61 23440.966 1050.9011 133.14424 - 80 5.817939 8115.7843 5997.9225 805.19356 2117.8618 901.84106 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.951 23834.833 1111.65 89.054921 - 100 7.207612 7496.2553 5770.3833 774.64747 1725.872 829.63908 1420.6659 325.4016 0 62.343574 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498472 - 120 8.656971 6986.593 5396.9479 724.51547 1589.6452 678.24993 1535.5197 325.88462 0 -9.6649617 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715636 - 140 10.075453 6549.0006 5126.6341 688.22709 1422.3665 724.95472 1477.7714 315.11964 0 -99.456486 513960.58 -514956.6 19747.307 24877.008 969.51239 30.977085 - 160 11.492728 6131.3317 5000.4421 671.2864 1130.8896 703.24858 1302.1192 314.93994 0 -258.4539 514042.29 -514973.25 23050.008 25142.654 948.73049 23.021806 - 180 12.899685 5749.9765 4700.9451 631.0803 1049.0314 674.94525 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.485 25400.048 893.75893 17.322076 - 200 14.301162 5429.601 4392.5738 589.68286 1037.0272 612.00108 1296.2432 303.16019 0 -300.38658 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486 - 220 15.696118 5133.8318 4290.7369 576.01173 843.09487 572.51989 1261.8055 289.99072 0 -383.71584 514078.3 -514975.81 12509.826 25814.229 817.78562 11.104636 - 240 17.080213 4850.3856 4120.3632 553.13985 730.0224 553.79224 1263.6533 278.92142 0 -487.76523 514091.35 -514969.93 10891.878 25996.167 785.87194 9.360776 - 260 18.465174 4583.9875 3911.0361 525.03865 672.95138 541.52251 1175.1552 273.43365 0 -475.23638 514139.68 -514981.61 8086.1512 26168.96 746.55574 7.4653786 - 280 19.852883 4349.224 3692.2792 495.67153 656.9448 598.81912 1148.0997 278.8781 0 -444.09603 514045.38 -514970.13 5124.6373 26323.056 705.04252 6.4783461 - 300 21.231065 4128.9017 3579.5067 480.53234 549.39506 584.06591 1089.5131 267.69425 0 -456.87099 514043.55 -514978.56 8350.7757 26456.831 683.9437 5.2650983 - 320 22.561911 3913.7712 3456.9151 464.07498 456.85609 556.31985 1103.3901 263.88855 0 -485.54294 514000.27 -514981.47 9117.6459 26592.844 660.74075 4.5694113 - 340 23.929412 3712.7166 3258.4133 437.42702 454.30336 533.72419 1069.0448 271.85689 0 -454.53939 514001.97 -514967.75 7187.6779 26736.819 622.98237 3.8812919 - 360 25.298241 3533.3834 3024.1004 405.9716 509.283 522.55431 1104.3208 276.30858 0 -456.06655 514036.53 -514974.36 4554.9866 26876.658 578.31181 3.3031408 - 380 26.653809 3367.1792 2971.2716 398.87957 395.9076 508.27241 1059.2248 257.85685 0 -499.68496 514032.55 -514962.31 5645.8914 27002.069 568.38695 2.8305175 - 400 27.984353 3204.91 2874.2403 385.85357 330.6697 543.88404 1018.8809 231.0702 0 -519.33317 514029.07 -514972.9 7250.7332 27123.905 549.89179 2.5832582 - 420 29.327209 3050.6948 2776.6044 372.74639 274.09045 517.42853 953.07587 226.06727 0 -505.60565 514057.02 -514973.9 4026.2599 27250.314 531.28066 2.3360848 - 440 30.659683 2916.2839 2640.2361 354.43958 276.04784 507.06292 983.97321 236.01275 0 -534.64355 514059.65 -514976.01 1708.709 27364.195 505.24974 2.0766005 - 460 31.992583 2787.525 2609.5902 350.32551 177.93474 485.64363 933.57925 234.95003 0 -560.61762 514069.83 -514985.45 3400.5279 27458.081 499.48923 1.8097259 - 480 33.31755 2662.4984 2514.178 337.51686 148.32032 464.67048 928.26208 239.37956 0 -570.38407 514070.86 -514984.47 5084.8141 27547.559 481.26944 1.6441427 - 500 34.613889 2540.5549 2433.5506 326.693 107.00428 473.2945 888.73268 239.40601 0 -565.68704 514057.33 -514986.07 3134.3501 27643.279 465.87942 1.4891047 - 520 35.938482 2432.2066 2375.3401 318.8785 56.866542 460.28751 838.60926 229.00792 0 -579.13212 514093.74 -514985.64 468.2133 27732.471 454.76753 1.3789356 - 540 37.265891 2328.8169 2275.0595 305.41629 53.757389 473.08203 875.54175 220.60944 0 -604.11384 514075.79 -514987.16 2632.7788 27804.408 435.55773 1.3457265 - 560 38.585909 2228.615 2278.3234 305.85446 -49.708475 455.58479 820.87878 215.10334 0 -604.72924 514052.45 -514989 3784.1482 27875.141 436.2741 1.1341618 - 580 39.864162 2134.4158 2127.9962 285.67372 6.4195621 480.68268 836.80009 219.13915 0 -563.30768 514019.28 -514986.18 1359.5813 27951.068 407.46382 1.1159366 - 600 41.132397 2048.4786 2102.9549 282.31205 -54.476369 486.301 796.4297 225.04029 0 -574.89865 514003.04 -514990.39 -91.415091 28017.963 402.69767 1.0358319 - 620 42.405012 1967.4398 2048.4364 274.99318 -80.996617 477.38045 786.20744 223.98682 0 -570.14553 513997.93 -514996.35 1828.8595 28070.312 392.2521 1.022392 - 640 43.643353 1888.1318 1981.566 266.01614 -93.434276 482.74658 801.17689 222.6863 0 -557.43781 513952.32 -514994.92 3812.5364 28123.574 379.47296 0.92888928 - 660 44.915581 1813.0614 1959.0105 262.98817 -145.94913 498.25019 750.64037 217.17325 0 -556.66234 513938.55 -514993.9 1151.2432 28187.531 375.17108 0.87739869 - 680 46.131009 1744.832 1911.6741 256.63347 -166.84215 497.042 725.1867 211.01897 0 -553.89849 513944.3 -514990.49 108.93436 28245.999 366.12859 0.80270448 - 700 47.378681 1678.1626 1915.3894 257.13223 -237.22675 490.51486 719.69339 202.0347 0 -569.53306 513909.13 -514989.07 2213.2126 28294.676 366.86703 0.7415387 - 720 48.690897 1612.159 1862.0857 249.97645 -249.92665 500.42275 728.44427 190.27551 0 -551.64449 513871.72 -514989.15 3052.5203 28347.921 356.64837 0.74199709 - 740 49.934569 1549.9154 1792.3586 240.61591 -242.44316 497.29161 738.6029 175.53735 0 -547.70029 513880.64 -514986.81 738.07583 28409.346 343.29748 0.7047584 - 760 51.094031 1493.142 1799.8956 241.62772 -306.75355 503.57846 709.28495 169.315 0 -559.17689 513862.16 -514991.92 -783.63021 28463.359 344.75885 0.66625263 - 780 52.252971 1437.0347 1824.9884 244.99631 -387.95371 510.42774 661.31982 170.22096 0 -556.6031 513818.26 -514991.58 1267.2418 28503.342 349.56302 0.68065177 - 800 53.379442 1382.5833 1736.7991 233.1573 -354.21576 514.27927 697.39594 172.11416 0 -554.93314 513805.74 -514988.82 1744.7887 28543.483 332.6636 0.66505935 - 820 54.535354 1332.0444 1690.9869 227.00722 -358.94246 509.37721 686.56084 172.95747 0 -552.9503 513815.42 -514990.31 -146.04973 28586.706 323.91193 0.59356881 - 840 55.662329 1285.5292 1685.7755 226.30763 -400.2463 507.19453 662.75433 170.55434 0 -559.51859 513807.26 -514988.49 -690.17907 28621.308 322.91069 0.59874377 - 860 56.818479 1239.7941 1704.701 228.84829 -464.90694 495.88426 658.89439 170.35 0 -574.82793 513772.87 -514988.08 747.19844 28645.708 326.53594 0.60530564 - 880 57.943864 1195.2063 1673.557 224.66734 -478.35068 498.99876 648.88199 170.51747 0 -557.50857 513743.81 -514983.05 1172.7738 28670.551 320.58027 0.57096305 - 900 59.0976 1153.211 1639.9315 220.15327 -486.72046 502.47627 643.51354 178.69816 0 -556.38628 513730.32 -514985.34 -511.45034 28697.8 314.13849 0.56088797 - 920 60.220959 1114.1597 1616.0109 216.94205 -501.85117 514.79499 630.19604 179.36393 0 -549.5453 513714.55 -514991.21 -1422.3991 28716.8 309.54311 0.58363424 - 940 61.375362 1076.2186 1627.0408 218.42275 -550.82218 512.57892 621.31041 171.65194 0 -553.00757 513686.04 -514989.39 298.61672 28723.941 311.6754 0.54200743 - 960 62.499341 1040.0389 1613.5611 216.61317 -573.52223 511.50602 601.98148 170.02159 0 -546.21393 513682.82 -514993.64 795.9161 28731.421 309.07527 0.57946382 - 980 63.655075 1005.556 1568.0264 210.50035 -562.47043 514.81982 629.32987 175.28567 0 -544.55487 513654.62 -514991.97 -1246.9263 28741.462 300.35589 0.55675479 - 1000 64.806202 973.43261 1565.2247 210.12423 -591.79208 505.29272 600.76239 165.17131 0 -554.93533 513685.36 -514993.44 -1299.5982 28742.028 299.81847 0.55749205 - 1020 65.904504 942.29451 1571.0425 210.90525 -628.74802 506.25414 614.54444 152.41332 0 -569.19989 513660.6 -514993.36 -197.56562 28733.474 300.93111 0.56370125 - 1040 67.002294 912.00673 1595.282 214.15928 -683.27525 489.63949 569.70488 159.39981 0 -590.61096 513680.38 -514991.79 467.80409 28724.916 305.58073 0.55701412 - 1060 68.131496 883.21094 1542.2424 207.03896 -659.03142 503.00762 589.40955 165.92561 0 -599.75208 513674.64 -514992.26 -2147.8302 28718.434 295.39729 0.59345978 - 1080 69.232333 856.19557 1533.4133 205.85369 -677.21769 507.87992 576.5184 168.18594 0 -578.48413 513634.34 -514985.66 -1762.0347 28699.147 293.70385 0.59551254 - 1100 70.364775 831.37376 1484.1452 199.23968 -652.77147 514.07523 608.66719 163.10107 0 -567.48676 513613.52 -514984.65 33.310994 28670.682 284.25195 0.61206838 - 1120 71.467535 808.52739 1521.0421 204.19292 -712.51473 513.69276 561.64386 163.23813 0 -559.45919 513591.61 -514983.24 -310.61111 28645.19 291.32265 0.61797603 - 1140 72.601129 786.87835 1489.4671 199.95412 -702.58878 523.98829 584.70722 162.29577 0 -549.08561 513559.92 -514984.41 -1685.4255 28620.437 285.26086 0.63846185 - 1160 73.705792 766.63847 1508.1762 202.46573 -741.53775 514.32182 584.88936 152.54558 0 -535.15913 513525.59 -514983.73 -1902.1776 28587.352 288.83351 0.67096701 - 1180 74.841457 749.02843 1510.9898 202.84344 -761.96133 536.04857 571.2202 147.21017 0 -519.34217 513485.23 -514982.33 867.83936 28547.617 289.35403 0.71492747 - 1200 75.948637 733.34578 1503.6833 201.86257 -770.33748 533.86604 589.40444 152.04389 0 -519.58392 513457.87 -514983.94 16.285861 28517.381 287.94489 0.73468233 - 1220 77.086539 718.25616 1498.0744 201.1096 -779.81819 559.89022 564.22113 156.14265 0 -507.10566 513432.51 -514985.47 -1279.2454 28491.203 286.86449 0.74672427 - 1240 78.196455 704.4456 1488.8421 199.87022 -784.3965 566.03391 579.8182 161.3278 0 -468.50406 513361.56 -514984.64 -54.414997 28461.145 285.0822 0.7757678 - 1260 79.336046 693.03071 1494.0932 200.57516 -801.06253 573.59408 573.29809 158.50778 0 -453.3769 513333.73 -514986.81 977.78497 28434.874 286.06644 0.82806578 - 1280 80.450187 683.34372 1478.8974 198.53519 -795.55372 580.51573 596.90975 153.51449 0 -437.44107 513297.84 -514986.89 809.72996 28418.785 283.14058 0.85789606 - 1300 81.562086 675.21003 1490.4096 200.08064 -815.19955 586.94949 575.877 144.63393 0 -412.94901 513274.99 -514984.7 -448.50658 28409.979 285.3107 0.94374006 - 1320 82.704837 668.21879 1489.4584 199.95295 -821.23962 576.22292 605.97557 140.59647 0 -423.93742 513262.85 -514982.94 -41.054413 28400.286 285.13719 0.9231239 - 1340 83.820401 662.582 1506.0415 202.17916 -843.45952 580.69502 578.24319 144.89986 0 -430.94868 513260.2 -514976.55 977.60126 28392.044 288.28069 1.0060194 - 1360 84.965785 658.24059 1527.9683 205.12273 -869.7277 577.91541 570.19843 152.39114 0 -451.12207 513259.47 -514978.58 371.63239 28390.774 292.47304 1.0318294 - 1380 86.080907 654.92452 1486.6437 199.57509 -831.71915 580.08964 585.152 157.63831 0 -437.00747 513263.59 -514981.18 -247.9673 28392.439 284.5256 1.0911219 - 1400 87.195704 652.93764 1510.6586 202.79899 -857.721 568.92903 573.37125 151.89337 0 -426.43036 513257.39 -514982.88 -51.617883 28392.618 289.11402 1.1268379 - 1420 88.34689 651.93794 1494.4977 200.62946 -842.55979 571.38046 600.63765 145.50987 0 -443.12588 513270.14 -514987.1 743.13616 28392.861 285.98783 1.1924311 - 1440 89.493044 651.84231 1520.3977 204.10641 -868.55537 569.30886 591.50444 144.87083 0 -452.53315 513268.23 -514989.93 461.56063 28397.854 290.94803 1.2038182 - 1460 90.608597 652.79726 1538.7134 206.56522 -885.91619 576.98896 569.0177 144.49629 0 -461.96923 513277.97 -514992.42 -706.12558 28404.942 294.4277 1.2773313 - 1480 91.757208 654.35279 1560.3813 209.47403 -906.02856 573.31257 551.02062 151.79154 0 -471.83285 513285.31 -514995.63 -636.13512 28406.735 298.57005 1.3040147 - 1500 92.886091 656.18474 1535.2238 206.09675 -879.03909 565.77757 581.30733 155.02848 0 -493.04533 513302.18 -514990.29 143.11549 28404.04 293.73748 1.3269254 - 1520 94.042872 658.68485 1540.4536 206.79882 -881.76871 562.4227 566.55678 153.51217 0 -481.25224 513306.12 -514989.13 320.11741 28402.365 294.71422 1.3871403 - 1540 95.163877 662.00561 1525.2953 204.7639 -863.28974 547.96338 591.50659 150.34534 0 -461.18073 513297.4 -514989.32 -131.34055 28402.834 291.79671 1.4143192 - 1560 96.312922 666.1124 1506.6675 202.2632 -840.55513 559.7266 593.99441 157.20165 0 -475.77029 513317.32 -514993.02 -361.762 28402.279 288.23662 1.3888658 - 1580 97.430754 670.56531 1535.7659 206.16953 -865.20063 562.32491 577.33497 164.90914 0 -495.18787 513321.56 -514996.14 281.32907 28399.686 293.815 1.3885206 - 1600 98.548553 676.03467 1559.0361 209.29344 -883.00142 570.63265 568.63747 171.76131 0 -497.53636 513299.62 -514996.12 -83.071675 28398.615 298.25471 1.4380743 - 1620 99.69614 681.61565 1551.6098 208.29649 -869.99417 572.80627 589.25676 175.66645 0 -486.29635 513275.79 -514997.22 -1208.1908 28396.28 296.81124 1.4843702 - 1640 100.81368 687.56466 1565.2232 210.12403 -877.65855 578.7743 586.81939 173.9181 0 -490.97778 513266.56 -514992.76 -587.86248 28386.365 299.44244 1.4342399 - 1660 101.96336 693.76095 1558.3222 209.1976 -864.56124 583.58497 605.24119 171.44101 0 -488.52963 513255.46 -514991.76 335.92415 28373.356 298.0981 1.4841753 - 1680 103.08285 699.76249 1608.1314 215.88426 -908.36892 585.35458 590.64567 171.79357 0 -478.93732 513211.41 -514988.64 91.212095 28363.527 307.67509 1.4177962 - 1700 104.23343 705.16423 1586.5697 212.9897 -881.40546 609.44211 582.01973 172.76356 0 -457.12517 513197.39 -514985.89 -662.76266 28354.912 303.56619 1.3605633 - 1720 105.38429 709.98606 1609.0843 216.01219 -899.09829 612.02708 597.82638 167.68834 0 -444.72348 513153.41 -514985.33 -92.038463 28343.124 307.84128 1.4562833 - 1740 106.50511 714.51622 1579.8945 212.09359 -865.37833 624.49924 619.60972 166.03466 0 -425.9731 513136.37 -514985.92 1173.1099 28332.574 302.27863 1.3790325 - 1760 107.65668 718.07347 1624.056 218.02206 -905.9825 608.96798 597.96224 154.72096 0 -409.37211 513132.37 -514990.63 786.32681 28330.712 310.74964 1.3669913 - 1780 108.77729 720.46707 1606.3817 215.64937 -885.91465 639.71765 615.06161 152.57928 0 -394.48439 513088.38 -514987.17 -271.86201 28334.236 307.3761 1.3327989 - 1800 109.92899 721.98649 1608.1038 215.88055 -886.11732 621.68949 602.68633 163.61329 0 -397.09967 513111.57 -514988.58 587.45646 28336.693 307.73281 1.2707867 - 1820 111.05093 722.92155 1567.2948 210.40212 -844.3732 657.9717 609.80843 174.58395 0 -387.74403 513087.19 -514986.18 1657.5204 28343.522 299.9292 1.2250789 - 1840 112.17289 723.61458 1561.6308 209.64177 -838.01626 621.38222 638.008 181.56394 0 -392.76804 513100.91 -514987.12 951.04423 28360.92 298.8574 1.192447 - 1860 113.32517 724.57888 1559.5079 209.35678 -834.92903 648.61916 621.88348 182.62731 0 -413.59874 513115.13 -514989.59 -474.05956 28382.975 298.4495 1.1946089 - 1880 114.44655 725.74322 1588.6378 213.26733 -862.89459 616.10137 598.6142 185.03327 0 -431.03949 513153.5 -514985.11 326.23753 28401.004 304.06324 1.1258592 - 1900 115.60092 726.63642 1552.6045 208.43002 -825.96805 615.20719 632.90186 175.31959 0 -439.29325 513177.07 -514987.17 1080.7061 28419.738 297.15171 1.1348451 - 1920 116.72882 727.57597 1579.3221 212.01674 -851.74611 606.50987 618.17792 169.75157 0 -442.63284 513179.83 -514983.38 -43.794187 28443.345 302.3028 1.0665772 - 1940 117.88137 728.52961 1573.1141 211.18335 -844.58454 624.72383 626.3057 166.98593 0 -453.41808 513175.12 -514984.3 -900.58801 28464.403 301.13166 1.0223996 - 1960 119.003 728.94698 1626.2629 218.31833 -897.31596 599.28223 602.89095 166.05528 0 -470.08979 513190.07 -514985.52 -260.33773 28477.732 311.33029 0.99933978 - 1980 120.15553 728.20483 1628.3695 218.60113 -900.16467 612.33461 601.10447 163.81406 0 -448.48915 513155.61 -514984.54 821.49207 28488.285 311.74795 0.96708127 - 2000 121.27853 726.32991 1617.7225 217.17182 -891.39259 608.69121 604.99032 169.22497 0 -445.16887 513154.27 -514983.4 -472.67394 28502.073 309.74198 0.88520672 -Loop time of 121.279 on 1 procs for 2000 steps with 3000 atoms - -Pair time (%) = 55.4018 (45.6815) -Bond time (%) = 7.86978 (6.48901) -Kspce time (%) = 13.9231 (11.4803) -Neigh time (%) = 2.17099 (1.79008) -Comm time (%) = 0.43024 (0.354754) -Outpt time (%) = 0.0126977 (0.0104699) -Other time (%) = 41.4699 (34.194) - -Nlocal: 3000 ave 3000 max 3000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 10468 ave 10468 max 10468 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 662422 ave 662422 max 662422 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 662422 -Ave neighs/atom = 220.807 -Ave special neighs/atom = 10.5 -Neighbor list builds = 63 -Dangerous builds = 0 diff --git a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 b/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 deleted file mode 100644 index 893c889b8b..0000000000 --- a/examples/USER/drude/ethanol/log.ethanol.nh.8Jul15.linux.4 +++ /dev/null @@ -1,263 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style hybrid/overlay lj/cut/coul/long 8.0 8.0 thole 2.600 8.0 -kspace_style pppm 1.0e-4 - -read_data data.ethanol - orthogonal box = (-14.0138 -14.0278 -14.0189) to (14.0169 14.0177 14.0857) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 3000 atoms - scanning bonds ... - 5 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 9 = max dihedrals/atom - reading bonds ... - 2750 bonds - reading angles ... - 3250 angles - reading dihedrals ... - 3000 dihedrals - 5 = max # of 1-2 neighbors - 6 = max # of 1-3 neighbors - 10 = max # of 1-4 neighbors - 11 = max # of special neighbors - - -pair_coeff 1 1 lj/cut/coul/long 0.065997 3.500000 # C3H C3H -pair_coeff 1 2 lj/cut/coul/long 0.065997 3.500000 # C3H CTO -pair_coeff 1 3 lj/cut/coul/long 0.044496 2.958040 # C3H H -pair_coeff 1 4 lj/cut/coul/long 0.105921 3.304542 # C3H OH -pair_coeff 1 5 lj/cut/coul/long 0.000000 0.000000 # C3H HO -pair_coeff 2 2 lj/cut/coul/long 0.065997 3.500000 # CTO CTO -pair_coeff 2 3 lj/cut/coul/long 0.044496 2.958040 # CTO H -pair_coeff 2 4 lj/cut/coul/long 0.105921 3.304542 # CTO OH -pair_coeff 2 5 lj/cut/coul/long 0.000000 0.000000 # CTO HO -pair_coeff 3 3 lj/cut/coul/long 0.029999 2.500000 # H H -pair_coeff 3 4 lj/cut/coul/long 0.071413 2.792848 # H OH -pair_coeff 3 5 lj/cut/coul/long 0.000000 0.000000 # H HO -pair_coeff 4 4 lj/cut/coul/long 0.169996 3.120000 # OH OH -pair_coeff 4 5 lj/cut/coul/long 0.000000 0.000000 # OH HO -pair_coeff 5 5 lj/cut/coul/long 0.000000 0.000000 # HO HO -pair_coeff * 6*8 lj/cut/coul/long 0.000000 0.000000 # No lj for drudes -pair_coeff 1 1 thole 2.051000 -pair_coeff 1 2 thole 1.580265 -pair_coeff 1 4 thole 1.416087 -pair_coeff 1 6 thole 2.051000 -pair_coeff 1 7 thole 1.580265 -pair_coeff 1 8 thole 1.416087 -pair_coeff 2 2 thole 1.217570 -pair_coeff 2 4 thole 1.091074 -pair_coeff 2 6 thole 1.580265 -pair_coeff 2 7 thole 1.217570 -pair_coeff 2 8 thole 1.091074 -pair_coeff 4 4 thole 0.977720 -pair_coeff 4 6 thole 1.416087 -pair_coeff 4 7 thole 1.091074 -pair_coeff 4 8 thole 0.977720 -pair_coeff 6 6 thole 2.051000 -pair_coeff 6 7 thole 1.580265 -pair_coeff 6 8 thole 1.416087 -pair_coeff 7 7 thole 1.217570 -pair_coeff 7 8 thole 1.091074 -pair_coeff 8 8 thole 0.977720 - -group gETHANOL molecule 1:250 -3000 atoms in group gETHANOL -group gATOMS type 1 2 3 4 5 -2250 atoms in group gATOMS -group gDRUDES type 6 7 8 -750 atoms in group gDRUDES - - -neighbor 2.0 bin - -variable vTEMP equal 300.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gATOMS create ${vTEMP} 12345 -velocity gATOMS create 300 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C N C N D D D - -fix fSHAKE gATOMS shake 0.0001 20 0 b 2 3 5 - 250 = # of size 2 clusters - 250 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -comm_modify vel yes -compute cTEMP_ATOM gATOMS temp -compute cTEMP all temp/drude - -fix fDTDIR all drude/transform/direct -fix fNPT gATOMS npt temp ${vTEMP} ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 ${vTEMP} 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso ${vPRESS} ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 ${vPRESS} 500 -fix fNPT gATOMS npt temp 300 300 100 iso 1 1 500 -fix_modify fNPT temp cTEMP_ATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1349) -fix fNVT gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 ${vTEMP_D} 100.0 -fix fNVT gDRUDES nvt temp 1 1 100.0 -fix fDTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 20 - -timestep 0.5 -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.379738 - grid = 30 30 30 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0289979 - estimated relative force accuracy = 8.73262e-05 - using double precision FFTs - 3d grid and FFT values/proc = 17908 7200 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 11 -New max number of 1-2 to 1-4 neighbors: 11 (+0) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 10 -Memory usage per processor = 13.7041 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume cTEMP[1] cTEMP[2] - 0 0 13868.828 2013.3852 270.28772 11855.443 3145.896 51.880809 0.00019113234 0 8481.5109 514734.14 -514557.98 170217.61 22094.109 381.62759 10.134301 - 20 0.48582006 11385.192 5995.2334 804.83256 5389.9589 2039.7325 2312.5375 131.6961 0 1710.3266 514098.34 -514902.67 75867.639 22408.275 975.26848 406.07565 - 40 0.99611902 9812.3727 6009.1747 806.70411 3803.198 1442.3489 1826.1439 275.19367 0 1288.2864 513934.98 -514963.76 48675.043 22980.115 1057.0177 221.56359 - 60 1.4878449 8857.9452 5779.5973 775.8844 3078.348 1190.8978 1938.6134 328.6837 0 619.31805 513970.98 -514970.15 39710.611 23440.966 1050.9011 133.14424 - 80 1.9926319 8115.7842 5997.9225 805.19356 2117.8617 901.84105 1587.5472 325.40763 0 288.34562 513957.43 -514942.71 37588.95 23834.833 1111.65 89.05492 - 100 2.476769 7496.2555 5770.3833 774.64747 1725.8722 829.63908 1420.6659 325.4016 0 62.343573 514051.62 -514963.79 27294.064 24225.918 1080.2687 60.498473 - 120 2.9719281 6986.5933 5396.9479 724.51547 1589.6454 678.24993 1535.5197 325.88462 0 -9.6649715 514027.05 -514967.4 21720.902 24578.195 1016.3014 42.715633 - 140 3.4472849 6549.0004 5126.6341 688.22709 1422.3663 724.95473 1477.7714 315.11964 0 -99.456489 513960.58 -514956.6 19747.305 24877.008 969.51239 30.977084 - 160 3.8980451 6131.3313 5000.4421 671.2864 1130.8892 703.24856 1302.1192 314.93994 0 -258.4539 514042.28 -514973.25 23050.008 25142.654 948.73049 23.021804 - 180 4.3219371 5749.9765 4700.9451 631.0803 1049.0314 674.94524 1301.4114 310.04938 0 -326.73679 514044.26 -514954.9 14225.484 25400.048 893.75892 17.322075 - 200 4.740237 5429.6012 4392.5738 589.68286 1037.0274 612.00109 1296.2432 303.16019 0 -300.38659 514093.7 -514967.69 10835.073 25622.866 836.16806 13.764486 - 220 5.15255 5133.8314 4290.7369 576.01173 843.09448 572.5199 1261.8055 289.99074 0 -383.71584 514078.3 -514975.81 12509.825 25814.229 817.78562 11.104636 - 240 5.5619049 4850.3859 4120.3634 553.13987 730.0225 553.79223 1263.6533 278.92141 0 -487.76524 514091.35 -514969.93 10891.878 25996.167 785.87197 9.3607763 - 260 5.9694359 4583.988 3911.0361 525.03865 672.95183 541.52258 1175.1553 273.43363 0 -475.23639 514139.68 -514981.61 8086.1508 26168.96 746.55574 7.4653781 - 280 6.3831999 4349.2238 3692.2792 495.67153 656.94461 598.81909 1148.0997 278.87809 0 -444.09603 514045.38 -514970.13 5124.6371 26323.056 705.04252 6.4783461 - 300 6.8002019 4128.9011 3579.5067 480.53234 549.39444 584.0659 1089.513 267.69426 0 -456.87099 514043.55 -514978.56 8350.7748 26456.831 683.94371 5.2650989 - 320 7.2020841 3913.7715 3456.9151 464.07498 456.85644 556.31985 1103.3901 263.8886 0 -485.54294 514000.27 -514981.47 9117.645 26592.844 660.74075 4.5694128 - 340 7.614501 3712.7165 3258.4132 437.42702 454.30329 533.72422 1069.0449 271.85681 0 -454.53938 514001.97 -514967.75 7187.6789 26736.819 622.98237 3.8812925 - 360 8.0251679 3533.3831 3024.1004 405.97159 509.28269 522.55432 1104.3208 276.30864 0 -456.06652 514036.53 -514974.36 4554.9866 26876.658 578.3118 3.3031414 - 380 8.4368989 3367.1791 2971.2717 398.87959 395.90735 508.27248 1059.2247 257.85692 0 -499.68504 514032.55 -514962.31 5645.8885 27002.069 568.38697 2.8305185 - 400 8.841274 3204.9102 2874.2407 385.85361 330.66952 543.884 1018.8809 231.07032 0 -519.33317 514029.07 -514972.9 7250.7314 27123.905 549.89185 2.58326 - 420 9.2528131 3050.6946 2776.6047 372.74643 274.08991 517.42853 953.07588 226.06762 0 -505.60561 514057.02 -514973.9 4026.258 27250.314 531.28072 2.3360857 - 440 9.6643951 2916.2842 2640.2367 354.43965 276.04748 507.06285 983.97334 236.01271 0 -534.64347 514059.65 -514976.01 1708.7076 27364.195 505.24986 2.0765971 - 460 10.070477 2787.525 2609.5902 350.3255 177.93484 485.64382 933.57906 234.95019 0 -560.61753 514069.83 -514985.45 3400.5283 27458.081 499.48921 1.8097272 - 480 10.475857 2662.4983 2514.1778 337.51682 148.3205 464.67048 928.2622 239.37954 0 -570.38391 514070.86 -514984.47 5084.8137 27547.559 481.26939 1.6441432 - 500 10.904204 2540.5544 2433.5504 326.69297 107.00399 473.29419 888.73276 239.40578 0 -565.68691 514057.33 -514986.07 3134.3575 27643.279 465.87938 1.4891037 - 520 11.343421 2432.2068 2375.3395 318.87842 56.867315 460.28707 838.60936 229.00812 0 -579.13202 514093.74 -514985.64 468.2212 27732.471 454.76741 1.3789343 - 540 11.792302 2328.8171 2275.0598 305.41633 53.757301 473.0817 875.54202 220.60952 0 -604.11383 514075.79 -514987.16 2632.7729 27804.408 435.55777 1.3457292 - 560 12.22888 2228.6146 2278.324 305.85454 -49.709377 455.5848 820.87873 215.10398 0 -604.72916 514052.45 -514989 3784.1433 27875.141 436.27421 1.1341637 - 580 12.654423 2134.4153 2127.9966 285.67378 6.418699 480.68271 836.79983 219.13997 0 -563.30761 514019.28 -514986.18 1359.5795 27951.068 407.46389 1.1159357 - 600 13.083667 2048.478 2102.9555 282.31212 -54.477504 486.30135 796.43014 225.04094 0 -574.89912 514003.04 -514990.39 -91.420338 28017.963 402.69778 1.0358317 - 620 13.5203 1967.44 2048.4369 274.99325 -80.99691 477.38009 786.20772 223.98767 0 -570.14552 513997.92 -514996.35 1828.852 28070.312 392.2522 1.022388 - 640 13.946543 1888.1309 1981.5653 266.01604 -93.434406 482.74621 801.17707 222.68721 0 -557.43764 513952.32 -514994.92 3812.5405 28123.574 379.47281 0.92888841 - 660 14.383896 1813.0614 1959.0076 262.98777 -145.94621 498.24936 750.64093 217.17501 0 -556.66175 513938.55 -514993.9 1151.2704 28187.531 375.17051 0.8773937 - 680 14.80455 1744.8321 1911.6727 256.63328 -166.84059 497.04089 725.18698 211.02114 0 -553.89822 513944.3 -514990.49 108.9445 28245.999 366.1283 0.80270876 - 700 15.246875 1678.1628 1915.389 257.13218 -237.22624 490.51443 719.69473 202.03683 0 -569.53274 513909.13 -514989.07 2213.2168 28294.676 366.86695 0.74153849 - 720 15.683303 1612.159 1862.0857 249.97646 -249.9267 500.42186 728.44302 190.2785 0 -551.64436 513871.73 -514989.15 3052.5153 28347.921 356.64838 0.74199104 - 740 16.103407 1549.912 1792.3564 240.61562 -242.44438 497.29156 738.60345 175.54129 0 -547.7015 513880.63 -514986.81 737.97658 28409.346 343.29706 0.70477013 - 760 16.533572 1493.1418 1799.8951 241.62766 -306.75333 503.57865 709.28516 169.31508 0 -559.17797 513862.16 -514991.92 -783.64904 28463.359 344.75876 0.66625709 - 780 16.963103 1437.0356 1824.9946 244.99715 -387.959 510.43018 661.31998 170.2197 0 -556.60498 513818.25 -514991.58 1267.2099 28503.341 349.56422 0.68065257 - 800 17.384911 1382.5837 1736.8044 233.15801 -354.22065 514.28158 697.39733 172.11237 0 -554.93413 513805.74 -514988.82 1744.7575 28543.482 332.66462 0.66506284 - 820 17.818295 1332.0449 1690.9863 227.00714 -358.94137 509.37962 686.56323 172.95557 0 -552.94994 513815.42 -514990.31 -146.04099 28586.704 323.91181 0.59356692 - 840 18.239769 1285.5293 1685.7656 226.30629 -400.23625 507.19659 662.75791 170.55111 0 -559.5183 513807.26 -514988.49 -690.12588 28621.306 322.90879 0.59871543 - 860 18.672279 1239.7943 1704.6913 228.84697 -464.89697 495.88249 658.89516 170.34465 0 -574.82534 513772.88 -514988.07 747.30519 28645.706 326.53407 0.60529545 - 880 19.094243 1195.2074 1673.5516 224.66662 -478.34417 498.99767 648.88222 170.51909 0 -557.50585 513743.81 -514983.05 1172.8191 28670.55 320.57923 0.57095732 - 900 19.530344 1153.213 1639.9317 220.1533 -486.71872 502.48114 643.51414 178.70544 0 -556.38218 513730.3 -514985.34 -511.40662 28697.799 314.13852 0.56091919 - 920 19.954644 1114.1622 1615.9735 216.93702 -501.81127 514.7973 630.19712 179.3982 0 -549.54237 513714.55 -514991.21 -1422.316 28716.8 309.53594 0.58362776 - 940 20.390261 1076.2212 1626.9734 218.41371 -550.75226 512.58732 621.31396 171.70796 0 -553.00677 513686.03 -514989.39 298.59388 28723.942 311.66248 0.54203006 - 960 20.813949 1040.0451 1613.5266 216.60854 -573.48149 511.51922 601.98585 170.02867 0 -546.21382 513682.83 -514993.63 795.90454 28731.424 309.06864 0.57947773 - 980 21.252467 1005.5683 1568.0671 210.50581 -562.49882 514.83412 629.32638 175.23649 0 -544.55558 513654.63 -514991.97 -1246.8402 28741.467 300.36369 0.55676445 - 1000 21.687328 973.43654 1565.2947 210.13362 -591.85814 505.31069 600.76156 165.13032 0 -554.93709 513685.33 -514993.45 -1299.6769 28742.033 299.8319 0.55747244 - 1020 22.104826 942.30585 1571.1252 210.91634 -628.81931 506.25625 614.52982 152.39206 0 -569.20109 513660.58 -514993.37 -197.40138 28733.481 300.94692 0.5637722 - 1040 22.524452 912.01118 1595.3373 214.16671 -683.32616 489.65166 569.71087 159.37841 0 -590.61264 513680.34 -514991.8 467.8096 28724.925 305.59134 0.55703469 - 1060 22.949422 883.20635 1542.2363 207.03814 -659.02996 503.02658 589.43979 165.92415 0 -599.75711 513674.6 -514992.27 -2148.0784 28718.444 295.39616 0.59339691 - 1080 23.371693 856.19688 1533.476 205.86212 -677.27914 507.92146 576.49892 168.14482 0 -578.48635 513634.3 -514985.66 -1762.3643 28699.157 293.71591 0.59543987 - 1100 23.796874 831.36718 1484.0494 199.22681 -652.68218 514.09435 608.64804 163.13622 0 -567.49464 513613.56 -514984.63 33.441222 28670.69 284.23352 0.61219688 - 1120 24.215957 808.52756 1520.8457 204.16656 -712.31817 513.70662 561.61909 163.36198 0 -559.46566 513591.68 -514983.22 -310.69178 28645.197 291.28494 0.61812087 - 1140 24.641242 786.87445 1489.3947 199.9444 -702.52028 523.97711 584.65081 162.32286 0 -549.07998 513560 -514984.39 -1685.574 28620.442 285.24697 0.63849523 - 1160 25.055568 766.64827 1508.2693 202.47822 -741.62101 514.35266 584.91055 152.45332 0 -535.165 513525.54 -514983.72 -1901.0493 28587.357 288.85135 0.67096559 - 1180 25.482658 749.02928 1511.1172 202.86054 -762.08788 536.05747 571.22043 147.19144 0 -519.37083 513485.14 -514982.32 866.88063 28547.627 289.37844 0.71496578 - 1200 25.894749 733.35099 1503.6268 201.85499 -770.27581 533.87098 589.37041 152.16808 0 -519.57804 513457.84 -514983.94 14.805399 28517.39 287.93411 0.73458768 - 1220 26.325628 718.27504 1498.0867 201.11126 -779.81165 559.91487 564.18647 156.27378 0 -507.13199 513432.42 -514985.48 -1279.1075 28491.202 286.86673 0.74700594 - 1240 26.738918 704.4507 1488.7649 199.85985 -784.31417 566.05166 579.79847 161.35046 0 -468.44357 513361.55 -514984.62 -53.3159 28461.135 285.06732 0.77592838 - 1260 27.171522 693.03769 1494.1149 200.57807 -801.07721 573.62194 573.3094 158.43371 0 -453.27917 513333.62 -514986.78 977.9179 28434.863 286.07064 0.82794452 - 1280 27.586875 683.35215 1479.0049 198.54962 -795.65277 580.54264 596.95031 153.53994 0 -437.44286 513297.62 -514986.86 808.24663 28418.774 283.16101 0.85830865 - 1300 28.005456 675.21985 1490.3973 200.079 -815.1775 586.97926 575.85031 144.74048 0 -412.9591 513274.88 -514984.67 -448.16581 28409.96 285.30833 0.9437975 - 1320 28.436763 668.22782 1489.1302 199.90889 -820.90236 576.19343 605.89694 140.779 0 -423.95547 513263.1 -514982.91 -40.766531 28400.261 285.0744 0.92283057 - 1340 28.854671 662.60827 1506.0283 202.17738 -843.42002 580.70797 578.1842 144.8341 0 -430.96333 513260.37 -514976.56 977.60336 28392.015 288.27815 1.0060347 - 1360 29.284718 658.23752 1527.6526 205.08035 -869.41511 577.91716 570.16602 152.14574 0 -451.11548 513260.04 -514978.56 374.82603 28390.744 292.41271 1.031412 - 1380 29.707547 654.96847 1486.4979 199.55551 -831.52939 580.08595 585.05597 157.33942 0 -437.07207 513264.24 -514981.18 -245.84993 28392.431 284.49746 1.0915693 - 1400 30.132399 652.9829 1510.7519 202.81151 -857.76902 568.8718 573.40304 151.53282 0 -426.40132 513257.71 -514982.89 -48.059208 28392.645 289.13172 1.1272637 - 1420 30.56509 652.00089 1494.6519 200.65015 -842.65097 571.38637 600.46686 145.25854 0 -443.09809 513270.44 -514987.1 744.84418 28392.941 286.01743 1.1922923 - 1440 30.993519 651.93656 1520.3356 204.09807 -868.39904 569.20772 591.53184 144.73613 0 -452.45231 513268.58 -514990 462.47894 28397.996 290.93612 1.2038241 - 1460 31.413554 652.8797 1538.7905 206.57555 -885.91076 576.968 569.3361 144.29397 0 -461.95958 513278 -514992.55 -703.88926 28405.143 294.44272 1.2767432 - 1480 31.854234 654.43984 1560.998 209.55681 -906.55813 573.32119 550.83703 151.55603 0 -471.87704 513285.3 -514995.69 -634.5939 28407.003 298.6883 1.3039308 - 1500 32.258767 656.25668 1535.2085 206.0947 -878.95186 565.7821 581.34544 155.11099 0 -493.26681 513302.34 -514990.27 141.09795 28404.376 293.73526 1.3252685 - 1520 32.667376 658.76245 1540.1255 206.75478 -881.36305 562.28162 566.2439 153.62339 0 -481.21787 513306.74 -514989.04 320.45957 28402.754 294.65144 1.3869014 - 1540 33.067487 662.13708 1524.8473 204.70375 -862.71024 547.98628 591.76817 150.15973 0 -460.97843 513297.6 -514989.25 -130.86158 28403.27 291.71099 1.413931 - 1560 33.480413 666.19858 1506.8716 202.29059 -840.67298 559.57219 594.04584 156.75269 0 -475.69342 513317.61 -514992.96 -357.4244 28402.761 288.27566 1.3890257 - 1580 33.881172 670.71346 1535.3958 206.11984 -864.68236 562.04024 577.64202 164.82634 0 -495.24757 513322.21 -514996.15 278.58466 28400.233 293.74325 1.3903967 - 1600 34.282713 676.13061 1559.338 209.33397 -883.20743 570.25038 568.59163 172.20015 0 -497.5923 513299.59 -514996.24 -86.394917 28399.201 298.31271 1.4378209 - 1620 34.693053 681.80099 1552.6868 208.44108 -870.88582 572.69475 589.3952 176.11924 0 -485.89655 513274.18 -514997.38 -1204.2981 28396.883 297.01677 1.4865321 - 1640 35.094327 687.72244 1565.9114 210.21642 -878.189 578.48421 587.25138 174.28163 0 -490.691 513265.29 -514992.8 -581.44816 28387.006 299.57429 1.4344443 - 1660 35.50466 693.90688 1558.2867 209.19283 -864.37979 583.51938 605.39763 171.58103 0 -488.26355 513255.15 -514991.76 341.26177 28374.079 298.09208 1.4823162 - 1680 35.905614 699.81947 1608.5571 215.9414 -908.73759 585.45342 590.42357 171.65094 0 -478.75081 513211.28 -514988.8 77.131096 28364.346 307.75695 1.4172031 - 1700 36.320681 705.27021 1587.164 213.06948 -881.89376 609.44479 581.8672 172.3033 0 -457.17018 513197.71 -514986.05 -666.39751 28355.734 303.6806 1.3594258 - 1720 36.728727 710.00906 1608.1379 215.88513 -898.12885 612.49125 598.01777 167.03198 0 -445.09105 513154.85 -514985.42 -87.720392 28343.913 307.66062 1.454487 - 1740 37.130271 714.53567 1580.0753 212.11786 -865.53967 624.57295 619.34825 165.15138 0 -426.77348 513138.14 -514985.98 1176.8164 28333.357 302.31339 1.3787996 - 1760 37.542675 718.03805 1624.8218 218.12487 -906.78379 608.77029 596.31671 153.7484 0 -409.62158 513134.59 -514990.59 800.3654 28331.535 310.89569 1.3688034 - 1780 37.943518 720.37511 1609.0275 216.00455 -888.65236 640.15257 613.63079 151.83793 0 -394.53333 513087.34 -514987.08 -257.84624 28335.192 307.88341 1.3325434 - 1800 38.353172 721.7956 1606.901 215.71908 -885.1054 621.86791 602.54827 163.37359 0 -396.5738 513111.86 -514988.19 600.83028 28337.874 307.50221 1.2708112 - 1820 38.755103 722.6791 1563.6639 209.9147 -840.98481 658.28036 609.55302 175.97253 0 -386.62661 513087.76 -514985.92 1673.6509 28345.014 299.23272 1.2261086 - 1840 39.156883 723.36526 1560.0643 209.43147 -836.69905 621.56238 639.2919 183.25684 0 -391.12333 513097.3 -514986.98 948.98786 28362.795 298.55837 1.1894608 - 1860 39.568864 724.34062 1560.3485 209.46963 -836.00792 648.95076 621.00344 183.45409 0 -412.61997 513112.89 -514989.69 -494.41519 28385.176 298.60946 1.1973936 - 1880 39.96934 725.55016 1589.2514 213.34971 -863.70126 617.1181 598.13412 185.78351 0 -430.81566 513151.32 -514985.25 301.61577 28403.364 304.1812 1.1250834 - 1900 40.379241 726.4494 1555.4145 208.80726 -828.96513 616.25066 631.90687 175.77829 0 -439.44651 513173.5 -514986.96 1079.4893 28422.072 297.69125 1.1328664 - 1920 40.778163 727.328 1577.4105 211.76012 -850.08251 606.30559 616.55697 170.46944 0 -442.17245 513181.84 -514983.08 4.4471417 28445.679 301.93699 1.065083 - 1940 41.186491 728.19228 1574.1105 211.3171 -845.91818 625.03022 624.89302 167.86917 0 -451.74938 513172.29 -514984.25 -891.08022 28467.03 301.3211 1.026012 - 1960 41.58233 728.61768 1624.4163 218.07043 -895.79862 599.93561 599.92993 167.38843 0 -465.99755 513188.14 -514985.2 -216.32489 28480.762 310.97645 0.99894847 - 1980 41.996931 727.92162 1627.8345 218.52931 -899.91293 612.92861 601.82319 165.16403 0 -447.59836 513151.59 -514983.82 865.41931 28491.981 311.64212 0.97473559 - 2000 42.398021 726.10625 1615.3704 216.85607 -889.26418 609.59944 604.55036 169.50136 0 -443.24252 513152.61 -514982.28 -436.06261 28506.736 309.2898 0.88821892 -Loop time of 42.3981 on 4 procs for 2000 steps with 3000 atoms - -Pair time (%) = 14.495 (34.1878) -Bond time (%) = 2.06082 (4.86065) -Kspce time (%) = 7.76109 (18.3053) -Neigh time (%) = 0.634993 (1.49769) -Comm time (%) = 1.07386 (2.53281) -Outpt time (%) = 0.0100121 (0.0236145) -Other time (%) = 16.3623 (38.5921) - -Nlocal: 750 ave 774 max 711 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 5796.5 ave 5864 max 5731 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 165579 ave 169096 max 157793 min -Histogram: 1 0 0 0 0 0 0 0 1 2 - -Total # of neighbors = 662315 -Ave neighs/atom = 220.772 -Ave special neighs/atom = 10.5 -Neighbor list builds = 63 -Dangerous builds = 0 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 new file mode 100644 index 0000000000..f68de51a79 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.1 @@ -0,0 +1,246 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +comm_modify vel yes +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes +fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix NVE DRUDES nve + +compute TEMP all temp/drude + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Per MPI rank memory allocation (min/avg/max) = 36.15 | 36.15 | 36.15 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 1.2941742 2882.4586 4527.8074 -1645.3488 561.72856 0 600.34616 155114.77 -157922.19 27167.701 14058.741 1013.3326 1438.6699 160.63128 + 40 2.6812835 1331.3822 3348.9313 -2017.5492 681.52311 0 553.09465 154668.62 -157920.79 17925.928 14484.215 749.4977 1105.2032 36.587791 + 60 4.0337768 297.35951 2604.4137 -2307.0542 583.99973 0 409.03992 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335647 + 80 5.3483341 -374.31059 2263.3247 -2637.6353 534.80336 0 212.27979 154543.18 -157927.9 6155.9233 15645.855 506.53672 755.45209 7.6929097 + 100 6.6217718 -905.58895 1911.7191 -2817.308 532.30402 0 87.570164 154497.48 -157934.66 2149.3102 16288.797 427.84665 639.27768 4.1289095 + 120 7.8588221 -1233.6892 1675.0884 -2908.7776 544.76423 0 59.500422 154422.72 -157935.76 233.49801 16915.818 374.88821 560.54178 2.8313109 + 140 8.9570706 -1463.4914 1468.7447 -2932.2361 539.69696 0 41.083518 154424.91 -157937.93 -1492.9875 17509.345 328.70809 491.66367 2.1395091 + 160 10.032995 -1695.7544 1385.9606 -3081.7149 552.9156 0 30.022825 154274.72 -157939.37 -3010.5044 18061.925 310.18082 463.9681 1.9858861 + 180 11.181687 -1818.1852 1253.1677 -3071.3529 559.57415 0 20.017285 154289.69 -157940.63 -3354.2207 18564.877 280.4615 419.5755 1.6725842 + 200 12.212811 -1949.6488 1210.0648 -3159.7136 570.0554 0 16.320167 154195.04 -157941.13 -4117.951 19014.456 270.81499 405.06855 1.7662371 + 220 13.224296 -2031.6068 1148.1459 -3179.7527 598.02848 0 30.832907 154127.13 -157935.75 -4514.6121 19406.767 256.95741 384.33718 1.6839577 + 240 14.315843 -2118.6272 1120.0031 -3238.6303 613.29235 0 59.889003 154030.6 -157942.41 -4415.1885 19738.97 250.659 374.93927 1.5971322 + 260 15.300218 -2203.4151 1065.8468 -3269.2619 614.19212 0 77.618884 153980.71 -157941.79 -4563.8872 20011.077 238.53871 356.80712 1.5248251 + 280 16.273073 -2317.9388 1033.2702 -3351.2091 650.51355 0 126.14935 153811.62 -157939.49 -4722.8063 20224.149 231.248 345.84878 1.5839508 + 300 17.240341 -2377.6039 992.48386 -3370.0878 688.02302 0 179.7828 153701.2 -157939.1 -4125.8573 20378.438 222.11992 332.08746 1.7406198 + 320 18.20275 -2419.6151 1023.0261 -3442.6412 720.31006 0 227.7006 153549.39 -157940.04 -4083.286 20479.24 228.95535 342.33558 1.7369708 + 340 19.161978 -2456.7614 1048.823 -3505.5844 754.12989 0 264.46876 153415.73 -157939.91 -3894.4573 20529.72 234.72874 351.04481 1.6271431 + 360 20.2149 -2504.7183 1041.9917 -3546.71 785.42914 0 335.38633 153271.5 -157939.03 -3464.0342 20531.324 233.19988 348.66948 1.7942822 + 380 21.17402 -2596.3611 1000.1227 -3596.4839 825.3161 0 390.15783 153129.43 -157941.39 -3357.8641 20490.649 223.82952 334.61582 1.8092697 + 400 22.139238 -2666.6886 1006.4834 -3673.172 866.01231 0 422.49717 152978.53 -157940.22 -3329.7321 20411.001 225.25305 336.79329 1.7220591 + 420 23.107117 -2676.0182 1036.9614 -3712.9796 909.17035 0 490.73558 152826 -157938.88 -2909.4385 20294.307 232.07409 346.93054 1.8970578 + 440 24.079176 -2731.6451 1054.3541 -3785.9992 935.99044 0 530.99271 152684.71 -157937.69 -2566.5271 20147.069 235.96661 352.81301 1.8018782 + 460 25.058476 -2808.7306 996.20963 -3804.9403 986.66566 0 582.2501 152565.84 -157939.7 -2490.6211 19973.642 222.95376 333.32458 1.7662208 + 480 26.045001 -2862.5602 1012.8284 -3875.3886 1005.2147 0 610.1273 152450.46 -157941.19 -2032.2463 19777.578 226.67307 338.84478 1.876307 + 500 27.043275 -2935.1165 989.42859 -3924.5451 1019.8833 0 633.91479 152362.53 -157940.87 -2210.2423 19561.788 221.43615 331.0551 1.7553824 + 520 28.052607 -2989.5984 969.48801 -3959.0864 1057.825 0 655.88112 152268.64 -157941.44 -2303.725 19328.454 216.97341 324.39473 1.6968168 + 540 29.169729 -3036.3745 1016.2059 -4052.5804 1091.3747 0 658.52433 152140.18 -157942.65 -2235.4034 19080.73 227.42896 340.04854 1.7349328 + 560 30.202366 -3093.8922 946.57093 -4040.4631 1140.9835 0 764.01213 151997.25 -157942.71 -1159.9486 18819.788 211.84452 316.62558 1.85871 + 580 31.245469 -3165.5156 988.32907 -4153.8446 1198.6661 0 795.79314 151795.81 -157944.12 -1299.7687 18555.467 221.19007 330.67963 1.7685771 + 600 32.305233 -3193.4945 981.48315 -4174.9776 1207.1636 0 842.25251 151717.63 -157942.02 -845.49527 18290.083 219.65794 328.37122 1.7920774 + 620 33.378728 -3254.0556 966.92094 -4220.9766 1219.0239 0 848.81235 151653.93 -157942.75 -633.10425 18027.72 216.39889 323.4395 1.8848743 + 640 34.465769 -3267.9659 1003.5996 -4271.5655 1273.644 0 929.19275 151468.58 -157942.99 146.55456 17770.457 224.60765 335.70351 1.9667214 + 660 35.565967 -3292.3649 1001.1012 -4293.4661 1299.7838 0 957.48532 151393.06 -157943.79 252.79622 17523.772 224.0485 334.86273 1.9719336 + 680 36.678817 -3311.7859 1008.4763 -4320.2622 1356.4829 0 987.54908 151279.12 -157943.41 715.95691 17290.15 225.69907 337.35795 1.9299071 + 700 37.804361 -3384.7539 970.95734 -4355.7113 1376.9176 0 1003.218 151209.28 -157945.12 602.03837 17070.444 217.30224 324.76399 1.9441468 + 720 38.944631 -3389.983 1003.4282 -4393.4112 1388.0708 0 1009.042 151153.78 -157944.31 799.15462 16864.409 224.5693 335.74485 1.7690575 + 740 40.095444 -3390.8892 1011.8969 -4402.786 1395.7801 0 1060.0508 151084.65 -157943.27 1475.2637 16672.377 226.4646 338.45322 2.034426 + 760 41.257411 -3430.7027 1037.7609 -4468.4636 1415.8714 0 1069.0374 150989.87 -157943.24 1304.5866 16496.661 232.25301 347.18143 1.9316673 + 780 42.432308 -3457.167 1031.0329 -4488.1999 1428.7433 0 1114.4772 150912.91 -157944.33 1885.5157 16338.236 230.74728 344.90463 1.9710957 + 800 43.614638 -3510.8663 985.5619 -4496.4282 1454.853 0 1136.1159 150858.74 -157946.14 1646.2494 16199.542 220.57078 329.56096 2.1492639 + 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-3765.0247 879.73583 -4644.7606 1542.4842 0 1151.7551 150607.39 -157946.39 1704.8479 15589.06 196.88668 294.16244 1.9413966 + 980 54.463265 -3768.795 907.84469 -4676.6397 1541.4855 0 1133.986 150593.62 -157945.73 1307.1066 15561.731 203.1775 303.56604 1.9940794 + 1000 55.701727 -3785.8075 880.81809 -4666.6256 1521.7209 0 1096.2695 150662.35 -157946.97 970.21043 15543.592 197.1289 294.56486 1.8627129 + 1020 56.889708 -3802.4725 921.96298 -4724.4355 1530.0248 0 1066.8927 150623.76 -157945.11 4.0693062 15531.676 206.33721 308.27171 2.0555342 + 1040 58.073551 -3805.5983 892.97259 -4698.5709 1517.1505 0 1090.904 150638.66 -157945.28 814.78747 15522.075 199.8491 298.65131 1.8449766 + 1060 59.268992 -3814.9754 904.37152 -4719.3469 1516.0462 0 1073.1076 150635.42 -157943.93 352.09813 15517.26 202.4002 302.40986 1.9760806 + 1080 60.368197 -3799.7772 900.93602 -4700.7132 1525.3102 0 1076.0639 150645.06 -157947.15 399.96911 15516.854 201.63133 301.25571 1.9793146 + 1100 61.57456 -3802.9637 891.80847 -4694.7721 1493.3846 0 1048.571 150708.35 -157945.08 296.41566 15520.259 199.58857 298.21614 1.9342423 + 1120 62.780309 -3783.7153 915.24553 -4698.9609 1504.5486 0 1057.5171 150684.14 -157945.17 489.89871 15526.377 204.83383 306.05465 1.9825112 + 1140 63.986179 -3799.4039 915.28328 -4714.6872 1498.182 0 1037.3595 150696.49 -157946.72 -57.392244 15535.825 204.84228 306.06136 1.9944283 + 1160 65.193113 -3821.1813 889.41687 -4710.5981 1485.5696 0 1035.222 150714.63 -157946.02 -132.88199 15546.599 199.05332 297.34747 2.0669157 + 1180 66.295017 -3815.3668 883.81796 -4699.1847 1475.1971 0 1029.0735 150742.62 -157946.07 -12.015088 15557.826 197.80027 295.60821 1.7888039 + 1200 67.501339 -3799.2243 924.83203 -4724.0563 1503.6728 0 1039.8081 150676.17 -157943.71 -279.42673 15568.706 206.97931 309.25452 2.0149166 + 1220 68.70749 -3793.2571 918.16669 -4711.4238 1500.7028 0 1072.1543 150660.33 -157944.61 396.95956 15579.039 205.48759 307.10011 1.8515828 + 1240 69.913097 -3807.1761 903.62796 -4710.804 1518.0566 0 1098.727 150617.61 -157945.19 571.77344 15592.05 202.23379 302.09539 2.1061249 + 1260 71.120192 -3813.0785 928.88909 -4741.9676 1522.8082 0 1080.2068 150602.14 -157947.12 143.45803 15608.285 207.88729 310.67334 1.8994019 + 1280 72.221799 -3825.0477 896.43989 -4721.4876 1498.3409 0 1057.1098 150667.73 -157944.67 -469.23041 15626.738 200.62509 299.78768 1.8986521 + 1300 73.424948 -3846.2307 907.67631 -4753.907 1477.8354 0 1013.4733 150700.69 -157945.9 -661.19665 15644.394 203.13982 303.56549 1.8822105 + 1320 74.627469 -3829.941 882.93628 -4712.8773 1476.7417 0 1016.2042 150741.02 -157946.85 -14.196904 15658.043 197.60295 295.24326 1.9271172 + 1340 75.833837 -3851.5034 857.32804 -4708.8314 1465.5881 0 1021.2072 150749.47 -157945.1 -96.242387 15669.364 191.87178 286.7037 1.8241831 + 1360 76.936204 -3860.3024 888.18647 -4748.4888 1464.1796 0 984.93111 150747.8 -157945.4 -974.33424 15678.357 198.77795 297.0089 1.9185093 + 1380 78.140865 -3836.5819 880.98802 -4717.5699 1461.9764 0 985.01748 150781.29 -157945.85 -872.9259 15682.263 197.16693 294.58145 1.9435476 + 1400 79.344863 -3828.5386 906.27947 -4734.8181 1482.8705 0 991.46422 150736.59 -157945.74 -1233.9461 15680.599 202.82721 303.0834 1.909166 + 1420 80.548134 -3814.3258 902.48807 -4716.8139 1475.6502 0 1014.0056 150738.18 -157944.65 -555.01708 15672.591 201.97868 301.83062 1.8708541 + 1440 81.755274 -3856.0851 862.48793 -4718.573 1498.2382 0 1065.2356 150663.3 -157945.35 32.56482 15661.106 193.02657 288.38598 1.9216938 + 1460 82.860741 -3844.5162 901.31045 -4745.8266 1509.4529 0 1079.4605 150610.73 -157945.47 187.59843 15650.274 201.71513 301.41292 1.9161214 + 1480 84.068614 -3830.9341 924.4504 -4755.3845 1492.3743 0 1043.7244 150654.84 -157946.33 -493.49005 15640.167 206.8939 309.17217 1.9235617 + 1500 85.277247 -3837.3277 905.31407 -4742.6418 1493.7224 0 1030.5512 150679.62 -157946.53 -614.09435 15628.452 202.61115 302.74791 1.9324006 + 1520 86.48688 -3826.0085 909.05297 -4735.0615 1484.1418 0 1034.4558 150691.85 -157945.51 -146.17552 15614.976 203.44792 304.03751 1.8618391 + 1540 87.592599 -3841.6696 938.60068 -4780.2703 1507.974 0 1041.0705 150616.87 -157946.18 -507.85898 15599.499 210.06076 313.85613 2.0498944 + 1560 88.805017 -3826.9957 909.65333 -4736.649 1544.8227 0 1126.866 150538.2 -157946.54 606.26354 15581.816 203.58228 304.19548 1.9487298 + 1580 90.020651 -3832.1768 912.93266 -4745.1095 1574.5895 0 1176.6062 150449.01 -157945.31 1282.9622 15569.746 204.3162 305.24469 2.0505914 + 1600 91.237675 -3854.9438 913.45738 -4768.4012 1573.5937 0 1137.9072 150465.94 -157945.85 833.4472 15566.901 204.43364 305.43089 2.0302658 + 1620 92.456385 -3858.2579 926.48289 -4784.7408 1547.7966 0 1104.6836 150506.72 -157943.94 175.66142 15569.538 207.34877 309.84283 1.9459647 + 1640 93.67173 -3891.1815 918.17278 -4809.3543 1552.442 0 1100.5019 150484.4 -157946.7 -21.914006 15574.644 205.48895 307.0691 1.9176872 + 1660 94.887992 -3919.3626 865.63387 -4784.9964 1520.4861 0 1071.2498 150569.18 -157945.91 76.169452 15580.674 193.73064 289.45503 1.8943961 + 1680 96.104407 -3895.1048 904.57852 -4799.6834 1528.5992 0 1025.321 150591.92 -157945.52 -806.96969 15586.13 202.44653 302.49383 1.9470391 + 1700 97.217725 -3867.858 892.51088 -4760.3689 1529.7738 0 1070.8486 150584.86 -157945.86 140.65618 15587.548 199.74577 298.38679 2.0642365 + 1720 98.434344 -3893.3744 901.29331 -4794.6677 1574.0498 0 1116.4639 150460.62 -157945.8 58.347282 15588.502 201.71129 301.37785 1.974756 + 1740 99.650283 -3863.7002 920.58199 -4784.2822 1591.6512 0 1158.7562 150411.66 -157946.35 690.62331 15590.533 206.02814 307.90557 1.8612258 + 1760 100.86726 -3861.1571 936.31333 -4797.4705 1577.1868 0 1147.145 150425.93 -157947.74 479.33327 15596.819 209.54885 313.12745 1.9725316 + 1780 102.08407 -3902.9055 937.9542 -4840.8597 1574.1479 0 1089.8436 150439.21 -157944.06 -423.26154 15606.503 209.91608 313.72161 1.8851726 + 1800 103.30044 -3924.3367 882.83761 -4807.1743 1548.9296 0 1083.4742 150506.67 -157946.25 -165.30212 15613.782 197.58087 295.18333 1.9807824 + 1820 104.51493 -3933.257 906.13467 -4839.3917 1566.2208 0 1066.4802 150474.1 -157946.19 -704.84936 15618.451 202.7948 303.015 1.948802 + 1840 105.73189 -3925.7774 886.11608 -4811.8935 1541.3194 0 1071.3574 150522.01 -157946.58 -603.17056 15617.998 198.3146 296.30423 1.9386975 + 1860 106.94721 -3888.206 921.52432 -4809.7304 1579.4857 0 1109.6812 150447.64 -157946.54 104.6013 15613.197 206.23903 308.2177 1.8692298 + 1880 108.06014 -3916.0862 918.21234 -4834.2985 1583.1417 0 1094.2365 150433.88 -157945.56 -253.01422 15607.47 205.49781 306.96538 2.1516579 + 1900 109.27602 -3899.0882 918.64022 -4817.7285 1556.1431 0 1115.1484 150457.92 -157946.94 -143.94816 15600.312 205.59357 307.17307 2.0233622 + 1920 110.49415 -3920.9798 896.1905 -4817.1703 1548.5569 0 1085.0712 150496.68 -157947.48 -337.28194 15592.107 200.56927 299.64783 2.0110119 + 1940 111.71421 -3968.3536 874.10309 -4842.4567 1572.4606 0 1094.9587 150436.32 -157946.19 -303.02321 15581.696 195.62607 292.28508 1.9167899 + 1960 112.93472 -3934.8475 883.5952 -4818.4427 1591.4146 0 1141.0692 150394.9 -157945.83 393.7304 15568.475 197.75042 295.48636 1.883029 + 1980 114.15483 -3907.4423 937.55746 -4844.9997 1643.691 0 1216.6376 150240.27 -157945.59 815.94743 15556.713 209.82728 313.50122 2.0597469 + 2000 115.37626 -3925.4165 915.08958 -4840.506 1623.4406 0 1190.2236 150292.14 -157946.31 519.99833 15550.966 204.79893 305.95187 2.083444 +Loop time of 115.376 on 1 procs for 2000 steps with 2500 atoms + +Performance: 1.498 ns/day, 16.024 hours/ns, 17.335 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 97.091 | 97.091 | 97.091 | 0.0 | 84.15 +Bond | 0.031897 | 0.031897 | 0.031897 | 0.0 | 0.03 +Kspace | 3.7648 | 3.7648 | 3.7648 | 0.0 | 3.26 +Neigh | 10.041 | 10.041 | 10.041 | 0.0 | 8.70 +Comm | 0.79701 | 0.79701 | 0.79701 | 0.0 | 0.69 +Output | 0.0071344 | 0.0071344 | 0.0071344 | 0.0 | 0.01 +Modify | 3.5966 | 3.5966 | 3.5966 | 0.0 | 3.12 +Other | | 0.0467 | | | 0.04 + +Nlocal: 2500 ave 2500 max 2500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21222 ave 21222 max 21222 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.30826e+06 ave 2.30826e+06 max 2.30826e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2308257 +Ave neighs/atom = 923.303 +Ave special neighs/atom = 4 +Neighbor list builds = 100 +Dangerous builds = 6 + +Total wall time: 0:01:55 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 new file mode 100644 index 0000000000..c6a45c4ab5 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.lang.g++.4 @@ -0,0 +1,246 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +comm_modify vel yes +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes +fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes +fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. +fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix NVE DRUDES nve + +compute TEMP all temp/drude + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 0.3966074 2915.1579 4579.5774 -1664.4194 561.91893 0 600.76451 155095.13 -157922.23 27379.771 14058.574 1024.9188 1455.9194 160.86778 + 40 0.81358027 1320.1722 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914 + 60 1.2173033 284.06793 2671.4324 -2387.3645 575.54155 0 387.8792 154580.74 -157931.53 12104.74 15031.425 597.87206 886.98502 18.450412 + 80 1.6120358 -462.53073 2214.284 -2676.8148 560.36346 0 254.65244 154447.22 -157939.05 6285.2446 15651.216 495.56131 739.13811 7.4024414 + 100 1.9901412 -965.1962 1839.8309 -2805.0271 544.5953 0 115.80813 154469.59 -157935.02 2361.9408 16295.72 411.75794 615.12768 4.1969771 + 120 2.4076366 -1316.6354 1649.5851 -2966.2205 554.66642 0 50.928948 154365.49 -157937.3 -493.85718 16925.293 369.18054 552.03453 2.7331858 + 140 2.7559175 -1590.9197 1440.667 -3031.5867 526.07695 0 -24.440541 154404.35 -157937.57 -2586.3198 17517.285 322.42423 482.1612 2.2975751 + 160 3.1113834 -1742.3406 1326.8813 -3069.2219 539.49038 0 -43.846686 154369.1 -157933.96 -3549.2199 18059.707 296.95875 444.11027 2.0644718 + 180 3.4379854 -1895.133 1224.1815 -3119.3145 555.27915 0 -18.261199 154275.94 -157932.27 -3762.2323 18545.519 273.97433 409.78407 1.8069068 + 200 3.772357 -2004.4681 1176.8827 -3181.3508 565.04401 0 0.21397152 154190.38 -157936.99 -4346.6082 18973.343 263.38877 393.94854 1.740057 + 220 4.0741081 -2094.1886 1098.386 -3192.5745 592.45711 0 36.50232 154113.36 -157934.89 -4135.0776 19341.735 245.82103 367.67719 1.6170754 + 240 4.3758588 -2178.9977 1086.8337 -3265.8313 617.63759 0 96.837785 153957.25 -157937.56 -4121.8002 19651.8 243.23561 363.77451 1.6722528 + 260 4.6875975 -2264.8204 1078.4367 -3343.2571 663.36053 0 167.77029 153763.13 -157937.51 -3799.2337 19907.053 241.35634 360.97449 1.6377088 + 280 4.9870708 -2325.8017 1097.4329 -3423.2346 717.74153 0 235.01385 153562.93 -157938.92 -3696.4866 20111.415 245.60773 367.30986 1.7042226 + 300 5.2866828 -2390.4714 1068.102 -3458.5734 751.64774 0 295.31519 153435.36 -157940.9 -3511.7651 20268.755 239.04342 357.49315 1.6658672 + 320 5.587172 -2455.1882 1041.7365 -3496.9247 765.89806 0 331.14936 153345 -157938.97 -3020.2521 20383.476 233.14276 348.62201 1.7179837 + 340 5.8844874 -2536.9586 1050.7417 -3587.7004 793.64691 0 352.69902 153205.76 -157939.81 -3447.4347 20457.614 235.15816 351.64191 1.7214644 + 360 6.1785333 -2603.5522 966.91828 -3570.4705 819.14562 0 391.00832 153158.88 -157939.51 -3164.7275 20490.766 216.3983 323.52165 1.7255664 + 380 6.475884 -2594.7716 1024.7965 -3619.5682 836.45788 0 434.31956 153047.12 -157937.46 -2902.8144 20485.924 229.35156 342.91613 1.7641391 + 400 6.7656763 -2647.3629 982.4772 -3629.8401 864.60508 0 479.09794 152963.5 -157937.04 -2535.5559 20447.667 219.88041 328.70004 1.8030439 + 420 7.0558476 -2687.5292 1023.0073 -3710.5365 928.03183 0 538.52272 152760.85 -157937.94 -2383.1875 20380.424 228.95113 342.29995 1.8044464 + 440 7.3502834 -2765.1784 999.349 -3764.5274 966.2891 0 577.16135 152631.19 -157939.17 -2390.6308 20286.677 223.65636 334.36519 1.794568 + 460 7.6480289 -2806.7277 1004.2012 -3810.9289 996.86402 0 599.42684 152532.82 -157940.04 -2476.2951 20168.787 224.74229 335.9677 1.8474231 + 480 7.9473393 -2830.1149 1013.7084 -3843.8233 1009.5457 0 624.67244 152464.69 -157942.73 -2208.5836 20027.763 226.87003 339.15378 1.8588625 + 500 8.2545588 -2849.2101 1033.8059 -3883.016 1018.8936 0 665.65423 152373.57 -157941.13 -1864.5049 19866.3 231.36788 345.90443 1.8323172 + 520 8.591975 -2883.363 982.80834 -3866.1713 1046.7496 0 716.08257 152311.55 -157940.55 -1180.4653 19690.017 219.95452 328.79387 1.8393955 + 540 8.9018662 -2922.4604 979.55307 -3902.0135 1068.293 0 739.88796 152230.57 -157940.76 -1048.6961 19504.92 219.22599 327.7909 1.6577051 + 560 9.2518864 -2966.9519 973.53114 -3940.4831 1078.4149 0 742.20771 152177.5 -157938.6 -840.75895 19313.099 217.87827 325.70841 1.7798986 + 580 9.5821679 -3053.0997 924.19412 -3977.2939 1102.7966 0 751.05657 152109.51 -157940.66 -919.12753 19115.431 206.83654 309.16882 1.7634757 + 600 9.9095862 -3062.7056 960.18758 -4022.8932 1105.4131 0 725.33328 152088.02 -157941.66 -1565.9872 18911.303 214.89195 321.19255 1.860965 + 620 10.237109 -3087.2168 1011.0151 -4098.2319 1138.4545 0 715.92859 151990.05 -157942.66 -1858.9668 18697.232 226.26725 338.29838 1.752463 + 640 10.571446 -3104.3903 1013.9671 -4118.3574 1151.4213 0 771.17657 151902.66 -157943.62 -1042.667 18472.317 226.92791 339.23913 1.8477429 + 660 10.904144 -3140.5527 1003.0482 -4143.6009 1209.2262 0 856.88154 151734.42 -157944.13 -209.63558 18243.884 224.48425 335.54573 1.90792 + 680 11.269296 -3178.318 984.55406 -4162.872 1244.5687 0 912.27932 151624.96 -157944.68 342.27035 18019.714 220.34522 329.38006 1.8427138 + 700 11.61204 -3220.4931 991.39835 -4211.8914 1287.1899 0 958.87881 151484.75 -157942.71 561.06968 17805.512 221.87699 331.61354 1.9544592 + 720 11.956387 -3270.5677 968.72596 -4239.2937 1318.9328 0 1005.2488 151379.5 -157942.98 980.32825 17604.484 216.80286 324.06313 1.8724276 + 740 12.307601 -3290.3786 992.65117 -4283.0298 1300.6067 0 994.6404 151364.88 -157943.15 981.03868 17418.67 222.15737 332.13302 1.7636245 + 760 12.709807 -3328.535 955.47413 -4284.0092 1326.3889 0 996.60158 151337.63 -157944.63 1057.2942 17247.311 213.83707 319.58671 1.9099364 + 780 13.073534 -3357.4814 992.18506 -4349.6664 1339.5541 0 988.34064 151267.55 -157945.11 569.82212 17090.619 222.05305 331.88822 1.9447924 + 800 13.464632 -3375.243 920.44154 -4295.6846 1344.9357 0 1033.5805 151270.88 -157945.08 1522.7002 16947.373 205.99671 307.8875 1.8152213 + 820 13.825511 -3384.8564 957.24296 -4342.0994 1353.9907 0 1040.4762 151209.02 -157945.59 1664.2884 16820.422 214.23294 320.13875 1.9919112 + 840 14.161551 -3422.503 978.5056 -4401.0087 1362.0589 0 1015.2074 151166.38 -157944.65 799.30788 16709.133 218.99156 327.32752 1.887971 + 860 14.533048 -3467.9469 967.207 -4435.1539 1359.5363 0 1012.6359 151135.59 -157942.92 781.21407 16610.402 216.46291 323.49791 1.9571626 + 880 14.90632 -3453.3858 998.28194 -4451.6677 1357.904 0 965.66218 151167.88 -157943.11 327.66041 16521.416 223.41755 333.88219 2.0414314 + 900 15.304111 -3462.8392 980.22919 -4443.0684 1356.3167 0 986.69144 151157.82 -157943.9 1027.2464 16438.193 219.37731 327.82432 2.0328217 + 920 15.679265 -3447.1555 973.44396 -4420.5994 1360.7957 0 1016.6188 151146.99 -157945 1288.3873 16362.953 217.85876 325.51992 2.1081109 + 940 16.057773 -3481.2586 989.56656 -4470.8252 1370.2709 0 978.71463 151124.98 -157944.79 462.51008 16297.794 221.46703 330.96437 2.0294765 + 960 16.417333 -3513.0231 967.65653 -4480.6797 1332.0395 0 924.14851 151207.66 -157944.53 130.65949 16238.731 216.56352 323.68471 1.8694768 + 980 16.809043 -3552.9742 930.52856 -4483.5028 1369.5671 0 943.1948 151148.51 -157944.78 162.05947 16182.544 208.2542 311.18346 1.9699974 + 1000 17.204374 -3547.8316 928.6749 -4476.5065 1345.2729 0 939.82999 151183.66 -157945.27 165.47858 16127.801 207.83935 310.6291 1.8515304 + 1020 17.596776 -3544.884 939.68436 -4484.5683 1339.8295 0 954.31534 151165.65 -157944.37 520.88879 16074.311 210.30329 314.30017 1.8816955 + 1040 17.979123 -3574.7347 918.01852 -4492.7532 1348.2798 0 985.63357 151118.04 -157944.71 667.98123 16024.2 205.45443 307.00947 1.9378696 + 1060 18.387169 -3558.0092 961.56557 -4519.5748 1357.9517 0 960.15956 151105.93 -157943.62 125.05193 15979.251 215.20035 321.61047 1.9569155 + 1080 18.773684 -3578.9948 924.98329 -4503.9781 1328.198 0 963.29308 151149.83 -157945.3 446.98896 15936.835 207.01316 309.36635 1.8873208 + 1100 19.16304 -3608.0441 897.53939 -4505.5835 1374.0861 0 1014.8258 151052.01 -157946.5 903.7649 15898.367 200.87116 300.13546 1.9333063 + 1120 19.575293 -3614.8945 952.97919 -4567.8736 1384.5634 0 1021.0735 150973.5 -157947.01 900.30601 15866.787 213.2787 318.78179 1.850125 + 1140 19.971095 -3618.8945 941.15802 -4560.0526 1413.1629 0 1052.0922 150920.8 -157946.1 946.48705 15842.856 210.6331 314.72329 2.0381081 + 1160 20.367334 -3593.6555 965.54035 -4559.1959 1410.1926 0 1056.4577 150917.31 -157943.16 1255.7185 15827.388 216.08991 322.92339 1.9871263 + 1180 20.80204 -3616.5746 928.17105 -4544.7457 1396.8419 0 1016.2295 150986.13 -157943.95 787.12503 15820.166 207.72659 310.40871 1.9519704 + 1200 21.354242 -3640.0065 913.1866 -4553.1931 1389.564 0 1003.0365 150999.43 -157945.23 124.9066 15819.562 204.37304 305.34426 2.0128932 + 1220 21.797356 -3633.6726 951.90864 -4585.5813 1378.6589 0 960.35277 151020.87 -157945.46 18.165228 15822.414 213.03911 318.39602 1.9062762 + 1240 22.183053 -3647.5993 945.94087 -4593.5401 1389.2708 0 951.90886 151011.29 -157946.01 -36.466949 15826.558 211.70351 316.39869 1.8959 + 1260 22.604321 -3652.8431 945.01497 -4597.8581 1429.1559 0 1004.3575 150913.05 -157944.42 362.05633 15830.563 211.49629 316.0745 1.946701 + 1280 22.99465 -3653.7982 950.39456 -4604.1928 1435.3114 0 1049.5949 150856.36 -157945.46 625.62312 15836.724 212.70025 317.85889 1.9726129 + 1300 23.381442 -3629.7936 957.73231 -4587.5259 1443.1612 0 1053.2561 150860.98 -157944.93 702.06174 15846.916 214.34246 320.25498 2.0929604 + 1320 23.76752 -3646.7132 952.84473 -4599.5579 1452.1034 0 1053.24 150842.08 -157946.98 574.37181 15862.45 213.24861 318.70565 1.9106871 + 1340 24.144538 -3671.1813 963.35534 -4634.5366 1444.4873 0 998.25657 150869.14 -157946.42 -322.65814 15883.001 215.6009 322.16079 2.04787 + 1360 24.525885 -3706.8433 911.96869 -4618.812 1408.7597 0 994.56958 150923.67 -157945.81 -57.178556 15902.95 204.10046 304.98731 1.9206183 + 1380 24.900833 -3729.8666 893.54172 -4623.4083 1421.5285 0 989.13168 150911.03 -157945.1 -299.2294 15921.536 199.97647 298.78606 1.9572022 + 1400 25.273009 -3793.6665 896.59455 -4690.261 1407.5033 0 927.03218 150922.27 -157947.07 -1625.2355 15935.372 200.6597 299.82059 1.9326242 + 1420 25.649713 -3798.9041 894.49834 -4693.4024 1387.2314 0 908.98338 150956.58 -157946.2 -1336.2681 15939.126 200.19057 299.08979 1.99336 + 1440 26.019568 -3770.2203 926.96956 -4697.1899 1408.3234 0 930.94218 150909.09 -157945.54 -1479.4839 15931.76 207.45769 309.99863 1.9420101 + 1460 26.391048 -3765.611 925.8388 -4691.4498 1453.7458 0 991.60997 150809.05 -157945.85 -840.19764 15915.083 207.20462 309.58977 2.0206113 + 1480 26.764417 -3775.5533 897.45722 -4673.0106 1448.3682 0 1017.1514 150806.55 -157945.08 -350.56805 15893.71 200.85277 300.10571 1.945031 + 1500 27.13281 -3774.5729 890.65309 -4665.226 1446.7764 0 1001.4176 150830.42 -157943.84 -410.46342 15870.464 199.32999 297.86004 1.8712264 + 1520 27.500265 -3789.599 873.98319 -4663.5822 1442.1868 0 1012.8814 150826.03 -157944.68 24.399796 15844.317 195.59923 292.31265 1.7812003 + 1540 27.868039 -3799.4214 879.9876 -4679.409 1470.7765 0 1043.5857 150751.8 -157945.57 -117.3494 15817.531 196.94303 294.27937 1.8764714 + 1560 28.237804 -3808.5737 884.02221 -4692.5959 1476.2544 0 1031.065 150745.8 -157945.71 -134.38328 15790.497 197.84599 295.60533 1.9624808 + 1580 28.614069 -3810.3826 881.02258 -4691.4052 1494.8044 0 1056.2914 150703.91 -157946.41 143.72796 15761.802 197.17466 294.61532 1.9194335 + 1600 28.98594 -3811.3999 900.38301 -4711.7829 1484.7896 0 1008.1585 150740.82 -157945.55 -606.18902 15732.936 201.50757 301.08426 1.975131 + 1620 29.390152 -3806.3652 923.83116 -4730.1964 1451.5712 0 974.75532 150788.99 -157945.52 -803.66402 15700.793 206.75531 308.94868 1.9548773 + 1640 29.770757 -3780.4823 926.08598 -4706.5682 1473.3966 0 1001.2541 150764.99 -157946.2 -267.61953 15664.228 207.25994 309.69886 1.9804041 + 1660 30.150359 -3781.8554 904.38999 -4686.2453 1480.8669 0 1044.4828 150733.32 -157944.92 334.93631 15626.039 202.40434 302.41882 1.9682532 + 1680 30.535691 -3806.1604 913.1776 -4719.338 1495.1709 0 1047.1796 150684.96 -157946.64 187.42287 15589.003 204.37102 305.37701 1.9489831 + 1700 30.914774 -3833.9683 889.78762 -4723.756 1506.0651 0 1085.1426 150631.7 -157946.67 484.91155 15553.147 199.1363 297.62268 1.7777001 + 1720 31.295628 -3842.1369 894.05081 -4736.1877 1523.554 0 1111.0586 150574.13 -157944.93 644.7439 15520.678 200.09041 298.99568 1.8760829 + 1740 31.688478 -3846.6021 868.65036 -4715.2525 1537.3591 0 1138.8056 150555.14 -157946.56 899.91638 15492.771 194.40573 290.47895 1.8712221 + 1760 32.046871 -3857.9528 883.26637 -4741.2192 1542.993 0 1087.2616 150575.49 -157946.97 551.51344 15470.089 197.67683 295.29782 2.0345443 + 1780 32.474213 -3871.4941 935.07928 -4806.5734 1526.7468 0 1036.0478 150576.57 -157945.93 -636.02229 15449.192 209.27266 312.71251 1.9801693 + 1800 32.86394 -3840.4408 916.271 -4756.7118 1576.9326 0 1100.9058 150511.02 -157945.57 628.83596 15425.726 205.06333 306.41471 1.9480945 + 1820 33.2544 -3863.8057 928.94676 -4792.7524 1566.8662 0 1091.867 150492.97 -157944.46 127.39479 15404.045 207.90019 310.61713 2.0438685 + 1840 33.654639 -3866.4315 882.39729 -4748.8287 1571.1231 0 1116.2191 150510.49 -157946.66 775.21837 15384.034 197.48232 295.08631 1.8701078 + 1860 34.049358 -3854.7362 943.50575 -4798.2419 1598.0765 0 1094.2606 150455.31 -157945.89 -185.76137 15367.771 211.15852 315.55119 1.9664963 + 1880 34.452703 -3862.4907 910.1166 -4772.6073 1551.4788 0 1069.6982 150551.3 -157945.09 75.157314 15353.364 203.68596 304.30419 2.0643731 + 1900 34.820253 -3879.6568 921.99593 -4801.6528 1541.8636 0 1071.1404 150530.01 -157944.67 -243.29034 15340.544 206.34458 308.28647 2.0409636 + 1920 35.24159 -3914.6053 894.91511 -4809.5205 1545.6295 0 1087.8419 150502.25 -157945.24 585.4907 15327.629 200.28384 299.29163 1.8721306 + 1940 35.641894 -3916.7204 893.69522 -4810.4157 1558.0228 0 1078.6893 150498.47 -157945.6 -213.58892 15315.774 200.01082 298.82901 1.9662798 + 1960 36.036489 -3916.4155 889.43523 -4805.8507 1569.5342 0 1087.2216 150483.46 -157946.07 197.26075 15304.142 199.05743 297.4414 1.897782 + 1980 36.439917 -3885.2222 890.76008 -4775.9823 1562.1737 0 1087.3549 150520.37 -157945.88 448.96019 15293.261 199.35393 297.81895 2.0239285 + 2000 36.842032 -3890.9997 883.71903 -4774.7187 1561.3244 0 1092.1688 150517.76 -157945.97 292.74093 15284.861 197.77813 295.50959 1.9186189 +Loop time of 36.8421 on 4 procs for 2000 steps with 2500 atoms + +Performance: 4.690 ns/day, 5.117 hours/ns, 54.286 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.965 | 26.526 | 28.829 | 27.6 | 72.00 +Bond | 0.011653 | 0.012315 | 0.013344 | 0.6 | 0.03 +Kspace | 1.5367 | 3.8315 | 5.3771 | 72.2 | 10.40 +Neigh | 2.6221 | 2.6225 | 2.6227 | 0.0 | 7.12 +Comm | 1.2339 | 1.2536 | 1.2758 | 1.3 | 3.40 +Output | 0.0057538 | 0.0073775 | 0.012186 | 3.2 | 0.02 +Modify | 2.4848 | 2.5068 | 2.5296 | 1.2 | 6.80 +Other | | 0.08209 | | | 0.22 + +Nlocal: 625 ave 639 max 613 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Nghost: 13529.2 ave 13635 max 13449 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 587190 ave 645917 max 526348 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 2348759 +Ave neighs/atom = 939.504 +Ave special neighs/atom = 4 +Neighbor list builds = 102 +Dangerous builds = 7 + +Total wall time: 0:00:36 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 new file mode 100644 index 0000000000..54fe5ecb01 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.1 @@ -0,0 +1,252 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +comm_modify vel yes +compute TATOM ATOMS temp/com +compute TEMP all temp/drude + +fix DTDIR all drude/transform/direct +fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix_modify RIGID temp TATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1338) +fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 1 100.0 +fix DTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 3375 1000 +Per MPI rank memory allocation (min/avg/max) = 36.15 | 36.15 | 36.15 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 1.3635511 3742.6843 5338.7884 -1596.1041 567.30749 0 662.23765 155098.37 -157924.01 31679.425 13979.574 1194.8318 1690.2246 201.65659 + 40 2.8319206 2752.8326 4407.7651 -1654.9326 793.00136 0 870.3308 154593.76 -157912.03 27394.569 14278.56 986.46689 1450.7477 55.932383 + 60 4.2769592 1995.5898 3982.037 -1986.4472 660.67727 0 750.60931 154536.67 -157934.4 22230.525 14691.401 891.18805 1315.7323 40.317105 + 80 5.6864653 1376.4611 3451.5427 -2075.0816 617.739 0 606.36728 154625.69 -157924.88 17342.361 15201.343 772.46234 1147.1933 21.455572 + 100 7.0593393 885.62035 3037.6307 -2152.0103 536.23281 0 448.92338 154793.05 -157930.22 13263.277 15783.251 679.82798 1011.6853 14.753602 + 120 8.3966329 487.59021 2926.9825 -2439.3923 534.45241 0 332.92674 154624.58 -157931.35 8680.1218 16409.225 655.06468 977.01117 9.8615821 + 140 9.6922171 159.94255 2531.0921 -2371.1495 507.26507 0 248.61566 154802.72 -157929.75 6400.0155 17052.819 566.4636 845.55884 7.140197 + 160 10.950651 -100.91956 2408.1664 -2509.0859 490.99483 0 134.36058 154800.6 -157935.04 3836.9925 17698.151 538.95257 805.1915 5.3968131 + 180 12.172047 -313.40678 2221.7371 -2535.1439 469.97826 0 75.806422 154853.24 -157934.17 1959.0003 18334.826 497.22932 743.13919 4.4151403 + 200 13.369177 -490.93825 2067.2564 -2558.1946 455.16083 0 77.543554 154841.16 -157932.06 1193.4025 18956.449 462.65622 691.72198 3.5993868 + 220 14.438093 -642.88359 1962.7222 -2605.6058 481.40176 0 64.823738 154779.31 -157931.14 258.47931 19559.018 439.26127 657.06568 2.7739198 + 240 15.577558 -770.43472 1795.7362 -2566.1709 467.25739 0 68.825446 154830.01 -157932.26 19.605411 20139.418 401.88945 601.23804 2.3884997 + 260 16.688265 -878.62151 1752.9509 -2631.5724 476.39236 0 71.926651 154747.16 -157927.05 -779.07206 20696.166 392.31402 587.06568 2.0260792 + 280 17.682964 -971.81622 1649.6272 -2621.4434 473.84812 0 58.450385 154779.58 -157933.32 -1008.5258 21226.441 369.18995 552.55677 1.7179235 + 300 18.755012 -1057.4737 1581.0153 -2638.4889 480.33302 0 92.047223 154721.85 -157932.72 -1272.4892 21728.979 353.83447 529.64527 1.5051853 + 320 19.774572 -1132.8157 1506.8725 -2639.6882 477.53234 0 107.39639 154707.65 -157932.27 -1097.9626 22203.697 337.24116 504.84512 1.3587573 + 340 20.69206 -1199.489 1494.9584 -2694.4474 479.87519 0 106.49874 154656.38 -157937.2 -1428.8049 22652.416 334.57476 500.90442 1.2462835 + 360 21.652272 -1264.9018 1440.9759 -2705.8778 491.74088 0 107.21802 154624.72 -157929.55 -1585.5815 23073.033 322.49337 482.81675 1.2016239 + 380 22.541014 -1323.4812 1376.8139 -2700.295 497.62389 0 130.73162 154602.95 -157931.6 -1822.4176 23465.34 308.13377 461.36583 1.0533711 + 400 23.429899 -1373.4313 1375.7746 -2749.2059 504.5216 0 124.40122 154554.57 -157932.7 -2024.2519 23828.151 307.90118 461.05182 0.98409512 + 420 24.30185 -1426.2004 1375.0825 -2801.2829 515.4234 0 141.95789 154473.92 -157932.58 -2211.7434 24159.844 307.74628 460.87881 0.86572884 + 440 25.220268 -1475.8906 1324.8476 -2800.7382 535.08125 0 196.94504 154398.6 -157931.36 -1603.3424 24460.372 296.50361 443.98822 0.94139759 + 460 26.069995 -1526.8146 1312.6512 -2839.4658 567.30401 0 263.15706 154263.01 -157932.94 -1446.573 24734.601 293.77403 439.95008 0.83440493 + 480 26.912804 -1575.0902 1310.7022 -2885.7924 595.89933 0 312.71625 154137.37 -157931.78 -1115.9617 24986.067 293.33784 439.29118 0.84448526 + 500 27.750046 -1625.867 1316.9545 -2942.8215 622.71944 0 334.05272 154029.75 -157929.34 -1178.3349 25218.467 294.73713 441.38984 0.84223525 + 520 28.580007 -1677.8147 1275.1901 -2953.0048 636.81498 0 364.43482 153975.25 -157929.51 -1185.7191 25432.383 285.39015 427.42176 0.75616765 + 540 29.461706 -1724.6335 1253.4762 -2978.1096 632.62875 0 336.7701 153984.65 -157932.16 -1475.652 25627.637 280.53054 420.14989 0.73078744 + 560 30.284055 -1768.8039 1262.2867 -3031.0907 642.26972 0 309.98943 153946.77 -157930.12 -1811.8157 25800.729 282.50237 423.09732 0.74744177 + 580 31.099254 -1811.2401 1227.9083 -3039.1484 678.22201 0 368.41929 153846.44 -157932.23 -1409.4088 25948.882 274.80841 411.53414 0.80732891 + 600 31.912324 -1853.2774 1206.9943 -3060.2717 700.63403 0 436.68693 153737.89 -157935.48 -992.41608 26077.285 270.12781 404.5385 0.76616257 + 620 32.720867 -1895.189 1204.3588 -3099.5478 691.72649 0 400.33253 153741.91 -157933.52 -1388.6703 26189.589 269.53797 403.65884 0.75715127 + 640 33.582986 -1935.0173 1187.9183 -3122.9356 705.21393 0 424.23263 153679.52 -157931.9 -1350.2348 26282.622 265.85856 398.13366 0.77665339 + 660 34.390937 -1971.7086 1162.7479 -3134.4565 702.26031 0 428.42789 153668.92 -157934.06 -1188.7971 26357.244 260.22536 389.70613 0.74337722 + 680 35.194277 -2009.3204 1181.9615 -3191.282 730.54911 0 440.01944 153571.31 -157933.16 -1362.8153 26413.989 264.52542 396.12452 0.79816042 + 700 35.997317 -2050.9709 1191.8391 -3242.8101 753.00327 0 467.6939 153468.36 -157931.87 -1482.0887 26451.007 266.73604 399.41272 0.84921753 + 720 36.797657 -2089.4271 1150.0076 -3239.4347 754.31976 0 503.35736 153436.75 -157933.87 -1244.458 26468.888 257.37407 385.38778 0.83191363 + 740 37.600469 -2125.3798 1154.3541 -3279.7339 774.13557 0 529.42004 153350.85 -157934.14 -1118.7575 26470.499 258.34683 386.83315 0.85749243 + 760 38.401939 -2161.7135 1130.3511 -3292.0647 796.77441 0 536.43801 153307.45 -157932.73 -1175.0129 26456.703 252.9749 378.79415 0.83045948 + 780 39.260591 -2198.2814 1150.3816 -3348.6631 831.65486 0 563.13944 153188.89 -157932.35 -1176.261 26427.139 257.45777 385.51594 0.82651674 + 800 40.064371 -2234.1521 1110.6647 -3344.8168 855.23508 0 601.01417 153131.92 -157932.98 -862.30786 26382.746 248.56904 372.17004 0.86990233 + 820 40.870016 -2267.8439 1102.4715 -3370.3153 860.65298 0 594.70187 153108.56 -157934.23 -1010.8125 26326.235 246.73537 369.40044 0.91177598 + 840 41.681368 -2299.1566 1078.3708 -3377.5273 859.59901 0 593.35932 153101.25 -157931.73 -865.53535 26257.386 241.34159 361.33643 0.86924241 + 860 42.495518 -2331.8875 1107.384 -3439.2715 881.30207 0 614.64915 152998.03 -157933.26 -1071.9258 26177.36 247.83481 371.04249 0.92379597 + 880 43.30765 -2362.8811 1111.5783 -3474.4594 878.94272 0 592.04533 152990.05 -157935.5 -1381.2745 26084.115 248.77351 372.40018 1.0226212 + 900 44.121972 -2394.8169 1068.126 -3462.9429 875.67985 0 600.20259 152996.32 -157935.15 -1082.6484 25975.468 239.0488 357.84385 0.98060155 + 920 44.942671 -2427.7497 1051.3836 -3479.1333 900.00235 0 630.10877 152926.67 -157935.91 -1219.7107 25853.048 235.30182 352.19248 1.049881 + 940 45.823624 -2454.734 1033.0018 -3487.7359 898.98611 0 622.98212 152924.56 -157934.26 -1017.3685 25716.622 231.18793 346.03843 1.0245683 + 960 46.651637 -2482.3376 1051.4989 -3533.8365 882.79039 0 607.4772 152907.91 -157932.02 -1287.7224 25567.669 235.32761 352.20104 1.1100984 + 980 47.483709 -2510.9021 1063.1436 -3574.0457 917.45654 0 628.78148 152815.06 -157935.34 -1318.0782 25404.812 237.93373 356.07751 1.1703057 + 1000 48.3218 -2539.3123 1076.5262 -3615.8385 929.24497 0 620.5376 152770.95 -157936.57 -1437.1421 25228.96 240.92878 360.5539 1.1966823 + 1020 49.120018 -2568.5635 1047.1393 -3615.7027 927.28535 0 622.11842 152769.9 -157935 -1455.4685 25039.532 234.35192 350.71529 1.1564745 + 1040 49.90245 -2600.2331 1062.6806 -3662.9136 955.48542 0 644.04662 152672.56 -157935.01 -1384.5306 24836.175 237.83009 355.87178 1.2710552 + 1060 50.69897 -2630.1462 1061.5152 -3691.6614 986.58819 0 682.07977 152579.13 -157939.46 -1344.1472 24620.038 237.56929 355.4358 1.3611209 + 1080 51.503865 -2659.3124 1028.5625 -3687.8749 1013.1448 0 748.60853 152486.11 -157935.74 -632.77731 24393.781 230.1944 344.4159 1.2910154 + 1100 52.317019 -2686.7631 1046.6402 -3733.4033 1010.8277 0 734.27617 152460.31 -157938.82 -853.90087 24163.398 234.24022 350.47672 1.2987412 + 1120 53.191877 -2717.3602 1100.2788 -3817.639 1053.1519 0 729.94563 152339.1 -157939.84 -1341.3046 23928.078 246.24466 368.47141 1.2986799 + 1140 54.021756 -2749.0229 1075.5657 -3824.5886 1053.2247 0 772.2959 152288.35 -157938.46 -589.3316 23686.107 240.71381 360.21003 1.2399432 + 1160 54.861993 -2781.7214 1067.9567 -3849.6781 1074.5488 0 806.08569 152208.08 -157938.39 -831.19568 23442.775 239.0109 357.6544 1.2458686 + 1180 55.710942 -2810.148 1089.8079 -3899.9559 1109.6809 0 845.87985 152083.25 -157938.76 -222.17835 23198.413 243.90125 365.01942 1.1770946 + 1200 56.57052 -2842.1991 1074.027 -3916.2261 1125.4801 0 878.8665 152014.69 -157935.26 -448.25353 22957.682 240.36945 359.7275 1.1726032 + 1220 57.436566 -2870.9683 1065.5007 -3936.469 1121.3024 0 895.48147 151984.11 -157937.36 -49.04933 22721.016 238.46125 356.86483 1.1771853 + 1240 58.31029 -2898.6134 1082.9239 -3981.5374 1156.8878 0 872.68215 151926.15 -157937.26 -519.72203 22490.6 242.3606 362.72866 1.139753 + 1260 59.192157 -2928.7913 1040.5848 -3969.3761 1145.0651 0 909.81511 151912.71 -157936.97 -29.590267 22264.147 232.88502 348.55509 1.0791106 + 1280 60.142411 -2955.6846 1022.8912 -3978.5758 1140.672 0 883.63602 151933.74 -157936.62 -175.91605 22043.467 228.92516 342.58962 1.1383994 + 1300 61.07528 -2981.9373 1075.9497 -4057.887 1158.7075 0 849.86519 151871.92 -157938.38 -934.6555 21827.24 240.79975 360.40764 1.1023778 + 1320 62.024172 -3008.7547 1034.6665 -4043.4212 1150.8314 0 884.82764 151858.67 -157937.75 -365.70526 21611.763 231.56049 346.60301 1.0123134 + 1340 62.982555 -3034.4981 1059.0543 -4093.5524 1167.4937 0 873.78686 151802.9 -157937.73 -607.20768 21399.603 237.01853 354.83546 0.91062335 + 1360 63.941291 -3061.6404 1086.842 -4148.4824 1203.2944 0 877.27308 151711.62 -157940.67 -877.19102 21189.111 243.23747 364.15541 0.91512372 + 1380 64.90951 -3092.7485 1046.5902 -4139.3388 1239.0597 0 915.00432 151646.1 -157939.51 -519.03533 20978.348 234.22904 350.66459 0.8894947 + 1400 65.889121 -3121.488 1051.0689 -4172.5569 1298.7247 0 989.25234 151480.54 -157941.07 -54.596483 20769.447 235.23138 352.15827 0.90714599 + 1420 66.880954 -3149.3299 1046.1867 -4195.5166 1316.5513 0 1013.5453 151416.57 -157942.18 -12.199056 20566.196 234.13872 350.49775 0.95239313 + 1440 67.876446 -3172.8201 1046.5913 -4219.4114 1319.1146 0 989.68846 151410.33 -157938.54 -145.84664 20369.571 234.22928 350.68677 0.84585946 + 1460 68.88107 -3200.8425 1052.2514 -4253.0939 1296.3997 0 914.27128 151478.83 -157942.59 -1047.6067 20177.139 235.49603 352.58952 0.83805114 + 1480 69.894247 -3229.1329 1032.538 -4261.6708 1273.6899 0 884.58641 151521.54 -157941.48 -877.62887 19983.452 231.08411 345.95296 0.88426485 + 1500 71.009717 -3256.5597 1060.231 -4316.7907 1291.1374 0 874.13592 151461.84 -157943.91 -1479.1729 19788.536 237.28186 355.23846 0.89410552 + 1520 72.041054 -3283.4789 1004.9547 -4288.4336 1248.3551 0 849.40507 151555.63 -157941.83 -1210.342 19590.335 224.91093 336.73148 0.81999833 + 1540 73.084395 -3307.2541 1008.328 -4315.5821 1259.4211 0 846.2933 151520.12 -157941.42 -1328.6534 19389.457 225.66587 337.86416 0.81796565 + 1560 74.135646 -3333.4164 1009.8078 -4343.2242 1290.3482 0 843.72954 151464.8 -157942.1 -1492.5376 19185.011 225.99706 338.35783 0.82352496 + 1580 75.198241 -3359.5746 1031.9507 -4391.5253 1301.979 0 907.32598 151341.72 -157942.55 -931.21229 18977.005 230.95268 345.78871 0.81873619 + 1600 76.272058 -3383.7255 977.90216 -4361.6277 1350.9107 0 1005.0889 151225.61 -157943.23 -265.11417 18769.775 218.85651 327.62822 0.87537743 + 1620 77.356282 -3399.3062 994.75129 -4394.0575 1387.4383 0 1059.1407 151101.4 -157942.03 574.54697 18568.615 222.62738 333.25885 0.91918263 + 1640 78.448545 -3415.8361 1023.468 -4439.304 1398.4672 0 1052.931 151054.15 -157944.85 470.27927 18377.301 229.05423 342.8805 0.94357863 + 1660 79.550247 -3434.561 975.54176 -4410.1027 1429.1617 0 1081.052 151023.2 -157943.52 1049.9178 18195.592 218.32825 326.8381 0.87189374 + 1680 80.667191 -3451.4085 987.31735 -4438.7259 1473.5691 0 1116.4474 150914.31 -157943.05 1058.2306 18025.735 220.96365 330.80265 0.84371639 + 1700 81.797154 -3467.686 964.72099 -4432.407 1455.6679 0 1109.6516 150945 -157942.73 1282.6999 17867.835 215.90654 323.18716 0.91347876 + 1720 82.926758 -3484.8522 984.05698 -4468.9092 1459.9348 0 1102.3739 150911.78 -157943 919.74849 17722.037 220.23397 329.6527 0.95604421 + 1740 84.064705 -3497.8606 976.97179 -4474.8324 1401.3809 0 1034.3626 151032.67 -157943.25 535.35483 17586.464 218.64829 327.27748 0.95261024 + 1760 85.25497 -3516.3474 990.65511 -4507.0025 1393.0104 0 1015.5429 151026.85 -157942.4 -45.078457 17457.877 221.71065 331.88315 0.92222263 + 1780 86.432811 -3532.5203 981.67325 -4514.1936 1381.8497 0 1018.8916 151028.12 -157943.05 419.25311 17333.542 219.70049 328.86023 0.94159899 + 1800 87.629265 -3551.0627 978.09831 -4529.161 1409.4225 0 1023.8144 150980.45 -157942.84 -136.21958 17214.117 218.90041 327.67684 0.90973891 + 1820 88.810324 -3566.367 953.86873 -4520.2357 1386.004 0 1027.6913 151009.66 -157943.59 272.29498 17097.552 213.47778 319.53574 0.93491142 + 1840 89.996806 -3581.9401 989.35892 -4571.299 1438.2511 0 1011.4985 150924.05 -157945.1 -277.89182 16984.647 221.42056 331.39393 1.0309706 + 1860 91.192728 -3597.0855 939.72505 -4536.8105 1424.7503 0 1045.0751 150938.2 -157944.83 769.1418 16874.282 210.31239 314.73818 1.0402053 + 1880 92.395072 -3609.1452 988.80243 -4597.9477 1452.2757 0 1054.8324 150839.43 -157944.48 448.42199 16769.952 221.29601 331.17499 1.095477 + 1900 93.599308 -3623.9274 981.88757 -4605.815 1467.8981 0 1058.3428 150811.66 -157943.72 440.93441 16671.114 219.74845 328.86095 1.0839713 + 1920 94.800441 -3637.4995 962.46738 -4599.9668 1472.6584 0 1100.9414 150770.55 -157944.12 927.11674 16577.506 215.40217 322.39885 0.97801499 + 1940 96.006696 -3649.8745 932.46317 -4582.3377 1482.9302 0 1127.1576 150751.01 -157943.44 1275.661 16490.871 208.68717 312.30264 1.0388692 + 1960 97.217233 -3660.5717 957.9057 -4618.4774 1471.5387 0 1090.5959 150763.08 -157943.69 926.00133 16412.162 214.38126 320.81698 1.081062 + 1980 98.432616 -3673.974 955.97217 -4629.9462 1448.9016 0 1043.2494 150823.46 -157945.55 585.7993 16339.534 213.94853 320.15896 1.0997884 + 2000 99.651307 -3687.9477 943.17863 -4631.1263 1431.8862 0 1028.9334 150853.1 -157945.05 406.94681 16271.378 211.08531 315.85857 1.1166274 +Loop time of 99.6513 on 1 procs for 2000 steps with 2500 atoms + +Performance: 1.734 ns/day, 13.840 hours/ns, 20.070 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 78.424 | 78.424 | 78.424 | 0.0 | 78.70 +Bond | 0.032606 | 0.032606 | 0.032606 | 0.0 | 0.03 +Kspace | 3.7865 | 3.7865 | 3.7865 | 0.0 | 3.80 +Neigh | 9.511 | 9.511 | 9.511 | 0.0 | 9.54 +Comm | 0.71185 | 0.71185 | 0.71185 | 0.0 | 0.71 +Output | 0.0071998 | 0.0071998 | 0.0071998 | 0.0 | 0.01 +Modify | 7.1361 | 7.1361 | 7.1361 | 0.0 | 7.16 +Other | | 0.04205 | | | 0.04 + +Nlocal: 2500 ave 2500 max 2500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 20897 ave 20897 max 20897 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.20428e+06 ave 2.20428e+06 max 2.20428e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2204275 +Ave neighs/atom = 881.71 +Ave special neighs/atom = 4 +Neighbor list builds = 122 +Dangerous builds = 16 + +Total wall time: 0:01:39 diff --git a/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 new file mode 100644 index 0000000000..332359e659 --- /dev/null +++ b/examples/USER/drude/swm4-ndp/log.27Nov18.swm4-ndp.nh.g++.4 @@ -0,0 +1,252 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +special_bonds lj/coul 0.0 0.0 0.5 + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-3 + +read_data data.swm4-ndp + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2500 atoms + scanning bonds ... + 1 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 2000 bonds + reading angles ... + 500 angles + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 3 = max # of 1-4 neighbors + 4 = max # of special neighbors + +pair_coeff 1 1 0.210939 3.183950 # ODw ODw +pair_coeff * 2* 0.000000 0.0 + +group ATOMS type 1:3 +2000 atoms in group ATOMS +group CORES type 1 +500 atoms in group CORES +group DRUDES type 4 +500 atoms in group DRUDES + +variable TK equal 300.0 +variable TDK equal 1.0 +variable PBAR equal 1.0 + +neighbor 2.0 bin + +timestep 1.0 + +fix DRUDE all drude C N N D + +velocity ATOMS create ${TK} 12345 +velocity ATOMS create 300 12345 +velocity DRUDES create ${TDK} 12345 +velocity DRUDES create 1 12345 + +delete_bonds ATOMS multi +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Rebuild special list taking Drude particles into account +Old max number of 1-2 to 1-4 neighbors: 4 +New max number of 1-2 to 1-4 neighbors: 4 (+0) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + 2000 total bonds, 500 turned on, 1500 turned off + 500 total angles, 0 turned on, 500 turned off + 0 total dihedrals, 0 turned on, 0 turned off + 0 total impropers, 0 turned on, 0 turned off + +comm_modify vel yes +compute TATOM ATOMS temp/com +compute TEMP all temp/drude + +fix DTDIR all drude/transform/direct +fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 +fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 +500 rigid bodies with 2000 atoms + 0.832099 = max distance from body owner to body atom +fix_modify RIGID temp TATOM press thermo_press +WARNING: Temperature for fix modify is not for group all (src/RIGID/fix_rigid_nh_small.cpp:1338) +fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 ${TDK} 100.0 +fix NVT DRUDES nvt temp 1 1 100.0 +fix DTINV all drude/transform/inverse + +thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] +thermo 20 + +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.217457 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.197288 + estimated relative force accuracy = 0.000594128 + using double precision FFTs + 3d grid and FFT values/proc = 1500 300 +Per MPI rank memory allocation (min/avg/max) = 18.29 | 18.3 | 18.3 Mbytes +Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp c_TEMP[1] c_TEMP[2] + 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 + 20 0.45823026 3742.7989 5338.7966 -1595.9977 567.29056 0 662.23349 155098.48 -157924 31679.045 13979.575 1194.8336 1690.2267 201.65776 + 40 0.95719695 2752.9392 4407.9332 -1654.994 792.86724 0 870.27523 154593.92 -157912.06 27392.303 14278.564 986.5045 1450.7624 56.079839 + 60 1.4402499 1995.9776 3980.851 -1984.8734 660.64219 0 750.43211 154538.47 -157934.42 22242.677 14691.413 890.92262 1315.3403 40.305318 + 80 1.9050057 1377.133 3449.7879 -2072.6549 617.64238 0 605.75691 154628.64 -157924.69 17345.359 15201.397 772.06961 1146.6088 21.447181 + 100 2.3745039 886.38999 3038.411 -2152.021 537.89929 0 450.99966 154789.13 -157930.05 13299.226 15783.335 680.00261 1011.6773 15.016235 + 120 2.8589215 488.05512 2928.1336 -2440.0785 536.23142 0 334.886 154620.05 -157931.25 8694.3495 16409.509 655.32232 977.40122 9.853881 + 140 3.2965367 160.14918 2538.5119 -2378.3627 509.19544 0 249.89187 154793.34 -157930.79 6363.0936 17053.486 568.12418 847.92535 7.2744487 + 160 3.7223189 -103.57483 2403.1617 -2506.7365 494.69852 0 144.07166 154790.83 -157936.34 4017.2081 17699.095 537.83252 803.44789 5.3901447 + 180 4.1554348 -315.60495 2216.8001 -2532.405 477.29347 0 80.852028 154842.41 -157932.96 1958.2418 18336.716 496.1244 741.47039 4.4401782 + 200 4.5533779 -490.60343 2058.8989 -2549.5023 470.22934 0 80.797892 154831.65 -157932.18 1260.3909 18960.132 460.78579 688.924 3.5878094 + 220 4.9085493 -644.11131 2001.1202 -2645.2315 494.11411 0 53.067462 154741.64 -157934.05 -16.783051 19564.819 447.8548 669.94702 2.7746354 + 240 5.2955835 -773.77077 1911.0789 -2684.8496 491.56671 0 36.573942 154722.87 -157935.86 -773.28467 20144.754 427.70337 639.97783 2.2990474 + 260 5.7046614 -886.74825 1719.7065 -2606.4547 462.97836 0 47.58745 154814.53 -157931.55 -695.31939 20696.484 384.87384 575.96438 1.9230094 + 280 6.0633757 -983.59043 1659.2126 -2642.803 476.05207 0 65.528 154749.28 -157933.67 -1099.7766 21220.608 371.33519 555.77921 1.7044743 + 300 6.4097662 -1069.381 1531.6365 -2601.0175 487.38768 0 130.0599 154709.01 -157927.47 -548.94313 21717.512 342.78339 513.13082 1.4029607 + 320 6.7455602 -1144.854 1562.925 -2707.779 508.98546 0 127.16624 154591.4 -157935.34 -1515.6429 22190.677 349.78582 523.6096 1.414493 + 340 7.0504746 -1216.4848 1511.8539 -2728.3386 518.41635 0 144.67031 154541.86 -157933.28 -1346.5299 22636.537 338.356 506.57907 1.2331509 + 360 7.3652327 -1279.8842 1434.5465 -2714.4306 524.92137 0 153.81139 154537.16 -157930.32 -1445.625 23056.451 321.05444 480.69079 1.1396531 + 380 7.6638732 -1340.1922 1391.8227 -2732.0149 537.12747 0 180.48607 154482.89 -157932.52 -1316.0441 23450.122 311.49278 466.4254 1.0045437 + 400 7.9763258 -1398.97 1401.3049 -2800.275 547.10484 0 190.74701 154394.07 -157932.19 -1697.8502 23818.202 313.61492 469.64586 0.92579849 + 420 8.2703266 -1450.483 1357.937 -2808.4199 555.88824 0 178.22829 154390.11 -157932.65 -1958.9883 24158.533 303.90908 455.10587 0.90768013 + 440 8.5902264 -1501.4161 1341.5516 -2842.9677 573.14949 0 195.16753 154320.41 -157931.7 -1876.025 24469.636 300.24201 449.65628 0.81297929 + 460 8.8937869 -1551.3256 1326.1262 -2877.4518 581.25352 0 206.82716 154267.73 -157933.26 -2033.2771 24752.01 296.78977 444.48443 0.8068672 + 480 9.1780484 -1598.4261 1289.0614 -2887.4875 599.31424 0 250.55266 154195.32 -157932.67 -1734.9907 25004.733 288.4946 432.05986 0.78706924 + 500 9.4627533 -1647.1265 1310.6504 -2957.7768 620.75343 0 278.84436 154075.73 -157933.11 -1819.9564 25230.755 293.32624 439.2975 0.79707067 + 520 9.744127 -1694.4448 1256.1824 -2950.6272 640.46082 0 300.05753 154043.8 -157934.95 -1676.1925 25430.395 281.13621 421.05228 0.74177674 + 540 10.022904 -1741.636 1235.1581 -2976.794 663.79651 0 343.79844 153947.6 -157931.99 -1450.0194 25605.442 276.43091 414.00136 0.73713962 + 560 10.317977 -1784.6341 1213.4226 -2998.0567 667.043 0 361.93171 153904.04 -157931.07 -1633.3649 25757.73 271.56648 406.71944 0.71740617 + 580 10.599227 -1824.7401 1203.2527 -3027.9928 695.49991 0 399.21355 153809.37 -157932.08 -1210.3391 25887.112 269.29042 403.29611 0.74045254 + 600 10.872629 -1865.8971 1201.7743 -3067.6714 714.59075 0 432.45767 153718.17 -157932.89 -1199.4783 25998.228 268.95956 402.78195 0.77684613 + 620 11.144566 -1905.4349 1175.2733 -3080.7082 746.97979 0 456.14057 153649.58 -157933.41 -952.82994 26092.511 263.02858 393.89597 0.76773558 + 640 11.426686 -1943.5065 1165.9307 -3109.4372 755.41374 0 483.29607 153585.09 -157933.23 -984.52156 26172.87 260.93768 390.78613 0.7189019 + 660 11.699499 -1980.6601 1149.4782 -3130.1383 744.34638 0 460.44858 153597.74 -157932.67 -1312.9908 26238.692 257.25559 385.23533 0.78159645 + 680 12.011345 -2017.8555 1159.1341 -3176.9896 734.22636 0 422.37481 153599.86 -157933.45 -1747.0103 26285.639 259.41659 388.49552 0.73989774 + 700 12.310963 -2054.4791 1156.1376 -3210.6166 733.10466 0 423.00212 153565.55 -157932.27 -1636.1386 26309.504 258.74596 387.47025 0.77987596 + 720 12.582198 -2091.6681 1174.8015 -3266.4696 739.49203 0 428.4236 153500.55 -157934.93 -1696.6642 26311.163 262.923 393.72409 0.79497316 + 740 12.970993 -2130.5966 1159.8063 -3290.403 749.2778 0 449.89501 153443.16 -157932.74 -1820.153 26290.013 259.56704 388.70043 0.78112554 + 760 13.328577 -2169.5713 1138.8137 -3308.385 783.90384 0 538.06269 153303 -157933.35 -1011.1163 26246.385 254.86884 381.62657 0.84363887 + 780 13.701648 -2205.5168 1142.2259 -3347.7427 832.2034 0 585.43846 153169.83 -157935.21 -877.81856 26188.431 255.63251 382.73539 0.91548041 + 800 14.064343 -2244.3113 1142.1063 -3386.4176 846.00692 0 618.31624 153083.94 -157934.68 -661.72264 26119.157 255.60573 382.69013 0.92572469 + 820 14.33644 -2280.7153 1109.9081 -3390.6234 858.49264 0 654.04808 153031.02 -157934.18 -465.91138 26042.068 248.39971 371.86079 0.98075233 + 840 14.635953 -2313.2679 1104.4689 -3417.7368 870.71302 0 653.66264 152993.54 -157935.66 -613.02846 25959.467 247.1824 370.05309 0.94666727 + 860 14.907509 -2345.7077 1108.2969 -3454.0045 887.72574 0 641.79104 152948.54 -157932.06 -761.70678 25870.075 248.03912 371.27357 1.0741475 + 880 15.183513 -2377.4774 1063.4515 -3440.9289 869.82787 0 628.04321 152993.89 -157932.69 -855.49925 25771.822 238.00263 356.26939 0.99311617 + 900 15.507916 -2408.6686 1102.0685 -3510.7371 895.2471 0 633.04968 152893.8 -157932.84 -816.76925 25662.984 246.64518 369.19309 1.0560774 + 920 15.786689 -2440.9159 1064.6296 -3505.5455 907.99426 0 640.59576 152879.85 -157933.98 -771.43262 25544.45 238.26628 356.60949 1.103337 + 940 16.081306 -2471.511 1069.129 -3540.64 935.37062 0 676.1306 152783.76 -157935.9 -835.05654 25417.183 239.27326 358.07731 1.186596 + 960 16.361392 -2501.4199 1106.6503 -3608.0702 940.89653 0 655.04578 152730.01 -157934.03 -1188.2588 25280.379 247.6706 370.62835 1.259746 + 980 16.6468 -2536.7151 1106.7401 -3643.4553 955.83568 0 689.00094 152647 -157935.3 -1034.563 25131.304 247.69072 370.65118 1.2744144 + 1000 16.935502 -2570.2795 1086.764 -3657.0436 980.59572 0 714.89208 152582.49 -157935.02 -778.85654 24971.385 243.22002 363.90242 1.3687958 + 1020 17.227137 -2602.1046 1057.6875 -3659.7921 986.13374 0 727.61595 152561.35 -157934.9 -733.05283 24804.434 236.71263 354.20236 1.2597408 + 1040 17.498504 -2630.2834 1061.6996 -3691.9831 979.55337 0 702.15346 152561.09 -157934.78 -845.34279 24631.58 237.61056 355.56436 1.2277288 + 1060 17.773529 -2662.6359 1059.732 -3722.3679 987.68613 0 704.67809 152519.16 -157933.89 -870.46195 24451.603 237.17019 354.91872 1.1988053 + 1080 18.050301 -2692.4034 1097.314 -3789.7174 1025.2827 0 758.27603 152361.94 -157935.22 -859.61672 24264.679 245.58112 367.45939 1.3334136 + 1100 18.32944 -2721.6082 1035.0808 -3756.689 1024.3757 0 793.48607 152361.85 -157936.4 -398.00889 24072.334 231.65321 346.6143 1.2677215 + 1120 18.641844 -2749.785 1044.4525 -3794.2375 1055.3749 0 824.30266 152262.04 -157935.96 -237.96338 23879.17 233.75062 349.76962 1.2451155 + 1140 18.960959 -2772.8286 1065.2495 -3838.078 1064.0529 0 819.37794 152214.82 -157936.33 -419.50711 23686.912 238.40502 356.77133 1.1955971 + 1160 19.294018 -2799.8843 1046.0072 -3845.8914 1068.2773 0 805.55181 152215.61 -157935.33 -627.01178 23494.818 234.09856 350.34221 1.1430413 + 1180 19.649965 -2828.7115 1062.1027 -3890.8142 1081.854 0 768.64664 152195.11 -157936.43 -1113.3883 23300.677 237.70076 355.77198 1.0829394 + 1200 19.96859 -2856.704 1046.499 -3903.203 1081.2546 0 753.81059 152196.72 -157934.99 -1184.6559 23100.615 234.20861 350.52914 1.0991524 + 1220 20.326653 -2886.057 1023.9211 -3909.9781 1088.5712 0 740.41133 152197.78 -157936.75 -1477.5653 22893.4 229.15565 343.00067 1.0072919 + 1240 20.659779 -2913.7708 995.31097 -3909.0818 1069.874 0 758.11146 152202.13 -157939.2 -1090.4758 22677.17 222.75264 333.41163 0.98913753 + 1260 20.982659 -2936.9388 1011.886 -3948.8248 1101.8407 0 796.10406 152091.56 -157938.33 -917.17194 22454.903 226.46216 338.97372 0.98612749 + 1280 21.296781 -2960.7771 994.15899 -3954.9361 1129.3448 0 823.90727 152029.43 -157937.61 -820.42886 22229.299 222.49482 333.04692 0.94562797 + 1300 21.610997 -2984.3569 1049.8825 -4034.2394 1141.808 0 815.97434 151946.6 -157938.63 -777.81536 22002.292 234.96586 351.7259 0.97584665 + 1320 21.939147 -3010.5287 1015.4181 -4025.9468 1162.122 0 814.19766 151933.87 -157936.14 -896.97771 21774.771 227.25266 340.00602 1.1005558 + 1340 22.290971 -3038.0553 985.5931 -4023.6484 1161.8588 0 834.2486 151919.16 -157938.92 -776.69761 21546.055 220.57776 330.09107 1.0139801 + 1360 22.647999 -3060.107 995.10747 -4055.2145 1155.9364 0 823.15336 151904.81 -157939.11 -1060.7954 21316.783 222.70709 333.36443 0.91659915 + 1380 23.10948 -3084.6301 1045.0151 -4129.6452 1182.7352 0 811.15693 151815.78 -157939.31 -1245.9569 21085.59 233.87652 350.01917 1.0453875 + 1400 23.508905 -3109.9777 987.57375 -4097.5514 1174.5153 0 826.73317 151839.75 -157938.55 -936.38803 20851.737 221.02103 330.8031 0.91405623 + 1420 23.906708 -3133.4897 996.08018 -4129.5698 1204.428 0 883.9796 151722.31 -157940.29 -279.27606 20617.831 222.92479 333.68351 0.93320818 + 1440 24.340815 -3156.6284 1002.5391 -4159.1675 1256.8861 0 938.67074 151584.42 -157939.15 -252.37357 20388.73 224.3703 335.78661 1.0353205 + 1460 24.814756 -3174.2482 1025.2447 -4199.493 1219.0264 0 890.12474 151633.42 -157942.07 -472.20532 20165.369 229.45188 343.47039 0.91379457 + 1480 25.194546 -3199.1381 1019.3011 -4218.4392 1263.6197 0 907.8062 151551.73 -157941.59 -357.34642 19946.233 228.12168 341.47893 0.95052162 + 1500 25.6163 -3221.8311 999.94752 -4221.7787 1277.1026 0 966.69277 151477.62 -157943.19 163.84163 19732.291 223.79031 334.84833 1.1106364 + 1520 26.062775 -3240.6737 1026.9402 -4267.6139 1307.0169 0 971.17205 151397.27 -157943.07 300.59837 19526.783 229.83132 344.05076 0.92328807 + 1540 26.51185 -3263.1162 1054.1755 -4317.2916 1310.0417 0 972.81145 151342.02 -157942.16 -71.812538 19330.083 235.92663 353.19321 0.92162655 + 1560 26.975349 -3285.1217 1012.3967 -4297.5183 1317.4278 0 1037.4478 151290.29 -157942.68 862.26427 19140.892 226.57645 339.17946 0.91729521 + 1580 27.358741 -3305.5601 989.56962 -4295.1297 1340.9939 0 1081.7847 151223.92 -157941.82 1218.8084 18963.059 221.46771 331.53455 0.89110049 + 1600 27.75085 -3325.3691 1029.8506 -4355.2197 1351.2586 0 1061.6722 151170.95 -157939.1 749.81991 18797.795 230.48267 344.98106 1.0044287 + 1620 28.144375 -3345.1891 1016.654 -4361.8431 1337.3071 0 1043.5237 151199.64 -157942.31 600.76159 18642.93 227.52925 340.61677 0.89914217 + 1640 28.539596 -3364.6709 980.13009 -4344.801 1354.0177 0 1066.4673 151176.84 -157942.13 1010.3991 18496.839 219.35513 328.33786 0.95094445 + 1660 28.935194 -3382.7945 996.82121 -4379.6158 1343.4606 0 1016.5523 151199.22 -157938.85 546.93155 18360.15 223.09063 333.92162 0.96051901 + 1680 29.338179 -3403.1864 976.66081 -4379.8472 1355.1038 0 1029.6963 151176.44 -157941.09 748.54459 18230.922 218.57869 327.20355 0.89183674 + 1700 29.743355 -3417.6904 994.06517 -4411.7556 1368.1157 0 1013.9323 151145.57 -157939.38 351.45668 18109.291 222.47382 332.98346 0.9529814 + 1720 30.14859 -3434.6282 979.89215 -4414.5203 1377.0869 0 1043.321 151104.18 -157939.11 1004.1915 17993.82 219.30187 328.11073 1.0747474 + 1740 30.591568 -3451.0422 966.54361 -4417.5858 1376.9794 0 1050.8109 151097.44 -157942.82 1079.9737 17886.467 216.31444 323.72083 1.0159044 + 1760 31.006144 -3469.3784 980.75469 -4450.1331 1396.5756 0 1015.9581 151078.09 -157940.75 190.14272 17786.919 219.49491 328.49844 0.97971363 + 1780 31.424875 -3485.9292 1008.375 -4494.3041 1373.9658 0 984.95385 151090.2 -157943.42 -155.51723 17691.03 225.67639 337.7992 0.97942677 + 1800 31.849784 -3502.475 976.23102 -4478.706 1385.4591 0 994.63329 151084.94 -157943.74 288.55406 17597.361 218.48251 327.04845 0.91364963 + 1820 32.275504 -3520.5204 971.19507 -4491.7155 1407.4082 0 1049.909 150992.97 -157942.01 526.1499 17507.18 217.35545 325.30923 0.99414761 + 1840 32.701591 -3535.2936 982.97322 -4518.2668 1419.0124 0 1050.2222 150955.57 -157943.08 420.31843 17421.408 219.99142 329.22593 1.0824421 + 1860 33.133267 -3551.8598 947.45359 -4499.3134 1430.136 0 1069.4805 150943.73 -157942.66 669.02599 17340.063 212.04206 317.36556 0.97096264 + 1880 33.56593 -3564.7527 963.54319 -4528.2959 1418.0293 0 1050.1008 150947.78 -157944.21 529.33841 17263.982 215.64294 322.72997 0.96836521 + 1900 34.00203 -3580.0607 963.5239 -4543.5846 1424.6268 0 1048.9836 150925.17 -157942.36 464.00157 17192.083 215.63863 322.69033 1.0695571 + 1920 34.44279 -3593.8573 957.94124 -4551.7986 1437.3475 0 1061.2427 150893.58 -157943.97 400.78058 17123.621 214.38922 320.8512 1.015936 + 1940 34.877758 -3608.3005 951.71962 -4560.0201 1421.2611 0 1059.2678 150903.97 -157944.52 332.6227 17058.096 212.9968 318.72703 1.0660417 + 1960 35.315982 -3623.3562 948.66706 -4572.0233 1438.6049 0 1066.4475 150868.57 -157945.64 448.04656 16995.11 212.31364 317.61154 1.1874864 + 1980 35.79727 -3635.1448 958.32383 -4593.4687 1448.1655 0 1056.2971 150846.27 -157944.2 110.28409 16935.142 214.47484 320.97102 1.0535213 + 2000 36.231822 -3649.7345 959.87855 -4609.6131 1458.7554 0 1080.5488 150796.28 -157945.2 615.27816 16877.582 214.82279 321.49302 1.0526861 +Loop time of 36.2319 on 4 procs for 2000 steps with 2500 atoms + +Performance: 4.769 ns/day, 5.032 hours/ns, 55.200 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 19.246 | 21.089 | 23.446 | 32.8 | 58.21 +Bond | 0.012314 | 0.012709 | 0.013402 | 0.4 | 0.04 +Kspace | 2.0259 | 4.3875 | 6.228 | 72.1 | 12.11 +Neigh | 2.6629 | 2.6673 | 2.6718 | 0.3 | 7.36 +Comm | 0.95863 | 0.96795 | 0.97884 | 0.9 | 2.67 +Output | 0.0071304 | 0.0093493 | 0.0142 | 2.9 | 0.03 +Modify | 7.0096 | 7.0134 | 7.0186 | 0.1 | 19.36 +Other | | 0.08472 | | | 0.23 + +Nlocal: 625 ave 683 max 565 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 12687 ave 12923 max 12461 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 531145 ave 625145 max 458041 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 2124581 +Ave neighs/atom = 849.832 +Ave special neighs/atom = 4 +Neighbor list builds = 122 +Dangerous builds = 16 + +Total wall time: 0:00:36 diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 deleted file mode 100644 index e66f4c69c2..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.1 +++ /dev/null @@ -1,230 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -comm_modify vel yes -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes -fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix NVE DRUDES nve - -compute TEMP all temp/drude - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 24.8361 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 1.529202 2882.459 4527.8074 -1645.3484 561.72857 0 600.34616 155114.77 -157922.19 27167.702 14058.741 1013.3326 1438.6699 160.63128 - 40 3.073256 1331.3826 3348.9313 -2017.5487 681.52309 0 553.09465 154668.62 -157920.79 17925.93 14484.215 749.4977 1105.2032 36.587791 - 60 4.584862 297.35979 2604.4137 -2307.0539 583.99971 0 409.0399 154634.74 -157934.83 13017.752 15026.564 582.87312 864.55899 18.335649 - 80 6.053256 -374.31023 2263.3247 -2637.635 534.80338 0 212.27981 154543.18 -157927.9 6155.9261 15645.855 506.53672 755.45209 7.6929084 - 100 7.4787509 -905.58889 1911.7191 -2817.308 532.30405 0 87.570168 154497.48 -157934.66 2149.3099 16288.797 427.84666 639.27768 4.1289101 - 120 8.8570309 -1233.6894 1675.0881 -2908.7775 544.7643 0 59.500519 154422.72 -157935.76 233.4994 16915.818 374.88816 560.54169 2.8313123 - 140 10.102229 -1463.4927 1468.7443 -2932.237 539.69692 0 41.083584 154424.91 -157937.93 -1492.9865 17509.345 328.70799 491.66353 2.1394958 - 160 11.319324 -1695.7535 1385.9603 -3081.7137 552.91518 0 30.022893 154274.72 -157939.37 -3010.4983 18061.925 310.18075 463.968 1.9858941 - 180 12.62008 -1818.1958 1253.169 -3071.3648 559.57456 0 20.01719 154289.67 -157940.63 -3354.4536 18564.877 280.4618 419.57594 1.6725953 - 200 13.836408 -1949.6497 1210.0669 -3159.7167 570.055 0 16.319449 154195.04 -157941.13 -4118.0013 19014.456 270.81546 405.06925 1.766255 - 220 15.032024 -2031.6125 1148.1454 -3179.7579 598.02981 0 30.833041 154127.13 -157935.75 -4514.7299 19406.767 256.9573 384.33701 1.6839691 - 240 16.302775 -2118.6259 1120.0048 -3238.6307 613.2903 0 59.888138 154030.6 -157942.41 -4415.1944 19738.97 250.65937 374.93983 1.5971234 - 260 17.465169 -2203.4348 1065.8476 -3269.2823 614.19171 0 77.619746 153980.69 -157941.79 -4564.2677 20011.077 238.53887 356.80737 1.5247856 - 280 18.614435 -2317.9282 1033.2676 -3351.1958 650.51218 0 126.14976 153811.64 -157939.49 -4722.7543 20224.149 231.24742 345.8479 1.5839508 - 300 19.757547 -2377.6306 992.4842 -3370.1148 688.02217 0 179.77994 153701.18 -157939.1 -4126.4983 20378.439 222.12 332.08757 1.7406267 - 320 20.888309 -2419.6547 1023.0345 -3442.6892 720.31567 0 227.70007 153549.33 -157940.04 -4083.8776 20479.241 228.95722 342.33844 1.7368676 - 340 22.018005 -2456.7661 1048.83 -3505.5961 754.13021 0 264.44865 153415.74 -157939.91 -3894.7125 20529.721 234.73031 351.04714 1.6271854 - 360 23.241519 -2504.7475 1041.9912 -3546.7386 785.42547 0 335.38743 153271.47 -157939.03 -3464.4465 20531.323 233.19976 348.66924 1.7943874 - 380 24.370763 -2596.2223 1000.109 -3596.3313 825.31479 0 390.18238 153129.56 -157941.39 -3355.5804 20490.646 223.82645 334.61119 1.8093168 - 400 25.499192 -2666.6702 1006.474 -3673.1442 865.9858 0 422.51674 152978.57 -157940.21 -3329.4637 20411.001 225.25095 336.79016 1.7220267 - 420 26.635042 -2675.8885 1036.9567 -3712.8452 909.14044 0 490.71452 152826.18 -157938.88 -2907.7096 20294.317 232.07303 346.92895 1.8970394 - 440 27.774963 -2731.5399 1054.4488 -3785.9886 935.99349 0 530.9675 152684.75 -157937.7 -2566.587 20147.094 235.9878 352.84462 1.8021906 - 460 28.922784 -2808.5929 996.20283 -3804.7957 986.6991 0 582.25374 152565.95 -157939.7 -2489.2912 19973.682 222.95224 333.32237 1.7660757 - 480 30.07189 -2862.64 1012.7035 -3875.3436 1005.1596 0 610.07691 152450.62 -157941.2 -2031.6453 19777.635 226.64513 338.80268 1.8767218 - 500 31.210731 -2935.4679 989.23412 -3924.702 1019.9115 0 633.87354 152362.4 -157940.89 -2214.2821 19561.863 221.39263 330.98935 1.7563884 - 520 32.363073 -2989.4684 968.83888 -3958.3072 1057.5825 0 655.88302 152269.68 -157941.45 -2298.887 19328.548 216.82813 324.17678 1.6971802 - 540 33.631173 -3036.6833 1016.2589 -4052.9421 1091.2498 0 658.37327 152140.1 -157942.67 -2240.561 19080.875 227.44082 340.06628 1.7350202 - 560 34.815099 -3093.7794 947.7515 -4041.5309 1141.2318 0 764.1603 151995.79 -157942.71 -1157.5191 18819.961 212.10873 317.02152 1.858938 - 580 36.012327 -3166.4133 987.9563 -4154.3696 1199.2171 0 796.34125 151794.12 -157944.05 -1304.4967 18555.635 221.10665 330.55449 1.7687509 - 600 37.228579 -3194.8572 979.66264 -4174.5199 1206.8265 0 842.68836 151717.96 -157941.99 -843.16439 18290.222 219.25051 327.76152 1.7899831 - 620 38.457464 -3255.2052 965.87596 -4221.0812 1218.8406 0 849.13897 151653.64 -157942.7 -628.0114 18027.862 216.16502 323.08905 1.8846337 - 640 39.700987 -3269.6729 1003.1309 -4272.8038 1273.0417 0 928.68865 151468.54 -157943.07 117.71698 17770.578 224.50275 335.54575 1.9677468 - 660 40.961165 -3293.6967 1002.4504 -4296.1471 1299.7531 0 955.60765 151392.37 -157943.87 207.76414 17523.763 224.35045 335.3089 1.9848634 - 680 42.237597 -3310.539 1011.7934 -4322.3324 1358.9202 0 986.69345 151275.62 -157943.56 677.05046 17289.864 226.44145 338.46824 1.9349743 - 700 43.530486 -3380.6882 976.5597 -4357.2479 1378.7945 0 1003.8845 151205.15 -157945.07 605.30766 17069.732 218.55607 326.63938 1.9523301 - 720 44.837568 -3385.7377 1005.1302 -4390.8679 1389.9512 0 1012.3035 151151.06 -157944.19 817.35931 16863.381 224.95021 336.31657 1.7675955 - 740 46.162222 -3378.6942 1023.8252 -4402.5194 1400.0688 0 1063.4211 151077.64 -157943.65 1513.5741 16671.518 229.13418 342.45655 2.0311926 - 760 47.500172 -3425.4378 1036.4011 -4461.8389 1408.8321 0 1068.7339 151003.75 -157943.15 1350.0894 16496.502 231.9487 346.7108 1.9605952 - 780 48.851472 -3453.9533 1021.8895 -4475.8428 1425.2091 0 1104.5857 150938.44 -157944.08 1801.2205 16339.019 228.70097 341.83264 1.9802343 - 800 50.2129 -3497.6136 979.31494 -4476.9285 1441.1399 0 1119.8292 150908.27 -157946.17 1649.8638 16200.982 219.17269 327.47284 2.1340593 - 820 51.586885 -3545.7792 969.50276 -4515.282 1479.3831 0 1103.1191 150847.98 -157945.76 1410.2174 16081.771 216.97671 324.23659 2.0229826 - 840 52.968935 -3562.4777 972.83071 -4535.3084 1470.5582 0 1079.9217 150857.46 -157943.25 1608.0813 15977.891 217.72151 325.33963 2.0498221 - 860 54.3603 -3569.1307 987.8631 -4556.9938 1446.8392 0 1055.8137 150885.62 -157945.27 1110.2002 15887.947 221.08579 330.4231 1.9689916 - 880 55.752677 -3612.6783 957.13055 -4569.8088 1435.3619 0 1056.264 150883.35 -157944.78 914.27883 15809.361 214.20778 320.06673 2.0614732 - 900 57.105164 -3660.821 939.51428 -4600.3353 1463.6114 0 1070.121 150812.25 -157946.31 1261.3306 15740.285 210.26522 314.20385 1.967446 - 920 58.464501 -3685.0371 941.21956 -4626.2567 1483.8487 0 1096.8187 150737.38 -157944.31 1236.4144 15680.989 210.64687 314.81024 1.89883 - 940 59.82202 -3719.0907 915.61639 -4634.7071 1515.6474 0 1104.1119 150691.39 -157945.86 1066.5855 15632.292 204.91683 306.20627 1.9280979 - 960 61.189826 -3752.7758 893.54303 -4646.3189 1517.1996 0 1125.6182 150656.81 -157945.94 1449.4275 15593.029 199.97676 298.74917 2.0320058 - 980 62.459059 -3752.1139 925.61635 -4677.7302 1528.3468 0 1137.3575 150600.83 -157944.27 1493.1803 15564.263 207.15484 309.5242 2.0018169 - 1000 63.8395 -3737.7642 905.82477 -4643.589 1505.254 0 1110.1192 150686.75 -157945.72 1296.1084 15546.258 202.72544 302.92529 1.9202879 - 1020 65.169118 -3767.2178 892.14155 -4659.3593 1493.2162 0 1085.8721 150707.12 -157945.57 922.80521 15537.177 199.66311 298.24598 2.0980372 - 1040 66.474103 -3783.5702 891.57404 -4675.1442 1484.1631 0 1076.2171 150710.25 -157945.77 707.15481 15535.102 199.5361 298.15469 1.8998396 - 1060 67.68596 -3816.1219 868.55884 -4684.6807 1478.7568 0 1060.3026 150723.2 -157946.94 638.16846 15538.641 194.38525 290.46937 1.8282435 - 1080 69.003517 -3807.3485 875.34276 -4682.6913 1482.2148 0 1055.6143 150725.66 -157946.19 416.14661 15546.427 195.90351 292.75831 1.802085 - 1100 70.315532 -3814.5517 894.42504 -4708.9768 1492.6318 0 1053.4891 150692.22 -157947.31 341.55654 15557.253 200.17416 299.12904 1.8640462 - 1120 71.62724 -3837.42 886.31149 -4723.7315 1497.9422 0 1047.1133 150677.33 -157946.12 4.9308474 15569.465 198.35833 296.42678 1.8247148 - 1140 72.956868 -3802.3965 899.40687 -4701.8034 1479.6329 0 1020.1254 150744.44 -157946 -142.99064 15582.446 201.2891 300.81318 1.8383791 - 1160 74.274932 -3810.7658 902.84695 -4713.6127 1472.5916 0 1018.8174 150740.5 -157945.52 12.783208 15594.928 202.059 301.90406 1.9647721 - 1180 75.595463 -3786.4338 929.44447 -4715.8783 1477.4053 0 1016.2942 150735.81 -157945.39 -53.70556 15606.416 208.01158 310.85718 1.9043666 - 1200 76.915409 -3800.0338 897.43664 -4697.4705 1483.1401 0 1059.31 150706.14 -157946.06 534.37576 15617.028 200.84816 300.11638 1.9100302 - 1220 78.119883 -3799.6824 882.65153 -4682.3339 1488.5302 0 1036.1696 150739.15 -157946.19 155.57627 15628.242 197.53922 295.16257 1.8974641 - 1240 79.419663 -3800.7533 911.18613 -4711.9394 1475.5968 0 1005.3229 150752.61 -157945.47 -457.64009 15638.953 203.92533 304.69739 1.9733514 - 1260 80.721954 -3763.5149 950.12041 -4713.6353 1441.6787 0 964.69517 150825.9 -157945.91 -604.24646 15647.017 212.6389 317.74138 2.0086447 - 1280 82.018768 -3770.742 937.09634 -4707.8384 1445.4659 0 949.37244 150842.61 -157945.28 -993.94783 15650.702 209.72409 313.39122 1.9703726 - 1300 83.314893 -3777.4899 904.34062 -4681.8306 1435.5873 0 967.49755 150860.85 -157945.76 -640.04936 15648.293 202.39329 302.46077 1.8535337 - 1320 84.617907 -3766.6204 885.81908 -4652.4395 1416.0678 0 971.89494 150906.86 -157947.27 -366.46049 15641.654 198.24813 296.26647 1.8149522 - 1340 85.931152 -3774.8032 919.58694 -4694.3901 1425.1776 0 939.16654 150887.07 -157945.81 -950.33698 15631.589 205.80544 307.5014 2.0019282 - 1360 87.242691 -3787.4243 922.65238 -4710.0767 1430.1028 0 964.01827 150842.71 -157946.91 -767.13405 15614.998 206.4915 308.53756 1.9863831 - 1380 88.556261 -3792.754 900.77391 -4693.5279 1420.8035 0 953.09514 150878.52 -157945.95 -1072.9667 15593.378 201.59505 301.19366 1.9946415 - 1400 89.868914 -3772.1032 910.85489 -4682.9581 1401.9732 0 959.20659 150901.09 -157945.23 -640.48972 15566.828 203.85119 304.58411 1.9776581 - 1420 91.085535 -3782.5246 898.64718 -4681.1718 1436.1885 0 1010.9254 150817.16 -157945.45 -21.80524 15536.721 201.11908 300.5555 1.8440133 - 1440 92.406331 -3775.4206 919.73488 -4695.1554 1446.1057 0 1018.1835 150785.23 -157944.68 46.810177 15507.157 205.83855 307.4904 2.123189 - 1460 93.732761 -3757.7457 938.91361 -4696.6593 1451.5945 0 1008.6517 150787.38 -157944.28 -175.88589 15478.297 210.13079 313.97065 2.030827 - 1480 95.057074 -3776.8625 933.4271 -4710.2896 1469.7064 0 1033.8521 150731.34 -157945.19 171.44717 15450.004 208.9029 312.19981 1.8912834 - 1500 96.391192 -3764.5196 945.12068 -4709.6403 1483.0898 0 1052.3029 150699.59 -157944.62 431.18844 15423.716 211.51995 316.14058 1.85565 - 1520 97.721669 -3760.514 960.29952 -4720.8136 1507.6965 0 1068.2902 150648.96 -157945.76 714.27148 15402.108 214.917 321.14587 2.0294443 - 1540 99.056402 -3787.9932 950.73472 -4738.728 1514.4781 0 1058.2368 150635.29 -157946.73 547.92963 15384.955 212.77638 318.01984 1.8639142 - 1560 100.30064 -3822.5612 921.12091 -4743.6821 1519.8628 0 1084.8337 150596.5 -157944.88 479.4088 15370.571 206.14875 308.02344 1.987069 - 1580 101.63827 -3832.4207 936.50822 -4768.9289 1562.5808 0 1124.0034 150490.87 -157946.38 833.06708 15360.019 209.59246 313.15266 2.0528778 - 1600 102.98354 -3862.3688 922.42346 -4784.7923 1571.2038 0 1110.9988 150479.2 -157946.19 674.29885 15354.399 206.44026 308.48417 1.9395764 - 1620 104.32562 -3863.8731 946.37539 -4810.2485 1562.9498 0 1094.323 150478.98 -157946.5 -224.35579 15352.811 211.80075 316.51174 1.9551706 - 1640 105.66368 -3834.5163 952.04367 -4786.5599 1536.5144 0 1078.6783 150544.66 -157946.41 -30.565669 15352.152 213.06933 318.41145 1.9589345 - 1660 107.00124 -3859.131 892.31028 -4751.4413 1515.0462 0 1076.4059 150603.91 -157946.81 227.01045 15352.058 199.70087 298.41871 1.8658052 - 1680 108.2363 -3858.2995 918.6578 -4776.9573 1533.9319 0 1064.9106 150570.69 -157946.49 335.15388 15352.595 205.5975 307.20976 1.9617869 - 1700 109.5659 -3850.0817 929.25672 -4779.3384 1552.5519 0 1094.2161 150519.21 -157945.31 393.76719 15353.331 207.96956 310.72982 2.0330981 - 1720 110.90017 -3890.603 917.87519 -4808.4781 1566.3302 0 1075.6092 150495.91 -157946.33 -76.371955 15355.997 205.42235 306.92393 2.0083539 - 1740 112.13829 -3891.5259 936.37478 -4827.9007 1568.2195 0 1085.8514 150464.14 -157946.11 0.9297943 15358.36 209.5626 313.09836 2.0719603 - 1760 113.46951 -3881.0244 903.38798 -4784.4124 1524.2547 0 1079.0557 150557.47 -157945.19 192.41461 15360.098 202.18008 302.05776 2.0203699 - 1780 114.81068 -3885.7248 910.74799 -4796.4728 1532.8732 0 1055.4583 150560.36 -157945.17 -530.84683 15362.305 203.82727 304.58876 1.8966227 - 1800 116.14689 -3907.0506 885.50025 -4792.5508 1533.7624 0 1068.2841 150550.77 -157945.37 240.13827 15362.751 198.17677 296.0834 1.9671724 - 1820 117.48197 -3898.1244 894.18625 -4792.3107 1521.378 0 1059.1428 150574.05 -157946.88 34.574046 15361.495 200.12072 298.96924 2.0234207 - 1840 118.82815 -3874.3766 895.94028 -4770.3169 1523.7865 0 1077.7882 150573.72 -157945.61 324.16201 15359.092 200.51327 299.59285 1.9530985 - 1860 120.06522 -3892.2617 891.17198 -4783.4337 1526.1544 0 1091.1167 150543.11 -157943.82 574.32363 15357.261 199.44612 297.92332 2.0928308 - 1880 121.40834 -3906.8943 911.93286 -4818.8271 1552.4086 0 1113.1993 150462.35 -157946.79 279.12422 15356.96 204.09245 304.90059 2.0679776 - 1900 122.76151 -3922.7591 879.82965 -4802.5888 1550.6607 0 1108.3657 150485.77 -157947.38 356.47291 15359.386 196.90768 294.18644 1.9563556 - 1920 124.11267 -3960.2437 869.21003 -4829.4537 1521.5339 0 1036.9974 150558.9 -157946.89 -839.29936 15362.76 194.53099 290.66184 1.8802157 - 1940 125.45713 -3954.661 876.75754 -4831.4186 1506.7448 0 1007.0383 150601.14 -157946.34 -1316.6937 15361.338 196.22014 293.17781 1.9123591 - 1960 126.70769 -3938.7558 876.41976 -4815.1756 1481.7627 0 996.84388 150652.15 -157945.93 -887.63902 15352.095 196.14454 293.08662 1.8680915 - 1980 128.05176 -3911.4383 894.43818 -4805.8765 1516.4382 0 1037.517 150585.32 -157945.15 -176.75144 15336.185 200.1771 299.12472 1.8815139 - 2000 129.4091 -3920.2641 888.06919 -4808.3333 1495.9942 0 1040.703 150601.72 -157946.75 -243.72475 15316.676 198.75171 296.94612 1.9653682 -Loop time of 129.409 on 1 procs for 2000 steps with 2500 atoms - -Pair time (%) = 109.108 (84.3128) -Bond time (%) = 0.0499372 (0.0385887) -Kspce time (%) = 3.30969 (2.55754) -Neigh time (%) = 9.70209 (7.49723) -Comm time (%) = 0.829103 (0.640684) -Outpt time (%) = 0.00999022 (0.00771987) -Other time (%) = 6.39989 (4.94547) - -Nlocal: 2500 ave 2500 max 2500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21780 ave 21780 max 21780 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.34087e+06 ave 2.34087e+06 max 2.34087e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2340869 -Ave neighs/atom = 936.348 -Ave special neighs/atom = 4 -Neighbor list builds = 100 -Dangerous builds = 6 - diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 deleted file mode 100644 index b43b75cc35..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.lang.8Jul15.linux.4 +++ /dev/null @@ -1,230 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -comm_modify vel yes -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes -fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes -fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500. -fix NPH ATOMS rigid/nph/small molecule iso 1 1 500. -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix NVE DRUDES nve - -compute TEMP all temp/drude - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 15.0906 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 0.47649789 2915.1578 4579.5774 -1664.4195 561.91893 0 600.76451 155095.13 -157922.23 27379.77 14058.574 1024.9188 1455.9194 160.86778 - 40 0.97488093 1320.1721 3337.6372 -2017.4651 726.83344 0 585.5439 154587.28 -157917.12 18749.425 14485.651 746.97006 1101.4061 36.530914 - 60 1.4631288 284.06852 2671.4325 -2387.3639 575.54157 0 387.8792 154580.74 -157931.53 12104.741 15031.425 597.87207 886.98502 18.450413 - 80 1.937151 -462.53017 2214.284 -2676.8142 560.36347 0 254.65245 154447.22 -157939.05 6285.2465 15651.216 495.56131 739.13811 7.4024411 - 100 2.3922298 -965.19662 1839.831 -2805.0276 544.59528 0 115.80812 154469.59 -157935.02 2361.9397 16295.72 411.75795 615.12769 4.196977 - 120 2.832803 -1316.6351 1649.585 -2966.2202 554.6664 0 50.928925 154365.49 -157937.3 -493.85523 16925.293 369.18052 552.0345 2.7331855 - 140 3.2340388 -1590.9162 1440.6669 -3031.5831 526.07679 0 -24.44055 154404.35 -157937.57 -2586.2431 17517.285 322.42421 482.16117 2.297578 - 160 3.6521859 -1742.3401 1326.8812 -3069.2213 539.49044 0 -43.846659 154369.1 -157933.96 -3549.2196 18059.707 296.95874 444.11026 2.0644677 - 180 4.033325 -1895.1332 1224.1816 -3119.3148 555.27887 0 -18.261233 154275.94 -157932.27 -3762.2304 18545.518 273.97437 409.78413 1.806893 - 200 4.4333398 -2004.4682 1176.8828 -3181.351 565.0443 0 0.21425471 154190.38 -157936.99 -4346.6036 18973.342 263.38879 393.94856 1.7400558 - 220 4.8055639 -2094.1888 1098.3856 -3192.5744 592.45764 0 36.50238 154113.36 -157934.89 -4135.0794 19341.735 245.82095 367.67707 1.617053 - 240 5.1688328 -2178.9829 1086.8322 -3265.8151 617.63697 0 96.836936 153957.27 -157937.56 -4121.5262 19651.8 243.23528 363.77401 1.6722646 - 260 5.5313618 -2264.8265 1078.4348 -3343.2613 663.35817 0 167.76882 153763.13 -157937.52 -3799.3346 19907.052 241.35592 360.97385 1.6377289 - 280 5.8937738 -2325.7764 1097.4356 -3423.212 717.74089 0 235.0127 153562.96 -157938.92 -3696.0526 20111.414 245.60833 367.31076 1.7042318 - 300 6.254128 -2390.4932 1068.1054 -3458.5986 751.64681 0 295.31516 153435.34 -157940.9 -3512.2095 20268.754 239.04419 357.49427 1.665921 - 320 6.6138928 -2455.1776 1041.7419 -3496.9195 765.8972 0 331.14997 153345 -157938.97 -3020.0674 20383.474 233.14397 348.62385 1.7179273 - 340 6.9748628 -2536.9935 1050.7304 -3587.7239 793.64536 0 352.69908 153205.74 -157939.81 -3447.9127 20457.612 235.15562 351.6381 1.7214573 - 360 7.3319299 -2603.5606 966.90943 -3570.47 819.14306 0 391.00909 153158.89 -157939.51 -3164.629 20490.764 216.39631 323.51872 1.7254892 - 380 7.691319 -2594.787 1024.7927 -3619.5797 836.44816 0 434.32118 153047.12 -157937.47 -2902.9345 20485.923 229.35071 342.91482 1.7641915 - 400 8.044276 -2647.3896 982.46478 -3629.8543 864.59805 0 479.08516 152963.5 -157937.04 -2535.9236 20447.668 219.87764 328.69587 1.8030508 - 420 8.3971269 -2687.5263 1023.0437 -3710.57 928.04551 0 538.49845 152760.83 -157937.94 -2383.6292 20380.427 228.95928 342.31215 1.8044964 - 440 8.753284 -2765.2192 999.28342 -3764.5026 966.26754 0 577.15359 152631.24 -157939.17 -2391.0923 20286.676 223.64168 334.34309 1.7947669 - 460 9.1102748 -2806.7385 1004.2311 -3810.9696 996.86893 0 599.41867 152532.79 -157940.05 -2476.5754 20168.782 224.74899 335.97767 1.8475589 - 480 9.471664 -2830.2582 1013.6925 -3843.9506 1009.5553 0 624.64584 152464.58 -157942.73 -2210.7254 20027.747 226.86645 339.14841 1.8588685 - 500 9.8365009 -2865.4993 1024.473 -3889.9723 1017.2606 0 658.56598 152375.13 -157940.93 -2047.5735 19865.992 229.27916 342.78576 1.8103481 - 520 10.207523 -2918.9299 973.10292 -3892.0328 1049.357 0 699.16951 152300.27 -157940.83 -1453.4121 19688.211 217.78243 325.51403 1.8799495 - 540 10.583098 -2970.1121 925.84385 -3895.956 1077.9578 0 758.25478 152208.67 -157940.84 -821.19447 19499.417 207.20575 309.67486 1.8442683 - 560 10.962813 -3008.9942 954.33133 -3963.3255 1114.7309 0 751.85274 152112.75 -157942.66 -1023.0801 19304.314 213.58131 319.23167 1.8463043 - 580 11.351938 -3069.9822 951.38041 -4021.3626 1127.8186 0 765.20411 152027.82 -157942.2 -954.30565 19101.694 212.92089 318.20155 1.9391088 - 600 11.74351 -3090.3867 973.25557 -4063.6423 1123.3487 0 744.86978 152009.46 -157941.32 -1226.2333 18891.444 217.81659 325.5949 1.8227604 - 620 12.138507 -3114.2347 1002.2136 -4116.4483 1159.4812 0 766.24573 151899.05 -157941.23 -1406.6638 18672.922 224.29746 335.32178 1.8002314 - 640 12.53874 -3160.3172 973.01388 -4133.3311 1181.5814 0 805.79135 151821.94 -157942.65 -1444.0821 18448.163 217.7625 325.51017 1.8464735 - 660 12.945363 -3185.1871 975.57462 -4160.7618 1177.1798 0 795.84414 151809.59 -157943.38 -962.08053 18220.064 218.3356 326.36793 1.8252243 - 680 13.358243 -3226.8034 977.21534 -4204.0187 1215.3088 0 862.3869 151662.05 -157943.76 -538.09214 17991.009 218.7028 326.90984 1.8513045 - 700 13.774714 -3267.0358 979.72611 -4246.7619 1229.2873 0 878.80049 151588.58 -157943.43 -526.4724 17765.058 219.26471 327.74412 1.86738 - 720 14.198356 -3275.0063 987.91851 -4262.9248 1260.2342 0 905.19546 151515.01 -157943.36 -285.51035 17544.004 221.09819 330.48021 1.8901628 - 740 14.624448 -3298.9204 992.679 -4291.5994 1283.7665 0 917.78414 151449.24 -157942.39 351.98558 17329.448 222.1636 332.09658 1.843264 - 760 15.05056 -3316.7113 1010.6458 -4327.3571 1296.6728 0 951.2091 151368.47 -157943.71 419.51796 17123.095 226.18459 338.07068 1.9518407 - 780 15.504961 -3294.5707 1053.9493 -4348.52 1300.722 0 975.60682 151317.15 -157942 1040.7668 16927.715 235.87602 352.49204 2.1793007 - 800 15.933704 -3363.0539 987.22337 -4350.2773 1325.1641 0 1013.664 151255.26 -157944.36 1462.6199 16747.7 220.94262 330.24432 1.8985721 - 820 16.364414 -3437.2117 980.5397 -4417.7514 1350.8684 0 1029.953 151144.46 -157943.03 817.95684 16584.026 219.4468 327.9943 1.9129039 - 840 16.799625 -3465.5868 981.23685 -4446.8236 1388.7125 0 1043.4314 151066.43 -157945.4 1366.0731 16434.707 219.60282 328.17006 2.0308095 - 860 17.241996 -3460.2301 1020.3681 -4480.5981 1418.4709 0 1090.9207 150954.21 -157944.2 1450.0443 16300.524 228.36046 341.31823 2.0218282 - 880 17.688347 -3499.5491 994.43799 -4493.9871 1444.4283 0 1113.276 150893.43 -157945.12 2227.6739 16183.439 222.55726 332.59403 2.0408296 - 900 18.136371 -3526.9176 952.87144 -4479.789 1443.8422 0 1118.5107 150902.72 -157944.87 2220.1643 16085.505 213.25458 318.69359 1.9574553 - 920 18.599828 -3545.2479 976.95271 -4522.2006 1443.4309 0 1118.3924 150859.69 -157943.71 2107.6215 16006.466 218.64402 326.75181 1.9926282 - 940 19.064528 -3560.4406 994.62379 -4555.0644 1431.3624 0 1098.4902 150860.38 -157945.3 1495.9356 15944.46 222.59885 332.62316 2.0953461 - 960 19.529192 -3590.569 964.78915 -4555.3582 1431.9284 0 1092.1793 150866.87 -157946.34 1559.1687 15897.003 215.92179 322.6406 2.0442546 - 980 19.991661 -3599.6592 986.56344 -4586.2227 1435.7543 0 1034.8682 150889.35 -157946.2 679.01087 15862.242 220.79492 330.01359 1.9307016 - 1000 20.427668 -3634.9266 939.78172 -4574.7083 1424.4834 0 1022.664 150924.73 -157946.59 733.04572 15834.345 210.32508 314.30018 1.9584145 - 1020 20.873712 -3669.298 934.76265 -4604.0606 1452.3 0 1016.3445 150873.46 -157946.16 143.60284 15811.749 209.2018 312.55492 2.0808526 - 1040 21.319204 -3682.4175 935.86127 -4618.2788 1447.0344 0 1035.4526 150844.58 -157945.34 515.93558 15792.261 209.44767 312.98247 1.9790896 - 1060 21.766855 -3704.0833 901.03929 -4605.1226 1476.4857 0 1067.779 150794.42 -157943.8 1092.0636 15777.267 201.65444 301.3325 1.8948719 - 1080 22.214459 -3699.4923 921.66268 -4621.155 1475.7351 0 1079.7576 150767.2 -157943.85 1003.4205 15769.569 206.27 308.27973 1.8458618 - 1100 22.662445 -3667.6761 957.47147 -4625.1476 1507.2355 0 1102.9252 150708.15 -157943.46 927.20789 15768.898 214.28408 320.17339 2.0742837 - 1120 23.085055 -3668.1399 935.38917 -4603.5291 1507.3367 0 1080.9826 150753.9 -157945.75 810.87137 15775.175 209.34202 312.79082 2.0279075 - 1140 23.534417 -3710.7149 937.22068 -4647.9356 1499.5413 0 1020.4759 150776.54 -157944.49 -138.27816 15786.277 209.75191 313.34734 2.1346658 - 1160 23.985544 -3711.7493 900.74897 -4612.4983 1430.3269 0 990.84122 150911.11 -157944.78 8.4592568 15798.538 201.58947 301.24561 1.8661211 - 1180 24.439474 -3729.7115 928.82825 -4658.5398 1435.7711 0 937.43508 150913.97 -157945.72 -905.33202 15809.125 207.87367 310.65722 1.8872897 - 1200 24.895124 -3738.2838 909.79315 -4648.077 1436.4199 0 938.10918 150922.8 -157945.41 -1112.9968 15812.511 203.61357 304.28121 1.8714711 - 1220 25.352201 -3757.8302 907.08742 -4664.9176 1424.1514 0 930.13653 150924.86 -157944.06 -1078.0621 15807.893 203.00803 303.40134 1.8521625 - 1240 25.780748 -3778.5355 905.88168 -4684.4171 1453.9568 0 959.37689 150846.21 -157943.96 -975.25032 15795.393 202.73818 303.00695 1.778808 - 1260 26.238145 -3773.7584 879.94641 -4653.7048 1473.5812 0 1002.67 150815.41 -157945.36 -360.58922 15776.466 196.93381 294.2433 1.9174557 - 1280 26.696751 -3755.4956 904.13603 -4659.6316 1493.7103 0 1017.8327 150773.94 -157945.12 -256.88128 15755.525 202.3475 302.35592 1.9294965 - 1300 27.158244 -3754.9246 903.51795 -4658.4425 1498.1329 0 1006.1786 150782.15 -157944.9 -455.2258 15732.436 202.20917 302.19365 1.8353806 - 1320 27.619539 -3758.1232 913.25769 -4671.3808 1500.2049 0 1032.0703 150739.71 -157943.37 -251.62277 15706.775 204.38895 305.38485 1.9968111 - 1340 28.079132 -3784.7481 937.61449 -4722.3626 1505.7439 0 993.46365 150723.27 -157944.84 -853.9871 15680.38 209.84005 313.60153 1.8911101 - 1360 28.514251 -3808.7787 864.89279 -4673.6715 1475.0618 0 1009.2569 150785.65 -157943.64 -331.64382 15650.208 193.56478 289.20988 1.8929896 - 1380 28.975972 -3798.7281 892.2622 -4690.9903 1465.561 0 993.58051 150793.83 -157943.96 -567.64508 15617.156 199.69011 298.39786 1.8757635 - 1400 29.439238 -3807.9228 893.51775 -4701.4406 1459.3875 0 1000.4434 150784.38 -157945.65 -456.80001 15580.856 199.97111 298.79789 1.925086 - 1420 29.904427 -3818.6783 890.66153 -4709.3398 1515.8208 0 1064.6851 150655.36 -157945.21 450.86768 15542.76 199.33188 297.83132 1.927452 - 1440 30.368352 -3822.016 910.79285 -4732.8089 1539.2325 0 1076.0339 150597.99 -157946.07 429.02044 15506.302 203.83731 304.53724 2.0216852 - 1460 30.835555 -3821.2117 931.47963 -4752.6914 1540.1582 0 1089.9477 150561.76 -157944.55 645.54716 15472.89 208.46705 311.56653 1.8487206 - 1480 31.306455 -3838.255 920.25737 -4758.5124 1546.6509 0 1107.4468 150533.86 -157946.47 556.76352 15443.298 205.95549 307.74395 1.9637305 - 1500 31.747528 -3839.4323 942.18813 -4781.6204 1557.1836 0 1105.7209 150502.68 -157947.21 535.34633 15417.723 210.86364 315.07463 2.0384198 - 1520 32.218974 -3827.551 925.42642 -4752.9774 1555.4578 0 1097.174 150540.89 -157946.5 680.16246 15396 207.11233 309.42351 2.0793499 - 1540 32.691924 -3836.1802 885.40721 -4721.5874 1558.3851 0 1144.6478 150521.13 -157945.75 1216.5367 15378.972 198.15595 296.02524 2.015983 - 1560 33.164075 -3830.4342 955.31807 -4785.7523 1574.0464 0 1105.7294 150481.06 -157946.59 169.17645 15369.126 213.80214 319.4694 2.0400237 - 1580 33.636497 -3808.4082 948.31996 -4756.7281 1556.8058 0 1079.1205 150552.4 -157945.06 603.87966 15363.124 212.23595 317.13706 2.0112224 - 1600 34.111529 -3835.9681 925.63461 -4761.6027 1575.0508 0 1091.3896 150517.16 -157945.2 356.94873 15359.871 207.15893 309.60148 1.8514712 - 1620 34.558112 -3865.8357 866.45292 -4732.2886 1577.3357 0 1137.1716 150497.63 -157944.43 945.81112 15359.844 193.91394 289.72922 1.8926829 - 1640 35.029171 -3849.5025 884.49282 -4733.9954 1547.0606 0 1101.4292 150561.92 -157944.41 703.96326 15365.598 197.95131 295.76038 1.913597 - 1660 35.495665 -3861.3162 906.62112 -4767.9373 1547.2773 0 1074.8986 150555.48 -157945.6 46.512723 15375.298 202.90367 303.1667 1.9573677 - 1680 35.959871 -3857.7679 907.8657 -4765.6336 1547.7327 0 1089.3299 150543.52 -157946.22 383.48079 15386.165 203.18221 303.5736 2.0202069 - 1700 36.428885 -3869.0902 891.82145 -4760.9117 1512.1728 0 1012.6239 150658.31 -157944.02 -488.95961 15397.869 199.59147 298.24425 1.8990607 - 1720 36.903833 -3870.4685 893.82411 -4764.2926 1485.7646 0 989.27762 150706.25 -157945.59 -542.70653 15406.338 200.03967 298.80302 2.1113341 - 1740 37.380529 -3847.3408 893.93384 -4741.2746 1509.8117 0 1031.6641 150663.04 -157945.79 -307.1162 15410.521 200.06423 298.90093 2.0090208 - 1760 37.827319 -3840.438 868.84851 -4709.2865 1474.404 0 1018.599 150744.2 -157946.49 -276.44721 15412.838 194.45008 290.51398 1.9203414 - 1780 38.297568 -3842.0322 910.50606 -4752.5383 1494.2187 0 1002.3762 150696.05 -157945.18 -585.57252 15412.983 203.77313 304.47127 1.9624414 - 1800 38.76671 -3861.9431 881.98228 -4743.9254 1471.6721 0 978.01808 150752.55 -157946.17 -711.07254 15409.636 197.38944 294.90206 1.9749925 - 1820 39.233968 -3890.8613 856.10452 -4746.9658 1505.1405 0 991.9875 150701.72 -157945.82 -509.17282 15401.428 191.59795 286.24213 1.9311068 - 1840 39.704207 -3860.2881 907.57785 -4767.866 1492.5264 0 999.80677 150685.45 -157945.65 -697.50098 15387.414 203.11779 303.52338 1.9123566 - 1860 40.174673 -3879.0681 938.58496 -4817.653 1532.9628 0 1046.6919 150550.41 -157947.72 -311.83188 15369.15 210.05724 313.84514 2.0580305 - 1880 40.646746 -3871.1182 925.64972 -4796.7679 1531.6363 0 1064.5321 150553.96 -157946.9 136.0161 15350.638 207.16231 309.48972 2.0957912 - 1900 41.120691 -3868.9005 949.1652 -4818.0657 1593.1686 0 1150.4095 150384.01 -157945.65 753.94006 15333.301 212.42512 317.39691 2.0615952 - 1920 41.59464 -3868.6343 954.03473 -4822.669 1610.5603 0 1192.2159 150320.88 -157946.33 1209.5547 15321.106 213.51493 319.06152 2.011006 - 1940 42.037294 -3884.0548 926.13369 -4810.1885 1595.5448 0 1167.6153 150372.25 -157945.6 1289.8018 15318.433 207.27062 309.70304 1.9619634 - 1960 42.507917 -3889.403 953.52537 -4842.9284 1598.8799 0 1116.9498 150388.89 -157947.65 327.93587 15323.804 213.40093 318.9112 1.9579466 - 1980 42.973861 -3911.0951 911.40927 -4822.5043 1553.4244 0 1085.4519 150485.64 -157947.02 169.14591 15332.113 203.97527 304.77814 1.9637281 - 2000 43.43889 -3892.0279 902.31728 -4794.3452 1534.2125 0 1088.703 150530.25 -157947.51 473.37009 15341.654 201.94046 301.71557 1.9929295 -Loop time of 43.4389 on 4 procs for 2000 steps with 2500 atoms - -Pair time (%) = 30.8131 (70.9343) -Bond time (%) = 0.0167851 (0.0386406) -Kspce time (%) = 2.78529 (6.41196) -Neigh time (%) = 2.7229 (6.26835) -Comm time (%) = 2.36382 (5.4417) -Outpt time (%) = 0.00704503 (0.0162182) -Other time (%) = 4.72998 (10.8888) - -Nlocal: 625 ave 641 max 600 min -Histogram: 1 0 0 0 0 0 0 2 0 1 -Nghost: 13465.2 ave 13518 max 13362 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Neighs: 585334 ave 608376 max 546210 min -Histogram: 1 0 0 0 0 0 1 0 1 1 - -Total # of neighbors = 2341334 -Ave neighs/atom = 936.534 -Ave special neighs/atom = 4 -Neighbor list builds = 100 -Dangerous builds = 7 - diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 deleted file mode 100644 index 5180a5ff69..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.1 +++ /dev/null @@ -1,236 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -comm_modify vel yes -compute TATOM ATOMS temp/com -compute TEMP all temp/drude - -fix DTDIR all drude/transform/direct -fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix_modify RIGID temp TATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395) -fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 1 100.0 -fix DTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 3375 1000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 24.8361 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 1.5779378 3742.6839 5338.7884 -1596.1045 567.30749 0 662.23765 155098.36 -157924.01 31679.424 13979.574 1194.8318 1690.2246 201.65659 - 40 3.2595179 2752.8331 4407.7651 -1654.932 793.00135 0 870.33079 154593.76 -157912.03 27394.571 14278.56 986.46688 1450.7477 55.932382 - 60 4.9160559 1995.591 3982.0372 -1986.4462 660.67737 0 750.60932 154536.67 -157934.4 22230.527 14691.401 891.1881 1315.7324 40.317107 - 80 6.5368109 1376.4607 3451.5429 -2075.0822 617.73899 0 606.3673 154625.69 -157924.88 17342.36 15201.343 772.46238 1147.1933 21.455584 - 100 8.1206679 885.61474 3037.6308 -2152.0161 536.23281 0 448.92334 154793.04 -157930.22 13263.15 15783.251 679.82802 1011.6854 14.7536 - 120 9.6622779 487.58833 2926.9844 -2439.396 534.45257 0 332.92672 154624.58 -157931.35 8680.1072 16409.225 655.06511 977.0118 9.8615914 - 140 11.151044 159.92993 2531.0941 -2371.1641 507.26614 0 248.61605 154802.7 -157929.75 6399.7614 17052.819 566.46405 845.55948 7.1402545 - 160 12.594065 -100.92554 2408.1685 -2509.0941 490.99513 0 134.36067 154800.59 -157935.04 3836.8939 17698.15 538.95306 805.19219 5.3968881 - 180 13.99897 -313.40437 2221.7416 -2535.1459 469.97779 0 75.805558 154853.24 -157934.17 1959.0151 18334.826 497.23032 743.14066 4.4151864 - 200 15.366489 -490.94535 2067.2605 -2558.2059 455.16264 0 77.545085 154841.14 -157932.06 1193.2843 18956.449 462.65715 691.7234 3.5993432 - 220 16.600555 -642.90899 1962.7268 -2605.6358 481.409 0 64.82886 154779.27 -157931.14 257.97318 19559.017 439.26229 657.06726 2.7738353 - 240 17.905356 -770.44499 1795.759 -2566.204 467.25833 0 68.82314 154829.98 -157932.26 19.366424 20139.417 401.89456 601.24562 2.3886434 - 260 19.179106 -878.63388 1752.9497 -2631.5836 476.38325 0 71.933328 154747.16 -157927.06 -779.27927 20696.165 392.31375 587.06527 2.0260796 - 280 20.338816 -971.86313 1649.5511 -2621.4143 473.83718 0 58.460942 154779.6 -157933.32 -1008.6839 21226.44 369.17293 552.5314 1.7176302 - 300 21.569212 -1057.5245 1580.9766 -2638.5012 480.33124 0 92.042617 154721.84 -157932.72 -1273.0871 21728.981 353.82581 529.63244 1.5049172 - 320 22.749114 -1132.8131 1507.0527 -2639.8658 477.51281 0 107.39942 154707.48 -157932.26 -1098.1682 22203.702 337.28149 504.90539 1.3591193 - 340 23.866651 -1199.4814 1495.1233 -2694.6047 479.99745 0 106.51864 154656.08 -157937.2 -1429.2857 22652.428 334.61166 500.95977 1.2462004 - 360 25.082959 -1264.8469 1440.8985 -2705.7454 491.71868 0 107.29672 154624.8 -157929.57 -1584.3973 23073.056 322.47604 482.79111 1.2009575 - 380 26.115491 -1323.6479 1376.047 -2699.695 497.4857 0 130.64748 154603.75 -157931.58 -1822.0261 23465.375 307.96215 461.10877 1.0530068 - 400 27.098619 -1373.3921 1374.977 -2748.3691 504.29487 0 124.46131 154555.55 -157932.67 -2021.5919 23828.229 307.72267 460.78429 0.98399317 - 420 28.070089 -1426.0355 1375.3813 -2801.4168 515.478 0 142.00079 154473.71 -157932.61 -2208.8244 24160.02 307.81316 460.97813 0.86759754 - 440 29.088747 -1476.2448 1329.2669 -2805.5117 535.72651 0 196.6858 154393.5 -157931.42 -1618.3009 24460.675 297.49266 445.47247 0.93805929 - 460 30.039555 -1527.7744 1320.4118 -2848.1861 568.66085 0 263.35802 154252.43 -157932.64 -1494.5444 24734.828 295.51087 442.54962 0.84234766 - 480 30.98472 -1576.2009 1300.9323 -2877.1332 594.86236 0 314.31593 154144.87 -157931.19 -1089.6762 24985.934 291.15132 436.02273 0.82622001 - 500 31.921181 -1626.4788 1317.6697 -2944.1486 623.62396 0 334.61944 154026.32 -157928.71 -1168.0859 25218.234 294.89719 441.63818 0.82542904 - 520 32.850868 -1678.487 1262.6568 -2941.1438 633.47682 0 363.44379 153992.91 -157930.98 -1163.3304 25431.978 282.58518 423.21273 0.76490406 - 540 33.831238 -1726.1374 1271.5003 -2997.6376 640.74261 0 345.52688 153948.98 -157932.89 -1537.3705 25626.826 284.56437 426.19842 0.72713952 - 560 34.751061 -1771.2597 1269.233 -3040.4927 644.30805 0 317.8435 153929.28 -157931.92 -1722.5181 25799.253 284.05695 425.41542 0.77189915 - 580 35.665466 -1815.0265 1246.413 -3061.4395 683.24088 0 371.72686 153815.69 -157932.1 -1494.5382 25947.498 278.94979 417.73291 0.82565978 - 600 36.573731 -1858.3541 1196.3137 -3054.6678 696.06741 0 437.52527 153744.09 -157932.35 -954.95797 26075.526 267.73745 400.95599 0.76490653 - 620 37.479106 -1899.6548 1179.8195 -3079.4743 696.68256 0 400.17078 153755.86 -157932.18 -1545.546 26187.542 264.04602 395.42296 0.76404516 - 640 38.439799 -1936.5953 1175.0129 -3111.6082 690.67817 0 392.53009 153736.67 -157931.49 -1651.1722 26278.598 262.97029 393.82361 0.73771389 - 660 39.342719 -1974.4946 1176.582 -3151.0766 687.10898 0 368.78109 153725.56 -157932.53 -1642.1352 26346.954 263.32147 394.35652 0.72471807 - 680 40.233007 -2011.9427 1170.7634 -3182.7062 704.7553 0 376.83243 153670.03 -157934.32 -1891.1355 26391.697 262.01926 392.39338 0.74699214 - 700 41.124436 -2051.0351 1135.0688 -3186.1039 725.49013 0 408.02789 153612.64 -157932.26 -1554.558 26411.443 254.03072 380.39243 0.79925352 - 720 42.014817 -2087.2728 1127.2712 -3214.544 747.73788 0 483.80639 153486.98 -157933.07 -1246.9189 26409.313 252.28561 377.77086 0.81053421 - 740 42.908141 -2122.8783 1145.0602 -3267.9385 791.69089 0 545.96341 153327.46 -157933.05 -1064.8488 26390.224 256.26683 383.71741 0.85313379 - 760 43.799068 -2155.8658 1189.0654 -3344.9312 789.63603 0 492.27945 153309.89 -157936.74 -1502.4138 26356.52 266.11528 398.4847 0.84422302 - 780 44.690825 -2197.1759 1166.0016 -3363.1774 813.89866 0 521.14986 153239.56 -157937.79 -1316.1431 26304.488 260.95354 390.75511 0.82849551 - 800 45.65434 -2236.6034 1147.1342 -3383.7376 858.77647 0 581.50775 153111.46 -157935.49 -1059.9568 26235.547 256.73099 384.3699 0.93971538 - 820 46.655089 -2273.5686 1128.3309 -3401.8996 876.66305 0 635.8842 153020.42 -157934.87 -522.03009 26154.47 252.52277 378.09253 0.87820184 - 840 47.581215 -2310.5392 1107.1453 -3417.6845 906.73 0 663.59923 152946.29 -157934.31 -660.73299 26066.561 247.78139 370.96848 0.9116362 - 860 48.461532 -2342.7319 1130.0857 -3472.8176 942.10066 0 680.8635 152839.09 -157934.87 -541.95751 25971.767 252.91551 378.61448 1.0117334 - 880 49.348792 -2377.0856 1100.1359 -3477.2215 941.37588 0 700.77054 152814.73 -157934.1 -443.18233 25871.504 246.21267 368.56741 1.0107473 - 900 50.240716 -2408.6694 1120.4615 -3529.131 953.77939 0 683.49952 152768.93 -157935.34 -805.27426 25765.603 250.76159 375.35036 1.0825367 - 920 51.130132 -2442.8312 1111.7289 -3554.56 950.77289 0 674.01395 152754.6 -157933.95 -905.29746 25651.192 248.80721 372.46424 0.9955159 - 940 52.02236 -2475.7651 1083.1001 -3558.8652 929.08218 0 652.94438 152792.16 -157933.05 -788.57962 25527.175 242.40003 362.8243 1.0666862 - 960 52.924057 -2508.9913 1065.8755 -3574.8668 958.92048 0 698.81111 152699.64 -157932.24 -628.47136 25394.225 238.54512 356.97396 1.2103698 - 980 53.828788 -2536.4577 1080.5323 -3616.99 965.47688 0 709.51639 152642.64 -157934.62 -711.96055 25254.689 241.82535 361.89287 1.2066617 - 1000 54.736123 -2567.3495 1049.6524 -3617.0019 961.00327 0 711.26219 152645.74 -157935.01 -767.44539 25108.887 234.91437 351.52221 1.2288643 - 1020 55.707224 -2595.1206 1073.4918 -3668.6124 974.79134 0 682.20149 152609.52 -157935.12 -1086.5823 24955.503 240.24966 359.53972 1.1890491 - 1040 56.677394 -2626.5258 1072.5969 -3699.1227 1013.3934 0 711.73335 152511.92 -157936.17 -993.59976 24792.452 240.04939 359.23966 1.1887504 - 1060 57.582305 -2655.4118 1059.0687 -3714.4806 1011.7018 0 747.43846 152460.24 -157933.86 -555.51961 24621.133 237.02176 354.6316 1.3280226 - 1080 58.451085 -2684.3286 1093.9034 -3778.232 1041.5624 0 765.98574 152348.29 -157934.07 -993.29607 24444.559 244.81782 366.39031 1.183205 - 1100 59.320593 -2716.1558 1073.5935 -3789.7493 1046.6309 0 741.4524 152358.32 -157936.15 -1031.9439 24260.537 240.27243 359.559 1.2187426 - 1120 60.197434 -2748.4358 1043.9493 -3792.3851 1050.7685 0 732.61894 152361.65 -157937.42 -1173.2273 24068.431 233.638 349.62448 1.1977845 - 1140 61.088693 -2777.1545 1036.6106 -3813.7651 1060.884 0 757.21086 152307.36 -157939.22 -1043.4335 23867.228 231.99557 347.17994 1.1628589 - 1160 62.010573 -2805.5456 1027.0164 -3832.5621 1057.9262 0 777.84714 152269.56 -157937.89 -729.25379 23659.194 229.84839 343.97766 1.1301417 - 1180 62.973114 -2832.7144 1030.8608 -3863.5752 1084.2376 0 767.80175 152221.94 -157937.56 -1365.8515 23446.354 230.70875 345.24169 1.1814637 - 1200 63.943778 -2860.0062 1032.0824 -3892.0886 1078.2587 0 781.38106 152185.86 -157937.59 -1050.1069 23225.033 230.98216 345.65138 1.1817665 - 1220 64.923382 -2887.3006 1026.4756 -3913.7762 1073.1543 0 809.51178 152141.13 -157937.57 -956.1976 22997.996 229.72734 343.81693 1.0887098 - 1240 65.912183 -2912.0696 1020.0729 -3932.1425 1095.3889 0 826.297 152085.57 -157939.4 -534.84968 22767.897 228.2944 341.63565 1.15531 - 1260 66.908861 -2938.0025 1009.7902 -3947.7927 1120.1948 0 846.76965 152025.28 -157940.04 -581.84084 22538.229 225.99312 338.22714 1.0731061 - 1280 67.970707 -2960.3724 1046.6347 -4007.0071 1144.3297 0 866.43256 151921.62 -157939.39 -368.35961 22310.088 234.239 350.59018 1.0681573 - 1300 68.984941 -2983.8905 1039.0599 -4022.9504 1162.4788 0 878.40157 151876.66 -157940.49 -408.4644 22085.613 232.54373 348.07145 1.0232144 - 1320 70.043952 -3009.5808 969.8918 -3979.4726 1186.5907 0 935.08613 151836.22 -157937.36 431.8242 21865.457 217.06378 324.88371 0.98977725 - 1340 71.117119 -3028.1057 1016.1027 -4044.2084 1215.7197 0 933.65661 151744.63 -157938.22 -118.90908 21653.612 227.40587 340.39676 0.96927182 - 1360 72.19871 -3048.8293 986.21586 -4035.0452 1231.0917 0 974.10814 151697.47 -157937.72 485.3122 21448.458 220.71713 330.39668 0.91660237 - 1380 73.289545 -3067.6975 1046.3647 -4114.0622 1252.358 0 948.20869 151626.66 -157941.29 -131.77945 21251.912 234.17856 350.55699 0.95332826 - 1400 74.389534 -3091.6437 1003.804 -4095.4478 1223.2343 0 914.21639 151708.69 -157941.59 -228.59592 21060.319 224.6534 336.27611 0.95868112 - 1420 75.496459 -3117.9845 1017.2871 -4135.2716 1252.8701 0 934.95412 151617.13 -157940.22 -328.62774 20872.161 227.67095 340.80959 0.93833238 - 1440 76.611495 -3137.2342 990.73612 -4127.9703 1224.5861 0 925.81135 151661.05 -157939.42 -23.294916 20687.614 221.72878 331.93708 0.86871384 - 1460 77.73649 -3159.4947 1040.535 -4200.0297 1218.936 0 881.92261 151636.87 -157937.75 -581.29505 20507.346 232.87387 348.59778 0.96029886 - 1480 78.872562 -3183.8273 1037.9432 -4221.7705 1246.5207 0 908.21966 151561.59 -157938.1 -884.42345 20328.04 232.29381 347.7323 0.95226246 - 1500 80.110645 -3206.5826 1008.5663 -4215.1489 1236.8936 0 929.15034 151558.28 -157939.47 -91.502556 20149.349 225.7192 337.88949 0.92718943 - 1520 81.168804 -3228.1152 994.3422 -4222.4574 1276.2214 0 948.25706 151492.45 -157939.39 -262.49453 19974.554 222.53583 333.16141 0.83959152 - 1540 82.328931 -3248.9878 997.70762 -4246.6954 1273.2453 0 944.04689 151475.31 -157939.3 -310.12487 19802.717 223.28901 334.28865 0.84316615 - 1560 83.500822 -3268.9264 1001.6639 -4270.5903 1283.2174 0 972.25539 151413.47 -157939.53 -368.92162 19633.499 224.17444 335.57814 0.91870789 - 1580 84.681217 -3289.8506 972.05937 -4261.9099 1290.892 0 995.40503 151394.08 -157942.29 309.3174 19467.313 217.54888 325.64947 0.91261747 - 1600 85.872982 -3306.0485 999.0593 -4305.1078 1336.2852 0 1018.2817 151281.27 -157940.94 78.176324 19307.332 223.59152 334.68976 0.94786237 - 1620 87.166941 -3323.911 1023.7518 -4347.6628 1346.5659 0 1012.0297 151235.76 -157942.02 401.58054 19152.885 229.11774 342.98696 0.92107142 - 1640 88.373719 -3346.3201 1013.0953 -4359.4153 1368.3551 0 1038.3633 151174.74 -157940.87 115.49888 19004.339 226.7328 339.39185 0.96123977 - 1660 89.588199 -3366.6764 980.18808 -4346.8645 1385.5623 0 1066.3348 151143.21 -157941.97 785.51107 18860.969 219.3681 328.38652 0.89253119 - 1680 90.812635 -3382.4343 999.75094 -4382.1852 1367.9173 0 1045.8848 151142.33 -157938.32 549.73441 18726.008 223.74631 334.953 0.88544944 - 1700 92.044767 -3400.8462 996.00209 -4396.8483 1351.6629 0 1019.0394 151174.27 -157941.83 32.327852 18598.28 222.90731 333.67893 0.91827006 - 1720 93.284649 -3418.3313 989.38116 -4407.7125 1347.9882 0 1026.3475 151161.41 -157943.46 700.69172 18474.978 221.42553 331.45637 0.92100955 - 1740 94.538928 -3435.1347 964.16624 -4399.301 1357.6456 0 1051.1466 151135.74 -157943.84 477.68306 18358.2 215.78238 322.997 0.92157841 - 1760 95.90276 -3452.4681 996.08241 -4448.5506 1365.9896 0 1001.3994 151128.36 -157944.3 -77.655143 18246.618 222.92529 333.72093 0.88815023 - 1780 97.200704 -3470.0186 947.16368 -4417.1823 1357.1769 0 1006.9477 151162.27 -157943.57 100.19368 18137.3 211.97718 317.3159 0.87577473 - 1800 98.461648 -3484.6818 988.75293 -4473.4348 1367.5971 0 995.1924 151106.14 -157942.36 -208.37477 18030.204 221.28494 331.23294 0.94635825 - 1820 99.729642 -3503.5324 959.4974 -4463.0298 1386.9033 0 1035.1867 151057.26 -157942.38 196.09637 17924.392 214.73749 321.44422 0.89454363 - 1840 101.00392 -3518.4137 985.10207 -4503.5157 1425.227 0 1062.1927 150951.14 -157942.08 189.40933 17821.795 220.46787 330.02248 0.91769756 - 1860 102.28783 -3531.6076 978.71334 -4510.3209 1447.6145 0 1081.8026 150905.2 -157944.94 369.13672 17723.495 219.03805 327.84302 0.99005655 - 1880 103.57975 -3546.6803 982.10151 -4528.7818 1416.6032 0 1040.8725 150959.42 -157945.68 206.83653 17629.384 219.79633 328.97668 0.9960403 - 1900 104.81168 -3563.7438 961.75306 -4525.4969 1426.2883 0 1055.2567 150936.42 -157943.46 223.06115 17537.856 215.24231 322.15829 0.97986655 - 1920 106.04042 -3579.7815 953.8957 -4533.6772 1420.242 0 1053.3469 150938.67 -157945.93 264.48404 17448.909 213.48382 319.52979 0.96489929 - 1940 107.27692 -3592.4628 995.11883 -4587.5816 1434.5738 0 1036.2736 150885.59 -157944.02 -203.71783 17362.885 222.70964 333.32982 1.0238542 - 1960 108.52049 -3607.1225 959.8186 -4566.9411 1454.811 0 1091.6157 150830.59 -157943.96 412.09226 17278.194 214.80937 321.46995 1.0586113 - 1980 109.76987 -3621.5836 950.82575 -4572.4094 1481.3655 0 1148.5036 150742.3 -157944.58 1156.6083 17197.362 212.79675 318.42806 1.1085537 - 2000 111.02457 -3632.4321 939.77229 -4572.2044 1484.3457 0 1154.0077 150733.65 -157944.21 1008.3019 17124.028 210.32297 314.7467 1.0548599 -Loop time of 111.025 on 1 procs for 2000 steps with 2500 atoms - -Pair time (%) = 87.5509 (78.8572) -Bond time (%) = 0.0493031 (0.0444073) -Kspce time (%) = 3.35179 (3.01896) -Neigh time (%) = 9.36055 (8.43106) -Comm time (%) = 0.69479 (0.625798) -Outpt time (%) = 0.0108259 (0.00975088) -Other time (%) = 10.0064 (9.01281) - -Nlocal: 2500 ave 2500 max 2500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 20348 ave 20348 max 20348 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.09326e+06 ave 2.09326e+06 max 2.09326e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2093261 -Ave neighs/atom = 837.304 -Ave special neighs/atom = 4 -Neighbor list builds = 120 -Dangerous builds = 16 - diff --git a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 b/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 deleted file mode 100644 index eb91fb883c..0000000000 --- a/examples/USER/drude/swm4-ndp/log.swm4-ndp.nh.8Jul15.linux.4 +++ /dev/null @@ -1,236 +0,0 @@ -LAMMPS (8 Jul 2015) -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-3 - -read_data data.swm4-ndp - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2500 atoms - scanning bonds ... - 1 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 2000 bonds - reading angles ... - 500 angles - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 3 = max # of 1-4 neighbors - 4 = max # of special neighbors - -pair_coeff 1 1 0.210939 3.183950 # ODw ODw -pair_coeff * 2* 0.000000 0.0 - -group ATOMS type 1:3 -2000 atoms in group ATOMS -group CORES type 1 -500 atoms in group CORES -group DRUDES type 4 -500 atoms in group DRUDES - -variable TK equal 300.0 -variable TDK equal 1.0 -variable PBAR equal 1.0 - -neighbor 2.0 bin - -timestep 1.0 - -fix DRUDE all drude C N N D - -velocity ATOMS create ${TK} 12345 -velocity ATOMS create 300 12345 -velocity DRUDES create ${TDK} 12345 -velocity DRUDES create 1 12345 - -delete_bonds ATOMS multi -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - 2000 total bonds, 500 turned on, 1500 turned off - 500 total angles, 0 turned on, 500 turned off - 0 total dihedrals, 0 turned on, 0 turned off - 0 total impropers, 0 turned on, 0 turned off - -comm_modify vel yes -compute TATOM ATOMS temp/com -compute TEMP all temp/drude - -fix DTDIR all drude/transform/direct -fix RIGID ATOMS rigid/npt/small molecule temp ${TK} ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 ${TK} 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso ${PBAR} ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 ${PBAR} 500 -fix RIGID ATOMS rigid/npt/small molecule temp 300 300 100 iso 1 1 500 -500 rigid bodies with 2000 atoms - 0.832099 = max distance from body owner to body atom -fix_modify RIGID temp TATOM press thermo_press -WARNING: Temperature for fix modify is not for group all (../fix_rigid_nh_small.cpp:1395) -fix NVT DRUDES nvt temp ${TDK} ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 ${TDK} 100.0 -fix NVT DRUDES nvt temp 1 1 100.0 -fix DTINV all drude/transform/inverse - -thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2] -thermo 20 - -run 2000 -PPPM initialization ... - G vector (1/distance) = 0.217457 - grid = 10 10 10 - stencil order = 5 - estimated absolute RMS force accuracy = 0.197288 - estimated relative force accuracy = 0.000594128 - using double precision FFTs - 3d grid and FFT values/proc = 1500 300 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 4 -New max number of 1-2 to 1-4 neighbors: 4 (+0) -Memory usage per processor = 15.0906 Mbytes -Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] - 0 0 4568.0415 903.41148 3664.63 623.46454 0 2890.2449 157955.66 -157804.74 244591.08 13824 202.18534 295.64644 14.858785 - 20 0.60629702 3742.7991 5338.7966 -1595.9975 567.29055 0 662.23349 155098.48 -157924 31679.046 13979.575 1194.8336 1690.2267 201.65776 - 40 1.2431891 2752.9388 4407.9332 -1654.9944 792.86725 0 870.27523 154593.92 -157912.06 27392.302 14278.564 986.5045 1450.7624 56.079837 - 60 1.875339 1995.9775 3980.851 -1984.8735 660.64216 0 750.43214 154538.47 -157934.42 22242.676 14691.413 890.92262 1315.3403 40.305321 - 80 2.471236 1377.1261 3449.7879 -2072.6618 617.64243 0 605.75693 154628.63 -157924.69 17345.214 15201.397 772.06962 1146.6088 21.44718 - 100 3.0357449 886.38995 3038.4108 -2152.0208 537.89929 0 450.99962 154789.13 -157930.05 13299.227 15783.335 680.00257 1011.6773 15.016231 - 120 3.585844 488.055 2928.1336 -2440.0786 536.23164 0 334.88597 154620.05 -157931.25 8694.3472 16409.509 655.3223 977.40122 9.8538294 - 140 4.117424 160.14918 2538.5116 -2378.3624 509.19396 0 249.89205 154793.34 -157930.79 6363.1137 17053.486 568.1241 847.92526 7.2744139 - 160 4.6321139 -103.57595 2403.1613 -2506.7372 494.69822 0 144.07174 154790.83 -157936.34 4017.2005 17699.095 537.83243 803.44775 5.3901399 - 180 5.126441 -315.61252 2216.7944 -2532.4069 477.29447 0 80.852363 154842.41 -157932.96 1958.1627 18336.716 496.12314 741.4685 4.440167 - 200 5.6090059 -490.61276 2058.9074 -2549.5202 470.23217 0 80.799455 154831.63 -157932.18 1260.1943 18960.132 460.78771 688.92684 3.5878733 - 220 6.0495639 -644.09355 2001.1189 -2645.2125 494.11524 0 53.071997 154741.65 -157934.05 -16.373549 19564.819 447.85452 669.94663 2.7746068 - 240 6.5042329 -773.76581 1911.0759 -2684.8417 491.56501 0 36.579309 154722.88 -157935.86 -773.18555 20144.755 427.70271 639.97688 2.2989541 - 260 6.9512041 -886.818 1719.7038 -2606.5218 462.97731 0 47.595907 154814.45 -157931.55 -696.23419 20696.487 384.87324 575.96351 1.9229602 - 280 7.3921249 -983.57561 1659.2167 -2642.7923 476.06924 0 65.542713 154749.27 -157933.68 -1099.4208 21220.613 371.3361 555.78067 1.7042918 - 300 7.8054619 -1069.4015 1531.598 -2600.9995 487.38132 0 130.06616 154709.03 -157927.47 -548.86446 21717.521 342.77477 513.11788 1.4030219 - 320 8.2272029 -1144.9139 1562.933 -2707.8469 509.00464 0 127.16899 154591.31 -157935.33 -1516.7077 22190.692 349.78761 523.61225 1.4145866 - 340 8.6145689 -1216.4369 1511.7737 -2728.2106 518.42214 0 144.71934 154541.92 -157933.27 -1345.493 22636.556 338.33806 506.55234 1.2328234 - 360 9.0159991 -1279.8637 1435.4044 -2715.2681 525.01973 0 153.83119 154536.21 -157930.33 -1447.797 23056.471 321.24646 480.9789 1.1390786 - 380 9.4004741 -1340.2241 1391.5909 -2731.815 536.93555 0 180.52081 154483.31 -157932.58 -1315.0222 23450.141 311.4409 466.34776 1.004293 - 400 9.7971771 -1398.7544 1401.1636 -2799.918 547.12264 0 190.99461 154394.23 -157932.27 -1686.7786 23818.238 313.5833 469.59825 0.92621346 - 420 10.175245 -1450.5676 1355.0166 -2805.5842 555.43355 0 178.57277 154392.99 -157932.58 -1948.3006 24158.665 303.2555 454.12588 0.90821389 - 440 10.550016 -1501.2755 1336.6037 -2837.8792 573.29095 0 195.76657 154324.78 -157931.72 -1845.698 24470.004 299.13465 447.99648 0.8127319 - 460 10.93798 -1551.1246 1327.3311 -2878.4557 580.57019 0 206.92238 154267.88 -157933.83 -2059.7154 24752.911 297.05944 444.88976 0.80466605 - 480 11.304226 -1597.9166 1280.274 -2878.1906 596.27629 0 247.5201 154210.94 -157932.93 -1714.1239 25006.108 286.52794 429.10945 0.79188456 - 500 11.66949 -1645.4221 1303.9947 -2949.4168 620.22431 0 275.42964 154086.38 -157931.45 -1833.6239 25232.592 291.83668 437.06941 0.78754301 - 520 12.030775 -1692.7733 1261.2365 -2954.0098 639.32812 0 295.13753 154045.85 -157934.32 -1715.0443 25432.412 282.26732 422.73896 0.75950535 - 540 12.389967 -1739.3602 1247.1301 -2986.4903 666.88476 0 341.37591 153937.16 -157931.91 -1556.9492 25607.225 279.11027 418.00746 0.75767537 - 560 12.765452 -1783.4916 1212.3647 -2995.8563 669.09681 0 366.501 153899.16 -157930.62 -1543.0147 25758.368 271.3297 406.37068 0.70509124 - 580 13.122579 -1824.6061 1200.7205 -3025.3267 699.41498 0 409.47507 153794.95 -157929.16 -1053.8519 25887.592 268.72372 402.43012 0.77346975 - 600 13.47702 -1864.0982 1206.4231 -3070.5213 726.9912 0 439.25863 153695.5 -157932.27 -1130.6737 26000.4 269.99996 404.33899 0.78190692 - 620 13.82937 -1902.6883 1167.061 -3069.7493 741.54351 0 453.21801 153667.95 -157932.46 -921.61026 26097.341 261.19065 391.14672 0.7561126 - 640 14.180362 -1941.2814 1168.4808 -3109.7622 758.6291 0 484.81029 153578.39 -157931.59 -1084.6877 26180.233 261.50841 391.64626 0.70968727 - 660 14.527615 -1977.9114 1159.1979 -3137.1094 746.51288 0 452.2958 153598.59 -157934.51 -1424.6628 26247.07 259.43088 388.52145 0.73088365 - 680 14.875155 -2015.8231 1149.125 -3164.9481 730.41157 0 417.95266 153620.83 -157934.15 -1485.3138 26293.983 257.17653 385.144 0.72723522 - 700 15.22063 -2052.4439 1175.9011 -3228.345 735.43016 0 393.72125 153577.95 -157935.44 -1936.2883 26318.916 263.16908 394.10321 0.77446426 - 720 15.565813 -2092.4868 1137.4051 -3229.892 739.27374 0 431.22089 153537.92 -157938.3 -1669.6367 26318.64 254.5536 381.18868 0.77432854 - 740 15.926298 -2128.2671 1117.2535 -3245.5206 763.39303 0 451.2336 153475.75 -157935.89 -1554.5185 26294.984 250.04362 374.42691 0.77695221 - 760 16.273413 -2164.5578 1132.9117 -3297.4695 791.93983 0 493.17297 153351.43 -157934.01 -1464.3621 26250.086 253.54797 379.63211 0.87260304 - 780 16.620524 -2201.7367 1138.2941 -3340.0308 832.89022 0 542.69718 153217.14 -157932.76 -1185.0268 26186.538 254.75255 381.43046 0.88724559 - 800 16.968419 -2236.9734 1127.0464 -3364.0197 849.94855 0 579.03844 153137.36 -157930.36 -957.1991 26107.922 252.23529 377.65702 0.8873688 - 820 17.320858 -2274.0191 1152.6791 -3426.6982 878.53555 0 605.98285 153020.89 -157932.1 -1004.5494 26016.264 257.97196 386.24526 0.90940959 - 840 17.671788 -2312.5555 1157.6702 -3470.2257 915.53242 0 653.69994 152892.11 -157931.56 -793.45868 25912.528 259.08897 387.88866 0.97141875 - 860 18.021136 -2351.0088 1136.5124 -3487.5212 921.37408 0 665.09396 152857.19 -157931.18 -528.38134 25800.163 254.35382 380.78143 0.98986969 - 880 18.370286 -2387.3364 1155.2826 -3542.619 934.02359 0 660.06761 152795.05 -157931.76 -775.58796 25681.702 258.55463 386.99987 1.1470186 - 900 18.737898 -2425.9324 1151.5543 -3577.4867 936.00838 0 670.95003 152749.78 -157934.22 -883.49007 25555.357 257.72021 385.72656 1.1920669 - 920 19.09607 -2461.264 1119.906 -3581.17 931.8496 0 682.4928 152739.5 -157935.01 -890.93067 25420.635 250.63726 375.12148 1.1675653 - 940 19.45002 -2496.7293 1081.4763 -3578.2056 971.61744 0 731.21429 152653.33 -157934.36 -483.6151 25277.795 242.03662 362.20568 1.2144341 - 960 19.805087 -2527.097 1111.841 -3638.938 964.7058 0 704.68407 152623.89 -157932.22 -841.64397 25129.524 248.8323 372.33505 1.3291216 - 980 20.160533 -2560.1354 1096.9132 -3657.0486 954.19645 0 693.42648 152627.51 -157932.19 -949.1276 24974.275 245.49142 367.3853 1.2126954 - 1000 20.518917 -2592.9079 1053.7186 -3646.6266 959.23242 0 684.31399 152644.74 -157934.91 -869.15319 24811.035 235.8244 352.90011 1.2013298 - 1020 20.849072 -2623.091 1066.4493 -3689.5404 998.09604 0 709.32917 152535.4 -157932.37 -881.38225 24640.265 238.67355 357.17132 1.2006706 - 1040 21.194962 -2652.822 1083.618 -3736.44 1011.32 0 727.70427 152458.99 -157934.45 -815.2175 24461.841 242.51594 362.90994 1.2429114 - 1060 21.530151 -2683.6347 1074.3994 -3758.0341 1029.3659 0 763.93884 152381.4 -157932.73 -616.78933 24277.069 240.45279 359.82116 1.235143 - 1080 21.868091 -2715.2991 1094.3032 -3809.6022 1068.1764 0 785.28284 152272.57 -157935.63 -541.23611 24088.232 244.9073 366.48583 1.2604348 - 1100 22.209137 -2747.0371 1066.1644 -3813.2016 1080.2369 0 833.94072 152208.13 -157935.51 -217.98411 23897.246 238.60979 357.0619 1.2283546 - 1120 22.551618 -2774.9066 1084.3361 -3859.2427 1113.055 0 847.43384 152114.69 -157934.42 -77.787494 23707.475 242.67665 363.13214 1.2803322 - 1140 22.899431 -2803.21 1072.4113 -3875.6213 1090.9217 0 807.02034 152161.17 -157934.73 -668.47773 23520.606 240.00786 359.14316 1.2572349 - 1160 23.252016 -2834.8697 1052.5943 -3887.464 1096.5034 0 789.77107 152162.88 -157936.62 -589.78074 23331.777 235.57277 352.55512 1.1369148 - 1180 23.609597 -2863.7817 1031.8109 -3895.5926 1087.1932 0 789.79657 152165.44 -157938.03 -586.94333 23140.391 230.92139 345.60929 1.0837566 - 1200 23.970129 -2891.3631 1042.111 -3933.4741 1093.7082 0 775.83298 152136.1 -157939.12 -1109.7168 22947.229 233.22659 349.07035 1.0726257 - 1220 24.3333 -2919.3393 1043.3795 -3962.7187 1095.6802 0 760.56643 152121.29 -157940.25 -1189.6331 22748.747 233.51046 349.50414 1.0560945 - 1240 24.699158 -2942.4201 1015.5889 -3958.009 1114.7861 0 821.20595 152042.69 -157936.69 -581.49954 22545.116 227.29088 340.1868 1.0444581 - 1260 25.06694 -2965.9906 1011.5209 -3977.5115 1137.3984 0 850.69736 151972.34 -157937.95 -557.09399 22340.759 226.38045 338.85243 0.98374803 - 1280 25.506043 -2989.5484 1016.7798 -4006.3282 1160.9102 0 882.24024 151890.5 -157939.98 -93.844073 22136.859 227.55742 340.60408 1.0089629 - 1300 25.885481 -3011.5964 1043.7628 -4055.3592 1184.2311 0 891.6381 151808.85 -157940.08 -307.32007 21936.757 233.59626 349.6133 1.0504806 - 1320 26.286564 -3035.1132 1037.5333 -4072.6466 1179.597 0 903.59052 151784.33 -157940.16 -91.53774 21739.794 232.20209 347.62923 0.8833997 - 1340 26.707803 -3061.1043 1034.7198 -4095.8241 1231.5568 0 955.77666 151655.57 -157938.72 53.261099 21546.978 231.57242 346.58931 1.0307605 - 1360 27.133179 -3085.252 983.77833 -4069.0303 1230.971 0 968.86383 151669.63 -157938.5 197.66951 21360.266 220.17161 329.49241 1.002352 - 1380 27.554558 -3101.9696 1037.9918 -4139.9614 1216.6215 0 897.01691 151685.79 -157939.39 -392.64446 21180.32 232.3047 347.61632 1.0380526 - 1400 27.956349 -3124.8379 1003.328 -4128.1659 1199.4883 0 863.54306 151748.07 -157939.27 -548.32584 21003.378 224.54686 336.16828 0.85494391 - 1420 28.361482 -3146.8927 1020.9417 -4167.8344 1210.319 0 850.57584 151710.13 -157938.86 -1093.8532 20825.938 228.48885 342.04449 0.9178739 - 1440 28.768238 -3170.6554 993.33274 -4163.9882 1239.5959 0 893.87046 151642.2 -157939.65 -436.10089 20645.122 222.30991 332.79717 0.88336557 - 1460 29.177687 -3191.0873 980.2106 -4171.2979 1257.3639 0 955.42122 151554.27 -157938.35 -139.1763 20465.429 219.37314 328.30589 0.99602014 - 1480 29.586943 -3208.4185 993.92387 -4202.3424 1243.9183 0 936.28667 151555.9 -157938.45 -261.1948 20289.512 222.4422 333.01034 0.85071989 - 1500 29.995233 -3229.0775 1028.0284 -4257.1059 1272.6443 0 960.80911 151449.75 -157940.31 -307.25416 20116.744 230.07487 344.43881 0.88683413 - 1520 30.435761 -3250.8294 998.11977 -4248.9491 1282.1976 0 990.08774 151419.81 -157941.05 64.772936 19947.298 223.38125 334.38841 0.90320757 - 1540 30.853458 -3268.3168 1004.1599 -4272.4768 1299.4164 0 987.20608 151381.91 -157941.01 -80.22578 19782.738 224.73305 336.30685 1.007422 - 1560 31.279241 -3289.0826 966.08591 -4255.1685 1287.1272 0 982.95309 151416.22 -157941.47 198.4371 19622.918 216.21201 323.54353 0.99939162 - 1580 31.708028 -3306.2125 979.26815 -4285.4807 1288.5111 0 952.23769 151415.68 -157941.91 -206.26434 19467.717 219.16222 328.0518 0.90689318 - 1600 32.140092 -3325.1219 984.21128 -4309.3331 1308.258 0 963.95207 151360.81 -157942.35 -284.04656 19314.766 220.2685 329.66568 0.9610293 - 1620 32.5727 -3340.9024 1013.5306 -4354.433 1318.1025 0 944.3489 151325.17 -157942.05 -653.005 19163.698 226.83023 339.47468 1.0097397 - 1640 32.982791 -3360.2312 974.13546 -4334.3667 1312.594 0 986.63361 151308.68 -157942.28 343.78235 19013.496 218.01352 326.28924 0.99083786 - 1660 33.419277 -3375.6484 982.60503 -4358.2535 1345.3148 0 970.47388 151266.28 -157940.32 -374.81541 18867.836 219.90902 329.06869 1.0301828 - 1680 33.858902 -3394.428 981.74052 -4376.1685 1319.3919 0 955.09161 151289.81 -157940.47 -162.3498 18724.14 219.71554 328.81202 0.99514477 - 1700 34.30191 -3412.8462 973.87976 -4386.7259 1341.294 0 965.41854 151248.54 -157941.98 -351.70824 18582.062 217.95629 326.03525 1.1973975 - 1720 34.776698 -3429.9352 986.76909 -4416.7043 1362.6752 0 1013.2358 151149.58 -157942.2 37.299904 18441.349 220.84095 330.4706 1.0534043 - 1740 35.222457 -3446.5561 971.25044 -4417.8065 1381.6012 0 1046.8608 151096.61 -157942.88 336.29665 18304.289 217.36784 325.28479 1.0839935 - 1760 35.644247 -3463.1798 999.75562 -4462.9354 1395.5442 0 1012.1296 151070.28 -157940.88 -252.71902 18172.322 223.74736 334.82695 1.1205298 - 1780 36.095301 -3481.5453 991.5153 -4473.0606 1403.686 0 1029.7008 151037.13 -157943.57 -108.73918 18043.082 221.90316 332.00846 1.1669904 - 1800 36.548801 -3496.9886 965.33662 -4462.3252 1390.3088 0 1050.6761 151040.12 -157943.43 539.62368 17917.488 216.04432 323.23991 1.1447201 - 1820 37.00671 -3510.113 991.32596 -4501.439 1392.0482 0 1034.7898 151015.68 -157943.96 152.36115 17797.781 221.86078 332.04409 1.050451 - 1840 37.465953 -3528.9352 974.95032 -4503.8855 1387.6457 0 1012.5199 151036.63 -157940.68 -250.11127 17681.765 218.19588 326.4633 1.104675 - 1860 37.926741 -3545.3967 970.46573 -4515.8624 1391.3683 0 1035.1551 151000.11 -157942.49 -218.15781 17567.52 217.19222 325.05524 1.0190724 - 1880 38.391252 -3561.7398 933.83134 -4495.5711 1404.458 0 1032.7156 151010.9 -157943.64 -1.9885562 17454.833 208.99337 312.70412 1.1301542 - 1900 38.856336 -3574.6165 984.6503 -4559.2668 1422.0814 0 1060.3245 150900.79 -157942.46 190.15103 17344.24 220.36676 329.66505 1.2027369 - 1920 39.32352 -3589.0687 963.85062 -4552.9193 1427.8662 0 1075.6986 150887.22 -157943.7 506.81653 17237.394 215.71175 322.81523 1.0733524 - 1940 39.79544 -3604.8214 970.89136 -4575.7128 1416.926 0 1037.9197 150913.56 -157944.12 -60.261935 17135.412 217.28748 325.12481 1.144127 - 1960 40.270815 -3620.548 963.48434 -4584.0323 1401.1546 0 1016.5609 150941.43 -157943.17 -388.03612 17035.264 215.62977 322.67138 1.1152888 - 1980 40.749353 -3638.3971 977.90456 -4616.3017 1415.5473 0 1009.486 150904.71 -157946.04 -640.67547 16934.97 218.85705 327.48198 1.1614525 - 2000 41.229238 -3654.2588 957.08437 -4611.3432 1418.1059 0 1031.2688 150883.23 -157943.95 -595.60403 16834.098 214.19745 320.55039 1.0631632 -Loop time of 41.2293 on 4 procs for 2000 steps with 2500 atoms - -Pair time (%) = 23.5391 (57.0932) -Bond time (%) = 0.0153775 (0.0372976) -Kspce time (%) = 3.17798 (7.70806) -Neigh time (%) = 2.51543 (6.10108) -Comm time (%) = 1.6585 (4.02262) -Outpt time (%) = 0.00876421 (0.0212572) -Other time (%) = 10.3141 (25.0165) - -Nlocal: 625 ave 632 max 619 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Nghost: 12577 ave 12644 max 12511 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 532752 ave 581561 max 492708 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 2131009 -Ave neighs/atom = 852.404 -Ave special neighs/atom = 4 -Neighbor list builds = 120 -Dangerous builds = 16 - diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 new file mode 100644 index 0000000000..08cc2f0f5c --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.1 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 new file mode 100644 index 0000000000..08cc2f0f5c --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.lang.g++.4 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Langevin) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 new file mode 100644 index 0000000000..a6807f8ee1 --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.1 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 new file mode 100644 index 0000000000..a6807f8ee1 --- /dev/null +++ b/examples/USER/drude/toluene/log.27Nov18.toluene.nh.g++.4 @@ -0,0 +1,14 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 250 toluene system for drude polarizability example (Nose-Hoover) + +units real +boundary p p p + +atom_style full +bond_style harmonic +angle_style harmonic +dihedral_style opls +improper_style opls +ERROR: Unknown improper style opls (src/force.cpp:634) +Last command: improper_style opls diff --git a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 b/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 deleted file mode 100644 index bc51063341..0000000000 --- a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.1 +++ /dev/null @@ -1,251 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 4.311986 8083.3901 4729.9995 328.37487 3353.3906 1812.5186 685.40417 646.10358 50.083281 804.80656 1305984.8 -1306630.3 16960.287 48631.318 448.67988 116.22125 - 100 8.756623 6206.7865 3683.944 255.75365 2522.8425 977.52675 777.45439 838.58809 68.086914 471.97862 1306097.1 -1306707.9 15657.142 48631.318 380.53159 35.760643 - 150 13.134938 5386.0219 3582.482 248.70976 1803.5399 752.25928 803.04832 643.43249 49.76684 131.97853 1306139.2 -1306716.2 15140.102 48631.318 383.61303 10.880935 - 200 17.508189 4846.4097 3254.3932 225.93257 1592.0166 700.43329 812.26722 657.52279 51.044716 -64.045174 1306160.5 -1306725.7 13844.277 48631.318 351.90677 3.8489009 - 250 21.871676 4473.215 3091.5333 214.6262 1381.6817 688.24707 842.63267 590.45999 48.22798 -214.02425 1306156.6 -1306730.5 8808.7402 48631.318 335.32872 1.8372171 - 300 26.226064 4191.8834 2883.8468 200.2078 1308.0367 734.36657 856.15482 584.87904 47.590787 -343.44615 1306163.4 -1306734.9 3389.3777 48631.318 313.03581 1.3011826 - 350 30.568716 3972.0739 2756.8392 191.39044 1215.2347 664.4688 866.06348 580.13632 48.515297 -378.8729 1306173.3 -1306738.3 8458.1149 48631.318 299.31146 1.1345329 - 400 34.845648 3838.3528 2731.3975 189.62419 1106.9552 684.0318 870.67752 548.93014 44.038787 -460.1537 1306160.4 -1306741 6697.9188 48631.318 296.54405 1.1332149 - 450 39.17477 3731.18 2607.8585 181.04762 1123.3216 719.57572 894.99915 571.99504 47.625227 -537.60494 1306171.9 -1306745.2 2450.4224 48631.318 283.13713 1.0721818 - 500 43.497489 3607.0055 2565.9469 178.13796 1041.0586 717.36452 841.34375 551.39834 45.985413 -542.47313 1306170.9 -1306743.4 3077.1849 48631.318 278.59462 1.0410963 - 550 47.812038 3513.8132 2548.7259 176.94241 965.08736 673.81272 852.38161 522.99297 44.276434 -552.27379 1306171.2 -1306747.4 4659.7275 48631.318 276.70124 1.0757459 - 600 52.124423 3386.9627 2471.0692 171.55118 915.89348 689.99732 833.61298 517.49343 43.023588 -594.96363 1306170.6 -1306743.8 2159.7328 48631.318 268.27854 1.0287605 - 650 56.370068 3374.3191 2413.6719 167.56644 960.64717 703.32428 874.12028 535.41271 43.256032 -617.25815 1306168.6 -1306746.8 1262.4757 48631.318 261.99584 1.0950976 - 700 60.667476 3342.9467 2412.9563 167.51676 929.99042 683.70355 882.22521 527.03932 43.661355 -616.70117 1306161 -1306751 2950.9009 48631.318 261.92814 1.0771869 - 750 64.964696 3327.7938 2414.3547 167.61385 913.43902 695.12778 863.48248 542.99202 46.408369 -639.60076 1306160.7 -1306755.6 1583.0277 48631.318 262.09771 1.0464936 - 800 69.256916 3391.689 2452.2049 170.24155 939.48407 694.2176 892.61592 557.53726 45.495129 -654.56675 1306155.2 -1306751 1232.1671 48631.318 266.20601 1.0640309 - 850 73.527972 3386.8618 2486.6928 172.63584 900.16902 696.7684 880.27643 545.11446 46.474227 -665.90464 1306154.7 -1306757.3 1129.2062 48631.318 269.97945 1.027015 - 900 77.775993 3368.0724 2416.7145 167.77767 951.35789 718.66654 893.18396 537.79136 46.404626 -641.29596 1306152.9 -1306756.3 1673.0743 48631.318 262.34697 1.0597091 - 950 82.028341 3300.4793 2409.5613 167.28107 890.918 728.06888 890.51193 515.08456 44.36547 -671.13741 1306142.3 -1306758.2 1038.6579 48631.318 261.57036 1.0567234 - 1000 86.189789 3333.2955 2452.2486 170.24458 881.04692 699.8414 915.33862 506.83261 41.77374 -665.68264 1306141.6 -1306758.7 467.42142 48631.318 266.19104 1.0987814 - 1050 90.384168 3303.87 2376.9713 165.01854 926.89875 706.12941 930.65844 524.73304 42.644613 -657.19573 1306139.3 -1306759.4 1737.6624 48631.318 258.00246 1.0954432 - 1100 94.549452 3367.668 2454.9154 170.42973 912.75259 715.68494 935.8363 516.52205 43.261761 -671.86101 1306137.9 -1306764.6 961.79199 48631.318 266.492 1.0797548 - 1150 98.65493 3350.0898 2485.3993 172.54604 864.69051 699.23072 933.76405 510.60424 42.381362 -684.53513 1306127.1 -1306763.8 -272.48178 48631.318 269.82496 1.0512421 - 1200 102.82045 3309.6871 2398.9577 166.54492 910.72944 705.58979 934.53183 531.90967 45.872142 -664.58495 1306126.9 -1306769.5 627.31931 48631.318 260.41866 1.0531639 - 1250 106.9899 3304.504 2491.6998 172.98344 812.80426 710.83366 881.33764 494.90045 41.71618 -672.49264 1306123.8 -1306767.3 136.11723 48631.318 270.51026 1.0516137 - 1300 111.16224 3318.9543 2462.0621 170.92588 856.89219 709.17314 932.87209 503.80373 43.426006 -680.2474 1306121.2 -1306773.3 1276.2503 48631.318 267.28591 1.0510113 - 1350 115.27184 3314.8515 2434.8483 169.03659 880.00316 710.91641 922.28347 540.40795 44.753548 -686.09335 1306124.5 -1306776.7 -438.87694 48631.318 264.31236 1.0731666 - 1400 119.44228 3349.0785 2457.7697 170.62788 891.30875 711.28064 936.58607 516.63511 42.396287 -653.09763 1306113.8 -1306776.3 350.79618 48631.318 266.80555 1.0745043 - 1450 123.61267 3364.1486 2459.8741 170.77397 904.27455 696.57265 946.32098 538.55368 44.69075 -652.75091 1306111 -1306780.1 502.47466 48631.318 267.03201 1.0789056 - 1500 127.72962 3341.9369 2454.3302 170.3891 887.60672 726.46979 903.40815 557.73064 47.536125 -667.65025 1306100.7 -1306780.6 -248.0975 48631.318 266.44821 1.044725 - 1550 131.91041 3270.4282 2437.7916 169.24093 832.63655 691.49462 910.83807 523.17366 44.83093 -654.48655 1306100.5 -1306783.7 490.32965 48631.318 264.63652 1.0662604 - 1600 136.0834 3252.0725 2429.6805 168.67782 822.39196 689.68155 898.22828 535.31963 43.84399 -660.93277 1306100.1 -1306783.9 1729.5956 48631.318 263.74523 1.0817172 - 1650 140.26444 3239.748 2442.6258 169.57653 797.12222 671.1832 907.1659 507.03947 43.048028 -648.14001 1306103.3 -1306786.5 970.43988 48631.318 265.15987 1.0708872 - 1700 144.3855 3202.9157 2410.267 167.33006 792.64869 686.40974 882.40791 527.02899 43.819792 -656.82001 1306096 -1306786.2 -107.50166 48631.318 261.64368 1.062837 - 1750 148.56592 3214.6107 2366.3264 164.27953 848.28434 696.38228 915.58636 538.2236 47.852688 -652.7697 1306093.6 -1306790.6 -164.14366 48631.318 256.84519 1.0937744 - 1800 152.74611 3209.5771 2421.4089 168.10357 788.16819 683.61816 869.45802 532.77927 45.708374 -658.39221 1306103.1 -1306788.1 277.61781 48631.318 262.83282 1.1036154 - 1850 156.86567 3146.3973 2362.3333 164.00232 784.064 697.87032 875.8451 523.54452 43.851379 -665.83106 1306101.5 -1306792.7 497.88657 48631.318 256.42683 1.0654271 - 1900 161.0419 3141.5496 2367.1077 164.33378 774.44186 693.39945 878.97447 515.65653 44.619392 -668.11692 1306103.8 -1306793.9 -1427.3998 48631.318 256.94212 1.0727903 - 1950 165.22235 3134.6473 2295.577 159.36784 839.07025 699.62719 905.76937 519.32307 46.109334 -645.08933 1306104.9 -1306791.6 1744.2846 48631.318 249.19694 1.0064565 - 2000 169.4 3146.866 2361.3821 163.93628 785.48386 682.24124 889.6864 534.94877 46.855983 -678.1614 1306104 -1306794.1 699.8735 48631.318 256.32873 1.0559143 -Loop time of 169.4 on 1 procs for 2000 steps with 5500 atoms - -Performance: 0.510 ns/day, 47.056 hours/ns, 11.806 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 107.93 | 107.93 | 107.93 | 0.0 | 63.71 -Bond | 19.76 | 19.76 | 19.76 | 0.0 | 11.66 -Kspace | 34.926 | 34.926 | 34.926 | 0.0 | 20.62 -Neigh | 1.9932 | 1.9932 | 1.9932 | 0.0 | 1.18 -Comm | 0.73555 | 0.73555 | 0.73555 | 0.0 | 0.43 -Output | 0.0065863 | 0.0065863 | 0.0065863 | 0.0 | 0.00 -Modify | 3.9135 | 3.9135 | 3.9135 | 0.0 | 2.31 -Other | | 0.133 | | | 0.08 - -Nlocal: 5500 ave 5500 max 5500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 13219 ave 13219 max 13219 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.33739e+06 ave 1.33739e+06 max 1.33739e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1337388 -Ave neighs/atom = 243.161 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 32 -Dangerous builds = 0 -Total wall time: 0:02:49 diff --git a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 b/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 deleted file mode 100644 index cebe687c11..0000000000 --- a/examples/USER/drude/toluene/log.toluene.lang.11Aug17.linux.4 +++ /dev/null @@ -1,251 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Langevin) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -fix fLANG all langevin/drude ${vTEMP} 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 ${vTEMP_D} 20.0 260514 zero yes -fix fLANG all langevin/drude 260 100.0 200611 1 20.0 260514 zero yes -fix fNPH all nve - -compute cTEMP all temp/drude - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 34263 16000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 1.0658228 8014.6879 4671.7498 324.33095 3342.9381 1798.7991 670.22837 651.99307 50.352024 819.34616 1305984.9 -1306632.7 17255.952 48631.318 442.52888 116.12397 - 100 2.136163 6185.5007 3697.0414 256.66292 2488.4593 974.42931 774.88353 840.46625 66.896007 427.27085 1306105.5 -1306701 15044.739 48631.318 381.93582 35.802658 - 150 3.202647 5418.0644 3628.2714 251.88864 1789.7929 764.02696 804.61034 641.14915 47.995428 108.05084 1306138.9 -1306714.9 15258.194 48631.318 388.65363 10.777816 - 200 4.2728949 4838.4235 3303.8964 229.36927 1534.5271 702.10438 772.85348 625.99718 52.299187 -63.792745 1306166.5 -1306721.4 13487.722 48631.318 357.35337 3.7423617 - 250 5.3275268 4461.2438 3084.8973 214.16551 1376.3465 693.85145 823.23815 599.85313 48.280277 -230.56822 1306167.8 -1306726.1 8779.0061 48631.318 334.59262 1.8620294 - 300 6.3794398 4179.6462 2885.0738 200.29299 1294.5724 739.337 868.84011 555.04912 44.838819 -354.73738 1306171.3 -1306730 4410.8735 48631.318 313.17473 1.2892347 - 350 7.427706 3934.3968 2756.2421 191.34899 1178.1546 666.16877 877.32996 548.99846 45.087026 -404.32209 1306179 -1306734.1 8477.8828 48631.318 299.22663 1.1698531 - 400 8.4820418 3800.4769 2674.8317 185.69716 1125.6452 693.29433 841.29833 579.61438 48.325361 -470.18802 1306170.5 -1306737.2 6265.7532 48631.318 290.39105 1.1303952 - 450 9.528651 3685.28 2616.9074 181.67583 1068.3726 702.68328 886.66644 555.74511 46.160811 -557.70651 1306176.6 -1306741.7 2701.7737 48631.318 284.11064 1.091646 - 500 10.579133 3582.6591 2517.6443 174.78461 1065.0148 701.82101 894.9429 554.06012 46.074357 -570.49878 1306181.8 -1306743.2 3643.7426 48631.318 273.31525 1.0831346 - 550 11.629649 3542.0402 2527.0386 175.4368 1015.0016 688.73877 916.2381 521.69932 44.014375 -580.05437 1306171 -1306746.6 2928.6632 48631.318 274.34257 1.0740018 - 600 12.684143 3507.0443 2519.9749 174.94641 987.06936 711.58734 894.63276 525.57884 42.944226 -603.24423 1306161.2 -1306745.7 2082.9907 48631.318 273.57124 1.0784841 - 650 13.737965 3416.2001 2445.9361 169.80635 970.26394 706.95207 891.76446 540.90369 45.970985 -626.32832 1306160.2 -1306749.2 1912.8783 48631.318 265.5023 1.1021764 - 700 14.777375 3419.7572 2446.117 169.81891 973.64019 664.17579 936.51992 551.67148 45.696531 -634.70926 1306159.6 -1306749.4 2215.7085 48631.318 265.53614 1.0774684 - 750 15.795347 3418.6537 2449.343 170.04287 969.31069 706.12432 899.61553 553.21874 45.793213 -642.75298 1306158.1 -1306750.8 1022.2516 48631.318 265.89304 1.0681488 - 800 16.835794 3385.2449 2465.4963 171.16429 919.74864 692.34918 888.91243 530.24204 45.132243 -638.54787 1306154.6 -1306753 1601.1391 48631.318 267.64361 1.0797553 - 850 17.87536 3397.1124 2426.3129 168.44403 970.79951 717.48898 878.71057 580.26487 46.675101 -646.96926 1306150.9 -1306756.3 1048.7905 48631.318 263.38063 1.0785255 - 900 18.899639 3324.2064 2447.5004 169.91495 876.70599 683.62339 881.77789 531.98758 43.646731 -648.59248 1306144.4 -1306760.2 2221.5859 48631.318 265.69596 1.0608373 - 950 19.938468 3316.6329 2398.6988 166.52695 917.93405 702.84237 885.96473 540.35376 45.671318 -638.80334 1306144.4 -1306762.5 1955.2237 48631.318 260.38167 1.0687233 - 1000 20.973543 3287.4205 2384.191 165.51976 903.22949 705.56988 889.96387 535.23674 44.902139 -661.28175 1306150.4 -1306761.6 90.200683 48631.318 258.81506 1.0477545 - 1050 21.990961 3297.7806 2392.0372 166.06448 905.74339 697.33157 889.75086 537.2395 46.319713 -636.03286 1306135.9 -1306764.8 1893.8234 48631.318 259.67633 1.0344207 - 1100 23.006456 3240.651 2370.2217 164.54996 870.42931 693.87289 897.0846 526.89184 43.778979 -657.83716 1306132.1 -1306765.5 799.62979 48631.318 257.28711 1.0618941 - 1150 24.014558 3232.457 2377.9797 165.08855 854.47728 692.51558 897.77048 520.3269 43.903959 -657.38369 1306126.9 -1306769.6 178.21408 48631.318 258.13876 1.0479172 - 1200 25.010178 3238.4266 2392.0623 166.06622 846.36427 695.98996 887.237 522.01974 42.355716 -660.92843 1306124.7 -1306765 1006.1877 48631.318 259.66037 1.0698925 - 1250 26.01949 3198.3364 2332.7551 161.94888 865.58134 690.81786 897.35028 524.47996 44.421121 -640.92419 1306116.3 -1306766.8 2073.9672 48631.318 253.227 1.0326937 - 1300 27.026911 3237.6809 2386.3739 165.67131 851.30706 672.11785 901.04813 530.2964 44.020263 -655.33033 1306125.7 -1306766.5 579.46013 48631.318 259.05838 1.0374113 - 1350 28.033721 3285.9536 2371.155 164.61476 914.79862 718.12968 928.41764 524.02349 43.89896 -657.10221 1306127.3 -1306769.9 518.88041 48631.318 257.36737 1.0993197 - 1400 29.026742 3272.2173 2391.4158 166.02134 880.80147 712.59883 896.13616 532.95785 45.989768 -658.37495 1306125.6 -1306774.1 961.2067 48631.318 259.5968 1.0557033 - 1450 30.032566 3244.2627 2356.0955 163.56926 888.16727 714.72692 901.18382 534.59787 45.517573 -655.58258 1306124.5 -1306776.8 596.10558 48631.318 255.75173 1.058657 - 1500 31.03878 3244.8598 2408.5382 167.21004 836.32161 695.63105 867.27743 527.37333 44.496971 -648.96393 1306125.2 -1306774.7 443.71088 48631.318 261.45495 1.0648973 - 1550 32.041435 3239.3658 2367.1336 164.33557 872.23223 704.16965 884.5938 544.41685 46.110791 -654.61963 1306124.1 -1306776.5 -446.5562 48631.318 256.96289 1.0409003 - 1600 33.058977 3221.4258 2334.2656 162.05375 887.1602 713.8296 885.80472 533.86753 45.413663 -633.58824 1306119.6 -1306777.8 1527.9489 48631.318 253.36367 1.0817678 - 1650 34.080875 3224.4472 2385.9055 165.63879 838.54168 681.01628 879.88017 536.75983 43.884394 -643.24788 1306114 -1306773.8 1314.2208 48631.318 258.97106 1.1033457 - 1700 35.095047 3178.6575 2352.4294 163.31475 826.2281 700.79494 854.06687 549.39826 46.155483 -662.57181 1306115.2 -1306776.9 -187.36898 48631.318 255.35015 1.0638209 - 1750 36.093828 3219.473 2371.9421 164.6694 847.53093 699.44953 891.26068 541.91687 45.714235 -679.13432 1306120.3 -1306771.9 -618.32924 48631.318 257.48034 1.0512601 - 1800 37.110101 3202.0094 2371.8909 164.66585 830.11842 698.44522 858.38216 550.82008 46.315893 -667.77838 1306119.2 -1306775.3 -9.4963278 48631.318 257.46873 1.0619052 - 1850 38.121337 3202.0111 2366.6984 164.30536 835.31277 714.69988 849.6778 553.24258 46.502994 -667.44162 1306114.9 -1306776.3 131.11108 48631.318 256.90165 1.0656162 - 1900 39.132607 3228.7805 2365.934 164.25229 862.84648 720.68418 890.65533 554.75943 45.736726 -685.52803 1306115.1 -1306778.5 -82.525994 48631.318 256.81451 1.0726218 - 1950 40.127507 3218.4068 2443.0023 169.60267 775.40452 673.40001 874.63022 529.69964 43.166847 -680.57322 1306115.4 -1306780.3 622.76654 48631.318 265.20173 1.0693092 - 2000 41.138176 3257.463 2375.6246 164.92505 881.83842 677.60747 933.47776 547.01076 46.507189 -665.56273 1306123.7 -1306780.9 1829.3477 48631.318 257.88171 1.0500311 -Loop time of 41.1383 on 4 procs for 2000 steps with 5500 atoms - -Performance: 2.100 ns/day, 11.427 hours/ns, 48.617 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 21.082 | 22.483 | 24.145 | 26.6 | 54.65 -Bond | 4.9992 | 5.0781 | 5.1544 | 2.7 | 12.34 -Kspace | 9.1202 | 10.806 | 12.272 | 39.7 | 26.27 -Neigh | 0.45045 | 0.45076 | 0.45094 | 0.0 | 1.10 -Comm | 0.85982 | 0.87287 | 0.88725 | 1.2 | 2.12 -Output | 0.0036495 | 0.004005 | 0.0049655 | 0.9 | 0.01 -Modify | 1.4009 | 1.401 | 1.4013 | 0.0 | 3.41 -Other | | 0.04245 | | | 0.10 - -Nlocal: 1375 ave 1398 max 1361 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 7745.75 ave 7788 max 7697 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 334374 ave 348629 max 319495 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 1337494 -Ave neighs/atom = 243.181 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 31 -Dangerous builds = 0 -Total wall time: 0:00:41 diff --git a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 b/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 deleted file mode 100644 index 6070b858be..0000000000 --- a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.1 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 42.06 | 42.06 | 42.06 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 4.462481 6863.642 4633.9267 321.70512 2229.7153 735.2547 604.6946 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839843 - 100 8.8666639 6628.0722 4376.1868 303.81182 2251.8853 598.11249 651.43051 919.41359 74.216826 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129702 - 150 13.323556 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32475 45.531175 288.99128 1306173.9 -1306720 18303.624 48631.318 514.21215 0.0061921467 - 200 17.710109 5997.6194 4565.6288 316.96362 1431.9906 524.2765 591.79843 718.11015 56.374558 88.660843 1306183 -1306730.3 17986.182 48631.318 496.75522 0.00681205 - 250 22.154451 5648.1758 4433.1558 307.76682 1215.02 502.13687 578.85369 665.27326 49.096119 -19.019967 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619539 - 300 26.524393 5317.8584 4075.2077 282.91669 1242.6506 602.55113 637.40817 647.27074 44.769726 -123.22347 1306183.3 -1306749.5 3571.1867 48631.318 443.3952 0.0071733829 - 350 30.881443 4996.709 3935.7988 273.23838 1060.9102 455.75196 634.36552 638.77826 45.831053 -157.6304 1306198.1 -1306754.3 13525.264 48631.318 428.22739 0.0063722044 - 400 35.218285 4695.9297 3742.6585 259.82983 953.27122 457.49584 620.73047 591.94411 42.495713 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.005787501 - 450 39.545502 4417.8027 3513.6374 243.9303 904.16528 519.61263 580.76003 624.06933 45.631271 -286.60025 1306184.3 -1306763.6 2956.9012 48631.318 382.29486 0.0057536613 - 500 43.868895 4165.0012 3333.7203 231.43976 831.28089 465.5234 579.36085 580.60005 42.34515 -254.82269 1306183.9 -1306765.6 5818.5565 48631.318 362.71904 0.0059224891 - 550 48.242395 3934.5209 3211.9362 222.98504 722.58462 431.14864 581.46511 517.2025 39.188196 -265.47041 1306182.7 -1306763.6 8537.9404 48631.318 349.46863 0.0055762504 - 600 52.542171 3714.8655 3121.0494 216.67532 593.81611 425.12998 539.89496 490.30508 34.564566 -305.82069 1306175.2 -1306765.5 7402.7677 48631.318 339.57967 0.0057486673 - 650 56.830079 3516.2452 2930.7498 203.46399 585.49537 511.91461 512.48859 521.40636 37.766801 -391.65392 1306163.5 -1306770 381.72879 48631.318 318.87447 0.0054629243 - 700 61.119511 3342.7694 2864.1576 198.8409 478.6118 451.54683 498.82407 489.17207 35.23127 -375.78886 1306153.8 -1306774.2 3691.2716 48631.318 311.62801 0.0071278731 - 750 65.401576 3181.7673 2786.7104 193.46422 395.05691 409.83192 508.19542 454.56182 32.890716 -379.80692 1306149 -1306779.6 7428.3698 48631.318 303.20195 0.006233194 - 800 69.680899 3032.4158 2699.8707 187.43547 332.54509 453.40673 486.16575 441.1235 32.847786 -437.39338 1306144.4 -1306788 1701.7652 48631.318 293.75377 0.0056528223 - 850 73.96463 2898.4928 2563.6959 177.98169 334.7969 463.66637 486.19929 453.38803 34.062233 -455.86062 1306144.2 -1306790.9 -285.03665 48631.318 278.9376 0.0052777781 - 900 78.229548 2780.3555 2528.3241 175.52604 252.03136 396.92692 451.76463 435.59744 33.035257 -413.46176 1306142.9 -1306794.7 3836.4341 48631.318 275.08801 0.0070306435 - 950 82.482848 2679.3417 2456.8817 170.56624 222.45998 385.66656 434.6516 418.37977 32.156722 -387.2201 1306136.9 -1306798.1 5510.2309 48631.318 267.31515 0.0064042654 - 1000 86.722726 2593.4365 2367.4477 164.35738 225.98882 427.8524 453.27435 415.48809 31.097577 -436.62051 1306131.8 -1306796.9 1166.3909 48631.318 257.58464 0.0059160543 - 1050 90.888482 2524.7788 2305.0253 160.02377 219.75349 432.90807 438.86657 412.79356 30.892593 -414.29436 1306119.4 -1306800.8 1698.2687 48631.318 250.79245 0.0065593259 - 1100 95.024656 2471.8176 2311.0953 160.44518 160.72227 378.43572 453.3435 392.48525 29.012472 -409.64374 1306119.6 -1306802.5 4190.91 48631.318 251.45323 0.0059713432 - 1150 99.165724 2433.9279 2279.0766 158.22231 154.8513 395.30434 436.87933 414.39389 31.118973 -428.90902 1306110.2 -1306804.2 3274.8924 48631.318 247.96893 0.0069039065 - 1200 103.31062 2411.3777 2238.4638 155.40282 172.91381 453.61551 460.27693 408.59237 31.237062 -482.78549 1306110.2 -1306808.2 -523.10179 48631.318 243.55012 0.0068754631 - 1250 107.40149 2402.1932 2286.0576 158.70696 116.13565 416.44979 462.75875 391.75373 29.446705 -477.67214 1306102.2 -1306808.8 484.04837 48631.318 248.72579 0.011679749 - 1300 111.55448 2406.5029 2261.2729 156.98631 145.23005 408.68043 437.74725 400.4567 30.448106 -418.44274 1306096.8 -1306810.5 4490.4165 48631.318 245.99228 0.076574936 - 1350 115.71244 2459.1398 2317.5855 160.89575 141.55434 651.84862 447.40877 400.66793 29.060967 -461.45124 1305884.3 -1306810.3 693.59782 48631.318 250.14098 3.5622064 - 1400 119.88515 2479.5991 2285.6701 158.68006 193.929 582.54021 457.54475 430.29254 30.183876 -449.49979 1305955.6 -1306812.8 930.31169 48631.318 247.21826 2.5935077 - 1450 124.05689 2498.3537 2286.4924 158.73715 211.86128 434.79588 477.9598 402.79356 31.070492 -406.60813 1306086.4 -1306814.5 2933.4418 48631.318 248.74646 0.058608522 - 1500 128.29115 2546.66 2423.6257 168.25747 123.03432 392.07474 456.01536 385.97457 29.255586 -417.92459 1306089.9 -1306812.3 3333.3497 48631.318 263.694 0.011243575 - 1550 132.46344 2596.5481 2325.2227 161.42596 271.32542 462.52464 469.53612 461.20308 34.616094 -423.51186 1306080.4 -1306813.4 2155.0566 48631.318 252.98739 0.011191115 - 1600 136.64497 2646.7844 2387.8797 165.77585 258.90469 424.6071 484.95314 449.56642 33.318144 -395.67454 1306077 -1306814.8 1291.5449 48631.318 259.80403 0.012426122 - 1650 140.83234 2700.2847 2387.3033 165.73584 312.98138 431.00741 496.39504 455.52303 32.724808 -357.63815 1306070.3 -1306815.3 5007.2365 48631.318 259.70198 0.081729799 - 1700 145.02103 2777.9556 2386.7756 165.6992 391.18003 636.61544 523.12627 482.84847 35.186128 -391.10505 1305919.7 -1306815.2 2192.7076 48631.318 258.14043 2.7318649 - 1750 149.22218 2829.5998 2559.2796 177.67509 270.32019 684.587 479.93609 446.30457 31.888933 -385.84966 1305832.5 -1306819.1 1683.1471 48631.318 276.95798 2.6465587 - 1800 153.41978 2835.768 2465.6959 171.17815 370.07208 470.05934 508.38934 479.71489 37.826868 -369.0767 1306062.8 -1306819.6 3023.0762 48631.318 268.22249 0.097440318 - 1850 157.62632 2857.7601 2504.3893 173.86439 353.37083 436.06841 516.10132 487.71301 36.514956 -385.43181 1306078.9 -1306816.5 2950.5189 48631.318 272.47825 0.016816883 - 1900 161.8372 2867.791 2528.8957 175.56572 338.89527 446.38065 509.27013 485.03036 37.283587 -402.68445 1306076.6 -1306812.9 3161.5045 48631.318 275.1476 0.011615474 - 1950 166.10858 2861.34 2513.9103 174.52538 347.4297 470.9855 536.84666 467.9604 36.049051 -430.05716 1306079.3 -1306813.6 738.77866 48631.318 273.51233 0.020075246 - 2000 170.32286 2838.0367 2530.4481 175.6735 307.58858 423.18694 516.91384 454.72628 35.048394 -387.67176 1306074.6 -1306809.3 4321.7103 48631.318 275.24492 0.13775419 -Loop time of 170.323 on 1 procs for 2000 steps with 5500 atoms - -Performance: 0.507 ns/day, 47.312 hours/ns, 11.742 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 105.66 | 105.66 | 105.66 | 0.0 | 62.04 -Bond | 19.802 | 19.802 | 19.802 | 0.0 | 11.63 -Kspace | 35.029 | 35.029 | 35.029 | 0.0 | 20.57 -Neigh | 2.7502 | 2.7502 | 2.7502 | 0.0 | 1.61 -Comm | 0.62654 | 0.62654 | 0.62654 | 0.0 | 0.37 -Output | 0.006705 | 0.006705 | 0.006705 | 0.0 | 0.00 -Modify | 6.3072 | 6.3072 | 6.3072 | 0.0 | 3.70 -Other | | 0.1366 | | | 0.08 - -Nlocal: 5500 ave 5500 max 5500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 15407 ave 15407 max 15407 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.30509e+06 ave 1.30509e+06 max 1.30509e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1305088 -Ave neighs/atom = 237.289 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 44 -Dangerous builds = 0 -Total wall time: 0:02:50 diff --git a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 b/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 deleted file mode 100644 index 673f867ab4..0000000000 --- a/examples/USER/drude/toluene/log.toluene.nh.11Aug17.linux.4 +++ /dev/null @@ -1,259 +0,0 @@ -LAMMPS (11 Aug 2017) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) - using 1 OpenMP thread(s) per MPI task -# 250 toluene system for drude polarizability example (Nose-Hoover) - -units real -boundary p p p - -atom_style full -bond_style harmonic -angle_style harmonic -dihedral_style opls -improper_style opls -special_bonds lj/coul 0.0 0.0 0.5 - -pair_style lj/cut/thole/long 2.600 8.0 8.0 -pair_modify mix geometric tail yes -kspace_style pppm 1.0e-4 - -read_data data.toluene extra/special/per/atom 1 - orthogonal box = (-18.2908 -18.1636 -18.223) to (18.3357 18.1621 18.3287) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 5500 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 8 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 5500 bonds - reading angles ... - 6000 angles - reading dihedrals ... - 6000 dihedrals - reading impropers ... - 1500 impropers - 5 = max # of 1-2 neighbors - 10 = max # of 1-3 neighbors - 16 = max # of 1-4 neighbors - 20 = max # of special neighbors - -comm_modify vel yes - -group gTOLUENE molecule 1:250 -5500 atoms in group gTOLUENE -group gCORES type 1 2 3 4 5 6 7 -3750 atoms in group gCORES -group gDRUDES type 8 9 10 11 12 -1750 atoms in group gDRUDES - -pair_coeff 1 1 0.069998 3.550000 1.620000 # CAT CAT -pair_coeff 1 2 0.069998 3.550000 1.620000 # CAT CAO -pair_coeff 1 3 0.069998 3.550000 1.620000 # CAT CAM -pair_coeff 1 4 0.069998 3.550000 1.620000 # CAT CAP -pair_coeff 1 5 0.067968 3.524911 1.620000 # CAT CTT -pair_coeff 1 6 0.045825 2.931041 0.000000 # CAT HAT -pair_coeff 1 7 0.045825 2.931041 0.000000 # CAT HT -pair_coeff 2 2 0.069998 3.550000 1.620000 # CAO CAO -pair_coeff 2 3 0.069998 3.550000 1.620000 # CAO CAM -pair_coeff 2 4 0.069998 3.550000 1.620000 # CAO CAP -pair_coeff 2 5 0.067968 3.524911 1.620000 # CAO CTT -pair_coeff 2 6 0.045825 2.931041 0.000000 # CAO HAT -pair_coeff 2 7 0.045825 2.931041 0.000000 # CAO HT -pair_coeff 3 3 0.069998 3.550000 1.620000 # CAM CAM -pair_coeff 3 4 0.069998 3.550000 1.620000 # CAM CAP -pair_coeff 3 5 0.067968 3.524911 1.620000 # CAM CTT -pair_coeff 3 6 0.045825 2.931041 0.000000 # CAM HAT -pair_coeff 3 7 0.045825 2.931041 0.000000 # CAM HT -pair_coeff 4 4 0.069998 3.550000 1.620000 # CAP CAP -pair_coeff 4 5 0.067968 3.524911 1.620000 # CAP CTT -pair_coeff 4 6 0.045825 2.931041 0.000000 # CAP HAT -pair_coeff 4 7 0.045825 2.931041 0.000000 # CAP HT -pair_coeff 5 5 0.065997 3.500000 1.620000 # CTT CTT -pair_coeff 5 6 0.044496 2.910326 0.000000 # CTT HAT -pair_coeff 5 7 0.044496 2.910326 0.000000 # CTT HT -pair_coeff 6 6 0.029999 2.420000 0.000000 # HAT HAT -pair_coeff 6 7 0.029999 2.420000 0.000000 # HAT HT -pair_coeff 7 7 0.029999 2.420000 0.000000 # HT HT -pair_coeff 1 8 0.000000 0.000000 1.620000 # CAT D_CAT -pair_coeff 1 9 0.000000 0.000000 1.620000 # CAT D_CAO -pair_coeff 1 10 0.000000 0.000000 1.620000 # CAT D_CAM -pair_coeff 1 11 0.000000 0.000000 1.620000 # CAT D_CAP -pair_coeff 1 12 0.000000 0.000000 1.620000 # CAT D_CTT -pair_coeff 2 8 0.000000 0.000000 1.620000 # CAO D_CAT -pair_coeff 2 9 0.000000 0.000000 1.620000 # CAO D_CAO -pair_coeff 2 10 0.000000 0.000000 1.620000 # CAO D_CAM -pair_coeff 2 11 0.000000 0.000000 1.620000 # CAO D_CAP -pair_coeff 2 12 0.000000 0.000000 1.620000 # CAO D_CTT -pair_coeff 3 8 0.000000 0.000000 1.620000 # CAM D_CAT -pair_coeff 3 9 0.000000 0.000000 1.620000 # CAM D_CAO -pair_coeff 3 10 0.000000 0.000000 1.620000 # CAM D_CAM -pair_coeff 3 11 0.000000 0.000000 1.620000 # CAM D_CAP -pair_coeff 3 12 0.000000 0.000000 1.620000 # CAM D_CTT -pair_coeff 4 8 0.000000 0.000000 1.620000 # CAP D_CAT -pair_coeff 4 9 0.000000 0.000000 1.620000 # CAP D_CAO -pair_coeff 4 10 0.000000 0.000000 1.620000 # CAP D_CAM -pair_coeff 4 11 0.000000 0.000000 1.620000 # CAP D_CAP -pair_coeff 4 12 0.000000 0.000000 1.620000 # CAP D_CTT -pair_coeff 5 8 0.000000 0.000000 1.620000 # CTT D_CAT -pair_coeff 5 9 0.000000 0.000000 1.620000 # CTT D_CAO -pair_coeff 5 10 0.000000 0.000000 1.620000 # CTT D_CAM -pair_coeff 5 11 0.000000 0.000000 1.620000 # CTT D_CAP -pair_coeff 5 12 0.000000 0.000000 1.620000 # CTT D_CTT -pair_coeff 8 8 0.000000 0.000000 1.620000 # D_CAT D_CAT -pair_coeff 8 9 0.000000 0.000000 1.620000 # D_CAT D_CAO -pair_coeff 8 10 0.000000 0.000000 1.620000 # D_CAT D_CAM -pair_coeff 8 11 0.000000 0.000000 1.620000 # D_CAT D_CAP -pair_coeff 8 12 0.000000 0.000000 1.620000 # D_CAT D_CTT -pair_coeff 9 9 0.000000 0.000000 1.620000 # D_CAO D_CAO -pair_coeff 9 10 0.000000 0.000000 1.620000 # D_CAO D_CAM -pair_coeff 9 11 0.000000 0.000000 1.620000 # D_CAO D_CAP -pair_coeff 9 12 0.000000 0.000000 1.620000 # D_CAO D_CTT -pair_coeff 10 10 0.000000 0.000000 1.620000 # D_CAM D_CAM -pair_coeff 10 11 0.000000 0.000000 1.620000 # D_CAM D_CAP -pair_coeff 10 12 0.000000 0.000000 1.620000 # D_CAM D_CTT -pair_coeff 11 11 0.000000 0.000000 1.620000 # D_CAP D_CAP -pair_coeff 11 12 0.000000 0.000000 1.620000 # D_CAP D_CTT -pair_coeff 12 12 0.000000 0.000000 1.620000 # D_CTT D_CTT - - -neighbor 2.0 bin - -variable vTEMP equal 260.0 -variable vTEMP_D equal 1.0 -variable vPRESS equal 1.0 - -velocity gCORES create ${vTEMP} 12345 -velocity gCORES create 260 12345 -velocity gDRUDES create ${vTEMP_D} 12345 -velocity gDRUDES create 1 12345 - -fix fDRUDE all drude C C C C C N N D D D D D - -fix fSHAKE gCORES shake 0.0001 20 0 b 4 6 7 8 - 1250 = # of size 2 clusters - 0 = # of size 3 clusters - 250 = # of size 4 clusters - 0 = # of frozen angles - -compute cTEMP_CORE gCORES temp/com -compute cTEMP all temp/drude - -fix fDIRECT all drude/transform/direct -fix fNVT1 gCORES nvt temp ${vTEMP} ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 ${vTEMP} 100.0 -fix fNVT1 gCORES nvt temp 260 260 100.0 -fix fNVT2 gDRUDES nvt temp ${vTEMP_D} ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 ${vTEMP_D} 20.0 -fix fNVT2 gDRUDES nvt temp 1 1 20.0 -fix fINVERSE all drude/transform/inverse - -fix fMOMENTUM all momentum 100 linear 1 1 1 - -thermo_style custom step cpu etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press vol c_cTEMP[1] c_cTEMP[2] -thermo 50 - -timestep 0.5 -run 2000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.382011 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0325934 - estimated relative force accuracy = 9.8154e-05 - using double precision FFTs - 3d grid and FFT values/proc = 34263 16000 -Rebuild special list taking Drude particles into account -Old max number of 1-2 to 1-4 neighbors: 19 -New max number of 1-2 to 1-4 neighbors: 20 (+1) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10 - ghost atom cutoff = 10 - binsize = 5, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/thole/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 18 | 18 | 18 Mbytes -Step CPU TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Volume c_cTEMP[1] c_cTEMP[2] - 0 0 14386.197 2910.7282 202.07402 11475.469 6565.4851 20.333365 1.0706727e-06 1.3894617e-07 4972.8631 1306116.6 -1306199.8 40273.68 48631.318 314.89553 3.1777821 - 50 1.1419601 6863.6417 4633.9267 321.70512 2229.715 735.2547 604.69459 648.35773 49.039129 824.06033 1306091.3 -1306722.9 17914.827 48631.318 504.18525 0.0086839775 - 100 2.3001912 6628.0719 4376.1868 303.81182 2251.8851 598.11248 651.43051 919.41359 74.216825 589.6504 1306135.1 -1306716 17450.721 48631.318 476.14276 0.0075129701 - 150 3.473469 6336.1884 4726.0692 328.10201 1610.1192 560.01225 621.30109 640.32474 45.531174 288.99129 1306173.9 -1306720 18303.624 48631.318 514.21215 0.006192153 - 200 4.6296241 5997.6192 4565.6288 316.96362 1431.9903 524.27651 591.79844 718.11014 56.374557 88.66084 1306183 -1306730.3 17986.183 48631.318 496.75522 0.0068120542 - 250 5.7982912 5648.1756 4433.1557 307.76682 1215.0199 502.13686 578.8537 665.27326 49.096119 -19.019961 1306179.2 -1306740.5 11771.328 48631.318 482.34141 0.0071619522 - 300 6.9468622 5317.8583 4075.2077 282.91669 1242.6505 602.55113 637.40818 647.27073 44.769725 -123.22347 1306183.3 -1306749.5 3571.1872 48631.318 443.3952 0.0071733908 - 350 8.0925181 4996.7094 3935.7988 273.23838 1060.9106 455.75195 634.3655 638.77824 45.831051 -157.63039 1306198.1 -1306754.3 13525.265 48631.318 428.22739 0.0063722017 - 400 9.2309761 4695.9294 3742.6584 259.82983 953.27093 457.49585 620.73048 591.94413 42.495714 -183.91838 1306186.7 -1306762.2 10901.217 48631.318 407.21326 0.0057875 - 450 10.363872 4417.8018 3513.6374 243.9303 904.1644 519.61261 580.76003 624.06933 45.631272 -286.60025 1306184.3 -1306763.6 2956.9021 48631.318 382.29485 0.0057536673 - 500 11.493601 4165.0005 3333.7203 231.43976 831.28022 465.52341 579.36085 580.60004 42.345149 -254.82269 1306183.9 -1306765.6 5818.5549 48631.318 362.71904 0.0059224858 - 550 12.636785 3934.5207 3211.9362 222.98504 722.58446 431.14864 581.46511 517.20249 39.188194 -265.4704 1306182.7 -1306763.6 8537.9415 48631.318 349.46863 0.0055762027 - 600 13.759642 3714.8658 3121.0493 216.67532 593.81649 425.12998 539.89497 490.30506 34.564567 -305.82067 1306175.2 -1306765.5 7402.7688 48631.318 339.57967 0.005748668 - 650 14.880794 3516.2453 2930.7499 203.464 585.49542 511.91457 512.48857 521.40634 37.766798 -391.65394 1306163.5 -1306770 381.72898 48631.318 318.87448 0.0054629381 - 700 15.99791 3342.7693 2864.1576 198.8409 478.61174 451.54685 498.82406 489.17206 35.231269 -375.78888 1306153.8 -1306774.2 3691.2706 48631.318 311.62801 0.0071278792 - 750 17.111346 3181.7665 2786.7104 193.46422 395.05608 409.83191 508.19537 454.56183 32.890719 -379.80694 1306149 -1306779.6 7428.3698 48631.318 303.20196 0.0062331873 - 800 18.219225 3032.4162 2699.8707 187.43547 332.54543 453.40674 486.16573 441.12346 32.847783 -437.39291 1306144.4 -1306788 1701.7675 48631.318 293.75377 0.0056528077 - 850 19.320825 2898.4936 2563.6961 177.9817 334.79757 463.66634 486.19928 453.38802 34.062236 -455.86081 1306144.2 -1306790.9 -285.04073 48631.318 278.93762 0.0052778244 - 900 20.41979 2780.3551 2528.3241 175.52604 252.03099 396.92693 451.7645 435.59756 33.035261 -413.46181 1306142.9 -1306794.7 3836.4347 48631.318 275.08801 0.0070307677 - 950 21.517533 2679.3418 2456.8821 170.56626 222.45967 385.66649 434.6516 418.37957 32.156706 -387.22039 1306136.9 -1306798.1 5510.2277 48631.318 267.31518 0.0064041284 - 1000 22.614275 2593.435 2367.4471 164.35734 225.98798 427.85237 453.27432 415.48822 31.097611 -436.61808 1306131.8 -1306796.9 1166.3709 48631.318 257.58457 0.0059160188 - 1050 23.688642 2524.7784 2305.0257 160.0238 219.75264 432.90797 438.8666 412.79338 30.892595 -414.29467 1306119.4 -1306800.8 1698.2602 48631.318 250.7925 0.0065595368 - 1100 24.750163 2471.818 2311.095 160.44516 160.72297 378.43554 453.3434 392.485 29.012487 -409.64322 1306119.6 -1306802.5 4190.9174 48631.318 251.4532 0.0059713928 - 1150 25.813605 2433.9311 2279.0768 158.22233 154.85433 395.30409 436.87935 414.39367 31.118959 -428.90913 1306110.2 -1306804.2 3274.9237 48631.318 247.96895 0.0069037916 - 1200 26.876952 2411.3772 2238.4639 155.40283 172.91329 453.61525 460.27658 408.59192 31.237007 -482.78468 1306110.2 -1306808.2 -523.10237 48631.318 243.55013 0.0068752641 - 1250 27.929701 2402.1937 2286.0559 158.70685 116.13778 416.44884 462.75935 391.75448 29.446777 -477.6718 1306102.2 -1306808.8 484.0561 48631.318 248.72561 0.011679662 - 1300 29.000999 2406.5014 2261.274 156.98639 145.22737 408.678 437.74824 400.45662 30.448139 -418.44472 1306096.8 -1306810.5 4490.4105 48631.318 245.9924 0.076575975 - 1350 30.07322 2459.141 2317.5852 160.89573 141.55579 651.85736 447.40791 400.66662 29.060882 -461.45016 1305884.3 -1306810.3 693.5247 48631.318 250.14112 3.5619231 - 1400 31.14859 2479.6103 2285.6714 158.68015 193.93893 582.54135 457.54445 430.29301 30.184026 -449.49877 1305955.6 -1306812.8 930.44669 48631.318 247.21806 2.5941109 - 1450 32.226914 2498.357 2286.4857 158.73668 211.87137 434.79636 477.95951 402.79572 31.070593 -406.60139 1306086.4 -1306814.5 2933.5045 48631.318 248.74572 0.058613153 - 1500 33.410717 2546.6608 2423.6247 168.25741 123.03609 392.07322 456.01243 385.97344 29.255562 -417.91413 1306089.9 -1306812.3 3333.391 48631.318 263.6939 0.011242005 - 1550 34.466176 2596.5534 2325.2208 161.42583 271.33259 462.52172 469.54241 461.20405 34.616224 -423.51068 1306080.4 -1306813.4 2155.1194 48631.318 252.98718 0.011190963 - 1600 35.524206 2646.7837 2387.8846 165.77619 258.8991 424.60563 484.95051 449.57767 33.318683 -395.68293 1306077 -1306814.8 1291.42 48631.318 259.80456 0.01242131 - 1650 36.582854 2700.2921 2387.3119 165.73643 312.98026 431.01369 496.39909 455.52591 32.725057 -357.65832 1306070.3 -1306815.3 5006.9348 48631.318 259.70291 0.081728845 - 1700 37.641527 2777.9572 2386.7777 165.69934 391.1795 636.55763 523.11512 482.8483 35.185863 -391.0955 1305919.8 -1306815.2 2192.6733 48631.318 258.1403 2.7324891 - 1750 38.722299 2829.6167 2559.2488 177.67295 270.36793 684.60746 479.95058 446.29664 31.887359 -385.83616 1305832.5 -1306819 1683.6061 48631.318 276.955 2.6459088 - 1800 39.800548 2835.7772 2465.7031 171.17865 370.07414 470.05306 508.38361 479.70121 37.826988 -369.0694 1306062.8 -1306819.6 3022.9801 48631.318 268.22328 0.097437593 - 1850 40.878327 2857.76 2504.4099 173.86582 353.35016 436.05857 516.10495 487.70907 36.514477 -385.43957 1306078.9 -1306816.5 2950.6415 48631.318 272.48049 0.016822774 - 1900 41.9583 2867.7843 2528.8424 175.56202 338.94193 446.38058 509.30719 485.04661 37.284135 -402.67104 1306076.5 -1306812.9 3161.5835 48631.318 275.1418 0.011620333 - 1950 43.058281 2861.3388 2513.8846 174.5236 347.45414 470.99292 536.81741 467.97736 36.047648 -430.00695 1306079.3 -1306813.6 739.25154 48631.318 273.50953 0.020089235 - 2000 44.142059 2838.068 2530.3189 175.66453 307.74914 423.19157 516.85371 454.76945 35.048253 -387.49234 1306074.6 -1306809.3 4324.0966 48631.318 275.23081 0.13784772 -Loop time of 44.1421 on 4 procs for 2000 steps with 5500 atoms - -Performance: 1.957 ns/day, 12.262 hours/ns, 45.308 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 21.008 | 22.592 | 23.892 | 21.7 | 51.18 -Bond | 4.8951 | 5.1338 | 5.2542 | 6.4 | 11.63 -Kspace | 9.1158 | 10.514 | 12.296 | 35.3 | 23.82 -Neigh | 0.63826 | 0.63849 | 0.63875 | 0.0 | 1.45 -Comm | 0.78008 | 0.80146 | 0.84186 | 2.7 | 1.82 -Output | 0.0036852 | 0.0040929 | 0.0052037 | 1.0 | 0.01 -Modify | 4.3966 | 4.4074 | 4.4147 | 0.3 | 9.98 -Other | | 0.05088 | | | 0.12 - -Nlocal: 1375 ave 1415 max 1340 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 8101 ave 8147 max 8056 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 326274 ave 342552 max 306832 min -Histogram: 1 0 0 0 1 0 1 0 0 1 - -Total # of neighbors = 1305095 -Ave neighs/atom = 237.29 -Ave special neighs/atom = 15.6364 -Neighbor list builds = 44 -Dangerous builds = 0 -Total wall time: 0:00:44 diff --git a/examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane b/examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane new file mode 100644 index 0000000000..6483512de1 --- /dev/null +++ b/examples/USER/fep/C7inEthanol/fep01/data.init_conf_with_heptane @@ -0,0 +1,2783 @@ +LAMMPS data file via write_data, version 27 Nov 2018, timestep = 1100100 + +383 atoms +8 atom types +342 bonds +9 bond types +562 angles +14 angle types +534 dihedrals +11 dihedral types +348 impropers +11 improper types + +-5.0514130135769175e-01 1.5783110029075640e+01 xlo xhi +-8.0620338035756767e-01 1.5482047948350324e+01 ylo yhi +-8.6275306635756799e-01 1.5425498262350324e+01 zlo zhi + +Masses + +1 12.0112 +2 12.0112 +3 15.9994 +4 1.00797 +5 1.00797 +6 12.0112 +7 12.0112 +8 1.00797 + +Pair Coeffs # lj/class2/coul/long + +1 lj/class2/coul/long 0.054 4.01 +2 lj/class2/coul/long 0.054 4.01 +3 lj/class2/coul/long 0.24 3.535 +4 lj/class2/coul/long 0.02 2.995 +5 lj/class2/coul/long 0.013 1.098 +6 lj/class2/coul/long 0.054 4.01 +7 lj/class2/coul/long 0.054 4.01 +8 lj/class2/coul/long 0.02 2.995 + +Bond Coeffs # class2 + +1 1.53 299.67 -501.77 679.81 +2 1.101 345 -691.89 844.6 +3 1.101 345 -691.89 844.6 +4 1.42 400.395 -835.195 1313.01 +5 0.965 532.506 -1282.9 2004.77 +6 1.53 299.67 -501.77 679.81 +7 1.101 345 -691.89 844.6 +8 1.53 299.67 -501.77 679.81 +9 1.101 345 -691.89 844.6 + +Angle Coeffs # class2 + +1 110.77 41.453 -10.604 5.129 +2 107.66 39.641 -12.921 -2.4318 +3 110.77 41.453 -10.604 5.129 +4 111.27 54.5381 -8.3642 -13.0838 +5 107.66 39.641 -12.921 -2.4318 +6 108.728 58.5446 -10.8088 -12.4006 +7 105.8 52.7061 -12.109 -9.8681 +8 110.77 41.453 -10.604 5.129 +9 107.66 39.641 -12.921 -2.4318 +10 112.67 39.516 -7.443 -9.5583 +11 110.77 41.453 -10.604 5.129 +12 110.77 41.453 -10.604 5.129 +13 107.66 39.641 -12.921 -2.4318 +14 112.67 39.516 -7.443 -9.5583 + +BondBond Coeffs + +1 3.3872 1.53 1.101 +2 5.3316 1.101 1.101 +3 3.3872 1.53 1.101 +4 11.4318 1.53 1.42 +5 5.3316 1.101 1.101 +6 23.1979 1.42 1.101 +7 -9.6879 1.42 0.965 +8 3.3872 1.53 1.101 +9 5.3316 1.101 1.101 +10 0 1.53 1.53 +11 3.3872 1.53 1.101 +12 3.3872 1.53 1.101 +13 5.3316 1.101 1.101 +14 0 1.53 1.53 + +BondAngle Coeffs + +1 20.754 11.421 1.53 1.101 +2 18.103 18.103 1.101 1.101 +3 20.754 11.421 1.53 1.101 +4 2.6868 20.4033 1.53 1.42 +5 18.103 18.103 1.101 1.101 +6 55.327 4.6189 1.42 1.101 +7 28.58 18.9277 1.42 0.965 +8 20.754 11.421 1.53 1.101 +9 18.103 18.103 1.101 1.101 +10 8.016 8.016 1.53 1.53 +11 20.754 11.421 1.53 1.101 +12 20.754 11.421 1.53 1.101 +13 18.103 18.103 1.101 1.101 +14 8.016 8.016 1.53 1.53 + +Dihedral Coeffs # class2 + +1 -0.1432 0 0.0617 0 -0.1083 0 +2 -0.1435 0 0.253 0 -0.0905 0 +3 -0.6732 0 -0.4778 0 -0.167 0 +4 0.1863 0 -0.4338 0 -0.2121 0 +5 0 0 0.0316 0 -0.1681 0 +6 -0.1432 0 0.0617 0 -0.1083 0 +7 0 0 0.0514 0 -0.143 0 +8 0 0 0.0316 0 -0.1681 0 +9 0 0 0.0316 0 -0.1681 0 +10 -0.1432 0 0.0617 0 -0.1083 0 +11 0 0 0.0514 0 -0.143 0 + +AngleAngleTorsion Coeffs + +1 -12.564 110.77 110.77 +2 -20.2006 110.77 111.27 +3 -12.1038 111.27 105.8 +4 -10.5093 108.728 105.8 +5 -16.164 110.77 112.67 +6 -12.564 110.77 110.77 +7 -22.045 112.67 112.67 +8 -16.164 112.67 110.77 +9 -16.164 112.67 110.77 +10 -12.564 110.77 110.77 +11 -22.045 112.67 112.67 + +EndBondTorsion Coeffs + +1 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 +2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.101 1.42 +3 -0.58 0.9004 0 0 0.5343 0.9025 1.53 0.965 +4 -1.7554 1.3145 0.2263 0.2493 0.6803 0 1.101 0.965 +5 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53 +6 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101 +7 -0.0732 0 0 -0.0732 0 0 1.53 1.53 +8 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101 +9 0.2486 0.2422 -0.0925 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290 289 292 294 +347 1 290 289 293 294 +348 2 292 289 293 294 diff --git a/examples/USER/fep/C7inEthanol/fep01/in.insertion b/examples/USER/fep/C7inEthanol/fep01/in.insertion new file mode 100644 index 0000000000..243d837515 --- /dev/null +++ b/examples/USER/fep/C7inEthanol/fep01/in.insertion @@ -0,0 +1,57 @@ +# LAMMPS atomistic input script + +echo screen +units real +atom_style full + +pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5 +bond_style class2 +angle_style class2 +dihedral_style class2 +improper_style class2 +pair_modify mix sixthpower tail yes +special_bonds lj/coul 0 0 1 + +read_data data.init_conf_without_heptane + +pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 0.0 +pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 0.0 +pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0 +pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0 +pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0 + +pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 0.0 +pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 0.0 +pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 0.0 +pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0 +pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 0.0 + +pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0 +pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 0.0 +pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 0.0 +pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 0.0 +pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 0.0 + +timestep 1.0 +kspace_style pppm 1.0e-5 + +variable lambda equal ramp(0.0,1.0) +variable q1 equal -0.1590*v_lambda +variable q2 equal -0.1060*v_lambda +variable q3 equal 0.0530*v_lambda + +fix ADAPT all adapt/fep 10 & + pair lj/class2/coul/long/soft lambda 1*5 6*8 v_lambda & + atom charge 6 v_q1 & + atom charge 7 v_q2 & + atom charge 8 v_q3 & + after yes + +thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3 +thermo_modify line one +thermo 100 + +fix 1 all nvt temp 300 300 100 +run 100000 + +write_data data.after_heptane_insertion diff --git a/examples/USER/fep/C7inEthanol/fep01/log.lammps b/examples/USER/fep/C7inEthanol/fep01/log.lammps new file mode 100644 index 0000000000..fbd4a49a3e --- /dev/null +++ b/examples/USER/fep/C7inEthanol/fep01/log.lammps @@ -0,0 +1,1125 @@ +LAMMPS (27 Nov 2018) +# LAMMPS atomistic input script + +echo screen + orthogonal box = (-0.505141 -0.806203 -0.862753) to (15.7831 15.482 15.4255) + 4 by 2 by 2 MPI processor grid +WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:580) + reading atoms ... + 383 atoms + reading velocities ... + 383 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + scanning impropers ... + 4 = max impropers/atom + reading bonds ... + 342 bonds + reading angles ... + 562 angles + reading dihedrals ... + 534 dihedrals + reading impropers ... + 348 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of special neighbors +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.288287 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00279394 + estimated relative force accuracy = 8.41388e-06 + using double precision FFTs + 3d grid and FFT values/proc = 1296 90 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5 + ghost atom cutoff = 11.5 + binsize = 5.75, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/class2/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/class2/coul/long/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.61 | 13.92 | 14.89 Mbytes +Step S/CPU Temp Press Volume TotEng PotEng v_lambda v_q1 v_q2 v_q3 + 0 0 301.82904 533.3184 4321.3892 -79.144423 -422.82793 1 -0.159 -0.106 0.053 + 100 799.51858 297.06821 2966.9114 4321.3892 -67.550969 -405.81346 0.999 -0.158841 -0.105894 0.052947 + 200 1111.1841 310.89475 -1076.6004 4321.3892 -32.998901 -387.00525 0.998 -0.158682 -0.105788 0.052894 + 300 1459.1789 313.65424 320.85082 4321.3892 -29.026776 -386.17527 0.997 -0.158523 -0.105682 0.052841 + 400 1415.1559 311.37233 -4525.9921 4321.3892 -43.910969 -398.46112 0.996 -0.158364 -0.105576 0.052788 + 500 1489.9869 288.38744 -1783.6133 4321.3892 -59.978436 -388.3564 0.995 -0.158205 -0.10547 0.052735 + 600 1372.2162 300.78589 2406.4287 4321.3892 -58.529306 -401.025 0.994 -0.158046 -0.105364 0.052682 + 700 1273.4802 302.48787 1188.4083 4321.3892 -19.664773 -364.09847 0.993 -0.157887 -0.105258 0.052629 + 800 1379.5701 324.19685 3525.573 4321.3892 -6.5601902 -375.71324 0.992 -0.157728 -0.105152 0.052576 + 900 1417.4117 302.20264 580.80929 4321.3892 -31.492626 -375.60153 0.991 -0.157569 -0.105046 0.052523 + 1000 1423.0943 288.09813 -3390.5518 4321.3892 -50.795041 -378.84358 0.99 -0.15741 -0.10494 0.05247 + 1100 1339.6567 279.41478 -1585.8135 4321.3892 -65.305421 -383.46649 0.989 -0.157251 -0.104834 0.052417 + 1200 1283.0804 297.57659 -5628.1846 4321.3892 -61.457533 -400.2989 0.988 -0.157092 -0.104728 0.052364 + 1300 1374.8154 302.95867 2800.3971 4321.3892 -25.223933 -370.19371 0.987 -0.156933 -0.104622 0.052311 + 1400 1548.7979 314.63757 169.32405 4321.3892 -9.2461401 -367.51433 0.986 -0.156774 -0.104516 0.052258 + 1500 1543.4384 302.78598 2667.3171 4321.3892 -28.872419 -373.64556 0.985 -0.156615 -0.10441 0.052205 + 1600 1505.9924 307.4754 -3144.1719 4321.3892 -42.805804 -392.91864 0.984 -0.156456 -0.104304 0.052152 + 1700 1519.2347 291.11376 -51.878589 4321.3892 -44.622256 -376.1046 0.983 -0.156297 -0.104198 0.052099 + 1800 1442.3107 297.91891 1568.4932 4321.3892 -38.314165 -377.54533 0.982 -0.156138 -0.104092 0.052046 + 1900 1416.7513 299.44141 -3439.0539 4321.3892 -34.396006 -375.36079 0.981 -0.155979 -0.103986 0.051993 + 2000 1320.1308 311.55135 -4036.9906 4321.3892 -38.635681 -393.38969 0.98 -0.15582 -0.10388 0.05194 + 2100 1352.1874 294.77184 1722.2251 4321.3892 -52.682147 -388.32983 0.979 -0.155661 -0.103774 0.051887 + 2200 1398.9382 275.77965 -798.41267 4321.3892 -87.333361 -401.35522 0.978 -0.155502 -0.103668 0.051834 + 2300 1401.8526 288.31697 1440.4268 4321.3892 -95.443884 -423.7416 0.977 -0.155343 -0.103562 0.051781 + 2400 1410.2793 300.6133 1047.3407 4321.3892 -67.450573 -409.74975 0.976 -0.155184 -0.103456 0.051728 + 2500 1342.2665 304.4924 4512.7456 4321.3892 -46.485002 -393.20119 0.975 -0.155025 -0.10335 0.051675 + 2600 1399.6709 304.59021 -1440.2459 4321.3892 -41.296463 -388.12403 0.974 -0.154866 -0.103244 0.051622 + 2700 1393.5595 307.63992 1801.3517 4321.3892 -35.974699 -386.27487 0.973 -0.154707 -0.103138 0.051569 + 2800 1416.1276 301.99824 680.3111 4321.3892 -37.283922 -381.16009 0.972 -0.154548 -0.103032 0.051516 + 2900 1467.076 290.21584 -655.51621 4321.3892 -55.113989 -385.5739 0.971 -0.154389 -0.102926 0.051463 + 3000 1507.7721 284.82664 2047.2406 4321.3892 -81.291143 -405.61453 0.97 -0.15423 -0.10282 0.05141 + 3100 1470.3382 285.07726 -4149.6477 4321.3892 -85.012313 -409.62108 0.969 -0.154071 -0.102714 0.051357 + 3200 1514.1911 299.64651 1428.5333 4321.3892 -52.958903 -394.15722 0.968 -0.153912 -0.102608 0.051304 + 3300 1511.3429 311.60785 36.886282 4321.3892 -40.626937 -395.44527 0.967 -0.153753 -0.102502 0.051251 + 3400 1570.8737 299.11947 3828.1184 4321.3892 -43.612199 -384.2104 0.966 -0.153594 -0.102396 0.051198 + 3500 1588.4825 297.08441 2021.8438 4321.3892 -52.83333 -391.11427 0.965 -0.153435 -0.10229 0.051145 + 3600 1514.3641 294.38448 510.47993 4321.3892 -76.148011 -411.35462 0.964 -0.153276 -0.102184 0.051092 + 3700 1579.6325 267.42535 1976.3472 4321.3892 -92.292608 -396.80168 0.963 -0.153117 -0.102078 0.051039 + 3800 1579.4417 305.93263 -2594.8587 4321.3892 -60.46367 -408.8198 0.962 -0.152958 -0.101972 0.050986 + 3900 1556.0604 295.41636 -2413.3469 4321.3892 -39.598538 -375.98011 0.961 -0.152799 -0.101866 0.050933 + 4000 1480.4195 291.39244 23.97447 4321.3892 -39.171532 -370.9712 0.96 -0.15264 -0.10176 0.05088 + 4100 1427.5893 302.95007 -136.92129 4321.3892 -61.300632 -406.26062 0.959 -0.152481 -0.101654 0.050827 + 4200 1507.0531 290.0336 -1924.0805 4321.3892 -78.49136 -408.74376 0.958 -0.152322 -0.101548 0.050774 + 4300 1530.443 301.52983 1346.5118 4321.3892 -65.981817 -409.32462 0.957 -0.152163 -0.101442 0.050721 + 4400 1522.4039 296.09695 2033.2832 4321.3892 -38.949103 -376.10565 0.956 -0.152004 -0.101336 0.050668 + 4500 1469.3288 299.67261 -2870.5264 4321.3892 -36.881907 -378.10995 0.955 -0.151845 -0.10123 0.050615 + 4600 1476.1078 317.35258 -43.577562 4321.3892 -46.136233 -407.49591 0.954 -0.151686 -0.101124 0.050562 + 4700 1521.8164 285.69675 -2599.4101 4321.3892 -67.71719 -393.03135 0.953 -0.151527 -0.101018 0.050509 + 4800 1567.0075 297.89711 -3002.7695 4321.3892 -82.138424 -421.34476 0.952 -0.151368 -0.100912 0.050456 + 4900 1603.8725 292.54174 392.88991 4321.3892 -77.729344 -410.83769 0.951 -0.151209 -0.100806 0.050403 + 5000 1596.5842 324.83308 522.49599 4321.3892 -37.736703 -407.6142 0.95 -0.15105 -0.1007 0.05035 + 5100 1606.1392 312.9193 -878.4909 4321.3892 -35.650262 -391.96191 0.949 -0.150891 -0.100594 0.050297 + 5200 1596.9711 301.10369 4932.6479 4321.3892 -53.77998 -396.63755 0.948 -0.150732 -0.100488 0.050244 + 5300 1465.77 299.48781 -279.78852 4321.3892 -74.767934 -415.78555 0.947 -0.150573 -0.100382 0.050191 + 5400 1373.2951 283.80778 -213.42159 4321.3892 -98.619463 -421.78271 0.946 -0.150414 -0.100276 0.050138 + 5500 1420.5231 264.12997 -2228.6488 4321.3892 -130.10614 -430.86286 0.945 -0.150255 -0.10017 0.050085 + 5600 1515.9938 266.04428 -2171.6706 4321.3892 -108.55638 -411.49288 0.944 -0.150096 -0.100064 0.050032 + 5700 1549.72 276.23021 1058.2904 4321.3892 -77.55162 -392.08652 0.943 -0.149937 -0.099958 0.049979 + 5800 1522.7747 296.33023 2834.8108 4321.3892 -52.620617 -390.0428 0.942 -0.149778 -0.099852 0.049926 + 5900 1501.6416 310.56588 2024.1237 4321.3892 -35.466522 -389.0984 0.941 -0.149619 -0.099746 0.049873 + 6000 1518.1573 305.31866 90.498107 4321.3892 -37.024388 -384.68142 0.94 -0.14946 -0.09964 0.04982 + 6100 1492.5011 298.08903 1653.7952 4321.3892 -59.680839 -399.1057 0.939 -0.149301 -0.099534 0.049767 + 6200 1441.766 282.17236 -1566.1626 4321.3892 -77.565829 -398.86687 0.938 -0.149142 -0.099428 0.049714 + 6300 1425.2832 297.96681 -2194.5697 4321.3892 -58.623811 -397.90951 0.937 -0.148983 -0.099322 0.049661 + 6400 1555.6883 320.41355 286.39321 4321.3892 -19.662831 -384.50795 0.936 -0.148824 -0.099216 0.049608 + 6500 1569.0293 301.95644 -1411.1846 4321.3892 -24.09389 -367.92246 0.935 -0.148665 -0.09911 0.049555 + 6600 1459.2486 303.94603 428.05651 4321.3892 -48.559803 -394.65386 0.934 -0.148506 -0.099004 0.049502 + 6700 1407.3379 307.53794 1933.383 4321.3892 -65.054887 -415.23894 0.933 -0.148347 -0.098898 0.049449 + 6800 1396.4378 283.43758 -1552.7689 4321.3892 -67.772351 -390.51406 0.932 -0.148188 -0.098792 0.049396 + 6900 1312.334 294.20856 -86.309891 4321.3892 -60.748487 -395.75478 0.931 -0.148029 -0.098686 0.049343 + 7000 1328.9804 309.35057 -1620.5208 4321.3892 -35.894847 -388.14288 0.93 -0.14787 -0.09858 0.04929 + 7100 1271.3608 307.56399 -1880.8175 4321.3892 -18.413736 -368.62745 0.929 -0.147711 -0.098474 0.049237 + 7200 1280.4326 306.93914 -851.36608 4321.3892 -46.917022 -396.41924 0.928 -0.147552 -0.098368 0.049184 + 7300 1365.3317 299.9729 828.31029 4321.3892 -75.239942 -416.80992 0.927 -0.147393 -0.098262 0.049131 + 7400 1450.2442 315.71577 -2258.2975 4321.3892 -77.889538 -437.38543 0.926 -0.147234 -0.098156 0.049078 + 7500 1506.8723 300.07141 -1066.1338 4321.3892 -81.309686 -422.99183 0.925 -0.147075 -0.09805 0.049025 + 7600 1479.5677 300.46763 2522.7745 4321.3892 -59.141607 -401.27491 0.924 -0.146916 -0.097944 0.048972 + 7700 1486.7071 313.96637 534.54997 4321.3892 -32.408256 -389.91217 0.923 -0.146757 -0.097838 0.048919 + 7800 1460.0973 321.9645 5106.3828 4321.3892 -36.110275 -402.72141 0.922 -0.146598 -0.097732 0.048866 + 7900 1473.6768 307.50736 -3942.5615 4321.3892 -65.330897 -415.48013 0.921 -0.146439 -0.097626 0.048813 + 8000 1504.0498 294.39848 -1832.9535 4321.3892 -70.459732 -405.68229 0.92 -0.14628 -0.09752 0.04876 + 8100 1468.7781 304.28718 -189.43195 4321.3892 -55.133331 -401.61584 0.919 -0.146121 -0.097414 0.048707 + 8200 1557.1646 319.02283 4230.5317 4321.3892 -47.629777 -410.89132 0.918 -0.145962 -0.097308 0.048654 + 8300 1556.6952 293.4999 181.18352 4321.3892 -69.981799 -404.18117 0.917 -0.145803 -0.097202 0.048601 + 8400 1451.0615 274.30746 1400.9176 4321.3892 -92.417033 -404.76255 0.916 -0.145644 -0.097096 0.048548 + 8500 1390.1269 299.11094 -1413.3952 4321.3892 -73.457265 -414.04575 0.915 -0.145485 -0.09699 0.048495 + 8600 1526.8274 293.96637 -966.76211 4321.3892 -62.221729 -396.95226 0.914 -0.145326 -0.096884 0.048442 + 8700 1502.3239 300.59003 2603.3929 4321.3892 -51.141883 -393.41456 0.913 -0.145167 -0.096778 0.048389 + 8800 1477.6603 308.15475 -3167.6166 4321.3892 -51.633564 -402.51996 0.912 -0.145008 -0.096672 0.048336 + 8900 1404.4793 281.16982 486.65033 4321.3892 -84.815835 -404.97531 0.911 -0.144849 -0.096566 0.048283 + 9000 1424.7846 298.03984 -324.86358 4321.3892 -100.12166 -439.49052 0.91 -0.14469 -0.09646 0.04823 + 9100 1459.1724 296.61591 2439.8998 4321.3892 -85.458332 -423.2058 0.909 -0.144531 -0.096354 0.048177 + 9200 1531.9879 285.76254 -703.26192 4321.3892 -70.24585 -395.63492 0.908 -0.144372 -0.096248 0.048124 + 9300 1531.1159 309.08622 480.80176 4321.3892 -59.014943 -410.96197 0.907 -0.144213 -0.096142 0.048071 + 9400 1364.9221 302.81366 4047.2007 4321.3892 -46.537085 -391.34175 0.906 -0.144054 -0.096036 0.048018 + 9500 1319.5761 315.47312 -2178.3733 4321.3892 -40.286299 -399.5059 0.905 -0.143895 -0.09593 0.047965 + 9600 1391.9897 283.75501 5823.4447 4321.3892 -60.734392 -383.83755 0.904 -0.143736 -0.095824 0.047912 + 9700 1404.1358 290.17475 -1708.2225 4321.3892 -80.431455 -410.84458 0.903 -0.143577 -0.095718 0.047859 + 9800 1445.6242 292.05836 44.59996 4321.3892 -62.767593 -395.32553 0.902 -0.143418 -0.095612 0.047806 + 9900 1365.5774 298.31941 -223.25286 4321.3892 -35.976309 -375.6635 0.901 -0.143259 -0.095506 0.047753 + 10000 1343.7083 299.18429 1708.9208 4321.3892 -34.382217 -375.05423 0.9 -0.1431 -0.0954 0.0477 + 10100 1282.9797 308.71854 -652.52818 4321.3892 -46.004329 -397.5327 0.899 -0.142941 -0.095294 0.047647 + 10200 1278.3479 312.09094 2652.1454 4321.3892 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1078.2676 307.26587 -1181.6991 4321.3892 -78.786952 -428.6612 0.019 -0.003021 -0.002014 0.001007 + 98200 1247.6092 289.07166 202.07604 4321.3892 -73.395206 -402.55228 0.018 -0.002862 -0.001908 0.000954 + 98300 1200.7015 285.31381 -2299.6769 4321.3892 -45.2464 -370.12452 0.017 -0.002703 -0.001802 0.000901 + 98400 1085.8992 311.10198 -3232.7903 4321.3892 -33.607942 -387.85026 0.016 -0.002544 -0.001696 0.000848 + 98500 1091.9796 292.79852 -1965.1408 4321.3892 -38.555567 -371.95629 0.015 -0.002385 -0.00159 0.000795 + 98600 1144.6557 290.76805 -4137.567 4321.3892 -50.778851 -381.86754 0.014 -0.002226 -0.001484 0.000742 + 98700 1170.8695 283.83023 2206.1755 4321.3892 -58.562343 -381.75115 0.013 -0.002067 -0.001378 0.000689 + 98800 1193.8331 287.40594 1967.1514 4321.3892 -74.339987 -401.60034 0.012 -0.001908 -0.001272 0.000636 + 98900 1230.3623 289.38887 -1622.2824 4321.3892 -78.82881 -408.34707 0.011 -0.001749 -0.001166 0.000583 + 99000 1266.8669 310.73931 4085.1571 4321.3892 -53.129655 -406.95901 0.01 -0.00159 -0.00106 0.00053 + 99100 1251.781 306.15188 1860.7013 4321.3892 -29.112509 -377.71829 0.009 -0.001431 -0.000954 0.000477 + 99200 1152.1594 314.46538 -138.58309 4321.3892 -26.023578 -384.09569 0.008 -0.001272 -0.000848 0.000424 + 99300 1195.7914 294.0181 2065.5118 4321.3892 -49.077056 -383.86648 0.007 -0.001113 -0.000742 0.000371 + 99400 1266.2656 287.47157 -2921.4005 4321.3892 -65.534324 -392.86941 0.006 -0.000954 -0.000636 0.000318 + 99500 1269.4126 292.64019 -2312.8277 4321.3892 -58.326345 -391.54679 0.005 -0.000795 -0.00053 0.000265 + 99600 1296.8191 302.22068 2864.3077 4321.3892 -44.992409 -389.12186 0.004 -0.000636 -0.000424 0.000212 + 99700 1410.231 300.25576 552.56231 4321.3892 -32.773166 -374.66523 0.003 -0.000477 -0.000318 0.000159 + 99800 1435.524 336.9684 -1254.1072 4321.3892 -4.899367 -388.59499 0.002 -0.000318 -0.000212 0.000106 + 99900 1433.3697 319.25818 3463.0802 4321.3892 8.0883629 -355.44117 0.001 -0.000159 -0.000106 5.3e-05 + 100000 1318.7622 291.43698 -2961.7602 4321.3892 -27.295831 -359.14621 0 -0 -0 0 +Loop time of 78.283 on 16 procs for 100000 steps with 383 atoms + +Performance: 110.369 ns/day, 0.217 hours/ns, 1277.417 timesteps/s +94.1% CPU use with 16 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.43 | 19.194 | 29.637 | 81.5 | 24.52 +Bond | 3.2625 | 3.4917 | 4.0461 | 11.0 | 4.46 +Kspace | 29.911 | 40.821 | 44.717 | 57.6 | 52.14 +Neigh | 0.96168 | 0.96819 | 0.97633 | 0.5 | 1.24 +Comm | 10.348 | 10.581 | 10.846 | 4.3 | 13.52 +Output | 0.030217 | 0.031298 | 0.040418 | 1.3 | 0.04 +Modify | 1.8451 | 1.9233 | 1.9863 | 3.6 | 2.46 +Other | | 1.273 | | | 1.63 + +Nlocal: 23.9375 ave 37 max 16 min +Histogram: 3 3 2 2 1 2 0 1 1 1 +Nghost: 2317.44 ave 2369 max 2273 min +Histogram: 3 3 1 1 0 1 2 1 2 2 +Neighs: 5966.62 ave 8863 max 4086 min +Histogram: 4 2 2 0 2 1 2 1 0 2 + +Total # of neighbors = 95466 +Ave neighs/atom = 249.258 +Ave special neighs/atom = 4.72063 +Neighbor list builds = 3058 +Dangerous builds = 0 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.288285 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00277417 + estimated relative force accuracy = 8.35432e-06 + using double precision FFTs + 3d grid and FFT values/proc = 1296 90 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5 + ghost atom cutoff = 11.5 + binsize = 5.75, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/class2/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/class2/coul/long/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Total wall time: 0:01:18 diff --git a/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane b/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane new file mode 100644 index 0000000000..6483512de1 --- /dev/null +++ b/examples/USER/fep/C7inEthanol/fep10/data.init_conf_with_heptane @@ -0,0 +1,2783 @@ +LAMMPS data file via write_data, version 27 Nov 2018, timestep = 1100100 + +383 atoms +8 atom types +342 bonds +9 bond types +562 angles +14 angle types +534 dihedrals +11 dihedral types +348 impropers +11 improper types + +-5.0514130135769175e-01 1.5783110029075640e+01 xlo xhi +-8.0620338035756767e-01 1.5482047948350324e+01 ylo yhi +-8.6275306635756799e-01 1.5425498262350324e+01 zlo zhi + +Masses + +1 12.0112 +2 12.0112 +3 15.9994 +4 1.00797 +5 1.00797 +6 12.0112 +7 12.0112 +8 1.00797 + +Pair Coeffs # lj/class2/coul/long + +1 lj/class2/coul/long 0.054 4.01 +2 lj/class2/coul/long 0.054 4.01 +3 lj/class2/coul/long 0.24 3.535 +4 lj/class2/coul/long 0.02 2.995 +5 lj/class2/coul/long 0.013 1.098 +6 lj/class2/coul/long 0.054 4.01 +7 lj/class2/coul/long 0.054 4.01 +8 lj/class2/coul/long 0.02 2.995 + +Bond Coeffs # class2 + +1 1.53 299.67 -501.77 679.81 +2 1.101 345 -691.89 844.6 +3 1.101 345 -691.89 844.6 +4 1.42 400.395 -835.195 1313.01 +5 0.965 532.506 -1282.9 2004.77 +6 1.53 299.67 -501.77 679.81 +7 1.101 345 -691.89 844.6 +8 1.53 299.67 -501.77 679.81 +9 1.101 345 -691.89 844.6 + +Angle Coeffs # class2 + +1 110.77 41.453 -10.604 5.129 +2 107.66 39.641 -12.921 -2.4318 +3 110.77 41.453 -10.604 5.129 +4 111.27 54.5381 -8.3642 -13.0838 +5 107.66 39.641 -12.921 -2.4318 +6 108.728 58.5446 -10.8088 -12.4006 +7 105.8 52.7061 -12.109 -9.8681 +8 110.77 41.453 -10.604 5.129 +9 107.66 39.641 -12.921 -2.4318 +10 112.67 39.516 -7.443 -9.5583 +11 110.77 41.453 -10.604 5.129 +12 110.77 41.453 -10.604 5.129 +13 107.66 39.641 -12.921 -2.4318 +14 112.67 39.516 -7.443 -9.5583 + +BondBond Coeffs + +1 3.3872 1.53 1.101 +2 5.3316 1.101 1.101 +3 3.3872 1.53 1.101 +4 11.4318 1.53 1.42 +5 5.3316 1.101 1.101 +6 23.1979 1.42 1.101 +7 -9.6879 1.42 0.965 +8 3.3872 1.53 1.101 +9 5.3316 1.101 1.101 +10 0 1.53 1.53 +11 3.3872 1.53 1.101 +12 3.3872 1.53 1.101 +13 5.3316 1.101 1.101 +14 0 1.53 1.53 + +BondAngle Coeffs + +1 20.754 11.421 1.53 1.101 +2 18.103 18.103 1.101 1.101 +3 20.754 11.421 1.53 1.101 +4 2.6868 20.4033 1.53 1.42 +5 18.103 18.103 1.101 1.101 +6 55.327 4.6189 1.42 1.101 +7 28.58 18.9277 1.42 0.965 +8 20.754 11.421 1.53 1.101 +9 18.103 18.103 1.101 1.101 +10 8.016 8.016 1.53 1.53 +11 20.754 11.421 1.53 1.101 +12 20.754 11.421 1.53 1.101 +13 18.103 18.103 1.101 1.101 +14 8.016 8.016 1.53 1.53 + +Dihedral Coeffs # class2 + +1 -0.1432 0 0.0617 0 -0.1083 0 +2 -0.1435 0 0.253 0 -0.0905 0 +3 -0.6732 0 -0.4778 0 -0.167 0 +4 0.1863 0 -0.4338 0 -0.2121 0 +5 0 0 0.0316 0 -0.1681 0 +6 -0.1432 0 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292 289 293 294 diff --git a/examples/USER/fep/C7inEthanol/fep10/in.deletion b/examples/USER/fep/C7inEthanol/fep10/in.deletion new file mode 100644 index 0000000000..a7f09d09ba --- /dev/null +++ b/examples/USER/fep/C7inEthanol/fep10/in.deletion @@ -0,0 +1,57 @@ +# LAMMPS atomistic input script + +echo screen +units real +atom_style full + +pair_style hybrid lj/class2/coul/long 9.5 lj/class2/coul/long/soft 2 0.5 0.5 9.5 +bond_style class2 +angle_style class2 +dihedral_style class2 +improper_style class2 +pair_modify mix sixthpower tail yes +special_bonds lj/coul 0 0 1 + +read_data data.init_conf_with_heptane + +pair_coeff 1 6 lj/class2/coul/long/soft 0.054 4.01 1.0 +pair_coeff 2 6 lj/class2/coul/long/soft 0.054 4.01 1.0 +pair_coeff 3 6 lj/class2/coul/long/soft 0.10615754 3.80912744 1.0 +pair_coeff 4 6 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0 +pair_coeff 5 6 lj/class2/coul/long/soft 0.00108740 3.57275476 1.0 + +pair_coeff 1 7 lj/class2/coul/long/soft 0.054 4.01 1.0 +pair_coeff 2 7 lj/class2/coul/long/soft 0.054 4.01 1.0 +pair_coeff 3 7 lj/class2/coul/long/soft 0.10615754 3.80912744 1.0 +pair_coeff 4 7 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0 +pair_coeff 5 7 lj/class2/coul/long/soft 0.00108740 3.57275476 1.0 + +pair_coeff 1 8 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0 +pair_coeff 2 8 lj/class2/coul/long/soft 0.02333374 3.66909137 1.0 +pair_coeff 3 8 lj/class2/coul/long/soft 0.06151694 3.31892497 1.0 +pair_coeff 4 8 lj/class2/coul/long/soft 0.02 2.995 1.0 +pair_coeff 5 8 lj/class2/coul/long/soft 0.00158519 2.66932028 1.0 + +timestep 1.0 +kspace_style pppm 1.0e-5 + +variable lambda equal ramp(1.0,0.0) +variable q1 equal -0.1590*v_lambda +variable q2 equal -0.1060*v_lambda +variable q3 equal 0.0530*v_lambda + +fix ADAPT all adapt/fep 10 & + pair lj/class2/coul/long/soft lambda 1*5 6*8 v_lambda & + atom charge 6 v_q1 & + atom charge 7 v_q2 & + atom charge 8 v_q3 & + after yes + +thermo_style custom step spcpu temp press vol etotal pe v_lambda v_q1 v_q2 v_q3 +thermo_modify line one +thermo 100 + +fix 1 all nvt temp 300 300 100 +run 100000 + +write_data data.after_heptane_deletion diff --git a/examples/USER/fep/C7inEthanol/fep10/log.lammps b/examples/USER/fep/C7inEthanol/fep10/log.lammps new file mode 100644 index 0000000000..fbd4a49a3e --- /dev/null +++ b/examples/USER/fep/C7inEthanol/fep10/log.lammps @@ -0,0 +1,1125 @@ +LAMMPS (27 Nov 2018) +# LAMMPS atomistic input script + +echo screen + orthogonal box = (-0.505141 -0.806203 -0.862753) to (15.7831 15.482 15.4255) + 4 by 2 by 2 MPI processor grid +WARNING: Pair style in data file differs from currently defined pair style (../read_data.cpp:580) + reading atoms ... + 383 atoms + reading velocities ... + 383 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 9 = max dihedrals/atom + scanning impropers ... + 4 = max impropers/atom + reading bonds ... + 342 bonds + reading angles ... + 562 angles + reading dihedrals ... + 534 dihedrals + reading impropers ... + 348 impropers + 4 = max # of 1-2 neighbors + 6 = max # of 1-3 neighbors + 10 = max # of special neighbors +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.288287 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00279394 + estimated relative force accuracy = 8.41388e-06 + using double precision FFTs + 3d grid and FFT values/proc = 1296 90 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5 + ghost atom cutoff = 11.5 + binsize = 5.75, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/class2/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/class2/coul/long/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.61 | 13.92 | 14.89 Mbytes +Step S/CPU Temp Press Volume TotEng PotEng v_lambda v_q1 v_q2 v_q3 + 0 0 301.82904 533.3184 4321.3892 -79.144423 -422.82793 1 -0.159 -0.106 0.053 + 100 799.51858 297.06821 2966.9114 4321.3892 -67.550969 -405.81346 0.999 -0.158841 -0.105894 0.052947 + 200 1111.1841 310.89475 -1076.6004 4321.3892 -32.998901 -387.00525 0.998 -0.158682 -0.105788 0.052894 + 300 1459.1789 313.65424 320.85082 4321.3892 -29.026776 -386.17527 0.997 -0.158523 -0.105682 0.052841 + 400 1415.1559 311.37233 -4525.9921 4321.3892 -43.910969 -398.46112 0.996 -0.158364 -0.105576 0.052788 + 500 1489.9869 288.38744 -1783.6133 4321.3892 -59.978436 -388.3564 0.995 -0.158205 -0.10547 0.052735 + 600 1372.2162 300.78589 2406.4287 4321.3892 -58.529306 -401.025 0.994 -0.158046 -0.105364 0.052682 + 700 1273.4802 302.48787 1188.4083 4321.3892 -19.664773 -364.09847 0.993 -0.157887 -0.105258 0.052629 + 800 1379.5701 324.19685 3525.573 4321.3892 -6.5601902 -375.71324 0.992 -0.157728 -0.105152 0.052576 + 900 1417.4117 302.20264 580.80929 4321.3892 -31.492626 -375.60153 0.991 -0.157569 -0.105046 0.052523 + 1000 1423.0943 288.09813 -3390.5518 4321.3892 -50.795041 -378.84358 0.99 -0.15741 -0.10494 0.05247 + 1100 1339.6567 279.41478 -1585.8135 4321.3892 -65.305421 -383.46649 0.989 -0.157251 -0.104834 0.052417 + 1200 1283.0804 297.57659 -5628.1846 4321.3892 -61.457533 -400.2989 0.988 -0.157092 -0.104728 0.052364 + 1300 1374.8154 302.95867 2800.3971 4321.3892 -25.223933 -370.19371 0.987 -0.156933 -0.104622 0.052311 + 1400 1548.7979 314.63757 169.32405 4321.3892 -9.2461401 -367.51433 0.986 -0.156774 -0.104516 0.052258 + 1500 1543.4384 302.78598 2667.3171 4321.3892 -28.872419 -373.64556 0.985 -0.156615 -0.10441 0.052205 + 1600 1505.9924 307.4754 -3144.1719 4321.3892 -42.805804 -392.91864 0.984 -0.156456 -0.104304 0.052152 + 1700 1519.2347 291.11376 -51.878589 4321.3892 -44.622256 -376.1046 0.983 -0.156297 -0.104198 0.052099 + 1800 1442.3107 297.91891 1568.4932 4321.3892 -38.314165 -377.54533 0.982 -0.156138 -0.104092 0.052046 + 1900 1416.7513 299.44141 -3439.0539 4321.3892 -34.396006 -375.36079 0.981 -0.155979 -0.103986 0.051993 + 2000 1320.1308 311.55135 -4036.9906 4321.3892 -38.635681 -393.38969 0.98 -0.15582 -0.10388 0.05194 + 2100 1352.1874 294.77184 1722.2251 4321.3892 -52.682147 -388.32983 0.979 -0.155661 -0.103774 0.051887 + 2200 1398.9382 275.77965 -798.41267 4321.3892 -87.333361 -401.35522 0.978 -0.155502 -0.103668 0.051834 + 2300 1401.8526 288.31697 1440.4268 4321.3892 -95.443884 -423.7416 0.977 -0.155343 -0.103562 0.051781 + 2400 1410.2793 300.6133 1047.3407 4321.3892 -67.450573 -409.74975 0.976 -0.155184 -0.103456 0.051728 + 2500 1342.2665 304.4924 4512.7456 4321.3892 -46.485002 -393.20119 0.975 -0.155025 -0.10335 0.051675 + 2600 1399.6709 304.59021 -1440.2459 4321.3892 -41.296463 -388.12403 0.974 -0.154866 -0.103244 0.051622 + 2700 1393.5595 307.63992 1801.3517 4321.3892 -35.974699 -386.27487 0.973 -0.154707 -0.103138 0.051569 + 2800 1416.1276 301.99824 680.3111 4321.3892 -37.283922 -381.16009 0.972 -0.154548 -0.103032 0.051516 + 2900 1467.076 290.21584 -655.51621 4321.3892 -55.113989 -385.5739 0.971 -0.154389 -0.102926 0.051463 + 3000 1507.7721 284.82664 2047.2406 4321.3892 -81.291143 -405.61453 0.97 -0.15423 -0.10282 0.05141 + 3100 1470.3382 285.07726 -4149.6477 4321.3892 -85.012313 -409.62108 0.969 -0.154071 -0.102714 0.051357 + 3200 1514.1911 299.64651 1428.5333 4321.3892 -52.958903 -394.15722 0.968 -0.153912 -0.102608 0.051304 + 3300 1511.3429 311.60785 36.886282 4321.3892 -40.626937 -395.44527 0.967 -0.153753 -0.102502 0.051251 + 3400 1570.8737 299.11947 3828.1184 4321.3892 -43.612199 -384.2104 0.966 -0.153594 -0.102396 0.051198 + 3500 1588.4825 297.08441 2021.8438 4321.3892 -52.83333 -391.11427 0.965 -0.153435 -0.10229 0.051145 + 3600 1514.3641 294.38448 510.47993 4321.3892 -76.148011 -411.35462 0.964 -0.153276 -0.102184 0.051092 + 3700 1579.6325 267.42535 1976.3472 4321.3892 -92.292608 -396.80168 0.963 -0.153117 -0.102078 0.051039 + 3800 1579.4417 305.93263 -2594.8587 4321.3892 -60.46367 -408.8198 0.962 -0.152958 -0.101972 0.050986 + 3900 1556.0604 295.41636 -2413.3469 4321.3892 -39.598538 -375.98011 0.961 -0.152799 -0.101866 0.050933 + 4000 1480.4195 291.39244 23.97447 4321.3892 -39.171532 -370.9712 0.96 -0.15264 -0.10176 0.05088 + 4100 1427.5893 302.95007 -136.92129 4321.3892 -61.300632 -406.26062 0.959 -0.152481 -0.101654 0.050827 + 4200 1507.0531 290.0336 -1924.0805 4321.3892 -78.49136 -408.74376 0.958 -0.152322 -0.101548 0.050774 + 4300 1530.443 301.52983 1346.5118 4321.3892 -65.981817 -409.32462 0.957 -0.152163 -0.101442 0.050721 + 4400 1522.4039 296.09695 2033.2832 4321.3892 -38.949103 -376.10565 0.956 -0.152004 -0.101336 0.050668 + 4500 1469.3288 299.67261 -2870.5264 4321.3892 -36.881907 -378.10995 0.955 -0.151845 -0.10123 0.050615 + 4600 1476.1078 317.35258 -43.577562 4321.3892 -46.136233 -407.49591 0.954 -0.151686 -0.101124 0.050562 + 4700 1521.8164 285.69675 -2599.4101 4321.3892 -67.71719 -393.03135 0.953 -0.151527 -0.101018 0.050509 + 4800 1567.0075 297.89711 -3002.7695 4321.3892 -82.138424 -421.34476 0.952 -0.151368 -0.100912 0.050456 + 4900 1603.8725 292.54174 392.88991 4321.3892 -77.729344 -410.83769 0.951 -0.151209 -0.100806 0.050403 + 5000 1596.5842 324.83308 522.49599 4321.3892 -37.736703 -407.6142 0.95 -0.15105 -0.1007 0.05035 + 5100 1606.1392 312.9193 -878.4909 4321.3892 -35.650262 -391.96191 0.949 -0.150891 -0.100594 0.050297 + 5200 1596.9711 301.10369 4932.6479 4321.3892 -53.77998 -396.63755 0.948 -0.150732 -0.100488 0.050244 + 5300 1465.77 299.48781 -279.78852 4321.3892 -74.767934 -415.78555 0.947 -0.150573 -0.100382 0.050191 + 5400 1373.2951 283.80778 -213.42159 4321.3892 -98.619463 -421.78271 0.946 -0.150414 -0.100276 0.050138 + 5500 1420.5231 264.12997 -2228.6488 4321.3892 -130.10614 -430.86286 0.945 -0.150255 -0.10017 0.050085 + 5600 1515.9938 266.04428 -2171.6706 4321.3892 -108.55638 -411.49288 0.944 -0.150096 -0.100064 0.050032 + 5700 1549.72 276.23021 1058.2904 4321.3892 -77.55162 -392.08652 0.943 -0.149937 -0.099958 0.049979 + 5800 1522.7747 296.33023 2834.8108 4321.3892 -52.620617 -390.0428 0.942 -0.149778 -0.099852 0.049926 + 5900 1501.6416 310.56588 2024.1237 4321.3892 -35.466522 -389.0984 0.941 -0.149619 -0.099746 0.049873 + 6000 1518.1573 305.31866 90.498107 4321.3892 -37.024388 -384.68142 0.94 -0.14946 -0.09964 0.04982 + 6100 1492.5011 298.08903 1653.7952 4321.3892 -59.680839 -399.1057 0.939 -0.149301 -0.099534 0.049767 + 6200 1441.766 282.17236 -1566.1626 4321.3892 -77.565829 -398.86687 0.938 -0.149142 -0.099428 0.049714 + 6300 1425.2832 297.96681 -2194.5697 4321.3892 -58.623811 -397.90951 0.937 -0.148983 -0.099322 0.049661 + 6400 1555.6883 320.41355 286.39321 4321.3892 -19.662831 -384.50795 0.936 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4321.3892 -77.889538 -437.38543 0.926 -0.147234 -0.098156 0.049078 + 7500 1506.8723 300.07141 -1066.1338 4321.3892 -81.309686 -422.99183 0.925 -0.147075 -0.09805 0.049025 + 7600 1479.5677 300.46763 2522.7745 4321.3892 -59.141607 -401.27491 0.924 -0.146916 -0.097944 0.048972 + 7700 1486.7071 313.96637 534.54997 4321.3892 -32.408256 -389.91217 0.923 -0.146757 -0.097838 0.048919 + 7800 1460.0973 321.9645 5106.3828 4321.3892 -36.110275 -402.72141 0.922 -0.146598 -0.097732 0.048866 + 7900 1473.6768 307.50736 -3942.5615 4321.3892 -65.330897 -415.48013 0.921 -0.146439 -0.097626 0.048813 + 8000 1504.0498 294.39848 -1832.9535 4321.3892 -70.459732 -405.68229 0.92 -0.14628 -0.09752 0.04876 + 8100 1468.7781 304.28718 -189.43195 4321.3892 -55.133331 -401.61584 0.919 -0.146121 -0.097414 0.048707 + 8200 1557.1646 319.02283 4230.5317 4321.3892 -47.629777 -410.89132 0.918 -0.145962 -0.097308 0.048654 + 8300 1556.6952 293.4999 181.18352 4321.3892 -69.981799 -404.18117 0.917 -0.145803 -0.097202 0.048601 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-0.007632 -0.005088 0.002544 + 95300 1313.8364 307.27814 -2352.9934 4321.3892 -54.373095 -404.26132 0.047 -0.007473 -0.004982 0.002491 + 95400 1201.8365 298.47877 -2718.7005 4321.3892 -45.986629 -385.85528 0.046 -0.007314 -0.004876 0.002438 + 95500 1103.6045 306.69668 -741.22716 4321.3892 -37.949989 -387.17613 0.045 -0.007155 -0.00477 0.002385 + 95600 1035.5871 286.79853 -1438.1728 4321.3892 -27.503416 -354.07213 0.044 -0.006996 -0.004664 0.002332 + 95700 1013.5068 320.48771 -5332.312 4321.3892 1.4199032 -363.50966 0.043 -0.006837 -0.004558 0.002279 + 95800 962.97959 304.6672 4340.0573 4321.3892 -20.784782 -367.70001 0.042 -0.006678 -0.004452 0.002226 + 95900 994.9843 299.96049 1484.318 4321.3892 -52.16709 -393.72294 0.041 -0.006519 -0.004346 0.002173 + 96000 1050.3279 294.67736 1439.7438 4321.3892 -48.622496 -384.1626 0.04 -0.00636 -0.00424 0.00212 + 96100 1088.3112 304.24734 -1088.2219 4321.3892 -36.639733 -383.07688 0.039 -0.006201 -0.004134 0.002067 + 96200 1132.9303 303.40913 326.74855 4321.3892 -18.241844 -363.72455 0.038 -0.006042 -0.004028 0.002014 + 96300 1230.6357 299.38135 -2205.1375 4321.3892 -14.056249 -354.95264 0.037 -0.005883 -0.003922 0.001961 + 96400 1209.7709 301.6218 130.93366 4321.3892 -45.370521 -388.81805 0.036 -0.005724 -0.003816 0.001908 + 96500 1204.9443 292.54592 -682.29661 4321.3892 -62.29541 -395.4085 0.035 -0.005565 -0.00371 0.001855 + 96600 1289.3438 300.5615 -174.9403 4321.3892 -57.725164 -399.96536 0.034 -0.005406 -0.003604 0.001802 + 96700 1338.818 308.2797 -1794.2828 4321.3892 -28.915577 -379.94425 0.033 -0.005247 -0.003498 0.001749 + 96800 1359.4009 305.91475 1486.7387 4321.3892 -8.4642777 -356.80006 0.032 -0.005088 -0.003392 0.001696 + 96900 1407.6407 306.58372 544.53377 4321.3892 -25.698784 -374.79629 0.031 -0.004929 -0.003286 0.001643 + 97000 1385.4966 288.17608 2812.0548 4321.3892 -36.040522 -364.17782 0.03 -0.00477 -0.00318 0.00159 + 97100 1184.017 311.13508 3386.5961 4321.3892 -35.636018 -389.91602 0.029 -0.004611 -0.003074 0.001537 + 97200 1052.5132 302.83751 -450.40793 4321.3892 -48.013358 -392.84518 0.028 -0.004452 -0.002968 0.001484 + 97300 936.51847 296.05186 2250.9701 4321.3892 -65.08671 -402.19191 0.027 -0.004293 -0.002862 0.001431 + 97400 879.09894 281.15562 204.89405 4321.3892 -79.023788 -399.1671 0.026 -0.004134 -0.002756 0.001378 + 97500 868.33473 269.68695 -3949.5957 4321.3892 -90.496345 -397.58063 0.025 -0.003975 -0.00265 0.001325 + 97600 915.76128 283.95639 441.03454 4321.3892 -55.42154 -378.754 0.024 -0.003816 -0.002544 0.001272 + 97700 896.34506 289.78136 -6167.1083 4321.3892 -37.414959 -367.38014 0.023 -0.003657 -0.002438 0.001219 + 97800 923.57325 298.24796 -2426.5007 4321.3892 -29.79808 -369.40392 0.022 -0.003498 -0.002332 0.001166 + 97900 939.86442 304.1769 -769.76822 4321.3892 -28.013008 -374.36994 0.021 -0.003339 -0.002226 0.001113 + 98000 965.49764 315.25564 4166.1952 4321.3892 -55.957081 -414.92904 0.02 -0.00318 -0.00212 0.00106 + 98100 1078.2676 307.26587 -1181.6991 4321.3892 -78.786952 -428.6612 0.019 -0.003021 -0.002014 0.001007 + 98200 1247.6092 289.07166 202.07604 4321.3892 -73.395206 -402.55228 0.018 -0.002862 -0.001908 0.000954 + 98300 1200.7015 285.31381 -2299.6769 4321.3892 -45.2464 -370.12452 0.017 -0.002703 -0.001802 0.000901 + 98400 1085.8992 311.10198 -3232.7903 4321.3892 -33.607942 -387.85026 0.016 -0.002544 -0.001696 0.000848 + 98500 1091.9796 292.79852 -1965.1408 4321.3892 -38.555567 -371.95629 0.015 -0.002385 -0.00159 0.000795 + 98600 1144.6557 290.76805 -4137.567 4321.3892 -50.778851 -381.86754 0.014 -0.002226 -0.001484 0.000742 + 98700 1170.8695 283.83023 2206.1755 4321.3892 -58.562343 -381.75115 0.013 -0.002067 -0.001378 0.000689 + 98800 1193.8331 287.40594 1967.1514 4321.3892 -74.339987 -401.60034 0.012 -0.001908 -0.001272 0.000636 + 98900 1230.3623 289.38887 -1622.2824 4321.3892 -78.82881 -408.34707 0.011 -0.001749 -0.001166 0.000583 + 99000 1266.8669 310.73931 4085.1571 4321.3892 -53.129655 -406.95901 0.01 -0.00159 -0.00106 0.00053 + 99100 1251.781 306.15188 1860.7013 4321.3892 -29.112509 -377.71829 0.009 -0.001431 -0.000954 0.000477 + 99200 1152.1594 314.46538 -138.58309 4321.3892 -26.023578 -384.09569 0.008 -0.001272 -0.000848 0.000424 + 99300 1195.7914 294.0181 2065.5118 4321.3892 -49.077056 -383.86648 0.007 -0.001113 -0.000742 0.000371 + 99400 1266.2656 287.47157 -2921.4005 4321.3892 -65.534324 -392.86941 0.006 -0.000954 -0.000636 0.000318 + 99500 1269.4126 292.64019 -2312.8277 4321.3892 -58.326345 -391.54679 0.005 -0.000795 -0.00053 0.000265 + 99600 1296.8191 302.22068 2864.3077 4321.3892 -44.992409 -389.12186 0.004 -0.000636 -0.000424 0.000212 + 99700 1410.231 300.25576 552.56231 4321.3892 -32.773166 -374.66523 0.003 -0.000477 -0.000318 0.000159 + 99800 1435.524 336.9684 -1254.1072 4321.3892 -4.899367 -388.59499 0.002 -0.000318 -0.000212 0.000106 + 99900 1433.3697 319.25818 3463.0802 4321.3892 8.0883629 -355.44117 0.001 -0.000159 -0.000106 5.3e-05 + 100000 1318.7622 291.43698 -2961.7602 4321.3892 -27.295831 -359.14621 0 -0 -0 0 +Loop time of 78.283 on 16 procs for 100000 steps with 383 atoms + +Performance: 110.369 ns/day, 0.217 hours/ns, 1277.417 timesteps/s +94.1% CPU use with 16 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.43 | 19.194 | 29.637 | 81.5 | 24.52 +Bond | 3.2625 | 3.4917 | 4.0461 | 11.0 | 4.46 +Kspace | 29.911 | 40.821 | 44.717 | 57.6 | 52.14 +Neigh | 0.96168 | 0.96819 | 0.97633 | 0.5 | 1.24 +Comm | 10.348 | 10.581 | 10.846 | 4.3 | 13.52 +Output | 0.030217 | 0.031298 | 0.040418 | 1.3 | 0.04 +Modify | 1.8451 | 1.9233 | 1.9863 | 3.6 | 2.46 +Other | | 1.273 | | | 1.63 + +Nlocal: 23.9375 ave 37 max 16 min +Histogram: 3 3 2 2 1 2 0 1 1 1 +Nghost: 2317.44 ave 2369 max 2273 min +Histogram: 3 3 1 1 0 1 2 1 2 2 +Neighs: 5966.62 ave 8863 max 4086 min +Histogram: 4 2 2 0 2 1 2 1 0 2 + +Total # of neighbors = 95466 +Ave neighs/atom = 249.258 +Ave special neighs/atom = 4.72063 +Neighbor list builds = 3058 +Dangerous builds = 0 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.288285 + grid = 10 10 10 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00277417 + estimated relative force accuracy = 8.35432e-06 + using double precision FFTs + 3d grid and FFT values/proc = 1296 90 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.5 + ghost atom cutoff = 11.5 + binsize = 5.75, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/class2/coul/long, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/class2/coul/long/soft, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Total wall time: 0:01:18 diff --git a/examples/USER/fep/README b/examples/USER/fep/README index 187c26be80..64c46f2b03 100644 --- a/examples/USER/fep/README +++ b/examples/USER/fep/README @@ -9,3 +9,6 @@ compute fep examples * `CC-CO` -- free energy difference of transforming ethane into methanol, in water (more complex). FEP, TI and BAR methods. + +* 'C7inEthanol' -- insertion / deletion of a hexane molecule in ethanol. + The hexane is described by the lj/class2/coul/long/soft potential. diff --git a/examples/USER/misc/entropy/log.entropy b/examples/USER/misc/entropy/log.entropy index c380c62a73..333214ada8 100644 --- a/examples/USER/misc/entropy/log.entropy +++ b/examples/USER/misc/entropy/log.entropy @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (4 Jan 2019) units metal atom_style full @@ -45,10 +45,10 @@ fix 1 all nph x 1. 1. 10. fix 2 all temp/csvr 350. 350. 0.1 64582 run 1000 -WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) -WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) -WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) -WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139) +WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -56,27 +56,27 @@ Neighbor list info ... ghost atom cutoff = 13.2 binsize = 6.6, bins = 21 6 6 5 neighbor lists, perpetual/occasional/extra = 5 0 0 - (1) pair eam/fs, perpetual + (1) pair eam/fs, perpetual, half/full from (2) attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard + pair build: halffull/newton + stencil: none + bin: none (2) compute entropy/atom, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (3) compute entropy/atom, perpetual, copy from (2) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (4) compute entropy/atom, perpetual attributes: full, newton on, ghost pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard - (3) compute entropy/atom, perpetual, copy from (2) - attributes: full, newton on, ghost - pair build: copy - stencil: none - bin: none - (4) compute entropy/atom, perpetual, copy from (2) - attributes: full, newton on, ghost - pair build: copy - stencil: none - bin: none - (5) compute entropy/atom, perpetual, copy from (2) + (5) compute entropy/atom, perpetual, copy from (4) attributes: full, newton on, ghost pair build: copy stencil: none @@ -85,34 +85,34 @@ Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.002 -Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes +Per MPI rank memory allocation (min/avg/max) = 19.6 | 19.6 | 19.6 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75 - 500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18 - 1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18 -Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms + 500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09 + 1000 348.99683 -4276.2282 0 -4091.4971 149.38771 166965.86 +Loop time of 4.4394 on 4 procs for 1000 steps with 4096 atoms -Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 38.924 ns/day, 0.617 hours/ns, 225.256 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.2832 | 4.3257 | 4.3839 | 1.8 | 80.95 -Bond | 0.00018309 | 0.00019825 | 0.00021418 | 0.0 | 0.00 -Neigh | 0.42195 | 0.42512 | 0.42739 | 0.3 | 7.96 -Comm | 0.051679 | 0.1101 | 0.14916 | 10.8 | 2.06 -Output | 0.40909 | 0.4091 | 0.40911 | 0.0 | 7.66 -Modify | 0.060869 | 0.061921 | 0.06327 | 0.4 | 1.16 -Other | | 0.01161 | | | 0.22 +Pair | 3.5298 | 3.5931 | 3.6669 | 2.6 | 80.94 +Bond | 8.2099e-05 | 0.00011444 | 0.00014673 | 0.0 | 0.00 +Neigh | 0.43384 | 0.4445 | 0.45558 | 1.4 | 10.01 +Comm | 0.048904 | 0.11122 | 0.16728 | 12.7 | 2.51 +Output | 0.22595 | 0.22595 | 0.22596 | 0.0 | 5.09 +Modify | 0.053103 | 0.053795 | 0.054549 | 0.3 | 1.21 +Other | | 0.01068 | | | 0.24 Nlocal: 1024 ave 1040 max 1001 min Histogram: 1 0 0 0 0 0 2 0 0 1 Nghost: 4614.25 ave 4700 max 4540 min Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 121747 ave 126398 max 116931 min +Neighs: 121747 ave 126398 max 116930 min Histogram: 1 0 0 1 0 0 1 0 0 1 -FullNghs: 243494 ave 252523 max 233842 min +FullNghs: 243494 ave 252523 max 233841 min Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 973974 @@ -121,4 +121,4 @@ Ave special neighs/atom = 0 Neighbor list builds = 13 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:04 diff --git a/examples/USER/misc/lebedeva/2particles.dat b/examples/USER/misc/lebedeva/2particles.dat new file mode 100644 index 0000000000..43eabd7d24 --- /dev/null +++ b/examples/USER/misc/lebedeva/2particles.dat @@ -0,0 +1,14 @@ +Ideal graphene structure in YZ plane created with create_graphen.pl + +2 atoms + +2 atom types + + 0.0 20 xlo xhi + 0.0 20 ylo yhi + 0.0 5 zlo zhi + +Atoms + + 1 1 10 10 0.0 + 2 2 0 0 3.35 diff --git a/examples/USER/misc/lebedeva/2particles.in b/examples/USER/misc/lebedeva/2particles.in new file mode 100644 index 0000000000..81cca2e473 --- /dev/null +++ b/examples/USER/misc/lebedeva/2particles.in @@ -0,0 +1,63 @@ +# After running LAMMPS with this input script a number of dump files is created. +# To extract the data from there I used grep script: +# grep '^2 ' *cfg > LammpsResult.dat +# After that after removing some text from LammpsResult.dat, +# the data can be viewed by lebedeva00.plot +# +# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland +# Email: softquake@gmail.com + + +# ---------- Start simulation --------------------- +clear +units metal +dimension 3 +boundary f f f +atom_style atomic + +# ========================== Create Atomistic Structure =========================== + +region whole block 0 20 0 20 0 10 +create_box 2 whole + +read_data 2particles.dat add append + +region graphite block INF INF INF INF 0 10 units box +group graphite type 1 2 +group graphene1 type 1 +group graphene2 type 2 + +pair_style hybrid/overlay lebedeva/z 20 +pair_coeff * * none +pair_coeff 1 2 lebedeva/z CC.Lebedeva C C + +mass 1 12.01 # Carbon +mass 2 12.01 # Carbon + +neighbor 0.3 bin +neigh_modify delay 1 check yes + +compute peratom all pe/atom + +dump 1 all custom 1 dump_lebedeva_*.cfg id x y z c_peratom fx fy fz +dump_modify 1 pad 3 + +thermo 10 +thermo_style custom step pe press temp +thermo_modify lost ignore + +label STEP_LOOP + +variable MYSTEP loop 0 400 pad # in degrees +variable DELTA_STEP equal 0.05 + +displace_atoms graphene2 move ${DELTA_STEP} ${DELTA_STEP} 0 + +run 1 + +next MYSTEP +jump SELF STEP_LOOP + +print "all done" + + diff --git a/examples/USER/misc/lebedeva/CC.Lebedeva b/examples/USER/misc/lebedeva/CC.Lebedeva new file mode 100644 index 0000000000..930f7b4328 --- /dev/null +++ b/examples/USER/misc/lebedeva/CC.Lebedeva @@ -0,0 +1,14 @@ +# Lebedeva Potential. Original values from Lebedeva. May be played with ;) +# +# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin, +# Modeling of graphene-based NEMS +# Physica E 44 (6), 949 (2012) +# https://doi.org/10.1016/j.physe.2011.07.018 +# +# Parameters must be in this order as here, otherwise their values may be changed. +# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C +# A B C z0 alpha D1 D2 lambda1 lambda2 S +# These are values according to Levedeva et al +#C C 10.510 11.6523.34 35.883 3.34 4.16 -0.86232 0.10049 0.48703 0.46445 1.0 +# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162 +C C 14.558 21.204 1.8 3.198 4.16 -0.862 0.10049 0.6 0.4 1.0 diff --git a/examples/USER/misc/lebedeva/LammpsResult.dat b/examples/USER/misc/lebedeva/LammpsResult.dat new file mode 100644 index 0000000000..ff9dfe1949 --- /dev/null +++ b/examples/USER/misc/lebedeva/LammpsResult.dat @@ -0,0 +1,400 @@ +dump_lebedeva_000.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07 +dump_lebedeva_001.cfg:2 0.05 0.05 3.35 -7.28468e-07 4.85145e-07 4.85145e-07 -1.6334e-07 +dump_lebedeva_002.cfg:2 0.1 0.1 3.35 -7.5313e-07 5.01468e-07 5.01468e-07 -1.69689e-07 +dump_lebedeva_003.cfg:2 0.15 0.15 3.35 -7.78625e-07 5.18417e-07 5.18417e-07 -1.76314e-07 +dump_lebedeva_004.cfg:2 0.2 0.2 3.35 -8.04983e-07 5.36017e-07 5.36017e-07 -1.8323e-07 +dump_lebedeva_005.cfg:2 0.25 0.25 3.35 -8.32238e-07 5.54298e-07 5.54298e-07 -1.90451e-07 +dump_lebedeva_006.cfg:2 0.3 0.3 3.35 -8.60425e-07 5.73288e-07 5.73288e-07 -1.97991e-07 +dump_lebedeva_007.cfg:2 0.35 0.35 3.35 -8.89579e-07 5.93019e-07 5.93019e-07 -2.05867e-07 +dump_lebedeva_008.cfg:2 0.4 0.4 3.35 -9.19739e-07 6.13522e-07 6.13522e-07 -2.14094e-07 +dump_lebedeva_009.cfg:2 0.45 0.45 3.35 -9.50945e-07 6.34832e-07 6.34832e-07 -2.2269e-07 +dump_lebedeva_010.cfg:2 0.5 0.5 3.35 -9.83237e-07 6.56984e-07 6.56984e-07 -2.31673e-07 +dump_lebedeva_011.cfg:2 0.55 0.55 3.35 -1.01666e-06 6.80016e-07 6.80016e-07 -2.41064e-07 +dump_lebedeva_012.cfg:2 0.6 0.6 3.35 -1.05125e-06 7.03966e-07 7.03966e-07 -2.50881e-07 +dump_lebedeva_013.cfg:2 0.65 0.65 3.35 -1.08707e-06 7.28875e-07 7.28875e-07 -2.61148e-07 +dump_lebedeva_014.cfg:2 0.7 0.7 3.35 -1.12416e-06 7.54787e-07 7.54787e-07 -2.71886e-07 +dump_lebedeva_015.cfg:2 0.75 0.75 3.35 -1.16257e-06 7.81747e-07 7.81747e-07 -2.83119e-07 +dump_lebedeva_016.cfg:2 0.8 0.8 3.35 -1.20235e-06 8.09802e-07 8.09802e-07 -2.94873e-07 +dump_lebedeva_017.cfg:2 0.85 0.85 3.35 -1.24357e-06 8.39001e-07 8.39001e-07 -3.07175e-07 +dump_lebedeva_018.cfg:2 0.9 0.9 3.35 -1.28627e-06 8.69398e-07 8.69398e-07 -3.20053e-07 +dump_lebedeva_019.cfg:2 0.95 0.95 3.35 -1.33053e-06 9.01046e-07 9.01046e-07 -3.33537e-07 +dump_lebedeva_020.cfg:2 1 1 3.35 -1.3764e-06 9.34005e-07 9.34005e-07 -3.47657e-07 +dump_lebedeva_021.cfg:2 1.05 1.05 3.35 -1.42395e-06 9.68333e-07 9.68333e-07 -3.62449e-07 +dump_lebedeva_022.cfg:2 1.1 1.1 3.35 -1.47325e-06 1.0041e-06 1.0041e-06 -3.77946e-07 +dump_lebedeva_023.cfg:2 1.15 1.15 3.35 -1.52438e-06 1.04136e-06 1.04136e-06 -3.94187e-07 +dump_lebedeva_024.cfg:2 1.2 1.2 3.35 -1.57742e-06 1.08019e-06 1.08019e-06 -4.1121e-07 +dump_lebedeva_025.cfg:2 1.25 1.25 3.35 -1.63243e-06 1.12067e-06 1.12067e-06 -4.29058e-07 +dump_lebedeva_026.cfg:2 1.3 1.3 3.35 -1.68951e-06 1.16288e-06 1.16288e-06 -4.47775e-07 +dump_lebedeva_027.cfg:2 1.35 1.35 3.35 -1.74875e-06 1.20689e-06 1.20689e-06 -4.67407e-07 +dump_lebedeva_028.cfg:2 1.4 1.4 3.35 -1.81023e-06 1.25279e-06 1.25279e-06 -4.88004e-07 +dump_lebedeva_029.cfg:2 1.45 1.45 3.35 -1.87406e-06 1.30067e-06 1.30067e-06 -5.0962e-07 +dump_lebedeva_030.cfg:2 1.5 1.5 3.35 -1.94033e-06 1.35063e-06 1.35063e-06 -5.32308e-07 +dump_lebedeva_031.cfg:2 1.55 1.55 3.35 -2.00916e-06 1.40277e-06 1.40277e-06 -5.56129e-07 +dump_lebedeva_032.cfg:2 1.6 1.6 3.35 -2.08065e-06 1.4572e-06 1.4572e-06 -5.81145e-07 +dump_lebedeva_033.cfg:2 1.65 1.65 3.35 -2.15492e-06 1.51402e-06 1.51402e-06 -6.07422e-07 +dump_lebedeva_034.cfg:2 1.7 1.7 3.35 -2.23209e-06 1.57336e-06 1.57336e-06 -6.3503e-07 +dump_lebedeva_035.cfg:2 1.75 1.75 3.35 -2.3123e-06 1.63533e-06 1.63533e-06 -6.64045e-07 +dump_lebedeva_036.cfg:2 1.8 1.8 3.35 -2.39567e-06 1.70008e-06 1.70008e-06 -6.94545e-07 +dump_lebedeva_037.cfg:2 1.85 1.85 3.35 -2.48236e-06 1.76774e-06 1.76774e-06 -7.26615e-07 +dump_lebedeva_038.cfg:2 1.9 1.9 3.35 -2.5725e-06 1.83844e-06 1.83844e-06 -7.60344e-07 +dump_lebedeva_039.cfg:2 1.95 1.95 3.35 -2.66625e-06 1.91236e-06 1.91236e-06 -7.95827e-07 +dump_lebedeva_040.cfg:2 2 2 3.35 -2.76379e-06 1.98965e-06 1.98965e-06 -8.33165e-07 +dump_lebedeva_041.cfg:2 2.05 2.05 3.35 -2.86528e-06 2.07047e-06 2.07047e-06 -8.72464e-07 +dump_lebedeva_042.cfg:2 2.1 2.1 3.35 -2.9709e-06 2.15503e-06 2.15503e-06 -9.1384e-07 +dump_lebedeva_043.cfg:2 2.15 2.15 3.35 -3.08085e-06 2.24349e-06 2.24349e-06 -9.57413e-07 +dump_lebedeva_044.cfg:2 2.2 2.2 3.35 -3.19532e-06 2.33607e-06 2.33607e-06 -1.00331e-06 +dump_lebedeva_045.cfg:2 2.25 2.25 3.35 -3.31452e-06 2.43298e-06 2.43298e-06 -1.05167e-06 +dump_lebedeva_046.cfg:2 2.3 2.3 3.35 -3.43869e-06 2.53444e-06 2.53444e-06 -1.10265e-06 +dump_lebedeva_047.cfg:2 2.35 2.35 3.35 -3.56805e-06 2.6407e-06 2.6407e-06 -1.15638e-06 +dump_lebedeva_048.cfg:2 2.4 2.4 3.35 -3.70284e-06 2.752e-06 2.752e-06 -1.21305e-06 +dump_lebedeva_049.cfg:2 2.45 2.45 3.35 -3.84334e-06 2.86861e-06 2.86861e-06 -1.27283e-06 +dump_lebedeva_050.cfg:2 2.5 2.5 3.35 -3.9898e-06 2.99082e-06 2.99082e-06 -1.3359e-06 +dump_lebedeva_051.cfg:2 2.55 2.55 3.35 -4.14252e-06 3.11892e-06 3.11892e-06 -1.40247e-06 +dump_lebedeva_052.cfg:2 2.6 2.6 3.35 -4.30179e-06 3.25323e-06 3.25323e-06 -1.47275e-06 +dump_lebedeva_053.cfg:2 2.65 2.65 3.35 -4.46795e-06 3.39408e-06 3.39408e-06 -1.54696e-06 +dump_lebedeva_054.cfg:2 2.7 2.7 3.35 -4.64132e-06 3.54184e-06 3.54184e-06 -1.62536e-06 +dump_lebedeva_055.cfg:2 2.75 2.75 3.35 -4.82225e-06 3.69686e-06 3.69686e-06 -1.70821e-06 +dump_lebedeva_056.cfg:2 2.8 2.8 3.35 -5.01113e-06 3.85956e-06 3.85956e-06 -1.79577e-06 +dump_lebedeva_057.cfg:2 2.85 2.85 3.35 -5.20835e-06 4.03036e-06 4.03036e-06 -1.88835e-06 +dump_lebedeva_058.cfg:2 2.9 2.9 3.35 -5.41431e-06 4.2097e-06 4.2097e-06 -1.98627e-06 +dump_lebedeva_059.cfg:2 2.95 2.95 3.35 -5.62947e-06 4.39805e-06 4.39805e-06 -2.08985e-06 +dump_lebedeva_060.cfg:2 3 3 3.35 -5.85427e-06 4.59593e-06 4.59593e-06 -2.19948e-06 +dump_lebedeva_061.cfg:2 3.05 3.05 3.35 -6.08923e-06 4.80386e-06 4.80386e-06 -2.31553e-06 +dump_lebedeva_062.cfg:2 3.1 3.1 3.35 -6.33484e-06 5.02241e-06 5.02241e-06 -2.43842e-06 +dump_lebedeva_063.cfg:2 3.15 3.15 3.35 -6.59165e-06 5.25219e-06 5.25219e-06 -2.56859e-06 +dump_lebedeva_064.cfg:2 3.2 3.2 3.35 -6.86025e-06 5.49384e-06 5.49384e-06 -2.70652e-06 +dump_lebedeva_065.cfg:2 3.25 3.25 3.35 -7.14125e-06 5.74802e-06 5.74802e-06 -2.85272e-06 +dump_lebedeva_066.cfg:2 3.3 3.3 3.35 -7.43528e-06 6.01548e-06 6.01548e-06 -3.00774e-06 +dump_lebedeva_067.cfg:2 3.35 3.35 3.35 -7.74303e-06 6.29696e-06 6.29696e-06 -3.17215e-06 +dump_lebedeva_068.cfg:2 3.4 3.4 3.35 -8.06522e-06 6.5933e-06 6.5933e-06 -3.3466e-06 +dump_lebedeva_069.cfg:2 3.45 3.45 3.35 -8.40262e-06 6.90535e-06 6.90535e-06 -3.53174e-06 +dump_lebedeva_070.cfg:2 3.5 3.5 3.35 -8.75603e-06 7.23404e-06 7.23404e-06 -3.72831e-06 +dump_lebedeva_071.cfg:2 3.55 3.55 3.35 -9.12632e-06 7.58035e-06 7.58035e-06 -3.93708e-06 +dump_lebedeva_072.cfg:2 3.6 3.6 3.35 -9.51438e-06 7.94533e-06 7.94533e-06 -4.15889e-06 +dump_lebedeva_073.cfg:2 3.65 3.65 3.35 -9.92118e-06 8.33009e-06 8.33009e-06 -4.39462e-06 +dump_lebedeva_074.cfg:2 3.7 3.7 3.35 -1.03477e-05 8.73582e-06 8.73582e-06 -4.64524e-06 +dump_lebedeva_075.cfg:2 3.75 3.75 3.35 -1.07951e-05 9.16377e-06 9.16377e-06 -4.91178e-06 +dump_lebedeva_076.cfg:2 3.8 3.8 3.35 -1.12645e-05 9.61529e-06 9.61529e-06 -5.19536e-06 +dump_lebedeva_077.cfg:2 3.85 3.85 3.35 -1.17571e-05 1.00918e-05 1.00918e-05 -5.49717e-06 +dump_lebedeva_078.cfg:2 3.9 3.9 3.35 -1.22741e-05 1.05949e-05 1.05949e-05 -5.8185e-06 +dump_lebedeva_079.cfg:2 3.95 3.95 3.35 -1.2817e-05 1.11261e-05 1.11261e-05 -6.16074e-06 +dump_lebedeva_080.cfg:2 4 4 3.35 -1.33872e-05 1.16872e-05 1.16872e-05 -6.52537e-06 +dump_lebedeva_081.cfg:2 4.05 4.05 3.35 -1.39863e-05 1.22801e-05 1.22801e-05 -6.91402e-06 +dump_lebedeva_082.cfg:2 4.1 4.1 3.35 -1.46158e-05 1.29067e-05 1.29067e-05 -7.32841e-06 +dump_lebedeva_083.cfg:2 4.15 4.15 3.35 -1.52776e-05 1.35692e-05 1.35692e-05 -7.77041e-06 +dump_lebedeva_084.cfg:2 4.2 4.2 3.35 -1.59734e-05 1.42698e-05 1.42698e-05 -8.24204e-06 +dump_lebedeva_085.cfg:2 4.25 4.25 3.35 -1.67052e-05 1.50109e-05 1.50109e-05 -8.74547e-06 +dump_lebedeva_086.cfg:2 4.3 4.3 3.35 -1.74752e-05 1.57951e-05 1.57951e-05 -9.28307e-06 +dump_lebedeva_087.cfg:2 4.35 4.35 3.35 -1.82855e-05 1.66251e-05 1.66251e-05 -9.85736e-06 +dump_lebedeva_088.cfg:2 4.4 4.4 3.35 -1.91385e-05 1.75039e-05 1.75039e-05 -1.04711e-05 +dump_lebedeva_089.cfg:2 4.45 4.45 3.35 -2.00367e-05 1.84346e-05 1.84346e-05 -1.11272e-05 +dump_lebedeva_090.cfg:2 4.5 4.5 3.35 -2.09829e-05 1.94207e-05 1.94207e-05 -1.1829e-05 +dump_lebedeva_091.cfg:2 4.55 4.55 3.35 -2.19798e-05 2.04656e-05 2.04656e-05 -1.25798e-05 +dump_lebedeva_092.cfg:2 4.6 4.6 3.35 -2.30305e-05 2.15733e-05 2.15733e-05 -1.33834e-05 +dump_lebedeva_093.cfg:2 4.65 4.65 3.35 -2.41382e-05 2.27478e-05 2.27478e-05 -1.42439e-05 +dump_lebedeva_094.cfg:2 4.7 4.7 3.35 -2.53065e-05 2.39936e-05 2.39936e-05 -1.51657e-05 +dump_lebedeva_095.cfg:2 4.75 4.75 3.35 -2.65389e-05 2.53153e-05 2.53153e-05 -1.61536e-05 +dump_lebedeva_096.cfg:2 4.8 4.8 3.35 -2.78393e-05 2.67182e-05 2.67182e-05 -1.72127e-05 +dump_lebedeva_097.cfg:2 4.85 4.85 3.35 -2.92121e-05 2.82074e-05 2.82074e-05 -1.83485e-05 +dump_lebedeva_098.cfg:2 4.9 4.9 3.35 -3.06616e-05 2.9789e-05 2.9789e-05 -1.95673e-05 +dump_lebedeva_099.cfg:2 4.95 4.95 3.35 -3.21926e-05 3.1469e-05 3.1469e-05 -2.08755e-05 +dump_lebedeva_100.cfg:2 5 5 3.35 -3.38103e-05 3.32542e-05 3.32542e-05 -2.22803e-05 +dump_lebedeva_101.cfg:2 5.05 5.05 3.35 -3.55199e-05 3.51516e-05 3.51516e-05 -2.37895e-05 +dump_lebedeva_102.cfg:2 5.1 5.1 3.35 -3.73274e-05 3.7169e-05 3.7169e-05 -2.54115e-05 +dump_lebedeva_103.cfg:2 5.15 5.15 3.35 -3.9239e-05 3.93146e-05 3.93146e-05 -2.71554e-05 +dump_lebedeva_104.cfg:2 5.2 5.2 3.35 -4.12612e-05 4.15971e-05 4.15971e-05 -2.90313e-05 +dump_lebedeva_105.cfg:2 5.25 5.25 3.35 -4.34011e-05 4.4026e-05 4.4026e-05 -3.10499e-05 +dump_lebedeva_106.cfg:2 5.3 5.3 3.35 -4.56664e-05 4.66115e-05 4.66115e-05 -3.32231e-05 +dump_lebedeva_107.cfg:2 5.35 5.35 3.35 -4.80651e-05 4.93643e-05 4.93643e-05 -3.55636e-05 +dump_lebedeva_108.cfg:2 5.4 5.4 3.35 -5.06058e-05 5.22962e-05 5.22962e-05 -3.80853e-05 +dump_lebedeva_109.cfg:2 5.45 5.45 3.35 -5.32979e-05 5.54196e-05 5.54196e-05 -4.08035e-05 +dump_lebedeva_110.cfg:2 5.5 5.5 3.35 -5.61512e-05 5.8748e-05 5.8748e-05 -4.37346e-05 +dump_lebedeva_111.cfg:2 5.55 5.55 3.35 -5.91763e-05 6.22957e-05 6.22957e-05 -4.68968e-05 +dump_lebedeva_112.cfg:2 5.6 5.6 3.35 -6.23847e-05 6.60782e-05 6.60782e-05 -5.03095e-05 +dump_lebedeva_113.cfg:2 5.65 5.65 3.35 -6.57883e-05 7.01119e-05 7.01119e-05 -5.39942e-05 +dump_lebedeva_114.cfg:2 5.7 5.7 3.35 -6.94003e-05 7.44146e-05 7.44146e-05 -5.79742e-05 +dump_lebedeva_115.cfg:2 5.75 5.75 3.35 -7.32346e-05 7.90054e-05 7.90054e-05 -6.22749e-05 +dump_lebedeva_116.cfg:2 5.8 5.8 3.35 -7.7306e-05 8.39045e-05 8.39045e-05 -6.69239e-05 +dump_lebedeva_117.cfg:2 5.85 5.85 3.35 -8.16306e-05 8.91338e-05 8.91338e-05 -7.19515e-05 +dump_lebedeva_118.cfg:2 5.9 5.9 3.35 -8.62253e-05 9.47167e-05 9.47167e-05 -7.73906e-05 +dump_lebedeva_119.cfg:2 5.95 5.95 3.35 -9.11085e-05 0.000100678 0.000100678 -8.32771e-05 +dump_lebedeva_120.cfg:2 6 6 3.35 -9.62998e-05 0.000107044 0.000107044 -8.96501e-05 +dump_lebedeva_121.cfg:2 6.05 6.05 3.35 -0.00010182 0.000113845 0.000113845 -9.65522e-05 +dump_lebedeva_122.cfg:2 6.1 6.1 3.35 -0.000107692 0.000121109 0.000121109 -0.00010403 +dump_lebedeva_123.cfg:2 6.15 6.15 3.35 -0.000113939 0.000128869 0.000128869 -0.000112134 +dump_lebedeva_124.cfg:2 6.2 6.2 3.35 -0.000120588 0.000137161 0.000137161 -0.00012092 +dump_lebedeva_125.cfg:2 6.25 6.25 3.35 -0.000127665 0.00014602 0.00014602 -0.000130447 +dump_lebedeva_126.cfg:2 6.3 6.3 3.35 -0.0001352 0.000155486 0.000155486 -0.000140781 +dump_lebedeva_127.cfg:2 6.35 6.35 3.35 -0.000143224 0.000165599 0.000165599 -0.000151993 +dump_lebedeva_128.cfg:2 6.4 6.4 3.35 -0.000151771 0.000176402 0.000176402 -0.000164159 +dump_lebedeva_129.cfg:2 6.45 6.45 3.35 -0.000160877 0.000187942 0.000187942 -0.000177363 +dump_lebedeva_130.cfg:2 6.5 6.5 3.35 -0.000170579 0.000200265 0.000200265 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15.45 15.45 3.35 -2.19798e-05 -2.04656e-05 -2.04656e-05 -1.25798e-05 +dump_lebedeva_310.cfg:2 15.5 15.5 3.35 -2.09829e-05 -1.94207e-05 -1.94207e-05 -1.1829e-05 +dump_lebedeva_311.cfg:2 15.55 15.55 3.35 -2.00367e-05 -1.84346e-05 -1.84346e-05 -1.11272e-05 +dump_lebedeva_312.cfg:2 15.6 15.6 3.35 -1.91385e-05 -1.75039e-05 -1.75039e-05 -1.04711e-05 +dump_lebedeva_313.cfg:2 15.65 15.65 3.35 -1.82855e-05 -1.66251e-05 -1.66251e-05 -9.85736e-06 +dump_lebedeva_314.cfg:2 15.7 15.7 3.35 -1.74752e-05 -1.57951e-05 -1.57951e-05 -9.28307e-06 +dump_lebedeva_315.cfg:2 15.75 15.75 3.35 -1.67052e-05 -1.50109e-05 -1.50109e-05 -8.74547e-06 +dump_lebedeva_316.cfg:2 15.8 15.8 3.35 -1.59734e-05 -1.42698e-05 -1.42698e-05 -8.24204e-06 +dump_lebedeva_317.cfg:2 15.85 15.85 3.35 -1.52776e-05 -1.35692e-05 -1.35692e-05 -7.77041e-06 +dump_lebedeva_318.cfg:2 15.9 15.9 3.35 -1.46158e-05 -1.29067e-05 -1.29067e-05 -7.32841e-06 +dump_lebedeva_319.cfg:2 15.95 15.95 3.35 -1.39863e-05 -1.22801e-05 -1.22801e-05 -6.91402e-06 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-5.62947e-06 -4.39805e-06 -4.39805e-06 -2.08985e-06 +dump_lebedeva_342.cfg:2 17.1 17.1 3.35 -5.41431e-06 -4.2097e-06 -4.2097e-06 -1.98627e-06 +dump_lebedeva_343.cfg:2 17.15 17.15 3.35 -5.20835e-06 -4.03036e-06 -4.03036e-06 -1.88835e-06 +dump_lebedeva_344.cfg:2 17.2 17.2 3.35 -5.01113e-06 -3.85956e-06 -3.85956e-06 -1.79577e-06 +dump_lebedeva_345.cfg:2 17.25 17.25 3.35 -4.82225e-06 -3.69686e-06 -3.69686e-06 -1.70821e-06 +dump_lebedeva_346.cfg:2 17.3 17.3 3.35 -4.64132e-06 -3.54184e-06 -3.54184e-06 -1.62536e-06 +dump_lebedeva_347.cfg:2 17.35 17.35 3.35 -4.46795e-06 -3.39408e-06 -3.39408e-06 -1.54696e-06 +dump_lebedeva_348.cfg:2 17.4 17.4 3.35 -4.30179e-06 -3.25323e-06 -3.25323e-06 -1.47275e-06 +dump_lebedeva_349.cfg:2 17.45 17.45 3.35 -4.14252e-06 -3.11892e-06 -3.11892e-06 -1.40247e-06 +dump_lebedeva_350.cfg:2 17.5 17.5 3.35 -3.9898e-06 -2.99082e-06 -2.99082e-06 -1.3359e-06 +dump_lebedeva_351.cfg:2 17.55 17.55 3.35 -3.84334e-06 -2.86861e-06 -2.86861e-06 -1.27283e-06 +dump_lebedeva_352.cfg:2 17.6 17.6 3.35 -3.70284e-06 -2.752e-06 -2.752e-06 -1.21305e-06 +dump_lebedeva_353.cfg:2 17.65 17.65 3.35 -3.56805e-06 -2.6407e-06 -2.6407e-06 -1.15638e-06 +dump_lebedeva_354.cfg:2 17.7 17.7 3.35 -3.43869e-06 -2.53444e-06 -2.53444e-06 -1.10265e-06 +dump_lebedeva_355.cfg:2 17.75 17.75 3.35 -3.31452e-06 -2.43298e-06 -2.43298e-06 -1.05167e-06 +dump_lebedeva_356.cfg:2 17.8 17.8 3.35 -3.19532e-06 -2.33607e-06 -2.33607e-06 -1.00331e-06 +dump_lebedeva_357.cfg:2 17.85 17.85 3.35 -3.08085e-06 -2.24349e-06 -2.24349e-06 -9.57413e-07 +dump_lebedeva_358.cfg:2 17.9 17.9 3.35 -2.9709e-06 -2.15503e-06 -2.15503e-06 -9.1384e-07 +dump_lebedeva_359.cfg:2 17.95 17.95 3.35 -2.86528e-06 -2.07047e-06 -2.07047e-06 -8.72464e-07 +dump_lebedeva_360.cfg:2 18 18 3.35 -2.76379e-06 -1.98965e-06 -1.98965e-06 -8.33165e-07 +dump_lebedeva_361.cfg:2 18.05 18.05 3.35 -2.66625e-06 -1.91236e-06 -1.91236e-06 -7.95827e-07 +dump_lebedeva_362.cfg:2 18.1 18.1 3.35 -2.5725e-06 -1.83844e-06 -1.83844e-06 -7.60344e-07 +dump_lebedeva_363.cfg:2 18.15 18.15 3.35 -2.48236e-06 -1.76774e-06 -1.76774e-06 -7.26615e-07 +dump_lebedeva_364.cfg:2 18.2 18.2 3.35 -2.39567e-06 -1.70008e-06 -1.70008e-06 -6.94545e-07 +dump_lebedeva_365.cfg:2 18.25 18.25 3.35 -2.3123e-06 -1.63533e-06 -1.63533e-06 -6.64045e-07 +dump_lebedeva_366.cfg:2 18.3 18.3 3.35 -2.23209e-06 -1.57336e-06 -1.57336e-06 -6.3503e-07 +dump_lebedeva_367.cfg:2 18.35 18.35 3.35 -2.15492e-06 -1.51402e-06 -1.51402e-06 -6.07422e-07 +dump_lebedeva_368.cfg:2 18.4 18.4 3.35 -2.08065e-06 -1.4572e-06 -1.4572e-06 -5.81145e-07 +dump_lebedeva_369.cfg:2 18.45 18.45 3.35 -2.00916e-06 -1.40277e-06 -1.40277e-06 -5.56129e-07 +dump_lebedeva_370.cfg:2 18.5 18.5 3.35 -1.94033e-06 -1.35063e-06 -1.35063e-06 -5.32308e-07 +dump_lebedeva_371.cfg:2 18.55 18.55 3.35 -1.87406e-06 -1.30067e-06 -1.30067e-06 -5.0962e-07 +dump_lebedeva_372.cfg:2 18.6 18.6 3.35 -1.81023e-06 -1.25279e-06 -1.25279e-06 -4.88004e-07 +dump_lebedeva_373.cfg:2 18.65 18.65 3.35 -1.74875e-06 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-1.20235e-06 -8.09802e-07 -8.09802e-07 -2.94873e-07 +dump_lebedeva_385.cfg:2 19.25 19.25 3.35 -1.16257e-06 -7.81747e-07 -7.81747e-07 -2.83119e-07 +dump_lebedeva_386.cfg:2 19.3 19.3 3.35 -1.12416e-06 -7.54787e-07 -7.54787e-07 -2.71886e-07 +dump_lebedeva_387.cfg:2 19.35 19.35 3.35 -1.08707e-06 -7.28875e-07 -7.28875e-07 -2.61148e-07 +dump_lebedeva_388.cfg:2 19.4 19.4 3.35 -1.05125e-06 -7.03966e-07 -7.03966e-07 -2.50881e-07 +dump_lebedeva_389.cfg:2 19.45 19.45 3.35 -1.01666e-06 -6.80016e-07 -6.80016e-07 -2.41064e-07 +dump_lebedeva_390.cfg:2 19.5 19.5 3.35 -9.83237e-07 -6.56984e-07 -6.56984e-07 -2.31673e-07 +dump_lebedeva_391.cfg:2 19.55 19.55 3.35 -9.50945e-07 -6.34832e-07 -6.34832e-07 -2.2269e-07 +dump_lebedeva_392.cfg:2 19.6 19.6 3.35 -9.19739e-07 -6.13522e-07 -6.13522e-07 -2.14094e-07 +dump_lebedeva_393.cfg:2 19.65 19.65 3.35 -8.89579e-07 -5.93019e-07 -5.93019e-07 -2.05867e-07 +dump_lebedeva_394.cfg:2 19.7 19.7 3.35 -8.60425e-07 -5.73288e-07 -5.73288e-07 -1.97991e-07 +dump_lebedeva_395.cfg:2 19.75 19.75 3.35 -8.32238e-07 -5.54298e-07 -5.54298e-07 -1.90451e-07 +dump_lebedeva_396.cfg:2 19.8 19.8 3.35 -8.04983e-07 -5.36017e-07 -5.36017e-07 -1.8323e-07 +dump_lebedeva_397.cfg:2 19.85 19.85 3.35 -7.78625e-07 -5.18417e-07 -5.18417e-07 -1.76314e-07 +dump_lebedeva_398.cfg:2 19.9 19.9 3.35 -7.5313e-07 -5.01468e-07 -5.01468e-07 -1.69689e-07 +dump_lebedeva_399.cfg:2 19.95 19.95 3.35 -7.28468e-07 -4.85145e-07 -4.85145e-07 -1.6334e-07 diff --git a/examples/USER/misc/lebedeva/LebDer.pl b/examples/USER/misc/lebedeva/LebDer.pl new file mode 100755 index 0000000000..5b449358d3 --- /dev/null +++ b/examples/USER/misc/lebedeva/LebDer.pl @@ -0,0 +1,90 @@ +#!/usr/bin/perl +# Computes potential energy of atom as a function of distance from another atom +# and computes numerical derivates of potential. +# The script was used to check if results from LAMMPS (using 2particles.in) +# are the same as these computed b this script. +# Prints results to STDOUT. +# Hence, use it like this: +# ./LebDer.pl > PerlResult.dat +# After that use lebedeva00.plot +# +# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland +# Email: softquake@gmail.com + +# Parameters used by ZJK for Lebedeva +my $LEB_A = -14.558; +my $LEB_B = 21.204; +my $LEB_alpha = 4.16; +my $LEB_C = 1.8; +my $LEB_D1 = -0.862; +my $LEB_D2 = 0.10049; # has very strong influence on position of minimum +my $LEB_lambda1 = 0.6; # has influance on splitting of AB-AA. +my $LEB_lambda2 = 0.4; # has strong influence on position of minimum +my $LEB_z0 = 3.198; +my $LEBSCALE =1.0; + +$Z0=3.35; + +$CX0 = 10; +$CY0 = 10; + +for (my $t=0; $t<400; $t++) { + my $X0 = 0.001 + 0.05*$t; + my $Y0 = 0.001 + 0.05*$t; + my $Z = $Z0; + print $X0, "\t", $Y0, "\t", $Z, "\t",&LEB($X0, $Y0, $Z), "\t", &DLEBX($X0, $Y0, $Z),"\t",&DLEBY($X0, $Y0, $Z), "\t", &DLEBZ($X0, $Y0, $Z),"\n"; +} + +############################################################################################### + +sub LEB { + my $x = shift; + my $y = shift; + my $z = shift; + + my $rho2 = ($x-$CX0)*($x-$CX0) + ($y-$CY0)*($y-$CY0); + my $r = sqrt($rho2 + ($Z0)*($Z0)); + my $zr = ($LEB_z0/$r)*($LEB_z0/$r); + my $zr6 = $zr*$zr*$zr; + + my $ONE = $LEB_C*(1+$LEB_D1*$rho2+$LEB_D2*$rho2*$rho2); + my $TWO = exp(-$LEB_lambda1*$rho2)*exp(-$LEB_lambda2*($z*$z-$LEB_z0*$LEB_z0)); + my $U = $LEB_A*$zr6 +$LEB_B*exp(-$LEB_alpha*($r-$LEB_z0)) + $ONE*$TWO; + return $U; +} + +sub DLEBX { # finding derivative at $x + my $x = shift; + my $y = shift; + my $z = shift; + + my $h = 0.0001; + + my $D = (&LEB($x+$h, $y, $z)-&LEB($x-$h, $y, $z))/(2*$h); + + return $D; +} + +sub DLEBY { # finding derivative at $y + my $x = shift; + my $y = shift; + my $z = shift; + + my $h = 0.0001; + + my $D = (&LEB($x, $y+$h, $z)-&LEB($x, $y-$h, $z))/(2*$h); + + return $D; +} + +sub DLEBZ { # finding derivative at $z + my $x = shift; + my $y = shift; + my $z = shift; + + my $h = 0.0001; + + my $D = (&LEB($x, $y, $z+$h)-&LEB($x, $y, $z-$h))/(2*$h); + + return $D; +} diff --git a/examples/USER/misc/lebedeva/lebedeva00.plot b/examples/USER/misc/lebedeva/lebedeva00.plot new file mode 100644 index 0000000000..a598c3e6b1 --- /dev/null +++ b/examples/USER/misc/lebedeva/lebedeva00.plot @@ -0,0 +1,34 @@ +# Author: Zbigniew Koziol, National Center for Nuclear Research, Poland +# Email: softquake@gmail.com + +set term x11; +unset log +unset title +set size 1.0,1.0 + +set encoding iso_8859_1 +#set term postscript eps enhanced color "Helvetica" 18; +#set output "lebedeva00.eps" + +set zero 1e-018; + +set xlabel "x,y [{\305}]" font "Helvetica,18"; +set ylabel "U [eV/atom]" font "Helvetica,18"; + +set key font ",18" + +set key right +set key top + +set pointsize 1.2 + +set xrange [0:20] +set yrange [-0.002:0.001] +#set yrange [-0.01:0.01] +#set yrange [*:*] + +plot \ + "LamppsResult.dat" u 2:5 t "Leb LAMMPS",\ + "PerlResult.dat" u 1:($4*0.001/2.) w l t "Leb Perl" + +exit diff --git a/examples/USER/mofff/log.17Jan18.hkust1.g++.1 b/examples/USER/mofff/log.27Nov18.hkust1.g++.1 similarity index 97% rename from examples/USER/mofff/log.17Jan18.hkust1.g++.1 rename to examples/USER/mofff/log.27Nov18.hkust1.g++.1 index 13074b5054..49fb746116 100644 --- a/examples/USER/mofff/log.17Jan18.hkust1.g++.1 +++ b/examples/USER/mofff/log.27Nov18.hkust1.g++.1 @@ -1,5 +1,7 @@ -LAMMPS (17 Jan 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task clear + using 1 OpenMP thread(s) per MPI task units real boundary p p p atom_style full @@ -119,7 +121,7 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0 # ------------------------ MOF-FF FORCE FIELD END -------------------------- run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -132,13 +134,13 @@ Neighbor list info ... pair build: half/bin/newton/tri stencil: half/bin/3d/newton/tri bin: standard -WARNING: Inconsistent image flags (../domain.cpp:786) +WARNING: Inconsistent image flags (src/domain.cpp:782) Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.23 | 21.23 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11833.81 343.7619 -11490.048 -5.8508834 Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +314.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total diff --git a/examples/USER/mofff/log.17Jan18.hkust1.g++.4 b/examples/USER/mofff/log.27Nov18.hkust1.g++.4 similarity index 96% rename from examples/USER/mofff/log.17Jan18.hkust1.g++.4 rename to examples/USER/mofff/log.27Nov18.hkust1.g++.4 index bba6ff5c2e..832bdfea94 100644 --- a/examples/USER/mofff/log.17Jan18.hkust1.g++.4 +++ b/examples/USER/mofff/log.27Nov18.hkust1.g++.4 @@ -1,5 +1,7 @@ -LAMMPS (17 Jan 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task clear + using 1 OpenMP thread(s) per MPI task units real boundary p p p atom_style full @@ -119,7 +121,7 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0 # ------------------------ MOF-FF FORCE FIELD END -------------------------- run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -132,13 +134,13 @@ Neighbor list info ... pair build: half/bin/newton/tri stencil: half/bin/3d/newton/tri bin: standard -WARNING: Inconsistent image flags (../domain.cpp:786) +WARNING: Inconsistent image flags (src/domain.cpp:782) Per MPI rank memory allocation (min/avg/max) = 20.68 | 20.68 | 20.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11833.81 343.7619 -11490.048 -5.8508834 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 624 atoms +Loop time of 2.01464e-05 on 4 procs for 0 steps with 624 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +86.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -149,7 +151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 2.015e-05 | | |100.00 Nlocal: 156 ave 156 max 156 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/mofff/log.17Jan18.hkust1_long.g++.1 b/examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 similarity index 96% rename from examples/USER/mofff/log.17Jan18.hkust1_long.g++.1 rename to examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 index 8f5d33c067..d67c0a11c5 100644 --- a/examples/USER/mofff/log.17Jan18.hkust1_long.g++.1 +++ b/examples/USER/mofff/log.27Nov18.hkust1_long.g++.1 @@ -1,5 +1,7 @@ -LAMMPS (17 Jan 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task clear + using 1 OpenMP thread(s) per MPI task units real boundary p p p atom_style full @@ -120,9 +122,9 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0 # ------------------------ MOF-FF FORCE FIELD END -------------------------- run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.267593 estimated absolute RMS force accuracy = 0.000333665 estimated relative force accuracy = 1.00482e-06 @@ -140,13 +142,13 @@ Neighbor list info ... pair build: half/bin/newton/tri stencil: half/bin/3d/newton/tri bin: standard -WARNING: Inconsistent image flags (../domain.cpp:786) +WARNING: Inconsistent image flags (src/domain.cpp:782) Per MPI rank memory allocation (min/avg/max) = 34.64 | 34.64 | 34.64 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16541.109 343.7619 -16197.347 -629.64956 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 624 atoms +Loop time of 1.19209e-06 on 1 procs for 0 steps with 624 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +167.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -158,7 +160,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.192e-06 | | |100.00 Nlocal: 624 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/mofff/log.17Jan18.hkust1_long.g++.4 b/examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 similarity index 96% rename from examples/USER/mofff/log.17Jan18.hkust1_long.g++.4 rename to examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 index 8201f7da00..235db2fcda 100644 --- a/examples/USER/mofff/log.17Jan18.hkust1_long.g++.4 +++ b/examples/USER/mofff/log.27Nov18.hkust1_long.g++.4 @@ -1,5 +1,7 @@ -LAMMPS (17 Jan 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task clear + using 1 OpenMP thread(s) per MPI task units real boundary p p p atom_style full @@ -120,9 +122,9 @@ special_bonds lj 0.0 0.0 1.0 coul 1.0 1.0 1.0 # ------------------------ MOF-FF FORCE FIELD END -------------------------- run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.267593 estimated absolute RMS force accuracy = 0.000333665 estimated relative force accuracy = 1.00482e-06 @@ -140,13 +142,13 @@ Neighbor list info ... pair build: half/bin/newton/tri stencil: half/bin/3d/newton/tri bin: standard -WARNING: Inconsistent image flags (../domain.cpp:786) +WARNING: Inconsistent image flags (src/domain.cpp:782) Per MPI rank memory allocation (min/avg/max) = 34.1 | 34.1 | 34.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16541.109 343.7619 -16197.347 -629.64956 -Loop time of 6.13928e-06 on 4 procs for 0 steps with 624 atoms +Loop time of 2.71797e-05 on 4 procs for 0 steps with 624 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +84.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -158,7 +160,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 6.139e-06 | | |100.00 +Other | | 2.718e-05 | | |100.00 Nlocal: 156 ave 156 max 156 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/README.md b/examples/USER/phonon/dynamical_matrix_command/Silicon/README.md new file mode 100755 index 0000000000..15ae158c62 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/README.md @@ -0,0 +1,21 @@ +# LAMMPS LATTICE DYNAMICS COMMANDS + +## DYNAMICAL MATRIX CALCULATOR + +This directory contains the ingredients to calculate a dynamical matrix. + +Example: +``` +NP=4 #number of processors +mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon +``` + +To test out a different silicon example: +``` +LMP_FILE=amorphous_silicon.lmp +cp lmp_bank/$LMP_FILE ./silicon_input_file.lmp +NP=4 #number of processors +mpirun -np $NP lmp_mpi -in in.silicon -out out.silicon +``` + +## Requires: MANYBODY and MOLECULE packages diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff b/examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff new file mode 100755 index 0000000000..3bc19f0581 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/Si.opt.tersoff @@ -0,0 +1,66 @@ +# Tersoff parameters for various elements and mixtures +# multiple entries can be added to this file, LAMMPS reads the ones it needs +# these entries are in LAMMPS "metal" units: +# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms +# other quantities are unitless + +# Aidan Thompson (athomps at sandia.gov) takes full blame for this +# file. It specifies various potentials published by J. Tersoff for +# silicon, carbon and germanium. Since Tersoff published several +# different silicon potentials, I refer to them using atom types +# Si(B), Si(C) and Si(D). The last two are almost almost identical but +# refer to two different publications. These names should be used in +# the LAMMPS command when the file is invoked. For example: +# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials +# can be used pure silicon, pure carbon, pure germanium, binary SiC, +# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will +# generate an error if this file is used with any combination +# involving C and Ge, since there are no entries for the GeC +# interactions (Tersoff did not publish parameters for this +# cross-interaction.) + +# format of a single entry (one or more lines): +# element 1, element 2, element 3, +# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A + +# The original Tersoff potential for Silicon, Si(B) +# J. Tersoff, PRB, 37, 6991 (1988) + +Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956 + 0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7 + +# The later Tersoff potential for Silicon, Si(C) +# J. Tersoff, PRB, 38, 9902 (1988) + +Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734 + 1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8 + +# The later Tersoff potential for Carbon, Silicon, and Germanium +# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248) +# The Si and C parameters are very close to those in SiC.tersoff + +C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6 +Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8 +Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0 + +C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111 +C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0 +C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0 + +Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111 +Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0 +Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0 + +Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347 +Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0 +Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0 + +Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347 +Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0 +Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0 + +# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) +# element 1, element 2, element 3, +# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A +C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6 + diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp b/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp new file mode 100755 index 0000000000..f3b895f168 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/ff-silicon.lmp @@ -0,0 +1,19 @@ +############################# +#Atoms types - mass - charge# +############################# +#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!# + +variable Si equal 1 + +############# +#Atom Masses# +############# + +mass ${Si} 28.08550 + +########################### +#Pair Potentials - Tersoff# +########################### + +pair_style tersoff +pair_coeff * * Si.opt.tersoff Si(D) diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon b/examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon new file mode 100755 index 0000000000..cda0ee8c58 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/in.silicon @@ -0,0 +1,89 @@ +###############################mm +# Atom style - charge/vdw/bonded# +################################# +atom_style full + +############################################## +#Units Metal : eV - ps - angstrom - bar# +# Real : kcal/mol - fs - angstrom - atm# +############################################## +units metal + +############ +#Run number# +############ +variable run_no equal 0 # is it a restart? +variable res_no equal ${run_no}-1 # restart file number + +####################################### +#Random Seeds and Domain Decomposition# +####################################### +variable iseed0 equal 2357 +variable iseed1 equal 26488 +variable iseed2 equal 10669 +processors * * * + +########### +#Data File# +########### +variable inpfile string silicon_input_file.lmp +variable resfile string final_restart.${res_no} +variable ff_file string ff-silicon.lmp + +########## +#Run Type# +########## +variable minimise equal 0 #Energy Minimization + +############################### +#Molecular Dynamics Parameters# +############################### +neighbor 1 bin + +################################ +#Energy Minimization Parameters# +################################ +variable mtraj equal 1 # trajectory output frequency - all system +variable etol equal 1e-5 # % change in energy +variable ftol equal 1e-5 # max force threshold (force units) +variable maxiter equal 10000 # max # of iterations + +######################## +#3D Periodic Simulation# +######################## +boundary p p p + +############################# +#Reading the input structure# +############################# +if "${run_no} == 0" then "read_data ${inpfile}" else "read_restart ${resfile}" + +############# +#Force Field# +############# +include ${ff_file} + +###################### +#Thermodynamic Output# +###################### +variable str_basic string 'step time pe temp press' + +##################### +#Energy Minimization# +##################### +if "${minimise} <= 0 || ${run_no} > 0" then "jump SELF end_minimise" + print "Doing CG minimisation" + dump mdcd all dcd ${mtraj} min.dcd + dump_modify mdcd unwrap yes + min_style cg + min_modify line quadratic + minimize ${etol} ${ftol} ${maxiter} ${maxiter} + reset_timestep 0 + undump mdcd +label end_minimise + +################## +#Dynamical Matrix# +################## +dynamical_matrix all eskm 0.000001 file dynmat.dat binary no + diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp b/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp new file mode 100755 index 0000000000..036ece0279 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/lmp_bank/amorphous_silicon.lmp @@ -0,0 +1,534 @@ +LAMMPS description + + 512 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 1 atom types + 0 bond types + 0 angle types + 0 dihedral types + 0 improper types + + + 0.0000000 21.848000 xlo xhi + 0.0000000 21.848000 ylo yhi + 0.0000000 21.848000 zlo zhi + + Atoms + + 1 1 1 0.0000000 6.2030000 5.5980000 12.9980000 + 2 2 1 0.0000000 21.3100000 5.6310000 21.1380000 + 3 3 1 0.0000000 19.5320000 6.1170000 3.6940000 + 4 4 1 0.0000000 4.3700000 14.0260000 0.0900000 + 5 5 1 0.0000000 10.1930000 7.4590000 2.3530000 + 6 6 1 0.0000000 17.5070000 14.1860000 3.6790000 + 7 7 1 0.0000000 11.2050000 15.9160000 15.0480000 + 8 8 1 0.0000000 8.6050000 19.8970000 21.0040000 + 9 9 1 0.0000000 15.0360000 17.5650000 1.3640000 + 10 10 1 0.0000000 12.0450000 3.3600000 7.2720000 + 11 11 1 0.0000000 7.1330000 17.4130000 18.0480000 + 12 12 1 0.0000000 8.7340000 6.3830000 3.8480000 + 13 13 1 0.0000000 13.0940000 3.2490000 3.5840000 + 14 14 1 0.0000000 11.3200000 7.2770000 20.4120000 + 15 15 1 0.0000000 19.7770000 8.9110000 0.3000000 + 16 16 1 0.0000000 11.9710000 20.8500000 1.5140000 + 17 17 1 0.0000000 10.4480000 10.3650000 15.4040000 + 18 18 1 0.0000000 9.2060000 9.4670000 10.2240000 + 19 19 1 0.0000000 8.4360000 13.6240000 17.6570000 + 20 20 1 0.0000000 18.2020000 21.1230000 0.1380000 + 21 21 1 0.0000000 3.2970000 19.5740000 14.7410000 + 22 22 1 0.0000000 12.5330000 17.3580000 7.5960000 + 23 23 1 0.0000000 1.4040000 18.1060000 3.1510000 + 24 24 1 0.0000000 17.7440000 13.1530000 16.7940000 + 25 25 1 0.0000000 12.1070000 12.6630000 18.0340000 + 26 26 1 0.0000000 8.7270000 17.1140000 10.4200000 + 27 27 1 0.0000000 13.2330000 16.0380000 13.9210000 + 28 28 1 0.0000000 15.2360000 14.8650000 7.0150000 + 29 29 1 0.0000000 5.5190000 20.8660000 19.9260000 + 30 30 1 0.0000000 16.5810000 9.7460000 15.1710000 + 31 31 1 0.0000000 2.0500000 13.8550000 21.8010000 + 32 32 1 0.0000000 21.2670000 20.8970000 13.6740000 + 33 33 1 0.0000000 9.6900000 6.7650000 0.1950000 + 34 34 1 0.0000000 11.2570000 13.2440000 2.8190000 + 35 35 1 0.0000000 10.7810000 12.7310000 12.1920000 + 36 36 1 0.0000000 16.2630000 7.4100000 1.5360000 + 37 37 1 0.0000000 19.6100000 18.1440000 19.6830000 + 38 38 1 0.0000000 8.1790000 0.1200000 10.1620000 + 39 39 1 0.0000000 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-0.06099862 -193.17561189 +858.96245049 858.96245041 -1273.17866553 +-0.12013444 -0.12013475 83.09915550 +-861.58531232 -861.58531217 -1275.71087655 +2.81780737 2.81780753 5404.30474547 diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon b/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon new file mode 100755 index 0000000000..9920ddac51 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/results/out.silicon @@ -0,0 +1,58 @@ +LAMMPS (16 Jul 2018) +Reading data file ... + orthogonal box = (0 0 0) to (5.431 5.431 5.431) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4 + ghost atom cutoff = 4 + binsize = 2, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Calculating Dynamical Matrix... +Dynamical Matrix calculation took 0.001183 seconds +Finished Calculating Dynamical Matrix +Loop time of 1.22396e+06 on 4 procs for 0 steps with 8 atoms + +0.0% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00016781 | 0.00041345 | 0.00051464 | 0.0 | 0.00 +Bond | 1.9255e-06 | 2.1775e-06 | 2.4787e-06 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.00056143 | 0.00066602 | 0.00090865 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.224e+06 | | |100.00 + +Nlocal: 2 ave 3 max 1 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 56 ave 57 max 55 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 32 ave 48 max 16 min +Histogram: 1 0 0 0 0 2 0 0 0 1 + +Total # of neighbors = 128 +Ave neighs/atom = 16 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp b/examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp new file mode 100755 index 0000000000..5066049895 --- /dev/null +++ b/examples/USER/phonon/dynamical_matrix_command/Silicon/silicon_input_file.lmp @@ -0,0 +1,29 @@ +LAMMPS description + + 8 atoms + 0 bonds + 0 angles + 0 dihedrals + 0 impropers + + 1 atom types + 0 bond types + 0 angle types + 0 dihedral types + 0 improper types + + + 0.0000000 5.4310000 xlo xhi + 0.0000000 5.4310000 ylo yhi + 0.0000000 5.4310000 zlo zhi + + Atoms + + 1 1 1 0.0000000 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7 1 37 36 42 38 + 8 2 42 37 43 53 + 9 1 44 43 62 45 + 10 2 62 44 63 70 + 11 1 64 63 79 65 + 12 2 79 64 80 81 diff --git a/examples/USER/plumed/in.peptide-plumed b/examples/USER/plumed/in.peptide-plumed new file mode 100644 index 0000000000..6972c0cfca --- /dev/null +++ b/examples/USER/plumed/in.peptide-plumed @@ -0,0 +1,41 @@ +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +group one id 2 4 5 6 +group two id 80 82 83 84 +group ref id 37 +group colvar union one two ref + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 2 all plumed plumedfile plumed.dat outfile p.log +fix 2a ref setforce 0.0 0.0 0.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + +#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_2 +thermo 10 +variable step equal step +variable pe equal pe + +run 101 diff --git a/examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1 b/examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1 new file mode 100644 index 0000000000..eb67b96fce --- /dev/null +++ b/examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1 @@ -0,0 +1,161 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 2 all plumed plumedfile plumed.dat outfile p.log +fix 2a ref setforce 0.0 0.0 0.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_2 +thermo 10 +variable step equal step +variable pe equal pe + +run 101 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 10648 3375 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 18.74 | 18.74 | 18.74 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0 + 10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504 + 20 279.08532 -5226.4036 -6349.1917 1122.7881 -6441.0169 20.764378 0.52605302 + 30 282.32141 -5222.3866 -6358.1939 1135.8073 -6448.9785 22.945165 0.65106011 + 40 276.34173 -5218.7623 -6330.5128 1111.7504 -6423.7566 15.655345 0.23795099 + 50 286.12741 -5215.9248 -6367.0439 1151.1192 -6449.2655 17.420975 0.42646205 + 60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815 + 70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896 + 80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348 + 90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014 +SHAKE stats (type/ave/delta) on step 100 + 4 1.111 2.06868e-06 + 6 0.996999 2.09521e-06 + 8 1.08 1.10835e-06 + 10 1.111 2.46599e-06 + 12 1.08 8.86314e-07 + 14 0.959999 0 + 18 0.9572 9.14098e-06 + 31 104.52 0.000760401 + 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372 + 101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332 +Loop time of 2.73445 on 1 procs for 101 steps with 2004 atoms + +Performance: 6.383 ns/day, 3.760 hours/ns, 36.936 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2617 | 2.2617 | 2.2617 | 0.0 | 82.71 +Bond | 0.0044148 | 0.0044148 | 0.0044148 | 0.0 | 0.16 +Kspace | 0.17883 | 0.17883 | 0.17883 | 0.0 | 6.54 +Neigh | 0.23945 | 0.23945 | 0.23945 | 0.0 | 8.76 +Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.43 +Output | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.01 +Modify | 0.0365 | 0.0365 | 0.0365 | 0.0 | 1.33 +Other | | 0.001611 | | | 0.06 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11134 ave 11134 max 11134 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 707961 ave 707961 max 707961 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 707961 +Ave neighs/atom = 353.274 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 8 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4 b/examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4 new file mode 100644 index 0000000000..72b851c2ff --- /dev/null +++ b/examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4 @@ -0,0 +1,161 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +group peptide type <= 12 +84 atoms in group peptide +group one id 2 4 5 6 +4 atoms in group one +group two id 80 82 83 84 +4 atoms in group two +group ref id 37 +1 atoms in group ref +group colvar union one two ref +9 atoms in group colvar + +fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 + +fix 2 all plumed plumedfile plumed.dat outfile p.log +fix 2a ref setforce 0.0 0.0 0.0 + +fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles + +#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz +#dump_modify 1 sort id + +thermo_style custom step temp etotal pe ke epair ebond f_2 +thermo 10 +variable step equal step +variable pe equal pe + +run 101 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +SHAKE stats (type/ave/delta) on step 0 + 4 1.111 1.44264e-05 + 6 0.996998 7.26967e-06 + 8 1.08 1.32536e-05 + 10 1.111 1.22749e-05 + 12 1.08 1.11767e-05 + 14 0.96 0 + 18 0.957206 4.37979e-05 + 31 104.519 0.00396029 +Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.87 | 16.06 Mbytes +Step Temp TotEng PotEng KinEng E_pair E_bond f_2 + 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0 + 10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504 + 20 279.08532 -5226.4036 -6349.1917 1122.7881 -6441.0169 20.764378 0.52605302 + 30 282.32141 -5222.3866 -6358.1939 1135.8073 -6448.9785 22.945165 0.65106011 + 40 276.34173 -5218.7623 -6330.5128 1111.7504 -6423.7566 15.655345 0.23795099 + 50 286.12741 -5215.9248 -6367.0439 1151.1192 -6449.2655 17.420975 0.42646205 + 60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815 + 70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896 + 80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348 + 90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014 +SHAKE stats (type/ave/delta) on step 100 + 4 1.111 2.06868e-06 + 6 0.996999 2.09521e-06 + 8 1.08 1.10835e-06 + 10 1.111 2.46599e-06 + 12 1.08 8.86314e-07 + 14 0.959999 0 + 18 0.9572 9.14098e-06 + 31 104.52 0.000760401 + 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372 + 101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332 +Loop time of 0.812799 on 4 procs for 101 steps with 2004 atoms + +Performance: 21.472 ns/day, 1.118 hours/ns, 124.262 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.57957 | 0.59988 | 0.62504 | 2.6 | 73.80 +Bond | 0.00080013 | 0.0017412 | 0.0028315 | 2.1 | 0.21 +Kspace | 0.075724 | 0.10008 | 0.12023 | 6.4 | 12.31 +Neigh | 0.067733 | 0.067947 | 0.068168 | 0.1 | 8.36 +Comm | 0.01375 | 0.014175 | 0.014681 | 0.3 | 1.74 +Output | 0.00025511 | 0.00051183 | 0.001277 | 0.0 | 0.06 +Modify | 0.026406 | 0.026436 | 0.026462 | 0.0 | 3.25 +Other | | 0.002027 | | | 0.25 + +Nlocal: 501 ave 512 max 492 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 6570.25 ave 6604 max 6529 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 176990 ave 181122 max 173551 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 707961 +Ave neighs/atom = 353.274 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 8 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/plumed/plumed.dat b/examples/USER/plumed/plumed.dat new file mode 100644 index 0000000000..0437836d03 --- /dev/null +++ b/examples/USER/plumed/plumed.dat @@ -0,0 +1,4 @@ +UNITS LENGTH=A ENERGY=kcal/mol +dd: DISTANCE ATOMS=45,48 +RESTRAINT ARG=dd KAPPA=2000 AT=6.0 +PRINT ARG=dd FILE=colvar diff --git a/examples/USER/plumed/reference/colvar b/examples/USER/plumed/reference/colvar new file mode 100644 index 0000000000..df282364f5 --- /dev/null +++ b/examples/USER/plumed/reference/colvar @@ -0,0 +1,103 @@ +#! FIELDS time dd + 0.000000 5.985554 + 0.002000 6.002880 + 0.004000 6.022015 + 0.006000 6.029922 + 0.008000 6.020103 + 0.010000 5.996906 + 0.012000 5.972734 + 0.014000 5.960079 + 0.016000 5.963714 + 0.018000 5.978140 + 0.020000 5.991813 + 0.022000 5.995155 + 0.024000 5.987021 + 0.026000 5.975340 + 0.028000 5.971456 + 0.030000 5.981945 + 0.032000 6.003550 + 0.034000 6.024743 + 0.036000 6.032990 + 0.038000 6.022936 + 0.040000 6.000131 + 0.042000 5.977800 + 0.044000 5.968692 + 0.046000 5.977224 + 0.048000 5.996934 + 0.050000 6.014800 + 0.052000 6.019586 + 0.054000 6.008803 + 0.056000 5.989809 + 0.058000 5.974484 + 0.060000 5.971140 + 0.062000 5.979074 + 0.064000 5.989379 + 0.066000 5.991356 + 0.068000 5.980176 + 0.070000 5.960625 + 0.072000 5.944401 + 0.074000 5.942614 + 0.076000 5.958402 + 0.078000 5.984574 + 0.080000 6.007964 + 0.082000 6.017667 + 0.084000 6.011795 + 0.086000 5.998304 + 0.088000 5.989405 + 0.090000 5.993275 + 0.092000 6.008545 + 0.094000 6.025183 + 0.096000 6.031186 + 0.098000 6.020651 + 0.100000 5.997952 + 0.102000 5.975230 + 0.104000 5.964757 + 0.106000 5.971150 + 0.108000 5.988568 + 0.110000 6.004676 + 0.112000 6.008731 + 0.114000 5.998481 + 0.116000 5.981406 + 0.118000 5.969615 + 0.120000 5.971827 + 0.122000 5.987658 + 0.124000 6.007888 + 0.126000 6.020477 + 0.128000 6.018377 + 0.130000 6.004046 + 0.132000 5.987682 + 0.134000 5.980338 + 0.136000 5.986534 + 0.138000 6.001303 + 0.140000 6.013589 + 0.142000 6.013717 + 0.144000 6.000028 + 0.146000 5.980283 + 0.148000 5.966836 + 0.150000 5.968670 + 0.152000 5.985459 + 0.154000 6.007612 + 0.156000 6.022374 + 0.158000 6.022034 + 0.160000 6.008851 + 0.162000 5.993355 + 0.164000 5.987212 + 0.166000 5.995452 + 0.168000 6.013111 + 0.170000 6.028386 + 0.172000 6.030387 + 0.174000 6.016468 + 0.176000 5.994191 + 0.178000 5.976616 + 0.180000 5.973983 + 0.182000 5.987185 + 0.184000 6.007275 + 0.186000 6.021338 + 0.188000 6.020837 + 0.190000 6.006955 + 0.192000 5.989433 + 0.194000 5.979796 + 0.196000 5.983601 + 0.198000 5.996921 + 0.200000 6.009310 + 0.202000 6.011114 diff --git a/examples/USER/plumed/reference/p.log b/examples/USER/plumed/reference/p.log new file mode 100644 index 0000000000..79d0bbd84c --- /dev/null +++ b/examples/USER/plumed/reference/p.log @@ -0,0 +1,57 @@ +PLUMED: PLUMED is starting +PLUMED: Version: 2.4.2 (git: Unknown) compiled on Jul 11 2018 at 19:09:03 +PLUMED: Please cite this paper when using PLUMED [1] +PLUMED: For further information see the PLUMED web page at http://www.plumed.org +PLUMED: Root: /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2/ +PLUMED: For installed feature, see /Users/gareth/MD_code/lammps-permanent/lammps/lib/plumed/plumed2-2.4.2//src/config/config.txt +PLUMED: Molecular dynamics engine: LAMMPS +PLUMED: Precision of reals: 8 +PLUMED: Running over 1 node +PLUMED: Number of threads: 1 +PLUMED: Cache line size: 512 +PLUMED: Number of atoms: 2004 +PLUMED: File suffix: +PLUMED: FILE: plumed.dat +PLUMED: Action UNITS +PLUMED: with label @0 +PLUMED: length: A +PLUMED: energy: kcal/mol +PLUMED: time: ps +PLUMED: charge: e +PLUMED: mass: amu +PLUMED: using physical units +PLUMED: inside PLUMED, Boltzmann constant is 0.001987 +PLUMED: Action DISTANCE +PLUMED: with label dd +PLUMED: between atoms 45 48 +PLUMED: using periodic boundary conditions +PLUMED: Action RESTRAINT +PLUMED: with label @2 +PLUMED: with arguments dd +PLUMED: added component to this action: @2.bias +PLUMED: at 6.000000 +PLUMED: with harmonic force constant 2000.000000 +PLUMED: and linear force constant 0.000000 +PLUMED: added component to this action: @2.force2 +PLUMED: Action PRINT +PLUMED: with label @3 +PLUMED: with stride 1 +PLUMED: with arguments dd +PLUMED: on file colvar +PLUMED: with format %f +PLUMED: END FILE: plumed.dat +PLUMED: Timestep: 0.002000 +PLUMED: KbT has not been set by the MD engine +PLUMED: It should be set by hand where needed +PLUMED: Relevant bibliography: +PLUMED: [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014) +PLUMED: Please read and cite where appropriate! +PLUMED: Finished setup +PLUMED: Cycles Total Average Minumum Maximum +PLUMED: 1 0.020354 0.020354 0.020354 0.020354 +PLUMED: 1 Prepare dependencies 102 0.000256 0.000003 0.000001 0.000006 +PLUMED: 2 Sharing data 102 0.010002 0.000098 0.000078 0.000546 +PLUMED: 3 Waiting for data 102 0.001398 0.000014 0.000011 0.000072 +PLUMED: 4 Calculating (forward loop) 102 0.001797 0.000018 0.000013 0.000058 +PLUMED: 5 Applying (backward loop) 102 0.002666 0.000026 0.000022 0.000062 +PLUMED: 6 Update 102 0.001126 0.000011 0.000007 0.000055 diff --git a/examples/USER/ptm/ptm_example.in b/examples/USER/ptm/ptm_example.in new file mode 100644 index 0000000000..07e4f2acaa --- /dev/null +++ b/examples/USER/ptm/ptm_example.in @@ -0,0 +1,47 @@ +# LAMMPS Input File for Grain Boundaries +# Mark Tschopp, Dec2009 +# Modified by PM Larsen to demonstrate the use of PTM in LAMMPS +# This file will generate a single Sigma5(310) STGB and run PTM + +# ---------- Initialize Simulation --------------------- +clear +units metal +dimension 3 +boundary p p p +atom_style atomic + +# ---------- Create Sigma5(310) Structure --------- +lattice fcc 4.05 +region whole block 0.000000 12.807225 -64.0361225 64.0361225 0.000000 4.050000 units box +create_box 2 whole +region upper block INF INF 0.000000 64.0361225 INF INF units box +lattice fcc 4.05 orient x 0 3 1 orient y 0 -1 3 orient z 1 0 0 +create_atoms 1 region upper +region lower block INF INF -64.0361225 0.000000 INF INF units box +lattice fcc 4.05 orient x 0 3 -1 orient y 0 1 3 orient z 1 0 0 +create_atoms 2 region lower +group upper type 1 +group lower type 2 + +mass 1 1.0 +mass 2 1.0 + +# ---------- Define Interatomic Potential --------------------- +pair_style lj/cut 2.5 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 + +# ---------- Displace atoms and delete overlapping atoms --------------------- +displace_atoms upper move 0 0 0 units lattice +delete_atoms overlap 0.35 lower upper + +# ---------- Define PTM settings (default structures, RMSD threshold of 0.1) ------------------- +compute ptm all ptm/atom default 0.1 + +# ---------- Dump data into Data file ------------- +reset_timestep 0 +dump 1 all cfg 10000 dump.ptm_example_*.cfg mass type xs ys zs c_ptm[1] c_ptm[2] c_ptm[3] c_ptm[4] c_ptm[5] c_ptm[6] c_ptm[7] +dump_modify 1 element Al Al +run 1 + +print "All done" diff --git a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod b/examples/USER/qtb/methane_qbmsst/methane_qtb.mod index 9ed62b74b5..181fb99d00 100644 --- a/examples/USER/qtb/methane_qbmsst/methane_qtb.mod +++ b/examples/USER/qtb/methane_qbmsst/methane_qtb.mod @@ -38,8 +38,9 @@ mass 2 1.007970 ## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax" #Pair Potentials -pair_style reax 10.0 1 1 1.0e-6 -pair_coeff * * ffield.reax 1 2 +pair_style reax/c NULL +pair_coeff * * ffield.reax C H +fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c #Neighbor Style neighbor 2.5 bin diff --git a/examples/USER/qtb/methane_qtb/methane_qtb.in b/examples/USER/qtb/methane_qtb/methane_qtb.in index 7389b65f19..f0ea94a221 100644 --- a/examples/USER/qtb/methane_qtb/methane_qtb.in +++ b/examples/USER/qtb/methane_qtb/methane_qtb.in @@ -44,8 +44,9 @@ mass 2 1.007970 ## This part defines the reax pair potential in methane, force field coefficients are specified in "ffield.reax" #Pair Potentials -pair_style reax 10.0 1 1 1.0e-6 -pair_coeff * * ffield.reax 1 2 +pair_style reax/c NULL +pair_coeff * * ffield.reax C H +fix 0 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c #Neighbor Style neighbor 2.5 bin diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 deleted file mode 100644 index 20d3faaf7f..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.16 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49647271 0 0.49647271 0 0 - 10 300 0.051135063 0.014582562 0.44286522 0.02180093 0.46466616 0 0.0043601861 - 20 300 0.10210872 0.058693359 0.37869251 0.087746571 0.46643909 0 0.017549314 - 30 300 0.15278506 0.13468789 0.26730177 0.2013584 0.46866017 0 0.040271679 - 40 300 0.19430375 0.50949535 0.083356437 0.76169555 0.84505198 0 0.15233911 - 50 300 0.23220921 1.1731116 -0.055261984 1.7538018 1.6985399 0 0.35076037 - 60 300 0.27002859 1.3589639 -0.33351524 2.031651 1.6981358 0 0.4063302 - 70 300 0.30781388 1.6482648 -0.76570045 2.4641559 1.6984554 0 0.49283118 - 80 300 0.34566283 2.8640899 -2.4038488 4.2818144 1.8779656 0 0.85636288 - 90 300 0.38424087 93.168442 -2.5911448 139.28682 136.69568 0 27.857364 - 100 300 0.42331123 94.146897 -1.3480439 140.74961 139.40157 0 28.149922 -Loop time of 0.423331 on 16 procs for 100 steps with 300 atoms - -Performance: 102047.913 tau/day, 236.222 timesteps/s -99.2% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5988e-05 | 3.6508e-05 | 5.5075e-05 | 0.0 | 0.01 -Kspace | 0.41852 | 0.41925 | 0.41976 | 0.1 | 99.04 -Neigh | 0.00023413 | 0.00056887 | 0.0012875 | 0.0 | 0.13 -Comm | 0.0019519 | 0.0022772 | 0.0027158 | 0.5 | 0.54 -Output | 0.00028276 | 0.00030752 | 0.0003624 | 0.0 | 0.07 -Modify | 8.3685e-05 | 0.0001286 | 0.00018764 | 0.0 | 0.03 -Other | | 0.000758 | | | 0.18 - -Nlocal: 18.75 ave 39 max 6 min -Histogram: 6 1 1 0 1 2 2 1 1 1 -Nghost: 122.812 ave 195 max 63 min -Histogram: 8 0 0 0 0 0 0 1 3 4 -Neighs: 160.625 ave 598 max 13 min -Histogram: 8 2 1 1 1 0 0 2 0 1 - -Total # of neighbors = 2570 -Ave neighs/atom = 8.56667 -Neighbor list builds = 23 -Dangerous builds = 16 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 deleted file mode 100644 index d26138522a..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.ewald.8 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49647271 0 0.49647271 0 0 - 10 300 0.057411432 0.014718629 0.45088339 0.02200435 0.47288774 0 0.00440087 - 20 300 0.11482716 0.05922597 0.38470912 0.088542825 0.47325194 0 0.017708565 - 30 300 0.17278481 0.13587829 0.27058048 0.20313804 0.47371852 0 0.040627608 - 40 300 0.23021507 0.51353118 0.088432648 0.76772911 0.85616176 0 0.15354582 - 50 300 0.28812647 1.1760001 -0.058088247 1.7581201 1.7000319 0 0.35162403 - 60 300 0.34651113 1.3627885 -0.33736672 2.0373688 1.7000021 0 0.40747376 - 70 300 0.40509939 1.6529365 -0.77082139 2.4711401 1.7003187 0 0.49422802 - 80 300 0.46342874 2.9569837 -2.4624654 4.4206907 1.9582253 0 0.88413814 - 90 300 0.52329254 81.642726 -2.5370215 122.05588 119.51885 0 24.411175 - 100 300 0.58335209 85.047974 -1.128107 127.14672 126.01861 0 25.429344 -Loop time of 0.583369 on 8 procs for 100 steps with 300 atoms - -Performance: 74052.598 tau/day, 171.418 timesteps/s -99.7% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.0531e-05 | 4.6492e-05 | 4.8876e-05 | 0.0 | 0.01 -Kspace | 0.57805 | 0.5785 | 0.57893 | 0.0 | 99.17 -Neigh | 0.00062275 | 0.00091892 | 0.0013313 | 0.0 | 0.16 -Comm | 0.002604 | 0.0028289 | 0.0031538 | 0.3 | 0.48 -Output | 0.0002265 | 0.0002434 | 0.00029039 | 0.0 | 0.04 -Modify | 0.00016117 | 0.00017747 | 0.00019884 | 0.0 | 0.03 -Other | | 0.00065 | | | 0.11 - -Nlocal: 37.5 ave 46 max 31 min -Histogram: 2 0 0 2 1 0 2 0 0 1 -Nghost: 203.875 ave 212 max 192 min -Histogram: 1 0 1 0 0 2 1 0 0 3 -Neighs: 321.625 ave 599 max 112 min -Histogram: 1 2 0 1 1 0 1 1 0 1 - -Total # of neighbors = 2573 -Ave neighs/atom = 8.57667 -Neighbor list builds = 23 -Dangerous builds = 16 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 deleted file mode 100644 index c9c1e0d155..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ... - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 - 10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 - 20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 - 30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 - 40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 - 50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 - 60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 - 70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 - 80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 - 90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 - 100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 -Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms - -Performance: 183509.107 tau/day, 424.790 timesteps/s -97.9% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.2425e-05 | 4.4718e-05 | 6.1274e-05 | 0.0 | 0.02 -Kspace | 0.23097 | 0.23143 | 0.2318 | 0.1 | 98.31 -Neigh | 0.00015116 | 0.00035347 | 0.00075746 | 0.0 | 0.15 -Comm | 0.0020316 | 0.002282 | 0.0025339 | 0.3 | 0.97 -Output | 0.00034404 | 0.00037053 | 0.00042701 | 0.0 | 0.16 -Modify | 9.3937e-05 | 0.00014532 | 0.00018811 | 0.0 | 0.06 -Other | | 0.0007878 | | | 0.33 - -Nlocal: 18.75 ave 36 max 6 min -Histogram: 4 3 1 0 0 1 2 1 2 2 -Nghost: 127 ave 196 max 71 min -Histogram: 8 0 0 0 0 0 0 1 6 1 -Neighs: 153.688 ave 491 max 10 min -Histogram: 8 1 1 1 1 1 0 0 0 3 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 deleted file mode 100644 index 1a9bc77146..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ... - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 - 10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 - 20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 - 30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 - 40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 - 50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 - 60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 - 70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 - 80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 - 90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 - 100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 -Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms - -Performance: 110479.760 tau/day, 255.740 timesteps/s -99.6% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 8.0109e-05 | 8.1539e-05 | 8.297e-05 | 0.0 | 0.02 -Kspace | 0.38534 | 0.38582 | 0.3863 | 0.1 | 98.67 -Neigh | 0.0014851 | 0.0019699 | 0.0024548 | 1.1 | 0.50 -Comm | 0.0019314 | 0.0020101 | 0.0020888 | 0.2 | 0.51 -Output | 0.00014496 | 0.00017297 | 0.00020099 | 0.0 | 0.04 -Modify | 0.0005033 | 0.00052273 | 0.00054216 | 0.0 | 0.13 -Other | | 0.0004461 | | | 0.11 - -Nlocal: 150 ave 159 max 141 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 392 ave 395 max 389 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 1229.5 ave 1773 max 686 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 deleted file mode 100644 index eae3f2b840..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.4 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ... - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 - 10 300 0.029414415 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 - 20 300 0.058616877 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 - 30 300 0.087769508 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 - 40 300 0.1168611 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 - 50 300 0.14482284 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 - 60 300 0.17198443 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 - 70 300 0.19868851 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 - 80 300 0.22835517 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 - 90 300 0.26023602 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 - 100 300 0.29043221 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 -Loop time of 0.290448 on 4 procs for 100 steps with 300 atoms - -Performance: 148735.741 tau/day, 344.296 timesteps/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.9605e-05 | 6.187e-05 | 6.4135e-05 | 0.0 | 0.02 -Kspace | 0.28551 | 0.28584 | 0.28604 | 0.0 | 98.41 -Neigh | 0.00077796 | 0.0010615 | 0.0013225 | 0.7 | 0.37 -Comm | 0.002372 | 0.0024325 | 0.002497 | 0.1 | 0.84 -Output | 0.00025368 | 0.0002659 | 0.00029516 | 0.0 | 0.09 -Modify | 0.00030279 | 0.00031865 | 0.00033021 | 0.0 | 0.11 -Other | | 0.0004706 | | | 0.16 - -Nlocal: 75 ave 81 max 70 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 282.5 ave 290 max 274 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Neighs: 614.75 ave 981 max 285 min -Histogram: 1 1 0 0 0 0 0 1 0 1 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 deleted file mode 100644 index feb7e2a5a6..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8 +++ /dev/null @@ -1,99 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -kspace_style scafacos fmm 1.0e-3 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ... - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 - 10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 - 20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 - 30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 - 40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 - 50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 - 60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 - 70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 - 80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 - 90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 - 100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 -Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms - -Performance: 147513.337 tau/day, 341.466 timesteps/s -98.4% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.7207e-05 | 5.5045e-05 | 6.9618e-05 | 0.0 | 0.02 -Kspace | 0.28739 | 0.28773 | 0.2881 | 0.0 | 98.25 -Neigh | 0.00040698 | 0.00060901 | 0.00082922 | 0.0 | 0.21 -Comm | 0.0029533 | 0.0031788 | 0.0034056 | 0.3 | 1.09 -Output | 0.00029063 | 0.00030866 | 0.00035119 | 0.0 | 0.11 -Modify | 0.00018978 | 0.00022188 | 0.00026703 | 0.0 | 0.08 -Other | | 0.0007486 | | | 0.26 - -Nlocal: 37.5 ave 45 max 31 min -Histogram: 1 1 1 1 1 0 1 0 1 1 -Nghost: 200 ave 209 max 189 min -Histogram: 1 0 0 0 1 4 0 0 0 2 -Neighs: 307.375 ave 514 max 115 min -Histogram: 2 1 0 1 1 0 0 0 1 2 - -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 deleted file mode 100644 index d6e7cbea37..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.313 | 3.501 | 3.689 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 - 10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 - 20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 - 30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 - 40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 - 50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 - 60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 - 70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 - 80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 - 90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 - 100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 -Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms - -Performance: 272716.448 tau/day, 631.288 timesteps/s -99.4% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.718e-05 | 3.7491e-05 | 5.6744e-05 | 0.0 | 0.02 -Kspace | 0.15435 | 0.15482 | 0.15516 | 0.1 | 97.74 -Neigh | 0.00014806 | 0.0003508 | 0.00074744 | 0.0 | 0.22 -Comm | 0.0016866 | 0.0019967 | 0.0023787 | 0.5 | 1.26 -Output | 0.00027871 | 0.00033027 | 0.00038028 | 0.0 | 0.21 -Modify | 8.0347e-05 | 0.00011933 | 0.00016522 | 0.0 | 0.08 -Other | | 0.0007506 | | | 0.47 - -Nlocal: 18.75 ave 33 max 6 min -Histogram: 2 6 0 0 0 0 2 1 2 3 -Nghost: 128.875 ave 198 max 71 min -Histogram: 7 1 0 0 0 0 0 1 5 2 -Neighs: 153.812 ave 490 max 14 min -Histogram: 8 0 3 0 1 1 0 0 1 2 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 deleted file mode 100644 index fb863797f3..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.2 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.354 | 3.354 | 3.355 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 - 10 300 0.044083834 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 - 20 300 0.088379145 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 - 30 300 0.13264704 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 - 40 300 0.17687225 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 - 50 300 0.22116137 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 - 60 300 0.26515126 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 - 70 300 0.30891085 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 - 80 300 0.35292292 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 - 90 300 0.39845228 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 - 100 300 0.44492316 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 -Loop time of 0.444937 on 2 procs for 100 steps with 300 atoms - -Performance: 97092.373 tau/day, 224.751 timesteps/s -100.0% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.7248e-05 | 7.844e-05 | 7.9632e-05 | 0.0 | 0.02 -Kspace | 0.43932 | 0.43979 | 0.44026 | 0.1 | 98.84 -Neigh | 0.0014915 | 0.0019662 | 0.0024409 | 1.1 | 0.44 -Comm | 0.0019331 | 0.0019941 | 0.0020552 | 0.1 | 0.45 -Output | 0.00013781 | 0.00016308 | 0.00018835 | 0.0 | 0.04 -Modify | 0.00050378 | 0.00050449 | 0.00050521 | 0.0 | 0.11 -Other | | 0.0004425 | | | 0.10 - -Nlocal: 150 ave 157 max 143 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 399 ave 402 max 396 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 1230.5 ave 1756 max 705 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 deleted file mode 100644 index a6f9228673..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8 +++ /dev/null @@ -1,92 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task - -units lj -atom_style charge - -read_data data.cloud_wall - orthogonal box = (0 0 0) to (10 10 10) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 300 atoms - -velocity all set 0.0 0.0 0.0 mom no - -pair_style zero 1.0 -pair_coeff * * - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 - -thermo_style custom step atoms cpu temp pe ke etotal ecoul press - -run_style verlet - -#dump simple all custom 1000 id x y z vx vy vz -#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass -#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass -#dump_modify dmpvtk pad 7 - -thermo 10 -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.317 | 3.317 | 3.317 Mbytes -Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press - 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 - 10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 - 20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 - 30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 - 40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 - 50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 - 60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 - 70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 - 80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 - 90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 - 100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 -Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms - -Performance: 216363.074 tau/day, 500.840 timesteps/s -99.4% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.5061e-05 | 4.7535e-05 | 5.3167e-05 | 0.0 | 0.02 -Kspace | 0.19551 | 0.19584 | 0.19611 | 0.0 | 98.08 -Neigh | 0.00041366 | 0.00060952 | 0.00082064 | 0.0 | 0.31 -Comm | 0.0021496 | 0.0022282 | 0.0024025 | 0.2 | 1.12 -Output | 0.0002346 | 0.00024167 | 0.00027847 | 0.0 | 0.12 -Modify | 0.00016665 | 0.00017652 | 0.0001924 | 0.0 | 0.09 -Other | | 0.0005245 | | | 0.26 - -Nlocal: 37.5 ave 42 max 33 min -Histogram: 2 1 0 1 0 0 1 0 1 2 -Nghost: 202.25 ave 212 max 194 min -Histogram: 1 0 2 1 0 2 0 1 0 1 -Neighs: 307.625 ave 505 max 129 min -Histogram: 3 0 0 1 1 0 0 0 1 2 - -Total # of neighbors = 2461 -Ave neighs/atom = 8.20333 -Neighbor list builds = 15 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 deleted file mode 100644 index 2fc46da3cd..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.16 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 2 by 2 by 4 MPI processor grid - 4096 atoms - Time spent = 0.000462294 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475938 0 0.50185691 -nan - 10 1.500011 -1.747529 0 0.50193816 -nan - 20 1.5000023 -1.7475152 0 0.50193898 -nan - 30 1.4999308 -1.747404 0 0.50194285 -nan - 40 1.4997722 -1.7471622 0 0.50194686 -nan - 50 1.4995835 -1.746878 0 0.50194808 -nan - 60 1.4996054 -1.7469114 0 0.50194749 -nan - 70 1.5004341 -1.7481558 0 0.50194592 -nan - 80 1.5033218 -1.7524875 0 0.50194458 -nan - 90 1.5108306 -1.7637462 0 0.50194636 -nan - 100 1.5292479 -1.7913449 0 0.50196695 -nan -Loop time of 80.2777 on 16 procs for 100 steps with 4096 atoms - -Performance: 538.132 tau/day, 1.246 timesteps/s -99.8% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0003705 | 0.00039807 | 0.00048542 | 0.0 | 0.00 -Kspace | 80.262 | 80.263 | 80.264 | 0.0 | 99.98 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010191 | 0.011419 | 0.012416 | 0.6 | 0.01 -Output | 0.00028253 | 0.00033158 | 0.0004065 | 0.0 | 0.00 -Modify | 0.00082541 | 0.0008464 | 0.00087833 | 0.0 | 0.00 -Other | | 0.001511 | | | 0.00 - -Nlocal: 256 ave 256 max 256 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Nghost: 2816 ave 2816 max 2816 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Neighs: 32768 ave 32768 max 32768 min -Histogram: 16 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:01:22 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 deleted file mode 100644 index b6bf41de24..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.2 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 1 by 1 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000344753 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475938 0 0.50185691 11.99707 - 10 1.500011 -1.747529 0 0.50193816 11.997158 - 20 1.5000023 -1.7475152 0 0.50193898 11.997089 - 30 1.4999308 -1.747404 0 0.50194285 11.996517 - 40 1.4997722 -1.7471622 0 0.50194686 11.995248 - 50 1.4995835 -1.746878 0 0.50194808 11.993739 - 60 1.4996054 -1.7469114 0 0.50194749 11.993914 - 70 1.5004341 -1.7481558 0 0.50194592 12.000543 - 80 1.5033218 -1.7524875 0 0.50194458 12.023638 - 90 1.5108306 -1.7637462 0 0.50194636 12.083694 - 100 1.5292479 -1.7913449 0 0.50196695 12.230996 -Loop time of 566.796 on 2 procs for 100 steps with 4096 atoms - -Performance: 76.218 tau/day, 0.176 timesteps/s -100.0% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0010231 | 0.0010413 | 0.0010595 | 0.1 | 0.00 -Kspace | 566.77 | 566.77 | 566.77 | 0.0 | 99.99 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.019707 | 0.01982 | 0.019932 | 0.1 | 0.00 -Output | 0.0002656 | 0.00029266 | 0.00031972 | 0.0 | 0.00 -Modify | 0.0055575 | 0.0055707 | 0.0055838 | 0.0 | 0.00 -Other | | 0.002497 | | | 0.00 - -Nlocal: 2048 ave 2048 max 2048 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Nghost: 7168 ave 7168 max 7168 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Neighs: 262144 ave 262144 max 262144 min -Histogram: 2 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:09:38 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 deleted file mode 100644 index 4a1a5b91ed..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.8 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 2 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000232935 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos ewald 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver ewald ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475938 0 0.50185691 -nan - 10 1.500011 -1.747529 0 0.50193816 -nan - 20 1.5000023 -1.7475152 0 0.50193898 -nan - 30 1.4999308 -1.747404 0 0.50194285 -nan - 40 1.4997722 -1.7471622 0 0.50194686 -nan - 50 1.4995835 -1.746878 0 0.50194808 -nan - 60 1.4996054 -1.7469114 0 0.50194749 -nan - 70 1.5004341 -1.7481558 0 0.50194592 -nan - 80 1.5033218 -1.7524875 0 0.50194458 -nan - 90 1.5108306 -1.7637462 0 0.50194636 -nan - 100 1.5292479 -1.7913449 0 0.50196695 -nan -Loop time of 154.44 on 8 procs for 100 steps with 4096 atoms - -Performance: 279.720 tau/day, 0.647 timesteps/s -99.9% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00049257 | 0.00051311 | 0.00059295 | 0.0 | 0.00 -Kspace | 154.42 | 154.42 | 154.42 | 0.0 | 99.99 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.012076 | 0.013177 | 0.014308 | 0.8 | 0.01 -Output | 0.00025177 | 0.00028065 | 0.00030136 | 0.0 | 0.00 -Modify | 0.0015776 | 0.0017182 | 0.0018268 | 0.2 | 0.00 -Other | | 0.001309 | | | 0.00 - -Nlocal: 512 ave 512 max 512 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 3584 ave 3584 max 3584 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 65536 ave 65536 max 65536 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:02:38 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 deleted file mode 100644 index 4bd0c3d4f3..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.16 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 2 by 2 by 4 MPI processor grid - 4096 atoms - Time spent = 0.000400543 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475646 0 0.50188608 10.44368 - 10 1.5000016 -1.7475671 0 0.50188602 10.44369 - 20 1.4999827 -1.7475388 0 0.50188592 10.443564 - 30 1.4999016 -1.7474173 0 0.5018858 10.443023 - 40 1.4997356 -1.7471685 0 0.50188572 10.441917 - 50 1.4995414 -1.7468771 0 0.5018858 10.440623 - 60 1.4995587 -1.7469027 0 0.50188622 10.440739 - 70 1.5003837 -1.7481389 0 0.50188727 10.446238 - 80 1.5032684 -1.7524625 0 0.50188958 10.465466 - 90 1.5107749 -1.763714 0 0.50189507 10.515502 - 100 1.52919 -1.791306 0 0.50191895 10.638261 -Loop time of 4.23774 on 16 procs for 100 steps with 4096 atoms - -Performance: 10194.102 tau/day, 23.597 timesteps/s -99.6% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00038028 | 0.00040729 | 0.00046206 | 0.0 | 0.01 -Kspace | 4.2206 | 4.2211 | 4.2216 | 0.0 | 99.61 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011439 | 0.012491 | 0.013172 | 0.4 | 0.29 -Output | 0.00042915 | 0.000489 | 0.00061274 | 0.0 | 0.01 -Modify | 0.00093102 | 0.00099151 | 0.0010982 | 0.0 | 0.02 -Other | | 0.002255 | | | 0.05 - -Nlocal: 256 ave 256 max 256 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Nghost: 2816 ave 2816 max 2816 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Neighs: 32768 ave 32768 max 32768 min -Histogram: 16 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:06 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 deleted file mode 100644 index 50dcc99393..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.2 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 1 by 1 by 2 MPI processor grid - 4096 atoms - Time spent = 0.0003407 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475646 0 0.50188608 10.44368 - 10 1.5000016 -1.7475671 0 0.50188602 10.44369 - 20 1.4999827 -1.7475388 0 0.50188592 10.443564 - 30 1.4999016 -1.7474173 0 0.5018858 10.443023 - 40 1.4997356 -1.7471685 0 0.50188572 10.441917 - 50 1.4995414 -1.7468771 0 0.5018858 10.440623 - 60 1.4995587 -1.7469027 0 0.50188622 10.440739 - 70 1.5003837 -1.7481389 0 0.50188727 10.446238 - 80 1.5032684 -1.7524625 0 0.50188958 10.465466 - 90 1.5107749 -1.763714 0 0.50189507 10.515502 - 100 1.52919 -1.791306 0 0.50191895 10.638261 -Loop time of 17.9401 on 2 procs for 100 steps with 4096 atoms - -Performance: 2408.014 tau/day, 5.574 timesteps/s -99.9% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0010042 | 0.0010235 | 0.0010428 | 0.1 | 0.01 -Kspace | 17.912 | 17.912 | 17.912 | 0.0 | 99.84 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.018252 | 0.018528 | 0.018804 | 0.2 | 0.10 -Output | 0.00034094 | 0.00035989 | 0.00037885 | 0.0 | 0.00 -Modify | 0.0055602 | 0.0056567 | 0.0057533 | 0.1 | 0.03 -Other | | 0.002716 | | | 0.02 - -Nlocal: 2048 ave 2048 max 2048 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Nghost: 7168 ave 7168 max 7168 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Neighs: 262144 ave 262144 max 262144 min -Histogram: 2 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:19 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 deleted file mode 100644 index 02a5528c59..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.8 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 2 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000236988 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475646 0 0.50188608 10.44368 - 10 1.5000016 -1.7475671 0 0.50188602 10.44369 - 20 1.4999827 -1.7475388 0 0.50188592 10.443564 - 30 1.4999016 -1.7474173 0 0.5018858 10.443023 - 40 1.4997356 -1.7471685 0 0.50188572 10.441917 - 50 1.4995414 -1.7468771 0 0.5018858 10.440623 - 60 1.4995587 -1.7469027 0 0.50188622 10.440739 - 70 1.5003837 -1.7481389 0 0.50188727 10.446238 - 80 1.5032684 -1.7524625 0 0.50188958 10.465466 - 90 1.5107749 -1.763714 0 0.50189507 10.515502 - 100 1.52919 -1.791306 0 0.50191895 10.638261 -Loop time of 5.96037 on 8 procs for 100 steps with 4096 atoms - -Performance: 7247.876 tau/day, 16.777 timesteps/s -99.8% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00049591 | 0.0005368 | 0.00056005 | 0.0 | 0.01 -Kspace | 5.94 | 5.941 | 5.9419 | 0.0 | 99.68 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013702 | 0.014631 | 0.015768 | 0.6 | 0.25 -Output | 0.00044751 | 0.00048846 | 0.00058961 | 0.0 | 0.01 -Modify | 0.0016675 | 0.0017205 | 0.0017893 | 0.1 | 0.03 -Other | | 0.001971 | | | 0.03 - -Nlocal: 512 ave 512 max 512 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 3584 ave 3584 max 3584 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 65536 ave 65536 max 65536 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:07 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 deleted file mode 100644 index 6e6e8f6e94..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.16 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 2 by 2 by 4 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 2 by 2 by 4 MPI processor grid - 4096 atoms - Time spent = 0.000361443 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.501 | 3.501 | 3.501 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7477245 0 0.50172614 10.443537 - 10 1.5000176 -1.7475898 0 0.50188725 10.443798 - 20 1.5000161 -1.7475262 0 0.50194874 10.443843 - 30 1.4999486 -1.7474019 0 0.50197176 10.443413 - 40 1.4997889 -1.7471525 0 0.50198161 10.442357 - 50 1.4995945 -1.7468614 0 0.50198122 10.441061 - 60 1.499609 -1.7468813 0 0.50198309 10.44116 - 70 1.5004314 -1.7481179 0 0.50197962 10.446638 - 80 1.5033149 -1.7524495 0 0.50197233 10.46585 - 90 1.5108219 -1.7637095 0 0.50197005 10.515883 - 100 1.529239 -1.7913105 0 0.501988 10.638649 -Loop time of 1.56685 on 16 procs for 100 steps with 4096 atoms - -Performance: 27571.239 tau/day, 63.822 timesteps/s -99.8% CPU use with 16 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00036407 | 0.00040755 | 0.00047517 | 0.0 | 0.03 -Kspace | 1.5521 | 1.553 | 1.5536 | 0.0 | 99.12 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.009537 | 0.010175 | 0.011894 | 0.6 | 0.65 -Output | 0.000319 | 0.00039139 | 0.00052881 | 0.0 | 0.02 -Modify | 0.00086999 | 0.00097834 | 0.0010362 | 0.0 | 0.06 -Other | | 0.001859 | | | 0.12 - -Nlocal: 256 ave 256 max 256 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Nghost: 2816 ave 2816 max 2816 min -Histogram: 16 0 0 0 0 0 0 0 0 0 -Neighs: 32768 ave 32768 max 32768 min -Histogram: 16 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 deleted file mode 100644 index 72a53c48ff..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.2 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 1 by 1 by 2 MPI processor grid - 4096 atoms - Time spent = 0.0003438 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7477245 0 0.50172614 10.443537 - 10 1.5000176 -1.7475898 0 0.50188725 10.443798 - 20 1.5000161 -1.7475262 0 0.50194874 10.443843 - 30 1.4999486 -1.7474019 0 0.50197176 10.443413 - 40 1.4997889 -1.7471525 0 0.50198161 10.442357 - 50 1.4995945 -1.7468614 0 0.50198122 10.441061 - 60 1.499609 -1.7468813 0 0.50198309 10.44116 - 70 1.5004314 -1.7481179 0 0.50197962 10.446638 - 80 1.5033149 -1.7524495 0 0.50197233 10.46585 - 90 1.5108219 -1.7637095 0 0.50197005 10.515883 - 100 1.529239 -1.7913105 0 0.501988 10.638649 -Loop time of 9.38943 on 2 procs for 100 steps with 4096 atoms - -Performance: 4600.920 tau/day, 10.650 timesteps/s -99.9% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0010064 | 0.0010065 | 0.0010066 | 0.0 | 0.01 -Kspace | 9.3602 | 9.3603 | 9.3604 | 0.0 | 99.69 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.019444 | 0.01968 | 0.019916 | 0.2 | 0.21 -Output | 0.00033355 | 0.00035357 | 0.0003736 | 0.0 | 0.00 -Modify | 0.0055819 | 0.0056176 | 0.0056534 | 0.0 | 0.06 -Other | | 0.002495 | | | 0.03 - -Nlocal: 2048 ave 2048 max 2048 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Nghost: 7168 ave 7168 max 7168 min -Histogram: 2 0 0 0 0 0 0 0 0 0 -Neighs: 262144 ave 262144 max 262144 min -Histogram: 2 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:11 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 deleted file mode 100644 index b5e889dfc1..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.8 +++ /dev/null @@ -1,102 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.NaCl - orthogonal box = (0 0 0) to (1 1 1) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 8 atoms - -replicate 8 8 8 - orthogonal box = (0 0 0) to (8 8 8) - 2 by 2 by 2 MPI processor grid - 4096 atoms - Time spent = 0.000324488 secs - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance field - -timestep 0.005 -thermo 10 - -run 100 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 8 8 8 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.508 | 3.508 | 3.508 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7477245 0 0.50172614 10.443537 - 10 1.5000176 -1.7475898 0 0.50188725 10.443798 - 20 1.5000161 -1.7475262 0 0.50194874 10.443843 - 30 1.4999486 -1.7474019 0 0.50197176 10.443413 - 40 1.4997889 -1.7471525 0 0.50198161 10.442357 - 50 1.4995945 -1.7468614 0 0.50198122 10.441061 - 60 1.499609 -1.7468813 0 0.50198309 10.44116 - 70 1.5004314 -1.7481179 0 0.50197962 10.446638 - 80 1.5033149 -1.7524495 0 0.50197233 10.46585 - 90 1.5108219 -1.7637095 0 0.50197005 10.515883 - 100 1.529239 -1.7913105 0 0.501988 10.638649 -Loop time of 2.88506 on 8 procs for 100 steps with 4096 atoms - -Performance: 14973.700 tau/day, 34.661 timesteps/s -99.6% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.000489 | 0.00051507 | 0.00052857 | 0.0 | 0.02 -Kspace | 2.8657 | 2.866 | 2.8664 | 0.0 | 99.34 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.014354 | 0.014851 | 0.015097 | 0.2 | 0.51 -Output | 0.00037169 | 0.00042769 | 0.00054169 | 0.0 | 0.01 -Modify | 0.0015774 | 0.0016578 | 0.0018044 | 0.2 | 0.06 -Other | | 0.001645 | | | 0.06 - -Nlocal: 512 ave 512 max 512 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Nghost: 3584 ave 3584 max 3584 min -Histogram: 8 0 0 0 0 0 0 0 0 0 -Neighs: 65536 ave 65536 max 65536 min -Histogram: 8 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 524288 -Ave neighs/atom = 128 -Neighbor list builds = 0 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 b/examples/USER/scafacos/log.08Aug18.scafacos.g++.p3m.2 deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 deleted file mode 100644 index 1ffab0ca6a..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.2 +++ /dev/null @@ -1,105 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos direct 0.001 - -timestep 0.005 -thermo 1 -run 20 -Setting up ScaFaCoS with solver direct ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777512 0 272.51604 0.17462195 - 5 286.36222 -4.382053 0 424.73173 0.26918926 - 6 481.42206 -4.3095567 0 717.1014 0.45274088 - 7 488.59167 -3.8685194 0 728.2861 0.45956866 - 8 497.85287 -3.0417966 0 742.99073 0.46838116 - 9 499.61615 -3.419003 0 745.2558 0.46983345 - 10 502.63684 -2.8360961 0 750.36521 0.47280809 - 11 504.4846 -2.7628105 0 753.20736 0.47462793 - 12 506.54485 -2.8460356 0 756.21142 0.47651441 - 13 508.27211 -2.730935 0 758.91482 0.47813752 - 14 510.57045 -2.6094877 0 762.48033 0.48031431 - 15 513.14798 -2.7150827 0 766.23717 0.48275229 - 16 515.78124 -2.3961811 0 770.50201 0.48526333 - 17 515.70265 -2.2982683 0 770.48215 0.48526617 - 18 515.7081 -2.1515983 0 770.63699 0.48530393 - 19 515.74906 -2.0581436 0 770.79182 0.48530977 - 20 515.70883 -1.8922577 0 770.89742 0.48527105 -Loop time of 0.284007 on 2 procs for 20 steps with 1000 atoms - -Performance: 30421.778 tau/day, 70.421 timesteps/s -99.1% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00022578 | 0.00022626 | 0.00022674 | 0.0 | 0.08 -Kspace | 0.18253 | 0.20503 | 0.22752 | 5.0 | 72.19 -Neigh | 0.05363 | 0.076239 | 0.098848 | 8.2 | 26.84 -Comm | 0.0014737 | 0.0016443 | 0.0018148 | 0.4 | 0.58 -Output | 0.000247 | 0.00032353 | 0.00040007 | 0.0 | 0.11 -Modify | 0.00029159 | 0.00029731 | 0.00030303 | 0.0 | 0.10 -Other | | 0.0002506 | | | 0.09 - -Nlocal: 500 ave 516 max 484 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 456.5 ave 475 max 438 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 123908 ave 172139 max 75678 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 deleted file mode 100644 index e72ade73b5..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.8 +++ /dev/null @@ -1,105 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos direct 0.001 - -timestep 0.005 -thermo 1 -run 20 -Setting up ScaFaCoS with solver direct ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777512 0 272.51604 0.17462195 - 5 286.36222 -4.382053 0 424.73173 0.26918926 - 6 481.42206 -4.3095567 0 717.1014 0.45274088 - 7 488.59167 -3.8685194 0 728.2861 0.45956866 - 8 497.85287 -3.0417966 0 742.99073 0.46838116 - 9 499.61615 -3.419003 0 745.2558 0.46983345 - 10 502.63684 -2.8360961 0 750.36521 0.47280809 - 11 504.4846 -2.7628105 0 753.20736 0.47462793 - 12 506.54485 -2.8460356 0 756.21142 0.47651441 - 13 508.27211 -2.730935 0 758.91482 0.47813752 - 14 510.57045 -2.6094877 0 762.48033 0.48031431 - 15 513.14798 -2.7150827 0 766.23717 0.48275229 - 16 515.78124 -2.3961811 0 770.50201 0.48526333 - 17 515.70265 -2.2982683 0 770.48215 0.48526617 - 18 515.7081 -2.1515983 0 770.63699 0.48530393 - 19 515.74906 -2.0581436 0 770.79182 0.48530977 - 20 515.70883 -1.8922577 0 770.89742 0.48527105 -Loop time of 0.0883947 on 8 procs for 20 steps with 1000 atoms - -Performance: 97743.448 tau/day, 226.258 timesteps/s -99.2% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0002284 | 0.00024167 | 0.00029922 | 0.0 | 0.27 -Kspace | 0.055725 | 0.063153 | 0.071883 | 2.4 | 71.44 -Neigh | 0.012251 | 0.021348 | 0.029026 | 4.3 | 24.15 -Comm | 0.0025573 | 0.0029825 | 0.0034359 | 0.5 | 3.37 -Output | 0.00034451 | 0.00044149 | 0.00057721 | 0.0 | 0.50 -Modify | 7.8917e-05 | 8.437e-05 | 8.9407e-05 | 0.0 | 0.10 -Other | | 0.0001439 | | | 0.16 - -Nlocal: 125 ave 133 max 113 min -Histogram: 2 0 0 0 0 1 1 0 2 2 -Nghost: 773.625 ave 788 max 764 min -Histogram: 1 1 2 1 1 0 0 0 1 1 -Neighs: 30977.1 ave 50690 max 10447 min -Histogram: 1 1 1 0 1 1 0 0 2 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 deleted file mode 100644 index e8e614004d..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.2 +++ /dev/null @@ -1,109 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ... - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.0015676581 - 1 18.780412 -10.770009 0 17.372438 0.016719188 - 2 65.294131 -11.084501 0 86.758754 0.06035827 - 3 121.92555 -7.0612033 0 175.64423 0.1140457 - 4 185.71165 -5.8781334 0 272.41077 0.17455524 - 5 286.28339 -4.3800108 0 424.61565 0.26911306 - 6 481.28097 -4.3052012 0 716.89433 0.45262045 - 7 487.26022 -3.8672741 0 726.29216 0.45830216 - 8 493.65478 -3.0242687 0 736.71742 0.46443761 - 9 495.66203 -3.4336343 0 739.31592 0.46613014 - 10 498.41831 -2.8837072 0 743.99613 0.46887706 - 11 499.20944 -2.7724783 0 745.29287 0.46966875 - 12 500.97345 -2.8281484 0 747.88057 0.47126462 - 13 507.46412 -2.7752775 0 757.65971 0.47728761 - 14 525.35729 -2.5749814 0 784.67292 0.49422171 - 15 563.9578 -2.9982381 0 842.09253 0.53043696 - 16 645.47602 -2.5519203 0 964.69389 0.60730795 - 17 647.09276 -2.2568468 0 967.41166 0.60891914 - 18 647.12596 -2.2791003 0 967.43915 0.60900309 - 19 647.24862 -2.2495226 0 967.65253 0.60908339 - 20 647.51175 -2.0239179 0 968.27244 0.60932598 -Loop time of 0.701186 on 2 procs for 20 steps with 1000 atoms - -Performance: 12321.981 tau/day, 28.523 timesteps/s -99.7% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00022388 | 0.00022912 | 0.00023437 | 0.0 | 0.03 -Kspace | 0.60189 | 0.62405 | 0.64621 | 2.8 | 89.00 -Neigh | 0.051681 | 0.073973 | 0.096265 | 8.2 | 10.55 -Comm | 0.0016983 | 0.0018919 | 0.0020854 | 0.4 | 0.27 -Output | 0.00034356 | 0.00044572 | 0.00054789 | 0.0 | 0.06 -Modify | 0.00031281 | 0.0003171 | 0.00032139 | 0.0 | 0.05 -Other | | 0.0002786 | | | 0.04 - -Nlocal: 500 ave 509 max 491 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 455.5 ave 467 max 444 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 122171 ave 171834 max 72508 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 244342 -Ave neighs/atom = 244.342 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 deleted file mode 100644 index 22d1140813..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.8 +++ /dev/null @@ -1,109 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos fmm 0.001 -kspace_modify scafacos tolerance energy_rel -kspace_modify scafacos fmm_tuning 1 -ScaFaCoS setting fmm inhomogen tuning ... - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver fmm ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.0015676581 - 1 18.780412 -10.770009 0 17.372438 0.016719188 - 2 65.294131 -11.084501 0 86.758754 0.06035827 - 3 121.92555 -7.0612033 0 175.64423 0.1140457 - 4 185.71165 -5.8781334 0 272.41077 0.17455524 - 5 286.28339 -4.3800108 0 424.61565 0.26911306 - 6 481.28097 -4.3052012 0 716.89433 0.45262045 - 7 487.26022 -3.8672741 0 726.29216 0.45830216 - 8 493.65478 -3.0242687 0 736.71742 0.46443761 - 9 495.66203 -3.4336343 0 739.31592 0.46613014 - 10 498.41831 -2.8837072 0 743.99613 0.46887706 - 11 499.20944 -2.7724783 0 745.29287 0.46966875 - 12 500.97345 -2.8281484 0 747.88057 0.47126462 - 13 507.46412 -2.7752775 0 757.65971 0.47728761 - 14 525.35729 -2.5749814 0 784.67292 0.49422171 - 15 563.9578 -2.9982381 0 842.09253 0.53043696 - 16 645.47602 -2.5519203 0 964.69389 0.60730795 - 17 647.09276 -2.2568468 0 967.41166 0.60891914 - 18 647.12596 -2.2791003 0 967.43915 0.60900309 - 19 647.24862 -2.2495226 0 967.65253 0.60908339 - 20 647.51175 -2.0239179 0 968.27244 0.60932598 -Loop time of 0.569395 on 8 procs for 20 steps with 1000 atoms - -Performance: 15174.000 tau/day, 35.125 timesteps/s -99.3% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00021982 | 0.00023353 | 0.0002408 | 0.0 | 0.04 -Kspace | 0.53679 | 0.54466 | 0.55292 | 0.8 | 95.66 -Neigh | 0.011844 | 0.02033 | 0.028357 | 4.2 | 3.57 -Comm | 0.0028894 | 0.0031579 | 0.0034704 | 0.4 | 0.55 -Output | 0.0005579 | 0.00067073 | 0.0008719 | 0.0 | 0.12 -Modify | 0.0001018 | 0.00011405 | 0.00012612 | 0.0 | 0.02 -Other | | 0.0002268 | | | 0.04 - -Nlocal: 125 ave 137 max 111 min -Histogram: 1 1 0 0 0 2 2 1 0 1 -Nghost: 768.875 ave 788 max 761 min -Histogram: 4 0 2 0 0 0 1 0 0 1 -Neighs: 30542.8 ave 48077 max 10011 min -Histogram: 1 1 1 0 1 1 0 0 0 3 - -Total # of neighbors = 244342 -Ave neighs/atom = 244.342 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 deleted file mode 100644 index bd7e7fee1f..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.2 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 1 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 6.48 | 6.861 | 7.243 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777511 0 272.51603 0.17462194 - 5 286.36221 -4.3820531 0 424.73172 0.26918925 - 6 481.42203 -4.3095567 0 717.10136 0.45274086 - 7 488.59165 -3.8685193 0 728.28607 0.45956865 - 8 497.85288 -3.0417938 0 742.99075 0.46838117 - 9 499.61619 -3.4190063 0 745.25585 0.46983349 - 10 502.63691 -2.8360951 0 750.36531 0.47280815 - 11 504.4847 -2.7628089 0 753.20751 0.47462802 - 12 506.54494 -2.8460319 0 756.21157 0.4765145 - 13 508.2722 -2.7309328 0 758.91497 0.47813761 - 14 510.57053 -2.6094792 0 762.48045 0.48031438 - 15 513.14804 -2.7150819 0 766.23726 0.48275234 - 16 515.78127 -2.3961749 0 770.50206 0.48526336 - 17 515.70267 -2.2982581 0 770.48219 0.48526619 - 18 515.70813 -2.1516075 0 770.63702 0.48530395 - 19 515.74908 -2.0581483 0 770.79185 0.48530979 - 20 515.70881 -1.892235 0 770.89742 0.48527104 -Loop time of 0.701267 on 2 procs for 20 steps with 1000 atoms - -Performance: 12320.557 tau/day, 28.520 timesteps/s -99.6% CPU use with 2 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0002265 | 0.00022769 | 0.00022888 | 0.0 | 0.03 -Kspace | 0.60195 | 0.62374 | 0.64554 | 2.8 | 88.95 -Neigh | 0.05268 | 0.074592 | 0.096504 | 8.0 | 10.64 -Comm | 0.0015199 | 0.0016934 | 0.0018668 | 0.4 | 0.24 -Output | 0.00031519 | 0.00041544 | 0.0005157 | 0.0 | 0.06 -Modify | 0.00029492 | 0.00030565 | 0.00031638 | 0.0 | 0.04 -Other | | 0.000288 | | | 0.04 - -Nlocal: 500 ave 516 max 484 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 456.5 ave 475 max 438 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 123908 ave 172139 max 75678 min -Histogram: 1 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 deleted file mode 100644 index 8a7e591f9a..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.4 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777511 0 272.51603 0.17462194 - 5 286.36221 -4.3820531 0 424.73172 0.26918925 - 6 481.42203 -4.3095567 0 717.10136 0.45274086 - 7 488.59165 -3.8685193 0 728.28607 0.45956865 - 8 497.85288 -3.0417938 0 742.99075 0.46838117 - 9 499.61619 -3.4190063 0 745.25585 0.46983349 - 10 502.63691 -2.8360951 0 750.36531 0.47280815 - 11 504.4847 -2.7628089 0 753.20751 0.47462802 - 12 506.54494 -2.8460319 0 756.21157 0.4765145 - 13 508.2722 -2.7309328 0 758.91497 0.47813761 - 14 510.57053 -2.6094792 0 762.48045 0.48031438 - 15 513.14804 -2.7150819 0 766.23726 0.48275234 - 16 515.78127 -2.3961749 0 770.50206 0.48526336 - 17 515.70267 -2.2982581 0 770.48219 0.48526619 - 18 515.70813 -2.1516075 0 770.63702 0.48530395 - 19 515.74908 -2.0581483 0 770.79185 0.48530979 - 20 515.70881 -1.892235 0 770.89742 0.48527104 -Loop time of 0.427495 on 4 procs for 20 steps with 1000 atoms - -Performance: 20210.785 tau/day, 46.784 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0002327 | 0.00023341 | 0.00023437 | 0.0 | 0.05 -Kspace | 0.36897 | 0.38411 | 0.39988 | 1.9 | 89.85 -Neigh | 0.023831 | 0.039796 | 0.055124 | 6.1 | 9.31 -Comm | 0.0022776 | 0.0025444 | 0.0028152 | 0.4 | 0.60 -Output | 0.00033784 | 0.0004344 | 0.00057077 | 0.0 | 0.10 -Modify | 0.00016117 | 0.00016713 | 0.00017095 | 0.0 | 0.04 -Other | | 0.0002093 | | | 0.05 - -Nlocal: 250 ave 259 max 238 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Nghost: 672.25 ave 683 max 663 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 61954.2 ave 97157 max 25016 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 b/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 deleted file mode 100644 index 13922c09ac..0000000000 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.8 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) - using 1 OpenMP thread(s) per MPI task -# Point dipoles in a 2d box - -units lj -atom_style charge - -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) - 2 by 2 by 2 MPI processor grid - reading atoms ... - 1000 atoms -change_box all boundary f f f - -velocity all create 1.5 49893 - -neighbor 1.0 bin -neigh_modify delay 0 - -fix 1 all nve - -# LAMMPS computes pairwise and long-range Coulombics - -#pair_style coul/long 3.0 -#pair_coeff * * -#kspace_style pppm 1.0e-3 - -# Scafacos computes entire long-range Coulombics -# use dummy pair style to perform atom sorting - -pair_style zero 1.0 -pair_coeff * * - -#fix 2 all scafacos p3m tolerance field 0.001 - -kspace_style scafacos p2nfft 0.001 -kspace_modify scafacos tolerance potential - -timestep 0.005 -thermo 1 - -run 20 -Setting up ScaFaCoS with solver p2nfft ... -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2 - ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair zero, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.164 | 4.26 | 4.546 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777511 0 272.51603 0.17462194 - 5 286.36221 -4.3820531 0 424.73172 0.26918925 - 6 481.42203 -4.3095567 0 717.10136 0.45274086 - 7 488.59165 -3.8685193 0 728.28607 0.45956865 - 8 497.85288 -3.0417938 0 742.99075 0.46838117 - 9 499.61619 -3.4190063 0 745.25585 0.46983349 - 10 502.63691 -2.8360951 0 750.36531 0.47280815 - 11 504.4847 -2.7628089 0 753.20751 0.47462802 - 12 506.54494 -2.8460319 0 756.21157 0.4765145 - 13 508.2722 -2.7309328 0 758.91497 0.47813761 - 14 510.57053 -2.6094792 0 762.48045 0.48031438 - 15 513.14804 -2.7150819 0 766.23726 0.48275234 - 16 515.78127 -2.3961749 0 770.50206 0.48526336 - 17 515.70267 -2.2982581 0 770.48219 0.48526619 - 18 515.70813 -2.1516075 0 770.63702 0.48530395 - 19 515.74908 -2.0581483 0 770.79185 0.48530979 - 20 515.70881 -1.892235 0 770.89742 0.48527104 -Loop time of 0.242145 on 8 procs for 20 steps with 1000 atoms - -Performance: 35681.038 tau/day, 82.595 timesteps/s -99.2% CPU use with 8 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0002315 | 0.00023672 | 0.00024652 | 0.0 | 0.10 -Kspace | 0.20915 | 0.21666 | 0.22564 | 1.3 | 89.48 -Neigh | 0.012218 | 0.021341 | 0.029026 | 4.3 | 8.81 -Comm | 0.0028954 | 0.0031248 | 0.0033553 | 0.3 | 1.29 -Output | 0.00039291 | 0.00049406 | 0.00066066 | 0.0 | 0.20 -Modify | 8.7976e-05 | 9.2953e-05 | 9.7752e-05 | 0.0 | 0.04 -Other | | 0.0001938 | | | 0.08 - -Nlocal: 125 ave 133 max 113 min -Histogram: 2 0 0 0 0 1 1 0 2 2 -Nghost: 773.625 ave 788 max 764 min -Histogram: 1 1 2 1 1 0 0 0 1 1 -Neighs: 30977.1 ave 50690 max 10447 min -Histogram: 1 1 1 0 1 1 0 0 2 1 - -Total # of neighbors = 247817 -Ave neighs/atom = 247.817 -Neighbor list builds = 19 -Dangerous builds = 18 -Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 new file mode 100644 index 0000000000..e0b10de95e --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.1 @@ -0,0 +1,92 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49647271 0 0.49647271 0 0 + 10 300 0.13361073 0.015454603 0.47336798 0.023104631 0.49647261 0 0.0046209262 + 20 300 0.26624846 0.062286838 0.40335451 0.093118823 0.49647334 0 0.018623765 + 30 300 0.39882493 0.14309258 0.2825546 0.21392341 0.49647801 0 0.042784682 + 40 300 0.53216863 0.52823732 0.08958779 0.78971479 0.87930258 0 0.15794296 + 50 300 0.66626191 1.1912156 -0.082808834 1.7808674 1.6980585 0 0.35617347 + 60 300 0.80045819 1.3877079 -0.37658402 2.0746234 1.6980393 0 0.41492467 + 70 300 0.93514919 1.7017671 -0.84569366 2.5441418 1.6984482 0 0.50882837 + 80 300 1.0722892 15.128456 -3.370646 22.617042 19.246396 0 4.5234083 + 90 300 1.2106726 41.994547 -2.2024419 62.781847 60.579406 0 12.556369 + 100 300 1.3514247 41.352114 -0.92449496 61.821411 60.896916 0 12.364282 +Loop time of 1.35144 on 1 procs for 100 steps with 300 atoms + +Performance: 31966.000 tau/day, 73.995 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.718e-05 | 2.718e-05 | 2.718e-05 | 0.0 | 0.00 +Kspace | 1.3486 | 1.3486 | 1.3486 | 0.0 | 99.79 +Neigh | 0.0019956 | 0.0019956 | 0.0019956 | 0.0 | 0.15 +Comm | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.02 +Output | 0.00013924 | 0.00013924 | 0.00013924 | 0.0 | 0.01 +Modify | 0.00023341 | 0.00023341 | 0.00023341 | 0.0 | 0.02 +Other | | 0.000195 | | | 0.01 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 374 ave 374 max 374 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2465 ave 2465 max 2465 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2465 +Ave neighs/atom = 8.21667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 new file mode 100644 index 0000000000..f881ed003a --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.ewald.g++.4 @@ -0,0 +1,92 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos ewald 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver ewald ... +WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49647271 0 0.49647271 0 0 + 10 300 0.04107213 0.015454603 0.47336798 0.023104631 0.49647261 0 0.0046209262 + 20 300 0.083310604 0.062286838 0.40335451 0.093118823 0.49647334 0 0.018623765 + 30 300 0.12387085 0.14309258 0.2825546 0.21392341 0.49647801 0 0.042784682 + 40 300 0.1672492 0.52823732 0.08958779 0.78971479 0.87930258 0 0.15794296 + 50 300 0.21049809 1.1912156 -0.082808834 1.7808674 1.6980585 0 0.35617347 + 60 300 0.25216699 1.3877079 -0.37658402 2.0746234 1.6980393 0 0.41492467 + 70 300 0.29355645 1.7017671 -0.84569366 2.5441418 1.6984482 0 0.50882837 + 80 300 0.33713698 15.128456 -3.370646 22.617042 19.246396 0 4.5234083 + 90 300 0.38109112 41.994547 -2.2024419 62.781847 60.579406 0 12.556369 + 100 300 0.4267664 41.352114 -0.92449496 61.821411 60.896916 0 12.364282 +Loop time of 0.426857 on 4 procs for 100 steps with 300 atoms + +Performance: 101204.784 tau/day, 234.270 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6689e-05 | 1.8835e-05 | 2.2173e-05 | 0.0 | 0.00 +Kspace | 0.42368 | 0.42384 | 0.42405 | 0.0 | 99.29 +Neigh | 0.00040579 | 0.00056726 | 0.00075126 | 0.0 | 0.13 +Comm | 0.0010395 | 0.0010909 | 0.001189 | 0.2 | 0.26 +Output | 0.00015545 | 0.00034326 | 0.00090313 | 0.0 | 0.08 +Modify | 9.8705e-05 | 0.00010544 | 0.00011539 | 0.0 | 0.02 +Other | | 0.0008868 | | | 0.21 + +Nlocal: 75 ave 81 max 70 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 282.5 ave 290 max 274 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 616.25 ave 983 max 283 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2465 +Ave neighs/atom = 8.21667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 similarity index 51% rename from examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 index 714ce85a5f..da0c698187 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units lj atom_style charge @@ -59,41 +58,41 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 - 10 300 0.063865185 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823 - 20 300 0.12760854 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642 - 30 300 0.19143319 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548 - 40 300 0.25553131 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903 - 50 300 0.31961966 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462 - 60 300 0.38388991 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911 - 70 300 0.44797421 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274 - 80 300 0.50961447 15.358343 -3.368063 22.960722 19.592659 0 4.4798757 - 90 300 0.57181501 42.280432 -2.1623864 63.209247 61.04686 0 12.56977 - 100 300 0.63501096 41.48079 -0.89904529 62.013782 61.114736 0 12.372788 -Loop time of 0.635022 on 1 procs for 100 steps with 300 atoms + 10 300 0.025602102 0.015455672 0.47336221 0.023106229 0.49646844 0 0.020399986 + 20 300 0.051156282 0.062291145 0.40334518 0.093125262 0.49647044 0 0.032069892 + 30 300 0.076699495 0.14310262 0.28254543 0.21393842 0.49648385 0 0.052205865 + 40 300 0.10232902 0.52932294 0.089676201 0.79133779 0.88101399 0 0.16125676 + 50 300 0.12800455 1.1962334 -0.082794531 1.788369 1.7055744 0 0.35491397 + 60 300 0.1537931 1.3927481 -0.37659486 2.0821585 1.7055636 0 0.40387853 + 70 300 0.17947531 1.7068337 -0.84572368 2.5517165 1.7059928 0 0.4821525 + 80 300 0.20517826 15.509932 -3.369527 23.187348 19.817821 0 4.5251521 + 90 300 0.23049045 42.26862 -2.0785273 63.191586 61.113059 0 12.569033 + 100 300 0.25625205 41.459415 -0.88546313 61.981825 61.096362 0 12.36685 +Loop time of 0.256263 on 1 procs for 100 steps with 300 atoms -Performance: 68029.122 tau/day, 157.475 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 168576.488 tau/day, 390.223 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.01 -Kspace | 0.62877 | 0.62877 | 0.62877 | 0.0 | 99.01 -Neigh | 0.0035319 | 0.0035319 | 0.0035319 | 0.0 | 0.56 -Comm | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 0.16 -Output | 0.00014758 | 0.00014758 | 0.00014758 | 0.0 | 0.02 -Modify | 0.0010428 | 0.0010428 | 0.0010428 | 0.0 | 0.16 -Other | | 0.0004218 | | | 0.07 +Pair | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.01 +Kspace | 0.25335 | 0.25335 | 0.25335 | 0.0 | 98.86 +Neigh | 0.0020251 | 0.0020251 | 0.0020251 | 0.0 | 0.79 +Comm | 0.00027776 | 0.00027776 | 0.00027776 | 0.0 | 0.11 +Output | 0.00014305 | 0.00014305 | 0.00014305 | 0.0 | 0.06 +Modify | 0.0002346 | 0.0002346 | 0.0002346 | 0.0 | 0.09 +Other | | 0.0002046 | | | 0.08 Nlocal: 300 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 374 ave 374 max 374 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2459 ave 2459 max 2459 min +Neighs: 2461 ave 2461 max 2461 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2459 -Ave neighs/atom = 8.19667 +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 Neighbor list builds = 15 Dangerous builds = 0 Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 new file mode 100644 index 0000000000..30fa988863 --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.fmm.g++.4 @@ -0,0 +1,98 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +kspace_style scafacos fmm 1.0e-3 +kspace_modify scafacos tolerance energy_rel +kspace_modify scafacos fmm_tuning 1 +ScaFaCoS setting fmm inhomogen tuning ... + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver fmm ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49646402 0 0.49646402 0 0.016548801 + 10 300 0.01548481 0.015455672 0.47336221 0.023106229 0.49646844 0 0.020399986 + 20 300 0.031042576 0.062291145 0.40334518 0.093125262 0.49647044 0 0.032069892 + 30 300 0.044115782 0.14310262 0.28254543 0.21393842 0.49648385 0 0.052205865 + 40 300 0.059348583 0.52932294 0.089676201 0.79133779 0.88101399 0 0.16125676 + 50 300 0.071757555 1.1962334 -0.082794531 1.788369 1.7055744 0 0.35491397 + 60 300 0.088143587 1.3927481 -0.37659486 2.0821585 1.7055636 0 0.40387853 + 70 300 0.099860907 1.7068337 -0.84572368 2.5517165 1.7059928 0 0.4821525 + 80 300 0.11159992 15.509932 -3.369527 23.187348 19.817821 0 4.5251521 + 90 300 0.12841201 42.26862 -2.0785273 63.191586 61.113059 0 12.569033 + 100 300 0.14122367 41.459415 -0.88546313 61.981825 61.096362 0 12.36685 +Loop time of 0.141343 on 4 procs for 100 steps with 300 atoms + +Performance: 305639.349 tau/day, 707.498 timesteps/s +94.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5988e-05 | 2.9087e-05 | 3.2663e-05 | 0.0 | 0.02 +Kspace | 0.13587 | 0.13743 | 0.13808 | 0.2 | 97.23 +Neigh | 0.00041199 | 0.00057679 | 0.00076771 | 0.0 | 0.41 +Comm | 0.001039 | 0.0015332 | 0.0029936 | 2.2 | 1.08 +Output | 0.00017786 | 0.00044322 | 0.0012352 | 0.0 | 0.31 +Modify | 0.00017333 | 0.00018805 | 0.00020623 | 0.0 | 0.13 +Other | | 0.001146 | | | 0.81 + +Nlocal: 75 ave 80 max 71 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 282.5 ave 290 max 275 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 615.25 ave 970 max 292 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2461 +Ave neighs/atom = 8.20333 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 similarity index 64% rename from examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 index f47f24edee..10c2fa166b 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units lj @@ -52,31 +51,31 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 - 10 300 0.071435928 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 - 20 300 0.14302707 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 - 30 300 0.21480989 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 - 40 300 0.28638172 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 - 50 300 0.35810781 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 - 60 300 0.42993116 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 - 70 300 0.50181961 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 - 80 300 0.57404566 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 - 90 300 0.64724708 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 - 100 300 0.72128963 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 -Loop time of 0.721302 on 1 procs for 100 steps with 300 atoms + 10 300 0.028267145 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.056742668 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.085426331 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.11415625 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.14363861 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.17313194 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.20299363 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.23256087 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.26286936 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.29372239 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.293738 on 1 procs for 100 steps with 300 atoms -Performance: 59891.733 tau/day, 138.638 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 147070.013 tau/day, 340.440 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.893e-05 | 8.893e-05 | 8.893e-05 | 0.0 | 0.01 -Kspace | 0.71502 | 0.71502 | 0.71502 | 0.0 | 99.13 -Neigh | 0.0035415 | 0.0035415 | 0.0035415 | 0.0 | 0.49 -Comm | 0.001024 | 0.001024 | 0.001024 | 0.0 | 0.14 -Output | 0.00015044 | 0.00015044 | 0.00015044 | 0.0 | 0.02 -Modify | 0.0010409 | 0.0010409 | 0.0010409 | 0.0 | 0.14 -Other | | 0.0004385 | | | 0.06 +Pair | 4.3869e-05 | 4.3869e-05 | 4.3869e-05 | 0.0 | 0.01 +Kspace | 0.29081 | 0.29081 | 0.29081 | 0.0 | 99.00 +Neigh | 0.0019989 | 0.0019989 | 0.0019989 | 0.0 | 0.68 +Comm | 0.0003159 | 0.0003159 | 0.0003159 | 0.0 | 0.11 +Output | 0.00016809 | 0.00016809 | 0.00016809 | 0.0 | 0.06 +Modify | 0.00021863 | 0.00021863 | 0.00021863 | 0.0 | 0.07 +Other | | 0.0001831 | | | 0.06 Nlocal: 300 ave 300 max 300 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 similarity index 64% rename from examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 rename to examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 index d5a07e0324..aa828ed159 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.4 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p2nfft.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units lj @@ -52,31 +51,31 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press 0 300 0 0 0.49683273 0 0.49683273 0 0.016561091 - 10 300 0.02743125 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 - 20 300 0.05494833 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 - 30 300 0.082517862 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 - 40 300 0.11015558 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 - 50 300 0.13790298 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 - 60 300 0.1660006 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 - 70 300 0.1937964 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 - 80 300 0.22181106 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 - 90 300 0.25105524 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 - 100 300 0.28086019 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 -Loop time of 0.280875 on 4 procs for 100 steps with 300 atoms + 10 300 0.013789177 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984 + 20 300 0.025422812 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581 + 30 300 0.039611578 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382 + 40 300 0.051841736 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862 + 50 300 0.07456398 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982 + 60 300 0.087505341 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499 + 70 300 0.10280418 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445 + 80 300 0.1173315 20.692093 -3.32971 30.93468 27.60497 0 6.0759456 + 90 300 0.13260174 48.999403 -2.1632167 73.254107 71.090891 0 14.578714 + 100 300 0.14577007 51.199785 -0.81127924 76.543678 75.732399 0 15.281693 +Loop time of 0.145873 on 4 procs for 100 steps with 300 atoms -Performance: 153805.254 tau/day, 356.031 timesteps/s -99.7% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 296148.120 tau/day, 685.528 timesteps/s +92.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.6744e-05 | 6.0022e-05 | 6.4135e-05 | 0.0 | 0.02 -Kspace | 0.27651 | 0.27682 | 0.27714 | 0.0 | 98.56 -Neigh | 0.00079465 | 0.001082 | 0.0014107 | 0.8 | 0.39 -Comm | 0.0019372 | 0.002014 | 0.0020835 | 0.1 | 0.72 -Output | 0.00018406 | 0.00019914 | 0.00023413 | 0.0 | 0.07 -Modify | 0.0002749 | 0.00028563 | 0.00029325 | 0.0 | 0.10 -Other | | 0.0004173 | | | 0.15 +Pair | 2.3842e-05 | 2.5034e-05 | 2.7657e-05 | 0.0 | 0.02 +Kspace | 0.14221 | 0.14239 | 0.14264 | 0.0 | 97.61 +Neigh | 0.00041676 | 0.0005784 | 0.00076866 | 0.0 | 0.40 +Comm | 0.0013564 | 0.0014941 | 0.0016375 | 0.3 | 1.02 +Output | 0.00017166 | 0.00033867 | 0.00083518 | 0.0 | 0.23 +Modify | 0.00012016 | 0.00012261 | 0.0001266 | 0.0 | 0.08 +Other | | 0.0009243 | | | 0.63 Nlocal: 75 ave 81 max 69 min Histogram: 1 0 0 0 1 1 0 0 0 1 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 new file mode 100644 index 0000000000..9410529284 --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.1 @@ -0,0 +1,92 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p3m ... +WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.34 | 3.34 | 3.34 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49619864 0 0.49619864 0 0 + 10 300 0.018853664 0.015458704 0.47310664 0.023110763 0.4962174 0 0.0046221526 + 20 300 0.037713289 0.062303961 0.40312435 0.093144421 0.49626877 0 0.018628884 + 30 300 0.055995226 0.14313464 0.28239193 0.21398628 0.49637821 0 0.042797257 + 40 300 0.074442625 0.53306643 0.089950137 0.79693431 0.88688444 0 0.15938686 + 50 300 0.093066454 1.1925037 -0.08272797 1.7827931 1.7000651 0 0.35655861 + 60 300 0.11158967 1.3890617 -0.37645444 2.0766472 1.7001927 0 0.41532944 + 70 300 0.1300416 1.7033725 -0.84587122 2.5465418 1.7006706 0 0.50930837 + 80 300 0.14844203 15.906218 -3.3586154 23.779796 20.421181 0 4.7559592 + 90 300 0.1676445 42.749883 -2.2769116 63.911076 61.634164 0 12.782215 + 100 300 0.1866703 42.25523 -0.84978755 63.171569 62.321782 0 12.634314 +Loop time of 0.186683 on 1 procs for 100 steps with 300 atoms + +Performance: 231408.103 tau/day, 535.667 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7657e-05 | 2.7657e-05 | 2.7657e-05 | 0.0 | 0.01 +Kspace | 0.18368 | 0.18368 | 0.18368 | 0.0 | 98.39 +Neigh | 0.0020967 | 0.0020967 | 0.0020967 | 0.0 | 1.12 +Comm | 0.00027132 | 0.00027132 | 0.00027132 | 0.0 | 0.15 +Output | 0.00013709 | 0.00013709 | 0.00013709 | 0.0 | 0.07 +Modify | 0.0002718 | 0.0002718 | 0.0002718 | 0.0 | 0.15 +Other | | 0.0001974 | | | 0.11 + +Nlocal: 300 ave 300 max 300 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 374 ave 374 max 374 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2478 ave 2478 max 2478 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2478 +Ave neighs/atom = 8.26 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 new file mode 100644 index 0000000000..2dc5c07b2b --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.cw.p3m.g++.4 @@ -0,0 +1,92 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style charge + +read_data data.cloud_wall + orthogonal box = (0 0 0) to (10 10 10) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 300 atoms + +velocity all set 0.0 0.0 0.0 mom no + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 + +thermo_style custom step atoms cpu temp pe ke etotal ecoul press + +run_style verlet + +#dump simple all custom 1000 id x y z vx vy vz +#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass +#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass +#dump_modify dmpvtk pad 7 + +thermo 10 +run 100 +Setting up ScaFaCoS with solver p3m ... +WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.333 | 3.333 | 3.333 Mbytes +Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press + 0 300 0 0 0.49601855 0 0.49601855 0 0 + 10 300 0.0080001354 0.015443077 0.47292202 0.0230874 0.49600942 0 0.00461748 + 20 300 0.018443823 0.062241297 0.40294626 0.093050739 0.495997 0 0.018610148 + 30 300 0.029161692 0.14299426 0.28226416 0.21377642 0.49604058 0 0.042755283 + 40 300 0.037320137 0.53371718 0.089969593 0.79790718 0.88787677 0 0.15958144 + 50 300 0.045557499 1.195874 -0.082570725 1.7878316 1.7052608 0 0.35756631 + 60 300 0.054044962 1.3923357 -0.37594466 2.0815419 1.7055972 0 0.41630838 + 70 300 0.064656734 1.7063617 -0.84481819 2.5510108 1.7061926 0 0.51020216 + 80 300 0.073246241 13.884845 -3.3804644 20.757843 17.377379 0 4.1515687 + 90 300 0.081598997 40.561354 -2.1801816 60.639224 58.459042 0 12.127845 + 100 300 0.092384577 39.972453 -0.95590215 59.758818 58.802916 0 11.951764 +Loop time of 0.0924569 on 4 procs for 100 steps with 300 atoms + +Performance: 467244.853 tau/day, 1081.585 timesteps/s +96.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.812e-05 | 1.955e-05 | 2.1935e-05 | 0.0 | 0.02 +Kspace | 0.087202 | 0.087385 | 0.087595 | 0.1 | 94.51 +Neigh | 0.00039053 | 0.00056016 | 0.00074887 | 0.0 | 0.61 +Comm | 0.00095391 | 0.001252 | 0.001538 | 0.6 | 1.35 +Output | 0.00015235 | 0.00026172 | 0.00058818 | 0.0 | 0.28 +Modify | 9.7275e-05 | 0.00010461 | 0.00011683 | 0.0 | 0.11 +Other | | 0.002874 | | | 3.11 + +Nlocal: 75 ave 81 max 70 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 284 ave 290 max 277 min +Histogram: 1 0 0 1 0 0 0 1 0 1 +Neighs: 619.25 ave 986 max 285 min +Histogram: 1 1 0 0 0 0 0 1 0 1 + +Total # of neighbors = 2477 +Ave neighs/atom = 8.25667 +Neighbor list builds = 15 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 b/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 similarity index 79% rename from examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 index 13212ede0c..e6cd7c506f 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box @@ -16,7 +15,7 @@ replicate 8 8 8 orthogonal box = (0 0 0) to (8 8 8) 1 by 1 by 1 MPI processor grid 4096 atoms - Time spent = 0.000498772 secs + Time spent = 0.000287294 secs velocity all create 1.5 49893 @@ -47,6 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... +WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -72,21 +72,21 @@ Step Temp E_pair E_mol TotEng Press 80 1.5033218 -1.7524875 0 0.50194458 12.023638 90 1.5108306 -1.7637462 0 0.50194636 12.083694 100 1.5292479 -1.7913449 0 0.50196695 12.230996 -Loop time of 1121.22 on 1 procs for 100 steps with 4096 atoms +Loop time of 427.03 on 1 procs for 100 steps with 4096 atoms -Performance: 38.530 tau/day, 0.089 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 101.164 tau/day, 0.234 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0015197 | 0.0015197 | 0.0015197 | 0.0 | 0.00 -Kspace | 1121.2 | 1121.2 | 1121.2 | 0.0 |100.00 +Pair | 0.0003655 | 0.0003655 | 0.0003655 | 0.0 | 0.00 +Kspace | 427.02 | 427.02 | 427.02 | 0.0 |100.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013699 | 0.013699 | 0.013699 | 0.0 | 0.00 -Output | 0.00038314 | 0.00038314 | 0.00038314 | 0.0 | 0.00 -Modify | 0.011126 | 0.011126 | 0.011126 | 0.0 | 0.00 -Other | | 0.00418 | | | 0.00 +Comm | 0.0047293 | 0.0047293 | 0.0047293 | 0.0 | 0.00 +Output | 0.00025916 | 0.00025916 | 0.00025916 | 0.0 | 0.00 +Modify | 0.0029993 | 0.0029993 | 0.0029993 | 0.0 | 0.00 +Other | | 0.00181 | | | 0.00 Nlocal: 4096 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -99,4 +99,4 @@ Total # of neighbors = 524288 Ave neighs/atom = 128 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:18:57 +Total wall time: 0:07:10 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 b/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 similarity index 76% rename from examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 rename to examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 index 26c1953afa..39e0387491 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.ewald.4 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.ewald.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box @@ -16,7 +15,7 @@ replicate 8 8 8 orthogonal box = (0 0 0) to (8 8 8) 1 by 2 by 2 MPI processor grid 4096 atoms - Time spent = 0.000261068 secs + Time spent = 0.000125408 secs velocity all create 1.5 49893 @@ -47,6 +46,7 @@ thermo 10 run 100 Setting up ScaFaCoS with solver ewald ... +WARNING: Virial computation for Ewald not available (src/USER-SCAFACOS/scafacos.cpp:107) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -61,32 +61,32 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes Step Temp E_pair E_mol TotEng Press - 0 1.5 -1.7475938 0 0.50185691 -nan - 10 1.500011 -1.747529 0 0.50193816 -nan - 20 1.5000023 -1.7475152 0 0.50193898 -nan - 30 1.4999308 -1.747404 0 0.50194285 -nan - 40 1.4997722 -1.7471622 0 0.50194686 -nan - 50 1.4995835 -1.746878 0 0.50194808 -nan - 60 1.4996054 -1.7469114 0 0.50194749 -nan - 70 1.5004341 -1.7481558 0 0.50194592 -nan - 80 1.5033218 -1.7524875 0 0.50194458 -nan - 90 1.5108306 -1.7637462 0 0.50194636 -nan - 100 1.5292479 -1.7913449 0 0.50196695 -nan -Loop time of 295.996 on 4 procs for 100 steps with 4096 atoms + 0 1.5 -1.7475938 0 0.50185691 11.99707 + 10 1.500011 -1.747529 0 0.50193816 11.997158 + 20 1.5000023 -1.7475152 0 0.50193898 11.997089 + 30 1.4999308 -1.747404 0 0.50194285 11.996517 + 40 1.4997722 -1.7471622 0 0.50194686 11.995248 + 50 1.4995835 -1.746878 0 0.50194808 11.993739 + 60 1.4996054 -1.7469114 0 0.50194749 11.993914 + 70 1.5004341 -1.7481558 0 0.50194592 12.000543 + 80 1.5033218 -1.7524875 0 0.50194458 12.023638 + 90 1.5108306 -1.7637462 0 0.50194636 12.083694 + 100 1.5292479 -1.7913449 0 0.50196695 12.230996 +Loop time of 113.519 on 4 procs for 100 steps with 4096 atoms -Performance: 145.948 tau/day, 0.338 timesteps/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 380.555 tau/day, 0.881 timesteps/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00071096 | 0.00071985 | 0.00072813 | 0.0 | 0.00 -Kspace | 295.98 | 295.98 | 295.98 | 0.0 | 99.99 +Pair | 0.00022793 | 0.00023127 | 0.00023508 | 0.0 | 0.00 +Kspace | 113.51 | 113.51 | 113.51 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013666 | 0.013736 | 0.013795 | 0.0 | 0.00 -Output | 0.00023484 | 0.00025135 | 0.00029254 | 0.0 | 0.00 -Modify | 0.0029099 | 0.002973 | 0.0030224 | 0.1 | 0.00 -Other | | 0.001821 | | | 0.00 +Comm | 0.0084581 | 0.0085486 | 0.0086188 | 0.1 | 0.01 +Output | 0.00019598 | 0.00046694 | 0.0012727 | 0.0 | 0.00 +Modify | 0.0016849 | 0.0017331 | 0.0017881 | 0.1 | 0.00 +Other | | 0.002307 | | | 0.00 Nlocal: 1024 ave 1024 max 1024 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -99,4 +99,4 @@ Total # of neighbors = 524288 Ave neighs/atom = 128 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:05:02 +Total wall time: 0:01:54 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 b/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 similarity index 79% rename from examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 index 598585ae95..b9ae654659 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box @@ -16,7 +15,7 @@ replicate 8 8 8 orthogonal box = (0 0 0) to (8 8 8) 1 by 1 by 1 MPI processor grid 4096 atoms - Time spent = 0.000518799 secs + Time spent = 0.000326395 secs velocity all create 1.5 49893 @@ -72,21 +71,21 @@ Step Temp E_pair E_mol TotEng Press 80 1.5032684 -1.7524625 0 0.50188958 10.465466 90 1.5107749 -1.763714 0 0.50189507 10.515502 100 1.52919 -1.791306 0 0.50191895 10.638261 -Loop time of 34.7058 on 1 procs for 100 steps with 4096 atoms +Loop time of 9.55733 on 1 procs for 100 steps with 4096 atoms -Performance: 1244.749 tau/day, 2.881 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 4520.093 tau/day, 10.463 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0015228 | 0.0015228 | 0.0015228 | 0.0 | 0.00 -Kspace | 34.675 | 34.675 | 34.675 | 0.0 | 99.91 +Pair | 0.0003767 | 0.0003767 | 0.0003767 | 0.0 | 0.00 +Kspace | 9.5472 | 9.5472 | 9.5472 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013741 | 0.013741 | 0.013741 | 0.0 | 0.04 -Output | 0.00041246 | 0.00041246 | 0.00041246 | 0.0 | 0.00 -Modify | 0.01107 | 0.01107 | 0.01107 | 0.0 | 0.03 -Other | | 0.004232 | | | 0.01 +Comm | 0.0047688 | 0.0047688 | 0.0047688 | 0.0 | 0.05 +Output | 0.00027132 | 0.00027132 | 0.00027132 | 0.0 | 0.00 +Modify | 0.0029824 | 0.0029824 | 0.0029824 | 0.0 | 0.03 +Other | | 0.001692 | | | 0.02 Nlocal: 4096 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -99,4 +98,4 @@ Total # of neighbors = 524288 Ave neighs/atom = 128 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:35 +Total wall time: 0:00:10 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 b/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 similarity index 79% rename from examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 rename to examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 index 27fdfcedcb..7ee8d3d068 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.fmm.4 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.fmm.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box @@ -16,7 +15,7 @@ replicate 8 8 8 orthogonal box = (0 0 0) to (8 8 8) 1 by 2 by 2 MPI processor grid 4096 atoms - Time spent = 0.000270367 secs + Time spent = 0.00015521 secs velocity all create 1.5 49893 @@ -72,21 +71,21 @@ Step Temp E_pair E_mol TotEng Press 80 1.5032684 -1.7524625 0 0.50188958 10.465466 90 1.5107749 -1.763714 0 0.50189507 10.515502 100 1.52919 -1.791306 0 0.50191895 10.638261 -Loop time of 10.0781 on 4 procs for 100 steps with 4096 atoms +Loop time of 3.05974 on 4 procs for 100 steps with 4096 atoms -Performance: 4286.533 tau/day, 9.923 timesteps/s -99.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 14118.863 tau/day, 32.683 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00071096 | 0.00073177 | 0.00075269 | 0.0 | 0.01 -Kspace | 10.056 | 10.057 | 10.057 | 0.0 | 99.79 +Pair | 0.00021482 | 0.0002175 | 0.00022054 | 0.0 | 0.01 +Kspace | 3.0468 | 3.0468 | 3.0468 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.01492 | 0.015036 | 0.015207 | 0.1 | 0.15 -Output | 0.00036311 | 0.00039428 | 0.00046515 | 0.0 | 0.00 -Modify | 0.002944 | 0.0030704 | 0.0033708 | 0.3 | 0.03 -Other | | 0.002214 | | | 0.02 +Comm | 0.0081758 | 0.0082486 | 0.0083146 | 0.1 | 0.27 +Output | 0.00019073 | 0.00049388 | 0.0013943 | 0.0 | 0.02 +Modify | 0.001507 | 0.0015851 | 0.0017498 | 0.2 | 0.05 +Other | | 0.002385 | | | 0.08 Nlocal: 1024 ave 1024 max 1024 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -99,4 +98,4 @@ Total # of neighbors = 524288 Ave neighs/atom = 128 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:04 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 b/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 new file mode 100644 index 0000000000..6b36f0ba91 --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.g++.1 @@ -0,0 +1,102 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000253677 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +#kspace_style scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p3m ... +WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475752 0 0.5018755 11.99707 + 10 1.5000018 -1.7475779 0 0.50187548 11.997085 + 20 1.4999833 -1.7475525 0 0.5018731 11.996936 + 30 1.4999006 -1.7474414 0 0.5018603 11.996276 + 40 1.49973 -1.7471989 0 0.50184695 11.994911 + 50 1.4995292 -1.7469064 0 0.50183822 11.993305 + 60 1.49954 -1.7469273 0 0.50183355 11.993391 + 70 1.5003599 -1.7481583 0 0.50183215 11.999949 + 80 1.5032409 -1.752478 0 0.50183276 12.022991 + 90 1.5107445 -1.7637257 0 0.50183781 12.083005 + 100 1.5291568 -1.7913136 0 0.50186158 12.230268 +Loop time of 2.98552 on 1 procs for 100 steps with 4096 atoms + +Performance: 14469.821 tau/day, 33.495 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0003686 | 0.0003686 | 0.0003686 | 0.0 | 0.01 +Kspace | 2.9749 | 2.9749 | 2.9749 | 0.0 | 99.65 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0049963 | 0.0049963 | 0.0049963 | 0.0 | 0.17 +Output | 0.00027728 | 0.00027728 | 0.00027728 | 0.0 | 0.01 +Modify | 0.0031269 | 0.0031269 | 0.0031269 | 0.0 | 0.10 +Other | | 0.001828 | | | 0.06 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 b/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 new file mode 100644 index 0000000000..23f55fc5a6 --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.g++.4 @@ -0,0 +1,102 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.00012064 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +#kspace_style scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p3m ... +WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475814 0 0.50186926 11.99707 + 10 1.5000019 -1.7475841 0 0.50186935 11.997085 + 20 1.4999837 -1.747556 0 0.50187017 11.99694 + 30 1.4999022 -1.7474323 0 0.50187181 11.996288 + 40 1.4997327 -1.7471824 0 0.50186744 11.994932 + 50 1.4995318 -1.7468908 0 0.50185778 11.993326 + 60 1.499542 -1.7469166 0 0.5018472 11.993407 + 70 1.5003608 -1.7481509 0 0.50184084 11.999956 + 80 1.5032406 -1.7524717 0 0.5018387 12.022989 + 90 1.5107432 -1.7637208 0 0.5018408 12.082995 + 100 1.5291549 -1.7913103 0 0.50186206 12.230252 +Loop time of 1.04979 on 4 procs for 100 steps with 4096 atoms + +Performance: 41150.904 tau/day, 95.257 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00021386 | 0.00022691 | 0.00023532 | 0.0 | 0.02 +Kspace | 1.0351 | 1.0353 | 1.0354 | 0.0 | 98.61 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0092776 | 0.0094286 | 0.0095558 | 0.1 | 0.90 +Output | 0.00019121 | 0.00050998 | 0.0014408 | 0.0 | 0.05 +Modify | 0.0019102 | 0.0019451 | 0.0019991 | 0.1 | 0.19 +Other | | 0.002431 | | | 0.23 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 similarity index 69% rename from examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 index b0a47e4f98..2d3ca0d588 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.1 @@ -1,13 +1,12 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj atom_style charge -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) +read_data data.hammersley_sphere + orthogonal box = (-51.5 -51.5 -51.5) to (51.5 51.5 51.5) 1 by 1 by 1 MPI processor grid reading atoms ... 1000 atoms @@ -45,51 +44,51 @@ Neighbor list info ... max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 + binsize = 1, bins = 103 103 103 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777512 0 272.51604 0.17462195 - 5 286.36222 -4.382053 0 424.73173 0.26918926 - 6 481.42206 -4.3095567 0 717.1014 0.45274088 - 7 488.59167 -3.8685194 0 728.2861 0.45956866 - 8 497.85287 -3.0417966 0 742.99073 0.46838116 - 9 499.61615 -3.419003 0 745.2558 0.46983345 - 10 502.63684 -2.8360961 0 750.36521 0.47280809 - 11 504.4846 -2.7628105 0 753.20736 0.47462793 - 12 506.54485 -2.8460356 0 756.21142 0.47651441 - 13 508.27211 -2.730935 0 758.91482 0.47813752 - 14 510.57045 -2.6094877 0 762.48033 0.48031431 - 15 513.14798 -2.7150827 0 766.23717 0.48275229 - 16 515.78124 -2.3961811 0 770.50201 0.48526333 - 17 515.70265 -2.2982683 0 770.48215 0.48526617 - 18 515.7081 -2.1515983 0 770.63699 0.48530393 - 19 515.74906 -2.0581436 0 770.79182 0.48530977 - 20 515.70883 -1.8922577 0 770.89742 0.48527105 -Loop time of 0.465839 on 1 procs for 20 steps with 1000 atoms + 0 1.5 -0.62417787 0 1.6235721 0.0015226607 + 1 18.780041 -10.770002 0 17.371889 0.01623671 + 2 65.289192 -11.084705 0 86.751149 0.058612772 + 3 121.92987 -7.0625759 0 175.64933 0.11076005 + 4 185.78164 -5.8777512 0 272.51604 0.16958509 + 5 286.36222 -4.382053 0 424.73173 0.26142467 + 6 481.42206 -4.3095567 0 717.1014 0.43968187 + 7 488.59167 -3.8685194 0 728.2861 0.4463127 + 8 497.85287 -3.0417966 0 742.99073 0.45487101 + 9 499.61615 -3.419003 0 745.2558 0.45628141 + 10 502.63684 -2.8360961 0 750.36521 0.45917024 + 11 504.4846 -2.7628105 0 753.20736 0.46093759 + 12 506.54485 -2.8460356 0 756.21142 0.46276966 + 13 508.27211 -2.730935 0 758.91482 0.46434596 + 14 510.57045 -2.6094877 0 762.48033 0.46645996 + 15 513.14798 -2.7150827 0 766.23717 0.46882762 + 16 515.78124 -2.3961811 0 770.50201 0.47126623 + 17 515.70265 -2.2982683 0 770.48215 0.47126898 + 18 515.7081 -2.1515983 0 770.63699 0.47130565 + 19 515.74906 -2.0581436 0 770.79182 0.47131132 + 20 515.70883 -1.8922577 0 770.89742 0.47127372 +Loop time of 0.139386 on 1 procs for 20 steps with 1000 atoms -Performance: 18547.165 tau/day, 42.933 timesteps/s -99.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 61985.954 tau/day, 143.486 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00021982 | 0.00021982 | 0.00021982 | 0.0 | 0.05 -Kspace | 0.3218 | 0.3218 | 0.3218 | 0.0 | 69.08 -Neigh | 0.14249 | 0.14249 | 0.14249 | 0.0 | 30.59 -Comm | 0.00014853 | 0.00014853 | 0.00014853 | 0.0 | 0.03 -Output | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.06 -Modify | 0.00055146 | 0.00055146 | 0.00055146 | 0.0 | 0.12 -Other | | 0.0003715 | | | 0.08 +Pair | 5.4359e-05 | 5.4359e-05 | 5.4359e-05 | 0.0 | 0.04 +Kspace | 0.1018 | 0.1018 | 0.1018 | 0.0 | 73.03 +Neigh | 0.037074 | 0.037074 | 0.037074 | 0.0 | 26.60 +Comm | 4.6492e-05 | 4.6492e-05 | 4.6492e-05 | 0.0 | 0.03 +Output | 0.00016332 | 0.00016332 | 0.00016332 | 0.0 | 0.12 +Modify | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.10 +Other | | 0.0001132 | | | 0.08 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 similarity index 64% rename from examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 rename to examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 index 1235c0a3cd..085958d351 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.direct.4 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.direct.g++.4 @@ -1,13 +1,12 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj atom_style charge -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) +read_data data.hammersley_sphere + orthogonal box = (-51.5 -51.5 -51.5) to (51.5 51.5 51.5) 1 by 2 by 2 MPI processor grid reading atoms ... 1000 atoms @@ -45,58 +44,58 @@ Neighbor list info ... max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 + binsize = 1, bins = 103 103 103 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.882 | 5.463 | 7.161 Mbytes Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777512 0 272.51604 0.17462195 - 5 286.36222 -4.382053 0 424.73173 0.26918926 - 6 481.42206 -4.3095567 0 717.1014 0.45274088 - 7 488.59167 -3.8685194 0 728.2861 0.45956866 - 8 497.85287 -3.0417966 0 742.99073 0.46838116 - 9 499.61615 -3.419003 0 745.2558 0.46983345 - 10 502.63684 -2.8360961 0 750.36521 0.47280809 - 11 504.4846 -2.7628105 0 753.20736 0.47462793 - 12 506.54485 -2.8460356 0 756.21142 0.47651441 - 13 508.27211 -2.730935 0 758.91482 0.47813752 - 14 510.57045 -2.6094877 0 762.48033 0.48031431 - 15 513.14798 -2.7150827 0 766.23717 0.48275229 - 16 515.78124 -2.3961811 0 770.50201 0.48526333 - 17 515.70265 -2.2982683 0 770.48215 0.48526617 - 18 515.7081 -2.1515983 0 770.63699 0.48530393 - 19 515.74906 -2.0581436 0 770.79182 0.48530977 - 20 515.70883 -1.8922577 0 770.89742 0.48527105 -Loop time of 0.161335 on 4 procs for 20 steps with 1000 atoms + 0 1.5 -0.62417787 0 1.6235721 0.0015226607 + 1 18.780041 -10.770002 0 17.371889 0.01623671 + 2 65.289192 -11.084705 0 86.751149 0.058612772 + 3 121.92987 -7.0625759 0 175.64933 0.11076005 + 4 185.78164 -5.8777512 0 272.51604 0.16958509 + 5 286.36222 -4.382053 0 424.73173 0.26142467 + 6 481.42206 -4.3095567 0 717.1014 0.43968187 + 7 488.59167 -3.8685194 0 728.2861 0.4463127 + 8 497.85287 -3.0417966 0 742.99073 0.45487101 + 9 499.61615 -3.419003 0 745.2558 0.45628141 + 10 502.63684 -2.8360961 0 750.36521 0.45917024 + 11 504.4846 -2.7628105 0 753.20736 0.46093759 + 12 506.54485 -2.8460356 0 756.21142 0.46276966 + 13 508.27211 -2.730935 0 758.91482 0.46434596 + 14 510.57045 -2.6094877 0 762.48033 0.46645996 + 15 513.14798 -2.7150827 0 766.23717 0.46882762 + 16 515.78124 -2.3961811 0 770.50201 0.47126623 + 17 515.70265 -2.2982683 0 770.48215 0.47126898 + 18 515.7081 -2.1515983 0 770.63699 0.47130565 + 19 515.74906 -2.0581436 0 770.79182 0.47131132 + 20 515.70883 -1.8922577 0 770.89742 0.47127372 +Loop time of 0.100977 on 4 procs for 20 steps with 1000 atoms -Performance: 53553.228 tau/day, 123.966 timesteps/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 85564.440 tau/day, 198.066 timesteps/s +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00022721 | 0.00023353 | 0.000247 | 0.0 | 0.14 -Kspace | 0.10295 | 0.11808 | 0.13377 | 3.5 | 73.19 -Neigh | 0.023849 | 0.039717 | 0.055031 | 6.1 | 24.62 -Comm | 0.0023148 | 0.0025774 | 0.0028391 | 0.4 | 1.60 -Output | 0.00029063 | 0.00038403 | 0.00050664 | 0.0 | 0.24 -Modify | 0.00015664 | 0.00015944 | 0.00016165 | 0.0 | 0.10 -Other | | 0.0001805 | | | 0.11 +Pair | 5.1975e-05 | 5.3406e-05 | 5.4836e-05 | 0.0 | 0.05 +Kspace | 0.07448 | 0.084484 | 0.08939 | 2.0 | 83.67 +Neigh | 0.006777 | 0.012519 | 0.023358 | 5.7 | 12.40 +Comm | 0.0011938 | 0.0020879 | 0.0029798 | 1.8 | 2.07 +Output | 0.00024247 | 0.00065064 | 0.0016594 | 0.0 | 0.64 +Modify | 1.812e-05 | 5.3406e-05 | 0.00014162 | 0.0 | 0.05 +Other | | 0.001127 | | | 1.12 -Nlocal: 250 ave 259 max 238 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Nghost: 672.25 ave 683 max 663 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 61954.2 ave 97157 max 25016 min -Histogram: 1 0 0 1 0 0 1 0 0 1 +Nlocal: 250 ave 518 max 78 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Nghost: 659 ave 791 max 430 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 61954.2 ave 115962 max 19730 min +Histogram: 1 0 1 0 0 1 0 0 0 1 Total # of neighbors = 247817 Ave neighs/atom = 247.817 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 similarity index 65% rename from examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 index 4bef247e26..94ac525119 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.1 @@ -1,13 +1,12 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj atom_style charge -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) +read_data data.hammersley_sphere + orthogonal box = (-51.5 -51.5 -51.5) to (51.5 51.5 51.5) 1 by 1 by 1 MPI processor grid reading atoms ... 1000 atoms @@ -49,51 +48,51 @@ Neighbor list info ... max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 + binsize = 1, bins = 103 103 103 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.0015676581 - 1 18.780412 -10.770009 0 17.372438 0.016719188 - 2 65.294131 -11.084501 0 86.758754 0.06035827 - 3 121.92555 -7.0612033 0 175.64423 0.1140457 - 4 185.71165 -5.8781334 0 272.41077 0.17455524 - 5 286.28339 -4.3800108 0 424.61565 0.26911306 - 6 481.28097 -4.3052012 0 716.89433 0.45262045 - 7 487.26022 -3.8672741 0 726.29216 0.45830216 - 8 493.65478 -3.0242687 0 736.71742 0.46443761 - 9 495.66203 -3.4336343 0 739.31592 0.46613014 - 10 498.41831 -2.8837072 0 743.99613 0.46887706 - 11 499.20944 -2.7724783 0 745.29287 0.46966875 - 12 500.97345 -2.8281484 0 747.88057 0.47126462 - 13 507.46412 -2.7752775 0 757.65971 0.47728761 - 14 525.35729 -2.5749814 0 784.67292 0.49422171 - 15 563.9578 -2.9982381 0 842.09253 0.53043696 - 16 645.47602 -2.5519203 0 964.69389 0.60730795 - 17 647.09276 -2.2568468 0 967.41166 0.60891914 - 18 647.12596 -2.2791003 0 967.43915 0.60900309 - 19 647.24862 -2.2495226 0 967.65253 0.60908339 - 20 647.51175 -2.0239179 0 968.27244 0.60932598 -Loop time of 0.797289 on 1 procs for 20 steps with 1000 atoms + 0 1.5 -0.62417141 0 1.6235786 0.00152244 + 1 18.780412 -10.770009 0 17.372438 0.016236934 + 2 65.294131 -11.084501 0 86.758754 0.058617275 + 3 121.92555 -7.0612033 0 175.64423 0.11075612 + 4 185.71165 -5.8781334 0 272.41077 0.16952031 + 5 286.28339 -4.3800108 0 424.61565 0.26135067 + 6 481.28097 -4.3052012 0 716.89433 0.43956491 + 7 487.26022 -3.8672741 0 726.29216 0.44508273 + 8 493.65478 -3.0242687 0 736.71742 0.45104121 + 9 495.66203 -3.4336343 0 739.31592 0.45268492 + 10 498.41831 -2.8837072 0 743.99613 0.4553526 + 11 499.20944 -2.7724783 0 745.29287 0.45612146 + 12 500.97345 -2.8281484 0 747.88057 0.4576713 + 13 507.46412 -2.7752775 0 757.65971 0.46352056 + 14 525.35729 -2.5749814 0 784.67292 0.47996621 + 15 563.9578 -2.9982381 0 842.09253 0.51513685 + 16 645.47602 -2.5519203 0 964.69389 0.58979054 + 17 647.09276 -2.2568468 0 967.41166 0.59135526 + 18 647.12596 -2.2791003 0 967.43915 0.59143679 + 19 647.24862 -2.2495226 0 967.65253 0.59151478 + 20 647.51175 -2.0239179 0 968.27244 0.59175037 +Loop time of 0.345449 on 1 procs for 20 steps with 1000 atoms -Performance: 10836.721 tau/day, 25.085 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 25010.947 tau/day, 57.896 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00022364 | 0.00022364 | 0.00022364 | 0.0 | 0.03 -Kspace | 0.6524 | 0.6524 | 0.6524 | 0.0 | 81.83 -Neigh | 0.14312 | 0.14312 | 0.14312 | 0.0 | 17.95 -Comm | 0.00020337 | 0.00020337 | 0.00020337 | 0.0 | 0.03 -Output | 0.00036621 | 0.00036621 | 0.00036621 | 0.0 | 0.05 -Modify | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.07 -Other | | 0.0003934 | | | 0.05 +Pair | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.02 +Kspace | 0.30702 | 0.30702 | 0.30702 | 0.0 | 88.88 +Neigh | 0.037661 | 0.037661 | 0.037661 | 0.0 | 10.90 +Comm | 5.4598e-05 | 5.4598e-05 | 5.4598e-05 | 0.0 | 0.02 +Output | 0.00032878 | 0.00032878 | 0.00032878 | 0.0 | 0.10 +Modify | 0.00016141 | 0.00016141 | 0.00016141 | 0.0 | 0.05 +Other | | 0.0001564 | | | 0.05 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -106,4 +105,4 @@ Total # of neighbors = 244342 Ave neighs/atom = 244.342 Neighbor list builds = 19 Dangerous builds = 18 -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 similarity index 60% rename from examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 rename to examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 index e3f5bf44c9..79137934ab 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.fmm.4 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.fmm.g++.4 @@ -1,13 +1,12 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj atom_style charge -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) +read_data data.hammersley_sphere + orthogonal box = (-51.5 -51.5 -51.5) to (51.5 51.5 51.5) 1 by 2 by 2 MPI processor grid reading atoms ... 1000 atoms @@ -49,58 +48,58 @@ Neighbor list info ... max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 + binsize = 1, bins = 103 103 103 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.837 | 5.123 | 5.6 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.882 | 5.463 | 7.161 Mbytes Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417141 0 1.6235786 0.0015676581 - 1 18.780412 -10.770009 0 17.372438 0.016719188 - 2 65.294131 -11.084501 0 86.758754 0.06035827 - 3 121.92555 -7.0612033 0 175.64423 0.1140457 - 4 185.71165 -5.8781334 0 272.41077 0.17455524 - 5 286.28339 -4.3800108 0 424.61565 0.26911306 - 6 481.28097 -4.3052012 0 716.89433 0.45262045 - 7 487.26022 -3.8672741 0 726.29216 0.45830216 - 8 493.65478 -3.0242687 0 736.71742 0.46443761 - 9 495.66203 -3.4336343 0 739.31592 0.46613014 - 10 498.41831 -2.8837072 0 743.99613 0.46887706 - 11 499.20944 -2.7724783 0 745.29287 0.46966875 - 12 500.97345 -2.8281484 0 747.88057 0.47126462 - 13 507.46412 -2.7752775 0 757.65971 0.47728761 - 14 525.35729 -2.5749814 0 784.67292 0.49422171 - 15 563.9578 -2.9982381 0 842.09253 0.53043696 - 16 645.47602 -2.5519203 0 964.69389 0.60730795 - 17 647.09276 -2.2568468 0 967.41166 0.60891914 - 18 647.12596 -2.2791003 0 967.43915 0.60900309 - 19 647.24862 -2.2495226 0 967.65253 0.60908339 - 20 647.51175 -2.0239179 0 968.27244 0.60932598 -Loop time of 0.666895 on 4 procs for 20 steps with 1000 atoms + 0 1.5 -0.62417141 0 1.6235786 0.00152244 + 1 18.780412 -10.770009 0 17.372438 0.016236934 + 2 65.294131 -11.084501 0 86.758754 0.058617275 + 3 121.92555 -7.0612033 0 175.64423 0.11075612 + 4 185.71165 -5.8781334 0 272.41077 0.16952031 + 5 286.28339 -4.3800108 0 424.61565 0.26135067 + 6 481.28097 -4.3052012 0 716.89433 0.43956491 + 7 487.26022 -3.8672741 0 726.29216 0.44508273 + 8 493.65478 -3.0242687 0 736.71742 0.45104121 + 9 495.66203 -3.4336343 0 739.31592 0.45268492 + 10 498.41831 -2.8837072 0 743.99613 0.4553526 + 11 499.20944 -2.7724783 0 745.29287 0.45612146 + 12 500.97345 -2.8281484 0 747.88057 0.4576713 + 13 507.46412 -2.7752775 0 757.65971 0.46352056 + 14 525.35729 -2.5749814 0 784.67292 0.47996621 + 15 563.9578 -2.9982381 0 842.09253 0.51513685 + 16 645.47602 -2.5519203 0 964.69389 0.58979054 + 17 647.09276 -2.2568468 0 967.41166 0.59135526 + 18 647.12596 -2.2791003 0 967.43915 0.59143679 + 19 647.24862 -2.2495226 0 967.65253 0.59151478 + 20 647.51175 -2.0239179 0 968.27244 0.59175037 +Loop time of 0.357618 on 4 procs for 20 steps with 1000 atoms -Performance: 12955.555 tau/day, 29.990 timesteps/s -99.5% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 24159.843 tau/day, 55.926 timesteps/s +96.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0002284 | 0.00024879 | 0.00025725 | 0.0 | 0.04 -Kspace | 0.6085 | 0.62278 | 0.6386 | 1.6 | 93.38 -Neigh | 0.023998 | 0.040044 | 0.054552 | 6.2 | 6.00 -Comm | 0.0025489 | 0.0028656 | 0.0031898 | 0.4 | 0.43 -Output | 0.0004077 | 0.00053912 | 0.00071406 | 0.0 | 0.08 -Modify | 0.00017953 | 0.00018525 | 0.00020218 | 0.0 | 0.03 -Other | | 0.0002366 | | | 0.04 +Pair | 5.9605e-05 | 6.2883e-05 | 6.8426e-05 | 0.0 | 0.02 +Kspace | 0.32759 | 0.3385 | 0.34421 | 1.1 | 94.65 +Neigh | 0.0090706 | 0.014676 | 0.025457 | 5.3 | 4.10 +Comm | 0.0013905 | 0.0015741 | 0.0017447 | 0.3 | 0.44 +Output | 0.00034785 | 0.00099462 | 0.0026579 | 0.0 | 0.28 +Modify | 5.2929e-05 | 8.3923e-05 | 0.00015783 | 0.0 | 0.02 +Other | | 0.001731 | | | 0.48 -Nlocal: 250 ave 259 max 240 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 668.75 ave 679 max 657 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Neighs: 61085.5 ave 95363 max 24964 min -Histogram: 1 0 0 1 0 0 0 1 0 1 +Nlocal: 250 ave 512 max 84 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 655.75 ave 784 max 433 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 61085.5 ave 111012 max 21779 min +Histogram: 1 0 1 0 0 1 0 0 0 1 Total # of neighbors = 244342 Ave neighs/atom = 244.342 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 similarity index 52% rename from examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 index f8a85c6c6b..9fa1677017 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.hsph.g++.p2nfft.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.1 @@ -1,13 +1,12 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj atom_style charge -read_data data.hammersley_shphere - orthogonal box = (-50.5 -50.5 -50.5) to (51.5 51.5 51.5) +read_data data.hammersley_sphere + orthogonal box = (-51.5 -51.5 -51.5) to (51.5 51.5 51.5) 1 by 1 by 1 MPI processor grid reading atoms ... 1000 atoms @@ -47,51 +46,51 @@ Neighbor list info ... max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2 ghost atom cutoff = 2 - binsize = 1, bins = 102 102 102 + binsize = 1, bins = 103 103 103 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair zero, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes Step Temp E_pair E_mol TotEng Press - 0 1.5 -0.62417787 0 1.6235721 0.0015678854 - 1 18.780041 -10.770002 0 17.371889 0.016718957 - 2 65.289192 -11.084705 0 86.751149 0.060353634 - 3 121.92987 -7.0625759 0 175.64933 0.11404974 - 4 185.78164 -5.8777511 0 272.51603 0.17462194 - 5 286.36221 -4.3820531 0 424.73172 0.26918925 - 6 481.42203 -4.3095567 0 717.10136 0.45274086 - 7 488.59165 -3.8685193 0 728.28607 0.45956865 - 8 497.85288 -3.0417938 0 742.99075 0.46838117 - 9 499.61619 -3.4190063 0 745.25585 0.46983349 - 10 502.63691 -2.8360951 0 750.36531 0.47280815 - 11 504.4847 -2.7628089 0 753.20751 0.47462802 - 12 506.54494 -2.8460319 0 756.21157 0.4765145 - 13 508.2722 -2.7309328 0 758.91497 0.47813761 - 14 510.57053 -2.6094792 0 762.48045 0.48031438 - 15 513.14804 -2.7150819 0 766.23726 0.48275234 - 16 515.78127 -2.3961749 0 770.50206 0.48526336 - 17 515.70267 -2.2982581 0 770.48219 0.48526619 - 18 515.70813 -2.1516075 0 770.63702 0.48530395 - 19 515.74908 -2.0581483 0 770.79185 0.48530979 - 20 515.70881 -1.892235 0 770.89742 0.48527104 -Loop time of 1.06008 on 1 procs for 20 steps with 1000 atoms + 0 1.5 -0.62417787 0 1.6235721 0.0015226607 + 1 18.780041 -10.770002 0 17.371889 0.01623671 + 2 65.289192 -11.084705 0 86.751149 0.058612772 + 3 121.92987 -7.0625759 0 175.64933 0.11076005 + 4 185.78164 -5.8777511 0 272.51603 0.16958509 + 5 286.36221 -4.3820531 0 424.73172 0.26142466 + 6 481.42203 -4.3095567 0 717.10136 0.43968184 + 7 488.59165 -3.8685193 0 728.28608 0.44631269 + 8 497.85288 -3.0417938 0 742.99075 0.45487102 + 9 499.61619 -3.4190062 0 745.25585 0.45628145 + 10 502.63691 -2.8360951 0 750.36531 0.45917031 + 11 504.4847 -2.762809 0 753.20751 0.46093768 + 12 506.54494 -2.846032 0 756.21156 0.46276975 + 13 508.2722 -2.7309328 0 758.91496 0.46434604 + 14 510.57052 -2.6094795 0 762.48045 0.46646002 + 15 513.14804 -2.715082 0 766.23725 0.46882767 + 16 515.78127 -2.396175 0 770.50206 0.47126626 + 17 515.70267 -2.2982584 0 770.48219 0.47126901 + 18 515.70813 -2.1516073 0 770.63702 0.47130567 + 19 515.74908 -2.0581482 0 770.79185 0.47131134 + 20 515.70881 -1.8922354 0 770.89742 0.47127371 +Loop time of 0.313936 on 1 procs for 20 steps with 1000 atoms -Performance: 8150.306 tau/day, 18.866 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 27521.533 tau/day, 63.707 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00022078 | 0.00022078 | 0.00022078 | 0.0 | 0.02 -Kspace | 0.91611 | 0.91611 | 0.91611 | 0.0 | 86.42 -Neigh | 0.14232 | 0.14232 | 0.14232 | 0.0 | 13.43 -Comm | 0.00015092 | 0.00015092 | 0.00015092 | 0.0 | 0.01 -Output | 0.00033736 | 0.00033736 | 0.00033736 | 0.0 | 0.03 -Modify | 0.00056243 | 0.00056243 | 0.00056243 | 0.0 | 0.05 -Other | | 0.0003803 | | | 0.04 +Pair | 5.7697e-05 | 5.7697e-05 | 5.7697e-05 | 0.0 | 0.02 +Kspace | 0.27613 | 0.27613 | 0.27613 | 0.0 | 87.96 +Neigh | 0.037193 | 0.037193 | 0.037193 | 0.0 | 11.85 +Comm | 4.9591e-05 | 4.9591e-05 | 4.9591e-05 | 0.0 | 0.02 +Output | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.07 +Modify | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.05 +Other | | 0.0001338 | | | 0.04 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -104,4 +103,4 @@ Total # of neighbors = 247817 Ave neighs/atom = 247.817 Neighbor list builds = 19 Dangerous builds = 18 -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 new file mode 100644 index 0000000000..a41a3d9685 --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.hsph.p2nfft.g++.4 @@ -0,0 +1,106 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.hammersley_sphere + orthogonal box = (-51.5 -51.5 -51.5) to (51.5 51.5 51.5) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 1000 atoms +change_box all boundary f f f + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p2nfft 0.001 +kspace_modify scafacos tolerance potential + +timestep 0.005 +thermo 1 + +run 20 +Setting up ScaFaCoS with solver p2nfft ... +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 103 103 103 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.882 | 5.463 | 7.161 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -0.62417787 0 1.6235721 0.0015226607 + 1 18.780041 -10.770002 0 17.371889 0.01623671 + 2 65.289192 -11.084705 0 86.751149 0.058612772 + 3 121.92987 -7.0625759 0 175.64933 0.11076005 + 4 185.78164 -5.8777511 0 272.51603 0.16958509 + 5 286.36221 -4.3820531 0 424.73172 0.26142466 + 6 481.42203 -4.3095567 0 717.10136 0.43968184 + 7 488.59165 -3.8685193 0 728.28608 0.44631269 + 8 497.85288 -3.0417938 0 742.99075 0.45487102 + 9 499.61619 -3.4190062 0 745.25585 0.45628145 + 10 502.63691 -2.8360951 0 750.36531 0.45917031 + 11 504.4847 -2.762809 0 753.20751 0.46093768 + 12 506.54494 -2.846032 0 756.21156 0.46276975 + 13 508.2722 -2.7309328 0 758.91496 0.46434604 + 14 510.57052 -2.6094795 0 762.48045 0.46646002 + 15 513.14804 -2.715082 0 766.23725 0.46882767 + 16 515.78127 -2.396175 0 770.50206 0.47126626 + 17 515.70267 -2.2982584 0 770.48219 0.47126901 + 18 515.70813 -2.1516073 0 770.63702 0.47130567 + 19 515.74908 -2.0581482 0 770.79185 0.47131134 + 20 515.70881 -1.8922354 0 770.89742 0.47127371 +Loop time of 0.283172 on 4 procs for 20 steps with 1000 atoms + +Performance: 30511.451 tau/day, 70.628 timesteps/s +94.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.8413e-05 | 6.2227e-05 | 6.8665e-05 | 0.0 | 0.02 +Kspace | 0.2548 | 0.26559 | 0.27139 | 1.2 | 93.79 +Neigh | 0.0083673 | 0.014062 | 0.024744 | 5.3 | 4.97 +Comm | 0.0013778 | 0.0014804 | 0.0015941 | 0.2 | 0.52 +Output | 0.00029898 | 0.00072974 | 0.0017858 | 0.0 | 0.26 +Modify | 3.6001e-05 | 6.3002e-05 | 0.00013065 | 0.0 | 0.02 +Other | | 0.001181 | | | 0.42 + +Nlocal: 250 ave 518 max 78 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Nghost: 659 ave 791 max 430 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Neighs: 61954.2 ave 115962 max 19730 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 247817 +Ave neighs/atom = 247.817 +Neighbor list builds = 19 +Dangerous builds = 18 +Total wall time: 0:00:00 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 b/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 similarity index 80% rename from examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 rename to examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 index 1876a0e52b..2993de6329 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.1 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box @@ -16,7 +15,7 @@ replicate 8 8 8 orthogonal box = (0 0 0) to (8 8 8) 1 by 1 by 1 MPI processor grid 4096 atoms - Time spent = 0.00049448 secs + Time spent = 0.000288725 secs velocity all create 1.5 49893 @@ -72,21 +71,21 @@ Step Temp E_pair E_mol TotEng Press 80 1.5033149 -1.7524495 0 0.50197233 10.46585 90 1.5108219 -1.7637095 0 0.50197005 10.515883 100 1.529239 -1.7913105 0 0.501988 10.638649 -Loop time of 18.1113 on 1 procs for 100 steps with 4096 atoms +Loop time of 7.17417 on 1 procs for 100 steps with 4096 atoms -Performance: 2385.257 tau/day, 5.521 timesteps/s -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 6021.602 tau/day, 13.939 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0014985 | 0.0014985 | 0.0014985 | 0.0 | 0.01 -Kspace | 18.079 | 18.079 | 18.079 | 0.0 | 99.82 +Pair | 0.00037169 | 0.00037169 | 0.00037169 | 0.0 | 0.01 +Kspace | 7.1639 | 7.1639 | 7.1639 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.014229 | 0.014229 | 0.014229 | 0.0 | 0.08 -Output | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.00 -Modify | 0.011227 | 0.011227 | 0.011227 | 0.0 | 0.06 -Other | | 0.004455 | | | 0.02 +Comm | 0.0048451 | 0.0048451 | 0.0048451 | 0.0 | 0.07 +Output | 0.00030565 | 0.00030565 | 0.00030565 | 0.0 | 0.00 +Modify | 0.0029933 | 0.0029933 | 0.0029933 | 0.0 | 0.04 +Other | | 0.001761 | | | 0.02 Nlocal: 4096 ave 4096 max 4096 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -99,4 +98,4 @@ Total # of neighbors = 524288 Ave neighs/atom = 128 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:21 +Total wall time: 0:00:07 diff --git a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 b/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 similarity index 79% rename from examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 rename to examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 index bf4494df8b..19db90d822 100644 --- a/examples/USER/scafacos/log.08Aug18.scafacos.g++.p2nfft.4 +++ b/examples/USER/scafacos/log.27Nov18.scafacos.p2nfft.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (2 Aug 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box @@ -16,7 +15,7 @@ replicate 8 8 8 orthogonal box = (0 0 0) to (8 8 8) 1 by 2 by 2 MPI processor grid 4096 atoms - Time spent = 0.000260592 secs + Time spent = 0.000186443 secs velocity all create 1.5 49893 @@ -72,21 +71,21 @@ Step Temp E_pair E_mol TotEng Press 80 1.5033149 -1.7524495 0 0.50197233 10.46585 90 1.5108219 -1.7637095 0 0.50197005 10.515883 100 1.529239 -1.7913105 0 0.501988 10.638649 -Loop time of 5.09997 on 4 procs for 100 steps with 4096 atoms +Loop time of 2.28914 on 4 procs for 100 steps with 4096 atoms -Performance: 8470.643 tau/day, 19.608 timesteps/s -99.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 18871.750 tau/day, 43.685 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00069928 | 0.00071001 | 0.00073647 | 0.0 | 0.01 -Kspace | 5.0795 | 5.0796 | 5.0797 | 0.0 | 99.60 +Pair | 0.00019193 | 0.00020188 | 0.00020981 | 0.0 | 0.01 +Kspace | 2.2771 | 2.2771 | 2.2772 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.014101 | 0.014216 | 0.014331 | 0.1 | 0.28 -Output | 0.00030541 | 0.00033581 | 0.00039625 | 0.0 | 0.01 -Modify | 0.0030217 | 0.0030621 | 0.0030868 | 0.0 | 0.06 -Other | | 0.002036 | | | 0.04 +Comm | 0.0075378 | 0.007587 | 0.0076075 | 0.0 | 0.33 +Output | 0.00019574 | 0.00051248 | 0.0014374 | 0.0 | 0.02 +Modify | 0.0014074 | 0.0014608 | 0.0014906 | 0.1 | 0.06 +Other | | 0.002247 | | | 0.10 Nlocal: 1024 ave 1024 max 1024 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -99,4 +98,4 @@ Total # of neighbors = 524288 Ave neighs/atom = 128 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:02 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 b/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 new file mode 100644 index 0000000000..92e85e072e --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.1 @@ -0,0 +1,102 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 1 by 1 MPI processor grid + 4096 atoms + Time spent = 0.000295162 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p3m ... +WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.813 | 5.813 | 5.813 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475754 0 0.5018753 11.99707 + 10 1.5000018 -1.7475781 0 0.50187528 11.997085 + 20 1.4999833 -1.7475525 0 0.50187314 11.996937 + 30 1.4999008 -1.7474408 0 0.50186112 11.996277 + 40 1.4997303 -1.7471984 0 0.5018478 11.994913 + 50 1.4995294 -1.7469059 0 0.50183901 11.993306 + 60 1.4995402 -1.7469269 0 0.50183416 11.993392 + 70 1.50036 -1.7481582 0 0.50183238 11.99995 + 80 1.5032409 -1.7524778 0 0.50183303 12.022991 + 90 1.5107445 -1.7637255 0 0.50183801 12.083005 + 100 1.5291568 -1.7913136 0 0.50186158 12.230268 +Loop time of 2.98343 on 1 procs for 100 steps with 4096 atoms + +Performance: 14479.957 tau/day, 33.518 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.00035572 | 0.00035572 | 0.00035572 | 0.0 | 0.01 +Kspace | 2.9729 | 2.9729 | 2.9729 | 0.0 | 99.65 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.005022 | 0.005022 | 0.005022 | 0.0 | 0.17 +Output | 0.00027037 | 0.00027037 | 0.00027037 | 0.0 | 0.01 +Modify | 0.003046 | 0.003046 | 0.003046 | 0.0 | 0.10 +Other | | 0.00182 | | | 0.06 + +Nlocal: 4096 ave 4096 max 4096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9728 ave 9728 max 9728 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 524288 ave 524288 max 524288 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 b/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 new file mode 100644 index 0000000000..18199eca16 --- /dev/null +++ b/examples/USER/scafacos/log.27Nov18.scafacos.p3m.g++.4 @@ -0,0 +1,102 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Point dipoles in a 2d box + +units lj +atom_style charge + +read_data data.NaCl + orthogonal box = (0 0 0) to (1 1 1) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 8 atoms + +replicate 8 8 8 + orthogonal box = (0 0 0) to (8 8 8) + 1 by 2 by 2 MPI processor grid + 4096 atoms + Time spent = 0.000118017 secs + +velocity all create 1.5 49893 + +neighbor 1.0 bin +neigh_modify delay 0 + +fix 1 all nve + +# LAMMPS computes pairwise and long-range Coulombics + +#pair_style coul/long 3.0 +#pair_coeff * * +#kspace_style pppm 1.0e-3 + +# Scafacos computes entire long-range Coulombics +# use dummy pair style to perform atom sorting + +pair_style zero 1.0 +pair_coeff * * + +#fix 2 all scafacos p3m tolerance field 0.001 + +kspace_style scafacos p3m 0.001 +kspace_modify scafacos tolerance field + +timestep 0.005 +thermo 10 + +run 100 +Setting up ScaFaCoS with solver p3m ... +WARNING: Virial computation for P3M not available (src/USER-SCAFACOS/scafacos.cpp:104) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2 + ghost atom cutoff = 2 + binsize = 1, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.008 | 4.008 | 4.008 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.5 -1.7475797 0 0.50187096 11.99707 + 10 1.5000019 -1.7475825 0 0.50187094 11.997085 + 20 1.4999837 -1.7475551 0 0.50187104 11.99694 + 30 1.4999024 -1.7474348 0 0.50186949 11.996289 + 40 1.4997328 -1.747187 0 0.50186299 11.994934 + 50 1.499532 -1.7468958 0 0.50185295 11.993327 + 60 1.4995421 -1.74692 0 0.50184401 11.993408 + 70 1.5003611 -1.7481536 0 0.5018387 11.999959 + 80 1.5032412 -1.7524745 0 0.50183679 12.022994 + 90 1.510744 -1.763723 0 0.50183979 12.083002 + 100 1.5291558 -1.7913123 0 0.5018614 12.23026 +Loop time of 1.10005 on 4 procs for 100 steps with 4096 atoms + +Performance: 39271.030 tau/day, 90.905 timesteps/s +96.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0002172 | 0.00022924 | 0.0002377 | 0.0 | 0.02 +Kspace | 1.0848 | 1.0849 | 1.085 | 0.0 | 98.62 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.010176 | 0.01062 | 0.01088 | 0.3 | 0.97 +Output | 0.00019169 | 0.0003345 | 0.00075459 | 0.0 | 0.03 +Modify | 0.001878 | 0.0018976 | 0.0019398 | 0.1 | 0.17 +Other | | 0.002097 | | | 0.19 + +Nlocal: 1024 ave 1024 max 1024 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5120 ave 5120 max 5120 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 131072 ave 131072 max 131072 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 524288 +Ave neighs/atom = 128 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/USER/sdpd/2d-diffusion-in-shear-flow/in.lammps b/examples/USER/sdpd/2d-diffusion-in-shear-flow/in.lammps new file mode 100644 index 0000000000..138f7b5338 --- /dev/null +++ b/examples/USER/sdpd/2d-diffusion-in-shear-flow/in.lammps @@ -0,0 +1,61 @@ +dimension 2 +units micro +atom_style meso + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable Lf equal $R*3 +variable Lb equal $R*4 +variable wall_velocity equal 0.01 # micrometers/microsecond +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable mass equal $a*$a*$a*${rho_0} +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h + +region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box +create_box 4 box +lattice sq $a + +create_atoms 1 box + +region sphere sphere 0 0 0 $R units box +set region sphere type 2 + +region upper_wall block INF INF +${Lf} INF INF INF units box +set region upper_wall type 3 + +region lower_wall block INF INF INF -${Lf} INF INF units box +set region lower_wall type 4 + +group fluid type 1 +group sphere type 2 +group upper_wall type 3 +group lower_wall type 4 + +mass * ${mass} +set group all meso/rho ${rho_0} + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_coeff * * ${rho_0} ${c_0} ${h} + +fix 1 fluid meso +fix 2 sphere rigid/meso single +fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box +fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box + +fix 2d all enforce2d + +neighbor ${skin} bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 diff --git a/examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 b/examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 new file mode 100644 index 0000000000..cd01601292 --- /dev/null +++ b/examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.1 @@ -0,0 +1,247 @@ +LAMMPS (24 Oct 2018) +dimension 2 +units micro +atom_style meso + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable Lf equal $R*3 +variable Lf equal 0.5*3 +variable Lb equal $R*4 +variable Lb equal 0.5*4 +variable wall_velocity equal 0.01 # micrometers/microsecond +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -2 ${Lb} 0 ${a} units box +region box block -2 2 -2 2 0 ${a} units box +region box block -2 2 -2 2 0 0.1 units box +create_box 4 box +Created orthogonal box = (-2 -2 0) to (2 2 0.1) + 1 by 1 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 1600 atoms + Time spent = 0.00169706 secs + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 + 81 settings made for type + +region upper_wall block INF INF +${Lf} INF INF INF units box +region upper_wall block INF INF +1.5 INF INF INF units box +set region upper_wall type 3 + 200 settings made for type + +region lower_wall block INF INF INF -${Lf} INF INF units box +region lower_wall block INF INF INF -1.5 INF INF units box +set region lower_wall type 4 + 240 settings made for type + +group fluid type 1 +1079 atoms in group fluid +group sphere type 2 +81 atoms in group sphere +group upper_wall type 3 +200 atoms in group upper_wall +group lower_wall type 4 +240 atoms in group lower_wall + +mass * ${mass} +mass * 0.001 +set group all meso/rho ${rho_0} +set group all meso/rho 1 + 1600 settings made for meso/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid meso +fix 2 sphere rigid/meso single +1 rigid bodies with 81 atoms +fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box +fix 3 upper_wall meso/move linear +0.01 0 0 units box +fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box +fix 4 lower_wall meso/move linear -0.01 0 0 units box + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 15 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.937 | 6.937 | 6.937 Mbytes +Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 0 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 5 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 6 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 9 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 10 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 11 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 12 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 14 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 15 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 16 0 + 4900 4.9 16 0 + 5000 5 16 0 + 5100 5.1 17 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 17 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 19 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 20 0 + 6100 6.1 20 0 + 6200 6.2 21 0 + 6300 6.3 21 0 + 6400 6.4 21 0 + 6500 6.5 22 0 + 6600 6.6 22 0 + 6700 6.7 22 0 + 6800 6.8 23 0 + 6900 6.9 23 0 + 7000 7 23 0 + 7100 7.1 24 0 + 7200 7.2 24 0 + 7300 7.3 25 0 + 7400 7.4 25 0 + 7500 7.5 25 0 + 7600 7.6 26 0 + 7700 7.7 26 0 + 7800 7.8 26 0 + 7900 7.9 27 0 + 8000 8 27 0 + 8100 8.1 27 0 + 8200 8.2 28 0 + 8300 8.3 28 0 + 8400 8.4 28 0 + 8500 8.5 29 0 + 8600 8.6 29 0 + 8700 8.7 30 0 + 8800 8.8 30 0 + 8900 8.9 30 0 + 9000 9 31 0 + 9100 9.1 31 0 + 9200 9.2 31 0 + 9300 9.3 32 0 + 9400 9.4 32 0 + 9500 9.5 32 0 + 9600 9.6 33 0 + 9700 9.7 33 0 + 9800 9.8 33 0 + 9900 9.9 34 0 + 10000 10 34 0 +Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms + +Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 143.08 | 143.08 | 143.08 | 0.0 | 99.22 +Neigh | 0.033195 | 0.033195 | 0.033195 | 0.0 | 0.02 +Comm | 0.24139 | 0.24139 | 0.24139 | 0.0 | 0.17 +Output | 0.11687 | 0.11687 | 0.11687 | 0.0 | 0.08 +Modify | 0.61566 | 0.61566 | 0.61566 | 0.0 | 0.43 +Other | | 0.117 | | | 0.08 + +Nlocal: 1600 ave 1600 max 1600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 993 ave 993 max 993 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 73236 ave 73236 max 73236 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 73236 +Ave neighs/atom = 45.7725 +Neighbor list builds = 34 +Dangerous builds = 0 +Total wall time: 0:02:24 diff --git a/examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 b/examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 new file mode 100644 index 0000000000..77823e00fc --- /dev/null +++ b/examples/USER/sdpd/2d-diffusion-in-shear-flow/log.24Oct18.2d-diffusion-in-shear-flow.g++.4 @@ -0,0 +1,247 @@ +LAMMPS (24 Oct 2018) +dimension 2 +units micro +atom_style meso + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable Lf equal $R*3 +variable Lf equal 0.5*3 +variable Lb equal $R*4 +variable Lb equal 0.5*4 +variable wall_velocity equal 0.01 # micrometers/microsecond +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -${Lb} ${Lb} 0 ${a} units box +region box block -2 2 -2 ${Lb} 0 ${a} units box +region box block -2 2 -2 2 0 ${a} units box +region box block -2 2 -2 2 0 0.1 units box +create_box 4 box +Created orthogonal box = (-2 -2 0) to (2 2 0.1) + 2 by 2 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 1600 atoms + Time spent = 0.000589566 secs + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 + 81 settings made for type + +region upper_wall block INF INF +${Lf} INF INF INF units box +region upper_wall block INF INF +1.5 INF INF INF units box +set region upper_wall type 3 + 200 settings made for type + +region lower_wall block INF INF INF -${Lf} INF INF units box +region lower_wall block INF INF INF -1.5 INF INF units box +set region lower_wall type 4 + 240 settings made for type + +group fluid type 1 +1079 atoms in group fluid +group sphere type 2 +81 atoms in group sphere +group upper_wall type 3 +200 atoms in group upper_wall +group lower_wall type 4 +240 atoms in group lower_wall + +mass * ${mass} +mass * 0.001 +set group all meso/rho ${rho_0} +set group all meso/rho 1 + 1600 settings made for meso/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid meso +fix 2 sphere rigid/meso single +1 rigid bodies with 81 atoms +fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box +fix 3 upper_wall meso/move linear +0.01 0 0 units box +fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box +fix 4 lower_wall meso/move linear -0.01 0 0 units box + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 15 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes +Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 1 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 4 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 5 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 6 0 + 2200 2.2 6 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 7 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 8 0 + 2900 2.9 9 0 + 3000 3 9 0 + 3100 3.1 9 0 + 3200 3.2 10 0 + 3300 3.3 10 0 + 3400 3.4 10 0 + 3500 3.5 11 0 + 3600 3.6 11 0 + 3700 3.7 11 0 + 3800 3.8 12 0 + 3900 3.9 12 0 + 4000 4 12 0 + 4100 4.1 13 0 + 4200 4.2 13 0 + 4300 4.3 13 0 + 4400 4.4 14 0 + 4500 4.5 14 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 15 0 + 4900 4.9 16 0 + 5000 5 16 0 + 5100 5.1 17 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 17 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 18 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 20 0 + 6100 6.1 20 0 + 6200 6.2 20 0 + 6300 6.3 21 0 + 6400 6.4 21 0 + 6500 6.5 21 0 + 6600 6.6 22 0 + 6700 6.7 22 0 + 6800 6.8 22 0 + 6900 6.9 23 0 + 7000 7 23 0 + 7100 7.1 23 0 + 7200 7.2 24 0 + 7300 7.3 24 0 + 7400 7.4 25 0 + 7500 7.5 25 0 + 7600 7.6 25 0 + 7700 7.7 25 0 + 7800 7.8 26 0 + 7900 7.9 26 0 + 8000 8 26 0 + 8100 8.1 27 0 + 8200 8.2 27 0 + 8300 8.3 27 0 + 8400 8.4 28 0 + 8500 8.5 28 0 + 8600 8.6 28 0 + 8700 8.7 29 0 + 8800 8.8 29 0 + 8900 8.9 29 0 + 9000 9 30 0 + 9100 9.1 30 0 + 9200 9.2 31 0 + 9300 9.3 31 0 + 9400 9.4 31 0 + 9500 9.5 32 0 + 9600 9.6 32 0 + 9700 9.7 32 0 + 9800 9.8 32 0 + 9900 9.9 33 0 + 10000 10 33 0 +Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms + +Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s +94.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 51.576 | 53.662 | 55.484 | 23.9 | 84.86 +Neigh | 0.011519 | 0.012395 | 0.013405 | 0.7 | 0.02 +Comm | 6.8389 | 8.5423 | 10.517 | 56.1 | 13.51 +Output | 0.12342 | 0.12513 | 0.1302 | 0.8 | 0.20 +Modify | 0.58708 | 0.69128 | 0.78806 | 11.3 | 1.09 +Other | | 0.2038 | | | 0.32 + +Nlocal: 400 ave 411 max 388 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 552.25 ave 567 max 539 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 18298.8 ave 18781 max 17829 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 73195 +Ave neighs/atom = 45.7469 +Neighbor list builds = 33 +Dangerous builds = 0 +Total wall time: 0:01:03 diff --git a/examples/USER/sdpd/2d-diffusion/in.lammps b/examples/USER/sdpd/2d-diffusion/in.lammps new file mode 100644 index 0000000000..6ef36a0cf6 --- /dev/null +++ b/examples/USER/sdpd/2d-diffusion/in.lammps @@ -0,0 +1,49 @@ +dimension 2 +units micro +atom_style meso + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable L equal $R*3 +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable mass equal $a*$a*$a*${rho_0} +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h + +region box block -$L $L -$L $L 0 $a units box +create_box 2 box +lattice sq $a + +create_atoms 1 box + +region sphere sphere 0 0 0 $R units box +set region sphere type 2 + +group fluid type 1 +group sphere type 2 + +mass * ${mass} +set group all meso/rho ${rho_0} + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_coeff * * ${rho_0} ${c_0} ${h} + +fix 1 fluid meso +fix 2 sphere rigid/meso single + +fix 2d all enforce2d + +neighbor ${skin} bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 diff --git a/examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 b/examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 new file mode 100644 index 0000000000..d44c0fd6f4 --- /dev/null +++ b/examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1 @@ -0,0 +1,226 @@ +LAMMPS (24 Oct 2018) +dimension 2 +units micro +atom_style meso + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable L equal $R*3 +variable L equal 0.5*3 +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -$L $L -$L $L 0 $a units box +region box block -1.5 $L -$L $L 0 $a units box +region box block -1.5 1.5 -$L $L 0 $a units box +region box block -1.5 1.5 -1.5 $L 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 0.1 units box +create_box 2 box +Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) + 1 by 1 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 900 atoms + Time spent = 0.0015769 secs + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 + 81 settings made for type + +group fluid type 1 +819 atoms in group fluid +group sphere type 2 +81 atoms in group sphere + +mass * ${mass} +mass * 0.001 +set group all meso/rho ${rho_0} +set group all meso/rho 1 + 900 settings made for meso/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid meso +fix 2 sphere rigid/meso single +1 rigid bodies with 81 atoms + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 12 12 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.137 | 6.137 | 6.137 Mbytes +Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 1 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 4 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 6 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 7 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 7 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 8 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 10 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 11 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 12 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 13 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 14 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 15 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 16 0 + 4900 4.9 16 0 + 5000 5 17 0 + 5100 5.1 17 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 18 0 + 5500 5.5 18 0 + 5600 5.6 18 0 + 5700 5.7 19 0 + 5800 5.8 19 0 + 5900 5.9 19 0 + 6000 6 19 0 + 6100 6.1 20 0 + 6200 6.2 20 0 + 6300 6.3 20 0 + 6400 6.4 21 0 + 6500 6.5 21 0 + 6600 6.6 21 0 + 6700 6.7 21 0 + 6800 6.8 22 0 + 6900 6.9 22 0 + 7000 7 22 0 + 7100 7.1 23 0 + 7200 7.2 23 0 + 7300 7.3 23 0 + 7400 7.4 24 0 + 7500 7.5 24 0 + 7600 7.6 24 0 + 7700 7.7 25 0 + 7800 7.8 25 0 + 7900 7.9 26 0 + 8000 8 26 0 + 8100 8.1 26 0 + 8200 8.2 26 0 + 8300 8.3 27 0 + 8400 8.4 27 0 + 8500 8.5 27 0 + 8600 8.6 28 0 + 8700 8.7 28 0 + 8800 8.8 28 0 + 8900 8.9 29 0 + 9000 9 29 0 + 9100 9.1 29 0 + 9200 9.2 30 0 + 9300 9.3 30 0 + 9400 9.4 30 0 + 9500 9.5 30 0 + 9600 9.6 31 0 + 9700 9.7 31 0 + 9800 9.8 32 0 + 9900 9.9 32 0 + 10000 10 32 0 +Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms + +Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s +99.8% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 80.306 | 80.306 | 80.306 | 0.0 | 99.21 +Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.02 +Comm | 0.16939 | 0.16939 | 0.16939 | 0.0 | 0.21 +Output | 0.070281 | 0.070281 | 0.070281 | 0.0 | 0.09 +Modify | 0.3154 | 0.3154 | 0.3154 | 0.0 | 0.39 +Other | | 0.067 | | | 0.08 + +Nlocal: 900 ave 900 max 900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 762 ave 762 max 762 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 40697 ave 40697 max 40697 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 40697 +Ave neighs/atom = 45.2189 +Neighbor list builds = 32 +Dangerous builds = 0 +Total wall time: 0:01:20 diff --git a/examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 b/examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 new file mode 100644 index 0000000000..f904b78ab4 --- /dev/null +++ b/examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4 @@ -0,0 +1,226 @@ +LAMMPS (24 Oct 2018) +dimension 2 +units micro +atom_style meso + +variable R equal 0.5 # radius of sphere micrometers +variable a equal $R/5 # lattice spacing micrometers +variable a equal 0.5/5 +variable L equal $R*3 +variable L equal 0.5*3 +variable T equal 300. +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 100. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.5 # kernel function cutoff micrometers +variable h equal 0.1*4.5 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 1e-3 # timestep microseconds +variable skin equal 0.2*$h +variable skin equal 0.2*0.45 + +region box block -$L $L -$L $L 0 $a units box +region box block -1.5 $L -$L $L 0 $a units box +region box block -1.5 1.5 -$L $L 0 $a units box +region box block -1.5 1.5 -1.5 $L 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 $a units box +region box block -1.5 1.5 -1.5 1.5 0 0.1 units box +create_box 2 box +Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1) + 2 by 2 by 1 MPI processor grid +lattice sq $a +lattice sq 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 900 atoms + Time spent = 0.0010246 secs + +region sphere sphere 0 0 0 $R units box +region sphere sphere 0 0 0 0.5 units box +set region sphere type 2 + 81 settings made for type + +group fluid type 1 +819 atoms in group fluid +group sphere type 2 +81 atoms in group sphere + +mass * ${mass} +mass * 0.001 +set group all meso/rho ${rho_0} +set group all meso/rho 1 + 900 settings made for meso/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 100 ${h} +pair_coeff * * 1 100 0.45 + +fix 1 fluid meso +fix 2 sphere rigid/meso single +1 rigid bodies with 81 atoms + +fix 2d all enforce2d + +neighbor ${skin} bin +neighbor 0.09 bin +neigh_modify delay 0 every 1 check yes +timestep ${dt} +timestep 0.001 + +dump dump_id all atom 100 dump.lammpstrj + +thermo 100 +thermo_style custom step time nbuild ndanger + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.54 + ghost atom cutoff = 0.54 + binsize = 0.27, bins = 12 12 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes +Step Time Nbuild Ndanger + 0 0 0 0 + 100 0.1 0 0 + 200 0.2 0 0 + 300 0.3 0 0 + 400 0.4 1 0 + 500 0.5 1 0 + 600 0.6 1 0 + 700 0.7 2 0 + 800 0.8 2 0 + 900 0.9 2 0 + 1000 1 3 0 + 1100 1.1 3 0 + 1200 1.2 3 0 + 1300 1.3 4 0 + 1400 1.4 4 0 + 1500 1.5 5 0 + 1600 1.6 5 0 + 1700 1.7 5 0 + 1800 1.8 6 0 + 1900 1.9 6 0 + 2000 2 6 0 + 2100 2.1 7 0 + 2200 2.2 7 0 + 2300 2.3 7 0 + 2400 2.4 8 0 + 2500 2.5 8 0 + 2600 2.6 8 0 + 2700 2.7 9 0 + 2800 2.8 9 0 + 2900 2.9 9 0 + 3000 3 9 0 + 3100 3.1 10 0 + 3200 3.2 10 0 + 3300 3.3 10 0 + 3400 3.4 11 0 + 3500 3.5 11 0 + 3600 3.6 11 0 + 3700 3.7 12 0 + 3800 3.8 12 0 + 3900 3.9 12 0 + 4000 4 13 0 + 4100 4.1 13 0 + 4200 4.2 13 0 + 4300 4.3 14 0 + 4400 4.4 14 0 + 4500 4.5 15 0 + 4600 4.6 15 0 + 4700 4.7 15 0 + 4800 4.8 16 0 + 4900 4.9 16 0 + 5000 5 16 0 + 5100 5.1 16 0 + 5200 5.2 17 0 + 5300 5.3 17 0 + 5400 5.4 18 0 + 5500 5.5 18 0 + 5600 5.6 19 0 + 5700 5.7 19 0 + 5800 5.8 19 0 + 5900 5.9 20 0 + 6000 6 20 0 + 6100 6.1 20 0 + 6200 6.2 21 0 + 6300 6.3 21 0 + 6400 6.4 21 0 + 6500 6.5 22 0 + 6600 6.6 22 0 + 6700 6.7 22 0 + 6800 6.8 23 0 + 6900 6.9 23 0 + 7000 7 23 0 + 7100 7.1 24 0 + 7200 7.2 24 0 + 7300 7.3 24 0 + 7400 7.4 25 0 + 7500 7.5 25 0 + 7600 7.6 25 0 + 7700 7.7 26 0 + 7800 7.8 26 0 + 7900 7.9 26 0 + 8000 8 27 0 + 8100 8.1 27 0 + 8200 8.2 27 0 + 8300 8.3 28 0 + 8400 8.4 28 0 + 8500 8.5 28 0 + 8600 8.6 28 0 + 8700 8.7 29 0 + 8800 8.8 29 0 + 8900 8.9 29 0 + 9000 9 30 0 + 9100 9.1 30 0 + 9200 9.2 31 0 + 9300 9.3 31 0 + 9400 9.4 31 0 + 9500 9.5 31 0 + 9600 9.6 32 0 + 9700 9.7 32 0 + 9800 9.8 32 0 + 9900 9.9 33 0 + 10000 10 33 0 +Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms + +Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s +48.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 56.528 | 57.936 | 58.729 | 11.0 | 83.95 +Neigh | 0.013157 | 0.013382 | 0.013551 | 0.1 | 0.02 +Comm | 8.9594 | 9.7555 | 11.113 | 26.7 | 14.14 +Output | 0.14644 | 0.15009 | 0.15809 | 1.2 | 0.22 +Modify | 0.72913 | 0.91574 | 1.0524 | 12.4 | 1.33 +Other | | 0.2389 | | | 0.35 + +Nlocal: 225 ave 229 max 223 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 442 ave 444 max 439 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 10188.8 ave 10437 max 9932 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 40755 +Ave neighs/atom = 45.2833 +Neighbor list builds = 33 +Dangerous builds = 0 +Total wall time: 0:01:09 diff --git a/examples/USER/sdpd/README b/examples/USER/sdpd/README new file mode 100644 index 0000000000..72feff15dc --- /dev/null +++ b/examples/USER/sdpd/README @@ -0,0 +1,24 @@ +Smoothed Dissipative Particle Dynamics examples + +equipartition-verification: + This example verifies the equipartition theorem. + It simulates a periodic box of water with no solid bodies. + If equipartition theorem holds true, the average of each component of + translational kinetic energy should be equal to k_B T, and therefore + vx_sq_check, vy_sq_check, and vz_sq_check should fluctuate near 1. + +2d-diffusion: + This example demonstrates the free diffusion of a disk in 2D. + The 3D simulation is similar but takes much longer to complete. + As with other statistical experiments you need an ensemble to + extract meaningful average quantities. + For a more realistic simulation you should increase the resolution + of the disk/sphere which also necessitates reduction of timestep. + +2d-diffusion-in-shear-flow: + This example demonstrates the diffusion of a disk in shear flow in 2D. + The 3D simulation is similar but takes much longer to complete. + As with other statistical experiments you need an ensemble to + extract meaningful average quantities. + For a more realistic simulation you should increase the resolution + of the disk/sphere which also necessitates reduction of timestep. diff --git a/examples/USER/sdpd/equipartition-verification/in.lammps b/examples/USER/sdpd/equipartition-verification/in.lammps new file mode 100644 index 0000000000..0d06723f59 --- /dev/null +++ b/examples/USER/sdpd/equipartition-verification/in.lammps @@ -0,0 +1,45 @@ +dimension 3 +units micro +atom_style meso + +variable a equal 0.1 # lattice spacing micrometers +variable L equal $a*10 +variable T equal 300. +variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin) +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 10. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.0 # kernel function cutoff micrometers +variable mass equal $a*$a*$a*${rho_0} +variable dt equal 5e-4 # timestep microseconds +variable skin equal 0.1*$h + +region box block -$L $L -$L $L -$L $L units box +create_box 1 box +lattice sc $a + +create_atoms 1 box + +mass * ${mass} +set group all meso/rho ${rho_0} + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_coeff * * ${rho_0} ${c_0} ${h} + +variable vx_sq atom vx*vx +variable vy_sq atom vy*vy +variable vz_sq atom vz*vz +compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq +variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T +variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T +variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T + +fix 1 all meso + +neighbor ${skin} bin +timestep ${dt} + +thermo 10 +thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check + +run 200 diff --git a/examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.1 b/examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.1 new file mode 100644 index 0000000000..06ffd699bc --- /dev/null +++ b/examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.1 @@ -0,0 +1,146 @@ +LAMMPS (24 Oct 2018) +dimension 3 +units micro +atom_style meso + +variable a equal 0.1 # lattice spacing micrometers +variable L equal $a*10 +variable L equal 0.1*10 +variable T equal 300. +variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin) +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 10. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.0 # kernel function cutoff micrometers +variable h equal 0.1*4.0 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 5e-4 # timestep microseconds +variable skin equal 0.1*$h +variable skin equal 0.1*0.4 + +region box block -$L $L -$L $L -$L $L units box +region box block -1 $L -$L $L -$L $L units box +region box block -1 1 -$L $L -$L $L units box +region box block -1 1 -1 $L -$L $L units box +region box block -1 1 -1 1 -$L $L units box +region box block -1 1 -1 1 -1 $L units box +region box block -1 1 -1 1 -1 1 units box +create_box 1 box +Created orthogonal box = (-1 -1 -1) to (1 1 1) + 1 by 1 by 1 MPI processor grid +lattice sc $a +lattice sc 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 8000 atoms + Time spent = 0.00285411 secs + +mass * ${mass} +mass * 0.001 +set group all meso/rho ${rho_0} +set group all meso/rho 1 + 8000 settings made for meso/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 10 ${h} +pair_coeff * * 1 10 0.4 + +variable vx_sq atom vx*vx +variable vy_sq atom vy*vy +variable vz_sq atom vz*vz +compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq +variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T +variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T +variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T +variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300 +variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T +variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T +variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T +variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300 +variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T +variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T +variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T +variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300 + +fix 1 all meso + +neighbor ${skin} bin +neighbor 0.04 bin +timestep ${dt} +timestep 0.0005 + +thermo 10 +thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check + +run 200 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.44 + ghost atom cutoff = 0.44 + binsize = 0.22, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes +Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check + 0 0 0 0 0 + 10 0.005 0.70973271 0.71495693 0.71910087 + 20 0.01 0.90418096 0.88845437 0.89659567 + 30 0.015 0.9590736 0.97880338 0.9619016 + 40 0.02 0.98533774 0.96057682 0.95600448 + 50 0.025 0.96433662 0.96650071 0.95509683 + 60 0.03 0.96598029 0.96373656 0.96734888 + 70 0.035 0.95433045 0.98004764 0.96255924 + 80 0.04 0.97872906 0.95987289 0.96623598 + 90 0.045 0.99913888 0.99255731 0.95616142 + 100 0.05 0.98872675 0.97141018 0.95338841 + 110 0.055 0.97794592 0.97389258 0.98473719 + 120 0.06 0.98389266 0.96716284 0.95504862 + 130 0.065 0.98572886 0.96680923 0.95599065 + 140 0.07 0.97602684 0.97580081 0.9886878 + 150 0.075 0.99172003 0.95027467 0.96028033 + 160 0.08 0.96793247 0.94590928 0.95644301 + 170 0.085 0.94167619 0.98048861 0.93439426 + 180 0.09 0.97277934 0.97383622 0.96900866 + 190 0.095 0.96647288 1.0027643 0.96230782 + 200 0.1 0.94864291 0.95902585 0.96398175 +Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms + +Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s +99.7% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 59.92 | 59.92 | 59.92 | 0.0 | 99.68 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11154 | 0.11154 | 0.11154 | 0.0 | 0.19 +Output | 0.0063498 | 0.0063498 | 0.0063498 | 0.0 | 0.01 +Modify | 0.043546 | 0.043546 | 0.043546 | 0.0 | 0.07 +Other | | 0.02811 | | | 0.05 + +Nlocal: 8000 ave 8000 max 8000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 16389 ave 16389 max 16389 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1456000 +Ave neighs/atom = 182 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:01:00 diff --git a/examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.4 b/examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.4 new file mode 100644 index 0000000000..88509f0fd1 --- /dev/null +++ b/examples/USER/sdpd/equipartition-verification/log.24Oct18.equipartition.g++.4 @@ -0,0 +1,146 @@ +LAMMPS (24 Oct 2018) +dimension 3 +units micro +atom_style meso + +variable a equal 0.1 # lattice spacing micrometers +variable L equal $a*10 +variable L equal 0.1*10 +variable T equal 300. +variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin) +variable rho_0 equal 1. # density picograms/micrometer^3 +variable c_0 equal 10. # speed of sound micrometers/microsecond +variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond) +variable h equal $a*4.0 # kernel function cutoff micrometers +variable h equal 0.1*4.0 +variable mass equal $a*$a*$a*${rho_0} +variable mass equal 0.1*$a*$a*${rho_0} +variable mass equal 0.1*0.1*$a*${rho_0} +variable mass equal 0.1*0.1*0.1*${rho_0} +variable mass equal 0.1*0.1*0.1*1 +variable dt equal 5e-4 # timestep microseconds +variable skin equal 0.1*$h +variable skin equal 0.1*0.4 + +region box block -$L $L -$L $L -$L $L units box +region box block -1 $L -$L $L -$L $L units box +region box block -1 1 -$L $L -$L $L units box +region box block -1 1 -1 $L -$L $L units box +region box block -1 1 -1 1 -$L $L units box +region box block -1 1 -1 1 -1 $L units box +region box block -1 1 -1 1 -1 1 units box +create_box 1 box +Created orthogonal box = (-1 -1 -1) to (1 1 1) + 1 by 2 by 2 MPI processor grid +lattice sc $a +lattice sc 0.1 +Lattice spacing in x,y,z = 0.1 0.1 0.1 + +create_atoms 1 box +Created 8000 atoms + Time spent = 0.00252754 secs + +mass * ${mass} +mass * 0.001 +set group all meso/rho ${rho_0} +set group all meso/rho 1 + 8000 settings made for meso/rho + +pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed +pair_style sdpd/taitwater/isothermal 300 ${mu} 76787 +pair_style sdpd/taitwater/isothermal 300 1 76787 +pair_coeff * * ${rho_0} ${c_0} ${h} +pair_coeff * * 1 ${c_0} ${h} +pair_coeff * * 1 10 ${h} +pair_coeff * * 1 10 0.4 + +variable vx_sq atom vx*vx +variable vy_sq atom vy*vy +variable vz_sq atom vz*vz +compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq +variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T +variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T +variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T +variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300 +variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T +variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T +variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T +variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300 +variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T +variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T +variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T +variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300 + +fix 1 all meso + +neighbor ${skin} bin +neighbor 0.04 bin +timestep ${dt} +timestep 0.0005 + +thermo 10 +thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check + +run 200 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0.44 + ghost atom cutoff = 0.44 + binsize = 0.22, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sdpd/taitwater/isothermal, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes +Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check + 0 0 0 0 0 + 10 0.005 0.71224819 0.71470372 0.7008956 + 20 0.01 0.90627589 0.90683966 0.90116506 + 30 0.015 0.938505 0.95884272 0.93337542 + 40 0.02 0.94394649 0.93668038 0.96468004 + 50 0.025 0.97152309 0.97546161 0.95107762 + 60 0.03 0.94710871 0.95678322 0.97285504 + 70 0.035 0.96253148 0.95838642 0.95450883 + 80 0.04 0.97581495 0.95278681 0.95099478 + 90 0.045 0.96251614 0.9740684 0.96081505 + 100 0.05 0.94191275 0.97137523 0.94084858 + 110 0.055 0.953406 0.95739684 0.98574522 + 120 0.06 0.99001614 0.99608287 0.9839996 + 130 0.065 0.96575225 0.94309655 0.92847798 + 140 0.07 0.97642687 0.97458638 0.94696406 + 150 0.075 0.99316381 0.96876814 0.95440106 + 160 0.08 0.94589744 0.95264791 0.95495169 + 170 0.085 0.97599092 0.95336014 0.97687718 + 180 0.09 0.97214242 0.9726305 0.9726035 + 190 0.095 0.97577583 0.96523645 0.9756968 + 200 0.1 0.96386053 0.97268854 0.94582436 +Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms + +Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s +73.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10 +Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08 +Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10 +Other | | 0.1226 | | | 0.38 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 8469 ave 8469 max 8469 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 364000 ave 376628 max 351184 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 1456000 +Ave neighs/atom = 182 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:32 diff --git a/examples/USER/smtbq/data.Alpha b/examples/USER/smtbq/data.Alpha old mode 100755 new mode 100644 diff --git a/examples/USER/smtbq/ffield.smtbq.Al b/examples/USER/smtbq/ffield.smtbq.Al old mode 100755 new mode 100644 diff --git a/examples/USER/smtbq/ffield.smtbq.Al2O3 b/examples/USER/smtbq/ffield.smtbq.Al2O3 old mode 100755 new mode 100644 diff --git a/examples/USER/smtbq/ffield.smtbq.TiO2 b/examples/USER/smtbq/ffield.smtbq.TiO2 old mode 100755 new mode 100644 diff --git a/examples/USER/smtbq/in.smtbq.Al b/examples/USER/smtbq/in.smtbq.Al old mode 100755 new mode 100644 diff --git a/examples/USER/smtbq/in.smtbq.Al2O3 b/examples/USER/smtbq/in.smtbq.Al2O3 old mode 100755 new mode 100644 diff --git a/examples/USER/smtbq/in.smtbq.TiO2 b/examples/USER/smtbq/in.smtbq.TiO2 old mode 100755 new mode 100644 diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 deleted file mode 100644 index e6d3b30cdb..0000000000 --- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.1 +++ /dev/null @@ -1,284 +0,0 @@ -LAMMPS (22 Sep 2017) -# biaxial NPT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -# these commads show the different methods that may be used to impose -# a constant stress through isotropic or anisotropic coupling -fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z -#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281, bins = 11 11 11 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes -Step c_1_press[1] c_1_press[2] c_1_press[3] - 0 6.3937851 7.0436438 6.4461087 - 50 7.9020345 7.303289 14.733929 - 100 8.3214325 8.385843 13.166247 - 150 5.7168419 5.6083988 9.7224198 - 200 3.8875348 4.0840705 7.9912973 - 250 4.2933724 4.2410519 7.7200953 - 300 4.5452314 4.2434949 8.6709832 - 350 5.446489 5.6166962 11.300536 - 400 6.0682558 5.7787878 12.106852 - 450 5.3884296 5.5066688 9.9100012 - 500 4.8046418 4.7115986 9.9769201 - 550 4.9043933 4.6240966 9.319336 - 600 4.6843238 4.9571246 9.5325487 - 650 5.1952989 5.195648 9.6187047 - 700 5.4163364 5.2938289 10.136655 - 750 5.6723178 5.0670261 11.415221 - 800 5.9379901 5.6402916 10.815209 - 850 5.0695389 5.3021432 10.742859 - 900 4.6498962 4.7111912 9.8453523 - 950 4.4811641 5.170132 9.421765 - 1000 4.7501483 4.2420772 9.3510803 - 1050 4.5973379 5.2046799 9.8632975 - 1100 4.7879562 4.9051316 9.8658626 - 1150 5.0528771 5.5048545 10.110913 - 1200 4.9926563 5.2482081 9.9610863 - 1250 4.8476232 4.8498859 9.5752989 - 1300 5.2932038 5.0594534 10.869545 - 1350 5.4720421 5.0830442 10.69386 - 1400 4.8175566 4.9863651 10.041898 - 1450 4.6307145 4.5615459 9.231299 - 1500 5.0296259 4.5433558 8.7180513 - 1550 4.8708444 5.1601014 10.256791 - 1600 5.5098593 5.316773 10.224386 - 1650 5.5055907 5.0516814 10.272037 - 1700 4.6965552 5.2436628 9.8272905 - 1750 5.0212307 4.740601 8.9738802 - 1800 4.7756351 5.199734 9.9929449 - 1850 4.7107092 5.177203 10.580427 - 1900 5.0935608 4.5286844 9.3036832 - 1950 4.8035855 4.894359 9.4423987 - 2000 4.5643937 4.7480477 9.4384251 - 2050 4.9314701 4.990414 10.151815 - 2100 5.9828824 5.8188026 12.262691 - 2150 5.5337303 5.4598468 10.136112 - 2200 4.892172 4.8699674 9.1629905 - 2250 4.5680591 4.5740533 9.5633545 - 2300 5.0023535 4.3948659 8.9645774 - 2350 5.2533056 4.9803884 10.255653 - 2400 5.3330196 5.3888322 10.021617 - 2450 5.2095527 4.8765336 10.135381 - 2500 5.221153 5.2974568 10.2493 - 2550 5.385331 5.0801192 10.490479 - 2600 5.3274988 5.0253548 10.147587 - 2650 4.718677 5.2710337 9.7549521 - 2700 4.5811521 4.6083971 8.1923164 - 2750 4.4743752 4.3319737 8.8690805 - 2800 5.0215013 5.2262961 9.8627954 - 2850 6.1005107 5.5994942 11.170661 - 2900 5.9673524 5.362124 10.401699 - 2950 5.5400849 5.7523993 10.292536 - 3000 4.9202636 5.1210431 10.125839 - 3050 4.5286487 5.3586164 9.8634322 - 3100 4.5719961 5.1615414 9.8027972 - 3150 5.4091919 4.8581943 9.96938 - 3200 5.522125 5.3564838 9.7638407 - 3250 4.9019062 5.2514758 9.2993079 - 3300 5.2375918 5.1439012 9.4313575 - 3350 4.750235 4.8692016 10.54193 - 3400 5.5793211 5.4184157 11.021389 - 3450 4.9022614 5.3166498 9.4629659 - 3500 4.6348617 4.4650979 9.0665548 - 3550 4.7922405 4.8961269 10.255446 - 3600 4.8914457 5.1158894 9.4736084 - 3650 5.062771 4.6725475 10.263484 - 3700 5.4842823 5.7793971 10.342915 - 3750 5.3136012 5.063065 10.398307 - 3800 4.9372149 4.9270414 9.5304748 - 3850 5.2144752 5.1716455 9.7575725 - 3900 5.0892665 5.1697057 9.918052 - 3950 5.1124507 5.354702 9.791366 - 4000 5.1255084 5.1143653 10.913101 - 4050 5.1891698 4.9913681 9.6871728 - 4100 4.7663368 4.2435014 8.3815668 - 4150 4.8060033 4.3415868 9.6553386 - 4200 4.8548303 4.8006768 9.5995801 - 4250 5.0976366 5.2683175 10.386444 - 4300 5.8921937 5.5134696 10.788143 - 4350 5.8323871 5.5255869 11.199128 - 4400 5.2464655 5.0005905 10.311055 - 4450 4.9264849 5.2499854 10.26702 - 4500 4.4431895 4.536981 8.7489096 - 4550 4.5180914 4.2080277 8.6525529 - 4600 5.1782188 5.1224059 10.683341 - 4650 5.4156233 4.8714464 10.473939 - 4700 5.3107669 5.224614 10.569391 - 4750 4.9538022 5.2509475 10.288918 - 4800 4.6976945 4.8107142 9.8299772 - 4850 5.1227936 5.0737571 10.440452 - 4900 4.7580514 4.6375995 9.1971008 - 4950 5.0647601 4.6470735 9.583131 - 5000 5.196231 5.7531491 10.409807 - 5050 5.6691323 5.7163652 12.335701 - 5100 5.3603738 5.4887106 10.961712 - 5150 4.455028 4.6494465 9.8096968 - 5200 4.7596912 4.4804896 9.3762885 - 5250 5.3144927 5.0113772 9.553101 - 5300 5.3445266 4.8262035 9.1220802 - 5350 5.1540657 5.5982676 10.765178 - 5400 5.1773418 5.2684381 10.452351 - 5450 4.8946859 5.3283747 9.8015564 - 5500 5.2009608 4.7183522 9.4558009 - 5550 5.4158589 5.5005458 10.539505 - 5600 4.7196831 5.4181991 9.6439249 - 5650 4.8333571 4.8601728 8.9350189 - 5700 5.4395698 4.9730096 10.669681 - 5750 5.2947443 5.6973259 10.020539 - 5800 5.4391993 5.5255143 10.264969 - 5850 4.9921388 5.2643827 10.217028 - 5900 5.0048643 4.7952641 8.9718929 - 5950 5.1843818 4.5987295 9.6858944 - 6000 5.0343993 4.946933 9.7436708 - 6050 4.6202714 5.3502658 10.752915 - 6100 5.6914422 5.3621964 10.281827 - 6150 5.1928763 5.9652686 10.923881 - 6200 5.0030409 5.2013891 10.056308 - 6250 4.9699876 5.2363753 9.9964211 - 6300 4.9129606 4.4558458 9.0419952 - 6350 4.6623958 4.4078264 8.528649 - 6400 4.9811441 5.1183207 10.261751 - 6450 5.3644017 5.5153937 10.401295 - 6500 5.6674981 5.7427566 11.928777 - 6550 5.1622364 5.3212928 10.067198 - 6600 4.5954278 5.1645397 10.16724 - 6650 4.9192712 5.0413326 9.95656 - 6700 4.6179845 4.5656214 9.3798952 - 6750 4.7287495 4.5071148 8.7890116 - 6800 4.8600442 4.8083512 10.245595 - 6850 5.0515531 5.1609272 10.553855 - 6900 5.1159742 5.1359869 10.594699 - 6950 4.8908884 5.0592418 9.5698704 - 7000 4.7654136 4.7530776 8.9439321 - 7050 4.779293 4.7534957 9.7244349 - 7100 5.2265831 5.6869073 10.32717 - 7150 5.4019177 5.15174 10.457567 - 7200 4.9817102 5.0596098 10.337574 - 7250 5.1836654 5.6065238 10.723108 - 7300 4.2916569 4.457143 8.5419099 - 7350 4.3906104 4.5439294 9.0805415 - 7400 4.998572 5.3386063 10.491418 - 7450 5.1109022 5.0506801 10.636116 - 7500 5.0248381 5.019932 10.217023 - 7550 5.0109265 5.1438717 9.9032426 - 7600 4.6628614 4.6204146 8.9459669 - 7650 4.8930717 5.0650009 10.049331 - 7700 4.9373454 5.6265835 10.210644 - 7750 5.5001067 5.3133253 10.667995 - 7800 5.0816102 5.0125753 10.591986 - 7850 4.9638046 5.1969015 9.9728333 - 7900 4.8438207 4.9217213 8.9978809 - 7950 4.7318805 4.6248537 8.6806596 - 8000 5.2808543 5.2892613 10.932535 - 8050 5.9609722 5.87087 10.47602 - 8100 5.2190231 5.6693244 11.244536 - 8150 5.3481127 5.2849903 10.222845 - 8200 4.7833053 4.7404657 9.2034474 - 8250 4.5461994 4.510467 10.294452 - 8300 4.6025175 4.8332817 8.7967546 - 8350 5.0389897 5.6642908 10.243402 - 8400 4.8414338 4.8925143 9.3653631 - 8450 5.5087429 4.7830361 10.831666 - 8500 5.2678146 5.1697789 9.9105782 - 8550 5.1211843 4.9097801 9.4165956 - 8600 5.8239149 5.0821022 10.803261 - 8650 5.3620154 5.5831747 11.16202 - 8700 5.1625813 4.8791404 10.537681 - 8750 4.5622461 5.0157549 10.013227 - 8800 4.4051517 5.0224553 9.6364273 - 8850 4.1711629 4.635617 8.5470244 - 8900 4.7049907 5.2458435 10.100728 - 8950 4.8568883 5.2360772 9.2306469 - 9000 5.0091899 5.2203574 10.718541 - 9050 5.1037824 4.9022451 10.24271 - 9100 5.0789015 4.9331454 9.173614 - 9150 5.3865455 5.3427553 11.40199 - 9200 5.5089482 5.9423232 10.976063 - 9250 5.1353552 5.0650262 10.040607 - 9300 4.6761948 4.9155175 9.6413722 - 9350 4.4780834 4.3934708 8.7049819 - 9400 4.2561799 4.7906324 9.046134 - 9450 5.6162819 5.2881846 9.9040868 - 9500 5.7554547 5.6111262 10.23849 - 9550 5.4230462 5.5656045 10.908006 - 9600 5.5045685 4.9818892 9.8929535 - 9650 5.0541481 5.0183351 9.5226021 - 9700 4.9712829 5.2395398 9.9996693 - 9750 5.0960017 5.4419775 10.914719 - 9800 5.0790688 5.6378474 10.00789 - 9850 4.9661747 5.114502 9.4585052 - 9900 5.0133498 4.7456254 9.4572653 - 9950 5.3318846 4.6643122 10.096292 - 10000 5.2227687 4.8924305 9.5894615 -Loop time of 4.78247 on 1 procs for 10000 steps with 500 atoms - -Performance: 903298.340 tau/day, 2090.968 timesteps/s -99.2% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.73894 | 0.73894 | 0.73894 | 0.0 | 15.45 -Neigh | 2.9092 | 2.9092 | 2.9092 | 0.0 | 60.83 -Comm | 0.32306 | 0.32306 | 0.32306 | 0.0 | 6.76 -Output | 0.003392 | 0.003392 | 0.003392 | 0.0 | 0.07 -Modify | 0.6959 | 0.6959 | 0.6959 | 0.0 | 14.55 -Other | | 0.112 | | | 2.34 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 905 ave 905 max 905 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3340 ave 3340 max 3340 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3340 -Ave neighs/atom = 6.68 -Neighbor list builds = 4580 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:04 diff --git a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 deleted file mode 100644 index 9be4413a96..0000000000 --- a/examples/USER/uef/npt_biaxial/log.22Sep17.npt_biaxial.g++.4 +++ /dev/null @@ -1,284 +0,0 @@ -LAMMPS (22 Sep 2017) -# biaxial NPT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -# these commads show the different methods that may be used to impose -# a constant stress through isotropic or anisotropic coupling -fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z -#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281, bins = 11 11 11 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes -Step c_1_press[1] c_1_press[2] c_1_press[3] - 0 6.3937851 7.0436438 6.4461087 - 50 7.9020345 7.303289 14.733929 - 100 8.3214325 8.385843 13.166247 - 150 5.7168419 5.6083988 9.7224198 - 200 3.8875348 4.0840705 7.9912973 - 250 4.2933724 4.2410519 7.7200953 - 300 4.5452314 4.2434949 8.6709832 - 350 5.446489 5.6166962 11.300536 - 400 6.0682558 5.7787878 12.106852 - 450 5.3884296 5.5066688 9.9100012 - 500 4.8046418 4.7115986 9.9769201 - 550 4.9043933 4.6240966 9.319336 - 600 4.6843238 4.9571246 9.5325487 - 650 5.1952989 5.195648 9.6187047 - 700 5.4163364 5.2938289 10.136655 - 750 5.6723178 5.0670261 11.415221 - 800 5.9379901 5.6402916 10.815209 - 850 5.0695389 5.3021432 10.742859 - 900 4.6498961 4.7111912 9.8453524 - 950 4.4811637 5.1701321 9.4217645 - 1000 4.750149 4.2420768 9.3510788 - 1050 4.5973376 5.2046787 9.8633025 - 1100 4.7879517 4.9051339 9.8658578 - 1150 5.0528775 5.5048671 10.110905 - 1200 4.9926841 5.2482049 9.9610519 - 1250 4.8475836 4.8499116 9.5753651 - 1300 5.2930219 5.0593566 10.869335 - 1350 5.4722342 5.0830411 10.693439 - 1400 4.8165803 4.9851498 10.04213 - 1450 4.6276458 4.5642988 9.2306141 - 1500 5.0196773 4.5470773 8.7204145 - 1550 4.878246 5.1583406 10.263895 - 1600 5.4921049 5.3126759 10.274755 - 1650 5.4363266 5.1708866 9.9880665 - 1700 4.9186005 5.2841155 9.5911223 - 1750 4.9105668 4.7112031 8.9221295 - 1800 4.9833291 4.886821 9.6573393 - 1850 5.0729703 4.8331712 10.094971 - 1900 5.7220173 5.9330299 10.580261 - 1950 5.3176022 5.7140521 11.11604 - 2000 5.3247727 5.5172893 10.622834 - 2050 5.2055235 4.8768078 9.9819356 - 2100 4.4604981 4.1427844 7.8106592 - 2150 4.4406592 4.8264893 9.6662695 - 2200 5.2350836 5.1039145 10.36006 - 2250 5.3777857 5.3274609 11.357157 - 2300 5.4888334 5.9555482 10.76346 - 2350 4.6122564 4.7356468 9.0833059 - 2400 4.6670237 4.4895588 9.0619648 - 2450 4.2201177 4.2558397 9.4898835 - 2500 5.452448 5.4336384 10.50224 - 2550 5.012581 5.316158 10.324517 - 2600 5.0880279 5.1264772 10.085103 - 2650 4.8885834 5.2368982 9.6002032 - 2700 5.1549266 5.3419678 11.335447 - 2750 5.497105 5.3643445 9.9990393 - 2800 4.8826744 4.9875712 10.125435 - 2850 4.8617121 5.1282348 9.5629401 - 2900 4.7883446 4.6187804 9.0562496 - 2950 4.7656266 5.1293592 10.693811 - 3000 5.2676745 5.110172 9.3512146 - 3050 4.5749222 4.8413907 10.311305 - 3100 5.0794819 5.265009 9.1598496 - 3150 5.2078869 5.1879882 10.412548 - 3200 5.0187616 4.6226213 9.7266174 - 3250 5.1541897 4.5157063 9.8355764 - 3300 5.0721396 5.3545282 10.174356 - 3350 5.3984495 5.3222207 10.008886 - 3400 5.1263226 5.1189192 10.361534 - 3450 5.1251845 4.8312752 9.6546597 - 3500 5.1133696 5.2646289 10.320765 - 3550 4.9884235 5.3861707 9.1944042 - 3600 5.196909 5.203186 10.085965 - 3650 5.4717592 5.2205442 10.251283 - 3700 5.4429771 5.3027898 11.385714 - 3750 5.5688484 5.5980199 10.558193 - 3800 4.5239453 4.7021545 8.952588 - 3850 4.6438079 4.6409958 9.3890154 - 3900 5.1108473 4.8787691 10.665694 - 3950 5.6398426 5.4386578 10.668189 - 4000 5.063697 4.9663173 10.513266 - 4050 4.8770847 4.4603573 9.8101845 - 4100 4.3950768 4.3579384 8.3402845 - 4150 4.3355402 5.0429352 10.323111 - 4200 4.7688478 5.051487 9.0632339 - 4250 4.9879366 5.3367146 10.409554 - 4300 5.4578199 5.4889206 10.418789 - 4350 5.6598068 5.4538572 10.842349 - 4400 5.3705312 5.3796871 10.430547 - 4450 4.663804 5.058851 9.2705923 - 4500 4.3439039 4.3523422 8.1747925 - 4550 4.5414802 4.3750772 9.2702452 - 4600 4.9216199 5.2897069 10.747727 - 4650 5.5154852 5.9628437 10.5168 - 4700 5.45199 5.382787 10.654544 - 4750 4.7525419 5.4701385 9.3189378 - 4800 5.3696365 4.6134207 9.4455676 - 4850 5.2444123 5.035993 9.4148435 - 4900 5.6006507 4.8536828 10.283579 - 4950 5.155711 4.978634 10.58973 - 5000 5.0854607 4.9853307 9.2414296 - 5050 5.1098462 4.7349164 9.8739001 - 5100 5.1989395 5.0217416 9.8780949 - 5150 5.612116 5.2165007 10.338464 - 5200 5.0571356 5.3109846 10.685262 - 5250 5.4832657 5.0371665 8.9420853 - 5300 4.5312549 4.9629392 8.2478064 - 5350 5.1617038 5.0533699 10.452218 - 5400 5.7873394 5.6776926 11.926526 - 5450 5.7002516 5.243239 10.940265 - 5500 4.7896799 4.898544 10.163856 - 5550 4.9155627 4.9567495 9.4445476 - 5600 4.2447343 4.5045912 8.7732992 - 5650 5.070197 4.7343938 9.9908239 - 5700 4.9609446 5.0901934 10.812786 - 5750 5.4001631 5.5552888 10.085896 - 5800 5.4209837 4.7153245 9.6865245 - 5850 4.9801041 5.180338 9.8930439 - 5900 5.3423595 5.2341361 10.294159 - 5950 5.683047 5.6830131 10.24313 - 6000 5.0618789 5.4533644 10.713412 - 6050 5.4034888 4.6341621 10.031976 - 6100 5.1934299 4.7525347 9.1287151 - 6150 5.0092398 4.806931 10.024305 - 6200 5.3046516 5.3083532 9.6396223 - 6250 5.2824046 4.7957557 10.305279 - 6300 5.3007029 5.0071874 11.175322 - 6350 5.1128883 4.990408 9.3439118 - 6400 5.0543602 4.9971378 9.8259954 - 6450 4.8843692 4.9116343 10.08132 - 6500 4.5966453 4.8042861 9.160272 - 6550 4.8510961 4.7096646 9.8009968 - 6600 5.658307 5.2330511 10.739519 - 6650 5.2374409 5.3241249 10.291779 - 6700 4.9006975 5.0036186 9.9872029 - 6750 5.2209104 5.1826025 9.5671875 - 6800 4.5238727 4.3070529 8.6072303 - 6850 4.2617247 4.7551571 9.7302077 - 6900 5.6499354 4.8714257 10.723511 - 6950 5.6881769 5.1800721 10.18134 - 7000 5.588834 5.0104896 10.304105 - 7050 4.9404045 4.8589121 9.7096741 - 7100 5.2208179 4.9339808 9.7737491 - 7150 5.4507842 5.046485 10.734783 - 7200 4.9737171 5.5760486 9.1627431 - 7250 4.5967409 4.750471 9.315832 - 7300 5.5147308 5.3202861 10.542679 - 7350 5.7730418 5.5363574 10.384376 - 7400 4.9879586 5.2837443 9.4485798 - 7450 5.1862431 4.8357842 10.017598 - 7500 5.4528245 5.1864957 10.941774 - 7550 5.4202434 5.1089468 10.128264 - 7600 4.8063537 4.8723653 9.0364984 - 7650 4.3144701 4.6148377 9.4939315 - 7700 4.9033831 5.5327473 9.9054613 - 7750 5.0693093 5.0768222 10.473081 - 7800 5.0591805 5.6009473 10.006225 - 7850 5.15269 5.468248 10.404619 - 7900 5.1971759 5.0615117 9.9614488 - 7950 4.9771238 4.886213 9.4730722 - 8000 4.7731123 5.1111433 9.9550597 - 8050 5.1655183 5.4432364 9.6649669 - 8100 5.4597006 5.4026039 11.631184 - 8150 5.3229643 5.4394219 9.9830611 - 8200 4.5420712 4.9359646 9.0121988 - 8250 4.5455108 4.3883996 10.304568 - 8300 5.219721 5.1571958 10.305462 - 8350 4.7291561 4.7391636 9.0768372 - 8400 5.3262934 5.8221591 11.065466 - 8450 4.7583026 5.2282086 10.291955 - 8500 4.9174536 4.5701979 10.140444 - 8550 4.459922 4.8293188 9.4438719 - 8600 4.7962584 4.5811071 9.5158666 - 8650 4.6097275 4.431952 9.4350505 - 8700 5.166554 5.2000584 11.162202 - 8750 5.2353596 5.1668944 10.829751 - 8800 5.3150111 4.9983333 9.8402224 - 8850 4.9571197 4.9196589 9.4880549 - 8900 4.902223 4.7539187 10.002425 - 8950 4.9531983 5.0517321 9.7838444 - 9000 5.4003802 4.9900303 10.550808 - 9050 4.9254643 5.0678701 10.24321 - 9100 4.9902263 4.9056928 9.0326566 - 9150 5.1003677 5.1555374 10.049056 - 9200 5.2358131 5.5834504 10.354698 - 9250 5.5781649 5.1188429 10.361369 - 9300 5.2100192 5.0737267 10.074694 - 9350 5.1462976 4.8010759 9.0279769 - 9400 5.0177693 5.4890092 10.03612 - 9450 5.2507957 5.541141 10.639854 - 9500 5.836784 4.9498236 10.288015 - 9550 5.4698183 5.8761209 10.979924 - 9600 5.0534023 5.0043428 10.436057 - 9650 4.3619773 4.5413125 9.047513 - 9700 4.3777508 4.7902251 8.9501908 - 9750 4.6851974 4.3152085 8.825764 - 9800 5.7312665 4.850913 10.247637 - 9850 6.2290614 5.5480801 10.934907 - 9900 6.0316892 6.1098926 11.562223 - 9950 5.6370814 5.3933342 11.148805 - 10000 4.6429923 5.0853156 9.4267693 -Loop time of 3.06414 on 4 procs for 10000 steps with 500 atoms - -Performance: 1409858.531 tau/day, 3263.561 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.27954 | 0.30916 | 0.3866 | 8.1 | 10.09 -Neigh | 1.0657 | 1.129 | 1.2853 | 8.5 | 36.85 -Comm | 0.56334 | 0.80526 | 0.89816 | 15.6 | 26.28 -Output | 0.0032749 | 0.0041527 | 0.006541 | 2.1 | 0.14 -Modify | 0.6522 | 0.67016 | 0.69843 | 2.1 | 21.87 -Other | | 0.1464 | | | 4.78 - -Nlocal: 125 ave 130 max 122 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Nghost: 459.75 ave 470 max 448 min -Histogram: 1 0 0 0 0 1 1 0 0 1 -Neighs: 837 ave 867 max 811 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 3348 -Ave neighs/atom = 6.696 -Neighbor list builds = 4589 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 b/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 new file mode 100644 index 0000000000..640a28f9b5 --- /dev/null +++ b/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.1 @@ -0,0 +1,285 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# biaxial NPT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +# these commads show the different methods that may be used to impose +# a constant stress through isotropic or anisotropic coupling +fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z +#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 7.9021894 7.3034499 14.734246 + 100 8.3198606 8.3842654 13.16397 + 150 5.7076656 5.5982431 9.7076087 + 200 3.8796305 4.0770762 7.9770769 + 250 4.2919032 4.238322 7.7197548 + 300 4.5471904 4.2439152 8.6784073 + 350 5.4499339 5.6138035 11.342244 + 400 6.0971324 5.7822211 12.109875 + 450 5.3647873 5.5491216 10.23872 + 500 4.7330582 4.9093422 9.5012486 + 550 4.7299281 4.8129828 8.9138674 + 600 5.0292698 5.1135021 10.070768 + 650 5.1900397 5.5845625 11.350623 + 700 5.1727128 5.2582562 10.567787 + 750 4.9027287 5.191078 10.36931 + 800 4.388688 4.9604327 10.059407 + 850 4.5645376 5.0369956 9.0534539 + 900 4.5706965 4.6288161 9.4845585 + 950 4.7846561 4.9221506 9.3307162 + 1000 5.2833925 5.0190193 9.8590467 + 1050 5.1489396 5.2489756 10.687019 + 1100 5.7646259 5.602148 11.94447 + 1150 4.9866799 5.6939822 10.344135 + 1200 4.5833981 4.5773728 9.4777252 + 1250 4.7783135 4.9004848 9.2356004 + 1300 4.2398409 4.615078 8.7232141 + 1350 5.0506617 5.1063295 8.9250218 + 1400 5.7596032 5.6925832 11.16017 + 1450 5.7463278 5.8799898 11.91113 + 1500 5.4673173 5.8848951 11.6597 + 1550 5.0514131 5.1189654 10.546707 + 1600 4.9176147 4.1974593 8.7559871 + 1650 4.7931674 4.0362562 9.2200844 + 1700 4.7777009 4.60455 9.3914386 + 1750 4.9917958 4.7710286 10.165995 + 1800 5.2878704 5.5858079 11.379962 + 1850 5.4762341 5.3559539 10.721841 + 1900 4.6136909 4.5841745 9.7970945 + 1950 4.6842216 4.6974096 9.4870028 + 2000 5.184473 4.9322483 9.8842281 + 2050 4.5704007 4.8389652 9.6076323 + 2100 4.731755 5.1286396 9.6765813 + 2150 4.9627984 5.2100464 10.411354 + 2200 5.5505018 5.2407864 10.814884 + 2250 5.1845435 5.3669868 10.41897 + 2300 4.7670519 5.0308883 9.2387629 + 2350 4.9576226 4.8044307 10.012093 + 2400 4.8229281 5.4438547 10.382479 + 2450 5.248646 5.0912182 9.6595448 + 2500 4.5705024 5.2219593 9.7339159 + 2550 4.8641037 4.8403069 10.837472 + 2600 4.992522 4.9890222 10.285939 + 2650 5.0975741 4.8716384 9.1436874 + 2700 5.0915762 4.8597862 10.084163 + 2750 5.2367693 5.3621151 9.0409101 + 2800 5.622419 5.0745161 10.864692 + 2850 5.4124822 5.1270063 10.529586 + 2900 4.9512714 4.9771705 10.399134 + 2950 4.9086056 5.0481759 10.175282 + 3000 4.7222615 4.9375912 9.9580179 + 3050 4.5538609 4.3906993 8.8014332 + 3100 4.5597935 4.8460914 9.0447372 + 3150 4.5797444 4.9881963 8.9865982 + 3200 5.344343 5.9378413 10.300797 + 3250 5.7394225 5.729666 10.393771 + 3300 5.7241388 5.6422002 11.420378 + 3350 5.7371735 5.5517544 10.421863 + 3400 4.7912531 5.1087978 10.044837 + 3450 4.7552647 5.1176239 9.4485297 + 3500 4.6004309 4.3453595 8.9125932 + 3550 4.9184353 5.1436174 9.7470471 + 3600 5.1448379 5.4587206 10.165912 + 3650 5.6421488 4.7860491 10.10303 + 3700 5.3222064 4.9006491 9.5460889 + 3750 5.092313 5.2169901 9.9356306 + 3800 4.9801751 5.5561465 10.128499 + 3850 5.3094304 5.3782291 10.264236 + 3900 5.3126758 5.188821 11.351077 + 3950 4.8915881 5.1644345 10.288019 + 4000 4.5416371 4.6946129 9.3622014 + 4050 4.5022234 4.4690638 10.012634 + 4100 4.4299746 4.7336989 9.3569727 + 4150 4.7581629 4.8536378 9.0409304 + 4200 4.9710073 5.1630615 10.407298 + 4250 5.6374144 5.4881368 10.247062 + 4300 5.1408355 5.2940493 10.43495 + 4350 5.3459236 6.1022236 11.70019 + 4400 4.969296 5.3035229 9.0524362 + 4450 4.6229598 4.8806514 8.8791459 + 4500 4.9518994 4.9395758 9.7992747 + 4550 4.7885188 5.4827408 10.569473 + 4600 5.1209124 5.1413191 9.96529 + 4650 4.642043 4.6618949 10.76236 + 4700 5.1144846 5.499524 9.8381957 + 4750 4.8799532 5.3405099 10.623812 + 4800 4.6075583 4.9659041 9.7525443 + 4850 4.5846434 4.5795043 8.9731754 + 4900 4.9225237 4.7748458 9.9316644 + 4950 4.9244884 5.2020183 10.120389 + 5000 5.6517752 5.2456778 10.778682 + 5050 5.690954 5.93441 11.019793 + 5100 5.414263 4.9849471 10.286106 + 5150 4.6403857 4.6021283 8.6873358 + 5200 4.4356878 4.8433705 9.0391816 + 5250 4.9737985 4.587079 9.9192911 + 5300 5.8002123 5.311289 10.44249 + 5350 5.307608 5.2150013 10.758409 + 5400 5.5956239 5.7062478 10.239561 + 5450 4.9762354 4.8541637 9.5752211 + 5500 4.4187604 4.8494725 9.4936376 + 5550 4.8266999 4.8436252 9.8148366 + 5600 5.0972098 5.3722443 9.5084475 + 5650 5.6753757 5.5321731 11.580265 + 5700 5.4238765 5.7052353 10.573799 + 5750 4.971213 4.7631056 10.309824 + 5800 4.5834127 4.6186465 8.6771163 + 5850 4.5848316 4.6314011 9.304245 + 5900 4.9686648 4.9363314 9.20327 + 5950 5.5225484 5.4699081 9.8202357 + 6000 5.1154967 5.4159103 11.365369 + 6050 6.2280757 5.9528656 10.896266 + 6100 4.9952626 4.8579703 9.9255705 + 6150 4.9072665 4.9180355 9.3070012 + 6200 4.9980254 4.6451563 9.6882833 + 6250 4.9274701 4.843916 9.248074 + 6300 4.7151735 4.8269527 10.215966 + 6350 5.3385638 4.9034159 10.242033 + 6400 5.1869704 5.1267673 9.3800463 + 6450 5.1033726 4.7937297 9.8448947 + 6500 5.5449526 5.2691074 10.689638 + 6550 5.2074561 5.060495 9.6009695 + 6600 5.0396844 5.1516197 9.8904407 + 6650 5.1593731 5.4506319 10.462558 + 6700 4.5221329 4.5495865 8.9180743 + 6750 4.5110386 4.5741907 9.3171993 + 6800 4.7533826 4.876553 9.7084497 + 6850 5.0605867 4.973688 9.662081 + 6900 5.2087631 5.1959274 10.13267 + 6950 5.6362175 5.6963964 11.29584 + 7000 5.576673 5.9467144 11.050861 + 7050 5.0264206 5.2946524 9.6572419 + 7100 4.3402188 4.5108706 10.089382 + 7150 4.3936062 4.7647229 10.059301 + 7200 4.4855959 4.8454956 8.7993639 + 7250 4.6376839 4.510911 9.34682 + 7300 5.1789012 5.5962982 9.8488588 + 7350 5.1642017 5.7861968 11.256613 + 7400 5.579834 5.4968053 10.458099 + 7450 5.149371 5.1220487 10.334194 + 7500 4.8048448 5.3089412 9.5345436 + 7550 4.2194278 4.6923534 8.8959444 + 7600 4.6725406 5.0908615 10.476709 + 7650 5.4411341 6.0356547 9.8581093 + 7700 5.4495963 4.9208089 10.165184 + 7750 5.0399074 5.1009352 9.9838045 + 7800 5.5620123 5.44628 11.417925 + 7850 4.9256715 4.8516742 9.6209317 + 7900 4.5979669 4.4223413 9.3118322 + 7950 4.7917041 4.1972832 9.5471092 + 8000 5.1301858 4.9674852 10.424156 + 8050 5.748976 5.406546 10.373017 + 8100 5.3810447 5.4890332 10.586819 + 8150 4.9586471 5.4037102 9.9944559 + 8200 4.8044905 4.9263889 9.8245965 + 8250 5.1890626 4.8840094 9.7558687 + 8300 5.1432598 4.9320019 9.5772204 + 8350 5.4751159 5.4465332 10.829543 + 8400 5.2404265 5.8728396 10.05644 + 8450 4.4832074 4.4327489 8.9569293 + 8500 4.7544224 4.8037462 9.8855364 + 8550 5.4523169 5.2905182 9.1832957 + 8600 5.263837 5.5303415 10.025825 + 8650 5.9855618 5.8626459 10.979494 + 8700 5.5999724 6.0400058 10.170144 + 8750 4.9578968 5.5337422 10.757767 + 8800 4.9516411 5.0981136 10.107278 + 8850 5.3097468 4.8852969 9.7556365 + 8900 4.9022802 4.5332799 9.9128314 + 8950 4.5798287 4.9654454 9.3983545 + 9000 4.6863328 4.6733925 9.2061315 + 9050 5.3305895 5.1208488 10.303653 + 9100 5.2508029 4.9931355 10.111519 + 9150 5.8456247 5.4272407 11.050285 + 9200 5.5908453 4.9848894 10.085967 + 9250 5.1045049 5.2151002 9.4749781 + 9300 5.0960954 5.135387 10.252554 + 9350 5.2143619 5.011559 10.041876 + 9400 5.0022922 4.999297 9.9435905 + 9450 4.5307558 4.8357118 9.2329515 + 9500 5.2777602 4.9195148 9.6776364 + 9550 5.4997839 5.5573251 10.338272 + 9600 5.4457202 5.0366677 10.150373 + 9650 4.8065991 4.8888395 9.4042123 + 9700 4.6046806 4.9965077 10.156526 + 9750 5.3833033 5.329118 10.51264 + 9800 5.1963178 4.9792777 10.438061 + 9850 5.3142717 5.2298222 10.296422 + 9900 4.918227 5.1840342 9.0013389 + 9950 4.5248956 4.7735581 8.9338178 + 10000 5.3267032 4.9182263 10.19245 +Loop time of 3.73058 on 1 procs for 10000 steps with 500 atoms + +Performance: 1157997.888 tau/day, 2680.551 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.52144 | 0.52144 | 0.52144 | 0.0 | 13.98 +Neigh | 2.2369 | 2.2369 | 2.2369 | 0.0 | 59.96 +Comm | 0.24337 | 0.24337 | 0.24337 | 0.0 | 6.52 +Output | 0.0015652 | 0.0015652 | 0.0015652 | 0.0 | 0.04 +Modify | 0.64512 | 0.64512 | 0.64512 | 0.0 | 17.29 +Other | | 0.0822 | | | 2.20 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 912 ave 912 max 912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3370 ave 3370 max 3370 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3370 +Ave neighs/atom = 6.74 +Neighbor list builds = 4581 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 b/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 new file mode 100644 index 0000000000..65919b8955 --- /dev/null +++ b/examples/USER/uef/npt_biaxial/log.27Nov18.npt_biaxial.g++.4 @@ -0,0 +1,285 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# biaxial NPT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +# these commads show the different methods that may be used to impose +# a constant stress through isotropic or anisotropic coupling +fix 1 all npt/uef temp 0.722 0.722 0.5 iso 10 10 5 erate 0.5 0.5 ext z +#fix 1 all npt/uef temp 0.722 0.722 0.5 z 10 10 5 erate 0.5 0.5 ext xyz + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 7.9021894 7.3034499 14.734246 + 100 8.3198606 8.3842654 13.16397 + 150 5.7076656 5.5982431 9.7076087 + 200 3.8796305 4.0770762 7.9770769 + 250 4.2919032 4.238322 7.7197548 + 300 4.5471904 4.2439152 8.6784073 + 350 5.4499339 5.6138035 11.342244 + 400 6.0971324 5.7822211 12.109875 + 450 5.3647873 5.5491216 10.23872 + 500 4.7330582 4.9093422 9.5012486 + 550 4.7299281 4.8129828 8.9138674 + 600 5.0292698 5.1135021 10.070768 + 650 5.1900397 5.5845625 11.350623 + 700 5.1727128 5.2582562 10.567787 + 750 4.9027287 5.191078 10.36931 + 800 4.388688 4.9604327 10.059407 + 850 4.5645375 5.0369956 9.053454 + 900 4.5706968 4.6288162 9.4845589 + 950 4.7846558 4.9221509 9.3307157 + 1000 5.2833916 5.0190189 9.8590443 + 1050 5.1489424 5.2489801 10.687018 + 1100 5.7646249 5.6021408 11.944487 + 1150 4.9866349 5.6939763 10.344098 + 1200 4.5834696 4.5773711 9.4777656 + 1250 4.7782628 4.9003931 9.2354794 + 1300 4.2398086 4.6156458 8.7235594 + 1350 5.0516664 5.106151 8.925344 + 1400 5.7599281 5.693153 11.161569 + 1450 5.74929 5.8792255 11.905985 + 1500 5.4770201 5.8663899 11.634664 + 1550 5.0842872 5.0979505 10.526591 + 1600 4.8431505 4.2339226 8.7429902 + 1650 4.733907 4.1990477 9.0573593 + 1700 5.2670297 4.8937733 9.5161206 + 1750 5.0933882 5.0840957 10.003455 + 1800 5.0762036 5.3282866 10.370587 + 1850 5.5253602 5.8193463 11.162205 + 1900 4.9830867 5.1984155 9.9505494 + 1950 5.0833879 5.0020521 9.4919371 + 2000 5.1066344 5.1579719 9.8668875 + 2050 5.3988406 5.5046098 10.419135 + 2100 5.2433191 5.1605828 10.335759 + 2150 4.9353676 4.3373911 9.6748317 + 2200 4.5278686 4.7876115 10.186293 + 2250 5.3058781 5.1020131 10.807037 + 2300 5.3049465 5.4198068 9.4589098 + 2350 4.9691623 4.6449463 9.6883654 + 2400 5.0591959 4.6871509 10.501085 + 2450 5.6485626 5.7934938 10.40336 + 2500 4.8529542 4.8645589 9.7522638 + 2550 4.6185478 4.6833643 9.9536174 + 2600 5.3007332 5.5198106 9.9052474 + 2650 5.0990987 5.1565356 10.46545 + 2700 4.7312547 4.9440008 9.8533728 + 2750 5.1788563 5.2765759 10.151495 + 2800 4.9110276 4.7663836 9.1840513 + 2850 5.2237628 5.1726783 11.249313 + 2900 5.2809505 5.5441058 10.201093 + 2950 5.3076988 5.6051526 10.514995 + 3000 5.1184905 5.5419286 10.601518 + 3050 4.6911631 5.3808828 10.457661 + 3100 4.8607911 4.9603546 9.4301575 + 3150 4.5154241 4.2391572 8.793511 + 3200 4.9225855 4.8553117 10.097738 + 3250 5.2806657 5.0883118 10.019105 + 3300 5.6211399 5.4189754 10.031345 + 3350 5.3272587 5.3012125 10.511112 + 3400 5.1537795 5.2751757 10.586364 + 3450 4.9755489 4.7379757 9.5319067 + 3500 4.639772 4.2724622 8.6134078 + 3550 4.429646 4.4744424 9.6934076 + 3600 4.7884194 5.0029165 10.298349 + 3650 5.187187 5.3525308 10.776252 + 3700 5.4484919 5.252409 10.249911 + 3750 5.4023844 5.4702812 10.510152 + 3800 5.5390275 5.5558904 11.637892 + 3850 5.0607613 4.7094507 10.655553 + 3900 4.7039017 4.6735214 9.2616315 + 3950 4.4841881 4.177444 8.2781294 + 4000 4.4476096 4.644048 9.2288327 + 4050 5.3377013 5.4161214 10.327745 + 4100 5.5088439 5.472021 10.160241 + 4150 5.2563495 5.7227923 10.944344 + 4200 5.7697457 5.9285173 11.01361 + 4250 5.5588517 5.6191129 10.10097 + 4300 4.7979693 5.160914 8.9640624 + 4350 4.5787515 4.921702 9.3202685 + 4400 4.7553573 4.6660054 9.1421637 + 4450 5.1209721 5.6522 10.972614 + 4500 5.4707365 5.73796 11.766141 + 4550 5.3811545 5.1951701 10.080047 + 4600 4.6186413 4.6707428 10.171706 + 4650 4.5253667 4.2958906 8.357902 + 4700 4.7727574 5.0615193 9.9593597 + 4750 5.1177598 4.818905 10.331896 + 4800 5.7793785 5.4309352 10.528804 + 4850 5.2737538 5.3926071 10.911118 + 4900 4.9248662 5.1161409 9.9553052 + 4950 4.5438154 4.5542986 9.7231827 + 5000 4.5792931 5.037416 9.4471877 + 5050 5.4657934 4.6463368 10.525459 + 5100 5.1929248 5.3150781 10.600995 + 5150 5.2424553 5.6037815 11.400125 + 5200 5.3554776 5.1462851 10.312698 + 5250 4.5621722 4.6536715 8.9629186 + 5300 4.3302701 4.0032142 8.2178001 + 5350 4.4089902 4.4070826 9.98944 + 5400 5.4923486 5.243049 9.8450519 + 5450 5.9651716 5.7058525 10.868126 + 5500 5.7119235 5.8769703 11.394999 + 5550 5.2139995 5.1454474 11.033523 + 5600 4.7379338 4.942432 9.4940872 + 5650 4.5231066 4.4487457 8.7695323 + 5700 4.708033 4.6389279 9.6186407 + 5750 4.9251705 5.2008226 9.7552276 + 5800 5.1820518 5.1298277 9.9062279 + 5850 5.1682714 5.5417945 10.510452 + 5900 5.3240541 5.447607 10.196406 + 5950 5.0230117 5.2275764 10.023658 + 6000 4.7808616 4.9572765 9.3874738 + 6050 5.3665339 5.0259733 10.08598 + 6100 4.3792707 4.498684 9.2981408 + 6150 5.5644405 5.0701965 9.6641099 + 6200 5.5089344 5.2024156 10.681185 + 6250 5.2016449 5.1923702 10.58283 + 6300 5.0820055 4.9044561 9.2080884 + 6350 5.2807998 5.3178136 10.960667 + 6400 5.2356859 5.3937694 10.444279 + 6450 4.9141004 5.0424402 9.8583318 + 6500 4.730159 4.3778519 8.3347658 + 6550 4.4680692 4.1557934 8.2081388 + 6600 5.1035106 5.5797859 10.011564 + 6650 6.0395438 5.9206816 11.127476 + 6700 5.8615491 6.3110504 11.394217 + 6750 5.6633011 5.4526334 11.052886 + 6800 5.0080995 5.057409 10.062444 + 6850 4.7698449 4.6981695 9.4610313 + 6900 4.7354667 4.37141 9.9744222 + 6950 4.7911975 5.0203879 9.7662892 + 7000 5.2428984 5.5119167 10.442666 + 7050 4.682975 4.9969905 9.7644109 + 7100 5.01603 5.0199261 10.21075 + 7150 5.1231276 4.9029064 9.6731597 + 7200 5.0505154 4.7700974 9.368416 + 7250 4.5832902 4.862384 9.3573655 + 7300 4.9754198 4.8922117 10.281497 + 7350 5.3775547 5.0882575 9.6564673 + 7400 4.7805076 5.1817965 10.671837 + 7450 4.9477584 4.8112232 10.521294 + 7500 5.0159196 4.5830513 10.315726 + 7550 4.5457712 4.3742672 8.2750411 + 7600 4.5562458 4.7579489 9.4828599 + 7650 5.0911757 5.4088122 10.241168 + 7700 5.8998331 5.158098 10.533196 + 7750 5.2573341 5.6316362 11.582955 + 7800 5.5208399 5.5724767 10.552019 + 7850 4.2579682 4.4297565 9.0720476 + 7900 4.4805314 4.2668697 8.5308736 + 7950 5.0361726 4.7345663 9.053936 + 8000 4.9653741 5.0377825 9.7367426 + 8050 5.6899681 5.2423091 10.791377 + 8100 5.7463021 5.7578506 10.412899 + 8150 5.2759991 5.4104042 10.070985 + 8200 5.458295 5.8367826 11.164512 + 8250 5.0428079 5.1837655 9.9204724 + 8300 4.6809536 4.5537928 9.4697904 + 8350 4.8813528 4.8364418 10.099128 + 8400 4.7682666 5.2049648 9.5798138 + 8450 5.0663986 4.5988946 9.4560847 + 8500 4.9165971 4.860584 9.5549796 + 8550 5.3481259 5.3835901 10.844579 + 8600 5.5975372 5.5878997 10.943816 + 8650 4.3283508 4.7046268 8.8049918 + 8700 5.089621 4.7172523 9.9647935 + 8750 5.1012591 4.5471991 9.9327107 + 8800 5.268596 5.2408733 10.867265 + 8850 5.4760815 4.9428094 10.748623 + 8900 4.6100656 5.146025 10.553286 + 8950 4.4411237 5.0226732 9.6226103 + 9000 4.3935196 4.591527 8.462486 + 9050 4.5657639 4.7316578 10.336313 + 9100 4.8547926 4.7683761 10.473456 + 9150 5.2718858 5.1274542 9.4487204 + 9200 5.6536596 5.0085121 10.538513 + 9250 4.8978022 5.5399287 11.227994 + 9300 5.1949276 5.2477679 9.4501652 + 9350 4.614631 4.5123768 8.9589058 + 9400 4.9004056 5.2279931 9.6976631 + 9450 5.2069446 5.0233778 9.9944637 + 9500 5.9550777 5.5494597 11.15982 + 9550 5.0613169 5.0592065 9.7027551 + 9600 5.1136537 4.826222 10.615866 + 9650 4.7063369 5.1309647 9.3445464 + 9700 5.03856 4.8819472 9.6814972 + 9750 4.5600617 4.8391307 10.209608 + 9800 4.9439503 4.9625294 10.613186 + 9850 5.4817844 5.1051439 10.055569 + 9900 5.0079108 4.8100264 9.0562123 + 9950 4.8676477 4.6891998 9.3252737 + 10000 4.9643649 5.9339432 10.816137 +Loop time of 1.53648 on 4 procs for 10000 steps with 500 atoms + +Performance: 2811615.788 tau/day, 6508.370 timesteps/s +94.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13145 | 0.13475 | 0.13936 | 0.9 | 8.77 +Neigh | 0.56509 | 0.57539 | 0.58617 | 1.2 | 37.45 +Comm | 0.34317 | 0.35857 | 0.37377 | 2.4 | 23.34 +Output | 0.0018919 | 0.0046901 | 0.012948 | 7.0 | 0.31 +Modify | 0.38306 | 0.39165 | 0.39657 | 0.8 | 25.49 +Other | | 0.07143 | | | 4.65 + +Nlocal: 125 ave 128 max 122 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 457.5 ave 468 max 453 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Neighs: 850.75 ave 868 max 824 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 3403 +Ave neighs/atom = 6.806 +Neighbor list builds = 4589 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 deleted file mode 100644 index 2c13448192..0000000000 --- a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.1 +++ /dev/null @@ -1,281 +0,0 @@ -LAMMPS (22 Sep 2017) -# uniaxial NVT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281, bins = 11 11 11 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes -Step c_1_press[1] c_1_press[2] c_1_press[3] - 0 6.3937851 7.0436438 6.4461087 - 50 10.369902 10.999889 6.5437384 - 100 12.411384 13.145871 7.8892802 - 150 12.88182 12.114068 7.5155182 - 200 10.375571 10.979773 6.5624056 - 250 10.158901 10.251273 5.4525068 - 300 10.011314 9.8371382 5.4031393 - 350 9.4890008 9.7992108 5.054963 - 400 9.1715116 9.2647886 4.9600208 - 450 9.8495961 9.3353483 4.986786 - 500 9.5903809 8.576173 4.8252116 - 550 8.8057509 9.7152078 4.9089022 - 600 8.9743682 10.031277 4.8924072 - 650 10.233852 9.3059527 5.1977058 - 700 9.2361906 9.6439971 5.0923763 - 750 10.449751 9.5911465 5.2548714 - 800 9.8366857 9.9873885 4.9456956 - 850 10.266351 9.9620134 5.0602713 - 900 9.6325813 9.3910946 5.1466624 - 950 9.1911919 9.1519006 4.8275345 - 1000 9.2871712 9.8508501 5.2674099 - 1050 9.7052035 10.291793 5.160359 - 1100 9.9425552 10.361827 5.5520484 - 1150 10.377563 10.26588 5.5997436 - 1200 9.6368269 10.354413 5.4137873 - 1250 9.2071055 9.1706334 4.9800411 - 1300 9.7140516 8.7257777 4.8536943 - 1350 10.145983 9.8247797 4.8921813 - 1400 9.1998975 9.6935675 5.2269871 - 1450 9.4838136 8.9035726 4.6867121 - 1500 9.066389 9.811658 4.8875316 - 1550 10.007083 9.8946118 5.204609 - 1600 9.722137 9.9291588 5.326712 - 1650 9.7424614 9.6995966 5.3577819 - 1700 9.7185135 9.5922931 5.385856 - 1750 9.6368481 8.1414594 5.0046079 - 1800 9.8065782 9.6798036 4.92473 - 1850 9.0463737 10.024205 5.6495695 - 1900 9.0774484 10.527582 5.0363426 - 1950 9.1691461 10.049703 4.8517514 - 2000 9.7619602 10.049532 5.2088038 - 2050 9.9203348 9.8056395 5.7699852 - 2100 9.1455665 9.5864018 5.1410542 - 2150 8.8501135 9.7917307 5.141824 - 2200 9.1433685 9.8168548 5.1742441 - 2250 9.3248968 10.454532 5.5456356 - 2300 10.210505 9.361499 5.0935226 - 2350 9.5041186 9.598986 5.2451005 - 2400 8.968896 9.2811921 4.7799868 - 2450 9.8201159 10.133892 4.9981817 - 2500 9.4421084 9.7875766 5.4124809 - 2550 9.6410643 9.9148309 5.0603288 - 2600 9.3810676 9.5346849 5.3233836 - 2650 9.2340337 8.7233538 5.0361302 - 2700 9.405597 9.7848488 4.7537042 - 2750 9.9447412 9.2366502 4.9736459 - 2800 10.189443 9.452684 5.624362 - 2850 9.6680124 9.0941543 5.0101469 - 2900 8.4350889 9.1595018 4.7706866 - 2950 9.0056117 9.3498593 4.7655963 - 3000 9.4795416 9.7400747 5.4705868 - 3050 9.6605264 9.4558374 5.1240166 - 3100 9.681451 9.7966554 5.3174458 - 3150 9.7887528 9.7371194 4.9349103 - 3200 9.9720054 9.5592538 5.2306417 - 3250 10.185023 9.9436037 5.4127312 - 3300 9.9670676 9.6069307 5.026261 - 3350 9.0090411 9.5975249 4.8881019 - 3400 9.6535707 9.748683 4.9933873 - 3450 9.7774977 9.7570511 4.8512619 - 3500 9.7250053 10.36386 5.4057249 - 3550 9.567788 9.773413 5.3936671 - 3600 9.2094148 9.0211247 5.2328675 - 3650 9.3512098 9.73407 4.576624 - 3700 9.159074 9.2611591 5.2996448 - 3750 9.4772798 8.9792211 5.1007079 - 3800 9.3898357 9.1150609 5.2126508 - 3850 9.2466312 9.1460651 4.867472 - 3900 9.9316993 9.3061137 5.1219265 - 3950 9.2550913 9.780254 5.371885 - 4000 10.005356 9.7328972 5.2535791 - 4050 9.5228242 9.5134113 5.4181393 - 4100 9.576808 10.082425 5.1272491 - 4150 10.20265 9.6667058 5.529118 - 4200 9.9443671 10.09427 5.6163734 - 4250 9.4956875 9.9462818 5.0820085 - 4300 10.350144 10.003702 5.1621505 - 4350 10.119486 9.8691507 5.4913457 - 4400 9.4991604 10.516185 5.2512264 - 4450 9.0812854 9.2835603 5.1695714 - 4500 9.7538478 8.5298834 4.5954607 - 4550 9.8920394 9.3581299 5.202587 - 4600 9.2694921 9.3338291 5.201958 - 4650 10.925818 9.5062049 4.8694531 - 4700 11.020014 10.130224 5.582409 - 4750 9.5005142 9.3571561 5.456739 - 4800 9.6670147 9.6628702 5.0451252 - 4850 9.134147 9.1308788 4.7950594 - 4900 9.7466206 8.6171443 4.8716275 - 4950 9.0397505 9.1996036 5.2010502 - 5000 9.6898652 9.8914655 5.3959279 - 5050 10.06771 9.7523891 5.3690408 - 5100 10.000963 9.6279379 5.4077384 - 5150 9.8686159 10.179702 5.0686824 - 5200 9.8866247 9.725152 5.4350049 - 5250 9.2068346 10.214424 5.3187713 - 5300 9.713992 9.8069045 5.496359 - 5350 9.423852 9.364085 5.2144606 - 5400 9.4350241 9.5584633 5.0339001 - 5450 10.555124 10.784922 5.1938072 - 5500 9.4147344 10.33187 5.4360602 - 5550 9.8514653 9.6575827 5.4959779 - 5600 9.3138107 9.6592624 4.941387 - 5650 9.1224809 8.7112257 5.0435936 - 5700 8.8289158 10.749686 4.8916132 - 5750 9.7200279 10.030606 5.2033161 - 5800 9.8439873 9.6289015 5.5131934 - 5850 9.6257294 9.4128988 4.9196038 - 5900 9.7490214 9.5776313 5.0301815 - 5950 9.1430855 10.108944 5.1406243 - 6000 9.3358644 9.5633737 4.9787073 - 6050 9.4432774 8.9464304 5.1466052 - 6100 8.8878373 9.5048946 4.9190238 - 6150 9.6451898 9.2419823 5.0159841 - 6200 9.5042173 8.9414307 5.2634247 - 6250 9.0896505 9.7230651 5.3340322 - 6300 8.8100599 8.8781352 5.4117914 - 6350 9.3104601 9.0233294 5.3136432 - 6400 9.368101 9.6387362 4.7833216 - 6450 10.334343 9.8384149 5.3606204 - 6500 9.8824036 10.022627 6.0857086 - 6550 9.7034443 10.026765 5.17604 - 6600 9.3757845 9.899268 5.2301359 - 6650 10.540821 10.4343 5.5287065 - 6700 9.6317649 9.8923579 5.6045768 - 6750 9.5982772 10.07897 5.1221451 - 6800 10.239883 10.189967 5.3167447 - 6850 10.017271 9.7680902 5.229621 - 6900 9.6200416 10.129301 5.1998759 - 6950 9.0361417 8.923798 5.1652612 - 7000 9.3153521 9.063054 4.6860773 - 7050 8.6434091 9.0363436 4.7811975 - 7100 9.4955395 9.3830541 5.022538 - 7150 9.3392402 9.1847119 5.1544622 - 7200 9.4676321 9.8370036 4.8854442 - 7250 9.5115882 10.350324 4.9780525 - 7300 9.6025583 9.6247917 5.473794 - 7350 9.8919524 10.049446 4.9816931 - 7400 9.6814319 9.9410894 5.265078 - 7450 9.4130955 10.191436 5.2531256 - 7500 9.8114668 8.8461635 5.0562894 - 7550 10.321567 9.4730124 5.2043655 - 7600 9.5059024 9.8330367 5.0749721 - 7650 10.067084 10.606423 5.5598818 - 7700 10.896159 10.084281 5.5159718 - 7750 9.754306 10.162301 5.2475876 - 7800 9.7278145 9.801009 5.0685504 - 7850 9.8639905 10.323104 5.2458864 - 7900 9.7246799 9.1377357 5.1841319 - 7950 10.381792 9.6977533 5.0977386 - 8000 9.7265224 9.2999829 4.7925571 - 8050 9.5203288 9.3144956 4.7539211 - 8100 9.6900973 9.6614063 5.304712 - 8150 9.713677 9.9154149 4.8178575 - 8200 9.4733597 9.8948632 5.036112 - 8250 9.7783036 9.9554334 5.3355682 - 8300 9.4034783 9.9156801 5.5539279 - 8350 9.2984025 9.2013949 5.0753991 - 8400 9.9299078 9.6166801 5.115776 - 8450 9.526737 9.3312125 4.7800587 - 8500 9.581956 10.065906 4.9756092 - 8550 9.2767953 9.326006 5.3024978 - 8600 9.799968 8.4660845 5.0199109 - 8650 9.8985354 10.127852 4.9098064 - 8700 8.7952691 10.521133 5.6840528 - 8750 9.8299997 9.5588553 5.3085734 - 8800 9.0811776 9.5704532 5.1684993 - 8850 9.8303571 9.7618932 5.1251259 - 8900 9.9238794 9.9654863 5.2999683 - 8950 10.851304 9.9682289 5.4133763 - 9000 9.5523794 9.1890766 5.1469144 - 9050 9.7461948 8.9611236 4.9490826 - 9100 10.138917 9.6757567 5.0473544 - 9150 9.4869835 9.4786575 5.0142464 - 9200 10.263518 10.079135 5.1493398 - 9250 9.8691684 9.0908275 5.3221203 - 9300 9.8586707 9.4177643 5.1525265 - 9350 9.3375816 9.9167208 5.4846207 - 9400 9.5603903 9.4813199 4.6237495 - 9450 10.30892 9.5217736 5.6163214 - 9500 9.327949 9.9831649 4.8923915 - 9550 9.8421656 9.3202702 5.3352046 - 9600 8.8543704 9.4556702 4.6430041 - 9650 10.103399 9.2161072 4.8658062 - 9700 9.507811 9.9647378 5.227369 - 9750 9.4988096 8.9942893 5.2491418 - 9800 9.8007958 9.234452 5.1740203 - 9850 9.6029685 10.076042 5.023107 - 9900 9.4035691 10.13782 5.2775777 - 9950 9.6517135 10.355994 5.3035779 - 10000 9.9157616 9.7741952 5.5269431 -Loop time of 3.47119 on 1 procs for 10000 steps with 500 atoms - -Performance: 1244529.812 tau/day, 2880.856 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.53077 | 0.53077 | 0.53077 | 0.0 | 15.29 -Neigh | 2.219 | 2.219 | 2.219 | 0.0 | 63.93 -Comm | 0.21866 | 0.21866 | 0.21866 | 0.0 | 6.30 -Output | 0.0027909 | 0.0027909 | 0.0027909 | 0.0 | 0.08 -Modify | 0.41956 | 0.41956 | 0.41956 | 0.0 | 12.09 -Other | | 0.08042 | | | 2.32 - -Nlocal: 500 ave 500 max 500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 908 ave 908 max 908 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3489 ave 3489 max 3489 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3489 -Ave neighs/atom = 6.978 -Neighbor list builds = 4567 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 b/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 deleted file mode 100644 index 276eb2f443..0000000000 --- a/examples/USER/uef/nvt_uniaxial/log.22Sep17.npt_uniaxial.g++.4 +++ /dev/null @@ -1,281 +0,0 @@ -LAMMPS (22 Sep 2017) -# uniaxial NVT deformation of WCA fluid - -units lj -atom_style atomic - - -pair_style lj/cut 1.122562 -read_data data.wca - orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 500 atoms - reading velocities ... - 500 velocities -pair_coeff 1 1 1.0 1.0 -pair_modify shift yes - -neighbor 0.5 bin -neigh_modify delay 0 - -change_box all triclinic - triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) - -fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 - -fix 2 all momentum 100 linear 1 1 1 - -#dump 1 all atom 25 dump.lammpstrj - -#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs - -thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] - -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.62256 - ghost atom cutoff = 1.62256 - binsize = 0.811281, bins = 11 11 11 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton/tri - stencil: half/bin/3d/newton/tri - bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes -Step c_1_press[1] c_1_press[2] c_1_press[3] - 0 6.3937851 7.0436438 6.4461087 - 50 10.369902 10.999889 6.5437384 - 100 12.411384 13.145871 7.8892802 - 150 12.88182 12.114068 7.5155182 - 200 10.375571 10.979773 6.5624056 - 250 10.158901 10.251273 5.4525068 - 300 10.011314 9.8371382 5.4031393 - 350 9.4890008 9.7992108 5.054963 - 400 9.1715116 9.2647886 4.9600208 - 450 9.8495961 9.3353483 4.986786 - 500 9.5903809 8.576173 4.8252116 - 550 8.8057509 9.7152078 4.9089022 - 600 8.9743682 10.031277 4.8924072 - 650 10.233852 9.3059527 5.1977058 - 700 9.2361906 9.6439971 5.0923762 - 750 10.449751 9.5911465 5.2548714 - 800 9.8366858 9.9873885 4.9456956 - 850 10.266351 9.9620134 5.0602713 - 900 9.6325811 9.3910947 5.1466627 - 950 9.1911906 9.1518996 4.8275336 - 1000 9.2871726 9.8508561 5.2674079 - 1050 9.7052019 10.291782 5.1603609 - 1100 9.9425827 10.361848 5.5520588 - 1150 10.37757 10.265891 5.5997246 - 1200 9.6367069 10.354451 5.4138749 - 1250 9.2075006 9.1705136 4.9806417 - 1300 9.7126123 8.7247301 4.8528533 - 1350 10.146034 9.8319205 4.8958266 - 1400 9.19638 9.7052094 5.2332913 - 1450 9.4667073 8.9014702 4.7073387 - 1500 9.0949401 9.8381729 4.8904182 - 1550 10.068959 9.8096692 5.1613658 - 1600 10.131443 9.7086921 5.0913546 - 1650 9.9557572 9.9183989 5.2635245 - 1700 9.3820418 8.6135867 4.9395498 - 1750 8.9486365 9.3433293 5.2674469 - 1800 10.352322 10.354432 5.3335153 - 1850 8.9629784 9.6172224 5.0824828 - 1900 8.5429652 9.749815 5.1577895 - 1950 8.9828002 8.9631646 5.0948426 - 2000 9.4171989 9.7122117 5.1386251 - 2050 9.767299 9.6146113 4.8965319 - 2100 10.049399 10.02243 5.3856622 - 2150 9.2639644 10.09669 5.3020322 - 2200 9.1916162 10.841127 5.0271109 - 2250 9.9859708 8.519568 5.24568 - 2300 9.9462279 9.5850706 5.0632906 - 2350 9.8043011 9.7605126 5.3148323 - 2400 9.089818 9.6474522 5.0012486 - 2450 9.655874 9.3255636 4.8291262 - 2500 9.0259445 9.3074827 5.1593031 - 2550 9.1610478 9.7356492 5.0741161 - 2600 9.3153881 9.3936949 5.4830363 - 2650 9.6212696 9.598252 4.7172875 - 2700 9.318906 9.665656 5.1917527 - 2750 9.6613838 9.7106796 5.1843146 - 2800 10.231844 9.9407641 4.6940455 - 2850 10.008093 9.2781076 5.2624957 - 2900 10.464168 9.808666 5.1457978 - 2950 9.7080601 9.6972304 5.406456 - 3000 9.6851209 10.050737 5.1198394 - 3050 8.9093581 9.213428 5.233108 - 3100 8.8098921 9.6607476 4.9625331 - 3150 8.6608386 9.7503441 5.0737533 - 3200 9.7004403 9.6748778 5.0734462 - 3250 10.077054 10.318711 5.3233841 - 3300 10.63887 9.4901739 5.516542 - 3350 10.232909 9.3407073 5.4989967 - 3400 9.8854134 9.9542625 5.1982468 - 3450 9.9388203 9.3394716 4.8135833 - 3500 9.2514026 9.5857527 5.4605449 - 3550 8.3940282 9.0549836 4.6951548 - 3600 8.7696659 9.6262816 4.6302087 - 3650 9.0695173 8.8520895 5.0814723 - 3700 9.4700744 9.2777557 4.6825004 - 3750 9.0221844 9.3407486 5.3984156 - 3800 9.1478369 9.1420043 5.3024474 - 3850 9.2652818 9.700053 5.3355364 - 3900 10.248456 9.2480211 5.2375956 - 3950 9.8259922 9.6130415 5.5978761 - 4000 9.404877 9.7931698 5.3767927 - 4050 10.131713 9.7047295 5.2964594 - 4100 9.8128638 9.4253237 5.5308166 - 4150 10.25183 9.1333595 5.1957555 - 4200 10.449736 9.295762 4.7863033 - 4250 9.7304858 9.4482515 5.356439 - 4300 9.2773777 9.4110855 4.9879246 - 4350 8.9325082 9.3429549 5.0410132 - 4400 9.2603855 9.7905381 4.7436126 - 4450 8.7600443 9.9160722 5.196316 - 4500 9.0824514 10.036035 4.873051 - 4550 9.3884333 9.6644343 5.1154951 - 4600 9.8181676 9.6385118 5.3639835 - 4650 9.1574799 9.5386974 4.7487094 - 4700 10.275911 9.5383553 5.1084297 - 4750 9.2476854 9.3353591 5.4773008 - 4800 9.3422407 9.1931821 4.9210291 - 4850 9.9033126 9.6443642 5.1334553 - 4900 9.8469467 9.6836455 5.5101146 - 4950 10.211229 9.760253 5.0151668 - 5000 9.3256273 10.109873 5.4129479 - 5050 9.9704879 9.8504809 5.2191163 - 5100 9.4820718 9.711504 4.9633504 - 5150 9.2952171 9.6955742 5.3214246 - 5200 9.8400791 9.4763906 4.9149518 - 5250 10.080112 9.5634741 5.1701348 - 5300 9.4221014 9.8149742 5.3605931 - 5350 8.8228402 10.121343 5.3192212 - 5400 9.7318719 10.508763 5.0044083 - 5450 8.7429847 9.6583774 5.033313 - 5500 9.9243256 10.239521 5.2956506 - 5550 9.6088558 9.8555986 5.359257 - 5600 10.904352 10.72033 5.7874034 - 5650 9.4774477 9.7246962 5.596949 - 5700 9.8527139 9.2188245 4.6518586 - 5750 9.7932375 9.2763721 4.6663307 - 5800 9.5630073 9.1704583 5.4784197 - 5850 10.159996 9.5206168 5.0012706 - 5900 9.1667978 9.6891715 5.1959301 - 5950 9.2194131 9.2170699 5.1653264 - 6000 9.5917124 9.2038051 5.1004966 - 6050 9.4141124 9.9166471 5.0535712 - 6100 10.231166 9.7746591 5.2399634 - 6150 9.6054192 9.34446 5.0711646 - 6200 9.9279645 8.9546561 5.4698039 - 6250 9.1581437 8.95439 4.9336111 - 6300 8.9257232 9.0665473 5.188718 - 6350 9.7685695 9.0822789 4.8454457 - 6400 9.5140226 9.5073414 5.3420644 - 6450 9.5379198 9.3316002 5.1940338 - 6500 10.216584 9.8982859 5.2790157 - 6550 10.221286 10.913585 5.4521496 - 6600 10.925166 10.088055 5.2079758 - 6650 10.012501 9.3870455 5.1740433 - 6700 10.176139 9.4869588 5.3783369 - 6750 9.2819415 8.1431975 4.8256476 - 6800 9.790723 9.7932943 5.3602927 - 6850 9.1327199 9.8354267 5.1356642 - 6900 9.240909 9.3854618 5.1767268 - 6950 10.652806 9.4355671 5.1314851 - 7000 9.1676917 10.055501 5.2824651 - 7050 9.6486488 9.1063089 4.9596976 - 7100 9.3733678 9.5875095 5.0882285 - 7150 9.282243 9.354934 4.6752644 - 7200 8.7370777 10.1445 5.0217245 - 7250 9.563419 9.929442 5.1720916 - 7300 9.9128346 9.2426863 5.3595023 - 7350 9.9319949 9.9479477 5.4844629 - 7400 9.4671739 9.2380048 5.3274217 - 7450 9.7531193 9.4075641 4.9426738 - 7500 10.331422 9.4704554 5.3036636 - 7550 8.7724434 9.663179 4.9492563 - 7600 10.222748 9.1674852 4.8135992 - 7650 9.5288583 8.5866929 5.0342955 - 7700 8.8832847 8.8035037 4.6184473 - 7750 9.4847076 9.7969656 5.0035855 - 7800 9.2782486 9.1283641 5.3151299 - 7850 8.962989 8.7729872 5.0374817 - 7900 9.6336556 9.4975426 4.9832641 - 7950 10.125279 10.044247 5.2740873 - 8000 9.9705097 9.6925988 5.2344188 - 8050 9.7836318 9.5794261 4.9174534 - 8100 10.79561 10.04809 5.1604639 - 8150 9.7261726 10.372878 5.3083843 - 8200 10.338569 10.08189 5.6555172 - 8250 9.7833315 9.9834209 5.3790753 - 8300 9.5857944 9.6052323 5.0689289 - 8350 9.6706688 9.6189242 4.7725678 - 8400 10.570423 9.5786093 5.1894242 - 8450 9.6514599 10.168359 5.0733592 - 8500 10.273682 9.9179284 5.4014563 - 8550 9.3120287 10.146837 4.9895115 - 8600 9.511943 9.644112 5.462624 - 8650 10.380674 9.1117114 5.156727 - 8700 10.068596 8.7687113 5.1440814 - 8750 9.2484971 9.2477678 4.9318794 - 8800 9.7298469 8.9480303 5.1151321 - 8850 9.7299502 10.415138 4.7902908 - 8900 10.966912 10.732962 5.4793574 - 8950 10.328384 9.9501313 5.6238396 - 9000 9.7385041 9.8319224 5.1926497 - 9050 9.7971055 9.5740203 5.1111302 - 9100 9.7789727 9.9281901 5.1786549 - 9150 9.9306964 9.3360599 4.9524547 - 9200 9.8798841 10.240752 5.1691344 - 9250 10.185445 9.4934917 4.9188964 - 9300 8.9184663 8.9349408 4.8079511 - 9350 9.6552187 9.9846949 4.9619969 - 9400 10.304306 9.2298208 5.2822855 - 9450 9.8379613 10.041703 5.4186514 - 9500 10.221443 9.5342818 4.8929802 - 9550 9.9723047 10.072856 5.4169676 - 9600 9.3923879 9.2984387 5.4452785 - 9650 8.9072589 9.7482374 4.7835208 - 9700 9.8370121 10.205922 5.0385145 - 9750 9.4274542 9.4653248 5.6340681 - 9800 9.7668106 9.3265705 5.3154126 - 9850 10.422549 10.362922 5.361592 - 9900 9.6264407 9.9790162 5.6381052 - 9950 10.35018 9.8853593 5.2639184 - 10000 9.6190853 9.7903758 5.1583115 -Loop time of 1.32471 on 4 procs for 10000 steps with 500 atoms - -Performance: 3261084.476 tau/day, 7548.807 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.1301 | 0.13489 | 0.13886 | 0.9 | 10.18 -Neigh | 0.5654 | 0.575 | 0.5883 | 1.3 | 43.41 -Comm | 0.35135 | 0.37147 | 0.38856 | 2.4 | 28.04 -Output | 0.0028336 | 0.0032777 | 0.004292 | 1.0 | 0.25 -Modify | 0.16328 | 0.16711 | 0.17231 | 0.8 | 12.61 -Other | | 0.07297 | | | 5.51 - -Nlocal: 125 ave 128 max 122 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 477 ave 489 max 469 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 861 ave 877 max 848 min -Histogram: 1 0 1 0 0 1 0 0 0 1 - -Total # of neighbors = 3444 -Ave neighs/atom = 6.888 -Neighbor list builds = 4560 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 b/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 new file mode 100644 index 0000000000..0d97a3793a --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.1 @@ -0,0 +1,282 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.742 | 2.742 | 2.742 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 10.369902 10.999889 6.5437384 + 100 12.411384 13.145871 7.8892802 + 150 12.88182 12.114068 7.5155182 + 200 10.375571 10.979773 6.5624056 + 250 10.158901 10.251273 5.4525068 + 300 10.011314 9.8371382 5.4031393 + 350 9.4890008 9.7992108 5.054963 + 400 9.1715116 9.2647886 4.9600208 + 450 9.8495961 9.3353483 4.986786 + 500 9.5903809 8.576173 4.8252116 + 550 8.8057509 9.7152078 4.9089022 + 600 8.9743682 10.031277 4.8924072 + 650 10.233852 9.3059527 5.1977058 + 700 9.2361906 9.6439971 5.0923763 + 750 10.449751 9.5911465 5.2548714 + 800 9.8366857 9.9873885 4.9456956 + 850 10.266351 9.9620134 5.0602713 + 900 9.6325813 9.3910946 5.1466624 + 950 9.1911919 9.1519006 4.8275345 + 1000 9.2871712 9.8508501 5.2674099 + 1050 9.7052036 10.291793 5.1603591 + 1100 9.9425548 10.361827 5.5520486 + 1150 10.377563 10.265879 5.5997431 + 1200 9.6368288 10.354415 5.413788 + 1250 9.2071084 9.1706343 4.9800415 + 1300 9.7140475 8.725759 4.8536998 + 1350 10.145943 9.8247688 4.8921964 + 1400 9.1998769 9.6934121 5.2269945 + 1450 9.4838819 8.9036871 4.6868425 + 1500 9.0660596 9.8119073 4.8875027 + 1550 10.008516 9.8942392 5.2035321 + 1600 9.7143761 9.9244983 5.3261192 + 1650 9.7387193 9.6991715 5.3519995 + 1700 9.7244046 9.6152132 5.3981523 + 1750 9.5710027 8.0741432 4.9456613 + 1800 9.9774654 9.6678929 4.9160721 + 1850 9.8364707 9.6445265 5.314823 + 1900 9.1249414 9.9271775 5.1286354 + 1950 9.6652829 9.0384584 5.2340419 + 2000 9.5265979 10.26158 5.2813427 + 2050 9.9173922 9.5527322 4.8940699 + 2100 9.9415753 9.8016834 5.4442305 + 2150 9.5497688 9.9967881 5.3150264 + 2200 10.334645 9.9712509 5.361381 + 2250 9.7205034 9.7973449 5.0447949 + 2300 9.2264367 9.7244096 5.1908235 + 2350 9.3549971 8.9425394 5.0163909 + 2400 9.1923971 8.6026816 4.9142184 + 2450 9.3318993 9.2876986 5.2092509 + 2500 9.2703657 9.7375808 4.9579591 + 2550 9.1967438 10.010085 4.9842759 + 2600 9.5606002 10.387986 5.7530846 + 2650 9.609164 9.4442273 5.5362122 + 2700 9.093698 8.9706057 4.8616368 + 2750 9.0180363 10.16255 4.7751355 + 2800 9.8966449 9.6404143 5.2088441 + 2850 9.7039267 9.6911675 5.1261088 + 2900 9.2003002 10.333632 5.1375334 + 2950 9.7470703 9.6392635 5.2311731 + 3000 9.0259323 9.0011546 5.0023767 + 3050 9.4620827 9.8701001 5.0220394 + 3100 9.1559748 9.5498091 5.1765241 + 3150 10.100442 9.8148718 5.2819275 + 3200 9.6668354 9.470653 5.3759397 + 3250 9.3371207 9.3274667 4.9318779 + 3300 9.091848 9.5112327 5.2200157 + 3350 9.1269693 9.6133794 5.1310717 + 3400 9.1027229 9.416857 5.0819883 + 3450 9.2658402 9.0401432 5.0990609 + 3500 10.377313 9.5626011 5.202188 + 3550 9.2947039 9.505877 5.5438005 + 3600 9.076374 9.5507698 5.1345649 + 3650 10.333552 9.0606354 5.0508117 + 3700 9.8802406 9.7469806 5.5088992 + 3750 9.7912998 9.2253084 5.5336078 + 3800 9.5643045 9.7834307 5.0726418 + 3850 9.8238806 9.9734109 5.4322981 + 3900 9.6518341 9.0747014 5.6444988 + 3950 9.1405553 9.3360768 4.8837062 + 4000 9.3606196 9.9269401 5.1633636 + 4050 9.4414403 9.9408674 5.2935162 + 4100 9.6568918 9.6131494 5.0426715 + 4150 9.864223 9.2610429 5.1413271 + 4200 10.292607 9.2650093 4.9732741 + 4250 9.7702935 10.274775 5.3607379 + 4300 9.4790352 8.8735538 4.8580655 + 4350 9.5504854 10.340269 4.4428322 + 4400 9.5556697 9.2862997 5.1467218 + 4450 9.6741368 10.007913 5.3062768 + 4500 9.938524 9.1645202 5.3414548 + 4550 9.9970823 9.6116985 5.0880012 + 4600 10.035008 9.8767746 5.1253207 + 4650 10.109616 10.971392 5.3742955 + 4700 10.080373 10.656347 5.4138717 + 4750 10.252518 10.563308 5.0535706 + 4800 9.3426418 9.4491805 5.1587548 + 4850 9.2885747 9.7058018 4.9715619 + 4900 9.2136015 9.0234401 4.7395994 + 4950 9.1361149 9.6758285 4.9981501 + 5000 9.5474982 9.0493007 5.2137701 + 5050 9.635291 9.7591762 4.8415939 + 5100 9.5719703 9.5689732 5.1787863 + 5150 9.4201066 10.449653 5.222846 + 5200 9.1962218 9.6566128 5.4026011 + 5250 8.6281903 9.0441148 5.1187247 + 5300 9.6429057 9.6840319 4.9475686 + 5350 10.388834 9.417967 5.224683 + 5400 10.047564 10.073369 5.2814251 + 5450 9.2430362 9.8508143 5.4960461 + 5500 9.9812959 9.4140317 5.0437339 + 5550 10.045822 10.077244 5.3796453 + 5600 9.6625863 9.5277882 5.0780914 + 5650 9.0185037 8.8319729 4.7626372 + 5700 9.16337 9.4156456 4.6766204 + 5750 9.3777054 9.292911 5.3348738 + 5800 8.8347896 9.0603847 5.2325469 + 5850 9.307492 10.066699 4.8439039 + 5900 9.6261925 9.8782796 5.5750224 + 5950 8.7773987 9.5456497 5.0858933 + 6000 9.7327023 9.9029484 5.202036 + 6050 9.370819 9.3128466 5.3681069 + 6100 9.4568801 9.3082668 5.1480307 + 6150 10.336417 9.4569418 5.152047 + 6200 9.4969856 9.7198161 5.1648394 + 6250 9.4844976 9.6958021 5.2628856 + 6300 9.2406959 9.9330467 5.205557 + 6350 9.9508721 9.4577577 5.1630178 + 6400 9.6759763 8.9531754 5.274062 + 6450 9.4062719 8.8404288 5.2379186 + 6500 9.553735 9.0313724 4.8620144 + 6550 9.1947496 9.289295 4.834747 + 6600 9.7299026 9.6968225 4.9198957 + 6650 10.467984 11.039001 5.0952273 + 6700 9.8488093 10.142611 5.3922943 + 6750 9.7484714 9.2403353 4.9210254 + 6800 8.7424625 9.4374325 5.1391373 + 6850 8.7654476 9.3003008 5.0486754 + 6900 9.5001642 9.5361838 5.0300213 + 6950 9.3807018 9.4573472 4.8452481 + 7000 9.6055795 10.087276 4.9469866 + 7050 9.5823321 9.439522 5.2882226 + 7100 9.8653958 9.4652195 5.7972727 + 7150 9.9148149 9.2324819 5.049893 + 7200 8.9502172 8.8138734 4.9123769 + 7250 8.8968143 9.2721861 5.0210042 + 7300 10.356078 9.6753595 4.9074775 + 7350 8.9771028 9.5585959 4.7967768 + 7400 9.8494816 9.7347288 5.3771897 + 7450 8.6771311 8.8770175 5.2917845 + 7500 9.612851 9.1856901 4.8593785 + 7550 9.4248312 9.5312938 5.1662239 + 7600 10.284524 9.6561627 5.000118 + 7650 10.322322 9.8314081 5.6316726 + 7700 9.3491815 9.103061 4.7351973 + 7750 9.7524148 9.3729475 5.3109482 + 7800 9.5120985 9.7507452 4.797863 + 7850 9.0245453 10.008972 5.0798698 + 7900 9.7587351 9.5831457 4.9297543 + 7950 10.122804 9.2235043 5.4337028 + 8000 9.7771103 9.567766 5.1963733 + 8050 9.7806594 10.298163 4.895879 + 8100 10.448182 10.515639 5.3289479 + 8150 9.8343933 10.008423 5.3820067 + 8200 9.5352286 10.361378 4.7917095 + 8250 9.5998667 9.548455 5.3325917 + 8300 8.6800132 8.9296257 5.1167116 + 8350 9.5002383 9.3974769 4.7360673 + 8400 9.1465982 9.9114657 4.8444228 + 8450 9.4052506 9.8253802 5.0409773 + 8500 9.8500797 9.3743233 5.4810341 + 8550 10.397958 9.9150945 5.2311945 + 8600 10.050509 10.469527 5.3628699 + 8650 9.8765677 9.9046431 5.2097096 + 8700 9.4719729 9.4809771 5.1901684 + 8750 10.655877 9.3045558 5.0291182 + 8800 9.3839631 9.0770977 5.4169863 + 8850 8.5563701 9.5609016 4.9363846 + 8900 9.1540031 9.1138085 5.0313556 + 8950 9.0683988 9.0612961 5.4303556 + 9000 9.0034656 9.3514159 5.1108578 + 9050 9.6175649 10.008811 5.4158707 + 9100 9.6318001 9.8674826 5.1353951 + 9150 9.6137113 9.0624145 4.8918834 + 9200 9.6383354 9.6193304 5.1957729 + 9250 9.9634948 9.5555506 5.1157666 + 9300 9.4959396 9.2081906 4.7966165 + 9350 9.4990471 9.6393468 5.038926 + 9400 9.8650474 9.5013204 5.1687108 + 9450 10.096601 9.7576279 5.1541738 + 9500 10.287174 9.1309869 5.2725889 + 9550 9.6880559 10.46627 5.2567677 + 9600 9.4560894 10.118705 5.504487 + 9650 9.4243792 9.1251893 5.356545 + 9700 9.2088034 9.5449084 4.7599797 + 9750 9.18092 9.4732177 4.7610484 + 9800 9.7077531 9.3400296 5.1136769 + 9850 9.2906762 9.2543264 5.1607448 + 9900 9.3504492 9.4905057 4.8533019 + 9950 10.121028 9.4893638 5.0876648 + 10000 9.6330262 9.8877889 5.255801 +Loop time of 3.55576 on 1 procs for 10000 steps with 500 atoms + +Performance: 1214931.314 tau/day, 2812.341 timesteps/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.48327 | 0.48327 | 0.48327 | 0.0 | 13.59 +Neigh | 2.239 | 2.239 | 2.239 | 0.0 | 62.97 +Comm | 0.24938 | 0.24938 | 0.24938 | 0.0 | 7.01 +Output | 0.0024805 | 0.0024805 | 0.0024805 | 0.0 | 0.07 +Modify | 0.49693 | 0.49693 | 0.49693 | 0.0 | 13.98 +Other | | 0.08466 | | | 2.38 + +Nlocal: 500 ave 500 max 500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 894 ave 894 max 894 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3473 ave 3473 max 3473 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3473 +Ave neighs/atom = 6.946 +Neighbor list builds = 4571 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:03 diff --git a/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 b/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 new file mode 100644 index 0000000000..475aa9a02d --- /dev/null +++ b/examples/USER/uef/nvt_uniaxial/log.27Nov18.nvt_uniaxial.g++.4 @@ -0,0 +1,282 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# uniaxial NVT deformation of WCA fluid + +units lj +atom_style atomic + + +pair_style lj/cut 1.122562 +read_data data.wca + orthogonal box = (0 0 0) to (8.39798 8.39798 8.39798) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 500 atoms + reading velocities ... + 500 velocities +pair_coeff 1 1 1.0 1.0 +pair_modify shift yes + +neighbor 0.5 bin +neigh_modify delay 0 + +change_box all triclinic + triclinic box = (0 0 0) to (8.39798 8.39798 8.39798) with tilt (0 0 0) + +fix 1 all nvt/uef temp 0.722 0.722 0.5 erate -0.5 -0.5 + +fix 2 all momentum 100 linear 1 1 1 + +#dump 1 all atom 25 dump.lammpstrj + +#dump 2 all cfg/uef 25 dump.*.cfg mass type xs ys zs + +thermo_style custom step c_1_press[1] c_1_press[2] c_1_press[3] + +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.62256 + ghost atom cutoff = 1.62256 + binsize = 0.811281, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.71 | 2.71 | 2.71 Mbytes +Step c_1_press[1] c_1_press[2] c_1_press[3] + 0 6.3937851 7.0436438 6.4461087 + 50 10.369902 10.999889 6.5437384 + 100 12.411384 13.145871 7.8892802 + 150 12.88182 12.114068 7.5155182 + 200 10.375571 10.979773 6.5624056 + 250 10.158901 10.251273 5.4525068 + 300 10.011314 9.8371382 5.4031393 + 350 9.4890008 9.7992108 5.054963 + 400 9.1715116 9.2647886 4.9600208 + 450 9.8495961 9.3353483 4.986786 + 500 9.5903809 8.576173 4.8252116 + 550 8.8057509 9.7152078 4.9089022 + 600 8.9743682 10.031277 4.8924072 + 650 10.233852 9.3059527 5.1977058 + 700 9.2361906 9.6439971 5.0923762 + 750 10.449751 9.5911465 5.2548714 + 800 9.8366858 9.9873884 4.9456956 + 850 10.266351 9.9620134 5.0602713 + 900 9.6325811 9.3910947 5.1466627 + 950 9.1911905 9.1518997 4.8275336 + 1000 9.2871725 9.8508562 5.2674079 + 1050 9.7052017 10.291782 5.1603605 + 1100 9.9425819 10.36185 5.552059 + 1150 10.377567 10.265893 5.5997253 + 1200 9.6367074 10.354441 5.4138714 + 1250 9.2075345 9.1705121 4.9806597 + 1300 9.7125304 8.7247864 4.8527961 + 1350 10.146279 9.8320637 4.8957733 + 1400 9.1958551 9.7053733 5.2334299 + 1450 9.4652827 8.9011309 4.7064679 + 1500 9.097059 9.8376542 4.8890705 + 1550 10.073762 9.8105951 5.1618299 + 1600 10.132035 9.7140421 5.0910485 + 1650 9.9272143 9.8919667 5.1764704 + 1700 9.387078 8.5379185 4.9433787 + 1750 9.2411549 9.6783579 5.1290917 + 1800 10.111692 9.9975429 4.96325 + 1850 9.4723913 9.3032011 5.0282162 + 1900 9.1909638 9.8626554 4.9377276 + 1950 9.5697796 9.7975713 4.8435878 + 2000 9.8478931 9.0884861 5.2329856 + 2050 9.4412451 9.3925057 5.0522524 + 2100 9.9067445 9.8587735 4.979452 + 2150 10.200525 9.3061345 5.2583418 + 2200 9.7020113 9.5542846 5.5306109 + 2250 9.6915356 10.520416 5.3194622 + 2300 9.2391264 9.464931 5.0772628 + 2350 10.054609 9.7850417 5.653202 + 2400 9.3803459 9.4323134 4.7562131 + 2450 9.1007052 9.6904074 5.2520835 + 2500 9.2586085 9.1371198 5.1371392 + 2550 9.091608 9.3685259 5.1482359 + 2600 8.9237293 9.0406832 5.2104216 + 2650 9.7360268 9.2519429 5.0398315 + 2700 9.9929147 9.036125 4.9901821 + 2750 9.2907663 9.3352821 4.9289845 + 2800 9.5368804 10.008157 4.8400379 + 2850 9.278721 9.5887435 5.3877385 + 2900 9.6424072 9.329667 4.6934542 + 2950 9.1689315 9.9502359 5.2742219 + 3000 9.6407238 9.6896783 5.4236624 + 3050 9.4180757 9.6335563 4.9475952 + 3100 9.3014748 9.8883475 5.3334153 + 3150 9.2596884 9.3730863 4.7044615 + 3200 9.4852847 10.063705 5.1115729 + 3250 9.5837854 9.8570045 5.2152566 + 3300 10.4346 9.5070868 5.3051491 + 3350 9.2432868 9.1515564 5.1465518 + 3400 9.9697276 9.4093982 4.82531 + 3450 10.209003 10.231731 5.0156036 + 3500 10.308668 10.368321 5.8799821 + 3550 9.4034117 9.7554506 5.2690776 + 3600 9.3545829 8.9994226 5.0278441 + 3650 8.7888087 9.1237694 5.0935882 + 3700 9.0666265 9.1732984 4.877327 + 3750 9.4200226 8.6735321 4.8452306 + 3800 9.465348 9.4091671 5.0179 + 3850 8.9727774 9.0192234 4.8767313 + 3900 9.436289 10.157156 5.269109 + 3950 8.5421593 9.4062573 5.2140073 + 4000 9.3051483 8.8716005 4.7590488 + 4050 9.0535105 9.1280971 5.1646893 + 4100 9.5480831 10.259875 5.1875536 + 4150 9.9237867 10.269757 5.6394637 + 4200 9.7126407 9.5984958 5.2415146 + 4250 10.12528 9.5182979 5.5850325 + 4300 8.9818181 9.144527 5.0107697 + 4350 9.3098797 9.8024806 4.8397827 + 4400 9.2427164 9.699184 5.1366641 + 4450 9.9356359 10.651145 5.1151886 + 4500 9.7524551 9.9912434 5.2412686 + 4550 10.078703 9.5328151 5.2060043 + 4600 9.3983698 9.6152 4.9376041 + 4650 9.9963375 9.5887427 4.9306202 + 4700 10.012303 9.7114835 5.0668394 + 4750 9.6449888 9.496676 5.299027 + 4800 9.7912528 9.6515788 5.1308053 + 4850 10.063515 9.4960168 5.2149877 + 4900 9.5951954 9.2870056 4.928229 + 4950 10.20955 10.184708 5.2096074 + 5000 10.732623 9.8250159 5.3978002 + 5050 10.439323 9.6161959 4.9561115 + 5100 10.26424 9.4611487 5.6919308 + 5150 9.4638719 9.8167726 5.1475905 + 5200 9.8482876 9.4899672 5.1930896 + 5250 9.7150245 9.6183215 4.920446 + 5300 8.722617 9.3382522 4.7819079 + 5350 9.0836368 9.4113687 5.1447731 + 5400 9.6207733 9.5737842 5.0414277 + 5450 9.3552951 9.3288804 5.2373326 + 5500 9.2143176 9.024929 4.6883468 + 5550 10.372758 9.1381198 4.8012855 + 5600 9.5520148 9.7896053 5.1547238 + 5650 9.6980784 10.951142 5.0241161 + 5700 10.611679 9.6523346 5.5326608 + 5750 9.1742649 9.6494073 5.5851624 + 5800 9.953586 9.9617747 4.7007718 + 5850 10.702009 11.067871 5.1330231 + 5900 9.8673283 9.7543507 5.2206639 + 5950 10.16692 10.060199 5.0400651 + 6000 9.9341281 9.6212713 5.1712869 + 6050 9.9281773 9.4342521 5.4660461 + 6100 9.567855 9.7513309 4.7343918 + 6150 8.795041 9.9236745 5.0766601 + 6200 8.692139 9.1845134 5.1633685 + 6250 9.0701253 9.7521268 4.8172065 + 6300 9.4583102 9.3188937 5.1569152 + 6350 8.6428721 9.2062944 4.9110217 + 6400 9.3818856 9.4262935 4.9271667 + 6450 9.4895013 9.5741062 5.0173634 + 6500 9.9822263 9.1903289 5.4171946 + 6550 10.010639 9.4613863 5.6106556 + 6600 8.847069 9.180382 5.0007521 + 6650 8.8684678 9.3900848 4.6876604 + 6700 9.7575413 10.054084 4.6587676 + 6750 10.115414 9.4226624 5.4854908 + 6800 9.8529501 9.4369048 5.2366418 + 6850 10.25008 10.202239 4.929119 + 6900 10.405896 10.46272 5.2636294 + 6950 9.3342275 9.9980868 5.4788629 + 7000 9.9933544 9.3374018 4.8181134 + 7050 10.115734 10.072388 5.6490688 + 7100 10.240083 9.4087789 4.6102705 + 7150 9.2524065 9.7472716 5.0925137 + 7200 9.264148 9.9229773 5.0557618 + 7250 10.05753 9.2914209 4.6450615 + 7300 10.147183 9.8973958 5.1521105 + 7350 10.557244 9.5876788 5.2394875 + 7400 9.0062903 9.1139724 4.9104291 + 7450 10.026016 9.1880235 5.0812661 + 7500 9.770617 9.7098832 5.0578123 + 7550 8.865352 9.5783696 5.127484 + 7600 10.606037 9.9212374 5.1338765 + 7650 9.2293794 9.74635 5.3595397 + 7700 10.136014 10.510875 4.8300321 + 7750 9.9974018 9.5151713 5.0779843 + 7800 10.168972 9.5247801 5.1045215 + 7850 10.487704 9.9748481 4.9660756 + 7900 9.7134418 9.6505576 5.3677417 + 7950 9.5874439 9.6696709 4.7790879 + 8000 8.9025499 9.3980684 4.9181099 + 8050 8.9385458 9.4324137 4.8704298 + 8100 9.429405 9.6231169 4.8712228 + 8150 9.471228 9.1507346 4.9513613 + 8200 9.0945803 9.2568274 4.9583007 + 8250 9.0486717 10.276196 5.0469026 + 8300 9.5270225 9.3578605 5.0959132 + 8350 10.019204 10.255987 5.3215538 + 8400 9.3804378 9.572985 5.3114559 + 8450 9.7622725 10.933028 5.0042871 + 8500 9.980802 10.387463 5.624029 + 8550 10.177065 10.736812 5.6835861 + 8600 9.4853991 9.4572634 5.2662391 + 8650 10.021383 9.6398577 5.0548533 + 8700 10.417762 10.551382 5.1401022 + 8750 9.2932185 9.6410107 5.1252967 + 8800 10.411184 10.005891 5.5464139 + 8850 9.1394978 9.0334923 5.2709589 + 8900 9.2577227 9.1885981 4.7441276 + 8950 9.5694417 9.420939 5.1766071 + 9000 9.3252516 9.6541534 4.76132 + 9050 10.129917 10.38226 5.5151239 + 9100 9.9469348 8.7671772 5.1494135 + 9150 9.6919911 8.6522594 5.0200023 + 9200 9.4052126 9.3008012 5.0004827 + 9250 9.599934 9.5285434 4.6368794 + 9300 9.9175442 9.8256117 4.9899989 + 9350 9.5819019 9.7558559 5.2795764 + 9400 10.133518 10.376403 5.2600124 + 9450 9.6970983 9.672896 5.3803885 + 9500 9.6338577 9.8443768 5.5143033 + 9550 9.0843344 10.00471 5.3399662 + 9600 9.5235958 9.7746182 5.0639295 + 9650 9.6467057 9.3897673 5.0335239 + 9700 10.070033 8.9260067 4.9535787 + 9750 9.9158669 10.292546 4.9937494 + 9800 9.5814408 9.8764893 5.2999138 + 9850 9.4928079 9.2662598 5.5435789 + 9900 8.8291515 8.9602162 5.08972 + 9950 9.5382191 9.9064194 5.0468896 + 10000 10.212615 9.4812174 5.0704059 +Loop time of 1.34397 on 4 procs for 10000 steps with 500 atoms + +Performance: 3214349.906 tau/day, 7440.625 timesteps/s +95.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.11223 | 0.11662 | 0.12747 | 1.8 | 8.68 +Neigh | 0.57426 | 0.59024 | 0.62229 | 2.5 | 43.92 +Comm | 0.30675 | 0.35437 | 0.37755 | 4.8 | 26.37 +Output | 0.0025589 | 0.0054465 | 0.014064 | 6.7 | 0.41 +Modify | 0.17845 | 0.18351 | 0.19314 | 1.3 | 13.65 +Other | | 0.09378 | | | 6.98 + +Nlocal: 125 ave 132 max 120 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 462.75 ave 467 max 457 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 863.25 ave 919 max 834 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 3453 +Ave neighs/atom = 6.906 +Neighbor list builds = 4557 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/USER/yaff/README b/examples/USER/yaff/README new file mode 100644 index 0000000000..af43a61e08 --- /dev/null +++ b/examples/USER/yaff/README @@ -0,0 +1,7 @@ +mof5: + NPT simulation of MOF5 using a QuickFF force field + +mil53al: + NPT simulation of MIL-53(Al) using a QuickFF force field. + If the pressure is high enough (for instance 2000 atm), + a phase transition from large pore to narrow pore is observed diff --git a/examples/USER/yaff/mil53al/lammps.data b/examples/USER/yaff/mil53al/lammps.data new file mode 100644 index 0000000000..7b73c99357 --- /dev/null +++ b/examples/USER/yaff/mil53al/lammps.data @@ -0,0 +1,1545 @@ +Generated by yaff2lammps + + 152 atoms + 184 bonds + 736 angles + 288 dihedrals + 64 impropers + + 8 atom types + 8 bond types + 34 angle types + 9 dihedral types + 3 improper types + + 0.0000000000000000000000000000000000 13.3259954452999984653160936431959271 xlo xhi + 0.0000000000000000000000000000000000 17.0769005354000000806991010904312134 ylo yhi + 0.0000000000000000000000000000000000 12.5451650575000002163505996577441692 zlo zhi + 0.2406519637999999794431005284423009 -0.0003290864999999999263892436207612 0.0000597691999999999968857904153463 xy xz yz + +Masses + + 1 15.99940000 # O_HY + 2 15.99940000 # O_CA + 3 1.00794000 # H_HY + 4 1.00794000 # H_PH + 5 26.98153860 # AL + 6 12.01070000 # C_PH + 7 12.01070000 # C_PC + 8 12.01070000 # C_CA + +Bond Coeffs + + 1 567.89714613 0.99006574 + 2 149.93642745 1.86984652 + 3 111.04240192 1.91161348 + 4 389.90538840 1.09141352 + 5 491.67603879 1.38895490 + 6 451.37211172 1.40304450 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283 9 136 152 24 82 + 284 9 136 152 36 88 + 285 6 36 152 136 116 + 286 6 36 152 136 104 + 287 6 24 152 136 116 + 288 6 24 152 136 104 + +Impropers + + 1 3 89 49 122 93 + 2 3 90 121 50 94 + 3 3 91 51 123 95 + 4 3 92 124 52 96 + 5 3 93 89 125 53 + 6 3 94 90 54 126 + 7 3 95 91 127 55 + 8 3 96 128 92 56 + 9 3 97 57 129 101 + 10 3 98 58 102 130 + 11 3 99 59 131 103 + 12 3 100 60 132 104 + 13 3 101 97 61 134 + 14 3 102 98 133 62 + 15 3 103 99 135 63 + 16 3 104 100 136 64 + 17 3 105 65 109 126 + 18 3 106 66 125 110 + 19 3 107 67 127 111 + 20 3 108 128 68 112 + 21 3 109 105 121 69 + 22 3 110 106 70 122 + 23 3 111 107 123 71 + 24 3 112 124 108 72 + 25 3 113 73 133 117 + 26 3 114 74 118 134 + 27 3 115 75 135 119 + 28 3 116 76 136 120 + 29 3 117 113 130 77 + 30 3 118 129 114 78 + 31 3 119 115 131 79 + 32 3 120 116 132 80 + 33 1 121 137 90 109 + 34 1 122 89 138 110 + 35 1 123 91 139 111 + 36 1 124 92 140 112 + 37 1 125 106 141 93 + 38 1 126 105 94 142 + 39 1 127 107 143 95 + 40 1 128 108 144 96 + 41 1 129 97 145 118 + 42 1 130 98 117 146 + 43 1 131 99 147 119 + 44 1 132 100 148 120 + 45 1 133 113 149 102 + 46 1 134 114 101 150 + 47 1 135 115 151 103 + 48 1 136 116 152 104 + 49 2 137 121 10 29 + 50 2 138 9 122 30 + 51 2 139 11 123 31 + 52 2 140 124 12 32 + 53 2 141 26 13 125 + 54 2 142 25 14 126 + 55 2 143 27 127 15 + 56 2 144 128 28 16 + 57 2 145 17 129 38 + 58 2 146 18 37 130 + 59 2 147 19 131 39 + 60 2 148 20 132 40 + 61 2 149 33 133 22 + 62 2 150 34 21 134 + 63 2 151 35 135 23 + 64 2 152 36 136 24 diff --git a/examples/USER/yaff/mil53al/lammps.in b/examples/USER/yaff/mil53al/lammps.in new file mode 100644 index 0000000000..a2b6329bbd --- /dev/null +++ b/examples/USER/yaff/mil53al/lammps.in @@ -0,0 +1,42 @@ +######################################### +#General settings +######################################### +units real +atom_style full +boundary p p p +dielectric 1 + +######################################### +#Force field and system specification +######################################### +special_bonds lj 0.000000 0.000000 1.000000 coul 1.000000 1.000000 1.000000 +pair_style mm3/switch3/coulgauss/long 12.0000 4.0000 +pair_modify table 16 # Accuracy of the table used for real space electrostatics +pair_modify mix arithmetic +pair_modify tail no +bond_style harmonic +angle_style hybrid cosine/periodic cross harmonic cosine/squared +dihedral_style fourier +improper_style distharm +box tilt large + +read_data lammps.data # Data file location +kspace_style pppm 0.0000001 # Ewald accuracy +neighbor 2.0 multi +neigh_modify every 2 delay 4 check yes + +######################################### +#Output settings +######################################### +thermo 100 # Provide output every n steps +thermo_style custom step time etotal ke temp pe emol evdwl ecoul elong etail vol press +thermo_modify line multi format float %20.12f + +######################################### +#Sampling options +######################################### +timestep 0.5 # in femtosecond +velocity all create 0.0 5 # initial temperature in Kelvin and random seed +fix 1 all npt temp 300.0 300.0 100.0 tri 2000.0 2000.0 1000.0 tchain 3 mtk yes nreset 1000 +fix_modify 1 energy yes # Add thermo/barostat contributions to energy +run 10000 diff --git a/examples/USER/yaff/mof5/lammps.data b/examples/USER/yaff/mof5/lammps.data new file mode 100644 index 0000000000..acc6f7d3d2 --- /dev/null +++ b/examples/USER/yaff/mof5/lammps.data @@ -0,0 +1,4315 @@ +Generated by yaff2lammps + + 424 atoms + 512 bonds + 1824 angles + 1248 dihedrals + 192 impropers + + 7 atom types + 7 bond types + 29 angle types + 11 dihedral types + 3 improper types + + 0.0000000000000000000000000000000000 26.4070248643267468935391661943867803 xlo xhi + 0.0000000000000000000000000000000000 26.4070252891212220447414438240230083 ylo yhi + 0.0000000000000000000000000000000000 26.4070257154843517355402582325041294 zlo zhi + -0.0000000007111492372846892652846758 -0.0000000000659408828932501509572980 -0.0000000000464737531820980317620204 xy xz yz + +Masses + + 1 65.40900000 # Zn + 2 15.99940000 # O_CE + 3 15.99940000 # O_CA + 4 12.01070000 # C_CA + 5 12.01070000 # C_PH + 6 12.01070000 # C_PC + 7 1.00794000 # H_PH + +Bond Coeffs + + 1 682.36094515 1.27102391 + 2 499.48089314 1.38650552 + 3 328.64606795 1.49449724 + 4 465.15110963 1.39880394 + 5 406.68075027 1.08330871 + 6 107.02127303 2.03268653 + 7 113.67644184 1.98848069 + +Angle Coeffs + + 1 cross 193.48062339 101.27328163 101.27328163 1.27218805 1.27218805 123.91120600 + 2 cross 90.86010618 104.60333096 43.56504880 1.27186911 1.49086906 118.21448172 + 3 cross 90.86010618 43.56504880 104.60333096 1.49086906 1.27186911 118.21448172 + 4 cross 130.81104940 12.67739461 16.17645862 1.39837427 1.38759779 120.07946149 + 5 cross 130.81104940 16.17645862 12.67739461 1.38759779 1.39837427 120.07946149 + 6 cross 11.41676921 30.63883886 25.17734414 1.08331485 1.39837427 119.52155527 + 7 cross 11.41676921 25.17734414 30.63883886 1.39837427 1.08331485 119.52155527 + 8 cross 12.44667401 28.35704887 28.27577085 1.38759779 1.08331485 120.41324047 + 9 cross 12.44667401 28.27577085 28.35704887 1.08331485 1.38759779 120.41324047 + 10 cross 75.95522848 37.17414513 10.05189907 1.49086906 1.39837427 119.94754556 + 11 cross 75.95522848 10.05189907 37.17414513 1.39837427 1.49086906 119.94754556 + 12 cross 144.65705708 -7.34407121 -7.34407121 1.39837427 1.39837427 119.90241395 + 13 cross 20.17000841 2.28355442 -7.92322284 1.98727825 2.03828701 109.42277782 + 14 cross 20.17000841 -7.92322284 2.28355442 2.03828701 1.98727825 109.42277782 + 15 cross 22.09014578 27.25520258 27.25520258 1.98727825 1.98727825 108.41474547 + 16 cross 35.09855972 13.51120456 13.51120456 2.03828701 2.03828701 110.23699695 + 17 cross 60.09401332 6.52883112 6.33031133 1.27250698 1.98727825 133.24307044 + 18 cross 60.09401332 6.33031133 6.52883112 1.98727825 1.27250698 133.24307044 + 19 mm3 89.55892156 124.04066786 + 20 mm3 66.99975548 120.08429731 + 21 mm3 36.80738383 120.34964823 + 22 mm3 78.98317285 118.11635047 + 23 mm3 45.56202376 120.27481067 + 24 mm3 38.05295940 119.66571944 + 25 mm3 69.51816469 119.99726194 + 26 mm3 10.37923783 135.02173615 + 27 mm3 7.08946285 108.92035063 + 28 mm3 9.10447143 107.51166462 + 29 mm3 29.71892770 109.45766072 + +Dihedral Coeffs + + 1 1 3.64767899 2 -180.00000000 + 2 1 2.35495004 2 -180.00000000 + 3 1 0.77392291 2 -180.00000000 + 4 1 4.23729765 2 -180.00000000 + 5 1 3.96491674 2 -180.00000000 + 6 1 3.27183804 2 -180.00000000 + 7 1 2.21748040 2 -180.00000000 + 8 1 5.15273943 2 -180.00000000 + 9 1 0.07197799 2 -180.00000000 + 10 1 1.18073306 2 -180.00000000 + 11 1 0.13801067 3 -180.00000000 + +Improper Coeffs + + 1 27.54315214 0.30000000 + 2 196.72513766 0.20000000 + 3 21.31242806 0.10000000 + +Pair Coeffs + + 1 0.276000000000 2.290000000000 2.073000000000 # Zn + 2 0.059000000000 1.820000000000 1.132500000000 # O_CE + 3 0.059000000000 1.820000000000 1.132500000000 # O_CA 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255 168 + 177 1 313 241 169 262 + 178 1 314 170 261 242 + 179 1 315 243 171 264 + 180 1 316 172 263 244 + 181 1 317 245 260 173 + 182 1 318 259 246 174 + 183 1 319 258 247 175 + 184 1 320 257 176 248 + 185 1 321 265 177 280 + 186 1 322 178 279 266 + 187 1 323 267 278 179 + 188 1 324 268 180 277 + 189 1 325 269 181 274 + 190 1 326 273 270 182 + 191 1 327 276 271 183 + 192 1 328 275 184 272 diff --git a/examples/USER/yaff/mof5/lammps.in b/examples/USER/yaff/mof5/lammps.in new file mode 100644 index 0000000000..1decfd77e4 --- /dev/null +++ b/examples/USER/yaff/mof5/lammps.in @@ -0,0 +1,42 @@ +######################################### +#General settings +######################################### +units real +atom_style full +boundary p p p +dielectric 1 + +######################################### +#Force field and system specification +######################################### +special_bonds lj 0.000000 0.000000 1.000000 coul 1.000000 1.000000 1.000000 +pair_style mm3/switch3/coulgauss/long 12.0000 4.0000 +pair_modify table 16 # Accuracy of the table used for real space electrostatics +pair_modify mix arithmetic +pair_modify tail no +bond_style mm3 +angle_style hybrid cross mm3 +dihedral_style fourier +improper_style distharm +box tilt large + +read_data lammps.data # Data file location +kspace_style pppm 0.0000001 # Ewald accuracy +neighbor 2.0 multi +neigh_modify every 2 delay 4 check yes + +######################################### +#Output settings +######################################### +thermo 10 # Provide output every n steps +thermo_style custom step time etotal ke temp pe emol evdwl ecoul elong etail vol press +thermo_modify line multi format float %20.12f + +######################################### +#Sampling options +######################################### +timestep 0.5 # in femtosecond +velocity all create 0.0 5 # initial temperature in Kelvin and random seed +fix 1 all npt temp 300.0 300.0 100.0 tri 1.0 1.0 1000.0 tchain 3 mtk yes nreset 1000 +fix_modify 1 energy yes # Add thermo/barostat contributions to energy +run 100 diff --git a/examples/airebo/CH.airebo b/examples/airebo/CH.airebo new file mode 120000 index 0000000000..60249102a5 --- /dev/null +++ b/examples/airebo/CH.airebo @@ -0,0 +1 @@ +../../potentials/CH.airebo \ No newline at end of file diff --git a/examples/airebo/CH.airebo-m b/examples/airebo/CH.airebo-m new file mode 120000 index 0000000000..21f734dd05 --- /dev/null +++ b/examples/airebo/CH.airebo-m @@ -0,0 +1 @@ +../../potentials/CH.airebo-m \ No newline at end of file diff --git a/examples/airebo/in.airebo b/examples/airebo/in.airebo index 5b0e36ff4a..7615412430 100644 --- a/examples/airebo/in.airebo +++ b/examples/airebo/in.airebo @@ -1,22 +1,22 @@ # AIREBO polyethelene benchmark -units metal -atom_style atomic +units metal +atom_style atomic -read_data data.airebo +read_data data.airebo -replicate 17 16 2 +replicate 17 16 2 -neighbor 0.5 bin -neigh_modify delay 5 every 1 +neighbor 0.5 bin +neigh_modify delay 5 every 1 -pair_style airebo 3.0 1 1 -pair_coeff * * ../../potentials/CH.airebo C H +pair_style airebo 3.0 1 1 +pair_coeff * * CH.airebo C H -velocity all create 300.0 761341 +velocity all create 300.0 761341 -fix 1 all nve -timestep 0.0005 +fix 1 all nve +timestep 0.0005 -thermo 10 -run 100 +thermo 10 +run 100 diff --git a/examples/airebo/in.airebo-m b/examples/airebo/in.airebo-m index 3ec29482a7..562b74e6fc 100644 --- a/examples/airebo/in.airebo-m +++ b/examples/airebo/in.airebo-m @@ -1,22 +1,22 @@ # AIREBO polyethelene benchmark -units metal -atom_style atomic +units metal +atom_style atomic -read_data data.airebo +read_data data.airebo -replicate 17 16 2 +replicate 17 16 2 -neighbor 0.5 bin -neigh_modify delay 5 every 1 +neighbor 0.5 bin +neigh_modify delay 5 every 1 -pair_style airebo/morse 3.0 1 1 -pair_coeff * * ../../potentials/CH.airebo-m C H +pair_style airebo/morse 3.0 1 1 +pair_coeff * * CH.airebo-m C H -velocity all create 300.0 761341 +velocity all create 300.0 761341 -fix 1 all nve -timestep 0.0005 +fix 1 all nve +timestep 0.0005 -thermo 10 -run 100 +thermo 10 +run 100 diff --git a/examples/airebo/log.23Jun17.airebo-m.g++.1 b/examples/airebo/log.27Nov18.airebo-m.g++.1 similarity index 80% rename from examples/airebo/log.23Jun17.airebo-m.g++.1 rename to examples/airebo/log.27Nov18.airebo-m.g++.1 index 1483fcb4a6..44d8b9d59c 100644 --- a/examples/airebo/log.23Jun17.airebo-m.g++.1 +++ b/examples/airebo/log.27Nov18.airebo-m.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -15,6 +15,7 @@ replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms + Time spent = 0.00141144 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 80 164.28396 -138709.5 0 -138016.4 -1524.7353 90 180.26403 -138776.42 0 -138015.9 -27143.467 100 164.05694 -138706.58 0 -138014.44 5157.5516 -Loop time of 117.672 on 1 procs for 100 steps with 32640 atoms +Loop time of 64.6107 on 1 procs for 100 steps with 32640 atoms -Performance: 0.037 ns/day, 653.734 hours/ns, 0.850 timesteps/s -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.067 ns/day, 358.948 hours/ns, 1.548 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 108.31 | 108.31 | 108.31 | 0.0 | 92.04 -Neigh | 9.2199 | 9.2199 | 9.2199 | 0.0 | 7.84 -Comm | 0.052942 | 0.052942 | 0.052942 | 0.0 | 0.04 -Output | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.00 -Modify | 0.060962 | 0.060962 | 0.060962 | 0.0 | 0.05 -Other | | 0.02656 | | | 0.02 +Pair | 59.916 | 59.916 | 59.916 | 0.0 | 92.73 +Neigh | 4.6347 | 4.6347 | 4.6347 | 0.0 | 7.17 +Comm | 0.025572 | 0.025572 | 0.025572 | 0.0 | 0.04 +Output | 0.00098896 | 0.00098896 | 0.00098896 | 0.0 | 0.00 +Modify | 0.022327 | 0.022327 | 0.022327 | 0.0 | 0.03 +Other | | 0.01076 | | | 0.02 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -83,4 +84,4 @@ Total # of neighbors = 22210922 Ave neighs/atom = 680.482 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:02:00 +Total wall time: 0:01:05 diff --git a/examples/airebo/log.23Jun17.airebo-m.g++.4 b/examples/airebo/log.27Nov18.airebo-m.g++.4 similarity index 80% rename from examples/airebo/log.23Jun17.airebo-m.g++.4 rename to examples/airebo/log.27Nov18.airebo-m.g++.4 index 3a3d922bcb..a4cc55211b 100644 --- a/examples/airebo/log.23Jun17.airebo-m.g++.4 +++ b/examples/airebo/log.27Nov18.airebo-m.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -15,6 +15,7 @@ replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms + Time spent = 0.000637531 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 80 164.28396 -138709.5 0 -138016.4 -1524.7353 90 180.26403 -138776.42 0 -138015.9 -27143.467 100 164.05694 -138706.58 0 -138014.44 5157.5516 -Loop time of 32.9268 on 4 procs for 100 steps with 32640 atoms +Loop time of 18.1922 on 4 procs for 100 steps with 32640 atoms -Performance: 0.131 ns/day, 182.927 hours/ns, 3.037 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.237 ns/day, 101.068 hours/ns, 5.497 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 28.045 | 28.537 | 29.42 | 10.4 | 86.67 -Neigh | 3.163 | 3.237 | 3.3761 | 4.7 | 9.83 -Comm | 0.09883 | 1.1206 | 1.6862 | 60.4 | 3.40 -Output | 0.00099325 | 0.0011329 | 0.0012462 | 0.3 | 0.00 -Modify | 0.016013 | 0.016726 | 0.017257 | 0.4 | 0.05 -Other | | 0.01459 | | | 0.04 +Pair | 15.968 | 16.084 | 16.308 | 3.4 | 88.41 +Neigh | 1.6017 | 1.6334 | 1.7006 | 3.1 | 8.98 +Comm | 0.1603 | 0.45122 | 0.59951 | 26.0 | 2.48 +Output | 0.00042605 | 0.00073195 | 0.0016003 | 0.0 | 0.00 +Modify | 0.0092106 | 0.010544 | 0.014411 | 2.2 | 0.06 +Other | | 0.01193 | | | 0.07 Nlocal: 8160 ave 8167 max 8153 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -83,4 +84,4 @@ Total # of neighbors = 22210922 Ave neighs/atom = 680.482 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:33 +Total wall time: 0:00:18 diff --git a/examples/airebo/log.23Jun17.airebo.g++.1 b/examples/airebo/log.27Nov18.airebo.g++.1 similarity index 80% rename from examples/airebo/log.23Jun17.airebo.g++.1 rename to examples/airebo/log.27Nov18.airebo.g++.1 index 0ef895dc28..3713c8a8f8 100644 --- a/examples/airebo/log.23Jun17.airebo.g++.1 +++ b/examples/airebo/log.27Nov18.airebo.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -15,6 +15,7 @@ replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 1 by 1 by 1 MPI processor grid 32640 atoms + Time spent = 0.00144172 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 80 157.16184 -138695.77 0 -138032.72 19824.698 90 196.15907 -138860.65 0 -138033.07 -7950.8462 100 178.31875 -138784.89 0 -138032.57 30997.671 -Loop time of 110.107 on 1 procs for 100 steps with 32640 atoms +Loop time of 57.9914 on 1 procs for 100 steps with 32640 atoms -Performance: 0.039 ns/day, 611.705 hours/ns, 0.908 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.074 ns/day, 322.174 hours/ns, 1.724 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 100.76 | 100.76 | 100.76 | 0.0 | 91.51 -Neigh | 9.1909 | 9.1909 | 9.1909 | 0.0 | 8.35 -Comm | 0.058134 | 0.058134 | 0.058134 | 0.0 | 0.05 -Output | 0.0015941 | 0.0015941 | 0.0015941 | 0.0 | 0.00 -Modify | 0.062212 | 0.062212 | 0.062212 | 0.0 | 0.06 -Other | | 0.03123 | | | 0.03 +Pair | 53.275 | 53.275 | 53.275 | 0.0 | 91.87 +Neigh | 4.6548 | 4.6548 | 4.6548 | 0.0 | 8.03 +Comm | 0.026622 | 0.026622 | 0.026622 | 0.0 | 0.05 +Output | 0.00097251 | 0.00097251 | 0.00097251 | 0.0 | 0.00 +Modify | 0.022773 | 0.022773 | 0.022773 | 0.0 | 0.04 +Other | | 0.01089 | | | 0.02 Nlocal: 32640 ave 32640 max 32640 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -83,4 +84,4 @@ Total # of neighbors = 22217840 Ave neighs/atom = 680.694 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:01:52 +Total wall time: 0:00:59 diff --git a/examples/airebo/log.23Jun17.airebo.g++.4 b/examples/airebo/log.27Nov18.airebo.g++.4 similarity index 80% rename from examples/airebo/log.23Jun17.airebo.g++.4 rename to examples/airebo/log.27Nov18.airebo.g++.4 index 486b48a004..335690684a 100644 --- a/examples/airebo/log.23Jun17.airebo.g++.4 +++ b/examples/airebo/log.27Nov18.airebo.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (23 Jun 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # AIREBO polyethelene benchmark @@ -15,6 +15,7 @@ replicate 17 16 2 orthogonal box = (-2.1 -2.1 0) to (69.3 65.1 51.158) 2 by 2 by 1 MPI processor grid 32640 atoms + Time spent = 0.00262594 secs neighbor 0.5 bin neigh_modify delay 5 every 1 @@ -55,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 80 157.16184 -138695.77 0 -138032.72 19824.698 90 196.15907 -138860.65 0 -138033.07 -7950.8462 100 178.31875 -138784.89 0 -138032.57 30997.671 -Loop time of 30.1916 on 4 procs for 100 steps with 32640 atoms +Loop time of 16.4395 on 4 procs for 100 steps with 32640 atoms -Performance: 0.143 ns/day, 167.731 hours/ns, 3.312 timesteps/s -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.263 ns/day, 91.331 hours/ns, 6.083 timesteps/s +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 26.083 | 26.31 | 26.795 | 5.5 | 87.14 -Neigh | 3.1781 | 3.2134 | 3.2775 | 2.2 | 10.64 -Comm | 0.086296 | 0.63643 | 0.88995 | 40.2 | 2.11 -Output | 0.00074124 | 0.0010698 | 0.0013616 | 0.7 | 0.00 -Modify | 0.015335 | 0.016373 | 0.017565 | 0.8 | 0.05 -Other | | 0.01457 | | | 0.05 +Pair | 14.263 | 14.349 | 14.483 | 2.3 | 87.28 +Neigh | 1.6071 | 1.6283 | 1.6636 | 1.7 | 9.90 +Comm | 0.26261 | 0.43435 | 0.52323 | 16.1 | 2.64 +Output | 0.00042105 | 0.0007121 | 0.001538 | 0.0 | 0.00 +Modify | 0.00898 | 0.009112 | 0.0093675 | 0.2 | 0.06 +Other | | 0.0184 | | | 0.11 Nlocal: 8160 ave 8174 max 8146 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -83,4 +84,4 @@ Total # of neighbors = 22217840 Ave neighs/atom = 680.694 Neighbor list builds = 8 Dangerous builds = 0 -Total wall time: 0:00:30 +Total wall time: 0:00:16 diff --git a/examples/atm/in.atm b/examples/atm/in.atm index 131528dce3..e0041d9d2a 100644 --- a/examples/atm/in.atm +++ b/examples/atm/in.atm @@ -1,31 +1,31 @@ # Axilrod-Teller-Muto potential example -variable x index 1 -variable y index 1 -variable z index 1 +variable x index 1 +variable y index 1 +variable z index 1 -variable xx equal 10*$x -variable yy equal 10*$y -variable zz equal 10*$z +variable xx equal 10*$x +variable yy equal 10*$y +variable zz equal 10*$z -units lj -atom_style atomic +units lj +atom_style atomic -lattice fcc 0.65 -region box block 0 ${xx} 0 ${yy} 0 ${zz} -create_box 1 box -create_atoms 1 box +lattice fcc 0.65 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box -pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff * * atm * 0.072 +pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff * * atm * 0.072 -mass * 1.0 -velocity all create 1.033 12345678 loop geom +mass * 1.0 +velocity all create 1.033 12345678 loop geom -fix 1 all nvt temp 1.033 1.033 0.05 +fix 1 all nvt temp 1.033 1.033 0.05 timestep 0.002 -thermo 5 +thermo 5 -run 25 +run 25 diff --git a/examples/atm/log.27Aug18.g++.1 b/examples/atm/log.27Nov18.atm.g++.1 similarity index 82% rename from examples/atm/log.27Aug18.g++.1 rename to examples/atm/log.27Nov18.atm.g++.1 index 46215e108c..69bdb2f266 100644 --- a/examples/atm/log.27Aug18.g++.1 +++ b/examples/atm/log.27Nov18.atm.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (22 Aug 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Axilrod-Teller-Muto potential example variable x index 1 @@ -26,7 +27,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms - Time spent = 0.00139618 secs + Time spent = 0.000354767 secs pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 pair_coeff * * lj/cut 1.0 1.0 @@ -66,20 +67,20 @@ Step Temp E_pair E_mol TotEng Press 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469 -Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms +Loop time of 11.3218 on 1 procs for 25 steps with 4000 atoms -Performance: 270.846 tau/day, 1.567 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 381.565 tau/day, 2.208 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97 +Pair | 11.319 | 11.319 | 11.319 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01 -Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00 -Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01 -Other | | 0.0006771 | | | 0.00 +Comm | 0.0010235 | 0.0010235 | 0.0010235 | 0.0 | 0.01 +Output | 0.00010943 | 0.00010943 | 0.00010943 | 0.0 | 0.00 +Modify | 0.0012162 | 0.0012162 | 0.0012162 | 0.0 | 0.01 +Other | | 0.0004497 | | | 0.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -97,4 +98,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:16 +Total wall time: 0:00:11 diff --git a/examples/atm/log.27Aug18.g++.4 b/examples/atm/log.27Nov18.atm.g++.4 similarity index 81% rename from examples/atm/log.27Aug18.g++.4 rename to examples/atm/log.27Nov18.atm.g++.4 index d84f17ee2b..1248040847 100644 --- a/examples/atm/log.27Aug18.g++.4 +++ b/examples/atm/log.27Nov18.atm.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (22 Aug 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Axilrod-Teller-Muto potential example variable x index 1 @@ -26,7 +27,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms - Time spent = 0.000900984 secs + Time spent = 0.000210762 secs pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5 pair_coeff * * lj/cut 1.0 1.0 @@ -66,20 +67,20 @@ Step Temp E_pair E_mol TotEng Press 15 1.0376519 -4.84599 0 -3.2899013 -4.0278711 20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052 25 1.0347886 -4.84473 0 -3.2929351 -3.8044469 -Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms +Loop time of 2.95263 on 4 procs for 25 steps with 4000 atoms -Performance: 993.935 tau/day, 5.752 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1463.102 tau/day, 8.467 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41 +Pair | 2.8823 | 2.9082 | 2.9447 | 1.4 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55 -Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00 -Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02 -Other | | 0.0003656 | | | 0.01 +Comm | 0.0066586 | 0.043249 | 0.069202 | 11.8 | 1.46 +Output | 7.3671e-05 | 0.00015199 | 0.00038099 | 0.0 | 0.01 +Modify | 0.00061488 | 0.0006243 | 0.00063872 | 0.0 | 0.02 +Other | | 0.0004148 | | | 0.01 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -97,4 +98,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:04 +Total wall time: 0:00:03 diff --git a/examples/balance/log.27Nov18.balance.bond.fast.g++.2 b/examples/balance/log.27Nov18.balance.bond.fast.g++.2 new file mode 100644 index 0000000000..0cc1495368 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.bond.fast.g++.2 @@ -0,0 +1,242 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 +variable v index 5 +variable w index 2 + +units lj +dimension 2 +atom_style bond +boundary f f p + +lattice hex 0.85 +Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 +region box block 0 $x 0 $y -0.5 0.5 +region box block 0 50 0 $y -0.5 0.5 +region box block 0 50 0 20 -0.5 0.5 +create_box 1 box bond/types 1 extra/bond/per/atom 6 +Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) + 2 by 1 by 1 MPI processor grid +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 10 +create_atoms 1 region circle +Created 361 atoms + Time spent = 0.000778913 secs +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes +velocity all set 5 $w 0 sum yes +velocity all set 5 2 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +bond_style harmonic +bond_coeff 1 10.0 1.2 + +# need to preserve 1-3, 1-4 pairwise interactions during hard collisions + +special_bonds lj/coul 0 1 1 + 0 = max # of 1-2 neighbors + 1 = max # of special neighbors +create_bonds many all all 1 1.0 1.5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Added 1014 bonds, new total = 1014 + 6 = max # of 1-2 neighbors + 6 = max # of special neighbors + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 + +comm_style tiled +comm_modify cutoff 10.0 # because bonds stretch a long ways +fix 10 all balance 50 0.9 rcb + +#compute 1 all property/atom proc +#variable p atom (c_1%10)+1 +#dump 2 all custom 50 tmp.dump id v_p x y z + +#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string # "red green blue yellow white # purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 10 + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.156 | 5.167 | 5.177 Mbytes +Step Temp E_pair Press f_10[3] f_10 + 0 25.701528 -2.2032569 3.1039469 2 1.0193906 + 100 27.623422 -6.228166 2.6542136 1.0803324 1.0027701 + 200 33.35302 -15.746749 3.2018248 1.1246537 1.0027701 + 300 39.17734 -24.1557 4.9116986 1.1468144 1.0027701 + 400 41.660701 -27.615203 8.6214678 1.2077562 1.0027701 + 500 37.154935 -24.096954 3.2656298 1.2243767 1.0083102 + 600 35.062196 -21.527799 2.3688444 1.1800554 1.0027701 + 700 36.962955 -22.265373 3.0233424 1.1800554 1.0083102 + 800 38.514356 -24.625735 5.2876402 1.2077562 1.0027701 + 900 37.840168 -24.069158 4.443617 1.2022161 1.0083102 + 1000 36.429396 -23.978878 7.2603394 1.1966759 1.0027701 + 1100 34.75827 -22.743232 6.6304628 1.1745152 1.0083102 + 1200 31.057199 -21.46544 3.7869701 1.1634349 1.0083102 + 1300 33.127345 -22.426161 5.824726 1.0858726 1.0027701 + 1400 31.678654 -21.604473 3.2219261 1.0360111 1.0083102 + 1500 28.345212 -18.030807 0.93335223 1.1191136 1.0027701 + 1600 26.031412 -15.389052 0.82549542 1.1080332 1.0027701 + 1700 25.082832 -13.48625 1.0006592 1.0858726 1.0027701 + 1800 25.673875 -13.965883 0.54607043 1.0692521 1.0027701 + 1900 26.530842 -13.979318 2.0285449 1.1024931 1.0027701 + 2000 25.910771 -14.244515 1.9592232 1.1191136 1.0027701 + 2100 28.505636 -16.220559 1.7154775 1.1191136 1.0027701 + 2200 28.142753 -15.564302 2.9946076 1.1135734 1.0027701 + 2300 26.606225 -13.734442 1.4589278 1.0083102 1.0083102 + 2400 25.664988 -12.389759 1.3450183 1.0360111 1.0027701 + 2500 25.145328 -11.815173 0.48162788 1.0360111 1.0027701 + 2600 26.654868 -13.916929 2.8361012 1.0581717 1.0083102 + 2700 27.3758 -15.495452 4.1206412 1.0360111 1.0027701 + 2800 23.60864 -14.520038 1.8948923 1.0193906 1.0027701 + 2900 20.604557 -12.901121 0.17526991 1.0138504 1.0027701 + 3000 20.852473 -12.756946 -0.44987285 1.0360111 1.0027701 + 3100 21.934986 -12.797691 0.76186765 1.0415512 1.0027701 + 3200 23.293263 -12.368233 0.021937309 1.0526316 1.0027701 + 3300 22.091492 -10.88605 0.013006632 1.0415512 1.0083102 + 3400 23.535429 -10.937804 2.0738989 1.0360111 1.0027701 + 3500 24.503573 -12.202994 1.126785 1.0581717 1.0027701 + 3600 23.54503 -12.745709 0.39022194 1.0858726 1.0027701 + 3700 22.658187 -10.986188 -0.18869692 1.0692521 1.0027701 + 3800 21.282045 -9.7879088 -0.061253454 1.0193906 1.0027701 + 3900 20.571754 -9.1157993 -1.0178917 1.0526316 1.0027701 + 4000 23.779702 -10.230328 1.0778525 1.0581717 1.0083102 + 4100 23.675854 -10.63724 0.59402249 1.0415512 1.0027701 + 4200 24.058963 -11.89505 0.3866378 1.0526316 1.0027701 + 4300 22.683721 -11.358978 1.8269036 1.0470914 1.0083102 + 4400 23.002345 -11.081443 0.4529456 1.0415512 1.0027701 + 4500 21.984542 -10.233276 -0.60718244 1.0415512 1.0083102 + 4600 22.079237 -9.979061 0.53013572 1.0415512 1.0027701 + 4700 22.336961 -10.323583 -0.37512832 1.0249307 1.0027701 + 4800 23.351699 -10.143724 0.95694397 1.0470914 1.0027701 + 4900 23.643954 -10.687354 1.6062522 1.0858726 1.0083102 + 5000 25.158132 -11.532398 1.3083639 1.0914127 1.0027701 + 5100 23.755521 -10.978548 0.60587307 1.0470914 1.0027701 + 5200 21.842692 -10.443216 -0.41185899 1.0637119 1.0027701 + 5300 22.828066 -10.871114 1.1754353 1.0470914 1.0027701 + 5400 24.883977 -12.39165 0.65101173 1.0470914 1.0027701 + 5500 22.908286 -11.419431 1.4712698 1.0637119 1.0027701 + 5600 22.718634 -12.083974 1.5706808 1.0526316 1.0027701 + 5700 23.080763 -11.464882 1.2979578 1.0304709 1.0083102 + 5800 21.877026 -11.483185 0.279772 1.0360111 1.0027701 + 5900 22.526809 -10.868636 0.37121786 1.0637119 1.0083102 + 6000 22.908857 -10.311118 0.58244569 1.0526316 1.0083102 + 6100 22.399847 -10.222706 0.87875674 1.0858726 1.0027701 + 6200 22.623463 -10.035541 -0.25811274 1.0304709 1.0027701 + 6300 21.518006 -10.017552 -0.98187611 1.0470914 1.0083102 + 6400 21.269816 -11.297716 0.20058535 1.0138504 1.0027701 + 6500 23.362834 -11.263306 0.47670072 1.0692521 1.0027701 + 6600 23.705236 -12.358492 -0.63286237 1.0027701 1.0027701 + 6700 22.410623 -10.849516 0.57027834 1.0581717 1.0083102 + 6800 21.661639 -9.3981379 0.38726515 1.0470914 1.0027701 + 6900 21.856521 -8.8451751 0.053822789 1.0304709 1.0027701 + 7000 21.069495 -8.6443387 -0.10412144 1.0193906 1.0027701 + 7100 22.305494 -10.098469 -0.22662961 1.0581717 1.0027701 + 7200 23.52884 -11.055929 -0.099869868 1.0692521 1.0027701 + 7300 24.042008 -11.411758 2.0528788 1.0415512 1.0027701 + 7400 22.870777 -12.408763 0.33346225 1.0249307 1.0027701 + 7500 21.290152 -10.963058 0.26940112 1.0083102 1.0027701 + 7600 21.702686 -10.36214 0.84057004 1.0083102 1.0027701 + 7700 22.478034 -10.832724 -0.70855164 1.0747922 1.0027701 + 7800 22.856853 -11.161008 -0.88354803 1.0083102 1.0083102 + 7900 22.579842 -10.789899 0.40865274 1.0360111 1.0027701 + 8000 24.364281 -12.116023 -0.44788445 1.0249307 1.0083102 + 8100 22.993409 -10.261331 0.44712215 1.0193906 1.0027701 + 8200 23.006207 -10.723372 1.2357091 1.0415512 1.0083102 + 8300 23.292233 -10.041314 2.143692 1.0581717 1.0027701 + 8400 21.658087 -10.089378 -0.25838681 1.0083102 1.0027701 + 8500 23.268456 -10.356603 0.089787317 1.0526316 1.0083102 + 8600 22.572019 -10.32801 0.12320758 1.0526316 1.0027701 + 8700 22.970465 -10.662456 0.57027398 1.0581717 1.0083102 + 8800 23.515552 -10.415842 1.0048598 1.0138504 1.0083102 + 8900 22.733961 -10.343495 0.19917627 1.0360111 1.0083102 + 9000 21.835458 -9.8740971 -1.0653164 1.0193906 1.0027701 + 9100 22.062821 -9.2303832 0.21428267 1.0415512 1.0083102 + 9200 23.020404 -10.321542 -0.48757848 1.0193906 1.0083102 + 9300 22.529362 -9.2916938 0.57056277 1.0415512 1.0027701 + 9400 23.301911 -10.538876 0.80637627 1.0138504 1.0027701 + 9500 21.984286 -9.4754676 -0.19048233 1.0193906 1.0027701 + 9600 23.710224 -10.274983 0.72268146 1.0249307 1.0027701 + 9700 22.317038 -9.3509008 -0.45727658 1.0360111 1.0027701 + 9800 23.41615 -10.026331 -0.45909049 1.0415512 1.0027701 + 9900 22.130299 -11.18528 -0.15359132 1.0747922 1.0027701 + 10000 23.273859 -11.337403 0.4036321 1.0304709 1.0083102 +Loop time of 1.18289 on 2 procs for 10000 steps with 361 atoms + +Performance: 3652073.393 tau/day, 8453.874 timesteps/s +97.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.25191 | 0.25685 | 0.2618 | 1.0 | 21.71 +Bond | 0.097655 | 0.098332 | 0.099009 | 0.2 | 8.31 +Neigh | 0.53258 | 0.53993 | 0.54728 | 1.0 | 45.65 +Comm | 0.13457 | 0.15372 | 0.17288 | 4.9 | 13.00 +Output | 0.0013587 | 0.0016007 | 0.0018427 | 0.6 | 0.14 +Modify | 0.074109 | 0.074314 | 0.074518 | 0.1 | 6.28 +Other | | 0.05813 | | | 4.91 + +Nlocal: 180.5 ave 182 max 179 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 172.5 ave 175 max 170 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 1421 ave 1488 max 1354 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 2842 +Ave neighs/atom = 7.87258 +Ave special neighs/atom = 5.61773 +Neighbor list builds = 4884 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/balance/log.27Nov18.balance.bond.fast.g++.4 b/examples/balance/log.27Nov18.balance.bond.fast.g++.4 new file mode 100644 index 0000000000..5cd072cf66 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.bond.fast.g++.4 @@ -0,0 +1,242 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 +variable v index 5 +variable w index 2 + +units lj +dimension 2 +atom_style bond +boundary f f p + +lattice hex 0.85 +Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 +region box block 0 $x 0 $y -0.5 0.5 +region box block 0 50 0 $y -0.5 0.5 +region box block 0 50 0 20 -0.5 0.5 +create_box 1 box bond/types 1 extra/bond/per/atom 6 +Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) + 2 by 2 by 1 MPI processor grid +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 10 +create_atoms 1 region circle +Created 361 atoms + Time spent = 0.00067687 secs +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes +velocity all set 5 $w 0 sum yes +velocity all set 5 2 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +bond_style harmonic +bond_coeff 1 10.0 1.2 + +# need to preserve 1-3, 1-4 pairwise interactions during hard collisions + +special_bonds lj/coul 0 1 1 + 0 = max # of 1-2 neighbors + 1 = max # of special neighbors +create_bonds many all all 1 1.0 1.5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Added 1014 bonds, new total = 1014 + 6 = max # of 1-2 neighbors + 6 = max # of special neighbors + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 + +comm_style tiled +comm_modify cutoff 10.0 # because bonds stretch a long ways +fix 10 all balance 50 0.9 rcb + +#compute 1 all property/atom proc +#variable p atom (c_1%10)+1 +#dump 2 all custom 50 tmp.dump id v_p x y z + +#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string # "red green blue yellow white # purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 10 + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.141 | 5.174 Mbytes +Step Temp E_pair Press f_10[3] f_10 + 0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316 + 100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102 + 200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906 + 300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906 + 400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102 + 500 37.154928 -24.096946 3.2656177 1.3296399 1.0304709 + 600 35.059873 -21.524223 2.3729526 1.3296399 1.0083102 + 700 36.735117 -22.012675 3.266197 1.3296399 1.0083102 + 800 39.218223 -25.076176 4.7162461 1.4182825 1.0193906 + 900 38.003628 -24.598176 3.4651756 1.4958449 1.0083102 + 1000 37.599298 -25.117714 4.6714491 1.2963989 1.0193906 + 1100 35.587211 -24.476201 4.8766816 1.2077562 1.0083102 + 1200 33.05745 -21.457847 4.7304313 1.2188366 1.0193906 + 1300 35.505899 -20.103017 7.0543469 1.1523546 1.0193906 + 1400 32.687958 -18.411286 2.8022421 1.1523546 1.0083102 + 1500 30.681103 -13.979491 1.5780815 1.1523546 1.0083102 + 1600 28.134276 -12.408217 1.4370834 1.2188366 1.0193906 + 1700 29.150676 -12.486223 1.7118526 1.1745152 1.0083102 + 1800 29.456937 -11.386522 2.0484739 1.1966759 1.0193906 + 1900 28.029998 -11.168436 0.38519481 1.1080332 1.0193906 + 2000 29.476997 -12.337678 1.8878345 1.1523546 1.0083102 + 2100 30.113294 -12.201714 2.8003366 1.1634349 1.0193906 + 2200 31.599067 -13.710787 2.5654923 1.2188366 1.0083102 + 2300 31.333799 -12.269386 1.9573739 1.1412742 1.0193906 + 2400 28.587094 -10.98229 2.090581 1.1745152 1.0083102 + 2500 28.012332 -11.416553 2.3293146 1.1855956 1.0083102 + 2600 28.703189 -13.33369 2.7247345 1.1080332 1.0083102 + 2700 26.933934 -13.546384 0.71447362 1.0415512 1.0304709 + 2800 24.556936 -12.231427 0.012081842 1.0526316 1.0193906 + 2900 24.362943 -10.921093 -0.6063159 1.0858726 1.0193906 + 3000 24.583358 -10.025143 0.35975315 1.0637119 1.0083102 + 3100 26.119046 -10.124317 0.75140102 1.0415512 1.0193906 + 3200 27.665317 -11.418452 0.39942176 1.1301939 1.0083102 + 3300 27.771434 -9.9777413 0.94693011 1.1080332 1.0083102 + 3400 25.692188 -9.9016885 2.2582772 1.0415512 1.0083102 + 3500 27.009276 -10.504438 0.98279258 1.1301939 1.0083102 + 3600 26.082843 -9.4359595 -0.030819747 1.1301939 1.0083102 + 3700 23.956851 -8.4601884 -0.45748969 1.0858726 1.0304709 + 3800 24.92141 -8.3315871 -0.19512647 1.0969529 1.0083102 + 3900 26.048044 -9.6299934 0.40522014 1.0858726 1.0083102 + 4000 26.558961 -10.032084 0.56213613 1.1745152 1.0083102 + 4100 26.949686 -10.133598 1.0140825 1.0747922 1.0083102 + 4200 25.868196 -9.3971859 1.2758465 1.0969529 1.0083102 + 4300 24.563369 -9.5992996 0.17389949 1.1191136 1.0193906 + 4400 24.032818 -10.002668 0.10233743 1.0969529 1.0083102 + 4500 25.281577 -9.948799 0.7590423 1.1523546 1.0083102 + 4600 25.010901 -10.195479 -0.24424931 1.0747922 1.0193906 + 4700 25.062368 -9.2973021 1.1755931 1.0858726 1.0193906 + 4800 25.70912 -8.890895 1.0780397 1.1080332 1.0193906 + 4900 26.027757 -10.205469 1.0644859 1.1080332 1.0083102 + 5000 25.845739 -9.8511049 0.49059257 1.1301939 1.0193906 + 5100 25.614064 -9.0396911 0.40825814 1.0526316 1.0304709 + 5200 25.548135 -9.000613 0.81571441 1.1080332 1.0083102 + 5300 26.592601 -9.2385129 1.4983434 1.0637119 1.0193906 + 5400 26.230779 -9.8226036 1.0072462 1.0858726 1.0083102 + 5500 26.809887 -9.9569954 1.4074968 1.0415512 1.0083102 + 5600 25.722206 -10.240487 -0.5216434 1.0747922 1.0193906 + 5700 24.973866 -9.0820997 0.92104357 1.0193906 1.0083102 + 5800 24.257134 -9.5439897 -0.75290789 1.0858726 1.0083102 + 5900 25.524917 -8.9920216 1.2049479 1.1191136 1.0083102 + 6000 24.816532 -9.5865764 -0.66634446 1.0637119 1.0193906 + 6100 27.034385 -9.4017037 1.0769494 1.0969529 1.0083102 + 6200 24.19144 -8.2292864 0.97913204 1.0415512 1.0193906 + 6300 26.112877 -9.1531212 0.77578963 1.0526316 1.0193906 + 6400 25.820541 -9.9662231 -0.092724413 1.0969529 1.0193906 + 6500 26.181404 -9.5875764 -0.30106405 1.1634349 1.0083102 + 6600 27.770851 -8.8366116 0.94545206 1.0304709 1.0193906 + 6700 26.065489 -9.8223382 0.24640067 1.0526316 1.0193906 + 6800 27.468165 -10.160923 2.7263738 1.0747922 1.0304709 + 6900 27.317955 -10.356911 1.131609 1.0526316 1.0304709 + 7000 26.343789 -9.9153453 1.0385354 1.0858726 1.0193906 + 7100 24.366577 -8.9243936 0.37685043 1.0526316 1.0193906 + 7200 25.570042 -8.9195237 0.44206575 1.0637119 1.0193906 + 7300 24.635046 -8.4524117 -0.20581694 1.0193906 1.0193906 + 7400 27.161863 -7.9885934 1.1323072 1.0858726 1.0193906 + 7500 26.8044 -9.5703931 0.69476535 1.0858726 1.0193906 + 7600 27.381006 -10.702178 -0.20230101 1.0526316 1.0083102 + 7700 26.507406 -9.828117 0.50115907 1.0415512 1.0193906 + 7800 25.945271 -8.9912842 0.89121191 1.0747922 1.0083102 + 7900 24.498681 -7.7193231 -0.63874494 1.0858726 1.0083102 + 8000 24.517408 -7.6046107 -0.91642337 1.0415512 1.0083102 + 8100 26.388387 -8.1883906 0.093136981 1.1080332 1.0193906 + 8200 26.261054 -8.7223732 -0.086859057 1.0747922 1.0083102 + 8300 26.287026 -9.2583895 0.79506804 1.0858726 1.0083102 + 8400 24.691375 -9.0701909 -0.40058151 1.0637119 1.0193906 + 8500 25.390612 -7.9499801 0.59874113 1.1412742 1.0193906 + 8600 26.84383 -8.5520984 0.37618599 1.0637119 1.0083102 + 8700 25.685137 -7.688836 0.035978149 1.0415512 1.0193906 + 8800 26.614591 -9.0444146 0.20671465 1.0193906 1.0083102 + 8900 25.782718 -8.2594705 0.54378816 1.0747922 1.0304709 + 9000 26.026886 -8.6777252 0.25418163 1.1191136 1.0083102 + 9100 27.246916 -9.0307861 1.211131 1.0526316 1.0193906 + 9200 27.282948 -9.180029 -0.0056269613 1.0747922 1.0083102 + 9300 27.029692 -8.7791461 0.35971649 1.0304709 1.0083102 + 9400 26.549013 -7.5083174 0.77607249 1.0969529 1.0193906 + 9500 25.533731 -9.2763668 0.28360762 1.0969529 1.0083102 + 9600 27.997538 -9.2766769 1.6968428 1.0637119 1.0083102 + 9700 26.977436 -9.21372 1.8007256 1.0637119 1.0083102 + 9800 25.547091 -9.1024445 -0.29158273 1.0969529 1.0193906 + 9900 26.378841 -8.7645665 1.0385835 1.1080332 1.0083102 + 10000 26.699368 -8.5450739 0.19591452 1.0526316 1.0193906 +Loop time of 0.916576 on 4 procs for 10000 steps with 361 atoms + +Performance: 4713193.307 tau/day, 10910.170 timesteps/s +92.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.10915 | 0.12374 | 0.14167 | 3.5 | 13.50 +Bond | 0.047075 | 0.049849 | 0.054161 | 1.2 | 5.44 +Neigh | 0.31176 | 0.3246 | 0.3384 | 1.7 | 35.41 +Comm | 0.24271 | 0.26717 | 0.30549 | 4.9 | 29.15 +Output | 0.0017068 | 0.0021075 | 0.0031145 | 1.3 | 0.23 +Modify | 0.064639 | 0.065705 | 0.067641 | 0.5 | 7.17 +Other | | 0.08341 | | | 9.10 + +Nlocal: 90.25 ave 92 max 89 min +Histogram: 1 0 0 2 0 0 0 0 0 1 +Nghost: 248.25 ave 264 max 230 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 569.5 ave 657 max 519 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 2278 +Ave neighs/atom = 6.31025 +Ave special neighs/atom = 5.61773 +Neighbor list builds = 4964 +Dangerous builds = 14 +Total wall time: 0:00:00 diff --git a/examples/balance/log.27Nov18.balance.bond.slow.g++.2 b/examples/balance/log.27Nov18.balance.bond.slow.g++.2 new file mode 100644 index 0000000000..5e23613f1f --- /dev/null +++ b/examples/balance/log.27Nov18.balance.bond.slow.g++.2 @@ -0,0 +1,541 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 + +# careful not to slam into wall too hard + +variable v index 0.3 +variable w index 0.08 + +units lj +dimension 2 +atom_style bond +boundary f f p + +lattice hex 0.85 +Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 +region box block 0 $x 0 $y -0.5 0.5 +region box block 0 50 0 $y -0.5 0.5 +region box block 0 50 0 20 -0.5 0.5 +create_box 1 box bond/types 1 extra/bond/per/atom 6 +Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) + 2 by 1 by 1 MPI processor grid +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 10 +create_atoms 1 region circle +Created 361 atoms + Time spent = 0.000762701 secs +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes +velocity all set 0.3 $w 0 sum yes +velocity all set 0.3 0.08 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +bond_style harmonic +bond_coeff 1 10.0 1.2 + +create_bonds many all all 1 1.0 1.5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Added 1014 bonds, new total = 1014 + 6 = max # of 1-2 neighbors + 30 = max # of 1-3 neighbors + 180 = max # of 1-4 neighbors + 36 = max # of special neighbors + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 + +comm_style tiled +fix 10 all balance 50 0.9 rcb + +#compute 1 all property/atom proc +#variable p atom (c_1%10)+1 +#dump 2 all custom 50 tmp.dump id v_p x y z + +#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string # "red green blue yellow white # purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 40000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.079 | 7.108 | 7.137 Mbytes +Step Temp E_pair Press f_10[3] f_10 + 0 0.57437856 0 0.26099453 2 1.0193906 + 100 0.29756515 0 0.10149401 1.0027701 1.0027701 + 200 0.35394813 0 0.075159099 1.0027701 1.0083102 + 300 0.39245849 0 0.033002384 1.0027701 1.0027701 + 400 0.34078347 0 -0.020825841 1.0083102 1.0027701 + 500 0.35201095 0 -0.062637506 1.0027701 1.0027701 + 600 0.34014717 0 -0.11122965 1.0249307 1.0027701 + 700 0.3323524 0 -0.11598015 1.0083102 1.0027701 + 800 0.35116047 0 -0.096162395 1.0138504 1.0027701 + 900 0.35695352 0 -0.01385176 1.0249307 1.0027701 + 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1.0083102 1.0027701 + 29400 0.34846892 0 0.020765104 1.0027701 1.0027701 + 29500 0.3416255 0 0.022650856 1.0083102 1.0027701 + 29600 0.33725496 0 0.020693083 1.0027701 1.0027701 + 29700 0.34480638 0 0.024317128 1.0138504 1.0027701 + 29800 0.31459471 0 0.023097895 1.0027701 1.0027701 + 29900 0.33014448 0 0.03114046 1.0138504 1.0027701 + 30000 0.33741498 0 0.015624314 1.0083102 1.0027701 + 30100 0.32598657 0 -0.0018860541 1.0138504 1.0027701 + 30200 0.34855815 0 0.0017983372 1.0027701 1.0027701 + 30300 0.33375921 0 0.0010991235 1.0083102 1.0083102 + 30400 0.35008944 0 -0.0027316177 1.0027701 1.0027701 + 30500 0.33279729 0 -0.0035788551 1.0027701 1.0027701 + 30600 0.33868746 0 -0.0016249482 1.0027701 1.0027701 + 30700 0.33597034 0 -0.0014524001 1.0193906 1.0083102 + 30800 0.3227257 0 0.016353457 1.0193906 1.0027701 + 30900 0.32676516 0 0.027396654 1.0027701 1.0027701 + 31000 0.34083982 0 0.031606413 1.0138504 1.0083102 + 31100 0.32165238 0 0.013583368 1.0027701 1.0027701 + 31200 0.3428492 0 0.020486611 1.0138504 1.0027701 + 31300 0.32372541 0 0.01215566 1.0027701 1.0027701 + 31400 0.32734692 0 0.016229397 1.0083102 1.0027701 + 31500 0.33089262 0 0.0060426618 1.0027701 1.0027701 + 31600 0.34273493 0 -0.013456537 1.0083102 1.0083102 + 31700 0.32723905 0 -0.019243766 1.0027701 1.0027701 + 31800 0.33636488 0 0.0027814902 1.0027701 1.0083102 + 31900 0.32834805 0 0.00706877 1.0083102 1.0027701 + 32000 0.33995148 0 0.0018383309 1.0083102 1.0083102 + 32100 0.33412282 0 0.0076455933 1.0027701 1.0083102 + 32200 0.34334884 0 0.023586129 1.0083102 1.0027701 + 32300 0.32778925 0 0.020564321 1.0193906 1.0083102 + 32400 0.33163443 0 0.038878463 1.0083102 1.0027701 + 32500 0.32290345 0 0.022247461 1.0027701 1.0027701 + 32600 0.34113954 0 0.010966365 1.0138504 1.0027701 + 32700 0.33390633 0 0.0037777555 1.0083102 1.0083102 + 32800 0.34385341 0 0.010556575 1.0138504 1.0083102 + 32900 0.32137047 0 0.00022027143 1.0138504 1.0027701 + 33000 0.32079172 0 -0.017261272 1.0083102 1.0027701 + 33100 0.33570882 0 -0.0051942206 1.0027701 1.0027701 + 33200 0.34320894 0 -0.011515281 1.0138504 1.0027701 + 33300 0.32794746 0 -0.0018153673 1.0027701 1.0027701 + 33400 0.33060982 0 0.027118146 1.0027701 1.0027701 + 33500 0.33641809 0 0.02143035 1.0083102 1.0027701 + 33600 0.33643061 0 0.020833068 1.0083102 1.0027701 + 33700 0.3485949 0 0.030918751 1.0083102 1.0027701 + 33800 0.3283985 0 0.01947613 1.0193906 1.0027701 + 33900 0.31959761 0 0.021128147 1.0027701 1.0027701 + 34000 0.33897984 0 0.015270986 1.0027701 1.0083102 + 34100 0.32392267 0 0.0020130852 1.0083102 1.0027701 + 34200 0.33084514 0 -0.024316708 1.0027701 1.0027701 + 34300 0.3342259 0 -0.0059047764 1.0138504 1.0027701 + 34400 0.33385098 0 0.0063818721 1.0027701 1.0027701 + 34500 0.33255603 0 -0.01023837 1.0027701 1.0083102 + 34600 0.34766173 0 0.0056703013 1.0083102 1.0027701 + 34700 0.339822 0 0.0061648559 1.0083102 1.0027701 + 34800 0.33902329 0 0.030037037 1.0027701 1.0083102 + 34900 0.3216153 0 0.027996689 1.0027701 1.0027701 + 35000 0.32701056 0 0.024778517 1.0083102 1.0027701 + 35100 0.3124942 0 0.011316548 1.0027701 1.0027701 + 35200 0.34486416 0 0.011670127 1.0027701 1.0027701 + 35300 0.33275353 0 0.020491246 1.0027701 1.0027701 + 35400 0.33618763 0 0.014678874 1.0083102 1.0027701 + 35500 0.32352282 0 -0.018568683 1.0027701 1.0027701 + 35600 0.32617903 0 -0.012796912 1.0083102 1.0027701 + 35700 0.32378048 0 -0.021318585 1.0027701 1.0083102 + 35800 0.3371086 0 -0.0023678632 1.0027701 1.0083102 + 35900 0.33818476 0 0.011197742 1.0083102 1.0027701 + 36000 0.35142144 0 0.022520935 1.0083102 1.0027701 + 36100 0.35147297 0 0.020277852 1.0083102 1.0027701 + 36200 0.33489465 0 0.014564878 1.0193906 1.0027701 + 36300 0.33841515 0 0.036439962 1.0027701 1.0027701 + 36400 0.32301096 0 0.019966746 1.0027701 1.0027701 + 36500 0.35612028 0 0.036509556 1.0027701 1.0027701 + 36600 0.33841597 0 -0.0042180605 1.0083102 1.0083102 + 36700 0.34477654 0 -0.0052770853 1.0193906 1.0083102 + 36800 0.33804317 0 -0.013751733 1.0027701 1.0027701 + 36900 0.35003816 0 -0.0021184393 1.0027701 1.0027701 + 37000 0.32965041 0 -0.020900951 1.0083102 1.0027701 + 37100 0.34653095 0 -0.013667977 1.0027701 1.0027701 + 37200 0.35019871 0 -0.0071740923 1.0027701 1.0027701 + 37300 0.34859745 0 0.02006041 1.0138504 1.0027701 + 37400 0.35739859 0 0.020892822 1.0083102 1.0027701 + 37500 0.34128859 0 0.041072111 1.0083102 1.0083102 + 37600 0.33781905 0 0.023376738 1.0083102 1.0083102 + 37700 0.32961874 0 0.030953741 1.0138504 1.0027701 + 37800 0.343987 0 0.029579795 1.0083102 1.0027701 + 37900 0.33610448 0 0.036836828 1.0138504 1.0027701 + 38000 0.32757228 0 0.020902031 1.0027701 1.0027701 + 38100 0.32735808 0 0.019544751 1.0138504 1.0083102 + 38200 0.35646953 0 0.044607528 1.0027701 1.0083102 + 38300 0.32509773 0 0.03610738 1.0138504 1.0027701 + 38400 0.32111741 0 0.034474043 1.0083102 1.0083102 + 38500 0.30590608 0 0.053461212 1.0083102 1.0027701 + 38600 0.32322402 0 0.053453832 1.0138504 1.0083102 + 38700 0.33843057 0 0.076264534 1.0027701 1.0027701 + 38800 0.31350741 0 0.064733869 1.0083102 1.0027701 + 38900 0.31943061 0 0.067836769 1.0083102 1.0027701 + 39000 0.33775583 0 0.0788316 1.0083102 1.0083102 + 39100 0.34256036 0 0.075874935 1.0027701 1.0027701 + 39200 0.33128527 0 0.071610976 1.0193906 1.0027701 + 39300 0.34519653 0 0.046257301 1.0083102 1.0083102 + 39400 0.34351844 0 0.052422917 1.0027701 1.0027701 + 39500 0.35716037 0 0.048916058 1.0083102 1.0027701 + 39600 0.34000737 0 0.016149089 1.0083102 1.0027701 + 39700 0.34587892 0 0.021619621 1.0083102 1.0083102 + 39800 0.34878036 0 0.0092881327 1.0083102 1.0027701 + 39900 0.35225411 0 -0.011341599 1.0083102 1.0027701 + 40000 0.36309266 0 0.0050869295 1.0304709 1.0027701 +Loop time of 1.30389 on 2 procs for 40000 steps with 361 atoms + +Performance: 13252650.572 tau/day, 30677.432 timesteps/s +97.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.041365 | 0.041785 | 0.042204 | 0.2 | 3.20 +Bond | 0.35501 | 0.37082 | 0.38664 | 2.6 | 28.44 +Neigh | 0.30901 | 0.31013 | 0.31125 | 0.2 | 23.78 +Comm | 0.12939 | 0.15871 | 0.18803 | 7.4 | 12.17 +Output | 0.00489 | 0.005671 | 0.0064521 | 1.0 | 0.43 +Modify | 0.28208 | 0.28362 | 0.28516 | 0.3 | 21.75 +Other | | 0.1332 | | | 10.21 + +Nlocal: 180.5 ave 181 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 52.5 ave 53 max 52 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 0 +Ave neighs/atom = 0 +Ave special neighs/atom = 31.0249 +Neighbor list builds = 3079 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/balance/log.5Oct16.balance.bond.slow.g++.4 b/examples/balance/log.27Nov18.balance.bond.slow.g++.4 similarity index 85% rename from examples/balance/log.5Oct16.balance.bond.slow.g++.4 rename to examples/balance/log.27Nov18.balance.bond.slow.g++.4 index 7e50516242..c799657e53 100644 --- a/examples/balance/log.5Oct16.balance.bond.slow.g++.4 +++ b/examples/balance/log.27Nov18.balance.bond.slow.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d circle of particles inside a box with LJ walls variable b index 0 @@ -31,6 +32,7 @@ region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) region circle sphere 11 6.7735026918962581988 0.0 10 create_atoms 1 region circle Created 361 atoms + Time spent = 0.000665188 secs mass 1 1.0 velocity all create 0.5 87287 loop geom @@ -44,14 +46,24 @@ pair_coeff 1 1 10.0 1.0 2.5 bond_style harmonic bond_coeff 1 10.0 1.2 -create_bonds all all 1 1.0 1.5 +create_bonds many all all 1 1.0 1.5 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 42 29 1 + binsize = 1.4, bins = 42 29 1 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command create_bonds, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard Added 1014 bonds, new total = 1014 6 = max # of 1-2 neighbors 30 = max # of 1-3 neighbors @@ -84,106 +96,111 @@ thermo 100 run 40000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 42 29 1 -Memory usage per processor = 6.41878 Mbytes + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.02 | 7.048 | 7.096 Mbytes Step Temp E_pair Press f_10[3] f_10 0 0.57437856 0 0.26099453 3.2354571 1.0526316 100 0.29756515 0 0.10149401 1.0193906 1.0083102 - 200 0.35394813 0 0.075159099 1.0304709 1.0083102 - 300 0.39245849 0 0.033002384 1.0304709 1.0193906 + 200 0.35394813 0 0.075159099 1.0304709 1.0193906 + 300 0.39245849 0 0.033002384 1.0083102 1.0193906 400 0.34078347 0 -0.020825841 1.0304709 1.0083102 500 0.35201095 0 -0.062637506 1.0193906 1.0083102 600 0.34014717 0 -0.11122965 1.0415512 1.0083102 700 0.3323524 0 -0.11598015 1.0193906 1.0083102 - 800 0.35116047 0 -0.096162395 1.0083102 1.0193906 + 800 0.35116047 0 -0.096162395 1.0193906 1.0193906 900 0.35695352 0 -0.01385176 1.0526316 1.0193906 1000 0.36986539 0 0.056772858 1.0083102 1.0083102 - 1100 0.34584644 0 0.084941323 1.0193906 1.0083102 - 1200 0.31921435 0 0.10545078 1.0415512 1.0193906 - 1300 0.32952819 0 0.124902 1.0083102 1.0083102 + 1100 0.34584644 0 0.084941323 1.0304709 1.0083102 + 1200 0.31921435 0 0.10545078 1.0415512 1.0083102 + 1300 0.32952819 0 0.124902 1.0083102 1.0193906 1400 0.34497365 0 0.12662081 1.0193906 1.0083102 - 1500 0.33429243 0 0.096230972 1.0526316 1.0193906 + 1500 0.33429243 0 0.096230972 1.0193906 1.0193906 1600 0.33765387 0 0.025800542 1.0304709 1.0083102 1700 0.35134464 0 -0.04422593 1.0415512 1.0083102 - 1800 0.35003859 0 -0.096745576 1.0304709 1.0193906 + 1800 0.35003859 0 -0.096745576 1.0304709 1.0083102 1900 0.33839618 0 -0.095465943 1.0193906 1.0083102 2000 0.33732078 0 -0.094652802 1.0083102 1.0083102 2100 0.34552238 0 -0.076729261 1.0304709 1.0083102 - 2200 0.34893142 0 -0.036853228 1.0304709 1.0193906 - 2300 0.35379341 0 0.021124847 1.0304709 1.0304709 - 2400 0.34829744 0 0.09230184 1.0304709 1.0193906 + 2200 0.34893142 0 -0.036853228 1.0304709 1.0083102 + 2300 0.35379341 0 0.021124847 1.0304709 1.0193906 + 2400 0.34829744 0 0.09230184 1.0304709 1.0083102 2500 0.33038141 0 0.1399855 1.0193906 1.0193906 - 2600 0.30983019 0 0.12754742 1.0193906 1.0083102 - 2700 0.32992561 0 0.10485138 1.0415512 1.0304709 + 2600 0.30983019 0 0.12754742 1.0083102 1.0083102 + 2700 0.32992561 0 0.10485138 1.0415512 1.0083102 2800 0.34604747 0 0.066174138 1.0083102 1.0083102 2900 0.3444791 0 0.036590652 1.0193906 1.0193906 - 3000 0.34721342 0 -0.023793368 1.0193906 1.0083102 + 3000 0.34721342 0 -0.023793368 1.0193906 1.0193906 3100 0.33404314 0 -0.08374223 1.0415512 1.0083102 - 3200 0.33019355 0 -0.12715599 1.0083102 1.0083102 + 3200 0.33019355 0 -0.12715599 1.0083102 1.0304709 3300 0.33515177 0 -0.12217394 1.0193906 1.0083102 3400 0.33628481 0 -0.070877624 1.0193906 1.0083102 3500 0.34257038 0 -0.021612062 1.0304709 1.0083102 3600 0.32838009 0 0.030131228 1.0083102 1.0083102 - 3700 0.34462142 0 0.074586378 1.0415512 1.0083102 + 3700 0.34462142 0 0.074586378 1.0526316 1.0193906 3800 0.30891825 0 0.10605673 1.0304709 1.0083102 - 3900 0.33847951 0 0.13956139 1.0415512 1.0193906 + 3900 0.33847951 0 0.13956139 1.0083102 1.0083102 4000 0.32952079 0 0.12688129 1.0193906 1.0304709 4100 0.32646772 0 0.081089042 1.0304709 1.0193906 4200 0.35399503 0 0.013422873 1.0083102 1.0083102 - 4300 0.33154914 0 -0.050919508 1.0083102 1.0193906 - 4400 0.34113556 0 -0.083171 1.0415512 1.0083102 - 4500 0.32651708 0 -0.1063133 1.0193906 1.0083102 - 4600 0.34359609 0 -0.1076395 1.0083102 1.0193906 + 4300 0.33154914 0 -0.050919508 1.0193906 1.0193906 + 4400 0.34113556 0 -0.083171 1.0304709 1.0083102 + 4500 0.32651708 0 -0.1063133 1.0304709 1.0083102 + 4600 0.34359609 0 -0.1076395 1.0083102 1.0083102 4700 0.34973537 0 -0.088231606 1.0415512 1.0083102 4800 0.35198515 0 -0.020901044 1.0415512 1.0083102 - 4900 0.35187284 0 0.043645941 1.0193906 1.0083102 + 4900 0.35187284 0 0.043645941 1.0415512 1.0083102 5000 0.34887336 0 0.095698609 1.0193906 1.0083102 - 5100 0.30308163 0 0.11649328 1.0083102 1.0083102 + 5100 0.30308163 0 0.11649328 1.0193906 1.0083102 5200 0.32401285 0 0.12072411 1.0193906 1.0083102 - 5300 0.33025072 0 0.10933161 1.0304709 1.0083102 + 5300 0.33025072 0 0.10933161 1.0193906 1.0083102 5400 0.33288012 0 0.078356448 1.0083102 1.0193906 5500 0.35142492 0 0.036958063 1.0193906 1.0083102 5600 0.35125368 0 -0.041371343 1.0304709 1.0083102 5700 0.34547744 0 -0.096450846 1.0637119 1.0083102 - 5800 0.30939887 0 -0.12356656 1.0083102 1.0083102 - 5900 0.32315628 0 -0.11338676 1.0193906 1.0304709 - 6000 0.34117485 0 -0.066198961 1.0193906 1.0193906 + 5800 0.30939887 0 -0.12356656 1.0083102 1.0193906 + 5900 0.32315628 0 -0.11338676 1.0193906 1.0193906 + 6000 0.34117485 0 -0.066198961 1.0193906 1.0083102 6100 0.35298043 0 -0.016172816 1.0304709 1.0193906 6200 0.35130653 0 0.027660468 1.0415512 1.0083102 - 6300 0.35398766 0 0.087221238 1.0083102 1.0193906 - 6400 0.30963379 0 0.11990957 1.0193906 1.0083102 + 6300 0.35398766 0 0.087221238 1.0083102 1.0083102 + 6400 0.30963379 0 0.11990957 1.0415512 1.0083102 6500 0.3174541 0 0.14103528 1.0193906 1.0193906 - 6600 0.31989791 0 0.11575506 1.0415512 1.0193906 - 6700 0.33811477 0 0.060747353 1.0083102 1.0193906 - 6800 0.3424043 0 0.010357152 1.0304709 1.0083102 + 6600 0.31989791 0 0.11575506 1.0304709 1.0193906 + 6700 0.33811477 0 0.060747353 1.0415512 1.0193906 + 6800 0.3424043 0 0.010357152 1.0193906 1.0083102 6900 0.34804319 0 -0.042621786 1.0193906 1.0083102 - 7000 0.35357865 0 -0.067248959 1.0304709 1.0083102 + 7000 0.35357865 0 -0.067248959 1.0083102 1.0083102 7100 0.33556885 0 -0.10983726 1.0193906 1.0083102 7200 0.33531101 0 -0.112179 1.0304709 1.0083102 7300 0.35742607 0 -0.078405267 1.0304709 1.0193906 7400 0.34577559 0 -0.01985432 1.0193906 1.0083102 7500 0.3498641 0 0.052289439 1.0526316 1.0083102 7600 0.33773715 0 0.092939035 1.0083102 1.0193906 - 7700 0.33093497 0 0.11924405 1.0193906 1.0083102 + 7700 0.33093497 0 0.11924405 1.0304709 1.0083102 7800 0.31435814 0 0.12701724 1.0083102 1.0304709 - 7900 0.33132217 0 0.10793075 1.0193906 1.0083102 - 8000 0.33451798 0 0.077993125 1.0304709 1.0083102 - 8100 0.35188371 0 0.019929977 1.0193906 1.0193906 + 7900 0.33132217 0 0.10793075 1.0083102 1.0083102 + 8000 0.33451798 0 0.077993125 1.0304709 1.0193906 + 8100 0.35188371 0 0.019929977 1.0193906 1.0083102 8200 0.33645742 0 -0.039302079 1.0193906 1.0193906 - 8300 0.3415632 0 -0.098067982 1.0304709 1.0083102 - 8400 0.30619282 0 -0.12952879 1.0193906 1.0193906 + 8300 0.3415632 0 -0.098067982 1.0193906 1.0083102 + 8400 0.30619282 0 -0.12952879 1.0304709 1.0193906 8500 0.34446484 0 -0.098084709 1.0083102 1.0083102 8600 0.33761673 0 -0.07069818 1.0193906 1.0083102 - 8700 0.34495452 0 -0.022458056 1.0193906 1.0193906 - 8800 0.33502983 0 0.027742411 1.0304709 1.0083102 - 8900 0.35418591 0 0.092390134 1.0083102 1.0083102 + 8700 0.34495452 0 -0.022458056 1.0193906 1.0083102 + 8800 0.33502983 0 0.027742411 1.0193906 1.0083102 + 8900 0.35418591 0 0.092390134 1.0083102 1.0193906 9000 0.31648387 0 0.12467398 1.0193906 1.0083102 - 9100 0.33994825 0 0.14460327 1.0193906 1.0193906 + 9100 0.33994825 0 0.14460327 1.0193906 1.0083102 9200 0.33822571 0 0.11273284 1.0193906 1.0083102 9300 0.33260773 0 0.060063671 1.0083102 1.0193906 9400 0.36140305 0 0.021427642 1.0193906 1.0083102 @@ -192,78 +209,78 @@ Step Temp E_pair Press f_10[3] f_10 9700 0.32088235 0 -0.12027075 1.0193906 1.0083102 9800 0.3320823 0 -0.11602794 1.0415512 1.0083102 9900 0.33916442 0 -0.080281044 1.0083102 1.0083102 - 10000 0.34852268 0 -0.01000914 1.0193906 1.0193906 + 10000 0.34852268 0 -0.01000914 1.0193906 1.0083102 10100 0.32955942 0 0.04258493 1.0083102 1.0083102 10200 0.34487898 0 0.086971308 1.0304709 1.0083102 - 10300 0.32325593 0 0.11558149 1.0304709 1.0083102 - 10400 0.30927871 0 0.12239437 1.0083102 1.0193906 + 10300 0.32325593 0 0.11558149 1.0304709 1.0193906 + 10400 0.30927871 0 0.12239437 1.0083102 1.0083102 10500 0.33176799 0 0.12285937 1.0193906 1.0083102 - 10600 0.35120027 0 0.084897432 1.0083102 1.0083102 + 10600 0.35120027 0 0.084897432 1.0415512 1.0083102 10700 0.33129697 0 0.0053089279 1.0193906 1.0193906 10800 0.36028769 0 -0.04280715 1.0193906 1.0083102 - 10900 0.35552287 0 -0.084955999 1.0193906 1.0304709 + 10900 0.35552287 0 -0.084955999 1.0193906 1.0193906 11000 0.3406024 0 -0.096554577 1.0083102 1.0083102 - 11100 0.33041202 0 -0.10703492 1.0304709 1.0083102 - 11200 0.32442686 0 -0.084328121 1.0304709 1.0083102 - 11300 0.35952468 0 -0.020191965 1.0304709 1.0193906 - 11400 0.34610624 0 0.03440148 1.0193906 1.0083102 - 11500 0.3415612 0 0.1041929 1.0193906 1.0193906 - 11600 0.34040042 0 0.13215705 1.0304709 1.0193906 - 11700 0.33555094 0 0.12738686 1.0083102 1.0304709 - 11800 0.3458647 0 0.10963398 1.0193906 1.0193906 + 11100 0.33041202 0 -0.10703492 1.0304709 1.0193906 + 11200 0.32442686 0 -0.084328121 1.0304709 1.0193906 + 11300 0.35952468 0 -0.020191965 1.0304709 1.0083102 + 11400 0.34610624 0 0.03440148 1.0193906 1.0193906 + 11500 0.3415612 0 0.1041929 1.0193906 1.0083102 + 11600 0.34040042 0 0.13215705 1.0304709 1.0083102 + 11700 0.33555094 0 0.12738686 1.0415512 1.0193906 + 11800 0.3458647 0 0.10963398 1.0083102 1.0193906 11900 0.33836678 0 0.067253864 1.0193906 1.0193906 12000 0.34853314 0 0.03201448 1.0193906 1.0083102 - 12100 0.34600048 0 -0.034833402 1.0304709 1.0083102 + 12100 0.34600048 0 -0.034833402 1.0304709 1.0193906 12200 0.33145631 0 -0.09865675 1.0193906 1.0193906 - 12300 0.32848884 0 -0.1248489 1.0193906 1.0193906 + 12300 0.32848884 0 -0.1248489 1.0193906 1.0083102 12400 0.3321344 0 -0.11266575 1.0083102 1.0083102 12500 0.32622305 0 -0.061634993 1.0304709 1.0083102 12600 0.36213537 0 -0.0090593315 1.0526316 1.0083102 12700 0.34673866 0 0.036734645 1.0193906 1.0083102 12800 0.34606618 0 0.086267678 1.0193906 1.0083102 - 12900 0.34271431 0 0.12415522 1.0304709 1.0083102 + 12900 0.34271431 0 0.12415522 1.0193906 1.0083102 13000 0.31993287 0 0.13879926 1.0193906 1.0193906 13100 0.3422918 0 0.11978905 1.0083102 1.0083102 - 13200 0.33055236 0 0.062620483 1.0193906 1.0083102 - 13300 0.34652207 0 0.0043833459 1.0304709 1.0193906 - 13400 0.33574661 0 -0.04691024 1.0304709 1.0193906 - 13500 0.33940837 0 -0.074241604 1.0304709 1.0193906 + 13200 0.33055236 0 0.062620483 1.0083102 1.0083102 + 13300 0.34652207 0 0.0043833459 1.0304709 1.0083102 + 13400 0.33574661 0 -0.04691024 1.0304709 1.0083102 + 13500 0.33940837 0 -0.074241604 1.0304709 1.0083102 13600 0.32093414 0 -0.1078027 1.0193906 1.0083102 13700 0.34336597 0 -0.10544097 1.0193906 1.0083102 13800 0.35806461 0 -0.072531559 1.0193906 1.0083102 - 13900 0.35209713 0 -0.018851408 1.0083102 1.0083102 + 13900 0.35209713 0 -0.018851408 1.0193906 1.0083102 14000 0.35702629 0 0.061046366 1.0083102 1.0083102 14100 0.33234093 0 0.094086465 1.0083102 1.0083102 - 14200 0.3459466 0 0.12186656 1.0193906 1.0083102 + 14200 0.3459466 0 0.12186656 1.0193906 1.0193906 14300 0.3327428 0 0.11396572 1.0193906 1.0083102 14400 0.32409443 0 0.10658903 1.0193906 1.0193906 - 14500 0.35022184 0 0.083558031 1.0083102 1.0193906 - 14600 0.34823843 0 0.024605569 1.0083102 1.0083102 + 14500 0.35022184 0 0.083558031 1.0083102 1.0083102 + 14600 0.34823843 0 0.024605569 1.0083102 1.0193906 14700 0.35298973 0 -0.040418888 1.0193906 1.0083102 14800 0.33679845 0 -0.10067728 1.0193906 1.0083102 - 14900 0.32790966 0 -0.10925568 1.0193906 1.0083102 + 14900 0.32790966 0 -0.10925568 1.0193906 1.0193906 15000 0.34208495 0 -0.09568004 1.0193906 1.0083102 15100 0.33647529 0 -0.055652929 1.0083102 1.0083102 - 15200 0.35328398 0 -0.020236536 1.0193906 1.0193906 - 15300 0.34252669 0 0.026434179 1.0083102 1.0193906 + 15200 0.35328398 0 -0.020236536 1.0415512 1.0193906 + 15300 0.34252669 0 0.026434179 1.0304709 1.0083102 15400 0.34409435 0 0.094410599 1.0304709 1.0083102 - 15500 0.32288994 0 0.12034455 1.0415512 1.0083102 + 15500 0.32288994 0 0.12034455 1.0304709 1.0193906 15600 0.32109689 0 0.13645185 1.0193906 1.0083102 - 15700 0.33681572 0 0.098607746 1.0415512 1.0083102 - 15800 0.33635195 0 0.05570715 1.0193906 1.0193906 - 15900 0.34289757 0 0.013849092 1.0304709 1.0193906 + 15700 0.33681572 0 0.098607746 1.0415512 1.0193906 + 15800 0.33635195 0 0.05570715 1.0193906 1.0083102 + 15900 0.34289757 0 0.013849092 1.0304709 1.0083102 16000 0.34225547 0 -0.035597548 1.0304709 1.0083102 16100 0.33660991 0 -0.076931881 1.0193906 1.0193906 - 16200 0.32802152 0 -0.12765884 1.0083102 1.0083102 + 16200 0.32802152 0 -0.12765884 1.0083102 1.0193906 16300 0.3469374 0 -0.10785455 1.0083102 1.0083102 16400 0.34053641 0 -0.070259853 1.0193906 1.0083102 - 16500 0.34610591 0 -0.014315306 1.0193906 1.0083102 + 16500 0.34610591 0 -0.014315306 1.0193906 1.0193906 16600 0.35109001 0 0.041251169 1.0304709 1.0083102 16700 0.34336905 0 0.077996627 1.0193906 1.0083102 16800 0.33277414 0 0.11053634 1.0083102 1.0083102 16900 0.32183338 0 0.11680626 1.0193906 1.0083102 17000 0.34044352 0 0.10806555 1.0193906 1.0083102 - 17100 0.32967873 0 0.067759786 1.0304709 1.0193906 + 17100 0.32967873 0 0.067759786 1.0193906 1.0193906 17200 0.36172278 0 -0.0048631904 1.0304709 1.0083102 17300 0.35619435 0 -0.04215545 1.0193906 1.0083102 17400 0.34540936 0 -0.093994174 1.0193906 1.0083102 @@ -271,13 +288,13 @@ Step Temp E_pair Press f_10[3] f_10 17600 0.3544756 0 -0.085660403 1.0193906 1.0083102 17700 0.34505209 0 -0.069640515 1.0304709 1.0193906 17800 0.36291124 0 -0.0063088133 1.0083102 1.0193906 - 17900 0.34255705 0 0.046794555 1.0304709 1.0083102 + 17900 0.34255705 0 0.046794555 1.0304709 1.0193906 18000 0.34163238 0 0.11767705 1.0193906 1.0193906 18100 0.3466445 0 0.1351712 1.0415512 1.0193906 18200 0.33037668 0 0.12703659 1.0083102 1.0083102 18300 0.33677404 0 0.10956306 1.0083102 1.0304709 18400 0.34978954 0 0.087193072 1.0193906 1.0193906 - 18500 0.33354363 0 0.051095814 1.0526316 1.0083102 + 18500 0.33354363 0 0.051095814 1.0526316 1.0193906 18600 0.34651729 0 0.0056245561 1.0304709 1.0193906 18700 0.32622232 0 -0.047319269 1.0083102 1.0193906 18800 0.32978847 0 -0.054929416 1.0304709 1.0193906 @@ -298,12 +315,12 @@ Step Temp E_pair Press f_10[3] f_10 20300 0.34195438 0 0.072811099 1.0304709 1.0193906 20400 0.31249563 0 0.10063541 1.0415512 1.0083102 20500 0.31544938 0 0.1405794 1.0083102 1.0083102 - 20600 0.30071644 0 0.12763486 1.0193906 1.0304709 + 20600 0.30071644 0 0.12763486 1.0193906 1.0193906 20700 0.2890265 0 0.1136651 1.0083102 1.0083102 20800 0.28962296 0 0.094481978 1.0193906 1.0083102 20900 0.29447212 0 0.0967165 1.0193906 1.0193906 21000 0.31159961 0 0.067307231 1.0083102 1.0083102 - 21100 0.30490648 0 0.017689358 1.0083102 1.0193906 + 21100 0.30490648 0 0.017689358 1.0083102 1.0304709 21200 0.30687262 0 -0.016055512 1.0193906 1.0193906 21300 0.30083286 0 -0.0014988997 1.0193906 1.0083102 21400 0.32070426 0 0.015960302 1.0083102 1.0083102 @@ -316,7 +333,7 @@ Step Temp E_pair Press f_10[3] f_10 22100 0.34857705 0 0.032731746 1.0193906 1.0083102 22200 0.34750227 0 0.0056917695 1.0193906 1.0083102 22300 0.34766017 0 -0.0027090483 1.0193906 1.0083102 - 22400 0.33426062 0 -0.023196063 1.0304709 1.0193906 + 22400 0.33426062 0 -0.023196063 1.0304709 1.0083102 22500 0.34174625 0 -0.025019717 1.0083102 1.0083102 22600 0.3356145 0 -0.029707418 1.0304709 1.0193906 22700 0.3362653 0 -0.035815733 1.0193906 1.0193906 @@ -328,13 +345,13 @@ Step Temp E_pair Press f_10[3] f_10 23300 0.32965664 0 0.035989589 1.0193906 1.0083102 23400 0.30927749 0 0.024581106 1.0193906 1.0083102 23500 0.32890632 0 0.01092479 1.0304709 1.0193906 - 23600 0.34137438 0 0.0094839745 1.0193906 1.0083102 + 23600 0.34137438 0 0.0094839745 1.0193906 1.0193906 23700 0.34512638 0 -0.012392771 1.0304709 1.0193906 - 23800 0.31781354 0 -0.012908449 1.0193906 1.0193906 + 23800 0.31781354 0 -0.012908449 1.0193906 1.0083102 23900 0.32405513 0 -0.015018071 1.0415512 1.0193906 24000 0.33549728 0 -0.012812915 1.0193906 1.0193906 - 24100 0.31368736 0 -0.020818372 1.0304709 1.0193906 - 24200 0.33533836 0 0.0056121057 1.0083102 1.0083102 + 24100 0.31368736 0 -0.020818372 1.0083102 1.0083102 + 24200 0.33533836 0 0.0056121057 1.0304709 1.0193906 24300 0.32530627 0 0.018183931 1.0415512 1.0083102 24400 0.31930662 0 0.027446878 1.0083102 1.0193906 24500 0.33540302 0 0.040307455 1.0304709 1.0083102 @@ -344,14 +361,14 @@ Step Temp E_pair Press f_10[3] f_10 24900 0.34727253 0 0.01670543 1.0193906 1.0083102 25000 0.35120105 0 0.0038617562 1.0193906 1.0083102 25100 0.32706871 0 -0.021196623 1.0415512 1.0193906 - 25200 0.32915282 0 -0.017146508 1.0193906 1.0083102 - 25300 0.32577518 0 -0.01312495 1.0193906 1.0304709 - 25400 0.33286855 0 0.0014726193 1.0193906 1.0193906 + 25200 0.32915282 0 -0.017146508 1.0083102 1.0193906 + 25300 0.32577518 0 -0.01312495 1.0193906 1.0083102 + 25400 0.33286855 0 0.0014726193 1.0415512 1.0193906 25500 0.33002601 0 0.0080974022 1.0193906 1.0083102 25600 0.34127655 0 0.014296091 1.0526316 1.0083102 - 25700 0.34048065 0 0.022513032 1.0193906 1.0193906 - 25800 0.33029079 0 0.038733531 1.0193906 1.0083102 - 25900 0.33031324 0 0.026156982 1.0304709 1.0193906 + 25700 0.34048065 0 0.022513032 1.0193906 1.0083102 + 25800 0.33029079 0 0.038733531 1.0526316 1.0083102 + 25900 0.33031324 0 0.026156982 1.0083102 1.0193906 26000 0.32967371 0 0.028727383 1.0083102 1.0193906 26100 0.33775718 0 0.015607478 1.0083102 1.0193906 26200 0.35097144 0 0.012291703 1.0083102 1.0083102 @@ -360,20 +377,20 @@ Step Temp E_pair Press f_10[3] f_10 26500 0.33580127 0 -0.0074168555 1.0193906 1.0193906 26600 0.33063188 0 -0.020378601 1.0083102 1.0193906 26700 0.33581846 0 -0.00084397268 1.0083102 1.0193906 - 26800 0.32998532 0 0.015932208 1.0304709 1.0304709 + 26800 0.32998532 0 0.015932208 1.0304709 1.0193906 26900 0.33825444 0 0.010428603 1.0304709 1.0083102 - 27000 0.32081518 0 0.019818223 1.0304709 1.0193906 + 27000 0.32081518 0 0.019818223 1.0415512 1.0193906 27100 0.31448098 0 0.020093416 1.0193906 1.0083102 - 27200 0.32643684 0 0.021934917 1.0083102 1.0083102 + 27200 0.32643684 0 0.021934917 1.0193906 1.0083102 27300 0.33289466 0 0.023713072 1.0415512 1.0083102 27400 0.32310744 0 0.024110945 1.0415512 1.0083102 - 27500 0.33115619 0 0.0025776713 1.0304709 1.0083102 - 27600 0.33295887 0 -0.010710764 1.0304709 1.0193906 - 27700 0.32968876 0 -0.0064595905 1.0193906 1.0083102 + 27500 0.33115619 0 0.0025776713 1.0304709 1.0193906 + 27600 0.33295887 0 -0.010710764 1.0193906 1.0193906 + 27700 0.32968876 0 -0.0064595905 1.0193906 1.0193906 27800 0.34064581 0 -0.0086519116 1.0193906 1.0083102 - 27900 0.33559187 0 -0.0055753593 1.0083102 1.0083102 + 27900 0.33559187 0 -0.0055753593 1.0526316 1.0083102 28000 0.32300727 0 -0.0004153384 1.0304709 1.0083102 - 28100 0.32147461 0 -0.0058543412 1.0083102 1.0193906 + 28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102 28200 0.35532383 0 0.013646951 1.0304709 1.0083102 28300 0.31507942 0 0.026532255 1.0415512 1.0193906 28400 0.32711006 0 0.033214981 1.0193906 1.0083102 @@ -396,66 +413,66 @@ Step Temp E_pair Press f_10[3] f_10 30100 0.32598657 0 -0.0018860541 1.0415512 1.0193906 30200 0.34855815 0 0.0017983372 1.0083102 1.0083102 30300 0.33375921 0 0.0010991235 1.0083102 1.0193906 - 30400 0.35008944 0 -0.0027316177 1.0415512 1.0083102 + 30400 0.35008944 0 -0.0027316177 1.0193906 1.0083102 30500 0.33279729 0 -0.0035788551 1.0193906 1.0193906 30600 0.33868746 0 -0.0016249482 1.0083102 1.0193906 30700 0.33597034 0 -0.0014524001 1.0193906 1.0193906 - 30800 0.3227257 0 0.016353457 1.0415512 1.0193906 + 30800 0.3227257 0 0.016353457 1.0193906 1.0193906 30900 0.32676516 0 0.027396654 1.0193906 1.0083102 31000 0.34083982 0 0.031606413 1.0415512 1.0193906 - 31100 0.32165238 0 0.013583368 1.0193906 1.0083102 - 31200 0.3428492 0 0.020486611 1.0304709 1.0193906 + 31100 0.32165238 0 0.013583368 1.0083102 1.0083102 + 31200 0.3428492 0 0.020486611 1.0304709 1.0083102 31300 0.32372541 0 0.01215566 1.0083102 1.0083102 31400 0.32734692 0 0.016229397 1.0083102 1.0083102 31500 0.33089262 0 0.0060426618 1.0083102 1.0083102 31600 0.34273493 0 -0.013456537 1.0083102 1.0193906 - 31700 0.32723905 0 -0.019243766 1.0193906 1.0193906 + 31700 0.32723905 0 -0.019243766 1.0193906 1.0083102 31800 0.33636488 0 0.0027814902 1.0083102 1.0083102 - 31900 0.32834805 0 0.00706877 1.0083102 1.0083102 + 31900 0.32834805 0 0.00706877 1.0083102 1.0193906 32000 0.33995148 0 0.0018383309 1.0193906 1.0193906 32100 0.33412282 0 0.0076455933 1.0083102 1.0083102 32200 0.34334884 0 0.023586129 1.0083102 1.0083102 32300 0.32778925 0 0.020564321 1.0193906 1.0083102 32400 0.33163443 0 0.038878463 1.0193906 1.0083102 - 32500 0.32290345 0 0.022247461 1.0193906 1.0193906 - 32600 0.34113954 0 0.010966365 1.0304709 1.0083102 + 32500 0.32290345 0 0.022247461 1.0193906 1.0083102 + 32600 0.34113954 0 0.010966365 1.0304709 1.0193906 32700 0.33390633 0 0.0037777555 1.0193906 1.0083102 32800 0.34385341 0 0.010556575 1.0193906 1.0193906 - 32900 0.32137047 0 0.00022027143 1.0526316 1.0193906 - 33000 0.32079172 0 -0.017261272 1.0193906 1.0193906 + 32900 0.32137047 0 0.00022027143 1.0304709 1.0193906 + 33000 0.32079172 0 -0.017261272 1.0193906 1.0083102 33100 0.33570882 0 -0.0051942206 1.0083102 1.0083102 - 33200 0.34320894 0 -0.011515281 1.0304709 1.0193906 - 33300 0.32794746 0 -0.0018153673 1.0083102 1.0083102 + 33200 0.34320894 0 -0.011515281 1.0193906 1.0083102 + 33300 0.32794746 0 -0.0018153673 1.0083102 1.0193906 33400 0.33060982 0 0.027118146 1.0193906 1.0083102 - 33500 0.33641809 0 0.02143035 1.0083102 1.0083102 - 33600 0.33643061 0 0.020833068 1.0193906 1.0083102 + 33500 0.33641809 0 0.02143035 1.0083102 1.0193906 + 33600 0.33643061 0 0.020833068 1.0304709 1.0083102 33700 0.3485949 0 0.030918751 1.0193906 1.0083102 33800 0.3283985 0 0.01947613 1.0193906 1.0083102 - 33900 0.31959761 0 0.021128147 1.0083102 1.0193906 + 33900 0.31959761 0 0.021128147 1.0083102 1.0304709 34000 0.33897984 0 0.015270986 1.0193906 1.0083102 34100 0.32392267 0 0.0020130852 1.0304709 1.0193906 - 34200 0.33084514 0 -0.024316708 1.0193906 1.0083102 + 34200 0.33084514 0 -0.024316708 1.0193906 1.0193906 34300 0.3342259 0 -0.0059047764 1.0193906 1.0304709 34400 0.33385098 0 0.0063818721 1.0193906 1.0083102 34500 0.33255603 0 -0.01023837 1.0083102 1.0304709 34600 0.34766173 0 0.0056703013 1.0193906 1.0083102 - 34700 0.339822 0 0.0061648559 1.0083102 1.0193906 + 34700 0.339822 0 0.0061648559 1.0193906 1.0193906 34800 0.33902329 0 0.030037037 1.0415512 1.0193906 - 34900 0.3216153 0 0.027996689 1.0304709 1.0083102 - 35000 0.32701056 0 0.024778517 1.0193906 1.0193906 - 35100 0.3124942 0 0.011316548 1.0193906 1.0193906 - 35200 0.34486416 0 0.011670127 1.0193906 1.0193906 + 34900 0.3216153 0 0.027996689 1.0083102 1.0083102 + 35000 0.32701056 0 0.024778517 1.0193906 1.0083102 + 35100 0.3124942 0 0.011316548 1.0304709 1.0193906 + 35200 0.34486416 0 0.011670127 1.0083102 1.0083102 35300 0.33275353 0 0.020491246 1.0193906 1.0193906 35400 0.33618763 0 0.014678874 1.0083102 1.0083102 35500 0.32352282 0 -0.018568683 1.0193906 1.0193906 - 35600 0.32617903 0 -0.012796912 1.0193906 1.0193906 - 35700 0.32378048 0 -0.021318585 1.0193906 1.0083102 + 35600 0.32617903 0 -0.012796912 1.0193906 1.0304709 + 35700 0.32378048 0 -0.021318585 1.0193906 1.0193906 35800 0.3371086 0 -0.0023678632 1.0193906 1.0193906 35900 0.33818476 0 0.011197742 1.0193906 1.0083102 36000 0.35142144 0 0.022520935 1.0083102 1.0193906 36100 0.35147297 0 0.020277852 1.0193906 1.0083102 - 36200 0.33489465 0 0.014564878 1.0415512 1.0083102 - 36300 0.33841515 0 0.036439962 1.0193906 1.0193906 + 36200 0.33489465 0 0.014564878 1.0415512 1.0193906 + 36300 0.33841515 0 0.036439962 1.0193906 1.0083102 36400 0.32301096 0 0.019966746 1.0304709 1.0083102 36500 0.35612028 0 0.036509556 1.0083102 1.0083102 36600 0.33841597 0 -0.0042180605 1.0193906 1.0193906 @@ -464,9 +481,9 @@ Step Temp E_pair Press f_10[3] f_10 36900 0.35003816 0 -0.0021184393 1.0083102 1.0083102 37000 0.32965041 0 -0.020900951 1.0193906 1.0083102 37100 0.34653095 0 -0.013667977 1.0193906 1.0083102 - 37200 0.35019871 0 -0.0071740923 1.0083102 1.0193906 + 37200 0.35019871 0 -0.0071740923 1.0193906 1.0304709 37300 0.34859745 0 0.02006041 1.0304709 1.0083102 - 37400 0.35739859 0 0.020892822 1.0193906 1.0083102 + 37400 0.35739859 0 0.020892822 1.0304709 1.0083102 37500 0.34128859 0 0.041072111 1.0193906 1.0193906 37600 0.33781905 0 0.023376738 1.0193906 1.0083102 37700 0.32961874 0 0.030953741 1.0193906 1.0083102 @@ -493,21 +510,21 @@ Step Temp E_pair Press f_10[3] f_10 39800 0.34878036 0 0.0092881327 1.0083102 1.0193906 39900 0.35225411 0 -0.011341599 1.0083102 1.0193906 40000 0.36309266 0 0.0050869295 1.0304709 1.0083102 -Loop time of 1.17534 on 4 procs for 40000 steps with 361 atoms +Loop time of 1.12306 on 4 procs for 40000 steps with 361 atoms -Performance: 14702186.196 tau/day, 34032.838 timesteps/s -99.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 15386559.518 tau/day, 35617.036 timesteps/s +90.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.019205 | 0.020313 | 0.022204 | 0.8 | 1.73 -Bond | 0.21255 | 0.23651 | 0.26839 | 4.9 | 20.12 -Neigh | 0.16301 | 0.16427 | 0.16578 | 0.3 | 13.98 -Comm | 0.33528 | 0.37951 | 0.4139 | 5.3 | 32.29 -Output | 0.0084457 | 0.0089972 | 0.010254 | 0.8 | 0.77 -Modify | 0.15906 | 0.16078 | 0.16308 | 0.4 | 13.68 -Other | | 0.205 | | | 17.44 +Pair | 0.023094 | 0.023348 | 0.023582 | 0.1 | 2.08 +Bond | 0.17827 | 0.19268 | 0.21984 | 3.7 | 17.16 +Neigh | 0.18144 | 0.18231 | 0.18323 | 0.1 | 16.23 +Comm | 0.23759 | 0.28095 | 0.30794 | 5.0 | 25.02 +Output | 0.0062952 | 0.013342 | 0.034226 | 10.4 | 1.19 +Modify | 0.2379 | 0.24327 | 0.25076 | 0.9 | 21.66 +Other | | 0.1871 | | | 16.66 Nlocal: 90.25 ave 91 max 89 min Histogram: 1 0 0 0 0 1 0 0 0 2 diff --git a/examples/balance/log.27Nov18.balance.clock.dynamic.g++.2 b/examples/balance/log.27Nov18.balance.clock.dynamic.g++.2 new file mode 100644 index 0000000000..781a609bd2 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.clock.dynamic.g++.2 @@ -0,0 +1,227 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000549078 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes +fix p all property/atom d_WEIGHT +compute p all property/atom d_WEIGHT +fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT +variable maximb equal f_0[1] +variable iter equal f_0[2] +variable prev equal f_0[3] +variable final equal f_0 + +#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}" + +fix 1 all nve + +#dump id all atom 50 dump.melt +#dump id all custom 50 dump.lammpstrj id type x y z c_p + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 500 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.753 | 4.944 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137 + 300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137 + 350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137 + 400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137 + 450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137 + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 +Loop time of 3.7099 on 2 procs for 500 steps with 4000 atoms + +Performance: 58222.644 tau/day, 134.775 timesteps/s +99.2% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5145 | 2.5951 | 2.6756 | 5.0 | 69.95 +Neigh | 0.8388 | 0.88634 | 0.93387 | 5.0 | 23.89 +Comm | 0.17027 | 0.20258 | 0.23489 | 7.2 | 5.46 +Output | 0.00029612 | 0.00032723 | 0.00035834 | 0.0 | 0.01 +Modify | 0.016136 | 0.017057 | 0.017979 | 0.7 | 0.46 +Other | | 0.008504 | | | 0.23 + +Nlocal: 2000 ave 2157 max 1843 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10465.5 ave 10840 max 10091 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298070 ave 305706 max 290433 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596139 +Ave neighs/atom = 149.035 +Neighbor list builds = 51 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.944 | 4.947 | 4.951 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 + 550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137 + 600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137 + 650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137 + 700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137 + 750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137 + 800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137 + 850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137 + 900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137 + 950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137 + 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137 +Loop time of 3.70634 on 2 procs for 500 steps with 4000 atoms + +Performance: 58278.514 tau/day, 134.904 timesteps/s +99.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5536 | 2.6173 | 2.6811 | 3.9 | 70.62 +Neigh | 0.82942 | 0.88683 | 0.94424 | 6.1 | 23.93 +Comm | 0.16927 | 0.17474 | 0.1802 | 1.3 | 4.71 +Output | 0.00030422 | 0.00033307 | 0.00036192 | 0.0 | 0.01 +Modify | 0.016714 | 0.017824 | 0.018933 | 0.8 | 0.48 +Other | | 0.009277 | | | 0.25 + +Nlocal: 2000 ave 2136 max 1864 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10413.5 ave 10877 max 9950 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 300836 ave 312313 max 289358 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 601671 +Ave neighs/atom = 150.418 +Neighbor list builds = 51 +Dangerous builds = 0 +fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.951 | 5.142 | 5.334 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137 + 1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137 + 1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137 + 1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137 + 1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137 + 1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418133 4738.2137 + 1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137 + 1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137 + 1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137 + 1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137 + 1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137 +Loop time of 4.8272 on 2 procs for 500 steps with 4000 atoms + +Performance: 44746.478 tau/day, 103.580 timesteps/s +98.5% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9951 | 2.6814 | 3.3676 | 41.9 | 55.55 +Neigh | 0.82826 | 0.90961 | 0.99095 | 8.5 | 18.84 +Comm | 0.44043 | 1.2083 | 1.9762 | 69.9 | 25.03 +Output | 0.00034881 | 0.0003655 | 0.00038218 | 0.0 | 0.01 +Modify | 0.016762 | 0.01755 | 0.018337 | 0.6 | 0.36 +Other | | 0.01001 | | | 0.21 + +Nlocal: 2000 ave 2564 max 1436 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10334 ave 10752 max 9916 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 302958 ave 499873 max 106044 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 605917 +Ave neighs/atom = 151.479 +Neighbor list builds = 51 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.955 | 5.336 | 5.717 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137 + 1550 0.53713591 -6.2504068 0 -5.4449044 -1.7647087 4738.2137 + 1600 0.5467956 -6.2646482 0 -5.4446599 -1.8115778 4738.2137 + 1650 0.53806575 -6.2519004 0 -5.4450036 -1.7409135 4738.2137 + 1700 0.5347949 -6.2468958 0 -5.444904 -1.7162322 4738.2137 + 1750 0.53714528 -6.2506529 0 -5.4451365 -1.7340402 4738.2137 + 1800 0.5274989 -6.2358675 0 -5.444817 -1.6874989 4738.2137 + 1850 0.54585906 -6.2629475 0 -5.4443636 -1.7758918 4738.2137 + 1900 0.5301071 -6.2387551 0 -5.4437932 -1.6381903 4738.2137 + 1950 0.54288149 -6.2582818 0 -5.4441632 -1.7367819 4738.2137 + 2000 0.52766162 -6.2348587 0 -5.4435642 -1.5589151 4738.2137 +Loop time of 4.90351 on 2 procs for 500 steps with 4000 atoms + +Performance: 44050.062 tau/day, 101.968 timesteps/s +98.1% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9937 | 2.6502 | 3.3067 | 40.3 | 54.05 +Neigh | 0.81645 | 0.88655 | 0.95664 | 7.4 | 18.08 +Comm | 0.61197 | 1.3389 | 2.0659 | 62.8 | 27.31 +Output | 0.00036287 | 0.0003773 | 0.00039172 | 0.0 | 0.01 +Modify | 0.016585 | 0.017429 | 0.018274 | 0.6 | 0.36 +Other | | 0.01003 | | | 0.20 + +Nlocal: 2000 ave 2564 max 1436 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10256 ave 10620 max 9892 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 303988 ave 502064 max 105911 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 607975 +Ave neighs/atom = 151.994 +Neighbor list builds = 51 +Dangerous builds = 0 +Total wall time: 0:00:17 diff --git a/examples/balance/log.5Oct16.balance.clock.dynamic.g++.4 b/examples/balance/log.27Nov18.balance.clock.dynamic.g++.4 similarity index 57% rename from examples/balance/log.5Oct16.balance.clock.dynamic.g++.4 rename to examples/balance/log.27Nov18.balance.clock.dynamic.g++.4 index f9b5f55ea2..94780b14df 100644 --- a/examples/balance/log.5Oct16.balance.clock.dynamic.g++.4 +++ b/examples/balance/log.27Nov18.balance.clock.dynamic.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000421762 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -51,13 +53,18 @@ fix 1 all nve thermo 50 run 500 Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 -Memory usage per processor = 3.0442 Mbytes + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.691 | 4.072 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137 @@ -70,34 +77,34 @@ Step Temp E_pair E_mol TotEng Press Volume 400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137 450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 -Loop time of 2.33547 on 4 procs for 500 steps with 4000 atoms +Loop time of 2.69458 on 4 procs for 500 steps with 4000 atoms -Performance: 92486.710 tau/day, 214.090 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 80160.913 tau/day, 185.558 timesteps/s +94.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1405 | 1.4342 | 1.6755 | 19.8 | 61.41 -Neigh | 0.26612 | 0.40331 | 0.57095 | 21.3 | 17.27 -Comm | 0.3676 | 0.47776 | 0.60114 | 14.4 | 20.46 -Output | 0.00025606 | 0.00029331 | 0.00032091 | 0.1 | 0.01 -Modify | 0.0068483 | 0.008993 | 0.012159 | 2.3 | 0.39 -Other | | 0.01091 | | | 0.47 +Pair | 1.0903 | 1.4509 | 1.7199 | 22.5 | 53.84 +Neigh | 0.31688 | 0.47906 | 0.71852 | 24.2 | 17.78 +Comm | 0.60463 | 0.72402 | 0.84257 | 12.7 | 26.87 +Output | 0.00035119 | 0.00067121 | 0.0015202 | 0.0 | 0.02 +Modify | 0.00811 | 0.010936 | 0.014029 | 2.7 | 0.41 +Other | | 0.02904 | | | 1.08 -Nlocal: 1000 ave 1541 max 597 min +Nlocal: 1000 ave 1504 max 634 min Histogram: 2 0 0 0 0 0 1 0 0 1 -Nghost: 8756.5 ave 9859 max 8068 min +Nghost: 8759.25 ave 9896 max 8021 min Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 149308 ave 164475 max 126288 min -Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 149308 ave 179946 max 116419 min +Histogram: 1 1 0 0 0 0 0 0 1 1 Total # of neighbors = 597231 Ave neighs/atom = 149.308 Neighbor list builds = 50 Dangerous builds = 0 run 500 -Memory usage per processor = 3.06519 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137 @@ -110,27 +117,27 @@ Step Temp E_pair E_mol TotEng Press Volume 900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137 950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137 -Loop time of 2.16422 on 4 procs for 500 steps with 4000 atoms +Loop time of 2.64502 on 4 procs for 500 steps with 4000 atoms -Performance: 99804.786 tau/day, 231.030 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 81662.873 tau/day, 189.034 timesteps/s +93.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1704 | 1.3643 | 1.5256 | 13.9 | 63.04 -Neigh | 0.252 | 0.39989 | 0.57798 | 23.0 | 18.48 -Comm | 0.36005 | 0.38026 | 0.399 | 2.7 | 17.57 -Output | 0.00026989 | 0.00029516 | 0.00030947 | 0.1 | 0.01 -Modify | 0.0062692 | 0.0085821 | 0.011907 | 2.6 | 0.40 -Other | | 0.01089 | | | 0.50 +Pair | 1.1279 | 1.4127 | 1.6268 | 18.0 | 53.41 +Neigh | 0.32225 | 0.49572 | 0.76053 | 26.2 | 18.74 +Comm | 0.64504 | 0.6974 | 0.75498 | 5.7 | 26.37 +Output | 0.00035477 | 0.00062996 | 0.001343 | 0.0 | 0.02 +Modify | 0.0077929 | 0.010538 | 0.013856 | 2.6 | 0.40 +Other | | 0.02803 | | | 1.06 -Nlocal: 1000 ave 1546 max 611 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Nghost: 8720 ave 9802 max 8007 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 150170 ave 167512 max 125941 min -Histogram: 1 0 0 1 0 0 0 0 0 2 +Nlocal: 1000 ave 1437 max 597 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Nghost: 8674 ave 9370 max 8013 min +Histogram: 1 0 1 0 0 0 0 1 0 1 +Neighs: 150170 ave 187030 max 102149 min +Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 600678 Ave neighs/atom = 150.169 @@ -138,7 +145,7 @@ Neighbor list builds = 53 Dangerous builds = 0 fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT run 500 -Memory usage per processor = 3.04802 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137 1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137 @@ -150,71 +157,71 @@ Step Temp E_pair E_mol TotEng Press Volume 1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137 1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137 1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137 - 1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137 -Loop time of 2.17454 on 4 procs for 500 steps with 4000 atoms + 1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137 +Loop time of 2.61342 on 4 procs for 500 steps with 4000 atoms -Performance: 99331.198 tau/day, 229.933 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 82650.254 tau/day, 191.320 timesteps/s +93.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1909 | 1.3814 | 1.5474 | 12.7 | 63.53 -Neigh | 0.24882 | 0.38781 | 0.5563 | 22.6 | 17.83 -Comm | 0.35985 | 0.38559 | 0.4055 | 3.0 | 17.73 -Output | 0.00030994 | 0.00033677 | 0.00035214 | 0.1 | 0.02 -Modify | 0.0060136 | 0.008362 | 0.011491 | 2.6 | 0.38 -Other | | 0.01102 | | | 0.51 +Pair | 1.222 | 1.4442 | 1.5812 | 12.3 | 55.26 +Neigh | 0.29672 | 0.48201 | 0.73859 | 27.6 | 18.44 +Comm | 0.59138 | 0.65738 | 0.70906 | 6.5 | 25.15 +Output | 0.00036502 | 0.00091559 | 0.0020845 | 0.0 | 0.04 +Modify | 0.0095406 | 0.012674 | 0.017643 | 2.8 | 0.48 +Other | | 0.01621 | | | 0.62 -Nlocal: 1000 ave 1555 max 581 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 8695.5 ave 9791 max 8011 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 150494 ave 160074 max 132359 min -Histogram: 1 0 0 0 0 0 1 0 0 2 +Nlocal: 1000 ave 1446 max 670 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 8641 ave 9376 max 8019 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 150494 ave 184085 max 105390 min +Histogram: 1 0 1 0 0 0 0 0 0 2 Total # of neighbors = 601974 Ave neighs/atom = 150.494 Neighbor list builds = 51 Dangerous builds = 0 run 500 -Memory usage per processor = 3.06519 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.269 | 4.458 Mbytes Step Temp E_pair E_mol TotEng Press Volume - 1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137 + 1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866984 4738.2137 1550 0.55327018 -6.2750125 0 -5.4453148 -1.9506585 4738.2137 - 1600 0.54419003 -6.2612622 0 -5.4451812 -1.8559437 4738.2137 - 1650 0.54710035 -6.2661979 0 -5.4457525 -1.8882833 4738.2137 - 1700 0.53665692 -6.2504957 0 -5.4457116 -1.8068001 4738.2137 - 1750 0.54864726 -6.2681127 0 -5.4453476 -1.8662658 4738.2137 - 1800 0.54476256 -6.2615132 0 -5.4445736 -1.8352921 4738.2137 - 1850 0.54142913 -6.2555501 0 -5.4436094 -1.8005632 4738.2137 - 1900 0.53992543 -6.2541365 0 -5.4444509 -1.7768749 4738.2137 - 1950 0.54666257 -6.2641014 0 -5.4443125 -1.7947215 4738.2137 - 2000 0.54557432 -6.2625445 0 -5.4443876 -1.8072402 4738.2137 -Loop time of 2.13804 on 4 procs for 500 steps with 4000 atoms + 1600 0.5441901 -6.2612622 0 -5.4451811 -1.8559436 4738.2137 + 1650 0.54710046 -6.2661938 0 -5.4457483 -1.8882766 4738.2137 + 1700 0.5366569 -6.2504957 0 -5.4457116 -1.8067998 4738.2137 + 1750 0.5486468 -6.2681121 0 -5.4453476 -1.8662631 4738.2137 + 1800 0.54476176 -6.2615037 0 -5.4445653 -1.8352743 4738.2137 + 1850 0.5414305 -6.2555519 0 -5.4436091 -1.8005747 4738.2137 + 1900 0.53992655 -6.2541344 0 -5.444447 -1.7768718 4738.2137 + 1950 0.54666071 -6.2640943 0 -5.4443082 -1.7947052 4738.2137 + 2000 0.54556196 -6.2625262 0 -5.4443879 -1.8071631 4738.2137 +Loop time of 2.81593 on 4 procs for 500 steps with 4000 atoms -Performance: 101026.937 tau/day, 233.859 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 76706.532 tau/day, 177.561 timesteps/s +90.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2063 | 1.3671 | 1.4849 | 9.7 | 63.94 -Neigh | 0.25593 | 0.41674 | 0.59932 | 24.5 | 19.49 -Comm | 0.25287 | 0.33513 | 0.39698 | 9.9 | 15.67 -Output | 0.00024056 | 0.00026721 | 0.00028205 | 0.1 | 0.01 -Modify | 0.0058651 | 0.0082419 | 0.011365 | 2.7 | 0.39 -Other | | 0.01061 | | | 0.50 +Pair | 1.2508 | 1.4839 | 1.6521 | 13.4 | 52.70 +Neigh | 0.34188 | 0.54016 | 0.82358 | 27.6 | 19.18 +Comm | 0.70575 | 0.75254 | 0.80167 | 4.6 | 26.72 +Output | 0.00041604 | 0.001362 | 0.0041099 | 4.3 | 0.05 +Modify | 0.010564 | 0.013653 | 0.018 | 2.7 | 0.48 +Other | | 0.02432 | | | 0.86 -Nlocal: 1000 ave 1513 max 612 min +Nlocal: 1000 ave 1555 max 569 min Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 8685.25 ave 9861 max 7992 min +Nghost: 8672.75 ave 9821 max 7993 min Histogram: 2 0 0 0 1 0 0 0 0 1 -Neighs: 151657 ave 173252 max 122114 min -Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 151656 ave 164603 max 133455 min +Histogram: 1 0 0 0 0 0 1 1 0 1 -Total # of neighbors = 606628 -Ave neighs/atom = 151.657 +Total # of neighbors = 606625 +Ave neighs/atom = 151.656 Neighbor list builds = 56 Dangerous builds = 0 -Total wall time: 0:00:08 +Total wall time: 0:00:10 diff --git a/examples/balance/log.27Nov18.balance.clock.static.g++.2 b/examples/balance/log.27Nov18.balance.clock.static.g++.2 new file mode 100644 index 0000000000..6f96ac4fef --- /dev/null +++ b/examples/balance/log.27Nov18.balance.clock.static.g++.2 @@ -0,0 +1,195 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +variable factor index 1.0 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000517368 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes + +group fast type 1 +2600 atoms in group fast +group slow type 2 +1400 atoms in group slow +balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000522375 seconds + iteration count = 1 + time weight factor: 1 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -6.9453205 0 -5.4456955 -5.6812358 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 +Loop time of 1.96356 on 2 procs for 250 steps with 4000 atoms + +Performance: 55002.186 tau/day, 127.320 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0024 | 1.243 | 1.4835 | 21.6 | 63.30 +Neigh | 0.3963 | 0.41601 | 0.43572 | 3.1 | 21.19 +Comm | 0.032948 | 0.29324 | 0.55353 | 48.1 | 14.93 +Output | 0.00013924 | 0.00014722 | 0.00015521 | 0.0 | 0.01 +Modify | 0.0072696 | 0.0073524 | 0.0074351 | 0.1 | 0.37 +Other | | 0.003842 | | | 0.20 + +Nlocal: 2000 ave 2051 max 1949 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10443 ave 10506 max 10380 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298332 ave 363449 max 233215 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596664 +Ave neighs/atom = 149.166 +Neighbor list builds = 24 +Dangerous builds = 0 +balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt + rebalancing time: 0.000424623 seconds + iteration count = 3 + time weight factor: 1 + initial/final max load/proc = 1.91926 1.6972 + initial/final imbalance factor = 1.15689 1.02304 + x cuts: 0 0.4375 1 + y cuts: 0 1 + z cuts: 0 1 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.685 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 + 300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 + 350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 + 400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 + 450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 +Loop time of 1.84751 on 2 procs for 250 steps with 4000 atoms + +Performance: 58457.127 tau/day, 135.317 timesteps/s +99.5% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1214 | 1.2291 | 1.3368 | 9.7 | 66.53 +Neigh | 0.37418 | 0.41926 | 0.46434 | 7.0 | 22.69 +Comm | 0.033842 | 0.18738 | 0.34091 | 35.5 | 10.14 +Output | 0.00016665 | 0.00018752 | 0.00020838 | 0.0 | 0.01 +Modify | 0.0062993 | 0.0072798 | 0.0082603 | 1.1 | 0.39 +Other | | 0.00428 | | | 0.23 + +Nlocal: 2000 ave 2284 max 1716 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10450 ave 10742 max 10158 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298063 ave 326003 max 270123 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596126 +Ave neighs/atom = 149.031 +Neighbor list builds = 25 +Dangerous builds = 0 +balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt + rebalancing time: 0.000502825 seconds + iteration count = 3 + time weight factor: 1 + initial/final max load/proc = 1.80118 1.79434 + initial/final imbalance factor = 1.0927 1.08854 + x cuts: 0 0.507812 1 + y cuts: 0 1 + z cuts: 0 1 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 + 550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 + 600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 + 650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 + 700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 + 750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 +Loop time of 2.03694 on 2 procs for 250 steps with 4000 atoms + +Performance: 53020.655 tau/day, 122.733 timesteps/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.92132 | 1.2301 | 1.5389 | 27.8 | 60.39 +Neigh | 0.3924 | 0.42313 | 0.45386 | 4.7 | 20.77 +Comm | 0.032816 | 0.37246 | 0.71211 | 55.7 | 18.29 +Output | 0.00013733 | 0.00014532 | 0.0001533 | 0.0 | 0.01 +Modify | 0.0069692 | 0.0072372 | 0.0075052 | 0.3 | 0.36 +Other | | 0.003856 | | | 0.19 + +Nlocal: 2000 ave 2097 max 1903 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10439.5 ave 10561 max 10318 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 299628 ave 378859 max 220397 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 599256 +Ave neighs/atom = 149.814 +Neighbor list builds = 25 +Dangerous builds = 0 +Total wall time: 0:00:05 diff --git a/examples/balance/log.5Oct16.balance.clock.static.g++.4 b/examples/balance/log.27Nov18.balance.clock.static.g++.4 similarity index 59% rename from examples/balance/log.5Oct16.balance.clock.static.g++.4 rename to examples/balance/log.27Nov18.balance.clock.static.g++.4 index 1348e396df..45bae5631f 100644 --- a/examples/balance/log.5Oct16.balance.clock.static.g++.4 +++ b/examples/balance/log.27Nov18.balance.clock.static.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000427961 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -36,13 +38,18 @@ group slow type 2 1400 atoms in group slow balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 - rebalancing time: 0.000463963 seconds + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000848055 seconds iteration count = 2 time weight factor: 1 initial/final max load/proc = 1200 1200 @@ -63,7 +70,7 @@ fix 1 all nve thermo 50 run 250 -Memory usage per processor = 2.77892 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.426 | 3.713 | 4.188 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 -6.9453205 0 -5.4456955 -5.6812358 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 @@ -71,20 +78,20 @@ Step Temp E_pair E_mol TotEng Press 150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 -Loop time of 1.40211 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.50594 on 4 procs for 250 steps with 4000 atoms -Performance: 77026.670 tau/day, 178.302 timesteps/s -98.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 71716.080 tau/day, 166.009 timesteps/s +96.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.35738 | 0.65181 | 1.1696 | 41.3 | 46.49 -Neigh | 0.13196 | 0.17021 | 0.20914 | 7.5 | 12.14 -Comm | 0.034142 | 0.57176 | 0.88483 | 44.5 | 40.78 -Output | 0.0001142 | 0.0001266 | 0.00014806 | 0.1 | 0.01 -Modify | 0.0023732 | 0.0032824 | 0.0044029 | 1.3 | 0.23 -Other | | 0.004928 | | | 0.35 +Pair | 0.34764 | 0.66777 | 1.2288 | 43.4 | 44.34 +Neigh | 0.1594 | 0.20524 | 0.2451 | 7.5 | 13.63 +Comm | 0.039175 | 0.62421 | 0.93047 | 45.4 | 41.45 +Output | 0.00015855 | 0.00024235 | 0.00047231 | 0.0 | 0.02 +Modify | 0.0028908 | 0.0039527 | 0.0049407 | 1.2 | 0.26 +Other | | 0.004522 | | | 0.30 Nlocal: 1000 ave 1263 max 712 min Histogram: 1 0 0 0 1 0 1 0 0 1 @@ -98,16 +105,16 @@ Ave neighs/atom = 149.325 Neighbor list builds = 23 Dangerous builds = 0 balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt - rebalancing time: 0.000343084 seconds - iteration count = 5 + rebalancing time: 0.000421047 seconds + iteration count = 4 time weight factor: 1 - initial/final max load/proc = 1.35965 0.878579 - initial/final imbalance factor = 1.65405 1.06882 - x cuts: 0 0.304688 0.460938 0.634766 1 + initial/final max load/proc = 1.45871 0.956175 + initial/final imbalance factor = 1.6709 1.09526 + x cuts: 0 0.296875 0.453125 0.628906 1 y cuts: 0 1 z cuts: 0 1 run 250 -Memory usage per processor = 2.78273 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.787 | 3.907 | 4.192 Mbytes Step Temp E_pair E_mol TotEng Press 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 @@ -115,43 +122,43 @@ Step Temp E_pair E_mol TotEng Press 400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 -Loop time of 1.06588 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.24397 on 4 procs for 250 steps with 4000 atoms -Performance: 101324.291 tau/day, 234.547 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 86819.073 tau/day, 200.970 timesteps/s +95.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.45977 | 0.64931 | 0.82184 | 17.0 | 60.92 -Neigh | 0.11586 | 0.17099 | 0.23942 | 12.5 | 16.04 -Comm | 0.10905 | 0.23692 | 0.35707 | 18.4 | 22.23 -Output | 0.00011897 | 0.00014734 | 0.00017262 | 0.2 | 0.01 -Modify | 0.0020723 | 0.0032738 | 0.0047829 | 2.0 | 0.31 -Other | | 0.005239 | | | 0.49 +Pair | 0.4612 | 0.67729 | 0.88321 | 20.9 | 54.45 +Neigh | 0.14175 | 0.20919 | 0.28903 | 13.7 | 16.82 +Comm | 0.19855 | 0.34785 | 0.48428 | 18.8 | 27.96 +Output | 0.00016665 | 0.00030792 | 0.00066757 | 0.0 | 0.02 +Modify | 0.0027177 | 0.0053391 | 0.010109 | 4.1 | 0.43 +Other | | 0.003992 | | | 0.32 -Nlocal: 1000 ave 1435 max 639 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 8679.75 ave 9430 max 7994 min +Nlocal: 1000 ave 1462 max 652 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 8657 ave 9421 max 7969 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 149356 ave 195930 max 106343 min Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 149356 ave 184268 max 102258 min -Histogram: 1 0 0 0 1 0 0 0 1 1 Total # of neighbors = 597424 Ave neighs/atom = 149.356 Neighbor list builds = 24 Dangerous builds = 0 balance 1.0 shift x 5 1.1 weight time 1.0 # out unweighted.txt - rebalancing time: 0.000194073 seconds - iteration count = 4 + rebalancing time: 0.000288963 seconds + iteration count = 5 time weight factor: 1 - initial/final max load/proc = 0.948736 0.898491 - initial/final imbalance factor = 1.15657 1.09532 - x cuts: 0 0.314453 0.451172 0.602173 1 + initial/final max load/proc = 1.03814 0.978524 + initial/final imbalance factor = 1.17108 1.10383 + x cuts: 0 0.301758 0.448242 0.60144 1 y cuts: 0 1 z cuts: 0 1 run 250 -Memory usage per processor = 2.7999 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.804 | 3.927 | 4.209 Mbytes Step Temp E_pair E_mol TotEng Press 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 @@ -159,27 +166,27 @@ Step Temp E_pair E_mol TotEng Press 650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 -Loop time of 1.02789 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.14445 on 4 procs for 250 steps with 4000 atoms -Performance: 105069.856 tau/day, 243.217 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 94368.537 tau/day, 218.446 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.51012 | 0.64726 | 0.75553 | 11.2 | 62.97 -Neigh | 0.10374 | 0.17664 | 0.25597 | 15.7 | 17.19 -Comm | 0.10147 | 0.19583 | 0.28425 | 16.9 | 19.05 -Output | 0.00011802 | 0.000139 | 0.00015593 | 0.1 | 0.01 -Modify | 0.0017936 | 0.0032012 | 0.0047436 | 2.3 | 0.31 -Other | | 0.004817 | | | 0.47 +Pair | 0.52287 | 0.67351 | 0.79602 | 13.2 | 58.85 +Neigh | 0.14306 | 0.21848 | 0.31638 | 16.2 | 19.09 +Comm | 0.19457 | 0.24404 | 0.29562 | 7.2 | 21.32 +Output | 0.00016236 | 0.00029993 | 0.00065851 | 0.0 | 0.03 +Modify | 0.0024104 | 0.0038835 | 0.0057485 | 2.3 | 0.34 +Other | | 0.004232 | | | 0.37 -Nlocal: 1000 ave 1518 max 524 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Nghost: 8714.5 ave 9870 max 7980 min +Nlocal: 1000 ave 1522 max 593 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 8754 ave 9866 max 8002 min Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 149124 ave 173877 max 119242 min -Histogram: 1 0 0 1 0 0 0 1 0 1 +Neighs: 149124 ave 182694 max 120516 min +Histogram: 1 0 1 0 0 0 1 0 0 1 Total # of neighbors = 596497 Ave neighs/atom = 149.124 diff --git a/examples/balance/log.27Nov18.balance.g++.2 b/examples/balance/log.27Nov18.balance.g++.2 new file mode 100644 index 0000000000..6b0d0baa88 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.g++.2 @@ -0,0 +1,209 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 +variable v index 5 +variable w index 2 + +units lj +dimension 2 +atom_style atomic +boundary f f p + +lattice hex 0.85 +Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 +region box block 0 $x 0 $y -0.5 0.5 +region box block 0 50 0 $y -0.5 0.5 +region box block 0 50 0 20 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) + 2 by 1 by 1 MPI processor grid +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 10 +create_atoms 1 region circle +Created 361 atoms + Time spent = 0.000478506 secs +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes +velocity all set 5 $w 0 sum yes +velocity all set 5 2 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 + +comm_style tiled +fix 10 all balance 50 0.9 rcb + +#compute 1 all property/atom proc +#variable p atom c_1%10 +#dump 2 all custom 50 tmp.dump id v_p x y z + +#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string # "red green blue yellow white # purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.061 | 3.065 | 3.07 Mbytes +Step Temp E_pair Press f_10[3] f_10 + 0 25.701528 -29.143179 -1.2407285 2 1.0193906 + 100 26.269576 -29.713313 7.9052334 1.1135734 1.0027701 + 200 26.368336 -29.809962 1.6412462 1.0803324 1.0027701 + 300 26.479082 -29.920083 2.3678653 1.1578947 1.0083102 + 400 26.522239 -29.965537 6.6787858 1.1578947 1.0083102 + 500 25.725591 -29.168034 0.67065285 1.1024931 1.0083102 + 600 26.247693 -29.692706 7.9887712 1.1301939 1.0027701 + 700 26.237368 -29.676926 1.5987214 1.1578947 1.0027701 + 800 25.889643 -29.431589 4.6160859 1.1523546 1.0027701 + 900 23.635295 -27.372963 9.029962 1.1468144 1.0027701 + 1000 22.571904 -25.87422 1.8936085 1.1191136 1.0083102 + 1100 17.493795 -21.447274 9.502619 1.0747922 1.0027701 + 1200 17.214459 -20.726965 6.3578919 1.0193906 1.0083102 + 1300 16.424217 -19.757401 3.9026861 1.0083102 1.0027701 + 1400 15.051731 -18.13464 1.7558146 1.0249307 1.0027701 + 1500 13.966718 -17.051915 1.4843674 1.0470914 1.0027701 + 1600 13.615641 -16.582695 1.7845355 1.0415512 1.0027701 + 1700 13.278822 -16.278248 1.8263176 1.0470914 1.0083102 + 1800 12.680841 -15.81089 2.0096239 1.0415512 1.0027701 + 1900 12.039167 -14.99225 1.4379549 1.0360111 1.0027701 + 2000 12.298923 -15.188233 1.6287319 1.0249307 1.0027701 + 2100 12.048347 -14.947484 1.0583787 1.0304709 1.0027701 + 2200 12.024664 -14.91864 1.0617555 1.0304709 1.0027701 + 2300 11.878263 -14.769923 1.2892425 1.0360111 1.0027701 + 2400 11.578448 -14.525725 1.2925126 1.0083102 1.0027701 + 2500 11.948793 -14.736647 1.5473169 1.0249307 1.0027701 + 2600 11.933924 -14.725605 1.3673896 1.0249307 1.0027701 + 2700 11.622855 -14.414518 1.3035925 1.0304709 1.0083102 + 2800 10.600538 -13.451379 1.3422508 1.0138504 1.0027701 + 2900 10.404739 -13.242902 1.3070821 1.0083102 1.0027701 + 3000 10.73199 -13.60699 0.92518136 1.0138504 1.0027701 + 3100 10.807664 -13.624775 1.3037969 1.0193906 1.0027701 + 3200 10.393964 -13.212022 0.72081929 1.0027701 1.0027701 + 3300 9.8733371 -12.65719 1.1606833 1.0138504 1.0027701 + 3400 9.6206594 -12.349773 0.69859994 1.0138504 1.0027701 + 3500 9.5882688 -12.32291 1.0028888 1.0138504 1.0027701 + 3600 9.693129 -12.441628 0.94751509 1.0193906 1.0083102 + 3700 9.3727837 -12.162354 1.9639195 1.0027701 1.0027701 + 3800 9.1011581 -11.860999 1.0253876 1.0083102 1.0027701 + 3900 8.6637799 -11.44226 1.4848652 1.0027701 1.0027701 + 4000 9.0454579 -11.770928 0.82719098 1.0083102 1.0083102 + 4100 8.5574492 -11.30614 0.82422479 1.0193906 1.0027701 + 4200 8.5903538 -11.322978 0.45091349 1.0027701 1.0027701 + 4300 8.540208 -11.282844 0.55403945 1.0027701 1.0027701 + 4400 7.7043293 -10.372194 0.80170046 1.0027701 1.0027701 + 4500 7.3429905 -9.9970461 0.77097228 1.0193906 1.0027701 + 4600 7.35485 -9.9992837 0.66531873 1.0027701 1.0027701 + 4700 7.3278467 -9.9885021 0.99577458 1.0193906 1.0027701 + 4800 7.8179777 -10.468758 0.56434522 1.0138504 1.0083102 + 4900 7.571002 -10.215558 0.81064116 1.0138504 1.0027701 + 5000 7.5326417 -10.224594 0.86387082 1.0083102 1.0027701 + 5100 7.8120521 -10.468885 0.86739094 1.0027701 1.0027701 + 5200 7.2949975 -10.041278 1.0298349 1.0027701 1.0027701 + 5300 7.6564811 -10.297993 0.71060925 1.0027701 1.0083102 + 5400 7.7359804 -10.373635 0.61872932 1.0027701 1.0083102 + 5500 7.6511513 -10.279058 0.87569767 1.0027701 1.0027701 + 5600 7.2927879 -9.9378811 1.1573049 1.0083102 1.0083102 + 5700 7.1836162 -9.8357325 0.43012076 1.0083102 1.0083102 + 5800 7.3405818 -9.9780947 0.69346928 1.0083102 1.0027701 + 5900 7.6636501 -10.323536 0.82554433 1.0027701 1.0027701 + 6000 7.3515582 -9.9803466 1.09521 1.0138504 1.0027701 + 6100 7.0275875 -9.6739554 0.48460922 1.0027701 1.0027701 + 6200 7.1449226 -9.7541904 0.83007096 1.0193906 1.0083102 + 6300 7.036185 -9.6445595 1.0982599 1.0193906 1.0027701 + 6400 7.1288989 -9.7501637 1.0103414 1.0138504 1.0027701 + 6500 6.6559525 -9.256798 0.58741228 1.0027701 1.0027701 + 6600 7.0559949 -9.6563848 0.53504661 1.0027701 1.0027701 + 6700 7.124289 -9.7613906 0.70816625 1.0027701 1.0027701 + 6800 7.0141849 -9.6298357 0.55987809 1.0083102 1.0027701 + 6900 6.8617323 -9.4376408 0.62371253 1.0193906 1.0083102 + 7000 6.7496366 -9.3379578 0.83540012 1.0027701 1.0083102 + 7100 7.0418565 -9.664915 0.68231111 1.0083102 1.0027701 + 7200 6.6175362 -9.2066737 0.31371885 1.0138504 1.0027701 + 7300 7.076179 -9.6917457 1.0827515 1.0083102 1.0027701 + 7400 6.5263123 -9.1321276 1.1892921 1.0027701 1.0027701 + 7500 6.8072952 -9.3976358 0.60458526 1.0138504 1.0027701 + 7600 6.610006 -9.1934492 0.54359615 1.0193906 1.0027701 + 7700 6.3533198 -8.943515 0.91970357 1.0138504 1.0027701 + 7800 6.7226774 -9.3164434 0.81151352 1.0027701 1.0083102 + 7900 6.2329222 -8.8531998 0.59439797 1.0083102 1.0027701 + 8000 6.5818943 -9.2025911 0.66303132 1.0083102 1.0027701 + 8100 6.372739 -8.9403406 0.81325975 1.0138504 1.0027701 + 8200 6.462003 -9.0346265 0.54917879 1.0083102 1.0027701 + 8300 6.5947825 -9.2171877 0.9005455 1.0027701 1.0027701 + 8400 6.7803374 -9.4179158 0.37270772 1.0027701 1.0027701 + 8500 6.7122886 -9.3363107 0.77011047 1.0083102 1.0027701 + 8600 6.8286386 -9.4264779 0.35815593 1.0027701 1.0027701 + 8700 6.4796483 -9.0676554 0.84568363 1.0138504 1.0027701 + 8800 6.551896 -9.1793668 1.0319947 1.0083102 1.0027701 + 8900 6.1879163 -8.7590749 0.34445309 1.0027701 1.0027701 + 9000 6.2374494 -8.7872159 0.46749314 1.0027701 1.0027701 + 9100 6.3605933 -8.9335681 0.86786624 1.0027701 1.0027701 + 9200 6.4387791 -9.0144583 0.56089061 1.0083102 1.0027701 + 9300 6.2745383 -8.9019836 0.58565081 1.0083102 1.0027701 + 9400 6.1957924 -8.7638279 0.65785826 1.0027701 1.0083102 + 9500 6.079287 -8.6556289 0.47532552 1.0083102 1.0027701 + 9600 6.7679205 -9.3427341 0.48539851 1.0083102 1.0027701 + 9700 6.4007616 -8.9753463 0.58689382 1.0138504 1.0027701 + 9800 6.2137021 -8.7670545 0.80327882 1.0249307 1.0027701 + 9900 6.063559 -8.6359278 0.34977555 1.0083102 1.0027701 + 10000 6.5604562 -9.1417599 0.49589297 1.0083102 1.0027701 +Loop time of 0.469504 on 2 procs for 10000 steps with 361 atoms + +Performance: 9201197.252 tau/day, 21299.068 timesteps/s +94.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13648 | 0.14553 | 0.15459 | 2.4 | 31.00 +Neigh | 0.13867 | 0.14128 | 0.1439 | 0.7 | 30.09 +Comm | 0.05533 | 0.06494 | 0.07455 | 3.8 | 13.83 +Output | 0.0012147 | 0.0013802 | 0.0015457 | 0.4 | 0.29 +Modify | 0.071393 | 0.071421 | 0.07145 | 0.0 | 15.21 +Other | | 0.04494 | | | 9.57 + +Nlocal: 180.5 ave 181 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 30 ave 34 max 26 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 579.5 ave 644 max 515 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 1159 +Ave neighs/atom = 3.21053 +Neighbor list builds = 3510 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/balance/log.27Nov18.balance.g++.4 b/examples/balance/log.27Nov18.balance.g++.4 new file mode 100644 index 0000000000..7889eff888 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.g++.4 @@ -0,0 +1,209 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d circle of particles inside a box with LJ walls + +variable b index 0 + +variable x index 50 +variable y index 20 +variable d index 20 +variable v index 5 +variable w index 2 + +units lj +dimension 2 +atom_style atomic +boundary f f p + +lattice hex 0.85 +Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 +region box block 0 $x 0 $y -0.5 0.5 +region box block 0 50 0 $y -0.5 0.5 +region box block 0 50 0 20 -0.5 0.5 +create_box 1 box +Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) + 2 by 2 by 1 MPI processor grid +region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) +region circle sphere 11 6.7735026918962581988 0.0 10 +create_atoms 1 region circle +Created 361 atoms + Time spent = 0.000404358 secs +mass 1 1.0 + +velocity all create 0.5 87287 loop geom +velocity all set $v $w 0 sum yes +velocity all set 5 $w 0 sum yes +velocity all set 5 2 0 sum yes + +pair_style lj/cut 2.5 +pair_coeff 1 1 10.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve + +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 +fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 +fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 + +comm_style tiled +fix 10 all balance 50 0.9 rcb + +#compute 1 all property/atom proc +#variable p atom c_1%10 +#dump 2 all custom 50 tmp.dump id v_p x y z + +#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 +#variable colors string # "red green blue yellow white # purple pink orange lime gray" +#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} + +thermo_style custom step temp epair press f_10[3] f_10 +thermo 100 + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 42 29 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.041 | 3.047 | 3.059 Mbytes +Step Temp E_pair Press f_10[3] f_10 + 0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316 + 100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709 + 200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102 + 300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906 + 400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102 + 500 25.725591 -29.168034 0.67065285 1.2520776 1.0193906 + 600 26.247693 -29.692706 7.9887712 1.3074792 1.0193906 + 700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102 + 800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102 + 900 23.635295 -27.372963 9.029962 1.1634349 1.0083102 + 1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906 + 1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906 + 1200 17.214459 -20.726965 6.3578918 1.0304709 1.0083102 + 1300 16.42412 -19.757358 3.9027527 1.1191136 1.0193906 + 1400 15.030721 -18.114099 1.7564242 1.1523546 1.0193906 + 1500 13.81681 -16.902783 1.1577715 1.0858726 1.0083102 + 1600 13.686443 -16.661545 1.5415714 1.0969529 1.0083102 + 1700 13.019794 -16.066239 2.0360985 1.0526316 1.0083102 + 1800 12.297559 -15.3505 2.3411708 1.0858726 1.0083102 + 1900 12.279142 -15.287559 1.6641576 1.0415512 1.0083102 + 2000 12.230052 -15.192836 1.0975388 1.0415512 1.0193906 + 2100 11.697549 -14.599737 1.6237216 1.0969529 1.0083102 + 2200 11.682062 -14.610972 1.4641234 1.0747922 1.0083102 + 2300 11.075799 -13.986408 1.3034228 1.0637119 1.0083102 + 2400 11.362073 -14.290331 1.4934327 1.0304709 1.0083102 + 2500 11.100258 -14.006922 1.5476543 1.0415512 1.0193906 + 2600 11.12995 -14.013738 1.648208 1.0526316 1.0193906 + 2700 10.709161 -13.560172 1.396234 1.0193906 1.0083102 + 2800 10.827433 -13.654426 1.0691842 1.0304709 1.0083102 + 2900 10.653946 -13.622298 1.0985321 1.0304709 1.0083102 + 3000 10.277755 -13.110194 0.80184675 1.0304709 1.0083102 + 3100 9.9099809 -12.702359 1.0351594 1.0304709 1.0193906 + 3200 9.7539825 -12.558768 0.54465848 1.0526316 1.0083102 + 3300 10.126666 -12.949441 0.64914734 1.0304709 1.0083102 + 3400 9.5324496 -12.338741 1.2896056 1.0193906 1.0193906 + 3500 9.4041639 -12.170248 0.72157285 1.0304709 1.0083102 + 3600 9.2601291 -12.094438 1.1638062 1.0415512 1.0193906 + 3700 9.7052324 -12.503428 1.0681965 1.0193906 1.0193906 + 3800 9.1757619 -11.95576 1.2517655 1.0637119 1.0083102 + 3900 9.2622488 -12.036744 0.49874718 1.0193906 1.0083102 + 4000 8.8510215 -11.634558 1.0887428 1.0415512 1.0193906 + 4100 8.3821331 -11.145234 0.91008971 1.0193906 1.0083102 + 4200 8.2295054 -10.970304 0.5181043 1.0304709 1.0083102 + 4300 8.2161013 -10.942353 0.42128421 1.0304709 1.0193906 + 4400 7.7366945 -10.4592 0.79646198 1.0304709 1.0193906 + 4500 7.6089407 -10.446852 1.0059975 1.0083102 1.0193906 + 4600 7.6662499 -10.406613 1.7369986 1.0193906 1.0083102 + 4700 7.9515739 -10.665324 0.73173058 1.0193906 1.0083102 + 4800 7.7580664 -10.520311 1.1065958 1.0304709 1.0083102 + 4900 7.561205 -10.291568 0.97923495 1.0083102 1.0193906 + 5000 7.4169102 -10.130439 1.1566293 1.0193906 1.0193906 + 5100 7.5994418 -10.310725 1.1081236 1.0193906 1.0193906 + 5200 7.4637026 -10.211945 0.46308591 1.0193906 1.0083102 + 5300 7.5864081 -10.289039 0.55146387 1.0415512 1.0083102 + 5400 7.2190688 -9.8943729 0.56255805 1.0193906 1.0193906 + 5500 7.3953465 -10.112294 0.49166363 1.0193906 1.0193906 + 5600 7.3584536 -10.027488 0.69227871 1.0193906 1.0193906 + 5700 6.932639 -9.6121874 0.67344283 1.0304709 1.0083102 + 5800 7.088604 -9.7715725 0.20307999 1.0193906 1.0193906 + 5900 6.9761247 -9.6446998 0.90406994 1.0083102 1.0083102 + 6000 6.8763621 -9.5236579 0.57873884 1.0415512 1.0083102 + 6100 6.939987 -9.5929188 0.36904108 1.0304709 1.0083102 + 6200 6.820038 -9.4635599 0.63193653 1.0304709 1.0083102 + 6300 6.8288347 -9.4833639 0.41971515 1.0415512 1.0304709 + 6400 6.8690672 -9.5446244 1.0201589 1.0415512 1.0193906 + 6500 6.4727631 -9.1148404 0.80775699 1.0193906 1.0193906 + 6600 6.7113328 -9.3554765 0.61684835 1.0083102 1.0083102 + 6700 6.5896516 -9.2696941 0.58593745 1.0526316 1.0193906 + 6800 6.5609717 -9.2314045 1.2897992 1.0193906 1.0083102 + 6900 6.6225137 -9.2809347 0.47677707 1.0415512 1.0083102 + 7000 6.6617661 -9.3147214 0.72415312 1.0304709 1.0193906 + 7100 6.5773856 -9.2843036 0.7800794 1.0304709 1.0083102 + 7200 6.7300254 -9.4233488 0.73403634 1.0193906 1.0193906 + 7300 6.8497011 -9.4992354 0.97755826 1.0304709 1.0193906 + 7400 6.5848304 -9.2649536 0.89449647 1.0526316 1.0193906 + 7500 6.6468599 -9.3004561 0.53259674 1.0304709 1.0083102 + 7600 6.7096387 -9.3824628 0.40095675 1.0193906 1.0083102 + 7700 6.6205931 -9.2612947 0.44113095 1.0083102 1.0083102 + 7800 6.444935 -9.073124 0.47355329 1.0193906 1.0083102 + 7900 6.6143353 -9.2763501 0.57936627 1.0193906 1.0083102 + 8000 6.5718284 -9.2099799 0.88048189 1.0637119 1.0083102 + 8100 6.9155381 -9.5644544 0.36029314 1.0415512 1.0083102 + 8200 6.4217261 -9.0582117 0.4577164 1.0193906 1.0193906 + 8300 6.4639521 -9.0911283 0.50560328 1.0193906 1.0193906 + 8400 6.2047897 -8.8357836 0.71150301 1.0083102 1.0083102 + 8500 6.5688691 -9.2701491 0.5963871 1.0193906 1.0083102 + 8600 6.6803448 -9.3311473 0.47008064 1.0304709 1.0083102 + 8700 6.4794219 -9.1136868 0.97764575 1.0193906 1.0193906 + 8800 6.3899651 -9.0655629 0.72557611 1.0083102 1.0193906 + 8900 6.4446062 -9.1121453 0.53050589 1.0193906 1.0083102 + 9000 6.7012614 -9.3365992 0.63041848 1.0415512 1.0083102 + 9100 6.3982388 -9.0510004 0.34575359 1.0415512 1.0083102 + 9200 6.9775773 -9.6647109 0.97993232 1.0304709 1.0193906 + 9300 6.5504231 -9.2113542 0.58697844 1.0193906 1.0193906 + 9400 6.6900283 -9.3954145 0.40867465 1.0083102 1.0193906 + 9500 6.3553229 -8.9965934 0.60133843 1.0526316 1.0193906 + 9600 6.4861076 -9.1404384 1.0033387 1.0193906 1.0193906 + 9700 6.469481 -9.1202491 0.85523385 1.0083102 1.0193906 + 9800 6.5508552 -9.188341 0.6068644 1.0304709 1.0083102 + 9900 6.4355199 -9.1044882 0.83288252 1.0304709 1.0193906 + 10000 6.4850092 -9.1433721 0.58691238 1.0193906 1.0193906 +Loop time of 0.418243 on 4 procs for 10000 steps with 361 atoms + +Performance: 10328920.895 tau/day, 23909.539 timesteps/s +87.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.062269 | 0.073833 | 0.096031 | 4.9 | 17.65 +Neigh | 0.066658 | 0.072882 | 0.084956 | 2.7 | 17.43 +Comm | 0.10814 | 0.13013 | 0.14677 | 4.4 | 31.11 +Output | 0.0015733 | 0.0017747 | 0.0023153 | 0.7 | 0.42 +Modify | 0.060045 | 0.060904 | 0.061674 | 0.3 | 14.56 +Other | | 0.07872 | | | 18.82 + +Nlocal: 90.25 ave 92 max 89 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 33.25 ave 57 max 13 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Neighs: 309.25 ave 496 max 125 min +Histogram: 1 0 0 1 0 0 1 0 0 1 + +Total # of neighbors = 1237 +Ave neighs/atom = 3.42659 +Neighbor list builds = 3620 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/balance/log.27Nov18.balance.group.dynamic.g++.2 b/examples/balance/log.27Nov18.balance.group.dynamic.g++.2 new file mode 100644 index 0000000000..b88593b718 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.group.dynamic.g++.2 @@ -0,0 +1,110 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +variable factor index 1.0 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000552893 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes + +group fast type 1 +2600 atoms in group fast +group slow type 2 +1400 atoms in group slow +balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt +balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000512123 seconds + iteration count = 1 + group weights: fast=1 slow=1 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 +fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} +fix 0 all balance 10 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0 + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.437 | 4.628 | 4.819 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137 +Loop time of 1.95661 on 2 procs for 250 steps with 4000 atoms + +Performance: 55197.383 tau/day, 127.772 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0628 | 1.263 | 1.4632 | 17.8 | 64.55 +Neigh | 0.42332 | 0.43486 | 0.44639 | 1.7 | 22.22 +Comm | 0.033167 | 0.2449 | 0.45664 | 42.8 | 12.52 +Output | 0.00015879 | 0.00017142 | 0.00018406 | 0.0 | 0.01 +Modify | 0.010039 | 0.010042 | 0.010045 | 0.0 | 0.51 +Other | | 0.003658 | | | 0.19 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 10441 ave 10457 max 10425 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298332 ave 349156 max 247508 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596664 +Ave neighs/atom = 149.166 +Neighbor list builds = 25 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/balance/log.5Oct16.balance.group.dynamic.g++.4 b/examples/balance/log.27Nov18.balance.group.dynamic.g++.4 similarity index 73% rename from examples/balance/log.5Oct16.balance.group.dynamic.g++.4 rename to examples/balance/log.27Nov18.balance.group.dynamic.g++.4 index b7b893e5fd..ec6fc449c4 100644 --- a/examples/balance/log.5Oct16.balance.group.dynamic.g++.4 +++ b/examples/balance/log.27Nov18.balance.group.dynamic.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000427008 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -37,13 +39,18 @@ group slow type 2 balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted.txt balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0 Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 - rebalancing time: 0.000472069 seconds + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000735044 seconds iteration count = 2 group weights: fast=1 slow=1 initial/final max load/proc = 1200 1200 @@ -66,7 +73,7 @@ fix 1 all nve thermo 50 run 250 -Memory usage per processor = 2.9192 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.566 | 3.947 | 4.329 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137 @@ -74,20 +81,20 @@ Step Temp E_pair E_mol TotEng Press Volume 150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137 200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137 -Loop time of 1.40299 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.48981 on 4 procs for 250 steps with 4000 atoms -Performance: 76978.657 tau/day, 178.191 timesteps/s -99.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 72492.623 tau/day, 167.807 timesteps/s +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.22572 | 0.65681 | 1.1571 | 45.2 | 46.82 -Neigh | 0.16769 | 0.18555 | 0.20139 | 3.0 | 13.23 -Comm | 0.033973 | 0.55042 | 0.99983 | 51.1 | 39.23 -Output | 0.00012207 | 0.00013012 | 0.00014353 | 0.1 | 0.01 -Modify | 0.0053966 | 0.0054266 | 0.0054569 | 0.0 | 0.39 -Other | | 0.004645 | | | 0.33 +Pair | 0.22803 | 0.67101 | 1.1622 | 43.7 | 45.04 +Neigh | 0.20611 | 0.2259 | 0.23756 | 2.5 | 15.16 +Comm | 0.085412 | 0.58198 | 1.045 | 47.7 | 39.06 +Output | 0.00016332 | 0.00028861 | 0.0006516 | 0.0 | 0.02 +Modify | 0.0069213 | 0.0070978 | 0.0072331 | 0.1 | 0.48 +Other | | 0.003534 | | | 0.24 Nlocal: 1000 ave 1001 max 999 min Histogram: 1 0 0 0 0 2 0 0 0 1 diff --git a/examples/balance/log.27Nov18.balance.group.static.g++.2 b/examples/balance/log.27Nov18.balance.group.static.g++.2 new file mode 100644 index 0000000000..eb7a506e2c --- /dev/null +++ b/examples/balance/log.27Nov18.balance.group.static.g++.2 @@ -0,0 +1,146 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +variable factor index 1.0 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.00050807 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes + +balance 1.0 shift x 5 1.1 # out unweighted.txt +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000545979 seconds + iteration count = 1 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +balance 1.0 x uniform + rebalancing time: 0.000159502 seconds + iteration count = 0 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +variable weight atom (type==1)*1.0+(type==2)*v_factor +balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt + rebalancing time: 0.000320673 seconds + iteration count = 1 + weight variable: weight + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +balance 1.0 x uniform + rebalancing time: 0.000132561 seconds + iteration count = 0 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +group fast type 1 +2600 atoms in group fast +group slow type 2 +1400 atoms in group slow +balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt +balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0 + rebalancing time: 0.000235796 seconds + iteration count = 1 + group weights: fast=1 slow=1 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -6.9453205 0 -5.4456955 -5.6812358 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 +Loop time of 1.99136 on 2 procs for 250 steps with 4000 atoms + +Performance: 54234.216 tau/day, 125.542 timesteps/s +99.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0081 | 1.262 | 1.5159 | 22.6 | 63.37 +Neigh | 0.40357 | 0.41713 | 0.43069 | 2.1 | 20.95 +Comm | 0.033287 | 0.30076 | 0.56822 | 48.8 | 15.10 +Output | 0.00014162 | 0.00015128 | 0.00016093 | 0.0 | 0.01 +Modify | 0.0072243 | 0.0073462 | 0.007468 | 0.1 | 0.37 +Other | | 0.003961 | | | 0.20 + +Nlocal: 2000 ave 2051 max 1949 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10443 ave 10506 max 10380 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298332 ave 363449 max 233215 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596664 +Ave neighs/atom = 149.166 +Neighbor list builds = 24 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/balance/log.5Oct16.balance.group.static.g++.4 b/examples/balance/log.27Nov18.balance.group.static.g++.4 similarity index 74% rename from examples/balance/log.5Oct16.balance.group.static.g++.4 rename to examples/balance/log.27Nov18.balance.group.static.g++.4 index be7a8dfc28..d792f1af93 100644 --- a/examples/balance/log.5Oct16.balance.group.static.g++.4 +++ b/examples/balance/log.27Nov18.balance.group.static.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000426769 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -32,13 +34,18 @@ neigh_modify every 2 delay 4 check yes balance 1.0 shift x 5 1.1 # out unweighted.txt Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 - rebalancing time: 0.00113606 seconds + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000867605 seconds iteration count = 2 initial/final max load/proc = 1200 1200 initial/final imbalance factor = 1.2 1.2 @@ -47,7 +54,7 @@ Neighbor list info ... z cuts: 0 1 balance 1.0 x uniform - rebalancing time: 0.00050211 seconds + rebalancing time: 0.000295401 seconds iteration count = 0 initial/final max load/proc = 1200 1200 initial/final imbalance factor = 1.2 1.2 @@ -57,7 +64,7 @@ balance 1.0 x uniform variable weight atom (type==1)*1.0+(type==2)*v_factor balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt - rebalancing time: 0.000926018 seconds + rebalancing time: 0.000428915 seconds iteration count = 2 weight variable: weight initial/final max load/proc = 1200 1200 @@ -67,7 +74,7 @@ balance 1.0 shift x 5 1.1 weight var weight # out weighted_var.txt z cuts: 0 1 balance 1.0 x uniform - rebalancing time: 0.000455856 seconds + rebalancing time: 0.000236273 seconds iteration count = 0 initial/final max load/proc = 1200 1200 initial/final imbalance factor = 1.2 1.2 @@ -81,7 +88,7 @@ group slow type 2 1400 atoms in group slow balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow ${factor} # out weighted_group.txt balance 1.0 shift x 5 1.1 weight group 2 fast 1.0 slow 1.0 - rebalancing time: 0.00071907 seconds + rebalancing time: 0.000319958 seconds iteration count = 2 group weights: fast=1 slow=1 initial/final max load/proc = 1200 1200 @@ -102,7 +109,7 @@ fix 1 all nve thermo 50 run 250 -Memory usage per processor = 2.77892 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.426 | 3.713 | 4.188 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 -6.9453205 0 -5.4456955 -5.6812358 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 @@ -110,20 +117,20 @@ Step Temp E_pair E_mol TotEng Press 150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 -Loop time of 1.42478 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.45972 on 4 procs for 250 steps with 4000 atoms -Performance: 75800.979 tau/day, 175.465 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 73986.752 tau/day, 171.266 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.35155 | 0.65282 | 1.1868 | 42.1 | 45.82 -Neigh | 0.12951 | 0.16927 | 0.20492 | 7.4 | 11.88 -Comm | 0.03706 | 0.59419 | 0.90483 | 44.8 | 41.70 -Output | 0.00011921 | 0.00013947 | 0.00015664 | 0.1 | 0.01 -Modify | 0.0023413 | 0.0032853 | 0.0043154 | 1.2 | 0.23 -Other | | 0.005085 | | | 0.36 +Pair | 0.34936 | 0.66325 | 1.1729 | 40.9 | 45.44 +Neigh | 0.15811 | 0.20835 | 0.24806 | 7.4 | 14.27 +Comm | 0.04955 | 0.57875 | 0.86745 | 43.6 | 39.65 +Output | 0.00015831 | 0.00028872 | 0.00064492 | 0.0 | 0.02 +Modify | 0.0030367 | 0.0040676 | 0.0050561 | 1.1 | 0.28 +Other | | 0.005014 | | | 0.34 Nlocal: 1000 ave 1263 max 712 min Histogram: 1 0 0 0 1 0 1 0 0 1 diff --git a/examples/balance/log.27Nov18.balance.kspace.g++.2 b/examples/balance/log.27Nov18.balance.kspace.g++.2 new file mode 100644 index 0000000000..13e24ed17a --- /dev/null +++ b/examples/balance/log.27Nov18.balance.kspace.g++.2 @@ -0,0 +1,117 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +#atom_style charge +processors * 1 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000510931 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type +#set type 1:2 charge 0.0 + +velocity all create 1.0 87287 + +pair_style lj/long/coul/long long off 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +kspace_style pppm/disp 1.0e-4 +kspace_modify gewald/disp 0.1 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes + +group fast type 1 +2600 atoms in group fast +group slow type 2 +1400 atoms in group slow +fix 0 all balance 20 1.0 shift x 5 1.0 weight group 2 fast 1.0 slow 2.0 weight time 0.66 + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 500 +PPPMDisp initialization ... + Dispersion G vector (1/distance) = 0.1 + Dispersion grid = 2 2 2 + Dispersion stencil order = 5 + Dispersion estimated absolute RMS force accuracy = 1.01251 + Dispersion estimated absolute real space RMS force accuracy = 1.01251 + Dispersion estimated absolute kspace RMS force accuracy = 7.29446e-07 + Disperion estimated relative force accuracy = 1.01251 + using double precision FFTs + 3d grid and FFT values/proc dispersion = 294 4 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/long/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.846 | 5.014 | 5.182 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 52.148338 0 53.647963 94.09503 4738.2137 + 50 17.747599 42.836975 0 69.451719 143.44398 4738.2137 + 100 9.0390947 49.78615 0 63.341402 117.79296 4738.2137 + 150 13.456072 47.810527 0 67.989589 140.52068 4738.2137 + 200 11.358932 52.542448 0 69.576586 142.87196 4738.2137 + 250 13.204593 48.601437 0 68.403375 134.97484 4738.2137 + 300 12.061996 50.642194 0 68.730665 133.27077 4738.2137 + 350 14.107163 50.201375 0 71.356829 143.54662 4738.2137 + 400 12.053939 50.221116 0 68.297504 132.01999 4738.2137 + 450 13.523963 50.829687 0 71.11056 143.8183 4738.2137 + 500 13.135822 50.150114 0 69.848921 137.26364 4738.2137 +Loop time of 6.95261 on 2 procs for 500 steps with 4000 atoms + +Performance: 31067.471 tau/day, 71.915 timesteps/s +99.5% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8521 | 3.0997 | 3.3472 | 14.1 | 44.58 +Kspace | 1.1859 | 1.303 | 1.4202 | 10.3 | 18.74 +Neigh | 2.2324 | 2.387 | 2.5417 | 10.0 | 34.33 +Comm | 0.1003 | 0.12513 | 0.14996 | 7.0 | 1.80 +Output | 0.00033641 | 0.00036693 | 0.00039744 | 0.0 | 0.01 +Modify | 0.026408 | 0.02737 | 0.028331 | 0.6 | 0.39 +Other | | 0.009989 | | | 0.14 + +Nlocal: 2000 ave 2316 max 1684 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 9543.5 ave 9675 max 9412 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 254445 ave 276022 max 232868 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 508890 +Ave neighs/atom = 127.222 +Neighbor list builds = 124 +Dangerous builds = 97 +Total wall time: 0:00:06 diff --git a/examples/balance/log.5Oct16.balance.kspace.g++.4 b/examples/balance/log.27Nov18.balance.kspace.g++.4 similarity index 58% rename from examples/balance/log.5Oct16.balance.kspace.g++.4 rename to examples/balance/log.27Nov18.balance.kspace.g++.4 index 0a98c0d14f..7745b3e602 100644 --- a/examples/balance/log.5Oct16.balance.kspace.g++.4 +++ b/examples/balance/log.27Nov18.balance.kspace.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000432491 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -61,50 +63,55 @@ PPPMDisp initialization ... using double precision FFTs 3d grid and FFT values/proc dispersion = 294 4 Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 -Memory usage per processor = 3.32692 Mbytes + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/long/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.291 | 4.423 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 52.148338 0 53.647963 94.09503 4738.2137 50 17.850656 42.620113 0 69.389403 142.80556 4738.2137 100 9.4607189 49.700118 0 63.887649 117.51739 4738.2137 150 13.992056 47.731988 0 68.714825 140.56926 4738.2137 - 200 11.617635 52.509395 0 69.931491 142.6933 4738.2137 - 250 13.536262 48.330072 0 68.629389 133.91619 4738.2137 - 300 12.619739 50.32635 0 69.251226 132.46483 4738.2137 - 350 14.513905 50.104058 0 71.869473 143.37708 4738.2137 - 400 12.410226 49.786147 0 68.396832 130.38693 4738.2137 - 450 13.812498 51.076195 0 71.789763 144.8252 4738.2137 - 500 13.278792 50.270368 0 70.183575 136.8547 4738.2137 -Loop time of 5.24456 on 4 procs for 500 steps with 4000 atoms + 200 11.617635 52.509394 0 69.93149 142.6933 4738.2137 + 250 13.536287 48.33108 0 68.630434 133.91794 4738.2137 + 300 12.619985 50.328139 0 69.253384 132.46719 4738.2137 + 350 14.497923 50.092405 0 71.833853 143.39356 4738.2137 + 400 12.228079 50.202361 0 68.539894 131.75614 4738.2137 + 450 14.01349 50.908526 0 71.923506 144.25732 4738.2137 + 500 13.277341 50.381613 0 70.292644 137.20282 4738.2137 +Loop time of 6.17838 on 4 procs for 500 steps with 4000 atoms -Performance: 41185.531 tau/day, 95.337 timesteps/s -98.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 34960.628 tau/day, 80.927 timesteps/s +93.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.64469 | 1.5898 | 2.5249 | 68.8 | 30.31 -Kspace | 0.63052 | 2.3872 | 3.9848 | 97.6 | 45.52 -Neigh | 0.2153 | 0.986 | 1.9625 | 76.8 | 18.80 -Comm | 0.094079 | 0.25333 | 0.3749 | 23.9 | 4.83 -Output | 0.0002811 | 0.00035048 | 0.00040078 | 0.3 | 0.01 -Modify | 0.013268 | 0.016651 | 0.021077 | 2.6 | 0.32 -Other | | 0.01122 | | | 0.21 +Pair | 0.74813 | 1.6453 | 2.5052 | 65.7 | 26.63 +Kspace | 1.036 | 2.9098 | 4.5974 | 94.8 | 47.10 +Neigh | 0.27464 | 1.2099 | 2.4155 | 84.8 | 19.58 +Comm | 0.1711 | 0.36843 | 0.5217 | 25.2 | 5.96 +Output | 0.00052595 | 0.0053349 | 0.0074508 | 3.8 | 0.09 +Modify | 0.023363 | 0.027308 | 0.032521 | 2.3 | 0.44 +Other | | 0.01228 | | | 0.20 -Nlocal: 1000 ave 2010 max 228 min +Nlocal: 1000 ave 2002 max 241 min Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 7559.75 ave 9255 max 5915 min +Nghost: 7608 ave 9312 max 5850 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 127415 ave 215720 max 45292 min +Neighs: 127345 ave 211903 max 47616 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Total # of neighbors = 509660 -Ave neighs/atom = 127.415 +Total # of neighbors = 509381 +Ave neighs/atom = 127.345 Neighbor list builds = 124 Dangerous builds = 97 -Total wall time: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/balance/log.27Nov18.balance.neigh.dynamic.g++.2 b/examples/balance/log.27Nov18.balance.neigh.dynamic.g++.2 new file mode 100644 index 0000000000..aef8d90889 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.neigh.dynamic.g++.2 @@ -0,0 +1,228 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000553608 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes +fix p all property/atom d_WEIGHT +fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.8 weight store WEIGHT +compute p all property/atom d_WEIGHT +variable maximb equal f_0[1] +variable iter equal f_0[2] +variable prev equal f_0[3] +variable final equal f_0 + +#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}" + +fix 1 all nve + +#dump id all atom 50 dump.melt +#dump id all custom 50 dump.lammpstrj id type x y z c_p + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mp4 c_p type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 amap 0.0 2.0 cf 0.1 3 min blue 0.5 green max red + +thermo 50 +run 500 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65) +Per MPI rank memory allocation (min/avg/max) = 4.562 | 4.753 | 4.944 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137 + 300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137 + 350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137 + 400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137 + 450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137 + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 +Loop time of 3.92718 on 2 procs for 500 steps with 4000 atoms + +Performance: 55001.290 tau/day, 127.318 timesteps/s +99.2% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2902 | 2.6102 | 2.9303 | 19.8 | 66.47 +Neigh | 0.89715 | 0.89718 | 0.8972 | 0.0 | 22.85 +Comm | 0.074355 | 0.39408 | 0.7138 | 50.9 | 10.03 +Output | 0.0003202 | 0.00035989 | 0.00039959 | 0.0 | 0.01 +Modify | 0.016438 | 0.016832 | 0.017226 | 0.3 | 0.43 +Other | | 0.008523 | | | 0.22 + +Nlocal: 2000 ave 2056 max 1944 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10457.5 ave 10508 max 10407 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298070 ave 333007 max 263132 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596139 +Ave neighs/atom = 149.035 +Neighbor list builds = 51 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 + 550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137 + 600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137 + 650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137 + 700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137 + 750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137 + 800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137 + 850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137 + 900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137 + 950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137 + 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137 +Loop time of 3.83028 on 2 procs for 500 steps with 4000 atoms + +Performance: 56392.741 tau/day, 130.539 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.263 | 2.5605 | 2.858 | 18.6 | 66.85 +Neigh | 0.8789 | 0.88341 | 0.88791 | 0.5 | 23.06 +Comm | 0.068052 | 0.36076 | 0.65347 | 48.7 | 9.42 +Output | 0.0003016 | 0.0003438 | 0.000386 | 0.0 | 0.01 +Modify | 0.016381 | 0.016829 | 0.017277 | 0.3 | 0.44 +Other | | 0.008426 | | | 0.22 + +Nlocal: 2000 ave 2049 max 1951 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10389 ave 10436 max 10342 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 300836 ave 335987 max 265684 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 601671 +Ave neighs/atom = 150.418 +Neighbor list builds = 51 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137 + 1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137 + 1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137 + 1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137 + 1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137 + 1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 4738.2137 + 1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137 + 1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137 + 1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137 + 1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137 + 1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137 +Loop time of 3.81946 on 2 procs for 500 steps with 4000 atoms + +Performance: 56552.445 tau/day, 130.908 timesteps/s +99.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2594 | 2.5549 | 2.8504 | 18.5 | 66.89 +Neigh | 0.86746 | 0.87203 | 0.8766 | 0.5 | 22.83 +Comm | 0.06715 | 0.36699 | 0.66684 | 49.5 | 9.61 +Output | 0.00029325 | 0.00033867 | 0.00038409 | 0.0 | 0.01 +Modify | 0.016529 | 0.016817 | 0.017105 | 0.2 | 0.44 +Other | | 0.008371 | | | 0.22 + +Nlocal: 2000 ave 2034 max 1966 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10386 ave 10936 max 9836 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 302958 ave 337188 max 268729 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 605917 +Ave neighs/atom = 151.479 +Neighbor list builds = 51 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.758 | 4.946 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137 + 1550 0.53713593 -6.2504069 0 -5.4449044 -1.764709 4738.2137 + 1600 0.54679556 -6.2646482 0 -5.4446599 -1.8115775 4738.2137 + 1650 0.53806577 -6.2519006 0 -5.4450037 -1.7409142 4738.2137 + 1700 0.5347951 -6.2468962 0 -5.4449041 -1.7162331 4738.2137 + 1750 0.53714568 -6.2506577 0 -5.4451406 -1.7340499 4738.2137 + 1800 0.52749839 -6.2358664 0 -5.4448167 -1.6874961 4738.2137 + 1850 0.54585956 -6.2629394 0 -5.4443547 -1.7758764 4738.2137 + 1900 0.53010831 -6.2387561 0 -5.4437925 -1.6381825 4738.2137 + 1950 0.54288557 -6.2583073 0 -5.4441826 -1.7368524 4738.2137 + 2000 0.52765923 -6.2348572 0 -5.4435663 -1.5588839 4738.2137 +Loop time of 3.78423 on 2 procs for 500 steps with 4000 atoms + +Performance: 57078.976 tau/day, 132.127 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2449 | 2.5388 | 2.8328 | 18.4 | 67.09 +Neigh | 0.85527 | 0.85828 | 0.86129 | 0.3 | 22.68 +Comm | 0.065453 | 0.36215 | 0.65885 | 49.3 | 9.57 +Output | 0.00030518 | 0.00032794 | 0.00035071 | 0.0 | 0.01 +Modify | 0.016444 | 0.016597 | 0.01675 | 0.1 | 0.44 +Other | | 0.008044 | | | 0.21 + +Nlocal: 2000 ave 2031 max 1969 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10334 ave 10921 max 9747 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 303988 ave 338808 max 269168 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 607976 +Ave neighs/atom = 151.994 +Neighbor list builds = 51 +Dangerous builds = 0 + +Total wall time: 0:00:15 diff --git a/examples/balance/log.5Oct16.balance.neigh.dynamic.g++.4 b/examples/balance/log.27Nov18.balance.neigh.dynamic.g++.4 similarity index 71% rename from examples/balance/log.5Oct16.balance.neigh.dynamic.g++.4 rename to examples/balance/log.27Nov18.balance.neigh.dynamic.g++.4 index 979da10e6c..08a59785d4 100644 --- a/examples/balance/log.5Oct16.balance.neigh.dynamic.g++.4 +++ b/examples/balance/log.27Nov18.balance.neigh.dynamic.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000430107 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -51,14 +53,19 @@ fix 1 all nve thermo 50 run 500 Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 -WARNING: Balance weight neigh skipped b/c no list found (../imbalance_neigh.cpp:67) -Memory usage per processor = 3.0442 Mbytes + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65) +Per MPI rank memory allocation (min/avg/max) = 3.691 | 4.072 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137 @@ -71,20 +78,20 @@ Step Temp E_pair E_mol TotEng Press Volume 400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137 450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 -Loop time of 2.30888 on 4 procs for 500 steps with 4000 atoms +Loop time of 2.45924 on 4 procs for 500 steps with 4000 atoms -Performance: 93551.974 tau/day, 216.555 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 87831.985 tau/day, 203.315 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.0928 | 1.4128 | 1.6873 | 21.3 | 61.19 -Neigh | 0.26037 | 0.38342 | 0.55053 | 20.2 | 16.61 -Comm | 0.33912 | 0.49342 | 0.644 | 18.3 | 21.37 -Output | 0.00029206 | 0.00033247 | 0.00037789 | 0.2 | 0.01 -Modify | 0.0062437 | 0.0082552 | 0.010971 | 2.2 | 0.36 -Other | | 0.01067 | | | 0.46 +Pair | 1.1372 | 1.4179 | 1.6656 | 18.1 | 57.66 +Neigh | 0.30681 | 0.46841 | 0.69372 | 24.1 | 19.05 +Comm | 0.46019 | 0.55206 | 0.6052 | 7.7 | 22.45 +Output | 0.00034404 | 0.0005753 | 0.001132 | 0.0 | 0.02 +Modify | 0.007339 | 0.0099927 | 0.013719 | 2.7 | 0.41 +Other | | 0.01029 | | | 0.42 Nlocal: 1000 ave 1549 max 605 min Histogram: 2 0 0 0 0 0 1 0 0 1 @@ -98,7 +105,7 @@ Ave neighs/atom = 149.308 Neighbor list builds = 50 Dangerous builds = 0 run 500 -Memory usage per processor = 3.06519 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137 @@ -111,20 +118,20 @@ Step Temp E_pair E_mol TotEng Press Volume 900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137 950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137 -Loop time of 2.16949 on 4 procs for 500 steps with 4000 atoms +Loop time of 2.389 on 4 procs for 500 steps with 4000 atoms -Performance: 99562.401 tau/day, 230.469 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 90414.542 tau/day, 209.293 timesteps/s +97.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1466 | 1.3644 | 1.5476 | 15.2 | 62.89 -Neigh | 0.25492 | 0.38744 | 0.57253 | 22.1 | 17.86 -Comm | 0.34836 | 0.39805 | 0.45037 | 6.7 | 18.35 -Output | 0.00028539 | 0.00031531 | 0.00037646 | 0.2 | 0.01 -Modify | 0.0060055 | 0.008239 | 0.011282 | 2.5 | 0.38 -Other | | 0.01107 | | | 0.51 +Pair | 1.2112 | 1.381 | 1.5214 | 11.0 | 57.81 +Neigh | 0.29746 | 0.48382 | 0.74669 | 27.5 | 20.25 +Comm | 0.40449 | 0.50032 | 0.57922 | 9.4 | 20.94 +Output | 0.00033617 | 0.00064272 | 0.0013907 | 0.0 | 0.03 +Modify | 0.0070128 | 0.010942 | 0.015494 | 3.7 | 0.46 +Other | | 0.01223 | | | 0.51 Nlocal: 1000 ave 1569 max 595 min Histogram: 2 0 0 0 0 0 1 0 0 1 @@ -138,7 +145,7 @@ Ave neighs/atom = 150.169 Neighbor list builds = 53 Dangerous builds = 0 run 500 -Memory usage per processor = 3.06519 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137 1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137 @@ -151,20 +158,20 @@ Step Temp E_pair E_mol TotEng Press Volume 1400 0.53726924 -6.2518379 0 -5.4461355 -1.8544028 4738.2137 1450 0.54525935 -6.2632653 0 -5.4455808 -1.9072158 4738.2137 1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137 -Loop time of 2.17283 on 4 procs for 500 steps with 4000 atoms +Loop time of 2.45895 on 4 procs for 500 steps with 4000 atoms -Performance: 99409.423 tau/day, 230.114 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 87842.291 tau/day, 203.339 timesteps/s +95.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1581 | 1.3768 | 1.574 | 15.8 | 63.37 -Neigh | 0.24753 | 0.3727 | 0.54533 | 21.2 | 17.15 -Comm | 0.33306 | 0.40373 | 0.47481 | 9.3 | 18.58 -Output | 0.00036979 | 0.0003832 | 0.00039721 | 0.0 | 0.02 -Modify | 0.0059896 | 0.0082257 | 0.011168 | 2.5 | 0.38 -Other | | 0.01095 | | | 0.50 +Pair | 1.2592 | 1.4017 | 1.5327 | 11.0 | 57.01 +Neigh | 0.28831 | 0.47661 | 0.75988 | 28.7 | 19.38 +Comm | 0.41426 | 0.54907 | 0.6044 | 10.6 | 22.33 +Output | 0.0003705 | 0.00060898 | 0.0012109 | 0.0 | 0.02 +Modify | 0.014004 | 0.016774 | 0.020669 | 1.9 | 0.68 +Other | | 0.01415 | | | 0.58 Nlocal: 1000 ave 1543 max 605 min Histogram: 2 0 0 0 0 0 1 0 0 1 @@ -178,7 +185,7 @@ Ave neighs/atom = 150.494 Neighbor list builds = 51 Dangerous builds = 0 run 500 -Memory usage per processor = 3.06519 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.097 | 4.288 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1500 0.54223346 -6.2591057 0 -5.4459588 -1.8866985 4738.2137 1550 0.55327018 -6.2750126 0 -5.4453148 -1.9506585 4738.2137 @@ -191,20 +198,20 @@ Step Temp E_pair E_mol TotEng Press Volume 1900 0.53992511 -6.254136 0 -5.4444508 -1.7768715 4738.2137 1950 0.54665895 -6.2640958 0 -5.4443124 -1.7946993 4738.2137 2000 0.5455751 -6.2625337 0 -5.4443756 -1.8072242 4738.2137 -Loop time of 2.20474 on 4 procs for 500 steps with 4000 atoms +Loop time of 2.42708 on 4 procs for 500 steps with 4000 atoms -Performance: 97970.946 tau/day, 226.785 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 88995.678 tau/day, 206.009 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1731 | 1.3783 | 1.5498 | 14.7 | 62.51 -Neigh | 0.26429 | 0.40654 | 0.59777 | 22.6 | 18.44 -Comm | 0.36731 | 0.40043 | 0.44935 | 5.2 | 18.16 -Output | 0.00030565 | 0.00033122 | 0.00039625 | 0.2 | 0.02 -Modify | 0.0059974 | 0.008266 | 0.01132 | 2.6 | 0.37 -Other | | 0.01088 | | | 0.49 +Pair | 1.2482 | 1.3902 | 1.5329 | 10.6 | 57.28 +Neigh | 0.31099 | 0.50813 | 0.78451 | 28.1 | 20.94 +Comm | 0.37293 | 0.5011 | 0.58684 | 11.2 | 20.65 +Output | 0.00033593 | 0.00060582 | 0.0012991 | 0.0 | 0.02 +Modify | 0.007091 | 0.0097566 | 0.013303 | 2.7 | 0.40 +Other | | 0.01727 | | | 0.71 Nlocal: 1000 ave 1539 max 607 min Histogram: 2 0 0 0 0 0 1 0 0 1 @@ -218,4 +225,4 @@ Ave neighs/atom = 151.655 Neighbor list builds = 56 Dangerous builds = 0 -Total wall time: 0:00:08 +Total wall time: 0:00:09 diff --git a/examples/balance/log.27Nov18.balance.neigh.rcb.g++.2 b/examples/balance/log.27Nov18.balance.neigh.rcb.g++.2 new file mode 100644 index 0000000000..42b04f818c --- /dev/null +++ b/examples/balance/log.27Nov18.balance.neigh.rcb.g++.2 @@ -0,0 +1,141 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000511885 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +comm_style tiled + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes +fix p all property/atom d_WEIGHT +fix 0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT +compute p all property/atom d_WEIGHT +variable maximb equal f_0[1] +variable iter equal f_0[2] +variable prev equal f_0[3] +variable final equal f_0 + +#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}" + +fix 1 all nve + +#dump id all atom 50 dump.melt +#dump id all custom 50 dump.lammpstrj id type x y z c_p + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 + +run 250 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65) +Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.329 | 4.52 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137 +Loop time of 1.80309 on 2 procs for 250 steps with 4000 atoms + +Performance: 59897.213 tau/day, 138.651 timesteps/s +97.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2185 | 1.2646 | 1.3106 | 4.1 | 70.13 +Neigh | 0.43131 | 0.43248 | 0.43365 | 0.2 | 23.99 +Comm | 0.045418 | 0.090311 | 0.1352 | 14.9 | 5.01 +Output | 0.00017476 | 0.00021195 | 0.00024915 | 0.0 | 0.01 +Modify | 0.011012 | 0.01103 | 0.011048 | 0.0 | 0.61 +Other | | 0.004476 | | | 0.25 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 10412.5 ave 10414 max 10411 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298332 ave 299797 max 296867 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596664 +Ave neighs/atom = 149.166 +Neighbor list builds = 25 +Dangerous builds = 0 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.929 | 4.929 | 4.93 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137 + 300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137 + 350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137 + 400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137 + 450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137 + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 +Loop time of 1.77097 on 2 procs for 250 steps with 4000 atoms + +Performance: 60983.669 tau/day, 141.166 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2353 | 1.2515 | 1.2678 | 1.5 | 70.67 +Neigh | 0.44235 | 0.44303 | 0.44371 | 0.1 | 25.02 +Comm | 0.045978 | 0.061555 | 0.077133 | 6.3 | 3.48 +Output | 0.0001564 | 0.00016713 | 0.00017786 | 0.0 | 0.01 +Modify | 0.010305 | 0.01031 | 0.010315 | 0.0 | 0.58 +Other | | 0.004365 | | | 0.25 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Nghost: 10466.5 ave 10470 max 10463 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 298070 ave 349236 max 246903 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 596139 +Ave neighs/atom = 149.035 +Neighbor list builds = 26 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/balance/log.5Oct16.balance.neigh.rcb.g++.4 b/examples/balance/log.27Nov18.balance.neigh.rcb.g++.4 similarity index 60% rename from examples/balance/log.5Oct16.balance.neigh.rcb.g++.4 rename to examples/balance/log.27Nov18.balance.neigh.rcb.g++.4 index 0ab49c229f..4a2a747773 100644 --- a/examples/balance/log.5Oct16.balance.neigh.rcb.g++.4 +++ b/examples/balance/log.27Nov18.balance.neigh.rcb.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000440836 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -54,14 +56,19 @@ thermo 50 run 250 Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 -WARNING: Balance weight neigh skipped b/c no list found (../imbalance_neigh.cpp:67) -Memory usage per processor = 2.90262 Mbytes + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65) +Per MPI rank memory allocation (min/avg/max) = 3.917 | 3.927 | 3.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137 @@ -69,34 +76,34 @@ Step Temp E_pair E_mol TotEng Press Volume 150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137 200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137 -Loop time of 0.956315 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.0693 on 4 procs for 250 steps with 4000 atoms -Performance: 112933.523 tau/day, 261.420 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 101000.295 tau/day, 233.797 timesteps/s +89.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.5859 | 0.6311 | 0.66986 | 4.1 | 65.99 -Neigh | 0.16996 | 0.18014 | 0.19678 | 2.4 | 18.84 -Comm | 0.078254 | 0.13416 | 0.18229 | 10.9 | 14.03 -Output | 0.00025582 | 0.0002594 | 0.00026608 | 0.0 | 0.03 -Modify | 0.0051248 | 0.0054137 | 0.0057077 | 0.3 | 0.57 -Other | | 0.005242 | | | 0.55 +Pair | 0.58255 | 0.65493 | 0.72281 | 8.3 | 61.25 +Neigh | 0.214 | 0.22344 | 0.23158 | 1.4 | 20.90 +Comm | 0.10451 | 0.17801 | 0.25967 | 17.3 | 16.65 +Output | 0.00015521 | 0.00020903 | 0.00034142 | 0.0 | 0.02 +Modify | 0.007113 | 0.0073407 | 0.0076027 | 0.2 | 0.69 +Other | | 0.005369 | | | 0.50 -Nlocal: 1000 ave 1103 max 932 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Nghost: 7617 ave 7871 max 7360 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 149349 ave 169737 max 137211 min -Histogram: 2 0 0 0 1 0 0 0 0 1 +Nlocal: 1000 ave 1005 max 996 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 7674 ave 7679 max 7670 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 149349 ave 149991 max 147960 min +Histogram: 1 0 0 0 0 0 0 1 0 2 Total # of neighbors = 597396 Ave neighs/atom = 149.349 Neighbor list builds = 25 Dangerous builds = 0 run 250 -Memory usage per processor = 2.90266 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.922 | 4.004 | 4.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137 300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137 @@ -104,31 +111,31 @@ Step Temp E_pair E_mol TotEng Press Volume 400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137 450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 -Loop time of 0.97826 on 4 procs for 250 steps with 4000 atoms +Loop time of 0.999028 on 4 procs for 250 steps with 4000 atoms -Performance: 110400.094 tau/day, 255.556 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 108105.088 tau/day, 250.243 timesteps/s +93.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.62013 | 0.63258 | 0.63864 | 0.9 | 64.66 -Neigh | 0.17712 | 0.18068 | 0.18788 | 1.0 | 18.47 -Comm | 0.14206 | 0.15504 | 0.17108 | 2.7 | 15.85 -Output | 0.00014997 | 0.00018102 | 0.000247 | 0.3 | 0.02 -Modify | 0.0047612 | 0.0049355 | 0.0050402 | 0.1 | 0.50 -Other | | 0.004845 | | | 0.50 +Pair | 0.60256 | 0.6507 | 0.68091 | 3.8 | 65.13 +Neigh | 0.21602 | 0.21945 | 0.22516 | 0.8 | 21.97 +Comm | 0.087366 | 0.11787 | 0.16957 | 9.6 | 11.80 +Output | 0.00016737 | 0.00028127 | 0.00057006 | 0.0 | 0.03 +Modify | 0.0065138 | 0.0066211 | 0.0067828 | 0.1 | 0.66 +Other | | 0.004103 | | | 0.41 -Nlocal: 1000 ave 1003 max 997 min +Nlocal: 1000 ave 1005 max 994 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 7675.75 ave 7703 max 7648 min Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 7662.75 ave 7668 max 7656 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Neighs: 149308 ave 151009 max 146887 min -Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 149308 ave 173909 max 124842 min +Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 597231 Ave neighs/atom = 149.308 Neighbor list builds = 25 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/balance/log.27Nov18.balance.neigh.static.g++.2 b/examples/balance/log.27Nov18.balance.neigh.static.g++.2 new file mode 100644 index 0000000000..de3aae921c --- /dev/null +++ b/examples/balance/log.27Nov18.balance.neigh.static.g++.2 @@ -0,0 +1,211 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +variable factor index 1.0 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 2 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000495195 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes + +balance 1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65) + rebalancing time: 0.000623703 seconds + iteration count = 1 + neigh weight factor: 0.8 + initial/final max load/proc = 2000 2000 + initial/final imbalance factor = 1 1 + x cuts: 0 0.5 1 + y cuts: 0 1 + z cuts: 0 1 + +fix 1 all nve + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 post no +Per MPI rank memory allocation (min/avg/max) = 4.297 | 4.488 | 4.678 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1 -6.9453205 0 -5.4456955 -5.6812358 + 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 + 100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 + 150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 + 200 0.536665 -6.2530113 0 -5.448215 -1.933468 + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 +Loop time of 1.97176 on 2 procs for 250 steps with 4000 atoms + +balance 1.0 shift x 10 1.0 weight neigh 0.8 + rebalancing time: 0.000482321 seconds + iteration count = 10 + neigh weight factor: 0.8 + initial/final max load/proc = 290759 262123 + initial/final imbalance factor = 1.10982 1.00052 + x cuts: 0 0.45166 1 + y cuts: 0 1 + z cuts: 0 1 +run 250 post no +Per MPI rank memory allocation (min/avg/max) = 4.304 | 4.492 | 4.681 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 + 300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 + 350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 + 400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 + 450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 +Loop time of 1.77716 on 2 procs for 250 steps with 4000 atoms + +balance 1.0 shift x 10 1.0 weight neigh 0.8 + rebalancing time: 0.000497341 seconds + iteration count = 10 + neigh weight factor: 0.8 + initial/final max load/proc = 296648 269016 + initial/final imbalance factor = 1.10642 1.00336 + x cuts: 0 0.501461 1 + y cuts: 0 1 + z cuts: 0 1 +run 250 post no +Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes +Step Temp E_pair E_mol TotEng Press + 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 + 550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 + 600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 + 650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 + 700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 + 750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 +Loop time of 2.0039 on 2 procs for 250 steps with 4000 atoms + +balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6 + rebalancing time: 0.000368118 seconds + iteration count = 10 + neigh weight factor: 0.8 + time weight factor: 0.6 + initial/final max load/proc = 168.493 167.093 + initial/final imbalance factor = 1.00948 1.00109 + x cuts: 0 0.499991 1 + y cuts: 0 1 + z cuts: 0 1 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes +Step Temp E_pair E_mol TotEng Press + 750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 + 800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 + 850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 + 900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 + 950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 + 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 +Loop time of 2.0382 on 2 procs for 250 steps with 4000 atoms + +Performance: 52987.998 tau/day, 122.657 timesteps/s +98.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.96918 | 1.257 | 1.5449 | 25.7 | 61.67 +Neigh | 0.40421 | 0.42672 | 0.44923 | 3.4 | 20.94 +Comm | 0.032542 | 0.34306 | 0.65358 | 53.0 | 16.83 +Output | 0.00014377 | 0.00015366 | 0.00016356 | 0.0 | 0.01 +Modify | 0.0070617 | 0.007337 | 0.0076122 | 0.3 | 0.36 +Other | | 0.003878 | | | 0.19 + +Nlocal: 2000 ave 2056 max 1944 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10403.5 ave 10525 max 10282 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 300836 ave 365656 max 236015 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 601671 +Ave neighs/atom = 150.418 +Neighbor list builds = 25 +Dangerous builds = 0 +balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6 + rebalancing time: 0.000344753 seconds + iteration count = 10 + neigh weight factor: 0.8 + time weight factor: 0.6 + initial/final max load/proc = 170.235 168.809 + initial/final imbalance factor = 1.01037 1.00191 + x cuts: 0 0.49755 1 + y cuts: 0 1 + z cuts: 0 1 +run 250 +Per MPI rank memory allocation (min/avg/max) = 4.681 | 4.683 | 4.686 Mbytes +Step Temp E_pair E_mol TotEng Press + 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 + 1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 + 1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 + 1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 + 1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 + 1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418134 +Loop time of 2.01086 on 2 procs for 250 steps with 4000 atoms + +Performance: 53708.387 tau/day, 124.325 timesteps/s +98.9% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.0037 | 1.2615 | 1.5192 | 23.0 | 62.73 +Neigh | 0.40846 | 0.4277 | 0.44695 | 2.9 | 21.27 +Comm | 0.033029 | 0.31012 | 0.5872 | 49.8 | 15.42 +Output | 0.00014424 | 0.00015259 | 0.00016093 | 0.0 | 0.01 +Modify | 0.007298 | 0.0074347 | 0.0075715 | 0.2 | 0.37 +Other | | 0.003999 | | | 0.20 + +Nlocal: 2000 ave 2038 max 1962 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 10391 ave 10489 max 10293 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 301104 ave 358264 max 243943 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 602207 +Ave neighs/atom = 150.552 +Neighbor list builds = 25 +Dangerous builds = 0 + +Total wall time: 0:00:09 diff --git a/examples/balance/log.5Oct16.balance.neigh.static.g++.4 b/examples/balance/log.27Nov18.balance.neigh.static.g++.4 similarity index 64% rename from examples/balance/log.5Oct16.balance.neigh.static.g++.4 rename to examples/balance/log.27Nov18.balance.neigh.static.g++.4 index 0e9550ceb5..3a9ab43cb1 100644 --- a/examples/balance/log.5Oct16.balance.neigh.static.g++.4 +++ b/examples/balance/log.27Nov18.balance.neigh.static.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000429153 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -32,14 +34,19 @@ neigh_modify every 2 delay 4 check yes balance 1.0 shift x 10 1.0 weight neigh 0.8 # out weighted_var.txt Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 -WARNING: Balance weight neigh skipped b/c no list found (../imbalance_neigh.cpp:67) - rebalancing time: 0.00039506 seconds + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +WARNING: Balance weight neigh skipped b/c no list found (src/imbalance_neigh.cpp:65) + rebalancing time: 0.000684023 seconds iteration count = 3 neigh weight factor: 0.8 initial/final max load/proc = 1200 1000 @@ -60,7 +67,7 @@ fix 1 all nve thermo 50 run 250 post no -Memory usage per processor = 2.77892 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.426 | 3.802 | 4.188 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 -6.9453205 0 -5.4456955 -5.6812358 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 @@ -68,11 +75,10 @@ Step Temp E_pair E_mol TotEng Press 150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 -Loop time of 1.41104 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.44749 on 4 procs for 250 steps with 4000 atoms -98.7% CPU use with 4 MPI tasks x no OpenMP threads balance 1.0 shift x 10 1.0 weight neigh 0.8 - rebalancing time: 0.000409126 seconds + rebalancing time: 0.000543356 seconds iteration count = 10 neigh weight factor: 0.8 initial/final max load/proc = 220132 125739 @@ -81,7 +87,7 @@ balance 1.0 shift x 10 1.0 weight neigh 0.8 y cuts: 0 1 z cuts: 0 1 run 250 post no -Memory usage per processor = 2.78273 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.814 | 3.999 | 4.192 Mbytes Step Temp E_pair E_mol TotEng Press 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 @@ -89,11 +95,10 @@ Step Temp E_pair E_mol TotEng Press 400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 -Loop time of 1.06236 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.19834 on 4 procs for 250 steps with 4000 atoms -99.4% CPU use with 4 MPI tasks x no OpenMP threads balance 1.0 shift x 10 1.0 weight neigh 0.8 - rebalancing time: 0.000265121 seconds + rebalancing time: 0.000308752 seconds iteration count = 10 neigh weight factor: 0.8 initial/final max load/proc = 147109 128929 @@ -102,7 +107,7 @@ balance 1.0 shift x 10 1.0 weight neigh 0.8 y cuts: 0 1 z cuts: 0 1 run 250 post no -Memory usage per processor = 2.7999 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.832 | 4.018 | 4.209 Mbytes Step Temp E_pair E_mol TotEng Press 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 @@ -110,21 +115,20 @@ Step Temp E_pair E_mol TotEng Press 650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 -Loop time of 1.02794 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.23246 on 4 procs for 250 steps with 4000 atoms -99.6% CPU use with 4 MPI tasks x no OpenMP threads balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6 - rebalancing time: 0.000314951 seconds + rebalancing time: 0.000306845 seconds iteration count = 10 neigh weight factor: 0.8 time weight factor: 0.6 - initial/final max load/proc = 109.37 93.2369 - initial/final imbalance factor = 1.17599 1.00252 - x cuts: 0 0.31323 0.448651 0.560211 1 + initial/final max load/proc = 114.116 101.665 + initial/final imbalance factor = 1.12567 1.00285 + x cuts: 0 0.30983 0.449501 0.588031 1 y cuts: 0 1 z cuts: 0 1 run 250 -Memory usage per processor = 2.7999 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.832 | 4.018 | 4.209 Mbytes Step Temp E_pair E_mol TotEng Press 750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 @@ -132,44 +136,44 @@ Step Temp E_pair E_mol TotEng Press 900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 -Loop time of 1.0482 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.13265 on 4 procs for 250 steps with 4000 atoms -Performance: 103033.455 tau/day, 238.503 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 95351.673 tau/day, 220.721 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.59706 | 0.65768 | 0.71098 | 5.8 | 62.74 -Neigh | 0.094988 | 0.17834 | 0.28455 | 19.8 | 17.01 -Comm | 0.057361 | 0.20341 | 0.34531 | 28.7 | 19.41 -Output | 0.00013709 | 0.00020045 | 0.0002768 | 0.4 | 0.02 -Modify | 0.0016088 | 0.0032223 | 0.0052993 | 2.8 | 0.31 -Other | | 0.005343 | | | 0.51 +Pair | 0.64092 | 0.67347 | 0.70289 | 3.5 | 59.46 +Neigh | 0.11654 | 0.22172 | 0.35287 | 22.2 | 19.58 +Comm | 0.068215 | 0.22827 | 0.36221 | 28.0 | 20.15 +Output | 0.00016975 | 0.00031555 | 0.00065875 | 0.0 | 0.03 +Modify | 0.00214 | 0.004007 | 0.0062947 | 3.0 | 0.35 +Other | | 0.004862 | | | 0.43 -Nlocal: 1000 ave 1684 max 506 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Nghost: 8706.25 ave 10207 max 7655 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 150170 ave 163204 max 140236 min +Nlocal: 1000 ave 1651 max 529 min Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 8692.5 ave 9709 max 8037 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 150170 ave 154877 max 145634 min +Histogram: 1 0 0 1 0 0 1 0 0 1 Total # of neighbors = 600681 Ave neighs/atom = 150.17 Neighbor list builds = 25 Dangerous builds = 0 balance 1.0 shift x 10 1.0 weight neigh 0.8 weight time 0.6 - rebalancing time: 0.000258207 seconds + rebalancing time: 0.000319719 seconds iteration count = 10 neigh weight factor: 0.8 time weight factor: 0.6 - initial/final max load/proc = 96.6033 94.7484 - initial/final imbalance factor = 1.0231 1.00345 - x cuts: 0 0.315478 0.450068 0.579538 1 + initial/final max load/proc = 102.192 99.2749 + initial/final imbalance factor = 1.03206 1.0026 + x cuts: 0 0.312695 0.449907 0.587625 1 y cuts: 0 1 z cuts: 0 1 run 250 -Memory usage per processor = 2.7999 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.832 | 4.019 | 4.209 Mbytes Step Temp E_pair E_mol TotEng Press 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 @@ -177,31 +181,31 @@ Step Temp E_pair E_mol TotEng Press 1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 -Loop time of 1.02694 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.16447 on 4 procs for 250 steps with 4000 atoms -Performance: 105166.691 tau/day, 243.441 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 92745.661 tau/day, 214.689 timesteps/s +97.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.6025 | 0.64932 | 0.70125 | 5.6 | 63.23 -Neigh | 0.093299 | 0.17549 | 0.27782 | 19.3 | 17.09 -Comm | 0.05188 | 0.19352 | 0.31909 | 28.5 | 18.84 -Output | 0.00022793 | 0.00024354 | 0.00027609 | 0.1 | 0.02 -Modify | 0.0016394 | 0.0032356 | 0.0052338 | 2.8 | 0.32 -Other | | 0.005129 | | | 0.50 +Pair | 0.61612 | 0.67903 | 0.73112 | 5.1 | 58.31 +Neigh | 0.11722 | 0.22257 | 0.35236 | 22.3 | 19.11 +Comm | 0.099441 | 0.25198 | 0.42338 | 28.4 | 21.64 +Output | 0.00018501 | 0.0012686 | 0.0040495 | 4.5 | 0.11 +Modify | 0.0020952 | 0.0044899 | 0.0086782 | 4.0 | 0.39 +Other | | 0.005134 | | | 0.44 -Nlocal: 1000 ave 1659 max 494 min +Nlocal: 1000 ave 1631 max 523 min Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 8646.75 ave 9782 max 7837 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 149995 ave 165511 max 134186 min -Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 8693.75 ave 9752 max 8002 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 149995 ave 161500 max 141963 min +Histogram: 2 0 0 0 0 0 1 0 0 1 Total # of neighbors = 599979 Ave neighs/atom = 149.995 Neighbor list builds = 25 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/balance/log.5Oct16.balance.var.dynamic.g++.2 b/examples/balance/log.27Nov18.balance.var.dynamic.g++.2 similarity index 61% rename from examples/balance/log.5Oct16.balance.var.dynamic.g++.2 rename to examples/balance/log.27Nov18.balance.var.dynamic.g++.2 index 8015823c6d..c488a725e0 100644 --- a/examples/balance/log.5Oct16.balance.var.dynamic.g++.2 +++ b/examples/balance/log.27Nov18.balance.var.dynamic.g++.2 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 2 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000491142 secs mass * 1.0 region long block 3 6 0 10 0 10 @@ -36,13 +38,18 @@ group slow type 2 1400 atoms in group slow balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT Neighbor list info ... - 1 neighbor list requests update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 7 7 7 - rebalancing time: 0.001688 seconds + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.000805378 seconds iteration count = 10 group weights: fast=0.8 slow=2.5 storing weight in atom property d_WEIGHT @@ -74,7 +81,7 @@ fix 1 all nve thermo 50 run 500 -Memory usage per processor = 3.23652 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.708 | 4.876 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137 @@ -87,26 +94,26 @@ Step Temp E_pair E_mol TotEng Press Volume 400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137 450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 -Loop time of 4.87829 on 2 procs for 500 steps with 4000 atoms +Loop time of 5.01752 on 2 procs for 500 steps with 4000 atoms -Performance: 44277.854 tau/day, 102.495 timesteps/s -99.2% CPU use with 2 MPI tasks x no OpenMP threads +Performance: 43049.176 tau/day, 99.651 timesteps/s +98.5% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.4978 | 2.6788 | 3.8597 | 72.2 | 54.91 -Neigh | 0.6012 | 0.75888 | 0.91656 | 18.1 | 15.56 -Comm | 0.073541 | 1.4134 | 2.7532 | 112.7 | 28.97 -Output | 0.00026584 | 0.00027144 | 0.00027704 | 0.0 | 0.01 -Modify | 0.013387 | 0.015078 | 0.01677 | 1.4 | 0.31 -Other | | 0.01191 | | | 0.24 +Pair | 1.4325 | 2.6317 | 3.8309 | 73.9 | 52.45 +Neigh | 0.72307 | 0.89995 | 1.0768 | 18.6 | 17.94 +Comm | 0.08143 | 1.4587 | 2.836 | 114.0 | 29.07 +Output | 0.00034356 | 0.00034773 | 0.00035191 | 0.0 | 0.01 +Modify | 0.015713 | 0.017661 | 0.01961 | 1.5 | 0.35 +Other | | 0.009141 | | | 0.18 -Nlocal: 2000 ave 2452 max 1548 min +Nlocal: 2000 ave 2500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 10456.5 ave 11082 max 9831 min +Nghost: 10457 ave 11055 max 9859 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 298070 ave 470560 max 125579 min +Neighs: 298070 ave 483758 max 112381 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 596139 @@ -114,7 +121,7 @@ Ave neighs/atom = 149.035 Neighbor list builds = 51 Dangerous builds = 0 run 500 -Memory usage per processor = 3.24422 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.092 | 5.269 | 5.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137 550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137 @@ -127,26 +134,26 @@ Step Temp E_pair E_mol TotEng Press Volume 900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137 950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137 -Loop time of 5.11308 on 2 procs for 500 steps with 4000 atoms +Loop time of 5.38962 on 2 procs for 500 steps with 4000 atoms -Performance: 42244.620 tau/day, 97.788 timesteps/s -98.9% CPU use with 2 MPI tasks x no OpenMP threads +Performance: 40077.052 tau/day, 92.771 timesteps/s +98.0% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.0421 | 2.5613 | 4.0806 | 94.9 | 50.09 -Neigh | 0.51289 | 0.72321 | 0.93354 | 24.7 | 14.14 -Comm | 0.069973 | 1.8016 | 3.5332 | 129.0 | 35.24 -Output | 0.000283 | 0.00028694 | 0.00029087 | 0.0 | 0.01 -Modify | 0.012173 | 0.015003 | 0.017834 | 2.3 | 0.29 -Other | | 0.01164 | | | 0.23 +Pair | 0.93627 | 2.5477 | 4.1591 | 101.0 | 47.27 +Neigh | 0.61458 | 0.87078 | 1.127 | 27.5 | 16.16 +Comm | 0.072418 | 1.9424 | 3.8124 | 134.2 | 36.04 +Output | 0.00034833 | 0.00035048 | 0.00035262 | 0.0 | 0.01 +Modify | 0.014652 | 0.018169 | 0.021687 | 2.6 | 0.34 +Other | | 0.01024 | | | 0.19 -Nlocal: 2000 ave 2497 max 1503 min +Nlocal: 2000 ave 2561 max 1439 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 10396.5 ave 10916 max 9877 min +Nghost: 10257 ave 11109 max 9405 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 300836 ave 484375 max 117296 min +Neighs: 300836 ave 498670 max 103001 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 601671 @@ -155,20 +162,20 @@ Neighbor list builds = 51 Dangerous builds = 0 balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT - rebalancing time: 0.000527143 seconds + rebalancing time: 0.000744104 seconds iteration count = 10 group weights: fast=0.8 slow=2.5 storing weight in atom property d_WEIGHT - initial/final max load/proc = 4318.1 2791.9 - initial/final imbalance factor = 1.54771 1.00068 - x cuts: 0 0.454292 1 + initial/final max load/proc = 4428.8 2798.1 + initial/final imbalance factor = 1.58738 1.0029 + x cuts: 0 0.45485 1 y cuts: 0 1 z cuts: 0 1 fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT run 500 -Memory usage per processor = 3.24422 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.098 | 5.464 | 5.83 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137 1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137 @@ -179,22 +186,22 @@ Step Temp E_pair E_mol TotEng Press Volume 1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137 1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137 1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137 - 1450 0.54218439 -6.2574683 0 -5.444395 -1.7901188 4738.2137 - 1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000345 4738.2137 -Loop time of 5.31552 on 2 procs for 500 steps with 4000 atoms + 1450 0.54218439 -6.2574683 0 -5.444395 -1.7901189 4738.2137 + 1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137 +Loop time of 5.50675 on 2 procs for 500 steps with 4000 atoms -Performance: 40635.746 tau/day, 94.064 timesteps/s -98.8% CPU use with 2 MPI tasks x no OpenMP threads +Performance: 39224.584 tau/day, 90.798 timesteps/s +98.0% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.157 | 2.6457 | 4.1345 | 91.5 | 49.77 -Neigh | 0.42836 | 0.74879 | 1.0692 | 37.0 | 14.09 -Comm | 0.079503 | 1.8922 | 3.7049 | 131.8 | 35.60 -Output | 0.000386 | 0.00045156 | 0.00051713 | 0.3 | 0.01 -Modify | 0.010813 | 0.015272 | 0.019732 | 3.6 | 0.29 -Other | | 0.01305 | | | 0.25 +Pair | 1.1091 | 2.6165 | 4.124 | 93.2 | 47.51 +Neigh | 0.49666 | 0.88338 | 1.2701 | 41.1 | 16.04 +Comm | 0.079062 | 1.9768 | 3.8745 | 135.0 | 35.90 +Output | 0.00032926 | 0.00041151 | 0.00049376 | 0.0 | 0.01 +Modify | 0.012776 | 0.018102 | 0.023428 | 4.0 | 0.33 +Other | | 0.01156 | | | 0.21 Nlocal: 2000 ave 3010 max 990 min Histogram: 1 0 0 0 0 0 0 0 0 1 @@ -208,43 +215,43 @@ Ave neighs/atom = 151.479 Neighbor list builds = 51 Dangerous builds = 0 run 500 -Memory usage per processor = 3.26138 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.847 | 5.872 | 5.897 Mbytes Step Temp E_pair E_mol TotEng Press Volume - 1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000345 4738.2137 + 1500 0.54200616 -6.2571433 0 -5.4443373 -1.8000345 4738.2137 1550 0.5371361 -6.250403 0 -5.4449003 -1.7647032 4738.2137 - 1600 0.54679572 -6.2646443 0 -5.4446558 -1.8115723 4738.2137 - 1650 0.5380659 -6.2519009 0 -5.4450038 -1.7409149 4738.2137 - 1700 0.53479444 -6.2469033 0 -5.4449122 -1.7162442 4738.2137 - 1750 0.53714076 -6.2506512 0 -5.4451415 -1.7340198 4738.2137 - 1800 0.5275053 -6.2358817 0 -5.4448216 -1.6875364 4738.2137 - 1850 0.54585433 -6.2629377 0 -5.4443609 -1.7758622 4738.2137 - 1900 0.53011157 -6.2387715 0 -5.4438029 -1.6382145 4738.2137 - 1950 0.54287707 -6.2583052 0 -5.4441932 -1.7367502 4738.2137 - 2000 0.52771203 -6.2349621 0 -5.443592 -1.5593714 4738.2137 -Loop time of 5.52542 on 2 procs for 500 steps with 4000 atoms + 1600 0.54679571 -6.2646443 0 -5.4446558 -1.8115722 4738.2137 + 1650 0.53806587 -6.2519009 0 -5.4450039 -1.7409152 4738.2137 + 1700 0.53479436 -6.2469032 0 -5.4449122 -1.7162441 4738.2137 + 1750 0.53714071 -6.2506513 0 -5.4451416 -1.7340205 4738.2137 + 1800 0.52750533 -6.2358819 0 -5.4448217 -1.687537 4738.2137 + 1850 0.54585346 -6.262937 0 -5.4443615 -1.7758597 4738.2137 + 1900 0.53011247 -6.2387653 0 -5.4437954 -1.6382086 4738.2137 + 1950 0.54287683 -6.2583097 0 -5.4441981 -1.7367469 4738.2137 + 2000 0.52771288 -6.2349676 0 -5.4435962 -1.5593804 4738.2137 +Loop time of 5.80884 on 2 procs for 500 steps with 4000 atoms -Performance: 39092.050 tau/day, 90.491 timesteps/s -98.9% CPU use with 2 MPI tasks x no OpenMP threads +Performance: 37184.695 tau/day, 86.076 timesteps/s +97.7% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.71557 | 2.5165 | 4.3174 | 113.5 | 45.54 -Neigh | 0.33034 | 0.71217 | 1.094 | 45.2 | 12.89 -Comm | 0.079871 | 2.2671 | 4.4544 | 145.3 | 41.03 -Output | 0.00027609 | 0.00034881 | 0.00042152 | 0.4 | 0.01 -Modify | 0.0095153 | 0.015319 | 0.021122 | 4.7 | 0.28 -Other | | 0.01399 | | | 0.25 +Pair | 0.71314 | 2.5435 | 4.3738 | 114.8 | 43.79 +Neigh | 0.39935 | 0.85806 | 1.3168 | 49.5 | 14.77 +Comm | 0.082629 | 2.3761 | 4.6695 | 148.8 | 40.90 +Output | 0.00034571 | 0.00044024 | 0.00053477 | 0.0 | 0.01 +Modify | 0.011643 | 0.018227 | 0.024811 | 4.9 | 0.31 +Other | | 0.01257 | | | 0.22 -Nlocal: 2000 ave 3030 max 970 min +Nlocal: 2000 ave 3032 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 10272.5 ave 12222 max 8323 min +Nghost: 10266 ave 12245 max 8287 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 303996 ave 524806 max 83185 min +Neighs: 303998 ave 525128 max 82868 min Histogram: 1 0 0 0 0 0 0 0 0 1 -Total # of neighbors = 607991 -Ave neighs/atom = 151.998 +Total # of neighbors = 607996 +Ave neighs/atom = 151.999 Neighbor list builds = 51 Dangerous builds = 0 -Total wall time: 0:00:20 +Total wall time: 0:00:21 diff --git a/examples/balance/log.27Nov18.balance.var.dynamic.g++.4 b/examples/balance/log.27Nov18.balance.var.dynamic.g++.4 new file mode 100644 index 0000000000..66c1183481 --- /dev/null +++ b/examples/balance/log.27Nov18.balance.var.dynamic.g++.4 @@ -0,0 +1,257 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic +processors * 1 1 + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 3 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 4 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000424862 secs +mass * 1.0 + +region long block 3 6 0 10 0 10 +set region long type 2 + 1400 settings made for type + +velocity all create 1.0 87287 + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_coeff * 2 1.0 1.0 5.0 + +neighbor 0.3 bin +neigh_modify every 2 delay 4 check yes +fix p all property/atom d_WEIGHT +compute p all property/atom d_WEIGHT + +group fast type 1 +2600 atoms in group fast +group slow type 2 +1400 atoms in group slow +balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.3 + ghost atom cutoff = 5.3 + binsize = 2.65, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + rebalancing time: 0.00115108 seconds + iteration count = 10 + group weights: fast=0.8 slow=2.5 + storing weight in atom property d_WEIGHT + initial/final max load/proc = 2160 1620 + initial/final imbalance factor = 1.54839 1.16129 + x cuts: 0 0.300049 0.449951 0.599854 1 + y cuts: 0 1 + z cuts: 0 1 +variable lastweight atom c_p + +fix 0 all balance 50 1.0 shift x 10 1.0 weight var lastweight weight time 0.5 weight store WEIGHT +variable maximb equal f_0[1] +variable iter equal f_0[2] +variable prev equal f_0[3] +variable final equal f_0 + +#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}" + +fix 1 all nve + +#dump id all atom 50 dump.melt +#dump id all custom 50 dump.lammpstrj id type x y z c_p + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.132 | 4.192 | 4.274 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137 + 50 0.48653399 -6.1788509 0 -5.4492324 -1.6017778 4738.2137 + 100 0.53411175 -6.249885 0 -5.4489177 -1.9317606 4738.2137 + 150 0.53646658 -6.2527206 0 -5.4482219 -1.9689568 4738.2137 + 200 0.54551611 -6.2656326 0 -5.4475631 -2.0042104 4738.2137 + 250 0.54677719 -6.2671162 0 -5.4471555 -2.0015995 4738.2137 + 300 0.5477618 -6.2678071 0 -5.4463698 -1.997842 4738.2137 + 350 0.55600296 -6.2801497 0 -5.4463538 -2.0394056 4738.2137 + 400 0.53241503 -6.2453665 0 -5.4469436 -1.878594 4738.2137 + 450 0.5439158 -6.2623 0 -5.4466302 -1.9744161 4738.2137 + 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 +Loop time of 2.66424 on 4 procs for 500 steps with 4000 atoms + +Performance: 81073.650 tau/day, 187.670 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1083 | 1.3909 | 1.7318 | 24.2 | 52.21 +Neigh | 0.19732 | 0.45425 | 0.7722 | 38.2 | 17.05 +Comm | 0.24921 | 0.79627 | 1.3351 | 60.3 | 29.89 +Output | 0.00041294 | 0.00065368 | 0.0011899 | 0.0 | 0.02 +Modify | 0.0071657 | 0.010935 | 0.015748 | 3.6 | 0.41 +Other | | 0.01124 | | | 0.42 + +Nlocal: 1000 ave 1870 max 299 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 8679.25 ave 10190 max 7374 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 149308 ave 215125 max 81132 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 597231 +Ave neighs/atom = 149.308 +Neighbor list builds = 50 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.134 | 4.387 | 4.664 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 500 0.55526241 -6.2793396 0 -5.4466542 -2.0595015 4738.2137 + 550 0.53879347 -6.2554274 0 -5.4474393 -1.9756834 4738.2137 + 600 0.54275982 -6.2616799 0 -5.4477437 -1.9939993 4738.2137 + 650 0.54526651 -6.265098 0 -5.4474027 -2.0303672 4738.2137 + 700 0.54369381 -6.263201 0 -5.4478642 -1.9921967 4738.2137 + 750 0.54452777 -6.2640839 0 -5.4474964 -1.9658675 4738.2137 + 800 0.55061744 -6.2725556 0 -5.4468359 -2.0100922 4738.2137 + 850 0.55371614 -6.2763992 0 -5.4460326 -2.0065329 4738.2137 + 900 0.54756622 -6.2668303 0 -5.4456863 -1.9796122 4738.2137 + 950 0.54791593 -6.2673161 0 -5.4456477 -1.9598278 4738.2137 + 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137 +Loop time of 3.02509 on 4 procs for 500 steps with 4000 atoms + +Performance: 71402.836 tau/day, 165.284 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.6808 | 1.3385 | 1.959 | 52.5 | 44.25 +Neigh | 0.13127 | 0.4678 | 0.86924 | 48.5 | 15.46 +Comm | 0.19735 | 1.1921 | 2.1903 | 85.9 | 39.41 +Output | 0.00045371 | 0.00090569 | 0.0013952 | 0.0 | 0.03 +Modify | 0.0062041 | 0.011167 | 0.01691 | 4.5 | 0.37 +Other | | 0.01462 | | | 0.48 + +Nlocal: 1000 ave 1935 max 262 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 8739.75 ave 10498 max 7333 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 150170 ave 231608 max 72161 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 600678 +Ave neighs/atom = 150.169 +Neighbor list builds = 53 +Dangerous builds = 0 + +balance 1.0 shift x 10 1.0 weight group 2 fast 0.8 slow 2.5 weight store WEIGHT + rebalancing time: 0.000575304 seconds + iteration count = 10 + group weights: fast=0.8 slow=2.5 + storing weight in atom property d_WEIGHT + initial/final max load/proc = 2318.1 1408.1 + initial/final imbalance factor = 1.66172 1.00939 + x cuts: 0 0.337054 0.454419 0.59556 1 + y cuts: 0 1 + z cuts: 0 1 + +fix 0 all balance 50 1.0 shift x 5 1.0 weight var lastweight weight neigh 0.5 weight store WEIGHT + +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.136 | 4.393 | 4.673 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 1000 0.54173198 -6.2586101 0 -5.4462153 -1.9007466 4738.2137 + 1050 0.54629742 -6.2657526 0 -5.4465113 -1.945821 4738.2137 + 1100 0.55427881 -6.2781733 0 -5.446963 -2.0021027 4738.2137 + 1150 0.54730654 -6.267257 0 -5.4465025 -1.9420678 4738.2137 + 1200 0.5388281 -6.2547963 0 -5.4467562 -1.890178 4738.2137 + 1250 0.54848768 -6.2694237 0 -5.4468979 -1.9636797 4738.2137 + 1300 0.54134321 -6.2590728 0 -5.447261 -1.917027 4738.2137 + 1350 0.53564389 -6.2501521 0 -5.4468871 -1.8642306 4738.2137 + 1400 0.53726925 -6.2518379 0 -5.4461355 -1.8544028 4738.2137 + 1450 0.54525929 -6.2632653 0 -5.4455808 -1.9072158 4738.2137 + 1500 0.54223341 -6.2591056 0 -5.4459588 -1.8866983 4738.2137 +Loop time of 3.07108 on 4 procs for 500 steps with 4000 atoms + +Performance: 70333.514 tau/day, 162.809 timesteps/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.77463 | 1.3897 | 2.1328 | 51.3 | 45.25 +Neigh | 0.13416 | 0.45546 | 0.80534 | 46.9 | 14.83 +Comm | 0.17763 | 1.2036 | 2.1448 | 83.6 | 39.19 +Output | 0.00039482 | 0.00067067 | 0.0013118 | 0.0 | 0.02 +Modify | 0.0058403 | 0.010695 | 0.015841 | 4.5 | 0.35 +Other | | 0.01099 | | | 0.36 + +Nlocal: 1000 ave 1955 max 199 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 8729 ave 10472 max 7399 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 150494 ave 251670 max 54664 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 601974 +Ave neighs/atom = 150.494 +Neighbor list builds = 51 +Dangerous builds = 0 +run 500 +Per MPI rank memory allocation (min/avg/max) = 4.136 | 4.393 | 4.673 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 1500 0.54223341 -6.2591056 0 -5.4459588 -1.8866983 4738.2137 + 1550 0.55327047 -6.2750129 0 -5.4453147 -1.9506601 4738.2137 + 1600 0.54419056 -6.2612631 0 -5.4451813 -1.8559469 4738.2137 + 1650 0.54710007 -6.2661977 0 -5.4457528 -1.8882828 4738.2137 + 1700 0.53665429 -6.250492 0 -5.4457118 -1.8067907 4738.2137 + 1750 0.54864943 -6.2681198 0 -5.4453514 -1.8662924 4738.2137 + 1800 0.54477002 -6.2615118 0 -5.4445611 -1.835304 4738.2137 + 1850 0.54143129 -6.2555621 0 -5.4436182 -1.8005839 4738.2137 + 1900 0.53994573 -6.254175 0 -5.4444588 -1.7770422 4738.2137 + 1950 0.54665379 -6.2640981 0 -5.4443224 -1.7946205 4738.2137 + 2000 0.54548501 -6.2623919 0 -5.4443689 -1.8063177 4738.2137 +Loop time of 3.48709 on 4 procs for 500 steps with 4000 atoms + +Performance: 61942.848 tau/day, 143.386 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.42099 | 1.3571 | 2.3564 | 80.4 | 38.92 +Neigh | 0.083965 | 0.4942 | 0.96204 | 58.6 | 14.17 +Comm | 0.25895 | 1.6131 | 2.9631 | 106.2 | 46.26 +Output | 0.00042915 | 0.00068706 | 0.0012567 | 0.0 | 0.02 +Modify | 0.0051193 | 0.010964 | 0.017898 | 5.5 | 0.31 +Other | | 0.01109 | | | 0.32 + +Nlocal: 1000 ave 2036 max 127 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 8722.75 ave 10448 max 7456 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 151642 ave 269558 max 35372 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 606566 +Ave neighs/atom = 151.642 +Neighbor list builds = 56 +Dangerous builds = 0 +Total wall time: 0:00:12 diff --git a/examples/balance/log.5Oct16.balance.bond.fast.g++.4 b/examples/balance/log.5Oct16.balance.bond.fast.g++.4 deleted file mode 100644 index 17df4227b4..0000000000 --- a/examples/balance/log.5Oct16.balance.bond.fast.g++.4 +++ /dev/null @@ -1,225 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d circle of particles inside a box with LJ walls - -variable b index 0 - -variable x index 50 -variable y index 20 -variable d index 20 -variable v index 5 -variable w index 2 - -units lj -dimension 2 -atom_style bond -boundary f f p - -lattice hex 0.85 -Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 -region box block 0 $x 0 $y -0.5 0.5 -region box block 0 50 0 $y -0.5 0.5 -region box block 0 50 0 20 -0.5 0.5 -create_box 1 box bond/types 1 extra/bond/per/atom 6 -Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) - 2 by 2 by 1 MPI processor grid -region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) -region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) -region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) -region circle sphere 11 6.7735026918962581988 0.0 10 -create_atoms 1 region circle -Created 361 atoms -mass 1 1.0 - -velocity all create 0.5 87287 loop geom -velocity all set $v $w 0 sum yes -velocity all set 5 $w 0 sum yes -velocity all set 5 2 0 sum yes - -pair_style lj/cut 2.5 -pair_coeff 1 1 10.0 1.0 2.5 - -bond_style harmonic -bond_coeff 1 10.0 1.2 - -# need to preserve 1-3, 1-4 pairwise interactions during hard collisions - -special_bonds lj/coul 0 1 1 - 0 = max # of 1-2 neighbors - 1 = max # of special neighbors -create_bonds all all 1 1.0 1.5 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 42 29 1 -Added 1014 bonds, new total = 1014 - 6 = max # of 1-2 neighbors - 6 = max # of special neighbors - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 -fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 -fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 -fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 - -comm_style tiled -comm_modify cutoff 10.0 # because bonds stretch a long ways -fix 10 all balance 50 0.9 rcb - -#compute 1 all property/atom proc -#variable p atom (c_1%10)+1 -#dump 2 all custom 50 tmp.dump id v_p x y z - -#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 -#variable colors string # "red green blue yellow white # purple pink orange lime gray" -#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} - -thermo_style custom step temp epair press f_10[3] f_10 -thermo 100 - -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 10 - binsize = 1.4 -> bins = 42 29 1 -Memory usage per processor = 4.49479 Mbytes -Step Temp E_pair Press f_10[3] f_10 - 0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316 - 100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102 - 200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906 - 300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906 - 400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102 - 500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906 - 600 35.05989 -21.524279 2.3728488 1.3296399 1.0083102 - 700 36.705654 -21.984526 3.2984899 1.3296399 1.0083102 - 800 39.631254 -25.783472 4.1595658 1.3961219 1.0083102 - 900 38.122407 -24.836728 5.3619155 1.3628809 1.0083102 - 1000 38.369965 -25.098561 4.5613077 1.3074792 1.0083102 - 1100 36.448264 -25.295817 4.0134469 1.1966759 1.0193906 - 1200 33.216313 -21.813423 4.48954 1.1634349 1.0304709 - 1300 30.361077 -20.323335 4.8079549 1.0637119 1.0083102 - 1400 29.368132 -18.532543 3.8449914 1.1191136 1.0083102 - 1500 27.699395 -15.990271 2.1565226 1.1523546 1.0304709 - 1600 25.304973 -14.626675 0.91025038 1.1301939 1.0083102 - 1700 26.335273 -14.499134 1.2878263 1.1855956 1.0083102 - 1800 25.755278 -13.121269 0.78425366 1.1745152 1.0193906 - 1900 25.454743 -13.903724 -0.16644734 1.1080332 1.0083102 - 2000 25.54829 -13.271068 1.9214248 1.0969529 1.0083102 - 2100 26.663083 -13.423796 1.9699997 1.1080332 1.0083102 - 2200 27.707332 -13.759474 1.5528121 1.1412742 1.0304709 - 2300 26.649636 -14.246313 0.91466777 1.1412742 1.0193906 - 2400 25.92802 -13.16271 1.0298936 1.1301939 1.0193906 - 2500 24.992275 -12.299161 1.3078979 1.1301939 1.0083102 - 2600 26.235185 -13.363142 2.0756764 1.2188366 1.0083102 - 2700 27.235116 -15.57943 2.1120604 1.1745152 1.0083102 - 2800 25.313585 -14.352196 2.1442169 1.0637119 1.0083102 - 2900 23.472278 -13.686216 0.69404738 1.0637119 1.0193906 - 3000 21.02552 -11.646464 0.56287643 1.0747922 1.0083102 - 3100 20.746946 -10.721207 -0.67351842 1.0858726 1.0193906 - 3200 20.330655 -10.307715 -0.30221601 1.0637119 1.0083102 - 3300 22.84995 -11.104879 0.0039310975 1.1191136 1.0083102 - 3400 23.23878 -11.827018 0.80792932 1.1301939 1.0193906 - 3500 25.262491 -12.191616 0.83249221 1.0747922 1.0193906 - 3600 25.08542 -13.10456 1.3164581 1.0969529 1.0193906 - 3700 22.649046 -11.300822 0.20123604 1.0526316 1.0193906 - 3800 20.516849 -9.7738907 -0.45160364 1.0637119 1.0083102 - 3900 20.227823 -9.8156456 -1.4386994 1.0637119 1.0083102 - 4000 21.511004 -9.6074826 0.83933362 1.1080332 1.0083102 - 4100 24.569081 -12.671563 0.60105671 1.0858726 1.0193906 - 4200 24.739215 -11.654269 0.66172409 1.0969529 1.0083102 - 4300 22.433043 -10.921392 1.2813391 1.1634349 1.0083102 - 4400 22.520504 -10.59901 0.10799908 1.0193906 1.0083102 - 4500 21.799185 -9.5801426 0.057062661 1.1191136 1.0193906 - 4600 22.537171 -9.9647087 -0.70915155 1.1412742 1.0083102 - 4700 22.380783 -10.974234 -0.73703011 1.0858726 1.0083102 - 4800 23.991602 -11.171402 1.3314176 1.0415512 1.0193906 - 4900 23.077116 -12.281132 0.73818416 1.0858726 1.0083102 - 5000 23.180253 -11.702364 0.84176858 1.1080332 1.0193906 - 5100 21.079712 -11.204743 0.50038687 1.0747922 1.0083102 - 5200 21.348945 -10.802581 -0.28651467 1.1634349 1.0193906 - 5300 21.332913 -10.352697 0.46738209 1.0858726 1.0193906 - 5400 22.283885 -10.635637 -0.31446485 1.0415512 1.0083102 - 5500 21.404737 -9.7733531 0.61106958 1.0858726 1.0193906 - 5600 23.013417 -10.291315 1.0562031 1.0969529 1.0083102 - 5700 22.087964 -10.931365 0.071180576 1.0415512 1.0193906 - 5800 24.011278 -11.080032 1.3901123 1.0637119 1.0193906 - 5900 22.320482 -10.616071 0.57726663 1.1412742 1.0193906 - 6000 23.348377 -12.116776 0.59306932 1.1191136 1.0193906 - 6100 22.20822 -11.545749 0.035299394 1.0747922 1.0193906 - 6200 22.810467 -10.598645 0.3296656 1.0415512 1.0083102 - 6300 21.398957 -10.058479 0.66795602 1.0415512 1.0193906 - 6400 21.945005 -10.358622 -1.0094405 1.0415512 1.0083102 - 6500 22.906408 -10.767788 1.0948374 1.0858726 1.0083102 - 6600 23.326617 -11.264481 0.82773039 1.0747922 1.0083102 - 6700 22.491386 -10.27014 0.043938534 1.0526316 1.0193906 - 6800 22.294374 -10.664685 0.048726237 1.1191136 1.0083102 - 6900 22.221286 -10.697394 1.0354647 1.0415512 1.0193906 - 7000 21.693738 -10.009277 0.64426437 1.0858726 1.0083102 - 7100 22.775615 -11.372061 0.069159076 1.1191136 1.0193906 - 7200 22.274683 -11.583382 -0.35907789 1.0858726 1.0193906 - 7300 21.410706 -11.005479 -0.66394825 1.1080332 1.0083102 - 7400 21.910735 -9.9354265 0.78899083 1.0526316 1.0083102 - 7500 21.526738 -9.7787506 -0.38232161 1.0415512 1.0083102 - 7600 21.833898 -10.289457 0.058939882 1.0747922 1.0193906 - 7700 21.606736 -9.6807332 0.50127515 1.0526316 1.0083102 - 7800 22.294657 -10.790285 0.8685065 1.0637119 1.0083102 - 7900 23.269713 -11.375434 0.84634431 1.0969529 1.0304709 - 8000 22.865151 -10.960251 1.0270422 1.0526316 1.0304709 - 8100 21.656008 -10.504825 1.2228537 1.0304709 1.0193906 - 8200 24.494122 -12.282009 0.16316531 1.0526316 1.0193906 - 8300 22.974267 -11.287149 -0.035076799 1.0747922 1.0193906 - 8400 21.052237 -11.243181 -0.099450689 1.0747922 1.0193906 - 8500 22.661383 -11.090107 -0.22913242 1.0969529 1.0193906 - 8600 21.403272 -9.5267458 -0.28047198 1.0637119 1.0193906 - 8700 22.786699 -10.403836 0.40752047 1.0415512 1.0193906 - 8800 24.504694 -10.706052 1.1870205 1.0969529 1.0193906 - 8900 23.22256 -11.182967 0.64166445 1.0747922 1.0304709 - 9000 23.734203 -10.422277 1.3143506 1.1191136 1.0304709 - 9100 23.517258 -11.247418 -0.13540081 1.0193906 1.0193906 - 9200 23.128204 -9.9181617 1.0928284 1.1412742 1.0083102 - 9300 23.281107 -10.523942 0.011923998 1.0969529 1.0193906 - 9400 21.800282 -10.359413 -0.62145559 1.1412742 1.0193906 - 9500 24.910955 -11.786562 1.6227559 1.1301939 1.0193906 - 9600 24.331432 -11.802048 0.62882542 1.1191136 1.0083102 - 9700 22.340782 -10.531555 0.29842716 1.0415512 1.0193906 - 9800 22.371239 -10.384104 0.34253854 1.0415512 1.0083102 - 9900 22.289367 -9.9488634 0.29499176 1.1412742 1.0083102 - 10000 22.518865 -10.279548 -0.48356734 1.1745152 1.0083102 -Loop time of 0.879172 on 4 procs for 10000 steps with 361 atoms - -Performance: 4913715.115 tau/day, 11374.341 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.11586 | 0.13009 | 0.14055 | 2.7 | 14.80 -Bond | 0.054003 | 0.058475 | 0.063238 | 1.8 | 6.65 -Neigh | 0.2865 | 0.29554 | 0.3049 | 1.2 | 33.62 -Comm | 0.20988 | 0.24193 | 0.27748 | 4.9 | 27.52 -Output | 0.0021532 | 0.0023131 | 0.00266 | 0.4 | 0.26 -Modify | 0.043945 | 0.045592 | 0.047122 | 0.6 | 5.19 -Other | | 0.1052 | | | 11.97 - -Nlocal: 90.25 ave 91 max 90 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 250.25 ave 257 max 247 min -Histogram: 1 1 1 0 0 0 0 0 0 1 -Neighs: 624.75 ave 739 max 519 min -Histogram: 1 0 0 1 0 0 1 0 0 1 - -Total # of neighbors = 2499 -Ave neighs/atom = 6.92244 -Ave special neighs/atom = 5.61773 -Neighbor list builds = 4881 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/balance/log.5Oct16.balance.g++.4 b/examples/balance/log.5Oct16.balance.g++.4 deleted file mode 100644 index 692666c3f8..0000000000 --- a/examples/balance/log.5Oct16.balance.g++.4 +++ /dev/null @@ -1,202 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d circle of particles inside a box with LJ walls - -variable b index 0 - -variable x index 50 -variable y index 20 -variable d index 20 -variable v index 5 -variable w index 2 - -units lj -dimension 2 -atom_style atomic -boundary f f p - -lattice hex 0.85 -Lattice spacing in x,y,z = 1.16553 2.01877 1.16553 -region box block 0 $x 0 $y -0.5 0.5 -region box block 0 50 0 $y -0.5 0.5 -region box block 0 50 0 20 -0.5 0.5 -create_box 1 box -Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767) - 2 by 2 by 1 MPI processor grid -region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) -region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2) -region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2) -region circle sphere 11 6.7735026918962581988 0.0 10 -create_atoms 1 region circle -Created 361 atoms -mass 1 1.0 - -velocity all create 0.5 87287 loop geom -velocity all set $v $w 0 sum yes -velocity all set 5 $w 0 sum yes -velocity all set 5 2 0 sum yes - -pair_style lj/cut 2.5 -pair_coeff 1 1 10.0 1.0 2.5 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 all nve - -fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5 -fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5 -fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5 -fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5 - -comm_style tiled -fix 10 all balance 50 0.9 rcb - -#compute 1 all property/atom proc -#variable p atom c_1%10 -#dump 2 all custom 50 tmp.dump id v_p x y z - -#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02 -#variable colors string # "red green blue yellow white # purple pink orange lime gray" -#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors} - -thermo_style custom step temp epair press f_10[3] f_10 -thermo 100 - -run 10000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 42 29 1 -Memory usage per processor = 2.48839 Mbytes -Step Temp E_pair Press f_10[3] f_10 - 0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316 - 100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709 - 200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102 - 300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906 - 400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102 - 500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102 - 600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102 - 700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102 - 800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102 - 900 23.635295 -27.372963 9.029962 1.1634349 1.0083102 - 1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906 - 1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906 - 1200 17.214458 -20.726965 6.3578918 1.0304709 1.0193906 - 1300 16.42404 -19.757268 3.9028429 1.1191136 1.0083102 - 1400 15.012286 -18.095045 1.7699868 1.0858726 1.0193906 - 1500 13.853156 -16.929243 1.0730365 1.0858726 1.0193906 - 1600 13.655251 -16.659753 2.1723498 1.0747922 1.0083102 - 1700 12.675328 -15.550697 1.8710911 1.0415512 1.0193906 - 1800 12.657349 -15.825827 1.9350712 1.0193906 1.0193906 - 1900 12.857141 -15.773 1.7624119 1.0193906 1.0304709 - 2000 11.856547 -14.727128 1.7186493 1.1080332 1.0083102 - 2100 12.113322 -14.953592 1.4400251 1.0415512 1.0193906 - 2200 11.545208 -14.363826 1.1597272 1.0969529 1.0083102 - 2300 11.433966 -14.302533 1.5537689 1.0969529 1.0083102 - 2400 11.577739 -14.385288 1.3175128 1.0526316 1.0193906 - 2500 11.308903 -14.130976 1.0372 1.0304709 1.0193906 - 2600 11.03881 -13.846505 1.498497 1.0304709 1.0083102 - 2700 10.70089 -13.790867 1.4450907 1.0637119 1.0083102 - 2800 10.805792 -13.563219 1.2192081 1.0415512 1.0083102 - 2900 10.421157 -13.168851 1.402862 1.0304709 1.0083102 - 3000 10.400588 -13.097548 1.0337744 1.0526316 1.0083102 - 3100 10.358923 -13.069844 0.90449608 1.0637119 1.0304709 - 3200 10.006549 -12.712754 1.2690601 1.0415512 1.0083102 - 3300 9.6601046 -12.398878 0.9892202 1.0193906 1.0083102 - 3400 9.8691691 -12.644347 1.0763164 1.0526316 1.0193906 - 3500 9.4257858 -12.095325 1.3422009 1.0747922 1.0193906 - 3600 9.8117461 -12.559789 1.0175443 1.0415512 1.0083102 - 3700 9.1821286 -11.849911 1.4515013 1.0415512 1.0083102 - 3800 9.3099882 -12.081373 0.90072272 1.0193906 1.0193906 - 3900 9.478143 -12.141401 1.0850242 1.0193906 1.0083102 - 4000 9.2104886 -11.866265 0.69822096 1.0304709 1.0083102 - 4100 8.8886161 -11.56296 0.89116764 1.0083102 1.0083102 - 4200 8.7477884 -11.435867 1.155131 1.0415512 1.0083102 - 4300 8.8404671 -11.475073 0.73376033 1.0193906 1.0083102 - 4400 9.0720052 -11.722172 1.1153459 1.0193906 1.0193906 - 4500 8.4943391 -11.10353 0.98158121 1.0304709 1.0193906 - 4600 8.6208392 -11.25783 0.52722218 1.0304709 1.0304709 - 4700 8.355727 -10.974506 0.9215792 1.0526316 1.0083102 - 4800 7.9464294 -10.531082 0.96217105 1.0193906 1.0193906 - 4900 8.1538037 -10.74077 0.93322839 1.0526316 1.0083102 - 5000 8.0560766 -10.668117 0.89914093 1.0083102 1.0083102 - 5100 7.8109289 -10.391977 0.89999269 1.0637119 1.0083102 - 5200 7.5452618 -10.199853 0.85038647 1.0415512 1.0083102 - 5300 7.5551774 -10.134568 0.48669864 1.0193906 1.0193906 - 5400 7.5427574 -10.109261 0.51382249 1.0304709 1.0083102 - 5500 7.3322385 -9.8794018 0.39341727 1.0304709 1.0193906 - 5600 7.1576966 -9.7228317 0.49695339 1.0637119 1.0193906 - 5700 6.9753083 -9.5665538 0.63845281 1.0637119 1.0193906 - 5800 7.2002518 -9.7545436 0.8869362 1.0304709 1.0083102 - 5900 6.7877615 -9.4201982 1.150461 1.0415512 1.0083102 - 6000 7.2316113 -9.7609318 0.56956179 1.0083102 1.0083102 - 6100 6.8517997 -9.3662525 0.69127091 1.0083102 1.0193906 - 6200 6.7332571 -9.2601934 0.64092541 1.0747922 1.0193906 - 6300 7.2653962 -9.812989 1.0089331 1.0415512 1.0193906 - 6400 6.9924469 -9.5198187 0.50623927 1.0193906 1.0083102 - 6500 6.7976268 -9.3171977 0.37708413 1.0304709 1.0193906 - 6600 7.1400261 -9.6453688 0.51672188 1.0415512 1.0193906 - 6700 7.0874791 -9.6159675 0.23431446 1.0193906 1.0083102 - 6800 7.0934248 -9.6288017 0.73112796 1.0083102 1.0193906 - 6900 7.0402806 -9.6881643 0.65441466 1.0193906 1.0193906 - 7000 6.6077988 -9.1981347 0.81515889 1.0193906 1.0083102 - 7100 6.6804693 -9.1892523 0.46231433 1.0193906 1.0083102 - 7200 6.7050761 -9.2536735 0.68422675 1.0083102 1.0083102 - 7300 6.6980524 -9.2116982 0.77722939 1.0083102 1.0193906 - 7400 6.9237141 -9.4504319 0.50584321 1.0083102 1.0193906 - 7500 6.7457236 -9.2517367 0.41774845 1.0193906 1.0083102 - 7600 6.140572 -8.6271314 0.47012282 1.0193906 1.0193906 - 7700 6.3154289 -8.8060017 0.30256453 1.0193906 1.0083102 - 7800 6.4817555 -9.0034539 0.48964815 1.0193906 1.0193906 - 7900 6.5509105 -9.046808 0.26620539 1.0304709 1.0083102 - 8000 6.1907919 -8.7009493 0.36431296 1.0193906 1.0083102 - 8100 6.6773106 -9.1825184 0.63034715 1.0193906 1.0083102 - 8200 6.3651832 -8.865283 0.41221098 1.0193906 1.0193906 - 8300 6.5319342 -9.0474918 0.50861431 1.0193906 1.0193906 - 8400 6.0026097 -8.4829924 0.61261898 1.0304709 1.0193906 - 8500 6.264053 -8.7484184 0.22150916 1.0193906 1.0193906 - 8600 6.4822013 -8.9786803 0.79519176 1.0415512 1.0083102 - 8700 6.1133663 -8.5901382 0.66131133 1.0193906 1.0193906 - 8800 5.7750595 -8.2366077 0.54475083 1.0415512 1.0193906 - 8900 5.7948059 -8.2720683 0.66374336 1.0083102 1.0083102 - 9000 6.0180401 -8.4602116 0.35964058 1.0193906 1.0083102 - 9100 5.6468037 -8.1226322 0.33562506 1.0083102 1.0083102 - 9200 6.0286609 -8.4948458 0.81948932 1.0083102 1.0083102 - 9300 5.3272121 -7.7564142 0.59727196 1.0193906 1.0083102 - 9400 5.3686107 -7.8108198 0.49158335 1.0193906 1.0083102 - 9500 5.5578127 -7.9767984 0.54325782 1.0083102 1.0083102 - 9600 5.3535292 -7.7952435 0.51871219 1.0083102 1.0083102 - 9700 5.2229146 -7.6572219 0.82526944 1.0193906 1.0193906 - 9800 5.5316834 -7.9694409 -0.06268606 1.0193906 1.0083102 - 9900 5.3195142 -7.7834343 0.98223661 1.0083102 1.0083102 - 10000 5.4133458 -7.8543365 0.23338829 1.0304709 1.0083102 -Loop time of 0.41562 on 4 procs for 10000 steps with 361 atoms - -Performance: 10394107.789 tau/day, 24060.435 timesteps/s -98.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.061998 | 0.074455 | 0.095533 | 4.7 | 17.91 -Neigh | 0.065831 | 0.070617 | 0.081226 | 2.4 | 16.99 -Comm | 0.11365 | 0.14064 | 0.16052 | 5.3 | 33.84 -Output | 0.0021498 | 0.0023028 | 0.0026829 | 0.5 | 0.55 -Modify | 0.040329 | 0.04214 | 0.043329 | 0.5 | 10.14 -Other | | 0.08546 | | | 20.56 - -Nlocal: 90.25 ave 91 max 90 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 22 ave 25 max 18 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Neighs: 252.75 ave 342 max 132 min -Histogram: 1 0 0 1 0 0 0 0 0 2 - -Total # of neighbors = 1011 -Ave neighs/atom = 2.80055 -Neighbor list builds = 3495 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/body/data.squares b/examples/body/data.squares old mode 100755 new mode 100644 diff --git a/examples/body/in.squares b/examples/body/in.squares old mode 100755 new mode 100644 diff --git a/examples/body/in.wall2d b/examples/body/in.wall2d old mode 100755 new mode 100644 diff --git a/examples/body/log.5Oct16.body.g++.1 b/examples/body/log.27Nov18.body.g++.1 similarity index 90% rename from examples/body/log.5Oct16.body.g++.1 rename to examples/body/log.27Nov18.body.g++.1 index e7b7b381c3..adb2c5dd6f 100644 --- a/examples/body/log.5Oct16.body.g++.1 +++ b/examples/body/log.27Nov18.body.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d polygon nparticle bodies units lj @@ -14,7 +15,7 @@ read_data data.body velocity all create 1.44 87287 loop geom -pair_style body 5.0 +pair_style body/nparticle 5.0 pair_coeff * * 1.0 1.0 neighbor 0.5 bin @@ -33,13 +34,18 @@ fix 2 all enforce2d thermo 100 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 - binsize = 2.75 -> bins = 12 12 1 -Memory usage per processor = 4.44944 Mbytes + binsize = 2.75, bins = 12 12 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/nparticle, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.772 | 4.772 | 4.772 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -0.63799525 0 0.78760475 -0.15028724 100 1.642337 -1.0003869 0 0.62552682 0.16140818 @@ -142,20 +148,20 @@ Step Temp E_pair E_mol TotEng Press 9800 1.6713187 -1.6842507 0 -0.029645137 0.17982115 9900 1.7707351 -1.6638268 0 0.089200949 0.2983883 10000 1.6466807 -1.592436 0 0.037777866 0.12761693 -Loop time of 2.33651 on 1 procs for 10000 steps with 100 atoms +Loop time of 1.76365 on 1 procs for 10000 steps with 100 atoms -Performance: 1848909.758 tau/day, 4279.884 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2449465.017 tau/day, 5670.058 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.1308 | 2.1308 | 2.1308 | 0.0 | 91.20 -Neigh | 0.011168 | 0.011168 | 0.011168 | 0.0 | 0.48 -Comm | 0.02469 | 0.02469 | 0.02469 | 0.0 | 1.06 -Output | 0.00063729 | 0.00063729 | 0.00063729 | 0.0 | 0.03 -Modify | 0.15896 | 0.15896 | 0.15896 | 0.0 | 6.80 -Other | | 0.01025 | | | 0.44 +Pair | 1.5533 | 1.5533 | 1.5533 | 0.0 | 88.08 +Neigh | 0.01155 | 0.01155 | 0.01155 | 0.0 | 0.65 +Comm | 0.042146 | 0.042146 | 0.042146 | 0.0 | 2.39 +Output | 0.00089574 | 0.00089574 | 0.00089574 | 0.0 | 0.05 +Modify | 0.14124 | 0.14124 | 0.14124 | 0.0 | 8.01 +Other | | 0.01448 | | | 0.82 Nlocal: 100 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -168,4 +174,4 @@ Total # of neighbors = 467 Ave neighs/atom = 4.67 Neighbor list builds = 468 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:01 diff --git a/examples/body/log.5Oct16.body.g++.4 b/examples/body/log.27Nov18.body.g++.4 similarity index 90% rename from examples/body/log.5Oct16.body.g++.4 rename to examples/body/log.27Nov18.body.g++.4 index 2a2e17ccba..24ed0a5436 100644 --- a/examples/body/log.5Oct16.body.g++.4 +++ b/examples/body/log.27Nov18.body.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d polygon nparticle bodies units lj @@ -14,7 +15,7 @@ read_data data.body velocity all create 1.44 87287 loop geom -pair_style body 5.0 +pair_style body/nparticle 5.0 pair_coeff * * 1.0 1.0 neighbor 0.5 bin @@ -33,13 +34,18 @@ fix 2 all enforce2d thermo 100 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.5 ghost atom cutoff = 5.5 - binsize = 2.75 -> bins = 12 12 1 -Memory usage per processor = 4.43864 Mbytes + binsize = 2.75, bins = 12 12 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/nparticle, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.759 | 4.759 | 4.759 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -0.63799525 0 0.78760475 -0.15028724 100 1.642337 -1.0003869 0 0.62552682 0.16140818 @@ -142,20 +148,20 @@ Step Temp E_pair E_mol TotEng Press 9800 1.7799071 -1.7889616 0 -0.026853542 0.3169291 9900 1.5838158 -1.718909 0 -0.15093133 0.46050618 10000 1.6100625 -1.7018091 0 -0.10784725 0.10312591 -Loop time of 0.849795 on 4 procs for 10000 steps with 100 atoms +Loop time of 0.715445 on 4 procs for 10000 steps with 100 atoms -Performance: 5083579.790 tau/day, 11767.546 timesteps/s -99.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 6038199.147 tau/day, 13977.313 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.47067 | 0.53757 | 0.61119 | 7.9 | 63.26 -Neigh | 0.0030298 | 0.0032511 | 0.0035295 | 0.3 | 0.38 -Comm | 0.1592 | 0.23416 | 0.30247 | 12.4 | 27.56 -Output | 0.0015244 | 0.0016521 | 0.0018895 | 0.4 | 0.19 -Modify | 0.039954 | 0.0415 | 0.044199 | 0.8 | 4.88 -Other | | 0.03166 | | | 3.73 +Pair | 0.35395 | 0.40307 | 0.45588 | 5.9 | 56.34 +Neigh | 0.0033705 | 0.0036112 | 0.0039394 | 0.4 | 0.50 +Comm | 0.17564 | 0.22399 | 0.26912 | 7.8 | 31.31 +Output | 0.0014601 | 0.0024824 | 0.0054784 | 3.5 | 0.35 +Modify | 0.038037 | 0.039219 | 0.04163 | 0.7 | 5.48 +Other | | 0.04308 | | | 6.02 Nlocal: 25 ave 28 max 23 min Histogram: 1 0 1 0 1 0 0 0 0 1 diff --git a/examples/body/log.9Jul18.body.cubes.g++.1 b/examples/body/log.27Nov18.cubes.g++.1 similarity index 82% rename from examples/body/log.9Jul18.body.cubes.g++.1 rename to examples/body/log.27Nov18.cubes.g++.1 index c9a799c0b5..588f95f69d 100644 --- a/examples/body/log.9Jul18.body.cubes.g++.1 +++ b/examples/body/log.27Nov18.cubes.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (29 Jun 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d rounded cubes variable r index 3 @@ -23,7 +24,7 @@ replicate 3 3 3 orthogonal box = (0 0 0) to (18 18 18) 1 by 1 by 1 MPI processor grid 54 atoms - Time spent = 0.000217915 secs + Time spent = 0.000426769 secs velocity all create 1.2 187287 dist gaussian mom yes rot yes @@ -82,7 +83,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.953 | 4.953 | 4.953 Mbytes Step KinEng PotEng TotEng c_p2 c_1_temp 0 1.7666667 0 1.7666667 0.01090535 0.59439252 1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694 @@ -95,20 +96,20 @@ Step KinEng PotEng TotEng c_p2 c_1_temp 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 -Loop time of 38.5686 on 1 procs for 10000 steps with 54 atoms +Loop time of 51.5779 on 1 procs for 10000 steps with 54 atoms -Performance: 22401.653 tau/day, 259.278 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 16751.376 tau/day, 193.882 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 38.426 | 38.426 | 38.426 | 0.0 | 99.63 -Neigh | 0.0043154 | 0.0043154 | 0.0043154 | 0.0 | 0.01 -Comm | 0.047616 | 0.047616 | 0.047616 | 0.0 | 0.12 -Output | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00 -Modify | 0.082948 | 0.082948 | 0.082948 | 0.0 | 0.22 -Other | | 0.007761 | | | 0.02 +Pair | 51.377 | 51.377 | 51.377 | 0.0 | 99.61 +Neigh | 0.0063686 | 0.0063686 | 0.0063686 | 0.0 | 0.01 +Comm | 0.072127 | 0.072127 | 0.072127 | 0.0 | 0.14 +Output | 0.0002768 | 0.0002768 | 0.0002768 | 0.0 | 0.00 +Modify | 0.10849 | 0.10849 | 0.10849 | 0.0 | 0.21 +Other | | 0.01404 | | | 0.03 Nlocal: 54 ave 54 max 54 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -122,4 +123,4 @@ Ave neighs/atom = 1.85185 Neighbor list builds = 268 Dangerous builds = 0 -Total wall time: 0:00:38 +Total wall time: 0:00:51 diff --git a/examples/body/log.9Jul18.body.cubes.g++.4 b/examples/body/log.27Nov18.cubes.g++.4 similarity index 84% rename from examples/body/log.9Jul18.body.cubes.g++.4 rename to examples/body/log.27Nov18.cubes.g++.4 index e2407e9725..f10a4c8a0a 100644 --- a/examples/body/log.9Jul18.body.cubes.g++.4 +++ b/examples/body/log.27Nov18.cubes.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (29 Jun 2018) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d rounded cubes variable r index 3 @@ -23,7 +24,7 @@ replicate 3 3 3 orthogonal box = (0 0 0) to (18 18 18) 1 by 2 by 2 MPI processor grid 54 atoms - Time spent = 0.00103807 secs + Time spent = 0.000776052 secs velocity all create 1.2 187287 dist gaussian mom yes rot yes @@ -95,20 +96,20 @@ Step KinEng PotEng TotEng c_p2 c_1_temp 8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056 9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914 10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679 -Loop time of 20.5306 on 4 procs for 10000 steps with 54 atoms +Loop time of 25.5798 on 4 procs for 10000 steps with 54 atoms -Performance: 42083.509 tau/day, 487.078 timesteps/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 33776.718 tau/day, 390.934 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.5288 | 10.878 | 19.952 | 159.0 | 52.98 -Neigh | 0.0014424 | 0.0016552 | 0.0021195 | 0.7 | 0.01 -Comm | 0.50623 | 9.5805 | 12.93 | 169.4 | 46.66 -Output | 0.00011921 | 0.00014341 | 0.00021386 | 0.0 | 0.00 -Modify | 0.044663 | 0.047684 | 0.05382 | 1.6 | 0.23 -Other | | 0.023 | | | 0.11 +Pair | 9.256 | 13.423 | 24.653 | 177.1 | 52.47 +Neigh | 0.0021949 | 0.0024942 | 0.0031152 | 0.7 | 0.01 +Comm | 0.73678 | 11.948 | 16.096 | 187.4 | 46.71 +Output | 0.00023246 | 0.00041932 | 0.0009768 | 0.0 | 0.00 +Modify | 0.12505 | 0.15661 | 0.18165 | 6.0 | 0.61 +Other | | 0.04968 | | | 0.19 Nlocal: 13.5 ave 17 max 9 min Histogram: 1 0 0 1 0 0 0 0 1 1 @@ -122,4 +123,4 @@ Ave neighs/atom = 1.85185 Neighbor list builds = 268 Dangerous builds = 0 -Total wall time: 0:00:20 +Total wall time: 0:00:25 diff --git a/examples/body/log.27Nov18.pour3d.g++.1 b/examples/body/log.27Nov18.pour3d.g++.1 new file mode 100644 index 0000000000..10a4999d14 --- /dev/null +++ b/examples/body/log.27Nov18.pour3d.g++.1 @@ -0,0 +1,74 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg +Created orthogonal box = (0 0 0) to (50 50 50) + 1 by 1 by 1 MPI processor grid + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 5 + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 +Read molecule object: + 1 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 2 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 3 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 4 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 +ERROR: Unknown fix style pour (src/modify.cpp:898) +Last command: fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 diff --git a/examples/body/log.27Nov18.pour3d.g++.4 b/examples/body/log.27Nov18.pour3d.g++.4 new file mode 100644 index 0000000000..eb65f99bc2 --- /dev/null +++ b/examples/body/log.27Nov18.pour3d.g++.4 @@ -0,0 +1,74 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# pouring 3d rounded polyhedron bodies + +variable steps index 6000 + +units lj +boundary p p fm +comm_modify vel yes + +atom_style body rounded/polyhedron 1 8 +atom_modify map array + +region reg block 0 50 0 50 0 50 units box +create_box 4 reg +Created orthogonal box = (0 0 0) to (50 50 50) + 1 by 2 by 2 MPI processor grid + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 5 +variable c_n equal 20 +variable c_t equal 5 +variable mu equal 0 +variable A_ua equal 1 + +pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} +pair_style body/rounded/polyhedron 20 5 0 1 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 5 + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +fix 1 all nve/body +fix 2 all gravity 1.0 spherical 0.0 -180.0 + +molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 +Read molecule object: + 1 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 2 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 3 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 +Read molecule object: + 1 atoms with max type 4 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 + +region slab block 5 45 5 45 25 35 units box +fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 +ERROR: Unknown fix style pour (src/modify.cpp:898) +Last command: fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 diff --git a/examples/body/log.27Nov18.squares.g++.1 b/examples/body/log.27Nov18.squares.g++.1 new file mode 100644 index 0000000000..cc334b416c --- /dev/null +++ b/examples/body/log.27Nov18.squares.g++.1 @@ -0,0 +1,222 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.000279665 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.38428256 0.0014168922 0.38569945 0.0020468171 + 2000 0.41372193 0.015263236 0.42898517 0.0029343462 + 3000 0.54844547 0.014870378 0.56331585 0.001978353 + 4000 0.73816048 0.031668204 0.76982869 0.0025939718 + 5000 0.84536165 0.011504649 0.8568663 0.0037990517 + 6000 0.73776478 0.14445932 0.8822241 0.0086538113 + 7000 0.52022565 0.069507637 0.58973329 0.0072098694 + 8000 0.72653213 0.12783368 0.85436581 0.023907183 + 9000 0.87685727 0.1239819 1.0008392 0.0064590959 + 10000 0.7250918 0.097243508 0.82233531 0.0012448267 + 11000 0.62302234 0.05597557 0.67899791 0.00080239872 + 12000 0.57159363 0.18199602 0.75358965 0.01033626 + 13000 0.7505295 0.071545266 0.82207477 0.011480236 + 14000 0.84703598 0.15914379 1.0061798 0.032814039 + 15000 0.41905013 0.090552572 0.5096027 0.015717153 + 16000 0.41805189 0.042916881 0.46096877 0.020702707 + 17000 0.59966233 0.05285043 0.65251275 0.016526024 + 18000 0.54282285 0.20835047 0.75117332 0.036414059 + 19000 0.777922 0.034754101 0.8126761 0.036467537 + 20000 0.54703924 0.14633506 0.6933743 0.012917248 + 21000 0.49337931 0.1858754 0.67925471 0.037890735 + 22000 0.64916623 0.19281344 0.84197967 0.011996773 + 23000 0.66958738 0.20459682 0.8741842 0.023639466 + 24000 0.63729755 0.1111959 0.74849345 0.025049919 + 25000 0.60094316 0.13375799 0.73470115 0.035286376 + 26000 0.35419589 0.22049451 0.5746904 0.0024215291 + 27000 0.33789786 0.18494942 0.52284728 0.0066457643 + 28000 0.32376056 0.13151726 0.45527782 0.010773856 + 29000 0.36198203 0.11044834 0.47243037 0.063012638 + 30000 0.22624436 0.19690087 0.42314523 0.037422734 + 31000 0.32284312 0.059623656 0.38246677 0.0287682 + 32000 0.4457193 0.042396136 0.48811544 0.022025252 + 33000 0.61078662 0.059447221 0.67023384 0.030335089 + 34000 0.63157762 0.062056279 0.6936339 0.044624352 + 35000 0.69577644 0.086216204 0.78199264 0.0319995 + 36000 0.76814336 0.062105963 0.83024933 0.044316891 + 37000 0.58641664 0.095034548 0.68145119 0.03234133 + 38000 0.48772813 0.12911854 0.61684667 0.038732146 + 39000 0.74957742 0.09823432 0.84781174 0.053181162 + 40000 0.57881374 0.2932491 0.87206284 0.065740126 + 41000 0.4415176 0.22899179 0.67050939 0.026159841 + 42000 0.5260339 0.2048105 0.7308444 0.046294432 + 43000 0.33493572 0.32500572 0.65994144 -0.01250241 + 44000 0.46467243 0.07907132 0.54374375 0.13386238 + 45000 0.48135518 0.2618908 0.74324598 -0.016767159 + 46000 0.27223209 0.24562643 0.51785852 0.052118439 + 47000 0.26402739 0.1838767 0.44790409 -0.0015878764 + 48000 0.10229166 0.25519169 0.35748335 -0.033927088 + 49000 0.24313495 0.16578185 0.40891679 0.12414926 + 50000 0.27400066 0.27688032 0.55088098 0.10421157 + 51000 0.43081855 0.18111733 0.61193587 0.16373371 + 52000 0.81969298 0.060995894 0.88068887 0.057285357 + 53000 0.99936159 0.029137886 1.0284995 0.19425015 + 54000 0.69750047 0.038079774 0.73558024 -0.089236384 + 55000 0.54823746 0.056369886 0.60460734 -0.021320579 + 56000 0.6752322 0.050322917 0.72555512 0.25303548 + 57000 0.90328009 0.061107142 0.96438723 -0.1962713 + 58000 0.81463148 0.050387847 0.86501933 0.35952157 + 59000 0.61636455 0.064910223 0.68127478 -0.27208497 + 60000 0.62573918 0.052264617 0.67800379 0.4493407 + 61000 0.81065726 0.071269668 0.88192693 -0.34643283 + 62000 0.86420318 0.052799365 0.91700254 0.48308047 + 63000 0.67848508 0.069087342 0.74757242 -0.31814526 + 64000 0.61430417 0.052109373 0.66641354 0.38336646 + 65000 0.75782937 0.063488206 0.82131757 -0.19113322 + 66000 0.88735857 0.051779306 0.93913787 0.29410996 + 67000 0.70684373 0.061786313 0.76863005 -0.16503578 + 68000 0.58571951 0.052402151 0.63812166 0.30173228 + 69000 0.64997491 0.064435462 0.71441037 -0.1920633 + 70000 0.75071821 0.053416991 0.8041352 0.3846747 + 71000 0.8124718 0.06877986 0.88125166 -0.26852566 + 72000 0.71352066 0.05358784 0.7671085 0.41321806 + 73000 0.55151827 0.066470642 0.61798891 -0.2211738 + 74000 0.65473635 0.061946814 0.71668316 0.29536873 + 75000 0.88704613 0.059476353 0.94652248 -0.0312656 + 76000 0.76899803 0.057351665 0.8263497 0.017885214 + 77000 0.65149455 0.05407174 0.70556629 0.25192449 + 78000 0.68614394 0.074251169 0.76039511 -0.19369404 + 79000 0.97451567 0.06262739 1.0371431 0.4217182 + 80000 0.88207775 0.070157004 0.95223476 -0.27318477 + 81000 0.69294455 0.062623957 0.75556851 0.40150141 + 82000 0.70748016 0.073924331 0.78140449 -0.17128794 + 83000 0.78180774 0.063513978 0.84532172 0.22033652 + 84000 0.80170993 0.065812223 0.86752216 0.083202913 + 85000 0.64788122 0.070348079 0.7182293 -0.066913668 + 86000 0.56575431 0.064865112 0.63061942 0.33905786 + 87000 0.78205358 0.07983702 0.8618906 -0.22844912 + 88000 0.87426443 0.065703482 0.93996791 0.448573 + 89000 0.73269893 0.079827385 0.81252632 -0.24183162 + 90000 0.66703106 0.065630146 0.73266121 0.35410109 + 91000 0.73107154 0.07402702 0.80509856 -0.085492997 + 92000 1.043635 0.067156523 1.1107915 0.14311135 + 93000 0.86063344 0.065607238 0.92624068 0.20750649 + 94000 0.68304235 0.075962239 0.75900459 -0.14594625 + 95000 0.7069191 0.067125732 0.77404483 0.39459759 + 96000 0.79860046 0.090957588 0.88955805 -0.24202125 + 97000 0.81366777 0.071387081 0.88505485 0.32217266 + 98000 0.61885746 0.041524228 0.66038169 0.31635364 + 99000 0.57007759 0.055438456 0.62551604 -0.21172902 + 100000 0.80462394 0.045542313 0.85016626 0.099207503 +Loop time of 6.34495 on 1 procs for 100000 steps with 32 atoms + +Performance: 1361713.788 tau/day, 15760.576 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0158 | 5.0158 | 5.0158 | 0.0 | 79.05 +Neigh | 0.0072868 | 0.0072868 | 0.0072868 | 0.0 | 0.11 +Comm | 0.18669 | 0.18669 | 0.18669 | 0.0 | 2.94 +Output | 0.00098681 | 0.00098681 | 0.00098681 | 0.0 | 0.02 +Modify | 1.0417 | 1.0417 | 1.0417 | 0.0 | 16.42 +Other | | 0.09245 | | | 1.46 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 35 ave 35 max 35 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 61 ave 61 max 61 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 61 +Ave neighs/atom = 1.90625 +Neighbor list builds = 1545 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/body/log.27Nov18.squares.g++.4 b/examples/body/log.27Nov18.squares.g++.4 new file mode 100644 index 0000000000..62c6206677 --- /dev/null +++ b/examples/body/log.27Nov18.squares.g++.4 @@ -0,0 +1,222 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000400782 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 1 +variable c_t equal 1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 + +fix 2 all enforce2d + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.38428256 0.0014168922 0.38569945 0.0020468171 + 2000 0.41372193 0.015263236 0.42898517 0.0029343462 + 3000 0.54844547 0.014870378 0.56331585 0.001978353 + 4000 0.73816048 0.031668204 0.76982869 0.0025939718 + 5000 0.84536165 0.011504649 0.8568663 0.0037990517 + 6000 0.73776478 0.14445932 0.8822241 0.0086538113 + 7000 0.52022565 0.069507637 0.58973329 0.0072098694 + 8000 0.72653213 0.12783367 0.85436581 0.023907185 + 9000 0.87685728 0.12398193 1.0008392 0.0064591005 + 10000 0.72509641 0.097241969 0.82233837 0.0012418726 + 11000 0.62314955 0.056042914 0.67919247 0.0018880786 + 12000 0.57157436 0.18187429 0.75344865 0.0096135623 + 13000 0.7489742 0.08262775 0.83160195 0.009183917 + 14000 0.78835138 0.18761048 0.97596186 0.023684357 + 15000 0.40408761 0.079431327 0.48351893 0.025285348 + 16000 0.4071013 0.13207058 0.53917188 0.02015488 + 17000 0.48417067 0.16699781 0.65116848 0.059188189 + 18000 0.60038567 0.18317457 0.78356024 -0.046456387 + 19000 0.73796958 0.064271521 0.8022411 0.090257204 + 20000 0.62508659 0.14486336 0.76994994 0.04948543 + 21000 0.5596837 0.10018831 0.65987201 0.044961962 + 22000 0.30731517 0.1386103 0.44592547 0.015096596 + 23000 0.34371843 0.1486761 0.49239453 0.026100892 + 24000 0.33484204 0.25428479 0.58912683 0.01974393 + 25000 0.48714744 0.32743616 0.8145836 0.037925893 + 26000 0.33255994 0.29851422 0.63107417 0.049419529 + 27000 0.21735889 0.18816203 0.40552093 0.050622152 + 28000 0.31911317 0.12559898 0.44471215 -0.0036236361 + 29000 0.53280161 0.055185441 0.58798705 0.083856225 + 30000 0.52916941 0.28697284 0.81614225 0.055873213 + 31000 0.47861645 0.21932568 0.69794214 0.02762301 + 32000 0.46786314 0.041856438 0.50971958 0.029923804 + 33000 0.69944716 0.039356744 0.7388039 0.028174645 + 34000 0.39964317 0.1027175 0.50236068 0.039495865 + 35000 0.70199237 0.10421859 0.80621095 0.015943417 + 36000 0.45053533 0.078626602 0.52916193 0.0073950287 + 37000 0.41587918 0.056551665 0.47243084 0.034091318 + 38000 0.58663473 0.039228671 0.6258634 0.033093641 + 39000 0.72480658 0.14792564 0.87273222 0.030903741 + 40000 0.51163285 0.13445292 0.64608577 -0.03114559 + 41000 0.56273761 0.16720374 0.72994135 0.027968528 + 42000 0.61850184 0.10584389 0.72434573 -0.036301799 + 43000 0.60039772 0.11984289 0.72024062 0.080894236 + 44000 0.57499839 0.068211092 0.64320948 0.049726122 + 45000 0.69937239 0.16287141 0.8622438 0.044921114 + 46000 0.23303785 0.2391726 0.47221045 0.021668935 + 47000 0.27051781 0.10690378 0.37742159 0.11963476 + 48000 0.408895 0.079919688 0.48881469 0.087484004 + 49000 0.74363181 0.040819422 0.78445123 0.011937456 + 50000 0.84482316 0.10205256 0.94687572 0.064133262 + 51000 0.84923574 0.089882984 0.93911872 0.062696388 + 52000 0.66278324 0.0331554 0.69593864 0.035150337 + 53000 0.64737251 0.039608076 0.68698058 0.057687461 + 54000 0.68931435 0.042661403 0.73197576 0.069664795 + 55000 0.84523308 0.10293275 0.94816583 0.047343755 + 56000 0.80033937 0.1534797 0.95381907 0.070206074 + 57000 0.6214799 0.1174575 0.7389374 0.078530452 + 58000 0.64228495 0.088089896 0.73037485 0.060245994 + 59000 0.89376363 0.065171887 0.95893552 0.071658895 + 60000 0.90162992 0.016564761 0.91819468 0.089245946 + 61000 0.72439995 0.0076508835 0.73205083 0.031430213 + 62000 0.71590702 0.0046728326 0.72057986 0.10153514 + 63000 0.74491219 0.0046757926 0.74958798 0.077145851 + 64000 0.77173614 0.008265632 0.78000178 -0.049932265 + 65000 0.72789092 0.0053605745 0.73325149 0.27060389 + 66000 0.63001101 0.013871945 0.64388296 -0.17766692 + 67000 0.65887071 0.0069105692 0.66578128 0.31632918 + 68000 0.89042862 0.0026334652 0.89306209 -0.050495873 + 69000 0.83442374 0.0059232957 0.84034703 -0.21871692 + 70000 0.65149642 0.004885383 0.65638181 0.50428108 + 71000 0.66888808 0.01125057 0.68013865 -0.29575772 + 72000 0.74941609 0.0026616299 0.75207772 0.34800716 + 73000 0.7898844 0.0048982026 0.7947826 -0.096872644 + 74000 0.68823538 0.0021467794 0.69038216 0.12272852 + 75000 0.5238808 0.0046112795 0.52849208 0.25760316 + 76000 0.65512889 0.014567969 0.66969686 -0.24622674 + 77000 0.82292373 0.0092471048 0.83217083 0.4002304 + 78000 0.76305221 0.01101937 0.77407158 -0.10704945 + 79000 0.66279814 0.0090486405 0.67184678 0.037466134 + 80000 0.65808885 0.010000569 0.66808942 0.31742291 + 81000 0.91357798 0.046226814 0.95980479 -0.20945693 + 82000 0.87611859 -0.016794871 0.85932372 0.31759733 + 83000 0.66285455 -0.017921021 0.64493353 0.27065273 + 84000 0.67460715 -0.0076174891 0.66698966 -0.024772659 + 85000 0.77786135 0.0014316505 0.779293 -0.21635327 + 86000 0.83246393 0.087489797 0.91995372 -0.13431455 + 87000 0.62935573 0.045088823 0.67444455 0.037766395 + 88000 0.55264538 -0.024625272 0.52802011 0.18121213 + 89000 0.74171392 -0.012629926 0.729084 -0.27666424 + 90000 0.82542165 -0.02296567 0.80245598 -0.30497174 + 91000 0.72958657 -0.026275093 0.70331147 -0.27624518 + 92000 0.6319558 0.022568297 0.65452409 -0.33539318 + 93000 0.66685301 0.021889807 0.68874282 -0.39890762 + 94000 0.91243243 0.0078218509 0.92025428 -0.27213648 + 95000 0.81125179 -0.0096756295 0.80157616 -0.099802335 + 96000 0.63354907 -0.018329423 0.61521965 0.18199604 + 97000 0.66812347 -0.016650228 0.65147324 0.49878257 + 98000 0.81490013 -0.0049164866 0.80998365 -0.13473106 + 99000 0.82131147 0.0043198846 0.82563136 -0.3083957 + 100000 0.50880983 -0.010467027 0.4983428 0.060606332 +Loop time of 4.3169 on 4 procs for 100000 steps with 32 atoms + +Performance: 2001435.573 tau/day, 23164.764 timesteps/s +95.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2078 | 1.3972 | 1.6653 | 15.1 | 32.36 +Neigh | 0.0030954 | 0.003284 | 0.0034814 | 0.3 | 0.08 +Comm | 1.074 | 1.3595 | 1.6003 | 16.2 | 31.49 +Output | 0.001703 | 0.0030067 | 0.0068843 | 4.1 | 0.07 +Modify | 1.2071 | 1.2647 | 1.3062 | 3.6 | 29.30 +Other | | 0.2893 | | | 6.70 + +Nlocal: 8 ave 9 max 6 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 17.75 ave 20 max 16 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 14 ave 18 max 7 min +Histogram: 1 0 0 0 0 0 0 1 1 1 + +Total # of neighbors = 56 +Ave neighs/atom = 1.75 +Neighbor list builds = 1566 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/body/log.27Nov18.wall2d.g++.1 b/examples/body/log.27Nov18.wall2d.g++.1 new file mode 100644 index 0000000000..1987280bee --- /dev/null +++ b/examples/body/log.27Nov18.wall2d.g++.1 @@ -0,0 +1,224 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 1 by 1 by 1 MPI processor grid + 32 atoms + Time spent = 0.000318766 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.51467204 0.00099202506 0.51566407 0.013452386 + 2000 0.55674899 0.0040762275 0.56082522 0.0034529066 + 3000 0.7546177 0.02259362 0.77721132 0.003650781 + 4000 0.72710218 0.10284108 0.82994326 0.0059629371 + 5000 0.5771012 0.069052145 0.64615335 0.00053937622 + 6000 0.53848154 0.041891239 0.58037277 0.0018693312 + 7000 0.61777556 0.033379829 0.65115538 0.0027584418 + 8000 0.47427227 0.059558934 0.5338312 0.017087187 + 9000 0.46822364 0.064382578 0.53260622 0.023258465 + 10000 0.46511051 0.027799371 0.49290988 0.015319493 + 11000 0.58686703 0.088016891 0.67488392 0.0088428936 + 12000 0.49962603 0.09879099 0.59841702 0.00074311497 + 13000 0.53160049 0.069625775 0.60122626 0.017019775 + 14000 0.49574902 0.041214164 0.53696318 0.0060355978 + 15000 0.56620415 0.13621516 0.70241931 0.045583297 + 16000 0.40942564 0.11469877 0.52412441 0.029905784 + 17000 0.608066 0.096938921 0.70500493 0.018509814 + 18000 0.45622168 0.057018077 0.51323975 0.0034035281 + 19000 0.48763322 0.057832224 0.54546545 0.0022972169 + 20000 0.41577025 0.14480819 0.56057844 0.023882542 + 21000 0.58565738 0.1601676 0.74582498 0.01702799 + 22000 0.60430354 0.16740706 0.7717106 -0.0047632836 + 23000 0.45659601 0.13740896 0.59400497 0.0191143 + 24000 0.42741367 0.25490516 0.68231884 0.051459175 + 25000 0.40851048 0.077823072 0.48633355 0.024392284 + 26000 0.53392894 0.14504323 0.67897217 0.028964572 + 27000 0.39775205 0.13101153 0.52876358 0.0080564916 + 28000 0.63138106 0.17706612 0.80844718 0.017594524 + 29000 0.57897788 0.26855503 0.84753292 0.019310624 + 30000 0.37401002 0.2274666 0.60147663 0.0044804008 + 31000 0.60924323 0.23142663 0.84066986 0.088271242 + 32000 0.60310397 0.35719837 0.96030234 0.0096762289 + 33000 0.47468105 0.17727177 0.65195282 0.0078486602 + 34000 0.42270829 0.20131235 0.62402064 0.090216203 + 35000 0.49578606 0.1697981 0.66558416 0.079099134 + 36000 0.50744538 0.29600416 0.80344954 0.018819487 + 37000 0.66728184 0.28166655 0.94894838 -0.01679437 + 38000 0.38972905 0.25798163 0.64771068 0.040442456 + 39000 0.38292839 0.21774389 0.60067228 0.016754932 + 40000 0.61770336 0.34202184 0.9597252 0.10986262 + 41000 0.42252651 0.13424708 0.5567736 0.040987711 + 42000 0.67513868 0.29515562 0.9702943 0.0013757417 + 43000 0.36768915 0.20349753 0.57118668 0.031443504 + 44000 0.49371025 0.095615653 0.5893259 0.032289477 + 45000 0.42144079 0.28894639 0.71038718 0.040302569 + 46000 0.36360136 0.33117431 0.69477567 0.010881881 + 47000 0.4206309 0.19557595 0.61620685 0.051137535 + 48000 0.4131465 0.37027912 0.78342561 0.11903042 + 49000 0.544703 0.38013565 0.92483865 0.054939742 + 50000 0.47394272 0.32384493 0.79778764 0.088363602 + 51000 0.55377533 0.38103395 0.93480927 0.097981664 + 52000 0.60648433 0.30877364 0.91525797 0.088877781 + 53000 0.62933509 0.33187159 0.96120668 0.10275954 + 54000 0.55077522 0.39050008 0.94127529 0.066721412 + 55000 0.41646397 0.34545572 0.76191969 0.011056796 + 56000 0.44244954 0.39274744 0.83519698 0.039963853 + 57000 0.41963092 0.33483982 0.75447073 0.032555938 + 58000 0.37941475 0.36905323 0.74846798 0.043952263 + 59000 0.53008564 0.32843795 0.85852359 0.080787301 + 60000 0.43408908 0.19840268 0.63249176 0.06421165 + 61000 0.56287814 0.31500577 0.87788391 0.12031895 + 62000 0.5185192 0.18275672 0.70127592 -0.0086212356 + 63000 0.57275413 0.45147395 1.0242281 0.054617465 + 64000 0.28322907 0.33687722 0.62010629 0.07268947 + 65000 0.40230876 0.37989067 0.78219943 -0.029604066 + 66000 0.58601209 0.52721274 1.1132248 -0.00037054404 + 67000 0.52669356 0.44276199 0.96945554 0.18969356 + 68000 0.41566831 0.47320489 0.8888732 0.040635264 + 69000 0.52140574 0.4261935 0.94759923 0.016566201 + 70000 0.42034133 0.55867009 0.97901142 0.047465899 + 71000 0.48720036 0.43749264 0.924693 0.15984789 + 72000 0.5244238 0.55854139 1.0829652 0.10155994 + 73000 0.69990219 0.57313852 1.2730407 0.11108648 + 74000 0.38274347 0.23359664 0.61634011 0.027968087 + 75000 0.47493369 0.49472607 0.96965976 0.10961568 + 76000 0.57064727 0.37996383 0.9506111 0.034746271 + 77000 0.50401727 0.34437588 0.84839315 0.015116686 + 78000 0.59504118 0.44154772 1.0365889 0.059341875 + 79000 0.4920801 0.58935767 1.0814378 0.12139906 + 80000 0.56992818 0.38916606 0.95909424 0.073618074 + 81000 0.38446945 0.77314417 1.1576136 0.12173381 + 82000 0.48734531 0.56198203 1.0493273 0.1080115 + 83000 0.5516933 0.56743096 1.1191243 0.13936805 + 84000 0.53336893 0.62914863 1.1625176 0.0084970895 + 85000 0.46456977 0.77446084 1.2390306 0.18024688 + 86000 0.58067599 0.53109608 1.1117721 0.012492021 + 87000 0.55096446 0.61715622 1.1681207 0.13264723 + 88000 0.56548774 0.74463701 1.3101247 0.14491188 + 89000 0.52492634 0.58482194 1.1097483 0.21155245 + 90000 0.64973565 0.85514474 1.5048804 0.036911953 + 91000 0.55367722 0.74046971 1.2941469 0.23918851 + 92000 0.44863249 0.56773761 1.0163701 0.00042860088 + 93000 0.64728356 0.66594086 1.3132244 0.0022850006 + 94000 0.65255497 0.82136644 1.4739214 0.10037643 + 95000 0.62266654 0.82642147 1.449088 0.11964602 + 96000 0.50656004 0.83312844 1.3396885 0.078491084 + 97000 0.47126712 0.70469684 1.175964 0.12956056 + 98000 0.48661103 1.0121726 1.4987837 0.043537851 + 99000 0.48379797 0.9520931 1.4358911 0.082047522 + 100000 0.54266361 1.0959698 1.6386334 -0.13092175 +Loop time of 3.8532 on 1 procs for 100000 steps with 32 atoms + +Performance: 2242290.202 tau/day, 25952.433 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3917 | 2.3917 | 2.3917 | 0.0 | 62.07 +Neigh | 0.012386 | 0.012386 | 0.012386 | 0.0 | 0.32 +Comm | 0.11307 | 0.11307 | 0.11307 | 0.0 | 2.93 +Output | 0.0010369 | 0.0010369 | 0.0010369 | 0.0 | 0.03 +Modify | 1.246 | 1.246 | 1.246 | 0.0 | 32.34 +Other | | 0.08895 | | | 2.31 + +Nlocal: 32 ave 32 max 32 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 55 ave 55 max 55 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 55 +Ave neighs/atom = 1.71875 +Neighbor list builds = 2886 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/body/log.27Nov18.wall2d.g++.4 b/examples/body/log.27Nov18.wall2d.g++.4 new file mode 100644 index 0000000000..d9a27cb1e4 --- /dev/null +++ b/examples/body/log.27Nov18.wall2d.g++.4 @@ -0,0 +1,224 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d rounded polygon bodies + +variable r index 4 +variable steps index 100000 +variable T index 0.5 +variable P index 0.1 +variable seed index 980411 + +units lj +dimension 2 + +atom_style body rounded/polygon 1 6 +atom_modify map array +read_data data.squares + orthogonal box = (0 0 -0.5) to (12 12 0.5) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 2 atoms + 2 bodies + +replicate $r $r 1 +replicate 4 $r 1 +replicate 4 4 1 + orthogonal box = (0 0 -0.5) to (48 48 0.5) + 2 by 2 by 1 MPI processor grid + 32 atoms + Time spent = 0.000329733 secs + +velocity all create $T ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 ${seed} dist gaussian mom yes rot yes +velocity all create 0.5 980411 dist gaussian mom yes rot yes + +change_box all boundary p f p + +variable cut_inner equal 0.5 +variable k_n equal 100 +variable k_na equal 2 +variable c_n equal 0.1 +variable c_t equal 0.1 +variable mu equal 0.1 +variable delta_ua equal 0.5 + +pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} +pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 +pair_coeff * * ${k_n} ${k_na} +pair_coeff * * 100 ${k_na} +pair_coeff * * 100 2 + +comm_modify vel yes + +neighbor 0.5 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.001 + +#fix 1 all nve/body +#fix 1 all nvt/body temp $T $T 1.0 +fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 +fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 + +fix 2 all enforce2d +fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 + +#compute 1 all body/local id 1 2 3 +#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] + +thermo_style custom step ke pe etotal press +thermo 1000 + +#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 +#dump_modify 2 pad 6 + +run ${steps} +run 100000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.15685 + ghost atom cutoff = 6.15685 + binsize = 3.07843, bins = 16 16 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair body/rounded/polygon, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes +Step KinEng PotEng TotEng Press + 0 0.484375 0.25 0.734375 0.0067274306 + 1000 0.51467204 0.00099202506 0.51566407 0.013452386 + 2000 0.55674899 0.0040762275 0.56082522 0.0034529066 + 3000 0.7546177 0.02259362 0.77721132 0.003650781 + 4000 0.72710218 0.10284108 0.82994326 0.0059629371 + 5000 0.57710119 0.069052154 0.64615335 0.00053937664 + 6000 0.53848104 0.041891152 0.58037219 0.0018693259 + 7000 0.61777485 0.033380825 0.65115568 0.0027584782 + 8000 0.47427732 0.059553658 0.53383098 0.017087698 + 9000 0.46820943 0.064379697 0.53258913 0.02325702 + 10000 0.46605511 0.02332689 0.489382 0.013699209 + 11000 0.57547516 0.090133398 0.66560855 0.0083913962 + 12000 0.465348 0.084853345 0.55020135 0.006231552 + 13000 0.55340889 0.07116165 0.62457054 0.030622563 + 14000 0.58866362 0.052281859 0.64094548 0.0079106838 + 15000 0.51757672 0.12255618 0.6401329 0.014005369 + 16000 0.42696011 0.086987541 0.51394765 -0.0017128649 + 17000 0.37612579 0.13054778 0.50667357 0.0046284992 + 18000 0.47659682 0.14670523 0.62330205 0.02206928 + 19000 0.47897909 0.15540332 0.63438241 0.02544138 + 20000 0.59377323 0.15357757 0.7473508 0.030262926 + 21000 0.52781204 0.22074491 0.74855695 -0.0022170167 + 22000 0.44843285 0.12779345 0.5762263 0.0097268482 + 23000 0.60400735 0.18098124 0.78498858 0.05778325 + 24000 0.58254338 0.1570243 0.73956769 0.022530491 + 25000 0.60524318 0.23660272 0.8418459 0.062530421 + 26000 0.45892702 0.34294121 0.80186823 0.038657393 + 27000 0.58418023 0.19551937 0.7796996 -0.0055396645 + 28000 0.45655369 0.26718934 0.72374303 0.006593108 + 29000 0.50277299 0.1747088 0.67748179 0.016059369 + 30000 0.38640717 0.1631573 0.54956447 0.036055723 + 31000 0.46944541 0.22076826 0.69021367 0.014334038 + 32000 0.53862858 0.26867594 0.80730452 0.057406282 + 33000 0.45666352 0.21796554 0.67462906 0.056555205 + 34000 0.51644038 0.21866786 0.73510824 0.015713 + 35000 0.50489584 0.1596236 0.66451945 0.040400644 + 36000 0.41723489 0.16227853 0.57951342 0.02863261 + 37000 0.481638 0.28830624 0.76994424 0.038381986 + 38000 0.6036094 0.33479287 0.93840227 0.0032059452 + 39000 0.47822122 0.18876355 0.66698476 0.029252649 + 40000 0.54949607 0.35011086 0.89960693 0.093909148 + 41000 0.54876522 0.27501735 0.82378257 -0.0084167014 + 42000 0.67801592 0.18102522 0.85904114 -0.0058395209 + 43000 0.54342066 0.34322081 0.88664146 0.12263806 + 44000 0.46672513 0.29749157 0.76421671 0.051073701 + 45000 0.4679867 0.25820875 0.72619545 0.069790993 + 46000 0.59598501 0.22285276 0.81883777 0.050578807 + 47000 0.48858341 0.29811577 0.78669917 0.080971431 + 48000 0.41238073 0.29362937 0.7060101 0.031893588 + 49000 0.61516435 0.33082609 0.94599044 -0.010710982 + 50000 0.57576635 0.37137185 0.94713819 0.062160249 + 51000 0.54614001 0.36960628 0.91574629 -0.0083424769 + 52000 0.42232354 0.25214442 0.67446796 0.028666126 + 53000 0.43025129 0.24479385 0.67504514 0.030342054 + 54000 0.54614922 0.29602426 0.84217348 0.083070642 + 55000 0.60719748 0.3577285 0.96492598 0.053799744 + 56000 0.47073149 0.31070429 0.78143579 0.083895368 + 57000 0.56861582 0.33249784 0.90111366 0.032324233 + 58000 0.75061035 0.33313728 1.0837476 0.031039937 + 59000 0.59473893 0.48870773 1.0834467 0.039503585 + 60000 0.55252481 0.38350562 0.93603043 0.0027643882 + 61000 0.45010855 0.43945065 0.8895592 0.028168222 + 62000 0.63942467 0.53372899 1.1731537 0.13790959 + 63000 0.69407873 0.37980402 1.0738828 0.035919608 + 64000 0.54898275 0.39910419 0.94808693 0.0015016851 + 65000 0.58229838 0.42300361 1.005302 0.089787193 + 66000 0.53443537 0.5597136 1.094149 -0.015781756 + 67000 0.59212426 0.56172146 1.1538457 0.030464683 + 68000 0.68164926 0.48724393 1.1688932 0.071465948 + 69000 0.59721737 0.49476309 1.0919805 0.07575647 + 70000 0.52314551 0.31950477 0.84265028 0.11206672 + 71000 0.53230509 0.53846575 1.0707708 0.0047204701 + 72000 0.71341933 0.4924749 1.2058942 0.116568 + 73000 0.70498496 0.54121008 1.246195 0.11210249 + 74000 0.54188682 0.61729607 1.1591829 0.044083048 + 75000 0.44073609 0.42072284 0.86145893 -0.041508511 + 76000 0.51225567 0.36848317 0.88073884 -0.028636748 + 77000 0.6517329 0.5503086 1.2020415 0.049605026 + 78000 0.60053898 0.52760266 1.1281416 0.094361256 + 79000 0.51560788 0.46563043 0.98123832 -0.03336136 + 80000 0.53357884 0.60743981 1.1410186 0.027259883 + 81000 0.6256228 0.40412923 1.029752 0.083274981 + 82000 0.6903519 0.69599412 1.386346 0.168747 + 83000 0.62621394 0.50082841 1.1270424 0.12294403 + 84000 0.5682146 0.73827702 1.3064916 0.085884707 + 85000 0.48179077 0.73669563 1.2184864 0.065002035 + 86000 0.61101399 0.80673836 1.4177523 0.037555163 + 87000 0.52278725 0.71608722 1.2388745 0.020943688 + 88000 0.53318823 0.50916748 1.0423557 -0.01946691 + 89000 0.56428713 0.56042234 1.1247095 0.040998134 + 90000 0.58720508 0.66023073 1.2474358 0.040313529 + 91000 0.61509407 0.86254343 1.4776375 0.15215034 + 92000 0.5640475 0.57694543 1.1409929 0.10238679 + 93000 0.60586378 0.67978456 1.2856483 -0.043948113 + 94000 0.75406595 0.74795347 1.5020194 0.015341415 + 95000 0.4974314 0.60192267 1.0993541 -0.018173218 + 96000 0.50048302 0.82845218 1.3289352 0.045394283 + 97000 0.65335222 0.6470855 1.3004377 0.011624967 + 98000 0.65693072 0.45222133 1.109152 0.13763684 + 99000 0.60573344 0.50284289 1.1085763 0.12853674 + 100000 0.50677068 0.58143063 1.0882013 0.11351254 +Loop time of 3.24642 on 4 procs for 100000 steps with 32 atoms + +Performance: 2661396.711 tau/day, 30803.203 timesteps/s +94.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.64148 | 0.70244 | 0.76391 | 6.5 | 21.64 +Neigh | 0.0049012 | 0.0050417 | 0.0052478 | 0.2 | 0.16 +Comm | 0.79447 | 0.88412 | 0.97443 | 8.1 | 27.23 +Output | 0.001776 | 0.0031438 | 0.0072262 | 4.2 | 0.10 +Modify | 1.325 | 1.3684 | 1.4049 | 2.4 | 42.15 +Other | | 0.2833 | | | 8.73 + +Nlocal: 8 ave 9 max 7 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 14 ave 15 max 13 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 13.25 ave 16 max 11 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 53 +Ave neighs/atom = 1.65625 +Neighbor list builds = 2654 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/body/log.9Jul18.body.pour3d.g++.1 b/examples/body/log.9Jul18.body.pour3d.g++.1 deleted file mode 100644 index 213dd2e18f..0000000000 --- a/examples/body/log.9Jul18.body.pour3d.g++.1 +++ /dev/null @@ -1,138 +0,0 @@ -LAMMPS (29 Jun 2018) -# pouring 3d rounded polyhedron bodies - -variable steps index 6000 - -units lj -boundary p p fm -comm_modify vel yes - -atom_style body rounded/polyhedron 1 8 -atom_modify map array - -region reg block 0 50 0 50 0 50 units box -create_box 4 reg -Created orthogonal box = (0 0 0) to (50 50 50) - 1 by 1 by 1 MPI processor grid - -variable cut_inner equal 0.5 -variable k_n equal 100 -variable k_na equal 5 -variable c_n equal 20 -variable c_t equal 5 -variable mu equal 0 -variable A_ua equal 1 - -pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner} -pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner} -pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner} -pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner} -pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner} -pair_style body/rounded/polyhedron 20 5 0 1 0.5 -pair_coeff * * ${k_n} ${k_na} -pair_coeff * * 100 ${k_na} -pair_coeff * * 100 5 - -neighbor 0.5 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.001 - -fix 1 all nve/body -fix 2 all gravity 1.0 spherical 0.0 -180.0 - -molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3 -Read molecule object: - 1 atoms with max type 1 - 0 bonds with max type 0 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -Read molecule object: - 1 atoms with max type 2 - 0 bonds with max type 0 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -Read molecule object: - 1 atoms with max type 3 - 0 bonds with max type 0 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -Read molecule object: - 1 atoms with max type 4 - 0 bonds with max type 0 - 0 angles with max type 0 - 0 dihedrals with max type 0 - 0 impropers with max type 0 - -region slab block 5 45 5 45 25 35 units box -fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25 -Particle insertion: 134 every 4472 steps, 500 by step 13417 - -fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL - -#compute 1 all body/local type 1 2 3 -#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4] -#dump 10 all custom 1000 tmp.dump id type x y z radius - -thermo_style custom step atoms ke pe etotal press - -thermo 1000 - -#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15 -#dump_modify 2 pad 6 - -run ${steps} -run 6000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 5 - ghost atom cutoff = 5 - binsize = 2.5, bins = 20 20 20 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair body/rounded/polyhedron, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes -Step Atoms KinEng PotEng TotEng Press - 0 0 -0 0 0 0 - 1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06 - 2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08 - 3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11 - 4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13 - 5000 268 -0 0.014969705 0.014969705 3.0797164e-05 - 6000 268 -0 0.042467887 0.042467887 0.00056148005 -Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms - -Performance: 816716.196 tau/day, 9452.734 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21 -Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66 -Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49 -Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02 -Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09 -Other | | 0.009719 | | | 1.53 - -Nlocal: 268 ave 268 max 268 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3 ave 3 max 3 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 68 ave 68 max 68 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 68 -Ave neighs/atom = 0.253731 -Neighbor list builds = 168 -Dangerous builds = 0 - - -Total wall time: 0:00:00 diff --git a/examples/body/log.9Jul18.body.squares.g++.1 b/examples/body/log.9Jul18.body.squares.g++.1 deleted file mode 100644 index 7b539797bd..0000000000 --- a/examples/body/log.9Jul18.body.squares.g++.1 +++ /dev/null @@ -1,221 +0,0 @@ -LAMMPS (29 Jun 2018) -# 2d rounded polygon bodies - -variable r index 4 -variable steps index 100000 -variable T index 0.5 -variable P index 0.1 -variable seed index 980411 - -units lj -dimension 2 - -atom_style body rounded/polygon 1 6 -atom_modify map array -read_data data.squares - orthogonal box = (0 0 -0.5) to (12 12 0.5) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2 atoms - 2 bodies - -replicate $r $r 1 -replicate 4 $r 1 -replicate 4 4 1 - orthogonal box = (0 0 -0.5) to (48 48 0.5) - 1 by 1 by 1 MPI processor grid - 32 atoms - Time spent = 0.00020504 secs - -velocity all create $T ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 980411 dist gaussian mom yes rot yes - -variable cut_inner equal 0.5 -variable k_n equal 100 -variable k_na equal 2 -variable c_n equal 1 -variable c_t equal 1 -variable mu equal 0.1 -variable delta_ua equal 0.5 - -pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} -pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 -pair_coeff * * ${k_n} ${k_na} -pair_coeff * * 100 ${k_na} -pair_coeff * * 100 2 - -comm_modify vel yes - -neighbor 0.5 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.001 - -#fix 1 all nve/body -#fix 1 all nvt/body temp $T $T 1.0 -fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 - -fix 2 all enforce2d - -#compute 1 all body/local id 1 2 3 -#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] - -thermo_style custom step ke pe etotal press -thermo 1000 - -#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 -#dump_modify 2 pad 6 - -run ${steps} -run 100000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.15685 - ghost atom cutoff = 6.15685 - binsize = 3.07843, bins = 16 16 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair body/rounded/polygon, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes -Step KinEng PotEng TotEng Press - 0 0.484375 0.25 0.734375 0.0067274306 - 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 - 2000 0.42284177 0.01346585 0.43630762 0.0029377883 - 3000 0.58154405 0.011321689 0.59286574 0.003667871 - 4000 0.73518304 0.034603175 0.76978621 0.0018689207 - 5000 0.84367476 0.025292163 0.86896692 0.0089161373 - 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 - 7000 0.56206452 0.10453031 0.66659483 0.010255161 - 8000 0.64538994 0.088817673 0.73420761 0.0037633655 - 9000 0.90540819 0.063696004 0.96910419 0.0077673359 - 10000 0.68632042 0.093265016 0.77958544 0.0057864838 - 11000 0.59118074 0.025654748 0.61683549 0.012518759 - 12000 0.67522767 0.038176401 0.71340407 0.01741153 - 13000 0.7644843 0.10429844 0.86878274 0.013161339 - 14000 0.56152694 0.067836655 0.62936359 0.016852121 - 15000 0.41895506 0.019513348 0.43846841 0.015225695 - 16000 0.55799421 0.1564559 0.71445011 0.011703561 - 17000 0.59391964 0.034450221 0.62836986 0.026215002 - 18000 0.75911858 0.030885726 0.7900043 0.018396366 - 19000 0.64417995 0.12110912 0.76528907 0.010247952 - 20000 0.57751435 0.16965651 0.74717086 0.023392323 - 21000 0.7613368 0.13405354 0.89539034 0.021498982 - 22000 0.57676692 0.18011879 0.75688571 0.024469161 - 23000 0.54043723 0.11842026 0.65885749 0.019799067 - 24000 0.62276061 0.038967924 0.66172853 0.019080086 - 25000 0.53157536 0.11651937 0.64809473 0.017019298 - 26000 0.72213293 0.039012448 0.76114538 0.015434904 - 27000 0.62157832 0.13697494 0.75855326 0.028711011 - 28000 0.41323738 0.16301101 0.57624839 0.041792632 - 29000 0.45774328 0.17569066 0.63343394 0.019975231 - 30000 0.78901796 0.099791386 0.88880934 0.024116947 - 31000 0.85205397 0.11977547 0.97182945 0.026667489 - 32000 0.37137095 0.1232622 0.49463315 0.00087637364 - 33000 0.26860871 0.26056381 0.52917252 0.036110517 - 34000 0.3018636 0.21336905 0.51523265 0.040315549 - 35000 0.39915129 0.28245957 0.68161085 0.034876856 - 36000 0.25761236 0.2352705 0.49288286 0.022772767 - 37000 0.1071233 0.31692858 0.42405188 0.017994666 - 38000 0.083729577 0.28473145 0.36846103 -0.0045370431 - 39000 0.070355565 0.26682083 0.33717639 0.017921556 - 40000 0.075894079 0.20077896 0.27667304 0.014873186 - 41000 0.05891028 0.15989064 0.21880092 0.025547873 - 42000 0.1225107 0.16583605 0.28834675 0.038842785 - 43000 0.17049189 0.14323991 0.3137318 0.029550161 - 44000 0.26823939 0.15208257 0.42032196 0.028113612 - 45000 0.10172203 0.1729706 0.27469264 -0.013769913 - 46000 0.14841355 0.19085074 0.33926429 -0.00073741985 - 47000 0.27654927 0.19097937 0.46752864 0.04021431 - 48000 0.53432331 0.080769923 0.61509323 0.029932845 - 49000 0.69111634 0.13064951 0.82176585 0.028985406 - 50000 0.24520806 0.18317453 0.42838258 0.05179746 - 51000 0.23541368 0.14281364 0.37822732 0.071884238 - 52000 0.25464996 0.095730242 0.3503802 0.034488204 - 53000 0.53677633 0.1058745 0.64265084 0.059932498 - 54000 0.32970921 0.27979128 0.60950049 0.062869716 - 55000 0.49094054 0.096735015 0.58767556 0.04728005 - 56000 0.54398249 0.2216472 0.76562969 0.056712022 - 57000 0.60869068 0.2338422 0.84253288 0.077143302 - 58000 0.72175509 0.18687368 0.90862877 0.019357656 - 59000 0.79442757 0.092502981 0.88693055 0.066882632 - 60000 0.6810555 0.077699385 0.75875488 0.095975173 - 61000 0.63178834 0.05071143 0.68249977 0.043586668 - 62000 0.76589344 0.044615704 0.81050914 0.085718411 - 63000 0.84815889 0.030527848 0.87868674 0.053072795 - 64000 0.7309043 0.051938637 0.78284294 0.058887766 - 65000 0.62498816 0.034474465 0.65946262 0.068446407 - 66000 0.69817494 0.068546004 0.76672094 0.062634433 - 67000 0.86444275 0.010184259 0.87462701 0.073635055 - 68000 0.77820319 0.0079319524 0.78613515 0.090330925 - 69000 0.56938919 0.0092629332 0.57865213 0.061838729 - 70000 0.61870712 0.010047381 0.6287545 0.066501338 - 71000 0.71651803 0.0088366199 0.72535465 0.079136316 - 72000 0.76278925 0.008828151 0.77161741 0.063672771 - 73000 0.75447428 0.0083985526 0.76287283 0.078256913 - 74000 0.66185251 0.0091910052 0.67104351 0.069840511 - 75000 0.58458829 0.0097671568 0.59435544 0.076123422 - 76000 0.7487564 0.0100022 0.7587586 0.076171741 - 77000 0.89505465 0.009250681 0.90430533 0.074921699 - 78000 0.73738164 0.0092029279 0.74658457 0.078835344 - 79000 0.65735281 0.010099528 0.66745233 0.077940627 - 80000 0.70247542 0.010306464 0.71278189 0.079560093 - 81000 0.74839505 0.010199092 0.75859415 0.080835104 - 82000 0.75193767 0.010274058 0.76221173 0.081086684 - 83000 0.71392598 0.010495573 0.72442156 0.082746145 - 84000 0.58498928 0.011027388 0.59601667 0.08356465 - 85000 0.59022869 0.011729474 0.60195817 0.084519397 - 86000 0.81753578 0.011208964 0.82874475 0.085490261 - 87000 0.83480682 0.010542579 0.8453494 0.086268527 - 88000 0.67322538 0.011170734 0.68439611 0.08751623 - 89000 0.62637389 0.012033316 0.6384072 0.088548094 - 90000 0.92828557 0.011750388 0.94003596 0.089199823 - 91000 0.96072564 0.010324509 0.97105015 0.090204803 - 92000 0.72105071 0.011484152 0.73253486 0.09140819 - 93000 0.65762527 0.012558219 0.67018349 0.092453474 - 94000 0.73991591 0.01261909 0.752535 0.093373477 - 95000 0.91791653 0.011980455 0.92989699 0.094182136 - 96000 0.76562561 0.011807085 0.7774327 0.095323684 - 97000 0.57292104 0.013610205 0.58653124 0.096505977 - 98000 0.68141076 0.013863204 0.69527396 0.097380069 - 99000 0.82390969 0.013002341 0.83691203 0.098235926 - 100000 0.77639728 0.012989342 0.78938662 0.099274147 -Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms - -Performance: 2221655.884 tau/day, 25713.610 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58 -Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13 -Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35 -Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03 -Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98 -Other | | 0.03616 | | | 0.93 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21 ave 21 max 21 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 57 ave 57 max 57 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 57 -Ave neighs/atom = 1.78125 -Neighbor list builds = 1445 -Dangerous builds = 0 -Total wall time: 0:00:03 diff --git a/examples/body/log.9Jul18.body.squares.g++.4 b/examples/body/log.9Jul18.body.squares.g++.4 deleted file mode 100644 index 56d7734b7b..0000000000 --- a/examples/body/log.9Jul18.body.squares.g++.4 +++ /dev/null @@ -1,221 +0,0 @@ -LAMMPS (29 Jun 2018) -# 2d rounded polygon bodies - -variable r index 4 -variable steps index 100000 -variable T index 0.5 -variable P index 0.1 -variable seed index 980411 - -units lj -dimension 2 - -atom_style body rounded/polygon 1 6 -atom_modify map array -read_data data.squares - orthogonal box = (0 0 -0.5) to (12 12 0.5) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 2 atoms - 2 bodies - -replicate $r $r 1 -replicate 4 $r 1 -replicate 4 4 1 - orthogonal box = (0 0 -0.5) to (48 48 0.5) - 2 by 2 by 1 MPI processor grid - 32 atoms - Time spent = 0.000324011 secs - -velocity all create $T ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 980411 dist gaussian mom yes rot yes - -variable cut_inner equal 0.5 -variable k_n equal 100 -variable k_na equal 2 -variable c_n equal 1 -variable c_t equal 1 -variable mu equal 0.1 -variable delta_ua equal 0.5 - -pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner} -pair_style body/rounded/polygon 1 1 0.1 0.5 0.5 -pair_coeff * * ${k_n} ${k_na} -pair_coeff * * 100 ${k_na} -pair_coeff * * 100 2 - -comm_modify vel yes - -neighbor 0.5 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.001 - -#fix 1 all nve/body -#fix 1 all nvt/body temp $T $T 1.0 -fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0 - -fix 2 all enforce2d - -#compute 1 all body/local id 1 2 3 -#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] - -thermo_style custom step ke pe etotal press -thermo 1000 - -#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 -#dump_modify 2 pad 6 - -run ${steps} -run 100000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.15685 - ghost atom cutoff = 6.15685 - binsize = 3.07843, bins = 16 16 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair body/rounded/polygon, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes -Step KinEng PotEng TotEng Press - 0 0.484375 0.25 0.734375 0.0067274306 - 1000 0.39423376 0.0017918048 0.39602557 0.0021941612 - 2000 0.42284177 0.01346585 0.43630762 0.0029377883 - 3000 0.58154405 0.011321689 0.59286574 0.003667871 - 4000 0.73518304 0.034603175 0.76978621 0.0018689207 - 5000 0.84367476 0.025292163 0.86896692 0.0089161373 - 6000 0.70803236 0.0085631016 0.71659546 0.0045552895 - 7000 0.56206452 0.10453031 0.66659483 0.010255161 - 8000 0.64538994 0.088817673 0.73420761 0.0037633655 - 9000 0.90540819 0.063696004 0.96910419 0.0077673359 - 10000 0.68632042 0.093265016 0.77958544 0.0057864837 - 11000 0.59118074 0.025654748 0.61683549 0.012518759 - 12000 0.67522767 0.038176401 0.71340407 0.01741153 - 13000 0.7644843 0.10429844 0.86878274 0.013161339 - 14000 0.56152694 0.067836656 0.6293636 0.016852113 - 15000 0.41895505 0.019513353 0.43846841 0.015225696 - 16000 0.55799443 0.15645637 0.7144508 0.011703646 - 17000 0.59385248 0.03451986 0.62837234 0.025482966 - 18000 0.75902169 0.031103586 0.79012527 0.018263354 - 19000 0.64266826 0.12535314 0.76802141 0.014884119 - 20000 0.57836261 0.16581188 0.74417449 0.024667165 - 21000 0.78281936 0.11877527 0.90159464 -0.0090089213 - 22000 0.5312006 0.13300874 0.66420934 0.025797278 - 23000 0.56458861 0.084369128 0.64895774 0.024630917 - 24000 0.65126875 0.06122992 0.71249867 0.034377198 - 25000 0.55173441 0.15694886 0.70868327 0.021634086 - 26000 0.59121615 0.17071182 0.76192797 0.024758366 - 27000 0.6394843 0.17442949 0.81391378 0.034919937 - 28000 0.31144221 0.41243036 0.72387256 0.074115225 - 29000 0.13516917 0.3075419 0.44271107 0.023861298 - 30000 0.14094934 0.24407203 0.38502137 0.037030438 - 31000 0.26313749 0.087395422 0.35053291 0.042347005 - 32000 0.51602457 0.063012079 0.57903664 0.018550299 - 33000 0.55628829 0.200213 0.75650129 0.026507686 - 34000 0.97399408 0.082504517 1.0564986 0.037889878 - 35000 0.64710533 0.17662002 0.82372535 0.058295508 - 36000 0.45769083 0.08241194 0.54010277 0.014957415 - 37000 0.72850105 0.053874061 0.78237512 0.037194593 - 38000 0.44177995 0.28939498 0.73117493 0.045194029 - 39000 0.46828451 0.077630686 0.54591519 0.089849009 - 40000 0.46786451 0.092828423 0.56069294 0.028042052 - 41000 0.71861856 0.097085715 0.81570427 0.036473296 - 42000 0.74121021 0.10553127 0.84674148 0.054058843 - 43000 0.62945489 0.12770673 0.75716161 0.047267994 - 44000 0.49900638 0.085150056 0.58415644 0.054798793 - 45000 0.70199572 0.063415877 0.7654116 0.038363546 - 46000 0.49513142 0.10649384 0.60162526 0.059392561 - 47000 0.3858898 0.079458749 0.46534855 0.051825764 - 48000 0.62585854 0.028585902 0.65444444 0.054074424 - 49000 0.65934482 0.51865062 1.1779954 -0.035272836 - 50000 0.5420438 0.082056756 0.62410056 0.031187494 - 51000 0.36685223 0.14224019 0.50909241 0.073790397 - 52000 0.19044627 0.15368389 0.34413016 0.059034266 - 53000 0.26847678 0.075693324 0.3441701 0.032276915 - 54000 0.3593711 0.19034549 0.54971659 0.070827883 - 55000 0.21659198 0.1929074 0.40949939 0.035916364 - 56000 0.28242715 0.12313241 0.40555956 0.062083926 - 57000 0.34067475 0.14711992 0.48779467 0.059321458 - 58000 0.4842796 0.16143425 0.64571385 0.059048247 - 59000 0.84438871 0.076546849 0.92093556 0.048046901 - 60000 0.92794849 0.054331626 0.98228012 0.058392272 - 61000 0.6916736 0.076168342 0.76784194 0.058654987 - 62000 0.63317965 0.094506389 0.72768604 0.061044719 - 63000 0.63317266 0.038785593 0.67195825 0.097236147 - 64000 0.81696668 0.121811 0.93877769 0.064935373 - 65000 0.82644758 0.25188344 1.078331 0.093352359 - 66000 0.64975019 0.17930857 0.82905876 0.058805254 - 67000 0.63487678 0.16877059 0.80364737 0.070254696 - 68000 0.79140717 0.11631004 0.9077172 0.064646394 - 69000 0.85687272 0.057835331 0.91470805 0.071057291 - 70000 0.67785976 0.040686768 0.71854653 0.074687222 - 71000 0.60594577 0.032193155 0.63813893 0.069349268 - 72000 0.77586745 0.024068533 0.79993598 0.083394193 - 73000 0.88877625 0.025746326 0.91452258 0.081511105 - 74000 0.73507888 0.036574786 0.77165367 0.075360233 - 75000 0.68787782 0.042098622 0.72997644 0.068651098 - 76000 0.72515745 0.04360868 0.76876613 0.069594624 - 77000 0.77580944 0.041826702 0.81763614 0.071937144 - 78000 0.76640394 0.039285046 0.80568899 0.074274921 - 79000 0.62504309 0.039593585 0.66463667 0.076443295 - 80000 0.60001642 0.043468215 0.64348464 0.094547719 - 81000 0.82175037 0.045608873 0.86735924 0.080186295 - 82000 0.85783276 0.042692576 0.90052534 0.081576548 - 83000 0.71367707 0.042172193 0.75584926 0.08256625 - 84000 0.68532406 0.044724759 0.73004882 0.083672013 - 85000 0.72576789 0.046982462 0.77275035 0.084789331 - 86000 0.75597701 0.04765086 0.80362787 0.085758056 - 87000 0.74190598 0.047629096 0.78953507 0.086679976 - 88000 0.60967704 0.049906172 0.65958321 0.085526191 - 89000 0.54490288 0.054768238 0.59967112 0.090604027 - 90000 0.75398341 0.057153453 0.81113686 0.091900858 - 91000 0.84577472 0.052753512 0.89852823 0.091913909 - 92000 0.7176235 0.050677427 0.76830093 0.092032507 - 93000 0.61699446 0.054097013 0.67109147 0.092071275 - 94000 0.76330752 0.057398618 0.82070614 0.092435043 - 95000 0.98754458 0.053801311 1.0413459 0.093526707 - 96000 0.7405897 0.052135628 0.79272533 0.095011929 - 97000 0.65587599 0.057011962 0.71288795 0.096692123 - 98000 0.72345634 0.060700171 0.78415651 0.097510345 - 99000 0.88283624 0.061795247 0.94463149 0.09799633 - 100000 0.86303812 0.058912988 0.92195111 0.09892993 -Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms - -Performance: 3084895.573 tau/day, 35704.810 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94 -Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06 -Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42 -Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03 -Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06 -Other | | 0.1536 | | | 5.48 - -Nlocal: 8 ave 10 max 4 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 17.25 ave 19 max 15 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 13.5 ave 21 max 5 min -Histogram: 1 0 0 0 1 0 1 0 0 1 - -Total # of neighbors = 54 -Ave neighs/atom = 1.6875 -Neighbor list builds = 1443 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.1 b/examples/body/log.9Jul18.body.wall2d.g++.1 deleted file mode 100644 index f22c366380..0000000000 --- a/examples/body/log.9Jul18.body.wall2d.g++.1 +++ /dev/null @@ -1,223 +0,0 @@ -LAMMPS (29 Jun 2018) -# 2d rounded polygon bodies - -variable r index 4 -variable steps index 100000 -variable T index 0.5 -variable P index 0.1 -variable seed index 980411 - -units lj -dimension 2 - -atom_style body rounded/polygon 1 6 -atom_modify map array -read_data data.squares - orthogonal box = (0 0 -0.5) to (12 12 0.5) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2 atoms - 2 bodies - -replicate $r $r 1 -replicate 4 $r 1 -replicate 4 4 1 - orthogonal box = (0 0 -0.5) to (48 48 0.5) - 1 by 1 by 1 MPI processor grid - 32 atoms - Time spent = 0.00029707 secs - -velocity all create $T ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 980411 dist gaussian mom yes rot yes - -change_box all boundary p f p - -variable cut_inner equal 0.5 -variable k_n equal 100 -variable k_na equal 2 -variable c_n equal 0.1 -variable c_t equal 0.1 -variable mu equal 0.1 -variable delta_ua equal 0.5 - -pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 -pair_coeff * * ${k_n} ${k_na} -pair_coeff * * 100 ${k_na} -pair_coeff * * 100 2 - -comm_modify vel yes - -neighbor 0.5 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.001 - -#fix 1 all nve/body -#fix 1 all nvt/body temp $T $T 1.0 -fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 - -fix 2 all enforce2d -fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 - -#compute 1 all body/local id 1 2 3 -#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] - -thermo_style custom step ke pe etotal press -thermo 1000 - -#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 -#dump_modify 2 pad 6 - -run ${steps} -run 100000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.15685 - ghost atom cutoff = 6.15685 - binsize = 3.07843, bins = 16 16 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair body/rounded/polygon, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes -Step KinEng PotEng TotEng Press - 0 0.484375 0.25 0.734375 0.0067274306 - 1000 0.49241101 0.0031318767 0.49554289 0.017768281 - 2000 0.56118632 0.0026068888 0.56379321 0.003410416 - 3000 0.75565115 0.025578366 0.78122951 0.0071862988 - 4000 0.72298647 0.093150646 0.81613712 0.003190158 - 5000 0.51684166 0.049164868 0.56600653 0.0096960168 - 6000 0.56627905 0.048132853 0.6144119 0.020733586 - 7000 0.58122129 0.018223718 0.59944501 0.0038160759 - 8000 0.64297977 0.025934821 0.66891459 0.0041091784 - 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 - 10000 0.35738377 0.078487805 0.43587158 3.9079782e-05 - 11000 0.41529308 0.13619284 0.55148592 -0.0067482285 - 12000 0.43274718 0.071315497 0.50406268 0.007006378 - 13000 0.4748331 0.069904647 0.54473775 0.0010384372 - 14000 0.6287791 0.12721033 0.75598943 0.0047792448 - 15000 0.4692413 0.12344005 0.59268136 0.018033616 - 16000 0.43157074 0.14306789 0.57463862 0.042356676 - 17000 0.53085999 0.22126296 0.75212294 0.027509646 - 18000 0.52688968 0.13225282 0.6591425 0.0021558013 - 19000 0.55032328 0.12513047 0.67545375 0.025036251 - 20000 0.48465097 0.1431055 0.62775647 0.017193781 - 21000 0.53166734 0.21928574 0.75095307 0.011564317 - 22000 0.62177353 0.09296159 0.71473512 0.017660922 - 23000 0.6972939 0.12434123 0.82163514 0.024432327 - 24000 0.42767372 0.22152311 0.64919684 -0.013712449 - 25000 0.4816037 0.19272865 0.67433236 0.052386055 - 26000 0.72642579 0.19697046 0.92339625 0.020407694 - 27000 0.39649144 0.15058326 0.5470747 0.023705766 - 28000 0.44896324 0.18500106 0.6339643 -0.0089410286 - 29000 0.5565759 0.11085772 0.66743362 0.048437166 - 30000 0.58173584 0.21773281 0.79946865 0.0057357773 - 31000 0.49199415 0.23601982 0.72801397 0.046744152 - 32000 0.55665496 0.20542161 0.76207658 -0.0038756805 - 33000 0.62730739 0.24460524 0.87191263 0.045330682 - 34000 0.58107044 0.16395278 0.74502322 -0.0049496051 - 35000 0.56838849 0.21842922 0.78681771 0.0062086036 - 36000 0.45910273 0.28464172 0.74374445 -0.011700747 - 37000 0.37092037 0.27646862 0.647389 0.022305679 - 38000 0.7278047 0.30674438 1.0345491 0.07698342 - 39000 0.5132923 0.27395066 0.78724295 0.026898634 - 40000 0.62348649 0.24424644 0.86773293 0.039403899 - 41000 0.3658401 0.15512326 0.52096337 0.022559003 - 42000 0.4912253 0.35712978 0.84835508 -0.010336341 - 43000 0.70225957 0.36314638 1.0654059 0.004148866 - 44000 0.56958157 0.25488927 0.82447084 0.067537066 - 45000 0.45854352 0.30149439 0.76003791 -0.017002401 - 46000 0.62787247 0.34567995 0.97355242 0.11894801 - 47000 0.61348914 0.29378625 0.90727539 0.067873976 - 48000 0.71301829 0.34135284 1.0543711 0.021077736 - 49000 0.53520804 0.30593196 0.84113999 0.0059257647 - 50000 0.44966403 0.35370793 0.80337195 0.0020395669 - 51000 0.5236113 0.32296924 0.84658054 -0.051011506 - 52000 0.53905573 0.351771 0.89082672 0.013720106 - 53000 0.55978158 0.41293947 0.97272106 0.068558589 - 54000 0.52170459 0.2718066 0.7935112 0.0093138985 - 55000 0.61078876 0.43353897 1.0443277 0.045377392 - 56000 0.51300655 0.33182278 0.84482933 -0.018418487 - 57000 0.54882822 0.38380093 0.93262915 0.10249946 - 58000 0.72106212 0.45361279 1.1746749 0.030313481 - 59000 0.55871447 0.63823029 1.1969448 0.019079703 - 60000 0.49395192 0.58283102 1.0767829 0.0179349 - 61000 0.45991079 0.62540573 1.0853165 0.074398804 - 62000 0.4655788 0.60862262 1.0742014 0.11472976 - 63000 0.55634524 0.63069255 1.1870378 -0.0025676135 - 64000 0.57688903 0.45435264 1.0312417 0.0083813852 - 65000 0.57168922 0.42217005 0.99385927 0.044931269 - 66000 0.6206044 0.46727538 1.0878798 0.019686229 - 67000 0.61037155 0.41840109 1.0287726 0.0195109 - 68000 0.63848598 0.41305347 1.0515395 0.072940144 - 69000 0.49244916 0.3834095 0.87585866 0.07963677 - 70000 0.41847062 0.51907975 0.93755037 0.18447904 - 71000 0.45198986 0.52973709 0.98172695 0.078419371 - 72000 0.47064262 0.37808165 0.84872427 -0.00046308054 - 73000 0.6690143 0.37549359 1.0445079 0.061208432 - 74000 0.60444955 0.33779636 0.94224592 -0.068840321 - 75000 0.61762382 0.3916421 1.0092659 0.16253292 - 76000 0.63657961 0.50277989 1.1393595 0.013857508 - 77000 0.52524028 0.43597896 0.96121924 -0.03296482 - 78000 0.43803533 0.33172284 0.76975817 0.078763029 - 79000 0.67156089 0.55272177 1.2242827 0.080822223 - 80000 0.68678238 0.46061627 1.1473987 0.0027036992 - 81000 0.64956678 0.44959229 1.0991591 0.11201483 - 82000 0.51060477 0.43508342 0.9456882 0.028000608 - 83000 0.59550548 0.69026083 1.2857663 -0.0015809004 - 84000 0.64222145 0.38768816 1.0299096 0.014153173 - 85000 0.7661229 0.43445261 1.2005755 0.048034534 - 86000 0.60025257 0.53027929 1.1305319 0.0056865157 - 87000 0.46220939 0.47470035 0.93690974 0.075311946 - 88000 0.54123847 0.62899839 1.1702369 0.13260162 - 89000 0.61212272 0.6114241 1.2235468 0.033284822 - 90000 0.63924773 0.6916249 1.3308726 0.045088296 - 91000 0.49316865 0.51037033 1.003539 0.023203598 - 92000 0.57572123 0.43496319 1.0106844 0.297092 - 93000 0.65187559 0.56815972 1.2200353 0.1538215 - 94000 0.64107331 0.58948521 1.2305585 0.031117778 - 95000 0.64584158 0.6364688 1.2823104 0.096154676 - 96000 0.60509093 0.601487 1.2065779 0.03457172 - 97000 0.68837218 0.77974186 1.468114 0.17801164 - 98000 0.62725266 0.64137144 1.2686241 0.17449001 - 99000 0.46861221 0.67000291 1.1386151 0.2429588 - 100000 0.5879119 0.7140612 1.3019731 0.064634257 -Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms - -Performance: 3447804.126 tau/day, 39905.140 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41 -Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35 -Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35 -Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05 -Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34 -Other | | 0.03781 | | | 1.51 - -Nlocal: 32 ave 32 max 32 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 20 ave 20 max 20 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 57 ave 57 max 57 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 57 -Ave neighs/atom = 1.78125 -Neighbor list builds = 2705 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/body/log.9Jul18.body.wall2d.g++.4 b/examples/body/log.9Jul18.body.wall2d.g++.4 deleted file mode 100644 index 7239fd4dcd..0000000000 --- a/examples/body/log.9Jul18.body.wall2d.g++.4 +++ /dev/null @@ -1,223 +0,0 @@ -LAMMPS (29 Jun 2018) -# 2d rounded polygon bodies - -variable r index 4 -variable steps index 100000 -variable T index 0.5 -variable P index 0.1 -variable seed index 980411 - -units lj -dimension 2 - -atom_style body rounded/polygon 1 6 -atom_modify map array -read_data data.squares - orthogonal box = (0 0 -0.5) to (12 12 0.5) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 2 atoms - 2 bodies - -replicate $r $r 1 -replicate 4 $r 1 -replicate 4 4 1 - orthogonal box = (0 0 -0.5) to (48 48 0.5) - 2 by 2 by 1 MPI processor grid - 32 atoms - Time spent = 0.000386 secs - -velocity all create $T ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 ${seed} dist gaussian mom yes rot yes -velocity all create 0.5 980411 dist gaussian mom yes rot yes - -change_box all boundary p f p - -variable cut_inner equal 0.5 -variable k_n equal 100 -variable k_na equal 2 -variable c_n equal 0.1 -variable c_t equal 0.1 -variable mu equal 0.1 -variable delta_ua equal 0.5 - -pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner} -pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5 -pair_coeff * * ${k_n} ${k_na} -pair_coeff * * 100 ${k_na} -pair_coeff * * 100 2 - -comm_modify vel yes - -neighbor 0.5 bin -neigh_modify every 1 delay 0 check yes - -timestep 0.001 - -#fix 1 all nve/body -#fix 1 all nvt/body temp $T $T 1.0 -fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0 -fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0 - -fix 2 all enforce2d -fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0 - -#compute 1 all body/local id 1 2 3 -#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4] - -thermo_style custom step ke pe etotal press -thermo 1000 - -#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0 -#dump_modify 2 pad 6 - -run ${steps} -run 100000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6.15685 - ghost atom cutoff = 6.15685 - binsize = 3.07843, bins = 16 16 1 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair body/rounded/polygon, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/2d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes -Step KinEng PotEng TotEng Press - 0 0.484375 0.25 0.734375 0.0067274306 - 1000 0.49241101 0.0031318767 0.49554289 0.017768281 - 2000 0.56118632 0.0026068888 0.56379321 0.003410416 - 3000 0.75565115 0.025578366 0.78122951 0.0071862988 - 4000 0.72298647 0.093150646 0.81613712 0.003190158 - 5000 0.51684166 0.049164868 0.56600653 0.0096960168 - 6000 0.56627905 0.048132853 0.6144119 0.020733586 - 7000 0.58122129 0.018223718 0.59944501 0.0038160759 - 8000 0.64297977 0.025934821 0.66891459 0.0041091784 - 9000 0.41748404 0.0077890042 0.42527305 0.0039270065 - 10000 0.35738377 0.078487805 0.43587158 3.9079865e-05 - 11000 0.41529307 0.13619284 0.55148591 -0.0067482285 - 12000 0.43274718 0.071315527 0.50406271 0.007006369 - 13000 0.4748324 0.069905666 0.54473807 0.0010385254 - 14000 0.62603727 0.098905625 0.7249429 0.0048876764 - 15000 0.44512086 0.10415235 0.54927321 0.01902062 - 16000 0.47460177 0.18053316 0.65513493 0.045013976 - 17000 0.52742676 0.10110706 0.62853382 0.013615471 - 18000 0.46111734 0.096118795 0.55723613 0.0073676834 - 19000 0.59668439 0.13652292 0.73320731 0.029403553 - 20000 0.46840192 0.11611719 0.58451911 -0.00034412499 - 21000 0.53550533 0.096457461 0.6319628 0.0019785732 - 22000 0.46599715 0.13206373 0.59806087 0.031970672 - 23000 0.49280776 0.20404726 0.69685501 0.03657433 - 24000 0.60901688 0.18255214 0.79156902 0.044955017 - 25000 0.47345185 0.13671357 0.61016542 0.020313539 - 26000 0.47653832 0.12448225 0.60102057 0.01878099 - 27000 0.50008212 0.24740634 0.74748845 0.021862639 - 28000 0.41627204 0.2519463 0.66821834 0.054683701 - 29000 0.55608273 0.23100212 0.78708485 -0.0043318497 - 30000 0.53884537 0.3001584 0.83900377 -0.012838186 - 31000 0.53036238 0.2300328 0.76039518 -0.0061688449 - 32000 0.42666792 0.20536256 0.63203048 0.045305282 - 33000 0.62908185 0.1652033 0.79428515 0.0072777588 - 34000 0.47028154 0.388736 0.85901754 0.04332288 - 35000 0.54602322 0.2775624 0.82358562 0.02898206 - 36000 0.59860544 0.21824655 0.81685199 0.0025936194 - 37000 0.62467827 0.11983499 0.74451326 0.050052743 - 38000 0.72594229 0.36584781 1.0917901 0.04280621 - 39000 0.51129656 0.23859043 0.74988699 0.050817447 - 40000 0.53263836 0.24212889 0.77476725 0.036245922 - 41000 0.50288088 0.36668283 0.86956371 0.018381415 - 42000 0.46653688 0.21974887 0.68628574 0.012661062 - 43000 0.61738785 0.32131037 0.93869821 0.012709433 - 44000 0.56603903 0.26515554 0.83119457 0.03315102 - 45000 0.56231638 0.32111693 0.88343331 0.06079756 - 46000 0.7096208 0.2570131 0.96663391 0.048770468 - 47000 0.588755 0.1880748 0.7768298 0.035962604 - 48000 0.56296339 0.25783519 0.82079858 0.053019928 - 49000 0.419885 0.42328618 0.84317118 0.038105269 - 50000 0.63073351 0.41426285 1.0449964 0.0015271048 - 51000 0.59357935 0.184222 0.77780136 0.015996218 - 52000 0.60608471 0.36247533 0.96856003 0.10984665 - 53000 0.5227842 0.27686739 0.79965159 0.02761699 - 54000 0.39435923 0.34197355 0.73633278 0.061183263 - 55000 0.46748455 0.34230903 0.80979358 0.077441382 - 56000 0.59819827 0.29212061 0.89031889 0.043772353 - 57000 0.61682559 0.32788566 0.94471124 0.03992069 - 58000 0.52702478 0.24891506 0.77593984 0.058480883 - 59000 0.66925719 0.4109031 1.0801603 0.072434423 - 60000 0.66807714 0.39233068 1.0604078 0.082370324 - 61000 0.5724275 0.43308567 1.0055132 0.0072945426 - 62000 0.49433556 0.38453743 0.87887299 0.0036097443 - 63000 0.57575143 0.54067119 1.1164226 0.073339638 - 64000 0.68045383 0.38246533 1.0629192 0.025314593 - 65000 0.59843527 0.42928622 1.0277215 -0.030096445 - 66000 0.60274797 0.50186417 1.1046121 0.069797184 - 67000 0.47450407 0.52689807 1.0014021 0.008758012 - 68000 0.5514135 0.64113187 1.1925454 0.093863314 - 69000 0.52008074 0.45749565 0.97757639 -0.066061381 - 70000 0.69042662 0.50416006 1.1945867 0.014128617 - 71000 0.63925854 0.35153425 0.9907928 -0.01134957 - 72000 0.52088835 0.47626986 0.99715821 0.10198133 - 73000 0.46333852 0.5515537 1.0148922 0.00060582772 - 74000 0.53481418 0.50409531 1.0389095 0.00919451 - 75000 0.67182749 0.50380162 1.1756291 0.043301985 - 76000 0.70492289 0.4112122 1.1161351 0.14880484 - 77000 0.59781817 0.50197661 1.0997948 -0.057111711 - 78000 0.51677429 0.4348232 0.95159749 -0.0074619446 - 79000 0.50663297 0.55000424 1.0566372 0.0052071216 - 80000 0.59392006 0.48394003 1.0778601 -0.018990234 - 81000 0.66323593 0.40358336 1.0668193 -0.02961345 - 82000 0.61596979 0.49177944 1.1077492 0.1314853 - 83000 0.63917554 0.61656584 1.2557414 0.11908351 - 84000 0.49305291 0.46161646 0.95466937 0.033558488 - 85000 0.52552044 0.54250555 1.068026 0.13015174 - 86000 0.55140914 0.38924725 0.94065638 0.047412499 - 87000 0.60952504 0.52603688 1.1355619 0.039230066 - 88000 0.50119735 0.547539 1.0487364 0.019659933 - 89000 0.40331401 0.50331134 0.90662535 -0.056906034 - 90000 0.47067839 0.51306911 0.9837475 0.11918166 - 91000 0.45564995 0.38693455 0.8425845 0.12040045 - 92000 0.64163032 0.34232532 0.98395564 0.0057051641 - 93000 0.70375593 0.53646186 1.2402178 0.16044241 - 94000 0.53378112 0.51971406 1.0534952 0.11389004 - 95000 0.47055342 0.50396004 0.97451346 0.079424215 - 96000 0.59543473 0.40204536 0.99748009 0.096813093 - 97000 0.64821917 0.50051728 1.1487365 0.054071312 - 98000 0.55723937 0.4945909 1.0518303 0.047316424 - 99000 0.56044424 0.50773312 1.0681774 0.0149959 - 100000 0.68254229 0.32704484 1.0095871 0.0069212661 -Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms - -Performance: 3926501.701 tau/day, 45445.622 timesteps/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80 -Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14 -Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88 -Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05 -Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78 -Other | | 0.1618 | | | 7.36 - -Nlocal: 8 ave 9 max 7 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 12.75 ave 14 max 12 min -Histogram: 2 0 0 0 0 1 0 0 0 1 -Neighs: 11 ave 19 max 5 min -Histogram: 1 0 0 2 0 0 0 0 0 1 - -Total # of neighbors = 44 -Ave neighs/atom = 1.375 -Neighbor list builds = 2663 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/cmap/log.11Apr17.cmap.g++.1 b/examples/cmap/log.11Apr17.cmap.g++.1 deleted file mode 100644 index 9b4fc29991..0000000000 --- a/examples/cmap/log.11Apr17.cmap.g++.1 +++ /dev/null @@ -1,205 +0,0 @@ -LAMMPS (31 Mar 2017) -# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016 - -units real -neigh_modify delay 2 every 1 -#newton off - -boundary p p p - -atom_style full -bond_style harmonic -angle_style charmm -dihedral_style charmmfsw -improper_style harmonic - -pair_style lj/charmmfsw/coul/charmmfsh 8 12 -pair_modify mix arithmetic - -fix cmap all cmap charmm22.cmap -Reading potential file charmm22.cmap with DATE: 2016-09-26 -fix_modify cmap energy yes - -read_data gagg.data fix cmap crossterm CMAP - orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 34 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 12 = max dihedrals/atom - scanning impropers ... - 1 = max impropers/atom - reading bonds ... - 33 bonds - reading angles ... - 57 angles - reading dihedrals ... - 75 dihedrals - reading impropers ... - 7 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 13 = max # of 1-4 neighbors - 16 = max # of special neighbors - -special_bonds charmm -fix 1 all nve - -#fix 1 all nvt temp 300 300 100.0 -#fix 2 all shake 1e-9 500 0 m 1.0 - -velocity all create 0.0 12345678 dist uniform - -thermo 1000 -thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp -timestep 2.0 - -run 100000 -Neighbor list info ... - update every 1 steps, delay 2 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 12 12 12 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/charmmfsw/coul/charmmfsh, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 14.96 | 14.96 | 14.96 Mbytes -Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro - 0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023 - 1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656 - 2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496 - 3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693 - 4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243 - 5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518 - 6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782 - 7000 18.186024 -0.84205608 0.58996182 3.0329585 4.7221473 -2.5733243 0.10047631 - 8000 18.214306 -1.1360938 0.72597611 3.7493028 4.7319958 -2.8957969 0.2006046 - 9000 17.248408 -0.48641993 0.90266229 2.9721743 4.7651056 -2.1473354 0.1302043 - 10000 17.760655 -1.2968444 0.92384663 3.7007455 4.7378947 -2.2147779 0.06940579 - 11000 17.633929 -0.57368413 0.84872849 3.4277114 4.285393 -2.236944 0.17204973 - 12000 18.305835 -1.0675148 0.75879532 2.8853173 4.685027 -2.409087 0.087538866 - 13000 17.391558 -0.9975291 0.66671947 3.8065638 5.2285578 -2.4198822 0.06253594 - 14000 17.483387 -0.67727643 0.91966477 3.7317031 4.7770445 -2.6080027 0.11487095 - 15000 18.131749 -1.1918751 1.0025684 3.1238131 4.789742 -2.2546745 0.13782813 - 16000 16.972343 -0.43926531 0.60644597 3.7551592 4.8658618 -2.2627659 0.12353145 - 17000 18.080785 -1.2073565 0.7867072 3.5671106 4.43754 -2.5092904 0.17429146 - 18000 17.474576 -0.97836065 0.8678524 3.7961537 4.3409032 -1.8922572 0.134048 - 19000 17.000911 -1.2286864 0.83615834 3.9322908 4.9319492 -2.3281576 0.056689619 - 20000 17.043286 -0.8506561 0.80966589 3.5087339 4.8603878 -2.3365263 0.096794824 - 21000 17.314495 -1.1430889 0.95363892 4.2446032 4.2756745 -2.1829483 0.17119518 - 22000 18.954881 -0.998673 0.58688334 2.71536 4.6634319 -2.6862804 0.20328442 - 23000 17.160427 -0.97803282 0.86894041 4.0897736 4.3146238 -2.1962289 0.075339092 - 24000 17.602026 -1.0833323 0.94888776 3.7341878 4.3084335 -2.1640414 0.081493681 - 25000 17.845584 -1.3432612 0.93497086 3.8911043 4.468032 -2.3475883 0.093204333 - 26000 17.833261 -1.1020534 0.77931087 3.7628141 4.512381 -2.3134761 0.15568465 - 27000 17.68607 -1.3222026 1.1985872 3.5817624 4.6360755 -2.3492774 0.08427906 - 28000 18.326649 -1.2669291 0.74809075 3.2624429 4.4698564 -2.3679076 0.14677293 - 29000 17.720933 -1.0773886 0.83099482 3.7652834 4.6584594 -2.8255303 0.23092596 - 30000 18.201999 -1.0168706 1.0637455 3.453095 4.3738593 -2.8063214 0.18658217 - 31000 17.823502 -1.2685768 0.84805585 3.8600661 4.2195821 -2.1169716 0.12517101 - 32000 16.883133 -0.62062648 0.84434922 3.5042683 5.1264906 -2.2674699 0.030138165 - 33000 17.805715 -1.679553 1.2430372 4.314677 4.2523894 -2.3008321 0.18591872 - 34000 16.723767 -0.54189072 1.1282827 3.8542159 4.3026559 -2.2186336 0.05392425 - 35000 17.976909 -0.72092075 0.5876319 2.9726396 5.0881439 -2.491692 0.17356291 - 36000 18.782492 -1.514246 0.63237955 3.2777164 4.6077164 -2.502574 0.082537318 - 37000 17.247716 -0.6344626 0.79885976 3.452491 4.7618281 -2.3902444 0.11450271 - 38000 17.996494 -1.6712877 1.0111769 4.1689136 4.46963 -2.4076725 0.11875756 - 39000 17.586857 -0.74508086 0.95970486 3.7395038 4.6011357 -2.9854953 0.30143284 - 40000 17.494879 -0.30772446 0.72047991 3.2604877 4.7283734 -2.3812495 0.16399034 - 41000 15.855772 -0.49642605 0.82496448 4.5139653 4.76884 -2.214141 0.10899661 - 42000 17.898568 -1.3078863 1.1505144 4.0429873 4.3889581 -2.8696559 0.23336417 - 43000 19.014372 -1.6325979 1.1553166 3.5660772 4.4047997 -2.9302044 0.13672127 - 44000 18.250782 -0.97211613 0.72714301 3.2258362 4.7257298 -2.5533613 0.11968073 - 45000 17.335174 0.24746331 1.0415866 3.3220992 4.5251095 -3.0415216 0.24453084 - 46000 17.72846 -0.9541418 0.88153841 3.7893452 4.5251883 -2.4003613 0.051809816 - 47000 18.226762 -0.67057787 0.84352989 3.0609522 4.5449078 -2.4694254 0.073703949 - 48000 17.838074 -0.88768441 1.3812262 3.5890492 4.5827868 -3.0137515 0.21417113 - 49000 17.973733 -0.75118705 0.69667886 3.3989025 4.7058886 -2.8243945 0.26665792 - 50000 17.461583 -0.65040016 0.68943524 2.9374743 5.6971777 -2.4438011 0.1697603 - 51000 16.79766 -0.010684434 0.89795555 3.959039 4.56763 -2.5101098 0.15048853 - 52000 17.566543 -0.7262764 0.74354418 3.3423185 4.8426523 -2.4187649 0.16908776 - 53000 17.964274 -0.9270914 1.065952 3.0397181 4.4682262 -2.2179503 0.07873406 - 54000 17.941256 -0.5807578 0.76516121 3.7262371 4.6975126 -3.179899 0.24433708 - 55000 17.079478 -0.48559832 0.95364453 3.0414645 5.2811414 -2.7064882 0.30102814 - 56000 17.632179 -0.75403299 0.97577942 3.3672363 4.4851336 -2.3683659 0.051117638 - 57000 16.17128 -0.44699325 0.76341543 4.267716 5.0881056 -2.4122329 0.16671692 - 58000 16.899276 -0.76481024 1.0400825 3.973493 4.8823309 -2.4270284 0.048716383 - 59000 18.145412 -0.84968335 0.71698306 3.2024358 4.6115739 -2.2520353 0.19466966 - 60000 17.578258 -1.0067331 0.72822527 3.5375208 4.9110255 -2.2319607 0.11922362 - 61000 17.434762 -1.0244393 0.90593099 3.8446915 4.8571191 -2.6228357 0.23259208 - 62000 17.580489 -1.1135917 0.79577432 3.7043524 4.6058114 -2.351492 0.042904152 - 63000 18.207335 -1.1512268 0.82684507 3.4114738 4.351069 -2.1878441 0.082922105 - 64000 18.333083 -1.1182287 0.74058959 3.6905164 4.3226172 -2.7110393 0.14721704 - 65000 16.271579 -0.7122151 1.0200168 4.6983643 4.3681131 -2.194921 0.12831024 - 66000 17.316444 -0.5729385 0.85254108 3.5769963 4.5526705 -2.3321328 0.040452643 - 67000 17.19011 -0.8814312 1.1381258 3.8605789 4.4183813 -2.299607 0.091527355 - 68000 18.223367 -1.362189 0.74472056 3.259165 4.486512 -2.2181134 0.048952796 - 69000 17.646348 -0.91647162 0.73990335 3.9313692 5.2663097 -3.3816778 0.27769877 - 70000 18.173493 -1.3107718 0.96484426 3.219728 4.5045124 -2.3349534 0.082327407 - 71000 17.0627 -0.58509083 0.85964129 3.8490884 4.437895 -2.1673348 0.24151404 - 72000 17.809764 -0.35128902 0.65479258 3.3945008 4.6160508 -2.5486166 0.10829531 - 73000 18.27769 -1.0739758 0.80890957 3.6070901 4.6256762 -2.4576547 0.080025736 - 74000 18.109437 -1.0691837 0.66679323 3.5923203 4.4825716 -2.5048169 0.21372319 - 75000 17.914569 -1.3500765 1.2993494 3.362421 4.4160377 -2.1278163 0.19397641 - 76000 16.563928 -0.16539261 1.0067302 3.5742755 4.8581915 -2.1362429 0.059822408 - 77000 18.130477 -0.38361279 0.43406954 3.4725995 4.7005855 -2.8836242 0.11958174 - 78000 16.746204 -1.1732959 0.7455507 3.6296638 5.6344113 -2.459208 0.16099803 - 79000 18.243999 -1.5850155 1.0108545 3.4727867 4.3367411 -2.316686 0.070480814 - 80000 16.960715 -0.84100929 0.91604996 3.862215 4.780949 -2.3711596 0.073916605 - 81000 17.697722 -1.1126605 0.952804 3.7114455 4.4216316 -2.2770085 0.091372066 - 82000 17.835901 -1.3091474 0.71867629 3.8168122 5.0150205 -2.4730634 0.062592852 - 83000 19.168418 -1.476938 0.75592316 3.2304519 4.3946471 -2.2991395 0.13083324 - 84000 17.945778 -1.5223622 1.0859941 3.4334011 5.0286682 -2.7550892 0.2476269 - 85000 17.950251 -0.85843846 0.86888218 3.3101287 4.5511879 -2.3640013 0.12080834 - 86000 17.480699 -0.97493649 0.85049761 3.4973085 4.6344922 -2.343121 0.2009677 - 87000 17.980244 -1.114983 0.88796989 3.4113329 4.3535853 -2.2535412 0.14494917 - 88000 18.023866 -1.226683 0.62339706 3.7649269 4.5923973 -2.3923523 0.10464375 - 89000 16.362829 -0.311462 1.0265375 4.0101723 4.4184777 -2.0314129 0.056570704 - 90000 17.533149 -0.41526788 1.0362029 3.4247412 4.2734431 -2.4776658 0.16960663 - 91000 17.719099 -1.1956801 1.0069945 3.2380672 4.8982805 -2.2154906 0.12950936 - 92000 17.762654 -1.170027 0.95814525 3.5217717 4.5405343 -2.5983677 0.15037754 - 93000 17.393958 -0.45641026 0.6579069 3.6002204 4.5942053 -2.5559641 0.12026544 - 94000 16.8182 -0.92962066 0.86801362 4.2914398 4.659848 -2.5251987 0.18000415 - 95000 17.642086 -0.7994896 0.7003756 3.8036697 4.5252487 -2.4166307 0.15686517 - 96000 18.114292 -1.5102104 1.2635908 3.2764427 5.0659496 -2.2777806 0.054309645 - 97000 18.575765 -1.6015311 0.69500699 3.1649317 4.9945742 -2.4012125 0.067373724 - 98000 16.578893 -0.78030229 0.91524222 4.4429655 4.4622392 -2.4052655 0.15355705 - 99000 17.26063 -0.57832833 0.7098846 3.9000046 4.5576484 -2.5333026 0.25517222 - 100000 18.377235 -0.89109577 0.68988617 2.8751751 4.4115591 -2.3560731 0.12185212 -Loop time of 2.96043 on 1 procs for 100000 steps with 34 atoms - -Performance: 5836.990 ns/day, 0.004 hours/ns, 33778.875 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.074 | 1.074 | 1.074 | 0.0 | 36.28 -Bond | 1.6497 | 1.6497 | 1.6497 | 0.0 | 55.72 -Neigh | 0.007576 | 0.007576 | 0.007576 | 0.0 | 0.26 -Comm | 0.012847 | 0.012847 | 0.012847 | 0.0 | 0.43 -Output | 0.0010746 | 0.0010746 | 0.0010746 | 0.0 | 0.04 -Modify | 0.16485 | 0.16485 | 0.16485 | 0.0 | 5.57 -Other | | 0.05037 | | | 1.70 - -Nlocal: 34 ave 34 max 34 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 395 ave 395 max 395 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 395 -Ave neighs/atom = 11.6176 -Ave special neighs/atom = 9.52941 -Neighbor list builds = 253 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/cmap/log.11Apr17.cmap.g++.4 b/examples/cmap/log.11Apr17.cmap.g++.4 deleted file mode 100644 index ec471d5a7e..0000000000 --- a/examples/cmap/log.11Apr17.cmap.g++.4 +++ /dev/null @@ -1,205 +0,0 @@ -LAMMPS (31 Mar 2017) -# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016 - -units real -neigh_modify delay 2 every 1 -#newton off - -boundary p p p - -atom_style full -bond_style harmonic -angle_style charmm -dihedral_style charmmfsw -improper_style harmonic - -pair_style lj/charmmfsw/coul/charmmfsh 8 12 -pair_modify mix arithmetic - -fix cmap all cmap charmm22.cmap -Reading potential file charmm22.cmap with DATE: 2016-09-26 -fix_modify cmap energy yes - -read_data gagg.data fix cmap crossterm CMAP - orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 34 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 12 = max dihedrals/atom - scanning impropers ... - 1 = max impropers/atom - reading bonds ... - 33 bonds - reading angles ... - 57 angles - reading dihedrals ... - 75 dihedrals - reading impropers ... - 7 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 13 = max # of 1-4 neighbors - 16 = max # of special neighbors - -special_bonds charmm -fix 1 all nve - -#fix 1 all nvt temp 300 300 100.0 -#fix 2 all shake 1e-9 500 0 m 1.0 - -velocity all create 0.0 12345678 dist uniform - -thermo 1000 -thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp -timestep 2.0 - -run 100000 -Neighbor list info ... - update every 1 steps, delay 2 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 12 12 12 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/charmmfsw/coul/charmmfsh, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes -Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro - 0 16.287573 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023 - 1000 18.816462 -0.84379243 0.78931817 2.7554247 4.4371421 -2.7762038 0.12697656 - 2000 18.091571 -1.045888 0.72306589 3.0951524 4.6725102 -2.3580092 0.22712496 - 3000 17.835596 -1.2171641 0.72666403 2.6696491 5.4373798 -2.0737041 0.075101693 - 4000 16.211232 -0.42713611 0.99472642 3.8961462 5.2009895 -2.5626866 0.17356243 - 5000 17.72183 -0.57081189 0.90733068 3.4376382 4.5457582 -2.3727543 0.12354518 - 6000 18.753977 -1.5772499 0.81468321 2.9236782 4.6033216 -2.3380859 0.12835782 - 7000 18.186024 -0.84205609 0.58996181 3.0329584 4.7221473 -2.5733244 0.10047631 - 8000 18.214306 -1.1360934 0.72597583 3.7493032 4.7319959 -2.8957975 0.20060467 - 9000 17.248415 -0.48642024 0.90266262 2.9721744 4.7651003 -2.1473349 0.13020438 - 10000 17.760663 -1.2968458 0.92384687 3.7007432 4.7378917 -2.2147799 0.06940514 - 11000 17.63395 -0.57366075 0.84871737 3.4276851 4.2853865 -2.2369491 0.17205075 - 12000 18.305713 -1.0672299 0.75876262 2.8852171 4.6850229 -2.4090072 0.087568888 - 13000 17.383367 -0.99678627 0.66712651 3.8060954 5.233865 -2.4180629 0.062014239 - 14000 17.510901 -0.68723297 0.92448551 3.7550867 4.7321218 -2.6059088 0.11504409 - 15000 18.080165 -1.13316 0.99982253 3.09947 4.8171402 -2.2713372 0.14580371 - 16000 17.383245 -0.4535296 0.57826268 3.6453593 4.6541138 -2.2434512 0.13285609 - 17000 17.111153 -0.3414839 0.73667584 3.7485311 4.6262965 -2.6166049 0.12635815 - 18000 16.862046 -1.3592061 1.2371142 4.4878937 4.2937117 -2.2112584 0.066145125 - 19000 18.313891 -1.654238 0.90644101 3.3934089 4.550735 -2.1862171 0.081267736 - 20000 19.083561 -1.3081747 0.56257812 2.7633848 4.6211438 -2.5196707 0.13763071 - 21000 18.23741 -1.051353 0.64408722 3.1735565 4.6912533 -2.2491947 0.099394904 - 22000 17.914515 -0.89769621 0.61793801 3.1224992 4.8683543 -2.282475 0.14524537 - 23000 16.756122 -0.98277883 1.2554905 3.7916115 4.7301443 -2.3094994 0.10226772 - 24000 16.109857 -0.54593177 0.86934462 4.4293574 4.926985 -2.2652264 0.11414331 - 25000 18.590559 -1.497327 1.1898361 2.9134403 4.7854107 -2.4437918 0.067416154 - 26000 18.493391 -1.0533797 0.4889578 3.6563013 4.6171721 -2.3240835 0.11607829 - 27000 18.646522 -1.1229601 0.67956815 2.7937638 4.8991207 -2.4068997 0.10109147 - 28000 18.545103 -1.7237438 0.72488022 3.8041665 4.6459974 -2.4339333 0.21943258 - 29000 17.840505 -1.0909667 0.88133248 3.3698456 5.0311644 -2.5116617 0.08102693 - 30000 17.649527 -0.65409177 0.86781692 3.24112 4.9903073 -2.6234925 0.14799777 - 31000 18.156812 -0.77476556 0.83192789 2.9620784 4.9160635 -2.8571635 0.22283201 - 32000 18.251583 -1.3384075 0.8059007 3.2588176 4.4365328 -2.1875071 0.087883637 - 33000 17.702785 -0.88311587 0.98573641 3.4645713 4.2650091 -2.0909158 0.14233004 - 34000 17.123413 -1.4873429 1.0419563 4.2628178 4.6318762 -2.2292095 0.105354 - 35000 18.162061 -1.0136007 0.82436129 3.6365024 4.5801677 -2.6856989 0.28648222 - 36000 17.65618 -1.094718 0.8872444 3.5075241 4.6382423 -2.3895134 0.18116961 - 37000 17.336475 -1.0657995 0.98869254 3.9252927 4.4383632 -2.2048244 0.22285949 - 38000 17.369467 -0.97623132 0.6712095 4.1349304 4.597754 -2.4088341 0.14608514 - 39000 18.170206 -1.2344285 0.77546195 3.6451049 4.7482287 -2.9895286 0.25768859 - 40000 16.210866 -0.81407781 0.99246271 4.2676233 5.0253763 -2.2929865 0.13348624 - 41000 17.641798 -1.0868157 0.80119513 3.4302526 5.280872 -2.4025406 0.22747391 - 42000 18.349848 -1.613759 1.1497004 3.7800682 4.3237683 -2.8676401 0.2120425 - 43000 19.130245 -1.196778 0.71845659 2.9325758 4.3684415 -2.433424 0.12240982 - 44000 18.061321 -1.2410101 1.0329373 3.0751569 4.7138313 -2.2880904 0.075814461 - 45000 18.162713 -1.4414622 1.009159 4.2298758 4.589593 -2.8502298 0.21606844 - 46000 18.591574 -0.99730412 1.0955215 3.3965004 4.359466 -3.1049731 0.17322629 - 47000 18.380259 -1.2717381 0.72291269 3.3958016 4.6099628 -2.4605065 0.19825185 - 48000 18.130478 -1.5051279 1.2087492 3.2488529 4.6690881 -2.2518174 0.05633061 - 49000 16.419912 -0.89320635 0.98926144 4.0388252 4.9919488 -2.1699511 0.15646479 - 50000 16.453196 -1.0433497 0.778346 4.6078069 4.7320614 -2.3760788 0.17161976 - 51000 18.245221 -0.89550444 0.9310446 3.0758194 4.3944595 -2.3082379 0.19983428 - 52000 17.839632 -1.0221781 0.76425017 3.3331547 4.5368437 -2.0988773 0.21098435 - 53000 18.693035 -1.4231915 0.76333082 3.1612761 4.583242 -2.4485762 0.089191206 - 54000 16.334672 -0.36309884 1.0200365 4.6700448 4.1628702 -2.1713841 0.11431995 - 55000 17.33842 -0.61522682 0.89847366 3.4970659 4.673495 -2.4743036 0.068004878 - 56000 17.790294 -1.0150845 0.73697112 3.6000297 4.5988343 -2.4822509 0.11434632 - 57000 18.913486 -1.0985507 1.0231848 2.7483267 4.4421755 -2.574424 0.1763388 - 58000 17.586896 -0.98284126 0.96965633 3.3330357 4.5325543 -2.1936869 0.083230915 - 59000 17.77788 -1.1649953 0.83092298 3.8004148 4.3940176 -2.3136642 0.017207608 - 60000 17.013042 -0.21728023 1.1688832 3.5374476 4.5462244 -2.4425301 0.15028297 - 61000 17.236242 -1.1342147 1.0301086 3.685948 4.6842331 -2.328108 0.070210812 - 62000 17.529852 -1.2961547 1.0323133 3.4474598 5.1435839 -2.4553423 0.060842687 - 63000 18.754704 -1.1816999 0.51806039 3.140172 4.5832701 -2.2713213 0.06327871 - 64000 17.54594 -1.3592836 0.9694558 4.1363258 4.3547729 -2.3818433 0.12634448 - 65000 16.962312 -0.54192775 0.90321315 4.0788618 4.2008255 -2.1376711 0.039504515 - 66000 18.078619 -1.3552947 1.0716861 3.3285374 4.7229362 -2.3331115 0.21978698 - 67000 17.132732 -1.4376876 0.91486534 4.4461852 4.6894176 -2.3655045 0.068150385 - 68000 18.69286 -1.2856207 0.3895394 3.0620063 4.9922992 -2.3459189 0.079879643 - 69000 18.329552 -1.1545957 0.88632275 3.1741058 4.4562418 -2.7094867 0.25329613 - 70000 16.681168 -0.94434373 1.2450393 4.5737944 4.4902996 -2.4581775 0.15313095 - 71000 17.375032 -1.0514442 1.0741595 3.4896146 4.8407713 -2.5302576 0.13640847 - 72000 17.833013 -0.9047134 0.87067876 3.1658924 4.8825932 -2.4398117 0.2343991 - 73000 17.421411 -1.2190741 0.73706811 4.2895 4.6464636 -2.3872727 0.19696525 - 74000 17.383158 -0.34208984 0.71333984 3.2718891 4.2718495 -2.2484281 0.10827022 - 75000 17.20885 -1.2710479 1.125102 3.8414467 5.3222741 -2.375505 0.12910797 - 76000 16.811578 -0.545162 0.59076961 3.9118604 4.8031296 -2.2777895 0.063015508 - 77000 16.679231 -0.080955983 0.7253398 3.4203454 5.0987608 -2.379614 0.12961874 - 78000 18.164524 -1.3115525 0.92526408 3.5764487 4.3814882 -2.3712488 0.073436724 - 79000 17.738686 -1.0697859 1.2186866 3.0593848 4.6551053 -2.2505871 0.075340661 - 80000 16.767483 -0.84777477 1.03128 4.1982958 4.6992227 -2.4146425 0.079774219 - 81000 16.257265 0.62803774 0.84032194 3.3873471 5.0961071 -2.7219776 0.20467848 - 82000 18.232082 -1.2129302 0.50746051 3.9207128 4.5073437 -2.599371 0.094522372 - 83000 16.618985 -0.60917055 0.8825847 3.805497 4.9560959 -2.2194726 0.14852687 - 84000 17.90762 -0.82336075 0.90504161 3.0324198 4.7444271 -2.5036073 0.15860682 - 85000 16.699883 -0.50297228 0.83405307 3.8598996 4.7971968 -2.2427788 0.10338668 - 86000 16.353038 -0.0096880616 0.80705167 4.0865115 4.5364338 -2.4548873 0.098456203 - 87000 17.887331 -0.75281219 1.0030148 4.0117123 4.3443074 -2.9774392 0.16190152 - 88000 18.583708 -1.4867053 0.86324814 3.3971237 4.3526221 -2.221239 0.14459352 - 89000 17.684828 -1.283764 1.0021118 3.5426808 4.9057005 -2.3921967 0.05844702 - 90000 17.2597 -0.84306489 0.99797936 3.8896866 4.4315457 -2.5662899 0.18270206 - 91000 16.705581 -0.44704047 0.75239556 3.470805 4.976868 -2.1894571 0.12312848 - 92000 17.548071 -1.2222664 0.92898812 4.0813773 4.3432647 -2.1631158 0.14071343 - 93000 17.163675 -0.94994776 0.96876981 3.9137692 4.4388666 -2.1260232 0.13187968 - 94000 18.842071 -1.2822113 0.58767049 3.1393475 4.5820965 -2.7264682 0.10406266 - 95000 18.112287 -1.1011381 0.63546648 3.4672667 4.486275 -2.2991936 0.041589685 - 96000 17.102713 -0.6877313 0.8389032 3.6892719 4.5676004 -2.1905327 0.13507011 - 97000 16.778253 -1.2902153 1.1588744 4.2820083 4.9537657 -2.4798159 0.35696636 - 98000 18.34638 -1.2908146 1.185356 3.0739807 4.4575453 -2.3959144 0.22407922 - 99000 17.995148 -1.3939639 0.7727299 3.8774144 4.4345458 -2.1142776 0.13550099 - 100000 18.444746 -1.2456693 0.86061526 3.468696 4.5264336 -2.4239851 0.074369539 -Loop time of 2.52011 on 4 procs for 100000 steps with 34 atoms - -Performance: 6856.851 ns/day, 0.004 hours/ns, 39680.850 timesteps/s -98.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.072506 | 0.28131 | 0.69088 | 46.2 | 11.16 -Bond | 0.050544 | 0.45307 | 0.9416 | 57.6 | 17.98 -Neigh | 0.0060885 | 0.0061619 | 0.0062056 | 0.1 | 0.24 -Comm | 0.44686 | 1.3679 | 2.0111 | 53.5 | 54.28 -Output | 0.0028057 | 0.0029956 | 0.003264 | 0.3 | 0.12 -Modify | 0.028202 | 0.095174 | 0.15782 | 19.8 | 3.78 -Other | | 0.3135 | | | 12.44 - -Nlocal: 8.5 ave 14 max 2 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 25.5 ave 32 max 20 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 98.75 ave 242 max 31 min -Histogram: 2 0 1 0 0 0 0 0 0 1 - -Total # of neighbors = 395 -Ave neighs/atom = 11.6176 -Ave special neighs/atom = 9.52941 -Neighbor list builds = 246 -Dangerous builds = 0 -Total wall time: 0:00:02 diff --git a/examples/cmap/log.27Nov18.cmap.g++.1 b/examples/cmap/log.27Nov18.cmap.g++.1 new file mode 100644 index 0000000000..c2c90059c4 --- /dev/null +++ b/examples/cmap/log.27Nov18.cmap.g++.1 @@ -0,0 +1,207 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016 + +units real +neigh_modify delay 2 every 1 +#newton off + +boundary p p p + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmmfsw +improper_style harmonic + +pair_style lj/charmmfsw/coul/charmmfsh 8 12 +Switching to CHARMM coulomb energy conversion constant (src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp:55) +pair_modify mix arithmetic + +fix cmap all cmap charmm22.cmap +Reading potential file charmm22.cmap with DATE: 2016-09-26 +fix_modify cmap energy yes + +read_data gagg.data fix cmap crossterm CMAP + orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 34 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 12 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 33 bonds + reading angles ... + 57 angles + reading dihedrals ... + 75 dihedrals + reading impropers ... + 7 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 13 = max # of 1-4 neighbors + 16 = max # of special neighbors + +special_bonds charmm +fix 1 all nve + +#fix 1 all nvt temp 300 300 100.0 +#fix 2 all shake 1e-9 500 0 m 1.0 + +velocity all create 0.0 12345678 dist uniform + +thermo 1000 +thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp +timestep 2.0 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmmfsw/coul/charmmfsh, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 14.96 | 14.96 | 14.96 Mbytes +Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro + 0 16.28796 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023 + 1000 18.817034 -0.84376064 0.78927748 2.7554954 4.4369572 -2.7762224 0.12700913 + 2000 18.091506 -1.0458619 0.72328506 3.0956514 4.6724302 -2.3582544 0.22717594 + 3000 17.841047 -1.2177066 0.72658478 2.6693344 5.4322049 -2.0735857 0.075472354 + 4000 16.203768 -0.43010212 0.99813471 3.9020929 5.2015958 -2.562376 0.17393693 + 5000 17.74278 -0.58387686 0.9095749 3.4440437 4.5474453 -2.3771369 0.12369887 + 6000 18.84065 -1.5987004 0.81046711 2.9214019 4.5243733 -2.3180496 0.12365723 + 7000 18.84546 -0.96510756 0.57164583 3.0069325 4.6579161 -2.8966842 0.186473 + 8000 16.965729 -0.85937109 0.62698075 3.6416157 5.2427548 -2.4812956 0.14018019 + 9000 16.847152 -0.23916172 0.76630295 3.8009862 4.4066861 -2.2021529 0.1798796 + 10000 17.553635 -1.2829068 1.1657706 3.9123497 5.0547767 -2.9598952 0.34416632 + 11000 17.985843 -1.5465483 0.84770758 3.3368358 5.662125 -2.6329553 0.24353243 + 12000 17.803319 -1.0407393 0.74246545 3.6148795 4.7651004 -2.5084817 0.10619442 + 13000 18.979266 -1.3899293 0.54141439 2.8249302 4.7550121 -2.5037554 0.11955235 + 14000 17.009105 -0.79638876 0.94514282 3.8784001 4.5107273 -2.2861709 0.076774568 + 15000 16.52792 -0.099911028 0.73468109 3.6878436 5.0897919 -2.6694045 0.1846061 + 16000 18.602333 -1.2207715 0.73683889 3.5724426 4.2967652 -2.1185335 0.14454439 + 17000 18.548631 -1.4459452 0.87132388 3.1082541 4.4173372 -2.1488103 0.05085499 + 18000 18.274944 -0.9082365 0.78279222 3.2003259 4.2230915 -2.0279073 0.067678678 + 19000 18.363395 -1.5446376 0.84278631 3.5192748 4.5827839 -2.3655766 0.16111203 + 20000 17.92959 -0.78977685 0.83244452 3.3573732 4.5008538 -2.7568218 0.18551385 + 21000 16.294685 -0.43068016 1.0820062 4.1094083 4.6392086 -2.4608104 0.1504371 + 22000 17.945194 -1.12622 0.86476498 3.3577152 4.673294 -2.4760964 0.081229709 + 23000 18.59629 -1.3692394 0.67592321 3.493029 4.5943035 -2.221834 0.13764568 + 24000 17.636587 -0.46892268 0.59584902 3.2114851 4.7133747 -2.4081857 0.26633414 + 25000 16.620668 -0.75136289 1.0243884 4.0835198 5.1451753 -2.6824535 0.24777903 + 26000 18.59225 -1.0967117 0.56177724 3.2556596 4.3523235 -2.4816091 0.1788868 + 27000 19.188088 -1.871277 0.96616357 3.0120122 4.3122826 -2.2148745 0.10347086 + 28000 17.912724 -0.90553766 1.1257482 3.2754041 4.2225708 -2.4365707 0.1807316 + 29000 17.81248 -1.1502128 0.95470623 3.4118416 4.6659831 -2.1613317 0.11462518 + 30000 17.018989 -0.89064809 0.84950442 4.1712342 4.4636021 -2.3306882 0.15623897 + 31000 18.547066 -1.5339831 0.89944952 3.3517223 4.7396826 -2.6121868 0.15212539 + 32000 17.200059 -1.0016932 0.81295912 4.0695758 4.5595904 -2.3605079 0.1387539 + 33000 17.531814 -0.70849955 0.75743835 3.226091 4.476408 -2.1190694 0.055884538 + 34000 18.325131 -1.2897672 0.89479605 3.1671187 4.2968993 -1.9697837 0.17312732 + 35000 18.289817 -1.0149458 0.75194781 3.4275427 4.5914578 -2.3206357 0.12126296 + 36000 17.111721 -0.59386121 0.84127598 3.5534448 5.0274338 -2.36455 0.090112107 + 37000 17.748767 -0.91029178 0.77689229 3.8018169 4.7249541 -2.4255194 0.054726961 + 38000 17.2172 -0.43070288 0.88086005 3.5586613 4.3203841 -2.0587465 0.050764106 + 39000 18.482481 -0.75351762 0.87677942 2.9007389 4.7178108 -2.6463003 0.25313342 + 40000 18.465192 -1.4076534 0.92705504 3.3546181 4.4030743 -2.3873054 0.071878288 + 41000 18.12592 -1.5839327 0.6979962 3.2851401 5.2815413 -2.3054411 0.11390788 + 42000 18.376705 -1.0077349 0.70647799 2.9499245 4.6421626 -2.3504786 0.17673009 + 43000 16.929642 -0.72975766 0.90203733 3.7176511 4.7292387 -2.2860424 0.084829761 + 44000 17.271104 -0.99868378 1.0201679 4.1153184 4.2727269 -2.1172719 0.1029166 + 45000 18.230889 -1.0093287 0.85777597 2.8550682 4.3913999 -2.0720155 0.073553812 + 46000 18.241544 -1.7077516 0.95512232 3.8878131 4.3812806 -2.3031674 0.10194331 + 47000 18.12818 -0.83919194 0.71483948 2.7541388 4.7432398 -2.2644558 0.053413336 + 48000 17.965762 -0.92946694 0.70540637 3.4567259 4.5010549 -2.3038276 0.15002746 + 49000 16.815211 0.19052416 1.0076747 3.1045662 4.9638411 -2.3712162 0.1057081 + 50000 17.193025 -0.89817177 1.2261029 3.7515175 4.4880145 -2.2643247 0.29712734 + 51000 18.665005 -0.84670757 0.56076732 3.0839868 4.458076 -2.2261738 0.046374416 + 52000 17.619937 -0.89986585 0.64159147 3.7530936 4.8769799 -2.3791391 0.13429701 + 53000 16.916466 -0.58872911 0.96495189 3.6755814 4.7419669 -2.3886804 0.20915197 + 54000 17.199476 -0.88155666 0.64336469 3.927811 4.8019389 -2.2773601 0.18734294 + 55000 18.158496 -0.81126798 0.68333055 2.9741959 4.4463001 -2.1864535 0.071857857 + 56000 17.860471 -1.6993 1.2366001 3.7857634 4.7701817 -2.4192649 0.15619688 + 57000 18.444698 -0.82854071 0.63506471 3.1823771 4.4432216 -2.2987011 0.1407306 + 58000 18.047238 -1.4404915 1.0095109 3.7328328 4.6385391 -2.1656547 0.068584173 + 59000 16.990212 -0.81630542 0.73745944 4.2847598 5.1556617 -2.4218952 0.044901478 + 60000 18.164864 -0.68273809 0.60589655 3.1085907 4.5637459 -2.2379342 0.11464892 + 61000 17.772457 -1.1890999 0.80411722 3.7218185 4.7750335 -2.4439724 0.11358571 + 62000 17.192042 -0.095008686 0.71713238 3.2284848 4.9345758 -2.4377098 0.12788027 + 63000 16.877969 -0.62181425 0.8931036 3.6147379 5.3541158 -2.302381 0.072736635 + 64000 17.934695 -1.1664658 0.74610888 3.5102215 4.6537266 -2.3495291 0.18818648 + 65000 17.034947 -0.59670985 0.7590603 3.4896411 5.0725358 -2.3057016 0.067650159 + 66000 18.259418 -0.57940688 0.55125252 3.2917088 4.4949827 -2.3128319 0.17052154 + 67000 16.656512 -1.1797815 0.88985636 4.3326457 4.7143632 -2.4187476 0.35820295 + 68000 18.218359 -0.98502226 0.8053151 2.8694875 4.6774476 -2.2750794 0.027475615 + 69000 18.591716 -1.2961393 0.85778116 3.4232791 4.3626988 -2.2150059 0.047420611 + 70000 18.282862 -1.5115081 1.1486318 3.1099158 4.5945816 -2.1742452 0.15701805 + 71000 17.722244 -1.3606013 0.98913854 3.9050958 4.4617942 -2.1980629 0.16665753 + 72000 17.578225 -1.0672968 1.1898075 3.3110576 4.6292013 -2.1893929 0.15802869 + 73000 17.700619 -1.1203382 0.68447774 3.7617044 4.5508307 -2.2031338 0.046795482 + 74000 18.864586 -1.3377627 0.54243736 3.1047677 4.6094993 -2.2506839 0.0618695 + 75000 17.252732 -0.75791613 0.79934329 3.6289993 4.8336985 -2.3716023 0.048355835 + 76000 15.625117 -0.17710917 1.0083339 4.5957493 4.3952808 -2.0145142 0.2165007 + 77000 18.663599 -1.214034 0.73808593 3.1282966 4.1967921 -2.04274 0.20129707 + 78000 16.687112 -0.81273153 1.0670946 3.5384094 5.3755076 -2.1922472 0.025711096 + 79000 18.169502 -1.443215 1.1859821 3.4043489 4.3415317 -2.3447052 0.11854425 + 80000 18.787124 -1.6654307 1.0501597 3.0298408 4.2077733 -1.9985344 0.26128514 + 81000 17.807683 -1.3429276 0.83231514 3.8051489 4.659607 -2.3866437 0.20196892 + 82000 17.331324 -0.78827019 0.95190013 3.7412416 4.3529018 -2.307155 0.073785492 + 83000 17.597954 -0.36573657 0.84239516 3.1227374 4.5709276 -2.2732398 0.12571923 + 84000 17.961063 -1.2301714 0.65709128 3.5308724 4.5505295 -2.4116051 0.14784451 + 85000 18.034924 -1.1445169 1.1114893 3.2704327 4.4570221 -2.3336871 0.084147643 + 86000 18.35847 -1.0687438 0.71638387 3.2994265 4.7224093 -2.6523985 0.2338977 + 87000 17.297387 -0.36290631 0.67031988 3.9566445 4.6234059 -2.8008118 0.22786876 + 88000 17.179923 -0.40756603 1.0448818 3.4777257 4.454146 -2.420876 0.18845717 + 89000 17.548178 -1.2104623 0.81223923 3.8553959 4.8092953 -2.3606086 0.16057241 + 90000 18.203445 -1.2476535 0.93776844 3.3519306 4.5880767 -2.3299626 0.13273664 + 91000 17.577661 -0.9536919 0.98278572 3.6805268 4.269043 -2.2758847 0.16458677 + 92000 17.249982 -1.2620718 1.2379068 4.077245 4.6893055 -2.3623079 0.080584665 + 93000 17.263474 -1.1194017 0.56075789 3.9937658 4.9398469 -2.458799 0.1178667 + 94000 17.794002 -0.94808955 0.82296171 3.4988835 4.723922 -2.4525227 0.093849723 + 95000 17.380526 -1.3184326 1.2273125 4.01341 4.3749028 -2.1577427 0.12183053 + 96000 17.421883 -1.0247407 0.98739686 4.1656417 4.5509065 -2.5533884 0.15050166 + 97000 18.097453 -0.82643049 0.58678318 3.5934164 4.2844244 -2.187686 0.1173314 + 98000 17.110826 -0.9875292 1.1047966 3.5373119 4.9434687 -2.3951197 0.051018748 + 99000 17.497671 -0.72505537 1.1343346 3.3335263 4.7133241 -2.3170405 0.18322857 + 100000 17.502653 -1.2246734 0.85121721 4.132924 4.6912393 -2.605162 0.24425609 +Loop time of 2.20757 on 1 procs for 100000 steps with 34 atoms + +Performance: 7827.606 ns/day, 0.003 hours/ns, 45298.646 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.80344 | 0.80344 | 0.80344 | 0.0 | 36.39 +Bond | 1.0867 | 1.0867 | 1.0867 | 0.0 | 49.22 +Neigh | 0.0081377 | 0.0081377 | 0.0081377 | 0.0 | 0.37 +Comm | 0.017823 | 0.017823 | 0.017823 | 0.0 | 0.81 +Output | 0.0011017 | 0.0011017 | 0.0011017 | 0.0 | 0.05 +Modify | 0.21444 | 0.21444 | 0.21444 | 0.0 | 9.71 +Other | | 0.07595 | | | 3.44 + +Nlocal: 34 ave 34 max 34 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 395 ave 395 max 395 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 395 +Ave neighs/atom = 11.6176 +Ave special neighs/atom = 9.52941 +Neighbor list builds = 230 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/cmap/log.27Nov18.cmap.g++.4 b/examples/cmap/log.27Nov18.cmap.g++.4 new file mode 100644 index 0000000000..63d94b86c8 --- /dev/null +++ b/examples/cmap/log.27Nov18.cmap.g++.4 @@ -0,0 +1,207 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016 + +units real +neigh_modify delay 2 every 1 +#newton off + +boundary p p p + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmmfsw +improper_style harmonic + +pair_style lj/charmmfsw/coul/charmmfsh 8 12 +Switching to CHARMM coulomb energy conversion constant (src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp:55) +pair_modify mix arithmetic + +fix cmap all cmap charmm22.cmap +Reading potential file charmm22.cmap with DATE: 2016-09-26 +fix_modify cmap energy yes + +read_data gagg.data fix cmap crossterm CMAP + orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 34 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 12 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 33 bonds + reading angles ... + 57 angles + reading dihedrals ... + 75 dihedrals + reading impropers ... + 7 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 13 = max # of 1-4 neighbors + 16 = max # of special neighbors + +special_bonds charmm +fix 1 all nve + +#fix 1 all nvt temp 300 300 100.0 +#fix 2 all shake 1e-9 500 0 m 1.0 + +velocity all create 0.0 12345678 dist uniform + +thermo 1000 +thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp +timestep 2.0 + +run 100000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmmfsw/coul/charmmfsh, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 14.94 | 15.57 | 16.2 Mbytes +Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro + 0 16.28796 -0.85933785 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023 + 1000 18.817034 -0.84376064 0.78927748 2.7554954 4.4369572 -2.7762224 0.12700913 + 2000 18.091506 -1.0458619 0.72328506 3.0956514 4.6724302 -2.3582544 0.22717594 + 3000 17.841047 -1.2177066 0.72658478 2.6693344 5.4322049 -2.0735857 0.075472354 + 4000 16.203768 -0.43010212 0.99813471 3.9020929 5.2015958 -2.562376 0.17393693 + 5000 17.74278 -0.58387686 0.9095749 3.4440437 4.5474453 -2.3771369 0.12369887 + 6000 18.84065 -1.5987004 0.81046711 2.9214019 4.5243733 -2.3180496 0.12365723 + 7000 18.84546 -0.96510756 0.57164583 3.0069325 4.6579161 -2.8966842 0.186473 + 8000 16.965729 -0.85937109 0.62698075 3.6416157 5.2427548 -2.4812956 0.14018019 + 9000 16.847152 -0.23916171 0.76630294 3.8009862 4.406686 -2.2021529 0.17987959 + 10000 17.553634 -1.2829064 1.1657706 3.91235 5.0547763 -2.9598949 0.34416627 + 11000 17.985844 -1.546548 0.84770734 3.3368355 5.6621242 -2.6329556 0.24353209 + 12000 17.803315 -1.0407428 0.74246591 3.6148861 4.7651023 -2.5084818 0.10619443 + 13000 18.979298 -1.3899069 0.54140353 2.824908 4.7549927 -2.5037439 0.1195534 + 14000 17.009076 -0.79641495 0.94514807 3.8784683 4.5107542 -2.2861686 0.076775119 + 15000 16.527651 -0.10009622 0.73467885 3.6878968 5.0899041 -2.6692893 0.18460865 + 16000 18.604151 -1.2210802 0.73655927 3.5718605 4.2964962 -2.1189359 0.14449313 + 17000 18.546852 -1.4467993 0.87198724 3.1105181 4.4184817 -2.1495741 0.051004484 + 18000 18.269987 -0.90581341 0.7831269 3.2002375 4.2239607 -2.0289403 0.067912952 + 19000 18.365165 -1.5425052 0.84132905 3.5171046 4.582444 -2.3624811 0.15993488 + 20000 17.919207 -0.79257338 0.83410115 3.3693164 4.4968189 -2.7465541 0.1841698 + 21000 16.278922 -0.44214815 1.0902282 4.1142335 4.6450522 -2.4508096 0.14648872 + 22000 17.980488 -1.1391025 0.8652074 3.3488636 4.6605505 -2.4768211 0.082465921 + 23000 18.89971 -1.3694963 0.64862919 3.3841726 4.4302445 -2.2592268 0.13555028 + 24000 17.161166 -0.55945806 0.69448645 3.4675689 5.0748468 -2.5837022 0.2986302 + 25000 17.156172 -0.68212797 0.95625815 3.9473369 4.6696376 -2.597154 0.27829376 + 26000 17.825866 -0.73781842 0.75572313 3.303994 4.6064489 -2.4678257 0.1101394 + 27000 18.616198 -1.1970872 0.74929218 2.7266748 4.5928796 -2.3031488 0.10452726 + 28000 17.263879 -1.1343882 1.3560474 3.5869107 4.954875 -2.3468498 0.055318117 + 29000 18.218484 -0.64810872 0.68572616 3.3763474 4.5347093 -2.5532561 0.044134638 + 30000 17.213834 -1.1463665 0.81650849 4.5021522 4.5992871 -2.40695 0.04205291 + 31000 17.8559 -0.99467757 0.71511439 3.5755686 4.9305642 -2.6691079 0.15067927 + 32000 17.632612 -0.8302854 1.2248328 3.4735959 4.6212801 -2.7231143 0.34288338 + 33000 17.176657 -0.64567669 0.97026796 3.3935778 4.5587216 -2.2673303 0.14591296 + 34000 17.928014 -0.78865694 0.54309368 3.508016 4.7763531 -2.4383684 0.18688827 + 35000 17.961344 -1.3258434 0.79791264 3.6021659 4.7174496 -2.4153924 0.14281974 + 36000 17.363519 -0.87152419 0.86057615 3.9176779 4.3965038 -2.1041204 0.12738842 + 37000 16.06135 -1.0007854 1.3152379 4.9256357 4.4181047 -2.2698823 0.20913478 + 38000 16.980479 -0.95646429 0.81311125 3.9783382 5.1047807 -2.5399437 0.20183215 + 39000 18.494869 -0.90369184 0.71368 2.9713413 4.7252974 -2.4204755 0.15716213 + 40000 17.879106 -0.86166372 0.89882312 3.4726397 4.3971385 -2.3460741 0.13021249 + 41000 18.035763 -1.2809432 0.91931903 3.4005222 4.5201606 -2.411653 0.10482408 + 42000 17.688254 -1.0984284 0.93541053 3.723003 4.6284132 -2.2978157 0.098932073 + 43000 17.162211 -1.2347977 1.0781323 4.0892528 4.6269303 -2.3550598 0.05480233 + 44000 17.368788 -0.62753591 0.95568557 3.2537525 4.6683551 -2.316093 0.17116275 + 45000 17.28803 -0.76881568 0.92524577 3.6089685 4.3707256 -2.2940853 0.054227805 + 46000 17.659642 -1.0636933 0.62134856 3.7988149 4.642663 -2.2567824 0.059618876 + 47000 17.520356 -0.73678104 0.65813025 3.5138815 4.6758778 -2.2989321 0.099899312 + 48000 16.812802 -0.88677379 0.9634123 3.5723247 5.1067533 -2.3228969 0.1375947 + 49000 16.689302 -0.84108162 0.97663708 4.5288711 4.2042907 -2.0960932 0.12712083 + 50000 17.34708 -0.99417589 0.74282621 4.0884892 4.4655725 -2.3445562 0.040137606 + 51000 18.386747 -1.4258618 0.7415682 3.5702618 4.3472793 -2.3531028 0.076627832 + 52000 18.62586 -1.3545312 0.8226399 2.8749248 4.6581056 -2.1415891 0.074885964 + 53000 18.142099 -1.0903937 1.0355955 3.39219 4.3761473 -2.3714216 0.12991324 + 54000 18.452949 -1.2117507 0.79702906 3.0176388 4.4872416 -2.3195176 0.073698473 + 55000 17.317369 -0.89629461 0.7135235 4.0285995 4.8471482 -2.3306208 0.067829904 + 56000 17.331139 -0.70400555 0.92933471 3.1428751 5.1938451 -2.3960347 0.10207963 + 57000 17.769688 -0.69097945 0.6761737 3.6233451 4.3309071 -2.588033 0.33444943 + 58000 17.808019 -0.50062525 0.84330344 3.0780006 4.4191107 -2.2626852 0.23176683 + 59000 16.974427 -0.22275961 1.1171381 3.6002905 4.8457806 -2.4506404 0.086485736 + 60000 18.426097 -1.1640712 0.89526359 3.0738119 4.3475275 -2.2585607 0.17344541 + 61000 18.347861 -1.1389796 0.94799071 3.3858595 4.3778565 -2.4264935 0.022565214 + 62000 17.472407 -0.054270199 0.78119769 3.5192829 4.5922308 -2.7152004 0.077668809 + 63000 18.451352 -0.99265328 0.65501446 3.1607389 4.4871585 -2.3972756 0.1095194 + 64000 17.664837 -1.3148668 0.94502551 3.7697825 4.6332111 -2.4479629 0.2841013 + 65000 17.857844 -0.82183909 0.94533467 3.3987595 4.7509642 -2.9322189 0.15667848 + 66000 16.809282 -0.11096144 0.79005552 4.2974065 4.667357 -2.85833 0.08678995 + 67000 18.331716 -0.77668223 0.85848669 2.630497 4.6984372 -2.6328844 0.20335427 + 68000 17.818595 -0.93709899 0.87885516 3.3973927 4.4542279 -2.2667437 0.18791512 + 69000 18.115509 -1.440213 1.347904 3.3737104 4.3392351 -2.3748603 0.15273089 + 70000 17.230663 -0.76722679 0.77580436 3.920298 4.3064374 -2.057197 0.1064338 + 71000 17.972819 -0.56240735 0.69337989 3.2513062 4.5245288 -2.5597279 0.27216928 + 72000 18.432872 -1.3313091 0.84535471 3.1727393 4.483952 -2.4128395 0.1378963 + 73000 17.697723 -0.97837773 1.0529842 3.8074009 4.72378 -2.7174621 0.17825868 + 74000 18.504521 -1.1231346 0.88277801 3.0479334 4.3481094 -2.2732739 0.086093125 + 75000 17.934978 -1.4213334 0.9145673 3.8583169 4.5864462 -2.3243695 0.081450732 + 76000 18.508287 -0.98310739 0.64131006 3.2474703 4.4350548 -2.2768941 0.11216496 + 77000 16.846831 -1.1997156 0.97525037 4.5115234 4.4822983 -2.2271894 0.15009063 + 78000 18.298764 -0.89093904 1.151268 2.9546969 4.5531473 -2.6022807 0.17136053 + 79000 17.440102 -0.84471365 0.79902079 3.7146172 4.5874272 -2.3161711 0.074592893 + 80000 16.96787 -0.76797183 1.1525337 3.4597685 5.140513 -2.6897182 0.21382322 + 81000 17.081167 -1.0035883 0.9417994 4.3325391 4.7180405 -2.6083103 0.19511734 + 82000 16.507622 -1.05195 1.1260094 4.2926577 4.7646789 -2.4006964 0.14462259 + 83000 17.693074 -0.86921671 0.78469232 3.2635421 4.7625581 -2.1472473 0.089898176 + 84000 17.485199 -0.63086362 0.84462236 3.7419011 4.3478352 -2.2855255 0.12993625 + 85000 17.791978 -1.2653364 0.83896065 3.8569475 4.7233956 -2.4464365 0.10326311 + 86000 17.859089 -0.81401354 0.81139105 3.4899076 4.5074402 -2.3756207 0.13928587 + 87000 17.922335 -1.381674 1.1201002 4.0246458 4.8013529 -3.0706282 0.14319694 + 88000 17.891848 -1.1065441 0.95945646 3.8687633 4.2747388 -2.2353028 0.2196999 + 89000 17.618833 -0.74803168 1.0695045 2.8694377 4.9185961 -2.2867946 0.14163937 + 90000 18.321207 -1.332528 0.81671672 3.921007 4.2555562 -2.4712797 0.071633057 + 91000 18.553104 -1.3004122 0.9317915 3.1911912 4.3221185 -2.2542173 0.090485864 + 92000 17.39548 -0.87272071 0.96671708 3.8750471 4.3904352 -2.5461358 0.1301959 + 93000 17.706773 -1.0859407 0.96681042 3.5302332 4.5674911 -2.2899428 0.051797638 + 94000 18.315271 -1.0896814 0.82594056 3.253212 4.6972747 -2.3528794 0.14073237 + 95000 17.512959 -1.2251671 1.1726435 3.870858 4.2950784 -2.3334602 0.063946067 + 96000 17.196402 -1.350795 1.0149203 4.5463081 4.46194 -2.2969009 0.057997074 + 97000 18.119424 -1.1822278 1.0710466 2.9669136 4.5028366 -2.3136825 0.10116804 + 98000 18.611528 -1.1675308 0.86166718 3.8663186 4.5385301 -3.2887663 0.17772415 + 99000 17.221377 -0.72476724 1.0463603 3.2816006 4.9591142 -2.6471303 0.23335447 + 100000 17.500556 -1.0148716 1.2155656 3.5359122 4.5111603 -2.2594507 0.14328565 +Loop time of 2.16745 on 4 procs for 100000 steps with 34 atoms + +Performance: 7972.502 ns/day, 0.003 hours/ns, 46137.167 timesteps/s +94.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.058708 | 0.22252 | 0.54183 | 40.5 | 10.27 +Bond | 0.038348 | 0.31503 | 0.66653 | 48.0 | 14.53 +Neigh | 0.0070002 | 0.007808 | 0.0096803 | 1.2 | 0.36 +Comm | 0.42884 | 1.1121 | 1.5566 | 42.8 | 51.31 +Output | 0.002564 | 0.0036213 | 0.0063593 | 2.6 | 0.17 +Modify | 0.036094 | 0.12956 | 0.22792 | 25.9 | 5.98 +Other | | 0.3768 | | | 17.38 + +Nlocal: 8.5 ave 15 max 2 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 25.5 ave 32 max 19 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 98.75 ave 271 max 18 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 395 +Ave neighs/atom = 11.6176 +Ave special neighs/atom = 9.52941 +Neighbor list builds = 236 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/colloid/log.27Nov18.colloid.g++.1 b/examples/colloid/log.27Nov18.colloid.g++.1 new file mode 100644 index 0000000000..7eae97eff6 --- /dev/null +++ b/examples/colloid/log.27Nov18.colloid.g++.1 @@ -0,0 +1,153 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.01 +Lattice spacing in x,y,z = 10 10 10 +region box block 0 30 0 30 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -5) to (300 300 5) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 900 atoms + Time spent = 0.000598431 secs + +set group all type/fraction 2 0.96 23984 + 861 settings made for type/fraction + +set type 1 mass 9 + 39 settings made for mass +set type 2 mass 1 + 861 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 +comm_modify mode multi + +# colloid potential + +pair_style colloid 12.5 +pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5 +pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0 +pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5 + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.5 + ghost atom cutoff = 13.5 + binsize = 1.75, bins = 172 172 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000 + 1000 1.9572809 -0.00036743274 1.9547388 0.017982269 98935.161 + 2000 2.068567 -0.0010518227 2.0652168 0.019466739 96307.439 + 3000 2.1787472 0.0045846363 2.180911 0.029249545 68560.31 + 4000 2.1979309 0.0017234058 2.1972121 0.048831814 42699.657 + 5000 2.1541368 0.0068842503 2.1586276 0.07471981 28571.492 + 6000 2.1113173 0.0024196693 2.1113911 0.091799816 21611.61 + 7000 2.0788416 0.0060975475 2.0826293 0.11638141 17868.699 + 8000 2.0587325 0.011431711 2.0678767 0.136977 15515.134 + 9000 2.0608274 0.00084150047 2.0593791 0.1448357 13890.944 + 10000 2.0446145 0.016230031 2.0585728 0.17785946 12557.927 + 11000 2.0481772 0.008961682 2.0548631 0.1925805 11482.879 + 12000 2.0536702 0.0065675004 2.0579558 0.19987216 10543.356 + 13000 2.0483659 0.0071445135 2.0532344 0.22867229 9777.939 + 14000 2.0334727 0.020440289 2.0516536 0.25700656 9138.0619 + 15000 2.0221794 0.032212195 2.0521448 0.28477019 8585.7952 + 16000 2.029058 0.024040298 2.0508438 0.28585812 8095.1269 + 17000 2.0270567 0.025118634 2.049923 0.30905216 7689.7819 + 18000 2.0123899 0.037421737 2.0475757 0.3636938 7364.3469 + 19000 2.019082 0.032220518 2.0490591 0.35887838 7063.0831 + 20000 2.0383387 0.013928928 2.0500028 0.35029696 6810.6189 + 21000 2.0113975 0.039874446 2.0490371 0.41652382 6555.842 + 22000 2.0292399 0.029463117 2.0564483 0.40823941 6292.2335 + 23000 2.0271279 0.033537888 2.0584134 0.4359853 6051.2547 + 24000 2.0075928 0.044388917 2.0497511 0.46590892 5890.69 + 25000 2.0345451 0.017490239 2.0497748 0.44508598 5798.4911 + 26000 1.9933171 0.070984054 2.0620863 0.53325353 5618.279 + 27000 2.0437208 0.022615819 2.0640658 0.50130607 5440.3246 + 28000 2.0101461 0.054907742 2.0628204 0.55318766 5304.6714 + 29000 2.0231122 0.043194685 2.0640589 0.54438745 5197.9144 + 30000 2.0036611 0.062982451 2.0644173 0.5791539 5071.4318 + 31000 2.0118619 0.055674047 2.0653006 0.63370324 4956.3038 + 32000 2.0291738 0.035314054 2.0622333 0.59475403 4852.8359 + 33000 1.9954345 0.075707165 2.0689245 0.6809065 4761.5146 + 34000 2.0141897 0.04990827 2.0618599 0.61183102 4681.1535 + 35000 2.0002914 0.072549616 2.0706185 0.78205667 4595.2138 + 36000 2.0048956 0.065248982 2.067917 0.74763198 4502.7759 + 37000 2.0229016 0.049698006 2.070352 0.6949933 4422.5382 + 38000 2.0291924 0.048408539 2.0753463 0.67746901 4353.6336 + 39000 2.0057251 0.071071345 2.0745679 0.781985 4293.9239 + 40000 2.0314588 0.052600075 2.0818017 0.71759858 4247.5894 + 41000 2.0229153 0.059717009 2.0803846 0.73068778 4179.9404 + 42000 2.003508 0.080215578 2.0814975 0.81505369 4124.3279 + 43000 2.0034351 0.079898162 2.0811072 0.81862672 4075.4928 + 44000 2.0151423 0.074554369 2.0874576 0.84679645 4014.0973 + 45000 2.0210784 0.073589668 2.0924224 0.82507573 3960.3663 + 46000 2.0192162 0.069599489 2.0865721 0.87813695 3915.513 + 47000 2.019728 0.071103706 2.0885875 0.90918917 3864.3408 + 48000 2.0138563 0.073940136 2.0855588 0.86312211 3819.3487 + 49000 2.0257679 0.066368453 2.0898855 0.99155677 3794.5614 + 50000 2.0054884 0.089153801 2.0924139 0.99114819 3770.4528 +Loop time of 9.13278 on 1 procs for 50000 steps with 900 atoms + +Performance: 2365106.031 tau/day, 5474.782 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.0125 | 4.0125 | 4.0125 | 0.0 | 43.93 +Neigh | 1.4242 | 1.4242 | 1.4242 | 0.0 | 15.59 +Comm | 0.45633 | 0.45633 | 0.45633 | 0.0 | 5.00 +Output | 0.00083971 | 0.00083971 | 0.00083971 | 0.0 | 0.01 +Modify | 2.8978 | 2.8978 | 2.8978 | 0.0 | 31.73 +Other | | 0.3412 | | | 3.74 + +Nlocal: 900 ave 900 max 900 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 571 ave 571 max 571 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5952 ave 5952 max 5952 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5952 +Ave neighs/atom = 6.61333 +Neighbor list builds = 3099 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:09 diff --git a/examples/colloid/log.27Nov18.colloid.g++.4 b/examples/colloid/log.27Nov18.colloid.g++.4 new file mode 100644 index 0000000000..af1e412ae9 --- /dev/null +++ b/examples/colloid/log.27Nov18.colloid.g++.4 @@ -0,0 +1,153 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Big colloid particles and small LJ particles + +units lj +atom_style sphere +dimension 2 + +lattice sq 0.01 +Lattice spacing in x,y,z = 10 10 10 +region box block 0 30 0 30 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -5) to (300 300 5) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 900 atoms + Time spent = 0.000492334 secs + +set group all type/fraction 2 0.96 23984 + 861 settings made for type/fraction + +set type 1 mass 9 + 39 settings made for mass +set type 2 mass 1 + 861 settings made for mass + +velocity all create 1.44 87287 loop geom + +# multi neighbor and comm for efficiency + +neighbor 1 multi +neigh_modify delay 0 +comm_modify mode multi + +# colloid potential + +pair_style colloid 12.5 +pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5 +pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0 +pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5 + +fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +#dump 1 all atom 1000 dump.colloid + +#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 + +#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 +#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 + +thermo_style custom step temp epair etotal press vol +thermo 1000 + +timestep 0.005 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.5 + ghost atom cutoff = 13.5 + binsize = 1.75, bins = 172 172 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair colloid, perpetual + attributes: half, newton on + pair build: half/multi/newton + stencil: half/multi/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.344 | 4.344 | 4.345 Mbytes +Step Temp E_pair TotEng Press Volume + 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000 + 1000 1.9572809 -0.00036743274 1.9547388 0.017982269 98935.161 + 2000 2.068567 -0.0010518227 2.0652168 0.019466739 96307.439 + 3000 2.1787472 0.0045846363 2.180911 0.029249545 68560.31 + 4000 2.1979309 0.0017234058 2.1972121 0.048831814 42699.657 + 5000 2.1541368 0.0068842504 2.1586276 0.07471981 28571.492 + 6000 2.1113175 0.0024194723 2.1113911 0.091799767 21611.61 + 7000 2.0788795 0.0060577432 2.0826274 0.11639395 17868.707 + 8000 2.0537762 0.01651572 2.0680099 0.13601134 15517.28 + 9000 2.0427394 0.019556597 2.0600262 0.15430942 13881.26 + 10000 2.050769 0.010396598 2.058887 0.16312819 12594.101 + 11000 2.0439348 0.018189464 2.0598533 0.2172647 11494.35 + 12000 2.0493504 0.010908719 2.0579821 0.21333624 10567.11 + 13000 2.0474606 0.013141328 2.0583269 0.2321885 9768.8239 + 14000 2.0370325 0.020936303 2.0557055 0.27034432 9105.9607 + 15000 2.0077835 0.045753549 2.0513062 0.3078643 8580.9799 + 16000 2.0184593 0.035585101 2.0518017 0.28738263 8120.9005 + 17000 2.0071721 0.044732393 2.0496743 0.32368949 7762.8875 + 18000 2.0085194 0.043117932 2.0494056 0.35526658 7442.6597 + 19000 2.0263547 0.029022667 2.0531258 0.3691966 7124.1683 + 20000 2.0285624 0.03264145 2.0589499 0.39783282 6810.1273 + 21000 2.0212924 0.039016129 2.0580626 0.42089074 6535.8717 + 22000 2.0285415 0.030259995 2.0565475 0.42080619 6301.8013 + 23000 2.0344885 0.02346797 2.0556959 0.4345206 6100.1797 + 24000 2.0219939 0.031317084 2.0510643 0.41301645 5921.1948 + 25000 2.034277 0.023680834 2.0556976 0.47443175 5749.5789 + 26000 2.0143035 0.051903569 2.063969 0.47278476 5570.3177 + 27000 2.0091763 0.054826231 2.0617701 0.53731629 5405.5081 + 28000 2.0306603 0.030512009 2.058916 0.50158605 5292.5739 + 29000 1.9905878 0.063609393 2.0519854 0.62105081 5217.6324 + 30000 2.0047307 0.057002418 2.0595056 0.59872107 5125.6009 + 31000 2.0076871 0.064365243 2.0698216 0.56914126 4971.7382 + 32000 2.0399769 0.031886115 2.0695964 0.55523269 4850.6347 + 33000 2.0196607 0.042847913 2.0602646 0.5749789 4770.7458 + 34000 2.0079696 0.067168038 2.0729066 0.70228842 4704.8088 + 35000 2.0264945 0.043126775 2.0673696 0.62754917 4625.3307 + 36000 2.029471 0.050993168 2.0782092 0.65985012 4513.2576 + 37000 2.0211356 0.053873626 2.0727635 0.75743646 4426.8691 + 38000 1.9933609 0.08028105 2.0714271 0.729473 4388.5022 + 39000 2.0046836 0.076855879 2.079312 0.83705993 4291.7229 + 40000 2.0321953 0.046360451 2.0762978 0.71726696 4229.9223 + 41000 2.0332458 0.051512927 2.0824996 0.78613181 4157.4167 + 42000 1.9750553 0.097198273 2.0700591 0.84569229 4123.0833 + 43000 2.0234742 0.056757566 2.0779835 0.78732804 4096.6281 + 44000 1.9966481 0.094296711 2.0887263 0.86811037 4021.0355 + 45000 2.0099144 0.077843813 2.085525 0.87222128 3961.2649 + 46000 1.9959281 0.090282388 2.0839928 0.90564582 3916.4041 + 47000 2.0174181 0.067872225 2.0830488 0.86559533 3889.8008 + 48000 2.0066047 0.094875259 2.0992504 0.99089696 3835.3328 + 49000 2.0031392 0.094024663 2.0949381 1.0600075 3789.3375 + 50000 2.0307693 0.059124989 2.0876379 0.85398261 3770.4556 +Loop time of 4.0156 on 4 procs for 50000 steps with 900 atoms + +Performance: 5379021.062 tau/day, 12451.438 timesteps/s +94.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.8857 | 0.95678 | 0.99748 | 4.6 | 23.83 +Neigh | 0.34187 | 0.39239 | 0.42858 | 5.1 | 9.77 +Comm | 0.95431 | 1.0287 | 1.1204 | 6.3 | 25.62 +Output | 0.0010757 | 0.0037161 | 0.011632 | 7.5 | 0.09 +Modify | 1.3279 | 1.3522 | 1.3823 | 1.7 | 33.67 +Other | | 0.2818 | | | 7.02 + +Nlocal: 225 ave 251 max 186 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 302.75 ave 330 max 288 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Neighs: 1487.5 ave 1689 max 1191 min +Histogram: 1 0 0 0 0 1 0 0 1 1 + +Total # of neighbors = 5950 +Ave neighs/atom = 6.61111 +Neighbor list builds = 3097 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/colloid/log.5Oct16.colloid.g++.1 b/examples/colloid/log.5Oct16.colloid.g++.1 deleted file mode 100644 index e4c31be124..0000000000 --- a/examples/colloid/log.5Oct16.colloid.g++.1 +++ /dev/null @@ -1,146 +0,0 @@ -LAMMPS (5 Oct 2016) -# Big colloid particles and small LJ particles - -units lj -atom_style sphere -dimension 2 - -lattice sq 0.01 -Lattice spacing in x,y,z = 10 10 10 -region box block 0 30 0 30 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -5) to (300 300 5) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 900 atoms - -set group all type/fraction 2 0.96 23984 - 861 settings made for type/fraction - -set type 1 mass 9 - 39 settings made for mass -set type 2 mass 1 - 861 settings made for mass - -velocity all create 1.44 87287 loop geom - -# multi neighbor and comm for efficiency - -neighbor 1 multi -neigh_modify delay 0 -comm_modify mode multi - -# colloid potential - -pair_style colloid 12.5 -pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5 -pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0 -pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5 - -fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -#dump 1 all atom 1000 dump.colloid - -#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 - -#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 - -thermo_style custom step temp epair etotal press vol -thermo 1000 - -timestep 0.005 - -run 50000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13.5 - ghost atom cutoff = 13.5 - binsize = 1.75 -> bins = 172 172 6 -Memory usage per processor = 3.86192 Mbytes -Step Temp E_pair TotEng Press Volume - 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000 - 1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011 - 2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014 - 3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78 - 4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579 - 5000 2.1407629 0.016107912 2.1544922 0.076141728 28576.1 - 6000 2.1131357 0.00050904012 2.1112969 0.095060602 21598.175 - 7000 2.0717026 0.013639823 2.0830406 0.11782618 17864.757 - 8000 2.0557671 0.015637275 2.0691201 0.13461012 15542.602 - 9000 2.052181 0.011294709 2.0611955 0.15150744 13852.149 - 10000 2.0531753 0.005995461 2.0568894 0.17005868 12487.961 - 11000 2.0458212 0.013960278 2.0575083 0.18853479 11391.15 - 12000 2.0405323 0.01846093 2.056726 0.20856764 10532.913 - 13000 2.0169788 0.041436672 2.0561744 0.23593917 9743.2413 - 14000 2.0381291 0.017030208 2.0528947 0.23907374 9093.804 - 15000 2.0400498 0.010140701 2.0479238 0.27667462 8571.3248 - 16000 2.0280005 0.024278921 2.0500261 0.31642444 8133.8701 - 17000 2.0330813 0.018237365 2.0490597 0.30128788 7764.8228 - 18000 2.0239878 0.02723825 2.0489771 0.30818234 7455.765 - 19000 2.0213402 0.035515393 2.0546096 0.39654991 7096.9286 - 20000 2.024466 0.032163441 2.0543801 0.37550172 6782.3498 - 21000 2.033932 0.017240839 2.0489129 0.39674508 6520.0345 - 22000 2.0204921 0.033630164 2.0518773 0.41617948 6306.7194 - 23000 2.0103922 0.046109389 2.0542679 0.44503939 6108.8439 - 24000 2.0063543 0.049507774 2.0536328 0.4949354 5923.2093 - 25000 1.9953872 0.066107231 2.0592773 0.5424389 5746.6695 - 26000 2.0416248 0.020853398 2.0602097 0.46642685 5593.8186 - 27000 2.0280574 0.037040684 2.0628447 0.49730884 5433.376 - 28000 2.0039648 0.055918617 2.0576568 0.56893257 5281.5584 - 29000 2.0042398 0.056161548 2.0581744 0.55361133 5164.0991 - 30000 2.031788 0.030776854 2.0603073 0.58478846 5056.2821 - 31000 2.0220647 0.044025601 2.0638435 0.60571441 4939.9798 - 32000 2.0115578 0.0548283 2.064151 0.62749615 4859.2601 - 33000 1.9905768 0.071616735 2.0599817 0.64066244 4787.7818 - 34000 2.0209823 0.052197269 2.0709341 0.68260584 4705.5825 - 35000 1.995165 0.078611977 2.0715601 0.69333031 4599.9346 - 36000 1.994471 0.079545726 2.0718006 0.7510532 4523.7494 - 37000 1.9939754 0.083417982 2.0751779 0.73746747 4449.8485 - 38000 1.9808613 0.098188975 2.0768493 0.89305039 4362.0588 - 39000 2.0056223 0.070537588 2.0739314 0.75049166 4320.201 - 40000 2.0490165 0.033488307 2.0802281 0.71809099 4259.8017 - 41000 2.0170375 0.066555481 2.0813519 0.80145545 4165.276 - 42000 2.034609 0.050123688 2.082472 0.7318767 4099.5342 - 43000 2.027217 0.053657298 2.0786218 0.79779536 4050.1962 - 44000 2.0107551 0.07427185 2.0827928 0.88949517 4022.2995 - 45000 2.035579 0.054511708 2.087829 0.85058092 3982.0592 - 46000 1.9855666 0.1079948 2.0913552 0.96268676 3937.279 - 47000 1.9938397 0.095380271 2.0870046 0.94036115 3882.9266 - 48000 2.0056151 0.087885527 2.0912722 0.94935203 3824.2309 - 49000 2.0079615 0.089440768 2.0951712 0.97596247 3781.8079 - 50000 1.9875181 0.10628651 2.0915963 1.1315334 3749.1501 -Loop time of 8.34943 on 1 procs for 50000 steps with 900 atoms - -Performance: 2587004.175 tau/day, 5988.436 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.9819 | 3.9819 | 3.9819 | 0.0 | 47.69 -Neigh | 1.3743 | 1.3743 | 1.3743 | 0.0 | 16.46 -Comm | 0.31324 | 0.31324 | 0.31324 | 0.0 | 3.75 -Output | 0.00052619 | 0.00052619 | 0.00052619 | 0.0 | 0.01 -Modify | 2.3748 | 2.3748 | 2.3748 | 0.0 | 28.44 -Other | | 0.3047 | | | 3.65 - -Nlocal: 900 ave 900 max 900 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 548 ave 548 max 548 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 6073 ave 6073 max 6073 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 6073 -Ave neighs/atom = 6.74778 -Neighbor list builds = 3122 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:08 diff --git a/examples/colloid/log.5Oct16.colloid.g++.4 b/examples/colloid/log.5Oct16.colloid.g++.4 deleted file mode 100644 index d3ce819286..0000000000 --- a/examples/colloid/log.5Oct16.colloid.g++.4 +++ /dev/null @@ -1,146 +0,0 @@ -LAMMPS (5 Oct 2016) -# Big colloid particles and small LJ particles - -units lj -atom_style sphere -dimension 2 - -lattice sq 0.01 -Lattice spacing in x,y,z = 10 10 10 -region box block 0 30 0 30 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -5) to (300 300 5) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 900 atoms - -set group all type/fraction 2 0.96 23984 - 861 settings made for type/fraction - -set type 1 mass 9 - 39 settings made for mass -set type 2 mass 1 - 861 settings made for mass - -velocity all create 1.44 87287 loop geom - -# multi neighbor and comm for efficiency - -neighbor 1 multi -neigh_modify delay 0 -comm_modify mode multi - -# colloid potential - -pair_style colloid 12.5 -pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5 -pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0 -pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5 - -fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -#dump 1 all atom 1000 dump.colloid - -#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5 - -#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5 -#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5 - -thermo_style custom step temp epair etotal press vol -thermo 1000 - -timestep 0.005 - -run 50000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13.5 - ghost atom cutoff = 13.5 - binsize = 1.75 -> bins = 172 172 6 -Memory usage per processor = 3.76692 Mbytes -Step Temp E_pair TotEng Press Volume - 0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000 - 1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011 - 2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014 - 3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78 - 4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579 - 5000 2.1407629 0.016107891 2.1544922 0.076141723 28576.1 - 6000 2.1131348 0.00051000844 2.1112968 0.095061489 21598.174 - 7000 2.0735911 0.011894403 2.0831815 0.11729552 17864.933 - 8000 2.0619661 0.0060168177 2.0656919 0.1295732 15547.781 - 9000 2.0595354 0.0024157411 2.0596627 0.14657861 13836.694 - 10000 2.0425447 0.018278949 2.0585541 0.1740235 12474.354 - 11000 2.0460068 0.012079252 2.0558127 0.19227728 11392.874 - 12000 2.0372027 0.019110617 2.0540498 0.21648482 10523.896 - 13000 2.0416804 0.015790699 2.0552026 0.24604625 9785.1314 - 14000 2.0466943 0.0064454505 2.0508656 0.22777839 9165.8411 - 15000 2.0436536 0.015576669 2.0569595 0.28266826 8582.5053 - 16000 2.0335541 0.01998798 2.0512825 0.2894612 8114.5044 - 17000 2.0109406 0.039132968 2.0478392 0.34665262 7758.9312 - 18000 2.016964 0.038362354 2.0530852 0.37108874 7399.6774 - 19000 2.0399584 0.012731426 2.0504232 0.32979629 7081.8066 - 20000 2.0260154 0.027880228 2.0516445 0.36371005 6812.6037 - 21000 2.0321966 0.023814364 2.053753 0.36376888 6556.4552 - 22000 1.9850947 0.072749763 2.0556388 0.52542507 6293.5003 - 23000 2.0360536 0.02395391 2.0577452 0.42540507 6061.6557 - 24000 2.0237181 0.032711377 2.0541809 0.43998497 5883.2886 - 25000 2.0145711 0.042376354 2.0547091 0.54706192 5715.4423 - 26000 2.00533 0.049986982 2.0530888 0.55453953 5564.0132 - 27000 2.0266398 0.035044901 2.0594329 0.51842026 5431.0259 - 28000 2.0321757 0.029913711 2.0598314 0.49663872 5305.2909 - 29000 1.9964359 0.066498777 2.0607164 0.56461185 5174.9947 - 30000 1.982908 0.082624709 2.0633294 0.65815484 5046.1903 - 31000 2.0141773 0.049027808 2.0609671 0.58512256 4980.1474 - 32000 1.9938427 0.076695158 2.0683225 0.64309333 4844.0907 - 33000 2.012869 0.054851302 2.0654838 0.63073652 4749.9868 - 34000 1.9867827 0.083467738 2.0680429 0.7840696 4656.3038 - 35000 2.0013706 0.067630614 2.0667775 0.72991936 4566.7052 - 36000 2.0106349 0.063148106 2.071549 0.73927159 4495.7351 - 37000 2.0245299 0.053399546 2.07568 0.7189467 4423.018 - 38000 2.0133929 0.062427506 2.0735833 0.74002573 4351.9277 - 39000 1.9874796 0.088021324 2.0732926 0.79349127 4293.1815 - 40000 2.0240342 0.057908137 2.0796935 0.75182186 4235.9306 - 41000 1.9973584 0.077969812 2.0731089 0.83868109 4218.8397 - 42000 2.0034131 0.079826384 2.0810134 0.78010078 4179.2254 - 43000 2.0438594 0.047617472 2.0892059 0.77402823 4089.0577 - 44000 2.021871 0.066506327 2.0861308 0.82593265 3999.9932 - 45000 2.0052391 0.07876379 2.0817748 0.84100298 3958.8163 - 46000 2.0163501 0.073621087 2.0877308 0.8621767 3920.4982 - 47000 2.020619 0.067706551 2.0860804 0.92651509 3885.827 - 48000 2.0168306 0.082111421 2.0967011 0.9214563 3829.1155 - 49000 2.0007804 0.098241181 2.0967985 0.93140657 3755.3901 - 50000 2.0213773 0.071280328 2.0904116 0.9408025 3734.5105 -Loop time of 3.66837 on 4 procs for 50000 steps with 900 atoms - -Performance: 5888181.024 tau/day, 13630.049 timesteps/s -98.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0038 | 1.0256 | 1.0441 | 1.4 | 27.96 -Neigh | 0.33784 | 0.35406 | 0.36994 | 2.1 | 9.65 -Comm | 0.82073 | 0.85742 | 0.88285 | 2.5 | 23.37 -Output | 0.00096369 | 0.0010209 | 0.0011663 | 0.3 | 0.03 -Modify | 1.178 | 1.1807 | 1.1825 | 0.1 | 32.19 -Other | | 0.2496 | | | 6.80 - -Nlocal: 225 ave 234 max 208 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 305.25 ave 313 max 299 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Neighs: 1501.75 ave 1627 max 1408 min -Histogram: 1 0 1 0 1 0 0 0 0 1 - -Total # of neighbors = 6007 -Ave neighs/atom = 6.67444 -Neighbor list builds = 3071 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/comb/ffield.comb b/examples/comb/ffield.comb deleted file mode 100644 index 2e685a9ed4..0000000000 --- a/examples/comb/ffield.comb +++ /dev/null @@ -1,98 +0,0 @@ -# DATE: 2011-02-22 DATE: 2010-12-17 CONTRIBUTOR: Tzu-Ray Shan, tnshan@sandia.gov CITATION: Shan, Devine, Sinnott and Phillpot, Phys Rev B, 81, 125328 (2010) -# COMB parameters for various elements (Si, Cu, Hf, Ti, O) and mixtures (their oxides and alloys) -# Edited by Tzu-Ray Shan from MSE, Univ. FL in Apr 2010 -# -# Elements currently available: Si, Cu, Hf, Ti -# Oxides currently available: Si-O, Cu-O, Hf-O, Ti-O -# Other interactions available: Cu-Ti, Cu-Si, Si-Hf -# -# Si parameter set from (JG Yu, SB Sinnott, SR Phillpot, Phys. Rev. B 75 085311 2007) -# ,and (TR Shan, BD Devine, SR Phillpot, SB Sinnott, to be sub to Phys. Rev. B) -# O parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010) -# Cu parameter set from (BD Devine, TR Shan, SB Sinnott, SR Phillpot, to be sub to Phys. Rev. B) -# Hf parameter set from (TR Shan, BD Devine, SB Sinnott, SR Phillpot, Phys. Rev. B 81 125328 2010) -# Ti parameter set from (TR Shan, SR Phillpot, SB Sinnott, in preparation) -# -# Multiple entries can be added to this file, LAMMPS reads the ones it needs -# Only M-O are added in the potential table, using mixing rules to generate desired alloy (A-B) parameters -# 8 entries for a desired A-B type: AAA, BBB, AAB, ABA, ABB, BAA, BBA, BBA -# 27 entries for a system containing three elements A, B and C -# These entries are in LAMMPS "metal" units -# -Hf Hf Hf 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.85 0.20 2.069563 2.069563 707.53 707.53 0 0 0.008 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0 -Ti Ti Ti 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.43 0.05 2.082408 2.082408 546.386 546.386 0 0 0.0084 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 2.46820415900968 0 0.151351003255176 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0 -O O O 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.8 0.2 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0 -Cu Cu Cu 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 3.0 0.05 2.794608 2.794608 952.693 952.693 0.077 0.0095 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0 -Si Si Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0 -Zr Zr Zr 1 0 1 0 1 0 0.929 0.929 39.9454 39.9454 3.8 0.31 1.857 1.857 382.6 382.6 0 0 0 0 0 0 1 1 1 1 -4 4 1.64 -1.5 -4 4 1.64 -1.5 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0 -U U U 1 0 1 0 4.346966 0.77617 0.832 0.832 162.6 162.6 3.9 0.15 1.835 1.835 795.6 795.6 0 0 0 0 0 0 1 1 1 1 -4 4 2 -2 -4 4 2 -2 0 3.139520d0 0 0.009410d0 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0 -# -Si O O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 109.47 0.3122 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0 -O Si Si 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 143.73 2.6 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0 -Si O Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0 -O Si O 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.20 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0 -Si Si O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.80 0.25 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0 -O O Si 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.25 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0 -# -Si Cu Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 3.05 0.15 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -7 1 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0 -Cu Si Si 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 3.05 0.15 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -7 1 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0 -Si Cu Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 3.05 0.15 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -7 1 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0 -Cu Si Cu 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 3.05 0.15 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1 1 1 1 -7 1 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0 -Si Si Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 2.90 0.10 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0 -Cu Cu Si 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 3.25 0.10 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -7 1 0.1677645 -0.161007 -7 1 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0 -# -Si O Cu 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 2.80 0.25 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1.276957 0.452693 1.032042 1.354486 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0 -Cu O Si 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.55 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.100000 1.097775 0.584713 1.666072 -7 1 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0 -Si Cu O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.681711 471.18 146.987 3.05 0.15 2.4799 2.794608 1830.8 952.693 0 0 0 0 0 0 1.276957 0.452693 1.032042 1.354486 -4 4 1.651725 -1.658949 -7 1 0.1677645 -0.161007 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 0.72571 2.999911 0.274649 12 0 -Cu Si O 1 0 1 0 1 0.140835 1.681711 1.7322 146.987 471.18 3.05 0.15 2.794608 2.4799 952.693 1830.8 0 0 0 0 0 0 1.0 1.0 1.0 1.0 -7 1 0.1677645 -0.161007 -4 4 1.651725 -1.658949 0 5.946437 0 0 0 0.454784 0.72571 -0.499378 0.274649 2.999911 12 0 -O Si Cu 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 2.80 0.25 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1.0 1.0 1.0 1.0 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0 -O Cu Si 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.55 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.100000 1.097775 0.584713 1.666072 -1.8349 5.5046 0.00148 -0.00112 -7 1 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0 -# -Cu O O 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.80 0.15 2.794608 5.36 952.693 3326.69 0 0 0 180.0 2.518789 0 0.100000 1.097775 0.584713 1.666072 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0 -O Cu Cu 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.80 0.15 5.36 2.794608 3326.69 952.693 0 0 0 109.47 0.007858 0 0.100000 1.097775 0.584713 1.666072 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0 -Cu O Cu 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.80 0.15 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.100000 1.097775 0.584713 1.666072 -6 2 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0 -O Cu O 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.80 0.15 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.100000 1.097775 0.584713 1.666072 -1.8349 5.5046 0.00148 -0.00112 -6 2 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0 -Cu Cu O 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 3.30 0.15 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -6 2 0.1677645 -0.161007 -6 2 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0 -O O Cu 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.20 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0 -# -Si Hf Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0 -Hf Si Si 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0 -Si Hf Si 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0 -Hf Si Hf 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0 -Si Si Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 1.7322 471.18 471.18 3.26 0.15 2.4799 2.4799 1830.8 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 1.651725 -1.658949 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -0.499378 2.999911 2.999911 12 0 -Hf Hf Si 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.26 0.15 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.92875 4.83958 4.83958 12 0 -# -Si O Hf 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 2.68 471.18 260.893 3.196 0.21 2.4799 5.36 1830.8 3326.69 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -1.8349 5.5046 0.00148 -0.00112 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.922011 2.999911 0.971086 12 0 -Hf O Si 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.196 0.21 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.28 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.719131 -3.92875 -3.922011 4.83958 0.971086 12 0.32 -Si Hf O 3 100390 16.218 -0.59826 0.78734 1.0999E-06 1.7322 0.959614 471.18 55.9421 3.26 0.15 2.4799 2.069563 1830.8 707.53 0 0 0 0 0 0 1 1 1 1 -4 4 1.651725 -1.658949 -4 4 0.26152 -0.25918 0 3.625144859 0 0.087067714 0 0.772871 -0.499378 -3.92875 2.999911 4.83958 12 0 -Hf Si O 1 0 1 0 1.011011 0.046511 0.959614 1.7322 55.9421 471.18 3.26 0.15 2.069563 2.4799 707.53 1830.8 0 0 0 0 0 0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 1.651725 -1.658949 0 3.13952 0 0.00941 0 0.719131 -3.92875 -0.499378 4.83958 2.999911 12 0 -O Si Hf 1 6.6 1 -0.229 1 2 2.68 1.7322 260.893 471.18 3.196 0.21 5.36 2.4799 3326.69 1830.8 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 1.651725 -1.658949 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -0.499378 0.971086 2.999911 12 0 -O Hf Si 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.196 0.21 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.28 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.30 -# -Hf O O 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.30 0.075 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.28 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.32 -O Hf Hf 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.30 0.075 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.28 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.32 -Hf O Hf 1 0 1 0 1.011011 0.046511 0.959614 2.68 55.9421 260.893 3.30 0.075 2.069563 5.36 707.53 3326.69 0 0 0 0 0 0.28 1 1 1 1 -4 4 0.26152 -0.25918 -1.8349 5.5046 0.00148 -0.00112 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.922011 4.83958 0.971086 12 0.32 -O Hf O 1 6.6 1 -0.229 1 2 2.68 0.959614 260.893 55.9421 3.30 0.075 5.36 2.069563 3326.69 707.53 0 0 0 0 0 0.28 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -4 4 0.26152 -0.25918 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.92875 0.971086 4.83958 12 0.32 -Hf Hf O 1 0 1 0 1.011011 0.046511 0.959614 0.959614 55.9421 55.9421 3.30 0.075 2.069563 2.069563 707.53 707.53 0 0 0 0 0 0.0 1 1 1 1 -4 4 0.26152 -0.25918 -4 4 0.26152 -0.25918 0 3.13952 0 0.00941 0 0.679131 -3.92875 -3.92875 4.83958 4.83958 12 0.0 -O O Hf 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.10 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0.0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0.0 -# -Ti O O 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 90 0.403105 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0 -O Ti Ti 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 130.54 0.202777 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0 -Ti O Ti 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0 -O Ti O 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0 -Ti Ti O 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.43 0.05 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0 -O O Ti 1 6.6 1 -0.229 1 2 2.68 2.68 260.893 260.893 2.80 0.10 5.36 5.36 3326.69 3326.69 0 0 0 0 0 0 1 1 1 1 -1.8349 5.5046 0.00148 -0.00112 -1.8349 5.5046 0.00148 -0.00112 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 -3.922011 0.971086 0.971086 12 0 -# -Ti Cu Cu 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 4.45 0.10 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 0.098179 1.662238 0.104821 10.000363 -4 4 2.508854 -2.511416 -7.2 0.8 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0 -Cu Ti Ti 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 4.45 0.10 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 0.098179 1.662238 0.104821 10.000363 -7.2 0.8 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0 -Ti Cu Ti 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 4.45 0.10 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 0.098179 1.662238 0.104821 10.000363 -4 4 2.508854 -2.511416 -7.2 0.8 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0 -Cu Ti Cu 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 4.45 0.10 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 0.098179 1.662238 0.104821 10.000363 -7.2 0.8 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0 -Ti Ti Cu 1 0 1 0 1.255016 0.089078 1.226342 1.226342 99.3916 99.3916 3.41 0.15 2.082408 2.082408 546.386 546.386 0 0 0 0 0 0 1 1 1 1 -4 4 2.508854 -2.511416 -4 4 2.508854 -2.511416 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.392632 1.78349 1.78349 12 0 -Cu Cu Ti 1 0 1 0 1 0.140835 1.681711 1.681711 146.987 146.987 3.25 0.10 2.794608 2.794608 952.693 952.693 0 0 0 0 0 0 1 1 1 1 -7.2 0.8 0.1677645 -0.161007 -7.2 0.8 0.1677645 -0.161007 0 5.946437 0 0 0 0.454784 0.72571 0.72571 0.274649 0.274649 12 0 -# -Ti O Cu 1 0 1 0 1.255016 0.089078 1.226342 2.68 99.3916 260.893 3.25 0.10 2.082408 5.36 546.386 3326.69 0 0 0 0 0 8.45 0.088406 0.969934 0.296577 1.326746 -4 4 2.508854 -2.511416 -1.8349 5.5046 0.00148 -0.00112 0 1.943430774 0 0.254695274 0 0.873685 0.392632 -3.922011 1.78349 0.971086 12 0 -Cu O Ti 1 0 1 0 1 0.140835 1.681711 2.68 146.987 260.893 2.55 0.10 2.794608 5.36 952.693 3326.69 0 0 0 0 0 0 0.100000 1.097775 0.584713 1.666072 -7.2 0.8 0.1677645 -0.161007 -1.8349 5.5046 0.00148 -0.00112 0 5.946437 0 0 0 0.454784 0.72571 -3.922011 0.274649 0.971086 12 0 -Ti Cu O 1 0 1 0 1.255016 0.089078 1.226342 1.681711 99.3916 146.987 4.45 0.10 2.082408 2.794608 546.386 952.693 0 0 0 0 0 0 0.098179 1.662238 0.104821 10.000363 -4 4 2.508854 -2.511416 -7.2 0.8 0.1677645 -0.161007 0 1.943430774 0 0.254695274 0 0.873685 0.392632 0.72571 1.78349 0.274649 12 0 -Cu Ti O 1 0 1 0 1 0.140835 1.681711 1.226342 146.987 99.3916 4.45 0.10 2.794608 2.082408 952.693 546.386 0 0 0 0 0 0 0.098179 1.662238 0.104821 10.000363 -7.2 0.8 0.1677645 -0.161007 -4 4 2.508854 -2.511416 0 5.946437 0 0 0 0.454784 0.72571 0.392632 0.274649 1.78349 12 0 -O Ti Cu 1 6.6 1 -0.229 1 2 2.68 1.226342 260.893 99.3916 3.25 0.10 5.36 2.082408 3326.69 546.386 0 0 0 0 0 0.00 0.088406 0.969934 0.296577 1.326746 -1.8349 5.5046 0.00148 -0.00112 -4 4 2.508854 -2.511416 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.392632 0.971086 1.78349 12 0 -O Cu Ti 1 6.6 1 -0.229 1 2 2.68 1.681711 260.893 146.987 2.55 0.10 5.36 2.794608 3326.69 952.693 0 0 0 0 0 0 0.100000 1.097775 0.584713 1.666072 -1.8349 5.5046 0.00148 -0.00112 -7.2 0.8 0.1677645 -0.161007 5.63441383 7.689598017 4.51426991 1.330079082 0 2.243072 -3.922011 0.72571 0.971086 0.274649 12 0 diff --git a/examples/comb/ffield.comb b/examples/comb/ffield.comb new file mode 120000 index 0000000000..09ef443f91 --- /dev/null +++ b/examples/comb/ffield.comb @@ -0,0 +1 @@ +../../potentials/ffield.comb \ No newline at end of file diff --git a/examples/comb/ffield.comb3 b/examples/comb/ffield.comb3 deleted file mode 100644 index 3c69fe9a2b..0000000000 --- a/examples/comb/ffield.comb3 +++ /dev/null @@ -1,523 +0,0 @@ - # DATE: 2014-02-01 DATE: 2013-11-04 CONTRIBUTOR: Tzu-Ray Shan, tnshan@sandia.gov CITATION: Liang, Shan, Cheng, Devine, Noordhoek, Li, Lu, Phillpot and Sinnott, Mater Sci Eng Rep, 74, 255-279 (2013) - # ffield.comb3 file for LAMMPS/COMB3, converted from COMB3 code parameters O Cu N C H Ti Zn Zr - # Converted on: 2014-01-30 - # - # Please cite the following publication for the use of LAMMPS-COMB3. - # Tao Liang, Tzu-Ray Shan, Yu-Ting Cheng, Bryce D. Devine, Mark Noordhoek, Yangzhong Li, Zhize Lu, Simon R. Phillpot,and Susan B. Sinnott, "Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials", Materials Science and Engineering: Reports, 74 (2013) 255-279. - # List of Changes since 2013-Sep: - # 1) CH4 has been changed. - # 2) Include ZrO2 force fields - # 3) Change correction terms from Legendre polynomials and bond bending to 6th order polynomials. - # -O O O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O Zn 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O O Zr 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.1823933E+00 0.9323800E-02 -0.1534590E-01 0.1691170E-01 -0.1317600E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O Cu Zr 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O N O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O N Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 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0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O C O 3 1 3 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 0.9882114E-01 0.1756465E-01 -0.2570172E-01 -0.1543155E+01 -0.9607860E-03 -0.7667515E+00 0.2371642E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 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0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 0.9882114E-01 0.1756465E-01 -0.2570172E-01 -0.1543155E+01 -0.9607860E-03 -0.7667515E+00 0.2371642E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O C C 3 1 1 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 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0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 0.9882114E-01 0.1756465E-01 -0.2570172E-01 -0.1543155E+01 -0.9607860E-03 -0.7667515E+00 0.2371642E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -O C Ti 3 1 2 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 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0.2900000E+01 0.1999999E+00 0.2725394E+02 0.2296021E+02 0.1245935E+02 -0.1753586E+02 0.5192187E+01 -0.1653414E+01 0.1298779E+01 0.1225438E+00 -0.4639774E+01 -0.2839011E+00 0.4639774E+01 -0.2061724E+00 0.6113230E-01 0.2061476E+01 0.3501339E+00 -0.3704719E+01 -0.6328295E+00 0.1819703E+01 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 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0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 -0.1261294E+01 0.1861535E+00 -0.1392390E-01 -0.9679700E-02 0.5166700E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu O Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu O 2 2 3 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu Cu 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4356100E-01 0.0000000E+00 0.4919500E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu N 2 2 3 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu C 2 2 1 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu H 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu Ti 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu Zn 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Cu Zr 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu N Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C O 2 1 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 -0.1098346E+00 0.4752372E+00 -0.8442600E-02 0.8754500E-02 0.3760100E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C Cu 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C N 2 1 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C C 2 1 1 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C H 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C Ti 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C Zn 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu C Zr 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H O 2 2 3 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H Cu 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H N 2 2 3 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H C 2 2 1 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H H 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H Ti 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H Zn 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu H Zr 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8454920E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Ti Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zn Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Cu Zr Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O Zn 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N O Zr 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Cu Zr 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N Zn 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N N Zr 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C O 3 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C Cu 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C N 3 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C C 3 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C H 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C Ti 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C Zn 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N C Zr 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N H Zr 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Ti Zr 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.5066036E+01 0.2800000E+01 0.2000000E+00 0.0000000E+00 0.2300000E-04 0.1728730E-01 0.4126639E+00 0.2633349E+00 -0.1032680E+00 0.2487740E-01 -0.5651670E-01 -0.3633110E-01 0.7137000E-02 0.6461960E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zn Zr 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -N Zr Zr 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O O 1 3 3 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O Cu 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1927749E+01 0.4492100E-02 0.7269000E-03 -0.1982700E-02 0.3811860E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O N 1 3 3 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O C 1 3 1 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 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0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O Ti 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O Zn 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C O Zr 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2502470E+01 0.6121492E-02 0.4192692E-01 -0.2181554E-02 0.6907540E+01 0.5222031E+01 0.2132357E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu O 1 2 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 -0.4855090E+00 0.3652260E-01 -0.9130700E-02 -0.1658200E-02 0.2825080E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu Cu 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu N 1 2 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu C 1 2 1 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu H 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu Ti 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu Zn 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Cu Zr 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 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0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C H O 1 2 3 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 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0.2070231E+00 -0.2066751E-01 0.1739971E+00 0.4435496E+00 -0.4620521E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C H Zn 1 2 2 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.1555865E+00 -0.1104684E-01 0.2070231E+00 -0.2066751E-01 0.1739971E+00 0.4435496E+00 -0.4620521E-01 0.0000000E+00 0.0000000E+00 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Ti Cu 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Ti N 1 2 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -C Ti C 1 2 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 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0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Cu Zn 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 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0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H N Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H C O 2 1 3 0 0 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.3251163E+00 0.1750000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H C Cu 2 1 2 0 0 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.3251163E+00 0.1750000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H C N 2 1 3 0 0 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.3251163E+00 0.1750000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H C C 2 1 1 0 0 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.3251163E+00 0.1750000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6366328E+00 -0.1273266E+01 0.6366328E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H C H 2 1 2 0 0 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.3251163E+00 0.1750000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5145789E+00 -0.1029158E+01 0.5145789E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H C Ti 2 1 2 0 0 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 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0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Ti Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zn Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 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0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zr Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 0.1005881E+01 0.9799900E-01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1510666E+01 0.1549729E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2029568E+01 0.2697819E+03 0.4498000E-03 0.2800000E+01 0.2000001E+00 0.4379410E+00 0.9582117E+00 0.1036535E+00 -0.7001700E+00 0.2999763E+00 0.1651448E+00 0.1011453E+00 -0.1624493E+00 0.4351683E+01 -0.2971600E-02 -0.4351683E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zr N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 0.1005881E+01 0.9799900E-01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1510666E+01 0.1549729E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2029568E+01 0.2697819E+03 0.4498000E-03 0.2800000E+01 0.2000001E+00 0.4379410E+00 0.9582117E+00 0.1036535E+00 -0.7001700E+00 0.2999763E+00 0.1651448E+00 0.1011453E+00 -0.1624493E+00 0.4351683E+01 -0.2971600E-02 -0.4351683E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zr C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 0.1005881E+01 0.9799900E-01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1510666E+01 0.1549729E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2029568E+01 0.2697819E+03 0.4498000E-03 0.2800000E+01 0.2000001E+00 0.4379410E+00 0.9582117E+00 0.1036535E+00 -0.7001700E+00 0.2999763E+00 0.1651448E+00 0.1011453E+00 -0.1624493E+00 0.4351683E+01 -0.2971600E-02 -0.4351683E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zr H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 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0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 0.1005881E+01 0.9799900E-01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1510666E+01 0.1549729E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2029568E+01 0.2697819E+03 0.4498000E-03 0.2800000E+01 0.2000001E+00 0.4379410E+00 0.9582117E+00 0.1036535E+00 -0.7001700E+00 0.2999763E+00 0.1651448E+00 0.1011453E+00 -0.1624493E+00 0.4351683E+01 -0.2971600E-02 -0.4351683E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zr Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 0.1005881E+01 0.9799900E-01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1510666E+01 0.1549729E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2029568E+01 0.2697819E+03 0.4498000E-03 0.2800000E+01 0.2000001E+00 0.4379410E+00 0.9582117E+00 0.1036535E+00 -0.7001700E+00 0.2999763E+00 0.1651448E+00 0.1011453E+00 -0.1624493E+00 0.4351683E+01 -0.2971600E-02 -0.4351683E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -H Zr Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 0.1005881E+01 0.9799900E-01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1510666E+01 0.1549729E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2029568E+01 0.2697819E+03 0.4498000E-03 0.2800000E+01 0.2000001E+00 0.4379410E+00 0.9582117E+00 0.1036535E+00 -0.7001700E+00 0.2999763E+00 0.1651448E+00 0.1011453E+00 -0.1624493E+00 0.4351683E+01 -0.2971600E-02 -0.4351683E+01 -0.2179000E-01 0.8986300E-02 0.3036884E+00 -0.2740163E+00 -0.9159242E+00 0.3626548E+00 0.7262178E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti O Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2129506E+01 0.2125257E+03 0.2142030E+01 0.1834730E+03 0.2030774E+01 0.1819432E+03 0.2868830E+01 0.1556206E+04 0.7912737E+00 0.3000000E+01 0.2000000E+00 0.4997810E-01 0.1546093E+00 0.4452330E-01 0.1693955E+00 0.1796268E+00 -0.2398841E+00 0.1848422E+00 -0.3457300E-02 -0.2265040E-01 0.1666560E-01 -0.3002200E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Cu Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti N Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.2453223E+01 0.1048055E+03 0.1766886E+01 0.1359923E+03 0.2439896E+01 0.3011201E+02 0.3178150E+01 0.1661766E+04 0.2297286E+01 0.2800000E+01 0.2000000E+00 0.2600000E-05 0.2240000E-04 -0.1131598E+00 0.3359560E-01 0.2616125E+00 0.2691128E+00 0.2251859E+00 -0.3203870E-01 -0.8235410E-01 0.2447850E-01 -0.7318660E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C O 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C Cu 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C N 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C C 2 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C H 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C Ti 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti C Zn 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 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0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti H Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.4356100E-01 0.0000000E+00 0.4919500E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Ti Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zn Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Ti Zr Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.3022933E+01 0.0000000E+00 0.3000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn O Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Cu Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn N Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C O 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C Cu 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C N 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C C 2 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C H 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C Ti 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C Zn 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn C Zr 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn H Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Ti Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 -0.6320000E-04 0.0000000E+00 0.1327400E-02 0.0000000E+00 -0.3982300E-02 0.0000000E+00 0.2920300E-02 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zn Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zn Zr Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.2106498E+01 0.4591872E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1347245E+01 0.1273479E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3598641E+01 0.4490868E+04 0.2460319E+01 0.2900000E+01 0.1999999E+00 0.5639262E+00 0.9034689E+00 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0.1000000E+01 -Zr Cu Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1264685E+01 0.1080820E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2266721E+01 0.5995921E+03 0.1769288E+01 0.3577135E+01 0.1269172E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr N Zr 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2400415E+01 0.4887068E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3519722E+01 0.1965532E+04 0.2905018E+01 0.2865151E+01 0.1375146E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr C O 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 0.2417269E+00 0.3186964E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1840783E+01 0.6151236E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2570545E+01 0.1860857E+04 0.1840783E+01 0.2790000E+01 0.1500000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr C Cu 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 0.2417269E+00 0.3186964E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1840783E+01 0.6151236E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2570545E+01 0.1860857E+04 0.1840783E+01 0.2790000E+01 0.1500000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr C N 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 0.2417269E+00 0.3186964E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1840783E+01 0.6151236E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2570545E+01 0.1860857E+04 0.1840783E+01 0.2790000E+01 0.1500000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr C C 2 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 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0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Ti Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1120556E+01 0.1153115E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1978709E+01 0.5105993E+03 0.1625159E+01 0.3908963E+01 0.1000265E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zn Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1713420E+01 0.4276226E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2229990E+01 0.1162104E+04 0.2218023E+01 0.3656498E+01 0.1000958E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 -Zr Zr Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 diff --git a/examples/comb/ffield.comb3 b/examples/comb/ffield.comb3 new file mode 120000 index 0000000000..5adce311f5 --- /dev/null +++ b/examples/comb/ffield.comb3 @@ -0,0 +1 @@ +../../potentials/ffield.comb3 \ No newline at end of file diff --git a/examples/comb/log.5Oct16.comb.Cu.g++.1 b/examples/comb/log.27Nov18.comb.Cu.g++.1 similarity index 80% rename from examples/comb/log.5Oct16.comb.Cu.g++.1 rename to examples/comb/log.27Nov18.comb.Cu.g++.1 index 0c419fa142..d5a334a1b5 100644 --- a/examples/comb/log.5Oct16.comb.Cu.g++.1 +++ b/examples/comb/log.27Nov18.comb.Cu.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pure Cu crystal, structure created by LAMMPS, qeq off units metal @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 0) to (14.46 14.46 14.46) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 256 atoms + Time spent = 0.000869274 secs mass 1 63.54 pair_style comb @@ -42,13 +44,18 @@ thermo 1 run 10 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 1 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 3 3 3 -Memory usage per processor = 6.4805 Mbytes + binsize = 6.25, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.469 | 7.469 | 7.469 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0 1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0 @@ -61,20 +68,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0 9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0 10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0 -Loop time of 0.244011 on 1 procs for 10 steps with 256 atoms +Loop time of 0.169334 on 1 procs for 10 steps with 256 atoms -Performance: 0.708 ns/day, 33.890 hours/ns, 40.982 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.020 ns/day, 23.519 hours/ns, 59.055 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.24357 | 0.24357 | 0.24357 | 0.0 | 99.82 +Pair | 0.16875 | 0.16875 | 0.16875 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00023103 | 0.00023103 | 0.00023103 | 0.0 | 0.09 -Output | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 0.05 -Modify | 4.7445e-05 | 4.7445e-05 | 4.7445e-05 | 0.0 | 0.02 -Other | | 5.651e-05 | | | 0.02 +Comm | 0.00034857 | 0.00034857 | 0.00034857 | 0.0 | 0.21 +Output | 0.0001359 | 0.0001359 | 0.0001359 | 0.0 | 0.08 +Modify | 4.1485e-05 | 4.1485e-05 | 4.1485e-05 | 0.0 | 0.02 +Other | | 5.889e-05 | | | 0.03 Nlocal: 256 ave 256 max 256 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/comb/log.5Oct16.comb.Cu.g++.4 b/examples/comb/log.27Nov18.comb.Cu.g++.4 similarity index 80% rename from examples/comb/log.5Oct16.comb.Cu.g++.4 rename to examples/comb/log.27Nov18.comb.Cu.g++.4 index d9b3aed9b0..bd37372709 100644 --- a/examples/comb/log.5Oct16.comb.Cu.g++.4 +++ b/examples/comb/log.27Nov18.comb.Cu.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pure Cu crystal, structure created by LAMMPS, qeq off units metal @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 0) to (14.46 14.46 14.46) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 256 atoms + Time spent = 0.000329494 secs mass 1 63.54 pair_style comb @@ -42,13 +44,18 @@ thermo 1 run 10 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 1 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 3 3 3 -Memory usage per processor = 6.35565 Mbytes + binsize = 6.25, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.951 | 6.951 | 6.951 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0 1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0 @@ -61,20 +68,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0 9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0 10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0 -Loop time of 0.0643001 on 4 procs for 10 steps with 256 atoms +Loop time of 0.0479479 on 4 procs for 10 steps with 256 atoms -Performance: 2.687 ns/day, 8.931 hours/ns, 155.521 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.604 ns/day, 6.659 hours/ns, 208.560 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.062855 | 0.063074 | 0.063304 | 0.1 | 98.09 +Pair | 0.043196 | 0.044313 | 0.045375 | 0.4 | 92.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00061822 | 0.00085837 | 0.0010862 | 0.6 | 1.33 -Output | 0.00021434 | 0.00023013 | 0.00025868 | 0.1 | 0.36 -Modify | 1.4782e-05 | 1.6153e-05 | 1.7405e-05 | 0.0 | 0.03 -Other | | 0.0001218 | | | 0.19 +Comm | 0.0020213 | 0.0028703 | 0.0042944 | 1.7 | 5.99 +Output | 0.00023198 | 0.00052303 | 0.00077415 | 0.0 | 1.09 +Modify | 1.4782e-05 | 1.657e-05 | 1.812e-05 | 0.0 | 0.03 +Other | | 0.0002254 | | | 0.47 Nlocal: 64 ave 64 max 64 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.1 b/examples/comb/log.27Nov18.comb.Cu2O.elastic.g++.1 similarity index 81% rename from examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.1 rename to examples/comb/log.27Nov18.comb.Cu2O.elastic.g++.1 index 0a1d16e25f..3c44febf60 100644 --- a/examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.1 +++ b/examples/comb/log.27Nov18.comb.Cu2O.elastic.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Cu2O crystal, qeq on, minimizes, then calculates elastic constants units metal @@ -44,31 +45,36 @@ fix 2 all qeq/comb 1 0.0001 run 2 Neighbor list info ... - 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 6.39852 Mbytes + binsize = 6.25, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.865 | 9.865 | 9.865 Mbytes Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568 1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568 2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568 -Loop time of 0.661607 on 1 procs for 2 steps with 1296 atoms +Loop time of 0.598454 on 1 procs for 2 steps with 1296 atoms -Performance: 0.052 ns/day, 459.449 hours/ns, 3.023 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.058 ns/day, 415.593 hours/ns, 3.342 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.26068 | 0.26068 | 0.26068 | 0.0 | 39.40 +Pair | 0.17797 | 0.17797 | 0.17797 | 0.0 | 29.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00010204 | 0.00010204 | 0.00010204 | 0.0 | 0.02 -Output | 5.4836e-05 | 5.4836e-05 | 5.4836e-05 | 0.0 | 0.01 -Modify | 0.40072 | 0.40072 | 0.40072 | 0.0 | 60.57 -Other | | 4.601e-05 | | | 0.01 +Comm | 0.00016093 | 0.00016093 | 0.00016093 | 0.0 | 0.03 +Output | 9.1314e-05 | 9.1314e-05 | 9.1314e-05 | 0.0 | 0.02 +Modify | 0.42019 | 0.42019 | 0.42019 | 0.0 | 70.21 +Other | | 3.576e-05 | | | 0.01 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -87,15 +93,8 @@ Dangerous builds not checked unfix 1 fix 1 all box/relax aniso 0.0 vmax 0.001 minimize 1.0e-14 1.0e-20 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 8.27781 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 11.74 | 11.74 | 11.74 Mbytes Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568 3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169 @@ -122,9 +121,9 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913 25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914 -Loop time of 29.3376 on 1 procs for 24 steps with 1296 atoms +Loop time of 28.4763 on 1 procs for 24 steps with 1296 atoms -99.9% CPU use with 1 MPI tasks x no OpenMP threads +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -138,12 +137,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.5417 | 7.5417 | 7.5417 | 0.0 | 25.71 -Neigh | 0.071155 | 0.071155 | 0.071155 | 0.0 | 0.24 -Comm | 0.0031855 | 0.0031855 | 0.0031855 | 0.0 | 0.01 -Output | 0.00070429 | 0.00070429 | 0.00070429 | 0.0 | 0.00 -Modify | 21.709 | 21.709 | 21.709 | 0.0 | 74.00 -Other | | 0.01167 | | | 0.04 +Pair | 5.1932 | 5.1932 | 5.1932 | 0.0 | 18.24 +Neigh | 0.078665 | 0.078665 | 0.078665 | 0.0 | 0.28 +Comm | 0.0045877 | 0.0045877 | 0.0045877 | 0.0 | 0.02 +Output | 0.0010743 | 0.0010743 | 0.0010743 | 0.0 | 0.00 +Modify | 23.184 | 23.184 | 23.184 | 0.0 | 81.42 +Other | | 0.0143 | | | 0.05 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -163,31 +162,24 @@ min_modify dmax 0.2 line quadratic unfix 1 fix 1 all nve run 1 -Neighbor list info ... - 1 neighbor list requests - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 6.65281 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.12 | 10.12 | 10.12 Mbytes Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914 27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914 -Loop time of 0.273439 on 1 procs for 1 steps with 1296 atoms +Loop time of 0.236144 on 1 procs for 1 steps with 1296 atoms -Performance: 0.063 ns/day, 379.776 hours/ns, 3.657 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.073 ns/day, 327.978 hours/ns, 4.235 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.14151 | 0.14151 | 0.14151 | 0.0 | 51.75 +Pair | 0.097929 | 0.097929 | 0.097929 | 0.0 | 41.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 4.8876e-05 | 4.8876e-05 | 4.8876e-05 | 0.0 | 0.02 -Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.01 -Modify | 0.13185 | 0.13185 | 0.13185 | 0.0 | 48.22 -Other | | 1.192e-05 | | | 0.00 +Comm | 6.8903e-05 | 6.8903e-05 | 6.8903e-05 | 0.0 | 0.03 +Output | 4.673e-05 | 4.673e-05 | 4.673e-05 | 0.0 | 0.02 +Modify | 0.13809 | 0.13809 | 0.13809 | 0.0 | 58.48 +Other | | 1.216e-05 | | | 0.01 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -216,9 +208,9 @@ fix 2 all deform 1 x scale 1.0001 remap x compute perfx all stress/atom NULL pair compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6] thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) run 10 -Memory usage per processor = 7.02781 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.49 | 10.49 | 10.49 Mbytes Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81 28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81 @@ -231,20 +223,20 @@ Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27 36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76 37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25 -Loop time of 1.55219 on 1 procs for 10 steps with 1296 atoms +Loop time of 1.09542 on 1 procs for 10 steps with 1296 atoms -Performance: 0.111 ns/day, 215.582 hours/ns, 6.443 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.158 ns/day, 152.141 hours/ns, 9.129 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.5493 | 1.5493 | 1.5493 | 0.0 | 99.81 +Pair | 1.0913 | 1.0913 | 1.0913 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00050259 | 0.00050259 | 0.00050259 | 0.0 | 0.03 -Output | 0.0021405 | 0.0021405 | 0.0021405 | 0.0 | 0.14 -Modify | 0.00018573 | 0.00018573 | 0.00018573 | 0.0 | 0.01 -Other | | 0.0001054 | | | 0.01 +Comm | 0.00068784 | 0.00068784 | 0.00068784 | 0.0 | 0.06 +Output | 0.0030589 | 0.0030589 | 0.0030589 | 0.0 | 0.28 +Modify | 0.0003252 | 0.0003252 | 0.0003252 | 0.0 | 0.03 +Other | | 8.798e-05 | | | 0.01 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -267,7 +259,7 @@ compute perfz all stress/atom NULL pair compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6] thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] run 10 -Memory usage per processor = 7.77781 Mbytes +Per MPI rank memory allocation (min/avg/max) = 11.24 | 11.24 | 11.24 Mbytes Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74 38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74 @@ -280,20 +272,20 @@ Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23 46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72 47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22 -Loop time of 1.55291 on 1 procs for 10 steps with 1296 atoms +Loop time of 1.09885 on 1 procs for 10 steps with 1296 atoms -Performance: 0.111 ns/day, 215.682 hours/ns, 6.440 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.157 ns/day, 152.618 hours/ns, 9.100 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.5499 | 1.5499 | 1.5499 | 0.0 | 99.81 +Pair | 1.0947 | 1.0947 | 1.0947 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00050187 | 0.00050187 | 0.00050187 | 0.0 | 0.03 -Output | 0.0021739 | 0.0021739 | 0.0021739 | 0.0 | 0.14 -Modify | 0.00018835 | 0.00018835 | 0.00018835 | 0.0 | 0.01 -Other | | 0.0001068 | | | 0.01 +Comm | 0.00070024 | 0.00070024 | 0.00070024 | 0.0 | 0.06 +Output | 0.0030808 | 0.0030808 | 0.0030808 | 0.0 | 0.28 +Modify | 0.00032425 | 0.00032425 | 0.00032425 | 0.0 | 0.03 +Other | | 8.869e-05 | | | 0.01 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -316,7 +308,7 @@ compute perfyz all stress/atom NULL pair compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6] thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] run 10 -Memory usage per processor = 8.54308 Mbytes +Per MPI rank memory allocation (min/avg/max) = 12.01 | 12.01 | 12.01 Mbytes Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72 48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72 @@ -329,20 +321,20 @@ Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443 56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203 -Loop time of 1.55278 on 1 procs for 10 steps with 1296 atoms +Loop time of 1.09597 on 1 procs for 10 steps with 1296 atoms -Performance: 0.111 ns/day, 215.664 hours/ns, 6.440 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.158 ns/day, 152.219 hours/ns, 9.124 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.5499 | 1.5499 | 1.5499 | 0.0 | 99.81 +Pair | 1.0917 | 1.0917 | 1.0917 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00050759 | 0.00050759 | 0.00050759 | 0.0 | 0.03 -Output | 0.0021291 | 0.0021291 | 0.0021291 | 0.0 | 0.14 -Modify | 0.00018358 | 0.00018358 | 0.00018358 | 0.0 | 0.01 -Other | | 0.0001001 | | | 0.01 +Comm | 0.00068474 | 0.00068474 | 0.00068474 | 0.0 | 0.06 +Output | 0.0030637 | 0.0030637 | 0.0030637 | 0.0 | 0.28 +Modify | 0.00032473 | 0.00032473 | 0.00032473 | 0.0 | 0.03 +Other | | 0.0001802 | | | 0.02 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -365,7 +357,7 @@ compute perfxy all stress/atom NULL pair compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6] thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] run 10 -Memory usage per processor = 9.29308 Mbytes +Per MPI rank memory allocation (min/avg/max) = 12.76 | 12.76 | 12.76 Mbytes Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083 58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083 @@ -378,20 +370,20 @@ Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109 66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113 67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116 -Loop time of 1.55248 on 1 procs for 10 steps with 1296 atoms +Loop time of 1.09696 on 1 procs for 10 steps with 1296 atoms -Performance: 0.111 ns/day, 215.622 hours/ns, 6.441 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.158 ns/day, 152.356 hours/ns, 9.116 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.5495 | 1.5495 | 1.5495 | 0.0 | 99.81 +Pair | 1.0927 | 1.0927 | 1.0927 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00049877 | 0.00049877 | 0.00049877 | 0.0 | 0.03 -Output | 0.0021408 | 0.0021408 | 0.0021408 | 0.0 | 0.14 -Modify | 0.00018549 | 0.00018549 | 0.00018549 | 0.0 | 0.01 -Other | | 0.0001054 | | | 0.01 +Comm | 0.0007906 | 0.0007906 | 0.0007906 | 0.0 | 0.07 +Output | 0.0030892 | 0.0030892 | 0.0030892 | 0.0 | 0.28 +Modify | 0.00032568 | 0.00032568 | 0.00032568 | 0.0 | 0.03 +Other | | 8.726e-05 | | | 0.01 Nlocal: 1296 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -406,4 +398,4 @@ Total # of neighbors = 862272 Ave neighs/atom = 665.333 Neighbor list builds = 0 Dangerous builds not checked -Total wall time: 0:00:43 +Total wall time: 0:00:40 diff --git a/examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.4 b/examples/comb/log.27Nov18.comb.Cu2O.elastic.g++.4 similarity index 81% rename from examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.4 rename to examples/comb/log.27Nov18.comb.Cu2O.elastic.g++.4 index 453a7e0e6c..30c4e79a9e 100644 --- a/examples/comb/log.5Oct16.comb.Cu2O.elastic.g++.4 +++ b/examples/comb/log.27Nov18.comb.Cu2O.elastic.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Cu2O crystal, qeq on, minimizes, then calculates elastic constants units metal @@ -44,31 +45,36 @@ fix 2 all qeq/comb 1 0.0001 run 2 Neighbor list info ... - 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 6.28094 Mbytes + binsize = 6.25, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.411 Mbytes Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568 1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568 2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568 -Loop time of 0.168944 on 4 procs for 2 steps with 1296 atoms +Loop time of 0.198435 on 4 procs for 2 steps with 1296 atoms -Performance: 0.205 ns/day, 117.322 hours/ns, 11.838 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.174 ns/day, 137.802 hours/ns, 10.079 timesteps/s +92.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.064867 | 0.065282 | 0.065606 | 0.1 | 38.64 +Pair | 0.043778 | 0.049896 | 0.064625 | 3.9 | 25.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00026083 | 0.00059474 | 0.001004 | 1.1 | 0.35 -Output | 7.1049e-05 | 7.3791e-05 | 8.1062e-05 | 0.0 | 0.04 -Modify | 0.10295 | 0.10296 | 0.10297 | 0.0 | 60.94 -Other | | 3.177e-05 | | | 0.02 +Comm | 0.0020771 | 0.016784 | 0.022921 | 6.6 | 8.46 +Output | 7.4863e-05 | 0.00012481 | 0.00026703 | 0.0 | 0.06 +Modify | 0.13153 | 0.13154 | 0.13155 | 0.0 | 66.29 +Other | | 8.988e-05 | | | 0.05 Nlocal: 324 ave 324 max 324 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -87,15 +93,8 @@ Dangerous builds not checked unfix 1 fix 1 all box/relax aniso 0.0 vmax 0.001 minimize 1.0e-14 1.0e-20 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 8.15594 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 9.286 | 9.286 | 9.286 Mbytes Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568 3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169 @@ -122,9 +121,9 @@ Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913 25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914 -Loop time of 7.60393 on 4 procs for 24 steps with 1296 atoms +Loop time of 7.68847 on 4 procs for 24 steps with 1296 atoms -99.9% CPU use with 4 MPI tasks x no OpenMP threads +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -138,12 +137,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.8378 | 1.8844 | 1.9098 | 2.1 | 24.78 -Neigh | 0.017217 | 0.01784 | 0.018236 | 0.3 | 0.23 -Comm | 0.011872 | 0.03777 | 0.08501 | 14.8 | 0.50 -Output | 0.00087929 | 0.00090992 | 0.00099182 | 0.2 | 0.01 -Modify | 5.6557 | 5.6558 | 5.6559 | 0.0 | 74.38 -Other | | 0.007261 | | | 0.10 +Pair | 1.2491 | 1.3017 | 1.3281 | 2.7 | 16.93 +Neigh | 0.019151 | 0.019765 | 0.020248 | 0.3 | 0.26 +Comm | 0.037999 | 0.064493 | 0.11782 | 12.3 | 0.84 +Output | 0.0011022 | 0.0016249 | 0.0031886 | 2.2 | 0.02 +Modify | 6.2904 | 6.2905 | 6.2907 | 0.0 | 81.82 +Other | | 0.01031 | | | 0.13 Nlocal: 324 ave 328 max 318 min Histogram: 1 0 0 0 1 0 0 0 0 2 @@ -163,31 +162,24 @@ min_modify dmax 0.2 line quadratic unfix 1 fix 1 all nve run 1 -Neighbor list info ... - 1 neighbor list requests - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 6.53094 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.661 | 7.661 | 7.661 Mbytes Step Temp TotEng PotEng E_vdwl E_coul c_q1 c_q2 Lx Ly Lz Volume 26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914 27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914 -Loop time of 0.0698364 on 4 procs for 1 steps with 1296 atoms +Loop time of 0.0626205 on 4 procs for 1 steps with 1296 atoms -Performance: 0.247 ns/day, 96.995 hours/ns, 14.319 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.276 ns/day, 86.973 hours/ns, 15.969 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.034876 | 0.035652 | 0.036197 | 0.3 | 51.05 +Pair | 0.024917 | 0.025476 | 0.025981 | 0.2 | 40.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00012708 | 0.00067472 | 0.0014517 | 2.0 | 0.97 -Output | 3.5048e-05 | 3.6299e-05 | 3.9101e-05 | 0.0 | 0.05 -Modify | 0.033457 | 0.033461 | 0.033464 | 0.0 | 47.91 -Other | | 1.24e-05 | | | 0.02 +Comm | 9.3937e-05 | 0.00060064 | 0.0011597 | 0.0 | 0.96 +Output | 4.5061e-05 | 6.8903e-05 | 0.00013781 | 0.0 | 0.11 +Modify | 0.036391 | 0.036391 | 0.036393 | 0.0 | 58.11 +Other | | 8.357e-05 | | | 0.13 Nlocal: 324 ave 328 max 318 min Histogram: 1 0 0 0 1 0 0 0 0 2 @@ -216,9 +208,9 @@ fix 2 all deform 1 x scale 1.0001 remap x compute perfx all stress/atom NULL pair compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6] thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) run 10 -Memory usage per processor = 6.90594 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.036 | 8.036 | 8.036 Mbytes Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81 28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81 @@ -231,20 +223,20 @@ Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27 36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76 37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25 -Loop time of 0.395692 on 4 procs for 10 steps with 1296 atoms +Loop time of 0.296792 on 4 procs for 10 steps with 1296 atoms -Performance: 0.437 ns/day, 54.957 hours/ns, 25.272 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.582 ns/day, 41.221 hours/ns, 33.694 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.37577 | 0.38538 | 0.39123 | 1.0 | 97.39 +Pair | 0.26413 | 0.27686 | 0.29205 | 2.0 | 93.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0016012 | 0.0074702 | 0.017095 | 7.0 | 1.89 -Output | 0.0026791 | 0.0027133 | 0.0027606 | 0.1 | 0.69 -Modify | 5.6028e-05 | 5.8174e-05 | 6.1035e-05 | 0.0 | 0.01 -Other | | 7.373e-05 | | | 0.02 +Comm | 0.00092983 | 0.016655 | 0.029568 | 8.3 | 5.61 +Output | 0.0028515 | 0.003047 | 0.0036252 | 0.6 | 1.03 +Modify | 0.00010395 | 0.00011069 | 0.00011992 | 0.0 | 0.04 +Other | | 0.0001195 | | | 0.04 Nlocal: 324 ave 328 max 318 min Histogram: 1 0 0 0 1 0 0 0 0 2 @@ -267,7 +259,7 @@ compute perfz all stress/atom NULL pair compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6] thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] run 10 -Memory usage per processor = 7.65594 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.786 | 8.786 | 8.786 Mbytes Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74 38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74 @@ -280,20 +272,20 @@ Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23 46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72 47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22 -Loop time of 0.395265 on 4 procs for 10 steps with 1296 atoms +Loop time of 0.298517 on 4 procs for 10 steps with 1296 atoms -Performance: 0.437 ns/day, 54.898 hours/ns, 25.300 timesteps/s -100.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.579 ns/day, 41.461 hours/ns, 33.499 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.37558 | 0.38392 | 0.39002 | 1.0 | 97.13 +Pair | 0.26417 | 0.27784 | 0.29233 | 1.9 | 93.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0023744 | 0.0084905 | 0.016869 | 6.7 | 2.15 -Output | 0.0026851 | 0.0027224 | 0.0027671 | 0.1 | 0.69 -Modify | 5.3167e-05 | 5.6148e-05 | 5.8651e-05 | 0.0 | 0.01 -Other | | 7.594e-05 | | | 0.02 +Comm | 0.0020907 | 0.017109 | 0.030962 | 7.9 | 5.73 +Output | 0.0031412 | 0.003336 | 0.003916 | 0.6 | 1.12 +Modify | 0.00010443 | 0.00010878 | 0.00011301 | 0.0 | 0.04 +Other | | 0.0001191 | | | 0.04 Nlocal: 324 ave 328 max 318 min Histogram: 1 0 0 0 1 0 0 0 0 2 @@ -316,7 +308,7 @@ compute perfyz all stress/atom NULL pair compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6] thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] run 10 -Memory usage per processor = 8.42123 Mbytes +Per MPI rank memory allocation (min/avg/max) = 9.552 | 9.552 | 9.552 Mbytes Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72 48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72 @@ -329,20 +321,20 @@ Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443 56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203 -Loop time of 0.395982 on 4 procs for 10 steps with 1296 atoms +Loop time of 0.313155 on 4 procs for 10 steps with 1296 atoms -Performance: 0.436 ns/day, 54.997 hours/ns, 25.254 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.552 ns/day, 43.494 hours/ns, 31.933 timesteps/s +95.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.37606 | 0.38505 | 0.39068 | 1.0 | 97.24 +Pair | 0.26394 | 0.28147 | 0.29254 | 2.1 | 89.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0021853 | 0.0078424 | 0.016867 | 6.7 | 1.98 -Output | 0.0029173 | 0.0029593 | 0.0030072 | 0.1 | 0.75 -Modify | 5.3167e-05 | 5.4538e-05 | 5.722e-05 | 0.0 | 0.01 -Other | | 7.403e-05 | | | 0.02 +Comm | 0.01504 | 0.027947 | 0.046101 | 7.0 | 8.92 +Output | 0.0028515 | 0.0034934 | 0.0053933 | 1.9 | 1.12 +Modify | 0.0001061 | 0.00010973 | 0.00011516 | 0.0 | 0.04 +Other | | 0.0001362 | | | 0.04 Nlocal: 324 ave 328 max 318 min Histogram: 1 0 0 0 1 0 0 0 0 2 @@ -365,7 +357,7 @@ compute perfxy all stress/atom NULL pair compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6] thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] run 10 -Memory usage per processor = 9.17123 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.3 | 10.3 | 10.3 Mbytes Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083 58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083 @@ -378,20 +370,20 @@ Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109 66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113 67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116 -Loop time of 0.393499 on 4 procs for 10 steps with 1296 atoms +Loop time of 0.298849 on 4 procs for 10 steps with 1296 atoms -Performance: 0.439 ns/day, 54.653 hours/ns, 25.413 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.578 ns/day, 41.507 hours/ns, 33.462 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.37563 | 0.38304 | 0.38942 | 1.0 | 97.34 +Pair | 0.26403 | 0.27705 | 0.29235 | 2.0 | 92.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0013115 | 0.0077351 | 0.015176 | 6.8 | 1.97 -Output | 0.002558 | 0.0025953 | 0.0026426 | 0.1 | 0.66 -Modify | 5.1975e-05 | 5.4598e-05 | 5.8174e-05 | 0.0 | 0.01 -Other | | 7.737e-05 | | | 0.02 +Comm | 0.00092888 | 0.017273 | 0.030558 | 8.4 | 5.78 +Output | 0.0032196 | 0.0042848 | 0.0053816 | 1.2 | 1.43 +Modify | 0.00010204 | 0.00010765 | 0.0001123 | 0.0 | 0.04 +Other | | 0.0001339 | | | 0.04 Nlocal: 324 ave 328 max 318 min Histogram: 1 0 0 0 1 0 0 0 0 2 diff --git a/examples/comb/log.5Oct16.comb.HfO2.g++.1 b/examples/comb/log.27Nov18.comb.HfO2.g++.1 similarity index 76% rename from examples/comb/log.5Oct16.comb.HfO2.g++.1 rename to examples/comb/log.27Nov18.comb.HfO2.g++.1 index 2db94329dd..2844a91523 100644 --- a/examples/comb/log.5Oct16.comb.HfO2.g++.1 +++ b/examples/comb/log.27Nov18.comb.HfO2.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task units metal atom_style charge dimension 3 @@ -39,30 +40,35 @@ fix 1 all nvt temp 300.0 300.0 0.1 thermo 1 run 1 Neighbor list info ... - 1 neighbor list requests update every 10 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 6.5933 Mbytes + binsize = 6.25, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8 -Loop time of 0.165626 on 1 procs for 1 steps with 1500 atoms +Loop time of 0.128487 on 1 procs for 1 steps with 1500 atoms -Performance: 0.104 ns/day, 230.036 hours/ns, 6.038 timesteps/s -100.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.134 ns/day, 178.455 hours/ns, 7.783 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.16548 | 0.16548 | 0.16548 | 0.0 | 99.91 +Pair | 0.12826 | 0.12826 | 0.12826 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 6.8188e-05 | 6.8188e-05 | 6.8188e-05 | 0.0 | 0.04 -Output | 2.8133e-05 | 2.8133e-05 | 2.8133e-05 | 0.0 | 0.02 -Modify | 3.5763e-05 | 3.5763e-05 | 3.5763e-05 | 0.0 | 0.02 -Other | | 1.597e-05 | | | 0.01 +Comm | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 0.07 +Output | 4.8399e-05 | 4.8399e-05 | 4.8399e-05 | 0.0 | 0.04 +Modify | 7.1526e-05 | 7.1526e-05 | 7.1526e-05 | 0.0 | 0.06 +Other | | 1.192e-05 | | | 0.01 Nlocal: 1500 ave 1500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -79,7 +85,7 @@ Neighbor list builds = 0 Dangerous builds = 0 fix 2 all qeq/comb 1 0.003 file fq.out run 5 -Memory usage per processor = 7.2183 Mbytes +Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 @@ -87,20 +93,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 -Loop time of 1.12494 on 1 procs for 5 steps with 1500 atoms +Loop time of 0.95807 on 1 procs for 5 steps with 1500 atoms -Performance: 0.077 ns/day, 312.485 hours/ns, 4.445 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.090 ns/day, 266.130 hours/ns, 5.219 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.82774 | 0.82774 | 0.82774 | 0.0 | 73.58 +Pair | 0.64289 | 0.64289 | 0.64289 | 0.0 | 67.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00032425 | 0.00032425 | 0.00032425 | 0.0 | 0.03 -Output | 0.00013924 | 0.00013924 | 0.00013924 | 0.0 | 0.01 -Modify | 0.29665 | 0.29665 | 0.29665 | 0.0 | 26.37 -Other | | 8.941e-05 | | | 0.01 +Comm | 0.00040817 | 0.00040817 | 0.00040817 | 0.0 | 0.04 +Output | 0.00024867 | 0.00024867 | 0.00024867 | 0.0 | 0.03 +Modify | 0.31447 | 0.31447 | 0.31447 | 0.0 | 32.82 +Other | | 5.698e-05 | | | 0.01 Nlocal: 1500 ave 1500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -123,21 +129,14 @@ fix 1 all box/relax aniso 0.0 vmax 0.0002 #minimize 1.0e-12 1.0e-18 1000 10000 minimize 1.0e-4 1.0e-6 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 8.3433 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 12.59 | 12.59 | 12.59 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 -Loop time of 0.628066 on 1 procs for 1 steps with 1500 atoms +Loop time of 0.57271 on 1 procs for 1 steps with 1500 atoms -100.0% CPU use with 1 MPI tasks x no OpenMP threads +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -151,12 +150,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.33072 | 0.33072 | 0.33072 | 0.0 | 52.66 +Pair | 0.25711 | 0.25711 | 0.25711 | 0.0 | 44.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00013089 | 0.00013089 | 0.00013089 | 0.0 | 0.02 +Comm | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0.29688 | 0.29688 | 0.29688 | 0.0 | 47.27 -Other | | 0.0003412 | | | 0.05 +Modify | 0.31493 | 0.31493 | 0.31493 | 0.0 | 54.99 +Other | | 0.0005131 | | | 0.09 Nlocal: 1500 ave 1500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -184,14 +183,7 @@ min_modify dmax 0.005 line quadratic velocity all create 300.1 2398378 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 10 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 7.2183 Mbytes +Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 @@ -204,20 +196,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 -Loop time of 2.25256 on 1 procs for 10 steps with 1500 atoms +Loop time of 1.93286 on 1 procs for 10 steps with 1500 atoms -Performance: 0.077 ns/day, 312.855 hours/ns, 4.439 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.089 ns/day, 268.453 hours/ns, 5.174 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.6582 | 1.6582 | 1.6582 | 0.0 | 73.62 +Pair | 1.2975 | 1.2975 | 1.2975 | 0.0 | 67.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00064015 | 0.00064015 | 0.00064015 | 0.0 | 0.03 -Output | 0.00028682 | 0.00028682 | 0.00028682 | 0.0 | 0.01 -Modify | 0.59326 | 0.59326 | 0.59326 | 0.0 | 26.34 -Other | | 0.0001378 | | | 0.01 +Comm | 0.00082493 | 0.00082493 | 0.00082493 | 0.0 | 0.04 +Output | 0.00050569 | 0.00050569 | 0.00050569 | 0.0 | 0.03 +Modify | 0.63389 | 0.63389 | 0.63389 | 0.0 | 32.80 +Other | | 0.0001204 | | | 0.01 Nlocal: 1500 ave 1500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -232,4 +224,4 @@ Total # of neighbors = 1037500 Ave neighs/atom = 691.667 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:10 +Total wall time: 0:00:09 diff --git a/examples/comb/log.5Oct16.comb.HfO2.g++.4 b/examples/comb/log.27Nov18.comb.HfO2.g++.4 similarity index 76% rename from examples/comb/log.5Oct16.comb.HfO2.g++.4 rename to examples/comb/log.27Nov18.comb.HfO2.g++.4 index 370982c81e..07f8f00521 100644 --- a/examples/comb/log.5Oct16.comb.HfO2.g++.4 +++ b/examples/comb/log.27Nov18.comb.HfO2.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task units metal atom_style charge dimension 3 @@ -39,30 +40,35 @@ fix 1 all nvt temp 300.0 300.0 0.1 thermo 1 run 1 Neighbor list info ... - 1 neighbor list requests update every 10 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 6.45428 Mbytes + binsize = 6.25, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.595 | 7.595 | 7.596 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8 -Loop time of 0.0431705 on 4 procs for 1 steps with 1500 atoms +Loop time of 0.0343346 on 4 procs for 1 steps with 1500 atoms -Performance: 0.400 ns/day, 59.959 hours/ns, 23.164 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.503 ns/day, 47.687 hours/ns, 29.125 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.041113 | 0.041747 | 0.04291 | 0.3 | 96.70 +Pair | 0.032358 | 0.033033 | 0.034117 | 0.4 | 96.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00016999 | 0.0013372 | 0.001966 | 1.9 | 3.10 -Output | 4.2915e-05 | 4.4703e-05 | 4.7922e-05 | 0.0 | 0.10 -Modify | 1.502e-05 | 2.3365e-05 | 2.9087e-05 | 0.1 | 0.05 -Other | | 1.83e-05 | | | 0.04 +Comm | 0.00012684 | 0.0012044 | 0.0018878 | 2.0 | 3.51 +Output | 4.3392e-05 | 4.6432e-05 | 5.1737e-05 | 0.0 | 0.14 +Modify | 2.1935e-05 | 2.3842e-05 | 2.5511e-05 | 0.0 | 0.07 +Other | | 2.718e-05 | | | 0.08 Nlocal: 375 ave 375 max 375 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -79,7 +85,7 @@ Neighbor list builds = 0 Dangerous builds = 0 fix 2 all qeq/comb 1 0.003 file fq.out run 5 -Memory usage per processor = 7.07928 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.22 | 8.22 | 8.221 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 @@ -87,20 +93,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 -Loop time of 0.282798 on 4 procs for 5 steps with 1500 atoms +Loop time of 0.264002 on 4 procs for 5 steps with 1500 atoms -Performance: 0.306 ns/day, 78.555 hours/ns, 17.680 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.327 ns/day, 73.334 hours/ns, 18.939 timesteps/s +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.20467 | 0.20595 | 0.20674 | 0.2 | 72.83 +Pair | 0.16374 | 0.17099 | 0.17738 | 1.2 | 64.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0016997 | 0.0024779 | 0.003768 | 1.7 | 0.88 -Output | 0.00022483 | 0.00023055 | 0.00024247 | 0.0 | 0.08 -Modify | 0.074072 | 0.074082 | 0.074091 | 0.0 | 26.20 -Other | | 5.567e-05 | | | 0.02 +Comm | 0.0030768 | 0.0093628 | 0.016711 | 5.1 | 3.55 +Output | 0.00022531 | 0.00034034 | 0.00068116 | 0.0 | 0.13 +Modify | 0.083183 | 0.083188 | 0.083197 | 0.0 | 31.51 +Other | | 0.0001165 | | | 0.04 Nlocal: 375 ave 375 max 375 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -123,21 +129,14 @@ fix 1 all box/relax aniso 0.0 vmax 0.0002 #minimize 1.0e-12 1.0e-18 1000 10000 minimize 1.0e-4 1.0e-6 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 8.20428 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 9.345 | 9.345 | 9.346 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998 7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 -Loop time of 0.159283 on 4 procs for 1 steps with 1500 atoms +Loop time of 0.15331 on 4 procs for 1 steps with 1500 atoms -99.8% CPU use with 4 MPI tasks x no OpenMP threads +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -151,12 +150,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.082013 | 0.082956 | 0.083975 | 0.3 | 52.08 +Pair | 0.065077 | 0.066851 | 0.06825 | 0.5 | 43.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0003221 | 0.0013521 | 0.0022871 | 2.2 | 0.85 +Comm | 0.0013995 | 0.0027977 | 0.0045724 | 2.4 | 1.82 Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0.074703 | 0.074712 | 0.074719 | 0.0 | 46.91 -Other | | 0.000263 | | | 0.17 +Modify | 0.083279 | 0.083284 | 0.083293 | 0.0 | 54.32 +Other | | 0.0003769 | | | 0.25 Nlocal: 375 ave 375 max 375 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -184,14 +183,7 @@ min_modify dmax 0.005 line quadratic velocity all create 300.1 2398378 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 10 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 5 5 5 -Memory usage per processor = 7.07928 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.22 | 8.22 | 8.221 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 @@ -204,20 +196,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz c_q1 c_q2 15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923 -Loop time of 0.572819 on 4 procs for 10 steps with 1500 atoms +Loop time of 0.555816 on 4 procs for 10 steps with 1500 atoms -Performance: 0.302 ns/day, 79.558 hours/ns, 17.458 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.311 ns/day, 77.197 hours/ns, 17.992 timesteps/s +92.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.41014 | 0.41529 | 0.42112 | 0.6 | 72.50 +Pair | 0.33358 | 0.35381 | 0.36898 | 2.2 | 63.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0017653 | 0.0076357 | 0.012777 | 4.8 | 1.33 -Output | 0.00045943 | 0.00046003 | 0.00046039 | 0.0 | 0.08 -Modify | 0.1493 | 0.14933 | 0.14935 | 0.0 | 26.07 -Other | | 0.0001076 | | | 0.02 +Comm | 0.005245 | 0.02059 | 0.041362 | 9.1 | 3.70 +Output | 0.00058889 | 0.00082082 | 0.0015032 | 0.0 | 0.15 +Modify | 0.1798 | 0.18018 | 0.18053 | 0.1 | 32.42 +Other | | 0.0004114 | | | 0.07 Nlocal: 375 ave 375 max 375 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/comb/log.5Oct16.comb.Si.elastic.g++.1 b/examples/comb/log.27Nov18.comb.Si.elastic.g++.1 similarity index 80% rename from examples/comb/log.5Oct16.comb.Si.elastic.g++.1 rename to examples/comb/log.27Nov18.comb.Si.elastic.g++.1 index 939210b353..47d1f5f03d 100644 --- a/examples/comb/log.5Oct16.comb.Si.elastic.g++.1 +++ b/examples/comb/log.27Nov18.comb.Si.elastic.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg units metal @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 512 atoms + Time spent = 0.000361919 secs mass 1 29.0 change_box all triclinic triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0) @@ -34,15 +36,20 @@ thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz thermo_modify norm yes thermo 1 minimize 1.0e-14 1.0e-20 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 4 4 4 -Memory usage per processor = 7.60455 Mbytes + binsize = 6.25, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.98 | 8.98 | 8.98 Mbytes Step Temp TotEng PotEng E_vdwl E_coul 0 1 -4.6295947 -4.6297237 -4.6297237 0 1 1 -4.6295965 -4.6297255 -4.6297255 0 @@ -50,9 +57,9 @@ Step Temp TotEng PotEng E_vdwl E_coul 3 1 -4.6295965 -4.6297255 -4.6297255 0 4 1 -4.6295965 -4.6297255 -4.6297255 0 5 1 -4.6295965 -4.6297255 -4.6297255 0 -Loop time of 0.201077 on 1 procs for 5 steps with 512 atoms +Loop time of 0.150557 on 1 procs for 5 steps with 512 atoms -99.9% CPU use with 1 MPI tasks x no OpenMP threads +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -66,12 +73,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.1996 | 0.1996 | 0.1996 | 0.0 | 99.27 +Pair | 0.14823 | 0.14823 | 0.14823 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.15 -Output | 2.861e-05 | 2.861e-05 | 2.861e-05 | 0.0 | 0.01 +Comm | 0.00061703 | 0.00061703 | 0.00061703 | 0.0 | 0.41 +Output | 6.8903e-05 | 6.8903e-05 | 6.8903e-05 | 0.0 | 0.05 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.001153 | | | 0.57 +Other | | 0.001645 | | | 1.09 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -90,32 +97,25 @@ min_modify dmax 0.2 line quadratic unfix 1 run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - 1 neighbor list requests - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 4 4 4 -Memory usage per processor = 5.97955 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.355 | 7.355 | 7.355 Mbytes Step Temp TotEng PotEng E_vdwl E_coul 5 1 -4.6295965 -4.6297255 -4.6297255 0 6 1 -4.6295965 -4.6297255 -4.6297255 0 -Loop time of 0.018162 on 1 procs for 1 steps with 512 atoms +Loop time of 0.0137405 on 1 procs for 1 steps with 512 atoms -Performance: 0.951 ns/day, 25.225 hours/ns, 55.060 timesteps/s -99.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.258 ns/day, 19.084 hours/ns, 72.777 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.018118 | 0.018118 | 0.018118 | 0.0 | 99.76 +Pair | 0.013664 | 0.013664 | 0.013664 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.15 -Output | 8.1062e-06 | 8.1062e-06 | 8.1062e-06 | 0.0 | 0.04 -Modify | 2.1458e-06 | 2.1458e-06 | 2.1458e-06 | 0.0 | 0.01 -Other | | 6.914e-06 | | | 0.04 +Comm | 4.2915e-05 | 4.2915e-05 | 4.2915e-05 | 0.0 | 0.31 +Output | 2.4319e-05 | 2.4319e-05 | 2.4319e-05 | 0.0 | 0.18 +Modify | 2.3842e-07 | 2.3842e-07 | 2.3842e-07 | 0.0 | 0.00 +Other | | 8.821e-06 | | | 0.06 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -140,9 +140,9 @@ fix 2 all deform 1 x scale 1.0001 remap x compute perfx all stress/atom NULL pair compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6] thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) run 10 -Memory usage per processor = 6.72955 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.105 | 8.105 | 8.105 Mbytes Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 6 21.727916 21.727916 21.727916 0 0 0 -4.5569391e-06 -9.3041736e-06 -3.863262e-06 5.3686749e-06 -1.5078216e-06 5.1674734e-06 7 21.728133 21.727916 21.727916 0 0 0 -2.4800435e-06 -9.5067314e-06 -2.1562734e-06 5.5972954e-06 -2.3715124e-06 3.9555507e-06 @@ -155,20 +155,20 @@ Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 14 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.18 541206.18 5.6537455e-06 -1.9222461e-06 4.3649131e-06 15 21.729871 21.727916 21.727916 0 0 0 1169613.3 618507.19 618507.19 5.5850663e-06 -2.204341e-06 6.1719985e-06 16 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.66 695804.66 -1.3406996e-05 2.5348334e-06 6.2581356e-06 -Loop time of 0.199118 on 1 procs for 10 steps with 512 atoms +Loop time of 0.15253 on 1 procs for 10 steps with 512 atoms -Performance: 0.868 ns/day, 27.655 hours/ns, 50.221 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.133 ns/day, 21.185 hours/ns, 65.561 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.19755 | 0.19755 | 0.19755 | 0.0 | 99.21 +Pair | 0.15014 | 0.15014 | 0.15014 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00027704 | 0.00027704 | 0.00027704 | 0.0 | 0.14 -Output | 0.0011551 | 0.0011551 | 0.0011551 | 0.0 | 0.58 -Modify | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.04 -Other | | 5.865e-05 | | | 0.03 +Comm | 0.00041151 | 0.00041151 | 0.00041151 | 0.0 | 0.27 +Output | 0.0017772 | 0.0017772 | 0.0017772 | 0.0 | 1.17 +Modify | 0.00014377 | 0.00014377 | 0.00014377 | 0.0 | 0.09 +Other | | 5.341e-05 | | | 0.04 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -191,7 +191,7 @@ compute perfz all stress/atom NULL pair compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6] thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] run 10 -Memory usage per processor = 7.47955 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.855 | 8.855 | 8.855 Mbytes Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 16 21.730089 21.727916 21.727916 0 0 0 1462009.5 773098.59 773098.59 4.2549849e-06 -8.3746497e-07 7.0310015e-06 17 21.730089 21.727916 21.728133 0 0 0 1462009.5 773098.59 773098.59 5.1784721e-06 -2.3038152e-06 5.7172699e-06 @@ -204,20 +204,20 @@ Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 24 21.730089 21.727916 21.729654 0 0 0 2003022 1314132.4 1796319.1 2.3497113e-06 -2.3680104e-06 4.7932602e-06 25 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 6.941166e-06 -1.1601937e-06 4.9355658e-06 26 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 5.7633476e-06 -8.4264935e-07 4.0350137e-06 -Loop time of 0.199616 on 1 procs for 10 steps with 512 atoms +Loop time of 0.152854 on 1 procs for 10 steps with 512 atoms -Performance: 0.866 ns/day, 27.724 hours/ns, 50.096 timesteps/s -100.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.130 ns/day, 21.230 hours/ns, 65.422 timesteps/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.19798 | 0.19798 | 0.19798 | 0.0 | 99.18 +Pair | 0.15047 | 0.15047 | 0.15047 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00028658 | 0.00028658 | 0.00028658 | 0.0 | 0.14 -Output | 0.0012088 | 0.0012088 | 0.0012088 | 0.0 | 0.61 -Modify | 7.987e-05 | 7.987e-05 | 7.987e-05 | 0.0 | 0.04 -Other | | 5.698e-05 | | | 0.03 +Comm | 0.00043082 | 0.00043082 | 0.00043082 | 0.0 | 0.28 +Output | 0.0017312 | 0.0017312 | 0.0017312 | 0.0 | 1.13 +Modify | 0.00015283 | 0.00015283 | 0.00015283 | 0.0 | 0.10 +Other | | 7.296e-05 | | | 0.05 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -240,7 +240,7 @@ compute perfyz all stress/atom NULL pair compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6] thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] run 10 -Memory usage per processor = 8.24482 Mbytes +Per MPI rank memory allocation (min/avg/max) = 9.621 | 9.621 | 9.621 Mbytes Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 26 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 4.8476018e-06 4.2828413e-07 5.75372e-06 27 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 5.088922e-06 -2.3012471e-06 5.6950612e-06 @@ -253,20 +253,20 @@ Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 34 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 4.8447261e-06 -1.9614792e-06 1705.6275 35 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 5.1297449e-06 -2.114135e-06 1949.2885 36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 4.5571577e-06 -1.8415232e-06 2192.9496 -Loop time of 0.199427 on 1 procs for 10 steps with 512 atoms +Loop time of 0.149663 on 1 procs for 10 steps with 512 atoms -Performance: 0.866 ns/day, 27.698 hours/ns, 50.144 timesteps/s -100.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.155 ns/day, 20.787 hours/ns, 66.817 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.19785 | 0.19785 | 0.19785 | 0.0 | 99.21 +Pair | 0.14745 | 0.14745 | 0.14745 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00027561 | 0.00027561 | 0.00027561 | 0.0 | 0.14 -Output | 0.0011613 | 0.0011613 | 0.0011613 | 0.0 | 0.58 -Modify | 7.6056e-05 | 7.6056e-05 | 7.6056e-05 | 0.0 | 0.04 -Other | | 6.199e-05 | | | 0.03 +Comm | 0.00038886 | 0.00038886 | 0.00038886 | 0.0 | 0.26 +Output | 0.0016539 | 0.0016539 | 0.0016539 | 0.0 | 1.11 +Modify | 0.00012946 | 0.00012946 | 0.00012946 | 0.0 | 0.09 +Other | | 4.387e-05 | | | 0.03 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -289,7 +289,7 @@ compute perfxy all stress/atom NULL pair compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6] thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] run 10 -Memory usage per processor = 8.99482 Mbytes +Per MPI rank memory allocation (min/avg/max) = 10.37 | 10.37 | 10.37 Mbytes Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1293854e-06 -1.6748595e-06 2436.6106 37 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1236563e-06 -3.3624188e-06 2436.6106 @@ -302,20 +302,20 @@ Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 44 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00091806693 2436.6106 45 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.001049945 2436.6106 46 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011787861 2436.6106 -Loop time of 0.200513 on 1 procs for 10 steps with 512 atoms +Loop time of 0.150095 on 1 procs for 10 steps with 512 atoms -Performance: 0.862 ns/day, 27.849 hours/ns, 49.872 timesteps/s -100.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.151 ns/day, 20.847 hours/ns, 66.624 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.19893 | 0.19893 | 0.19893 | 0.0 | 99.21 +Pair | 0.14786 | 0.14786 | 0.14786 | 0.0 | 98.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.14 -Output | 0.0011744 | 0.0011744 | 0.0011744 | 0.0 | 0.59 -Modify | 7.4387e-05 | 7.4387e-05 | 7.4387e-05 | 0.0 | 0.04 -Other | | 6.08e-05 | | | 0.03 +Comm | 0.00038791 | 0.00038791 | 0.00038791 | 0.0 | 0.26 +Output | 0.0016763 | 0.0016763 | 0.0016763 | 0.0 | 1.12 +Modify | 0.00012708 | 0.00012708 | 0.00012708 | 0.0 | 0.08 +Other | | 4.101e-05 | | | 0.03 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -330,4 +330,4 @@ Total # of neighbors = 212992 Ave neighs/atom = 416 Neighbor list builds = 0 Dangerous builds not checked -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/comb/log.5Oct16.comb.Si.elastic.g++.4 b/examples/comb/log.27Nov18.comb.Si.elastic.g++.4 similarity index 79% rename from examples/comb/log.5Oct16.comb.Si.elastic.g++.4 rename to examples/comb/log.27Nov18.comb.Si.elastic.g++.4 index b539f2ec17..96e7a86615 100644 --- a/examples/comb/log.5Oct16.comb.Si.elastic.g++.4 +++ b/examples/comb/log.27Nov18.comb.Si.elastic.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg units metal @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 512 atoms + Time spent = 0.000349045 secs mass 1 29.0 change_box all triclinic triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0) @@ -34,23 +36,28 @@ thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz thermo_modify norm yes thermo 1 minimize 1.0e-14 1.0e-20 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 4 4 4 -Memory usage per processor = 7.52233 Mbytes + binsize = 6.25, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.115 | 8.117 | 8.119 Mbytes Step Temp TotEng PotEng E_vdwl E_coul 0 1 -4.6295947 -4.6297237 -4.6297237 0 1 1 -4.6295965 -4.6297255 -4.6297255 0 2 1 -4.6295965 -4.6297255 -4.6297255 0 3 1 -4.6295965 -4.6297255 -4.6297255 0 -Loop time of 0.0423422 on 4 procs for 3 steps with 512 atoms +Loop time of 0.0321558 on 4 procs for 3 steps with 512 atoms -97.4% CPU use with 4 MPI tasks x no OpenMP threads +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -64,12 +71,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.026049 | 0.03263 | 0.041219 | 3.0 | 77.06 +Pair | 0.018856 | 0.024412 | 0.030752 | 2.7 | 75.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00049615 | 0.0090721 | 0.015641 | 5.7 | 21.43 -Output | 3.314e-05 | 3.5107e-05 | 4.1008e-05 | 0.1 | 0.08 +Comm | 0.00067329 | 0.0070035 | 0.012553 | 5.0 | 21.78 +Output | 2.9802e-05 | 3.8147e-05 | 6.2227e-05 | 0.0 | 0.12 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0006052 | | | 1.43 +Other | | 0.0007022 | | | 2.18 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 @@ -88,32 +95,25 @@ min_modify dmax 0.2 line quadratic unfix 1 run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - 1 neighbor list requests - update every 20 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 4 4 4 -Memory usage per processor = 5.89733 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 6.49 | 6.492 | 6.494 Mbytes Step Temp TotEng PotEng E_vdwl E_coul 3 1 -4.6295965 -4.6297255 -4.6297255 0 4 1 -4.6295965 -4.6297255 -4.6297255 0 -Loop time of 0.00589204 on 4 procs for 1 steps with 512 atoms +Loop time of 0.00449681 on 4 procs for 1 steps with 512 atoms -Performance: 2.933 ns/day, 8.183 hours/ns, 169.721 timesteps/s -101.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.843 ns/day, 6.246 hours/ns, 222.380 timesteps/s +86.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.003751 | 0.0046486 | 0.0057852 | 1.1 | 78.90 +Pair | 0.0026906 | 0.003392 | 0.0043435 | 1.0 | 75.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 7.391e-05 | 0.001206 | 0.0021 | 2.1 | 20.47 -Output | 1.9073e-05 | 2.0742e-05 | 2.1935e-05 | 0.0 | 0.35 -Modify | 0 | 7.1526e-07 | 1.9073e-06 | 0.1 | 0.01 -Other | | 1.597e-05 | | | 0.27 +Comm | 0.00013089 | 0.0010685 | 0.0017493 | 1.8 | 23.76 +Output | 1.6212e-05 | 1.9789e-05 | 2.7895e-05 | 0.0 | 0.44 +Modify | 0 | 2.9802e-07 | 4.7684e-07 | 0.0 | 0.01 +Other | | 1.621e-05 | | | 0.36 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 @@ -138,9 +138,9 @@ fix 2 all deform 1 x scale 1.0001 remap x compute perfx all stress/atom NULL pair compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6] thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) run 10 -Memory usage per processor = 6.64733 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.24 | 7.242 | 7.244 Mbytes Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 4 21.727916 21.727916 21.727916 0 0 0 0.036618297 0.036625051 0.036618342 -1.7136998e-07 -3.2302114e-06 -1.7543151e-06 5 21.728133 21.727916 21.727916 0 0 0 0.036618988 0.036625612 0.036619564 -1.1309366e-06 -2.412817e-06 -2.6316468e-06 @@ -153,20 +153,20 @@ Step Lx Ly Lz Xy Xz Yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6] 12 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.21 541206.21 -9.1665744e-07 -1.59238e-06 -7.7617215e-06 13 21.729871 21.727916 21.727916 0 0 0 1169613.4 618507.22 618507.22 -1.1565806e-06 -2.0309366e-06 -6.6873647e-06 14 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.69 695804.69 1.8915845e-06 7.7289624e-06 -6.2492306e-06 -Loop time of 0.0653707 on 4 procs for 10 steps with 512 atoms +Loop time of 0.0540967 on 4 procs for 10 steps with 512 atoms -Performance: 2.643 ns/day, 9.079 hours/ns, 152.974 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.194 ns/day, 7.513 hours/ns, 184.854 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.041152 | 0.050811 | 0.063103 | 3.5 | 77.73 +Pair | 0.03044 | 0.038641 | 0.049502 | 3.5 | 71.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00078726 | 0.013075 | 0.02272 | 6.9 | 20.00 -Output | 0.0013869 | 0.0014045 | 0.0014176 | 0.0 | 2.15 -Modify | 2.9087e-05 | 3.32e-05 | 3.5048e-05 | 0.0 | 0.05 -Other | | 4.774e-05 | | | 0.07 +Comm | 0.0010123 | 0.011967 | 0.020209 | 6.4 | 22.12 +Output | 0.0033484 | 0.0033884 | 0.0034938 | 0.1 | 6.26 +Modify | 3.7432e-05 | 4.5538e-05 | 5.2452e-05 | 0.0 | 0.08 +Other | | 5.442e-05 | | | 0.10 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 @@ -189,7 +189,7 @@ compute perfz all stress/atom NULL pair compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6] thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] run 10 -Memory usage per processor = 7.39733 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.99 | 7.992 | 7.994 Mbytes Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 14 21.730089 21.727916 21.727916 0 0 0 1462009.6 773098.62 773098.62 -6.2271887e-07 -3.134065e-06 -1.4448086e-06 15 21.730089 21.727916 21.728133 0 0 0 1462009.6 773098.62 773098.62 -1.4749588e-06 -2.1972704e-06 -2.7974026e-06 @@ -202,20 +202,20 @@ Step Lx Ly Lz Xy Xz Yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6] 22 21.730089 21.727916 21.729654 0 0 0 2003022.1 1314132.4 1796319.1 -2.1981227e-06 -2.7285159e-06 -2.0486576e-06 23 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 -3.6986662e-06 -2.430512e-06 -2.6914988e-06 24 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 -7.1345705e-06 -2.6113355e-06 -1.261254e-06 -Loop time of 0.065423 on 4 procs for 10 steps with 512 atoms +Loop time of 0.0533404 on 4 procs for 10 steps with 512 atoms -Performance: 2.641 ns/day, 9.087 hours/ns, 152.851 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.240 ns/day, 7.408 hours/ns, 187.475 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.041187 | 0.050801 | 0.063128 | 3.5 | 77.65 +Pair | 0.030974 | 0.038825 | 0.04982 | 3.5 | 72.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00077367 | 0.013104 | 0.022709 | 6.9 | 20.03 -Output | 0.0014305 | 0.0014462 | 0.0014589 | 0.0 | 2.21 -Modify | 2.0504e-05 | 2.7299e-05 | 3.1233e-05 | 0.1 | 0.04 -Other | | 4.494e-05 | | | 0.07 +Comm | 0.0017583 | 0.012849 | 0.020708 | 6.1 | 24.09 +Output | 0.0015182 | 0.0015638 | 0.0016725 | 0.2 | 2.93 +Modify | 4.1723e-05 | 4.7386e-05 | 5.3883e-05 | 0.0 | 0.09 +Other | | 5.519e-05 | | | 0.10 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 @@ -238,7 +238,7 @@ compute perfyz all stress/atom NULL pair compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6] thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] run 10 -Memory usage per processor = 8.16262 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.755 | 8.757 | 8.759 Mbytes Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 24 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 -3.9610575e-06 -3.188829e-06 -5.7973926e-07 25 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 -4.4960939e-06 -2.549801e-06 -1.5603844e-06 @@ -251,20 +251,20 @@ Step Lx Ly Lz Xy Xz Yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6] 32 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 -6.62009e-06 -8.621625e-06 1705.6275 33 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 -6.712501e-06 -8.7315457e-06 1949.2885 34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.3958831e-06 -7.1670331e-06 2192.9496 -Loop time of 0.0656388 on 4 procs for 10 steps with 512 atoms +Loop time of 0.0527849 on 4 procs for 10 steps with 512 atoms -Performance: 2.633 ns/day, 9.116 hours/ns, 152.349 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.274 ns/day, 7.331 hours/ns, 189.448 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.040685 | 0.050668 | 0.063339 | 3.6 | 77.19 +Pair | 0.031353 | 0.038631 | 0.04922 | 3.3 | 73.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00077748 | 0.013466 | 0.023423 | 7.0 | 20.52 -Output | 0.0013893 | 0.0014307 | 0.001461 | 0.1 | 2.18 -Modify | 2.1935e-05 | 2.6524e-05 | 3.0994e-05 | 0.1 | 0.04 -Other | | 4.733e-05 | | | 0.07 +Comm | 0.0018575 | 0.012532 | 0.019807 | 5.9 | 23.74 +Output | 0.0014849 | 0.0015269 | 0.0016224 | 0.1 | 2.89 +Modify | 3.624e-05 | 4.2975e-05 | 5.0306e-05 | 0.0 | 0.08 +Other | | 5.269e-05 | | | 0.10 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 @@ -287,7 +287,7 @@ compute perfxy all stress/atom NULL pair compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6] thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] run 10 -Memory usage per processor = 8.91262 Mbytes +Per MPI rank memory allocation (min/avg/max) = 9.505 | 9.507 | 9.509 Mbytes Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.1581426e-06 -1.1350015e-05 2436.6106 35 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.7014652e-06 -1.1032048e-05 2436.6106 @@ -300,20 +300,20 @@ Step Lx Ly Lz Xy Xz Yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6] 42 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00093156087 2436.6106 43 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.0010618138 2436.6106 44 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011926577 2436.6106 -Loop time of 0.0657181 on 4 procs for 10 steps with 512 atoms +Loop time of 0.0532025 on 4 procs for 10 steps with 512 atoms -Performance: 2.629 ns/day, 9.128 hours/ns, 152.165 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3.248 ns/day, 7.389 hours/ns, 187.961 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.040015 | 0.050405 | 0.063468 | 3.7 | 76.70 +Pair | 0.031092 | 0.039043 | 0.049599 | 3.4 | 73.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00079203 | 0.013852 | 0.024224 | 7.1 | 21.08 -Output | 0.0013652 | 0.001386 | 0.0014119 | 0.1 | 2.11 -Modify | 2.0981e-05 | 2.5392e-05 | 3.2902e-05 | 0.1 | 0.04 -Other | | 4.965e-05 | | | 0.08 +Comm | 0.0009048 | 0.012022 | 0.020445 | 6.4 | 22.60 +Output | 0.0015302 | 0.0020386 | 0.0026102 | 1.1 | 3.83 +Modify | 3.8862e-05 | 4.4942e-05 | 5.1498e-05 | 0.0 | 0.08 +Other | | 5.406e-05 | | | 0.10 Nlocal: 128 ave 164 max 100 min Histogram: 1 0 0 2 0 0 0 0 0 1 diff --git a/examples/comb/log.5Oct16.comb.Si.g++.1 b/examples/comb/log.27Nov18.comb.Si.g++.1 similarity index 80% rename from examples/comb/log.5Oct16.comb.Si.g++.1 rename to examples/comb/log.27Nov18.comb.Si.g++.1 index 517c7ba306..1a37d41a9a 100644 --- a/examples/comb/log.5Oct16.comb.Si.g++.1 +++ b/examples/comb/log.27Nov18.comb.Si.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pure Si crystal, structure created by LAMMPS, qeq off units metal @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 0) to (21.72 21.72 21.72) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 512 atoms + Time spent = 0.000380754 secs mass 1 29.0 pair_style comb @@ -42,13 +44,18 @@ thermo 1 run 10 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 1 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 4 4 4 -Memory usage per processor = 6.47955 Mbytes + binsize = 6.25, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.855 | 7.855 | 7.855 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0 1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0 @@ -61,20 +68,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0 9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0 10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0 -Loop time of 0.187379 on 1 procs for 10 steps with 512 atoms +Loop time of 0.135568 on 1 procs for 10 steps with 512 atoms -Performance: 0.922 ns/day, 26.025 hours/ns, 53.368 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1.275 ns/day, 18.829 hours/ns, 73.764 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.18685 | 0.18685 | 0.18685 | 0.0 | 99.72 +Pair | 0.13472 | 0.13472 | 0.13472 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00025797 | 0.00025797 | 0.00025797 | 0.0 | 0.14 -Output | 0.00011826 | 0.00011826 | 0.00011826 | 0.0 | 0.06 -Modify | 8.297e-05 | 8.297e-05 | 8.297e-05 | 0.0 | 0.04 -Other | | 7.2e-05 | | | 0.04 +Comm | 0.00044823 | 0.00044823 | 0.00044823 | 0.0 | 0.33 +Output | 0.00023055 | 0.00023055 | 0.00023055 | 0.0 | 0.17 +Modify | 8.7976e-05 | 8.7976e-05 | 8.7976e-05 | 0.0 | 0.06 +Other | | 8.512e-05 | | | 0.06 Nlocal: 512 ave 512 max 512 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/comb/log.5Oct16.comb.Si.g++.4 b/examples/comb/log.27Nov18.comb.Si.g++.4 similarity index 80% rename from examples/comb/log.5Oct16.comb.Si.g++.4 rename to examples/comb/log.27Nov18.comb.Si.g++.4 index 0c91786f20..2cbe145f85 100644 --- a/examples/comb/log.5Oct16.comb.Si.g++.4 +++ b/examples/comb/log.27Nov18.comb.Si.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pure Si crystal, structure created by LAMMPS, qeq off units metal @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 0) to (21.72 21.72 21.72) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 512 atoms + Time spent = 0.000349522 secs mass 1 29.0 pair_style comb @@ -42,13 +44,18 @@ thermo 1 run 10 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 1 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.5 ghost atom cutoff = 12.5 - binsize = 6.25 -> bins = 4 4 4 -Memory usage per processor = 6.39352 Mbytes + binsize = 6.25, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.99 | 6.99 | 6.99 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0 1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0 @@ -61,20 +68,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz 8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0 9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0 10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0 -Loop time of 0.0527902 on 4 procs for 10 steps with 512 atoms +Loop time of 0.0424338 on 4 procs for 10 steps with 512 atoms -Performance: 3.273 ns/day, 7.332 hours/ns, 189.429 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 4.072 ns/day, 5.894 hours/ns, 235.661 timesteps/s +93.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.045993 | 0.047917 | 0.051259 | 0.9 | 90.77 +Pair | 0.034115 | 0.035889 | 0.040149 | 1.3 | 84.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0010545 | 0.0044153 | 0.0063219 | 3.0 | 8.36 -Output | 0.00030351 | 0.00033081 | 0.00036931 | 0.1 | 0.63 -Modify | 2.3365e-05 | 2.6286e-05 | 2.8372e-05 | 0.0 | 0.05 -Other | | 0.0001011 | | | 0.19 +Comm | 0.0015998 | 0.0058764 | 0.0076761 | 3.2 | 13.85 +Output | 0.00023532 | 0.00029427 | 0.00042939 | 0.0 | 0.69 +Modify | 2.7418e-05 | 2.9385e-05 | 3.1948e-05 | 0.0 | 0.07 +Other | | 0.0003446 | | | 0.81 Nlocal: 128 ave 128 max 128 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/comb/log.5Oct16.comb3.g++.1 b/examples/comb/log.27Nov18.comb3.g++.1 similarity index 77% rename from examples/comb/log.5Oct16.comb3.g++.1 rename to examples/comb/log.27Nov18.comb3.g++.1 index d6342dbf54..10120130d1 100644 --- a/examples/comb/log.5Oct16.comb3.g++.1 +++ b/examples/comb/log.27Nov18.comb3.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Graphene-OH on Cu2O (110) surface units metal @@ -40,18 +41,23 @@ velocity all create 300.0 2398378 thermo 10 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 4 4 6 -Memory usage per processor = 4.95036 Mbytes + binsize = 6.5, bins = 4 4 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb3, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 12.04 | 12.04 | 12.04 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz 0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162 10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162 20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162 - 30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162 + 30 906.42367 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162 40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162 50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162 60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162 @@ -59,20 +65,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz 80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162 90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162 100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162 -Loop time of 44.821 on 1 procs for 100 steps with 682 atoms +Loop time of 32.3303 on 1 procs for 100 steps with 682 atoms -Performance: 0.039 ns/day, 622.513 hours/ns, 2.231 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.053 ns/day, 449.032 hours/ns, 3.093 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 10.702 | 10.702 | 10.702 | 0.0 | 23.88 +Pair | 8.3833 | 8.3833 | 8.3833 | 0.0 | 25.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0028968 | 0.0028968 | 0.0028968 | 0.0 | 0.01 -Output | 0.00018311 | 0.00018311 | 0.00018311 | 0.0 | 0.00 -Modify | 34.115 | 34.115 | 34.115 | 0.0 | 76.11 -Other | | 0.001503 | | | 0.00 +Comm | 0.003716 | 0.003716 | 0.003716 | 0.0 | 0.01 +Output | 0.00026011 | 0.00026011 | 0.00026011 | 0.0 | 0.00 +Modify | 23.942 | 23.942 | 23.942 | 0.0 | 74.05 +Other | | 0.001301 | | | 0.00 Nlocal: 682 ave 682 max 682 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -87,4 +93,4 @@ Total # of neighbors = 355216 Ave neighs/atom = 520.845 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:47 +Total wall time: 0:00:34 diff --git a/examples/comb/log.5Oct16.comb3.g++.4 b/examples/comb/log.27Nov18.comb3.g++.4 similarity index 79% rename from examples/comb/log.5Oct16.comb3.g++.4 rename to examples/comb/log.27Nov18.comb3.g++.4 index 39c032b9c5..2e87771f1f 100644 --- a/examples/comb/log.5Oct16.comb3.g++.4 +++ b/examples/comb/log.27Nov18.comb3.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Graphene-OH on Cu2O (110) surface units metal @@ -40,13 +41,18 @@ velocity all create 300.0 2398378 thermo 10 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 4 4 6 -Memory usage per processor = 4.95436 Mbytes + binsize = 6.5, bins = 4 4 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair comb3, perpetual + attributes: full, newton on, ghost + pair build: full/bin/ghost + stencil: full/ghost/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.978 | 9.688 | 10.4 Mbytes Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz 0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162 10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162 @@ -59,20 +65,20 @@ Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz 80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162 90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162 100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162 -Loop time of 20.2521 on 4 procs for 100 steps with 682 atoms +Loop time of 15.9617 on 4 procs for 100 steps with 682 atoms -Performance: 0.085 ns/day, 281.279 hours/ns, 4.938 timesteps/s -99.0% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.108 ns/day, 221.691 hours/ns, 6.265 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.1898 | 3.3988 | 4.7081 | 65.6 | 16.78 +Pair | 2.2602 | 3.3385 | 4.4367 | 57.4 | 20.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.013637 | 1.3219 | 2.5298 | 105.1 | 6.53 -Output | 0.00034475 | 0.00035816 | 0.00038099 | 0.1 | 0.00 -Modify | 15.528 | 15.528 | 15.529 | 0.0 | 76.68 -Other | | 0.002504 | | | 0.01 +Comm | 0.09019 | 1.1876 | 2.265 | 96.2 | 7.44 +Output | 0.00035334 | 0.0005967 | 0.0013168 | 0.0 | 0.00 +Modify | 11.432 | 11.432 | 11.432 | 0.0 | 71.62 +Other | | 0.002874 | | | 0.02 Nlocal: 170.5 ave 245 max 100 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -87,4 +93,4 @@ Total # of neighbors = 355216 Ave neighs/atom = 520.845 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:21 +Total wall time: 0:00:16 diff --git a/examples/controller/in.controller b/examples/controller/in.controller.temp old mode 100755 new mode 100644 similarity index 100% rename from examples/controller/in.controller rename to examples/controller/in.controller.temp diff --git a/examples/controller/in.controller.wall b/examples/controller/in.controller.wall new file mode 100644 index 0000000000..4e60b3e7de --- /dev/null +++ b/examples/controller/in.controller.wall @@ -0,0 +1,46 @@ +# 3d Lennard-Jones melt, thermostatted by fix controller + +units lj +atom_style atomic +boundary p p m +processors * * 1 +lattice fcc 0.8442 +region box block 0 10 0 10 -4 14 +region slab block 0 10 0 10 0 10 +create_box 1 box +create_atoms 1 region slab +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 2 every 2 check yes + +fix 1 all nve +fix 3 all langevin 1.5 1.5 0.5 412513 + +variable zhi internal $(10.5*zlat) +variable kwall equal 20.0 +fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5 + +variable pzz equal pzz +fix ave all ave/time 10 10 100 v_pzz +# equilibrate + +thermo_style custom step temp pxx pyy pzz f_ave v_zhi +thermo 500 +run 2500 + +# use time averaged pressure for control +#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi + +# use instantaneous pressure for control +fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi + +# run with controller + +run 5000 + diff --git a/examples/controller/log.5Oct16.controller.g++.1 b/examples/controller/log.27Nov18.controller.temp.g++.1 similarity index 81% rename from examples/controller/log.5Oct16.controller.g++.1 rename to examples/controller/log.27Nov18.controller.temp.g++.1 index 5b30a14007..64b9beda3b 100644 --- a/examples/controller/log.5Oct16.controller.g++.1 +++ b/examples/controller/log.27Nov18.controller.temp.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt, thermostatted by fix controller units lj @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.00062418 secs mass 1 1.0 velocity all create 1.44 87287 loop geom @@ -32,13 +34,18 @@ fix tstat all langevin v_tcontrol 0.5 0.5 2938940 thermo 50 run 500 Neighbor list info ... - 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 12 -Memory usage per processor = 2.19271 Mbytes + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 50 0.61784238 -5.9328913 0 -5.0063594 -0.8309723 @@ -51,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 400 0.49885979 -6.157314 0 -5.4092114 -2.1544075 450 0.50261633 -6.1458076 0 -5.3920716 -2.1080502 500 0.51198903 -6.1441158 0 -5.3763242 -2.0677941 -Loop time of 1.51804 on 1 procs for 500 steps with 4000 atoms +Loop time of 1.55006 on 1 procs for 500 steps with 4000 atoms -Performance: 142288.277 tau/day, 329.371 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 139349.249 tau/day, 322.568 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2152 | 1.2152 | 1.2152 | 0.0 | 80.05 -Neigh | 0.16464 | 0.16464 | 0.16464 | 0.0 | 10.85 -Comm | 0.022342 | 0.022342 | 0.022342 | 0.0 | 1.47 -Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.01 -Modify | 0.10936 | 0.10936 | 0.10936 | 0.0 | 7.20 -Other | | 0.006292 | | | 0.41 +Pair | 1.2115 | 1.2115 | 1.2115 | 0.0 | 78.16 +Neigh | 0.18784 | 0.18784 | 0.18784 | 0.0 | 12.12 +Comm | 0.027217 | 0.027217 | 0.027217 | 0.0 | 1.76 +Output | 0.00033712 | 0.00033712 | 0.00033712 | 0.0 | 0.02 +Modify | 0.1171 | 0.1171 | 0.1171 | 0.0 | 7.55 +Other | | 0.006078 | | | 0.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -90,7 +97,7 @@ fix 10 all controller 100 1.0 0.5 0.0 0.0 c_thermo_t # run with controller run 2500 -Memory usage per processor = 2.19271 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 500 0.51198903 -6.1441158 0 -5.3763242 -2.0677941 550 0.50342035 -6.1446822 0 -5.3897404 -2.0872641 @@ -143,20 +150,20 @@ Step Temp E_pair E_mol TotEng Press 2900 1.5287303 -4.8393493 0 -2.546827 5.3276564 2950 1.5175567 -4.8779763 0 -2.6022104 5.1592321 3000 1.5038518 -4.8714664 0 -2.6162526 5.1494048 -Loop time of 7.82673 on 1 procs for 2500 steps with 4000 atoms +Loop time of 7.9877 on 1 procs for 2500 steps with 4000 atoms -Performance: 137988.733 tau/day, 319.418 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 135207.915 tau/day, 312.981 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.2774 | 6.2774 | 6.2774 | 0.0 | 80.21 -Neigh | 0.85491 | 0.85491 | 0.85491 | 0.0 | 10.92 -Comm | 0.11304 | 0.11304 | 0.11304 | 0.0 | 1.44 -Output | 0.00090504 | 0.00090504 | 0.00090504 | 0.0 | 0.01 -Modify | 0.55013 | 0.55013 | 0.55013 | 0.0 | 7.03 -Other | | 0.0303 | | | 0.39 +Pair | 6.2628 | 6.2628 | 6.2628 | 0.0 | 78.41 +Neigh | 0.97669 | 0.97669 | 0.97669 | 0.0 | 12.23 +Comm | 0.13389 | 0.13389 | 0.13389 | 0.0 | 1.68 +Output | 0.0015631 | 0.0015631 | 0.0015631 | 0.0 | 0.02 +Modify | 0.58344 | 0.58344 | 0.58344 | 0.0 | 7.30 +Other | | 0.02927 | | | 0.37 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/controller/log.5Oct16.controller.g++.4 b/examples/controller/log.27Nov18.controller.temp.g++.4 similarity index 81% rename from examples/controller/log.5Oct16.controller.g++.4 rename to examples/controller/log.27Nov18.controller.temp.g++.4 index 21e1f58f36..9584c0a8a0 100644 --- a/examples/controller/log.5Oct16.controller.g++.4 +++ b/examples/controller/log.27Nov18.controller.temp.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt, thermostatted by fix controller units lj @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000405788 secs mass 1 1.0 velocity all create 1.44 87287 loop geom @@ -32,13 +34,18 @@ fix tstat all langevin v_tcontrol 0.5 0.5 2938940 thermo 50 run 500 Neighbor list info ... - 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 12 -Memory usage per processor = 2.10344 Mbytes + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 50 0.61546984 -5.9273631 0 -5.0043892 -0.80234884 @@ -51,20 +58,20 @@ Step Temp E_pair E_mol TotEng Press 400 0.50869337 -6.1435002 0 -5.3806509 -2.0654599 450 0.50821435 -6.1436659 0 -5.381535 -2.0660991 500 0.51057155 -6.138733 0 -5.3730671 -2.0305015 -Loop time of 0.474689 on 4 procs for 500 steps with 4000 atoms +Loop time of 0.469437 on 4 procs for 500 steps with 4000 atoms -Performance: 455034.992 tau/day, 1053.322 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 460125.812 tau/day, 1065.106 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.31692 | 0.32816 | 0.35039 | 2.3 | 69.13 -Neigh | 0.042872 | 0.044288 | 0.046693 | 0.7 | 9.33 -Comm | 0.043676 | 0.070658 | 0.084897 | 6.0 | 14.89 -Output | 0.00025439 | 0.0002867 | 0.00030446 | 0.1 | 0.06 -Modify | 0.02728 | 0.028604 | 0.030571 | 0.8 | 6.03 -Other | | 0.002697 | | | 0.57 +Pair | 0.31917 | 0.32582 | 0.32979 | 0.7 | 69.41 +Neigh | 0.048915 | 0.051251 | 0.053828 | 0.8 | 10.92 +Comm | 0.054731 | 0.059151 | 0.069726 | 2.5 | 12.60 +Output | 0.00028014 | 0.00033808 | 0.00048709 | 0.0 | 0.07 +Modify | 0.02967 | 0.031206 | 0.033305 | 0.8 | 6.65 +Other | | 0.00167 | | | 0.36 Nlocal: 1000 ave 1027 max 969 min Histogram: 1 0 0 1 0 0 0 0 1 1 @@ -90,7 +97,7 @@ fix 10 all controller 100 1.0 0.5 0.0 0.0 c_thermo_t # run with controller run 2500 -Memory usage per processor = 2.10344 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 500 0.51057155 -6.138733 0 -5.3730671 -2.0305015 550 0.50420106 -6.1501845 0 -5.394072 -2.095219 @@ -143,20 +150,20 @@ Step Temp E_pair E_mol TotEng Press 2900 1.4994026 -4.8400966 0 -2.591555 5.3231654 2950 1.5057915 -4.8842358 0 -2.6261131 5.1645778 3000 1.5038806 -4.8661399 0 -2.610883 5.2228747 -Loop time of 2.33203 on 4 procs for 2500 steps with 4000 atoms +Loop time of 2.39888 on 4 procs for 2500 steps with 4000 atoms -Performance: 463116.726 tau/day, 1072.029 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 450209.527 tau/day, 1042.152 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.6173 | 1.6621 | 1.7135 | 3.2 | 71.27 -Neigh | 0.2201 | 0.22394 | 0.23011 | 0.9 | 9.60 -Comm | 0.22619 | 0.29012 | 0.33801 | 8.8 | 12.44 -Output | 0.001302 | 0.0013426 | 0.0013707 | 0.1 | 0.06 -Modify | 0.13805 | 0.14195 | 0.14664 | 0.9 | 6.09 -Other | | 0.01257 | | | 0.54 +Pair | 1.6469 | 1.6659 | 1.7027 | 1.7 | 69.45 +Neigh | 0.25338 | 0.26008 | 0.26833 | 1.2 | 10.84 +Comm | 0.24458 | 0.30644 | 0.33939 | 6.6 | 12.77 +Output | 0.0012605 | 0.0020466 | 0.0043511 | 2.9 | 0.09 +Modify | 0.15009 | 0.15611 | 0.16933 | 2.0 | 6.51 +Other | | 0.008278 | | | 0.35 Nlocal: 1000 ave 1014 max 988 min Histogram: 2 0 0 0 0 0 0 0 1 1 diff --git a/examples/controller/log.27Nov18.controller.wall.g++.1 b/examples/controller/log.27Nov18.controller.wall.g++.1 new file mode 100644 index 0000000000..ac660f2fdb --- /dev/null +++ b/examples/controller/log.27Nov18.controller.wall.g++.1 @@ -0,0 +1,142 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt, thermostatted by fix controller + +units lj +atom_style atomic +boundary p p m +processors * * 1 +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 -4 14 +region slab block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region slab +Created 4200 atoms + Time spent = 0.000752687 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 2 every 2 check yes + +fix 1 all nve +fix 3 all langevin 1.5 1.5 0.5 412513 + +variable zhi internal $(10.5*zlat) +variable zhi internal 17.635760009516324942 +variable kwall equal 20.0 +fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5 +fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5 +fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5 + +variable pzz equal pzz +fix ave all ave/time 10 10 100 v_pzz +# equilibrate + +thermo_style custom step temp pxx pyy pzz f_ave v_zhi +thermo 500 +run 2500 +Neighbor list info ... + update every 2 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.639 | 3.639 | 3.639 Mbytes +Step Temp Pxx Pyy Pzz f_ave v_zhi + 0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576 + 500 1.4850596 3.1161377 2.9246345 2.9122136 2.9795403 17.63576 + 1000 1.4706875 2.4918963 2.4698964 2.3538419 2.5181301 17.63576 + 1500 1.4978967 1.9196563 2.0442863 1.978316 1.9215971 17.63576 + 2000 1.4738152 1.6424128 1.5875245 1.7098788 1.6222172 17.63576 + 2500 1.5012535 1.3324666 1.3078613 1.30772 1.3830807 17.63576 +Loop time of 9.88972 on 1 procs for 2500 steps with 4200 atoms + +Performance: 109204.308 tau/day, 252.788 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.9583 | 5.9583 | 5.9583 | 0.0 | 60.25 +Neigh | 3.0444 | 3.0444 | 3.0444 | 0.0 | 30.78 +Comm | 0.095146 | 0.095146 | 0.095146 | 0.0 | 0.96 +Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00 +Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 7.45 +Other | | 0.05447 | | | 0.55 + +Nlocal: 4200 ave 4200 max 4200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3278 ave 3278 max 3278 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 125488 ave 125488 max 125488 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 125488 +Ave neighs/atom = 29.8781 +Neighbor list builds = 414 +Dangerous builds = 0 + +# use time averaged pressure for control +#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi + +# use instantaneous pressure for control +fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi + +# run with controller + +run 5000 +Per MPI rank memory allocation (min/avg/max) = 3.645 | 3.645 | 3.645 Mbytes +Step Temp Pxx Pyy Pzz f_ave v_zhi + 2500 1.5012535 1.332723 1.3081129 1.3079716 1.3830807 17.63576 + 3000 1.4976659 1.2148748 1.2873541 1.4929784 1.337029 17.052206 + 3500 1.5099561 1.2602054 1.2429245 1.3566909 1.2922544 15.926241 + 4000 1.4993048 1.3600782 1.2700229 1.441161 1.3958688 15.38517 + 4500 1.5361306 1.4939463 1.4981484 1.6511208 1.4778535 15.14012 + 5000 1.4858931 1.3755603 1.4202936 1.3321859 1.4463033 14.710626 + 5500 1.495093 1.5412773 1.3726815 1.3337702 1.4661477 14.551062 + 6000 1.4867063 1.4204076 1.4972286 1.5325972 1.5125403 14.727292 + 6500 1.5036424 1.4449136 1.5290335 1.5163832 1.4974 14.866821 + 7000 1.5376638 1.4409843 1.4434687 1.3927467 1.5097986 14.730925 + 7500 1.4880255 1.4006281 1.4538957 1.4700911 1.4904586 14.531748 +Loop time of 18.1541 on 1 procs for 5000 steps with 4200 atoms + +Performance: 118981.600 tau/day, 275.420 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.685 | 10.685 | 10.685 | 0.0 | 58.86 +Neigh | 5.6863 | 5.6863 | 5.6863 | 0.0 | 31.32 +Comm | 0.19485 | 0.19485 | 0.19485 | 0.0 | 1.07 +Output | 0.0003798 | 0.0003798 | 0.0003798 | 0.0 | 0.00 +Modify | 1.479 | 1.479 | 1.479 | 0.0 | 8.15 +Other | | 0.1086 | | | 0.60 + +Nlocal: 4200 ave 4200 max 4200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3252 ave 3252 max 3252 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 126902 ave 126902 max 126902 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 126902 +Ave neighs/atom = 30.2148 +Neighbor list builds = 815 +Dangerous builds = 0 + +Total wall time: 0:00:28 diff --git a/examples/controller/log.27Nov18.controller.wall.g++.2 b/examples/controller/log.27Nov18.controller.wall.g++.2 new file mode 100644 index 0000000000..acecf705fd --- /dev/null +++ b/examples/controller/log.27Nov18.controller.wall.g++.2 @@ -0,0 +1,142 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt, thermostatted by fix controller + +units lj +atom_style atomic +boundary p p m +processors * * 1 +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 -4 14 +region slab block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 -6.71838) to (16.796 16.796 23.5143) + 2 by 1 by 1 MPI processor grid +create_atoms 1 region slab +Created 4200 atoms + Time spent = 0.00055027 secs +mass 1 1.0 + +velocity all create 1.44 87287 loop geom + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify delay 2 every 2 check yes + +fix 1 all nve +fix 3 all langevin 1.5 1.5 0.5 412513 + +variable zhi internal $(10.5*zlat) +variable zhi internal 17.635760009516324942 +variable kwall equal 20.0 +fix 2 all wall/harmonic zlo -0.5 ${kwall} 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5 +fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi ${kwall} 0.0 2.5 +fix 2 all wall/harmonic zlo -0.5 20 0.0 2.5 zhi v_zhi 20 0.0 2.5 + +variable pzz equal pzz +fix ave all ave/time 10 10 100 v_pzz +# equilibrate + +thermo_style custom step temp pxx pyy pzz f_ave v_zhi +thermo 500 +run 2500 +Neighbor list info ... + update every 2 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes +Step Temp Pxx Pyy Pzz f_ave v_zhi + 0 1.44 -2.8234811 -2.8425184 -2.7022745 0 17.63576 + 500 1.4685077 2.9959993 2.9101136 2.9557017 2.9691654 17.63576 + 1000 1.4660014 2.3677693 2.4832805 2.3853443 2.495998 17.63576 + 1500 1.503875 1.9958194 1.8192177 1.8732779 1.9196618 17.63576 + 2000 1.508944 1.6772869 1.6171356 1.5363361 1.6221247 17.63576 + 2500 1.4754205 1.4808824 1.3803411 1.3538329 1.433588 17.63576 +Loop time of 5.20209 on 2 procs for 2500 steps with 4200 atoms + +Performance: 207608.821 tau/day, 480.576 timesteps/s +99.2% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0816 | 3.1008 | 3.1199 | 1.1 | 59.61 +Neigh | 1.5272 | 1.5364 | 1.5455 | 0.7 | 29.53 +Comm | 0.12968 | 0.15815 | 0.18662 | 7.2 | 3.04 +Output | 0.00012827 | 0.00048637 | 0.00084448 | 0.0 | 0.01 +Modify | 0.3743 | 0.37516 | 0.37602 | 0.1 | 7.21 +Other | | 0.03114 | | | 0.60 + +Nlocal: 2100 ave 2121 max 2079 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2593 ave 2606 max 2580 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 62766.5 ave 63603 max 61930 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 125533 +Ave neighs/atom = 29.8888 +Neighbor list builds = 410 +Dangerous builds = 0 + +# use time averaged pressure for control +#fix 10 all controller 100 -0.05 20.0 0.0 0.0 f_ave 1.5 zhi + +# use instantaneous pressure for control +fix 10 all controller 100 -0.05 50.0 0.0 0.0 v_pzz 1.5 zhi + +# run with controller + +run 5000 +Per MPI rank memory allocation (min/avg/max) = 3.208 | 3.208 | 3.208 Mbytes +Step Temp Pxx Pyy Pzz f_ave v_zhi + 2500 1.4754205 1.482216 1.3815843 1.3550522 1.433588 17.63576 + 3000 1.4805196 1.4121967 1.3859531 1.4360385 1.3724589 16.755204 + 3500 1.4909046 1.3658062 1.3441219 1.3839841 1.3998033 15.699356 + 4000 1.500835 1.4985308 1.4043943 1.3989491 1.4418757 15.030304 + 4500 1.5371526 1.4614358 1.4941526 1.455191 1.5121676 14.738878 + 5000 1.4766657 1.4037866 1.2404757 1.3679074 1.4173969 14.670117 + 5500 1.48302 1.5591058 1.3928461 1.3952178 1.5334476 14.58675 + 6000 1.5191325 1.4416274 1.5290468 1.5077685 1.5176605 14.560389 + 6500 1.495773 1.6695592 1.6621934 1.6073908 1.5508856 14.668722 + 7000 1.5033866 1.48723 1.5054815 1.4755225 1.5024653 14.676533 + 7500 1.5512429 1.6282941 1.7399228 1.6351273 1.6851571 14.671092 +Loop time of 9.76074 on 2 procs for 5000 steps with 4200 atoms + +Performance: 221294.755 tau/day, 512.256 timesteps/s +98.5% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5979 | 5.6281 | 5.6583 | 1.3 | 57.66 +Neigh | 2.9053 | 2.9335 | 2.9618 | 1.6 | 30.05 +Comm | 0.31645 | 0.37703 | 0.43762 | 9.9 | 3.86 +Output | 0.00025439 | 0.0009656 | 0.0016768 | 0.0 | 0.01 +Modify | 0.75674 | 0.75966 | 0.76258 | 0.3 | 7.78 +Other | | 0.06145 | | | 0.63 + +Nlocal: 2100 ave 2109 max 2091 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 2578 ave 2578 max 2578 min +Histogram: 2 0 0 0 0 0 0 0 0 0 +Neighs: 63578.5 ave 64145 max 63012 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 127157 +Ave neighs/atom = 30.2755 +Neighbor list builds = 816 +Dangerous builds = 0 + +Total wall time: 0:00:14 diff --git a/examples/coreshell/log.9Nov16.coreshell.dsf.g++.1 b/examples/coreshell/log.27Nov18.coreshell.dsf.g++.1 similarity index 84% rename from examples/coreshell/log.9Nov16.coreshell.dsf.g++.1 rename to examples/coreshell/log.27Nov18.coreshell.dsf.g++.1 index f58970fff0..12fd548f02 100644 --- a/examples/coreshell/log.9Nov16.coreshell.dsf.g++.1 +++ b/examples/coreshell/log.27Nov18.coreshell.dsf.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (27 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Testsystem for core-shell model compared to Mitchel and Finchham # Hendrik Heenen, June 2014 @@ -68,12 +69,17 @@ thermo_modify temp CSequ velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 22 ghost atom cutoff = 22 - binsize = 11 -> bins = 3 3 3 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/dsf/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard velocity all scale 1427 temp CSequ fix thermoberendsen all temp/berendsen 1427 1427 0.4 @@ -84,7 +90,7 @@ fix_modify thermoberendsen temp CSequ timestep 0.002 run 500 -Memory usage per processor = 7.04355 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.3517686e-14 2.942091e-15 13990.5 50 -633.9898 -666.02679 32.03699 1152.7858 -4578.5681 -668.50431 37.800204 -706.30452 0 2.4775226 14.568073 4.3012389 13990.5 @@ -97,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 400 -625.02586 -661.46042 36.434568 1311.0236 -868.2031 -664.40231 43.21398 -707.61629 0 2.9418875 14.945389 2.7493413 13990.5 450 -624.3278 -660.50844 36.180639 1301.8865 -2203.3944 -663.49896 40.008669 -703.50763 0 2.9905179 14.158866 1.7299899 13990.5 500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5 -Loop time of 10.7162 on 1 procs for 500 steps with 432 atoms +Loop time of 8.43387 on 1 procs for 500 steps with 432 atoms -Performance: 8.063 ns/day, 2.977 hours/ns, 46.658 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 10.244 ns/day, 2.343 hours/ns, 59.285 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 10.478 | 10.478 | 10.478 | 0.0 | 97.78 -Bond | 0.0029511 | 0.0029511 | 0.0029511 | 0.0 | 0.03 -Neigh | 0.14159 | 0.14159 | 0.14159 | 0.0 | 1.32 -Comm | 0.074382 | 0.074382 | 0.074382 | 0.0 | 0.69 -Output | 0.00054097 | 0.00054097 | 0.00054097 | 0.0 | 0.01 -Modify | 0.010588 | 0.010588 | 0.010588 | 0.0 | 0.10 -Other | | 0.007748 | | | 0.07 +Pair | 8.1175 | 8.1175 | 8.1175 | 0.0 | 96.25 +Bond | 0.0019796 | 0.0019796 | 0.0019796 | 0.0 | 0.02 +Neigh | 0.21242 | 0.21242 | 0.21242 | 0.0 | 2.52 +Comm | 0.085533 | 0.085533 | 0.085533 | 0.0 | 1.01 +Output | 0.00041103 | 0.00041103 | 0.00041103 | 0.0 | 0.00 +Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 0.14 +Other | | 0.003863 | | | 0.05 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -131,7 +137,7 @@ unfix thermoberendsen # ------------------------ Dynamic Run ------------------------------- run 1000 -Memory usage per processor = 7.04355 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5 550 -623.5004 -660.74472 37.244326 1340.1611 -1413.4326 -663.99669 41.875014 -705.8717 0 3.2519651 15.097948 2.278405 13990.5 @@ -154,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 1400 -623.50803 -660.03912 36.53109 1314.4968 362.97431 -663.24909 45.772904 -709.02199 0 3.2099708 14.566488 1.9170714 13990.5 1450 -623.51243 -659.65548 36.143052 1300.534 2853.0755 -663.0534 51.355353 -714.40875 0 3.3979157 15.890282 2.5251359 13990.5 1500 -623.51621 -661.87741 38.361201 1380.3496 740.04973 -665.00896 46.208742 -711.2177 0 3.1315492 15.168927 2.4710846 13990.5 -Loop time of 22.2766 on 1 procs for 1000 steps with 432 atoms +Loop time of 16.907 on 1 procs for 1000 steps with 432 atoms -Performance: 7.757 ns/day, 3.094 hours/ns, 44.890 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 10.221 ns/day, 2.348 hours/ns, 59.147 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.8 | 21.8 | 21.8 | 0.0 | 97.86 -Bond | 0.005852 | 0.005852 | 0.005852 | 0.0 | 0.03 -Neigh | 0.30423 | 0.30423 | 0.30423 | 0.0 | 1.37 -Comm | 0.14388 | 0.14388 | 0.14388 | 0.0 | 0.65 -Output | 0.0010855 | 0.0010855 | 0.0010855 | 0.0 | 0.00 -Modify | 0.0064189 | 0.0064189 | 0.0064189 | 0.0 | 0.03 -Other | | 0.01527 | | | 0.07 +Pair | 16.247 | 16.247 | 16.247 | 0.0 | 96.09 +Bond | 0.0039518 | 0.0039518 | 0.0039518 | 0.0 | 0.02 +Neigh | 0.46795 | 0.46795 | 0.46795 | 0.0 | 2.77 +Comm | 0.17146 | 0.17146 | 0.17146 | 0.0 | 1.01 +Output | 0.00082397 | 0.00082397 | 0.00082397 | 0.0 | 0.00 +Modify | 0.0065799 | 0.0065799 | 0.0065799 | 0.0 | 0.04 +Other | | 0.009467 | | | 0.06 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -182,4 +188,4 @@ Ave neighs/atom = 687.803 Ave special neighs/atom = 1 Neighbor list builds = 44 Dangerous builds = 0 -Total wall time: 0:00:33 +Total wall time: 0:00:25 diff --git a/examples/coreshell/log.9Nov16.coreshell.dsf.g++.4 b/examples/coreshell/log.27Nov18.coreshell.dsf.g++.4 similarity index 85% rename from examples/coreshell/log.9Nov16.coreshell.dsf.g++.4 rename to examples/coreshell/log.27Nov18.coreshell.dsf.g++.4 index ccf1b4b035..fddddee49b 100644 --- a/examples/coreshell/log.9Nov16.coreshell.dsf.g++.4 +++ b/examples/coreshell/log.27Nov18.coreshell.dsf.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (26 Jan 2017) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Testsystem for core-shell model compared to Mitchel and Finchham # Hendrik Heenen, June 2014 @@ -74,7 +75,8 @@ Neighbor list info ... ghost atom cutoff = 22 binsize = 11, bins = 3 3 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair born/coul/dsf/cs, half, perpetual + (1) pair born/coul/dsf/cs, perpetual + attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard @@ -88,7 +90,7 @@ fix_modify thermoberendsen temp CSequ timestep 0.002 run 500 -Memory usage per processor = 6.8559 Mbytes +Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.5814015e-14 3.2317898e-15 13990.5 50 -634.07021 -666.11867 32.048452 1153.1982 -4560.945 -668.28236 37.756542 -706.0389 0 2.163691 13.802484 3.022372 13990.5 @@ -101,21 +103,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 400 -625.09344 -661.26404 36.1706 1301.5253 -729.96729 -664.10334 43.468765 -707.57211 0 2.8392963 13.663555 1.9067551 13990.5 450 -624.46214 -660.01362 35.551477 1279.2474 -1617.7158 -663.06571 41.644856 -704.71057 0 3.0520921 14.527005 1.7280213 13990.5 500 -623.49246 -659.2527 35.76024 1286.7593 -935.99238 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5 -Loop time of 4.09864 on 4 procs for 500 steps with 432 atoms +Loop time of 2.44013 on 4 procs for 500 steps with 432 atoms -Performance: 21.080 ns/day, 1.139 hours/ns, 121.992 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 35.408 ns/day, 0.678 hours/ns, 204.907 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.3804 | 3.568 | 3.8354 | 8.9 | 87.05 -Bond | 0.00074339 | 0.00079519 | 0.00087976 | 0.0 | 0.02 -Neigh | 0.045851 | 0.046084 | 0.046361 | 0.1 | 1.12 -Comm | 0.20413 | 0.47123 | 0.65875 | 24.3 | 11.50 -Output | 0.00044298 | 0.00046057 | 0.00051165 | 0.0 | 0.01 -Modify | 0.0064909 | 0.0067219 | 0.0069766 | 0.2 | 0.16 -Other | | 0.005345 | | | 0.13 +Pair | 2.0321 | 2.1124 | 2.1759 | 3.6 | 86.57 +Bond | 0.00069523 | 0.00071579 | 0.00074148 | 0.0 | 0.03 +Neigh | 0.060491 | 0.060606 | 0.060709 | 0.0 | 2.48 +Comm | 0.19263 | 0.25562 | 0.33556 | 10.4 | 10.48 +Output | 0.00041246 | 0.00057316 | 0.0010512 | 0.0 | 0.02 +Modify | 0.0059495 | 0.0062472 | 0.006577 | 0.4 | 0.26 +Other | | 0.00394 | | | 0.16 Nlocal: 108 ave 114 max 105 min Histogram: 1 1 1 0 0 0 0 0 0 1 @@ -135,7 +137,7 @@ unfix thermoberendsen # ------------------------ Dynamic Run ------------------------------- run 1000 -Memory usage per processor = 6.85787 Mbytes +Per MPI rank memory allocation (min/avg/max) = 6.883 | 6.948 | 7.138 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 500 -623.49319 -659.2527 35.759511 1286.7331 -936.04802 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5 550 -623.44059 -663.57938 40.138795 1444.3127 -935.73484 -666.2789 42.563337 -708.84224 0 2.6995167 13.918509 2.3189805 13990.5 @@ -158,21 +160,21 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 1400 -623.47124 -661.45375 37.982513 1366.7233 -379.56023 -664.6321 43.788306 -708.42041 0 3.1783497 14.251126 1.7415409 13990.5 1450 -623.46671 -660.17518 36.708464 1320.8792 -374.37056 -662.92706 44.083648 -707.01071 0 2.7518803 15.210167 1.9984277 13990.5 1500 -623.50515 -659.06488 35.559725 1279.5442 260.37822 -662.39548 45.779764 -708.17524 0 3.3306005 14.682396 2.4201107 13990.5 -Loop time of 8.26746 on 4 procs for 1000 steps with 432 atoms +Loop time of 5.16152 on 4 procs for 1000 steps with 432 atoms -Performance: 20.901 ns/day, 1.148 hours/ns, 120.956 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 33.478 ns/day, 0.717 hours/ns, 193.741 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.706 | 7.1568 | 7.6597 | 12.7 | 86.57 -Bond | 0.0014617 | 0.0015531 | 0.0016506 | 0.2 | 0.02 -Neigh | 0.10511 | 0.10522 | 0.10532 | 0.0 | 1.27 -Comm | 0.48547 | 0.98841 | 1.4393 | 34.0 | 11.96 -Output | 0.0012085 | 0.0012462 | 0.0013196 | 0.1 | 0.02 -Modify | 0.0021446 | 0.0021989 | 0.0022545 | 0.1 | 0.03 -Other | | 0.01204 | | | 0.15 +Pair | 4.0761 | 4.2795 | 4.6259 | 10.9 | 82.91 +Bond | 0.0013907 | 0.0014481 | 0.0015037 | 0.1 | 0.03 +Neigh | 0.13612 | 0.13618 | 0.13624 | 0.0 | 2.64 +Comm | 0.38391 | 0.73074 | 0.93346 | 26.3 | 14.16 +Output | 0.00096703 | 0.0014517 | 0.0028937 | 2.2 | 0.03 +Modify | 0.0022988 | 0.0024452 | 0.0025537 | 0.2 | 0.05 +Other | | 0.009786 | | | 0.19 Nlocal: 108 ave 114 max 94 min Histogram: 1 0 0 0 0 0 0 0 1 2 @@ -186,4 +188,4 @@ Ave neighs/atom = 687.484 Ave special neighs/atom = 1 Neighbor list builds = 46 Dangerous builds = 0 -Total wall time: 0:00:12 +Total wall time: 0:00:07 diff --git a/examples/coreshell/log.27Nov18.coreshell.g++.1 b/examples/coreshell/log.27Nov18.coreshell.g++.1 new file mode 100644 index 0000000000..ac37069a1d --- /dev/null +++ b/examples/coreshell/log.27Nov18.coreshell.g++.1 @@ -0,0 +1,218 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Testsystem for core-shell model compared to Mitchel and Finchham +# Hendrik Heenen, June 2014 + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + orthogonal box = (0 0 0) to (24.096 24.096 24.096) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 432 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 216 bonds + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +group cores type 1 2 +216 atoms in group cores +group shells type 3 4 +216 atoms in group shells + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +kspace_style ewald 1.0e-6 +pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol + +compute CStemp all temp/cs cores shells +compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CStemp press thermo_press_lmp + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 22 + ghost atom cutoff = 22 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/long/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +velocity all scale 1427 temp CStemp + +# thermostating using the core/shell decoupling + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CStemp + +# 2 fmsec timestep + +timestep 0.002 +run 500 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5 + 50 -634.17327 -666.17818 32.004909 1151.6314 -4029.8418 -667.9562 37.809071 989.23283 -1694.9981 1.7780231 9.7133792 2.191797 13990.5 + 100 -631.93507 -661.91226 29.977186 1078.6679 -3171.7799 -664.06719 39.33341 991.36934 -1694.7699 2.1549313 11.091423 2.1704389 13990.5 + 150 -630.16811 -663.12417 32.956056 1185.8565 143.26508 -665.48036 46.253769 982.97454 -1694.7087 2.3561935 11.467913 2.1652595 13990.5 + 200 -628.62323 -663.64922 35.025998 1260.3391 -1622.4126 -665.96878 41.661879 986.81675 -1694.4474 2.3195587 10.597709 2.9538262 13990.5 + 250 -627.31045 -662.01825 34.7078 1248.8894 -1509.6621 -664.50312 42.101718 987.90197 -1694.5068 2.4848739 10.392757 1.6933711 13990.5 + 300 -626.57622 -660.97494 34.39872 1237.7678 -1637.8094 -663.48087 41.653234 989.53228 -1694.6664 2.5059303 11.204361 2.2809738 13990.5 + 350 -625.91962 -665.35837 39.438749 1419.123 -1351.4779 -667.6167 41.582456 985.53382 -1694.733 2.2583289 10.83106 1.8963347 13990.5 + 400 -625.24849 -660.77642 35.527934 1278.4003 -424.45104 -663.12602 43.890331 987.75201 -1694.7684 2.3495966 11.521966 2.175931 13990.5 + 450 -624.67743 -662.88678 38.209353 1374.8857 1109.0155 -665.43212 46.964803 982.35208 -1694.749 2.5453383 11.002405 2.0014356 13990.5 + 500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5 +Loop time of 6.53907 on 1 procs for 500 steps with 432 atoms + +Performance: 13.213 ns/day, 1.816 hours/ns, 76.463 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.6198 | 5.6198 | 5.6198 | 0.0 | 85.94 +Bond | 0.0020258 | 0.0020258 | 0.0020258 | 0.0 | 0.03 +Kspace | 0.57813 | 0.57813 | 0.57813 | 0.0 | 8.84 +Neigh | 0.23532 | 0.23532 | 0.23532 | 0.0 | 3.60 +Comm | 0.086898 | 0.086898 | 0.086898 | 0.0 | 1.33 +Output | 0.00044823 | 0.00044823 | 0.00044823 | 0.0 | 0.01 +Modify | 0.012434 | 0.012434 | 0.012434 | 0.0 | 0.19 +Other | | 0.004004 | | | 0.06 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9338 ave 9338 max 9338 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 297354 ave 297354 max 297354 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 297354 +Ave neighs/atom = 688.319 +Ave special neighs/atom = 1 +Neighbor list builds = 22 +Dangerous builds = 0 + +unfix thermoberendsen + +# ------------------------ Dynamic Run ------------------------------- + +run 1000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5 + 550 -624.30709 -662.13368 37.826594 1361.1129 327.40639 -664.76823 45.306662 984.72847 -1694.8034 2.6345475 10.879928 1.9751611 13990.5 + 600 -624.30993 -661.84513 37.535201 1350.6277 -983.48045 -664.36158 42.366067 987.87918 -1694.6068 2.5164439 10.210733 1.7891188 13990.5 + 650 -624.30501 -659.20528 34.90027 1255.8151 556.10903 -661.96404 46.567866 986.0511 -1694.583 2.7587602 13.154392 2.1649995 13990.5 + 700 -624.30909 -661.85126 37.54217 1350.8784 -134.38128 -664.38499 44.382232 985.80624 -1694.5735 2.5337309 10.991718 2.0394718 13990.5 + 750 -624.30994 -660.52853 36.218591 1303.2522 1197.4475 -663.29728 47.437035 984.08807 -1694.8224 2.7687507 11.683138 2.075797 13990.5 + 800 -624.30475 -659.88119 35.576433 1280.1454 358.11619 -662.81702 45.487454 986.41325 -1694.7177 2.9358301 11.519677 3.7837385 13990.5 + 850 -624.3061 -663.63946 39.333359 1415.3307 -33.011248 -666.10531 44.296094 984.32445 -1694.7258 2.4658499 11.039607 1.9232237 13990.5 + 900 -624.3004 -659.038 34.737607 1249.962 373.33796 -662.10263 45.838541 986.93651 -1694.8777 3.0646238 12.13843 2.4692874 13990.5 + 950 -624.30802 -663.36014 39.052124 1405.2111 290.61832 -665.78004 45.269372 983.76386 -1694.8133 2.4198995 11.723515 2.0708786 13990.5 + 1000 -624.30213 -659.49404 35.191918 1266.3094 -920.00206 -662.25664 42.950066 989.20183 -1694.4085 2.7625985 11.442653 1.8492839 13990.5 + 1050 -624.30371 -659.3839 35.080191 1262.2891 284.04674 -662.15204 45.828093 986.77381 -1694.7539 2.7681351 12.123317 1.8741591 13990.5 + 1100 -624.3052 -660.69507 36.389872 1309.4153 -282.65356 -663.18011 44.45192 987.28618 -1694.9182 2.4850386 11.032596 1.9763392 13990.5 + 1150 -624.30478 -657.75327 33.448496 1203.5759 1331.9067 -660.51356 48.445972 985.91346 -1694.873 2.7602894 13.583395 2.4702797 13990.5 + 1200 -624.30892 -664.76096 40.452036 1455.5841 -1970.8297 -666.85506 39.983487 988.02113 -1694.8597 2.0941031 9.5654747 1.9888352 13990.5 + 1250 -624.30486 -661.48101 37.176152 1337.708 1864.8469 -664.22952 48.84895 981.57501 -1694.6535 2.7485121 11.090466 1.9610957 13990.5 + 1300 -624.3122 -662.74179 38.429588 1382.8104 1775.1061 -665.4945 48.300257 980.84489 -1694.6396 2.7527096 11.276872 1.7562916 13990.5 + 1350 -624.30198 -659.95211 35.65013 1282.7973 -154.85356 -662.68735 44.54654 987.24605 -1694.4799 2.7352371 11.229424 2.4657127 13990.5 + 1400 -624.30362 -659.14451 34.840882 1253.6781 -159.66669 -662.01516 44.455993 988.18506 -1694.6562 2.87065 11.536771 1.6678 13990.5 + 1450 -624.30238 -661.91803 37.615642 1353.5222 993.97328 -664.55469 46.579213 983.57987 -1694.7138 2.6366597 11.343434 2.3751981 13990.5 + 1500 -624.31198 -659.70757 35.395599 1273.6385 2948.584 -662.67607 51.30697 980.45677 -1694.4398 2.9684904 11.953269 2.2096873 13990.5 +Loop time of 13.2154 on 1 procs for 1000 steps with 432 atoms + +Performance: 13.076 ns/day, 1.835 hours/ns, 75.669 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.363 | 11.363 | 11.363 | 0.0 | 85.98 +Bond | 0.0040638 | 0.0040638 | 0.0040638 | 0.0 | 0.03 +Kspace | 1.1573 | 1.1573 | 1.1573 | 0.0 | 8.76 +Neigh | 0.50039 | 0.50039 | 0.50039 | 0.0 | 3.79 +Comm | 0.17365 | 0.17365 | 0.17365 | 0.0 | 1.31 +Output | 0.00093961 | 0.00093961 | 0.00093961 | 0.0 | 0.01 +Modify | 0.0068541 | 0.0068541 | 0.0068541 | 0.0 | 0.05 +Other | | 0.009295 | | | 0.07 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9380 ave 9380 max 9380 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 296922 ave 296922 max 296922 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 296922 +Ave neighs/atom = 687.319 +Ave special neighs/atom = 1 +Neighbor list builds = 47 +Dangerous builds = 0 +Total wall time: 0:00:19 diff --git a/examples/coreshell/log.27Nov18.coreshell.g++.4 b/examples/coreshell/log.27Nov18.coreshell.g++.4 new file mode 100644 index 0000000000..597ffc2660 --- /dev/null +++ b/examples/coreshell/log.27Nov18.coreshell.g++.4 @@ -0,0 +1,218 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Testsystem for core-shell model compared to Mitchel and Finchham +# Hendrik Heenen, June 2014 + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + orthogonal box = (0 0 0) to (24.096 24.096 24.096) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 432 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 216 bonds + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +group cores type 1 2 +216 atoms in group cores +group shells type 3 4 +216 atoms in group shells + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +kspace_style ewald 1.0e-6 +pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol + +compute CStemp all temp/cs cores shells +compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CStemp press thermo_press_lmp + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 22 + ghost atom cutoff = 22 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/long/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +velocity all scale 1427 temp CStemp + +# thermostating using the core/shell decoupling + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CStemp + +# 2 fmsec timestep + +timestep 0.002 +run 500 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 15.58 | 15.58 | 15.58 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5 + 50 -634.17349 -666.17817 32.004686 1151.6234 -4029.8405 -667.9562 37.809075 989.23283 -1694.9981 1.778024 9.7133822 2.1917966 13990.5 + 100 -631.93517 -661.91227 29.977104 1078.665 -3171.8044 -664.0672 39.333371 991.36937 -1694.7699 2.1549315 11.091441 2.1704346 13990.5 + 150 -630.16822 -663.12423 32.956001 1185.8545 143.24615 -665.48041 46.253736 982.97453 -1694.7087 2.3561828 11.467862 2.1651517 13990.5 + 200 -628.6223 -663.6493 35.026994 1260.375 -1622.4428 -665.96885 41.661825 986.81675 -1694.4474 2.3195537 10.597709 2.9538132 13990.5 + 250 -627.31146 -662.01843 34.706968 1248.8595 -1509.7149 -664.50329 42.10159 987.90193 -1694.5068 2.4848612 10.392642 1.693337 13990.5 + 300 -626.57661 -660.97479 34.398178 1237.7483 -1637.8266 -663.48071 41.653258 989.53241 -1694.6664 2.5059269 11.20455 2.2814851 13990.5 + 350 -625.91971 -665.3583 39.438589 1419.1172 -1351.5076 -667.61665 41.582479 985.53388 -1694.733 2.2583457 10.831559 1.8963688 13990.5 + 400 -625.24855 -660.7758 35.527253 1278.3758 -423.70384 -663.1256 43.89223 987.7506 -1694.7684 2.349799 11.523597 2.1775994 13990.5 + 450 -624.6774 -662.88749 38.210092 1374.9123 1108.7784 -665.43272 46.964156 982.35233 -1694.7492 2.5452316 11.002239 2.001871 13990.5 + 500 -624.30227 -661.97992 37.677648 1355.7533 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5 +Loop time of 1.9801 on 4 procs for 500 steps with 432 atoms + +Performance: 43.634 ns/day, 0.550 hours/ns, 252.513 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3316 | 1.4349 | 1.5717 | 7.8 | 72.46 +Bond | 0.00071955 | 0.00073642 | 0.00075316 | 0.0 | 0.04 +Kspace | 0.20621 | 0.33644 | 0.43824 | 15.7 | 16.99 +Neigh | 0.065812 | 0.065825 | 0.065829 | 0.0 | 3.32 +Comm | 0.11763 | 0.12492 | 0.12828 | 1.2 | 6.31 +Output | 0.0004766 | 0.0020956 | 0.0069461 | 6.1 | 0.11 +Modify | 0.0063045 | 0.0071256 | 0.0079646 | 1.0 | 0.36 +Other | | 0.008101 | | | 0.41 + +Nlocal: 108 ave 119 max 102 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Nghost: 6516 ave 6545 max 6491 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 74337.8 ave 81248 max 69989 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 297351 +Ave neighs/atom = 688.312 +Ave special neighs/atom = 1 +Neighbor list builds = 22 +Dangerous builds = 0 + +unfix thermoberendsen + +# ------------------------ Dynamic Run ------------------------------- + +run 1000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 15.59 | 15.65 | 15.84 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 500 -624.30215 -661.97992 37.677763 1355.7575 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5 + 550 -624.307 -662.13312 37.826117 1361.0957 331.61441 -664.76755 45.316291 984.7202 -1694.804 2.6344363 10.876847 1.9725627 13990.5 + 600 -624.30999 -661.82604 37.516052 1349.9386 -977.02006 -664.34278 42.382897 987.88146 -1694.6071 2.5167365 10.214195 1.7874159 13990.5 + 650 -624.30519 -659.19917 34.89398 1255.5887 549.29026 -661.95827 46.555452 986.06834 -1694.5821 2.7590968 13.15971 2.150802 13990.5 + 700 -624.30925 -661.91134 37.60209 1353.0346 -173.75617 -664.45296 44.284848 985.83333 -1694.5711 2.5416162 10.971743 1.9844905 13990.5 + 750 -624.30957 -660.4111 36.101528 1299.0399 1224.7615 -663.20844 47.513495 984.09149 -1694.8134 2.7973427 11.760288 2.1436426 13990.5 + 800 -624.30443 -660.29859 35.994159 1295.1764 274.44426 -663.2484 45.216978 986.25498 -1694.7204 2.9498134 11.512509 4.0054687 13990.5 + 850 -624.30771 -663.64907 39.341363 1415.6187 339.0107 -666.13161 45.126833 983.39086 -1694.6493 2.4825413 11.020953 2.1719529 13990.5 + 900 -624.30318 -658.79061 34.487426 1240.9597 326.93573 -661.83606 45.870868 987.13858 -1694.8455 3.0454534 12.639272 1.9516031 13990.5 + 950 -624.30275 -663.63565 39.332892 1415.3139 -668.82258 -665.98818 43.090661 985.63359 -1694.7124 2.3525337 11.014784 2.0742438 13990.5 + 1000 -624.30302 -660.58037 36.27735 1305.3665 -725.43356 -663.2066 42.991534 988.36047 -1694.5586 2.6262239 10.521127 1.8763991 13990.5 + 1050 -624.30291 -660.75751 36.454601 1311.7445 834.87442 -663.66586 46.551242 984.37581 -1694.5929 2.908347 11.20897 2.1312758 13990.5 + 1100 -624.30709 -663.05705 38.749955 1394.3381 -709.57897 -665.5853 42.840927 986.33077 -1694.757 2.5282501 10.630015 2.6077838 13990.5 + 1150 -624.31167 -663.16861 38.856933 1398.1875 -202.93169 -665.68694 43.83137 985.37199 -1694.8903 2.5183367 10.924515 2.9847813 13990.5 + 1200 -624.30447 -660.45656 36.152088 1300.8592 -490.40029 -663.44614 43.512278 987.25887 -1694.2173 2.9895748 11.017505 2.1685389 13990.5 + 1250 -624.3046 -661.95895 37.654347 1354.9149 -1405.9374 -664.49438 41.407094 988.59571 -1694.4972 2.5354305 11.05786 2.0138426 13990.5 + 1300 -624.30002 -659.01152 34.711493 1249.0223 414.13124 -661.65532 45.873988 986.98863 -1694.5179 2.6438076 11.612439 2.2823703 13990.5 + 1350 -624.31114 -659.05277 34.741631 1250.1068 795.03396 -661.48604 46.584896 986.7784 -1694.8493 2.43327 10.382832 1.616191 13990.5 + 1400 -624.30512 -661.30058 36.995459 1331.2062 -1144.6328 -663.78961 41.970109 989.12976 -1694.8895 2.4890256 9.9264597 2.1371617 13990.5 + 1450 -624.30479 -657.8718 33.567014 1207.8406 980.42716 -660.87614 47.207833 986.87048 -1694.9545 3.004339 11.783025 2.7986076 13990.5 + 1500 -624.30058 -658.54923 34.248643 1232.3676 -728.22612 -661.1865 43.605107 989.73327 -1694.5249 2.6372721 11.688084 2.5466244 13990.5 +Loop time of 4.08004 on 4 procs for 1000 steps with 432 atoms + +Performance: 42.353 ns/day, 0.567 hours/ns, 245.096 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.7379 | 2.8952 | 3.2162 | 11.5 | 70.96 +Bond | 0.0014176 | 0.0015033 | 0.0016136 | 0.2 | 0.04 +Kspace | 0.47825 | 0.7808 | 0.93251 | 20.9 | 19.14 +Neigh | 0.13731 | 0.13815 | 0.13904 | 0.2 | 3.39 +Comm | 0.23139 | 0.25066 | 0.2586 | 2.2 | 6.14 +Output | 0.0010233 | 0.0015535 | 0.0031006 | 2.3 | 0.04 +Modify | 0.0025311 | 0.0026742 | 0.0028279 | 0.2 | 0.07 +Other | | 0.00951 | | | 0.23 + +Nlocal: 108 ave 116 max 98 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 6461.75 ave 6504 max 6437 min +Histogram: 2 0 0 0 1 0 0 0 0 1 +Neighs: 74412.8 ave 81159 max 68634 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 297651 +Ave neighs/atom = 689.007 +Ave special neighs/atom = 1 +Neighbor list builds = 46 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.1 b/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.1 new file mode 100644 index 0000000000..109e556b7a --- /dev/null +++ b/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.1 @@ -0,0 +1,278 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Testsystem for core-shell model compared to Mitchell and Fincham +# Hendrik Heenen, June 2014 + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + orthogonal box = (0 0 0) to (24.096 24.096 24.096) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 432 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 216 bonds + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +group cores type 1 2 +216 atoms in group cores +group shells type 3 4 +216 atoms in group shells + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +kspace_style ewald 1.0e-6 +pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol + +compute CStemp all temp/cs cores shells +compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CStemp press thermo_press_lmp + +# 2 fmsec timestep + +timestep 0.002 + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 22 + ghost atom cutoff = 22 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/long/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +velocity all scale 1427 temp CStemp + +# thermostating using the core/shell decoupling + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CStemp + +run 500 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5 + 50 -634.17327 -666.17818 32.004909 1151.6314 -4029.8418 -667.9562 37.809071 989.23283 -1694.9981 1.7780231 9.7133792 2.191797 13990.5 + 100 -631.93507 -661.91226 29.977186 1078.6679 -3171.7799 -664.06719 39.33341 991.36934 -1694.7699 2.1549313 11.091423 2.1704389 13990.5 + 150 -630.16811 -663.12417 32.956056 1185.8565 143.26508 -665.48036 46.253769 982.97454 -1694.7087 2.3561935 11.467913 2.1652595 13990.5 + 200 -628.62323 -663.64922 35.025998 1260.3391 -1622.4126 -665.96878 41.661879 986.81675 -1694.4474 2.3195587 10.597709 2.9538262 13990.5 + 250 -627.31045 -662.01825 34.7078 1248.8894 -1509.6621 -664.50312 42.101718 987.90197 -1694.5068 2.4848739 10.392757 1.6933711 13990.5 + 300 -626.57622 -660.97494 34.39872 1237.7678 -1637.8094 -663.48087 41.653234 989.53228 -1694.6664 2.5059303 11.204361 2.2809738 13990.5 + 350 -625.91962 -665.35837 39.438749 1419.123 -1351.4779 -667.6167 41.582456 985.53382 -1694.733 2.2583289 10.83106 1.8963347 13990.5 + 400 -625.24849 -660.77642 35.527934 1278.4003 -424.45104 -663.12602 43.890331 987.75201 -1694.7684 2.3495966 11.521966 2.175931 13990.5 + 450 -624.67743 -662.88678 38.209353 1374.8857 1109.0155 -665.43212 46.964803 982.35208 -1694.749 2.5453383 11.002405 2.0014356 13990.5 + 500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5 +Loop time of 6.42035 on 1 procs for 500 steps with 432 atoms + +Performance: 13.457 ns/day, 1.783 hours/ns, 77.877 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5082 | 5.5082 | 5.5082 | 0.0 | 85.79 +Bond | 0.0019779 | 0.0019779 | 0.0019779 | 0.0 | 0.03 +Kspace | 0.57472 | 0.57472 | 0.57472 | 0.0 | 8.95 +Neigh | 0.23256 | 0.23256 | 0.23256 | 0.0 | 3.62 +Comm | 0.086275 | 0.086275 | 0.086275 | 0.0 | 1.34 +Output | 0.00044322 | 0.00044322 | 0.00044322 | 0.0 | 0.01 +Modify | 0.012263 | 0.012263 | 0.012263 | 0.0 | 0.19 +Other | | 0.003893 | | | 0.06 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9338 ave 9338 max 9338 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 297354 ave 297354 max 297354 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 297354 +Ave neighs/atom = 688.319 +Ave special neighs/atom = 1 +Neighbor list builds = 22 +Dangerous builds = 0 + +unfix thermoberendsen +unfix nve + +fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4 +fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar + +run 500 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5 + 550 -615.79469 -659.53309 43.738406 1573.8374 1470.2728 -662.39233 46.796275 985.55051 -1694.7391 2.8592421 11.816222 2.0435827 13959.536 + 600 -620.1583 -658.0606 37.902298 1363.8369 -1976.0423 -660.62151 39.901722 994.0484 -1694.5716 2.5609098 10.333069 1.7024274 14344.949 + 650 -614.79177 -655.16909 40.377318 1452.8955 1369.3632 -658.06385 47.296696 989.25356 -1694.6141 2.8947623 12.7805 2.1488232 14305.838 + 700 -619.96986 -659.64497 39.675118 1427.6282 455.78012 -662.19977 45.29754 986.93209 -1694.4294 2.554791 10.780261 2.0068563 14432.96 + 750 -616.0691 -654.36205 38.29295 1377.8937 -241.86552 -657.41633 43.727007 993.62088 -1694.7642 3.0542755 11.706048 3.3689413 14829.924 + 800 -614.16673 -652.57617 38.409441 1382.0854 -552.93403 -655.00904 42.769389 996.79939 -1694.5778 2.4328709 11.05387 1.3686986 15324.864 + 850 -611.92307 -653.97912 42.056053 1513.3013 -685.21581 -656.44468 42.244804 996.03742 -1694.7269 2.4655655 11.681335 1.9879277 15467.594 + 900 -615.2753 -658.9358 43.660499 1571.034 -243.69139 -661.50959 43.098716 989.8049 -1694.4132 2.573788 10.674681 1.6541594 14964.747 + 950 -617.05845 -655.42907 38.370623 1380.6886 607.78657 -658.13583 45.497112 991.02201 -1694.6549 2.7067567 12.70332 2.4561886 14472.808 + 1000 -618.16527 -657.57073 39.405466 1417.9254 416.69904 -660.62844 45.155689 988.77163 -1694.5558 3.0577092 11.730529 1.8247965 14362.255 +Loop time of 6.22988 on 1 procs for 500 steps with 432 atoms + +Performance: 13.869 ns/day, 1.731 hours/ns, 80.258 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2759 | 5.2759 | 5.2759 | 0.0 | 84.69 +Bond | 0.0028615 | 0.0028615 | 0.0028615 | 0.0 | 0.05 +Kspace | 0.57661 | 0.57661 | 0.57661 | 0.0 | 9.26 +Neigh | 0.24735 | 0.24735 | 0.24735 | 0.0 | 3.97 +Comm | 0.083591 | 0.083591 | 0.083591 | 0.0 | 1.34 +Output | 0.0004077 | 0.0004077 | 0.0004077 | 0.0 | 0.01 +Modify | 0.03937 | 0.03937 | 0.03937 | 0.0 | 0.63 +Other | | 0.003794 | | | 0.06 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 9025 ave 9025 max 9025 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 290026 ave 290026 max 290026 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 290026 +Ave neighs/atom = 671.356 +Ave special neighs/atom = 1 +Neighbor list builds = 24 +Dangerous builds = 0 + +unfix npt_equ + +# ------------------------ Dynamic Run ------------------------------- + +fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4 +fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar +run 1000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175163 + estimated absolute RMS force accuracy = 1.51081e-05 + estimated relative force accuracy = 1.0492e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 1000 -618.16527 -657.57073 39.405466 1417.9254 428.20902 -660.62844 45.155689 987.86858 -1693.6527 3.0577092 11.730529 1.8247964 14362.255 + 1050 -624.47216 -659.74932 35.277161 1269.3767 1023.4005 -662.65642 47.132969 983.86865 -1693.658 2.9071018 11.128238 2.4855361 14240.043 + 1100 -617.14258 -658.07887 40.936282 1473.0087 -664.49152 -660.92582 42.224469 990.57675 -1693.727 2.8469569 11.75658 2.4149634 14408.926 + 1150 -619.61978 -657.61169 37.991909 1367.0614 -465.46433 -660.31084 43.105221 989.99318 -1693.4092 2.699159 10.782062 2.1690057 14554.158 + 1200 -615.99237 -657.2408 41.248432 1484.2407 -813.35983 -660.07564 41.678196 991.8399 -1693.5937 2.8348373 10.545446 2.1121233 14555.425 + 1250 -626.68392 -658.41883 31.734906 1141.9159 -539.79478 -660.84299 44.20365 988.80199 -1693.8486 2.4241661 11.395962 2.135851 14575.926 + 1300 -617.50678 -657.21802 39.711239 1428.928 1685.6002 -659.90723 48.138182 985.72575 -1693.7712 2.6892077 12.721388 1.8776177 14369.009 + 1350 -622.21239 -658.79581 36.583414 1316.3796 -799.75314 -661.51494 42.733724 989.2771 -1693.5258 2.7191347 11.211319 2.3809801 14613.392 + 1400 -614.34638 -654.89562 40.549232 1459.0815 1192.2924 -657.82292 46.886633 988.93592 -1693.6455 2.927306 11.818277 2.0357932 15050.984 + 1450 -614.74459 -651.08463 36.340044 1307.6224 -941.42354 -653.80733 42.373988 997.48406 -1693.6654 2.7226961 11.57117 1.9107106 15667.952 + 1500 -608.59499 -648.39988 39.804894 1432.2979 -1036.978 -651.42193 41.284322 1000.5742 -1693.2804 3.0220531 10.965804 1.9225015 15657.799 + 1550 -616.75971 -653.701 36.941282 1329.2567 956.80287 -656.37213 46.958724 990.63147 -1693.9623 2.6711387 11.270035 2.1646421 15283.769 + 1600 -614.00249 -655.22129 41.218796 1483.1743 162.86851 -658.03388 44.578553 990.97117 -1693.5836 2.8125894 12.001595 2.1613558 15014.979 + 1650 -620.21853 -658.7696 38.551071 1387.1817 -15.994219 -661.3575 44.417732 988.12137 -1693.8966 2.5879024 11.60402 2.2188998 14421.685 + 1700 -621.65896 -660.14043 38.481472 1384.6773 374.01196 -662.88364 45.046442 985.61668 -1693.5468 2.7432107 11.020422 2.0354876 13843.115 + 1750 -626.52363 -662.7125 36.188873 1302.1828 246.87832 -665.23873 45.613954 983.17191 -1694.0246 2.5262291 12.801515 2.4291407 13584.377 + 1800 -620.84342 -658.64915 37.805737 1360.3624 1419.6927 -661.54346 47.476679 984.72199 -1693.7421 2.8943029 13.331926 2.1690676 13249.778 + 1850 -618.96345 -661.03809 42.074638 1513.9701 1692.1613 -663.74409 47.099139 982.71413 -1693.5574 2.7060076 11.521214 1.6552929 13269.978 + 1900 -622.60007 -658.68592 36.085857 1298.476 -1580.4079 -661.4614 41.163528 991.0778 -1693.7027 2.7754739 10.427911 1.946547 14057.045 + 1950 -613.97975 -656.9327 42.952955 1545.5745 -1163.9497 -659.48701 40.688202 993.61603 -1693.7912 2.5543044 10.621596 2.2183688 14489.331 + 2000 -613.52562 -654.78948 41.263864 1484.796 646.07695 -657.76756 45.489785 990.40525 -1693.6626 2.978081 12.135455 2.3293 14760.827 +Loop time of 12.672 on 1 procs for 1000 steps with 432 atoms + +Performance: 13.636 ns/day, 1.760 hours/ns, 78.914 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.73 | 10.73 | 10.73 | 0.0 | 84.67 +Bond | 0.0057325 | 0.0057325 | 0.0057325 | 0.0 | 0.05 +Kspace | 1.1532 | 1.1532 | 1.1532 | 0.0 | 9.10 +Neigh | 0.52571 | 0.52571 | 0.52571 | 0.0 | 4.15 +Comm | 0.17069 | 0.17069 | 0.17069 | 0.0 | 1.35 +Output | 0.00081754 | 0.00081754 | 0.00081754 | 0.0 | 0.01 +Modify | 0.078469 | 0.078469 | 0.078469 | 0.0 | 0.62 +Other | | 0.007788 | | | 0.06 + +Nlocal: 432 ave 432 max 432 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 8927 ave 8927 max 8927 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 281696 ave 281696 max 281696 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 281696 +Ave neighs/atom = 652.074 +Ave special neighs/atom = 1 +Neighbor list builds = 50 +Dangerous builds = 0 +Total wall time: 0:00:25 diff --git a/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.4 b/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.4 new file mode 100644 index 0000000000..679ee19a39 --- /dev/null +++ b/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.4 @@ -0,0 +1,278 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Testsystem for core-shell model compared to Mitchell and Fincham +# Hendrik Heenen, June 2014 + +# ------------------------ INITIALIZATION ---------------------------- + +units metal +dimension 3 +boundary p p p +atom_style full + +# ----------------------- ATOM DEFINITION ---------------------------- + +fix csinfo all property/atom i_CSID +read_data data.coreshell fix csinfo NULL CS-Info + orthogonal box = (0 0 0) to (24.096 24.096 24.096) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 432 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 216 bonds + 1 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + +group cores type 1 2 +216 atoms in group cores +group shells type 3 4 +216 atoms in group shells + +neighbor 2.0 bin +comm_modify vel yes + +# ------------------------ FORCE FIELDS ------------------------------ + +kspace_style ewald 1.0e-6 +pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D +pair_coeff * * 0.0 1.000 0.00 0.00 0.00 +pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na +pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl +pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl + +bond_style harmonic +bond_coeff 1 63.014 0.0 +bond_coeff 2 25.724 0.0 + +# ------------------------ Equilibration Run ------------------------------- + +reset_timestep 0 + +thermo 50 +thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol + +compute CStemp all temp/cs cores shells +compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar + +# output via chunk method + +#compute prop all property/atom i_CSID +#compute cs_chunk all chunk/atom c_prop +#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 +#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector + +thermo_modify temp CStemp press thermo_press_lmp + +# 2 fmsec timestep + +timestep 0.002 + +# velocity bias option + +velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 22 + ghost atom cutoff = 22 + binsize = 11, bins = 3 3 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair born/coul/long/cs, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +velocity all scale 1427 temp CStemp + +# thermostating using the core/shell decoupling + +fix thermoberendsen all temp/berendsen 1427 1427 0.4 +fix nve all nve +fix_modify thermoberendsen temp CStemp + +run 500 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 15.58 | 15.58 | 15.58 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5 + 50 -634.17349 -666.17817 32.004686 1151.6234 -4029.8405 -667.9562 37.809075 989.23283 -1694.9981 1.778024 9.7133822 2.1917966 13990.5 + 100 -631.93517 -661.91227 29.977104 1078.665 -3171.8044 -664.0672 39.333371 991.36937 -1694.7699 2.1549315 11.091441 2.1704346 13990.5 + 150 -630.16822 -663.12423 32.956001 1185.8545 143.24615 -665.48041 46.253736 982.97453 -1694.7087 2.3561828 11.467862 2.1651517 13990.5 + 200 -628.6223 -663.6493 35.026994 1260.375 -1622.4428 -665.96885 41.661825 986.81675 -1694.4474 2.3195537 10.597709 2.9538132 13990.5 + 250 -627.31146 -662.01843 34.706968 1248.8595 -1509.7149 -664.50329 42.10159 987.90193 -1694.5068 2.4848612 10.392642 1.693337 13990.5 + 300 -626.57661 -660.97479 34.398178 1237.7483 -1637.8266 -663.48071 41.653258 989.53241 -1694.6664 2.5059269 11.20455 2.2814851 13990.5 + 350 -625.91971 -665.3583 39.438589 1419.1172 -1351.5076 -667.61665 41.582479 985.53388 -1694.733 2.2583457 10.831559 1.8963688 13990.5 + 400 -625.24855 -660.7758 35.527253 1278.3758 -423.70384 -663.1256 43.89223 987.7506 -1694.7684 2.349799 11.523597 2.1775994 13990.5 + 450 -624.6774 -662.88749 38.210092 1374.9123 1108.7784 -665.43272 46.964156 982.35233 -1694.7492 2.5452316 11.002239 2.001871 13990.5 + 500 -624.30227 -661.97992 37.677648 1355.7533 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5 +Loop time of 1.9161 on 4 procs for 500 steps with 432 atoms + +Performance: 45.092 ns/day, 0.532 hours/ns, 260.946 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3101 | 1.4046 | 1.5088 | 5.9 | 73.31 +Bond | 0.00073409 | 0.00074953 | 0.00076699 | 0.0 | 0.04 +Kspace | 0.20996 | 0.30779 | 0.39708 | 12.0 | 16.06 +Neigh | 0.065428 | 0.065516 | 0.065591 | 0.0 | 3.42 +Comm | 0.12002 | 0.12628 | 0.13124 | 1.2 | 6.59 +Output | 0.00047278 | 0.00062203 | 0.0010662 | 0.0 | 0.03 +Modify | 0.0061893 | 0.0064721 | 0.0066924 | 0.2 | 0.34 +Other | | 0.004042 | | | 0.21 + +Nlocal: 108 ave 119 max 102 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Nghost: 6516 ave 6545 max 6491 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 74337.8 ave 81248 max 69989 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 297351 +Ave neighs/atom = 688.312 +Ave special neighs/atom = 1 +Neighbor list builds = 22 +Dangerous builds = 0 + +unfix thermoberendsen +unfix nve + +fix npt_equ all npt temp 1427 1427 0.04 iso 0 0 0.4 +fix_modify npt_equ temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar + +run 500 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.175257 + estimated absolute RMS force accuracy = 1.49563e-05 + estimated relative force accuracy = 1.03866e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 15.59 | 15.65 | 15.84 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 500 -624.30215 -661.97992 37.677763 1355.7575 -998.38049 -664.60501 42.373269 987.58935 -1694.5676 2.6250971 11.151918 2.8270144 13990.5 + 550 -615.79609 -659.53283 43.736746 1573.7776 1474.8922 -662.39181 46.806896 985.54114 -1694.7399 2.858983 11.812288 2.0388938 13959.445 + 600 -620.14312 -658.02816 37.88504 1363.2159 -1969.137 -660.59055 39.918958 994.06227 -1694.5718 2.5623852 10.344301 1.7265857 14345.491 + 650 -614.8194 -655.14772 40.328319 1451.1323 1362.2165 -658.04338 47.289196 989.28021 -1694.6128 2.8956629 12.77476 2.1533941 14308.181 + 700 -620.02982 -659.67169 39.641877 1426.4321 437.18253 -662.22416 45.260412 986.94645 -1694.431 2.5524634 10.78512 2.0136405 14434.476 + 750 -616.07569 -654.50017 38.424477 1382.6265 -256.57498 -657.55133 43.657506 993.54515 -1694.754 3.0511562 11.572553 3.3391993 14823.696 + 800 -614.14966 -652.72914 38.579477 1388.2038 -584.44437 -655.14057 42.618194 996.80921 -1694.568 2.4114337 10.916418 1.4113651 15315.148 + 850 -612.16455 -653.84169 41.677135 1499.6667 -441.98725 -656.42973 42.922374 995.29998 -1694.6521 2.5880353 11.829353 2.135168 15445.115 + 900 -615.1092 -656.96201 41.85281 1505.988 374.2354 -659.60969 44.82627 989.96538 -1694.4013 2.6476821 11.074704 1.5105804 14959.613 + 950 -620.11829 -657.30032 37.18203 1337.9196 237.21273 -659.92487 44.925824 990.04501 -1694.8957 2.6245445 11.636019 2.6504684 14536.194 + 1000 -614.74144 -660.36077 45.619322 1641.5183 890.12037 -663.18359 45.139971 986.56616 -1694.8897 2.8228194 11.867666 2.4545613 14093.503 +Loop time of 1.93169 on 4 procs for 500 steps with 432 atoms + +Performance: 44.728 ns/day, 0.537 hours/ns, 258.841 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.239 | 1.3639 | 1.4951 | 8.2 | 70.61 +Bond | 0.0009706 | 0.0010555 | 0.0010962 | 0.2 | 0.05 +Kspace | 0.22414 | 0.34623 | 0.46491 | 15.4 | 17.92 +Neigh | 0.069416 | 0.069507 | 0.06959 | 0.0 | 3.60 +Comm | 0.11461 | 0.12363 | 0.13004 | 1.6 | 6.40 +Output | 0.00040793 | 0.0006547 | 0.001394 | 0.0 | 0.03 +Modify | 0.022097 | 0.022964 | 0.023674 | 0.4 | 1.19 +Other | | 0.003751 | | | 0.19 + +Nlocal: 108 ave 130 max 94 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 6344.5 ave 6406 max 6272 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 72679.5 ave 88315 max 61830 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 290718 +Ave neighs/atom = 672.958 +Ave special neighs/atom = 1 +Neighbor list builds = 24 +Dangerous builds = 0 + +unfix npt_equ + +# ------------------------ Dynamic Run ------------------------------- + +fix npt_dyn all npt temp 1427 1427 0.04 iso 0 0 0.4 +fix_modify npt_dyn temp CStemp press thermo_press_lmp # pressure for correct kinetic scalar +run 1000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.17523 + estimated absolute RMS force accuracy = 1.49925e-05 + estimated relative force accuracy = 1.04117e-06 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +Per MPI rank memory allocation (min/avg/max) = 15.59 | 15.71 | 15.84 Mbytes +Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume + 1000 -614.74144 -660.36077 45.619322 1641.5183 897.55556 -663.18359 45.139971 986.31352 -1694.6371 2.8228194 11.867665 2.4545613 14093.503 + 1050 -618.94984 -658.03173 39.081888 1406.2821 5.4174147 -660.68647 43.84377 989.81944 -1694.3497 2.6547475 10.009866 1.6559553 14124.735 + 1100 -616.115 -652.50083 36.385826 1309.2698 246.27221 -655.60386 44.678646 993.96562 -1694.2481 3.1030335 12.845497 2.1365385 14269.044 + 1150 -612.77698 -655.40444 42.627458 1533.8622 -394.23637 -658.16511 42.232098 993.95417 -1694.3514 2.7606635 10.588799 2.0797438 14526.576 + 1200 -614.12785 -652.61572 38.487865 1384.9074 -1232.5709 -655.35877 40.844849 997.88225 -1694.0859 2.7430549 11.246738 2.4837618 14939.435 + 1250 -612.01665 -651.53067 39.514016 1421.8313 -532.88057 -654.28679 42.767165 997.1403 -1694.1943 2.7561288 12.258706 3.8726564 15369.672 + 1300 -616.56459 -654.91454 38.349957 1379.945 -41.331568 -657.57515 44.211159 992.57496 -1694.3613 2.6606091 11.147615 2.3545887 15492.237 + 1350 -609.61162 -652.77366 43.162036 1553.0979 672.33089 -655.82423 44.690532 993.39227 -1693.907 3.0505702 11.680426 1.9918324 15294.141 + 1400 -616.08355 -652.13969 36.056138 1297.4066 -1202.7428 -654.77053 41.470863 998.3537 -1694.5951 2.6308398 10.12054 1.9139605 15206.436 + 1450 -613.53416 -655.92542 42.391264 1525.3632 -225.70273 -658.53945 42.800387 993.30095 -1694.6408 2.61403 10.475263 1.5543043 14786.088 + 1500 -618.90281 -658.01769 39.114877 1407.4691 1689.1895 -660.56762 47.983304 985.87237 -1694.4233 2.5499298 12.160031 2.121879 14225.24 + 1550 -619.95625 -660.95261 40.996357 1475.1703 162.48311 -663.63715 44.435076 986.14893 -1694.2212 2.6845396 11.400162 2.1028833 14097.469 + 1600 -621.01142 -658.90113 37.889708 1363.3839 -1426.7573 -661.45407 41.336331 991.32904 -1694.1194 2.5529431 10.96667 1.8785672 14124.398 + 1650 -616.93204 -657.21145 40.27941 1449.3725 1600.8152 -659.95623 47.433021 987.26391 -1694.6532 2.7447834 12.068379 2.0232824 13868.26 + 1700 -613.94971 -656.25711 42.307399 1522.3455 -17.243012 -658.67143 43.416284 992.19931 -1694.287 2.4143179 10.33501 1.9231274 14268.199 + 1750 -614.52671 -652.83727 38.310551 1378.5271 -1505.7623 -655.2978 40.639683 998.21477 -1694.1523 2.4605373 10.777496 1.8915025 14892.754 + 1800 -608.85779 -650.27052 41.412727 1490.1526 -426.82921 -653.21627 42.824093 998.13559 -1694.176 2.9457492 12.624136 2.1758155 15177.014 + 1850 -614.3254 -653.44307 39.117675 1407.5698 -10.449183 -656.43604 44.1397 993.33969 -1693.9154 2.992966 11.306721 2.0406266 14987.262 + 1900 -617.0898 -655.8162 38.726395 1393.4904 -810.27608 -658.56819 42.357417 993.51569 -1694.4413 2.751989 11.117505 1.8829772 14850.207 + 1950 -615.58194 -657.41631 41.834372 1505.3246 1466.9904 -660.21529 47.446402 986.51421 -1694.1759 2.7989828 12.408148 2.0449602 14609.998 + 2000 -617.98223 -655.26933 37.287095 1341.7001 -728.80528 -658.12982 42.660772 993.38817 -1694.1788 2.8604933 11.117049 2.0691895 14608.511 +Loop time of 4.08624 on 4 procs for 1000 steps with 432 atoms + +Performance: 42.288 ns/day, 0.568 hours/ns, 244.724 timesteps/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5272 | 2.7629 | 3.169 | 14.9 | 67.62 +Bond | 0.001961 | 0.0021452 | 0.0023017 | 0.3 | 0.05 +Kspace | 0.48303 | 0.85591 | 1.0735 | 24.7 | 20.95 +Neigh | 0.14933 | 0.14943 | 0.14956 | 0.0 | 3.66 +Comm | 0.22499 | 0.25699 | 0.27433 | 3.8 | 6.29 +Output | 0.00085068 | 0.001357 | 0.0028689 | 2.4 | 0.03 +Modify | 0.048769 | 0.049731 | 0.051893 | 0.6 | 1.22 +Other | | 0.00775 | | | 0.19 + +Nlocal: 108 ave 118 max 100 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 6291.25 ave 6323 max 6256 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 71221.2 ave 77896 max 66643 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 284885 +Ave neighs/atom = 659.456 +Ave special neighs/atom = 1 +Neighbor list builds = 50 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 b/examples/coreshell/log.27Nov18.coreshell.wolf.g++.1 similarity index 51% rename from examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 rename to examples/coreshell/log.27Nov18.coreshell.wolf.g++.1 index 35c30913fc..de23733aca 100644 --- a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.1 +++ b/examples/coreshell/log.27Nov18.coreshell.wolf.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (22 Sep 2017) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Testsystem for core-shell model compared to Mitchel and Finchham # Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. @@ -92,31 +93,31 @@ run 500 Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5 - 50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858939 9.6844521 2.2001656 13990.5 + 50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858938 9.684452 2.2001656 13990.5 100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5 - 150 -630.82538 -663.70056 32.875182 1182.9464 -74.330324 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5 + 150 -630.82538 -663.70056 32.875182 1182.9464 -74.33032 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5 200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5 - 250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400986 13990.5 + 250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400987 13990.5 300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5 - 350 -626.27558 -665.04303 38.767448 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5 + 350 -626.27558 -665.04303 38.767449 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5 400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5 - 450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068929 13990.5 - 500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5 -Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms + 450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068928 13990.5 + 500 -623.87093 -660.24145 36.370525 1308.7192 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5 +Loop time of 9.56959 on 1 procs for 500 steps with 432 atoms -Performance: 7.381 ns/day, 3.252 hours/ns, 42.711 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 9.029 ns/day, 2.658 hours/ns, 52.249 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 11.535 | 11.535 | 11.535 | 0.0 | 98.54 -Bond | 0.001443 | 0.001443 | 0.001443 | 0.0 | 0.01 -Neigh | 0.10952 | 0.10952 | 0.10952 | 0.0 | 0.94 -Comm | 0.048796 | 0.048796 | 0.048796 | 0.0 | 0.42 -Output | 0.00038695 | 0.00038695 | 0.00038695 | 0.0 | 0.00 -Modify | 0.0067511 | 0.0067511 | 0.0067511 | 0.0 | 0.06 -Other | | 0.004243 | | | 0.04 +Pair | 9.2366 | 9.2366 | 9.2366 | 0.0 | 96.52 +Bond | 0.0020828 | 0.0020828 | 0.0020828 | 0.0 | 0.02 +Neigh | 0.22581 | 0.22581 | 0.22581 | 0.0 | 2.36 +Comm | 0.087387 | 0.087387 | 0.087387 | 0.0 | 0.91 +Output | 0.00043035 | 0.00043035 | 0.00043035 | 0.0 | 0.00 +Modify | 0.013176 | 0.013176 | 0.013176 | 0.0 | 0.14 +Other | | 0.004087 | | | 0.04 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -138,53 +139,53 @@ unfix thermoberendsen run 1000 Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume - 500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5 - 550 -623.95762 -659.99899 36.041371 1296.8752 -442.62446 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5 - 600 -624.04214 -661.21748 37.175332 1337.6785 47.615854 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185464 13990.5 - 650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3823 -664.31138 40.933446 -705.24482 0 2.4588298 9.7960191 1.4159904 13990.5 - 700 -624.02941 -661.57484 37.54543 1350.9958 -124.09512 -663.95322 44.666402 -708.61962 0 2.3783801 10.518712 2.0854584 13990.5 - 750 -624.03935 -661.11619 37.076837 1334.1344 -1163.2721 -663.82553 42.1219 -705.94743 0 2.7093404 10.634859 1.9381654 13990.5 - 800 -623.98709 -659.43647 35.44938 1275.5737 -285.65702 -662.23782 44.650233 -706.88805 0 2.8013482 11.83459 3.4506407 13990.5 - 850 -623.96081 -661.77923 37.818422 1360.8188 -814.33212 -664.38161 42.860208 -707.24181 0 2.6023728 10.766451 2.9211132 13990.5 - 900 -623.96136 -662.98419 39.022831 1404.157 308.13105 -665.65877 45.053188 -710.71195 0 2.6745786 11.028799 1.8494322 13990.5 - 950 -623.91048 -660.63828 36.7278 1321.575 -445.31526 -663.79806 43.94833 -707.74639 0 3.1597729 11.852051 1.8238458 13990.5 - 1000 -623.90541 -661.03474 37.129332 1336.0233 522.57958 -663.50212 45.863261 -709.36538 0 2.4673781 10.949291 1.8614095 13990.5 - 1050 -624.01134 -660.99076 36.979422 1330.6291 -1710.2829 -663.67762 41.056102 -704.73372 0 2.6868521 10.86533 2.2154165 13990.5 - 1100 -624.02639 -660.86661 36.840225 1325.6204 1151.0236 -663.5066 47.207185 -710.71378 0 2.6399847 11.298044 1.8900703 13990.5 - 1150 -624.04418 -661.29819 37.254006 1340.5094 161.09847 -663.73735 45.222561 -708.95991 0 2.4391651 11.261119 2.2245673 13990.5 - 1200 -624.08628 -662.39932 38.313043 1378.6168 -1405.0927 -664.93121 41.728112 -706.65933 0 2.5318927 10.458041 2.1153159 13990.5 - 1250 -624.03036 -661.25661 37.226248 1339.5106 63.407721 -663.72719 45.086961 -708.81415 0 2.4705832 11.766021 2.2297809 13990.5 - 1300 -623.97475 -661.55998 37.585229 1352.4278 -763.66781 -663.80645 42.870244 -706.6767 0 2.2464703 10.098322 1.7614596 13990.5 - 1350 -623.93123 -660.30786 36.376631 1308.9389 -2389.8052 -663.04725 39.749029 -702.79628 0 2.7393936 10.879364 2.6622521 13990.5 - 1400 -623.86468 -658.44644 34.581765 1244.3543 2262.7586 -660.95368 50.10608 -711.05976 0 2.5072434 11.528291 1.7861906 13990.5 - 1450 -623.85494 -661.47216 37.617217 1353.5789 -1435.0174 -664.13587 41.701767 -705.83764 0 2.6637191 11.297444 2.0038345 13990.5 - 1500 -623.79928 -659.70124 35.901959 1291.8588 -198.39562 -662.57415 44.358482 -706.93263 0 2.872907 11.075746 2.2821286 13990.5 -Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms + 500 -623.87093 -660.24145 36.370525 1308.7192 410.85327 -662.86944 45.869201 -708.73864 0 2.6279857 10.592786 1.8162328 13990.5 + 550 -623.95762 -659.99899 36.041371 1296.8752 -442.62441 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5 + 600 -624.04214 -661.21748 37.175332 1337.6785 47.61587 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185465 13990.5 + 650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3824 -664.31138 40.933446 -705.24482 0 2.4588297 9.7960192 1.4159906 13990.5 + 700 -624.02941 -661.57484 37.545431 1350.9958 -124.09619 -663.95322 44.666399 -708.61962 0 2.3783802 10.518712 2.0854583 13990.5 + 750 -624.03935 -661.11619 37.076842 1334.1346 -1163.274 -663.82553 42.121895 -705.94743 0 2.70934 10.634855 1.9381646 13990.5 + 800 -623.98709 -659.43647 35.449379 1275.5736 -285.65541 -662.23781 44.650237 -706.88805 0 2.8013481 11.83459 3.4506393 13990.5 + 850 -623.96081 -661.77923 37.81842 1360.8187 -814.33165 -664.3816 42.860208 -707.24181 0 2.6023716 10.766441 2.9211138 13990.5 + 900 -623.96136 -662.9842 39.02284 1404.1573 308.1419 -665.65877 45.053211 -710.71198 0 2.674576 11.028802 1.8494293 13990.5 + 950 -623.91049 -660.63827 36.727782 1321.5743 -445.29549 -663.79804 43.948376 -707.74641 0 3.1597692 11.852029 1.8238312 13990.5 + 1000 -623.90541 -661.03472 37.129304 1336.0223 522.59285 -663.50211 45.8633 -709.36541 0 2.4673901 10.949322 1.8613502 13990.5 + 1050 -624.01134 -660.99086 36.979522 1330.6327 -1710.3266 -663.6777 41.055997 -704.7337 0 2.6868396 10.865335 2.2154562 13990.5 + 1100 -624.02639 -660.86653 36.840144 1325.6175 1151.2194 -663.50657 47.207655 -710.71423 0 2.6400422 11.298226 1.8901962 13990.5 + 1150 -624.04418 -661.29792 37.253732 1340.4996 161.18555 -663.7371 45.222823 -708.95992 0 2.4391845 11.26132 2.2249572 13990.5 + 1200 -624.08629 -662.39857 38.312276 1378.5891 -1404.3216 -664.93056 41.729944 -706.6605 0 2.5319943 10.45796 2.1150356 13990.5 + 1250 -624.03031 -661.25639 37.226081 1339.5046 61.673399 -663.72681 45.083327 -708.81014 0 2.4704185 11.764377 2.2300033 13990.5 + 1300 -623.97477 -661.56221 37.587436 1352.5072 -766.14948 -663.8091 42.864064 -706.67316 0 2.2468911 10.098925 1.7609776 13990.5 + 1350 -623.93106 -660.2936 36.362535 1308.4317 -2387.7331 -663.03485 39.756427 -702.79127 0 2.7412491 10.88663 2.66284 13990.5 + 1400 -623.86405 -658.43845 34.574407 1244.0896 2274.8627 -660.9465 50.133006 -711.0795 0 2.5080438 11.530504 1.7943496 13990.5 + 1450 -623.85491 -661.52972 37.674807 1355.6511 -1417.2183 -664.20085 41.731022 -705.93187 0 2.6711331 11.299254 1.9911762 13990.5 + 1500 -623.80036 -659.86071 36.060348 1297.5581 -193.90288 -662.71759 44.340486 -707.05807 0 2.8568759 11.042693 2.2234298 13990.5 +Loop time of 19.4477 on 1 procs for 1000 steps with 432 atoms -Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 8.885 ns/day, 2.701 hours/ns, 51.420 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 23.069 | 23.069 | 23.069 | 0.0 | 98.54 -Bond | 0.0029275 | 0.0029275 | 0.0029275 | 0.0 | 0.01 -Neigh | 0.22821 | 0.22821 | 0.22821 | 0.0 | 0.97 -Comm | 0.097941 | 0.097941 | 0.097941 | 0.0 | 0.42 -Output | 0.00074033 | 0.00074033 | 0.00074033 | 0.0 | 0.00 -Modify | 0.0042015 | 0.0042015 | 0.0042015 | 0.0 | 0.02 -Other | | 0.00865 | | | 0.04 +Pair | 18.754 | 18.754 | 18.754 | 0.0 | 96.43 +Bond | 0.0046136 | 0.0046136 | 0.0046136 | 0.0 | 0.02 +Neigh | 0.49116 | 0.49116 | 0.49116 | 0.0 | 2.53 +Comm | 0.17734 | 0.17734 | 0.17734 | 0.0 | 0.91 +Output | 0.00094318 | 0.00094318 | 0.00094318 | 0.0 | 0.00 +Modify | 0.007426 | 0.007426 | 0.007426 | 0.0 | 0.04 +Other | | 0.0122 | | | 0.06 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 9388 ave 9388 max 9388 min +Nghost: 9382 ave 9382 max 9382 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 297212 ave 297212 max 297212 min +Neighs: 297191 ave 297191 max 297191 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 297212 -Ave neighs/atom = 687.991 +Total # of neighbors = 297191 +Ave neighs/atom = 687.942 Ave special neighs/atom = 1 Neighbor list builds = 45 Dangerous builds = 0 -Total wall time: 0:00:35 +Total wall time: 0:00:29 diff --git a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 b/examples/coreshell/log.27Nov18.coreshell.wolf.g++.4 similarity index 54% rename from examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 rename to examples/coreshell/log.27Nov18.coreshell.wolf.g++.4 index 84f854cf67..e099e7ca4e 100644 --- a/examples/coreshell/log.22Sep17.coreshell.wolf.g++.4 +++ b/examples/coreshell/log.27Nov18.coreshell.wolf.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (22 Sep 2017) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Testsystem for core-shell model compared to Mitchel and Finchham # Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation. @@ -94,29 +95,29 @@ Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fm 0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.3530839e-14 3.6429193e-15 13990.5 50 -635.62704 -667.67108 32.044047 1153.0397 -4532.6842 -669.45828 37.771018 -707.2293 0 1.787201 9.6848095 2.2028349 13990.5 100 -632.76343 -662.83014 30.066711 1081.8893 -3493.0827 -664.98212 39.195967 -704.17809 0 2.151977 11.060773 2.1578583 13990.5 - 150 -630.82533 -663.70172 32.876385 1182.9897 -75.706974 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5 + 150 -630.82533 -663.70172 32.876385 1182.9897 -75.706966 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5 200 -629.15463 -664.55009 35.395466 1273.6337 -1707.9185 -666.88117 41.794868 -708.67604 0 2.331082 10.596229 3.0031523 13990.5 - 250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.841604 13990.5 - 300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160685 1.2472271 13990.5 + 250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.8416041 13990.5 + 300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160684 1.2472271 13990.5 350 -626.2729 -665.01858 38.745682 1394.1844 -1433.1302 -667.44315 41.864785 -709.30793 0 2.4245625 10.312641 1.9815612 13990.5 - 400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039276 11.076154 2.1819703 13990.5 - 450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6101 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5 - 500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 -Loop time of 4.63313 on 4 procs for 500 steps with 432 atoms + 400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039277 11.076154 2.1819702 13990.5 + 450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6102 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5 + 500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 +Loop time of 3.06159 on 4 procs for 500 steps with 432 atoms -Performance: 18.648 ns/day, 1.287 hours/ns, 107.919 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 28.221 ns/day, 0.850 hours/ns, 163.314 timesteps/s +95.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.8133 | 3.5934 | 4.4255 | 36.3 | 77.56 -Bond | 0.00042245 | 0.00050305 | 0.00059825 | 0.0 | 0.01 -Neigh | 0.0411 | 0.041561 | 0.04202 | 0.2 | 0.90 -Comm | 0.15622 | 0.9884 | 1.7686 | 69.2 | 21.33 -Output | 0.00028311 | 0.00031345 | 0.00040011 | 0.0 | 0.01 -Modify | 0.0039899 | 0.00403 | 0.0040654 | 0.0 | 0.09 -Other | | 0.004911 | | | 0.11 +Pair | 2.3967 | 2.4786 | 2.5323 | 3.3 | 80.96 +Bond | 0.00078011 | 0.00080734 | 0.00087595 | 0.0 | 0.03 +Neigh | 0.065675 | 0.065807 | 0.06593 | 0.0 | 2.15 +Comm | 0.43311 | 0.49538 | 0.58587 | 8.0 | 16.18 +Output | 0.00041747 | 0.00060827 | 0.0011797 | 0.0 | 0.02 +Modify | 0.0073676 | 0.016077 | 0.024872 | 6.9 | 0.53 +Other | | 0.004283 | | | 0.14 Nlocal: 108 ave 112 max 106 min Histogram: 2 0 0 1 0 0 0 0 0 1 @@ -138,53 +139,53 @@ unfix thermoberendsen run 1000 Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume - 500 -623.86344 -660.20235 36.338906 1307.5814 462.72862 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 - 550 -623.95339 -660.07946 36.126069 1299.9229 -362.67288 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461377 13990.5 - 600 -624.04508 -661.27298 37.227902 1339.5701 110.39823 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5 + 500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5 + 550 -623.95339 -660.07946 36.126069 1299.9229 -362.67285 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461376 13990.5 + 600 -624.04508 -661.27298 37.227902 1339.5701 110.39822 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5 650 -623.9608 -661.50573 37.544934 1350.9779 -1594.4701 -663.91531 41.226571 -705.14188 0 2.4095736 10.022027 1.6264014 13990.5 - 700 -624.00658 -663.55636 39.549777 1423.1181 -588.9804 -665.88666 43.124023 -709.01068 0 2.3302979 9.924587 2.1027837 13990.5 - 750 -623.99813 -659.97695 35.978816 1294.6243 -364.1415 -662.75959 43.973556 -706.73315 0 2.782646 11.487832 1.8799695 13990.5 - 800 -624.01235 -661.04908 37.036728 1332.6911 -85.655852 -663.49204 44.570117 -708.06215 0 2.4429547 11.213149 1.6792926 13990.5 - 850 -624.02581 -659.39933 35.373519 1272.844 -1090.9179 -662.11969 42.375064 -704.49476 0 2.7203673 11.214629 2.2907474 13990.5 - 900 -624.09244 -663.33386 39.241421 1412.0225 303.76207 -666.00593 45.332458 -711.33839 0 2.6720667 11.897188 2.0599033 13990.5 - 950 -624.04544 -661.11578 37.070341 1333.9007 1637.6438 -663.61305 48.65892 -712.27197 0 2.49727 12.343774 2.429225 13990.5 - 1000 -623.95457 -661.51816 37.563586 1351.6491 -851.77182 -663.83594 42.813468 -706.64941 0 2.317782 10.251422 1.6922864 13990.5 - 1050 -623.98731 -662.01988 38.032562 1368.5242 -2123.9075 -664.72609 39.917382 -704.64348 0 2.706218 9.600838 1.7365559 13990.5 - 1100 -623.9653 -659.32023 35.354929 1272.1751 -436.90576 -662.14454 44.057776 -706.20232 0 2.8243167 11.267546 2.6807602 13990.5 - 1150 -624.02273 -665.13902 41.116293 1479.486 -128.13268 -667.4769 44.013761 -711.49066 0 2.3378768 10.406604 1.5102324 13990.5 - 1200 -623.97328 -663.08042 39.107135 1407.1905 -539.63284 -665.67946 43.319308 -708.99877 0 2.599042 10.632657 1.4608707 13990.5 - 1250 -623.92529 -661.81902 37.893723 1363.5284 1708.0621 -664.63624 48.396874 -713.03311 0 2.8172251 11.369352 1.8836979 13990.5 - 1300 -623.99283 -662.19734 38.204509 1374.7114 -820.77291 -664.34556 42.656202 -707.00176 0 2.1482151 10.186898 1.7081329 13990.5 - 1350 -623.99798 -658.70752 34.709535 1248.9519 776.28486 -662.01647 46.925412 -708.94188 0 3.3089536 12.457581 2.5027978 13990.5 - 1400 -623.96941 -662.15959 38.190183 1374.1959 880.21756 -664.90452 46.628183 -711.5327 0 2.7449282 11.918894 3.0466188 13990.5 - 1450 -623.95068 -662.25435 38.303671 1378.2795 -391.56711 -664.7631 43.644066 -708.40716 0 2.5087493 10.465803 1.8744864 13990.5 - 1500 -624.00637 -661.48756 37.481185 1348.684 430.69453 -664.32151 45.704366 -710.02587 0 2.8339501 11.650821 2.0752813 13990.5 -Loop time of 6.7003 on 4 procs for 1000 steps with 432 atoms + 700 -624.00658 -663.55636 39.549777 1423.1181 -588.98052 -665.88666 43.124023 -709.01068 0 2.3302979 9.9245872 2.1027837 13990.5 + 750 -623.99813 -659.97694 35.978814 1294.6243 -364.14087 -662.75959 43.973558 -706.73315 0 2.782646 11.487833 1.8799696 13990.5 + 800 -624.01235 -661.04908 37.03673 1332.6912 -85.65751 -663.49204 44.570113 -708.06215 0 2.4429544 11.213146 1.6792935 13990.5 + 850 -624.02581 -659.39932 35.373517 1272.8439 -1090.9176 -662.11969 42.375065 -704.49476 0 2.7203674 11.21463 2.2907477 13990.5 + 900 -624.09244 -663.33388 39.241435 1412.0231 303.76293 -666.00594 45.332457 -711.3384 0 2.6720661 11.89718 2.0599025 13990.5 + 950 -624.04544 -661.11578 37.070343 1333.9007 1637.6353 -663.61305 48.6589 -712.27195 0 2.4972693 12.343765 2.4292305 13990.5 + 1000 -623.95457 -661.51817 37.563599 1351.6495 -851.76774 -663.83595 42.813476 -706.64943 0 2.3177804 10.251415 1.6922809 13990.5 + 1050 -623.98731 -662.01986 38.032541 1368.5235 -2123.915 -664.72608 39.917367 -704.64345 0 2.7062234 9.6008351 1.7364324 13990.5 + 1100 -623.9653 -659.3203 35.355002 1272.1777 -436.97572 -662.14462 44.05761 -706.20223 0 2.8243234 11.267511 2.6807914 13990.5 + 1150 -624.02272 -665.13875 41.116028 1479.4764 -128.02349 -667.47666 44.014064 -711.49073 0 2.337912 10.406786 1.5105446 13990.5 + 1200 -623.97327 -663.08066 39.107391 1407.1997 -539.90459 -665.67972 43.318696 -708.99842 0 2.5990577 10.632743 1.4609102 13990.5 + 1250 -623.92529 -661.81994 37.894649 1363.5617 1707.6307 -664.63708 48.39571 -713.03279 0 2.8171362 11.368475 1.8834293 13990.5 + 1300 -623.99279 -662.19655 38.203765 1374.6846 -820.5362 -664.34485 42.656892 -707.00174 0 2.1482931 10.187738 1.7086422 13990.5 + 1350 -623.99805 -658.70847 34.710418 1248.9836 775.25351 -662.01721 46.922474 -708.93969 0 3.3087449 12.454651 2.5036539 13990.5 + 1400 -623.96952 -662.16086 38.191338 1374.2374 880.29949 -664.90588 46.628569 -711.53444 0 2.7450171 11.920421 3.0464811 13990.5 + 1450 -623.9503 -662.26105 38.310754 1378.5344 -394.54404 -664.76894 43.635444 -708.40439 0 2.5078923 10.460115 1.8699789 13990.5 + 1500 -624.00558 -661.4861 37.480516 1348.66 438.34419 -664.32045 45.721579 -710.04203 0 2.8343497 11.655942 2.0688262 13990.5 +Loop time of 6.53617 on 4 procs for 1000 steps with 432 atoms -Performance: 25.790 ns/day, 0.931 hours/ns, 149.247 timesteps/s -99.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 26.438 ns/day, 0.908 hours/ns, 152.995 timesteps/s +93.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.9613 | 6.0752 | 6.2064 | 4.1 | 90.67 -Bond | 0.00087095 | 0.00088993 | 0.00091671 | 0.0 | 0.01 -Neigh | 0.06494 | 0.064964 | 0.064987 | 0.0 | 0.97 -Comm | 0.41743 | 0.54863 | 0.6626 | 13.8 | 8.19 -Output | 0.00053867 | 0.00059268 | 0.00074867 | 0.0 | 0.01 -Modify | 0.0013288 | 0.0013592 | 0.0013841 | 0.1 | 0.02 -Other | | 0.008613 | | | 0.13 +Pair | 4.8738 | 5.0908 | 5.4162 | 10.1 | 77.89 +Bond | 0.0016415 | 0.0017839 | 0.0019331 | 0.3 | 0.03 +Neigh | 0.15882 | 0.15886 | 0.15894 | 0.0 | 2.43 +Comm | 0.93524 | 1.2478 | 1.4524 | 19.3 | 19.09 +Output | 0.00097799 | 0.0018684 | 0.0036883 | 2.5 | 0.03 +Modify | 0.0027459 | 0.0028836 | 0.0030859 | 0.2 | 0.04 +Other | | 0.03211 | | | 0.49 Nlocal: 108 ave 116 max 102 min Histogram: 2 0 0 0 0 0 0 1 0 1 Nghost: 6504.5 ave 6624 max 6380 min Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 74267 ave 79230 max 70993 min +Neighs: 74267.8 ave 79232 max 70988 min Histogram: 2 0 0 0 0 1 0 0 0 1 -Total # of neighbors = 297068 -Ave neighs/atom = 687.657 +Total # of neighbors = 297071 +Ave neighs/atom = 687.664 Ave special neighs/atom = 1 Neighbor list builds = 45 Dangerous builds = 0 -Total wall time: 0:00:11 +Total wall time: 0:00:09 diff --git a/examples/coreshell/log.5Oct16.coreshell.g++.1 b/examples/coreshell/log.5Oct16.coreshell.g++.1 deleted file mode 100644 index e1caf994b9..0000000000 --- a/examples/coreshell/log.5Oct16.coreshell.g++.1 +++ /dev/null @@ -1,209 +0,0 @@ -LAMMPS (5 Oct 2016) -# Testsystem for core-shell model compared to Mitchel and Finchham -# Hendrik Heenen, June 2014 - -# ------------------------ INITIALIZATION ---------------------------- - -units metal -dimension 3 -boundary p p p -atom_style full - -# ----------------------- ATOM DEFINITION ---------------------------- - -fix csinfo all property/atom i_CSID -read_data data.coreshell fix csinfo NULL CS-Info - orthogonal box = (0 0 0) to (24.096 24.096 24.096) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 432 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 216 bonds - 1 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -group cores type 1 2 -216 atoms in group cores -group shells type 3 4 -216 atoms in group shells - -neighbor 2.0 bin -comm_modify vel yes - -# ------------------------ FORCE FIELDS ------------------------------ - -kspace_style ewald 1.0e-6 -pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D -pair_coeff * * 0.0 1.000 0.00 0.00 0.00 -pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na -pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl -pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl - -bond_style harmonic -bond_coeff 1 63.014 0.0 -bond_coeff 2 25.724 0.0 - -# ------------------------ Equilibration Run ------------------------------- - -reset_timestep 0 - -thermo 50 -thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol - -compute CSequ all temp/cs cores shells - -# output via chunk method - -#compute prop all property/atom i_CSID -#compute cs_chunk all chunk/atom c_prop -#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 -#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector - -thermo_modify temp CSequ - -# velocity bias option - -velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.175257 - estimated absolute RMS force accuracy = 1.49563e-05 - estimated relative force accuracy = 1.03866e-06 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 22 - ghost atom cutoff = 22 - binsize = 11 -> bins = 3 3 3 -velocity all scale 1427 temp CSequ - -fix thermoberendsen all temp/berendsen 1427 1427 0.4 -fix nve all nve -fix_modify thermoberendsen temp CSequ - -# 2 fmsec timestep - -timestep 0.002 -run 500 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.175257 - estimated absolute RMS force accuracy = 1.49563e-05 - estimated relative force accuracy = 1.03866e-06 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -Memory usage per processor = 15.7472 Mbytes -Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume - 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5 - 50 -634.17327 -666.17818 32.004909 1151.6314 -4030.3308 -667.95621 37.809071 989.23282 -1694.9981 1.7780231 9.7133792 2.1917971 13990.5 - 100 -631.93508 -661.91226 29.977186 1078.6679 -3172.6296 -664.0672 39.333409 991.36934 -1694.7699 2.1549314 11.091424 2.1704389 13990.5 - 150 -630.1681 -663.12416 32.956057 1185.8565 142.25543 -665.48036 46.253767 982.97455 -1694.7087 2.3561935 11.467914 2.1652594 13990.5 - 200 -628.62323 -663.64923 35.025998 1260.3391 -1623.5465 -665.96879 41.661877 986.81675 -1694.4474 2.3195587 10.597709 2.9538263 13990.5 - 250 -627.31045 -662.01825 34.707801 1248.8894 -1510.5567 -664.50313 42.101716 987.90197 -1694.5068 2.4848735 10.392755 1.6933702 13990.5 - 300 -626.57622 -660.97494 34.398716 1237.7677 -1638.6653 -663.48087 41.653234 989.53228 -1694.6664 2.5059308 11.204363 2.2809764 13990.5 - 350 -625.91962 -665.35838 39.438756 1419.1232 -1352.4038 -667.6167 41.582459 985.53381 -1694.733 2.2583269 10.83105 1.8963306 13990.5 - 400 -625.24851 -660.77642 35.527912 1278.3995 -425.3358 -663.12602 43.890329 987.75201 -1694.7684 2.3495978 11.521967 2.1759207 13990.5 - 450 -624.67742 -662.88674 38.209317 1374.8844 1108.0844 -665.43207 46.964873 982.35206 -1694.749 2.5453361 11.002418 2.0014401 13990.5 - 500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5 -Loop time of 8.64071 on 1 procs for 500 steps with 432 atoms - -Performance: 9.999 ns/day, 2.400 hours/ns, 57.866 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.824 | 7.824 | 7.824 | 0.0 | 90.55 -Bond | 0.0024104 | 0.0024104 | 0.0024104 | 0.0 | 0.03 -Kspace | 0.53534 | 0.53534 | 0.53534 | 0.0 | 6.20 -Neigh | 0.19522 | 0.19522 | 0.19522 | 0.0 | 2.26 -Comm | 0.066091 | 0.066091 | 0.066091 | 0.0 | 0.76 -Output | 0.0003643 | 0.0003643 | 0.0003643 | 0.0 | 0.00 -Modify | 0.011435 | 0.011435 | 0.011435 | 0.0 | 0.13 -Other | | 0.005869 | | | 0.07 - -Nlocal: 432 ave 432 max 432 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 9338 ave 9338 max 9338 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 297354 ave 297354 max 297354 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 297354 -Ave neighs/atom = 688.319 -Ave special neighs/atom = 1 -Neighbor list builds = 22 -Dangerous builds = 0 - -unfix thermoberendsen - -# ------------------------ Dynamic Run ------------------------------- - -run 1000 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.175257 - estimated absolute RMS force accuracy = 1.49563e-05 - estimated relative force accuracy = 1.03866e-06 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -Memory usage per processor = 15.7472 Mbytes -Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume - 500 -624.30218 -661.97851 37.676336 1355.7061 -999.37887 -664.60374 42.373166 987.59022 -1694.5671 2.6252269 11.153982 2.8270477 13990.5 - 550 -624.30708 -662.13355 37.826467 1361.1083 326.46254 -664.76811 45.306636 984.72863 -1694.8034 2.6345547 10.879989 1.9751675 13990.5 - 600 -624.30994 -661.8449 37.534969 1350.6193 -984.35215 -664.36139 42.366573 987.8789 -1694.6069 2.516489 10.211098 1.7890339 13990.5 - 650 -624.30501 -659.20596 34.900952 1255.8396 554.8226 -661.96471 46.567453 986.05088 -1694.583 2.7587454 13.15403 2.1657286 13990.5 - 700 -624.30907 -661.85064 37.541572 1350.8569 -135.38668 -664.3843 44.382641 985.80654 -1694.5735 2.5336521 10.991882 2.0402026 13990.5 - 750 -624.30999 -660.52853 36.21854 1303.2503 1196.4145 -663.29701 47.437312 984.08773 -1694.822 2.7684838 11.681986 2.0756933 13990.5 - 800 -624.30488 -659.87594 35.571053 1279.9518 361.87762 -662.81183 45.49882 986.40712 -1694.7178 2.935891 11.519352 3.7801343 13990.5 - 850 -624.30607 -663.64735 39.341278 1415.6157 -42.214824 -666.11278 44.277011 984.33678 -1694.7266 2.4654311 11.03941 1.9211474 13990.5 - 900 -624.30048 -659.04455 34.744072 1250.1946 386.10592 -662.10941 45.864611 986.90301 -1694.877 3.0648637 12.126864 2.467969 13990.5 - 950 -624.30795 -663.3468 39.038856 1404.7337 289.90291 -665.76693 45.27444 983.7762 -1694.8176 2.420128 11.735744 2.053808 13990.5 - 1000 -624.303 -659.5513 35.248296 1268.3381 -896.7132 -662.30776 42.985505 989.11655 -1694.4098 2.7564586 11.38686 1.8136876 13990.5 - 1050 -624.30433 -659.21593 34.911606 1256.223 273.26272 -661.98578 45.834363 986.93885 -1694.759 2.7698415 12.201066 1.9804734 13990.5 - 1100 -624.3035 -660.37975 36.076254 1298.1305 40.2604 -662.88712 45.266447 986.77782 -1694.9314 2.5073688 11.366839 2.2452799 13990.5 - 1150 -624.30832 -658.16356 33.855242 1218.2119 905.45817 -660.85689 47.381273 986.61927 -1694.8574 2.6933378 13.157497 2.3062872 13990.5 - 1200 -624.30971 -665.57285 41.263142 1484.77 -2010.9356 -667.71783 39.858615 987.32002 -1694.8965 2.1449751 9.3563352 1.7115187 13990.5 - 1250 -624.3069 -662.41936 38.112468 1371.3994 223.85833 -665.01906 45.021425 984.67299 -1694.7135 2.5997021 10.137667 1.8129534 13990.5 - 1300 -624.3116 -661.73044 37.418835 1346.4405 524.83698 -664.46475 45.716001 983.98856 -1694.1693 2.734311 11.475107 2.5468008 13990.5 - 1350 -624.30917 -661.34529 37.036121 1332.6693 399.81653 -663.86813 45.373759 985.3362 -1694.5781 2.5228434 10.819603 2.2048214 13990.5 - 1400 -624.31545 -660.75213 36.43668 1311.0996 193.18853 -663.43944 45.172084 985.90744 -1694.519 2.6873128 10.597955 1.9090871 13990.5 - 1450 -624.30419 -660.88131 36.577122 1316.1532 530.40423 -663.62017 46.21726 984.89723 -1694.7347 2.7388564 12.015146 2.6454091 13990.5 - 1500 -624.30236 -660.40336 36.100999 1299.0209 -759.2259 -663.48374 43.382233 987.65506 -1694.521 3.0803837 12.48163 2.2113083 13990.5 -Loop time of 17.2383 on 1 procs for 1000 steps with 432 atoms - -Performance: 10.024 ns/day, 2.394 hours/ns, 58.011 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 15.619 | 15.619 | 15.619 | 0.0 | 90.61 -Bond | 0.0048032 | 0.0048032 | 0.0048032 | 0.0 | 0.03 -Kspace | 1.068 | 1.068 | 1.068 | 0.0 | 6.20 -Neigh | 0.39623 | 0.39623 | 0.39623 | 0.0 | 2.30 -Comm | 0.13052 | 0.13052 | 0.13052 | 0.0 | 0.76 -Output | 0.00067472 | 0.00067472 | 0.00067472 | 0.0 | 0.00 -Modify | 0.0071197 | 0.0071197 | 0.0071197 | 0.0 | 0.04 -Other | | 0.01175 | | | 0.07 - -Nlocal: 432 ave 432 max 432 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 9327 ave 9327 max 9327 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 297525 ave 297525 max 297525 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 297525 -Ave neighs/atom = 688.715 -Ave special neighs/atom = 1 -Neighbor list builds = 45 -Dangerous builds = 0 -Total wall time: 0:00:25 diff --git a/examples/coreshell/log.5Oct16.coreshell.g++.4 b/examples/coreshell/log.5Oct16.coreshell.g++.4 deleted file mode 100644 index 117b6e08d5..0000000000 --- a/examples/coreshell/log.5Oct16.coreshell.g++.4 +++ /dev/null @@ -1,209 +0,0 @@ -LAMMPS (5 Oct 2016) -# Testsystem for core-shell model compared to Mitchel and Finchham -# Hendrik Heenen, June 2014 - -# ------------------------ INITIALIZATION ---------------------------- - -units metal -dimension 3 -boundary p p p -atom_style full - -# ----------------------- ATOM DEFINITION ---------------------------- - -fix csinfo all property/atom i_CSID -read_data data.coreshell fix csinfo NULL CS-Info - orthogonal box = (0 0 0) to (24.096 24.096 24.096) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 432 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 216 bonds - 1 = max # of 1-2 neighbors - 0 = max # of 1-3 neighbors - 0 = max # of 1-4 neighbors - 1 = max # of special neighbors - -group cores type 1 2 -216 atoms in group cores -group shells type 3 4 -216 atoms in group shells - -neighbor 2.0 bin -comm_modify vel yes - -# ------------------------ FORCE FIELDS ------------------------------ - -kspace_style ewald 1.0e-6 -pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D -pair_coeff * * 0.0 1.000 0.00 0.00 0.00 -pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na -pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl -pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl - -bond_style harmonic -bond_coeff 1 63.014 0.0 -bond_coeff 2 25.724 0.0 - -# ------------------------ Equilibration Run ------------------------------- - -reset_timestep 0 - -thermo 50 -thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol - -compute CSequ all temp/cs cores shells - -# output via chunk method - -#compute prop all property/atom i_CSID -#compute cs_chunk all chunk/atom c_prop -#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 -#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector - -thermo_modify temp CSequ - -# velocity bias option - -velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.175257 - estimated absolute RMS force accuracy = 1.49563e-05 - estimated relative force accuracy = 1.03866e-06 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 22 - ghost atom cutoff = 22 - binsize = 11 -> bins = 3 3 3 -velocity all scale 1427 temp CSequ - -fix thermoberendsen all temp/berendsen 1427 1427 0.4 -fix nve all nve -fix_modify thermoberendsen temp CSequ - -# 2 fmsec timestep - -timestep 0.002 -run 500 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.175257 - estimated absolute RMS force accuracy = 1.49563e-05 - estimated relative force accuracy = 1.03866e-06 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -Memory usage per processor = 15.2111 Mbytes -Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume - 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.9851021e-14 4.2188475e-15 13990.5 - 50 -634.17349 -666.17817 32.004686 1151.6234 -4030.346 -667.9562 37.809075 989.23283 -1694.9981 1.7780241 9.7133824 2.1917971 13990.5 - 100 -631.93518 -661.91229 29.977104 1078.665 -3172.6554 -664.06722 39.333371 991.36935 -1694.7699 2.1549316 11.09144 2.1704351 13990.5 - 150 -630.16821 -663.12421 32.956001 1185.8545 142.23746 -665.48039 46.253735 982.97455 -1694.7087 2.3561823 11.467862 2.1651502 13990.5 - 200 -628.62229 -663.64928 35.026994 1260.375 -1623.495 -665.96883 41.661825 986.81676 -1694.4474 2.3195535 10.597709 2.9538127 13990.5 - 250 -627.31146 -662.01843 34.706969 1248.8595 -1510.677 -664.50329 42.10159 987.90193 -1694.5068 2.4848607 10.392642 1.6933333 13990.5 - 300 -626.57662 -660.97479 34.398174 1237.7482 -1638.7013 -663.48072 41.653268 989.53239 -1694.6664 2.5059279 11.204558 2.2814875 13990.5 - 350 -625.91972 -665.3583 39.438581 1419.1169 -1352.428 -667.61665 41.5825 985.53386 -1694.733 2.2583465 10.831573 1.8963653 13990.5 - 400 -625.24854 -660.77581 35.527271 1278.3764 -424.57407 -663.12561 43.89225 987.75056 -1694.7684 2.3497967 11.523588 2.1775908 13990.5 - 450 -624.67739 -662.88749 38.210098 1374.9125 1107.8255 -665.43273 46.964166 982.35231 -1694.7492 2.5452345 11.00224 2.0018738 13990.5 - 500 -624.30227 -661.98003 37.677766 1355.7576 -999.27326 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5 -Loop time of 2.40619 on 4 procs for 500 steps with 432 atoms - -Performance: 35.907 ns/day, 0.668 hours/ns, 207.797 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.7876 | 1.9016 | 2.0542 | 7.0 | 79.03 -Bond | 0.00064754 | 0.0006901 | 0.00074625 | 0.1 | 0.03 -Kspace | 0.16854 | 0.31596 | 0.42594 | 16.5 | 13.13 -Neigh | 0.051607 | 0.051768 | 0.051931 | 0.1 | 2.15 -Comm | 0.11933 | 0.12412 | 0.12769 | 0.9 | 5.16 -Output | 0.00039911 | 0.00042087 | 0.00047565 | 0.2 | 0.02 -Modify | 0.0059447 | 0.0063215 | 0.0067348 | 0.4 | 0.26 -Other | | 0.005341 | | | 0.22 - -Nlocal: 108 ave 119 max 102 min -Histogram: 1 1 1 0 0 0 0 0 0 1 -Nghost: 6516 ave 6545 max 6491 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Neighs: 74337.8 ave 81248 max 69989 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 297351 -Ave neighs/atom = 688.312 -Ave special neighs/atom = 1 -Neighbor list builds = 22 -Dangerous builds = 0 - -unfix thermoberendsen - -# ------------------------ Dynamic Run ------------------------------- - -run 1000 -Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.175257 - estimated absolute RMS force accuracy = 1.49563e-05 - estimated relative force accuracy = 1.03866e-06 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -Memory usage per processor = 15.213 Mbytes -Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume - 500 -624.30215 -661.98003 37.677882 1355.7618 -999.26443 -664.60512 42.373091 987.58943 -1694.5676 2.6250858 11.151835 2.8270448 13990.5 - 550 -624.30702 -662.13315 37.826126 1361.096 330.71041 -664.76759 45.316349 984.7201 -1694.804 2.6344423 10.876902 1.9726348 13990.5 - 600 -624.31001 -661.82602 37.516015 1349.9373 -978.11503 -664.34272 42.382797 987.88159 -1694.6071 2.5166949 10.21416 1.787289 13990.5 - 650 -624.30516 -659.19843 34.893268 1255.5631 548.43865 -661.95754 46.556222 986.06829 -1694.582 2.7591048 13.16005 2.1511562 13990.5 - 700 -624.30926 -661.91108 37.601819 1353.0248 -175.1339 -664.4528 44.284398 985.834 -1694.5712 2.5417263 10.972065 1.9847042 13990.5 - 750 -624.30955 -660.4096 36.100048 1298.9866 1222.5932 -663.20741 47.511377 984.09471 -1694.8135 2.7978144 11.761903 2.1481489 13990.5 - 800 -624.30447 -660.30683 36.002357 1295.4714 270.6639 -663.25589 45.210122 986.25515 -1694.7212 2.9490566 11.50988 4.0037749 13990.5 - 850 -624.30774 -663.65149 39.343757 1415.7049 339.356 -666.13397 45.12874 983.38616 -1694.6489 2.4824719 11.01305 2.1691298 13990.5 - 900 -624.30311 -658.78647 34.483353 1240.8132 309.88983 -661.8322 45.836842 987.17541 -1694.8445 3.045732 12.635589 1.9594437 13990.5 - 950 -624.303 -663.59545 39.292454 1413.8588 -649.78872 -665.94289 43.141981 985.63193 -1694.7168 2.347436 11.012602 2.0685819 13990.5 - 1000 -624.3032 -660.59776 36.294555 1305.9856 -753.87453 -663.22012 42.930848 988.41708 -1694.568 2.6223608 10.526403 1.8887197 13990.5 - 1050 -624.3023 -660.7017 36.399405 1309.7584 790.88591 -663.6376 46.453299 984.4785 -1694.5694 2.9359001 11.210429 2.1822375 13990.5 - 1100 -624.30545 -662.76291 38.457457 1383.8132 -853.19698 -665.29416 42.533854 986.84955 -1694.6776 2.5312537 10.517674 2.6445601 13990.5 - 1150 -624.31539 -663.03811 38.722722 1393.3582 -380.13868 -665.58847 43.476852 985.81618 -1694.8815 2.5503626 10.818389 1.9559813 13990.5 - 1200 -624.3093 -659.85835 35.549055 1279.1603 44.140107 -662.93041 44.773497 986.67501 -1694.3789 3.0720506 11.310516 2.2601607 13990.5 - 1250 -624.30277 -663.46462 39.161852 1409.1594 -352.57297 -666.0144 43.477124 984.93408 -1694.4256 2.5497829 10.720231 1.8458373 13990.5 - 1300 -624.30329 -660.15937 35.85608 1290.2079 -348.83001 -662.73568 43.884677 988.07413 -1694.6945 2.5763161 11.369766 2.2580977 13990.5 - 1350 -624.30469 -662.72631 38.421619 1382.5236 1338.9038 -665.20399 47.35379 982.28307 -1694.8408 2.4776776 10.587886 1.7677665 13990.5 - 1400 -624.30499 -662.12513 37.820139 1360.8806 132.00801 -664.73589 44.55252 985.34275 -1694.6312 2.6107622 11.193448 2.1613441 13990.5 - 1450 -624.30207 -661.42856 37.126485 1335.9209 2069.8075 -664.07373 49.544418 981.20445 -1694.8226 2.6451763 13.011189 3.3987593 13990.5 - 1500 -624.29727 -656.99924 32.701969 1176.7137 504.56835 -660.08591 46.605885 987.7602 -1694.452 3.0866635 13.271242 3.025272 13990.5 -Loop time of 4.96339 on 4 procs for 1000 steps with 432 atoms - -Performance: 34.815 ns/day, 0.689 hours/ns, 201.475 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.6491 | 3.8484 | 4.2642 | 12.4 | 77.54 -Bond | 0.0013638 | 0.0014506 | 0.0016019 | 0.2 | 0.03 -Kspace | 0.3347 | 0.73521 | 0.92903 | 27.3 | 14.81 -Neigh | 0.10979 | 0.11008 | 0.11042 | 0.1 | 2.22 -Comm | 0.23785 | 0.25289 | 0.2601 | 1.8 | 5.10 -Output | 0.0008378 | 0.00088245 | 0.00098872 | 0.2 | 0.02 -Modify | 0.0022187 | 0.0024077 | 0.0026662 | 0.3 | 0.05 -Other | | 0.01206 | | | 0.24 - -Nlocal: 108 ave 112 max 102 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 6500.75 ave 6612 max 6392 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Neighs: 74275 ave 77543 max 69706 min -Histogram: 1 0 0 0 0 1 0 1 0 1 - -Total # of neighbors = 297100 -Ave neighs/atom = 687.731 -Ave special neighs/atom = 1 -Neighbor list builds = 45 -Dangerous builds = 0 -Total wall time: 0:00:07 diff --git a/examples/crack/log.5Oct16.crack.g++.1 b/examples/crack/log.27Nov18.crack.g++.1 similarity index 81% rename from examples/crack/log.5Oct16.crack.g++.1 rename to examples/crack/log.27Nov18.crack.g++.1 index b65db9dda6..418b5fc0f6 100644 --- a/examples/crack/log.5Oct16.crack.g++.1 +++ b/examples/crack/log.27Nov18.crack.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d LJ crack simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 8141 atoms + Time spent = 0.00162196 secs mass 1 1.0 mass 2 1.0 @@ -76,7 +78,7 @@ fix 2 boundary setforce NULL 0.0 0.0 timestep 0.003 thermo 200 thermo_modify temp new -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) neigh_modify exclude type 2 3 @@ -90,13 +92,18 @@ neigh_modify exclude type 2 3 run 5000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 80 56 1 -Memory usage per processor = 2.48017 Mbytes + binsize = 1.4, bins = 80 56 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917 200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101 @@ -124,20 +131,20 @@ Step Temp E_pair E_mol TotEng Press Volume 4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925 4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122 5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637 -Loop time of 6.89346 on 1 procs for 5000 steps with 8141 atoms +Loop time of 7.02888 on 1 procs for 5000 steps with 8141 atoms -Performance: 188004.255 tau/day, 725.325 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 184382.046 tau/day, 711.350 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.8036 | 5.8036 | 5.8036 | 0.0 | 84.19 -Neigh | 0.37434 | 0.37434 | 0.37434 | 0.0 | 5.43 -Comm | 0.004128 | 0.004128 | 0.004128 | 0.0 | 0.06 -Output | 0.00077105 | 0.00077105 | 0.00077105 | 0.0 | 0.01 -Modify | 0.53619 | 0.53619 | 0.53619 | 0.0 | 7.78 -Other | | 0.1744 | | | 2.53 +Pair | 5.8668 | 5.8668 | 5.8668 | 0.0 | 83.47 +Neigh | 0.29717 | 0.29717 | 0.29717 | 0.0 | 4.23 +Comm | 0.0045955 | 0.0045955 | 0.0045955 | 0.0 | 0.07 +Output | 0.0011108 | 0.0011108 | 0.0011108 | 0.0 | 0.02 +Modify | 0.65277 | 0.65277 | 0.65277 | 0.0 | 9.29 +Other | | 0.2064 | | | 2.94 Nlocal: 8141 ave 8141 max 8141 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -150,4 +157,4 @@ Total # of neighbors = 71389 Ave neighs/atom = 8.76907 Neighbor list builds = 100 Dangerous builds = 0 -Total wall time: 0:00:06 +Total wall time: 0:00:07 diff --git a/examples/crack/log.5Oct16.crack.g++.4 b/examples/crack/log.27Nov18.crack.g++.4 similarity index 81% rename from examples/crack/log.5Oct16.crack.g++.4 rename to examples/crack/log.27Nov18.crack.g++.4 index 00fb8d3e49..998f560b85 100644 --- a/examples/crack/log.5Oct16.crack.g++.4 +++ b/examples/crack/log.27Nov18.crack.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d LJ crack simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 8141 atoms + Time spent = 0.00064826 secs mass 1 1.0 mass 2 1.0 @@ -76,7 +78,7 @@ fix 2 boundary setforce NULL 0.0 0.0 timestep 0.003 thermo 200 thermo_modify temp new -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) neigh_modify exclude type 2 3 @@ -90,13 +92,18 @@ neigh_modify exclude type 2 3 run 5000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 80 56 1 -Memory usage per processor = 2.48163 Mbytes + binsize = 1.4, bins = 80 56 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.069 | 3.069 | 3.069 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917 200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331 @@ -124,20 +131,20 @@ Step Temp E_pair E_mol TotEng Press Volume 4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949 4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155 5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031 -Loop time of 1.97398 on 4 procs for 5000 steps with 8141 atoms +Loop time of 2.06204 on 4 procs for 5000 steps with 8141 atoms -Performance: 656540.037 tau/day, 2532.948 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 628504.111 tau/day, 2424.784 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.4909 | 1.5203 | 1.5671 | 2.3 | 77.02 -Neigh | 0.10125 | 0.10271 | 0.10657 | 0.7 | 5.20 -Comm | 0.076516 | 0.13066 | 0.15771 | 8.8 | 6.62 -Output | 0.00077796 | 0.00082064 | 0.00091672 | 0.2 | 0.04 -Modify | 0.13725 | 0.14082 | 0.14325 | 0.6 | 7.13 -Other | | 0.07865 | | | 3.98 +Pair | 1.4844 | 1.5266 | 1.5909 | 3.6 | 74.03 +Neigh | 0.081047 | 0.085878 | 0.093027 | 1.5 | 4.16 +Comm | 0.12993 | 0.19571 | 0.25179 | 11.6 | 9.49 +Output | 0.00072265 | 0.00096798 | 0.0016601 | 0.0 | 0.05 +Modify | 0.16787 | 0.17024 | 0.17234 | 0.4 | 8.26 +Other | | 0.0826 | | | 4.01 Nlocal: 2035.25 ave 2064 max 2015 min Histogram: 1 1 0 0 0 1 0 0 0 1 @@ -150,4 +157,4 @@ Total # of neighbors = 71400 Ave neighs/atom = 8.77042 Neighbor list builds = 106 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/deposit/log.5Oct16.deposit.atom.g++.1 b/examples/deposit/log.27Nov18.deposit.atom.g++.1 similarity index 89% rename from examples/deposit/log.5Oct16.deposit.atom.g++.1 rename to examples/deposit/log.27Nov18.deposit.atom.g++.1 index 0ce6ac3c9c..2ed7f60dbe 100644 --- a/examples/deposit/log.5Oct16.deposit.atom.g++.1 +++ b/examples/deposit/log.27Nov18.deposit.atom.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms + Time spent = 0.000444174 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 @@ -30,7 +32,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp -compute_modify add dynamic yes extra 0 +compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 @@ -43,7 +45,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom @@ -55,13 +57,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 3 3 6 -Memory usage per processor = 2.54053 Mbytes + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.126 | 3.126 | 3.126 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746 @@ -164,20 +171,20 @@ Step Atoms Temp E_pair TotEng Press 9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109 9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384 10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643 -Loop time of 5.63963 on 1 procs for 10000 steps with 450 atoms +Loop time of 6.17726 on 1 procs for 10000 steps with 450 atoms -Performance: 766007.688 tau/day, 1773.166 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 699339.360 tau/day, 1618.841 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.1973 | 3.1973 | 3.1973 | 0.0 | 56.69 -Neigh | 2.1646 | 2.1646 | 2.1646 | 0.0 | 38.38 -Comm | 0.11922 | 0.11922 | 0.11922 | 0.0 | 2.11 -Output | 0.00081301 | 0.00081301 | 0.00081301 | 0.0 | 0.01 -Modify | 0.11702 | 0.11702 | 0.11702 | 0.0 | 2.07 -Other | | 0.04063 | | | 0.72 +Pair | 3.1708 | 3.1708 | 3.1708 | 0.0 | 51.33 +Neigh | 2.6376 | 2.6376 | 2.6376 | 0.0 | 42.70 +Comm | 0.18927 | 0.18927 | 0.18927 | 0.0 | 3.06 +Output | 0.0013239 | 0.0013239 | 0.0013239 | 0.0 | 0.02 +Modify | 0.13663 | 0.13663 | 0.13663 | 0.0 | 2.21 +Other | | 0.04162 | | | 0.67 Nlocal: 450 ave 450 max 450 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -190,4 +197,4 @@ Total # of neighbors = 29176 Ave neighs/atom = 64.8356 Neighbor list builds = 1143 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/deposit/log.5Oct16.deposit.atom.g++.4 b/examples/deposit/log.27Nov18.deposit.atom.g++.4 similarity index 89% rename from examples/deposit/log.5Oct16.deposit.atom.g++.4 rename to examples/deposit/log.27Nov18.deposit.atom.g++.4 index 34b855f2ed..dd41ecedbd 100644 --- a/examples/deposit/log.5Oct16.deposit.atom.g++.4 +++ b/examples/deposit/log.27Nov18.deposit.atom.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # sample surface deposition script for atoms units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms + Time spent = 0.000353813 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 @@ -30,7 +32,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp -compute_modify add dynamic yes extra 0 +compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 1.0 1.0 0.1 587283 @@ -43,7 +45,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom @@ -55,13 +57,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 3 3 6 -Memory usage per processor = 2.60645 Mbytes + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.4396 | 2.389 | 3.192 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131 @@ -164,20 +171,20 @@ Step Atoms Temp E_pair TotEng Press 9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592 9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329 10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403 -Loop time of 4.38653 on 4 procs for 10000 steps with 450 atoms +Loop time of 5.30178 on 4 procs for 10000 steps with 450 atoms -Performance: 984832.436 tau/day, 2279.705 timesteps/s -98.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 814820.053 tau/day, 1886.158 timesteps/s +94.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0022979 | 0.81396 | 2.0831 | 95.7 | 18.56 -Neigh | 0.0083807 | 0.57856 | 1.7676 | 93.7 | 13.19 -Comm | 0.3792 | 2.1868 | 3.8575 | 85.0 | 49.85 -Output | 0.001919 | 0.008881 | 0.025856 | 10.5 | 0.20 -Modify | 0.0053477 | 0.035994 | 0.08146 | 16.2 | 0.82 -Other | | 0.7623 | | | 17.38 +Pair | 0.0030358 | 0.8503 | 2.2484 | 100.1 | 16.04 +Neigh | 0.0085447 | 0.74813 | 2.3721 | 111.4 | 14.11 +Comm | 0.50519 | 2.6696 | 4.6851 | 95.8 | 50.35 +Output | 0.0024836 | 0.012219 | 0.029616 | 9.5 | 0.23 +Modify | 0.014966 | 0.047625 | 0.094656 | 14.8 | 0.90 +Other | | 0.9739 | | | 18.37 Nlocal: 112.5 ave 250 max 9 min Histogram: 2 0 0 0 0 0 1 0 0 1 @@ -190,4 +197,4 @@ Total # of neighbors = 29661 Ave neighs/atom = 65.9133 Neighbor list builds = 1164 Dangerous builds = 0 -Total wall time: 0:00:04 +Total wall time: 0:00:05 diff --git a/examples/deposit/log.5Oct16.deposit.molecule.g++.1 b/examples/deposit/log.27Nov18.deposit.molecule.g++.1 similarity index 87% rename from examples/deposit/log.5Oct16.deposit.molecule.g++.1 rename to examples/deposit/log.27Nov18.deposit.molecule.g++.1 index 3c8aa85d92..c006119370 100644 --- a/examples/deposit/log.5Oct16.deposit.molecule.g++.1 +++ b/examples/deposit/log.27Nov18.deposit.molecule.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # sample surface deposition script for molecules units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms + Time spent = 0.000686646 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 @@ -33,7 +35,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp -compute_modify add dynamic yes extra 0 +compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 @@ -41,11 +43,11 @@ fix 3 mobile nve molecule dimer molecule.dimer Read molecule dimer: - 2 atoms with 3 types - 1 bonds with 1 types - 0 angles with 0 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 fix 5 addatoms wall/reflect zhi EDGE @@ -53,7 +55,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add lost/bond ignore lost warn -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom @@ -65,13 +67,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 3 3 6 -Memory usage per processor = 3.56565 Mbytes + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.152 | 4.152 | 4.152 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914 @@ -174,21 +181,21 @@ Step Atoms Temp E_pair TotEng Press 9800 546 0.26835398 -7.2214231 -6.8757262 -0.86029096 9900 548 0.31676744 -7.264604 -6.884266 -0.74053962 10000 550 0.31368419 -7.2759575 -6.8979611 -0.76153366 -Loop time of 6.51779 on 1 procs for 10000 steps with 550 atoms +Loop time of 7.42799 on 1 procs for 10000 steps with 550 atoms -Performance: 662801.655 tau/day, 1534.263 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 581583.611 tau/day, 1346.258 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.0744 | 4.0744 | 4.0744 | 0.0 | 62.51 -Bond | 0.01209 | 0.01209 | 0.01209 | 0.0 | 0.19 -Neigh | 2.1316 | 2.1316 | 2.1316 | 0.0 | 32.70 -Comm | 0.13266 | 0.13266 | 0.13266 | 0.0 | 2.04 -Output | 0.0008409 | 0.0008409 | 0.0008409 | 0.0 | 0.01 -Modify | 0.12403 | 0.12403 | 0.12403 | 0.0 | 1.90 -Other | | 0.04216 | | | 0.65 +Pair | 4.1961 | 4.1961 | 4.1961 | 0.0 | 56.49 +Bond | 0.011222 | 0.011222 | 0.011222 | 0.0 | 0.15 +Neigh | 2.8258 | 2.8258 | 2.8258 | 0.0 | 38.04 +Comm | 0.20406 | 0.20406 | 0.20406 | 0.0 | 2.75 +Output | 0.0014198 | 0.0014198 | 0.0014198 | 0.0 | 0.02 +Modify | 0.14606 | 0.14606 | 0.14606 | 0.0 | 1.97 +Other | | 0.04341 | | | 0.58 Nlocal: 550 ave 550 max 550 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -202,4 +209,4 @@ Ave neighs/atom = 72.2 Ave special neighs/atom = 0.363636 Neighbor list builds = 877 Dangerous builds = 0 -Total wall time: 0:00:06 +Total wall time: 0:00:07 diff --git a/examples/deposit/log.5Oct16.deposit.molecule.g++.4 b/examples/deposit/log.27Nov18.deposit.molecule.g++.4 similarity index 87% rename from examples/deposit/log.5Oct16.deposit.molecule.g++.4 rename to examples/deposit/log.27Nov18.deposit.molecule.g++.4 index c2affc26e3..c0c3ae35ff 100644 --- a/examples/deposit/log.5Oct16.deposit.molecule.g++.4 +++ b/examples/deposit/log.27Nov18.deposit.molecule.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # sample surface deposition script for molecules units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms + Time spent = 0.000594139 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 @@ -33,7 +35,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp -compute_modify add dynamic yes extra 0 +compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 @@ -41,11 +43,11 @@ fix 3 mobile nve molecule dimer molecule.dimer Read molecule dimer: - 2 atoms with 3 types - 1 bonds with 1 types - 0 angles with 0 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 fix 5 addatoms wall/reflect zhi EDGE @@ -53,7 +55,7 @@ fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add lost/bond ignore lost warn -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom @@ -65,13 +67,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 3 3 6 -Memory usage per processor = 3.63985 Mbytes + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.441 | 3.16 | 4.226 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 0.83994737 -6.8946578 -6.8874992 -0.73775337 @@ -174,21 +181,21 @@ Step Atoms Temp E_pair TotEng Press 9800 546 0.28129876 -7.3140275 -6.9098746 -0.82726219 9900 548 0.28891495 -7.3235633 -6.9092268 -0.88128702 10000 550 0.29861445 -7.3507915 -6.9161229 -0.73192335 -Loop time of 5.59197 on 4 procs for 10000 steps with 550 atoms +Loop time of 6.59998 on 4 procs for 10000 steps with 550 atoms -Performance: 772536.289 tau/day, 1788.278 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 654547.468 tau/day, 1515.156 timesteps/s +95.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0012441 | 1.0454 | 2.9987 | 119.8 | 18.70 -Bond | 0.0012348 | 0.0039268 | 0.010973 | 6.5 | 0.07 -Neigh | 0.0049584 | 0.57381 | 1.8059 | 96.8 | 10.26 -Comm | 0.62167 | 2.892 | 5.0562 | 98.9 | 51.72 -Output | 0.0021472 | 0.014835 | 0.048822 | 16.2 | 0.27 -Modify | 0.0069871 | 0.038206 | 0.074167 | 15.4 | 0.68 -Other | | 1.024 | | | 18.31 +Pair | 0.0020502 | 1.124 | 3.2865 | 126.5 | 17.03 +Bond | 0.0019848 | 0.0045845 | 0.011024 | 5.5 | 0.07 +Neigh | 0.0055914 | 0.79469 | 2.5826 | 118.4 | 12.04 +Comm | 0.541 | 3.3411 | 6.0178 | 116.5 | 50.62 +Output | 0.0026808 | 0.018505 | 0.055692 | 15.9 | 0.28 +Modify | 0.017398 | 0.054306 | 0.10289 | 15.9 | 0.82 +Other | | 1.263 | | | 19.13 Nlocal: 137.5 ave 299 max 2 min Histogram: 2 0 0 0 0 0 0 1 0 1 @@ -202,4 +209,4 @@ Ave neighs/atom = 71.9345 Ave special neighs/atom = 0.363636 Neighbor list builds = 884 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/deposit/log.5Oct16.deposit.molecule.shake.g++.1 b/examples/deposit/log.27Nov18.deposit.molecule.shake.g++.1 similarity index 88% rename from examples/deposit/log.5Oct16.deposit.molecule.shake.g++.1 rename to examples/deposit/log.27Nov18.deposit.molecule.shake.g++.1 index 508aaa9df1..e2150860d1 100644 --- a/examples/deposit/log.5Oct16.deposit.molecule.shake.g++.1 +++ b/examples/deposit/log.27Nov18.deposit.molecule.shake.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # sample surface deposition script for molecules units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms + Time spent = 0.000657082 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 @@ -33,7 +35,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp -compute_modify add dynamic yes extra 0 +compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 @@ -41,11 +43,11 @@ fix 3 mobile nve molecule dimer molecule.dimer.shake Read molecule dimer: - 2 atoms with 3 types - 1 bonds with 1 types - 0 angles with 0 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6 fix 5 addatoms wall/reflect zhi EDGE @@ -58,7 +60,7 @@ fix 6 all shake 0.0001 20 1000 b 1 mol dimer thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add lost/bond ignore lost warn -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom @@ -70,14 +72,19 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 3 3 6 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard SHAKE stats (type/ave/delta) on step 0 -Memory usage per processor = 4.44065 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914 @@ -200,21 +207,21 @@ SHAKE stats (type/ave/delta) on step 9000 SHAKE stats (type/ave/delta) on step 10000 1 1 2.44249e-15 10000 550 0.31059632 -6.7463923 -6.6052122 -0.75225652 -Loop time of 6.31791 on 1 procs for 10000 steps with 550 atoms +Loop time of 7.11276 on 1 procs for 10000 steps with 550 atoms -Performance: 683770.197 tau/day, 1582.801 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 607358.878 tau/day, 1405.923 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.9451 | 3.9451 | 3.9451 | 0.0 | 62.44 -Bond | 0.012146 | 0.012146 | 0.012146 | 0.0 | 0.19 -Neigh | 2.0103 | 2.0103 | 2.0103 | 0.0 | 31.82 -Comm | 0.13071 | 0.13071 | 0.13071 | 0.0 | 2.07 -Output | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.01 -Modify | 0.1759 | 0.1759 | 0.1759 | 0.0 | 2.78 -Other | | 0.04281 | | | 0.68 +Pair | 3.9705 | 3.9705 | 3.9705 | 0.0 | 55.82 +Bond | 0.011102 | 0.011102 | 0.011102 | 0.0 | 0.16 +Neigh | 2.6732 | 2.6732 | 2.6732 | 0.0 | 37.58 +Comm | 0.20071 | 0.20071 | 0.20071 | 0.0 | 2.82 +Output | 0.0015368 | 0.0015368 | 0.0015368 | 0.0 | 0.02 +Modify | 0.21124 | 0.21124 | 0.21124 | 0.0 | 2.97 +Other | | 0.0444 | | | 0.62 Nlocal: 550 ave 550 max 550 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -228,4 +235,4 @@ Ave neighs/atom = 66.2873 Ave special neighs/atom = 0.363636 Neighbor list builds = 839 Dangerous builds = 0 -Total wall time: 0:00:06 +Total wall time: 0:00:07 diff --git a/examples/deposit/log.5Oct16.deposit.molecule.shake.g++.4 b/examples/deposit/log.27Nov18.deposit.molecule.shake.g++.4 similarity index 88% rename from examples/deposit/log.5Oct16.deposit.molecule.shake.g++.4 rename to examples/deposit/log.27Nov18.deposit.molecule.shake.g++.4 index 3947e4eec1..066d6f78a5 100644 --- a/examples/deposit/log.5Oct16.deposit.molecule.shake.g++.4 +++ b/examples/deposit/log.27Nov18.deposit.molecule.shake.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # sample surface deposition script for molecules units lj @@ -15,6 +16,7 @@ Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874) region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate Created 350 atoms + Time spent = 0.000810623 secs pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 @@ -33,7 +35,7 @@ group mobile region mobile 150 atoms in group mobile compute add addatoms temp -compute_modify add dynamic yes extra 0 +compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 @@ -41,11 +43,11 @@ fix 3 mobile nve molecule dimer molecule.dimer.shake Read molecule dimer: - 2 atoms with 3 types - 1 bonds with 1 types - 0 angles with 0 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 2 atoms with max type 3 + 1 bonds with max type 1 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6 fix 5 addatoms wall/reflect zhi EDGE @@ -58,7 +60,7 @@ fix 6 all shake 0.0001 20 1000 b 1 mol dimer thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add lost/bond ignore lost warn -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 50 dump.deposit.atom @@ -70,14 +72,19 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.3 ghost atom cutoff = 5.3 - binsize = 2.65 -> bins = 3 3 6 + binsize = 2.65, bins = 3 3 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard SHAKE stats (type/ave/delta) on step 0 -Memory usage per processor = 4.51485 Mbytes +Per MPI rank memory allocation (min/avg/max) = 0.4411 | 3.816 | 5.101 Mbytes Step Atoms Temp E_pair TotEng Press 0 350 0 -6.9215833 -6.9215833 -1.0052629 100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337 @@ -200,21 +207,21 @@ SHAKE stats (type/ave/delta) on step 9000 SHAKE stats (type/ave/delta) on step 10000 1 1 2.55351e-15 10000 550 0.30296128 -6.7756768 -6.6379672 -0.84420968 -Loop time of 5.7633 on 4 procs for 10000 steps with 550 atoms +Loop time of 6.71355 on 4 procs for 10000 steps with 550 atoms -Performance: 749570.876 tau/day, 1735.118 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 643474.692 tau/day, 1489.525 timesteps/s +95.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0014243 | 1.0038 | 2.9203 | 118.9 | 17.42 -Bond | 0.001431 | 0.004068 | 0.010644 | 6.0 | 0.07 -Neigh | 0.0053701 | 0.53209 | 1.6663 | 92.7 | 9.23 -Comm | 0.60632 | 2.7675 | 4.853 | 97.7 | 48.02 -Output | 0.0026648 | 0.003988 | 0.0067949 | 2.6 | 0.07 -Modify | 0.43492 | 1.2606 | 3.3556 | 108.4 | 21.87 -Other | | 0.1912 | | | 3.32 +Pair | 0.0023715 | 1.0684 | 3.1403 | 123.9 | 15.91 +Bond | 0.0018587 | 0.0045958 | 0.011149 | 5.6 | 0.07 +Neigh | 0.0059454 | 0.74298 | 2.4218 | 114.9 | 11.07 +Comm | 0.53191 | 3.1926 | 5.7443 | 113.9 | 47.55 +Output | 0.0028977 | 0.0060919 | 0.010627 | 4.2 | 0.09 +Modify | 0.47242 | 1.5021 | 4.1679 | 126.1 | 22.37 +Other | | 0.1969 | | | 2.93 Nlocal: 137.5 ave 300 max 2 min Histogram: 2 0 0 0 0 0 0 1 0 1 @@ -228,4 +235,4 @@ Ave neighs/atom = 66.8055 Ave special neighs/atom = 0.363636 Neighbor list builds = 833 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/dipole/log.5Oct16.dipole.g++.1 b/examples/dipole/log.27Nov18.dipole.g++.1 similarity index 76% rename from examples/dipole/log.5Oct16.dipole.g++.1 rename to examples/dipole/log.27Nov18.dipole.g++.1 index fc620f23fd..cc82422a9c 100644 --- a/examples/dipole/log.5Oct16.dipole.g++.1 +++ b/examples/dipole/log.27Nov18.dipole.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 200 atoms + Time spent = 0.00140882 secs # need both mass settings due to hybrid atom style @@ -46,13 +48,18 @@ thermo 500 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 13 13 2 -Memory usage per processor = 4.47689 Mbytes + binsize = 1.4, bins = 13 13 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/dipole/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair c_erot TotEng Press 0 0 -2.1909822 0 -2.1909822 -2.5750971 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899 @@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press 9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949 9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561 10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978 -Loop time of 1.05484 on 1 procs for 10000 steps with 200 atoms +Loop time of 0.851938 on 1 procs for 10000 steps with 200 atoms -Performance: 4095400.088 tau/day, 9480.093 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 5070791.481 tau/day, 11737.943 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.88325 | 0.88325 | 0.88325 | 0.0 | 83.73 -Neigh | 0.038596 | 0.038596 | 0.038596 | 0.0 | 3.66 -Comm | 0.034257 | 0.034257 | 0.034257 | 0.0 | 3.25 -Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.01 -Modify | 0.083041 | 0.083041 | 0.083041 | 0.0 | 7.87 -Other | | 0.01556 | | | 1.48 +Pair | 0.64889 | 0.64889 | 0.64889 | 0.0 | 76.17 +Neigh | 0.04038 | 0.04038 | 0.04038 | 0.0 | 4.74 +Comm | 0.058003 | 0.058003 | 0.058003 | 0.0 | 6.81 +Output | 0.00021219 | 0.00021219 | 0.00021219 | 0.0 | 0.02 +Modify | 0.083454 | 0.083454 | 0.083454 | 0.0 | 9.80 +Other | | 0.021 | | | 2.47 Nlocal: 200 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -101,4 +108,4 @@ Total # of neighbors = 1625 Ave neighs/atom = 8.125 Neighbor list builds = 673 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/dipole/log.5Oct16.dipole.g++.4 b/examples/dipole/log.27Nov18.dipole.g++.4 similarity index 77% rename from examples/dipole/log.5Oct16.dipole.g++.4 rename to examples/dipole/log.27Nov18.dipole.g++.4 index b573253fbc..f33bfde451 100644 --- a/examples/dipole/log.5Oct16.dipole.g++.4 +++ b/examples/dipole/log.27Nov18.dipole.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Point dipoles in a 2d box units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 200 atoms + Time spent = 0.00139761 secs # need both mass settings due to hybrid atom style @@ -46,13 +48,18 @@ thermo 500 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 13 13 2 -Memory usage per processor = 4.47621 Mbytes + binsize = 1.4, bins = 13 13 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/dipole/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair c_erot TotEng Press 0 0 -2.1909822 0 -2.1909822 -2.5750971 500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899 @@ -75,20 +82,20 @@ Step Temp E_pair c_erot TotEng Press 9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391 9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721 10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509 -Loop time of 0.406978 on 4 procs for 10000 steps with 200 atoms +Loop time of 0.396069 on 4 procs for 10000 steps with 200 atoms -Performance: 10614834.981 tau/day, 24571.377 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 10907185.759 tau/day, 25248.115 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.18518 | 0.23558 | 0.25487 | 6.0 | 57.88 -Neigh | 0.0090437 | 0.011033 | 0.011971 | 1.1 | 2.71 -Comm | 0.086857 | 0.10807 | 0.16262 | 9.6 | 26.56 -Output | 0.00029182 | 0.00031263 | 0.00035739 | 0.1 | 0.08 -Modify | 0.022396 | 0.025649 | 0.026865 | 1.2 | 6.30 -Other | | 0.02633 | | | 6.47 +Pair | 0.13746 | 0.17338 | 0.19067 | 5.1 | 43.77 +Neigh | 0.0096052 | 0.011424 | 0.012275 | 1.0 | 2.88 +Comm | 0.12394 | 0.14718 | 0.1914 | 7.1 | 37.16 +Output | 0.00037861 | 0.00056618 | 0.0011225 | 0.0 | 0.14 +Modify | 0.021838 | 0.024665 | 0.026625 | 1.1 | 6.23 +Other | | 0.03886 | | | 9.81 Nlocal: 50 ave 53 max 41 min Histogram: 1 0 0 0 0 0 0 0 0 3 diff --git a/examples/dreiding/in.dreiding b/examples/dreiding/in.dreiding index 4b811248d4..db0738fd32 100644 --- a/examples/dreiding/in.dreiding +++ b/examples/dreiding/in.dreiding @@ -2,28 +2,28 @@ units real atom_style full boundary p p p dielectric 1 -special_bonds lj/coul 0.0 0.0 1.0 +special_bonds lj/coul 0.0 0.0 1.0 pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5 -bond_style harmonic -angle_style harmonic +bond_style harmonic +angle_style harmonic dihedral_style harmonic improper_style none -kspace_style pppm 0.001 +kspace_style pppm 0.001 read_data data.dreiding -pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 -pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 -pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 -pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 -pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 -pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 -pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 -pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 -pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 -pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 -pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 +pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 +pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 +pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 +pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 +pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 +pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 +pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 +pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 +pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 +pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 +pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 pair_modify mix arithmetic neighbor 2.0 multi neigh_modify every 2 delay 4 check yes @@ -33,7 +33,11 @@ variable sname index ch3oh.box.dreiding compute hb all pair hbond/dreiding/lj variable C_hbond equal c_hb[1] #number hbonds variable E_hbond equal c_hb[2] #hbond energy -thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol -thermo_modify line multi format float %14.6f +thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol +thermo_modify line multi format float %14.6f -run 0 +fix 1 all nve + +thermo 10 + +run 100 diff --git a/examples/dreiding/log.27Nov18.dreiding.g++.1 b/examples/dreiding/log.27Nov18.dreiding.g++.1 new file mode 100644 index 0000000000..bbc2105238 --- /dev/null +++ b/examples/dreiding/log.27Nov18.dreiding.g++.1 @@ -0,0 +1,198 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full +boundary p p p +dielectric 1 +special_bonds lj/coul 0.0 0.0 1.0 + +pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5 +bond_style harmonic +angle_style harmonic +dihedral_style harmonic +improper_style none +kspace_style pppm 0.001 + +read_data data.dreiding + orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 384 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 3 = max dihedrals/atom + reading bonds ... + 320 bonds + reading angles ... + 448 angles + reading dihedrals ... + 192 dihedrals + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 5 = max # of special neighbors + +pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 +pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 +pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 +pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 +pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 +pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 +pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 +pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 +pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 +pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 +pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 +pair_modify mix arithmetic +neighbor 2.0 multi +neigh_modify every 2 delay 4 check yes +variable input index in.ch3oh.box.dreiding +variable sname index ch3oh.box.dreiding + +compute hb all pair hbond/dreiding/lj +variable C_hbond equal c_hb[1] #number hbonds +variable E_hbond equal c_hb[2] #hbond energy +thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol +thermo_modify line multi format float %14.6f + +fix 1 all nve + +thermo 10 + +run 100 +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.142073 + grid = 3 3 3 + stencil order = 5 + estimated absolute RMS force accuracy = 0.154715 + estimated relative force accuracy = 0.00046592 + using double precision FFTs + 3d grid and FFT values/proc = 512 27 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.5 + ghost atom cutoff = 13.5 + binsize = 6.75, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair hbond/dreiding/lj, perpetual, skip from (3) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/coul/long, perpetual, half/full from (3) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: full, newton on + pair build: full/multi + stencil: full/multi/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 +PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 +E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 +E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 +v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 +---------------- Step 10 ----- CPU = 0.0306 (sec) ---------------- +TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522 +PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481 +E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883 +E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278 +v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335 +---------------- Step 20 ----- CPU = 0.0597 (sec) ---------------- +TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407 +PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582 +E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103 +E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343 +v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335 +---------------- Step 30 ----- CPU = 0.0889 (sec) ---------------- +TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412 +PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630 +E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697 +E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068 +v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335 +---------------- Step 40 ----- CPU = 0.1178 (sec) ---------------- +TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037 +PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583 +E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713 +E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393 +v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335 +---------------- Step 50 ----- CPU = 0.1467 (sec) ---------------- +TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734 +PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041 +E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518 +E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967 +v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335 +---------------- Step 60 ----- CPU = 0.1755 (sec) ---------------- +TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489 +PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008 +E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312 +E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165 +v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335 +---------------- Step 70 ----- CPU = 0.2044 (sec) ---------------- +TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019 +PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999 +E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572 +E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544 +v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335 +---------------- Step 80 ----- CPU = 0.2333 (sec) ---------------- +TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689 +PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918 +E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346 +E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370 +v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335 +---------------- Step 90 ----- CPU = 0.2622 (sec) ---------------- +TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574 +PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914 +E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267 +E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223 +v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335 +---------------- Step 100 ----- CPU = 0.2911 (sec) ---------------- +TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054 +PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059 +E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719 +E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795 +v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335 +Loop time of 0.291149 on 1 procs for 100 steps with 384 atoms + +Performance: 29.676 ns/day, 0.809 hours/ns, 343.467 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.255 | 0.255 | 0.255 | 0.0 | 87.59 +Bond | 0.0042725 | 0.0042725 | 0.0042725 | 0.0 | 1.47 +Kspace | 0.027151 | 0.027151 | 0.027151 | 0.0 | 9.33 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0034399 | 0.0034399 | 0.0034399 | 0.0 | 1.18 +Output | 0.00025988 | 0.00025988 | 0.00025988 | 0.0 | 0.09 +Modify | 0.00059223 | 0.00059223 | 0.00059223 | 0.0 | 0.20 +Other | | 0.0004294 | | | 0.15 + +Nlocal: 384 ave 384 max 384 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4637 ave 4637 max 4637 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 101854 ave 101854 max 101854 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 5624 ave 5624 max 5624 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 101854 +Ave neighs/atom = 265.245 +Ave special neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/dreiding/log.27Nov18.dreiding.g++.4 b/examples/dreiding/log.27Nov18.dreiding.g++.4 new file mode 100644 index 0000000000..f765d71fbe --- /dev/null +++ b/examples/dreiding/log.27Nov18.dreiding.g++.4 @@ -0,0 +1,198 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full +boundary p p p +dielectric 1 +special_bonds lj/coul 0.0 0.0 1.0 + +pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5 +bond_style harmonic +angle_style harmonic +dihedral_style harmonic +improper_style none +kspace_style pppm 0.001 + +read_data data.dreiding + orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697) + 2 by 1 by 2 MPI processor grid + reading atoms ... + 384 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 3 = max dihedrals/atom + reading bonds ... + 320 bonds + reading angles ... + 448 angles + reading dihedrals ... + 192 dihedrals + 4 = max # of 1-2 neighbors + 3 = max # of 1-3 neighbors + 5 = max # of special neighbors + +pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 +pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 +pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 +pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 +pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 +pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 +pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 +pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 +pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 +pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 +pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 +pair_modify mix arithmetic +neighbor 2.0 multi +neigh_modify every 2 delay 4 check yes +variable input index in.ch3oh.box.dreiding +variable sname index ch3oh.box.dreiding + +compute hb all pair hbond/dreiding/lj +variable C_hbond equal c_hb[1] #number hbonds +variable E_hbond equal c_hb[2] #hbond energy +thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol +thermo_modify line multi format float %14.6f + +fix 1 all nve + +thermo 10 + +run 100 +PPPM initialization ... +WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.142073 + grid = 3 3 3 + stencil order = 5 + estimated absolute RMS force accuracy = 0.154715 + estimated relative force accuracy = 0.00046592 + using double precision FFTs + 3d grid and FFT values/proc = 392 12 +Neighbor list info ... + update every 2 steps, delay 4 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 13.5 + ghost atom cutoff = 13.5 + binsize = 6.75, bins = 3 3 3 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair hbond/dreiding/lj, perpetual, skip from (3) + attributes: full, newton on + pair build: skip + stencil: none + bin: none + (2) pair lj/cut/coul/long, perpetual, half/full from (3) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: full, newton on + pair build: full/multi + stencil: full/multi/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 +PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 +E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 +E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 +v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 +---------------- Step 10 ----- CPU = 0.0112 (sec) ---------------- +TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522 +PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481 +E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883 +E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278 +v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335 +---------------- Step 20 ----- CPU = 0.0206 (sec) ---------------- +TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407 +PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582 +E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103 +E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343 +v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335 +---------------- Step 30 ----- CPU = 0.0299 (sec) ---------------- +TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412 +PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630 +E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697 +E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068 +v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335 +---------------- Step 40 ----- CPU = 0.0403 (sec) ---------------- +TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037 +PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583 +E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713 +E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393 +v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335 +---------------- Step 50 ----- CPU = 0.0494 (sec) ---------------- +TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734 +PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041 +E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518 +E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967 +v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335 +---------------- Step 60 ----- CPU = 0.0588 (sec) ---------------- +TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489 +PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008 +E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312 +E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165 +v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335 +---------------- Step 70 ----- CPU = 0.0680 (sec) ---------------- +TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019 +PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999 +E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572 +E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544 +v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335 +---------------- Step 80 ----- CPU = 0.0790 (sec) ---------------- +TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689 +PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918 +E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346 +E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370 +v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335 +---------------- Step 90 ----- CPU = 0.0883 (sec) ---------------- +TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574 +PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914 +E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267 +E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223 +v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335 +---------------- Step 100 ----- CPU = 0.0976 (sec) ---------------- +TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054 +PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059 +E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719 +E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795 +v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335 +Loop time of 0.0976357 on 4 procs for 100 steps with 384 atoms + +Performance: 88.492 ns/day, 0.271 hours/ns, 1024.215 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.055383 | 0.065178 | 0.07438 | 2.7 | 66.76 +Bond | 0.00099874 | 0.0011503 | 0.001229 | 0.3 | 1.18 +Kspace | 0.013823 | 0.022918 | 0.032308 | 4.4 | 23.47 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.0064669 | 0.0072899 | 0.0078194 | 0.6 | 7.47 +Output | 0.00039268 | 0.00043893 | 0.00056481 | 0.0 | 0.45 +Modify | 0.000175 | 0.00019002 | 0.00020623 | 0.0 | 0.19 +Other | | 0.0004706 | | | 0.48 + +Nlocal: 96 ave 104 max 87 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 3063.25 ave 3108 max 3024 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 25463.5 ave 28799 max 22471 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +FullNghs: 1406 ave 1664 max 1237 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 101854 +Ave neighs/atom = 265.245 +Ave special neighs/atom = 4 +Neighbor list builds = 0 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/dreiding/log.5Oct16.dreiding.g++.1 b/examples/dreiding/log.5Oct16.dreiding.g++.1 deleted file mode 100644 index 5208fe7d1c..0000000000 --- a/examples/dreiding/log.5Oct16.dreiding.g++.1 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (5 Oct 2016) -units real -atom_style full -boundary p p p -dielectric 1 -special_bonds lj/coul 0.0 0.0 1.0 - -pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5 -bond_style harmonic -angle_style harmonic -dihedral_style harmonic -improper_style none -kspace_style pppm 0.001 - -read_data data.dreiding - orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 384 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 3 = max dihedrals/atom - reading bonds ... - 320 bonds - reading angles ... - 448 angles - reading dihedrals ... - 192 dihedrals - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 5 = max # of special neighbors - -pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 -pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 -pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 -pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 -pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 -pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 -pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 -pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 -pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 -pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 -pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 -pair_modify mix arithmetic -neighbor 2.0 multi -neigh_modify every 2 delay 4 check yes -variable input index in.ch3oh.box.dreiding -variable sname index ch3oh.box.dreiding - -compute hb all pair hbond/dreiding/lj -variable C_hbond equal c_hb[1] #number hbonds -variable E_hbond equal c_hb[2] #hbond energy -thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol -thermo_modify line multi format float %14.6f - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -PPPM initialization ... -WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297) -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.142073 - grid = 3 3 3 - stencil order = 5 - estimated absolute RMS force accuracy = 0.154715 - estimated relative force accuracy = 0.00046592 - using double precision FFTs - 3d grid and FFT values/proc = 512 27 -Neighbor list info ... - 3 neighbor list requests - update every 2 steps, delay 4 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13.5 - ghost atom cutoff = 13.5 - binsize = 6.75 -> bins = 3 3 3 -Memory usage per processor = 9.19186 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 -PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 -E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 -E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 -v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 384 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Bond | 0 | 0 | 0 | 0.0 | 0.00 -Kspace | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 384 ave 384 max 384 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4637 ave 4637 max 4637 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 101854 ave 101854 max 101854 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 203708 ave 203708 max 203708 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 203708 -Ave neighs/atom = 530.49 -Ave special neighs/atom = 4 -Neighbor list builds = 0 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/dreiding/log.5Oct16.dreiding.g++.4 b/examples/dreiding/log.5Oct16.dreiding.g++.4 deleted file mode 100644 index 551b8cbb1b..0000000000 --- a/examples/dreiding/log.5Oct16.dreiding.g++.4 +++ /dev/null @@ -1,118 +0,0 @@ -LAMMPS (5 Oct 2016) -units real -atom_style full -boundary p p p -dielectric 1 -special_bonds lj/coul 0.0 0.0 1.0 - -pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5 -bond_style harmonic -angle_style harmonic -dihedral_style harmonic -improper_style none -kspace_style pppm 0.001 - -read_data data.dreiding - orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 384 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 3 = max dihedrals/atom - reading bonds ... - 320 bonds - reading angles ... - 448 angles - reading dihedrals ... - 192 dihedrals - 4 = max # of 1-2 neighbors - 3 = max # of 1-3 neighbors - 5 = max # of special neighbors - -pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 -pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 -pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 -pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 -pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 -pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 -pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 -pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 -pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 -pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 -pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4 -pair_modify mix arithmetic -neighbor 2.0 multi -neigh_modify every 2 delay 4 check yes -variable input index in.ch3oh.box.dreiding -variable sname index ch3oh.box.dreiding - -compute hb all pair hbond/dreiding/lj -variable C_hbond equal c_hb[1] #number hbonds -variable E_hbond equal c_hb[2] #hbond energy -thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol -thermo_modify line multi format float %14.6f - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -PPPM initialization ... -WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297) -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) - G vector (1/distance) = 0.142073 - grid = 3 3 3 - stencil order = 5 - estimated absolute RMS force accuracy = 0.154715 - estimated relative force accuracy = 0.00046592 - using double precision FFTs - 3d grid and FFT values/proc = 392 12 -Neighbor list info ... - 3 neighbor list requests - update every 2 steps, delay 4 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 13.5 - ghost atom cutoff = 13.5 - binsize = 6.75 -> bins = 3 3 3 -Memory usage per processor = 9.05502 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 -PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 -E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 -E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 -v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 -Loop time of 4.52995e-06 on 4 procs for 0 steps with 384 atoms - -0.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Bond | 0 | 0 | 0 | 0.0 | 0.00 -Kspace | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 4.53e-06 | | |100.00 - -Nlocal: 96 ave 104 max 87 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 3063.25 ave 3108 max 3024 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 25463.5 ave 28799 max 22471 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -FullNghs: 50927 ave 55516 max 46073 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 203708 -Ave neighs/atom = 530.49 -Ave special neighs/atom = 4 -Neighbor list builds = 0 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/eim/ffield.eim b/examples/eim/ffield.eim deleted file mode 100644 index b29bee83a4..0000000000 --- a/examples/eim/ffield.eim +++ /dev/null @@ -1,145 +0,0 @@ - global: 2.0000e+00 -1.6450e+00 1.6450e+00 ### DATE: 2010-08-31 CONTRIBUTOR: Xiaowang Zhou, xzhou@sandia.gov CITATION: Zhou, unknown -element: Li 3 6.9410e+00 9.8000e-01 1.1220e+00 1.1220e+00 -1.6500e+00 0.0000e+00 -element: Na 11 2.2990e+01 9.3000e-01 1.3690e+00 1.3690e+00 -1.1100e+00 0.0000e+00 -element: K 19 3.9100e+01 8.2000e-01 1.6910e+00 1.6910e+00 -9.3400e-01 0.0000e+00 -element: Rb 37 8.5470e+01 8.2000e-01 1.8350e+00 1.8350e+00 -8.9200e-01 0.0000e+00 -element: Cs 55 1.3290e+02 7.9000e-01 2.0040e+00 2.0040e+00 -8.2000e-01 0.0000e+00 -element: F 9 1.9000e+01 3.9800e+00 9.5600e-01 9.5600e-01 -8.2000e-01 0.0000e+00 -element: Cl 17 3.5450e+01 3.1600e+00 1.4470e+00 1.4470e+00 -1.2660e+00 0.0000e+00 -element: Br 35 7.9900e+01 2.9600e+00 1.6070e+00 1.6070e+00 -1.1620e+00 0.0000e+00 -element: Id 53 1.2690e+02 2.6600e+00 1.8500e+00 1.8500e+00 -1.1100e+00 0.0000e+00 - pair: Li Li 6.0490e+00 6.0490e+00 -2.5330e-01 3.6176e+00 7.5536e+00 & - 3.5017e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.0637e+00 & - 3.3271e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Li Na 6.2550e+00 6.2550e+00 -2.1173e-01 3.8107e+00 7.6502e+00 & - 3.9066e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.2391e+00 & - 4.1481e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Li K 6.5500e+00 6.5500e+00 -1.9593e-01 4.1243e+00 8.3560e+00 & - 4.1457e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.4670e+00 & - 3.1840e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Li Rb 6.6870e+00 6.6870e+00 -1.8748e-01 4.2997e+00 8.8253e+00 & - 4.1380e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.5690e+00 & - 4.7482e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Li Cs 6.1460e+00 6.1460e+00 -1.8290e-01 3.9687e+00 9.7602e+00 & - 5.5766e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.3351e+00 & - 5.9605e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Li F 4.5000e+00 4.5000e+00 -1.2681e+00 1.9644e+00 1.3467e+01 & - 5.2272e+00 5.4300e+00 2.1778e-02 2.0090e+00 5.4840e+00 & - 6.9987e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Li Cl 4.5000e+00 4.5000e+00 -1.1727e+00 2.3957e+00 1.3116e+01 & - 5.0004e+00 6.9360e+00 2.1778e-02 2.5660e+00 5.9750e+00 & - 1.5717e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Li Br 4.7580e+00 4.7580e+00 -8.5748e-01 2.6727e+00 1.4436e+01 & - 9.1593e+00 7.4250e+00 2.1778e-02 2.7470e+00 6.1350e+00 & - 1.9827e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Li Id 5.2390e+00 5.2390e+00 -8.7986e-01 2.9537e+00 1.7362e+01 & - 1.0904e+01 8.1770e+00 2.1778e-02 3.0250e+00 6.3780e+00 & - 1.9661e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Na Na 6.4610e+00 6.4610e+00 -1.7698e-01 4.0039e+00 7.7467e+00 & - 4.3115e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.4144e+00 & - 5.1719e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Na K 6.7560e+00 6.7560e+00 -1.6377e-01 4.3174e+00 8.4525e+00 & - 4.5506e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.6423e+00 & - 3.9698e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Na Rb 6.8930e+00 6.8930e+00 -1.5671e-01 4.4929e+00 8.9219e+00 & - 4.5430e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.7443e+00 & - 5.9200e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Na Cs 6.3520e+00 6.3520e+00 -1.5288e-01 4.1619e+00 9.8567e+00 & - 5.9816e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.5104e+00 & - 7.4315e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Na F 4.5000e+00 4.5000e+00 -1.1620e+00 2.1974e+00 1.1049e+01 & - 4.1424e+00 6.2360e+00 2.1778e-02 2.3070e+00 5.7310e+00 & - 4.9728e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Na Cl 4.8740e+00 4.8740e+00 -8.9972e-01 2.6668e+00 9.4654e+00 & - 4.9503e+00 7.6060e+00 2.1778e-02 2.8140e+00 6.2220e+00 & - 7.7787e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Na Br 5.1630e+00 5.1630e+00 -8.0673e-01 2.7422e+00 8.1178e+00 & - 3.3460e+00 8.0580e+00 2.1778e-02 2.9810e+00 6.3820e+00 & - 4.0042e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Na Id 5.5960e+00 5.5960e+00 -7.2203e-01 3.0252e+00 9.7019e+00 & - 4.4260e+00 8.7330e+00 2.1778e-02 3.2310e+00 6.6250e+00 & - 5.9680e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: K K 7.0510e+00 7.0510e+00 -1.5155e-01 4.6310e+00 9.1583e+00 & - 4.7898e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.8702e+00 & - 3.0471e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: K Rb 7.1880e+00 7.1880e+00 -1.4502e-01 4.8065e+00 9.6276e+00 & - 4.7821e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.9722e+00 & - 4.5441e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: K Cs 6.6460e+00 6.6460e+00 -1.4147e-01 4.4755e+00 1.0563e+01 & - 6.2207e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.7383e+00 & - 5.7043e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: K F 4.6140e+00 4.6140e+00 -1.0775e+00 2.5856e+00 1.0225e+01 & - 5.4019e+00 7.2010e+00 2.1778e-02 2.6640e+00 6.0530e+00 & - 1.0410e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: K Cl 5.4370e+00 5.4370e+00 -8.1301e-01 3.0910e+00 1.2573e+01 & - 7.0710e+00 8.4850e+00 2.1778e-02 3.1390e+00 6.5440e+00 & - 1.4487e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: K Br 5.7030e+00 5.7030e+00 -6.7522e-01 3.2878e+00 1.7293e+01 & - 1.0996e+01 8.9010e+00 2.1778e-02 3.2930e+00 6.7040e+00 & - 1.1194e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: K Id 6.1070e+00 6.1070e+00 -6.0446e-01 3.5269e+00 1.4089e+01 & - 9.0912e+00 9.5310e+00 2.1778e-02 3.5260e+00 6.9470e+00 & - 3.0858e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Rb Rb 7.3250e+00 7.3250e+00 -1.3877e-01 4.9819e+00 1.0097e+01 & - 4.7744e+00 0.0000e+00 2.1778e-02 2.0000e+00 8.0742e+00 & - 6.7765e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Rb Cs 6.7840e+00 6.7840e+00 -1.3538e-01 4.6509e+00 1.1032e+01 & - 6.2130e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.8403e+00 & - 8.5066e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Rb F 4.8760e+00 4.8760e+00 -1.0823e+00 2.7541e+00 1.3747e+01 & - 7.6226e+00 7.6090e+00 2.1778e-02 2.8150e+00 6.1970e+00 & - 1.6872e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Rb Cl 5.6900e+00 5.6900e+00 -7.8153e-01 3.2541e+00 1.5328e+01 & - 7.5403e+00 8.8790e+00 2.1778e-02 3.2850e+00 6.6880e+00 & - 5.1848e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Rb Br 5.9480e+00 5.9480e+00 -6.4488e-01 3.4287e+00 1.4880e+01 & - 9.5493e+00 9.2820e+00 2.1778e-02 3.4340e+00 6.8480e+00 & - 1.3768e-02 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Rb Id 6.3440e+00 6.3440e+00 -5.3162e-01 3.6720e+00 1.5074e+01 & - 9.7627e+00 9.9010e+00 2.1778e-02 3.6630e+00 7.0910e+00 & - 7.4616e-02 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Cs Cs 6.2420e+00 6.2420e+00 -1.3207e-01 4.3199e+00 1.1967e+01 & - 7.6516e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.6064e+00 & - 1.0679e+00 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Cs F 5.2050e+00 5.2050e+00 -9.8283e-01 3.0007e+00 1.3854e+01 & - 7.7871e+00 8.1230e+00 2.1778e-02 3.0050e+00 6.3660e+00 & - 2.3092e-01 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Cs Cl 5.9750e+00 5.9750e+00 -5.8967e-01 3.4958e+00 1.1434e+01 & - 6.9253e+00 9.3250e+00 2.1778e-02 3.4500e+00 6.8570e+00 & - 2.1629e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Cs Br 6.2320e+00 6.2320e+00 -5.5406e-01 3.6322e+00 1.2533e+01 & - 8.0448e+00 9.7250e+00 2.1778e-02 3.5980e+00 7.0170e+00 & - 2.1997e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: Cs Id 6.6210e+00 6.6210e+00 -5.3436e-01 3.8333e+00 1.2407e+01 & - 7.9302e+00 1.0334e+01 2.1778e-02 3.8230e+00 7.2600e+00 & - 2.0446e+00 6.0000e-01 2.0000e+00 2.0000e+00 - pair: F F 6.0090e+00 6.0090e+00 -1.3323e-01 4.0026e+00 7.7698e+00 & - 2.9898e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.0273e+00 & - 1.0029e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: F Cl 6.2890e+00 6.2890e+00 -1.6693e-01 4.3780e+00 8.0429e+00 & - 3.2973e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.2844e+00 & - 4.0767e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: F Br 6.4380e+00 6.4380e+00 -1.6007e-01 4.3642e+00 8.0224e+00 & - 4.1481e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.3941e+00 & - 4.3519e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: F Id 6.6670e+00 6.6670e+00 -1.5664e-01 4.6057e+00 8.3941e+00 & - 4.1673e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.5606e+00 & - 3.8866e-01 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Cl Cl 6.5690e+00 6.5690e+00 -2.0915e-01 4.7534e+00 8.3161e+00 & - 3.6047e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.5415e+00 & - 1.6571e+00 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Cl Br 6.7180e+00 6.7180e+00 -2.0056e-01 4.7396e+00 8.2956e+00 & - 4.4555e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.6512e+00 & - 1.7690e+00 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Cl Id 6.9470e+00 6.9470e+00 -1.9626e-01 4.9811e+00 8.6672e+00 & - 4.4747e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.8177e+00 & - 1.5798e+00 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Br Br 6.8670e+00 6.8670e+00 -1.9232e-01 4.7259e+00 8.2751e+00 & - 5.3064e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.7610e+00 & - 1.8884e+00 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Br Id 7.0960e+00 7.0960e+00 -1.8820e-01 4.9674e+00 8.6467e+00 & - 5.3256e+00 0.0000e+00 2.1778e-02 2.0000e+00 7.9274e+00 & - 1.6865e+00 6.0000e-01 2.0000e+00 1.0000e+00 - pair: Id Id 7.3250e+00 7.3250e+00 -1.8417e-01 5.2089e+00 9.0184e+00 & - 5.3448e+00 0.0000e+00 2.1778e-02 2.0000e+00 8.0939e+00 & - 1.5062e+00 6.0000e-01 2.0000e+00 1.0000e+00 diff --git a/examples/eim/ffield.eim b/examples/eim/ffield.eim new file mode 120000 index 0000000000..46a319baeb --- /dev/null +++ b/examples/eim/ffield.eim @@ -0,0 +1 @@ +../../potentials/ffield.eim \ No newline at end of file diff --git a/examples/eim/log.27Nov18.eim.g++.1 b/examples/eim/log.27Nov18.eim.g++.1 new file mode 100644 index 0000000000..e36d3f4d5f --- /dev/null +++ b/examples/eim/log.27Nov18.eim.g++.1 @@ -0,0 +1,94 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# NaCl test problem for embedded atom method (EIM) potential + +units metal +atom_style atomic + +boundary p p p + +lattice diamond 5.0 +Lattice spacing in x,y,z = 5 5 5 +read_data data.eim + orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2000 atoms + reading velocities ... + 2000 velocities + +pair_style eim +pair_coeff * * Na Cl ffield.eim Na Cl +Reading potential file ffield.eim with DATE: 2010-08-31 + +neighbor 0.3 bin +neigh_modify delay 0 + +timestep 0.001 +thermo_style custom step pe pxx pyy pzz temp +thermo 50 + +velocity all create 1400.0 43454 dist gaussian mom yes +fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1 + +#dump id all atom 100 dump.eim + +#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Na Cl + +#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Na Cl + +run 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.906 + ghost atom cutoff = 7.906 + binsize = 3.953, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eim, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.169 | 3.169 | 3.169 Mbytes +Step PotEng Pxx Pyy Pzz Temp + 0 -5660.4738 -118151.29 -117613.39 -118064.41 1400 + 50 -5773.8755 1024.91 1034.0269 838.0568 891.54632 + 100 -5742.8536 806.6806 769.72456 836.8687 838.72572 + 150 -5738.7736 -355.86552 -362.389 -155.34159 900.47212 + 200 -5704.2318 -227.29937 -538.51196 -762.1005 834.64611 + 250 -5724.4788 502.49466 657.68817 529.01376 966.07978 + 300 -5718.6085 457.03928 186.13362 725.43587 934.80653 + 350 -5722.7713 -318.51677 -377.15809 125.76892 865.12488 + 400 -5743.7387 -2.3555301 61.330533 -402.22943 840.67167 + 450 -5751.2518 -437.13614 -374.77859 236.60865 743.10367 + 500 -5780.5268 -750.96919 -793.62966 -1722.9652 712.74134 +Loop time of 6.10824 on 1 procs for 500 steps with 2000 atoms + +Performance: 7.072 ns/day, 3.393 hours/ns, 81.857 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.5778 | 5.5778 | 5.5778 | 0.0 | 91.32 +Neigh | 0.43316 | 0.43316 | 0.43316 | 0.0 | 7.09 +Comm | 0.027343 | 0.027343 | 0.027343 | 0.0 | 0.45 +Output | 0.00038743 | 0.00038743 | 0.00038743 | 0.0 | 0.01 +Modify | 0.060761 | 0.060761 | 0.060761 | 0.0 | 0.99 +Other | | 0.008835 | | | 0.14 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4198 ave 4198 max 4198 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 99451 ave 99451 max 99451 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 99451 +Ave neighs/atom = 49.7255 +Neighbor list builds = 90 +Dangerous builds = 10 +Total wall time: 0:00:06 diff --git a/examples/eim/log.27Nov18.eim.g++.4 b/examples/eim/log.27Nov18.eim.g++.4 new file mode 100644 index 0000000000..08abee78b5 --- /dev/null +++ b/examples/eim/log.27Nov18.eim.g++.4 @@ -0,0 +1,94 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# NaCl test problem for embedded atom method (EIM) potential + +units metal +atom_style atomic + +boundary p p p + +lattice diamond 5.0 +Lattice spacing in x,y,z = 5 5 5 +read_data data.eim + orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2000 atoms + reading velocities ... + 2000 velocities + +pair_style eim +pair_coeff * * Na Cl ffield.eim Na Cl +Reading potential file ffield.eim with DATE: 2010-08-31 + +neighbor 0.3 bin +neigh_modify delay 0 + +timestep 0.001 +thermo_style custom step pe pxx pyy pzz temp +thermo 50 + +velocity all create 1400.0 43454 dist gaussian mom yes +fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1 + +#dump id all atom 100 dump.eim + +#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Na Cl + +#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Na Cl + +run 500 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.906 + ghost atom cutoff = 7.906 + binsize = 3.953, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eim, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.051 | 3.051 | 3.051 Mbytes +Step PotEng Pxx Pyy Pzz Temp + 0 -5660.4738 -118151.29 -117613.39 -118064.41 1400 + 50 -5773.8755 1024.91 1034.0269 838.0568 891.54632 + 100 -5742.8536 806.6806 769.72456 836.8687 838.72572 + 150 -5738.7736 -355.86552 -362.389 -155.34159 900.47212 + 200 -5704.2318 -227.29937 -538.51196 -762.1005 834.64611 + 250 -5724.4788 502.49466 657.68817 529.01376 966.07978 + 300 -5718.6085 457.03928 186.13362 725.43587 934.80653 + 350 -5722.7713 -318.51677 -377.15809 125.76892 865.12488 + 400 -5743.7387 -2.3555301 61.330533 -402.22943 840.67167 + 450 -5751.2518 -437.13614 -374.77859 236.60865 743.10367 + 500 -5780.5268 -750.96919 -793.62966 -1722.9652 712.74134 +Loop time of 1.79017 on 4 procs for 500 steps with 2000 atoms + +Performance: 24.132 ns/day, 0.995 hours/ns, 279.303 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5775 | 1.584 | 1.5959 | 0.6 | 88.48 +Neigh | 0.10838 | 0.10882 | 0.10955 | 0.1 | 6.08 +Comm | 0.050677 | 0.062797 | 0.069371 | 2.9 | 3.51 +Output | 0.00031972 | 0.00056875 | 0.0013139 | 0.0 | 0.03 +Modify | 0.027115 | 0.02819 | 0.028965 | 0.4 | 1.57 +Other | | 0.005774 | | | 0.32 + +Nlocal: 500 ave 501 max 499 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2180.25 ave 2183 max 2177 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 24862.8 ave 25154 max 24659 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 99451 +Ave neighs/atom = 49.7255 +Neighbor list builds = 90 +Dangerous builds = 10 +Total wall time: 0:00:01 diff --git a/examples/eim/log.5Oct16.eim.g++.1 b/examples/eim/log.5Oct16.eim.g++.1 deleted file mode 100644 index 7963101f8e..0000000000 --- a/examples/eim/log.5Oct16.eim.g++.1 +++ /dev/null @@ -1,88 +0,0 @@ -LAMMPS (5 Oct 2016) -# NaCl test problem for embedded atom method (EIM) potential - -units metal -atom_style atomic - -boundary p p p - -lattice diamond 5.0 -Lattice spacing in x,y,z = 5 5 5 -read_data data.eim - orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2000 atoms - reading velocities ... - 2000 velocities - -pair_style eim -pair_coeff * * Na Cl ffield.eim Na Cl -Reading potential file ffield.eim with DATE: 2010-08-31 - -neighbor 0.3 bin -neigh_modify delay 0 - -timestep 0.001 -thermo_style custom step pe pxx pyy pzz temp -thermo 50 - -velocity all create 1400.0 43454 dist gaussian mom yes -fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1 - -#dump id all atom 100 dump.eim - -#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 element Na Cl - -#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 element Na Cl - -run 500 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.906 - ghost atom cutoff = 7.906 - binsize = 3.953 -> bins = 10 10 10 -Memory usage per processor = 2.76959 Mbytes -Step PotEng Pxx Pyy Pzz Temp - 0 -5660.4738 -118151.29 -117613.39 -118064.41 1400 - 50 -5773.8661 889.73924 898.43321 703.5365 891.68472 - 100 -5742.8192 866.6183 817.86837 889.72898 838.77403 - 150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672 - 200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705 - 250 -5724.4679 375.50199 546.99196 405.29298 966.14585 - 300 -5718.5442 428.47856 361.93998 752.00729 934.57116 - 350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075 - 400 -5743.6862 173.43552 288.02324 107.96614 840.48912 - 450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176 - 500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129 -Loop time of 5.86191 on 1 procs for 500 steps with 2000 atoms - -Performance: 7.370 ns/day, 3.257 hours/ns, 85.296 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.4001 | 5.4001 | 5.4001 | 0.0 | 92.12 -Neigh | 0.37572 | 0.37572 | 0.37572 | 0.0 | 6.41 -Comm | 0.019177 | 0.019177 | 0.019177 | 0.0 | 0.33 -Output | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.00 -Modify | 0.057656 | 0.057656 | 0.057656 | 0.0 | 0.98 -Other | | 0.008926 | | | 0.15 - -Nlocal: 2000 ave 2000 max 2000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4194 ave 4194 max 4194 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 99537 ave 99537 max 99537 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 99537 -Ave neighs/atom = 49.7685 -Neighbor list builds = 89 -Dangerous builds = 10 -Total wall time: 0:00:05 diff --git a/examples/eim/log.5Oct16.eim.g++.4 b/examples/eim/log.5Oct16.eim.g++.4 deleted file mode 100644 index 57713509e2..0000000000 --- a/examples/eim/log.5Oct16.eim.g++.4 +++ /dev/null @@ -1,88 +0,0 @@ -LAMMPS (5 Oct 2016) -# NaCl test problem for embedded atom method (EIM) potential - -units metal -atom_style atomic - -boundary p p p - -lattice diamond 5.0 -Lattice spacing in x,y,z = 5 5 5 -read_data data.eim - orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2000 atoms - reading velocities ... - 2000 velocities - -pair_style eim -pair_coeff * * Na Cl ffield.eim Na Cl -Reading potential file ffield.eim with DATE: 2010-08-31 - -neighbor 0.3 bin -neigh_modify delay 0 - -timestep 0.001 -thermo_style custom step pe pxx pyy pzz temp -thermo 50 - -velocity all create 1400.0 43454 dist gaussian mom yes -fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1 - -#dump id all atom 100 dump.eim - -#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 element Na Cl - -#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 element Na Cl - -run 500 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7.906 - ghost atom cutoff = 7.906 - binsize = 3.953 -> bins = 10 10 10 -Memory usage per processor = 2.70056 Mbytes -Step PotEng Pxx Pyy Pzz Temp - 0 -5660.4738 -118151.29 -117613.39 -118064.41 1400 - 50 -5773.8661 889.73924 898.43321 703.5365 891.68472 - 100 -5742.8192 866.6183 817.86837 889.72898 838.77403 - 150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672 - 200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705 - 250 -5724.4679 375.50199 546.99196 405.29298 966.14585 - 300 -5718.5442 428.47856 361.93998 752.00729 934.57116 - 350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075 - 400 -5743.6862 173.43552 288.02324 107.96614 840.48912 - 450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176 - 500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129 -Loop time of 1.56761 on 4 procs for 500 steps with 2000 atoms - -Performance: 27.558 ns/day, 0.871 hours/ns, 318.957 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.3749 | 1.3896 | 1.4073 | 1.1 | 88.65 -Neigh | 0.093211 | 0.094616 | 0.096788 | 0.5 | 6.04 -Comm | 0.034484 | 0.05451 | 0.070809 | 6.2 | 3.48 -Output | 0.00025511 | 0.00026953 | 0.00029612 | 0.1 | 0.02 -Modify | 0.023773 | 0.023898 | 0.024043 | 0.1 | 1.52 -Other | | 0.004684 | | | 0.30 - -Nlocal: 500 ave 501 max 498 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 2179.25 ave 2182 max 2175 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Neighs: 24884.2 ave 25164 max 24622 min -Histogram: 1 0 0 1 0 1 0 0 0 1 - -Total # of neighbors = 99537 -Ave neighs/atom = 49.7685 -Neighbor list builds = 89 -Dangerous builds = 10 -Total wall time: 0:00:01 diff --git a/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 new file mode 100644 index 0000000000..cf7d851f64 --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.1 @@ -0,0 +1,192 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# GayBerne ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.000507116 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style gayberne 1.0 3.0 1.0 4.0 +pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gayberne, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839 + 500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214 + 600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035 + 700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157 + 800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484 + 900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691 + 1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324 + 1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906 + 1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606 + 1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407 + 1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026 + 1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803 + 1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587 + 1700 1.9434093 -3.2434441 -1.3043926 0.72465776 1136.9866 + 1800 1.9731416 -3.2692426 -1.3364608 0.52887378 1162.1022 + 1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306 + 2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713 +Loop time of 0.950695 on 1 procs for 2000 steps with 400 atoms + +Performance: 363523.513 tau/day, 2103.724 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.72638 | 0.72638 | 0.72638 | 0.0 | 76.40 +Neigh | 0.015026 | 0.015026 | 0.015026 | 0.0 | 1.58 +Comm | 0.015169 | 0.015169 | 0.015169 | 0.0 | 1.60 +Output | 0.0004487 | 0.0004487 | 0.0004487 | 0.0 | 0.05 +Modify | 0.18921 | 0.18921 | 0.18921 | 0.0 | 19.90 +Other | | 0.004463 | | | 0.47 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 247 ave 247 max 247 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3021 ave 3021 max 3021 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3021 +Ave neighs/atom = 7.5525 +Neighbor list builds = 137 +Dangerous builds = 80 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.763 | 4.763 | 4.763 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.894614 -3.3964158 -1.4932323 0.69021871 1125.7713 + 2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713 + 2200 1.9098636 -3.4103342 -1.5286928 0.58806422 1125.7713 + 2300 1.9069018 -3.4099451 -1.6100279 0.63472569 1125.7713 + 2400 1.9773111 -3.4856999 -1.5268537 0.68904663 1125.7713 + 2500 2.0027582 -3.5144592 -1.4900208 0.59925433 1125.7713 + 2600 1.9616623 -3.4744355 -1.5230915 0.26873349 1125.7713 + 2700 1.8601168 -3.3625754 -1.4872109 0.68399005 1125.7713 + 2800 1.8194253 -3.319084 -1.5148077 0.62537226 1125.7713 + 2900 1.8465082 -3.3451652 -1.5508026 0.60163613 1125.7713 + 3000 1.8894551 -3.3918005 -1.5180435 0.61243969 1125.7713 + 3100 1.866554 -3.3662479 -1.5275331 0.54334005 1125.7713 + 3200 1.8233715 -3.3204693 -1.5180055 0.82717864 1125.7713 + 3300 1.7945158 -3.2898507 -1.4976351 0.56745564 1125.7713 + 3400 1.8242025 -3.3242538 -1.5070312 1.0550995 1125.7713 + 3500 1.860405 -3.3595757 -1.5138968 0.56959347 1125.7713 + 3600 1.76951 -3.2635375 -1.5302852 0.47091998 1125.7713 + 3700 1.7874111 -3.2838743 -1.4858244 0.74507678 1125.7713 + 3800 1.8084002 -3.3081089 -1.5294313 0.63717641 1125.7713 + 3900 1.9201118 -3.4261733 -1.4874713 0.4111663 1125.7713 + 4000 1.9130445 -3.4170846 -1.49357 0.35783848 1125.7713 +Loop time of 1.05944 on 1 procs for 2000 steps with 400 atoms + +Performance: 326208.857 tau/day, 1887.783 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.91753 | 0.91753 | 0.91753 | 0.0 | 86.60 +Neigh | 0.0072479 | 0.0072479 | 0.0072479 | 0.0 | 0.68 +Comm | 0.016155 | 0.016155 | 0.016155 | 0.0 | 1.52 +Output | 0.00042105 | 0.00042105 | 0.00042105 | 0.0 | 0.04 +Modify | 0.11222 | 0.11222 | 0.11222 | 0.0 | 10.59 +Other | | 0.005868 | | | 0.55 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 243 ave 243 max 243 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3073 ave 3073 max 3073 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3073 +Ave neighs/atom = 7.6825 +Neighbor list builds = 46 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:02 diff --git a/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 new file mode 100644 index 0000000000..e15ce8474f --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.gayberne.g++.4 @@ -0,0 +1,192 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# GayBerne ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.000466347 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style gayberne 1.0 3.0 1.0 4.0 +pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gayberne, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1707875 -0.00045989278 2.2870073 0.066725499 13701.839 + 500 1.9710982 -0.014545321 2.0486111 0.12205188 8490.5214 + 600 2.0818888 -0.21572832 1.8356955 0.22333255 4697.3035 + 700 2.1551458 -0.68175426 1.4003368 0.60385996 2541.157 + 800 1.8879651 -1.6357045 0.21794544 1.0826917 1444.4484 + 900 2.1993533 -3.0664068 -0.91036919 3.2142529 925.96691 + 1000 1.4285977 -4.3962037 -2.9651113 3.1830461 744.91324 + 1100 1.933074 -4.9398703 -3.0147256 1.4694937 715.30906 + 1200 2.0872875 -4.5711608 -2.4689861 1.4091154 757.68606 + 1300 1.8950043 -4.1568789 -2.2487345 0.19138859 846.69407 + 1400 2.1773467 -3.7905723 -1.6164698 0.55639059 930.77026 + 1500 1.934954 -3.5505876 -1.6187812 0.2572587 1020.2803 + 1600 2.083004 -3.2707357 -1.1794873 0.68661802 1088.5587 + 1700 1.9434093 -3.2434441 -1.3043926 0.72465775 1136.9866 + 1800 1.9731416 -3.2692426 -1.3364608 0.52887379 1162.1022 + 1900 2.0618126 -3.2264372 -1.162807 0.93455596 1155.8306 + 2000 1.894614 -3.3964158 -1.4932323 0.69021875 1125.7713 +Loop time of 0.349687 on 4 procs for 2000 steps with 400 atoms + +Performance: 988313.640 tau/day, 5719.408 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.17051 | 0.19038 | 0.20513 | 3.1 | 54.44 +Neigh | 0.0039656 | 0.0043136 | 0.0049045 | 0.6 | 1.23 +Comm | 0.054327 | 0.071206 | 0.087044 | 4.9 | 20.36 +Output | 0.00043106 | 0.00062788 | 0.0012097 | 0.0 | 0.18 +Modify | 0.072846 | 0.077488 | 0.081302 | 1.2 | 22.16 +Other | | 0.005673 | | | 1.62 + +Nlocal: 100 ave 112 max 84 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 146.75 ave 156 max 137 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 755.25 ave 889 max 589 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 3021 +Ave neighs/atom = 7.5525 +Neighbor list builds = 137 +Dangerous builds = 80 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.74 | 4.74 | 4.74 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.894614 -3.3964158 -1.4932323 0.69021875 1125.7713 + 2100 1.8880098 -3.3875135 -1.4857102 0.21017294 1125.7713 + 2200 1.9098636 -3.4103342 -1.5286928 0.58806421 1125.7713 + 2300 1.9069019 -3.4099452 -1.610028 0.63472573 1125.7713 + 2400 1.9773106 -3.4856993 -1.5268537 0.68904883 1125.7713 + 2500 2.0027578 -3.5144588 -1.4900205 0.59925475 1125.7713 + 2600 1.9616631 -3.4744364 -1.5230915 0.26873516 1125.7713 + 2700 1.8601136 -3.362572 -1.487211 0.68399725 1125.7713 + 2800 1.8194391 -3.3190986 -1.5148092 0.62533318 1125.7713 + 2900 1.846505 -3.3451617 -1.5508267 0.60156074 1125.7713 + 3000 1.8894747 -3.3918215 -1.5180241 0.61210219 1125.7713 + 3100 1.866832 -3.3665537 -1.5276291 0.54222093 1125.7713 + 3200 1.8233362 -3.320323 -1.5177672 0.82891257 1125.7713 + 3300 1.7946952 -3.2899252 -1.4974666 0.56782835 1125.7713 + 3400 1.8283468 -3.3286169 -1.5065958 1.0370934 1125.7713 + 3500 1.8538134 -3.3526037 -1.5116661 0.58945341 1125.7713 + 3600 1.7851382 -3.2811082 -1.5306837 0.462114 1125.7713 + 3700 1.7664573 -3.2622701 -1.4774432 0.86540402 1125.7713 + 3800 1.8574677 -3.3592552 -1.5196884 0.45146881 1125.7713 + 3900 1.9139087 -3.4196718 -1.5054647 0.79636137 1125.7713 + 4000 1.9081675 -3.4146407 -1.5285325 0.69377107 1125.7713 +Loop time of 0.379139 on 4 procs for 2000 steps with 400 atoms + +Performance: 911539.742 tau/day, 5275.114 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.20177 | 0.23758 | 0.28816 | 7.4 | 62.66 +Neigh | 0.0015984 | 0.001946 | 0.0022459 | 0.6 | 0.51 +Comm | 0.046169 | 0.093409 | 0.13456 | 11.9 | 24.64 +Output | 0.00048614 | 0.00087821 | 0.0016096 | 0.0 | 0.23 +Modify | 0.02563 | 0.029633 | 0.034698 | 2.0 | 7.82 +Other | | 0.01569 | | | 4.14 + +Nlocal: 100 ave 117 max 87 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 152.5 ave 169 max 131 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 771.25 ave 988 max 612 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 3085 +Ave neighs/atom = 7.7125 +Neighbor list builds = 45 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 new file mode 100644 index 0000000000..be1a711218 --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.1 @@ -0,0 +1,189 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# RESquared ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.000540733 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style resquared 4.0 +pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair resquared, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.752 | 4.752 | 4.752 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864 + 500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958 + 600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892 + 700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262 + 800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933 + 900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139 + 1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133 + 1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229 + 1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187 + 1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057 + 1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359 + 1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976 + 1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576 + 1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102 + 1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953 + 1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914 + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 +Loop time of 1.62265 on 1 procs for 2000 steps with 400 atoms + +Performance: 212984.850 tau/day, 1232.551 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4048 | 1.4048 | 1.4048 | 0.0 | 86.57 +Neigh | 0.014643 | 0.014643 | 0.014643 | 0.0 | 0.90 +Comm | 0.011678 | 0.011678 | 0.011678 | 0.0 | 0.72 +Output | 0.00046086 | 0.00046086 | 0.00046086 | 0.0 | 0.03 +Modify | 0.18748 | 0.18748 | 0.18748 | 0.0 | 11.55 +Other | | 0.003623 | | | 0.22 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 213 ave 213 max 213 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1884 ave 1884 max 1884 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1884 +Ave neighs/atom = 4.71 +Neighbor list builds = 177 +Dangerous builds = 144 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.754 | 4.754 | 4.754 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 + 2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751 + 2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751 + 2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751 + 2400 1.9752559 0.16967804 2.1177286 1.3037679 1669.0751 + 2500 1.978203 0.16642164 2.1631435 1.2908362 1669.0751 + 2600 1.9587508 0.18695272 2.1506896 1.3513902 1669.0751 + 2700 1.9654455 0.17997217 2.1247901 1.3360491 1669.0751 + 2800 1.9870267 0.15716583 2.1207709 1.2045103 1669.0751 + 2900 1.923066 0.22448724 2.1353571 1.4964299 1669.0751 + 3000 2.0042113 0.13903206 2.1149788 1.2100652 1669.0751 + 3100 1.9543697 0.19149442 2.0984704 1.3409703 1669.0751 + 3200 1.9991114 0.14441985 2.1292353 1.175647 1669.0751 + 3300 1.9629782 0.18246606 2.1463675 1.3162684 1669.0751 + 3400 1.9403528 0.2063029 2.1687044 1.4952816 1669.0751 + 3500 1.9887416 0.15531264 2.1485278 1.2530419 1669.0751 + 3600 1.9732723 0.1717156 2.1755741 1.2958545 1669.0751 + 3700 2.0072829 0.13576753 2.1212377 1.1421359 1669.0751 + 3800 1.9581273 0.18762532 2.1743415 1.3711091 1669.0751 + 3900 1.9761639 0.16862987 2.1429576 1.3036491 1669.0751 + 4000 1.9615823 0.18390729 2.12447 1.4179639 1669.0751 +Loop time of 2.70201 on 1 procs for 2000 steps with 400 atoms + +Performance: 127904.684 tau/day, 740.189 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.563 | 2.563 | 2.563 | 0.0 | 94.85 +Neigh | 0.0056589 | 0.0056589 | 0.0056589 | 0.0 | 0.21 +Comm | 0.014635 | 0.014635 | 0.014635 | 0.0 | 0.54 +Output | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.02 +Modify | 0.11246 | 0.11246 | 0.11246 | 0.0 | 4.16 +Other | | 0.00584 | | | 0.22 + +Nlocal: 400 ave 400 max 400 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 206 ave 206 max 206 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1872 ave 1872 max 1872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1872 +Ave neighs/atom = 4.68 +Neighbor list builds = 50 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/ellipse/log.27Nov18.ellipse.resquared.g++.4 b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.4 new file mode 100644 index 0000000000..c32aa28653 --- /dev/null +++ b/examples/ellipse/log.27Nov18.ellipse.resquared.g++.4 @@ -0,0 +1,189 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# RESquared ellipsoids in LJ background fluid + +units lj +atom_style ellipsoid +dimension 2 + +lattice sq 0.02 +Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 +region box block 0 20 0 20 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 400 atoms + Time spent = 0.00047946 secs + +set group all type/fraction 2 0.1 95392 + 45 settings made for type/fraction +set type 1 mass 1.0 + 355 settings made for mass +set type 2 mass 1.5 + 45 settings made for mass +set type 1 shape 1 1 1 + 355 settings made for shape +set type 2 shape 3 1 1 + 45 settings made for shape +set group all quat/random 18238 + 400 settings made for quat/random + +compute rot all temp/asphere +group spheroid type 1 +355 atoms in group spheroid +variable dof equal count(spheroid)+2 +compute_modify rot extra/dof ${dof} +compute_modify rot extra/dof 357 + +velocity all create 2.4 87287 loop geom + +pair_style resquared 4.0 +pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 +pair_coeff 1 2 3.0 1 1 1 1 0 0 0 +pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 + +neighbor 0.8 bin + +thermo_style custom step c_rot epair etotal press vol +thermo 100 + +timestep 0.002 + +compute q all property/atom quatw quati quatj quatk + +#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] + +#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 + +#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 +#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 + +fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 +fix 2 all enforce2d + +compute_modify 1_temp extra/dof ${dof} +compute_modify 1_temp extra/dof 357 + +# equilibrate to shrink box around dilute system + +run 2000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.8 + ghost atom cutoff = 4.8 + binsize = 2.4, bins = 59 59 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair resquared, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.738 | 4.738 | 4.738 Mbytes +Step c_rot E_pair TotEng Press Volume + 0 2.2718861 0 2.394 0.04788 20000 + 100 1.7443419 0 1.8381003 0.035765442 20557.278 + 200 2.2768798 0 2.3992621 0.046544845 20618.928 + 300 1.8573086 0 1.9571389 0.04239709 18464.842 + 400 2.1706741 -2.5275641e-05 2.2873225 0.066771565 13701.864 + 500 2.012561 0.0079467721 2.063898 0.10816504 8501.4958 + 600 2.1428003 0.083982458 2.2020759 0.3340759 4786.6892 + 700 2.0449292 0.17309565 2.1718849 0.78086274 2774.9262 + 800 1.9528849 0.31804014 2.2520272 1.8059473 1826.0933 + 900 1.6296095 0.24347613 1.8589813 1.7120274 1518.1139 + 1000 1.9349826 0.13913538 2.1125467 1.3044646 1519.7133 + 1100 2.1040629 0.11218748 2.2384236 1.0097965 1751.5229 + 1200 1.7801858 0.051922127 1.8564589 0.54836207 2198.0187 + 1300 2.3147158 0.049339841 2.390002 0.48871848 2754.4057 + 1400 1.754921 0.025804182 1.785499 0.28804529 3305.8359 + 1500 2.3701432 0.070771258 2.4523449 0.42290556 3531.1976 + 1600 1.7628065 0.054682596 1.830609 0.36138713 3319.2576 + 1700 2.2969598 0.130209 2.454872 0.73541699 2721.9102 + 1800 1.8253139 0.23039663 2.0810243 1.2065009 2155.7953 + 1900 2.017999 0.16257657 2.1664889 1.1654021 1815.9914 + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 +Loop time of 0.513811 on 4 procs for 2000 steps with 400 atoms + +Performance: 672620.799 tau/day, 3892.481 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.3553 | 0.36778 | 0.37737 | 1.4 | 71.58 +Neigh | 0.0039301 | 0.0040173 | 0.004127 | 0.1 | 0.78 +Comm | 0.056627 | 0.065564 | 0.076112 | 3.0 | 12.76 +Output | 0.00041318 | 0.00061768 | 0.0012202 | 0.0 | 0.12 +Modify | 0.070257 | 0.072503 | 0.074547 | 0.6 | 14.11 +Other | | 0.003331 | | | 0.65 + +Nlocal: 100 ave 108 max 96 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 123.5 ave 125 max 122 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 471 ave 518 max 433 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 1884 +Ave neighs/atom = 4.71 +Neighbor list builds = 177 +Dangerous builds = 144 + +# run dynamics on dense system + +unfix 1 +fix 1 all nve/asphere + +run 2000 +Per MPI rank memory allocation (min/avg/max) = 4.739 | 4.739 | 4.739 Mbytes +Step c_rot E_pair TotEng Press Volume + 2000 1.973946 0.17086654 2.1754835 1.2957284 1669.0751 + 2100 2.0234333 0.11888043 2.165674 1.056689 1669.0751 + 2200 1.9652317 0.18018588 2.1288332 1.3191509 1669.0751 + 2300 1.9982484 0.1453846 2.1438911 1.2670661 1669.0751 + 2400 1.9752559 0.16967804 2.1177286 1.303768 1669.0751 + 2500 1.978203 0.16642165 2.1631435 1.2908362 1669.0751 + 2600 1.9587508 0.18695271 2.1506896 1.3513902 1669.0751 + 2700 1.9654455 0.17997218 2.1247901 1.3360492 1669.0751 + 2800 1.9870267 0.15716584 2.1207709 1.2045104 1669.0751 + 2900 1.9230662 0.22448703 2.1353571 1.4964289 1669.0751 + 3000 2.0042113 0.13903204 2.1149787 1.210065 1669.0751 + 3100 1.9543694 0.19149467 2.0984705 1.3409714 1669.0751 + 3200 1.9991114 0.14441984 2.1292354 1.1756471 1669.0751 + 3300 1.9629781 0.18246618 2.1463676 1.3162687 1669.0751 + 3400 1.940353 0.20630269 2.1687038 1.4952819 1669.0751 + 3500 1.9887413 0.15531296 2.1485274 1.2530446 1669.0751 + 3600 1.9732704 0.17171758 2.1755757 1.295861 1669.0751 + 3700 2.0072863 0.13576402 2.1212392 1.1421254 1669.0751 + 3800 1.9581337 0.18761851 2.1743384 1.3710796 1669.0751 + 3900 1.9761519 0.16864273 2.142963 1.3037308 1669.0751 + 4000 1.9615865 0.18390288 2.1244667 1.4179575 1669.0751 +Loop time of 0.846017 on 4 procs for 2000 steps with 400 atoms + +Performance: 408502.313 tau/day, 2364.018 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.63647 | 0.67097 | 0.74711 | 5.4 | 79.31 +Neigh | 0.0015061 | 0.0015807 | 0.0017054 | 0.2 | 0.19 +Comm | 0.058258 | 0.1341 | 0.16808 | 12.1 | 15.85 +Output | 0.00045156 | 0.00077933 | 0.0016997 | 0.0 | 0.09 +Modify | 0.028721 | 0.029793 | 0.03152 | 0.6 | 3.52 +Other | | 0.0088 | | | 1.04 + +Nlocal: 100 ave 106 max 97 min +Histogram: 1 1 1 0 0 0 0 0 0 1 +Nghost: 114 ave 117 max 111 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 468 ave 528 max 431 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 1872 +Ave neighs/atom = 4.68 +Neighbor list builds = 50 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 b/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 deleted file mode 100644 index ad23b08f43..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.1 +++ /dev/null @@ -1,185 +0,0 @@ -LAMMPS (5 Oct 2016) -# GayBerne ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style gayberne 1.0 3.0 1.0 4.0 -pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.17878 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473 - 500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548 - 600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955 - 700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873 - 800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961 - 900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895 - 1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136 - 1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574 - 1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454 - 1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577 - 1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639 - 1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387 - 1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271 - 1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473 - 1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051 - 1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372 - 2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026 -Loop time of 1.01022 on 1 procs for 2000 steps with 400 atoms - -Performance: 342102.068 tau/day, 1979.757 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.80465 | 0.80465 | 0.80465 | 0.0 | 79.65 -Neigh | 0.014326 | 0.014326 | 0.014326 | 0.0 | 1.42 -Comm | 0.011179 | 0.011179 | 0.011179 | 0.0 | 1.11 -Output | 0.00032926 | 0.00032926 | 0.00032926 | 0.0 | 0.03 -Modify | 0.17561 | 0.17561 | 0.17561 | 0.0 | 17.38 -Other | | 0.004126 | | | 0.41 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 249 ave 249 max 249 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3031 ave 3031 max 3031 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3031 -Ave neighs/atom = 7.5775 -Neighbor list builds = 140 -Dangerous builds = 80 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.18892 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026 - 2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026 - 2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026 - 2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026 - 2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026 - 2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026 - 2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026 - 2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026 - 2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026 - 2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026 - 3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026 - 3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026 - 3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026 - 3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026 - 3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026 - 3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026 - 3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026 - 3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026 - 3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026 - 3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026 - 4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026 -Loop time of 1.13656 on 1 procs for 2000 steps with 400 atoms - -Performance: 304074.636 tau/day, 1759.691 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.0076 | 1.0076 | 1.0076 | 0.0 | 88.65 -Neigh | 0.0065663 | 0.0065663 | 0.0065663 | 0.0 | 0.58 -Comm | 0.011639 | 0.011639 | 0.011639 | 0.0 | 1.02 -Output | 0.00035858 | 0.00035858 | 0.00035858 | 0.0 | 0.03 -Modify | 0.10463 | 0.10463 | 0.10463 | 0.0 | 9.21 -Other | | 0.00581 | | | 0.51 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 219 ave 219 max 219 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3046 ave 3046 max 3046 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3046 -Ave neighs/atom = 7.615 -Neighbor list builds = 47 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:02 diff --git a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 b/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 deleted file mode 100644 index 7217a863d3..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.gayberne.g++.4 +++ /dev/null @@ -1,185 +0,0 @@ -LAMMPS (5 Oct 2016) -# GayBerne ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style gayberne 1.0 3.0 1.0 4.0 -pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.16784 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473 - 500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548 - 600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955 - 700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873 - 800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961 - 900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895 - 1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136 - 1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574 - 1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454 - 1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577 - 1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639 - 1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387 - 1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271 - 1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473 - 1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051 - 1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372 - 2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026 -Loop time of 0.348825 on 4 procs for 2000 steps with 400 atoms - -Performance: 990754.062 tau/day, 5733.530 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.18317 | 0.20567 | 0.22597 | 3.3 | 58.96 -Neigh | 0.0036285 | 0.0038322 | 0.0039773 | 0.2 | 1.10 -Comm | 0.043543 | 0.06339 | 0.085499 | 5.9 | 18.17 -Output | 0.00044894 | 0.00046825 | 0.00051665 | 0.1 | 0.13 -Modify | 0.069605 | 0.070677 | 0.071795 | 0.3 | 20.26 -Other | | 0.004791 | | | 1.37 - -Nlocal: 100 ave 113 max 85 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 149.75 ave 160 max 141 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 757.75 ave 885 max 592 min -Histogram: 1 0 0 1 0 0 0 0 1 1 - -Total # of neighbors = 3031 -Ave neighs/atom = 7.5775 -Neighbor list builds = 140 -Dangerous builds = 80 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.16867 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026 - 2100 2.0067383 -3.4164295 -1.402453 0.63163513 1121.7026 - 2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026 - 2300 2.0418708 -3.4552617 -1.4277716 0.58834191 1121.7026 - 2400 2.0126625 -3.4242024 -1.3839097 0.80723766 1121.7026 - 2500 1.9403968 -3.3489494 -1.3995212 0.79492647 1121.7026 - 2600 2.0459318 -3.4600945 -1.4229599 0.69698729 1121.7026 - 2700 2.0032338 -3.4126541 -1.4297892 0.44208354 1121.7026 - 2800 1.9367789 -3.3456765 -1.4171038 0.6873665 1121.7026 - 2900 1.9870979 -3.3983434 -1.4218523 0.42398659 1121.7026 - 3000 1.965491 -3.376773 -1.3835208 0.66112051 1121.7026 - 3100 1.9307633 -3.3342121 -1.3895745 0.45224657 1121.7026 - 3200 1.8918453 -3.2949278 -1.4157216 0.56825582 1121.7026 - 3300 1.8824584 -3.2844031 -1.4066487 0.85795659 1121.7026 - 3400 1.8871451 -3.2878452 -1.4156691 0.91410213 1121.7026 - 3500 1.9297625 -3.3340904 -1.3901995 0.6754809 1121.7026 - 3600 1.8994197 -3.3009141 -1.3964162 0.58676937 1121.7026 - 3700 1.9181765 -3.3204193 -1.3956433 0.54632736 1121.7026 - 3800 1.9278078 -3.3300748 -1.3999307 0.48904879 1121.7026 - 3900 1.888321 -3.2896024 -1.3848249 0.49521159 1121.7026 - 4000 1.8372182 -3.2347372 -1.4091759 0.61895915 1121.7026 -Loop time of 0.380732 on 4 procs for 2000 steps with 400 atoms - -Performance: 907726.114 tau/day, 5253.045 timesteps/s -98.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.24119 | 0.25802 | 0.28318 | 3.0 | 67.77 -Neigh | 0.001538 | 0.0017161 | 0.0018811 | 0.3 | 0.45 -Comm | 0.055332 | 0.081399 | 0.098741 | 5.6 | 21.38 -Output | 0.0005157 | 0.00053984 | 0.00058794 | 0.1 | 0.14 -Modify | 0.026189 | 0.027282 | 0.029091 | 0.7 | 7.17 -Other | | 0.01177 | | | 3.09 - -Nlocal: 100 ave 106 max 92 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 148 ave 152 max 145 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Neighs: 760.25 ave 815 max 713 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 3041 -Ave neighs/atom = 7.6025 -Neighbor list builds = 46 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:00 diff --git a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1 b/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1 deleted file mode 100644 index 51028b326e..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.1 +++ /dev/null @@ -1,182 +0,0 @@ -LAMMPS (5 Oct 2016) -# RESquared ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style resquared 4.0 -pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.17878 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499 - 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241 - 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723 - 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757 - 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943 - 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585 - 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058 - 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608 - 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358 - 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014 - 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144 - 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855 - 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472 - 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401 - 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099 - 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221 - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 -Loop time of 1.69003 on 1 procs for 2000 steps with 400 atoms - -Performance: 204492.823 tau/day, 1183.408 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.4827 | 1.4827 | 1.4827 | 0.0 | 87.73 -Neigh | 0.014216 | 0.014216 | 0.014216 | 0.0 | 0.84 -Comm | 0.0084538 | 0.0084538 | 0.0084538 | 0.0 | 0.50 -Output | 0.0003345 | 0.0003345 | 0.0003345 | 0.0 | 0.02 -Modify | 0.18062 | 0.18062 | 0.18062 | 0.0 | 10.69 -Other | | 0.003745 | | | 0.22 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 216 ave 216 max 216 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1929 ave 1929 max 1929 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1929 -Ave neighs/atom = 4.8225 -Neighbor list builds = 177 -Dangerous builds = 146 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.18079 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 - 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587 - 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587 - 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587 - 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587 - 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587 - 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587 - 2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587 - 2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587 - 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587 - 3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587 - 3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587 - 3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587 - 3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587 - 3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587 - 3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587 - 3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587 - 3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587 - 3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587 - 3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587 - 4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587 -Loop time of 2.86686 on 1 procs for 2000 steps with 400 atoms - -Performance: 120550.133 tau/day, 697.628 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.7349 | 2.7349 | 2.7349 | 0.0 | 95.40 -Neigh | 0.0052247 | 0.0052247 | 0.0052247 | 0.0 | 0.18 -Comm | 0.011207 | 0.011207 | 0.011207 | 0.0 | 0.39 -Output | 0.00036931 | 0.00036931 | 0.00036931 | 0.0 | 0.01 -Modify | 0.10925 | 0.10925 | 0.10925 | 0.0 | 3.81 -Other | | 0.005949 | | | 0.21 - -Nlocal: 400 ave 400 max 400 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 204 ave 204 max 204 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1857 ave 1857 max 1857 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1857 -Ave neighs/atom = 4.6425 -Neighbor list builds = 48 -Dangerous builds = 0 -Total wall time: 0:00:04 diff --git a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.4 b/examples/ellipse/log.5Oct16.ellipse.resquared.g++.4 deleted file mode 100644 index fa93b41fa3..0000000000 --- a/examples/ellipse/log.5Oct16.ellipse.resquared.g++.4 +++ /dev/null @@ -1,182 +0,0 @@ -LAMMPS (5 Oct 2016) -# RESquared ellipsoids in LJ background fluid - -units lj -atom_style ellipsoid -dimension 2 - -lattice sq 0.02 -Lattice spacing in x,y,z = 7.07107 7.07107 7.07107 -region box block 0 20 0 20 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 400 atoms - -set group all type/fraction 2 0.1 95392 - 45 settings made for type/fraction -set type 1 mass 1.0 - 355 settings made for mass -set type 2 mass 1.5 - 45 settings made for mass -set type 1 shape 1 1 1 - 355 settings made for shape -set type 2 shape 3 1 1 - 45 settings made for shape -set group all quat/random 18238 - 400 settings made for quat/random - -compute rot all temp/asphere -group spheroid type 1 -355 atoms in group spheroid -variable dof equal count(spheroid)+2 -compute_modify rot extra ${dof} -compute_modify rot extra 357 - -velocity all create 2.4 87287 loop geom - -pair_style resquared 4.0 -pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5 -pair_coeff 1 2 3.0 1 1 1 1 0 0 0 -pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0 - -neighbor 0.8 bin - -thermo_style custom step c_rot epair etotal press vol -thermo 100 - -timestep 0.002 - -compute q all property/atom quatw quati quatj quatk - -#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4] - -#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0 - -#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5 -#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0 - -fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1 -fix 2 all enforce2d - -compute_modify 1_temp extra ${dof} -compute_modify 1_temp extra 357 - -# equilibrate to shrink box around dilute system - -run 2000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.8 - ghost atom cutoff = 4.8 - binsize = 2.4 -> bins = 59 59 3 -Memory usage per processor = 4.16784 Mbytes -Step c_rot E_pair TotEng Press Volume - 0 2.2718861 0 2.394 0.04788 20000 - 100 1.7443002 0 1.8380563 0.03576216 20558.672 - 200 2.2770454 0 2.3994366 0.046545139 20620.298 - 300 1.8573283 0 1.9571597 0.04240689 18460.771 - 400 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499 - 500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241 - 600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723 - 700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757 - 800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943 - 900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585 - 1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058 - 1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608 - 1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358 - 1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014 - 1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144 - 1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855 - 1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472 - 1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401 - 1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099 - 1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221 - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 -Loop time of 0.529177 on 4 procs for 2000 steps with 400 atoms - -Performance: 653089.670 tau/day, 3779.454 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.36797 | 0.3809 | 0.38796 | 1.2 | 71.98 -Neigh | 0.0037003 | 0.0038002 | 0.0038807 | 0.1 | 0.72 -Comm | 0.057266 | 0.063631 | 0.076821 | 3.1 | 12.02 -Output | 0.00050998 | 0.00052881 | 0.00056648 | 0.1 | 0.10 -Modify | 0.075577 | 0.076514 | 0.078309 | 0.4 | 14.46 -Other | | 0.0038 | | | 0.72 - -Nlocal: 100 ave 108 max 95 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Nghost: 125.75 ave 128 max 123 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 482.25 ave 535 max 442 min -Histogram: 1 1 0 0 0 1 0 0 0 1 - -Total # of neighbors = 1929 -Ave neighs/atom = 4.8225 -Neighbor list builds = 177 -Dangerous builds = 146 - -# run dynamics on dense system - -unfix 1 -fix 1 all nve/asphere - -run 2000 -Memory usage per processor = 4.16867 Mbytes -Step c_rot E_pair TotEng Press Volume - 2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587 - 2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587 - 2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587 - 2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587 - 2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587 - 2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587 - 2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587 - 2700 1.9608664 0.18459944 2.1483889 1.3461096 1654.9587 - 2800 2.005755 0.13729992 2.1214078 1.1596183 1654.9587 - 2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587 - 3000 1.9606373 0.18480426 2.1301691 1.3280548 1654.9587 - 3100 1.9824235 0.16187647 2.1284433 1.2590074 1654.9587 - 3200 1.9389485 0.20774113 2.1063219 1.4587339 1654.9587 - 3300 1.984931 0.15929453 2.1301897 1.2415169 1654.9587 - 3400 1.9596864 0.18578934 2.1215072 1.3738204 1654.9587 - 3500 1.9671165 0.17804604 2.0934256 1.3147236 1654.9587 - 3600 1.9702644 0.17471548 2.156925 1.3331072 1654.9587 - 3700 1.9104013 0.2379238 2.1305421 1.5831938 1654.9587 - 3800 1.9129623 0.23512612 2.1445951 1.565741 1654.9587 - 3900 1.9868116 0.15724371 2.1658058 1.2581725 1654.9587 - 4000 2.0058633 0.13728433 2.1534403 1.1352037 1654.9587 -Loop time of 0.822603 on 4 procs for 2000 steps with 400 atoms - -Performance: 420129.522 tau/day, 2431.305 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.67029 | 0.69125 | 0.73659 | 3.2 | 84.03 -Neigh | 0.0013115 | 0.0014372 | 0.0016122 | 0.3 | 0.17 -Comm | 0.046684 | 0.092118 | 0.1133 | 9.0 | 11.20 -Output | 0.00053906 | 0.00055629 | 0.00059342 | 0.1 | 0.07 -Modify | 0.026623 | 0.027991 | 0.029785 | 0.8 | 3.40 -Other | | 0.009251 | | | 1.12 - -Nlocal: 100 ave 103 max 96 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 118 ave 122 max 115 min -Histogram: 1 0 1 0 1 0 0 0 0 1 -Neighs: 464.25 ave 489 max 449 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 1857 -Ave neighs/atom = 4.6425 -Neighbor list builds = 48 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/flow/log.5Oct16.flow.couette.g++.1 b/examples/flow/log.27Nov18.flow.couette.g++.1 similarity index 80% rename from examples/flow/log.5Oct16.flow.couette.g++.1 rename to examples/flow/log.27Nov18.flow.couette.g++.1 index a9d3a9929f..9045771f7c 100644 --- a/examples/flow/log.5Oct16.flow.couette.g++.1 +++ b/examples/flow/log.27Nov18.flow.couette.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000395536 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 4 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47395 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.402333 0 0.30957177 2.4852035 571.54286 9500 0.99889786 -0.46870263 0 0.24241751 2.3763314 571.54286 10000 1 -0.43338695 0 0.27851782 2.405424 571.54286 -Loop time of 0.281614 on 1 procs for 10000 steps with 420 atoms +Loop time of 0.293461 on 1 procs for 10000 steps with 420 atoms -Performance: 9204085.735 tau/day, 35509.590 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 8832531.296 tau/day, 34076.124 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12437 | 0.12437 | 0.12437 | 0.0 | 44.16 -Neigh | 0.062146 | 0.062146 | 0.062146 | 0.0 | 22.07 -Comm | 0.0076008 | 0.0076008 | 0.0076008 | 0.0 | 2.70 -Output | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 0.05 -Modify | 0.067444 | 0.067444 | 0.067444 | 0.0 | 23.95 -Other | | 0.01991 | | | 7.07 +Pair | 0.11085 | 0.11085 | 0.11085 | 0.0 | 37.77 +Neigh | 0.059952 | 0.059952 | 0.059952 | 0.0 | 20.43 +Comm | 0.010563 | 0.010563 | 0.010563 | 0.0 | 3.60 +Output | 0.00021076 | 0.00021076 | 0.00021076 | 0.0 | 0.07 +Modify | 0.089026 | 0.089026 | 0.089026 | 0.0 | 30.34 +Other | | 0.02286 | | | 7.79 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/flow/log.5Oct16.flow.couette.g++.4 b/examples/flow/log.27Nov18.flow.couette.g++.4 similarity index 80% rename from examples/flow/log.5Oct16.flow.couette.g++.4 rename to examples/flow/log.27Nov18.flow.couette.g++.4 index 84bd03560d..01f1e81d46 100644 --- a/examples/flow/log.5Oct16.flow.couette.g++.4 +++ b/examples/flow/log.27Nov18.flow.couette.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.00031352 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 4 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47768 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.048 | 3.048 | 3.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.45171969 0 0.26018507 2.5525861 571.54286 9500 1.0322994 -0.40989898 0 0.32499991 2.6021234 571.54286 10000 1 -0.42489516 0 0.28700961 2.619505 571.54286 -Loop time of 0.134939 on 4 procs for 10000 steps with 420 atoms +Loop time of 0.172876 on 4 procs for 10000 steps with 420 atoms -Performance: 19208643.416 tau/day, 74107.421 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 14993379.796 tau/day, 57844.829 timesteps/s +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.024453 | 0.030829 | 0.036954 | 3.5 | 22.85 -Neigh | 0.0152 | 0.016832 | 0.018415 | 1.2 | 12.47 -Comm | 0.040894 | 0.049385 | 0.058308 | 3.7 | 36.60 -Output | 0.00027037 | 0.00029039 | 0.0003438 | 0.2 | 0.22 -Modify | 0.017885 | 0.018734 | 0.019774 | 0.6 | 13.88 -Other | | 0.01887 | | | 13.98 +Pair | 0.024842 | 0.030136 | 0.036735 | 3.1 | 17.43 +Neigh | 0.014276 | 0.015892 | 0.017287 | 1.1 | 9.19 +Comm | 0.065952 | 0.075937 | 0.084912 | 3.2 | 43.93 +Output | 0.00034285 | 0.00042874 | 0.00067973 | 0.0 | 0.25 +Modify | 0.024682 | 0.026202 | 0.028216 | 1.0 | 15.16 +Other | | 0.02428 | | | 14.05 Nlocal: 105 ave 113 max 97 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/flow/log.5Oct16.flow.pois.g++.1 b/examples/flow/log.27Nov18.flow.pois.g++.1 similarity index 80% rename from examples/flow/log.5Oct16.flow.pois.g++.1 rename to examples/flow/log.27Nov18.flow.pois.g++.1 index 8a8748f984..45eed1d841 100644 --- a/examples/flow/log.5Oct16.flow.pois.g++.1 +++ b/examples/flow/log.27Nov18.flow.pois.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000394583 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 7 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47395 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.74461165 0 -0.032706889 2.574656 498.14523 9500 1.2047533 -0.75768848 0 0.09998113 2.4174997 501.8877 10000 1 -0.67361996 0 0.038284798 2.2310948 507.57444 -Loop time of 0.313724 on 1 procs for 10000 steps with 420 atoms +Loop time of 0.353337 on 1 procs for 10000 steps with 420 atoms -Performance: 8262038.165 tau/day, 31875.147 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 7335771.903 tau/day, 28301.589 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.13662 | 0.13662 | 0.13662 | 0.0 | 43.55 -Neigh | 0.034956 | 0.034956 | 0.034956 | 0.0 | 11.14 -Comm | 0.0064242 | 0.0064242 | 0.0064242 | 0.0 | 2.05 -Output | 0.00014639 | 0.00014639 | 0.00014639 | 0.0 | 0.05 -Modify | 0.11616 | 0.11616 | 0.11616 | 0.0 | 37.03 -Other | | 0.01941 | | | 6.19 +Pair | 0.12053 | 0.12053 | 0.12053 | 0.0 | 34.11 +Neigh | 0.033673 | 0.033673 | 0.033673 | 0.0 | 9.53 +Comm | 0.00895 | 0.00895 | 0.00895 | 0.0 | 2.53 +Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.07 +Modify | 0.16577 | 0.16577 | 0.16577 | 0.0 | 46.92 +Other | | 0.02418 | | | 6.84 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/flow/log.5Oct16.flow.pois.g++.4 b/examples/flow/log.27Nov18.flow.pois.g++.4 similarity index 80% rename from examples/flow/log.5Oct16.flow.pois.g++.4 rename to examples/flow/log.27Nov18.flow.pois.g++.4 index 20c3293b82..6e0c58614a 100644 --- a/examples/flow/log.5Oct16.flow.pois.g++.4 +++ b/examples/flow/log.27Nov18.flow.pois.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2-d LJ flow simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.00031805 secs mass 1 1.0 mass 2 1.0 @@ -75,7 +77,7 @@ fix 7 all enforce2d timestep 0.003 thermo 500 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.flow @@ -87,13 +89,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 10000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 37 32 1 -Memory usage per processor = 2.47768 Mbytes + binsize = 0.71123, bins = 37 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.048 | 3.048 | 3.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1 0 0 0.71190476 0.52314537 571.54286 500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659 @@ -116,20 +123,20 @@ Step Temp E_pair E_mol TotEng Press Volume 9000 1 -0.8200207 0 -0.10811593 2.6210027 502.60511 9500 1.2167146 -0.77385956 0 0.092325373 2.5938179 500.86068 10000 1 -0.73082779 0 -0.018923029 2.735112 505.69856 -Loop time of 0.225282 on 4 procs for 10000 steps with 420 atoms +Loop time of 0.208663 on 4 procs for 10000 steps with 420 atoms -Performance: 11505578.988 tau/day, 44388.808 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 12421919.467 tau/day, 47924.072 timesteps/s +95.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.032012 | 0.033154 | 0.035252 | 0.7 | 14.72 -Neigh | 0.0094411 | 0.0097138 | 0.010069 | 0.2 | 4.31 -Comm | 0.080785 | 0.085431 | 0.088782 | 1.0 | 37.92 -Output | 0.0003736 | 0.00039834 | 0.00046349 | 0.2 | 0.18 -Modify | 0.062812 | 0.064686 | 0.066481 | 0.6 | 28.71 -Other | | 0.0319 | | | 14.16 +Pair | 0.031368 | 0.032216 | 0.033688 | 0.5 | 15.44 +Neigh | 0.0093348 | 0.0097306 | 0.010144 | 0.3 | 4.66 +Comm | 0.059824 | 0.065823 | 0.07057 | 1.8 | 31.55 +Output | 0.00033283 | 0.00043827 | 0.00073981 | 0.0 | 0.21 +Modify | 0.067317 | 0.071492 | 0.075636 | 1.3 | 34.26 +Other | | 0.02896 | | | 13.88 Nlocal: 105 ave 106 max 103 min Histogram: 1 0 0 0 0 0 1 0 0 2 diff --git a/examples/friction/log.5Oct16.friction.g++.1 b/examples/friction/log.27Nov18.friction.g++.1 similarity index 81% rename from examples/friction/log.5Oct16.friction.g++.1 rename to examples/friction/log.27Nov18.friction.g++.1 index 27c3d34dcc..6e7422b4f8 100644 --- a/examples/friction/log.5Oct16.friction.g++.1 +++ b/examples/friction/log.27Nov18.friction.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d friction simulation dimension 2 @@ -39,12 +40,16 @@ region hi-half-sphere intersect 2 hi-asperity below-hi create_atoms 1 region lo-slab Created 750 atoms + Time spent = 0.000692606 secs create_atoms 1 region hi-slab Created 750 atoms + Time spent = 0.000464201 secs create_atoms 2 region lo-half-sphere Created 112 atoms + Time spent = 0.000610352 secs create_atoms 3 region hi-half-sphere Created 112 atoms + Time spent = 0.000571966 secs # LJ potentials @@ -94,7 +99,7 @@ fix 4 all enforce2d timestep 0.0025 thermo 1000 thermo_modify temp new -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.friction @@ -106,13 +111,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 20000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 41 31 1 -Memory usage per processor = 2.47434 Mbytes + binsize = 1.4, bins = 41 31 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.058 | 3.058 | 3.058 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.1 -3.1333672 0 -3.0920969 -1.1437663 2444.9333 1000 0.1 -3.0915072 0 -3.0502369 0.0099866805 2444.9333 @@ -135,20 +145,20 @@ Step Temp E_pair E_mol TotEng Press Volume 18000 0.11159326 -3.0416392 0 -2.9955843 -0.22725121 2444.9333 19000 0.11530974 -3.0457005 0 -2.9981118 -0.36488457 2444.9333 20000 0.1131733 -3.0417814 0 -2.9950744 -0.27902539 2444.9333 -Loop time of 5.78572 on 1 procs for 20000 steps with 1724 atoms +Loop time of 5.95046 on 1 procs for 20000 steps with 1724 atoms -Performance: 746665.546 tau/day, 3456.785 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 725993.862 tau/day, 3361.083 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.7167 | 4.7167 | 4.7167 | 0.0 | 81.52 -Neigh | 0.30734 | 0.30734 | 0.30734 | 0.0 | 5.31 -Comm | 0.036082 | 0.036082 | 0.036082 | 0.0 | 0.62 -Output | 0.00039339 | 0.00039339 | 0.00039339 | 0.0 | 0.01 -Modify | 0.57194 | 0.57194 | 0.57194 | 0.0 | 9.89 -Other | | 0.1533 | | | 2.65 +Pair | 4.7314 | 4.7314 | 4.7314 | 0.0 | 79.51 +Neigh | 0.3022 | 0.3022 | 0.3022 | 0.0 | 5.08 +Comm | 0.046376 | 0.046376 | 0.046376 | 0.0 | 0.78 +Output | 0.00047255 | 0.00047255 | 0.00047255 | 0.0 | 0.01 +Modify | 0.69477 | 0.69477 | 0.69477 | 0.0 | 11.68 +Other | | 0.1752 | | | 2.94 Nlocal: 1724 ave 1724 max 1724 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/friction/log.5Oct16.friction.g++.4 b/examples/friction/log.27Nov18.friction.g++.4 similarity index 81% rename from examples/friction/log.5Oct16.friction.g++.4 rename to examples/friction/log.27Nov18.friction.g++.4 index 7dbecb1bc7..1ac945bb8a 100644 --- a/examples/friction/log.5Oct16.friction.g++.4 +++ b/examples/friction/log.27Nov18.friction.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d friction simulation dimension 2 @@ -39,12 +40,16 @@ region hi-half-sphere intersect 2 hi-asperity below-hi create_atoms 1 region lo-slab Created 750 atoms + Time spent = 0.000427008 secs create_atoms 1 region hi-slab Created 750 atoms + Time spent = 0.000396729 secs create_atoms 2 region lo-half-sphere Created 112 atoms + Time spent = 0.000207663 secs create_atoms 3 region hi-half-sphere Created 112 atoms + Time spent = 0.000194788 secs # LJ potentials @@ -94,7 +99,7 @@ fix 4 all enforce2d timestep 0.0025 thermo 1000 thermo_modify temp new -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 500 dump.friction @@ -106,13 +111,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 20000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 41 31 1 -Memory usage per processor = 2.47775 Mbytes + binsize = 1.4, bins = 41 31 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.051 | 3.051 | 3.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.1 -3.1333672 0 -3.0920969 -1.1437663 2444.9333 1000 0.081947197 -3.0926906 0 -3.0588707 -0.021905504 2444.9333 @@ -135,20 +145,20 @@ Step Temp E_pair E_mol TotEng Press Volume 18000 0.11086121 -3.0462098 0 -3.0004571 -0.19272619 2444.9333 19000 0.11407977 -3.046791 0 -2.99971 -0.29824356 2444.9333 20000 0.11532037 -3.0463959 0 -2.9988028 -0.3435294 2444.9333 -Loop time of 1.90668 on 4 procs for 20000 steps with 1724 atoms +Loop time of 1.98982 on 4 procs for 20000 steps with 1724 atoms -Performance: 2265719.994 tau/day, 10489.444 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2171051.815 tau/day, 10051.166 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.0349 | 1.1944 | 1.3574 | 10.5 | 62.64 -Neigh | 0.070767 | 0.082252 | 0.094675 | 3.0 | 4.31 -Comm | 0.19432 | 0.3776 | 0.54764 | 20.4 | 19.80 -Output | 0.00043559 | 0.00045842 | 0.00052333 | 0.2 | 0.02 -Modify | 0.12252 | 0.14002 | 0.15438 | 3.1 | 7.34 -Other | | 0.112 | | | 5.87 +Pair | 1.0746 | 1.214 | 1.3479 | 8.9 | 61.01 +Neigh | 0.073977 | 0.083197 | 0.096277 | 2.9 | 4.18 +Comm | 0.22466 | 0.37933 | 0.52711 | 17.6 | 19.06 +Output | 0.00045776 | 0.00078875 | 0.0017807 | 0.0 | 0.04 +Modify | 0.16952 | 0.18621 | 0.20218 | 2.8 | 9.36 +Other | | 0.1263 | | | 6.35 Nlocal: 431 ave 479 max 377 min Histogram: 1 1 0 0 0 0 0 0 0 2 diff --git a/examples/gcmc/log.30Mar18.gcmc.co2.g++.1 b/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 similarity index 60% rename from examples/gcmc/log.30Mar18.gcmc.co2.g++.1 rename to examples/gcmc/log.27Nov18.gcmc.co2.g++.1 index 46afe5ea2a..4ed9056d04 100644 --- a/examples/gcmc/log.30Mar18.gcmc.co2.g++.1 +++ b/examples/gcmc/log.27Nov18.gcmc.co2.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # GCMC for CO2 molecular fluid, rigid/small/nvt dynamics # Rigid CO2 TraPPE model @@ -46,7 +46,7 @@ Read molecule co2mol: 0 impropers with max type 0 create_atoms 0 box mol co2mol 464563 units box Created 24 atoms - Time spent = 0.00241756 secs + Time spent = 0.00134993 secs # rigid CO2 TraPPE model @@ -118,16 +118,16 @@ thermo 1000 run 20000 Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.164636 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) +WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -143,54 +143,54 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 15.62 | 15.62 | 15.62 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO 0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0 8 16 - 1000 330.05964 -376.0111 -13.936335 13.773831 0.65771539 27 0.21142067 0.21453147 0 0 9 18 - 2000 293.79769 -321.3209 -19.049256 13.720163 0.73079488 30 0.25170944 0.25426294 0 0 10 20 - 3000 348.9085 259.04079 -0.23347965 2.4267366 0.14615898 6 0.22016906 0.23200597 0 0 2 4 - 4000 360.54577 -329.12072 -16.584234 15.046059 0.65771539 27 0.19173099 0.19785362 0 0 9 18 - 5000 275.58628 -58.283006 -12.520856 11.500585 0.65771539 27 0.16490585 0.17329884 0 0 9 18 - 6000 338.59574 364.93514 -19.866569 17.494353 0.80387436 33 0.17971759 0.18331589 0 0 11 22 - 7000 286.11586 -1252.5069 -19.588667 13.361427 0.73079488 30 0.15729895 0.16220459 0 0 10 20 - 8000 454.86786 -642.89382 -20.818357 21.242037 0.73079488 30 0.15500235 0.15802382 0 0 10 20 - 9000 326.36695 -364.71382 -31.376162 18.48392 0.87695385 36 0.14203985 0.14510714 0 0 12 24 - 10000 348.46961 -387.75245 -21.068466 18.00451 0.80387436 33 0.14000907 0.14343389 0 0 11 22 - 11000 409.74257 -15.843895 -20.648252 21.170323 0.80387436 33 0.14689306 0.15117074 0 0 11 22 - 12000 523.93502 1003.0729 -6.0563102 14.055757 0.43847693 18 0.15337575 0.1580166 0 0 6 12 - 13000 278.14441 -717.1097 -2.3488496 4.6982087 0.29231795 12 0.15952356 0.16422306 0 0 4 8 - 14000 367.89375 1239.0841 -11.203323 13.524997 0.5846359 24 0.17002439 0.17460294 0 0 8 16 - 15000 197.05319 -471.14343 -9.3890758 6.2653668 0.51155641 21 0.17702612 0.18155802 0 0 7 14 - 16000 138.17147 -935.93437 -2.3846783 2.3338898 0.29231795 12 0.17884346 0.18268758 0 0 4 8 - 17000 245.61833 -166.1694 -5.0970057 5.3690384 0.36539744 15 0.18909252 0.19317817 0 0 5 10 - 18000 232.0142 -175.732 -14.320198 9.6822635 0.65771539 27 0.18977089 0.19280537 0 0 9 18 - 19000 362.01189 864.87258 -6.4515321 9.7117982 0.43847693 18 0.19207244 0.19488984 0 0 6 12 - 20000 441.19548 186.19779 -18.147268 20.603546 0.73079488 30 0.19713351 0.199073 0 0 10 20 -Loop time of 16.4949 on 1 procs for 20000 steps with 30 atoms + 1000 267.9799 -73.919548 -3.6735999 5.8578459 0.36539744 15 0.23663972 0.2494423 0 0 5 10 + 2000 409.06596 -98.033864 -6.7570039 10.974131 0.43847693 18 0.29379544 0.29816284 0 0 6 12 + 3000 279.3225 -836.47758 -26.434976 15.819539 0.87695385 36 0.23798567 0.24203908 0 0 12 24 + 4000 333.6181 606.63478 -30.35312 18.894592 0.87695385 36 0.19121778 0.19481508 0 0 12 24 + 5000 405.98741 -103.97582 -14.180277 16.942399 0.65771539 27 0.15272841 0.15982952 0 0 9 18 + 6000 283.5835 -240.01076 -6.7198093 7.607777 0.43847693 18 0.1606796 0.16536735 0 0 6 12 + 7000 142.00717 154.95914 -0.74192319 0.98769159 0.14615898 6 0.19501993 0.20103405 0 0 2 4 + 8000 376.67702 -118.12474 -10.774631 13.847899 0.5846359 24 0.20133396 0.20468352 0 0 8 16 + 9000 305.43166 -1095.8633 -10.388279 9.7112935 0.51155641 21 0.19445239 0.19869334 0 0 7 14 + 10000 244.08225 -179.31274 -12.974988 8.9732748 0.5846359 24 0.19098971 0.19586397 0 0 8 16 + 11000 305.03389 -568.94714 -21.745425 14.244887 0.73079488 30 0.18517522 0.18978828 0 0 10 20 + 12000 318.29735 767.76579 -37.184231 21.189508 1.0231128 42 0.17256426 0.17580267 0 0 14 28 + 13000 411.21707 433.01125 -4.5149215 8.9889065 0.36539744 15 0.16329385 0.16767604 0 0 5 10 + 14000 304.29535 148.28607 -2.3505844 6.6516754 0.36539744 15 0.17435868 0.17897674 0 0 5 10 + 15000 338.00555 2384.1424 -21.438264 17.463859 0.80387436 33 0.17237066 0.17634112 0 0 11 22 + 16000 613.56062 610.93867 -0.057364228 1.2192718 0.073079488 3 0.17128158 0.1758886 0 0 1 2 + 17000 432.63323 -980.52384 -15.79844 18.054365 0.65771539 27 0.17145651 0.17504846 0 0 9 18 + 18000 181.74572 -352.81765 -1.8617959 2.1669979 0.21923846 9 0.17292463 0.17654774 0 0 3 6 + 19000 208.55292 -248.38735 -4.2287767 4.5588154 0.36539744 15 0.18168324 0.18454331 0 0 5 10 + 20000 304.73317 -649.9896 -16.532405 12.716924 0.65771539 27 0.18085983 0.18345574 0 0 9 18 +Loop time of 21.0434 on 1 procs for 20000 steps with 27 atoms -Performance: 104.760 ns/day, 0.229 hours/ns, 1212.498 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 82.116 ns/day, 0.292 hours/ns, 950.415 timesteps/s +98.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.8955 | 1.8955 | 1.8955 | 0.0 | 11.49 -Bond | 0.026564 | 0.026564 | 0.026564 | 0.0 | 0.16 -Kspace | 0.21215 | 0.21215 | 0.21215 | 0.0 | 1.29 -Neigh | 0.088336 | 0.088336 | 0.088336 | 0.0 | 0.54 -Comm | 0.19828 | 0.19828 | 0.19828 | 0.0 | 1.20 -Output | 0.001025 | 0.001025 | 0.001025 | 0.0 | 0.01 -Modify | 14.024 | 14.024 | 14.024 | 0.0 | 85.02 -Other | | 0.0491 | | | 0.30 +Pair | 2.2373 | 2.2373 | 2.2373 | 0.0 | 10.63 +Bond | 0.022895 | 0.022895 | 0.022895 | 0.0 | 0.11 +Kspace | 0.16756 | 0.16756 | 0.16756 | 0.0 | 0.80 +Neigh | 0.11436 | 0.11436 | 0.11436 | 0.0 | 0.54 +Comm | 0.26988 | 0.26988 | 0.26988 | 0.0 | 1.28 +Output | 0.0014684 | 0.0014684 | 0.0014684 | 0.0 | 0.01 +Modify | 18.193 | 18.193 | 18.193 | 0.0 | 86.45 +Other | | 0.03692 | | | 0.18 -Nlocal: 30 ave 30 max 30 min +Nlocal: 27 ave 27 max 27 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2094 ave 2094 max 2094 min +Nghost: 2081 ave 2081 max 2081 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 7664 ave 7664 max 7664 min +Neighs: 6264 ave 6264 max 6264 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 7664 -Ave neighs/atom = 255.467 +Total # of neighbors = 6264 +Ave neighs/atom = 232 Ave special neighs/atom = 2 -Neighbor list builds = 20076 +Neighbor list builds = 20177 Dangerous builds = 0 -Total wall time: 0:00:16 +Total wall time: 0:00:21 diff --git a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 b/examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 similarity index 54% rename from examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 rename to examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 index 2f11cb116e..86b8fa7b45 100644 --- a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.1 +++ b/examples/gcmc/log.27Nov18.gcmc.h2o.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # fix gcmc example with fix shake @@ -43,7 +43,7 @@ Read molecule h2omol: 0 impropers with max type 0 create_atoms 0 box mol h2omol 464563 units box Created 24 atoms - Time spent = 0.00204968 secs + Time spent = 0.00128841 secs # rigid SPC/E water model @@ -69,9 +69,9 @@ velocity all create 338.0 54654 timestep 1.0 minimize 0.0 0.0 100 1000 -WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 @@ -92,41 +92,41 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 338 -4.1890564 9.2628112e-06 18.98377 739.06991 - 100 338 -30.182886 0.85607237 -6.1539961 -2535.3207 -Loop time of 0.0512006 on 1 procs for 100 steps with 24 atoms + 100 338 -36.122455 0.67828405 -12.271354 573.22675 +Loop time of 0.0461962 on 1 procs for 100 steps with 24 atoms -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = - -4.18904713252 -28.9258064504 -29.3268133965 - Force two-norm initial, final = 18.0027 42.4511 - Force max component initial, final = 5.8993 16.0523 - Final line search alpha, max atom move = 0.00353207 0.056698 - Iterations, force evaluations = 100 238 + -4.18904713252 -34.586018764 -35.4441713339 + Force two-norm initial, final = 18.0027 42.115 + Force max component initial, final = 5.8993 15.4907 + Final line search alpha, max atom move = 0.00127226 0.0197082 + Iterations, force evaluations = 100 239 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.04303 | 0.04303 | 0.04303 | 0.0 | 84.04 -Bond | 0.00047088 | 0.00047088 | 0.00047088 | 0.0 | 0.92 -Kspace | 0.0029728 | 0.0029728 | 0.0029728 | 0.0 | 5.81 -Neigh | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.90 -Comm | 0.003406 | 0.003406 | 0.003406 | 0.0 | 6.65 -Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.04 +Pair | 0.038526 | 0.038526 | 0.038526 | 0.0 | 83.40 +Bond | 0.00031209 | 0.00031209 | 0.00031209 | 0.0 | 0.68 +Kspace | 0.0019636 | 0.0019636 | 0.0019636 | 0.0 | 4.25 +Neigh | 0.00055456 | 0.00055456 | 0.00055456 | 0.0 | 1.20 +Comm | 0.0040288 | 0.0040288 | 0.0040288 | 0.0 | 8.72 +Output | 1.5259e-05 | 1.5259e-05 | 1.5259e-05 | 0.0 | 0.03 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0008392 | | | 1.64 +Other | | 0.0007958 | | | 1.72 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2047 ave 2047 max 2047 min +Nghost: 2011 ave 2011 max 2011 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 4936 ave 4936 max 4936 min +Neighs: 4921 ave 4921 max 4921 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 4936 -Ave neighs/atom = 205.667 +Total # of neighbors = 4921 +Ave neighs/atom = 205.042 Ave special neighs/atom = 2 Neighbor list builds = 2 Dangerous builds = 0 @@ -150,7 +150,7 @@ compute_modify mynvt_temp dynamic/dof yes run 1000 Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 @@ -158,36 +158,36 @@ Ewald initialization ... kxmax kymax kzmax = 2 2 2 Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp E_pair E_mol TotEng Press - 0 518.26667 -30.182886 0 -7.0100684 993.1985 - 1000 326.9865 -62.258443 0 -47.638173 -5.3439918 -Loop time of 0.139436 on 1 procs for 1000 steps with 24 atoms + 0 518.26667 -36.122455 0 -12.949638 703.43827 + 1000 260.39219 -55.141232 0 -43.498537 -1698.672 +Loop time of 0.140376 on 1 procs for 1000 steps with 24 atoms -Performance: 619.641 ns/day, 0.039 hours/ns, 7171.773 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 615.489 ns/day, 0.039 hours/ns, 7123.720 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.10588 | 0.10588 | 0.10588 | 0.0 | 75.94 -Bond | 0.00015759 | 0.00015759 | 0.00015759 | 0.0 | 0.11 -Kspace | 0.011144 | 0.011144 | 0.011144 | 0.0 | 7.99 -Neigh | 0.00459 | 0.00459 | 0.00459 | 0.0 | 3.29 -Comm | 0.011396 | 0.011396 | 0.011396 | 0.0 | 8.17 -Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.01 -Modify | 0.0043328 | 0.0043328 | 0.0043328 | 0.0 | 3.11 -Other | | 0.001914 | | | 1.37 +Pair | 0.10434 | 0.10434 | 0.10434 | 0.0 | 74.33 +Bond | 0.00013041 | 0.00013041 | 0.00013041 | 0.0 | 0.09 +Kspace | 0.008199 | 0.008199 | 0.008199 | 0.0 | 5.84 +Neigh | 0.0061581 | 0.0061581 | 0.0061581 | 0.0 | 4.39 +Comm | 0.015352 | 0.015352 | 0.015352 | 0.0 | 10.94 +Output | 1.4305e-05 | 1.4305e-05 | 1.4305e-05 | 0.0 | 0.01 +Modify | 0.004544 | 0.004544 | 0.004544 | 0.0 | 3.24 +Other | | 0.001639 | | | 1.17 Nlocal: 24 ave 24 max 24 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1660 ave 1660 max 1660 min +Nghost: 1776 ave 1776 max 1776 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5112 ave 5112 max 5112 min +Neighs: 5073 ave 5073 max 5073 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 5112 -Ave neighs/atom = 213 +Total # of neighbors = 5073 +Ave neighs/atom = 211.375 Ave special neighs/atom = 2 -Neighbor list builds = 25 +Neighbor list builds = 27 Dangerous builds = 0 reset_timestep 0 @@ -224,67 +224,67 @@ thermo 1000 run 20000 Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.170448 estimated absolute RMS force accuracy = 0.0332064 estimated relative force accuracy = 0.0001 KSpace vectors: actual max1d max3d = 16 2 62 kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) +WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487) 0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc 0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472) +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471) Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH - 0 326.9865 -4.3508819 -62.258443 14.62027 0.23910963 24 0 0 0 0 8 16 - 1000 354.423 -3760.1354 -235.34169 51.766914 0.74721761 75 0.046175467 0.011949811 0 0 25 50 - 2000 335.19661 -3018.659 -270.44089 52.955344 0.80699501 81 0.026473882 0.0068755525 0 0 27 54 - 3000 333.47175 2657.2052 -336.48359 64.611037 0.98632724 99 0.022634978 0.0060076096 0 0 33 66 - 4000 321.48504 2055.4786 -345.06113 62.288579 0.98632724 99 0.016897769 0.0045269353 0 0 33 66 - 5000 333.45735 1918.5375 -368.5463 66.596193 1.0162159 102 0.013784412 0.0036569014 0 0 34 68 - 6000 301.90666 -698.74074 -371.32122 60.295069 1.0162159 102 0.01160439 0.0030159847 0 0 34 68 - 7000 336.42505 1537.9483 -378.51731 69.194524 1.0461046 105 0.010174953 0.0025995783 0 0 35 70 - 8000 338.95331 -1032.1084 -390.7067 69.714524 1.0461046 105 0.0089594585 0.002260114 0 0 35 70 - 9000 311.44605 -1494.7788 -383.9272 64.056945 1.0461046 105 0.007938083 0.0020156323 0 0 35 70 - 10000 330.70877 2082.4597 -366.57249 68.018822 1.0461046 105 0.0071412985 0.0018148454 0 0 35 70 - 11000 286.34718 2238.3752 -370.91119 60.601806 1.0759934 108 0.0066641451 0.0016519521 0 0 36 72 - 12000 371.02522 3048.7157 -398.51333 78.522854 1.0759934 108 0.0061145907 0.0015128339 0 0 36 72 - 13000 392.87611 4486.1134 -387.07077 83.147323 1.0759934 108 0.0056427384 0.0013968431 0 0 36 72 - 14000 332.80747 3586.2698 -406.12151 70.434545 1.0759934 108 0.0052496417 0.0012945729 0 0 36 72 - 15000 325.61844 4198.3864 -387.5733 68.913077 1.0759934 108 0.0048934679 0.0012098238 0 0 36 72 - 16000 254.10285 1560.976 -409.98615 55.292559 1.1058821 111 0.0047204383 0.0011320612 0 0 37 74 - 17000 367.46414 2750.8283 -412.22037 79.959878 1.1058821 111 0.0044407568 0.0010659592 0 0 37 74 - 18000 407.74215 2308.5027 -408.73046 88.724338 1.1058821 111 0.0042016342 0.0010049017 0 0 37 74 - 19000 341.53799 5777.9814 -407.00637 74.31837 1.1058821 111 0.0039877848 0.00095025921 0 0 37 74 - 20000 395.75303 3159.4677 -403.82798 86.115516 1.1058821 111 0.0037874635 0.00090297077 0 0 37 74 -Loop time of 231.351 on 1 procs for 20000 steps with 111 atoms + 0 260.39219 -1699.3643 -55.141232 11.642695 0.23910963 24 0 0 0 0 8 16 + 1000 340.44409 -2560.1501 -280.70157 53.784356 0.80699501 81 0.054205983 0.015933081 0 0 27 54 + 2000 302.57602 592.41718 -310.37771 53.213377 0.89666113 90 0.030546787 0.0078577743 0 0 30 60 + 3000 270.18045 -817.18659 -346.75773 50.737466 0.95643854 96 0.021969243 0.0060076096 0 0 32 64 + 4000 334.17192 1153.3017 -335.25519 62.75449 0.95643854 96 0.016400775 0.0045269353 0 0 32 64 + 5000 360.36872 -647.99689 -336.2928 67.674015 0.95643854 96 0.012996731 0.0036569014 0 0 32 64 + 6000 282.37822 -986.51765 -341.91848 53.028098 0.95643854 96 0.010941282 0.0030159847 0 0 32 64 + 7000 363.01448 2952.0391 -358.72963 70.335018 0.98632724 99 0.0098923151 0.0028884203 0 0 33 66 + 8000 331.70391 323.34886 -382.04165 68.223498 1.0461046 105 0.0092083323 0.0025112378 0 0 35 70 + 9000 337.2032 -3637.5257 -390.66472 69.35457 1.0461046 105 0.0081585853 0.0022395915 0 0 35 70 + 10000 373.67063 3081.3271 -380.5107 76.855041 1.0461046 105 0.0073396679 0.0020164949 0 0 35 70 + 11000 336.64665 5535.9451 -405.21548 71.247059 1.0759934 108 0.0068442571 0.0018355023 0 0 36 72 + 12000 306.51164 1448.1757 -410.3655 64.869362 1.0759934 108 0.0062798499 0.0016809265 0 0 36 72 + 13000 319.03497 177.44405 -406.17113 67.519768 1.0759934 108 0.0057952448 0.0015520479 0 0 36 72 + 14000 309.89701 -1022.6798 -384.20239 65.585833 1.0759934 108 0.005391524 0.0014384143 0 0 36 72 + 15000 398.91559 2058.9251 -404.32604 84.425503 1.0759934 108 0.0050257238 0.0013442486 0 0 36 72 + 16000 318.98778 873.46142 -392.13338 67.50978 1.0759934 108 0.0047204383 0.0012578458 0 0 36 72 + 17000 333.16025 2347.0215 -387.73943 70.509206 1.0759934 108 0.0044407568 0.0011843991 0 0 36 72 + 18000 353.23789 -2305.787 -382.1633 74.758389 1.0759934 108 0.0042016342 0.0011165574 0 0 36 72 + 19000 322.70939 5619.9631 -381.81328 68.297412 1.0759934 108 0.0039877848 0.0010558436 0 0 36 72 + 20000 371.07261 3916.1113 -389.76357 78.532884 1.0759934 108 0.0037874635 0.0010033009 0 0 36 72 +Loop time of 242.59 on 1 procs for 20000 steps with 108 atoms -Performance: 7.469 ns/day, 3.213 hours/ns, 86.449 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 7.123 ns/day, 3.369 hours/ns, 82.444 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 39.09 | 39.09 | 39.09 | 0.0 | 16.90 -Bond | 0.092728 | 0.092728 | 0.092728 | 0.0 | 0.04 -Kspace | 0.87751 | 0.87751 | 0.87751 | 0.0 | 0.38 -Neigh | 3.9658 | 3.9658 | 3.9658 | 0.0 | 1.71 -Comm | 1.0608 | 1.0608 | 1.0608 | 0.0 | 0.46 -Output | 0.00096035 | 0.00096035 | 0.00096035 | 0.0 | 0.00 -Modify | 186.07 | 186.07 | 186.07 | 0.0 | 80.43 -Other | | 0.1892 | | | 0.08 +Pair | 38.279 | 38.279 | 38.279 | 0.0 | 15.78 +Bond | 0.055672 | 0.055672 | 0.055672 | 0.0 | 0.02 +Kspace | 0.60623 | 0.60623 | 0.60623 | 0.0 | 0.25 +Neigh | 4.4189 | 4.4189 | 4.4189 | 0.0 | 1.82 +Comm | 1.2719 | 1.2719 | 1.2719 | 0.0 | 0.52 +Output | 0.00096583 | 0.00096583 | 0.00096583 | 0.0 | 0.00 +Modify | 197.85 | 197.85 | 197.85 | 0.0 | 81.56 +Other | | 0.1098 | | | 0.05 -Nlocal: 111 ave 111 max 111 min +Nlocal: 108 ave 108 max 108 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 8070 ave 8070 max 8070 min +Nghost: 8000 ave 8000 max 8000 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 105469 ave 105469 max 105469 min +Neighs: 100006 ave 100006 max 100006 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 105469 -Ave neighs/atom = 950.171 +Total # of neighbors = 100006 +Ave neighs/atom = 925.981 Ave special neighs/atom = 2 -Neighbor list builds = 20910 +Neighbor list builds = 20903 Dangerous builds = 0 -Total wall time: 0:03:51 +Total wall time: 0:04:02 diff --git a/examples/gcmc/log.30Mar18.gcmc.lj.g++.1 b/examples/gcmc/log.27Nov18.gcmc.lj.g++.1 similarity index 90% rename from examples/gcmc/log.30Mar18.gcmc.lj.g++.1 rename to examples/gcmc/log.27Nov18.gcmc.lj.g++.1 index 20a25c0f95..1a6651fd4e 100644 --- a/examples/gcmc/log.30Mar18.gcmc.lj.g++.1 +++ b/examples/gcmc/log.27Nov18.gcmc.lj.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # GCMC for LJ simple fluid, no dynamics # T = 2.0 @@ -112,20 +112,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v 8000 2.2135488 2.0878792 -3.0471089 3.2707661 0.536 67 0.067926473 0.067738312 0.1135594 0.52736 1.4348314 0.034380623 62.43 9000 1.8904287 0.52639383 -3.3548657 2.7920177 0.52 65 0.06818197 0.068003094 0.11356319 0.53072 1.4528143 0.021683615 63.23 10000 2.2353281 0.73275312 -3.2197702 3.3006016 0.512 64 0.068465059 0.068208485 0.11414748 0.52712 1.4143492 0.03497858 62.44 -Loop time of 21.2409 on 1 procs for 10000 steps with 64 atoms +Loop time of 27.8547 on 1 procs for 10000 steps with 64 atoms -Performance: 203381.368 tau/day, 470.790 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 155090.656 tau/day, 359.006 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.45931 | 0.45931 | 0.45931 | 0.0 | 2.16 -Neigh | 1.1637 | 1.1637 | 1.1637 | 0.0 | 5.48 -Comm | 0.17294 | 0.17294 | 0.17294 | 0.0 | 0.81 -Output | 0.00027394 | 0.00027394 | 0.00027394 | 0.0 | 0.00 -Modify | 19.416 | 19.416 | 19.416 | 0.0 | 91.41 -Other | | 0.02919 | | | 0.14 +Pair | 0.43892 | 0.43892 | 0.43892 | 0.0 | 1.58 +Neigh | 1.278 | 1.278 | 1.278 | 0.0 | 4.59 +Comm | 0.24105 | 0.24105 | 0.24105 | 0.0 | 0.87 +Output | 0.00032067 | 0.00032067 | 0.00032067 | 0.0 | 0.00 +Modify | 25.88 | 25.88 | 25.88 | 0.0 | 92.91 +Other | | 0.01693 | | | 0.06 Nlocal: 64 ave 64 max 64 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -138,4 +138,4 @@ Total # of neighbors = 2423 Ave neighs/atom = 37.8594 Neighbor list builds = 10000 Dangerous builds = 0 -Total wall time: 0:00:21 +Total wall time: 0:00:27 diff --git a/examples/gcmc/log.30Mar18.gcmc.lj.g++.4 b/examples/gcmc/log.27Nov18.gcmc.lj.g++.4 similarity index 90% rename from examples/gcmc/log.30Mar18.gcmc.lj.g++.4 rename to examples/gcmc/log.27Nov18.gcmc.lj.g++.4 index 819d0ed086..6e59f3d484 100644 --- a/examples/gcmc/log.30Mar18.gcmc.lj.g++.4 +++ b/examples/gcmc/log.27Nov18.gcmc.lj.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (30 Mar 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # GCMC for LJ simple fluid, no dynamics # T = 2.0 @@ -112,20 +112,20 @@ Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_rhoav v_pav v 8000 1.947817 0.74570466 -3.0935809 2.8753489 0.504 63 0.068034071 0.067855883 0.11217045 0.53304 1.4924302 0.012298733 63.45 9000 1.8942389 1.3367401 -2.8925016 2.7962574 0.504 63 0.068117479 0.067943081 0.11236152 0.536 1.4091106 0.0011494886 63.73 10000 2.2092799 0.95517153 -2.9117781 3.2586879 0.48 60 0.068264792 0.068016591 0.11310789 0.52272 1.4774174 0.051284873 62.04 -Loop time of 29.2417 on 4 procs for 10000 steps with 60 atoms +Loop time of 26.0069 on 4 procs for 10000 steps with 60 atoms -Performance: 147733.999 tau/day, 341.977 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 166109.741 tau/day, 384.513 timesteps/s +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.11648 | 0.1221 | 0.13001 | 1.5 | 0.42 -Neigh | 0.34452 | 0.35618 | 0.36328 | 1.2 | 1.22 -Comm | 0.63561 | 0.65617 | 0.67542 | 1.8 | 2.24 -Output | 0.00056601 | 0.00069755 | 0.00074744 | 0.0 | 0.00 -Modify | 28.069 | 28.076 | 28.082 | 0.1 | 96.01 -Other | | 0.03094 | | | 0.11 +Pair | 0.10309 | 0.115 | 0.1225 | 2.2 | 0.44 +Neigh | 0.3907 | 0.40447 | 0.41957 | 1.7 | 1.56 +Comm | 0.44236 | 0.46678 | 0.49472 | 2.8 | 1.79 +Output | 0.0011411 | 0.0062903 | 0.0080109 | 3.7 | 0.02 +Modify | 25 | 25.002 | 25.005 | 0.0 | 96.14 +Other | | 0.01231 | | | 0.05 Nlocal: 15 ave 16 max 14 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -138,4 +138,4 @@ Total # of neighbors = 2116 Ave neighs/atom = 35.2667 Neighbor list builds = 10000 Dangerous builds = 0 -Total wall time: 0:00:29 +Total wall time: 0:00:26 diff --git a/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 b/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 deleted file mode 100644 index a824945cbf..0000000000 --- a/examples/gcmc/log.30Mar18.gcmc.co2.g++.4 +++ /dev/null @@ -1,131 +0,0 @@ -LAMMPS (30 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics -# Rigid CO2 TraPPE model -# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of -# mixtures containing alkanes, carbon dioxide and -# nitrogen AIChE J., 47,1676-1682 (2001)]. - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid -molecule co2mol CO2.txt -Read molecule co2mol: - 3 atoms with max type 2 - 2 bonds with max type 1 - 1 angles with max type 1 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -create_atoms 0 box mol co2mol 464563 units box -Created 24 atoms - Time spent = 0.00257635 secs - -# rigid CO2 TraPPE model - -pair_coeff 1 1 0.053649 2.8 -pair_coeff 2 2 0.156973 3.05 -bond_coeff 1 0 1.16 -angle_coeff 1 0 180 - -# masses - -mass 1 12.0107 -mass 2 15.9994 - -# MD settings - -group co2 type 1 2 -24 atoms in group co2 -neighbor 2.0 bin -neigh_modify every 1 delay 10 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -# rigid constraints with thermostat - -fix myrigidnvt co2 rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol -fix myrigidnvt co2 rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol -8 rigid bodies with 24 atoms - 1.16 = max distance from body owner to body atom - -# dynamically update fix rigid/nvt/small temperature ndof -fix_modify myrigidnvt dynamic/dof yes - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc co2 gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt -fix mygcmc co2 gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt - -# atom counts - -variable carbon atom "type==1" -variable oxygen atom "type==2" -group carbon dynamic co2 var carbon -dynamic group carbon defined -group oxygen dynamic co2 var oxygen -dynamic group oxygen defined -variable nC equal count(carbon) -variable nO equal count(oxygen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) - -# dynamically update default temperature ndof -compute_modify thermo_temp dynamic/dof yes - -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nC v_nO -thermo 1000 - -# run - -run 20000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.164636 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721) -Last command: run 20000 diff --git a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 b/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 deleted file mode 100644 index c5caf57113..0000000000 --- a/examples/gcmc/log.30Mar18.gcmc.h2o.g++.4 +++ /dev/null @@ -1,237 +0,0 @@ -LAMMPS (30 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# fix gcmc example with fix shake - -# variables available on command line - -variable mu index -8.1 -variable disp index 0.5 -variable temp index 338.0 -variable lbox index 10.0 -variable spacing index 5.0 - -# global model settings - -units real -atom_style full -boundary p p p -pair_style lj/cut/coul/long 14 -pair_modify mix arithmetic tail yes -kspace_style ewald 0.0001 -bond_style harmonic -angle_style harmonic - -# box, start molecules on simple cubic lattice - -lattice sc ${spacing} -lattice sc 5.0 -Lattice spacing in x,y,z = 5 5 5 -region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 ${lbox} 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 ${lbox} units box -region box block 0 10.0 0 10.0 0 10.0 units box -create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 -Created orthogonal box = (0 0 0) to (10 10 10) - 1 by 2 by 2 MPI processor grid - -molecule h2omol H2O.txt -Read molecule h2omol: - 3 atoms with max type 2 - 2 bonds with max type 1 - 1 angles with max type 1 - 0 dihedrals with max type 0 - 0 impropers with max type 0 -create_atoms 0 box mol h2omol 464563 units box -Created 24 atoms - Time spent = 0.00285625 secs - -# rigid SPC/E water model - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_coeff 1 1000 1.0 -angle_coeff 1 100 109.47 - -# masses - -mass 1 15.9994 -mass 2 1.0 - -# MD settings - -group h2o type 1 2 -24 atoms in group h2o -neighbor 2.0 bin -neigh_modify every 1 delay 1 check yes -velocity all create ${temp} 54654 -velocity all create 338.0 54654 -timestep 1.0 - -minimize 0.0 0.0 100 1000 -WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168) -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 16 - ghost atom cutoff = 16 - binsize = 8, bins = 2 2 2 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 11.85 | 11.85 | 11.85 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 338 -4.9610706 9.2628112e-06 18.211756 730.90791 - 100 338 -15.742442 0.14954269 7.579918 -637.49568 -Loop time of 0.0695416 on 4 procs for 100 steps with 24 atoms - -94.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = max iterations - Energy initial, next-to-last, final = - -4.96106135393 -15.5388622715 -15.592899346 - Force two-norm initial, final = 15.474 18.1478 - Force max component initial, final = 5.80042 7.56514 - Final line search alpha, max atom move = 0.00151131 0.0114333 - Iterations, force evaluations = 100 328 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0093951 | 0.017625 | 0.028943 | 5.3 | 25.34 -Bond | 0.00035357 | 0.00042325 | 0.00055075 | 0.0 | 0.61 -Kspace | 0.00664 | 0.019695 | 0.029924 | 6.1 | 28.32 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.022505 | 0.02509 | 0.027851 | 1.3 | 36.08 -Output | 3.3855e-05 | 3.5942e-05 | 4.1485e-05 | 0.0 | 0.05 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.006672 | | | 9.59 - -Nlocal: 6 ave 8 max 3 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Nghost: 1722 ave 1725 max 1720 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 1256.75 ave 2101 max 667 min -Histogram: 1 0 1 0 1 0 0 0 0 1 - -Total # of neighbors = 5027 -Ave neighs/atom = 209.458 -Ave special neighs/atom = 2 -Neighbor list builds = 0 -Dangerous builds = 0 -reset_timestep 0 - -# rigid constraints with thermostat - -fix mynvt h2o nvt temp ${temp} ${temp} 100 -fix mynvt h2o nvt temp 338.0 ${temp} 100 -fix mynvt h2o nvt temp 338.0 338.0 100 -fix wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 8 = # of frozen angles - -# important to make temperature dofs dynamic - -compute_modify thermo_temp dynamic/dof yes -compute_modify mynvt_temp dynamic/dof yes - -run 1000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -Per MPI rank memory allocation (min/avg/max) = 11.6 | 11.6 | 11.6 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 518.26667 -15.742442 0 7.4303753 -613.0781 - 1000 369.81793 -54.202682 0 -37.667327 294.98832 -Loop time of 0.191619 on 4 procs for 1000 steps with 24 atoms - -Performance: 450.894 ns/day, 0.053 hours/ns, 5218.680 timesteps/s -96.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.015873 | 0.028989 | 0.040172 | 5.3 | 15.13 -Bond | 0.00024271 | 0.00027657 | 0.00034404 | 0.0 | 0.14 -Kspace | 0.022896 | 0.034492 | 0.047924 | 5.1 | 18.00 -Neigh | 0.0025764 | 0.0025961 | 0.0026152 | 0.0 | 1.35 -Comm | 0.068467 | 0.070095 | 0.071535 | 0.4 | 36.58 -Output | 4.8161e-05 | 5.0783e-05 | 5.7936e-05 | 0.0 | 0.03 -Modify | 0.049141 | 0.049894 | 0.05072 | 0.3 | 26.04 -Other | | 0.005226 | | | 2.73 - -Nlocal: 6 ave 8 max 3 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 1331.5 ave 1369 max 1290 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 1259.75 ave 1642 max 428 min -Histogram: 1 0 0 0 0 0 0 1 0 2 - -Total # of neighbors = 5039 -Ave neighs/atom = 209.958 -Ave special neighs/atom = 2 -Neighbor list builds = 27 -Dangerous builds = 0 -reset_timestep 0 - -# gcmc - -variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans) -fix mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert ${tfac} group h2o shake wshake -fix mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol h2omol tfac_insert 1.66666666666667 group h2o shake wshake - -# atom counts - -variable oxygen atom "type==1" -variable hydrogen atom "type==2" -group oxygen dynamic all var oxygen -dynamic group oxygen defined -group hydrogen dynamic all var hydrogen -dynamic group hydrogen defined -variable nO equal count(oxygen) -variable nH equal count(hydrogen) - -# output - -variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1) -variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1) -variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1) -variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1) -thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH -thermo 1000 - -# run - -run 20000 -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.170448 - estimated absolute RMS force accuracy = 0.0332064 - estimated relative force accuracy = 0.0001 - KSpace vectors: actual max1d max3d = 16 2 62 - kxmax kymax kzmax = 2 2 2 -WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:485) -0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc -0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc -ERROR: fix gcmc does currently not support full_energy option with molecules on more than 1 MPI process. (../fix_gcmc.cpp:721) -Last command: run 20000 diff --git a/examples/granregion/log.27Nov18.granregion.box.g++.1 b/examples/granregion/log.27Nov18.granregion.box.g++.1 new file mode 100644 index 0000000000..ef004b7398 --- /dev/null +++ b/examples/granregion/log.27Nov18.granregion.box.g++.1 @@ -0,0 +1,475 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# pouring spheres into container box + +units lj +atom_style sphere +boundary f f f +dimension 3 +comm_modify vel yes + +region box block -10 10 -10 10 -10 10 units box +create_box 2 box +Created orthogonal box = (-10 -10 -10) to (10 10 10) + 1 by 1 by 1 MPI processor grid + +pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 +pair_coeff * * gran/hooke + +region container block -6 6 -6 6 -6 6 units box +fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 2 all nve/sphere +fix 3 all gravity 1.0 vector 0 0 -1 + +region slab block -2 2 -2 2 -2 2 units box +fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore +Particle insertion: 48 every 566 steps, 100 by step 1133 + +timestep 0.005 + +compute 1 all temp +compute_modify 1 dynamic/dof yes + +compute 2 all temp/sphere +compute_modify 2 dynamic/dof yes + +thermo 100 +thermo_style custom step atoms temp c_1 c_2 press +thermo_modify lost ignore +compute_modify thermo_temp dynamic/dof yes + +#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03 +#dump_modify 2 pad 5 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 31 31 31 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke, perpetual + attributes: half, newton on, size + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.5855 | 0.5855 | 0.5855 Mbytes +Step Atoms Temp c_1 c_2 Press + 0 0 0 0 0 0 + 100 21 0.54270729 0.54270729 0.26473526 0.0013567682 + 200 21 0.87606961 0.87606961 0.42735103 0.002190174 + 300 21 1.1428374 1.1428374 0.55748167 0.0028570936 + 400 21 1.3543103 1.3543103 0.66829516 0.0033857758 + 500 21 1.0677786 1.0677786 0.53582407 0.0045048164 + 600 56 0.6744286 0.6744286 0.3502938 0.0047464584 + 700 56 0.75569283 0.75569283 0.39779462 0.0051953882 + 800 56 0.61597505 0.61597505 0.32943642 0.0086022783 + 900 56 0.65260802 0.65260802 0.34474044 0.0059298996 + 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337 + 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094 + 1200 81 0.39112346 0.39112346 0.21690172 0.0086559316 + 1300 81 0.33302617 0.33302617 0.19109398 0.0033381104 + 1400 81 0.3933533 0.3933533 0.21221692 0.004135078 + 1500 81 0.35495297 0.35495297 0.19925984 0.0037374946 + 1600 81 0.34150606 0.34150606 0.19025811 0.0053492835 + 1700 100 0.2561647 0.2561647 0.14186278 0.0090767057 + 1800 100 0.21124278 0.21124278 0.12154878 0.0028545759 + 1900 100 0.21793955 0.21793955 0.12173867 0.0029049155 + 2000 100 0.25530858 0.25530858 0.13892272 0.0035528009 + 2100 100 0.24671808 0.24671808 0.13687783 0.0076812435 + 2200 100 0.22465216 0.22465216 0.12513603 0.0042528715 + 2300 100 0.19362854 0.19362854 0.10914305 0.0061173739 + 2400 100 0.061627608 0.061627608 0.045907717 0.0010422721 + 2500 100 0.052700901 0.052700901 0.038883014 0.0019341647 + 2600 100 0.037332018 0.037332018 0.028357146 0.0028364476 + 2700 100 0.033526602 0.033526602 0.024609055 0.00044524562 + 2800 100 0.0194148 0.0194148 0.014491377 0.00056526591 + 2900 100 0.012346108 0.012346108 0.009857017 0.00081855699 + 3000 100 0.0107344 0.0107344 0.008669364 0.00040371396 + 3100 100 0.0092678291 0.0092678291 0.0073003108 0.00033287397 + 3200 100 0.0085847001 0.0085847001 0.0064045591 0.00023253547 + 3300 100 0.0049475182 0.0049475182 0.0041173627 0.00019876269 + 3400 100 0.0030471097 0.0030471097 0.0026940466 0.00013462604 + 3500 100 0.0031188371 0.0031188371 0.002612223 0.00026148578 + 3600 100 0.0017616584 0.0017616584 0.0017464137 0.00019049724 + 3700 100 0.0015475923 0.0015475923 0.0015560356 0.00025062814 + 3800 100 0.0012547887 0.0012547887 0.0012622678 0.00014132236 + 3900 100 0.0010047282 0.0010047282 0.0010379262 9.7665594e-05 + 4000 100 0.00080895307 0.00080895307 0.00088263027 8.1278842e-05 + 4100 100 0.00079078739 0.00079078739 0.00085810727 8.1271694e-05 + 4200 100 0.00075192318 0.00075192318 0.00083085046 8.9352453e-05 + 4300 100 0.00063546457 0.00063546457 0.00073222177 8.9264255e-05 + 4400 100 0.00062398391 0.00062398391 0.00071312118 8.4200615e-05 + 4500 100 0.00056464934 0.00056464934 0.00066087801 9.2097641e-05 + 4600 100 0.00066951894 0.00066951894 0.00071633313 8.2457941e-05 + 4700 100 0.001128837 0.001128837 0.00095293877 0.00011716361 + 4800 100 0.00049580391 0.00049580391 0.00056710488 0.00010718794 + 4900 100 0.00054374371 0.00054374371 0.00058671699 5.6580257e-05 + 5000 100 0.00043016232 0.00043016232 0.00050264172 2.8640786e-05 +Loop time of 0.0807264 on 1 procs for 5000 steps with 100 atoms + +Performance: 26757050.955 tau/day, 61937.618 timesteps/s +97.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0089066 | 0.0089066 | 0.0089066 | 0.0 | 11.03 +Neigh | 0.017107 | 0.017107 | 0.017107 | 0.0 | 21.19 +Comm | 0.00091505 | 0.00091505 | 0.00091505 | 0.0 | 1.13 +Output | 0.00051451 | 0.00051451 | 0.00051451 | 0.0 | 0.64 +Modify | 0.047671 | 0.047671 | 0.047671 | 0.0 | 59.05 +Other | | 0.005612 | | | 6.95 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 158 ave 158 max 158 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 158 +Ave neighs/atom = 1.58 +Neighbor list builds = 310 +Dangerous builds = 0 + +region container delete +variable theta equal (step-5000)*(4.0*PI/5000) +region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1 +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes +Step Atoms Temp c_1 c_2 Press + 5000 100 0.00043016232 0.00043016232 0.00050264172 2.8677624e-05 + 5100 100 0.56489668 0.56489668 0.31137762 0.011848041 + 5200 100 0.66068288 0.66068288 0.35915482 0.010199755 + 5300 100 0.74068022 0.74068022 0.39643217 0.010806409 + 5400 100 0.80913562 0.80913562 0.42748505 0.01190892 + 5500 100 0.89409135 0.89409135 0.46135116 0.013093474 + 5600 100 0.97585093 0.97585093 0.50021126 0.013588886 + 5700 100 1.0151954 1.0151954 0.5174624 0.01601347 + 5800 100 1.0452728 1.0452728 0.53122496 0.01879329 + 5900 100 1.0881689 1.0881689 0.55152229 0.017120714 + 6000 100 1.1133186 1.1133186 0.5638022 0.017284617 + 6100 100 1.1532099 1.1532099 0.58310076 0.017031384 + 6200 100 1.1798849 1.1798849 0.5959516 0.017971323 + 6300 100 1.19387 1.19387 0.60173877 0.020140984 + 6400 100 1.2126705 1.2126705 0.61086899 0.018426638 + 6500 100 1.2137646 1.2137646 0.61284198 0.019127381 + 6600 100 1.2339012 1.2339012 0.62199324 0.019378799 + 6700 100 1.2439326 1.2439326 0.62488425 0.021049447 + 6800 100 1.2489549 1.2489549 0.6278167 0.019552409 + 6900 100 1.2733303 1.2733303 0.63898149 0.020237284 + 7000 100 1.2835029 1.2835029 0.6440245 0.020798586 + 7100 100 1.2866111 1.2866111 0.64522896 0.020355019 + 7200 100 1.2886381 1.2886381 0.6467497 0.02062322 + 7300 100 1.2885085 1.2885085 0.64617988 0.020350755 + 7400 100 1.2912349 1.2912349 0.64691898 0.020197503 + 7500 100 1.2963062 1.2963062 0.64926335 0.020349791 + 7600 100 1.3016488 1.3016488 0.65150178 0.021001457 + 7700 100 1.3009311 1.3009311 0.65106234 0.021546471 + 7800 100 1.3016987 1.3016987 0.65143099 0.020994967 + 7900 100 1.3028811 1.3028811 0.65164558 0.022200425 + 8000 100 1.3087855 1.3087855 0.65439023 0.021310808 + 8100 100 1.3102001 1.3102001 0.65514941 0.021177764 + 8200 100 1.3133931 1.3133931 0.65681861 0.021591267 + 8300 100 1.3148898 1.3148898 0.65775353 0.021335384 + 8400 100 1.3160355 1.3160355 0.65845913 0.021238095 + 8500 100 1.3171797 1.3171797 0.65934185 0.021172983 + 8600 100 1.3176785 1.3176785 0.65964311 0.020747457 + 8700 100 1.3180425 1.3180425 0.66019624 0.021275913 + 8800 100 1.3287501 1.3287501 0.66444242 0.021832635 + 8900 100 1.3249847 1.3249847 0.6625848 0.021337451 + 9000 100 1.326216 1.326216 0.66297827 0.021470663 + 9100 100 1.3261662 1.3261662 0.66303852 0.021423573 + 9200 100 1.3312132 1.3312132 0.6653609 0.021385943 + 9300 100 1.3300976 1.3300976 0.66504574 0.021489888 + 9400 100 1.3377335 1.3377335 0.66820989 0.021565001 + 9500 100 1.3421956 1.3421956 0.67027168 0.022402346 + 9600 100 1.3464217 1.3464217 0.67228206 0.021991922 + 9700 100 1.3470623 1.3470623 0.67258349 0.022035729 + 9800 100 1.3446725 1.3446725 0.67135725 0.022295251 + 9900 100 1.343146 1.343146 0.67066672 0.022049041 + 10000 100 1.3435397 1.3435397 0.67093067 0.022451365 +Loop time of 0.247549 on 1 procs for 5000 steps with 100 atoms + +Performance: 8725560.044 tau/day, 20198.056 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.031783 | 0.031783 | 0.031783 | 0.0 | 12.84 +Neigh | 0.038383 | 0.038383 | 0.038383 | 0.0 | 15.51 +Comm | 0.0012343 | 0.0012343 | 0.0012343 | 0.0 | 0.50 +Output | 0.00056028 | 0.00056028 | 0.00056028 | 0.0 | 0.23 +Modify | 0.1687 | 0.1687 | 0.1687 | 0.0 | 68.15 +Other | | 0.00689 | | | 2.78 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 199 ave 199 max 199 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 199 +Ave neighs/atom = 1.99 +Neighbor list builds = 621 +Dangerous builds = 0 + +region container delete +region container block -6 6 -6 6 -6 6 units box +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes +Step Atoms Temp c_1 c_2 Press + 10000 100 1.3435397 1.3435397 0.67093067 0.022411116 + 10100 100 0.31352763 0.31352763 0.18877908 0.01321582 + 10200 100 0.13367611 0.13367611 0.090010637 0.0074171016 + 10300 100 0.068195658 0.068195658 0.052632714 0.0019696287 + 10400 100 0.053814936 0.053814936 0.043037586 0.0017121584 + 10500 100 0.04032072 0.04032072 0.032944572 0.0011809154 + 10600 100 0.029178161 0.029178161 0.023951873 0.0007804529 + 10700 100 0.025978206 0.025978206 0.021045025 0.00099531465 + 10800 100 0.023205036 0.023205036 0.01898502 0.00040036401 + 10900 100 0.019994638 0.019994638 0.016451227 0.00027385559 + 11000 100 0.017838131 0.017838131 0.014730762 0.00040399762 + 11100 100 0.014863196 0.014863196 0.012314308 0.00019097464 + 11200 100 0.012131256 0.012131256 0.010102122 0.00018514926 + 11300 100 0.010881385 0.010881385 0.0090013541 0.00016579157 + 11400 100 0.0076519814 0.0076519814 0.0064604568 0.00035399997 + 11500 100 0.0067507315 0.0067507315 0.0057378868 0.00049116726 + 11600 100 0.0053146649 0.0053146649 0.0047005938 0.00019625233 + 11700 100 0.0044162463 0.0044162463 0.0039534657 0.00012548039 + 11800 100 0.0037025387 0.0037025387 0.0033604103 6.2969827e-05 + 11900 100 0.0032632211 0.0032632211 0.0030406641 8.1600622e-05 + 12000 100 0.0028944057 0.0028944057 0.0026875858 6.6435833e-05 + 12100 100 0.0027644728 0.0027644728 0.0025859762 5.5899271e-05 + 12200 100 0.002480367 0.002480367 0.0023685117 6.0201418e-05 + 12300 100 0.0024136475 0.0024136475 0.0023107986 4.4386874e-05 + 12400 100 0.0021911567 0.0021911567 0.0021413262 5.0213175e-05 + 12500 100 0.0019775905 0.0019775905 0.0019927698 0.00035250097 + 12600 100 0.0017410363 0.0017410363 0.001830428 5.7885177e-05 + 12700 100 0.0015749276 0.0015749276 0.0016816771 4.5530192e-05 + 12800 100 0.0015187705 0.0015187705 0.0016218625 4.0589413e-05 + 12900 100 0.0014778376 0.0014778376 0.001580232 4.0085455e-05 + 13000 100 0.0014693491 0.0014693491 0.0015681809 4.0407656e-05 + 13100 100 0.0014434495 0.0014434495 0.0015356278 5.7849212e-05 + 13200 100 0.0014121959 0.0014121959 0.0015058758 3.2720737e-05 + 13300 100 0.0012876041 0.0012876041 0.0013838998 3.7725702e-05 + 13400 100 0.0012304951 0.0012304951 0.0013373457 3.6784546e-05 + 13500 100 0.0011954303 0.0011954303 0.0012877627 3.6584963e-05 + 13600 100 0.0011028947 0.0011028947 0.0011955404 2.3767582e-05 + 13700 100 0.0010611762 0.0010611762 0.0011504675 3.485879e-05 + 13800 100 0.0010080835 0.0010080835 0.0010997919 3.7905404e-05 + 13900 100 0.00096495712 0.00096495712 0.0010530767 3.5273885e-05 + 14000 100 0.00094945029 0.00094945029 0.0010409175 3.3718395e-05 + 14100 100 0.00092386757 0.00092386757 0.0010217415 3.3313256e-05 + 14200 100 0.00088928389 0.00088928389 0.000983023 3.290941e-05 + 14300 100 0.00082696485 0.00082696485 0.00092690771 3.1651431e-05 + 14400 100 0.00081086188 0.00081086188 0.00091681096 3.1845632e-05 + 14500 100 0.00077732305 0.00077732305 0.00087592983 4.8087361e-05 + 14600 100 0.00073386005 0.00073386005 0.00082546873 3.0892065e-05 + 14700 100 0.00068701098 0.00068701098 0.00075953521 0.00010208859 + 14800 100 0.00065860451 0.00065860451 0.00073738846 2.9272912e-05 + 14900 100 0.00064706564 0.00064706564 0.00072748391 2.9817955e-05 + 15000 100 0.00064227996 0.00064227996 0.00070964586 3.2547768e-05 +Loop time of 0.0840213 on 1 procs for 5000 steps with 100 atoms + +Performance: 25707757.817 tau/day, 59508.699 timesteps/s +98.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.01004 | 0.01004 | 0.01004 | 0.0 | 11.95 +Neigh | 0.0057366 | 0.0057366 | 0.0057366 | 0.0 | 6.83 +Comm | 0.00086808 | 0.00086808 | 0.00086808 | 0.0 | 1.03 +Output | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 0.59 +Modify | 0.060893 | 0.060893 | 0.060893 | 0.0 | 72.47 +Other | | 0.005989 | | | 7.13 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151 ave 151 max 151 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151 +Ave neighs/atom = 1.51 +Neighbor list builds = 92 +Dangerous builds = 0 + +region container delete +variable theta equal (step-15000)*(4.0*PI/5000) +region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1 +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes +Step Atoms Temp c_1 c_2 Press + 15000 100 0.00064227996 0.00064227996 0.00070964586 3.2291286e-05 + 15100 100 0.81230775 0.81230775 0.53266834 0.010948517 + 15200 100 0.87957637 0.87957637 0.57559572 0.012401402 + 15300 100 1.0262431 1.0262431 0.66535656 0.015239294 + 15400 100 1.2863564 1.2863564 0.82026439 0.020115365 + 15500 100 1.4721549 1.4721549 0.92138954 0.022400442 + 15600 100 1.7140429 1.7140429 1.0103822 0.02558084 + 15700 100 1.8963287 1.8963287 1.0916756 0.032032318 + 15800 100 2.0741177 2.0741177 1.1706233 0.034251942 + 15900 100 2.1434733 2.1434733 1.2054242 0.030132271 + 16000 100 2.1409892 2.1409892 1.2019761 0.030914205 + 16100 100 2.2496058 2.2496058 1.2476438 0.030939743 + 16200 100 2.233356 2.233356 1.2499888 0.030097445 + 16300 100 2.2673491 2.2673491 1.272321 0.030968524 + 16400 100 2.3735648 2.3735648 1.3126117 0.034532377 + 16500 100 2.4510087 2.4510087 1.3588349 0.036685351 + 16600 100 2.497406 2.497406 1.3811443 0.032019982 + 16700 100 2.6800518 2.6800518 1.4661941 0.037455527 + 16800 100 2.8673997 2.8673997 1.5558303 0.03606532 + 16900 100 3.1229488 3.1229488 1.6918439 0.039753213 + 17000 100 3.117815 3.117815 1.6996841 0.046210837 + 17100 100 3.3336225 3.3336225 1.7834517 0.047865361 + 17200 100 3.1773164 3.1773164 1.7113961 0.047778334 + 17300 100 3.4336759 3.4336759 1.8343073 0.049673718 + 17400 100 3.3142326 3.3142326 1.7796613 0.055329946 + 17500 100 3.3205493 3.3205493 1.7853946 0.043558145 + 17600 100 3.2764553 3.2764553 1.7640702 0.051463316 + 17700 100 3.1909643 3.1909643 1.7407995 0.043248948 + 17800 100 3.1958324 3.1958324 1.735056 0.050123145 + 17900 100 3.2431806 3.2431806 1.7380638 0.050838878 + 18000 100 3.2967417 3.2967417 1.7705821 0.042176084 + 18100 100 3.4270672 3.4270672 1.8459819 0.043589925 + 18200 100 3.3638494 3.3638494 1.8159436 0.048949648 + 18300 100 3.3192279 3.3192279 1.8122198 0.043629595 + 18400 100 3.2627211 3.2627211 1.796316 0.045504529 + 18500 100 3.5669172 3.5669172 1.9257062 0.048460393 + 18600 100 3.5546411 3.5546411 1.9154318 0.046890968 + 18700 100 3.7288485 3.7288485 2.011106 0.046906531 + 18800 100 3.6800347 3.6800347 1.9936406 0.049985172 + 18900 100 3.7151898 3.7151898 2.007659 0.050394561 + 19000 100 3.9693368 3.9693368 2.1311549 0.053710204 + 19100 100 3.6907732 3.6907732 1.9939387 0.05480136 + 19200 100 3.8808777 3.8808777 2.0790125 0.055093552 + 19300 100 3.8422142 3.8422142 2.0756951 0.058090774 + 19400 100 3.7836875 3.7836875 2.0399805 0.06965907 + 19500 100 4.0480195 4.0480195 2.169214 0.053420651 + 19600 100 3.965917 3.965917 2.1245227 0.059077084 + 19700 100 3.8980869 3.8980869 2.0956306 0.050857062 + 19800 100 4.008079 4.008079 2.1501421 0.054938689 + 19900 100 3.7244506 3.7244506 2.0080877 0.055481507 + 20000 100 3.8146094 3.8146094 2.0541416 0.053187111 +Loop time of 0.210396 on 1 procs for 5000 steps with 100 atoms + +Performance: 10266363.999 tau/day, 23764.731 timesteps/s +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.013991 | 0.013991 | 0.013991 | 0.0 | 6.65 +Neigh | 0.056947 | 0.056947 | 0.056947 | 0.0 | 27.07 +Comm | 0.0013928 | 0.0013928 | 0.0013928 | 0.0 | 0.66 +Output | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.26 +Modify | 0.13027 | 0.13027 | 0.13027 | 0.0 | 61.92 +Other | | 0.007249 | | | 3.45 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 144 ave 144 max 144 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 144 +Ave neighs/atom = 1.44 +Neighbor list builds = 910 +Dangerous builds = 0 + +region container delete +region container block -6 6 -6 6 -6 6 units box +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.836 | 5.836 | 5.836 Mbytes +Step Atoms Temp c_1 c_2 Press + 20000 100 3.8146094 3.8146094 2.0541416 0.052956687 + 20100 100 1.3848453 1.3848453 0.82244153 0.017544632 + 20200 100 0.89469578 0.89469578 0.55929611 0.0111604 + 20300 100 0.83962013 0.83962013 0.52665461 0.010396174 + 20400 100 0.77264252 0.77264252 0.48961142 0.0095493901 + 20500 100 0.78613208 0.78613208 0.48683715 0.012166835 + 20600 100 0.88411633 0.88411633 0.52854942 0.011725323 + 20700 100 0.89833225 0.89833225 0.52549693 0.012193413 + 20800 100 0.90216089 0.90216089 0.51167019 0.014289685 + 20900 100 0.98665057 0.98665057 0.5468893 0.013794318 + 21000 100 0.7576342 0.7576342 0.42758791 0.011720156 + 21100 100 0.3821563 0.3821563 0.23426423 0.005324458 + 21200 100 0.17486973 0.17486973 0.12876582 0.0029726352 + 21300 100 0.17940562 0.17940562 0.12400155 0.0026179917 + 21400 100 0.15526876 0.15526876 0.10526802 0.002341177 + 21500 100 0.079493361 0.079493361 0.062289324 0.0017379534 + 21600 100 0.057299519 0.057299519 0.047939171 0.0020095941 + 21700 100 0.056900097 0.056900097 0.045799124 0.0017782068 + 21800 100 0.039847861 0.039847861 0.035138066 0.0018265057 + 21900 100 0.03919167 0.03919167 0.031815619 0.0012160098 + 22000 100 0.025499317 0.025499317 0.022126202 0.0010056809 + 22100 100 0.018956113 0.018956113 0.017843095 0.0016109368 + 22200 100 0.017337018 0.017337018 0.016063068 0.00042537508 + 22300 100 0.014785686 0.014785686 0.013007571 0.00049466367 + 22400 100 0.011754087 0.011754087 0.010399793 0.00042349151 + 22500 100 0.010362474 0.010362474 0.009077435 0.00025198478 + 22600 100 0.0089484896 0.0089484896 0.0079474121 0.00035239475 + 22700 100 0.0089936432 0.0089936432 0.0077908763 0.00018548371 + 22800 100 0.0068663718 0.0068663718 0.0064061667 0.00025641972 + 22900 100 0.0050272392 0.0050272392 0.0046676214 0.00040466013 + 23000 100 0.0049250142 0.0049250142 0.0044849467 0.00035704909 + 23100 100 0.0050508148 0.0050508148 0.0043117775 0.00030051828 + 23200 100 0.0037293467 0.0037293467 0.0033592517 0.00038108923 + 23300 100 0.0032823722 0.0032823722 0.0030511575 0.00040421775 + 23400 100 0.0026913866 0.0026913866 0.0025493429 9.2813733e-05 + 23500 100 0.0025590632 0.0025590632 0.0024466447 8.4695125e-05 + 23600 100 0.0025270441 0.0025270441 0.0024236554 8.4237376e-05 + 23700 100 0.0026406527 0.0026406527 0.0024501963 0.00015009901 + 23800 100 0.0024633391 0.0024633391 0.0023470594 3.8990761e-05 + 23900 100 0.0029505606 0.0029505606 0.0025122613 4.9810757e-05 + 24000 100 0.0019535519 0.0019535519 0.0019112421 3.5804751e-05 + 24100 100 0.0017505151 0.0017505151 0.001726233 2.380737e-05 + 24200 100 0.0015864857 0.0015864857 0.0015479949 1.963276e-05 + 24300 100 0.0014535898 0.0014535898 0.0014221262 3.6607862e-05 + 24400 100 0.0013744934 0.0013744934 0.0013523293 1.4522467e-05 + 24500 100 0.0013286378 0.0013286378 0.0013097089 3.2389792e-05 + 24600 100 0.0012093624 0.0012093624 0.0011617482 4.848694e-05 + 24700 100 0.0011817062 0.0011817062 0.0011409092 3.8898899e-05 + 24800 100 0.0011142524 0.0011142524 0.0010877723 1.4560662e-05 + 24900 100 0.0010941199 0.0010941199 0.0010614415 7.0209336e-05 + 25000 100 0.0010773559 0.0010773559 0.0010389783 1.3332279e-05 +Loop time of 0.0912137 on 1 procs for 5000 steps with 100 atoms + +Performance: 23680652.416 tau/day, 54816.325 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.010053 | 0.010053 | 0.010053 | 0.0 | 11.02 +Neigh | 0.017597 | 0.017597 | 0.017597 | 0.0 | 19.29 +Comm | 0.00092912 | 0.00092912 | 0.00092912 | 0.0 | 1.02 +Output | 0.00049806 | 0.00049806 | 0.00049806 | 0.0 | 0.55 +Modify | 0.056085 | 0.056085 | 0.056085 | 0.0 | 61.49 +Other | | 0.006052 | | | 6.63 + +Nlocal: 100 ave 100 max 100 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 143 ave 143 max 143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 143 +Ave neighs/atom = 1.43 +Neighbor list builds = 289 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/granregion/log.27Nov18.granregion.box.g++.4 b/examples/granregion/log.27Nov18.granregion.box.g++.4 new file mode 100644 index 0000000000..170c8be867 --- /dev/null +++ b/examples/granregion/log.27Nov18.granregion.box.g++.4 @@ -0,0 +1,475 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# pouring spheres into container box + +units lj +atom_style sphere +boundary f f f +dimension 3 +comm_modify vel yes + +region box block -10 10 -10 10 -10 10 units box +create_box 2 box +Created orthogonal box = (-10 -10 -10) to (10 10 10) + 1 by 2 by 2 MPI processor grid + +pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 +pair_coeff * * gran/hooke + +region container block -6 6 -6 6 -6 6 units box +fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 2 all nve/sphere +fix 3 all gravity 1.0 vector 0 0 -1 + +region slab block -2 2 -2 2 -2 2 units box +fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore +Particle insertion: 48 every 566 steps, 100 by step 1133 + +timestep 0.005 + +compute 1 all temp +compute_modify 1 dynamic/dof yes + +compute 2 all temp/sphere +compute_modify 2 dynamic/dof yes + +thermo 100 +thermo_style custom step atoms temp c_1 c_2 press +thermo_modify lost ignore +compute_modify thermo_temp dynamic/dof yes + +#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03 +#dump_modify 2 pad 5 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 31 31 31 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke, perpetual + attributes: half, newton on, size + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 0.4834 | 0.4834 | 0.4834 Mbytes +Step Atoms Temp c_1 c_2 Press + 0 0 0 0 0 0 + 100 21 0.54270729 0.54270729 0.26473526 0.0013567682 + 200 21 0.87606961 0.87606961 0.42735103 0.002190174 + 300 21 1.1428374 1.1428374 0.55748167 0.0028570936 + 400 21 1.3543103 1.3543103 0.66829516 0.0033857758 + 500 21 1.0677786 1.0677786 0.53582407 0.0045048164 + 600 56 0.6744286 0.6744286 0.3502938 0.0047464584 + 700 56 0.75569283 0.75569283 0.39779462 0.0051953882 + 800 56 0.61597505 0.61597505 0.32943642 0.0086022783 + 900 56 0.65260802 0.65260802 0.34474044 0.0059298996 + 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337 + 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094 + 1200 81 0.39112346 0.39112346 0.21690172 0.0086559316 + 1300 81 0.33302617 0.33302617 0.19109398 0.0033381104 + 1400 81 0.3933533 0.3933533 0.21221692 0.004135078 + 1500 81 0.35495297 0.35495297 0.19925984 0.0037374946 + 1600 81 0.34150606 0.34150606 0.19025811 0.0053492835 + 1700 100 0.2561647 0.2561647 0.14186278 0.0090767057 + 1800 100 0.21124278 0.21124278 0.12154878 0.002854576 + 1900 100 0.21793955 0.21793955 0.12173867 0.0029049175 + 2000 100 0.25530858 0.25530858 0.13892272 0.0035528022 + 2100 100 0.24671805 0.24671805 0.13687782 0.0076812357 + 2200 100 0.22465212 0.22465212 0.12513612 0.0042526344 + 2300 100 0.19362805 0.19362805 0.10914275 0.0061175383 + 2400 100 0.061626039 0.061626039 0.045905953 0.0010393593 + 2500 100 0.052690575 0.052690575 0.038879745 0.0018543933 + 2600 100 0.037256691 0.037256691 0.02833916 0.0027683815 + 2700 100 0.033416362 0.033416362 0.024551243 0.00046725913 + 2800 100 0.019617758 0.019617758 0.014619416 0.00064550316 + 2900 100 0.012313874 0.012313874 0.0098188153 0.00033470181 + 3000 100 0.010948455 0.010948455 0.0087981878 0.00034401243 + 3100 100 0.009359431 0.009359431 0.0073642412 0.00045497356 + 3200 100 0.008129885 0.008129885 0.0061460516 0.00029944201 + 3300 100 0.0050682533 0.0050682533 0.0042692811 0.00026543293 + 3400 100 0.0031539312 0.0031539312 0.0027256511 0.00012475748 + 3500 100 0.0023621311 0.0023621311 0.0021691817 0.0001186392 + 3600 100 0.0018305354 0.0018305354 0.0018004128 0.00015926282 + 3700 100 0.0016522492 0.0016522492 0.0017231072 0.0002193159 + 3800 100 0.0011715102 0.0011715102 0.0012739973 0.0001747857 + 3900 100 0.0010607606 0.0010607606 0.0010974725 0.00012476088 + 4000 100 0.00087570802 0.00087570802 0.00095828935 6.5544103e-05 + 4100 100 0.00078598203 0.00078598203 0.00088068743 9.4560761e-05 + 4200 100 0.00088317454 0.00088317454 0.00092784605 8.1108122e-05 + 4300 100 0.0015013254 0.0015013254 0.0012069505 8.8289686e-05 + 4400 100 0.00070054041 0.00070054041 0.00079451193 5.195712e-05 + 4500 100 0.00096259073 0.00096259073 0.00091232511 3.4895669e-05 + 4600 100 0.00056641848 0.00056641848 0.00069083146 3.9657253e-05 + 4700 100 0.0005455099 0.0005455099 0.00064816699 2.8131762e-05 + 4800 100 0.00048254366 0.00048254366 0.00057192255 4.7914432e-05 + 4900 100 0.00037108125 0.00037108125 0.00048035333 6.4711817e-05 + 5000 100 0.00031290399 0.00031290399 0.00042398478 4.6025975e-05 +Loop time of 0.075416 on 4 procs for 5000 steps with 100 atoms + +Performance: 28641126.336 tau/day, 66298.904 timesteps/s +93.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0022948 | 0.0041364 | 0.0061705 | 2.8 | 5.48 +Neigh | 0.0043123 | 0.0057145 | 0.0070784 | 1.8 | 7.58 +Comm | 0.014259 | 0.018658 | 0.024313 | 3.3 | 24.74 +Output | 0.0011525 | 0.001404 | 0.0015383 | 0.4 | 1.86 +Modify | 0.0030508 | 0.014543 | 0.026602 | 9.5 | 19.28 +Other | | 0.03096 | | | 41.05 + +Nlocal: 25 ave 51 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5.5 ave 12 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 39.75 ave 84 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 159 +Ave neighs/atom = 1.59 +Neighbor list builds = 310 +Dangerous builds = 0 + +region container delete +variable theta equal (step-5000)*(4.0*PI/5000) +region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1 +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes +Step Atoms Temp c_1 c_2 Press + 5000 100 0.00031290399 0.00031290399 0.00042398478 4.4282259e-05 + 5100 100 0.62661084 0.62661084 0.33840611 0.012020153 + 5200 100 0.67371678 0.67371678 0.36218522 0.0093514044 + 5300 100 0.75892331 0.75892331 0.4000747 0.010693252 + 5400 100 0.86207426 0.86207426 0.44630388 0.013540097 + 5500 100 0.96205334 0.96205334 0.49432848 0.017375079 + 5600 100 1.0261194 1.0261194 0.52203912 0.016045333 + 5700 100 1.0584366 1.0584366 0.53794336 0.018621676 + 5800 100 1.0881674 1.0881674 0.55300469 0.01930602 + 5900 100 1.1214233 1.1214233 0.56613492 0.021141141 + 6000 100 1.1666836 1.1666836 0.58759377 0.017655361 + 6100 100 1.1785775 1.1785775 0.59365148 0.01829443 + 6200 100 1.2092305 1.2092305 0.60798809 0.018752443 + 6300 100 1.2331787 1.2331787 0.62003386 0.020291021 + 6400 100 1.2561616 1.2561616 0.63143643 0.019899235 + 6500 100 1.284432 1.284432 0.6460504 0.02083284 + 6600 100 1.2678801 1.2678801 0.63882384 0.019456553 + 6700 100 1.2662641 1.2662641 0.63676836 0.020235578 + 6800 100 1.2785484 1.2785484 0.64129093 0.020335162 + 6900 100 1.2916608 1.2916608 0.64764298 0.020154225 + 7000 100 1.2907774 1.2907774 0.64724849 0.020550885 + 7100 100 1.3074473 1.3074473 0.65460147 0.020847362 + 7200 100 1.3124592 1.3124592 0.65641332 0.020897348 + 7300 100 1.3206191 1.3206191 0.66011491 0.021444077 + 7400 100 1.3273988 1.3273988 0.66350669 0.02129418 + 7500 100 1.3343911 1.3343911 0.66707269 0.021337376 + 7600 100 1.3368998 1.3368998 0.66869327 0.021415901 + 7700 100 1.330658 1.330658 0.66535295 0.021500761 + 7800 100 1.330801 1.330801 0.66555123 0.022806058 + 7900 100 1.3392828 1.3392828 0.66926796 0.02194009 + 8000 100 1.3432728 1.3432728 0.67142337 0.022393719 + 8100 100 1.3411612 1.3411612 0.66989302 0.022366895 + 8200 100 1.3427451 1.3427451 0.67054285 0.021966329 + 8300 100 1.3418147 1.3418147 0.67023132 0.022513459 + 8400 100 1.346493 1.346493 0.67247837 0.022705366 + 8500 100 1.3513958 1.3513958 0.6749092 0.022834077 + 8600 100 1.3520297 1.3520297 0.67506261 0.023227676 + 8700 100 1.3517157 1.3517157 0.67485073 0.023043414 + 8800 100 1.3530071 1.3530071 0.67547212 0.022933766 + 8900 100 1.3550454 1.3550454 0.67657277 0.022744182 + 9000 100 1.3554069 1.3554069 0.67673505 0.022802134 + 9100 100 1.3556675 1.3556675 0.67698335 0.022868449 + 9200 100 1.3534709 1.3534709 0.67600677 0.022537792 + 9300 100 1.3525103 1.3525103 0.67569499 0.022687849 + 9400 100 1.3612673 1.3612673 0.67967213 0.022703588 + 9500 100 1.3649439 1.3649439 0.68147385 0.023498539 + 9600 100 1.3629376 1.3629376 0.68063814 0.023515579 + 9700 100 1.3648924 1.3648924 0.68137104 0.023641856 + 9800 100 1.3662063 1.3662063 0.68196538 0.023576884 + 9900 100 1.3689695 1.3689695 0.68326751 0.023572622 + 10000 100 1.3701139 1.3701139 0.68383343 0.023720885 +Loop time of 0.174251 on 4 procs for 5000 steps with 100 atoms + +Performance: 12395939.906 tau/day, 28694.305 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0024631 | 0.010709 | 0.020461 | 8.0 | 6.15 +Neigh | 0.0078361 | 0.012368 | 0.016955 | 4.0 | 7.10 +Comm | 0.0059071 | 0.013641 | 0.023547 | 6.6 | 7.83 +Output | 0.0011749 | 0.0021775 | 0.0030091 | 1.4 | 1.25 +Modify | 0.015055 | 0.055709 | 0.097013 | 17.2 | 31.97 +Other | | 0.07965 | | | 45.71 + +Nlocal: 25 ave 51 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 4.5 ave 10 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 49.25 ave 101 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 197 +Ave neighs/atom = 1.97 +Neighbor list builds = 627 +Dangerous builds = 0 + +region container delete +region container block -6 6 -6 6 -6 6 units box +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes +Step Atoms Temp c_1 c_2 Press + 10000 100 1.3701139 1.3701139 0.68383343 0.023895921 + 10100 100 0.25960098 0.25960098 0.15183967 0.0049554084 + 10200 100 0.15017576 0.15017576 0.10081112 0.0045433238 + 10300 100 0.10129671 0.10129671 0.078049099 0.0014012658 + 10400 100 0.06742425 0.06742425 0.055603816 0.0010184792 + 10500 100 0.053446366 0.053446366 0.045338293 0.00089291689 + 10600 100 0.041898231 0.041898231 0.036081995 0.00060703885 + 10700 100 0.03580041 0.03580041 0.031118724 0.00067731964 + 10800 100 0.030933755 0.030933755 0.026372348 0.00039362325 + 10900 100 0.027278004 0.027278004 0.022868898 0.0003680788 + 11000 100 0.021566952 0.021566952 0.017994879 0.0013056062 + 11100 100 0.019143625 0.019143625 0.015833865 0.00050998112 + 11200 100 0.015659868 0.015659868 0.013119379 0.00012755696 + 11300 100 0.013554605 0.013554605 0.01147808 0.00027393437 + 11400 100 0.01204033 0.01204033 0.010273026 0.00033430792 + 11500 100 0.010958991 0.010958991 0.0093924566 0.00049023273 + 11600 100 0.01012553 0.01012553 0.0084556996 0.00021457333 + 11700 100 0.0083584131 0.0083584131 0.0071118766 7.7149089e-05 + 11800 100 0.007044883 0.007044883 0.0058675523 0.00036165381 + 11900 100 0.0059875106 0.0059875106 0.0050610372 7.4095443e-05 + 12000 100 0.0045180275 0.0045180275 0.0039006565 0.00014607704 + 12100 100 0.0036631356 0.0036631356 0.0031154279 7.031064e-05 + 12200 100 0.0034443424 0.0034443424 0.0029190637 0.00020974475 + 12300 100 0.0030853504 0.0030853504 0.0026315266 3.4873541e-05 + 12400 100 0.0025451749 0.0025451749 0.0022290833 0.00041551536 + 12500 100 0.0021624857 0.0021624857 0.0019127734 2.6760761e-05 + 12600 100 0.0020637862 0.0020637862 0.0018186641 4.9446655e-05 + 12700 100 0.0019889538 0.0019889538 0.0017604689 3.326943e-05 + 12800 100 0.0018706349 0.0018706349 0.0016669237 2.3327318e-05 + 12900 100 0.0017472824 0.0017472824 0.001579469 8.816765e-05 + 13000 100 0.0016034824 0.0016034824 0.0014549852 3.5407524e-05 + 13100 100 0.00151798 0.00151798 0.0013826659 1.8754149e-05 + 13200 100 0.0013049781 0.0013049781 0.0012137907 0.00015263775 + 13300 100 0.0012270536 0.0012270536 0.0011590841 4.77636e-06 + 13400 100 0.0011395128 0.0011395128 0.0010860297 2.5606328e-05 + 13500 100 0.0010858414 0.0010858414 0.0010486713 5.8563931e-05 + 13600 100 0.0010474389 0.0010474389 0.001015904 1.4319658e-05 + 13700 100 0.00099241549 0.00099241549 0.00097825038 1.2281142e-05 + 13800 100 0.00084449252 0.00084449252 0.00084141963 1.0451215e-05 + 13900 100 0.00084004792 0.00084004792 0.00083755495 3.7174162e-05 + 14000 100 0.00082183505 0.00082183505 0.00082027058 1.0170209e-05 + 14100 100 0.00082377076 0.00082377076 0.00080489795 1.181976e-05 + 14200 100 0.00076903208 0.00076903208 0.00076216608 4.4590341e-05 + 14300 100 0.00075173269 0.00075173269 0.00074828209 2.2134371e-05 + 14400 100 0.00074379148 0.00074379148 0.00074072001 1.5746014e-05 + 14500 100 0.00072454029 0.00072454029 0.0007174429 8.9830398e-06 + 14600 100 0.00072372648 0.00072372648 0.00071678769 9.1111512e-06 + 14700 100 0.00071541587 0.00071541587 0.00070893868 7.8446375e-05 + 14800 100 0.0006820307 0.0006820307 0.00066675502 8.4401299e-06 + 14900 100 0.00067050627 0.00067050627 0.00065751846 0.0001228548 + 15000 100 0.00064977132 0.00064977132 0.00062305247 7.8887775e-06 +Loop time of 0.0746691 on 4 procs for 5000 steps with 100 atoms + +Performance: 28927619.905 tau/day, 66962.083 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0021737 | 0.0042608 | 0.0063519 | 3.2 | 5.71 +Neigh | 0.0012126 | 0.0019009 | 0.0026193 | 1.6 | 2.55 +Comm | 0.0023425 | 0.0092477 | 0.016876 | 7.2 | 12.38 +Output | 0.0010619 | 0.0017995 | 0.0030522 | 1.8 | 2.41 +Modify | 0.00097013 | 0.017151 | 0.03415 | 12.3 | 22.97 +Other | | 0.04031 | | | 53.98 + +Nlocal: 25 ave 55 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 3.75 ave 9 max 0 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Neighs: 42.5 ave 88 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 170 +Ave neighs/atom = 1.7 +Neighbor list builds = 97 +Dangerous builds = 0 + +region container delete +variable theta equal (step-15000)*(4.0*PI/5000) +region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1 +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.733 | 5.734 Mbytes +Step Atoms Temp c_1 c_2 Press + 15000 100 0.00064977132 0.00064977132 0.00062305247 7.9405607e-06 + 15100 100 1.0123899 1.0123899 0.66185504 0.014587215 + 15200 100 1.0332828 1.0332828 0.67443308 0.014002815 + 15300 100 1.0804076 1.0804076 0.72450056 0.016985272 + 15400 100 1.2868163 1.2868163 0.8708132 0.022190597 + 15500 100 1.5180471 1.5180471 0.99613124 0.026761866 + 15600 100 1.5422016 1.5422016 1.0021746 0.024490139 + 15700 100 1.7142241 1.7142241 1.0611146 0.0301368 + 15800 100 1.8747057 1.8747057 1.1207858 0.027612699 + 15900 100 1.9294819 1.9294819 1.1289025 0.027270228 + 16000 100 1.953275 1.953275 1.1264475 0.031568811 + 16100 100 2.0434228 2.0434228 1.1665365 0.026358952 + 16200 100 2.2129393 2.2129393 1.2448327 0.029613382 + 16300 100 2.2558224 2.2558224 1.2373264 0.028306021 + 16400 100 2.367398 2.367398 1.293448 0.029659303 + 16500 100 2.4221549 2.4221549 1.3198966 0.032541712 + 16600 100 2.510283 2.510283 1.3618001 0.034740544 + 16700 100 2.6776293 2.6776293 1.4508262 0.034556341 + 16800 100 2.8095841 2.8095841 1.5190571 0.035183782 + 16900 100 2.8485646 2.8485646 1.5344387 0.037153336 + 17000 100 3.0298285 3.0298285 1.6321623 0.040745906 + 17100 100 3.0218054 3.0218054 1.6187189 0.042082135 + 17200 100 3.1981705 3.1981705 1.7090597 0.041770208 + 17300 100 3.3178559 3.3178559 1.7723201 0.044604756 + 17400 100 3.3940903 3.3940903 1.8229846 0.049231759 + 17500 100 3.3274817 3.3274817 1.7870996 0.051649102 + 17600 100 3.3204358 3.3204358 1.791527 0.043875639 + 17700 100 3.2185649 3.2185649 1.7480866 0.049941218 + 17800 100 3.2507826 3.2507826 1.7727758 0.048622479 + 17900 100 3.2432767 3.2432767 1.7796296 0.044343902 + 18000 100 3.0841272 3.0841272 1.6978832 0.045344433 + 18100 100 3.0953909 3.0953909 1.699898 0.040070963 + 18200 100 3.1405704 3.1405704 1.7316463 0.042528194 + 18300 100 3.1904871 3.1904871 1.7555188 0.041141165 + 18400 100 3.3256779 3.3256779 1.8243767 0.043908318 + 18500 100 3.5161823 3.5161823 1.9150861 0.045165166 + 18600 100 3.5668273 3.5668273 1.9217975 0.048127705 + 18700 100 3.6648305 3.6648305 1.9685241 0.051205352 + 18800 100 3.9000502 3.9000502 2.0886668 0.05262835 + 18900 100 4.0217758 4.0217758 2.1465498 0.054502839 + 19000 100 3.8431174 3.8431174 2.0581611 0.054852333 + 19100 100 4.1721454 4.1721454 2.2221193 0.053831555 + 19200 100 3.9061181 3.9061181 2.096323 0.058077678 + 19300 100 4.0191085 4.0191085 2.1408069 0.05475437 + 19400 100 3.8840871 3.8840871 2.0887677 0.061905092 + 19500 100 3.8388062 3.8388062 2.0567095 0.051076414 + 19600 100 3.6331742 3.6331742 1.9574769 0.04748008 + 19700 100 3.6996954 3.6996954 1.9887285 0.053305043 + 19800 100 3.8649872 3.8649872 2.0827424 0.060484008 + 19900 100 3.8305733 3.8305733 2.0700281 0.052926584 + 20000 100 3.7948463 3.7948463 2.0657301 0.048516953 +Loop time of 0.156359 on 4 procs for 5000 steps with 100 atoms + +Performance: 13814330.011 tau/day, 31977.616 timesteps/s +94.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0040646 | 0.0058124 | 0.0074518 | 1.6 | 3.72 +Neigh | 0.014813 | 0.018389 | 0.020829 | 1.6 | 11.76 +Comm | 0.031892 | 0.034103 | 0.036658 | 1.0 | 21.81 +Output | 0.0013497 | 0.0019822 | 0.003484 | 2.0 | 1.27 +Modify | 0.031006 | 0.046878 | 0.056364 | 4.5 | 29.98 +Other | | 0.0492 | | | 31.46 + +Nlocal: 25 ave 37 max 10 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 3.75 ave 6 max 2 min +Histogram: 1 0 1 0 0 1 0 0 0 1 +Neighs: 36.25 ave 57 max 9 min +Histogram: 1 0 0 0 0 0 2 0 0 1 + +Total # of neighbors = 145 +Ave neighs/atom = 1.45 +Neighbor list builds = 921 +Dangerous builds = 0 + +region container delete +region container block -6 6 -6 6 -6 6 units box +run 5000 +Per MPI rank memory allocation (min/avg/max) = 5.733 | 5.734 | 5.734 Mbytes +Step Atoms Temp c_1 c_2 Press + 20000 100 3.7948463 3.7948463 2.0657301 0.048381317 + 20100 100 1.1359931 1.1359931 0.70170151 0.015300556 + 20200 100 0.87354617 0.87354617 0.55969299 0.012181983 + 20300 100 0.84424484 0.84424484 0.52849351 0.017724782 + 20400 100 0.82422562 0.82422562 0.50175766 0.0098154181 + 20500 100 0.83731289 0.83731289 0.49814627 0.010465327 + 20600 100 0.93125924 0.93125924 0.53803834 0.011624902 + 20700 100 1.0810919 1.0810919 0.60974741 0.01425935 + 20800 100 1.0646343 1.0646343 0.60037545 0.013418132 + 20900 100 1.0608055 1.0608055 0.58353908 0.015119612 + 21000 100 0.68173094 0.68173094 0.3941588 0.0099947535 + 21100 100 0.35407592 0.35407592 0.21306735 0.0043859494 + 21200 100 0.19247432 0.19247432 0.12989264 0.0031808422 + 21300 100 0.13493768 0.13493768 0.093987634 0.0025990872 + 21400 100 0.085735857 0.085735857 0.062091707 0.001434207 + 21500 100 0.074307566 0.074307566 0.05224051 0.0022163094 + 21600 100 0.069932382 0.069932382 0.045388838 0.0020296572 + 21700 100 0.041749712 0.041749712 0.031422931 0.001211155 + 21800 100 0.03378055 0.03378055 0.026248846 0.0020596463 + 21900 100 0.030608528 0.030608528 0.022868294 0.0016282878 + 22000 100 0.025632448 0.025632448 0.019606402 0.0011659657 + 22100 100 0.013785062 0.013785062 0.011561769 0.00069006322 + 22200 100 0.013139066 0.013139066 0.010559726 0.00038424576 + 22300 100 0.01455318 0.01455318 0.011094558 0.00054735929 + 22400 100 0.0096885414 0.0096885414 0.008012617 0.00055875777 + 22500 100 0.0081193116 0.0081193116 0.006802973 0.00052914932 + 22600 100 0.0057159621 0.0057159621 0.0048680253 0.00054864875 + 22700 100 0.0052344376 0.0052344376 0.0045511708 0.00026333033 + 22800 100 0.0054554177 0.0054554177 0.0045005479 0.0002085972 + 22900 100 0.0039455776 0.0039455776 0.0035287888 0.00022514017 + 23000 100 0.0042620461 0.0042620461 0.0035747729 0.00020030999 + 23100 100 0.0035303095 0.0035303095 0.0031995108 0.00016007298 + 23200 100 0.0029747457 0.0029747457 0.0027095904 0.00029775807 + 23300 100 0.0032404433 0.0032404433 0.002769389 0.00019627995 + 23400 100 0.0024965262 0.0024965262 0.0022343473 0.00018870133 + 23500 100 0.00251617 0.00251617 0.0022533604 0.0002661237 + 23600 100 0.0025923653 0.0025923653 0.0022887204 0.00018475201 + 23700 100 0.0023016545 0.0023016545 0.0019829032 0.00014888334 + 23800 100 0.0028358441 0.0028358441 0.0021790504 0.00064613131 + 23900 100 0.0016682403 0.0016682403 0.0014930521 8.8407075e-05 + 24000 100 0.0016341577 0.0016341577 0.0014597606 0.00011262081 + 24100 100 0.0015433636 0.0015433636 0.0013981581 8.364568e-05 + 24200 100 0.0015033978 0.0015033978 0.0013582013 8.4539006e-05 + 24300 100 0.0014513098 0.0014513098 0.0012943981 0.00010546194 + 24400 100 0.0013293352 0.0013293352 0.001206366 8.4967509e-05 + 24500 100 0.0013732518 0.0013732518 0.001202532 0.00014787559 + 24600 100 0.00091890041 0.00091890041 0.00084499923 0.00010080638 + 24700 100 0.00083467915 0.00083467915 0.00077071316 5.3934025e-05 + 24800 100 0.00080701934 0.00080701934 0.0007477161 5.3982095e-05 + 24900 100 0.00080620771 0.00080620771 0.0007471026 5.3581294e-05 + 25000 100 0.00080568604 0.00080568604 0.00074625735 5.3574637e-05 +Loop time of 0.0792506 on 4 procs for 5000 steps with 100 atoms + +Performance: 27255302.560 tau/day, 63090.978 timesteps/s +95.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0023611 | 0.0047854 | 0.0077851 | 3.4 | 6.04 +Neigh | 0.0042653 | 0.005571 | 0.0067258 | 1.5 | 7.03 +Comm | 0.0077977 | 0.013373 | 0.019515 | 4.4 | 16.87 +Output | 0.0010924 | 0.0017727 | 0.0030222 | 1.8 | 2.24 +Modify | 0.0023608 | 0.015964 | 0.030545 | 10.5 | 20.14 +Other | | 0.03778 | | | 47.68 + +Nlocal: 25 ave 50 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 5 ave 10 max 0 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 35.75 ave 78 max 0 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 143 +Ave neighs/atom = 1.43 +Neighbor list builds = 287 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/granregion/log.27Nov18.granregion.funnel.g++.1 b/examples/granregion/log.27Nov18.granregion.funnel.g++.1 new file mode 100644 index 0000000000..0268ed000a --- /dev/null +++ b/examples/granregion/log.27Nov18.granregion.funnel.g++.1 @@ -0,0 +1,601 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# pour particles into cone-shaped funnel, settle them, let them run out bottom + +variable name string funnel_pour + +thermo_modify flush yes +units si +variable PI equal 3.141592653589 +variable seed equal 14314 + +############################################### +# Geometry-related parameters +############################################### + +variable xlo equal 10 +variable xhi equal 40 +variable ylo equal 10 +variable yhi equal 40 +variable zlo equal -20 +variable zhi equal 50 + +variable xc equal 25 +variable yc equal 25 + +variable zconehi equal 50 +variable zconelo equal 10 +variable zcyllo equal 0 +variable radconelo equal 2 +variable radconehi equal 20 + +################################################ +# Particle sizes +################################################ + +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.25 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.5 + +variable skin equal ${rhi} +variable skin equal 0.5 + +############################################### +# Granular contact parameters +############################################### + +variable coeffRes equal 0.1 +variable coeffFric equal 0.5 + +variable density equal 1.0 +variable EYoung equal 10^5 +variable Poisson equal 2.0/7.0 +variable GShear equal ${EYoung}/(2*(1+${Poisson})) +variable GShear equal 100000/(2*(1+${Poisson})) +variable GShear equal 100000/(2*(1+0.285714285714286)) + +variable gravity equal 1.0 + +variable reff equal 0.5*(${rhi}+${rlo}) +variable reff equal 0.5*(0.5+${rlo}) +variable reff equal 0.5*(0.5+0.25) +variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3 +variable meff equal 1*4.0/3.0*${PI}*${reff}^3 +variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3 +variable meff equal 1*4.0/3.0*3.141592653589*0.375^3 +variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25 +variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5 + +## Typical way to set kn, kt, etc.: +variable kn equal 4.0*${GShear}/(3*(1-${Poisson})) +variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson})) +variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286)) +variable kt equal 4.0*${GShear}/(2-${Poisson}) +variable kt equal 4.0*38888.8888888889/(2-${Poisson}) +variable kt equal 4.0*38888.8888888889/(2-0.285714285714286) + +variable a equal (-2.0*log(${coeffRes})/${PI})^2 +variable a equal (-2.0*log(0.1)/${PI})^2 +variable a equal (-2.0*log(0.1)/3.141592653589)^2 +variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556)) +variable gamma_t equal ${gamma_n}*0.5 +variable gamma_t equal 903.503751814138*0.5 + +variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0) + +variable dt equal ${tcol}*0.05 +variable dt equal 0.00210943016014969*0.05 +timestep ${dt} +timestep 0.000105471508007485 + +############################################### +variable dumpfreq equal 1000 +variable logfreq equal 1000 + +newton off +atom_style sphere + +boundary p p f + +region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} +region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} +region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi} +region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi} +region boxreg block 10 40 10 40 ${zlo} ${zhi} +region boxreg block 10 40 10 40 -20 ${zhi} +region boxreg block 10 40 10 40 -20 50 +create_box 1 boxreg +Created orthogonal box = (10 10 -20) to (40 40 50) + 1 by 1 by 1 MPI processor grid + +pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 +pair_coeff * * + +neighbor ${skin} bin +neighbor 0.5 bin +thermo ${logfreq} +thermo 1000 + +comm_style brick +comm_modify mode multi group all vel yes +balance 1.1 shift xyz 20 1.1 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 30, bins = 1 1 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +fix bal all balance 10000 1.1 shift xyz 20 1.01 + +####################### Options specific to pouring ######################### + +# insertion region for fix/pour + +region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box +region insreg cylinder z 25 ${yc} 10 30 50 side in units box +region insreg cylinder z 25 25 10 30 50 side in units box + +# define cone and cylinder regions - see lammps doc on region command +# note new open options + +region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open +region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 2 0 10 side in units box open 2 + +region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open +region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2 + +region hopreg union 2 conereg cylreg + +fix grav all gravity ${gravity} vector 0 0 -1 +fix grav all gravity 1 vector 0 0 -1 +fix 1 all nve/sphere + + +fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg + +fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1 +Particle insertion: 3000 every 59965 steps, 2000 by step 1 + +#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z + +#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0 +#dump_modify 2 pad 6 + +thermo_style custom step cpu atoms ke +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) +thermo_modify flush yes lost warn + +# Initial run to fill up the cone + +run 20000 +Per MPI rank memory allocation (min/avg/max) = 6.649 | 6.649 | 6.649 Mbytes +Step CPU Atoms KinEng + 0 0 0 -0 + 1000 0.63593698 2000 -0 + 2000 1.0282419 2000 -0 + 3000 1.4184453 2000 -0 + 4000 1.8055785 2000 -0 + 5000 2.1941335 2000 -0 + 6000 2.5804653 2000 -0 + 7000 2.9660621 2000 -0 + 8000 3.3506265 2000 -0 + 9000 3.7344413 2000 -0 + 10000 4.1212304 2000 -0 + 11000 4.5044594 2000 -0 + 12000 4.8875456 2000 -0 + 13000 5.2698007 2000 -0 + 14000 5.6527214 2000 -0 + 15000 6.0349295 2000 -0 + 16000 6.4172938 2000 -0 + 17000 6.8001184 2000 -0 + 18000 7.1826644 2000 -0 + 19000 7.5654378 2000 -0 + 20000 7.9511659 2000 -0 +Loop time of 7.95118 on 1 procs for 20000 steps with 2000 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.6189 | 0.6189 | 0.6189 | 0.0 | 7.78 +Neigh | 0.09361 | 0.09361 | 0.09361 | 0.0 | 1.18 +Comm | 0.016098 | 0.016098 | 0.016098 | 0.0 | 0.20 +Output | 0.00048828 | 0.00048828 | 0.00048828 | 0.0 | 0.01 +Modify | 6.9973 | 6.9973 | 6.9973 | 0.0 | 88.00 +Other | | 0.2248 | | | 2.83 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1537 ave 1537 max 1537 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1537 +Ave neighs/atom = 0.7685 +Neighbor list builds = 69 +Dangerous builds = 0 +unfix ins +run 150000 +Per MPI rank memory allocation (min/avg/max) = 12.77 | 12.77 | 12.77 Mbytes +Step CPU Atoms KinEng + 20000 0 2000 6443.7665 + 21000 0.3826313 2000 6572.3531 + 22000 0.76688981 2000 6723.8376 + 23000 1.1534231 2000 6853.1812 + 24000 1.5391715 2000 6976.0209 + 25000 1.9263508 2000 7096.9955 + 26000 2.3168406 2000 7215.5795 + 27000 2.7065961 2000 7349.2382 + 28000 3.096664 2000 7471.8719 + 29000 3.4905531 2000 7574.8228 + 30000 3.8877606 2000 7659.3836 + 31000 4.2839894 2000 7703.6856 + 32000 4.6859732 2000 7644.279 + 33000 5.0932801 2000 7526.6944 + 34000 5.5045564 2000 7370.0821 + 35000 5.9206297 2000 7193.0457 + 36000 6.343729 2000 6990.9899 + 37000 6.7719142 2000 6849.2841 + 38000 7.2016783 2000 6701.7433 + 39000 7.6354482 2000 6538.9557 + 40000 8.078445 2000 6381.9346 + 41000 8.5191586 2000 6217.5253 + 42000 8.9630713 2000 6093.5344 + 43000 9.4097741 2000 5943.0479 + 44000 9.8652256 2000 5841.0782 + 45000 10.331057 2000 5652.8319 + 46000 10.803253 2000 5476.1466 + 47000 11.278766 2000 5267.7855 + 48000 11.759121 2000 5131.4036 + 49000 12.248896 2000 4972.7696 + 50000 12.747719 2000 4867.0868 + 51000 13.246704 2000 4681.897 + 52000 13.757842 2000 4506.8185 + 53000 14.276078 2000 4346.8045 + 54000 14.795933 2000 4193.8194 + 55000 15.311241 2000 4058.2049 + 56000 15.828737 2000 3879.0325 + 57000 16.359453 2000 3696.3154 + 58000 16.905406 2000 3504.0399 + 59000 17.460454 2000 3284.6522 + 60000 18.027276 2000 3061.0727 + 61000 18.586931 2000 2874.2926 + 62000 19.158563 2000 2653.0722 + 63000 19.738442 2000 2437.4941 + 64000 20.331411 2000 2124.1876 + 65000 20.936204 2000 1864.5661 + 66000 21.547443 2000 1610.2335 + 67000 22.166888 2000 1390.0428 + 68000 22.789106 2000 1163.7679 + 69000 23.416016 2000 933.0928 + 70000 24.038879 2000 745.66667 + 71000 24.663115 2000 605.58458 + 72000 25.294193 2000 444.31183 + 73000 25.932019 2000 357.19162 + 74000 26.568184 2000 291.16762 + 75000 27.203393 2000 230.58362 + 76000 27.836079 2000 197.59502 + 77000 28.467344 2000 166.55702 + 78000 29.099997 2000 139.89052 + 79000 29.741694 2000 117.1145 + 80000 30.388097 2000 100.12353 + 81000 31.036193 2000 85.233155 + 82000 31.688463 2000 71.145302 + 83000 32.343411 2000 61.545348 + 84000 32.999346 2000 54.099358 + 85000 33.652976 2000 46.922028 + 86000 34.306931 2000 41.606645 + 87000 34.967787 2000 37.462793 + 88000 35.633721 2000 33.698298 + 89000 36.310035 2000 29.340455 + 90000 36.995441 2000 26.072122 + 91000 37.67904 2000 23.20848 + 92000 38.367699 2000 21.015862 + 93000 39.058641 2000 20.134175 + 94000 39.749342 2000 19.196075 + 95000 40.442651 2000 18.285127 + 96000 41.140177 2000 17.476411 + 97000 41.840761 2000 16.55882 + 98000 42.543845 2000 15.444541 + 99000 43.256415 2000 14.41642 + 100000 43.97382 2000 13.818738 + 101000 44.684596 2000 12.878373 + 102000 45.401082 2000 12.11804 + 103000 46.120936 2000 11.016885 + 104000 46.83935 2000 10.531044 + 105000 47.559419 2000 10.46735 + 106000 48.286016 2000 10.246007 + 107000 49.012266 2000 9.6423041 + 108000 49.74013 2000 9.3948808 + 109000 50.471961 2000 9.5178141 + 110000 51.206152 2000 9.4143884 + 111000 51.939123 2000 9.5058226 + 112000 52.673443 2000 9.6911516 + 113000 53.410485 2000 9.7756849 + 114000 54.152537 2000 9.3876232 + 115000 54.891784 2000 8.6725333 + 116000 55.631474 2000 8.6691065 + 117000 56.371762 2000 8.0156055 + 118000 57.110131 2000 7.9150786 + 119000 57.8533 2000 7.5310892 + 120000 58.599064 2000 7.2940498 + 121000 59.340753 2000 6.8347898 + 122000 60.084676 2000 6.696484 + 123000 60.826952 2000 6.7799146 + 124000 61.569413 2000 6.7901567 + 125000 62.316334 2000 6.7532108 + 126000 63.061374 2000 6.762162 + 127000 63.806385 2000 6.6317366 + 128000 64.555969 2000 6.8246399 + 129000 65.308131 2000 6.9130358 + 130000 66.060967 2000 7.1750566 + 131000 66.809725 2000 6.9507379 + 132000 67.559796 2000 6.7987445 + 133000 68.314249 2000 6.8535775 + 134000 69.065513 2000 7.0255144 + 135000 69.817604 2000 6.7381064 + 136000 70.572079 2000 6.5567748 + 137000 71.324444 2000 6.2655395 + 138000 72.079147 2000 6.1923013 + 139000 72.831323 2000 6.0958081 + 140000 73.59117 2000 5.9185709 + 141000 74.343753 2000 5.9151241 + 142000 75.096509 2000 5.4743035 + 143000 75.852151 2000 5.438642 + 144000 76.605005 2000 4.6646664 + 145000 77.357571 2000 4.6899837 + 146000 78.113125 2000 4.5357917 + 147000 78.867751 2000 4.5993842 + 148000 79.625344 2000 4.7076884 + 149000 80.37992 2000 4.8306642 + 150000 81.143175 2000 4.8282147 + 151000 81.899326 2000 4.546308 + 152000 82.658645 2000 4.6700755 + 153000 83.41837 2000 4.7557633 + 154000 84.17509 2000 4.9004538 + 155000 84.934161 2000 5.0552949 + 156000 85.695466 2000 4.0672495 + 157000 86.453115 2000 3.5819543 + 158000 87.212663 2000 3.3533477 + 159000 87.967768 2000 3.3281001 + 160000 88.729631 2000 3.0831743 + 161000 89.498983 2000 3.0519269 + 162000 90.259424 2000 3.0951675 + 163000 91.019656 2000 2.9868352 + 164000 91.776359 2000 2.9195788 + 165000 92.536374 2000 2.5637813 + 166000 93.296332 2000 2.5553272 + 167000 94.05653 2000 2.0752912 + 168000 94.814559 2000 1.9689845 + 169000 95.576005 2000 1.9117916 + 170000 96.337863 2000 1.8568914 +Loop time of 96.3379 on 1 procs for 150000 steps with 2000 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 37.121 | 37.121 | 37.121 | 0.0 | 38.53 +Neigh | 0.8454 | 0.8454 | 0.8454 | 0.0 | 0.88 +Comm | 0.11506 | 0.11506 | 0.11506 | 0.0 | 0.12 +Output | 0.004431 | 0.004431 | 0.004431 | 0.0 | 0.00 +Modify | 56.517 | 56.517 | 56.517 | 0.0 | 58.67 +Other | | 1.735 | | | 1.80 + +Nlocal: 2000 ave 2000 max 2000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 15524 ave 15524 max 15524 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 15524 +Ave neighs/atom = 7.762 +Neighbor list builds = 388 +Dangerous builds = 0 + +# remove "plug" - need to redefine cylinder region & union + +region cylreg delete +region hopreg delete +region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open +region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2 + +region hopreg union 2 cylreg conereg + +unfix hopper3 +fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg + +run 100000 +Per MPI rank memory allocation (min/avg/max) = 18.64 | 18.64 | 18.64 Mbytes +Step CPU Atoms KinEng + 170000 0 2000 1.8568914 + 171000 0.75704765 2000 2.4011583 + 172000 1.5101345 2000 3.176628 + 173000 2.2556529 2000 4.5364486 + 174000 2.9946566 2000 6.5494125 + 175000 3.7253478 2000 9.1934319 + 176000 4.4570525 2000 12.25765 + 177000 5.1876664 2000 15.799657 + 178000 5.9178619 2000 19.982558 + 179000 6.6439464 2000 24.927165 + 180000 7.3749168 2000 30.428362 + 181000 8.1011977 2000 36.74232 + 182000 8.8207343 2000 43.820448 + 183000 9.5397925 2000 50.903222 + 184000 10.253098 2000 59.425781 + 185000 10.965505 2000 69.143119 + 186000 11.673319 2000 79.210705 + 187000 12.373966 2000 90.411346 + 188000 13.075475 2000 102.35389 + 189000 13.770632 2000 114.93888 + 190000 14.469445 2000 128.63341 + 191000 15.158381 2000 143.44526 + 192000 15.846267 2000 159.04574 + 193000 16.527754 2000 174.3114 + 194000 17.204808 2000 190.42123 + 195000 17.881059 2000 207.70459 + 196000 18.556555 2000 224.90931 + 197000 19.229818 2000 242.64914 + 198000 19.905086 2000 261.48312 + 199000 20.578518 2000 281.28308 + 200000 21.25632 2000 302.95108 + 201000 21.921347 2000 325.95534 + 202000 22.583873 2000 350.6874 + 203000 23.244724 2000 376.31773 + 204000 23.904842 2000 404.21947 + 205000 24.562788 2000 432.96116 + 206000 25.217762 2000 462.4113 + 207000 25.875814 2000 491.91207 + 208000 26.531285 2000 522.15395 + 209000 27.184766 2000 553.1024 + 210000 27.842961 2000 585.7133 + 211000 28.489339 2000 619.96357 + 212000 29.139612 2000 653.96189 + 213000 29.783866 2000 689.8027 + 214000 30.426881 2000 727.28401 + 215000 31.06706 2000 766.40354 + 216000 31.706399 2000 805.65433 + 217000 32.343033 2000 845.40981 + 218000 32.989384 2000 884.24637 + 219000 33.633664 2000 923.5998 + 220000 34.285172 2000 965.01779 + 221000 34.931959 2000 1009.1763 + 222000 35.571624 2000 1054.7789 + 223000 36.207868 2000 1101.9922 + 224000 36.836062 2000 1151.1205 + 225000 37.464514 2000 1201.3979 + 226000 38.09746 2000 1252.4054 + 227000 38.732507 1999 1296.6784 + 228000 39.371367 1997 1342.3466 + 229000 40.012553 1992 1368.8559 + 230000 40.652111 1977 1360.2259 + 231000 41.275478 1965 1340.3793 + 232000 41.892734 1953 1318.8318 + 233000 42.50588 1938 1295.5667 + 234000 43.121427 1924 1270.0641 + 235000 43.740727 1914 1258.296 + 236000 44.359241 1902 1224.3945 + 237000 44.979463 1899 1248.3905 + 238000 45.597358 1885 1206.9229 + 239000 46.210114 1875 1195.5429 + 240000 46.818148 1861 1142.6591 + 241000 47.411079 1851 1131.5523 + 242000 48.002522 1841 1116.8741 + 243000 48.594254 1830 1099.9978 + 244000 49.191798 1822 1078.6068 + 245000 49.791332 1814 1072.1498 + 246000 50.389728 1803 1020.7842 + 247000 50.984212 1794 1000.1936 + 248000 51.571047 1781 942.02462 + 249000 52.149428 1772 916.83697 + 250000 52.726202 1758 825.10751 + 251000 53.29913 1748 789.06351 + 252000 53.871912 1739 753.92258 + 253000 54.441009 1729 697.83686 + 254000 55.010203 1718 648.98541 + 255000 55.573602 1710 620.38129 + 256000 56.134709 1705 622.43466 + 257000 56.701827 1700 595.79102 + 258000 57.264463 1698 608.49223 + 259000 57.827817 1695 614.0119 + 260000 58.398994 1690 601.50438 + 261000 58.964611 1687 608.5892 + 262000 59.526765 1683 597.07884 + 263000 60.082729 1682 618.65041 + 264000 60.640105 1678 615.47784 + 265000 61.195717 1675 605.27658 + 266000 61.751087 1671 583.69853 + 267000 62.305546 1669 600.11043 + 268000 62.86105 1666 598.79807 + 269000 63.417551 1663 588.40338 + 270000 63.974486 1660 579.59387 +Loop time of 63.9745 on 1 procs for 100000 steps with 1660 atoms + +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 26.514 | 26.514 | 26.514 | 0.0 | 41.44 +Neigh | 0.60324 | 0.60324 | 0.60324 | 0.0 | 0.94 +Comm | 0.075881 | 0.075881 | 0.075881 | 0.0 | 0.12 +Output | 0.0029137 | 0.0029137 | 0.0029137 | 0.0 | 0.00 +Modify | 35.686 | 35.686 | 35.686 | 0.0 | 55.78 +Other | | 1.092 | | | 1.71 + +Nlocal: 1660 ave 1660 max 1660 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 11681 ave 11681 max 11681 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 11681 +Ave neighs/atom = 7.03675 +Neighbor list builds = 249 +Dangerous builds = 0 +Total wall time: 0:02:48 diff --git a/examples/granregion/log.27Nov18.granregion.funnel.g++.4 b/examples/granregion/log.27Nov18.granregion.funnel.g++.4 new file mode 100644 index 0000000000..67c307d212 --- /dev/null +++ b/examples/granregion/log.27Nov18.granregion.funnel.g++.4 @@ -0,0 +1,601 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +# pour particles into cone-shaped funnel, settle them, let them run out bottom + +variable name string funnel_pour + +thermo_modify flush yes +units si +variable PI equal 3.141592653589 +variable seed equal 14314 + +############################################### +# Geometry-related parameters +############################################### + +variable xlo equal 10 +variable xhi equal 40 +variable ylo equal 10 +variable yhi equal 40 +variable zlo equal -20 +variable zhi equal 50 + +variable xc equal 25 +variable yc equal 25 + +variable zconehi equal 50 +variable zconelo equal 10 +variable zcyllo equal 0 +variable radconelo equal 2 +variable radconehi equal 20 + +################################################ +# Particle sizes +################################################ + +variable rlo equal 0.25 +variable rhi equal 0.5 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.25 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.5 + +variable skin equal ${rhi} +variable skin equal 0.5 + +############################################### +# Granular contact parameters +############################################### + +variable coeffRes equal 0.1 +variable coeffFric equal 0.5 + +variable density equal 1.0 +variable EYoung equal 10^5 +variable Poisson equal 2.0/7.0 +variable GShear equal ${EYoung}/(2*(1+${Poisson})) +variable GShear equal 100000/(2*(1+${Poisson})) +variable GShear equal 100000/(2*(1+0.285714285714286)) + +variable gravity equal 1.0 + +variable reff equal 0.5*(${rhi}+${rlo}) +variable reff equal 0.5*(0.5+${rlo}) +variable reff equal 0.5*(0.5+0.25) +variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3 +variable meff equal 1*4.0/3.0*${PI}*${reff}^3 +variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3 +variable meff equal 1*4.0/3.0*3.141592653589*0.375^3 +variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo} +variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25 +variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi} +variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5 + +## Typical way to set kn, kt, etc.: +variable kn equal 4.0*${GShear}/(3*(1-${Poisson})) +variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson})) +variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286)) +variable kt equal 4.0*${GShear}/(2-${Poisson}) +variable kt equal 4.0*38888.8888888889/(2-${Poisson}) +variable kt equal 4.0*38888.8888888889/(2-0.285714285714286) + +variable a equal (-2.0*log(${coeffRes})/${PI})^2 +variable a equal (-2.0*log(0.1)/${PI})^2 +variable a equal (-2.0*log(0.1)/3.141592653589)^2 +variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556)) +variable gamma_t equal ${gamma_n}*0.5 +variable gamma_t equal 903.503751814138*0.5 + +variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0) +variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0) + +variable dt equal ${tcol}*0.05 +variable dt equal 0.00210943016014969*0.05 +timestep ${dt} +timestep 0.000105471508007485 + +############################################### +variable dumpfreq equal 1000 +variable logfreq equal 1000 + +newton off +atom_style sphere + +boundary p p f + +region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} +region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} +region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi} +region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi} +region boxreg block 10 40 10 40 ${zlo} ${zhi} +region boxreg block 10 40 10 40 -20 ${zhi} +region boxreg block 10 40 10 40 -20 50 +create_box 1 boxreg +Created orthogonal box = (10 10 -20) to (40 40 50) + 1 by 1 by 4 MPI processor grid + +pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 +pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 +pair_coeff * * + +neighbor ${skin} bin +neighbor 0.5 bin +thermo ${logfreq} +thermo 1000 + +comm_style brick +comm_modify mode multi group all vel yes +balance 1.1 shift xyz 20 1.1 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 30, bins = 1 1 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +fix bal all balance 10000 1.1 shift xyz 20 1.01 + +####################### Options specific to pouring ######################### + +# insertion region for fix/pour + +region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box +region insreg cylinder z 25 ${yc} 10 30 50 side in units box +region insreg cylinder z 25 25 10 30 50 side in units box + +# define cone and cylinder regions - see lammps doc on region command +# note new open options + +region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open +region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2 +region cylreg cylinder z 25 25 2 0 10 side in units box open 2 + +region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open +region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2 +region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2 + +region hopreg union 2 conereg cylreg + +fix grav all gravity ${gravity} vector 0 0 -1 +fix grav all gravity 1 vector 0 0 -1 +fix 1 all nve/sphere + + +fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg + +fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density} +fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1 +Particle insertion: 3000 every 59965 steps, 2000 by step 1 + +#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z + +#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0 +#dump_modify 2 pad 6 + +thermo_style custom step cpu atoms ke +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) +thermo_modify flush yes lost warn + +# Initial run to fill up the cone + +run 20000 +Per MPI rank memory allocation (min/avg/max) = 6.05 | 6.05 | 6.05 Mbytes +Step CPU Atoms KinEng + 0 0 0 -0 + 1000 0.63366675 2000 -0 + 2000 1.0221362 2000 -0 + 3000 1.3905275 2000 -0 + 4000 1.7514329 2000 -0 + 5000 2.1040537 2000 -0 + 6000 2.4468088 2000 -0 + 7000 2.7853072 2000 -0 + 8000 3.1109948 2000 -0 + 9000 3.4281557 2000 -0 + 10000 3.7435207 2000 -0 + 11000 3.8612552 2000 -0 + 12000 3.9786677 2000 -0 + 13000 4.0988154 2000 -0 + 14000 4.2249811 2000 -0 + 15000 4.3562138 2000 -0 + 16000 4.4940333 2000 -0 + 17000 4.6394637 2000 -0 + 18000 4.7909062 2000 -0 + 19000 4.9482198 2000 -0 + 20000 5.1116607 2000 -0 +Loop time of 5.11176 on 4 procs for 20000 steps with 2000 atoms + +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.050997 | 0.14884 | 0.36048 | 32.0 | 2.91 +Neigh | 0.01374 | 0.025199 | 0.043743 | 7.0 | 0.49 +Comm | 0.063387 | 0.1781 | 0.29748 | 22.6 | 3.48 +Output | 0.0016627 | 0.0060938 | 0.015082 | 6.8 | 0.12 +Modify | 1.1198 | 1.987 | 3.7195 | 72.6 | 38.87 +Other | | 2.767 | | | 54.12 + +Nlocal: 500 ave 505 max 493 min +Histogram: 1 0 0 0 0 1 0 1 0 1 +Nghost: 159.25 ave 254 max 71 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 397.5 ave 616 max 214 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 1590 +Ave neighs/atom = 0.795 +Neighbor list builds = 69 +Dangerous builds = 0 +unfix ins +run 150000 +Per MPI rank memory allocation (min/avg/max) = 12.37 | 12.51 | 12.7 Mbytes +Step CPU Atoms KinEng + 20000 0 2000 6443.7665 + 21000 0.11261106 2000 6572.3531 + 22000 0.23091817 2000 6723.8376 + 23000 0.35577631 2000 6853.1812 + 24000 0.48790455 2000 6976.0209 + 25000 0.63509274 2000 7096.9955 + 26000 0.78251743 2000 7215.5795 + 27000 0.93707466 2000 7349.2382 + 28000 1.1032445 2000 7471.8719 + 29000 1.2721858 2000 7574.8228 + 30000 1.449265 2000 7659.3836 + 31000 1.5742557 2000 7703.6856 + 32000 1.7076068 2000 7644.279 + 33000 1.8527873 2000 7526.6944 + 34000 2.009855 2000 7370.0821 + 35000 2.1766446 2000 7193.0459 + 36000 2.3557482 2000 6990.9912 + 37000 2.5468907 2000 6849.286 + 38000 2.7480681 2000 6701.7548 + 39000 2.9574037 2000 6538.6915 + 40000 3.1807711 2000 6382.3209 + 41000 3.3486595 2000 6216.424 + 42000 3.5162592 2000 6091.29 + 43000 3.687057 2000 5945.3256 + 44000 3.8662596 2000 5840.875 + 45000 4.0557241 2000 5649.763 + 46000 4.2541051 2000 5476.2837 + 47000 4.4571214 2000 5277.0701 + 48000 4.6628008 2000 5123.9796 + 49000 4.8686502 2000 4968.3344 + 50000 5.0788848 2000 4869.5754 + 51000 5.2552598 2000 4704.8517 + 52000 5.4428713 2000 4522.8978 + 53000 5.6520596 2000 4393.8047 + 54000 5.8613031 2000 4235.438 + 55000 6.0776098 2000 4082.3073 + 56000 6.2998042 2000 3901.0483 + 57000 6.5321434 2000 3718.0882 + 58000 6.7745438 2000 3504.621 + 59000 7.0237701 2000 3285.7484 + 60000 7.2791855 2000 3047.3386 + 61000 7.489058 2000 2875.4032 + 62000 7.7044094 2000 2647.83 + 63000 7.9194827 2000 2396.5343 + 64000 8.1429474 2000 2107.2113 + 65000 8.3745618 2000 1858.1977 + 66000 8.610673 2000 1615.8096 + 67000 8.8505244 2000 1416.5065 + 68000 9.0955915 2000 1206.8534 + 69000 9.3609676 2000 953.93974 + 70000 9.6382594 2000 766.9148 + 71000 9.8719468 2000 611.45063 + 72000 10.095534 2000 464.94805 + 73000 10.317962 2000 364.31415 + 74000 10.547287 2000 298.77524 + 75000 10.764052 2000 245.73022 + 76000 10.978769 2000 207.8035 + 77000 11.199921 2000 179.1305 + 78000 11.410296 2000 151.21032 + 79000 11.624499 2000 124.49675 + 80000 11.849562 2000 106.71504 + 81000 12.077449 2000 93.299034 + 82000 12.306904 2000 81.220408 + 83000 12.539016 2000 67.383955 + 84000 12.773108 2000 57.287165 + 85000 13.009487 2000 49.255887 + 86000 13.252544 2000 44.082536 + 87000 13.502564 2000 40.193574 + 88000 13.747198 2000 36.903867 + 89000 13.993028 2000 33.55332 + 90000 14.240036 2000 30.730912 + 91000 14.472719 2000 28.650574 + 92000 14.708542 2000 26.377609 + 93000 14.948106 2000 24.433165 + 94000 15.186653 2000 22.933076 + 95000 15.428022 2000 22.31788 + 96000 15.676323 2000 20.829124 + 97000 15.916326 2000 19.401354 + 98000 16.160197 2000 18.943699 + 99000 16.404796 2000 17.690599 + 100000 16.659731 2000 17.215943 + 101000 16.904498 2000 15.948087 + 102000 17.150993 2000 15.140324 + 103000 17.39584 2000 14.885674 + 104000 17.643707 2000 14.414752 + 105000 17.889343 2000 14.270676 + 106000 18.136159 2000 13.943799 + 107000 18.383653 2000 13.840145 + 108000 18.630952 2000 12.826341 + 109000 18.878218 2000 12.209012 + 110000 19.125558 2000 11.916194 + 111000 19.3726 2000 11.970849 + 112000 19.621494 2000 11.56909 + 113000 19.869978 2000 11.390562 + 114000 20.123402 2000 11.276545 + 115000 20.370963 2000 11.171298 + 116000 20.619975 2000 11.686225 + 117000 20.869585 2000 11.379805 + 118000 21.118875 2000 10.539511 + 119000 21.36837 2000 10.064595 + 120000 21.629511 2000 10.003722 + 121000 21.877867 2000 9.6974586 + 122000 22.127922 2000 9.7156209 + 123000 22.378215 2000 9.615256 + 124000 22.630463 2000 8.8979008 + 125000 22.882154 2000 8.2220003 + 126000 23.135763 2000 8.3153866 + 127000 23.392389 2000 8.0945497 + 128000 23.645521 2000 7.8942467 + 129000 23.89965 2000 7.4794776 + 130000 24.153195 2000 7.3635341 + 131000 24.406239 2000 7.5757743 + 132000 24.66016 2000 7.7047492 + 133000 24.914093 2000 8.0142133 + 134000 25.173429 2000 8.1716714 + 135000 25.433318 2000 7.7803343 + 136000 25.692997 2000 6.3545482 + 137000 25.947787 2000 6.313769 + 138000 26.200427 2000 6.4948596 + 139000 26.452514 2000 6.6183259 + 140000 26.714963 2000 6.7922281 + 141000 26.968235 2000 7.0752448 + 142000 27.220962 2000 7.2328717 + 143000 27.474819 2000 7.626453 + 144000 27.728029 2000 7.4576787 + 145000 27.981958 2000 7.124435 + 146000 28.236591 2000 7.2581589 + 147000 28.489842 2000 7.0622049 + 148000 28.744432 2000 7.1672801 + 149000 28.998739 2000 7.3248363 + 150000 29.253511 2000 7.0092266 + 151000 29.50567 2000 6.8124438 + 152000 29.759836 2000 6.9808705 + 153000 30.015359 2000 7.1516731 + 154000 30.275488 2000 6.6245443 + 155000 30.533407 2000 5.5867165 + 156000 30.788683 2000 5.318949 + 157000 31.043126 2000 5.1195805 + 158000 31.297011 2000 5.2045485 + 159000 31.551327 2000 5.24992 + 160000 31.807728 2000 5.3270577 + 161000 32.061371 2000 4.995281 + 162000 32.315467 2000 5.0755874 + 163000 32.57628 2000 5.0788135 + 164000 32.83119 2000 4.5917317 + 165000 33.085634 2000 4.6255452 + 166000 33.344148 2000 4.2563299 + 167000 33.599342 2000 3.3808566 + 168000 33.853488 2000 3.218931 + 169000 34.121464 2000 3.0839289 + 170000 34.378727 2000 3.0358838 +Loop time of 34.3788 on 4 procs for 150000 steps with 2000 atoms + +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.5861 | 10.058 | 12.152 | 68.4 | 29.26 +Neigh | 0.17612 | 0.25274 | 0.30005 | 9.2 | 0.74 +Comm | 1.5024 | 2.6626 | 3.4174 | 44.9 | 7.74 +Output | 0.006542 | 0.019532 | 0.046425 | 11.5 | 0.06 +Modify | 11.945 | 14.674 | 16.29 | 42.7 | 42.68 +Other | | 6.711 | | | 19.52 + +Nlocal: 500 ave 508 max 489 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Nghost: 446.75 ave 708 max 191 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 4498 ave 5441 max 3786 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 17992 +Ave neighs/atom = 8.996 +Neighbor list builds = 403 +Dangerous builds = 0 + +# remove "plug" - need to redefine cylinder region & union + +region cylreg delete +region hopreg delete +region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open +region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2 +region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2 + +region hopreg union 2 cylreg conereg + +unfix hopper3 +fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg +fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg + +run 100000 +Per MPI rank memory allocation (min/avg/max) = 13.68 | 15.35 | 16.59 Mbytes +Step CPU Atoms KinEng + 170000 0 2000 3.0358838 + 171000 0.25455499 2000 3.7725185 + 172000 0.50768304 2000 4.727285 + 173000 0.76122355 2000 5.9840449 + 174000 1.0141416 2000 8.0335022 + 175000 1.2750733 2000 10.177259 + 176000 1.5277736 2000 13.655163 + 177000 1.7810826 2000 17.987975 + 178000 2.0348532 2000 23.266471 + 179000 2.2915859 2000 29.266364 + 180000 2.547174 2000 35.84089 + 181000 2.8009758 2000 43.130989 + 182000 3.0531759 2000 51.177142 + 183000 3.3130636 2000 60.031831 + 184000 3.5651338 2000 69.52374 + 185000 3.8185399 2000 79.941907 + 186000 4.070199 2000 91.195382 + 187000 4.3204038 2000 102.1696 + 188000 4.5699775 2000 112.73657 + 189000 4.8184452 2000 123.57252 + 190000 5.0653601 2000 135.59942 + 191000 5.3119307 2000 147.37757 + 192000 5.5574484 2000 159.12931 + 193000 5.8029084 2000 170.90271 + 194000 6.0463562 2000 185.71189 + 195000 6.2883332 2000 201.83733 + 196000 6.5281694 2000 218.30785 + 197000 6.7682493 2000 236.05694 + 198000 7.0084231 2000 255.23099 + 199000 7.2519951 2000 273.94566 + 200000 7.5010133 2000 293.91107 + 201000 7.7396591 2000 316.52142 + 202000 7.9784184 2000 340.91391 + 203000 8.224021 2000 364.81801 + 204000 8.4597676 2000 390.06478 + 205000 8.6934731 2000 415.90918 + 206000 8.9342225 2000 441.0995 + 207000 9.1714027 2000 467.40314 + 208000 9.4081488 2000 494.93631 + 209000 9.6457636 2000 524.70539 + 210000 9.8831718 2000 556.52058 + 211000 10.118018 2000 589.36821 + 212000 10.3541 2000 622.6887 + 213000 10.587226 2000 657.05888 + 214000 10.820744 2000 691.14292 + 215000 11.055785 2000 726.94959 + 216000 11.298702 2000 762.92802 + 217000 11.534793 2000 801.23648 + 218000 11.769849 2000 841.1559 + 219000 12.000917 2000 882.4342 + 220000 12.232812 2000 924.8466 + 221000 12.461166 2000 968.86229 + 222000 12.698451 2000 1013.1381 + 223000 12.930287 2000 1058.2988 + 224000 13.172862 2000 1105.2911 + 225000 13.405001 2000 1152.8617 + 226000 13.633187 1999 1197.6777 + 227000 13.857126 1998 1243.1211 + 228000 14.079622 1992 1262.1402 + 229000 14.303362 1987 1281.9162 + 230000 14.530392 1973 1264.0674 + 231000 14.756486 1964 1277.8347 + 232000 14.984495 1953 1266.7926 + 233000 15.213102 1940 1244.0038 + 234000 15.441666 1925 1206.4472 + 235000 15.667547 1914 1193.33 + 236000 15.895047 1901 1160.4096 + 237000 16.120833 1890 1141.6816 + 238000 16.346628 1883 1149.1584 + 239000 16.573303 1877 1141.7514 + 240000 16.801035 1871 1146.8662 + 241000 17.024775 1866 1152.561 + 242000 17.248651 1858 1148.2529 + 243000 17.47241 1847 1114.7239 + 244000 17.70222 1832 1070.9996 + 245000 17.926477 1824 1066.7549 + 246000 18.157588 1813 1027.1865 + 247000 18.378868 1804 1011.5024 + 248000 18.599988 1797 993.10451 + 249000 18.819007 1787 951.89778 + 250000 19.044634 1777 926.30475 + 251000 19.254408 1764 875.07091 + 252000 19.465788 1755 824.89358 + 253000 19.676327 1742 742.51957 + 254000 19.887648 1731 708.30958 + 255000 20.094912 1722 690.09761 + 256000 20.299963 1713 638.00218 + 257000 20.506153 1705 596.86839 + 258000 20.713994 1701 583.71937 + 259000 20.919755 1691 549.0049 + 260000 21.123122 1688 549.4278 + 261000 21.332215 1684 535.35719 + 262000 21.533673 1682 546.74031 + 263000 21.737042 1678 532.69324 + 264000 21.941306 1676 537.89254 + 265000 22.15135 1676 559.50898 + 266000 22.358371 1670 540.21452 + 267000 22.563236 1668 557.19857 + 268000 22.764648 1665 569.52869 + 269000 22.96391 1658 543.77057 + 270000 23.172415 1656 550.23716 +Loop time of 23.1725 on 4 procs for 100000 steps with 1656 atoms + +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.3849 | 7.3002 | 10.192 | 91.3 | 31.50 +Neigh | 0.14271 | 0.16781 | 0.19054 | 4.5 | 0.72 +Comm | 1.086 | 1.9721 | 2.6157 | 42.7 | 8.51 +Output | 0.0018437 | 0.013918 | 0.041359 | 13.5 | 0.06 +Modify | 8.6598 | 9.3198 | 9.8874 | 16.6 | 40.22 +Other | | 4.399 | | | 18.98 + +Nlocal: 414 ave 454 max 385 min +Histogram: 2 0 0 0 0 0 1 0 0 1 +Nghost: 395.25 ave 645 max 157 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 3498.5 ave 4524 max 2034 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 13994 +Ave neighs/atom = 8.45048 +Neighbor list builds = 240 +Dangerous builds = 0 +Total wall time: 0:01:02 diff --git a/examples/granregion/log.27Nov18.granregion.mixer.g++.1 b/examples/granregion/log.27Nov18.granregion.mixer.g++.1 new file mode 100644 index 0000000000..f2ba9d7122 --- /dev/null +++ b/examples/granregion/log.27Nov18.granregion.mixer.g++.1 @@ -0,0 +1,602 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable name string mixer + +thermo_modify flush yes +variable seed equal 14314 + +############################################### +# Particle parameters +################################################ + +variable rlo equal 0.3 +variable rhi equal 0.6 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.3 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.6 +variable skin equal ${rhi} +variable skin equal 0.6 + +variable coeffRes equal 0.1 +variable coeffFric equal 0.5 + +variable kn equal 10^5 +variable kt equal 0.2*${kn} +variable kt equal 0.2*100000 + +variable gravity equal 1.0 +variable density equal 1.0 + +variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo} +variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3 +variable a equal (-2.0*log(${coeffRes})/PI)^2 +variable a equal (-2.0*log(0.1)/PI)^2 +variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351)) +variable gamma_t equal ${gamma_n}*0.5 +variable gamma_t equal 806.699778405191*0.5 + +variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) +variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0) +variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0) +variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0) + +variable dt equal ${tcol}*0.02 +variable dt equal 0.00236257621510454*0.02 +timestep ${dt} +timestep 4.72515243020908e-05 + +############################################### + +variable dumpfreq equal 1000 +variable logfreq equal 1000 + +newton on +atom_style sphere + +boundary p p f + +region boxreg block 0 20 0 20 0 20 +create_box 1 boxreg +Created orthogonal box = (0 0 0) to (20 20 20) + 1 by 1 by 1 MPI processor grid + +pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 +pair_coeff * * + +neighbor ${skin} bin +neighbor 0.6 bin +thermo ${logfreq} +thermo 1000 + +comm_style brick +comm_modify mode multi group all vel yes +balance 1.1 shift xyz 20 1.1 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 20, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +fix bal all balance 10000 1.1 shift xyz 20 1.01 + +####################### Options specific to pouring ######################### + +region insreg cylinder z 10 10 8 10 18 side in units box +region cylreg cylinder z 10 10 10 0 20 side in units box + +variable theta equal (step/400000)*2*PI + +region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box +region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box + +region mixer intersect 3 cylreg b1 b2 side in + +fix grav all gravity ${gravity} vector 0 0 -1 +fix grav all gravity 1 vector 0 0 -1 +fix 1 all nve/sphere + +fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer + +fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1 +Particle insertion: 444 every 84653 steps, 1000 by step 169307 + +#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z + +#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0 +#dump_modify 2 pad 6 + +thermo_style custom step cpu atoms ke v_theta +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) +thermo_modify flush yes lost warn + +run 200000 +Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes +Step CPU Atoms KinEng v_theta + 0 0 0 -0 0 + 1000 0.15327144 444 -0 0.015707963 + 2000 0.30070925 444 -0 0.031415927 + 3000 0.44653535 444 -0 0.04712389 + 4000 0.59226131 444 -0 0.062831853 + 5000 0.73794818 444 -0 0.078539816 + 6000 0.88327622 444 -0 0.09424778 + 7000 1.0286083 444 -0 0.10995574 + 8000 1.1740625 444 -0 0.12566371 + 9000 1.3224797 444 -0 0.14137167 + 10000 1.4717772 444 -0 0.15707963 + 11000 1.6204555 444 -0 0.1727876 + 12000 1.7690799 444 -0 0.18849556 + 13000 1.918304 444 -0 0.20420352 + 14000 2.0670426 444 -0 0.21991149 + 15000 2.2157068 444 -0 0.23561945 + 16000 2.3642888 444 -0 0.25132741 + 17000 2.5129776 444 -0 0.26703538 + 18000 2.6614521 444 -0 0.28274334 + 19000 2.8100598 444 -0 0.2984513 + 20000 2.9591351 444 -0 0.31415927 + 21000 3.1073661 444 -0 0.32986723 + 22000 3.2557554 444 -0 0.34557519 + 23000 3.4041324 444 -0 0.36128316 + 24000 3.5526814 444 -0 0.37699112 + 25000 3.700824 444 -0 0.39269908 + 26000 3.8496137 444 -0 0.40840704 + 27000 3.9986103 444 -0 0.42411501 + 28000 4.1475384 444 -0 0.43982297 + 29000 4.2963772 444 -0 0.45553093 + 30000 4.4454341 444 -0 0.4712389 + 31000 4.5942066 444 -0 0.48694686 + 32000 4.7434044 444 -0 0.50265482 + 33000 4.893549 444 -0 0.51836279 + 34000 5.0427935 444 -0 0.53407075 + 35000 5.1920972 444 -0 0.54977871 + 36000 5.3411844 444 -0 0.56548668 + 37000 5.4904606 444 -0 0.58119464 + 38000 5.6397707 444 -0 0.5969026 + 39000 5.7900345 444 -0 0.61261057 + 40000 5.9405882 444 -0 0.62831853 + 41000 6.089345 444 -0 0.64402649 + 42000 6.2388933 444 -0 0.65973446 + 43000 6.3888056 444 -0 0.67544242 + 44000 6.5379841 444 -0 0.69115038 + 45000 6.6875141 444 -0 0.70685835 + 46000 6.8370855 444 -0 0.72256631 + 47000 6.9866009 444 -0 0.73827427 + 48000 7.1364653 444 -0 0.75398224 + 49000 7.2859883 444 -0 0.7696902 + 50000 7.4368248 444 -0 0.78539816 + 51000 7.5870779 444 -0 0.80110613 + 52000 7.7370813 444 -0 0.81681409 + 53000 7.8879561 444 -0 0.83252205 + 54000 8.0383027 444 -0 0.84823002 + 55000 8.1916294 444 -0 0.86393798 + 56000 8.3458471 444 -0 0.87964594 + 57000 8.5010631 444 -0 0.89535391 + 58000 8.6560545 444 -0 0.91106187 + 59000 8.8110209 444 -0 0.92676983 + 60000 8.9674675 444 -0 0.9424778 + 61000 9.1231239 444 -0 0.95818576 + 62000 9.2785382 444 -0 0.97389372 + 63000 9.4343674 444 -0 0.98960169 + 64000 9.5911541 444 -0 1.0053096 + 65000 9.7477772 444 -0 1.0210176 + 66000 9.9050307 444 -0 1.0367256 + 67000 10.063978 444 -0 1.0524335 + 68000 10.221835 444 -0 1.0681415 + 69000 10.37944 444 -0 1.0838495 + 70000 10.537409 444 -0 1.0995574 + 71000 10.695649 444 -0 1.1152654 + 72000 10.85453 444 -0 1.1309734 + 73000 11.013438 444 -0 1.1466813 + 74000 11.172689 444 -0 1.1623893 + 75000 11.332172 444 -0 1.1780972 + 76000 11.492824 444 -0 1.1938052 + 77000 11.653915 444 -0 1.2095132 + 78000 11.815798 444 -0 1.2252211 + 79000 11.97868 444 -0 1.2409291 + 80000 12.141392 444 -0 1.2566371 + 81000 12.30536 444 -0 1.272345 + 82000 12.468797 444 -0 1.288053 + 83000 12.633028 444 -0 1.303761 + 84000 12.797936 444 -0 1.3194689 + 85000 13.019726 888 -0 1.3351769 + 86000 13.333436 888 -0 1.3508848 + 87000 13.648179 888 -0 1.3665928 + 88000 13.962435 888 -0 1.3823008 + 89000 14.276158 888 -0 1.3980087 + 90000 14.590669 888 -0 1.4137167 + 91000 14.904268 888 -0 1.4294247 + 92000 15.216788 888 -0 1.4451326 + 93000 15.529868 888 -0 1.4608406 + 94000 15.843157 888 -0 1.4765485 + 95000 16.156564 888 -0 1.4922565 + 96000 16.469569 888 -0 1.5079645 + 97000 16.784048 888 -0 1.5236724 + 98000 17.100451 888 -0 1.5393804 + 99000 17.416338 888 -0 1.5550884 + 100000 17.733482 888 -0 1.5707963 + 101000 18.052522 888 -0 1.5865043 + 102000 18.371428 888 -0 1.6022123 + 103000 18.690222 888 -0 1.6179202 + 104000 19.009665 888 -0 1.6336282 + 105000 19.328189 888 -0 1.6493361 + 106000 19.647804 888 -0 1.6650441 + 107000 19.96805 888 -0 1.6807521 + 108000 20.286857 888 -0 1.69646 + 109000 20.607965 888 -0 1.712168 + 110000 20.931749 888 -0 1.727876 + 111000 21.251903 888 -0 1.7435839 + 112000 21.572158 888 -0 1.7592919 + 113000 21.892612 888 -0 1.7749998 + 114000 22.214408 888 -0 1.7907078 + 115000 22.535498 888 -0 1.8064158 + 116000 22.856752 888 -0 1.8221237 + 117000 23.178885 888 -0 1.8378317 + 118000 23.501127 888 -0 1.8535397 + 119000 23.8241 888 -0 1.8692476 + 120000 24.147258 888 -0 1.8849556 + 121000 24.472969 888 -0 1.9006636 + 122000 24.799108 888 -0 1.9163715 + 123000 25.125275 888 -0 1.9320795 + 124000 25.453866 888 -0 1.9477874 + 125000 25.784766 888 -0 1.9634954 + 126000 26.117013 888 -0 1.9792034 + 127000 26.448734 888 -0 1.9949113 + 128000 26.780032 888 -0 2.0106193 + 129000 27.113678 888 -0 2.0263273 + 130000 27.450001 888 -0 2.0420352 + 131000 27.782047 888 -0 2.0577432 + 132000 28.114287 888 -0 2.0734512 + 133000 28.446648 888 -0 2.0891591 + 134000 28.780438 888 -0 2.1048671 + 135000 29.116443 888 -0 2.120575 + 136000 29.451848 888 -0 2.136283 + 137000 29.787778 888 -0 2.151991 + 138000 30.12804 888 -0 2.1676989 + 139000 30.46814 888 -0 2.1834069 + 140000 30.808946 888 -0 2.1991149 + 141000 31.147584 888 -0 2.2148228 + 142000 31.486475 888 -0 2.2305308 + 143000 31.826754 888 -0 2.2462387 + 144000 32.165796 888 -0 2.2619467 + 145000 32.506074 888 -0 2.2776547 + 146000 32.847604 888 -0 2.2933626 + 147000 33.188988 888 -0 2.3090706 + 148000 33.532869 888 -0 2.3247786 + 149000 33.876629 888 -0 2.3404865 + 150000 34.221172 888 -0 2.3561945 + 151000 34.562559 888 -0 2.3719025 + 152000 34.904679 888 -0 2.3876104 + 153000 35.247727 888 -0 2.4033184 + 154000 35.591228 888 -0 2.4190263 + 155000 35.949192 888 -0 2.4347343 + 156000 36.320157 888 -0 2.4504423 + 157000 36.693571 888 -0 2.4661502 + 158000 37.069463 888 -0 2.4818582 + 159000 37.44221 888 -0 2.4975662 + 160000 37.81863 888 -0 2.5132741 + 161000 38.195121 888 -0 2.5289821 + 162000 38.573424 888 -0 2.54469 + 163000 38.950044 888 -0 2.560398 + 164000 39.331977 888 -0 2.576106 + 165000 39.714367 888 -0 2.5918139 + 166000 40.097099 888 -0 2.6075219 + 167000 40.477443 888 -0 2.6232299 + 168000 40.860404 888 -0 2.6389378 + 169000 41.244357 888 -0 2.6546458 + 170000 41.658126 1000 -0 2.6703538 + 171000 42.082517 1000 -0 2.6860617 + 172000 42.507502 1000 -0 2.7017697 + 173000 42.93363 1000 -0 2.7174776 + 174000 43.361133 1000 -0 2.7331856 + 175000 43.792381 1000 -0 2.7488936 + 176000 44.223827 1000 -0 2.7646015 + 177000 44.656581 1000 -0 2.7803095 + 178000 45.087615 1000 -0 2.7960175 + 179000 45.521129 1000 -0 2.8117254 + 180000 45.957808 1000 -0 2.8274334 + 181000 46.391451 1000 -0 2.8431414 + 182000 46.825486 1000 -0 2.8588493 + 183000 47.26091 1000 -0 2.8745573 + 184000 47.694263 1000 -0 2.8902652 + 185000 48.123312 1000 -0 2.9059732 + 186000 48.554081 1000 -0 2.9216812 + 187000 48.982617 1000 -0 2.9373891 + 188000 49.414355 1000 -0 2.9530971 + 189000 49.84753 1000 -0 2.9688051 + 190000 50.284462 1000 -0 2.984513 + 191000 50.71899 1000 -0 3.000221 + 192000 51.157278 1000 -0 3.0159289 + 193000 51.586171 1000 -0 3.0316369 + 194000 52.011691 1000 -0 3.0473449 + 195000 52.437732 1000 -0 3.0630528 + 196000 52.863703 1000 -0 3.0787608 + 197000 53.290403 1000 -0 3.0944688 + 198000 53.7191 1000 -0 3.1101767 + 199000 54.147195 1000 -0 3.1258847 + 200000 54.575967 1000 -0 3.1415927 +Loop time of 54.576 on 1 procs for 200000 steps with 1000 atoms + +Performance: 14960.907 tau/day, 3664.615 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.7989 | 3.7989 | 3.7989 | 0.0 | 6.96 +Neigh | 0.067629 | 0.067629 | 0.067629 | 0.0 | 0.12 +Comm | 0.63734 | 0.63734 | 0.63734 | 0.0 | 1.17 +Output | 0.0049303 | 0.0049303 | 0.0049303 | 0.0 | 0.01 +Modify | 49.1 | 49.1 | 49.1 | 0.0 | 89.97 +Other | | 0.9668 | | | 1.77 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 196 ave 196 max 196 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3910 ave 3910 max 3910 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3910 +Ave neighs/atom = 3.91 +Neighbor list builds = 219 +Dangerous builds = 0 +unfix ins +run 200000 +Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes +Step CPU Atoms KinEng v_theta + 200000 0 1000 0.93873133 3.1415927 + 201000 0.4261198 1000 0.93239566 3.1573006 + 202000 0.84928846 1000 0.90333835 3.1730086 + 203000 1.2720087 1000 0.89351493 3.1887165 + 204000 1.6929317 1000 0.87648478 3.2044245 + 205000 2.114043 1000 0.86818482 3.2201325 + 206000 2.5357664 1000 0.86033251 3.2358404 + 207000 2.9579847 1000 0.85442625 3.2515484 + 208000 3.3812878 1000 0.8517451 3.2672564 + 209000 3.8124611 1000 0.84406987 3.2829643 + 210000 4.2440236 1000 0.83964642 3.2986723 + 211000 4.6781921 1000 0.82994066 3.3143802 + 212000 5.1116509 1000 0.82908369 3.3300882 + 213000 5.5468135 1000 0.83115482 3.3457962 + 214000 5.9802556 1000 0.82680518 3.3615041 + 215000 6.4107294 1000 0.8223909 3.3772121 + 216000 6.8419023 1000 0.81872537 3.3929201 + 217000 7.2763367 1000 0.82446065 3.408628 + 218000 7.7160695 1000 0.82278874 3.424336 + 219000 8.1540956 1000 0.83017397 3.440044 + 220000 8.5917952 1000 0.82232305 3.4557519 + 221000 9.0296218 1000 0.82584132 3.4714599 + 222000 9.4719794 1000 0.82143909 3.4871678 + 223000 9.9180939 1000 0.82925587 3.5028758 + 224000 10.361852 1000 0.84546265 3.5185838 + 225000 10.803539 1000 0.84436452 3.5342917 + 226000 11.248456 1000 0.84849375 3.5499997 + 227000 11.695092 1000 0.8409057 3.5657077 + 228000 12.136044 1000 0.83139305 3.5814156 + 229000 12.579807 1000 0.83098473 3.5971236 + 230000 13.02219 1000 0.81335147 3.6128316 + 231000 13.463863 1000 0.78946649 3.6285395 + 232000 13.906293 1000 0.78807613 3.6442475 + 233000 14.348807 1000 0.79086655 3.6599554 + 234000 14.793175 1000 0.79358862 3.6756634 + 235000 15.238316 1000 0.79444252 3.6913714 + 236000 15.683342 1000 0.79392156 3.7070793 + 237000 16.12611 1000 0.80416034 3.7227873 + 238000 16.5711 1000 0.80365093 3.7384953 + 239000 17.014355 1000 0.80860323 3.7542032 + 240000 17.454467 1000 0.80245788 3.7699112 + 241000 17.89162 1000 0.79602568 3.7856191 + 242000 18.330859 1000 0.79023692 3.8013271 + 243000 18.769301 1000 0.79066782 3.8170351 + 244000 19.211293 1000 0.77671368 3.832743 + 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5.9376101 + 379000 80.307228 1000 0.67317549 5.9533181 + 380000 80.767418 1000 0.67691049 5.969026 + 381000 81.227579 1000 0.69231691 5.984734 + 382000 81.686924 1000 0.69998609 6.000442 + 383000 82.145783 1000 0.69328258 6.0161499 + 384000 82.604827 1000 0.69903908 6.0318579 + 385000 83.056443 1000 0.69455744 6.0475659 + 386000 83.507131 1000 0.68865933 6.0632738 + 387000 83.95695 1000 0.68630439 6.0789818 + 388000 84.404079 1000 0.6800564 6.0946897 + 389000 84.851053 1000 0.66747339 6.1103977 + 390000 85.298614 1000 0.65695883 6.1261057 + 391000 85.744507 1000 0.65659359 6.1418136 + 392000 86.191348 1000 0.65933663 6.1575216 + 393000 86.632782 1000 0.65170236 6.1732296 + 394000 87.074105 1000 0.65631817 6.1889375 + 395000 87.5177 1000 0.66205838 6.2046455 + 396000 87.963111 1000 0.65512694 6.2203535 + 397000 88.408348 1000 0.65266011 6.2360614 + 398000 88.854042 1000 0.64593806 6.2517694 + 399000 89.298754 1000 0.64940473 6.2674773 + 400000 89.745445 1000 0.66033435 6.2831853 +Loop time of 89.7455 on 1 procs for 200000 steps with 1000 atoms + +Performance: 9098.023 tau/day, 2228.525 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 10.924 | 10.924 | 10.924 | 0.0 | 12.17 +Neigh | 0.10266 | 0.10266 | 0.10266 | 0.0 | 0.11 +Comm | 1.9424 | 1.9424 | 1.9424 | 0.0 | 2.16 +Output | 0.0056458 | 0.0056458 | 0.0056458 | 0.0 | 0.01 +Modify | 75.442 | 75.442 | 75.442 | 0.0 | 84.06 +Other | | 1.329 | | | 1.48 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 272 ave 272 max 272 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4933 ave 4933 max 4933 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4933 +Ave neighs/atom = 4.933 +Neighbor list builds = 171 +Dangerous builds = 0 +Total wall time: 0:02:24 diff --git a/examples/granregion/log.27Nov18.granregion.mixer.g++.4 b/examples/granregion/log.27Nov18.granregion.mixer.g++.4 new file mode 100644 index 0000000000..be690a7df5 --- /dev/null +++ b/examples/granregion/log.27Nov18.granregion.mixer.g++.4 @@ -0,0 +1,602 @@ +LAMMPS (27 Nov 2018) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +variable name string mixer + +thermo_modify flush yes +variable seed equal 14314 + +############################################### +# Particle parameters +################################################ + +variable rlo equal 0.3 +variable rhi equal 0.6 +variable dlo equal 2.0*${rlo} +variable dlo equal 2.0*0.3 +variable dhi equal 2.0*${rhi} +variable dhi equal 2.0*0.6 +variable skin equal ${rhi} +variable skin equal 0.6 + +variable coeffRes equal 0.1 +variable coeffFric equal 0.5 + +variable kn equal 10^5 +variable kt equal 0.2*${kn} +variable kt equal 0.2*100000 + +variable gravity equal 1.0 +variable density equal 1.0 + +variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo} +variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo} +variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3 +variable a equal (-2.0*log(${coeffRes})/PI)^2 +variable a equal (-2.0*log(0.1)/PI)^2 +variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a)) +variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351)) +variable gamma_t equal ${gamma_n}*0.5 +variable gamma_t equal 806.699778405191*0.5 + +variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) +variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0) +variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0) +variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0) + +variable dt equal ${tcol}*0.02 +variable dt equal 0.00236257621510454*0.02 +timestep ${dt} +timestep 4.72515243020908e-05 + +############################################### + +variable dumpfreq equal 1000 +variable logfreq equal 1000 + +newton on +atom_style sphere + +boundary p p f + +region boxreg block 0 20 0 20 0 20 +create_box 1 boxreg +Created orthogonal box = (0 0 0) to (20 20 20) + 1 by 2 by 2 MPI processor grid + +pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 +pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 +pair_coeff * * + +neighbor ${skin} bin +neighbor 0.6 bin +thermo ${logfreq} +thermo 1000 + +comm_style brick +comm_modify mode multi group all vel yes +balance 1.1 shift xyz 20 1.1 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 0 + ghost atom cutoff = 0 + binsize = 20, bins = 1 1 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton on, size, history + pair build: half/size/bin/newton + stencil: half/bin/3d/newton + bin: standard +fix bal all balance 10000 1.1 shift xyz 20 1.01 + +####################### Options specific to pouring ######################### + +region insreg cylinder z 10 10 8 10 18 side in units box +region cylreg cylinder z 10 10 10 0 20 side in units box + +variable theta equal (step/400000)*2*PI + +region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box +region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box + +region mixer intersect 3 cylreg b1 b2 side in + +fix grav all gravity ${gravity} vector 0 0 -1 +fix grav all gravity 1 vector 0 0 -1 +fix 1 all nve/sphere + +fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer +fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer + +fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density} +fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1 +Particle insertion: 444 every 84653 steps, 1000 by step 169307 + +#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z + +#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0 +#dump_modify 2 pad 6 + +thermo_style custom step cpu atoms ke v_theta +WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:705) +thermo_modify flush yes lost warn + +run 200000 +Per MPI rank memory allocation (min/avg/max) = 5.817 | 5.817 | 5.817 Mbytes +Step CPU Atoms KinEng v_theta + 0 0 0 -0 0 + 1000 0.096722603 444 -0 0.015707963 + 2000 0.18796778 444 -0 0.031415927 + 3000 0.27916241 444 -0 0.04712389 + 4000 0.37111688 444 -0 0.062831853 + 5000 0.46224833 444 -0 0.078539816 + 6000 0.55190682 444 -0 0.09424778 + 7000 0.64120579 444 -0 0.10995574 + 8000 0.73025131 444 -0 0.12566371 + 9000 0.82121348 444 -0 0.14137167 + 10000 0.91006637 444 -0 0.15707963 + 11000 0.97034311 444 -0 0.1727876 + 12000 1.030247 444 -0 0.18849556 + 13000 1.0894752 444 -0 0.20420352 + 14000 1.1483686 444 -0 0.21991149 + 15000 1.2138393 444 -0 0.23561945 + 16000 1.2744856 444 -0 0.25132741 + 17000 1.3361425 444 -0 0.26703538 + 18000 1.3998857 444 -0 0.28274334 + 19000 1.4625463 444 -0 0.2984513 + 20000 1.5255082 444 -0 0.31415927 + 21000 1.5845048 444 -0 0.32986723 + 22000 1.6437175 444 -0 0.34557519 + 23000 1.7022173 444 -0 0.36128316 + 24000 1.7614172 444 -0 0.37699112 + 25000 1.8209105 444 -0 0.39269908 + 26000 1.8818901 444 -0 0.40840704 + 27000 1.9439991 444 -0 0.42411501 + 28000 2.0067189 444 -0 0.43982297 + 29000 2.0697014 444 -0 0.45553093 + 30000 2.1327429 444 -0 0.4712389 + 31000 2.1904151 444 -0 0.48694686 + 32000 2.2478669 444 -0 0.50265482 + 33000 2.3062997 444 -0 0.51836279 + 34000 2.3723967 444 -0 0.53407075 + 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atoms + +Performance: 39328.699 tau/day, 9633.409 timesteps/s +98.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.57172 | 0.93292 | 1.2995 | 37.1 | 4.49 +Neigh | 0.015648 | 0.018747 | 0.02175 | 2.1 | 0.09 +Comm | 3.17 | 3.6151 | 4.0856 | 23.0 | 17.41 +Output | 0.0051017 | 0.012686 | 0.033359 | 10.6 | 0.06 +Modify | 12.36 | 13.269 | 14.095 | 21.8 | 63.91 +Other | | 2.912 | | | 14.03 + +Nlocal: 250 ave 270 max 230 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Nghost: 297 ave 337 max 234 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 982.5 ave 1580 max 496 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 3930 +Ave neighs/atom = 3.93 +Neighbor list builds = 218 +Dangerous builds = 0 +unfix ins +run 200000 +Per MPI rank memory allocation (min/avg/max) = 12 | 12.19 | 12.35 Mbytes +Step CPU Atoms KinEng v_theta + 200000 0 1000 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6.2831853 +Loop time of 33.7298 on 4 procs for 200000 steps with 1000 atoms + +Performance: 24207.249 tau/day, 5929.470 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.6748 | 2.6848 | 3.6646 | 58.4 | 7.96 +Neigh | 0.021206 | 0.026438 | 0.03191 | 3.1 | 0.08 +Comm | 6.133 | 7.3745 | 8.6652 | 45.0 | 21.86 +Output | 0.0053763 | 0.016101 | 0.044719 | 13.0 | 0.05 +Modify | 18.26 | 20.115 | 22.413 | 39.2 | 59.64 +Other | | 3.513 | | | 10.42 + +Nlocal: 250 ave 266 max 230 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 401.5 ave 476 max 325 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 1264 ave 1634 max 895 min +Histogram: 1 0 1 0 0 0 0 1 0 1 + +Total # of neighbors = 5056 +Ave neighs/atom = 5.056 +Neighbor list builds = 160 +Dangerous builds = 0 +Total wall time: 0:00:54 diff --git a/examples/granregion/log.6Oct16.granregion.box.g++.1 b/examples/granregion/log.6Oct16.granregion.box.g++.1 deleted file mode 100644 index ae2ec694e9..0000000000 --- a/examples/granregion/log.6Oct16.granregion.box.g++.1 +++ /dev/null @@ -1,468 +0,0 @@ -LAMMPS (5 Oct 2016) -# pouring spheres into container box - -units lj -atom_style sphere -boundary f f f -dimension 3 -comm_modify vel yes - -region box block -10 10 -10 10 -10 10 units box -create_box 2 box -Created orthogonal box = (-10 -10 -10) to (10 10 10) - 1 by 1 by 1 MPI processor grid - -pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 -pair_coeff * * gran/hooke - -region container block -6 6 -6 6 -6 6 units box -fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 2 all nve/sphere -fix 3 all gravity 1.0 vector 0 0 -1 - -region slab block -2 2 -2 2 -2 2 units box -fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore -Particle insertion: 48 every 566 steps, 100 by step 1133 - -timestep 0.005 - -compute 1 all temp -compute_modify 1 dynamic yes - -compute 2 all temp/sphere -compute_modify 2 dynamic yes - -thermo 100 -thermo_style custom step atoms temp c_1 c_2 press -thermo_modify lost ignore -compute_modify thermo_temp dynamic yes - -#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03 -#dump_modify 2 pad 5 - -run 5000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 1.3 - binsize = 0.65 -> bins = 31 31 31 -Memory usage per processor = 0.201172 Mbytes -Step Atoms Temp c_1 c_2 Press - 0 0 0 0 0 0 - 100 21 0.54270729 0.54270729 0.26473526 0.0013567682 - 200 21 0.87606961 0.87606961 0.42735103 0.002190174 - 300 21 1.1428374 1.1428374 0.55748167 0.0028570936 - 400 21 1.3543103 1.3543103 0.66829516 0.0033857758 - 500 21 1.0677786 1.0677786 0.53582407 0.0045048164 - 600 56 0.6744286 0.6744286 0.3502938 0.0047464584 - 700 56 0.75569283 0.75569283 0.39779462 0.0051953882 - 800 56 0.61597505 0.61597505 0.32943642 0.0086022783 - 900 56 0.65260802 0.65260802 0.34474044 0.0059298996 - 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337 - 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094 - 1200 81 0.39112377 0.39112377 0.21690744 0.0086559347 - 1300 81 0.33302801 0.33302801 0.19110222 0.0033381288 - 1400 81 0.39333146 0.39333146 0.21220965 0.0041348597 - 1500 81 0.35493951 0.35493951 0.19924958 0.00373736 - 1600 81 0.34154491 0.34154491 0.19031147 0.005349672 - 1700 100 0.25598828 0.25598828 0.14171498 0.0092236643 - 1800 100 0.2114074 0.2114074 0.12162965 0.0027213483 - 1900 100 0.21810423 0.21810423 0.12176698 0.0036436034 - 2000 100 0.2553198 0.2553198 0.13900087 0.0032844504 - 2100 100 0.24809937 0.24809937 0.13753654 0.0088764373 - 2200 100 0.22455642 0.22455642 0.12500977 0.0043517009 - 2300 100 0.19586874 0.19586874 0.11064996 0.0055178814 - 2400 100 0.059619074 0.059619074 0.045535036 0.00079051539 - 2500 100 0.052222462 0.052222462 0.038563852 0.00098981299 - 2600 100 0.036930777 0.036930777 0.027579114 0.0012285499 - 2700 100 0.027937818 0.027937818 0.020587353 0.00063085447 - 2800 100 0.02103783 0.02103783 0.015469157 0.00050316582 - 2900 100 0.010408128 0.010408128 0.0084894275 0.00035440391 - 3000 100 0.0077664382 0.0077664382 0.0068149074 0.0011153614 - 3100 100 0.0088789208 0.0088789208 0.0070143391 0.00032679783 - 3200 100 0.0077683432 0.0077683432 0.0059711038 0.00044762363 - 3300 100 0.00411 0.00411 0.00372409 0.00015328221 - 3400 100 0.0039192171 0.0039192171 0.0032409072 9.3603399e-05 - 3500 100 0.0023532199 0.0023532199 0.0020924799 0.00049044152 - 3600 100 0.0022544513 0.0022544513 0.0019545724 8.1086108e-05 - 3700 100 0.0012696379 0.0012696379 0.0013134108 5.0058058e-05 - 3800 100 0.0012035225 0.0012035225 0.0012490584 6.0331967e-05 - 3900 100 0.00080361803 0.00080361803 0.00094424552 6.7229227e-05 - 4000 100 0.00060715659 0.00060715659 0.00076521759 6.7029916e-05 - 4100 100 0.00058510487 0.00058510487 0.00073844578 5.5867098e-05 - 4200 100 0.00046832309 0.00046832309 0.00060848748 5.3853715e-05 - 4300 100 0.00045207186 0.00045207186 0.00057825336 4.8367831e-05 - 4400 100 0.00041874845 0.00041874845 0.00053103589 8.666037e-05 - 4500 100 0.00041136295 0.00041136295 0.00052246056 6.0456585e-05 - 4600 100 0.00041021147 0.00041021147 0.0005190668 4.8701604e-05 - 4700 100 0.00037176253 0.00037176253 0.00049156279 5.8874891e-05 - 4800 100 0.0003262417 0.0003262417 0.00045551846 5.0610728e-05 - 4900 100 0.00028093583 0.00028093583 0.00042099654 4.6558605e-05 - 5000 100 0.00027730599 0.00027730599 0.00041664922 4.7053044e-05 -Loop time of 0.081454 on 1 procs for 5000 steps with 100 atoms - -Performance: 26518022.146 tau/day, 61384.311 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0085223 | 0.0085223 | 0.0085223 | 0.0 | 10.46 -Neigh | 0.01466 | 0.01466 | 0.01466 | 0.0 | 18.00 -Comm | 0.00076532 | 0.00076532 | 0.00076532 | 0.0 | 0.94 -Output | 0.00052285 | 0.00052285 | 0.00052285 | 0.0 | 0.64 -Modify | 0.05317 | 0.05317 | 0.05317 | 0.0 | 65.28 -Other | | 0.003814 | | | 4.68 - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 158 ave 158 max 158 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 158 -Ave neighs/atom = 1.58 -Neighbor list builds = 306 -Dangerous builds = 0 - -region container delete -variable theta equal (step-5000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1 -run 5000 -Memory usage per processor = 5.26337 Mbytes -Step Atoms Temp c_1 c_2 Press - 5000 100 0.00027730599 0.00027730599 0.00041664922 4.705763e-05 - 5100 100 0.60717077 0.60717077 0.33118944 0.010686501 - 5200 100 0.64991179 0.64991179 0.35498767 0.011370453 - 5300 100 0.72038713 0.72038713 0.38745069 0.010507667 - 5400 100 0.81357499 0.81357499 0.42946808 0.012920419 - 5500 100 0.90488411 0.90488411 0.46803321 0.015077428 - 5600 100 0.99065617 0.99065617 0.50811954 0.015556572 - 5700 100 1.0701203 1.0701203 0.54641187 0.016464366 - 5800 100 1.1351242 1.1351242 0.57607707 0.017832476 - 5900 100 1.1883602 1.1883602 0.60022389 0.019571838 - 6000 100 1.2153421 1.2153421 0.61245652 0.020549414 - 6100 100 1.2369293 1.2369293 0.62229634 0.01827529 - 6200 100 1.2556883 1.2556883 0.63207905 0.020286322 - 6300 100 1.2618555 1.2618555 0.63610311 0.019844583 - 6400 100 1.2671678 1.2671678 0.63873131 0.019817249 - 6500 100 1.2875312 1.2875312 0.64728693 0.020097362 - 6600 100 1.3014055 1.3014055 0.65413071 0.020000886 - 6700 100 1.2904021 1.2904021 0.6485358 0.020009625 - 6800 100 1.2962767 1.2962767 0.65088367 0.021340143 - 6900 100 1.3056081 1.3056081 0.65490644 0.020455771 - 7000 100 1.3116731 1.3116731 0.65766216 0.020475061 - 7100 100 1.319457 1.319457 0.66105016 0.020937651 - 7200 100 1.3213585 1.3213585 0.66207982 0.02120792 - 7300 100 1.3232411 1.3232411 0.66392391 0.021040683 - 7400 100 1.3300163 1.3300163 0.66599805 0.021202273 - 7500 100 1.3350122 1.3350122 0.66894534 0.021161833 - 7600 100 1.3344633 1.3344633 0.6688403 0.020871936 - 7700 100 1.3492825 1.3492825 0.6751371 0.021415859 - 7800 100 1.3539647 1.3539647 0.67757279 0.021306442 - 7900 100 1.3527157 1.3527157 0.67722774 0.021793531 - 8000 100 1.3526931 1.3526931 0.67713399 0.022973395 - 8100 100 1.3568279 1.3568279 0.67936578 0.021422428 - 8200 100 1.3599258 1.3599258 0.68113142 0.021397012 - 8300 100 1.3601893 1.3601893 0.68165656 0.021643375 - 8400 100 1.3752164 1.3752164 0.68788213 0.022208765 - 8500 100 1.3821458 1.3821458 0.69165274 0.022015877 - 8600 100 1.3784691 1.3784691 0.68964478 0.022144188 - 8700 100 1.3801422 1.3801422 0.6904093 0.0220402 - 8800 100 1.3900051 1.3900051 0.6947875 0.02216362 - 8900 100 1.3897902 1.3897902 0.69427134 0.023078569 - 9000 100 1.3909918 1.3909918 0.69456955 0.022043699 - 9100 100 1.3925028 1.3925028 0.69519141 0.022180156 - 9200 100 1.3923277 1.3923277 0.69512657 0.022113729 - 9300 100 1.3945193 1.3945193 0.69625374 0.022344694 - 9400 100 1.3960782 1.3960782 0.69705144 0.022181158 - 9500 100 1.3932407 1.3932407 0.69560365 0.022129998 - 9600 100 1.3925489 1.3925489 0.69532399 0.022124653 - 9700 100 1.3935299 1.3935299 0.69581607 0.022258368 - 9800 100 1.3933949 1.3933949 0.69579137 0.022209028 - 9900 100 1.3934712 1.3934712 0.69587898 0.022214942 - 10000 100 1.3935828 1.3935828 0.69598655 0.022231414 -Loop time of 0.261407 on 1 procs for 5000 steps with 100 atoms - -Performance: 8262972.563 tau/day, 19127.251 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.042233 | 0.042233 | 0.042233 | 0.0 | 16.16 -Neigh | 0.035131 | 0.035131 | 0.035131 | 0.0 | 13.44 -Comm | 0.0010462 | 0.0010462 | 0.0010462 | 0.0 | 0.40 -Output | 0.00051785 | 0.00051785 | 0.00051785 | 0.0 | 0.20 -Modify | 0.17687 | 0.17687 | 0.17687 | 0.0 | 67.66 -Other | | 0.00561 | | | 2.15 - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 187 ave 187 max 187 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 187 -Ave neighs/atom = 1.87 -Neighbor list builds = 634 -Dangerous builds = 0 - -region container delete -region container block -6 6 -6 6 -6 6 units box -run 5000 -Memory usage per processor = 5.26337 Mbytes -Step Atoms Temp c_1 c_2 Press - 10000 100 1.3935828 1.3935828 0.69598655 0.02230659 - 10100 100 0.3402861 0.3402861 0.19584226 0.014767914 - 10200 100 0.19064555 0.19064555 0.12536788 0.0025413789 - 10300 100 0.13281358 0.13281358 0.10275768 0.002843208 - 10400 100 0.10124671 0.10124671 0.077914135 0.0017745353 - 10500 100 0.082636734 0.082636734 0.063857622 0.001419336 - 10600 100 0.066744462 0.066744462 0.051927437 0.0010830674 - 10700 100 0.060778462 0.060778462 0.047461784 0.0011418844 - 10800 100 0.043437178 0.043437178 0.032805669 0.0017050393 - 10900 100 0.036483219 0.036483219 0.027387805 0.00086936813 - 11000 100 0.027639076 0.027639076 0.021221241 0.00054920607 - 11100 100 0.023614696 0.023614696 0.018445634 0.00058724552 - 11200 100 0.020103248 0.020103248 0.015933089 0.00072830275 - 11300 100 0.018645345 0.018645345 0.014559759 0.0002319388 - 11400 100 0.015499672 0.015499672 0.01248828 0.00036020862 - 11500 100 0.013421296 0.013421296 0.010743248 0.00043093929 - 11600 100 0.011214892 0.011214892 0.0089653924 0.00059789544 - 11700 100 0.0086660806 0.0086660806 0.0070563902 0.00029684573 - 11800 100 0.0064777244 0.0064777244 0.0052946156 0.00046466386 - 11900 100 0.0059360881 0.0059360881 0.0048568813 8.361561e-05 - 12000 100 0.0045341025 0.0045341025 0.003883229 0.00016408047 - 12100 100 0.0042504415 0.0042504415 0.0036944958 6.5005147e-05 - 12200 100 0.0041367637 0.0041367637 0.0035928232 7.3025698e-05 - 12300 100 0.0037700129 0.0037700129 0.003283398 6.381318e-05 - 12400 100 0.0033494476 0.0033494476 0.0029274495 4.7731105e-05 - 12500 100 0.0030903175 0.0030903175 0.0027068073 6.797313e-05 - 12600 100 0.0026406999 0.0026406999 0.0023315387 0.0002371331 - 12700 100 0.0025020713 0.0025020713 0.0022367855 4.2787276e-05 - 12800 100 0.0022977381 0.0022977381 0.0020778307 3.9744567e-05 - 12900 100 0.002039634 0.002039634 0.0018862012 0.00011669223 - 13000 100 0.0018044702 0.0018044702 0.00171399 0.00013835538 - 13100 100 0.0016600965 0.0016600965 0.0015553191 3.2320019e-05 - 13200 100 0.0015596204 0.0015596204 0.001486374 1.9246911e-05 - 13300 100 0.001316505 0.001316505 0.0012105249 9.1469679e-05 - 13400 100 0.0012517536 0.0012517536 0.0011525753 4.815292e-05 - 13500 100 0.0010827608 0.0010827608 0.001038339 2.0913017e-05 - 13600 100 0.0009863908 0.0009863908 0.00095924929 9.7716736e-05 - 13700 100 0.00094543599 0.00094543599 0.00092425645 1.378887e-05 - 13800 100 0.00087893271 0.00087893271 0.00086801608 1.8981177e-05 - 13900 100 0.00080241572 0.00080241572 0.0007930026 5.0987122e-05 - 14000 100 0.00070705631 0.00070705631 0.00069238137 1.2900066e-05 - 14100 100 0.0006525032 0.0006525032 0.000637991 0.00010838464 - 14200 100 0.00059338444 0.00059338444 0.00057560454 7.3431324e-06 - 14300 100 0.00058641228 0.00058641228 0.00056944735 7.256852e-06 - 14400 100 0.00056221112 0.00056221112 0.00054625666 8.1343426e-06 - 14500 100 0.00055493127 0.00055493127 0.00053957583 1.1713058e-05 - 14600 100 0.00052854921 0.00052854921 0.00051816618 8.6527225e-06 - 14700 100 0.00052630581 0.00052630581 0.00051584277 6.4890475e-06 - 14800 100 0.00052563819 0.00052563819 0.00051493123 1.2687153e-05 - 14900 100 0.00052131364 0.00052131364 0.00050917244 7.4589995e-08 - 15000 100 0.00051902191 0.00051902191 0.00050725364 6.4228962e-06 -Loop time of 0.0895741 on 1 procs for 5000 steps with 100 atoms - -Performance: 24114113.723 tau/day, 55819.708 timesteps/s -99.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0098987 | 0.0098987 | 0.0098987 | 0.0 | 11.05 -Neigh | 0.0061045 | 0.0061045 | 0.0061045 | 0.0 | 6.81 -Comm | 0.00069976 | 0.00069976 | 0.00069976 | 0.0 | 0.78 -Output | 0.00049758 | 0.00049758 | 0.00049758 | 0.0 | 0.56 -Modify | 0.068435 | 0.068435 | 0.068435 | 0.0 | 76.40 -Other | | 0.003939 | | | 4.40 - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 160 ave 160 max 160 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 160 -Ave neighs/atom = 1.6 -Neighbor list builds = 111 -Dangerous builds = 0 - -region container delete -variable theta equal (step-15000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1 -run 5000 -Memory usage per processor = 5.26337 Mbytes -Step Atoms Temp c_1 c_2 Press - 15000 100 0.00051902191 0.00051902191 0.00050725364 6.4228962e-06 - 15100 100 1.1235353 1.1235353 0.72003773 0.013686681 - 15200 100 1.0778556 1.0778556 0.69137925 0.013478363 - 15300 100 1.069015 1.069015 0.69798184 0.014165255 - 15400 100 1.2249943 1.2249943 0.79096059 0.020933395 - 15500 100 1.5225664 1.5225664 0.94822282 0.023932611 - 15600 100 1.5867194 1.5867194 0.98143504 0.024565132 - 15700 100 1.6595267 1.6595267 1.0203985 0.025152432 - 15800 100 1.8188027 1.8188027 1.0857586 0.031597641 - 15900 100 1.9234102 1.9234102 1.1099361 0.032381895 - 16000 100 2.039435 2.039435 1.1656948 0.032501981 - 16100 100 2.17315 2.17315 1.2265552 0.032675825 - 16200 100 2.2017279 2.2017279 1.23995 0.028634878 - 16300 100 2.3510902 2.3510902 1.3055642 0.03248003 - 16400 100 2.373932 2.373932 1.3059254 0.031292969 - 16500 100 2.5010862 2.5010862 1.3607219 0.032322054 - 16600 100 2.4815092 2.4815092 1.3524159 0.031223889 - 16700 100 2.6549226 2.6549226 1.4383508 0.033713507 - 16800 100 2.8087564 2.8087564 1.5261538 0.036598837 - 16900 100 2.8653588 2.8653588 1.5649123 0.035890231 - 17000 100 2.903748 2.903748 1.5907716 0.038038745 - 17100 100 2.9679376 2.9679376 1.6195577 0.051771432 - 17200 100 2.9632377 2.9632377 1.6233074 0.039825751 - 17300 100 3.0436883 3.0436883 1.6591248 0.042862982 - 17400 100 3.0969015 3.0969015 1.6811582 0.042104811 - 17500 100 3.0827135 3.0827135 1.691414 0.045839327 - 17600 100 3.0854805 3.0854805 1.689399 0.041770144 - 17700 100 3.07523 3.07523 1.6685518 0.045104715 - 17800 100 2.9610899 2.9610899 1.6349099 0.039060791 - 17900 100 2.8002989 2.8002989 1.5665223 0.037917927 - 18000 100 2.9139644 2.9139644 1.6206891 0.050841302 - 18100 100 3.0134757 3.0134757 1.6673916 0.040967255 - 18200 100 3.0731184 3.0731184 1.6777507 0.043503474 - 18300 100 3.0915242 3.0915242 1.6843452 0.040157898 - 18400 100 3.098896 3.098896 1.6904524 0.039629218 - 18500 100 3.1651814 3.1651814 1.7290259 0.042604953 - 18600 100 3.353247 3.353247 1.8236992 0.045132486 - 18700 100 3.540156 3.540156 1.9078363 0.046602063 - 18800 100 3.6395129 3.6395129 1.9578976 0.045659959 - 18900 100 3.7638134 3.7638134 2.0179445 0.051061068 - 19000 100 3.7603453 3.7603453 2.003355 0.057123184 - 19100 100 3.9218495 3.9218495 2.0968869 0.057671742 - 19200 100 3.9924222 3.9924222 2.1321955 0.051824898 - 19300 100 3.9690887 3.9690887 2.1270643 0.054832867 - 19400 100 3.9408481 3.9408481 2.1146593 0.057020024 - 19500 100 3.8313782 3.8313782 2.0610797 0.055164704 - 19600 100 3.8317496 3.8317496 2.0668123 0.049840804 - 19700 100 3.6068628 3.6068628 1.964227 0.05142407 - 19800 100 3.5477437 3.5477437 1.9314948 0.051076014 - 19900 100 3.6526881 3.6526881 1.9855353 0.047130029 - 20000 100 3.7243709 3.7243709 2.0380212 0.048446835 -Loop time of 0.206397 on 1 procs for 5000 steps with 100 atoms - -Performance: 10465265.522 tau/day, 24225.152 timesteps/s -100.3% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.014297 | 0.014297 | 0.014297 | 0.0 | 6.93 -Neigh | 0.050213 | 0.050213 | 0.050213 | 0.0 | 24.33 -Comm | 0.0011115 | 0.0011115 | 0.0011115 | 0.0 | 0.54 -Output | 0.00051141 | 0.00051141 | 0.00051141 | 0.0 | 0.25 -Modify | 0.13415 | 0.13415 | 0.13415 | 0.0 | 65.00 -Other | | 0.006114 | | | 2.96 - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 142 ave 142 max 142 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 142 -Ave neighs/atom = 1.42 -Neighbor list builds = 899 -Dangerous builds = 0 - -region container delete -region container block -6 6 -6 6 -6 6 units box -run 5000 -Memory usage per processor = 5.26337 Mbytes -Step Atoms Temp c_1 c_2 Press - 20000 100 3.7243709 3.7243709 2.0380212 0.048156434 - 20100 100 1.1186527 1.1186527 0.69104385 0.014964891 - 20200 100 0.91445605 0.91445605 0.57005236 0.011324474 - 20300 100 0.8936601 0.8936601 0.55534411 0.011071843 - 20400 100 0.90773143 0.90773143 0.55999953 0.011254101 - 20500 100 0.91995508 0.91995508 0.55837916 0.011548541 - 20600 100 0.91682167 0.91682167 0.54095261 0.012563797 - 20700 100 0.97806337 0.97806337 0.56016442 0.012396925 - 20800 100 0.97778738 0.97778738 0.55606194 0.015441479 - 20900 100 0.77253213 0.77253213 0.44636799 0.011428992 - 21000 100 0.63053468 0.63053468 0.35995394 0.01005502 - 21100 100 0.25437539 0.25437539 0.16544433 0.004628738 - 21200 100 0.11828032 0.11828032 0.087911985 0.0037076362 - 21300 100 0.11219312 0.11219312 0.080957112 0.0015847347 - 21400 100 0.10765357 0.10765357 0.074676159 0.0022823419 - 21500 100 0.060787093 0.060787093 0.046135213 0.00091422949 - 21600 100 0.040447932 0.040447932 0.033050575 0.0013404194 - 21700 100 0.035227782 0.035227782 0.02916621 0.00138779 - 21800 100 0.03309101 0.03309101 0.026613861 0.00058184323 - 21900 100 0.031461843 0.031461843 0.024751985 0.0013090333 - 22000 100 0.021624144 0.021624144 0.017872639 0.0010893822 - 22100 100 0.016728267 0.016728267 0.01403934 0.00049128736 - 22200 100 0.016256915 0.016256915 0.013763903 0.00047288638 - 22300 100 0.01349256 0.01349256 0.011498343 0.0013508309 - 22400 100 0.010027007 0.010027007 0.0087924966 0.00030117996 - 22500 100 0.0107355 0.0107355 0.0088715062 0.001043188 - 22600 100 0.0095852245 0.0095852245 0.007965421 0.00028464236 - 22700 100 0.0072956464 0.0072956464 0.0062403843 0.00061636772 - 22800 100 0.0060874415 0.0060874415 0.0054788049 0.00021135824 - 22900 100 0.0059688159 0.0059688159 0.0049530273 0.00022094116 - 23000 100 0.0050218996 0.0050218996 0.0043518404 0.00022527705 - 23100 100 0.005022208 0.005022208 0.0043118432 0.00052482006 - 23200 100 0.0047096056 0.0047096056 0.0039698638 0.00026423471 - 23300 100 0.0039510068 0.0039510068 0.0034773285 0.0001891104 - 23400 100 0.0037308781 0.0037308781 0.0031763304 0.00027163016 - 23500 100 0.0036278619 0.0036278619 0.0030371899 0.00017961072 - 23600 100 0.0033598677 0.0033598677 0.0027586323 0.00015034494 - 23700 100 0.0028530843 0.0028530843 0.0024809444 0.00012294415 - 23800 100 0.0025388819 0.0025388819 0.0022812799 0.00018946676 - 23900 100 0.0021129272 0.0021129272 0.0019905358 0.00015816903 - 24000 100 0.0021010978 0.0021010978 0.0019864539 0.00017086049 - 24100 100 0.0022189886 0.0022189886 0.0020466911 0.00030932562 - 24200 100 0.0019226314 0.0019226314 0.0017933042 9.3246067e-05 - 24300 100 0.0016875781 0.0016875781 0.0015999656 9.9935458e-05 - 24400 100 0.0015929611 0.0015929611 0.001531011 9.7429139e-05 - 24500 100 0.0015143044 0.0015143044 0.0014044175 9.807117e-05 - 24600 100 0.0018595492 0.0018595492 0.0014740944 7.4734729e-05 - 24700 100 0.0011646988 0.0011646988 0.0010881356 6.1197025e-05 - 24800 100 0.0014641612 0.0014641612 0.0012316664 8.81462e-05 - 24900 100 0.001024996 0.001024996 0.00094311114 5.8776472e-05 - 25000 100 0.00097890442 0.00097890442 0.00090302317 3.3980657e-05 -Loop time of 0.0954661 on 1 procs for 5000 steps with 100 atoms - -Performance: 22625823.872 tau/day, 52374.592 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.01234 | 0.01234 | 0.01234 | 0.0 | 12.93 -Neigh | 0.015404 | 0.015404 | 0.015404 | 0.0 | 16.14 -Comm | 0.00077391 | 0.00077391 | 0.00077391 | 0.0 | 0.81 -Output | 0.000494 | 0.000494 | 0.000494 | 0.0 | 0.52 -Modify | 0.062222 | 0.062222 | 0.062222 | 0.0 | 65.18 -Other | | 0.004233 | | | 4.43 - -Nlocal: 100 ave 100 max 100 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 150 ave 150 max 150 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 150 -Ave neighs/atom = 1.5 -Neighbor list builds = 283 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/granregion/log.6Oct16.granregion.box.g++.4 b/examples/granregion/log.6Oct16.granregion.box.g++.4 deleted file mode 100644 index daaae2019e..0000000000 --- a/examples/granregion/log.6Oct16.granregion.box.g++.4 +++ /dev/null @@ -1,468 +0,0 @@ -LAMMPS (5 Oct 2016) -# pouring spheres into container box - -units lj -atom_style sphere -boundary f f f -dimension 3 -comm_modify vel yes - -region box block -10 10 -10 10 -10 10 units box -create_box 2 box -Created orthogonal box = (-10 -10 -10) to (10 10 10) - 1 by 2 by 2 MPI processor grid - -pair_style hybrid gran/hooke 4000.0 NULL 100.0 NULL 0.5 1 -pair_coeff * * gran/hooke - -region container block -6 6 -6 6 -6 6 units box -fix container all wall/gran/region hooke/history 4000.0 NULL 100.0 NULL 0.5 1 region container - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 2 all nve/sphere -fix 3 all gravity 1.0 vector 0 0 -1 - -region slab block -2 2 -2 2 -2 2 units box -fix ins all pour 100 2 4767548 vol 0.4 10 diam one 1.0 region slab ignore -Particle insertion: 48 every 566 steps, 100 by step 1133 - -timestep 0.005 - -compute 1 all temp -compute_modify 1 dynamic yes - -compute 2 all temp/sphere -compute_modify 2 dynamic yes - -thermo 100 -thermo_style custom step atoms temp c_1 c_2 press -thermo_modify lost ignore -compute_modify thermo_temp dynamic yes - -#dump 2 all image 100 image.*.jpg type type # zoom 1.4 adiam 1.0 box no 0.0 axes yes 0.9 0.03 -#dump_modify 2 pad 5 - -run 5000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 1.3 - binsize = 0.65 -> bins = 31 31 31 -Memory usage per processor = 0.0990257 Mbytes -Step Atoms Temp c_1 c_2 Press - 0 0 0 0 0 0 - 100 21 0.54270729 0.54270729 0.26473526 0.0013567682 - 200 21 0.87606961 0.87606961 0.42735103 0.002190174 - 300 21 1.1428374 1.1428374 0.55748167 0.0028570936 - 400 21 1.3543103 1.3543103 0.66829516 0.0033857758 - 500 21 1.0677786 1.0677786 0.53582407 0.0045048164 - 600 56 0.6744286 0.6744286 0.3502938 0.0047464584 - 700 56 0.75569283 0.75569283 0.39779462 0.0051953882 - 800 56 0.61597505 0.61597505 0.32943642 0.0086022783 - 900 56 0.65260802 0.65260802 0.34474044 0.0059298996 - 1000 56 0.51624952 0.51624952 0.28326898 0.0067827337 - 1100 56 0.46050076 0.46050076 0.25656319 0.0061891094 - 1200 81 0.39112377 0.39112377 0.21690744 0.0086559347 - 1300 81 0.33302801 0.33302801 0.19110222 0.0033381288 - 1400 81 0.39333146 0.39333146 0.21220965 0.0041348597 - 1500 81 0.35493951 0.35493951 0.19924958 0.00373736 - 1600 81 0.34154491 0.34154491 0.19031147 0.005349672 - 1700 100 0.25598828 0.25598828 0.14171498 0.0092236643 - 1800 100 0.2114074 0.2114074 0.12162965 0.0027213483 - 1900 100 0.21810423 0.21810423 0.12176698 0.0036436054 - 2000 100 0.2553198 0.2553198 0.13900087 0.0032844518 - 2100 100 0.24809936 0.24809936 0.13753654 0.0088764777 - 2200 100 0.22455625 0.22455625 0.12500973 0.0043515755 - 2300 100 0.19586871 0.19586871 0.11064996 0.0055176298 - 2400 100 0.059621411 0.059621411 0.045535517 0.00079910861 - 2500 100 0.052217518 0.052217518 0.038542594 0.0009759424 - 2600 100 0.036907358 0.036907358 0.027550263 0.0014047668 - 2700 100 0.027926944 0.027926944 0.020599405 0.00063362027 - 2800 100 0.020876282 0.020876282 0.015385856 0.00066161626 - 2900 100 0.010390963 0.010390963 0.0085038611 0.00026222195 - 3000 100 0.0080105974 0.0080105974 0.006995365 0.00059521652 - 3100 100 0.0087388005 0.0087388005 0.0069051613 0.00028045343 - 3200 100 0.0078828927 0.0078828927 0.0060159861 0.00014819289 - 3300 100 0.0039336821 0.0039336821 0.0036525886 0.0001439482 - 3400 100 0.0037684472 0.0037684472 0.0031531439 0.00010653386 - 3500 100 0.0023527874 0.0023527874 0.0020983632 6.3797052e-05 - 3600 100 0.0018768162 0.0018768162 0.0017248798 0.00014904114 - 3700 100 0.00135595 0.00135595 0.0013962044 6.2461444e-05 - 3800 100 0.0012673777 0.0012673777 0.0013074364 0.00028034063 - 3900 100 0.00081311806 0.00081311806 0.00095642595 7.9543605e-05 - 4000 100 0.00059774673 0.00059774673 0.00074849615 6.8190201e-05 - 4100 100 0.00052811986 0.00052811986 0.00067263919 5.012633e-05 - 4200 100 0.00049555855 0.00049555855 0.00061736675 4.9888372e-05 - 4300 100 0.00048274473 0.00048274473 0.00059050389 5.1381757e-05 - 4400 100 0.00047341333 0.00047341333 0.00058083446 5.02623e-05 - 4500 100 0.00046792237 0.00046792237 0.00057416894 4.9019652e-05 - 4600 100 0.00046035378 0.00046035378 0.00056694823 6.0353699e-05 - 4700 100 0.00038114933 0.00038114933 0.0004980117 6.5173515e-05 - 4800 100 0.0003783967 0.0003783967 0.00049488428 4.8463898e-05 - 4900 100 0.00027940611 0.00027940611 0.00041517649 5.0979155e-05 - 5000 100 0.00026071989 0.00026071989 0.00040045214 5.151673e-05 -Loop time of 0.0799825 on 4 procs for 5000 steps with 100 atoms - -Performance: 27005901.076 tau/day, 62513.660 timesteps/s -96.6% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00093961 | 0.0032012 | 0.0054553 | 3.8 | 4.00 -Neigh | 0.0032456 | 0.0046872 | 0.0061908 | 2.0 | 5.86 -Comm | 0.014328 | 0.02121 | 0.029619 | 4.7 | 26.52 -Output | 0.0011828 | 0.0014142 | 0.0015574 | 0.4 | 1.77 -Modify | 0.002455 | 0.013876 | 0.026567 | 9.6 | 17.35 -Other | | 0.03559 | | | 44.50 - -Nlocal: 25 ave 51 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 4.75 ave 11 max 0 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 39.5 ave 85 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 158 -Ave neighs/atom = 1.58 -Neighbor list builds = 305 -Dangerous builds = 0 - -region container delete -variable theta equal (step-5000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 0 0 1 -run 5000 -Memory usage per processor = 5.16122 Mbytes -Step Atoms Temp c_1 c_2 Press - 5000 100 0.00026071989 0.00026071989 0.00040045214 5.1497323e-05 - 5100 100 0.66352492 0.66352492 0.35750241 0.015948709 - 5200 100 0.6922229 0.6922229 0.37176131 0.011025479 - 5300 100 0.76307067 0.76307067 0.40325027 0.010979511 - 5400 100 0.83871418 0.83871418 0.43756084 0.012600965 - 5500 100 0.93090048 0.93090048 0.4817574 0.012306942 - 5600 100 0.98338567 0.98338567 0.50374148 0.015434412 - 5700 100 1.0455442 1.0455442 0.53265847 0.017959409 - 5800 100 1.1081511 1.1081511 0.56112842 0.018832417 - 5900 100 1.1724309 1.1724309 0.59276447 0.019257973 - 6000 100 1.1914813 1.1914813 0.60201665 0.019694573 - 6100 100 1.2417733 1.2417733 0.62578893 0.019616524 - 6200 100 1.2612898 1.2612898 0.63503847 0.020442394 - 6300 100 1.2657345 1.2657345 0.63714395 0.020498843 - 6400 100 1.2678009 1.2678009 0.63828941 0.019900919 - 6500 100 1.284156 1.284156 0.64724666 0.020147256 - 6600 100 1.3090278 1.3090278 0.65925035 0.02136883 - 6700 100 1.3122075 1.3122075 0.66136807 0.020782325 - 6800 100 1.3147107 1.3147107 0.66026206 0.022887611 - 6900 100 1.3185295 1.3185295 0.66157265 0.021249838 - 7000 100 1.3232771 1.3232771 0.66334852 0.021738995 - 7100 100 1.3375003 1.3375003 0.67017176 0.021997185 - 7200 100 1.3349835 1.3349835 0.66895884 0.022149977 - 7300 100 1.3388711 1.3388711 0.67061163 0.021662545 - 7400 100 1.338676 1.338676 0.67074642 0.021076102 - 7500 100 1.3409052 1.3409052 0.67205098 0.021664853 - 7600 100 1.3499236 1.3499236 0.67612412 0.021653422 - 7700 100 1.3479719 1.3479719 0.67510646 0.021873569 - 7800 100 1.3489138 1.3489138 0.67563223 0.021419315 - 7900 100 1.357018 1.357018 0.6795804 0.022201202 - 8000 100 1.3540513 1.3540513 0.67843711 0.02275761 - 8100 100 1.3560429 1.3560429 0.67947065 0.022421723 - 8200 100 1.3590694 1.3590694 0.6806094 0.022004213 - 8300 100 1.3592154 1.3592154 0.68083948 0.021923269 - 8400 100 1.3601392 1.3601392 0.68121418 0.022155184 - 8500 100 1.3622149 1.3622149 0.6824182 0.022126924 - 8600 100 1.3651697 1.3651697 0.68397342 0.022195287 - 8700 100 1.3679254 1.3679254 0.68540978 0.023609651 - 8800 100 1.3686254 1.3686254 0.68559712 0.02242291 - 8900 100 1.3761277 1.3761277 0.68897201 0.023594162 - 9000 100 1.379968 1.379968 0.69045216 0.022516846 - 9100 100 1.3784732 1.3784732 0.68955121 0.022836115 - 9200 100 1.376848 1.376848 0.6885551 0.02279321 - 9300 100 1.3799231 1.3799231 0.68964009 0.023105818 - 9400 100 1.3817992 1.3817992 0.69057466 0.023062265 - 9500 100 1.3836544 1.3836544 0.69156755 0.024363244 - 9600 100 1.388032 1.388032 0.69348762 0.024930983 - 9700 100 1.3943738 1.3943738 0.6965703 0.024448451 - 9800 100 1.3963094 1.3963094 0.6971039 0.02341203 - 9900 100 1.3995489 1.3995489 0.69881652 0.023502542 - 10000 100 1.3974742 1.3974742 0.69765474 0.02340004 -Loop time of 0.18267 on 4 procs for 5000 steps with 100 atoms - -Performance: 11824571.055 tau/day, 27371.692 timesteps/s -99.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0010765 | 0.012038 | 0.023519 | 9.9 | 6.59 -Neigh | 0.0057316 | 0.010541 | 0.015351 | 4.6 | 5.77 -Comm | 0.0067229 | 0.017007 | 0.028509 | 7.8 | 9.31 -Output | 0.0011928 | 0.002021 | 0.0027668 | 1.6 | 1.11 -Modify | 0.009697 | 0.053707 | 0.098413 | 19.0 | 29.40 -Other | | 0.08736 | | | 47.82 - -Nlocal: 25 ave 51 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 3.25 ave 8 max 0 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -Neighs: 46.75 ave 104 max 0 min -Histogram: 2 0 0 0 0 0 0 1 0 1 - -Total # of neighbors = 187 -Ave neighs/atom = 1.87 -Neighbor list builds = 633 -Dangerous builds = 0 - -region container delete -region container block -6 6 -6 6 -6 6 units box -run 5000 -Memory usage per processor = 5.16122 Mbytes -Step Atoms Temp c_1 c_2 Press - 10000 100 1.3974742 1.3974742 0.69765474 0.023347613 - 10100 100 0.34944285 0.34944285 0.20251378 0.019176827 - 10200 100 0.22524385 0.22524385 0.14368424 0.0033260831 - 10300 100 0.15243438 0.15243438 0.11070165 0.0064816535 - 10400 100 0.1143586 0.1143586 0.087867032 0.0024091961 - 10500 100 0.092025102 0.092025102 0.071291506 0.0030683413 - 10600 100 0.071051442 0.071051442 0.05700858 0.00100243 - 10700 100 0.058346771 0.058346771 0.04843626 0.0006073275 - 10800 100 0.048700232 0.048700232 0.039550383 0.00091511006 - 10900 100 0.036880936 0.036880936 0.029482183 0.0011698854 - 11000 100 0.028768807 0.028768807 0.023865852 0.0011980794 - 11100 100 0.022823005 0.022823005 0.018819891 0.0004639259 - 11200 100 0.016954703 0.016954703 0.014075803 0.00085142865 - 11300 100 0.015359685 0.015359685 0.01295219 0.00026241662 - 11400 100 0.012748378 0.012748378 0.011085291 0.00045626939 - 11500 100 0.010464459 0.010464459 0.0087024732 0.00029325411 - 11600 100 0.0099186727 0.0099186727 0.0080127406 0.00031388584 - 11700 100 0.0088308874 0.0088308874 0.0072317369 0.00017850972 - 11800 100 0.0081740195 0.0081740195 0.0066522963 0.00012282618 - 11900 100 0.0079005289 0.0079005289 0.0063346391 0.00010630403 - 12000 100 0.0066277573 0.0066277573 0.0054122601 5.4791661e-05 - 12100 100 0.00567928 0.00567928 0.0047331385 9.2668647e-05 - 12200 100 0.005282803 0.005282803 0.0043827202 8.7820361e-05 - 12300 100 0.0051590302 0.0051590302 0.0042806737 6.5433983e-05 - 12400 100 0.0049013329 0.0049013329 0.0040882737 6.2007733e-05 - 12500 100 0.0044725745 0.0044725745 0.0037535523 6.1132729e-05 - 12600 100 0.0043131884 0.0043131884 0.0035845765 5.3375706e-05 - 12700 100 0.0042020236 0.0042020236 0.0034902096 0.0001192142 - 12800 100 0.0041367453 0.0041367453 0.003433341 0.00011052418 - 12900 100 0.0039862367 0.0039862367 0.0033026224 5.2674711e-05 - 13000 100 0.0033163769 0.0033163769 0.0028118123 5.9042575e-05 - 13100 100 0.0030645983 0.0030645983 0.002571872 4.9521551e-05 - 13200 100 0.002808301 0.002808301 0.0023652684 3.4748246e-05 - 13300 100 0.002556475 0.002556475 0.0021699595 0.00042840611 - 13400 100 0.0023430405 0.0023430405 0.0019913198 2.2687303e-05 - 13500 100 0.0021422817 0.0021422817 0.0018017112 -6.7761855e-06 - 13600 100 0.0020993702 0.0020993702 0.001749657 2.5979707e-05 - 13700 100 0.0019871396 0.0019871396 0.0016647634 5.754995e-05 - 13800 100 0.0017311886 0.0017311886 0.0014696399 2.1585018e-05 - 13900 100 0.0016249641 0.0016249641 0.0013982224 2.0108931e-05 - 14000 100 0.0015874763 0.0015874763 0.0013613318 0.00018348921 - 14100 100 0.0013772541 0.0013772541 0.0012193388 1.9336869e-05 - 14200 100 0.0013587865 0.0013587865 0.0012054213 1.807845e-05 - 14300 100 0.0011824329 0.0011824329 0.0010348168 0.00017307518 - 14400 100 0.0011387278 0.0011387278 0.0010010725 1.4091757e-05 - 14500 100 0.0010441599 0.0010441599 0.00092205881 1.3630652e-05 - 14600 100 0.00096839518 0.00096839518 0.00086828535 1.2437299e-05 - 14700 100 0.00094215882 0.00094215882 0.00084418599 5.3989122e-05 - 14800 100 0.00077297853 0.00077297853 0.00070382005 8.5049867e-06 - 14900 100 0.00072181281 0.00072181281 0.00066110432 8.9324335e-06 - 15000 100 0.00070122327 0.00070122327 0.00063826734 3.4876262e-05 -Loop time of 0.0815294 on 4 procs for 5000 steps with 100 atoms - -Performance: 26493517.176 tau/day, 61327.586 timesteps/s -97.8% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.00076294 | 0.0033154 | 0.0062585 | 4.3 | 4.07 -Neigh | 0.0010953 | 0.0020078 | 0.002914 | 2.0 | 2.46 -Comm | 0.0021389 | 0.012184 | 0.023433 | 9.1 | 14.94 -Output | 0.0011332 | 0.0014591 | 0.0017147 | 0.7 | 1.79 -Modify | 0.00083971 | 0.017889 | 0.035367 | 12.7 | 21.94 -Other | | 0.04467 | | | 54.79 - -Nlocal: 25 ave 54 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 3.75 ave 8 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 37.5 ave 97 max 0 min -Histogram: 2 0 0 0 0 1 0 0 0 1 - -Total # of neighbors = 150 -Ave neighs/atom = 1.5 -Neighbor list builds = 120 -Dangerous builds = 0 - -region container delete -variable theta equal (step-15000)*(4.0*PI/5000) -region container block -6 6 -6 6 -6 6 units box rotate v_theta 0 0 0 1 1 1 -run 5000 -Memory usage per processor = 5.16122 Mbytes -Step Atoms Temp c_1 c_2 Press - 15000 100 0.00070122327 0.00070122327 0.00063826734 3.4742207e-05 - 15100 100 1.1981004 1.1981004 0.74046013 0.017300203 - 15200 100 1.2197457 1.2197457 0.75847511 0.016724637 - 15300 100 1.1794198 1.1794198 0.77076582 0.017228755 - 15400 100 1.4027714 1.4027714 0.87950036 0.021028602 - 15500 100 1.5514702 1.5514702 0.95040716 0.019935207 - 15600 100 1.8360404 1.8360404 1.0987247 0.02494663 - 15700 100 2.0317625 2.0317625 1.2004001 0.029286087 - 15800 100 2.0478625 2.0478625 1.189893 0.031660426 - 15900 100 2.1289888 2.1289888 1.2083316 0.028754408 - 16000 100 2.2261493 2.2261493 1.2550891 0.030665647 - 16100 100 2.3005184 2.3005184 1.29238 0.036511242 - 16200 100 2.4515818 2.4515818 1.3563253 0.033787104 - 16300 100 2.4524614 2.4524614 1.3571527 0.031905963 - 16400 100 2.5592541 2.5592541 1.405001 0.035688651 - 16500 100 2.5311864 2.5311864 1.3918694 0.032451265 - 16600 100 2.6471904 2.6471904 1.4481739 0.034763978 - 16700 100 2.7024085 2.7024085 1.4785065 0.037514299 - 16800 100 2.8116979 2.8116979 1.5403269 0.03585152 - 16900 100 2.9095374 2.9095374 1.5962283 0.038244982 - 17000 100 2.9228985 2.9228985 1.5978628 0.037971615 - 17100 100 2.983589 2.983589 1.6205713 0.038332341 - 17200 100 3.1245984 3.1245984 1.6925827 0.042532223 - 17300 100 3.1060575 3.1060575 1.6713928 0.052589575 - 17400 100 3.2494904 3.2494904 1.7567188 0.044783721 - 17500 100 3.2313349 3.2313349 1.7549177 0.044959213 - 17600 100 3.3928412 3.3928412 1.822978 0.052512199 - 17700 100 3.3064729 3.3064729 1.7924768 0.046624738 - 17800 100 3.1907518 3.1907518 1.7406131 0.042864325 - 17900 100 3.0224556 3.0224556 1.6641648 0.040151025 - 18000 100 3.105271 3.105271 1.7045599 0.047137803 - 18100 100 3.0293425 3.0293425 1.6626024 0.04198758 - 18200 100 3.139773 3.139773 1.7310307 0.040137164 - 18300 100 2.9732894 2.9732894 1.6555933 0.03777758 - 18400 100 3.1250324 3.1250324 1.739812 0.038542298 - 18500 100 3.1687407 3.1687407 1.7593494 0.041591022 - 18600 100 3.2880821 3.2880821 1.8169373 0.042503015 - 18700 100 3.4877047 3.4877047 1.9049979 0.048156272 - 18800 100 3.7982973 3.7982973 2.055323 0.049805341 - 18900 100 3.9922267 3.9922267 2.1260665 0.062688073 - 19000 100 3.8620284 3.8620284 2.0652184 0.064418518 - 19100 100 3.8757665 3.8757665 2.0615465 0.058600317 - 19200 100 3.9425495 3.9425495 2.1030375 0.053714175 - 19300 100 3.8589133 3.8589133 2.0485568 0.05531747 - 19400 100 3.9202395 3.9202395 2.0904529 0.056324297 - 19500 100 3.9748628 3.9748628 2.1114492 0.055590699 - 19600 100 3.8876771 3.8876771 2.0918436 0.052415532 - 19700 100 3.8975921 3.8975921 2.0755799 0.050647718 - 19800 100 3.7488333 3.7488333 2.0024562 0.056966734 - 19900 100 3.7818574 3.7818574 2.00915 0.050079148 - 20000 100 3.4510736 3.4510736 1.8525818 0.053548452 -Loop time of 0.156607 on 4 procs for 5000 steps with 100 atoms - -Performance: 13792452.627 tau/day, 31926.974 timesteps/s -98.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0030923 | 0.0049732 | 0.0071678 | 2.1 | 3.18 -Neigh | 0.012225 | 0.015592 | 0.017859 | 1.7 | 9.96 -Comm | 0.034876 | 0.037526 | 0.040807 | 1.1 | 23.96 -Output | 0.0013812 | 0.0015668 | 0.0017419 | 0.3 | 1.00 -Modify | 0.026932 | 0.044011 | 0.054787 | 5.0 | 28.10 -Other | | 0.05294 | | | 33.80 - -Nlocal: 25 ave 41 max 12 min -Histogram: 1 0 0 1 1 0 0 0 0 1 -Nghost: 3.25 ave 6 max 1 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 35.75 ave 59 max 9 min -Histogram: 1 0 0 0 0 1 1 0 0 1 - -Total # of neighbors = 143 -Ave neighs/atom = 1.43 -Neighbor list builds = 917 -Dangerous builds = 0 - -region container delete -region container block -6 6 -6 6 -6 6 units box -run 5000 -Memory usage per processor = 5.16122 Mbytes -Step Atoms Temp c_1 c_2 Press - 20000 100 3.4510736 3.4510736 1.8525818 0.053182767 - 20100 100 0.99241675 0.99241675 0.61590164 0.015233656 - 20200 100 0.92799489 0.92799489 0.55540992 0.011885237 - 20300 100 0.9171573 0.9171573 0.54477252 0.012926388 - 20400 100 0.86718407 0.86718407 0.5145422 0.011384414 - 20500 100 0.84470122 0.84470122 0.50181203 0.010482207 - 20600 100 0.93025469 0.93025469 0.53939952 0.011377044 - 20700 100 0.96631348 0.96631348 0.55772027 0.015287231 - 20800 100 0.90708015 0.90708015 0.52037018 0.014854537 - 20900 100 0.73319001 0.73319001 0.42824847 0.0092980012 - 21000 100 0.3371096 0.3371096 0.21272171 0.0061783554 - 21100 100 0.21771022 0.21771022 0.14128887 0.0082147558 - 21200 100 0.18133275 0.18133275 0.11945636 0.0055722731 - 21300 100 0.17117199 0.17117199 0.11048263 0.0027980106 - 21400 100 0.15741047 0.15741047 0.10346676 0.0023057723 - 21500 100 0.10045855 0.10045855 0.069905343 0.0023941181 - 21600 100 0.066094864 0.066094864 0.051285108 0.0022519002 - 21700 100 0.048622069 0.048622069 0.040662255 0.00073951939 - 21800 100 0.046829799 0.046829799 0.037431722 0.0015913976 - 21900 100 0.025308514 0.025308514 0.02092076 0.00064225773 - 22000 100 0.016326886 0.016326886 0.013588504 0.00087416572 - 22100 100 0.011892981 0.011892981 0.010417133 0.00080132313 - 22200 100 0.011974602 0.011974602 0.010342276 0.00044437732 - 22300 100 0.012567486 0.012567486 0.010294969 0.00048413872 - 22400 100 0.011676022 0.011676022 0.0091714238 0.00066567365 - 22500 100 0.0098737136 0.0098737136 0.0079252142 0.00024081335 - 22600 100 0.0052495523 0.0052495523 0.0047802341 0.00029167814 - 22700 100 0.0049396543 0.0049396543 0.0043570686 0.00019793167 - 22800 100 0.004469254 0.004469254 0.0038657445 0.00052965165 - 22900 100 0.0043837877 0.0043837877 0.0034611363 0.00045595698 - 23000 100 0.003439309 0.003439309 0.0028031344 0.00025784869 - 23100 100 0.0034805091 0.0034805091 0.0027537344 0.00012746906 - 23200 100 0.0045502061 0.0045502061 0.0032298328 0.00024006432 - 23300 100 0.0028553043 0.0028553043 0.0023107483 0.00012803066 - 23400 100 0.0022736412 0.0022736412 0.0018560302 0.0002706771 - 23500 100 0.0020966521 0.0020966521 0.0017106541 0.00014239612 - 23600 100 0.0018760993 0.0018760993 0.0015415318 0.00010892634 - 23700 100 0.0022362451 0.0022362451 0.0017014519 0.00012547256 - 23800 100 0.0017603403 0.0017603403 0.0014681398 0.00023372731 - 23900 100 0.0023396747 0.0023396747 0.0016700312 0.00017014305 - 24000 100 0.0012059144 0.0012059144 0.0009982224 3.6215959e-05 - 24100 100 0.0011739433 0.0011739433 0.00097155852 3.6169918e-05 - 24200 100 0.0011071139 0.0011071139 0.00092095478 8.8000847e-05 - 24300 100 0.0011078659 0.0011078659 0.00092073833 4.8706222e-05 - 24400 100 0.0011037562 0.0011037562 0.00091673546 3.7548502e-05 - 24500 100 0.00098422752 0.00098422752 0.00083054499 9.1151844e-05 - 24600 100 0.00097403646 0.00097403646 0.00082364881 5.0914687e-05 - 24700 100 0.00093082012 0.00093082012 0.00079047801 3.2230016e-05 - 24800 100 0.0009138973 0.0009138973 0.00075880177 2.8780789e-05 - 24900 100 0.0012881027 0.0012881027 0.00093025416 1.6385252e-05 - 25000 100 0.00076099168 0.00076099168 0.00065175575 9.417272e-06 -Loop time of 0.0846543 on 4 procs for 5000 steps with 100 atoms - -Performance: 25515528.493 tau/day, 59063.723 timesteps/s -98.9% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0010469 | 0.0037468 | 0.0067947 | 4.3 | 4.43 -Neigh | 0.0032442 | 0.0047541 | 0.0065064 | 2.0 | 5.62 -Comm | 0.0085762 | 0.016923 | 0.024509 | 5.8 | 19.99 -Output | 0.0011523 | 0.0014572 | 0.0016789 | 0.6 | 1.72 -Modify | 0.0017715 | 0.016296 | 0.031399 | 11.1 | 19.25 -Other | | 0.04148 | | | 49.00 - -Nlocal: 25 ave 50 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 6 ave 13 max 0 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 39 ave 80 max 0 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 156 -Ave neighs/atom = 1.56 -Neighbor list builds = 284 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/granregion/log.6Oct16.granregion.funnel.g++.1 b/examples/granregion/log.6Oct16.granregion.funnel.g++.1 deleted file mode 100644 index 86faeb3401..0000000000 --- a/examples/granregion/log.6Oct16.granregion.funnel.g++.1 +++ /dev/null @@ -1,608 +0,0 @@ -LAMMPS (5 Oct 2016) -# pour particles into cone-shaped funnel, settle them, let them run out bottom - -variable name string funnel_pour - -thermo_modify flush yes -units si -variable PI equal 3.141592653589 -variable seed equal 14314 - -############################################### -# Geometry-related parameters -############################################### - -variable xlo equal 10 -variable xhi equal 40 -variable ylo equal 10 -variable yhi equal 40 -variable zlo equal -20 -variable zhi equal 50 - -variable xc equal 25 -variable yc equal 25 - -variable zconehi equal 50 -variable zconelo equal 10 -variable zcyllo equal 0 -variable radconelo equal 2 -variable radconehi equal 20 - -################################################ -# Particle sizes -################################################ - -variable rlo equal 0.25 -variable rhi equal 0.5 -variable dlo equal 2.0*${rlo} -variable dlo equal 2.0*0.25 -variable dhi equal 2.0*${rhi} -variable dhi equal 2.0*0.5 - -variable skin equal ${rhi} -variable skin equal 0.5 - -############################################### -# Granular contact parameters -############################################### - -variable coeffRes equal 0.1 -variable coeffFric equal 0.5 - -variable density equal 1.0 -variable EYoung equal 10^5 -variable Poisson equal 2.0/7.0 -variable GShear equal ${EYoung}/(2*(1+${Poisson})) -variable GShear equal 100000/(2*(1+${Poisson})) -variable GShear equal 100000/(2*(1+0.285714285714286)) - -variable gravity equal 1.0 - -variable reff equal 0.5*(${rhi}+${rlo}) -variable reff equal 0.5*(0.5+${rlo}) -variable reff equal 0.5*(0.5+0.25) -variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3 -variable meff equal 1*4.0/3.0*${PI}*${reff}^3 -variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3 -variable meff equal 1*4.0/3.0*3.141592653589*0.375^3 -variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25 -variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5 - -## Typical way to set kn, kt, etc.: -variable kn equal 4.0*${GShear}/(3*(1-${Poisson})) -variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson})) -variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286)) -variable kt equal 4.0*${GShear}/(2-${Poisson}) -variable kt equal 4.0*38888.8888888889/(2-${Poisson}) -variable kt equal 4.0*38888.8888888889/(2-0.285714285714286) - -variable a equal (-2.0*log(${coeffRes})/${PI})^2 -variable a equal (-2.0*log(0.1)/${PI})^2 -variable a equal (-2.0*log(0.1)/3.141592653589)^2 -variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556)) -variable gamma_t equal ${gamma_n}*0.5 -variable gamma_t equal 903.503751814138*0.5 - -variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0) - -variable dt equal ${tcol}*0.05 -variable dt equal 0.00210943016014969*0.05 -timestep ${dt} -timestep 0.000105471508007485 - -############################################### -variable dumpfreq equal 1000 -variable logfreq equal 1000 - -newton off -atom_style sphere - -boundary p p f - -region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} -region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} -region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi} -region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi} -region boxreg block 10 40 10 40 ${zlo} ${zhi} -region boxreg block 10 40 10 40 -20 ${zhi} -region boxreg block 10 40 10 40 -20 50 -create_box 1 boxreg -Created orthogonal box = (10 10 -20) to (40 40 50) - 1 by 1 by 1 MPI processor grid - -pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 -pair_coeff * * - -neighbor ${skin} bin -neighbor 0.5 bin -thermo ${logfreq} -thermo 1000 - -comm_style brick -comm_modify mode multi group all vel yes -balance 1.1 shift xyz 20 1.1 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 0 - binsize = 30 -> bins = 1 1 3 -fix bal all balance 10000 1.1 shift xyz 20 1.01 - -####################### Options specific to pouring ######################### - -# insertion region for fix/pour - -region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box -region insreg cylinder z 25 ${yc} 10 30 50 side in units box -region insreg cylinder z 25 25 10 30 50 side in units box - -# define cone and cylinder regions - see lammps doc on region command -# note new open options - -region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open -region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 2 0 10 side in units box open 2 - -region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open -region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2 - -region hopreg union 2 conereg cylreg - -fix grav all gravity ${gravity} vector 0 0 -1 -fix grav all gravity 1 vector 0 0 -1 -fix 1 all nve/sphere - - -fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg - -fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1 -Particle insertion: 3000 every 59965 steps, 2000 by step 1 - -#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z - -#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0 -#dump_modify 2 pad 6 - -thermo_style custom step cpu atoms ke -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) -thermo_modify flush yes lost warn - -# Initial run to fill up the cone - -run 20000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.5 - ghost atom cutoff = 1.5 - binsize = 0.75 -> bins = 40 40 94 -Memory usage per processor = 3.59417 Mbytes -Step CPU Atoms KinEng - 0 0 0 -0 - 1000 0.54582715 2000 -0 - 2000 0.93155909 2000 -0 - 3000 1.3159981 2000 -0 - 4000 1.697911 2000 -0 - 5000 2.080133 2000 -0 - 6000 2.461525 2000 -0 - 7000 2.842278 2000 -0 - 8000 3.222302 2000 -0 - 9000 3.6018171 2000 -0 - 10000 3.9843922 2000 -0 - 11000 4.363066 2000 -0 - 12000 4.743022 2000 -0 - 13000 5.121953 2000 -0 - 14000 5.5021431 2000 -0 - 15000 5.8807089 2000 -0 - 16000 6.2604752 2000 -0 - 17000 6.640244 2000 -0 - 18000 7.0199981 2000 -0 - 19000 7.40029 2000 -0 - 20000 7.7834539 2000 -0 -Loop time of 7.78348 on 1 procs for 20000 steps with 2000 atoms - -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.64588 | 0.64588 | 0.64588 | 0.0 | 8.30 -Neigh | 0.097229 | 0.097229 | 0.097229 | 0.0 | 1.25 -Comm | 0.011505 | 0.011505 | 0.011505 | 0.0 | 0.15 -Output | 0.00041127 | 0.00041127 | 0.00041127 | 0.0 | 0.01 -Modify | 6.8117 | 6.8117 | 6.8117 | 0.0 | 87.51 -Other | | 0.2168 | | | 2.79 - -Nlocal: 2000 ave 2000 max 2000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1537 ave 1537 max 1537 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1537 -Ave neighs/atom = 0.7685 -Neighbor list builds = 69 -Dangerous builds = 0 -unfix ins -run 150000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.49993 - ghost atom cutoff = 1.49993 - binsize = 0.749963 -> bins = 41 41 94 -Memory usage per processor = 9.40639 Mbytes -Step CPU Atoms KinEng - 20000 0 2000 6443.7665 - 21000 0.37979388 2000 6572.3531 - 22000 0.76149178 2000 6723.8376 - 23000 1.1449339 2000 6853.1812 - 24000 1.529017 2000 6976.0209 - 25000 1.9145579 2000 7096.9955 - 26000 2.30124 2000 7215.5795 - 27000 2.6893978 2000 7349.2382 - 28000 3.0777299 2000 7471.8719 - 29000 3.4699018 2000 7574.7988 - 30000 3.8656738 2000 7660.2353 - 31000 4.2606828 2000 7703.5736 - 32000 4.6632309 2000 7643.5299 - 33000 5.0728998 2000 7520.14 - 34000 5.4878559 2000 7372.2247 - 35000 5.910604 2000 7192.1639 - 36000 6.340683 2000 6985.7075 - 37000 6.8159268 2000 6858.944 - 38000 7.2553098 2000 6717.0485 - 39000 7.699847 2000 6541.6874 - 40000 8.1524599 2000 6382.1661 - 41000 8.6083429 2000 6235.6681 - 42000 9.0669999 2000 6103.095 - 43000 9.5359929 2000 5951.0523 - 44000 10.012767 2000 5811.0158 - 45000 10.497891 2000 5627.7273 - 46000 10.988827 2000 5471.7262 - 47000 11.48741 2000 5299.1205 - 48000 11.990619 2000 5164.1642 - 49000 12.497663 2000 5006.5014 - 50000 13.020399 2000 4872.2336 - 51000 13.548012 2000 4694.5332 - 52000 14.082238 2000 4515.5164 - 53000 14.622731 2000 4384.7531 - 54000 15.170292 2000 4215.1354 - 55000 15.721908 2000 4063.0658 - 56000 16.285099 2000 3895.7872 - 57000 16.858606 2000 3693.0537 - 58000 17.440427 2000 3514.887 - 59000 18.03239 2000 3268.5625 - 60000 18.640969 2000 3049.7365 - 61000 19.245721 2000 2885.6786 - 62000 19.85574 2000 2652.9108 - 63000 20.47405 2000 2408.6484 - 64000 21.10165 2000 2126.9549 - 65000 21.743939 2000 1879.2829 - 66000 22.39462 2000 1645.0406 - 67000 23.059044 2000 1425.8023 - 68000 23.730976 2000 1160.2206 - 69000 24.410132 2000 961.78467 - 70000 25.096468 2000 785.64232 - 71000 25.778622 2000 626.09642 - 72000 26.474474 2000 468.40645 - 73000 27.171065 2000 358.58331 - 74000 27.860177 2000 299.43443 - 75000 28.544588 2000 246.40717 - 76000 29.226358 2000 206.30408 - 77000 29.902697 2000 176.97739 - 78000 30.577693 2000 144.25328 - 79000 31.269697 2000 115.11502 - 80000 31.977588 2000 97.780887 - 81000 32.685445 2000 82.593472 - 82000 33.397946 2000 72.226521 - 83000 34.114464 2000 62.978026 - 84000 34.831341 2000 55.350711 - 85000 35.545558 2000 51.162661 - 86000 36.266238 2000 46.100957 - 87000 36.99804 2000 41.19148 - 88000 37.743379 2000 36.31567 - 89000 38.499655 2000 32.456379 - 90000 39.270287 2000 30.16589 - 91000 40.035401 2000 27.36473 - 92000 40.799095 2000 25.488138 - 93000 41.564371 2000 23.674866 - 94000 42.335499 2000 22.219066 - 95000 43.114508 2000 20.982603 - 96000 43.897793 2000 19.840979 - 97000 44.685675 2000 19.092279 - 98000 45.483452 2000 18.20277 - 99000 46.282718 2000 17.512786 - 100000 47.085373 2000 16.921053 - 101000 47.888376 2000 16.228234 - 102000 48.698546 2000 15.958752 - 103000 49.51312 2000 15.640913 - 104000 50.330832 2000 14.016542 - 105000 51.146589 2000 13.484725 - 106000 51.96128 2000 13.369222 - 107000 52.781047 2000 12.965898 - 108000 53.604374 2000 12.268212 - 109000 54.424389 2000 11.492904 - 110000 55.253544 2000 11.110936 - 111000 56.077677 2000 10.05383 - 112000 56.904333 2000 10.159311 - 113000 57.729366 2000 10.071694 - 114000 58.559509 2000 9.820289 - 115000 59.391732 2000 9.4736012 - 116000 60.221045 2000 9.5616457 - 117000 61.052557 2000 8.6478552 - 118000 61.890195 2000 8.7425719 - 119000 62.726358 2000 8.4741204 - 120000 63.565646 2000 7.772287 - 121000 64.397804 2000 6.9466866 - 122000 65.231394 2000 6.7645153 - 123000 66.064887 2000 6.6568629 - 124000 66.901915 2000 6.7578346 - 125000 67.741833 2000 6.7845523 - 126000 68.582414 2000 6.8385357 - 127000 69.421944 2000 6.8984218 - 128000 70.262972 2000 7.031649 - 129000 71.108668 2000 6.5894805 - 130000 71.954121 2000 6.6452991 - 131000 72.795366 2000 6.7278453 - 132000 73.639866 2000 6.679577 - 133000 74.484945 2000 6.8049542 - 134000 75.326506 2000 6.9015567 - 135000 76.171268 2000 7.2052436 - 136000 77.015739 2000 7.5532841 - 137000 77.861613 2000 7.2577958 - 138000 78.706479 2000 7.5218509 - 139000 79.549466 2000 7.5221639 - 140000 80.398284 2000 7.6657717 - 141000 81.240794 2000 7.9761942 - 142000 82.087164 2000 8.2314258 - 143000 82.931215 2000 8.3019975 - 144000 83.777896 2000 8.0179905 - 145000 84.622383 2000 8.2517491 - 146000 85.469753 2000 6.9481522 - 147000 86.315756 2000 6.6131212 - 148000 87.164711 2000 6.7706881 - 149000 88.012004 2000 6.8104528 - 150000 88.861557 2000 6.7339102 - 151000 89.708494 2000 6.4777998 - 152000 90.558437 2000 6.3011889 - 153000 91.40365 2000 6.3101502 - 154000 92.249997 2000 6.5542552 - 155000 93.099774 2000 6.7687268 - 156000 93.945557 2000 6.7974687 - 157000 94.795065 2000 6.4615869 - 158000 95.645761 2000 6.5566144 - 159000 96.495711 2000 6.4371 - 160000 97.349979 2000 6.4540668 - 161000 98.19875 2000 6.6987231 - 162000 99.049934 2000 6.2464506 - 163000 99.902813 2000 4.7573102 - 164000 100.75416 2000 4.7782706 - 165000 101.60479 2000 4.9414064 - 166000 102.45183 2000 4.970526 - 167000 103.30172 2000 5.1492473 - 168000 104.15283 2000 5.3633229 - 169000 105.00583 2000 4.3464936 - 170000 105.85919 2000 3.6784016 -Loop time of 105.859 on 1 procs for 150000 steps with 2000 atoms - -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 46.786 | 46.786 | 46.786 | -nan | 44.20 -Neigh | 0.88556 | 0.88556 | 0.88556 | 0.0 | 0.84 -Comm | 0.080127 | 0.080127 | 0.080127 | 0.0 | 0.08 -Output | 0.0033967 | 0.0033967 | 0.0033967 | 0.0 | 0.00 -Modify | 56.418 | 56.418 | 56.418 | 0.0 | 53.29 -Other | | 1.687 | | | 1.59 - -Nlocal: 2000 ave 2000 max 2000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 15507 ave 15507 max 15507 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 15507 -Ave neighs/atom = 7.7535 -Neighbor list builds = 401 -Dangerous builds = 0 - -# remove "plug" - need to redefine cylinder region & union - -region cylreg delete -region hopreg delete -region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open -region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2 - -region hopreg union 2 cylreg conereg - -unfix hopper3 -fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg - -run 100000 -Memory usage per processor = 9.40667 Mbytes -Step CPU Atoms KinEng - 170000 0 2000 3.6784016 - 171000 0.84847808 2000 4.3936331 - 172000 1.6901879 2000 5.5750342 - 173000 2.523411 2000 6.8205762 - 174000 3.3501492 2000 8.9700613 - 175000 4.1766891 2000 11.336633 - 176000 4.9954321 2000 14.225242 - 177000 5.814229 2000 17.653262 - 178000 6.630548 2000 21.796078 - 179000 7.4493361 2000 26.660801 - 180000 8.2656369 2000 32.428193 - 181000 9.069953 2000 39.229088 - 182000 9.8759181 2000 46.242732 - 183000 10.674972 2000 54.604245 - 184000 11.47082 2000 63.96931 - 185000 12.259916 2000 74.132316 - 186000 13.046788 2000 84.690798 - 187000 13.832446 2000 95.486707 - 188000 14.612976 2000 106.68052 - 189000 15.391779 2000 118.91376 - 190000 16.160107 2000 131.90023 - 191000 16.919573 2000 146.30664 - 192000 17.677855 2000 161.10142 - 193000 18.4352 2000 174.91947 - 194000 19.188156 2000 191.47629 - 195000 19.937255 2000 208.19912 - 196000 20.687716 2000 224.80045 - 197000 21.43754 2000 243.29637 - 198000 22.18579 2000 262.88685 - 199000 22.932473 2000 282.34797 - 200000 23.680828 2000 302.78689 - 201000 24.428559 2000 323.48767 - 202000 25.167341 2000 345.99414 - 203000 25.904465 2000 368.54389 - 204000 26.635727 2000 393.49643 - 205000 27.366891 2000 417.82722 - 206000 28.094282 2000 443.67976 - 207000 28.821021 2000 470.35934 - 208000 29.545596 2000 499.01368 - 209000 30.267439 2000 528.99746 - 210000 30.993287 2000 561.03931 - 211000 31.713729 2000 594.0482 - 212000 32.42933 2000 628.20118 - 213000 33.14608 2000 662.585 - 214000 33.863882 2000 697.41408 - 215000 34.580495 2000 733.36799 - 216000 35.302571 2000 770.46796 - 217000 36.023821 2000 806.72007 - 218000 36.74189 2000 844.06965 - 219000 37.460105 2000 884.31774 - 220000 38.177705 2000 926.23771 - 221000 38.886587 2000 970.02095 - 222000 39.594003 2000 1015.3938 - 223000 40.29579 2000 1061.1281 - 224000 41.001112 2000 1107.9962 - 225000 41.706489 2000 1155.3656 - 226000 42.417622 1998 1196.6939 - 227000 43.133238 1996 1240.8434 - 228000 43.844991 1990 1260.0436 - 229000 44.545565 1986 1280.0431 - 230000 45.246651 1974 1285.222 - 231000 45.934355 1970 1311.8189 - 232000 46.624066 1960 1300.7922 - 233000 47.310339 1943 1282.113 - 234000 47.993433 1932 1261.0871 - 235000 48.66937 1918 1211.0667 - 236000 49.332954 1911 1232.6411 - 237000 49.99742 1898 1209.112 - 238000 50.664096 1888 1189.4002 - 239000 51.336205 1875 1151.415 - 240000 52.010198 1863 1108.0821 - 241000 52.680788 1856 1090.2279 - 242000 53.343069 1843 1062.9726 - 243000 53.996768 1830 1016.0933 - 244000 54.635882 1825 1023.5568 - 245000 55.271259 1817 1012.2897 - 246000 55.902793 1811 1019.8355 - 247000 56.541437 1802 996.81934 - 248000 57.182244 1793 971.29353 - 249000 57.827453 1785 947.98166 - 250000 58.473311 1771 898.58408 - 251000 59.1075 1762 851.46342 - 252000 59.73473 1754 826.46301 - 253000 60.362094 1747 808.08292 - 254000 60.989489 1737 778.86892 - 255000 61.616293 1720 702.90046 - 256000 62.243096 1709 665.14293 - 257000 62.866596 1703 628.63036 - 258000 63.48969 1702 645.42118 - 259000 64.119075 1696 617.03362 - 260000 64.752187 1692 607.96874 - 261000 65.374973 1690 619.83155 - 262000 65.991365 1688 622.09585 - 263000 66.608686 1682 612.86762 - 264000 67.220696 1681 636.53769 - 265000 67.830797 1678 638.33305 - 266000 68.439964 1675 635.97419 - 267000 69.043459 1672 634.91103 - 268000 69.643043 1669 638.50196 - 269000 70.250146 1667 646.16045 - 270000 70.86361 1664 659.62209 -Loop time of 70.8636 on 1 procs for 100000 steps with 1664 atoms - -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 33.501 | 33.501 | 33.501 | 0.0 | 47.27 -Neigh | 0.63279 | 0.63279 | 0.63279 | 0.0 | 0.89 -Comm | 0.055495 | 0.055495 | 0.055495 | 0.0 | 0.08 -Output | 0.0021648 | 0.0021648 | 0.0021648 | 0.0 | 0.00 -Modify | 35.602 | 35.602 | 35.602 | 0.0 | 50.24 -Other | | 1.07 | | | 1.51 - -Nlocal: 1664 ave 1664 max 1664 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 11687 ave 11687 max 11687 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 11687 -Ave neighs/atom = 7.02344 -Neighbor list builds = 261 -Dangerous builds = 0 -Total wall time: 0:03:04 diff --git a/examples/granregion/log.6Oct16.granregion.funnel.g++.4 b/examples/granregion/log.6Oct16.granregion.funnel.g++.4 deleted file mode 100644 index fcbd050b76..0000000000 --- a/examples/granregion/log.6Oct16.granregion.funnel.g++.4 +++ /dev/null @@ -1,608 +0,0 @@ -LAMMPS (5 Oct 2016) -# pour particles into cone-shaped funnel, settle them, let them run out bottom - -variable name string funnel_pour - -thermo_modify flush yes -units si -variable PI equal 3.141592653589 -variable seed equal 14314 - -############################################### -# Geometry-related parameters -############################################### - -variable xlo equal 10 -variable xhi equal 40 -variable ylo equal 10 -variable yhi equal 40 -variable zlo equal -20 -variable zhi equal 50 - -variable xc equal 25 -variable yc equal 25 - -variable zconehi equal 50 -variable zconelo equal 10 -variable zcyllo equal 0 -variable radconelo equal 2 -variable radconehi equal 20 - -################################################ -# Particle sizes -################################################ - -variable rlo equal 0.25 -variable rhi equal 0.5 -variable dlo equal 2.0*${rlo} -variable dlo equal 2.0*0.25 -variable dhi equal 2.0*${rhi} -variable dhi equal 2.0*0.5 - -variable skin equal ${rhi} -variable skin equal 0.5 - -############################################### -# Granular contact parameters -############################################### - -variable coeffRes equal 0.1 -variable coeffFric equal 0.5 - -variable density equal 1.0 -variable EYoung equal 10^5 -variable Poisson equal 2.0/7.0 -variable GShear equal ${EYoung}/(2*(1+${Poisson})) -variable GShear equal 100000/(2*(1+${Poisson})) -variable GShear equal 100000/(2*(1+0.285714285714286)) - -variable gravity equal 1.0 - -variable reff equal 0.5*(${rhi}+${rlo}) -variable reff equal 0.5*(0.5+${rlo}) -variable reff equal 0.5*(0.5+0.25) -variable meff equal ${density}*4.0/3.0*${PI}*${reff}^3 -variable meff equal 1*4.0/3.0*${PI}*${reff}^3 -variable meff equal 1*4.0/3.0*3.141592653589*${reff}^3 -variable meff equal 1*4.0/3.0*3.141592653589*0.375^3 -variable min_mass equal ${density}*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*${PI}*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*${rlo} -variable min_mass equal 1*4.0/3.0*3.141592653589*0.25*0.25*0.25 -variable max_mass equal ${density}*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*${PI}*${rhi}*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*${rhi}*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*${rhi}*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*${rhi} -variable max_mass equal 1*4.0/3.0*3.141592653589*0.5*0.5*0.5 - -## Typical way to set kn, kt, etc.: -variable kn equal 4.0*${GShear}/(3*(1-${Poisson})) -variable kn equal 4.0*38888.8888888889/(3*(1-${Poisson})) -variable kn equal 4.0*38888.8888888889/(3*(1-0.285714285714286)) -variable kt equal 4.0*${GShear}/(2-${Poisson}) -variable kt equal 4.0*38888.8888888889/(2-${Poisson}) -variable kt equal 4.0*38888.8888888889/(2-0.285714285714286) - -variable a equal (-2.0*log(${coeffRes})/${PI})^2 -variable a equal (-2.0*log(0.1)/${PI})^2 -variable a equal (-2.0*log(0.1)/3.141592653589)^2 -variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569556*2*72592.5925925926/0.0654498469497708/(1+0.25*0.405284734569556)) -variable gamma_t equal ${gamma_n}*0.5 -variable gamma_t equal 903.503751814138*0.5 - -variable tcol equal ${PI}/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/${min_mass}-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-${gamma_n}/4.0) -variable tcol equal 3.141592653589/sqrt(2*72592.5925925926/0.0654498469497708-903.503751814138/4.0) - -variable dt equal ${tcol}*0.05 -variable dt equal 0.00210943016014969*0.05 -timestep ${dt} -timestep 0.000105471508007485 - -############################################### -variable dumpfreq equal 1000 -variable logfreq equal 1000 - -newton off -atom_style sphere - -boundary p p f - -region boxreg block ${xlo} ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} -region boxreg block 10 ${xhi} ${ylo} ${yhi} ${zlo} ${zhi} -region boxreg block 10 40 ${ylo} ${yhi} ${zlo} ${zhi} -region boxreg block 10 40 10 ${yhi} ${zlo} ${zhi} -region boxreg block 10 40 10 40 ${zlo} ${zhi} -region boxreg block 10 40 10 40 -20 ${zhi} -region boxreg block 10 40 10 40 -20 50 -create_box 1 boxreg -Created orthogonal box = (10 10 -20) to (40 40 50) - 1 by 1 by 4 MPI processor grid - -pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 -pair_style gran/hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 -pair_coeff * * - -neighbor ${skin} bin -neighbor 0.5 bin -thermo ${logfreq} -thermo 1000 - -comm_style brick -comm_modify mode multi group all vel yes -balance 1.1 shift xyz 20 1.1 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 0 - binsize = 30 -> bins = 1 1 3 -fix bal all balance 10000 1.1 shift xyz 20 1.01 - -####################### Options specific to pouring ######################### - -# insertion region for fix/pour - -region insreg cylinder z ${xc} ${yc} 10 30 50 side in units box -region insreg cylinder z 25 ${yc} 10 30 50 side in units box -region insreg cylinder z 25 25 10 30 50 side in units box - -# define cone and cylinder regions - see lammps doc on region command -# note new open options - -region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 #Top is open -region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 2 -region cylreg cylinder z 25 25 2 0 10 side in units box open 2 - -region conereg cone z ${xc} ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 #Bottom and top are open -region conereg cone z 25 ${yc} ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 ${radconelo} ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 ${radconehi} ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 20 ${zconelo} ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 20 10 ${zconehi} side in units box open 1 open 2 -region conereg cone z 25 25 2 20 10 50 side in units box open 1 open 2 - -region hopreg union 2 conereg cylreg - -fix grav all gravity ${gravity} vector 0 0 -1 -fix grav all gravity 1 vector 0 0 -1 -fix 1 all nve/sphere - - -fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg - -fix ins all pour 2000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 ${dhi} dens ${density} ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens ${density} ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 ${density} -fix ins all pour 2000 1 42424 region insreg diam range 0.5 1 dens 1 1 -Particle insertion: 3000 every 59965 steps, 2000 by step 1 - -#dump 1 all custom ${dumpfreq} ${name}.dump # id type mass diameter x y z - -#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 3.0 # box no 0.0 axes no 0.0 0.0 -#dump_modify 2 pad 6 - -thermo_style custom step cpu atoms ke -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) -thermo_modify flush yes lost warn - -# Initial run to fill up the cone - -run 20000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.5 - ghost atom cutoff = 1.5 - binsize = 0.75 -> bins = 40 40 94 -Memory usage per processor = 2.99539 Mbytes -Step CPU Atoms KinEng - 0 0 0 -0 - 1000 0.53632808 2000 -0 - 2000 0.90599012 2000 -0 - 3000 1.2640941 2000 -0 - 4000 1.6225331 2000 -0 - 5000 1.9735272 2000 -0 - 6000 2.3156731 2000 -0 - 7000 2.6499262 2000 -0 - 8000 2.9751072 2000 -0 - 9000 3.2918322 2000 -0 - 10000 3.597712 2000 -0 - 11000 3.7157061 2000 -0 - 12000 3.833451 2000 -0 - 13000 3.9541111 2000 -0 - 14000 4.081727 2000 -0 - 15000 4.2142782 2000 -0 - 16000 4.3530872 2000 -0 - 17000 4.4987361 2000 -0 - 18000 4.6507492 2000 -0 - 19000 4.807373 2000 -0 - 20000 4.9710512 2000 -0 -Loop time of 4.97109 on 4 procs for 20000 steps with 2000 atoms - -98.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.067799 | 0.17326 | 0.37341 | 28.4 | 3.49 -Neigh | 0.013881 | 0.025808 | 0.045841 | 7.5 | 0.52 -Comm | 0.078163 | 0.1808 | 0.2915 | 21.0 | 3.64 -Output | 0.0011413 | 0.0027029 | 0.0036721 | 1.8 | 0.05 -Modify | 1.0146 | 1.8605 | 3.562 | 73.8 | 37.43 -Other | | 2.728 | | | 54.88 - -Nlocal: 500 ave 505 max 493 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 159.25 ave 254 max 71 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 397.5 ave 616 max 214 min -Histogram: 1 0 1 0 0 0 1 0 0 1 - -Total # of neighbors = 1590 -Ave neighs/atom = 0.795 -Neighbor list builds = 69 -Dangerous builds = 0 -unfix ins -run 150000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.49993 - ghost atom cutoff = 1.49993 - binsize = 0.749963 -> bins = 41 41 94 -Memory usage per processor = 9.39737 Mbytes -Step CPU Atoms KinEng - 20000 0 2000 6443.7665 - 21000 0.11240888 2000 6572.3531 - 22000 0.23014092 2000 6723.8376 - 23000 0.35371184 2000 6853.1812 - 24000 0.4838469 2000 6976.0209 - 25000 0.62193394 2000 7096.9955 - 26000 0.76781893 2000 7215.5795 - 27000 0.92212081 2000 7349.2382 - 28000 1.0841098 2000 7471.8719 - 29000 1.2593179 2000 7574.7988 - 30000 1.4459748 2000 7660.2353 - 31000 1.5759299 2000 7703.5736 - 32000 1.7189329 2000 7643.5299 - 33000 1.876133 2000 7520.14 - 34000 2.0453629 2000 7372.2247 - 35000 2.2281299 2000 7192.1638 - 36000 2.4208269 2000 6985.7056 - 37000 2.6258228 2000 6858.9422 - 38000 2.839473 2000 6717.0655 - 39000 3.065336 2000 6541.5809 - 40000 3.3090389 2000 6381.8513 - 41000 3.4969938 2000 6236.4297 - 42000 3.6888108 2000 6104.2528 - 43000 3.8874888 2000 5951.0314 - 44000 4.0956569 2000 5819.0972 - 45000 4.312974 2000 5620.6457 - 46000 4.5343778 2000 5479.332 - 47000 4.757262 2000 5295.328 - 48000 4.9850328 2000 5179.9559 - 49000 5.2210319 2000 5022.5562 - 50000 5.4699879 2000 4899.1332 - 51000 5.6774018 2000 4699.4456 - 52000 5.8900218 2000 4522.5719 - 53000 6.110677 2000 4402.8664 - 54000 6.3361218 2000 4256.1664 - 55000 6.5778289 2000 4093.6265 - 56000 6.8319149 2000 3933.0179 - 57000 7.0925779 2000 3738.4628 - 58000 7.3578169 2000 3535.7866 - 59000 7.6344049 2000 3298.4079 - 60000 7.9258108 2000 3058.9356 - 61000 8.1758959 2000 2888.0074 - 62000 8.4278228 2000 2652.4613 - 63000 8.6815088 2000 2435.0991 - 64000 8.9371588 2000 2147.9441 - 65000 9.208025 2000 1898.0657 - 66000 9.4795358 2000 1650.5794 - 67000 9.7519388 2000 1425.7284 - 68000 10.025867 2000 1193.3786 - 69000 10.313816 2000 940.55767 - 70000 10.610488 2000 761.5312 - 71000 10.879718 2000 599.1989 - 72000 11.154029 2000 453.25929 - 73000 11.424376 2000 345.73222 - 74000 11.697359 2000 273.72167 - 75000 11.966099 2000 222.44251 - 76000 12.230213 2000 190.79993 - 77000 12.481982 2000 157.71153 - 78000 12.73433 2000 131.99208 - 79000 12.986017 2000 111.10589 - 80000 13.243904 2000 96.736337 - 81000 13.500538 2000 81.24169 - 82000 13.765755 2000 66.640863 - 83000 14.032985 2000 53.07725 - 84000 14.308284 2000 45.942738 - 85000 14.586721 2000 38.811918 - 86000 14.861759 2000 34.59113 - 87000 15.135665 2000 31.04487 - 88000 15.417487 2000 27.659144 - 89000 15.698281 2000 24.596119 - 90000 15.97969 2000 22.004865 - 91000 16.266118 2000 20.541665 - 92000 16.557007 2000 18.938077 - 93000 16.846745 2000 17.293956 - 94000 17.133408 2000 16.443596 - 95000 17.42023 2000 15.518083 - 96000 17.709025 2000 14.264343 - 97000 18.001337 2000 13.410217 - 98000 18.292414 2000 13.036621 - 99000 18.583887 2000 12.523214 - 100000 18.880312 2000 12.371509 - 101000 19.176964 2000 11.828077 - 102000 19.474371 2000 11.510333 - 103000 19.770957 2000 11.289304 - 104000 20.070744 2000 10.370661 - 105000 20.372617 2000 10.217921 - 106000 20.673949 2000 9.3275222 - 107000 20.9765 2000 8.9156372 - 108000 21.276062 2000 8.5850821 - 109000 21.585305 2000 8.5326934 - 110000 21.89079 2000 8.0579504 - 111000 22.194207 2000 8.1084595 - 112000 22.501593 2000 7.9190174 - 113000 22.81251 2000 8.0127499 - 114000 23.118514 2000 8.1791911 - 115000 23.432862 2000 8.3333032 - 116000 23.735549 2000 8.4833817 - 117000 24.038329 2000 8.315498 - 118000 24.343247 2000 7.9460007 - 119000 24.643288 2000 7.5922134 - 120000 24.94731 2000 7.4089143 - 121000 25.253605 2000 7.5790659 - 122000 25.56672 2000 7.3778204 - 123000 25.870958 2000 7.1384456 - 124000 26.180729 2000 6.9151887 - 125000 26.493089 2000 6.4671685 - 126000 26.806734 2000 5.6773128 - 127000 27.10969 2000 5.5603057 - 128000 27.410973 2000 5.6376136 - 129000 27.712398 2000 5.5578044 - 130000 28.015943 2000 5.4632646 - 131000 28.319002 2000 4.9669466 - 132000 28.620558 2000 5.0191026 - 133000 28.923233 2000 4.7146653 - 134000 29.235178 2000 4.4835803 - 135000 29.542816 2000 4.5469703 - 136000 29.8518 2000 4.3349926 - 137000 30.159096 2000 4.423031 - 138000 30.464283 2000 4.3680646 - 139000 30.769279 2000 4.2461787 - 140000 31.074457 2000 4.4140001 - 141000 31.380334 2000 4.3991236 - 142000 31.683855 2000 4.572989 - 143000 31.987308 2000 4.7601702 - 144000 32.28998 2000 4.7790587 - 145000 32.594971 2000 4.8127728 - 146000 32.89855 2000 4.8750003 - 147000 33.205142 2000 4.9830109 - 148000 33.509096 2000 4.9960037 - 149000 33.812951 2000 5.2151503 - 150000 34.117585 2000 5.2745187 - 151000 34.420995 2000 4.8959892 - 152000 34.725788 2000 4.7600627 - 153000 35.032001 2000 4.6944719 - 154000 35.337093 2000 4.7647384 - 155000 35.645299 2000 4.312228 - 156000 35.953225 2000 3.8513036 - 157000 36.258107 2000 3.8798947 - 158000 36.570122 2000 3.7116749 - 159000 36.880424 2000 3.7246469 - 160000 37.187331 2000 3.8165318 - 161000 37.491939 2000 3.8954595 - 162000 37.806365 2000 4.0109691 - 163000 38.122006 2000 3.3864369 - 164000 38.437246 2000 3.4533589 - 165000 38.753073 2000 3.4967205 - 166000 39.068713 2000 3.5758702 - 167000 39.376388 2000 2.8913997 - 168000 39.685628 2000 2.507523 - 169000 39.99294 2000 2.4910068 - 170000 40.302393 2000 2.4992886 -Loop time of 40.3024 on 4 procs for 150000 steps with 2000 atoms - -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.9352 | 13.451 | 15.947 | 88.7 | 33.37 -Neigh | 0.15394 | 0.23292 | 0.28243 | 10.0 | 0.58 -Comm | 2.1471 | 3.534 | 4.4671 | 47.3 | 8.77 -Output | 0.0070386 | 0.011774 | 0.021483 | 5.4 | 0.03 -Modify | 10.816 | 14.404 | 16.047 | 55.2 | 35.74 -Other | | 8.669 | | | 21.51 - -Nlocal: 500 ave 542 max 430 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 449.5 ave 679 max 208 min -Histogram: 1 0 0 0 1 0 1 0 0 1 -Neighs: 4506.75 ave 5611 max 3508 min -Histogram: 1 0 1 0 0 0 1 0 0 1 - -Total # of neighbors = 18027 -Ave neighs/atom = 9.0135 -Neighbor list builds = 386 -Dangerous builds = 0 - -# remove "plug" - need to redefine cylinder region & union - -region cylreg delete -region hopreg delete -region cylreg cylinder z ${xc} ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 #Bottom & top are open -region cylreg cylinder z 25 ${yc} ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 ${radconelo} ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 ${zcyllo} ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 0 ${zconelo} side in units box open 1 open 2 -region cylreg cylinder z 25 25 2 0 10 side in units box open 1 open 2 - -region hopreg union 2 cylreg conereg - -unfix hopper3 -fix hopper3 all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 ${gamma_n} ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 ${gamma_t} ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 ${coeffFric} 1 region hopreg -fix hopper3 all wall/gran/region hertz/history 72592.5925925926 90740.7407407408 903.503751814138 451.751875907069 0.5 1 region hopreg - -run 100000 -Memory usage per processor = 9.41929 Mbytes -Step CPU Atoms KinEng - 170000 0 2000 2.4992886 - 171000 0.30864286 2000 3.6052039 - 172000 0.62273479 2000 4.8584577 - 173000 0.94411087 2000 6.5620833 - 174000 1.2588799 2000 8.8636423 - 175000 1.574302 2000 11.743197 - 176000 1.888201 2000 15.60405 - 177000 2.1948938 2000 20.29426 - 178000 2.508261 2000 25.069266 - 179000 2.8257489 2000 31.340924 - 180000 3.1444538 2000 38.454779 - 181000 3.4541628 2000 46.488676 - 182000 3.7632799 2000 55.279578 - 183000 4.0711808 2000 65.192327 - 184000 4.386853 2000 75.466011 - 185000 4.7000408 2000 86.06934 - 186000 5.00436 2000 97.157035 - 187000 5.3041189 2000 108.92242 - 188000 5.601872 2000 120.88599 - 189000 5.9027078 2000 134.09884 - 190000 6.2037618 2000 148.60143 - 191000 6.4879329 2000 163.96898 - 192000 6.7703898 2000 180.32931 - 193000 7.0603459 2000 198.83575 - 194000 7.3395619 2000 217.46631 - 195000 7.6245389 2000 235.34916 - 196000 7.911685 2000 253.61893 - 197000 8.1976559 2000 271.3908 - 198000 8.483418 2000 289.60064 - 199000 8.7664149 2000 309.44306 - 200000 9.0593698 2000 331.9367 - 201000 9.3373818 2000 354.86646 - 202000 9.612149 2000 380.56766 - 203000 9.8876739 2000 406.97399 - 204000 10.152671 2000 435.69917 - 205000 10.415859 2000 465.1954 - 206000 10.67967 2000 494.6045 - 207000 10.941435 2000 522.71704 - 208000 11.205367 2000 550.56072 - 209000 11.471415 2000 580.10547 - 210000 11.738137 2000 610.36222 - 211000 12.006432 2000 641.99128 - 212000 12.270102 2000 676.0736 - 213000 12.531937 2000 711.70118 - 214000 12.797442 2000 747.84561 - 215000 13.062646 2000 785.59575 - 216000 13.33019 2000 826.36549 - 217000 13.598467 2000 868.35085 - 218000 13.863022 2000 911.07041 - 219000 14.127777 2000 953.70251 - 220000 14.391496 2000 997.5717 - 221000 14.655347 2000 1043.5565 - 222000 14.923357 2000 1090.7944 - 223000 15.193349 2000 1140.1324 - 224000 15.462326 2000 1190.6956 - 225000 15.729748 1999 1238.1536 - 226000 15.996867 1998 1286.8076 - 227000 16.261762 1995 1326.9895 - 228000 16.527382 1989 1349.5997 - 229000 16.788356 1984 1370.593 - 230000 17.05426 1968 1344.3763 - 231000 17.320126 1962 1363.7958 - 232000 17.58387 1949 1340.1482 - 233000 17.850221 1940 1348.409 - 234000 18.116595 1929 1335.9703 - 235000 18.383276 1918 1328.201 - 236000 18.650066 1905 1309.6469 - 237000 18.916963 1896 1292.9758 - 238000 19.185209 1884 1266.3598 - 239000 19.453402 1872 1221.0069 - 240000 19.722178 1855 1166.1488 - 241000 19.98987 1842 1126.9482 - 242000 20.257783 1828 1107.128 - 243000 20.523743 1815 1060.6573 - 244000 20.793404 1805 1026.0259 - 245000 21.061462 1797 1009.4924 - 246000 21.325574 1790 995.26136 - 247000 21.587046 1782 976.04886 - 248000 21.840234 1778 989.11589 - 249000 22.09455 1762 903.62508 - 250000 22.356228 1748 852.03257 - 251000 22.602243 1738 807.41049 - 252000 22.852106 1722 738.82529 - 253000 23.097209 1712 706.05657 - 254000 23.341263 1696 626.53135 - 255000 23.58614 1692 613.89548 - 256000 23.83122 1686 598.9367 - 257000 24.076937 1683 589.27487 - 258000 24.321166 1681 591.42793 - 259000 24.566143 1678 595.25383 - 260000 24.820743 1677 617.50379 - 261000 25.057835 1675 623.39319 - 262000 25.294068 1673 627.08829 - 263000 25.526724 1669 623.52963 - 264000 25.766729 1667 626.44957 - 265000 26.005453 1664 631.58936 - 266000 26.244549 1660 605.22452 - 267000 26.478879 1657 611.76935 - 268000 26.71252 1655 611.73538 - 269000 26.951368 1652 624.58227 - 270000 27.186447 1648 625.97446 -Loop time of 27.1865 on 4 procs for 100000 steps with 1648 atoms - -99.2% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.6257 | 9.631 | 13.049 | 100.0 | 35.43 -Neigh | 0.1522 | 0.17549 | 0.19588 | 4.3 | 0.65 -Comm | 1.5797 | 2.7289 | 3.602 | 48.7 | 10.04 -Output | 0.0014181 | 0.007208 | 0.016675 | 6.8 | 0.03 -Modify | 7.7129 | 9.0949 | 10.256 | 31.9 | 33.45 -Other | | 5.549 | | | 20.41 - -Nlocal: 412 ave 436 max 388 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 391 ave 629 max 158 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 3406 ave 4479 max 2040 min -Histogram: 1 0 0 0 1 0 0 1 0 1 - -Total # of neighbors = 13624 -Ave neighs/atom = 8.26699 -Neighbor list builds = 260 -Dangerous builds = 0 -Total wall time: 0:01:12 diff --git a/examples/granregion/log.6Oct16.granregion.mixer.g++.1 b/examples/granregion/log.6Oct16.granregion.mixer.g++.1 deleted file mode 100644 index 3cfa3eb0fc..0000000000 --- a/examples/granregion/log.6Oct16.granregion.mixer.g++.1 +++ /dev/null @@ -1,609 +0,0 @@ -LAMMPS (5 Oct 2016) -variable name string mixer - -thermo_modify flush yes -variable seed equal 14314 - -############################################### -# Particle parameters -################################################ - -variable rlo equal 0.3 -variable rhi equal 0.6 -variable dlo equal 2.0*${rlo} -variable dlo equal 2.0*0.3 -variable dhi equal 2.0*${rhi} -variable dhi equal 2.0*0.6 -variable skin equal ${rhi} -variable skin equal 0.6 - -variable coeffRes equal 0.1 -variable coeffFric equal 0.5 - -variable kn equal 10^5 -variable kt equal 0.2*${kn} -variable kt equal 0.2*100000 - -variable gravity equal 1.0 -variable density equal 1.0 - -variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo} -variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3 -variable a equal (-2.0*log(${coeffRes})/PI)^2 -variable a equal (-2.0*log(0.1)/PI)^2 -variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351)) -variable gamma_t equal ${gamma_n}*0.5 -variable gamma_t equal 806.699778405191*0.5 - -variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) -variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0) -variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0) -variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0) - -variable dt equal ${tcol}*0.02 -variable dt equal 0.00236257621510454*0.02 -timestep ${dt} -timestep 4.72515243020908e-05 - -############################################### - -variable dumpfreq equal 1000 -variable logfreq equal 1000 - -newton on -atom_style sphere - -boundary p p f - -region boxreg block 0 20 0 20 0 20 -create_box 1 boxreg -Created orthogonal box = (0 0 0) to (20 20 20) - 1 by 1 by 1 MPI processor grid - -pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 -pair_coeff * * - -neighbor ${skin} bin -neighbor 0.6 bin -thermo ${logfreq} -thermo 1000 - -comm_style brick -comm_modify mode multi group all vel yes -balance 1.1 shift xyz 20 1.1 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 0 - binsize = 20 -> bins = 1 1 1 -fix bal all balance 10000 1.1 shift xyz 20 1.01 - -####################### Options specific to pouring ######################### - -region insreg cylinder z 10 10 8 10 18 side in units box -region cylreg cylinder z 10 10 10 0 20 side in units box - -variable theta equal (step/400000)*2*PI - -region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box -region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box - -region mixer intersect 3 cylreg b1 b2 side in - -fix grav all gravity ${gravity} vector 0 0 -1 -fix grav all gravity 1 vector 0 0 -1 -fix 1 all nve/sphere - -fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer - -fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1 -Particle insertion: 444 every 84653 steps, 1000 by step 169307 - -#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z - -#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0 -#dump_modify 2 pad 6 - -thermo_style custom step cpu atoms ke v_theta -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) -thermo_modify flush yes lost warn - -run 200000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.8 - ghost atom cutoff = 1.8 - binsize = 0.9 -> bins = 23 23 23 -Memory usage per processor = 2.80779 Mbytes -Step CPU Atoms KinEng v_theta - 0 0 0 -0 0 - 1000 0.16771817 444 -0 0.015707963 - 2000 0.33019304 444 -0 0.031415927 - 3000 0.4894321 444 -0 0.04712389 - 4000 0.64879322 444 -0 0.062831853 - 5000 0.80816507 444 -0 0.078539816 - 6000 0.96711302 444 -0 0.09424778 - 7000 1.1265812 444 -0 0.10995574 - 8000 1.286129 444 -0 0.12566371 - 9000 1.445487 444 -0 0.14137167 - 10000 1.6056392 444 -0 0.15707963 - 11000 1.7650061 444 -0 0.1727876 - 12000 1.9249642 444 -0 0.18849556 - 13000 2.0851831 444 -0 0.20420352 - 14000 2.244523 444 -0 0.21991149 - 15000 2.4043641 444 -0 0.23561945 - 16000 2.5638251 444 -0 0.25132741 - 17000 2.7155962 444 -0 0.26703538 - 18000 2.866904 444 -0 0.28274334 - 19000 3.0188181 444 -0 0.2984513 - 20000 3.17047 444 -0 0.31415927 - 21000 3.3214712 444 -0 0.32986723 - 22000 3.472692 444 -0 0.34557519 - 23000 3.6240032 444 -0 0.36128316 - 24000 3.7753551 444 -0 0.37699112 - 25000 3.926239 444 -0 0.39269908 - 26000 4.0782132 444 -0 0.40840704 - 27000 4.2301712 444 -0 0.42411501 - 28000 4.382267 444 -0 0.43982297 - 29000 4.5339992 444 -0 0.45553093 - 30000 4.6860211 444 -0 0.4712389 - 31000 4.8376751 444 -0 0.48694686 - 32000 4.989748 444 -0 0.50265482 - 33000 5.1418142 444 -0 0.51836279 - 34000 5.294476 444 -0 0.53407075 - 35000 5.4472861 444 -0 0.54977871 - 36000 5.5999811 444 -0 0.56548668 - 37000 5.7526181 444 -0 0.58119464 - 38000 5.9061031 444 -0 0.5969026 - 39000 6.0593271 444 -0 0.61261057 - 40000 6.2123802 444 -0 0.62831853 - 41000 6.3652351 444 -0 0.64402649 - 42000 6.5186551 444 -0 0.65973446 - 43000 6.672132 444 -0 0.67544242 - 44000 6.8245611 444 -0 0.69115038 - 45000 6.9778051 444 -0 0.70685835 - 46000 7.131258 444 -0 0.72256631 - 47000 7.2841291 444 -0 0.73827427 - 48000 7.4379101 444 -0 0.75398224 - 49000 7.5915 444 -0 0.7696902 - 50000 7.7461231 444 -0 0.78539816 - 51000 7.9047191 444 -0 0.80110613 - 52000 8.0634432 444 -0 0.81681409 - 53000 8.2226322 444 -0 0.83252205 - 54000 8.3817451 444 -0 0.84823002 - 55000 8.5419021 444 -0 0.86393798 - 56000 8.701194 444 -0 0.87964594 - 57000 8.8613491 444 -0 0.89535391 - 58000 9.0211501 444 -0 0.91106187 - 59000 9.180917 444 -0 0.92676983 - 60000 9.341964 444 -0 0.9424778 - 61000 9.5026722 444 -0 0.95818576 - 62000 9.6630561 444 -0 0.97389372 - 63000 9.8236201 444 -0 0.98960169 - 64000 9.9854801 444 -0 1.0053096 - 65000 10.148318 444 -0 1.0210176 - 66000 10.311267 444 -0 1.0367256 - 67000 10.476498 444 -0 1.0524335 - 68000 10.640768 444 -0 1.0681415 - 69000 10.804709 444 -0 1.0838495 - 70000 10.969271 444 -0 1.0995574 - 71000 11.133451 444 -0 1.1152654 - 72000 11.299253 444 -0 1.1309734 - 73000 11.463999 444 -0 1.1466813 - 74000 11.62903 444 -0 1.1623893 - 75000 11.795109 444 -0 1.1780972 - 76000 11.962154 444 -0 1.1938052 - 77000 12.1292 444 -0 1.2095132 - 78000 12.298106 444 -0 1.2252211 - 79000 12.46744 444 -0 1.2409291 - 80000 12.637916 444 -0 1.2566371 - 81000 12.808494 444 -0 1.272345 - 82000 12.97813 444 -0 1.288053 - 83000 13.149135 444 -0 1.303761 - 84000 13.32082 444 -0 1.3194689 - 85000 13.56205 888 -0 1.3351769 - 86000 13.908699 888 -0 1.3508848 - 87000 14.254615 888 -0 1.3665928 - 88000 14.600851 888 -0 1.3823008 - 89000 14.946295 888 -0 1.3980087 - 90000 15.291315 888 -0 1.4137167 - 91000 15.637396 888 -0 1.4294247 - 92000 15.981426 888 -0 1.4451326 - 93000 16.327519 888 -0 1.4608406 - 94000 16.675434 888 -0 1.4765485 - 95000 17.023515 888 -0 1.4922565 - 96000 17.372152 888 -0 1.5079645 - 97000 17.719346 888 -0 1.5236724 - 98000 18.067159 888 -0 1.5393804 - 99000 18.414599 888 -0 1.5550884 - 100000 18.764775 888 -0 1.5707963 - 101000 19.114239 888 -0 1.5865043 - 102000 19.464285 888 -0 1.6022123 - 103000 19.813956 888 -0 1.6179202 - 104000 20.163276 888 -0 1.6336282 - 105000 20.553808 888 -0 1.6493361 - 106000 20.904093 888 -0 1.6650441 - 107000 21.25918 888 -0 1.6807521 - 108000 21.615056 888 -0 1.69646 - 109000 21.971067 888 -0 1.712168 - 110000 22.326407 888 -0 1.727876 - 111000 22.68062 888 -0 1.7435839 - 112000 23.03653 888 -0 1.7592919 - 113000 23.39161 888 -0 1.7749998 - 114000 23.751273 888 -0 1.7907078 - 115000 24.106946 888 -0 1.8064158 - 116000 24.461182 888 -0 1.8221237 - 117000 24.797533 888 -0 1.8378317 - 118000 25.133924 888 -0 1.8535397 - 119000 25.472617 888 -0 1.8692476 - 120000 25.810786 888 -0 1.8849556 - 121000 26.147399 888 -0 1.9006636 - 122000 26.485868 888 -0 1.9163715 - 123000 26.82395 888 -0 1.9320795 - 124000 27.162345 888 -0 1.9477874 - 125000 27.501503 888 -0 1.9634954 - 126000 27.843318 888 -0 1.9792034 - 127000 28.183379 888 -0 1.9949113 - 128000 28.525406 888 -0 2.0106193 - 129000 28.869601 888 -0 2.0263273 - 130000 29.216232 888 -0 2.0420352 - 131000 29.562432 888 -0 2.0577432 - 132000 29.95624 888 -0 2.0734512 - 133000 30.308919 888 -0 2.0891591 - 134000 30.662184 888 -0 2.1048671 - 135000 31.015509 888 -0 2.120575 - 136000 31.366132 888 -0 2.136283 - 137000 31.71887 888 -0 2.151991 - 138000 32.0723 888 -0 2.1676989 - 139000 32.428657 888 -0 2.1834069 - 140000 32.781484 888 -0 2.1991149 - 141000 33.133593 888 -0 2.2148228 - 142000 33.487376 888 -0 2.2305308 - 143000 33.838656 888 -0 2.2462387 - 144000 34.188723 888 -0 2.2619467 - 145000 34.540083 888 -0 2.2776547 - 146000 34.895624 888 -0 2.2933626 - 147000 35.25153 888 -0 2.3090706 - 148000 35.607482 888 -0 2.3247786 - 149000 35.9642 888 -0 2.3404865 - 150000 36.321759 888 -0 2.3561945 - 151000 36.667172 888 -0 2.3719025 - 152000 37.013822 888 -0 2.3876104 - 153000 37.362735 888 -0 2.4033184 - 154000 37.712576 888 -0 2.4190263 - 155000 38.063528 888 -0 2.4347343 - 156000 38.414666 888 -0 2.4504423 - 157000 38.766119 888 -0 2.4661502 - 158000 39.115828 888 -0 2.4818582 - 159000 39.470874 888 -0 2.4975662 - 160000 39.827871 888 -0 2.5132741 - 161000 40.184885 888 -0 2.5289821 - 162000 40.543838 888 -0 2.54469 - 163000 40.901814 888 -0 2.560398 - 164000 41.258631 888 -0 2.576106 - 165000 41.619086 888 -0 2.5918139 - 166000 41.977332 888 -0 2.6075219 - 167000 42.33775 888 -0 2.6232299 - 168000 42.701344 888 -0 2.6389378 - 169000 43.067663 888 -0 2.6546458 - 170000 43.461687 1000 -0 2.6703538 - 171000 43.866086 1000 -0 2.6860617 - 172000 44.271406 1000 -0 2.7017697 - 173000 44.677085 1000 -0 2.7174776 - 174000 45.082441 1000 -0 2.7331856 - 175000 45.491593 1000 -0 2.7488936 - 176000 45.903002 1000 -0 2.7646015 - 177000 46.315031 1000 -0 2.7803095 - 178000 46.726531 1000 -0 2.7960175 - 179000 47.140818 1000 -0 2.8117254 - 180000 47.553784 1000 -0 2.8274334 - 181000 47.964021 1000 -0 2.8431414 - 182000 48.376739 1000 -0 2.8588493 - 183000 48.789612 1000 -0 2.8745573 - 184000 49.204073 1000 -0 2.8902652 - 185000 49.642401 1000 -0 2.9059732 - 186000 50.083479 1000 -0 2.9216812 - 187000 50.523357 1000 -0 2.9373891 - 188000 50.963685 1000 -0 2.9530971 - 189000 51.404166 1000 -0 2.9688051 - 190000 51.849094 1000 -0 2.984513 - 191000 52.291805 1000 -0 3.000221 - 192000 52.731855 1000 -0 3.0159289 - 193000 53.174104 1000 -0 3.0316369 - 194000 53.619739 1000 -0 3.0473449 - 195000 54.061019 1000 -0 3.0630528 - 196000 54.501149 1000 -0 3.0787608 - 197000 54.940486 1000 -0 3.0944688 - 198000 55.381843 1000 -0 3.1101767 - 199000 55.822243 1000 -0 3.1258847 - 200000 56.264319 1000 -0 3.1415927 -Loop time of 56.2643 on 1 procs for 200000 steps with 1000 atoms - -Performance: 14511.970 tau/day, 3554.650 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.6309 | 4.6309 | 4.6309 | 0.0 | 8.23 -Neigh | 0.071456 | 0.071456 | 0.071456 | 0.0 | 0.13 -Comm | 0.50064 | 0.50064 | 0.50064 | 0.0 | 0.89 -Output | 0.0039163 | 0.0039163 | 0.0039163 | 0.0 | 0.01 -Modify | 50.189 | 50.189 | 50.189 | 0.0 | 89.20 -Other | | 0.8688 | | | 1.54 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 183 ave 183 max 183 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3926 ave 3926 max 3926 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3926 -Ave neighs/atom = 3.926 -Neighbor list builds = 217 -Dangerous builds = 0 -unfix ins -run 200000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.79826 - ghost atom cutoff = 1.79826 - binsize = 0.899132 -> bins = 23 23 23 -Memory usage per processor = 8.62017 Mbytes -Step CPU Atoms KinEng v_theta - 200000 0 1000 0.90078559 3.1415927 - 201000 0.44072509 1000 0.90377135 3.1573006 - 202000 0.8800211 1000 0.89194106 3.1730086 - 203000 1.3210881 1000 0.8940532 3.1887165 - 204000 1.762887 1000 0.8967696 3.2044245 - 205000 2.2080901 1000 0.89758718 3.2201325 - 206000 2.6548181 1000 0.89434418 3.2358404 - 207000 3.1002531 1000 0.87633906 3.2515484 - 208000 3.547334 1000 0.86721615 3.2672564 - 209000 3.993988 1000 0.86214817 3.2829643 - 210000 4.4423161 1000 0.85463743 3.2986723 - 211000 4.889446 1000 0.85744914 3.3143802 - 212000 5.3357229 1000 0.84702799 3.3300882 - 213000 5.780273 1000 0.84375104 3.3457962 - 214000 6.2249129 1000 0.83820701 3.3615041 - 215000 6.670651 1000 0.83566708 3.3772121 - 216000 7.113143 1000 0.83620798 3.3929201 - 217000 7.5359521 1000 0.83581605 3.408628 - 218000 7.9623129 1000 0.84045719 3.424336 - 219000 8.3878851 1000 0.85410521 3.440044 - 220000 8.8153811 1000 0.84336839 3.4557519 - 221000 9.244349 1000 0.85145747 3.4714599 - 222000 9.6728511 1000 0.8476916 3.4871678 - 223000 10.104052 1000 0.8412701 3.5028758 - 224000 10.532736 1000 0.8390277 3.5185838 - 225000 10.959564 1000 0.8359107 3.5342917 - 226000 11.38617 1000 0.83920631 3.5499997 - 227000 11.814104 1000 0.83930526 3.5657077 - 228000 12.241758 1000 0.83152308 3.5814156 - 229000 12.67198 1000 0.81211079 3.5971236 - 230000 13.101597 1000 0.80395018 3.6128316 - 231000 13.532943 1000 0.79991397 3.6285395 - 232000 13.969412 1000 0.80828959 3.6442475 - 233000 14.403885 1000 0.80892923 3.6599554 - 234000 14.833452 1000 0.82048914 3.6756634 - 235000 15.266211 1000 0.8174713 3.6913714 - 236000 15.697822 1000 0.81898551 3.7070793 - 237000 16.133023 1000 0.82034714 3.7227873 - 238000 16.569559 1000 0.81950728 3.7384953 - 239000 17.006308 1000 0.82152915 3.7542032 - 240000 17.445493 1000 0.83217597 3.7699112 - 241000 17.885585 1000 0.83464253 3.7856191 - 242000 18.324268 1000 0.84326166 3.8013271 - 243000 18.763748 1000 0.84235055 3.8170351 - 244000 19.203869 1000 0.83325408 3.832743 - 245000 19.645 1000 0.82577315 3.848451 - 246000 20.08666 1000 0.83923456 3.864159 - 247000 20.530596 1000 0.84153419 3.8798669 - 248000 20.971984 1000 0.85768309 3.8955749 - 249000 21.413571 1000 0.86910799 3.9112829 - 250000 21.854153 1000 0.8775521 3.9269908 - 251000 22.302884 1000 0.87299296 3.9426988 - 252000 22.753789 1000 0.86613861 3.9584067 - 253000 23.202458 1000 0.85513456 3.9741147 - 254000 23.655372 1000 0.84629733 3.9898227 - 255000 24.108225 1000 0.84154885 4.0055306 - 256000 24.561535 1000 0.84162715 4.0212386 - 257000 25.012338 1000 0.83959672 4.0369466 - 258000 25.466506 1000 0.83577695 4.0526545 - 259000 25.919168 1000 0.83021368 4.0683625 - 260000 26.37215 1000 0.81106893 4.0840704 - 261000 26.823834 1000 0.79884608 4.0997784 - 262000 27.276505 1000 0.78360303 4.1154864 - 263000 27.728503 1000 0.77030843 4.1311943 - 264000 28.181969 1000 0.76127974 4.1469023 - 265000 28.636329 1000 0.75553065 4.1626103 - 266000 29.090593 1000 0.75332019 4.1783182 - 267000 29.549547 1000 0.74670528 4.1940262 - 268000 30.008774 1000 0.74216141 4.2097342 - 269000 30.463826 1000 0.74564756 4.2254421 - 270000 30.920159 1000 0.7416035 4.2411501 - 271000 31.377192 1000 0.73061389 4.256858 - 272000 31.836268 1000 0.71620113 4.272566 - 273000 32.291662 1000 0.70840181 4.288274 - 274000 32.743646 1000 0.70946906 4.3039819 - 275000 33.197723 1000 0.70418049 4.3196899 - 276000 33.651405 1000 0.69591327 4.3353979 - 277000 34.106289 1000 0.69499716 4.3511058 - 278000 34.564324 1000 0.69242545 4.3668138 - 279000 35.020887 1000 0.69690811 4.3825218 - 280000 35.478222 1000 0.70402124 4.3982297 - 281000 35.938226 1000 0.71936578 4.4139377 - 282000 36.39808 1000 0.72439386 4.4296456 - 283000 36.855587 1000 0.72221632 4.4453536 - 284000 37.309629 1000 0.70387029 4.4610616 - 285000 37.791869 1000 0.70505716 4.4767695 - 286000 38.277853 1000 0.70731734 4.4924775 - 287000 38.764774 1000 0.71149743 4.5081855 - 288000 39.24815 1000 0.70994023 4.5238934 - 289000 39.728005 1000 0.69794225 4.5396014 - 290000 40.206798 1000 0.6905751 4.5553093 - 291000 40.678802 1000 0.68652972 4.5710173 - 292000 41.147991 1000 0.6743341 4.5867253 - 293000 41.618836 1000 0.67357205 4.6024332 - 294000 42.08982 1000 0.66465346 4.6181412 - 295000 42.561323 1000 0.65587678 4.6338492 - 296000 43.034196 1000 0.65455827 4.6495571 - 297000 43.505748 1000 0.65135145 4.6652651 - 298000 43.975299 1000 0.65400349 4.6809731 - 299000 44.447556 1000 0.66186899 4.696681 - 300000 44.926073 1000 0.66844193 4.712389 - 301000 45.402658 1000 0.67720506 4.7280969 - 302000 45.880643 1000 0.68554918 4.7438049 - 303000 46.359444 1000 0.69321489 4.7595129 - 304000 46.841542 1000 0.70345329 4.7752208 - 305000 47.323539 1000 0.70172137 4.7909288 - 306000 47.809358 1000 0.70989191 4.8066368 - 307000 48.291664 1000 0.70546377 4.8223447 - 308000 48.770327 1000 0.70820389 4.8380527 - 309000 49.248974 1000 0.69637815 4.8537606 - 310000 49.72965 1000 0.68679532 4.8694686 - 311000 50.204503 1000 0.68824984 4.8851766 - 312000 50.683502 1000 0.68647935 4.9008845 - 313000 51.161407 1000 0.68289956 4.9165925 - 314000 51.638365 1000 0.68356788 4.9323005 - 315000 52.114341 1000 0.68269829 4.9480084 - 316000 52.590791 1000 0.67961769 4.9637164 - 317000 53.043198 1000 0.67437047 4.9794244 - 318000 53.499062 1000 0.66534726 4.9951323 - 319000 53.954004 1000 0.66052125 5.0108403 - 320000 54.409776 1000 0.65351962 5.0265482 - 321000 54.867935 1000 0.64155441 5.0422562 - 322000 55.324528 1000 0.63463177 5.0579642 - 323000 55.780399 1000 0.62945691 5.0736721 - 324000 56.239189 1000 0.63156746 5.0893801 - 325000 56.697767 1000 0.63883759 5.1050881 - 326000 57.155746 1000 0.64703516 5.120796 - 327000 57.618744 1000 0.65532057 5.136504 - 328000 58.083021 1000 0.66697061 5.152212 - 329000 58.547646 1000 0.66896271 5.1679199 - 330000 59.011518 1000 0.66551963 5.1836279 - 331000 59.478689 1000 0.65083894 5.1993358 - 332000 59.94887 1000 0.65171641 5.2150438 - 333000 60.416096 1000 0.65122777 5.2307518 - 334000 60.889826 1000 0.65844334 5.2464597 - 335000 61.363105 1000 0.66931264 5.2621677 - 336000 61.832482 1000 0.66847415 5.2778757 - 337000 62.300731 1000 0.65863495 5.2935836 - 338000 62.769011 1000 0.64977739 5.3092916 - 339000 63.232862 1000 0.6454395 5.3249995 - 340000 63.699228 1000 0.63484999 5.3407075 - 341000 64.165101 1000 0.62753448 5.3564155 - 342000 64.631118 1000 0.62781442 5.3721234 - 343000 65.099469 1000 0.63813963 5.3878314 - 344000 65.576568 1000 0.6485183 5.4035394 - 345000 66.054068 1000 0.67111606 5.4192473 - 346000 66.531747 1000 0.68435581 5.4349553 - 347000 67.007296 1000 0.69526046 5.4506633 - 348000 67.478242 1000 0.6876531 5.4663712 - 349000 67.944422 1000 0.67962108 5.4820792 - 350000 68.410281 1000 0.6800934 5.4977871 - 351000 68.862112 1000 0.67658657 5.5134951 - 352000 69.316476 1000 0.67043355 5.5292031 - 353000 69.76356 1000 0.66863154 5.544911 - 354000 70.212144 1000 0.65806572 5.560619 - 355000 70.658375 1000 0.6498301 5.576327 - 356000 71.103688 1000 0.64384284 5.5920349 - 357000 71.551545 1000 0.64228421 5.6077429 - 358000 72.001238 1000 0.6408188 5.6234508 - 359000 72.45158 1000 0.64388002 5.6391588 - 360000 72.906369 1000 0.64347896 5.6548668 - 361000 73.358316 1000 0.65055455 5.6705747 - 362000 73.814119 1000 0.65545061 5.6862827 - 363000 74.277034 1000 0.6667431 5.7019907 - 364000 74.737593 1000 0.6869856 5.7176986 - 365000 75.20209 1000 0.69651407 5.7334066 - 366000 75.667448 1000 0.70824091 5.7491146 - 367000 76.132389 1000 0.7144853 5.7648225 - 368000 76.596067 1000 0.71780876 5.7805305 - 369000 77.059749 1000 0.7159398 5.7962384 - 370000 77.519236 1000 0.70648968 5.8119464 - 371000 77.977404 1000 0.69796557 5.8276544 - 372000 78.434017 1000 0.69876891 5.8433623 - 373000 78.887217 1000 0.70908957 5.8590703 - 374000 79.341658 1000 0.70831124 5.8747783 - 375000 79.802381 1000 0.70631178 5.8904862 - 376000 80.265165 1000 0.70533876 5.9061942 - 377000 80.727821 1000 0.70097225 5.9219022 - 378000 81.187538 1000 0.70139806 5.9376101 - 379000 81.645627 1000 0.69691027 5.9533181 - 380000 82.105692 1000 0.69163881 5.969026 - 381000 82.56483 1000 0.68973183 5.984734 - 382000 83.025126 1000 0.68059207 6.000442 - 383000 83.482786 1000 0.68096466 6.0161499 - 384000 83.939808 1000 0.6698933 6.0318579 - 385000 84.418408 1000 0.66795846 6.0475659 - 386000 84.898757 1000 0.66153854 6.0632738 - 387000 85.376756 1000 0.66560025 6.0789818 - 388000 85.853575 1000 0.66671699 6.0946897 - 389000 86.32865 1000 0.66013733 6.1103977 - 390000 86.807772 1000 0.66181942 6.1261057 - 391000 87.290335 1000 0.66281334 6.1418136 - 392000 87.773899 1000 0.66657879 6.1575216 - 393000 88.248567 1000 0.66608992 6.1732296 - 394000 88.723817 1000 0.66128929 6.1889375 - 395000 89.200089 1000 0.65764538 6.2046455 - 396000 89.671826 1000 0.65073015 6.2203535 - 397000 90.142595 1000 0.64967355 6.2360614 - 398000 90.616654 1000 0.65193957 6.2517694 - 399000 91.093856 1000 0.64936977 6.2674773 - 400000 91.571678 1000 0.65849743 6.2831853 -Loop time of 91.5717 on 1 procs for 200000 steps with 1000 atoms - -Performance: 8916.580 tau/day, 2184.081 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 13.827 | 13.827 | 13.827 | 0.0 | 15.10 -Neigh | 0.097679 | 0.097679 | 0.097679 | 0.0 | 0.11 -Comm | 1.5668 | 1.5668 | 1.5668 | 0.0 | 1.71 -Output | 0.0042615 | 0.0042615 | 0.0042615 | 0.0 | 0.00 -Modify | 74.804 | 74.804 | 74.804 | 0.0 | 81.69 -Other | | 1.273 | | | 1.39 - -Nlocal: 1000 ave 1000 max 1000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 289 ave 289 max 289 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5091 ave 5091 max 5091 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5091 -Ave neighs/atom = 5.091 -Neighbor list builds = 160 -Dangerous builds = 0 -Total wall time: 0:02:27 diff --git a/examples/granregion/log.6Oct16.granregion.mixer.g++.4 b/examples/granregion/log.6Oct16.granregion.mixer.g++.4 deleted file mode 100644 index 726b31f8fe..0000000000 --- a/examples/granregion/log.6Oct16.granregion.mixer.g++.4 +++ /dev/null @@ -1,609 +0,0 @@ -LAMMPS (5 Oct 2016) -variable name string mixer - -thermo_modify flush yes -variable seed equal 14314 - -############################################### -# Particle parameters -################################################ - -variable rlo equal 0.3 -variable rhi equal 0.6 -variable dlo equal 2.0*${rlo} -variable dlo equal 2.0*0.3 -variable dhi equal 2.0*${rhi} -variable dhi equal 2.0*0.6 -variable skin equal ${rhi} -variable skin equal 0.6 - -variable coeffRes equal 0.1 -variable coeffFric equal 0.5 - -variable kn equal 10^5 -variable kt equal 0.2*${kn} -variable kt equal 0.2*100000 - -variable gravity equal 1.0 -variable density equal 1.0 - -variable min_mass equal ${density}*4.0/3.0*PI*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*PI*${rlo}*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*PI*0.3*${rlo}*${rlo} -variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*${rlo} -variable min_mass equal 1*4.0/3.0*PI*0.3*0.3*0.3 -variable a equal (-2.0*log(${coeffRes})/PI)^2 -variable a equal (-2.0*log(0.1)/PI)^2 -variable gamma_n equal sqrt($a*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*${kn}/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*100000/${min_mass}/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*$a)) -variable gamma_n equal sqrt(0.405284734569351*2*100000/0.113097335529233/(1+0.25*0.405284734569351)) -variable gamma_t equal ${gamma_n}*0.5 -variable gamma_t equal 806.699778405191*0.5 - -variable tcol equal PI/sqrt(2*${kn}/${min_mass}-${gamma_n}/4.0) -variable tcol equal PI/sqrt(2*100000/${min_mass}-${gamma_n}/4.0) -variable tcol equal PI/sqrt(2*100000/0.113097335529233-${gamma_n}/4.0) -variable tcol equal PI/sqrt(2*100000/0.113097335529233-806.699778405191/4.0) - -variable dt equal ${tcol}*0.02 -variable dt equal 0.00236257621510454*0.02 -timestep ${dt} -timestep 4.72515243020908e-05 - -############################################### - -variable dumpfreq equal 1000 -variable logfreq equal 1000 - -newton on -atom_style sphere - -boundary p p f - -region boxreg block 0 20 0 20 0 20 -create_box 1 boxreg -Created orthogonal box = (0 0 0) to (20 20 20) - 1 by 2 by 2 MPI processor grid - -pair_style gran/hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 -pair_style gran/hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 -pair_coeff * * - -neighbor ${skin} bin -neighbor 0.6 bin -thermo ${logfreq} -thermo 1000 - -comm_style brick -comm_modify mode multi group all vel yes -balance 1.1 shift xyz 20 1.1 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 0 - binsize = 20 -> bins = 1 1 1 -fix bal all balance 10000 1.1 shift xyz 20 1.01 - -####################### Options specific to pouring ######################### - -region insreg cylinder z 10 10 8 10 18 side in units box -region cylreg cylinder z 10 10 10 0 20 side in units box - -variable theta equal (step/400000)*2*PI - -region b1 block 2 18 9 11 0 4 side out rotate v_theta 10 10 0 0 0 1 units box -region b2 block 9 11 2 18 0 3.99999 side out rotate v_theta 10 10 0 0 0 1 units box - -region mixer intersect 3 cylreg b1 b2 side in - -fix grav all gravity ${gravity} vector 0 0 -1 -fix grav all gravity 1 vector 0 0 -1 -fix 1 all nve/sphere - -fix mixwall all wall/gran/region hertz/history ${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 ${gamma_n} ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 ${gamma_t} ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 ${coeffFric} 1 region mixer -fix mixwall all wall/gran/region hertz/history 100000 20000 806.699778405191 403.349889202595 0.5 1 region mixer - -fix ins all pour 1000 1 42424 region insreg diam range ${dlo} ${dhi} dens ${density} ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 ${dhi} dens ${density} ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens ${density} ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 ${density} -fix ins all pour 1000 1 42424 region insreg diam range 0.6 1.2 dens 1 1 -Particle insertion: 444 every 84653 steps, 1000 by step 169307 - -#dump 1 all custom ${dumpfreq} ${name}_pour.dump # id type mass diameter x y z - -#dump 2 all image 4000 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 zoom 1.5 # box no 0.0 axes no 0.0 0.0 -#dump_modify 2 pad 6 - -thermo_style custom step cpu atoms ke v_theta -WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:690) -thermo_modify flush yes lost warn - -run 200000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.8 - ghost atom cutoff = 1.8 - binsize = 0.9 -> bins = 23 23 23 -Memory usage per processor = 2.76258 Mbytes -Step CPU Atoms KinEng v_theta - 0 0 0 -0 0 - 1000 0.10398197 444 -0 0.015707963 - 2000 0.20485091 444 -0 0.031415927 - 3000 0.3069241 444 -0 0.04712389 - 4000 0.40875912 444 -0 0.062831853 - 5000 0.50989199 444 -0 0.078539816 - 6000 0.60949397 444 -0 0.09424778 - 7000 0.708915 444 -0 0.10995574 - 8000 0.80870605 444 -0 0.12566371 - 9000 0.90752602 444 -0 0.14137167 - 10000 1.0054469 444 -0 0.15707963 - 11000 1.072515 444 -0 0.1727876 - 12000 1.139096 444 -0 0.18849556 - 13000 1.2049479 444 -0 0.20420352 - 14000 1.2707851 444 -0 0.21991149 - 15000 1.3377919 444 -0 0.23561945 - 16000 1.405757 444 -0 0.25132741 - 17000 1.471797 444 -0 0.26703538 - 18000 1.538343 444 -0 0.28274334 - 19000 1.6035659 444 -0 0.2984513 - 20000 1.6690421 444 -0 0.31415927 - 21000 1.729399 444 -0 0.32986723 - 22000 1.7885301 444 -0 0.34557519 - 23000 1.8496239 444 -0 0.36128316 - 24000 1.913486 444 -0 0.37699112 - 25000 1.977428 444 -0 0.39269908 - 26000 2.04282 444 -0 0.40840704 - 27000 2.1089439 444 -0 0.42411501 - 28000 2.1759491 444 -0 0.43982297 - 29000 2.243813 444 -0 0.45553093 - 30000 2.312156 444 -0 0.4712389 - 31000 2.3742449 444 -0 0.48694686 - 32000 2.435447 444 -0 0.50265482 - 33000 2.495765 444 -0 0.51836279 - 34000 2.556865 444 -0 0.53407075 - 35000 2.6201291 444 -0 0.54977871 - 36000 2.6843281 444 -0 0.56548668 - 37000 2.7505059 444 -0 0.58119464 - 38000 2.817348 444 -0 0.5969026 - 39000 2.8837919 444 -0 0.61261057 - 40000 2.951216 444 -0 0.62831853 - 41000 3.012845 444 -0 0.64402649 - 42000 3.074688 444 -0 0.65973446 - 43000 3.13556 444 -0 0.67544242 - 44000 3.1965449 444 -0 0.69115038 - 45000 3.2582009 444 -0 0.70685835 - 46000 3.3201971 444 -0 0.72256631 - 47000 3.3819821 444 -0 0.73827427 - 48000 3.4455171 444 -0 0.75398224 - 49000 3.508738 444 -0 0.7696902 - 50000 3.5734961 444 -0 0.78539816 - 51000 3.6333289 444 -0 0.80110613 - 52000 3.694531 444 -0 0.81681409 - 53000 3.757041 444 -0 0.83252205 - 54000 3.820612 444 -0 0.84823002 - 55000 3.8852711 444 -0 0.86393798 - 56000 3.950211 444 -0 0.87964594 - 57000 4.015795 444 -0 0.89535391 - 58000 4.0818441 444 -0 0.91106187 - 59000 4.1476641 444 -0 0.92676983 - 60000 4.2141221 444 -0 0.9424778 - 61000 4.276612 444 -0 0.95818576 - 62000 4.339952 444 -0 0.97389372 - 63000 4.404351 444 -0 0.98960169 - 64000 4.4700999 444 -0 1.0053096 - 65000 4.5364759 444 -0 1.0210176 - 66000 4.605715 444 -0 1.0367256 - 67000 4.677629 444 -0 1.0524335 - 68000 4.7494669 444 -0 1.0681415 - 69000 4.8212609 444 -0 1.0838495 - 70000 4.894326 444 -0 1.0995574 - 71000 4.9639831 444 -0 1.1152654 - 72000 5.0345671 444 -0 1.1309734 - 73000 5.1048689 444 -0 1.1466813 - 74000 5.175498 444 -0 1.1623893 - 75000 5.2477591 444 -0 1.1780972 - 76000 5.3205409 444 -0 1.1938052 - 77000 5.394573 444 -0 1.2095132 - 78000 5.4685309 444 -0 1.2252211 - 79000 5.5431759 444 -0 1.2409291 - 80000 5.6212411 444 -0 1.2566371 - 81000 5.6890731 444 -0 1.272345 - 82000 5.7582159 444 -0 1.288053 - 83000 5.8298571 444 -0 1.303761 - 84000 5.9029069 444 -0 1.3194689 - 85000 6.0061591 888 -0 1.3351769 - 86000 6.1541281 888 -0 1.3508848 - 87000 6.3004079 888 -0 1.3665928 - 88000 6.4460659 888 -0 1.3823008 - 89000 6.591886 888 -0 1.3980087 - 90000 6.7376239 888 -0 1.4137167 - 91000 6.850734 888 -0 1.4294247 - 92000 6.9631939 888 -0 1.4451326 - 93000 7.0786369 888 -0 1.4608406 - 94000 7.1958089 888 -0 1.4765485 - 95000 7.3130219 888 -0 1.4922565 - 96000 7.430867 888 -0 1.5079645 - 97000 7.5498819 888 -0 1.5236724 - 98000 7.673686 888 -0 1.5393804 - 99000 7.7966969 888 -0 1.5550884 - 100000 7.921546 888 -0 1.5707963 - 101000 8.0396931 888 -0 1.5865043 - 102000 8.1583791 888 -0 1.6022123 - 103000 8.276613 888 -0 1.6179202 - 104000 8.3952639 888 -0 1.6336282 - 105000 8.514308 888 -0 1.6493361 - 106000 8.6361439 888 -0 1.6650441 - 107000 8.762326 888 -0 1.6807521 - 108000 8.8900061 888 -0 1.69646 - 109000 9.0179789 888 -0 1.712168 - 110000 9.1496761 888 -0 1.727876 - 111000 9.2728269 888 -0 1.7435839 - 112000 9.398078 888 -0 1.7592919 - 113000 9.519841 888 -0 1.7749998 - 114000 9.642343 888 -0 1.7907078 - 115000 9.7643859 888 -0 1.8064158 - 116000 9.8893411 888 -0 1.8221237 - 117000 10.01295 888 -0 1.8378317 - 118000 10.137574 888 -0 1.8535397 - 119000 10.263738 888 -0 1.8692476 - 120000 10.388673 888 -0 1.8849556 - 121000 10.507599 888 -0 1.9006636 - 122000 10.623901 888 -0 1.9163715 - 123000 10.740251 888 -0 1.9320795 - 124000 10.857467 888 -0 1.9477874 - 125000 10.975856 888 -0 1.9634954 - 126000 11.096002 888 -0 1.9792034 - 127000 11.217218 888 -0 1.9949113 - 128000 11.341925 888 -0 2.0106193 - 129000 11.467607 888 -0 2.0263273 - 130000 11.59517 888 -0 2.0420352 - 131000 11.71358 888 -0 2.0577432 - 132000 11.833024 888 -0 2.0734512 - 133000 11.954967 888 -0 2.0891591 - 134000 12.078482 888 -0 2.1048671 - 135000 12.202435 888 -0 2.120575 - 136000 12.327202 888 -0 2.136283 - 137000 12.453334 888 -0 2.151991 - 138000 12.583142 888 -0 2.1676989 - 139000 12.718396 888 -0 2.1834069 - 140000 12.854459 888 -0 2.1991149 - 141000 12.981024 888 -0 2.2148228 - 142000 13.108875 888 -0 2.2305308 - 143000 13.236802 888 -0 2.2462387 - 144000 13.36691 888 -0 2.2619467 - 145000 13.500126 888 -0 2.2776547 - 146000 13.633748 888 -0 2.2933626 - 147000 13.769077 888 -0 2.3090706 - 148000 13.90522 888 -0 2.3247786 - 149000 14.040417 888 -0 2.3404865 - 150000 14.176483 888 -0 2.3561945 - 151000 14.303389 888 -0 2.3719025 - 152000 14.432187 888 -0 2.3876104 - 153000 14.559857 888 -0 2.4033184 - 154000 14.691256 888 -0 2.4190263 - 155000 14.823413 888 -0 2.4347343 - 156000 14.956581 888 -0 2.4504423 - 157000 15.090666 888 -0 2.4661502 - 158000 15.228012 888 -0 2.4818582 - 159000 15.364569 888 -0 2.4975662 - 160000 15.501847 888 -0 2.5132741 - 161000 15.642772 888 -0 2.5289821 - 162000 15.783889 888 -0 2.54469 - 163000 15.926508 888 -0 2.560398 - 164000 16.07293 888 -0 2.576106 - 165000 16.221293 888 -0 2.5918139 - 166000 16.371738 888 -0 2.6075219 - 167000 16.523027 888 -0 2.6232299 - 168000 16.675525 888 -0 2.6389378 - 169000 16.830527 888 -0 2.6546458 - 170000 16.989955 1000 -0 2.6703538 - 171000 17.14772 1000 -0 2.6860617 - 172000 17.305565 1000 -0 2.7017697 - 173000 17.463517 1000 -0 2.7174776 - 174000 17.623862 1000 -0 2.7331856 - 175000 17.788165 1000 -0 2.7488936 - 176000 17.952028 1000 -0 2.7646015 - 177000 18.119269 1000 -0 2.7803095 - 178000 18.285714 1000 -0 2.7960175 - 179000 18.452439 1000 -0 2.8117254 - 180000 18.621119 1000 -0 2.8274334 - 181000 18.777982 1000 -0 2.8431414 - 182000 18.940248 1000 -0 2.8588493 - 183000 19.105385 1000 -0 2.8745573 - 184000 19.273934 1000 -0 2.8902652 - 185000 19.450922 1000 -0 2.9059732 - 186000 19.625563 1000 -0 2.9216812 - 187000 19.801329 1000 -0 2.9373891 - 188000 19.976869 1000 -0 2.9530971 - 189000 20.151134 1000 -0 2.9688051 - 190000 20.319214 1000 -0 2.984513 - 191000 20.485033 1000 -0 3.000221 - 192000 20.652254 1000 -0 3.0159289 - 193000 20.820876 1000 -0 3.0316369 - 194000 20.988597 1000 -0 3.0473449 - 195000 21.154705 1000 -0 3.0630528 - 196000 21.322634 1000 -0 3.0787608 - 197000 21.489394 1000 -0 3.0944688 - 198000 21.659512 1000 -0 3.1101767 - 199000 21.833228 1000 -0 3.1258847 - 200000 22.006487 1000 -0 3.1415927 -Loop time of 22.0065 on 4 procs for 200000 steps with 1000 atoms - -Performance: 37102.953 tau/day, 9088.222 timesteps/s -99.1% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.67692 | 1.166 | 1.6704 | 44.4 | 5.30 -Neigh | 0.01562 | 0.018723 | 0.0222 | 2.3 | 0.09 -Comm | 3.845 | 4.4454 | 5.0282 | 26.1 | 20.20 -Output | 0.0043464 | 0.0052906 | 0.0056455 | 0.8 | 0.02 -Modify | 12.239 | 13.152 | 14.347 | 25.1 | 59.76 -Other | | 3.22 | | | 14.63 - -Nlocal: 250 ave 257 max 244 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Nghost: 305.75 ave 372 max 242 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 982.5 ave 1380 max 572 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 3930 -Ave neighs/atom = 3.93 -Neighbor list builds = 216 -Dangerous builds = 0 -unfix ins -run 200000 -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.79826 - ghost atom cutoff = 1.79826 - binsize = 0.899132 -> bins = 23 23 23 -Memory usage per processor = 8.63577 Mbytes -Step CPU Atoms KinEng v_theta - 200000 0 1000 0.90316284 3.1415927 - 201000 0.16518497 1000 0.8867387 3.1573006 - 202000 0.33065486 1000 0.88745316 3.1730086 - 203000 0.4991529 1000 0.87793424 3.1887165 - 204000 0.6695168 1000 0.87009551 3.2044245 - 205000 0.83599901 1000 0.86431259 3.2201325 - 206000 1.001833 1000 0.85039776 3.2358404 - 207000 1.166487 1000 0.82897867 3.2515484 - 208000 1.3331649 1000 0.82069182 3.2672564 - 209000 1.5031869 1000 0.82349024 3.2829643 - 210000 1.6751509 1000 0.81859611 3.2986723 - 211000 1.846776 1000 0.82053992 3.3143802 - 212000 2.0198569 1000 0.82832647 3.3300882 - 213000 2.1932938 1000 0.82676865 3.3457962 - 214000 2.3676898 1000 0.82425781 3.3615041 - 215000 2.5424879 1000 0.83127148 3.3772121 - 216000 2.715348 1000 0.83925992 3.3929201 - 217000 2.8844988 1000 0.84390181 3.408628 - 218000 3.0485029 1000 0.85705713 3.424336 - 219000 3.211767 1000 0.85325946 3.440044 - 220000 3.3767338 1000 0.85641557 3.4557519 - 221000 3.5419538 1000 0.86922287 3.4714599 - 222000 3.710084 1000 0.89591143 3.4871678 - 223000 3.880873 1000 0.90395821 3.5028758 - 224000 4.054816 1000 0.91161431 3.5185838 - 225000 4.2260928 1000 0.92716425 3.5342917 - 226000 4.3996999 1000 0.91664886 3.5499997 - 227000 4.5679309 1000 0.9128853 3.5657077 - 228000 4.7353978 1000 0.91063998 3.5814156 - 229000 4.9045198 1000 0.90616712 3.5971236 - 230000 5.079206 1000 0.9042797 3.6128316 - 231000 5.252316 1000 0.91588137 3.6285395 - 232000 5.4218178 1000 0.92322871 3.6442475 - 233000 5.592988 1000 0.92370885 3.6599554 - 234000 5.753634 1000 0.91531408 3.6756634 - 235000 5.9159088 1000 0.91016621 3.6913714 - 236000 6.0817358 1000 0.89501073 3.7070793 - 237000 6.249059 1000 0.88504426 3.7227873 - 238000 6.4182718 1000 0.88268268 3.7384953 - 239000 6.5897119 1000 0.87811868 3.7542032 - 240000 6.758353 1000 0.88272663 3.7699112 - 241000 6.928581 1000 0.87751512 3.7856191 - 242000 7.0978079 1000 0.87017281 3.8013271 - 243000 7.268832 1000 0.86587613 3.8170351 - 244000 7.439904 1000 0.85157794 3.832743 - 245000 7.6105168 1000 0.8291738 3.848451 - 246000 7.7830069 1000 0.82315948 3.864159 - 247000 7.9578128 1000 0.81231703 3.8798669 - 248000 8.134944 1000 0.79931415 3.8955749 - 249000 8.3061719 1000 0.78877578 3.9112829 - 250000 8.476692 1000 0.78519942 3.9269908 - 251000 8.6525538 1000 0.78837716 3.9426988 - 252000 8.8288019 1000 0.79621044 3.9584067 - 253000 9.006846 1000 0.78744385 3.9741147 - 254000 9.1839809 1000 0.78810047 3.9898227 - 255000 9.3600328 1000 0.79053484 4.0055306 - 256000 9.538172 1000 0.79976932 4.0212386 - 257000 9.7188668 1000 0.81724577 4.0369466 - 258000 9.9032769 1000 0.81135963 4.0526545 - 259000 10.084928 1000 0.82017101 4.0683625 - 260000 10.266693 1000 0.82352898 4.0840704 - 261000 10.449515 1000 0.81662689 4.0997784 - 262000 10.630166 1000 0.82707216 4.1154864 - 263000 10.812056 1000 0.82001278 4.1311943 - 264000 10.991668 1000 0.81136264 4.1469023 - 265000 11.172162 1000 0.80507755 4.1626103 - 266000 11.353101 1000 0.80247583 4.1783182 - 267000 11.533476 1000 0.78870449 4.1940262 - 268000 11.716022 1000 0.77775428 4.2097342 - 269000 11.900351 1000 0.78170639 4.2254421 - 270000 12.083609 1000 0.78023258 4.2411501 - 271000 12.266298 1000 0.76257507 4.256858 - 272000 12.449454 1000 0.75871195 4.272566 - 273000 12.633748 1000 0.75909277 4.288274 - 274000 12.820916 1000 0.76329234 4.3039819 - 275000 13.004197 1000 0.76188557 4.3196899 - 276000 13.188507 1000 0.75974847 4.3353979 - 277000 13.372202 1000 0.75392834 4.3511058 - 278000 13.557712 1000 0.74837333 4.3668138 - 279000 13.747933 1000 0.74268307 4.3825218 - 280000 13.934871 1000 0.73840427 4.3982297 - 281000 14.11717 1000 0.73817851 4.4139377 - 282000 14.30208 1000 0.73666069 4.4296456 - 283000 14.485039 1000 0.74064713 4.4453536 - 284000 14.671087 1000 0.73916222 4.4610616 - 285000 14.863267 1000 0.73225442 4.4767695 - 286000 15.050005 1000 0.7312283 4.4924775 - 287000 15.234556 1000 0.72947519 4.5081855 - 288000 15.422593 1000 0.72469992 4.5238934 - 289000 15.609153 1000 0.70843645 4.5396014 - 290000 15.797906 1000 0.69731415 4.5553093 - 291000 15.983677 1000 0.69099822 4.5710173 - 292000 16.168935 1000 0.68855366 4.5867253 - 293000 16.355853 1000 0.69826256 4.6024332 - 294000 16.544831 1000 0.70211589 4.6181412 - 295000 16.733875 1000 0.7055847 4.6338492 - 296000 16.918698 1000 0.69692413 4.6495571 - 297000 17.100869 1000 0.68027227 4.6652651 - 298000 17.280404 1000 0.67254493 4.6809731 - 299000 17.46406 1000 0.67767946 4.696681 - 300000 17.652748 1000 0.68480172 4.712389 - 301000 17.84199 1000 0.67864643 4.7280969 - 302000 18.025759 1000 0.67656342 4.7438049 - 303000 18.208747 1000 0.67719641 4.7595129 - 304000 18.391225 1000 0.68049491 4.7752208 - 305000 18.576276 1000 0.68230722 4.7909288 - 306000 18.764125 1000 0.67985 4.8066368 - 307000 18.956063 1000 0.67790944 4.8223447 - 308000 19.147159 1000 0.6836647 4.8380527 - 309000 19.339173 1000 0.69705355 4.8537606 - 310000 19.530591 1000 0.69858847 4.8694686 - 311000 19.720214 1000 0.69448554 4.8851766 - 312000 19.907717 1000 0.68878539 4.9008845 - 313000 20.088793 1000 0.68810484 4.9165925 - 314000 20.268118 1000 0.68483484 4.9323005 - 315000 20.445564 1000 0.67732034 4.9480084 - 316000 20.627415 1000 0.67943319 4.9637164 - 317000 20.807826 1000 0.67326868 4.9794244 - 318000 20.983587 1000 0.67762092 4.9951323 - 319000 21.156655 1000 0.68914624 5.0108403 - 320000 21.331391 1000 0.69872806 5.0265482 - 321000 21.506313 1000 0.71510434 5.0422562 - 322000 21.679505 1000 0.71452122 5.0579642 - 323000 21.85396 1000 0.71765429 5.0736721 - 324000 22.02904 1000 0.72748838 5.0893801 - 325000 22.205191 1000 0.72974854 5.1050881 - 326000 22.38063 1000 0.73324928 5.120796 - 327000 22.555817 1000 0.72479525 5.136504 - 328000 22.729859 1000 0.71942855 5.152212 - 329000 22.903234 1000 0.71890587 5.1679199 - 330000 23.078575 1000 0.73495891 5.1836279 - 331000 23.252865 1000 0.74306733 5.1993358 - 332000 23.427175 1000 0.75274051 5.2150438 - 333000 23.604881 1000 0.75981346 5.2307518 - 334000 23.789045 1000 0.75410165 5.2464597 - 335000 23.971105 1000 0.74802374 5.2621677 - 336000 24.150954 1000 0.73111266 5.2778757 - 337000 24.331991 1000 0.72226021 5.2935836 - 338000 24.515157 1000 0.70866271 5.3092916 - 339000 24.69639 1000 0.70253496 5.3249995 - 340000 24.879524 1000 0.69381505 5.3407075 - 341000 25.061928 1000 0.68285569 5.3564155 - 342000 25.2437 1000 0.67262303 5.3721234 - 343000 25.423809 1000 0.67160137 5.3878314 - 344000 25.605531 1000 0.67658439 5.4035394 - 345000 25.78848 1000 0.67113748 5.4192473 - 346000 25.969866 1000 0.67506296 5.4349553 - 347000 26.152485 1000 0.67686518 5.4506633 - 348000 26.335445 1000 0.68878941 5.4663712 - 349000 26.522271 1000 0.70728493 5.4820792 - 350000 26.709942 1000 0.70870657 5.4977871 - 351000 26.889998 1000 0.71541489 5.5134951 - 352000 27.069872 1000 0.71827633 5.5292031 - 353000 27.249259 1000 0.7099127 5.544911 - 354000 27.428386 1000 0.70507946 5.560619 - 355000 27.607797 1000 0.70709703 5.576327 - 356000 27.788887 1000 0.70637714 5.5920349 - 357000 27.975344 1000 0.7088694 5.6077429 - 358000 28.164236 1000 0.70907948 5.6234508 - 359000 28.352999 1000 0.71504714 5.6391588 - 360000 28.539172 1000 0.71417205 5.6548668 - 361000 28.722691 1000 0.70716852 5.6705747 - 362000 28.906856 1000 0.70193967 5.6862827 - 363000 29.087598 1000 0.69786793 5.7019907 - 364000 29.268141 1000 0.68714789 5.7176986 - 365000 29.450765 1000 0.68170443 5.7334066 - 366000 29.633131 1000 0.67832571 5.7491146 - 367000 29.816219 1000 0.67809457 5.7648225 - 368000 29.999479 1000 0.66886004 5.7805305 - 369000 30.182675 1000 0.67233336 5.7962384 - 370000 30.36698 1000 0.67433369 5.8119464 - 371000 30.550787 1000 0.67478226 5.8276544 - 372000 30.736018 1000 0.67882814 5.8433623 - 373000 30.922576 1000 0.68494254 5.8590703 - 374000 31.107558 1000 0.69046765 5.8747783 - 375000 31.291329 1000 0.69398953 5.8904862 - 376000 31.474582 1000 0.68692367 5.9061942 - 377000 31.656979 1000 0.674184 5.9219022 - 378000 31.83851 1000 0.65899449 5.9376101 - 379000 32.019869 1000 0.65198402 5.9533181 - 380000 32.200375 1000 0.64366122 5.969026 - 381000 32.381651 1000 0.64443345 5.984734 - 382000 32.561897 1000 0.64655912 6.000442 - 383000 32.743947 1000 0.64894161 6.0161499 - 384000 32.927231 1000 0.65259561 6.0318579 - 385000 33.11882 1000 0.65230446 6.0475659 - 386000 33.311072 1000 0.64177598 6.0632738 - 387000 33.50435 1000 0.63900349 6.0789818 - 388000 33.695734 1000 0.64611067 6.0946897 - 389000 33.885915 1000 0.64943993 6.1103977 - 390000 34.076093 1000 0.66303716 6.1261057 - 391000 34.264909 1000 0.68916583 6.1418136 - 392000 34.45411 1000 0.71501556 6.1575216 - 393000 34.644116 1000 0.73685375 6.1732296 - 394000 34.834608 1000 0.74461041 6.1889375 - 395000 35.025693 1000 0.75251204 6.2046455 - 396000 35.217372 1000 0.75493054 6.2203535 - 397000 35.407008 1000 0.77028775 6.2360614 - 398000 35.594868 1000 0.7686439 6.2517694 - 399000 35.778411 1000 0.75167376 6.2674773 - 400000 35.962646 1000 0.73505917 6.2831853 -Loop time of 35.9627 on 4 procs for 200000 steps with 1000 atoms - -Performance: 22704.278 tau/day, 5561.323 timesteps/s -99.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.0549 | 3.4094 | 4.9773 | 72.1 | 9.48 -Neigh | 0.022087 | 0.026923 | 0.032716 | 2.9 | 0.07 -Comm | 7.3555 | 9.2143 | 10.854 | 53.0 | 25.62 -Output | 0.0046289 | 0.0058927 | 0.0071292 | 1.4 | 0.02 -Modify | 17.504 | 19.601 | 22.342 | 44.9 | 54.50 -Other | | 3.705 | | | 10.30 - -Nlocal: 250 ave 269 max 225 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Nghost: 408.5 ave 500 max 320 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Neighs: 1262.25 ave 1665 max 880 min -Histogram: 1 0 1 0 0 0 0 1 0 1 - -Total # of neighbors = 5049 -Ave neighs/atom = 5.049 -Neighbor list builds = 166 -Dangerous builds = 0 -Total wall time: 0:00:57 diff --git a/examples/hugoniostat/in.hugoniostat b/examples/hugoniostat/in.hugoniostat index affc97980c..01c2a246fc 100644 --- a/examples/hugoniostat/in.hugoniostat +++ b/examples/hugoniostat/in.hugoniostat @@ -15,7 +15,7 @@ units lj boundary p p p -atom_style atomic +atom_style atomic # Set up FCC lattice with z axis along <110> @@ -39,10 +39,10 @@ pair_coeff * * 1.0 0.8908987 fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100 thermo 100 -thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz +thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz min_modify line quadratic -minimize 0.0 1.0e-6 10000 100000 +minimize 0.0 1.0e-6 10000 100000 # Define initial velocity @@ -51,8 +51,6 @@ write_restart restart.equil # Start Run #1 -log log.nodrag - clear read_restart restart.equil @@ -87,22 +85,20 @@ thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)' -#dump id all atom 500 dump.hugoniostat +#dump id all atom 500 dump.hugoniostat -#dump 2 all image 500 image.*.jpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 +#dump 2 all image 500 image.*.jpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 -#dump 3 all movie 500 movie.mpg type type & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 +#dump 3 all movie 500 movie.mpg type type & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 -run 10000 +run 10000 # Start Run #2 -log log.drag - clear read_restart restart.equil @@ -137,12 +133,10 @@ thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)' -run 10000 +run 10000 # Start Run #3 -log log.nhchains - clear read_restart restart.equil @@ -177,5 +171,5 @@ thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)' -run 10000 +run 10000 diff --git a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 new file mode 100644 index 0000000000..2473641dea --- /dev/null +++ b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.1 @@ -0,0 +1,401 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# This script reproduces stress trajectories from Fig. 1 in +# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004) +# +# Three thermostatting scenarios are visited: undamped (nodrag), +# damped (drag) and Nose-Hoover chain (nhchains). +# +# The axial and shear stress trajectories are printed to the +# file "stress_vs_t.dat". For the damped case, the original figure +# seems to be a plot of 2*tau, rather than tau. +# +# The script also demonstrates how to +# orient a crystal along <110>, +# and how to use the lj/cubic pair style. + +units lj +boundary p p p + +atom_style atomic + +# Set up FCC lattice with z axis along <110> + +lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0 +Lattice spacing in x,y,z = 1.41421 2 2 + +region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice +create_box 1 mycell +Created orthogonal box = (0 0 0) to (7.07107 10 10) + 1 by 1 by 1 MPI processor grid +mass * 1.0 +create_atoms 1 box +Created 1000 atoms + Time spent = 0.000465155 secs + +# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987 + +pair_style lj/cubic +pair_coeff * * 1.0 0.8908987 + +# Relax box dimensions + +fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100 + +thermo 100 +thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz + +min_modify line quadratic +minimize 0.0 1.0e-6 10000 100000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.84754 + ghost atom cutoff = 1.84754 + binsize = 0.923769, bins = 8 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.247 | 4.247 | 4.247 Mbytes +Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz + 0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999 + 100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999 + 134 0 -6.3344257 -6.3344257 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199 +Loop time of 0.0724094 on 1 procs for 134 steps with 1000 atoms + +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = force tolerance + Energy initial, next-to-last, final = + -6.2937539309 -6.33442568056 -6.33442568056 + Force two-norm initial, final = 3395.29 5.83329e-10 + Force max component initial, final = 1960.27 3.42093e-10 + Final line search alpha, max atom move = 1 3.42093e-10 + Iterations, force evaluations = 134 137 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.054599 | 0.054599 | 0.054599 | 0.0 | 75.40 +Neigh | 0.0011106 | 0.0011106 | 0.0011106 | 0.0 | 1.53 +Comm | 0.002012 | 0.002012 | 0.002012 | 0.0 | 2.78 +Output | 1.955e-05 | 1.955e-05 | 1.955e-05 | 0.0 | 0.03 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.01467 | | | 20.26 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1724 ave 1724 max 1724 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 21000 ave 21000 max 21000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 21000 +Ave neighs/atom = 21 +Neighbor list builds = 1 +Dangerous builds = 0 + +# Define initial velocity + +velocity all create 0.01 87287 mom yes rot yes dist gaussian +write_restart restart.equil + +# Start Run #1 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/cubic from restart + 1000 atoms + +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes +timestep 0.001 +reset_timestep 0 + +# Pzz = 40.0, drag/damping term off + +fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0 + +# Specify reference state from paper, times 1000 atoms + +fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519 + +# Add fix energy to ouput etotal + +fix_modify myhug energy yes + +# Define output + +variable dele equal f_myhug[1] # energy delta [temperature] +variable us equal f_myhug[2] # shock velocity [distance/time] +variable up equal f_myhug[3] # particle velocity [distance/time] +variable pzz equal pzz # axial stress +variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress +variable time equal dt*step + +thermo 1000 +thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up + +fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)' + +#dump id all atom 500 dump.hugoniostat + +#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.74754 + ghost atom cutoff = 1.74754 + binsize = 0.873769, bins = 8 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes +Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up + 0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654 + 1000 0.0093381489 0.013993216 -2.170443 -6.3381216 129.15286 58.544417 8.3142516 -4.1816719 0.93744258 23.519053 3.7381989 + 2000 0.24794909 0.37155171 -5.8915802 -6.0429087 8.3850692 1.3744507 9.5938765 -0.5228803 -0.2435043 13.910468 0.4103393 + 3000 0.38920701 0.5832267 -3.768677 -6.6246124 72.742761 28.486747 8.623805 -3.439162 0.003825459 19.697379 2.5139668 + 4000 0.67009971 1.0041444 -4.2080644 -6.1365367 35.596179 3.9344133 8.7508422 -2.9326167 -0.58039603 14.529822 1.6677129 + 5000 0.41848975 0.62710689 -4.8393088 -6.1026724 30.626544 4.6387208 8.7827245 -1.8904705 -0.31996439 13.670884 1.5250343 + 6000 0.22410139 0.33581594 -3.7652941 -6.0923259 50.807437 7.2229456 8.2549488 -2.6628477 -0.017396966 14.4806 2.3884652 + 7000 0.095001485 0.14235972 -4.5436753 -6.7307217 35.8743 3.4938089 8.4476287 -2.3294061 -0.052272192 12.957528 1.8846881 + 8000 0.043277437 0.064851239 -4.6264096 -6.2447456 39.658659 6.7266325 8.4327483 -1.6831873 0.070488482 13.553882 1.9918311 + 9000 0.018271956 0.027380526 -4.4239627 -6.3085661 41.708324 5.9081923 8.3463321 -1.9119839 0.091057512 13.503882 2.1025305 + 10000 0.0082840001 0.012413574 -4.622252 -6.3316699 39.830379 6.5596321 8.4109569 -1.7218314 0.099435465 13.482451 2.0110543 +Loop time of 6.20702 on 1 procs for 10000 steps with 1000 atoms + +Performance: 139197.321 tau/day, 1611.080 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.0198 | 5.0198 | 5.0198 | 0.0 | 80.87 +Neigh | 0.21405 | 0.21405 | 0.21405 | 0.0 | 3.45 +Comm | 0.16164 | 0.16164 | 0.16164 | 0.0 | 2.60 +Output | 0.00053501 | 0.00053501 | 0.00053501 | 0.0 | 0.01 +Modify | 0.7419 | 0.7419 | 0.7419 | 0.0 | 11.95 +Other | | 0.06911 | | | 1.11 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1886 ave 1886 max 1886 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 20874 ave 20874 max 20874 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 20874 +Ave neighs/atom = 20.874 +Neighbor list builds = 188 +Dangerous builds = 0 + +# Start Run #2 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/cubic from restart + 1000 atoms + +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes +timestep 0.001 +reset_timestep 0 + +# Pzz = 40.0, drag/damping term on + +fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 + +# Specify reference state from paper, times 1000 atoms + +fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519 + +# Add fix energy to ouput etotal + +fix_modify myhug energy yes + +# Define output + +variable dele equal f_myhug[1] # energy delta [temperature] +variable us equal f_myhug[2] # shock velocity [distance/time] +variable up equal f_myhug[3] # particle velocity [distance/time] +variable pzz equal pzz # axial stress +variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress +variable time equal dt*step + +thermo 1000 +thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up + +fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)' + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.74754 + ghost atom cutoff = 1.74754 + binsize = 0.873769, bins = 8 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes +Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up + 0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654 + 1000 0.0062572991 0.0093765627 -5.9890874 -7.64465 18.918117 7.5844397 9.2338165 -1.6649392 0.02341947 13.976996 0.92138738 + 2000 0.006845108 0.010257394 -5.4565813 -7.9786876 37.064254 15.537266 8.9496404 -2.5323637 0.1023062 16.325405 1.5455017 + 3000 0.0073276109 0.010980425 -5.3663425 -7.9938818 39.907292 16.807488 8.9154852 -2.6385197 0.11818131 16.639049 1.6326833 + 4000 0.0069296915 0.010384143 -5.3623404 -8.0023271 40.010741 16.851482 8.9144328 -2.6503708 0.11868152 16.651571 1.6356847 + 5000 0.0076142476 0.01140995 -5.3631447 -8.0108329 39.997648 16.846756 8.9145416 -2.6590981 0.11841154 16.649778 1.6353255 + 6000 0.0077053839 0.011546518 -5.3628542 -8.0192007 39.991597 16.840313 8.9145803 -2.6678931 0.11818376 16.648851 1.6351691 + 7000 0.0077405662 0.011599239 -5.3623534 -8.0275624 40.000448 16.844008 8.9145774 -2.6768081 0.11809914 16.650669 1.6353525 + 8000 0.008067359 0.012088937 -5.3623759 -8.0359471 39.995327 16.840134 8.9146099 -2.6856601 0.11787118 16.649881 1.6352204 + 9000 0.0083223114 0.012470984 -5.3622992 -8.0443714 40.00571 16.847763 8.9146503 -2.6945431 0.11781538 16.652389 1.6353987 + 10000 0.0091249143 0.013673684 -5.3630142 -8.0529573 39.987196 16.837314 8.9146848 -2.7036168 0.11743028 16.648831 1.6349911 +Loop time of 5.48047 on 1 procs for 10000 steps with 1000 atoms + +Performance: 157650.687 tau/day, 1824.661 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.5166 | 4.5166 | 4.5166 | 0.0 | 82.41 +Neigh | 0.012162 | 0.012162 | 0.012162 | 0.0 | 0.22 +Comm | 0.14168 | 0.14168 | 0.14168 | 0.0 | 2.59 +Output | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.01 +Modify | 0.74394 | 0.74394 | 0.74394 | 0.0 | 13.57 +Other | | 0.06553 | | | 1.20 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1724 ave 1724 max 1724 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 21000 ave 21000 max 21000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 21000 +Ave neighs/atom = 21 +Neighbor list builds = 11 +Dangerous builds = 0 + +# Start Run #3 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421) + 1 by 1 by 1 MPI processor grid + restoring pair style lj/cubic from restart + 1000 atoms + +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes +timestep 0.001 +reset_timestep 0 + +# Pzz = 40.0, drag/damping term off, Nose-Hoover chains + +fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 + +# Specify reference state from paper, times 1000 atoms + +fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519 + +# Add fix energy to ouput etotal + +fix_modify myhug energy yes + +# Define output + +variable dele equal f_myhug[1] # energy delta [temperature] +variable us equal f_myhug[2] # shock velocity [distance/time] +variable up equal f_myhug[3] # particle velocity [distance/time] +variable pzz equal pzz # axial stress +variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress +variable time equal dt*step + +thermo 1000 +thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up + +fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)' + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.74754 + ghost atom cutoff = 1.74754 + binsize = 0.873769, bins = 8 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.771 | 2.771 | 2.771 Mbytes +Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up + 0 0.01 0.014985 -6.3344257 -6.3194407 0.014381062 -0.0002397183 9.8684199 0 -0.0048551451 2.3814196 0.0041108654 + 1000 0.0083300394 0.012482564 -5.5023188 -6.3233387 35.610076 14.886667 8.9677982 -0.83350251 0.093761848 16.159481 1.500112 + 2000 0.020386462 0.030549113 -5.2949349 -6.2805556 41.760388 17.563305 8.896033 -1.0161699 0.11780863 16.85284 1.6868235 + 3000 0.049693152 0.074465188 -5.3469434 -6.2493961 39.030372 16.123483 8.9325594 -0.9769179 0.073097387 16.601986 1.6003716 + 4000 0.11859514 0.17771482 -5.207077 -6.3242752 40.941558 16.507785 8.9213147 -1.2949131 0.018189678 16.904156 1.6487282 + 5000 0.13014573 0.19502337 -5.2610248 -6.269279 39.059628 15.609345 8.9431685 -1.2032776 -0.00023747376 16.701437 1.5920344 + 6000 0.1381307 0.20698886 -5.171005 -6.2931942 40.904837 16.242165 8.9222854 -1.3291781 -0.0044770368 16.905086 1.6471589 + 7000 0.12107326 0.18142828 -5.2602554 -6.2438099 39.060928 15.57765 8.9397525 -1.1649827 0.0055890257 16.671524 1.594944 + 8000 0.14333636 0.21478954 -5.1717123 -6.304602 40.876188 16.205815 8.9218142 -1.3476793 -0.0069396327 16.895033 1.6469846 + 9000 0.12159663 0.18221255 -5.2591911 -6.2587685 39.228648 15.677869 8.9376641 -1.18179 0.0077357066 16.688862 1.6001283 + 10000 0.15321883 0.22959841 -5.1881787 -6.3448453 40.666451 16.146177 8.922851 -1.386265 -0.0091929687 16.860705 1.6418699 +Loop time of 5.6426 on 1 procs for 10000 steps with 1000 atoms + +Performance: 153120.907 tau/day, 1772.233 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 4.5653 | 4.5653 | 4.5653 | 0.0 | 80.91 +Neigh | 0.10885 | 0.10885 | 0.10885 | 0.0 | 1.93 +Comm | 0.14695 | 0.14695 | 0.14695 | 0.0 | 2.60 +Output | 0.00055218 | 0.00055218 | 0.00055218 | 0.0 | 0.01 +Modify | 0.75364 | 0.75364 | 0.75364 | 0.0 | 13.36 +Other | | 0.0673 | | | 1.19 + +Nlocal: 1000 ave 1000 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1724 ave 1724 max 1724 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 20654 ave 20654 max 20654 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 20654 +Ave neighs/atom = 20.654 +Neighbor list builds = 94 +Dangerous builds = 0 + +Total wall time: 0:00:17 diff --git a/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 new file mode 100644 index 0000000000..30f1335ea9 --- /dev/null +++ b/examples/hugoniostat/log.27Nov18.hugoniostat.g++.4 @@ -0,0 +1,401 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# This script reproduces stress trajectories from Fig. 1 in +# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004) +# +# Three thermostatting scenarios are visited: undamped (nodrag), +# damped (drag) and Nose-Hoover chain (nhchains). +# +# The axial and shear stress trajectories are printed to the +# file "stress_vs_t.dat". For the damped case, the original figure +# seems to be a plot of 2*tau, rather than tau. +# +# The script also demonstrates how to +# orient a crystal along <110>, +# and how to use the lj/cubic pair style. + +units lj +boundary p p p + +atom_style atomic + +# Set up FCC lattice with z axis along <110> + +lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0 +Lattice spacing in x,y,z = 1.41421 2 2 + +region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice +create_box 1 mycell +Created orthogonal box = (0 0 0) to (7.07107 10 10) + 1 by 2 by 2 MPI processor grid +mass * 1.0 +create_atoms 1 box +Created 1000 atoms + Time spent = 0.0003438 secs + +# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987 + +pair_style lj/cubic +pair_coeff * * 1.0 0.8908987 + +# Relax box dimensions + +fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100 + +thermo 100 +thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz + +min_modify line quadratic +minimize 0.0 1.0e-6 10000 100000 +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.84754 + ghost atom cutoff = 1.84754 + binsize = 0.923769, bins = 8 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.211 | 4.211 | 4.211 Mbytes +Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz + 0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999 + 100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999 + 134 0 -6.3344257 -6.3344257 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199 +Loop time of 0.0269771 on 4 procs for 134 steps with 1000 atoms + +94.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = force tolerance + Energy initial, next-to-last, final = + -6.2937539309 -6.33442568056 -6.33442568056 + Force two-norm initial, final = 3395.29 5.80609e-10 + Force max component initial, final = 1960.27 3.41627e-10 + Final line search alpha, max atom move = 1 3.41627e-10 + Iterations, force evaluations = 134 137 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.011534 | 0.013897 | 0.016008 | 1.3 | 51.51 +Neigh | 0.00024176 | 0.00029498 | 0.00035191 | 0.0 | 1.09 +Comm | 0.0029764 | 0.0050126 | 0.0073018 | 2.2 | 18.58 +Output | 1.8835e-05 | 1.9968e-05 | 2.2888e-05 | 0.0 | 0.07 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.007753 | | | 28.74 + +Nlocal: 250 ave 305 max 205 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Nghost: 829 ave 874 max 774 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 5250 ave 6445 max 4305 min +Histogram: 1 0 0 2 0 0 0 0 0 1 + +Total # of neighbors = 21000 +Ave neighs/atom = 21 +Neighbor list builds = 1 +Dangerous builds = 0 + +# Define initial velocity + +velocity all create 0.01 87287 mom yes rot yes dist gaussian +write_restart restart.equil + +# Start Run #1 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421) + 1 by 2 by 2 MPI processor grid + restoring pair style lj/cubic from restart + 1000 atoms + +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes +timestep 0.001 +reset_timestep 0 + +# Pzz = 40.0, drag/damping term off + +fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0 + +# Specify reference state from paper, times 1000 atoms + +fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519 + +# Add fix energy to ouput etotal + +fix_modify myhug energy yes + +# Define output + +variable dele equal f_myhug[1] # energy delta [temperature] +variable us equal f_myhug[2] # shock velocity [distance/time] +variable up equal f_myhug[3] # particle velocity [distance/time] +variable pzz equal pzz # axial stress +variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress +variable time equal dt*step + +thermo 1000 +thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up + +fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)' + +#dump id all atom 500 dump.hugoniostat + +#dump 2 all image 500 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 500 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.74754 + ghost atom cutoff = 1.74754 + binsize = 0.873769, bins = 8 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes +Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up + 0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135 + 1000 0.010586668 0.015864122 -2.1721826 -6.3380886 129.03334 58.456626 8.3141284 -4.1817701 0.93542408 23.507246 3.7366154 + 2000 0.3321368 0.49770699 -5.584787 -6.0546694 12.097343 1.2026972 9.4615963 -0.96758935 -0.3571439 13.858218 0.5942385 + 3000 0.46981685 0.70402055 -3.9208474 -6.3911005 63.005989 22.559106 8.6828663 -3.1742737 -0.16958917 18.776521 2.2842567 + 4000 0.54866493 0.82217439 -4.1703408 -6.2427645 38.408608 4.9066022 8.6573289 -2.894598 -0.45434132 14.506935 1.8023166 + 5000 0.30625495 0.45892304 -4.7355785 -6.186448 35.000599 6.2097986 8.6658098 -1.9097925 -0.19603125 13.896448 1.7145489 + 6000 0.13938196 0.20886386 -4.303964 -5.7629121 50.370681 12.189231 8.3966581 -1.6678119 0.11451271 15.088809 2.2724852 + 7000 0.055349516 0.082941249 -5.2031342 -6.8043199 30.859256 6.5562297 8.6850282 -1.684127 0.020586458 13.152479 1.5971879 + 8000 0.027926794 0.0418483 -4.5281656 -5.4484008 48.145681 12.229919 8.4107051 -0.96208352 0.19922201 14.821877 2.2112219 + 9000 0.018195086 0.027265336 -4.9847444 -6.5712684 37.347655 8.7291385 8.5606968 -1.6137894 0.10912534 13.773573 1.8458438 + 10000 0.0082893467 0.012421586 -5.0130076 -6.6821423 36.46118 8.3386716 8.5689995 -1.6815563 0.1065388 13.651975 1.8180818 +Loop time of 2.01177 on 4 procs for 10000 steps with 1000 atoms + +Performance: 429472.539 tau/day, 4970.747 timesteps/s +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.2437 | 1.2651 | 1.2843 | 1.7 | 62.89 +Neigh | 0.051696 | 0.052503 | 0.053247 | 0.3 | 2.61 +Comm | 0.24826 | 0.26724 | 0.28867 | 3.5 | 13.28 +Output | 0.00058603 | 0.00085759 | 0.0016623 | 0.0 | 0.04 +Modify | 0.37363 | 0.37671 | 0.38189 | 0.5 | 18.73 +Other | | 0.04935 | | | 2.45 + +Nlocal: 250 ave 260 max 240 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 927.5 ave 934 max 921 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 5048.5 ave 5203 max 4889 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 20194 +Ave neighs/atom = 20.194 +Neighbor list builds = 175 +Dangerous builds = 0 + +# Start Run #2 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421) + 1 by 2 by 2 MPI processor grid + restoring pair style lj/cubic from restart + 1000 atoms + +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes +timestep 0.001 +reset_timestep 0 + +# Pzz = 40.0, drag/damping term on + +fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0 + +# Specify reference state from paper, times 1000 atoms + +fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519 + +# Add fix energy to ouput etotal + +fix_modify myhug energy yes + +# Define output + +variable dele equal f_myhug[1] # energy delta [temperature] +variable us equal f_myhug[2] # shock velocity [distance/time] +variable up equal f_myhug[3] # particle velocity [distance/time] +variable pzz equal pzz # axial stress +variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress +variable time equal dt*step + +thermo 1000 +thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up + +fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)' + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.74754 + ghost atom cutoff = 1.74754 + binsize = 0.873769, bins = 8 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes +Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up + 0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135 + 1000 0.0063089138 0.0094539073 -5.9892326 -7.6448129 18.914956 7.5823222 9.2337797 -1.6650342 0.023426454 13.975434 0.92133642 + 2000 0.0068813683 0.01031173 -5.4566765 -7.9789037 37.064192 15.537213 8.9495783 -2.5325388 0.10234565 16.32485 1.5455517 + 3000 0.0072427316 0.010853233 -5.3662818 -7.9940958 39.906002 16.80569 8.9154322 -2.6386672 0.11821344 16.638326 1.6327015 + 4000 0.0070936522 0.010629838 -5.3626164 -8.0025859 40.007994 16.850321 8.9143648 -2.6505993 0.11869226 16.650416 1.6356859 + 5000 0.0074091958 0.01110268 -5.3628943 -8.0110325 39.998199 16.845204 8.9144816 -2.6592409 0.11846422 16.649379 1.6353872 + 6000 0.0077388573 0.011596678 -5.3629264 -8.0194804 39.995216 16.842807 8.9145056 -2.6681507 0.11826582 16.648964 1.635306 + 7000 0.0076023298 0.011392091 -5.3621083 -8.0277598 39.998343 16.839762 8.9144789 -2.6770435 0.11810824 16.649386 1.6353924 + 8000 0.007691692 0.011526001 -5.361706 -8.0360632 40.000701 16.839078 8.9144843 -2.6858833 0.11795313 16.649923 1.6354361 + 9000 0.0082153298 0.012310672 -5.3620899 -8.0446091 40.006134 16.845865 8.914544 -2.6948299 0.11785259 16.651566 1.6354969 + 10000 0.0088368792 0.013242063 -5.3625357 -8.0530825 39.989575 16.835079 8.914577 -2.7037888 0.1174907 16.648402 1.6351306 +Loop time of 1.80214 on 4 procs for 10000 steps with 1000 atoms + +Performance: 479429.980 tau/day, 5548.958 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1353 | 1.1591 | 1.1787 | 1.5 | 64.32 +Neigh | 0.0028975 | 0.0029137 | 0.0029218 | 0.0 | 0.16 +Comm | 0.20882 | 0.22752 | 0.25213 | 3.4 | 12.62 +Output | 0.00058103 | 0.0007953 | 0.0014329 | 0.0 | 0.04 +Modify | 0.36598 | 0.36908 | 0.37078 | 0.3 | 20.48 +Other | | 0.04277 | | | 2.37 + +Nlocal: 250 ave 258 max 239 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 829 ave 840 max 821 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 5250 ave 5360 max 5090 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 21000 +Ave neighs/atom = 21 +Neighbor list builds = 10 +Dangerous builds = 0 + +# Start Run #3 + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0.0465206 0.06579 0.06579) to (7.02455 9.93421 9.93421) + 1 by 2 by 2 MPI processor grid + restoring pair style lj/cubic from restart + 1000 atoms + +neighbor 0.2 bin +neigh_modify every 1 delay 0 check yes +timestep 0.001 +reset_timestep 0 + +# Pzz = 40.0, drag/damping term off, Nose-Hoover chains + +fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 + +# Specify reference state from paper, times 1000 atoms + +fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519 + +# Add fix energy to ouput etotal + +fix_modify myhug energy yes + +# Define output + +variable dele equal f_myhug[1] # energy delta [temperature] +variable us equal f_myhug[2] # shock velocity [distance/time] +variable up equal f_myhug[3] # particle velocity [distance/time] +variable pzz equal pzz # axial stress +variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress +variable time equal dt*step + +thermo 1000 +thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up + +fix stress all print 10 "${time} ${pzz} ${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)' + +run 10000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.74754 + ghost atom cutoff = 1.74754 + binsize = 0.873769, bins = 8 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cubic, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.809 | 3.086 Mbytes +Step Temp KinEng E_pair TotEng Pzz v_tau Lz f_myhug v_dele v_us v_up + 0 0.01 0.014985 -6.3344257 -6.3194407 0.014347835 -0.00026463907 9.8684199 0 -0.0048551516 2.3786668 0.0041061135 + 1000 0.0078345827 0.011740122 -5.501714 -6.3232649 35.616592 14.888101 8.9677603 -0.833291 0.093891974 16.160626 1.5002802 + 2000 0.019260469 0.028861813 -5.2936047 -6.2784351 41.771445 17.563018 8.895899 -1.0136922 0.11811779 16.853929 1.687161 + 3000 0.048111305 0.072094791 -5.3454082 -6.2447367 39.061491 16.137184 8.932261 -0.97142325 0.073850675 16.606004 1.6012602 + 4000 0.11854629 0.17764161 -5.2071426 -6.3210422 40.843054 16.426156 8.9202992 -1.2915412 0.017621345 16.874925 1.6476105 + 5000 0.13634167 0.204308 -5.2645153 -6.3135608 39.098316 15.628006 8.9407716 -1.2533534 -0.00067532215 16.688495 1.5948471 + 6000 0.14222646 0.21312635 -5.1774703 -6.3289809 40.888616 16.260775 8.9214855 -1.3646369 -0.0041713956 16.89472 1.6475159 + 7000 0.12683662 0.19006468 -5.2679846 -6.2838171 39.084233 15.633883 8.939337 -1.2058972 0.0057260888 16.672835 1.5957701 + 8000 0.14531516 0.21775476 -5.1737923 -6.3237483 40.861161 16.191124 8.9199968 -1.3677107 -0.0065481979 16.876021 1.6482339 + 9000 0.12123357 0.18166851 -5.2546748 -6.2570254 39.276123 15.677988 8.9363522 -1.1840191 0.0075191856 16.687414 1.6022039 + 10000 0.14771416 0.22134967 -5.1833988 -6.3104954 40.578265 16.080163 8.9245634 -1.3484463 -0.0098090911 16.857414 1.6386293 +Loop time of 1.8702 on 4 procs for 10000 steps with 1000 atoms + +Performance: 461983.152 tau/day, 5347.027 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.1723 | 1.1812 | 1.1956 | 0.9 | 63.16 +Neigh | 0.028221 | 0.030409 | 0.035555 | 1.7 | 1.63 +Comm | 0.22963 | 0.24139 | 0.25155 | 1.6 | 12.91 +Output | 0.00055218 | 0.00077897 | 0.0014515 | 0.0 | 0.04 +Modify | 0.37165 | 0.37241 | 0.3732 | 0.1 | 19.91 +Other | | 0.04404 | | | 2.35 + +Nlocal: 250 ave 257 max 244 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Nghost: 832.25 ave 840 max 822 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 5144.25 ave 5282 max 4949 min +Histogram: 1 0 0 0 0 1 0 1 0 1 + +Total # of neighbors = 20577 +Ave neighs/atom = 20.577 +Neighbor list builds = 95 +Dangerous builds = 0 + +Total wall time: 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single 5 38 4 +create_atoms 1 single 42 19 4 +create_atoms 1 single 30.5 7.5 4 +create_atoms 1 single 42.5 7.5 4 +create_atoms 1 single 26.5 18.5 4 +create_atoms 1 single 18.5 1.5 4 +create_atoms 1 single 41.5 10.5 4 diff --git a/examples/hyper/global.000000.jpg b/examples/hyper/global.000000.jpg new file mode 100644 index 0000000000..3064ece7f1 Binary files /dev/null and b/examples/hyper/global.000000.jpg differ diff --git a/examples/hyper/global.041000.jpg b/examples/hyper/global.041000.jpg new file mode 100644 index 0000000000..1f5253865e Binary files /dev/null and b/examples/hyper/global.041000.jpg differ diff --git a/examples/hyper/global.045000.jpg b/examples/hyper/global.045000.jpg new file mode 100644 index 0000000000..fb545052cb Binary files /dev/null and b/examples/hyper/global.045000.jpg differ diff --git a/examples/hyper/global.048000.jpg b/examples/hyper/global.048000.jpg new file mode 100644 index 0000000000..506ea4a4bb Binary files /dev/null and b/examples/hyper/global.048000.jpg differ diff --git a/examples/hyper/global.089000.jpg b/examples/hyper/global.089000.jpg new file mode 100644 index 0000000000..094e8b5328 Binary files /dev/null and b/examples/hyper/global.089000.jpg differ diff --git a/examples/hyper/in.hyper.global b/examples/hyper/in.hyper.global new file mode 100644 index 0000000000..eba5c7bf89 --- /dev/null +++ b/examples/hyper/in.hyper.global @@ -0,0 +1,97 @@ +# 3d EAM surface for global HD + +# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92 +# hop event on (100) surface is same distance +# exchange event is 2 atoms moving same distance + +variable Tequil index 500.0 +variable Vmax index 0.5 +variable qfactor index 0.3 +variable cutbond index 3.2 +variable cutevent index 1.1 +variable steps index 100000 +variable nevent index 1000 +variable zoom index 1.8 +variable seed index 826626413 +variable tol index 1.0e-15 + +units metal +atom_style atomic +atom_modify map array +boundary p p p + +lattice fcc 3.92 +region box block 0 6 0 6 0 4 +create_box 3 box +create_atoms 1 box + +mass * 1.0 + +change_box all z final -0.1 5.0 boundary p p f +create_atoms 2 single 3.5 3.5 4 + +# define frozen substrate and mobile atoms + +group adatom type 2 +region base block INF INF INF INF 0 1.8 +set region base type 3 +group base type 3 +group mobile type 1 2 + +# pair style + +pair_style eam/alloy +pair_coeff * * ptvoterlammps.eam Pt Pt Pt + +neighbor 0.5 bin +neigh_modify every 1 delay 5 check yes + +fix 1 mobile nve +fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes + +timestep 0.005 + +compute tmobile mobile temp + +thermo 100 +thermo_modify temp tmobile + +# thermal equilibration + +run 1000 +reset_timestep 0 + +# pin base so will not move during quenches + +fix freeze base setforce 0.0 0.0 0.0 + +# event detection + +compute event all event/displace ${cutevent} + +# hyper/global + +fix HG mobile hyper/global ${cutbond} ${qfactor} ${Vmax} ${Tequil} + +# thermo output + +thermo_style custom step temp pe f_HG f_HG[*] + +thermo_modify lost ignore +thermo_modify temp tmobile + +thermo ${nevent} + +# dump output options + +region substrate block INF INF INF INF 1.8 3.8 +region adatoms block INF INF INF INF 3.8 INF +variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms) + +dump 1 all image 1000000 global.*.jpg v_acolor type & + zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01 +dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green + +# run + +hyper ${steps} ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1 diff --git a/examples/hyper/in.hyper.local b/examples/hyper/in.hyper.local new file mode 100644 index 0000000000..cdf478ac38 --- /dev/null +++ b/examples/hyper/in.hyper.local @@ -0,0 +1,118 @@ +# 3d EAM surface for local HD + +# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92 +# hop event on (100) surface is same distance +# exchange event is 2 atoms moving same distance + +variable Tequil index 400.0 +variable Vmax index 0.4 +variable qfactor index 0.3 +variable cutbond index 3.2 +variable Dcut index 10.0 +variable cutevent index 1.1 +variable alpha index 200.0 +variable boost index 4000.0 +variable ghostcut index 12.0 +variable steps index 1500 +variable nevent index 100 +variable nx index 8 +variable ny index 8 +variable zoom index 1.8 +variable seed index 826626413 +variable tol index 1.0e-15 +variable add index 37K + +units metal +atom_style atomic +atom_modify map array +boundary p p p +comm_modify cutoff ${ghostcut} + +lattice fcc 3.92 +region box block 0 6 0 6 0 4 +create_box 2 box +create_atoms 1 box + +mass * 1.0 + +change_box all z final -0.1 5.0 boundary p p f + +# replicate in xy + +replicate ${nx} ${ny} 1 + +# add adatoms + +include adatoms.list.${add} + +# define frozen substrate and mobile atoms + +region base block INF INF INF INF 0 1.8 +set region base type 2 +group base type 2 +group mobile type 1 + +# pair style + +pair_style eam/alloy +pair_coeff * * ptvoterlammps.eam Pt Pt + +neighbor 0.5 bin +neigh_modify every 1 delay 5 check yes + +fix 1 mobile nve +fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes + +timestep 0.005 + +compute tmobile mobile temp + +thermo 100 +thermo_modify temp tmobile + +# thermal equilibration + +run 1000 +reset_timestep 0 + +# pin base so will not move during quenches + +fix freeze base setforce 0.0 0.0 0.0 + +# event detection + +compute event all event/displace ${cutevent} + +# hyper/local + +fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} & + ${Dcut} ${alpha} ${boost} + +# thermo output + +thermo_style custom step temp pe f_HL f_HL[*] + +thermo_modify lost ignore +thermo_modify temp tmobile + +thermo ${nevent} + +# dump + +region substrate block INF INF INF INF 1.8 3.8 +region adatoms block INF INF INF INF 3.8 INF +variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms) + +dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 & + zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01 +dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green + +# test of histogramming and dump output of bias coeffs + +#fix histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL & +# mode vector kind local file tmp.histo +#dump 2 all local 1000 tmp.local f_HL + +# run + +hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1 diff --git a/examples/hyper/local.000000.jpg b/examples/hyper/local.000000.jpg new file mode 100644 index 0000000000..ef0ec0cd59 Binary files /dev/null and b/examples/hyper/local.000000.jpg differ diff --git a/examples/hyper/local.001200.jpg b/examples/hyper/local.001200.jpg new file mode 100644 index 0000000000..36bc9cd7bc Binary files /dev/null and b/examples/hyper/local.001200.jpg differ diff --git a/examples/hyper/log.25Mar19.hyper.global.g++.4 b/examples/hyper/log.25Mar19.hyper.global.g++.4 new file mode 100644 index 0000000000..6a066d0d66 --- /dev/null +++ b/examples/hyper/log.25Mar19.hyper.global.g++.4 @@ -0,0 +1,1250 @@ +LAMMPS (28 Feb 2019) +# 3d EAM surface for global HD + +# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92 +# hop event on (100) surface is same distance +# exchange event is 2 atoms moving same distance + +variable Tequil index 500.0 +variable Vmax index 0.5 +variable qfactor index 0.3 +variable cutbond index 3.2 +variable cutevent index 1.1 +variable steps index 100000 +variable nevent index 1000 +variable zoom index 1.8 +variable seed index 826626413 +variable tol index 1.0e-15 + +units metal +atom_style atomic +atom_modify map array +boundary p p p + +lattice fcc 3.92 +Lattice spacing in x,y,z = 3.92 3.92 3.92 +region box block 0 6 0 6 0 4 +create_box 3 box +Created orthogonal box = (0 0 0) to (23.52 23.52 15.68) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 576 atoms + Time spent = 0.000785828 secs + +mass * 1.0 + +change_box all z final -0.1 5.0 boundary p p f + orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6) +create_atoms 2 single 3.5 3.5 4 +Created 1 atoms + Time spent = 5.79357e-05 secs + +# define frozen substrate and mobile atoms + +group adatom type 2 +1 atoms in group adatom +region base block INF INF INF INF 0 1.8 +set region base type 3 + 288 settings made for type +group base type 3 +288 atoms in group base +group mobile type 1 2 +289 atoms in group mobile + +# pair style + +pair_style eam/alloy +pair_coeff * * ptvoterlammps.eam Pt Pt Pt + +neighbor 0.5 bin +neigh_modify every 1 delay 5 check yes + +fix 1 mobile nve +fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes +fix 2 mobile langevin 500.0 ${Tequil} 1.0 ${seed} zero yes +fix 2 mobile langevin 500.0 500.0 1.0 ${seed} zero yes +fix 2 mobile langevin 500.0 500.0 1.0 826626413 zero yes + +timestep 0.005 + +compute tmobile mobile temp + +thermo 100 +thermo_modify temp tmobile +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:487) + +# thermal equilibration + +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.07583 + ghost atom cutoff = 6.07583 + binsize = 3.03792, bins = 8 8 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.327 | 3.327 | 3.327 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -3213.9136 0 -3213.9136 -51843.125 + 100 223.70164 -3209.0653 0 -3200.7375 -26575.84 + 200 345.18355 -3206.1371 0 -3193.2869 -42327.268 + 300 411.05681 -3203.8465 0 -3188.5442 -32455.226 + 400 446.05938 -3202.2976 0 -3185.6922 -35377.683 + 500 435.52439 -3200.2131 0 -3183.9999 -31477.028 + 600 474.70282 -3199.4049 0 -3181.7332 -34761.287 + 700 492.00191 -3201.1592 0 -3182.8435 -33036.989 + 800 440.88631 -3198.37 0 -3181.9572 -34669.762 + 900 475.14414 -3198.5845 0 -3180.8964 -31191.883 + 1000 476.87852 -3197.3442 0 -3179.5914 -33731.074 +Loop time of 0.339602 on 4 procs for 1000 steps with 577 atoms + +Performance: 1272.077 ns/day, 0.019 hours/ns, 2944.623 timesteps/s +98.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.25294 | 0.26196 | 0.27409 | 1.5 | 77.14 +Neigh | 0.017554 | 0.018856 | 0.020498 | 0.8 | 5.55 +Comm | 0.027196 | 0.040838 | 0.050409 | 4.2 | 12.03 +Output | 0.00025296 | 0.0002721 | 0.00030828 | 0.0 | 0.08 +Modify | 0.013425 | 0.014212 | 0.014999 | 0.5 | 4.18 +Other | | 0.00346 | | | 1.02 + +Nlocal: 144.25 ave 147 max 141 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 527.5 ave 533 max 523 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Neighs: 3477.25 ave 3585 max 3399 min +Histogram: 1 0 1 0 1 0 0 0 0 1 + +Total # of neighbors = 13909 +Ave neighs/atom = 24.1057 +Neighbor list builds = 91 +Dangerous builds = 0 +reset_timestep 0 + +# pin base so will not move during quenches + +fix freeze base setforce 0.0 0.0 0.0 + +# event detection + +compute event all event/displace ${cutevent} +compute event all event/displace 1.1 + +# hyper/global + +fix HG mobile hyper/global ${cutbond} ${qfactor} ${Vmax} ${Tequil} +fix HG mobile hyper/global 3.2 ${qfactor} ${Vmax} ${Tequil} +fix HG mobile hyper/global 3.2 0.3 ${Vmax} ${Tequil} +fix HG mobile hyper/global 3.2 0.3 0.5 ${Tequil} +fix HG mobile hyper/global 3.2 0.3 0.5 500.0 + +# thermo output + +thermo_style custom step temp pe f_HG f_HG[*] +WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705) + +thermo_modify lost ignore +thermo_modify temp tmobile +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:487) + +thermo ${nevent} +thermo 1000 + +# dump output options + +region substrate block INF INF INF INF 1.8 3.8 +region adatoms block INF INF INF INF 3.8 INF +variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms) + +dump 1 all image 1000000 global.*.jpg v_acolor type zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01 +dump 1 all image 1000000 global.*.jpg v_acolor type zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01 +dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green + +# run + +hyper ${steps} ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1 +hyper 100000 ${nevent} HG event min ${tol} ${tol} 1000 1000 dump 1 +hyper 100000 1000 HG event min ${tol} ${tol} 1000 1000 dump 1 +hyper 100000 1000 HG event min 1.0e-15 ${tol} 1000 1000 dump 1 +hyper 100000 1000 HG event min 1.0e-15 1.0e-15 1000 1000 dump 1 +WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:133) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.07583 + ghost atom cutoff = 6.07583 + binsize = 3.03792, bins = 8 8 7 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix hyper/global, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.015 | 6.015 | 6.015 Mbytes +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 0 476.87852 -3197.3442 0 0 0 0 0 0 0 0 0 0 0 0 0 + 53 476.87852 -3217.9192 0 0 0 0 0 0 0 0 0 0 0 0 0 +Loop time of 0.0358047 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 0 476.87852 -3197.3442 0.33187212 2213.7063 0.17396269 129 131 6.0069324 0 0 0 3.3552688 0 0 0 + 1000 487.34979 -3198.3697 0.19401776 90.283981 0.23468448 543 548 6.0069324 0.165 0 0 3.9974111 6134.6092 0 0 +Loop time of 0.342707 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 1000 487.34979 -3198.3697 0.19401776 90.283981 0.23468448 543 548 6.0069324 0.165 0 0 3.9974111 6134.6092 0 0 + 1059 487.34979 -3217.9192 0.19401776 90.283981 0.23468448 543 548 6.0069324 0.15580737 0 0 3.9974111 6134.6092 0 0 +Loop time of 0.0359111 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 1000 487.34979 -3198.3697 0.19401776 90.283981 0.23468448 543 548 6.0069324 0.165 0 0 3.9974111 6134.6092 0 0 + 2000 522.93873 -3197.4748 0.1540961 35.745265 0.24952495 120 131 6.0069324 0.1645 0 0 4.0370436 10213.644 0 0 +Loop time of 0.305975 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 2000 522.93873 -3197.4748 0.1540961 35.745265 0.24952495 120 131 6.0069324 0.1645 0 0 4.0370436 10213.644 0 0 + 2057 522.93873 -3217.9192 0.1540961 35.745265 0.24952495 120 131 6.0069324 0.15994166 0 0 4.0370436 10213.644 0 0 +Loop time of 0.0335248 on 4 procs for 57 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 2000 522.93873 -3197.4748 0.1540961 35.745265 0.24952495 120 131 6.0069324 0.1645 0 0 4.0370436 10213.644 0 0 + 3000 485.3853 -3198.0446 0.081070047 6.563707 0.27460406 120 131 6.0069324 0.145 0 0 4.0370436 13331.739 0 0 +Loop time of 0.269706 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 3000 485.3853 -3198.0446 0.081070047 6.563707 0.27460406 120 131 6.0069324 0.145 0 0 4.0370436 13331.739 0 0 + 3059 485.3853 -3217.9192 0.081070047 6.563707 0.27460406 120 131 6.0069324 0.14220333 0 0 4.0370436 13331.739 0 0 +Loop time of 0.0265908 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 3000 485.3853 -3198.0446 0.081070047 6.563707 0.27460406 120 131 6.0069324 0.145 0 0 4.0370436 13331.739 0 0 + 4000 522.88476 -3199.0496 0.020170911 1.5970319 0.29388643 548 555 6.0069324 0.17575 0 0 4.0370436 14355.723 0 0 +Loop time of 0.229504 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 4000 522.88476 -3199.0496 0.020170911 1.5970319 0.29388643 548 555 6.0069324 0.17575 0 0 4.0370436 14355.723 0 0 + 4060 522.88476 -3217.9192 0.020170911 1.5970319 0.29388643 548 555 6.0069324 0.17315271 0 0 4.0370436 14355.723 0 0 +Loop time of 0.0280094 on 4 procs for 60 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 4000 522.88476 -3199.0496 0.020170911 1.5970319 0.29388643 548 555 6.0069324 0.17575 0 0 4.0370436 14355.723 0 0 + 5000 462.24647 -3197.3076 0.11575138 14.679837 0.26299192 130 132 6.0069324 0.1664 0 0 4.0370436 19342.466 0 0 +Loop time of 0.234847 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 5000 462.24647 -3197.3076 0.11575138 14.679837 0.26299192 130 132 6.0069324 0.1664 0 0 4.0370436 19342.466 0 0 + 5054 462.24647 -3217.9192 0.11575138 14.679837 0.26299192 130 132 6.0069324 0.16462208 0 0 4.0370436 19342.466 0 0 +Loop time of 0.026547 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 5000 462.24647 -3197.3076 0.11575138 14.679837 0.26299192 130 132 6.0069324 0.1664 0 0 4.0370436 19342.466 0 0 + 6000 463.33022 -3196.1897 0.37378421 5855.6457 0.15072771 122 123 6.0069324 0.15583333 0 0 4.0370436 22854.021 0 0 +Loop time of 0.244725 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 6000 463.33022 -3196.1897 0.37378421 5855.6457 0.15072771 122 123 6.0069324 0.15583333 0 0 4.0370436 22854.021 0 0 + 6054 463.33022 -3217.9192 0.37378421 5855.6457 0.15072771 122 123 6.0069324 0.15444334 0 0 4.0370436 22854.021 0 0 +Loop time of 0.0267512 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 6000 463.33022 -3196.1897 0.37378421 5855.6457 0.15072771 122 123 6.0069324 0.15583333 0 0 4.0370436 22854.021 0 0 + 7000 496.34089 -3198.1795 0.29031005 843.70994 0.19427864 547 552 6.0069324 0.14885714 0 0 4.1079381 27854.511 0 0 +Loop time of 0.229727 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 7000 496.34089 -3198.1795 0.29031005 843.70994 0.19427864 547 552 6.0069324 0.14885714 0 0 4.1079381 27854.511 0 0 + 7055 496.34089 -3217.9192 0.29031005 843.70994 0.19427864 547 552 6.0069324 0.14769667 0 0 4.1079381 27854.511 0 0 +Loop time of 0.0260235 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 7000 496.34089 -3198.1795 0.29031005 843.70994 0.19427864 547 552 6.0069324 0.14885714 0 0 4.1079381 27854.511 0 0 + 8000 468.63017 -3197.6685 0 1 0.31412476 275 556 6.0069324 0.14075 0.00175 0 4.1079381 31930.231 0 0 +Loop time of 0.230083 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 8000 468.63017 -3197.6685 0 1 0.31412476 275 556 6.0069324 0.14075 0.00175 0 4.1079381 31930.231 0 0 + 8056 468.63017 -3217.9192 0 1 0.31412476 275 556 6.0069324 0.1397716 0.0017378352 0 4.1079381 31930.231 0 0 +Loop time of 0.0261552 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 8000 468.63017 -3197.6685 0 1 0.31412476 275 556 6.0069324 0.14075 0.00175 0 4.1079381 31930.231 0 0 + 9000 467.53307 -3198.3982 0 1 0.3075376 543 544 6.0069324 0.14888889 0.0015555556 0 4.1079381 35292.432 0 0 +Loop time of 0.22948 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 9000 467.53307 -3198.3982 0 1 0.3075376 543 544 6.0069324 0.14888889 0.0015555556 0 4.1079381 35292.432 0 0 + 9051 467.53307 -3217.9192 0 1 0.3075376 543 544 6.0069324 0.14804994 0.0015467904 0 4.1079381 35292.432 0 0 +Loop time of 0.0240657 on 4 procs for 51 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 9000 467.53307 -3198.3982 0 1 0.3075376 543 544 6.0069324 0.14888889 0.0015555556 0 4.1079381 35292.432 0 0 + 10000 496.73768 -3197.9106 0.11921512 15.908682 0.26180389 543 548 6.0069324 0.1531 0.0014 0 4.1079381 40303.236 0 0 +Loop time of 0.237951 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 10000 496.73768 -3197.9106 0.11921512 15.908682 0.26180389 543 548 6.0069324 0.1531 0.0014 0 4.1079381 40303.236 0 0 + 10061 496.73768 -3217.9192 0.11921512 15.908682 0.26180389 543 548 6.0069324 0.15217175 0.0013915118 0 4.1079381 40303.236 0 0 +Loop time of 0.0275102 on 4 procs for 61 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 10000 496.73768 -3197.9106 0.11921512 15.908682 0.26180389 543 548 6.0069324 0.1531 0.0014 0 4.1079381 40303.236 0 0 + 11000 526.76049 -3199.3263 0.24399827 287.99939 0.21466325 408 419 6.0069324 0.15945455 0.0012727273 0 4.1079381 42710.668 0 0 +Loop time of 0.226262 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 11000 526.76049 -3199.3263 0.24399827 287.99939 0.21466325 408 419 6.0069324 0.15945455 0.0012727273 0 4.1079381 42710.668 0 0 + 11058 526.76049 -3217.9192 0.24399827 287.99939 0.21466325 408 419 6.0069324 0.15861819 0.0012660517 0 4.1079381 42710.668 0 0 +Loop time of 0.0257103 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 11000 526.76049 -3199.3263 0.24399827 287.99939 0.21466325 408 419 6.0069324 0.15945455 0.0012727273 0 4.1079381 42710.668 0 0 + 12000 488.24107 -3198.2441 0.34073209 2719.0951 0.16931693 409 400 6.0069324 0.15558333 0.0011666667 0 4.1079381 47154.117 0 0 +Loop time of 0.226415 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 12000 488.24107 -3198.2441 0.34073209 2719.0951 0.16931693 409 400 6.0069324 0.15558333 0.0011666667 0 4.1079381 47154.117 0 0 + 12053 488.24107 -3217.9192 0.34073209 2719.0951 0.16931693 409 400 6.0069324 0.1548992 0.0011615365 0 4.1079381 47154.117 0 0 +Loop time of 0.0232868 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 12000 488.24107 -3198.2441 0.34073209 2719.0951 0.16931693 409 400 6.0069324 0.15558333 0.0011666667 0 4.1079381 47154.117 0 0 + 13000 467.87203 -3197.0681 0 1 0.32542353 275 556 6.0069324 0.14869231 0.0015384615 0 4.1079381 54700.864 0 0 +Loop time of 0.234386 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 13000 467.87203 -3197.0681 0 1 0.32542353 275 556 6.0069324 0.14869231 0.0015384615 0 4.1079381 54700.864 0 0 + 13055 467.87203 -3217.9192 0 1 0.32542353 275 556 6.0069324 0.14806588 0.0015319801 0 4.1079381 54700.864 0 0 +Loop time of 0.0268174 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 13000 467.87203 -3197.0681 0 1 0.32542353 275 556 6.0069324 0.14869231 0.0015384615 0 4.1079381 54700.864 0 0 + 14000 494.97859 -3197.9767 0.061678009 4.1849114 0.2808878 544 555 6.0069324 0.16885714 0.0014285714 0 4.1079381 55284.212 0 0 +Loop time of 0.236772 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 14000 494.97859 -3197.9767 0.061678009 4.1849114 0.2808878 544 555 6.0069324 0.16885714 0.0014285714 0 4.1079381 55284.212 0 0 + 14059 494.97859 -3217.9192 0.061678009 4.1849114 0.2808878 544 555 6.0069324 0.16814852 0.0014225763 0 4.1079381 55284.212 0 0 +Loop time of 0.0262685 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 14000 494.97859 -3197.9767 0.061678009 4.1849114 0.2808878 544 555 6.0069324 0.16885714 0.0014285714 0 4.1079381 55284.212 0 0 + 15000 487.47593 -3196.3193 0 1 0.30681413 124 135 6.0069324 0.16526667 0.0013333333 0 4.1079381 58845.637 0 0 +Loop time of 0.228132 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 15000 487.47593 -3196.3193 0 1 0.30681413 124 135 6.0069324 0.16526667 0.0013333333 0 4.1079381 58845.637 0 0 + 15056 487.47593 -3217.9192 0 1 0.30681413 124 135 6.0069324 0.16465197 0.0013283741 0 4.1079381 58845.637 0 0 +Loop time of 0.0253892 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 15000 487.47593 -3196.3193 0 1 0.30681413 124 135 6.0069324 0.16526667 0.0013333333 0 4.1079381 58845.637 0 0 + 16000 514.29619 -3198.6976 0.15192442 33.988268 0.25030702 287 568 6.0069324 0.160375 0.00125 0 4.1079381 65959.225 0 0 +Loop time of 0.226636 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 16000 514.29619 -3198.6976 0.15192442 33.988268 0.25030702 287 568 6.0069324 0.160375 0.00125 0 4.1079381 65959.225 0 0 + 16057 514.29619 -3217.9192 0.15192442 33.988268 0.25030702 287 568 6.0069324 0.15980569 0.0012455627 0 4.1079381 65959.225 0 0 +Loop time of 0.0258105 on 4 procs for 57 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 16000 514.29619 -3198.6976 0.15192442 33.988268 0.25030702 287 568 6.0069324 0.160375 0.00125 0 4.1079381 65959.225 0 0 + 17000 518.58789 -3197.5021 0.1333678 22.094631 0.25689258 116 123 6.0069324 0.16088235 0.0011764706 0 4.1079381 70525.413 0 0 +Loop time of 0.233751 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 17000 518.58789 -3197.5021 0.1333678 22.094631 0.25689258 116 123 6.0069324 0.16088235 0.0011764706 0 4.1079381 70525.413 0 0 + 17052 518.58789 -3217.9192 0.1333678 22.094631 0.25689258 116 123 6.0069324 0.16039174 0.0011728829 0 4.1079381 70525.413 0 0 +Loop time of 0.0248473 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 17000 518.58789 -3197.5021 0.1333678 22.094631 0.25689258 116 123 6.0069324 0.16088235 0.0011764706 0 4.1079381 70525.413 0 0 + 18000 505.83228 -3198.9838 0.08205079 6.7148239 0.27428244 552 563 6.0069324 0.15644444 0.0011111111 0 4.1079381 73252.823 0 0 +Loop time of 0.240134 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 18000 505.83228 -3198.9838 0.08205079 6.7148239 0.27428244 552 563 6.0069324 0.15644444 0.0011111111 0 4.1079381 73252.823 0 0 + 18056 505.83228 -3217.9192 0.08205079 6.7148239 0.27428244 552 563 6.0069324 0.15595924 0.001107665 0 4.1079381 73252.823 0 0 +Loop time of 0.0243995 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 18000 505.83228 -3198.9838 0.08205079 6.7148239 0.27428244 552 563 6.0069324 0.15644444 0.0011111111 0 4.1079381 73252.823 0 0 + 19000 527.41862 -3198.5008 0.040305357 2.5483534 0.28765437 424 263 6.0069324 0.15589474 0.0010526316 0 4.1079381 75984.28 0 0 +Loop time of 0.22821 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 19000 527.41862 -3198.5008 0.040305357 2.5483534 0.28765437 424 263 6.0069324 0.15589474 0.0010526316 0 4.1079381 75984.28 0 0 + 19052 527.41862 -3217.9192 0.040305357 2.5483534 0.28765437 424 263 6.0069324 0.15546924 0.0010497586 0 4.1079381 75984.28 0 0 +Loop time of 0.0237539 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 19000 527.41862 -3198.5008 0.040305357 2.5483534 0.28765437 424 263 6.0069324 0.15589474 0.0010526316 0 4.1079381 75984.28 0 0 + 20000 451.64207 -3198.7796 0.047092391 2.9831142 0.28552298 570 403 6.0069324 0.15125 0.001 0 4.1079381 81688.471 0 0 +Loop time of 0.226179 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 20000 451.64207 -3198.7796 0.047092391 2.9831142 0.28552298 570 403 6.0069324 0.15125 0.001 0 4.1079381 81688.471 0 0 + 20053 451.64207 -3217.9192 0.047092391 2.9831142 0.28552298 570 403 6.0069324 0.15085025 0.000997357 0 4.1079381 81688.471 0 0 +Loop time of 0.0244102 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 20000 451.64207 -3198.7796 0.047092391 2.9831142 0.28552298 570 403 6.0069324 0.15125 0.001 0 4.1079381 81688.471 0 0 + 21000 469.69339 -3200.6427 0 1 0.3308786 267 268 6.0069324 0.14852381 0.00095238095 0 4.1079381 87660.496 0 0 +Loop time of 0.234504 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 21000 469.69339 -3200.6427 0 1 0.3308786 267 268 6.0069324 0.14852381 0.00095238095 0 4.1079381 87660.496 0 0 + 21050 469.69339 -3217.9192 0 1 0.3308786 267 268 6.0069324 0.14817102 0.00095011876 0 4.1079381 87660.496 0 0 +Loop time of 0.0231035 on 4 procs for 50 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 21000 469.69339 -3200.6427 0 1 0.3308786 267 268 6.0069324 0.14852381 0.00095238095 0 4.1079381 87660.496 0 0 + 22000 473.26326 -3199.3284 0 1 0.31249141 544 555 6.0069324 0.14786364 0.00090909091 0 4.1079381 91920.285 0 0 +Loop time of 0.235723 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 22000 473.26326 -3199.3284 0 1 0.31249141 544 555 6.0069324 0.14786364 0.00090909091 0 4.1079381 91920.285 0 0 + 22054 473.26326 -3217.9192 0 1 0.31249141 544 555 6.0069324 0.14750159 0.00090686497 0 4.1079381 91920.285 0 0 +Loop time of 0.024776 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 22000 473.26326 -3199.3284 0 1 0.31249141 544 555 6.0069324 0.14786364 0.00090909091 0 4.1079381 91920.285 0 0 + 23000 496.07543 -3198.2605 0.30577111 1207.9075 0.18697914 572 403 6.0069324 0.15665217 0.0011304348 0 4.1079381 92558.536 0 0 +Loop time of 0.229916 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 23000 496.07543 -3198.2605 0.30577111 1207.9075 0.18697914 572 403 6.0069324 0.15665217 0.0011304348 0 4.1079381 92558.536 0 0 + 23056 496.07543 -3217.9192 0.30577111 1207.9075 0.18697914 572 403 6.0069324 0.15627169 0.0011276891 0 4.1079381 92558.536 0 0 +Loop time of 0.0252325 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 23000 496.07543 -3198.2605 0.30577111 1207.9075 0.18697914 572 403 6.0069324 0.15665217 0.0011304348 0 4.1079381 92558.536 0 0 + 24000 465.43821 -3199.468 0 1 0.31415739 543 544 6.0069324 0.15466667 0.0010833333 0 4.1079381 97530.178 0 0 +Loop time of 0.231022 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 24000 465.43821 -3199.468 0 1 0.31415739 543 544 6.0069324 0.15466667 0.0010833333 0 4.1079381 97530.178 0 0 + 24054 465.43821 -3217.9192 0 1 0.31415739 543 544 6.0069324 0.15431945 0.0010809013 0 4.1079381 97530.178 0 0 +Loop time of 0.0246248 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 24000 465.43821 -3199.468 0 1 0.31415739 543 544 6.0069324 0.15466667 0.0010833333 0 4.1079381 97530.178 0 0 + 25000 489.80528 -3200.439 0.25812453 399.74019 0.20865662 543 544 6.0069324 0.15368 0.00104 0 4.1079381 103216.01 0 0 +Loop time of 0.239562 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 25000 489.80528 -3200.439 0.25812453 399.74019 0.20865662 543 544 6.0069324 0.15368 0.00104 0 4.1079381 103216.01 0 0 + 25060 489.80528 -3217.9192 0.25812453 399.74019 0.20865662 543 544 6.0069324 0.15331205 0.00103751 0 4.1079381 103216.01 0 0 +Loop time of 0.0290521 on 4 procs for 60 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 25000 489.80528 -3200.439 0.25812453 399.74019 0.20865662 543 544 6.0069324 0.15368 0.00104 0 4.1079381 103216.01 0 0 + 26000 454.33199 -3197.9264 0.15449017 36.073692 0.24938278 283 272 6.0069324 0.15788462 0.001 0 4.1079381 106857.47 0 0 +Loop time of 0.231679 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 26000 454.33199 -3197.9264 0.15449017 36.073692 0.24938278 283 272 6.0069324 0.15788462 0.001 0 4.1079381 106857.47 0 0 + 26053 454.33199 -3217.9192 0.15449017 36.073692 0.24938278 283 272 6.0069324 0.15756343 0.00099796569 0 4.1079381 106857.47 0 0 +Loop time of 0.0229361 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 26000 454.33199 -3197.9264 0.15449017 36.073692 0.24938278 283 272 6.0069324 0.15788462 0.001 0 4.1079381 106857.47 0 0 + 27000 493.26662 -3198.8515 0.17523126 58.378293 0.24178166 260 271 6.0069324 0.15388889 0.00096296296 0 4.1079381 114287.4 0 0 +Loop time of 0.228356 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 27000 493.26662 -3198.8515 0.17523126 58.378293 0.24178166 260 271 6.0069324 0.15388889 0.00096296296 0 4.1079381 114287.4 0 0 + 27056 493.26662 -3217.9192 0.17523126 58.378293 0.24178166 260 271 6.0069324 0.15357037 0.00096096984 0 4.1079381 114287.4 0 0 +Loop time of 0.0249045 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 27000 493.26662 -3198.8515 0.17523126 58.378293 0.24178166 260 271 6.0069324 0.15388889 0.00096296296 0 4.1079381 114287.4 0 0 + 28000 516.59709 -3198.7939 0.017083929 1.486614 0.29483028 543 548 6.0069324 0.15278571 0.00092857143 0 4.1079381 117735.24 0 0 +Loop time of 0.226666 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 28000 516.59709 -3198.7939 0.017083929 1.486614 0.29483028 543 548 6.0069324 0.15278571 0.00092857143 0 4.1079381 117735.24 0 0 + 28054 516.59709 -3217.9192 0.017083929 1.486614 0.29483028 543 548 6.0069324 0.15249162 0.00092678406 0 4.1079381 117735.24 0 0 +Loop time of 0.0245788 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 28000 516.59709 -3198.7939 0.017083929 1.486614 0.29483028 543 548 6.0069324 0.15278571 0.00092857143 0 4.1079381 117735.24 0 0 + 29000 498.78313 -3197.7551 0 1 0.43523955 543 544 6.0069324 0.15648276 0.00089655172 0 4.3557073 122569.32 0 0 +Loop time of 0.239195 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 29000 498.78313 -3197.7551 0 1 0.43523955 543 544 6.0069324 0.15648276 0.00089655172 0 4.3557073 122569.32 0 0 + 29059 498.78313 -3217.9192 0 1 0.43523955 543 544 6.0069324 0.15616504 0.00089473141 0 4.3557073 122569.32 0 0 +Loop time of 0.0290976 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 29000 498.78313 -3197.7551 0 1 0.43523955 543 544 6.0069324 0.15648276 0.00089655172 0 4.3557073 122569.32 0 0 + 30000 466.86137 -3199.5233 0.23621441 240.39961 0.21790229 126 127 6.0069324 0.15756667 0.00086666667 0 4.3557073 127229.34 0 0 +Loop time of 0.232616 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 30000 466.86137 -3199.5233 0.23621441 240.39961 0.21790229 126 127 6.0069324 0.15756667 0.00086666667 0 4.3557073 127229.34 0 0 + 30059 466.86137 -3217.9192 0.23621441 240.39961 0.21790229 126 127 6.0069324 0.15725739 0.00086496557 0 4.3557073 127229.34 0 0 +Loop time of 0.0269623 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 30000 466.86137 -3199.5233 0.23621441 240.39961 0.21790229 126 127 6.0069324 0.15756667 0.00086666667 0 4.3557073 127229.34 0 0 + 31000 471.12992 -3199.7598 0 1 0.30984418 567 572 6.0069324 0.15541935 0.00087096774 0 4.3557073 131258.9 0 0 +Loop time of 0.229214 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 31000 471.12992 -3199.7598 0 1 0.30984418 567 572 6.0069324 0.15541935 0.00087096774 0 4.3557073 131258.9 0 0 + 31053 471.12992 -3217.9192 0 1 0.30984418 567 572 6.0069324 0.15515409 0.00086948121 0 4.3557073 131258.9 0 0 +Loop time of 0.0240388 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 31000 471.12992 -3199.7598 0 1 0.30984418 567 572 6.0069324 0.15541935 0.00087096774 0 4.3557073 131258.9 0 0 + 32000 510.4372 -3198.4263 0.38770138 8088.2308 0.14217507 511 546 6.0069324 0.15328125 0.00084375 0 4.3557073 136077.46 0 0 +Loop time of 0.230157 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 32000 510.4372 -3198.4263 0.38770138 8088.2308 0.14217507 511 546 6.0069324 0.15328125 0.00084375 0 4.3557073 136077.46 0 0 + 32057 510.4372 -3217.9192 0.38770138 8088.2308 0.14217507 511 546 6.0069324 0.1530087 0.00084224974 0 4.3557073 136077.46 0 0 +Loop time of 0.0259738 on 4 procs for 57 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 32000 510.4372 -3198.4263 0.38770138 8088.2308 0.14217507 511 546 6.0069324 0.15328125 0.00084375 0 4.3557073 136077.46 0 0 + 33000 517.9664 -3198.8477 0.065094278 4.5302347 0.27979105 136 255 6.0069324 0.15212121 0.00081818182 0 4.3557073 140653.16 0 0 +Loop time of 0.240719 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 33000 517.9664 -3198.8477 0.065094278 4.5302347 0.27979105 136 255 6.0069324 0.15212121 0.00081818182 0 4.3557073 140653.16 0 0 + 33055 517.9664 -3217.9192 0.065094278 4.5302347 0.27979105 136 255 6.0069324 0.1518681 0.00081682045 0 4.3557073 140653.16 0 0 +Loop time of 0.0254009 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 33000 517.9664 -3198.8477 0.065094278 4.5302347 0.27979105 136 255 6.0069324 0.15212121 0.00081818182 0 4.3557073 140653.16 0 0 + 34000 539.21923 -3197.9619 0.10137745 10.515709 0.26786575 119 400 6.0069324 0.15088235 0.00079411765 0 4.3557073 146106.36 0 0 +Loop time of 0.228472 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 34000 539.21923 -3197.9619 0.10137745 10.515709 0.26786575 119 400 6.0069324 0.15088235 0.00079411765 0 4.3557073 146106.36 0 0 + 34053 539.21923 -3217.9192 0.10137745 10.515709 0.26786575 119 400 6.0069324 0.15064752 0.00079288168 0 4.3557073 146106.36 0 0 +Loop time of 0.0239374 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 34000 539.21923 -3197.9619 0.10137745 10.515709 0.26786575 119 400 6.0069324 0.15088235 0.00079411765 0 4.3557073 146106.36 0 0 + 35000 495.28481 -3198.2101 0.03728079 2.3756005 0.28859913 543 544 6.0069324 0.14882857 0.00077142857 0 4.3557073 152132.21 0 0 +Loop time of 0.227014 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 35000 495.28481 -3198.2101 0.03728079 2.3756005 0.28859913 543 544 6.0069324 0.14882857 0.00077142857 0 4.3557073 152132.21 0 0 + 35061 495.28481 -3217.9192 0.03728079 2.3756005 0.28859913 543 544 6.0069324 0.14856964 0.00077008642 0 4.3557073 152132.21 0 0 +Loop time of 0.0271087 on 4 procs for 61 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 35000 495.28481 -3198.2101 0.03728079 2.3756005 0.28859913 543 544 6.0069324 0.14882857 0.00077142857 0 4.3557073 152132.21 0 0 + 36000 522.02047 -3197.5464 0.023049198 1.7073613 0.29300366 132 139 6.0069324 0.14975 0.00075 0 4.3557073 155779.35 0 0 +Loop time of 0.230395 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 36000 522.02047 -3197.5464 0.023049198 1.7073613 0.29300366 132 139 6.0069324 0.14975 0.00075 0 4.3557073 155779.35 0 0 + 36058 522.02047 -3217.9192 0.023049198 1.7073613 0.29300366 132 139 6.0069324 0.14950912 0.00074879361 0 4.3557073 155779.35 0 0 +Loop time of 0.0274341 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 36000 522.02047 -3197.5464 0.023049198 1.7073613 0.29300366 132 139 6.0069324 0.14975 0.00075 0 4.3557073 155779.35 0 0 + 37000 493.66881 -3198.2972 0.29065621 850.51576 0.19411822 110 121 6.0069324 0.14783784 0.00072972973 0 4.3557073 159446.9 0 0 +Loop time of 0.239665 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 37000 493.66881 -3198.2972 0.29065621 850.51576 0.19411822 110 121 6.0069324 0.14783784 0.00072972973 0 4.3557073 159446.9 0 0 + 37055 493.66881 -3217.9192 0.29065621 850.51576 0.19411822 110 121 6.0069324 0.14761841 0.00072864661 0 4.3557073 159446.9 0 0 +Loop time of 0.0258739 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 37000 493.66881 -3198.2972 0.29065621 850.51576 0.19411822 110 121 6.0069324 0.14783784 0.00072972973 0 4.3557073 159446.9 0 0 + 38000 471.56021 -3200.0689 0.21390468 143.23918 0.22692985 546 559 6.0069324 0.1505 0.00071052632 0 4.3557073 161793.64 0 0 +Loop time of 0.231827 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 38000 471.56021 -3200.0689 0.21390468 143.23918 0.22692985 546 559 6.0069324 0.1505 0.00071052632 0 4.3557073 161793.64 0 0 + 38050 471.56021 -3217.9192 0.21390468 143.23918 0.22692985 546 559 6.0069324 0.15030223 0.00070959264 0 4.3557073 161793.64 0 0 +Loop time of 0.0234141 on 4 procs for 50 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 38000 471.56021 -3200.0689 0.21390468 143.23918 0.22692985 546 559 6.0069324 0.1505 0.00071052632 0 4.3557073 161793.64 0 0 + 39000 488.60708 -3198.2279 0.29546108 950.85261 0.19187758 410 412 6.0069324 0.14884615 0.00069230769 0 4.3557073 167145.63 0 0 +Loop time of 0.227483 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 39000 488.60708 -3198.2279 0.29546108 950.85261 0.19187758 410 412 6.0069324 0.14884615 0.00069230769 0 4.3557073 167145.63 0 0 + 39062 488.60708 -3217.9192 0.29546108 950.85261 0.19187758 410 412 6.0069324 0.1486099 0.00069120885 0 4.3557073 167145.63 0 0 +Loop time of 0.028059 on 4 procs for 62 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 39000 488.60708 -3198.2279 0.29546108 950.85261 0.19187758 410 412 6.0069324 0.14884615 0.00069230769 0 4.3557073 167145.63 0 0 + 40000 507.73002 -3196.8491 0.012490865 1.3362947 0.29622904 543 544 6.0069324 0.15095 0.000675 0 4.3557073 171194.28 0 0 +Loop time of 0.231293 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 40000 507.73002 -3196.8491 0.012490865 1.3362947 0.29622904 543 544 6.0069324 0.15095 0.000675 0 4.3557073 171194.28 0 0 + 40064 507.73002 -3217.9192 0.012490865 1.3362947 0.29622904 543 544 6.0069324 0.15070887 0.00067392173 0 4.3557073 171194.28 0 0 +Loop time of 0.0308156 on 4 procs for 64 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 40000 507.73002 -3196.8491 0.012490865 1.3362947 0.29622904 543 544 6.0069324 0.15095 0.000675 0 4.3557073 171194.28 0 0 + 41000 479.11448 -3200.241 0 1 0.94094448 542 544 6.0069324 0.16480488 0.00065853659 0 5.4178316 171224.32 0 0 +Loop time of 0.239781 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 41000 479.11448 -3200.241 0 1 0.94094448 542 544 6.0069324 0.16480488 0.00065853659 0 5.4178316 171224.32 0 0 + 41055 479.11448 -3217.9192 0 1 0.94094448 542 544 6.0069324 0.16458409 0.00065765437 0 5.4178316 171224.32 0 0 +Loop time of 0.0248787 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 41000 479.11448 -3200.241 0.31626598 1541.0515 0.18185743 398 404 6.0069324 0.16480488 0.00065853659 2.3326665 5.4178316 171224.32 1 2 + 42000 495.84675 -3198.6432 0.1729929 55.422961 0.24261343 275 264 6.0069324 0.1692381 0.0011190476 2.3326665 5.4178316 174484.67 1 2 +Loop time of 0.226913 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 42000 495.84675 -3198.6432 0.1729929 55.422961 0.24261343 275 264 6.0069324 0.1692381 0.0011190476 2.3326665 5.4178316 174484.67 1 2 + 42056 495.84675 -3217.9192 0.1729929 55.422961 0.24261343 275 264 6.0069324 0.16901274 0.0011175575 2.3326665 5.4178316 174484.67 1 2 +Loop time of 0.0239749 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 42000 495.84675 -3198.6432 0.1729929 55.422961 0.24261343 275 264 6.0069324 0.1692381 0.0011190476 2.3326665 5.4178316 174484.67 1 2 + 43000 533.30453 -3198.6415 0 1 0.34377427 263 577 6.0069324 0.17646512 0.0010930233 2.3326665 5.4178316 175038.14 1 2 +Loop time of 0.224798 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 43000 533.30453 -3198.6415 0 1 0.34377427 263 577 6.0069324 0.17646512 0.0010930233 2.3326665 5.4178316 175038.14 1 2 + 43054 533.30453 -3217.9192 0 1 0.34377427 263 577 6.0069324 0.17624379 0.0010916523 2.3326665 5.4178316 175038.14 1 2 +Loop time of 0.0243425 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 43000 533.30453 -3198.6415 0 1 0.34377427 263 577 6.0069324 0.17646512 0.0010930233 2.3326665 5.4178316 175038.14 1 2 + 44000 497.19886 -3199.3252 0 1 0.32411085 262 264 6.0069324 0.17947727 0.0010681818 2.3326665 5.4178316 175732.69 1 2 +Loop time of 0.23413 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 44000 497.19886 -3199.3252 0 1 0.32411085 262 264 6.0069324 0.17947727 0.0010681818 2.3326665 5.4178316 175732.69 1 2 + 44056 497.19886 -3217.9192 0 1 0.32411085 262 264 6.0069324 0.17924914 0.001066824 2.3326665 5.4178316 175732.69 1 2 +Loop time of 0.0264681 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 44000 497.19886 -3199.3252 0 1 0.32411085 262 264 6.0069324 0.17947727 0.0010681818 2.3326665 5.4178316 175732.69 1 2 + 45000 501.66497 -3198.3133 0 1 0.89133337 262 264 6.0069324 0.18806667 0.0010444444 2.3326665 5.4178316 175885.32 1 2 +Loop time of 0.233324 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 45000 501.66497 -3198.3133 0 1 0.89133337 262 264 6.0069324 0.18806667 0.0010444444 2.3326665 5.4178316 175885.32 1 2 + 45053 501.66497 -3217.9192 0 1 0.89133337 262 264 6.0069324 0.18784543 0.0010432158 2.3326665 5.4178316 175885.32 1 2 +Loop time of 0.0239007 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 45000 501.66497 -3198.3133 0.31380779 1455.5922 0.18306993 549 547 6.0069324 0.18806667 0.0010444444 2.332667 5.4178316 175885.32 2 4 + 46000 512.99827 -3198.7869 0.30973921 1324.4339 0.18505929 547 552 6.0069324 0.18545652 0.0010217391 2.332667 5.4178316 180703.66 2 4 +Loop time of 0.227399 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 46000 512.99827 -3198.7869 0.30973921 1324.4339 0.18505929 547 552 6.0069324 0.18545652 0.0010217391 2.332667 5.4178316 180703.66 2 4 + 46058 512.99827 -3217.9192 0.30973921 1324.4339 0.18505929 547 552 6.0069324 0.18522298 0.0010204525 2.332667 5.4178316 180703.66 2 4 +Loop time of 0.025696 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 46000 512.99827 -3198.7869 0.30973921 1324.4339 0.18505929 547 552 6.0069324 0.18545652 0.0010217391 2.332667 5.4178316 180703.66 2 4 + 47000 508.06284 -3198.0819 0.17828926 62.67216 0.24064067 271 544 6.0069324 0.18404255 0.001 2.332667 5.4178316 186245.92 2 4 +Loop time of 0.232521 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 47000 508.06284 -3198.0819 0.17828926 62.67216 0.24064067 271 544 6.0069324 0.18404255 0.001 2.332667 5.4178316 186245.92 2 4 + 47062 508.06284 -3217.9192 0.17828926 62.67216 0.24064067 271 544 6.0069324 0.18380009 0.00099868259 2.332667 5.4178316 186245.92 2 4 +Loop time of 0.0288792 on 4 procs for 62 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 47000 508.06284 -3198.0819 0.17828926 62.67216 0.24064067 271 544 6.0069324 0.18404255 0.001 2.332667 5.4178316 186245.92 2 4 + 48000 512.83356 -3200.0643 0 1 0.96810224 258 544 6.0069324 0.1921875 0.00097916667 2.332667 5.5485401 188226.87 2 4 +Loop time of 0.241704 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 48000 512.83356 -3200.0643 0 1 0.96810224 258 544 6.0069324 0.1921875 0.00097916667 2.332667 5.5485401 188226.87 2 4 + 48051 512.83356 -3217.9192 0 1 0.96810224 258 544 6.0069324 0.19198352 0.00097812741 2.332667 5.5485401 188226.87 2 4 +Loop time of 0.0259903 on 4 procs for 51 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 48000 512.83356 -3200.0643 0.36239559 4495.5483 0.15738105 280 407 6.0069324 0.1921875 0.00097916667 2.332667 5.5485401 188226.87 3 6 + 49000 490.9639 -3198.6936 0.21113624 134.32512 0.22802517 114 115 6.0069324 0.18993878 0.00095918367 2.332667 5.5485401 191519.1 3 6 +Loop time of 0.22826 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 49000 490.9639 -3198.6936 0.21113624 134.32512 0.22802517 114 115 6.0069324 0.18993878 0.00095918367 2.332667 5.5485401 191519.1 3 6 + 49054 490.9639 -3217.9192 0.21113624 134.32512 0.22802517 114 115 6.0069324 0.18972969 0.00095812778 2.332667 5.5485401 191519.1 3 6 +Loop time of 0.024157 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 49000 490.9639 -3198.6936 0.21113624 134.32512 0.22802517 114 115 6.0069324 0.18993878 0.00095918367 2.332667 5.5485401 191519.1 3 6 + 50000 502.62206 -3199.7905 0.22799901 198.66723 0.22126947 119 400 6.0069324 0.1885 0.00094 2.332667 5.5485401 195910.67 3 6 +Loop time of 0.226578 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 50000 502.62206 -3199.7905 0.22799901 198.66723 0.22126947 119 400 6.0069324 0.1885 0.00094 2.332667 5.5485401 195910.67 3 6 + 50059 502.62206 -3217.9192 0.22799901 198.66723 0.22126947 119 400 6.0069324 0.18827783 0.00093889211 2.332667 5.5485401 195910.67 3 6 +Loop time of 0.0268276 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 50000 502.62206 -3199.7905 0.22799901 198.66723 0.22126947 119 400 6.0069324 0.1885 0.00094 2.332667 5.5485401 195910.67 3 6 + 51000 508.29336 -3198.9059 0.14109933 26.437299 0.25416947 264 275 6.0069324 0.18907843 0.00092156863 2.332667 5.5485401 199067.94 3 6 +Loop time of 0.23022 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 51000 508.29336 -3198.9059 0.14109933 26.437299 0.25416947 264 275 6.0069324 0.18907843 0.00092156863 2.332667 5.5485401 199067.94 3 6 + 51055 508.29336 -3217.9192 0.14109933 26.437299 0.25416947 264 275 6.0069324 0.18887474 0.00092057585 2.332667 5.5485401 199067.94 3 6 +Loop time of 0.0267057 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 51000 508.29336 -3198.9059 0.14109933 26.437299 0.25416947 264 275 6.0069324 0.18907843 0.00092156863 2.332667 5.5485401 199067.94 3 6 + 52000 506.84322 -3198.7391 0 1 0.35895473 264 275 6.0069324 0.19369231 0.00090384615 2.332667 5.5485401 199119.85 3 6 +Loop time of 0.248939 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 52000 506.84322 -3198.7391 0 1 0.35895473 264 275 6.0069324 0.19369231 0.00090384615 2.332667 5.5485401 199119.85 3 6 + 52061 506.84322 -3217.9192 0 1 0.35895473 264 275 6.0069324 0.19346536 0.00090278712 2.332667 5.5485401 199119.85 3 6 +Loop time of 0.0283017 on 4 procs for 61 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 52000 506.84322 -3198.7391 0 1 0.35895473 264 275 6.0069324 0.19369231 0.00090384615 2.332667 5.5485401 199119.85 3 6 + 53000 477.74415 -3199.3706 0 1 0.31797782 264 275 6.0069324 0.1960566 0.00088679245 2.332667 5.5485401 200597.61 3 6 +Loop time of 0.226147 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 53000 477.74415 -3199.3706 0 1 0.31797782 264 275 6.0069324 0.1960566 0.00088679245 2.332667 5.5485401 200597.61 3 6 + 53056 477.74415 -3217.9192 0 1 0.31797782 264 275 6.0069324 0.19584967 0.00088585645 2.332667 5.5485401 200597.61 3 6 +Loop time of 0.0249364 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 53000 477.74415 -3199.3706 0 1 0.31797782 264 275 6.0069324 0.1960566 0.00088679245 2.332667 5.5485401 200597.61 3 6 + 54000 467.64603 -3198.6476 0.12868765 19.820426 0.25852702 575 280 6.0069324 0.19614815 0.00087037037 2.332667 5.5485401 203111.2 3 6 +Loop time of 0.242983 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 54000 467.64603 -3198.6476 0.12868765 19.820426 0.25852702 575 280 6.0069324 0.19614815 0.00087037037 2.332667 5.5485401 203111.2 3 6 + 54051 467.64603 -3217.9192 0.12868765 19.820426 0.25852702 575 280 6.0069324 0.19596307 0.00086954913 2.332667 5.5485401 203111.2 3 6 +Loop time of 0.0256515 on 4 procs for 51 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 54000 467.64603 -3198.6476 0.12868765 19.820426 0.25852702 575 280 6.0069324 0.19614815 0.00087037037 2.332667 5.5485401 203111.2 3 6 + 55000 504.56378 -3198.2318 0.01979034 1.582988 0.29400296 556 567 6.0069324 0.1934 0.00085454545 2.332667 5.5485401 209967.08 3 6 +Loop time of 0.243744 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 55000 504.56378 -3198.2318 0.01979034 1.582988 0.29400296 556 567 6.0069324 0.1934 0.00085454545 2.332667 5.5485401 209967.08 3 6 + 55057 504.56378 -3217.9192 0.01979034 1.582988 0.29400296 556 567 6.0069324 0.19319977 0.00085366075 2.332667 5.5485401 209967.08 3 6 +Loop time of 0.0273646 on 4 procs for 57 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 55000 504.56378 -3198.2318 0.01979034 1.582988 0.29400296 556 567 6.0069324 0.1934 0.00085454545 2.332667 5.5485401 209967.08 3 6 + 56000 564.45428 -3198.7813 0.20223936 109.26492 0.23151007 78 91 6.0069324 0.19246429 0.00083928571 2.332667 5.5485401 215831.27 3 6 +Loop time of 0.238614 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 56000 564.45428 -3198.7813 0.20223936 109.26492 0.23151007 78 91 6.0069324 0.19246429 0.00083928571 2.332667 5.5485401 215831.27 3 6 + 56052 564.45428 -3217.9192 0.20223936 109.26492 0.23151007 78 91 6.0069324 0.19228573 0.0008385071 2.332667 5.5485401 215831.27 3 6 +Loop time of 0.0241504 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 56000 564.45428 -3198.7813 0.20223936 109.26492 0.23151007 78 91 6.0069324 0.19246429 0.00083928571 2.332667 5.5485401 215831.27 3 6 + 57000 515.72168 -3198.6584 0.31159686 1382.7848 0.18415364 544 577 6.0069324 0.19210526 0.0008245614 2.332667 5.5485401 222695.11 3 6 +Loop time of 0.30046 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 57000 515.72168 -3198.6584 0.31159686 1382.7848 0.18415364 544 577 6.0069324 0.19210526 0.0008245614 2.332667 5.5485401 222695.11 3 6 + 57059 515.72168 -3217.9192 0.31159686 1382.7848 0.18415364 544 577 6.0069324 0.19190662 0.00082370879 2.332667 5.5485401 222695.11 3 6 +Loop time of 0.0361512 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 57000 515.72168 -3198.6584 0.31159686 1382.7848 0.18415364 544 577 6.0069324 0.19210526 0.0008245614 2.332667 5.5485401 222695.11 3 6 + 58000 493.40021 -3198.8621 0 1 0.30931038 275 577 6.0069324 0.18989655 0.00081034483 2.332667 5.5485401 225894.02 3 6 +Loop time of 0.304723 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 58000 493.40021 -3198.8621 0 1 0.30931038 275 577 6.0069324 0.18989655 0.00081034483 2.332667 5.5485401 225894.02 3 6 + 58055 493.40021 -3217.9192 0 1 0.30931038 275 577 6.0069324 0.18971665 0.00080957713 2.332667 5.5485401 225894.02 3 6 +Loop time of 0.034838 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 58000 493.40021 -3198.8621 0 1 0.30931038 275 577 6.0069324 0.18989655 0.00081034483 2.332667 5.5485401 225894.02 3 6 + 59000 459.13337 -3198.423 0.32299123 1801.3772 0.17849812 117 288 6.0069324 0.189 0.00079661017 2.332667 5.5485401 232785.62 3 6 +Loop time of 0.267864 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 59000 459.13337 -3198.423 0.32299123 1801.3772 0.17849812 117 288 6.0069324 0.189 0.00079661017 2.332667 5.5485401 232785.62 3 6 + 59052 459.13337 -3217.9192 0.32299123 1801.3772 0.17849812 117 288 6.0069324 0.18883357 0.00079590869 2.332667 5.5485401 232785.62 3 6 +Loop time of 0.0229472 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 59000 459.13337 -3198.423 0.32299123 1801.3772 0.17849812 117 288 6.0069324 0.189 0.00079661017 2.332667 5.5485401 232785.62 3 6 + 60000 491.26878 -3198.9291 0.28012983 666.16416 0.19893876 560 567 6.0069324 0.18678333 0.00078333333 2.332667 5.5485401 236949.88 3 6 +Loop time of 0.224423 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 60000 491.26878 -3198.9291 0.28012983 666.16416 0.19893876 560 567 6.0069324 0.18678333 0.00078333333 2.332667 5.5485401 236949.88 3 6 + 60051 491.26878 -3217.9192 0.28012983 666.16416 0.19893876 560 567 6.0069324 0.1866247 0.00078266807 2.332667 5.5485401 236949.88 3 6 +Loop time of 0.0231369 on 4 procs for 51 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 60000 491.26878 -3198.9291 0.28012983 666.16416 0.19893876 560 567 6.0069324 0.18678333 0.00078333333 2.332667 5.5485401 236949.88 3 6 + 61000 469.65564 -3198.3735 0.086199081 7.3934564 0.27291787 562 564 6.0069324 0.18445902 0.0007704918 2.332667 5.5485401 245720.88 3 6 +Loop time of 0.228656 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 61000 469.65564 -3198.3735 0.086199081 7.3934564 0.27291787 562 564 6.0069324 0.18445902 0.0007704918 2.332667 5.5485401 245720.88 3 6 + 61053 469.65564 -3217.9192 0.086199081 7.3934564 0.27291787 562 564 6.0069324 0.18429889 0.00076982294 2.332667 5.5485401 245720.88 3 6 +Loop time of 0.0245876 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 61000 469.65564 -3198.3735 0.086199081 7.3934564 0.27291787 562 564 6.0069324 0.18445902 0.0007704918 2.332667 5.5485401 245720.88 3 6 + 62000 520.14843 -3198.5458 0.35275062 3593.8982 0.16280322 116 123 6.0069324 0.18312903 0.00075806452 2.332667 5.5485401 250136.37 3 6 +Loop time of 0.232165 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 62000 520.14843 -3198.5458 0.35275062 3593.8982 0.16280322 116 123 6.0069324 0.18312903 0.00075806452 2.332667 5.5485401 250136.37 3 6 + 62056 520.14843 -3217.9192 0.35275062 3593.8982 0.16280322 116 123 6.0069324 0.18296377 0.00075738043 2.332667 5.5485401 250136.37 3 6 +Loop time of 0.0275648 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 62000 520.14843 -3198.5458 0.35275062 3593.8982 0.16280322 116 123 6.0069324 0.18312903 0.00075806452 2.332667 5.5485401 250136.37 3 6 + 63000 506.90141 -3196.9575 0.019630501 1.5771264 0.29405188 577 555 6.0069324 0.18190476 0.00074603175 2.332667 5.5485401 257004.48 3 6 +Loop time of 0.236446 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 63000 506.90141 -3196.9575 0.019630501 1.5771264 0.29405188 577 555 6.0069324 0.18190476 0.00074603175 2.332667 5.5485401 257004.48 3 6 + 63059 506.90141 -3217.9192 0.019630501 1.5771264 0.29405188 577 555 6.0069324 0.18173457 0.00074533374 2.332667 5.5485401 257004.48 3 6 +Loop time of 0.0258729 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 63000 506.90141 -3196.9575 0.019630501 1.5771264 0.29405188 577 555 6.0069324 0.18190476 0.00074603175 2.332667 5.5485401 257004.48 3 6 + 64000 435.29185 -3197.3025 0.08981574 8.0408468 0.27172259 266 267 6.0069324 0.18060937 0.000734375 2.332667 5.5485401 261196.79 3 6 +Loop time of 0.224694 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 64000 435.29185 -3197.3025 0.08981574 8.0408468 0.27172259 266 267 6.0069324 0.18060937 0.000734375 2.332667 5.5485401 261196.79 3 6 + 64053 435.29185 -3217.9192 0.08981574 8.0408468 0.27172259 266 267 6.0069324 0.18045993 0.00073376735 2.332667 5.5485401 261196.79 3 6 +Loop time of 0.023932 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 64000 435.29185 -3197.3025 0.08981574 8.0408468 0.27172259 266 267 6.0069324 0.18060937 0.000734375 2.332667 5.5485401 261196.79 3 6 + 65000 484.45338 -3198.1013 0.27900382 648.98038 0.19944752 85 87 6.0069324 0.17955385 0.00072307692 2.332667 5.5485401 267611.45 3 6 +Loop time of 0.225038 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 65000 484.45338 -3198.1013 0.27900382 648.98038 0.19944752 85 87 6.0069324 0.17955385 0.00072307692 2.332667 5.5485401 267611.45 3 6 + 65053 484.45338 -3217.9192 0.27900382 648.98038 0.19944752 85 87 6.0069324 0.17940756 0.00072248782 2.332667 5.5485401 267611.45 3 6 +Loop time of 0.0248089 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 65000 484.45338 -3198.1013 0.27900382 648.98038 0.19944752 85 87 6.0069324 0.17955385 0.00072307692 2.332667 5.5485401 267611.45 3 6 + 66000 497.23553 -3199.036 0.25525209 373.95984 0.20989193 412 411 6.0069324 0.17804545 0.00071212121 2.332667 5.5485401 274383.49 3 6 +Loop time of 0.233376 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 66000 497.23553 -3199.036 0.25525209 373.95984 0.20989193 412 411 6.0069324 0.17804545 0.00071212121 2.332667 5.5485401 274383.49 3 6 + 66058 497.23553 -3217.9192 0.25525209 373.95984 0.20989193 412 411 6.0069324 0.17788913 0.00071149596 2.332667 5.5485401 274383.49 3 6 +Loop time of 0.0279601 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 66000 497.23553 -3199.036 0.25525209 373.95984 0.20989193 412 411 6.0069324 0.17804545 0.00071212121 2.332667 5.5485401 274383.49 3 6 + 67000 488.34684 -3198.7152 0.27967841 659.2212 0.19914288 264 275 6.0069324 0.17935821 0.00070149254 2.332667 5.5485401 274635.62 3 6 +Loop time of 0.237521 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 67000 488.34684 -3198.7152 0.27967841 659.2212 0.19914288 264 275 6.0069324 0.17935821 0.00070149254 2.332667 5.5485401 274635.62 3 6 + 67055 488.34684 -3217.9192 0.27967841 659.2212 0.19914288 264 275 6.0069324 0.1792111 0.00070091716 2.332667 5.5485401 274635.62 3 6 +Loop time of 0.0262208 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 67000 488.34684 -3198.7152 0.27967841 659.2212 0.19914288 264 275 6.0069324 0.17935821 0.00070149254 2.332667 5.5485401 274635.62 3 6 + 68000 547.06201 -3198.7151 0.11427629 14.185774 0.26349624 261 263 6.0069324 0.17882353 0.00069117647 2.332667 5.5485401 277575.99 3 6 +Loop time of 0.224043 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 68000 547.06201 -3198.7151 0.11427629 14.185774 0.26349624 261 263 6.0069324 0.17882353 0.00069117647 2.332667 5.5485401 277575.99 3 6 + 68060 547.06201 -3217.9192 0.11427629 14.185774 0.26349624 261 263 6.0069324 0.17866588 0.00069056715 2.332667 5.5485401 277575.99 3 6 +Loop time of 0.0288572 on 4 procs for 60 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 68000 547.06201 -3198.7151 0.11427629 14.185774 0.26349624 261 263 6.0069324 0.17882353 0.00069117647 2.332667 5.5485401 277575.99 3 6 + 69000 508.94771 -3198.9475 0.10069537 10.350552 0.26809482 264 275 6.0069324 0.18095652 0.00068115942 2.332667 5.5485401 279847.52 3 6 +Loop time of 0.227692 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 69000 508.94771 -3198.9475 0.10069537 10.350552 0.26809482 264 275 6.0069324 0.18095652 0.00068115942 2.332667 5.5485401 279847.52 3 6 + 69056 508.94771 -3217.9192 0.10069537 10.350552 0.26809482 264 275 6.0069324 0.18080978 0.00068060704 2.332667 5.5485401 279847.52 3 6 +Loop time of 0.0247979 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 69000 508.94771 -3198.9475 0.10069537 10.350552 0.26809482 264 275 6.0069324 0.18095652 0.00068115942 2.332667 5.5485401 279847.52 3 6 + 70000 499.92534 -3198.5636 0.3528879 3605.3669 0.16272731 283 288 6.0069324 0.18142857 0.00072857143 2.332667 5.5485401 281504.52 3 6 +Loop time of 0.232204 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 70000 499.92534 -3198.5636 0.3528879 3605.3669 0.16272731 283 288 6.0069324 0.18142857 0.00072857143 2.332667 5.5485401 281504.52 3 6 + 70054 499.92534 -3217.9192 0.3528879 3605.3669 0.16272731 283 288 6.0069324 0.18128872 0.00072800982 2.332667 5.5485401 281504.52 3 6 +Loop time of 0.0249009 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 70000 499.92534 -3198.5636 0.3528879 3605.3669 0.16272731 283 288 6.0069324 0.18142857 0.00072857143 2.332667 5.5485401 281504.52 3 6 + 71000 506.70688 -3197.313 0.082678879 6.813425 0.27407627 541 543 6.0069324 0.18050704 0.00071830986 2.332667 5.5485401 286003.61 3 6 +Loop time of 0.229025 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 71000 506.70688 -3197.313 0.082678879 6.813425 0.27407627 541 543 6.0069324 0.18050704 0.00071830986 2.332667 5.5485401 286003.61 3 6 + 71059 506.70688 -3217.9192 0.082678879 6.813425 0.27407627 541 543 6.0069324 0.18035717 0.00071771345 2.332667 5.5485401 286003.61 3 6 +Loop time of 0.0265949 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 71000 506.70688 -3197.313 0.082678879 6.813425 0.27407627 541 543 6.0069324 0.18050704 0.00071830986 2.332667 5.5485401 286003.61 3 6 + 72000 464.23294 -3197.7357 0 1 0.31542276 275 577 6.0069324 0.18266667 0.00070833333 2.332667 5.5485401 286734.83 3 6 +Loop time of 0.228346 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 72000 464.23294 -3197.7357 0 1 0.31542276 275 577 6.0069324 0.18266667 0.00070833333 2.332667 5.5485401 286734.83 3 6 + 72053 464.23294 -3217.9192 0 1 0.31542276 275 577 6.0069324 0.1825323 0.0007078123 2.332667 5.5485401 286734.83 3 6 +Loop time of 0.026114 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 72000 464.23294 -3197.7357 0 1 0.31542276 275 577 6.0069324 0.18266667 0.00070833333 2.332667 5.5485401 286734.83 3 6 + 73000 529.30216 -3198.1231 0.1005148 10.307265 0.26815543 411 416 6.0069324 0.18394521 0.00069863014 2.332667 5.5485401 287872.93 3 6 +Loop time of 0.229123 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 73000 529.30216 -3198.1231 0.1005148 10.307265 0.26815543 411 416 6.0069324 0.18394521 0.00069863014 2.332667 5.5485401 287872.93 3 6 + 73054 529.30216 -3217.9192 0.1005148 10.307265 0.26815543 411 416 6.0069324 0.18380924 0.00069811372 2.332667 5.5485401 287872.93 3 6 +Loop time of 0.0243089 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 73000 529.30216 -3198.1231 0.1005148 10.307265 0.26815543 411 416 6.0069324 0.18394521 0.00069863014 2.332667 5.5485401 287872.93 3 6 + 74000 490.65557 -3199.6766 0.14904687 31.792497 0.25133954 111 116 6.0069324 0.18322973 0.00068918919 2.332667 5.5485401 294766.16 3 6 +Loop time of 0.236133 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 74000 490.65557 -3199.6766 0.14904687 31.792497 0.25133954 111 116 6.0069324 0.18322973 0.00068918919 2.332667 5.5485401 294766.16 3 6 + 74055 490.65557 -3217.9192 0.14904687 31.792497 0.25133954 111 116 6.0069324 0.18309365 0.00068867733 2.332667 5.5485401 294766.16 3 6 +Loop time of 0.0264881 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 74000 490.65557 -3199.6766 0.14904687 31.792497 0.25133954 111 116 6.0069324 0.18322973 0.00068918919 2.332667 5.5485401 294766.16 3 6 + 75000 475.22638 -3198.1558 0.37341486 5805.6632 0.15094809 563 564 6.0069324 0.18212 0.00073333333 2.332667 5.5485401 302150.54 3 6 +Loop time of 0.228974 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 75000 475.22638 -3198.1558 0.37341486 5805.6632 0.15094809 563 564 6.0069324 0.18212 0.00073333333 2.332667 5.5485401 302150.54 3 6 + 75053 475.22638 -3217.9192 0.37341486 5805.6632 0.15094809 563 564 6.0069324 0.18199139 0.00073281548 2.332667 5.5485401 302150.54 3 6 +Loop time of 0.0246332 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 75000 475.22638 -3198.1558 0.37341486 5805.6632 0.15094809 563 564 6.0069324 0.18212 0.00073333333 2.332667 5.5485401 302150.54 3 6 + 76000 523.91803 -3198.8966 0.038679316 2.4539737 0.28816267 263 264 6.0069324 0.18286842 0.00072368421 2.332667 5.5485401 304160.3 3 6 +Loop time of 0.223991 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 76000 523.91803 -3198.8966 0.038679316 2.4539737 0.28816267 263 264 6.0069324 0.18286842 0.00072368421 2.332667 5.5485401 304160.3 3 6 + 76058 523.91803 -3217.9192 0.038679316 2.4539737 0.28816267 263 264 6.0069324 0.18272897 0.00072313235 2.332667 5.5485401 304160.3 3 6 +Loop time of 0.0268497 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 76000 523.91803 -3198.8966 0.038679316 2.4539737 0.28816267 263 264 6.0069324 0.18286842 0.00072368421 2.332667 5.5485401 304160.3 3 6 + 77000 511.16512 -3199.1926 0 1 0.31251901 264 275 6.0069324 0.18790909 0.00071428571 2.332667 5.5485401 304174.43 3 6 +Loop time of 0.226324 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 77000 511.16512 -3199.1926 0 1 0.31251901 264 275 6.0069324 0.18790909 0.00071428571 2.332667 5.5485401 304174.43 3 6 + 77059 511.16512 -3217.9192 0 1 0.31251901 264 275 6.0069324 0.18776522 0.00071373882 2.332667 5.5485401 304174.43 3 6 +Loop time of 0.026314 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 77000 511.16512 -3199.1926 0 1 0.31251901 264 275 6.0069324 0.18790909 0.00071428571 2.332667 5.5485401 304174.43 3 6 + 78000 554.58169 -3199.0107 0.022175428 1.6730858 0.29327193 263 264 6.0069324 0.19037179 0.00094871795 2.332667 5.5485401 304438.98 3 6 +Loop time of 0.234504 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 78000 554.58169 -3199.0107 0.022175428 1.6730858 0.29327193 263 264 6.0069324 0.19037179 0.00094871795 2.332667 5.5485401 304438.98 3 6 + 78062 554.58169 -3217.9192 0.022175428 1.6730858 0.29327193 263 264 6.0069324 0.19022059 0.00094796444 2.332667 5.5485401 304438.98 3 6 +Loop time of 0.0297351 on 4 procs for 62 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 78000 554.58169 -3199.0107 0.022175428 1.6730858 0.29327193 263 264 6.0069324 0.19037179 0.00094871795 2.332667 5.5485401 304438.98 3 6 + 79000 523.97176 -3198.2366 0.1672356 48.490735 0.24473985 556 567 6.0069324 0.19017722 0.00093670886 2.332667 5.5485401 306076.23 3 6 +Loop time of 0.228044 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 79000 523.97176 -3198.2366 0.1672356 48.490735 0.24473985 556 567 6.0069324 0.19017722 0.00093670886 2.332667 5.5485401 306076.23 3 6 + 79057 523.97176 -3217.9192 0.1672356 48.490735 0.24473985 556 567 6.0069324 0.1900401 0.00093603349 2.332667 5.5485401 306076.23 3 6 +Loop time of 0.026444 on 4 procs for 57 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 79000 523.97176 -3198.2366 0.1672356 48.490735 0.24473985 556 567 6.0069324 0.19017722 0.00093670886 2.332667 5.5485401 306076.23 3 6 + 80000 479.09781 -3197.6134 0 1 0.30854872 263 577 6.0069324 0.1902125 0.000925 2.332667 5.5485401 308522.09 3 6 +Loop time of 0.224854 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 80000 479.09781 -3197.6134 0 1 0.30854872 263 577 6.0069324 0.1902125 0.000925 2.332667 5.5485401 308522.09 3 6 + 80059 479.09781 -3217.9192 0 1 0.30854872 263 577 6.0069324 0.19007232 0.00092431832 2.332667 5.5485401 308522.09 3 6 +Loop time of 0.0272751 on 4 procs for 59 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 80000 479.09781 -3197.6134 0 1 0.30854872 263 577 6.0069324 0.1902125 0.000925 2.332667 5.5485401 308522.09 3 6 + 81000 517.52613 -3198.2236 0.29863857 1023.6251 0.19038135 254 256 6.0069324 0.18996296 0.00091358025 2.332667 5.5485401 311171.12 3 6 +Loop time of 0.226269 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 81000 517.52613 -3198.2236 0.29863857 1023.6251 0.19038135 254 256 6.0069324 0.18996296 0.00091358025 2.332667 5.5485401 311171.12 3 6 + 81056 517.52613 -3217.9192 0.29863857 1023.6251 0.19038135 254 256 6.0069324 0.18983172 0.00091294907 2.332667 5.5485401 311171.12 3 6 +Loop time of 0.0258186 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 81000 517.52613 -3198.2236 0.29863857 1023.6251 0.19038135 254 256 6.0069324 0.18996296 0.00091358025 2.332667 5.5485401 311171.12 3 6 + 82000 503.95678 -3197.7481 0.091495497 8.3605139 0.27116565 263 264 6.0069324 0.18862195 0.0010365854 2.332667 5.5485401 315319.38 3 6 +Loop time of 0.235559 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 82000 503.95678 -3197.7481 0.091495497 8.3605139 0.27116565 263 264 6.0069324 0.18862195 0.0010365854 2.332667 5.5485401 315319.38 3 6 + 82055 503.95678 -3217.9192 0.091495497 8.3605139 0.27116565 263 264 6.0069324 0.18849552 0.0010358906 2.332667 5.5485401 315319.38 3 6 +Loop time of 0.0261242 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 82000 503.95678 -3197.7481 0.091495497 8.3605139 0.27116565 263 264 6.0069324 0.18862195 0.0010365854 2.332667 5.5485401 315319.38 3 6 + 83000 537.67639 -3197.6886 0 1 0.32414276 263 264 6.0069324 0.1896988 0.0010240964 2.332667 5.5485401 316613.84 3 6 +Loop time of 0.227873 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 83000 537.67639 -3197.6886 0 1 0.32414276 263 264 6.0069324 0.1896988 0.0010240964 2.332667 5.5485401 316613.84 3 6 + 83064 537.67639 -3217.9192 0 1 0.32414276 263 264 6.0069324 0.18955263 0.0010233073 2.332667 5.5485401 316613.84 3 6 +Loop time of 0.0301323 on 4 procs for 64 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 83000 537.67639 -3197.6886 0 1 0.32414276 263 264 6.0069324 0.1896988 0.0010240964 2.332667 5.5485401 316613.84 3 6 + 84000 510.26841 -3199.5428 0.23554832 236.71181 0.21817723 142 424 6.0069324 0.19 0.0010119048 2.332667 5.5485401 318598.08 3 6 +Loop time of 0.228573 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 84000 510.26841 -3199.5428 0.23554832 236.71181 0.21817723 142 424 6.0069324 0.19 0.0010119048 2.332667 5.5485401 318598.08 3 6 + 84052 510.26841 -3217.9192 0.23554832 236.71181 0.21817723 142 424 6.0069324 0.18988245 0.0010112787 2.332667 5.5485401 318598.08 3 6 +Loop time of 0.0254717 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 84000 510.26841 -3199.5428 0.23554832 236.71181 0.21817723 142 424 6.0069324 0.19 0.0010119048 2.332667 5.5485401 318598.08 3 6 + 85000 472.16876 -3197.5248 0 1 0.34247044 264 275 6.0069324 0.18970588 0.001 2.332667 5.5485401 323882.61 3 6 +Loop time of 0.231174 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 85000 472.16876 -3197.5248 0 1 0.34247044 264 275 6.0069324 0.18970588 0.001 2.332667 5.5485401 323882.61 3 6 + 85055 472.16876 -3217.9192 0 1 0.34247044 264 275 6.0069324 0.18958321 0.00099935336 2.332667 5.5485401 323882.61 3 6 +Loop time of 0.0253472 on 4 procs for 55 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 85000 472.16876 -3197.5248 0 1 0.34247044 264 275 6.0069324 0.18970588 0.001 2.332667 5.5485401 323882.61 3 6 + 86000 509.30024 -3198.3226 0.20619306 119.76563 0.22996793 275 276 6.0069324 0.19110465 0.00098837209 2.332667 5.5485401 325788.44 3 6 +Loop time of 0.241364 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 86000 509.30024 -3198.3226 0.20619306 119.76563 0.22996793 275 276 6.0069324 0.19110465 0.00098837209 2.332667 5.5485401 325788.44 3 6 + 86053 509.30024 -3217.9192 0.20619306 119.76563 0.22996793 275 276 6.0069324 0.19098695 0.00098776336 2.332667 5.5485401 325788.44 3 6 +Loop time of 0.0262635 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 86000 509.30024 -3198.3226 0.20619306 119.76563 0.22996793 275 276 6.0069324 0.19110465 0.00098837209 2.332667 5.5485401 325788.44 3 6 + 87000 478.57944 -3199.3497 0.19192384 86.001287 0.23548611 260 271 6.0069324 0.1897931 0.00097701149 2.332667 5.5485401 330047.59 3 6 +Loop time of 0.230381 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 87000 478.57944 -3199.3497 0.19192384 86.001287 0.23548611 260 271 6.0069324 0.1897931 0.00097701149 2.332667 5.5485401 330047.59 3 6 + 87058 478.57944 -3217.9192 0.19192384 86.001287 0.23548611 260 271 6.0069324 0.18966666 0.00097636059 2.332667 5.5485401 330047.59 3 6 +Loop time of 0.0275965 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 87000 478.57944 -3199.3497 0.19192384 86.001287 0.23548611 260 271 6.0069324 0.1897931 0.00097701149 2.332667 5.5485401 330047.59 3 6 + 88000 515.63138 -3198.9629 0.35491784 3779.2911 0.16160071 543 577 6.0069324 0.18827273 0.00096590909 2.332667 5.5485401 337304.34 3 6 +Loop time of 0.229339 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 88000 515.63138 -3198.9629 0.35491784 3779.2911 0.16160071 543 577 6.0069324 0.18827273 0.00096590909 2.332667 5.5485401 337304.34 3 6 + 88050 515.63138 -3217.9192 0.35491784 3779.2911 0.16160071 543 577 6.0069324 0.18816581 0.00096536059 2.332667 5.5485401 337304.34 3 6 +Loop time of 0.0253522 on 4 procs for 50 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 88000 515.63138 -3198.9629 0.35491784 3779.2911 0.16160071 543 577 6.0069324 0.18827273 0.00096590909 2.332667 5.5485401 337304.34 3 6 + 89000 520.37063 -3197.8234 0 1 0.92013924 262 275 6.0069324 0.19148315 0.0011123596 2.332667 5.5485401 339909.57 3 6 +Loop time of 0.234048 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 89000 520.37063 -3197.8234 0 1 0.92013924 262 275 6.0069324 0.19148315 0.0011123596 2.332667 5.5485401 339909.57 3 6 + 89052 520.37063 -3217.9192 0 1 0.92013924 262 275 6.0069324 0.19137133 0.00111171 2.332667 5.5485401 339909.57 3 6 +Loop time of 0.0242915 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 89000 520.37063 -3197.8234 0.34652166 3110.1454 0.16621101 111 112 6.0069324 0.19148315 0.0011123596 2.332667 5.5485401 339909.57 4 8 + 90000 455.69218 -3197.8262 0.30521336 1192.3721 0.18724742 416 415 6.0069324 0.1905 0.0011 2.332667 5.5485401 345606.41 4 8 +Loop time of 0.239736 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 90000 455.69218 -3197.8262 0.30521336 1192.3721 0.18724742 416 415 6.0069324 0.1905 0.0011 2.332667 5.5485401 345606.41 4 8 + 90058 455.69218 -3217.9192 0.30521336 1192.3721 0.18724742 416 415 6.0069324 0.19037731 0.0010992916 2.332667 5.5485401 345606.41 4 8 +Loop time of 0.027481 on 4 procs for 58 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 90000 455.69218 -3197.8262 0.30521336 1192.3721 0.18724742 416 415 6.0069324 0.1905 0.0011 2.332667 5.5485401 345606.41 4 8 + 91000 506.17768 -3197.1344 0.035696451 2.2898339 0.28909279 547 548 6.0069324 0.18983516 0.0010879121 2.332667 5.5485401 350825.27 4 8 +Loop time of 0.23396 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 91000 506.17768 -3197.1344 0.035696451 2.2898339 0.28909279 547 548 6.0069324 0.18983516 0.0010879121 2.332667 5.5485401 350825.27 4 8 + 91051 506.17768 -3217.9192 0.035696451 2.2898339 0.28909279 547 548 6.0069324 0.18972883 0.0010873027 2.332667 5.5485401 350825.27 4 8 +Loop time of 0.0249534 on 4 procs for 51 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 91000 506.17768 -3197.1344 0.035696451 2.2898339 0.28909279 547 548 6.0069324 0.18983516 0.0010879121 2.332667 5.5485401 350825.27 4 8 + 92000 478.3025 -3197.9483 0 1 0.30393958 544 556 6.0069324 0.19196739 0.001076087 2.332667 5.5485401 352816.62 4 8 +Loop time of 0.233376 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 92000 478.3025 -3197.9483 0 1 0.30393958 544 556 6.0069324 0.19196739 0.001076087 2.332667 5.5485401 352816.62 4 8 + 92060 478.3025 -3217.9192 0 1 0.30393958 544 556 6.0069324 0.19184228 0.0010753856 2.332667 5.5485401 352816.62 4 8 +Loop time of 0.0286014 on 4 procs for 60 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 92000 478.3025 -3197.9483 0 1 0.30393958 544 556 6.0069324 0.19196739 0.001076087 2.332667 5.5485401 352816.62 4 8 + 93000 485.23153 -3199.9299 0.16699022 48.215364 0.24483006 544 556 6.0069324 0.1942043 0.0010645161 2.332667 5.5485401 354391.05 4 8 +Loop time of 0.234626 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 93000 485.23153 -3199.9299 0.16699022 48.215364 0.24483006 544 556 6.0069324 0.1942043 0.0010645161 2.332667 5.5485401 354391.05 4 8 + 93056 485.23153 -3217.9192 0.16699022 48.215364 0.24483006 544 556 6.0069324 0.19408743 0.0010638755 2.332667 5.5485401 354391.05 4 8 +Loop time of 0.0261769 on 4 procs for 56 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 93000 485.23153 -3199.9299 0.16699022 48.215364 0.24483006 544 556 6.0069324 0.1942043 0.0010645161 2.332667 5.5485401 354391.05 4 8 + 94000 499.72991 -3199.3195 0 1 0.30394408 544 556 6.0069324 0.19443617 0.0010531915 2.332667 5.5485401 360147.54 4 8 +Loop time of 0.229448 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 94000 499.72991 -3199.3195 0 1 0.30394408 544 556 6.0069324 0.19443617 0.0010531915 2.332667 5.5485401 360147.54 4 8 + 94061 499.72991 -3217.9192 0 1 0.30394408 544 556 6.0069324 0.19431008 0.0010525085 2.332667 5.5485401 360147.54 4 8 +Loop time of 0.0281783 on 4 procs for 61 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 94000 499.72991 -3199.3195 0 1 0.30394408 544 556 6.0069324 0.19443617 0.0010531915 2.332667 5.5485401 360147.54 4 8 + 95000 509.83941 -3199.0903 0.078854869 6.234781 0.27532912 555 556 6.0069324 0.19681053 0.0010421053 2.332667 5.5485401 360599.28 4 8 +Loop time of 0.224206 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 95000 509.83941 -3199.0903 0.078854869 6.234781 0.27532912 555 556 6.0069324 0.19681053 0.0010421053 2.332667 5.5485401 360599.28 4 8 + 95060 509.83941 -3217.9192 0.078854869 6.234781 0.27532912 555 556 6.0069324 0.1966863 0.0010414475 2.332667 5.5485401 360599.28 4 8 +Loop time of 0.027992 on 4 procs for 60 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 95000 509.83941 -3199.0903 0.078854869 6.234781 0.27532912 555 556 6.0069324 0.19681053 0.0010421053 2.332667 5.5485401 360599.28 4 8 + 96000 486.83779 -3197.2106 0.31070799 1354.5503 0.18458755 136 431 6.0069324 0.19620833 0.00103125 2.332667 5.5485401 365489.89 4 8 +Loop time of 0.228167 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 96000 486.83779 -3197.2106 0.31070799 1354.5503 0.18458755 136 431 6.0069324 0.19620833 0.00103125 2.332667 5.5485401 365489.89 4 8 + 96053 486.83779 -3217.9192 0.31070799 1354.5503 0.18458755 136 431 6.0069324 0.19610007 0.001030681 2.332667 5.5485401 365489.89 4 8 +Loop time of 0.024569 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 96000 486.83779 -3197.2106 0.31070799 1354.5503 0.18458755 136 431 6.0069324 0.19620833 0.00103125 2.332667 5.5485401 365489.89 4 8 + 97000 499.91835 -3199.2446 0.2280334 198.82589 0.22125548 280 111 6.0069324 0.19491753 0.0010206186 2.332667 5.5485401 372336.45 4 8 +Loop time of 0.23889 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 97000 499.91835 -3199.2446 0.2280334 198.82589 0.22125548 280 111 6.0069324 0.19491753 0.0010206186 2.332667 5.5485401 372336.45 4 8 + 97052 499.91835 -3217.9192 0.2280334 198.82589 0.22125548 280 111 6.0069324 0.19481309 0.0010200717 2.332667 5.5485401 372336.45 4 8 +Loop time of 0.0262206 on 4 procs for 52 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 97000 499.91835 -3199.2446 0.2280334 198.82589 0.22125548 280 111 6.0069324 0.19491753 0.0010206186 2.332667 5.5485401 372336.45 4 8 + 98000 547.56456 -3197.2191 0.27848637 641.23302 0.19968088 430 136 6.0069324 0.1957449 0.0010102041 2.332667 5.5485401 377711.41 4 8 +Loop time of 0.239305 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 98000 547.56456 -3197.2191 0.27848637 641.23302 0.19968088 430 136 6.0069324 0.1957449 0.0010102041 2.332667 5.5485401 377711.41 4 8 + 98054 547.56456 -3217.9192 0.27848637 641.23302 0.19968088 430 136 6.0069324 0.1956371 0.0010096477 2.332667 5.5485401 377711.41 4 8 +Loop time of 0.0272166 on 4 procs for 54 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 98000 547.56456 -3197.2191 0.27848637 641.23302 0.19968088 430 136 6.0069324 0.1957449 0.0010102041 2.332667 5.5485401 377711.41 4 8 + 99000 504.19627 -3196.6567 0 1 0.33814873 287 276 6.0069324 0.19517172 0.001 2.332667 5.5485401 381676.19 4 8 +Loop time of 0.235176 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 99000 504.19627 -3196.6567 0 1 0.33814873 287 276 6.0069324 0.19517172 0.001 2.332667 5.5485401 381676.19 4 8 + 99053 504.19627 -3217.9192 0 1 0.33814873 287 276 6.0069324 0.19506729 0.00099946493 2.332667 5.5485401 381676.19 4 8 +Loop time of 0.0249114 on 4 procs for 53 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 99000 504.19627 -3196.6567 0 1 0.33814873 287 276 6.0069324 0.19517172 0.001 2.332667 5.5485401 381676.19 4 8 + 100000 542.04702 -3198.2211 0.37630331 6208.2061 0.14921597 563 564 6.0069324 0.19442 0.00099 2.332667 5.5485401 385211.4 4 8 +Loop time of 0.226452 on 4 procs for 1000 steps with 577 atoms + +Step Temp PotEng f_HG f_HG[1] f_HG[2] f_HG[3] f_HG[4] f_HG[5] f_HG[6] f_HG[7] f_HG[8] f_HG[9] f_HG[10] f_HG[11] f_HG[12] + 100000 542.04702 -3198.2211 0.37630331 6208.2061 0.14921597 563 564 6.0069324 0.19442 0.00099 2.332667 5.5485401 385211.4 4 8 + 100060 542.04702 -3217.9192 0.37630331 6208.2061 0.14921597 563 564 6.0069324 0.19430342 0.00098940636 2.332667 5.5485401 385211.4 4 8 +Loop time of 0.0303354 on 4 procs for 60 steps with 577 atoms + +Final hyper stats ... + +Cummulative quantities for fix hyper: + hyper time = 385211 + time boost factor = 770.423 + event timesteps = 4 + # of atoms in events = 8 +Quantities for this hyper run: + event timesteps = 4 + # of atoms in events = 8 + max length of any bond = 5.54854 + max drift distance of any atom = 2.33267 + fraction of biased bonds with zero bias = 0.19442 + fraction of biased bonds with negative strain = 0.00099 +Current quantities: + ave bonds/atom = 6.00693 + +Loop time of 26.6054 on 4 procs for 100000 steps with 577 atoms + +Performance: 1623.732 ns/day, 0.015 hours/ns, 3758.639 timesteps/s +100.6% CPU use with 4 MPI tasks x no OpenMP threads + +Hyper stats: + Dynamics time (%) = 23.5897 (88.665) + Quench time (%) = 2.6357 (9.90664) + Other time (%) = 0.875172 (3.28945) + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 18.942 | 19.435 | 20.026 | 10.1 | 73.05 +Neigh | 1.3021 | 1.3833 | 1.4611 | 6.2 | 5.20 +Comm | 2.1376 | 2.1725 | 2.2239 | 2.2 | 8.17 +Output | 0.0033467 | 0.0034443 | 0.0037186 | 0.3 | 0.01 +Modify | 2.0693 | 2.7356 | 3.2627 | 30.2 | 10.28 +Other | | 0.8752 | | | 3.29 + +Nlocal: 144.25 ave 152 max 139 min +Histogram: 1 1 0 0 1 0 0 0 0 1 +Nghost: 533.25 ave 538 max 526 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 3368.25 ave 3528 max 3240 min +Histogram: 1 1 0 0 0 0 1 0 0 1 + +Total # of neighbors = 13473 +Ave neighs/atom = 23.3501 +Neighbor list builds = 10072 +Dangerous builds = 0 +Total wall time: 0:00:27 diff --git a/examples/hyper/log.25Mar19.hyper.local.g++.16 b/examples/hyper/log.25Mar19.hyper.local.g++.16 new file mode 100644 index 0000000000..b56406f963 --- /dev/null +++ b/examples/hyper/log.25Mar19.hyper.local.g++.16 @@ -0,0 +1,1002 @@ +LAMMPS (28 Feb 2019) +# 3d EAM surface for local HD + +# nearest neighbor distance = a * sqrt(2)/2 = 2.77 Angs for Pt with a = 3.92 +# hop event on (100) surface is same distance +# exchange event is 2 atoms moving same distance + +variable Tequil index 400.0 +variable Vmax index 0.4 +variable qfactor index 0.3 +variable cutbond index 3.2 +variable Dcut index 10.0 +variable cutevent index 1.1 +variable alpha index 200.0 +variable boost index 4000.0 +variable ghostcut index 12.0 +variable steps index 1500 +variable nevent index 100 +variable nx index 8 +variable ny index 8 +variable zoom index 1.8 +variable seed index 826626413 +variable tol index 1.0e-15 +variable add index 37K + +units metal +atom_style atomic +atom_modify map array +boundary p p p +comm_modify cutoff ${ghostcut} +comm_modify cutoff 12.0 + +lattice fcc 3.92 +Lattice spacing in x,y,z = 3.92 3.92 3.92 +region box block 0 6 0 6 0 4 +create_box 2 box +Created orthogonal box = (0 0 0) to (23.52 23.52 15.68) + 2 by 4 by 2 MPI processor grid +create_atoms 1 box +Created 576 atoms + Time spent = 0.00110102 secs + +mass * 1.0 + +change_box all z final -0.1 5.0 boundary p p f + orthogonal box = (0 0 -0.392) to (23.52 23.52 19.6) + +# replicate in xy + +replicate ${nx} ${ny} 1 +replicate 8 ${ny} 1 +replicate 8 8 1 + orthogonal box = (0 0 -0.392) to (188.16 188.16 19.6) + 4 by 4 by 1 MPI processor grid + 36864 atoms + Time spent = 0.00289989 secs + +# add adatoms + +include adatoms.list.${add} +include adatoms.list.37K +create_atoms 1 single 27.5 9.5 4 +Created 1 atoms + Time spent = 0.000200033 secs +create_atoms 1 single 16 9 4 +Created 1 atoms + Time spent = 0.000183105 secs +create_atoms 1 single 10 12 4 +Created 1 atoms + Time spent = 0.000180006 secs +create_atoms 1 single 31 44 4 +Created 1 atoms + Time spent = 0.000190973 secs +create_atoms 1 single 13 17 4 +Created 1 atoms + Time spent = 0.000185013 secs +create_atoms 1 single 8.5 28.5 4 +Created 1 atoms + Time spent = 0.00018692 secs +create_atoms 1 single 23 26 4 +Created 1 atoms + Time spent = 0.000179052 secs +create_atoms 1 single 38 27 4 +Created 1 atoms + Time spent = 0.000191927 secs +create_atoms 1 single 37.5 4.5 4 +Created 1 atoms + Time spent = 0.000238895 secs +create_atoms 1 single 41.5 47.5 4 +Created 1 atoms + Time spent = 0.000191927 secs +create_atoms 1 single 20.5 37.5 4 +Created 1 atoms + Time spent = 0.000185966 secs +create_atoms 1 single 5 8 4 +Created 1 atoms + Time spent = 0.000170946 secs +create_atoms 1 single 2.5 16.5 4 +Created 1 atoms + Time spent = 0.000174046 secs +create_atoms 1 single 38.5 45.5 4 +Created 1 atoms + Time spent = 0.000172853 secs +create_atoms 1 single 9 0 4 +Created 1 atoms + Time spent = 0.000187159 secs +create_atoms 1 single 39 32 4 +Created 1 atoms + Time spent = 0.000180006 secs +create_atoms 1 single 45.5 11.5 4 +Created 1 atoms + Time spent = 0.000189066 secs +create_atoms 1 single 40 0 4 +Created 1 atoms + Time spent = 0.000170946 secs +create_atoms 1 single 44.5 2.5 4 +Created 1 atoms + Time spent = 0.000191927 secs +create_atoms 1 single 4.5 44.5 4 +Created 1 atoms + Time spent = 0.000169992 secs +create_atoms 1 single 24.5 13.5 4 +Created 1 atoms + Time spent = 0.000166893 secs +create_atoms 1 single 47.5 23.5 4 +Created 1 atoms + Time spent = 0.000181913 secs +create_atoms 1 single 1 20 4 +Created 1 atoms + Time spent = 0.000167131 secs +create_atoms 1 single 38.5 31.5 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 12.5 12.5 4 +Created 1 atoms + Time spent = 0.000165939 secs +create_atoms 1 single 2 27 4 +Created 1 atoms + Time spent = 0.000170231 secs +create_atoms 1 single 21 5 4 +Created 1 atoms + Time spent = 0.00018096 secs +create_atoms 1 single 47 12 4 +Created 1 atoms + Time spent = 0.000166178 secs +create_atoms 1 single 32.5 46.5 4 +Created 1 atoms + Time spent = 0.000166893 secs +create_atoms 1 single 9.5 40.5 4 +Created 1 atoms + Time spent = 0.000165939 secs +create_atoms 1 single 8.5 2.5 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 41.5 22.5 4 +Created 1 atoms + Time spent = 0.000175953 secs +create_atoms 1 single 29 11 4 +Created 1 atoms + Time spent = 0.000165939 secs +create_atoms 1 single 3.5 3.5 4 +Created 1 atoms + Time spent = 0.000174999 secs +create_atoms 1 single 5 21 4 +Created 1 atoms + Time spent = 0.0001719 secs +create_atoms 1 single 46.5 31.5 4 +Created 1 atoms + Time spent = 0.000169992 secs +create_atoms 1 single 35 46 4 +Created 1 atoms + Time spent = 0.000178099 secs +create_atoms 1 single 40.5 41.5 4 +Created 1 atoms + Time spent = 0.000168085 secs +create_atoms 1 single 10 22 4 +Created 1 atoms + Time spent = 0.000169992 secs +create_atoms 1 single 43.5 14.5 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 42 42 4 +Created 1 atoms + Time spent = 0.000184059 secs +create_atoms 1 single 4 26 4 +Created 1 atoms + Time spent = 0.000178814 secs +create_atoms 1 single 19 34 4 +Created 1 atoms + Time spent = 0.0001688 secs +create_atoms 1 single 33 9 4 +Created 1 atoms + Time spent = 0.000168085 secs +create_atoms 1 single 0.5 45.5 4 +Created 1 atoms + Time spent = 0.000169992 secs +create_atoms 1 single 30.5 32.5 4 +Created 1 atoms + Time spent = 0.000169992 secs +create_atoms 1 single 25.5 5.5 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 47.5 39.5 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 15 13 4 +Created 1 atoms + Time spent = 0.000174046 secs +create_atoms 1 single 21 21 4 +Created 1 atoms + Time spent = 0.000166893 secs +create_atoms 1 single 14 28 4 +Created 1 atoms + Time spent = 0.000170946 secs +create_atoms 1 single 9 34 4 +Created 1 atoms + Time spent = 0.000174999 secs +create_atoms 1 single 7 38 4 +Created 1 atoms + Time spent = 0.000167847 secs +create_atoms 1 single 11 35 4 +Created 1 atoms + Time spent = 0.000168085 secs +create_atoms 1 single 20.5 45.5 4 +Created 1 atoms + Time spent = 0.000177145 secs +create_atoms 1 single 30.5 31.5 4 +Created 1 atoms + Time spent = 0.000167131 secs +create_atoms 1 single 32.5 2.5 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 21.5 3.5 4 +Created 1 atoms + Time spent = 0.000166893 secs +create_atoms 1 single 23 12 4 +Created 1 atoms + Time spent = 0.000169039 secs +create_atoms 1 single 4.5 33.5 4 +Created 1 atoms + Time spent = 0.000178099 secs +create_atoms 1 single 46 43 4 +Created 1 atoms + Time spent = 0.000175953 secs +create_atoms 1 single 42.5 45.5 4 +Created 1 atoms + Time spent = 0.000169992 secs +create_atoms 1 single 4.5 10.5 4 +Created 1 atoms + Time spent = 0.000175953 secs +create_atoms 1 single 33.5 15.5 4 +Created 1 atoms + Time spent = 0.000158787 secs +create_atoms 1 single 24 5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 13 16 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 16.5 23.5 4 +Created 1 atoms + Time spent = 0.000160933 secs +create_atoms 1 single 45.5 28.5 4 +Created 1 atoms + Time spent = 0.000159025 secs +create_atoms 1 single 44.5 5.5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 27.5 46.5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 44.5 12.5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 12 41 4 +Created 1 atoms + Time spent = 0.000166893 secs +create_atoms 1 single 6 4 4 +Created 1 atoms + Time spent = 0.0001688 secs +create_atoms 1 single 31.5 10.5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 1 44 4 +Created 1 atoms + Time spent = 0.000157833 secs +create_atoms 1 single 31 4 4 +Created 1 atoms + Time spent = 0.000156879 secs +create_atoms 1 single 21 33 4 +Created 1 atoms + Time spent = 0.000172138 secs +create_atoms 1 single 3 33 4 +Created 1 atoms + Time spent = 0.000156879 secs +create_atoms 1 single 15 10 4 +Created 1 atoms + Time spent = 0.000156879 secs +create_atoms 1 single 28.5 22.5 4 +Created 1 atoms + Time spent = 0.000161886 secs +create_atoms 1 single 43 1 4 +Created 1 atoms + Time spent = 0.000166178 secs +create_atoms 1 single 3.5 0.5 4 +Created 1 atoms + Time spent = 0.000164986 secs +create_atoms 1 single 41 37 4 +Created 1 atoms + Time spent = 0.000160933 secs +create_atoms 1 single 18.5 43.5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 17 27 4 +Created 1 atoms + Time spent = 0.000159025 secs +create_atoms 1 single 3 5 4 +Created 1 atoms + Time spent = 0.000161171 secs +create_atoms 1 single 18.5 23.5 4 +Created 1 atoms + Time spent = 0.000164986 secs +create_atoms 1 single 31.5 14.5 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 41 31 4 +Created 1 atoms + Time spent = 0.000159979 secs +create_atoms 1 single 22 3 4 +Created 1 atoms + Time spent = 0.000158787 secs +create_atoms 1 single 14.5 40.5 4 +Created 1 atoms + Time spent = 0.000156879 secs +create_atoms 1 single 9 38 4 +Created 1 atoms + Time spent = 0.000155926 secs +create_atoms 1 single 36 42 4 +Created 1 atoms + Time spent = 0.000170231 secs +create_atoms 1 single 33 22 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 15.5 47.5 4 +Created 1 atoms + Time spent = 0.000162125 secs +create_atoms 1 single 3 0 4 +Created 1 atoms + Time spent = 0.000157118 secs +create_atoms 1 single 25.5 27.5 4 +Created 1 atoms + Time spent = 0.000159025 secs +create_atoms 1 single 2.5 28.5 4 +Created 1 atoms + Time spent = 0.000166178 secs +create_atoms 1 single 29.5 28.5 4 +Created 1 atoms + Time spent = 0.000160933 secs +create_atoms 1 single 44.5 18.5 4 +Created 1 atoms + Time spent = 0.000155926 secs +create_atoms 1 single 26 40 4 +Created 1 atoms + Time spent = 0.000157833 secs +create_atoms 1 single 41 27 4 +Created 1 atoms + Time spent = 0.000156879 secs +create_atoms 1 single 39.5 5.5 4 +Created 1 atoms + Time spent = 0.000167847 secs +create_atoms 1 single 3 38 4 +Created 1 atoms + Time spent = 0.000156164 secs +create_atoms 1 single 35 29 4 +Created 1 atoms + Time spent = 0.000154018 secs +create_atoms 1 single 11 19 4 +Created 1 atoms + Time spent = 0.000164032 secs +create_atoms 1 single 18 1 4 +Created 1 atoms + Time spent = 0.000154972 secs +create_atoms 1 single 39.5 40.5 4 +Created 1 atoms + Time spent = 0.000157118 secs +create_atoms 1 single 46 17 4 +Created 1 atoms + Time spent = 0.000164986 secs +create_atoms 1 single 1.5 23.5 4 +Created 1 atoms + Time spent = 0.00015521 secs +create_atoms 1 single 28.5 23.5 4 +Created 1 atoms + Time spent = 0.000153065 secs +create_atoms 1 single 10 28 4 +Created 1 atoms + Time spent = 0.000154018 secs +create_atoms 1 single 19 47 4 +Created 1 atoms + Time spent = 0.000159979 secs +create_atoms 1 single 10.5 16.5 4 +Created 1 atoms + Time spent = 0.000163078 secs +create_atoms 1 single 38 45 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 42.5 41.5 4 +Created 1 atoms + Time spent = 0.000159025 secs +create_atoms 1 single 47.5 42.5 4 +Created 1 atoms + Time spent = 0.000155926 secs +create_atoms 1 single 38 7 4 +Created 1 atoms + Time spent = 0.000154018 secs +create_atoms 1 single 10 44 4 +Created 1 atoms + Time spent = 0.000158072 secs +create_atoms 1 single 29.5 27.5 4 +Created 1 atoms + Time spent = 0.000159025 secs +create_atoms 1 single 45 30 4 +Created 1 atoms + Time spent = 0.000172138 secs +create_atoms 1 single 3 9 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 8.5 35.5 4 +Created 1 atoms + Time spent = 0.000148058 secs +create_atoms 1 single 24 44 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 47 4 4 +Created 1 atoms + Time spent = 0.000155926 secs +create_atoms 1 single 7.5 8.5 4 +Created 1 atoms + Time spent = 0.000146866 secs +create_atoms 1 single 32.5 41.5 4 +Created 1 atoms + Time spent = 0.000146151 secs +create_atoms 1 single 0.5 34.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 11 8 4 +Created 1 atoms + Time spent = 0.000146866 secs +create_atoms 1 single 2 40 4 +Created 1 atoms + Time spent = 0.000148058 secs +create_atoms 1 single 25 24 4 +Created 1 atoms + Time spent = 0.000154018 secs +create_atoms 1 single 47.5 6.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 39.5 28.5 4 +Created 1 atoms + Time spent = 0.000147104 secs +create_atoms 1 single 17 21 4 +Created 1 atoms + Time spent = 0.000150919 secs +create_atoms 1 single 32 43 4 +Created 1 atoms + Time spent = 0.000149012 secs +create_atoms 1 single 16.5 29.5 4 +Created 1 atoms + Time spent = 0.000154972 secs +create_atoms 1 single 34 34 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 11.5 3.5 4 +Created 1 atoms + Time spent = 0.000148058 secs +create_atoms 1 single 39 22 4 +Created 1 atoms + Time spent = 0.000148058 secs +create_atoms 1 single 24.5 36.5 4 +Created 1 atoms + Time spent = 0.000146151 secs +create_atoms 1 single 33 31 4 +Created 1 atoms + Time spent = 0.000149965 secs +create_atoms 1 single 35.5 35.5 4 +Created 1 atoms + Time spent = 0.000185966 secs +create_atoms 1 single 14.5 34.5 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 34 28 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 37 41 4 +Created 1 atoms + Time spent = 0.000146866 secs +create_atoms 1 single 33 46 4 +Created 1 atoms + Time spent = 0.000149965 secs +create_atoms 1 single 27.5 28.5 4 +Created 1 atoms + Time spent = 0.000149965 secs +create_atoms 1 single 40.5 22.5 4 +Created 1 atoms + Time spent = 0.000148773 secs +create_atoms 1 single 27.5 1.5 4 +Created 1 atoms + Time spent = 0.00014782 secs +create_atoms 1 single 12 2 4 +Created 1 atoms + Time spent = 0.000146151 secs +create_atoms 1 single 36 43 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 28.5 9.5 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 20.5 25.5 4 +Created 1 atoms + Time spent = 0.000154972 secs +create_atoms 1 single 3 3 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 38 33 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 3 20 4 +Created 1 atoms + Time spent = 0.000149012 secs +create_atoms 1 single 35 11 4 +Created 1 atoms + Time spent = 0.000154018 secs +create_atoms 1 single 5 25 4 +Created 1 atoms + Time spent = 0.00014782 secs +create_atoms 1 single 36.5 6.5 4 +Created 1 atoms + Time spent = 0.000152111 secs +create_atoms 1 single 19.5 24.5 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 27 41 4 +Created 1 atoms + Time spent = 0.000147104 secs +create_atoms 1 single 39.5 11.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 21.5 2.5 4 +Created 1 atoms + Time spent = 0.000152111 secs +create_atoms 1 single 46.5 15.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 13 24 4 +Created 1 atoms + Time spent = 0.000153065 secs +create_atoms 1 single 11 37 4 +Created 1 atoms + Time spent = 0.000146866 secs +create_atoms 1 single 11.5 31.5 4 +Created 1 atoms + Time spent = 0.000158787 secs +create_atoms 1 single 47 0 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 25.5 17.5 4 +Created 1 atoms + Time spent = 0.000144005 secs +create_atoms 1 single 32 11 4 +Created 1 atoms + Time spent = 0.000149012 secs +create_atoms 1 single 8 17 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 27.5 12.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 25 7 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 25.5 37.5 4 +Created 1 atoms + Time spent = 0.000161886 secs +create_atoms 1 single 12 15 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 1 7 4 +Created 1 atoms + Time spent = 0.000154972 secs +create_atoms 1 single 18.5 47.5 4 +Created 1 atoms + Time spent = 0.000162125 secs +create_atoms 1 single 5 38 4 +Created 1 atoms + Time spent = 0.000145197 secs +create_atoms 1 single 42 19 4 +Created 1 atoms + Time spent = 0.000147104 secs +create_atoms 1 single 30.5 7.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 42.5 7.5 4 +Created 1 atoms + Time spent = 0.000145912 secs +create_atoms 1 single 26.5 18.5 4 +Created 1 atoms + Time spent = 0.000150919 secs +create_atoms 1 single 18.5 1.5 4 +Created 1 atoms + Time spent = 0.000144958 secs +create_atoms 1 single 41.5 10.5 4 +Created 1 atoms + Time spent = 0.000151873 secs + +# define frozen substrate and mobile atoms + +region base block INF INF INF INF 0 1.8 +set region base type 2 + 18432 settings made for type +group base type 2 +18432 atoms in group base +group mobile type 1 +18616 atoms in group mobile + +# pair style + +pair_style eam/alloy +pair_coeff * * ptvoterlammps.eam Pt Pt + +neighbor 0.5 bin +neigh_modify every 1 delay 5 check yes + +fix 1 mobile nve +fix 2 mobile langevin ${Tequil} ${Tequil} 1.0 ${seed} zero yes +fix 2 mobile langevin 400.0 ${Tequil} 1.0 ${seed} zero yes +fix 2 mobile langevin 400.0 400.0 1.0 ${seed} zero yes +fix 2 mobile langevin 400.0 400.0 1.0 826626413 zero yes + +timestep 0.005 + +compute tmobile mobile temp + +thermo 100 +thermo_modify temp tmobile +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:487) + +# thermal equilibration + +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.07583 + ghost atom cutoff = 12 + binsize = 3.03792, bins = 62 62 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.359 | 3.359 | 3.36 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -206220.22 0 -206220.22 -52155.664 + 100 188.18127 -206044.43 0 -205591.63 -25068.83 + 200 274.34464 -205860.78 0 -205200.66 -40191.797 + 300 325.66286 -205750.01 0 -204966.4 -31510.222 + 400 352.48242 -205675.42 0 -204827.28 -35058.064 + 500 370.88571 -205619.66 0 -204727.25 -32735.022 + 600 388.62129 -205592.87 0 -204657.78 -33904.556 + 700 389.54874 -205579.73 0 -204642.4 -32769.852 + 800 395.56074 -205576.82 0 -204625.03 -33755.948 + 900 398.03458 -205564.48 0 -204606.74 -32777.103 + 1000 401.24089 -205562.85 0 -204597.4 -33785.341 +Loop time of 4.22555 on 16 procs for 1000 steps with 37048 atoms + +Performance: 102.235 ns/day, 0.235 hours/ns, 236.655 timesteps/s +98.5% CPU use with 16 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.2988 | 3.3283 | 3.3788 | 1.5 | 78.77 +Neigh | 0.22391 | 0.23756 | 0.28119 | 2.7 | 5.62 +Comm | 0.31341 | 0.3888 | 0.49372 | 8.0 | 9.20 +Output | 0.00041842 | 0.00042947 | 0.00048399 | 0.0 | 0.01 +Modify | 0.17166 | 0.2512 | 0.35242 | 9.5 | 5.94 +Other | | 0.0193 | | | 0.46 + +Nlocal: 2315.5 ave 2332 max 2297 min +Histogram: 2 0 0 3 4 0 2 1 2 2 +Nghost: 3186.31 ave 3205 max 3170 min +Histogram: 2 1 3 0 2 3 2 1 0 2 +Neighs: 55590.9 ave 56174 max 55103 min +Histogram: 2 2 1 1 4 1 3 0 0 2 + +Total # of neighbors = 889454 +Ave neighs/atom = 24.0082 +Neighbor list builds = 105 +Dangerous builds = 0 +reset_timestep 0 + +# pin base so will not move during quenches + +fix freeze base setforce 0.0 0.0 0.0 + +# event detection + +compute event all event/displace ${cutevent} +compute event all event/displace 1.1 + +# hyper/local + +fix HL mobile hyper/local ${cutbond} ${qfactor} ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost} +fix HL mobile hyper/local 3.2 ${qfactor} ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost} +fix HL mobile hyper/local 3.2 0.3 ${Vmax} ${Tequil} ${Dcut} ${alpha} ${boost} +fix HL mobile hyper/local 3.2 0.3 0.4 ${Tequil} ${Dcut} ${alpha} ${boost} +fix HL mobile hyper/local 3.2 0.3 0.4 400.0 ${Dcut} ${alpha} ${boost} +fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 ${alpha} ${boost} +fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 200.0 ${boost} +fix HL mobile hyper/local 3.2 0.3 0.4 400.0 10.0 200.0 4000.0 + +# thermo output + +thermo_style custom step temp pe f_HL f_HL[*] +WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:705) + +thermo_modify lost ignore +thermo_modify temp tmobile +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:487) + +thermo ${nevent} +thermo 100 + +# dump + +region substrate block INF INF INF INF 1.8 3.8 +region adatoms block INF INF INF INF 3.8 INF +variable acolor atom rmask(base)+2*rmask(substrate)+3*rmask(adatoms) + +dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 zoom ${zoom} adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01 +dump 1 all image 10000000 local.*.jpg v_acolor type size 1024 1024 zoom 1.8 adiam 2.5 view 0.0 0.0 up 0 1 0 axes yes 0.9 0.01 +dump_modify 1 pad 6 amap 1 3 sa 1 3 blue red green + +# test of histogramming and dump output of bias coeffs + +#fix histo all ave/histo 10 100 1000 0.9 1.1 100 f_HL # mode vector kind local file tmp.histo +#dump 2 all local 1000 tmp.local f_HL + +# run + +hyper ${steps} ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1 +hyper 1500 ${nevent} HL event min ${tol} ${tol} 1000 1000 dump 1 +hyper 1500 100 HL event min ${tol} ${tol} 1000 1000 dump 1 +hyper 1500 100 HL event min 1.0e-15 ${tol} 1000 1000 dump 1 +hyper 1500 100 HL event min 1.0e-15 1.0e-15 1000 1000 dump 1 +WARNING: Resetting reneighboring criteria during hyper (../hyper.cpp:133) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 6.07583 + ghost atom cutoff = 12 + binsize = 3.03792, bins = 62 62 7 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix hyper/local, occasional + attributes: full, newton on, cut 10 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) fix hyper/local, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 6.941 | 6.942 | 6.942 Mbytes +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 0 401.24089 -205562.85 0 0 0 1 0 0 0 0 0 0 0 1e+20 0 0 0 0 0 0 0 0 0 0 + 77 401.24089 -206534.96 0 0 0 1 0 0 0 0 0 0 0 1e+20 0 0 0 0 0 0 1540 0 0 0 +Loop time of 0.51152 on 16 procs for 77 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 0 401.24089 -205562.85 24.755808 79 0.18753621 0 6.0138739 705.15041 3.5350432 0 0 0 0 1e+20 0 0 0 0 0 0 0 0 0 0 + 100 400.6027 -205547.79 21.854739 92 0.43709939 0.99825259 6.0138739 705.15041 4.230764 92.74 0.03245633 0.0067931852 0.99890138 0.98969319 1.0024404 0 0 0 0 0 2000 0 0 0 +Loop time of 0.453073 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 100 400.6027 -205547.79 21.854739 92 0.43709939 0.99825259 6.0138739 705.15041 4.230764 92.74 0.03245633 0.0067931852 0.99890138 0.98969319 1.0024404 0 0 0 0 0 2000 0 0 0 + 177 400.6027 -206534.96 21.854739 92 0.43709939 0.99825259 6.0138739 705.15041 4.230764 52.39548 0.03245633 0.0067931852 0.56435106 0.98969319 1.0024404 0 0 0 0 0 3540 0 0 0 +Loop time of 0.494676 on 16 procs for 77 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 100 400.6027 -205547.79 21.854339 92 0.43709939 0.99825259 6.0138739 705.15041 4.230764 92.74 0.03245633 0.0067931852 0.99890138 0.98969319 1.0024404 0 0 0 0 0 2000 0 0 0 + 200 400.46944 -205544.7 23.349576 97 0.33740983 0.99723256 6.0138739 705.15041 4.230764 92.525 0.040097271 0.0058362605 0.99830632 0.98259113 1.0048777 0 0 0 0 0 4000 0 0 0 +Loop time of 0.450918 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 200 400.46944 -205544.7 23.349576 97 0.33740983 0.99723256 6.0138739 705.15041 4.230764 92.525 0.040097271 0.0058362605 0.99830632 0.98259113 1.0048777 0 0 0 0 0 4000 0 0 0 + 273 400.46944 -206534.96 23.349576 97 0.33740983 0.99723256 6.0138739 705.15041 4.230764 67.783883 0.040097271 0.0058362605 0.73135994 0.98259113 1.0048777 0 0 0 0 0 5460 0 0 0 +Loop time of 0.488918 on 16 procs for 73 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 200 400.46944 -205544.7 23.349184 97 0.33740983 0.99723256 6.0138739 705.15041 4.230764 92.525 0.040097271 0.0058362605 0.99830632 0.98259113 1.0048777 0 0 0 0 0 4000 0 0 0 + 300 396.89568 -205540.38 19.394419 94 0.35022551 0.99673595 6.0138739 705.15041 4.230764 93.376667 0.047799236 0.0063898904 0.99785232 0.97756247 1.0073497 0 0 0 0 0 6000 0 0 0 +Loop time of 0.45579 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 300 396.89568 -205540.38 19.394419 94 0.35022551 0.99673595 6.0138739 705.15041 4.230764 93.376667 0.047799236 0.0063898904 0.99785232 0.97756247 1.0073497 0 0 0 0 0 6000 0 0 0 + 373 396.89568 -206534.96 19.394419 94 0.35022551 0.99673595 6.0138739 705.15041 4.230764 75.101877 0.047799236 0.0063898904 0.80256219 0.97756247 1.0073497 0 0 0 0 0 7460 0 0 0 +Loop time of 0.49254 on 16 procs for 73 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 300 396.89568 -205540.38 19.394206 94 0.35022551 0.99673595 6.0138739 705.15041 4.230764 93.376667 0.047799236 0.0063898904 0.99785232 0.97756247 1.0073497 0 0 0 0 0 6000 0 0 0 + 400 399.1218 -205541.68 18.990804 94 0.3505205 0.99638391 6.0138739 705.15041 4.230764 93.3775 0.055982437 0.0068271264 0.99752641 0.97044214 1.0098482 0 0 0 0 0 8000 0 0 0 +Loop time of 0.452751 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 400 399.1218 -205541.68 18.990804 94 0.3505205 0.99638391 6.0138739 705.15041 4.230764 93.3775 0.055982437 0.0068271264 0.99752641 0.97044214 1.0098482 0 0 0 0 0 8000 0 0 0 + 475 399.1218 -206534.96 18.990804 94 0.3505205 0.99638391 6.0138739 705.15041 4.230764 78.633684 0.055982437 0.0068271264 0.84002224 0.97044214 1.0098482 0 0 0 0 0 9500 0 0 0 +Loop time of 0.4963 on 16 procs for 75 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 400 399.1218 -205541.68 18.990689 94 0.3505205 0.99638391 6.0138739 705.15041 4.230764 93.3775 0.055982437 0.0068271264 0.99752641 0.97044214 1.0098482 0 0 0 0 0 8000 0 0 0 + 500 399.61667 -205539.79 19.794362 99 0.33740217 0.99633812 6.0138739 705.15041 4.230764 93.222 0.063096694 0.0076591363 0.99729174 0.96745199 1.0123163 0 0 0 0 0 10000 0 0 0 +Loop time of 0.45226 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 500 399.61667 -205539.79 19.794362 99 0.33740217 0.99633812 6.0138739 705.15041 4.230764 93.222 0.063096694 0.0076591363 0.99729174 0.96745199 1.0123163 0 0 0 0 0 10000 0 0 0 + 577 399.61667 -206534.96 19.794362 99 0.33740217 0.99633812 6.0138739 705.15041 4.230764 80.781629 0.063096694 0.0076591363 0.86420428 0.96745199 1.0123163 0 0 0 0 0 11540 0 0 0 +Loop time of 0.518479 on 16 procs for 77 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 500 399.61667 -205539.79 19.79402 99 0.33740217 0.99633812 6.0138739 705.15041 4.230764 93.222 0.063096694 0.0076591363 0.99729174 0.96745199 1.0123163 0 0 0 0 0 10000 0 0 0 + 600 397.41676 -205529.51 20.336863 99 0.35185916 0.99625666 6.0138739 705.15041 4.230764 93.621667 0.066686842 0.0091859078 0.99712746 0.96713729 1.0148143 0 0 0 0 0 12000 0 0 0 +Loop time of 0.452059 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 600 397.41676 -205529.51 20.336863 99 0.35185916 0.99625666 6.0138739 705.15041 4.230764 93.621667 0.066686842 0.0091859078 0.99712746 0.96713729 1.0148143 0 0 0 0 0 12000 0 0 0 + 677 397.41676 -206534.96 20.336863 99 0.35185916 0.99625666 6.0138739 705.15041 4.230764 82.973412 0.066686842 0.0091859078 0.8837171 0.96713729 1.0148143 0 0 0 0 0 13540 0 0 0 +Loop time of 0.5171 on 16 procs for 77 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 600 397.41676 -205529.51 20.336526 99 0.35185916 0.99625666 6.0138739 705.15041 4.230764 93.621667 0.066686842 0.0091859078 0.99712746 0.96713729 1.0148143 0 0 0 0 0 12000 0 0 0 + 700 403.33442 -205550.89 18.955866 93 0.42542334 0.99592297 6.0138739 705.15041 4.230764 94.135714 0.068078003 0.0094089081 0.99698101 0.9641519 1.0173022 0 0 0 0 0 14000 0 0 0 +Loop time of 0.450117 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 700 403.33442 -205550.89 18.955866 93 0.42542334 0.99592297 6.0138739 705.15041 4.230764 94.135714 0.068078003 0.0094089081 0.99698101 0.9641519 1.0173022 0 0 0 0 0 14000 0 0 0 + 783 403.33442 -206534.96 18.955866 93 0.42542334 0.99592297 6.0138739 705.15041 4.230764 84.157088 0.068078003 0.0094089081 0.89129847 0.9641519 1.0173022 0 0 0 0 0 15660 0 0 0 +Loop time of 0.541959 on 16 procs for 83 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 700 403.33442 -205550.89 18.955589 93 0.42542334 0.99592297 6.0138739 705.15041 4.230764 94.135714 0.068078003 0.0094089081 0.99698101 0.9641519 1.0173022 0 0 0 0 0 14000 0 0 0 + 800 397.5897 -205530.58 19.298375 97 0.42432974 0.99573055 6.0138739 705.15041 4.2562861 94.69125 0.070492258 0.0098477948 0.99683461 0.96199283 1.0198015 0 0 0 0 0 16000 0 0 0 +Loop time of 0.454322 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 800 397.5897 -205530.58 19.298375 97 0.42432974 0.99573055 6.0138739 705.15041 4.2562861 94.69125 0.070492258 0.0098477948 0.99683461 0.96199283 1.0198015 0 0 0 0 0 16000 0 0 0 + 877 397.5897 -206534.96 19.298375 97 0.42432974 0.99573055 6.0138739 705.15041 4.2562861 86.377423 0.070492258 0.0098477948 0.90931322 0.96199283 1.0198015 0 0 0 0 0 17540 0 0 0 +Loop time of 0.502899 on 16 procs for 77 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 800 397.5897 -205530.58 19.29822 97 0.42432974 0.99573055 6.0138739 705.15041 4.2562861 94.69125 0.070492258 0.0098477948 0.99683461 0.96199283 1.0198015 0 0 0 0 0 16000 0 0 0 + 900 402.04231 -205545.55 18.434766 91 0.34927854 0.99563819 6.0138739 705.15041 4.2562861 94.956667 0.072594517 0.0091737752 0.99670822 0.95723843 1.0223007 0 0 0 0 0 18000 0 0 0 +Loop time of 0.451618 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 900 402.04231 -205545.55 18.434766 91 0.34927854 0.99563819 6.0138739 705.15041 4.2562861 94.956667 0.072594517 0.0091737752 0.99670822 0.95723843 1.0223007 0 0 0 0 0 18000 0 0 0 + 976 402.04231 -206534.96 18.434766 91 0.34927854 0.99563819 6.0138739 705.15041 4.2562861 87.5625 0.072594517 0.0091737752 0.91909569 0.95723843 1.0223007 0 0 0 0 0 19520 0 0 0 +Loop time of 0.493429 on 16 procs for 76 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 900 402.04231 -205545.55 18.434576 91 0.34927854 0.99563819 6.0138739 705.15041 4.2562861 94.956667 0.072594517 0.0091737752 0.99670822 0.95723843 1.0223007 0 0 0 0 0 18000 0 0 0 + 1000 403.13682 -205538.62 20.371378 100 0.36854432 0.99555559 6.0138739 705.15041 4.2562861 94.973 0.075589904 0.0088025018 0.99659567 0.95567008 1.0247999 0 0 0 0 0 20000 0 0 0 +Loop time of 0.452482 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1000 403.13682 -205538.62 20.371378 100 0.36854432 0.99555559 6.0138739 705.15041 4.2562861 94.973 0.075589904 0.0088025018 0.99659567 0.95567008 1.0247999 0 0 0 0 0 20000 0 0 0 + 1081 403.13682 -206534.96 20.371378 100 0.36854432 0.99555559 6.0138739 705.15041 4.2562861 87.856614 0.075589904 0.0088025018 0.92192014 0.95567008 1.0247999 0 0 0 0 0 21620 0 0 0 +Loop time of 0.521678 on 16 procs for 81 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1000 403.13682 -205538.62 20.371013 100 0.36854432 0.99555559 6.0138739 705.15041 4.2562861 94.973 0.075589904 0.0088025018 0.99659567 0.95567008 1.0247999 0 0 0 0 0 20000 0 0 0 + 1100 401.64961 -205531.15 16.838899 93 0.37998317 0.99541314 6.0138739 705.15041 4.2562861 95.323636 0.077697032 0.0088979171 0.99649521 0.95206312 1.0272987 0 0 0 0 0 22000 0 0 0 +Loop time of 0.452415 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1100 401.64961 -205531.15 16.838899 93 0.37998317 0.99541314 6.0138739 705.15041 4.2562861 95.323636 0.077697032 0.0088979171 0.99649521 0.95206312 1.0272987 0 0 0 0 0 22000 0 0 0 + 1179 401.64961 -206534.96 16.838899 93 0.37998317 0.99541314 6.0138739 705.15041 4.2562861 88.936387 0.077697032 0.0088979171 0.92972412 0.95206312 1.0272987 0 0 0 0 0 23580 0 0 0 +Loop time of 0.50337 on 16 procs for 79 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1100 401.64961 -205531.15 16.838708 93 0.37998317 0.99541314 6.0138739 705.15041 4.2562861 95.323636 0.077697032 0.0088979171 0.99649521 0.95206312 1.0272987 0 0 0 0 0 22000 0 0 0 + 1200 400.40964 -205539.37 19.135216 99 0.67128843 0.99558682 6.0138739 705.15041 4.6317552 95.505 0.080458266 0.0085684868 0.99641317 0.95050066 1.029798 0 0 0 0 0 24000 0 0 0 +Loop time of 0.44891 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1200 400.40964 -205539.37 19.135216 99 0.67128843 0.99558682 6.0138739 705.15041 4.6317552 95.505 0.080458266 0.0085684868 0.99641317 0.95050066 1.029798 0 0 0 0 0 24000 0 0 0 + 1276 400.40964 -206534.97 19.135216 99 0.67128843 0.99558682 6.0138739 705.15041 4.6317552 89.816614 0.080458266 0.0085684868 0.93706567 0.95050066 1.029798 0 0 0 0 0 25520 0 0 0 +Loop time of 0.508519 on 16 procs for 76 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1200 400.40964 -205539.37 19.448471 100 0.41040038 0.99558682 6.0138739 705.141 4.6317552 95.505 0.080458266 0.0085684868 0.99641317 0.95050066 1.029798 2.2953088 0 0 0 0 24000 1 2 6 + 1300 401.71843 -205549 19.86411 94 0.31328255 0.99531422 6.0138739 705.141 4.6317552 95.636923 0.080786307 0.0080834567 0.99634504 0.95016182 1.0314365 2.2953088 0 0 0 0 26000 1 2 6 +Loop time of 0.453256 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1300 401.71843 -205549 19.86411 94 0.31328255 0.99531422 6.0138739 705.141 4.6317552 95.636923 0.080786307 0.0080834567 0.99634504 0.95016182 1.0314365 2.2953088 0 0 0 0 26000 1 2 6 + 1376 401.71843 -206534.97 19.86411 94 0.31328255 0.99531422 6.0138739 705.141 4.6317552 90.354651 0.080786307 0.0080834567 0.94131435 0.95016182 1.0314365 2.2953088 0 0 0 0 27520 1 2 6 +Loop time of 0.502886 on 16 procs for 76 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1300 401.71843 -205549 19.863856 94 0.31328255 0.99531422 6.0138739 705.141 4.6317552 95.636923 0.080786307 0.0080834567 0.99634504 0.95016182 1.0314365 2.2953088 0 0 0 0 26000 1 2 6 + 1400 397.79762 -205534.95 19.064761 90 0.33635396 0.99488167 6.0138739 705.141 4.6317552 95.55 0.080145025 0.0081557898 0.99625782 0.94925079 1.0339117 2.2953088 0 0 0 0 28000 1 2 6 +Loop time of 0.453094 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1400 397.79762 -205534.95 19.064761 90 0.33635396 0.99488167 6.0138739 705.141 4.6317552 95.55 0.080145025 0.0081557898 0.99625782 0.94925079 1.0339117 2.2953088 0 0 0 0 28000 1 2 6 + 1477 397.79762 -206534.97 19.064761 90 0.33635396 0.99488167 6.0138739 705.141 4.6317552 90.56872 0.080145025 0.0081557898 0.94432021 0.94925079 1.0339117 2.2953088 0 0 0 0 29540 1 2 6 +Loop time of 0.515217 on 16 procs for 77 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1400 397.79762 -205534.95 19.064345 90 0.33635396 0.99488167 6.0138739 705.141 4.6317552 95.55 0.080145025 0.0081557898 0.99625782 0.94925079 1.0339117 2.2953088 0 0 0 0 28000 1 2 6 + 1500 400.56079 -205539.86 18.860257 93 0.35488977 0.99467946 6.0138739 705.141 4.6317552 95.578667 0.080575861 0.0083561185 0.99615829 0.94636637 1.0355154 2.2953088 0 0 0 0 30000 1 2 6 +Loop time of 0.450111 on 16 procs for 100 steps with 37048 atoms + +Step Temp PotEng f_HL f_HL[1] f_HL[2] f_HL[3] f_HL[4] f_HL[5] f_HL[6] f_HL[7] f_HL[8] f_HL[9] f_HL[10] f_HL[11] f_HL[12] f_HL[13] f_HL[14] f_HL[15] f_HL[16] f_HL[17] f_HL[18] f_HL[19] f_HL[20] f_HL[21] + 1500 400.56079 -205539.86 18.860257 93 0.35488977 0.99467946 6.0138739 705.141 4.6317552 95.578667 0.080575861 0.0083561185 0.99615829 0.94636637 1.0355154 2.2953088 0 0 0 0 30000 1 2 6 + 1584 400.56079 -206534.97 18.860257 93 0.35488977 0.99467946 6.0138739 705.141 4.6317552 90.510101 0.080575861 0.0083561185 0.94333171 0.94636637 1.0355154 2.2953088 0 0 0 0 31680 1 2 6 +Loop time of 0.566455 on 16 procs for 84 steps with 37048 atoms + +Final hyper stats ... + +Cummulative quantities for fix hyper: + hyper time = 30000 + time boost factor = 4000 + event timesteps = 1 + # of atoms in events = 2 +Quantities for this hyper run: + event timesteps = 1 + # of atoms in events = 2 + max length of any bond = 4.63176 + max drift distance of any atom = 2.29531 + fraction of biased bonds with zero bias = 0.0805759 + fraction of biased bonds with negative strain = 0.00835612 +Current quantities: + ave bonds/atom = 6.01387 +Cummulative quantities specific to fix hyper/local: + # of new bonds formed = 6 + max bonds/atom = 13 +Quantities for this hyper run specific to fix hyper/local: + ave biased bonds/step = 95.5787 + ave bias coeff of all bonds = 0.996158 + min bias coeff of any bond = 0.946366 + max bias coeff of any bond = 1.03552 + max dist from my subbox of any non-maxstrain bond ghost atom = 0 + max dist from my box of any bond ghost atom = 0 + count of bond ghost neighbors not found on reneighbor steps = 0 + bias overlaps = 0 + CPU time for bond builds = 0.0147002 +Current quantities specific to fix hyper/local: + neighbor bonds/bond = 705.141 + ave boost coeff for all bonds = 0.994679 + +Loop time of 14.9193 on 16 procs for 1500 steps with 37048 atoms + +Performance: 43.434 ns/day, 0.553 hours/ns, 100.541 timesteps/s +128.3% CPU use with 16 MPI tasks x no OpenMP threads + +Hyper stats: + Dynamics time (%) = 6.78318 (45.4657) + Quench time (%) = 7.66443 (51.3725) + Other time (%) = 0.189889 (1.27277) + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.726 | 11.881 | 12.051 | 2.6 | 79.64 +Neigh | 0.49995 | 0.52243 | 0.54427 | 1.9 | 3.50 +Comm | 0.34477 | 0.51495 | 0.62326 | 10.4 | 3.45 +Output | 0.0017493 | 0.0017652 | 0.0018535 | 0.1 | 0.01 +Modify | 1.7669 | 1.8088 | 1.8523 | 1.7 | 12.12 +Other | | 0.1899 | | | 1.27 + +Nlocal: 2315.5 ave 2353 max 2275 min +Histogram: 1 1 1 3 0 2 5 2 0 1 +Nghost: 3187.62 ave 3228 max 3148 min +Histogram: 1 0 2 4 2 2 1 3 0 1 +Neighs: 54002.8 ave 54567 max 53263 min +Histogram: 1 0 2 1 3 2 2 1 1 3 +FullNghs: 542996 ave 554820 max 527895 min +Histogram: 1 0 0 4 1 3 3 2 0 2 + +Total # of neighbors = 8687932 +Ave neighs/atom = 234.505 +Neighbor list builds = 166 +Dangerous builds = 0 +Total wall time: 0:00:19 diff --git a/examples/hyper/ptvoterlammps.eam b/examples/hyper/ptvoterlammps.eam new file mode 100644 index 0000000000..780f76c0da --- /dev/null +++ b/examples/hyper/ptvoterlammps.eam @@ -0,0 +1,1206 @@ +lammps potential file (eam alloy format) generated from Voter potential +lammps potential file (eam alloy format) generated from Voter potential +lammps potential file (eam alloy format) generated from Voter potential + 1 Pt + 2000 4.4701153864882436E-04 2000 2.7893112429014507E-03 5.5758331745599996E+00 + 78 195.100000 3.9200000000E+00 fcc + 0.0000000000000000E+00 -9.3726378237257005E-02 -1.4662876812087147E-01 -1.9347407019915208E-01 -2.3636618878752805E-01 + -2.7644724047124986E-01 -3.1435333587770409E-01 -3.5048959265680196E-01 -3.8513634620198733E-01 -4.1849879865649925E-01 + 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a/examples/indent/log.5Oct16.indent.g++.1 +++ b/examples/indent/log.27Nov18.indent.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d indenter simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000351191 secs mass 1 1.0 mass 2 1.0 @@ -57,7 +59,7 @@ fix 5 all enforce2d thermo 1000 thermo_modify temp new -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 250 dump.indent @@ -69,13 +71,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 30000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 17 15 1 -Memory usage per processor = 2.4697 Mbytes + binsize = 1.4, bins = 17 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333 1000 0.11974254 -3.0876892 0 -2.9853378 -0.037059247 440.78771 @@ -108,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press Volume 28000 0.1183178 -3.0017823 0 -2.9006488 1.3477212 474.08453 29000 0.118332 -2.9855957 0 -2.88445 1.4002777 478.49231 30000 0.11691453 -2.9721091 0 -2.872175 1.6266108 479.0394 -Loop time of 2.36919 on 1 procs for 30000 steps with 420 atoms +Loop time of 2.58797 on 1 procs for 30000 steps with 420 atoms -Performance: 3282134.431 tau/day, 12662.556 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3004676.853 tau/day, 11592.117 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.7824 | 1.7824 | 1.7824 | 0.0 | 75.23 -Neigh | 0.073035 | 0.073035 | 0.073035 | 0.0 | 3.08 -Comm | 0.023414 | 0.023414 | 0.023414 | 0.0 | 0.99 -Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.01 -Modify | 0.42744 | 0.42744 | 0.42744 | 0.0 | 18.04 -Other | | 0.06268 | | | 2.65 +Pair | 1.7803 | 1.7803 | 1.7803 | 0.0 | 68.79 +Neigh | 0.074505 | 0.074505 | 0.074505 | 0.0 | 2.88 +Comm | 0.038266 | 0.038266 | 0.038266 | 0.0 | 1.48 +Output | 0.00033927 | 0.00033927 | 0.00033927 | 0.0 | 0.01 +Modify | 0.61562 | 0.61562 | 0.61562 | 0.0 | 23.79 +Other | | 0.07897 | | | 3.05 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -139,7 +146,7 @@ Dangerous builds = 0 unfix 4 run 30000 -Memory usage per processor = 2.46978 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30000 0.11691453 -2.9721091 0 -2.872175 1.6267079 479.0108 31000 0.10925212 -3.0270482 0 -2.9336637 -0.33277278 488.93429 @@ -172,20 +179,20 @@ Step Temp E_pair E_mol TotEng Press Volume 58000 0.10703451 -3.04105 0 -2.949561 -0.2673909 482.03847 59000 0.11041464 -3.0439806 0 -2.9496023 -0.17616699 481.33957 60000 0.12014097 -3.05226 0 -2.949568 -0.21176633 481.15213 -Loop time of 2.11008 on 1 procs for 30000 steps with 420 atoms +Loop time of 2.20628 on 1 procs for 30000 steps with 420 atoms -Performance: 3685166.663 tau/day, 14217.464 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3524485.426 tau/day, 13597.552 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.7612 | 1.7612 | 1.7612 | 0.0 | 83.46 -Neigh | 0.072587 | 0.072587 | 0.072587 | 0.0 | 3.44 -Comm | 0.023835 | 0.023835 | 0.023835 | 0.0 | 1.13 -Output | 0.00023365 | 0.00023365 | 0.00023365 | 0.0 | 0.01 -Modify | 0.19556 | 0.19556 | 0.19556 | 0.0 | 9.27 -Other | | 0.05669 | | | 2.69 +Pair | 1.7599 | 1.7599 | 1.7599 | 0.0 | 79.77 +Neigh | 0.074152 | 0.074152 | 0.074152 | 0.0 | 3.36 +Comm | 0.037216 | 0.037216 | 0.037216 | 0.0 | 1.69 +Output | 0.00033259 | 0.00033259 | 0.00033259 | 0.0 | 0.02 +Modify | 0.25688 | 0.25688 | 0.25688 | 0.0 | 11.64 +Other | | 0.07779 | | | 3.53 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/indent/log.5Oct16.indent.g++.4 b/examples/indent/log.27Nov18.indent.g++.4 similarity index 82% rename from examples/indent/log.5Oct16.indent.g++.4 rename to examples/indent/log.27Nov18.indent.g++.4 index 3d96cf6185..1f0556475b 100644 --- a/examples/indent/log.5Oct16.indent.g++.4 +++ b/examples/indent/log.27Nov18.indent.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d indenter simulation dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.00031352 secs mass 1 1.0 mass 2 1.0 @@ -57,7 +59,7 @@ fix 5 all enforce2d thermo 1000 thermo_modify temp new -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 250 dump.indent @@ -69,13 +71,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 30000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 17 15 1 -Memory usage per processor = 2.47636 Mbytes + binsize = 1.4, bins = 17 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.047 | 3.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333 1000 0.11573595 -3.0964873 0 -2.9975606 -0.20448672 441.83732 @@ -108,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press Volume 28000 0.11718062 -2.993818 0 -2.8936565 1.143781 478.94786 29000 0.10922042 -2.9873887 0 -2.8940313 1.6184815 473.13968 30000 0.11475456 -2.9749758 0 -2.876888 1.8682946 472.49357 -Loop time of 1.05783 on 4 procs for 30000 steps with 420 atoms +Loop time of 1.15893 on 4 procs for 30000 steps with 420 atoms -Performance: 7350928.409 tau/day, 28360.063 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 6709635.246 tau/day, 25885.938 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.40826 | 0.46628 | 0.5198 | 6.6 | 44.08 -Neigh | 0.017807 | 0.019817 | 0.021682 | 1.1 | 1.87 -Comm | 0.22255 | 0.26884 | 0.31893 | 8.2 | 25.41 -Output | 0.0005722 | 0.00060749 | 0.00070214 | 0.2 | 0.06 -Modify | 0.18744 | 0.19364 | 0.20341 | 1.5 | 18.31 -Other | | 0.1086 | | | 10.27 +Pair | 0.39848 | 0.4603 | 0.53798 | 8.6 | 39.72 +Neigh | 0.018286 | 0.020391 | 0.022765 | 1.4 | 1.76 +Comm | 0.18903 | 0.27493 | 0.34712 | 13.2 | 23.72 +Output | 0.00055623 | 0.00077116 | 0.0014129 | 0.0 | 0.07 +Modify | 0.28166 | 0.29302 | 0.30362 | 1.5 | 25.28 +Other | | 0.1095 | | | 9.45 Nlocal: 105 ave 115 max 90 min Histogram: 1 0 0 0 1 0 0 0 0 2 @@ -139,7 +146,7 @@ Dangerous builds = 0 unfix 4 run 30000 -Memory usage per processor = 2.47641 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.047 | 3.048 | 3.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30000 0.11475456 -2.9749758 0 -2.876888 1.8675667 472.67773 31000 0.11574891 -3.0442299 0 -2.9452921 -0.72600606 489.16618 @@ -172,20 +179,20 @@ Step Temp E_pair E_mol TotEng Press Volume 58000 0.11858604 -3.0812503 0 -2.9798874 -0.17502776 463.2168 59000 0.11344551 -3.0768536 0 -2.9798847 -0.32382437 465.29204 60000 0.11637998 -3.0793607 0 -2.9798836 -0.45942931 466.04868 -Loop time of 0.87344 on 4 procs for 30000 steps with 420 atoms +Loop time of 0.903556 on 4 procs for 30000 steps with 420 atoms -Performance: 8902734.020 tau/day, 34346.968 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 8605992.311 tau/day, 33202.131 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.38824 | 0.45201 | 0.49914 | 6.9 | 51.75 -Neigh | 0.0175 | 0.020234 | 0.022472 | 1.5 | 2.32 -Comm | 0.21322 | 0.26426 | 0.33067 | 10.0 | 30.25 -Output | 0.00049305 | 0.00051773 | 0.00058699 | 0.2 | 0.06 -Modify | 0.04793 | 0.053404 | 0.05745 | 1.8 | 6.11 -Other | | 0.08302 | | | 9.50 +Pair | 0.3899 | 0.45567 | 0.53041 | 8.7 | 50.43 +Neigh | 0.017401 | 0.021048 | 0.024747 | 2.1 | 2.33 +Comm | 0.17915 | 0.26432 | 0.34168 | 13.8 | 29.25 +Output | 0.00051928 | 0.00093985 | 0.0021935 | 0.0 | 0.10 +Modify | 0.067609 | 0.075224 | 0.08228 | 2.4 | 8.33 +Other | | 0.08635 | | | 9.56 Nlocal: 105 ave 112 max 98 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -198,4 +205,4 @@ Total # of neighbors = 3569 Ave neighs/atom = 8.49762 Neighbor list builds = 634 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/indent/log.5Oct16.indent.min.g++.1 b/examples/indent/log.27Nov18.indent.min.g++.1 similarity index 77% rename from examples/indent/log.5Oct16.indent.min.g++.1 rename to examples/indent/log.27Nov18.indent.min.g++.1 index e988892da1..ce5b0b1b61 100644 --- a/examples/indent/log.5Oct16.indent.min.g++.1 +++ b/examples/indent/log.27Nov18.indent.min.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d indenter simulation with minimization instead of dynamics dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000453234 secs mass * 1.0 @@ -57,24 +59,29 @@ thermo 10 #dump_modify 3 pad 4 minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 17 15 1 -Memory usage per processor = 3.5947 Mbytes + binsize = 1.4, bins = 17 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333 10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558 20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033 30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033 35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082 -Loop time of 0.00874686 on 1 procs for 35 steps with 420 atoms +Loop time of 0.00889349 on 1 procs for 35 steps with 420 atoms -102.9% CPU use with 1 MPI tasks x no OpenMP threads +98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -88,12 +95,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0074182 | 0.0074182 | 0.0074182 | 0.0 | 84.81 -Neigh | 0.00042582 | 0.00042582 | 0.00042582 | 0.0 | 4.87 -Comm | 7.2718e-05 | 7.2718e-05 | 7.2718e-05 | 0.0 | 0.83 -Output | 2.2173e-05 | 2.2173e-05 | 2.2173e-05 | 0.0 | 0.25 -Modify | 0.00011134 | 0.00011134 | 0.00011134 | 0.0 | 1.27 -Other | | 0.0006967 | | | 7.96 +Pair | 0.0073352 | 0.0073352 | 0.0073352 | 0.0 | 82.48 +Neigh | 0.00039649 | 0.00039649 | 0.00039649 | 0.0 | 4.46 +Comm | 9.8944e-05 | 9.8944e-05 | 9.8944e-05 | 0.0 | 1.11 +Output | 2.718e-05 | 2.718e-05 | 2.718e-05 | 0.0 | 0.31 +Modify | 0.00016856 | 0.00016856 | 0.00016856 | 0.0 | 1.90 +Other | | 0.0008671 | | | 9.75 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -114,8 +121,8 @@ fix 4 all indent $k sphere 10 13.0 0 6.0 fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.5947 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574 40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534 @@ -127,9 +134,9 @@ Step Temp E_pair E_mol TotEng Press Volume 100 0 -3.1812307 0 -3.1805381 -0.15305004 434.96379 110 0 -3.1812588 0 -3.1805938 -0.12504604 432.50683 111 0 -3.1812728 0 -3.1805961 -0.12407116 432.50683 -Loop time of 0.02054 on 1 procs for 76 steps with 420 atoms +Loop time of 0.0211506 on 1 procs for 76 steps with 420 atoms -97.4% CPU use with 1 MPI tasks x no OpenMP threads +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -143,12 +150,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.015534 | 0.015534 | 0.015534 | 0.0 | 75.63 -Neigh | 0.0021462 | 0.0021462 | 0.0021462 | 0.0 | 10.45 -Comm | 0.00019169 | 0.00019169 | 0.00019169 | 0.0 | 0.93 -Output | 6.2704e-05 | 6.2704e-05 | 6.2704e-05 | 0.0 | 0.31 -Modify | 0.00095463 | 0.00095463 | 0.00095463 | 0.0 | 4.65 -Other | | 0.001651 | | | 8.04 +Pair | 0.015347 | 0.015347 | 0.015347 | 0.0 | 72.56 +Neigh | 0.002106 | 0.002106 | 0.002106 | 0.0 | 9.96 +Comm | 0.00025511 | 0.00025511 | 0.00025511 | 0.0 | 1.21 +Output | 7.1287e-05 | 7.1287e-05 | 7.1287e-05 | 0.0 | 0.34 +Modify | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 6.55 +Other | | 0.001985 | | | 9.38 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -166,8 +173,8 @@ fix 4 all indent ${k1} sphere 10 12.5 0 6.0 fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.5947 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -3.1812728 0 -0.21796953 -0.12362158 434.07977 120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832 @@ -179,9 +186,9 @@ Step Temp E_pair E_mol TotEng Press Volume 180 0 -3.1041304 0 -3.0969544 1.3751461 430.37017 190 0 -3.1043441 0 -3.0970791 1.392095 430.37017 193 0 -3.1043345 0 -3.0970891 1.3934777 430.37017 -Loop time of 0.0210519 on 1 procs for 82 steps with 420 atoms +Loop time of 0.0218823 on 1 procs for 82 steps with 420 atoms -104.5% CPU use with 1 MPI tasks x no OpenMP threads +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -195,12 +202,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.01655 | 0.01655 | 0.01655 | 0.0 | 78.62 -Neigh | 0.0016158 | 0.0016158 | 0.0016158 | 0.0 | 7.68 -Comm | 0.00016141 | 0.00016141 | 0.00016141 | 0.0 | 0.77 -Output | 5.4359e-05 | 5.4359e-05 | 5.4359e-05 | 0.0 | 0.26 -Modify | 0.0010245 | 0.0010245 | 0.0010245 | 0.0 | 4.87 -Other | | 0.001646 | | | 7.82 +Pair | 0.016445 | 0.016445 | 0.016445 | 0.0 | 75.15 +Neigh | 0.0015912 | 0.0015912 | 0.0015912 | 0.0 | 7.27 +Comm | 0.00024986 | 0.00024986 | 0.00024986 | 0.0 | 1.14 +Output | 7.1526e-05 | 7.1526e-05 | 7.1526e-05 | 0.0 | 0.33 +Modify | 0.0014741 | 0.0014741 | 0.0014741 | 0.0 | 6.74 +Other | | 0.002051 | | | 9.37 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -218,8 +225,8 @@ fix 4 all indent ${k1} sphere 10 12.0 0 6.0 fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.5947 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes Step Temp E_pair E_mol TotEng Press Volume 193 0 -3.1043345 0 2.0111862 1.3910056 431.13503 200 0 -2.5918177 0 -1.931934 5.51119 430.91952 @@ -235,9 +242,9 @@ Step Temp E_pair E_mol TotEng Press Volume 300 0 -3.1107855 0 -3.1043751 1.0663324 470.76888 310 0 -3.1124671 0 -3.1059633 1.0375877 473.02275 316 0 -3.1126981 0 -3.1061297 1.0266662 473.02275 -Loop time of 0.0372601 on 1 procs for 123 steps with 420 atoms +Loop time of 0.0387044 on 1 procs for 123 steps with 420 atoms -99.3% CPU use with 1 MPI tasks x no OpenMP threads +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -251,12 +258,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.028822 | 0.028822 | 0.028822 | 0.0 | 77.35 -Neigh | 0.0035007 | 0.0035007 | 0.0035007 | 0.0 | 9.40 -Comm | 0.00031781 | 0.00031781 | 0.00031781 | 0.0 | 0.85 -Output | 8.1539e-05 | 8.1539e-05 | 8.1539e-05 | 0.0 | 0.22 -Modify | 0.0017815 | 0.0017815 | 0.0017815 | 0.0 | 4.78 -Other | | 0.002757 | | | 7.40 +Pair | 0.028596 | 0.028596 | 0.028596 | 0.0 | 73.88 +Neigh | 0.0035679 | 0.0035679 | 0.0035679 | 0.0 | 9.22 +Comm | 0.00047278 | 0.00047278 | 0.00047278 | 0.0 | 1.22 +Output | 0.0001111 | 0.0001111 | 0.0001111 | 0.0 | 0.29 +Modify | 0.0025539 | 0.0025539 | 0.0025539 | 0.0 | 6.60 +Other | | 0.003402 | | | 8.79 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -274,8 +281,8 @@ fix 4 all indent ${k1} sphere 10 11.4 0 6.0 fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.5947 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes Step Temp E_pair E_mol TotEng Press Volume 316 0 -3.1126981 0 5.3552772 1.0307152 471.16452 320 0 -2.7131804 0 0.70918694 3.910187 471.16482 @@ -294,9 +301,9 @@ Step Temp E_pair E_mol TotEng Press Volume 450 0 -3.0420658 0 -3.0294992 1.6461313 493.96169 460 0 -3.0443144 0 -3.0312966 1.6701433 493.56812 465 0 -3.0444584 0 -3.0313908 1.6713796 493.56812 -Loop time of 0.0447221 on 1 procs for 149 steps with 420 atoms +Loop time of 0.046638 on 1 procs for 149 steps with 420 atoms -96.1% CPU use with 1 MPI tasks x no OpenMP threads +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -310,12 +317,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.034669 | 0.034669 | 0.034669 | 0.0 | 77.52 -Neigh | 0.0041096 | 0.0041096 | 0.0041096 | 0.0 | 9.19 -Comm | 0.00039029 | 0.00039029 | 0.00039029 | 0.0 | 0.87 -Output | 0.00010586 | 0.00010586 | 0.00010586 | 0.0 | 0.24 -Modify | 0.0021372 | 0.0021372 | 0.0021372 | 0.0 | 4.78 -Other | | 0.00331 | | | 7.40 +Pair | 0.034523 | 0.034523 | 0.034523 | 0.0 | 74.02 +Neigh | 0.0042307 | 0.0042307 | 0.0042307 | 0.0 | 9.07 +Comm | 0.00056744 | 0.00056744 | 0.00056744 | 0.0 | 1.22 +Output | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 0.30 +Modify | 0.0030701 | 0.0030701 | 0.0030701 | 0.0 | 6.58 +Other | | 0.004109 | | | 8.81 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -333,8 +340,8 @@ fix 4 all indent ${k1} sphere 10 11.2 0 6.0 fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.59478 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.168 | 4.168 | 4.168 Mbytes Step Temp E_pair E_mol TotEng Press Volume 465 0 -3.0444584 0 -2.5580192 1.6715946 493.50462 470 0 -2.9426683 0 -2.8814986 2.6421083 493.54443 @@ -357,9 +364,9 @@ Step Temp E_pair E_mol TotEng Press Volume 640 0 -3.0778611 0 -3.0710808 1.1946248 520.31492 650 0 -3.0781525 0 -3.0715363 1.2031624 520.31492 651 0 -3.0781525 0 -3.0715363 1.2031624 520.31492 -Loop time of 0.055048 on 1 procs for 186 steps with 420 atoms +Loop time of 0.0571101 on 1 procs for 186 steps with 420 atoms -99.9% CPU use with 1 MPI tasks x no OpenMP threads +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -373,12 +380,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.042811 | 0.042811 | 0.042811 | 0.0 | 77.77 -Neigh | 0.0048847 | 0.0048847 | 0.0048847 | 0.0 | 8.87 -Comm | 0.00049543 | 0.00049543 | 0.00049543 | 0.0 | 0.90 -Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.24 -Modify | 0.0026782 | 0.0026782 | 0.0026782 | 0.0 | 4.87 -Other | | 0.004047 | | | 7.35 +Pair | 0.042337 | 0.042337 | 0.042337 | 0.0 | 74.13 +Neigh | 0.0050063 | 0.0050063 | 0.0050063 | 0.0 | 8.77 +Comm | 0.00071383 | 0.00071383 | 0.00071383 | 0.0 | 1.25 +Output | 0.00017142 | 0.00017142 | 0.00017142 | 0.0 | 0.30 +Modify | 0.0038519 | 0.0038519 | 0.0038519 | 0.0 | 6.74 +Other | | 0.005029 | | | 8.81 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -396,8 +403,8 @@ fix 4 all indent ${k1} sphere 10 11.0 0 6.0 fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.59487 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.169 | 4.169 | 4.169 Mbytes Step Temp E_pair E_mol TotEng Press Volume 651 0 -3.0781525 0 -2.6488207 1.2032064 520.29591 660 0 -3.0085949 0 -2.9796645 1.9715308 520.26872 @@ -415,9 +422,9 @@ Step Temp E_pair E_mol TotEng Press Volume 780 0 -3.065994 0 -3.0566273 1.931796 521.52157 790 0 -3.0675084 0 -3.0577936 1.9283059 520.99202 799 0 -3.0677005 0 -3.057959 1.9288603 520.99202 -Loop time of 0.043978 on 1 procs for 148 steps with 420 atoms +Loop time of 0.0457094 on 1 procs for 148 steps with 420 atoms -100.0% CPU use with 1 MPI tasks x no OpenMP threads +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -431,12 +438,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.034369 | 0.034369 | 0.034369 | 0.0 | 78.15 -Neigh | 0.0036526 | 0.0036526 | 0.0036526 | 0.0 | 8.31 -Comm | 0.00038934 | 0.00038934 | 0.00038934 | 0.0 | 0.89 -Output | 9.3699e-05 | 9.3699e-05 | 9.3699e-05 | 0.0 | 0.21 -Modify | 0.0021935 | 0.0021935 | 0.0021935 | 0.0 | 4.99 -Other | | 0.00328 | | | 7.46 +Pair | 0.03413 | 0.03413 | 0.03413 | 0.0 | 74.67 +Neigh | 0.0037162 | 0.0037162 | 0.0037162 | 0.0 | 8.13 +Comm | 0.00058603 | 0.00058603 | 0.00058603 | 0.0 | 1.28 +Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.28 +Modify | 0.0031106 | 0.0031106 | 0.0031106 | 0.0 | 6.81 +Other | | 0.00404 | | | 8.84 Nlocal: 420 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/indent/log.5Oct16.indent.min.g++.4 b/examples/indent/log.27Nov18.indent.min.g++.4 similarity index 76% rename from examples/indent/log.5Oct16.indent.min.g++.4 rename to examples/indent/log.27Nov18.indent.min.g++.4 index 4ea1a37d25..b0dca95501 100644 --- a/examples/indent/log.5Oct16.indent.min.g++.4 +++ b/examples/indent/log.27Nov18.indent.min.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d indenter simulation with minimization instead of dynamics dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 420 atoms + Time spent = 0.000312805 secs mass * 1.0 @@ -57,24 +59,29 @@ thermo 10 #dump_modify 3 pad 4 minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 17 15 1 -Memory usage per processor = 3.60136 Mbytes + binsize = 1.4, bins = 17 15 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333 10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558 20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033 30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033 35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082 -Loop time of 0.00329685 on 4 procs for 35 steps with 420 atoms +Loop time of 0.00425965 on 4 procs for 35 steps with 420 atoms -75.8% CPU use with 4 MPI tasks x no OpenMP threads +91.0% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -88,12 +95,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0018942 | 0.0019329 | 0.0019758 | 0.1 | 58.63 -Neigh | 0.00011587 | 0.000121 | 0.00012612 | 0.0 | 3.67 -Comm | 0.00034523 | 0.00040966 | 0.00046587 | 0.3 | 12.43 -Output | 4.3869e-05 | 4.667e-05 | 5.2929e-05 | 0.1 | 1.42 -Modify | 2.4796e-05 | 3.7432e-05 | 5.0306e-05 | 0.2 | 1.14 -Other | | 0.0007492 | | | 22.73 +Pair | 0.0018404 | 0.0020409 | 0.002239 | 0.3 | 47.91 +Neigh | 0.00011182 | 0.00011867 | 0.00012565 | 0.0 | 2.79 +Comm | 0.00071144 | 0.0010059 | 0.0013125 | 0.7 | 23.62 +Output | 4.1723e-05 | 4.4882e-05 | 5.1022e-05 | 0.0 | 1.05 +Modify | 4.7445e-05 | 5.6326e-05 | 6.4611e-05 | 0.0 | 1.32 +Other | | 0.0009929 | | | 23.31 Nlocal: 105 ave 111 max 99 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -114,8 +121,8 @@ fix 4 all indent $k sphere 10 13.0 0 6.0 fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.60136 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574 40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534 @@ -127,9 +134,9 @@ Step Temp E_pair E_mol TotEng Press Volume 100 0 -3.1812307 0 -3.1805381 -0.15305002 434.96379 110 0 -3.1812588 0 -3.1805938 -0.12504601 432.50683 111 0 -3.1812728 0 -3.1805961 -0.12407115 432.50683 -Loop time of 0.00908947 on 4 procs for 76 steps with 420 atoms +Loop time of 0.009408 on 4 procs for 76 steps with 420 atoms -96.2% CPU use with 4 MPI tasks x no OpenMP threads +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -143,12 +150,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0037253 | 0.0040306 | 0.0043435 | 0.5 | 44.34 -Neigh | 0.00058532 | 0.00061685 | 0.00064421 | 0.1 | 6.79 -Comm | 0.0012383 | 0.0015994 | 0.0019143 | 0.8 | 17.60 -Output | 0.00012493 | 0.0001325 | 0.00015235 | 0.1 | 1.46 -Modify | 0.00026274 | 0.00028539 | 0.00030255 | 0.1 | 3.14 -Other | | 0.002425 | | | 26.68 +Pair | 0.0035956 | 0.0040194 | 0.0043173 | 0.5 | 42.72 +Neigh | 0.00058937 | 0.00061256 | 0.00065064 | 0.0 | 6.51 +Comm | 0.0012782 | 0.0017276 | 0.0023015 | 1.0 | 18.36 +Output | 0.00012088 | 0.00013882 | 0.00018907 | 0.0 | 1.48 +Modify | 0.00037575 | 0.00040001 | 0.00041938 | 0.0 | 4.25 +Other | | 0.00251 | | | 26.68 Nlocal: 105 ave 111 max 99 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -166,8 +173,8 @@ fix 4 all indent ${k1} sphere 10 12.5 0 6.0 fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.60136 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes Step Temp E_pair E_mol TotEng Press Volume 111 0 -3.1812728 0 -0.21796955 -0.12362156 434.07977 120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832 @@ -179,9 +186,9 @@ Step Temp E_pair E_mol TotEng Press Volume 180 0 -3.1041304 0 -3.0969544 1.3751455 430.37021 190 0 -3.1043441 0 -3.0970791 1.3920926 430.37021 193 0 -3.1043346 0 -3.0970891 1.3934753 430.37021 -Loop time of 0.00948715 on 4 procs for 82 steps with 420 atoms +Loop time of 0.00970888 on 4 procs for 82 steps with 420 atoms -100.1% CPU use with 4 MPI tasks x no OpenMP threads +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -195,12 +202,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0037739 | 0.0042151 | 0.0046482 | 0.6 | 44.43 -Neigh | 0.00041008 | 0.0004425 | 0.00048161 | 0.1 | 4.66 -Comm | 0.0013449 | 0.0018466 | 0.0023468 | 1.1 | 19.46 -Output | 0.00012422 | 0.00013196 | 0.00015044 | 0.1 | 1.39 -Modify | 0.00026131 | 0.00028855 | 0.00030518 | 0.1 | 3.04 -Other | | 0.002563 | | | 27.01 +Pair | 0.0038064 | 0.0043663 | 0.0049345 | 0.7 | 44.97 +Neigh | 0.00041938 | 0.00044787 | 0.00046825 | 0.0 | 4.61 +Comm | 0.0012298 | 0.0018778 | 0.0025084 | 1.2 | 19.34 +Output | 0.00010872 | 0.00013095 | 0.00019455 | 0.0 | 1.35 +Modify | 0.0003829 | 0.00042218 | 0.00045204 | 0.0 | 4.35 +Other | | 0.002464 | | | 25.38 Nlocal: 105 ave 112 max 98 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -218,8 +225,8 @@ fix 4 all indent ${k1} sphere 10 12.0 0 6.0 fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.60136 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.172 Mbytes Step Temp E_pair E_mol TotEng Press Volume 193 0 -3.1043346 0 2.0111873 1.3910032 431.13505 200 0 -2.5918062 0 -1.93191 5.511262 430.91953 @@ -235,9 +242,9 @@ Step Temp E_pair E_mol TotEng Press Volume 300 0 -3.1109522 0 -3.1046995 1.064904 470.50807 310 0 -3.1123989 0 -3.105985 1.0430839 470.40952 313 0 -3.1125022 0 -3.1060453 1.0390872 470.40952 -Loop time of 0.016437 on 4 procs for 120 steps with 420 atoms +Loop time of 0.0169249 on 4 procs for 120 steps with 420 atoms -95.8% CPU use with 4 MPI tasks x no OpenMP threads +95.2% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -251,12 +258,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0060949 | 0.0071945 | 0.008219 | 1.2 | 43.77 -Neigh | 0.00081253 | 0.00092614 | 0.0010352 | 0.3 | 5.63 -Comm | 0.0022275 | 0.0035025 | 0.0047491 | 2.1 | 21.31 -Output | 0.00018907 | 0.00019854 | 0.00022316 | 0.1 | 1.21 -Modify | 0.00045967 | 0.00049853 | 0.0005331 | 0.1 | 3.03 -Other | | 0.004117 | | | 25.05 +Pair | 0.0061595 | 0.0073055 | 0.0083787 | 1.2 | 43.16 +Neigh | 0.00085759 | 0.00095439 | 0.0010619 | 0.0 | 5.64 +Comm | 0.0020378 | 0.0032984 | 0.0046635 | 2.1 | 19.49 +Output | 0.00016832 | 0.00020832 | 0.00032616 | 0.0 | 1.23 +Modify | 0.0006628 | 0.00078654 | 0.00090957 | 0.0 | 4.65 +Other | | 0.004372 | | | 25.83 Nlocal: 105 ave 123 max 90 min Histogram: 2 0 0 0 0 0 0 0 1 1 @@ -274,8 +281,8 @@ fix 4 all indent ${k1} sphere 10 11.4 0 6.0 fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.60136 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.172 | 4.173 Mbytes Step Temp E_pair E_mol TotEng Press Volume 313 0 -3.1125022 0 5.3341053 1.0377311 471.02427 320 0 -2.402824 0 -0.86170235 6.1550233 471.02943 @@ -289,9 +296,9 @@ Step Temp E_pair E_mol TotEng Press Volume 400 0 -3.0098108 0 -2.9963408 2.0798685 490.87751 410 0 -3.0142937 0 -3.0017605 2.0015139 491.52711 417 0 -3.0148998 0 -3.0024932 1.9909706 492.48053 -Loop time of 0.0132418 on 4 procs for 104 steps with 420 atoms +Loop time of 0.0135124 on 4 procs for 104 steps with 420 atoms -94.4% CPU use with 4 MPI tasks x no OpenMP threads +90.7% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -305,12 +312,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0043645 | 0.0054896 | 0.0065427 | 1.4 | 41.46 -Neigh | 0.00071716 | 0.00088716 | 0.0010509 | 0.5 | 6.70 -Comm | 0.0017078 | 0.0030243 | 0.0044179 | 2.3 | 22.84 -Output | 0.00015879 | 0.00016719 | 0.00018978 | 0.1 | 1.26 -Modify | 0.00033998 | 0.00038028 | 0.00042176 | 0.2 | 2.87 -Other | | 0.003293 | | | 24.87 +Pair | 0.0043001 | 0.0056325 | 0.0068884 | 1.5 | 41.68 +Neigh | 0.0007472 | 0.00091684 | 0.0010941 | 0.0 | 6.79 +Comm | 0.0015268 | 0.0030602 | 0.0046747 | 2.4 | 22.65 +Output | 0.00014591 | 0.00017387 | 0.00025606 | 0.0 | 1.29 +Modify | 0.00047064 | 0.00054699 | 0.00062537 | 0.0 | 4.05 +Other | | 0.003182 | | | 23.55 Nlocal: 105 ave 121 max 89 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -328,8 +335,8 @@ fix 4 all indent ${k1} sphere 10 11.2 0 6.0 fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.60141 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.173 | 4.173 Mbytes Step Temp E_pair E_mol TotEng Press Volume 417 0 -3.0148998 0 -2.4816986 1.9918498 492.26314 420 0 -2.9209943 0 -2.7871779 2.8201475 492.26417 @@ -352,9 +359,9 @@ Step Temp E_pair E_mol TotEng Press Volume 590 0 -3.114722 0 -3.1095528 0.90665975 515.99746 600 0 -3.1149189 0 -3.1096744 0.88783587 515.99746 605 0 -3.1149612 0 -3.1097106 0.88187936 515.99746 -Loop time of 0.0257494 on 4 procs for 188 steps with 420 atoms +Loop time of 0.0262601 on 4 procs for 188 steps with 420 atoms -98.0% CPU use with 4 MPI tasks x no OpenMP threads +95.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -368,12 +375,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0080748 | 0.010793 | 0.013608 | 2.6 | 41.91 -Neigh | 0.000983 | 0.0012598 | 0.0015397 | 0.8 | 4.89 -Comm | 0.003365 | 0.0064785 | 0.0095432 | 3.8 | 25.16 -Output | 0.0002985 | 0.00031477 | 0.00035667 | 0.1 | 1.22 -Modify | 0.00062346 | 0.0007531 | 0.00086522 | 0.4 | 2.92 -Other | | 0.00615 | | | 23.89 +Pair | 0.0080013 | 0.010975 | 0.013789 | 2.6 | 41.79 +Neigh | 0.001025 | 0.001315 | 0.0016329 | 0.8 | 5.01 +Comm | 0.0033126 | 0.0065627 | 0.010028 | 3.9 | 24.99 +Output | 0.00025845 | 0.00032175 | 0.00050783 | 0.0 | 1.23 +Modify | 0.00088954 | 0.0010915 | 0.0012805 | 0.6 | 4.16 +Other | | 0.005994 | | | 22.83 Nlocal: 105 ave 125 max 84 min Histogram: 2 0 0 0 0 0 0 0 0 2 @@ -391,8 +398,8 @@ fix 4 all indent ${k1} sphere 10 11.0 0 6.0 fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0 fix_modify 4 energy yes minimize 1.0e-6 1.0e-6 1000 1000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -Memory usage per processor = 3.60141 Mbytes +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) +Per MPI rank memory allocation (min/avg/max) = 4.172 | 4.173 | 4.173 Mbytes Step Temp E_pair E_mol TotEng Press Volume 605 0 -3.1149612 0 -2.7562264 0.88153856 516.19694 610 0 -3.0480145 0 -3.0046036 1.5377628 516.18952 @@ -408,9 +415,9 @@ Step Temp E_pair E_mol TotEng Press Volume 710 0 -3.0738836 0 -3.0635305 1.6674853 516.40455 720 0 -3.0744809 0 -3.0640016 1.6430059 516.40455 729 0 -3.074692 0 -3.0641622 1.6351234 517.12194 -Loop time of 0.017405 on 4 procs for 124 steps with 420 atoms +Loop time of 0.0187363 on 4 procs for 124 steps with 420 atoms -97.7% CPU use with 4 MPI tasks x no OpenMP threads +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero @@ -424,12 +431,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0049167 | 0.0073144 | 0.0095913 | 2.7 | 42.02 -Neigh | 0.00037408 | 0.00051659 | 0.00065827 | 0.6 | 2.97 -Comm | 0.0021894 | 0.0047411 | 0.0072858 | 3.6 | 27.24 -Output | 0.00018907 | 0.0001967 | 0.00021863 | 0.1 | 1.13 -Modify | 0.00040865 | 0.00051677 | 0.00060606 | 0.4 | 2.97 -Other | | 0.004119 | | | 23.67 +Pair | 0.0051301 | 0.0074221 | 0.0098505 | 2.6 | 39.61 +Neigh | 0.00038052 | 0.00054228 | 0.00068402 | 0.0 | 2.89 +Comm | 0.0018504 | 0.004572 | 0.007129 | 3.8 | 24.40 +Output | 0.00017834 | 0.00021213 | 0.00030828 | 0.0 | 1.13 +Modify | 0.00057554 | 0.00075471 | 0.00091839 | 0.0 | 4.03 +Other | | 0.005233 | | | 27.93 Nlocal: 105 ave 131 max 78 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/kim/in.kim.lj.lmp b/examples/kim/in.kim.lj.lmp.newton-off similarity index 77% rename from examples/kim/in.kim.lj.lmp rename to examples/kim/in.kim.lj.lmp.newton-off index 8879024590..197755294a 100644 --- a/examples/kim/in.kim.lj.lmp +++ b/examples/kim/in.kim.lj.lmp.newton-off @@ -10,6 +10,7 @@ variable zz equal 20*$z units metal atom_style atomic +newton off lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} @@ -17,13 +18,12 @@ create_box 1 box create_atoms 1 box pair_style lj/cut 8.1500 -pair_coeff 1 1 0.0031 2.7400 -pair_modify shift yes +pair_coeff 1 1 0.0104 3.4000 -#pair_style kim KIMvirial ex_model_Ne_P_fastLJ -#pair_coeff * * Ne +#pair_style kim LennardJones_Ar +#pair_coeff * * Ar -mass 1 20.18 +mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin diff --git a/examples/kim/in.kim.lj b/examples/kim/in.kim.lj.lmp.newton-on similarity index 73% rename from examples/kim/in.kim.lj rename to examples/kim/in.kim.lj.lmp.newton-on index f33b258be8..f9f79e2bb2 100644 --- a/examples/kim/in.kim.lj +++ b/examples/kim/in.kim.lj.lmp.newton-on @@ -10,20 +10,20 @@ variable zz equal 20*$z units metal atom_style atomic +newton on lattice fcc 4.4300 region box block 0 ${xx} 0 ${yy} 0 ${zz} create_box 1 box create_atoms 1 box -#pair_style lj/cut 8.1500 -#pair_coeff 1 1 0.0031 2.7400 -#pair_modify shift yes +pair_style lj/cut 8.1500 +pair_coeff 1 1 0.0104 3.4000 -pair_style kim KIMvirial ex_model_Ne_P_fastLJ -pair_coeff * * Ne +#pair_style kim LennardJones_Ar +#pair_coeff * * Ar -mass 1 20.18 +mass 1 39.95 velocity all create 200.0 232345 loop geom neighbor 0.3 bin diff --git a/examples/kim/in.kim.lj.newton-off b/examples/kim/in.kim.lj.newton-off new file mode 100644 index 0000000000..82cf5ba602 --- /dev/null +++ b/examples/kim/in.kim.lj.newton-off @@ -0,0 +1,41 @@ +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units metal +atom_style atomic +newton off + +lattice fcc 4.4300 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +#pair_style lj/cut 8.1500 +#pair_coeff 1 1 0.0104 3.4000 + +pair_style kim LennardJones_Ar +pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.kim.lj.newton-on b/examples/kim/in.kim.lj.newton-on new file mode 100644 index 0000000000..3a95f1dbb0 --- /dev/null +++ b/examples/kim/in.kim.lj.newton-on @@ -0,0 +1,41 @@ +# 3d Lennard-Jones melt +# +# This example requires that the example models provided with +# the kim-api package are installed. see the ./lib/kim/README or +# ./lib/kim/Install.py files for details on how to install these +# example models. +# + +variable x index 1 +variable y index 1 +variable z index 1 + +variable xx equal 20*$x +variable yy equal 20*$y +variable zz equal 20*$z + +units metal +atom_style atomic +newton on + +lattice fcc 4.4300 +region box block 0 ${xx} 0 ${yy} 0 ${zz} +create_box 1 box +create_atoms 1 box + +#pair_style lj/cut 8.1500 +#pair_coeff 1 1 0.0104 3.4000 + +pair_style kim LennardJones_Ar +pair_coeff * * Ar + +mass 1 39.95 +velocity all create 200.0 232345 loop geom + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 all nve +#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0 + +run 100 diff --git a/examples/kim/in.query b/examples/kim/in.query new file mode 100644 index 0000000000..33272dc298 --- /dev/null +++ b/examples/kim/in.query @@ -0,0 +1,11 @@ + +# example for performing a query to the OpenKIM test database to retrieve +# a parameter to be used in the input. here it requests the aluminium +# lattice constant for a specific test used for a specific model and then +# assigns it to the variable 'latconst' + +units metal +info variables out log +kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"] +info variables out log +lattice fcc ${latconst} diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 new file mode 100644 index 0000000000..5925fd750d --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.1 @@ -0,0 +1,55 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +Created 32000 atoms + Time spent = 0.004499 secs +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 2.92885 on 1 procs for 100 steps with 32000 atoms + +Performance: 2.950 ns/day, 8.136 hours/ns, 34.143 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5638 | 2.5638 | 2.5638 | 0.0 | 87.54 +Neigh | 0.31935 | 0.31935 | 0.31935 | 0.0 | 10.90 +Comm | 0.006833 | 0.006833 | 0.006833 | 0.0 | 0.23 +Output | 0.000107 | 0.000107 | 0.000107 | 0.0 | 0.00 +Modify | 0.027806 | 0.027806 | 0.027806 | 0.0 | 0.95 +Other | | 0.01091 | | | 0.37 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2370499 +Ave neighs/atom = 74.0781 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 new file mode 100644 index 0000000000..c1ca108c7b --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-off.4 @@ -0,0 +1,55 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +Created 32000 atoms + Time spent = 0.001039 secs +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton off + pair build: half/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 0.778581 on 4 procs for 100 steps with 32000 atoms + +Performance: 11.097 ns/day, 2.163 hours/ns, 128.439 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.65171 | 0.65891 | 0.67656 | 1.3 | 84.63 +Neigh | 0.07924 | 0.079548 | 0.07997 | 0.1 | 10.22 +Comm | 0.006755 | 0.0069015 | 0.007072 | 0.2 | 0.89 +Output | 4.6e-05 | 9.725e-05 | 0.000203 | 0.0 | 0.01 +Modify | 0.006841 | 0.006941 | 0.007015 | 0.1 | 0.89 +Other | | 0.02618 | | | 3.36 + +Nlocal: 8000 ave 8018 max 7967 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 9131 ave 9164 max 9113 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 630904 ave 632094 max 628209 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 2523614 +Ave neighs/atom = 78.8629 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 new file mode 100644 index 0000000000..53555743d7 --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.1 @@ -0,0 +1,55 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +Created 32000 atoms + Time spent = 0.003479 secs +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 2.17978 on 1 procs for 100 steps with 32000 atoms + +Performance: 3.964 ns/day, 6.055 hours/ns, 45.876 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9892 | 1.9892 | 1.9892 | 0.0 | 91.26 +Neigh | 0.14506 | 0.14506 | 0.14506 | 0.0 | 6.65 +Comm | 0.011049 | 0.011049 | 0.011049 | 0.0 | 0.51 +Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00 +Modify | 0.02347 | 0.02347 | 0.02347 | 0.0 | 1.08 +Other | | 0.01094 | | | 0.50 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.12688e+06 ave 2.12688e+06 max 2.12688e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2126875 +Ave neighs/atom = 66.4648 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:02 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 new file mode 100644 index 0000000000..f0fdf66193 --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.lmp.newton-on.4 @@ -0,0 +1,55 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +Created 32000 atoms + Time spent = 0.000919 secs +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 0.63515 on 4 procs for 100 steps with 32000 atoms + +Performance: 13.603 ns/day, 1.764 hours/ns, 157.443 timesteps/s +99.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.55365 | 0.5566 | 0.55868 | 0.2 | 87.63 +Neigh | 0.041495 | 0.0418 | 0.04211 | 0.1 | 6.58 +Comm | 0.019086 | 0.021075 | 0.023898 | 1.2 | 3.32 +Output | 4.4e-05 | 5.025e-05 | 6e-05 | 0.0 | 0.01 +Modify | 0.009315 | 0.0093595 | 0.009422 | 0.0 | 1.47 +Other | | 0.006263 | | | 0.99 + +Nlocal: 8000 ave 8018 max 7967 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 9131 ave 9164 max 9113 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 531719 ave 533273 max 529395 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 2126875 +Ave neighs/atom = 66.4648 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 new file mode 100644 index 0000000000..0ab258fe0d --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.1 @@ -0,0 +1,59 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +Created 32000 atoms + Time spent = 0.003446 secs +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 3.01669 on 1 procs for 100 steps with 32000 atoms + +Performance: 2.864 ns/day, 8.380 hours/ns, 33.149 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.6562 | 2.6562 | 2.6562 | 0.0 | 88.05 +Neigh | 0.31903 | 0.31903 | 0.31903 | 0.0 | 10.58 +Comm | 0.00634 | 0.00634 | 0.00634 | 0.0 | 0.21 +Output | 9.1e-05 | 9.1e-05 | 9.1e-05 | 0.0 | 0.00 +Modify | 0.024723 | 0.024723 | 0.024723 | 0.0 | 0.82 +Other | | 0.01032 | | | 0.34 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 new file mode 100644 index 0000000000..c17ea6afb7 --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.newton-off.4 @@ -0,0 +1,65 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +Created 32000 atoms + Time spent = 0.000921 secs +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 0.890192 on 4 procs for 100 steps with 32000 atoms + +Performance: 9.706 ns/day, 2.473 hours/ns, 112.335 timesteps/s +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.77867 | 0.77906 | 0.7794 | 0.0 | 87.52 +Neigh | 0.087831 | 0.088176 | 0.088805 | 0.1 | 9.91 +Comm | 0.006358 | 0.0065898 | 0.006815 | 0.3 | 0.74 +Output | 4.9e-05 | 5.975e-05 | 6.8e-05 | 0.0 | 0.01 +Modify | 0.010265 | 0.010429 | 0.010678 | 0.2 | 1.17 +Other | | 0.005874 | | | 0.66 + +Nlocal: 8000 ave 8018 max 7967 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 9131 ave 9164 max 9113 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 new file mode 100644 index 0000000000..59d018e12a --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.1 @@ -0,0 +1,59 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 1 by 1 MPI processor grid +Created 32000 atoms + Time spent = 0.003089 secs +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 3.05849 on 1 procs for 100 steps with 32000 atoms + +Performance: 2.825 ns/day, 8.496 hours/ns, 32.696 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.6786 | 2.6786 | 2.6786 | 0.0 | 87.58 +Neigh | 0.33105 | 0.33105 | 0.33105 | 0.0 | 10.82 +Comm | 0.012602 | 0.012602 | 0.012602 | 0.0 | 0.41 +Output | 9.5e-05 | 9.5e-05 | 9.5e-05 | 0.0 | 0.00 +Modify | 0.024858 | 0.024858 | 0.024858 | 0.0 | 0.81 +Other | | 0.01132 | | | 0.37 + +Nlocal: 32000 ave 32000 max 32000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 19911 ave 19911 max 19911 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 new file mode 100644 index 0000000000..da8c9f0faa --- /dev/null +++ b/examples/kim/log.06Feb2019.in.kim.lj.newton-on.4 @@ -0,0 +1,65 @@ +LAMMPS (1 Feb 2019) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) + using 1 OpenMP thread(s) per MPI task +Lattice spacing in x,y,z = 4.43 4.43 4.43 +Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) + 1 by 2 by 2 MPI processor grid +Created 32000 atoms + Time spent = 0.000893 secs +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097) +WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102) +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8.45 + ghost atom cutoff = 8.45 + binsize = 4.225, bins = 21 21 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair kim, perpetual + attributes: full, newton off, cut 8.45 + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Setting up Verlet run ... + Unit style : metal + Current step : 0 + Time step : 0.001 +Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 200 6290.8194 0 7118.0584 129712.25 + 100 95.179725 6718.814 0 7112.496 133346.59 +Loop time of 0.903182 on 4 procs for 100 steps with 32000 atoms + +Performance: 9.566 ns/day, 2.509 hours/ns, 110.720 timesteps/s +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.76173 | 0.76349 | 0.76597 | 0.2 | 84.53 +Neigh | 0.088773 | 0.088938 | 0.089074 | 0.0 | 9.85 +Comm | 0.032018 | 0.03452 | 0.03638 | 0.9 | 3.82 +Output | 4e-05 | 4.425e-05 | 5.2e-05 | 0.0 | 0.00 +Modify | 0.009278 | 0.0093917 | 0.009528 | 0.1 | 1.04 +Other | | 0.006797 | | | 0.75 + +Nlocal: 8000 ave 8018 max 7967 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 9131 ave 9164 max 9113 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 4253750 +Ave neighs/atom = 132.93 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/kim/log.22Mar2019.query.g++.1 b/examples/kim/log.22Mar2019.query.g++.1 new file mode 100644 index 0000000000..034bb13bba --- /dev/null +++ b/examples/kim/log.22Mar2019.query.g++.1 @@ -0,0 +1,34 @@ +LAMMPS (28 Feb 2019) + +# example for performing a query to the OpenKIM test database to retrieve +# a parameter to be used in the input. here it requests the aluminium +# lattice constant for a specific test used for a specific model and then +# assigns it to the variable 'latconst' + +units metal +info variables out log + +Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info +Printed on Fri Mar 22 20:00:56 2019 + + +Variable information: + +Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info + +kim_query latconst get_test_result test=TE_156715955670 species=["Al"] model=MO_800509458712 prop=structure-cubic-crystal-npt keys=["a"] units=["angstrom"] +info variables out log + +Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info +Printed on Fri Mar 22 20:00:57 2019 + + +Variable information: +Variable[ 0]: latconst , style = string , def = 4.03208274841 + +Info-Info-Info-Info-Info-Info-Info-Info-Info-Info-Info + +lattice fcc ${latconst} +lattice fcc 4.03208274841 +Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 +Total wall time: 0:00:00 diff --git a/examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.1 b/examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.1 deleted file mode 100644 index efae0587a1..0000000000 --- a/examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.1 +++ /dev/null @@ -1,33 +0,0 @@ -LAMMPS (15 May 2015) -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - master list distance cutoff = 8.45 -Setting up run ... -Memory usage per processor = 9.18789 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 -741.55469 0 85.684388 -34.939092 - 100 108.37517 -362.56658 0 85.694308 3963.7892 -Loop time of 2.95205 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 2.52074 (85.3894) -Neigh time (%) = 0.347949 (11.7867) -Comm time (%) = 0.0228171 (0.772925) -Outpt time (%) = 0.000188828 (0.00639649) -Other time (%) = 0.0603588 (2.04464) - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 20131 ave 20131 max 20131 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1.88909e+06 ave 1.88909e+06 max 1.88909e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1889091 -Ave neighs/atom = 59.0341 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.4 b/examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.4 deleted file mode 100644 index 12c1c76695..0000000000 --- a/examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.4 +++ /dev/null @@ -1,33 +0,0 @@ -LAMMPS (15 May 2015) -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - master list distance cutoff = 8.45 -Setting up run ... -Memory usage per processor = 4.58461 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 -741.55469 0 85.684388 -34.939092 - 100 108.37517 -362.56658 0 85.694308 3963.7892 -Loop time of 6.15911 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 1.76201 (28.6083) -Neigh time (%) = 0.265002 (4.30261) -Comm time (%) = 3.64452 (59.1729) -Outpt time (%) = 0.0169877 (0.275815) -Other time (%) = 0.470582 (7.64042) - -Nlocal: 8000 ave 8010 max 7989 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 9240.25 ave 9249 max 9228 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Neighs: 472273 ave 473390 max 471652 min -Histogram: 2 0 0 1 0 0 0 0 0 1 - -Total # of neighbors = 1889091 -Ave neighs/atom = 59.0341 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/examples/kim/log.28Jun15.kim.lj.ubuntu.1 b/examples/kim/log.28Jun15.kim.lj.ubuntu.1 deleted file mode 100644 index 95284453b1..0000000000 --- a/examples/kim/log.28Jun15.kim.lj.ubuntu.1 +++ /dev/null @@ -1,33 +0,0 @@ -LAMMPS (15 May 2015) -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 1 by 1 MPI processor grid -Created 32000 atoms -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - master list distance cutoff = 8.45 -Setting up run ... -Memory usage per processor = 9.43789 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 -741.55469 0 85.684388 -34.939092 - 100 108.37517 -362.56658 0 85.694308 3963.7892 -Loop time of 3.79746 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 3.18686 (83.9207) -Neigh time (%) = 0.524724 (13.8178) -Comm time (%) = 0.0244031 (0.642616) -Outpt time (%) = 0.000174046 (0.00458321) -Other time (%) = 0.061305 (1.61437) - -Nlocal: 32000 ave 32000 max 32000 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 20131 ave 20131 max 20131 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.09236e+06 ave 2.09236e+06 max 2.09236e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2092355 -Ave neighs/atom = 65.3861 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/examples/kim/log.28Jun15.kim.lj.ubuntu.4 b/examples/kim/log.28Jun15.kim.lj.ubuntu.4 deleted file mode 100644 index 7eaf58aad4..0000000000 --- a/examples/kim/log.28Jun15.kim.lj.ubuntu.4 +++ /dev/null @@ -1,33 +0,0 @@ -LAMMPS (15 May 2015) -Lattice spacing in x,y,z = 4.43 4.43 4.43 -Created orthogonal box = (0 0 0) to (88.6 88.6 88.6) - 1 by 2 by 2 MPI processor grid -Created 32000 atoms -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - master list distance cutoff = 8.45 -Setting up run ... -Memory usage per processor = 4.70961 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 200 -741.55469 0 85.684388 -34.939092 - 100 108.37517 -362.56658 0 85.694308 3963.7892 -Loop time of 7.25305 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 2.52571 (34.8227) -Neigh time (%) = 0.500287 (6.8976) -Comm time (%) = 3.70236 (51.0456) -Outpt time (%) = 0.00146681 (0.0202234) -Other time (%) = 0.523229 (7.21391) - -Nlocal: 8000 ave 8010 max 7989 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Nghost: 9240.25 ave 9249 max 9228 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -Neighs: 555266 ave 555920 max 554805 min -Histogram: 2 0 0 0 0 1 0 0 0 1 - -Total # of neighbors = 2221065 -Ave neighs/atom = 69.4083 -Neighbor list builds = 5 -Dangerous builds = 0 diff --git a/examples/meam/Ni.meam b/examples/meam/Ni.meam deleted file mode 100644 index 7fd8d19f52..0000000000 --- a/examples/meam/Ni.meam +++ /dev/null @@ -1,3 +0,0 @@ -# DATE: 2007-06-11 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Unknown -rc = 4.0 -delr = 0.1 diff --git a/examples/meam/Ni.meam b/examples/meam/Ni.meam new file mode 120000 index 0000000000..5283388f64 --- /dev/null +++ b/examples/meam/Ni.meam @@ -0,0 +1 @@ +../../potentials/Ni.meam \ No newline at end of file diff --git a/examples/meam/SiC.meam b/examples/meam/SiC.meam deleted file mode 100644 index d07903c52a..0000000000 --- a/examples/meam/SiC.meam +++ /dev/null @@ -1,12 +0,0 @@ -# DATE: 2007-06-11 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Unknown -lattce(1,2) = 'dia' -Ec(1,2) = 6.4325 -alpha(1,2) = 4.37 -re(1,2) = 1.8878 -rho0(2) = 2.25 -rc = 4.0 -delr = 0.1 -Cmax(1,2,1) = 4.0 -Cmax(1,2,2) = 4.0 -Cmax(2,2,1) = 4.0 -Cmax(1,1,2) = 4.0 diff --git a/examples/meam/SiC.meam b/examples/meam/SiC.meam new file mode 120000 index 0000000000..288d5d0433 --- /dev/null +++ b/examples/meam/SiC.meam @@ -0,0 +1 @@ +../../potentials/SiC.meam \ No newline at end of file diff --git a/examples/meam/in.meam b/examples/meam/in.meam deleted file mode 100644 index b4463be365..0000000000 --- a/examples/meam/in.meam +++ /dev/null @@ -1,30 +0,0 @@ -# Test of MEAM potential for SiC system - -units metal -boundary p p p - -atom_style atomic - -read_data data.meam - -pair_style meam -pair_coeff * * library.meam Si C SiC.meam Si C - -neighbor 0.3 bin -neigh_modify delay 10 - -fix 1 all nve -thermo 10 -timestep 0.001 - -#dump 1 all atom 50 dump.meam - -#dump 2 all image 10 image.*.jpg element element & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 element Si C - -#dump 3 all movie 10 movie.mpg element element & -# axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 element Si C - -run 100 diff --git a/examples/meam/library.meam b/examples/meam/library.meam deleted file mode 100644 index 38a52bed0a..0000000000 --- a/examples/meam/library.meam +++ /dev/null @@ -1,178 +0,0 @@ -# DATE: 2012-06-29 DATE: 2007-06-11 CONTRIBUTOR: Greg Wagner, gjwagne@sandia.gov CITATION: Baskes, Phys Rev B, 46, 2727-2742 (1992) -# meam data from vax files fcc,bcc,dia 11/4/92 -# elt lat z ielement atwt -# alpha b0 b1 b2 b3 alat esub asub -# t0 t1 t2 t3 rozero ibar - -'AlS' 'fcc' 12. 13 26.9815 -4.64 2.04 3.00 6.0 1.50 4.05 3.353 1.07 -1.0 +4.50 -2.30 8.01 1.0 -5 -'SiS' 'dia' 4. 14 28.086 -4.87 4.4 5.5 5.5 5.5 5.431 4.63 1. -1.0 2.05 4.47 -1.80 2.2 -5 -'MgS' 'hcp' 12. 12 24.305 -5.52 4.0 3.0 0.2 1.2 3.194 1.51 0.80 -1.0 10.04 9.49 -4.3 0.63 -5 -'CuS' 'fcc' 12. 29 63.54 -5.11 3.634 2.20 6 2.20 3.62 3.54 1.07 -1.0 4.91 2.49 2.95 1.10 -5 -'FeS' 'bcc' 8 26 55.847 -5.0270 3.500 2 1.00 1 2.851 4.28 0.5550 -1 -1.6 12.5 -1.40 1.0 -5 -'Sn5' 'dia' 4. 50 118. -5.09 5.00 16.0 04.0 5.0 6.483 3.14 1.00 -1.0 2.00 5.756 -0.30 1. 0 -'Sn' 'dia' 4. 50 118. -5.09 5.42 8.0 5.0 6.0 6.483 3.14 1.12 -1.0 3.0 5.707 +0.30 1. 0 -'Cu' 'fcc' 12. 29 63.54 -5.10570729 3.634 2.20 6 2.20 3.62 3.54 1.07 -1.0 3.13803254 2.49438711 2.95269237 1. 0 -'Ag' 'fcc' 12. 47 107.870 -5.89222008 4.456 2.20 6 2.20 4.08 2.85 1.06 -1.0 5.54097609 2.45015783 1.28843988 1. 0 -'Au' 'fcc' 12. 79 196.967 -6.34090112 5.449 2.20 6 2.20 4.07 3.93 1.04 -1.0 1.58956328 1.50776392 2.60609758 1. 0 -'Ni1' 'fcc' 12. 28 58.71 -4.99 2.45 2.20 6 2.20 3.52 4.45 1.10 -1.0 3.57 1.60 3.70 1.0 0 -'Ni2' 'fcc' 12. 28 58.71 -4.99 2.45 2.20 6 2.20 3.52 4.45 1.10 -1.0 3.57 1.60 3.70 1.0 3 -'Ni3' 'fcc' 12. 28 58.71 -4.99 2.45 1.50 6 1.50 3.52 4.45 1.10 -1.0 3.57 1.60 3.70 1.0 3 -'Ni4' 'fcc' 12. 28 58.71 -4.99 2.45 1.50 6 1.50 3.52 4.45 1.10 -1.0 3.57 1.60 3.70 1.0 0 -'Ni' 'fcc' 12. 28 58.71 -4.99 2.64 1.50 4.50 1.50 3.52 4.45 1.10 -1.0 1.692 4.987 3.683 1.0 1 -'Nix' 'fcc' 12. 28 58.71 -4.99 2.64 1.50 4.50 1.50 3.52 4.45 1.10 -1.0 0.00 0.000 3.683 1.0 1 -'Ni' 'fcc' 12. 28 58.71 -4.99 3.25 0.80 4 1.50 3.52 4.45 1.07 -1.0 -4.052 13.14 3.786 1.0 1 -'Pd' 'fcc' 12. 46 106.4 -6.43230473 4.975 2.20 6 2.20 3.89 3.91 1.01 -1.0 2.33573516 1.38343023 4.47989049 1. 0 -'Pt' 'fcc' 12. 78 195.09 -6.44221724 4.673 2.20 6 2.20 3.92 5.77 1.04 -1.0 2.73335406 -1.3759593 3.29322278 1. 0 -'Al' 'fcc' 12. 13 26.9815 -4.61 2.21 2.20 6.0 2.20 4.05 3.58 1.07 -1.0 -1.78 -2.21 8.01 0.6 0 -'Al' 'fcc' 12. 13 26.9815 -4.69 1.56 4.00 5.5 0.60 4.05 3.36 1.09 -1.0 -0.251 -3.450 8.298 0.6 1 -'Al' 'fcc' 12. 13 26.9815 -4.69 1.58 1.00 6.0 0.60 4.05 3.36 1.09 -1.0 -0.808 -2.614 8.298 0.6 1 -'Pb' 'fcc' 12. 82 207.19 -6.0564428 5.306 2.20 6 2.20 4.95 2.04 1.01 -1.0 2.74022352 3.06323991 1.2 1. 0 -'Rh' 'fcc' 12. 45 102.905 -6.0045385 1.131 1.00 2 1.00 3.8 5.75 1.05 -1.0 2.9900 4.60231784 4.8 1. 0 -'Ir' 'fcc' 12. 77 192.2 -6.52315787 1.13 1.00 2 1.00 3.84 6.93 1.05 -1.0 1.50000 8.09942666 4.8 1. 0 -'Li' 'bcc' 8. 3 6.939 -2.97244804 1.425 1.00 1.00169907 1.00 3.509 1.65 0.87 -1.0 0.26395017 0.44431129 -0.2 1. 0 -'Na' 'bcc' 8. 11 22.9898 -3.64280541 2.313 1.00 1.00173951 1.00 4.291 1.13 0.9 -1.0 3.55398839 0.68807569 -0.2 1. 0 -'K' 'bcc' 8. 19 39.102 -3.90128376 2.687 1.00 1.00186667 1.00 5.344 0.94 0.92 -1.0 5.09756981 0.69413264 -0.2 1. 0 -'V' 'bcc' 8. 23 50.942 -4.83265262 4.113 1.00 1.00095022 1.00 3.04 5.3 1 -1.0 4.20161301 4.09946561 -1 1. 0 -'Nb' 'bcc' 8. 41 92.906 -4.79306197 4.374 1.00 1.00101441 1.00 3.301 7.47 1 -1.0 3.75762849 3.82514598 -1 1. 0 -'Ta' 'bcc' 8. 73 180.948 -4.89528669 3.709 1.00 1.00099783 1.00 3.303 8.09 0.99 -1.0 6.08617812 3.35255804 -2.9 1. 0 -'Cr' 'bcc' 8. 24 51.996 -5.12169218 3.224 1.00 1.00048646 1.00 2.885 4.1 0.94 -1.0 -0.207535 12.2600006 -1.9 1. 0 -'Mo' 'bcc' 8. 42 95.94 -5.84872871 4.481 1.00 1.00065204 1.00 3.15 6.81 0.99 -1.0 3.47727181 9.48582009 -2.9 1. 0 -'W' 'bcc' 8. 74 183.85 -5.62777409 3.978 1.00 1.00065894 1.00 3.165 8.66 0.98 -1.0 3.16353338 8.24586928 -2.7 1. 0 -'WL' 'bcc' 8 74 183.85 -5.6831 6.54 1 1 1 3.1639 8.66 0.4 -1 -0.6 0.3 -8.7 1 3 -'Fe' 'bcc' 8. 26 55.847 -5.07292627 2.935 1.00 1.00080073 1.00 2.866 4.29 0.89 -1.0 5.13579244 4.12042448 -2.7 1. 0 -'Si' 'dia' 4. 14 28.086 -4.87 4.8 4.8 4.8 4.8 5.431 4.63 1. -1.0 3.30 5.105 -0.80 1. 1 -'Si97' 'dia' 4. 14 28.086 -4.87 4.4 5.5 5.5 5.5 5.431 4.63 1. -1.0 3.13 4.47 -1.80 2.05 0 -'Si92' 'dia' 4. 14 28.086 -4.87 4.4 5.5 5.5 5.5 5.431 4.63 1. -1.0 3.13 4.47 -1.80 2.35 0 -'Six' 'dia' 4 14 28.086 -4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.0 -1.0 2.05 4.47 -1.8 2.05 0 -'Sixb' 'dia' 4 14 28.086 -4.87 4.4 5.5 5.5 5.5 5.431 4.63 1.0 -1.0 2.05 4.47 -1.8 2.5 0 -'Mg' 'hcp' 12. 12 24.305 -5.45 2.70 0.0 0.35 3.0 3.20 1.55 1.11 -1.0 8.00 04.1 -02.0 1.0 0 -'C' 'dia' 4. 6 12.0111 -4.38 4.10 4.200 5.00 3.00 3.567 7.37 1.000 -1.0 5.0 9.34 -1.00 2.25 1 -'C' 'dia' 4. 6 12.0111 -4.38 5.20 3.87 4.00 4.50 3.567 7.37 1.278 -1.0 15. 2.09 -6.00 2.5 1 -'C' 'dia' 4. 6 12.0111 -4.38 4.50 4.00 3.50 4.80 3.567 7.37 1.00 -1.0 10.5 1.54 -8.75 3.2 1 -'C' 'dia' 4. 6 12.0111 -4.38 3.30 2.80 1.50 3.20 3.567 7.37 1.00 -1.0 10.3 1.54 -8.80 2.5 1 -'C' 'dia' 4. 6 12.0111 -4.38 4.60 3.45 4.00 4.20 3.567 7.37 1.061 -1.0 15.0 1.74 -8.00 2.5 1 -'C' 'dia' 4. 6 12.0111 -4.38 4.50 4.00 3.50 4.80 3.567 7.37 1.00 -1.0 10.5 1.54 -8.75 3.2 1 -'h' 'dim' 1. 1 1.0079 -2.96 2.70 3.5 3.4 3.4 0.74 2.235 2.27 -1.0 0.19 0.00 0.00 20.00 0 -'h' 'dim' 1. 1 1.0079 -2.96 2.00 4.0 4.0 0.0 0.74 2.235 1.00 -1.0 -0.60 -0.80 -0.0 01.0 1 -'H' 'dim' 1. 1 1.0079 -2.96 2.96 3.0 3.0 3.0 0.74 2.235 2.50 -1.0 0.20 -0.10 0.0 0.5 0 -'H' 'dim' 1. 1 1.0079 -2.96 2.0 3.0 4.0 0.0 0.74 2.225 1.00 -1.0 -0.5 -1.00 0.0 0.15 1 -'H' 'dim' 1. 1 1.0079 -2.96 2.00 2.0 2.0 2.0 0.74 2.235 1.00 -1.0 -0.60 -0.80 -0.0 01.0 2 -'Hni' 'dim' 1. 1 1.0079 -2.96 2.96 3.0 3.0 3.0 0.74 2.235 2.50 -1.0 0.2 -0.1 0.0 0.5 0 -'Hni' 'dim' 1. 1 1.0079 -2.96 2.96 3.0 2.0 3.0 0.74 2.235 36.4 -1.0 0.2 6.0 0.0 22.8 0 -'Vac' 'fcc' 12. 1 1. -0 0 0.0 0 0.0 1E+08 0 1 -0 0 0 0 1. 0 -'zz' 'zzz' 99. 1 1. -0 0 0.0 0 0.0 0. 0. 0. -0 0 0 0 1. 0 - diff --git a/examples/meam/library.meam b/examples/meam/library.meam new file mode 120000 index 0000000000..86fb601d6b --- /dev/null +++ b/examples/meam/library.meam @@ -0,0 +1 @@ +../../potentials/library.meam \ No newline at end of file diff --git a/examples/meam/log.19May17.meam.g++.1 b/examples/meam/log.19May17.meam.g++.1 deleted file mode 100644 index a98de97f8e..0000000000 --- a/examples/meam/log.19May17.meam.g++.1 +++ /dev/null @@ -1,95 +0,0 @@ -LAMMPS (19 May 2017) - using 1 OpenMP thread(s) per MPI task -# Test of MEAM potential for SiC system - -units metal -boundary p p p - -atom_style atomic - -read_data data.meam - orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 128 atoms - -pair_style meam -pair_coeff * * library.meam Si C SiC.meam Si C -Reading potential file library.meam with DATE: 2012-06-29 -Reading potential file SiC.meam with DATE: 2007-06-11 - -neighbor 0.3 bin -neigh_modify delay 10 - -fix 1 all nve -thermo 10 -timestep 0.001 - -#dump 1 all atom 50 dump.meam - -#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 element Si C - -#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 element Si C - -run 100 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.3 - ghost atom cutoff = 4.3 - binsize = 2.15, bins = 6 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -636.38121 0 -636.38121 -76571.819 - 10 1807.8862 -666.21959 0 -636.54126 -150571.49 - 20 1932.4467 -668.2581 0 -636.53498 -120223.52 - 30 1951.3652 -668.58139 0 -636.54771 -100508.4 - 40 2172.5974 -672.22715 0 -636.5617 -110753.34 - 50 2056.9149 -670.33108 0 -636.56468 -105418.07 - 60 1947.9564 -668.52788 0 -636.55015 -111413.04 - 70 1994.7712 -669.28849 0 -636.54225 -109645.76 - 80 2126.0903 -671.43755 0 -636.53557 -97475.831 - 90 2065.755 -670.4349 0 -636.52338 -95858.837 - 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.0864418 on 1 procs for 100 steps with 128 atoms - -Performance: 99.952 ns/day, 0.240 hours/ns, 1156.848 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.082592 | 0.082592 | 0.082592 | 0.0 | 95.55 -Neigh | 0.0028124 | 0.0028124 | 0.0028124 | 0.0 | 3.25 -Comm | 0.00049043 | 0.00049043 | 0.00049043 | 0.0 | 0.57 -Output | 0.00014329 | 0.00014329 | 0.00014329 | 0.0 | 0.17 -Modify | 0.00025415 | 0.00025415 | 0.00025415 | 0.0 | 0.29 -Other | | 0.0001497 | | | 0.17 - -Nlocal: 128 ave 128 max 128 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 543 ave 543 max 543 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1526 ave 1526 max 1526 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 3052 ave 3052 max 3052 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3052 -Ave neighs/atom = 23.8438 -Neighbor list builds = 10 -Dangerous builds = 10 -Total wall time: 0:00:00 diff --git a/examples/meam/log.19May17.meam.g++.4 b/examples/meam/log.19May17.meam.g++.4 deleted file mode 100644 index adc34d08aa..0000000000 --- a/examples/meam/log.19May17.meam.g++.4 +++ /dev/null @@ -1,95 +0,0 @@ -LAMMPS (19 May 2017) - using 1 OpenMP thread(s) per MPI task -# Test of MEAM potential for SiC system - -units metal -boundary p p p - -atom_style atomic - -read_data data.meam - orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 128 atoms - -pair_style meam -pair_coeff * * library.meam Si C SiC.meam Si C -Reading potential file library.meam with DATE: 2012-06-29 -Reading potential file SiC.meam with DATE: 2007-06-11 - -neighbor 0.3 bin -neigh_modify delay 10 - -fix 1 all nve -thermo 10 -timestep 0.001 - -#dump 1 all atom 50 dump.meam - -#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 element Si C - -#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 element Si C - -run 100 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.3 - ghost atom cutoff = 4.3 - binsize = 2.15, bins = 6 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -636.38121 0 -636.38121 -76571.819 - 10 1807.8862 -666.21959 0 -636.54126 -150571.49 - 20 1932.4467 -668.2581 0 -636.53498 -120223.52 - 30 1951.3652 -668.58139 0 -636.54771 -100508.4 - 40 2172.5974 -672.22715 0 -636.5617 -110753.34 - 50 2056.9149 -670.33108 0 -636.56468 -105418.07 - 60 1947.9564 -668.52788 0 -636.55015 -111413.04 - 70 1994.7712 -669.28849 0 -636.54225 -109645.76 - 80 2126.0903 -671.43755 0 -636.53557 -97475.831 - 90 2065.755 -670.4349 0 -636.52338 -95858.837 - 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.0389078 on 4 procs for 100 steps with 128 atoms - -Performance: 222.063 ns/day, 0.108 hours/ns, 2570.177 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.031958 | 0.033267 | 0.034691 | 0.6 | 85.50 -Neigh | 0.00079155 | 0.00086409 | 0.00098801 | 0.0 | 2.22 -Comm | 0.0025704 | 0.0041765 | 0.005573 | 1.9 | 10.73 -Output | 0.0002749 | 0.00029588 | 0.00033569 | 0.0 | 0.76 -Modify | 9.4891e-05 | 0.00010347 | 0.00011587 | 0.0 | 0.27 -Other | | 0.000201 | | | 0.52 - -Nlocal: 32 ave 36 max 30 min -Histogram: 1 2 0 0 0 0 0 0 0 1 -Nghost: 293.75 ave 305 max 285 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Neighs: 381.5 ave 413 max 334 min -Histogram: 1 0 0 0 1 0 0 0 0 2 -FullNghs: 763 ave 866 max 678 min -Histogram: 1 0 1 0 0 1 0 0 0 1 - -Total # of neighbors = 3052 -Ave neighs/atom = 23.8438 -Neighbor list builds = 10 -Dangerous builds = 10 -Total wall time: 0:00:00 diff --git a/examples/meam/log.19May17.meam.shear.g++.1 b/examples/meam/log.19May17.meam.shear.g++.1 deleted file mode 100644 index 77b9688455..0000000000 --- a/examples/meam/log.19May17.meam.shear.g++.1 +++ /dev/null @@ -1,207 +0,0 @@ -LAMMPS (19 May 2017) - using 1 OpenMP thread(s) per MPI task -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -Lattice spacing in x,y,z = 3.52 3.52 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box -Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) - 1 by 1 by 1 MPI processor grid - -lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 -Lattice spacing in x,y,z = 3.52 4.97803 4.97803 -create_atoms 1 box -Created 1912 atoms - -pair_style meam -pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 -Reading potential file library.meam with DATE: 2012-06-29 -Reading potential file Ni.meam with DATE: 2007-06-11 - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 0.9 INF INF -region upper block INF INF 6.1 INF INF INF -group lower region lower -264 atoms in group lower -group upper region upper -264 atoms in group upper -group boundary union lower upper -528 atoms in group boundary -group mobile subtract all boundary -1384 atoms in group mobile - -set group lower type 2 - 264 settings made for type -set group upper type 3 - 264 settings made for type - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -compute new3d mobile temp -compute new2d mobile temp/partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) - -timestep 0.001 -run 100 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.3 - ghost atom cutoff = 4.3 - binsize = 2.15, bins = 27 17 5 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 - 25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02 - 50 300 -8149.7654 0 -8096.1353 10633.141 19684.382 - 75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745 - 100 300 -8173.6884 0 -8120.0584 5952.521 19886.589 -Loop time of 1.58103 on 1 procs for 100 steps with 1912 atoms - -Performance: 5.465 ns/day, 4.392 hours/ns, 63.250 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.5561 | 1.5561 | 1.5561 | 0.0 | 98.42 -Neigh | 0.018544 | 0.018544 | 0.018544 | 0.0 | 1.17 -Comm | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 0.09 -Output | 0.00011396 | 0.00011396 | 0.00011396 | 0.0 | 0.01 -Modify | 0.0038245 | 0.0038245 | 0.0038245 | 0.0 | 0.24 -Other | | 0.001096 | | | 0.07 - -Nlocal: 1912 ave 1912 max 1912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1672 ave 1672 max 1672 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23806 ave 23806 max 23806 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 47612 ave 47612 max 47612 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 47612 -Ave neighs/atom = 24.9017 -Neighbor list builds = 5 -Dangerous builds = 0 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -#dump 1 all atom 500 dump.meam.shear - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 2 pad 4 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 3 pad 4 - -thermo 100 -thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) - -reset_timestep 0 -run 3000 -Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297 - 100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53 - 200 306.69894 -8177.1357 0 -8140.584 874.24259 20047.24 - 300 295.68229 -8172.9213 0 -8137.6825 -1049.0836 20091.759 - 400 308.99958 -8169.6355 0 -8132.8096 -1785.9335 20121.698 - 500 303.85723 -8163.984 0 -8127.7709 -150.56268 20183.813 - 600 300 -8157.7632 0 -8122.0099 1492.5742 20279.887 - 700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302 - 800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519 - 900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992 - 1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243 - 1100 304.14047 -8096.5041 0 -8060.2573 9646.6976 20888.167 - 1200 302.78457 -8080.5931 0 -8044.5079 11516.209 20995.917 - 1300 308.67054 -8061.6724 0 -8024.8857 11496.479 21130.013 - 1400 309.8301 -8046.27 0 -8009.3452 12926.835 21247.271 - 1500 300 -8035.0321 0 -7999.2788 15346.455 21370.637 - 1600 300 -8030.6657 0 -7994.9123 14802.869 21496.446 - 1700 300 -8024.5251 0 -7988.7718 13176.923 21611.262 - 1800 300 -8022.9963 0 -7987.243 10260.665 21741.956 - 1900 300 -8028.0522 0 -7992.2988 6955.1367 21867.765 - 2000 300 -8037.2708 0 -8001.5175 3520.3749 21987.467 - 2100 300 -8035.9945 0 -8000.2412 3237.6121 22109.611 - 2200 300 -8036.1882 0 -8000.4348 4295.1386 22223.205 - 2300 300 -8032.7689 0 -7997.0155 6231.2346 22355.121 - 2400 300 -8034.6621 0 -7998.9088 8585.3799 22468.716 - 2500 300 -8031.7774 0 -7996.0241 11627.871 22587.196 - 2600 300 -8024.032 0 -7988.2786 16254.69 22716.669 - 2700 308.64215 -8017.407 0 -7980.6237 18440.226 22835.149 - 2800 300 -8015.7348 0 -7979.9814 17601.716 22957.293 - 2900 305.82558 -8013.7448 0 -7977.2972 14123.494 23089.209 - 3000 300 -8011.0289 0 -7975.2755 9957.2884 23205.247 -Loop time of 51.9315 on 1 procs for 3000 steps with 1912 atoms - -Performance: 4.991 ns/day, 4.808 hours/ns, 57.768 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 50.918 | 50.918 | 50.918 | 0.0 | 98.05 -Neigh | 0.81033 | 0.81033 | 0.81033 | 0.0 | 1.56 -Comm | 0.047331 | 0.047331 | 0.047331 | 0.0 | 0.09 -Output | 0.0011976 | 0.0011976 | 0.0011976 | 0.0 | 0.00 -Modify | 0.11889 | 0.11889 | 0.11889 | 0.0 | 0.23 -Other | | 0.03606 | | | 0.07 - -Nlocal: 1912 ave 1912 max 1912 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1672 ave 1672 max 1672 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23557 ave 23557 max 23557 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 47114 ave 47114 max 47114 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 47114 -Ave neighs/atom = 24.6412 -Neighbor list builds = 221 -Dangerous builds = 0 -Total wall time: 0:00:53 diff --git a/examples/meam/log.19May17.meam.shear.g++.4 b/examples/meam/log.19May17.meam.shear.g++.4 deleted file mode 100644 index 84cb94f4b9..0000000000 --- a/examples/meam/log.19May17.meam.shear.g++.4 +++ /dev/null @@ -1,207 +0,0 @@ -LAMMPS (19 May 2017) - using 1 OpenMP thread(s) per MPI task -# 3d metal shear simulation - -units metal -boundary s s p - -atom_style atomic -lattice fcc 3.52 -Lattice spacing in x,y,z = 3.52 3.52 3.52 -region box block 0 16.0 0 10.0 0 2.828427 -create_box 3 box -Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) - 2 by 2 by 1 MPI processor grid - -lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 -Lattice spacing in x,y,z = 3.52 4.97803 4.97803 -create_atoms 1 box -Created 1912 atoms - -pair_style meam -pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 -Reading potential file library.meam with DATE: 2012-06-29 -Reading potential file Ni.meam with DATE: 2007-06-11 - -neighbor 0.3 bin -neigh_modify delay 5 - -region lower block INF INF INF 0.9 INF INF -region upper block INF INF 6.1 INF INF INF -group lower region lower -264 atoms in group lower -group upper region upper -264 atoms in group upper -group boundary union lower upper -528 atoms in group boundary -group mobile subtract all boundary -1384 atoms in group mobile - -set group lower type 2 - 264 settings made for type -set group upper type 3 - 264 settings made for type - -# void - -#region void cylinder z 8 5 2.5 INF INF -#delete_atoms region void - -# temp controllers - -compute new3d mobile temp -compute new2d mobile temp/partial 0 1 1 - -# equilibrate - -velocity mobile create 300.0 5812775 temp new3d -fix 1 all nve -fix 2 boundary setforce 0.0 0.0 0.0 - -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new3d - -thermo 25 -thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) - -timestep 0.001 -run 100 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 4.3 - ghost atom cutoff = 4.3 - binsize = 2.15, bins = 27 17 5 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair meam, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - bin: standard - (2) pair meam, perpetual, half/full from (1) - attributes: half, newton on - pair build: halffull/newton - stencil: none - bin: none -Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 - 25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02 - 50 300 -8150.0685 0 -8096.4384 10317.407 19685.743 - 75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814 - 100 300 -8176.5141 0 -8122.884 4162.2559 19873.327 -Loop time of 0.482293 on 4 procs for 100 steps with 1912 atoms - -Performance: 17.914 ns/day, 1.340 hours/ns, 207.343 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.44374 | 0.45604 | 0.46922 | 1.4 | 94.56 -Neigh | 0.0047338 | 0.0049097 | 0.0051899 | 0.2 | 1.02 -Comm | 0.0054841 | 0.019044 | 0.031472 | 6.9 | 3.95 -Output | 0.00012755 | 0.00013644 | 0.00015831 | 0.0 | 0.03 -Modify | 0.0011139 | 0.0011852 | 0.0012643 | 0.2 | 0.25 -Other | | 0.0009753 | | | 0.20 - -Nlocal: 478 ave 492 max 465 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 809 ave 822 max 795 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 5916 ave 6133 max 5658 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -FullNghs: 11832 ave 12277 max 11299 min -Histogram: 1 0 0 1 0 0 0 0 1 1 - -Total # of neighbors = 47328 -Ave neighs/atom = 24.7531 -Neighbor list builds = 5 -Dangerous builds = 0 - -# shear - -velocity upper set 1.0 0 0 -velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes - -unfix 3 -fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 -fix_modify 3 temp new2d - -#dump 1 all atom 500 dump.meam.shear - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 2 pad 4 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 -#dump_modify 3 pad 4 - -thermo 100 -thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) - -reset_timestep 0 -run 3000 -Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93 - 100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765 - 200 306.11682 -8176.7719 0 -8140.2895 -1370.6886 19948.877 - 300 300 -8172.6262 0 -8136.8729 -1735.9765 20085.714 - 400 306.88489 -8168.435 0 -8131.8611 -933.02058 20117.012 - 500 308.99003 -8166.2906 0 -8129.4658 -1049.3138 20198.256 - 600 304.23435 -8158.0946 0 -8121.8366 583.93595 20328.848 - 700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046 - 800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183 - 900 304.61422 -8126.9246 0 -8090.6214 6654.0963 20640.213 - 1000 300 -8113.8464 0 -8078.0931 7760.1239 20768.465 - 1100 300.17873 -8097.7469 0 -8061.9722 8438.126 20874.731 - 1200 306.01441 -8083.3367 0 -8046.8665 10835.586 20994.432 - 1300 300 -8067.022 0 -8031.2686 11216.067 21126.348 - 1400 300 -8053.223 0 -8017.4697 10570.206 21253.378 - 1500 300 -8043.4849 0 -8007.7315 11360.766 21375.523 - 1600 300 -8034.621 0 -7998.8676 11371.584 21498.889 - 1700 300 -8028.6783 0 -7992.925 9596.524 21613.705 - 1800 300 -8033.0818 0 -7997.3285 8767.2651 21743.178 - 1900 303.18912 -8035.194 0 -7999.0606 8059.9558 21859.215 - 2000 300 -8025.0327 0 -7989.2794 9305.7521 21980.138 - 2100 300 -8041.4626 0 -8005.7092 6623.8789 22108.39 - 2200 300 -8040.3133 0 -8004.5599 7512.9368 22225.648 - 2300 300 -8055.6567 0 -8019.9033 8281.354 22344.128 - 2400 304.05922 -8050.289 0 -8014.0518 11964.826 22476.044 - 2500 305.75646 -8037.0481 0 -8000.6087 16594.032 22595.746 - 2600 307.71105 -8031.2253 0 -7994.5529 18381.745 22708.119 - 2700 307.397 -8026.5338 0 -7989.8988 13944.653 22829.042 - 2800 309.3455 -8020.2305 0 -7983.3634 7037.4046 22954.851 - 2900 301.2859 -8010.4731 0 -7974.5665 3843.8972 23072.109 - 3000 303.29908 -8000.0395 0 -7963.8929 364.90172 23207.69 -Loop time of 14.5278 on 4 procs for 3000 steps with 1912 atoms - -Performance: 17.842 ns/day, 1.345 hours/ns, 206.500 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 13.872 | 13.929 | 13.998 | 1.4 | 95.88 -Neigh | 0.20891 | 0.21114 | 0.21272 | 0.3 | 1.45 -Comm | 0.25364 | 0.32377 | 0.37706 | 8.9 | 2.23 -Output | 0.0011427 | 0.0012097 | 0.0013931 | 0.3 | 0.01 -Modify | 0.033687 | 0.033991 | 0.034694 | 0.2 | 0.23 -Other | | 0.02871 | | | 0.20 - -Nlocal: 478 ave 509 max 445 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Nghost: 804 ave 845 max 759 min -Histogram: 1 1 0 0 0 0 0 0 1 1 -Neighs: 5827 ave 6177 max 5496 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -FullNghs: 11654 ave 12330 max 11039 min -Histogram: 1 0 0 1 0 1 0 0 0 1 - -Total # of neighbors = 46616 -Ave neighs/atom = 24.3808 -Neighbor list builds = 223 -Dangerous builds = 0 -Total wall time: 0:00:15 diff --git a/examples/meam/log.19May17.meamc.g++.1 b/examples/meam/log.27Nov18.meamc.g++.1 similarity index 83% rename from examples/meam/log.19May17.meamc.g++.1 rename to examples/meam/log.27Nov18.meamc.g++.1 index 4aa1f7bcc3..2fcd24077b 100644 --- a/examples/meam/log.19May17.meamc.g++.1 +++ b/examples/meam/log.27Nov18.meamc.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (19 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system @@ -64,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press 80 2126.0903 -671.43755 0 -636.53557 -97475.832 90 2065.7549 -670.4349 0 -636.52338 -95858.836 100 2051.4553 -670.20799 0 -636.53122 -107068.89 -Loop time of 0.0778153 on 1 procs for 100 steps with 128 atoms +Loop time of 0.0780671 on 1 procs for 100 steps with 128 atoms -Performance: 111.032 ns/day, 0.216 hours/ns, 1285.094 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 110.674 ns/day, 0.217 hours/ns, 1280.950 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.073801 | 0.073801 | 0.073801 | 0.0 | 94.84 -Neigh | 0.0029731 | 0.0029731 | 0.0029731 | 0.0 | 3.82 -Comm | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.61 -Output | 0.00015664 | 0.00015664 | 0.00015664 | 0.0 | 0.20 -Modify | 0.00025702 | 0.00025702 | 0.00025702 | 0.0 | 0.33 -Other | | 0.0001504 | | | 0.19 +Pair | 0.074199 | 0.074199 | 0.074199 | 0.0 | 95.05 +Neigh | 0.0026548 | 0.0026548 | 0.0026548 | 0.0 | 3.40 +Comm | 0.00068045 | 0.00068045 | 0.00068045 | 0.0 | 0.87 +Output | 0.00020933 | 0.00020933 | 0.00020933 | 0.0 | 0.27 +Modify | 0.00021243 | 0.00021243 | 0.00021243 | 0.0 | 0.27 +Other | | 0.0001111 | | | 0.14 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/meam/log.19May17.meamc.g++.4 b/examples/meam/log.27Nov18.meamc.g++.4 similarity index 83% rename from examples/meam/log.19May17.meamc.g++.4 rename to examples/meam/log.27Nov18.meamc.g++.4 index 3701fb80d8..b97f18b25c 100644 --- a/examples/meam/log.19May17.meamc.g++.4 +++ b/examples/meam/log.27Nov18.meamc.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (19 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system @@ -64,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press 80 2126.0903 -671.43755 0 -636.53557 -97475.832 90 2065.7549 -670.4349 0 -636.52338 -95858.836 100 2051.4553 -670.20799 0 -636.53122 -107068.89 -Loop time of 0.037066 on 4 procs for 100 steps with 128 atoms +Loop time of 0.0317811 on 4 procs for 100 steps with 128 atoms -Performance: 233.097 ns/day, 0.103 hours/ns, 2697.887 timesteps/s -97.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 271.859 ns/day, 0.088 hours/ns, 3146.521 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.029985 | 0.031596 | 0.033021 | 0.8 | 85.24 -Neigh | 0.0007906 | 0.00085384 | 0.00088596 | 0.0 | 2.30 -Comm | 0.0025654 | 0.0040313 | 0.0057514 | 2.2 | 10.88 -Output | 0.00027013 | 0.00029153 | 0.00033426 | 0.0 | 0.79 -Modify | 9.5367e-05 | 0.00010639 | 0.00012016 | 0.0 | 0.29 -Other | | 0.0001866 | | | 0.50 +Pair | 0.027395 | 0.027726 | 0.028188 | 0.2 | 87.24 +Neigh | 0.00073433 | 0.00077397 | 0.00084281 | 0.0 | 2.44 +Comm | 0.0024559 | 0.0028514 | 0.003237 | 0.5 | 8.97 +Output | 0.00018358 | 0.00020361 | 0.00026178 | 0.0 | 0.64 +Modify | 8.44e-05 | 9.0241e-05 | 9.5129e-05 | 0.0 | 0.28 +Other | | 0.0001359 | | | 0.43 Nlocal: 32 ave 36 max 30 min Histogram: 1 2 0 0 0 0 0 0 0 1 diff --git a/examples/meam/log.19May17.meamc.shear.g++.1 b/examples/meam/log.27Nov18.meamc.shear.g++.1 similarity index 61% rename from examples/meam/log.19May17.meamc.shear.g++.1 rename to examples/meam/log.27Nov18.meamc.shear.g++.1 index 5eb06592d8..4aff7d2399 100644 --- a/examples/meam/log.19May17.meamc.shear.g++.1 +++ b/examples/meam/log.27Nov18.meamc.shear.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (19 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation @@ -17,6 +17,7 @@ lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms + Time spent = 0.000667334 secs pair_style meam/c pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 @@ -63,7 +64,7 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 @@ -91,20 +92,20 @@ Step Temp E_pair E_mol TotEng Press Volume 50 300 -8149.7654 0 -8096.1353 10633.139 19684.382 75 304.80657 -8163.4557 0 -8108.9665 7045.4555 19759.745 100 300 -8173.6884 0 -8120.0584 5952.5197 19886.589 -Loop time of 1.46986 on 1 procs for 100 steps with 1912 atoms +Loop time of 1.24344 on 1 procs for 100 steps with 1912 atoms -Performance: 5.878 ns/day, 4.083 hours/ns, 68.034 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 6.948 ns/day, 3.454 hours/ns, 80.422 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.445 | 1.445 | 1.445 | 0.0 | 98.31 -Neigh | 0.018564 | 0.018564 | 0.018564 | 0.0 | 1.26 -Comm | 0.0012956 | 0.0012956 | 0.0012956 | 0.0 | 0.09 -Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.01 -Modify | 0.0038197 | 0.0038197 | 0.0038197 | 0.0 | 0.26 -Other | | 0.001095 | | | 0.07 +Pair | 1.2191 | 1.2191 | 1.2191 | 0.0 | 98.05 +Neigh | 0.017918 | 0.017918 | 0.017918 | 0.0 | 1.44 +Comm | 0.0016081 | 0.0016081 | 0.0016081 | 0.0 | 0.13 +Output | 0.00010872 | 0.00010872 | 0.00010872 | 0.0 | 0.01 +Modify | 0.0035257 | 0.0035257 | 0.0035257 | 0.0 | 0.28 +Other | | 0.001145 | | | 0.09 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -139,7 +140,7 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 @@ -155,53 +156,53 @@ Step Temp E_pair E_mol TotEng Press Volume 700 300 -8148.1314 0 -8112.3781 3507.1949 20435.297 800 300 -8139.1805 0 -8103.4272 3628.5908 20509.519 900 305.03217 -8126.7741 0 -8090.421 5313.7881 20638.992 - 1000 303.7648 -8112.1574 0 -8075.9554 7433.3181 20767.243 - 1100 302.39719 -8096.1399 0 -8060.1009 9681.7685 20888.167 - 1200 304.04919 -8080.7022 0 -8044.4663 11621.974 21011.532 - 1300 303.56395 -8062.0984 0 -8025.9203 11410.793 21125.127 - 1400 309.92338 -8046.0008 0 -8009.0648 12408.158 21246.05 - 1500 300 -8034.7094 0 -7998.956 14845.312 21363.308 - 1600 300 -8028.4585 0 -7992.7051 15120.908 21489.117 - 1700 308.23904 -8015.9618 0 -7979.2265 14714.73 21612.483 - 1800 300 -8013.5458 0 -7977.7924 11955.065 21737.07 - 1900 300 -8012.2984 0 -7976.545 6667.1353 21854.329 - 2000 300 -8025.6019 0 -7989.8485 2006.6545 21981.359 - 2100 300 -8027.6823 0 -7991.9289 16.47633 22109.611 - 2200 300 -8029.6905 0 -7993.9372 -603.98293 22224.427 - 2300 300 -8033.2663 0 -7997.513 -464.68645 22351.457 - 2400 300 -8040.6863 0 -8004.9329 -640.54641 22467.494 - 2500 300 -8037.0332 0 -8001.2799 1504.2444 22587.196 - 2600 300 -8036.0909 0 -8000.3375 4190.2052 22708.119 - 2700 308.97892 -8028.5269 0 -7991.7035 5755.7418 22832.706 - 2800 305.27189 -8023.8286 0 -7987.4469 2611.7551 22962.179 - 2900 301.94251 -8017.4523 0 -7981.4675 358.11928 23078.216 - 3000 305.67682 -8009.853 0 -7973.4231 -2345.487 23197.918 -Loop time of 48.351 on 1 procs for 3000 steps with 1912 atoms + 1000 303.7648 -8112.1574 0 -8075.9554 7433.3182 20767.243 + 1100 302.39719 -8096.1399 0 -8060.1009 9681.7687 20888.167 + 1200 304.0492 -8080.7022 0 -8044.4663 11621.974 21011.532 + 1300 303.56399 -8062.0984 0 -8025.9203 11410.792 21125.127 + 1400 309.92342 -8046.0009 0 -8009.0649 12408.16 21246.05 + 1500 300 -8034.7095 0 -7998.9562 14845.279 21363.308 + 1600 300 -8028.4584 0 -7992.7051 15120.946 21489.117 + 1700 308.24098 -8015.9617 0 -7979.2262 14714.985 21612.483 + 1800 300 -8013.5445 0 -7977.7911 11955.097 21737.07 + 1900 300 -8012.2934 0 -7976.5401 6668.5401 21854.329 + 2000 300 -8025.5575 0 -7989.8041 1991.1401 21981.359 + 2100 300 -8027.6564 0 -7991.9031 15.137723 22109.611 + 2200 300 -8029.7898 0 -7994.0364 -583.82386 22225.648 + 2300 300 -8033.278 0 -7997.5247 -657.14777 22344.128 + 2400 300 -8040.6711 0 -8004.9178 -826.53135 22473.601 + 2500 300 -8037.7007 0 -8001.9473 547.23901 22594.524 + 2600 306.30094 -8036.6072 0 -8000.1029 2870.9529 22721.555 + 2700 309.00737 -8033.9906 0 -7997.1638 4440.4698 22832.706 + 2800 300 -8030.7816 0 -7995.0282 1519.7066 22956.072 + 2900 307.99687 -8026.5913 0 -7989.8849 -1143.0985 23089.209 + 3000 300 -8021.6011 0 -7985.8477 -4089.7884 23199.139 +Loop time of 40.4198 on 1 procs for 3000 steps with 1912 atoms -Performance: 5.361 ns/day, 4.477 hours/ns, 62.046 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 6.413 ns/day, 3.743 hours/ns, 74.221 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 47.356 | 47.356 | 47.356 | 0.0 | 97.94 -Neigh | 0.79977 | 0.79977 | 0.79977 | 0.0 | 1.65 -Comm | 0.043133 | 0.043133 | 0.043133 | 0.0 | 0.09 -Output | 0.0011899 | 0.0011899 | 0.0011899 | 0.0 | 0.00 -Modify | 0.11648 | 0.11648 | 0.11648 | 0.0 | 0.24 -Other | | 0.03404 | | | 0.07 +Pair | 39.44 | 39.44 | 39.44 | 0.0 | 97.58 +Neigh | 0.78059 | 0.78059 | 0.78059 | 0.0 | 1.93 +Comm | 0.0537 | 0.0537 | 0.0537 | 0.0 | 0.13 +Output | 0.00090766 | 0.00090766 | 0.00090766 | 0.0 | 0.00 +Modify | 0.1089 | 0.1089 | 0.1089 | 0.0 | 0.27 +Other | | 0.03561 | | | 0.09 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1662 ave 1662 max 1662 min +Nghost: 1658 ave 1658 max 1658 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23143 ave 23143 max 23143 min +Neighs: 23146 ave 23146 max 23146 min Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 46286 ave 46286 max 46286 min +FullNghs: 46292 ave 46292 max 46292 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 46286 -Ave neighs/atom = 24.2082 -Neighbor list builds = 220 +Total # of neighbors = 46292 +Ave neighs/atom = 24.2113 +Neighbor list builds = 222 Dangerous builds = 0 -Total wall time: 0:00:49 +Total wall time: 0:00:41 diff --git a/examples/meam/log.19May17.meamc.shear.g++.4 b/examples/meam/log.27Nov18.meamc.shear.g++.4 similarity index 61% rename from examples/meam/log.19May17.meamc.shear.g++.4 rename to examples/meam/log.27Nov18.meamc.shear.g++.4 index 136459a44a..702e13f554 100644 --- a/examples/meam/log.19May17.meamc.shear.g++.4 +++ b/examples/meam/log.27Nov18.meamc.shear.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (19 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation @@ -17,6 +17,7 @@ lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms + Time spent = 0.000405788 secs pair_style meam/c pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 @@ -63,7 +64,7 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 @@ -91,20 +92,20 @@ Step Temp E_pair E_mol TotEng Press Volume 50 300 -8150.0685 0 -8096.4384 10317.406 19685.743 75 307.76021 -8164.6669 0 -8109.6496 6289.7123 19757.814 100 300 -8176.5141 0 -8122.884 4162.2548 19873.327 -Loop time of 0.435874 on 4 procs for 100 steps with 1912 atoms +Loop time of 0.360204 on 4 procs for 100 steps with 1912 atoms -Performance: 19.822 ns/day, 1.211 hours/ns, 229.424 timesteps/s -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 23.986 ns/day, 1.001 hours/ns, 277.621 timesteps/s +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.4092 | 0.41563 | 0.42184 | 0.7 | 95.35 -Neigh | 0.0048575 | 0.004932 | 0.0049984 | 0.1 | 1.13 -Comm | 0.0069079 | 0.013151 | 0.019513 | 4.2 | 3.02 -Output | 0.00012398 | 0.00013405 | 0.00015688 | 0.0 | 0.03 -Modify | 0.0011275 | 0.0011509 | 0.0011735 | 0.1 | 0.26 -Other | | 0.0008795 | | | 0.20 +Pair | 0.33423 | 0.33889 | 0.34311 | 0.7 | 94.08 +Neigh | 0.0045969 | 0.004706 | 0.0048506 | 0.1 | 1.31 +Comm | 0.010211 | 0.014394 | 0.019267 | 3.4 | 4.00 +Output | 0.00011277 | 0.00017589 | 0.00036049 | 0.0 | 0.05 +Modify | 0.0010302 | 0.0010442 | 0.0010614 | 0.0 | 0.29 +Other | | 0.0009908 | | | 0.28 Nlocal: 478 ave 492 max 465 min Histogram: 2 0 0 0 0 0 0 0 1 1 @@ -139,7 +140,7 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 @@ -156,52 +157,52 @@ Step Temp E_pair E_mol TotEng Press Volume 800 307.88628 -8139.1709 0 -8102.4776 4311.4142 20513.183 900 303.37209 -8126.9382 0 -8090.7829 6712.7316 20640.213 1000 300 -8113.7973 0 -8078.044 7630.2594 20750.143 - 1100 300.07815 -8098.1383 0 -8062.3756 8423.7063 20879.616 + 1100 300.07815 -8098.1383 0 -8062.3756 8423.7061 20879.616 1200 300 -8083.3163 0 -8047.563 10772.917 21000.539 - 1300 300 -8066.6741 0 -8030.9208 10834.336 21128.791 - 1400 300 -8050.8799 0 -8015.1265 10842.382 21257.043 - 1500 300 -8040.3206 0 -8004.5673 11852.589 21362.087 - 1600 300 -8033.2471 0 -7997.4937 11298.745 21492.782 - 1700 300 -8030.6375 0 -7994.8842 10850.43 21610.04 - 1800 300 -8035.1631 0 -7999.4097 9985.6107 21734.628 - 1900 308.56562 -8040.1954 0 -8003.4213 9865.7107 21859.215 - 2000 300 -8030.1651 0 -7994.4117 11817.502 21980.138 - 2100 300 -8031.6147 0 -7995.8613 12791.357 22101.061 - 2200 300 -8033.7793 0 -7998.0259 13823.043 22234.198 - 2300 300 -8040.5964 0 -8004.8431 16204.549 22350.236 - 2400 309.42867 -8045.9414 0 -8009.0644 18506.386 22465.051 - 2500 300 -8054.2629 0 -8018.5095 20099.612 22593.303 - 2600 300 -8054.9562 0 -8019.2028 20036.318 22721.555 - 2700 300 -8051.4788 0 -8015.7254 16993.437 22844.921 - 2800 300 -8050.6908 0 -8014.9374 9048.5896 22964.622 - 2900 309.90783 -8044.3096 0 -8007.3754 5017.0198 23080.659 - 3000 300 -8035.8165 0 -8000.0632 2084.8999 23207.69 -Loop time of 13.4901 on 4 procs for 3000 steps with 1912 atoms + 1300 300 -8066.6742 0 -8030.9208 10834.324 21128.791 + 1400 300 -8050.8799 0 -8015.1265 10842.369 21257.043 + 1500 300 -8040.3207 0 -8004.5673 11852.581 21362.087 + 1600 300 -8033.2463 0 -7997.493 11298.907 21492.782 + 1700 300 -8030.6375 0 -7994.8841 10850.25 21610.04 + 1800 300 -8035.1637 0 -7999.4104 9985.4993 21734.628 + 1900 308.60398 -8040.1957 0 -8003.417 9865.6907 21859.215 + 2000 300 -8030.1598 0 -7994.4064 11817.286 21980.138 + 2100 300 -8031.581 0 -7995.8276 12782.733 22101.061 + 2200 300 -8033.981 0 -7998.2276 13853.626 22220.762 + 2300 300 -8040.0125 0 -8004.2591 16329.98 22350.236 + 2400 308.4546 -8046.1468 0 -8009.3859 18839.675 22467.494 + 2500 300 -8051.022 0 -8015.2686 19977.441 22598.189 + 2600 300 -8049.9219 0 -8014.1686 20982.796 22720.333 + 2700 300 -8047.5121 0 -8011.7587 17432.464 22833.928 + 2800 300 -8047.4546 0 -8011.7013 10733.925 22967.065 + 2900 303.07072 -8039.2015 0 -8003.0822 6498.2787 23079.438 + 3000 300 -8033.2092 0 -7997.4558 2413.3858 23210.132 +Loop time of 11.5481 on 4 procs for 3000 steps with 1912 atoms -Performance: 19.214 ns/day, 1.249 hours/ns, 222.386 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 22.445 ns/day, 1.069 hours/ns, 259.782 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 12.851 | 12.919 | 12.945 | 1.1 | 95.76 -Neigh | 0.20449 | 0.20777 | 0.21169 | 0.6 | 1.54 -Comm | 0.27479 | 0.30264 | 0.36667 | 6.8 | 2.24 -Output | 0.0010171 | 0.0010971 | 0.0012388 | 0.3 | 0.01 -Modify | 0.033248 | 0.033878 | 0.034567 | 0.3 | 0.25 -Other | | 0.02594 | | | 0.19 +Pair | 10.828 | 10.919 | 11.062 | 2.7 | 94.55 +Neigh | 0.19748 | 0.20277 | 0.20818 | 0.9 | 1.76 +Comm | 0.21506 | 0.36705 | 0.46467 | 15.6 | 3.18 +Output | 0.0008328 | 0.0015925 | 0.0038536 | 3.3 | 0.01 +Modify | 0.030773 | 0.031848 | 0.033535 | 0.6 | 0.28 +Other | | 0.02569 | | | 0.22 -Nlocal: 478 ave 506 max 450 min +Nlocal: 478 ave 499 max 457 min Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 790.5 ave 822 max 751 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 5829.5 ave 6014 max 5672 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -FullNghs: 11659 ave 12027 max 11320 min -Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 796.5 ave 832 max 755 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 5807.25 ave 5840 max 5774 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +FullNghs: 11614.5 ave 11687 max 11558 min +Histogram: 1 1 0 0 0 1 0 0 0 1 -Total # of neighbors = 46636 -Ave neighs/atom = 24.3912 -Neighbor list builds = 220 +Total # of neighbors = 46458 +Ave neighs/atom = 24.2981 +Neighbor list builds = 218 Dangerous builds = 0 -Total wall time: 0:00:13 +Total wall time: 0:00:11 diff --git a/examples/melt/log.5Oct16.melt.g++.1 b/examples/melt/log.27Nov18.melt.g++.1 similarity index 66% rename from examples/melt/log.5Oct16.melt.g++.1 rename to examples/melt/log.27Nov18.melt.g++.1 index b4aefdceb4..69b39e6011 100644 --- a/examples/melt/log.5Oct16.melt.g++.1 +++ b/examples/melt/log.27Nov18.melt.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000645638 secs mass 1 1.0 velocity all create 3.0 87287 @@ -35,13 +37,18 @@ fix 1 all nve thermo 50 run 250 Neighbor list info ... - 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 12 -Memory usage per processor = 2.19271 Mbytes + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 @@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 -Loop time of 0.724365 on 1 procs for 250 steps with 4000 atoms +Loop time of 0.729809 on 1 procs for 250 steps with 4000 atoms -Performance: 149096.106 tau/day, 345.130 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 147983.915 tau/day, 342.555 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.61654 | 0.61654 | 0.61654 | 0.0 | 85.11 -Neigh | 0.081313 | 0.081313 | 0.081313 | 0.0 | 11.23 -Comm | 0.010941 | 0.010941 | 0.010941 | 0.0 | 1.51 -Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.01 -Modify | 0.012401 | 0.012401 | 0.012401 | 0.0 | 1.71 -Other | | 0.003077 | | | 0.42 +Pair | 0.60661 | 0.60661 | 0.60661 | 0.0 | 83.12 +Neigh | 0.092198 | 0.092198 | 0.092198 | 0.0 | 12.63 +Comm | 0.013581 | 0.013581 | 0.013581 | 0.0 | 1.86 +Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.02 +Modify | 0.014395 | 0.014395 | 0.014395 | 0.0 | 1.97 +Other | | 0.002878 | | | 0.39 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/melt/log.5Oct16.melt.g++.4 b/examples/melt/log.27Nov18.melt.g++.4 similarity index 66% rename from examples/melt/log.5Oct16.melt.g++.4 rename to examples/melt/log.27Nov18.melt.g++.4 index 0335725187..927895b1cd 100644 --- a/examples/melt/log.5Oct16.melt.g++.4 +++ b/examples/melt/log.27Nov18.melt.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt units lj @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.00041604 secs mass 1 1.0 velocity all create 3.0 87287 @@ -35,13 +37,18 @@ fix 1 all nve thermo 50 run 250 Neighbor list info ... - 1 neighbor list requests update every 20 steps, delay 0 steps, check no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 12 -Memory usage per processor = 2.10344 Mbytes + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 @@ -49,20 +56,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 -Loop time of 0.210997 on 4 procs for 250 steps with 4000 atoms +Loop time of 0.223329 on 4 procs for 250 steps with 4000 atoms -Performance: 511855.365 tau/day, 1184.850 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 483592.231 tau/day, 1119.426 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.15475 | 0.16099 | 0.1682 | 1.2 | 76.30 -Neigh | 0.020829 | 0.021108 | 0.021522 | 0.2 | 10.00 -Comm | 0.01674 | 0.024412 | 0.030987 | 3.3 | 11.57 -Output | 0.00011587 | 0.0001238 | 0.00013185 | 0.1 | 0.06 -Modify | 0.0031242 | 0.0031361 | 0.0031476 | 0.0 | 1.49 -Other | | 0.001227 | | | 0.58 +Pair | 0.15881 | 0.16314 | 0.16859 | 0.9 | 73.05 +Neigh | 0.02472 | 0.025218 | 0.025828 | 0.3 | 11.29 +Comm | 0.025185 | 0.030091 | 0.034351 | 1.9 | 13.47 +Output | 0.00015163 | 0.00019169 | 0.00030899 | 0.0 | 0.09 +Modify | 0.0037532 | 0.0038366 | 0.0040054 | 0.2 | 1.72 +Other | | 0.00085 | | | 0.38 Nlocal: 1000 ave 1010 max 982 min Histogram: 1 0 0 0 0 0 1 0 0 2 diff --git a/examples/micelle/log.27Nov18.micelle.g++.1 b/examples/micelle/log.27Nov18.micelle.g++.1 new file mode 100644 index 0000000000..30a965e041 --- /dev/null +++ b/examples/micelle/log.27Nov18.micelle.g++.1 @@ -0,0 +1,255 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.167265 on 1 procs for 1000 steps with 1200 atoms + +Performance: 2582728.958 tau/day, 5978.539 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.096171 | 0.096171 | 0.096171 | 0.0 | 57.50 +Bond | 0.006212 | 0.006212 | 0.006212 | 0.0 | 3.71 +Neigh | 0.024826 | 0.024826 | 0.024826 | 0.0 | 14.84 +Comm | 0.0047672 | 0.0047672 | 0.0047672 | 0.0 | 2.85 +Output | 0.00029063 | 0.00029063 | 0.00029063 | 0.0 | 0.17 +Modify | 0.028771 | 0.028771 | 0.028771 | 0.0 | 17.20 +Other | | 0.006227 | | | 3.72 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 195 ave 195 max 195 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 3136 ave 3136 max 3136 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3136 +Ave neighs/atom = 2.61333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 92 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 1000 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 60000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 1000 0.45 -1.9727655 0.058608715 -1.4645318 1.9982298 + 2000 0.46465361 -1.9897467 0.067008449 -1.4584719 1.5873463 + 3000 0.46175071 -2.0129279 0.057865385 -1.4936966 1.41269 + 4000 0.44386154 -2.0280304 0.067167835 -1.5173709 1.4022093 + 5000 0.46127582 -2.0556041 0.068318674 -1.526394 1.1416711 + 6000 0.45354052 -2.0463246 0.05461954 -1.5385425 1.1650258 + 7000 0.44082313 -2.040263 0.060218047 -1.5395891 1.3258681 + 8000 0.44353466 -2.0423792 0.061769402 -1.5374447 1.2696989 + 9000 0.46192977 -2.0761348 0.064999109 -1.5495908 0.9205826 + 10000 0.45278646 -2.0589872 0.059623919 -1.5469542 1.075581 + 11000 0.45583355 -2.0661957 0.058197558 -1.5525445 1.127643 + 12000 0.45881198 -2.0921508 0.066937896 -1.5667833 0.98383574 + 13000 0.45339481 -2.079088 0.06292782 -1.5631432 1.0188637 + 14000 0.43601312 -2.0624084 0.057999616 -1.568759 1.1452177 + 15000 0.45941503 -2.0746606 0.062523373 -1.553105 0.86928343 + 16000 0.45 -2.0743162 0.05517924 -1.569512 0.86849848 + 17000 0.45603004 -2.0657683 0.058711872 -1.5514064 0.95544551 + 18000 0.45320383 -2.1009711 0.060716634 -1.5874283 0.8343521 + 19000 0.44072983 -2.0846408 0.062893297 -1.581385 0.90776246 + 20000 0.44452441 -2.0921415 0.060341571 -1.587646 0.98180005 + 21000 0.45964557 -2.0837047 0.054459432 -1.5699827 1.0213779 + 22000 0.46351849 -2.1053613 0.058392027 -1.5838371 0.81579487 + 23000 0.45576065 -2.1001888 0.057646538 -1.5871614 0.76090085 + 24000 0.44671746 -2.0848717 0.058192801 -1.5803337 0.77003809 + 25000 0.44371239 -2.0870872 0.054804981 -1.5889396 0.92295746 + 26000 0.45381188 -2.097021 0.057195346 -1.586392 0.7743058 + 27000 0.46158533 -2.1071056 0.061289644 -1.5846153 0.78981802 + 28000 0.46534671 -2.1056151 0.054934755 -1.5857214 0.80778664 + 29000 0.4505804 -2.0949318 0.065503451 -1.5792234 0.78274755 + 30000 0.45730883 -2.1029161 0.063461968 -1.5825264 0.82507857 + 31000 0.4620071 -2.1124989 0.059980378 -1.5908964 0.78583986 + 32000 0.46934619 -2.1107818 0.056442616 -1.5853842 0.70535653 + 33000 0.45800203 -2.1062502 0.054317859 -1.594312 0.726293 + 34000 0.44634295 -2.110401 0.057764968 -1.606665 0.85401059 + 35000 0.4431929 -2.1274759 0.062048133 -1.6226042 0.64243758 + 36000 0.46049645 -2.1300979 0.068463634 -1.6015216 0.57252544 + 37000 0.45366344 -2.0977407 0.053788554 -1.5906668 0.78046879 + 38000 0.44155077 -2.1166674 0.056888683 -1.6185959 0.53429042 + 39000 0.45631012 -2.096949 0.04860872 -1.5924104 0.86494908 + 40000 0.44684402 -2.1229137 0.067190397 -1.6092516 0.65110818 + 41000 0.4479377 -2.1105264 0.059375259 -1.6035867 0.79092862 + 42000 0.46143191 -2.1174539 0.057418393 -1.5989882 0.69762908 + 43000 0.4356786 -2.085826 0.056534028 -1.5939764 0.89541946 + 44000 0.45806826 -2.126423 0.060905733 -1.6078307 0.66389027 + 45000 0.44343688 -2.1116384 0.065870114 -1.602701 0.83947585 + 46000 0.43844672 -2.1096265 0.064158652 -1.6073865 0.77278902 + 47000 0.45794928 -2.1142786 0.058919562 -1.5977914 0.62611933 + 48000 0.45412335 -2.1106058 0.059153304 -1.5977076 0.66190677 + 49000 0.45927883 -2.1197656 0.068354598 -1.5925149 0.56008845 + 50000 0.44117285 -2.1020783 0.064763249 -1.5965099 0.85935147 + 51000 0.45325398 -2.1125154 0.062295387 -1.5973438 0.80951782 + 52000 0.43896579 -2.1039004 0.057475908 -1.6078245 0.84753768 + 53000 0.45180671 -2.1092446 0.063528598 -1.5942857 0.67065038 + 54000 0.4554341 -2.1185135 0.059603337 -1.6038556 0.76399618 + 55000 0.43861159 -2.0986406 0.057733879 -1.6026606 0.77334084 + 56000 0.45522991 -2.1207166 0.063287543 -1.6025785 0.78669598 + 57000 0.46125513 -2.1150202 0.06026261 -1.5938868 0.78148646 + 58000 0.45236938 -2.1088894 0.062678374 -1.5942186 0.75643518 + 59000 0.43927269 -2.1274165 0.055355076 -1.6331548 0.63495311 + 60000 0.45331102 -2.1336193 0.051244399 -1.6294416 0.56706921 +Loop time of 13.9361 on 1 procs for 60000 steps with 1200 atoms + +Performance: 1859917.639 tau/day, 4305.365 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.2211 | 9.2211 | 9.2211 | 0.0 | 66.17 +Bond | 0.33763 | 0.33763 | 0.33763 | 0.0 | 2.42 +Neigh | 2.3772 | 2.3772 | 2.3772 | 0.0 | 17.06 +Comm | 0.37693 | 0.37693 | 0.37693 | 0.0 | 2.70 +Output | 0.0011795 | 0.0011795 | 0.0011795 | 0.0 | 0.01 +Modify | 1.2727 | 1.2727 | 1.2727 | 0.0 | 9.13 +Other | | 0.3493 | | | 2.51 + +Nlocal: 1200 ave 1200 max 1200 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 405 ave 405 max 405 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9565 ave 9565 max 9565 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9565 +Ave neighs/atom = 7.97083 +Ave special neighs/atom = 0.5 +Neighbor list builds = 4876 +Dangerous builds = 0 +Total wall time: 0:00:14 diff --git a/examples/micelle/log.27Nov18.micelle.g++.4 b/examples/micelle/log.27Nov18.micelle.g++.4 new file mode 100644 index 0000000000..c9509df4b2 --- /dev/null +++ b/examples/micelle/log.27Nov18.micelle.g++.4 @@ -0,0 +1,255 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d micelle simulation + +dimension 2 + +neighbor 0.3 bin +neigh_modify delay 5 + +atom_style bond + +# Soft potential push-off + +read_data data.micelle + orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 1200 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 300 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +pair_style soft 1.12246 +pair_coeff * * 0.0 1.12246 + +bond_style harmonic +bond_coeff 1 50.0 0.75 + +velocity all create 0.45 2349852 + +variable prefactor equal ramp(1.0,20.0) + +fix 1 all nve +fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 +fix 3 all adapt 1 pair soft a * * v_prefactor +fix 4 all enforce2d + +thermo 50 +run 1000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.42246 + ghost atom cutoff = 1.42246 + binsize = 0.71123, bins = 51 51 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair soft, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 + 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 + 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 + 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 + 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 + 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 + 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 + 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 + 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 + 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 + 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 + 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 + 600 0.45 0.58193041 0.088386617 1.119942 5.131481 + 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 + 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 + 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 + 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 + 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 + 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 + 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 + 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 +Loop time of 0.0641922 on 4 procs for 1000 steps with 1200 atoms + +Performance: 6729792.131 tau/day, 15578.223 timesteps/s +90.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.020663 | 0.021445 | 0.022477 | 0.5 | 33.41 +Bond | 0.0014422 | 0.0015128 | 0.001569 | 0.1 | 2.36 +Neigh | 0.0067129 | 0.0067645 | 0.0068202 | 0.1 | 10.54 +Comm | 0.018454 | 0.019275 | 0.020386 | 0.5 | 30.03 +Output | 0.00038171 | 0.00040019 | 0.00044632 | 0.0 | 0.62 +Modify | 0.010561 | 0.010904 | 0.011309 | 0.3 | 16.99 +Other | | 0.003891 | | | 6.06 + +Nlocal: 300 ave 305 max 292 min +Histogram: 1 0 0 0 0 0 1 0 1 1 +Nghost: 100.25 ave 108 max 93 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Neighs: 784 ave 815 max 739 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 3136 +Ave neighs/atom = 2.61333 +Ave special neighs/atom = 0.5 +Neighbor list builds = 92 +Dangerous builds = 0 + +unfix 3 + +# Main run + +pair_style lj/cut 2.5 + +# solvent/head - full-size and long-range + +pair_coeff 1 1 1.0 1.0 2.5 +pair_coeff 2 2 1.0 1.0 2.5 +pair_coeff 1 2 1.0 1.0 2.5 + +# tail/tail - size-averaged and long-range + +pair_coeff 3 3 1.0 0.75 2.5 +pair_coeff 4 4 1.0 0.50 2.5 +pair_coeff 3 4 1.0 0.67 2.5 + +# solvent/tail - full-size and repulsive + +pair_coeff 1 3 1.0 1.0 1.12246 +pair_coeff 1 4 1.0 1.0 1.12246 + +# head/tail - size-averaged and repulsive + +pair_coeff 2 3 1.0 0.88 1.12246 +pair_coeff 2 4 1.0 0.75 1.12246 + +thermo 1000 + +#dump 1 all atom 2000 dump.micelle + +#dump 2 all image 2000 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +#dump 3 all movie 2000 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 + +reset_timestep 0 +run 60000 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 26 26 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 + 1000 0.45 -1.9727661 0.05860859 -1.4645325 1.9982402 + 2000 0.45146247 -1.9766043 0.059408886 -1.4661092 1.7398826 + 3000 0.43338517 -2.0028125 0.059884381 -1.5099041 1.4716488 + 4000 0.46674519 -2.0200954 0.066548679 -1.4871905 1.2506693 + 5000 0.45 -2.0207125 0.055926205 -1.5151613 1.3047457 + 6000 0.45447759 -2.0585234 0.068004883 -1.5364197 1.1859762 + 7000 0.43183018 -2.0170545 0.060800296 -1.5247839 1.3074223 + 8000 0.46657547 -2.053224 0.063224367 -1.523813 1.1785643 + 9000 0.45 -2.0691221 0.054959029 -1.564538 1.1833657 + 10000 0.4428252 -2.0473987 0.054306905 -1.5506356 1.181794 + 11000 0.45407036 -2.0746151 0.065849667 -1.5550734 1.1008545 + 12000 0.46061944 -2.0580809 0.063129643 -1.5347156 1.0206491 + 13000 0.45159068 -2.0640832 0.060059758 -1.5528091 1.0813494 + 14000 0.44141594 -2.0467255 0.062785088 -1.5428923 1.1465772 + 15000 0.454361 -2.0908595 0.057471037 -1.5794061 0.84297781 + 16000 0.44061091 -2.0521452 0.064644196 -1.5472573 1.1478647 + 17000 0.45118383 -2.081348 0.058660999 -1.5718791 1.0101404 + 18000 0.44664866 -2.0845745 0.060435731 -1.5778623 0.96142277 + 19000 0.45515339 -2.0914006 0.062174016 -1.5744525 0.87623323 + 20000 0.45624408 -2.0837697 0.059263054 -1.5686428 0.92810644 + 21000 0.46791657 -2.1062007 0.067355929 -1.5713181 0.88318793 + 22000 0.43907391 -2.1005271 0.065885144 -1.5959339 0.77211644 + 23000 0.43967354 -2.0723459 0.057613471 -1.5754253 1.0371548 + 24000 0.45716384 -2.0987126 0.055157377 -1.5867723 0.89670061 + 25000 0.45828285 -2.1041616 0.057736138 -1.5885245 0.79952286 + 26000 0.45 -2.0743463 0.072455519 -1.5522658 0.88260204 + 27000 0.46581599 -2.0804974 0.058113258 -1.5569564 0.93053891 + 28000 0.46904194 -2.0920124 0.059748792 -1.5636125 0.79359618 + 29000 0.46093196 -2.118556 0.063942334 -1.5940659 0.67707604 + 30000 0.45733724 -2.1197827 0.066939064 -1.5958875 0.66886075 + 31000 0.44580762 -2.0977175 0.056969121 -1.5953123 0.81042562 + 32000 0.44403029 -2.1032264 0.063465127 -1.596101 0.71796412 + 33000 0.45834072 -2.0934132 0.066035391 -1.569419 0.77873998 + 34000 0.44981563 -2.0910902 0.07138738 -1.5702621 0.75679805 + 35000 0.45383392 -2.0926654 0.067553478 -1.5716562 0.9064517 + 36000 0.44447198 -2.1107114 0.062718917 -1.6038909 0.8538349 + 37000 0.45838527 -2.1166464 0.062442606 -1.5962005 0.7300635 + 38000 0.45014075 -2.1096258 0.059293718 -1.6005665 0.73988246 + 39000 0.44377026 -2.080309 0.063545781 -1.5733628 0.99775641 + 40000 0.44577324 -2.1134607 0.065271179 -1.6027878 0.64113168 + 41000 0.45 -2.0937983 0.060881377 -1.5832919 0.78849829 + 42000 0.46866695 -2.1142283 0.056417605 -1.5895343 0.73788436 + 43000 0.43211727 -2.0819893 0.061463358 -1.5887688 0.95853724 + 44000 0.44138397 -2.0921314 0.059643895 -1.5914713 0.89486208 + 45000 0.45 -2.117209 0.054804331 -1.6127797 0.78564885 + 46000 0.44285245 -2.1090975 0.057629006 -1.6089851 0.64549424 + 47000 0.45537009 -2.1164296 0.068582324 -1.5928567 0.73629413 + 48000 0.45046732 -2.1006362 0.057249591 -1.5932947 0.74317593 + 49000 0.45425966 -2.1191703 0.064247719 -1.6010414 0.70962368 + 50000 0.45506149 -2.1184671 0.064911797 -1.5988731 0.69958156 + 51000 0.46047417 -2.1019719 0.058468259 -1.5834132 0.87219271 + 52000 0.43808317 -2.092294 0.057280941 -1.597295 0.84156893 + 53000 0.45012337 -2.1175234 0.064002667 -1.6037725 0.64562439 + 54000 0.43854679 -2.1236444 0.061316257 -1.6241468 0.72478117 + 55000 0.46382438 -2.1016563 0.060724666 -1.5774938 0.83311209 + 56000 0.44951533 -2.0946157 0.055075217 -1.5903998 0.90066109 + 57000 0.45937401 -2.0983442 0.061558996 -1.577794 0.58606161 + 58000 0.446669 -2.1146838 0.062385166 -1.6060019 0.73443388 + 59000 0.43847747 -2.1197461 0.060460257 -1.6211738 0.7230937 + 60000 0.45294215 -2.1258513 0.061895006 -1.6113915 0.70722168 +Loop time of 4.56226 on 4 procs for 60000 steps with 1200 atoms + +Performance: 5681397.232 tau/day, 13151.382 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.2114 | 2.2527 | 2.3592 | 4.1 | 49.38 +Bond | 0.083713 | 0.09234 | 0.10244 | 2.3 | 2.02 +Neigh | 0.72491 | 0.7277 | 0.72957 | 0.2 | 15.95 +Comm | 0.79464 | 0.90036 | 0.94957 | 6.5 | 19.74 +Output | 0.0014119 | 0.0024976 | 0.0057502 | 3.8 | 0.05 +Modify | 0.33757 | 0.35202 | 0.36946 | 2.1 | 7.72 +Other | | 0.2346 | | | 5.14 + +Nlocal: 300 ave 306 max 289 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 227.25 ave 250 max 216 min +Histogram: 2 0 1 0 0 0 0 0 0 1 +Neighs: 2373.25 ave 2489 max 2283 min +Histogram: 1 1 0 0 0 1 0 0 0 1 + +Total # of neighbors = 9493 +Ave neighs/atom = 7.91083 +Ave special neighs/atom = 0.5 +Neighbor list builds = 4888 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/micelle/log.5Oct16.micelle.g++.1 b/examples/micelle/log.5Oct16.micelle.g++.1 deleted file mode 100644 index 5dfc652d68..0000000000 --- a/examples/micelle/log.5Oct16.micelle.g++.1 +++ /dev/null @@ -1,244 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 51 51 1 -Memory usage per processor = 3.45296 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.192637 on 1 procs for 1000 steps with 1200 atoms - -Performance: 2242560.228 tau/day, 5191.112 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.13348 | 0.13348 | 0.13348 | 0.0 | 69.29 -Bond | 0.0066328 | 0.0066328 | 0.0066328 | 0.0 | 3.44 -Neigh | 0.023894 | 0.023894 | 0.023894 | 0.0 | 12.40 -Comm | 0.0032849 | 0.0032849 | 0.0032849 | 0.0 | 1.71 -Output | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 0.10 -Modify | 0.020029 | 0.020029 | 0.020029 | 0.0 | 10.40 -Other | | 0.005115 | | | 2.66 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 195 ave 195 max 195 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 3136 ave 3136 max 3136 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 1000 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 60000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 26 26 1 -Memory usage per processor = 3.45296 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299 - 2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107 - 3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132 - 4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127 - 5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421 - 6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692 - 7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802 - 8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472 - 9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529 - 10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481 - 11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264 - 12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813 - 13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127 - 14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319 - 15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211 - 16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991 - 17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012 - 18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585 - 19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228 - 20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418 - 21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595 - 22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955 - 23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876 - 24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833 - 25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274 - 26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526 - 27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018 - 28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478 - 29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706 - 30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298 - 31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692 - 32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441 - 33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371 - 34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708 - 35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163 - 36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748 - 37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072 - 38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145 - 39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475 - 40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301 - 41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478 - 42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466 - 43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235 - 44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091 - 45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898 - 46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901 - 47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542 - 48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782 - 49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201 - 50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821 - 51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581 - 52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576 - 53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136 - 54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217 - 55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948 - 56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945 - 57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456 - 58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379 - 59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834 - 60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428 -Loop time of 13.6136 on 1 procs for 60000 steps with 1200 atoms - -Performance: 1903978.372 tau/day, 4407.357 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 9.3684 | 9.3684 | 9.3684 | 0.0 | 68.82 -Bond | 0.39461 | 0.39461 | 0.39461 | 0.0 | 2.90 -Neigh | 2.211 | 2.211 | 2.211 | 0.0 | 16.24 -Comm | 0.2552 | 0.2552 | 0.2552 | 0.0 | 1.87 -Output | 0.00065112 | 0.00065112 | 0.00065112 | 0.0 | 0.00 -Modify | 1.0819 | 1.0819 | 1.0819 | 0.0 | 7.95 -Other | | 0.3019 | | | 2.22 - -Nlocal: 1200 ave 1200 max 1200 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 417 ave 417 max 417 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9495 ave 9495 max 9495 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9495 -Ave neighs/atom = 7.9125 -Ave special neighs/atom = 0.5 -Neighbor list builds = 4885 -Dangerous builds = 0 -Total wall time: 0:00:13 diff --git a/examples/micelle/log.5Oct16.micelle.g++.4 b/examples/micelle/log.5Oct16.micelle.g++.4 deleted file mode 100644 index 960489aad0..0000000000 --- a/examples/micelle/log.5Oct16.micelle.g++.4 +++ /dev/null @@ -1,244 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d micelle simulation - -dimension 2 - -neighbor 0.3 bin -neigh_modify delay 5 - -atom_style bond - -# Soft potential push-off - -read_data data.micelle - orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 1200 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 300 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -pair_style soft 1.12246 -pair_coeff * * 0.0 1.12246 - -bond_style harmonic -bond_coeff 1 50.0 0.75 - -velocity all create 0.45 2349852 - -variable prefactor equal ramp(1.0,20.0) - -fix 1 all nve -fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0 -fix 3 all adapt 1 pair soft a * * v_prefactor -fix 4 all enforce2d - -thermo 50 -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.42246 - ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 51 51 1 -Memory usage per processor = 3.55365 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518 - 50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852 - 100 0.45 0.73046745 0.054836584 1.234929 2.3196516 - 150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416 - 200 0.45 0.78481891 0.076931503 1.3113754 3.0412388 - 250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024 - 300 0.45 0.76820218 0.066727591 1.2845548 3.7861054 - 350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621 - 400 0.45 0.68527759 0.090724527 1.2256271 4.4725214 - 450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211 - 500 0.45 0.64883009 0.078376672 1.1768318 4.7919294 - 550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705 - 600 0.45 0.58193041 0.088386617 1.119942 5.131481 - 650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294 - 700 0.45 0.50856787 0.088471208 1.0466641 5.2550165 - 750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763 - 800 0.45 0.49926696 0.085958476 1.0348504 5.4665914 - 850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932 - 900 0.45 0.47785593 0.10150857 1.0289895 5.7765975 - 950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245 - 1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568 -Loop time of 0.0670803 on 4 procs for 1000 steps with 1200 atoms - -Performance: 6440046.660 tau/day, 14907.515 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.033971 | 0.034628 | 0.036162 | 0.5 | 51.62 -Bond | 0.001687 | 0.0017596 | 0.0018852 | 0.2 | 2.62 -Neigh | 0.0068789 | 0.0069902 | 0.0070932 | 0.1 | 10.42 -Comm | 0.011152 | 0.012883 | 0.013872 | 0.9 | 19.20 -Output | 0.00035501 | 0.00038034 | 0.00044274 | 0.2 | 0.57 -Modify | 0.0065997 | 0.0067009 | 0.0068605 | 0.1 | 9.99 -Other | | 0.003738 | | | 5.57 - -Nlocal: 300 ave 305 max 292 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Nghost: 100.25 ave 108 max 93 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Neighs: 784 ave 815 max 739 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 3136 -Ave neighs/atom = 2.61333 -Ave special neighs/atom = 0.5 -Neighbor list builds = 92 -Dangerous builds = 0 - -unfix 3 - -# Main run - -pair_style lj/cut 2.5 - -# solvent/head - full-size and long-range - -pair_coeff 1 1 1.0 1.0 2.5 -pair_coeff 2 2 1.0 1.0 2.5 -pair_coeff 1 2 1.0 1.0 2.5 - -# tail/tail - size-averaged and long-range - -pair_coeff 3 3 1.0 0.75 2.5 -pair_coeff 4 4 1.0 0.50 2.5 -pair_coeff 3 4 1.0 0.67 2.5 - -# solvent/tail - full-size and repulsive - -pair_coeff 1 3 1.0 1.0 1.12246 -pair_coeff 1 4 1.0 1.0 1.12246 - -# head/tail - size-averaged and repulsive - -pair_coeff 2 3 1.0 0.88 1.12246 -pair_coeff 2 4 1.0 0.75 1.12246 - -thermo 1000 - -#dump 1 all atom 2000 dump.micelle - -#dump 2 all image 2000 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -#dump 3 all movie 2000 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75 - -reset_timestep 0 -run 60000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 26 26 1 -Memory usage per processor = 3.55365 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686 - 1000 0.45 -1.9727663 0.058608449 -1.4645328 1.9982389 - 2000 0.45428051 -1.9704547 0.062434911 -1.4541178 1.7134222 - 3000 0.46748648 -2.0088544 0.065086237 -1.4766712 1.4648627 - 4000 0.45608936 -2.032563 0.057148422 -1.5197053 1.3833681 - 5000 0.46134038 -2.0250107 0.061983009 -1.5020718 1.3378201 - 6000 0.45254634 -2.0414745 0.071656389 -1.5176489 1.2670697 - 7000 0.46380932 -2.0463598 0.060057501 -1.5228795 1.1029258 - 8000 0.46495917 -2.0570216 0.058074076 -1.5343758 1.1187483 - 9000 0.45771237 -2.0510911 0.061803881 -1.5319563 1.1540073 - 10000 0.45 -2.0568306 0.06114562 -1.54606 1.128504 - 11000 0.43977142 -2.0442503 0.061128391 -1.543717 1.2268919 - 12000 0.4412548 -2.051046 0.065150223 -1.5450087 1.0681597 - 13000 0.46384147 -2.0657072 0.064678941 -1.5375734 0.99078604 - 14000 0.43330137 -2.0693058 0.06542588 -1.5709397 1.0252118 - 15000 0.44825078 -2.078972 0.059800283 -1.5712944 0.76305383 - 16000 0.45607271 -2.085101 0.058347214 -1.5710611 0.99903698 - 17000 0.45329523 -2.0865426 0.057674526 -1.5759505 0.90245709 - 18000 0.46719329 -2.076619 0.062698678 -1.5471164 0.95433376 - 19000 0.45253889 -2.0741652 0.06154596 -1.5604575 1.0606446 - 20000 0.43708811 -2.1005493 0.063453064 -1.6003723 0.65980174 - 21000 0.43630563 -2.0780131 0.05595505 -1.586116 0.86690426 - 22000 0.44050783 -2.0766368 0.057980992 -1.578515 0.99638367 - 23000 0.44657992 -2.0731942 0.058890194 -1.5680963 0.92620975 - 24000 0.45645869 -2.0957688 0.065464986 -1.5742255 0.88631971 - 25000 0.46007071 -2.0928226 0.058133397 -1.5750019 0.75468418 - 26000 0.46316546 -2.0945456 0.064110354 -1.5676557 0.84437166 - 27000 0.44780223 -2.0966995 0.063284428 -1.585986 0.89645525 - 28000 0.43945645 -2.0909433 0.062357411 -1.5894957 0.92336874 - 29000 0.44332217 -2.0885003 0.063832997 -1.5817146 0.86508766 - 30000 0.44865024 -2.0899642 0.057319345 -1.5843685 0.76862889 - 31000 0.45702135 -2.0941006 0.059669304 -1.5777908 0.76171188 - 32000 0.46630168 -2.1066612 0.051622888 -1.5891252 0.72214981 - 33000 0.44966822 -2.1086408 0.061298737 -1.5980486 0.7056562 - 34000 0.45599464 -2.11216 0.045835595 -1.6107098 0.75827582 - 35000 0.44021366 -2.1082791 0.066290667 -1.6021416 0.85079438 - 36000 0.46531913 -2.1228506 0.054779097 -1.6031402 0.60391389 - 37000 0.44777064 -2.1193684 0.062074675 -1.6098962 0.68654583 - 38000 0.46608897 -2.1243843 0.052889984 -1.6057938 0.6517974 - 39000 0.44921432 -2.1050268 0.059790015 -1.5963968 0.74248261 - 40000 0.44407222 -2.0930539 0.055687841 -1.5936639 0.69821332 - 41000 0.4377755 -2.0929451 0.056403441 -1.599131 0.90040574 - 42000 0.46403029 -2.1245032 0.058491534 -1.6023681 0.6984091 - 43000 0.45456147 -2.0966395 0.055922733 -1.5865341 0.86499812 - 44000 0.45619203 -2.1150101 0.054818604 -1.6043796 0.71197595 - 45000 0.44806278 -2.1067617 0.057539822 -1.6015324 0.7644258 - 46000 0.46326243 -2.1204997 0.060566953 -1.5970563 0.68822898 - 47000 0.43464277 -2.1257611 0.069053137 -1.6224273 0.60024032 - 48000 0.46986944 -2.1245871 0.058768355 -1.5963409 0.58191819 - 49000 0.4428734 -2.1203847 0.059089451 -1.6187909 0.60806508 - 50000 0.43813854 -2.12123 0.066218857 -1.6172377 0.42860822 - 51000 0.4514578 -2.1304644 0.057932769 -1.62145 0.62355123 - 52000 0.44155257 -2.1248047 0.062563155 -1.6210569 0.81276016 - 53000 0.4467801 -2.1254575 0.056774655 -1.6222751 0.6115287 - 54000 0.43972332 -2.1036785 0.061427338 -1.6028943 0.75225909 - 55000 0.44933771 -2.104883 0.058556755 -1.5973629 0.75480805 - 56000 0.45 -2.1212286 0.057392665 -1.614211 0.56759345 - 57000 0.43127001 -2.0978236 0.04986292 -1.61705 0.71828346 - 58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906 - 59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859 - 60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066 -Loop time of 4.56204 on 4 procs for 60000 steps with 1200 atoms - -Performance: 5681665.051 tau/day, 13152.002 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.3705 | 2.4423 | 2.4948 | 2.9 | 53.54 -Bond | 0.084795 | 0.10292 | 0.11359 | 3.4 | 2.26 -Neigh | 0.63938 | 0.64418 | 0.64857 | 0.4 | 14.12 -Comm | 0.81947 | 0.8785 | 0.9618 | 5.7 | 19.26 -Output | 0.0012863 | 0.0013551 | 0.0015438 | 0.3 | 0.03 -Modify | 0.26717 | 0.27596 | 0.28816 | 1.5 | 6.05 -Other | | 0.2168 | | | 4.75 - -Nlocal: 300 ave 305 max 293 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Nghost: 211 ave 215 max 205 min -Histogram: 1 0 0 0 0 0 1 0 1 1 -Neighs: 2448.75 ave 2531 max 2414 min -Histogram: 2 1 0 0 0 0 0 0 0 1 - -Total # of neighbors = 9795 -Ave neighs/atom = 8.1625 -Ave special neighs/atom = 0.5 -Neighbor list builds = 4880 -Dangerous builds = 0 -Total wall time: 0:00:04 diff --git a/examples/min/log.5Oct16.min.box.g++.1 b/examples/min/log.27Nov18.min.box.g++.1 similarity index 84% rename from examples/min/log.5Oct16.min.box.g++.1 rename to examples/min/log.27Nov18.min.box.g++.1 index 29294567ae..7e2151c6cb 100644 --- a/examples/min/log.5Oct16.min.box.g++.1 +++ b/examples/min/log.27Nov18.min.box.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d Lennard-Jones melt and subsequent energy minimization, # followed by box relaxation to a target stress state # @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 800 atoms + Time spent = 0.000453234 secs mass 1 1.0 velocity all create 5.0 87287 loop geom @@ -40,13 +42,18 @@ thermo 100 run 1000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 22 22 1 -Memory usage per processor = 2.47843 Mbytes + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.056 | 3.056 | 3.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 5 -2.461717 0 2.532033 5.0190509 100 3.2788864 -0.74311698 0 2.5316708 15.912832 @@ -59,20 +66,20 @@ Step Temp E_pair E_mol TotEng Press 800 3.3016275 -0.76569171 0 2.5318087 15.639335 900 3.4639203 -0.92788002 0 2.5317104 14.765912 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 -Loop time of 0.202646 on 1 procs for 1000 steps with 800 atoms +Loop time of 0.210142 on 1 procs for 1000 steps with 800 atoms -Performance: 2131796.155 tau/day, 4934.713 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2055749.118 tau/day, 4758.679 timesteps/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12926 | 0.12926 | 0.12926 | 0.0 | 63.79 -Neigh | 0.051169 | 0.051169 | 0.051169 | 0.0 | 25.25 -Comm | 0.0044918 | 0.0044918 | 0.0044918 | 0.0 | 2.22 -Output | 9.3222e-05 | 9.3222e-05 | 9.3222e-05 | 0.0 | 0.05 -Modify | 0.011879 | 0.011879 | 0.011879 | 0.0 | 5.86 -Other | | 0.005755 | | | 2.84 +Pair | 0.12951 | 0.12951 | 0.12951 | 0.0 | 61.63 +Neigh | 0.053642 | 0.053642 | 0.053642 | 0.0 | 25.53 +Comm | 0.0062521 | 0.0062521 | 0.0062521 | 0.0 | 2.98 +Output | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 0.06 +Modify | 0.0142 | 0.0142 | 0.0142 | 0.0 | 6.76 +Other | | 0.006405 | | | 3.05 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -98,7 +105,7 @@ thermo 50 # atoms only minimize 1.0e-6 0.001 1000 10000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp E_pair E_mol TotEng Press 1000 0 -0.79078181 0 -0.79078181 12.79527 1050 0 -2.8361415 0 -2.8361415 -1.1950285 @@ -111,9 +118,9 @@ Step Temp E_pair E_mol TotEng Press 1400 0 -2.9131297 0 -2.9131297 -1.0962069 1450 0 -2.9167506 0 -2.9167506 -1.0259809 1475 0 -2.9169436 0 -2.9169436 -1.0125744 -Loop time of 0.232023 on 1 procs for 475 steps with 800 atoms +Loop time of 0.234897 on 1 procs for 475 steps with 800 atoms -100.0% CPU use with 1 MPI tasks x no OpenMP threads +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -127,12 +134,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.18865 | 0.18865 | 0.18865 | 0.0 | 81.30 -Neigh | 0.020881 | 0.020881 | 0.020881 | 0.0 | 9.00 -Comm | 0.0028429 | 0.0028429 | 0.0028429 | 0.0 | 1.23 -Output | 7.0095e-05 | 7.0095e-05 | 7.0095e-05 | 0.0 | 0.03 -Modify | 0.0020018 | 0.0020018 | 0.0020018 | 0.0 | 0.86 -Other | | 0.01758 | | | 7.58 +Pair | 0.18533 | 0.18533 | 0.18533 | 0.0 | 78.90 +Neigh | 0.02206 | 0.02206 | 0.02206 | 0.0 | 9.39 +Comm | 0.0041955 | 0.0041955 | 0.0041955 | 0.0 | 1.79 +Output | 0.000108 | 0.000108 | 0.000108 | 0.0 | 0.05 +Modify | 0.002362 | 0.002362 | 0.002362 | 0.0 | 1.01 +Other | | 0.02084 | | | 8.87 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -156,7 +163,7 @@ thermo_style custom step temp pe pxx pyy pxy f_3 v_emin # anisotropic volume relaxation to hydrostatic target minimize 0.0 10.0e0 10000 100000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1475 0 -2.9169436 -1.0208231 -1.0043256 0.042048233 0 -2.9169436 1500 0 -2.9112018 1.4420862 1.4721681 0.065929095 -0.087730988 -2.9989327 @@ -164,9 +171,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1600 0 -2.924265 1.4545702 1.5281333 0.053590255 -0.12032598 -3.044591 1650 0 -2.9289538 1.4528452 1.5692678 0.038096542 -0.12516914 -3.054123 1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 -0.12731783 -3.060769 -Loop time of 0.109303 on 1 procs for 224 steps with 800 atoms +Loop time of 0.112146 on 1 procs for 224 steps with 800 atoms -99.7% CPU use with 1 MPI tasks x no OpenMP threads +97.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -180,12 +187,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.086675 | 0.086675 | 0.086675 | 0.0 | 79.30 -Neigh | 0.0040114 | 0.0040114 | 0.0040114 | 0.0 | 3.67 -Comm | 0.0010419 | 0.0010419 | 0.0010419 | 0.0 | 0.95 -Output | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 | 0.0 | 0.09 -Modify | 0.00085473 | 0.00085473 | 0.00085473 | 0.0 | 0.78 -Other | | 0.01662 | | | 15.21 +Pair | 0.084376 | 0.084376 | 0.084376 | 0.0 | 75.24 +Neigh | 0.0042746 | 0.0042746 | 0.0042746 | 0.0 | 3.81 +Comm | 0.0015385 | 0.0015385 | 0.0015385 | 0.0 | 1.37 +Output | 0.0001235 | 0.0001235 | 0.0001235 | 0.0 | 0.11 +Modify | 0.0011208 | 0.0011208 | 0.0011208 | 0.0 | 1.00 +Other | | 0.02071 | | | 18.47 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -202,13 +209,13 @@ Dangerous builds = 0 fix 3 all box/relax aniso 1.5 vmax 1.0e-3 minimize 0.0 10.0 10000 100000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 0 -2.9334511 1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 9.09619e-05 -2.9335086 -Loop time of 0.000785828 on 1 procs for 1 steps with 800 atoms +Loop time of 0.000793934 on 1 procs for 1 steps with 800 atoms -127.3% CPU use with 1 MPI tasks x no OpenMP threads +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -222,12 +229,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00063896 | 0.00063896 | 0.00063896 | 0.0 | 81.31 +Pair | 0.00061846 | 0.00061846 | 0.00061846 | 0.0 | 77.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.76 +Comm | 1.0014e-05 | 1.0014e-05 | 1.0014e-05 | 0.0 | 1.26 Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 | 0.0 | 0.79 -Other | | 0.0001347 | | | 17.14 +Modify | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 | 0.0 | 0.96 +Other | | 0.0001578 | | | 19.88 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -246,7 +253,7 @@ Dangerous builds = 0 fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 minimize 0.0 10.0 10000 100000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 -3.5527137e-17 -2.9335996 1750 0 -2.9306696 0.95043712 1.984164 0.04474671 -0.014282691 -2.9449523 @@ -254,9 +261,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1850 0 -2.935585 0.98224846 1.9920507 0.047038767 -0.021070874 -2.9566559 1900 0 -2.9380757 0.96811097 1.9677247 0.068809483 -0.024274947 -2.9623506 1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 -0.025108208 -2.9642387 -Loop time of 0.0971339 on 1 procs for 213 steps with 800 atoms +Loop time of 0.0997889 on 1 procs for 213 steps with 800 atoms -100.9% CPU use with 1 MPI tasks x no OpenMP threads +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -270,12 +277,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.076124 | 0.076124 | 0.076124 | 0.0 | 78.37 -Neigh | 0.0027554 | 0.0027554 | 0.0027554 | 0.0 | 2.84 -Comm | 0.00085568 | 0.00085568 | 0.00085568 | 0.0 | 0.88 -Output | 0.00012589 | 0.00012589 | 0.00012589 | 0.0 | 0.13 -Modify | 0.00077486 | 0.00077486 | 0.00077486 | 0.0 | 0.80 -Other | | 0.0165 | | | 16.98 +Pair | 0.074305 | 0.074305 | 0.074305 | 0.0 | 74.46 +Neigh | 0.0028846 | 0.0028846 | 0.0028846 | 0.0 | 2.89 +Comm | 0.0012925 | 0.0012925 | 0.0012925 | 0.0 | 1.30 +Output | 0.00016117 | 0.00016117 | 0.00016117 | 0.0 | 0.16 +Modify | 0.00090647 | 0.00090647 | 0.00090647 | 0.0 | 0.91 +Other | | 0.02024 | | | 20.28 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -290,7 +297,7 @@ Neighbor list builds = 11 Dangerous builds = 0 minimize 0.0 1.0 10000 100000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 7.1054274e-17 -2.9391305 1950 0 -2.9397224 0.98880561 2.0105792 0.10042798 -0.0026601558 -2.9423825 @@ -382,9 +389,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 6250 0 -3.0378032 0.99964291 1.9971778 0.033045048 -0.037140636 -3.0749439 6300 0 -3.0377782 0.9965492 1.9980669 0.032201395 -0.037170252 -3.0749485 6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 -0.037163869 -3.0749493 -Loop time of 2.27089 on 1 procs for 4401 steps with 800 atoms +Loop time of 2.33993 on 1 procs for 4401 steps with 800 atoms -99.9% CPU use with 1 MPI tasks x no OpenMP threads +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -398,12 +405,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.8251 | 1.8251 | 1.8251 | 0.0 | 80.37 -Neigh | 0.027037 | 0.027037 | 0.027037 | 0.0 | 1.19 -Comm | 0.019059 | 0.019059 | 0.019059 | 0.0 | 0.84 -Output | 0.0027676 | 0.0027676 | 0.0027676 | 0.0 | 0.12 -Modify | 0.018233 | 0.018233 | 0.018233 | 0.0 | 0.80 -Other | | 0.3786 | | | 16.67 +Pair | 1.7909 | 1.7909 | 1.7909 | 0.0 | 76.54 +Neigh | 0.028373 | 0.028373 | 0.028373 | 0.0 | 1.21 +Comm | 0.029514 | 0.029514 | 0.029514 | 0.0 | 1.26 +Output | 0.0037448 | 0.0037448 | 0.0037448 | 0.0 | 0.16 +Modify | 0.021746 | 0.021746 | 0.021746 | 0.0 | 0.93 +Other | | 0.4657 | | | 19.90 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -418,7 +425,7 @@ Neighbor list builds = 109 Dangerous builds = 0 minimize 0.0 1.0e-2 10000 100000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 3.5527137e-17 -3.0377854 6350 0 -3.0377426 0.9995618 1.9997582 0.032364722 -4.5395813e-05 -3.037788 @@ -454,9 +461,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 7850 0 -3.0378352 1.0000397 2.0000524 0.033753896 -7.5318252e-05 -3.0379105 7900 0 -3.0378354 1.0000486 2.0000488 0.033742064 -7.5113089e-05 -3.0379105 7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 -7.491864e-05 -3.0379105 -Loop time of 0.831561 on 1 procs for 1590 steps with 800 atoms +Loop time of 0.85351 on 1 procs for 1590 steps with 800 atoms -99.9% CPU use with 1 MPI tasks x no OpenMP threads +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -470,12 +477,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.67727 | 0.67727 | 0.67727 | 0.0 | 81.45 -Neigh | 0.0004921 | 0.0004921 | 0.0004921 | 0.0 | 0.06 -Comm | 0.0065284 | 0.0065284 | 0.0065284 | 0.0 | 0.79 -Output | 0.0010114 | 0.0010114 | 0.0010114 | 0.0 | 0.12 -Modify | 0.0067346 | 0.0067346 | 0.0067346 | 0.0 | 0.81 -Other | | 0.1395 | | | 16.78 +Pair | 0.66264 | 0.66264 | 0.66264 | 0.0 | 77.64 +Neigh | 0.00052071 | 0.00052071 | 0.00052071 | 0.0 | 0.06 +Comm | 0.010136 | 0.010136 | 0.010136 | 0.0 | 1.19 +Output | 0.0012524 | 0.0012524 | 0.0012524 | 0.0 | 0.15 +Modify | 0.0080862 | 0.0080862 | 0.0080862 | 0.0 | 0.95 +Other | | 0.1709 | | | 20.02 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -494,7 +501,7 @@ Dangerous builds = 0 fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100 minimize 0.0 1.0e-4 10000 100000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 0 -3.0378356 7950 0 -3.0378364 1.000001 2.0000015 0.03373689 8.3404927e-07 -3.0378356 @@ -515,9 +522,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 8700 0 -3.0378364 1 1.9999997 0.033725586 4.9116894e-09 -3.0378364 8750 0 -3.0378364 0.99999991 2 0.033725386 7.3634181e-10 -3.0378364 8753 0 -3.0378364 1 2 0.033725385 -1.0901182e-09 -3.0378364 -Loop time of 0.445577 on 1 procs for 849 steps with 800 atoms +Loop time of 0.457836 on 1 procs for 849 steps with 800 atoms -99.9% CPU use with 1 MPI tasks x no OpenMP threads +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -531,12 +538,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.36325 | 0.36325 | 0.36325 | 0.0 | 81.52 +Pair | 0.3559 | 0.3559 | 0.3559 | 0.0 | 77.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0034921 | 0.0034921 | 0.0034921 | 0.0 | 0.78 -Output | 0.00052595 | 0.00052595 | 0.00052595 | 0.0 | 0.12 -Modify | 0.0036132 | 0.0036132 | 0.0036132 | 0.0 | 0.81 -Other | | 0.07469 | | | 16.76 +Comm | 0.0054362 | 0.0054362 | 0.0054362 | 0.0 | 1.19 +Output | 0.00070548 | 0.00070548 | 0.00070548 | 0.0 | 0.15 +Modify | 0.004298 | 0.004298 | 0.004298 | 0.0 | 0.94 +Other | | 0.09149 | | | 19.98 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/min/log.5Oct16.min.box.g++.4 b/examples/min/log.27Nov18.min.box.g++.4 similarity index 84% rename from examples/min/log.5Oct16.min.box.g++.4 rename to examples/min/log.27Nov18.min.box.g++.4 index 090b5ad79c..f6dacb0129 100644 --- a/examples/min/log.5Oct16.min.box.g++.4 +++ b/examples/min/log.27Nov18.min.box.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d Lennard-Jones melt and subsequent energy minimization, # followed by box relaxation to a target stress state # @@ -14,6 +15,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 800 atoms + Time spent = 0.000339985 secs mass 1 1.0 velocity all create 5.0 87287 loop geom @@ -40,13 +42,18 @@ thermo 100 run 1000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 22 22 1 -Memory usage per processor = 2.47676 Mbytes + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.049 | 3.049 | 3.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 5 -2.461717 0 2.532033 5.0190509 100 3.2788864 -0.74311698 0 2.5316708 15.912832 @@ -59,20 +66,20 @@ Step Temp E_pair E_mol TotEng Press 800 3.3016408 -0.76570603 0 2.5318077 15.639259 900 3.4621697 -0.92610292 0 2.5317391 14.773473 1000 3.3058424 -0.77076863 0 2.5309414 15.708171 -Loop time of 0.066087 on 4 procs for 1000 steps with 800 atoms +Loop time of 0.0739716 on 4 procs for 1000 steps with 800 atoms -Performance: 6536837.061 tau/day, 15131.567 timesteps/s -98.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 5840081.570 tau/day, 13518.707 timesteps/s +96.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.032169 | 0.032534 | 0.032995 | 0.2 | 49.23 -Neigh | 0.013092 | 0.013286 | 0.01348 | 0.1 | 20.10 -Comm | 0.011925 | 0.012799 | 0.013343 | 0.5 | 19.37 -Output | 0.00017333 | 0.00018448 | 0.00021172 | 0.1 | 0.28 -Modify | 0.0029421 | 0.0029953 | 0.0030239 | 0.1 | 4.53 -Other | | 0.004288 | | | 6.49 +Pair | 0.031443 | 0.032581 | 0.034717 | 0.7 | 44.04 +Neigh | 0.01403 | 0.014414 | 0.01483 | 0.2 | 19.49 +Comm | 0.013565 | 0.015975 | 0.01834 | 1.4 | 21.60 +Output | 0.00017476 | 0.00018531 | 0.00020695 | 0.0 | 0.25 +Modify | 0.0037742 | 0.0043355 | 0.0058382 | 1.3 | 5.86 +Other | | 0.006481 | | | 8.76 Nlocal: 200 ave 202 max 196 min Histogram: 1 0 0 0 0 0 0 0 2 1 @@ -98,7 +105,7 @@ thermo 50 # atoms only minimize 1.0e-6 0.001 1000 10000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp E_pair E_mol TotEng Press 1000 0 -0.77076863 0 -0.77076863 12.920868 1050 0 -2.8318266 0 -2.8318266 -1.1892931 @@ -107,9 +114,9 @@ Step Temp E_pair E_mol TotEng Press 1200 0 -2.8831122 0 -2.8831122 -1.1004001 1250 0 -2.8877971 0 -2.8877971 -1.0596414 1300 0 -2.8887969 0 -2.8887969 -1.0448381 -Loop time of 0.0501025 on 4 procs for 300 steps with 800 atoms +Loop time of 0.0533715 on 4 procs for 300 steps with 800 atoms -99.8% CPU use with 4 MPI tasks x no OpenMP threads +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -123,12 +130,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.030059 | 0.030357 | 0.030755 | 0.2 | 60.59 -Neigh | 0.0037379 | 0.0037849 | 0.0038264 | 0.1 | 7.55 -Comm | 0.0061991 | 0.0067289 | 0.0071735 | 0.5 | 13.43 -Output | 7.3195e-05 | 7.7724e-05 | 8.9407e-05 | 0.1 | 0.16 -Modify | 0.00036192 | 0.00037038 | 0.00037956 | 0.0 | 0.74 -Other | | 0.008784 | | | 17.53 +Pair | 0.029885 | 0.031269 | 0.033625 | 0.8 | 58.59 +Neigh | 0.0038524 | 0.0040049 | 0.0040805 | 0.1 | 7.50 +Comm | 0.0062668 | 0.0087315 | 0.010314 | 1.7 | 16.36 +Output | 7.9632e-05 | 8.3268e-05 | 9.346e-05 | 0.0 | 0.16 +Modify | 0.00043797 | 0.00044793 | 0.00045705 | 0.0 | 0.84 +Other | | 0.008835 | | | 16.55 Nlocal: 200 ave 202 max 196 min Histogram: 1 0 0 0 0 0 1 0 0 2 @@ -152,15 +159,15 @@ thermo_style custom step temp pe pxx pyy pxy f_3 v_emin # anisotropic volume relaxation to hydrostatic target minimize 0.0 10.0e0 10000 100000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1300 0 -2.8887969 -0.93904343 -1.1506328 -0.0037265764 0 -2.8887969 1350 0 -2.889313 1.555657 1.4414453 -0.025585726 -0.10933729 -2.9986503 1400 0 -2.8958621 1.5320803 1.476774 0.0041557664 -0.1208966 -3.0167587 1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 -0.12088872 -3.0171446 -Loop time of 0.0163901 on 4 procs for 103 steps with 800 atoms +Loop time of 0.0172202 on 4 procs for 103 steps with 800 atoms -97.6% CPU use with 4 MPI tasks x no OpenMP threads +96.4% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -174,12 +181,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0086238 | 0.0087494 | 0.0088425 | 0.1 | 53.38 -Neigh | 0.00099087 | 0.0010223 | 0.0010412 | 0.1 | 6.24 -Comm | 0.0017323 | 0.0018613 | 0.002028 | 0.3 | 11.36 -Output | 7.3195e-05 | 7.4625e-05 | 7.8917e-05 | 0.0 | 0.46 -Modify | 9.7513e-05 | 0.00010496 | 0.00011063 | 0.1 | 0.64 -Other | | 0.004578 | | | 27.93 +Pair | 0.0085471 | 0.0087811 | 0.0090215 | 0.2 | 50.99 +Neigh | 0.0010307 | 0.0011456 | 0.0013525 | 0.4 | 6.65 +Comm | 0.0017407 | 0.0020964 | 0.0024772 | 0.6 | 12.17 +Output | 7.5102e-05 | 7.695e-05 | 8.1301e-05 | 0.0 | 0.45 +Modify | 0.00012064 | 0.0001241 | 0.00012684 | 0.0 | 0.72 +Other | | 0.004996 | | | 29.01 Nlocal: 200 ave 202 max 198 min Histogram: 1 0 0 0 0 2 0 0 0 1 @@ -196,13 +203,13 @@ Dangerous builds = 0 fix 3 all box/relax aniso 1.5 vmax 1.0e-3 minimize 0.0 10.0 10000 100000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 0 -2.8962558 1404 0 -2.8963678 1.49615 1.499767 0.0037848845 9.6365079e-05 -2.8962714 -Loop time of 0.000319898 on 4 procs for 1 steps with 800 atoms +Loop time of 0.000330448 on 4 procs for 1 steps with 800 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -216,12 +223,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00016475 | 0.0001657 | 0.00016618 | 0.0 | 51.80 +Pair | 0.00016141 | 0.00016457 | 0.00016809 | 0.0 | 49.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 2.9802e-05 | 3.1531e-05 | 3.4094e-05 | 0.0 | 9.86 +Comm | 2.861e-05 | 3.3557e-05 | 3.7193e-05 | 0.0 | 10.16 Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 2.1458e-06 | 2.563e-06 | 3.3379e-06 | 0.0 | 0.80 -Other | | 0.0001201 | | | 37.54 +Modify | 2.1458e-06 | 2.3842e-06 | 2.6226e-06 | 0.0 | 0.72 +Other | | 0.0001299 | | | 39.32 Nlocal: 200 ave 202 max 197 min Histogram: 1 0 0 0 0 0 1 0 1 1 @@ -240,16 +247,16 @@ Dangerous builds = 0 fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 minimize 0.0 10.0 10000 100000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1404 0 -2.8963678 1.49615 1.499767 0.0037848845 -7.1054274e-17 -2.8963678 1450 0 -2.8925305 0.94584654 2.0945709 -0.029336194 -0.016086454 -2.9086169 1500 0 -2.8975934 1.0123866 2.009477 -0.036498498 -0.01841842 -2.9160118 1550 0 -2.903576 1.0046986 1.9380791 -0.037683327 -0.020970768 -2.9245468 1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 -0.024234721 -2.9303646 -Loop time of 0.0294311 on 4 procs for 188 steps with 800 atoms +Loop time of 0.0321782 on 4 procs for 188 steps with 800 atoms -101.1% CPU use with 4 MPI tasks x no OpenMP threads +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -263,12 +270,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.016194 | 0.016255 | 0.0163 | 0.0 | 55.23 -Neigh | 0.00050688 | 0.0005179 | 0.00053 | 0.0 | 1.76 -Comm | 0.0030935 | 0.0031458 | 0.0031939 | 0.1 | 10.69 -Output | 0.00011897 | 0.00012201 | 0.00013018 | 0.0 | 0.41 -Modify | 0.00016952 | 0.0001781 | 0.00018668 | 0.0 | 0.61 -Other | | 0.009212 | | | 31.30 +Pair | 0.015791 | 0.016377 | 0.01695 | 0.3 | 50.90 +Neigh | 0.00053954 | 0.00056165 | 0.00057793 | 0.0 | 1.75 +Comm | 0.0027378 | 0.0033152 | 0.0039263 | 0.8 | 10.30 +Output | 0.00014901 | 0.00015163 | 0.00015783 | 0.0 | 0.47 +Modify | 0.00021982 | 0.00022542 | 0.0002315 | 0.0 | 0.70 +Other | | 0.01155 | | | 35.88 Nlocal: 200 ave 202 max 196 min Histogram: 1 0 0 0 0 0 0 0 2 1 @@ -283,7 +290,7 @@ Neighbor list builds = 8 Dangerous builds = 0 minimize 0.0 1.0 10000 100000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 3.5527137e-17 -2.9061298 1600 0 -2.9046586 1.0529014 2.0593731 -0.050860896 -0.0020973121 -2.9067559 @@ -378,9 +385,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 6050 0 -3.0313105 0.9590106 1.959899 0.10814531 -0.084790331 -3.1161008 6100 0 -3.0313244 0.9580272 1.9605104 0.10879691 -0.08493735 -3.1162617 6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -0.084945274 -3.1162837 -Loop time of 0.833589 on 4 procs for 4538 steps with 800 atoms +Loop time of 0.937381 on 4 procs for 4538 steps with 800 atoms -99.7% CPU use with 4 MPI tasks x no OpenMP threads +95.6% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -394,12 +401,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.45739 | 0.47006 | 0.47928 | 1.2 | 56.39 -Neigh | 0.006587 | 0.0068482 | 0.0069439 | 0.2 | 0.82 -Comm | 0.089155 | 0.097262 | 0.11111 | 2.7 | 11.67 -Output | 0.0035946 | 0.0036807 | 0.0039296 | 0.2 | 0.44 -Modify | 0.0051167 | 0.0053424 | 0.005434 | 0.2 | 0.64 -Other | | 0.2504 | | | 30.04 +Pair | 0.45297 | 0.47262 | 0.48939 | 2.1 | 50.42 +Neigh | 0.0071242 | 0.0072536 | 0.0073645 | 0.1 | 0.77 +Comm | 0.12672 | 0.1453 | 0.17041 | 4.8 | 15.50 +Output | 0.0040541 | 0.0063651 | 0.013254 | 5.0 | 0.68 +Modify | 0.0063808 | 0.0065207 | 0.0066283 | 0.1 | 0.70 +Other | | 0.2993 | | | 31.93 Nlocal: 200 ave 203 max 197 min Histogram: 1 0 0 1 0 0 1 0 0 1 @@ -414,7 +421,7 @@ Neighbor list builds = 104 Dangerous builds = 0 minimize 0.0 1.0e-2 10000 100000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -3.5527137e-17 -3.0313384 6150 0 -3.0304428 0.9947235 1.9969091 0.10935746 -0.00091797415 -3.0313608 @@ -448,9 +455,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 7550 0 -3.0303533 1.0000018 1.9999949 0.10769873 -0.0010415749 -3.0313949 7600 0 -3.0303529 1.0000017 2.0000034 0.10770161 -0.0010419517 -3.0313949 7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 -0.0010421819 -3.0313949 -Loop time of 0.279601 on 4 procs for 1477 steps with 800 atoms +Loop time of 0.311816 on 4 procs for 1477 steps with 800 atoms -99.9% CPU use with 4 MPI tasks x no OpenMP threads +96.2% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -464,12 +471,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.15759 | 0.16061 | 0.16246 | 0.5 | 57.44 +Pair | 0.16143 | 0.16413 | 0.16779 | 0.6 | 52.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.026405 | 0.029149 | 0.033293 | 1.5 | 10.43 -Output | 0.0011969 | 0.0012203 | 0.0012867 | 0.1 | 0.44 -Modify | 0.0017877 | 0.0018381 | 0.0019131 | 0.1 | 0.66 -Other | | 0.08679 | | | 31.04 +Comm | 0.03717 | 0.042433 | 0.05037 | 2.5 | 13.61 +Output | 0.0012872 | 0.0017485 | 0.0031171 | 1.9 | 0.56 +Modify | 0.0022309 | 0.0022756 | 0.002321 | 0.1 | 0.73 +Other | | 0.1012 | | | 32.46 Nlocal: 200 ave 203 max 197 min Histogram: 1 0 0 1 0 0 1 0 0 1 @@ -488,7 +495,7 @@ Dangerous builds = 0 fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100 minimize 0.0 1.0e-4 10000 100000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 3.5527137e-17 -3.0303527 7650 0 -3.030353 0.9999904 2.0000076 0.10770145 2.9878713e-07 -3.0303527 @@ -504,9 +511,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 8150 0 -3.0303532 1.0000003 2.0000002 0.10770398 -1.4421314e-09 -3.0303532 8200 0 -3.0303532 1.0000001 2.0000001 0.10770407 7.0744514e-10 -3.0303532 8201 0 -3.0303532 0.99999993 2 0.10770406 3.9670625e-09 -3.0303532 -Loop time of 0.118568 on 4 procs for 594 steps with 800 atoms +Loop time of 0.129036 on 4 procs for 594 steps with 800 atoms -99.7% CPU use with 4 MPI tasks x no OpenMP threads +95.5% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = force tolerance @@ -520,12 +527,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.063769 | 0.065702 | 0.068746 | 0.7 | 55.41 +Pair | 0.06542 | 0.066275 | 0.068163 | 0.4 | 51.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011877 | 0.015052 | 0.017311 | 1.6 | 12.69 -Output | 0.0004735 | 0.00048357 | 0.00051045 | 0.1 | 0.41 -Modify | 0.00073504 | 0.00075912 | 0.00081396 | 0.1 | 0.64 -Other | | 0.03657 | | | 30.84 +Comm | 0.015691 | 0.016819 | 0.018781 | 0.9 | 13.03 +Output | 0.00052595 | 0.00067312 | 0.0011091 | 0.0 | 0.52 +Modify | 0.00091577 | 0.0009293 | 0.0009408 | 0.0 | 0.72 +Other | | 0.04434 | | | 34.36 Nlocal: 200 ave 203 max 197 min Histogram: 1 0 0 1 0 0 1 0 0 1 diff --git a/examples/min/log.5Oct16.min.g++.1 b/examples/min/log.27Nov18.min.g++.1 similarity index 73% rename from examples/min/log.5Oct16.min.g++.1 rename to examples/min/log.27Nov18.min.g++.1 index 9d38693274..98c3ca3b93 100644 --- a/examples/min/log.5Oct16.min.g++.1 +++ b/examples/min/log.27Nov18.min.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d Lennard-Jones melt and subsequent energy minimization units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 800 atoms + Time spent = 0.000434637 secs mass 1 1.0 velocity all create 5.0 87287 loop geom @@ -39,13 +41,18 @@ thermo 100 run 1000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 22 22 1 -Memory usage per processor = 2.47843 Mbytes + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.056 | 3.056 | 3.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 5 -2.461717 0 2.532033 5.0190509 100 3.2788864 -0.74311698 0 2.5316708 15.912832 @@ -58,20 +65,20 @@ Step Temp E_pair E_mol TotEng Press 800 3.3016275 -0.76569171 0 2.5318087 15.639335 900 3.4639203 -0.92788002 0 2.5317104 14.765912 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 -Loop time of 0.201747 on 1 procs for 1000 steps with 800 atoms +Loop time of 0.206744 on 1 procs for 1000 steps with 800 atoms -Performance: 2141296.412 tau/day, 4956.705 timesteps/s -99.6% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 2089538.727 tau/day, 4836.895 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12879 | 0.12879 | 0.12879 | 0.0 | 63.84 -Neigh | 0.051049 | 0.051049 | 0.051049 | 0.0 | 25.30 -Comm | 0.0043695 | 0.0043695 | 0.0043695 | 0.0 | 2.17 -Output | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 | 0.0 | 0.04 -Modify | 0.011838 | 0.011838 | 0.011838 | 0.0 | 5.87 -Other | | 0.005622 | | | 2.79 +Pair | 0.12643 | 0.12643 | 0.12643 | 0.0 | 61.15 +Neigh | 0.053694 | 0.053694 | 0.053694 | 0.0 | 25.97 +Comm | 0.0061328 | 0.0061328 | 0.0061328 | 0.0 | 2.97 +Output | 0.00011373 | 0.00011373 | 0.00011373 | 0.0 | 0.06 +Modify | 0.014107 | 0.014107 | 0.014107 | 0.0 | 6.82 +Other | | 0.006263 | | | 3.03 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -91,7 +98,7 @@ neigh_modify delay 0 every 1 check yes thermo 50 minimize 1.0e-6 0.001 1000 10000 -Memory usage per processor = 3.60343 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes Step Temp E_pair E_mol TotEng Press 1000 3.3256788 -0.79078181 0 2.5307399 15.599298 1050 3.3256788 -2.8361415 0 0.48538014 1.6090001 @@ -104,9 +111,9 @@ Step Temp E_pair E_mol TotEng Press 1400 3.3256788 -2.9131297 0 0.40839199 1.7078217 1450 3.3256788 -2.9167506 0 0.40477104 1.7780477 1475 3.3256788 -2.9169436 0 0.4045781 1.7914542 -Loop time of 0.231352 on 1 procs for 475 steps with 800 atoms +Loop time of 0.233542 on 1 procs for 475 steps with 800 atoms -99.8% CPU use with 1 MPI tasks x no OpenMP threads +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -120,12 +127,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.18807 | 0.18807 | 0.18807 | 0.0 | 81.29 -Neigh | 0.02088 | 0.02088 | 0.02088 | 0.0 | 9.03 -Comm | 0.0028048 | 0.0028048 | 0.0028048 | 0.0 | 1.21 -Output | 6.9618e-05 | 6.9618e-05 | 6.9618e-05 | 0.0 | 0.03 -Modify | 0.0020773 | 0.0020773 | 0.0020773 | 0.0 | 0.90 -Other | | 0.01745 | | | 7.54 +Pair | 0.18404 | 0.18404 | 0.18404 | 0.0 | 78.80 +Neigh | 0.02204 | 0.02204 | 0.02204 | 0.0 | 9.44 +Comm | 0.0040922 | 0.0040922 | 0.0040922 | 0.0 | 1.75 +Output | 0.00010443 | 0.00010443 | 0.00010443 | 0.0 | 0.04 +Modify | 0.0023651 | 0.0023651 | 0.0023651 | 0.0 | 1.01 +Other | | 0.0209 | | | 8.95 Nlocal: 800 ave 800 max 800 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/min/log.5Oct16.min.g++.4 b/examples/min/log.27Nov18.min.g++.4 similarity index 71% rename from examples/min/log.5Oct16.min.g++.4 rename to examples/min/log.27Nov18.min.g++.4 index c58633b77c..43171cd28d 100644 --- a/examples/min/log.5Oct16.min.g++.4 +++ b/examples/min/log.27Nov18.min.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d Lennard-Jones melt and subsequent energy minimization units lj @@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 2 by 2 by 1 MPI processor grid create_atoms 1 box Created 800 atoms + Time spent = 0.000340223 secs mass 1 1.0 velocity all create 5.0 87287 loop geom @@ -39,13 +41,18 @@ thermo 100 run 1000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 22 22 1 -Memory usage per processor = 2.47676 Mbytes + binsize = 1.4, bins = 22 22 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.049 | 3.049 | 3.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 5 -2.461717 0 2.532033 5.0190509 100 3.2788864 -0.74311698 0 2.5316708 15.912832 @@ -58,20 +65,20 @@ Step Temp E_pair E_mol TotEng Press 800 3.3016408 -0.76570603 0 2.5318077 15.639259 900 3.4621697 -0.92610292 0 2.5317391 14.773473 1000 3.3058424 -0.77076863 0 2.5309414 15.708171 -Loop time of 0.162444 on 4 procs for 1000 steps with 800 atoms +Loop time of 0.0730537 on 4 procs for 1000 steps with 800 atoms -Performance: 2659379.051 tau/day, 6155.970 timesteps/s -78.3% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 5913456.756 tau/day, 13688.557 timesteps/s +95.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.032602 | 0.033969 | 0.034999 | 0.5 | 20.91 -Neigh | 0.013433 | 0.013719 | 0.013862 | 0.1 | 8.45 -Comm | 0.08291 | 0.088224 | 0.099287 | 2.2 | 54.31 -Output | 0.00084209 | 0.00093055 | 0.00097394 | 0.2 | 0.57 -Modify | 0.0030942 | 0.0033001 | 0.0035179 | 0.3 | 2.03 -Other | | 0.0223 | | | 13.73 +Pair | 0.031481 | 0.031893 | 0.032234 | 0.2 | 43.66 +Neigh | 0.014234 | 0.014466 | 0.014672 | 0.1 | 19.80 +Comm | 0.017078 | 0.01775 | 0.018055 | 0.3 | 24.30 +Output | 0.00017548 | 0.00027454 | 0.00056386 | 0.0 | 0.38 +Modify | 0.0038447 | 0.0038754 | 0.0038893 | 0.0 | 5.30 +Other | | 0.004795 | | | 6.56 Nlocal: 200 ave 202 max 196 min Histogram: 1 0 0 0 0 0 0 0 2 1 @@ -91,7 +98,7 @@ neigh_modify delay 0 every 1 check yes thermo 50 minimize 1.0e-6 0.001 1000 10000 -Memory usage per processor = 3.60176 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes Step Temp E_pair E_mol TotEng Press 1000 3.3058424 -0.77076863 0 2.5309414 15.708171 1050 3.3058424 -2.8318266 0 0.46988351 1.5980106 @@ -100,9 +107,9 @@ Step Temp E_pair E_mol TotEng Press 1200 3.3058424 -2.8831122 0 0.41859789 1.6869035 1250 3.3058424 -2.8877971 0 0.413913 1.7276622 1300 3.3058424 -2.8887969 0 0.41291311 1.7424655 -Loop time of 0.048058 on 4 procs for 300 steps with 800 atoms +Loop time of 0.055995 on 4 procs for 300 steps with 800 atoms -98.8% CPU use with 4 MPI tasks x no OpenMP threads +96.0% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -116,12 +123,12 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.03076 | 0.031581 | 0.032226 | 0.3 | 65.71 -Neigh | 0.0037913 | 0.0038914 | 0.0039353 | 0.1 | 8.10 -Comm | 0.004194 | 0.0049016 | 0.0058777 | 1.0 | 10.20 -Output | 6.3181e-05 | 6.6817e-05 | 7.7009e-05 | 0.1 | 0.14 -Modify | 0.00035 | 0.00036556 | 0.0003829 | 0.1 | 0.76 -Other | | 0.007252 | | | 15.09 +Pair | 0.029709 | 0.030492 | 0.031057 | 0.3 | 54.45 +Neigh | 0.0040245 | 0.0042111 | 0.0046084 | 0.4 | 7.52 +Comm | 0.010827 | 0.011703 | 0.012587 | 0.6 | 20.90 +Output | 9.8228e-05 | 0.00024104 | 0.00066733 | 0.0 | 0.43 +Modify | 0.0004456 | 0.00045222 | 0.00045633 | 0.0 | 0.81 +Other | | 0.008895 | | | 15.89 Nlocal: 200 ave 202 max 196 min Histogram: 1 0 0 0 0 0 1 0 0 2 diff --git a/examples/msst/log.5Oct16.msst.g++.1 b/examples/msst/log.27Nov18.msst.g++.1 similarity index 79% rename from examples/msst/log.5Oct16.msst.g++.1 rename to examples/msst/log.27Nov18.msst.g++.1 index 64af995896..4b18e67702 100644 --- a/examples/msst/log.5Oct16.msst.g++.1 +++ b/examples/msst/log.27Nov18.msst.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # LJ test of msst shock dynamics # Energy in eV, time in ps, distance in angstroms. @@ -20,6 +21,7 @@ Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602) 1 by 1 by 1 MPI processor grid create_atoms 1 region box1 Created 23328 atoms + Time spent = 0.00902033 secs mass 1 40.00 @@ -37,13 +39,18 @@ thermo 10 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 17 17 17 -Memory usage per processor = 8.03726 Mbytes + binsize = 6, bins = 17 17 17 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.86 | 17.86 | 17.86 Mbytes Step Temp E_pair E_mol TotEng Press 0 600 -1943.9014 0 -134.75058 992.06384 10 586.44651 -1917.3971 0 -149.11346 1306.17 @@ -56,20 +63,20 @@ Step Temp E_pair E_mol TotEng Press 80 300.28534 -1056.589 0 -151.15321 8324.8812 90 305.83368 -1073.3097 0 -151.14426 8175.2478 100 304.06857 -1067.9843 0 -151.14112 8191.234 -Loop time of 3.5066 on 1 procs for 100 steps with 23328 atoms +Loop time of 3.49498 on 1 procs for 100 steps with 23328 atoms -Performance: 4.928 ns/day, 4.870 hours/ns, 28.518 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 4.944 ns/day, 4.854 hours/ns, 28.612 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.3534 | 3.3534 | 3.3534 | 0.0 | 95.63 -Neigh | 0.066456 | 0.066456 | 0.066456 | 0.0 | 1.90 -Comm | 0.01981 | 0.01981 | 0.01981 | 0.0 | 0.56 -Output | 0.00096083 | 0.00096083 | 0.00096083 | 0.0 | 0.03 -Modify | 0.037752 | 0.037752 | 0.037752 | 0.0 | 1.08 -Other | | 0.02825 | | | 0.81 +Pair | 3.354 | 3.354 | 3.354 | 0.0 | 95.97 +Neigh | 0.074059 | 0.074059 | 0.074059 | 0.0 | 2.12 +Comm | 0.020118 | 0.020118 | 0.020118 | 0.0 | 0.58 +Output | 0.0010924 | 0.0010924 | 0.0010924 | 0.0 | 0.03 +Modify | 0.034063 | 0.034063 | 0.034063 | 0.0 | 0.97 +Other | | 0.01168 | | | 0.33 Nlocal: 23328 ave 23328 max 23328 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -118,7 +125,7 @@ Fix MSST v0 = 8.97521e+05 Fix MSST p0 = 8.10679e+03 Fix MSST e0 = to be -1.51141e+02 Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02 -Memory usage per processor = 8.04369 Mbytes +Per MPI rank memory allocation (min/avg/max) = 18.99 | 18.99 | 18.99 Mbytes Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst 100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318 110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721 @@ -131,20 +138,20 @@ Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lg 180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622 190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999 200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149 -Loop time of 4.74363 on 1 procs for 100 steps with 23328 atoms +Loop time of 5.50267 on 1 procs for 100 steps with 23328 atoms -Performance: 3.643 ns/day, 6.588 hours/ns, 21.081 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3.140 ns/day, 7.643 hours/ns, 18.173 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.366 | 3.366 | 3.366 | 0.0 | 70.96 -Neigh | 0.13476 | 0.13476 | 0.13476 | 0.0 | 2.84 -Comm | 0.017403 | 0.017403 | 0.017403 | 0.0 | 0.37 -Output | 0.011465 | 0.011465 | 0.011465 | 0.0 | 0.24 -Modify | 1.1866 | 1.1866 | 1.1866 | 0.0 | 25.01 -Other | | 0.02743 | | | 0.58 +Pair | 4.7512 | 4.7512 | 4.7512 | 0.0 | 86.34 +Neigh | 0.14916 | 0.14916 | 0.14916 | 0.0 | 2.71 +Comm | 0.020737 | 0.020737 | 0.020737 | 0.0 | 0.38 +Output | 0.010999 | 0.010999 | 0.010999 | 0.0 | 0.20 +Modify | 0.55965 | 0.55965 | 0.55965 | 0.0 | 10.17 +Other | | 0.01089 | | | 0.20 Nlocal: 23328 ave 23328 max 23328 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -157,4 +164,4 @@ Total # of neighbors = 2183494 Ave neighs/atom = 93.5997 Neighbor list builds = 2 Dangerous builds = 0 -Total wall time: 0:00:08 +Total wall time: 0:00:09 diff --git a/examples/msst/log.5Oct16.msst.g++.4 b/examples/msst/log.27Nov18.msst.g++.4 similarity index 79% rename from examples/msst/log.5Oct16.msst.g++.4 rename to examples/msst/log.27Nov18.msst.g++.4 index 6026141ace..c2ed0fcb5e 100644 --- a/examples/msst/log.5Oct16.msst.g++.4 +++ b/examples/msst/log.27Nov18.msst.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # LJ test of msst shock dynamics # Energy in eV, time in ps, distance in angstroms. @@ -20,6 +21,7 @@ Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602) 1 by 2 by 2 MPI processor grid create_atoms 1 region box1 Created 23328 atoms + Time spent = 0.00104165 secs mass 1 40.00 @@ -37,13 +39,18 @@ thermo 10 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 17 17 17 -Memory usage per processor = 5.24184 Mbytes + binsize = 6, bins = 17 17 17 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 600 -1943.9014 0 -134.75058 992.06384 10 586.47212 -1917.4465 0 -149.08565 1305.7368 @@ -56,20 +63,20 @@ Step Temp E_pair E_mol TotEng Press 80 299.37658 -1053.8476 0 -151.1519 8352.9467 90 304.24026 -1068.4941 0 -151.13319 8218.1594 100 301.9683 -1061.6332 0 -151.12284 8244.1277 -Loop time of 0.933851 on 4 procs for 100 steps with 23328 atoms +Loop time of 0.978562 on 4 procs for 100 steps with 23328 atoms -Performance: 18.504 ns/day, 1.297 hours/ns, 107.083 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 17.659 ns/day, 1.359 hours/ns, 102.191 timesteps/s +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.83046 | 0.85727 | 0.86953 | 1.7 | 91.80 -Neigh | 0.01685 | 0.017314 | 0.017519 | 0.2 | 1.85 -Comm | 0.028471 | 0.041764 | 0.070721 | 8.3 | 4.47 -Output | 0.00049806 | 0.00062126 | 0.00067735 | 0.3 | 0.07 -Modify | 0.0090787 | 0.009689 | 0.0099437 | 0.4 | 1.04 -Other | | 0.007188 | | | 0.77 +Pair | 0.86406 | 0.88129 | 0.89922 | 1.4 | 90.06 +Neigh | 0.019231 | 0.019453 | 0.019816 | 0.2 | 1.99 +Comm | 0.043947 | 0.06197 | 0.079005 | 5.1 | 6.33 +Output | 0.00057197 | 0.00082499 | 0.0015628 | 0.0 | 0.08 +Modify | 0.0091414 | 0.0092927 | 0.0094769 | 0.1 | 0.95 +Other | | 0.005727 | | | 0.59 Nlocal: 5832 ave 5850 max 5813 min Histogram: 1 0 0 0 1 1 0 0 0 1 @@ -118,7 +125,7 @@ Fix MSST v0 = 8.97521e+05 Fix MSST p0 = 8.18624e+03 Fix MSST e0 = to be -1.51123e+02 Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02 -Memory usage per processor = 5.24184 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.534 | 8.534 | 8.534 Mbytes Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lgr_pos f_msst 100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034 110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557 @@ -131,20 +138,20 @@ Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng v_dhug v_dray v_lgr_vel v_lg 180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462 190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801 200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378 -Loop time of 1.23008 on 4 procs for 100 steps with 23328 atoms +Loop time of 1.57102 on 4 procs for 100 steps with 23328 atoms -Performance: 14.048 ns/day, 1.708 hours/ns, 81.295 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 10.999 ns/day, 2.182 hours/ns, 63.653 timesteps/s +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.83631 | 0.84345 | 0.85189 | 0.8 | 68.57 -Neigh | 0.033866 | 0.03409 | 0.034339 | 0.1 | 2.77 -Comm | 0.029796 | 0.038609 | 0.045779 | 3.5 | 3.14 -Output | 0.0036259 | 0.0036446 | 0.0036905 | 0.0 | 0.30 -Modify | 0.30399 | 0.30447 | 0.30495 | 0.1 | 24.75 -Other | | 0.00582 | | | 0.47 +Pair | 1.2237 | 1.2543 | 1.3264 | 3.7 | 79.84 +Neigh | 0.038648 | 0.039684 | 0.041811 | 0.6 | 2.53 +Comm | 0.026617 | 0.10771 | 0.14194 | 14.3 | 6.86 +Output | 0.0035126 | 0.0045422 | 0.0076261 | 2.6 | 0.29 +Modify | 0.15787 | 0.15969 | 0.16403 | 0.6 | 10.16 +Other | | 0.005042 | | | 0.32 Nlocal: 5832 ave 5874 max 5803 min Histogram: 2 0 0 0 0 1 0 0 0 1 diff --git a/examples/nb3b/log.5Oct16.nb3b.g++.1 b/examples/nb3b/log.27Nov18.nb3b.g++.1 similarity index 71% rename from examples/nb3b/log.5Oct16.nb3b.g++.1 rename to examples/nb3b/log.27Nov18.nb3b.g++.1 index a156b3400c..d4a8cffc42 100644 --- a/examples/nb3b/log.5Oct16.nb3b.g++.1 +++ b/examples/nb3b/log.27Nov18.nb3b.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # test of NB3B pair style with pair hybrid and KSpace solver units real @@ -57,26 +58,46 @@ thermo 50 ### Minimize forces in structure ### minimize 1.0e-06 1.0e-08 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) EwaldDisp initialization ... -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) - G vector = 0.269426 -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) + G vector = 0.269426 accuracy = 0.0332064 +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) Neighbor list info ... - 4 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 4 4 4 + binsize = 6, bins = 4 4 4 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair nb3b/harmonic, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair lj/cut/coul/long, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) pair nb3b/harmonic, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (4) pair lj/cut/coul/long, perpetual, copy from (2) + attributes: half, newton on + pair build: copy + stencil: none + bin: none vectors: nbox = 6, nkvec = 478 -Memory usage per processor = 17.039 Mbytes +Per MPI rank memory allocation (min/avg/max) = 32.37 | 32.37 | 32.37 Mbytes Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume 0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72822 22.5907 22.359 23.4708 0 0 0 11855.229 4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.43 22.5907 22.359 23.4708 0 0 0 11855.229 -Loop time of 0.434716 on 1 procs for 4 steps with 1400 atoms +Loop time of 0.562063 on 1 procs for 4 steps with 1400 atoms -98.4% CPU use with 1 MPI tasks x no OpenMP threads +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -90,14 +111,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.35925 | 0.35925 | 0.35925 | 0.0 | 82.64 -Bond | 0.00031662 | 0.00031662 | 0.00031662 | 0.0 | 0.07 -Kspace | 0.074097 | 0.074097 | 0.074097 | 0.0 | 17.04 +Pair | 0.47517 | 0.47517 | 0.47517 | 0.0 | 84.54 +Bond | 0.00020051 | 0.00020051 | 0.00020051 | 0.0 | 0.04 +Kspace | 0.085509 | 0.085509 | 0.085509 | 0.0 | 15.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00059676 | 0.00059676 | 0.00059676 | 0.0 | 0.14 +Comm | 0.00077796 | 0.00077796 | 0.00077796 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0004592 | | | 0.11 +Other | | 0.0004046 | | | 0.07 Nlocal: 1400 ave 1400 max 1400 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -123,38 +144,31 @@ fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0 run 100 EwaldDisp initialization ... -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) - G vector = 0.269426 -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) -Neighbor list info ... - 4 neighbor list requests - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6 -> bins = 4 4 4 -Memory usage per processor = 16.664 Mbytes +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) + G vector = 0.269426 accuracy = 0.0332064 +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) +Per MPI rank memory allocation (min/avg/max) = 31.99 | 31.99 | 31.99 Mbytes Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume 4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.1472 22.5907 22.359 23.4708 0 0 0 11855.229 50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229 100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229 104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229 -Loop time of 7.88523 on 1 procs for 100 steps with 1400 atoms +Loop time of 10.7036 on 1 procs for 100 steps with 1400 atoms -Performance: 1.096 ns/day, 21.903 hours/ns, 12.682 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.807 ns/day, 29.732 hours/ns, 9.343 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.9318 | 6.9318 | 6.9318 | 0.0 | 87.91 -Bond | 0.0063558 | 0.0063558 | 0.0063558 | 0.0 | 0.08 -Kspace | 0.81841 | 0.81841 | 0.81841 | 0.0 | 10.38 -Neigh | 0.1015 | 0.1015 | 0.1015 | 0.0 | 1.29 -Comm | 0.013201 | 0.013201 | 0.013201 | 0.0 | 0.17 -Output | 9.7752e-05 | 9.7752e-05 | 9.7752e-05 | 0.0 | 0.00 -Modify | 0.0064344 | 0.0064344 | 0.0064344 | 0.0 | 0.08 -Other | | 0.007411 | | | 0.09 +Pair | 9.5983 | 9.5983 | 9.5983 | 0.0 | 89.67 +Bond | 0.0037653 | 0.0037653 | 0.0037653 | 0.0 | 0.04 +Kspace | 0.95057 | 0.95057 | 0.95057 | 0.0 | 8.88 +Neigh | 0.11977 | 0.11977 | 0.11977 | 0.0 | 1.12 +Comm | 0.018144 | 0.018144 | 0.018144 | 0.0 | 0.17 +Output | 0.00011969 | 0.00011969 | 0.00011969 | 0.0 | 0.00 +Modify | 0.0061135 | 0.0061135 | 0.0061135 | 0.0 | 0.06 +Other | | 0.006855 | | | 0.06 Nlocal: 1400 ave 1400 max 1400 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -170,4 +184,4 @@ Ave neighs/atom = 850.439 Ave special neighs/atom = 0.8 Neighbor list builds = 2 Dangerous builds = 0 -Total wall time: 0:00:08 +Total wall time: 0:00:11 diff --git a/examples/nb3b/log.5Oct16.nb3b.g++.4 b/examples/nb3b/log.27Nov18.nb3b.g++.4 similarity index 71% rename from examples/nb3b/log.5Oct16.nb3b.g++.4 rename to examples/nb3b/log.27Nov18.nb3b.g++.4 index f63a40486d..e2c1f77844 100644 --- a/examples/nb3b/log.5Oct16.nb3b.g++.4 +++ b/examples/nb3b/log.27Nov18.nb3b.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # test of NB3B pair style with pair hybrid and KSpace solver units real @@ -57,26 +58,46 @@ thermo 50 ### Minimize forces in structure ### minimize 1.0e-06 1.0e-08 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) EwaldDisp initialization ... -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) - G vector = 0.269426 -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) + G vector = 0.269426 accuracy = 0.0332064 +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) Neighbor list info ... - 4 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 4 4 4 + binsize = 6, bins = 4 4 4 + 4 neighbor lists, perpetual/occasional/extra = 4 0 0 + (1) pair nb3b/harmonic, perpetual + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) pair lj/cut/coul/long, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) pair nb3b/harmonic, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none + (4) pair lj/cut/coul/long, perpetual, copy from (2) + attributes: half, newton on + pair build: copy + stencil: none + bin: none vectors: nbox = 6, nkvec = 478 -Memory usage per processor = 16.9507 Mbytes +Per MPI rank memory allocation (min/avg/max) = 20.64 | 21.18 | 22.02 Mbytes Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume 0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72822 22.5907 22.359 23.4708 0 0 0 11855.229 4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.43 22.5907 22.359 23.4708 0 0 0 11855.229 -Loop time of 0.129448 on 4 procs for 4 steps with 1400 atoms +Loop time of 0.164255 on 4 procs for 4 steps with 1400 atoms -99.4% CPU use with 4 MPI tasks x no OpenMP threads +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance @@ -90,14 +111,14 @@ Minimization stats: MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.082641 | 0.0934 | 0.10605 | 3.3 | 72.15 -Bond | 7.2002e-05 | 7.9215e-05 | 8.6546e-05 | 0.1 | 0.06 -Kspace | 0.021445 | 0.032612 | 0.04218 | 4.9 | 25.19 +Pair | 0.11101 | 0.12473 | 0.13747 | 3.3 | 75.93 +Bond | 5.8889e-05 | 6.2823e-05 | 6.6757e-05 | 0.0 | 0.04 +Kspace | 0.025273 | 0.036047 | 0.047969 | 5.3 | 21.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0015318 | 0.0030052 | 0.0042045 | 2.1 | 2.32 +Comm | 0.001081 | 0.0030527 | 0.0048478 | 2.8 | 1.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.0003518 | | | 0.27 +Other | | 0.000367 | | | 0.22 Nlocal: 350 ave 399 max 305 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -123,38 +144,31 @@ fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0 run 100 EwaldDisp initialization ... -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) - G vector = 0.269426 -WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:216) -Neighbor list info ... - 4 neighbor list requests - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6 -> bins = 4 4 4 -Memory usage per processor = 16.5757 Mbytes +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) + G vector = 0.269426 accuracy = 0.0332064 +WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:218) +Per MPI rank memory allocation (min/avg/max) = 20.26 | 20.8 | 21.65 Mbytes Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume 4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.1472 22.5907 22.359 23.4708 0 0 0 11855.229 50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229 100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229 104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229 -Loop time of 2.3186 on 4 procs for 100 steps with 1400 atoms +Loop time of 3.0299 on 4 procs for 100 steps with 1400 atoms -Performance: 3.726 ns/day, 6.441 hours/ns, 43.129 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2.852 ns/day, 8.416 hours/ns, 33.004 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.7054 | 1.8352 | 1.9875 | 8.4 | 79.15 -Bond | 0.0015972 | 0.0017807 | 0.0019476 | 0.3 | 0.08 -Kspace | 0.21511 | 0.22245 | 0.23383 | 1.6 | 9.59 -Neigh | 0.026175 | 0.026182 | 0.026186 | 0.0 | 1.13 -Comm | 0.062151 | 0.21516 | 0.34573 | 24.7 | 9.28 -Output | 0.0001421 | 0.00016701 | 0.00020218 | 0.2 | 0.01 -Modify | 0.0021067 | 0.0031134 | 0.0037572 | 1.2 | 0.13 -Other | | 0.01456 | | | 0.63 +Pair | 2.424 | 2.5288 | 2.6552 | 6.3 | 83.46 +Bond | 0.0011241 | 0.0011699 | 0.0011907 | 0.1 | 0.04 +Kspace | 0.24584 | 0.25484 | 0.26259 | 1.5 | 8.41 +Neigh | 0.031059 | 0.031067 | 0.031075 | 0.0 | 1.03 +Comm | 0.070014 | 0.19745 | 0.30262 | 22.7 | 6.52 +Output | 0.00011683 | 0.0002265 | 0.00050616 | 0.0 | 0.01 +Modify | 0.0022085 | 0.0030763 | 0.0039916 | 1.3 | 0.10 +Other | | 0.01331 | | | 0.44 Nlocal: 350 ave 357 max 340 min Histogram: 1 0 0 0 0 0 1 1 0 1 @@ -170,4 +184,4 @@ Ave neighs/atom = 850.439 Ave special neighs/atom = 0.8 Neighbor list builds = 2 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:03 diff --git a/examples/nemd/log.27Nov18.nemd.g++.1 b/examples/nemd/log.27Nov18.nemd.g++.1 new file mode 100644 index 0000000000..c0989db969 --- /dev/null +++ b/examples/nemd/log.27Nov18.nemd.g++.1 @@ -0,0 +1,137 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d NEMD simulation + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000332355 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +#dump 1 all custom 5000 dump.nemd id type x y z + +#dump 2 all image 1000 image.*.jpg type type adiam 1.2 +#dump_modify 2 pad 5 + +#dump 3 all movie 1000 movie.mpg type type adiam 1.2 +#dump_modify 3 pad 5 + +thermo 1000 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.065 | 3.065 | 3.065 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 0 0 1.431 1.2080502 189.52855 + 1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855 + 2000 0.99104643 0.37634349 0 1.3611959 7.8993387 189.52855 + 3000 1.0749743 0.21908728 0 1.2873429 6.2659517 189.52855 + 4000 1.0986742 0.27147022 0 1.3632777 5.8778262 189.52855 + 5000 1.071838 0.23413372 0 1.2992728 5.9120887 189.52855 + 6000 1.0013194 0.26923671 0 1.2642979 6.2802759 189.52855 + 7000 0.94110685 0.3224557 0 1.2576806 6.1864166 189.52855 + 8000 0.97391513 0.28793383 0 1.255762 6.5071893 189.52855 + 9000 0.95346063 0.31050593 0 1.2580074 6.3321512 189.52855 + 10000 0.96236447 0.26298203 0 1.2193317 6.4083918 189.52855 + 11000 0.9511149 0.27571527 0 1.2208857 6.0949768 189.52855 + 12000 1.0186935 0.18134918 0 1.1936758 5.1269128 189.52855 + 13000 0.96350682 0.23171507 0 1.1892 5.7367267 189.52855 + 14000 0.94740402 0.27357945 0 1.2150622 6.0156532 189.52855 + 15000 0.87951545 0.27745111 0 1.1514696 6.297405 189.52855 + 16000 0.93216196 0.27020559 0 1.1965415 6.6188833 189.52855 + 17000 0.94109936 0.24756193 0 1.1827794 5.8993088 189.52855 + 18000 0.97325239 0.27996398 0 1.2471335 6.1486561 189.52855 + 19000 1.0494686 0.27132686 0 1.3142363 6.6757065 189.52855 + 20000 1.0391862 0.25195457 0 1.2846459 6.143235 189.52855 + 21000 0.96407137 0.27359166 0 1.2316376 5.9577116 189.52855 + 22000 0.97954534 0.31920255 0 1.2926257 6.5320163 189.52855 + 23000 0.97585473 0.24154424 0 1.2112999 6.0839179 189.52855 + 24000 1.0522109 0.1646952 0 1.2103298 5.0388687 189.52855 + 25000 0.93707172 0.25655806 0 1.1877731 5.819887 189.52855 + 26000 0.89798775 0.26629627 0 1.1586716 6.0393558 189.52855 + 27000 0.93259926 0.24542428 0 1.1721948 5.3560986 189.52855 + 28000 0.8428223 0.20784302 0 1.0453977 4.956911 189.52855 + 29000 0.81653505 0.21924932 0 1.030681 5.271501 189.52855 + 30000 0.90157811 0.15070734 0 1.0466506 4.476142 189.52855 + 31000 0.86580039 0.21115151 0 1.0715407 5.0056915 189.52855 + 32000 0.89768096 0.28377249 0 1.1758429 5.8449711 189.52855 + 33000 1.0504011 0.29009694 0 1.333933 6.1319155 189.52855 + 34000 1.2009765 0.19137934 0 1.3848498 4.9643885 189.52855 + 35000 1.208705 0.27071222 0 1.4718628 6.2162389 189.52855 + 36000 1.2211309 0.28389521 0 1.497394 6.5090715 189.52855 + 37000 1.1384381 0.42795547 0 1.5592783 8.5129272 189.52855 + 38000 1.2198334 0.34335732 0 1.5555668 7.2940883 189.52855 + 39000 1.1562045 0.35783089 0 1.5068091 7.340999 189.52855 + 40000 1.2145924 0.28410558 0 1.4911068 6.234986 189.52855 + 41000 1.1240878 0.34663237 0 1.4636946 7.1720193 189.52855 + 42000 1.2491422 0.26815889 0 1.509494 6.1390803 189.52855 + 43000 1.1387564 0.33755832 0 1.4691975 7.0577597 189.52855 + 44000 1.0031598 0.4081807 0 1.4050708 8.2732113 189.52855 + 45000 1.0166213 0.29131017 0 1.3015776 6.1907807 189.52855 + 46000 0.96251302 0.31483519 0 1.2713325 6.6987235 189.52855 + 47000 0.89809294 0.30909884 0 1.2015787 6.3997583 189.52855 + 48000 0.86736217 0.31917648 0 1.1811176 7.1584774 189.52855 + 49000 0.91979053 0.21099403 0 1.1250359 5.4968259 189.52855 + 50000 0.87079959 0.24059333 0 1.1059504 5.6039305 189.52855 +Loop time of 1.54353 on 1 procs for 50000 steps with 160 atoms + +Performance: 13993916.675 tau/day, 32393.326 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.20172 | 0.20172 | 0.20172 | 0.0 | 13.07 +Neigh | 0.16634 | 0.16634 | 0.16634 | 0.0 | 10.78 +Comm | 0.068928 | 0.068928 | 0.068928 | 0.0 | 4.47 +Output | 0.00059891 | 0.00059891 | 0.00059891 | 0.0 | 0.04 +Modify | 1.0123 | 1.0123 | 1.0123 | 0.0 | 65.59 +Other | | 0.09361 | | | 6.06 + +Nlocal: 160 ave 160 max 160 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 73 ave 73 max 73 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 353 ave 353 max 353 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 353 +Ave neighs/atom = 2.20625 +Neighbor list builds = 5273 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/nemd/log.27Nov18.nemd.g++.4 b/examples/nemd/log.27Nov18.nemd.g++.4 new file mode 100644 index 0000000000..68543882b7 --- /dev/null +++ b/examples/nemd/log.27Nov18.nemd.g++.4 @@ -0,0 +1,137 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d NEMD simulation + +units lj +atom_style atomic +dimension 2 + +lattice sq2 0.8442 +Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 +region box prism 0 10 0 8 -0.5 0.5 0 0 0 +create_box 2 box +Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) + 2 by 2 by 1 MPI processor grid +create_atoms 1 box +Created 160 atoms + Time spent = 0.000308275 secs +mass * 1.0 + +velocity all create 1.44 87287 loop geom + +region slice block 4 6 INF INF INF INF +set region slice type 2 + 40 settings made for type + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 1.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 + +fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 +fix 2 all deform 1 xy erate 0.01 remap v + +#dump 1 all custom 5000 dump.nemd id type x y z + +#dump 2 all image 1000 image.*.jpg type type adiam 1.2 +#dump_modify 2 pad 5 + +#dump 3 all movie 1000 movie.mpg type type adiam 1.2 +#dump_modify 3 pad 5 + +thermo 1000 + +run 50000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.3 + ghost atom cutoff = 1.3 + binsize = 0.65, bins = 24 19 3 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/2d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 1.44 0 0 1.431 1.2080502 189.52855 + 1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855 + 2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855 + 3000 1.09088 0.24816112 0 1.3322231 5.7001547 189.52855 + 4000 1.0110684 0.29868377 0 1.303433 7.3312319 189.52855 + 5000 0.91033678 0.28330698 0 1.1879542 6.1840352 189.52855 + 6000 0.93416074 0.22661127 0 1.1549335 5.3619735 189.52855 + 7000 0.93305734 0.19203739 0 1.1192631 5.2497547 189.52855 + 8000 0.88944438 0.19421381 0 1.0780992 4.9733446 189.52855 + 9000 0.86949257 0.21207681 0 1.0761351 5.4687076 189.52855 + 10000 0.80088203 0.24071142 0 1.0365879 5.334545 189.52855 + 11000 0.88899727 0.19972767 0 1.0831687 4.8832207 189.52855 + 12000 0.93045817 0.17883252 0 1.1034753 4.9081709 189.52855 + 13000 0.9724196 0.19089684 0 1.1572388 5.3460903 189.52855 + 14000 0.93902186 0.25513773 0 1.1882907 6.3338337 189.52855 + 15000 0.91879903 0.31605547 0 1.229112 6.2085671 189.52855 + 16000 0.9860058 0.26863362 0 1.2484769 6.514688 189.52855 + 17000 1.0354756 0.23445357 0 1.2634574 6.1519296 189.52855 + 18000 1.0244774 0.27511827 0 1.2931927 6.2230002 189.52855 + 19000 1.1581216 0.21558936 0 1.3664727 5.5458237 189.52855 + 20000 1.0552168 0.29344488 0 1.3420666 6.4880315 189.52855 + 21000 0.97925435 0.31583414 0 1.2889681 6.7584093 189.52855 + 22000 1.0112494 0.26246834 0 1.2673974 5.4112008 189.52855 + 23000 1.0463332 0.26049752 0 1.3002911 6.1359606 189.52855 + 24000 1.1130319 0.19848564 0 1.3045611 5.7088487 189.52855 + 25000 1.0355662 0.28048951 0 1.3095834 6.4596476 189.52855 + 26000 1.0823932 0.21784218 0 1.2934704 5.106334 189.52855 + 27000 0.99719525 0.32679678 0 1.3177596 6.7399277 189.52855 + 28000 1.0665868 0.25002709 0 1.3099477 6.2732557 189.52855 + 29000 1.0312798 0.30650087 0 1.3313351 7.0581024 189.52855 + 30000 1.0388277 0.29812912 0 1.3304641 6.2533028 189.52855 + 31000 1.0461658 0.21344416 0 1.2530714 5.3631154 189.52855 + 32000 1.0233681 0.27545017 0 1.2924222 5.9612896 189.52855 + 33000 1.1353086 0.20278244 0 1.3309953 5.7619128 189.52855 + 34000 1.0374791 0.29661216 0 1.327607 6.5124409 189.52855 + 35000 1.0752783 0.21684443 0 1.2854022 5.4759171 189.52855 + 36000 1.0383445 0.27068641 0 1.3025412 6.8367218 189.52855 + 37000 0.97341144 0.24034988 0 1.2076775 6.1335996 189.52855 + 38000 0.9285918 0.2737544 0 1.1965425 5.8750327 189.52855 + 39000 0.84869423 0.30079207 0 1.144182 6.8909326 189.52855 + 40000 0.88237131 0.26049171 0 1.1373482 6.3932981 189.52855 + 41000 0.90368591 0.21064132 0 1.1086792 5.5627232 189.52855 + 42000 0.93436749 0.20367569 0 1.1322034 5.1420052 189.52855 + 43000 0.91378588 0.26155533 0 1.16963 6.366756 189.52855 + 44000 0.91673608 0.25967314 0 1.1706796 6.0846334 189.52855 + 45000 1.0233334 0.25463562 0 1.2715732 6.0924255 189.52855 + 46000 0.96184729 0.35422095 0 1.3100567 7.0249175 189.52855 + 47000 1.134079 0.26196034 0 1.3889514 6.3476756 189.52855 + 48000 1.0552136 0.303812 0 1.3524305 6.6968927 189.52855 + 49000 1.1282184 0.2100955 0 1.3312626 5.8658659 189.52855 + 50000 1.0493816 0.31540438 0 1.3582274 6.6348173 189.52855 +Loop time of 1.09903 on 4 procs for 50000 steps with 160 atoms + +Performance: 19653623.953 tau/day, 45494.500 timesteps/s +94.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.057854 | 0.05974 | 0.062726 | 0.7 | 5.44 +Neigh | 0.047791 | 0.049863 | 0.054819 | 1.3 | 4.54 +Comm | 0.3581 | 0.38553 | 0.39784 | 2.6 | 35.08 +Output | 0.001116 | 0.0014414 | 0.0023859 | 1.4 | 0.13 +Modify | 0.41102 | 0.42642 | 0.4493 | 2.3 | 38.80 +Other | | 0.176 | | | 16.02 + +Nlocal: 40 ave 42 max 39 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Nghost: 36.5 ave 37 max 36 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 87.5 ave 94 max 81 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 350 +Ave neighs/atom = 2.1875 +Neighbor list builds = 5276 +Dangerous builds = 0 +Total wall time: 0:00:01 diff --git a/examples/nemd/log.5Oct16.nemd.g++.1 b/examples/nemd/log.5Oct16.nemd.g++.1 deleted file mode 100644 index fb5abee6e2..0000000000 --- a/examples/nemd/log.5Oct16.nemd.g++.1 +++ /dev/null @@ -1,130 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d NEMD simulation - -units lj -atom_style atomic -dimension 2 - -lattice sq2 0.8442 -Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 -region box prism 0 10 0 8 -0.5 0.5 0 0 0 -create_box 2 box -Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 160 atoms -mass * 1.0 - -velocity all create 1.44 87287 loop geom - -region slice block 4 6 INF INF INF INF -set region slice type 2 - 40 settings made for type - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 1.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 - -fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 -fix 2 all deform 1 xy erate 0.01 remap v - -#dump 1 all custom 5000 dump.nemd id type x y z - -#dump 2 all image 1000 image.*.jpg type type adiam 1.2 -#dump_modify 2 pad 5 - -#dump 3 all movie 1000 movie.mpg type type adiam 1.2 -#dump_modify 3 pad 5 - -thermo 1000 - -run 50000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 1.3 - binsize = 0.65 -> bins = 24 19 3 -Memory usage per processor = 2.49357 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1.44 0 0 1.431 1.2080502 189.52855 - 1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855 - 2000 1.0158438 0.33502643 0 1.3445212 7.2638652 189.52855 - 3000 1.0968167 0.3149227 0 1.4048843 7.0653223 189.52855 - 4000 1.0070993 0.40611915 0 1.4069241 7.7283521 189.52855 - 5000 1.1153133 0.2674828 0 1.3758254 6.2949171 189.52855 - 6000 1.0170665 0.25843673 0 1.2691466 6.049412 189.52855 - 7000 1.0224605 0.20974914 0 1.2258193 5.5104976 189.52855 - 8000 0.96149374 0.24035439 0 1.1958388 5.4179146 189.52855 - 9000 0.87759014 0.2590493 0 1.1311545 5.8711239 189.52855 - 10000 0.83791968 0.23477897 0 1.0674617 5.666904 189.52855 - 11000 0.87702487 0.22958877 0 1.1011322 5.9068062 189.52855 - 12000 0.81507294 0.26375817 0 1.0737369 5.9166925 189.52855 - 13000 0.85655284 0.24676491 0 1.0979643 5.6918734 189.52855 - 14000 0.84369293 0.27818471 0 1.1166046 6.4146184 189.52855 - 15000 0.90052173 0.19836095 0 1.0932544 5.2690913 189.52855 - 16000 0.83836874 0.26921637 0 1.1023453 5.9579526 189.52855 - 17000 0.90492897 0.21933098 0 1.1186041 5.6042194 189.52855 - 18000 0.90113412 0.24880908 0 1.1443111 6.0634846 189.52855 - 19000 1.0160445 0.17252962 0 1.1822239 5.3149334 189.52855 - 20000 0.96217234 0.2414377 0 1.1975965 5.476653 189.52855 - 21000 0.98229664 0.27569118 0 1.2518485 5.9340174 189.52855 - 22000 1.0551763 0.26997615 0 1.3185576 6.2094112 189.52855 - 23000 1.051999 0.34076639 0 1.3861904 7.082385 189.52855 - 24000 1.1350071 0.23701844 0 1.3649317 6.1829742 189.52855 - 25000 1.0946409 0.33366032 0 1.4214597 7.1907559 189.52855 - 26000 1.1511799 0.24626808 0 1.3902531 5.8469984 189.52855 - 27000 1.1009203 0.25653085 0 1.3505704 6.1504287 189.52855 - 28000 1.0521302 0.2876798 0 1.3332342 5.9906187 189.52855 - 29000 1.0518465 0.21853 0 1.2638025 5.6577549 189.52855 - 30000 0.97264625 0.28758145 0 1.2541487 6.5769804 189.52855 - 31000 1.0133579 0.31575837 0 1.3227828 6.6650893 189.52855 - 32000 1.0714324 0.28757036 0 1.3523063 6.2682059 189.52855 - 33000 1.0739451 0.28062459 0 1.3478575 6.6862746 189.52855 - 34000 1.0056867 0.38289586 0 1.382297 7.1120131 189.52855 - 35000 1.0911349 0.26370939 0 1.3480247 6.1476048 189.52855 - 36000 1.0618618 0.28269593 0 1.3379211 6.9414608 189.52855 - 37000 1.0704991 0.29974994 0 1.3635585 7.0834346 189.52855 - 38000 1.1087507 0.2682201 0 1.3700411 5.8506019 189.52855 - 39000 1.1303733 0.22362416 0 1.3469326 5.2500269 189.52855 - 40000 1.0174248 0.28956571 0 1.3006316 6.4491571 189.52855 - 41000 0.95981887 0.29162143 0 1.2454414 6.4658646 189.52855 - 42000 0.88302144 0.30432252 0 1.1818251 6.7401923 189.52855 - 43000 0.93164419 0.25110308 0 1.1769245 5.9067383 189.52855 - 44000 0.98352598 0.23322873 0 1.2106077 5.5606585 189.52855 - 45000 1.0247245 0.26503082 0 1.2833508 6.533394 189.52855 - 46000 0.93004532 0.32277782 0 1.2470104 6.4689179 189.52855 - 47000 1.0653176 0.29185413 0 1.3505135 6.9534569 189.52855 - 48000 1.0401524 0.3420245 0 1.3756759 6.8016042 189.52855 - 49000 1.0023407 0.31833091 0 1.314407 6.7385662 189.52855 - 50000 1.0566272 0.28657142 0 1.3365947 6.261203 189.52855 -Loop time of 1.14585 on 1 procs for 50000 steps with 160 atoms - -Performance: 18850616.224 tau/day, 43635.686 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.19375 | 0.19375 | 0.19375 | 0.0 | 16.91 -Neigh | 0.17407 | 0.17407 | 0.17407 | 0.0 | 15.19 -Comm | 0.046638 | 0.046638 | 0.046638 | 0.0 | 4.07 -Output | 0.0003221 | 0.0003221 | 0.0003221 | 0.0 | 0.03 -Modify | 0.66586 | 0.66586 | 0.66586 | 0.0 | 58.11 -Other | | 0.06522 | | | 5.69 - -Nlocal: 160 ave 160 max 160 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 71 ave 71 max 71 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 362 ave 362 max 362 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 362 -Ave neighs/atom = 2.2625 -Neighbor list builds = 5256 -Dangerous builds = 0 -Total wall time: 0:00:01 diff --git a/examples/nemd/log.5Oct16.nemd.g++.4 b/examples/nemd/log.5Oct16.nemd.g++.4 deleted file mode 100644 index 7738d64e2e..0000000000 --- a/examples/nemd/log.5Oct16.nemd.g++.4 +++ /dev/null @@ -1,130 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d NEMD simulation - -units lj -atom_style atomic -dimension 2 - -lattice sq2 0.8442 -Lattice spacing in x,y,z = 1.53919 1.53919 1.53919 -region box prism 0 10 0 8 -0.5 0.5 0 0 0 -create_box 2 box -Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0) - 2 by 2 by 1 MPI processor grid -create_atoms 1 box -Created 160 atoms -mass * 1.0 - -velocity all create 1.44 87287 loop geom - -region slice block 4 6 INF INF INF INF -set region slice type 2 - 40 settings made for type - -pair_style lj/cut 2.5 -pair_coeff * * 1.0 1.0 1.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 - -fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1 -fix 2 all deform 1 xy erate 0.01 remap v - -#dump 1 all custom 5000 dump.nemd id type x y z - -#dump 2 all image 1000 image.*.jpg type type adiam 1.2 -#dump_modify 2 pad 5 - -#dump 3 all movie 1000 movie.mpg type type adiam 1.2 -#dump_modify 3 pad 5 - -thermo 1000 - -run 50000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 1.3 - binsize = 0.65 -> bins = 24 19 3 -Memory usage per processor = 2.49198 Mbytes -Step Temp E_pair E_mol TotEng Press Volume - 0 1.44 0 0 1.431 1.2080502 189.52855 - 1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855 - 2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855 - 3000 1.0895801 0.24812344 0 1.3308937 5.6987334 189.52855 - 4000 1.0231536 0.23938192 0 1.2561408 5.6395384 189.52855 - 5000 0.92980496 0.29549086 0 1.2194845 6.7361058 189.52855 - 6000 0.94654468 0.27175873 0 1.2123875 6.1830354 189.52855 - 7000 1.04513 0.19555104 0 1.234149 5.3099904 189.52855 - 8000 0.90165043 0.33774203 0 1.2337571 6.8441345 189.52855 - 9000 1.0559475 0.21527383 0 1.2646217 5.3936713 189.52855 - 10000 1.0316023 0.25162907 0 1.2767839 6.0630699 189.52855 - 11000 1.0057873 0.1929355 0 1.1924366 5.1939416 189.52855 - 12000 0.95976424 0.23631857 0 1.1900843 5.1197849 189.52855 - 13000 0.96228689 0.2359206 0 1.1921932 5.8485377 189.52855 - 14000 0.92347491 0.28934379 0 1.207047 6.7279587 189.52855 - 15000 0.98798195 0.25310368 0 1.2349107 5.5744542 189.52855 - 16000 0.93800257 0.39455603 0 1.3266961 7.5939651 189.52855 - 17000 1.1781148 0.21856228 0 1.3893138 5.8347428 189.52855 - 18000 1.1292943 0.26429204 0 1.3865283 6.0510955 189.52855 - 19000 1.1047406 0.37926848 0 1.4771045 8.1596576 189.52855 - 20000 1.1716353 0.34662527 0 1.5109379 7.4616642 189.52855 - 21000 1.1630831 0.35981763 0 1.5156314 7.1024447 189.52855 - 22000 1.1249714 0.28308559 0 1.4010259 6.4004855 189.52855 - 23000 1.1062056 0.28618757 0 1.3854794 6.4957851 189.52855 - 24000 1.0588756 0.31727536 0 1.369533 6.987661 189.52855 - 25000 1.0379506 0.30773124 0 1.3391947 6.3814122 189.52855 - 26000 1.0316899 0.25596718 0 1.281209 6.4851096 189.52855 - 27000 0.95909019 0.32282679 0 1.2759227 6.480673 189.52855 - 28000 1.0224651 0.24795447 0 1.2640291 5.5846145 189.52855 - 29000 0.98739892 0.24878333 0 1.230011 5.6749101 189.52855 - 30000 1.0099165 0.22964407 0 1.2332486 5.3791167 189.52855 - 31000 0.93350481 0.2879577 0 1.2156281 6.2148818 189.52855 - 32000 0.99089487 0.22340991 0 1.2081117 5.639 189.52855 - 33000 0.89519123 0.26943351 0 1.1590298 6.3869898 189.52855 - 34000 0.891093 0.28473528 0 1.1702589 6.0284238 189.52855 - 35000 0.83575157 0.25811245 0 1.0886406 6.4030425 189.52855 - 36000 0.81108815 0.26558543 0 1.0716043 6.3037393 189.52855 - 37000 0.92476501 0.18404704 0 1.1030323 5.3793557 189.52855 - 38000 0.85121163 0.2792429 0 1.1251345 5.9668051 189.52855 - 39000 0.90345348 0.2399627 0 1.1377696 6.1440023 189.52855 - 40000 0.93871579 0.2217328 0 1.1545816 4.9454727 189.52855 - 41000 1.0132854 0.25226008 0 1.2592124 6.2541531 189.52855 - 42000 0.98600788 0.27213553 0 1.2519809 6.0321859 189.52855 - 43000 1.0635948 0.27086236 0 1.3278097 6.6622232 189.52855 - 44000 1.0332292 0.36613701 0 1.3929085 7.4935675 189.52855 - 45000 1.1168224 0.3374366 0 1.4472788 7.3625776 189.52855 - 46000 1.0725949 0.37916007 0 1.4450513 6.8897095 189.52855 - 47000 1.0940234 0.35474661 0 1.4419324 7.4781317 189.52855 - 48000 1.1093597 0.26705754 0 1.3694837 5.8401116 189.52855 - 49000 1.0803976 0.29555751 0 1.3692026 6.4769008 189.52855 - 50000 1.0150244 0.29822696 0 1.3069075 6.4417197 189.52855 -Loop time of 0.89762 on 4 procs for 50000 steps with 160 atoms - -Performance: 24063642.337 tau/day, 55702.876 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.049302 | 0.050204 | 0.051269 | 0.3 | 5.59 -Neigh | 0.047954 | 0.048719 | 0.049847 | 0.3 | 5.43 -Comm | 0.32267 | 0.33536 | 0.34668 | 1.5 | 37.36 -Output | 0.00076675 | 0.00081015 | 0.00093508 | 0.3 | 0.09 -Modify | 0.30312 | 0.31088 | 0.31853 | 1.0 | 34.63 -Other | | 0.1516 | | | 16.89 - -Nlocal: 40 ave 42 max 38 min -Histogram: 1 0 1 0 0 0 0 1 0 1 -Nghost: 35.5 ave 37 max 34 min -Histogram: 1 0 0 1 0 0 1 0 0 1 -Neighs: 88.75 ave 96 max 79 min -Histogram: 1 0 1 0 0 0 0 0 0 2 - -Total # of neighbors = 355 -Ave neighs/atom = 2.21875 -Neighbor list builds = 5284 -Dangerous builds = 0 -Total wall time: 0:00:00 diff --git a/examples/obstacle/log.5Oct16.obstacle.g++.1 b/examples/obstacle/log.27Nov18.obstacle.g++.1 similarity index 82% rename from examples/obstacle/log.5Oct16.obstacle.g++.1 rename to examples/obstacle/log.27Nov18.obstacle.g++.1 index 7d1a1a8c7d..68db45ee7e 100644 --- a/examples/obstacle/log.5Oct16.obstacle.g++.1 +++ b/examples/obstacle/log.27Nov18.obstacle.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d LJ obstacle flow dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 840 atoms + Time spent = 0.0004704 secs mass 1 1.0 mass 2 1.0 @@ -80,7 +82,7 @@ fix 9 all enforce2d timestep 0.003 thermo 1000 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 100 dump.obstacle @@ -92,13 +94,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 25000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 73 32 1 -Memory usage per processor = 2.47903 Mbytes + binsize = 0.71123, bins = 73 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.055 | 3.055 | 3.055 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1.0027471 0 0 0.68849216 0.46317653 1143.0857 1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728 @@ -126,20 +133,20 @@ Step Temp E_pair E_mol TotEng Press Volume 23000 1 -0.39249509 0 0.29411089 0.97187435 1459.6771 24000 1 -0.33410442 0 0.35250156 0.93960021 1463.5903 25000 1 -0.37437615 0 0.31222983 0.9644765 1464.9391 -Loop time of 1.64517 on 1 procs for 25000 steps with 769 atoms +Loop time of 1.98053 on 1 procs for 25000 steps with 769 atoms -Performance: 3938793.608 tau/day, 15195.963 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 3271856.949 tau/day, 12622.905 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.5054 | 0.5054 | 0.5054 | 0.0 | 30.72 -Neigh | 0.17887 | 0.17887 | 0.17887 | 0.0 | 10.87 -Comm | 0.022527 | 0.022527 | 0.022527 | 0.0 | 1.37 -Output | 0.00023794 | 0.00023794 | 0.00023794 | 0.0 | 0.01 -Modify | 0.85127 | 0.85127 | 0.85127 | 0.0 | 51.74 -Other | | 0.08687 | | | 5.28 +Pair | 0.46219 | 0.46219 | 0.46219 | 0.0 | 23.34 +Neigh | 0.17 | 0.17 | 0.17 | 0.0 | 8.58 +Comm | 0.029093 | 0.029093 | 0.029093 | 0.0 | 1.47 +Output | 0.00041389 | 0.00041389 | 0.00041389 | 0.0 | 0.02 +Modify | 1.22 | 1.22 | 1.22 | 0.0 | 61.60 +Other | | 0.09888 | | | 4.99 Nlocal: 769 ave 769 max 769 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/obstacle/log.5Oct16.obstacle.g++.4 b/examples/obstacle/log.27Nov18.obstacle.g++.4 similarity index 82% rename from examples/obstacle/log.5Oct16.obstacle.g++.4 rename to examples/obstacle/log.27Nov18.obstacle.g++.4 index 5bd84740e4..ed80fabf9b 100644 --- a/examples/obstacle/log.5Oct16.obstacle.g++.4 +++ b/examples/obstacle/log.27Nov18.obstacle.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d LJ obstacle flow dimension 2 @@ -18,6 +19,7 @@ Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089) 4 by 1 by 1 MPI processor grid create_atoms 1 box Created 840 atoms + Time spent = 0.000343561 secs mass 1 1.0 mass 2 1.0 @@ -80,7 +82,7 @@ fix 9 all enforce2d timestep 0.003 thermo 1000 thermo_modify temp mobile -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) #dump 1 all atom 100 dump.obstacle @@ -92,13 +94,18 @@ WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474 run 25000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.42246 ghost atom cutoff = 1.42246 - binsize = 0.71123 -> bins = 73 32 1 -Memory usage per processor = 2.47142 Mbytes + binsize = 0.71123, bins = 73 32 1 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.043 | 3.043 | 3.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 1.0004177 0 0 0.68689281 0.46210058 1143.0857 1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239 @@ -126,20 +133,20 @@ Step Temp E_pair E_mol TotEng Press Volume 23000 1 -0.37327871 0 0.31332728 1.0623185 1453.1342 24000 1 -0.40040333 0 0.28620265 0.94983886 1459.4461 25000 1 -0.37645924 0 0.31014674 1.0526044 1458.7191 -Loop time of 0.821326 on 4 procs for 25000 steps with 769 atoms +Loop time of 0.950647 on 4 procs for 25000 steps with 769 atoms -Performance: 7889678.376 tau/day, 30438.574 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 6816413.742 tau/day, 26297.893 timesteps/s +95.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.064561 | 0.12703 | 0.20657 | 15.5 | 15.47 -Neigh | 0.036315 | 0.04798 | 0.06249 | 4.4 | 5.84 -Comm | 0.14793 | 0.21791 | 0.27951 | 10.6 | 26.53 -Output | 0.00043583 | 0.00046438 | 0.00054574 | 0.2 | 0.06 -Modify | 0.27754 | 0.31239 | 0.3371 | 3.9 | 38.03 -Other | | 0.1156 | | | 14.07 +Pair | 0.068658 | 0.11988 | 0.18819 | 13.5 | 12.61 +Neigh | 0.034307 | 0.046836 | 0.063159 | 5.0 | 4.93 +Comm | 0.1325 | 0.21714 | 0.27078 | 11.3 | 22.84 +Output | 0.00052547 | 0.00096804 | 0.0022867 | 0.0 | 0.10 +Modify | 0.37752 | 0.41834 | 0.48768 | 6.5 | 44.01 +Other | | 0.1475 | | | 15.51 Nlocal: 192.25 ave 243 max 151 min Histogram: 1 1 0 0 0 0 1 0 0 1 diff --git a/examples/peptide/log.5Oct16.peptide.g++.1 b/examples/peptide/log.27Nov18.peptide.g++.1 similarity index 67% rename from examples/peptide/log.5Oct16.peptide.g++.1 rename to examples/peptide/log.27Nov18.peptide.g++.1 index 19b9646778..3999ca36cb 100644 --- a/examples/peptide/log.5Oct16.peptide.g++.1 +++ b/examples/peptide/log.27Nov18.peptide.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real @@ -70,7 +71,7 @@ group peptide type <= 12 run 300 PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 @@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 10648 3375 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 @@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 -Memory usage per processor = 15.5934 Mbytes +Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ----------------- Step 50 ----- CPU = 0.9457 (sec) ---------------- +---------------- Step 50 ----- CPU = 1.0190 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 @@ -114,77 +120,77 @@ SHAKE stats (type/ave/delta) on step 100 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ----------------- Step 100 ----- CPU = 1.9163 (sec) ---------------- +---------------- Step 100 ----- CPU = 2.0505 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 ----------------- Step 150 ----- CPU = 2.9286 (sec) ---------------- -TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 +---------------- Step 150 ----- CPU = 3.1208 (sec) ---------------- +TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1829 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18698e-07 - 6 0.997 1.50562e-07 - 8 1.08 6.57498e-08 + 6 0.997 1.50563e-07 + 8 1.08 6.57499e-08 10 1.111 5.54188e-07 - 12 1.08 1.98839e-07 + 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 31 104.52 0.000388335 ----------------- Step 200 ----- CPU = 3.8703 (sec) ---------------- -TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 +---------------- Step 200 ----- CPU = 4.1320 (sec) ---------------- +TotEng = -5308.4468 KinEng = 1100.4873 Temp = 273.5421 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 -E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3400 ----------------- Step 250 ----- CPU = 4.8652 (sec) ---------------- -TotEng = -5294.1569 KinEng = 1071.0938 Temp = 266.2359 -PotEng = -6365.2507 E_bond = 14.2013 E_angle = 39.1996 +E_coul = 26736.1319 E_long = -33902.3837 Press = -1470.3401 +---------------- Step 250 ----- CPU = 5.2131 (sec) ---------------- +TotEng = -5294.1568 KinEng = 1071.0940 Temp = 266.2360 +PotEng = -6365.2508 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4590 -E_coul = 26714.0040 E_long = -33908.7139 Press = -189.6059 +E_coul = 26714.0039 E_long = -33908.7139 Press = -189.6057 SHAKE stats (type/ave/delta) on step 300 - 4 1.111 3.79044e-06 + 4 1.111 3.79043e-06 6 0.997001 3.6052e-06 8 1.08 2.09369e-06 10 1.111 5.6484e-06 - 12 1.08 2.10677e-06 + 12 1.08 2.10676e-06 14 0.96 0 - 18 0.957202 7.72576e-06 - 31 104.52 0.000806204 ----------------- Step 300 ----- CPU = 5.8596 (sec) ---------------- -TotEng = -5251.3637 KinEng = 1123.7718 Temp = 279.3298 -PotEng = -6375.1355 E_bond = 14.2206 E_angle = 38.4274 -E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3473 -E_coul = 26745.4074 E_long = -33909.0791 Press = -471.5505 -Loop time of 5.85959 on 1 procs for 300 steps with 2004 atoms + 18 0.957202 7.72571e-06 + 31 104.52 0.000806203 +---------------- Step 300 ----- CPU = 6.2919 (sec) ---------------- +TotEng = -5251.3662 KinEng = 1123.7719 Temp = 279.3299 +PotEng = -6375.1381 E_bond = 14.2206 E_angle = 38.4274 +E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3476 +E_coul = 26745.4045 E_long = -33909.0791 Press = -471.5904 +Loop time of 6.29195 on 1 procs for 300 steps with 2004 atoms -Performance: 8.847 ns/day, 2.713 hours/ns, 51.198 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 8.239 ns/day, 2.913 hours/ns, 47.680 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.6289 | 4.6289 | 4.6289 | 0.0 | 79.00 -Bond | 0.013405 | 0.013405 | 0.013405 | 0.0 | 0.23 -Kspace | 0.47821 | 0.47821 | 0.47821 | 0.0 | 8.16 -Neigh | 0.64447 | 0.64447 | 0.64447 | 0.0 | 11.00 -Comm | 0.026137 | 0.026137 | 0.026137 | 0.0 | 0.45 -Output | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.00 -Modify | 0.062095 | 0.062095 | 0.062095 | 0.0 | 1.06 -Other | | 0.006195 | | | 0.11 +Pair | 4.8228 | 4.8228 | 4.8228 | 0.0 | 76.65 +Bond | 0.0094063 | 0.0094063 | 0.0094063 | 0.0 | 0.15 +Kspace | 0.523 | 0.523 | 0.523 | 0.0 | 8.31 +Neigh | 0.82602 | 0.82602 | 0.82602 | 0.0 | 13.13 +Comm | 0.03742 | 0.03742 | 0.03742 | 0.0 | 0.59 +Output | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.00 +Modify | 0.068182 | 0.068182 | 0.068182 | 0.0 | 1.08 +Other | | 0.00493 | | | 0.08 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11185 ave 11185 max 11185 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 708018 ave 708018 max 708018 min +Neighs: 708019 ave 708019 max 708019 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 708018 -Ave neighs/atom = 353.302 +Total # of neighbors = 708019 +Ave neighs/atom = 353.303 Ave special neighs/atom = 2.34032 Neighbor list builds = 26 Dangerous builds = 0 -Total wall time: 0:00:05 +Total wall time: 0:00:06 diff --git a/examples/peptide/log.5Oct16.peptide.g++.4 b/examples/peptide/log.27Nov18.peptide.g++.4 similarity index 64% rename from examples/peptide/log.5Oct16.peptide.g++.4 rename to examples/peptide/log.27Nov18.peptide.g++.4 index 5d43e6e546..bb9e3771c4 100644 --- a/examples/peptide/log.5Oct16.peptide.g++.4 +++ b/examples/peptide/log.27Nov18.peptide.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real @@ -70,7 +71,7 @@ group peptide type <= 12 run 300 PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 @@ -79,12 +80,17 @@ WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) using double precision FFTs 3d grid and FFT values/proc = 4312 960 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 - binsize = 6 -> bins = 5 5 5 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard SHAKE stats (type/ave/delta) on step 0 4 1.111 1.44264e-05 6 0.996998 7.26967e-06 @@ -94,13 +100,13 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 -Memory usage per processor = 14.8928 Mbytes +Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ----------------- Step 50 ----- CPU = 0.2741 (sec) ---------------- +---------------- Step 50 ----- CPU = 0.2858 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 @@ -114,65 +120,65 @@ SHAKE stats (type/ave/delta) on step 100 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ----------------- Step 100 ----- CPU = 0.5371 (sec) ---------------- +---------------- Step 100 ----- CPU = 0.5744 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 -E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6819 ----------------- Step 150 ----- CPU = 0.8054 (sec) ---------------- -TotEng = -5287.2799 KinEng = 1098.6028 Temp = 273.0737 -PotEng = -6385.8827 E_bond = 17.4925 E_angle = 32.8594 +E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6820 +---------------- Step 150 ----- CPU = 0.8756 (sec) ---------------- +TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 +PotEng = -6385.8826 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 -E_coul = 26717.2655 E_long = -33907.2821 Press = -333.1830 +E_coul = 26717.2656 E_long = -33907.2821 Press = -333.1828 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18699e-07 6 0.997 1.50563e-07 - 8 1.08 6.57501e-08 - 10 1.111 5.54188e-07 - 12 1.08 1.98841e-07 + 8 1.08 6.575e-08 + 10 1.111 5.54187e-07 + 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 - 31 104.52 0.000388336 ----------------- Step 200 ----- CPU = 1.0652 (sec) ---------------- -TotEng = -5308.4465 KinEng = 1100.4875 Temp = 273.5422 -PotEng = -6408.9340 E_bond = 18.2714 E_angle = 33.3040 + 31 104.52 0.000388335 +---------------- Step 200 ----- CPU = 1.1602 (sec) ---------------- +TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 +PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 -E_coul = 26736.1321 E_long = -33902.3837 Press = -1470.3400 ----------------- Step 250 ----- CPU = 1.3409 (sec) ---------------- -TotEng = -5294.1570 KinEng = 1071.0939 Temp = 266.2360 -PotEng = -6365.2509 E_bond = 14.2013 E_angle = 39.1996 -E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4591 -E_coul = 26714.0037 E_long = -33908.7139 Press = -189.6059 +E_coul = 26736.1320 E_long = -33902.3837 Press = -1470.3400 +---------------- Step 250 ----- CPU = 1.4629 (sec) ---------------- +TotEng = -5294.1567 KinEng = 1071.0938 Temp = 266.2359 +PotEng = -6365.2505 E_bond = 14.2013 E_angle = 39.1996 +E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4589 +E_coul = 26714.0043 E_long = -33908.7139 Press = -189.6068 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.79043e-06 - 6 0.997001 3.60519e-06 - 8 1.08 2.09368e-06 - 10 1.111 5.64839e-06 - 12 1.08 2.10676e-06 + 6 0.997001 3.6052e-06 + 8 1.08 2.09369e-06 + 10 1.111 5.6484e-06 + 12 1.08 2.10677e-06 14 0.96 0 - 18 0.957202 7.72573e-06 - 31 104.52 0.000806208 ----------------- Step 300 ----- CPU = 1.6199 (sec) ---------------- -TotEng = -5251.3639 KinEng = 1123.7721 Temp = 279.3299 -PotEng = -6375.1360 E_bond = 14.2206 E_angle = 38.4274 -E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3470 -E_coul = 26745.4071 E_long = -33909.0790 Press = -471.5569 -Loop time of 1.61992 on 4 procs for 300 steps with 2004 atoms + 18 0.957202 7.72579e-06 + 31 104.52 0.000806203 +---------------- Step 300 ----- CPU = 1.7662 (sec) ---------------- +TotEng = -5251.3662 KinEng = 1123.7712 Temp = 279.3297 +PotEng = -6375.1374 E_bond = 14.2206 E_angle = 38.4274 +E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3474 +E_coul = 26745.4053 E_long = -33909.0790 Press = -471.5904 +Loop time of 1.76629 on 4 procs for 300 steps with 2004 atoms -Performance: 32.002 ns/day, 0.750 hours/ns, 185.194 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 29.350 ns/day, 0.818 hours/ns, 169.847 timesteps/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.1484 | 1.17 | 1.1865 | 1.5 | 72.23 -Bond | 0.0011752 | 0.003831 | 0.0069602 | 4.0 | 0.24 -Kspace | 0.16316 | 0.1798 | 0.20413 | 3.9 | 11.10 -Neigh | 0.16885 | 0.16895 | 0.16902 | 0.0 | 10.43 -Comm | 0.046479 | 0.047215 | 0.047759 | 0.2 | 2.91 -Output | 0.00024033 | 0.00025702 | 0.00030375 | 0.2 | 0.02 -Modify | 0.04556 | 0.045949 | 0.046353 | 0.2 | 2.84 -Other | | 0.003923 | | | 0.24 +Pair | 1.2044 | 1.2351 | 1.2721 | 2.3 | 69.92 +Bond | 0.0013924 | 0.0034139 | 0.0057151 | 3.2 | 0.19 +Kspace | 0.17476 | 0.21195 | 0.2407 | 5.3 | 12.00 +Neigh | 0.21273 | 0.21286 | 0.21293 | 0.0 | 12.05 +Comm | 0.042942 | 0.046074 | 0.047584 | 0.9 | 2.61 +Output | 0.00025845 | 0.00033492 | 0.00055695 | 0.0 | 0.02 +Modify | 0.049944 | 0.051619 | 0.054278 | 0.8 | 2.92 +Other | | 0.004988 | | | 0.28 Nlocal: 501 ave 508 max 490 min Histogram: 1 0 0 0 0 0 1 1 0 1 diff --git a/examples/peri/log.6Jul17.peri.eps.g++.1 b/examples/peri/log.27Nov18.peri.eps.g++.1 similarity index 65% rename from examples/peri/log.6Jul17.peri.eps.g++.1 rename to examples/peri/log.27Nov18.peri.eps.g++.1 index 6aa4314d53..379f3f75c9 100644 --- a/examples/peri/log.6Jul17.peri.eps.g++.1 +++ b/examples/peri/log.27Nov18.peri.eps.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 1 by 1 by 1 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.00100374 secs pair_style peri/eps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 50.29 | 50.29 | 50.29 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 - 100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 - 200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 - 300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 - 400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 - 500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 - 600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 - 700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 - 800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 - 900 1.3166045e+28 1911868.6 0 9.524241e+08 1.9729649e+14 3.2117896e-06 - 1000 1.3159578e+28 1995827.6 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 -Loop time of 72.5574 on 1 procs for 1000 steps with 3487 atoms + 100 9.7403734e+24 248692.93 0 951891.49 9.3703576e+11 5.0030006e-07 + 200 1.220493e+27 1011231.9 0 89123756 1.0636834e+14 5.5224782e-07 + 300 2.7274231e+27 4549425.2 0 2.0145358e+08 1.7250255e+14 7.6097098e-07 + 400 3.3665092e+27 13347641 0 2.5639011e+08 1.5828139e+14 1.0236725e-06 + 500 3.8995641e+27 14196430 0 2.9572238e+08 1.5145191e+14 1.2392314e-06 + 600 4.6668832e+27 23135807 0 3.6005775e+08 1.478168e+14 1.5195473e-06 + 700 1.1847301e+28 8126622 0 8.6343315e+08 2.9204301e+14 1.9524671e-06 + 800 1.2328889e+28 4646514.3 0 8.9472087e+08 2.2467312e+14 2.6410944e-06 + 900 1.2277283e+28 2668877.7 0 8.8901759e+08 1.671177e+14 3.5358262e-06 + 1000 1.2260912e+28 1587002.9 0 8.8675386e+08 1.29707e+14 4.5495712e-06 +Loop time of 34.8143 on 1 procs for 1000 steps with 3487 atoms -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads +96.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 71.779 | 71.779 | 71.779 | 0.0 | 98.93 -Neigh | 0.5596 | 0.5596 | 0.5596 | 0.0 | 0.77 -Comm | 0.0040631 | 0.0040631 | 0.0040631 | 0.0 | 0.01 -Output | 0.00056624 | 0.00056624 | 0.00056624 | 0.0 | 0.00 -Modify | 0.18403 | 0.18403 | 0.18403 | 0.0 | 0.25 -Other | | 0.03016 | | | 0.04 +Pair | 34.045 | 34.045 | 34.045 | 0.0 | 97.79 +Neigh | 0.63254 | 0.63254 | 0.63254 | 0.0 | 1.82 +Comm | 0.0025852 | 0.0025852 | 0.0025852 | 0.0 | 0.01 +Output | 0.00035906 | 0.00035906 | 0.00035906 | 0.0 | 0.00 +Modify | 0.11784 | 0.11784 | 0.11784 | 0.0 | 0.34 +Other | | 0.01593 | | | 0.05 Nlocal: 3487 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 569177 ave 569177 max 569177 min +Neighs: 546591 ave 546591 max 546591 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 -Neighbor list builds = 40 +Neighbor list builds = 45 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:12 +Total wall time: 0:00:34 diff --git a/examples/peri/log.6Jul17.peri.eps.g++.4 b/examples/peri/log.27Nov18.peri.eps.g++.4 similarity index 62% rename from examples/peri/log.6Jul17.peri.eps.g++.4 rename to examples/peri/log.27Nov18.peri.eps.g++.4 index 1423ec4637..bccd5cd25a 100644 --- a/examples/peri/log.6Jul17.peri.eps.g++.4 +++ b/examples/peri/log.27Nov18.peri.eps.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 2 by 1 by 2 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.000587225 secs pair_style peri/eps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 10.0e8 @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 44.77 | 45.04 | 45.14 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 - 100 8.3466308e+24 247103.03 0 849681.45 8.0295601e+11 5.0030006e-07 - 200 1.1784921e+27 1098605.6 0 86178912 1.0246967e+14 5.5353162e-07 - 300 2.6263212e+27 4118581.6 0 1.9372377e+08 1.662415e+14 7.6036043e-07 - 400 3.3085888e+27 9397203.3 0 2.4825816e+08 1.561692e+14 1.0196674e-06 - 500 3.9151799e+27 18408722 0 3.0106204e+08 1.5298661e+14 1.2317127e-06 - 600 6.2936721e+27 11346143 0 4.6571282e+08 1.9645007e+14 1.5419242e-06 - 700 1.2721597e+28 3830223.2 0 9.2225588e+08 3.0235577e+14 2.0250441e-06 - 800 1.3190107e+28 2831668.7 0 9.5508099e+08 2.4853932e+14 2.5542553e-06 - 900 1.3166045e+28 1911869.3 0 9.524241e+08 1.9729649e+14 3.2117896e-06 - 1000 1.3159578e+28 1995833.9 0 9.5204114e+08 1.6722163e+14 3.7875695e-06 -Loop time of 29.6266 on 4 procs for 1000 steps with 3487 atoms + 100 2.3613868e+26 2297417.8 0 19345263 2.2716828e+13 5.0030006e-07 + 200 3.9573281e+27 28896934 0 3.1459311e+08 3.6928392e+14 5.1576607e-07 + 300 8.7809254e+27 38915502 0 6.7284747e+08 6.4053658e+14 6.5979263e-07 + 400 1.3210949e+28 35344681 0 9.8909868e+08 7.0953264e+14 8.9613355e-07 + 500 1.7324732e+28 21092574 0 1.2718379e+09 7.4083646e+14 1.1255254e-06 + 600 2.1194595e+28 11349855 0 1.5414769e+09 6.6250164e+14 1.5397467e-06 + 700 2.316318e+28 2515600.8 0 1.6747631e+09 5.0111859e+14 2.2246862e-06 + 800 2.363319e+28 1731461.2 0 1.7079109e+09 4.0277805e+14 2.8240193e-06 + 900 2.3668922e+28 870525.69 0 1.7096296e+09 3.1718257e+14 3.5915363e-06 + 1000 2.3654433e+28 789707.52 0 1.7085028e+09 2.5538989e+14 4.4577935e-06 +Loop time of 5.11902 on 4 procs for 1000 steps with 3487 atoms -98.8% CPU use with 4 MPI tasks x 1 OpenMP threads +90.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 25.905 | 26.18 | 26.326 | 3.2 | 88.37 -Neigh | 0.15352 | 0.1872 | 0.22394 | 7.6 | 0.63 -Comm | 3.0374 | 3.1471 | 3.3731 | 7.5 | 10.62 -Output | 0.00047588 | 0.00062978 | 0.00097752 | 0.0 | 0.00 -Modify | 0.073521 | 0.081854 | 0.093222 | 2.7 | 0.28 -Other | | 0.02989 | | | 0.10 +Pair | 3.1161 | 3.9019 | 4.7582 | 30.3 | 76.22 +Neigh | 0.0701 | 0.080061 | 0.089326 | 3.0 | 1.56 +Comm | 0.22296 | 1.0644 | 1.8357 | 57.0 | 20.79 +Output | 0.00028729 | 0.00058514 | 0.0013847 | 0.0 | 0.01 +Modify | 0.041605 | 0.043229 | 0.044626 | 0.6 | 0.84 +Other | | 0.02887 | | | 0.56 -Nlocal: 871.75 ave 908 max 838 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 1368.25 ave 1402 max 1332 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 142294 ave 159233 max 124729 min +Nlocal: 871.75 ave 947 max 799 min Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1011 ave 1087 max 936 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 91271.8 ave 92650 max 90045 min +Histogram: 1 1 0 0 0 0 1 0 0 1 FullNghs: 302269 ave 346070 max 260820 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 -Neighbor list builds = 40 +Neighbor list builds = 24 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:29 +Total wall time: 0:00:05 diff --git a/examples/peri/log.6Jul17.peri.lps.g++.1 b/examples/peri/log.27Nov18.peri.lps.g++.1 similarity index 66% rename from examples/peri/log.6Jul17.peri.lps.g++.1 rename to examples/peri/log.27Nov18.peri.lps.g++.1 index 4b2ac532d1..0b9f4b4e0b 100644 --- a/examples/peri/log.6Jul17.peri.lps.g++.1 +++ b/examples/peri/log.27Nov18.peri.lps.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 1 by 1 by 1 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.00101972 secs pair_style peri/lps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 @@ -72,35 +73,35 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 34.91 | 34.91 | 34.91 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 - 100 1.684629e+24 133446.65 0 255067.11 1.6206343e+11 5.0030006e-07 - 200 1.1380148e+27 684478.05 0 82842557 9.9178307e+13 5.5225839e-07 - 300 2.5659218e+27 5944645.9 0 1.9118934e+08 1.6231114e+14 7.6086254e-07 - 400 2.9916164e+27 13677434 0 2.2965481e+08 1.4081705e+14 1.0224963e-06 - 500 3.3570343e+27 11130894 0 2.5348933e+08 1.2577633e+14 1.2846002e-06 - 600 3.9506165e+27 6986672.5 0 2.9219831e+08 1.2659956e+14 1.5019096e-06 - 700 7.8366157e+27 11716082 0 5.7747436e+08 1.9480124e+14 1.9361899e-06 - 800 8.2483231e+27 4671647.2 0 6.0015282e+08 1.7040064e+14 2.3297298e-06 - 900 8.2720965e+27 1249680.9 0 5.9844715e+08 1.4117116e+14 2.8202052e-06 - 1000 8.2441462e+27 2278265.6 0 5.9745788e+08 1.234652e+14 3.213751e-06 -Loop time of 62.3833 on 1 procs for 1000 steps with 3487 atoms + 100 2.0851116e+24 132640.06 0 283173.04 2.0059034e+11 5.0030006e-07 + 200 1.1421456e+27 733330.77 0 83189631 9.9580342e+13 5.5202528e-07 + 300 2.5694547e+27 6192900.7 0 1.9169265e+08 1.6253438e+14 7.6086363e-07 + 400 3.0375813e+27 7013786 0 2.2630957e+08 1.4286927e+14 1.0232935e-06 + 500 3.4006176e+27 5347550.9 0 2.5085245e+08 1.2727968e+14 1.2859078e-06 + 600 3.7690314e+27 8040942.9 0 2.8014319e+08 1.2082801e+14 1.5013199e-06 + 700 7.6688193e+27 8282231 0 5.6192658e+08 1.9074258e+14 1.935049e-06 + 800 8.2147783e+27 3439316.5 0 5.9649874e+08 1.6954721e+14 2.3319342e-06 + 900 8.1767735e+27 1827759 0 5.9214346e+08 1.38875e+14 2.8337987e-06 + 1000 8.1478191e+27 1415059 0 5.8964042e+08 1.2086486e+14 3.2445347e-06 +Loop time of 27.5943 on 1 procs for 1000 steps with 3487 atoms -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 61.608 | 61.608 | 61.608 | 0.0 | 98.76 -Neigh | 0.57177 | 0.57177 | 0.57177 | 0.0 | 0.92 -Comm | 0.0030825 | 0.0030825 | 0.0030825 | 0.0 | 0.00 -Output | 0.00051951 | 0.00051951 | 0.00051951 | 0.0 | 0.00 -Modify | 0.17278 | 0.17278 | 0.17278 | 0.0 | 0.28 -Other | | 0.02745 | | | 0.04 +Pair | 26.946 | 26.946 | 26.946 | 0.0 | 97.65 +Neigh | 0.52412 | 0.52412 | 0.52412 | 0.0 | 1.90 +Comm | 0.001683 | 0.001683 | 0.001683 | 0.0 | 0.01 +Output | 0.00032282 | 0.00032282 | 0.00032282 | 0.0 | 0.00 +Modify | 0.10716 | 0.10716 | 0.10716 | 0.0 | 0.39 +Other | | 0.01544 | | | 0.06 Nlocal: 3487 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 576568 ave 576568 max 576568 min +Neighs: 578212 ave 578212 max 578212 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -112,4 +113,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:02 +Total wall time: 0:00:27 diff --git a/examples/peri/log.6Jul17.peri.lps.g++.4 b/examples/peri/log.27Nov18.peri.lps.g++.4 similarity index 61% rename from examples/peri/log.6Jul17.peri.lps.g++.4 rename to examples/peri/log.27Nov18.peri.lps.g++.4 index 04244f0123..4f8b53f246 100644 --- a/examples/peri/log.6Jul17.peri.lps.g++.4 +++ b/examples/peri/log.27Nov18.peri.lps.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 2 by 1 by 2 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.000591278 secs pair_style peri/lps pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 29.4 | 29.66 | 29.76 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 - 100 1.684629e+24 133446.65 0 255067.11 1.6206343e+11 5.0030006e-07 - 200 1.1380148e+27 684478.05 0 82842557 9.9178307e+13 5.5225839e-07 - 300 2.5659218e+27 5944645.9 0 1.9118934e+08 1.6231114e+14 7.6086254e-07 - 400 2.9916164e+27 13677434 0 2.2965481e+08 1.4081705e+14 1.0224963e-06 - 500 3.3570343e+27 11130894 0 2.5348933e+08 1.2577633e+14 1.2846002e-06 - 600 3.9506165e+27 6986672.5 0 2.9219831e+08 1.2659956e+14 1.5019096e-06 - 700 7.8366157e+27 11716082 0 5.7747436e+08 1.9480124e+14 1.9361899e-06 - 800 8.2483231e+27 4671647.2 0 6.0015282e+08 1.7040064e+14 2.3297298e-06 - 900 8.2720965e+27 1249680.9 0 5.9844715e+08 1.4117116e+14 2.8202052e-06 - 1000 8.2441489e+27 2277476.2 0 5.9745729e+08 1.2346524e+14 3.213751e-06 -Loop time of 23.2656 on 4 procs for 1000 steps with 3487 atoms + 100 2.1708413e+26 2019616.1 0 17691833 2.0883757e+13 5.0030006e-07 + 200 2.6858201e+27 23091889 0 2.1699255e+08 2.5837916e+14 5.0030006e-07 + 300 7.7773248e+27 36337377 0 5.9781519e+08 5.5903929e+14 6.6957466e-07 + 400 1.2392524e+28 26946130 0 9.2161463e+08 5.8015586e+14 1.0280783e-06 + 500 1.6748989e+28 24398485 0 1.2335785e+09 5.5317919e+14 1.4572494e-06 + 600 2.1137718e+28 12455731 0 1.5384766e+09 5.144781e+14 1.9774354e-06 + 700 2.2843381e+28 3012521.8 0 1.6521724e+09 4.1591669e+14 2.6434138e-06 + 800 2.30994e+28 1986584 0 1.6696295e+09 3.1911076e+14 3.4839376e-06 + 900 2.3325118e+28 935517.5 0 1.684874e+09 2.5083968e+14 4.4754707e-06 + 1000 2.3453028e+28 646658.88 0 1.6938195e+09 1.9996924e+14 5.6447777e-06 +Loop time of 3.68562 on 4 procs for 1000 steps with 3487 atoms -99.2% CPU use with 4 MPI tasks x 1 OpenMP threads +97.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.801 | 21.119 | 21.525 | 6.3 | 90.78 -Neigh | 0.13851 | 0.18557 | 0.22747 | 8.5 | 0.80 -Comm | 1.5175 | 1.8689 | 2.1386 | 18.0 | 8.03 -Output | 0.00049806 | 0.00059026 | 0.00071931 | 0.0 | 0.00 -Modify | 0.063441 | 0.066235 | 0.069135 | 0.9 | 0.28 -Other | | 0.02496 | | | 0.11 +Pair | 2.3895 | 2.9098 | 3.4454 | 22.8 | 78.95 +Neigh | 0.089031 | 0.10631 | 0.12931 | 5.1 | 2.88 +Comm | 0.084373 | 0.61215 | 1.1154 | 48.5 | 16.61 +Output | 0.00026274 | 0.00058717 | 0.0014296 | 0.0 | 0.02 +Modify | 0.030758 | 0.032229 | 0.034897 | 0.9 | 0.87 +Other | | 0.02456 | | | 0.67 -Nlocal: 871.75 ave 939 max 805 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Nghost: 1343.25 ave 1410 max 1276 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 144142 ave 176488 max 113797 min -Histogram: 1 0 1 0 0 0 1 0 0 1 +Nlocal: 871.75 ave 955 max 804 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1052.5 ave 1144 max 960 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 94652.8 ave 98974 max 91771 min +Histogram: 1 1 0 0 1 0 0 0 0 1 FullNghs: 302269 ave 346070 max 260820 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 -Neighbor list builds = 37 +Neighbor list builds = 31 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:23 +Total wall time: 0:00:03 diff --git a/examples/peri/log.6Jul17.peri.pmb.g++.1 b/examples/peri/log.27Nov18.peri.pmb.g++.1 similarity index 80% rename from examples/peri/log.6Jul17.peri.pmb.g++.1 rename to examples/peri/log.27Nov18.peri.pmb.g++.1 index 84a439674b..d00ff7e97c 100644 --- a/examples/peri/log.6Jul17.peri.pmb.g++.1 +++ b/examples/peri/log.27Nov18.peri.pmb.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 1 by 1 by 1 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.000993729 secs pair_style peri/pmb pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 @@ -79,28 +80,28 @@ Step Temp E_pair E_mol TotEng Press Volume 500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06 600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06 700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06 - 800 1.2424839e+28 2407365.1 0 8.994088e+08 2.3787786e+14 2.5138992e-06 - 900 1.2358397e+28 4532424.3 0 8.9673716e+08 1.9097316e+14 3.1145903e-06 - 1000 1.2341048e+28 3219355.8 0 8.9417154e+08 1.5968585e+14 3.7196039e-06 -Loop time of 28.565 on 1 procs for 1000 steps with 3487 atoms + 800 1.2424839e+28 2407361.6 0 8.994088e+08 2.3787786e+14 2.5138992e-06 + 900 1.2358395e+28 4532520.6 0 8.9673706e+08 1.9097312e+14 3.1145903e-06 + 1000 1.2341057e+28 3219939.5 0 8.9417279e+08 1.5968597e+14 3.7196039e-06 +Loop time of 15.3451 on 1 procs for 1000 steps with 3487 atoms -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 27.721 | 27.721 | 27.721 | 0.0 | 97.04 -Neigh | 0.66353 | 0.66353 | 0.66353 | 0.0 | 2.32 -Comm | 0.0027969 | 0.0027969 | 0.0027969 | 0.0 | 0.01 -Output | 0.00042295 | 0.00042295 | 0.00042295 | 0.0 | 0.00 -Modify | 0.1566 | 0.1566 | 0.1566 | 0.0 | 0.55 -Other | | 0.02086 | | | 0.07 +Pair | 14.575 | 14.575 | 14.575 | 0.0 | 94.98 +Neigh | 0.65203 | 0.65203 | 0.65203 | 0.0 | 4.25 +Comm | 0.0019367 | 0.0019367 | 0.0019367 | 0.0 | 0.01 +Output | 0.00032711 | 0.00032711 | 0.00032711 | 0.0 | 0.00 +Modify | 0.10225 | 0.10225 | 0.10225 | 0.0 | 0.67 +Other | | 0.01342 | | | 0.09 Nlocal: 3487 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 567132 ave 567132 max 567132 min +Neighs: 567140 ave 567140 max 567140 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -112,4 +113,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:28 +Total wall time: 0:00:15 diff --git a/examples/peri/log.6Jul17.peri.pmb.g++.4 b/examples/peri/log.27Nov18.peri.pmb.g++.4 similarity index 77% rename from examples/peri/log.6Jul17.peri.pmb.g++.4 rename to examples/peri/log.27Nov18.peri.pmb.g++.4 index 637b2cc26a..da5b6e0e97 100644 --- a/examples/peri/log.6Jul17.peri.pmb.g++.4 +++ b/examples/peri/log.27Nov18.peri.pmb.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 2 by 1 by 2 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.000591755 secs pair_style peri/pmb pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 @@ -79,29 +80,29 @@ Step Temp E_pair E_mol TotEng Press Volume 500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06 600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06 700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06 - 800 1.2424839e+28 2407365.2 0 8.994088e+08 2.3787786e+14 2.5138992e-06 - 900 1.2358397e+28 4532423 0 8.9673716e+08 1.9097316e+14 3.1145903e-06 - 1000 1.2341048e+28 3219408.7 0 8.9417158e+08 1.5968585e+14 3.7196039e-06 -Loop time of 9.59889 on 4 procs for 1000 steps with 3487 atoms + 800 1.2424839e+28 2407361.5 0 8.994088e+08 2.3787786e+14 2.5138992e-06 + 900 1.2358395e+28 4532520.1 0 8.9673706e+08 1.9097312e+14 3.1145903e-06 + 1000 1.2341057e+28 3219974.3 0 8.9417286e+08 1.5968598e+14 3.7196039e-06 +Loop time of 4.86638 on 4 procs for 1000 steps with 3487 atoms -99.2% CPU use with 4 MPI tasks x 1 OpenMP threads +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.9131 | 8.1341 | 8.3286 | 6.7 | 84.74 -Neigh | 0.19736 | 0.22539 | 0.25643 | 5.6 | 2.35 -Comm | 0.92843 | 1.1536 | 1.402 | 18.4 | 12.02 -Output | 0.00053358 | 0.00059688 | 0.00070548 | 0.0 | 0.01 -Modify | 0.060774 | 0.06358 | 0.068375 | 1.2 | 0.66 -Other | | 0.02165 | | | 0.23 +Pair | 3.524 | 3.9207 | 4.4499 | 17.8 | 80.57 +Neigh | 0.12891 | 0.16928 | 0.21015 | 9.0 | 3.48 +Comm | 0.1204 | 0.70321 | 1.1349 | 46.1 | 14.45 +Output | 0.00028253 | 0.00053787 | 0.0012429 | 0.0 | 0.01 +Modify | 0.03231 | 0.033227 | 0.034578 | 0.5 | 0.68 +Other | | 0.03944 | | | 0.81 -Nlocal: 871.75 ave 920 max 829 min -Histogram: 1 0 0 0 2 0 0 0 0 1 -Nghost: 1343.25 ave 1386 max 1295 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 141783 ave 157099 max 127518 min -Histogram: 2 0 0 0 0 0 0 0 1 1 +Nlocal: 871.75 ave 920 max 824 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 1343.25 ave 1391 max 1295 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 141785 ave 170754 max 115891 min +Histogram: 1 1 0 0 0 0 0 1 0 1 FullNghs: 302269 ave 346070 max 260820 min Histogram: 1 0 0 0 2 0 0 0 0 1 @@ -112,4 +113,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:09 +Total wall time: 0:00:04 diff --git a/examples/peri/log.6Jul17.peri.ves.g++.1 b/examples/peri/log.27Nov18.peri.ves.g++.1 similarity index 65% rename from examples/peri/log.6Jul17.peri.ves.g++.1 rename to examples/peri/log.27Nov18.peri.ves.g++.1 index 3d1d156d4a..8f39af5bbb 100644 --- a/examples/peri/log.6Jul17.peri.ves.g++.1 +++ b/examples/peri/log.27Nov18.peri.ves.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 1 by 1 by 1 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.000948906 secs pair_style peri/ves pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 65.41 | 65.41 | 65.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 - 100 8.3392177e+24 247040.57 0 849083.8 8.0224286e+11 5.0030006e-07 - 200 1.1849022e+27 1158030.5 0 86701105 1.0301578e+14 5.5359205e-07 - 300 2.6287222e+27 4389155.1 0 1.9416767e+08 1.6636212e+14 7.6050375e-07 - 400 3.2718778e+27 7458219 0 2.4366885e+08 1.5439709e+14 1.0199269e-06 - 500 3.8413187e+27 6151611.4 0 2.8347258e+08 1.5008974e+14 1.2318007e-06 - 600 6.1409926e+27 18424316 0 4.6176842e+08 1.9507512e+14 1.5151227e-06 - 700 1.0046131e+28 11478344 0 7.3675086e+08 2.4228512e+14 1.9956447e-06 - 800 1.0402132e+28 4421233.6 0 7.5539495e+08 2.0512303e+14 2.4407262e-06 - 900 1.0419515e+28 7223261.3 0 7.594519e+08 1.6647307e+14 3.0124137e-06 - 1000 1.0503737e+28 2621490.6 0 7.6093049e+08 1.4315634e+14 3.5313793e-06 -Loop time of 77.2175 on 1 procs for 1000 steps with 3487 atoms + 100 9.7323839e+24 248625.39 0 951247.15 9.3626715e+11 5.0030006e-07 + 200 1.2061753e+27 1013477.4 0 88092352 1.0509747e+14 5.5236899e-07 + 300 2.7144154e+27 3853028.1 0 1.998181e+08 1.7162586e+14 7.6121038e-07 + 400 3.40253e+27 12536380 0 2.5817934e+08 1.5995767e+14 1.0237832e-06 + 500 3.9896399e+27 9604773.5 0 2.9763367e+08 1.5530851e+14 1.2363731e-06 + 600 5.1484768e+27 20065080 0 3.9175529e+08 1.6320898e+14 1.5182588e-06 + 700 1.1341683e+28 8156461.7 0 8.269603e+08 2.765964e+14 1.9735225e-06 + 800 1.1679489e+28 4475262.6 0 8.4766672e+08 2.1589017e+14 2.6037667e-06 + 900 1.1714785e+28 2839888 0 8.4857954e+08 1.7092697e+14 3.2986395e-06 + 1000 1.1716494e+28 1690965.6 0 8.4755402e+08 1.3801485e+14 4.0858554e-06 +Loop time of 27.0077 on 1 procs for 1000 steps with 3487 atoms -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 76.421 | 76.421 | 76.421 | 0.0 | 98.97 -Neigh | 0.56616 | 0.56616 | 0.56616 | 0.0 | 0.73 -Comm | 0.0038247 | 0.0038247 | 0.0038247 | 0.0 | 0.00 -Output | 0.00051951 | 0.00051951 | 0.00051951 | 0.0 | 0.00 -Modify | 0.19434 | 0.19434 | 0.19434 | 0.0 | 0.25 -Other | | 0.03197 | | | 0.04 +Pair | 26.294 | 26.294 | 26.294 | 0.0 | 97.36 +Neigh | 0.5863 | 0.5863 | 0.5863 | 0.0 | 2.17 +Comm | 0.0051315 | 0.0051315 | 0.0051315 | 0.0 | 0.02 +Output | 0.00033832 | 0.00033832 | 0.00033832 | 0.0 | 0.00 +Modify | 0.10736 | 0.10736 | 0.10736 | 0.0 | 0.40 +Other | | 0.01489 | | | 0.06 Nlocal: 3487 ave 3487 max 3487 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 561942 ave 561942 max 561942 min +Neighs: 539960 ave 539960 max 539960 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 -Neighbor list builds = 37 +Neighbor list builds = 42 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:01:17 +Total wall time: 0:00:27 diff --git a/examples/peri/log.6Jul17.peri.ves.g++.4 b/examples/peri/log.27Nov18.peri.ves.g++.4 similarity index 61% rename from examples/peri/log.6Jul17.peri.ves.g++.4 rename to examples/peri/log.27Nov18.peri.ves.g++.4 index bd05d58e9f..c71d41da9c 100644 --- a/examples/peri/log.6Jul17.peri.ves.g++.4 +++ b/examples/peri/log.27Nov18.peri.ves.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (6 Jul 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # small Peridynamic cylinder hit by projectile @@ -18,6 +18,7 @@ Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005) 2 by 1 by 2 MPI processor grid create_atoms 1 region target Created 3487 atoms + Time spent = 0.000587225 secs pair_style peri/ves pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 @@ -72,44 +73,44 @@ Peridynamic bonds: Per MPI rank memory allocation (min/avg/max) = 59.9 | 60.16 | 60.26 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0 0 0 0 0 5.0030006e-07 - 100 8.3392177e+24 247040.57 0 849083.8 8.0224286e+11 5.0030006e-07 - 200 1.1849022e+27 1158030.5 0 86701105 1.0301578e+14 5.5359205e-07 - 300 2.6287222e+27 4389155.1 0 1.9416767e+08 1.6636212e+14 7.6050375e-07 - 400 3.2718778e+27 7458219 0 2.4366885e+08 1.5439709e+14 1.0199269e-06 - 500 3.8413187e+27 6151611.4 0 2.8347258e+08 1.5008974e+14 1.2318007e-06 - 600 6.1409926e+27 18424316 0 4.6176842e+08 1.9507512e+14 1.5151227e-06 - 700 1.0046131e+28 11478344 0 7.3675086e+08 2.4228512e+14 1.9956447e-06 - 800 1.0402132e+28 4421233.6 0 7.5539495e+08 2.0512303e+14 2.4407262e-06 - 900 1.0419515e+28 7223258.7 0 7.594519e+08 1.6647307e+14 3.0124137e-06 - 1000 1.0503738e+28 2621480.4 0 7.6093057e+08 1.4315636e+14 3.5313793e-06 -Loop time of 25.9768 on 4 procs for 1000 steps with 3487 atoms + 100 2.3611484e+26 2297126.2 0 19343251 2.2714535e+13 5.0030006e-07 + 200 3.9696282e+27 27477818 0 3.1406199e+08 3.7046187e+14 5.1572409e-07 + 300 8.8025822e+27 32485477 0 6.6798094e+08 7.1158578e+14 5.9537958e-07 + 400 1.3288413e+28 37587857 0 9.9693436e+08 7.7688957e+14 8.2323713e-07 + 500 1.777552e+28 24842920 0 1.3081325e+09 7.3838229e+14 1.1586497e-06 + 600 2.1408855e+28 11023553 0 1.5566189e+09 6.4536834e+14 1.5966028e-06 + 700 2.2659932e+28 3494159 0 1.63941e+09 4.9466351e+14 2.2047524e-06 + 800 2.285628e+28 2220143.6 0 1.6523112e+09 3.8214902e+14 2.8786171e-06 + 900 2.2903476e+28 904133.04 0 1.6544025e+09 2.790555e+14 3.9502258e-06 + 1000 2.29097e+28 617974.86 0 1.6545656e+09 2.2599918e+14 4.8789193e-06 +Loop time of 3.73704 on 4 procs for 1000 steps with 3487 atoms -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads +98.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 22.455 | 23.348 | 24.175 | 14.1 | 89.88 -Neigh | 0.14472 | 0.18294 | 0.2299 | 8.6 | 0.70 -Comm | 1.4715 | 2.3485 | 3.2075 | 44.8 | 9.04 -Output | 0.000489 | 0.00059682 | 0.0007987 | 0.0 | 0.00 -Modify | 0.063634 | 0.071411 | 0.076907 | 1.9 | 0.27 -Other | | 0.02506 | | | 0.10 +Pair | 2.3248 | 2.876 | 3.5364 | 25.9 | 76.96 +Neigh | 0.072288 | 0.081806 | 0.091866 | 3.1 | 2.19 +Comm | 0.078943 | 0.72589 | 1.2634 | 50.3 | 19.42 +Output | 0.00028825 | 0.00057435 | 0.001307 | 0.0 | 0.02 +Modify | 0.031366 | 0.032767 | 0.035145 | 0.8 | 0.88 +Other | | 0.02002 | | | 0.54 -Nlocal: 871.75 ave 896 max 852 min -Histogram: 2 0 0 0 0 0 0 1 0 1 -Nghost: 1293.25 ave 1313 max 1269 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 140486 ave 167239 max 121255 min -Histogram: 2 0 0 0 0 0 1 0 0 1 +Nlocal: 871.75 ave 978 max 770 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 1004.75 ave 1107 max 906 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 90070.2 ave 94639 max 83936 min +Histogram: 1 0 0 0 0 1 0 1 0 1 FullNghs: 302269 ave 346070 max 260820 min Histogram: 1 0 0 0 2 0 0 0 0 1 Total # of neighbors = 1209076 Ave neighs/atom = 346.738 -Neighbor list builds = 37 +Neighbor list builds = 25 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:26 +Total wall time: 0:00:03 diff --git a/examples/pour/log.5Oct16.pour.2d.g++.1 b/examples/pour/log.27Nov18.pour.2d.g++.1 similarity index 78% rename from examples/pour/log.5Oct16.pour.2d.g++.1 rename to examples/pour/log.27Nov18.pour.2d.g++.1 index f80a61a55f..d8b615816f 100644 --- a/examples/pour/log.5Oct16.pour.2d.g++.1 +++ b/examples/pour/log.27Nov18.pour.2d.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pour 2d granular particles into container dimension 2 @@ -40,7 +41,7 @@ compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo 1000 thermo_modify lost ignore norm no -compute_modify thermo_temp dynamic yes +compute_modify thermo_temp dynamic/dof yes #dump id all atom 250 dump.pour @@ -52,13 +53,18 @@ compute_modify thermo_temp dynamic yes run 25000 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.2 ghost atom cutoff = 1.2 - binsize = 0.6 -> bins = 167 84 2 -Memory usage per processor = 2.75186 Mbytes + binsize = 0.6, bins = 167 84 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.804 | 5.804 | 5.804 Mbytes Step Atoms KinEng c_1 Volume 0 0 -0 0 5000 1000 224 201.77464 0 5000 @@ -86,20 +92,20 @@ Step Atoms KinEng c_1 Volume 23000 1000 16.115382 7.9435503 5000 24000 1000 11.971003 5.9411126 5000 25000 1000 10.404117 4.3811155 5000 -Loop time of 3.00132 on 1 procs for 25000 steps with 1000 atoms +Loop time of 2.72875 on 1 procs for 25000 steps with 1000 atoms -Performance: 719682.852 tau/day, 8329.663 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 791570.958 tau/day, 9161.701 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2554 | 1.2554 | 1.2554 | 0.0 | 41.83 -Neigh | 0.4288 | 0.4288 | 0.4288 | 0.0 | 14.29 -Comm | 0.0078034 | 0.0078034 | 0.0078034 | 0.0 | 0.26 -Output | 0.0003016 | 0.0003016 | 0.0003016 | 0.0 | 0.01 -Modify | 1.177 | 1.177 | 1.177 | 0.0 | 39.21 -Other | | 0.132 | | | 4.40 +Pair | 0.95597 | 0.95597 | 0.95597 | 0.0 | 35.03 +Neigh | 0.38475 | 0.38475 | 0.38475 | 0.0 | 14.10 +Comm | 0.010862 | 0.010862 | 0.010862 | 0.0 | 0.40 +Output | 0.00054383 | 0.00054383 | 0.00054383 | 0.0 | 0.02 +Modify | 1.2364 | 1.2364 | 1.2364 | 0.0 | 45.31 +Other | | 0.1402 | | | 5.14 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -112,4 +118,4 @@ Total # of neighbors = 2374 Ave neighs/atom = 2.374 Neighbor list builds = 2089 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/pour/log.5Oct16.pour.2d.g++.4 b/examples/pour/log.27Nov18.pour.2d.g++.4 similarity index 78% rename from examples/pour/log.5Oct16.pour.2d.g++.4 rename to examples/pour/log.27Nov18.pour.2d.g++.4 index ee88b94284..a491cf4866 100644 --- a/examples/pour/log.5Oct16.pour.2d.g++.4 +++ b/examples/pour/log.27Nov18.pour.2d.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pour 2d granular particles into container dimension 2 @@ -40,7 +41,7 @@ compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo 1000 thermo_modify lost ignore norm no -compute_modify thermo_temp dynamic yes +compute_modify thermo_temp dynamic/dof yes #dump id all atom 250 dump.pour @@ -52,13 +53,18 @@ compute_modify thermo_temp dynamic yes run 25000 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.2 ghost atom cutoff = 1.2 - binsize = 0.6 -> bins = 167 84 2 -Memory usage per processor = 2.7174 Mbytes + binsize = 0.6, bins = 167 84 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.77 | 5.77 | 5.77 Mbytes Step Atoms KinEng c_1 Volume 0 0 -0 0 5000 1000 224 201.77464 0 5000 @@ -86,20 +92,20 @@ Step Atoms KinEng c_1 Volume 23000 1000 11.97674 5.2548063 5000 24000 1000 7.8974699 3.7396899 5000 25000 1000 6.1288038 2.2056805 5000 -Loop time of 0.974647 on 4 procs for 25000 steps with 1000 atoms +Loop time of 0.901039 on 4 procs for 25000 steps with 1000 atoms -Performance: 2216187.157 tau/day, 25650.314 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2397232.992 tau/day, 27745.752 timesteps/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.29556 | 0.31544 | 0.33654 | 3.0 | 32.36 -Neigh | 0.10012 | 0.10782 | 0.11355 | 1.7 | 11.06 -Comm | 0.081835 | 0.087606 | 0.098412 | 2.2 | 8.99 -Output | 0.00039244 | 0.00043273 | 0.0004766 | 0.2 | 0.04 -Modify | 0.28155 | 0.29814 | 0.31262 | 2.2 | 30.59 -Other | | 0.1652 | | | 16.95 +Pair | 0.21557 | 0.22754 | 0.23651 | 1.9 | 25.25 +Neigh | 0.098304 | 0.10178 | 0.10595 | 1.0 | 11.30 +Comm | 0.051792 | 0.066485 | 0.079589 | 3.8 | 7.38 +Output | 0.00052619 | 0.00061941 | 0.00082016 | 0.0 | 0.07 +Modify | 0.31782 | 0.32767 | 0.33815 | 1.5 | 36.37 +Other | | 0.1769 | | | 19.64 Nlocal: 250 ave 267 max 232 min Histogram: 1 0 0 0 1 1 0 0 0 1 diff --git a/examples/pour/log.5Oct16.pour.2d.molecule.g++.1 b/examples/pour/log.27Nov18.pour.2d.molecule.g++.1 similarity index 78% rename from examples/pour/log.5Oct16.pour.2d.molecule.g++.1 rename to examples/pour/log.27Nov18.pour.2d.molecule.g++.1 index c4533f3f0c..5eff1843e7 100644 --- a/examples/pour/log.5Oct16.pour.2d.molecule.g++.1 +++ b/examples/pour/log.27Nov18.pour.2d.molecule.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pour 2d granular particles into container dimension 2 @@ -34,11 +35,11 @@ fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NU molecule object molecule.vshape Read molecule object: - 5 atoms with 1 types - 0 bonds with 0 types - 0 angles with 0 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 5 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 fix 3 all rigid/small molecule mol object 0 rigid bodies with 0 atoms 2.23607 = max distance from body owner to body atom @@ -55,7 +56,7 @@ compute 1 all erotate/sphere compute Tsphere all temp/sphere thermo_style custom step atoms ke c_1 vol thermo_modify lost ignore norm no temp Tsphere -compute_modify Tsphere dynamic yes +compute_modify Tsphere dynamic/dof yes thermo 1000 @@ -73,13 +74,18 @@ thermo 1000 run 25000 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.2 ghost atom cutoff = 2.5 - binsize = 0.6 -> bins = 167 84 2 -Memory usage per processor = 2.75807 Mbytes + binsize = 0.6, bins = 167 84 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.81 | 5.81 | 5.81 Mbytes Step Atoms KinEng c_1 Volume 0 0 -0 0 5000 1000 130 259.24123 2.3772821e-30 5000 @@ -106,21 +112,21 @@ Step Atoms KinEng c_1 Volume 22000 1040 1262.0253 1.6097601 5000 23000 1040 1042.7 3.1078701 5000 24000 1040 1167.4717 1.4954047 5000 - 25000 1170 1214.9087 2.4525541 5000 -Loop time of 3.19438 on 1 procs for 25000 steps with 1170 atoms + 25000 1170 1214.9087 2.4525535 5000 +Loop time of 3.36515 on 1 procs for 25000 steps with 1170 atoms -Performance: 676187.595 tau/day, 7826.245 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 641872.369 tau/day, 7429.078 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.87733 | 0.87733 | 0.87733 | 0.0 | 27.46 -Neigh | 0.25913 | 0.25913 | 0.25913 | 0.0 | 8.11 -Comm | 0.0095103 | 0.0095103 | 0.0095103 | 0.0 | 0.30 -Output | 0.00043368 | 0.00043368 | 0.00043368 | 0.0 | 0.01 -Modify | 1.941 | 1.941 | 1.941 | 0.0 | 60.76 -Other | | 0.107 | | | 3.35 +Pair | 0.73922 | 0.73922 | 0.73922 | 0.0 | 21.97 +Neigh | 0.22808 | 0.22808 | 0.22808 | 0.0 | 6.78 +Comm | 0.013331 | 0.013331 | 0.013331 | 0.0 | 0.40 +Output | 0.00082207 | 0.00082207 | 0.00082207 | 0.0 | 0.02 +Modify | 2.2694 | 2.2694 | 2.2694 | 0.0 | 67.44 +Other | | 0.1143 | | | 3.40 Nlocal: 1170 ave 1170 max 1170 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/pour/log.5Oct16.pour.2d.molecule.g++.4 b/examples/pour/log.27Nov18.pour.2d.molecule.g++.4 similarity index 78% rename from examples/pour/log.5Oct16.pour.2d.molecule.g++.4 rename to examples/pour/log.27Nov18.pour.2d.molecule.g++.4 index 604fd71673..2fae548aab 100644 --- a/examples/pour/log.5Oct16.pour.2d.molecule.g++.4 +++ b/examples/pour/log.27Nov18.pour.2d.molecule.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pour 2d granular particles into container dimension 2 @@ -34,11 +35,11 @@ fix ywalls all wall/gran hertz/history 4000.0 NULL 100.0 NULL 0 1 yplane 0 NU molecule object molecule.vshape Read molecule object: - 5 atoms with 1 types - 0 bonds with 0 types - 0 angles with 0 types - 0 dihedrals with 0 types - 0 impropers with 0 types + 5 atoms with max type 1 + 0 bonds with max type 0 + 0 angles with max type 0 + 0 dihedrals with max type 0 + 0 impropers with max type 0 fix 3 all rigid/small molecule mol object 0 rigid bodies with 0 atoms 2.23607 = max distance from body owner to body atom @@ -55,7 +56,7 @@ compute 1 all erotate/sphere compute Tsphere all temp/sphere thermo_style custom step atoms ke c_1 vol thermo_modify lost ignore norm no temp Tsphere -compute_modify Tsphere dynamic yes +compute_modify Tsphere dynamic/dof yes thermo 1000 @@ -73,13 +74,18 @@ thermo 1000 run 25000 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.2 ghost atom cutoff = 2.5 - binsize = 0.6 -> bins = 167 84 2 -Memory usage per processor = 2.72041 Mbytes + binsize = 0.6, bins = 167 84 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hertz/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/2d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.773 | 5.773 | 5.773 Mbytes Step Atoms KinEng c_1 Volume 0 0 -0 0 5000 1000 130 259.24123 2.3773387e-30 5000 @@ -106,21 +112,21 @@ Step Atoms KinEng c_1 Volume 22000 1040 1226.7461 1.2299974 5000 23000 1040 1106.7165 3.1057108 5000 24000 1040 1161.9203 2.0994962 5000 - 25000 1170 1187.5093 2.959617 5000 -Loop time of 1.20622 on 4 procs for 25000 steps with 1170 atoms + 25000 1170 1187.5093 2.9596172 5000 +Loop time of 1.4211 on 4 procs for 25000 steps with 1170 atoms -Performance: 1790713.641 tau/day, 20725.852 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1519946.444 tau/day, 17591.973 timesteps/s +94.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.22275 | 0.23039 | 0.23778 | 1.1 | 19.10 -Neigh | 0.064599 | 0.067646 | 0.069656 | 0.7 | 5.61 -Comm | 0.079895 | 0.092342 | 0.10857 | 3.5 | 7.66 -Output | 0.00061584 | 0.00065601 | 0.00075412 | 0.2 | 0.05 -Modify | 0.69333 | 0.69728 | 0.70102 | 0.3 | 57.81 -Other | | 0.1179 | | | 9.78 +Pair | 0.19053 | 0.21869 | 0.23582 | 3.7 | 15.39 +Neigh | 0.06394 | 0.066575 | 0.070017 | 0.9 | 4.68 +Comm | 0.055579 | 0.070079 | 0.080658 | 3.4 | 4.93 +Output | 0.0012593 | 0.0031545 | 0.0088205 | 5.8 | 0.22 +Modify | 0.89034 | 0.9006 | 0.91315 | 0.9 | 63.37 +Other | | 0.162 | | | 11.40 Nlocal: 292.5 ave 296 max 285 min Histogram: 1 0 0 0 0 0 0 0 1 2 diff --git a/examples/pour/log.5Oct16.pour.g++.1 b/examples/pour/log.27Nov18.pour.g++.1 similarity index 77% rename from examples/pour/log.5Oct16.pour.g++.1 rename to examples/pour/log.27Nov18.pour.g++.1 index 23e2acd6dd..a1ebc335cd 100644 --- a/examples/pour/log.5Oct16.pour.g++.1 +++ b/examples/pour/log.27Nov18.pour.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pour granular particles into chute container, then induce flow atom_style sphere @@ -36,7 +37,7 @@ compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo 1000 thermo_modify lost ignore norm no -compute_modify thermo_temp dynamic yes +compute_modify thermo_temp dynamic/dof yes #dump id all atom 1000 dump.pour @@ -48,13 +49,18 @@ compute_modify thermo_temp dynamic yes run 25000 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.2 ghost atom cutoff = 1.2 - binsize = 0.6 -> bins = 34 34 28 -Memory usage per processor = 2.90017 Mbytes + binsize = 0.6, bins = 34 34 28 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.955 | 5.955 | 5.955 Mbytes Step Atoms KinEng c_1 Volume 0 0 -0 0 6600 1000 402 768.04606 0 6600 @@ -82,20 +88,20 @@ Step Atoms KinEng c_1 Volume 23000 3000 446.47658 39.719019 6600 24000 3000 331.57201 24.034747 6600 25000 3000 239.90493 18.457205 6600 -Loop time of 9.8391 on 1 procs for 25000 steps with 3000 atoms +Loop time of 8.66761 on 1 procs for 25000 steps with 3000 atoms -Performance: 219532.250 tau/day, 2540.883 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 249203.592 tau/day, 2884.301 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.5009 | 5.5009 | 5.5009 | 0.0 | 55.91 -Neigh | 1.57 | 1.57 | 1.57 | 0.0 | 15.96 -Comm | 0.20079 | 0.20079 | 0.20079 | 0.0 | 2.04 -Output | 0.00048852 | 0.00048852 | 0.00048852 | 0.0 | 0.00 -Modify | 2.2916 | 2.2916 | 2.2916 | 0.0 | 23.29 -Other | | 0.2752 | | | 2.80 +Pair | 4.5311 | 4.5311 | 4.5311 | 0.0 | 52.28 +Neigh | 1.4556 | 1.4556 | 1.4556 | 0.0 | 16.79 +Comm | 0.2322 | 0.2322 | 0.2322 | 0.0 | 2.68 +Output | 0.00084257 | 0.00084257 | 0.00084257 | 0.0 | 0.01 +Modify | 2.1642 | 2.1642 | 2.1642 | 0.0 | 24.97 +Other | | 0.2837 | | | 3.27 Nlocal: 3000 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -112,7 +118,7 @@ Dangerous builds = 0 unfix ins fix 2 all gravity 1.0 chute 26.0 run 25000 -Memory usage per processor = 7.31316 Mbytes +Per MPI rank memory allocation (min/avg/max) = 13.24 | 13.24 | 13.24 Mbytes Step Atoms KinEng c_1 Volume 25000 3000 239.90493 18.457205 6600 26000 3000 86.453151 19.990229 6600 @@ -140,20 +146,20 @@ Step Atoms KinEng c_1 Volume 48000 3000 16184.643 202.00907 6600 49000 3000 17573.204 215.30429 6600 50000 3000 19117.749 232.28939 6600 -Loop time of 18.9367 on 1 procs for 25000 steps with 3000 atoms +Loop time of 16.4345 on 1 procs for 25000 steps with 3000 atoms -Performance: 114064.182 tau/day, 1320.187 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 131430.508 tau/day, 1521.186 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 12.058 | 12.058 | 12.058 | 0.0 | 63.68 -Neigh | 2.3177 | 2.3177 | 2.3177 | 0.0 | 12.24 -Comm | 0.4221 | 0.4221 | 0.4221 | 0.0 | 2.23 -Output | 0.00076723 | 0.00076723 | 0.00076723 | 0.0 | 0.00 -Modify | 3.6817 | 3.6817 | 3.6817 | 0.0 | 19.44 -Other | | 0.4563 | | | 2.41 +Pair | 9.893 | 9.893 | 9.893 | 0.0 | 60.20 +Neigh | 2.1448 | 2.1448 | 2.1448 | 0.0 | 13.05 +Comm | 0.47991 | 0.47991 | 0.47991 | 0.0 | 2.92 +Output | 0.0011523 | 0.0011523 | 0.0011523 | 0.0 | 0.01 +Modify | 3.4635 | 3.4635 | 3.4635 | 0.0 | 21.07 +Other | | 0.4522 | | | 2.75 Nlocal: 3000 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -166,4 +172,4 @@ Total # of neighbors = 13997 Ave neighs/atom = 4.66567 Neighbor list builds = 836 Dangerous builds = 0 -Total wall time: 0:00:28 +Total wall time: 0:00:25 diff --git a/examples/pour/log.5Oct16.pour.g++.4 b/examples/pour/log.27Nov18.pour.g++.4 similarity index 77% rename from examples/pour/log.5Oct16.pour.g++.4 rename to examples/pour/log.27Nov18.pour.g++.4 index 28e463121a..004bf92608 100644 --- a/examples/pour/log.5Oct16.pour.g++.4 +++ b/examples/pour/log.27Nov18.pour.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Pour granular particles into chute container, then induce flow atom_style sphere @@ -36,7 +37,7 @@ compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo 1000 thermo_modify lost ignore norm no -compute_modify thermo_temp dynamic yes +compute_modify thermo_temp dynamic/dof yes #dump id all atom 1000 dump.pour @@ -48,13 +49,18 @@ compute_modify thermo_temp dynamic yes run 25000 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.2 ghost atom cutoff = 1.2 - binsize = 0.6 -> bins = 34 34 28 -Memory usage per processor = 2.7753 Mbytes + binsize = 0.6, bins = 34 34 28 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair gran/hooke/history, perpetual + attributes: half, newton off, size, history + pair build: half/size/bin/newtoff + stencil: half/bin/3d/newtoff + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.83 | 5.83 | 5.83 Mbytes Step Atoms KinEng c_1 Volume 0 0 -0 0 6600 1000 402 768.04606 0 6600 @@ -82,20 +88,20 @@ Step Atoms KinEng c_1 Volume 23000 3000 456.26221 36.394458 6600 24000 3000 334.38331 26.256087 6600 25000 3000 233.7217 18.768345 6600 -Loop time of 3.00537 on 4 procs for 25000 steps with 3000 atoms +Loop time of 2.79912 on 4 procs for 25000 steps with 3000 atoms -Performance: 718714.211 tau/day, 8318.452 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 771671.423 tau/day, 8931.382 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.328 | 1.3659 | 1.4112 | 2.9 | 45.45 -Neigh | 0.39528 | 0.40948 | 0.42265 | 1.6 | 13.62 -Comm | 0.36134 | 0.36901 | 0.37668 | 0.9 | 12.28 -Output | 0.00052094 | 0.00060934 | 0.0006752 | 0.2 | 0.02 -Modify | 0.5892 | 0.60403 | 0.61671 | 1.3 | 20.10 -Other | | 0.2564 | | | 8.53 +Pair | 1.0916 | 1.1431 | 1.1982 | 4.0 | 40.84 +Neigh | 0.37439 | 0.39186 | 0.41149 | 2.6 | 14.00 +Comm | 0.32241 | 0.32795 | 0.33831 | 1.1 | 11.72 +Output | 0.00068283 | 0.0029467 | 0.0094671 | 6.9 | 0.11 +Modify | 0.5813 | 0.5952 | 0.60947 | 1.5 | 21.26 +Other | | 0.3381 | | | 12.08 Nlocal: 750 ave 765 max 730 min Histogram: 1 0 0 0 1 0 0 0 1 1 @@ -112,7 +118,7 @@ Dangerous builds = 0 unfix ins fix 2 all gravity 1.0 chute 26.0 run 25000 -Memory usage per processor = 7.16682 Mbytes +Per MPI rank memory allocation (min/avg/max) = 12.16 | 12.39 | 13.06 Mbytes Step Atoms KinEng c_1 Volume 25000 3000 233.7217 18.768345 6600 26000 3000 80.58756 21.114703 6600 @@ -140,20 +146,20 @@ Step Atoms KinEng c_1 Volume 48000 3000 15555.796 204.40316 6600 49000 3000 16694.338 208.98934 6600 50000 3000 17936.665 192.19442 6600 -Loop time of 5.5877 on 4 procs for 25000 steps with 3000 atoms +Loop time of 5.65089 on 4 procs for 25000 steps with 3000 atoms -Performance: 386563.121 tau/day, 4474.110 timesteps/s -99.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 382240.368 tau/day, 4424.078 timesteps/s +94.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.9862 | 3.0411 | 3.0685 | 1.9 | 54.42 -Neigh | 0.58638 | 0.60065 | 0.61313 | 1.2 | 10.75 -Comm | 0.49186 | 0.50314 | 0.51344 | 1.2 | 9.00 -Output | 0.00076151 | 0.0010245 | 0.0012021 | 0.5 | 0.02 -Modify | 0.93086 | 0.95139 | 0.96527 | 1.3 | 17.03 -Other | | 0.4904 | | | 8.78 +Pair | 2.5656 | 2.5853 | 2.6068 | 0.9 | 45.75 +Neigh | 0.57736 | 0.59939 | 0.61824 | 1.9 | 10.61 +Comm | 0.58146 | 0.63908 | 0.70461 | 5.5 | 11.31 +Output | 0.00081015 | 0.002184 | 0.0061922 | 5.0 | 0.04 +Modify | 0.91975 | 0.93371 | 0.95875 | 1.5 | 16.52 +Other | | 0.8912 | | | 15.77 Nlocal: 750 ave 758 max 741 min Histogram: 1 0 0 0 0 2 0 0 0 1 diff --git a/examples/python/log.27Nov18.fix_python_invoke.g++.1 b/examples/python/log.27Nov18.fix_python_invoke.g++.1 new file mode 100644 index 0000000000..094c667a5d --- /dev/null +++ b/examples/python/log.27Nov18.fix_python_invoke.g++.1 @@ -0,0 +1,100 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000678539 secs +mass 1 1.0 + +velocity all create 3.0 87287 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +python end_of_step_callback here """ +from __future__ import print_function +from lammps import lammps +def end_of_step_callback(lmp): + L = lammps(ptr=lmp) + t = L.extract_global("ntimestep", 0) + print("### END OF STEP ###", t) +def post_force_callback(lmp, v): + L = lammps(ptr=lmp) + t = L.extract_global("ntimestep", 0) + print("### POST_FORCE ###", t) +""" + +fix 1 all nve +fix 2 all python/invoke 50 end_of_step end_of_step_callback +fix 3 all python/invoke 50 post_force post_force_callback + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 + 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 + 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 + 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 +Loop time of 0.732007 on 1 procs for 250 steps with 4000 atoms + +Performance: 147539.519 tau/day, 341.527 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.60651 | 0.60651 | 0.60651 | 0.0 | 82.86 +Neigh | 0.092702 | 0.092702 | 0.092702 | 0.0 | 12.66 +Comm | 0.013686 | 0.013686 | 0.013686 | 0.0 | 1.87 +Output | 0.00016069 | 0.00016069 | 0.00016069 | 0.0 | 0.02 +Modify | 0.016055 | 0.016055 | 0.016055 | 0.0 | 2.19 +Other | | 0.00289 | | | 0.39 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5499 ave 5499 max 5499 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151513 ave 151513 max 151513 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151513 +Ave neighs/atom = 37.8783 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/python/log.27Nov18.fix_python_invoke.g++.4 b/examples/python/log.27Nov18.fix_python_invoke.g++.4 new file mode 100644 index 0000000000..17c48e0f48 --- /dev/null +++ b/examples/python/log.27Nov18.fix_python_invoke.g++.4 @@ -0,0 +1,100 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000408888 secs +mass 1 1.0 + +velocity all create 3.0 87287 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +python end_of_step_callback here """ +from __future__ import print_function +from lammps import lammps +def end_of_step_callback(lmp): + L = lammps(ptr=lmp) + t = L.extract_global("ntimestep", 0) + print("### END OF STEP ###", t) +def post_force_callback(lmp, v): + L = lammps(ptr=lmp) + t = L.extract_global("ntimestep", 0) + print("### POST_FORCE ###", t) +""" + +fix 1 all nve +fix 2 all python/invoke 50 end_of_step end_of_step_callback +fix 3 all python/invoke 50 post_force post_force_callback + +#dump id all atom 50 dump.melt + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 + 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 + 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 + 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 + 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 +Loop time of 0.227907 on 4 procs for 250 steps with 4000 atoms + +Performance: 473877.870 tau/day, 1096.940 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15923 | 0.16507 | 0.17227 | 1.2 | 72.43 +Neigh | 0.02438 | 0.025177 | 0.025757 | 0.4 | 11.05 +Comm | 0.022418 | 0.030157 | 0.036685 | 2.9 | 13.23 +Output | 0.00052595 | 0.00092125 | 0.0011675 | 0.0 | 0.40 +Modify | 0.0053911 | 0.0057266 | 0.006294 | 0.5 | 2.51 +Other | | 0.0008523 | | | 0.37 + +Nlocal: 1000 ave 1010 max 982 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 2703.75 ave 2713 max 2689 min +Histogram: 1 0 0 0 0 0 0 2 0 1 +Neighs: 37915.5 ave 39239 max 36193 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 151662 +Ave neighs/atom = 37.9155 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/python/log.27Nov18.fix_python_move_nve_melt.g++.1 b/examples/python/log.27Nov18.fix_python_move_nve_melt.g++.1 new file mode 100644 index 0000000000..414ac69747 --- /dev/null +++ b/examples/python/log.27Nov18.fix_python_move_nve_melt.g++.1 @@ -0,0 +1,77 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000658989 secs +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all python/move py_nve.NVE + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 + 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 + 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 + 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 +Loop time of 12.0574 on 1 procs for 250 steps with 4000 atoms + +Performance: 8957.186 tau/day, 20.734 timesteps/s +98.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.61686 | 0.61686 | 0.61686 | 0.0 | 5.12 +Neigh | 0.094026 | 0.094026 | 0.094026 | 0.0 | 0.78 +Comm | 0.015743 | 0.015743 | 0.015743 | 0.0 | 0.13 +Output | 0.00021815 | 0.00021815 | 0.00021815 | 0.0 | 0.00 +Modify | 11.328 | 11.328 | 11.328 | 0.0 | 93.95 +Other | | 0.002812 | | | 0.02 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5499 ave 5499 max 5499 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151513 ave 151513 max 151513 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151513 +Ave neighs/atom = 37.8783 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:12 diff --git a/examples/python/log.27Nov18.fix_python_move_nve_melt.g++.4 b/examples/python/log.27Nov18.fix_python_move_nve_melt.g++.4 new file mode 100644 index 0000000000..8a8f4e4f33 --- /dev/null +++ b/examples/python/log.27Nov18.fix_python_move_nve_melt.g++.4 @@ -0,0 +1,77 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.00041604 secs +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all python/move py_nve.NVE + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 + 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 + 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 + 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 + 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 +Loop time of 3.60532 on 4 procs for 250 steps with 4000 atoms + +Performance: 29955.711 tau/day, 69.342 timesteps/s +95.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15953 | 0.16556 | 0.16945 | 0.9 | 4.59 +Neigh | 0.024014 | 0.024431 | 0.024704 | 0.2 | 0.68 +Comm | 0.10837 | 0.26844 | 0.38063 | 19.1 | 7.45 +Output | 0.00021553 | 0.0063262 | 0.0088348 | 4.5 | 0.18 +Modify | 3.0299 | 3.138 | 3.3038 | 5.7 | 87.04 +Other | | 0.002585 | | | 0.07 + +Nlocal: 1000 ave 1010 max 982 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 2703.75 ave 2713 max 2689 min +Histogram: 1 0 0 0 0 0 0 2 0 1 +Neighs: 37915.5 ave 39239 max 36193 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 151662 +Ave neighs/atom = 37.9155 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:03 diff --git a/examples/python/log.27Nov18.fix_python_move_nve_melt_opt.g++.1 b/examples/python/log.27Nov18.fix_python_move_nve_melt_opt.g++.1 new file mode 100644 index 0000000000..e3c9ee4aa2 --- /dev/null +++ b/examples/python/log.27Nov18.fix_python_move_nve_melt_opt.g++.1 @@ -0,0 +1,77 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000703096 secs +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all python/move py_nve.NVE_Opt + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 + 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 + 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 + 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 +Loop time of 0.806998 on 1 procs for 250 steps with 4000 atoms + +Performance: 133829.286 tau/day, 309.790 timesteps/s +95.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.60639 | 0.60639 | 0.60639 | 0.0 | 75.14 +Neigh | 0.092807 | 0.092807 | 0.092807 | 0.0 | 11.50 +Comm | 0.013782 | 0.013782 | 0.013782 | 0.0 | 1.71 +Output | 0.00021243 | 0.00021243 | 0.00021243 | 0.0 | 0.03 +Modify | 0.091672 | 0.091672 | 0.091672 | 0.0 | 11.36 +Other | | 0.00213 | | | 0.26 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5499 ave 5499 max 5499 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151513 ave 151513 max 151513 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151513 +Ave neighs/atom = 37.8783 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/python/log.27Nov18.fix_python_move_nve_melt_opt.g++.4 b/examples/python/log.27Nov18.fix_python_move_nve_melt_opt.g++.4 new file mode 100644 index 0000000000..b4fbdcbc44 --- /dev/null +++ b/examples/python/log.27Nov18.fix_python_move_nve_melt_opt.g++.4 @@ -0,0 +1,77 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms + Time spent = 0.000407457 secs +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 2.5 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all python/move py_nve.NVE_Opt + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 + 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 + 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 + 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 + 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 +Loop time of 0.283796 on 4 procs for 250 steps with 4000 atoms + +Performance: 380554.630 tau/day, 880.913 timesteps/s +93.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.16068 | 0.16297 | 0.167 | 0.6 | 57.42 +Neigh | 0.024281 | 0.02511 | 0.027018 | 0.7 | 8.85 +Comm | 0.033199 | 0.035637 | 0.03814 | 1.3 | 12.56 +Output | 0.00044489 | 0.00057381 | 0.00065589 | 0.0 | 0.20 +Modify | 0.056902 | 0.058489 | 0.06128 | 0.7 | 20.61 +Other | | 0.001018 | | | 0.36 + +Nlocal: 1000 ave 1010 max 982 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 2703.75 ave 2713 max 2689 min +Histogram: 1 0 0 0 0 0 0 2 0 1 +Neighs: 37915.5 ave 39239 max 36193 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 151662 +Ave neighs/atom = 37.9155 +Neighbor list builds = 12 +Dangerous builds not checked +Total wall time: 0:00:00 diff --git a/examples/python/log.27Nov18.pair_python_coulomb.g++.1 b/examples/python/log.27Nov18.pair_python_coulomb.g++.1 new file mode 100644 index 0000000000..e1f0aba1bf --- /dev/null +++ b/examples/python/log.27Nov18.pair_python_coulomb.g++.1 @@ -0,0 +1,178 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay coul/cut 12.0 python 12.0 + +pair_coeff * * coul/cut +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create combined lj/coul table for all atom types +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + +# switch to tabulated potential +pair_style table linear 2000 pppm +pair_coeff 1 1 spce.table OW-OW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) +pair_coeff 1 2 spce.table OW-HW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) +pair_coeff 2 2 spce.table HW-HW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 25.18 | 25.18 | 25.18 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -18173.499 0 -18173.499 -2019.6011 + 10 146.87683 -19431.334 0 -18118.336 -4804.774 + 20 183.13008 -19192.694 0 -17555.612 -5105.075 + 30 205.91102 -18124.567 0 -16283.836 -4052.5955 + 40 241.34432 -18154.089 0 -15996.604 -3187.3994 + 50 265.93905 -19712.779 0 -17335.431 -2716.3264 + 60 273.67861 -21092.479 0 -18645.943 -2266.2648 + 70 288.39213 -19794.592 0 -17216.526 -1207.5782 + 80 300.36209 -20235.73 0 -17550.658 -1345.2669 + 90 303.8567 -21670.331 0 -18954.02 -2207.0831 + 100 304.10875 -19847.214 0 -17128.649 -1431.7749 +Loop time of 5.78394 on 1 procs for 100 steps with 4500 atoms + +Performance: 1.494 ns/day, 16.066 hours/ns, 17.289 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.4417 | 5.4417 | 5.4417 | 0.0 | 94.08 +Bond | 9.5844e-05 | 9.5844e-05 | 9.5844e-05 | 0.0 | 0.00 +Neigh | 0.26895 | 0.26895 | 0.26895 | 0.0 | 4.65 +Comm | 0.019179 | 0.019179 | 0.019179 | 0.0 | 0.33 +Output | 0.00039768 | 0.00039768 | 0.00039768 | 0.0 | 0.01 +Modify | 0.050508 | 0.050508 | 0.050508 | 0.0 | 0.87 +Other | | 0.003098 | | | 0.05 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21269 ave 21269 max 21269 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.59772e+06 ave 2.59772e+06 max 2.59772e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2597720 +Ave neighs/atom = 577.271 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:06 diff --git a/examples/python/log.27Nov18.pair_python_coulomb.g++.4 b/examples/python/log.27Nov18.pair_python_coulomb.g++.4 new file mode 100644 index 0000000000..6558085246 --- /dev/null +++ b/examples/python/log.27Nov18.pair_python_coulomb.g++.4 @@ -0,0 +1,178 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay coul/cut 12.0 python 12.0 + +pair_coeff * * coul/cut +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create combined lj/coul table for all atom types +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + +# switch to tabulated potential +pair_style table linear 2000 pppm +pair_coeff 1 1 spce.table OW-OW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) +pair_coeff 1 2 spce.table OW-HW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) +pair_coeff 2 2 spce.table HW-HW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.01 | 10.01 | 10.01 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -18173.499 0 -18173.499 -2019.6011 + 10 146.87683 -19431.334 0 -18118.336 -4804.774 + 20 183.13008 -19192.694 0 -17555.612 -5105.075 + 30 205.91102 -18124.567 0 -16283.836 -4052.5955 + 40 241.34432 -18154.089 0 -15996.604 -3187.3994 + 50 265.93905 -19712.779 0 -17335.431 -2716.3264 + 60 273.67861 -21092.479 0 -18645.943 -2266.2648 + 70 288.39213 -19794.592 0 -17216.526 -1207.5782 + 80 300.36209 -20235.73 0 -17550.658 -1345.2669 + 90 303.8567 -21670.331 0 -18954.02 -2207.0831 + 100 304.10875 -19847.214 0 -17128.649 -1431.7749 +Loop time of 1.64676 on 4 procs for 100 steps with 4500 atoms + +Performance: 5.247 ns/day, 4.574 hours/ns, 60.725 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4241 | 1.4506 | 1.5134 | 3.0 | 88.09 +Bond | 9.8705e-05 | 0.00010312 | 0.00010729 | 0.0 | 0.01 +Neigh | 0.071698 | 0.071712 | 0.07172 | 0.0 | 4.35 +Comm | 0.027696 | 0.090501 | 0.11691 | 12.1 | 5.50 +Output | 0.00032783 | 0.00048846 | 0.00096679 | 0.0 | 0.03 +Modify | 0.030543 | 0.030691 | 0.030788 | 0.1 | 1.86 +Other | | 0.002627 | | | 0.16 + +Nlocal: 1125 ave 1163 max 1097 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 12265.5 ave 12299 max 12233 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 649430 ave 681781 max 630283 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 2597720 +Ave neighs/atom = 577.271 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:01 diff --git a/examples/python/log.4May17.pair_python_hybrid.g++.1 b/examples/python/log.27Nov18.pair_python_hybrid.g++.1 similarity index 65% rename from examples/python/log.4May17.pair_python_hybrid.g++.1 rename to examples/python/log.27Nov18.pair_python_hybrid.g++.1 index 718f794a57..bc56a98bba 100644 --- a/examples/python/log.4May17.pair_python_hybrid.g++.1 +++ b/examples/python/log.27Nov18.pair_python_hybrid.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones hybrid @@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.00073123 secs mass * 1.0 region half block -0.1 4.9 0 10 0 10 set region half type 2 @@ -53,7 +54,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 @@ -61,20 +62,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 -Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms +Loop time of 5.56562 on 1 procs for 250 steps with 4000 atoms -Performance: 10758.705 tau/day, 24.904 timesteps/s -98.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 19404.856 tau/day, 44.919 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.913 | 9.913 | 9.913 | 0.0 | 98.75 -Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95 -Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13 -Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00 -Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14 -Other | | 0.003027 | | | 0.03 +Pair | 5.4305 | 5.4305 | 5.4305 | 0.0 | 97.57 +Neigh | 0.10441 | 0.10441 | 0.10441 | 0.0 | 1.88 +Comm | 0.013915 | 0.013915 | 0.013915 | 0.0 | 0.25 +Output | 0.00019979 | 0.00019979 | 0.00019979 | 0.0 | 0.00 +Modify | 0.014502 | 0.014502 | 0.014502 | 0.0 | 0.26 +Other | | 0.002061 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -89,14 +90,60 @@ Neighbor list builds = 12 Dangerous builds not checked write_data hybrid.data +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard write_restart hybrid.restart +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard clear using 1 OpenMP thread(s) per MPI task read_restart hybrid.restart + restoring atom style atomic from restart orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid + restoring pair style hybrid from restart 4000 atoms pair_style hybrid lj/cut 2.5 python 2.5 @@ -129,7 +176,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.281 | 4.281 | 4.281 Mbytes Step Temp E_pair E_mol TotEng Press 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 300 1.645592 -4.7496711 0 -2.2819002 5.8734193 @@ -137,20 +184,20 @@ Step Temp E_pair E_mol TotEng Press 400 1.6540555 -4.7622999 0 -2.281837 5.8200413 450 1.6264734 -4.7200865 0 -2.2809863 5.9546991 500 1.6366891 -4.7350979 0 -2.2806781 5.9369284 -Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms +Loop time of 5.56525 on 1 procs for 250 steps with 4000 atoms -Performance: 10713.932 tau/day, 24.801 timesteps/s -98.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 19406.123 tau/day, 44.922 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69 -Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98 -Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14 -Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00 -Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13 -Other | | 0.004348 | | | 0.04 +Pair | 5.3122 | 5.3122 | 5.3122 | 0.0 | 95.45 +Neigh | 0.21918 | 0.21918 | 0.21918 | 0.0 | 3.94 +Comm | 0.015959 | 0.015959 | 0.015959 | 0.0 | 0.29 +Output | 0.00018764 | 0.00018764 | 0.00018764 | 0.0 | 0.00 +Modify | 0.014443 | 0.014443 | 0.014443 | 0.0 | 0.26 +Other | | 0.00326 | | | 0.06 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -211,7 +258,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.781 | 3.781 | 3.781 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.6275257 -4.7224992 0 -2.281821 5.9567365 50 1.6454666 -4.7497515 0 -2.2821686 5.8729175 @@ -219,20 +266,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6537193 -4.7627023 0 -2.2827434 5.8177704 200 1.6258731 -4.7205017 0 -2.2823017 5.952511 250 1.6370862 -4.7373176 0 -2.2823022 5.925807 -Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms +Loop time of 5.44427 on 1 procs for 250 steps with 4000 atoms -Performance: 10868.626 tau/day, 25.159 timesteps/s -98.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 19837.379 tau/day, 45.920 timesteps/s +99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74 -Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97 -Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13 -Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00 -Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13 -Other | | 0.002994 | | | 0.03 +Pair | 5.3082 | 5.3082 | 5.3082 | 0.0 | 97.50 +Neigh | 0.10536 | 0.10536 | 0.10536 | 0.0 | 1.94 +Comm | 0.01346 | 0.01346 | 0.01346 | 0.0 | 0.25 +Output | 0.00019431 | 0.00019431 | 0.00019431 | 0.0 | 0.00 +Modify | 0.015079 | 0.015079 | 0.015079 | 0.0 | 0.28 +Other | | 0.002012 | | | 0.04 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -247,4 +294,4 @@ Neighbor list builds = 12 Dangerous builds not checked shell rm hybrid.data hybrid.restart -Total wall time: 0:00:30 +Total wall time: 0:00:16 diff --git a/examples/python/log.4May17.pair_python_hybrid.g++.4 b/examples/python/log.27Nov18.pair_python_hybrid.g++.4 similarity index 65% rename from examples/python/log.4May17.pair_python_hybrid.g++.4 rename to examples/python/log.27Nov18.pair_python_hybrid.g++.4 index 32d9fc1740..b959f608ee 100644 --- a/examples/python/log.4May17.pair_python_hybrid.g++.4 +++ b/examples/python/log.27Nov18.pair_python_hybrid.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones hybrid @@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000420809 secs mass * 1.0 region half block -0.1 4.9 0 10 0 10 set region half type 2 @@ -53,7 +54,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.968 | 3.968 | 3.968 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 @@ -61,20 +62,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 -Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.53377 on 4 procs for 250 steps with 4000 atoms -Performance: 39742.745 tau/day, 91.997 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 70414.718 tau/day, 162.997 timesteps/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35 -Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93 -Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53 -Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01 -Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13 -Other | | 0.001337 | | | 0.05 +Pair | 1.3644 | 1.406 | 1.4448 | 3.2 | 91.67 +Neigh | 0.027066 | 0.027591 | 0.028437 | 0.3 | 1.80 +Comm | 0.055296 | 0.095109 | 0.13733 | 12.4 | 6.20 +Output | 0.00022817 | 0.00030088 | 0.00042033 | 0.0 | 0.02 +Modify | 0.0037878 | 0.0038549 | 0.0040336 | 0.2 | 0.25 +Other | | 0.0008861 | | | 0.06 Nlocal: 1000 ave 1010 max 982 min Histogram: 1 0 0 0 0 0 1 0 0 2 @@ -89,14 +90,60 @@ Neighbor list builds = 12 Dangerous builds not checked write_data hybrid.data +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard write_restart hybrid.restart +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard clear using 1 OpenMP thread(s) per MPI task read_restart hybrid.restart + restoring atom style atomic from restart orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid + restoring pair style hybrid from restart 4000 atoms pair_style hybrid lj/cut 2.5 python 2.5 @@ -129,7 +176,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.626 | 3.626 | 3.626 Mbytes Step Temp E_pair E_mol TotEng Press 250 1.6323462 -4.7292062 0 -2.2812991 5.9762168 300 1.6451788 -4.7488091 0 -2.2816578 5.8375485 @@ -137,20 +184,20 @@ Step Temp E_pair E_mol TotEng Press 400 1.6388136 -4.7387093 0 -2.2811035 5.9331084 450 1.6431295 -4.7452215 0 -2.2811435 5.8929898 500 1.643316 -4.7454222 0 -2.2810644 5.8454817 -Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.51785 on 4 procs for 250 steps with 4000 atoms -Performance: 39155.038 tau/day, 90.637 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 71153.411 tau/day, 164.707 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13 -Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90 -Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76 -Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01 -Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13 -Other | | 0.002039 | | | 0.07 +Pair | 1.2893 | 1.3741 | 1.416 | 4.2 | 90.53 +Neigh | 0.055474 | 0.056676 | 0.057363 | 0.3 | 3.73 +Comm | 0.039187 | 0.081666 | 0.16742 | 17.6 | 5.38 +Output | 0.00014877 | 0.0002687 | 0.00061893 | 0.0 | 0.02 +Modify | 0.003741 | 0.0037862 | 0.0038075 | 0.0 | 0.25 +Other | | 0.001315 | | | 0.09 Nlocal: 1000 ave 1012 max 983 min Histogram: 1 0 0 0 0 0 2 0 0 1 @@ -211,7 +258,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.126 | 3.126 | 3.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.6323462 -4.7292062 0 -2.2812991 5.9762168 50 1.6450626 -4.7488948 0 -2.2819177 5.8370409 @@ -219,20 +266,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6384234 -4.7389689 0 -2.2819482 5.9315273 200 1.6428814 -4.7460743 0 -2.2823683 5.8888228 250 1.6432631 -4.7466603 0 -2.2823818 5.8398819 -Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms +Loop time of 1.53622 on 4 procs for 250 steps with 4000 atoms -Performance: 39715.257 tau/day, 91.933 timesteps/s -98.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 70302.534 tau/day, 162.737 timesteps/s +97.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52 -Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92 -Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37 -Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01 -Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13 -Other | | 0.001215 | | | 0.04 +Pair | 1.2893 | 1.3875 | 1.4506 | 5.1 | 90.32 +Neigh | 0.026512 | 0.02714 | 0.027651 | 0.2 | 1.77 +Comm | 0.053684 | 0.11665 | 0.21515 | 17.6 | 7.59 +Output | 0.00017214 | 0.00029582 | 0.0006547 | 0.0 | 0.02 +Modify | 0.0037682 | 0.0037964 | 0.0038147 | 0.0 | 0.25 +Other | | 0.0008581 | | | 0.06 Nlocal: 1000 ave 1013 max 989 min Histogram: 1 0 0 1 0 1 0 0 0 1 @@ -247,4 +294,4 @@ Neighbor list builds = 12 Dangerous builds not checked shell rm hybrid.data hybrid.restart -Total wall time: 0:00:08 +Total wall time: 0:00:04 diff --git a/examples/python/log.4May17.pair_python_long.g++.1 b/examples/python/log.27Nov18.pair_python_long.g++.1 similarity index 63% rename from examples/python/log.4May17.pair_python_long.g++.1 rename to examples/python/log.27Nov18.pair_python_long.g++.1 index e2d7cf1bde..ad3532b2e8 100644 --- a/examples/python/log.4May17.pair_python_long.g++.1 +++ b/examples/python/log.27Nov18.pair_python_long.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full @@ -48,8 +48,8 @@ fix 2 all nvt temp 300.0 300.0 100.0 # create only lj/cut table for the oxygen atoms from python shell rm -f spce.table -WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) -WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) +WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308) +WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308) pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW Neighbor list info ... update every 1 steps, delay 10 steps, check yes @@ -69,11 +69,13 @@ pair_style hybrid/overlay coul/long 12.0 table linear 2000 kspace_style pppm 1.0e-6 pair_coeff * * coul/long pair_coeff 1 1 table spce.table OW-OW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) thermo 10 run 100 PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 @@ -98,35 +100,35 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes +Per MPI rank memory allocation (min/avg/max) = 36.57 | 36.57 | 36.57 Mbytes Step Temp E_pair E_mol TotEng Press - 0 0 -16690.032 0 -16690.032 -1268.9538 - 10 120.58553 -17767.504 0 -16689.536 -4063.8589 - 20 136.11736 -17882.557 0 -16665.742 -5124.6758 - 30 137.00764 -17872.318 0 -16647.545 -5337.2022 - 40 153.38868 -17999.269 0 -16628.059 -5213.6001 - 50 167.70342 -18103.06 0 -16603.883 -4460.6632 - 60 163.07134 -18034.856 0 -16577.088 -3285.0037 - 70 169.59286 -18064.636 0 -16548.57 -2606.407 - 80 182.92893 -18153.499 0 -16518.215 -2385.5152 - 90 191.2793 -18195.356 0 -16485.425 -2235.3701 - 100 194.68587 -18192.458 0 -16452.073 -1948.3746 -Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms + 0 0 -16690.019 0 -16690.019 -1268.9124 + 10 120.58553 -17767.489 0 -16689.521 -4063.8136 + 20 136.11736 -17882.538 0 -16665.724 -5124.6194 + 30 137.00764 -17872.302 0 -16647.529 -5337.1515 + 40 153.38867 -17999.256 0 -16628.046 -5213.5616 + 50 167.70342 -18103.046 0 -16603.87 -4460.6216 + 60 163.07134 -18034.842 0 -16577.074 -3284.9621 + 70 169.59286 -18064.622 0 -16548.556 -2606.3642 + 80 182.92892 -18153.485 0 -16518.202 -2385.4747 + 90 191.2793 -18195.343 0 -16485.411 -2235.3292 + 100 194.68587 -18192.446 0 -16452.061 -1948.3379 +Loop time of 7.00522 on 1 procs for 100 steps with 4500 atoms -Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 1.233 ns/day, 19.459 hours/ns, 14.275 timesteps/s +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32 -Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00 -Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36 -Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11 -Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30 -Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01 -Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83 -Other | | 0.005364 | | | 0.07 +Pair | 5.5664 | 5.5664 | 5.5664 | 0.0 | 79.46 +Bond | 0.00011444 | 0.00011444 | 0.00011444 | 0.0 | 0.00 +Kspace | 1.0814 | 1.0814 | 1.0814 | 0.0 | 15.44 +Neigh | 0.28011 | 0.28011 | 0.28011 | 0.0 | 4.00 +Comm | 0.020573 | 0.020573 | 0.020573 | 0.0 | 0.29 +Output | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01 +Modify | 0.052692 | 0.052692 | 0.052692 | 0.0 | 0.75 +Other | | 0.003407 | | | 0.05 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -135,7 +137,7 @@ Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2601769 +Total # of neighbors = 2601768 Ave neighs/atom = 578.171 Ave special neighs/atom = 2 Neighbor list builds = 3 @@ -143,4 +145,4 @@ Dangerous builds = 0 shell rm spce.table -Total wall time: 0:00:08 +Total wall time: 0:00:07 diff --git a/examples/python/log.4May17.pair_python_long.g++.4 b/examples/python/log.27Nov18.pair_python_long.g++.4 similarity index 63% rename from examples/python/log.4May17.pair_python_long.g++.4 rename to examples/python/log.27Nov18.pair_python_long.g++.4 index 35347da713..50ce2e5f3d 100644 --- a/examples/python/log.4May17.pair_python_long.g++.4 +++ b/examples/python/log.27Nov18.pair_python_long.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full @@ -48,8 +48,8 @@ fix 2 all nvt temp 300.0 300.0 100.0 # create only lj/cut table for the oxygen atoms from python shell rm -f spce.table -WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) -WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) +WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308) +WARNING: Shell command 'rm' failed with error 'No such file or directory' (src/input.cpp:1308) pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW Neighbor list info ... update every 1 steps, delay 10 steps, check yes @@ -69,11 +69,13 @@ pair_style hybrid/overlay coul/long 12.0 table linear 2000 kspace_style pppm 1.0e-6 pair_coeff * * coul/long pair_coeff 1 1 table spce.table OW-OW +WARNING: 1 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (src/pair_table.cpp:481) thermo 10 run 100 PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 @@ -98,44 +100,44 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes +Per MPI rank memory allocation (min/avg/max) = 13.5 | 13.5 | 13.5 Mbytes Step Temp E_pair E_mol TotEng Press - 0 0 -16690.032 0 -16690.032 -1268.9538 - 10 120.58553 -17767.504 0 -16689.536 -4063.8589 - 20 136.11736 -17882.557 0 -16665.742 -5124.6758 - 30 137.00764 -17872.318 0 -16647.545 -5337.2022 - 40 153.38868 -17999.269 0 -16628.059 -5213.6001 - 50 167.70342 -18103.06 0 -16603.883 -4460.6632 - 60 163.07134 -18034.856 0 -16577.088 -3285.0037 - 70 169.59286 -18064.636 0 -16548.57 -2606.407 - 80 182.92893 -18153.499 0 -16518.215 -2385.5152 - 90 191.2793 -18195.356 0 -16485.425 -2235.3701 - 100 194.68587 -18192.458 0 -16452.073 -1948.3746 -Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms + 0 0 -16690.019 0 -16690.019 -1268.9124 + 10 120.58553 -17767.489 0 -16689.521 -4063.8136 + 20 136.11736 -17882.538 0 -16665.724 -5124.6194 + 30 137.00764 -17872.302 0 -16647.529 -5337.1515 + 40 153.38867 -17999.256 0 -16628.046 -5213.5616 + 50 167.70342 -18103.046 0 -16603.87 -4460.6216 + 60 163.07134 -18034.842 0 -16577.074 -3284.9621 + 70 169.59286 -18064.622 0 -16548.556 -2606.3642 + 80 182.92892 -18153.485 0 -16518.202 -2385.4747 + 90 191.2793 -18195.343 0 -16485.411 -2235.3292 + 100 194.68587 -18192.446 0 -16452.061 -1948.3379 +Loop time of 2.26946 on 4 procs for 100 steps with 4500 atoms -Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 3.807 ns/day, 6.304 hours/ns, 44.063 timesteps/s +95.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49 -Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01 -Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86 -Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83 -Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68 -Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02 -Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95 -Other | | 0.003775 | | | 0.16 +Pair | 1.4676 | 1.53 | 1.6054 | 4.5 | 67.42 +Bond | 9.7752e-05 | 0.00012088 | 0.00013947 | 0.0 | 0.01 +Kspace | 0.51974 | 0.59375 | 0.65496 | 7.2 | 26.16 +Neigh | 0.075271 | 0.075279 | 0.075287 | 0.0 | 3.32 +Comm | 0.028602 | 0.029937 | 0.031052 | 0.5 | 1.32 +Output | 0.00035477 | 0.00062722 | 0.0014365 | 0.0 | 0.03 +Modify | 0.03581 | 0.035956 | 0.036059 | 0.1 | 1.58 +Other | | 0.003819 | | | 0.17 Nlocal: 1125 ave 1154 max 1092 min Histogram: 1 0 0 0 1 0 0 1 0 1 Nghost: 12256.2 ave 12296 max 12213 min Histogram: 1 0 1 0 0 0 0 0 1 1 -Neighs: 650442 ave 678831 max 626373 min +Neighs: 650442 ave 678830 max 626373 min Histogram: 1 0 0 0 2 0 0 0 0 1 -Total # of neighbors = 2601769 +Total # of neighbors = 2601768 Ave neighs/atom = 578.171 Ave special neighs/atom = 2 Neighbor list builds = 3 diff --git a/examples/python/log.4May17.pair_python_melt.g++.1 b/examples/python/log.27Nov18.pair_python_melt.g++.1 similarity index 73% rename from examples/python/log.4May17.pair_python_melt.g++.1 rename to examples/python/log.27Nov18.pair_python_melt.g++.1 index d234ce93b5..c656624fb1 100644 --- a/examples/python/log.4May17.pair_python_melt.g++.1 +++ b/examples/python/log.27Nov18.pair_python_melt.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000694513 secs mass * 1.0 velocity all create 3.0 87287 @@ -39,7 +40,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 @@ -47,20 +48,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 -Loop time of 20.9283 on 1 procs for 250 steps with 4000 atoms +Loop time of 11.5979 on 1 procs for 250 steps with 4000 atoms -Performance: 5160.475 tau/day, 11.946 timesteps/s -98.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 9312.020 tau/day, 21.556 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.809 | 20.809 | 20.809 | 0.0 | 99.43 -Neigh | 0.088638 | 0.088638 | 0.088638 | 0.0 | 0.42 -Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.06 -Output | 0.0002737 | 0.0002737 | 0.0002737 | 0.0 | 0.00 -Modify | 0.014334 | 0.014334 | 0.014334 | 0.0 | 0.07 -Other | | 0.003089 | | | 0.01 +Pair | 11.474 | 11.474 | 11.474 | 0.0 | 98.94 +Neigh | 0.092903 | 0.092903 | 0.092903 | 0.0 | 0.80 +Comm | 0.01373 | 0.01373 | 0.01373 | 0.0 | 0.12 +Output | 0.00021935 | 0.00021935 | 0.00021935 | 0.0 | 0.00 +Modify | 0.014506 | 0.014506 | 0.014506 | 0.0 | 0.13 +Other | | 0.002072 | | | 0.02 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -81,8 +82,10 @@ clear using 1 OpenMP thread(s) per MPI task read_restart melt.restart + restoring atom style atomic from restart orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid + pair style python stores no restart info 4000 atoms pair_style python 2.5 @@ -104,7 +107,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.36 | 3.36 | 3.36 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.396 | 3.396 | 3.396 Mbytes Step Temp E_pair E_mol TotEng Press 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 300 1.645592 -4.7496711 0 -2.2819002 5.8734193 @@ -112,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press 400 1.6540555 -4.7622999 0 -2.281837 5.8200413 450 1.6264734 -4.7200865 0 -2.2809863 5.9546991 500 1.6366891 -4.7350979 0 -2.2806781 5.9369284 -Loop time of 21.1422 on 1 procs for 250 steps with 4000 atoms +Loop time of 11.6299 on 1 procs for 250 steps with 4000 atoms -Performance: 5108.279 tau/day, 11.825 timesteps/s -98.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 9286.409 tau/day, 21.496 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.925 | 20.925 | 20.925 | 0.0 | 98.97 -Neigh | 0.18452 | 0.18452 | 0.18452 | 0.0 | 0.87 -Comm | 0.014836 | 0.014836 | 0.014836 | 0.0 | 0.07 -Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.00 -Modify | 0.01366 | 0.01366 | 0.01366 | 0.0 | 0.06 -Other | | 0.004355 | | | 0.02 +Pair | 11.403 | 11.403 | 11.403 | 0.0 | 98.05 +Neigh | 0.19289 | 0.19289 | 0.19289 | 0.0 | 1.66 +Comm | 0.015828 | 0.015828 | 0.015828 | 0.0 | 0.14 +Output | 0.00018644 | 0.00018644 | 0.00018644 | 0.0 | 0.00 +Modify | 0.014582 | 0.014582 | 0.014582 | 0.0 | 0.13 +Other | | 0.003107 | | | 0.03 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -175,7 +178,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.86 | 2.86 | 2.86 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.896 | 2.896 | 2.896 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.6275257 -4.7224992 0 -2.281821 5.9567365 50 1.6454666 -4.7497515 0 -2.2821686 5.8729175 @@ -183,20 +186,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6537193 -4.7627023 0 -2.2827434 5.8177704 200 1.6258731 -4.7205017 0 -2.2823017 5.952511 250 1.6370862 -4.7373176 0 -2.2823022 5.925807 -Loop time of 21.1026 on 1 procs for 250 steps with 4000 atoms +Loop time of 11.6243 on 1 procs for 250 steps with 4000 atoms -Performance: 5117.845 tau/day, 11.847 timesteps/s -98.7% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 9290.855 tau/day, 21.507 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 20.984 | 20.984 | 20.984 | 0.0 | 99.44 -Neigh | 0.088639 | 0.088639 | 0.088639 | 0.0 | 0.42 -Comm | 0.012881 | 0.012881 | 0.012881 | 0.0 | 0.06 -Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00 -Modify | 0.013523 | 0.013523 | 0.013523 | 0.0 | 0.06 -Other | | 0.003033 | | | 0.01 +Pair | 11.501 | 11.501 | 11.501 | 0.0 | 98.94 +Neigh | 0.093333 | 0.093333 | 0.093333 | 0.0 | 0.80 +Comm | 0.013483 | 0.013483 | 0.013483 | 0.0 | 0.12 +Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.00 +Modify | 0.014475 | 0.014475 | 0.014475 | 0.0 | 0.12 +Other | | 0.001968 | | | 0.02 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -211,4 +214,4 @@ Neighbor list builds = 12 Dangerous builds not checked shell rm melt.data melt.restart -Total wall time: 0:01:05 +Total wall time: 0:00:35 diff --git a/examples/python/log.4May17.pair_python_melt.g++.4 b/examples/python/log.27Nov18.pair_python_melt.g++.4 similarity index 73% rename from examples/python/log.4May17.pair_python_melt.g++.4 rename to examples/python/log.27Nov18.pair_python_melt.g++.4 index 58dae340bd..ca89640d30 100644 --- a/examples/python/log.4May17.pair_python_melt.g++.4 +++ b/examples/python/log.27Nov18.pair_python_melt.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000413418 secs mass * 1.0 velocity all create 3.0 87287 @@ -39,7 +40,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733681 0 -2.2744931 -3.7033504 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 @@ -47,20 +48,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 -Loop time of 5.65922 on 4 procs for 250 steps with 4000 atoms +Loop time of 3.21263 on 4 procs for 250 steps with 4000 atoms -Performance: 19083.895 tau/day, 44.176 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 33617.340 tau/day, 77.818 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.4529 | 5.5207 | 5.5575 | 1.7 | 97.55 -Neigh | 0.023164 | 0.023376 | 0.023883 | 0.2 | 0.41 -Comm | 0.073318 | 0.1099 | 0.17804 | 12.2 | 1.94 -Output | 0.00023365 | 0.00026143 | 0.00030684 | 0.0 | 0.00 -Modify | 0.0036483 | 0.0037143 | 0.003896 | 0.2 | 0.07 -Other | | 0.001274 | | | 0.02 +Pair | 2.9309 | 2.9942 | 3.1071 | 3.9 | 93.20 +Neigh | 0.024111 | 0.024518 | 0.024765 | 0.2 | 0.76 +Comm | 0.075799 | 0.1889 | 0.25258 | 15.5 | 5.88 +Output | 0.00018406 | 0.00030106 | 0.00065088 | 0.0 | 0.01 +Modify | 0.0038259 | 0.0038511 | 0.0038726 | 0.0 | 0.12 +Other | | 0.0009047 | | | 0.03 Nlocal: 1000 ave 1010 max 982 min Histogram: 1 0 0 0 0 0 1 0 0 2 @@ -81,8 +82,10 @@ clear using 1 OpenMP thread(s) per MPI task read_restart melt.restart + restoring atom style atomic from restart orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid + pair style python stores no restart info 4000 atoms pair_style python 2.5 @@ -104,7 +107,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.815 | 2.816 | 2.816 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.829 | 2.83 | 2.83 Mbytes Step Temp E_pair E_mol TotEng Press 250 1.6323462 -4.7292062 0 -2.2812991 5.9762168 300 1.6451788 -4.7488091 0 -2.2816578 5.8375485 @@ -112,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press 400 1.6388136 -4.7387093 0 -2.2811035 5.9331084 450 1.6431295 -4.7452215 0 -2.2811435 5.8929898 500 1.643316 -4.7454222 0 -2.2810644 5.8454817 -Loop time of 5.70169 on 4 procs for 250 steps with 4000 atoms +Loop time of 3.16401 on 4 procs for 250 steps with 4000 atoms -Performance: 18941.760 tau/day, 43.847 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 34133.894 tau/day, 79.014 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.3919 | 5.4905 | 5.6136 | 3.7 | 96.30 -Neigh | 0.046791 | 0.047817 | 0.048795 | 0.3 | 0.84 -Comm | 0.034221 | 0.1575 | 0.25635 | 22.1 | 2.76 -Output | 0.00020409 | 0.00023448 | 0.00026131 | 0.0 | 0.00 -Modify | 0.0035028 | 0.0035674 | 0.0036926 | 0.1 | 0.06 -Other | | 0.002079 | | | 0.04 +Pair | 2.9254 | 2.9723 | 3.0639 | 3.2 | 93.94 +Neigh | 0.04915 | 0.050266 | 0.050704 | 0.3 | 1.59 +Comm | 0.044051 | 0.13579 | 0.18379 | 15.0 | 4.29 +Output | 0.00016141 | 0.00028008 | 0.00063109 | 0.0 | 0.01 +Modify | 0.0037544 | 0.003895 | 0.0041802 | 0.3 | 0.12 +Other | | 0.001474 | | | 0.05 Nlocal: 1000 ave 1012 max 983 min Histogram: 1 0 0 0 0 0 2 0 0 1 @@ -175,7 +178,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.315 | 2.316 | 2.316 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.329 | 2.33 | 2.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.6323462 -4.7292062 0 -2.2812991 5.9762168 50 1.6450626 -4.7488948 0 -2.2819177 5.8370409 @@ -183,20 +186,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6384234 -4.7389689 0 -2.2819482 5.9315273 200 1.6428814 -4.7460743 0 -2.2823683 5.8888228 250 1.6432631 -4.7466603 0 -2.2823818 5.8398819 -Loop time of 5.69568 on 4 procs for 250 steps with 4000 atoms +Loop time of 3.16461 on 4 procs for 250 steps with 4000 atoms -Performance: 18961.751 tau/day, 43.893 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 34127.383 tau/day, 78.999 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.4041 | 5.5245 | 5.6139 | 3.2 | 96.99 -Neigh | 0.022658 | 0.022986 | 0.023398 | 0.2 | 0.40 -Comm | 0.053521 | 0.14309 | 0.26385 | 20.2 | 2.51 -Output | 0.00027037 | 0.00029504 | 0.00033665 | 0.0 | 0.01 -Modify | 0.0035288 | 0.0035585 | 0.0035827 | 0.0 | 0.06 -Other | | 0.001275 | | | 0.02 +Pair | 2.9135 | 2.9842 | 3.0594 | 3.1 | 94.30 +Neigh | 0.024132 | 0.024319 | 0.024553 | 0.1 | 0.77 +Comm | 0.075955 | 0.15106 | 0.22174 | 13.9 | 4.77 +Output | 0.00016856 | 0.00028443 | 0.00062919 | 0.0 | 0.01 +Modify | 0.0037944 | 0.0038335 | 0.0038977 | 0.1 | 0.12 +Other | | 0.0008717 | | | 0.03 Nlocal: 1000 ave 1013 max 989 min Histogram: 1 0 0 1 0 1 0 0 0 1 @@ -211,4 +214,4 @@ Neighbor list builds = 12 Dangerous builds not checked shell rm melt.data melt.restart -Total wall time: 0:00:17 +Total wall time: 0:00:09 diff --git a/examples/python/log.4May17.pair_python_spce.g++.1 b/examples/python/log.27Nov18.pair_python_spce.g++.1 similarity index 79% rename from examples/python/log.4May17.pair_python_spce.g++.1 rename to examples/python/log.27Nov18.pair_python_spce.g++.1 index 540c06853f..c64f599fc3 100644 --- a/examples/python/log.4May17.pair_python_spce.g++.1 +++ b/examples/python/log.27Nov18.pair_python_spce.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full @@ -52,7 +52,7 @@ fix 2 all nvt temp 300.0 300.0 100.0 thermo 10 run 100 PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 @@ -77,7 +77,7 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 Mbytes +Per MPI rank memory allocation (min/avg/max) = 41.15 | 41.15 | 41.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16692.369 0 -16692.369 -1289.222 10 120.56861 -17769.719 0 -16691.902 -4082.7098 @@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press 80 182.94811 -18155.978 0 -16520.523 -2393.3156 90 191.29902 -18197.887 0 -16487.779 -2242.7104 100 194.70949 -18195.021 0 -16454.425 -1955.2916 -Loop time of 23.5385 on 1 procs for 100 steps with 4500 atoms +Loop time of 15.3744 on 1 procs for 100 steps with 4500 atoms -Performance: 0.367 ns/day, 65.385 hours/ns, 4.248 timesteps/s -98.9% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.562 ns/day, 42.707 hours/ns, 6.504 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 21.642 | 21.642 | 21.642 | 0.0 | 91.94 -Bond | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.00 -Kspace | 1.5436 | 1.5436 | 1.5436 | 0.0 | 6.56 -Neigh | 0.25623 | 0.25623 | 0.25623 | 0.0 | 1.09 -Comm | 0.024325 | 0.024325 | 0.024325 | 0.0 | 0.10 -Output | 0.00064301 | 0.00064301 | 0.00064301 | 0.0 | 0.00 -Modify | 0.065919 | 0.065919 | 0.065919 | 0.0 | 0.28 -Other | | 0.005401 | | | 0.02 +Pair | 13.914 | 13.914 | 13.914 | 0.0 | 90.50 +Bond | 0.00013375 | 0.00013375 | 0.00013375 | 0.0 | 0.00 +Kspace | 1.0852 | 1.0852 | 1.0852 | 0.0 | 7.06 +Neigh | 0.29811 | 0.29811 | 0.29811 | 0.0 | 1.94 +Comm | 0.020503 | 0.020503 | 0.020503 | 0.0 | 0.13 +Output | 0.00045133 | 0.00045133 | 0.00045133 | 0.0 | 0.00 +Modify | 0.052513 | 0.052513 | 0.052513 | 0.0 | 0.34 +Other | | 0.00348 | | | 0.02 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -119,4 +119,4 @@ Ave neighs/atom = 578.169 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 -Total wall time: 0:00:24 +Total wall time: 0:00:15 diff --git a/examples/python/log.4May17.pair_python_spce.g++.4 b/examples/python/log.27Nov18.pair_python_spce.g++.4 similarity index 79% rename from examples/python/log.4May17.pair_python_spce.g++.4 rename to examples/python/log.27Nov18.pair_python_spce.g++.4 index 332c079ec1..44a1e27be4 100644 --- a/examples/python/log.4May17.pair_python_spce.g++.4 +++ b/examples/python/log.27Nov18.pair_python_spce.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full @@ -52,7 +52,7 @@ fix 2 all nvt temp 300.0 300.0 100.0 thermo 10 run 100 PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.279652 grid = 40 40 40 stencil order = 5 @@ -77,7 +77,7 @@ Neighbor list info ... pair build: skip stencil: none bin: none -Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes +Per MPI rank memory allocation (min/avg/max) = 14.64 | 14.64 | 14.64 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16692.369 0 -16692.369 -1289.222 10 120.56861 -17769.719 0 -16691.902 -4082.7098 @@ -90,22 +90,22 @@ Step Temp E_pair E_mol TotEng Press 80 182.94811 -18155.978 0 -16520.523 -2393.3156 90 191.29902 -18197.887 0 -16487.779 -2242.7104 100 194.70949 -18195.021 0 -16454.425 -1955.2916 -Loop time of 6.4942 on 4 procs for 100 steps with 4500 atoms +Loop time of 4.36104 on 4 procs for 100 steps with 4500 atoms -Performance: 1.330 ns/day, 18.039 hours/ns, 15.398 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 1.981 ns/day, 12.114 hours/ns, 22.930 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.4084 | 5.572 | 5.8013 | 7.2 | 85.80 -Bond | 0.00012994 | 0.0001421 | 0.00016356 | 0.0 | 0.00 -Kspace | 0.52942 | 0.75773 | 0.92078 | 19.5 | 11.67 -Neigh | 0.071055 | 0.07116 | 0.071278 | 0.0 | 1.10 -Comm | 0.040311 | 0.041255 | 0.041817 | 0.3 | 0.64 -Output | 0.00040603 | 0.00048071 | 0.00058675 | 0.0 | 0.01 -Modify | 0.047507 | 0.047629 | 0.047772 | 0.1 | 0.73 -Other | | 0.003771 | | | 0.06 +Pair | 3.5019 | 3.6105 | 3.738 | 4.4 | 82.79 +Bond | 0.00010133 | 0.00013196 | 0.00017118 | 0.0 | 0.00 +Kspace | 0.47082 | 0.59641 | 0.70417 | 10.8 | 13.68 +Neigh | 0.081036 | 0.081042 | 0.081047 | 0.0 | 1.86 +Comm | 0.030113 | 0.03092 | 0.03135 | 0.3 | 0.71 +Output | 0.00034952 | 0.00064117 | 0.001514 | 0.0 | 0.01 +Modify | 0.036583 | 0.037553 | 0.038021 | 0.3 | 0.86 +Other | | 0.00388 | | | 0.09 Nlocal: 1125 ave 1154 max 1092 min Histogram: 1 0 0 0 1 0 0 1 0 1 @@ -119,4 +119,4 @@ Ave neighs/atom = 578.169 Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 -Total wall time: 0:00:06 +Total wall time: 0:00:04 diff --git a/examples/python/log.4May17.pair_python_table.g++.1 b/examples/python/log.27Nov18.pair_python_table.g++.1 similarity index 77% rename from examples/python/log.4May17.pair_python_table.g++.1 rename to examples/python/log.27Nov18.pair_python_table.g++.1 index c594a8e90a..86f98384cb 100644 --- a/examples/python/log.4May17.pair_python_table.g++.1 +++ b/examples/python/log.27Nov18.pair_python_table.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000697136 secs mass * 1.0 velocity all create 3.0 87287 @@ -38,7 +39,7 @@ Neighbor list info ... pair_style table linear 2000 pair_coeff 1 1 lj_1_1.table LJ WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (src/pair_table.cpp:481) neighbor 0.3 bin neigh_modify every 20 delay 0 check no @@ -59,7 +60,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.221 | 3.221 | 3.221 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733629 0 -2.2744879 -3.7032813 50 1.6758731 -4.7953067 0 -2.2821255 5.6706553 @@ -67,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.632425 -4.7284533 0 -2.2804279 5.9595684 200 1.6631578 -4.7749889 0 -2.2808759 5.7365839 250 1.6277062 -4.7224727 0 -2.2815238 5.9572913 -Loop time of 0.996739 on 1 procs for 250 steps with 4000 atoms +Loop time of 0.94897 on 1 procs for 250 steps with 4000 atoms -Performance: 108353.298 tau/day, 250.818 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 113807.650 tau/day, 263.444 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.87985 | 0.87985 | 0.87985 | 0.0 | 88.27 -Neigh | 0.08799 | 0.08799 | 0.08799 | 0.0 | 8.83 -Comm | 0.012301 | 0.012301 | 0.012301 | 0.0 | 1.23 -Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01 -Modify | 0.013656 | 0.013656 | 0.013656 | 0.0 | 1.37 -Other | | 0.002808 | | | 0.28 +Pair | 0.82415 | 0.82415 | 0.82415 | 0.0 | 86.85 +Neigh | 0.093798 | 0.093798 | 0.093798 | 0.0 | 9.88 +Comm | 0.013542 | 0.013542 | 0.013542 | 0.0 | 1.43 +Output | 0.00017834 | 0.00017834 | 0.00017834 | 0.0 | 0.02 +Modify | 0.014418 | 0.014418 | 0.014418 | 0.0 | 1.52 +Other | | 0.002882 | | | 0.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -96,4 +97,4 @@ Dangerous builds not checked shell rm lj_1_1.table -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/python/log.4May17.pair_python_table.g++.4 b/examples/python/log.27Nov18.pair_python_table.g++.4 similarity index 78% rename from examples/python/log.4May17.pair_python_table.g++.4 rename to examples/python/log.27Nov18.pair_python_table.g++.4 index e509fc7f6a..3d7ad148e4 100644 --- a/examples/python/log.4May17.pair_python_table.g++.4 +++ b/examples/python/log.27Nov18.pair_python_table.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (4 May 2017) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt @@ -13,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000404596 secs mass * 1.0 velocity all create 3.0 87287 @@ -38,7 +39,7 @@ Neighbor list info ... pair_style table linear 2000 pair_coeff 1 1 lj_1_1.table LJ WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:476) + Should only be flagged at inflection points (src/pair_table.cpp:481) neighbor 0.3 bin neigh_modify every 20 delay 0 check no @@ -59,7 +60,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.705 | 2.705 | 2.705 Mbytes Step Temp E_pair E_mol TotEng Press 0 3 -6.7733629 0 -2.2744879 -3.7032813 50 1.675395 -4.7945736 0 -2.2821094 5.6620623 @@ -67,20 +68,20 @@ Step Temp E_pair E_mol TotEng Press 150 1.6595852 -4.7697199 0 -2.2809644 5.7837898 200 1.6371471 -4.7363942 0 -2.2812874 5.924977 250 1.6315623 -4.7278268 0 -2.2810951 5.9807196 -Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms +Loop time of 0.285577 on 4 procs for 250 steps with 4000 atoms -Performance: 370058.286 tau/day, 856.616 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 378181.086 tau/day, 875.419 timesteps/s +96.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06 -Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96 -Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30 -Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05 -Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22 -Other | | 0.001211 | | | 0.42 +Pair | 0.2111 | 0.21779 | 0.22447 | 1.0 | 76.26 +Neigh | 0.024165 | 0.024465 | 0.0247 | 0.1 | 8.57 +Comm | 0.03147 | 0.038356 | 0.044902 | 2.5 | 13.43 +Output | 0.00016117 | 0.00022227 | 0.00040102 | 0.0 | 0.08 +Modify | 0.0037565 | 0.0038704 | 0.0040345 | 0.2 | 1.36 +Other | | 0.0008699 | | | 0.30 Nlocal: 1000 ave 1010 max 981 min Histogram: 1 0 0 0 0 0 1 0 0 2 diff --git a/examples/python/log.5Oct16.python.g++.1 b/examples/python/log.27Nov18.python.g++.1 similarity index 53% rename from examples/python/log.5Oct16.python.g++.1 rename to examples/python/log.27Nov18.python.g++.1 index 1f58c69165..facbd73bab 100644 --- a/examples/python/log.5Oct16.python.g++.1 +++ b/examples/python/log.27Nov18.python.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt with Python functions added units lj @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.00072813 secs mass 1 1.0 velocity all create 1.44 87287 loop geom @@ -26,30 +28,35 @@ fix 1 all nve run 10 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 12 -Memory usage per processor = 2.69271 Mbytes + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.721 | 3.721 | 3.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638 -Loop time of 0.0323398 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.0312054 on 1 procs for 10 steps with 4000 atoms -Performance: 133581.484 tau/day, 309.216 timesteps/s -102.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 138437.508 tau/day, 320.457 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.024638 | 0.024638 | 0.024638 | 0.0 | 76.18 -Neigh | 0.0063899 | 0.0063899 | 0.0063899 | 0.0 | 19.76 -Comm | 0.00049949 | 0.00049949 | 0.00049949 | 0.0 | 1.54 -Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.06 -Modify | 0.00050044 | 0.00050044 | 0.00050044 | 0.0 | 1.55 -Other | | 0.0002944 | | | 0.91 +Pair | 0.022328 | 0.022328 | 0.022328 | 0.0 | 71.55 +Neigh | 0.0073318 | 0.0073318 | 0.0073318 | 0.0 | 23.50 +Comm | 0.0006578 | 0.0006578 | 0.0006578 | 0.0 | 2.11 +Output | 2.6941e-05 | 2.6941e-05 | 2.6941e-05 | 0.0 | 0.09 +Modify | 0.00057721 | 0.00057721 | 0.00057721 | 0.0 | 1.85 +Other | | 0.0002832 | | | 0.91 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -67,13 +74,14 @@ Dangerous builds = 0 # example of catching a syntax error python simple here """ +from __future__ import print_function def simple(): - import exceptions - print "Inside simple function" + foo = 0 + print("Inside simple function") try: foo += 1 - except Exception, e: - print "FOO error:",e + except Exception as e: + print("FOO error:", e) """ python simple invoke @@ -110,31 +118,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.0 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 1.3 - binsize = 0.65 -> bins = 26 26 26 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 10 1.1259767 0.016557378 0 1.7051002 1.2784679 20 0.87608998 0.39300382 0 1.7068103 6.0488236 -Loop time of 0.0046258 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.00488138 on 1 procs for 10 steps with 4000 atoms -Performance: 933893.067 tau/day, 2161.790 timesteps/s -86.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 884995.276 tau/day, 2048.600 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.001574 | 0.001574 | 0.001574 | 0.0 | 34.03 -Neigh | 0.0020421 | 0.0020421 | 0.0020421 | 0.0 | 44.14 -Comm | 0.00025463 | 0.00025463 | 0.00025463 | 0.0 | 5.50 -Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.39 -Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 10.73 -Other | | 0.000241 | | | 5.21 +Pair | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 35.17 +Neigh | 0.0020256 | 0.0020256 | 0.0020256 | 0.0 | 41.50 +Comm | 0.00028539 | 0.00028539 | 0.00028539 | 0.0 | 5.85 +Output | 2.6703e-05 | 2.6703e-05 | 2.6703e-05 | 0.0 | 0.55 +Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 11.76 +Other | | 0.0002532 | | | 5.19 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -151,31 +152,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.1 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.4 - ghost atom cutoff = 1.4 - binsize = 0.7 -> bins = 24 24 24 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 20 0.87608998 -0.33042884 0 0.9833776 8.5817494 30 1.0155079 -0.83166219 0 0.69121891 7.9905553 -Loop time of 0.00619817 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.00647616 on 1 procs for 10 steps with 4000 atoms -Performance: 696980.162 tau/day, 1613.380 timesteps/s -96.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 667061.565 tau/day, 1544.124 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0029786 | 0.0029786 | 0.0029786 | 0.0 | 48.06 -Neigh | 0.002203 | 0.002203 | 0.002203 | 0.0 | 35.54 -Comm | 0.00025678 | 0.00025678 | 0.00025678 | 0.0 | 4.14 -Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.29 -Modify | 0.00049472 | 0.00049472 | 0.00049472 | 0.0 | 7.98 -Other | | 0.0002472 | | | 3.99 +Pair | 0.0030439 | 0.0030439 | 0.0030439 | 0.0 | 47.00 +Neigh | 0.002295 | 0.002295 | 0.002295 | 0.0 | 35.44 +Comm | 0.00028467 | 0.00028467 | 0.00028467 | 0.0 | 4.40 +Output | 2.3842e-05 | 2.3842e-05 | 2.3842e-05 | 0.0 | 0.37 +Modify | 0.0005753 | 0.0005753 | 0.0005753 | 0.0 | 8.88 +Other | | 0.0002534 | | | 3.91 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -192,31 +186,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.2 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.5 - ghost atom cutoff = 1.5 - binsize = 0.75 -> bins = 23 23 23 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 30 1.0155079 -2.0616558 0 -0.53877467 7.6238572 40 1.0490928 -2.1868324 0 -0.61358669 7.2084131 -Loop time of 0.00750899 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.00802207 on 1 procs for 10 steps with 4000 atoms -Performance: 575310.153 tau/day, 1331.736 timesteps/s -93.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 538514.378 tau/day, 1246.561 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.004189 | 0.004189 | 0.004189 | 0.0 | 55.79 -Neigh | 0.0022991 | 0.0022991 | 0.0022991 | 0.0 | 30.62 -Comm | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 3.45 -Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.24 -Modify | 0.00049615 | 0.00049615 | 0.00049615 | 0.0 | 6.61 -Other | | 0.0002475 | | | 3.30 +Pair | 0.0044219 | 0.0044219 | 0.0044219 | 0.0 | 55.12 +Neigh | 0.0024219 | 0.0024219 | 0.0024219 | 0.0 | 30.19 +Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 3.75 +Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.32 +Modify | 0.00059366 | 0.00059366 | 0.00059366 | 0.0 | 7.40 +Other | | 0.0002577 | | | 3.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -233,31 +220,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.3 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.6 - ghost atom cutoff = 1.6 - binsize = 0.8 -> bins = 21 21 21 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 40 1.0490928 -3.0667608 0 -1.493515 6.2796311 50 1.0764484 -3.1173704 0 -1.5031014 6.0850409 -Loop time of 0.00869107 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.00908327 on 1 procs for 10 steps with 4000 atoms -Performance: 497061.786 tau/day, 1150.606 timesteps/s -103.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 475599.593 tau/day, 1100.925 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0049038 | 0.0049038 | 0.0049038 | 0.0 | 56.42 -Neigh | 0.0027289 | 0.0027289 | 0.0027289 | 0.0 | 31.40 -Comm | 0.00028753 | 0.00028753 | 0.00028753 | 0.0 | 3.31 -Output | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 | 0.0 | 0.23 -Modify | 0.00049758 | 0.00049758 | 0.00049758 | 0.0 | 5.73 -Other | | 0.0002532 | | | 2.91 +Pair | 0.0049157 | 0.0049157 | 0.0049157 | 0.0 | 54.12 +Neigh | 0.0029771 | 0.0029771 | 0.0029771 | 0.0 | 32.78 +Comm | 0.00033617 | 0.00033617 | 0.00033617 | 0.0 | 3.70 +Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.25 +Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 6.34 +Other | | 0.0002553 | | | 2.81 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -274,31 +254,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.4 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.7 - ghost atom cutoff = 1.7 - binsize = 0.85 -> bins = 20 20 20 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 50 1.0764484 -3.6112241 0 -1.9969552 5.4223348 60 1.1101013 -3.6616014 0 -1.9968657 5.2348251 -Loop time of 0.00934482 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.0096159 on 1 procs for 10 steps with 4000 atoms -Performance: 462288.386 tau/day, 1070.112 timesteps/s -96.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 449256.007 tau/day, 1039.944 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0055761 | 0.0055761 | 0.0055761 | 0.0 | 59.67 -Neigh | 0.002676 | 0.002676 | 0.002676 | 0.0 | 28.64 -Comm | 0.00032163 | 0.00032163 | 0.00032163 | 0.0 | 3.44 -Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.19 -Modify | 0.00049901 | 0.00049901 | 0.00049901 | 0.0 | 5.34 -Other | | 0.0002542 | | | 2.72 +Pair | 0.0054793 | 0.0054793 | 0.0054793 | 0.0 | 56.98 +Neigh | 0.0028973 | 0.0028973 | 0.0028973 | 0.0 | 30.13 +Comm | 0.00038075 | 0.00038075 | 0.00038075 | 0.0 | 3.96 +Output | 2.3127e-05 | 2.3127e-05 | 2.3127e-05 | 0.0 | 0.24 +Modify | 0.00057387 | 0.00057387 | 0.00057387 | 0.0 | 5.97 +Other | | 0.0002615 | | | 2.72 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -315,31 +288,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.5 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.8 - ghost atom cutoff = 1.8 - binsize = 0.9 -> bins = 19 19 19 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 60 1.1101013 -3.9655053 0 -2.3007696 4.7849008 70 1.1122144 -3.9657095 0 -2.297805 4.8014106 -Loop time of 0.0103869 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.0107083 on 1 procs for 10 steps with 4000 atoms -Performance: 415906.746 tau/day, 962.747 timesteps/s -96.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 403424.172 tau/day, 933.852 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0063703 | 0.0063703 | 0.0063703 | 0.0 | 61.33 -Neigh | 0.002893 | 0.002893 | 0.002893 | 0.0 | 27.85 -Comm | 0.00034499 | 0.00034499 | 0.00034499 | 0.0 | 3.32 -Output | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 | 0.0 | 0.17 -Modify | 0.00050139 | 0.00050139 | 0.00050139 | 0.0 | 4.83 -Other | | 0.0002594 | | | 2.50 +Pair | 0.0062652 | 0.0062652 | 0.0062652 | 0.0 | 58.51 +Neigh | 0.0031667 | 0.0031667 | 0.0031667 | 0.0 | 29.57 +Comm | 0.00041771 | 0.00041771 | 0.00041771 | 0.0 | 3.90 +Output | 2.265e-05 | 2.265e-05 | 2.265e-05 | 0.0 | 0.21 +Modify | 0.0005734 | 0.0005734 | 0.0005734 | 0.0 | 5.35 +Other | | 0.0002627 | | | 2.45 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -356,31 +322,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.6 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.9 - ghost atom cutoff = 1.9 - binsize = 0.95 -> bins = 18 18 18 -Memory usage per processor = 2.78761 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.816 | 3.816 | 3.816 Mbytes Step Temp E_pair E_mol TotEng Press 70 1.1122144 -4.1752688 0 -2.5073643 4.4755409 80 1.117224 -4.1831357 0 -2.5077187 4.446079 -Loop time of 0.0116282 on 1 procs for 10 steps with 4000 atoms +Loop time of 0.0121632 on 1 procs for 10 steps with 4000 atoms -Performance: 371512.205 tau/day, 859.982 timesteps/s -103.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 355170.795 tau/day, 822.155 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0074186 | 0.0074186 | 0.0074186 | 0.0 | 63.80 -Neigh | 0.0030658 | 0.0030658 | 0.0030658 | 0.0 | 26.37 -Comm | 0.00036025 | 0.00036025 | 0.00036025 | 0.0 | 3.10 -Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.15 -Modify | 0.0005033 | 0.0005033 | 0.0005033 | 0.0 | 4.33 -Other | | 0.000263 | | | 2.26 +Pair | 0.0074623 | 0.0074623 | 0.0074623 | 0.0 | 61.35 +Neigh | 0.0033951 | 0.0033951 | 0.0033951 | 0.0 | 27.91 +Comm | 0.00043678 | 0.00043678 | 0.00043678 | 0.0 | 3.59 +Output | 2.408e-05 | 2.408e-05 | 2.408e-05 | 0.0 | 0.20 +Modify | 0.00057578 | 0.00057578 | 0.00057578 | 0.0 | 4.73 +Other | | 0.0002692 | | | 2.21 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/python/log.5Oct16.python.g++.4 b/examples/python/log.27Nov18.python.g++.4 similarity index 53% rename from examples/python/log.5Oct16.python.g++.4 rename to examples/python/log.27Nov18.python.g++.4 index 816fbf977b..cd451e49b7 100644 --- a/examples/python/log.5Oct16.python.g++.4 +++ b/examples/python/log.27Nov18.python.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d Lennard-Jones melt with Python functions added units lj @@ -12,6 +13,7 @@ Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 4000 atoms + Time spent = 0.000517368 secs mass 1 1.0 velocity all create 1.44 87287 loop geom @@ -26,30 +28,35 @@ fix 1 all nve run 10 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 12 -Memory usage per processor = 2.60344 Mbytes + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.205 | 3.205 | 3.205 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 10 1.1259767 -6.3010653 0 -4.6125225 -2.5704638 -Loop time of 0.00930309 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00902343 on 4 procs for 10 steps with 4000 atoms -Performance: 464361.693 tau/day, 1074.911 timesteps/s -96.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 478753.753 tau/day, 1108.226 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0064399 | 0.0064787 | 0.0065157 | 0.0 | 69.64 -Neigh | 0.0017071 | 0.0017205 | 0.0017281 | 0.0 | 18.49 -Comm | 0.00073171 | 0.00077122 | 0.00081086 | 0.1 | 8.29 -Output | 1.9789e-05 | 2.3663e-05 | 2.9087e-05 | 0.1 | 0.25 -Modify | 0.00012827 | 0.00012904 | 0.00013018 | 0.0 | 1.39 -Other | | 0.0001799 | | | 1.93 +Pair | 0.0058084 | 0.0058863 | 0.0059605 | 0.1 | 65.23 +Neigh | 0.0019183 | 0.0019591 | 0.0020542 | 0.1 | 21.71 +Comm | 0.00081086 | 0.00084025 | 0.00090694 | 0.0 | 9.31 +Output | 2.1458e-05 | 2.9743e-05 | 4.53e-05 | 0.0 | 0.33 +Modify | 0.00015211 | 0.00015229 | 0.00015259 | 0.0 | 1.69 +Other | | 0.0001558 | | | 1.73 Nlocal: 1000 ave 1013 max 989 min Histogram: 1 0 1 0 0 1 0 0 0 1 @@ -67,13 +74,14 @@ Dangerous builds = 0 # example of catching a syntax error python simple here """ +from __future__ import print_function def simple(): - import exceptions - print "Inside simple function" + foo = 0 + print("Inside simple function") try: foo += 1 - except Exception, e: - print "FOO error:",e + except Exception as e: + print("FOO error:", e) """ python simple invoke @@ -110,31 +118,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.0 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.3 - ghost atom cutoff = 1.3 - binsize = 0.65 -> bins = 26 26 26 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 10 1.1259767 0.016557378 0 1.7051002 1.2784679 20 0.87608998 0.39300382 0 1.7068103 6.0488236 -Loop time of 0.00152922 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00153601 on 4 procs for 10 steps with 4000 atoms -Performance: 2824975.566 tau/day, 6539.295 timesteps/s -130.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2812478.584 tau/day, 6510.367 timesteps/s +91.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00040293 | 0.0004105 | 0.00041485 | 0.0 | 26.84 -Neigh | 0.00057507 | 0.00060332 | 0.00062108 | 0.1 | 39.45 -Comm | 0.0002377 | 0.00025356 | 0.00026774 | 0.1 | 16.58 -Output | 1.9073e-05 | 1.9789e-05 | 2.1935e-05 | 0.0 | 1.29 -Modify | 0.00012994 | 0.00013161 | 0.00013328 | 0.0 | 8.61 -Other | | 0.0001104 | | | 7.22 +Pair | 0.00042677 | 0.00043494 | 0.00044322 | 0.0 | 28.32 +Neigh | 0.00051236 | 0.00051689 | 0.00052524 | 0.0 | 33.65 +Comm | 0.00025344 | 0.00026941 | 0.00027728 | 0.0 | 17.54 +Output | 1.7881e-05 | 2.3544e-05 | 3.9339e-05 | 0.0 | 1.53 +Modify | 0.00015187 | 0.00015521 | 0.00016356 | 0.0 | 10.10 +Other | | 0.000136 | | | 8.86 Nlocal: 1000 ave 1015 max 987 min Histogram: 1 0 0 1 0 1 0 0 0 1 @@ -151,31 +152,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.1 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.4 - ghost atom cutoff = 1.4 - binsize = 0.7 -> bins = 24 24 24 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 20 0.87608998 -0.33042884 0 0.9833776 8.5817494 30 1.0155079 -0.83166219 0 0.69121891 7.9905553 -Loop time of 0.00186676 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00198567 on 4 procs for 10 steps with 4000 atoms -Performance: 2314172.647 tau/day, 5356.881 timesteps/s -107.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 2175589.035 tau/day, 5036.086 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00075388 | 0.00077951 | 0.00079727 | 0.1 | 41.76 -Neigh | 0.00057292 | 0.00058091 | 0.00058484 | 0.0 | 31.12 -Comm | 0.00022578 | 0.00024849 | 0.00028563 | 0.1 | 13.31 -Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 1.00 -Modify | 0.00012493 | 0.00012845 | 0.00013137 | 0.0 | 6.88 -Other | | 0.0001107 | | | 5.93 +Pair | 0.00076985 | 0.00078291 | 0.00079393 | 0.0 | 39.43 +Neigh | 0.0005703 | 0.00057709 | 0.00058103 | 0.0 | 29.06 +Comm | 0.00030351 | 0.00031525 | 0.00033665 | 0.0 | 15.88 +Output | 1.9073e-05 | 2.4378e-05 | 4.0054e-05 | 0.0 | 1.23 +Modify | 0.00014806 | 0.00015008 | 0.00015354 | 0.0 | 7.56 +Other | | 0.000136 | | | 6.85 Nlocal: 1000 ave 1019 max 983 min Histogram: 1 0 1 0 0 0 1 0 0 1 @@ -192,31 +186,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.2 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.5 - ghost atom cutoff = 1.5 - binsize = 0.75 -> bins = 23 23 23 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 30 1.0155079 -2.0616558 0 -0.53877467 7.6238572 40 1.0490928 -2.1868324 0 -0.61358669 7.2084131 -Loop time of 0.00224304 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00232226 on 4 procs for 10 steps with 4000 atoms -Performance: 1925955.918 tau/day, 4458.231 timesteps/s -89.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1860259.570 tau/day, 4306.156 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0010781 | 0.0011036 | 0.0011303 | 0.1 | 49.20 -Neigh | 0.00060606 | 0.00060952 | 0.00061703 | 0.0 | 27.17 -Comm | 0.00023556 | 0.0002715 | 0.00029659 | 0.1 | 12.10 -Output | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 | 0.0 | 0.83 -Modify | 0.00012541 | 0.00012833 | 0.00013351 | 0.0 | 5.72 -Other | | 0.0001114 | | | 4.97 +Pair | 0.0010829 | 0.0010984 | 0.0011158 | 0.0 | 47.30 +Neigh | 0.00060892 | 0.00061285 | 0.00062037 | 0.0 | 26.39 +Comm | 0.00027418 | 0.00030226 | 0.00031734 | 0.0 | 13.02 +Output | 1.7881e-05 | 2.3305e-05 | 3.8624e-05 | 0.0 | 1.00 +Modify | 0.00014758 | 0.00014979 | 0.0001533 | 0.0 | 6.45 +Other | | 0.0001357 | | | 5.84 Nlocal: 1000 ave 1013 max 984 min Histogram: 1 0 0 1 0 0 0 0 1 1 @@ -233,31 +220,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.3 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.6 - ghost atom cutoff = 1.6 - binsize = 0.8 -> bins = 21 21 21 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 40 1.0490928 -3.0667608 0 -1.493515 6.2796311 50 1.0764484 -3.1173704 0 -1.5031014 6.0850409 -Loop time of 0.00257862 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00268328 on 4 procs for 10 steps with 4000 atoms -Performance: 1675317.210 tau/day, 3878.049 timesteps/s -77.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1609968.749 tau/day, 3726.780 timesteps/s +99.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0012422 | 0.0012776 | 0.0013103 | 0.1 | 49.55 -Neigh | 0.0007019 | 0.00072145 | 0.00073099 | 0.0 | 27.98 -Comm | 0.00027132 | 0.00031221 | 0.00036168 | 0.2 | 12.11 -Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.74 -Modify | 0.00012279 | 0.00012654 | 0.00012875 | 0.0 | 4.91 -Other | | 0.0001217 | | | 4.72 +Pair | 0.0012326 | 0.0012579 | 0.0012789 | 0.1 | 46.88 +Neigh | 0.00073671 | 0.00076056 | 0.00077105 | 0.0 | 28.34 +Comm | 0.00031805 | 0.00035089 | 0.0003984 | 0.0 | 13.08 +Output | 1.7405e-05 | 2.2769e-05 | 3.8147e-05 | 0.0 | 0.85 +Modify | 0.00014949 | 0.00015247 | 0.00015497 | 0.0 | 5.68 +Other | | 0.0001387 | | | 5.17 Nlocal: 1000 ave 1013 max 974 min Histogram: 1 0 0 0 0 0 0 1 0 2 @@ -274,31 +254,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.4 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.7 - ghost atom cutoff = 1.7 - binsize = 0.85 -> bins = 20 20 20 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 50 1.0764484 -3.6112241 0 -1.9969552 5.4223348 60 1.1101013 -3.6616014 0 -1.9968657 5.2348251 -Loop time of 0.00283062 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00504404 on 4 procs for 10 steps with 4000 atoms -Performance: 1526164.943 tau/day, 3532.789 timesteps/s -97.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 856455.812 tau/day, 1982.537 timesteps/s +88.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0014381 | 0.0014688 | 0.0015128 | 0.1 | 51.89 -Neigh | 0.00070405 | 0.000714 | 0.00071907 | 0.0 | 25.22 -Comm | 0.00032473 | 0.00037426 | 0.0004046 | 0.2 | 13.22 -Output | 1.8835e-05 | 1.961e-05 | 2.1935e-05 | 0.0 | 0.69 -Modify | 0.00012612 | 0.00012892 | 0.00013089 | 0.0 | 4.55 -Other | | 0.000125 | | | 4.42 +Pair | 0.0013909 | 0.001602 | 0.0021472 | 0.8 | 31.76 +Neigh | 0.00074077 | 0.00075352 | 0.00076365 | 0.0 | 14.94 +Comm | 0.00083065 | 0.0018672 | 0.0025668 | 1.7 | 37.02 +Output | 2.1458e-05 | 2.7359e-05 | 4.4346e-05 | 0.0 | 0.54 +Modify | 0.00014758 | 0.0001505 | 0.00015235 | 0.0 | 2.98 +Other | | 0.0006434 | | | 12.76 Nlocal: 1000 ave 1016 max 981 min Histogram: 1 0 0 0 1 0 1 0 0 1 @@ -315,31 +288,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.5 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.8 - ghost atom cutoff = 1.8 - binsize = 0.9 -> bins = 19 19 19 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 60 1.1101013 -3.9655053 0 -2.3007696 4.7849008 70 1.1122144 -3.9657095 0 -2.297805 4.8014106 -Loop time of 0.00313491 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.003398 on 4 procs for 10 steps with 4000 atoms -Performance: 1378031.621 tau/day, 3189.888 timesteps/s -87.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1271335.633 tau/day, 2942.907 timesteps/s +98.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0016167 | 0.001663 | 0.0016985 | 0.1 | 53.05 -Neigh | 0.00075388 | 0.00076818 | 0.00078201 | 0.0 | 24.50 -Comm | 0.00037456 | 0.00042272 | 0.00048018 | 0.2 | 13.48 -Output | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 | 0.0 | 0.61 -Modify | 0.00012636 | 0.00012881 | 0.00013304 | 0.0 | 4.11 -Other | | 0.0001331 | | | 4.25 +Pair | 0.0015702 | 0.0016137 | 0.001651 | 0.1 | 47.49 +Neigh | 0.00080371 | 0.00082165 | 0.00084138 | 0.0 | 24.18 +Comm | 0.0005908 | 0.00064844 | 0.00071096 | 0.0 | 19.08 +Output | 1.7643e-05 | 2.3365e-05 | 4.0293e-05 | 0.0 | 0.69 +Modify | 0.00014853 | 0.00015211 | 0.00015593 | 0.0 | 4.48 +Other | | 0.0001387 | | | 4.08 Nlocal: 1000 ave 1022 max 982 min Histogram: 1 0 0 1 0 1 0 0 0 1 @@ -356,31 +322,24 @@ pair_style lj/cut ${cut} pair_style lj/cut 1.6 pair_coeff * * 1.0 1.0 run 10 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 1.9 - ghost atom cutoff = 1.9 - binsize = 0.95 -> bins = 18 18 18 -Memory usage per processor = 2.63679 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.238 | 3.238 | 3.238 Mbytes Step Temp E_pair E_mol TotEng Press 70 1.1122144 -4.1752688 0 -2.5073643 4.4755409 80 1.117224 -4.1831357 0 -2.5077187 4.446079 -Loop time of 0.00345927 on 4 procs for 10 steps with 4000 atoms +Loop time of 0.00420767 on 4 procs for 10 steps with 4000 atoms -Performance: 1248816.671 tau/day, 2890.779 timesteps/s -79.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 1026696.317 tau/day, 2376.612 timesteps/s +95.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0019331 | 0.0019561 | 0.0019834 | 0.0 | 56.55 -Neigh | 0.00081587 | 0.00081897 | 0.00082588 | 0.0 | 23.67 -Comm | 0.00037837 | 0.00040215 | 0.00041842 | 0.1 | 11.63 -Output | 1.812e-05 | 1.9312e-05 | 2.1935e-05 | 0.0 | 0.56 -Modify | 0.00012708 | 0.00013059 | 0.00013423 | 0.0 | 3.78 -Other | | 0.0001321 | | | 3.82 +Pair | 0.0019023 | 0.00194 | 0.0019965 | 0.1 | 46.11 +Neigh | 0.00088286 | 0.00088775 | 0.00089431 | 0.0 | 21.10 +Comm | 0.0010023 | 0.0010559 | 0.0010967 | 0.1 | 25.09 +Output | 2.0027e-05 | 2.6524e-05 | 4.53e-05 | 0.0 | 0.63 +Modify | 0.00014782 | 0.00015038 | 0.00015473 | 0.0 | 3.57 +Other | | 0.0001471 | | | 3.50 Nlocal: 1000 ave 1013 max 987 min Histogram: 1 0 1 0 0 0 0 1 0 1 diff --git a/examples/python/log.4May17.pair_python_coulomb.1 b/examples/python/log.4May17.pair_python_coulomb.1 deleted file mode 100644 index 97826eda47..0000000000 --- a/examples/python/log.4May17.pair_python_coulomb.1 +++ /dev/null @@ -1,178 +0,0 @@ -LAMMPS (4 May 2017) - using 1 OpenMP thread(s) per MPI task -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style hybrid/overlay python 12.0 coul/long 12.0 -kspace_style pppm 1.0e-6 - -pair_coeff * * coul/long -pair_coeff * * python potentials.LJCutSPCE OW NULL - -pair_modify table 0 - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -# create combined lj/coul table for all atom types -# generate tabulated potential from python variant -pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 -PPPM initialization ... -WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.279652 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.000394206 - estimated relative force accuracy = 1.18714e-06 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 6 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair python, perpetual, skip from (2) - attributes: half, newton on - pair build: skip - stencil: none - bin: none - (2) pair coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 -PPPM initialization ... -WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.279652 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.000394206 - estimated relative force accuracy = 1.18714e-06 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 -PPPM initialization ... -WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.279652 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.000394206 - estimated relative force accuracy = 1.18714e-06 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 - -# switch to tabulated potential -pair_style table linear 2000 pppm -pair_coeff 1 1 spce.table OW-OW -pair_coeff 1 2 spce.table OW-HW -pair_coeff 2 2 spce.table HW-HW - -thermo 10 -run 100 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.279652 - grid = 40 40 40 - stencil order = 5 - estimated absolute RMS force accuracy = 0.000394674 - estimated relative force accuracy = 1.18855e-06 - using double precision FFTs - 3d grid and FFT values/proc = 103823 64000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair table, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -100272.97 0 -100272.97 -1282.0708 - 10 120.61568 -101350.63 0 -100272.39 -4077.5051 - 20 136.11379 -101465.43 0 -100248.65 -5136.5677 - 30 137.01602 -101455.3 0 -100230.46 -5347.8311 - 40 153.424 -101582.46 0 -100210.93 -5223.1676 - 50 167.73654 -101686.24 0 -100186.77 -4468.6687 - 60 163.11642 -101618.16 0 -100159.99 -3291.7815 - 70 169.64512 -101647.89 0 -100131.35 -2611.638 - 80 182.9979 -101737.01 0 -100101.11 -2390.6293 - 90 191.33873 -101778.71 0 -100068.24 -2239.386 - 100 194.7458 -101775.84 0 -100034.92 -1951.9128 -Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms - -Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51 -Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00 -Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24 -Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02 -Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32 -Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01 -Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83 -Other | | 0.005243 | | | 0.07 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21216 ave 21216 max 21216 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2601766 -Ave neighs/atom = 578.17 -Ave special neighs/atom = 2 -Neighbor list builds = 3 -Dangerous builds = 0 - -shell rm spce.table - -Total wall time: 0:00:07 diff --git a/examples/python/log.4May17.pair_python_coulomb.g++.1 b/examples/python/log.4May17.pair_python_coulomb.g++.1 deleted file mode 100644 index b08d4b939c..0000000000 --- a/examples/python/log.4May17.pair_python_coulomb.g++.1 +++ /dev/null @@ -1,138 +0,0 @@ -LAMMPS (4 May 2017) - using 1 OpenMP thread(s) per MPI task -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style hybrid/overlay coul/cut 12.0 python 12.0 - -pair_coeff * * coul/cut -pair_coeff * * python py_pot.LJCutSPCE OW NULL - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -# create combined lj/coul table for all atom types -# generate tabulated potential from python variant -pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 6 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair coul/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) pair python, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 -pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 - -# switch to tabulated potential -pair_style table linear 2000 pppm -pair_coeff 1 1 spce.table OW-OW -pair_coeff 1 2 spce.table OW-HW -pair_coeff 2 2 spce.table HW-HW - -thermo 10 -run 100 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair table, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -18284.922 0 -18284.922 -2080.7739 - 10 146.83806 -19552.072 0 -18239.421 -4865.31 - 20 183.15761 -18706.872 0 -17069.543 -4865.6695 - 30 205.96203 -18901.541 0 -17060.354 -4454.8634 - 40 241.62768 -18323.117 0 -16163.099 -3269.1475 - 50 265.98384 -19883.562 0 -17505.813 -2788.5194 - 60 274.01897 -21320.575 0 -18870.996 -2387.0708 - 70 288.7601 -19849.269 0 -17267.913 -1235.818 - 80 300.64724 -20958.602 0 -18270.981 -1714.7988 - 90 304.19113 -21580.4 0 -18861.099 -2144.1614 - 100 304.22027 -21239.014 0 -18519.452 -2092.6759 -Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms - -Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 5.698 | 5.698 | 5.698 | 0.0 | 94.67 -Bond | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.00 -Neigh | 0.23235 | 0.23235 | 0.23235 | 0.0 | 3.86 -Comm | 0.018961 | 0.018961 | 0.018961 | 0.0 | 0.32 -Output | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.01 -Modify | 0.063452 | 0.063452 | 0.063452 | 0.0 | 1.05 -Other | | 0.005146 | | | 0.09 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21285 ave 21285 max 21285 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2597662 -Ave neighs/atom = 577.258 -Ave special neighs/atom = 2 -Neighbor list builds = 3 -Dangerous builds = 0 - -shell rm spce.table - -Total wall time: 0:00:06 diff --git a/examples/python/log.4May17.pair_python_coulomb.g++.4 b/examples/python/log.4May17.pair_python_coulomb.g++.4 deleted file mode 100644 index b002d5c1ab..0000000000 --- a/examples/python/log.4May17.pair_python_coulomb.g++.4 +++ /dev/null @@ -1,138 +0,0 @@ -LAMMPS (4 May 2017) - using 1 OpenMP thread(s) per MPI task -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style hybrid/overlay coul/cut 12.0 python 12.0 - -pair_coeff * * coul/cut -pair_coeff * * python py_pot.LJCutSPCE OW NULL - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -# create combined lj/coul table for all atom types -# generate tabulated potential from python variant -pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 6 6 6 - 2 neighbor lists, perpetual/occasional/extra = 2 0 0 - (1) pair coul/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard - (2) pair python, perpetual, skip from (1) - attributes: half, newton on - pair build: skip - stencil: none - bin: none -pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 -pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 - -# switch to tabulated potential -pair_style table linear 2000 pppm -pair_coeff 1 1 spce.table OW-OW -pair_coeff 1 2 spce.table OW-HW -pair_coeff 2 2 spce.table HW-HW - -thermo 10 -run 100 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7, bins = 6 6 6 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair table, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 9.962 | 9.963 | 9.963 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -18284.922 0 -18284.922 -2080.7739 - 10 146.83806 -19552.072 0 -18239.421 -4865.31 - 20 183.15761 -18706.872 0 -17069.543 -4865.6695 - 30 205.96203 -18901.541 0 -17060.354 -4454.8634 - 40 241.62768 -18323.117 0 -16163.099 -3269.1475 - 50 265.98384 -19883.562 0 -17505.813 -2788.5194 - 60 274.01897 -21320.575 0 -18870.996 -2387.0708 - 70 288.7601 -19849.269 0 -17267.913 -1235.818 - 80 300.64724 -20958.602 0 -18270.981 -1714.7988 - 90 304.19113 -21580.4 0 -18861.099 -2144.1614 - 100 304.22027 -21239.014 0 -18519.452 -2092.6759 -Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms - -Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s -99.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26 -Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01 -Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70 -Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65 -Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02 -Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18 -Other | | 0.003148 | | | 0.18 - -Nlocal: 1125 ave 1162 max 1098 min -Histogram: 1 1 0 0 0 1 0 0 0 1 -Nghost: 12267.8 ave 12302 max 12238 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 649416 ave 681458 max 630541 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 2597662 -Ave neighs/atom = 577.258 -Ave special neighs/atom = 2 -Neighbor list builds = 3 -Dangerous builds = 0 - -shell rm spce.table - -Total wall time: 0:00:01 diff --git a/examples/qeq/ffield.reax.cho b/examples/qeq/ffield.reax.cho old mode 100755 new mode 100644 diff --git a/examples/qeq/log.5Oct16.qeq.buck.g++.1 b/examples/qeq/log.27Nov18.qeq.buck.g++.1 similarity index 60% rename from examples/qeq/log.5Oct16.qeq.buck.g++.1 rename to examples/qeq/log.27Nov18.qeq.buck.g++.1 index 2dbd6674ae..4d5225ccc3 100644 --- a/examples/qeq/log.5Oct16.qeq.buck.g++.1 +++ b/examples/qeq/log.27Nov18.qeq.buck.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with # that defines and uses charges, in this case pair_style buck/coul/long @@ -14,6 +15,7 @@ replicate 2 2 2 orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) 1 by 1 by 1 MPI processor grid 9600 atoms + Time spent = 0.00114894 secs pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 @@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 run 100 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.305064 estimated absolute RMS force accuracy = 2.07629e-05 estimated relative force accuracy = 1.44191e-06 KSpace vectors: actual max1d max3d = 13556 20 34460 kxmax kymax kzmax = 18 18 20 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 8 8 9 -Memory usage per processor = 110.875 Mbytes + binsize = 6.5, bins = 8 8 9 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix qeq/fire, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes Step PotEng c_q1 c_q2 v_qtot S/CPU 0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0 - 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64960264 - 20 -27975.085 0.85968531 -0.42984266 -8.8220986e-11 0.55300005 - 30 -28552.628 0.86755661 -0.4337783 1.4142643e-10 0.52434987 - 40 -29133.643 0.87426387 -0.43713193 1.6871127e-10 0.52326849 - 50 -29697.011 0.8794039 -0.43970195 1.2460077e-10 0.52083626 - 60 -30342.001 0.88478594 -0.44239297 -4.3655746e-11 0.52824882 - 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.56010601 - 80 -31792.732 0.89506635 -0.44753317 -3.774403e-11 0.60040973 - 90 -32424.749 0.89714841 -0.44857421 -1.0004442e-10 0.57758717 - 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59560798 -Loop time of 178.401 on 1 procs for 100 steps with 9600 atoms + 10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877 + 20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179 + 30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643 + 40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341 + 50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127 + 60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762 + 70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546 + 80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079 + 90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419 + 100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001 +Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms -Performance: 0.005 ns/day, 4955.597 hours/ns, 0.561 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 15.042 | 15.042 | 15.042 | 0.0 | 8.43 -Kspace | 98.245 | 98.245 | 98.245 | 0.0 | 55.07 +Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48 +Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.019511 | 0.019511 | 0.019511 | 0.0 | 0.01 -Output | 0.0020375 | 0.0020375 | 0.0020375 | 0.0 | 0.00 -Modify | 65.083 | 65.083 | 65.083 | 0.0 | 36.48 -Other | | 0.009152 | | | 0.01 +Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01 +Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00 +Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11 +Other | | 0.007197 | | | 0.00 Nlocal: 9600 ave 9600 max 9600 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -103,4 +115,4 @@ Total # of neighbors = 2940800 Ave neighs/atom = 306.333 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:03:02 +Total wall time: 0:03:01 diff --git a/examples/qeq/log.5Oct16.qeq.buck.g++.4 b/examples/qeq/log.27Nov18.qeq.buck.g++.4 similarity index 57% rename from examples/qeq/log.5Oct16.qeq.buck.g++.4 rename to examples/qeq/log.27Nov18.qeq.buck.g++.4 index 0f628740bd..947c3caeaf 100644 --- a/examples/qeq/log.5Oct16.qeq.buck.g++.4 +++ b/examples/qeq/log.27Nov18.qeq.buck.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with # that defines and uses charges, in this case pair_style buck/coul/long @@ -14,6 +15,7 @@ replicate 2 2 2 orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405) 1 by 2 by 2 MPI processor grid 9600 atoms + Time spent = 0.000675201 secs pair_style buck/coul/long 12.0 pair_coeff 2 2 1388.77 .3623188 175.0 @@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2 run 100 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.305064 estimated absolute RMS force accuracy = 2.07629e-05 estimated relative force accuracy = 1.44191e-06 KSpace vectors: actual max1d max3d = 13556 20 34460 kxmax kymax kzmax = 18 18 20 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 8 8 9 -Memory usage per processor = 46.867 Mbytes + binsize = 6.5, bins = 8 8 9 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair buck/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) fix qeq/fire, perpetual, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes Step PotEng c_q1 c_q2 v_qtot S/CPU 0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0 - 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.561772 - 20 -27975.085 0.85968531 -0.42984266 9.777068e-11 2.1470405 - 30 -28552.627 0.86755661 -0.4337783 1.2823875e-10 2.0585052 - 40 -29133.643 0.87426387 -0.43713193 1.5506885e-10 2.0319632 - 50 -29697.01 0.8794039 -0.43970195 2.1873348e-10 2.0350244 - 60 -30342 0.88478594 -0.44239297 1.891749e-10 2.0793976 - 70 -31081.139 0.89069733 -0.44534866 1.4688339e-10 2.1759002 - 80 -31792.732 0.89506635 -0.44753317 1.4142643e-10 2.3320978 - 90 -32424.752 0.89714841 -0.44857421 9.9134922e-11 2.2673305 - 100 -32998.353 0.89755721 -0.44877861 1.5097612e-10 2.3389389 -Loop time of 45.6331 on 4 procs for 100 steps with 9600 atoms + 10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312 + 20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316 + 30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335 + 40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139 + 50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263 + 60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722 + 70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406 + 80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813 + 90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145 + 100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486 +Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms -Performance: 0.019 ns/day, 1267.586 hours/ns, 2.191 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.8297 | 3.8983 | 3.938 | 2.1 | 8.54 -Kspace | 24.434 | 24.579 | 24.78 | 2.9 | 53.86 +Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22 +Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.078239 | 0.31795 | 0.53069 | 30.8 | 0.70 -Output | 0.00097322 | 0.0010365 | 0.0011294 | 0.2 | 0.00 -Modify | 16.831 | 16.832 | 16.832 | 0.0 | 36.88 -Other | | 0.005259 | | | 0.01 +Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75 +Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00 +Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03 +Other | | 0.01409 | | | 0.03 Nlocal: 2400 ave 2400 max 2400 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -103,4 +115,4 @@ Total # of neighbors = 2940800 Ave neighs/atom = 306.333 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:46 +Total wall time: 0:00:49 diff --git a/examples/qeq/log.5Oct16.qeq.reaxc.g++.1 b/examples/qeq/log.27Nov18.qeq.reaxc.g++.1 similarity index 76% rename from examples/qeq/log.5Oct16.qeq.reaxc.g++.1 rename to examples/qeq/log.27Nov18.qeq.reaxc.g++.1 index 493b4b62d8..c88acc39f2 100644 --- a/examples/qeq/log.5Oct16.qeq.reaxc.g++.1 +++ b/examples/qeq/log.27Nov18.qeq.reaxc.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with pair reax/c # You can comment in/out various versions below # @@ -54,13 +55,23 @@ timestep 0.25 run 10 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 - binsize = 5.5 -> bins = 5 5 5 -Memory usage per processor = 15.8004 Mbytes + binsize = 5.5, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes Step PotEng c_q1 c_q2 c_q3 v_qtot 0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16 1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15 @@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot 8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15 9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16 10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15 -Loop time of 0.0398569 on 1 procs for 10 steps with 105 atoms +Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms -Performance: 5.419 ns/day, 4.429 hours/ns, 250.898 timesteps/s -100.3% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.034917 | 0.034917 | 0.034917 | 0.0 | 87.61 +Pair | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 3.2663e-05 | 3.2663e-05 | 3.2663e-05 | 0.0 | 0.08 -Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.43 -Modify | 0.0047123 | 0.0047123 | 0.0047123 | 0.0 | 11.82 -Other | | 2.527e-05 | | | 0.06 +Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16 +Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85 +Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57 +Other | | 2.694e-05 | | | 0.08 Nlocal: 105 ave 105 max 105 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/qeq/log.5Oct16.qeq.reaxc.g++.4 b/examples/qeq/log.27Nov18.qeq.reaxc.g++.4 similarity index 76% rename from examples/qeq/log.5Oct16.qeq.reaxc.g++.4 rename to examples/qeq/log.27Nov18.qeq.reaxc.g++.4 index 834c8170c8..c54a99577e 100644 --- a/examples/qeq/log.5Oct16.qeq.reaxc.g++.4 +++ b/examples/qeq/log.27Nov18.qeq.reaxc.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # This example demonstrates the use of various fix qeq variants with pair reax/c # You can comment in/out various versions below # @@ -54,13 +55,23 @@ timestep 0.25 run 10 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11 ghost atom cutoff = 11 - binsize = 5.5 -> bins = 5 5 5 -Memory usage per processor = 11.6046 Mbytes + binsize = 5.5, bins = 5 5 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/reax, perpetual, copy from (1) + attributes: half, newton off, ghost + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes Step PotEng c_q1 c_q2 c_q3 v_qtot 0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15 1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15 @@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot 8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16 9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16 10 -10186.168 0.095747223 -0.15684634 -0.091183742 0 -Loop time of 0.0217528 on 4 procs for 10 steps with 105 atoms +Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms -Performance: 9.930 ns/day, 2.417 hours/ns, 459.710 timesteps/s -93.1% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s +92.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.012203 | 0.014022 | 0.015427 | 1.0 | 64.46 +Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00011754 | 0.0015323 | 0.0033445 | 3.0 | 7.04 -Output | 0.00041366 | 0.00044626 | 0.00048447 | 0.1 | 2.05 -Modify | 0.0056725 | 0.0056758 | 0.0056815 | 0.0 | 26.09 -Other | | 7.629e-05 | | | 0.35 +Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45 +Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50 +Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27 +Other | | 0.0002902 | | | 1.57 Nlocal: 26.25 ave 35 max 15 min Histogram: 1 0 0 1 0 0 0 0 0 2 diff --git a/examples/rdf-adf/log.10Oct2018.spce.g++.2 b/examples/rdf-adf/log.27Nov18.spce.g++.1 similarity index 52% rename from examples/rdf-adf/log.10Oct2018.spce.g++.2 rename to examples/rdf-adf/log.27Nov18.spce.g++.1 index d19e69a031..70adb9d1c5 100644 --- a/examples/rdf-adf/log.10Oct2018.spce.g++.2 +++ b/examples/rdf-adf/log.27Nov18.spce.g++.1 @@ -1,12 +1,13 @@ -LAMMPS (10 Oct 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task +# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom) + units real atom_style full read_data data.spce orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 2 by 1 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 4500 atoms scanning bonds ... @@ -65,7 +66,7 @@ PPPM initialization ... estimated absolute RMS force accuracy = 0.000394674 estimated relative force accuracy = 1.18855e-06 using double precision FFTs - 3d grid and FFT values/proc = 59643 32000 + 3d grid and FFT values/proc = 103823 64000 Neighbor list info ... update every 1 steps, delay 2 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -78,39 +79,39 @@ Neighbor list info ... pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 25.06 | 25.25 | 25.44 Mbytes +Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -16692.369 0 -14010.534 -112.83562 - 100 283.44729 -17008.717 0 -14474.854 -162.06374 - 200 298.75279 -16765.544 0 -14094.858 428.79127 - 300 296.6501 -16589.155 0 -13937.267 547.40768 - 400 303.83151 -16625.028 0 -13908.942 237.9775 - 500 298.01615 -16717.015 0 -14052.915 230.7095 -Loop time of 21.4041 on 2 procs for 500 steps with 4500 atoms + 100 283.44729 -17008.717 0 -14474.854 -162.06378 + 200 298.75279 -16765.543 0 -14094.858 428.7917 + 300 296.65014 -16589.155 0 -13937.267 547.40796 + 400 303.82963 -16625.011 0 -13908.942 237.93694 + 500 298.00057 -16716.887 0 -14052.926 231.55014 +Loop time of 38.2796 on 1 procs for 500 steps with 4500 atoms -Performance: 4.037 ns/day, 5.946 hours/ns, 23.360 timesteps/s -94.8% CPU use with 2 MPI tasks x 1 OpenMP threads +Performance: 2.257 ns/day, 10.633 hours/ns, 13.062 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 14.892 | 15.034 | 15.176 | 3.7 | 70.24 -Bond | 0.00056624 | 0.00059342 | 0.0006206 | 0.0 | 0.00 -Kspace | 3.987 | 4.1321 | 4.2773 | 7.1 | 19.31 -Neigh | 1.7494 | 1.7496 | 1.7497 | 0.0 | 8.17 -Comm | 0.20554 | 0.20637 | 0.2072 | 0.2 | 0.96 -Output | 0.00015688 | 0.00036144 | 0.00056601 | 0.0 | 0.00 -Modify | 0.25707 | 0.2606 | 0.26413 | 0.7 | 1.22 -Other | | 0.02059 | | | 0.10 +Pair | 28.428 | 28.428 | 28.428 | 0.0 | 74.26 +Bond | 0.00056672 | 0.00056672 | 0.00056672 | 0.0 | 0.00 +Kspace | 5.3161 | 5.3161 | 5.3161 | 0.0 | 13.89 +Neigh | 4.1185 | 4.1185 | 4.1185 | 0.0 | 10.76 +Comm | 0.12788 | 0.12788 | 0.12788 | 0.0 | 0.33 +Output | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00 +Modify | 0.26748 | 0.26748 | 0.26748 | 0.0 | 0.70 +Other | | 0.02102 | | | 0.05 -Nlocal: 2250 ave 2258 max 2242 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 16319 ave 16381 max 16257 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 1.30073e+06 ave 1.32386e+06 max 1.2776e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21248 ave 21248 max 21248 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60146e+06 ave 2.60146e+06 max 2.60146e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2601457 +Total # of neighbors = 2601459 Ave neighs/atom = 578.102 Ave special neighs/atom = 2 Neighbor list builds = 45 @@ -119,7 +120,7 @@ Dangerous builds = 0 reset_timestep 0 compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H -compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 1 2 1 0.0 1.2 1.5 2.5 +compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector @@ -132,7 +133,7 @@ PPPM initialization ... estimated absolute RMS force accuracy = 0.000394674 estimated relative force accuracy = 1.18855e-06 using double precision FFTs - 3d grid and FFT values/proc = 59643 32000 + 3d grid and FFT values/proc = 103823 64000 Neighbor list info ... update every 1 steps, delay 2 steps, check yes max neighbors/atom: 2000, page size: 100000 @@ -155,48 +156,48 @@ Neighbor list info ... pair build: full/bin stencil: full/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 26.78 | 26.78 | 26.78 Mbytes +Per MPI rank memory allocation (min/avg/max) = 36.67 | 36.67 | 36.67 Mbytes Step Temp E_pair E_mol TotEng Press - 0 298.01615 -16717.015 0 -14052.915 230.81371 - 100 307.1766 -16759.33 0 -14013.341 454.2771 - 200 298.94628 -16674.186 0 -14001.771 114.20846 - 300 293.13091 -16581.542 0 -13961.113 272.85574 - 400 294.47017 -16556.872 0 -13924.471 180.3252 - 500 305.57174 -16647.976 0 -13916.333 -444.14856 - 600 302.53992 -16670.304 0 -13965.764 114.82353 - 700 306.56761 -16616.508 0 -13875.962 534.02537 - 800 299.06297 -16644.133 0 -13970.675 83.643063 - 900 301.15522 -16674.021 0 -13981.859 325.04538 - 1000 298.14963 -16701.663 0 -14036.369 356.0601 -Loop time of 53.3181 on 2 procs for 1000 steps with 4500 atoms + 0 298.00057 -16716.887 0 -14052.926 231.6595 + 100 307.31045 -16761.022 0 -14013.835 449.26027 + 200 299.52847 -16679.165 0 -14001.546 148.44719 + 300 293.68499 -16583.548 0 -13958.166 140.79069 + 400 306.76266 -16658.573 0 -13916.284 481.26934 + 500 294.75648 -16640.446 0 -14005.485 585.05479 + 600 303.19282 -16629.985 0 -13919.608 328.23667 + 700 300.28233 -16590.155 0 -13905.797 -176.71076 + 800 292.36899 -16620.826 0 -14007.208 -194.83408 + 900 304.92802 -16633.331 0 -13907.443 479.49808 + 1000 300.64529 -16598.233 0 -13910.63 904.96137 +Loop time of 107.579 on 1 procs for 1000 steps with 4500 atoms -Performance: 3.241 ns/day, 7.405 hours/ns, 18.755 timesteps/s -97.3% CPU use with 2 MPI tasks x 1 OpenMP threads +Performance: 1.606 ns/day, 14.942 hours/ns, 9.295 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 28.831 | 29.365 | 29.899 | 9.9 | 55.07 -Bond | 0.00097084 | 0.0010794 | 0.001188 | 0.3 | 0.00 -Kspace | 7.3086 | 7.8356 | 8.3626 | 18.8 | 14.70 -Neigh | 3.7241 | 3.7245 | 3.7248 | 0.0 | 6.99 -Comm | 0.32839 | 0.33495 | 0.34151 | 1.1 | 0.63 -Output | 0.00043344 | 0.0015392 | 0.002645 | 2.8 | 0.00 -Modify | 12.013 | 12.014 | 12.015 | 0.0 | 22.53 -Other | | 0.04153 | | | 0.08 +Pair | 58.928 | 58.928 | 58.928 | 0.0 | 54.78 +Bond | 0.0012271 | 0.0012271 | 0.0012271 | 0.0 | 0.00 +Kspace | 10.698 | 10.698 | 10.698 | 0.0 | 9.94 +Neigh | 8.7649 | 8.7649 | 8.7649 | 0.0 | 8.15 +Comm | 0.2608 | 0.2608 | 0.2608 | 0.0 | 0.24 +Output | 0.00043702 | 0.00043702 | 0.00043702 | 0.0 | 0.00 +Modify | 28.883 | 28.883 | 28.883 | 0.0 | 26.85 +Other | | 0.04301 | | | 0.04 -Nlocal: 2250 ave 2251 max 2249 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Nghost: 16300 ave 16358 max 16242 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -Neighs: 1.301e+06 ave 1.31594e+06 max 1.28606e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 1 -FullNghs: 2.602e+06 ave 2.60923e+06 max 2.59476e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 1 +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21275 ave 21275 max 21275 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60217e+06 ave 2.60217e+06 max 2.60217e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 5.20478e+06 ave 5.20478e+06 max 5.20478e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 5203998 -Ave neighs/atom = 1156.44 +Total # of neighbors = 5204784 +Ave neighs/atom = 1156.62 Ave special neighs/atom = 2 -Neighbor list builds = 93 +Neighbor list builds = 94 Dangerous builds = 0 -Total wall time: 0:01:14 +Total wall time: 0:02:26 diff --git a/examples/rdf-adf/log.27Nov18.spce.g++.4 b/examples/rdf-adf/log.27Nov18.spce.g++.4 new file mode 100644 index 0000000000..4fa0369e19 --- /dev/null +++ b/examples/rdf-adf/log.27Nov18.spce.g++.4 @@ -0,0 +1,203 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom) + +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style lj/cut/coul/long 12.0 12.0 +pair_coeff * * 0.0 1.0 +pair_coeff 1 1 0.15535 3.166 +kspace_style pppm 1.0e-6 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +# need to set bond/angle inclusion to > 0.0 +# so that intramolecular pairs are included in neighbor lists (required for second ADF) +special_bonds lj/coul 1.0e-100 1.0e-100 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin +timestep 2.0 +neigh_modify every 1 delay 2 check yes + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +velocity all create 300.0 6244325 + +thermo 100 +run 500 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 34263 16000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.1 | 13.1 | 13.1 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 300 -16692.369 0 -14010.534 -112.83562 + 100 283.44729 -17008.717 0 -14474.854 -162.06378 + 200 298.75279 -16765.543 0 -14094.858 428.79175 + 300 296.65013 -16589.155 0 -13937.267 547.40809 + 400 303.82993 -16625.014 0 -13908.942 237.957 + 500 298.00206 -16716.893 0 -14052.919 231.33112 +Loop time of 12.5516 on 4 procs for 500 steps with 4500 atoms + +Performance: 6.884 ns/day, 3.487 hours/ns, 39.836 timesteps/s +94.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.739 | 7.9051 | 8.2663 | 7.5 | 62.98 +Bond | 0.00061631 | 0.00064486 | 0.00070524 | 0.0 | 0.01 +Kspace | 2.7001 | 3.0573 | 3.2239 | 11.9 | 24.36 +Neigh | 1.1736 | 1.174 | 1.1743 | 0.0 | 9.35 +Comm | 0.18222 | 0.1869 | 0.19248 | 0.8 | 1.49 +Output | 0.00017595 | 0.00032246 | 0.00076079 | 0.0 | 0.00 +Modify | 0.20354 | 0.20467 | 0.20652 | 0.2 | 1.63 +Other | | 0.02259 | | | 0.18 + +Nlocal: 1125 ave 1132 max 1114 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Nghost: 12241 ave 12298 max 12196 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 650366 ave 671163 max 631441 min +Histogram: 1 0 0 1 0 1 0 0 0 1 + +Total # of neighbors = 2601464 +Ave neighs/atom = 578.103 +Ave special neighs/atom = 2 +Neighbor list builds = 45 +Dangerous builds = 0 + +reset_timestep 0 + +compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H +compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O +fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector +fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector + +run 1000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 34263 16000 +Neighbor list info ... + update every 1 steps, delay 2 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 3 neighbor lists, perpetual/occasional/extra = 1 2 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute rdf, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none + (3) compute adf, occasional + attributes: full, newton on + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 13.96 | 13.96 | 13.96 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 298.00206 -16716.893 0 -14052.919 231.44272 + 100 307.28155 -16760.647 0 -14013.72 452.38436 + 200 299.05168 -16674.695 0 -14001.338 177.44237 + 300 292.7564 -16573.946 0 -13956.865 122.27796 + 400 299.2644 -16578.318 0 -13903.059 482.03304 + 500 296.04028 -16623.179 0 -13976.742 89.968145 + 600 300.30911 -16664.206 0 -13979.608 132.70079 + 700 292.39517 -16703.749 0 -14089.897 825.267 + 800 298.75851 -16661.684 0 -13990.948 468.68671 + 900 301.55689 -16644.846 0 -13949.093 -72.16965 + 1000 298.2852 -16682.077 0 -14015.572 0.69725342 +Loop time of 32.3106 on 4 procs for 1000 steps with 4500 atoms + +Performance: 5.348 ns/day, 4.488 hours/ns, 30.950 timesteps/s +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 15.647 | 15.876 | 16.119 | 4.3 | 49.13 +Bond | 0.0011718 | 0.0012704 | 0.001348 | 0.2 | 0.00 +Kspace | 5.286 | 5.5364 | 5.7729 | 7.5 | 17.13 +Neigh | 2.3892 | 2.3962 | 2.3991 | 0.3 | 7.42 +Comm | 0.34641 | 0.35514 | 0.35988 | 0.9 | 1.10 +Output | 0.00047851 | 0.00069892 | 0.0013568 | 0.0 | 0.00 +Modify | 8.0882 | 8.0963 | 8.1047 | 0.3 | 25.06 +Other | | 0.04887 | | | 0.15 + +Nlocal: 1125 ave 1137 max 1114 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Nghost: 12206.2 ave 12239 max 12169 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 650464 ave 655962 max 641444 min +Histogram: 1 0 0 0 0 0 0 2 0 1 +FullNghs: 1.30095e+06 ave 1.31925e+06 max 1.28413e+06 min +Histogram: 1 0 1 0 0 0 1 0 0 1 + +Total # of neighbors = 5203786 +Ave neighs/atom = 1156.4 +Ave special neighs/atom = 2 +Neighbor list builds = 94 +Dangerous builds = 0 +Total wall time: 0:00:45 diff --git a/examples/rdf-adf/spce-adf.dat.ref b/examples/rdf-adf/spce-adf.dat.ref index 2c6b53c291..0109e13ccb 100644 --- a/examples/rdf-adf/spce-adf.dat.ref +++ b/examples/rdf-adf/spce-adf.dat.ref @@ -12,38 +12,38 @@ 8 30 0 0 0 0 9 34 0 0 0 0 10 38 0 0 0 0 -11 42 2.66805e-05 0.00123333 0 0 -12 46 0.00168251 0.07888 0 0 -13 50 0.00730338 0.41588 0 0 -14 54 0.00883969 0.82378 0 0 -15 58 0.00712558 1.15264 0 0 -16 62 0.00681516 1.46717 0 0 -17 66 0.00753965 1.81511 0 0 -18 70 0.0086394 2.21377 0 0 -19 74 0.00958735 2.65613 0 0 -20 78 0.0102438 3.12873 5.076e-06 2e-05 -21 82 0.0108097 3.62739 2.62642e-05 0.000123333 -22 86 0.0112538 4.14651 0.000100091 0.000516667 -23 90 0.0115997 4.68151 0.000173925 0.0012 -24 94 0.0118726 5.22921 0.00025685 0.00221 -25 98 0.0118616 5.77635 0.000341943 0.00355333 -26 102 0.0117868 6.32011 0.000488452 0.00547333 -27 106 0.0115064 6.85083 0.000753934 0.00843667 -28 110 0.0111827 7.36672 0.00118587 0.0130967 -29 114 0.0106304 7.85709 0.00157663 0.0192933 -30 118 0.0100947 8.32278 0.00223856 0.0280933 -31 122 0.009349 8.75409 0.00295997 0.0397267 -32 126 0.008637 9.15256 0.00363466 0.05401 -33 130 0.00785049 9.51475 0.00480604 0.0728967 -34 134 0.00712391 9.8434 0.00617924 0.09718 -35 138 0.00633303 10.1356 0.00801778 0.12869 -36 142 0.00574158 10.4005 0.0105777 0.170257 -37 146 0.00509275 10.6354 0.0138935 0.224857 -38 150 0.0045349 10.8446 0.0182593 0.296613 -39 154 0.00398109 11.0283 0.0234156 0.38863 -40 158 0.00334665 11.1827 0.0283932 0.500213 -41 162 0.00273371 11.3088 0.032517 0.627997 -42 166 0.00212695 11.407 0.0330644 0.757927 -43 170 0.00153822 11.4779 0.0292715 0.872957 -44 174 0.000912858 11.52 0.0205789 0.953827 -45 178 0.000296337 11.5337 0.00728348 0.98245 +11 42 2.37636e-05 0.00109333 0 0 +12 46 0.00169251 0.0789867 0 0 +13 50 0.00730134 0.414993 0 0 +14 54 0.00880551 0.820173 0 0 +15 58 0.0071375 1.14866 0 0 +16 62 0.0066689 1.45561 0 0 +17 66 0.00746703 1.79925 0 0 +18 70 0.00857042 2.19363 0 0 +19 74 0.0093992 2.62615 0 0 +20 78 0.0101772 3.09435 4.23471e-06 1.66667e-05 +21 82 0.0108355 3.59288 3.04321e-05 0.000136667 +22 86 0.0113606 4.11563 9.22188e-05 0.0005 +23 90 0.0117079 4.65431 0.000176849 0.00119667 +24 94 0.0119884 5.2059 0.000230899 0.00210667 +25 98 0.012007 5.75831 0.000312922 0.00334 +26 102 0.0117876 6.30063 0.000482843 0.00524333 +27 106 0.011572 6.83302 0.000770416 0.00828 +28 110 0.0111902 7.34792 0.00113941 0.01277 +29 114 0.0106638 7.83854 0.00161896 0.01915 +30 118 0.0100445 8.30067 0.00220659 0.0278433 +31 122 0.0092193 8.72479 0.00273188 0.0386067 +32 126 0.00860698 9.12078 0.00353887 0.05255 +33 130 0.00788729 9.48369 0.00463824 0.0708233 +34 134 0.0071613 9.81317 0.00589308 0.09404 +35 138 0.00645327 10.1101 0.00794474 0.125337 +36 142 0.00575866 10.3751 0.0103074 0.16594 +37 146 0.00512532 10.6109 0.0139526 0.220907 +38 150 0.0045258 10.8192 0.0181886 0.292553 +39 154 0.00394488 11.0007 0.0234856 0.385067 +40 158 0.00336751 11.1557 0.0285798 0.497653 +41 162 0.00274518 11.282 0.0325617 0.625923 +42 166 0.00211836 11.3794 0.0335082 0.757917 +43 170 0.00149999 11.4485 0.0296222 0.874607 +44 174 0.000895422 11.4897 0.0205701 0.955633 +45 178 0.00028968 11.503 0.00741112 0.984827 diff --git a/examples/rdf-adf/spce-rdf.dat.ref b/examples/rdf-adf/spce-rdf.dat.ref index 204e5ffc73..7c978e1635 100644 --- a/examples/rdf-adf/spce-rdf.dat.ref +++ b/examples/rdf-adf/spce-rdf.dat.ref @@ -14,91 +14,91 @@ 10 1.14 0 0 0 0 0 2 11 1.26 0 0 0 0 0 2 12 1.38 0 0 0 0 0 2 -13 1.5 0 0 0.00146316 0.000333333 0.0485606 2.01107 -14 1.62 0 0 3.77986 1.00467 0.691259 2.1948 -15 1.74 0 0 0.087001 1.03133 1.5081 2.6572 -16 1.86 0 0 0.261354 1.12287 1.29225 3.10993 -17 1.98 0 0 0.557712 1.3442 0.791284 3.42407 -18 2.1 0 0 0.890071 1.74153 0.441155 3.62107 -19 2.22 0 0 1.18482 2.3326 0.280275 3.76093 -20 2.34 0 0 1.33539 3.07273 0.203573 3.8738 -21 2.46 0.0296137 0.00906667 1.31236 3.8766 0.199433 3.996 -22 2.58 0.910251 0.3156 1.12596 4.6352 0.252635 4.16627 -23 2.7 2.74616 1.3284 0.92755 5.3196 0.399944 4.46147 -24 2.82 2.69277 2.41173 0.776668 5.94473 0.620912 4.9614 -25 2.94 1.69749 3.154 0.715559 6.57073 0.927784 5.77333 -26 3.06 1.12844 3.68853 0.734337 7.26667 1.28373 6.99033 -27 3.18 0.894502 4.14613 0.785685 8.0708 1.53008 8.55687 -28 3.3 0.830879 4.60387 0.853285 9.01127 1.55205 10.2681 -29 3.42 0.837147 5.0992 0.940998 10.1252 1.42789 11.9589 -30 3.54 0.87264 5.6524 1.02352 11.4233 1.30488 13.6145 -31 3.66 0.890146 6.2556 1.10007 12.9147 1.15043 15.1747 -32 3.78 0.923629 6.9232 1.14816 14.5751 1.05067 16.6945 -33 3.9 0.948076 7.65267 1.1789 16.3898 0.995284 18.2271 -34 4.02 1.02003 8.48653 1.14251 18.2584 0.987649 19.843 -35 4.14 1.05003 9.39693 1.09918 20.1651 0.973183 21.5317 -36 4.26 1.0578 10.368 1.05588 22.1043 0.968154 23.3104 -37 4.38 1.08788 11.4237 1.04202 24.1275 0.95294 25.1612 -38 4.5 1.0991 12.5496 1.02603 26.2302 0.948747 27.1062 -39 4.62 1.08758 13.7239 1.0199 28.4333 0.952182 29.1637 -40 4.74 1.08319 14.9549 1.0085 30.7265 0.958425 31.3437 -41 4.86 1.06718 16.23 1.0021 33.1219 0.966773 33.6555 -42 4.98 1.0236 17.5141 0.983127 35.5894 0.975683 36.1051 -43 5.1 0.979245 18.8025 0.968484 38.1387 0.993353 38.7208 -44 5.22 0.967438 20.136 0.960781 40.7882 1.0117 41.5116 -45 5.34 0.9397 21.4915 0.95327 43.5392 1.02048 44.4575 -46 5.46 0.933775 22.8996 0.957903 46.4292 1.02138 47.5401 -47 5.58 0.905728 24.3261 0.96475 49.4692 1.01134 50.7279 -48 5.7 0.908316 25.8189 0.985709 52.7103 1.00699 54.0401 -49 5.82 0.922062 27.3988 0.992001 56.1108 0.993731 57.4477 -50 5.94 0.933444 29.0648 1.00316 59.6929 0.985977 60.9695 -51 6.06 0.967112 30.8613 1.00148 63.4149 0.975667 64.5968 -52 6.18 0.995762 32.7851 1.00378 67.2946 0.966562 68.3339 -53 6.3 1.01856 34.83 1.01103 71.3556 0.980183 72.2723 -54 6.42 1.02375 36.9644 1.00763 75.5586 0.975791 76.3439 -55 6.54 1.02443 39.1808 1.0048 79.9079 0.988272 80.6231 -56 6.66 1.04424 41.5237 0.994556 84.3723 0.992933 85.0817 -57 6.78 1.02624 43.91 0.993082 88.9922 1.00275 89.7481 -58 6.9 1.05342 46.4469 0.995881 93.7905 1.0039 94.5867 -59 7.02 1.04804 49.0595 1.0028 98.7917 1.0061 99.606 -60 7.14 1.03565 51.7301 0.999035 103.946 1.00976 104.817 -61 7.26 1.01185 54.4279 0.999229 109.276 1.01388 110.227 -62 7.38 1.00714 57.2025 0.997563 114.774 1.02243 115.864 -63 7.5 0.997335 60.0403 1.00429 120.491 1.01948 121.67 -64 7.62 0.98964 62.9469 1.00029 126.369 1.01107 127.613 -65 7.74 0.986472 65.9363 1.01014 132.493 1.0127 133.755 -66 7.86 0.976805 68.9888 1.0082 138.797 1.00837 140.061 -67 7.98 0.980184 72.1461 1.00972 145.304 1.00029 146.51 -68 8.1 0.99097 75.4349 1.00403 151.97 0.999714 153.15 -69 8.22 0.988581 78.8137 1.00883 158.869 1.00011 159.991 -70 8.34 1.0046 82.3483 1.00269 165.927 0.994842 166.996 -71 8.46 0.987279 85.9225 0.997968 173.155 0.990283 174.171 -72 8.58 1.00046 89.648 0.999277 180.6 0.990097 181.55 -73 8.7 1.00036 93.478 0.999683 188.257 0.987047 189.113 -74 8.82 1.00138 97.4184 0.995158 196.091 0.991812 196.923 -75 8.94 1.02075 101.545 0.999836 204.178 0.991287 204.944 -76 9.06 1.00201 105.705 0.99005 212.403 0.996973 213.228 -77 9.18 0.990377 109.927 0.994103 220.881 1.00126 221.77 -78 9.3 1.0021 114.311 0.998366 229.619 0.997051 230.5 -79 9.42 1.00911 118.841 0.996714 238.57 1.00147 239.496 -80 9.54 1.00129 123.45 0.997009 247.752 1.00442 248.751 -81 9.66 0.994425 128.144 0.999099 257.187 1.0036 258.231 -82 9.78 0.99875 132.976 1.00089 266.876 1.00798 267.991 -83 9.9 1.00475 137.958 1.00485 276.842 1.00223 277.935 -84 10.02 1.00821 143.078 1.00531 287.057 1.00199 288.119 -85 10.14 1.00146 148.286 1.00396 297.503 1.00607 298.591 -86 10.26 0.987716 153.546 1.00115 308.168 1.00195 309.269 -87 10.38 0.996668 158.978 0.999956 319.072 0.999207 320.167 -88 10.5 1.00737 164.595 1.00266 330.259 0.999525 331.323 -89 10.62 1.00322 170.319 1.00368 341.714 0.991347 342.642 -90 10.74 1.00197 176.165 1.00151 353.405 1.00118 354.333 -91 10.86 1.01265 182.206 0.997669 365.313 1.00021 366.275 -92 10.98 1.00566 188.339 1.00218 377.54 0.998434 378.46 -93 11.1 1.00615 194.61 0.998681 389.992 1.00219 390.96 -94 11.22 0.989815 200.913 0.994781 402.666 0.996803 403.664 -95 11.34 0.995666 207.389 0.998115 415.655 0.99786 416.654 -96 11.46 0.990077 213.966 0.999458 428.938 1.00053 429.956 -97 11.58 0.992053 220.695 0.997809 442.479 0.994388 443.455 -98 11.7 1.00038 227.622 0.999064 456.319 1.00445 457.374 -99 11.82 0.99774 234.673 1.00106 470.473 0.998027 471.49 -100 11.94 1.00539 241.923 0.99896 484.885 1.00035 485.927 +13 1.5 0 0 0.00175579 0.0004 0.0526561 2.012 +14 1.62 0 0 3.78111 1.00507 0.697028 2.19727 +15 1.74 0 0 0.0891761 1.0324 1.47939 2.65087 +16 1.86 0 0 0.258879 1.12307 1.31357 3.11107 +17 1.98 0 0 0.547465 1.34033 0.778689 3.4202 +18 2.1 0 0 0.913219 1.748 0.445036 3.61893 +19 2.22 0 0 1.17666 2.335 0.280275 3.7588 +20 2.34 0 0 1.32397 3.0688 0.200928 3.8702 +21 2.46 0.0344041 0.0105333 1.298 3.86387 0.19965 3.99253 +22 2.58 0.933215 0.3248 1.14238 4.63353 0.260351 4.168 +23 2.7 2.69772 1.31973 0.918695 5.3114 0.409066 4.46993 +24 2.82 2.69973 2.40587 0.788843 5.94633 0.622485 4.97113 +25 2.94 1.68742 3.14373 0.716931 6.57353 0.921309 5.7774 +26 3.06 1.17854 3.702 0.725122 7.26073 1.28872 6.99913 +27 3.18 0.877821 4.15107 0.783927 8.06307 1.52077 8.55613 +28 3.3 0.823134 4.60453 0.856914 9.00753 1.55623 10.2719 +29 3.42 0.848865 5.1068 0.944321 10.1254 1.42361 11.9577 +30 3.54 0.859179 5.65147 1.02168 11.4212 1.28943 13.5937 +31 3.66 0.902739 6.2632 1.1038 12.9177 1.14738 15.1497 +32 3.78 0.926027 6.93253 1.1595 14.5944 1.0656 16.6912 +33 3.9 0.958993 7.6704 1.17188 16.3983 0.99537 18.2239 +34 4.02 0.998828 8.48693 1.14666 18.2737 0.993965 19.8501 +35 4.14 1.04388 9.392 1.10034 20.1824 0.968649 21.5309 +36 4.26 1.06085 10.3659 1.0577 22.125 0.960389 23.2954 +37 4.38 1.07881 11.4128 1.03302 24.1307 0.96849 25.1764 +38 4.5 1.08582 12.5251 1.01926 26.2195 0.952324 27.1287 +39 4.62 1.10128 13.7141 1.01049 28.4023 0.950238 29.1821 +40 4.74 1.08014 14.9417 1.00533 30.6883 0.95441 31.3529 +41 4.86 1.06986 16.22 1.00062 33.0801 0.95827 33.6443 +42 4.98 1.03848 17.5228 0.984535 35.5512 0.980463 36.106 +43 5.1 0.978536 18.8103 0.979628 38.1299 0.98282 38.6939 +44 5.22 0.971985 20.15 0.961821 40.7822 1.01254 41.4871 +45 5.34 0.94275 21.5099 0.957683 43.5459 1.02253 44.4389 +46 5.46 0.91839 22.8948 0.956334 46.4312 1.01667 47.5073 +47 5.58 0.913178 24.3331 0.97006 49.4879 1.02157 50.7274 +48 5.7 0.917321 25.8407 0.98508 52.7269 1.00299 54.0264 +49 5.82 0.906654 27.3941 0.985116 56.1039 0.993109 57.4319 +50 5.94 0.926646 29.048 1.00072 59.6772 0.984428 60.9482 +51 6.06 0.976372 30.8617 1.00731 63.4209 0.983091 64.6031 +52 6.18 0.988791 32.772 1.00833 67.3182 0.970493 68.3554 +53 6.3 1.01384 34.8075 1.0079 71.3666 0.975255 72.274 +54 6.42 1.02791 36.9505 1.00939 75.5769 0.983508 76.3777 +55 6.54 1.03645 39.1929 1.00148 79.9119 0.990828 80.668 +56 6.66 1.04864 41.5457 0.998046 84.3919 0.993913 85.131 +57 6.78 1.03771 43.9587 0.997997 89.0347 0.998581 89.778 +58 6.9 1.04218 46.4685 0.993391 93.821 1.00659 94.6295 +59 7.02 1.05285 49.0931 1.00509 98.8336 1.01027 99.6697 +60 7.14 1.02748 51.7427 0.998338 103.984 1.01201 104.893 +61 7.26 1.0231 54.4704 0.998866 109.312 1.0124 110.295 +62 7.38 1.01372 57.2632 1.00397 114.846 1.0199 115.918 +63 7.5 0.988947 60.0771 1.00531 120.569 1.02265 121.741 +64 7.62 0.980062 62.9556 1.00466 126.472 1.01237 127.692 +65 7.74 0.989464 65.954 1.00649 132.574 1.00737 133.802 +66 7.86 0.989093 69.0449 1.00774 138.875 1.00819 140.107 +67 7.98 0.98097 72.2048 1.00692 145.364 0.999231 146.549 +68 8.1 0.977431 75.4487 1.00046 152.007 1.00085 153.196 +69 8.22 0.985577 78.8172 1.00522 158.88 0.995709 160.007 +70 8.34 0.992739 82.31 1.00494 165.954 0.989474 166.974 +71 8.46 0.991994 85.9013 0.997194 173.177 0.993918 174.176 +72 8.58 1.00368 89.6388 0.998087 180.612 0.989104 181.547 +73 8.7 1.0116 93.5119 0.998012 188.257 0.990205 189.134 +74 8.82 1.00751 97.4764 0.991686 196.064 0.989992 196.931 +75 8.94 1.00977 101.559 1.00219 204.17 0.994295 204.976 +76 9.06 0.999123 105.707 0.994424 212.431 0.997422 213.264 +77 9.18 0.998916 109.965 0.994158 220.909 0.999422 221.79 +78 9.3 0.994577 114.316 0.996797 229.634 1.00194 230.563 +79 9.42 1.00825 118.842 0.999476 238.609 0.999165 239.538 +80 9.54 0.998167 123.437 1.0022 247.84 1.00643 248.811 +81 9.66 0.997363 128.145 0.999346 257.277 1.00494 258.304 +82 9.78 1.0017 132.991 0.998169 266.939 1.00407 268.026 +83 9.9 1.00266 137.962 0.999727 276.855 1.00037 277.952 +84 10.02 0.997976 143.03 1.00404 287.057 1.00406 288.157 +85 10.14 0.999388 148.228 1.00641 297.529 1.00094 298.576 +86 10.26 0.999911 153.552 1.00311 308.215 0.999732 309.229 +87 10.38 1.00403 159.024 0.997204 319.088 0.999567 320.132 +88 10.5 1.00586 164.634 1.00433 330.294 0.997524 331.265 +89 10.62 1.00479 170.366 1.00278 341.739 0.999381 342.676 +90 10.74 1.0057 176.234 1.00313 353.449 0.999143 354.343 +91 10.86 0.99951 182.197 1.00108 365.397 1.00255 366.313 +92 10.98 1.004 188.319 1.00128 377.613 0.998276 378.496 +93 11.1 1.0075 194.599 0.996323 390.036 1.00332 391.011 +94 11.22 0.998232 200.955 0.997973 402.75 1.00385 403.804 +95 11.34 0.99788 207.446 0.996466 415.718 1.00156 416.842 +96 11.46 0.994593 214.053 0.999307 428.999 0.999586 430.132 +97 11.58 0.998619 220.827 0.999303 442.56 0.998194 443.682 +98 11.7 0.993817 227.708 0.99877 456.397 0.9981 457.514 +99 11.82 1.00212 234.79 1.00325 470.581 0.994609 471.581 +100 11.94 0.999696 241.999 0.999589 485.003 0.998572 485.993 diff --git a/examples/reax/README b/examples/reax/README index fe9d33df94..e839f0ea99 100644 --- a/examples/reax/README +++ b/examples/reax/README @@ -1,12 +1,8 @@ This directory contains input files for two short ReaxFF simulations (RDX and TATB crystals) using the ReaxFF parameterization developed for nitramines. The parameter file ffield.reax is the same as that in -subdirectory RDX (see below). Input files for both pair_style reax and -pair_style reax/c are provided. - -In addition, each subdirectory contains validated parameter files for -a particular published version of ReaxFF. In all cases, the examples -use pair_style reax/c. +subdirectory RDX (see below). In addition, each subdirectory contains +validated parameter files for a particular published version of ReaxFF. Disclaimer: Using these force fields for systems they have not been explicitly trained against may produce unrealistic results. Please diff --git a/examples/reax/in.reax.rdx b/examples/reax/in.reaxc.rdx-shielded similarity index 68% rename from examples/reax/in.reax.rdx rename to examples/reax/in.reaxc.rdx-shielded index 768b8e4546..3354b92eab 100644 --- a/examples/reax/in.reax.rdx +++ b/examples/reax/in.reaxc.rdx-shielded @@ -1,16 +1,15 @@ # ReaxFF potential for RDX system +# this run is equivalent to reax/in.reax.rdx units real atom_style charge read_data data.rdx -# reax args: hbcut hbnewflag tripflag precision +pair_style reax/c control.reax_c.rdx +pair_coeff * * ffield.reax C H O N -pair_style reax 6.0 1 1 1.0e-6 -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax +compute reax all pair reax/c variable eb equal c_reax[1] variable ea equal c_reax[2] @@ -31,15 +30,16 @@ neighbor 2.5 bin neigh_modify every 10 delay 0 check no fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c thermo 10 -thermo_style custom step temp epair etotal press & - v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb & - v_et v_eco v_ew v_ep v_efi v_eqeq +thermo_style custom step temp epair etotal press & + v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa & + v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq timestep 1.0 -#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs +#dump 1 all atom 10 dump.reaxc.rdx #dump 2 all image 25 image.*.jpg type type & # axes yes 0.8 0.02 view 60 -30 diff --git a/examples/reax/in.reax.tatb b/examples/reax/in.reaxc.tatb-shielded similarity index 72% rename from examples/reax/in.reax.tatb rename to examples/reax/in.reaxc.tatb-shielded index a9a4cd9e5e..2ff4d34f7a 100644 --- a/examples/reax/in.reax.tatb +++ b/examples/reax/in.reaxc.tatb-shielded @@ -1,15 +1,15 @@ # ReaxFF potential for TATB system +# this run is equivalent to reax/in.reax.tatb, units real atom_style charge read_data data.tatb -# reax args: hbcut hbnewflag tripflag precision -pair_style reax 6.0 1 1 1.0e-6 -pair_coeff * * ffield.reax 1 2 3 4 +pair_style reax/c control.reax_c.tatb +pair_coeff * * ffield.reax C H O N -compute reax all pair reax +compute reax all pair reax/c variable eb equal c_reax[1] variable ea equal c_reax[2] @@ -30,6 +30,8 @@ neighbor 2.5 bin neigh_modify delay 0 every 5 check no fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c +fix 4 all reax/c/bonds 5 bonds.reaxc thermo 5 thermo_style custom step temp epair etotal press & @@ -38,7 +40,7 @@ thermo_style custom step temp epair etotal press & timestep 0.0625 -#dump 1 all custom 100 dump.reax.tatb id type q x y z +#dump 1 all custom 100 dump.reaxc.tatb id type q x y z #dump 2 all image 5 image.*.jpg type type & # axes yes 0.8 0.02 view 60 -30 @@ -48,6 +50,6 @@ timestep 0.0625 # axes yes 0.8 0.02 view 60 -30 #dump_modify 3 pad 3 -fix 2 all reax/bonds 25 bonds.reax.tatb +fix 3 all reax/c/species 1 5 5 species.tatb run 25 diff --git a/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1 b/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1 new file mode 100644 index 0000000000..9e991a5d6e --- /dev/null +++ b/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.1 @@ -0,0 +1,116 @@ +LAMMPS (4 Jan 2019) +# ReaxFF potential for RDX system +# this run is equivalent to reax/in.reax.rdx + +units real + +atom_style charge +read_data data.rdx + orthogonal box = (35 35 35) to (48 48 48) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 21 atoms + +pair_style reax/c control.reax_c.rdx +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reax/c + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxc.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.54 | 15.54 | 15.54 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79939 0 168.88404 + 10 1288.6115 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.1252289 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934 + 20 538.95832 -1942.7037 -1910.5731 -10725.665 -2803.7395 7.9078296 0.077926657 0 81.61005 0.22951928 -57.5571 0 30.331204 -10.178049 878.99014 -159.69088 0 89.31512 + 30 463.09535 -1933.5765 -1905.9685 -33255.521 -2749.8591 -8.0154561 0.027628873 0 81.62739 0.11972409 -50.262289 0 20.820315 -9.6327029 851.88723 -149.49502 0 79.205749 + 40 885.49232 -1958.9126 -1906.1229 -4814.704 -2795.644 9.1506683 0.13747502 0 70.947988 0.2436053 -57.862679 0 19.076499 -11.141216 873.73896 -159.99392 0 92.434085 + 50 861.16622 -1954.4599 -1903.1204 -1896.7878 -2784.8448 3.8269901 0.15793272 0 79.851828 3.3492155 -78.066128 0 32.628996 -7.9565333 872.81832 -190.98567 0 114.75995 + 60 1167.7852 -1971.843 -1902.2241 -3482.6875 -2705.8632 -17.121673 0.22749075 0 44.507672 7.856086 -74.788945 0 16.256491 -4.6046463 835.83056 -188.33693 0 114.19414 + 70 1439.997 -1989.3024 -1903.4553 23845.434 -2890.7895 31.958869 0.26671726 0 85.758681 3.1803462 -71.002898 0 24.35711 -10.311314 905.86781 -175.38471 0 106.79648 + 80 502.39629 -1930.7545 -1900.8035 -20356.384 -2703.8111 -18.66263 0.11286065 0 99.804114 2.0329076 -76.171338 0 19.23692 -6.2786691 826.47429 -166.03132 0 92.539464 + 90 749.08722 -1946.9837 -1902.3259 17798.557 -2863.7579 42.068808 0.24338058 0 96.181716 0.96183793 -69.955449 0 24.615308 -11.58277 903.68837 -190.13841 0 120.6914 + 100 1109.6997 -1968.5874 -1902.4313 -4490.2776 -2755.896 -7.1232734 0.21757686 0 61.806176 7.0827207 -75.645383 0 20.114879 -6.2371839 863.56324 -198.56967 0 122.09951 +Loop time of 0.657427 on 1 procs for 100 steps with 21 atoms + +Performance: 13.142 ns/day, 1.826 hours/ns, 152.108 timesteps/s +99.3% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.59308 | 0.59308 | 0.59308 | 0.0 | 90.21 +Neigh | 0.020665 | 0.020665 | 0.020665 | 0.0 | 3.14 +Comm | 0.0015757 | 0.0015757 | 0.0015757 | 0.0 | 0.24 +Output | 0.00039387 | 0.00039387 | 0.00039387 | 0.0 | 0.06 +Modify | 0.04156 | 0.04156 | 0.04156 | 0.0 | 6.32 +Other | | 0.000154 | | | 0.02 + +Nlocal: 21 ave 21 max 21 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 546 ave 546 max 546 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1096 ave 1096 max 1096 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 1306 ave 1306 max 1306 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1306 +Ave neighs/atom = 62.1905 +Neighbor list builds = 10 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4 b/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4 new file mode 100644 index 0000000000..1492865c17 --- /dev/null +++ b/examples/reax/log.4Jan19.reaxc.rdx-shielded.g++.4 @@ -0,0 +1,116 @@ +LAMMPS (4 Jan 2019) +# ReaxFF potential for RDX system +# this run is equivalent to reax/in.reax.rdx + +units real + +atom_style charge +read_data data.rdx + orthogonal box = (35 35 35) to (48 48 48) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 21 atoms + +pair_style reax/c control.reax_c.rdx +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reax/c + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify every 10 delay 0 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c + +thermo 10 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 1.0 + +#dump 1 all atom 10 dump.reaxc.rdx + +#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +run 100 +Neighbor list info ... + update every 10 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 3 3 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.62 | 12.08 | 13.84 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -1884.3081 -1884.3081 27186.178 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79987 0 168.88452 + 10 1288.6116 -1989.6644 -1912.8422 -19456.355 -2734.6769 -15.60722 0.2017796 0 54.629559 3.1252284 -77.7067 0 14.933902 -5.8108544 843.92073 -180.43321 0 107.75934 + 20 538.95818 -1942.7037 -1910.5731 -10725.629 -2803.7394 7.9078295 0.077926694 0 81.61005 0.22951941 -57.557106 0 30.331206 -10.178049 878.9901 -159.68969 0 89.313929 + 30 463.09529 -1933.5765 -1905.9685 -33255.529 -2749.859 -8.0154758 0.027628845 0 81.627406 0.1197241 -50.26229 0 20.82031 -9.6327013 851.88715 -149.49497 0 79.205706 + 40 885.49462 -1958.9125 -1906.1227 -4814.6528 -2795.6439 9.1506212 0.13747486 0 70.94804 0.24360501 -57.862675 0 19.076509 -11.141214 873.7389 -159.99391 0 92.434076 + 50 861.16112 -1954.4601 -1903.121 -1896.6704 -2784.8452 3.8270543 0.15793292 0 79.851662 3.3492078 -78.066133 0 32.628979 -7.9565431 872.81857 -190.9857 0 114.75999 + 60 1167.7837 -1971.8434 -1902.2245 -3482.8961 -2705.8635 -17.121601 0.22749083 0 44.507696 7.8559922 -74.789025 0 16.256492 -4.6046625 835.83053 -188.33688 0 114.19412 + 70 1439.9917 -1989.3024 -1903.4555 23845.887 -2890.7894 31.958677 0.26671714 0 85.758424 3.1804092 -71.002955 0 24.357221 -10.311284 905.86805 -175.38496 0 106.7967 + 80 502.39695 -1930.7548 -1900.8039 -20356.331 -2703.8113 -18.662598 0.11286102 0 99.803743 2.0329429 -76.171299 0 19.236922 -6.2786652 826.4744 -166.03139 0 92.539525 + 90 749.08478 -1946.984 -1902.3264 17798.605 -2863.7581 42.068587 0.24338052 0 96.181622 0.96184063 -69.955519 0 24.615456 -11.582749 903.68853 -190.13827 0 120.69126 + 100 1109.6952 -1968.5879 -1902.4321 -4490.2728 -2755.8985 -7.1225966 0.21757682 0 61.805902 7.0826502 -75.64544 0 20.115369 -6.2372513 863.56451 -198.56956 0 122.09944 +Loop time of 0.634333 on 4 procs for 100 steps with 21 atoms + +Performance: 13.621 ns/day, 1.762 hours/ns, 157.646 timesteps/s +93.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.53395 | 0.5352 | 0.53805 | 0.2 | 84.37 +Neigh | 0.0088253 | 0.012023 | 0.016203 | 2.4 | 1.90 +Comm | 0.0051677 | 0.0081 | 0.0093861 | 1.9 | 1.28 +Output | 0.00049353 | 0.00054371 | 0.00058222 | 0.0 | 0.09 +Modify | 0.074155 | 0.078299 | 0.081472 | 0.9 | 12.34 +Other | | 0.0001715 | | | 0.03 + +Nlocal: 5.25 ave 15 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 355.5 ave 432 max 282 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 298.75 ave 822 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +FullNghs: 326.5 ave 927 max 0 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 1306 +Ave neighs/atom = 62.1905 +Neighbor list builds = 10 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:00 diff --git a/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1 b/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1 new file mode 100644 index 0000000000..86dc1c323a --- /dev/null +++ b/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.1 @@ -0,0 +1,114 @@ +LAMMPS (4 Jan 2019) +# ReaxFF potential for TATB system +# this run is equivalent to reax/in.reax.tatb, + +units real + +atom_style charge +read_data data.tatb + triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 384 atoms + +pair_style reax/c control.reax_c.tatb +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reax/c + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c +fix 4 all reax/c/bonds 5 bonds.reaxc + +thermo 5 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxc.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reax/c/species 1 5 5 species.tatb + +run 25 +Neighbor list info ... + update every 5 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 169.6 | 169.6 | 169.6 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -44760.998 -44760.998 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 + 5 0.61603942 -44761.698 -44760.994 8934.628 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 + 10 2.3525549 -44763.227 -44760.541 12288.614 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9684 0 6381.7061 + 15 4.9013311 -44766.36 -44760.764 17716.982 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2449 0 6370.4111 + 20 7.8294673 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5142 0 6355.2654 + 25 10.697904 -44772.904 -44760.691 34232.821 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3541 0 6336.8349 +Loop time of 7.80985 on 1 procs for 25 steps with 384 atoms + +Performance: 0.017 ns/day, 1388.418 hours/ns, 3.201 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.003 | 5.003 | 5.003 | 0.0 | 64.06 +Neigh | 1.1164 | 1.1164 | 1.1164 | 0.0 | 14.29 +Comm | 0.0065806 | 0.0065806 | 0.0065806 | 0.0 | 0.08 +Output | 0.00029969 | 0.00029969 | 0.00029969 | 0.0 | 0.00 +Modify | 1.6831 | 1.6831 | 1.6831 | 0.0 | 21.55 +Other | | 0.0004976 | | | 0.01 + +Nlocal: 384 ave 384 max 384 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7559 ave 7559 max 7559 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 286828 ave 286828 max 286828 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 336304 ave 336304 max 336304 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 336304 +Ave neighs/atom = 875.792 +Neighbor list builds = 5 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:08 diff --git a/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4 b/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4 new file mode 100644 index 0000000000..7dc9867f5a --- /dev/null +++ b/examples/reax/log.4Jan19.reaxc.tatb-shielded.g++.4 @@ -0,0 +1,114 @@ +LAMMPS (4 Jan 2019) +# ReaxFF potential for TATB system +# this run is equivalent to reax/in.reax.tatb, + +units real + +atom_style charge +read_data data.tatb + triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 384 atoms + +pair_style reax/c control.reax_c.tatb +pair_coeff * * ffield.reax C H O N +Reading potential file ffield.reax with DATE: 2010-02-19 + +compute reax all pair reax/c + +variable eb equal c_reax[1] +variable ea equal c_reax[2] +variable elp equal c_reax[3] +variable emol equal c_reax[4] +variable ev equal c_reax[5] +variable epen equal c_reax[6] +variable ecoa equal c_reax[7] +variable ehb equal c_reax[8] +variable et equal c_reax[9] +variable eco equal c_reax[10] +variable ew equal c_reax[11] +variable ep equal c_reax[12] +variable efi equal c_reax[13] +variable eqeq equal c_reax[14] + +neighbor 2.5 bin +neigh_modify delay 0 every 5 check no + +fix 1 all nve +fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c +fix 4 all reax/c/bonds 5 bonds.reaxc + +thermo 5 +thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + +timestep 0.0625 + +#dump 1 all custom 100 dump.reaxc.tatb id type q x y z + +#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 + +#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 + +fix 3 all reax/c/species 1 5 5 species.tatb + +run 25 +Neighbor list info ... + update every 5 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12.5 + ghost atom cutoff = 12.5 + binsize = 6.25, bins = 5 4 3 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair reax/c, perpetual + attributes: half, newton off, ghost + pair build: half/bin/newtoff/ghost + stencil: half/ghost/bin/3d/newtoff + bin: standard + (2) fix qeq/shielded, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 113 | 113 | 113 Mbytes +Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq + 0 0 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0277 + 5 0.61603968 -44761.698 -44760.994 8934.6336 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 + 10 2.3525543 -44763.227 -44760.541 12288.588 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9756 0 6381.7133 + 15 4.9013233 -44766.36 -44760.764 17716.934 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2627 0 6370.4289 + 20 7.8294615 -44769.686 -44760.747 25205.586 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4958 0 6355.2471 + 25 10.697919 -44772.904 -44760.691 34232.898 -61069.308 490.25887 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3285 0 6336.8093 +Loop time of 4.34178 on 4 procs for 25 steps with 384 atoms + +Performance: 0.031 ns/day, 771.872 hours/ns, 5.758 timesteps/s +96.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.1756 | 3.1763 | 3.1771 | 0.0 | 73.16 +Neigh | 0.58917 | 0.59661 | 0.6035 | 0.9 | 13.74 +Comm | 0.0088837 | 0.010178 | 0.011116 | 0.8 | 0.23 +Output | 0.00036407 | 0.0019013 | 0.003552 | 2.7 | 0.04 +Modify | 0.54882 | 0.55637 | 0.56413 | 0.8 | 12.81 +Other | | 0.0004123 | | | 0.01 + +Nlocal: 96 ave 96 max 96 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Nghost: 5118 ave 5118 max 5118 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +Neighs: 79754 ave 79754 max 79754 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 84076 ave 84076 max 84076 min +Histogram: 4 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 336304 +Ave neighs/atom = 875.792 +Neighbor list builds = 5 +Dangerous builds not checked + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:04 diff --git a/examples/reax/log.8March18.reax.rdx.g++.1 b/examples/reax/log.8March18.reax.rdx.g++.1 deleted file mode 100644 index c2edc5d51f..0000000000 --- a/examples/reax/log.8March18.reax.rdx.g++.1 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for RDX system - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 21 atoms - -# reax args: hbcut hbnewflag tripflag precision - -pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 3 3 3 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair reax, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.278 | 3.278 | 3.278 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1885.1269 -1885.1269 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79973 0 168.8842 - 10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.02023 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.5115 - 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134186 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574159 - 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179958 0.049322453 0 78.853173 0.13604393 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.86177 - 40 647.45528 -1951.1994 -1912.6006 -5883.713 -2798.3556 17.334814 0.15102862 0 63.235117 0.18070924 -54.598957 0 17.325007 -12.052278 883.0167 -164.21335 0 96.777424 - 50 716.38088 -1949.4735 -1906.7656 5473.1969 -2800.9309 9.2056861 0.15413274 0 85.371466 3.2986127 -78.253597 0 34.861774 -8.553123 882.01431 -193.85254 0 117.21068 - 60 1175.2705 -1975.961 -1905.8958 -1939.4966 -2726.5816 -11.651996 0.24296786 0 48.320654 7.1799691 -75.363638 0 16.520127 -4.8869441 844.75401 -194.23297 0 119.73841 - 70 1156.701 -1975.3497 -1906.3916 24628.304 -2880.5225 25.652501 0.26894311 0 83.724852 7.1049152 -68.70096 0 24.750735 -8.6338267 911.20079 -183.40562 0 113.21047 - 80 840.23677 -1955.4769 -1905.3851 -17731.334 -2755.7299 -8.0167723 0.1386797 0 86.147417 2.2387319 -76.945843 0 23.595869 -7.260968 853.63487 -167.88288 0 94.603961 - 90 365.79122 -1926.4061 -1904.599 898.38479 -2842.1832 47.368107 0.23109002 0 92.288071 0.38031213 -61.361485 0 18.476336 -12.25546 900.24233 -186.48046 0 116.88827 - 100 801.32158 -1953.418 -1905.6462 -2417.6887 -2802.7247 4.6676477 0.18046575 0 76.729987 5.4177322 -77.102566 0 24.997175 -7.7554074 898.67337 -196.89114 0 120.38946 -Loop time of 0.463306 on 1 procs for 100 steps with 21 atoms - -Performance: 18.649 ns/day, 1.287 hours/ns, 215.840 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.46143 | 0.46143 | 0.46143 | 0.0 | 99.60 -Neigh | 0.00087953 | 0.00087953 | 0.00087953 | 0.0 | 0.19 -Comm | 0.00042653 | 0.00042653 | 0.00042653 | 0.0 | 0.09 -Output | 0.00034237 | 0.00034237 | 0.00034237 | 0.0 | 0.07 -Modify | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.02 -Other | | 0.000124 | | | 0.03 - -Nlocal: 21 ave 21 max 21 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 546 ave 546 max 546 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1106 ave 1106 max 1106 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 1106 -Ave neighs/atom = 52.6667 -Neighbor list builds = 10 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reax.rdx.g++.4 b/examples/reax/log.8March18.reax.rdx.g++.4 deleted file mode 100644 index 9526e25661..0000000000 --- a/examples/reax/log.8March18.reax.rdx.g++.4 +++ /dev/null @@ -1,107 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for RDX system - -units real - -atom_style charge -read_data data.rdx - orthogonal box = (35 35 35) to (48 48 48) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 21 atoms - -# reax args: hbcut hbnewflag tripflag precision - -pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify every 10 delay 0 check no - -fix 1 all nve - -thermo 10 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 1.0 - -#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs - -#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -run 100 -Neighbor list info ... - update every 10 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 3 3 3 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair reax, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.262 | 3.36 | 3.647 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88428 - 10 1281.7558 -1989.1322 -1912.7187 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51152 - 20 516.83079 -1941.677 -1910.8655 -12525.412 -2801.8626 7.410797 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78695 -158.93385 0 88.574168 - 30 467.26411 -1940.978 -1913.1215 -35957.489 -2755.021 -6.9179959 0.049322449 0 78.853173 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861765 - 40 647.45479 -1951.1995 -1912.6007 -5883.7199 -2798.3556 17.334805 0.15102868 0 63.235116 0.18070946 -54.59897 0 17.32501 -12.052277 883.0166 -164.21339 0 96.777473 - 50 716.37927 -1949.466 -1906.7582 5473.2486 -2800.9309 9.2056758 0.15413278 0 85.37143 3.2986099 -78.253596 0 34.861773 -8.5531243 882.01424 -193.85223 0 117.21791 - 60 1175.2698 -1975.9612 -1905.896 -1939.5206 -2726.5818 -11.651942 0.24296793 0 48.320679 7.1799538 -75.36365 0 16.520134 -4.8869515 844.75405 -194.23289 0 119.7383 - 70 1156.6963 -1975.3494 -1906.3915 24628.423 -2880.5221 25.65242 0.26894312 0 83.724787 7.1049615 -68.700925 0 24.750729 -8.6338123 911.2006 -183.40591 0 113.21091 - 80 840.238 -1955.4788 -1905.387 -17731.371 -2755.7301 -8.0167357 0.13868007 0 86.147246 2.2387405 -76.945868 0 23.595868 -7.2609697 853.6349 -167.88312 0 94.602512 - 90 365.78645 -1926.4072 -1904.6004 898.36945 -2842.1831 47.368307 0.23108998 0 92.288039 0.38031101 -61.361464 0 18.476388 -12.255481 900.24216 -186.48066 0 116.88716 - 100 801.31322 -1953.4165 -1905.6452 -2417.2041 -2802.7247 4.6678077 0.18046498 0 76.730367 5.4176812 -77.102592 0 24.9973 -7.7554425 898.6732 -196.89097 0 120.39043 -Loop time of 0.404551 on 4 procs for 100 steps with 21 atoms - -Performance: 21.357 ns/day, 1.124 hours/ns, 247.188 timesteps/s -97.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.2191 | 0.28038 | 0.39839 | 13.2 | 69.31 -Neigh | 5.8651e-05 | 0.00025928 | 0.00062203 | 0.0 | 0.06 -Comm | 0.0046599 | 0.12307 | 0.1845 | 19.9 | 30.42 -Output | 0.00055337 | 0.00062728 | 0.00071192 | 0.0 | 0.16 -Modify | 5.3167e-05 | 7.844e-05 | 0.00010109 | 0.0 | 0.02 -Other | | 0.0001363 | | | 0.03 - -Nlocal: 5.25 ave 15 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 -Nghost: 355.5 ave 432 max 282 min -Histogram: 1 0 0 0 1 1 0 0 0 1 -Neighs: 301.25 ave 827 max 0 min -Histogram: 1 0 2 0 0 0 0 0 0 1 - -Total # of neighbors = 1205 -Ave neighs/atom = 57.381 -Neighbor list builds = 10 -Dangerous builds not checked -Total wall time: 0:00:00 diff --git a/examples/reax/log.8March18.reax.tatb.g++.1 b/examples/reax/log.8March18.reax.tatb.g++.1 deleted file mode 100644 index 53d77cd1da..0000000000 --- a/examples/reax/log.8March18.reax.tatb.g++.1 +++ /dev/null @@ -1,103 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for TATB system - -units real - -atom_style charge -read_data data.tatb - triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 384 atoms - -# reax args: hbcut hbnewflag tripflag precision -pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve - -thermo 5 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reax.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 2 all reax/bonds 25 bonds.reax.tatb - -run 25 -Neighbor list info ... - update every 5 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 5 4 3 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair reax, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.764 | 7.764 | 7.764 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231 - 5 0.63682806 -44767.737 -44767.01 8391.5964 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2728 0 6388.8127 - 10 2.4306958 -44769.409 -44766.634 11717.376 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0693 0 6381.7942 - 15 5.0590493 -44772.631 -44766.855 17125.067 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28962 -1566.5961 252.97781 -654.93836 18835.335 -8719.3013 0 6370.4551 - 20 8.067859 -44775.936 -44766.725 24620.627 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3748 0 6355.1614 - 25 10.975538 -44777.233 -44764.702 34381.173 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.23109 -1582.8552 253.88696 -653.46042 18790.855 -8683.8691 0 6336.3409 -Loop time of 7.80129 on 1 procs for 25 steps with 384 atoms - -Performance: 0.017 ns/day, 1386.896 hours/ns, 3.205 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 7.7384 | 7.7384 | 7.7384 | 0.0 | 99.19 -Neigh | 0.058615 | 0.058615 | 0.058615 | 0.0 | 0.75 -Comm | 0.0022428 | 0.0022428 | 0.0022428 | 0.0 | 0.03 -Output | 0.00033212 | 0.00033212 | 0.00033212 | 0.0 | 0.00 -Modify | 0.0013618 | 0.0013618 | 0.0013618 | 0.0 | 0.02 -Other | | 0.0003309 | | | 0.00 - -Nlocal: 384 ave 384 max 384 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 7559 ave 7559 max 7559 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 286828 ave 286828 max 286828 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 286828 -Ave neighs/atom = 746.948 -Neighbor list builds = 5 -Dangerous builds not checked -Total wall time: 0:00:08 diff --git a/examples/reax/log.8March18.reax.tatb.g++.4 b/examples/reax/log.8March18.reax.tatb.g++.4 deleted file mode 100644 index e3acac9d0e..0000000000 --- a/examples/reax/log.8March18.reax.tatb.g++.4 +++ /dev/null @@ -1,103 +0,0 @@ -LAMMPS (8 Mar 2018) - using 1 OpenMP thread(s) per MPI task -# ReaxFF potential for TATB system - -units real - -atom_style charge -read_data data.tatb - triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 384 atoms - -# reax args: hbcut hbnewflag tripflag precision -pair_style reax 6.0 1 1 1.0e-6 -WARNING: The pair_style reax command is unsupported. Please switch to pair_style reax/c instead (../pair_reax.cpp:49) -pair_coeff * * ffield.reax 1 2 3 4 - -compute reax all pair reax - -variable eb equal c_reax[1] -variable ea equal c_reax[2] -variable elp equal c_reax[3] -variable emol equal c_reax[4] -variable ev equal c_reax[5] -variable epen equal c_reax[6] -variable ecoa equal c_reax[7] -variable ehb equal c_reax[8] -variable et equal c_reax[9] -variable eco equal c_reax[10] -variable ew equal c_reax[11] -variable ep equal c_reax[12] -variable efi equal c_reax[13] -variable eqeq equal c_reax[14] - -neighbor 2.5 bin -neigh_modify delay 0 every 5 check no - -fix 1 all nve - -thermo 5 -thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - -timestep 0.0625 - -#dump 1 all custom 100 dump.reax.tatb id type q x y z - -#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 3 - -#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 3 - -fix 2 all reax/bonds 25 bonds.reax.tatb - -run 25 -Neighbor list info ... - update every 5 steps, delay 0 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12.5 - ghost atom cutoff = 12.5 - binsize = 6.25, bins = 5 4 3 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair reax, perpetual - attributes: half, newton off - pair build: half/bin/newtoff - stencil: half/bin/3d/newtoff - bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes -Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq - 0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231 - 5 0.63682727 -44767.816 -44767.089 8391.1708 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3973 0 6388.8581 - 10 2.4306941 -44769.405 -44766.63 11717.306 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.08 0 6381.8083 - 15 5.0590444 -44772.6 -44766.824 17125.207 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.2653 0 6370.4505 - 20 8.0678523 -44775.983 -44766.772 24620.114 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.5228 0 6355.2629 - 25 10.975532 -44777.234 -44764.704 34381.065 -61068.889 490.53151 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.898 0 6336.3682 -Loop time of 3.74388 on 4 procs for 25 steps with 384 atoms - -Performance: 0.036 ns/day, 665.579 hours/ns, 6.678 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.478 | 3.6025 | 3.7215 | 4.8 | 96.22 -Neigh | 0.012731 | 0.01299 | 0.013174 | 0.2 | 0.35 -Comm | 0.0073411 | 0.12653 | 0.25119 | 25.4 | 3.38 -Output | 0.00050354 | 0.00081849 | 0.0011628 | 0.0 | 0.02 -Modify | 0.00049281 | 0.00082356 | 0.001157 | 0.0 | 0.02 -Other | | 0.0002663 | | | 0.01 - -Nlocal: 96 ave 96 max 96 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 5118 ave 5118 max 5118 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 79754 ave 79754 max 79754 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 319016 -Ave neighs/atom = 830.771 -Neighbor list builds = 5 -Dangerous builds not checked -Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.1 b/examples/rigid/log.20Apr18.rigid.poems.g++.1 deleted file mode 100644 index 0cba72a2dd..0000000000 --- a/examples/rigid/log.20Apr18.rigid.poems.g++.1 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (20 Apr 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384277 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184717 - 1150 20849.582 206.01695 0 3680.9472 -0.86699146 - 1200 21815.003 45.317414 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064078 - 1300 20780.781 217.36506 0 3680.8286 6.0538615 - 1350 20558.971 254.36482 0 3680.8601 -3.6773954 - 1400 21485.029 99.812918 0 3680.6511 -16.185473 - 1450 21771.107 52.159607 0 3680.6775 -2.4756675 - 1500 21520.948 93.503927 0 3680.3286 2.1023577 - 1550 21351.418 121.68138 0 3680.2511 5.515995 - 1600 20778.805 216.92177 0 3680.0559 15.089187 - 1650 21477.638 100.21836 0 3679.8247 -1.1045739 - 1700 18501.339 596.47922 0 3680.0357 -15.679682 - 1750 18563.642 587.3479 0 3681.2882 33.532211 - 1800 19110.186 494.82336 0 3679.8543 18.024046 - 1850 21364.191 119.23543 0 3679.9339 2.5291075 - 1900 20146.627 322.14849 0 3679.9197 5.7313175 - 1950 20692.671 231.25345 0 3680.0319 4.297772 - 2000 20943.905 189.11218 0 3679.7629 -22.64509 - 2050 19668.055 401.83025 0 3679.8394 3.6251438 - 2100 20280.434 299.76289 0 3679.8353 7.4807805 - 2150 19181.835 483.52621 0 3680.4987 22.62081 - 2200 21300.18 130.7021 0 3680.7322 4.710193 - 2250 20486.914 266.64414 0 3681.1299 -8.6458025 - 2300 18653.082 572.25481 0 3681.1017 -5.2636982 - 2350 21513.563 95.608298 0 3681.2021 -9.3624751 - 2400 21466.205 103.57569 0 3681.2765 -29.559707 - 2450 20100.204 332.25468 0 3682.2886 35.739592 - 2500 20764.513 221.64794 0 3682.4001 -12.46688 - 2550 20436.771 276.13128 0 3682.2598 -22.419404 - 2600 21466.252 104.57185 0 3682.2806 -10.080362 - 2650 20817.269 212.81674 0 3682.3615 5.1374497 - 2700 18565.157 588.46125 0 3682.6541 22.283866 - 2750 20780.743 218.76366 0 3682.2208 -8.0046411 - 2800 21032.22 176.82368 0 3682.1936 -7.078895 - 2850 16817.729 879.49153 0 3682.4464 33.140849 - 2900 19309.511 463.89319 0 3682.145 7.9225025 - 2950 20544.978 257.86831 0 3682.0314 2.0523059 - 3000 20616.438 246.0975 0 3682.1706 -0.2824889 - 3050 18648.596 574.37266 0 3682.4721 -5.8677065 - 3100 19147.135 490.76826 0 3681.9574 -1.9922835 - 3150 18568.022 587.36965 0 3682.0399 14.694505 - 3200 19720.841 395.38315 0 3682.1899 5.9162402 - 3250 19008.557 514.50687 0 3682.5998 -3.4702895 - 3300 21708.937 64.231264 0 3682.3874 -5.4808611 - 3350 20548.477 257.62974 0 3682.3759 9.7818301 - 3400 20508.84 264.0153 0 3682.1553 -12.578182 - 3450 18736.579 559.11222 0 3681.8754 21.920437 - 3500 21444.82 107.82706 0 3681.9638 0.093050651 - 3550 20439.241 275.31015 0 3681.8503 -3.0785302 - 3600 21547.1 90.778361 0 3681.9617 -5.9189729 - 3650 15623.305 1079.996 0 3683.8802 36.064752 - 3700 19912.452 363.09483 0 3681.8368 5.4802367 - 3750 21289.7 133.2258 0 3681.5091 -10.884642 - 3800 20214.875 312.09245 0 3681.2382 8.6419893 - 3850 19853.031 372.13835 0 3680.9769 2.6229234 - 3900 17863.409 703.8716 0 3681.1064 -1.4250404 - 3950 19926.351 359.87227 0 3680.9307 -14.60997 - 4000 17595.665 747.85423 0 3680.4651 24.228859 - 4050 18408.194 611.80934 0 3679.8416 4.4236034 - 4100 17506.503 762.1286 0 3679.8792 5.0526379 - 4150 18479.134 600.76034 0 3680.6159 -6.6523095 - 4200 18475.322 601.95797 0 3681.1783 1.3292995 - 4250 18301.378 630.34119 0 3680.5709 2.5387332 - 4300 19384.541 449.98455 0 3680.7414 5.8750989 - 4350 18717.888 561.31715 0 3680.9651 3.7948584 - 4400 18893.773 532.20993 0 3681.172 10.963539 - 4450 20269.613 302.15984 0 3680.4286 -10.145642 - 4500 19151.762 489.32407 0 3681.2845 21.695364 - 4550 19914.708 361.54065 0 3680.6587 -4.2298372 - 4600 21153.44 154.99598 0 3680.5693 2.3172078 - 4650 21021.611 176.81454 0 3680.4164 1.9128023 - 4700 21707.966 62.767734 0 3680.762 -5.2080189 - 4750 16517.674 927.53839 0 3680.484 17.329608 - 4800 21654.604 71.574174 0 3680.6749 -6.0650166 - 4850 18135.978 657.28622 0 3679.9493 5.4803307 - 4900 20389.048 282.49215 0 3680.6668 -2.8570431 - 4950 17159.074 820.81472 0 3680.6604 31.273877 - 5000 20788.159 215.88415 0 3680.5773 4.6345196 - 5050 21366.767 119.68693 0 3680.8148 -9.9482889 - 5100 20668.21 236.17655 0 3680.8782 3.8118334 - 5150 20468.573 269.83696 0 3681.2657 -26.625943 - 5200 19493.142 432.49135 0 3681.3483 -7.6677112 - 5250 19626.594 410.09767 0 3681.1967 7.3622341 - 5300 20771.914 219.12484 0 3681.1105 -7.0871793 - 5350 21152.459 155.26401 0 3680.6738 5.9030557 - 5400 21376.189 117.91075 0 3680.6088 -1.2004513 - 5450 21455.06 105.15166 0 3680.995 -9.1675471 - 5500 21227.896 143.35739 0 3681.3401 -6.646305 - 5550 21149.831 156.61404 0 3681.5858 -12.953136 - 5600 21364.198 120.94695 0 3681.6466 1.0372254 - 5650 20219.777 311.34588 0 3681.3088 6.5026316 - 5700 21163.024 154.3001 0 3681.4708 -0.47587262 - 5750 19583.077 418.40745 0 3682.2535 24.609517 - 5800 18801.324 548.79742 0 3682.3515 -12.082631 - 5850 20875.4 203.07604 0 3682.3093 -8.1191161 - 5900 20737.053 226.2734 0 3682.4489 -7.6845943 - 5950 21260.028 139.21888 0 3682.5568 -2.2977046 - 6000 19823.84 378.71803 0 3682.6914 -1.1163373 - 6050 20487.214 268.03474 0 3682.5704 4.313979 - 6100 17853.211 707.10918 0 3682.6443 16.762322 - 6150 21322.705 129.06 0 3682.8441 2.7500936 - 6200 21609.008 81.580972 0 3683.0823 0.37062555 - 6250 20364.115 289.30707 0 3683.3262 13.176034 - 6300 20201.9 316.16558 0 3683.149 -1.6318339 - 6350 21151.879 157.75018 0 3683.0634 -23.337621 - 6400 21453.129 107.45563 0 3682.9772 -0.60776225 - 6450 21105.382 165.1926 0 3682.7562 4.244932 - 6500 20746.748 224.6945 0 3682.4859 0.2929158 - 6550 20913.725 197.29847 0 3682.9194 -15.792862 - 6600 17956.374 690.52623 0 3683.2552 15.445255 - 6650 20270.609 303.60078 0 3682.0357 -0.26503277 - 6700 21442.931 109.08904 0 3682.9109 -2.8409166 - 6750 20907.994 198.30695 0 3682.9726 0.91664072 - 6800 20431.208 277.98326 0 3683.1845 -1.8537161 - 6850 20312.052 297.88656 0 3683.2285 3.1028547 - 6900 19458.401 439.97157 0 3683.0385 -4.1856293 - 6950 20507.759 264.99217 0 3682.952 -1.4597973 - 7000 20782.356 219.47456 0 3683.2006 -7.1967021 - 7050 20560.324 256.07109 0 3682.7917 -10.720013 - 7100 21652.145 74.086415 0 3682.7772 -0.61455054 - 7150 20134.823 326.40272 0 3682.2065 11.689827 - 7200 20778.071 219.16459 0 3682.1765 -1.796567 - 7250 20153.065 323.13721 0 3681.9814 -0.1215538 - 7300 19524.938 427.99711 0 3682.1534 -3.1139903 - 7350 20554.595 256.63855 0 3682.4044 10.023083 - 7400 18778.53 552.29852 0 3682.0534 -1.7145222 - 7450 18972.509 520.15393 0 3682.2388 1.4489874 - 7500 17680.668 736.20139 0 3682.9794 15.096954 - 7550 19070.785 504.65403 0 3683.1182 2.2707533 - 7600 20805.541 214.54957 0 3682.1398 -3.4306308 - 7650 18473.262 604.25322 0 3683.1301 2.2083367 - 7700 19294.016 466.99211 0 3682.6615 2.2666382 - 7750 20995.664 183.47108 0 3682.7484 -13.935938 - 7800 21042.433 175.06619 0 3682.1384 0.49855811 - 7850 19343.054 459.21955 0 3683.0618 7.9049312 - 7900 18382.898 619.01969 0 3682.8361 1.7996366 - 7950 16092.435 1000.6563 0 3682.7287 29.993154 - 8000 17551.635 757.47719 0 3682.7498 8.1753011 - 8050 20309.875 298.25877 0 3683.2379 -1.9545317 - 8100 21746.174 59.002125 0 3683.3645 -2.6980678 - 8150 21478.427 103.44202 0 3683.1799 -10.930392 - 8200 20986.729 185.46995 0 3683.2581 -14.298403 - 8250 20744.064 225.47546 0 3682.8194 -6.4982356 - 8300 19887.982 368.35069 0 3683.0143 1.5899179 - 8350 21871.414 37.899202 0 3683.1348 -2.0554107 - 8400 20002.858 348.98887 0 3682.7985 8.2963084 - 8450 21553.861 90.985193 0 3683.2953 2.8575186 - 8500 21605.143 82.347635 0 3683.2048 -4.711565 - 8550 20151.76 324.4703 0 3683.097 -8.5109459 - 8600 20564.158 255.77814 0 3683.1378 -1.3815408 - 8650 19316.602 463.61706 0 3683.0507 -2.6895635 - 8700 18157.859 656.69518 0 3683.0051 19.428927 - 8750 18752.43 557.67555 0 3683.0805 1.9765973 - 8800 20903.812 199.07408 0 3683.0428 1.9011523 - 8850 20132.963 327.56826 0 3683.0621 3.0389961 - 8900 21667.171 71.80023 0 3682.9954 -2.0042246 - 8950 20346.973 292.00907 0 3683.1712 7.5582361 - 9000 17889.448 695.59406 0 3677.1688 7.5315391 - 9050 19446.144 441.90609 0 3682.9302 5.9819228 - 9100 20384.34 285.05862 0 3682.4486 9.8610378 - 9150 20023.515 344.98587 0 3682.2384 -0.40175043 - 9200 17786.795 718.76166 0 3683.2275 10.984317 - 9250 20843.023 208.42263 0 3682.2597 -7.4709344 - 9300 21670.622 70.503925 0 3682.2742 -6.2303366 - 9350 20642.313 241.21277 0 3681.5983 4.7423898 - 9400 19228.566 476.44753 0 3681.2085 10.836639 - 9450 21215.705 146.40003 0 3682.3509 -9.091421 - 9500 21543.685 91.725901 0 3682.3401 -1.0608492 - 9550 20143.22 324.98532 0 3682.1887 -5.995164 - 9600 21234.294 142.96512 0 3682.0142 0.004838125 - 9650 21025.207 177.8801 0 3682.0813 -5.4857701 - 9700 20638.235 242.46577 0 3682.1716 -1.6014085 - 9750 18374.191 620.54322 0 3682.9084 13.864712 - 9800 19730.262 393.89083 0 3682.2679 5.7601754 - 9850 21547.855 91.283379 0 3682.5926 2.1989329 - 9900 20959.935 189.28821 0 3682.6108 2.1174676 - 9950 21191.026 150.79441 0 3682.6321 8.3829825 - 10000 20776.574 220.03769 0 3682.8 -1.8404787 -Loop time of 3.0852 on 1 procs for 10000 steps with 81 atoms - -Performance: 28004.636 tau/day, 3241.277 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.17336 | 0.17336 | 0.17336 | 0.0 | 5.62 -Neigh | 0.1094 | 0.1094 | 0.1094 | 0.0 | 3.55 -Comm | 0.010163 | 0.010163 | 0.010163 | 0.0 | 0.33 -Output | 0.0030687 | 0.0030687 | 0.0030687 | 0.0 | 0.10 -Modify | 2.7782 | 2.7782 | 2.7782 | 0.0 | 90.05 -Other | | 0.01105 | | | 0.36 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 82 ave 82 max 82 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 887 ave 887 max 887 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 887 -Ave neighs/atom = 10.9506 -Neighbor list builds = 992 -Dangerous builds = 939 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems.g++.4 b/examples/rigid/log.20Apr18.rigid.poems.g++.4 deleted file mode 100644 index e2fb6b65b6..0000000000 --- a/examples/rigid/log.20Apr18.rigid.poems.g++.4 +++ /dev/null @@ -1,338 +0,0 @@ -LAMMPS (20 Apr 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 36 45 -10 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 -1 clusters, 9 bodies, 8 joints, 81 atoms - -# 2 chains of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 37 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 -#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 217.7783 3430.3907 0 3466.6871 -2.7403788 - 50 13679.637 1404.2468 0 3684.1863 12.446066 - 100 16777.225 888.87665 0 3685.0808 -31.828677 - 150 19595.365 418.45042 0 3684.3446 40.709078 - 200 18524.188 596.47273 0 3683.8375 -0.8159371 - 250 21015.789 180.96521 0 3683.5967 -10.042469 - 300 20785.513 219.25314 0 3683.5053 2.6452719 - 350 21072.46 171.2554 0 3683.3321 7.0609024 - 400 19956.414 356.36381 0 3682.4328 19.320259 - 450 20724.42 227.73284 0 3681.8028 8.1259249 - 500 20152.578 322.71466 0 3681.4777 5.4929878 - 550 20017.022 345.29701 0 3681.4673 5.4661666 - 600 17897.743 698.72196 0 3681.6791 3.2854742 - 650 17297.758 796.60256 0 3679.5623 15.191113 - 700 18581.934 584.29715 0 3681.2861 5.1588289 - 750 21774.158 52.821062 0 3681.8474 -10.775664 - 800 21604.055 81.188546 0 3681.8644 -3.2045743 - 850 17821.483 711.53827 0 3681.7854 7.4384277 - 900 21033.292 175.98127 0 3681.5299 -16.345167 - 950 20968.166 186.59847 0 3681.2929 -2.330456 - 1000 20490.66 266.19375 0 3681.3037 11.787983 - 1050 20222.396 310.94072 0 3681.34 -8.3459539 - 1100 21321.687 127.61533 0 3681.2299 -1.2184717 - 1150 20849.582 206.01695 0 3680.9472 -0.86699147 - 1200 21815.003 45.317414 0 3681.1512 1.5988314 - 1250 18655.437 572.41453 0 3681.654 10.064078 - 1300 20780.781 217.36506 0 3680.8286 6.0538614 - 1350 20558.971 254.36483 0 3680.8601 -3.6773951 - 1400 21485.029 99.812917 0 3680.6511 -16.185473 - 1450 21771.107 52.15961 0 3680.6775 -2.4756673 - 1500 21520.948 93.503926 0 3680.3286 2.1023576 - 1550 21351.418 121.68137 0 3680.2511 5.5159947 - 1600 20778.805 216.92177 0 3680.0559 15.089188 - 1650 21477.638 100.21836 0 3679.8247 -1.1045741 - 1700 18501.339 596.4792 0 3680.0357 -15.679682 - 1750 18563.642 587.34785 0 3681.2882 33.53221 - 1800 19110.185 494.82342 0 3679.8543 18.024046 - 1850 21364.191 119.23548 0 3679.9339 2.5291079 - 1900 20146.626 322.14873 0 3679.9197 5.7313282 - 1950 20692.672 231.2533 0 3680.0319 4.2977759 - 2000 20943.904 189.11231 0 3679.7629 -22.645089 - 2050 19668.052 401.83077 0 3679.8394 3.6251598 - 2100 20280.434 299.76292 0 3679.8353 7.4807838 - 2150 19181.841 483.52513 0 3680.4987 22.620829 - 2200 21300.185 130.70136 0 3680.7321 4.7101928 - 2250 20486.897 266.64698 0 3681.1299 -8.6459184 - 2300 18653.018 572.26538 0 3681.1017 -5.2635489 - 2350 21513.576 95.606125 0 3681.202 -9.3627078 - 2400 21466.185 103.579 0 3681.2764 -29.55912 - 2450 20100.274 332.24291 0 3682.2886 35.736349 - 2500 20764.562 221.63964 0 3682.4 -12.465656 - 2550 20437.187 276.06174 0 3682.2596 -22.421308 - 2600 21466.269 104.56898 0 3682.2805 -10.080867 - 2650 20819.865 212.38395 0 3682.3615 5.1305357 - 2700 18565.57 588.39438 0 3682.656 22.28768 - 2750 20789.153 217.36229 0 3682.2211 -8.051962 - 2800 21045.639 174.58656 0 3682.193 -7.0803377 - 2850 16845.227 874.90505 0 3682.4429 32.992098 - 2900 19319.232 462.27119 0 3682.1432 7.9276373 - 2950 20558.495 255.61185 0 3682.0277 1.9151653 - 3000 20615.868 246.18886 0 3682.1668 -0.016805532 - 3050 18695.136 566.5914 0 3682.4474 -7.3528355 - 3100 19381.554 451.57712 0 3681.8361 -2.0887636 - 3150 19080.633 502.00742 0 3682.1129 5.2518182 - 3200 20969.083 187.13559 0 3681.9828 12.156446 - 3250 20474.81 269.6876 0 3682.156 1.4067779 - 3300 18836.313 542.79266 0 3682.1781 -9.1497216 - 3350 21397.694 116.27473 0 3682.557 -6.4412585 - 3400 20886.812 201.52507 0 3682.6604 6.3038335 - 3450 21604.639 81.93055 0 3682.7038 2.3769444 - 3500 20847.621 207.85705 0 3682.4605 -2.758021 - 3550 20627.979 244.69999 0 3682.6964 -0.33497747 - 3600 19265.519 471.27582 0 3682.1956 2.3506222 - 3650 20351.848 290.65727 0 3682.6319 3.5445062 - 3700 18507.473 597.72931 0 3682.3082 -21.283074 - 3750 20344.017 291.60622 0 3682.2757 6.5366987 - 3800 20672.372 237.18966 0 3682.585 6.7310703 - 3850 21366.943 122.07461 0 3683.2318 -3.5870721 - 3900 20890.294 201.69901 0 3683.4147 -9.5644117 - 3950 20684.181 235.91733 0 3683.2809 -4.8913079 - 4000 21499.086 100.67563 0 3683.8566 1.1969651 - 4050 18549.152 590.04529 0 3681.5707 -9.1914883 - 4100 18436.457 604.2601 0 3677.003 3.6486137 - 4150 19332.655 462.03124 0 3684.1404 -11.280758 - 4200 21199.837 150.66602 0 3683.9722 0.14505208 - 4250 19088.228 501.77395 0 3683.1453 1.6869973 - 4300 16617.942 913.86736 0 3683.5244 9.1792322 - 4350 19765.761 388.52744 0 3682.821 -4.1982973 - 4400 20181.964 320.06096 0 3683.7216 5.3685715 - 4450 20132.04 328.29106 0 3683.631 6.3340995 - 4500 21026.359 179.13858 0 3683.5317 -15.365253 - 4550 19273.765 471.36221 0 3683.6564 -0.71397595 - 4600 20064.71 339.29348 0 3683.4117 -4.8121056 - 4650 19821.01 380.27685 0 3683.7784 11.857115 - 4700 18724.367 563.42963 0 3684.1575 13.250333 - 4750 20467.467 273.2046 0 3684.449 -1.8076823 - 4800 19630.315 412.48507 0 3684.2042 -9.0412254 - 4850 19483.424 437.0206 0 3684.258 11.22465 - 4900 18504.179 600.28485 0 3684.3146 -5.2345686 - 4950 21436.13 111.62139 0 3684.3098 -5.8197915 - 5000 18022.817 680.57727 0 3684.38 19.238942 - 5050 20750.212 226.15635 0 3684.525 -0.73974419 - 5100 20569.533 255.21358 0 3683.4691 -18.332775 - 5150 21447.046 109.3048 0 3683.8124 -2.5745966 - 5200 18985.753 519.77191 0 3684.0641 9.7821968 - 5250 21334.568 128.16597 0 3683.9273 -0.61310451 - 5300 18836.476 544.54018 0 3683.9528 -17.979429 - 5350 18574.391 587.20088 0 3682.9327 40.990206 - 5400 21003.047 183.40176 0 3683.9096 6.1115776 - 5450 20693.875 234.62783 0 3683.607 5.4472209 - 5500 17673.479 738.99306 0 3684.5729 -28.621738 - 5550 19265.837 472.34663 0 3683.3195 -6.609151 - 5600 20800.947 217.12409 0 3683.9486 2.6477049 - 5650 21746.371 59.453265 0 3683.8485 1.5272163 - 5700 20448.97 275.57425 0 3683.736 -7.9864104 - 5750 19776.152 387.64417 0 3683.6695 -16.604848 - 5800 15779.293 1055.4995 0 3685.3817 20.365883 - 5850 21008.009 182.52093 0 3683.8557 -6.6727217 - 5900 21566.123 89.588216 0 3683.9421 -7.8944316 - 5950 21591.695 85.284975 0 3683.9009 -2.4895203 - 6000 17737.17 726.79112 0 3682.9861 1.5643841 - 6050 16648.524 907.73295 0 3682.487 3.0853478 - 6100 19917.439 363.6324 0 3683.2056 4.358303 - 6150 21767.004 56.152017 0 3683.986 -8.8722559 - 6200 17654.098 742.15421 0 3684.5039 9.7673482 - 6250 20125.754 329.65218 0 3683.9445 5.5050658 - 6300 20160.047 323.44453 0 3683.4524 4.852504 - 6350 20509.459 264.29515 0 3682.5383 2.5335834 - 6400 17199.686 817.09171 0 3683.7061 8.3428304 - 6450 18748.366 558.82243 0 3683.5501 0.23782614 - 6500 19133.519 494.28383 0 3683.2037 8.1586096 - 6550 20311.228 297.30741 0 3682.5122 -1.7015056 - 6600 18879.49 536.62652 0 3683.2082 5.0874769 - 6650 18189.35 651.42447 0 3682.9828 -15.223564 - 6700 19925.861 361.90598 0 3682.8828 0.26811015 - 6750 19420.312 445.30915 0 3682.0278 5.5725626 - 6800 19925.024 361.87412 0 3682.7114 -3.9763013 - 6850 16196.938 985.7242 0 3685.2138 2.8265047 - 6900 19779.752 386.51634 0 3683.1416 16.798629 - 6950 21043.144 176.83133 0 3684.0221 -4.193188 - 7000 18555.362 589.47043 0 3682.0307 14.516315 - 7050 21225.883 147.54974 0 3685.1969 -13.466586 - 7100 21234.667 145.92615 0 3685.0373 -5.1951121 - 7150 21483.472 104.62556 0 3685.2042 -5.6904048 - 7200 21014.278 182.97687 0 3685.3566 1.044649 - 7250 18588.789 587.96259 0 3686.094 22.707132 - 7300 20202.932 318.14401 0 3685.2994 -10.795766 - 7350 18304.22 634.7344 0 3685.4377 -1.6801482 - 7400 20967.579 190.67822 0 3685.2747 -0.94800692 - 7450 20991.588 186.07163 0 3684.6696 -1.411476 - 7500 19056.583 507.18197 0 3683.2791 3.2026014 - 7550 18542.455 594.92944 0 3685.3386 -27.908724 - 7600 19895.73 367.08589 0 3683.0409 4.1334366 - 7650 20384.942 285.88041 0 3683.3707 -7.515362 - 7700 20683.189 235.46294 0 3682.6611 10.876437 - 7750 20729.325 228.204 0 3683.0915 3.8844308 - 7800 21667.475 71.752748 0 3682.9985 -15.457992 - 7850 19043.652 508.96807 0 3682.9101 -5.8335792 - 7900 21079.827 169.61123 0 3682.9158 -1.3216223 - 7950 20713.266 230.43917 0 3682.6502 -0.20026535 - 8000 20606.41 248.06357 0 3682.4652 4.2844844 - 8050 20284.503 302.0469 0 3682.7973 6.3402329 - 8100 21859.537 39.514865 0 3682.7711 -13.302141 - 8150 18495.181 600.26329 0 3682.7934 9.9318242 - 8200 21458.549 105.63828 0 3682.0631 -7.7419285 - 8250 18704.511 564.30958 0 3681.728 14.680489 - 8300 20689.366 233.57049 0 3681.7982 2.3067527 - 8350 20692.974 232.67005 0 3681.499 4.2743386 - 8400 20240.086 307.5395 0 3680.8872 1.9694217 - 8450 19075.969 501.34689 0 3680.6751 11.056078 - 8500 21456.727 103.36067 0 3679.4818 -3.4512371 - 8550 20393.16 279.84781 0 3678.7078 6.3282998 - 8600 20898.88 195.43751 0 3678.5842 -14.393947 - 8650 20297.482 295.3169 0 3678.2306 -0.96829147 - 8700 21079.56 164.72934 0 3677.9893 -8.339122 - 8750 21142.519 154.18527 0 3677.9384 -4.6169442 - 8800 20143.871 320.23161 0 3677.5435 6.5710426 - 8850 21030.065 172.88831 0 3677.8992 1.3973883 - 8900 19814.648 375.22097 0 3677.6624 2.6996208 - 8950 17392.382 778.87517 0 3677.6055 11.963975 - 9000 19209.163 476.44659 0 3677.9738 8.7050034 - 9050 20143.824 320.17051 0 3677.4745 -5.8044332 - 9100 21400.78 110.99404 0 3677.7908 -3.0027429 - 9150 21834.471 38.970732 0 3678.0493 -2.5838117 - 9200 21344.715 120.55831 0 3678.0108 4.8187829 - 9250 20998.277 178.31959 0 3678.0324 -1.2009012 - 9300 21141.788 154.4658 0 3678.0971 -21.693564 - 9350 21439.398 105.00432 0 3678.2374 -16.113694 - 9400 21296.282 128.83877 0 3678.2191 -2.9990284 - 9450 19050.623 503.10319 0 3678.207 15.622525 - 9500 20845.847 203.77117 0 3678.079 -1.7504827 - 9550 18808.956 543.38757 0 3678.2135 -2.6611868 - 9600 20612.559 242.57373 0 3678.0002 -0.1650541 - 9650 20522.637 257.28926 0 3677.7288 6.8876074 - 9700 20970.074 182.75754 0 3677.7699 -4.5350279 - 9750 18297.505 625.06808 0 3674.6522 32.429153 - 9800 21042.472 170.78969 0 3677.8684 5.4901963 - 9850 20444.092 270.84839 0 3678.197 6.9444494 - 9900 21597.787 78.901871 0 3678.533 2.3445932 - 9950 18376.854 616.35469 0 3679.1636 -8.55063 - 10000 21490.054 97.234379 0 3678.9101 -0.36115606 -Loop time of 3.38095 on 4 procs for 10000 steps with 81 atoms - -Performance: 25554.943 tau/day, 2957.748 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.015775 | 0.043664 | 0.1024 | 16.8 | 1.29 -Neigh | 0.012822 | 0.029038 | 0.061576 | 11.5 | 0.86 -Comm | 0.18256 | 0.2516 | 0.30898 | 10.5 | 7.44 -Output | 0.0063725 | 0.0069898 | 0.0081069 | 0.8 | 0.21 -Modify | 2.9608 | 3.0171 | 3.0947 | 2.8 | 89.24 -Other | | 0.03255 | | | 0.96 - -Nlocal: 20.25 ave 81 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 -Nghost: 45.5 ave 82 max 12 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 218.75 ave 875 max 0 min -Histogram: 3 0 0 0 0 0 0 0 0 1 - -Total # of neighbors = 875 -Ave neighs/atom = 10.8025 -Neighbor list builds = 993 -Dangerous builds = 945 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.1 b/examples/rigid/log.20Apr18.rigid.poems2.g++.1 deleted file mode 100644 index 9062b78def..0000000000 --- a/examples/rigid/log.20Apr18.rigid.poems2.g++.1 +++ /dev/null @@ -1,342 +0,0 @@ -LAMMPS (20 Apr 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -WARNING: More than one fix poems (../fix_poems.cpp:363) -WARNING: More than one fix poems (../fix_poems.cpp:363) -WARNING: One or more atoms are time integrated more than once (../modify.cpp:279) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12167.633 1505.5478 0 3758.8133 35.125973 - 100 17556.978 512.66277 0 3763.9549 11.137534 - 150 19579.586 138.04942 0 3763.8987 -29.953971 - 200 19757.51 105.30542 0 3764.1036 -0.030645317 - 250 18218.374 390.10747 0 3763.8804 13.711001 - 300 19383.039 174.40688 0 3763.8586 5.7240693 - 350 20125.986 36.972611 0 3764.0071 1.9559205 - 400 18888.816 266.10975 0 3764.0386 9.6362168 - 450 19307.656 188.2511 0 3763.743 1.9326206 - 500 16331.197 738.56392 0 3762.8597 9.1715579 - 550 19318.722 186.16172 0 3763.7027 3.0115336 - 600 19455.268 161.20621 0 3764.0336 0.55208034 - 650 18487.011 340.03216 0 3763.5528 -8.0359122 - 700 17321.201 556.32471 0 3763.9545 -13.631751 - 750 18979.187 249.04389 0 3763.7082 -2.6072455 - 800 19342.456 181.85552 0 3763.7918 8.1918726 - 850 19070.641 232.19342 0 3763.7936 7.3148472 - 900 19478.873 156.65987 0 3763.8586 2.4284987 - 950 19912.415 76.437437 0 3763.9216 -1.4667227 - 1000 16003.749 802.39753 0 3766.0548 46.642188 - 1050 19859.583 86.64176 0 3764.3424 -2.1961943 - 1100 19229.575 203.61488 0 3764.6473 -10.632365 - 1150 18821.6 279.15861 0 3764.64 -0.89495035 - 1200 19392.695 173.59744 0 3764.8373 1.8508753 - 1250 16459.624 717.32104 0 3765.3995 33.478127 - 1300 19343.863 182.59043 0 3764.7874 0.75890736 - 1350 20019.643 57.503573 0 3764.8448 0.31444671 - 1400 18549.582 329.31436 0 3764.4221 10.738303 - 1450 15163.926 957.47585 0 3765.6103 -17.92346 - 1500 19223.688 204.15177 0 3764.0939 -1.6134528 - 1550 18147.996 404.12677 0 3764.8668 8.4194783 - 1600 18615.043 317.42469 0 3764.6548 -2.3288917 - 1650 20120.654 38.887903 0 3764.935 -8.7620301 - 1700 19450.907 162.98262 0 3765.0025 2.3254748 - 1750 19374.631 177.37975 0 3765.2744 8.9328771 - 1800 19424.404 167.93963 0 3765.0514 0.081227378 - 1850 17936.203 442.85082 0 3764.3699 6.6011902 - 1900 19982.595 64.406292 0 3764.8868 -2.95296 - 1950 16215.781 761.92636 0 3764.8487 13.995056 - 2000 18584.444 322.1163 0 3763.6801 7.1653369 - 2050 20107.965 41.025841 0 3764.723 -0.31088772 - 2100 20002.324 60.594786 0 3764.7288 -6.7919989 - 2150 16949.875 626.57523 0 3765.4409 3.50855 - 2200 20010.954 58.808121 0 3764.5403 -10.862112 - 2250 18982.734 247.00818 0 3762.3293 -0.53817452 - 2300 18401.254 354.88774 0 3762.5274 1.0921595 - 2350 19390.545 172.93755 0 3763.7793 -3.3523777 - 2400 16080.137 786.51156 0 3764.3147 -16.202632 - 2450 18870.17 268.79443 0 3763.2704 11.201845 - 2500 19688.736 117.49945 0 3763.5616 4.3786781 - 2550 18869.811 268.97474 0 3763.3842 -5.6659314 - 2600 17021.088 611.38597 0 3763.4393 6.3051835 - 2650 18743.998 292.7827 0 3763.8934 2.4233167 - 2700 19745.629 106.63088 0 3763.2289 -0.34816161 - 2750 19527.584 147.21131 0 3763.4306 -1.6219417 - 2800 18195.354 392.99533 0 3762.5053 24.376674 - 2850 18550.094 327.77867 0 3762.9812 4.2654596 - 2900 20174.105 27.269108 0 3763.2144 1.7109311 - 2950 17744.679 476.70478 0 3762.7564 0.46336417 - 3000 19161.715 214.56545 0 3763.0311 2.3774967 - 3050 18357.87 363.54089 0 3763.1465 7.5885138 - 3100 18851.02 272.19735 0 3763.1269 8.0560784 - 3150 19586.208 136.32381 0 3763.3995 -10.118566 - 3200 19300.444 189.2076 0 3763.3639 -12.590066 - 3250 18680.955 303.88073 0 3763.3168 -1.0138975 - 3300 18444.612 347.49752 0 3763.1664 8.9271155 - 3350 19006.554 243.54359 0 3763.2757 4.7398999 - 3400 17842.797 459.11352 0 3763.3351 28.63048 - 3450 19801.317 96.103613 0 3763.0141 4.0933253 - 3500 18599.338 318.61343 0 3762.9353 6.3657111 - 3550 19737.266 107.84071 0 3762.89 1.3861757 - 3600 19002.648 244.0525 0 3763.0613 8.7615304 - 3650 19154.418 215.94396 0 3763.0584 -2.6243193 - 3700 19036.117 237.84014 0 3763.047 -5.6841944 - 3750 20045.863 50.759281 0 3762.9562 -2.1930939 - 3800 19331.877 182.69303 0 3762.6703 0.57474959 - 3850 18193.947 393.70074 0 3762.9502 -4.1144639 - 3900 19675.638 119.2295 0 3762.8663 0.46172332 - 3950 19506.743 150.36614 0 3762.7259 5.8020668 - 4000 17985.008 431.80897 0 3762.366 10.755615 - 4050 19947.208 68.962683 0 3762.8902 -2.0041629 - 4100 19936.06 70.997196 0 3762.8602 -6.6295574 - 4150 19011.006 242.10402 0 3762.6608 -12.682711 - 4200 18108.183 409.44214 0 3762.8094 -0.42654932 - 4250 18734.162 293.70086 0 3762.9901 8.8549986 - 4300 16619.218 686.30953 0 3763.9426 43.405681 - 4350 18818.184 277.95188 0 3762.8007 20.953883 - 4400 18649.616 307.93211 0 3761.5647 -3.6011031 - 4450 18626.995 313.23564 0 3762.6792 -2.5430627 - 4500 18133.284 405.27778 0 3763.2934 3.057056 - 4550 19985.929 61.792735 0 3762.8908 1.9540846 - 4600 18664.305 306.02805 0 3762.3809 1.2395242 - 4650 19822.408 92.030223 0 3762.8466 -1.0496216 - 4700 19218.014 203.93895 0 3762.8305 0.74203538 - 4750 19425.781 165.36374 0 3762.7306 4.0113982 - 4800 18604.891 317.55244 0 3762.9026 16.671366 - 4850 19648.156 124.29963 0 3762.8471 4.1073 - 4900 18928.508 257.76023 0 3763.0394 -4.3547566 - 4950 19795.841 97.135231 0 3763.0317 -10.401888 - 5000 20150.671 31.452661 0 3763.0584 -3.352706 - 5050 18694.789 300.8954 0 3762.8933 11.690808 - 5100 16936.745 627.00902 0 3763.4434 -0.56880353 - 5150 18446.99 346.49004 0 3762.5992 8.409244 - 5200 18532.691 330.61677 0 3762.5966 10.358529 - 5250 18342.743 366.3264 0 3763.1306 -9.5622676 - 5300 20038.203 52.234825 0 3763.0131 -3.6974868 - 5350 19337.092 182.06755 0 3763.0106 -0.045248915 - 5400 19561.005 140.5518 0 3762.9602 1.3850963 - 5450 19415.557 167.29181 0 3762.7654 2.6966013 - 5500 18646.823 309.81657 0 3762.9319 7.4858844 - 5550 19165.312 214.07271 0 3763.2046 1.4335924 - 5600 18879.507 266.90953 0 3763.1146 7.8746695 - 5650 19824.482 91.786842 0 3762.9872 -2.4395467 - 5700 19699.85 114.8239 0 3762.9442 4.2779932 - 5750 19535.697 145.24886 0 3762.9706 5.9452722 - 5800 18275.446 378.66191 0 3763.0038 11.965062 - 5850 19931.992 71.873259 0 3762.9828 -2.3097575 - 5900 18528.705 331.64793 0 3762.8897 -18.312104 - 5950 16535.446 701.02536 0 3763.1451 -14.797902 - 6000 18678.807 303.76763 0 3762.806 -3.2732626 - 6050 16661.525 677.73561 0 3763.2031 17.862761 - 6100 18100.317 410.39139 0 3762.3019 -4.9765779 - 6150 16487.861 707.08907 0 3760.3967 32.53899 - 6200 16823.279 647.56578 0 3762.9878 -9.8237219 - 6250 18418.096 351.89624 0 3762.6548 -2.0149855 - 6300 18822.067 277.01314 0 3762.5811 5.3782716 - 6350 19300.198 188.57243 0 3762.6832 -1.9316023 - 6400 18425.789 350.70367 0 3762.8868 2.6884393 - 6450 18708.506 297.50643 0 3762.0447 -13.808707 - 6500 19528.099 146.10805 0 3762.4226 -1.5991505 - 6550 19701.841 114.01327 0 3762.5023 4.4322487 - 6600 18892.934 262.83827 0 3761.5297 10.689265 - 6650 19041.669 235.52692 0 3761.7619 -1.1425512 - 6700 19352.162 178.40501 0 3762.1388 -0.55130997 - 6750 16177.653 765.61942 0 3761.481 4.6526477 - 6800 19007.323 242.63753 0 3762.5122 3.6202242 - 6850 14255.206 1125.4974 0 3765.3503 -31.10433 - 6900 18481.408 340.4703 0 3762.9532 0.53246054 - 6950 19227.569 202.33363 0 3762.9946 -0.94126626 - 7000 18771.85 286.70279 0 3762.9714 3.151759 - 7050 18689.51 301.95602 0 3762.9765 8.0511724 - 7100 18599.258 318.83229 0 3763.1394 -0.86222116 - 7150 17739.189 478.35458 0 3763.3896 11.976827 - 7200 19492.829 153.62536 0 3763.4084 -8.6815909 - 7250 18797.718 282.17319 0 3763.232 -19.897633 - 7300 18353.871 364.09362 0 3762.9585 5.4538454 - 7350 19040.053 237.34144 0 3763.2772 6.5600248 - 7400 19452.586 160.98629 0 3763.317 -9.0542585 - 7450 19033.845 238.45033 0 3763.2365 3.2654681 - 7500 18137.358 404.80969 0 3763.5796 -7.2639486 - 7550 16863.391 642.47654 0 3765.3267 31.248679 - 7600 16374.538 731.74039 0 3764.0622 29.566291 - 7650 19837.917 89.823014 0 3763.5114 -2.6605403 - 7700 15593.154 876.08807 0 3763.7093 -9.7668717 - 7750 16609.929 687.32679 0 3763.2396 1.0775966 - 7800 17513.384 519.87756 0 3763.0968 3.4979836 - 7850 20022.015 56.036771 0 3763.8173 -4.316185 - 7900 17681.324 489.71547 0 3764.0347 5.1978443 - 7950 18320.382 371.17872 0 3763.8421 6.1860655 - 8000 20014.059 57.688322 0 3763.9956 -9.0623854 - 8050 16203.013 762.61545 0 3763.1735 31.662714 - 8100 18749.745 291.57889 0 3763.7538 -14.015057 - 8150 19411.326 169.05845 0 3763.7485 -4.3392799 - 8200 17994.991 431.56932 0 3763.9751 6.8158642 - 8250 19325.923 185.1137 0 3763.9883 9.4923883 - 8300 17354.302 550.33316 0 3764.0927 6.1636399 - 8350 19900.895 78.431831 0 3763.7828 -4.5224196 - 8400 17775.757 471.62915 0 3763.4361 12.949899 - 8450 19909.324 76.935162 0 3763.8471 -2.950115 - 8500 18601.933 318.79405 0 3763.5965 6.0173542 - 8550 18685.758 303.59497 0 3763.9205 2.7277487 - 8600 19297.521 190.12606 0 3763.741 4.8998933 - 8650 17396.37 542.14326 0 3763.6932 39.937715 - 8700 17134.714 590.99465 0 3764.0898 10.37328 - 8750 14348.104 1106.7544 0 3763.8106 -3.8604659 - 8800 19830.924 90.929138 0 3763.3225 0.26603444 - 8850 18551.537 326.53747 0 3762.0072 -1.5369982 - 8900 20040.322 52.066026 0 3763.2367 -12.667979 - 8950 19314.585 186.54793 0 3763.3228 -0.64755555 - 9000 19117.66 222.84553 0 3763.153 5.2990011 - 9050 19072.016 231.26038 0 3763.1152 -1.6513695 - 9100 19284.933 191.73976 0 3763.0237 -3.932358 - 9150 17356.576 548.61808 0 3762.7988 1.3659056 - 9200 18939.549 255.43703 0 3762.761 3.3037106 - 9250 19621.961 129.5012 0 3763.1976 1.667 - 9300 16898.033 633.79921 0 3763.0647 7.5941845 - 9350 19662.75 122.10836 0 3763.3584 -3.3144828 - 9400 16118.338 778.70243 0 3763.5799 9.8684537 - 9450 17362.374 548.18847 0 3763.443 6.8117548 - 9500 17873.057 453.37389 0 3763.1993 9.5651746 - 9550 19282.305 192.593 0 3763.3901 -4.987757 - 9600 18236.48 386.36263 0 3763.4886 8.8658343 - 9650 17695.571 486.6517 0 3763.6093 12.471421 - 9700 19044.003 237.04652 0 3763.7138 0.84430497 - 9750 17937.299 442.4372 0 3764.1592 3.981475 - 9800 18179.761 396.86987 0 3763.4923 -11.397273 - 9850 19157.292 215.8937 0 3763.5404 -7.7648682 - 9900 19719.066 111.98124 0 3763.6602 5.5378968 - 9950 18103.235 410.65473 0 3763.1056 28.201374 - 10000 18479.903 341.32548 0 3763.5297 -5.0581298 -Loop time of 3.14341 on 1 procs for 10000 steps with 81 atoms - -Performance: 27486.104 tau/day, 3181.262 timesteps/s -99.3% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.12201 | 0.12201 | 0.12201 | 0.0 | 3.88 -Neigh | 0.077269 | 0.077269 | 0.077269 | 0.0 | 2.46 -Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 0.39 -Output | 0.0032048 | 0.0032048 | 0.0032048 | 0.0 | 0.10 -Modify | 2.9172 | 2.9172 | 2.9172 | 0.0 | 92.80 -Other | | 0.01151 | | | 0.37 - -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 67 ave 67 max 67 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 599 ave 599 max 599 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 599 -Ave neighs/atom = 7.39506 -Neighbor list builds = 993 -Dangerous builds = 945 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.poems2.g++.4 b/examples/rigid/log.20Apr18.rigid.poems2.g++.4 deleted file mode 100644 index 812b101841..0000000000 --- a/examples/rigid/log.20Apr18.rigid.poems2.g++.4 +++ /dev/null @@ -1,342 +0,0 @@ -LAMMPS (20 Apr 2018) - using 1 OpenMP thread(s) per MPI task -# Simple rigid body system - -units lj -atom_style atomic - -pair_style lj/cut 2.5 - -read_data data.rigid - orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 81 atoms - -velocity all create 100.0 4928459 - -# unconnected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 10 18 -#group clump3 id <> 19 27 -#group clump4 id <> 28 36 -#group clump5 id <> 37 45 -#group clump6 id <> 46 54 -#group clump7 id <> 55 63 -#group clump8 id <> 64 72 -#group clump9 id <> 73 81 - -#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 1 chain of connected bodies - -#group clump1 id <> 1 9 -#group clump2 id <> 9 18 -#group clump3 id <> 18 27 -#group clump4 id <> 27 36 -#group clump5 id <> 36 45 -#group clump6 id <> 45 54 -#group clump7 id <> 54 63 -#group clump8 id <> 63 72 -#group clump9 id <> 72 81 - -#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 - -# 2 chains of connected bodies - -group clump1 id <> 1 9 -9 atoms in group clump1 -group clump2 id <> 9 18 -10 atoms in group clump2 -group clump3 id <> 18 27 -10 atoms in group clump3 -group clump4 id <> 27 36 -10 atoms in group clump4 -group clump5 id <> 37 45 -9 atoms in group clump5 -group clump6 id <> 45 54 -10 atoms in group clump6 -group clump7 id <> 54 63 -10 atoms in group clump7 -group clump8 id <> 63 72 -10 atoms in group clump8 -group clump9 id <> 72 81 -10 atoms in group clump9 - -fix 1 all poems group clump1 clump2 clump3 clump4 -1 clusters, 4 bodies, 3 joints, 36 atoms -fix 2 all poems group clump5 clump6 clump7 clump8 clump9 -1 clusters, 5 bodies, 4 joints, 45 atoms - -neigh_modify exclude group clump1 clump1 -neigh_modify exclude group clump2 clump2 -neigh_modify exclude group clump3 clump3 -neigh_modify exclude group clump4 clump4 -neigh_modify exclude group clump5 clump5 -neigh_modify exclude group clump6 clump6 -neigh_modify exclude group clump7 clump7 -neigh_modify exclude group clump8 clump8 -neigh_modify exclude group clump9 clump9 - -thermo 100 - -#dump 1 all atom 50 dump.rigid.poems2 - -#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 2 pad 5 - -#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 -#dump_modify 3 pad 5 - -timestep 0.0001 -thermo 50 -run 10000 -WARNING: More than one fix poems (../fix_poems.cpp:363) -WARNING: More than one fix poems (../fix_poems.cpp:363) -WARNING: One or more atoms are time integrated more than once (../modify.cpp:279) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 18 18 18 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 196.00047 3632.2347 0 3668.5311 -2.7403788 - 50 12167.633 1505.5478 0 3758.8133 35.125973 - 100 17556.978 512.66277 0 3763.9549 11.137534 - 150 19579.586 138.04942 0 3763.8987 -29.953971 - 200 19757.51 105.30542 0 3764.1036 -0.030645317 - 250 18218.374 390.10747 0 3763.8804 13.711001 - 300 19383.039 174.40688 0 3763.8586 5.7240693 - 350 20125.986 36.972611 0 3764.0071 1.9559205 - 400 18888.816 266.10975 0 3764.0386 9.6362168 - 450 19307.656 188.2511 0 3763.743 1.9326206 - 500 16331.197 738.56392 0 3762.8597 9.1715579 - 550 19318.722 186.16172 0 3763.7027 3.0115336 - 600 19455.268 161.20621 0 3764.0336 0.55208034 - 650 18487.011 340.03216 0 3763.5528 -8.0359122 - 700 17321.201 556.32471 0 3763.9545 -13.631751 - 750 18979.187 249.04389 0 3763.7082 -2.6072455 - 800 19342.456 181.85552 0 3763.7918 8.1918726 - 850 19070.641 232.19342 0 3763.7936 7.3148472 - 900 19478.873 156.65987 0 3763.8586 2.4284987 - 950 19912.415 76.437437 0 3763.9216 -1.4667227 - 1000 16003.749 802.39753 0 3766.0548 46.642188 - 1050 19859.583 86.64176 0 3764.3424 -2.1961943 - 1100 19229.575 203.61488 0 3764.6473 -10.632365 - 1150 18821.6 279.15861 0 3764.64 -0.89495035 - 1200 19392.695 173.59744 0 3764.8373 1.8508753 - 1250 16459.624 717.32104 0 3765.3995 33.478127 - 1300 19343.863 182.59043 0 3764.7874 0.75890736 - 1350 20019.643 57.503573 0 3764.8448 0.31444671 - 1400 18549.582 329.31436 0 3764.4221 10.738303 - 1450 15163.926 957.47584 0 3765.6103 -17.923459 - 1500 19223.688 204.15172 0 3764.0939 -1.6134536 - 1550 18147.996 404.12676 0 3764.8668 8.4194774 - 1600 18615.043 317.42466 0 3764.6548 -2.3288957 - 1650 20120.654 38.887927 0 3764.935 -8.7620244 - 1700 19450.906 162.98284 0 3765.0025 2.3254707 - 1750 19374.632 177.37954 0 3765.2744 8.9328778 - 1800 19424.403 167.93971 0 3765.0514 0.081234023 - 1850 17936.311 442.83087 0 3764.3699 6.600894 - 1900 19982.596 64.40607 0 3764.8868 -2.9530102 - 1950 16215.95 761.89459 0 3764.8482 13.994238 - 2000 18584.39 322.12621 0 3763.68 7.1654863 - 2050 20107.966 41.025634 0 3764.723 -0.31093298 - 2100 20002.346 60.590652 0 3764.7288 -6.7919499 - 2150 16949.612 626.62391 0 3765.441 3.5094585 - 2200 20010.952 58.808492 0 3764.5403 -10.862255 - 2250 18982.727 247.00941 0 3762.3292 -0.53796622 - 2300 18401.351 354.86992 0 3762.5275 1.0919209 - 2350 19390.5 172.94589 0 3763.7793 -3.3526281 - 2400 16081.648 786.23133 0 3764.3143 -16.197875 - 2450 18870.722 268.69249 0 3763.2707 11.192419 - 2500 19687.71 117.6898 0 3763.562 4.387789 - 2550 18872.129 268.54506 0 3763.3838 -5.6577428 - 2600 17017.179 612.11028 0 3763.4397 6.3187623 - 2650 18766.343 288.63699 0 3763.8856 2.3968008 - 2700 19737.998 108.02069 0 3763.2054 -0.30752024 - 2750 19508.797 150.69812 0 3763.4384 -1.6171126 - 2800 18394.822 355.73011 0 3762.1787 21.193311 - 2850 18561.108 325.76417 0 3763.0065 3.9331499 - 2900 20124.042 36.554163 0 3763.2286 0.54133121 - 2950 15727.607 849.90471 0 3762.4245 13.885323 - 3000 17991.206 431.32693 0 3763.0317 9.9953567 - 3050 18834.86 275.34241 0 3763.2795 9.1519305 - 3100 18986.272 247.38123 0 3763.3575 -1.8754521 - 3150 19979.145 63.575968 0 3763.4177 -11.800026 - 3200 19953.846 68.376593 0 3763.5332 -6.7719573 - 3250 15646.02 867.19502 0 3764.6062 16.433911 - 3300 16946.252 625.14854 0 3763.3433 4.3975456 - 3350 19006.567 243.97026 0 3763.7048 5.3392405 - 3400 18082.133 414.87059 0 3763.4138 15.143954 - 3450 18273.719 379.36162 0 3763.3836 5.4465204 - 3500 19783.17 100.06678 0 3763.6167 1.9588505 - 3550 19794.99 97.904519 0 3763.6435 -3.0349395 - 3600 18357.708 363.98291 0 3763.5585 -2.1229788 - 3650 19647.179 125.48949 0 3763.8559 1.2967845 - 3700 18806.632 281.78709 0 3764.4967 5.125718 - 3750 18982.747 248.97053 0 3764.294 -0.72036085 - 3800 19597.926 135.04805 0 3764.2935 -3.2129291 - 3850 18914.042 261.7133 0 3764.3136 -12.163282 - 3900 18646.326 311.16482 0 3764.1881 5.1808943 - 3950 18589.554 321.36256 0 3763.8726 4.9554103 - 4000 17877.615 453.02456 0 3763.694 9.8457113 - 4050 19440.059 164.15739 0 3764.1684 -5.4054486 - 4100 18505.545 337.36023 0 3764.313 4.8468985 - 4150 19220.307 204.85944 0 3764.1755 -6.5040818 - 4200 19058.915 234.79578 0 3764.2245 3.1852011 - 4250 19867.025 85.136186 0 3764.2149 5.6156236 - 4300 16989.857 616.86564 0 3763.1355 -3.4041875 - 4350 19782.09 100.85847 0 3764.2085 3.2531098 - 4400 19879.56 82.559198 0 3763.9593 1.6340828 - 4450 19409.95 169.46676 0 3763.9019 -1.824265 - 4500 19742.977 107.72786 0 3763.8347 -0.72711698 - 4550 17166.529 585.04113 0 3764.028 -0.38806102 - 4600 19604.596 133.61426 0 3764.0949 -5.2712214 - 4650 18865.608 270.23956 0 3763.8707 1.5751363 - 4700 20190.139 25.270932 0 3764.1855 -10.159924 - 4750 20043.487 52.56327 0 3764.3201 -4.713579 - 4800 19361.931 178.70311 0 3764.246 4.2460799 - 4850 19460.365 160.29083 0 3764.0621 3.5079181 - 4900 18252.89 384.16194 0 3764.3268 4.1870604 - 4950 19516.947 150.07365 0 3764.3231 4.0238527 - 5000 19041.145 238.27335 0 3764.4113 8.2280019 - 5050 19519.408 149.66793 0 3764.3731 -0.088904966 - 5100 18087.848 415.34004 0 3764.9416 8.9482852 - 5150 19392.463 173.43121 0 3764.628 -6.6722716 - 5200 19683.968 119.46663 0 3764.6458 -2.0330852 - 5250 19675.404 121.09497 0 3764.6884 3.0627309 - 5300 18627.53 314.96107 0 3764.5038 5.2692141 - 5350 20022.616 56.725346 0 3764.6172 -7.7034469 - 5400 19353.4 180.6482 0 3764.6112 -2.3897589 - 5450 16966.649 622.29693 0 3764.2689 6.3601638 - 5500 17584.292 508.42495 0 3764.7753 5.949219 - 5550 19169.69 214.76864 0 3764.7113 3.3778997 - 5600 19491.814 155.19149 0 3764.7866 -0.20031164 - 5650 19079.585 231.70394 0 3764.9605 7.3017226 - 5700 19686.564 119.34 0 3765 0.98980357 - 5750 19639.909 127.89886 0 3764.919 2.3982612 - 5800 19474.109 158.55418 0 3764.8706 3.4940447 - 5850 16957.663 624.72623 0 3765.0342 10.739819 - 5900 19950.579 70.027987 0 3764.5796 4.6925057 - 5950 19759.601 105.38621 0 3764.5716 3.0958319 - 6000 19129.749 221.96406 0 3764.5102 -1.0612997 - 6050 16087.951 785.36134 0 3764.6115 -15.255986 - 6100 18851.976 272.98306 0 3764.0896 4.9341766 - 6150 19532.23 147.4113 0 3764.4909 1.3206073 - 6200 18051.604 421.79367 0 3764.6833 2.587863 - 6250 18922.77 259.81211 0 3764.0287 10.363589 - 6300 18402.504 356.81518 0 3764.6864 8.3589218 - 6350 19315.369 187.64457 0 3764.5647 1.0716382 - 6400 19700.59 116.50438 0 3764.7618 2.165408 - 6450 19596.362 135.79675 0 3764.7527 1.6466783 - 6500 20217.677 20.884953 0 3764.8993 -3.5893732 - 6550 18278.991 379.95981 0 3764.9582 7.0433091 - 6600 20142.999 34.761283 0 3764.9462 1.7083655 - 6650 20185.488 26.899017 0 3764.9524 -0.65741058 - 6700 17942.962 441.72909 0 3764.4999 -3.691039 - 6750 16435.681 720.9581 0 3764.6028 -9.4583249 - 6800 17825.95 463.58979 0 3764.6916 6.1557503 - 6850 19440.75 164.52796 0 3764.6669 -11.921703 - 6900 18824.905 278.4897 0 3764.5832 -1.4668322 - 6950 19069.14 233.25502 0 3764.5772 6.8149838 - 7000 18983.209 249.29193 0 3764.701 15.140158 - 7050 15623.103 872.33684 0 3765.5041 7.3268767 - 7100 20090.283 44.006184 0 3764.429 2.6959947 - 7150 15535.27 888.39683 0 3765.2987 -4.1285644 - 7200 19425.575 167.19079 0 3764.5195 4.9190857 - 7250 18684.497 304.24754 0 3764.3396 7.3927682 - 7300 17632.518 498.82765 0 3764.1087 5.1101854 - 7350 18969.793 251.66375 0 3764.5884 -3.7865508 - 7400 17700.626 486.89931 0 3764.7931 -8.8531288 - 7450 17897.361 450.31562 0 3764.6417 -3.6095062 - 7500 18795.228 284.03842 0 3764.6361 8.3567203 - 7550 18658.285 309.34015 0 3764.5781 0.4306691 - 7600 19230.039 203.5385 0 3764.6567 0.80253549 - 7650 19513.551 150.86999 0 3764.4906 0.32848159 - 7700 19494.849 154.28788 0 3764.4452 -4.2498631 - 7750 20011.058 58.832118 0 3764.5835 0.54896615 - 7800 19241.055 201.57548 0 3764.7338 -0.26200786 - 7850 19512.742 151.11436 0 3764.5851 2.7308876 - 7900 19688.007 118.68023 0 3764.6075 0.80454178 - 7950 16891.645 636.56823 0 3764.6507 -25.839253 - 8000 19425.572 167.33746 0 3764.6657 -2.8744687 - 8050 19444.916 163.57779 0 3764.4882 8.5388183 - 8100 19540.338 145.77731 0 3764.3585 5.5606379 - 8150 17997.991 429.85951 0 3762.8208 20.179487 - 8200 19463.886 159.50302 0 3763.9264 0.19577123 - 8250 19517.733 149.53457 0 3763.9295 2.3294314 - 8300 19236.221 201.66041 0 3763.9236 5.8204747 - 8350 18662.608 308.25544 0 3764.2939 5.4422482 - 8400 19030.046 239.38211 0 3763.4647 3.7940188 - 8450 18058.148 419.70672 0 3763.8081 4.4010713 - 8500 16866.001 641.00564 0 3764.3392 -19.894815 - 8550 19484.364 155.35821 0 3763.5737 4.2635496 - 8600 18562.912 326.16323 0 3763.7395 11.288271 - 8650 19256.188 197.67578 0 3763.6365 -4.1872666 - 8700 19653.945 124.27148 0 3763.8909 -7.4888761 - 8750 19590.834 136.12748 0 3764.0596 1.0605539 - 8800 19065.424 233.46882 0 3764.1029 1.8432113 - 8850 18961.297 252.69734 0 3764.0486 6.7414134 - 8900 19879.711 82.777822 0 3764.2058 0.12631864 - 8950 18689.712 302.80546 0 3763.8632 5.1584036 - 9000 19114.403 224.23511 0 3763.9393 -4.5856366 - 9050 17626.3 500.49518 0 3764.6248 -3.9436947 - 9100 18552.501 328.86032 0 3764.5087 -0.32810034 - 9150 15039.846 979.12961 0 3764.2862 16.571104 - 9200 19146.923 218.64681 0 3764.3733 -4.6264398 - 9250 17606.161 503.14852 0 3763.5487 13.13675 - 9300 18002.328 430.47362 0 3764.2381 4.9326117 - 9350 19980.452 64.168644 0 3764.2524 -5.6111349 - 9400 18953.798 254.44926 0 3764.4118 2.3662302 - 9450 17151.075 588.59472 0 3764.7197 4.3116983 - 9500 19128.858 221.38199 0 3763.763 3.6641306 - 9550 18217.322 390.53199 0 3764.1101 1.8537154 - 9600 19094.478 227.98925 0 3764.0038 3.972665 - 9650 19577.649 138.55507 0 3764.0456 4.0408247 - 9700 19331.361 184.31942 0 3764.2011 -4.7996733 - 9750 18999.798 245.87295 0 3764.3541 -0.26741334 - 9800 18987.181 248.37105 0 3764.5157 6.1717595 - 9850 20094.73 43.013036 0 3764.2593 -8.9770288 - 9900 18988.815 247.63984 0 3764.087 -6.3990966 - 9950 18290.808 377.34967 0 3764.5363 7.7453525 - 10000 19558.326 142.47047 0 3764.3828 3.4110829 -Loop time of 3.53831 on 4 procs for 10000 steps with 81 atoms - -Performance: 24418.438 tau/day, 2826.208 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0096724 | 0.035349 | 0.063574 | 10.3 | 1.00 -Neigh | 0.0091243 | 0.022333 | 0.037608 | 6.9 | 0.63 -Comm | 0.18063 | 0.2494 | 0.33202 | 12.6 | 7.05 -Output | 0.0060797 | 0.0065744 | 0.0074706 | 0.7 | 0.19 -Modify | 3.0943 | 3.1895 | 3.2828 | 4.0 | 90.14 -Other | | 0.0352 | | | 0.99 - -Nlocal: 20.25 ave 36 max 0 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 17.5 ave 37 max 1 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Neighs: 154.25 ave 393 max 0 min -Histogram: 2 0 0 0 0 1 0 0 0 1 - -Total # of neighbors = 617 -Ave neighs/atom = 7.61728 -Neighbor list builds = 993 -Dangerous builds = 948 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:03 diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.1 b/examples/rigid/log.20Apr18.rigid.tnr.g++.1 deleted file mode 100644 index 097fd132aa..0000000000 --- a/examples/rigid/log.20Apr18.rigid.tnr.g++.1 +++ /dev/null @@ -1,458 +0,0 @@ -LAMMPS (20 Apr 2018) - using 1 OpenMP thread(s) per MPI task -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule/intra rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule -800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 45 45 45 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 - 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 - 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 - 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 - 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 - 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 - 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 - 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 - 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 - 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 - 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 - 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 - 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 - 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 - 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 - 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 - 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 - 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 - 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 - 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 - 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 - 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216998 -0.0032636911 - 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 - 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738261 0.0090537939 0.013165402 - 2500 1.4153808 5.9421661 7.0538718 0.00015906308 7.0607216 62.244 62.244 62.244 0.0023516211 -0.0019814987 0.00010706678 - 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 - 2700 1.4138077 5.9369067 7.047377 0.0024268843 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960354 0.00049277379 - 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113032 0.0047214106 - 2900 1.3938659 5.921023 7.01583 0.0053751201 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566097 0.0064197134 - 3000 1.390221 5.9205014 7.0124455 -0.0010750973 6.9661486 62.244 62.244 62.244 0.0019519817 -0.0041878875 -0.0009893861 - 3100 1.4205722 5.9178284 7.0336117 0.0098735467 7.4587964 62.244 62.244 62.244 0.0040973349 0.012167268 0.013356037 - 3200 1.398418 5.9150349 7.0134173 0.0061541837 7.278435 62.244 62.244 62.244 0.0067621825 0.011952562 -0.00025219321 - 3300 1.4269859 5.9148727 7.0356937 0.006062387 7.2967584 62.244 62.244 62.244 0.012956233 -2.480748e-05 0.005255736 - 3400 1.434286 5.9356705 7.0622253 0.0002731615 7.0739885 62.244 62.244 62.244 -0.00054959543 0.0052526331 -0.0038835532 - 3500 1.4416808 5.9228153 7.0551783 0.0083383068 7.414251 62.244 62.244 62.244 0.0073994017 0.0030328023 0.014582716 - 3600 1.4136063 5.9039442 7.0142562 0.0019711852 7.0991414 62.244 62.244 62.244 -0.00032317688 0.0035029725 0.0027337599 - 3700 1.433382 5.91201 7.0378548 0.0071286927 7.3448378 62.244 62.244 62.244 0.0064768108 0.0046765006 0.010232767 - 3800 1.3659481 5.9032872 6.9761663 -0.0054034056 6.7434793 62.244 62.244 62.244 -0.007394357 -0.0082833116 -0.00053254832 - 3900 1.396322 5.9043001 7.0010362 0.005331024 7.2306062 62.244 62.244 62.244 0.0081855301 0.0048806234 0.0029269184 - 4000 1.412548 5.906066 7.0155468 0.0028450132 7.1380616 62.244 62.244 62.244 0.0052588387 0.00072412871 0.0025520721 - 4100 1.3943949 5.9040868 6.9993093 0.0058053193 7.2493039 62.244 62.244 62.244 0.0060583148 0.0024781972 0.0088794459 - 4200 1.4249768 5.8906369 7.0098798 0.0030209006 7.1399689 62.244 62.244 62.244 0.0061742017 -0.0020795681 0.0049680681 - 4300 1.3899827 5.8966327 6.9883897 0.0057278096 7.2350464 62.244 62.244 62.244 0.0049035059 0.0021868561 0.010093067 - 4400 1.4414361 5.8986386 7.0308094 0.0050941357 7.2501783 62.244 62.244 62.244 0.0057971901 0.0037941986 0.0056910185 - 4500 1.4093099 5.8922729 6.9992103 0.0012182325 7.0516711 62.244 62.244 62.244 0.0042896986 0.0014287789 -0.00206378 - 4600 1.3779677 5.892894 6.9752138 0.002057623 7.0638213 62.244 62.244 62.244 0.0029271755 -0.0031752166 0.0064209102 - 4700 1.4086418 5.9096898 7.0161024 -0.00052853259 6.9933422 62.244 62.244 62.244 -0.001862386 -0.0018129293 0.0020897176 - 4800 1.4394 5.9146102 7.0451818 0.015326441 7.7051846 62.244 62.244 62.244 0.014754936 0.017967956 0.013256431 - 4900 1.4496219 5.9074613 7.0460616 0.0075297868 7.370317 62.244 62.244 62.244 0.0092907193 0.0079794674 0.0053191736 - 5000 1.4280291 5.9106136 7.032254 -0.0013249587 6.9751972 62.244 62.244 62.244 -0.0044875103 0.0020723667 -0.0015597324 -Loop time of 6.73744 on 1 procs for 5000 steps with 5600 atoms - -Performance: 320596.735 tau/day, 742.122 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.52635 | 0.52635 | 0.52635 | 0.0 | 7.81 -Bond | 0.26628 | 0.26628 | 0.26628 | 0.0 | 3.95 -Neigh | 1.5927 | 1.5927 | 1.5927 | 0.0 | 23.64 -Comm | 0.16011 | 0.16011 | 0.16011 | 0.0 | 2.38 -Output | 0.0040634 | 0.0040634 | 0.0040634 | 0.0 | 0.06 -Modify | 4.0145 | 4.0145 | 4.0145 | 0.0 | 59.58 -Other | | 0.1735 | | | 2.57 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1352 ave 1352 max 1352 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5257 ave 5257 max 5257 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5257 -Ave neighs/atom = 0.93875 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 766 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule -800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4280291 5.9106136 7.032254 0.02814128 8.2441024 62.244 62.244 62.244 0.019873502 0.039656784 0.024893554 - 5100 1.4435659 5.8998386 7.0336823 0.0063929319 7.3089813 62.244 62.244 62.244 0.0089837757 0.0052773116 0.0049177085 - 5200 1.3970069 5.9117164 7.0089904 0.0065245686 7.289958 62.244 62.244 62.244 0.008502047 0.0043872479 0.0066844108 - 5300 1.433167 5.8796669 7.0053428 0.0076478538 7.3346825 62.244 62.244 62.244 0.0061384889 0.0070193789 0.0097856935 - 5400 1.4191626 5.8830864 6.9977626 0.0026371359 7.1113257 62.244 62.244 62.244 0.0024097043 -0.00082200506 0.0063237084 - 5500 1.409376 5.8753367 6.982326 0.010180815 7.4207427 62.244 62.244 62.244 0.010429709 0.0081711083 0.011941628 - 5600 1.4005678 5.882485 6.9825559 0.00036705268 6.9983623 62.244 62.244 62.244 -0.0034485466 0.0031079204 0.0014417843 - 5700 1.4116833 5.8842566 6.9930582 0.00053413233 7.0160595 62.244 62.244 62.244 0.0016669624 -0.0030741941 0.0030096286 - 5800 1.409035 5.894902 7.0016235 4.7080816e-05 7.003651 62.244 62.244 62.244 0.0018596854 -5.3937508e-05 -0.0016645054 - 5900 1.4150353 5.8928576 7.004292 0.0063467985 7.2776043 62.244 62.244 62.244 0.0055755751 0.0090839847 0.0043808358 - 6000 1.4374163 5.8778036 7.0068171 0.0031890481 7.1441472 62.244 62.244 62.244 0.0067647375 0.0015458579 0.0012565488 -Loop time of 1.41082 on 1 procs for 1000 steps with 5600 atoms - -Performance: 306205.780 tau/day, 708.810 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.149 | 0.149 | 0.149 | 0.0 | 10.56 -Bond | 0.053873 | 0.053873 | 0.053873 | 0.0 | 3.82 -Neigh | 0.35532 | 0.35532 | 0.35532 | 0.0 | 25.19 -Comm | 0.032433 | 0.032433 | 0.032433 | 0.0 | 2.30 -Output | 0.00080752 | 0.00080752 | 0.00080752 | 0.0 | 0.06 -Modify | 0.78447 | 0.78447 | 0.78447 | 0.0 | 55.60 -Other | | 0.03491 | | | 2.47 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1347 ave 1347 max 1347 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5592 ave 5592 max 5592 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5592 -Ave neighs/atom = 0.998571 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 -800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.4374163 5.8778036 7.0068171 -0.0020672233 6.9177963 62.244 62.244 62.244 0.034504923 -0.030001164 -0.010705429 - 6100 1.4393824 5.8852696 7.0158274 0.0055792227 7.2560855 62.244 62.244 62.244 0.0072602759 0.0074870643 0.0019903278 - 6200 1.4265711 5.8853532 7.0058484 0.0019366613 7.0892468 62.244 62.244 62.244 -0.0035411799 0.0047319741 0.0046191897 - 6300 1.4030198 5.8824874 6.9844843 0.0055760353 7.2246052 62.244 62.244 62.244 0.0031273033 0.0080002386 0.005600564 - 6400 1.3592064 5.8924876 6.9600714 0.0051450348 7.1816321 62.244 62.244 62.244 0.0042848197 0.0044005693 0.0067497155 - 6500 1.3946028 5.8798014 6.9751872 0.0051168754 7.1955353 62.244 62.244 62.244 0.0020473208 0.0038175566 0.0094857487 - 6600 1.3652122 5.8985637 6.9708648 0.0065480579 7.2528439 62.244 62.244 62.244 0.0056940621 0.0062242398 0.0077258719 - 6700 1.3808929 5.9047739 6.9893913 0.0074053719 7.308289 62.244 62.244 62.244 0.0049554161 0.012378296 0.0048824031 - 6800 1.4140879 5.891133 7.0018233 0.001592636 7.070407 62.244 62.244 62.244 -9.4421917e-05 -0.00029455229 0.0051668821 - 6900 1.4364121 5.8904988 7.0187235 0.00647853 7.2977086 62.244 62.244 62.244 0.0024458531 0.0073279625 0.0096617742 - 7000 1.4370567 5.8900758 7.0188069 0.00098705898 7.0613127 62.244 62.244 62.244 0.0024436343 -0.0011032284 0.001620771 -Loop time of 1.44111 on 1 procs for 1000 steps with 5600 atoms - -Performance: 299769.942 tau/day, 693.912 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.14928 | 0.14928 | 0.14928 | 0.0 | 10.36 -Bond | 0.053511 | 0.053511 | 0.053511 | 0.0 | 3.71 -Neigh | 0.35946 | 0.35946 | 0.35946 | 0.0 | 24.94 -Comm | 0.033026 | 0.033026 | 0.033026 | 0.0 | 2.29 -Output | 0.00081658 | 0.00081658 | 0.00081658 | 0.0 | 0.06 -Modify | 0.80995 | 0.80995 | 0.80995 | 0.0 | 56.20 -Other | | 0.03506 | | | 2.43 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1351 ave 1351 max 1351 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 5541 ave 5541 max 5541 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 5541 -Ave neighs/atom = 0.989464 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 153 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.4370567 5.8900758 7.0188069 -0.0033603557 6.8740999 62.244 62.244 62.244 -0.094745193 0.10894465 -0.024280521 - 7100 1.485379 5.864626 7.0313116 0.018625962 7.6475425 57.008236 57.008236 57.008236 0.023222208 0.015549704 0.017105973 - 7200 1.5367991 5.8157585 7.0228319 0.019179143 7.4580039 50.273593 50.273593 50.273593 0.019479917 0.008906575 0.029150938 - 7300 1.5692285 5.785208 7.0177529 0.026450106 7.4560147 45.27218 45.27218 45.27218 0.029705272 0.019989987 0.029655059 - 7400 1.5961415 5.7633541 7.0170377 0.049085262 7.6510208 41.665015 41.665015 41.665015 0.045248259 0.047932005 0.054075524 - 7500 1.5805951 5.7223115 6.9637843 0.022024393 7.1962354 38.952791 38.952791 38.952791 0.017398546 0.0097043058 0.038970326 - 7600 1.5679583 5.6928914 6.9244386 0.05023237 7.3717858 36.808633 36.808633 36.808633 0.029561593 0.080716323 0.040419195 - 7700 1.5214637 5.661404 6.8564322 0.038992847 7.1614257 35.25044 35.25044 35.25044 0.013961981 0.064676103 0.038340457 - 7800 1.5313649 5.6185256 6.8213307 0.053950562 7.1990319 33.971403 33.971403 33.971403 0.036690654 0.066107903 0.059053129 - 7900 1.5272701 5.5732963 6.7728851 0.067896988 7.2131774 33.115109 33.115109 33.115109 0.046486851 0.073976177 0.083227936 - 8000 1.4754162 5.5525858 6.7114461 0.036458901 6.9347086 32.48878 32.48878 32.48878 0.066065978 0.031260775 0.01204995 -Loop time of 3.09124 on 1 procs for 1000 steps with 5600 atoms - -Performance: 139749.554 tau/day, 323.494 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.38334 | 0.38334 | 0.38334 | 0.0 | 12.40 -Bond | 0.079063 | 0.079063 | 0.079063 | 0.0 | 2.56 -Neigh | 1.3711 | 1.3711 | 1.3711 | 0.0 | 44.35 -Comm | 0.07249 | 0.07249 | 0.07249 | 0.0 | 2.35 -Output | 0.00079656 | 0.00079656 | 0.00079656 | 0.0 | 0.03 -Modify | 1.1412 | 1.1412 | 1.1412 | 0.0 | 36.92 -Other | | 0.04324 | | | 1.40 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 2922 ave 2922 max 2922 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 24639 ave 24639 max 24639 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 24639 -Ave neighs/atom = 4.39982 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 335 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.784 | 7.784 | 7.784 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.4754162 5.5525858 6.7114461 -0.036273091 6.4893215 32.48878 32.48878 32.48878 -0.12886524 -0.13731772 0.15736368 - 8100 1.4842494 5.5359706 6.701769 0.040754696 6.9494736 32.246136 32.48878 32.48878 0.0098547221 0.069850343 0.042559024 - 8200 1.4385513 5.5252007 6.6551057 -0.0053954052 6.6228379 31.729684 32.48878 32.48878 0.029251386 -0.023427626 -0.022009975 - 8300 1.4426011 5.5073818 6.6404676 0.034683453 6.8437384 31.093797 32.48878 32.48878 0.028287259 0.027455229 0.048307871 - 8400 1.4194517 5.5015592 6.6164624 0.015869651 6.7074209 30.408624 32.48878 32.48878 0.020129982 0.00586219 0.021616782 - 8500 1.4584335 5.4424151 6.5879365 0.025786252 6.7324275 29.728548 32.48878 32.48878 0.051564744 0.0046756434 0.021118368 - 8600 1.4578973 5.4266016 6.5717019 0.061244725 6.9097759 29.286286 32.48878 32.48878 0.08652905 0.052448352 0.044756773 - 8700 1.4158345 5.4199695 6.5320317 0.076133238 6.9466617 28.894001 32.48878 32.48878 0.078560655 0.077921379 0.071917679 - 8800 1.4360707 5.3986549 6.5266116 0.05106059 6.7993343 28.337182 32.48878 32.48878 0.030158729 0.080651224 0.042371819 - 8900 1.424778 5.386975 6.5060619 0.0023828771 6.5185272 27.75397 32.48878 32.48878 -0.026562751 0.0076340254 0.026077357 - 9000 1.4273004 5.369067 6.490135 0.077698761 6.8879525 27.163833 32.48878 32.48878 0.056923916 0.050917329 0.12525504 -Loop time of 3.05599 on 1 procs for 1000 steps with 5600 atoms - -Performance: 141361.930 tau/day, 327.227 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.60397 | 0.60397 | 0.60397 | 0.0 | 19.76 -Bond | 0.080384 | 0.080384 | 0.080384 | 0.0 | 2.63 -Neigh | 1.1078 | 1.1078 | 1.1078 | 0.0 | 36.25 -Comm | 0.057267 | 0.057267 | 0.057267 | 0.0 | 1.87 -Output | 0.0007937 | 0.0007937 | 0.0007937 | 0.0 | 0.03 -Modify | 1.1674 | 1.1674 | 1.1674 | 0.0 | 38.20 -Other | | 0.03837 | | | 1.26 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3326 ave 3326 max 3326 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 31301 ave 31301 max 31301 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 31301 -Ave neighs/atom = 5.58946 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 168 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.787 | 7.787 | 7.787 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.4273004 5.369067 6.490135 0.075024718 6.8742614 27.163833 32.48878 32.48878 0.020257355 0.083191009 0.12162579 - 9100 1.425834 5.3711961 6.4911123 0.045582762 6.7236289 27.13015 32.448495 32.448495 0.047970965 0.045448278 0.043329042 - 9200 1.4609827 5.3288319 6.4763555 0.072880923 6.8414166 26.96611 32.252298 32.252298 0.053774659 0.093193782 0.071674329 - 9300 1.448717 5.3331013 6.4709909 0.048446002 6.7095138 26.811748 32.067676 32.067676 0.053340258 0.056657855 0.035339893 - 9400 1.441683 5.326611 6.4589758 0.014571871 6.5288665 26.578822 31.789089 31.789089 0.043939432 -0.038654064 0.038430244 - 9500 1.4651641 5.2943716 6.4451796 0.079668782 6.8205296 26.421077 31.600422 31.600422 0.10411792 0.075090335 0.059798087 - 9600 1.4617024 5.2886327 6.4367216 0.01137432 6.4894218 26.274239 31.424799 31.424799 0.023318055 0.015516795 -0.0047118896 - 9700 1.4381296 5.2798198 6.4093935 0.030371415 6.5484925 26.173039 31.303761 31.303761 0.05231569 0.025227191 0.013571362 - 9800 1.4412744 5.2674085 6.3994523 0.076731911 6.7476559 26.092768 31.207754 31.207754 0.05712947 0.077029719 0.096036545 - 9900 1.4427959 5.2666411 6.39988 0.034570225 6.5551479 26.003248 31.100686 31.100686 0.020955217 0.019879252 0.062876207 - 10000 1.4337411 5.258442 6.3845688 0.011619021 6.4367617 26.004486 31.102166 31.102166 0.018666906 0.01076669 0.005423467 -Loop time of 3.23963 on 1 procs for 1000 steps with 5600 atoms - -Performance: 133348.758 tau/day, 308.678 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.71266 | 0.71266 | 0.71266 | 0.0 | 22.00 -Bond | 0.0805 | 0.0805 | 0.0805 | 0.0 | 2.48 -Neigh | 1.2019 | 1.2019 | 1.2019 | 0.0 | 37.10 -Comm | 0.061646 | 0.061646 | 0.061646 | 0.0 | 1.90 -Output | 0.00080585 | 0.00080585 | 0.00080585 | 0.0 | 0.02 -Modify | 1.1436 | 1.1436 | 1.1436 | 0.0 | 35.30 -Other | | 0.03849 | | | 1.19 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3617 ave 3617 max 3617 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 35834 ave 35834 max 35834 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 35834 -Ave neighs/atom = 6.39893 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 162 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.793 | 7.793 | 7.793 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4337411 5.258442 6.3845688 0.26156311 7.559515 26.004486 31.102166 31.102166 0.31569183 0.56043401 -0.091436513 - 10100 1.4450694 5.2429626 6.3779872 0.026397674 6.4966895 26.018016 31.118349 31.102166 0.012890725 0.035887426 0.030414871 - 10200 1.4603735 5.2471262 6.3941713 0.041496848 6.5804213 25.993694 31.089259 31.102166 0.043043384 0.031851909 0.04959525 - 10300 1.4434562 5.2268279 6.3605855 0.073867581 6.6874051 25.808018 30.867184 31.102166 0.049265569 0.084151743 0.08818543 - 10400 1.4391471 5.209772 6.3401449 0.010656841 6.3865593 25.605881 30.625422 31.102166 -0.012411333 -0.014743822 0.059125677 - 10500 1.4239127 5.2146206 6.3330277 0.08346505 6.689122 25.342982 30.310987 31.102166 0.15420896 0.040839126 0.055347067 - 10600 1.4524651 5.1794989 6.3203324 -0.025909515 6.2120807 25.079294 29.995608 31.102166 -0.014573849 -0.056558124 -0.0065965719 - 10700 1.4455577 5.1721256 6.3075337 0.084888991 6.6555495 24.842844 29.712806 31.102166 0.10063515 0.067972312 0.08605951 - 10800 1.4598996 5.15251 6.2991829 0.11430526 6.7624231 24.700034 29.542001 31.102166 0.12408423 0.12316195 0.095669606 - 10900 1.4149128 5.1641212 6.2754594 0.045495923 6.4584246 24.605124 29.428485 31.102166 0.10001213 0.053235051 -0.016759411 - 11000 1.3909637 5.1566933 6.2492208 0.046382806 6.433354 24.446408 29.238657 31.102166 0.091440494 0.0046064525 0.043101472 -Loop time of 3.41971 on 1 procs for 1000 steps with 5600 atoms - -Performance: 126326.531 tau/day, 292.423 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.78521 | 0.78521 | 0.78521 | 0.0 | 22.96 -Bond | 0.080655 | 0.080655 | 0.080655 | 0.0 | 2.36 -Neigh | 1.2846 | 1.2846 | 1.2846 | 0.0 | 37.57 -Comm | 0.064334 | 0.064334 | 0.064334 | 0.0 | 1.88 -Output | 0.00080228 | 0.00080228 | 0.00080228 | 0.0 | 0.02 -Modify | 1.1651 | 1.1651 | 1.1651 | 0.0 | 34.07 -Other | | 0.03903 | | | 1.14 - -Nlocal: 5600 ave 5600 max 5600 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 3805 ave 3805 max 3805 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 40038 ave 40038 max 40038 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 40038 -Ave neighs/atom = 7.14964 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 162 -Dangerous builds = 0 - -Total wall time: 0:00:22 diff --git a/examples/rigid/log.20Apr18.rigid.tnr.g++.4 b/examples/rigid/log.20Apr18.rigid.tnr.g++.4 deleted file mode 100644 index 28457f51ee..0000000000 --- a/examples/rigid/log.20Apr18.rigid.tnr.g++.4 +++ /dev/null @@ -1,458 +0,0 @@ -LAMMPS (20 Apr 2018) - using 1 OpenMP thread(s) per MPI task -# Tethered nanorods - -atom_style molecular - -read_data data.rigid.tnr - orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 5600 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 1600 bonds - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -# Specify bond parameters - -bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 - -special_bonds fene - 2 = max # of 1-2 neighbors - 2 = max # of special neighbors - -# Specify initial velocities - -velocity all create 1.4 109345 - -# Specify rigid components - -group rods type 2 -4000 atoms in group rods -group tethers subtract all rods -1600 atoms in group tethers - -neigh_modify exclude molecule/intra rods delay 0 every 1 - -# Specify the pair potentials - -pair_style lj/cut 2.5 -pair_modify shift yes -pair_coeff * * 1.0 1.0 1.122 -pair_coeff 2 2 1.0 1.0 2.5 - -# Specify output - -thermo 100 -thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz -thermo_modify flush yes lost warn - -timestep 0.005 - -fix 1 rods rigid molecule -800 rigid bodies with 4000 atoms -fix 2 tethers nve -fix 3 all langevin 1.4 1.4 1.0 437624 - -run 5000 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4, bins = 45 45 45 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 - 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 - 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 - 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 - 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 - 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 - 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 - 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 - 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 - 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 - 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 - 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 - 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 - 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 - 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 - 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278431 - 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 - 1700 1.3612202 5.9676733 7.0368389 0.0001686213 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 - 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 - 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 - 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119435 -0.0036279901 - 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 - 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 - 2300 1.4048926 5.9444129 7.0478808 0.0062444035 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 - 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825028 - 2500 1.4200762 5.9359254 7.0513193 0.002831965 7.1732722 62.244 62.244 62.244 -0.00030414188 0.0039571831 0.0048428539 - 2600 1.3876469 5.9249124 7.0148347 -0.0017777223 6.9382806 62.244 62.244 62.244 -0.00047616388 -0.0025484917 -0.0023085112 - 2700 1.4099941 5.916763 7.0242378 0.0070716262 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048357 - 2800 1.4444643 5.9283432 7.0628925 0.0019400019 7.1464348 62.244 62.244 62.244 0.0014895075 0.0046367395 -0.0003062412 - 2900 1.3902832 5.9152516 7.0072446 -0.0021662211 6.9139606 62.244 62.244 62.244 -0.0012374413 -0.00056403267 -0.0046971892 - 3000 1.3711706 5.922146 6.999127 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093025 0.010147658 - 3100 1.3569137 5.9171753 6.9829583 -0.0028266781 6.861233 62.244 62.244 62.244 -0.0069507246 0.001008439 -0.0025377485 - 3200 1.4004275 5.905939 7.0058998 0.005439464 7.2401395 62.244 62.244 62.244 0.010352181 0.0057594129 0.00020679783 - 3300 1.3641217 5.9145275 6.985972 -0.0027212797 6.8687855 62.244 62.244 62.244 -0.00065933477 -0.0057712994 -0.0017332048 - 3400 1.3868722 5.9059546 6.9952684 0.0092591181 7.3939939 62.244 62.244 62.244 0.010690872 0.01075251 0.0063339724 - 3500 1.3939168 5.8992292 6.9940762 0.0074340103 7.3142071 62.244 62.244 62.244 0.010137319 0.0044252681 0.0077394433 - 3600 1.3982507 5.921946 7.020197 0.0056794467 7.2647712 62.244 62.244 62.244 0.0023367139 0.0080592038 0.0066424225 - 3700 1.4019908 5.9059954 7.007184 0.0065915246 7.291035 62.244 62.244 62.244 0.0049554227 0.010827006 0.0039921455 - 3800 1.3960735 5.9020788 6.9986197 0.0027763543 7.1181779 62.244 62.244 62.244 -0.0015907599 0.0025861989 0.007333624 - 3900 1.4352827 5.8986213 7.025959 0.0034983366 7.1766079 62.244 62.244 62.244 0.0030418079 0.002773833 0.0046793689 - 4000 1.4121839 5.9079032 7.017098 0.0050464926 7.2344152 62.244 62.244 62.244 0.0045546986 0.0064116168 0.0041731626 - 4100 1.3989613 5.9082377 7.0070468 0.00042898744 7.0255203 62.244 62.244 62.244 0.0025736361 0.0025182434 -0.0038049172 - 4200 1.3998851 5.8998106 6.9993454 0.0042770066 7.1835262 62.244 62.244 62.244 0.0013728904 0.0064694548 0.0049886746 - 4300 1.4076016 5.9044534 7.0100491 0.0066777871 7.2976147 62.244 62.244 62.244 0.0073579039 0.0048129651 0.0078624924 - 4400 1.3948857 5.9101851 7.0057931 0.0013429373 7.063624 62.244 62.244 62.244 -0.00084288143 0.0061856571 -0.0013139638 - 4500 1.4356157 5.8855608 7.01316 -0.0013707942 6.9541295 62.244 62.244 62.244 -0.0018523205 -0.0050195956 0.0027595334 - 4600 1.4148397 5.8957564 7.0070372 0.0072212968 7.318008 62.244 62.244 62.244 0.011376867 0.0074399971 0.0028470263 - 4700 1.3695106 5.8936708 6.969348 0.0017509017 7.0447471 62.244 62.244 62.244 -0.0061975951 0.0044076775 0.0070426225 - 4800 1.4142735 5.8887578 6.9995939 0.0081923232 7.35238 62.244 62.244 62.244 0.013343877 0.0054560473 0.0057770449 - 4900 1.4300042 5.8867398 7.0099315 0.0070875112 7.3151411 62.244 62.244 62.244 0.0080416381 0.0042409901 0.0089799056 - 5000 1.4286039 5.8964609 7.0185527 -0.003158533 6.8825368 62.244 62.244 62.244 0.0024975808 -0.0097503027 -0.0022228771 -Loop time of 3.4608 on 4 procs for 5000 steps with 5600 atoms - -Performance: 624133.913 tau/day, 1444.754 timesteps/s -98.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.083226 | 0.13336 | 0.18611 | 13.0 | 3.85 -Bond | 0.045169 | 0.066142 | 0.087486 | 7.8 | 1.91 -Neigh | 0.57772 | 0.57997 | 0.58211 | 0.3 | 16.76 -Comm | 0.19402 | 0.26217 | 0.32776 | 12.2 | 7.58 -Output | 0.0027087 | 0.0035715 | 0.0041978 | 0.9 | 0.10 -Modify | 2.1223 | 2.2156 | 2.2842 | 4.2 | 64.02 -Other | | 0.2 | | | 5.78 - -Nlocal: 1400 ave 1844 max 907 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 642 ave 714 max 581 min -Histogram: 1 1 0 0 0 0 1 0 0 1 -Neighs: 1307.25 ave 1883 max 682 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 5229 -Ave neighs/atom = 0.93375 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 762 -Dangerous builds = 0 - -# Replace fix rigid and fix langevin with new ones - -unfix 1 -unfix 3 - -fix 3 tethers langevin 1.4 1.4 1.0 198450 - -# Test different integrators for rods - -fix 1 rods rigid/nve molecule -800 rigid bodies with 4000 atoms -print "rigid/nve" -rigid/nve -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 5000 1.4286039 5.8964609 7.0185527 -0.017900244 6.2477142 62.244 62.244 62.244 -0.017934885 -0.027283526 -0.0084823215 - 5100 1.4251274 5.887521 7.0068821 0.0066290394 7.2923486 62.244 62.244 62.244 0.0033173534 0.0056467845 0.01092298 - 5200 1.4246222 5.8928547 7.0118192 -0.00025763331 7.0007247 62.244 62.244 62.244 -0.001891953 -0.0031121381 0.0042311911 - 5300 1.3905023 5.9024119 6.994577 0.0026824588 7.1100918 62.244 62.244 62.244 0.003106008 0.0040692376 0.00087213068 - 5400 1.4139617 5.8906493 7.0012405 0.003175173 7.137973 62.244 62.244 62.244 0.0034546577 0.003858524 0.0022123373 - 5500 1.4160473 5.8891813 7.0014106 0.0032907848 7.1431217 62.244 62.244 62.244 0.0014909385 0.0067546452 0.0016267707 - 5600 1.4185962 5.8932473 7.0074786 0.013015823 7.5679792 62.244 62.244 62.244 0.011297248 0.011426835 0.016323387 - 5700 1.4115847 5.892193 7.0009171 0.0080660065 7.3482637 62.244 62.244 62.244 0.0096534077 0.004127271 0.010417341 - 5800 1.3920238 5.8874957 6.9808558 0.0087013878 7.3555639 62.244 62.244 62.244 0.0070865796 0.0093328615 0.0096847223 - 5900 1.389416 5.8996657 6.9909775 0.0053218583 7.2201528 62.244 62.244 62.244 0.0050547275 0.0054113274 0.0054995198 - 6000 1.4079053 5.8795437 6.9853779 0.0066005053 7.2696156 62.244 62.244 62.244 0.0087434104 0.0013589366 0.0096991689 -Loop time of 0.793224 on 4 procs for 1000 steps with 5600 atoms - -Performance: 544612.641 tau/day, 1260.677 timesteps/s -98.6% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.018101 | 0.036068 | 0.051689 | 7.6 | 4.55 -Bond | 0.0083735 | 0.013206 | 0.017318 | 3.6 | 1.66 -Neigh | 0.12864 | 0.1293 | 0.13002 | 0.1 | 16.30 -Comm | 0.037184 | 0.056407 | 0.077999 | 7.4 | 7.11 -Output | 0.00048971 | 0.00072509 | 0.00083923 | 0.0 | 0.09 -Modify | 0.49526 | 0.51293 | 0.52997 | 2.2 | 64.66 -Other | | 0.04459 | | | 5.62 - -Nlocal: 1400 ave 1844 max 884 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 713.5 ave 818 max 656 min -Histogram: 1 1 1 0 0 0 0 0 0 1 -Neighs: 1315 ave 1956 max 573 min -Histogram: 1 0 1 0 0 0 0 0 0 2 - -Total # of neighbors = 5260 -Ave neighs/atom = 0.939286 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 156 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 -800 rigid bodies with 4000 atoms -print "rigid/nvt" -rigid/nvt -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 6000 1.4079053 5.8795437 6.9853779 0.010184208 7.4239406 62.244 62.244 62.244 0.0015995549 0.064769849 -0.035816779 - 6100 1.4031886 5.8721732 6.9743027 0.0039601 7.1448365 62.244 62.244 62.244 0.0019177243 0.0048575488 0.005105027 - 6200 1.4078378 5.8813987 6.9871798 -0.0019043091 6.9051745 62.244 62.244 62.244 -0.0012543967 -0.0035545317 -0.00090399881 - 6300 1.3898748 5.8818577 6.97353 0.0050781011 7.1922083 62.244 62.244 62.244 0.0037642013 0.0035169519 0.0079531499 - 6400 1.3901345 5.8620878 6.953964 -0.0013161864 6.897285 62.244 62.244 62.244 0.0024166375 -0.0023907165 -0.0039744801 - 6500 1.3990792 5.8647534 6.9636551 0.0025190902 7.0721348 62.244 62.244 62.244 0.003080505 -0.00072200043 0.0051987659 - 6600 1.3802747 5.8639204 6.9480523 0.0030906745 7.0811461 62.244 62.244 62.244 0.0041979458 0.0059358092 -0.00086173155 - 6700 1.392968 5.8692368 6.9633385 0.00060394401 6.9893462 62.244 62.244 62.244 0.0037955666 0.00058857296 -0.0025723075 - 6800 1.4139599 5.8777321 6.9883218 0.0064457022 7.2658932 62.244 62.244 62.244 0.0066202313 0.0077537688 0.0049631066 - 6900 1.3913822 5.8914016 6.9842578 0.0012411779 7.0377066 62.244 62.244 62.244 -0.0029791199 0.0027656154 0.0039370381 - 7000 1.4203244 5.8676225 6.9832112 0.0053040447 7.2116194 62.244 62.244 62.244 0.0024159021 0.0053958945 0.0081003375 -Loop time of 0.812983 on 4 procs for 1000 steps with 5600 atoms - -Performance: 531376.713 tau/day, 1230.039 timesteps/s -98.2% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.020489 | 0.038507 | 0.054352 | 7.9 | 4.74 -Bond | 0.0086164 | 0.013153 | 0.017908 | 3.5 | 1.62 -Neigh | 0.13205 | 0.13275 | 0.13353 | 0.1 | 16.33 -Comm | 0.039251 | 0.05774 | 0.079146 | 7.7 | 7.10 -Output | 0.00057149 | 0.00076026 | 0.00087905 | 0.0 | 0.09 -Modify | 0.51332 | 0.52873 | 0.54512 | 2.1 | 65.04 -Other | | 0.04134 | | | 5.09 - -Nlocal: 1400 ave 1861 max 953 min -Histogram: 2 0 0 0 0 0 0 0 1 1 -Nghost: 732.5 ave 799 max 634 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Neighs: 1478.5 ave 2087 max 852 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 5914 -Ave neighs/atom = 1.05607 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 154 -Dangerous builds = 0 -unfix 1 - -compute myTemp all temp - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt iso" -rigid/npt iso -fix_modify 1 temp myTemp - -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 7000 1.4203244 5.8676225 6.9832112 -0.040722281 5.2295869 62.244 62.244 62.244 -0.12474488 0.041369653 -0.038791619 - 7100 1.4820526 5.8454198 7.0094927 0.013935005 7.4687465 56.934813 56.934813 56.934813 0.011753675 0.011015866 0.019035475 - 7200 1.5504398 5.8024995 7.0202869 0.023075447 7.5454178 50.323226 50.323226 50.323226 0.02128889 0.024383628 0.023553823 - 7300 1.5422614 5.7803177 6.9916814 0.022398755 7.3670099 45.442117 45.442117 45.442117 0.011815608 0.027421849 0.027958808 - 7400 1.5762224 5.7500188 6.988057 0.044637382 7.5673845 41.732187 41.732187 41.732187 0.045858714 0.035776277 0.052277154 - 7500 1.5734284 5.7222605 6.9581042 0.029862564 7.2743396 38.996336 38.996336 38.996336 0.024440229 0.034455527 0.030691934 - 7600 1.5572312 5.6929606 6.9160823 0.050216724 7.366563 36.898208 36.898208 36.898208 0.059366814 0.056376093 0.034907266 - 7700 1.5225653 5.659289 6.8551824 0.042054552 7.1814902 35.15611 35.15611 35.15611 0.043735305 0.039349247 0.043079104 - 7800 1.5081978 5.629903 6.8145116 0.057013188 7.2106251 33.885255 33.885255 33.885255 0.055017894 0.053733429 0.062288242 - 7900 1.4721367 5.5821237 6.7384082 0.067262555 7.1645957 32.860322 32.860322 32.860322 0.097134972 0.066643481 0.03800921 - 8000 1.4710105 5.5302806 6.6856805 0.054118027 7.0029681 32.020862 32.020862 32.020862 0.039052412 0.059044234 0.064257435 -Loop time of 1.47728 on 4 procs for 1000 steps with 5600 atoms - -Performance: 292430.022 tau/day, 676.921 timesteps/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.064968 | 0.10073 | 0.1395 | 10.5 | 6.82 -Bond | 0.014031 | 0.019927 | 0.02572 | 3.7 | 1.35 -Neigh | 0.52043 | 0.52145 | 0.52214 | 0.1 | 35.30 -Comm | 0.069327 | 0.11344 | 0.15499 | 11.3 | 7.68 -Output | 0.00045276 | 0.00050163 | 0.00058174 | 0.0 | 0.03 -Modify | 0.65598 | 0.67559 | 0.69898 | 2.4 | 45.73 -Other | | 0.04563 | | | 3.09 - -Nlocal: 1400 ave 1711 max 1074 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 1617 ave 1748 max 1514 min -Histogram: 1 0 0 2 0 0 0 0 0 1 -Neighs: 6221.75 ave 8875 max 3829 min -Histogram: 2 0 0 0 0 0 0 0 1 1 - -Total # of neighbors = 24887 -Ave neighs/atom = 4.44411 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 340 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/npt x" -rigid/npt x -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.408 | 7.596 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 8000 1.4710105 5.5302806 6.6856805 0.19181859 7.81029 32.020862 32.020862 32.020862 0.26866704 0.14123342 0.16555531 - 8100 1.47531 5.5300767 6.6888537 0.072844262 7.1138998 31.868578 32.020862 32.020862 0.090224787 0.062332105 0.065975895 - 8200 1.448408 5.51143 6.6490768 0.069870568 7.0519422 31.491082 32.020862 32.020862 0.087940256 0.058037199 0.063634249 - 8300 1.4057002 5.4923673 6.5964694 0.065508742 6.9688194 31.043742 32.020862 32.020862 0.079268242 0.048811269 0.068446714 - 8400 1.3991297 5.4626242 6.5615657 -0.017027709 6.4660067 30.650474 32.020862 32.020862 0.0088006578 -0.001632039 -0.058251747 - 8500 1.4126457 5.4676374 6.5771949 0.012615987 6.6471389 30.279686 32.020862 32.020862 0.010145607 0.017449486 0.010252867 - 8600 1.4250925 5.4367644 6.5560982 0.057260287 6.8682646 29.775194 32.020862 32.020862 0.05660339 0.10551068 0.0096667873 - 8700 1.4259617 5.431439 6.5514555 0.060058224 6.8743509 29.36374 32.020862 32.020862 0.059243843 0.040552126 0.080378702 - 8800 1.4336545 5.3949149 6.5209738 0.052324111 6.7965365 28.763424 32.020862 32.020862 0.02607362 0.067534725 0.063363987 - 8900 1.4228767 5.3718196 6.489413 0.04039784 6.6975045 28.133143 32.020862 32.020862 0.038493401 0.059136317 0.023563801 - 9000 1.3840335 5.3851579 6.4722421 0.055356171 6.7513156 27.534332 32.020862 32.020862 0.067391117 0.061540537 0.03713686 -Loop time of 1.41644 on 4 procs for 1000 steps with 5600 atoms - -Performance: 304989.819 tau/day, 705.995 timesteps/s -98.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.111 | 0.15928 | 0.20768 | 11.1 | 11.25 -Bond | 0.014816 | 0.020169 | 0.024592 | 3.1 | 1.42 -Neigh | 0.40146 | 0.40175 | 0.40221 | 0.0 | 28.36 -Comm | 0.063586 | 0.11635 | 0.16698 | 14.1 | 8.21 -Output | 0.00045538 | 0.00050312 | 0.00063586 | 0.0 | 0.04 -Modify | 0.66405 | 0.67875 | 0.69575 | 1.6 | 47.92 -Other | | 0.03963 | | | 2.80 - -Nlocal: 1400 ave 1641 max 1120 min -Histogram: 1 0 1 0 0 0 0 0 0 2 -Nghost: 1593.5 ave 1674 max 1480 min -Histogram: 1 0 0 1 0 0 0 0 0 2 -Neighs: 7766.25 ave 10004 max 5618 min -Histogram: 2 0 0 0 0 0 0 0 0 2 - -Total # of neighbors = 31065 -Ave neighs/atom = 5.54732 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 168 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph iso" -rigid/nph iso -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.228 | 7.409 | 7.596 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 9000 1.3840335 5.3851579 6.4722421 0.16503405 7.3042475 27.534332 32.020862 32.020862 0.18505216 0.10781406 0.20223595 - 9100 1.3884253 5.3614209 6.4519546 -0.00091586458 6.4474179 27.373411 31.83372 31.83372 0.022761165 -0.0041100422 -0.021398716 - 9200 1.420492 5.3303864 6.4461068 0.059143817 6.7274082 27.005021 31.405303 31.405303 0.083033013 0.062389471 0.032008967 - 9300 1.4715513 5.2993502 6.4551749 -0.0012173753 6.4496031 26.66115 31.005402 31.005402 3.6757409e-05 -0.035942133 0.03225325 - 9400 1.446323 5.2997487 6.4357579 0.089723486 6.8324557 26.355721 30.650205 30.650205 0.074549411 0.091827859 0.10279319 - 9500 1.4429552 5.2778071 6.4111711 0.074185245 6.7328342 26.184941 30.451597 30.451597 0.081909739 0.072238574 0.068407422 - 9600 1.4570864 5.2601352 6.4045984 0.0580315 6.6544318 26.122769 30.379295 30.379295 0.060115487 0.027228888 0.086750125 - 9700 1.4421488 5.2741205 6.4068511 0.044711738 6.5981759 26.069954 30.317874 30.317874 0.093367845 0.025219144 0.015548226 - 9800 1.4305027 5.2831767 6.4067599 0.064007051 6.6787519 26.009567 30.247648 30.247648 0.1207317 0.021857174 0.049432283 - 9900 1.4457473 5.2513943 6.3869514 0.016264617 6.4551575 25.895064 30.114487 30.114487 0.055652525 0.015908352 -0.022767026 - 10000 1.4739193 5.2108898 6.3685744 0.066079547 6.6416503 25.768894 29.967759 29.967759 0.059174033 0.048716715 0.090347892 -Loop time of 1.47405 on 4 procs for 1000 steps with 5600 atoms - -Performance: 293069.938 tau/day, 678.403 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.14109 | 0.19261 | 0.2429 | 10.7 | 13.07 -Bond | 0.015511 | 0.020164 | 0.023957 | 2.5 | 1.37 -Neigh | 0.43698 | 0.43723 | 0.43759 | 0.0 | 29.66 -Comm | 0.064379 | 0.1184 | 0.17429 | 14.5 | 8.03 -Output | 0.00053048 | 0.00056964 | 0.00067139 | 0.0 | 0.04 -Modify | 0.65413 | 0.66598 | 0.68039 | 1.3 | 45.18 -Other | | 0.0391 | | | 2.65 - -Nlocal: 1400 ave 1629 max 1159 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Nghost: 1760.25 ave 1871 max 1635 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Neighs: 9467.75 ave 11967 max 6712 min -Histogram: 1 1 0 0 0 0 0 0 0 2 - -Total # of neighbors = 37871 -Ave neighs/atom = 6.76268 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 163 -Dangerous builds = 0 -unfix 1 - -fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all -800 rigid bodies with 4000 atoms -print "rigid/nph xy couple" -rigid/nph xy couple -run 1000 -Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes -Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz - 10000 1.4739193 5.2108898 6.3685744 0.15675952 7.0163882 25.768894 29.967759 29.967759 0.15485552 -0.045372029 0.36079506 - 10100 1.450711 5.2108741 6.3503298 0.0083383764 6.3849239 25.819477 30.026584 29.967759 0.0025039775 -0.0028716599 0.025382812 - 10200 1.4627819 5.2187046 6.3676414 0.031215755 6.4961258 25.717327 29.907789 29.967759 0.04657158 0.0023172248 0.044758461 - 10300 1.4689915 5.2231223 6.3769364 0.094530779 6.7645053 25.667024 29.84929 29.967759 0.10402187 0.089461211 0.090109255 - 10400 1.465366 5.211321 6.3622875 0.057765151 6.5976168 25.585426 29.754396 29.967759 0.025724468 0.03148259 0.1160884 - 10500 1.4206144 5.2096595 6.325476 0.029618225 6.4439115 25.348314 29.478648 29.967759 0.016757876 -0.021974627 0.094071428 - 10600 1.4490516 5.1686358 6.3067882 0.10186675 6.705618 25.082174 29.169143 29.967759 0.13985672 0.13649813 0.029245401 - 10700 1.42637 5.1516578 6.271995 0.12577606 6.7554051 24.851151 28.900476 29.967759 0.099699897 0.11678127 0.16084703 - 10800 1.4675204 5.1334029 6.2860615 0.054610838 6.494291 24.752517 28.78577 29.967759 0.018006539 0.090588468 0.055237507 - 10900 1.4312627 5.1332052 6.2573854 -0.0020120377 6.2496947 24.782913 28.821119 29.967759 -0.0035770106 0.047436898 -0.049896 - 11000 1.3986074 5.1272068 6.225738 0.045641244 6.3993661 24.72401 28.752618 29.967759 0.052336235 0.073561738 0.011025759 -Loop time of 1.50406 on 4 procs for 1000 steps with 5600 atoms - -Performance: 287222.965 tau/day, 664.868 timesteps/s -98.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.16856 | 0.21287 | 0.26569 | 9.4 | 14.15 -Bond | 0.016815 | 0.020397 | 0.023304 | 1.9 | 1.36 -Neigh | 0.44152 | 0.44161 | 0.44172 | 0.0 | 29.36 -Comm | 0.067729 | 0.1232 | 0.16886 | 13.0 | 8.19 -Output | 0.00045419 | 0.00048572 | 0.0005734 | 0.0 | 0.03 -Modify | 0.6568 | 0.66799 | 0.6841 | 1.3 | 44.41 -Other | | 0.0375 | | | 2.49 - -Nlocal: 1400 ave 1605 max 1229 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Nghost: 1859 ave 1964 max 1718 min -Histogram: 1 0 0 0 0 1 0 1 0 1 -Neighs: 10208.2 ave 13091 max 7670 min -Histogram: 1 1 0 0 0 0 1 0 0 1 - -Total # of neighbors = 40833 -Ave neighs/atom = 7.29161 -Ave special neighs/atom = 0.571429 -Neighbor list builds = 160 -Dangerous builds = 0 - -Total wall time: 0:00:10 diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 b/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 similarity index 90% rename from examples/rigid/log.20Apr18.rigid.atomfile.g++.4 rename to examples/rigid/log.27Nov18.rigid.atomfile.g++.1 index 70f86f32bb..e3e539eada 100644 --- a/examples/rigid/log.20Apr18.rigid.atomfile.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -10,7 +10,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 81 atoms @@ -106,7 +106,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -160,8 +160,8 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 2800 16738.585 -0.046813448 0 5269.5076 14.511073 @@ -169,7 +169,7 @@ Step Temp E_pair E_mol TotEng Press 2900 16738.465 -0.0026252725 0 5269.514 14.510277 2950 16738.476 -0.0082220764 0 5269.512 14.510223 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3050 16715.332 7.2419352 0 5269.476 14.870305 3100 16653.226 26.818761 0 5269.5009 14.496764 3150 16739.351 -0.30690375 0 5269.4886 13.643904 3200 16733.238 1.6025328 0 5269.4737 12.016934 @@ -179,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press 3400 16738.543 -0.042215005 0 5269.4991 12.092809 3450 16738.591 -0.059327511 0 5269.4972 12.092536 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 3700 16738.602 -0.070934368 0 5269.4889 12.025288 @@ -277,8 +277,8 @@ Step Temp E_pair E_mol TotEng Press 8300 16738.471 0 0 5269.5187 12.011719 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -298,38 +298,38 @@ Step Temp E_pair E_mol TotEng Press 9350 16738.48 0 0 5269.5214 12.011744 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589887 0 5269.4979 12.062708 - 9750 16738.013 0.135501 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.191483 on 4 procs for 10000 steps with 81 atoms +Loop time of 0.153749 on 1 procs for 10000 steps with 81 atoms -Performance: 451214.099 tau/day, 52223.854 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 561955.786 tau/day, 65041.179 timesteps/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0024264 | 0.0036595 | 0.0042815 | 1.2 | 1.91 -Neigh | 0.011347 | 0.012011 | 0.013367 | 0.7 | 6.27 -Comm | 0.081701 | 0.083476 | 0.087947 | 0.9 | 43.59 -Output | 0.0042565 | 0.0045614 | 0.0053556 | 0.7 | 2.38 -Modify | 0.075719 | 0.078165 | 0.080737 | 0.7 | 40.82 -Other | | 0.009611 | | | 5.02 +Pair | 0.0098538 | 0.0098538 | 0.0098538 | 0.0 | 6.41 +Neigh | 0.040308 | 0.040308 | 0.040308 | 0.0 | 26.22 +Comm | 0.013034 | 0.013034 | 0.013034 | 0.0 | 8.48 +Output | 0.0017202 | 0.0017202 | 0.0017202 | 0.0 | 1.12 +Modify | 0.083709 | 0.083709 | 0.083709 | 0.0 | 54.45 +Other | | 0.005123 | | | 3.33 -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 b/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 similarity index 92% rename from examples/rigid/log.20Apr18.rigid.atomfile.g++.1 rename to examples/rigid/log.27Nov18.rigid.atomfile.g++.4 index c66711c41c..1e28766101 100644 --- a/examples/rigid/log.20Apr18.rigid.atomfile.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.atomfile.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -10,7 +10,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms @@ -106,7 +106,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.109 | 4.109 | 4.109 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.08 | 4.174 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -160,7 +160,7 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 @@ -182,7 +182,7 @@ Step Temp E_pair E_mol TotEng Press 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 3750 16737.731 0.20706557 0 5269.4927 12.061948 3800 16738.578 -0.05582043 0 5269.4965 12.035665 3850 16738.471 -0.016307928 0 5269.5024 12.035302 @@ -278,7 +278,7 @@ Step Temp E_pair E_mol TotEng Press 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -299,37 +299,37 @@ Step Temp E_pair E_mol TotEng Press 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 9600 16738.549 -0.026814371 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589893 0 5269.4979 12.062708 - 9750 16738.013 0.13550102 0 5269.5101 11.407246 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.140447 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.202963 on 4 procs for 10000 steps with 81 atoms -Performance: 615179.112 tau/day, 71201.286 timesteps/s -98.2% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 425693.239 tau/day, 49270.051 timesteps/s +89.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.010351 | 0.010351 | 0.010351 | 0.0 | 7.37 -Neigh | 0.036597 | 0.036597 | 0.036597 | 0.0 | 26.06 -Comm | 0.0092356 | 0.0092356 | 0.0092356 | 0.0 | 6.58 -Output | 0.0023856 | 0.0023856 | 0.0023856 | 0.0 | 1.70 -Modify | 0.07586 | 0.07586 | 0.07586 | 0.0 | 54.01 -Other | | 0.006017 | | | 4.28 +Pair | 0.0025978 | 0.0033882 | 0.0042055 | 1.0 | 1.67 +Neigh | 0.012025 | 0.013416 | 0.01623 | 1.4 | 6.61 +Comm | 0.080375 | 0.087468 | 0.090782 | 1.4 | 43.10 +Output | 0.0031407 | 0.0039954 | 0.0065427 | 2.3 | 1.97 +Modify | 0.086613 | 0.087285 | 0.087619 | 0.1 | 43.01 +Other | | 0.00741 | | | 3.65 -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 b/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 similarity index 90% rename from examples/rigid/log.20Apr18.rigid.atomvar.g++.4 rename to examples/rigid/log.27Nov18.rigid.atomvar.g++.1 index 76344d0995..58834ebf3d 100644 --- a/examples/rigid/log.20Apr18.rigid.atomvar.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -10,7 +10,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 81 atoms @@ -106,7 +106,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -160,8 +160,8 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 2800 16738.585 -0.046813448 0 5269.5076 14.511073 @@ -169,7 +169,7 @@ Step Temp E_pair E_mol TotEng Press 2900 16738.465 -0.0026252725 0 5269.514 14.510277 2950 16738.476 -0.0082220764 0 5269.512 14.510223 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3050 16715.332 7.2419352 0 5269.476 14.870305 3100 16653.226 26.818761 0 5269.5009 14.496764 3150 16739.351 -0.30690375 0 5269.4886 13.643904 3200 16733.238 1.6025328 0 5269.4737 12.016934 @@ -179,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press 3400 16738.543 -0.042215005 0 5269.4991 12.092809 3450 16738.591 -0.059327511 0 5269.4972 12.092536 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 3700 16738.602 -0.070934368 0 5269.4889 12.025288 @@ -277,8 +277,8 @@ Step Temp E_pair E_mol TotEng Press 8300 16738.471 0 0 5269.5187 12.011719 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -298,38 +298,38 @@ Step Temp E_pair E_mol TotEng Press 9350 16738.48 0 0 5269.5214 12.011744 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589887 0 5269.4979 12.062708 - 9750 16738.013 0.135501 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.202733 on 4 procs for 10000 steps with 81 atoms +Loop time of 0.15622 on 1 procs for 10000 steps with 81 atoms -Performance: 426175.966 tau/day, 49325.922 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 553065.489 tau/day, 64012.209 timesteps/s +95.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0025222 | 0.0037088 | 0.0044038 | 1.2 | 1.83 -Neigh | 0.01135 | 0.012003 | 0.013654 | 0.9 | 5.92 -Comm | 0.088217 | 0.089948 | 0.091659 | 0.4 | 44.37 -Output | 0.0044014 | 0.0047023 | 0.0055132 | 0.7 | 2.32 -Modify | 0.080218 | 0.082638 | 0.084872 | 0.6 | 40.76 -Other | | 0.009733 | | | 4.80 +Pair | 0.0098181 | 0.0098181 | 0.0098181 | 0.0 | 6.28 +Neigh | 0.040912 | 0.040912 | 0.040912 | 0.0 | 26.19 +Comm | 0.013111 | 0.013111 | 0.013111 | 0.0 | 8.39 +Output | 0.0016305 | 0.0016305 | 0.0016305 | 0.0 | 1.04 +Modify | 0.085361 | 0.085361 | 0.085361 | 0.0 | 54.64 +Other | | 0.005387 | | | 3.45 -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 b/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 similarity index 92% rename from examples/rigid/log.20Apr18.rigid.atomvar.g++.1 rename to examples/rigid/log.27Nov18.rigid.atomvar.g++.4 index 99098d04d2..42b8a52768 100644 --- a/examples/rigid/log.20Apr18.rigid.atomvar.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -10,7 +10,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms @@ -106,7 +106,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.984 | 3.984 | 3.984 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.955 | 4.049 | 4.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -160,7 +160,7 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 @@ -182,7 +182,7 @@ Step Temp E_pair E_mol TotEng Press 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 3750 16737.731 0.20706557 0 5269.4927 12.061948 3800 16738.578 -0.05582043 0 5269.4965 12.035665 3850 16738.471 -0.016307928 0 5269.5024 12.035302 @@ -278,7 +278,7 @@ Step Temp E_pair E_mol TotEng Press 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -299,37 +299,37 @@ Step Temp E_pair E_mol TotEng Press 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 9600 16738.549 -0.026814371 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589893 0 5269.4979 12.062708 - 9750 16738.013 0.13550102 0 5269.5101 11.407246 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.139024 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.199799 on 4 procs for 10000 steps with 81 atoms -Performance: 621477.474 tau/day, 71930.263 timesteps/s -99.0% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 432434.078 tau/day, 50050.241 timesteps/s +91.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.010292 | 0.010292 | 0.010292 | 0.0 | 7.40 -Neigh | 0.036968 | 0.036968 | 0.036968 | 0.0 | 26.59 -Comm | 0.0091348 | 0.0091348 | 0.0091348 | 0.0 | 6.57 -Output | 0.0024047 | 0.0024047 | 0.0024047 | 0.0 | 1.73 -Modify | 0.074017 | 0.074017 | 0.074017 | 0.0 | 53.24 -Other | | 0.006207 | | | 4.46 +Pair | 0.002665 | 0.0034567 | 0.0040557 | 0.9 | 1.73 +Neigh | 0.012185 | 0.013168 | 0.014083 | 0.8 | 6.59 +Comm | 0.079331 | 0.082804 | 0.084927 | 0.7 | 41.44 +Output | 0.0031595 | 0.0039212 | 0.0061827 | 2.1 | 1.96 +Modify | 0.088465 | 0.090202 | 0.091938 | 0.4 | 45.15 +Other | | 0.006247 | | | 3.13 -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.4 b/examples/rigid/log.27Nov18.rigid.early.g++.1 similarity index 90% rename from examples/rigid/log.20Apr18.rigid.early.g++.4 rename to examples/rigid/log.27Nov18.rigid.early.g++.1 index c9513a211e..3c8022423f 100644 --- a/examples/rigid/log.20Apr18.rigid.early.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.early.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -9,7 +9,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 81 atoms @@ -105,7 +105,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -159,8 +159,8 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 2800 16738.585 -0.046813448 0 5269.5076 14.511073 @@ -168,7 +168,7 @@ Step Temp E_pair E_mol TotEng Press 2900 16738.465 -0.0026252725 0 5269.514 14.510277 2950 16738.476 -0.0082220764 0 5269.512 14.510223 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3050 16715.332 7.2419352 0 5269.476 14.870305 3100 16653.226 26.818761 0 5269.5009 14.496764 3150 16739.351 -0.30690375 0 5269.4886 13.643904 3200 16733.238 1.6025328 0 5269.4737 12.016934 @@ -178,7 +178,7 @@ Step Temp E_pair E_mol TotEng Press 3400 16738.543 -0.042215005 0 5269.4991 12.092809 3450 16738.591 -0.059327511 0 5269.4972 12.092536 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 3700 16738.602 -0.070934368 0 5269.4889 12.025288 @@ -276,8 +276,8 @@ Step Temp E_pair E_mol TotEng Press 8300 16738.471 0 0 5269.5187 12.011719 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -297,38 +297,38 @@ Step Temp E_pair E_mol TotEng Press 9350 16738.48 0 0 5269.5214 12.011744 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589887 0 5269.4979 12.062708 - 9750 16738.013 0.135501 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.170899 on 4 procs for 10000 steps with 81 atoms +Loop time of 0.152593 on 1 procs for 10000 steps with 81 atoms -Performance: 505560.431 tau/day, 58513.939 timesteps/s -96.4% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 566210.692 tau/day, 65533.645 timesteps/s +96.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0024047 | 0.0038016 | 0.0044513 | 1.3 | 2.22 -Neigh | 0.011313 | 0.012043 | 0.013355 | 0.7 | 7.05 -Comm | 0.066761 | 0.069035 | 0.071617 | 0.7 | 40.40 -Output | 0.0038884 | 0.0041398 | 0.0048923 | 0.7 | 2.42 -Modify | 0.071143 | 0.072567 | 0.074478 | 0.4 | 42.46 -Other | | 0.009313 | | | 5.45 +Pair | 0.0098324 | 0.0098324 | 0.0098324 | 0.0 | 6.44 +Neigh | 0.040376 | 0.040376 | 0.040376 | 0.0 | 26.46 +Comm | 0.012246 | 0.012246 | 0.012246 | 0.0 | 8.03 +Output | 0.0016036 | 0.0016036 | 0.0016036 | 0.0 | 1.05 +Modify | 0.083605 | 0.083605 | 0.083605 | 0.0 | 54.79 +Other | | 0.00493 | | | 3.23 -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.early.g++.1 b/examples/rigid/log.27Nov18.rigid.early.g++.4 similarity index 92% rename from examples/rigid/log.20Apr18.rigid.early.g++.1 rename to examples/rigid/log.27Nov18.rigid.early.g++.4 index 5402647b98..91f091b799 100644 --- a/examples/rigid/log.20Apr18.rigid.early.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.early.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -9,7 +9,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms @@ -105,7 +105,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -159,7 +159,7 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 @@ -181,7 +181,7 @@ Step Temp E_pair E_mol TotEng Press 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 3750 16737.731 0.20706557 0 5269.4927 12.061948 3800 16738.578 -0.05582043 0 5269.4965 12.035665 3850 16738.471 -0.016307928 0 5269.5024 12.035302 @@ -277,7 +277,7 @@ Step Temp E_pair E_mol TotEng Press 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -298,37 +298,37 @@ Step Temp E_pair E_mol TotEng Press 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 9600 16738.549 -0.026814371 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589893 0 5269.4979 12.062708 - 9750 16738.013 0.13550102 0 5269.5101 11.407246 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.142284 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.198859 on 4 procs for 10000 steps with 81 atoms -Performance: 607236.588 tau/day, 70282.013 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 434479.274 tau/day, 50286.953 timesteps/s +91.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.010693 | 0.010693 | 0.010693 | 0.0 | 7.52 -Neigh | 0.037908 | 0.037908 | 0.037908 | 0.0 | 26.64 -Comm | 0.0087049 | 0.0087049 | 0.0087049 | 0.0 | 6.12 -Output | 0.0025849 | 0.0025849 | 0.0025849 | 0.0 | 1.82 -Modify | 0.076329 | 0.076329 | 0.076329 | 0.0 | 53.65 -Other | | 0.006064 | | | 4.26 +Pair | 0.002526 | 0.0034331 | 0.0041001 | 1.0 | 1.73 +Neigh | 0.012097 | 0.013092 | 0.013992 | 0.8 | 6.58 +Comm | 0.075266 | 0.07972 | 0.084679 | 1.2 | 40.09 +Output | 0.0030892 | 0.0043746 | 0.0081537 | 3.3 | 2.20 +Modify | 0.088037 | 0.091924 | 0.095021 | 0.9 | 46.23 +Other | | 0.006316 | | | 3.18 -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.g++.4 b/examples/rigid/log.27Nov18.rigid.g++.1 similarity index 90% rename from examples/rigid/log.20Apr18.rigid.g++.4 rename to examples/rigid/log.27Nov18.rigid.g++.1 index ff72c213ed..9dff202069 100644 --- a/examples/rigid/log.20Apr18.rigid.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -9,7 +9,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 81 atoms @@ -103,7 +103,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -157,8 +157,8 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 2800 16738.585 -0.046813448 0 5269.5076 14.511073 @@ -166,7 +166,7 @@ Step Temp E_pair E_mol TotEng Press 2900 16738.465 -0.0026252725 0 5269.514 14.510277 2950 16738.476 -0.0082220764 0 5269.512 14.510223 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3050 16715.332 7.2419352 0 5269.476 14.870305 3100 16653.226 26.818761 0 5269.5009 14.496764 3150 16739.351 -0.30690375 0 5269.4886 13.643904 3200 16733.238 1.6025328 0 5269.4737 12.016934 @@ -176,7 +176,7 @@ Step Temp E_pair E_mol TotEng Press 3400 16738.543 -0.042215005 0 5269.4991 12.092809 3450 16738.591 -0.059327511 0 5269.4972 12.092536 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 3700 16738.602 -0.070934368 0 5269.4889 12.025288 @@ -274,8 +274,8 @@ Step Temp E_pair E_mol TotEng Press 8300 16738.471 0 0 5269.5187 12.011719 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -295,38 +295,38 @@ Step Temp E_pair E_mol TotEng Press 9350 16738.48 0 0 5269.5214 12.011744 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589887 0 5269.4979 12.062708 - 9750 16738.013 0.135501 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.194532 on 4 procs for 10000 steps with 81 atoms +Loop time of 0.152143 on 1 procs for 10000 steps with 81 atoms -Performance: 444142.918 tau/day, 51405.430 timesteps/s -96.3% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 567885.005 tau/day, 65727.431 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0025368 | 0.003831 | 0.0045376 | 1.2 | 1.97 -Neigh | 0.011299 | 0.012014 | 0.013005 | 0.6 | 6.18 -Comm | 0.081939 | 0.084112 | 0.087817 | 0.8 | 43.24 -Output | 0.0044608 | 0.0047221 | 0.0053811 | 0.6 | 2.43 -Modify | 0.078212 | 0.080219 | 0.082467 | 0.7 | 41.24 -Other | | 0.009634 | | | 4.95 +Pair | 0.0097773 | 0.0097773 | 0.0097773 | 0.0 | 6.43 +Neigh | 0.040602 | 0.040602 | 0.040602 | 0.0 | 26.69 +Comm | 0.012049 | 0.012049 | 0.012049 | 0.0 | 7.92 +Output | 0.0016172 | 0.0016172 | 0.0016172 | 0.0 | 1.06 +Modify | 0.083104 | 0.083104 | 0.083104 | 0.0 | 54.62 +Other | | 0.004994 | | | 3.28 -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.g++.1 b/examples/rigid/log.27Nov18.rigid.g++.4 similarity index 92% rename from examples/rigid/log.20Apr18.rigid.g++.1 rename to examples/rigid/log.27Nov18.rigid.g++.4 index ca76376e32..36e602f1f1 100644 --- a/examples/rigid/log.20Apr18.rigid.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -9,7 +9,7 @@ pair_style lj/cut 2.5 read_data data.rigid orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms @@ -103,7 +103,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.979 | 3.979 | 3.979 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.95 | 4.044 | 4.326 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -157,7 +157,7 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 @@ -179,7 +179,7 @@ Step Temp E_pair E_mol TotEng Press 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 3750 16737.731 0.20706557 0 5269.4927 12.061948 3800 16738.578 -0.05582043 0 5269.4965 12.035665 3850 16738.471 -0.016307928 0 5269.5024 12.035302 @@ -275,7 +275,7 @@ Step Temp E_pair E_mol TotEng Press 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -296,37 +296,37 @@ Step Temp E_pair E_mol TotEng Press 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 9600 16738.549 -0.026814371 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589893 0 5269.4979 12.062708 - 9750 16738.013 0.13550102 0 5269.5101 11.407246 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.155936 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.201762 on 4 procs for 10000 steps with 81 atoms -Performance: 554075.151 tau/day, 64129.068 timesteps/s -98.3% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 428226.262 tau/day, 49563.225 timesteps/s +89.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.013007 | 0.013007 | 0.013007 | 0.0 | 8.34 -Neigh | 0.041885 | 0.041885 | 0.041885 | 0.0 | 26.86 -Comm | 0.0094752 | 0.0094752 | 0.0094752 | 0.0 | 6.08 -Output | 0.002636 | 0.002636 | 0.002636 | 0.0 | 1.69 -Modify | 0.082249 | 0.082249 | 0.082249 | 0.0 | 52.75 -Other | | 0.006683 | | | 4.29 +Pair | 0.0025356 | 0.0033935 | 0.0042305 | 1.0 | 1.68 +Neigh | 0.012009 | 0.012959 | 0.015092 | 1.1 | 6.42 +Comm | 0.07666 | 0.086213 | 0.092506 | 2.0 | 42.73 +Output | 0.0032623 | 0.0052034 | 0.011 | 4.6 | 2.58 +Modify | 0.084815 | 0.087869 | 0.089999 | 0.6 | 43.55 +Other | | 0.006125 | | | 3.04 -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 b/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 similarity index 71% rename from examples/rigid/log.20Apr18.rigid.nve.early.g++.1 rename to examples/rigid/log.27Nov18.rigid.nve.early.g++.1 index 7e92b4e6ef..1e426d397e 100644 --- a/examples/rigid/log.20Apr18.rigid.nve.early.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -202,126 +202,126 @@ Step Temp E_pair E_mol TotEng Press 4600 16738.425 0 0 5269.5042 12.383376 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.048521421 0 5269.4761 12.385777 - 4800 16735.057 1.0347219 0 5269.4786 12.43543 - 4850 16735.441 0.92650928 0 5269.4913 12.418653 - 4900 16723.839 4.5908971 0 5269.5033 13.410103 - 4950 16738.531 -0.021537669 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 4750 16738.49 -0.04852143 0 5269.4761 12.385777 + 4800 16735.057 1.0347216 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908974 0 5269.5033 13.410103 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589697 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 5100 16738.404 0 0 5269.4976 13.090032 5150 16738.421 0 0 5269.5029 13.090073 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376397 0 5269.5075 13.090026 - 5350 16738.479 -0.020383842 0 5269.5007 13.089898 - 5400 16735.845 0.79889481 0 5269.4909 13.136244 - 5450 16735.558 0.87619898 0 5269.4778 12.324482 - 5500 16711.494 8.47243 0 5269.4984 12.65658 - 5550 16454.525 89.074845 0 5269.2031 16.996503 - 5600 16713.084 7.9801091 0 5269.5065 13.774971 - 5650 16738.676 -0.079987812 0 5269.5033 13.168292 - 5700 16446.281 91.866085 0 5269.399 23.764658 - 5750 16738.549 -0.039869082 0 5269.5034 13.378117 - 5800 16738.487 -0.014994464 0 5269.5086 13.378394 - 5850 16738.466 -0.0051267378 0 5269.512 13.378555 - 5900 16738.462 -0.0043689966 0 5269.5113 13.378568 - 5950 16738.528 -0.032727396 0 5269.5039 13.378192 - 6000 16702.774 10.969422 0 5269.2502 13.788847 - 6050 16682.271 17.483217 0 5269.3092 13.353098 - 6100 16738.508 -0.028838289 0 5269.5016 12.521077 - 6150 16738.425 -0.0067595568 0 5269.4974 12.521216 - 6200 16738.401 -0.0011499904 0 5269.4955 12.521247 - 6250 16738.455 0 0 5269.5136 12.521403 - 6300 16738.523 0 0 5269.5352 12.521573 - 6350 16738.503 0 0 5269.5287 12.521525 - 6400 16738.427 0 0 5269.5047 12.521337 - 6450 16738.399 0 0 5269.496 12.521268 - 6500 16738.425 0 0 5269.5042 12.521331 - 6550 16738.441 0 0 5269.5093 12.521372 - 6600 16738.42 0 0 5269.5025 12.521319 - 6650 16738.398 0 0 5269.4957 12.521266 - 6700 16738.435 0 0 5269.5074 12.521355 - 6750 16738.505 0 0 5269.5293 12.521527 - 6800 16738.508 0 0 5269.5303 12.521536 - 6850 16738.446 0 0 5269.5108 12.521384 - 6900 16738.414 0 0 5269.5009 12.521306 - 6950 16738.432 0 0 5269.5063 12.521348 - 7000 16738.444 0 0 5269.5102 12.521378 - 7050 16738.421 0 0 5269.5029 12.521322 - 7100 16738.393 0 0 5269.4941 12.521253 - 7150 16738.419 0 0 5269.5022 12.521315 - 7200 16738.489 0 0 5269.5244 12.521489 - 7250 16738.505 0 0 5269.5293 12.521528 - 7300 16738.443 0 0 5269.5098 12.521376 - 7350 16738.404 0 0 5269.4976 12.521281 - 7400 16738.43 0 0 5269.5058 12.521343 - 7450 16738.461 0 0 5269.5156 12.521421 - 7500 16738.447 0 0 5269.5109 12.521385 - 7550 16738.407 0 0 5269.4986 12.521288 - 7600 16738.412 0 0 5269.5002 12.5213 - 7650 16738.478 0 0 5269.5208 12.52146 - 7700 16738.51 0 0 5269.5309 12.521541 - 7750 16738.454 0 0 5269.5135 12.521405 - 7800 16738.398 0 0 5269.4958 12.521267 - 7850 16738.407 -0.0002118068 0 5269.4982 12.521283 - 7900 16738.441 -0.00021679441 0 5269.509 12.521366 - 7950 16738.446 -0.00023847865 0 5269.5107 12.52138 - 8000 16738.423 0 0 5269.5035 12.521326 - 8050 16738.423 0 0 5269.5034 12.521325 - 8100 16738.478 -0.00069624411 0 5269.52 12.521447 - 8150 16738.523 -0.0040058094 0 5269.531 12.521494 - 8200 16738.486 -0.0092298399 0 5269.5142 12.521327 - 8250 16738.458 -0.023189572 0 5269.4914 12.521008 - 8300 16738.513 -0.045847775 0 5269.4861 12.520773 - 8350 16723.734 4.5722877 0 5269.4516 12.849562 - 8400 16738.466 -0.020202622 0 5269.497 12.835807 - 8450 16738.437 -0.012822209 0 5269.4952 12.829975 - 8500 16738.408 -0.001683355 0 5269.4972 12.8301 - 8550 16738.464 -0.00097382251 0 5269.5155 12.830254 - 8600 16738.669 -0.050581166 0 5269.5304 12.829973 - 8650 15918.256 250.07455 0 5261.3774 24.539208 - 8700 16738.446 0.00084613367 0 5269.5116 10.591358 - 8750 16738.472 -0.010145611 0 5269.5089 10.590277 - 8800 16738.468 0 0 5269.5176 10.590497 - 8850 16738.508 0 0 5269.5303 10.590596 - 8900 16738.509 0 0 5269.5306 10.590599 - 8950 16738.496 0 0 5269.5266 10.590568 - 9000 16738.477 0 0 5269.5204 10.59052 - 9050 16738.455 0 0 5269.5135 10.590465 - 9100 16738.477 0 0 5269.5205 10.590519 - 9150 16738.512 0 0 5269.5315 10.590606 - 9200 16738.502 0 0 5269.5285 10.590583 - 9250 16738.493 0 0 5269.5254 10.590559 - 9300 16738.482 0 0 5269.522 10.590532 - 9350 16738.46 0 0 5269.5151 10.590478 - 9400 16738.48 0 0 5269.5216 10.590528 - 9450 16738.509 0 0 5269.5306 10.590599 - 9500 16738.49 0 0 5269.5247 10.590554 - 9550 16738.484 0 0 5269.5226 10.590536 - 9600 16738.483 0 0 5269.5223 10.590534 - 9650 16738.464 0 0 5269.5165 10.590489 - 9700 16738.484 0 0 5269.5228 10.590537 - 9750 16738.507 0 0 5269.53 10.590595 - 9800 16738.482 0 0 5269.522 10.590532 - 9850 16738.478 0 0 5269.5207 10.590521 - 9900 16738.487 -0.00030979882 0 5269.5233 10.590538 - 9950 16738.476 -0.00095967357 0 5269.5193 10.590496 - 10000 16738.494 -0.00062714625 0 5269.5253 10.590548 -Loop time of 0.166298 on 1 procs for 10000 steps with 81 atoms + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376391 0 5269.5075 13.090026 + 5350 16738.479 -0.020383841 0 5269.5007 13.089897 + 5400 16735.845 0.7988947 0 5269.4909 13.136244 + 5450 16735.558 0.87620022 0 5269.4778 12.324482 + 5500 16711.494 8.4724178 0 5269.4984 12.656579 + 5550 16454.525 89.074815 0 5269.2031 16.996503 + 5600 16713.084 7.9801418 0 5269.5065 13.774979 + 5650 16738.676 -0.079987748 0 5269.5033 13.168297 + 5700 16446.281 91.866085 0 5269.399 23.764663 + 5750 16738.549 -0.039869084 0 5269.5034 13.378122 + 5800 16738.487 -0.014994478 0 5269.5086 13.378399 + 5850 16738.466 -0.0051267616 0 5269.512 13.37856 + 5900 16738.462 -0.0043690142 0 5269.5113 13.378573 + 5950 16738.528 -0.032727415 0 5269.5039 13.378197 + 6000 16702.774 10.969438 0 5269.2502 13.788852 + 6050 16682.271 17.483137 0 5269.3092 13.353101 + 6100 16738.508 -0.028838222 0 5269.5016 12.521084 + 6150 16738.425 -0.0067595536 0 5269.4974 12.521223 + 6200 16738.401 -0.0011499893 0 5269.4955 12.521254 + 6250 16738.455 0 0 5269.5135 12.52141 + 6300 16738.523 0 0 5269.5352 12.52158 + 6350 16738.503 0 0 5269.5287 12.521531 + 6400 16738.427 0 0 5269.5047 12.521344 + 6450 16738.399 0 0 5269.496 12.521274 + 6500 16738.425 0 0 5269.5042 12.521337 + 6550 16738.441 0 0 5269.5093 12.521378 + 6600 16738.42 0 0 5269.5025 12.521326 + 6650 16738.398 0 0 5269.4957 12.521272 + 6700 16738.435 0 0 5269.5074 12.521362 + 6750 16738.505 0 0 5269.5293 12.521534 + 6800 16738.508 0 0 5269.5303 12.521543 + 6850 16738.446 0 0 5269.5108 12.521391 + 6900 16738.414 0 0 5269.5009 12.521312 + 6950 16738.432 0 0 5269.5063 12.521354 + 7000 16738.444 0 0 5269.5102 12.521385 + 7050 16738.421 0 0 5269.5029 12.521329 + 7100 16738.393 0 0 5269.4941 12.521259 + 7150 16738.419 0 0 5269.5022 12.521322 + 7200 16738.489 0 0 5269.5244 12.521495 + 7250 16738.505 0 0 5269.5293 12.521535 + 7300 16738.443 0 0 5269.5098 12.521383 + 7350 16738.404 0 0 5269.4976 12.521287 + 7400 16738.43 0 0 5269.5058 12.52135 + 7450 16738.461 0 0 5269.5156 12.521427 + 7500 16738.447 0 0 5269.5109 12.521392 + 7550 16738.407 0 0 5269.4986 12.521295 + 7600 16738.412 0 0 5269.5002 12.521306 + 7650 16738.478 0 0 5269.5208 12.521467 + 7700 16738.51 0 0 5269.5309 12.521547 + 7750 16738.454 0 0 5269.5135 12.521412 + 7800 16738.398 0 0 5269.4958 12.521273 + 7850 16738.407 -0.0002118108 0 5269.4982 12.521289 + 7900 16738.441 -0.00021679711 0 5269.509 12.521373 + 7950 16738.446 -0.00023848139 0 5269.5107 12.521386 + 8000 16738.423 0 0 5269.5035 12.521333 + 8050 16738.423 0 0 5269.5034 12.521332 + 8100 16738.478 -0.00069622994 0 5269.52 12.521454 + 8150 16738.523 -0.0040058408 0 5269.531 12.521501 + 8200 16738.486 -0.0092298229 0 5269.5142 12.521334 + 8250 16738.458 -0.023189671 0 5269.4914 12.521014 + 8300 16738.513 -0.045845677 0 5269.4861 12.520779 + 8350 16723.745 4.5690412 0 5269.4516 12.849325 + 8400 16738.466 -0.020158442 0 5269.497 12.835773 + 8450 16738.437 -0.012822892 0 5269.4952 12.829936 + 8500 16738.408 -0.0016837088 0 5269.4972 12.830061 + 8550 16738.464 -0.00097379467 0 5269.5155 12.830216 + 8600 16738.669 -0.050578079 0 5269.5304 12.829934 + 8650 15917.563 250.28318 0 5261.3678 24.54572 + 8700 16738.445 0.0012168759 0 5269.5117 10.589499 + 8750 16738.473 -0.010164589 0 5269.509 10.588414 + 8800 16738.468 0 0 5269.5177 10.588633 + 8850 16738.508 0 0 5269.5304 10.588733 + 8900 16738.509 0 0 5269.5307 10.588736 + 8950 16738.496 0 0 5269.5266 10.588705 + 9000 16738.477 0 0 5269.5204 10.588656 + 9050 16738.455 0 0 5269.5135 10.588602 + 9100 16738.477 0 0 5269.5206 10.588656 + 9150 16738.512 0 0 5269.5316 10.588743 + 9200 16738.502 0 0 5269.5285 10.58872 + 9250 16738.493 0 0 5269.5255 10.588696 + 9300 16738.482 0 0 5269.522 10.588669 + 9350 16738.46 0 0 5269.5151 10.588615 + 9400 16738.481 0 0 5269.5217 10.588665 + 9450 16738.509 0 0 5269.5307 10.588736 + 9500 16738.491 0 0 5269.5248 10.58869 + 9550 16738.484 0 0 5269.5227 10.588674 + 9600 16738.483 0 0 5269.5223 10.588671 + 9650 16738.464 0 0 5269.5166 10.588626 + 9700 16738.484 0 0 5269.5229 10.588674 + 9750 16738.507 0 0 5269.5301 10.588731 + 9800 16738.482 0 0 5269.5221 10.588669 + 9850 16738.478 0 0 5269.5208 10.588659 + 9900 16738.487 -0.00030979474 0 5269.5233 10.588675 + 9950 16738.476 -0.00095968581 0 5269.5193 10.588632 + 10000 16738.494 -0.00062717822 0 5269.5253 10.588684 +Loop time of 0.168577 on 1 procs for 10000 steps with 81 atoms -Performance: 519549.516 tau/day, 60133.046 timesteps/s -99.4% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 512524.843 tau/day, 59320.005 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.011685 | 0.011685 | 0.011685 | 0.0 | 7.03 -Neigh | 0.038539 | 0.038539 | 0.038539 | 0.0 | 23.17 -Comm | 0.0086315 | 0.0086315 | 0.0086315 | 0.0 | 5.19 -Output | 0.0026531 | 0.0026531 | 0.0026531 | 0.0 | 1.60 -Modify | 0.098759 | 0.098759 | 0.098759 | 0.0 | 59.39 -Other | | 0.00603 | | | 3.63 +Pair | 0.010812 | 0.010812 | 0.010812 | 0.0 | 6.41 +Neigh | 0.04144 | 0.04144 | 0.04144 | 0.0 | 24.58 +Comm | 0.012082 | 0.012082 | 0.012082 | 0.0 | 7.17 +Output | 0.0016394 | 0.0016394 | 0.0016394 | 0.0 | 0.97 +Modify | 0.097466 | 0.097466 | 0.097466 | 0.0 | 57.82 +Other | | 0.005139 | | | 3.05 Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 b/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 similarity index 72% rename from examples/rigid/log.20Apr18.rigid.nve.early.g++.4 rename to examples/rigid/log.27Nov18.rigid.nve.early.g++.4 index 1c3592990b..5b775d969a 100644 --- a/examples/rigid/log.20Apr18.rigid.nve.early.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.nve.early.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -202,126 +202,126 @@ Step Temp E_pair E_mol TotEng Press 4600 16738.425 0 0 5269.5042 12.383376 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.048521424 0 5269.4761 12.385777 - 4800 16735.057 1.0347218 0 5269.4786 12.43543 + 4750 16738.49 -0.048521428 0 5269.4761 12.385777 + 4800 16735.057 1.0347217 0 5269.4786 12.43543 4850 16735.441 0.92650925 0 5269.4913 12.418653 4900 16723.839 4.5908973 0 5269.5033 13.410103 - 4950 16738.531 -0.021537669 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 5100 16738.404 0 0 5269.4976 13.090032 5150 16738.421 0 0 5269.5029 13.090073 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376396 0 5269.5075 13.090026 - 5350 16738.479 -0.020383843 0 5269.5007 13.089898 - 5400 16735.845 0.79889489 0 5269.4909 13.136244 - 5450 16735.558 0.87619907 0 5269.4778 12.324482 - 5500 16711.494 8.4724273 0 5269.4984 12.656579 - 5550 16454.525 89.074821 0 5269.2031 16.996502 - 5600 16713.084 7.9801107 0 5269.5065 13.774972 - 5650 16738.676 -0.079987805 0 5269.5033 13.168292 - 5700 16446.281 91.866085 0 5269.399 23.764659 - 5750 16738.549 -0.039869082 0 5269.5034 13.378118 - 5800 16738.487 -0.014994465 0 5269.5086 13.378394 - 5850 16738.466 -0.0051267396 0 5269.512 13.378555 - 5900 16738.462 -0.004368998 0 5269.5113 13.378568 - 5950 16738.528 -0.032727397 0 5269.5039 13.378192 - 6000 16702.774 10.969422 0 5269.2502 13.788847 - 6050 16682.271 17.483223 0 5269.3092 13.353098 - 6100 16738.508 -0.028838294 0 5269.5016 12.521077 - 6150 16738.425 -0.0067595586 0 5269.4974 12.521216 - 6200 16738.401 -0.0011499906 0 5269.4955 12.521248 - 6250 16738.455 0 0 5269.5136 12.521404 - 6300 16738.523 0 0 5269.5352 12.521573 - 6350 16738.503 0 0 5269.5287 12.521525 - 6400 16738.427 0 0 5269.5047 12.521337 - 6450 16738.399 0 0 5269.496 12.521268 - 6500 16738.425 0 0 5269.5042 12.521331 - 6550 16738.441 0 0 5269.5093 12.521372 - 6600 16738.42 0 0 5269.5025 12.521319 - 6650 16738.398 0 0 5269.4957 12.521266 - 6700 16738.435 0 0 5269.5074 12.521355 - 6750 16738.505 0 0 5269.5293 12.521527 - 6800 16738.508 0 0 5269.5303 12.521536 - 6850 16738.446 0 0 5269.5108 12.521384 - 6900 16738.414 0 0 5269.5009 12.521306 - 6950 16738.432 0 0 5269.5063 12.521348 - 7000 16738.444 0 0 5269.5102 12.521379 - 7050 16738.421 0 0 5269.5029 12.521322 - 7100 16738.393 0 0 5269.4941 12.521253 - 7150 16738.419 0 0 5269.5022 12.521315 - 7200 16738.489 0 0 5269.5244 12.521489 - 7250 16738.505 0 0 5269.5293 12.521528 - 7300 16738.443 0 0 5269.5098 12.521377 - 7350 16738.404 0 0 5269.4976 12.521281 - 7400 16738.43 0 0 5269.5058 12.521344 - 7450 16738.461 0 0 5269.5156 12.521421 - 7500 16738.447 0 0 5269.5109 12.521385 - 7550 16738.407 0 0 5269.4986 12.521288 - 7600 16738.412 0 0 5269.5002 12.5213 - 7650 16738.478 0 0 5269.5208 12.521461 - 7700 16738.51 0 0 5269.5309 12.521541 - 7750 16738.454 0 0 5269.5135 12.521406 - 7800 16738.398 0 0 5269.4958 12.521267 - 7850 16738.407 -0.00021180715 0 5269.4982 12.521283 - 7900 16738.441 -0.0002167946 0 5269.509 12.521367 - 7950 16738.446 -0.0002384787 0 5269.5107 12.52138 - 8000 16738.423 0 0 5269.5035 12.521327 - 8050 16738.423 0 0 5269.5034 12.521325 - 8100 16738.478 -0.00069624484 0 5269.52 12.521448 - 8150 16738.523 -0.0040058183 0 5269.531 12.521494 - 8200 16738.486 -0.0092298512 0 5269.5142 12.521328 - 8250 16738.458 -0.023189661 0 5269.4914 12.521008 - 8300 16738.513 -0.045847765 0 5269.4861 12.520773 - 8350 16723.735 4.5720344 0 5269.4516 12.849543 - 8400 16738.466 -0.02019859 0 5269.497 12.835812 - 8450 16738.437 -0.012822198 0 5269.4952 12.829979 - 8500 16738.408 -0.0016833646 0 5269.4972 12.830104 - 8550 16738.464 -0.00097382606 0 5269.5155 12.830258 - 8600 16738.669 -0.050581176 0 5269.5304 12.829977 - 8650 15918.073 250.131 0 5261.3761 24.542327 - 8700 16738.446 0.00085039409 0 5269.5116 10.59114 - 8750 16738.472 -0.010146632 0 5269.5089 10.590059 - 8800 16738.468 0 0 5269.5176 10.590278 - 8850 16738.508 0 0 5269.5303 10.590378 - 8900 16738.509 0 0 5269.5306 10.590381 - 8950 16738.496 0 0 5269.5266 10.590349 - 9000 16738.477 0 0 5269.5204 10.590302 - 9050 16738.455 0 0 5269.5135 10.590247 - 9100 16738.477 0 0 5269.5205 10.590301 - 9150 16738.512 0 0 5269.5315 10.590388 - 9200 16738.502 0 0 5269.5285 10.590364 - 9250 16738.493 0 0 5269.5254 10.59034 - 9300 16738.482 0 0 5269.522 10.590314 - 9350 16738.46 0 0 5269.5151 10.59026 - 9400 16738.48 0 0 5269.5216 10.59031 - 9450 16738.509 0 0 5269.5306 10.590381 - 9500 16738.49 0 0 5269.5247 10.590335 - 9550 16738.484 0 0 5269.5226 10.590318 - 9600 16738.483 0 0 5269.5223 10.590316 - 9650 16738.464 0 0 5269.5165 10.590271 - 9700 16738.484 0 0 5269.5228 10.590319 - 9750 16738.507 0 0 5269.53 10.590376 - 9800 16738.482 0 0 5269.522 10.590314 - 9850 16738.478 0 0 5269.5207 10.590303 - 9900 16738.487 -0.00030979874 0 5269.5233 10.59032 - 9950 16738.476 -0.00095967134 0 5269.5192 10.590278 - 10000 16738.494 -0.00062714318 0 5269.5253 10.590329 -Loop time of 0.224811 on 4 procs for 10000 steps with 81 atoms + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 + 5350 16738.479 -0.020383842 0 5269.5007 13.089897 + 5400 16735.845 0.79889474 0 5269.4909 13.136244 + 5450 16735.558 0.87619992 0 5269.4778 12.324482 + 5500 16711.494 8.4724208 0 5269.4984 12.656579 + 5550 16454.525 89.074816 0 5269.2031 16.996503 + 5600 16713.084 7.9801334 0 5269.5065 13.774977 + 5650 16738.676 -0.079987764 0 5269.5033 13.168295 + 5700 16446.281 91.866085 0 5269.399 23.764662 + 5750 16738.549 -0.039869084 0 5269.5034 13.378121 + 5800 16738.487 -0.014994475 0 5269.5086 13.378397 + 5850 16738.466 -0.0051267556 0 5269.512 13.378559 + 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 + 5950 16738.528 -0.03272741 0 5269.5039 13.378195 + 6000 16702.774 10.969434 0 5269.2502 13.788851 + 6050 16682.271 17.483158 0 5269.3092 13.3531 + 6100 16738.508 -0.028838239 0 5269.5016 12.521082 + 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 + 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 + 6250 16738.455 0 0 5269.5135 12.521408 + 6300 16738.523 0 0 5269.5352 12.521578 + 6350 16738.503 0 0 5269.5287 12.52153 + 6400 16738.427 0 0 5269.5047 12.521342 + 6450 16738.399 0 0 5269.496 12.521273 + 6500 16738.425 0 0 5269.5042 12.521336 + 6550 16738.441 0 0 5269.5093 12.521377 + 6600 16738.42 0 0 5269.5025 12.521324 + 6650 16738.398 0 0 5269.4957 12.52127 + 6700 16738.435 0 0 5269.5074 12.52136 + 6750 16738.505 0 0 5269.5293 12.521532 + 6800 16738.508 0 0 5269.5303 12.521541 + 6850 16738.446 0 0 5269.5108 12.521389 + 6900 16738.414 0 0 5269.5009 12.521311 + 6950 16738.432 0 0 5269.5063 12.521353 + 7000 16738.444 0 0 5269.5102 12.521383 + 7050 16738.421 0 0 5269.5029 12.521327 + 7100 16738.393 0 0 5269.4941 12.521258 + 7150 16738.419 0 0 5269.5022 12.52132 + 7200 16738.489 0 0 5269.5244 12.521494 + 7250 16738.505 0 0 5269.5293 12.521533 + 7300 16738.443 0 0 5269.5098 12.521381 + 7350 16738.404 0 0 5269.4976 12.521285 + 7400 16738.43 0 0 5269.5058 12.521348 + 7450 16738.461 0 0 5269.5156 12.521425 + 7500 16738.447 0 0 5269.5109 12.52139 + 7550 16738.407 0 0 5269.4986 12.521293 + 7600 16738.412 0 0 5269.5002 12.521305 + 7650 16738.478 0 0 5269.5208 12.521465 + 7700 16738.51 0 0 5269.5309 12.521546 + 7750 16738.454 0 0 5269.5135 12.52141 + 7800 16738.398 0 0 5269.4958 12.521272 + 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 + 7900 16738.441 -0.0002167964 0 5269.509 12.521371 + 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 + 8000 16738.423 0 0 5269.5035 12.521331 + 8050 16738.423 0 0 5269.5034 12.52133 + 8100 16738.478 -0.00069623408 0 5269.52 12.521452 + 8150 16738.523 -0.0040058355 0 5269.531 12.521499 + 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 + 8250 16738.458 -0.023189665 0 5269.4914 12.521012 + 8300 16738.513 -0.045846242 0 5269.4861 12.520778 + 8350 16723.742 4.5698786 0 5269.4516 12.849386 + 8400 16738.466 -0.02016972 0 5269.497 12.835784 + 8450 16738.437 -0.012822703 0 5269.4952 12.829948 + 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 + 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 + 8600 16738.669 -0.050578946 0 5269.5304 12.829946 + 8650 15917.707 250.24016 0 5261.3702 24.544744 + 8700 16738.445 0.0010615265 0 5269.5117 10.589987 + 8750 16738.473 -0.010158834 0 5269.509 10.588904 + 8800 16738.468 0 0 5269.5176 10.589124 + 8850 16738.508 0 0 5269.5304 10.589223 + 8900 16738.509 0 0 5269.5306 10.589226 + 8950 16738.496 0 0 5269.5266 10.589195 + 9000 16738.477 0 0 5269.5204 10.589147 + 9050 16738.455 0 0 5269.5135 10.589092 + 9100 16738.477 0 0 5269.5206 10.589146 + 9150 16738.512 0 0 5269.5316 10.589233 + 9200 16738.502 0 0 5269.5285 10.58921 + 9250 16738.493 0 0 5269.5255 10.589186 + 9300 16738.482 0 0 5269.522 10.589159 + 9350 16738.46 0 0 5269.5151 10.589105 + 9400 16738.481 0 0 5269.5217 10.589155 + 9450 16738.509 0 0 5269.5307 10.589226 + 9500 16738.491 0 0 5269.5248 10.589181 + 9550 16738.484 0 0 5269.5227 10.589164 + 9600 16738.483 0 0 5269.5223 10.589161 + 9650 16738.464 0 0 5269.5166 10.589116 + 9700 16738.484 0 0 5269.5228 10.589164 + 9750 16738.507 0 0 5269.5301 10.589221 + 9800 16738.482 0 0 5269.5221 10.589159 + 9850 16738.478 0 0 5269.5208 10.589149 + 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 + 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 + 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 +Loop time of 0.213152 on 4 procs for 10000 steps with 81 atoms -Performance: 384323.005 tau/day, 44481.829 timesteps/s -95.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 405345.239 tau/day, 46914.958 timesteps/s +91.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0032673 | 0.0039269 | 0.0048387 | 1.1 | 1.75 -Neigh | 0.010401 | 0.012159 | 0.015022 | 1.6 | 5.41 -Comm | 0.087584 | 0.08909 | 0.090645 | 0.4 | 39.63 -Output | 0.0042956 | 0.0045624 | 0.0052695 | 0.6 | 2.03 -Modify | 0.10208 | 0.10506 | 0.10697 | 0.6 | 46.73 -Other | | 0.01001 | | | 4.45 +Pair | 0.0029514 | 0.0038354 | 0.005348 | 1.5 | 1.80 +Neigh | 0.01178 | 0.013139 | 0.0167 | 1.8 | 6.16 +Comm | 0.073879 | 0.078553 | 0.081131 | 1.0 | 36.85 +Output | 0.0031943 | 0.0037987 | 0.0055451 | 1.6 | 1.78 +Modify | 0.10553 | 0.10763 | 0.1096 | 0.4 | 50.49 +Other | | 0.0062 | | | 2.91 Nlocal: 20.25 ave 34 max 9 min Histogram: 2 0 0 0 0 0 0 1 0 1 diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.1 b/examples/rigid/log.27Nov18.rigid.nve.g++.1 similarity index 71% rename from examples/rigid/log.20Apr18.rigid.nve.g++.1 rename to examples/rigid/log.27Nov18.rigid.nve.g++.1 index 26fa4e7f68..c3805dc42e 100644 --- a/examples/rigid/log.20Apr18.rigid.nve.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.nve.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -200,126 +200,126 @@ Step Temp E_pair E_mol TotEng Press 4600 16738.425 0 0 5269.5042 12.383376 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.048521421 0 5269.4761 12.385777 - 4800 16735.057 1.0347219 0 5269.4786 12.43543 - 4850 16735.441 0.92650928 0 5269.4913 12.418653 - 4900 16723.839 4.5908971 0 5269.5033 13.410103 - 4950 16738.531 -0.021537669 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 4750 16738.49 -0.04852143 0 5269.4761 12.385777 + 4800 16735.057 1.0347216 0 5269.4786 12.43543 + 4850 16735.441 0.92650925 0 5269.4913 12.418653 + 4900 16723.839 4.5908974 0 5269.5033 13.410103 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589697 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 5100 16738.404 0 0 5269.4976 13.090032 5150 16738.421 0 0 5269.5029 13.090073 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376397 0 5269.5075 13.090026 - 5350 16738.479 -0.020383842 0 5269.5007 13.089898 - 5400 16735.845 0.79889481 0 5269.4909 13.136244 - 5450 16735.558 0.87619898 0 5269.4778 12.324482 - 5500 16711.494 8.47243 0 5269.4984 12.65658 - 5550 16454.525 89.074845 0 5269.2031 16.996503 - 5600 16713.084 7.9801091 0 5269.5065 13.774971 - 5650 16738.676 -0.079987812 0 5269.5033 13.168292 - 5700 16446.281 91.866085 0 5269.399 23.764658 - 5750 16738.549 -0.039869082 0 5269.5034 13.378117 - 5800 16738.487 -0.014994464 0 5269.5086 13.378394 - 5850 16738.466 -0.0051267378 0 5269.512 13.378555 - 5900 16738.462 -0.0043689966 0 5269.5113 13.378568 - 5950 16738.528 -0.032727396 0 5269.5039 13.378192 - 6000 16702.774 10.969422 0 5269.2502 13.788847 - 6050 16682.271 17.483217 0 5269.3092 13.353098 - 6100 16738.508 -0.028838289 0 5269.5016 12.521077 - 6150 16738.425 -0.0067595568 0 5269.4974 12.521216 - 6200 16738.401 -0.0011499904 0 5269.4955 12.521247 - 6250 16738.455 0 0 5269.5136 12.521403 - 6300 16738.523 0 0 5269.5352 12.521573 - 6350 16738.503 0 0 5269.5287 12.521525 - 6400 16738.427 0 0 5269.5047 12.521337 - 6450 16738.399 0 0 5269.496 12.521268 - 6500 16738.425 0 0 5269.5042 12.521331 - 6550 16738.441 0 0 5269.5093 12.521372 - 6600 16738.42 0 0 5269.5025 12.521319 - 6650 16738.398 0 0 5269.4957 12.521266 - 6700 16738.435 0 0 5269.5074 12.521355 - 6750 16738.505 0 0 5269.5293 12.521527 - 6800 16738.508 0 0 5269.5303 12.521536 - 6850 16738.446 0 0 5269.5108 12.521384 - 6900 16738.414 0 0 5269.5009 12.521306 - 6950 16738.432 0 0 5269.5063 12.521348 - 7000 16738.444 0 0 5269.5102 12.521378 - 7050 16738.421 0 0 5269.5029 12.521322 - 7100 16738.393 0 0 5269.4941 12.521253 - 7150 16738.419 0 0 5269.5022 12.521315 - 7200 16738.489 0 0 5269.5244 12.521489 - 7250 16738.505 0 0 5269.5293 12.521528 - 7300 16738.443 0 0 5269.5098 12.521376 - 7350 16738.404 0 0 5269.4976 12.521281 - 7400 16738.43 0 0 5269.5058 12.521343 - 7450 16738.461 0 0 5269.5156 12.521421 - 7500 16738.447 0 0 5269.5109 12.521385 - 7550 16738.407 0 0 5269.4986 12.521288 - 7600 16738.412 0 0 5269.5002 12.5213 - 7650 16738.478 0 0 5269.5208 12.52146 - 7700 16738.51 0 0 5269.5309 12.521541 - 7750 16738.454 0 0 5269.5135 12.521405 - 7800 16738.398 0 0 5269.4958 12.521267 - 7850 16738.407 -0.0002118068 0 5269.4982 12.521283 - 7900 16738.441 -0.00021679441 0 5269.509 12.521366 - 7950 16738.446 -0.00023847865 0 5269.5107 12.52138 - 8000 16738.423 0 0 5269.5035 12.521326 - 8050 16738.423 0 0 5269.5034 12.521325 - 8100 16738.478 -0.00069624411 0 5269.52 12.521447 - 8150 16738.523 -0.0040058094 0 5269.531 12.521494 - 8200 16738.486 -0.0092298399 0 5269.5142 12.521327 - 8250 16738.458 -0.023189572 0 5269.4914 12.521008 - 8300 16738.513 -0.045847775 0 5269.4861 12.520773 - 8350 16723.734 4.5722877 0 5269.4516 12.849562 - 8400 16738.466 -0.020202622 0 5269.497 12.835807 - 8450 16738.437 -0.012822209 0 5269.4952 12.829975 - 8500 16738.408 -0.001683355 0 5269.4972 12.8301 - 8550 16738.464 -0.00097382251 0 5269.5155 12.830254 - 8600 16738.669 -0.050581166 0 5269.5304 12.829973 - 8650 15918.256 250.07455 0 5261.3774 24.539208 - 8700 16738.446 0.00084613367 0 5269.5116 10.591358 - 8750 16738.472 -0.010145611 0 5269.5089 10.590277 - 8800 16738.468 0 0 5269.5176 10.590497 - 8850 16738.508 0 0 5269.5303 10.590596 - 8900 16738.509 0 0 5269.5306 10.590599 - 8950 16738.496 0 0 5269.5266 10.590568 - 9000 16738.477 0 0 5269.5204 10.59052 - 9050 16738.455 0 0 5269.5135 10.590465 - 9100 16738.477 0 0 5269.5205 10.590519 - 9150 16738.512 0 0 5269.5315 10.590606 - 9200 16738.502 0 0 5269.5285 10.590583 - 9250 16738.493 0 0 5269.5254 10.590559 - 9300 16738.482 0 0 5269.522 10.590532 - 9350 16738.46 0 0 5269.5151 10.590478 - 9400 16738.48 0 0 5269.5216 10.590528 - 9450 16738.509 0 0 5269.5306 10.590599 - 9500 16738.49 0 0 5269.5247 10.590554 - 9550 16738.484 0 0 5269.5226 10.590536 - 9600 16738.483 0 0 5269.5223 10.590534 - 9650 16738.464 0 0 5269.5165 10.590489 - 9700 16738.484 0 0 5269.5228 10.590537 - 9750 16738.507 0 0 5269.53 10.590595 - 9800 16738.482 0 0 5269.522 10.590532 - 9850 16738.478 0 0 5269.5207 10.590521 - 9900 16738.487 -0.00030979882 0 5269.5233 10.590538 - 9950 16738.476 -0.00095967357 0 5269.5193 10.590496 - 10000 16738.494 -0.00062714625 0 5269.5253 10.590548 -Loop time of 0.166547 on 1 procs for 10000 steps with 81 atoms + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376391 0 5269.5075 13.090026 + 5350 16738.479 -0.020383841 0 5269.5007 13.089897 + 5400 16735.845 0.7988947 0 5269.4909 13.136244 + 5450 16735.558 0.87620022 0 5269.4778 12.324482 + 5500 16711.494 8.4724178 0 5269.4984 12.656579 + 5550 16454.525 89.074815 0 5269.2031 16.996503 + 5600 16713.084 7.9801418 0 5269.5065 13.774979 + 5650 16738.676 -0.079987748 0 5269.5033 13.168297 + 5700 16446.281 91.866085 0 5269.399 23.764663 + 5750 16738.549 -0.039869084 0 5269.5034 13.378122 + 5800 16738.487 -0.014994478 0 5269.5086 13.378399 + 5850 16738.466 -0.0051267616 0 5269.512 13.37856 + 5900 16738.462 -0.0043690142 0 5269.5113 13.378573 + 5950 16738.528 -0.032727415 0 5269.5039 13.378197 + 6000 16702.774 10.969438 0 5269.2502 13.788852 + 6050 16682.271 17.483137 0 5269.3092 13.353101 + 6100 16738.508 -0.028838222 0 5269.5016 12.521084 + 6150 16738.425 -0.0067595536 0 5269.4974 12.521223 + 6200 16738.401 -0.0011499893 0 5269.4955 12.521254 + 6250 16738.455 0 0 5269.5135 12.52141 + 6300 16738.523 0 0 5269.5352 12.52158 + 6350 16738.503 0 0 5269.5287 12.521531 + 6400 16738.427 0 0 5269.5047 12.521344 + 6450 16738.399 0 0 5269.496 12.521274 + 6500 16738.425 0 0 5269.5042 12.521337 + 6550 16738.441 0 0 5269.5093 12.521378 + 6600 16738.42 0 0 5269.5025 12.521326 + 6650 16738.398 0 0 5269.4957 12.521272 + 6700 16738.435 0 0 5269.5074 12.521362 + 6750 16738.505 0 0 5269.5293 12.521534 + 6800 16738.508 0 0 5269.5303 12.521543 + 6850 16738.446 0 0 5269.5108 12.521391 + 6900 16738.414 0 0 5269.5009 12.521312 + 6950 16738.432 0 0 5269.5063 12.521354 + 7000 16738.444 0 0 5269.5102 12.521385 + 7050 16738.421 0 0 5269.5029 12.521329 + 7100 16738.393 0 0 5269.4941 12.521259 + 7150 16738.419 0 0 5269.5022 12.521322 + 7200 16738.489 0 0 5269.5244 12.521495 + 7250 16738.505 0 0 5269.5293 12.521535 + 7300 16738.443 0 0 5269.5098 12.521383 + 7350 16738.404 0 0 5269.4976 12.521287 + 7400 16738.43 0 0 5269.5058 12.52135 + 7450 16738.461 0 0 5269.5156 12.521427 + 7500 16738.447 0 0 5269.5109 12.521392 + 7550 16738.407 0 0 5269.4986 12.521295 + 7600 16738.412 0 0 5269.5002 12.521306 + 7650 16738.478 0 0 5269.5208 12.521467 + 7700 16738.51 0 0 5269.5309 12.521547 + 7750 16738.454 0 0 5269.5135 12.521412 + 7800 16738.398 0 0 5269.4958 12.521273 + 7850 16738.407 -0.0002118108 0 5269.4982 12.521289 + 7900 16738.441 -0.00021679711 0 5269.509 12.521373 + 7950 16738.446 -0.00023848139 0 5269.5107 12.521386 + 8000 16738.423 0 0 5269.5035 12.521333 + 8050 16738.423 0 0 5269.5034 12.521332 + 8100 16738.478 -0.00069622994 0 5269.52 12.521454 + 8150 16738.523 -0.0040058408 0 5269.531 12.521501 + 8200 16738.486 -0.0092298229 0 5269.5142 12.521334 + 8250 16738.458 -0.023189671 0 5269.4914 12.521014 + 8300 16738.513 -0.045845677 0 5269.4861 12.520779 + 8350 16723.745 4.5690412 0 5269.4516 12.849325 + 8400 16738.466 -0.020158442 0 5269.497 12.835773 + 8450 16738.437 -0.012822892 0 5269.4952 12.829936 + 8500 16738.408 -0.0016837088 0 5269.4972 12.830061 + 8550 16738.464 -0.00097379467 0 5269.5155 12.830216 + 8600 16738.669 -0.050578079 0 5269.5304 12.829934 + 8650 15917.563 250.28318 0 5261.3678 24.54572 + 8700 16738.445 0.0012168759 0 5269.5117 10.589499 + 8750 16738.473 -0.010164589 0 5269.509 10.588414 + 8800 16738.468 0 0 5269.5177 10.588633 + 8850 16738.508 0 0 5269.5304 10.588733 + 8900 16738.509 0 0 5269.5307 10.588736 + 8950 16738.496 0 0 5269.5266 10.588705 + 9000 16738.477 0 0 5269.5204 10.588656 + 9050 16738.455 0 0 5269.5135 10.588602 + 9100 16738.477 0 0 5269.5206 10.588656 + 9150 16738.512 0 0 5269.5316 10.588743 + 9200 16738.502 0 0 5269.5285 10.58872 + 9250 16738.493 0 0 5269.5255 10.588696 + 9300 16738.482 0 0 5269.522 10.588669 + 9350 16738.46 0 0 5269.5151 10.588615 + 9400 16738.481 0 0 5269.5217 10.588665 + 9450 16738.509 0 0 5269.5307 10.588736 + 9500 16738.491 0 0 5269.5248 10.58869 + 9550 16738.484 0 0 5269.5227 10.588674 + 9600 16738.483 0 0 5269.5223 10.588671 + 9650 16738.464 0 0 5269.5166 10.588626 + 9700 16738.484 0 0 5269.5229 10.588674 + 9750 16738.507 0 0 5269.5301 10.588731 + 9800 16738.482 0 0 5269.5221 10.588669 + 9850 16738.478 0 0 5269.5208 10.588659 + 9900 16738.487 -0.00030979474 0 5269.5233 10.588675 + 9950 16738.476 -0.00095968581 0 5269.5193 10.588632 + 10000 16738.494 -0.00062717822 0 5269.5253 10.588684 +Loop time of 0.171181 on 1 procs for 10000 steps with 81 atoms -Performance: 518773.777 tau/day, 60043.261 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 504728.317 tau/day, 58417.629 timesteps/s +97.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.011439 | 0.011439 | 0.011439 | 0.0 | 6.87 -Neigh | 0.038572 | 0.038572 | 0.038572 | 0.0 | 23.16 -Comm | 0.0085464 | 0.0085464 | 0.0085464 | 0.0 | 5.13 -Output | 0.0025046 | 0.0025046 | 0.0025046 | 0.0 | 1.50 -Modify | 0.099479 | 0.099479 | 0.099479 | 0.0 | 59.73 -Other | | 0.006005 | | | 3.61 +Pair | 0.011004 | 0.011004 | 0.011004 | 0.0 | 6.43 +Neigh | 0.041984 | 0.041984 | 0.041984 | 0.0 | 24.53 +Comm | 0.012262 | 0.012262 | 0.012262 | 0.0 | 7.16 +Output | 0.0017002 | 0.0017002 | 0.0017002 | 0.0 | 0.99 +Modify | 0.098894 | 0.098894 | 0.098894 | 0.0 | 57.77 +Other | | 0.005337 | | | 3.12 Nlocal: 81 ave 81 max 81 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/rigid/log.20Apr18.rigid.nve.g++.4 b/examples/rigid/log.27Nov18.rigid.nve.g++.4 similarity index 72% rename from examples/rigid/log.20Apr18.rigid.nve.g++.4 rename to examples/rigid/log.27Nov18.rigid.nve.g++.4 index 782457b427..bc79d9730f 100644 --- a/examples/rigid/log.20Apr18.rigid.nve.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.nve.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -200,126 +200,126 @@ Step Temp E_pair E_mol TotEng Press 4600 16738.425 0 0 5269.5042 12.383376 4650 16738.404 -0.0014438316 0 5269.4961 12.383299 4700 16738.444 -0.024020551 0 5269.4862 12.382975 - 4750 16738.49 -0.048521424 0 5269.4761 12.385777 - 4800 16735.057 1.0347218 0 5269.4786 12.43543 + 4750 16738.49 -0.048521428 0 5269.4761 12.385777 + 4800 16735.057 1.0347217 0 5269.4786 12.43543 4850 16735.441 0.92650925 0 5269.4913 12.418653 4900 16723.839 4.5908973 0 5269.5033 13.410103 - 4950 16738.531 -0.021537669 0 5269.5159 13.089982 - 5000 16738.45 -0.0042589693 0 5269.5077 13.090062 - 5050 16738.409 -0.00024692474 0 5269.4987 13.090038 + 4950 16738.531 -0.02153767 0 5269.5159 13.089982 + 5000 16738.45 -0.0042589696 0 5269.5077 13.090062 + 5050 16738.409 -0.00024692476 0 5269.4987 13.090038 5100 16738.404 0 0 5269.4976 13.090032 5150 16738.421 0 0 5269.5029 13.090073 5200 16738.44 0 0 5269.5087 13.090119 - 5250 16738.448 -0.0012793921 0 5269.5102 13.090114 - 5300 16738.456 -0.0064376396 0 5269.5075 13.090026 - 5350 16738.479 -0.020383843 0 5269.5007 13.089898 - 5400 16735.845 0.79889489 0 5269.4909 13.136244 - 5450 16735.558 0.87619907 0 5269.4778 12.324482 - 5500 16711.494 8.4724273 0 5269.4984 12.656579 - 5550 16454.525 89.074821 0 5269.2031 16.996502 - 5600 16713.084 7.9801107 0 5269.5065 13.774972 - 5650 16738.676 -0.079987805 0 5269.5033 13.168292 - 5700 16446.281 91.866085 0 5269.399 23.764659 - 5750 16738.549 -0.039869082 0 5269.5034 13.378118 - 5800 16738.487 -0.014994465 0 5269.5086 13.378394 - 5850 16738.466 -0.0051267396 0 5269.512 13.378555 - 5900 16738.462 -0.004368998 0 5269.5113 13.378568 - 5950 16738.528 -0.032727397 0 5269.5039 13.378192 - 6000 16702.774 10.969422 0 5269.2502 13.788847 - 6050 16682.271 17.483223 0 5269.3092 13.353098 - 6100 16738.508 -0.028838294 0 5269.5016 12.521077 - 6150 16738.425 -0.0067595586 0 5269.4974 12.521216 - 6200 16738.401 -0.0011499906 0 5269.4955 12.521248 - 6250 16738.455 0 0 5269.5136 12.521404 - 6300 16738.523 0 0 5269.5352 12.521573 - 6350 16738.503 0 0 5269.5287 12.521525 - 6400 16738.427 0 0 5269.5047 12.521337 - 6450 16738.399 0 0 5269.496 12.521268 - 6500 16738.425 0 0 5269.5042 12.521331 - 6550 16738.441 0 0 5269.5093 12.521372 - 6600 16738.42 0 0 5269.5025 12.521319 - 6650 16738.398 0 0 5269.4957 12.521266 - 6700 16738.435 0 0 5269.5074 12.521355 - 6750 16738.505 0 0 5269.5293 12.521527 - 6800 16738.508 0 0 5269.5303 12.521536 - 6850 16738.446 0 0 5269.5108 12.521384 - 6900 16738.414 0 0 5269.5009 12.521306 - 6950 16738.432 0 0 5269.5063 12.521348 - 7000 16738.444 0 0 5269.5102 12.521379 - 7050 16738.421 0 0 5269.5029 12.521322 - 7100 16738.393 0 0 5269.4941 12.521253 - 7150 16738.419 0 0 5269.5022 12.521315 - 7200 16738.489 0 0 5269.5244 12.521489 - 7250 16738.505 0 0 5269.5293 12.521528 - 7300 16738.443 0 0 5269.5098 12.521377 - 7350 16738.404 0 0 5269.4976 12.521281 - 7400 16738.43 0 0 5269.5058 12.521344 - 7450 16738.461 0 0 5269.5156 12.521421 - 7500 16738.447 0 0 5269.5109 12.521385 - 7550 16738.407 0 0 5269.4986 12.521288 - 7600 16738.412 0 0 5269.5002 12.5213 - 7650 16738.478 0 0 5269.5208 12.521461 - 7700 16738.51 0 0 5269.5309 12.521541 - 7750 16738.454 0 0 5269.5135 12.521406 - 7800 16738.398 0 0 5269.4958 12.521267 - 7850 16738.407 -0.00021180715 0 5269.4982 12.521283 - 7900 16738.441 -0.0002167946 0 5269.509 12.521367 - 7950 16738.446 -0.0002384787 0 5269.5107 12.52138 - 8000 16738.423 0 0 5269.5035 12.521327 - 8050 16738.423 0 0 5269.5034 12.521325 - 8100 16738.478 -0.00069624484 0 5269.52 12.521448 - 8150 16738.523 -0.0040058183 0 5269.531 12.521494 - 8200 16738.486 -0.0092298512 0 5269.5142 12.521328 - 8250 16738.458 -0.023189661 0 5269.4914 12.521008 - 8300 16738.513 -0.045847765 0 5269.4861 12.520773 - 8350 16723.735 4.5720344 0 5269.4516 12.849543 - 8400 16738.466 -0.02019859 0 5269.497 12.835812 - 8450 16738.437 -0.012822198 0 5269.4952 12.829979 - 8500 16738.408 -0.0016833646 0 5269.4972 12.830104 - 8550 16738.464 -0.00097382606 0 5269.5155 12.830258 - 8600 16738.669 -0.050581176 0 5269.5304 12.829977 - 8650 15918.073 250.131 0 5261.3761 24.542327 - 8700 16738.446 0.00085039409 0 5269.5116 10.59114 - 8750 16738.472 -0.010146632 0 5269.5089 10.590059 - 8800 16738.468 0 0 5269.5176 10.590278 - 8850 16738.508 0 0 5269.5303 10.590378 - 8900 16738.509 0 0 5269.5306 10.590381 - 8950 16738.496 0 0 5269.5266 10.590349 - 9000 16738.477 0 0 5269.5204 10.590302 - 9050 16738.455 0 0 5269.5135 10.590247 - 9100 16738.477 0 0 5269.5205 10.590301 - 9150 16738.512 0 0 5269.5315 10.590388 - 9200 16738.502 0 0 5269.5285 10.590364 - 9250 16738.493 0 0 5269.5254 10.59034 - 9300 16738.482 0 0 5269.522 10.590314 - 9350 16738.46 0 0 5269.5151 10.59026 - 9400 16738.48 0 0 5269.5216 10.59031 - 9450 16738.509 0 0 5269.5306 10.590381 - 9500 16738.49 0 0 5269.5247 10.590335 - 9550 16738.484 0 0 5269.5226 10.590318 - 9600 16738.483 0 0 5269.5223 10.590316 - 9650 16738.464 0 0 5269.5165 10.590271 - 9700 16738.484 0 0 5269.5228 10.590319 - 9750 16738.507 0 0 5269.53 10.590376 - 9800 16738.482 0 0 5269.522 10.590314 - 9850 16738.478 0 0 5269.5207 10.590303 - 9900 16738.487 -0.00030979874 0 5269.5233 10.59032 - 9950 16738.476 -0.00095967134 0 5269.5192 10.590278 - 10000 16738.494 -0.00062714318 0 5269.5253 10.590329 -Loop time of 0.22441 on 4 procs for 10000 steps with 81 atoms + 5250 16738.448 -0.001279392 0 5269.5102 13.090114 + 5300 16738.456 -0.0064376392 0 5269.5075 13.090026 + 5350 16738.479 -0.020383842 0 5269.5007 13.089897 + 5400 16735.845 0.79889474 0 5269.4909 13.136244 + 5450 16735.558 0.87619992 0 5269.4778 12.324482 + 5500 16711.494 8.4724208 0 5269.4984 12.656579 + 5550 16454.525 89.074816 0 5269.2031 16.996503 + 5600 16713.084 7.9801334 0 5269.5065 13.774977 + 5650 16738.676 -0.079987764 0 5269.5033 13.168295 + 5700 16446.281 91.866085 0 5269.399 23.764662 + 5750 16738.549 -0.039869084 0 5269.5034 13.378121 + 5800 16738.487 -0.014994475 0 5269.5086 13.378397 + 5850 16738.466 -0.0051267556 0 5269.512 13.378559 + 5900 16738.462 -0.0043690097 0 5269.5113 13.378572 + 5950 16738.528 -0.03272741 0 5269.5039 13.378195 + 6000 16702.774 10.969434 0 5269.2502 13.788851 + 6050 16682.271 17.483158 0 5269.3092 13.3531 + 6100 16738.508 -0.028838239 0 5269.5016 12.521082 + 6150 16738.425 -0.0067595542 0 5269.4974 12.521221 + 6200 16738.401 -0.0011499896 0 5269.4955 12.521252 + 6250 16738.455 0 0 5269.5135 12.521408 + 6300 16738.523 0 0 5269.5352 12.521578 + 6350 16738.503 0 0 5269.5287 12.52153 + 6400 16738.427 0 0 5269.5047 12.521342 + 6450 16738.399 0 0 5269.496 12.521273 + 6500 16738.425 0 0 5269.5042 12.521336 + 6550 16738.441 0 0 5269.5093 12.521377 + 6600 16738.42 0 0 5269.5025 12.521324 + 6650 16738.398 0 0 5269.4957 12.52127 + 6700 16738.435 0 0 5269.5074 12.52136 + 6750 16738.505 0 0 5269.5293 12.521532 + 6800 16738.508 0 0 5269.5303 12.521541 + 6850 16738.446 0 0 5269.5108 12.521389 + 6900 16738.414 0 0 5269.5009 12.521311 + 6950 16738.432 0 0 5269.5063 12.521353 + 7000 16738.444 0 0 5269.5102 12.521383 + 7050 16738.421 0 0 5269.5029 12.521327 + 7100 16738.393 0 0 5269.4941 12.521258 + 7150 16738.419 0 0 5269.5022 12.52132 + 7200 16738.489 0 0 5269.5244 12.521494 + 7250 16738.505 0 0 5269.5293 12.521533 + 7300 16738.443 0 0 5269.5098 12.521381 + 7350 16738.404 0 0 5269.4976 12.521285 + 7400 16738.43 0 0 5269.5058 12.521348 + 7450 16738.461 0 0 5269.5156 12.521425 + 7500 16738.447 0 0 5269.5109 12.52139 + 7550 16738.407 0 0 5269.4986 12.521293 + 7600 16738.412 0 0 5269.5002 12.521305 + 7650 16738.478 0 0 5269.5208 12.521465 + 7700 16738.51 0 0 5269.5309 12.521546 + 7750 16738.454 0 0 5269.5135 12.52141 + 7800 16738.398 0 0 5269.4958 12.521272 + 7850 16738.407 -0.00021180981 0 5269.4982 12.521288 + 7900 16738.441 -0.0002167964 0 5269.509 12.521371 + 7950 16738.446 -0.00023848065 0 5269.5107 12.521385 + 8000 16738.423 0 0 5269.5035 12.521331 + 8050 16738.423 0 0 5269.5034 12.52133 + 8100 16738.478 -0.00069623408 0 5269.52 12.521452 + 8150 16738.523 -0.0040058355 0 5269.531 12.521499 + 8200 16738.486 -0.0092298325 0 5269.5142 12.521332 + 8250 16738.458 -0.023189665 0 5269.4914 12.521012 + 8300 16738.513 -0.045846242 0 5269.4861 12.520778 + 8350 16723.742 4.5698786 0 5269.4516 12.849386 + 8400 16738.466 -0.02016972 0 5269.497 12.835784 + 8450 16738.437 -0.012822703 0 5269.4952 12.829948 + 8500 16738.408 -0.0016836132 0 5269.4972 12.830073 + 8550 16738.464 -0.00097380297 0 5269.5155 12.830227 + 8600 16738.669 -0.050578946 0 5269.5304 12.829946 + 8650 15917.707 250.24016 0 5261.3702 24.544744 + 8700 16738.445 0.0010615265 0 5269.5117 10.589987 + 8750 16738.473 -0.010158834 0 5269.509 10.588904 + 8800 16738.468 0 0 5269.5176 10.589124 + 8850 16738.508 0 0 5269.5304 10.589223 + 8900 16738.509 0 0 5269.5306 10.589226 + 8950 16738.496 0 0 5269.5266 10.589195 + 9000 16738.477 0 0 5269.5204 10.589147 + 9050 16738.455 0 0 5269.5135 10.589092 + 9100 16738.477 0 0 5269.5206 10.589146 + 9150 16738.512 0 0 5269.5316 10.589233 + 9200 16738.502 0 0 5269.5285 10.58921 + 9250 16738.493 0 0 5269.5255 10.589186 + 9300 16738.482 0 0 5269.522 10.589159 + 9350 16738.46 0 0 5269.5151 10.589105 + 9400 16738.481 0 0 5269.5217 10.589155 + 9450 16738.509 0 0 5269.5307 10.589226 + 9500 16738.491 0 0 5269.5248 10.589181 + 9550 16738.484 0 0 5269.5227 10.589164 + 9600 16738.483 0 0 5269.5223 10.589161 + 9650 16738.464 0 0 5269.5166 10.589116 + 9700 16738.484 0 0 5269.5228 10.589164 + 9750 16738.507 0 0 5269.5301 10.589221 + 9800 16738.482 0 0 5269.5221 10.589159 + 9850 16738.478 0 0 5269.5208 10.589149 + 9900 16738.487 -0.00030979591 0 5269.5233 10.589165 + 9950 16738.476 -0.0009596827 0 5269.5193 10.589123 + 10000 16738.494 -0.0006271698 0 5269.5253 10.589175 +Loop time of 0.212511 on 4 procs for 10000 steps with 81 atoms -Performance: 385008.767 tau/day, 44561.200 timesteps/s -97.6% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 406566.385 tau/day, 47056.295 timesteps/s +91.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0032785 | 0.0039999 | 0.0052714 | 1.3 | 1.78 -Neigh | 0.010548 | 0.012524 | 0.016082 | 1.9 | 5.58 -Comm | 0.082771 | 0.087847 | 0.091037 | 1.1 | 39.15 -Output | 0.0042846 | 0.0045864 | 0.0054133 | 0.7 | 2.04 -Modify | 0.10401 | 0.10533 | 0.10736 | 0.4 | 46.94 -Other | | 0.01013 | | | 4.51 +Pair | 0.0032909 | 0.0039915 | 0.0048544 | 0.9 | 1.88 +Neigh | 0.011434 | 0.01325 | 0.016991 | 1.9 | 6.24 +Comm | 0.076038 | 0.082493 | 0.088069 | 1.5 | 38.82 +Output | 0.0031183 | 0.0045295 | 0.0086036 | 3.5 | 2.13 +Modify | 0.099662 | 0.10206 | 0.10679 | 0.9 | 48.02 +Other | | 0.00619 | | | 2.91 Nlocal: 20.25 ave 34 max 9 min Histogram: 2 0 0 0 0 0 0 1 0 1 diff --git a/examples/rigid/log.27Nov18.rigid.poems.g++.1 b/examples/rigid/log.27Nov18.rigid.poems.g++.1 new file mode 100644 index 0000000000..e279b8a73e --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.poems.g++.1 @@ -0,0 +1,338 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.292 | 3.292 | 3.292 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384277 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184717 + 1150 20849.582 206.01695 0 3680.9472 -0.86699149 + 1200 21815.003 45.317414 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064078 + 1300 20780.781 217.36506 0 3680.8286 6.0538616 + 1350 20558.971 254.36482 0 3680.8601 -3.6773952 + 1400 21485.029 99.812921 0 3680.6511 -16.185473 + 1450 21771.107 52.15961 0 3680.6775 -2.4756673 + 1500 21520.948 93.503927 0 3680.3286 2.1023576 + 1550 21351.418 121.68137 0 3680.2511 5.5159947 + 1600 20778.805 216.92177 0 3680.0559 15.089188 + 1650 21477.638 100.21836 0 3679.8247 -1.1045746 + 1700 18501.339 596.47914 0 3680.0357 -15.679679 + 1750 18563.642 587.34785 0 3681.2882 33.532209 + 1800 19110.185 494.8234 0 3679.8543 18.024046 + 1850 21364.191 119.23545 0 3679.9339 2.5291103 + 1900 20146.626 322.14867 0 3679.9197 5.7313218 + 1950 20692.672 231.25325 0 3680.0319 4.2977763 + 2000 20943.904 189.11235 0 3679.7629 -22.645121 + 2050 19668.057 401.82994 0 3679.8394 3.6251916 + 2100 20280.442 299.76155 0 3679.8353 7.4807949 + 2150 19181.86 483.522 0 3680.4987 22.620507 + 2200 21300.161 130.70534 0 3680.7322 4.7102665 + 2250 20486.943 266.63931 0 3681.1299 -8.6456512 + 2300 18653.122 572.24819 0 3681.1018 -5.2637122 + 2350 21513.523 95.614901 0 3681.2021 -9.3621767 + 2400 21466.272 103.56446 0 3681.2765 -29.561368 + 2450 20100.105 332.27123 0 3682.2887 35.744287 + 2500 20764.395 221.6677 0 3682.4001 -12.468906 + 2550 20435.699 276.31055 0 3682.2603 -22.413697 + 2600 21466.467 104.53618 0 3682.2807 -10.078508 + 2650 20814.737 213.23892 0 3682.3617 5.1390411 + 2700 18565.761 588.3578 0 3682.6513 22.27664 + 2750 20772.36 220.1607 0 3682.2206 -7.9448198 + 2800 21018.563 179.10058 0 3682.1945 -7.0717829 + 2850 16789.412 884.21472 0 3682.4501 33.279015 + 2900 19304.363 464.75282 0 3682.1466 7.947554 + 2950 20513.758 263.07578 0 3682.0355 2.2361434 + 3000 20617.309 245.95251 0 3682.1706 -0.75213689 + 3050 18567.52 587.90473 0 3682.4914 -4.0112006 + 3100 18696.577 566.20617 0 3682.3023 -1.4814167 + 3150 19864.606 371.56078 0 3682.3284 8.9362836 + 3200 18902.643 532.04614 0 3682.4867 0.76630303 + 3250 21110.454 163.86212 0 3682.271 -1.6253894 + 3300 19369.939 454.05833 0 3682.3816 4.9066544 + 3350 19082.603 501.69905 0 3682.133 3.5982292 + 3400 19527.779 426.918 0 3681.5478 6.9612143 + 3450 19892.953 366.19989 0 3681.6921 3.0050426 + 3500 19708.981 396.84552 0 3681.6756 7.0757635 + 3550 20256.096 306.23937 0 3682.2554 -1.752138 + 3600 21289.889 133.93823 0 3682.253 -3.7462615 + 3650 18333.877 627.18028 0 3682.8264 -15.276791 + 3700 19829.133 377.33753 0 3682.1931 -6.269648 + 3750 20771.635 220.07171 0 3682.0109 -28.479036 + 3800 18373.813 619.79253 0 3682.0947 29.594781 + 3850 19320.99 461.92786 0 3682.0928 -5.3212101 + 3900 16119.825 995.68064 0 3682.3182 -8.4683118 + 3950 15556.948 1091.3655 0 3684.1902 20.98273 + 4000 20000.464 348.24891 0 3681.6596 7.1589745 + 4050 18870.219 536.59924 0 3681.6358 -3.7997025 + 4100 19889.518 367.49253 0 3682.4122 -14.091266 + 4150 15789.623 1051.3399 0 3682.9438 -4.4152389 + 4200 20548.889 256.83493 0 3681.6498 0.92234153 + 4250 20681.925 235.46113 0 3682.4487 -11.515773 + 4300 19330.404 460.80975 0 3682.5437 -22.351775 + 4350 19369.443 453.35405 0 3681.5945 29.418242 + 4400 20762.165 222.24133 0 3682.6021 2.6627047 + 4450 19984.657 350.71294 0 3681.4891 28.88731 + 4500 21167.58 154.25344 0 3682.1834 -3.0784322 + 4550 18133.576 660.73671 0 3682.9995 2.5305835 + 4600 19935.069 360.36826 0 3682.8798 2.4575034 + 4650 21413.76 113.86464 0 3682.8246 -5.1271547 + 4700 21716.333 63.609419 0 3682.9982 -2.4708049 + 4750 21352.947 124.36961 0 3683.1941 -0.29026265 + 4800 19043.788 508.8617 0 3682.8264 14.797006 + 4850 20516.121 263.78758 0 3683.1411 7.1348281 + 4900 20624.5 245.81827 0 3683.235 0.34708051 + 4950 20317.197 296.68937 0 3682.8889 -0.55065946 + 5000 18346.865 625.37246 0 3683.1832 7.3371413 + 5050 18867.53 538.49153 0 3683.0799 1.9249866 + 5100 18790.276 551.17224 0 3682.885 2.2333017 + 5150 20241.365 311.84683 0 3685.4076 -3.998004 + 5200 17685.058 739.76418 0 3687.2739 3.2835025 + 5250 18496.626 604.58166 0 3687.3526 -10.185776 + 5300 18420.042 617.82026 0 3687.8273 -16.392458 + 5350 18767.338 559.0349 0 3686.9246 4.5320767 + 5400 20423.245 284.90517 0 3688.7794 -8.6356656 + 5450 21080.398 176.18494 0 3689.5846 -16.450038 + 5500 16684.424 909.12643 0 3689.8637 49.94555 + 5550 20132.31 335.03663 0 3690.4216 -16.018038 + 5600 20430.923 285.17562 0 3690.3295 -5.0773675 + 5650 20479.943 276.55962 0 3689.8834 5.4334564 + 5700 20061.532 345.95553 0 3689.5441 -16.230658 + 5750 20523.759 268.92217 0 3689.5487 -4.4128812 + 5800 18900.356 537.65462 0 3687.7139 13.605549 + 5850 20280.502 310.27193 0 3690.3556 -4.7884959 + 5900 19050.26 515.66087 0 3690.7042 7.8864722 + 5950 19566.917 430.2997 0 3691.4525 31.715268 + 6000 18878.118 544.75449 0 3691.1076 -4.2415329 + 6050 19308.682 471.70734 0 3689.821 -10.561614 + 6100 18776.194 560.04764 0 3689.4133 -7.7286747 + 6150 21475.064 110.1508 0 3689.3281 -3.6506391 + 6200 19975 360.82675 0 3689.9934 10.282021 + 6250 21396.341 123.5341 0 3689.5909 -5.7215163 + 6300 18533.423 600.87422 0 3689.778 15.408027 + 6350 20653.152 247.19253 0 3689.3846 8.5607784 + 6400 19716.537 403.41487 0 3689.5044 13.165575 + 6450 21120.66 168.79838 0 3688.9084 -0.50382728 + 6500 19700.345 404.7155 0 3688.1064 13.941375 + 6550 10818.393 1892.037 0 3695.1025 38.423155 + 6600 18684.478 574.84755 0 3688.9273 5.9176985 + 6650 19219.732 486.04269 0 3689.3314 18.287659 + 6700 20058.587 344.88255 0 3687.9804 6.5372086 + 6750 21279.318 142.77333 0 3689.3264 2.498188 + 6800 20671.545 244.25024 0 3689.5078 -4.1356416 + 6850 21203.598 155.82001 0 3689.753 -0.0083061182 + 6900 21699.344 73.301497 0 3689.8588 -8.0309898 + 6950 20951.212 197.19403 0 3689.0627 0.76668303 + 7000 20166.275 329.02869 0 3690.0746 2.0083318 + 7050 21554.944 97.465792 0 3689.9564 -3.2420086 + 7100 20817.494 220.25476 0 3689.8372 0.17206182 + 7150 21481.11 109.84029 0 3690.0253 -3.6814741 + 7200 21266.824 145.53099 0 3690.0016 -2.060543 + 7250 19434.684 450.81331 0 3689.9273 9.4822765 + 7300 21246.525 148.96573 0 3690.0532 3.3208839 + 7350 19749.269 398.60049 0 3690.1454 1.0929662 + 7400 20354.792 297.70261 0 3690.168 1.547159 + 7450 19996.859 357.16723 0 3689.977 -0.68412025 + 7500 20179.628 326.53243 0 3689.8038 -2.4805507 + 7550 18765.184 561.65039 0 3689.1811 -1.7976428 + 7600 19457.496 447.04428 0 3689.9603 -1.9055522 + 7650 18206.823 655.57276 0 3690.0433 1.2797964 + 7700 19152.344 497.77422 0 3689.8315 18.145069 + 7750 21387.484 125.48654 0 3690.0673 -2.9915772 + 7800 18127.052 668.61425 0 3689.7896 9.044869 + 7850 21419.557 120.08889 0 3690.015 6.2651717 + 7900 21817.182 53.739819 0 3689.9368 -4.2387416 + 7950 18215.195 654.15494 0 3690.0208 -54.628049 + 8000 21523.503 102.58018 0 3689.8307 -4.84236 + 8050 20720.799 236.28689 0 3689.7535 -9.3725225 + 8100 21196.483 157.3232 0 3690.0704 -7.7222497 + 8150 20869.667 211.65308 0 3689.9309 -6.8438295 + 8200 17790.052 725.72497 0 3690.7336 -25.697688 + 8250 19634.94 417.71929 0 3690.2094 8.861604 + 8300 19135.784 500.92443 0 3690.2218 -3.1245167 + 8350 20191.718 324.93312 0 3690.2195 6.5736107 + 8400 20695.239 241.02378 0 3690.2302 -14.592221 + 8450 21793.857 57.609525 0 3689.9191 -11.509747 + 8500 21271.088 144.43102 0 3689.6124 -0.091587085 + 8550 20064.337 345.21754 0 3689.2737 9.5058471 + 8600 20282.86 308.2307 0 3688.7074 2.265529 + 8650 21223.055 151.24306 0 3688.419 1.7296834 + 8700 18875.342 542.42055 0 3688.3108 6.367148 + 8750 20922.65 201.55122 0 3688.6595 3.4208578 + 8800 21406.54 120.8539 0 3688.6106 1.8253729 + 8850 19868.524 377.05623 0 3688.477 16.327796 + 8900 20025.322 348.94892 0 3686.5025 17.063406 + 8950 21224.374 151.3567 0 3688.7524 -0.11028753 + 9000 21318.309 135.862 0 3688.9135 -0.50826819 + 9050 17538.618 768.00136 0 3691.1043 37.978645 + 9100 21247.861 147.84641 0 3689.1566 -6.7773259 + 9150 18455.677 613.08767 0 3689.0339 -3.4844751 + 9200 19486.859 441.03829 0 3688.8482 -18.602827 + 9250 21774.926 59.710446 0 3688.8648 -13.379919 + 9300 17628.877 750.72321 0 3688.8694 27.797974 + 9350 19827.334 383.85708 0 3688.4128 6.5459021 + 9400 20020.126 351.61742 0 3688.3051 -14.332562 + 9450 21596.338 88.904175 0 3688.2939 1.5779716 + 9500 18981.418 524.60141 0 3688.1711 5.4352409 + 9550 18652.616 579.05144 0 3687.8208 25.600729 + 9600 21198.037 155.23097 0 3688.2371 -3.3586596 + 9650 19958.317 361.32544 0 3687.7115 4.2910178 + 9700 19129.101 499.5993 0 3687.7828 13.267102 + 9750 21913.967 35.689587 0 3688.0174 -7.3222905 + 9800 21314.694 135.43794 0 3687.8869 -9.5613518 + 9850 20899.743 204.82802 0 3688.1185 -2.6321428 + 9900 20288.244 306.5013 0 3687.8753 3.6196618 + 9950 19271.015 475.88527 0 3687.7211 -1.8196764 + 10000 21122.24 167.82714 0 3688.2005 -3.8464842 +Loop time of 6.61148 on 1 procs for 10000 steps with 81 atoms + +Performance: 13068.179 tau/day, 1512.521 timesteps/s +97.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14595 | 0.14595 | 0.14595 | 0.0 | 2.21 +Neigh | 0.10704 | 0.10704 | 0.10704 | 0.0 | 1.62 +Comm | 0.013317 | 0.013317 | 0.013317 | 0.0 | 0.20 +Output | 0.0047956 | 0.0047956 | 0.0047956 | 0.0 | 0.07 +Modify | 6.3318 | 6.3318 | 6.3318 | 0.0 | 95.77 +Other | | 0.008603 | | | 0.13 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 95 ave 95 max 95 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 744 ave 744 max 744 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 744 +Ave neighs/atom = 9.18519 +Neighbor list builds = 992 +Dangerous builds = 941 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:06 diff --git a/examples/rigid/log.27Nov18.rigid.poems.g++.4 b/examples/rigid/log.27Nov18.rigid.poems.g++.4 new file mode 100644 index 0000000000..55ecca3067 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.poems.g++.4 @@ -0,0 +1,338 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 36 45 +10 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9 +1 clusters, 9 bodies, 8 joints, 81 atoms + +# 2 chains of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 37 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 +#fix 2 all poems group clump5 clump6 clump7 clump8 clump9 + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.263 | 3.357 | 3.638 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 217.7783 3430.3907 0 3466.6871 -2.7403788 + 50 13679.637 1404.2468 0 3684.1863 12.446066 + 100 16777.225 888.87665 0 3685.0808 -31.828677 + 150 19595.365 418.45042 0 3684.3446 40.709078 + 200 18524.188 596.47273 0 3683.8375 -0.8159371 + 250 21015.789 180.96521 0 3683.5967 -10.042469 + 300 20785.513 219.25314 0 3683.5053 2.6452719 + 350 21072.46 171.2554 0 3683.3321 7.0609024 + 400 19956.414 356.36381 0 3682.4328 19.320259 + 450 20724.42 227.73284 0 3681.8028 8.1259249 + 500 20152.578 322.71466 0 3681.4777 5.4929878 + 550 20017.022 345.29701 0 3681.4673 5.4661666 + 600 17897.743 698.72196 0 3681.6791 3.2854742 + 650 17297.758 796.60256 0 3679.5623 15.191113 + 700 18581.934 584.29715 0 3681.2861 5.1588289 + 750 21774.158 52.821062 0 3681.8474 -10.775664 + 800 21604.055 81.188546 0 3681.8644 -3.2045743 + 850 17821.483 711.53827 0 3681.7854 7.4384276 + 900 21033.292 175.98127 0 3681.5299 -16.345167 + 950 20968.166 186.59847 0 3681.2929 -2.330456 + 1000 20490.66 266.19375 0 3681.3037 11.787983 + 1050 20222.396 310.94072 0 3681.34 -8.3459539 + 1100 21321.687 127.61533 0 3681.2299 -1.2184718 + 1150 20849.582 206.01695 0 3680.9472 -0.8669916 + 1200 21815.003 45.317417 0 3681.1512 1.5988314 + 1250 18655.437 572.41453 0 3681.654 10.064076 + 1300 20780.781 217.36504 0 3680.8286 6.0538619 + 1350 20558.972 254.3648 0 3680.8601 -3.6773987 + 1400 21485.029 99.812949 0 3680.6511 -16.185471 + 1450 21771.108 52.15959 0 3680.6775 -2.4756681 + 1500 21520.948 93.503949 0 3680.3286 2.1023578 + 1550 21351.418 121.6814 0 3680.2511 5.5159978 + 1600 20778.805 216.92171 0 3680.0559 15.089182 + 1650 21477.639 100.2182 0 3679.8247 -1.1045944 + 1700 18501.343 596.47853 0 3680.0357 -15.67963 + 1750 18563.643 587.34767 0 3681.2882 33.532167 + 1800 19110.19 494.82264 0 3679.8543 18.024034 + 1850 21364.196 119.23454 0 3679.9339 2.5291491 + 1900 20146.643 322.14595 0 3679.9197 5.731152 + 1950 20692.67 231.25357 0 3680.0319 4.2977641 + 2000 20943.904 189.11223 0 3679.763 -22.645645 + 2050 19668.152 401.81407 0 3679.8394 3.6255896 + 2100 20280.572 299.73976 0 3679.8351 7.4809355 + 2150 19182.121 483.47905 0 3680.4992 22.615309 + 2200 21299.76 130.77281 0 3680.7327 4.7114154 + 2250 20487.784 266.4995 0 3681.1302 -8.6406776 + 2300 18655.125 571.91487 0 3681.1023 -5.2671669 + 2350 21512.614 95.766913 0 3681.2025 -9.3523428 + 2400 21467.773 103.31519 0 3681.2773 -29.600307 + 2450 20096.937 332.80159 0 3682.2911 35.890912 + 2500 20761.446 222.16118 0 3682.4022 -12.528127 + 2550 20409.6 280.67234 0 3682.2723 -22.277373 + 2600 21469.964 103.95529 0 3682.2826 -10.038267 + 2650 20708.138 231.00516 0 3682.3615 5.3659502 + 2700 18584.743 585.07862 0 3682.5357 21.785261 + 2750 20503.019 264.91491 0 3682.0847 -4.5583917 + 2800 20584.075 251.44664 0 3682.1258 -6.5084595 + 2850 17277.076 802.33356 0 3681.8462 15.519513 + 2900 19392.956 449.92915 0 3682.0885 -4.3829957 + 2950 18371.786 620.29835 0 3682.2626 7.2117592 + 3000 20412.015 280.25302 0 3682.2555 0.32492606 + 3050 20858.248 205.65269 0 3682.0273 4.5055715 + 3100 21561.094 88.438447 0 3681.9541 -3.7523733 + 3150 15471.278 1103.4497 0 3681.9961 -14.576367 + 3200 15386.973 1117.8815 0 3682.377 15.051163 + 3250 19741.037 392.04755 0 3682.2204 -2.6610995 + 3300 20870.191 203.58229 0 3681.9475 -4.7795545 + 3350 16648.228 907.66571 0 3682.3704 -8.9242511 + 3400 20104.016 331.58603 0 3682.2554 6.4783858 + 3450 21421.316 112.28228 0 3682.5015 -8.3484987 + 3500 19284.533 467.80739 0 3681.8962 -12.835452 + 3550 20160.125 322.4476 0 3682.4684 1.6574827 + 3600 16682.415 902.73752 0 3683.14 22.383296 + 3650 16762.19 890.14636 0 3683.8446 16.119412 + 3700 17858.568 707.37212 0 3683.8 -1.6582504 + 3750 20029.881 345.15986 0 3683.4733 -3.1415889 + 3800 20734 227.99158 0 3683.6582 -7.9580418 + 3850 20741.089 226.39408 0 3683.2423 8.3055765 + 3900 18671.251 571.42296 0 3683.2981 -3.7468858 + 3950 19547.209 423.14256 0 3681.0108 5.8312279 + 4000 19739.799 393.58799 0 3683.5544 18.604884 + 4050 20014.121 347.8176 0 3683.5044 9.93387 + 4100 20503.654 266.08691 0 3683.3626 8.1304118 + 4150 18309.702 632.29807 0 3683.9151 -0.0021480359 + 4200 20509.423 265.60353 0 3683.8408 -2.1658857 + 4250 21805.541 50.325935 0 3684.5828 1.082842 + 4300 21420.551 114.90431 0 3684.9962 -1.7985998 + 4350 20256.928 308.74187 0 3684.8966 -11.669472 + 4400 21633.488 79.629274 0 3685.2106 -0.96131785 + 4450 20793.327 219.66955 0 3685.2241 1.3752349 + 4500 18719.484 564.86754 0 3684.7816 2.6308699 + 4550 20966.335 190.68308 0 3685.0722 -18.587627 + 4600 19428.962 446.59618 0 3684.7565 -4.4051672 + 4650 18408.956 616.85009 0 3685.0095 2.777272 + 4700 19215.779 482.57562 0 3685.2054 19.441016 + 4750 20155.927 326.13401 0 3685.4553 6.1734993 + 4800 20918.085 199.31832 0 3685.6659 3.4407437 + 4850 20236.958 312.07276 0 3684.899 3.2612893 + 4900 21419.89 115.36879 0 3685.3505 -4.675951 + 4950 19707.901 401.14828 0 3685.7985 -10.730734 + 5000 19407.201 450.64394 0 3685.1775 17.518981 + 5050 21527.598 97.655186 0 3685.5882 -9.2294707 + 5100 21581.933 88.595517 0 3685.5843 -20.669485 + 5150 21161.214 158.48503 0 3685.3541 -2.7587502 + 5200 21166.679 157.24762 0 3685.0275 -18.180044 + 5250 20909.576 200.23507 0 3685.1644 -16.617303 + 5300 21911.746 33.236563 0 3685.1942 -5.8313967 + 5350 20857.303 208.87453 0 3685.0916 12.176312 + 5400 20958.96 191.96694 0 3685.1269 3.6116429 + 5450 20433.179 279.61178 0 3685.1415 13.324529 + 5500 19604.675 416.88499 0 3684.3308 21.536484 + 5550 18171.145 655.92915 0 3684.4534 -9.2269804 + 5600 19799.907 385.12116 0 3685.1056 22.202165 + 5650 19711.882 399.30581 0 3684.6194 15.93063 + 5700 17908.833 699.52405 0 3684.3295 0.35530356 + 5750 18606.518 583.538 0 3684.6243 -4.4540843 + 5800 21814.053 48.974627 0 3684.6501 -1.5206358 + 5850 18029.107 679.9357 0 3684.7868 12.137677 + 5900 21090.739 169.64502 0 3684.7682 -1.5051545 + 5950 21086.26 170.29075 0 3684.6674 -2.8164474 + 6000 21285.771 136.95608 0 3684.5846 -26.582739 + 6050 21203.994 150.87822 0 3684.8772 -2.6617226 + 6100 21481.553 104.57796 0 3684.8368 -16.524974 + 6150 20354.4 292.57675 0 3684.9767 2.7960207 + 6200 21326.591 130.75243 0 3685.1843 -1.5929194 + 6250 21505.087 101.07817 0 3685.2593 -3.7821931 + 6300 21296.273 135.6593 0 3685.0382 -0.55635908 + 6350 21295.389 135.86485 0 3685.0964 5.6614093 + 6400 16552.242 926.02655 0 3684.7336 14.177218 + 6450 20148.951 327.1151 0 3685.2736 7.4561085 + 6500 20962.151 191.79415 0 3685.486 -4.5436711 + 6550 21710.328 67.433972 0 3685.8219 -5.7678572 + 6600 20698.571 234.79099 0 3684.5528 -2.1984068 + 6650 17892.287 704.05484 0 3686.1026 11.525836 + 6700 21272.999 141.26589 0 3686.7657 0.44088069 + 6750 19558.993 426.46448 0 3686.2966 -16.907401 + 6800 20350.247 295.23951 0 3686.9474 1.1284348 + 6850 18665.05 573.5326 0 3684.3742 17.088712 + 6900 19769.199 392.1551 0 3687.0216 6.7562425 + 6950 19439.159 446.99138 0 3686.8512 -6.0105763 + 7000 19379.907 456.53471 0 3686.5192 -9.0505095 + 7050 19983.754 356.02523 0 3686.651 -5.6274314 + 7100 19867.737 375.47627 0 3686.7658 17.315482 + 7150 19258.794 477.47344 0 3687.2724 14.316676 + 7200 21282.428 139.96051 0 3687.0318 -0.77043459 + 7250 19828.603 381.98919 0 3686.7564 6.5142869 + 7300 20574.582 257.8245 0 3686.9215 -3.6547118 + 7350 21613.467 84.771568 0 3687.0161 -7.5188826 + 7400 21817.009 50.844944 0 3687.0131 -14.888864 + 7450 14937.538 1197.4257 0 3687.0154 1.7540499 + 7500 18326.914 632.40374 0 3686.8894 8.3397357 + 7550 13611.007 1418.4727 0 3686.9739 -19.379482 + 7600 19173.985 491.9482 0 3687.6123 17.229001 + 7650 16911.504 867.33649 0 3685.9204 -21.042834 + 7700 21752.116 61.143705 0 3686.4963 -10.344487 + 7750 20208.337 318.26355 0 3686.3197 13.385814 + 7800 21649.909 77.950987 0 3686.2692 -1.7911084 + 7850 20139.64 329.50319 0 3686.1098 -5.5805093 + 7900 21355.026 126.7642 0 3685.9352 -7.7062172 + 7950 21336.178 129.88925 0 3685.9188 -2.059298 + 8000 21047.596 177.71546 0 3685.6482 0.37963466 + 8050 19217.351 482.62331 0 3685.5152 6.5582595 + 8100 20499.057 268.7173 0 3685.2268 -1.1959737 + 8150 21494.301 102.83829 0 3685.2219 -1.6427647 + 8200 20074.928 339.19817 0 3685.0195 6.285123 + 8250 17335.157 793.47566 0 3682.6685 22.877381 + 8300 17340.544 794.62619 0 3684.7168 3.9147755 + 8350 20529.345 262.51162 0 3684.0691 4.031768 + 8400 18884.747 537.47827 0 3684.9361 22.853404 + 8450 20341.86 293.10484 0 3683.4148 0.33856656 + 8500 19300.282 467.58127 0 3684.2949 12.35507 + 8550 21631.936 78.254534 0 3683.5772 -10.992959 + 8600 20204.913 316.83233 0 3684.3178 20.74228 + 8650 21018.189 181.32054 0 3684.352 1.8412068 + 8700 20161.304 323.97907 0 3684.1964 -2.646629 + 8750 19081.79 504.00155 0 3684.2998 -10.088053 + 8800 20834.489 211.76247 0 3684.1773 14.896336 + 8850 20929.355 196.18335 0 3684.4092 -1.2602398 + 8900 21491.074 102.47788 0 3684.3235 -1.4696758 + 8950 20474.735 271.69461 0 3684.1504 -6.9489258 + 9000 21128.641 162.40732 0 3683.8474 -7.7928168 + 9050 18421.801 614.46442 0 3684.7646 24.40313 + 9100 19301.292 466.98873 0 3683.8707 4.4687046 + 9150 21575.705 88.213763 0 3684.1646 -0.94696984 + 9200 20004.776 350.05448 0 3684.1838 -7.3466605 + 9250 21384.079 120.14472 0 3684.1578 -8.3773844 + 9300 21980.599 20.702393 0 3684.1356 -12.666293 + 9350 21686.606 69.517984 0 3683.9524 -8.8366533 + 9400 20732.704 228.46247 0 3683.9131 -6.4080307 + 9450 19798.859 384.34696 0 3684.1568 7.6198484 + 9500 20270.695 305.22664 0 3683.6758 1.5862486 + 9550 16496.156 935.28481 0 3684.6441 15.001468 + 9600 20642.429 241.08853 0 3681.4934 -9.2159382 + 9650 21292.587 135.4474 0 3684.2119 -0.54770976 + 9700 18888.158 536.60518 0 3684.6315 5.3236926 + 9750 18750.018 559.35922 0 3684.3623 -9.9424949 + 9800 20544.772 259.71076 0 3683.8394 8.732202 + 9850 16698.125 901.90076 0 3684.9216 9.9553329 + 9900 21450.963 109.58687 0 3684.7474 -4.8001999 + 9950 20664.461 240.66995 0 3684.7468 -3.4840781 + 10000 18951.367 526.45428 0 3685.0155 21.512727 +Loop time of 8.99246 on 4 procs for 10000 steps with 81 atoms + +Performance: 9608.051 tau/day, 1112.043 timesteps/s +93.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.01308 | 0.038162 | 0.084123 | 14.4 | 0.42 +Neigh | 0.017227 | 0.032774 | 0.061983 | 10.0 | 0.36 +Comm | 1.329 | 1.5822 | 1.8017 | 13.5 | 17.60 +Output | 0.014984 | 0.029676 | 0.046035 | 6.6 | 0.33 +Modify | 6.8022 | 7.1104 | 7.4356 | 8.6 | 79.07 +Other | | 0.1992 | | | 2.22 + +Nlocal: 20.25 ave 81 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 +Nghost: 46.25 ave 95 max 14 min +Histogram: 2 0 0 0 0 1 0 0 0 1 +Neighs: 249.25 ave 997 max 0 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 997 +Ave neighs/atom = 12.3086 +Neighbor list builds = 993 +Dangerous builds = 943 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:09 diff --git a/examples/rigid/log.27Nov18.rigid.poems2.g++.1 b/examples/rigid/log.27Nov18.rigid.poems2.g++.1 new file mode 100644 index 0000000000..071e9bcc52 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.poems2.g++.1 @@ -0,0 +1,342 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 +1 clusters, 4 bodies, 3 joints, 36 atoms +fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +1 clusters, 5 bodies, 4 joints, 45 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) +WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) +WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.854 | 3.854 | 3.854 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12167.633 1505.5478 0 3758.8133 35.125973 + 100 17556.978 512.66277 0 3763.9549 11.137534 + 150 19579.586 138.04942 0 3763.8987 -29.953971 + 200 19757.51 105.30542 0 3764.1036 -0.030645317 + 250 18218.374 390.10747 0 3763.8804 13.711001 + 300 19383.039 174.40688 0 3763.8586 5.7240693 + 350 20125.986 36.972611 0 3764.0071 1.9559205 + 400 18888.816 266.10975 0 3764.0386 9.6362168 + 450 19307.656 188.2511 0 3763.743 1.9326206 + 500 16331.197 738.56392 0 3762.8597 9.1715579 + 550 19318.722 186.16172 0 3763.7027 3.0115336 + 600 19455.268 161.20621 0 3764.0336 0.55208034 + 650 18487.011 340.03216 0 3763.5528 -8.0359122 + 700 17321.201 556.32471 0 3763.9545 -13.631751 + 750 18979.187 249.04389 0 3763.7082 -2.6072455 + 800 19342.456 181.85552 0 3763.7918 8.1918726 + 850 19070.641 232.19342 0 3763.7936 7.3148472 + 900 19478.873 156.65987 0 3763.8586 2.4284987 + 950 19912.415 76.437437 0 3763.9216 -1.4667227 + 1000 16003.749 802.39753 0 3766.0548 46.642188 + 1050 19859.583 86.64176 0 3764.3424 -2.1961943 + 1100 19229.575 203.61488 0 3764.6473 -10.632365 + 1150 18821.6 279.15861 0 3764.64 -0.89495035 + 1200 19392.695 173.59744 0 3764.8373 1.8508753 + 1250 16459.624 717.32104 0 3765.3995 33.478127 + 1300 19343.863 182.59043 0 3764.7874 0.75890736 + 1350 20019.643 57.503573 0 3764.8448 0.31444671 + 1400 18549.582 329.31436 0 3764.4221 10.738303 + 1450 15163.926 957.47585 0 3765.6103 -17.923459 + 1500 19223.688 204.15175 0 3764.0939 -1.6134531 + 1550 18147.996 404.12677 0 3764.8668 8.4194779 + 1600 18615.043 317.42467 0 3764.6548 -2.3288934 + 1650 20120.654 38.887913 0 3764.935 -8.7620277 + 1700 19450.907 162.98272 0 3765.0025 2.3254731 + 1750 19374.632 177.37966 0 3765.2744 8.9328774 + 1800 19424.404 167.93966 0 3765.0514 0.081230261 + 1850 17936.249 442.84231 0 3764.3699 6.6010636 + 1900 19982.595 64.406198 0 3764.8868 -2.9529813 + 1950 16215.852 761.91287 0 3764.8485 13.994708 + 2000 18584.422 322.12049 0 3763.68 7.1654003 + 2050 20107.965 41.025754 0 3764.723 -0.3109069 + 2100 20002.333 60.593017 0 3764.7288 -6.7919784 + 2150 16949.762 626.59623 0 3765.441 3.508941 + 2200 20010.953 58.808279 0 3764.5403 -10.862172 + 2250 18982.73 247.00892 0 3762.3292 -0.53807815 + 2300 18401.298 354.87973 0 3762.5274 1.0920554 + 2350 19390.524 172.9415 0 3763.7793 -3.3524932 + 2400 16080.801 786.38838 0 3764.3146 -16.200514 + 2450 18870.412 268.74976 0 3763.2705 11.197736 + 2500 19688.29 117.58223 0 3763.5618 4.382644 + 2550 18870.825 268.78678 0 3763.384 -5.6623656 + 2600 17019.35 611.70808 0 3763.4395 6.3109641 + 2650 18753.285 291.0596 0 3763.8902 2.4120296 + 2700 19742.456 107.20901 0 3763.2193 -0.33061303 + 2750 19522.438 148.16759 0 3763.4339 -1.6254851 + 2800 18304.801 372.55152 0 3762.3295 22.6368 + 2850 18465.36 343.48495 0 3762.9961 4.4169272 + 2900 20151.999 31.372926 0 3763.2245 1.2013699 + 2950 15498.143 892.80071 0 3762.8272 13.263724 + 3000 18728.301 294.65113 0 3762.855 8.1897838 + 3050 18538.466 330.25223 0 3763.3015 8.5865739 + 3100 19081.409 229.5907 0 3763.1849 -4.8573813 + 3150 18498.802 337.11548 0 3762.8195 1.0555321 + 3200 19925.897 73.358029 0 3763.339 -7.7325108 + 3250 19780.108 100.23785 0 3763.2209 -5.5974972 + 3300 19221.043 203.82387 0 3763.2763 4.2703251 + 3350 19025.292 240.11329 0 3763.3156 5.7708328 + 3400 18153.696 401.52086 0 3763.3164 21.076943 + 3450 18611.375 316.50396 0 3763.0548 -3.5484945 + 3500 19931.319 71.969274 0 3762.9543 1.8764978 + 3550 19747.562 106.05439 0 3763.0103 -2.5506186 + 3600 18491.39 338.4134 0 3762.7449 -4.0527808 + 3650 19757.998 104.19207 0 3763.0806 1.4865598 + 3700 20108.003 39.345514 0 3763.0498 0.062827129 + 3750 19222.505 203.28065 0 3763.0039 0.33719277 + 3800 19286.383 191.08831 0 3762.6406 -0.1826802 + 3850 19450.083 161.09138 0 3762.9587 -0.2708263 + 3900 18002.304 429.25655 0 3763.0166 -4.6832439 + 3950 17186.829 582.26502 0 3765.0111 55.816834 + 4000 16826.434 645.84974 0 3761.856 19.675962 + 4050 19227.526 202.18151 0 3762.8344 -0.2596098 + 4100 19908.792 76.084531 0 3762.8978 -2.796813 + 4150 17821.329 462.63065 0 3762.8768 13.069155 + 4200 19917.133 74.574998 0 3762.9329 -6.4181155 + 4250 19012.618 241.96787 0 3762.823 4.0847974 + 4300 19077.34 229.98133 0 3762.8221 4.324323 + 4350 19361.128 177.47406 0 3762.8681 -7.377974 + 4400 18565.044 324.95107 0 3762.9223 2.5229032 + 4450 19352.406 178.98756 0 3762.7665 0.10862717 + 4500 18482.218 340.15496 0 3762.788 12.518301 + 4550 18359.732 362.83749 0 3762.7879 3.7500902 + 4600 19623.618 128.71624 0 3762.7196 -1.1328521 + 4650 17565.707 509.99904 0 3762.9078 1.7135935 + 4700 19876.052 81.892814 0 3762.6431 0.32476108 + 4750 19022.676 239.92262 0 3762.6403 -0.24613022 + 4800 18862.685 269.24248 0 3762.3324 6.2733979 + 4850 19899.174 77.426145 0 3762.4584 0.42535238 + 4900 18250.865 382.72867 0 3762.5185 23.308462 + 4950 18895.847 263.22651 0 3762.4575 8.0634675 + 5000 19096.705 225.69358 0 3762.1204 3.6816481 + 5050 16546.294 698.91312 0 3763.0416 17.453618 + 5100 19501.208 151.20999 0 3762.5449 -1.1231291 + 5150 19479.879 155.00669 0 3762.3917 -3.983378 + 5200 17397.818 541.23039 0 3763.0485 6.1109992 + 5250 18564.869 324.10557 0 3762.0442 9.2244762 + 5300 16271.663 747.52374 0 3760.7947 -6.5256602 + 5350 19831.418 89.851887 0 3762.3367 -2.3453958 + 5400 18723.697 294.67435 0 3762.0256 4.6822081 + 5450 19547.28 142.21934 0 3762.086 -5.5243408 + 5500 19415.447 166.68729 0 3762.1404 -9.5658991 + 5550 18492.721 337.54773 0 3762.1256 6.5184903 + 5600 19391.389 171.14375 0 3762.1416 -0.53835361 + 5650 18503.465 334.62751 0 3761.1951 4.6580363 + 5700 18153.344 399.91064 0 3761.6409 12.851587 + 5750 18342.297 365.14769 0 3761.8694 2.7148176 + 5800 19583.241 135.64969 0 3762.1758 -1.089608 + 5850 15967.283 804.18382 0 3761.088 11.278762 + 5900 19040.271 235.35509 0 3761.3312 5.1352158 + 5950 17920.962 443.17951 0 3761.8762 4.9621366 + 6000 19100.92 224.3946 0 3761.602 -9.537589 + 6050 17982.119 432.3251 0 3762.3472 -2.851617 + 6100 16233.096 755.46191 0 3761.5908 25.113316 + 6150 18316.543 370.01118 0 3761.9635 -1.7445703 + 6200 18483.464 339.13282 0 3761.9966 -2.0857447 + 6250 18609.406 315.56032 0 3761.7467 -12.289208 + 6300 17167.919 582.68212 0 3761.9264 -3.8263397 + 6350 17870.329 452.58116 0 3761.9013 -3.3843134 + 6400 19309.717 186.11786 0 3761.9913 -4.9462739 + 6450 17964.073 435.39924 0 3762.0794 12.272972 + 6500 18772.847 285.61959 0 3762.0727 6.7928648 + 6550 18915.116 259.41365 0 3762.213 -4.1449761 + 6600 19446.628 161.18763 0 3762.415 -2.1906581 + 6650 16348.787 734.99282 0 3762.546 -9.9624546 + 6700 19066.684 231.43863 0 3762.3061 -5.362833 + 6750 14890.323 1004.547 0 3762.0143 37.373013 + 6800 18235.19 385.253 0 3762.1401 0.21012662 + 6850 16447.997 716.11276 0 3762.0382 -9.2095411 + 6900 18343.362 364.81902 0 3761.7379 10.417932 + 6950 16014.084 797.13348 0 3762.7046 6.7906777 + 7000 19120.393 221.29236 0 3762.1059 -1.3461375 + 7050 18055.409 418.30136 0 3761.8957 1.5772317 + 7100 18407.231 353.41868 0 3762.1652 0.61071769 + 7150 18728.136 293.64021 0 3761.8136 5.1649654 + 7200 17706.628 483.07628 0 3762.0815 18.000708 + 7250 19349.505 178.89673 0 3762.1385 2.540201 + 7300 20016.293 55.389159 0 3762.1101 -1.5793163 + 7350 19398.573 169.86661 0 3762.1949 -5.060123 + 7400 19466.526 157.37407 0 3762.2862 1.7158273 + 7450 18440.348 347.09196 0 3761.9712 12.781963 + 7500 19989.907 60.555934 0 3762.3906 -1.5033319 + 7550 19667.28 120.27403 0 3762.363 -3.3502366 + 7600 18497.707 336.15863 0 3761.66 1.7887539 + 7650 17901.957 447.17282 0 3762.3501 0.016725252 + 7700 19758.725 103.3129 0 3762.3361 -23.534448 + 7750 19443.957 161.6532 0 3762.386 -10.323924 + 7800 19776.178 100.1773 0 3762.4324 6.0854422 + 7850 19242.512 198.86705 0 3762.2952 5.2823659 + 7900 19499.929 151.30366 0 3762.4017 12.299911 + 7950 19630.317 127.19541 0 3762.4393 8.0799632 + 8000 19872.384 82.421129 0 3762.4923 2.2126691 + 8050 17747.038 476.27982 0 3762.7683 -7.7042786 + 8100 18832.654 274.78106 0 3762.3095 13.882157 + 8150 19949.814 68.09711 0 3762.5072 -0.54410896 + 8200 17555.866 511.02517 0 3762.1115 6.2471175 + 8250 17800.1 465.9992 0 3762.314 13.583485 + 8300 19755.224 103.89732 0 3762.2721 -1.487243 + 8350 17583.61 506.17539 0 3762.3995 -9.7819128 + 8400 18529.003 330.75623 0 3762.0532 14.731228 + 8450 20155.902 29.797078 0 3762.3716 -8.5711085 + 8500 18047.548 420.54645 0 3762.685 7.3875118 + 8550 19790.794 97.493375 0 3762.4553 -3.3427911 + 8600 19997.902 59.172074 0 3762.4874 3.3479688 + 8650 19987.319 61.148363 0 3762.5037 -1.889232 + 8700 19363.91 176.41833 0 3762.3276 -9.4291288 + 8750 18712.689 296.3979 0 3761.7107 5.9221369 + 8800 19783.17 98.860518 0 3762.4105 -3.5262066 + 8850 18796.049 281.60057 0 3762.3504 -8.2913002 + 8900 16738.277 662.62261 0 3762.3035 8.5838631 + 8950 17869.613 452.25006 0 3761.4377 11.561101 + 9000 18682.512 302.27997 0 3762.0043 3.8878724 + 9050 17513.759 518.50265 0 3761.7914 23.05778 + 9100 17500.686 521.57944 0 3762.4473 -2.8435751 + 9150 19645.683 124.43597 0 3762.5254 -3.0193092 + 9200 18898.897 262.76552 0 3762.5612 3.5891701 + 9250 20114.279 37.614866 0 3762.4813 -0.58120871 + 9300 19562.613 139.54073 0 3762.2468 -3.2630158 + 9350 19679.811 118.05865 0 3762.468 -3.4644363 + 9400 19297.384 188.84527 0 3762.4349 0.40498037 + 9450 18267.029 379.52581 0 3762.309 -0.13762867 + 9500 19951.072 67.63844 0 3762.2814 -7.575539 + 9550 19134.562 218.46835 0 3761.9057 -1.9626244 + 9600 19089.093 227.29178 0 3762.3089 -1.94158 + 9650 16964.603 620.71289 0 3762.3061 16.987042 + 9700 18846.881 271.3129 0 3761.4761 3.4458802 + 9750 19309.225 186.0142 0 3761.7966 9.4048627 + 9800 16359.704 733.51007 0 3763.0849 15.870164 + 9850 19958.532 66.203725 0 3762.2282 6.0043645 + 9900 19864.564 83.502384 0 3762.1253 -0.65360617 + 9950 18996.789 244.25101 0 3762.1749 -2.4961826 + 10000 17933.494 441.33587 0 3762.3532 -6.0731708 +Loop time of 6.84978 on 1 procs for 10000 steps with 81 atoms + +Performance: 12613.550 tau/day, 1459.902 timesteps/s +96.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1054 | 0.1054 | 0.1054 | 0.0 | 1.54 +Neigh | 0.081336 | 0.081336 | 0.081336 | 0.0 | 1.19 +Comm | 0.017124 | 0.017124 | 0.017124 | 0.0 | 0.25 +Output | 0.0050254 | 0.0050254 | 0.0050254 | 0.0 | 0.07 +Modify | 6.6313 | 6.6313 | 6.6313 | 0.0 | 96.81 +Other | | 0.00962 | | | 0.14 + +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 71 ave 71 max 71 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 612 ave 612 max 612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 612 +Ave neighs/atom = 7.55556 +Neighbor list builds = 989 +Dangerous builds = 906 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:06 diff --git a/examples/rigid/log.27Nov18.rigid.poems2.g++.4 b/examples/rigid/log.27Nov18.rigid.poems2.g++.4 new file mode 100644 index 0000000000..36856d97ec --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.poems2.g++.4 @@ -0,0 +1,342 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple rigid body system + +units lj +atom_style atomic + +pair_style lj/cut 2.5 + +read_data data.rigid + orthogonal box = (-12 -12 -12) to (12 12 12) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 81 atoms + +velocity all create 100.0 4928459 + +# unconnected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 10 18 +#group clump3 id <> 19 27 +#group clump4 id <> 28 36 +#group clump5 id <> 37 45 +#group clump6 id <> 46 54 +#group clump7 id <> 55 63 +#group clump8 id <> 64 72 +#group clump9 id <> 73 81 + +#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 1 chain of connected bodies + +#group clump1 id <> 1 9 +#group clump2 id <> 9 18 +#group clump3 id <> 18 27 +#group clump4 id <> 27 36 +#group clump5 id <> 36 45 +#group clump6 id <> 45 54 +#group clump7 id <> 54 63 +#group clump8 id <> 63 72 +#group clump9 id <> 72 81 + +#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9 + +# 2 chains of connected bodies + +group clump1 id <> 1 9 +9 atoms in group clump1 +group clump2 id <> 9 18 +10 atoms in group clump2 +group clump3 id <> 18 27 +10 atoms in group clump3 +group clump4 id <> 27 36 +10 atoms in group clump4 +group clump5 id <> 37 45 +9 atoms in group clump5 +group clump6 id <> 45 54 +10 atoms in group clump6 +group clump7 id <> 54 63 +10 atoms in group clump7 +group clump8 id <> 63 72 +10 atoms in group clump8 +group clump9 id <> 72 81 +10 atoms in group clump9 + +fix 1 all poems group clump1 clump2 clump3 clump4 +1 clusters, 4 bodies, 3 joints, 36 atoms +fix 2 all poems group clump5 clump6 clump7 clump8 clump9 +1 clusters, 5 bodies, 4 joints, 45 atoms + +neigh_modify exclude group clump1 clump1 +neigh_modify exclude group clump2 clump2 +neigh_modify exclude group clump3 clump3 +neigh_modify exclude group clump4 clump4 +neigh_modify exclude group clump5 clump5 +neigh_modify exclude group clump6 clump6 +neigh_modify exclude group clump7 clump7 +neigh_modify exclude group clump8 clump8 +neigh_modify exclude group clump9 clump9 + +thermo 100 + +#dump 1 all atom 50 dump.rigid.poems2 + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 5 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 5 + +timestep 0.0001 +thermo 50 +run 10000 +WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) +WARNING: More than one fix poems (src/POEMS/fix_poems.cpp:363) +WARNING: One or more atoms are time integrated more than once (src/modify.cpp:283) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 18 18 18 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.919 | 4.201 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 196.00047 3632.2347 0 3668.5311 -2.7403788 + 50 12167.633 1505.5478 0 3758.8133 35.125973 + 100 17556.978 512.66277 0 3763.9549 11.137534 + 150 19579.586 138.04942 0 3763.8987 -29.953971 + 200 19757.51 105.30542 0 3764.1036 -0.030645317 + 250 18218.374 390.10747 0 3763.8804 13.711001 + 300 19383.039 174.40688 0 3763.8586 5.7240693 + 350 20125.986 36.972611 0 3764.0071 1.9559205 + 400 18888.816 266.10975 0 3764.0386 9.6362168 + 450 19307.656 188.2511 0 3763.743 1.9326206 + 500 16331.197 738.56392 0 3762.8597 9.1715579 + 550 19318.722 186.16172 0 3763.7027 3.0115336 + 600 19455.268 161.20621 0 3764.0336 0.55208034 + 650 18487.011 340.03216 0 3763.5528 -8.0359122 + 700 17321.201 556.32471 0 3763.9545 -13.631751 + 750 18979.187 249.04389 0 3763.7082 -2.6072455 + 800 19342.456 181.85552 0 3763.7918 8.1918726 + 850 19070.641 232.19342 0 3763.7936 7.3148472 + 900 19478.873 156.65987 0 3763.8586 2.4284987 + 950 19912.415 76.437437 0 3763.9216 -1.4667227 + 1000 16003.749 802.39753 0 3766.0548 46.642188 + 1050 19859.583 86.64176 0 3764.3424 -2.1961943 + 1100 19229.575 203.61488 0 3764.6473 -10.632365 + 1150 18821.6 279.15861 0 3764.64 -0.89495035 + 1200 19392.695 173.59744 0 3764.8373 1.8508753 + 1250 16459.624 717.32104 0 3765.3995 33.478127 + 1300 19343.863 182.59043 0 3764.7874 0.75890736 + 1350 20019.643 57.503573 0 3764.8448 0.31444671 + 1400 18549.582 329.31436 0 3764.4221 10.738303 + 1450 15163.926 957.47585 0 3765.6103 -17.923459 + 1500 19223.688 204.15176 0 3764.0939 -1.6134529 + 1550 18147.996 404.12677 0 3764.8668 8.4194781 + 1600 18615.043 317.42468 0 3764.6548 -2.3288926 + 1650 20120.654 38.887908 0 3764.935 -8.7620288 + 1700 19450.907 162.98267 0 3765.0025 2.3254739 + 1750 19374.631 177.3797 0 3765.2744 8.9328773 + 1800 19424.404 167.93965 0 3765.0514 0.081228843 + 1850 17936.227 442.84645 0 3764.3699 6.6011251 + 1900 19982.595 64.406244 0 3764.8868 -2.952971 + 1950 16215.818 761.91942 0 3764.8486 13.994877 + 2000 18584.433 322.11846 0 3763.6801 7.1653695 + 2050 20107.965 41.025796 0 3764.723 -0.31089763 + 2100 20002.329 60.593879 0 3764.7288 -6.7919882 + 2150 16949.817 626.58598 0 3765.4409 3.5087505 + 2200 20010.954 58.8082 0 3764.5403 -10.862143 + 2250 18982.732 247.00854 0 3762.3293 -0.53812607 + 2300 18401.276 354.88369 0 3762.5274 1.0921058 + 2350 19390.535 172.93951 0 3763.7793 -3.3524354 + 2400 16080.475 786.44896 0 3764.3146 -16.201558 + 2450 18870.293 268.77171 0 3763.2704 11.199749 + 2500 19688.508 117.54164 0 3763.5617 4.3806994 + 2550 18870.328 268.87896 0 3763.3841 -5.6641099 + 2600 17020.211 611.54841 0 3763.4394 6.3081434 + 2650 18748.838 291.88478 0 3763.8917 2.4175163 + 2700 19743.991 106.92945 0 3763.224 -0.33916964 + 2750 19525.446 147.60906 0 3763.4324 -1.6251174 + 2800 18257.411 381.40184 0 3762.4038 23.39495 + 2850 18496.796 337.65425 0 3762.9868 4.3657735 + 2900 20163.418 29.253902 0 3763.2203 1.4431917 + 2950 16823.317 646.69817 0 3762.1273 4.9041552 + 3000 19223.007 203.2529 0 3763.069 4.0414458 + 3050 17391.02 542.93746 0 3763.4968 15.139863 + 3100 19205.6 206.57791 0 3763.1705 4.8519241 + 3150 19835.659 90.247763 0 3763.5179 -14.900053 + 3200 18962.776 251.5838 0 3763.2089 -13.706561 + 3250 19418.837 167.29058 0 3763.3716 -2.0866468 + 3300 18628.291 313.69067 0 3763.3742 5.9919715 + 3350 17465.974 529.14439 0 3763.5841 14.122593 + 3400 18488.661 339.6186 0 3763.4448 21.526798 + 3450 19163.152 214.26098 0 3762.9928 4.1888096 + 3500 18000.27 429.81789 0 3763.2011 5.4734485 + 3550 19582.423 136.71887 0 3763.0935 -2.5335675 + 3600 19634.325 127.2219 0 3763.208 -1.9728322 + 3650 19428.114 165.40707 0 3763.2059 -2.3318779 + 3700 19861.116 85.356944 0 3763.3414 -3.9097609 + 3750 19337.239 182.43992 0 3763.4102 -3.3559651 + 3800 19493.146 153.40349 0 3763.2453 -0.71089657 + 3850 18607.616 317.74889 0 3763.6037 3.475832 + 3900 19719.59 111.5553 0 3763.3313 0.58876668 + 3950 19756.661 104.5522 0 3763.1931 3.7526698 + 4000 17904.708 447.1673 0 3762.854 12.270654 + 4050 19588.087 135.80435 0 3763.2279 0.94578945 + 4100 19065.901 232.38235 0 3763.1048 -2.7495195 + 4150 18775.075 286.2257 0 3763.0915 -3.7039858 + 4200 18800.725 281.46601 0 3763.0817 0.15619543 + 4250 19732.687 108.90618 0 3763.1075 3.0865861 + 4300 18278.151 377.63653 0 3762.4794 1.5768601 + 4350 17915.757 445.4804 0 3763.2133 -3.7040484 + 4400 15987.794 802.41575 0 3763.1183 22.252078 + 4450 19302.37 188.69495 0 3763.2079 0.91081327 + 4500 20039.32 52.304099 0 3763.2893 -2.0828905 + 4550 19535.953 145.4374 0 3763.2064 -3.3804255 + 4600 19700.723 114.79823 0 3763.0803 -1.1761163 + 4650 17804.641 465.85788 0 3763.0136 7.5947192 + 4700 19913.881 75.240289 0 3762.996 -2.1100557 + 4750 19982.484 62.535995 0 3762.996 -4.5821237 + 4800 17400.76 540.21707 0 3762.58 -5.8418778 + 4850 19199.88 206.90989 0 3762.4433 3.4536341 + 4900 19173.92 212.11327 0 3762.8392 5.0387071 + 4950 19236.635 200.57537 0 3762.9152 -1.4932783 + 5000 19077.616 230.04967 0 3762.9415 4.3742655 + 5050 19893.763 78.909747 0 3762.94 -1.5796711 + 5100 18884.746 265.68301 0 3762.8583 2.2767949 + 5150 17417.096 537.54036 0 3762.9286 -2.8632555 + 5200 18247.844 383.60092 0 3762.8312 10.384179 + 5250 19494.107 152.60532 0 3762.6251 -4.7617287 + 5300 18739.781 292.46206 0 3762.7919 23.210048 + 5350 19310.938 186.62363 0 3762.7232 14.895327 + 5400 19540.39 144.14287 0 3762.7336 6.094624 + 5450 20074.459 45.247888 0 3762.7403 -2.0871835 + 5500 19986.377 61.668045 0 3762.849 -2.4551918 + 5550 19038.904 237.07578 0 3762.7987 5.4250813 + 5600 19439.124 163.1438 0 3762.9816 4.1291468 + 5650 19480.321 155.58325 0 3763.0501 -3.5308058 + 5700 19869.291 83.651379 0 3763.1497 -7.8661592 + 5750 19991.447 61.068554 0 3763.1884 -6.8473586 + 5800 19454.072 160.36805 0 3762.9739 1.527662 + 5850 17994.409 430.95597 0 3763.2539 -5.6078082 + 5900 19209.794 205.74997 0 3763.1193 8.4113055 + 5950 19046.427 236.06321 0 3763.1793 10.463356 + 6000 19409.899 168.95271 0 3763.3785 2.542067 + 6050 18068.174 417.35443 0 3763.3125 10.498199 + 6100 19549.253 143.21885 0 3763.4509 2.3075797 + 6150 18464.719 344.0303 0 3763.4228 0.46469762 + 6200 19811.205 94.62725 0 3763.3689 1.2382763 + 6250 18715.36 297.26445 0 3763.0718 -3.4541762 + 6300 17115.664 594.09913 0 3763.6666 4.2065564 + 6350 18155.927 400.71764 0 3762.9264 1.1521258 + 6400 19873.093 83.169067 0 3763.3716 0.16383592 + 6450 19991.88 61.13218 0 3763.3321 -1.3008128 + 6500 19434.416 164.40698 0 3763.3728 -13.593422 + 6550 19855.253 86.645329 0 3763.544 -0.85704037 + 6600 19251.141 198.41152 0 3763.4376 4.3027745 + 6650 19741.815 107.69047 0 3763.582 4.994835 + 6700 19633.466 127.69333 0 3763.5203 6.3677145 + 6750 16231.353 757.83705 0 3763.6431 -1.5978692 + 6800 18863.396 270.1114 0 3763.3329 -11.915909 + 6850 19644.779 125.29421 0 3763.2163 -1.151217 + 6900 18883.642 266.06889 0 3763.0397 -4.3950749 + 6950 19042.364 236.54144 0 3762.9052 5.5718878 + 7000 18351.868 364.38028 0 3762.8743 7.8958273 + 7050 19981.031 62.840667 0 3763.0316 -5.8572298 + 7100 19796.372 97.073665 0 3763.0685 -3.5178361 + 7150 19805.385 95.235221 0 3762.899 -2.5481726 + 7200 18722.055 295.86113 0 3762.9084 13.826356 + 7250 19537.304 144.54234 0 3762.5616 1.2288666 + 7300 18787.328 283.49504 0 3762.6299 9.0044469 + 7350 18886.005 265.52121 0 3762.9295 6.6791881 + 7400 19891.864 79.239278 0 3762.9178 -2.3882842 + 7450 18164.752 399.07065 0 3762.9137 3.9400481 + 7500 18702.612 299.582 0 3763.0286 4.7987316 + 7550 19884.986 80.231665 0 3762.6365 -0.75016515 + 7600 19549.059 142.16243 0 3762.3586 -2.1035756 + 7650 18223.668 387.9047 0 3762.658 -17.064339 + 7700 19428.4 164.79531 0 3762.6473 -2.8342541 + 7750 19239.584 199.93029 0 3762.8163 3.1746033 + 7800 19458.005 159.46176 0 3762.7961 1.714515 + 7850 18320.308 369.77051 0 3762.4202 2.1422976 + 7900 18817.415 278.04812 0 3762.7546 0.94492621 + 7950 19892.761 79.115928 0 3762.9606 1.4948501 + 8000 19592.344 134.7639 0 3762.9758 -1.8520224 + 8050 19316.109 185.70579 0 3762.7631 -4.8061205 + 8100 19867.017 83.850395 0 3762.9277 -3.496391 + 8150 19129.936 220.29802 0 3762.8789 -2.8357376 + 8200 18449.554 346.30415 0 3762.8883 1.4417837 + 8250 18405.197 354.49049 0 3762.8602 6.7020283 + 8300 18310.437 372.25376 0 3763.0755 3.9043508 + 8350 18842.702 273.55075 0 3762.94 -10.987272 + 8400 18574.308 323.33378 0 3763.0204 12.008785 + 8450 15368.628 918.21692 0 3764.2591 34.80292 + 8500 18432.887 349.54013 0 3763.0378 0.00064258465 + 8550 15777.73 841.79263 0 3763.5945 15.473699 + 8600 17205.381 576.4515 0 3762.6331 2.3985544 + 8650 19773.742 101.48276 0 3763.2869 2.3978892 + 8700 19059.824 232.99716 0 3762.5941 5.2611349 + 8750 19006.086 243.41125 0 3763.0568 4.7880403 + 8800 19492.691 153.0188 0 3762.7763 1.9118755 + 8850 19625.883 128.44474 0 3762.8675 3.4157389 + 8900 19916.97 74.635094 0 3762.9629 -10.157254 + 8950 16012.956 798.16801 0 3763.5302 16.904998 + 9000 19364.051 177.00354 0 3762.9389 -13.373346 + 9050 19133.929 219.61882 0 3762.9389 -7.3824392 + 9100 18657.168 307.85939 0 3762.8905 9.3071421 + 9150 17975.904 434.21548 0 3763.0867 6.9609506 + 9200 19075.282 230.41699 0 3762.8767 7.0961232 + 9250 20115.276 37.578674 0 3762.6298 1.8678552 + 9300 18195.486 393.20682 0 3762.7413 13.272552 + 9350 19617.155 129.85893 0 3762.6653 -2.0849447 + 9400 19276.325 193.03425 0 3762.724 -2.8963555 + 9450 18642.803 310.4759 0 3762.8467 3.407984 + 9500 19175.951 211.72785 0 3762.8298 -0.39025564 + 9550 17669.191 490.85942 0 3762.9319 5.3867954 + 9600 18481.199 340.29485 0 3762.7391 8.9004886 + 9650 20091.442 42.504743 0 3763.1422 -1.3206133 + 9700 19651.405 124.04835 0 3763.1975 1.4000525 + 9750 19138.245 219.03637 0 3763.1558 5.8352794 + 9800 19189.146 209.67958 0 3763.2251 6.214691 + 9850 19899.376 78.096337 0 3763.166 -0.75102404 + 9900 19447.247 161.27279 0 3762.6149 -6.4166376 + 9950 19807.083 95.152663 0 3763.1309 -0.88933698 + 10000 18972.157 249.56342 0 3762.9258 1.9189241 +Loop time of 9.05599 on 4 procs for 10000 steps with 81 atoms + +Performance: 9540.646 tau/day, 1104.241 timesteps/s +94.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.009043 | 0.030098 | 0.048276 | 8.1 | 0.33 +Neigh | 0.012702 | 0.02622 | 0.04009 | 6.1 | 0.29 +Comm | 0.99902 | 1.2924 | 1.6008 | 24.3 | 14.27 +Output | 0.0057414 | 0.010684 | 0.024912 | 7.9 | 0.12 +Modify | 7.2674 | 7.5881 | 7.9123 | 10.6 | 83.79 +Other | | 0.1085 | | | 1.20 + +Nlocal: 20.25 ave 37 max 0 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 17.75 ave 33 max 4 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 144.75 ave 356 max 0 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 579 +Ave neighs/atom = 7.14815 +Neighbor list builds = 994 +Dangerous builds = 958 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:09 diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.4 b/examples/rigid/log.27Nov18.rigid.property.g++.1 similarity index 90% rename from examples/rigid/log.20Apr18.rigid.property.g++.4 rename to examples/rigid/log.27Nov18.rigid.property.g++.1 index c34324b19c..e6ab4ed102 100644 --- a/examples/rigid/log.20Apr18.rigid.property.g++.4 +++ b/examples/rigid/log.27Nov18.rigid.property.g++.1 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -12,7 +12,7 @@ fix 0 all property/atom i_bodies read_data data.rigid-property fix 0 NULL Bodies orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 2 by 2 MPI processor grid + 1 by 1 by 1 MPI processor grid reading atoms ... 81 atoms @@ -108,7 +108,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -162,8 +162,8 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722854e-05 0 5269.5046 14.510657 - 2650 16733.017 1.705148 0 5269.5067 14.596295 + 2600 16738.427 -7.972284e-05 0 5269.5046 14.510657 + 2650 16733.017 1.7051479 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 2800 16738.585 -0.046813448 0 5269.5076 14.511073 @@ -171,7 +171,7 @@ Step Temp E_pair E_mol TotEng Press 2900 16738.465 -0.0026252725 0 5269.514 14.510277 2950 16738.476 -0.0082220764 0 5269.512 14.510223 3000 16738.66 -0.071284779 0 5269.507 14.509758 - 3050 16715.332 7.2419351 0 5269.476 14.870305 + 3050 16715.332 7.2419352 0 5269.476 14.870305 3100 16653.226 26.818761 0 5269.5009 14.496764 3150 16739.351 -0.30690375 0 5269.4886 13.643904 3200 16733.238 1.6025328 0 5269.4737 12.016934 @@ -181,7 +181,7 @@ Step Temp E_pair E_mol TotEng Press 3400 16738.543 -0.042215005 0 5269.4991 12.092809 3450 16738.591 -0.059327511 0 5269.4972 12.092536 3500 16738.759 -0.11761245 0 5269.4918 12.09203 - 3550 16713.405 7.846062 0 5269.4737 12.389816 + 3550 16713.405 7.8460621 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 3700 16738.602 -0.070934368 0 5269.4889 12.025288 @@ -279,8 +279,8 @@ Step Temp E_pair E_mol TotEng Press 8300 16738.471 0 0 5269.5187 12.011719 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 - 8450 16738.473 -0.00039690664 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 + 8450 16738.473 -0.00039690666 0 5269.5189 12.011706 + 8500 16738.481 -0.0034646804 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532811 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -300,38 +300,38 @@ Step Temp E_pair E_mol TotEng Press 9350 16738.48 0 0 5269.5214 12.011744 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 - 9500 16738.481 -0.00037652437 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156159 0 5269.5203 12.011611 - 9600 16738.549 -0.026814369 0 5269.5163 12.011415 + 9500 16738.481 -0.00037652434 0 5269.5216 12.011692 + 9550 16738.493 -0.005315616 0 5269.5203 12.011611 + 9600 16738.549 -0.026814368 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589887 0 5269.4979 12.062708 - 9750 16738.013 0.135501 0 5269.5101 11.407245 - 9800 16738.512 -0.011620329 0 5269.5201 11.394973 - 9850 16738.489 -0.00067270548 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984569 0 5269.5242 11.395084 + 9700 16735.041 1.0589885 0 5269.4979 12.062708 + 9750 16738.013 0.13550123 0 5269.5101 11.407245 + 9800 16738.512 -0.011620328 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270523 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984554 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.206235 on 4 procs for 10000 steps with 81 atoms +Loop time of 0.156049 on 1 procs for 10000 steps with 81 atoms -Performance: 418940.303 tau/day, 48488.461 timesteps/s -97.1% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 553673.043 tau/day, 64082.528 timesteps/s +97.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0026572 | 0.004187 | 0.0050838 | 1.5 | 2.03 -Neigh | 0.012115 | 0.012789 | 0.013634 | 0.5 | 6.20 -Comm | 0.084275 | 0.089969 | 0.095318 | 1.5 | 43.62 -Output | 0.0048559 | 0.0051559 | 0.0059836 | 0.7 | 2.50 -Modify | 0.077074 | 0.083586 | 0.088022 | 1.5 | 40.53 -Other | | 0.01055 | | | 5.11 +Pair | 0.010187 | 0.010187 | 0.010187 | 0.0 | 6.53 +Neigh | 0.040601 | 0.040601 | 0.040601 | 0.0 | 26.02 +Comm | 0.013221 | 0.013221 | 0.013221 | 0.0 | 8.47 +Output | 0.0016611 | 0.0016611 | 0.0016611 | 0.0 | 1.06 +Modify | 0.085107 | 0.085107 | 0.085107 | 0.0 | 54.54 +Other | | 0.005271 | | | 3.38 -Nlocal: 20.25 ave 38 max 3 min -Histogram: 1 0 1 0 0 0 1 0 0 1 -Nghost: 27.25 ave 48 max 13 min -Histogram: 1 0 1 1 0 0 0 0 0 1 +Nlocal: 81 ave 81 max 81 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 84 ave 84 max 84 min +Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 +Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.20Apr18.rigid.property.g++.1 b/examples/rigid/log.27Nov18.rigid.property.g++.4 similarity index 92% rename from examples/rigid/log.20Apr18.rigid.property.g++.1 rename to examples/rigid/log.27Nov18.rigid.property.g++.4 index 76ef36825b..f63e34bc4b 100644 --- a/examples/rigid/log.20Apr18.rigid.property.g++.1 +++ b/examples/rigid/log.27Nov18.rigid.property.g++.4 @@ -1,4 +1,4 @@ -LAMMPS (20 Apr 2018) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Simple rigid body system @@ -12,7 +12,7 @@ fix 0 all property/atom i_bodies read_data data.rigid-property fix 0 NULL Bodies orthogonal box = (-12 -12 -12) to (12 12 12) - 1 by 1 by 1 MPI processor grid + 1 by 2 by 2 MPI processor grid reading atoms ... 81 atoms @@ -108,7 +108,7 @@ Neighbor list info ... pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 4.046 | 4.046 | 4.046 Mbytes +Per MPI rank memory allocation (min/avg/max) = 4.017 | 4.111 | 4.392 Mbytes Step Temp E_pair E_mol TotEng Press 0 115.29439 5235.9179 0 5272.2142 -2.7403788 50 14910.685 571.71558 0 5265.82 32.006171 @@ -162,7 +162,7 @@ Step Temp E_pair E_mol TotEng Press 2450 16738.464 -0.0023259756 0 5269.514 14.510746 2500 16738.468 -0.0051929186 0 5269.5127 14.510731 2550 16738.581 -0.044940117 0 5269.5085 14.510315 - 2600 16738.427 -7.9722839e-05 0 5269.5046 14.510657 + 2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657 2650 16733.017 1.705148 0 5269.5067 14.596295 2700 16738.761 -0.10614946 0 5269.5038 14.499584 2750 16733.973 1.4038179 0 5269.5064 14.598107 @@ -184,7 +184,7 @@ Step Temp E_pair E_mol TotEng Press 3550 16713.405 7.846062 0 5269.4737 12.389816 3600 16734.939 1.0821936 0 5269.4891 12.173591 3650 16738.808 -0.13663194 0 5269.4882 12.027009 - 3700 16738.602 -0.070934367 0 5269.4889 12.025288 + 3700 16738.602 -0.070934368 0 5269.4889 12.025288 3750 16737.731 0.20706557 0 5269.4927 12.061948 3800 16738.578 -0.05582043 0 5269.4965 12.035665 3850 16738.471 -0.016307928 0 5269.5024 12.035302 @@ -280,7 +280,7 @@ Step Temp E_pair E_mol TotEng Press 8350 16738.472 0 0 5269.5189 12.011723 8400 16738.472 0 0 5269.519 12.01172 8450 16738.473 -0.00039690663 0 5269.5189 12.011706 - 8500 16738.481 -0.0034646802 0 5269.5182 12.011643 + 8500 16738.481 -0.0034646803 0 5269.5182 12.011643 8550 16738.483 -0.0045307409 0 5269.5178 12.011621 8600 16738.474 -0.00076532813 0 5269.5189 12.011681 8650 16738.474 0 0 5269.5197 12.011699 @@ -301,37 +301,37 @@ Step Temp E_pair E_mol TotEng Press 9400 16738.48 0 0 5269.5215 12.011732 9450 16738.48 0 0 5269.5216 12.011715 9500 16738.481 -0.00037652438 0 5269.5216 12.011692 - 9550 16738.493 -0.0053156162 0 5269.5203 12.011611 + 9550 16738.493 -0.0053156163 0 5269.5203 12.011611 9600 16738.549 -0.026814371 0 5269.5163 12.011415 9650 16738.765 -0.10191523 0 5269.5092 12.011013 - 9700 16735.041 1.0589893 0 5269.4979 12.062708 - 9750 16738.013 0.13550102 0 5269.5101 11.407246 - 9800 16738.512 -0.011620328 0 5269.5201 11.394974 - 9850 16738.489 -0.00067270521 0 5269.5237 11.395098 - 9900 16738.489 -0.00024984561 0 5269.5242 11.395085 + 9700 16735.041 1.0589894 0 5269.4979 12.062708 + 9750 16738.013 0.13550109 0 5269.5101 11.407246 + 9800 16738.512 -0.011620327 0 5269.5201 11.394974 + 9850 16738.489 -0.00067270507 0 5269.5237 11.395098 + 9900 16738.489 -0.00024984555 0 5269.5242 11.395085 9950 16738.49 0 0 5269.5245 11.395076 10000 16738.49 0 0 5269.5246 11.395075 -Loop time of 0.140719 on 1 procs for 10000 steps with 81 atoms +Loop time of 0.198069 on 4 procs for 10000 steps with 81 atoms -Performance: 613990.898 tau/day, 71063.761 timesteps/s -97.1% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 436211.675 tau/day, 50487.462 timesteps/s +91.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.010882 | 0.010882 | 0.010882 | 0.0 | 7.73 -Neigh | 0.037245 | 0.037245 | 0.037245 | 0.0 | 26.47 -Comm | 0.0092154 | 0.0092154 | 0.0092154 | 0.0 | 6.55 -Output | 0.0024879 | 0.0024879 | 0.0024879 | 0.0 | 1.77 -Modify | 0.074702 | 0.074702 | 0.074702 | 0.0 | 53.09 -Other | | 0.006187 | | | 4.40 +Pair | 0.0026007 | 0.0034987 | 0.0043218 | 1.0 | 1.77 +Neigh | 0.012213 | 0.013261 | 0.014237 | 0.8 | 6.70 +Comm | 0.073581 | 0.082048 | 0.087982 | 2.1 | 41.42 +Output | 0.0047908 | 0.0058783 | 0.009093 | 2.4 | 2.97 +Modify | 0.081998 | 0.086993 | 0.09176 | 1.4 | 43.92 +Other | | 0.00639 | | | 3.23 -Nlocal: 81 ave 81 max 81 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 84 ave 84 max 84 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Nlocal: 20.25 ave 38 max 3 min +Histogram: 1 0 1 0 0 0 1 0 0 1 +Nghost: 27.25 ave 48 max 13 min +Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 +Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 diff --git a/examples/rigid/log.27Nov18.rigid.tnr.g++.1 b/examples/rigid/log.27Nov18.rigid.tnr.g++.1 new file mode 100644 index 0000000000..bf29e0b94b --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.tnr.g++.1 @@ -0,0 +1,458 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule +800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.769 | 7.769 | 7.769 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248 + 200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036 + 300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998 + 400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801 + 500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745 + 600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581 + 700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883 + 800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271 + 900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788 + 1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119 + 1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748 + 1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115 + 1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625 + 1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021 + 1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242 + 1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334 + 1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394292 0.009326014 + 1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797 + 1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268 + 2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673 + 2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825 + 2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911 + 2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709635 0.0044949165 0.0038341296 + 2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.008373826 0.0090537939 0.013165402 + 2500 1.4153808 5.9421661 7.0538718 0.00015906306 7.0607216 62.244 62.244 62.244 0.002351621 -0.0019814986 0.00010706677 + 2600 1.4014223 5.9431386 7.0438807 0.0070733749 7.3484816 62.244 62.244 62.244 0.0054143871 0.010055843 0.0057498948 + 2700 1.4138077 5.9369067 7.047377 0.0024268842 7.1518859 62.244 62.244 62.244 0.0052918436 0.0014960353 0.00049277371 + 2800 1.432192 5.9347676 7.0596777 0.0077670448 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113033 0.0047214106 + 2900 1.3938659 5.921023 7.01583 0.0053751198 7.2472989 62.244 62.244 62.244 0.0020490372 0.0076566093 0.006419713 + 3000 1.390221 5.9205014 7.0124455 -0.0010750977 6.9661485 62.244 62.244 62.244 0.0019519817 -0.0041878885 -0.00098938611 + 3100 1.4205722 5.9178284 7.0336117 0.0098735475 7.4587965 62.244 62.244 62.244 0.0040973361 0.012167268 0.013356039 + 3200 1.398418 5.9150349 7.0134173 0.0061541841 7.2784351 62.244 62.244 62.244 0.0067621815 0.011952563 -0.00025219251 + 3300 1.4269859 5.9148727 7.0356937 0.0060623879 7.2967584 62.244 62.244 62.244 0.012956234 -2.4806661e-05 0.0052557362 + 3400 1.434286 5.9356705 7.0622253 0.00027315892 7.0739884 62.244 62.244 62.244 -0.00054959866 0.0052526278 -0.0038835524 + 3500 1.4416809 5.9228153 7.0551783 0.0083382977 7.4142506 62.244 62.244 62.244 0.007399393 0.0030328007 0.014582699 + 3600 1.4136063 5.9039442 7.0142562 0.0019712004 7.0991421 62.244 62.244 62.244 -0.00032316149 0.0035029874 0.0027337752 + 3700 1.4333819 5.9120101 7.0378548 0.0071287182 7.3448389 62.244 62.244 62.244 0.0064768218 0.0046765361 0.010232797 + 3800 1.3659481 5.9032873 6.9761663 -0.0054033416 6.7434821 62.244 62.244 62.244 -0.0073943479 -0.0082831992 -0.00053247772 + 3900 1.3963222 5.9042998 7.0010361 0.0053310264 7.2306062 62.244 62.244 62.244 0.0081855739 0.0048806019 0.0029269034 + 4000 1.4125482 5.9060665 7.0155474 0.0028450296 7.138063 62.244 62.244 62.244 0.0052588294 0.00072395285 0.0025523065 + 4100 1.3943951 5.9040875 6.9993102 0.0058050223 7.2492919 62.244 62.244 62.244 0.0060579697 0.0024782584 0.0088788387 + 4200 1.4249768 5.8906371 7.0098801 0.0030210669 7.1399763 62.244 62.244 62.244 0.006174431 -0.002079586 0.0049683557 + 4300 1.3899801 5.8966397 6.9883947 0.0057285402 7.2350829 62.244 62.244 62.244 0.0049048136 0.0021882328 0.010092574 + 4400 1.4414352 5.898628 7.0307981 0.0050932552 7.2501291 62.244 62.244 62.244 0.0057941393 0.0037951842 0.0056904421 + 4500 1.4092913 5.8922803 6.9992031 0.0012238869 7.0519073 62.244 62.244 62.244 0.0042907674 0.0014412643 -0.0020603711 + 4600 1.3779868 5.8928757 6.9752105 0.0020701322 7.0643566 62.244 62.244 62.244 0.0029283254 -0.0031683908 0.006450462 + 4700 1.4084635 5.9098782 7.0161508 -0.00052129502 6.9937023 62.244 62.244 62.244 -0.0018460523 -0.0018286314 0.0021107986 + 4800 1.4393258 5.9148464 7.0453597 0.015311954 7.7047386 62.244 62.244 62.244 0.014718813 0.01801777 0.013199278 + 4900 1.4500008 5.9076899 7.0465879 0.0075111779 7.3700419 62.244 62.244 62.244 0.0091865271 0.0080981174 0.0052488891 + 5000 1.4279632 5.9111567 7.0327453 -0.0014189553 6.9716408 62.244 62.244 62.244 -0.0046013754 0.0019937576 -0.001649248 +Loop time of 6.84203 on 1 procs for 5000 steps with 5600 atoms + +Performance: 315695.745 tau/day, 730.777 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.53182 | 0.53182 | 0.53182 | 0.0 | 7.77 +Bond | 0.18231 | 0.18231 | 0.18231 | 0.0 | 2.66 +Neigh | 1.8709 | 1.8709 | 1.8709 | 0.0 | 27.34 +Comm | 0.18452 | 0.18452 | 0.18452 | 0.0 | 2.70 +Output | 0.0043087 | 0.0043087 | 0.0043087 | 0.0 | 0.06 +Modify | 3.8809 | 3.8809 | 3.8809 | 0.0 | 56.72 +Other | | 0.1873 | | | 2.74 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1351 ave 1351 max 1351 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5254 ave 5254 max 5254 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5254 +Ave neighs/atom = 0.938214 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 766 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule +800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4279632 5.9111567 7.0327453 0.027874409 8.2331015 62.244 62.244 62.244 0.018992956 0.039655696 0.024974575 + 5100 1.439608 5.9052128 7.0359478 0.0060989863 7.2985885 62.244 62.244 62.244 0.0087364157 0.004022839 0.0055377041 + 5200 1.4120672 5.9102569 7.01936 0.0064301432 7.2962614 62.244 62.244 62.244 0.0082738077 0.0038925667 0.0071240551 + 5300 1.4452434 5.8842166 7.0193778 0.008172419 7.3713068 62.244 62.244 62.244 0.0077715647 0.0068924406 0.0098532518 + 5400 1.4170243 5.887522 7.0005186 0.0008656658 7.0377968 62.244 62.244 62.244 -9.1800583e-05 -0.0020237513 0.0047125493 + 5500 1.4209082 5.8758921 6.9919394 0.0093634084 7.395156 62.244 62.244 62.244 0.0088769348 0.0087092521 0.010504038 + 5600 1.4132978 5.8798939 6.9899636 0.0014877766 7.0540317 62.244 62.244 62.244 -0.0023427923 0.004559371 0.002246751 + 5700 1.4065053 5.887541 6.9922756 0.0028083452 7.1132114 62.244 62.244 62.244 0.0025188632 0.000510969 0.0053952035 + 5800 1.4079051 5.8940739 6.999908 0.0015946158 7.0685769 62.244 62.244 62.244 0.0037830287 0.00021751956 0.00078329927 + 5900 1.4076047 5.8941577 6.9997558 0.005189853 7.2232465 62.244 62.244 62.244 -0.00093244616 0.0096403542 0.0068616509 + 6000 1.4322772 5.8903539 7.0153309 0.00029752476 7.0281432 62.244 62.244 62.244 0.001913333 -0.00073790796 -0.00028285075 +Loop time of 1.40593 on 1 procs for 1000 steps with 5600 atoms + +Performance: 307270.224 tau/day, 711.274 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.14844 | 0.14844 | 0.14844 | 0.0 | 10.56 +Bond | 0.036852 | 0.036852 | 0.036852 | 0.0 | 2.62 +Neigh | 0.40537 | 0.40537 | 0.40537 | 0.0 | 28.83 +Comm | 0.036592 | 0.036592 | 0.036592 | 0.0 | 2.60 +Output | 0.00085831 | 0.00085831 | 0.00085831 | 0.0 | 0.06 +Modify | 0.74053 | 0.74053 | 0.74053 | 0.0 | 52.67 +Other | | 0.03729 | | | 2.65 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1347 ave 1347 max 1347 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5399 ave 5399 max 5399 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5399 +Ave neighs/atom = 0.964107 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 +800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.4322772 5.8903539 7.0153309 0.012980585 7.574314 62.244 62.244 62.244 0.058317363 0.0073619377 -0.026737547 + 6100 1.4199699 5.8764035 6.9917138 0.0054065561 7.2245364 62.244 62.244 62.244 0.009227645 0.0019623802 0.0050296432 + 6200 1.3976825 5.8924426 6.9902474 0.00043900876 7.0091524 62.244 62.244 62.244 -0.0023073124 -0.00049925318 0.0041235918 + 6300 1.4077283 5.8847362 6.9904313 0.0066398301 7.2763625 62.244 62.244 62.244 0.0058018934 0.0091933877 0.0049242093 + 6400 1.3749203 5.8817073 6.9616336 0.0074967162 7.2844648 62.244 62.244 62.244 0.012281887 0.0039781589 0.0062301027 + 6500 1.3467096 5.8881264 6.9458946 -0.00011926349 6.9407588 62.244 62.244 62.244 0.0030721967 -0.0013265863 -0.0021034009 + 6600 1.3646558 5.8739857 6.9458497 0.0056064043 7.1872784 62.244 62.244 62.244 0.0059660337 0.0057680048 0.0050851745 + 6700 1.3927251 5.883612 6.9775229 0.0025583824 7.0876946 62.244 62.244 62.244 0.0030974706 0.0018499606 0.002727716 + 6800 1.4016999 5.9015886 7.0025488 0.0039070678 7.1707989 62.244 62.244 62.244 0.0068320586 0.0020056859 0.002883459 + 6900 1.4136745 5.8914714 7.001837 0.0051755091 7.22471 62.244 62.244 62.244 0.0028467792 0.0094052519 0.0032744962 + 7000 1.4286639 5.893567 7.0157059 0.0062957476 7.2868198 62.244 62.244 62.244 0.0047242086 0.0093408867 0.0048221474 +Loop time of 1.41045 on 1 procs for 1000 steps with 5600 atoms + +Performance: 306284.404 tau/day, 708.992 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.1497 | 0.1497 | 0.1497 | 0.0 | 10.61 +Bond | 0.036719 | 0.036719 | 0.036719 | 0.0 | 2.60 +Neigh | 0.40272 | 0.40272 | 0.40272 | 0.0 | 28.55 +Comm | 0.036315 | 0.036315 | 0.036315 | 0.0 | 2.57 +Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.06 +Modify | 0.747 | 0.747 | 0.747 | 0.0 | 52.96 +Other | | 0.03715 | | | 2.63 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1284 ave 1284 max 1284 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5677 ave 5677 max 5677 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5677 +Ave neighs/atom = 1.01375 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 151 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.77 | 7.77 | 7.77 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.4286639 5.893567 7.0157059 0.032101512 8.3980939 62.244 62.244 62.244 0.0040045405 0.040447803 0.051852194 + 7100 1.4709161 5.8870949 7.0424207 0.019697134 7.6953761 57.045689 57.045689 57.045689 0.012929484 0.020492532 0.025669387 + 7200 1.5163078 5.8421187 7.0330973 0.018916867 7.46241 50.277171 50.277171 50.277171 0.017823354 0.026688031 0.012239218 + 7300 1.5675309 5.7752739 7.0064855 0.022899743 7.3829781 45.154874 45.154874 45.154874 0.019324617 0.024318577 0.025056034 + 7400 1.5432228 5.7513096 6.9634284 0.024381819 7.272744 41.416613 41.416613 41.416613 0.032026791 0.022254425 0.018864241 + 7500 1.5511419 5.7072564 6.9255953 0.030632381 7.2405167 38.613262 38.613262 38.613262 0.041572196 0.012539031 0.037785916 + 7600 1.5437461 5.6656571 6.8781869 0.031293788 7.1486082 36.440994 36.440994 36.440994 0.036220762 0.02125772 0.036402883 + 7700 1.5873874 5.6134986 6.8603063 0.04807003 7.221002 34.765744 34.765744 34.765744 0.031608235 0.053442472 0.059159381 + 7800 1.5079648 5.601961 6.7863866 0.031128515 6.9971673 33.59594 33.59594 33.59594 0.032932226 0.015950578 0.044502741 + 7900 1.4737447 5.5644198 6.7219673 0.099246661 7.3415696 32.698542 32.698542 32.698542 0.071386679 0.10758014 0.11877317 + 8000 1.4727947 5.5161158 6.6729171 0.072190554 7.0973199 32.050043 32.050043 32.050043 0.072806068 0.06277287 0.080992723 +Loop time of 3.15299 on 1 procs for 1000 steps with 5600 atoms + +Performance: 137012.841 tau/day, 317.159 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.37069 | 0.37069 | 0.37069 | 0.0 | 11.76 +Bond | 0.05046 | 0.05046 | 0.05046 | 0.0 | 1.60 +Neigh | 1.4844 | 1.4844 | 1.4844 | 0.0 | 47.08 +Comm | 0.081178 | 0.081178 | 0.081178 | 0.0 | 2.57 +Output | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 0.03 +Modify | 1.1163 | 1.1163 | 1.1163 | 0.0 | 35.41 +Other | | 0.0491 | | | 1.56 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2954 ave 2954 max 2954 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 25585 ave 25585 max 25585 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 25585 +Ave neighs/atom = 4.56875 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 334 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.785 | 7.785 | 7.785 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4727947 5.5161158 6.6729171 0.13628586 7.4741313 32.050043 32.050043 32.050043 -0.030897367 0.27196335 0.1677916 + 8100 1.4522497 5.5136331 6.6542974 0.057107124 6.9895036 32.000184 32.050043 32.050043 0.049932793 0.056130194 0.065258384 + 8200 1.4407937 5.5014539 6.6331202 0.024119241 6.7733276 31.691157 32.050043 32.050043 0.041526366 0.022503949 0.0083274089 + 8300 1.4542258 5.496977 6.6391934 0.043395674 6.887667 31.215092 32.050043 32.050043 0.025407647 0.075227689 0.029551686 + 8400 1.4375595 5.4901345 6.6192605 0.013578023 6.6952098 30.494249 32.050043 32.050043 -0.0045150608 0.033500673 0.011748456 + 8500 1.4410736 5.4540565 6.5859426 0.017121222 6.679397 29.757445 32.050043 32.050043 0.035675932 -0.032105 0.047792733 + 8600 1.4372413 5.4150437 6.5439197 0.084045699 6.9949237 29.254706 32.050043 32.050043 0.10347392 0.073148157 0.075515024 + 8700 1.4299119 5.3982284 6.5213476 0.00045273296 6.5237411 28.822481 32.050043 32.050043 0.0093093459 0.0081538479 -0.016104995 + 8800 1.4677947 5.3637715 6.5166456 0.028621833 6.6651924 28.294159 32.050043 32.050043 0.033527613 0.036046563 0.016291323 + 8900 1.4625499 5.3483914 6.4971459 0.032843022 6.6649394 27.852402 32.050043 32.050043 0.040751528 0.055865445 0.0019120942 + 9000 1.4488382 5.3486741 6.4866589 0.087522574 6.9279711 27.488856 32.050043 32.050043 0.059432129 0.10936517 0.093770421 +Loop time of 3.09429 on 1 procs for 1000 steps with 5600 atoms + +Performance: 139611.779 tau/day, 323.175 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.57714 | 0.57714 | 0.57714 | 0.0 | 18.65 +Bond | 0.051715 | 0.051715 | 0.051715 | 0.0 | 1.67 +Neigh | 1.223 | 1.223 | 1.223 | 0.0 | 39.52 +Comm | 0.066183 | 0.066183 | 0.066183 | 0.0 | 2.14 +Output | 0.00086594 | 0.00086594 | 0.00086594 | 0.0 | 0.03 +Modify | 1.1355 | 1.1355 | 1.1355 | 0.0 | 36.70 +Other | | 0.03994 | | | 1.29 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3381 ave 3381 max 3381 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 31737 ave 31737 max 31737 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 31737 +Ave neighs/atom = 5.66732 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 169 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.788 | 7.788 | 7.788 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.4488382 5.3486741 6.4866589 0.20124138 7.5013717 27.488856 32.050043 32.050043 0.22160189 0.42145658 -0.039334342 + 9100 1.4408457 5.3612674 6.4929746 0.076331412 6.8758499 27.440968 31.994208 31.994208 0.083838068 0.041724506 0.10343166 + 9200 1.4870445 5.3340546 6.5020483 0.01010773 6.5521592 27.334266 31.869802 31.869802 0.024563803 -0.0068003493 0.012559737 + 9300 1.4376808 5.3295183 6.4587396 0.10720051 6.9752889 27.076116 31.568817 31.568817 0.11844426 0.10444301 0.09871425 + 9400 1.4621325 5.3011274 6.4495541 0.071127232 6.7846388 26.873295 31.332342 31.332342 0.091608834 0.02680694 0.094965923 + 9500 1.4463444 5.3005044 6.4365304 0.0011545049 6.4418432 26.664 31.088319 31.088319 -0.030551889 0.036011952 -0.0019965484 + 9600 1.4473406 5.2912939 6.4281024 0.066132857 6.7281169 26.537276 30.940568 30.940568 0.12276096 0.013455525 0.06218208 + 9700 1.4520445 5.2707214 6.4112246 0.077219765 6.757956 26.446587 30.834832 30.834832 0.073829267 0.11047347 0.047356559 + 9800 1.4825713 5.246644 6.4111243 0.061402527 6.6831281 26.327581 30.696078 30.696078 0.091860222 0.022619578 0.06972778 + 9900 1.4795219 5.2344495 6.3965347 0.086345107 6.7729623 26.187615 30.532888 30.532888 0.077396265 0.11142542 0.07021363 + 10000 1.4527053 5.2126819 6.3537041 0.045117764 6.5474705 26.057038 30.380645 30.380645 0.011087188 0.058029185 0.066236921 +Loop time of 3.25046 on 1 procs for 1000 steps with 5600 atoms + +Performance: 132904.162 tau/day, 307.649 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.68223 | 0.68223 | 0.68223 | 0.0 | 20.99 +Bond | 0.05211 | 0.05211 | 0.05211 | 0.0 | 1.60 +Neigh | 1.2617 | 1.2617 | 1.2617 | 0.0 | 38.82 +Comm | 0.069407 | 0.069407 | 0.069407 | 0.0 | 2.14 +Output | 0.00085688 | 0.00085688 | 0.00085688 | 0.0 | 0.03 +Modify | 1.1438 | 1.1438 | 1.1438 | 0.0 | 35.19 +Other | | 0.04037 | | | 1.24 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3756 ave 3756 max 3756 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 37360 ave 37360 max 37360 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 37360 +Ave neighs/atom = 6.67143 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 158 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.795 | 7.795 | 7.795 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.4527053 5.2126819 6.3537041 0.056937886 6.5982342 26.057038 30.380645 30.380645 -0.37001102 0.18554825 0.35527643 + 10100 1.4606958 5.2220088 6.3693071 0.10308269 6.8132489 26.093341 30.422971 30.380645 0.12567436 0.057087258 0.12648646 + 10200 1.4429187 5.2134399 6.3467753 0.022637194 6.4450326 26.195743 30.542365 30.380645 0.010739012 0.071921542 -0.014748971 + 10300 1.4559104 5.2293511 6.3728908 0.0079467818 6.4073504 26.182966 30.527467 30.380645 -0.014274944 0.032205181 0.0059101087 + 10400 1.4741126 5.2072221 6.3650586 0.095611559 6.7814715 26.240156 30.594148 30.380645 0.073579289 0.092441893 0.12081349 + 10500 1.4411698 5.2173262 6.3492878 0.010458046 6.3947259 26.208633 30.557393 30.380645 0.036794882 -0.0051462954 -0.00027444949 + 10600 1.4492728 5.1940541 6.3323802 0.042602534 6.5163992 26.132032 30.468083 30.380645 0.090116773 0.0022769844 0.035413845 + 10700 1.4599974 5.1895935 6.3363432 0.05533717 6.573197 26.013045 30.329352 30.380645 0.070180878 0.08084881 0.014981824 + 10800 1.4781084 5.1724704 6.3334454 0.031843587 6.4690539 25.947295 30.252692 30.380645 0.0041524129 0.077618702 0.013759645 + 10900 1.4410507 5.1708846 6.3027527 0.020221033 6.3881531 25.839719 30.127267 30.380645 -0.0014092876 0.014833141 0.047239245 + 11000 1.4150286 5.1756927 6.2871219 0.039768792 6.45242 25.63435 29.887821 30.380645 0.034930907 0.032278926 0.052096542 +Loop time of 3.43774 on 1 procs for 1000 steps with 5600 atoms + +Performance: 125663.855 tau/day, 290.889 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.75066 | 0.75066 | 0.75066 | 0.0 | 21.84 +Bond | 0.053177 | 0.053177 | 0.053177 | 0.0 | 1.55 +Neigh | 1.3577 | 1.3577 | 1.3577 | 0.0 | 39.49 +Comm | 0.07294 | 0.07294 | 0.07294 | 0.0 | 2.12 +Output | 0.00086403 | 0.00086403 | 0.00086403 | 0.0 | 0.03 +Modify | 1.1612 | 1.1612 | 1.1612 | 0.0 | 33.78 +Other | | 0.0412 | | | 1.20 + +Nlocal: 5600 ave 5600 max 5600 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 3904 ave 3904 max 3904 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 39666 ave 39666 max 39666 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 39666 +Ave neighs/atom = 7.08321 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 159 +Dangerous builds = 0 + +Total wall time: 0:00:22 diff --git a/examples/rigid/log.27Nov18.rigid.tnr.g++.4 b/examples/rigid/log.27Nov18.rigid.tnr.g++.4 new file mode 100644 index 0000000000..1fa53eb8d3 --- /dev/null +++ b/examples/rigid/log.27Nov18.rigid.tnr.g++.4 @@ -0,0 +1,458 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Tethered nanorods + +atom_style molecular + +read_data data.rigid.tnr + orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 5600 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 1600 bonds + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +# Specify bond parameters + +bond_style fene +bond_coeff 1 30.0 1.5 1.0 1.0 + +special_bonds fene + 2 = max # of 1-2 neighbors + 2 = max # of special neighbors + +# Specify initial velocities + +velocity all create 1.4 109345 + +# Specify rigid components + +group rods type 2 +4000 atoms in group rods +group tethers subtract all rods +1600 atoms in group tethers + +neigh_modify exclude molecule/intra rods delay 0 every 1 + +# Specify the pair potentials + +pair_style lj/cut 2.5 +pair_modify shift yes +pair_coeff * * 1.0 1.0 1.122 +pair_coeff 2 2 1.0 1.0 2.5 + +# Specify output + +thermo 100 +thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz +thermo_modify flush yes lost warn + +timestep 0.005 + +fix 1 rods rigid molecule +800 rigid bodies with 4000 atoms +fix 2 tethers nve +fix 3 all langevin 1.4 1.4 1.0 437624 + +run 5000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 45 45 45 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 7.216 | 7.384 | 7.552 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458 + 100 1.3999025 5.9707695 7.0703179 0.027293074 8.24564 62.244 62.244 62.244 0.017246307 0.04732529 0.017307624 + 200 1.4245544 5.9878446 7.1067558 0.0072016369 7.41688 62.244 62.244 62.244 0.0071370801 0.0084066589 0.0060611719 + 300 1.4212057 5.9942604 7.1105414 0.0023296933 7.210865 62.244 62.244 62.244 -0.0059197015 0.0040269953 0.008881786 + 400 1.4030116 5.9953214 7.0973119 0.0055751834 7.3373961 62.244 62.244 62.244 -0.0026920847 0.013323321 0.0060943141 + 500 1.4201338 5.9984777 7.1139168 -0.0018229523 7.035415 62.244 62.244 62.244 -0.0082217102 -0.00047319975 0.0032260529 + 600 1.425173 5.9902537 7.1096508 0.013367744 7.6853062 62.244 62.244 62.244 0.012971415 0.016298595 0.010833222 + 700 1.4181225 5.9840752 7.0979345 0.0014999758 7.1625279 62.244 62.244 62.244 -0.0015835387 0.0045967753 0.0014866907 + 800 1.4084205 5.9778462 7.084085 0.0063728488 7.3585191 62.244 62.244 62.244 0.0036202744 0.005593586 0.0099046859 + 900 1.3958301 5.9891019 7.0854517 0.0028974454 7.2102244 62.244 62.244 62.244 0.0087724642 0.0014508428 -0.001530971 + 1000 1.3937374 5.9794855 7.0741916 0.0087158481 7.4495223 62.244 62.244 62.244 0.014424783 0.0034958881 0.0082268735 + 1100 1.3729162 5.9916252 7.0699773 0.0030451966 7.2011127 62.244 62.244 62.244 0.00084635444 -0.00064448421 0.0089337195 + 1200 1.4427374 5.9713589 7.1045519 0.0042680608 7.2883474 62.244 62.244 62.244 0.0030884628 0.0031576538 0.0065580658 + 1300 1.3971469 5.9728674 7.0702514 0.0022809251 7.168475 62.244 62.244 62.244 0.00060902513 -0.00020572386 0.006439474 + 1400 1.4194118 5.9672631 7.082135 0.012945844 7.6396221 62.244 62.244 62.244 0.0082418827 0.016256336 0.014339314 + 1500 1.3866472 5.9728382 7.0619753 0.0010642438 7.1078049 62.244 62.244 62.244 0.0020316123 0.0020439035 -0.00088278432 + 1600 1.4184955 5.9539591 7.0681113 0.0077605409 7.4023036 62.244 62.244 62.244 0.0033721722 0.0057827512 0.014126699 + 1700 1.3612202 5.9676733 7.0368389 0.00016862131 7.0441002 62.244 62.244 62.244 0.0052525345 0.0007705269 -0.0055171975 + 1800 1.3641041 5.9521837 7.0236144 0.0057884587 7.2728829 62.244 62.244 62.244 0.0038061044 0.0044032908 0.009155981 + 1900 1.3594477 5.9646024 7.0323757 0.0044261926 7.2229809 62.244 62.244 62.244 0.0019417448 0.006871542 0.004465291 + 2000 1.3776971 5.9431816 7.0252888 -0.0012460593 6.9716298 62.244 62.244 62.244 -0.0010913822 0.00098119436 -0.0036279901 + 2100 1.3986245 5.9509735 7.0495181 0.007520633 7.3733792 62.244 62.244 62.244 0.008359824 0.0075919773 0.0066100978 + 2200 1.4033594 5.9548158 7.0570794 0.0016804284 7.1294438 62.244 62.244 62.244 -0.001842641 0.0032876741 0.0035962521 + 2300 1.4048926 5.9444129 7.0478808 0.0062444034 7.3167836 62.244 62.244 62.244 0.004383569 0.0065720464 0.007777595 + 2400 1.4044043 5.9370822 7.0401666 0.0034562836 7.1890046 62.244 62.244 62.244 0.0068959298 0.0041111713 -0.00063825026 + 2500 1.4200762 5.9359254 7.0513193 0.0028319649 7.1732722 62.244 62.244 62.244 -0.00030414203 0.0039571831 0.0048428538 + 2600 1.3876469 5.9249124 7.0148347 -0.0017777224 6.9382806 62.244 62.244 62.244 -0.00047616392 -0.0025484917 -0.0023085116 + 2700 1.4099941 5.916763 7.0242378 0.0070716263 7.3287634 62.244 62.244 62.244 0.012628756 0.0053812867 0.0032048359 + 2800 1.4444643 5.9283432 7.0628925 0.0019400024 7.1464349 62.244 62.244 62.244 0.0014895079 0.0046367397 -0.00030624055 + 2900 1.3902832 5.9152516 7.0072446 -0.002166221 6.9139606 62.244 62.244 62.244 -0.0012374412 -0.00056403267 -0.004697189 + 3000 1.3711706 5.922146 6.9991271 0.011101505 7.4771914 62.244 62.244 62.244 0.011063833 0.012093026 0.010147657 + 3100 1.3569137 5.9171753 6.9829583 -0.002826677 6.8612331 62.244 62.244 62.244 -0.0069507252 0.0010084399 -0.0025377458 + 3200 1.4004275 5.905939 7.0058998 0.005439467 7.2401397 62.244 62.244 62.244 0.010352184 0.0057594148 0.00020680265 + 3300 1.3641217 5.9145275 6.985972 -0.0027212811 6.8687855 62.244 62.244 62.244 -0.00065933677 -0.0057713008 -0.0017332057 + 3400 1.3868722 5.9059546 6.9952684 0.0092591256 7.3939943 62.244 62.244 62.244 0.010690877 0.010752519 0.006333981 + 3500 1.3939169 5.8992292 6.9940762 0.0074340028 7.3142068 62.244 62.244 62.244 0.010137307 0.0044252569 0.0077394447 + 3600 1.3982507 5.9219461 7.0201971 0.005679459 7.2647718 62.244 62.244 62.244 0.0023367243 0.008059221 0.0066424317 + 3700 1.4019908 5.9059957 7.0071843 0.0065915477 7.2910363 62.244 62.244 62.244 0.0049554109 0.010827005 0.0039922268 + 3800 1.3960736 5.902079 6.99862 0.0027763588 7.1181784 62.244 62.244 62.244 -0.0015907217 0.0025862003 0.0073335977 + 3900 1.4352825 5.8986215 7.025959 0.003498268 7.176605 62.244 62.244 62.244 0.0030416681 0.0027739509 0.0046791851 + 4000 1.4121845 5.907903 7.0170983 0.005046232 7.2344043 62.244 62.244 62.244 0.0045542682 0.0064113499 0.0041730779 + 4100 1.3989578 5.9082397 7.0070461 0.00042880001 7.0255115 62.244 62.244 62.244 0.0025735184 0.0025181486 -0.003805267 + 4200 1.3998829 5.8998147 6.9993477 0.0042777376 7.18356 62.244 62.244 62.244 0.0013744091 0.00646996 0.0049888436 + 4300 1.4076022 5.9044509 7.010047 0.0066789366 7.2976622 62.244 62.244 62.244 0.0073610616 0.0048139129 0.0078618353 + 4400 1.4161075 5.9064331 7.0187096 -0.0011844267 6.9677046 62.244 62.244 62.244 -0.0019088313 -0.0037556503 0.0021112015 + 4500 1.4292243 5.8980093 7.0205884 0.0018500416 7.1002567 62.244 62.244 62.244 0.0041144085 0.0010160497 0.00041966655 + 4600 1.3958775 5.8943133 6.9907003 0.0041485723 7.1693504 62.244 62.244 62.244 0.0033999287 0.0041620406 0.0048837475 + 4700 1.3856614 5.8886847 6.9770475 0.0013150314 7.0336767 62.244 62.244 62.244 -0.00051753674 0.0030875481 0.0013750828 + 4800 1.401683 5.9023505 7.0032974 0.002504877 7.1111649 62.244 62.244 62.244 0.0016543718 -0.0001813413 0.0060416007 + 4900 1.446628 5.9050553 7.0413042 -0.0026645902 6.9265589 62.244 62.244 62.244 -0.00069368076 -0.0073984763 9.8386402e-05 + 5000 1.4387091 5.9077604 7.0377893 0.0049468048 7.2508137 62.244 62.244 62.244 0.0042902506 0.0046715523 0.0058786114 +Loop time of 3.70354 on 4 procs for 5000 steps with 5600 atoms + +Performance: 583225.455 tau/day, 1350.059 timesteps/s +92.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.081073 | 0.13498 | 0.20108 | 14.4 | 3.64 +Bond | 0.032352 | 0.048566 | 0.066671 | 7.0 | 1.31 +Neigh | 0.71345 | 0.72477 | 0.73658 | 1.3 | 19.57 +Comm | 0.29998 | 0.37027 | 0.42722 | 8.9 | 10.00 +Output | 0.0026417 | 0.0048325 | 0.0085185 | 3.2 | 0.13 +Modify | 1.9807 | 2.1035 | 2.263 | 8.1 | 56.80 +Other | | 0.3166 | | | 8.55 + +Nlocal: 1400 ave 1868 max 905 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 648.25 ave 688 max 598 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Neighs: 1202.5 ave 1821 max 698 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 4810 +Ave neighs/atom = 0.858929 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 759 +Dangerous builds = 0 + +# Replace fix rigid and fix langevin with new ones + +unfix 1 +unfix 3 + +fix 3 tethers langevin 1.4 1.4 1.0 198450 + +# Test different integrators for rods + +fix 1 rods rigid/nve molecule +800 rigid bodies with 4000 atoms +print "rigid/nve" +rigid/nve +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 5000 1.4387091 5.9077604 7.0377893 0.0035977871 7.1927209 62.244 62.244 62.244 0.025518192 -0.016769871 0.0020450407 + 5100 1.4449405 5.8876257 7.022549 0.0023104502 7.122044 62.244 62.244 62.244 0.0045960664 0.0036845954 -0.0013493113 + 5200 1.4271652 5.9160022 7.036964 0.0020238904 7.1241189 62.244 62.244 62.244 -0.0022546188 0.00392213 0.0044041599 + 5300 1.4143299 5.9052666 7.016147 0.0064054214 7.2919838 62.244 62.244 62.244 0.0090997079 0.0026363579 0.0074801984 + 5400 1.4426441 5.9087558 7.0418754 0.0020465683 7.1300068 62.244 62.244 62.244 0.0043188307 3.0314417e-06 0.0018178427 + 5500 1.4281065 5.9038871 7.0255883 0.00058665945 7.0508516 62.244 62.244 62.244 0.005898925 0.00066013177 -0.0047990784 + 5600 1.4315628 5.902373 7.0267888 0.0096475978 7.4422435 62.244 62.244 62.244 0.0054175405 0.011780025 0.011745228 + 5700 1.4075482 5.9075587 7.0131124 0.0052150708 7.2376891 62.244 62.244 62.244 0.0030069124 0.0036690785 0.0089692215 + 5800 1.4215681 5.9048555 7.0214211 0.0015070444 7.086319 62.244 62.244 62.244 -5.6858344e-05 0.0023644208 0.0022135708 + 5900 1.3992461 5.8949367 6.9939696 0.0062425817 7.262794 62.244 62.244 62.244 0.0056972212 0.0095293238 0.0035012003 + 6000 1.385289 5.8972105 6.9852808 0.0043255163 7.1715506 62.244 62.244 62.244 0.0040215567 0.0026330714 0.0063219208 +Loop time of 0.84847 on 4 procs for 1000 steps with 5600 atoms + +Performance: 509151.820 tau/day, 1178.592 timesteps/s +94.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.020741 | 0.03547 | 0.053064 | 7.5 | 4.18 +Bond | 0.0064373 | 0.0096895 | 0.013065 | 3.0 | 1.14 +Neigh | 0.14992 | 0.15174 | 0.15392 | 0.4 | 17.88 +Comm | 0.068751 | 0.081259 | 0.10084 | 4.2 | 9.58 +Output | 0.00054288 | 0.00096381 | 0.0017593 | 0.0 | 0.11 +Modify | 0.45914 | 0.48587 | 0.51316 | 2.8 | 57.26 +Other | | 0.08348 | | | 9.84 + +Nlocal: 1400 ave 1868 max 935 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 633.75 ave 695 max 541 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +Neighs: 1263 ave 1799 max 710 min +Histogram: 1 1 0 0 0 0 0 0 0 2 + +Total # of neighbors = 5052 +Ave neighs/atom = 0.902143 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 153 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0 +800 rigid bodies with 4000 atoms +print "rigid/nvt" +rigid/nvt +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 6000 1.385289 5.8972105 6.9852808 0.0029190017 7.1109818 62.244 62.244 62.244 0.026575922 -0.075631452 0.057812535 + 6100 1.3829575 5.9055308 6.9917699 0.0022904842 7.090405 62.244 62.244 62.244 -0.00045870123 0.0040556461 0.0032745076 + 6200 1.3942692 5.90506 7.0001838 0.0046406766 7.2000253 62.244 62.244 62.244 0.0042263485 0.0051632793 0.0045324021 + 6300 1.4009885 5.902399 7.0028005 0.0077682466 7.3373246 62.244 62.244 62.244 0.0071636876 0.0098268446 0.0063142075 + 6400 1.3627532 5.9075588 6.9779284 0.0093180831 7.3791932 62.244 62.244 62.244 0.0062401458 0.01302262 0.0086914833 + 6500 1.3341203 5.9012967 6.9491767 0.01010805 7.3844599 62.244 62.244 62.244 0.0031876185 0.011099561 0.01603697 + 6600 1.3572847 5.8915298 6.9576042 -0.00034416901 6.9427833 62.244 62.244 62.244 0.0025579012 -0.0011308802 -0.0024595281 + 6700 1.366374 5.8985277 6.9717413 0.0029472772 7.0986599 62.244 62.244 62.244 0.0022469424 -0.00042869772 0.0070235868 + 6800 1.381673 5.8909304 6.9761606 -9.1063397e-05 6.9722391 62.244 62.244 62.244 -0.0048194377 -0.00080972169 0.0053559692 + 6900 1.4011472 5.8881927 6.9887188 0.0010086058 7.0321524 62.244 62.244 62.244 0.0012132619 -0.0025916747 0.0044042301 + 7000 1.3973658 5.8867938 6.9843498 0.0070015187 7.2858563 62.244 62.244 62.244 0.0058913402 0.0076802028 0.0074330131 +Loop time of 0.902266 on 4 procs for 1000 steps with 5600 atoms + +Performance: 478794.425 tau/day, 1108.320 timesteps/s +92.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.022644 | 0.037091 | 0.054025 | 7.4 | 4.11 +Bond | 0.0066526 | 0.0098482 | 0.012934 | 2.8 | 1.09 +Neigh | 0.15815 | 0.16028 | 0.16242 | 0.5 | 17.76 +Comm | 0.086046 | 0.10069 | 0.11568 | 3.7 | 11.16 +Output | 0.00047731 | 0.00090772 | 0.0016732 | 0.0 | 0.10 +Modify | 0.46692 | 0.49338 | 0.52973 | 3.5 | 54.68 +Other | | 0.1001 | | | 11.09 + +Nlocal: 1400 ave 1832 max 970 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 652.5 ave 749 max 561 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Neighs: 1407.5 ave 2071 max 748 min +Histogram: 1 1 0 0 0 0 0 0 1 1 + +Total # of neighbors = 5630 +Ave neighs/atom = 1.00536 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 149 +Dangerous builds = 0 +unfix 1 + +compute myTemp all temp + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt iso" +rigid/npt iso +fix_modify 1 temp myTemp + +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.217 | 7.395 | 7.573 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 7000 1.3973658 5.8867938 6.9843498 0.0026564535 7.0987447 62.244 62.244 62.244 0.033711862 -0.0068580786 -0.018884423 + 7100 1.463906 5.861189 7.0110088 0.011521299 7.3924648 57.022165 57.022165 57.022165 0.010788399 0.0093706759 0.014404821 + 7200 1.4950346 5.817724 6.9919936 0.023104537 7.516484 50.28164 50.28164 50.28164 0.023252537 0.018108267 0.027952807 + 7300 1.5103539 5.7757334 6.9620355 0.02265972 7.3367664 45.242961 45.242961 45.242961 0.023588139 0.022279352 0.022111669 + 7400 1.5583184 5.7576833 6.9816589 0.028383162 7.3460731 41.582206 41.582206 41.582206 0.027312172 0.029876235 0.027961079 + 7500 1.5988886 5.6930714 6.9489127 0.046500933 7.4415595 39.00204 39.00204 39.00204 0.057497139 0.031007247 0.050998413 + 7600 1.5458926 5.6844397 6.8986555 0.034168406 7.2068206 36.96428 36.96428 36.96428 0.037874991 0.027247969 0.037382258 + 7700 1.5179913 5.6416448 6.8339457 0.070322183 7.3856048 35.284894 35.284894 35.284894 0.054248771 0.10402305 0.052694729 + 7800 1.4797888 5.6045532 6.7668481 0.07801402 7.3126319 33.963465 33.963465 33.963465 0.096058241 0.061172194 0.076811627 + 7900 1.4846305 5.54982 6.7159177 0.065303374 7.1325712 32.936376 32.936376 32.936376 0.089117046 0.06069295 0.046100127 + 8000 1.4352665 5.5157472 6.6430722 0.065962965 7.0326574 32.099391 32.099391 32.099391 0.032126133 0.070109418 0.095653344 +Loop time of 1.72334 on 4 procs for 1000 steps with 5600 atoms + +Performance: 250675.661 tau/day, 580.268 timesteps/s +92.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.060282 | 0.099801 | 0.13824 | 10.8 | 5.79 +Bond | 0.0095227 | 0.013491 | 0.017217 | 3.2 | 0.78 +Neigh | 0.58793 | 0.59546 | 0.60654 | 1.0 | 34.55 +Comm | 0.17903 | 0.21403 | 0.24615 | 6.5 | 12.42 +Output | 0.00045562 | 0.00076783 | 0.0017018 | 0.0 | 0.04 +Modify | 0.64959 | 0.68513 | 0.70671 | 2.8 | 39.76 +Other | | 0.1147 | | | 6.65 + +Nlocal: 1400 ave 1768 max 981 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 1574 ave 1663 max 1447 min +Histogram: 1 0 0 1 0 0 0 0 0 2 +Neighs: 6338 ave 9521 max 3068 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 25352 +Ave neighs/atom = 4.52714 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 337 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/npt x" +rigid/npt x +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.226 | 7.412 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 8000 1.4352665 5.5157472 6.6430722 0.073641793 7.0780095 32.099391 32.099391 32.099391 0.13359913 0.13991003 -0.052583787 + 8100 1.4385682 5.5149882 6.6449064 0.092621097 7.1894426 31.952972 32.099391 32.099391 0.10729401 0.11619987 0.054369411 + 8200 1.42735 5.5149024 6.6360094 0.023903894 6.7756304 31.745099 32.099391 32.099391 0.051524189 0.013370811 0.006816681 + 8300 1.4335369 5.5031396 6.629106 0.024536474 6.7705237 31.324638 32.099391 32.099391 0.042356568 -0.0039258365 0.035178692 + 8400 1.4502714 5.4659017 6.6050122 0.06575457 6.9774701 30.785462 32.099391 32.099391 0.056998298 0.084852971 0.055412441 + 8500 1.4432366 5.4541505 6.5877355 0.03322226 6.7725932 30.241461 32.099391 32.099391 0.045871758 0.024443739 0.029351281 + 8600 1.436491 5.4272043 6.5554911 0.039811655 6.7732608 29.729098 32.099391 32.099391 0.037709456 0.060942551 0.020782958 + 8700 1.4099251 5.4106713 6.5180919 0.013490442 6.590596 29.209958 32.099391 32.099391 0.025833003 -0.0021161354 0.016754458 + 8800 1.3801478 5.3926425 6.4766747 0.028808964 6.6280205 28.552039 32.099391 32.099391 0.012603549 0.018713073 0.055110271 + 8900 1.4411695 5.3583474 6.4903088 0.053464468 6.7655624 27.980937 32.099391 32.099391 0.055084927 0.073292013 0.032016464 + 9000 1.4264395 5.3680298 6.4884216 0.066557314 6.8276318 27.69922 32.099391 32.099391 0.05380086 0.069450871 0.076420212 +Loop time of 1.45936 on 4 procs for 1000 steps with 5600 atoms + +Performance: 296020.704 tau/day, 685.233 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.097855 | 0.1563 | 0.20542 | 12.5 | 10.71 +Bond | 0.010222 | 0.01371 | 0.016844 | 2.6 | 0.94 +Neigh | 0.43646 | 0.44419 | 0.4668 | 2.0 | 30.44 +Comm | 0.10136 | 0.14589 | 0.19563 | 11.6 | 10.00 +Output | 0.00046229 | 0.00076181 | 0.0016556 | 0.0 | 0.05 +Modify | 0.59971 | 0.62524 | 0.65776 | 2.9 | 42.84 +Other | | 0.07327 | | | 5.02 + +Nlocal: 1400 ave 1680 max 1049 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Nghost: 1627.25 ave 1775 max 1488 min +Histogram: 1 1 0 0 0 0 0 1 0 1 +Neighs: 7842 ave 10600 max 4326 min +Histogram: 1 0 1 0 0 0 0 0 0 2 + +Total # of neighbors = 31368 +Ave neighs/atom = 5.60143 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 166 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph iso" +rigid/nph iso +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.227 | 7.412 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 9000 1.4264395 5.3680298 6.4884216 0.0098629166 6.5386881 27.69922 32.099391 32.099391 -0.32352455 -0.020288613 0.37340191 + 9100 1.4501008 5.3468478 6.4858243 0.059250929 6.7846766 27.60347 31.988431 31.988431 0.076039445 0.051409059 0.050304282 + 9200 1.4635102 5.3406895 6.4901983 0.035210102 6.6656151 27.490192 31.857158 31.857158 0.0079484246 0.066653954 0.031027926 + 9300 1.4503713 5.3595734 6.4987624 0.020794 6.6013231 27.398334 31.750708 31.750708 0.053098983 0.0019379163 0.0073450997 + 9400 1.4701421 5.3186993 6.4734172 0.039118143 6.6618027 27.181055 31.498913 31.498913 0.076457868 -0.0028405762 0.043737137 + 9500 1.4495442 5.323167 6.4617063 0.073591495 6.8091096 27.000921 31.290164 31.290164 0.037777789 0.097624306 0.085372389 + 9600 1.4668438 5.3002222 6.4523494 0.06758294 6.7648428 26.814997 31.074705 31.074705 0.057941415 0.09775976 0.047047645 + 9700 1.4926839 5.2883964 6.4608196 0.059125916 6.7288224 26.637713 30.869258 30.869258 0.049817515 0.032285203 0.095275031 + 9800 1.4644558 5.2702597 6.4205112 0.0076221617 6.4543756 26.460515 30.663911 30.663911 -0.0060723629 0.010616271 0.018322577 + 9900 1.4669549 5.2511861 6.4034006 0.044167302 6.5961243 26.30195 30.480157 30.480157 0.026274163 0.013826125 0.092401618 + 10000 1.460983 5.2470476 6.3945715 0.10536479 6.8483021 26.186495 30.346361 30.346361 0.088951294 0.11273872 0.11440435 +Loop time of 1.61361 on 4 procs for 1000 steps with 5600 atoms + +Performance: 267722.758 tau/day, 619.729 timesteps/s +93.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.13322 | 0.18643 | 0.259 | 12.5 | 11.55 +Bond | 0.012367 | 0.014462 | 0.016771 | 1.6 | 0.90 +Neigh | 0.46284 | 0.46471 | 0.46675 | 0.3 | 28.80 +Comm | 0.10183 | 0.17241 | 0.22246 | 12.4 | 10.68 +Output | 0.00044584 | 0.00074542 | 0.0016396 | 0.0 | 0.05 +Modify | 0.691 | 0.7057 | 0.72761 | 1.8 | 43.73 +Other | | 0.06915 | | | 4.29 + +Nlocal: 1400 ave 1633 max 1183 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 1747.75 ave 1847 max 1624 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 9290.75 ave 12454 max 6621 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 37163 +Ave neighs/atom = 6.63625 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 162 +Dangerous builds = 0 +unfix 1 + +fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all +800 rigid bodies with 4000 atoms +print "rigid/nph xy couple" +rigid/nph xy couple +run 1000 +Per MPI rank memory allocation (min/avg/max) = 7.229 | 7.413 | 7.597 Mbytes +Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz + 10000 1.460983 5.2470476 6.3945715 0.18376191 7.1859023 26.186495 30.346361 30.346361 0.015959435 0.68341409 -0.14808778 + 10100 1.4487259 5.2485513 6.3864479 0.060157728 6.6465409 26.238844 30.407026 30.346361 0.10289596 0.022823411 0.05475381 + 10200 1.4335646 5.2420513 6.3680395 0.013676852 6.4271554 26.235255 30.402867 30.346361 -0.017328522 0.040786509 0.017572569 + 10300 1.4334952 5.2377534 6.3636871 0.030978458 6.4967192 26.150168 30.304264 30.346361 0.044154015 0.036133394 0.012647966 + 10400 1.4209473 5.2242736 6.3403516 -0.00094467594 6.3363148 26.085773 30.22964 30.346361 0.030664991 0.018005544 -0.051504563 + 10500 1.4262805 5.2044624 6.3247294 0.045042501 6.5149748 25.934148 30.053928 30.346361 0.031103656 0.045410964 0.058612885 + 10600 1.4516048 5.2017459 6.3419036 0.069565209 6.6313867 25.741959 29.831208 30.346361 0.021768778 0.11302833 0.073898515 + 10700 1.4841074 5.1911212 6.356808 0.046866825 6.5493087 25.574636 29.637306 30.346361 0.073969059 0.064901506 0.0017299084 + 10800 1.4646257 5.1958815 6.3462665 0.050747116 6.5534926 25.500146 29.550982 30.346361 0.076646556 0.070734108 0.004860682 + 10900 1.461356 5.1821605 6.3299773 0.069060447 6.610166 25.417723 29.455466 30.346361 0.051399011 0.065631311 0.090151019 + 11000 1.4395386 5.1786243 6.3093047 -0.0087983274 6.2737059 25.383039 29.415273 30.346361 -0.060891892 0.037235898 -0.0027389884 +Loop time of 1.56065 on 4 procs for 1000 steps with 5600 atoms + +Performance: 276807.605 tau/day, 640.758 timesteps/s +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15892 | 0.20364 | 0.2564 | 9.2 | 13.05 +Bond | 0.011486 | 0.014652 | 0.01918 | 2.6 | 0.94 +Neigh | 0.43915 | 0.43981 | 0.44125 | 0.1 | 28.18 +Comm | 0.093711 | 0.14431 | 0.18183 | 9.9 | 9.25 +Output | 0.00044441 | 0.00073904 | 0.0016198 | 0.0 | 0.05 +Modify | 0.66889 | 0.68497 | 0.70418 | 1.5 | 43.89 +Other | | 0.07254 | | | 4.65 + +Nlocal: 1400 ave 1610 max 1237 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Nghost: 1832 ave 1919 max 1765 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 10008.2 ave 12428 max 7982 min +Histogram: 2 0 0 0 0 0 0 1 0 1 + +Total # of neighbors = 40033 +Ave neighs/atom = 7.14875 +Ave special neighs/atom = 0.571429 +Neighbor list builds = 157 +Dangerous builds = 0 + +Total wall time: 0:00:11 diff --git a/examples/shear/log.5Oct16.shear.g++.1 b/examples/shear/log.27Nov18.shear.g++.1 similarity index 78% rename from examples/shear/log.5Oct16.shear.g++.1 rename to examples/shear/log.27Nov18.shear.g++.1 index 2a9d4e4b93..37731131c1 100644 --- a/examples/shear/log.5Oct16.shear.g++.1 +++ b/examples/shear/log.27Nov18.shear.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal @@ -16,6 +17,7 @@ lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms + Time spent = 0.001899 secs pair_style eam pair_coeff * * Ni_u3.eam @@ -61,38 +63,43 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.1 ghost atom cutoff = 5.1 - binsize = 2.55 -> bins = 23 14 4 -Memory usage per processor = 2.88718 Mbytes + binsize = 2.55, bins = 23 14 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.49 | 3.49 | 3.49 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02 25 220.34459 -8272.5701 0 -8233.1798 5168.6655 19547.02 50 300 -8237.7876 0 -8184.1576 13741.264 19686.493 75 292.67269 -8229.8093 0 -8177.4891 14319.387 19744.946 100 300 -8245.8191 0 -8192.189 9034.8776 19778.592 -Loop time of 0.259133 on 1 procs for 100 steps with 1912 atoms +Loop time of 0.284035 on 1 procs for 100 steps with 1912 atoms -Performance: 33.342 ns/day, 0.720 hours/ns, 385.902 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 30.419 ns/day, 0.789 hours/ns, 352.069 timesteps/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.2446 | 0.2446 | 0.2446 | 0.0 | 94.39 -Neigh | 0.0086329 | 0.0086329 | 0.0086329 | 0.0 | 3.33 -Comm | 0.0014203 | 0.0014203 | 0.0014203 | 0.0 | 0.55 -Output | 5.8413e-05 | 5.8413e-05 | 5.8413e-05 | 0.0 | 0.02 -Modify | 0.0033374 | 0.0033374 | 0.0033374 | 0.0 | 1.29 -Other | | 0.001081 | | | 0.42 +Pair | 0.26775 | 0.26775 | 0.26775 | 0.0 | 94.27 +Neigh | 0.0096006 | 0.0096006 | 0.0096006 | 0.0 | 3.38 +Comm | 0.0018885 | 0.0018885 | 0.0018885 | 0.0 | 0.66 +Output | 9.8228e-05 | 9.8228e-05 | 9.8228e-05 | 0.0 | 0.03 +Modify | 0.0035083 | 0.0035083 | 0.0035083 | 0.0 | 1.24 +Other | | 0.001191 | | | 0.42 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -125,11 +132,11 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 -Memory usage per processor = 2.88909 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.492 | 3.492 | 3.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 298.42546 -8245.8191 0 -8210.2533 8056.2702 19786.12 100 300 -8260.779 0 -8225.0257 3180.8817 19817.51 @@ -162,20 +169,20 @@ Step Temp E_pair E_mol TotEng Press Volume 2800 306.61457 -8165.9986 0 -8129.457 -2360.5296 22954.851 2900 305.42952 -8161.9351 0 -8125.5347 -6928.3135 23081.881 3000 292.3109 -8156.8668 0 -8122.0298 -9481.3532 23197.918 -Loop time of 7.96699 on 1 procs for 3000 steps with 1912 atoms +Loop time of 8.5487 on 1 procs for 3000 steps with 1912 atoms -Performance: 32.534 ns/day, 0.738 hours/ns, 376.554 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 30.320 ns/day, 0.792 hours/ns, 350.931 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 7.3036 | 7.3036 | 7.3036 | 0.0 | 91.67 -Neigh | 0.48164 | 0.48164 | 0.48164 | 0.0 | 6.05 -Comm | 0.045735 | 0.045735 | 0.045735 | 0.0 | 0.57 -Output | 0.00060129 | 0.00060129 | 0.00060129 | 0.0 | 0.01 -Modify | 0.10228 | 0.10228 | 0.10228 | 0.0 | 1.28 -Other | | 0.03312 | | | 0.42 +Pair | 7.7964 | 7.7964 | 7.7964 | 0.0 | 91.20 +Neigh | 0.54999 | 0.54999 | 0.54999 | 0.0 | 6.43 +Comm | 0.061907 | 0.061907 | 0.061907 | 0.0 | 0.72 +Output | 0.00085449 | 0.00085449 | 0.00085449 | 0.0 | 0.01 +Modify | 0.10321 | 0.10321 | 0.10321 | 0.0 | 1.21 +Other | | 0.03637 | | | 0.43 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/shear/log.5Oct16.shear.g++.4 b/examples/shear/log.27Nov18.shear.g++.4 similarity index 78% rename from examples/shear/log.5Oct16.shear.g++.4 rename to examples/shear/log.27Nov18.shear.g++.4 index ac94b38918..f06a26ece5 100644 --- a/examples/shear/log.5Oct16.shear.g++.4 +++ b/examples/shear/log.27Nov18.shear.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal @@ -16,6 +17,7 @@ lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms + Time spent = 0.000388622 secs pair_style eam pair_coeff * * Ni_u3.eam @@ -61,38 +63,43 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.1 ghost atom cutoff = 5.1 - binsize = 2.55 -> bins = 23 14 4 -Memory usage per processor = 2.78742 Mbytes + binsize = 2.55, bins = 23 14 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.371 | 3.371 | 3.371 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02 25 219.81848 -8272.1577 0 -8232.8615 5206.8057 19547.02 50 300 -8238.3413 0 -8184.7112 13308.809 19688.933 75 294.78636 -8232.2217 0 -8179.5237 13192.782 19748.176 100 300 -8248.1223 0 -8194.4923 7352.0246 19816.321 -Loop time of 0.0729427 on 4 procs for 100 steps with 1912 atoms +Loop time of 0.0884107 on 4 procs for 100 steps with 1912 atoms -Performance: 118.449 ns/day, 0.203 hours/ns, 1370.938 timesteps/s -100.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 97.726 ns/day, 0.246 hours/ns, 1131.084 timesteps/s +94.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.063756 | 0.065014 | 0.06712 | 0.5 | 89.13 -Neigh | 0.0021732 | 0.0022199 | 0.0022831 | 0.1 | 3.04 -Comm | 0.0017257 | 0.0039253 | 0.0052609 | 2.1 | 5.38 -Output | 8.7023e-05 | 9.3579e-05 | 0.00010633 | 0.1 | 0.13 -Modify | 0.00090957 | 0.00092477 | 0.00093555 | 0.0 | 1.27 -Other | | 0.0007653 | | | 1.05 +Pair | 0.072181 | 0.073453 | 0.074266 | 0.3 | 83.08 +Neigh | 0.0026526 | 0.0028275 | 0.0029895 | 0.2 | 3.20 +Comm | 0.0081384 | 0.0091963 | 0.0099204 | 0.7 | 10.40 +Output | 9.8705e-05 | 0.00012231 | 0.00018597 | 0.0 | 0.14 +Modify | 0.00092363 | 0.00094259 | 0.00096059 | 0.0 | 1.07 +Other | | 0.001869 | | | 2.11 Nlocal: 478 ave 490 max 466 min Histogram: 1 0 1 0 0 0 0 1 0 1 @@ -125,11 +132,11 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 -Memory usage per processor = 2.78742 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.371 | 3.371 | 3.371 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 302.29407 -8248.1223 0 -8212.0956 6393.6774 19845.81 100 291.61298 -8259.5472 0 -8224.7933 -1300.9229 19874.36 @@ -162,20 +169,20 @@ Step Temp E_pair E_mol TotEng Press Volume 2800 306.09492 -8173.4147 0 -8136.935 -10981.226 22960.958 2900 303.27397 -8168.2141 0 -8132.0706 -8905.5017 23078.216 3000 301.48023 -8165.8151 0 -8129.8854 -10668.385 23201.582 -Loop time of 2.25377 on 4 procs for 3000 steps with 1912 atoms +Loop time of 2.66845 on 4 procs for 3000 steps with 1912 atoms -Performance: 115.007 ns/day, 0.209 hours/ns, 1331.105 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 97.135 ns/day, 0.247 hours/ns, 1124.248 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.8854 | 1.9462 | 2.0017 | 3.0 | 86.35 -Neigh | 0.11869 | 0.12531 | 0.13086 | 1.2 | 5.56 -Comm | 0.0676 | 0.13095 | 0.19879 | 13.0 | 5.81 -Output | 0.0006516 | 0.00068212 | 0.00076056 | 0.2 | 0.03 -Modify | 0.028034 | 0.028804 | 0.029825 | 0.5 | 1.28 -Other | | 0.02182 | | | 0.97 +Pair | 2.1584 | 2.2278 | 2.3244 | 4.0 | 83.49 +Neigh | 0.14134 | 0.15172 | 0.1614 | 2.0 | 5.69 +Comm | 0.11957 | 0.22852 | 0.30416 | 14.2 | 8.56 +Output | 0.00077462 | 0.0013641 | 0.0031083 | 2.7 | 0.05 +Modify | 0.028383 | 0.029401 | 0.030651 | 0.5 | 1.10 +Other | | 0.02965 | | | 1.11 Nlocal: 478 ave 509 max 446 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/shear/log.5Oct16.shear.void.g++.1 b/examples/shear/log.27Nov18.shear.void.g++.1 similarity index 78% rename from examples/shear/log.5Oct16.shear.void.g++.1 rename to examples/shear/log.27Nov18.shear.void.g++.1 index 2eb48c76d8..ea97045168 100644 --- a/examples/shear/log.5Oct16.shear.void.g++.1 +++ b/examples/shear/log.27Nov18.shear.void.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal @@ -16,6 +17,7 @@ lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms + Time spent = 0.000714779 secs pair_style eam pair_coeff * * Ni_u3.eam @@ -62,38 +64,43 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.1 ghost atom cutoff = 5.1 - binsize = 2.55 -> bins = 23 14 4 -Memory usage per processor = 2.86988 Mbytes + binsize = 2.55, bins = 23 14 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.469 | 3.469 | 3.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02 25 222.66197 -7321.4403 0 -7287.5071 562.28854 19547.02 50 300 -7292.2273 0 -7246.508 7555.5059 19688.542 75 292.67603 -7286.2016 0 -7241.5984 6825.409 19746.217 100 300 -7297.4174 0 -7251.698 1627.2455 19775.648 -Loop time of 0.228115 on 1 procs for 100 steps with 1708 atoms +Loop time of 0.248797 on 1 procs for 100 steps with 1708 atoms -Performance: 37.876 ns/day, 0.634 hours/ns, 438.375 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 34.727 ns/day, 0.691 hours/ns, 401.933 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.21523 | 0.21523 | 0.21523 | 0.0 | 94.35 -Neigh | 0.0075827 | 0.0075827 | 0.0075827 | 0.0 | 3.32 -Comm | 0.001266 | 0.001266 | 0.001266 | 0.0 | 0.55 -Output | 5.4121e-05 | 5.4121e-05 | 5.4121e-05 | 0.0 | 0.02 -Modify | 0.0030229 | 0.0030229 | 0.0030229 | 0.0 | 1.33 -Other | | 0.0009584 | | | 0.42 +Pair | 0.2343 | 0.2343 | 0.2343 | 0.0 | 94.17 +Neigh | 0.0084395 | 0.0084395 | 0.0084395 | 0.0 | 3.39 +Comm | 0.0016763 | 0.0016763 | 0.0016763 | 0.0 | 0.67 +Output | 0.0001018 | 0.0001018 | 0.0001018 | 0.0 | 0.04 +Modify | 0.0030863 | 0.0030863 | 0.0030863 | 0.0 | 1.24 +Other | | 0.001193 | | | 0.48 Nlocal: 1708 ave 1708 max 1708 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -126,11 +133,11 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 -Memory usage per processor = 2.86988 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.469 | 3.469 | 3.469 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 296.68961 -7297.4174 0 -7267.2741 785.80272 19779.424 100 290.29095 -7309.7136 0 -7280.2205 -5956.8739 19838.833 @@ -163,20 +170,20 @@ Step Temp E_pair E_mol TotEng Press Volume 2800 293.40764 -7248.9658 0 -7219.156 -17298.989 22959.736 2900 306.87934 -7249.3942 0 -7218.2158 -17152.689 23078.216 3000 308.14535 -7244.6151 0 -7213.308 -15383.029 23210.132 -Loop time of 6.91463 on 1 procs for 3000 steps with 1708 atoms +Loop time of 7.37965 on 1 procs for 3000 steps with 1708 atoms -Performance: 37.486 ns/day, 0.640 hours/ns, 433.863 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 35.124 ns/day, 0.683 hours/ns, 406.523 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 6.3607 | 6.3607 | 6.3607 | 0.0 | 91.99 -Neigh | 0.39249 | 0.39249 | 0.39249 | 0.0 | 5.68 -Comm | 0.040066 | 0.040066 | 0.040066 | 0.0 | 0.58 -Output | 0.0005281 | 0.0005281 | 0.0005281 | 0.0 | 0.01 -Modify | 0.092056 | 0.092056 | 0.092056 | 0.0 | 1.33 -Other | | 0.02877 | | | 0.42 +Pair | 6.7514 | 6.7514 | 6.7514 | 0.0 | 91.49 +Neigh | 0.45084 | 0.45084 | 0.45084 | 0.0 | 6.11 +Comm | 0.053905 | 0.053905 | 0.053905 | 0.0 | 0.73 +Output | 0.00081897 | 0.00081897 | 0.00081897 | 0.0 | 0.01 +Modify | 0.090654 | 0.090654 | 0.090654 | 0.0 | 1.23 +Other | | 0.032 | | | 0.43 Nlocal: 1708 ave 1708 max 1708 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/shear/log.5Oct16.shear.void.g++.4 b/examples/shear/log.27Nov18.shear.void.g++.4 similarity index 78% rename from examples/shear/log.5Oct16.shear.void.g++.4 rename to examples/shear/log.27Nov18.shear.void.g++.4 index 89c88d2ecf..cea6f6fc65 100644 --- a/examples/shear/log.5Oct16.shear.void.g++.4 +++ b/examples/shear/log.27Nov18.shear.void.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal @@ -16,6 +17,7 @@ lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms + Time spent = 0.000400543 secs pair_style eam pair_coeff * * Ni_u3.eam @@ -62,38 +64,43 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.1 ghost atom cutoff = 5.1 - binsize = 2.55 -> bins = 23 14 4 -Memory usage per processor = 2.7752 Mbytes + binsize = 2.55, bins = 23 14 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair eam, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02 25 220.57465 -7320.4003 0 -7286.7852 832.69858 19547.02 50 300 -7292.1121 0 -7246.3928 7101.9213 19686.075 75 295.2793 -7286.9013 0 -7241.9014 5282.1114 19746.39 100 300 -7301.0026 0 -7255.2833 -1939.7714 19790.975 -Loop time of 0.0665765 on 4 procs for 100 steps with 1708 atoms +Loop time of 0.0688287 on 4 procs for 100 steps with 1708 atoms -Performance: 129.776 ns/day, 0.185 hours/ns, 1502.032 timesteps/s -98.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 125.529 ns/day, 0.191 hours/ns, 1452.882 timesteps/s +96.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.056678 | 0.05843 | 0.061234 | 0.7 | 87.76 -Neigh | 0.001873 | 0.0019386 | 0.0019932 | 0.1 | 2.91 -Comm | 0.0016048 | 0.0044546 | 0.0062997 | 2.6 | 6.69 -Output | 8.2016e-05 | 8.6188e-05 | 9.6321e-05 | 0.1 | 0.13 -Modify | 0.0008502 | 0.00086212 | 0.00087571 | 0.0 | 1.29 -Other | | 0.0008054 | | | 1.21 +Pair | 0.059247 | 0.060771 | 0.062449 | 0.5 | 88.29 +Neigh | 0.0022693 | 0.0023552 | 0.0024772 | 0.2 | 3.42 +Comm | 0.0018966 | 0.0037905 | 0.005276 | 2.1 | 5.51 +Output | 8.297e-05 | 0.00011259 | 0.00019741 | 0.0 | 0.16 +Modify | 0.00082994 | 0.00084907 | 0.00086927 | 0.0 | 1.23 +Other | | 0.0009506 | | | 1.38 Nlocal: 427 ave 437 max 419 min Histogram: 1 1 0 0 0 0 1 0 0 1 @@ -126,11 +133,11 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 -Memory usage per processor = 2.7752 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 298.93143 -7301.0026 0 -7270.6316 -2766.8643 19799.958 100 301.13545 -7308.1131 0 -7277.5182 -8902.3332 19851.054 @@ -163,20 +170,20 @@ Step Temp E_pair E_mol TotEng Press Volume 2800 298.94765 -7255.6331 0 -7225.2605 -20555.015 22959.736 2900 294.98551 -7249.0201 0 -7219.05 -23986.374 23079.438 3000 291.21483 -7244.1837 0 -7214.5967 -25356.925 23197.918 -Loop time of 1.88696 on 4 procs for 3000 steps with 1708 atoms +Loop time of 2.21357 on 4 procs for 3000 steps with 1708 atoms -Performance: 137.364 ns/day, 0.175 hours/ns, 1589.856 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 117.096 ns/day, 0.205 hours/ns, 1355.278 timesteps/s +96.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.608 | 1.6534 | 1.6897 | 2.3 | 87.62 -Neigh | 0.099209 | 0.10261 | 0.10744 | 0.9 | 5.44 -Comm | 0.044314 | 0.086752 | 0.13601 | 11.1 | 4.60 -Output | 0.00059652 | 0.00062531 | 0.00070548 | 0.2 | 0.03 -Modify | 0.024703 | 0.025439 | 0.026699 | 0.5 | 1.35 -Other | | 0.01814 | | | 0.96 +Pair | 1.8072 | 1.86 | 1.9192 | 3.7 | 84.03 +Neigh | 0.11667 | 0.12264 | 0.13213 | 1.7 | 5.54 +Comm | 0.10804 | 0.17878 | 0.23557 | 13.3 | 8.08 +Output | 0.00073075 | 0.0012527 | 0.002811 | 2.5 | 0.06 +Modify | 0.024781 | 0.025831 | 0.02754 | 0.7 | 1.17 +Other | | 0.02508 | | | 1.13 Nlocal: 427 ave 450 max 403 min Histogram: 1 1 0 0 0 0 0 0 1 1 @@ -189,4 +196,4 @@ Total # of neighbors = 38325 Ave neighs/atom = 22.4385 Neighbor list builds = 215 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/snap/Mo_Chen_PRM2017.snap b/examples/snap/Mo_Chen_PRM2017.snap deleted file mode 100644 index e5e5f3e180..0000000000 --- a/examples/snap/Mo_Chen_PRM2017.snap +++ /dev/null @@ -1,7 +0,0 @@ - -# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) -# Generated by Materials Virtual Lab -# Definition of SNAP potential. -pair_style snap -pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo - diff --git a/examples/snap/Mo_Chen_PRM2017.snap b/examples/snap/Mo_Chen_PRM2017.snap new file mode 120000 index 0000000000..78422c66e2 --- /dev/null +++ b/examples/snap/Mo_Chen_PRM2017.snap @@ -0,0 +1 @@ +../../potentials/Mo_Chen_PRM2017.snap \ No newline at end of file diff --git a/examples/snap/Mo_Chen_PRM2017.snapcoeff b/examples/snap/Mo_Chen_PRM2017.snapcoeff deleted file mode 100644 index 577c45bd76..0000000000 --- a/examples/snap/Mo_Chen_PRM2017.snapcoeff +++ /dev/null @@ -1,35 +0,0 @@ -# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) -# Generated by Materials Virtual Lab -1 31 -Mo 0.5 1 --17.2757958404 -0.00431015861472 -0.0657685117891 -0.477733335702 -0.0152688837211 -0.77559888196 -0.284846429566 -0.148804982644 -0.0573702179736 -0.19281989434 -0.323441703578 -0.101324335724 -0.0139639846514 --0.0324444749083 -0.0349797952779 -0.0613023441282 -0.0881078513046 -0.118716074611 -0.0069662975532 --0.0174658914685 --0.0178902177779 -0.0195993756659 -0.0719238160707 -0.0344832661036 --0.0358616891662 --0.0292380783172 --0.0334933909866 -0.00595462520243 -0.0754556638328 --0.000972545258845 --0.0100170422751 diff --git a/examples/snap/Mo_Chen_PRM2017.snapcoeff b/examples/snap/Mo_Chen_PRM2017.snapcoeff new file mode 120000 index 0000000000..b2dfa99a06 --- /dev/null +++ b/examples/snap/Mo_Chen_PRM2017.snapcoeff @@ -0,0 +1 @@ +../../potentials/Mo_Chen_PRM2017.snapcoeff \ No newline at end of file diff --git a/examples/snap/Mo_Chen_PRM2017.snapparam b/examples/snap/Mo_Chen_PRM2017.snapparam deleted file mode 100644 index e618bc1dd4..0000000000 --- a/examples/snap/Mo_Chen_PRM2017.snapparam +++ /dev/null @@ -1,4 +0,0 @@ -# DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) -# Generated by Materials Virtual Lab -rcutfac 4.615858 -twojmax 6 diff --git a/examples/snap/Mo_Chen_PRM2017.snapparam b/examples/snap/Mo_Chen_PRM2017.snapparam new file mode 120000 index 0000000000..b1dc628e01 --- /dev/null +++ b/examples/snap/Mo_Chen_PRM2017.snapparam @@ -0,0 +1 @@ +../../potentials/Mo_Chen_PRM2017.snapparam \ No newline at end of file diff --git a/examples/snap/Ta06A.snap b/examples/snap/Ta06A.snap deleted file mode 100644 index edcc002524..0000000000 --- a/examples/snap/Ta06A.snap +++ /dev/null @@ -1,17 +0,0 @@ -# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) - -# Definition of SNAP potential Ta_Cand06A -# Assumes 1 LAMMPS atom type - -variable zblcutinner equal 4 -variable zblcutouter equal 4.8 -variable zblz equal 73 - -# Specify hybrid with SNAP, ZBL - -pair_style hybrid/overlay & -zbl ${zblcutinner} ${zblcutouter} & -snap -pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta - diff --git a/examples/snap/Ta06A.snap b/examples/snap/Ta06A.snap new file mode 120000 index 0000000000..cc26b99d64 --- /dev/null +++ b/examples/snap/Ta06A.snap @@ -0,0 +1 @@ +../../potentials/Ta06A.snap \ No newline at end of file diff --git a/examples/snap/Ta06A.snapcoeff b/examples/snap/Ta06A.snapcoeff deleted file mode 100644 index ad2dfa4bc5..0000000000 --- a/examples/snap/Ta06A.snapcoeff +++ /dev/null @@ -1,37 +0,0 @@ -# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) - -# LAMMPS SNAP coefficients for Ta_Cand06A - -1 31 -Ta 0.5 1 --2.92477 --0.01137 --0.00775 --0.04907 --0.15047 -0.09157 -0.05590 -0.05785 --0.11615 --0.17122 --0.10583 -0.03941 --0.11284 -0.03939 --0.07331 --0.06582 --0.09341 --0.10587 --0.15497 -0.04820 -0.00205 -0.00060 --0.04898 --0.05084 --0.03371 --0.01441 --0.01501 --0.00599 --0.06373 -0.03965 -0.01072 diff --git a/examples/snap/Ta06A.snapcoeff b/examples/snap/Ta06A.snapcoeff new file mode 120000 index 0000000000..311d582ec6 --- /dev/null +++ b/examples/snap/Ta06A.snapcoeff @@ -0,0 +1 @@ +../../potentials/Ta06A.snapcoeff \ No newline at end of file diff --git a/examples/snap/Ta06A.snapparam b/examples/snap/Ta06A.snapparam deleted file mode 100644 index 283629d658..0000000000 --- a/examples/snap/Ta06A.snapparam +++ /dev/null @@ -1,15 +0,0 @@ -# DATE: 2014-09-05 CONTRIBUTOR: Aidan Thompson athomps@sandia.gov CITATION: Thompson, Swiler, Trott, Foiles and Tucker, arxiv.org, 1409.3880 (2014) - -# LAMMPS SNAP parameters for Ta_Cand06A - -# required -rcutfac 4.67637 -twojmax 6 - -# optional - -rfac0 0.99363 -rmin0 0 -diagonalstyle 3 -bzeroflag 0 -quadraticflag 0 diff --git a/examples/snap/Ta06A.snapparam b/examples/snap/Ta06A.snapparam new file mode 120000 index 0000000000..e697069cba --- /dev/null +++ b/examples/snap/Ta06A.snapparam @@ -0,0 +1 @@ +../../potentials/Ta06A.snapparam \ No newline at end of file diff --git a/examples/snap/W_2940_2017_2.snap b/examples/snap/W_2940_2017_2.snap deleted file mode 100644 index 04b8d58094..0000000000 --- a/examples/snap/W_2940_2017_2.snap +++ /dev/null @@ -1,16 +0,0 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] -# -# Definition of SNAP+ZBL potential. -variable zblcutinner equal 4 -variable zblcutouter equal 4.8 -variable zblz equal 74 - -# Specify hybrid with SNAP and ZBL - -pair_style hybrid/overlay & -zbl ${zblcutinner} ${zblcutouter} & -snap -pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W - -#Nomenclature on the snap files are Element_DakotaID_Year_Month diff --git a/examples/snap/W_2940_2017_2.snap b/examples/snap/W_2940_2017_2.snap new file mode 120000 index 0000000000..907ee91562 --- /dev/null +++ b/examples/snap/W_2940_2017_2.snap @@ -0,0 +1 @@ +../../potentials/W_2940_2017_2.snap \ No newline at end of file diff --git a/examples/snap/W_2940_2017_2.snapcoeff b/examples/snap/W_2940_2017_2.snapcoeff deleted file mode 100644 index dcfea3feaf..0000000000 --- a/examples/snap/W_2940_2017_2.snapcoeff +++ /dev/null @@ -1,62 +0,0 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] -# -# LAMMPS SNAP coefficients for W - -1 56 -W 0.5 1 - 0.781170857801 - -0.001794941735 - -0.016628679036 - -0.066625537037 - -0.073716343967 - -0.062913923923 - 0.032552694672 - -0.134901744419 - -0.075076334103 - -0.148558616547 - -0.140808831101 - -0.166749145704 - -0.047487675984 - -0.049892090603 - -0.032483739965 - -0.114766534860 - -0.106759718242 - -0.125894850485 - -0.103409735225 - -0.095247335447 - -0.061998736346 - -0.053895610976 - -0.010799734206 - -0.011644828900 - -0.028316826924 - 0.011176085541 - 0.064619474684 - -0.023886279996 - -0.004099224312 - -0.056084222496 - -0.035551497650 - -0.056678501024 - -0.004905851656 - -0.015701146162 - -0.008462280779 - 0.016429018676 - 0.032432633993 - -0.010805361272 - -0.014841893457 - 0.019414134562 - -0.008112452759 - -0.002700775447 - 0.007032887063 - -0.009706065042 - 0.008385967833 - 0.028606085876 - -0.007003591067 - 0.006467260152 - -0.006666986361 - 0.029243285316 - 0.002477673872 - -0.000199497504 - 0.004068954075 - 0.006036129972 - -0.013010633924 - -0.008314173699 diff --git a/examples/snap/W_2940_2017_2.snapcoeff b/examples/snap/W_2940_2017_2.snapcoeff new file mode 120000 index 0000000000..5eff37c936 --- /dev/null +++ b/examples/snap/W_2940_2017_2.snapcoeff @@ -0,0 +1 @@ +../../potentials/W_2940_2017_2.snapcoeff \ No newline at end of file diff --git a/examples/snap/W_2940_2017_2.snapparam b/examples/snap/W_2940_2017_2.snapparam deleted file mode 100644 index 27ab61a266..0000000000 --- a/examples/snap/W_2940_2017_2.snapparam +++ /dev/null @@ -1,13 +0,0 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] -# -# required -rcutfac 4.73442 -twojmax 8 - -# optional - -rfac0 0.99363 -rmin0 0 -diagonalstyle 3 -bzeroflag 0 -quadraticflag 0 diff --git a/examples/snap/W_2940_2017_2.snapparam b/examples/snap/W_2940_2017_2.snapparam new file mode 120000 index 0000000000..af9dec2e52 --- /dev/null +++ b/examples/snap/W_2940_2017_2.snapparam @@ -0,0 +1 @@ +../../potentials/W_2940_2017_2.snapparam \ No newline at end of file diff --git a/examples/snap/W_2940_2017_2_He_JW2013.snap b/examples/snap/W_2940_2017_2_He_JW2013.snap deleted file mode 100644 index cb70916ec4..0000000000 --- a/examples/snap/W_2940_2017_2_He_JW2013.snap +++ /dev/null @@ -1,17 +0,0 @@ -# DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. "Quantum-Accurate Molecular Dynamics Potential for Tungsten" arXiv:1702.07042 [physics.comp-ph] -# -# Definition of SNAP+ZBL+Tabulated potential. -variable zblcutinner equal 4 -variable zblcutouter equal 4.8 -variable zblz equal 74 - -# Specify hybrid with SNAP and ZBL - -pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 -pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL -pair_coeff 2 2 table 1 He_He_JW2013.table HeHe -pair_coeff 1 2 table 2 W_He_JW2013.table WHe -#Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here -#This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. - diff --git a/examples/snap/W_2940_2017_2_He_JW2013.snap b/examples/snap/W_2940_2017_2_He_JW2013.snap new file mode 120000 index 0000000000..5e0f21ab3b --- /dev/null +++ b/examples/snap/W_2940_2017_2_He_JW2013.snap @@ -0,0 +1 @@ +../../potentials/W_2940_2017_2_He_JW2013.snap \ No newline at end of file diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 b/examples/snap/log.27Nov18.snap.Mo_Chen.g++.1 similarity index 86% rename from examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 rename to examples/snap/log.27Nov18.snap.Mo_Chen.g++.1 index c5e0f6abab..0ca8406d10 100644 --- a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.1 +++ b/examples/snap/log.27Nov18.snap.Mo_Chen.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000223637 secs + Time spent = 0.00029707 secs mass 1 183.84 @@ -95,20 +94,20 @@ Step Temp E_pair E_mol TotEng Press 80 87.224916 -22.378685 0 -22.367499 10247.68 90 62.623892 -22.37553 0 -22.367498 11250.067 100 45.9103 -22.373386 0 -22.367498 12011.726 -Loop time of 3.3917 on 1 procs for 100 steps with 128 atoms +Loop time of 7.00873 on 1 procs for 100 steps with 128 atoms -Performance: 1.274 ns/day, 18.843 hours/ns, 29.484 timesteps/s +Performance: 0.616 ns/day, 38.937 hours/ns, 14.268 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.3906 | 3.3906 | 3.3906 | 0.0 | 99.97 +Pair | 7.0068 | 7.0068 | 7.0068 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00039721 | 0.00039721 | 0.00039721 | 0.0 | 0.01 -Output | 0.00023007 | 0.00023007 | 0.00023007 | 0.0 | 0.01 -Modify | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.01 -Other | | 0.0002868 | | | 0.01 +Comm | 0.00083661 | 0.00083661 | 0.00083661 | 0.0 | 0.01 +Output | 0.00025535 | 0.00025535 | 0.00025535 | 0.0 | 0.00 +Modify | 0.00034285 | 0.00034285 | 0.00034285 | 0.0 | 0.00 +Other | | 0.0005035 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -124,4 +123,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:03 +Total wall time: 0:00:07 diff --git a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 b/examples/snap/log.27Nov18.snap.Mo_Chen.g++.4 similarity index 85% rename from examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 rename to examples/snap/log.27Nov18.snap.Mo_Chen.g++.4 index c25f1f5530..a8c3d6858c 100644 --- a/examples/snap/log.20Apr18.snap.Mo_Chen.g++.4 +++ b/examples/snap/log.27Nov18.snap.Mo_Chen.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (12.64 12.64 12.64) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000277281 secs + Time spent = 0.000289917 secs mass 1 183.84 @@ -95,20 +94,20 @@ Step Temp E_pair E_mol TotEng Press 80 83.449257 -22.378201 0 -22.367499 10047.619 90 58.862643 -22.375048 0 -22.367498 11012.233 100 42.41931 -22.372939 0 -22.367498 11740.641 -Loop time of 1.91636 on 4 procs for 100 steps with 128 atoms +Loop time of 2.15419 on 4 procs for 100 steps with 128 atoms -Performance: 2.254 ns/day, 10.646 hours/ns, 52.182 timesteps/s -97.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 2.005 ns/day, 11.968 hours/ns, 46.421 timesteps/s +92.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.8147 | 1.8411 | 1.8875 | 2.1 | 96.07 +Pair | 1.7677 | 1.9028 | 1.9897 | 6.2 | 88.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.022276 | 0.069629 | 0.095057 | 10.7 | 3.63 -Output | 0.00032496 | 0.00065821 | 0.0016179 | 0.0 | 0.03 -Modify | 0.00019503 | 0.00020915 | 0.00023341 | 0.0 | 0.01 -Other | | 0.00481 | | | 0.25 +Comm | 0.15367 | 0.24295 | 0.38029 | 17.6 | 11.28 +Output | 0.00034404 | 0.0012512 | 0.0017219 | 1.6 | 0.06 +Modify | 0.00018859 | 0.00021273 | 0.00023699 | 0.0 | 0.01 +Other | | 0.007011 | | | 0.33 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -124,4 +123,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/snap/log.20Apr18.snap.Ta06A.g++.1 b/examples/snap/log.27Nov18.snap.Ta06A.g++.1 similarity index 86% rename from examples/snap/log.20Apr18.snap.Ta06A.g++.1 rename to examples/snap/log.27Nov18.snap.Ta06A.g++.1 index d2296852a0..76cdc8641a 100644 --- a/examples/snap/log.20Apr18.snap.Ta06A.g++.1 +++ b/examples/snap/log.27Nov18.snap.Ta06A.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000328064 secs + Time spent = 0.000350714 secs mass 1 180.88 @@ -117,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 124.04276 -11.829003 0 -11.813094 1537.703 90 97.37622 -11.825582 0 -11.813094 1734.9662 100 75.007873 -11.822714 0 -11.813094 1930.8005 -Loop time of 2.53266 on 1 procs for 100 steps with 128 atoms +Loop time of 5.03244 on 1 procs for 100 steps with 128 atoms -Performance: 1.706 ns/day, 14.070 hours/ns, 39.484 timesteps/s -99.5% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.858 ns/day, 27.958 hours/ns, 19.871 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5313 | 2.5313 | 2.5313 | 0.0 | 99.95 +Pair | 5.0308 | 5.0308 | 5.0308 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00051379 | 0.00051379 | 0.00051379 | 0.0 | 0.02 -Output | 0.00023317 | 0.00023317 | 0.00023317 | 0.0 | 0.01 -Modify | 0.00023675 | 0.00023675 | 0.00023675 | 0.0 | 0.01 -Other | | 0.0003583 | | | 0.01 +Comm | 0.00070858 | 0.00070858 | 0.00070858 | 0.0 | 0.01 +Output | 0.00024676 | 0.00024676 | 0.00024676 | 0.0 | 0.00 +Modify | 0.0002749 | 0.0002749 | 0.0002749 | 0.0 | 0.01 +Other | | 0.0004299 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -146,4 +145,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:02 +Total wall time: 0:00:05 diff --git a/examples/snap/log.20Apr18.snap.Ta06A.g++.4 b/examples/snap/log.27Nov18.snap.Ta06A.g++.4 similarity index 87% rename from examples/snap/log.20Apr18.snap.Ta06A.g++.4 rename to examples/snap/log.27Nov18.snap.Ta06A.g++.4 index 4d26481d5d..4cc5b82c9b 100644 --- a/examples/snap/log.20Apr18.snap.Ta06A.g++.4 +++ b/examples/snap/log.27Nov18.snap.Ta06A.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000288486 secs + Time spent = 0.000299692 secs mass 1 180.88 @@ -117,20 +116,20 @@ Step Temp E_pair E_mol TotEng Press 80 121.80051 -11.828715 0 -11.813094 1627.6911 90 95.262635 -11.825311 0 -11.813094 1812.9327 100 73.194645 -11.822481 0 -11.813094 1995.2199 -Loop time of 1.3621 on 4 procs for 100 steps with 128 atoms +Loop time of 1.4959 on 4 procs for 100 steps with 128 atoms -Performance: 3.172 ns/day, 7.567 hours/ns, 73.416 timesteps/s -98.7% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 2.888 ns/day, 8.311 hours/ns, 66.850 timesteps/s +94.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.2867 | 1.309 | 1.35 | 2.1 | 96.10 +Pair | 1.2973 | 1.3263 | 1.3444 | 1.6 | 88.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0096083 | 0.050652 | 0.072999 | 10.9 | 3.72 -Output | 0.00031447 | 0.00060236 | 0.0014303 | 0.0 | 0.04 -Modify | 0.00014234 | 0.00016212 | 0.00018811 | 0.0 | 0.01 -Other | | 0.001728 | | | 0.13 +Comm | 0.14155 | 0.16475 | 0.19518 | 5.0 | 11.01 +Output | 0.00055361 | 0.0006234 | 0.00078511 | 0.0 | 0.04 +Modify | 0.00016427 | 0.00020635 | 0.00032949 | 0.0 | 0.01 +Other | | 0.004009 | | | 0.27 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/snap/log.20Apr18.snap.W.2940.g++.1 b/examples/snap/log.27Nov18.snap.W.2940.g++.1 similarity index 87% rename from examples/snap/log.20Apr18.snap.W.2940.g++.1 rename to examples/snap/log.27Nov18.snap.W.2940.g++.1 index 19b2bfb40d..d2c540c709 100644 --- a/examples/snap/log.20Apr18.snap.W.2940.g++.1 +++ b/examples/snap/log.27Nov18.snap.W.2940.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000190258 secs + Time spent = 0.000316143 secs mass 1 183.84 @@ -116,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press 80 58.605244 -10.997364 0 -10.989848 11289.914 90 39.754503 -10.994946 0 -10.989848 11824.945 100 32.524085 -10.994019 0 -10.989848 11932.118 -Loop time of 9.69738 on 1 procs for 100 steps with 128 atoms +Loop time of 18.7678 on 1 procs for 100 steps with 128 atoms -Performance: 0.445 ns/day, 53.874 hours/ns, 10.312 timesteps/s +Performance: 0.230 ns/day, 104.265 hours/ns, 5.328 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 9.6961 | 9.6961 | 9.6961 | 0.0 | 99.99 +Pair | 18.766 | 18.766 | 18.766 | 0.0 | 99.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00044036 | 0.00044036 | 0.00044036 | 0.0 | 0.00 -Output | 0.00024843 | 0.00024843 | 0.00024843 | 0.0 | 0.00 -Modify | 0.00023937 | 0.00023937 | 0.00023937 | 0.0 | 0.00 -Other | | 0.0003347 | | | 0.00 +Comm | 0.00081968 | 0.00081968 | 0.00081968 | 0.0 | 0.00 +Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00 +Modify | 0.0003283 | 0.0003283 | 0.0003283 | 0.0 | 0.00 +Other | | 0.0005233 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -145,4 +144,4 @@ Ave neighs/atom = 58 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:09 +Total wall time: 0:00:18 diff --git a/examples/snap/log.20Apr18.snap.W.2940.g++.4 b/examples/snap/log.27Nov18.snap.W.2940.g++.4 similarity index 87% rename from examples/snap/log.20Apr18.snap.W.2940.g++.4 rename to examples/snap/log.27Nov18.snap.W.2940.g++.4 index dfa63fc6ea..cdd063de28 100644 --- a/examples/snap/log.20Apr18.snap.W.2940.g++.4 +++ b/examples/snap/log.27Nov18.snap.W.2940.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000309944 secs + Time spent = 0.000297546 secs mass 1 183.84 @@ -116,20 +115,20 @@ Step Temp E_pair E_mol TotEng Press 80 56.127265 -10.997046 0 -10.989848 11551.687 90 38.025013 -10.994724 0 -10.989847 12069.936 100 31.768127 -10.993922 0 -10.989847 12145.648 -Loop time of 5.15615 on 4 procs for 100 steps with 128 atoms +Loop time of 5.38055 on 4 procs for 100 steps with 128 atoms -Performance: 0.838 ns/day, 28.645 hours/ns, 19.394 timesteps/s -98.9% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.803 ns/day, 29.892 hours/ns, 18.585 timesteps/s +96.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 5.0497 | 5.0762 | 5.092 | 0.8 | 98.45 +Pair | 4.8254 | 5.0245 | 5.2817 | 7.7 | 93.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.060802 | 0.07661 | 0.10305 | 6.1 | 1.49 -Output | 0.00040722 | 0.00078458 | 0.0018959 | 0.0 | 0.02 -Modify | 0.0002389 | 0.00024962 | 0.00027442 | 0.0 | 0.00 -Other | | 0.002315 | | | 0.04 +Comm | 0.093845 | 0.34915 | 0.5466 | 29.1 | 6.49 +Output | 0.00032616 | 0.0011846 | 0.0037167 | 4.2 | 0.02 +Modify | 0.00022507 | 0.00025326 | 0.0002687 | 0.0 | 0.00 +Other | | 0.005432 | | | 0.10 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 b/examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.1 similarity index 87% rename from examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 rename to examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.1 index 3f40936308..7d49043aa0 100644 --- a/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.1 +++ b/examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.1 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000431538 secs + Time spent = 0.000426054 secs mass 1 183.84 mass 2 4.0026 @@ -75,11 +74,11 @@ SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:481) + Should only be flagged at inflection points (src/pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:481) + Should only be flagged at inflection points (src/pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -151,20 +150,20 @@ Step Temp E_pair E_mol TotEng Press 80 85.903126 -10.410645 0 -10.399628 857.74986 90 65.223651 -10.407993 0 -10.399628 1494.2746 100 59.833542 -10.407302 0 -10.399628 1938.9164 -Loop time of 8.902 on 1 procs for 100 steps with 128 atoms +Loop time of 17.6435 on 1 procs for 100 steps with 128 atoms -Performance: 0.485 ns/day, 49.456 hours/ns, 11.233 timesteps/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 0.245 ns/day, 98.019 hours/ns, 5.668 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 8.9002 | 8.9002 | 8.9002 | 0.0 | 99.98 -Neigh | 0.00043058 | 0.00043058 | 0.00043058 | 0.0 | 0.00 -Comm | 0.00045776 | 0.00045776 | 0.00045776 | 0.0 | 0.01 -Output | 0.00025344 | 0.00025344 | 0.00025344 | 0.0 | 0.00 -Modify | 0.00022483 | 0.00022483 | 0.00022483 | 0.0 | 0.00 -Other | | 0.0003953 | | | 0.00 +Pair | 17.641 | 17.641 | 17.641 | 0.0 | 99.99 +Neigh | 0.00054359 | 0.00054359 | 0.00054359 | 0.0 | 0.00 +Comm | 0.00080729 | 0.00080729 | 0.00080729 | 0.0 | 0.00 +Output | 0.00026512 | 0.00026512 | 0.00026512 | 0.0 | 0.00 +Modify | 0.00033879 | 0.00033879 | 0.00033879 | 0.0 | 0.00 +Other | | 0.0005448 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -180,4 +179,4 @@ Ave neighs/atom = 53.5156 Neighbor list builds = 1 Dangerous builds = 0 -Total wall time: 0:00:09 +Total wall time: 0:00:17 diff --git a/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 b/examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.4 similarity index 88% rename from examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 rename to examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.4 index 4ec85a63d0..05db710266 100644 --- a/examples/snap/log.20Apr18.snap.hybrid.WSNAP.HePair.g++.4 +++ b/examples/snap/log.27Nov18.snap.hybrid.WSNAP.HePair.g++.4 @@ -1,5 +1,4 @@ -LAMMPS (20 Apr 2018) -OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) +LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Demonstrate SNAP Ta potential @@ -33,7 +32,7 @@ Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms - Time spent = 0.000274658 secs + Time spent = 0.000303984 secs mass 1 183.84 mass 2 4.0026 @@ -75,11 +74,11 @@ SNAP keyword quadraticflag 0 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:481) + Should only be flagged at inflection points (src/pair_table.cpp:481) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. - Should only be flagged at inflection points (../pair_table.cpp:481) + Should only be flagged at inflection points (src/pair_table.cpp:481) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. @@ -151,20 +150,20 @@ Step Temp E_pair E_mol TotEng Press 80 79.985938 -10.409886 0 -10.399628 2392.1106 90 62.568933 -10.407652 0 -10.399628 3141.7027 100 56.697933 -10.406899 0 -10.399628 3583.9538 -Loop time of 4.82103 on 4 procs for 100 steps with 128 atoms +Loop time of 4.7853 on 4 procs for 100 steps with 128 atoms -Performance: 0.896 ns/day, 26.783 hours/ns, 20.742 timesteps/s -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads +Performance: 0.903 ns/day, 26.585 hours/ns, 20.897 timesteps/s +97.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 4.4837 | 4.6734 | 4.7605 | 5.2 | 96.94 +Pair | 4.394 | 4.5813 | 4.7463 | 5.9 | 95.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.057389 | 0.14453 | 0.33421 | 29.4 | 3.00 -Output | 0.00038719 | 0.00073916 | 0.0017841 | 0.0 | 0.02 -Modify | 0.00018716 | 0.00022203 | 0.00026417 | 0.0 | 0.00 -Other | | 0.002119 | | | 0.04 +Comm | 0.035261 | 0.19515 | 0.38629 | 28.5 | 4.08 +Output | 0.00031662 | 0.00060844 | 0.0014563 | 0.0 | 0.01 +Modify | 0.00018692 | 0.0001924 | 0.00020123 | 0.0 | 0.00 +Other | | 0.008012 | | | 0.17 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/srd/log.5Oct16.srd.mixture.g++.1 b/examples/srd/log.27Nov18.srd.mixture.g++.1 similarity index 85% rename from examples/srd/log.5Oct16.srd.mixture.g++.1 rename to examples/srd/log.27Nov18.srd.mixture.g++.1 index d7c9fe5bab..6207a7948e 100644 --- a/examples/srd/log.5Oct16.srd.mixture.g++.1 +++ b/examples/srd/log.27Nov18.srd.mixture.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d SRD test: big + small particles units lj @@ -16,6 +17,7 @@ Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) 1 by 1 by 1 MPI processor grid create_atoms 1 region box Created 100 atoms + Time spent = 0.000496387 secs set type 1 mass 1.0 100 settings made for mass set type 1 diameter 1.0 @@ -40,30 +42,35 @@ fix 2 all enforce2d run 1000 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 2 -Memory usage per processor = 3.60175 Mbytes + binsize = 1.4, bins = 12 12 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.173 | 4.173 | 4.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -0.54272 0 0.88288 -0.041088 1000 1.8791467 -0.97185784 0 0.8884974 0.61487656 -Loop time of 0.0151019 on 1 procs for 1000 steps with 100 atoms +Loop time of 0.0159547 on 1 procs for 1000 steps with 100 atoms -Performance: 28605653.879 tau/day, 66216.791 timesteps/s -105.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 27076604.970 tau/day, 62677.326 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0079689 | 0.0079689 | 0.0079689 | 0.0 | 52.77 -Neigh | 0.0030537 | 0.0030537 | 0.0030537 | 0.0 | 20.22 -Comm | 0.001416 | 0.001416 | 0.001416 | 0.0 | 9.38 -Output | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 | 0.0 | 0.04 -Modify | 0.001749 | 0.001749 | 0.001749 | 0.0 | 11.58 -Other | | 0.0009084 | | | 6.01 +Pair | 0.0072021 | 0.0072021 | 0.0072021 | 0.0 | 45.14 +Neigh | 0.0030136 | 0.0030136 | 0.0030136 | 0.0 | 18.89 +Comm | 0.0022571 | 0.0022571 | 0.0022571 | 0.0 | 14.15 +Output | 9.5367e-06 | 9.5367e-06 | 9.5367e-06 | 0.0 | 0.06 +Modify | 0.0021653 | 0.0021653 | 0.0021653 | 0.0 | 13.57 +Other | | 0.001307 | | | 8.19 Nlocal: 100 ave 100 max 100 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -89,6 +96,7 @@ lattice sq 85.0 Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 create_atoms 2 region plane Created 21316 atoms + Time spent = 0.0168567 secs set type 2 mass 0.01 21316 settings made for mass set type 2 diameter 0.0 @@ -109,13 +117,23 @@ pair_coeff 1 2 0.0 1.0 0.5 delete_atoms overlap 0.5 small big Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 2 -WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:278) + binsize = 1.4, bins = 12 12 2 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:305) Deleted 6700 atoms, new total = 14716 # SRD run @@ -151,7 +169,7 @@ variable ebig equal etotal*atoms/count(big) thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) thermo 100 #dump 1 all atom 250 dump.srd.mixture @@ -173,18 +191,23 @@ SRD info: SRD per actual grid cell = 4.86648 SRD viscosity = 0.463448 big/SRD mass density ratio = 2.12808 -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2884) +WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2888) # of rescaled SRD velocities = 0 ave/max small velocity = 13.2944 24.262 ave/max big velocity = 1.69284 5.10989 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 2 -Memory usage per processor = 14.7783 Mbytes + binsize = 1.4, bins = 12 12 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.84 | 15.84 | 15.84 Mbytes Step Temp f_2[7] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487656 0 0 0 0 0 0 0 0 0 100 1.1596877 3969 0.00179671 -0.88368701 0.26440385 0.85824547 7578 83 83 0 14 12996 3000 1.0041859 0 @@ -237,20 +260,20 @@ Step Temp f_2[7] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] 4800 1.2169028 3969 0.0010831546 -1.0453368 0.15939704 0.42728069 7444 80 80 0 1560 12996 2997 1.0300677 0 4900 0.90968786 3969 -0.0010022199 -1.0480777 -0.14748667 0.37681568 7563 88 88 0 1592 12996 2997 1.0257714 0 5000 1.0856525 3969 0.0001301746 -1.0556395 0.019156494 0.55496941 7439 78 78 0 1633 12996 3008 1.0343075 0 -Loop time of 2.9124 on 1 procs for 5000 steps with 14716 atoms +Loop time of 3.59613 on 1 procs for 5000 steps with 14716 atoms -Performance: 148331.176 tau/day, 1716.796 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 120129.150 tau/day, 1390.384 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.041905 | 0.041905 | 0.041905 | 0.0 | 1.44 -Neigh | 0.0063758 | 0.0063758 | 0.0063758 | 0.0 | 0.22 -Comm | 0.027464 | 0.027464 | 0.027464 | 0.0 | 0.94 -Output | 0.0026662 | 0.0026662 | 0.0026662 | 0.0 | 0.09 -Modify | 2.7808 | 2.7808 | 2.7808 | 0.0 | 95.48 -Other | | 0.0532 | | | 1.83 +Pair | 0.043031 | 0.043031 | 0.043031 | 0.0 | 1.20 +Neigh | 0.0068874 | 0.0068874 | 0.0068874 | 0.0 | 0.19 +Comm | 0.035111 | 0.035111 | 0.035111 | 0.0 | 0.98 +Output | 0.0043986 | 0.0043986 | 0.0043986 | 0.0 | 0.12 +Modify | 3.46 | 3.46 | 3.46 | 0.0 | 96.22 +Other | | 0.04668 | | | 1.30 Nlocal: 14716 ave 14716 max 14716 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -266,4 +289,4 @@ Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:03 +Total wall time: 0:00:04 diff --git a/examples/srd/log.27Nov18.srd.mixture.g++.4 b/examples/srd/log.27Nov18.srd.mixture.g++.4 new file mode 100644 index 0000000000..835de98274 --- /dev/null +++ b/examples/srd/log.27Nov18.srd.mixture.g++.4 @@ -0,0 +1,292 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# 2d SRD test: big + small particles + +units lj +atom_style sphere +atom_modify first big +dimension 2 + +# create big particles with sigma 1.0 + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region box block 0 10 0 10 -0.5 0.5 +create_box 2 box +Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) + 2 by 2 by 1 MPI processor grid +create_atoms 1 region box +Created 100 atoms + Time spent = 0.000455379 secs +set type 1 mass 1.0 + 100 settings made for mass +set type 1 diameter 1.0 + 100 settings made for diameter + +group big type 1 +100 atoms in group big +velocity big create 1.44 87287 loop geom + +# equilibrate big particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +fix 1 big nve +fix 2 all enforce2d + +run 1000 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.171 | 4.171 | 4.171 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.44 -0.54272 0 0.88288 -0.041088 + 1000 1.8791467 -0.97185784 0 0.8884974 0.61487657 +Loop time of 0.0164104 on 4 procs for 1000 steps with 100 atoms + +Performance: 26324848.583 tau/day, 60937.149 timesteps/s +94.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0017555 | 0.0019422 | 0.0022526 | 0.4 | 11.84 +Neigh | 0.00085735 | 0.00090593 | 0.00096583 | 0.0 | 5.52 +Comm | 0.0088477 | 0.0094896 | 0.0098495 | 0.4 | 57.83 +Output | 2.1935e-05 | 2.3127e-05 | 2.6226e-05 | 0.0 | 0.14 +Modify | 0.00074744 | 0.00088817 | 0.0012014 | 0.0 | 5.41 +Other | | 0.003161 | | | 19.26 + +Nlocal: 25 ave 26 max 23 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 47 ave 48 max 46 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 114.75 ave 124 max 100 min +Histogram: 1 0 0 0 0 1 0 0 0 2 + +Total # of neighbors = 459 +Ave neighs/atom = 4.59 +Neighbor list builds = 129 +Dangerous builds = 0 + +unfix 1 +unfix 2 + +# add small particles as hi density lattice + +lattice sq 0.4 +Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 +region plane block 0 10 0 10 -0.001 0.001 +lattice sq 85.0 +Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 +create_atoms 2 region plane +Created 21316 atoms + Time spent = 0.00417233 secs +set type 2 mass 0.01 + 21316 settings made for mass +set type 2 diameter 0.0 + 21316 settings made for diameter + +group small type 2 +21316 atoms in group small + +velocity small create 1.0 593849 loop geom + +# delete overlaps +# must set 1-2 cutoff to non-zero value + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.5 + +delete_atoms overlap 0.5 small big +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 2 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) command delete_atoms, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/2d + bin: standard + (2) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +WARNING: Delete_atoms cutoff > minimum neighbor cutoff (src/delete_atoms.cpp:305) +Deleted 6700 atoms, new total = 14716 + +# SRD run + +reset_timestep 0 + +neighbor 0.3 bin +neigh_modify delay 0 every 1 check yes + +comm_modify mode multi group big vel yes +neigh_modify include big + +# no pairwise interactions with small particles + +pair_style lj/cut 2.5 +pair_coeff 1 1 1.0 1.0 +pair_coeff 2 2 0.0 1.0 0.0 +pair_coeff 1 2 0.0 1.0 0.0 + +# use fix SRD to push small particles out from inside big ones + +timestep 0.001 + +fix 1 big nve +fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip +fix 3 all enforce2d + +# diagnostics + +compute tbig big temp +variable pebig equal pe*atoms/count(big) +variable ebig equal etotal*atoms/count(big) +thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] + +thermo_modify temp tbig +WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) +thermo 100 + +#dump 1 all atom 250 dump.srd.mixture + +#dump 2 all image 250 image.*.jpg type type zoom 1.6 +#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2 + +#dump 3 all movie 250 movie.mpg type type zoom 1.6 +#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2 + +run 5000 +SRD info: + SRD/big particles = 14616 100 + big particle diameter max/min = 0.88 0.88 + SRD temperature & lamda = 1 0.2 + SRD max distance & max velocity = 0.8 40 + SRD grid counts: 63 63 1 + SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 + SRD per actual grid cell = 4.86648 + SRD viscosity = 0.463448 + big/SRD mass density ratio = 2.12808 +WARNING: Fix srd grid size > 1/4 of big particle diameter (src/SRD/fix_srd.cpp:2888) + # of rescaled SRD velocities = 0 + ave/max small velocity = 13.2944 24.262 + ave/max big velocity = 1.69284 5.10989 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 2 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/2d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.921 | 5.925 | 5.93 Mbytes +Step Temp f_2[7] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] + 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0 + 100 1.4044369 3969 0.0030633093 -0.93959598 0.4507966 0.78900119 7464 99 99 0 17 22500 3005 1.028131 0 + 200 1.1569383 3969 0.0010543995 -0.99020352 0.15516543 0.50132981 7393 82 82 0 43 22500 2996 1.014347 0 + 300 0.97802835 3969 -0.00019991154 -0.99766705 -0.029418982 0.35789515 7411 90 90 0 84 22500 3001 1.0213725 0 + 400 1.0992982 3969 0.00055034756 -1.007316 0.080989146 0.35177983 7443 78 78 0 107 22500 2993 1.0451641 0 + 500 1.0436705 3969 -7.4779704e-05 -1.0442384 -0.011004581 0.15132448 7504 94 94 0 141 22500 3007 1.0236992 0 + 600 1.0216461 3969 -0.00032426678 -1.0591487 -0.047719099 0.2200765 7508 111 111 0 179 22500 3007 1.0304838 0 + 700 1.1491339 3969 0.0012328743 -0.95621278 0.18142978 0.80670059 7448 95 95 0 201 22500 2978 1.0099113 0 + 800 1.0332166 3969 -0.00040684239 -1.0827554 -0.059870926 0.35939225 7453 113 113 0 235 22500 3024 1.0141565 0 + 900 1.0652211 3969 -6.1337025e-06 -1.0554715 -0.00090263566 0.51460169 7447 97 97 0 259 22500 2982 1.0192735 0 + 1000 0.92834993 3969 -0.00067681883 -1.0186671 -0.09960066 0.738738 7328 78 78 0 286 22500 2999 1.023841 0 + 1100 1.0386338 3969 -0.00018904027 -1.0560666 -0.027819166 0.57129719 7449 96 96 0 325 22500 3012 1.0373885 0 + 1200 0.92218024 3969 -0.00077989365 -1.0277276 -0.11476915 0.48613467 7507 100 100 0 355 22500 3003 1.0254889 0 + 1300 1.1835318 3969 0.00096836748 -1.0291915 0.14250496 0.62935386 7439 92 92 0 384 22500 2993 1.0289037 0 + 1400 1.0895805 3969 0.00022072203 -1.0462033 0.032481455 0.49130771 7492 80 80 0 426 22500 3005 1.0083895 0 + 1500 1.0713283 3969 0.00042008247 -0.99879571 0.061819337 0.63979877 7498 87 87 0 457 22500 3000 1.0009934 0 + 1600 0.97815063 3969 -0.0005425653 -1.048213 -0.079843909 0.3604669 7533 105 105 0 492 22500 3004 1.0375508 0 + 1700 1.1626991 3969 0.00048969595 -1.0790084 0.072063656 0.36261544 7493 87 87 0 519 22500 3014 1.0151507 0 + 1800 0.91077627 3969 -0.0012059339 -1.0791337 -0.17746523 0.14204134 7553 77 77 0 554 22500 3001 1.0393648 0 + 1900 1.0736324 3969 0.00048053532 -0.99218049 0.070715578 0.56468307 7660 96 96 0 579 22500 2990 1.0071005 0 + 2000 1.0529119 3969 -0.00019827686 -1.0715612 -0.029178422 0.28111275 7561 93 93 0 630 22500 3020 1.0201426 0 + 2100 0.9995282 3969 -0.00066769217 -1.0877905 -0.09825758 0.22578496 7488 83 83 0 671 22500 2993 1.0246877 0 + 2200 1.1492521 3969 0.00093648659 -0.99994625 0.13781337 0.66214341 7481 97 97 0 699 22500 2999 1.0420787 0 + 2300 1.174939 3969 0.00098605988 -1.0180811 0.14510857 0.57783443 7414 83 83 0 723 22500 2989 1.004816 0 + 2400 1.1382223 3969 0.00050867975 -1.0519828 0.074857312 0.41119597 7601 77 77 0 754 22500 2996 1.007891 0 + 2500 0.96793374 3969 -0.00075093709 -1.0687623 -0.1105079 0.12887172 7444 88 88 0 789 22500 2984 1.0268818 0 + 2600 1.0064799 3969 -0.00023588466 -1.0311279 -0.034712786 0.38564304 7483 83 83 0 831 22500 3047 1.0199727 0 + 2700 1.1198694 3969 0.00019125912 -1.080525 0.028145692 0.35649192 7372 72 72 0 863 22500 2991 0.99989809 0 + 2800 1.130996 3969 0.00083301498 -0.99709952 0.12258648 0.76321666 7293 95 95 0 895 22500 2997 1.0077098 0 + 2900 1.069281 3969 0.00033771134 -1.0088906 0.049697601 0.60669604 7485 86 86 0 929 22500 3004 1.0105564 0 + 3000 1.0864905 3969 5.9065123e-05 -1.0669336 0.0086920235 0.2448914 7367 88 88 0 965 22500 3018 1.0256143 0 + 3100 1.2930036 3969 0.0016599457 -1.035796 0.24427761 0.4417485 7502 103 103 0 1002 22500 2996 1.0207648 0 + 3200 0.99779215 3969 0.00017970488 -0.96136886 0.02644537 0.48688189 7463 89 89 0 1040 22500 2975 1.0226074 0 + 3300 1.1649719 3969 0.00083129956 -1.0309882 0.12233404 0.32895722 7504 92 92 0 1072 22500 2984 1.016696 0 + 3400 1.1428122 3969 0.00094373594 -0.99250387 0.13888018 0.62272115 7519 103 103 0 1092 22500 3005 1.0177259 0 + 3500 1.1207278 3969 0.00052216214 -1.0326791 0.076841381 0.51325294 7456 71 71 0 1127 22500 2986 1.0290334 0 + 3600 0.97869243 3969 -0.00058219044 -1.0545807 -0.085675146 0.44258567 7321 72 72 0 1164 22500 2976 1.031506 0 + 3700 1.0853936 3969 -4.3134698e-06 -1.0751745 -0.00063477022 0.37380213 7444 80 80 0 1194 22500 2985 1.0445746 0 + 3800 1.0351364 3969 -0.00012682002 -1.0434479 -0.018662834 0.42474168 7503 76 76 0 1226 22500 2986 1.0260769 0 + 3900 0.96833719 3969 -0.00039514299 -1.0168031 -0.058149242 0.42237112 7423 79 79 0 1276 22500 3014 1.0160914 0 + 4000 1.0465724 3969 0.00016394266 -1.0119808 0.024125802 0.46524856 7502 97 97 0 1299 22500 2984 1.0159361 0 + 4100 1.2417361 3969 0.0011421943 -1.0612334 0.16808531 0.39684717 7633 83 83 0 1328 22500 3015 1.0264492 0 + 4200 1.0974708 3969 0.00053755453 -1.0073895 0.079106524 0.52996179 7347 86 86 0 1363 22500 3020 1.0215105 0 + 4300 1.1082592 3969 0.00034118461 -1.0469679 0.050208728 0.40630088 7470 94 94 0 1400 22500 3012 1.0278618 0 + 4400 1.0021274 3969 -0.00027032597 -1.0318873 -0.039781169 0.50493986 7643 77 77 0 1434 22500 3006 1.0236688 0 + 4500 0.97643527 3969 -0.00024256014 -1.0023661 -0.03569515 0.55193268 7488 75 75 0 1476 22500 2998 1.0281645 0 + 4600 1.0333058 3969 -9.5227766e-05 -1.0369865 -0.014013718 0.37752045 7455 86 86 0 1507 22500 3003 1.0419695 0 + 4700 1.1320717 3969 0.00069912511 -1.0178677 0.10288325 0.42203645 7594 80 80 0 1531 22500 2989 1.0343185 0 + 4800 1.1326193 3969 0.0010771417 -0.96278098 0.15851217 0.59591984 7504 101 101 0 1560 22500 2998 1.0182951 0 + 4900 1.1174294 3969 0.00044360443 -1.0409743 0.065280828 0.30043772 7611 96 96 0 1590 22500 2996 1.0255445 0 + 5000 0.93845577 3969 -0.00055722 -1.0110717 -0.082000495 0.41966034 7582 83 83 0 1632 22500 2990 1.0290121 0 +Loop time of 1.15581 on 4 procs for 5000 steps with 14716 atoms + +Performance: 373763.989 tau/day, 4325.972 timesteps/s +95.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.0088997 | 0.011787 | 0.01474 | 1.9 | 1.02 +Neigh | 0.00226 | 0.0025237 | 0.002775 | 0.4 | 0.22 +Comm | 0.077973 | 0.084049 | 0.088172 | 1.3 | 7.27 +Output | 0.0065994 | 0.007837 | 0.011406 | 2.3 | 0.68 +Modify | 0.99157 | 0.99959 | 1.0146 | 0.9 | 86.48 +Other | | 0.05002 | | | 4.33 + +Nlocal: 3679 ave 3871 max 3455 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 46.5 ave 49 max 43 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 118.25 ave 151 max 84 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 473 +Ave neighs/atom = 0.0321419 +Neighbor list builds = 250 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:01 diff --git a/examples/srd/log.5Oct16.srd.pure.g++.1 b/examples/srd/log.27Nov18.srd.pure.g++.1 similarity index 90% rename from examples/srd/log.5Oct16.srd.pure.g++.1 rename to examples/srd/log.27Nov18.srd.pure.g++.1 index f840d923c8..d0f53429e5 100644 --- a/examples/srd/log.5Oct16.srd.pure.g++.1 +++ b/examples/srd/log.27Nov18.srd.pure.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d SRD only test units lj @@ -24,6 +25,7 @@ lattice sq 85.0 Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 create_atoms 1 region plane Created 21316 atoms + Time spent = 0.0160828 secs group empty type 2 0 atoms in group empty @@ -71,14 +73,7 @@ SRD info: big/SRD mass density ratio = 0 # of rescaled SRD velocities = 0 ave/max all velocity = 13.2735 24.2873 -Neighbor list info ... - 0 neighbor list requests - update every 1 steps, delay 1 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 0 - binsize = 15.8114 -> bins = 1 1 1 -Memory usage per processor = 5.16355 Mbytes +Per MPI rank memory allocation (min/avg/max) = 5.038 | 5.038 | 5.038 Mbytes Step Temp f_1[7] TotEng Press f_1[3] f_1[4] f_1[6] 0 1 0 0.99995309 85.26 0 0 0 100 0.97820615 3969 0.97816026 83.401857 0 0 0 @@ -131,20 +126,20 @@ Step Temp f_1[7] TotEng Press f_1[3] f_1[4] f_1[6] 4800 0.75446697 3969 0.75443157 64.325854 0 0 0 4900 0.75276753 3969 0.75273221 64.180959 0 0 0 5000 0.75113693 3969 0.75110169 64.041935 0 0 0 -Loop time of 8.07858 on 1 procs for 5000 steps with 21316 atoms +Loop time of 7.57583 on 1 procs for 5000 steps with 21316 atoms -Performance: 1069494.899 tau/day, 618.921 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1140469.459 tau/day, 659.994 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.00082159 | 0.00082159 | 0.00082159 | 0.0 | 0.01 -Comm | 0.38133 | 0.38133 | 0.38133 | 0.0 | 4.72 -Output | 0.0034697 | 0.0034697 | 0.0034697 | 0.0 | 0.04 -Modify | 6.265 | 6.265 | 6.265 | 0.0 | 77.55 -Other | | 1.428 | | | 17.68 +Neigh | 0.00093412 | 0.00093412 | 0.00093412 | 0.0 | 0.01 +Comm | 0.49229 | 0.49229 | 0.49229 | 0.0 | 6.50 +Output | 0.004915 | 0.004915 | 0.004915 | 0.0 | 0.06 +Modify | 5.9494 | 5.9494 | 5.9494 | 0.0 | 78.53 +Other | | 1.128 | | | 14.89 Nlocal: 21316 ave 21316 max 21316 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -160,4 +155,4 @@ Dangerous builds not checked Please see the log.cite file for references relevant to this simulation -Total wall time: 0:00:08 +Total wall time: 0:00:07 diff --git a/examples/srd/log.5Oct16.srd.pure.g++.4 b/examples/srd/log.27Nov18.srd.pure.g++.4 similarity index 90% rename from examples/srd/log.5Oct16.srd.pure.g++.4 rename to examples/srd/log.27Nov18.srd.pure.g++.4 index 3cce60cb25..82aea9a2f2 100644 --- a/examples/srd/log.5Oct16.srd.pure.g++.4 +++ b/examples/srd/log.27Nov18.srd.pure.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # 2d SRD only test units lj @@ -24,6 +25,7 @@ lattice sq 85.0 Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 create_atoms 1 region plane Created 21316 atoms + Time spent = 0.00763822 secs group empty type 2 0 atoms in group empty @@ -71,14 +73,7 @@ SRD info: big/SRD mass density ratio = 0 # of rescaled SRD velocities = 0 ave/max all velocity = 13.2735 24.2873 -Neighbor list info ... - 0 neighbor list requests - update every 1 steps, delay 1 steps, check no - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 0 - ghost atom cutoff = 0 - binsize = 15.8114 -> bins = 1 1 1 -Memory usage per processor = 2.29814 Mbytes +Per MPI rank memory allocation (min/avg/max) = 2.236 | 2.241 | 2.246 Mbytes Step Temp f_1[7] TotEng Press f_1[3] f_1[4] f_1[6] 0 1 0 0.99995309 85.26 0 0 0 100 0.97718565 3969 0.97713981 83.314849 0 0 0 @@ -131,20 +126,20 @@ Step Temp f_1[7] TotEng Press f_1[3] f_1[4] f_1[6] 4800 0.75699084 3969 0.75695533 64.541039 0 0 0 4900 0.75590428 3969 0.75586882 64.448399 0 0 0 5000 0.75435525 3969 0.75431986 64.316328 0 0 0 -Loop time of 2.01342 on 4 procs for 5000 steps with 21316 atoms +Loop time of 2.63242 on 4 procs for 5000 steps with 21316 atoms -Performance: 4291197.146 tau/day, 2483.332 timesteps/s -99.2% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3282146.784 tau/day, 1899.391 timesteps/s +90.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0.0011518 | 0.001229 | 0.0013053 | 0.2 | 0.06 -Comm | 0.2563 | 0.27904 | 0.2912 | 2.6 | 13.86 -Output | 0.0022588 | 0.0023048 | 0.0024054 | 0.1 | 0.11 -Modify | 1.3545 | 1.3589 | 1.3629 | 0.3 | 67.49 -Other | | 0.372 | | | 18.48 +Neigh | 0.0010204 | 0.001139 | 0.001276 | 0.3 | 0.04 +Comm | 0.48325 | 0.51859 | 0.56231 | 4.0 | 19.70 +Output | 0.0025201 | 0.0089323 | 0.028138 | 11.7 | 0.34 +Modify | 1.7822 | 1.8025 | 1.8257 | 1.5 | 68.47 +Other | | 0.3013 | | | 11.45 Nlocal: 5329 ave 5410 max 5266 min Histogram: 1 0 0 2 0 0 0 0 0 1 diff --git a/examples/srd/log.5Oct16.srd.mixture.g++.4 b/examples/srd/log.5Oct16.srd.mixture.g++.4 deleted file mode 100644 index 6962f331d5..0000000000 --- a/examples/srd/log.5Oct16.srd.mixture.g++.4 +++ /dev/null @@ -1,269 +0,0 @@ -LAMMPS (5 Oct 2016) -# 2d SRD test: big + small particles - -units lj -atom_style sphere -atom_modify first big -dimension 2 - -# create big particles with sigma 1.0 - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region box block 0 10 0 10 -0.5 0.5 -create_box 2 box -Created orthogonal box = (0 0 -0.790569) to (15.8114 15.8114 0.790569) - 2 by 2 by 1 MPI processor grid -create_atoms 1 region box -Created 100 atoms -set type 1 mass 1.0 - 100 settings made for mass -set type 1 diameter 1.0 - 100 settings made for diameter - -group big type 1 -100 atoms in group big -velocity big create 1.44 87287 loop geom - -# equilibrate big particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -fix 1 big nve -fix 2 all enforce2d - -run 1000 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 2 -Memory usage per processor = 3.60121 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 1.44 -0.54272 0 0.88288 -0.041088 - 1000 1.8791467 -0.97185784 0 0.8884974 0.61487657 -Loop time of 0.0114341 on 4 procs for 1000 steps with 100 atoms - -Performance: 37781795.071 tau/day, 87457.859 timesteps/s -94.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.001864 | 0.0021054 | 0.0024471 | 0.5 | 18.41 -Neigh | 0.00081182 | 0.00085837 | 0.00093675 | 0.2 | 7.51 -Comm | 0.005461 | 0.0057024 | 0.0059059 | 0.2 | 49.87 -Output | 1.3113e-05 | 1.3828e-05 | 1.5974e-05 | 0.0 | 0.12 -Modify | 0.00065017 | 0.00068271 | 0.00069666 | 0.1 | 5.97 -Other | | 0.002071 | | | 18.12 - -Nlocal: 25 ave 26 max 23 min -Histogram: 1 0 0 0 0 0 1 0 0 2 -Nghost: 47 ave 48 max 46 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 114.75 ave 124 max 100 min -Histogram: 1 0 0 0 0 1 0 0 0 2 - -Total # of neighbors = 459 -Ave neighs/atom = 4.59 -Neighbor list builds = 129 -Dangerous builds = 0 - -unfix 1 -unfix 2 - -# add small particles as hi density lattice - -lattice sq 0.4 -Lattice spacing in x,y,z = 1.58114 1.58114 1.58114 -region plane block 0 10 0 10 -0.001 0.001 -lattice sq 85.0 -Lattice spacing in x,y,z = 0.108465 0.108465 0.108465 -create_atoms 2 region plane -Created 21316 atoms -set type 2 mass 0.01 - 21316 settings made for mass -set type 2 diameter 0.0 - 21316 settings made for diameter - -group small type 2 -21316 atoms in group small - -velocity small create 1.0 593849 loop geom - -# delete overlaps -# must set 1-2 cutoff to non-zero value - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.5 - -delete_atoms overlap 0.5 small big -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 2 -WARNING: Delete_atoms cutoff > minimum neighbor cutoff (../delete_atoms.cpp:278) -Deleted 6700 atoms, new total = 14716 - -# SRD run - -reset_timestep 0 - -neighbor 0.3 bin -neigh_modify delay 0 every 1 check yes - -comm_modify mode multi group big vel yes -neigh_modify include big - -# no pairwise interactions with small particles - -pair_style lj/cut 2.5 -pair_coeff 1 1 1.0 1.0 -pair_coeff 2 2 0.0 1.0 0.0 -pair_coeff 1 2 0.0 1.0 0.0 - -# use fix SRD to push small particles out from inside big ones - -timestep 0.001 - -fix 1 big nve -fix 2 small srd 20 big 1.0 0.25 49894 radius 0.88 search 0.2 collision slip -fix 3 all enforce2d - -# diagnostics - -compute tbig big temp -variable pebig equal pe*atoms/count(big) -variable ebig equal etotal*atoms/count(big) -thermo_style custom step temp f_2[7] etotal v_pebig v_ebig press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] - -thermo_modify temp tbig -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) -thermo 100 - -#dump 1 all atom 250 dump.srd.mixture - -#dump 2 all image 250 image.*.jpg type type zoom 1.6 -#dump_modify 2 pad 4 adiam 1 1 adiam 2 0.2 - -#dump 3 all movie 250 movie.mpg type type zoom 1.6 -#dump_modify 3 pad 4 adiam 1 1 adiam 2 0.2 - -run 5000 -SRD info: - SRD/big particles = 14616 100 - big particle diameter max/min = 0.88 0.88 - SRD temperature & lamda = 1 0.2 - SRD max distance & max velocity = 0.8 40 - SRD grid counts: 63 63 1 - SRD grid size: request, actual (xyz) = 0.25, 0.250974 0.250974 1.58114 - SRD per actual grid cell = 4.86648 - SRD viscosity = 0.463448 - big/SRD mass density ratio = 2.12808 -WARNING: Fix srd grid size > 1/4 of big particle diameter (../fix_srd.cpp:2884) - # of rescaled SRD velocities = 0 - ave/max small velocity = 13.2944 24.262 - ave/max big velocity = 1.69284 5.10989 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 2.8 - ghost atom cutoff = 2.8 - binsize = 1.4 -> bins = 12 12 2 -Memory usage per processor = 5.3246 Mbytes -Step Temp f_2[7] TotEng v_pebig v_ebig Press f_2[1] f_2[2] f_2[3] f_2[4] f_2[5] f_2[6] f_2[8] f_2[9] f_2[10] - 0 1.8791467 0 0.0060376284 -0.97185784 0.8884974 0.61487657 0 0 0 0 0 0 0 0 0 - 100 1.4044369 3969 0.0030633093 -0.93959598 0.4507966 0.78900119 7464 99 99 0 17 22500 3005 1.028131 0 - 200 1.1569383 3969 0.0010543995 -0.99020352 0.15516543 0.50132981 7393 82 82 0 43 22500 2996 1.014347 0 - 300 0.97802835 3969 -0.00019991154 -0.99766705 -0.029418982 0.35789515 7411 90 90 0 84 22500 3001 1.0213725 0 - 400 1.0992982 3969 0.00055034756 -1.007316 0.080989146 0.35177983 7443 78 78 0 107 22500 2993 1.0451641 0 - 500 1.0436705 3969 -7.4779704e-05 -1.0442384 -0.011004581 0.15132448 7504 94 94 0 141 22500 3007 1.0236992 0 - 600 1.0216461 3969 -0.00032426678 -1.0591487 -0.047719099 0.2200765 7508 111 111 0 179 22500 3007 1.0304838 0 - 700 1.1491339 3969 0.0012328743 -0.95621278 0.18142978 0.80670059 7448 95 95 0 201 22500 2978 1.0099113 0 - 800 1.0332166 3969 -0.00040684239 -1.0827554 -0.059870926 0.35939225 7453 113 113 0 235 22500 3024 1.0141565 0 - 900 1.0652211 3969 -6.1337025e-06 -1.0554715 -0.00090263566 0.51460169 7447 97 97 0 259 22500 2982 1.0192735 0 - 1000 0.92834993 3969 -0.00067681883 -1.0186671 -0.09960066 0.738738 7328 78 78 0 286 22500 2999 1.023841 0 - 1100 1.0386338 3969 -0.00018904027 -1.0560666 -0.027819166 0.57129719 7449 96 96 0 325 22500 3012 1.0373885 0 - 1200 0.92218024 3969 -0.00077989365 -1.0277276 -0.11476915 0.48613467 7507 100 100 0 355 22500 3003 1.0254889 0 - 1300 1.1835318 3969 0.00096836748 -1.0291915 0.14250496 0.62935386 7439 92 92 0 384 22500 2993 1.0289037 0 - 1400 1.0895805 3969 0.00022072203 -1.0462033 0.032481455 0.49130771 7492 80 80 0 426 22500 3005 1.0083895 0 - 1500 1.0713283 3969 0.00042008247 -0.99879571 0.061819337 0.63979877 7498 87 87 0 457 22500 3000 1.0009934 0 - 1600 0.97815063 3969 -0.0005425653 -1.048213 -0.079843909 0.3604669 7533 105 105 0 492 22500 3004 1.0375508 0 - 1700 1.1626991 3969 0.00048969594 -1.0790084 0.072063654 0.36261544 7493 87 87 0 519 22500 3014 1.0151507 0 - 1800 0.91077626 3969 -0.001205934 -1.0791337 -0.17746525 0.14204132 7553 77 77 0 554 22500 3001 1.0393648 0 - 1900 1.073632 3969 0.00048053229 -0.99218055 0.070715131 0.56468311 7660 96 96 0 579 22500 2990 1.0071005 0 - 2000 1.0516743 3969 -0.00020689596 -1.0716044 -0.03044681 0.28030578 7561 96 96 0 631 22500 3020 1.0222307 0 - 2100 1.141885 3969 0.00040167415 -1.0713558 0.059110368 0.32604475 7569 69 69 0 662 22500 2968 1.0125404 0 - 2200 1.2228391 3969 0.0010327668 -1.0586288 0.15198196 0.36038619 7572 86 86 0 691 22500 2979 1.0235277 0 - 2300 1.1087892 3969 0.00043721167 -1.0333612 0.06434007 0.39699935 7512 68 68 0 716 22500 3022 1.0515275 0 - 2400 1.0637949 3969 0.00033715078 -1.0035418 0.049615108 0.47092535 7508 82 82 0 742 22500 2997 1.0295291 0 - 2500 1.0345185 3969 0.00023374535 -0.98977538 0.034397966 0.57463578 7514 89 89 0 778 22500 2986 1.0252443 0 - 2600 1.1040438 3969 0.00024293233 -1.0572534 0.035749922 0.38043986 7543 82 82 0 811 22500 2995 1.0181075 0 - 2700 0.96252159 3969 -0.00081483156 -1.072807 -0.11991061 0.2771083 7555 97 97 0 842 22500 2990 1.0125575 0 - 2800 0.98730039 3969 -0.00037330307 -1.0323627 -0.05493528 0.57796755 7359 88 88 0 866 22500 2981 1.0187945 0 - 2900 1.056508 3969 0.0003868833 -0.98900914 0.056933747 0.63280739 7485 84 84 0 906 22500 3009 1.0260952 0 - 3000 0.97367876 3969 -0.0002599408 -1.0021949 -0.038252888 0.66404419 7424 99 99 0 951 22500 2998 1.0143644 0 - 3100 0.97186052 3969 -0.00084858744 -1.08702 -0.12487813 0.33835871 7502 88 88 0 983 22500 3016 1.0292976 0 - 3200 0.97992936 3969 -0.0006672966 -1.0683294 -0.098199368 0.45138198 7326 72 72 0 1026 22500 3005 1.023367 0 - 3300 0.96722828 3969 -0.00034604616 -1.0084802 -0.050924152 0.58525322 7383 70 70 0 1053 22500 2986 1.034213 0 - 3400 1.1202892 3969 0.00043227098 -1.0454733 0.063612998 0.43718189 7364 85 85 0 1087 22500 2995 1.0158362 0 - 3500 0.79750662 3969 -0.0014948003 -1.0095064 -0.21997481 0.41132937 7511 90 90 0 1116 22500 2993 1.0182386 0 - 3600 1.0491778 3969 -0.00010433247 -1.0540396 -0.015353567 0.42315074 7489 95 95 0 1144 22500 2999 1.020922 0 - 3700 0.9610381 3969 -0.00021690291 -0.98334715 -0.031919432 0.55752687 7496 80 80 0 1172 22500 3019 1.0303605 0 - 3800 0.76471906 3969 -0.0017426239 -1.0135164 -0.25644453 0.32180761 7518 89 89 0 1213 22500 3008 1.0419804 0 - 3900 1.086591 3969 0.00018698809 -1.0482079 0.027517167 0.26073092 7462 98 98 0 1246 22500 3005 1.0261112 0 - 4000 0.82619819 3969 -0.0014452395 -1.0306176 -0.21268144 0.14915039 7545 98 98 0 1287 22500 3008 1.0352711 0 - 4100 0.95064219 3969 -0.00053545528 -1.0199334 -0.0787976 0.39089361 7572 85 85 0 1318 22500 3001 1.0372179 0 - 4200 0.90370321 3969 -0.0007185822 -1.0004127 -0.10574656 0.47384816 7460 61 61 0 1355 22500 2998 1.012362 0 - 4300 0.97729216 3969 -0.00029144098 -1.0104077 -0.042888455 0.46030155 7533 70 70 0 1388 22500 3007 1.0223284 0 - 4400 1.0140429 3969 4.720814e-06 -1.0032078 0.00069471498 0.55984871 7501 88 88 0 1412 22500 2995 1.0285533 0 - 4500 1.0498677 3969 0.00022703142 -1.0059591 0.033409944 0.61932234 7461 82 82 0 1442 22500 2994 1.0292131 0 - 4600 0.90182406 3969 -0.00092157839 -1.0284253 -0.13561948 0.59198635 7499 73 73 0 1483 22500 3020 1.0159894 0 - 4700 1.0138009 3969 -0.00028404538 -1.045463 -0.041800118 0.53428422 7407 78 78 0 1507 22500 3011 1.0058816 0 - 4800 1.0506575 3969 -0.00043345499 -1.1039381 -0.063787236 0.30643257 7543 87 87 0 1524 22500 2995 1.0210242 0 - 4900 1.1479137 3969 -0.00019383126 -1.1649587 -0.028524208 0.28842185 7416 91 91 0 1557 22500 2988 1.0063463 0 - 5000 0.9092746 3969 -0.00087214131 -1.0285262 -0.12834432 0.76635862 7389 85 85 0 1589 22500 3000 1.0157079 0 -Loop time of 0.845193 on 4 procs for 5000 steps with 14716 atoms - -Performance: 511125.916 tau/day, 5915.809 timesteps/s -99.3% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.0080214 | 0.010886 | 0.013055 | 1.7 | 1.29 -Neigh | 0.0015197 | 0.0018466 | 0.002033 | 0.5 | 0.22 -Comm | 0.058729 | 0.061718 | 0.063298 | 0.7 | 7.30 -Output | 0.0025218 | 0.0027084 | 0.0029843 | 0.3 | 0.32 -Modify | 0.71322 | 0.72561 | 0.73841 | 1.1 | 85.85 -Other | | 0.04242 | | | 5.02 - -Nlocal: 3679 ave 4013 max 3459 min -Histogram: 1 0 1 1 0 0 0 0 0 1 -Nghost: 48.25 ave 54 max 44 min -Histogram: 1 0 1 0 0 1 0 0 0 1 -Neighs: 117 ave 136 max 87 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 468 -Ave neighs/atom = 0.0318021 -Neighbor list builds = 250 -Dangerous builds = 0 - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:01 diff --git a/examples/streitz/log.5Oct16.streitz.ewald.g++.1 b/examples/streitz/log.27Nov18.streitz.ewald.g++.1 similarity index 56% rename from examples/streitz/log.5Oct16.streitz.ewald.g++.1 rename to examples/streitz/log.27Nov18.streitz.ewald.g++.1 index 5cb643146a..2e5c9fb093 100644 --- a/examples/streitz/log.5Oct16.streitz.ewald.g++.1 +++ b/examples/streitz/log.27Nov18.streitz.ewald.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Streitz-Mintmire potential with alpha-alumina # option to use with Ewald or Wolf sum # EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions @@ -61,47 +62,62 @@ fix 2 all nve run 100 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.310132 estimated absolute RMS force accuracy = 1.9688e-05 estimated relative force accuracy = 1.36725e-06 KSpace vectors: actual max1d max3d = 2541 11 6083 kxmax kymax kzmax = 10 11 10 Neighbor list info ... - 3 neighbor list requests update every 10 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 4 5 4 -Memory usage per processor = 79.7925 Mbytes + binsize = 6.5, bins = 4 5 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair coul/streitz, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair eam/alloy, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) fix qeq/slater, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 102.8 | 102.8 | 102.8 Mbytes Step Temp TotEng PotEng E_vdwl E_coul E_long c_q1 c_q2 v_qsum Press S/CPU - 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801924 2.8665317 -1.9110211 2.7284841e-12 -26072.585 0 - 10 272.45428 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 4.5474735e-13 -21774.211 1.0024289 - 20 219.94294 -6.3402438 -6.3686605 -2.7790335 10.192017 -13.781644 2.8638745 -1.9092497 1.3642421e-12 -16693.959 1.0737194 - 30 179.36108 -6.3401905 -6.363364 -2.7689124 10.190565 -13.785017 2.8639191 -1.9092794 1.0004442e-11 -12974.154 1.075669 - 40 162.68484 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 -3.6379788e-12 -12735.477 1.0762629 - 50 152.76246 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724802 2.8575298 -1.9050198 6.3664629e-12 -14532.643 1.0803062 - 60 138.38061 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671967 2.8519579 -1.9013053 3.1832315e-12 -15656.278 1.0800578 - 70 134.9572 -6.3401907 -6.3576272 -2.7740776 10.063528 -13.647077 2.849277 -1.899518 -2.7284841e-12 -14160.692 1.0792572 - 80 161.55083 -6.3401305 -6.3610029 -2.7741365 10.086552 -13.673419 2.8520585 -1.9013723 1.8189894e-12 -9666.5838 1.0798168 - 90 207.33012 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591984 -1.9061323 -3.1832315e-12 -2530.8605 1.0783069 - 100 233.80619 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811339 2.8668083 -1.9112055 9.094947e-13 6120.857 1.0726581 -Loop time of 93.5154 on 1 procs for 100 steps with 2160 atoms + 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801924 2.8665317 -1.9110211 -2.7284841e-12 -26072.585 0 + 10 272.45428 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 -3.6379788e-12 -21774.211 1.4901869 + 20 219.94294 -6.3402438 -6.3686605 -2.7790336 10.192017 -13.781644 2.8638745 -1.9092497 -2.7284841e-12 -16693.959 1.6439654 + 30 179.36108 -6.3401905 -6.363364 -2.7689124 10.190565 -13.785017 2.8639191 -1.9092794 -9.094947e-13 -12974.155 1.6560994 + 40 162.68484 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 3.1832315e-12 -12735.479 1.6506831 + 50 152.76247 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724801 2.8575297 -1.9050198 -3.6379788e-12 -14532.607 1.6531952 + 60 138.38062 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671967 2.851958 -1.9013053 1.3642421e-12 -15656.298 1.6555081 + 70 134.9572 -6.3401907 -6.3576272 -2.7740776 10.063527 -13.647077 2.8492769 -1.8995179 -2.7284841e-12 -14160.663 1.6525548 + 80 161.55081 -6.3401305 -6.3610029 -2.7741365 10.086552 -13.673419 2.8520584 -1.9013723 -4.5474735e-13 -9666.5594 1.6525076 + 90 207.33009 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591985 -1.9061323 4.0927262e-12 -2530.8853 1.6448945 + 100 233.80619 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811339 2.8668083 -1.9112055 -4.0927262e-12 6120.8481 1.635231 +Loop time of 61.2766 on 1 procs for 100 steps with 2160 atoms -Performance: 0.037 ns/day, 649.413 hours/ns, 1.069 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.056 ns/day, 425.532 hours/ns, 1.632 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 40.681 | 40.681 | 40.681 | 0.0 | 43.50 -Kspace | 4.9722 | 4.9722 | 4.9722 | 0.0 | 5.32 +Pair | 22.617 | 22.617 | 22.617 | 0.0 | 36.91 +Kspace | 5.3519 | 5.3519 | 5.3519 | 0.0 | 8.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010761 | 0.010761 | 0.010761 | 0.0 | 0.01 -Output | 0.00078893 | 0.00078893 | 0.00078893 | 0.0 | 0.00 -Modify | 47.848 | 47.848 | 47.848 | 0.0 | 51.17 -Other | | 0.002154 | | | 0.00 +Comm | 0.01263 | 0.01263 | 0.01263 | 0.0 | 0.02 +Output | 0.00089216 | 0.00089216 | 0.00089216 | 0.0 | 0.00 +Modify | 33.292 | 33.292 | 33.292 | 0.0 | 54.33 +Other | | 0.001862 | | | 0.00 Nlocal: 2160 ave 2160 max 2160 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -116,4 +132,4 @@ Total # of neighbors = 2357856 Ave neighs/atom = 1091.6 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:01:34 +Total wall time: 0:01:01 diff --git a/examples/streitz/log.5Oct16.streitz.ewald.g++.4 b/examples/streitz/log.27Nov18.streitz.ewald.g++.4 similarity index 53% rename from examples/streitz/log.5Oct16.streitz.ewald.g++.4 rename to examples/streitz/log.27Nov18.streitz.ewald.g++.4 index 01beb3d1ba..29b5133a19 100644 --- a/examples/streitz/log.5Oct16.streitz.ewald.g++.4 +++ b/examples/streitz/log.27Nov18.streitz.ewald.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Streitz-Mintmire potential with alpha-alumina # option to use with Ewald or Wolf sum # EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions @@ -61,47 +62,62 @@ fix 2 all nve run 100 Ewald initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) + using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.310132 estimated absolute RMS force accuracy = 1.9688e-05 estimated relative force accuracy = 1.36725e-06 KSpace vectors: actual max1d max3d = 2541 11 6083 kxmax kymax kzmax = 10 11 10 Neighbor list info ... - 3 neighbor list requests update every 10 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 4 5 4 -Memory usage per processor = 32.3255 Mbytes + binsize = 6.5, bins = 4 5 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair coul/streitz, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair eam/alloy, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) fix qeq/slater, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 38.08 | 38.08 | 38.08 Mbytes Step Temp TotEng PotEng E_vdwl E_coul E_long c_q1 c_q2 v_qsum Press S/CPU - 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801925 2.8665317 -1.9110211 4.5474735e-13 -26072.6 0 - 10 272.45429 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 4.5474735e-13 -21774.214 3.7998441 - 20 219.94295 -6.3402438 -6.3686605 -2.7790335 10.192018 -13.781645 2.8638746 -1.9092497 -4.5474735e-13 -16694.015 4.0421334 - 30 179.36109 -6.3401905 -6.363364 -2.7689124 10.190566 -13.785018 2.8639192 -1.9092795 9.094947e-13 -12974.238 4.1358956 - 40 162.68485 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 -4.5474735e-13 -12735.472 4.1616104 - 50 152.76249 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724801 2.8575297 -1.9050198 4.5474735e-13 -14532.583 4.052378 - 60 138.38062 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671968 2.851958 -1.9013053 4.5474735e-13 -15656.298 4.1601628 - 70 134.9572 -6.3401907 -6.3576272 -2.7740776 10.063527 -13.647077 2.8492769 -1.8995179 -1.3642421e-12 -14160.655 4.1215986 - 80 161.55082 -6.3401305 -6.3610029 -2.7741365 10.086553 -13.673419 2.8520585 -1.9013723 0 -9666.5793 4.1226863 - 90 207.3301 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591985 -1.9061323 0 -2530.8682 4.1248222 - 100 233.80619 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811339 2.8668082 -1.9112055 -4.5474735e-13 6120.8881 4.1438288 -Loop time of 24.4873 on 4 procs for 100 steps with 2160 atoms + 0 300 -6.3402658 -6.3790259 -2.7952901 10.218189 -13.801925 2.8665317 -1.9110211 9.094947e-13 -26072.6 0 + 10 272.45428 -6.340306 -6.3755071 -2.790294 10.191122 -13.776335 2.8636996 -1.9091331 0 -21774.211 5.2839781 + 20 219.94294 -6.3402438 -6.3686605 -2.7790336 10.192017 -13.781644 2.8638745 -1.9092497 0 -16693.959 6.0398147 + 30 179.36107 -6.3401905 -6.363364 -2.7689124 10.190565 -13.785017 2.8639191 -1.9092794 -9.094947e-13 -12974.157 6.0771654 + 40 162.68484 -6.340179 -6.3611979 -2.7652026 10.173296 -13.769291 2.8621763 -1.9081175 1.3642421e-12 -12735.472 5.9101566 + 50 152.76247 -6.3401898 -6.3599268 -2.7673924 10.132267 -13.724801 2.8575297 -1.9050198 -9.094947e-13 -14532.603 6.1598264 + 60 138.38062 -6.340206 -6.3580848 -2.7714511 10.085334 -13.671967 2.8519579 -1.9013053 -9.094947e-13 -15656.287 6.0492678 + 70 134.95719 -6.3401907 -6.3576272 -2.7740777 10.063528 -13.647077 2.8492769 -1.899518 4.5474735e-13 -14160.677 5.8316321 + 80 161.55082 -6.3401305 -6.3610029 -2.7741365 10.086552 -13.673419 2.8520584 -1.9013723 4.5474735e-13 -9666.5672 6.0547326 + 90 207.33012 -6.3400321 -6.3668192 -2.7713864 10.144722 -13.740155 2.8591984 -1.9061323 4.5474735e-13 -2530.8639 6.1225844 + 100 233.80623 -6.3399378 -6.3701456 -2.7659477 10.207141 -13.811338 2.8668082 -1.9112055 -4.5474735e-13 6120.8845 5.8372987 +Loop time of 16.8751 on 4 procs for 100 steps with 2160 atoms -Performance: 0.141 ns/day, 170.051 hours/ns, 4.084 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.205 ns/day, 117.188 hours/ns, 5.926 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 10.566 | 10.569 | 10.572 | 0.1 | 43.16 -Kspace | 1.2451 | 1.2531 | 1.2593 | 0.5 | 5.12 +Pair | 6.0459 | 6.0553 | 6.0662 | 0.3 | 35.88 +Kspace | 1.4116 | 1.4188 | 1.4243 | 0.4 | 8.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.032611 | 0.037556 | 0.042452 | 1.8 | 0.15 -Output | 0.00079513 | 0.00084209 | 0.00089383 | 0.1 | 0.00 -Modify | 12.626 | 12.626 | 12.626 | 0.0 | 51.56 -Other | | 0.001517 | | | 0.01 +Comm | 0.052984 | 0.057914 | 0.062647 | 1.8 | 0.34 +Output | 0.00076938 | 0.0010375 | 0.0018225 | 1.4 | 0.01 +Modify | 9.3406 | 9.3408 | 9.341 | 0.0 | 55.35 +Other | | 0.001289 | | | 0.01 Nlocal: 540 ave 540 max 540 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -116,4 +132,4 @@ Total # of neighbors = 2357856 Ave neighs/atom = 1091.6 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:24 +Total wall time: 0:00:17 diff --git a/examples/streitz/log.5Oct16.streitz.wolf.g++.1 b/examples/streitz/log.27Nov18.streitz.wolf.g++.1 similarity index 55% rename from examples/streitz/log.5Oct16.streitz.wolf.g++.1 rename to examples/streitz/log.27Nov18.streitz.wolf.g++.1 index b7f091e834..200113e6df 100644 --- a/examples/streitz/log.5Oct16.streitz.wolf.g++.1 +++ b/examples/streitz/log.27Nov18.streitz.wolf.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Streitz-Mintmire potential with alpha-alumina # option to use with Ewald or Wolf sum # EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions @@ -61,39 +62,54 @@ fix 2 all nve run 100 Neighbor list info ... - 3 neighbor list requests update every 10 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 4 5 4 -Memory usage per processor = 43.8231 Mbytes + binsize = 6.5, bins = 4 5 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair coul/streitz, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair eam/alloy, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) fix qeq/slater, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 66.79 | 66.79 | 66.79 Mbytes Step Temp TotEng PotEng E_vdwl E_coul E_long c_q1 c_q2 v_qsum Press S/CPU - 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 2.7284841e-12 -25874.942 0 - 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -5.9117156e-12 -21564.556 0.81612507 - 20 220.54622 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -2.7284841e-12 -16449.483 0.86358366 - 30 180.22122 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 -4.0927262e-12 -12688.515 0.86365801 - 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 5.9117156e-12 -12334.208 0.863544 - 50 153.73808 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 -1.3642421e-12 -13908.747 0.86145214 - 60 139.1264 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.9016079 -2.7284841e-12 -14717.564 0.86116198 - 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 4.5474735e-13 -12982.145 0.86628367 - 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 9.094947e-13 -8388.9494 0.86398157 - 90 205.15419 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 -9.094947e-13 -1208.0269 0.86058046 - 100 231.50843 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675277 -1.9116851 -1.8189894e-12 7331.3742 0.85974026 -Loop time of 116.581 on 1 procs for 100 steps with 2160 atoms + 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 -2.7284841e-12 -25874.942 0 + 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 4.5474735e-12 -21564.553 1.428018 + 20 220.54623 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -6.8212103e-12 -16449.483 1.5873243 + 30 180.22122 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 9.094947e-13 -12688.517 1.5892821 + 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 2.2737368e-12 -12334.25 1.5885841 + 50 153.73807 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 1.3642421e-12 -13908.751 1.5780942 + 60 139.1264 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.9016079 1.3642421e-12 -14717.538 1.5868676 + 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 -4.5474735e-13 -12982.184 1.589379 + 80 160.34289 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 -3.1832315e-12 -8388.9485 1.5812201 + 90 205.15422 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599386 -1.9066257 -4.0927262e-12 -1208.1523 1.580384 + 100 231.50846 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675277 -1.9116851 -3.6379788e-12 7331.391 1.5711353 +Loop time of 63.8366 on 1 procs for 100 steps with 2160 atoms -Performance: 0.030 ns/day, 809.593 hours/ns, 0.858 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.054 ns/day, 443.310 hours/ns, 1.567 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 68.334 | 68.334 | 68.334 | 0.0 | 58.61 +Pair | 30.658 | 30.658 | 30.658 | 0.0 | 48.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010072 | 0.010072 | 0.010072 | 0.0 | 0.01 -Output | 0.00077605 | 0.00077605 | 0.00077605 | 0.0 | 0.00 -Modify | 48.234 | 48.234 | 48.234 | 0.0 | 41.37 -Other | | 0.002206 | | | 0.00 +Comm | 0.012245 | 0.012245 | 0.012245 | 0.0 | 0.02 +Output | 0.00091052 | 0.00091052 | 0.00091052 | 0.0 | 0.00 +Modify | 33.164 | 33.164 | 33.164 | 0.0 | 51.95 +Other | | 0.001392 | | | 0.00 Nlocal: 2160 ave 2160 max 2160 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -108,4 +124,4 @@ Total # of neighbors = 2357856 Ave neighs/atom = 1091.6 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:01:57 +Total wall time: 0:01:04 diff --git a/examples/streitz/log.5Oct16.streitz.wolf.g++.4 b/examples/streitz/log.27Nov18.streitz.wolf.g++.4 similarity index 57% rename from examples/streitz/log.5Oct16.streitz.wolf.g++.4 rename to examples/streitz/log.27Nov18.streitz.wolf.g++.4 index 0d44412e9b..2629e864dd 100644 --- a/examples/streitz/log.5Oct16.streitz.wolf.g++.4 +++ b/examples/streitz/log.27Nov18.streitz.wolf.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Streitz-Mintmire potential with alpha-alumina # option to use with Ewald or Wolf sum # EAM (AlO.eam.alloy) includes 1994 SM and 2004 Zhou versions @@ -61,39 +62,54 @@ fix 2 all nve run 100 Neighbor list info ... - 3 neighbor list requests update every 10 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13 ghost atom cutoff = 13 - binsize = 6.5 -> bins = 4 5 4 -Memory usage per processor = 13.9811 Mbytes + binsize = 6.5, bins = 4 5 4 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair coul/streitz, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair eam/alloy, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none + (3) fix qeq/slater, perpetual, copy from (1) + attributes: full, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 19.73 | 19.73 | 19.73 Mbytes Step Temp TotEng PotEng E_vdwl E_coul E_long c_q1 c_q2 v_qsum Press S/CPU - 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 4.5474735e-13 -25874.956 0 - 10 272.66671 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -1.3642421e-12 -21564.555 3.1498495 - 20 220.54623 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 -1.3642421e-12 -16449.483 3.2884449 - 30 180.22123 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 1.3642421e-12 -12688.521 3.3407498 - 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 -9.094947e-13 -12334.216 3.2513632 - 50 153.73807 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 4.5474735e-13 -13908.735 3.2545821 - 60 139.12639 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.901608 0 -14717.582 3.3020584 - 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.849924 -1.8999493 -4.5474735e-13 -12982.152 3.3300311 - 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528608 -1.9019072 -4.5474735e-13 -8388.9691 3.3716067 - 90 205.15418 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 -1.3642421e-12 -1208.0315 3.2650044 - 100 231.50843 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675276 -1.9116851 0 7331.4547 3.2807764 -Loop time of 30.4655 on 4 procs for 100 steps with 2160 atoms + 0 300 -6.3403863 -6.3791464 -2.7952901 -3.5838563 0 2.8665317 -1.9110211 9.094947e-13 -25874.957 0 + 10 272.66672 -6.3403993 -6.375628 -2.7902909 -3.5853371 0 2.8636914 -1.9091276 -2.2737368e-12 -21564.553 5.2615137 + 20 220.54623 -6.3402616 -6.3687562 -2.7790072 -3.589749 0 2.863852 -1.9092346 9.094947e-13 -16449.483 5.6907174 + 30 180.22123 -6.3401053 -6.36339 -2.768798 -3.5945919 0 2.8639472 -1.9092981 4.5474735e-13 -12688.521 5.8240034 + 40 163.64074 -6.3399908 -6.3611332 -2.7648763 -3.5962569 0 2.8623043 -1.9082029 0 -12334.214 5.7924103 + 50 153.73807 -6.3399173 -6.3597803 -2.7667004 -3.5930799 0 2.8578231 -1.9052154 -2.7284841e-12 -13908.738 5.5609047 + 60 139.12639 -6.3398818 -6.357857 -2.7702921 -3.5875649 0 2.8524119 -1.9016079 9.094947e-13 -14717.539 5.8733718 + 70 134.93296 -6.3398533 -6.3572867 -2.7724725 -3.5848142 0 2.8499241 -1.8999494 -4.5474735e-13 -12982.215 5.8723225 + 80 160.3429 -6.3398152 -6.3605315 -2.7722306 -3.5883009 0 2.8528607 -1.9019071 0 -8388.8771 5.6759992 + 90 205.15422 -6.3397713 -6.3662773 -2.7693832 -3.596894 0 2.8599384 -1.9066256 0 -1208.0057 5.8210112 + 100 231.50845 -6.339741 -6.369652 -2.7640167 -3.6056353 0 2.8675277 -1.9116851 -4.5474735e-13 7331.3767 5.8173821 +Loop time of 17.5038 on 4 procs for 100 steps with 2160 atoms -Performance: 0.113 ns/day, 211.566 hours/ns, 3.282 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.197 ns/day, 121.554 hours/ns, 5.713 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 17.774 | 17.778 | 17.783 | 0.1 | 58.35 +Pair | 8.2231 | 8.2312 | 8.2384 | 0.2 | 47.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.033262 | 0.037797 | 0.041712 | 1.9 | 0.12 -Output | 0.0010474 | 0.0010778 | 0.0011182 | 0.1 | 0.00 -Modify | 12.647 | 12.647 | 12.647 | 0.0 | 41.51 -Other | | 0.001517 | | | 0.00 +Comm | 0.040039 | 0.046999 | 0.055306 | 2.5 | 0.27 +Output | 0.00074816 | 0.00099862 | 0.0017352 | 0.0 | 0.01 +Modify | 9.2234 | 9.2236 | 9.2237 | 0.0 | 52.69 +Other | | 0.001126 | | | 0.01 Nlocal: 540 ave 540 max 540 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -108,4 +124,4 @@ Total # of neighbors = 2357856 Ave neighs/atom = 1091.6 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:30 +Total wall time: 0:00:17 diff --git a/examples/threebody/BNC.tersoff b/examples/threebody/BNC.tersoff deleted file mode 100644 index 1630062524..0000000000 --- a/examples/threebody/BNC.tersoff +++ /dev/null @@ -1,74 +0,0 @@ -# DATE: 2013-03-21 CONTRIBUTOR: Cem Sevik CITATION: Kinaci, Haskins, Sevik and Cagin, Phys Rev B, 86, 115410 (2012) -# Tersoff parameters for B, C, and BN-C hybrid based graphene like nano structures -# multiple entries can be added to this file, LAMMPS reads the ones it needs - -# these entries are in LAMMPS "metal" units: -# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms -# other quantities are unitless - -# Cem Sevik (csevik at anadolu.edu.tr) takes full blame for this -# file. It specifies B-N, B-C, and N-C interaction parameters -# generated and published by the reseacrh group of Prof. Tahir Cagin. - -# 1. Physical Review B 84, 085409 2011 -# Characterization of thermal transport in low-dimensional boron nitride nanostructures, -# - -# 2. Physical Review B 86, 075403 2012 -# Influence of disorder on thermal transport properties of boron nitride nanostructures -# - -# 3. Physical Review B 86, 075403 2012, Please see for further information about B-C and N-C parameters -# Thermal conductivity of BN-C nanostructures -# - -# The file also specifies C-C, interaction parameters -# generated and published by the reseacrh group of Dr. D. A. Broido -# Physical Review B 81, 205441 2010 -# Optimized Tersoff and Brenner empirical potential parameters for -# lattice dynamics and phonon thermal transport in carbon nanotubes and graphene - -# Users in referring the full parameters can cite the full parameter paper (3) as: -# A. Kinaci, J. B. Haskins, C. Sevik, T. Cagin, Physical Review B 86, 115410 (2012) -# Thermal conductivity of BN-C nanostructures -# - -# format of a single entry (one or more lines): -# element 1, element 2, element 3, -# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A - -N B B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 -N B N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 -N B C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 - -B N B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 -B N N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 -B N C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.199 340.00 1.95 0.05 3.568 1380.0 - -N N B 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 -N N N 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 -N N C 3.0 1.0 0.0 17.7959 5.9484 0.00000 0.6184432 0.019251 2.6272721 138.77866 2.0 0.1 2.8293093 128.86866 - -B B B 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 -B B N 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 -B B C 3.0 1.0 0.0 0.52629 0.001587 0.5 3.9929061 1.6e-6 2.0774982 43.132016 2.0 0.1 2.2372578 40.0520156 - -C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 -C C B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 -C C N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2119 430.00 1.95 0.15 3.4879 1393.6 - -C B B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 -C B N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 -C B C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 - -C N B 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 -C N N 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 -C N C 3.0 1.0 0.0 3.8049e4 4.3484 -0.93000 0.72751 1.5724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 - -B C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 -B C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 -B C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 339.068910 1.95 0.10 3.5279 1386.78 - -N C C 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 -N C B 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 -N C N 3.0 1.0 0.0 25000 4.3484 -0.89000 0.72751 1.25724e-7 2.2054 387.575152 1.95 0.10 3.5279 1386.78 diff --git a/examples/threebody/BNC.tersoff b/examples/threebody/BNC.tersoff new file mode 120000 index 0000000000..4b27d18160 --- /dev/null +++ b/examples/threebody/BNC.tersoff @@ -0,0 +1 @@ +../../potentials/BNC.tersoff \ No newline at end of file diff --git a/examples/threebody/CdTeZnSeHgS0.sw b/examples/threebody/CdTeZnSeHgS0.sw deleted file mode 100644 index d6f05d41df..0000000000 --- a/examples/threebody/CdTeZnSeHgS0.sw +++ /dev/null @@ -1,233 +0,0 @@ -### DATE: 2013-08-09 CONTRIBUTOR: X. W. Zhou, xzhou@sandia.gov, CITATION: Zhou, Ward, Martin, van Swol, Cruz-Campa, and D. Zubia, Phys. Rev. B, 88, 085309 (2013). -# -# Note that the way the parameters can be entered is not unique. -# As one way, we assume that eps_ijk is equal to eps_ik and -# lambda_ijk is equal to sqrt(lambda_ij*eps_ij*lambda_ik*eps_ik)/eps_ik, -# and all other parameters in the ijk line are for ik. -# -# The twobody ik pair parameters are entered on the i*k lines, where * -# can be any species. This is consistent with the LAMMPS requirement -# that twobody ik parameters be defined on the ikk line. Entries on all -# the other i*k lines are ignored by LAMMPS -# -# These entries are in LAMMPS "metal" units: epsilon = eV; -# sigma = Angstroms; other quantities are unitless -# -# cutoff distance = 4.632 -# eps sigma a lambda gamma cos(theta) A B p q tol -Cd Cd Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Cd Te 1.385284e+00 2.352141e+00 1.810919e+00 3.002537e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Cd Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.251831e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Cd Se 1.352371e+00 2.045165e+00 1.953387e+00 3.038855e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Cd Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.058167e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Cd S 1.300376e+00 1.804151e+00 2.124568e+00 3.099013e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Te Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.517858e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Te Te 1.385284e+00 2.352141e+00 1.810919e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Te Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.602259e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Te Se 1.352371e+00 2.045165e+00 1.953387e+00 3.289311e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Te Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.475051e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Te S 1.300376e+00 1.804151e+00 2.124568e+00 3.354428e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Zn Cd 1.182358e+00 2.663951e+00 1.527956e+00 2.484224e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Zn Te 1.385284e+00 2.352141e+00 1.810919e+00 2.295069e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Zn Zn 6.908179e-01 2.238699e+00 1.812616e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Zn Se 1.352371e+00 2.045165e+00 1.953387e+00 2.322829e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Zn Hg 4.881231e-01 2.432694e+00 1.677987e+00 3.866344e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Zn S 1.300376e+00 1.804151e+00 2.124568e+00 2.368813e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Se Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.475816e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Se Te 1.385284e+00 2.352141e+00 1.810919e+00 3.211159e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Se Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.547256e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Se Se 1.352371e+00 2.045165e+00 1.953387e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Se Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.409618e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Se S 1.300376e+00 1.804151e+00 2.124568e+00 3.314338e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Hg Cd 1.182358e+00 2.663951e+00 1.527956e+00 2.088207e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Hg Te 1.385284e+00 2.352141e+00 1.810919e+00 1.929206e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Hg Zn 6.908179e-01 2.238699e+00 1.812616e+00 2.731909e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Hg Se 1.352371e+00 2.045165e+00 1.953387e+00 1.952541e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Hg Hg 4.881231e-01 2.432694e+00 1.677987e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd Hg S 1.300376e+00 1.804151e+00 2.124568e+00 1.991194e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd S Cd 1.182358e+00 2.663951e+00 1.527956e+00 3.408343e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.674460e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd S Te 1.385284e+00 2.352141e+00 1.810919e+00 3.148823e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd S Zn 6.908179e-01 2.238699e+00 1.812616e+00 4.458985e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd S Se 1.352371e+00 2.045165e+00 1.953387e+00 3.186911e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Cd S Hg 4.881231e-01 2.432694e+00 1.677987e+00 5.304605e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Cd S S 1.300376e+00 1.804151e+00 2.124568e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Cd Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Cd Te 1.849775e+00 2.905254e+00 1.594353e+00 2.812506e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Cd Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.076200e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Cd Se 1.295053e+00 2.231716e+00 1.809645e+00 3.361313e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Cd Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.485063e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Cd S 1.450015e+00 2.297301e+00 1.726905e+00 3.176630e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Te Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.755548e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Te Te 1.849775e+00 2.905254e+00 1.594353e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Te Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.554713e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Te Se 1.295053e+00 2.231716e+00 1.809645e+00 3.884177e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Te Hg 1.204715e+00 2.135591e+00 1.892491e+00 4.027176e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Te S 1.450015e+00 2.297301e+00 1.726905e+00 3.670765e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Zn Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.433620e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Zn Te 1.849775e+00 2.905254e+00 1.594353e+00 2.971408e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Zn Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Zn Se 1.295053e+00 2.231716e+00 1.809645e+00 3.551222e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Zn Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.681964e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Zn S 1.450015e+00 2.297301e+00 1.726905e+00 3.356105e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Se Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.142373e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Se Te 1.849775e+00 2.905254e+00 1.594353e+00 2.719366e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Se Zn 1.546239e+00 2.056363e+00 1.907922e+00 2.974328e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Se Se 1.295053e+00 2.231716e+00 1.809645e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Se Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.369652e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Se S 1.450015e+00 2.297301e+00 1.726905e+00 3.071433e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Hg Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.030791e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Hg Te 1.849775e+00 2.905254e+00 1.594353e+00 2.622805e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te Hg Zn 1.546239e+00 2.056363e+00 1.907922e+00 2.868714e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Hg Se 1.295053e+00 2.231716e+00 1.809645e+00 3.134597e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Hg Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te Hg S 1.450015e+00 2.297301e+00 1.726905e+00 2.962370e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te S Cd 1.385284e+00 2.352141e+00 1.810919e+00 3.325065e+01 1.200000e+00 -3.333333e-01 7.049600e+00 8.861252e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te S Te 1.849775e+00 2.905254e+00 1.594353e+00 2.877465e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.307283e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Te S Zn 1.546239e+00 2.056363e+00 1.907922e+00 3.147250e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te S Se 1.295053e+00 2.231716e+00 1.809645e+00 3.438949e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te S Hg 1.204715e+00 2.135591e+00 1.892491e+00 3.565557e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Te S S 1.450015e+00 2.297301e+00 1.726905e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Cd Cd 6.908179e-01 2.238699e+00 1.812616e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Cd Te 1.546239e+00 2.056363e+00 1.907922e+00 2.172335e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Cd Zn 1.392961e+00 2.367650e+00 1.525521e+00 2.288736e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Cd Se 1.691181e+00 2.028827e+00 1.836907e+00 2.077161e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Cd Hg 4.951616e-01 2.239186e+00 1.761363e+00 3.838766e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Cd S 2.208390e+00 2.323783e+00 1.589241e+00 1.817721e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Te Cd 6.908179e-01 2.238699e+00 1.812616e+00 4.862279e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Te Te 1.546239e+00 2.056363e+00 1.907922e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Te Zn 1.392961e+00 2.367650e+00 1.525521e+00 3.424146e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Te Se 1.691181e+00 2.028827e+00 1.836907e+00 3.107611e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Te Hg 4.951616e-01 2.239186e+00 1.761363e+00 5.743124e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Te S 2.208390e+00 2.323783e+00 1.589241e+00 2.719467e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Zn Cd 6.908179e-01 2.238699e+00 1.812616e+00 4.614993e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Zn Te 1.546239e+00 2.056363e+00 1.907922e+00 3.084711e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Zn Zn 1.392961e+00 2.367650e+00 1.525521e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Zn Se 1.691181e+00 2.028827e+00 1.836907e+00 2.949563e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Zn Hg 4.951616e-01 2.239186e+00 1.761363e+00 5.451040e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Zn S 2.208390e+00 2.323783e+00 1.589241e+00 2.581160e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Se Cd 6.908179e-01 2.238699e+00 1.812616e+00 5.085067e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Se Te 1.546239e+00 2.056363e+00 1.907922e+00 3.398914e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Se Zn 1.392961e+00 2.367650e+00 1.525521e+00 3.581039e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Se Se 1.691181e+00 2.028827e+00 1.836907e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Se Hg 4.951616e-01 2.239186e+00 1.761363e+00 6.006272e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Se S 2.208390e+00 2.323783e+00 1.589241e+00 2.844072e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Hg Cd 6.908179e-01 2.238699e+00 1.812616e+00 2.751535e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Hg Te 1.546239e+00 2.056363e+00 1.907922e+00 1.839156e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Hg Zn 1.392961e+00 2.367650e+00 1.525521e+00 1.937704e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Hg Se 1.691181e+00 2.028827e+00 1.836907e+00 1.758578e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Hg Hg 4.951616e-01 2.239186e+00 1.761363e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn Hg S 2.208390e+00 2.323783e+00 1.589241e+00 1.538930e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn S Cd 6.908179e-01 2.238699e+00 1.812616e+00 5.810847e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.010632e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn S Te 1.546239e+00 2.056363e+00 1.907922e+00 3.884033e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.255846e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Zn S Zn 1.392961e+00 2.367650e+00 1.525521e+00 4.092153e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.676279e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn S Se 1.691181e+00 2.028827e+00 1.836907e+00 3.713865e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn S Hg 4.951616e-01 2.239186e+00 1.761363e+00 6.863534e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Zn S S 2.208390e+00 2.323783e+00 1.589241e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Cd Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Cd Te 1.295053e+00 2.231716e+00 1.809645e+00 3.321142e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Cd Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.906271e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Cd Se 2.400781e+00 2.789002e+00 1.544925e+00 2.439242e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Cd Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.315126e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Cd S 1.307592e+00 2.229392e+00 1.747782e+00 3.305180e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Te Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.180382e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Te Te 1.295053e+00 2.231716e+00 1.809645e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Te Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.844016e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Te Se 2.400781e+00 2.789002e+00 1.544925e+00 2.386992e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Te Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.244113e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Te S 1.307592e+00 2.229392e+00 1.747782e+00 3.234380e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Zn Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.634382e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Zn Te 1.295053e+00 2.231716e+00 1.809645e+00 3.713938e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Zn Zn 1.691181e+00 2.028827e+00 1.836907e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Zn Se 2.400781e+00 2.789002e+00 1.544925e+00 2.727735e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Zn Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.707211e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Zn S 1.307592e+00 2.229392e+00 1.747782e+00 3.696088e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Se Cd 1.352371e+00 2.045165e+00 1.953387e+00 4.330238e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Se Te 1.295053e+00 2.231716e+00 1.809645e+00 4.425026e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Se Zn 1.691181e+00 2.028827e+00 1.836907e+00 3.872260e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Se Se 2.400781e+00 2.789002e+00 1.544925e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Se Hg 1.299758e+00 2.113406e+00 1.831821e+00 4.417011e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Se S 1.307592e+00 2.229392e+00 1.747782e+00 4.403758e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Hg Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.186153e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Hg Te 1.295053e+00 2.231716e+00 1.809645e+00 3.255898e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Hg Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.849177e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Hg Se 2.400781e+00 2.789002e+00 1.544925e+00 2.391323e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se Hg Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se Hg S 1.307592e+00 2.229392e+00 1.747782e+00 3.240249e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se S Cd 1.352371e+00 2.045165e+00 1.953387e+00 3.195742e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.116149e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se S Te 1.295053e+00 2.231716e+00 1.809645e+00 3.265696e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.005396e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se S Zn 1.691181e+00 2.028827e+00 1.836907e+00 2.857751e+01 1.200000e+00 -3.333333e-01 7.049600e+00 9.510930e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se S Se 2.400781e+00 2.789002e+00 1.544925e+00 2.398520e+01 1.200000e+00 -3.333333e-01 7.917000e+00 7.672131e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Se S Hg 1.299758e+00 2.113406e+00 1.831821e+00 3.259780e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Se S S 1.307592e+00 2.229392e+00 1.747782e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Cd Cd 4.881231e-01 2.432694e+00 1.677987e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Cd Te 1.204715e+00 2.135591e+00 1.892491e+00 2.068740e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Cd Zn 4.951616e-01 2.239186e+00 1.761363e+00 3.226819e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Cd Se 1.299758e+00 2.113406e+00 1.831821e+00 1.991668e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Cd Hg 1.272807e+00 2.699097e+00 1.498503e+00 2.012643e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Cd S 1.531211e+00 2.025045e+00 1.833708e+00 1.834976e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Te Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.105765e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Te Te 1.204715e+00 2.135591e+00 1.892491e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Te Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.069347e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Te Se 1.299758e+00 2.113406e+00 1.831821e+00 3.128919e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Te Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.161872e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Te S 1.531211e+00 2.025045e+00 1.833708e+00 2.882756e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Zn Cd 4.881231e-01 2.432694e+00 1.677987e+00 3.273348e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Zn Te 1.204715e+00 2.135591e+00 1.892491e+00 2.083602e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Zn Zn 4.951616e-01 2.239186e+00 1.761363e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Zn Se 1.299758e+00 2.113406e+00 1.831821e+00 2.005976e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Zn Hg 1.272807e+00 2.699097e+00 1.498503e+00 2.027102e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Zn S 1.531211e+00 2.025045e+00 1.833708e+00 1.848159e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Se Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.303345e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Se Te 1.204715e+00 2.135591e+00 1.892491e+00 3.375766e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Se Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.265518e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Se Se 1.299758e+00 2.113406e+00 1.831821e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Se Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.284228e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Se S 1.531211e+00 2.025045e+00 1.833708e+00 2.994311e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Hg Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.248074e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Hg Te 1.204715e+00 2.135591e+00 1.892491e+00 3.340584e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Hg Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.210641e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Hg Se 1.299758e+00 2.113406e+00 1.831821e+00 3.216129e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Hg Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg Hg S 1.531211e+00 2.025045e+00 1.833708e+00 2.963105e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg S Cd 4.881231e-01 2.432694e+00 1.677987e+00 5.756205e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.250999e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg S Te 1.204715e+00 2.135591e+00 1.892491e+00 3.664028e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.445180e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg S Zn 4.951616e-01 2.239186e+00 1.761363e+00 5.715148e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.461167e-01 4.000000e+00 0.000000e+00 0.000000e+00 -Hg S Se 1.299758e+00 2.113406e+00 1.831821e+00 3.527522e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.150200e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg S Hg 1.272807e+00 2.699097e+00 1.498503e+00 3.564673e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.211532e+00 4.000000e+00 0.000000e+00 0.000000e+00 -Hg S S 1.531211e+00 2.025045e+00 1.833708e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Cd Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Cd Te 1.450015e+00 2.297301e+00 1.726905e+00 3.077737e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Cd Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.493905e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Cd Se 1.307592e+00 2.229392e+00 1.747782e+00 3.241019e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Cd Hg 1.531211e+00 2.025045e+00 1.833708e+00 2.995023e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Cd S 2.434871e+00 2.423171e+00 1.711097e+00 2.375088e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Te Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.431904e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Te Te 1.450015e+00 2.297301e+00 1.726905e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Te Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.633490e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Te Se 1.307592e+00 2.229392e+00 1.747782e+00 3.422421e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Te Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.162656e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Te S 2.434871e+00 2.423171e+00 1.711097e+00 2.508023e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Zn Cd 1.300376e+00 1.804151e+00 2.124568e+00 4.235326e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Zn Te 1.450015e+00 2.297301e+00 1.726905e+00 4.010837e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Zn Zn 2.208390e+00 2.323783e+00 1.589241e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Zn Se 1.307592e+00 2.229392e+00 1.747782e+00 4.223622e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Zn Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.903046e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Zn S 2.434871e+00 2.423171e+00 1.711097e+00 3.095161e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Se Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.259006e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Se Te 1.450015e+00 2.297301e+00 1.726905e+00 3.086266e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Se Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.500815e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Se Se 1.307592e+00 2.229392e+00 1.747782e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Se Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.003322e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Se S 2.434871e+00 2.423171e+00 1.711097e+00 2.381670e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Hg Cd 1.300376e+00 1.804151e+00 2.124568e+00 3.526684e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Hg Te 1.450015e+00 2.297301e+00 1.726905e+00 3.339756e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Hg Zn 2.208390e+00 2.323783e+00 1.589241e+00 2.706220e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Hg Se 1.307592e+00 2.229392e+00 1.747782e+00 3.516939e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S Hg Hg 1.531211e+00 2.025045e+00 1.833708e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S Hg S 2.434871e+00 2.423171e+00 1.711097e+00 2.577288e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S S Cd 1.300376e+00 1.804151e+00 2.124568e+00 4.447203e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.540087e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S S Te 1.450015e+00 2.297301e+00 1.726905e+00 4.211484e+01 1.200000e+00 -3.333333e-01 7.049600e+00 7.794685e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S S Zn 2.208390e+00 2.323783e+00 1.589241e+00 3.412585e+01 1.200000e+00 -3.333333e-01 7.049600e+00 4.643181e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S S Se 1.307592e+00 2.229392e+00 1.747782e+00 4.434914e+01 1.200000e+00 -3.333333e-01 7.049600e+00 6.932325e-01 4.000000e+00 0.000000e+00 0.000000e+00 -S S Hg 1.531211e+00 2.025045e+00 1.833708e+00 4.098300e+01 1.200000e+00 -3.333333e-01 7.049600e+00 1.184541e+00 4.000000e+00 0.000000e+00 0.000000e+00 -S S S 2.434871e+00 2.423171e+00 1.711097e+00 3.250000e+01 1.200000e+00 -3.333333e-01 7.917000e+00 1.049688e+00 4.000000e+00 0.000000e+00 0.000000e+00 diff --git a/examples/threebody/InP.vashishta b/examples/threebody/InP.vashishta deleted file mode 100644 index 9fefd4ef19..0000000000 --- a/examples/threebody/InP.vashishta +++ /dev/null @@ -1,38 +0,0 @@ -# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002 -# -# Vashishta potential file for InP, Branicio, Rino, Gan and Tsuzuki, -# J. Phys Condensed Matter 21 (2009) 095002 -# -# These entries are in LAMMPS "metal" units: -# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge); -# lambda1, lambda4, rc, r0, gamma = Angstroms; -# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV; -# other quantities are unitless - -# element1 element2 element3 -# H eta Zi Zj lambda1 D lambda4 -# W rc B gamma r0 C cos(theta) - -In In In 273.584 7 -1.21 -1.21 4.5 0.0 2.75 - 0.0 6.0 0.0 0.0 0.0 0.0 0.0 - -P P P 1813.06 7 1.21 1.21 4.5 52.7067 2.75 - 0.0 6.0 0.0 0.0 0.0 0.0 -0.333333333333 - -In P P 4847.09 9 1.21 -1.21 4.5 26.3533 2.75 - 270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333 - -P In In 4847.09 9 1.21 -1.21 4.5 26.3533 2.75 - 270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333 - -In In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -In P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -P In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -P P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 diff --git a/examples/threebody/InP.vashishta b/examples/threebody/InP.vashishta new file mode 120000 index 0000000000..61b3b88359 --- /dev/null +++ b/examples/threebody/InP.vashishta @@ -0,0 +1 @@ +../../potentials/InP.vashishta \ No newline at end of file diff --git a/examples/threebody/Si.tersoff.mod b/examples/threebody/Si.tersoff.mod new file mode 120000 index 0000000000..668f7c83f1 --- /dev/null +++ b/examples/threebody/Si.tersoff.mod @@ -0,0 +1 @@ +../../potentials/Si.tersoff.mod \ No newline at end of file diff --git a/examples/threebody/Si.tersoff.modc b/examples/threebody/Si.tersoff.modc new file mode 120000 index 0000000000..eaf8b6e3ab --- /dev/null +++ b/examples/threebody/Si.tersoff.modc @@ -0,0 +1 @@ +../../potentials/Si.tersoff.modc \ No newline at end of file diff --git a/examples/threebody/in.threebody b/examples/threebody/in.threebody index db11bfec4c..a030523901 100644 --- a/examples/threebody/in.threebody +++ b/examples/threebody/in.threebody @@ -134,7 +134,7 @@ run 100 clear read_restart restart.equil - +newton on on pair_style tersoff/mod/c pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si diff --git a/examples/threebody/log.27Nov18.threebody.g++.1 b/examples/threebody/log.27Nov18.threebody.g++.1 new file mode 100644 index 0000000000..71a0e2369c --- /dev/null +++ b/examples/threebody/log.27Nov18.threebody.g++.1 @@ -0,0 +1,524 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple regression tests for threebody potentials + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# cubic diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 + +create_box 8 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8 +Created 512 atoms + Time spent = 0.000483751 secs + +mass * 28.06 + +velocity all create $t 5287287 mom yes rot yes dist gaussian +velocity all create 1800 5287287 mom yes rot yes dist gaussian + +# Equilibrate using Stillinger-Weber model for silicon + +pair_style sw +pair_coeff * * Si.sw Si Si Si Si Si Si Si Si +Reading potential file Si.sw with DATE: 2007-06-11 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.77118 + ghost atom cutoff = 4.77118 + binsize = 2.38559, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sw, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.982 | 2.982 | 2.982 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1800 -2220.3392 0 -2101.4457 12358.626 + 10 993.48824 -2166.8749 0 -2101.3265 14121.853 + 20 587.90768 -2139.6876 0 -2101.3093 11864.886 + 30 1030.8616 -2167.8446 0 -2101.3947 6649.2566 + 40 724.62874 -2145.9637 0 -2101.3436 5859.6447 + 50 490.9053 -2129.5491 0 -2101.3077 6326.5434 + 60 960.24533 -2159.427 0 -2101.3794 5733.9889 + 70 906.76518 -2154.3675 0 -2101.3496 8380.4834 + 80 800.7253 -2146.0714 0 -2101.3113 11515.737 + 90 1249.2719 -2173.9445 0 -2101.3818 11593.728 + 100 1080.3797 -2160.6174 0 -2101.3445 12414.602 +Loop time of 0.129171 on 1 procs for 100 steps with 512 atoms + +Performance: 66.888 ns/day, 0.359 hours/ns, 774.165 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.12468 | 0.12468 | 0.12468 | 0.0 | 96.52 +Neigh | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 1.33 +Comm | 0.00088573 | 0.00088573 | 0.00088573 | 0.0 | 0.69 +Output | 0.00011206 | 0.00011206 | 0.00011206 | 0.0 | 0.09 +Modify | 0.0014365 | 0.0014365 | 0.0014365 | 0.0 | 1.11 +Other | | 0.0003417 | | | 0.26 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1017 ave 1017 max 1017 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 14044 ave 14044 max 14044 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14044 +Ave neighs/atom = 27.4297 +Neighbor list builds = 2 +Dangerous builds = 0 + +write_restart restart.equil + +# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms + +pair_style sw +pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te +Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.632 + ghost atom cutoff = 5.632 + binsize = 2.816, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sw, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.758 | 2.758 | 2.758 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1080.3797 -621.93681 0 -562.66385 464005.01 + 110 1512.4547 -648.51133 0 -562.74194 463733.24 + 120 1959.7565 -675.18668 0 -562.8255 486580.33 + 130 1138.5498 -618.80419 0 -562.6427 515406.41 + 140 1827.3403 -662.43867 0 -562.78985 485719 + 150 1822.9803 -659.56725 0 -562.76627 465652.59 + 160 1128.3444 -611.92808 0 -562.65512 469836.33 + 170 1699.6402 -647.82381 0 -562.75353 467977.54 + 180 1840.047 -654.5552 0 -562.77005 488397.41 + 190 1312.0974 -617.70228 0 -562.6629 510856.48 + 200 1809.8409 -648.6173 0 -562.75377 490822.97 +Loop time of 0.399255 on 1 procs for 100 steps with 512 atoms + +Performance: 21.640 ns/day, 1.109 hours/ns, 250.467 timesteps/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.38979 | 0.38979 | 0.38979 | 0.0 | 97.63 +Neigh | 0.0061283 | 0.0061283 | 0.0061283 | 0.0 | 1.53 +Comm | 0.0013483 | 0.0013483 | 0.0013483 | 0.0 | 0.34 +Output | 0.00016642 | 0.00016642 | 0.00016642 | 0.0 | 0.04 +Modify | 0.0014937 | 0.0014937 | 0.0014937 | 0.0 | 0.37 +Other | | 0.0003231 | | | 0.08 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1386 ave 1386 max 1386 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 17388 ave 17388 max 17388 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 17388 +Ave neighs/atom = 33.9609 +Neighbor list builds = 5 +Dangerous builds = 0 + +# Test Vashishta model for In/P + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms + +pair_style vashishta +pair_coeff * * InP.vashishta In In In In P P P P +Reading potential file InP.vashishta with DATE: 2015-10-14 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.783 | 2.783 | 2.783 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1080.3797 -1491.8652 0 -1432.5922 358930.65 + 110 1299.3069 -1504.494 0 -1432.6803 347566.41 + 120 1396.3035 -1508.3817 0 -1432.672 336798.42 + 130 1055.9254 -1483.8342 0 -1432.5849 341035.18 + 140 1543.9033 -1513.8559 0 -1432.6931 314268.54 + 150 1242.5383 -1491.417 0 -1432.6036 311068.53 + 160 1240.1733 -1489.2495 0 -1432.6033 295776.98 + 170 1559.5037 -1507.824 0 -1432.6417 266170.25 + 180 1379.0358 -1493.4092 0 -1432.5869 251410.63 + 190 1465.8073 -1496.8564 0 -1432.6105 226461.31 + 200 1456.6383 -1493.8133 0 -1432.5852 208188.34 +Loop time of 0.198058 on 1 procs for 100 steps with 512 atoms + +Performance: 43.624 ns/day, 0.550 hours/ns, 504.903 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.18746 | 0.18746 | 0.18746 | 0.0 | 94.65 +Neigh | 0.00688 | 0.00688 | 0.00688 | 0.0 | 3.47 +Comm | 0.001718 | 0.001718 | 0.001718 | 0.0 | 0.87 +Output | 0.00013351 | 0.00013351 | 0.00013351 | 0.0 | 0.07 +Modify | 0.0015109 | 0.0015109 | 0.0015109 | 0.0 | 0.76 +Other | | 0.0003531 | | | 0.18 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1810 ave 1810 max 1810 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 36480 ave 36480 max 36480 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 36480 +Ave neighs/atom = 71.25 +Neighbor list builds = 4 +Dangerous builds = 0 + +# Test Tersoff model for B/N/C + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms + +variable fac equal 0.6 +change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap +change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap +change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap +change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap + orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724) + orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724) + orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792) + +pair_style tersoff +pair_coeff * * BNC.tersoff N N N C B B C B +Reading potential file BNC.tersoff with DATE: 2013-03-21 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.74 | 2.74 | 2.74 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1080.3797 -3249.8451 0 -3190.5722 1925371.8 + 110 1878.2843 -3300.7205 0 -3191.0964 1893058.6 + 120 1153.8494 -3250.2114 0 -3190.5436 1932141.4 + 130 1363.8664 -3261.6889 0 -3190.6116 1902268.1 + 140 1565.5505 -3273.0405 0 -3190.6982 1878817 + 150 1416.9458 -3261.1805 0 -3190.865 1916554.4 + 160 1288.6997 -3249.8279 0 -3190.4141 1933227.4 + 170 1768.3043 -3279.2164 0 -3190.4535 1898123.4 + 180 1375.1942 -3251.0929 0 -3190.3781 1896205.1 + 190 1527.0671 -3258.7679 0 -3190.4344 1900673.6 + 200 1586.8691 -3260.4713 0 -3190.434 1912454.8 +Loop time of 0.210082 on 1 procs for 100 steps with 512 atoms + +Performance: 41.127 ns/day, 0.584 hours/ns, 476.006 timesteps/s +98.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.20628 | 0.20628 | 0.20628 | 0.0 | 98.19 +Neigh | 0.00099182 | 0.00099182 | 0.00099182 | 0.0 | 0.47 +Comm | 0.00085139 | 0.00085139 | 0.00085139 | 0.0 | 0.41 +Output | 0.00013494 | 0.00013494 | 0.00013494 | 0.0 | 0.06 +Modify | 0.0014665 | 0.0014665 | 0.0014665 | 0.0 | 0.70 +Other | | 0.0003612 | | | 0.17 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1027 ave 1027 max 1027 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 14602 ave 14602 max 14602 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 14602 +Ave neighs/atom = 28.5195 +Neighbor list builds = 1 +Dangerous builds = 0 + +# Test Tersoff/Mod model for Si + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms + +pair_style tersoff/mod +pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si +Reading potential file Si.tersoff.mod with DATE: 2013-07-26 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/mod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.744 | 2.744 | 2.744 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1080.3797 -2307.5808 0 -2248.3078 18624.75 + 110 851.21757 -2290.7529 0 -2248.2817 21041.97 + 120 1074.6349 -2303.6437 0 -2248.321 15244.809 + 130 1006.5662 -2296.9866 0 -2248.3057 15954.09 + 140 855.64354 -2285.1581 0 -2248.2781 19346.662 + 150 1111.1546 -2300.024 0 -2248.314 14698.998 + 160 1114.7933 -2297.8629 0 -2248.3098 14414.14 + 170 853.9568 -2278.6047 0 -2248.2716 20120.632 + 180 1031.0925 -2288.3481 0 -2248.2949 18332.008 + 190 1230.3458 -2298.9946 0 -2248.3111 15520.302 + 200 1053.8799 -2284.8931 0 -2248.2816 20033.536 +Loop time of 0.158428 on 1 procs for 100 steps with 512 atoms + +Performance: 54.536 ns/day, 0.440 hours/ns, 631.200 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.15318 | 0.15318 | 0.15318 | 0.0 | 96.69 +Neigh | 0.0022631 | 0.0022631 | 0.0022631 | 0.0 | 1.43 +Comm | 0.00093651 | 0.00093651 | 0.00093651 | 0.0 | 0.59 +Output | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.12 +Modify | 0.0015035 | 0.0015035 | 0.0015035 | 0.0 | 0.95 +Other | | 0.0003462 | | | 0.22 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1001 ave 1001 max 1001 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 8872 ave 8872 max 8872 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8872 +Ave neighs/atom = 17.3281 +Neighbor list builds = 3 +Dangerous builds = 0 + +# Test Tersoff/Mod/C model for Si + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid + pair style sw stores no restart info + 512 atoms +newton on on +pair_style tersoff/mod/c +pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si +Reading potential file Si.tersoff.modc with DATE: 2016-11-09 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.20569 + ghost atom cutoff = 4.20569 + binsize = 2.10285, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/mod/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1080.3797 -2307.5509 0 -2248.2779 21368.36 + 110 846.70637 -2290.4239 0 -2248.2488 22856.37 + 120 1083.0906 -2304.1686 0 -2248.2895 17530.457 + 130 1008.7015 -2297.0835 0 -2248.2781 17698.498 + 140 811.71413 -2282.2528 0 -2248.2417 19986.737 + 150 1094.4969 -2298.9718 0 -2248.2836 15822.967 + 160 1100.1109 -2296.9461 0 -2248.2804 15213.75 + 170 801.20165 -2275.2175 0 -2248.2372 20153.957 + 180 994.63485 -2286.1145 0 -2248.2621 19167.021 + 190 1215.6425 -2298.2082 0 -2248.284 15895.654 + 200 992.20385 -2281.0372 0 -2248.2425 19643.792 +Loop time of 0.282035 on 1 procs for 100 steps with 512 atoms + +Performance: 30.634 ns/day, 0.783 hours/ns, 354.565 timesteps/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.27701 | 0.27701 | 0.27701 | 0.0 | 98.22 +Neigh | 0.0021927 | 0.0021927 | 0.0021927 | 0.0 | 0.78 +Comm | 0.00089169 | 0.00089169 | 0.00089169 | 0.0 | 0.32 +Output | 0.0001452 | 0.0001452 | 0.0001452 | 0.0 | 0.05 +Modify | 0.0014682 | 0.0014682 | 0.0014682 | 0.0 | 0.52 +Other | | 0.0003295 | | | 0.12 + +Nlocal: 512 ave 512 max 512 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 972 ave 972 max 972 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 8390 ave 8390 max 8390 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8390 +Ave neighs/atom = 16.3867 +Neighbor list builds = 3 +Dangerous builds = 0 + +Total wall time: 0:00:01 diff --git a/examples/threebody/log.27Nov18.threebody.g++.4 b/examples/threebody/log.27Nov18.threebody.g++.4 new file mode 100644 index 0000000000..429fc4fb9d --- /dev/null +++ b/examples/threebody/log.27Nov18.threebody.g++.4 @@ -0,0 +1,524 @@ +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task +# Simple regression tests for threebody potentials + +# NOTE: These are not intended to represent real materials + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# cubic diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 + +create_box 8 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid +create_atoms 1 region myreg basis 1 1 basis 2 2 basis 3 3 basis 4 4 basis 5 5 basis 6 6 basis 7 7 basis 8 8 +Created 512 atoms + Time spent = 0.000348091 secs + +mass * 28.06 + +velocity all create $t 5287287 mom yes rot yes dist gaussian +velocity all create 1800 5287287 mom yes rot yes dist gaussian + +# Equilibrate using Stillinger-Weber model for silicon + +pair_style sw +pair_coeff * * Si.sw Si Si Si Si Si Si Si Si +Reading potential file Si.sw with DATE: 2007-06-11 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.77118 + ghost atom cutoff = 4.77118 + binsize = 2.38559, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sw, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.957 | 2.957 | 2.957 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1800 -2220.3392 0 -2101.4457 12358.626 + 10 979.93888 -2165.9769 0 -2101.3242 14172.134 + 20 579.6159 -2139.1412 0 -2101.3085 11866.038 + 30 1027.5223 -2167.6187 0 -2101.3942 6885.6751 + 40 711.03138 -2145.0665 0 -2101.3405 6357.0866 + 50 497.18304 -2129.9748 0 -2101.3052 7137.6093 + 60 1008.411 -2162.5834 0 -2101.3804 6745.1775 + 70 947.58674 -2156.9872 0 -2101.3508 9678.1622 + 80 798.43683 -2145.8382 0 -2101.3074 12728.694 + 90 1259.2065 -2174.5324 0 -2101.3799 12033.395 + 100 1100.5203 -2161.8599 0 -2101.3468 12356.137 +Loop time of 0.0414283 on 4 procs for 100 steps with 512 atoms + +Performance: 208.553 ns/day, 0.115 hours/ns, 2413.811 timesteps/s +95.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.030011 | 0.032047 | 0.034036 | 0.8 | 77.36 +Neigh | 0.00043392 | 0.00045151 | 0.0004642 | 0.0 | 1.09 +Comm | 0.0050831 | 0.0067263 | 0.0091536 | 1.8 | 16.24 +Output | 0.00018191 | 0.00018775 | 0.00020432 | 0.0 | 0.45 +Modify | 0.00068116 | 0.0010136 | 0.001817 | 1.5 | 2.45 +Other | | 0.001002 | | | 2.42 + +Nlocal: 128 ave 132 max 126 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 525 ave 527 max 521 min +Histogram: 1 0 0 0 0 0 0 0 2 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 3507 ave 3596 max 3470 min +Histogram: 3 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 14028 +Ave neighs/atom = 27.3984 +Neighbor list builds = 2 +Dangerous builds = 0 + +write_restart restart.equil + +# Test Stillinger-Weber model for Cd/Te/Zn/Se/Hg/S + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid + pair style sw stores no restart info + 512 atoms + +pair_style sw +pair_coeff * * CdTeZnSeHgS0.sw Cd Zn Hg Cd Te S Se Te +Reading potential file CdTeZnSeHgS0.sw with DATE: 2013-08-09 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.632 + ghost atom cutoff = 5.632 + binsize = 2.816, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair sw, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.717 | 2.718 | 2.718 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1100.5203 -621.61663 0 -561.10352 462716.2 + 110 1478.2708 -644.61282 0 -561.16927 464567.29 + 120 1989.4577 -675.5312 0 -561.25985 486476.63 + 130 1185.4652 -620.23829 0 -561.09359 514103.86 + 140 1726.9774 -654.21952 0 -561.20676 488915.22 + 150 1863.2061 -660.66167 0 -561.21416 466985.15 + 160 1119.0313 -609.68409 0 -561.08624 471511.61 + 170 1708.2653 -646.79823 0 -561.18829 468697.42 + 180 1891.8451 -656.32585 0 -561.2042 489912.65 + 190 1345.7703 -618.29258 0 -561.09909 512364.68 + 200 1865.9507 -650.72167 0 -561.19281 491531.23 +Loop time of 0.117532 on 4 procs for 100 steps with 512 atoms + +Performance: 73.512 ns/day, 0.326 hours/ns, 850.834 timesteps/s +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.096347 | 0.10005 | 0.10244 | 0.8 | 85.13 +Neigh | 0.000947 | 0.0010053 | 0.0011535 | 0.3 | 0.86 +Comm | 0.0098422 | 0.012949 | 0.016335 | 2.2 | 11.02 +Output | 0.00017452 | 0.00022596 | 0.00037885 | 0.0 | 0.19 +Modify | 0.00078702 | 0.0013881 | 0.0021975 | 1.6 | 1.18 +Other | | 0.001909 | | | 1.62 + +Nlocal: 128 ave 133 max 125 min +Histogram: 1 0 2 0 0 0 0 0 0 1 +Nghost: 754.5 ave 759 max 748 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 4353 ave 4512 max 4252 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 17412 +Ave neighs/atom = 34.0078 +Neighbor list builds = 3 +Dangerous builds = 0 + +# Test Vashishta model for In/P + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid + pair style sw stores no restart info + 512 atoms + +pair_style vashishta +pair_coeff * * InP.vashishta In In In In P P P P +Reading potential file InP.vashishta with DATE: 2015-10-14 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7 + ghost atom cutoff = 7 + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.739 | 2.739 | 2.739 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1100.5203 -1495.2135 0 -1434.7004 357102.51 + 110 1238.7371 -1502.5372 0 -1434.7528 348870.19 + 120 1409.575 -1511.3137 0 -1434.7612 336831.6 + 130 1081.541 -1487.5554 0 -1434.6881 339244.71 + 140 1484.7455 -1512.0076 0 -1434.7646 313026.51 + 150 1263.0321 -1494.834 0 -1434.7018 306496.02 + 160 1253.4363 -1492.1804 0 -1434.7025 290683.01 + 170 1536.7348 -1508.3735 0 -1434.7312 261755.69 + 180 1342.0478 -1493.0615 0 -1434.6754 248519.54 + 190 1457.921 -1498.4355 0 -1434.6991 223607.39 + 200 1499.5384 -1498.7005 0 -1434.6898 204647.17 +Loop time of 0.060006 on 4 procs for 100 steps with 512 atoms + +Performance: 143.986 ns/day, 0.167 hours/ns, 1666.501 timesteps/s +95.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.043862 | 0.047754 | 0.04964 | 1.0 | 79.58 +Neigh | 0.0018079 | 0.0018883 | 0.0019724 | 0.1 | 3.15 +Comm | 0.0067413 | 0.0083464 | 0.011978 | 2.3 | 13.91 +Output | 0.00018859 | 0.00029892 | 0.00062919 | 0.0 | 0.50 +Modify | 0.00088429 | 0.0011829 | 0.0014911 | 0.8 | 1.97 +Other | | 0.0005357 | | | 0.89 + +Nlocal: 128 ave 129 max 127 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Nghost: 992.75 ave 1001 max 987 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 9116 ave 9213 max 9051 min +Histogram: 1 0 1 1 0 0 0 0 0 1 + +Total # of neighbors = 36464 +Ave neighs/atom = 71.2188 +Neighbor list builds = 4 +Dangerous builds = 0 + +# Test Tersoff model for B/N/C + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid + pair style sw stores no restart info + 512 atoms + +variable fac equal 0.6 +change_box all x scale ${fac} y scale ${fac} z scale ${fac} remap +change_box all x scale 0.6 y scale ${fac} z scale ${fac} remap +change_box all x scale 0.6 y scale 0.6 z scale ${fac} remap +change_box all x scale 0.6 y scale 0.6 z scale 0.6 remap + orthogonal box = (4.3448 0 0) to (17.3792 21.724 21.724) + orthogonal box = (4.3448 4.3448 0) to (17.3792 17.3792 21.724) + orthogonal box = (4.3448 4.3448 4.3448) to (17.3792 17.3792 17.3792) + +pair_style tersoff +pair_coeff * * BNC.tersoff N N N C B B C B +Reading potential file BNC.tersoff with DATE: 2013-03-21 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.699 | 2.699 | 2.699 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1100.5203 -3252.8699 0 -3192.3567 1930742.5 + 110 1858.7735 -3301.1227 0 -3192.8403 1901753.1 + 120 1107.7693 -3248.8236 0 -3192.2522 1953649.4 + 130 1315.4397 -3260.1471 0 -3192.2616 1898713.9 + 140 1541.4371 -3273.1832 0 -3192.41 1887352.3 + 150 1424.7104 -3262.9648 0 -3192.216 1960688.1 + 160 1291.2932 -3251.5548 0 -3192.0201 1914541.2 + 170 1719.1133 -3277.7936 0 -3192.33 1893926 + 180 1312.8066 -3248.6914 0 -3192.1477 1921417.4 + 190 1481.3472 -3257.1585 0 -3191.8991 1927045.6 + 200 1615.282 -3263.8377 0 -3192.055 1920616.3 +Loop time of 0.0635643 on 4 procs for 100 steps with 512 atoms + +Performance: 135.925 ns/day, 0.177 hours/ns, 1573.210 timesteps/s +97.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.051391 | 0.053262 | 0.05459 | 0.6 | 83.79 +Neigh | 0.00052404 | 0.00052798 | 0.00053144 | 0.0 | 0.83 +Comm | 0.0063059 | 0.0079132 | 0.0095143 | 1.5 | 12.45 +Output | 0.00017905 | 0.00029147 | 0.00062609 | 0.0 | 0.46 +Modify | 0.00064421 | 0.00096625 | 0.0012674 | 0.0 | 1.52 +Other | | 0.0006039 | | | 0.95 + +Nlocal: 128 ave 131 max 125 min +Histogram: 1 0 0 1 0 0 1 0 0 1 +Nghost: 526.75 ave 532 max 523 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 3646.5 ave 3722 max 3567 min +Histogram: 1 0 0 1 0 0 0 1 0 1 + +Total # of neighbors = 14586 +Ave neighs/atom = 28.4883 +Neighbor list builds = 2 +Dangerous builds = 0 + +# Test Tersoff/Mod model for Si + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid + pair style sw stores no restart info + 512 atoms + +pair_style tersoff/mod +pair_coeff * * Si.tersoff.mod Si Si Si Si Si Si Si Si +Reading potential file Si.tersoff.mod with DATE: 2013-07-26 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/mod, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1100.5203 -2308.936 0 -2248.4229 18087.231 + 110 821.82813 -2288.8477 0 -2248.3856 21245.995 + 120 1082.3774 -2304.2287 0 -2248.4366 15467.483 + 130 995.26561 -2296.2957 0 -2248.4145 16341.517 + 140 826.97009 -2283.3692 0 -2248.3897 19123.5 + 150 1048.4178 -2296.0496 0 -2248.4172 15060.312 + 160 1101.7884 -2297.2417 0 -2248.426 15070.879 + 170 859.48562 -2279.1747 0 -2248.383 21416.479 + 180 1041.679 -2289.2303 0 -2248.4038 19572.707 + 190 1278.0514 -2302.2822 0 -2248.4257 16006.173 + 200 1097.0682 -2287.8121 0 -2248.3929 20906.774 +Loop time of 0.046846 on 4 procs for 100 steps with 512 atoms + +Performance: 184.434 ns/day, 0.130 hours/ns, 2134.653 timesteps/s +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.037434 | 0.039142 | 0.041109 | 0.7 | 83.55 +Neigh | 0.0005877 | 0.00059921 | 0.00061464 | 0.0 | 1.28 +Comm | 0.0036416 | 0.0055436 | 0.0073476 | 1.8 | 11.83 +Output | 0.00016212 | 0.00027066 | 0.00059533 | 0.0 | 0.58 +Modify | 0.00063038 | 0.00065678 | 0.00067234 | 0.0 | 1.40 +Other | | 0.0006335 | | | 1.35 + +Nlocal: 128 ave 131 max 126 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Nghost: 518 ave 525 max 513 min +Histogram: 1 0 1 0 1 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2202 ave 2257 max 2175 min +Histogram: 1 1 1 0 0 0 0 0 0 1 + +Total # of neighbors = 8808 +Ave neighs/atom = 17.2031 +Neighbor list builds = 3 +Dangerous builds = 0 + +# Test Tersoff/Mod/C model for Si + +clear + using 1 OpenMP thread(s) per MPI task +read_restart restart.equil + restoring atom style atomic from restart + orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid + pair style sw stores no restart info + 512 atoms +newton on on +pair_style tersoff/mod/c +pair_coeff * * Si.tersoff.modc Si Si Si Si Si Si Si Si +Reading potential file Si.tersoff.modc with DATE: 2016-11-09 + +thermo 10 +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 +Resetting global fix info from restart file: + fix style: nvt, fix ID: 1 +fix_modify 1 energy yes +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes +run 100 +All restart file global fix info was re-assigned +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.20569 + ghost atom cutoff = 4.20569 + binsize = 2.10285, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair tersoff/mod/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.701 | 2.701 | 2.701 Mbytes +Step Temp E_pair E_mol TotEng Press + 100 1100.5203 -2308.5955 0 -2248.0824 20775.991 + 110 813.33618 -2287.9469 0 -2248.04 22564.16 + 120 1100.0902 -2305.051 0 -2248.092 17540.971 + 130 1022.9471 -2297.7384 0 -2248.0801 17985.336 + 140 761.99242 -2278.7251 0 -2248.0345 20462.975 + 150 1053.3973 -2296.1039 0 -2248.081 16130.559 + 160 1089.2622 -2296.1059 0 -2248.0833 15434.234 + 170 776.25788 -2273.4496 0 -2248.0321 20642.702 + 180 1016.1885 -2287.4305 0 -2248.0641 19276.936 + 190 1266.3943 -2301.3675 0 -2248.0865 16199.281 + 200 1012.4185 -2282.134 0 -2248.0423 20795.113 +Loop time of 0.0840016 on 4 procs for 100 steps with 512 atoms + +Performance: 102.855 ns/day, 0.233 hours/ns, 1190.454 timesteps/s +97.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.068133 | 0.071658 | 0.075315 | 1.0 | 85.31 +Neigh | 0.00057864 | 0.00058872 | 0.00060058 | 0.0 | 0.70 +Comm | 0.0049844 | 0.008617 | 0.012086 | 2.8 | 10.26 +Output | 0.0001626 | 0.00027418 | 0.00060463 | 0.0 | 0.33 +Modify | 0.00070477 | 0.0011689 | 0.0022428 | 1.8 | 1.39 +Other | | 0.001694 | | | 2.02 + +Nlocal: 128 ave 129 max 127 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 489.75 ave 501 max 481 min +Histogram: 1 0 0 1 1 0 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 2094.5 ave 2121 max 2060 min +Histogram: 1 0 0 1 0 0 0 0 0 2 + +Total # of neighbors = 8378 +Ave neighs/atom = 16.3633 +Neighbor list builds = 3 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/vashishta/InP.vashishta b/examples/vashishta/InP.vashishta deleted file mode 100644 index 9fefd4ef19..0000000000 --- a/examples/vashishta/InP.vashishta +++ /dev/null @@ -1,38 +0,0 @@ -# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002 -# -# Vashishta potential file for InP, Branicio, Rino, Gan and Tsuzuki, -# J. Phys Condensed Matter 21 (2009) 095002 -# -# These entries are in LAMMPS "metal" units: -# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge); -# lambda1, lambda4, rc, r0, gamma = Angstroms; -# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV; -# other quantities are unitless - -# element1 element2 element3 -# H eta Zi Zj lambda1 D lambda4 -# W rc B gamma r0 C cos(theta) - -In In In 273.584 7 -1.21 -1.21 4.5 0.0 2.75 - 0.0 6.0 0.0 0.0 0.0 0.0 0.0 - -P P P 1813.06 7 1.21 1.21 4.5 52.7067 2.75 - 0.0 6.0 0.0 0.0 0.0 0.0 -0.333333333333 - -In P P 4847.09 9 1.21 -1.21 4.5 26.3533 2.75 - 270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333 - -P In In 4847.09 9 1.21 -1.21 4.5 26.3533 2.75 - 270.105 6.0 4.34967 1.0 3.55 7.0 -0.333333333333 - -In In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -In P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -P In P 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -P P In 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 diff --git a/examples/vashishta/InP.vashishta b/examples/vashishta/InP.vashishta new file mode 120000 index 0000000000..61b3b88359 --- /dev/null +++ b/examples/vashishta/InP.vashishta @@ -0,0 +1 @@ +../../potentials/InP.vashishta \ No newline at end of file diff --git a/examples/vashishta/SiO.1990.vashishta b/examples/vashishta/SiO.1990.vashishta deleted file mode 100644 index f0f9ab354f..0000000000 --- a/examples/vashishta/SiO.1990.vashishta +++ /dev/null @@ -1,41 +0,0 @@ -# DATE: 2015-10-14 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov CITATION: P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo, Phys. Rev. B 41, 12197 (1990). -# -# Vashishta potential file for SiO2, P. Vashishta, R. K. Kalia, J. P. Rino, and I. Ebbsjo, -# Phys. Rev. B 41, 12197 (1990). -# -# These parameters, some inferred indirectly, give a good -# match to the energy-volume curve for alpha-quartz in Fig. 2 of the paper. -# -# These entries are in LAMMPS "metal" units: -# H = eV*Angstroms^eta; Zi, Zj = |e| (e = electronic charge); -# lambda1, lambda4, rc, r0, gamma = Angstroms; -# D = eV*Angstroms^4; W = eV*Angstroms^6; B = eV; -# other quantities are unitless -# -# element1 element2 element3 -# H eta Zi Zj lambda1 D lambda4 -# W rc B gamma r0 C cos(theta) - -Si Si Si 0.82023 11 1.6 1.6 999 0.0 4.43 - 0.0 10.0 0.0 0.0 0.0 0.0 0.0 - -O O O 743.848 7 -0.8 -0.8 999 22.1179 4.43 - 0.0 10.0 0.0 0.0 0.0 0.0 0.0 - -O Si Si 163.859 9 -0.8 1.6 999 44.2357 4.43 - 0.0 10.0 20.146 1.0 2.60 0.0 -0.77714596 - -Si O O 163.859 9 1.6 -0.8 999 44.2357 4.43 - 0.0 10.0 5.0365 1.0 2.60 0.0 -0.333333333333 - -Si O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -Si Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -O Si O 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - -O O Si 0.0 0.0 0.0 0.0 0.0 0.0 0.0 - 0.0 0.0 0.0 0.0 0.0 0.0 0.0 diff --git a/examples/vashishta/SiO.1990.vashishta b/examples/vashishta/SiO.1990.vashishta new file mode 120000 index 0000000000..ae56b2bf26 --- /dev/null +++ b/examples/vashishta/SiO.1990.vashishta @@ -0,0 +1 @@ +../../potentials/SiO.1990.vashishta \ No newline at end of file diff --git a/examples/vashishta/log.5Oct16.vashishta.inp.g++.1 b/examples/vashishta/log.27Nov18.vashishta.inp.g++.1 similarity index 85% rename from examples/vashishta/log.5Oct16.vashishta.inp.g++.1 rename to examples/vashishta/log.27Nov18.vashishta.inp.g++.1 index ac454470e9..158cf0b832 100644 --- a/examples/vashishta/log.5Oct16.vashishta.inp.g++.1 +++ b/examples/vashishta/log.27Nov18.vashishta.inp.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # calculate the energy volume curve for InP zincblende # define volume range and filename @@ -39,6 +40,7 @@ Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0) create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 Created 8 atoms + Time spent = 0.000331879 secs mass 1 114.76 mass 2 30.98 @@ -82,19 +84,24 @@ change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 -Memory usage per processor = 2.31867 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta, perpetual + attributes: full, newton on + pair build: full/nsq + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -24.633958 315900.5 160.72 Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +104.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -140,13 +147,13 @@ change_box all x scale 1.00149105588627 y scale 1.00149105588627 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -24.773834 306658.04 161.44 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -156,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -192,13 +199,13 @@ change_box all x scale 1.00148441583558 y scale 1.00148441583558 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -24.909615 297676.86 162.16 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -208,7 +215,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -244,13 +251,13 @@ change_box all x scale 1.00147783466245 y scale 1.00147783466245 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.041417 288949.17 162.88 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -260,7 +267,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -296,13 +303,13 @@ change_box all x scale 1.00147131158722 y scale 1.00147131158722 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.169352 280467.46 163.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -312,7 +319,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -348,13 +355,13 @@ change_box all x scale 1.00146484584395 y scale 1.00146484584395 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.29353 272224.44 164.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -364,7 +371,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -400,13 +407,13 @@ change_box all x scale 1.0014584366801 y scale 1.0014584366801 z scale 1.001458 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.414056 264213.09 165.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -416,7 +423,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -452,13 +459,13 @@ change_box all x scale 1.00145208335626 y scale 1.00145208335626 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.531033 256426.58 165.76 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -468,7 +475,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -504,13 +511,13 @@ change_box all x scale 1.00144578514582 y scale 1.00144578514582 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.644559 248858.32 166.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -520,7 +527,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -556,13 +563,13 @@ change_box all x scale 1.00143954133473 y scale 1.00143954133473 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.754685 240961.62 167.2 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -572,7 +579,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -608,13 +615,13 @@ change_box all x scale 1.00143335122124 y scale 1.00143335122124 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.861049 232444.2 167.92 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -624,7 +631,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -660,13 +667,13 @@ change_box all x scale 1.00142721411559 y scale 1.00142721411559 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -25.963633 224145.09 168.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -676,7 +683,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -712,13 +719,13 @@ change_box all x scale 1.00142112933981 y scale 1.00142112933981 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.062537 216058.21 169.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -728,7 +735,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -764,13 +771,13 @@ change_box all x scale 1.00141509622744 y scale 1.00141509622744 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.157853 208177.66 170.08 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -780,7 +787,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -816,13 +823,13 @@ change_box all x scale 1.00140911412325 y scale 1.00140911412325 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.249672 200497.73 170.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -832,7 +839,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -868,13 +875,13 @@ change_box all x scale 1.00140318238311 y scale 1.00140318238311 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.338085 193012.87 171.52 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -884,7 +891,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -920,13 +927,13 @@ change_box all x scale 1.00139730037362 y scale 1.00139730037362 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.423176 185717.71 172.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -936,7 +943,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -972,13 +979,13 @@ change_box all x scale 1.00139146747202 y scale 1.00139146747202 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.505031 178607.07 172.96 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -988,7 +995,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1024,13 +1031,13 @@ change_box all x scale 1.00138568306585 y scale 1.00138568306585 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.583731 171675.89 173.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1040,7 +1047,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1076,13 +1083,13 @@ change_box all x scale 1.00137994655284 y scale 1.00137994655284 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.659356 164919.29 174.4 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1092,7 +1099,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1128,13 +1135,13 @@ change_box all x scale 1.00137425734062 y scale 1.00137425734062 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.731982 158332.52 175.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1144,7 +1151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1180,13 +1187,13 @@ change_box all x scale 1.00136861484656 y scale 1.00136861484656 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.801686 151911 175.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1196,7 +1203,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1232,13 +1239,13 @@ change_box all x scale 1.00136301849755 y scale 1.00136301849755 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.868541 145650.26 176.56 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1248,7 +1255,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1284,13 +1291,13 @@ change_box all x scale 1.00135746772984 y scale 1.00135746772984 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.932617 139545.98 177.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1300,7 +1307,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1336,13 +1343,13 @@ change_box all x scale 1.00135196198879 y scale 1.00135196198879 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -26.993984 133593.97 178 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1352,7 +1359,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1388,13 +1395,13 @@ change_box all x scale 1.00134650072876 y scale 1.00134650072876 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.05271 127790.17 178.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1404,7 +1411,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1440,13 +1447,13 @@ change_box all x scale 1.00134108341287 y scale 1.00134108341287 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.108861 122130.61 179.44 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1456,7 +1463,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1492,13 +1499,13 @@ change_box all x scale 1.00133570951285 y scale 1.00133570951285 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.1625 116611.48 180.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1508,7 +1515,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1544,13 +1551,13 @@ change_box all x scale 1.00133037850885 y scale 1.00133037850885 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.213689 111229.06 180.88 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1560,7 +1567,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1596,13 +1603,13 @@ change_box all x scale 1.00132508988931 y scale 1.00132508988931 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.26249 105979.74 181.6 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1612,7 +1619,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1648,13 +1655,13 @@ change_box all x scale 1.00131984315076 y scale 1.00131984315076 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.308961 100860.02 182.32 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1664,7 +1671,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1700,13 +1707,13 @@ change_box all x scale 1.00131463779767 y scale 1.00131463779767 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.353159 95866.497 183.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1716,7 +1723,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1752,13 +1759,13 @@ change_box all x scale 1.00130947334229 y scale 1.00130947334229 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.395142 90995.879 183.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1768,7 +1775,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1804,13 +1811,13 @@ change_box all x scale 1.00130434930454 y scale 1.00130434930454 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.434962 86244.961 184.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1820,7 +1827,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1856,13 +1863,13 @@ change_box all x scale 1.00129926521177 y scale 1.00129926521177 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.472674 81610.631 185.2 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1872,7 +1879,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1908,13 +1915,13 @@ change_box all x scale 1.00129422059873 y scale 1.00129422059873 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.508329 77089.868 185.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1924,7 +1931,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1960,13 +1967,13 @@ change_box all x scale 1.00128921500731 y scale 1.00128921500731 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.541977 72679.738 186.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1976,7 +1983,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2012,13 +2019,13 @@ change_box all x scale 1.0012842479865 y scale 1.0012842479865 z scale 1.001284 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.573668 68377.392 187.36 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2028,7 +2035,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2064,13 +2071,13 @@ change_box all x scale 1.00127931909221 y scale 1.00127931909221 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.603449 64180.061 188.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2080,7 +2087,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2116,13 +2123,13 @@ change_box all x scale 1.00127442788711 y scale 1.00127442788711 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.631367 60085.056 188.8 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2132,7 +2139,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2168,13 +2175,13 @@ change_box all x scale 1.00126957394058 y scale 1.00126957394058 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.657467 56089.763 189.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2184,7 +2191,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2220,13 +2227,13 @@ change_box all x scale 1.0012647568285 y scale 1.0012647568285 z scale 1.001264 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.681794 52191.643 190.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2236,7 +2243,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2272,13 +2279,13 @@ change_box all x scale 1.00125997613317 y scale 1.00125997613317 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.70439 48388.229 190.96 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2288,7 +2295,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2324,13 +2331,13 @@ change_box all x scale 1.00125523144319 y scale 1.00125523144319 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.725298 44677.122 191.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2340,7 +2347,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2376,13 +2383,13 @@ change_box all x scale 1.00125052235334 y scale 1.00125052235334 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.744558 41055.991 192.4 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2392,7 +2399,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2428,13 +2435,13 @@ change_box all x scale 1.00124584846443 y scale 1.00124584846443 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.762211 37522.57 193.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2444,7 +2451,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2480,13 +2487,13 @@ change_box all x scale 1.00124120938324 y scale 1.00124120938324 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.778295 34074.656 193.84 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2496,7 +2503,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2532,13 +2539,13 @@ change_box all x scale 1.00123660472238 y scale 1.00123660472238 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.792849 30710.109 194.56 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2548,7 +2555,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2584,13 +2591,13 @@ change_box all x scale 1.00123203410018 y scale 1.00123203410018 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.805909 27426.844 195.28 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2600,7 +2607,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2636,13 +2643,13 @@ change_box all x scale 1.00122749714061 y scale 1.00122749714061 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.817512 24222.838 196 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2652,7 +2659,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2688,13 +2695,13 @@ change_box all x scale 1.00122299347313 y scale 1.00122299347313 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.827692 21096.12 196.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2704,7 +2711,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2740,13 +2747,13 @@ change_box all x scale 1.00121852273265 y scale 1.00121852273265 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.836484 18044.775 197.44 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2756,7 +2763,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2792,13 +2799,13 @@ change_box all x scale 1.00121408455937 y scale 1.00121408455937 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.843921 15066.941 198.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2808,7 +2815,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2844,13 +2851,13 @@ change_box all x scale 1.00120967859874 y scale 1.00120967859874 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.850036 12160.805 198.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2860,7 +2867,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2896,13 +2903,13 @@ change_box all x scale 1.00120530450131 y scale 1.00120530450131 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.854861 9324.604 199.6 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +279.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2912,7 +2919,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2948,13 +2955,13 @@ change_box all x scale 1.00120096192269 y scale 1.00120096192269 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.858427 6556.6223 200.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2964,7 +2971,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3000,13 +3007,13 @@ change_box all x scale 1.00119665052343 y scale 1.00119665052343 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.860764 3855.1909 201.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3016,7 +3023,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3052,13 +3059,13 @@ change_box all x scale 1.00119236996892 y scale 1.00119236996892 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.861902 1218.6858 201.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3068,7 +3075,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3104,13 +3111,13 @@ change_box all x scale 1.00118811992934 y scale 1.00118811992934 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.861869 -1354.4738 202.48 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3120,7 +3127,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3156,13 +3163,13 @@ change_box all x scale 1.00118390007955 y scale 1.00118390007955 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.860694 -3865.8261 203.2 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3172,7 +3179,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3208,13 +3215,13 @@ change_box all x scale 1.00117971009901 y scale 1.00117971009901 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.858404 -6316.8685 203.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3224,7 +3231,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3260,13 +3267,13 @@ change_box all x scale 1.00117554967171 y scale 1.00117554967171 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.855025 -8709.0584 204.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3276,7 +3283,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3312,13 +3319,13 @@ change_box all x scale 1.00117141848607 y scale 1.00117141848607 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.850585 -11043.815 205.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3328,7 +3335,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3364,13 +3371,13 @@ change_box all x scale 1.00116731623489 y scale 1.00116731623489 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.845108 -13322.519 206.08 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3380,7 +3387,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3416,13 +3423,13 @@ change_box all x scale 1.00116324261524 y scale 1.00116324261524 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.838619 -15546.516 206.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3432,7 +3439,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3468,13 +3475,13 @@ change_box all x scale 1.00115919732841 y scale 1.00115919732841 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.831143 -17717.116 207.52 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3484,7 +3491,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3520,13 +3527,13 @@ change_box all x scale 1.00115518007984 y scale 1.00115518007984 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.822703 -19835.593 208.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3536,7 +3543,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3572,13 +3579,13 @@ change_box all x scale 1.00115119057903 y scale 1.00115119057903 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.813323 -21903.19 208.96 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3588,7 +3595,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3624,13 +3631,13 @@ change_box all x scale 1.00114722853949 y scale 1.00114722853949 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.803024 -23921.116 209.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3640,7 +3647,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3676,13 +3683,13 @@ change_box all x scale 1.00114329367864 y scale 1.00114329367864 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.79183 -25890.55 210.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3692,7 +3699,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3728,13 +3735,13 @@ change_box all x scale 1.00113938571778 y scale 1.00113938571778 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.779761 -27812.639 211.12 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +279.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3744,7 +3751,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3780,13 +3787,13 @@ change_box all x scale 1.00113550438201 y scale 1.00113550438201 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.76684 -29688.502 211.84 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3796,7 +3803,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3832,13 +3839,13 @@ change_box all x scale 1.00113164940016 y scale 1.00113164940016 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.753085 -31519.227 212.56 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3848,7 +3855,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3884,13 +3891,13 @@ change_box all x scale 1.00112782050471 y scale 1.00112782050471 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.738517 -33305.877 213.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3900,7 +3907,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3936,13 +3943,13 @@ change_box all x scale 1.00112401743178 y scale 1.00112401743178 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.723157 -35049.484 214 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3952,7 +3959,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3988,13 +3995,13 @@ change_box all x scale 1.00112023992101 y scale 1.00112023992101 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.707022 -36751.057 214.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4004,7 +4011,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4040,13 +4047,13 @@ change_box all x scale 1.00111648771556 y scale 1.00111648771556 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.690132 -38411.578 215.44 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4056,7 +4063,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4092,13 +4099,13 @@ change_box all x scale 1.00111276056198 y scale 1.00111276056198 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.672509 -39943.013 216.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4108,7 +4115,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4144,13 +4151,13 @@ change_box all x scale 1.00110905821022 y scale 1.00110905821022 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.654292 -41126.388 216.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4160,7 +4167,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4196,13 +4203,13 @@ change_box all x scale 1.00110538041355 y scale 1.00110538041355 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.635551 -42275.674 217.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4212,7 +4219,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4248,13 +4255,13 @@ change_box all x scale 1.00110172692849 y scale 1.00110172692849 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.6163 -43391.705 218.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4264,7 +4271,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4300,13 +4307,13 @@ change_box all x scale 1.00109809751476 y scale 1.00109809751476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.596556 -44475.291 219.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4316,7 +4323,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4352,13 +4359,13 @@ change_box all x scale 1.00109449193525 y scale 1.00109449193525 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.576332 -45527.226 219.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4368,7 +4375,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4404,13 +4411,13 @@ change_box all x scale 1.00109090995595 y scale 1.00109090995595 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.555642 -46548.278 220.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4420,7 +4427,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4456,13 +4463,13 @@ change_box all x scale 1.00108735134592 y scale 1.00108735134592 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.5345 -47539.201 221.2 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4472,7 +4479,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4508,13 +4515,13 @@ change_box all x scale 1.00108381587718 y scale 1.00108381587718 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.512919 -48500.725 221.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4524,7 +4531,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4560,13 +4567,13 @@ change_box all x scale 1.00108030332476 y scale 1.00108030332476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.490913 -49433.564 222.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4576,7 +4583,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4612,13 +4619,13 @@ change_box all x scale 1.00107681346655 y scale 1.00107681346655 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.468494 -50338.414 223.36 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4628,7 +4635,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4664,13 +4671,13 @@ change_box all x scale 1.00107334608333 y scale 1.00107334608333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.445674 -51215.952 224.08 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4680,7 +4687,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4716,13 +4723,13 @@ change_box all x scale 1.00106990095868 y scale 1.00106990095868 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.422466 -52066.839 224.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4732,7 +4739,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4768,13 +4775,13 @@ change_box all x scale 1.00106647787897 y scale 1.00106647787897 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.398881 -52891.72 225.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4784,7 +4791,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4820,13 +4827,13 @@ change_box all x scale 1.00106307663326 y scale 1.00106307663326 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.374932 -53691.221 226.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4836,7 +4843,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4872,13 +4879,13 @@ change_box all x scale 1.00105969701333 y scale 1.00105969701333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.350628 -54465.955 226.96 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4888,7 +4895,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4924,13 +4931,13 @@ change_box all x scale 1.00105633881357 y scale 1.00105633881357 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.325983 -55216.518 227.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4940,7 +4947,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4976,13 +4983,13 @@ change_box all x scale 1.00105300183098 y scale 1.00105300183098 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.301005 -55943.493 228.4 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4992,7 +4999,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5028,13 +5035,13 @@ change_box all x scale 1.00104968586512 y scale 1.00104968586512 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.275705 -56647.446 229.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5044,7 +5051,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5080,13 +5087,13 @@ change_box all x scale 1.00104639071808 y scale 1.00104639071808 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.250095 -57328.932 229.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5096,7 +5103,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5132,13 +5139,13 @@ change_box all x scale 1.00104311619438 y scale 1.00104311619438 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.224183 -57988.489 230.56 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5148,7 +5155,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5184,13 +5191,13 @@ change_box all x scale 1.00103986210104 y scale 1.00103986210104 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.197979 -58626.644 231.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5200,7 +5207,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5236,13 +5243,13 @@ change_box all x scale 1.00103662824744 y scale 1.00103662824744 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.95 | 2.95 | 2.95 Mbytes Step Temp PotEng Press Volume 0 0 -27.171493 -59243.909 232 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5252,7 +5259,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/vashishta/log.5Oct16.vashishta.inp.g++.4 b/examples/vashishta/log.27Nov18.vashishta.inp.g++.4 similarity index 87% rename from examples/vashishta/log.5Oct16.vashishta.inp.g++.4 rename to examples/vashishta/log.27Nov18.vashishta.inp.g++.4 index c914a530c2..22c58edfef 100644 --- a/examples/vashishta/log.5Oct16.vashishta.inp.g++.4 +++ b/examples/vashishta/log.27Nov18.vashishta.inp.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # calculate the energy volume curve for InP zincblende # define volume range and filename @@ -39,6 +40,7 @@ Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0) create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 Created 8 atoms + Time spent = 0.00030756 secs mass 1 114.76 mass 2 30.98 @@ -82,19 +84,24 @@ change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 -Memory usage per processor = 2.33394 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta, perpetual + attributes: full, newton on + pair build: full/nsq + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -24.633958 315900.5 160.72 -Loop time of 2.5034e-05 on 4 procs for 0 steps with 8 atoms +Loop time of 2.14577e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +81.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -104,7 +111,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.503e-05 | | |100.00 +Other | | 2.146e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -140,13 +147,13 @@ change_box all x scale 1.00149105588627 y scale 1.00149105588627 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -24.773834 306658.04 161.44 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 3.01003e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +65.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -156,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 3.01e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -192,13 +199,13 @@ change_box all x scale 1.00148441583558 y scale 1.00148441583558 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -24.909615 297676.86 162.16 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 2.8193e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +64.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -208,7 +215,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 2.819e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -244,13 +251,13 @@ change_box all x scale 1.00147783466245 y scale 1.00147783466245 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.041417 288949.17 162.88 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +129.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -260,7 +267,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -296,13 +303,13 @@ change_box all x scale 1.00147131158722 y scale 1.00147131158722 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.169352 280467.46 163.6 Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +94.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -348,13 +355,13 @@ change_box all x scale 1.00146484584395 y scale 1.00146484584395 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.29353 272224.44 164.32 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -364,7 +371,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -400,13 +407,13 @@ change_box all x scale 1.0014584366801 y scale 1.0014584366801 z scale 1.001458 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.414056 264213.09 165.04 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +127.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -416,7 +423,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -452,13 +459,13 @@ change_box all x scale 1.00145208335626 y scale 1.00145208335626 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.531033 256426.58 165.76 Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -504,13 +511,13 @@ change_box all x scale 1.00144578514582 y scale 1.00144578514582 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.644559 248858.32 166.48 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.72853e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +101.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -520,7 +527,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.729e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -556,13 +563,13 @@ change_box all x scale 1.00143954133473 y scale 1.00143954133473 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.754685 240961.62 167.2 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -572,7 +579,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -608,13 +615,13 @@ change_box all x scale 1.00143335122124 y scale 1.00143335122124 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.861049 232444.2 167.92 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +121.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -624,7 +631,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -660,13 +667,13 @@ change_box all x scale 1.00142721411559 y scale 1.00142721411559 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -25.963633 224145.09 168.64 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -676,7 +683,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -712,13 +719,13 @@ change_box all x scale 1.00142112933981 y scale 1.00142112933981 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.062537 216058.21 169.36 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +91.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -728,7 +735,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -764,13 +771,13 @@ change_box all x scale 1.00141509622744 y scale 1.00141509622744 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.157853 208177.66 170.08 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +124.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -780,7 +787,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -816,13 +823,13 @@ change_box all x scale 1.00140911412325 y scale 1.00140911412325 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.249672 200497.73 170.8 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +121.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -832,7 +839,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -868,13 +875,13 @@ change_box all x scale 1.00140318238311 y scale 1.00140318238311 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.338085 193012.87 171.52 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +121.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -884,7 +891,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -920,13 +927,13 @@ change_box all x scale 1.00139730037362 y scale 1.00139730037362 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.423176 185717.71 172.24 -Loop time of 1.2517e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.3113e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +114.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -936,7 +943,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.252e-06 | | |100.00 +Other | | 1.311e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -972,13 +979,13 @@ change_box all x scale 1.00139146747202 y scale 1.00139146747202 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.505031 178607.07 172.96 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -988,7 +995,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1024,13 +1031,13 @@ change_box all x scale 1.00138568306585 y scale 1.00138568306585 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.583731 171675.89 173.68 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +125.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1040,7 +1047,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1076,13 +1083,13 @@ change_box all x scale 1.00137994655284 y scale 1.00137994655284 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.659356 164919.29 174.4 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +91.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1092,7 +1099,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1128,13 +1135,13 @@ change_box all x scale 1.00137425734062 y scale 1.00137425734062 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.731982 158332.52 175.12 Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +119.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1180,13 +1187,13 @@ change_box all x scale 1.00136861484656 y scale 1.00136861484656 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.801686 151911 175.84 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1196,7 +1203,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1232,13 +1239,13 @@ change_box all x scale 1.00136301849755 y scale 1.00136301849755 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.868541 145650.26 176.56 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +100.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1248,7 +1255,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1284,13 +1291,13 @@ change_box all x scale 1.00135746772984 y scale 1.00135746772984 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.932617 139545.98 177.28 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1300,7 +1307,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1336,13 +1343,13 @@ change_box all x scale 1.00135196198879 y scale 1.00135196198879 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -26.993984 133593.97 178 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +124.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1352,7 +1359,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1388,13 +1395,13 @@ change_box all x scale 1.00134650072876 y scale 1.00134650072876 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.05271 127790.17 178.72 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1404,7 +1411,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1440,13 +1447,13 @@ change_box all x scale 1.00134108341287 y scale 1.00134108341287 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.108861 122130.61 179.44 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +117.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1456,7 +1463,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1492,13 +1499,13 @@ change_box all x scale 1.00133570951285 y scale 1.00133570951285 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.1625 116611.48 180.16 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +129.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1508,7 +1515,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1544,13 +1551,13 @@ change_box all x scale 1.00133037850885 y scale 1.00133037850885 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.213689 111229.06 180.88 Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +118.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1596,13 +1603,13 @@ change_box all x scale 1.00132508988931 y scale 1.00132508988931 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.26249 105979.74 181.6 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1612,7 +1619,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1648,13 +1655,13 @@ change_box all x scale 1.00131984315076 y scale 1.00131984315076 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.308961 100860.02 182.32 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1664,7 +1671,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1700,13 +1707,13 @@ change_box all x scale 1.00131463779767 y scale 1.00131463779767 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.353159 95866.497 183.04 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.72853e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +101.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1716,7 +1723,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.729e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1752,13 +1759,13 @@ change_box all x scale 1.00130947334229 y scale 1.00130947334229 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.395142 90995.879 183.76 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1768,7 +1775,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1804,13 +1811,13 @@ change_box all x scale 1.00130434930454 y scale 1.00130434930454 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.434962 86244.961 184.48 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1820,7 +1827,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1856,13 +1863,13 @@ change_box all x scale 1.00129926521177 y scale 1.00129926521177 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.472674 81610.631 185.2 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1872,7 +1879,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1908,13 +1915,13 @@ change_box all x scale 1.00129422059873 y scale 1.00129422059873 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.508329 77089.868 185.92 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +100.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1924,7 +1931,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1960,13 +1967,13 @@ change_box all x scale 1.00128921500731 y scale 1.00128921500731 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.541977 72679.738 186.64 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1976,7 +1983,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2012,13 +2019,13 @@ change_box all x scale 1.0012842479865 y scale 1.0012842479865 z scale 1.001284 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.573668 68377.392 187.36 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +131.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2028,7 +2035,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2064,13 +2071,13 @@ change_box all x scale 1.00127931909221 y scale 1.00127931909221 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.603449 64180.061 188.08 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.3113e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +152.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2080,7 +2087,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.311e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2116,13 +2123,13 @@ change_box all x scale 1.00127442788711 y scale 1.00127442788711 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.631367 60085.056 188.8 -Loop time of 1.2517e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +102.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2132,7 +2139,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.252e-06 | | |100.00 +Other | | 2.205e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2168,13 +2175,13 @@ change_box all x scale 1.00126957394058 y scale 1.00126957394058 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.657467 56089.763 189.52 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2184,7 +2191,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2220,13 +2227,13 @@ change_box all x scale 1.0012647568285 y scale 1.0012647568285 z scale 1.001264 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.681794 52191.643 190.24 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2236,7 +2243,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2272,13 +2279,13 @@ change_box all x scale 1.00125997613317 y scale 1.00125997613317 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.70439 48388.229 190.96 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2288,7 +2295,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2324,13 +2331,13 @@ change_box all x scale 1.00125523144319 y scale 1.00125523144319 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.725298 44677.122 191.68 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +111.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2340,7 +2347,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2376,13 +2383,13 @@ change_box all x scale 1.00125052235334 y scale 1.00125052235334 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.744558 41055.991 192.4 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2392,7 +2399,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2428,13 +2435,13 @@ change_box all x scale 1.00124584846443 y scale 1.00124584846443 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.762211 37522.57 193.12 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +121.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2444,7 +2451,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2480,13 +2487,13 @@ change_box all x scale 1.00124120938324 y scale 1.00124120938324 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.778295 34074.656 193.84 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2496,7 +2503,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2532,13 +2539,13 @@ change_box all x scale 1.00123660472238 y scale 1.00123660472238 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.792849 30710.109 194.56 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +117.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2548,7 +2555,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2584,13 +2591,13 @@ change_box all x scale 1.00123203410018 y scale 1.00123203410018 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.805909 27426.844 195.28 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +125.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2600,7 +2607,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2636,13 +2643,13 @@ change_box all x scale 1.00122749714061 y scale 1.00122749714061 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.817512 24222.838 196 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2652,7 +2659,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2688,13 +2695,13 @@ change_box all x scale 1.00122299347313 y scale 1.00122299347313 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.827692 21096.12 196.72 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2704,7 +2711,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2740,13 +2747,13 @@ change_box all x scale 1.00121852273265 y scale 1.00121852273265 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.836484 18044.775 197.44 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +122.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2756,7 +2763,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2792,13 +2799,13 @@ change_box all x scale 1.00121408455937 y scale 1.00121408455937 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.843921 15066.941 198.16 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2808,7 +2815,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2844,13 +2851,13 @@ change_box all x scale 1.00120967859874 y scale 1.00120967859874 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.850036 12160.805 198.88 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +129.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2860,7 +2867,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2896,13 +2903,13 @@ change_box all x scale 1.00120530450131 y scale 1.00120530450131 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.854861 9324.604 199.6 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2912,7 +2919,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2948,13 +2955,13 @@ change_box all x scale 1.00120096192269 y scale 1.00120096192269 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.858427 6556.6223 200.32 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +93.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2964,7 +2971,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3000,13 +3007,13 @@ change_box all x scale 1.00119665052343 y scale 1.00119665052343 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.860764 3855.1909 201.04 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 2.02656e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3016,7 +3023,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 2.027e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3052,13 +3059,13 @@ change_box all x scale 1.00119236996892 y scale 1.00119236996892 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.861902 1218.6858 201.76 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3068,7 +3075,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3104,13 +3111,13 @@ change_box all x scale 1.00118811992934 y scale 1.00118811992934 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.861869 -1354.4738 202.48 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3120,7 +3127,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3156,13 +3163,13 @@ change_box all x scale 1.00118390007955 y scale 1.00118390007955 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.860694 -3865.8261 203.2 -Loop time of 1.2517e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +111.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3172,7 +3179,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.252e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3208,13 +3215,13 @@ change_box all x scale 1.00117971009901 y scale 1.00117971009901 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.858404 -6316.8685 203.92 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3224,7 +3231,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3260,13 +3267,13 @@ change_box all x scale 1.00117554967171 y scale 1.00117554967171 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.855025 -8709.0584 204.64 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +69.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3276,7 +3283,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3312,13 +3319,13 @@ change_box all x scale 1.00117141848607 y scale 1.00117141848607 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.850585 -11043.815 205.36 -Loop time of 5.00679e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -4993.2% CPU use with 4 MPI tasks x no OpenMP threads +118.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3328,7 +3335,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 5.007e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3364,13 +3371,13 @@ change_box all x scale 1.00116731623489 y scale 1.00116731623489 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.845108 -13322.519 206.08 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +121.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3380,7 +3387,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3416,13 +3423,13 @@ change_box all x scale 1.00116324261524 y scale 1.00116324261524 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.838619 -15546.516 206.8 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3432,7 +3439,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3468,13 +3475,13 @@ change_box all x scale 1.00115919732841 y scale 1.00115919732841 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.831143 -17717.116 207.52 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3484,7 +3491,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3520,13 +3527,13 @@ change_box all x scale 1.00115518007984 y scale 1.00115518007984 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.822703 -19835.593 208.24 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +121.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3536,7 +3543,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3572,13 +3579,13 @@ change_box all x scale 1.00115119057903 y scale 1.00115119057903 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.813323 -21903.19 208.96 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +117.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3588,7 +3595,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3624,13 +3631,13 @@ change_box all x scale 1.00114722853949 y scale 1.00114722853949 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.803024 -23921.116 209.68 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3640,7 +3647,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3676,13 +3683,13 @@ change_box all x scale 1.00114329367864 y scale 1.00114329367864 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.79183 -25890.55 210.4 -Loop time of 1.2517e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3692,7 +3699,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.252e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3728,13 +3735,13 @@ change_box all x scale 1.00113938571778 y scale 1.00113938571778 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.779761 -27812.639 211.12 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3744,7 +3751,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3780,13 +3787,13 @@ change_box all x scale 1.00113550438201 y scale 1.00113550438201 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.76684 -29688.502 211.84 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +117.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3796,7 +3803,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3832,13 +3839,13 @@ change_box all x scale 1.00113164940016 y scale 1.00113164940016 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.753085 -31519.227 212.56 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +87.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3848,7 +3855,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3884,13 +3891,13 @@ change_box all x scale 1.00112782050471 y scale 1.00112782050471 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.738517 -33305.877 213.28 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +118.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3900,7 +3907,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3936,13 +3943,13 @@ change_box all x scale 1.00112401743178 y scale 1.00112401743178 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.723157 -35049.484 214 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3952,7 +3959,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3988,13 +3995,13 @@ change_box all x scale 1.00112023992101 y scale 1.00112023992101 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.707022 -36751.057 214.72 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +117.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4004,7 +4011,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4040,13 +4047,13 @@ change_box all x scale 1.00111648771556 y scale 1.00111648771556 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.690132 -38411.578 215.44 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +83.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4056,7 +4063,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4092,13 +4099,13 @@ change_box all x scale 1.00111276056198 y scale 1.00111276056198 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.672509 -39943.013 216.16 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +122.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4108,7 +4115,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4144,13 +4151,13 @@ change_box all x scale 1.00110905821022 y scale 1.00110905821022 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.654292 -41126.388 216.88 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +129.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4160,7 +4167,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4196,13 +4203,13 @@ change_box all x scale 1.00110538041355 y scale 1.00110538041355 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.635551 -42275.674 217.6 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4212,7 +4219,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4248,13 +4255,13 @@ change_box all x scale 1.00110172692849 y scale 1.00110172692849 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.6163 -43391.705 218.32 -Loop time of 9.53674e-07 on 4 procs for 0 steps with 8 atoms +Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +149.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4264,7 +4271,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.669e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4300,13 +4307,13 @@ change_box all x scale 1.00109809751476 y scale 1.00109809751476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.596556 -44475.291 219.04 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +117.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4316,7 +4323,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4352,13 +4359,13 @@ change_box all x scale 1.00109449193525 y scale 1.00109449193525 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.576332 -45527.226 219.76 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +87.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4368,7 +4375,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4404,13 +4411,13 @@ change_box all x scale 1.00109090995595 y scale 1.00109090995595 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.555642 -46548.278 220.48 Loop time of 1.2517e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +119.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4456,13 +4463,13 @@ change_box all x scale 1.00108735134592 y scale 1.00108735134592 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.5345 -47539.201 221.2 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +109.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4472,7 +4479,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4508,13 +4515,13 @@ change_box all x scale 1.00108381587718 y scale 1.00108381587718 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.512919 -48500.725 221.92 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.96695e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +127.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4524,7 +4531,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.967e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4560,13 +4567,13 @@ change_box all x scale 1.00108030332476 y scale 1.00108030332476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.490913 -49433.564 222.64 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +131.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4576,7 +4583,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.907e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4612,13 +4619,13 @@ change_box all x scale 1.00107681346655 y scale 1.00107681346655 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.468494 -50338.414 223.36 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4628,7 +4635,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4664,13 +4671,13 @@ change_box all x scale 1.00107334608333 y scale 1.00107334608333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.445674 -51215.952 224.08 -Loop time of 3.57628e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +145.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4680,7 +4687,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.576e-06 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4716,13 +4723,13 @@ change_box all x scale 1.00106990095868 y scale 1.00106990095868 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.422466 -52066.839 224.8 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.72853e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +86.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4732,7 +4739,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.729e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4768,13 +4775,13 @@ change_box all x scale 1.00106647787897 y scale 1.00106647787897 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.398881 -52891.72 225.52 -Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4784,7 +4791,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.431e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4820,13 +4827,13 @@ change_box all x scale 1.00106307663326 y scale 1.00106307663326 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.374932 -53691.221 226.24 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4836,7 +4843,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4872,13 +4879,13 @@ change_box all x scale 1.00105969701333 y scale 1.00105969701333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.350628 -54465.955 226.96 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4888,7 +4895,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4924,13 +4931,13 @@ change_box all x scale 1.00105633881357 y scale 1.00105633881357 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.325983 -55216.518 227.68 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +100.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4940,7 +4947,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4976,13 +4983,13 @@ change_box all x scale 1.00105300183098 y scale 1.00105300183098 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.301005 -55943.493 228.4 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +127.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4992,7 +4999,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5028,13 +5035,13 @@ change_box all x scale 1.00104968586512 y scale 1.00104968586512 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.275705 -56647.446 229.12 -Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +100.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5044,7 +5051,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.848e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5080,13 +5087,13 @@ change_box all x scale 1.00104639071808 y scale 1.00104639071808 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.250095 -57328.932 229.84 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +122.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5096,7 +5103,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5132,13 +5139,13 @@ change_box all x scale 1.00104311619438 y scale 1.00104311619438 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.224183 -57988.489 230.56 -Loop time of 1.19209e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.78814e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +125.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5148,7 +5155,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 1.788e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5184,13 +5191,13 @@ change_box all x scale 1.00103986210104 y scale 1.00103986210104 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.197979 -58626.644 231.28 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +124.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5200,7 +5207,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5236,13 +5243,13 @@ change_box all x scale 1.00103662824744 y scale 1.00103662824744 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.33394 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 2.965 | 2.965 | 2.965 Mbytes Step Temp PotEng Press Volume 0 0 -27.171493 -59243.909 232 Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total diff --git a/examples/vashishta/log.5Oct16.vashishta.sio2.g++.1 b/examples/vashishta/log.27Nov18.vashishta.sio2.g++.1 similarity index 70% rename from examples/vashishta/log.5Oct16.vashishta.sio2.g++.1 rename to examples/vashishta/log.27Nov18.vashishta.sio2.g++.1 index a76309d776..b1bd70d1bf 100644 --- a/examples/vashishta/log.5Oct16.vashishta.sio2.g++.1 +++ b/examples/vashishta/log.27Nov18.vashishta.sio2.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # test Vashishta potential for quartz units metal @@ -16,6 +17,7 @@ replicate 4 4 4 triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0) 1 by 1 by 1 MPI processor grid 576 atoms + Time spent = 0.000259161 secs velocity all create 2000.0 277387 mom yes displace_atoms all move 0.05 0.9 0.4 units box @@ -35,13 +37,18 @@ timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.3 ghost atom cutoff = 10.3 - binsize = 5.15 -> bins = 6 4 5 -Memory usage per processor = 2.54081 Mbytes + binsize = 5.15, bins = 6 4 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.677 | 3.677 | 3.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 2000 -5280.875 0 -5132.2259 -20502.321 10 895.65237 -5198.402 0 -5131.833 419.34676 @@ -54,20 +61,20 @@ Step Temp E_pair E_mol TotEng Press 80 1020.1044 -5207.6763 0 -5131.8574 -13488.675 90 912.75535 -5199.651 0 -5131.8108 2715.5897 100 998.97588 -5206.1008 0 -5131.8523 6024.3651 -Loop time of 2.13995 on 1 procs for 100 steps with 576 atoms +Loop time of 1.20228 on 1 procs for 100 steps with 576 atoms -Performance: 4.037 ns/day, 5.944 hours/ns, 46.730 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 7.186 ns/day, 3.340 hours/ns, 83.176 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.0601 | 2.0601 | 2.0601 | 0.0 | 96.27 -Neigh | 0.074257 | 0.074257 | 0.074257 | 0.0 | 3.47 -Comm | 0.0039079 | 0.0039079 | 0.0039079 | 0.0 | 0.18 -Output | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 0.01 -Modify | 0.00091672 | 0.00091672 | 0.00091672 | 0.0 | 0.04 -Other | | 0.0006473 | | | 0.03 +Pair | 1.1142 | 1.1142 | 1.1142 | 0.0 | 92.67 +Neigh | 0.081275 | 0.081275 | 0.081275 | 0.0 | 6.76 +Comm | 0.0051043 | 0.0051043 | 0.0051043 | 0.0 | 0.42 +Output | 0.00019526 | 0.00019526 | 0.00019526 | 0.0 | 0.02 +Modify | 0.00081301 | 0.00081301 | 0.00081301 | 0.0 | 0.07 +Other | | 0.0006804 | | | 0.06 Nlocal: 576 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -83,4 +90,4 @@ Ave neighs/atom = 365.399 Neighbor list builds = 10 Dangerous builds = 10 -Total wall time: 0:00:02 +Total wall time: 0:00:01 diff --git a/examples/vashishta/log.5Oct16.sio2.g++.4 b/examples/vashishta/log.27Nov18.vashishta.sio2.g++.4 similarity index 71% rename from examples/vashishta/log.5Oct16.sio2.g++.4 rename to examples/vashishta/log.27Nov18.vashishta.sio2.g++.4 index baa2942bd0..ebac488d79 100644 --- a/examples/vashishta/log.5Oct16.sio2.g++.4 +++ b/examples/vashishta/log.27Nov18.vashishta.sio2.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # test Vashishta potential for quartz units metal @@ -16,6 +17,7 @@ replicate 4 4 4 triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0) 2 by 1 by 2 MPI processor grid 576 atoms + Time spent = 0.000181913 secs velocity all create 2000.0 277387 mom yes displace_atoms all move 0.05 0.9 0.4 units box @@ -35,13 +37,18 @@ timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.3 ghost atom cutoff = 10.3 - binsize = 5.15 -> bins = 6 4 5 -Memory usage per processor = 2.50221 Mbytes + binsize = 5.15, bins = 6 4 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.851 | 2.851 | 2.851 Mbytes Step Temp E_pair E_mol TotEng Press 0 2000 -5280.875 0 -5132.2259 -20502.321 10 895.65237 -5198.402 0 -5131.833 419.34676 @@ -54,20 +61,20 @@ Step Temp E_pair E_mol TotEng Press 80 1020.1044 -5207.6763 0 -5131.8574 -13488.675 90 912.75535 -5199.651 0 -5131.8108 2715.5897 100 998.97588 -5206.1008 0 -5131.8523 6024.3651 -Loop time of 0.595389 on 4 procs for 100 steps with 576 atoms +Loop time of 0.33693 on 4 procs for 100 steps with 576 atoms -Performance: 14.512 ns/day, 1.654 hours/ns, 167.957 timesteps/s -99.9% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 25.643 ns/day, 0.936 hours/ns, 296.798 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.51621 | 0.52629 | 0.53686 | 1.1 | 88.39 -Neigh | 0.017571 | 0.018024 | 0.018574 | 0.3 | 3.03 -Comm | 0.038951 | 0.050033 | 0.06044 | 3.7 | 8.40 -Output | 0.00020981 | 0.00022781 | 0.00025916 | 0.1 | 0.04 -Modify | 0.00025797 | 0.00027782 | 0.00031734 | 0.1 | 0.05 -Other | | 0.0005327 | | | 0.09 +Pair | 0.28209 | 0.28996 | 0.30024 | 1.3 | 86.06 +Neigh | 0.019293 | 0.020102 | 0.021493 | 0.6 | 5.97 +Comm | 0.014259 | 0.025857 | 0.034626 | 4.9 | 7.67 +Output | 0.00024128 | 0.00035256 | 0.00068545 | 0.0 | 0.10 +Modify | 0.00024343 | 0.00025165 | 0.00026345 | 0.0 | 0.07 +Other | | 0.0004103 | | | 0.12 Nlocal: 144 ave 146 max 143 min Histogram: 2 0 0 1 0 0 0 0 0 1 diff --git a/examples/vashishta/log.5Oct16.vashishta.table.inp.g++.1 b/examples/vashishta/log.27Nov18.vashishta.table.inp.g++.1 similarity index 85% rename from examples/vashishta/log.5Oct16.vashishta.table.inp.g++.1 rename to examples/vashishta/log.27Nov18.vashishta.table.inp.g++.1 index 2724f18090..e6566fe364 100644 --- a/examples/vashishta/log.5Oct16.vashishta.table.inp.g++.1 +++ b/examples/vashishta/log.27Nov18.vashishta.table.inp.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # calculate the energy volume curve for InP zincblende # define volume range and filename @@ -39,6 +40,7 @@ Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0) create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 Created 8 atoms + Time spent = 0.0003407 secs mass 1 114.76 mass 2 30.98 @@ -82,19 +84,24 @@ change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 -Memory usage per processor = 8.42218 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta/table, perpetual + attributes: full, newton on + pair build: full/nsq + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -24.633958 315900.51 160.72 -Loop time of 1.90735e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -104,7 +111,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 9.537e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -140,13 +147,13 @@ change_box all x scale 1.00149105588627 y scale 1.00149105588627 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -24.773834 306658.05 161.44 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -156,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -192,13 +199,13 @@ change_box all x scale 1.00148441583558 y scale 1.00148441583558 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -24.909614 297676.86 162.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -208,7 +215,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -244,13 +251,13 @@ change_box all x scale 1.00147783466245 y scale 1.00147783466245 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.041417 288949.18 162.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -260,7 +267,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -296,13 +303,13 @@ change_box all x scale 1.00147131158722 y scale 1.00147131158722 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.169352 280467.47 163.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -312,7 +319,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -348,13 +355,13 @@ change_box all x scale 1.00146484584395 y scale 1.00146484584395 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.29353 272224.45 164.32 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -364,7 +371,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -400,13 +407,13 @@ change_box all x scale 1.0014584366801 y scale 1.0014584366801 z scale 1.001458 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.414056 264213.09 165.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -416,7 +423,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -452,13 +459,13 @@ change_box all x scale 1.00145208335626 y scale 1.00145208335626 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.531033 256426.59 165.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -468,7 +475,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -504,13 +511,13 @@ change_box all x scale 1.00144578514582 y scale 1.00144578514582 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.644559 248858.32 166.48 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -520,7 +527,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -556,13 +563,13 @@ change_box all x scale 1.00143954133473 y scale 1.00143954133473 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.754685 240961.63 167.2 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -572,7 +579,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -608,13 +615,13 @@ change_box all x scale 1.00143335122124 y scale 1.00143335122124 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.861048 232444.2 167.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +3355.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -624,7 +631,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -660,13 +667,13 @@ change_box all x scale 1.00142721411559 y scale 1.00142721411559 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -25.963633 224145.1 168.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -676,7 +683,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -712,13 +719,13 @@ change_box all x scale 1.00142112933981 y scale 1.00142112933981 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.062537 216058.22 169.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -728,7 +735,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -764,13 +771,13 @@ change_box all x scale 1.00141509622744 y scale 1.00141509622744 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.157852 208177.67 170.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -780,7 +787,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -816,13 +823,13 @@ change_box all x scale 1.00140911412325 y scale 1.00140911412325 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.249672 200497.73 170.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -832,7 +839,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -868,13 +875,13 @@ change_box all x scale 1.00140318238311 y scale 1.00140318238311 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.338085 193012.87 171.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -884,7 +891,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -920,13 +927,13 @@ change_box all x scale 1.00139730037362 y scale 1.00139730037362 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.423176 185717.72 172.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -936,7 +943,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -972,13 +979,13 @@ change_box all x scale 1.00139146747202 y scale 1.00139146747202 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.505031 178607.08 172.96 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -988,7 +995,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1024,13 +1031,13 @@ change_box all x scale 1.00138568306585 y scale 1.00138568306585 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.583731 171675.9 173.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1040,7 +1047,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1076,13 +1083,13 @@ change_box all x scale 1.00137994655284 y scale 1.00137994655284 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.659356 164919.3 174.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1092,7 +1099,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1128,13 +1135,13 @@ change_box all x scale 1.00137425734062 y scale 1.00137425734062 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.731982 158332.53 175.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1144,7 +1151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1180,13 +1187,13 @@ change_box all x scale 1.00136861484656 y scale 1.00136861484656 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.801686 151911 175.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1196,7 +1203,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1232,13 +1239,13 @@ change_box all x scale 1.00136301849755 y scale 1.00136301849755 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.86854 145650.27 176.56 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1248,7 +1255,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1284,13 +1291,13 @@ change_box all x scale 1.00135746772984 y scale 1.00135746772984 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.932617 139545.99 177.28 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1300,7 +1307,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1336,13 +1343,13 @@ change_box all x scale 1.00135196198879 y scale 1.00135196198879 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -26.993984 133593.98 178 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1352,7 +1359,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1388,13 +1395,13 @@ change_box all x scale 1.00134650072876 y scale 1.00134650072876 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.05271 127790.17 178.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1404,7 +1411,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1440,13 +1447,13 @@ change_box all x scale 1.00134108341287 y scale 1.00134108341287 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.108861 122130.62 179.44 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1456,7 +1463,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1492,13 +1499,13 @@ change_box all x scale 1.00133570951285 y scale 1.00133570951285 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.162499 116611.48 180.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1508,7 +1515,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1544,13 +1551,13 @@ change_box all x scale 1.00133037850885 y scale 1.00133037850885 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.213689 111229.06 180.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1560,7 +1567,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1596,13 +1603,13 @@ change_box all x scale 1.00132508988931 y scale 1.00132508988931 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.262489 105979.74 181.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1612,7 +1619,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1648,13 +1655,13 @@ change_box all x scale 1.00131984315076 y scale 1.00131984315076 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.30896 100860.02 182.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1664,7 +1671,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1700,13 +1707,13 @@ change_box all x scale 1.00131463779767 y scale 1.00131463779767 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.353159 95866.501 183.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1716,7 +1723,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1752,13 +1759,13 @@ change_box all x scale 1.00130947334229 y scale 1.00130947334229 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.395142 90995.883 183.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1768,7 +1775,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1804,13 +1811,13 @@ change_box all x scale 1.00130434930454 y scale 1.00130434930454 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.434962 86244.965 184.48 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1820,7 +1827,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1856,13 +1863,13 @@ change_box all x scale 1.00129926521177 y scale 1.00129926521177 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.472674 81610.635 185.2 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1872,7 +1879,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1908,13 +1915,13 @@ change_box all x scale 1.00129422059873 y scale 1.00129422059873 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.508329 77089.873 185.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1924,7 +1931,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -1960,13 +1967,13 @@ change_box all x scale 1.00128921500731 y scale 1.00128921500731 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.541977 72679.744 186.64 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1976,7 +1983,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2012,13 +2019,13 @@ change_box all x scale 1.0012842479865 y scale 1.0012842479865 z scale 1.001284 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.573668 68377.396 187.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2028,7 +2035,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2064,13 +2071,13 @@ change_box all x scale 1.00127931909221 y scale 1.00127931909221 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.603449 64180.063 188.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2080,7 +2087,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2116,13 +2123,13 @@ change_box all x scale 1.00127442788711 y scale 1.00127442788711 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.631367 60085.061 188.8 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2132,7 +2139,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2168,13 +2175,13 @@ change_box all x scale 1.00126957394058 y scale 1.00126957394058 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.657467 56089.766 189.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2184,7 +2191,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2220,13 +2227,13 @@ change_box all x scale 1.0012647568285 y scale 1.0012647568285 z scale 1.001264 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.681794 52191.647 190.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2236,7 +2243,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2272,13 +2279,13 @@ change_box all x scale 1.00125997613317 y scale 1.00125997613317 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.70439 48388.232 190.96 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2288,7 +2295,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2324,13 +2331,13 @@ change_box all x scale 1.00125523144319 y scale 1.00125523144319 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.725298 44677.126 191.68 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2340,7 +2347,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2376,13 +2383,13 @@ change_box all x scale 1.00125052235334 y scale 1.00125052235334 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.744558 41055.991 192.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2392,7 +2399,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2428,13 +2435,13 @@ change_box all x scale 1.00124584846443 y scale 1.00124584846443 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.762211 37522.574 193.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2444,7 +2451,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2480,13 +2487,13 @@ change_box all x scale 1.00124120938324 y scale 1.00124120938324 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.778295 34074.66 193.84 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2496,7 +2503,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2532,13 +2539,13 @@ change_box all x scale 1.00123660472238 y scale 1.00123660472238 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.792849 30710.111 194.56 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2548,7 +2555,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2584,13 +2591,13 @@ change_box all x scale 1.00123203410018 y scale 1.00123203410018 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.805909 27426.844 195.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2600,7 +2607,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2636,13 +2643,13 @@ change_box all x scale 1.00122749714061 y scale 1.00122749714061 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.817512 24222.839 196 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2652,7 +2659,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2688,13 +2695,13 @@ change_box all x scale 1.00122299347313 y scale 1.00122299347313 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.827692 21096.122 196.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2704,7 +2711,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2740,13 +2747,13 @@ change_box all x scale 1.00121852273265 y scale 1.00121852273265 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.836484 18044.777 197.44 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2756,7 +2763,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2792,13 +2799,13 @@ change_box all x scale 1.00121408455937 y scale 1.00121408455937 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.843921 15066.943 198.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2808,7 +2815,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2844,13 +2851,13 @@ change_box all x scale 1.00120967859874 y scale 1.00120967859874 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.850036 12160.806 198.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2860,7 +2867,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2896,13 +2903,13 @@ change_box all x scale 1.00120530450131 y scale 1.00120530450131 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.854861 9324.6056 199.6 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2912,7 +2919,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -2948,13 +2955,13 @@ change_box all x scale 1.00120096192269 y scale 1.00120096192269 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.858427 6556.6252 200.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2964,7 +2971,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3000,13 +3007,13 @@ change_box all x scale 1.00119665052343 y scale 1.00119665052343 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.860764 3855.194 201.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3016,7 +3023,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3052,13 +3059,13 @@ change_box all x scale 1.00119236996892 y scale 1.00119236996892 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.861902 1218.687 201.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3068,7 +3075,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3104,13 +3111,13 @@ change_box all x scale 1.00118811992934 y scale 1.00118811992934 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.861869 -1354.4715 202.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3120,7 +3127,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3156,13 +3163,13 @@ change_box all x scale 1.00118390007955 y scale 1.00118390007955 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.860694 -3865.8233 203.2 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3172,7 +3179,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3208,13 +3215,13 @@ change_box all x scale 1.00117971009901 y scale 1.00117971009901 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.858403 -6316.8674 203.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3224,7 +3231,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3260,13 +3267,13 @@ change_box all x scale 1.00117554967171 y scale 1.00117554967171 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.855025 -8709.0557 204.64 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3276,7 +3283,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3312,13 +3319,13 @@ change_box all x scale 1.00117141848607 y scale 1.00117141848607 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.850585 -11043.813 205.36 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3328,7 +3335,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3364,13 +3371,13 @@ change_box all x scale 1.00116731623489 y scale 1.00116731623489 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.845108 -13322.517 206.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3380,7 +3387,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3416,13 +3423,13 @@ change_box all x scale 1.00116324261524 y scale 1.00116324261524 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.838619 -15546.513 206.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3432,7 +3439,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3468,13 +3475,13 @@ change_box all x scale 1.00115919732841 y scale 1.00115919732841 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.831143 -17717.114 207.52 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3484,7 +3491,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3520,13 +3527,13 @@ change_box all x scale 1.00115518007984 y scale 1.00115518007984 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.822703 -19835.592 208.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3536,7 +3543,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3572,13 +3579,13 @@ change_box all x scale 1.00115119057903 y scale 1.00115119057903 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.813323 -21903.187 208.96 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3588,7 +3595,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3624,13 +3631,13 @@ change_box all x scale 1.00114722853949 y scale 1.00114722853949 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.803024 -23921.114 209.68 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3640,7 +3647,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3676,13 +3683,13 @@ change_box all x scale 1.00114329367864 y scale 1.00114329367864 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.79183 -25890.548 210.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3692,7 +3699,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3728,13 +3735,13 @@ change_box all x scale 1.00113938571778 y scale 1.00113938571778 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.779761 -27812.637 211.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3744,7 +3751,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3780,13 +3787,13 @@ change_box all x scale 1.00113550438201 y scale 1.00113550438201 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.76684 -29688.5 211.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3796,7 +3803,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3832,13 +3839,13 @@ change_box all x scale 1.00113164940016 y scale 1.00113164940016 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.753085 -31519.225 212.56 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3848,7 +3855,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3884,13 +3891,13 @@ change_box all x scale 1.00112782050471 y scale 1.00112782050471 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.738517 -33305.874 213.28 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3900,7 +3907,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3936,13 +3943,13 @@ change_box all x scale 1.00112401743178 y scale 1.00112401743178 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.723157 -35049.482 214 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3952,7 +3959,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -3988,13 +3995,13 @@ change_box all x scale 1.00112023992101 y scale 1.00112023992101 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.707022 -36751.056 214.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4004,7 +4011,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4040,13 +4047,13 @@ change_box all x scale 1.00111648771556 y scale 1.00111648771556 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.690132 -38411.578 215.44 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4056,7 +4063,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4092,13 +4099,13 @@ change_box all x scale 1.00111276056198 y scale 1.00111276056198 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.672509 -39943.011 216.16 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4108,7 +4115,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4144,13 +4151,13 @@ change_box all x scale 1.00110905821022 y scale 1.00110905821022 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.654292 -41126.386 216.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4160,7 +4167,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4196,13 +4203,13 @@ change_box all x scale 1.00110538041355 y scale 1.00110538041355 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.635551 -42275.674 217.6 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4212,7 +4219,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4248,13 +4255,13 @@ change_box all x scale 1.00110172692849 y scale 1.00110172692849 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.6163 -43391.703 218.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4264,7 +4271,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4300,13 +4307,13 @@ change_box all x scale 1.00109809751476 y scale 1.00109809751476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.596556 -44475.29 219.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4316,7 +4323,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4352,13 +4359,13 @@ change_box all x scale 1.00109449193525 y scale 1.00109449193525 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.576332 -45527.224 219.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4368,7 +4375,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4404,13 +4411,13 @@ change_box all x scale 1.00109090995595 y scale 1.00109090995595 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.555642 -46548.278 220.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4420,7 +4427,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4456,13 +4463,13 @@ change_box all x scale 1.00108735134592 y scale 1.00108735134592 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.5345 -47539.199 221.2 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4472,7 +4479,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4508,13 +4515,13 @@ change_box all x scale 1.00108381587718 y scale 1.00108381587718 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.512919 -48500.724 221.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4524,7 +4531,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4560,13 +4567,13 @@ change_box all x scale 1.00108030332476 y scale 1.00108030332476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.490913 -49433.563 222.64 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4576,7 +4583,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4612,13 +4619,13 @@ change_box all x scale 1.00107681346655 y scale 1.00107681346655 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.468493 -50338.412 223.36 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4628,7 +4635,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4664,13 +4671,13 @@ change_box all x scale 1.00107334608333 y scale 1.00107334608333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.445674 -51215.951 224.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4680,7 +4687,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4716,13 +4723,13 @@ change_box all x scale 1.00106990095868 y scale 1.00106990095868 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.422466 -52066.839 224.8 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4732,7 +4739,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4768,13 +4775,13 @@ change_box all x scale 1.00106647787897 y scale 1.00106647787897 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.398881 -52891.72 225.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4784,7 +4791,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4820,13 +4827,13 @@ change_box all x scale 1.00106307663326 y scale 1.00106307663326 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.374932 -53691.22 226.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4836,7 +4843,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4872,13 +4879,13 @@ change_box all x scale 1.00105969701333 y scale 1.00105969701333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.350628 -54465.954 226.96 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4888,7 +4895,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4924,13 +4931,13 @@ change_box all x scale 1.00105633881357 y scale 1.00105633881357 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.325983 -55216.517 227.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4940,7 +4947,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -4976,13 +4983,13 @@ change_box all x scale 1.00105300183098 y scale 1.00105300183098 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.301005 -55943.492 228.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4992,7 +4999,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5028,13 +5035,13 @@ change_box all x scale 1.00104968586512 y scale 1.00104968586512 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.275705 -56647.446 229.12 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5044,7 +5051,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5080,13 +5087,13 @@ change_box all x scale 1.00104639071808 y scale 1.00104639071808 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.250095 -57328.932 229.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5096,7 +5103,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5132,13 +5139,13 @@ change_box all x scale 1.00104311619438 y scale 1.00104311619438 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.224183 -57988.488 230.56 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5148,7 +5155,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5184,13 +5191,13 @@ change_box all x scale 1.00103986210104 y scale 1.00103986210104 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.197979 -58626.642 231.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5200,7 +5207,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -5236,13 +5243,13 @@ change_box all x scale 1.00103662824744 y scale 1.00103662824744 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.42218 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.054 | 9.054 | 9.054 Mbytes Step Temp PotEng Press Volume 0 0 -27.171493 -59243.908 232 -Loop time of 0 on 1 procs for 0 steps with 8 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 8 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5252,7 +5259,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/vashishta/log.5Oct16.vashishta.table.inp.g++.4 b/examples/vashishta/log.27Nov18.vashishta.table.inp.g++.4 similarity index 85% rename from examples/vashishta/log.5Oct16.vashishta.table.inp.g++.4 rename to examples/vashishta/log.27Nov18.vashishta.table.inp.g++.4 index 528f7fbee3..b5bc469600 100644 --- a/examples/vashishta/log.5Oct16.vashishta.table.inp.g++.4 +++ b/examples/vashishta/log.27Nov18.vashishta.table.inp.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # calculate the energy volume curve for InP zincblende # define volume range and filename @@ -39,6 +40,7 @@ Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0) create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 Created 8 atoms + Time spent = 0.00137448 secs mass 1 114.76 mass 2 30.98 @@ -82,19 +84,24 @@ change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 -Memory usage per processor = 8.43745 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta/table, perpetual + attributes: full, newton on + pair build: full/nsq + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -24.633958 315900.51 160.72 -Loop time of 5.00679e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.20997e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +90.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -104,7 +111,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 5.007e-06 | | |100.00 +Other | | 1.21e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -140,13 +147,13 @@ change_box all x scale 1.00149105588627 y scale 1.00149105588627 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -24.773834 306658.05 161.44 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.23978e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -156,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.24e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -192,13 +199,13 @@ change_box all x scale 1.00148441583558 y scale 1.00148441583558 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -24.909614 297676.86 162.16 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.20401e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +103.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -208,7 +215,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.204e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -244,13 +251,13 @@ change_box all x scale 1.00147783466245 y scale 1.00147783466245 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.041417 288949.18 162.88 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2517e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +99.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -260,7 +267,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.252e-05 | | |100.00 Nlocal: 2 ave 2 max 2 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -296,13 +303,13 @@ change_box all x scale 1.00147131158722 y scale 1.00147131158722 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.169352 280467.47 163.6 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.20997e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +70.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -312,7 +319,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.21e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -348,13 +355,13 @@ change_box all x scale 1.00146484584395 y scale 1.00146484584395 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.29353 272224.45 164.32 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2517e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -364,7 +371,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.252e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -400,13 +407,13 @@ change_box all x scale 1.0014584366801 y scale 1.0014584366801 z scale 1.001458 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.414056 264213.09 165.04 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.20997e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +95.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -416,7 +423,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.21e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -452,13 +459,13 @@ change_box all x scale 1.00145208335626 y scale 1.00145208335626 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.531033 256426.59 165.76 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2517e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -468,7 +475,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 1.252e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -504,13 +511,13 @@ change_box all x scale 1.00144578514582 y scale 1.00144578514582 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.644559 248858.32 166.48 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2219e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -520,7 +527,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.222e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -556,13 +563,13 @@ change_box all x scale 1.00143954133473 y scale 1.00143954133473 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.754685 240961.63 167.2 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2219e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -572,7 +579,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.222e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -608,13 +615,13 @@ change_box all x scale 1.00143335122124 y scale 1.00143335122124 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.861048 232444.2 167.92 -Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.20997e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -624,7 +631,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.099e-06 | | |100.00 +Other | | 1.21e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -660,13 +667,13 @@ change_box all x scale 1.00142721411559 y scale 1.00142721411559 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -25.963633 224145.1 168.64 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.21593e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +106.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -676,7 +683,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.216e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -712,13 +719,13 @@ change_box all x scale 1.00142112933981 y scale 1.00142112933981 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.062537 216058.22 169.36 -Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.23382e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +99.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -728,7 +735,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.099e-06 | | |100.00 +Other | | 1.234e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -764,13 +771,13 @@ change_box all x scale 1.00141509622744 y scale 1.00141509622744 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.157852 208177.67 170.08 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2517e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +103.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -780,7 +787,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.252e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -816,13 +823,13 @@ change_box all x scale 1.00140911412325 y scale 1.00140911412325 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.249672 200497.73 170.8 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.77622e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +102.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -832,7 +839,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.776e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -868,13 +875,13 @@ change_box all x scale 1.00140318238311 y scale 1.00140318238311 z scale 1.0014 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.338085 193012.87 171.52 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +135.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -884,7 +891,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -920,13 +927,13 @@ change_box all x scale 1.00139730037362 y scale 1.00139730037362 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.423176 185717.72 172.24 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +129.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -936,7 +943,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -972,13 +979,13 @@ change_box all x scale 1.00139146747202 y scale 1.00139146747202 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.505031 178607.08 172.96 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +151.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -988,7 +995,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1024,13 +1031,13 @@ change_box all x scale 1.00138568306585 y scale 1.00138568306585 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.583731 171675.9 173.68 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +119.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1040,7 +1047,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.669e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1076,13 +1083,13 @@ change_box all x scale 1.00137994655284 y scale 1.00137994655284 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.659356 164919.3 174.4 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.16229e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +101.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1092,7 +1099,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.162e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1128,13 +1135,13 @@ change_box all x scale 1.00137425734062 y scale 1.00137425734062 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.731982 158332.53 175.12 -Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.28746e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +102.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1144,7 +1151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.099e-06 | | |100.00 +Other | | 1.287e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1180,13 +1187,13 @@ change_box all x scale 1.00136861484656 y scale 1.00136861484656 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.801686 151911 175.84 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.16229e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +73.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1196,7 +1203,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.162e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1232,13 +1239,13 @@ change_box all x scale 1.00136301849755 y scale 1.00136301849755 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.86854 145650.27 176.56 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.17421e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +70.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1248,7 +1255,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 1.174e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1284,13 +1291,13 @@ change_box all x scale 1.00135746772984 y scale 1.00135746772984 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.932617 139545.99 177.28 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.25766e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +69.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1300,7 +1307,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.258e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1336,13 +1343,13 @@ change_box all x scale 1.00135196198879 y scale 1.00135196198879 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -26.993984 133593.98 178 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.25766e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +93.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1352,7 +1359,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.258e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1388,13 +1395,13 @@ change_box all x scale 1.00134650072876 y scale 1.00134650072876 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.05271 127790.17 178.72 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.16229e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +94.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1404,7 +1411,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.162e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1440,13 +1447,13 @@ change_box all x scale 1.00134108341287 y scale 1.00134108341287 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.108861 122130.62 179.44 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.23978e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1456,7 +1463,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 1.24e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1492,13 +1499,13 @@ change_box all x scale 1.00133570951285 y scale 1.00133570951285 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.162499 116611.48 180.16 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.2517e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +95.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1508,7 +1515,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.252e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1544,13 +1551,13 @@ change_box all x scale 1.00133037850885 y scale 1.00133037850885 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.213689 111229.06 180.88 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.25766e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1560,7 +1567,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 1.258e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1596,13 +1603,13 @@ change_box all x scale 1.00132508988931 y scale 1.00132508988931 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.262489 105979.74 181.6 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.18613e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1612,7 +1619,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.186e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1648,13 +1655,13 @@ change_box all x scale 1.00131984315076 y scale 1.00131984315076 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.30896 100860.02 182.32 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 0.000160694 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +99.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1664,7 +1671,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 0.0001607 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1700,13 +1707,13 @@ change_box all x scale 1.00131463779767 y scale 1.00131463779767 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.353159 95866.501 183.04 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.16825e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +102.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1716,7 +1723,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.168e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1752,13 +1759,13 @@ change_box all x scale 1.00130947334229 y scale 1.00130947334229 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.395142 90995.883 183.76 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 5.47767e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +100.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1768,7 +1775,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 5.478e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1804,13 +1811,13 @@ change_box all x scale 1.00130434930454 y scale 1.00130434930454 z scale 1.0013 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.434962 86244.965 184.48 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.15633e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +105.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1820,7 +1827,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.156e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1856,13 +1863,13 @@ change_box all x scale 1.00129926521177 y scale 1.00129926521177 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.472674 81610.635 185.2 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.15633e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +93.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1872,7 +1879,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.156e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1908,13 +1915,13 @@ change_box all x scale 1.00129422059873 y scale 1.00129422059873 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.508329 77089.873 185.92 -Loop time of 2.5034e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.15037e-05 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +95.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1924,7 +1931,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.503e-06 | | |100.00 +Other | | 1.15e-05 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -1960,13 +1967,13 @@ change_box all x scale 1.00128921500731 y scale 1.00128921500731 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.541977 72679.744 186.64 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +139.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -1976,7 +1983,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2012,13 +2019,13 @@ change_box all x scale 1.0012842479865 y scale 1.0012842479865 z scale 1.001284 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.573668 68377.396 187.36 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +112.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2028,7 +2035,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2064,13 +2071,13 @@ change_box all x scale 1.00127931909221 y scale 1.00127931909221 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.603449 64180.063 188.08 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.3113e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +152.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2080,7 +2087,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.311e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2116,13 +2123,13 @@ change_box all x scale 1.00127442788711 y scale 1.00127442788711 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.631367 60085.061 188.8 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +122.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2132,7 +2139,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2168,13 +2175,13 @@ change_box all x scale 1.00126957394058 y scale 1.00126957394058 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.657467 56089.766 189.52 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +105.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2184,7 +2191,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2220,13 +2227,13 @@ change_box all x scale 1.0012647568285 y scale 1.0012647568285 z scale 1.001264 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.681794 52191.647 190.24 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.46386e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +106.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2236,7 +2243,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 8.464e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2272,13 +2279,13 @@ change_box all x scale 1.00125997613317 y scale 1.00125997613317 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.70439 48388.232 190.96 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.52346e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2288,7 +2295,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 8.523e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2324,13 +2331,13 @@ change_box all x scale 1.00125523144319 y scale 1.00125523144319 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.725298 44677.126 191.68 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.64267e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +86.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2340,7 +2347,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.643e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2376,13 +2383,13 @@ change_box all x scale 1.00125052235334 y scale 1.00125052235334 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.744558 41055.991 192.4 -Loop time of 2.5034e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.46386e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2392,7 +2399,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.503e-06 | | |100.00 +Other | | 8.464e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2428,13 +2435,13 @@ change_box all x scale 1.00124584846443 y scale 1.00124584846443 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.762211 37522.574 193.12 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.22544e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +94.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2444,7 +2451,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.225e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2480,13 +2487,13 @@ change_box all x scale 1.00124120938324 y scale 1.00124120938324 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.778295 34074.66 193.84 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.40425e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2496,7 +2503,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 8.404e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2532,13 +2539,13 @@ change_box all x scale 1.00123660472238 y scale 1.00123660472238 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.792849 30710.111 194.56 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.76188e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2548,7 +2555,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.762e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2584,13 +2591,13 @@ change_box all x scale 1.00123203410018 y scale 1.00123203410018 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.805909 27426.844 195.28 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.34465e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2600,7 +2607,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.345e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2636,13 +2643,13 @@ change_box all x scale 1.00122749714061 y scale 1.00122749714061 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.817512 24222.839 196 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.58307e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2652,7 +2659,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.583e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2688,13 +2695,13 @@ change_box all x scale 1.00122299347313 y scale 1.00122299347313 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.827692 21096.122 196.72 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.22544e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +106.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2704,7 +2711,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.225e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2740,13 +2747,13 @@ change_box all x scale 1.00121852273265 y scale 1.00121852273265 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.836484 18044.777 197.44 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.52346e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2756,7 +2763,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.523e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2792,13 +2799,13 @@ change_box all x scale 1.00121408455937 y scale 1.00121408455937 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.843921 15066.943 198.16 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.34465e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2808,7 +2815,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.345e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2844,13 +2851,13 @@ change_box all x scale 1.00120967859874 y scale 1.00120967859874 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.850036 12160.806 198.88 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.72853e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +130.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2860,7 +2867,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.729e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2896,13 +2903,13 @@ change_box all x scale 1.00120530450131 y scale 1.00120530450131 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.854861 9324.6056 199.6 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.43051e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +122.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2912,7 +2919,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -2948,13 +2955,13 @@ change_box all x scale 1.00120096192269 y scale 1.00120096192269 z scale 1.0012 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.858427 6556.6252 200.32 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.66893e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +89.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -2964,7 +2971,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.669e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3000,13 +3007,13 @@ change_box all x scale 1.00119665052343 y scale 1.00119665052343 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.860764 3855.194 201.04 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.96695e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +101.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3016,7 +3023,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.967e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3052,13 +3059,13 @@ change_box all x scale 1.00119236996892 y scale 1.00119236996892 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.861902 1218.687 201.76 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.22544e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +100.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3068,7 +3075,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.225e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3104,13 +3111,13 @@ change_box all x scale 1.00118811992934 y scale 1.00118811992934 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.861869 -1354.4715 202.48 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.40425e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3120,7 +3127,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 8.404e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3156,13 +3163,13 @@ change_box all x scale 1.00118390007955 y scale 1.00118390007955 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.860694 -3865.8233 203.2 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.22544e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +106.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3172,7 +3179,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.225e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3208,13 +3215,13 @@ change_box all x scale 1.00117971009901 y scale 1.00117971009901 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.858403 -6316.8674 203.92 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.16584e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3224,7 +3231,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.166e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3260,13 +3267,13 @@ change_box all x scale 1.00117554967171 y scale 1.00117554967171 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.855025 -8709.0557 204.64 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.10623e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +95.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3276,7 +3283,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.106e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3312,13 +3319,13 @@ change_box all x scale 1.00117141848607 y scale 1.00117141848607 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.850585 -11043.813 205.36 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.10623e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3328,7 +3335,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 8.106e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3364,13 +3371,13 @@ change_box all x scale 1.00116731623489 y scale 1.00116731623489 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.845108 -13322.517 206.08 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.22544e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +109.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3380,7 +3387,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.225e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3416,13 +3423,13 @@ change_box all x scale 1.00116324261524 y scale 1.00116324261524 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.838619 -15546.513 206.8 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.40425e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3432,7 +3439,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.404e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3468,13 +3475,13 @@ change_box all x scale 1.00115919732841 y scale 1.00115919732841 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.831143 -17717.114 207.52 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.52346e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +102.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3484,7 +3491,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.523e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3520,13 +3527,13 @@ change_box all x scale 1.00115518007984 y scale 1.00115518007984 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.822703 -19835.592 208.24 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.34465e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +92.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3536,7 +3543,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.345e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3572,13 +3579,13 @@ change_box all x scale 1.00115119057903 y scale 1.00115119057903 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.813323 -21903.187 208.96 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3588,7 +3595,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3624,13 +3631,13 @@ change_box all x scale 1.00114722853949 y scale 1.00114722853949 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.803024 -23921.114 209.68 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.16584e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3640,7 +3647,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.166e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3676,13 +3683,13 @@ change_box all x scale 1.00114329367864 y scale 1.00114329367864 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.79183 -25890.548 210.4 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.88109e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3692,7 +3699,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.881e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3728,13 +3735,13 @@ change_box all x scale 1.00113938571778 y scale 1.00113938571778 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.779761 -27812.637 211.12 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.40425e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +101.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3744,7 +3751,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 8.404e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3780,13 +3787,13 @@ change_box all x scale 1.00113550438201 y scale 1.00113550438201 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.76684 -29688.5 211.84 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +83.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3796,7 +3803,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3832,13 +3839,13 @@ change_box all x scale 1.00113164940016 y scale 1.00113164940016 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.753085 -31519.225 212.56 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +145.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3848,7 +3855,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3884,13 +3891,13 @@ change_box all x scale 1.00112782050471 y scale 1.00112782050471 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.738517 -33305.874 213.28 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.60933e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +124.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3900,7 +3907,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.609e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3936,13 +3943,13 @@ change_box all x scale 1.00112401743178 y scale 1.00112401743178 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.723157 -35049.482 214 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 0.00103354 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -3952,7 +3959,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 0.001034 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -3988,13 +3995,13 @@ change_box all x scale 1.00112023992101 y scale 1.00112023992101 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.707022 -36751.056 214.72 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.46386e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4004,7 +4011,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 8.464e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4040,13 +4047,13 @@ change_box all x scale 1.00111648771556 y scale 1.00111648771556 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.690132 -38411.578 215.44 -Loop time of 2.5034e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.04663e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4056,7 +4063,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.503e-06 | | |100.00 +Other | | 8.047e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4092,13 +4099,13 @@ change_box all x scale 1.00111276056198 y scale 1.00111276056198 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.672509 -39943.011 216.16 -Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.40425e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4108,7 +4115,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.099e-06 | | |100.00 +Other | | 8.404e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4144,13 +4151,13 @@ change_box all x scale 1.00110905821022 y scale 1.00110905821022 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.654292 -41126.386 216.88 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.04663e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +105.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4160,7 +4167,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.047e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4196,13 +4203,13 @@ change_box all x scale 1.00110538041355 y scale 1.00110538041355 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.635551 -42275.674 217.6 -Loop time of 2.44379e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.16584e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4212,7 +4219,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.444e-06 | | |100.00 +Other | | 8.166e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4248,13 +4255,13 @@ change_box all x scale 1.00110172692849 y scale 1.00110172692849 z scale 1.0011 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.6163 -43391.703 218.32 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.34465e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +104.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4264,7 +4271,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.345e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4300,13 +4307,13 @@ change_box all x scale 1.00109809751476 y scale 1.00109809751476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.596556 -44475.29 219.04 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +93.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4316,7 +4323,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4352,13 +4359,13 @@ change_box all x scale 1.00109449193525 y scale 1.00109449193525 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.576332 -45527.224 219.76 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.34465e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +56.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4368,7 +4375,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.345e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4404,13 +4411,13 @@ change_box all x scale 1.00109090995595 y scale 1.00109090995595 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.555642 -46548.278 220.48 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.52346e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4420,7 +4427,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 8.523e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4456,13 +4463,13 @@ change_box all x scale 1.00108735134592 y scale 1.00108735134592 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.5345 -47539.199 221.2 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.46386e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +106.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4472,7 +4479,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 8.464e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4508,13 +4515,13 @@ change_box all x scale 1.00108381587718 y scale 1.00108381587718 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.512919 -48500.724 221.92 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4524,7 +4531,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4560,13 +4567,13 @@ change_box all x scale 1.00108030332476 y scale 1.00108030332476 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.490913 -49433.563 222.64 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.58307e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +93.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4576,7 +4583,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 8.583e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4612,13 +4619,13 @@ change_box all x scale 1.00107681346655 y scale 1.00107681346655 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.468493 -50338.412 223.36 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +134.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4628,7 +4635,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4664,13 +4671,13 @@ change_box all x scale 1.00107334608333 y scale 1.00107334608333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.445674 -51215.951 224.08 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +127.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4680,7 +4687,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4716,13 +4723,13 @@ change_box all x scale 1.00106990095868 y scale 1.00106990095868 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.422466 -52066.839 224.8 -Loop time of 2.20537e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.54972e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4732,7 +4739,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.205e-06 | | |100.00 +Other | | 1.55e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4768,13 +4775,13 @@ change_box all x scale 1.00106647787897 y scale 1.00106647787897 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.398881 -52891.72 225.52 -Loop time of 2.6226e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 1.37091e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +127.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4784,7 +4791,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.623e-06 | | |100.00 +Other | | 1.371e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4820,13 +4827,13 @@ change_box all x scale 1.00106307663326 y scale 1.00106307663326 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.374932 -53691.22 226.24 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.52346e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +96.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4836,7 +4843,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.523e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4872,13 +4879,13 @@ change_box all x scale 1.00105969701333 y scale 1.00105969701333 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.350628 -54465.954 226.96 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.34465e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +107.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4888,7 +4895,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.345e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4924,13 +4931,13 @@ change_box all x scale 1.00105633881357 y scale 1.00105633881357 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.325983 -55216.517 227.68 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +105.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4940,7 +4947,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -4976,13 +4983,13 @@ change_box all x scale 1.00105300183098 y scale 1.00105300183098 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.301005 -55943.492 228.4 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +99.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -4992,7 +4999,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5028,13 +5035,13 @@ change_box all x scale 1.00104968586512 y scale 1.00104968586512 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.275705 -56647.446 229.12 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +108.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5044,7 +5051,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5080,13 +5087,13 @@ change_box all x scale 1.00104639071808 y scale 1.00104639071808 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.250095 -57328.932 229.84 -Loop time of 2.5034e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +102.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5096,7 +5103,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.503e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5132,13 +5139,13 @@ change_box all x scale 1.00104311619438 y scale 1.00104311619438 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.224183 -57988.488 230.56 -Loop time of 3.93391e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.46386e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +103.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5148,7 +5155,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.934e-06 | | |100.00 +Other | | 8.464e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5184,13 +5191,13 @@ change_box all x scale 1.00103986210104 y scale 1.00103986210104 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.197979 -58626.642 231.28 -Loop time of 2.80142e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.40425e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +101.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5200,7 +5207,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.801e-06 | | |100.00 +Other | | 8.404e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 @@ -5236,13 +5243,13 @@ change_box all x scale 1.00103662824744 y scale 1.00103662824744 z scale 1.0010 # no energy minimization needed for zincblende run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.43745 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.069 | 9.069 | 9.069 Mbytes Step Temp PotEng Press Volume 0 0 -27.171493 -59243.908 232 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 8 atoms +Loop time of 8.28505e-06 on 4 procs for 0 steps with 8 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +90.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -5252,7 +5259,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 8.285e-06 | | |100.00 Nlocal: 2 ave 5 max 1 min Histogram: 3 0 0 0 0 0 0 0 0 1 diff --git a/examples/vashishta/log.5Oct16.vashishta.table.sio2.g++.1 b/examples/vashishta/log.27Nov18.vashishta.table.sio2.g++.1 similarity index 72% rename from examples/vashishta/log.5Oct16.vashishta.table.sio2.g++.1 rename to examples/vashishta/log.27Nov18.vashishta.table.sio2.g++.1 index 778a9389f8..401f1f8efd 100644 --- a/examples/vashishta/log.5Oct16.vashishta.table.sio2.g++.1 +++ b/examples/vashishta/log.27Nov18.vashishta.table.sio2.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # test Vashishta potential for quartz units metal @@ -18,6 +19,7 @@ replicate 4 4 4 triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0) 1 by 1 by 1 MPI processor grid 576 atoms + Time spent = 0.000264406 secs velocity all create 2000.0 277387 mom yes displace_atoms all move 0.05 0.9 0.4 units box @@ -38,13 +40,18 @@ timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.3 ghost atom cutoff = 10.3 - binsize = 5.15 -> bins = 6 4 5 -Memory usage per processor = 8.64433 Mbytes + binsize = 5.15, bins = 6 4 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.78 | 9.78 | 9.78 Mbytes Step Temp E_pair E_mol TotEng Press 0 2000 -5280.8748 0 -5132.2257 -20501.94 10 895.65274 -5198.4018 0 -5131.8328 419.5556 @@ -57,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press 80 1020.1046 -5207.6761 0 -5131.8572 -13488.691 90 912.75537 -5199.6508 0 -5131.8106 2715.7189 100 998.97595 -5206.1006 0 -5131.8521 6024.5628 -Loop time of 0.57105 on 1 procs for 100 steps with 576 atoms +Loop time of 0.613275 on 1 procs for 100 steps with 576 atoms -Performance: 15.130 ns/day, 1.586 hours/ns, 175.116 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 14.088 ns/day, 1.704 hours/ns, 163.059 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.49037 | 0.49037 | 0.49037 | 0.0 | 85.87 -Neigh | 0.075116 | 0.075116 | 0.075116 | 0.0 | 13.15 -Comm | 0.0039296 | 0.0039296 | 0.0039296 | 0.0 | 0.69 -Output | 0.00010204 | 0.00010204 | 0.00010204 | 0.0 | 0.02 -Modify | 0.00090742 | 0.00090742 | 0.00090742 | 0.0 | 0.16 -Other | | 0.0006287 | | | 0.11 +Pair | 0.52478 | 0.52478 | 0.52478 | 0.0 | 85.57 +Neigh | 0.081344 | 0.081344 | 0.081344 | 0.0 | 13.26 +Comm | 0.0052247 | 0.0052247 | 0.0052247 | 0.0 | 0.85 +Output | 0.00029302 | 0.00029302 | 0.00029302 | 0.0 | 0.05 +Modify | 0.00088763 | 0.00088763 | 0.00088763 | 0.0 | 0.14 +Other | | 0.0007463 | | | 0.12 Nlocal: 576 ave 576 max 576 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/vashishta/log.5Oct16.vashishta.table.sio2.g++.4 b/examples/vashishta/log.27Nov18.vashishta.table.sio2.g++.4 similarity index 72% rename from examples/vashishta/log.5Oct16.vashishta.table.sio2.g++.4 rename to examples/vashishta/log.27Nov18.vashishta.table.sio2.g++.4 index 6a1af80724..4d1e7f5dcc 100644 --- a/examples/vashishta/log.5Oct16.vashishta.table.sio2.g++.4 +++ b/examples/vashishta/log.27Nov18.vashishta.table.sio2.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # test Vashishta potential for quartz units metal @@ -18,6 +19,7 @@ replicate 4 4 4 triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0) 2 by 1 by 2 MPI processor grid 576 atoms + Time spent = 0.000568867 secs velocity all create 2000.0 277387 mom yes displace_atoms all move 0.05 0.9 0.4 units box @@ -38,13 +40,18 @@ timestep 0.001 run 100 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.3 ghost atom cutoff = 10.3 - binsize = 5.15 -> bins = 6 4 5 -Memory usage per processor = 8.60573 Mbytes + binsize = 5.15, bins = 6 4 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair vashishta/table, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.954 | 8.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 2000 -5280.8748 0 -5132.2257 -20501.94 10 895.65274 -5198.4018 0 -5131.8328 419.5556 @@ -57,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press 80 1020.1046 -5207.6761 0 -5131.8572 -13488.691 90 912.75537 -5199.6508 0 -5131.8106 2715.7189 100 998.97595 -5206.1006 0 -5131.8521 6024.5628 -Loop time of 0.16443 on 4 procs for 100 steps with 576 atoms +Loop time of 0.245452 on 4 procs for 100 steps with 576 atoms -Performance: 52.545 ns/day, 0.457 hours/ns, 608.161 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 35.200 ns/day, 0.682 hours/ns, 407.412 timesteps/s +96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.12531 | 0.13171 | 0.13599 | 1.1 | 80.10 -Neigh | 0.017477 | 0.017983 | 0.018685 | 0.3 | 10.94 -Comm | 0.0094879 | 0.01374 | 0.020683 | 3.8 | 8.36 -Output | 0.00022864 | 0.00025094 | 0.00027585 | 0.1 | 0.15 -Modify | 0.00027609 | 0.00028592 | 0.00029564 | 0.0 | 0.17 -Other | | 0.0004643 | | | 0.28 +Pair | 0.18883 | 0.19598 | 0.21164 | 2.1 | 79.85 +Neigh | 0.01932 | 0.019972 | 0.020683 | 0.4 | 8.14 +Comm | 0.011552 | 0.028067 | 0.03599 | 5.9 | 11.43 +Output | 0.00027466 | 0.0005008 | 0.00109 | 0.0 | 0.20 +Modify | 0.00035977 | 0.00036436 | 0.00037313 | 0.0 | 0.15 +Other | | 0.0005662 | | | 0.23 Nlocal: 144 ave 146 max 143 min Histogram: 2 0 0 1 0 0 0 0 0 1 diff --git a/examples/vashishta/log.5Oct16.indiumphosphide.g++.1 b/examples/vashishta/log.5Oct16.indiumphosphide.g++.1 deleted file mode 100644 index 3887d186ff..0000000000 --- a/examples/vashishta/log.5Oct16.indiumphosphide.g++.1 +++ /dev/null @@ -1,5276 +0,0 @@ -LAMMPS (5 Oct 2016) -# calculate the energy volume curve for InP zincblende - -# define volume range and filename - -variable ndelta equal 100 -variable volatom_min equal 20.0 -variable volatom_max equal 29.0 -variable evsvolfile string evsvol.dat - -# set up cell - -units metal - -boundary p p p - -# setup loop variables for box volume - -variable amin equal ${volatom_min}^(1/3)*2 -variable amin equal 20^(1/3)*2 -variable delta equal (${volatom_max}-${volatom_min})/${ndelta} -variable delta equal (29-${volatom_min})/${ndelta} -variable delta equal (29-20)/${ndelta} -variable delta equal (29-20)/100 -variable scale equal (${delta}/v_volatom+1)^(1/3) -variable scale equal (0.09/v_volatom+1)^(1/3) - -# set up 8 atom InP zincblende unit cell - -lattice diamond ${amin} -lattice diamond 5.42883523318981 -Lattice spacing in x,y,z = 5.42884 5.42884 5.42884 - -region box prism 0 1 0 1 0 1 0 0 0 - -create_box 2 box -Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0) - 1 by 1 by 1 MPI processor grid - -create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 -Created 8 atoms - -mass 1 114.76 -mass 2 30.98 - -# choose potential - -pair_style vashishta -pair_coeff * * InP.vashishta In P -Reading potential file InP.vashishta with DATE: 2015-10-14 - -# setup neighbor style - -neighbor 1.0 nsq -neigh_modify once no every 1 delay 0 check yes - -# setup output - -thermo_style custom step temp pe press vol -thermo_modify norm no -variable volatom equal vol/atoms -variable eatom equal pe/atoms -print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile} -print "# Volume [A^3/atom] Energy [eV/atom]" file evsvol.dat -# Volume [A^3/atom] Energy [eV/atom] - -# loop over range of volumes - -label loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00149775560818 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale ${scale} remap -change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.00149775560818 remap - triclinic box = (-0.00406553 0 0) to (5.4329 5.42884 5.42884) with tilt (0 0 0) - triclinic box = (-0.00406553 -0.00406553 0) to (5.4329 5.4329 5.42884) with tilt (0 0 0) - triclinic box = (-0.00406553 -0.00406553 -0.00406553) to (5.4329 5.4329 5.4329) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7 - ghost atom cutoff = 7 -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -24.633958 315900.5 160.72 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.09 -3.07924477327226 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00149105588627 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00149105588627 y scale 1.00149105588627 z scale ${scale} remap -change_box all x scale 1.00149105588627 y scale 1.00149105588627 z scale 1.00149105588627 remap - triclinic box = (-0.00811894 -0.00406553 -0.00406553) to (5.43695 5.4329 5.4329) with tilt (0 0 0) - triclinic box = (-0.00811894 -0.00811894 -0.00406553) to (5.43695 5.43695 5.4329) with tilt (0 0 0) - triclinic box = (-0.00811894 -0.00811894 -0.00811894) to (5.43695 5.43695 5.43695) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -24.773834 306658.04 161.44 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.1799999999997 -3.09672920462219 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00148441583558 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00148441583558 y scale 1.00148441583558 z scale ${scale} remap -change_box all x scale 1.00148441583558 y scale 1.00148441583558 z scale 1.00148441583558 remap - triclinic box = (-0.0121603 -0.00811894 -0.00811894) to (5.441 5.43695 5.43695) with tilt (0 0 0) - triclinic box = (-0.0121603 -0.0121603 -0.00811894) to (5.441 5.441 5.43695) with tilt (0 0 0) - triclinic box = (-0.0121603 -0.0121603 -0.0121603) to (5.441 5.441 5.441) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -24.909615 297676.86 162.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.2699999999996 -3.11370182923915 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00147783466245 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00147783466245 y scale 1.00147783466245 z scale ${scale} remap -change_box all x scale 1.00147783466245 y scale 1.00147783466245 z scale 1.00147783466245 remap - triclinic box = (-0.0161898 -0.0121603 -0.0121603) to (5.44502 5.441 5.441) with tilt (0 0 0) - triclinic box = (-0.0161898 -0.0161898 -0.0121603) to (5.44502 5.44502 5.441) with tilt (0 0 0) - triclinic box = (-0.0161898 -0.0161898 -0.0161898) to (5.44502 5.44502 5.44502) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.041417 288949.17 162.88 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.3599999999999 -3.13017710427322 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00147131158722 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00147131158722 y scale 1.00147131158722 z scale ${scale} remap -change_box all x scale 1.00147131158722 y scale 1.00147131158722 z scale 1.00147131158722 remap - triclinic box = (-0.0202073 -0.0161898 -0.0161898) to (5.44904 5.44502 5.44502) with tilt (0 0 0) - triclinic box = (-0.0202073 -0.0202073 -0.0161898) to (5.44904 5.44904 5.44502) with tilt (0 0 0) - triclinic box = (-0.0202073 -0.0202073 -0.0202073) to (5.44904 5.44904 5.44904) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.169352 280467.46 163.6 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.4500000000002 -3.14616905711537 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00146484584395 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00146484584395 y scale 1.00146484584395 z scale ${scale} remap -change_box all x scale 1.00146484584395 y scale 1.00146484584395 z scale 1.00146484584395 remap - triclinic box = (-0.0242131 -0.0202073 -0.0202073) to (5.45305 5.44904 5.44904) with tilt (0 0 0) - triclinic box = (-0.0242131 -0.0242131 -0.0202073) to (5.45305 5.45305 5.44904) with tilt (0 0 0) - triclinic box = (-0.0242131 -0.0242131 -0.0242131) to (5.45305 5.45305 5.45305) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.29353 272224.44 164.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.5400000000003 -3.16169129950254 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.0014584366801 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.0014584366801 y scale 1.0014584366801 z scale ${scale} remap -change_box all x scale 1.0014584366801 y scale 1.0014584366801 z scale 1.0014584366801 remap - triclinic box = (-0.0282073 -0.0242131 -0.0242131) to (5.45704 5.45305 5.45305) with tilt (0 0 0) - triclinic box = (-0.0282073 -0.0282073 -0.0242131) to (5.45704 5.45704 5.45305) with tilt (0 0 0) - triclinic box = (-0.0282073 -0.0282073 -0.0282073) to (5.45704 5.45704 5.45704) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.414056 264213.09 165.04 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.6300000000001 -3.17675704110846 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00145208335626 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00145208335626 y scale 1.00145208335626 z scale ${scale} remap -change_box all x scale 1.00145208335626 y scale 1.00145208335626 z scale 1.00145208335626 remap - triclinic box = (-0.0321898 -0.0282073 -0.0282073) to (5.46103 5.45704 5.45704) with tilt (0 0 0) - triclinic box = (-0.0321898 -0.0321898 -0.0282073) to (5.46103 5.46103 5.45704) with tilt (0 0 0) - triclinic box = (-0.0321898 -0.0321898 -0.0321898) to (5.46103 5.46103 5.46103) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.531033 256426.58 165.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.7200000000001 -3.19137910264164 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00144578514582 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00144578514582 y scale 1.00144578514582 z scale ${scale} remap -change_box all x scale 1.00144578514582 y scale 1.00144578514582 z scale 1.00144578514582 remap - triclinic box = (-0.0361608 -0.0321898 -0.0321898) to (5.465 5.46103 5.46103) with tilt (0 0 0) - triclinic box = (-0.0361608 -0.0361608 -0.0321898) to (5.465 5.465 5.46103) with tilt (0 0 0) - triclinic box = (-0.0361608 -0.0361608 -0.0361608) to (5.465 5.465 5.465) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.644559 248858.32 166.48 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.8100000000003 -3.20556992846954 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00143954133473 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00143954133473 y scale 1.00143954133473 z scale ${scale} remap -change_box all x scale 1.00143954133473 y scale 1.00143954133473 z scale 1.00143954133473 remap - triclinic box = (-0.0401203 -0.0361608 -0.0361608) to (5.46896 5.465 5.465) with tilt (0 0 0) - triclinic box = (-0.0401203 -0.0401203 -0.0361608) to (5.46896 5.46896 5.465) with tilt (0 0 0) - triclinic box = (-0.0401203 -0.0401203 -0.0401203) to (5.46896 5.46896 5.46896) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.754685 240961.62 167.2 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.9000000000003 -3.21933565066766 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00143335122124 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00143335122124 y scale 1.00143335122124 z scale ${scale} remap -change_box all x scale 1.00143335122124 y scale 1.00143335122124 z scale 1.00143335122124 remap - triclinic box = (-0.0440686 -0.0401203 -0.0401203) to (5.4729 5.46896 5.46896) with tilt (0 0 0) - triclinic box = (-0.0440686 -0.0440686 -0.0401203) to (5.4729 5.4729 5.46896) with tilt (0 0 0) - triclinic box = (-0.0440686 -0.0440686 -0.0440686) to (5.4729 5.4729 5.4729) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.861049 232444.2 167.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.9900000000005 -3.23263106528897 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00142721411559 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00142721411559 y scale 1.00142721411559 z scale ${scale} remap -change_box all x scale 1.00142721411559 y scale 1.00142721411559 z scale 1.00142721411559 remap - triclinic box = (-0.0480055 -0.0440686 -0.0440686) to (5.47684 5.4729 5.4729) with tilt (0 0 0) - triclinic box = (-0.0480055 -0.0480055 -0.0440686) to (5.47684 5.47684 5.4729) with tilt (0 0 0) - triclinic box = (-0.0480055 -0.0480055 -0.0480055) to (5.47684 5.47684 5.47684) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -25.963633 224145.09 168.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.0800000000004 -3.24545418655742 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00142112933981 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00142112933981 y scale 1.00142112933981 z scale ${scale} remap -change_box all x scale 1.00142112933981 y scale 1.00142112933981 z scale 1.00142112933981 remap - triclinic box = (-0.0519313 -0.0480055 -0.0480055) to (5.48077 5.47684 5.47684) with tilt (0 0 0) - triclinic box = (-0.0519313 -0.0519313 -0.0480055) to (5.48077 5.48077 5.47684) with tilt (0 0 0) - triclinic box = (-0.0519313 -0.0519313 -0.0519313) to (5.48077 5.48077 5.48077) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.062537 216058.21 169.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.1700000000001 -3.2578171061398 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00141509622744 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00141509622744 y scale 1.00141509622744 z scale ${scale} remap -change_box all x scale 1.00141509622744 y scale 1.00141509622744 z scale 1.00141509622744 remap - triclinic box = (-0.0558459 -0.0519313 -0.0519313) to (5.48468 5.48077 5.48077) with tilt (0 0 0) - triclinic box = (-0.0558459 -0.0558459 -0.0519313) to (5.48468 5.48468 5.48077) with tilt (0 0 0) - triclinic box = (-0.0558459 -0.0558459 -0.0558459) to (5.48468 5.48468 5.48468) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.157853 208177.66 170.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.2600000000005 -3.26973157905241 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00140911412325 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00140911412325 y scale 1.00140911412325 z scale ${scale} remap -change_box all x scale 1.00140911412325 y scale 1.00140911412325 z scale 1.00140911412325 remap - triclinic box = (-0.0597495 -0.0558459 -0.0558459) to (5.48858 5.48468 5.48468) with tilt (0 0 0) - triclinic box = (-0.0597495 -0.0597495 -0.0558459) to (5.48858 5.48858 5.48468) with tilt (0 0 0) - triclinic box = (-0.0597495 -0.0597495 -0.0597495) to (5.48858 5.48858 5.48858) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.249672 200497.73 170.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.3500000000002 -3.28120903415515 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00140318238311 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00140318238311 y scale 1.00140318238311 z scale ${scale} remap -change_box all x scale 1.00140318238311 y scale 1.00140318238311 z scale 1.00140318238311 remap - triclinic box = (-0.0636422 -0.0597495 -0.0597495) to (5.49248 5.48858 5.48858) with tilt (0 0 0) - triclinic box = (-0.0636422 -0.0636422 -0.0597495) to (5.49248 5.49248 5.48858) with tilt (0 0 0) - triclinic box = (-0.0636422 -0.0636422 -0.0636422) to (5.49248 5.49248 5.49248) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.338085 193012.87 171.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.4400000000004 -3.29226058428118 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00139730037362 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00139730037362 y scale 1.00139730037362 z scale ${scale} remap -change_box all x scale 1.00139730037362 y scale 1.00139730037362 z scale 1.00139730037362 remap - triclinic box = (-0.067524 -0.0636422 -0.0636422) to (5.49636 5.49248 5.49248) with tilt (0 0 0) - triclinic box = (-0.067524 -0.067524 -0.0636422) to (5.49636 5.49636 5.49248) with tilt (0 0 0) - triclinic box = (-0.067524 -0.067524 -0.067524) to (5.49636 5.49636 5.49636) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.423176 185717.71 172.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.5300000000002 -3.3028970360141 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00139146747202 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00139146747202 y scale 1.00139146747202 z scale ${scale} remap -change_box all x scale 1.00139146747202 y scale 1.00139146747202 z scale 1.00139146747202 remap - triclinic box = (-0.071395 -0.067524 -0.067524) to (5.50023 5.49636 5.49636) with tilt (0 0 0) - triclinic box = (-0.071395 -0.071395 -0.067524) to (5.50023 5.50023 5.49636) with tilt (0 0 0) - triclinic box = (-0.071395 -0.071395 -0.071395) to (5.50023 5.50023 5.50023) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.505031 178607.07 172.96 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.6200000000004 -3.31312889912851 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00138568306585 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00138568306585 y scale 1.00138568306585 z scale ${scale} remap -change_box all x scale 1.00138568306585 y scale 1.00138568306585 z scale 1.00138568306585 remap - triclinic box = (-0.0752552 -0.071395 -0.071395) to (5.50409 5.50023 5.50023) with tilt (0 0 0) - triclinic box = (-0.0752552 -0.0752552 -0.071395) to (5.50409 5.50409 5.50023) with tilt (0 0 0) - triclinic box = (-0.0752552 -0.0752552 -0.0752552) to (5.50409 5.50409 5.50409) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.583731 171675.89 173.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.7100000000001 -3.32296639570479 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00137994655284 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00137994655284 y scale 1.00137994655284 z scale ${scale} remap -change_box all x scale 1.00137994655284 y scale 1.00137994655284 z scale 1.00137994655284 remap - triclinic box = (-0.0791048 -0.0752552 -0.0752552) to (5.50794 5.50409 5.50409) with tilt (0 0 0) - triclinic box = (-0.0791048 -0.0791048 -0.0752552) to (5.50794 5.50794 5.50409) with tilt (0 0 0) - triclinic box = (-0.0791048 -0.0791048 -0.0791048) to (5.50794 5.50794 5.50794) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.659356 164919.29 174.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.7999999999999 -3.33241946893207 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00137425734062 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00137425734062 y scale 1.00137425734062 z scale ${scale} remap -change_box all x scale 1.00137425734062 y scale 1.00137425734062 z scale 1.00137425734062 remap - triclinic box = (-0.0829438 -0.0791048 -0.0791048) to (5.51178 5.50794 5.50794) with tilt (0 0 0) - triclinic box = (-0.0829438 -0.0829438 -0.0791048) to (5.51178 5.51178 5.50794) with tilt (0 0 0) - triclinic box = (-0.0829438 -0.0829438 -0.0829438) to (5.51178 5.51178 5.51178) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.731982 158332.52 175.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 420 ave 420 max 420 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.89 -3.34149779161019 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00136861484656 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00136861484656 y scale 1.00136861484656 z scale ${scale} remap -change_box all x scale 1.00136861484656 y scale 1.00136861484656 z scale 1.00136861484656 remap - triclinic box = (-0.0867724 -0.0829438 -0.0829438) to (5.51561 5.51178 5.51178) with tilt (0 0 0) - triclinic box = (-0.0867724 -0.0867724 -0.0829438) to (5.51561 5.51561 5.51178) with tilt (0 0 0) - triclinic box = (-0.0867724 -0.0867724 -0.0867724) to (5.51561 5.51561 5.51561) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.801686 151911 175.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -21.9800000000002 -3.35021077436259 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00136301849755 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00136301849755 y scale 1.00136301849755 z scale ${scale} remap -change_box all x scale 1.00136301849755 y scale 1.00136301849755 z scale 1.00136301849755 remap - triclinic box = (-0.0905904 -0.0867724 -0.0867724) to (5.51943 5.51561 5.51561) with tilt (0 0 0) - triclinic box = (-0.0905904 -0.0905904 -0.0867724) to (5.51943 5.51943 5.51561) with tilt (0 0 0) - triclinic box = (-0.0905904 -0.0905904 -0.0905904) to (5.51943 5.51943 5.51943) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.868541 145650.26 176.56 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.0700000000002 -3.35856757357086 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00135746772984 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00135746772984 y scale 1.00135746772984 z scale ${scale} remap -change_box all x scale 1.00135746772984 y scale 1.00135746772984 z scale 1.00135746772984 remap - triclinic box = (-0.0943981 -0.0905904 -0.0905904) to (5.52323 5.51943 5.51943) with tilt (0 0 0) - triclinic box = (-0.0943981 -0.0943981 -0.0905904) to (5.52323 5.52323 5.51943) with tilt (0 0 0) - triclinic box = (-0.0943981 -0.0943981 -0.0943981) to (5.52323 5.52323 5.52323) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.932617 139545.98 177.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.1600000000005 -3.36657709904146 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00135196198879 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00135196198879 y scale 1.00135196198879 z scale ${scale} remap -change_box all x scale 1.00135196198879 y scale 1.00135196198879 z scale 1.00135196198879 remap - triclinic box = (-0.0981955 -0.0943981 -0.0943981) to (5.52703 5.52323 5.52323) with tilt (0 0 0) - triclinic box = (-0.0981955 -0.0981955 -0.0943981) to (5.52703 5.52703 5.52323) with tilt (0 0 0) - triclinic box = (-0.0981955 -0.0981955 -0.0981955) to (5.52703 5.52703 5.52703) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -26.993984 133593.97 178 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.2500000000003 -3.37424802141442 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00134650072876 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00134650072876 y scale 1.00134650072876 z scale ${scale} remap -change_box all x scale 1.00134650072876 y scale 1.00134650072876 z scale 1.00134650072876 remap - triclinic box = (-0.101983 -0.0981955 -0.0981955) to (5.53082 5.52703 5.52703) with tilt (0 0 0) - triclinic box = (-0.101983 -0.101983 -0.0981955) to (5.53082 5.53082 5.52703) with tilt (0 0 0) - triclinic box = (-0.101983 -0.101983 -0.101983) to (5.53082 5.53082 5.53082) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.05271 127790.17 178.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.34 -3.38158877932393 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00134108341287 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00134108341287 y scale 1.00134108341287 z scale ${scale} remap -change_box all x scale 1.00134108341287 y scale 1.00134108341287 z scale 1.00134108341287 remap - triclinic box = (-0.10576 -0.101983 -0.101983) to (5.53459 5.53082 5.53082) with tilt (0 0 0) - triclinic box = (-0.10576 -0.10576 -0.101983) to (5.53459 5.53459 5.53082) with tilt (0 0 0) - triclinic box = (-0.10576 -0.10576 -0.10576) to (5.53459 5.53459 5.53459) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.108861 122130.61 179.44 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.4299999999997 -3.38860758631982 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00133570951285 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00133570951285 y scale 1.00133570951285 z scale ${scale} remap -change_box all x scale 1.00133570951285 y scale 1.00133570951285 z scale 1.00133570951285 remap - triclinic box = (-0.109527 -0.10576 -0.10576) to (5.53836 5.53459 5.53459) with tilt (0 0 0) - triclinic box = (-0.109527 -0.109527 -0.10576) to (5.53836 5.53836 5.53459) with tilt (0 0 0) - triclinic box = (-0.109527 -0.109527 -0.109527) to (5.53836 5.53836 5.53836) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.1625 116611.48 180.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.5199999999998 -3.39531243755874 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00133037850885 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00133037850885 y scale 1.00133037850885 z scale ${scale} remap -change_box all x scale 1.00133037850885 y scale 1.00133037850885 z scale 1.00133037850885 remap - triclinic box = (-0.113284 -0.109527 -0.109527) to (5.54212 5.53836 5.53836) with tilt (0 0 0) - triclinic box = (-0.113284 -0.113284 -0.109527) to (5.54212 5.54212 5.53836) with tilt (0 0 0) - triclinic box = (-0.113284 -0.113284 -0.113284) to (5.54212 5.54212 5.54212) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.213689 111229.06 180.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.6099999999997 -3.40171111627368 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00132508988931 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00132508988931 y scale 1.00132508988931 z scale ${scale} remap -change_box all x scale 1.00132508988931 y scale 1.00132508988931 z scale 1.00132508988931 remap - triclinic box = (-0.117031 -0.113284 -0.113284) to (5.54587 5.54212 5.54212) with tilt (0 0 0) - triclinic box = (-0.117031 -0.117031 -0.113284) to (5.54587 5.54587 5.54212) with tilt (0 0 0) - triclinic box = (-0.117031 -0.117031 -0.117031) to (5.54587 5.54587 5.54587) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.26249 105979.74 181.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.6999999999996 -3.40781120002994 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00131984315076 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00131984315076 y scale 1.00131984315076 z scale ${scale} remap -change_box all x scale 1.00131984315076 y scale 1.00131984315076 z scale 1.00131984315076 remap - triclinic box = (-0.120768 -0.117031 -0.117031) to (5.5496 5.54587 5.54587) with tilt (0 0 0) - triclinic box = (-0.120768 -0.120768 -0.117031) to (5.5496 5.5496 5.54587) with tilt (0 0 0) - triclinic box = (-0.120768 -0.120768 -0.120768) to (5.5496 5.5496 5.5496) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.308961 100860.02 182.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.7899999999997 -3.4136200667752 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00131463779767 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00131463779767 y scale 1.00131463779767 z scale ${scale} remap -change_box all x scale 1.00131463779767 y scale 1.00131463779767 z scale 1.00131463779767 remap - triclinic box = (-0.124495 -0.120768 -0.120768) to (5.55333 5.5496 5.5496) with tilt (0 0 0) - triclinic box = (-0.124495 -0.124495 -0.120768) to (5.55333 5.55333 5.5496) with tilt (0 0 0) - triclinic box = (-0.124495 -0.124495 -0.124495) to (5.55333 5.55333 5.55333) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.353159 95866.497 183.04 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.88 -3.41914490069132 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00130947334229 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00130947334229 y scale 1.00130947334229 z scale ${scale} remap -change_box all x scale 1.00130947334229 y scale 1.00130947334229 z scale 1.00130947334229 remap - triclinic box = (-0.128212 -0.124495 -0.124495) to (5.55705 5.55333 5.55333) with tilt (0 0 0) - triclinic box = (-0.128212 -0.128212 -0.124495) to (5.55705 5.55705 5.55333) with tilt (0 0 0) - triclinic box = (-0.128212 -0.128212 -0.128212) to (5.55705 5.55705 5.55705) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.395142 90995.879 183.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -22.9699999999997 -3.424392697855 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00130434930454 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00130434930454 y scale 1.00130434930454 z scale ${scale} remap -change_box all x scale 1.00130434930454 y scale 1.00130434930454 z scale 1.00130434930454 remap - triclinic box = (-0.13192 -0.128212 -0.128212) to (5.56076 5.55705 5.55705) with tilt (0 0 0) - triclinic box = (-0.13192 -0.13192 -0.128212) to (5.56076 5.56076 5.55705) with tilt (0 0 0) - triclinic box = (-0.13192 -0.13192 -0.13192) to (5.56076 5.56076 5.56076) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.434962 86244.961 184.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.0599999999998 -3.42937027171443 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00129926521177 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00129926521177 y scale 1.00129926521177 z scale ${scale} remap -change_box all x scale 1.00129926521177 y scale 1.00129926521177 z scale 1.00129926521177 remap - triclinic box = (-0.135618 -0.13192 -0.13192) to (5.56445 5.56076 5.56076) with tilt (0 0 0) - triclinic box = (-0.135618 -0.135618 -0.13192) to (5.56445 5.56445 5.56076) with tilt (0 0 0) - triclinic box = (-0.135618 -0.135618 -0.135618) to (5.56445 5.56445 5.56445) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.472674 81610.631 185.2 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.1499999999995 -3.43408425838794 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00129422059873 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00129422059873 y scale 1.00129422059873 z scale ${scale} remap -change_box all x scale 1.00129422059873 y scale 1.00129422059873 z scale 1.00129422059873 remap - triclinic box = (-0.139307 -0.135618 -0.135618) to (5.56814 5.56445 5.56445) with tilt (0 0 0) - triclinic box = (-0.139307 -0.139307 -0.135618) to (5.56814 5.56814 5.56445) with tilt (0 0 0) - triclinic box = (-0.139307 -0.139307 -0.139307) to (5.56814 5.56814 5.56814) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.508329 77089.868 185.92 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.2399999999998 -3.43854112179202 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00128921500731 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00128921500731 y scale 1.00128921500731 z scale ${scale} remap -change_box all x scale 1.00128921500731 y scale 1.00128921500731 z scale 1.00128921500731 remap - triclinic box = (-0.142986 -0.139307 -0.139307) to (5.57182 5.56814 5.56814) with tilt (0 0 0) - triclinic box = (-0.142986 -0.142986 -0.139307) to (5.57182 5.57182 5.56814) with tilt (0 0 0) - triclinic box = (-0.142986 -0.142986 -0.142986) to (5.57182 5.57182 5.57182) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.541977 72679.738 186.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 560 ave 560 max 560 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.3299999999999 -3.4427471586037 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.0012842479865 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.0012842479865 y scale 1.0012842479865 z scale ${scale} remap -change_box all x scale 1.0012842479865 y scale 1.0012842479865 z scale 1.0012842479865 remap - triclinic box = (-0.146656 -0.142986 -0.142986) to (5.57549 5.57182 5.57182) with tilt (0 0 0) - triclinic box = (-0.146656 -0.146656 -0.142986) to (5.57549 5.57549 5.57182) with tilt (0 0 0) - triclinic box = (-0.146656 -0.146656 -0.146656) to (5.57549 5.57549 5.57549) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.573668 68377.392 187.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.4199999999997 -3.44670850306418 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00127931909221 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00127931909221 y scale 1.00127931909221 z scale ${scale} remap -change_box all x scale 1.00127931909221 y scale 1.00127931909221 z scale 1.00127931909221 remap - triclinic box = (-0.150316 -0.146656 -0.146656) to (5.57915 5.57549 5.57549) with tilt (0 0 0) - triclinic box = (-0.150316 -0.150316 -0.146656) to (5.57915 5.57915 5.57549) with tilt (0 0 0) - triclinic box = (-0.150316 -0.150316 -0.150316) to (5.57915 5.57915 5.57915) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.603449 64180.061 188.08 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.5100000000001 -3.45043113162863 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00127442788711 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00127442788711 y scale 1.00127442788711 z scale ${scale} remap -change_box all x scale 1.00127442788711 y scale 1.00127442788711 z scale 1.00127442788711 remap - triclinic box = (-0.153967 -0.150316 -0.150316) to (5.5828 5.57915 5.57915) with tilt (0 0 0) - triclinic box = (-0.153967 -0.153967 -0.150316) to (5.5828 5.5828 5.57915) with tilt (0 0 0) - triclinic box = (-0.153967 -0.153967 -0.153967) to (5.5828 5.5828 5.5828) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.631367 60085.056 188.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.5999999999998 -3.45392086746794 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00126957394058 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00126957394058 y scale 1.00126957394058 z scale ${scale} remap -change_box all x scale 1.00126957394058 y scale 1.00126957394058 z scale 1.00126957394058 remap - triclinic box = (-0.157608 -0.153967 -0.153967) to (5.58644 5.5828 5.5828) with tilt (0 0 0) - triclinic box = (-0.157608 -0.157608 -0.153967) to (5.58644 5.58644 5.5828) with tilt (0 0 0) - triclinic box = (-0.157608 -0.157608 -0.157608) to (5.58644 5.58644 5.58644) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.657467 56089.763 189.52 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.6899999999998 -3.45718338482772 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.0012647568285 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.0012647568285 y scale 1.0012647568285 z scale ${scale} remap -change_box all x scale 1.0012647568285 y scale 1.0012647568285 z scale 1.0012647568285 remap - triclinic box = (-0.161241 -0.157608 -0.157608) to (5.59008 5.58644 5.58644) with tilt (0 0 0) - triclinic box = (-0.161241 -0.161241 -0.157608) to (5.59008 5.59008 5.58644) with tilt (0 0 0) - triclinic box = (-0.161241 -0.161241 -0.161241) to (5.59008 5.59008 5.59008) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.681794 52191.643 190.24 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.78 -3.46022421324915 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00125997613317 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00125997613317 y scale 1.00125997613317 z scale ${scale} remap -change_box all x scale 1.00125997613317 y scale 1.00125997613317 z scale 1.00125997613317 remap - triclinic box = (-0.164864 -0.161241 -0.161241) to (5.5937 5.59008 5.59008) with tilt (0 0 0) - triclinic box = (-0.164864 -0.164864 -0.161241) to (5.5937 5.5937 5.59008) with tilt (0 0 0) - triclinic box = (-0.164864 -0.164864 -0.164864) to (5.5937 5.5937 5.5937) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.70439 48388.229 190.96 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.8699999999999 -3.46304874165698 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00125523144319 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00125523144319 y scale 1.00125523144319 z scale ${scale} remap -change_box all x scale 1.00125523144319 y scale 1.00125523144319 z scale 1.00125523144319 remap - triclinic box = (-0.168478 -0.164864 -0.164864) to (5.59731 5.5937 5.5937) with tilt (0 0 0) - triclinic box = (-0.168478 -0.168478 -0.164864) to (5.59731 5.59731 5.5937) with tilt (0 0 0) - triclinic box = (-0.168478 -0.168478 -0.168478) to (5.59731 5.59731 5.59731) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.725298 44677.122 191.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -23.9599999999996 -3.46566222231901 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00125052235334 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00125052235334 y scale 1.00125052235334 z scale ${scale} remap -change_box all x scale 1.00125052235334 y scale 1.00125052235334 z scale 1.00125052235334 remap - triclinic box = (-0.172083 -0.168478 -0.168478) to (5.60092 5.59731 5.59731) with tilt (0 0 0) - triclinic box = (-0.172083 -0.172083 -0.168478) to (5.60092 5.60092 5.59731) with tilt (0 0 0) - triclinic box = (-0.172083 -0.172083 -0.172083) to (5.60092 5.60092 5.60092) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.744558 41055.991 192.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.0499999999997 -3.46806977468166 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00124584846443 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00124584846443 y scale 1.00124584846443 z scale ${scale} remap -change_box all x scale 1.00124584846443 y scale 1.00124584846443 z scale 1.00124584846443 remap - triclinic box = (-0.175679 -0.172083 -0.172083) to (5.60451 5.60092 5.60092) with tilt (0 0 0) - triclinic box = (-0.175679 -0.175679 -0.172083) to (5.60451 5.60451 5.60092) with tilt (0 0 0) - triclinic box = (-0.175679 -0.175679 -0.175679) to (5.60451 5.60451 5.60451) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.762211 37522.57 193.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.1399999999998 -3.47027638908584 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00124120938324 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00124120938324 y scale 1.00124120938324 z scale ${scale} remap -change_box all x scale 1.00124120938324 y scale 1.00124120938324 z scale 1.00124120938324 remap - triclinic box = (-0.179267 -0.175679 -0.175679) to (5.6081 5.60451 5.60451) with tilt (0 0 0) - triclinic box = (-0.179267 -0.179267 -0.175679) to (5.6081 5.6081 5.60451) with tilt (0 0 0) - triclinic box = (-0.179267 -0.179267 -0.179267) to (5.6081 5.6081 5.6081) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.778295 34074.656 193.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.2299999999998 -3.47228693036723 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00123660472238 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00123660472238 y scale 1.00123660472238 z scale ${scale} remap -change_box all x scale 1.00123660472238 y scale 1.00123660472238 z scale 1.00123660472238 remap - triclinic box = (-0.182845 -0.179267 -0.179267) to (5.61168 5.6081 5.6081) with tilt (0 0 0) - triclinic box = (-0.182845 -0.182845 -0.179267) to (5.61168 5.61168 5.6081) with tilt (0 0 0) - triclinic box = (-0.182845 -0.182845 -0.182845) to (5.61168 5.61168 5.61168) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.792849 30710.109 194.56 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.3199999999999 -3.47410614134514 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00123203410018 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00123203410018 y scale 1.00123203410018 z scale ${scale} remap -change_box all x scale 1.00123203410018 y scale 1.00123203410018 z scale 1.00123203410018 remap - triclinic box = (-0.186414 -0.182845 -0.182845) to (5.61525 5.61168 5.61168) with tilt (0 0 0) - triclinic box = (-0.186414 -0.186414 -0.182845) to (5.61525 5.61525 5.61168) with tilt (0 0 0) - triclinic box = (-0.186414 -0.186414 -0.186414) to (5.61525 5.61525 5.61525) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.805909 27426.844 195.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.4099999999996 -3.47573864620345 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00122749714061 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00122749714061 y scale 1.00122749714061 z scale ${scale} remap -change_box all x scale 1.00122749714061 y scale 1.00122749714061 z scale 1.00122749714061 remap - triclinic box = (-0.189975 -0.186414 -0.186414) to (5.61881 5.61525 5.61525) with tilt (0 0 0) - triclinic box = (-0.189975 -0.189975 -0.186414) to (5.61881 5.61881 5.61525) with tilt (0 0 0) - triclinic box = (-0.189975 -0.189975 -0.189975) to (5.61881 5.61881 5.61881) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.817512 24222.838 196 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.4999999999996 -3.47718895376758 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00122299347313 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00122299347313 y scale 1.00122299347313 z scale ${scale} remap -change_box all x scale 1.00122299347313 y scale 1.00122299347313 z scale 1.00122299347313 remap - triclinic box = (-0.193527 -0.189975 -0.189975) to (5.62236 5.61881 5.61881) with tilt (0 0 0) - triclinic box = (-0.193527 -0.193527 -0.189975) to (5.62236 5.62236 5.61881) with tilt (0 0 0) - triclinic box = (-0.193527 -0.193527 -0.193527) to (5.62236 5.62236 5.62236) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.827692 21096.12 196.72 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.5899999999993 -3.4784614606809 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00121852273265 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00121852273265 y scale 1.00121852273265 z scale ${scale} remap -change_box all x scale 1.00121852273265 y scale 1.00121852273265 z scale 1.00121852273265 remap - triclinic box = (-0.197071 -0.193527 -0.193527) to (5.62591 5.62236 5.62236) with tilt (0 0 0) - triclinic box = (-0.197071 -0.197071 -0.193527) to (5.62591 5.62591 5.62236) with tilt (0 0 0) - triclinic box = (-0.197071 -0.197071 -0.197071) to (5.62591 5.62591 5.62591) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.836484 18044.775 197.44 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.6799999999993 -3.47956045448403 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00121408455937 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00121408455937 y scale 1.00121408455937 z scale ${scale} remap -change_box all x scale 1.00121408455937 y scale 1.00121408455937 z scale 1.00121408455937 remap - triclinic box = (-0.200605 -0.197071 -0.197071) to (5.62944 5.62591 5.62591) with tilt (0 0 0) - triclinic box = (-0.200605 -0.200605 -0.197071) to (5.62944 5.62944 5.62591) with tilt (0 0 0) - triclinic box = (-0.200605 -0.200605 -0.200605) to (5.62944 5.62944 5.62944) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.843921 15066.941 198.16 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.769999999999 -3.48049011660029 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00120967859874 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00120967859874 y scale 1.00120967859874 z scale ${scale} remap -change_box all x scale 1.00120967859874 y scale 1.00120967859874 z scale 1.00120967859874 remap - triclinic box = (-0.204132 -0.200605 -0.200605) to (5.63297 5.62944 5.62944) with tilt (0 0 0) - triclinic box = (-0.204132 -0.204132 -0.200605) to (5.63297 5.63297 5.62944) with tilt (0 0 0) - triclinic box = (-0.204132 -0.204132 -0.204132) to (5.63297 5.63297 5.63297) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.850036 12160.805 198.88 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.859999999999 -3.48125452523046 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00120530450131 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00120530450131 y scale 1.00120530450131 z scale ${scale} remap -change_box all x scale 1.00120530450131 y scale 1.00120530450131 z scale 1.00120530450131 remap - triclinic box = (-0.207649 -0.204132 -0.204132) to (5.63648 5.63297 5.63297) with tilt (0 0 0) - triclinic box = (-0.207649 -0.207649 -0.204132) to (5.63648 5.63648 5.63297) with tilt (0 0 0) - triclinic box = (-0.207649 -0.207649 -0.207649) to (5.63648 5.63648 5.63648) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.854861 9324.604 199.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -24.9499999999988 -3.4818576581599 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00120096192269 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00120096192269 y scale 1.00120096192269 z scale ${scale} remap -change_box all x scale 1.00120096192269 y scale 1.00120096192269 z scale 1.00120096192269 remap - triclinic box = (-0.211159 -0.207649 -0.207649) to (5.63999 5.63648 5.63648) with tilt (0 0 0) - triclinic box = (-0.211159 -0.211159 -0.207649) to (5.63999 5.63999 5.63648) with tilt (0 0 0) - triclinic box = (-0.211159 -0.211159 -0.211159) to (5.63999 5.63999 5.63999) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.858427 6556.6223 200.32 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.0399999999985 -3.48230339548106 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00119665052343 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00119665052343 y scale 1.00119665052343 z scale ${scale} remap -change_box all x scale 1.00119665052343 y scale 1.00119665052343 z scale 1.00119665052343 remap - triclinic box = (-0.21466 -0.211159 -0.211159) to (5.64349 5.63999 5.63999) with tilt (0 0 0) - triclinic box = (-0.21466 -0.21466 -0.211159) to (5.64349 5.64349 5.63999) with tilt (0 0 0) - triclinic box = (-0.21466 -0.21466 -0.21466) to (5.64349 5.64349 5.64349) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.860764 3855.1909 201.04 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.1299999999987 -3.48259552223389 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00119236996892 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00119236996892 y scale 1.00119236996892 z scale ${scale} remap -change_box all x scale 1.00119236996892 y scale 1.00119236996892 z scale 1.00119236996892 remap - triclinic box = (-0.218152 -0.21466 -0.21466) to (5.64699 5.64349 5.64349) with tilt (0 0 0) - triclinic box = (-0.218152 -0.218152 -0.21466) to (5.64699 5.64699 5.64349) with tilt (0 0 0) - triclinic box = (-0.218152 -0.218152 -0.218152) to (5.64699 5.64699 5.64699) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.861902 1218.6858 201.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.2199999999989 -3.48273773096731 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00118811992934 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00118811992934 y scale 1.00118811992934 z scale ${scale} remap -change_box all x scale 1.00118811992934 y scale 1.00118811992934 z scale 1.00118811992934 remap - triclinic box = (-0.221636 -0.218152 -0.218152) to (5.65047 5.64699 5.64699) with tilt (0 0 0) - triclinic box = (-0.221636 -0.221636 -0.218152) to (5.65047 5.65047 5.64699) with tilt (0 0 0) - triclinic box = (-0.221636 -0.221636 -0.221636) to (5.65047 5.65047 5.65047) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.861869 -1354.4738 202.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.3099999999989 -3.48273362422406 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00118390007955 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00118390007955 y scale 1.00118390007955 z scale ${scale} remap -change_box all x scale 1.00118390007955 y scale 1.00118390007955 z scale 1.00118390007955 remap - triclinic box = (-0.225112 -0.221636 -0.221636) to (5.65395 5.65047 5.65047) with tilt (0 0 0) - triclinic box = (-0.225112 -0.225112 -0.221636) to (5.65395 5.65395 5.65047) with tilt (0 0 0) - triclinic box = (-0.225112 -0.225112 -0.225112) to (5.65395 5.65395 5.65395) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.860694 -3865.8261 203.2 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.3999999999989 -3.48258671695145 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00117971009901 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00117971009901 y scale 1.00117971009901 z scale ${scale} remap -change_box all x scale 1.00117971009901 y scale 1.00117971009901 z scale 1.00117971009901 remap - triclinic box = (-0.22858 -0.225112 -0.225112) to (5.65742 5.65395 5.65395) with tilt (0 0 0) - triclinic box = (-0.22858 -0.22858 -0.225112) to (5.65742 5.65742 5.65395) with tilt (0 0 0) - triclinic box = (-0.22858 -0.22858 -0.22858) to (5.65742 5.65742 5.65742) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.858404 -6316.8685 203.92 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.4899999999987 -3.48230043884065 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00117554967171 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00117554967171 y scale 1.00117554967171 z scale ${scale} remap -change_box all x scale 1.00117554967171 y scale 1.00117554967171 z scale 1.00117554967171 remap - triclinic box = (-0.23204 -0.22858 -0.22858) to (5.66088 5.65742 5.65742) with tilt (0 0 0) - triclinic box = (-0.23204 -0.23204 -0.22858) to (5.66088 5.66088 5.65742) with tilt (0 0 0) - triclinic box = (-0.23204 -0.23204 -0.23204) to (5.66088 5.66088 5.66088) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.855025 -8709.0584 204.64 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.5799999999985 -3.48187813659671 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00117141848607 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00117141848607 y scale 1.00117141848607 z scale ${scale} remap -change_box all x scale 1.00117141848607 y scale 1.00117141848607 z scale 1.00117141848607 remap - triclinic box = (-0.235491 -0.23204 -0.23204) to (5.66433 5.66088 5.66088) with tilt (0 0 0) - triclinic box = (-0.235491 -0.235491 -0.23204) to (5.66433 5.66433 5.66088) with tilt (0 0 0) - triclinic box = (-0.235491 -0.235491 -0.235491) to (5.66433 5.66433 5.66433) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.850585 -11043.815 205.36 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.6699999999982 -3.48132307614154 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00116731623489 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00116731623489 y scale 1.00116731623489 z scale ${scale} remap -change_box all x scale 1.00116731623489 y scale 1.00116731623489 z scale 1.00116731623489 remap - triclinic box = (-0.238935 -0.235491 -0.235491) to (5.66777 5.66433 5.66433) with tilt (0 0 0) - triclinic box = (-0.238935 -0.238935 -0.235491) to (5.66777 5.66777 5.66433) with tilt (0 0 0) - triclinic box = (-0.238935 -0.238935 -0.238935) to (5.66777 5.66777 5.66777) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.845108 -13322.519 206.08 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.7599999999983 -3.48063844475218 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00116324261524 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00116324261524 y scale 1.00116324261524 z scale ${scale} remap -change_box all x scale 1.00116324261524 y scale 1.00116324261524 z scale 1.00116324261524 remap - triclinic box = (-0.24237 -0.238935 -0.238935) to (5.67121 5.66777 5.66777) with tilt (0 0 0) - triclinic box = (-0.24237 -0.24237 -0.238935) to (5.67121 5.67121 5.66777) with tilt (0 0 0) - triclinic box = (-0.24237 -0.24237 -0.24237) to (5.67121 5.67121 5.67121) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.838619 -15546.516 206.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.8499999999986 -3.47982735313635 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00115919732841 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00115919732841 y scale 1.00115919732841 z scale ${scale} remap -change_box all x scale 1.00115919732841 y scale 1.00115919732841 z scale 1.00115919732841 remap - triclinic box = (-0.245798 -0.24237 -0.24237) to (5.67463 5.67121 5.67121) with tilt (0 0 0) - triclinic box = (-0.245798 -0.245798 -0.24237) to (5.67463 5.67463 5.67121) with tilt (0 0 0) - triclinic box = (-0.245798 -0.245798 -0.245798) to (5.67463 5.67463 5.67463) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.831143 -17717.116 207.52 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -25.9399999999987 -3.47889283744737 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00115518007984 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00115518007984 y scale 1.00115518007984 z scale ${scale} remap -change_box all x scale 1.00115518007984 y scale 1.00115518007984 z scale 1.00115518007984 remap - triclinic box = (-0.249217 -0.245798 -0.245798) to (5.67805 5.67463 5.67463) with tilt (0 0 0) - triclinic box = (-0.249217 -0.249217 -0.245798) to (5.67805 5.67805 5.67463) with tilt (0 0 0) - triclinic box = (-0.249217 -0.249217 -0.249217) to (5.67805 5.67805 5.67805) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.822703 -19835.593 208.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.0299999999988 -3.47783786124029 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00115119057903 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00115119057903 y scale 1.00115119057903 z scale ${scale} remap -change_box all x scale 1.00115119057903 y scale 1.00115119057903 z scale 1.00115119057903 remap - triclinic box = (-0.252629 -0.249217 -0.249217) to (5.68146 5.67805 5.67805) with tilt (0 0 0) - triclinic box = (-0.252629 -0.252629 -0.249217) to (5.68146 5.68146 5.67805) with tilt (0 0 0) - triclinic box = (-0.252629 -0.252629 -0.252629) to (5.68146 5.68146 5.68146) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.813323 -21903.19 208.96 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.1199999999987 -3.47666531737132 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00114722853949 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00114722853949 y scale 1.00114722853949 z scale ${scale} remap -change_box all x scale 1.00114722853949 y scale 1.00114722853949 z scale 1.00114722853949 remap - triclinic box = (-0.256033 -0.252629 -0.252629) to (5.68487 5.68146 5.68146) with tilt (0 0 0) - triclinic box = (-0.256033 -0.256033 -0.252629) to (5.68487 5.68487 5.68146) with tilt (0 0 0) - triclinic box = (-0.256033 -0.256033 -0.256033) to (5.68487 5.68487 5.68487) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.803024 -23921.116 209.68 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.209999999999 -3.47537802984216 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00114329367864 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00114329367864 y scale 1.00114329367864 z scale ${scale} remap -change_box all x scale 1.00114329367864 y scale 1.00114329367864 z scale 1.00114329367864 remap - triclinic box = (-0.259429 -0.256033 -0.256033) to (5.68826 5.68487 5.68487) with tilt (0 0 0) - triclinic box = (-0.259429 -0.259429 -0.256033) to (5.68826 5.68826 5.68487) with tilt (0 0 0) - triclinic box = (-0.259429 -0.259429 -0.259429) to (5.68826 5.68826 5.68826) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.79183 -25890.55 210.4 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.2999999999991 -3.4739787555912 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00113938571778 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00113938571778 y scale 1.00113938571778 z scale ${scale} remap -change_box all x scale 1.00113938571778 y scale 1.00113938571778 z scale 1.00113938571778 remap - triclinic box = (-0.262817 -0.259429 -0.259429) to (5.69165 5.68826 5.68826) with tilt (0 0 0) - triclinic box = (-0.262817 -0.262817 -0.259429) to (5.69165 5.69165 5.68826) with tilt (0 0 0) - triclinic box = (-0.262817 -0.262817 -0.262817) to (5.69165 5.69165 5.69165) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.779761 -27812.639 211.12 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.3899999999989 -3.47247018623304 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00113550438201 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00113550438201 y scale 1.00113550438201 z scale ${scale} remap -change_box all x scale 1.00113550438201 y scale 1.00113550438201 z scale 1.00113550438201 remap - triclinic box = (-0.266198 -0.262817 -0.262817) to (5.69503 5.69165 5.69165) with tilt (0 0 0) - triclinic box = (-0.266198 -0.266198 -0.262817) to (5.69503 5.69503 5.69165) with tilt (0 0 0) - triclinic box = (-0.266198 -0.266198 -0.266198) to (5.69503 5.69503 5.69503) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.76684 -29688.502 211.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.4799999999987 -3.47085494974826 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00113164940016 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00113164940016 y scale 1.00113164940016 z scale ${scale} remap -change_box all x scale 1.00113164940016 y scale 1.00113164940016 z scale 1.00113164940016 remap - triclinic box = (-0.269571 -0.266198 -0.266198) to (5.69841 5.69503 5.69503) with tilt (0 0 0) - triclinic box = (-0.269571 -0.269571 -0.266198) to (5.69841 5.69841 5.69503) with tilt (0 0 0) - triclinic box = (-0.269571 -0.269571 -0.269571) to (5.69841 5.69841 5.69841) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.753085 -31519.227 212.56 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.5699999999991 -3.46913561212469 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00112782050471 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00112782050471 y scale 1.00112782050471 z scale ${scale} remap -change_box all x scale 1.00112782050471 y scale 1.00112782050471 z scale 1.00112782050471 remap - triclinic box = (-0.272937 -0.269571 -0.269571) to (5.70177 5.69841 5.69841) with tilt (0 0 0) - triclinic box = (-0.272937 -0.272937 -0.269571) to (5.70177 5.70177 5.69841) with tilt (0 0 0) - triclinic box = (-0.272937 -0.272937 -0.272937) to (5.70177 5.70177 5.70177) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.738517 -33305.877 213.28 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.6599999999992 -3.46731467895206 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00112401743178 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00112401743178 y scale 1.00112401743178 z scale ${scale} remap -change_box all x scale 1.00112401743178 y scale 1.00112401743178 z scale 1.00112401743178 remap - triclinic box = (-0.276294 -0.272937 -0.272937) to (5.70513 5.70177 5.70177) with tilt (0 0 0) - triclinic box = (-0.276294 -0.276294 -0.272937) to (5.70513 5.70513 5.70177) with tilt (0 0 0) - triclinic box = (-0.276294 -0.276294 -0.276294) to (5.70513 5.70513 5.70513) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.723157 -35049.484 214 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.7499999999995 -3.46539459697116 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00112023992101 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00112023992101 y scale 1.00112023992101 z scale ${scale} remap -change_box all x scale 1.00112023992101 y scale 1.00112023992101 z scale 1.00112023992101 remap - triclinic box = (-0.279645 -0.276294 -0.276294) to (5.70848 5.70513 5.70513) with tilt (0 0 0) - triclinic box = (-0.279645 -0.279645 -0.276294) to (5.70848 5.70848 5.70513) with tilt (0 0 0) - triclinic box = (-0.279645 -0.279645 -0.279645) to (5.70848 5.70848 5.70848) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.707022 -36751.057 214.72 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.8399999999993 -3.46337775557919 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00111648771556 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00111648771556 y scale 1.00111648771556 z scale ${scale} remap -change_box all x scale 1.00111648771556 y scale 1.00111648771556 z scale 1.00111648771556 remap - triclinic box = (-0.282988 -0.279645 -0.279645) to (5.71182 5.70848 5.70848) with tilt (0 0 0) - triclinic box = (-0.282988 -0.282988 -0.279645) to (5.71182 5.71182 5.70848) with tilt (0 0 0) - triclinic box = (-0.282988 -0.282988 -0.282988) to (5.71182 5.71182 5.71182) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.690132 -38411.578 215.44 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -26.9299999999997 -3.46126648829251 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00111276056198 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00111276056198 y scale 1.00111276056198 z scale ${scale} remap -change_box all x scale 1.00111276056198 y scale 1.00111276056198 z scale 1.00111276056198 remap - triclinic box = (-0.286323 -0.282988 -0.282988) to (5.71516 5.71182 5.71182) with tilt (0 0 0) - triclinic box = (-0.286323 -0.286323 -0.282988) to (5.71516 5.71516 5.71182) with tilt (0 0 0) - triclinic box = (-0.286323 -0.286323 -0.286323) to (5.71516 5.71516 5.71516) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.672509 -39943.013 216.16 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.0199999999998 -3.45906362981948 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00110905821022 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00110905821022 y scale 1.00110905821022 z scale ${scale} remap -change_box all x scale 1.00110905821022 y scale 1.00110905821022 z scale 1.00110905821022 remap - triclinic box = (-0.289651 -0.286323 -0.286323) to (5.71849 5.71516 5.71516) with tilt (0 0 0) - triclinic box = (-0.289651 -0.289651 -0.286323) to (5.71849 5.71849 5.71516) with tilt (0 0 0) - triclinic box = (-0.289651 -0.289651 -0.289651) to (5.71849 5.71849 5.71849) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.654292 -41126.388 216.88 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.1099999999995 -3.45678648875684 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00110538041355 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00110538041355 y scale 1.00110538041355 z scale ${scale} remap -change_box all x scale 1.00110538041355 y scale 1.00110538041355 z scale 1.00110538041355 remap - triclinic box = (-0.292972 -0.289651 -0.289651) to (5.72181 5.71849 5.71849) with tilt (0 0 0) - triclinic box = (-0.292972 -0.292972 -0.289651) to (5.72181 5.72181 5.71849) with tilt (0 0 0) - triclinic box = (-0.292972 -0.292972 -0.292972) to (5.72181 5.72181 5.72181) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.635551 -42275.674 217.6 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.1999999999992 -3.45444383466799 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00110172692849 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00110172692849 y scale 1.00110172692849 z scale ${scale} remap -change_box all x scale 1.00110172692849 y scale 1.00110172692849 z scale 1.00110172692849 remap - triclinic box = (-0.296285 -0.292972 -0.292972) to (5.72512 5.72181 5.72181) with tilt (0 0 0) - triclinic box = (-0.296285 -0.296285 -0.292972) to (5.72512 5.72512 5.72181) with tilt (0 0 0) - triclinic box = (-0.296285 -0.296285 -0.296285) to (5.72512 5.72512 5.72512) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.6163 -43391.705 218.32 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.2899999999996 -3.45203755895375 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00109809751476 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00109809751476 y scale 1.00109809751476 z scale ${scale} remap -change_box all x scale 1.00109809751476 y scale 1.00109809751476 z scale 1.00109809751476 remap - triclinic box = (-0.299591 -0.296285 -0.296285) to (5.72843 5.72512 5.72512) with tilt (0 0 0) - triclinic box = (-0.299591 -0.299591 -0.296285) to (5.72843 5.72843 5.72512) with tilt (0 0 0) - triclinic box = (-0.299591 -0.299591 -0.299591) to (5.72843 5.72843 5.72843) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.596556 -44475.291 219.04 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.3799999999999 -3.44956950680041 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00109449193525 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00109449193525 y scale 1.00109449193525 z scale ${scale} remap -change_box all x scale 1.00109449193525 y scale 1.00109449193525 z scale 1.00109449193525 remap - triclinic box = (-0.30289 -0.299591 -0.299591) to (5.73172 5.72843 5.72843) with tilt (0 0 0) - triclinic box = (-0.30289 -0.30289 -0.299591) to (5.73172 5.73172 5.72843) with tilt (0 0 0) - triclinic box = (-0.30289 -0.30289 -0.30289) to (5.73172 5.73172 5.73172) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.576332 -45527.226 219.76 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.4700000000001 -3.44704147836752 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00109090995595 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00109090995595 y scale 1.00109090995595 z scale ${scale} remap -change_box all x scale 1.00109090995595 y scale 1.00109090995595 z scale 1.00109090995595 remap - triclinic box = (-0.306181 -0.30289 -0.30289) to (5.73502 5.73172 5.73172) with tilt (0 0 0) - triclinic box = (-0.306181 -0.306181 -0.30289) to (5.73502 5.73502 5.73172) with tilt (0 0 0) - triclinic box = (-0.306181 -0.306181 -0.306181) to (5.73502 5.73502 5.73502) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.555642 -46548.278 220.48 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.5599999999998 -3.44445522994241 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00108735134592 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00108735134592 y scale 1.00108735134592 z scale ${scale} remap -change_box all x scale 1.00108735134592 y scale 1.00108735134592 z scale 1.00108735134592 remap - triclinic box = (-0.309466 -0.306181 -0.306181) to (5.7383 5.73502 5.73502) with tilt (0 0 0) - triclinic box = (-0.309466 -0.309466 -0.306181) to (5.7383 5.7383 5.73502) with tilt (0 0 0) - triclinic box = (-0.309466 -0.309466 -0.309466) to (5.7383 5.7383 5.7383) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.5345 -47539.201 221.2 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.6500000000002 -3.44181247506245 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00108381587718 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00108381587718 y scale 1.00108381587718 z scale ${scale} remap -change_box all x scale 1.00108381587718 y scale 1.00108381587718 z scale 1.00108381587718 remap - triclinic box = (-0.312743 -0.309466 -0.309466) to (5.74158 5.7383 5.7383) with tilt (0 0 0) - triclinic box = (-0.312743 -0.312743 -0.309466) to (5.74158 5.74158 5.7383) with tilt (0 0 0) - triclinic box = (-0.312743 -0.312743 -0.312743) to (5.74158 5.74158 5.74158) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.512919 -48500.725 221.92 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.74 -3.43911488560607 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00108030332476 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00108030332476 y scale 1.00108030332476 z scale ${scale} remap -change_box all x scale 1.00108030332476 y scale 1.00108030332476 z scale 1.00108030332476 remap - triclinic box = (-0.316013 -0.312743 -0.312743) to (5.74485 5.74158 5.74158) with tilt (0 0 0) - triclinic box = (-0.316013 -0.316013 -0.312743) to (5.74485 5.74485 5.74158) with tilt (0 0 0) - triclinic box = (-0.316013 -0.316013 -0.316013) to (5.74485 5.74485 5.74485) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.490913 -49433.564 222.64 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.8300000000003 -3.43636409285328 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00107681346655 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00107681346655 y scale 1.00107681346655 z scale ${scale} remap -change_box all x scale 1.00107681346655 y scale 1.00107681346655 z scale 1.00107681346655 remap - triclinic box = (-0.319277 -0.316013 -0.316013) to (5.74811 5.74485 5.74485) with tilt (0 0 0) - triclinic box = (-0.319277 -0.319277 -0.316013) to (5.74811 5.74811 5.74485) with tilt (0 0 0) - triclinic box = (-0.319277 -0.319277 -0.319277) to (5.74811 5.74811 5.74811) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.468494 -50338.414 223.36 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -27.9200000000003 -3.43356168851709 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00107334608333 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00107334608333 y scale 1.00107334608333 z scale ${scale} remap -change_box all x scale 1.00107334608333 y scale 1.00107334608333 z scale 1.00107334608333 remap - triclinic box = (-0.322533 -0.319277 -0.319277) to (5.75137 5.74811 5.74811) with tilt (0 0 0) - triclinic box = (-0.322533 -0.322533 -0.319277) to (5.75137 5.75137 5.74811) with tilt (0 0 0) - triclinic box = (-0.322533 -0.322533 -0.322533) to (5.75137 5.75137 5.75137) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.445674 -51215.952 224.08 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.0100000000003 -3.43070922574611 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00106990095868 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00106990095868 y scale 1.00106990095868 z scale ${scale} remap -change_box all x scale 1.00106990095868 y scale 1.00106990095868 z scale 1.00106990095868 remap - triclinic box = (-0.325782 -0.322533 -0.322533) to (5.75462 5.75137 5.75137) with tilt (0 0 0) - triclinic box = (-0.325782 -0.325782 -0.322533) to (5.75462 5.75462 5.75137) with tilt (0 0 0) - triclinic box = (-0.325782 -0.325782 -0.325782) to (5.75462 5.75462 5.75462) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.422466 -52066.839 224.8 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.0999999999999 -3.42780822009964 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00106647787897 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00106647787897 y scale 1.00106647787897 z scale ${scale} remap -change_box all x scale 1.00106647787897 y scale 1.00106647787897 z scale 1.00106647787897 remap - triclinic box = (-0.329024 -0.325782 -0.325782) to (5.75786 5.75462 5.75462) with tilt (0 0 0) - triclinic box = (-0.329024 -0.329024 -0.325782) to (5.75786 5.75786 5.75462) with tilt (0 0 0) - triclinic box = (-0.329024 -0.329024 -0.329024) to (5.75786 5.75786 5.75786) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.398881 -52891.72 225.52 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.1900000000001 -3.424860150496 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00106307663326 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00106307663326 y scale 1.00106307663326 z scale ${scale} remap -change_box all x scale 1.00106307663326 y scale 1.00106307663326 z scale 1.00106307663326 remap - triclinic box = (-0.33226 -0.329024 -0.329024) to (5.76109 5.75786 5.75786) with tilt (0 0 0) - triclinic box = (-0.33226 -0.33226 -0.329024) to (5.76109 5.76109 5.75786) with tilt (0 0 0) - triclinic box = (-0.33226 -0.33226 -0.33226) to (5.76109 5.76109 5.76109) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.374932 -53691.221 226.24 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.28 -3.42186646013476 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00105969701333 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00105969701333 y scale 1.00105969701333 z scale ${scale} remap -change_box all x scale 1.00105969701333 y scale 1.00105969701333 z scale 1.00105969701333 remap - triclinic box = (-0.335488 -0.33226 -0.33226) to (5.76432 5.76109 5.76109) with tilt (0 0 0) - triclinic box = (-0.335488 -0.335488 -0.33226) to (5.76432 5.76432 5.76109) with tilt (0 0 0) - triclinic box = (-0.335488 -0.335488 -0.335488) to (5.76432 5.76432 5.76432) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.350628 -54465.955 226.96 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.3700000000003 -3.41882855739378 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00105633881357 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00105633881357 y scale 1.00105633881357 z scale ${scale} remap -change_box all x scale 1.00105633881357 y scale 1.00105633881357 z scale 1.00105633881357 remap - triclinic box = (-0.33871 -0.335488 -0.335488) to (5.76755 5.76432 5.76432) with tilt (0 0 0) - triclinic box = (-0.33871 -0.33871 -0.335488) to (5.76755 5.76755 5.76432) with tilt (0 0 0) - triclinic box = (-0.33871 -0.33871 -0.33871) to (5.76755 5.76755 5.76755) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.325983 -55216.518 227.68 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.4600000000007 -3.4157478167018 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00105300183098 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00105300183098 y scale 1.00105300183098 z scale ${scale} remap -change_box all x scale 1.00105300183098 y scale 1.00105300183098 z scale 1.00105300183098 remap - triclinic box = (-0.341925 -0.33871 -0.33871) to (5.77076 5.76755 5.76755) with tilt (0 0 0) - triclinic box = (-0.341925 -0.341925 -0.33871) to (5.77076 5.77076 5.76755) with tilt (0 0 0) - triclinic box = (-0.341925 -0.341925 -0.341925) to (5.77076 5.77076 5.77076) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.301005 -55943.493 228.4 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.5500000000008 -3.41262557938724 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00104968586512 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00104968586512 y scale 1.00104968586512 z scale ${scale} remap -change_box all x scale 1.00104968586512 y scale 1.00104968586512 z scale 1.00104968586512 remap - triclinic box = (-0.345133 -0.341925 -0.341925) to (5.77397 5.77076 5.77076) with tilt (0 0 0) - triclinic box = (-0.345133 -0.345133 -0.341925) to (5.77397 5.77397 5.77076) with tilt (0 0 0) - triclinic box = (-0.345133 -0.345133 -0.345133) to (5.77397 5.77397 5.77397) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.275705 -56647.446 229.12 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.6400000000005 -3.40946315450402 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00104639071808 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00104639071808 y scale 1.00104639071808 z scale ${scale} remap -change_box all x scale 1.00104639071808 y scale 1.00104639071808 z scale 1.00104639071808 remap - triclinic box = (-0.348335 -0.345133 -0.345133) to (5.77717 5.77397 5.77397) with tilt (0 0 0) - triclinic box = (-0.348335 -0.348335 -0.345133) to (5.77717 5.77717 5.77397) with tilt (0 0 0) - triclinic box = (-0.348335 -0.348335 -0.348335) to (5.77717 5.77717 5.77717) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.250095 -57328.932 229.84 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.7300000000009 -3.40626181963491 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00104311619438 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00104311619438 y scale 1.00104311619438 z scale ${scale} remap -change_box all x scale 1.00104311619438 y scale 1.00104311619438 z scale 1.00104311619438 remap - triclinic box = (-0.351529 -0.348335 -0.348335) to (5.78036 5.77717 5.77717) with tilt (0 0 0) - triclinic box = (-0.351529 -0.351529 -0.348335) to (5.78036 5.78036 5.77717) with tilt (0 0 0) - triclinic box = (-0.351529 -0.351529 -0.351529) to (5.78036 5.78036 5.78036) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.224183 -57988.489 230.56 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.8200000000006 -3.40302282167349 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00103986210104 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00103986210104 y scale 1.00103986210104 z scale ${scale} remap -change_box all x scale 1.00103986210104 y scale 1.00103986210104 z scale 1.00103986210104 remap - triclinic box = (-0.354718 -0.351529 -0.351529) to (5.78355 5.78036 5.78036) with tilt (0 0 0) - triclinic box = (-0.354718 -0.354718 -0.351529) to (5.78355 5.78355 5.78036) with tilt (0 0 0) - triclinic box = (-0.354718 -0.354718 -0.354718) to (5.78355 5.78355 5.78355) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.197979 -58626.644 231.28 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -28.9100000000005 -3.39974737758459 - -next i -jump SELF loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00103662824744 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00103662824744 y scale 1.00103662824744 z scale ${scale} remap -change_box all x scale 1.00103662824744 y scale 1.00103662824744 z scale 1.00103662824744 remap - triclinic box = (-0.357899 -0.354718 -0.354718) to (5.78673 5.78355 5.78355) with tilt (0 0 0) - triclinic box = (-0.357899 -0.357899 -0.354718) to (5.78673 5.78673 5.78355) with tilt (0 0 0) - triclinic box = (-0.357899 -0.357899 -0.357899) to (5.78673 5.78673 5.78673) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 2.31867 Mbytes -Step Temp PotEng Press Volume - 0 0 -27.171493 -59243.909 232 -Loop time of 0 on 1 procs for 0 steps with 8 atoms - -0.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 - -Nlocal: 8 ave 8 max 8 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 272 ave 272 max 272 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 368 ave 368 max 368 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 368 -Ave neighs/atom = 46 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -29.0000000000008 -3.39643667514478 - -next i -jump SELF loop -Total wall time: 0:00:00 diff --git a/examples/vashishta/log.5Oct16.indiumphosphide.g++.4 b/examples/vashishta/log.5Oct16.indiumphosphide.g++.4 deleted file mode 100644 index 71dc3350e8..0000000000 --- a/examples/vashishta/log.5Oct16.indiumphosphide.g++.4 +++ /dev/null @@ -1,128 +0,0 @@ -LAMMPS (5 Oct 2016) -# calculate the energy volume curve for InP zincblende - -# define volume range and filename - -variable ndelta equal 100 -variable volatom_min equal 20.0 -variable volatom_max equal 29.0 -variable evsvolfile string evsvol.dat - -# set up cell - -units metal - -boundary p p p - -# setup loop variables for box volume - -variable amin equal ${volatom_min}^(1/3)*2 -variable amin equal 20^(1/3)*2 -variable delta equal (${volatom_max}-${volatom_min})/${ndelta} -variable delta equal (29-${volatom_min})/${ndelta} -variable delta equal (29-20)/${ndelta} -variable delta equal (29-20)/100 -variable scale equal (${delta}/v_volatom+1)^(1/3) -variable scale equal (0.09/v_volatom+1)^(1/3) - -# set up 8 atom InP zincblende unit cell - -lattice diamond ${amin} -lattice diamond 5.42883523318981 -Lattice spacing in x,y,z = 5.42884 5.42884 5.42884 - -region box prism 0 1 0 1 0 1 0 0 0 - -create_box 2 box -Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0) - 1 by 2 by 2 MPI processor grid - -create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 -Created 8 atoms - -mass 1 114.76 -mass 2 30.98 - -# choose potential - -pair_style vashishta -pair_coeff * * InP.vashishta In P -Reading potential file InP.vashishta with DATE: 2015-10-14 - -# setup neighbor style - -neighbor 1.0 nsq -neigh_modify once no every 1 delay 0 check yes - -# setup output - -thermo_style custom step temp pe press vol -thermo_modify norm no -variable volatom equal vol/atoms -variable eatom equal pe/atoms -print "# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile} -print "# Volume [A^3/atom] Energy [eV/atom]" file evsvol.dat -# Volume [A^3/atom] Energy [eV/atom] - -# loop over range of volumes - -label loop -variable i loop ${ndelta} -variable i loop 100 - -change_box all x scale ${scale} y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00149775560818 y scale ${scale} z scale ${scale} remap -change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale ${scale} remap -change_box all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.00149775560818 remap - triclinic box = (-0.00406553 0 0) to (5.4329 5.42884 5.42884) with tilt (0 0 0) - triclinic box = (-0.00406553 -0.00406553 0) to (5.4329 5.4329 5.42884) with tilt (0 0 0) - triclinic box = (-0.00406553 -0.00406553 -0.00406553) to (5.4329 5.4329 5.4329) with tilt (0 0 0) - -# calculate energy -# no energy minimization needed for zincblende - -run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 7 - ghost atom cutoff = 7 -Memory usage per processor = 2.33394 Mbytes -Step Temp PotEng Press Volume - 0 0 -24.633958 315900.5 160.72 -Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms - -0.0% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0 | 0 | 0 | 0.0 | 0.00 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0 | 0 | 0 | 0.0 | 0.00 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 3.099e-06 | | |100.00 - -Nlocal: 2 ave 2 max 2 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 320 ave 320 max 320 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 140 ave 140 max 140 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 560 -Ave neighs/atom = 70 -Neighbor list builds = 0 -Dangerous builds = 0 -print "${volatom} ${eatom}" append ${evsvolfile} -print "${volatom} ${eatom}" append evsvol.dat -20.09 -3.07924477327226 - -next i -jump SELF loop -ERROR: Label wasn't found in input script (../input.cpp:207) diff --git a/examples/vashishta/log.5Oct16.sio2.g++.1 b/examples/vashishta/log.5Oct16.sio2.g++.1 deleted file mode 100644 index d302760d95..0000000000 --- a/examples/vashishta/log.5Oct16.sio2.g++.1 +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS (5 Oct 2016) -# test Vashishta potential for quartz - -units metal -boundary p p p - -atom_style atomic - -read_data data.quartz - triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 9 atoms - -replicate 4 4 4 - triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0) - 1 by 1 by 1 MPI processor grid - 576 atoms -velocity all create 2000.0 277387 mom yes -displace_atoms all move 0.05 0.9 0.4 units box - -pair_style vashishta -pair_coeff * * SiO.1990.vashishta Si O -Reading potential file SiO.1990.vashishta with DATE: 2015-10-14 - -neighbor 0.3 bin -neigh_modify delay 10 - -fix 1 all nve -thermo 10 -timestep 0.001 - -#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz -#dump_modify 1 element Si O - -run 100 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.3 - ghost atom cutoff = 10.3 - binsize = 5.15 -> bins = 6 4 5 -Memory usage per processor = 2.54081 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 2000 -5280.875 0 -5132.2259 -20502.321 - 10 895.65237 -5198.402 0 -5131.833 419.34676 - 20 932.93463 -5201.1569 0 -5131.8169 -21407.961 - 30 936.09591 -5201.3998 0 -5131.8248 -32531.168 - 40 930.05159 -5201.0073 0 -5131.8816 -46445.212 - 50 904.64676 -5199.062 0 -5131.8245 -31402.385 - 60 1005.5353 -5206.5725 0 -5131.8365 -29790.442 - 70 941.02343 -5201.7644 0 -5131.8232 -23046.796 - 80 1020.1044 -5207.6763 0 -5131.8574 -13488.675 - 90 912.75535 -5199.651 0 -5131.8108 2715.5897 - 100 998.97588 -5206.1008 0 -5131.8523 6024.3651 -Loop time of 2.15298 on 1 procs for 100 steps with 576 atoms - -Performance: 4.013 ns/day, 5.981 hours/ns, 46.447 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.0719 | 2.0719 | 2.0719 | 0.0 | 96.23 -Neigh | 0.075195 | 0.075195 | 0.075195 | 0.0 | 3.49 -Comm | 0.0039992 | 0.0039992 | 0.0039992 | 0.0 | 0.19 -Output | 0.0001986 | 0.0001986 | 0.0001986 | 0.0 | 0.01 -Modify | 0.00095224 | 0.00095224 | 0.00095224 | 0.0 | 0.04 -Other | | 0.0007288 | | | 0.03 - -Nlocal: 576 ave 576 max 576 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 4926 ave 4926 max 4926 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 210470 ave 210470 max 210470 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 210470 -Ave neighs/atom = 365.399 -Neighbor list builds = 10 -Dangerous builds = 10 - -Total wall time: 0:00:02 diff --git a/examples/vashishta/log.5Oct16.vashishta.sio2.g++.4 b/examples/vashishta/log.5Oct16.vashishta.sio2.g++.4 deleted file mode 100644 index c16943f4dc..0000000000 --- a/examples/vashishta/log.5Oct16.vashishta.sio2.g++.4 +++ /dev/null @@ -1,86 +0,0 @@ -LAMMPS (5 Oct 2016) -# test Vashishta potential for quartz - -units metal -boundary p p p - -atom_style atomic - -read_data data.quartz - triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0) - 2 by 1 by 2 MPI processor grid - reading atoms ... - 9 atoms - -replicate 4 4 4 - triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0) - 2 by 1 by 2 MPI processor grid - 576 atoms -velocity all create 2000.0 277387 mom yes -displace_atoms all move 0.05 0.9 0.4 units box - -pair_style vashishta -pair_coeff * * SiO.1990.vashishta Si O -Reading potential file SiO.1990.vashishta with DATE: 2015-10-14 - -neighbor 0.3 bin -neigh_modify delay 10 - -fix 1 all nve -thermo 10 -timestep 0.001 - -#dump 1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz -#dump_modify 1 element Si O - -run 100 -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 10.3 - ghost atom cutoff = 10.3 - binsize = 5.15 -> bins = 6 4 5 -Memory usage per processor = 2.50221 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 2000 -5280.875 0 -5132.2259 -20502.321 - 10 895.65237 -5198.402 0 -5131.833 419.34676 - 20 932.93463 -5201.1569 0 -5131.8169 -21407.961 - 30 936.09591 -5201.3998 0 -5131.8248 -32531.168 - 40 930.05159 -5201.0073 0 -5131.8816 -46445.212 - 50 904.64676 -5199.062 0 -5131.8245 -31402.385 - 60 1005.5353 -5206.5725 0 -5131.8365 -29790.442 - 70 941.02343 -5201.7644 0 -5131.8232 -23046.796 - 80 1020.1044 -5207.6763 0 -5131.8574 -13488.675 - 90 912.75535 -5199.651 0 -5131.8108 2715.5897 - 100 998.97588 -5206.1008 0 -5131.8523 6024.3651 -Loop time of 0.592926 on 4 procs for 100 steps with 576 atoms - -Performance: 14.572 ns/day, 1.647 hours/ns, 168.655 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.52105 | 0.52662 | 0.5338 | 0.8 | 88.82 -Neigh | 0.017895 | 0.018018 | 0.018194 | 0.1 | 3.04 -Comm | 0.039864 | 0.047185 | 0.052807 | 2.6 | 7.96 -Output | 0.00022006 | 0.00027043 | 0.00031042 | 0.2 | 0.05 -Modify | 0.00026655 | 0.00027591 | 0.00029397 | 0.1 | 0.05 -Other | | 0.0005552 | | | 0.09 - -Nlocal: 144 ave 146 max 143 min -Histogram: 2 0 0 1 0 0 0 0 0 1 -Nghost: 3031 ave 3032 max 3030 min -Histogram: 1 0 0 0 0 2 0 0 0 1 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 52617.5 ave 53258 max 52208 min -Histogram: 2 0 0 0 1 0 0 0 0 1 - -Total # of neighbors = 210470 -Ave neighs/atom = 365.399 -Neighbor list builds = 10 -Dangerous builds = 10 - -Total wall time: 0:00:00 diff --git a/examples/voronoi/log.5Oct16.voronoi.2d.g++.1 b/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 similarity index 81% rename from examples/voronoi/log.5Oct16.voronoi.2d.g++.1 rename to examples/voronoi/log.27Nov18.voronoi.2d.g++.1 index 4366a725ca..a591db8b4f 100644 --- a/examples/voronoi/log.5Oct16.voronoi.2d.g++.1 +++ b/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems variable rcut equal 10.0 @@ -29,6 +30,7 @@ Created orthogonal box = (0 0 0) to (4 6.9282 10) 1 by 1 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms + Time spent = 0.000315905 secs mass 1 1.0 @@ -55,19 +57,24 @@ thermo 1 # run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 -Memory usage per processor = 2.37519 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.007 | 3.007 | 3.007 Mbytes c_volvor v_volsys Volume v_err 277.12813 277.12813 27.712813 5.6843419e-14 Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -98,13 +105,13 @@ Dangerous builds = 0 change_box all boundary f f p run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 7.05652 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.688 | 7.688 | 7.688 Mbytes c_volvor v_volsys Volume v_err 277.12813 277.12813 27.712813 3.4106051e-13 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms +Loop time of 4.76837e-07 on 1 procs for 0 steps with 32 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -114,7 +121,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 4.768e-07 | | |100.00 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/voronoi/log.5Oct16.voronoi.2d.g++.4 b/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 similarity index 79% rename from examples/voronoi/log.5Oct16.voronoi.2d.g++.4 rename to examples/voronoi/log.27Nov18.voronoi.2d.g++.4 index bdf134225c..841f8dcb81 100644 --- a/examples/voronoi/log.5Oct16.voronoi.2d.g++.4 +++ b/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Test volume definitions for 2d and finite systems variable rcut equal 10.0 @@ -29,6 +30,7 @@ Created orthogonal box = (0 0 0) to (4 6.9282 10) 2 by 2 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms + Time spent = 0.000319481 secs mass 1 1.0 @@ -55,19 +57,24 @@ thermo 1 # run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 20 -Memory usage per processor = 2.41069 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 3.042 | 3.042 | 3.042 Mbytes c_volvor v_volsys Volume v_err 277.12813 277.12813 27.712813 5.1159077e-13 -Loop time of 4.05312e-06 on 4 procs for 0 steps with 32 atoms +Loop time of 2.79546e-05 on 4 procs for 0 steps with 32 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +51.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -77,7 +84,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 4.053e-06 | | |100.00 +Other | | 2.795e-05 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -98,13 +105,13 @@ Dangerous builds = 0 change_box all boundary f f p run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 7.04625 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.678 | 7.678 | 7.678 Mbytes c_volvor v_volsys Volume v_err 277.12813 277.12813 27.712813 3.4106051e-13 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 32 atoms +Loop time of 1.88947e-05 on 4 procs for 0 steps with 32 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +47.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -114,7 +121,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 1.889e-05 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/voronoi/log.5Oct16.voronoi.data.g++.1 b/examples/voronoi/log.27Nov18.voronoi.data.g++.1 similarity index 82% rename from examples/voronoi/log.5Oct16.voronoi.data.g++.1 rename to examples/voronoi/log.27Nov18.voronoi.data.g++.1 index c3d5e2cc82..04bc629d87 100644 --- a/examples/voronoi/log.5Oct16.voronoi.data.g++.1 +++ b/examples/voronoi/log.27Nov18.voronoi.data.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Exercise different output data options variable len equal 4.0 @@ -25,6 +26,7 @@ Created orthogonal box = (0 0 0) to (4 6.9282 10) 1 by 1 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms + Time spent = 0.000315666 secs mass 1 1.0 @@ -63,19 +65,24 @@ thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] thermo 1 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.5 ghost atom cutoff = 3.5 -Memory usage per processor = 9.40674 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 10.04 | 10.04 | 10.04 Mbytes c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 277.12813 277.12813 27.712813 3.9790393e-13 0 186 12 36 0 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 32 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -85,7 +92,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -128,13 +135,13 @@ thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] thermo 1 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.15503 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.787 | 8.787 | 8.787 Mbytes c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] 1215.0706 0 186 12 36 0 -Loop time of 1.19209e-06 on 1 procs for 0 steps with 32 atoms +Loop time of 7.15256e-07 on 1 procs for 0 steps with 32 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +139.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -144,7 +151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.192e-06 | | |100.00 +Other | | 7.153e-07 | | |100.00 Nlocal: 32 ave 32 max 32 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/voronoi/log.5Oct16.voronoi.data.g++.4 b/examples/voronoi/log.27Nov18.voronoi.data.g++.4 similarity index 82% rename from examples/voronoi/log.5Oct16.voronoi.data.g++.4 rename to examples/voronoi/log.27Nov18.voronoi.data.g++.4 index 097ba91347..be028e4d2f 100644 --- a/examples/voronoi/log.5Oct16.voronoi.data.g++.4 +++ b/examples/voronoi/log.27Nov18.voronoi.data.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Exercise different output data options variable len equal 4.0 @@ -25,6 +26,7 @@ Created orthogonal box = (0 0 0) to (4 6.9282 10) 2 by 2 by 1 MPI processor grid create_atoms 1 region atoms Created 32 atoms + Time spent = 0.000311136 secs mass 1 1.0 @@ -63,19 +65,24 @@ thermo_style custom c_volvor v_volsys vol v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] thermo 1 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3.5 ghost atom cutoff = 3.5 -Memory usage per processor = 9.29039 Mbytes + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/nsq/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.922 | 9.922 | 9.922 Mbytes c_volvor v_volsys Volume v_err c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 277.12813 277.12813 27.712813 3.4106051e-13 0 186 12 36 0 -Loop time of 5.00679e-06 on 4 procs for 0 steps with 32 atoms +Loop time of 1.40667e-05 on 4 procs for 0 steps with 32 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +46.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -85,7 +92,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 5.007e-06 | | |100.00 +Other | | 1.407e-05 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -128,13 +135,13 @@ thermo_style custom c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] thermo 1 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.03996 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.671 | 8.671 | 8.671 Mbytes c_sumarea c_v2[3] c_v2[4] c_v2[5] c_v2[6] c_v2[7] 1215.0706 0 186 12 36 0 -Loop time of 1.90735e-06 on 4 procs for 0 steps with 32 atoms +Loop time of 2.71797e-05 on 4 procs for 0 steps with 32 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +57.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -144,7 +151,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-06 | | |100.00 +Other | | 2.718e-05 | | |100.00 Nlocal: 8 ave 8 max 8 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/examples/voronoi/log.5Oct16.voronoi.g++.1 b/examples/voronoi/log.27Nov18.voronoi.g++.1 similarity index 78% rename from examples/voronoi/log.5Oct16.voronoi.g++.1 rename to examples/voronoi/log.27Nov18.voronoi.g++.1 index b76e99038e..c1d56b0eb7 100644 --- a/examples/voronoi/log.5Oct16.voronoi.g++.1 +++ b/examples/voronoi/log.27Nov18.voronoi.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Test of Kawasaki Dynamics on LJ test system units metal @@ -19,6 +20,7 @@ Created orthogonal box = (0 0 0) to (10 10 10) 1 by 1 by 1 MPI processor grid create_atoms 1 box basis 1 2 Created 4000 atoms + Time spent = 0.00091362 secs mass 1 50 mass 2 50 @@ -60,20 +62,25 @@ compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t1 equal c_r0 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.3 ghost atom cutoff = 5 - binsize = 1.15 -> bins = 9 9 9 -Memory usage per processor = 8.74398 Mbytes + binsize = 1.15, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.02 | 11.02 | 11.02 Mbytes c_r0 1000 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms +Loop time of 1.43051e-06 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +209.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -83,7 +90,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -114,13 +121,13 @@ thermo_style custom c_r0 c_r1 variable t2a equal c_r0 variable t2b equal c_r1 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.74398 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 11.02 | 11.02 | 11.02 Mbytes c_r0 c_r1 1000 0 -Loop time of 0 on 1 procs for 0 steps with 4000 atoms +Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +167.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -130,7 +137,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 1.192e-06 | | |100.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -162,13 +169,13 @@ compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t3 equal c_r0 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.74398 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 11.02 | 11.02 | 11.02 Mbytes c_r0 1000 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms +Loop time of 1.43051e-06 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +279.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -178,7 +185,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.431e-06 | | |100.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -204,25 +211,25 @@ undump d1 compute v1 type2 voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.53036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.81 | 8.81 | 8.81 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 12000 0 0 0 0 0 0 12000 0 0 0 -Loop time of 0.454686 on 1 procs for 1 steps with 4000 atoms +Loop time of 0.314834 on 1 procs for 1 steps with 4000 atoms -Performance: 0.190 ns/day, 126.302 hours/ns, 2.199 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.274 ns/day, 87.454 hours/ns, 3.176 timesteps/s +98.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0058758 | 0.0058758 | 0.0058758 | 0.0 | 1.29 +Pair | 0.0057888 | 0.0057888 | 0.0057888 | 0.0 | 1.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.04 -Output | 0.44856 | 0.44856 | 0.44856 | 0.0 | 98.65 -Modify | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00 -Other | | 6.723e-05 | | | 0.01 +Comm | 0.00023079 | 0.00023079 | 0.00023079 | 0.0 | 0.07 +Output | 0.30878 | 0.30878 | 0.30878 | 0.0 | 98.08 +Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00 +Other | | 3.266e-05 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -242,25 +249,25 @@ uncompute v1 compute v1 all voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.53036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.81 | 8.81 | 8.81 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 48000 0 0 0 0 0 0 48000 0 0 0 -Loop time of 0.474271 on 1 procs for 1 steps with 4000 atoms +Loop time of 0.325299 on 1 procs for 1 steps with 4000 atoms -Performance: 0.182 ns/day, 131.742 hours/ns, 2.108 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.266 ns/day, 90.361 hours/ns, 3.074 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.005832 | 0.005832 | 0.005832 | 0.0 | 1.23 +Pair | 0.0057862 | 0.0057862 | 0.0057862 | 0.0 | 1.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00016904 | 0.00016904 | 0.00016904 | 0.0 | 0.04 -Output | 0.46822 | 0.46822 | 0.46822 | 0.0 | 98.72 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 5.007e-05 | | | 0.01 +Comm | 0.00022984 | 0.00022984 | 0.00022984 | 0.0 | 0.07 +Output | 0.31925 | 0.31925 | 0.31925 | 0.0 | 98.14 +Modify | 7.1526e-07 | 7.1526e-07 | 7.1526e-07 | 0.0 | 0.00 +Other | | 3.242e-05 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -283,25 +290,25 @@ displace_atoms all random 0.01 0.01 0.01 31423 compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.53036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.81 | 8.81 | 8.81 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 48000 0 0 0 0 0 0 48000 0 0 0 -Loop time of 0.465207 on 1 procs for 1 steps with 4000 atoms +Loop time of 0.340279 on 1 procs for 1 steps with 4000 atoms -Performance: 0.186 ns/day, 129.224 hours/ns, 2.150 timesteps/s -99.7% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.254 ns/day, 94.522 hours/ns, 2.939 timesteps/s +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.006129 | 0.006129 | 0.006129 | 0.0 | 1.32 +Pair | 0.0062513 | 0.0062513 | 0.0062513 | 0.0 | 1.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00016928 | 0.00016928 | 0.00016928 | 0.0 | 0.04 -Output | 0.45886 | 0.45886 | 0.45886 | 0.0 | 98.64 -Modify | 9.5367e-07 | 9.5367e-07 | 9.5367e-07 | 0.0 | 0.00 -Other | | 4.482e-05 | | | 0.01 +Comm | 0.00023031 | 0.00023031 | 0.00023031 | 0.0 | 0.07 +Output | 0.33376 | 0.33376 | 0.33376 | 0.0 | 98.09 +Modify | 7.1526e-07 | 7.1526e-07 | 7.1526e-07 | 0.0 | 0.00 +Other | | 3.171e-05 | | | 0.01 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -326,28 +333,29 @@ lattice bcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 create_atoms 1 box Created 2000 atoms + Time spent = 0.000280142 secs compute v1 all voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.53036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.81 | 8.81 | 8.81 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 12000 0 16000 0 0 0 0 12000 0 16000 0 -Loop time of 0.196673 on 1 procs for 1 steps with 2000 atoms +Loop time of 0.140848 on 1 procs for 1 steps with 2000 atoms -Performance: 0.439 ns/day, 54.631 hours/ns, 5.085 timesteps/s -100.2% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 0.613 ns/day, 39.125 hours/ns, 7.100 timesteps/s +98.4% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0014789 | 0.0014789 | 0.0014789 | 0.0 | 0.75 +Pair | 0.0014246 | 0.0014246 | 0.0014246 | 0.0 | 1.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 8.1062e-05 | 8.1062e-05 | 8.1062e-05 | 0.0 | 0.04 -Output | 0.19509 | 0.19509 | 0.19509 | 0.0 | 99.20 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.907e-05 | | | 0.01 +Comm | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.08 +Output | 0.13929 | 0.13929 | 0.13929 | 0.0 | 98.89 +Modify | 4.7684e-07 | 4.7684e-07 | 4.7684e-07 | 0.0 | 0.00 +Other | | 1.884e-05 | | | 0.01 Nlocal: 2000 ave 2000 max 2000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -372,6 +380,7 @@ lattice fcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 create_atoms 1 box basis 1 2 Created 4000 atoms + Time spent = 0.00044775 secs # # TEST 5: Occupation analysis @@ -397,13 +406,13 @@ variable d5d equal c_v1[257][2] thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.53036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 8.81 | 8.81 | 8.81 Mbytes c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 4000 4000 1 1 1 1 -Loop time of 0 on 1 procs for 0 steps with 4000 atoms +Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +251.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -413,7 +422,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0 | | | 0.00 +Other | | 1.192e-06 | | |100.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -464,13 +473,13 @@ set atom 13 x 4.4500000000000001776 y 6.4500000000000001776 z 0.4500000000000000 1 settings made for z run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 7.03036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.31 | 9.31 | 9.31 Mbytes c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 4000 4002 0 2 2 2 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms +Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +251.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -480,7 +489,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.192e-06 | | |100.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -511,13 +520,13 @@ set atom 13 x 3.25 y 0.25 z 0.25 1 settings made for z run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 7.03036 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.31 | 9.31 | 9.31 Mbytes c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 4000 4000 1 1 1 1 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +314.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -570,20 +579,25 @@ compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t6 equal c_r0 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.3 ghost atom cutoff = 5 - binsize = 1.15 -> bins = 14 9 9 -Memory usage per processor = 12.5794 Mbytes + binsize = 1.15, bins = 14 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.06 | 15.06 | 15.06 Mbytes c_r0 1000 -Loop time of 9.53674e-07 on 1 procs for 0 steps with 4000 atoms +Loop time of 1.19209e-06 on 1 procs for 0 steps with 4000 atoms -0.0% CPU use with 1 MPI tasks x no OpenMP threads +251.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -593,7 +607,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 9.537e-07 | | |100.00 +Other | | 1.192e-06 | | |100.00 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -616,4 +630,4 @@ undump d1 print TEST_DONE TEST_DONE -Total wall time: 0:00:06 +Total wall time: 0:00:04 diff --git a/examples/voronoi/log.5Oct16.voronoi.g++.4 b/examples/voronoi/log.27Nov18.voronoi.g++.4 similarity index 77% rename from examples/voronoi/log.5Oct16.voronoi.g++.4 rename to examples/voronoi/log.27Nov18.voronoi.g++.4 index ba5dfa48c0..37e861be70 100644 --- a/examples/voronoi/log.5Oct16.voronoi.g++.4 +++ b/examples/voronoi/log.27Nov18.voronoi.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (27 Nov 2018) + using 1 OpenMP thread(s) per MPI task # Test of Kawasaki Dynamics on LJ test system units metal @@ -19,6 +20,7 @@ Created orthogonal box = (0 0 0) to (10 10 10) 1 by 2 by 2 MPI processor grid create_atoms 1 box basis 1 2 Created 4000 atoms + Time spent = 0.000644922 secs mass 1 50 mass 2 50 @@ -60,20 +62,25 @@ compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t1 equal c_r0 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.3 ghost atom cutoff = 5 - binsize = 1.15 -> bins = 9 9 9 -Memory usage per processor = 8.20003 Mbytes + binsize = 1.15, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes c_r0 1000 -Loop time of 1.29938e-05 on 4 procs for 0 steps with 4000 atoms +Loop time of 2.08616e-06 on 4 procs for 0 steps with 4000 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +167.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -83,7 +90,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.299e-05 | | |100.00 +Other | | 2.086e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -114,13 +121,13 @@ thermo_style custom c_r0 c_r1 variable t2a equal c_r0 variable t2b equal c_r1 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.20003 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes c_r0 c_r1 1000 0 -Loop time of 1.66893e-06 on 4 procs for 0 steps with 4000 atoms +Loop time of 4.52995e-06 on 4 procs for 0 steps with 4000 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +132.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -130,7 +137,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.669e-06 | | |100.00 +Other | | 4.53e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -162,13 +169,13 @@ compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t3 equal c_r0 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 8.20003 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 9.228 | 9.228 | 9.228 Mbytes c_r0 1000 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 4000 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +162.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -178,7 +185,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -204,25 +211,25 @@ undump d1 compute v1 type2 voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.14663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 12000 0 0 0 0 0 0 12000 0 0 0 -Loop time of 0.277843 on 4 procs for 1 steps with 4000 atoms +Loop time of 0.181586 on 4 procs for 1 steps with 4000 atoms -Performance: 0.311 ns/day, 77.179 hours/ns, 3.599 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.476 ns/day, 50.441 hours/ns, 5.507 timesteps/s +98.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.0014799 | 0.0015165 | 0.001543 | 0.1 | 0.55 +Pair | 0.0015094 | 0.0015393 | 0.0016015 | 0.1 | 0.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00051594 | 0.00054592 | 0.00059509 | 0.1 | 0.20 -Output | 0.27569 | 0.27571 | 0.27571 | 0.0 | 99.23 -Modify | 0 | 4.7684e-07 | 9.5367e-07 | 0.1 | 0.00 -Other | | 7.474e-05 | | | 0.03 +Comm | 0.00039601 | 0.00046033 | 0.00049233 | 0.0 | 0.25 +Output | 0.17947 | 0.1795 | 0.17956 | 0.0 | 98.85 +Modify | 4.7684e-07 | 7.1526e-07 | 9.5367e-07 | 0.0 | 0.00 +Other | | 9e-05 | | | 0.05 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -242,25 +249,25 @@ uncompute v1 compute v1 all voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.14663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 48000 0 0 0 0 0 0 48000 0 0 0 -Loop time of 0.275933 on 4 procs for 1 steps with 4000 atoms +Loop time of 0.184754 on 4 procs for 1 steps with 4000 atoms -Performance: 0.313 ns/day, 76.648 hours/ns, 3.624 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.468 ns/day, 51.321 hours/ns, 5.413 timesteps/s +96.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.001452 | 0.0014912 | 0.0015581 | 0.1 | 0.54 +Pair | 0.0015123 | 0.0015253 | 0.0015385 | 0.0 | 0.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00044107 | 0.00050235 | 0.00053501 | 0.2 | 0.18 -Output | 0.27389 | 0.2739 | 0.27391 | 0.0 | 99.26 -Modify | 0 | 4.7684e-07 | 9.5367e-07 | 0.1 | 0.00 -Other | | 3.755e-05 | | | 0.01 +Comm | 0.00038028 | 0.00039649 | 0.00040984 | 0.0 | 0.21 +Output | 0.18271 | 0.18273 | 0.1828 | 0.0 | 98.91 +Modify | 7.1526e-07 | 8.9407e-07 | 9.5367e-07 | 0.0 | 0.00 +Other | | 0.0001001 | | | 0.05 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -283,25 +290,25 @@ displace_atoms all random 0.01 0.01 0.01 31423 compute v1 all voronoi/atom edge_histo 8 edge_threshold 0.1 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.14663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 48000 0 0 0 0 0 0 48000 0 0 0 -Loop time of 0.274319 on 4 procs for 1 steps with 4000 atoms +Loop time of 0.191424 on 4 procs for 1 steps with 4000 atoms -Performance: 0.315 ns/day, 76.200 hours/ns, 3.645 timesteps/s -99.6% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.451 ns/day, 53.173 hours/ns, 5.224 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.001529 | 0.0015675 | 0.0016341 | 0.1 | 0.57 +Pair | 0.0016205 | 0.0016853 | 0.0018284 | 0.2 | 0.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00042391 | 0.00048423 | 0.00051594 | 0.2 | 0.18 -Output | 0.27222 | 0.27223 | 0.27224 | 0.0 | 99.24 -Modify | 0 | 4.7684e-07 | 9.5367e-07 | 0.1 | 0.00 -Other | | 3.517e-05 | | | 0.01 +Comm | 0.00041676 | 0.00055587 | 0.00062323 | 0.0 | 0.29 +Output | 0.18905 | 0.18907 | 0.18915 | 0.0 | 98.77 +Modify | 1.1921e-06 | 1.2517e-06 | 1.4305e-06 | 0.0 | 0.00 +Other | | 0.0001094 | | | 0.06 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -326,28 +333,29 @@ lattice bcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 create_atoms 1 box Created 2000 atoms + Time spent = 0.000178576 secs compute v1 all voronoi/atom edge_histo 8 thermo_style custom c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] run 1 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.14663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes c_v1[1] c_v1[2] c_v1[3] c_v1[4] c_v1[5] c_v1[6] c_v1[7] 0 0 0 12000 0 16000 0 0 0 0 12000 0 16000 0 -Loop time of 0.119681 on 4 procs for 1 steps with 2000 atoms +Loop time of 0.0871635 on 4 procs for 1 steps with 2000 atoms -Performance: 0.722 ns/day, 33.245 hours/ns, 8.356 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 0.991 ns/day, 24.212 hours/ns, 11.473 timesteps/s +96.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.00036597 | 0.00036877 | 0.00037217 | 0.0 | 0.31 +Pair | 0.00038028 | 0.00038761 | 0.00040364 | 0.0 | 0.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.0002737 | 0.00027668 | 0.00027895 | 0.0 | 0.23 -Output | 0.11901 | 0.11902 | 0.11902 | 0.0 | 99.45 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.681e-05 | | | 0.01 +Comm | 0.00020146 | 0.00021631 | 0.00022292 | 0.0 | 0.25 +Output | 0.086468 | 0.086487 | 0.086541 | 0.0 | 99.22 +Modify | 4.7684e-07 | 7.1526e-07 | 9.5367e-07 | 0.0 | 0.00 +Other | | 7.224e-05 | | | 0.08 Nlocal: 500 ave 500 max 500 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -372,6 +380,7 @@ lattice fcc 1 origin 0.25 0.25 0.25 Lattice spacing in x,y,z = 1 1 1 create_atoms 1 box basis 1 2 Created 4000 atoms + Time spent = 0.000248909 secs # # TEST 5: Occupation analysis @@ -397,13 +406,13 @@ variable d5d equal c_v1[257][2] thermo_style custom c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.14663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.175 | 7.175 | 7.175 Mbytes c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 4000 4000 1 1 1 1 -Loop time of 2.14577e-06 on 4 procs for 0 steps with 4000 atoms +Loop time of 1.84774e-06 on 4 procs for 0 steps with 4000 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +189.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -413,7 +422,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.146e-06 | | |100.00 +Other | | 1.848e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -464,13 +473,13 @@ set atom 13 x 4.4500000000000001776 y 1.4499999999999999556 z 1.4499999999999999 1 settings made for z run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.64663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.675 | 7.675 | 7.675 Mbytes c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 4000 4002 0 2 2 2 -Loop time of 4.41074e-06 on 4 procs for 0 steps with 4000 atoms +Loop time of 1.72853e-06 on 4 procs for 0 steps with 4000 atoms -5662.3% CPU use with 4 MPI tasks x no OpenMP threads +188.0% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -480,7 +489,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 4.411e-06 | | |100.00 +Other | | 1.729e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -511,13 +520,13 @@ set atom 13 x 3.25 y 0.25 z 0.25 1 settings made for z run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) -Memory usage per processor = 6.64663 Mbytes +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) +Per MPI rank memory allocation (min/avg/max) = 7.675 | 7.675 | 7.675 Mbytes c_r0 c_r1 v_d5a v_d5b v_d5c v_d5d 4000 4000 1 1 1 1 -Loop time of 2.38419e-06 on 4 procs for 0 steps with 4000 atoms +Loop time of 1.49012e-06 on 4 procs for 0 steps with 4000 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +218.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -527,7 +536,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.384e-06 | | |100.00 +Other | | 1.49e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -570,20 +579,25 @@ compute r0 all reduce sum c_v1[1] thermo_style custom c_r0 variable t6 equal c_r0 run 0 -WARNING: No fixes defined, atoms won't move (../verlet.cpp:55) +WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.3 ghost atom cutoff = 5 - binsize = 1.15 -> bins = 14 9 9 -Memory usage per processor = 8.20784 Mbytes + binsize = 1.15, bins = 14 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton/tri + stencil: half/bin/3d/newton/tri + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.493 | 9.493 | 9.493 Mbytes c_r0 1000 -Loop time of 2.86102e-06 on 4 procs for 0 steps with 4000 atoms +Loop time of 1.96695e-06 on 4 procs for 0 steps with 4000 atoms -0.0% CPU use with 4 MPI tasks x no OpenMP threads +165.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -593,7 +607,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.861e-06 | | |100.00 +Other | | 1.967e-06 | | |100.00 Nlocal: 1000 ave 1000 max 1000 min Histogram: 4 0 0 0 0 0 0 0 0 0 @@ -616,4 +630,4 @@ undump d1 print TEST_DONE TEST_DONE -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/lib/Install.py b/lib/Install.py index d30cbffcf1..d5c41f9ad0 100644 --- a/lib/Install.py +++ b/lib/Install.py @@ -1,26 +1,28 @@ #!/usr/bin/env python -# install.py tool to do a generic build of a library -# soft linked to by many of the lib/Install.py files -# used to automate the steps described in the corresponding lib/README +""" +Install.py tool to do a generic build of a library +soft linked to by many of the lib/Install.py files +used to automate the steps described in the corresponding lib/README +""" from __future__ import print_function -import sys,os,subprocess +import sys, os, subprocess +from argparse import ArgumentParser -# help message +sys.path.append('..') +from install_helpers import get_cpus, fullpath -help = """ +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +HELP = """ Syntax from src dir: make lib-libname args="-m machine -e suffix" Syntax from lib dir: python Install.py -m machine -e suffix libname = name of lib dir (e.g. atc, h5md, meam, poems, etc) specify -m and optionally -e, order does not matter - -m = peform a clean followed by "make -f Makefile.machine" - machine = suffix of a lib/Makefile.* file - -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix - does not alter existing Makefile.machine - Examples: make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src @@ -28,48 +30,37 @@ make lib-colvars args="-m mpi" # build USER-COLVARS lib with same settings as i make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran) """ -# print error message or help +# parse and process arguments -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +parser.add_argument("-m", "--machine", + help="suffix of a /Makefile.* file used for compiling this library") +parser.add_argument("-e", "--extramake", + help="set EXTRAMAKE variable in /Makefile. to Makefile.lammps.") -# parse args +args = parser.parse_args() -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() +# print help message and exit, if neither build nor path options are given +if not args.machine and not args.extramake: + parser.print_help() + sys.exit(HELP) -machine = None -extraflag = 0 - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-m": - if iarg+2 > nargs: error() - machine = args[iarg+1] - iarg += 2 - elif args[iarg] == "-e": - if iarg+2 > nargs: error() - extraflag = 1 - suffix = args[iarg+1] - iarg += 2 - else: error() +machine = args.machine +extraflag = not args.extramake +suffix = args.extramake # set lib from working dir -cwd = os.getcwd() +cwd = fullpath('.') lib = os.path.basename(cwd) # create Makefile.auto as copy of Makefile.machine # reset EXTRAMAKE if requested if not os.path.exists("Makefile.%s" % machine): - error("lib/%s/Makefile.%s does not exist" % (lib,machine)) + sys.exit("lib/%s/Makefile.%s does not exist" % (lib, machine)) -lines = open("Makefile.%s" % machine,'r').readlines() -fp = open("Makefile.auto",'w') +lines = open("Makefile.%s" % machine, 'r').readlines() +fp = open("Makefile.auto", 'w') has_extramake = False for line in lines: @@ -77,25 +68,27 @@ for line in lines: if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=': has_extramake = True if extraflag: - line = line.replace(words[2],"Makefile.lammps.%s" % suffix) + line = line.replace(words[2], "Makefile.lammps.%s" % suffix) fp.write(line) fp.close() # make the library via Makefile.auto optionally with parallel make - -try: - import multiprocessing - n_cpus = multiprocessing.cpu_count() -except: - n_cpus = 1 +n_cpus = get_cpus() print("Building lib%s.a ..." % lib) cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus -txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT) -print(txt.decode('UTF-8')) +try: + txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT) + print(txt.decode('UTF-8')) +except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + +if os.path.exists("lib%s.a" % lib): + print("Build was successful") +else: + sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib)) -if os.path.exists("lib%s.a" % lib): print("Build was successful") -else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib)) if has_extramake and not os.path.exists("Makefile.lammps"): - print("lib/%s/Makefile.lammps was NOT created" % lib) + print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib) diff --git a/lib/README b/lib/README index 12c27b2a39..d89490e202 100644 --- a/lib/README +++ b/lib/README @@ -33,8 +33,6 @@ kokkos Kokkos package for GPU and many-core acceleration from Kokkos development team (Sandia) linalg set of BLAS and LAPACK routines needed by USER-ATC package from Axel Kohlmeyer (Temple U) -meam modified embedded atom method (MEAM) potential, MEAM package - from Greg Wagner (Sandia) message client/server communication library via MPI, sockets, files from Steve Plimpton (Sandia) molfile hooks to VMD molfile plugins, used by the USER-MOLFILE package @@ -51,8 +49,6 @@ qmmm quantum mechanics/molecular mechanics coupling interface from Axel Kohlmeyer (Temple U) quip interface to QUIP/libAtoms framework, USER-QUIP package from Albert Bartok-Partay and Gabor Csanyi (U Cambridge) -reax ReaxFF potential, REAX package - from Adri van Duin (Penn State) and Aidan Thompson (Sandia) smd hooks to Eigen library, used by USER-SMD package from Georg Ganzenmueller (Ernst Mach Institute, Germany) voronoi hooks to the Voro++ library, used by compute voronoi/atom command diff --git a/lib/atc/DenseVector.h b/lib/atc/DenseVector.h index bbca12997b..70e223d988 100644 --- a/lib/atc/DenseVector.h +++ b/lib/atc/DenseVector.h @@ -82,7 +82,7 @@ void DenseVector::resize(INDEX rows, INDEX cols, bool copy) /////////////////////////////////////////////////////////////////////////////// //* resizes the matrix and optionally zeros it out template -void DenseVector::reset(INDEX rows, INDEX cols, bool zero) +void DenseVector::reset(INDEX rows, INDEX /* cols */, bool zero) { if (_size!=rows) { @@ -94,7 +94,7 @@ void DenseVector::reset(INDEX rows, INDEX cols, bool zero) /////////////////////////////////////////////////////////////////////////////// //* resizes the matrix and optionally zeros it out template -void DenseVector::copy(const T * ptr, INDEX rows, INDEX cols) +void DenseVector::copy(const T * ptr, INDEX rows, INDEX /* cols */) { resize(rows, 1, false); memcpy(_data, ptr, this->size()*sizeof(T)); diff --git a/lib/colvars/Install.py b/lib/colvars/Install.py index 030644ceb5..e481536768 100644 --- a/lib/colvars/Install.py +++ b/lib/colvars/Install.py @@ -4,6 +4,13 @@ from __future__ import print_function import sys,os,subprocess +sys.path.append('..') +from install_helpers import get_cpus + +from argparse import ArgumentParser + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") # help message @@ -24,44 +31,33 @@ Examples: make lib-colvars args="-m mpi" # build COLVARS lib with default mpi compiler wrapper """ -# print error message or help - -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -machine = None -extraflag = False - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-m": - if iarg+2 > len(args): error() - machine = args[iarg+1] - iarg += 2 - elif args[iarg] == "-e": - if iarg+2 > len(args): error() - extraflag = True - suffix = args[iarg+1] - iarg += 2 - else: error() - # set lib from working dir cwd = os.getcwd() lib = os.path.basename(cwd) +# parse and process arguments + +parser.add_argument("-m", "--machine", + help="suffix of a /Makefile.* or of a src/MAKE/MACHINES/Makefile.* file used for compiling this library") +parser.add_argument("-e", "--extramake", + help="set EXTRAMAKE variable in /Makefile. to Makefile.lammps.") + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.machine and not args.extramake: + parser.print_help() + sys.exit(help) + +machine = args.machine +extraflag = args.extramake != None +suffix = args.extramake + def get_lammps_machine_flags(machine): """Parse Makefile.machine from LAMMPS, return dictionary of compiler flags""" if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine): - error("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine) + sys.exit("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine) lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine, 'r').readlines() machine_flags = {} @@ -107,7 +103,7 @@ if not os.path.exists("Makefile.%s" % machine): machine_flags = get_lammps_machine_flags(machine) gen_colvars_makefile_machine(machine, machine_flags) if not os.path.exists("Makefile.%s" % machine): - error("lib/%s/Makefile.%s does not exist" % (lib,machine)) + sys.exit("lib/%s/Makefile.%s does not exist" % (lib,machine)) # create Makefile.auto as copy of Makefile.machine # reset EXTRAMAKE if requested @@ -124,19 +120,18 @@ fp.close() # make the library via Makefile.auto optionally with parallel make -try: - import multiprocessing - n_cpus = multiprocessing.cpu_count() -except: - n_cpus = 1 +n_cpus = get_cpus() print("Building lib%s.a ..." % lib) -cmd = ["make -f Makefile.auto clean"] -print(subprocess.check_output(cmd, shell=True).decode('UTF-8')) -cmd = ["make -f Makefile.auto -j%d" % n_cpus] -print(subprocess.check_output(cmd, shell=True).decode('UTF-8')) +cmd = ["make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus] +try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True); + print(txt.decode('UTF-8')) +except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) if os.path.exists("lib%s.a" % lib): print("Build was successful") -else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib)) +else: sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib)) if not os.path.exists("Makefile.lammps"): print("lib/%s/Makefile.lammps was NOT created" % lib) diff --git a/lib/colvars/colvar.cpp b/lib/colvars/colvar.cpp index 22befdfd43..8b28eaa0df 100644 --- a/lib/colvars/colvar.cpp +++ b/lib/colvars/colvar.cpp @@ -21,10 +21,14 @@ colvar::colvar() - : prev_timestep(-1) { - // Initialize static array once and for all runave_os = NULL; + + prev_timestep = -1; + after_restart = false; + kinetic_energy = 0.0; + potential_energy = 0.0; + init_cv_requires(); } @@ -38,6 +42,7 @@ namespace { } } + int colvar::init(std::string const &conf) { cvm::log("Initializing a new collective variable.\n"); @@ -48,7 +53,7 @@ int colvar::init(std::string const &conf) colvarmodule *cv = cvm::main(); get_keyval(conf, "name", this->name, - (std::string("colvar")+cvm::to_str(cv->variables()->size()+1))); + (std::string("colvar")+cvm::to_str(cv->variables()->size()))); if ((cvm::colvar_by_name(this->name) != NULL) && (cvm::colvar_by_name(this->name) != this)) { @@ -63,9 +68,6 @@ int colvar::init(std::string const &conf) this->description = "colvar " + this->name; - kinetic_energy = 0.0; - potential_energy = 0.0; - error_code |= init_components(conf); if (error_code != COLVARS_OK) { return cvm::get_error(); @@ -260,7 +262,6 @@ int colvar::init(std::string const &conf) f_old.reset(); x_restart.type(value()); - after_restart = false; reset_bias_force(); @@ -282,8 +283,7 @@ int colvar::init(std::string const &conf) // Now that the children are defined we can solve dependencies enable(f_cv_active); - if (cvm::b_analysis) - parse_analysis(conf); + error_code |= parse_analysis(conf); if (cvm::debug()) cvm::log("Done initializing collective variable \""+this->name+"\".\n"); @@ -881,19 +881,7 @@ int colvar::parse_analysis(std::string const &conf) cvm::error("Error: runAveStride must be commensurate with the restart frequency.\n", INPUT_ERROR); } - get_keyval(conf, "runAveOutputFile", runave_outfile, - std::string(cvm::output_prefix()+"."+ - this->name+".runave.traj")); - - size_t const this_cv_width = x.output_width(cvm::cv_width); - cvm::proxy->backup_file(runave_outfile); - runave_os = cvm::proxy->output_stream(runave_outfile); - *runave_os << "# " << cvm::wrap_string("step", cvm::it_width-2) - << " " - << cvm::wrap_string("running average", this_cv_width) - << " " - << cvm::wrap_string("running stddev", this_cv_width) - << "\n"; + get_keyval(conf, "runAveOutputFile", runave_outfile, runave_outfile); } acf_length = 0; @@ -902,7 +890,6 @@ int colvar::parse_analysis(std::string const &conf) enable(f_cv_corrfunc); - std::string acf_colvar_name; get_keyval(conf, "corrFuncWithColvar", acf_colvar_name, this->name); if (acf_colvar_name == this->name) { cvm::log("Calculating auto-correlation function.\n"); @@ -918,8 +905,12 @@ int colvar::parse_analysis(std::string const &conf) } else if (acf_type_str == to_lower_cppstr(std::string("velocity"))) { acf_type = acf_vel; enable(f_cv_fdiff_velocity); - if (acf_colvar_name.size()) - (cvm::colvar_by_name(acf_colvar_name))->enable(f_cv_fdiff_velocity); + colvar *cv2 = cvm::colvar_by_name(acf_colvar_name); + if (cv2 == NULL) { + return cvm::error("Error: collective variable \""+acf_colvar_name+ + "\" is not defined at this time.\n", INPUT_ERROR); + } + cv2->enable(f_cv_fdiff_velocity); } else if (acf_type_str == to_lower_cppstr(std::string("coordinate_p2"))) { acf_type = acf_p2coor; } else { @@ -937,9 +928,7 @@ int colvar::parse_analysis(std::string const &conf) } get_keyval(conf, "corrFuncNormalize", acf_normalize, true); - get_keyval(conf, "corrFuncOutputFile", acf_outfile, - std::string(cvm::output_prefix()+"."+this->name+ - ".corrfunc.dat")); + get_keyval(conf, "corrFuncOutputFile", acf_outfile, acf_outfile); } return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } @@ -1389,9 +1378,9 @@ int colvar::calc_colvar_properties() { if (is_enabled(f_cv_fdiff_velocity)) { // calculate the velocity by finite differences - if (cvm::step_relative() == 0) + if (cvm::step_relative() == 0) { x_old = x; - else { + } else { v_fdiff = fdiff_velocity(x_old, x); v_reported = v_fdiff; } @@ -1486,7 +1475,6 @@ cvm::real colvar::update_forces_energy() return 0.; } } - prev_timestep = cvm::step_relative(); // Integrate with slow timestep (if time_step_factor != 1) cvm::real dt = cvm::dt() * cvm::real(time_step_factor); @@ -1547,8 +1535,18 @@ cvm::real colvar::update_forces_energy() // bypass the extended Lagrangian mass) f += fb_actual; + if (cvm::debug()) + cvm::log("Done updating colvar \""+this->name+"\".\n"); + return (potential_energy + kinetic_energy); +} + + +int colvar::end_of_step() +{ + if (cvm::debug()) + cvm::log("End of step for colvar \""+this->name+"\".\n"); + if (is_enabled(f_cv_fdiff_velocity)) { - // set it for the next step x_old = x; } @@ -1556,9 +1554,9 @@ cvm::real colvar::update_forces_energy() f_old = f; } - if (cvm::debug()) - cvm::log("Done updating colvar \""+this->name+"\".\n"); - return (potential_energy + kinetic_energy); + prev_timestep = cvm::step_relative(); + + return COLVARS_OK; } @@ -1966,6 +1964,10 @@ std::ostream & colvar::write_restart(std::ostream &os) { os << "}\n\n"; + if (runave_os) { + cvm::main()->proxy->flush_output_stream(runave_os); + } + return os; } @@ -2075,55 +2077,61 @@ std::ostream & colvar::write_traj(std::ostream &os) return os; } + int colvar::write_output_files() { - if (cvm::b_analysis) { + int error_code = COLVARS_OK; + if (is_enabled(f_cv_corrfunc)) { if (acf.size()) { - cvm::log("Writing acf to file \""+acf_outfile+"\".\n"); - + if (acf_outfile.size() == 0) { + acf_outfile = std::string(cvm::output_prefix()+"."+this->name+ + ".corrfunc.dat"); + } + cvm::log("Writing correlation function to file \""+acf_outfile+"\".\n"); cvm::backup_file(acf_outfile.c_str()); std::ostream *acf_os = cvm::proxy->output_stream(acf_outfile); if (!acf_os) return cvm::get_error(); - write_acf(*acf_os); + error_code |= write_acf(*acf_os); cvm::proxy->close_output_stream(acf_outfile); } - - if (runave_os) { - cvm::proxy->close_output_stream(runave_outfile); - runave_os = NULL; - } } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + + return error_code; } // ******************** ANALYSIS FUNCTIONS ******************** -void colvar::analyze() +int colvar::analyze() { + int error_code = COLVARS_OK; + if (is_enabled(f_cv_runave)) { - calc_runave(); + error_code |= calc_runave(); } if (is_enabled(f_cv_corrfunc)) { - calc_acf(); + error_code |= calc_acf(); } + + return error_code; } inline void history_add_value(size_t const &history_length, - std::list &history, - colvarvalue const &new_value) + std::list &history, + colvarvalue const &new_value) { history.push_front(new_value); if (history.size() > history_length) history.pop_back(); } + inline void history_incr(std::list< std::list > &history, - std::list< std::list >::iterator &history_p) + std::list< std::list >::iterator &history_p) { if ((++history_p) == history.end()) history_p = history.begin(); @@ -2133,18 +2141,21 @@ inline void history_incr(std::list< std::list > &history, int colvar::calc_acf() { // using here an acf_stride-long list of vectors for either - // coordinates(acf_x_history) or velocities (acf_v_history); each vector can + // coordinates (acf_x_history) or velocities (acf_v_history); each vector can // contain up to acf_length values, which are contiguous in memory // representation but separated by acf_stride in the time series; // the pointer to each vector is changed at every step + colvar const *cfcv = cvm::colvar_by_name(acf_colvar_name); + if (cfcv == NULL) { + return cvm::error("Error: collective variable \""+acf_colvar_name+ + "\" is not defined at this time.\n", INPUT_ERROR); + } + if (acf_x_history.empty() && acf_v_history.empty()) { // first-step operations - colvar *cfcv = (acf_colvar_name.size() ? - cvm::colvar_by_name(acf_colvar_name) : - this); if (colvarvalue::check_types(cfcv->value(), value())) { cvm::error("Error: correlation function between \""+cfcv->name+ "\" and \""+this->name+"\" cannot be calculated, " @@ -2153,7 +2164,8 @@ int colvar::calc_acf() } acf_nframes = 0; - cvm::log("Colvar \""+this->name+"\": initializing ACF calculation.\n"); + cvm::log("Colvar \""+this->name+"\": initializing correlation function " + "calculation.\n"); if (acf.size() < acf_length+1) acf.resize(acf_length+1, 0.0); @@ -2182,41 +2194,31 @@ int colvar::calc_acf() break; } - } else { - - colvar *cfcv = (acf_colvar_name.size() ? - cvm::colvar_by_name(acf_colvar_name) : - this); + } else if (cvm::step_relative() > prev_timestep) { switch (acf_type) { case acf_vel: - if (is_enabled(f_cv_fdiff_velocity)) { - // calc() should do this already, but this only happens in a - // simulation; better do it again in case a trajectory is - // being read - v_reported = v_fdiff = fdiff_velocity(x_old, cfcv->value()); - } - calc_vel_acf((*acf_v_history_p), cfcv->velocity()); - // store this value in the history - history_add_value(acf_length+acf_offset, *acf_v_history_p, cfcv->velocity()); - // if stride is larger than one, cycle among different histories + history_add_value(acf_length+acf_offset, *acf_v_history_p, + cfcv->velocity()); history_incr(acf_v_history, acf_v_history_p); break; case acf_coor: calc_coor_acf((*acf_x_history_p), cfcv->value()); - history_add_value(acf_length+acf_offset, *acf_x_history_p, cfcv->value()); + history_add_value(acf_length+acf_offset, *acf_x_history_p, + cfcv->value()); history_incr(acf_x_history, acf_x_history_p); break; case acf_p2coor: calc_p2coor_acf((*acf_x_history_p), cfcv->value()); - history_add_value(acf_length+acf_offset, *acf_x_history_p, cfcv->value()); + history_add_value(acf_length+acf_offset, *acf_x_history_p, + cfcv->value()); history_incr(acf_x_history, acf_x_history_p); break; @@ -2225,18 +2227,14 @@ int colvar::calc_acf() } } - if (is_enabled(f_cv_fdiff_velocity)) { - // set it for the next step - x_old = x; - } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); + return COLVARS_OK; } -int colvar::calc_vel_acf(std::list &v_list, - colvarvalue const &v) +void colvar::calc_vel_acf(std::list &v_list, + colvarvalue const &v) { - // loop over stored velocities and add to the ACF, but only the + // loop over stored velocities and add to the ACF, but only if the // length is sufficient to hold an entire row of ACF values if (v_list.size() >= acf_length+acf_offset) { std::list::iterator vs_i = v_list.begin(); @@ -2255,7 +2253,6 @@ int colvar::calc_vel_acf(std::list &v_list, acf_nframes++; } - return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); } @@ -2280,7 +2277,7 @@ void colvar::calc_coor_acf(std::list &x_list, void colvar::calc_p2coor_acf(std::list &x_list, - colvarvalue const &x) + colvarvalue const &x) { // same as above but with second order Legendre polynomial instead // of just the scalar product @@ -2301,20 +2298,46 @@ void colvar::calc_p2coor_acf(std::list &x_list, } -void colvar::write_acf(std::ostream &os) +int colvar::write_acf(std::ostream &os) { - if (!acf_nframes) - cvm::log("Warning: ACF was not calculated (insufficient frames).\n"); + if (!acf_nframes) { + return COLVARS_OK; + } + os.setf(std::ios::scientific, std::ios::floatfield); - os << "# Autocorrelation function for collective variable \"" - << this->name << "\"\n"; - // one frame is used for normalization, the statistical sample is - // hence decreased - os << "# nframes = " << (acf_normalize ? - acf_nframes - 1 : - acf_nframes) << "\n"; + os << "# "; + switch (acf_type) { + case acf_vel: + os << "Velocity"; + break; + case acf_coor: + os << "Coordinate"; + break; + case acf_p2coor: + os << "Coordinate (2nd Legendre poly)"; + break; + } + + if (acf_colvar_name == name) { + os << " autocorrelation function for variable \"" + << this->name << "\"\n"; + } else { + os << " correlation function between variables \"" // + << this->name << "\" and \"" << acf_colvar_name << "\"\n"; + } + + os << "# Number of samples = "; + if (acf_normalize) { + os << (acf_nframes-1) << " (one DoF is used for normalization)\n"; + } else { + os << acf_nframes << "\n"; + } + + os << "# " << cvm::wrap_string("step", cvm::it_width-2) << " " + << cvm::wrap_string("corrfunc(step)", cvm::cv_width) << "\n"; cvm::real const acf_norm = acf.front() / cvm::real(acf_nframes); + std::vector::iterator acf_i; size_t it = acf_offset; for (acf_i = acf.begin(); acf_i != acf.end(); ++acf_i) { @@ -2325,11 +2348,15 @@ void colvar::write_acf(std::ostream &os) (*acf_i)/(acf_norm * cvm::real(acf_nframes)) : (*acf_i)/(cvm::real(acf_nframes)) ) << "\n"; } + + return os.good() ? COLVARS_OK : FILE_ERROR; } -void colvar::calc_runave() +int colvar::calc_runave() { + int error_code = COLVARS_OK; + if (x_history.empty()) { runave.type(value().type()); @@ -2348,10 +2375,29 @@ void colvar::calc_runave() } else { - if ( (cvm::step_relative() % runave_stride) == 0) { + if ( (cvm::step_relative() % runave_stride) == 0 && + (cvm::step_relative() > prev_timestep) ) { if ((*x_history_p).size() >= runave_length-1) { + if (runave_os == NULL) { + if (runave_outfile.size() == 0) { + runave_outfile = std::string(cvm::output_prefix()+"."+ + this->name+".runave.traj"); + } + + size_t const this_cv_width = x.output_width(cvm::cv_width); + cvm::proxy->backup_file(runave_outfile); + runave_os = cvm::proxy->output_stream(runave_outfile); + runave_os->setf(std::ios::scientific, std::ios::floatfield); + *runave_os << "# " << cvm::wrap_string("step", cvm::it_width-2) + << " " + << cvm::wrap_string("running average", this_cv_width) + << " " + << cvm::wrap_string("running stddev", this_cv_width) + << "\n"; + } + runave = x; std::list::iterator xs_i; for (xs_i = (*x_history_p).begin(); @@ -2370,7 +2416,7 @@ void colvar::calc_runave() runave_variance *= 1.0 / cvm::real(runave_length-1); *runave_os << std::setw(cvm::it_width) << cvm::step_relative() - << " " + << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << runave << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) @@ -2381,6 +2427,7 @@ void colvar::calc_runave() } } + return error_code; } // Static members diff --git a/lib/colvars/colvar.h b/lib/colvars/colvar.h index 989d55124f..a67749d577 100644 --- a/lib/colvars/colvar.h +++ b/lib/colvars/colvar.h @@ -291,6 +291,9 @@ public: /// \brief Calculate the colvar's value and related quantities int calc(); + /// Carry out operations needed before next step is run + int end_of_step(); + /// \brief Calculate a subset of the colvar components (CVCs) currently active /// (default: all active CVCs) /// Note: both arguments refer to the sect of *active* CVCs, not all CVCs @@ -410,8 +413,9 @@ public: /// Read the analysis tasks int parse_analysis(std::string const &conf); + /// Perform analysis tasks - void analyze(); + int analyze(); /// Read the value from a collective variable trajectory file @@ -489,23 +493,23 @@ protected: acf_type_e acf_type; /// \brief Velocity ACF, scalar product between v(0) and v(t) - int calc_vel_acf(std::list &v_history, - colvarvalue const &v); + void calc_vel_acf(std::list &v_history, + colvarvalue const &v); /// \brief Coordinate ACF, scalar product between x(0) and x(t) /// (does not work with scalar numbers) void calc_coor_acf(std::list &x_history, - colvarvalue const &x); + colvarvalue const &x); /// \brief Coordinate ACF, second order Legendre polynomial between /// x(0) and x(t) (does not work with scalar numbers) void calc_p2coor_acf(std::list &x_history, - colvarvalue const &x); + colvarvalue const &x); /// Calculate the auto-correlation function (ACF) int calc_acf(); /// Save the ACF to a file - void write_acf(std::ostream &os); + int write_acf(std::ostream &os); /// Length of running average series size_t runave_length; @@ -521,7 +525,7 @@ protected: cvm::real runave_variance; /// Calculate the running average and its standard deviation - void calc_runave(); + int calc_runave(); /// If extended Lagrangian active: colvar energies (kinetic and harmonic potential) cvm::real kinetic_energy; diff --git a/lib/colvars/colvarbias.cpp b/lib/colvars/colvarbias.cpp index 29620fbee8..9363fcdcb6 100644 --- a/lib/colvars/colvarbias.cpp +++ b/lib/colvars/colvarbias.cpp @@ -236,6 +236,12 @@ void colvarbias::communicate_forces() } +int colvarbias::end_of_step() +{ + return COLVARS_OK; +} + + int colvarbias::change_configuration(std::string const &conf) { cvm::error("Error: change_configuration() not implemented.\n", diff --git a/lib/colvars/colvarbias.h b/lib/colvars/colvarbias.h index 083b9d7303..391826e79e 100644 --- a/lib/colvars/colvarbias.h +++ b/lib/colvars/colvarbias.h @@ -66,6 +66,9 @@ public: /// Send forces to the collective variables virtual void communicate_forces(); + /// Carry out operations needed before next step is run + virtual int end_of_step(); + /// Load new configuration - force constant and/or centers only virtual int change_configuration(std::string const &conf); diff --git a/lib/colvars/colvardeps.cpp b/lib/colvars/colvardeps.cpp index 80bd6670d3..d20ee6e55c 100644 --- a/lib/colvars/colvardeps.cpp +++ b/lib/colvars/colvardeps.cpp @@ -567,6 +567,9 @@ void colvardeps::init_cv_requires() { // Most features are available, so we set them so // and list exceptions below } + + feature_states[f_cv_fdiff_velocity].available = + cvm::main()->proxy->simulation_running(); } diff --git a/lib/colvars/colvarmodule.cpp b/lib/colvars/colvarmodule.cpp index 87b08b1ef8..d88a97a441 100644 --- a/lib/colvars/colvarmodule.cpp +++ b/lib/colvars/colvarmodule.cpp @@ -62,8 +62,6 @@ colvarmodule::colvarmodule(colvarproxy *proxy_in) use_scripted_forces = false; scripting_after_biases = false; - b_analysis = false; - colvarmodule::debug_gradients_step_size = 1.0e-07; colvarmodule::rotation::monitor_crossings = false; @@ -274,7 +272,12 @@ int colvarmodule::parse_global_params(std::string const &conf) } } - parse->get_keyval(conf, "analysis", b_analysis, b_analysis); + bool b_analysis = true; + if (parse->get_keyval(conf, "analysis", b_analysis, true, + colvarparse::parse_silent)) { + cvm::log("Warning: keyword \"analysis\" is deprecated: it is now set " + "to true; individual analyses are performed only if requested."); + } parse->get_keyval(conf, "debugGradientsStepSize", debug_gradients_step_size, debug_gradients_step_size, @@ -715,9 +718,7 @@ int colvarmodule::calc() error_code |= calc_biases(); error_code |= update_colvar_forces(); - if (cvm::b_analysis) { - error_code |= analyze(); - } + error_code |= analyze(); // write trajectory files, if needed if (cv_traj_freq && cv_traj_name.size()) { @@ -736,6 +737,8 @@ int colvarmodule::calc() write_output_files(); } + error_code |= end_of_step(); + return error_code; } @@ -1056,6 +1059,33 @@ int colvarmodule::analyze() } +int colvarmodule::end_of_step() +{ + if (cvm::debug()) { + cvm::log("colvarmodule::end_of_step(), step = "+cvm::to_str(it)+".\n"); + } + + for (std::vector::iterator cvi = variables_active()->begin(); + cvi != variables_active()->end(); + cvi++) { + cvm::increase_depth(); + (*cvi)->end_of_step(); + cvm::decrease_depth(); + } + + // perform bias-specific analysis + for (std::vector::iterator bi = biases.begin(); + bi != biases.end(); + bi++) { + cvm::increase_depth(); + (*bi)->end_of_step(); + cvm::decrease_depth(); + } + + return (cvm::get_error() ? COLVARS_ERROR : COLVARS_OK); +} + + int colvarmodule::setup() { if (this->size() == 0) return cvm::get_error(); @@ -1895,7 +1925,6 @@ long colvarmodule::it = 0; long colvarmodule::it_restart = 0; size_t colvarmodule::restart_out_freq = 0; size_t colvarmodule::cv_traj_freq = 0; -bool colvarmodule::b_analysis = false; bool colvarmodule::use_scripted_forces = false; bool colvarmodule::scripting_after_biases = true; diff --git a/lib/colvars/colvarmodule.h b/lib/colvars/colvarmodule.h index 3d93798e0a..99b797627e 100644 --- a/lib/colvars/colvarmodule.h +++ b/lib/colvars/colvarmodule.h @@ -422,6 +422,9 @@ public: /// Perform analysis int analyze(); + /// Carry out operations needed before next step is run + int end_of_step(); + /// \brief Read a collective variable trajectory (post-processing /// only, not called at runtime) int read_traj(char const *traj_filename, @@ -546,9 +549,6 @@ public: /// Frequency for collective variables trajectory output static size_t cv_traj_freq; - /// \brief True if only analysis is performed and not a run - static bool b_analysis; - /// Frequency for saving output restarts static size_t restart_out_freq; /// Output restart file name diff --git a/lib/colvars/colvars_version.h b/lib/colvars/colvars_version.h index a37d264a20..bd84d077d7 100644 --- a/lib/colvars/colvars_version.h +++ b/lib/colvars/colvars_version.h @@ -1,5 +1,5 @@ #ifndef COLVARS_VERSION -#define COLVARS_VERSION "2018-10-16" +#define COLVARS_VERSION "2018-11-16" // This file is part of the Collective Variables module (Colvars). // The original version of Colvars and its updates are located at: // https://github.com/colvars/colvars diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py index d1024c0085..d06a37567a 100644 --- a/lib/gpu/Install.py +++ b/lib/gpu/Install.py @@ -1,14 +1,23 @@ #!/usr/bin/env python -# Install.py tool to build the GPU library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to build the GPU library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,subprocess +import sys, os, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import get_cpus + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") # help message -help = """ +HELP = """ Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix" Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -b -o osuffix @@ -21,28 +30,8 @@ optionally uses Makefile.auto to build the GPU library -> libgpu.a and to copy a Makefile.lammps.esuffix -> Makefile.lammps optionally copies Makefile.auto to a new Makefile.osuffix - -m = use Makefile.machine as starting point, copy to Makefile.auto - default machine = linux - default for -h, -a, -p, -e settings are those in -m Makefile - -h = set CUDA_HOME variable in Makefile.auto to hdir - hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda - -a = set CUDA_ARCH variable in Makefile.auto to arch - use arch = sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) - or GeForce GTX 580 or similar - use arch = sm_30 for Kepler (K10) - use arch = sm_35 for Kepler (K40) or GeForce GTX Titan or similar - use arch = sm_37 for Kepler (dual K80) - use arch = sm_60 for Pascal (P100) - use arch = sm_70 for Volta - -p = set CUDA_PRECISION variable in Makefile.auto to precision - use precision = double or mixed or single - -e = set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.esuffix - -b = make the GPU library using Makefile.auto - first performs a "make clean" - then produces libgpu.a if successful - also copies EXTRAMAKE file -> Makefile.lammps - -e can set which Makefile.lammps.esuffix file is copied - -o = copy final Makefile.auto to Makefile.osuffix +See lib/gpu/README and the LAMMPS manual for more information +on which settings to use and how to build. Examples: @@ -51,74 +40,68 @@ make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk make lib-gpu args="-m mpi -a sm_35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings """ -# print error message or help +# parse and process arguments -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +parser.add_argument("-b", "--build", action="store_true", + help="build the GPU library from scratch from a customized Makefile.auto") +parser.add_argument("-m", "--machine", default='linux', + help="suffix of Makefile.machine used as base for customizing Makefile.auto") +parser.add_argument("-a", "--arch", default='sm_30', + choices=['sm_12', 'sm_13', 'sm_20', 'sm_21', 'sm_30', 'sm_35', 'sm_37', + 'sm_50', 'sm_52', 'sm_60', 'sm_61', 'sm_70', 'sm_75'], + help="set GPU architecture and instruction set (default: 'sm_30')") +parser.add_argument("-p", "--precision", default='mixed', choices=['single', 'mixed', 'double'], + help="set GPU kernel precision mode (default: mixed)") +parser.add_argument("-e", "--extramake", default='standard', + help="set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.") +parser.add_argument("-c", "--cuda", + help="set CUDA_HOME variable in Makefile.auto. Will be used if $CUDA_HOME environment variable is not set") +parser.add_argument("-o", "--output", + help="if set, copy final Makefile.auto to Makefile. for later re-use") -# parse args +args = parser.parse_args() -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() +# print help message and exit, if neither build nor output options are given +if not args.build and not args.output: + parser.print_help() + sys.exit(HELP) -isuffix = "linux" -hflag = aflag = pflag = eflag = 0 +hflag = 0 +eflag = 0 makeflag = 0 outflag = 0 -iarg = 0 -while iarg < nargs: - if args[iarg] == "-m": - if iarg+2 > nargs: error() - isuffix = args[iarg+1] - iarg += 2 - elif args[iarg] == "-h": - if iarg+2 > nargs: error() - hflag = 1 - hdir = args[iarg+1] - iarg += 2 - elif args[iarg] == "-a": - if iarg+2 > nargs: error() - aflag = 1 - arch = args[iarg+1] - iarg += 2 - elif args[iarg] == "-p": - if iarg+2 > nargs: error() - pflag = 1 - precision = args[iarg+1] - iarg += 2 - elif args[iarg] == "-e": - if iarg+2 > nargs: error() - eflag = 1 - lmpsuffix = args[iarg+1] - iarg += 2 - elif args[iarg] == "-b": - makeflag = 1 - iarg += 1 - elif args[iarg] == "-o": - if iarg+2 > nargs: error() - outflag = 1 - osuffix = args[iarg+1] - iarg += 2 - else: error() +if args.build: + makeflag = 1 -if pflag: - if precision == "double": precstr = "-D_DOUBLE_DOUBLE" - elif precision == "mixed": precstr = "-D_SINGLE_DOUBLE" - elif precision == "single": precstr = "-D_SINGLE_SINGLE" - else: error("Invalid precision setting") +isuffix = args.machine +arch = args.arch + +if args.precision == "double": + precstr = "-D_DOUBLE_DOUBLE" +elif args.precision == "mixed": + precstr = "-D_SINGLE_DOUBLE" +else: + precstr = "-D_SINGLE_SINGLE" + +lmpsuffix = args.extramake + +if args.cuda: + hflag = 1 + hdir = args.cuda + +if args.output: + outflag = 1 + osuffix = args.output # create Makefile.auto # reset EXTRAMAKE, CUDA_HOME, CUDA_ARCH, CUDA_PRECISION if requested if not os.path.exists("Makefile.%s" % isuffix): - error("lib/gpu/Makefile.%s does not exist" % isuffix) + sys.exit("lib/gpu/Makefile.%s does not exist" % isuffix) -lines = open("Makefile.%s" % isuffix,'r').readlines() -fp = open("Makefile.auto",'w') +lines = open("Makefile.%s" % isuffix, 'r').readlines() +fp = open("Makefile.auto", 'w') for line in lines: words = line.split() @@ -127,13 +110,13 @@ for line in lines: continue if hflag and words[0] == "CUDA_HOME" and words[1] == '=': - line = line.replace(words[2],hdir) - if aflag and words[0] == "CUDA_ARCH" and words[1] == '=': - line = line.replace(words[2],"-arch=%s" % arch) - if pflag and words[0] == "CUDA_PRECISION" and words[1] == '=': - line = line.replace(words[2],precstr) + line = line.replace(words[2], hdir) + if words[0] == "CUDA_ARCH" and words[1] == '=': + line = line.replace(words[2], "-arch=%s" % arch) + if words[0] == "CUDA_PRECISION" and words[1] == '=': + line = line.replace(words[2], precstr) if eflag and words[0] == "EXTRAMAKE" and words[1] == '=': - line = line.replace(words[2],"Makefile.lammps.%s" % lmpsuffix) + line = line.replace(words[2], "Makefile.lammps.%s" % lmpsuffix) fp.write(line) fp.close() @@ -143,19 +126,24 @@ fp.close() if makeflag: print("Building libgpu.a ...") - cmd = "rm -f libgpu.a" - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = "make -f Makefile.auto clean; make -f Makefile.auto" - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - print(txt.decode('UTF-8')) + if os.path.exists("libgpu.a"): + os.remove("libgpu.a") + n_cpus = get_cpus() + cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + if not os.path.exists("libgpu.a"): - error("Build of lib/gpu/libgpu.a was NOT successful") + sys.exit("Build of lib/gpu/libgpu.a was NOT successful") if not os.path.exists("Makefile.lammps"): - error("lib/gpu/Makefile.lammps was NOT created") + sys.exit("lib/gpu/Makefile.lammps was NOT created") # copy new Makefile.auto to Makefile.osuffix if outflag: print("Creating new Makefile.%s" % osuffix) - cmd = "cp Makefile.auto Makefile.%s" % osuffix - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + shutil.copyfile("Makefile.auto", "Makefile.%s" % osuffix) diff --git a/lib/gpu/Makefile.fermi b/lib/gpu/Makefile.fermi index 4cd9dd20a3..ce5ccaaf78 100644 --- a/lib/gpu/Makefile.fermi +++ b/lib/gpu/Makefile.fermi @@ -3,11 +3,11 @@ EXTRAMAKE = Makefile.lammps.standard CUDA_ARCH = -arch=sm_35 CUDA_PRECISION = -D_SINGLE_DOUBLE -CUDA_INCLUDE = -I$(CUDA_HOME)/include +CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -Xlinker -rpath -Xlinker $(CUDA_HOME)/lib64 -lcudart -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math --ftz=true +CUDA_OPTS = -DUNIX -O3 --use_fast_math --ftz=true -CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include +CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include CUDR_OPTS = -O3 -ffast-math -funroll-loops -DMPI_GERYON -DLAMMPS_SMALLBIG BIN_DIR = . diff --git a/lib/gpu/Makefile.linux b/lib/gpu/Makefile.linux index 9580bfd4ae..7001c6d8b9 100644 --- a/lib/gpu/Makefile.linux +++ b/lib/gpu/Makefile.linux @@ -13,13 +13,33 @@ endif NVCC = nvcc -# older CUDA -#CUDA_ARCH = -arch=sm_21 -# newer CUDA +# obsolete hardware. not supported by current drivers anymore. #CUDA_ARCH = -arch=sm_13 -# older CUDA #CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE -CUDA_ARCH = -arch=sm_35 + +# Fermi hardware +#CUDA_ARCH = -arch=sm_20 +#CUDA_ARCH = -arch=sm_21 + +# Kepler hardware +CUDA_ARCH = -arch=sm_30 +#CUDA_ARCH = -arch=sm_32 +#CUDA_ARCH = -arch=sm_35 +#CUDA_ARCH = -arch=sm_37 + +# Maxwell hardware +#CUDA_ARCH = -arch=sm_50 +#CUDA_ARCH = -arch=sm_52 + +# Pascal hardware +#CUDA_ARCH = -arch=sm_60 +#CUDA_ARCH = -arch=sm_61 + +# Volta hardware +#CUDA_ARCH = -arch=sm_70 + +# Turing hardware +#CUDA_ARCH = -arch=sm_75 # this setting should match LAMMPS Makefile # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL @@ -35,7 +55,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler -fPIC +CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler -fPIC CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.linux.double b/lib/gpu/Makefile.linux.double index defbe2bc9c..e65647f160 100644 --- a/lib/gpu/Makefile.linux.double +++ b/lib/gpu/Makefile.linux.double @@ -33,7 +33,7 @@ CUDA_PRECISION = -D_DOUBLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math +CUDA_OPTS = -DUNIX -O3 --use_fast_math CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.linux.mixed b/lib/gpu/Makefile.linux.mixed index 6289163ac8..a036b84ee3 100644 --- a/lib/gpu/Makefile.linux.mixed +++ b/lib/gpu/Makefile.linux.mixed @@ -33,7 +33,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math +CUDA_OPTS = -DUNIX -O3 --use_fast_math CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.linux.single b/lib/gpu/Makefile.linux.single index 4048bc8788..808647cea7 100644 --- a/lib/gpu/Makefile.linux.single +++ b/lib/gpu/Makefile.linux.single @@ -33,7 +33,7 @@ CUDA_PRECISION = -D_SINGLE_SINGLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math +CUDA_OPTS = -DUNIX -O3 --use_fast_math CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.linux_multi b/lib/gpu/Makefile.linux_multi index 02b405ac35..2f75ca0e2b 100644 --- a/lib/gpu/Makefile.linux_multi +++ b/lib/gpu/Makefile.linux_multi @@ -19,8 +19,13 @@ NVCC = nvcc #CUDA_ARCH = -arch=sm_13 # older CUDA #CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE +CUDA_ARCH = -arch=sm_30 -CUDA_ARCH = -gencode arch=compute_60,code=sm_60 -gencode arch=compute_61,code=sm_61 +CUDA_CODE = -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] \ + -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] \ + -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] + +CUDA_ARCH += $(CUDA_CODE) # this setting should match LAMMPS Makefile # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL @@ -36,7 +41,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98" +CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) -Xcompiler "-fPIC -std=c++98" CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.mac b/lib/gpu/Makefile.mac index 96f739633e..f9f8d5179a 100644 --- a/lib/gpu/Makefile.mac +++ b/lib/gpu/Makefile.mac @@ -15,7 +15,7 @@ CUDA_ARCH = -arch=sm_11 CUDA_PRECISION = -D_SINGLE_SINGLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib -CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 -Xptxas -v --use_fast_math +CUDA_OPTS = -DUNIX -DUCL_NO_EXIT -O3 --use_fast_math CUDR_CPP = mpic++ -m64 CUDR_OPTS = -O2 -g diff --git a/lib/gpu/Makefile.serial b/lib/gpu/Makefile.serial index 9348dc565a..99153fc471 100644 --- a/lib/gpu/Makefile.serial +++ b/lib/gpu/Makefile.serial @@ -35,7 +35,7 @@ CUDA_PRECISION = -D_SINGLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi_stubs -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC) +CUDA_OPTS = -DUNIX -O3 --use_fast_math $(LMP_INC) CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.shannon b/lib/gpu/Makefile.shannon index 2ddb0d1f04..22c2dc89d7 100644 --- a/lib/gpu/Makefile.shannon +++ b/lib/gpu/Makefile.shannon @@ -33,7 +33,7 @@ CUDA_PRECISION = -D_DOUBLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math +CUDA_OPTS = -DUNIX -O3 --use_fast_math CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK CUDR_OPTS = -O2 # -xHost -no-prec-div -ansi-alias diff --git a/lib/gpu/Makefile.xk7 b/lib/gpu/Makefile.xk7 index 1ee8e3225f..0b9f029399 100644 --- a/lib/gpu/Makefile.xk7 +++ b/lib/gpu/Makefile.xk7 @@ -15,7 +15,7 @@ CUDA_ARCH = -arch=sm_35 CUDA_PRECISION = -D_SINGLE_DOUBLE CUDA_INCLUDE = -I$(CUDA_HOME)/include CUDA_LIB = -L$(CUDA_HOME)/lib64 -CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math +CUDA_OPTS = -DUNIX -O3 --use_fast_math CUDR_CPP = CC -DCUDA_PROXY -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK CUDR_OPTS = -O2 -march=bdver1 -ftree-vectorize diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index 0d7214260d..233f43380f 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -880,7 +880,7 @@ $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_bor $(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR) $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H) - $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda + $(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda $(GPU_LIB): $(OBJS) $(CUDPP) $(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP) diff --git a/lib/gpu/README b/lib/gpu/README index 15b65516ac..6cc386270d 100644 --- a/lib/gpu/README +++ b/lib/gpu/README @@ -91,51 +91,14 @@ Performance Computers - Three-Body Potentials. Computer Physics Communications. ---- -NOTE: Installation of the CUDA SDK is not required. +NOTE: Installation of the CUDA SDK is not required, only the CUDA +toolkit itself or an OpenCL 1.2 compatible header and library. -Current styles supporting GPU acceleration: +Pair styles supporting GPU acceleration this this library +are marked in the list of Pair style potentials with a "g". +See the online version at: https://lammps.sandia.gov/doc/Commands_pair.html - 1 beck - 2 born/coul/long - 3 born/coul/wolf - 4 born - 5 buck/coul/cut - 6 buck/coul/long - 7 buck - 8 colloid - 9 coul/dsf - 10 coul/long - 11 eam/alloy - 12 eam/fs - 13 eam - 14 gauss - 15 gayberne - 16 lj96/cut - 17 lj/charmm/coul/long - 18 lj/class2/coul/long - 19 lj/class2 - 20 lj/cut/coul/cut - 21 lj/cut/coul/debye - 22 lj/cut/coul/dsf - 23 lj/cut/coul/long - 24 lj/cut/coul/msm - 25 lj/cut/dipole/cut - 26 lj/cut - 27 lj/expand - 28 lj/gromacs - 29 lj/sdk/coul/long - 30 lj/sdk - 31 lj/sf/dipole/sf - 32 mie/cut - 33 morse - 34 resquared - 35 soft - 36 sw - 37 table - 38 yukawa/colloid - 39 yukawa - 40 pppm - 41 ufm +In addition the (plain) pppm kspace style is supported as well. MULTIPLE LAMMPS PROCESSES @@ -165,7 +128,8 @@ that ships with the CUDA toolkit, but also with the CUDA driver library (libcuda.so) that ships with the Nvidia driver. If you are compiling LAMMPS on the head node of a GPU cluster, this library may not be installed, so you may need to copy it over from one of the compute nodes (best into -this directory). +this directory). Recent CUDA toolkits starting from CUDA 9 provide a dummy +libcuda.so library, that can be used for linking (but not for running). The gpu library supports 3 precision modes as determined by the CUDA_PRECISION variable: @@ -174,40 +138,37 @@ the CUDA_PRECISION variable: CUDA_PRECISION = -D_DOUBLE_DOUBLE # Double precision for all calculations CUDA_PRECISION = -D_SINGLE_DOUBLE # Accumulation of forces, etc. in double -NOTE: PPPM acceleration can only be run on GPUs with compute capability>=1.1. - You will get the error "GPU library not compiled for this accelerator." - when attempting to run PPPM on a GPU with compute capability 1.0. +As of CUDA 7.5 only GPUs with compute capability 2.0 (Fermi) or newer are +supported and as of CUDA 9.0 only compute capability 3.0 (Kepler) or newer +are supported. There are some limitations of this library for GPUs older +than that, which require additional preprocessor flag, and limit features, +but they are kept for historical reasons. There is no value in trying to +use those GPUs for production calculations. -NOTE: Double precision is only supported on certain GPUs (with - compute capability>=1.3). If you compile the GPU library for - a GPU with compute capability 1.1 and 1.2, then only single - precision FFTs are supported, i.e. LAMMPS has to be compiled - with -DFFT_SINGLE. For details on configuring FFT support in - LAMMPS, see http://lammps.sandia.gov/doc/Section_start.html#2_2_4 - -NOTE: For graphics cards with compute capability>=1.3 (e.g. Tesla C1060), - make sure that -arch=sm_13 is set on the CUDA_ARCH line. +You have to make sure that you set a CUDA_ARCH line suitable for your +hardware and CUDA toolkit version: e.g. -arch=sm_35 for Tesla K20 or K40 +or -arch=sm_52 GeForce GTX Titan X. A detailed list of GPU architectures +and CUDA compatible GPUs can be found e.g. here: +https://en.wikipedia.org/wiki/CUDA#GPUs_supported -NOTE: For newer graphics card (a.k.a. "Fermi", e.g. Tesla C2050), make - sure that either -arch=sm_20 or -arch=sm_21 is set on the - CUDA_ARCH line, depending on hardware and CUDA toolkit version. +NOTE: when compiling with CMake, all of the considerations listed below +are considered within the CMake configuration process, so no separate +compilation of the gpu library is required. Also this will build in support +for all compute architecture that are supported by the CUDA toolkit version +used to build the gpu library. -NOTE: The gayberne/gpu pair style will only be installed if the ASPHERE - package has been installed. - -NOTE: The cg/cmm/gpu and cg/cmm/coul/long/gpu pair styles will only be - installed if the USER-CG-CMM package has been installed. - -NOTE: The lj/cut/coul/long/gpu, cg/cmm/coul/long/gpu, coul/long/gpu, - lj/charmm/coul/long/gpu and pppm/gpu styles will only be installed - if the KSPACE package has been installed. +Please note the CUDA_CODE settings in Makefile.linux_multi, which allows +to compile this library with support for multiple GPUs. This list can be +extended for newer GPUs with newer CUDA toolkits and should allow to build +a single GPU library compatible with all GPUs that are worth using for +GPU acceleration and supported by the current CUDA toolkits and drivers. NOTE: The system-specific setting LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG, or LAMMPS_SMALLSMALL if specified when building LAMMPS (i.e. in src/MAKE/Makefile.foo) should be consistent with that specified when building libgpu.a (i.e. by LMP_INC in the lib/gpu/Makefile.bar). - EXAMPLE BUILD PROCESS + EXAMPLE CONVENTIONAL BUILD PROCESS -------------------------------- cd ~/lammps/lib/gpu diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index 6b4d0ab2a5..9397f3c6c5 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -237,7 +237,7 @@ int DeviceT::set_ocl_params(char *ocl_vendor) { " -DBLOCK_CELL_ID="+params[11]+ " -DMAX_BIO_SHARED_TYPES="+params[12]; } - _ocl_compile_string="-cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+ + _ocl_compile_string="-cl-std=CL1.2 -cl-fast-relaxed-math -cl-mad-enable "+std::string(OCL_INT_TYPE)+" "+ std::string(OCL_PRECISION_COMPILE)+" "+_ocl_vendor_string; #endif return 0; diff --git a/lib/gpu/lal_device.cu b/lib/gpu/lal_device.cu index 6761b23fbb..37d0758845 100644 --- a/lib/gpu/lal_device.cu +++ b/lib/gpu/lal_device.cu @@ -11,7 +11,7 @@ // // begin : // email : brownw@ornl.gov -// ***************************************************************************/ +// *************************************************************************** #ifdef NV_KERNEL #include "lal_preprocessor.h" @@ -42,3 +42,4 @@ __kernel void kernel_info(__global int *info) { info[13]=THREADS_PER_CHARGE; info[14]=BLOCK_ELLIPSE; } + diff --git a/lib/install_helpers.py b/lib/install_helpers.py new file mode 100644 index 0000000000..7990463736 --- /dev/null +++ b/lib/install_helpers.py @@ -0,0 +1,68 @@ +import hashlib,os,subprocess,sys + +# try to auto-detect the maximum number of available CPUs +def get_cpus(): + try: + import multiprocessing + n_cpus = multiprocessing.cpu_count() + except: + n_cpus = 1 + return n_cpus + +# expand to full path name +# process leading '~' or relative path + +def fullpath(path): + return os.path.abspath(os.path.expanduser(path)) + +def which(program): + def is_exe(fpath): + return os.path.isfile(fpath) and os.access(fpath, os.X_OK) + + fpath, fname = os.path.split(program) + if fpath: + if is_exe(program): + return program + else: + for path in os.environ["PATH"].split(os.pathsep): + path = path.strip('"') + exe_file = os.path.join(path, program) + if is_exe(exe_file): + return exe_file + + return None + +def geturl(url,fname): + success = False + + if which('curl') != None: + cmd = 'curl -L -o "%s" %s' % (fname,url) + try: + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + success = True + except subprocess.CalledProcessError as e: + print("Calling curl failed with: %s" % e.output.decode('UTF-8')) + + if not success and which('wget') != None: + cmd = 'wget -O "%s" %s' % (fname,url) + try: + subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + success = True + except subprocess.CalledProcessError as e: + print("Calling wget failed with: %s" % e.output.decode('UTF-8')) + + if not success: + error("Failed to download source code with 'curl' or 'wget'") + return + +def checkmd5sum(md5sum,fname): + with open(fname,'rb') as fh: + m = hashlib.md5() + while True: + data = fh.read(81920) + if not data: + break + m.update(data) + fh.close() + return m.hexdigest() == md5sum + diff --git a/lib/kim/.gitignore b/lib/kim/.gitignore index c1f57fe64c..bfd4b35d87 100644 --- a/lib/kim/.gitignore +++ b/lib/kim/.gitignore @@ -1,3 +1,2 @@ -/Makefile.KIM_DIR -/Makefile.KIM_Config +/kim-prefix.txt /installed-kim-api-* diff --git a/lib/kim/Install.py b/lib/kim/Install.py index d098250906..dfb6bc53dc 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -1,14 +1,28 @@ #!/usr/bin/env python -# install.py tool to download, compile, and setup the kim-api library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to download, compile, and setup the kim-api library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,subprocess +import sys, os, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import fullpath, geturl + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +thisdir = fullpath('.') +version = "kim-api-v2-2.0.1" # help message -help = """ +HELP = """ Syntax from src dir: make lib-kim args="-b -v version -a kim-name" or: make lib-kim args="-b -a everything" or: make lib-kim args="-n -a kim-name" @@ -18,157 +32,72 @@ Syntax from lib dir: python Install.py -b -v version -a kim-name or: python Install.py -n -a kim-name or: python Install.py -p /usr/local/open-kim -a kim-name -specify one or more options, order does not matter - - -v = version of KIM API library to use - default = kim-api-v1.9.5 (current as of May 2018) - -b = download and build base KIM API library with example Models - this will delete any previous installation in the current folder - -n = do NOT download and build base KIM API library. - Use an existing installation - -p = specify location of KIM API installation (implies -n) - -a = add single KIM model or model driver with kim-name - to existing KIM API lib (see example below). - If kim-name = everything, then rebuild KIM API library with - *all* available OpenKIM Models (make take a long time). - -vv = be more verbose about what is happening while the script runs - Examples: make lib-kim args="-b" # install KIM API lib with only example models -make lib-kim args="-a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # Ditto plus one model +make lib-kim args="-b -a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditto plus one model make lib-kim args="-b -a everything" # install KIM API lib with all models -make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # only add one model or model driver +make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005" # only add one model or model driver See the list of KIM model drivers here: -https://openkim.org/kim-items/model-drivers/alphabetical +https://openkim.org/browse/model-drivers/alphabetical See the list of all KIM models here: -https://openkim.org/kim-items/models/by-model-drivers - -See the list of example KIM models included by default here: -https://openkim.org/kim-api -in the "What is in the KIM API source package?" section +https://openkim.org/browse/models/by-model-drivers """ -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build base KIM API library with example Models.") +pgroup.add_argument("-n", "--nobuild", action="store_true", + help="use the previously downloaded and compiled base KIM API.") +pgroup.add_argument("-p", "--path", + help="specify location of existing KIM API installation.") +parser.add_argument("-v", "--version", default=version, + help="set version of KIM API library to download and build (default: %s)" % version) +parser.add_argument("-a", "--add", + help="add single KIM model or model driver. If adding 'everything', then all available OpenKIM models are added (may take a long time)") +parser.add_argument("-vv", "--verbose", action="store_true", + help="be more verbose about is happening while this script runs") -# expand to full path name -# process leading '~' or relative path +args = parser.parse_args() -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path and not args.nobuild: + parser.print_help() + sys.exit(HELP) -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) - - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program - else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file - - return None - -def geturl(url,fname): - success = False - - if which('curl') != None: - cmd = 'curl -L -o "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling curl failed with: %s" % e.output.decode('UTF-8')) - - if not success and which('wget') != None: - cmd = 'wget -O "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling wget failed with: %s" % e.output.decode('UTF-8')) - - if not success: - error("Failed to download source code with 'curl' or 'wget'") - return - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -thisdir = os.environ['PWD'] -version = "kim-api-v1.9.5" - -buildflag = False +buildflag = args.build +pathflag = args.path is not None +addflag = args.add is not None +addmodelname = args.add everythingflag = False -addflag = False -verboseflag = False -pathflag = False +if addflag and addmodelname == "everything": + everythingflag = True + buildflag = True +verboseflag = args.verbose -iarg = 0 -while iarg < len(args): - if args[iarg] == "-v": - if iarg+2 > len(args): error() - version = args[iarg+1] - iarg += 2 - elif args[iarg] == "-b": - buildflag = True - iarg += 1 - elif args[iarg] == "-n": - buildflag = False - iarg += 1 - elif args[iarg] == "-p": - if iarg+2 > len(args): error() - kimdir = fullpath(args[iarg+1]) - pathflag = True - buildflag = False - iarg += 2 - elif args[iarg] == "-a": - addflag = True - if iarg+2 > len(args): error() - addmodelname = args[iarg+1] - if addmodelname == "everything": - buildflag = True - everythingflag = True - addflag = False - iarg += 2 - elif args[iarg] == "-vv": - verboseflag = True - iarg += 1 - else: error() +if pathflag: + buildflag = False + kimdir = args.path + if not os.path.isdir(kimdir): + sys.exit("KIM API path %s does not exist" % kimdir) + kimdir = fullpath(kimdir) -thisdir = os.path.abspath(thisdir) url = "https://s3.openkim.org/kim-api/%s.txz" % version # set KIM API directory if pathflag: - if not os.path.isdir(kimdir): - print("\nkim-api is not installed at %s" % kimdir) - error() - # configure LAMMPS to use existing kim-api installation - with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile: - mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir) - mkfile.write(".DUMMY: print_dir\n\n") - mkfile.write("print_dir:\n") - mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") + with open("%s/kim-prefix.txt" % thisdir, 'w') as pffile: + pffile.write("%s" % kimdir) - print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir)) + print("Created %s/kim-prefix.txt\n using %s" % (thisdir,kimdir)) else: kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version) + if args.nobuild and not os.path.isdir(kimdir): + sys.exit("Cannot use -n/--nobuild without first building the KIM API with -b") # download KIM tarball, unpack, build KIM if buildflag: @@ -177,80 +106,72 @@ if buildflag: if os.path.isdir(kimdir): print("kim-api is already installed at %s.\nRemoving it for re-install" % kimdir) - cmd = 'rm -rf "%s"' % kimdir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + shutil.rmtree(kimdir) # configure LAMMPS to use kim-api to be installed - with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile: - mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir) - mkfile.write(".DUMMY: print_dir\n\n") - mkfile.write("print_dir:\n") - mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") + with open("%s/kim-prefix.txt" % thisdir, 'w') as pffile: + pffile.write("%s" % kimdir) - print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir)) + print("Created %s/kim-prefix.txt\n using %s" % (thisdir,kimdir)) # download entire kim-api tarball print("Downloading kim-api tarball ...") - geturl(url,"%s/%s.txz" % (thisdir,version)) + geturl(url, "%s/%s.txz" % (thisdir, version)) print("Unpacking kim-api tarball ...") - cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir,version,version) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'cd "%s"; rm -rf "%s"; tar -xJvf %s.txz' % (thisdir, version, version) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) # configure kim-api print("Configuring kim-api ...") - cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir,version,kimdir) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'cd "%s/%s" && mkdir build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX="%s" -DCMAKE_BUILD_TYPE=Release' % (thisdir,version,kimdir) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print(txt.decode("UTF-8")) # build kim-api print("Building kim-api ...") - cmd = 'cd "%s/%s"; make' % (thisdir,version) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print(txt.decode("UTF-8")) + cmd = 'cd "%s/%s/build" && make' % (thisdir, version) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + if verboseflag: + print(txt.decode("UTF-8")) # install kim-api print("Installing kim-api ...") - cmd = 'cd "%s/%s"; make install' % (thisdir,version) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print(txt.decode("UTF-8")) + cmd = 'cd "%s/%s/build" && make install' % (thisdir, version) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + if verboseflag: + print(txt.decode("UTF-8")) # remove source files - print("Building and installing example Models") - cmd = 'cd "%s/%s/examples"; make model-drivers-all-system' % (thisdir,version) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print (txt.decode("UTF-8")) - cmd = 'cd "%s/%s/examples"; make models-all-system' % (thisdir,version) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print (txt.decode("UTF-8")) - print("Removing kim-api source and build files ...") - cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir,version,version) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + cmd = 'cd "%s"; rm -rf %s; rm -rf %s.txz' % (thisdir, version, version) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) # add all OpenKIM models, if desired if everythingflag: print("Adding all OpenKIM models, this will take a while ...") - cmd = '%s/bin/kim-api-v1-collections-management install system OpenKIM' % (kimdir) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print(txt.decode("UTF-8")) + cmd = '%s/bin/kim-api-v2-collections-management install system OpenKIM' % (kimdir) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + if verboseflag: + print(txt.decode("UTF-8")) # add single OpenKIM model if addflag: - makefile_path = os.path.join(thisdir, "Makefile.KIM_DIR") - if os.path.isfile(makefile_path): - cmd = 'make --no-print-directory -f %s print_dir' % makefile_path + pf_path = os.path.join(thisdir, "kim-prefix.txt") + if os.path.isfile(pf_path): + cmd = 'cat %s' % pf_path kimdir = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) if not os.path.isdir(kimdir): - print("\nkim-api is not installed") - error() + sys.exit("\nkim-api is not installed") # download single model - cmd = '%s/bin/kim-api-v1-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print (txt.decode("UTF-8")) + cmd = '%s/bin/kim-api-v2-collections-management install system %s' % (kimdir.decode("UTF-8"), addmodelname) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + if verboseflag: + print(txt.decode("UTF-8")) diff --git a/lib/kim/Makefile.lammps b/lib/kim/Makefile.lammps index d73891d1e2..492b9ddfc6 100644 --- a/lib/kim/Makefile.lammps +++ b/lib/kim/Makefile.lammps @@ -5,8 +5,6 @@ # The KIM API package can be downloaded from https://openkim.org/kim-api # Follow the instructions in the INSTALL file to build and install the # KIM API. Add the openkim.org Models you are interested in using. -# Make sure the directory where the "kim-api-build-conifg" utility is -# located is on the PATH. # # As long as you have followed the KIM API build and install instructions, # there should not be any reason to change this file. @@ -16,17 +14,22 @@ # Settings that the LAMMPS build will import when this package is installed -include ../../lib/kim/Makefile.KIM_DIR +ifeq ($(strip $(shell pkg-config --version)),) + $(error 'pkg-config' not found, but is required to configure the KIM API) +endif +kim_PREFIX := $(shell cat ../../lib/kim/kim-prefix.txt 2> /dev/null) +kim_PREFIX := $(if $(kim_PREFIX),$(kim_PREFIX)/lib/pkgconfig,) +kim_PREFIX := $(if $(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX):$(shell printf -- "$${PKG_CONFIG_PATH}"),$(kim_PREFIX)) -ifeq ($(wildcard $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config),) - KIM_CONFIG_HELPER = kim-api-v1-build-config +# there is no usable libcurl installation +ifeq ($(shell curl-config --version 2> /dev/null),) +kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null) +kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null) else - KIM_CONFIG_HELPER = $(KIM_INSTALL_DIR)/bin/kim-api-v1-build-config -endif -ifeq ($(shell $(KIM_CONFIG_HELPER) --version 2> /dev/null),) - $(error $(KIM_CONFIG_HELPER) utility is not available. Something is wrong with your KIM API package setup) +kim_SYSINC := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --cflags libkim-api-v2 2> /dev/null) $(shell curl-config --cflags) -DLMP_KIM_CURL +kim_SYSLIB := $(shell export PKG_CONFIG_PATH="$(kim_PREFIX)"; pkg-config --libs libkim-api-v2 2> /dev/null) $(shell curl-config --libs) endif -kim_SYSINC = $(shell $(KIM_CONFIG_HELPER) --includes) -kim_SYSLIB = $(shell $(KIM_CONFIG_HELPER) --ldlibs) -kim_SYSPATH = $(shell $(KIM_CONFIG_HELPER) --ldflags) +ifeq ($(strip $(kim_SYSINC)),) + $(error 'pkg-config' could not find an installed KIM API library.) +endif diff --git a/lib/kim/README b/lib/kim/README index ce4ea1bdff..493758561d 100644 --- a/lib/kim/README +++ b/lib/kim/README @@ -3,10 +3,9 @@ is required to use the KIM package and its pair_style kim command in a LAMMPS input script. Information about the KIM project can be found at https://openkim.org. -The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and -James Sethna (Cornell U). Ryan Elliott is the main developer for the -KIM API and he also maintains the code that implements the pair_style -kim command. +The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn). +Ryan Elliott is the main developer for the KIM API and he also +maintains the code that implements the pair_style kim command. You can type "make lib-kim" from the src directory to see help on how to download and build this library via make commands, or you can @@ -14,6 +13,12 @@ do the same thing by typing "python Install.py" from within this directory, or you can do it manually by following the instructions below. +As of KIM API version 2, the KIM package also provides a LAMMPS command +to perform queries through the OpenKIM web API. This feature requires +that the CURL library (libcurl) development package and its configuration +query tool, curl-config, are installed. The provided Makefile.lammps +is set up to automatically detect this. + ----------------- Instructions: @@ -21,33 +26,34 @@ Instructions: 1. Configure lammps for use with the kim-api library installed in this directory # replace X.Y.Z as appropriate here and below -$ printf "KIM_INSTALL_DIR=${PWD}/installed-kim-api-vX.Y.Z\n" > ./Makefile.KIM_DIR +$ printf "${PWD}/installed-kim-api-vX-X.Y.Z" > ./kim-prefix.txt 2. Download and unpack the kim-api -$ wget http://s3.openkim.org/kim-api/kim-api-vX.Y.Z.txz -$ tar zxvf kim-api-vX.Y.Z.txz +$ wget http://s3.openkim.org/kim-api/kim-api-vX-X.Y.Z.txz +$ tar zxvf kim-api-vX-X.Y.Z.txz # configure the kim-api -$ cd kim-api-vX.Y.Z -$ ./configure --prefix=${PWD}/../installed-kim-api-vX.Y.Z +$ cd kim-api-vX-X.Y.Z +$ mkdir build && cd build +$ cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-vX-X.Y.Z 3. Build and install the kim-api and model $ make $ make install -$ cd .. 4. Remove source and build files -$ rm -rf kim-api-vX.Y.Z -$ rm -rf kim-api-vX.Y.Z.txz +$ cd ../../ +$ rm -rf kim-api-vX-X.Y.Z +$ rm -rf kim-api-vX-X.Y.Z.txz 5. To add items do the following (replace the kim item name with your desired value) -$ source ${PWD}/kim-api-vX.Y.Z/bin/kim-api-v1-activate -$ kim-api-v1-collections-management install system Pair_Johnson_Fe__MO_857282754307_002 +$ source ${PWD}/kim-api-vX-X.Y.Z/bin/kim-api-vX-activate +$ kim-api-vX-collections-management install system Pair_Johnson_Fe__MO_857282754307_002 ----------------- @@ -59,6 +65,6 @@ $ cd lammpos/src $ make yes-kim $ make g++ (or whatever target you wish) -Note that the Makefile.lammps and Makefile.KIM_DIR files in this directory -are required to allow the LAMMPS build to find the necessary KIM files. -You should not normally need to edit these files. +Note that the Makefile.lammps file in this directory is required to +allow the LAMMPS build to find the necessary KIM files. You should +not normally need to edit these files. diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index 145cc62706..9d503663ae 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,89 @@ # Change Log +## [2.8.00](https://github.com/kokkos/kokkos/tree/2.8.00) (2019-02-05) +[Full Changelog](https://github.com/kokkos/kokkos/compare/2.7.24...2.8.00) + +**Implemented enhancements:** + +- Capability, Tests: C++14 support and testing [\#1914](https://github.com/kokkos/kokkos/issues/1914) +- Capability: Add environment variables for all command line arguments [\#1798](https://github.com/kokkos/kokkos/issues/1798) +- Capability: --kokkos-ndevices not working for Slurm [\#1920](https://github.com/kokkos/kokkos/issues/1920) +- View: Undefined behavior when deep copying from and to an empty unmanaged view [\#1967](https://github.com/kokkos/kokkos/issues/1967) +- BuildSystem: nvcc\_wrapper should stop immediately if nvcc is not in PATH [\#1861](https://github.com/kokkos/kokkos/issues/1861) + +**Fixed bugs:** + +- Cuda: Fix Volta Issues 1 Non-deterministic behavior on Volta, runs fine on Pascal [\#1949](https://github.com/kokkos/kokkos/issues/1949) +- Cuda: Fix Volta Issues 2 CUDA Team Scan gives wrong values on Volta with -G compile flag [\#1942](https://github.com/kokkos/kokkos/issues/1942) +- Cuda: illegal warp sync in parallel\_reduce by functor on Turing 75 [\#1958](https://github.com/kokkos/kokkos/issues/1958) +- Threads: Pthreads backend does not handle RangePolicy with offset correctly [\#1976](https://github.com/kokkos/kokkos/issues/1976) +- Atomics: atomic\_fetch\_oper has no case for Kokkos::complex\ or other 16-byte types [\#1951](https://github.com/kokkos/kokkos/issues/1951) +- MDRangePolicy: Fix zero-length range [\#1948](https://github.com/kokkos/kokkos/issues/1948) +- TeamThreadRange: TeamThreadRange MaxLoc reduce doesnt compile [\#1909](https://github.com/kokkos/kokkos/issues/1909) + +## [2.7.24](https://github.com/kokkos/kokkos/tree/2.7.24) (2018-11-04) +[Full Changelog](https://github.com/kokkos/kokkos/compare/2.7.00...2.7.24) + +**Implemented enhancements:** + +- DualView: Add non-templated functions for sync, need\_sync, view, modify [\#1858](https://github.com/kokkos/kokkos/issues/1858) +- DualView: Avoid needlessly allocates and initializes modify\_host and modify\_device flag views [\#1831](https://github.com/kokkos/kokkos/issues/1831) +- DualView: Incorrect deduction of "not device type" [\#1659](https://github.com/kokkos/kokkos/issues/1659) +- BuildSystem: Add KOKKOS\_ENABLE\_CXX14 and KOKKOS\_ENABLE\_CXX17 [\#1602](https://github.com/kokkos/kokkos/issues/1602) +- BuildSystem: Installed kokkos\_generated\_settings.cmake contains build directories instead of install directories [\#1838](https://github.com/kokkos/kokkos/issues/1838) +- BuildSystem: KOKKOS\_ARCH: add ticks to printout of improper arch setting [\#1649](https://github.com/kokkos/kokkos/issues/1649) +- BuildSystem: Make core/src/Makefile for Cuda use needed nvcc\_wrapper [\#1296](https://github.com/kokkos/kokkos/issues/1296) +- Build: Support PGI as host compiler for NVCC [\#1828](https://github.com/kokkos/kokkos/issues/1828) +- Build: Many Warnings Fixed e.g.[\#1786](https://github.com/kokkos/kokkos/issues/1786) +- Capability: OffsetView with non-zero begin index [\#567](https://github.com/kokkos/kokkos/issues/567) +- Capability: Reductions into device side view [\#1788](https://github.com/kokkos/kokkos/issues/1788) +- Capability: Add max\_size to Kokkos::Array [\#1760](https://github.com/kokkos/kokkos/issues/1760) +- Capability: View Assignment: LayoutStride -\> LayoutLeft and LayoutStride -\> LayoutRight [\#1594](https://github.com/kokkos/kokkos/issues/1594) +- Capability: Atomic function allow implicit conversion of update argument [\#1571](https://github.com/kokkos/kokkos/issues/1571) +- Capability: Add team\_size\_max with tagged functors [\#663](https://github.com/kokkos/kokkos/issues/663) +- Capability: Fix allignment of views from Kokkos\_ScratchSpace should use different alignment [\#1700](https://github.com/kokkos/kokkos/issues/1700) +- Capabilitiy: create\_mirror\_view\_and\_copy for DynRankView [\#1651](https://github.com/kokkos/kokkos/issues/1651) +- Capability: DeepCopy HBWSpace / HostSpace [\#548](https://github.com/kokkos/kokkos/issues/548) +- ROCm: support team vector scan [\#1645](https://github.com/kokkos/kokkos/issues/1645) +- ROCm: Merge from rocm-hackathon2 [\#1636](https://github.com/kokkos/kokkos/issues/1636) +- ROCm: Add ParallelScanWithTotal [\#1611](https://github.com/kokkos/kokkos/issues/1611) +- ROCm: Implement MDRange in ROCm [\#1314](https://github.com/kokkos/kokkos/issues/1314) +- ROCm: Implement Reducers for Nested Parallelism Levels [\#963](https://github.com/kokkos/kokkos/issues/963) +- ROCm: Add asynchronous deep copy [\#959](https://github.com/kokkos/kokkos/issues/959) +- Tests: Memory pool test seems to allocate 8GB [\#1830](https://github.com/kokkos/kokkos/issues/1830) +- Tests: Add unit\_test for team\_broadcast [\#734](https://github.com/kokkos/kokkos/issues/734) + +**Fixed bugs:** + +- BuildSystem: Makefile.kokkos gets gcc-toolchain wrong if gcc is cached [\#1841](https://github.com/kokkos/kokkos/issues/1841) +- BuildSystem: kokkos\_generated\_settings.cmake placement is inconsistent [\#1771](https://github.com/kokkos/kokkos/issues/1771) +- BuildSystem: Invalid escape sequence \. in kokkos\_functions.cmake [\#1661](https://github.com/kokkos/kokkos/issues/1661) +- BuildSystem: Problem in Kokkos generated cmake file [\#1770](https://github.com/kokkos/kokkos/issues/1770) +- BuildSystem: invalid file names on windows [\#1671](https://github.com/kokkos/kokkos/issues/1671) +- Tests: reducers min/max\_loc test fails randomly due to multiple min values and thus multiple valid locations [\#1681](https://github.com/kokkos/kokkos/issues/1681) +- Tests: cuda.scatterview unit test causes "Bus error" when force\_uvm and enable\_lambda are enabled [\#1852](https://github.com/kokkos/kokkos/issues/1852) +- Tests: cuda.cxx11 unit test fails when force\_uvm and enable\_lambda are enabled [\#1850](https://github.com/kokkos/kokkos/issues/1850) +- Tests: threads.reduce\_device\_view\_range\_policy failing with Cuda/8.0.44 and RDC [\#1836](https://github.com/kokkos/kokkos/issues/1836) +- Build: compile error when compiling Kokkos with hwloc 2.0.1 \(on OSX 10.12.6, with g++ 7.2.0\) [\#1506](https://github.com/kokkos/kokkos/issues/1506) +- Build: dual\_view.view broken with UVM [\#1834](https://github.com/kokkos/kokkos/issues/1834) +- Build: White cuda/9.2 + gcc/7.2 warnings triggering errors [\#1833](https://github.com/kokkos/kokkos/issues/1833) +- Build: warning: enum constant in boolean context [\#1813](https://github.com/kokkos/kokkos/issues/1813) +- Capability: Fix overly conservative max\_team\_size thingy [\#1808](https://github.com/kokkos/kokkos/issues/1808) +- DynRankView: Ctors taking ViewAllocateWithoutInitializing broken [\#1783](https://github.com/kokkos/kokkos/issues/1783) +- Cuda: Apollo cuda.team\_broadcast test fail with clang-6.0 [\#1762](https://github.com/kokkos/kokkos/issues/1762) +- Cuda: Clang spurious test failure in impl\_view\_accessible [\#1753](https://github.com/kokkos/kokkos/issues/1753) +- Cuda: Kokkos::complex\ atomic deadlocks with Clang 6 Cuda build with -O0 [\#1752](https://github.com/kokkos/kokkos/issues/1752) +- Cuda: LayoutStride Test fails for UVM as default memory space [\#1688](https://github.com/kokkos/kokkos/issues/1688) +- Cuda: Scan wrong values on Volta [\#1676](https://github.com/kokkos/kokkos/issues/1676) +- Cuda: Kokkos::deep\_copy error with CudaUVM and Kokkos::Serial spaces [\#1652](https://github.com/kokkos/kokkos/issues/1652) +- Cuda: cudaErrorInvalidConfiguration with debug build [\#1647](https://github.com/kokkos/kokkos/issues/1647) +- Cuda: parallel\_for with TeamPolicy::team\_size\_recommended with launch bounds not working -- reported by Daniel Holladay [\#1283](https://github.com/kokkos/kokkos/issues/1283) +- Cuda: Using KOKKOS\_CLASS\_LAMBDA in a class with Kokkos::Random\_XorShift64\_Pool member data [\#1696](https://github.com/kokkos/kokkos/issues/1696) +- Long Build Times on Darwin [\#1721](https://github.com/kokkos/kokkos/issues/1721) +- Capability: Typo in Kokkos\_Sort.hpp - BinOp3D - wrong comparison [\#1720](https://github.com/kokkos/kokkos/issues/1720) +- Buffer overflow in SharedAllocationRecord in Kokkos\_HostSpace.cpp [\#1673](https://github.com/kokkos/kokkos/issues/1673) +- Serial unit test failure [\#1632](https://github.com/kokkos/kokkos/issues/1632) + ## [2.7.00](https://github.com/kokkos/kokkos/tree/2.7.00) (2018-05-24) [Full Changelog](https://github.com/kokkos/kokkos/compare/2.6.00...2.7.00) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 9e5308f1c3..236f523aec 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -11,7 +11,7 @@ IF(NOT KOKKOS_HAS_TRILINOS) # Define Project Name if this is a standalone build IF(NOT DEFINED ${PROJECT_NAME}) - project(Kokkos CXX) + project(Kokkos CXX) ENDIF() # Basic initialization (Used in KOKKOS_SETTINGS) @@ -22,7 +22,7 @@ IF(NOT KOKKOS_HAS_TRILINOS) include(${KOKKOS_SRC_PATH}/cmake/kokkos_functions.cmake) set_kokkos_cxx_compiler() set_kokkos_cxx_standard() - + #------------ GET OPTIONS AND KOKKOS_SETTINGS -------------------------------- # Add Kokkos' modules to CMake's module path. set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${Kokkos_SOURCE_DIR}/cmake/Modules/") @@ -34,7 +34,7 @@ IF(NOT KOKKOS_HAS_TRILINOS) #------------ GENERATE HEADER AND SOURCE FILES ------------------------------- execute_process( - COMMAND ${KOKKOS_SETTINGS} make -f ${KOKKOS_SRC_PATH}/cmake/Makefile.generate_cmake_settings CXX=${CMAKE_CXX_COMPILER} generate_build_settings + COMMAND ${KOKKOS_SETTINGS} make -f ${KOKKOS_SRC_PATH}/cmake/Makefile.generate_cmake_settings CXX=${CMAKE_CXX_COMPILER} PREFIX=${CMAKE_INSTALL_PREFIX} generate_build_settings WORKING_DIRECTORY "${Kokkos_BINARY_DIR}" OUTPUT_FILE ${Kokkos_BINARY_DIR}/core_src_make.out RESULT_VARIABLE GEN_SETTINGS_RESULT @@ -45,6 +45,7 @@ IF(NOT KOKKOS_HAS_TRILINOS) endif() include(${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake) install(FILES ${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake DESTINATION lib/cmake/Kokkos) + install(FILES ${Kokkos_BINARY_DIR}/kokkos_generated_settings.cmake DESTINATION ${CMAKE_INSTALL_PREFIX}) string(REPLACE " " ";" KOKKOS_TPL_INCLUDE_DIRS "${KOKKOS_GMAKE_TPL_INCLUDE_DIRS}") string(REPLACE " " ";" KOKKOS_TPL_LIBRARY_DIRS "${KOKKOS_GMAKE_TPL_LIBRARY_DIRS}") string(REPLACE " " ";" KOKKOS_TPL_LIBRARY_NAMES "${KOKKOS_GMAKE_TPL_LIBRARY_NAMES}") diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index 52cd3969f9..a90e86b9f8 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -11,22 +11,23 @@ KOKKOS_DEVICES ?= "OpenMP" #KOKKOS_DEVICES ?= "Pthreads" # Options: # Intel: KNC,KNL,SNB,HSW,BDW,SKX -# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72 +# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75 # ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2 # IBM: BGQ,Power7,Power8,Power9 # AMD-GPUS: Kaveri,Carrizo,Fiji,Vega -# AMD-CPUS: AMDAVX,Ryzen,Epyc +# AMD-CPUS: AMDAVX,Ryzen,EPYC KOKKOS_ARCH ?= "" # Options: yes,no KOKKOS_DEBUG ?= "no" # Options: hwloc,librt,experimental_memkind KOKKOS_USE_TPLS ?= "" -# Options: c++11,c++1z +# Options: c++11,c++14,c++1y,c++17,c++1z,c++2a KOKKOS_CXX_STANDARD ?= "c++11" # Options: aggressive_vectorization,disable_profiling,disable_deprecated_code,enable_large_mem_tests KOKKOS_OPTIONS ?= "" # Option for setting ETI path KOKKOS_ETI_PATH ?= ${KOKKOS_PATH}/core/src/eti +KOKKOS_CMAKE ?= "no" # Default settings specific options. # Options: force_uvm,use_ldg,rdc,enable_lambda @@ -41,7 +42,11 @@ kokkos_has_string=$(if $(findstring $2,$1),1,0) # Check for general settings. KOKKOS_INTERNAL_ENABLE_DEBUG := $(call kokkos_has_string,$(KOKKOS_DEBUG),yes) KOKKOS_INTERNAL_ENABLE_CXX11 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++11) +KOKKOS_INTERNAL_ENABLE_CXX14 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++14) +KOKKOS_INTERNAL_ENABLE_CXX1Y := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1y) +KOKKOS_INTERNAL_ENABLE_CXX17 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++17) KOKKOS_INTERNAL_ENABLE_CXX1Z := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1z) +KOKKOS_INTERNAL_ENABLE_CXX2A := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++2a) # Check for external libraries. KOKKOS_INTERNAL_USE_HWLOC := $(call kokkos_has_string,$(KOKKOS_USE_TPLS),hwloc) @@ -110,6 +115,18 @@ KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VE KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),apple-darwin) KOKKOS_INTERNAL_COMPILER_HCC := $(call kokkos_has_string,$(KOKKOS_CXX_VERSION),HCC) +# Check Host Compiler if using NVCC through nvcc_wrapper +ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER := $(strip $(shell echo $(CXX) | grep nvcc_wrapper | wc -l)) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC_WRAPPER), 1) + + KOKKOS_CXX_HOST_VERSION := $(strip $(shell $(CXX) $(CXXFLAGS) --host-version 2>&1)) + KOKKOS_INTERNAL_COMPILER_PGI := $(call kokkos_has_string,$(KOKKOS_CXX_HOST_VERSION),PGI) + KOKKOS_INTERNAL_COMPILER_INTEL := $(call kokkos_has_string,$(KOKKOS_CXX_HOST_VERSION),Intel Corporation) + KOKKOS_INTERNAL_COMPILER_CLANG := $(call kokkos_has_string,$(KOKKOS_CXX_HOST_VERSION),clang) + endif +endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 2) KOKKOS_INTERNAL_COMPILER_CLANG = 1 endif @@ -202,18 +219,34 @@ endif # Set C++11 flags. ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) KOKKOS_INTERNAL_CXX11_FLAG := --c++11 + KOKKOS_INTERNAL_CXX14_FLAG := --c++14 + #KOKKOS_INTERNAL_CXX17_FLAG := --c++17 else ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) KOKKOS_INTERNAL_CXX11_FLAG := -std=c++11 + KOKKOS_INTERNAL_CXX14_FLAG := -std=c++14 + KOKKOS_INTERNAL_CXX1Y_FLAG := -std=c++1y + #KOKKOS_INTERNAL_CXX17_FLAG := -std=c++17 + #KOKKOS_INTERNAL_CXX1Z_FLAG := -std=c++1Z + #KOKKOS_INTERNAL_CXX2A_FLAG := -std=c++2a else ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) KOKKOS_INTERNAL_CXX11_FLAG := -hstd=c++11 + KOKKOS_INTERNAL_CXX14_FLAG := -hstd=c++14 + #KOKKOS_INTERNAL_CXX1Y_FLAG := -hstd=c++1y + #KOKKOS_INTERNAL_CXX17_FLAG := -hstd=c++17 + #KOKKOS_INTERNAL_CXX1Z_FLAG := -hstd=c++1z + #KOKKOS_INTERNAL_CXX2A_FLAG := -hstd=c++2a else ifeq ($(KOKKOS_INTERNAL_COMPILER_HCC), 1) KOKKOS_INTERNAL_CXX11_FLAG := else KOKKOS_INTERNAL_CXX11_FLAG := --std=c++11 + KOKKOS_INTERNAL_CXX14_FLAG := --std=c++14 + KOKKOS_INTERNAL_CXX1Y_FLAG := --std=c++1y + KOKKOS_INTERNAL_CXX17_FLAG := --std=c++17 KOKKOS_INTERNAL_CXX1Z_FLAG := --std=c++1z + KOKKOS_INTERNAL_CXX2A_FLAG := --std=c++2a endif endif endif @@ -243,6 +276,7 @@ KOKKOS_INTERNAL_USE_ARCH_PASCAL61 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pas KOKKOS_INTERNAL_USE_ARCH_PASCAL60 := $(call kokkos_has_string,$(KOKKOS_ARCH),Pascal60) KOKKOS_INTERNAL_USE_ARCH_VOLTA70 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta70) KOKKOS_INTERNAL_USE_ARCH_VOLTA72 := $(call kokkos_has_string,$(KOKKOS_ARCH),Volta72) +KOKKOS_INTERNAL_USE_ARCH_TURING75 := $(call kokkos_has_string,$(KOKKOS_ARCH),Turing75) KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLER30) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER32) \ + $(KOKKOS_INTERNAL_USE_ARCH_KEPLER35) \ @@ -251,6 +285,7 @@ KOKKOS_INTERNAL_USE_ARCH_NVIDIA := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KEPLE + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \ + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \ + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \ + + $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53)) @@ -267,6 +302,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) + $(KOKKOS_INTERNAL_USE_ARCH_PASCAL60) \ + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA70) \ + $(KOKKOS_INTERNAL_USE_ARCH_VOLTA72) \ + + $(KOKKOS_INTERNAL_USE_ARCH_TURING75) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52) \ + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53)) @@ -298,7 +334,7 @@ KOKKOS_INTERNAL_USE_ARCH_IBM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ # AMD based. KOKKOS_INTERNAL_USE_ARCH_AMDAVX := $(call kokkos_has_string,$(KOKKOS_ARCH),AMDAVX) KOKKOS_INTERNAL_USE_ARCH_RYZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Ryzen) -KOKKOS_INTERNAL_USE_ARCH_EPYC := $(call kokkos_has_string,$(KOKKOS_ARCH),Epyc) +KOKKOS_INTERNAL_USE_ARCH_EPYC := $(call kokkos_has_string,$(KOKKOS_ARCH),EPYC) KOKKOS_INTERNAL_USE_ARCH_KAVERI := $(call kokkos_has_string,$(KOKKOS_ARCH),Kaveri) KOKKOS_INTERNAL_USE_ARCH_CARRIZO := $(call kokkos_has_string,$(KOKKOS_ARCH),Carrizo) KOKKOS_INTERNAL_USE_ARCH_FIJI := $(call kokkos_has_string,$(KOKKOS_ARCH),Fiji) @@ -308,12 +344,12 @@ KOKKOS_INTERNAL_USE_ARCH_GFX901 := $(call kokkos_has_string,$(KOKKOS_ARCH),gfx90 # Any AVX? KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM)) KOKKOS_INTERNAL_USE_ARCH_AVX := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)) -KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW)) +KOKKOS_INTERNAL_USE_ARCH_AVX2 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_EPYC)) KOKKOS_INTERNAL_USE_ARCH_AVX512MIC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNL)) KOKKOS_INTERNAL_USE_ARCH_AVX512XEON := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_SKX)) # Decide what ISA level we are able to support. -KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX)) +KOKKOS_INTERNAL_USE_ISA_X86_64 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM) + $(KOKKOS_INTERNAL_USE_ARCH_SNB) + $(KOKKOS_INTERNAL_USE_ARCH_HSW) + $(KOKKOS_INTERNAL_USE_ARCH_BDW) + $(KOKKOS_INTERNAL_USE_ARCH_KNL) + $(KOKKOS_INTERNAL_USE_ARCH_SKX) + $(KOKKOS_INTERNAL_USE_ARCH_EPYC)) KOKKOS_INTERNAL_USE_ISA_KNC := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_KNC)) KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER8) + $(KOKKOS_INTERNAL_USE_ARCH_POWER9)) KOKKOS_INTERNAL_USE_ISA_POWERPCBE := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_POWER7)) @@ -336,7 +372,9 @@ endif #CPPFLAGS is now unused KOKKOS_CPPFLAGS = -KOKKOS_CXXFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src -I$(KOKKOS_ETI_PATH) +ifneq ($(KOKKOS_CMAKE), yes) + KOKKOS_CXXFLAGS = -I./ -I$(KOKKOS_PATH)/core/src -I$(KOKKOS_PATH)/containers/src -I$(KOKKOS_PATH)/algorithms/src -I$(KOKKOS_ETI_PATH) +endif KOKKOS_TPL_INCLUDE_DIRS = KOKKOS_TPL_LIBRARY_DIRS = KOKKOS_TPL_LIBRARY_NAMES = @@ -347,9 +385,11 @@ endif KOKKOS_LIBS = -ldl KOKKOS_TPL_LIBRARY_NAMES += dl -KOKKOS_LDFLAGS = -L$(shell pwd) -# CXXLDFLAGS is used together with CXXFLAGS in a combined compile/link command -KOKKOS_CXXLDFLAGS = -L$(shell pwd) +ifneq ($(KOKKOS_CMAKE), yes) + KOKKOS_LDFLAGS = -L$(shell pwd) + # CXXLDFLAGS is used together with CXXFLAGS in a combined compile/link command + KOKKOS_CXXLDFLAGS = -L$(shell pwd) +endif KOKKOS_LINK_FLAGS = KOKKOS_SRC = KOKKOS_HEADERS = @@ -377,10 +417,12 @@ tmp := $(call kokkos_append_header,"/* Execution Spaces */") ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CUDA") + tmp := $(call kokkos_append_header,"\#define KOKKOS_COMPILER_CUDA_VERSION $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION)") endif ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) tmp := $(call kokkos_append_header,'\#define KOKKOS_ENABLE_ROCM') + tmp := $(call kokkos_append_header,'\#define KOKKOS_IMPL_ROCM_CLANG_WORKAROUND 1') endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) @@ -438,11 +480,25 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX11), 1) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG) tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX11") endif - +ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1) + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX14") +endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Y), 1) + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Y_FLAG) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX14") +endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX17), 1) + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX17_FLAG) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX17") +endif ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX1Z_FLAG) - tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX11") - tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX1Z") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX17") +endif +ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX2A), 1) + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX2A_FLAG) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ENABLE_CXX20") endif ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1) @@ -465,7 +521,9 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) ifneq ($(HWLOC_PATH),) - KOKKOS_CXXFLAGS += -I$(HWLOC_PATH)/include + ifneq ($(KOKKOS_CMAKE), yes) + KOKKOS_CXXFLAGS += -I$(HWLOC_PATH)/include + endif KOKKOS_LDFLAGS += -L$(HWLOC_PATH)/lib KOKKOS_CXXLDFLAGS += -L$(HWLOC_PATH)/lib KOKKOS_TPL_INCLUDE_DIRS += $(HWLOC_PATH)/include @@ -484,7 +542,9 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) ifneq ($(MEMKIND_PATH),) - KOKKOS_CXXFLAGS += -I$(MEMKIND_PATH)/include + ifneq ($(KOKKOS_CMAKE), yes) + KOKKOS_CXXFLAGS += -I$(MEMKIND_PATH)/include + endif KOKKOS_LDFLAGS += -L$(MEMKIND_PATH)/lib KOKKOS_CXXLDFLAGS += -L$(MEMKIND_PATH)/lib KOKKOS_TPL_INCLUDE_DIRS += $(MEMKIND_PATH)/include @@ -601,6 +661,19 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1) endif endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_EPYC), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AMD_EPYC") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_AMD_AVX2") + + ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) + KOKKOS_CXXFLAGS += -mavx2 + KOKKOS_LDFLAGS += -mavx2 + else + KOKKOS_CXXFLAGS += -march=znver1 -mtune=znver1 + KOKKOS_LDFLAGS += -march=znver1 -mtune=znver1 + endif +endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX), 1) tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV80") tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_ARMV8_THUNDERX") @@ -893,6 +966,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_VOLTA72") KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_72 endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_TURING75), 1) + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_TURING") + tmp := $(call kokkos_append_header,"\#define KOKKOS_ARCH_TURING75") + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_75 + endif ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) @@ -977,7 +1055,9 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_ETI), 1) endif KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp) ifneq ($(CUDA_PATH),) - KOKKOS_CXXFLAGS += -I$(CUDA_PATH)/include + ifneq ($(KOKKOS_CMAKE), yes) + KOKKOS_CXXFLAGS += -I$(CUDA_PATH)/include + endif KOKKOS_LDFLAGS += -L$(CUDA_PATH)/lib64 KOKKOS_CXXLDFLAGS += -L$(CUDA_PATH)/lib64 KOKKOS_TPL_INCLUDE_DIRS += $(CUDA_PATH)/include @@ -1032,7 +1112,9 @@ ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Qthreads/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Qthreads/*.hpp) ifneq ($(QTHREADS_PATH),) - KOKKOS_CXXFLAGS += -I$(QTHREADS_PATH)/include + ifneq ($(KOKKOS_CMAKE), yes) + KOKKOS_CXXFLAGS += -I$(QTHREADS_PATH)/include + endif KOKKOS_LDFLAGS += -L$(QTHREADS_PATH)/lib KOKKOS_CXXLDFLAGS += -L$(QTHREADS_PATH)/lib KOKKOS_TPL_INCLUDE_DIRS += $(QTHREADS_PATH)/include diff --git a/lib/kokkos/README b/lib/kokkos/README index 31d134bf0a..cb6ceb5581 100644 --- a/lib/kokkos/README +++ b/lib/kokkos/README @@ -52,44 +52,49 @@ For specifics see the LICENSE file contained in the repository or distribution. * GCC 4.8.4 * GCC 4.9.3 * GCC 5.1.0 - * GCC 5.3.0 + * GCC 5.5.0 * GCC 6.1.0 + * GCC 7.2.0 + * GCC 7.3.0 + * GCC 8.1.0 * Intel 15.0.2 * Intel 16.0.1 - * Intel 17.1.043 + * Intel 17.0.1 * Intel 17.4.196 - * Intel 18.0.128 + * Intel 18.2.128 * Clang 3.6.1 * Clang 3.7.1 * Clang 3.8.1 * Clang 3.9.0 * Clang 4.0.0 - * Clang 4.0.0 for CUDA (CUDA Toolkit 8.0.44) - * Clang 6.0.0 for CUDA (CUDA Toolkit 9.1) - * PGI 17.10 - * NVCC 7.0 for CUDA (with gcc 4.8.4) + * Clang 6.0.0 for CUDA (CUDA Toolkit 9.0) + * Clang 7.0.0 for CUDA (CUDA Toolkit 9.1) + * PGI 18.7 * NVCC 7.5 for CUDA (with gcc 4.8.4) * NVCC 8.0.44 for CUDA (with gcc 5.3.0) * NVCC 9.1 for CUDA (with gcc 6.1.0) + * NVCC 9.2 for CUDA (with gcc 7.2.0) + * NVCC 10.0 for CUDA (with gcc 7.4.0) ### Primary tested compilers on Power 8 are: - * GCC 5.4.0 (OpenMP,Serial) - * IBM XL 13.1.6 (OpenMP, Serial) - * NVCC 8.0.44 for CUDA (with gcc 5.4.0) - * NVCC 9.0.103 for CUDA (with gcc 6.3.0 and XL 13.1.6) + * GCC 6.4.0 (OpenMP,Serial) + * GCC 7.2.0 (OpenMP,Serial) + * IBM XL 16.1.0 (OpenMP, Serial) + * NVCC 9.2.88 for CUDA (with gcc 7.2.0 and XL 16.1.0) ### Primary tested compilers on Intel KNL are: - * GCC 6.2.0 * Intel 16.4.258 (with gcc 4.7.2) * Intel 17.2.174 (with gcc 4.9.3) - * Intel 18.0.128 (with gcc 4.9.3) + * Intel 18.2.199 (with gcc 4.9.3) -### Primary tested compilers on ARM - * GCC 6.1.0 +### Primary tested compilers on ARM (Cavium ThunderX2) + * GCC 7.2.0 + * ARM/Clang 18.4.0 ### Other compilers working: * X86: - Cygwin 2.1.0 64bit with gcc 4.9.3 + - GCC 8.1.0 (not warning free) ### Known non-working combinations: * Power8: @@ -106,7 +111,7 @@ GCC: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wignored-qualifiers -Wempty-body -Wclobbered -Wuninitialized Intel: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized Clang: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized -NVCC: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized +NVCC: -Wall -Wshadow -pedantic -Werror -Wsign-compare -Wtype-limits -Wuninitialized Other compilers are tested occasionally, in particular when pushing from develop to master branch, without -Werror and only for a select set of backends. diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index 5f1d88bfff..e14471a48a 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -697,6 +697,7 @@ namespace Kokkos { typedef Random_XorShift64 generator_type; typedef DeviceType device_type; + KOKKOS_INLINE_FUNCTION Random_XorShift64_Pool() { num_states_ = 0; } @@ -709,12 +710,14 @@ namespace Kokkos { #endif } + KOKKOS_INLINE_FUNCTION Random_XorShift64_Pool(const Random_XorShift64_Pool& src): locks_(src.locks_), state_(src.state_), num_states_(src.num_states_) {} + KOKKOS_INLINE_FUNCTION Random_XorShift64_Pool operator = (const Random_XorShift64_Pool& src) { locks_ = src.locks_; state_ = src.state_; @@ -958,6 +961,7 @@ namespace Kokkos { typedef DeviceType device_type; + KOKKOS_INLINE_FUNCTION Random_XorShift1024_Pool() { num_states_ = 0; } @@ -972,6 +976,7 @@ namespace Kokkos { #endif } + KOKKOS_INLINE_FUNCTION Random_XorShift1024_Pool(const Random_XorShift1024_Pool& src): locks_(src.locks_), state_(src.state_), @@ -979,6 +984,7 @@ namespace Kokkos { num_states_(src.num_states_) {} + KOKKOS_INLINE_FUNCTION Random_XorShift1024_Pool operator = (const Random_XorShift1024_Pool& src) { locks_ = src.locks_; state_ = src.state_; diff --git a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp index c952b1e541..8bdd876723 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Sort.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Sort.hpp @@ -246,8 +246,8 @@ public: { bin_count_atomic = Kokkos::View("Kokkos::SortImpl::BinSortFunctor::bin_count",bin_op.max_bins()); bin_count_const = bin_count_atomic; - bin_offsets = offset_type("Kokkos::SortImpl::BinSortFunctor::bin_offsets",bin_op.max_bins()); - sort_order = offset_type("PermutationVector",range_end-range_begin); + bin_offsets = offset_type(ViewAllocateWithoutInitializing("Kokkos::SortImpl::BinSortFunctor::bin_offsets"),bin_op.max_bins()); + sort_order = offset_type(ViewAllocateWithoutInitializing("Kokkos::SortImpl::BinSortFunctor::sort_order"),range_end-range_begin); } BinSort( const_key_view_type keys_ @@ -290,7 +290,7 @@ public: #ifdef KOKKOS_ENABLE_DEPRECATED_CODE scratch_view_type - sorted_values("Scratch", + sorted_values(ViewAllocateWithoutInitializing("Kokkos::SortImpl::BinSortFunctor::sorted_values"), len, values.extent(1), values.extent(2), @@ -301,7 +301,7 @@ public: values.extent(7)); #else scratch_view_type - sorted_values("Scratch", + sorted_values(ViewAllocateWithoutInitializing("Kokkos::SortImpl::BinSortFunctor::sorted_values"), values.rank_dynamic > 0 ? len : KOKKOS_IMPL_CTOR_DEFAULT_ARG, values.rank_dynamic > 1 ? values.extent(1) : KOKKOS_IMPL_CTOR_DEFAULT_ARG , values.rank_dynamic > 2 ? values.extent(2) : KOKKOS_IMPL_CTOR_DEFAULT_ARG, @@ -483,7 +483,7 @@ struct BinOp3D { if (keys(i1,0)>keys(i2,0)) return true; else if (keys(i1,0)==keys(i2,0)) { if (keys(i1,1)>keys(i2,1)) return true; - else if (keys(i1,1)==keys(i2,2)) { + else if (keys(i1,1)==keys(i2,1)) { if (keys(i1,2)>keys(i2,2)) return true; } } diff --git a/lib/kokkos/benchmarks/gups/Makefile b/lib/kokkos/benchmarks/gups/Makefile new file mode 100644 index 0000000000..7176111664 --- /dev/null +++ b/lib/kokkos/benchmarks/gups/Makefile @@ -0,0 +1,41 @@ +#Set your Kokkos path to something appropriate +KOKKOS_PATH = ${HOME}/git/kokkos-github-repo +KOKKOS_DEVICES = "Cuda" +KOKKOS_ARCH = "Pascal60" +KOKKOS_CUDA_OPTIONS = enable_lambda +#KOKKOS_DEVICES = "OpenMP" +#KOKKOS_ARCH = "Power8" + +SRC = gups-kokkos.cc + +default: build + echo "Start Build" + +CXXFLAGS = -O3 +CXX = ${HOME}/git/kokkos-github-repo/bin/nvcc_wrapper +#CXX = g++ + +LINK = ${CXX} + +LINKFLAGS = +EXE = gups-kokkos + +DEPFLAGS = -M + +OBJ = $(SRC:.cc=.o) +LIB = + +include $(KOKKOS_PATH)/Makefile.kokkos + +build: $(EXE) + +$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) + $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) + +clean: kokkos-clean + rm -f *.o $(EXE) + +# Compilation rules + +%.o:%.cc $(KOKKOS_CPP_DEPENDS) + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< diff --git a/lib/kokkos/benchmarks/gups/gups-kokkos.cc b/lib/kokkos/benchmarks/gups/gups-kokkos.cc new file mode 100644 index 0000000000..4602adda79 --- /dev/null +++ b/lib/kokkos/benchmarks/gups/gups-kokkos.cc @@ -0,0 +1,199 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// ************************************************************************ +//@HEADER +*/ + +#include "Kokkos_Core.hpp" +#include +#include +#include + +#include + +#define HLINE "-------------------------------------------------------------\n" + +#if defined(KOKKOS_ENABLE_CUDA) +typedef Kokkos::View::HostMirror GUPSHostArray; +typedef Kokkos::View GUPSDeviceArray; +#else +typedef Kokkos::View::HostMirror GUPSHostArray; +typedef Kokkos::View GUPSDeviceArray; +#endif + +typedef int GUPSIndex; + +double now() { + struct timeval now; + gettimeofday(&now, NULL); + + return (double) now.tv_sec + ((double) now.tv_usec * 1.0e-6); +} + +void randomize_indices(GUPSHostArray& indices, GUPSDeviceArray& dev_indices, const int64_t dataCount) { + for( GUPSIndex i = 0; i < indices.extent(0); ++i ) { + indices[i] = lrand48() % dataCount; + } + + Kokkos::deep_copy(dev_indices, indices); +} + +void run_gups(GUPSDeviceArray& indices, GUPSDeviceArray& data, const int64_t datum, + const bool performAtomics) { + + if( performAtomics ) { + Kokkos::parallel_for("bench-gups-atomic", indices.extent(0), KOKKOS_LAMBDA(const GUPSIndex i) { + Kokkos::atomic_fetch_xor( &data[indices[i]], datum ); + }); + } else { + Kokkos::parallel_for("bench-gups-non-atomic", indices.extent(0), KOKKOS_LAMBDA(const GUPSIndex i) { + data[indices[i]] ^= datum; + }); + } + + Kokkos::fence(); +} + +int run_benchmark(const GUPSIndex indicesCount, const GUPSIndex dataCount, const int repeats, + const bool useAtomics) { + + printf("Reports fastest timing per kernel\n"); + printf("Creating Views...\n"); + + printf("Memory Sizes:\n"); + printf("- Elements: %15" PRIu64 " (%12.4f MB)\n", static_cast(dataCount), + 1.0e-6 * ((double) dataCount * (double) sizeof(int64_t))); + printf("- Indices: %15" PRIu64 " (%12.4f MB)\n", static_cast(indicesCount), + 1.0e-6 * ((double) indicesCount * (double) sizeof(int64_t))); + printf(" - Atomics: %15s\n", (useAtomics ? "Yes" : "No") ); + printf("Benchmark kernels will be performed for %d iterations.\n", repeats); + + printf(HLINE); + + GUPSDeviceArray dev_indices("indices", indicesCount); + GUPSDeviceArray dev_data("data", dataCount); + int64_t datum = -1; + + GUPSHostArray indices = Kokkos::create_mirror_view(dev_indices); + GUPSHostArray data = Kokkos::create_mirror_view(dev_data); + + double gupsTime = 0.0; + + printf("Initializing Views...\n"); + +#if defined(KOKKOS_HAVE_OPENMP) + Kokkos::parallel_for("init-data", Kokkos::RangePolicy(0, dataCount), +#else + Kokkos::parallel_for("init-data", Kokkos::RangePolicy(0, dataCount), +#endif + KOKKOS_LAMBDA(const int i) { + + data[i] = 10101010101; + }); + +#if defined(KOKKOS_HAVE_OPENMP) + Kokkos::parallel_for("init-indices", Kokkos::RangePolicy(0, indicesCount), +#else + Kokkos::parallel_for("init-indices", Kokkos::RangePolicy(0, indicesCount), +#endif + KOKKOS_LAMBDA(const int i) { + + indices[i] = 0; + }); + + Kokkos::deep_copy(dev_data, data); + Kokkos::deep_copy(dev_indices, indices); + double start; + + printf("Starting benchmarking...\n"); + + for( GUPSIndex k = 0; k < repeats; ++k ) { + randomize_indices(indices, dev_indices, data.extent(0)); + + start = now(); + run_gups(dev_indices, dev_data, datum, useAtomics); + gupsTime += now() - start; + } + + Kokkos::deep_copy(indices, dev_indices); + Kokkos::deep_copy(data, dev_data); + + printf(HLINE); + printf("GUP/s Random: %18.6f\n", + (1.0e-9 * ((double) repeats) * (double) dev_indices.extent(0)) / gupsTime); + printf(HLINE); + + return 0; +} + +int main(int argc, char* argv[]) { + + printf(HLINE); + printf("Kokkos GUPS Benchmark\n"); + printf(HLINE); + + srand48(1010101); + + Kokkos::initialize(argc, argv); + + int64_t indices = 8192; + int64_t data = 33554432; + int64_t repeats = 10; + bool useAtomics = false; + + for( int i = 1; i < argc; ++i ) { + if( strcmp( argv[i], "--indices" ) == 0 ) { + indices = std::atoll(argv[i+1]); + ++i; + } else if( strcmp( argv[i], "--data" ) == 0 ) { + data = std::atoll(argv[i+1]); + ++i; + } else if( strcmp( argv[i], "--repeats" ) == 0 ) { + repeats = std::atoll(argv[i+1]); + ++i; + } else if( strcmp( argv[i], "--atomics" ) == 0 ) { + useAtomics = true; + } + } + + const int rc = run_benchmark(indices, data, repeats, useAtomics); + + Kokkos::finalize(); + + return rc; +} diff --git a/lib/kokkos/benchmarks/stream/Makefile b/lib/kokkos/benchmarks/stream/Makefile new file mode 100644 index 0000000000..04566b322d --- /dev/null +++ b/lib/kokkos/benchmarks/stream/Makefile @@ -0,0 +1,41 @@ +#Set your Kokkos path to something appropriate +KOKKOS_PATH = ${HOME}/git/kokkos-github-repo +#KOKKOS_DEVICES = "Cuda" +#KOKKOS_ARCH = "Pascal60" +#KOKKOS_CUDA_OPTIONS = enable_lambda +KOKKOS_DEVICES = "OpenMP" +KOKKOS_ARCH = "Power8" + +SRC = stream-kokkos.cc + +default: build + echo "Start Build" + +CXXFLAGS = -O3 +#CXX = ${HOME}/git/kokkos-github-repo/bin/nvcc_wrapper +CXX = g++ + +LINK = ${CXX} + +LINKFLAGS = +EXE = stream-kokkos + +DEPFLAGS = -M + +OBJ = $(SRC:.cc=.o) +LIB = + +include $(KOKKOS_PATH)/Makefile.kokkos + +build: $(EXE) + +$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) + $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) + +clean: kokkos-clean + rm -f *.o $(EXE) + +# Compilation rules + +%.o:%.cc $(KOKKOS_CPP_DEPENDS) + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< diff --git a/lib/kokkos/benchmarks/stream/stream-kokkos.cc b/lib/kokkos/benchmarks/stream/stream-kokkos.cc new file mode 100644 index 0000000000..370995432e --- /dev/null +++ b/lib/kokkos/benchmarks/stream/stream-kokkos.cc @@ -0,0 +1,265 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// ************************************************************************ +//@HEADER +*/ + +#include "Kokkos_Core.hpp" +#include +#include +#include + +#include + +#define STREAM_ARRAY_SIZE 100000000 +#define STREAM_NTIMES 20 + +#define HLINE "-------------------------------------------------------------\n" + +#if defined(KOKKOS_ENABLE_CUDA) +typedef Kokkos::View::HostMirror StreamHostArray; +typedef Kokkos::View StreamDeviceArray; +#else +typedef Kokkos::View::HostMirror StreamHostArray; +typedef Kokkos::View StreamDeviceArray; +#endif + +typedef int StreamIndex; + +double now() { + struct timeval now; + gettimeofday(&now, NULL); + + return (double) now.tv_sec + ((double) now.tv_usec * 1.0e-6); +} + +void perform_copy(StreamDeviceArray& a, StreamDeviceArray& b, StreamDeviceArray& c) { + + Kokkos::parallel_for("copy", a.extent(0), KOKKOS_LAMBDA(const StreamIndex i) { + c[i] = a[i]; + }); + + Kokkos::fence(); +} + +void perform_scale(StreamDeviceArray& a, StreamDeviceArray& b, StreamDeviceArray& c, + const double scalar) { + + Kokkos::parallel_for("copy", a.extent(0), KOKKOS_LAMBDA(const StreamIndex i) { + b[i] = scalar * c[i]; + }); + + Kokkos::fence(); +} + +void perform_add(StreamDeviceArray& a, StreamDeviceArray& b, StreamDeviceArray& c) { + Kokkos::parallel_for("add", a.extent(0), KOKKOS_LAMBDA(const StreamIndex i) { + c[i] = a[i] + b[i]; + }); + + Kokkos::fence(); +} + +void perform_triad(StreamDeviceArray& a, StreamDeviceArray& b, StreamDeviceArray& c, + const double scalar) { + + Kokkos::parallel_for("triad", a.extent(0), KOKKOS_LAMBDA(const StreamIndex i) { + a[i] = b[i] + scalar * c[i]; + }); + + Kokkos::fence(); +} + +int perform_validation(StreamHostArray& a, StreamHostArray& b, StreamHostArray& c, + const StreamIndex arraySize, const double scalar) { + + double ai = 1.0; + double bi = 2.0; + double ci = 0.0; + + for( StreamIndex i = 0; i < arraySize; ++i ) { + ci = ai; + bi = scalar * ci; + ci = ai + bi; + ai = bi + scalar * ci; + }; + + double aError = 0.0; + double bError = 0.0; + double cError = 0.0; + + for( StreamIndex i = 0; i < arraySize; ++i ) { + aError = std::abs( a[i] - ai ); + bError = std::abs( b[i] - bi ); + cError = std::abs( c[i] - ci ); + } + + double aAvgError = aError / (double) arraySize; + double bAvgError = bError / (double) arraySize; + double cAvgError = cError / (double) arraySize; + + const double epsilon = 1.0e-13; + int errorCount = 0; + + if( std::abs( aAvgError / ai ) > epsilon ) { + fprintf(stderr, "Error: validation check on View a failed.\n"); + errorCount++; + } + + if( std::abs( bAvgError / bi ) > epsilon ) { + fprintf(stderr, "Error: validation check on View b failed.\n"); + errorCount++; + } + + if( std::abs( cAvgError / ci ) > epsilon ) { + fprintf(stderr, "Error: validation check on View c failed.\n"); + errorCount++; + } + + if( errorCount == 0 ) { + printf("All solutions checked and verified.\n"); + } + + return errorCount; +} + +int run_benchmark() { + + printf("Reports fastest timing per kernel\n"); + printf("Creating Views...\n"); + + printf("Memory Sizes:\n"); + printf("- Array Size: %" PRIu64 "\n", static_cast(STREAM_ARRAY_SIZE)); + printf("- Per Array: %12.2f MB\n", 1.0e-6 * (double) STREAM_ARRAY_SIZE * (double) sizeof(double)); + printf("- Total: %12.2f MB\n", 3.0e-6 * (double) STREAM_ARRAY_SIZE * (double) sizeof(double)); + + printf("Benchmark kernels will be performed for %d iterations.\n", STREAM_NTIMES); + + printf(HLINE); + + StreamDeviceArray dev_a("a", STREAM_ARRAY_SIZE); + StreamDeviceArray dev_b("b", STREAM_ARRAY_SIZE); + StreamDeviceArray dev_c("c", STREAM_ARRAY_SIZE); + + StreamHostArray a = Kokkos::create_mirror_view(dev_a); + StreamHostArray b = Kokkos::create_mirror_view(dev_b); + StreamHostArray c = Kokkos::create_mirror_view(dev_c); + + const double scalar = 3.0; + + double copyTime = std::numeric_limits::max(); + double scaleTime = std::numeric_limits::max(); + double addTime = std::numeric_limits::max(); + double triadTime = std::numeric_limits::max(); + + printf("Initializing Views...\n"); + +#if defined(KOKKOS_HAVE_OPENMP) + Kokkos::parallel_for("init", Kokkos::RangePolicy(0, STREAM_ARRAY_SIZE), +#else + Kokkos::parallel_for("init", Kokkos::RangePolicy(0, STREAM_ARRAY_SIZE), +#endif + KOKKOS_LAMBDA(const int i) { + + a[i] = 1.0; + b[i] = 2.0; + c[i] = 0.0; + }); + + // Copy contents of a (from the host) to the dev_a (device) + Kokkos::deep_copy(dev_a, a); + Kokkos::deep_copy(dev_b, b); + Kokkos::deep_copy(dev_c, c); + + double start; + + printf("Starting benchmarking...\n"); + + for( StreamIndex k = 0; k < STREAM_NTIMES; ++k ) { + start = now(); + perform_copy(dev_a, dev_b, dev_c); + copyTime = std::min( copyTime, (now() - start) ); + + start = now(); + perform_scale(dev_a, dev_b, dev_c, scalar); + scaleTime = std::min( scaleTime, (now() - start) ); + + start = now(); + perform_add(dev_a, dev_b, dev_c); + addTime = std::min( addTime, (now() - start) ); + + start = now(); + perform_triad(dev_a, dev_b, dev_c, scalar); + triadTime = std::min( triadTime, (now() - start) ); + } + + Kokkos::deep_copy(a, dev_a); + Kokkos::deep_copy(b, dev_b); + Kokkos::deep_copy(c, dev_c); + + printf("Performing validation...\n"); + int rc = perform_validation(a, b, c, STREAM_ARRAY_SIZE, scalar); + + printf(HLINE); + + printf("Copy %11.2f MB/s\n", + ( 1.0e-06 * 2.0 * (double) sizeof(double) * (double) STREAM_ARRAY_SIZE) / copyTime ); + printf("Scale %11.2f MB/s\n", + ( 1.0e-06 * 2.0 * (double) sizeof(double) * (double) STREAM_ARRAY_SIZE) / scaleTime ); + printf("Add %11.2f MB/s\n", + ( 1.0e-06 * 3.0 * (double) sizeof(double) * (double) STREAM_ARRAY_SIZE) / addTime ); + printf("Triad %11.2f MB/s\n", + ( 1.0e-06 * 3.0 * (double) sizeof(double) * (double) STREAM_ARRAY_SIZE) / triadTime ); + + printf(HLINE); + + return rc; +} + +int main(int argc, char* argv[]) { + + printf(HLINE); + printf("Kokkos STREAM Benchmark\n"); + printf(HLINE); + + Kokkos::initialize(argc, argv); + const int rc = run_benchmark(); + Kokkos::finalize(); + + return rc; +} diff --git a/lib/kokkos/bin/hpcbind b/lib/kokkos/bin/hpcbind index 92f9f81ac9..b185a92821 100755 --- a/lib/kokkos/bin/hpcbind +++ b/lib/kokkos/bin/hpcbind @@ -125,18 +125,20 @@ function show_help { echo " --openmp-ratio=N/D Ratio of the cpuset to use for OpenMP" echo " Default: 1" echo " --openmp-places= Op=threads|cores|sockets. Default: threads" - echo " --no-openmp-proc-bind Set OMP_PROC_BIND to false and unset OMP_PLACES" - echo " --force-openmp-num-threads=N" + echo " --openmp-num-threads=N" echo " Override logic for selecting OMP_NUM_THREADS" - echo " --force-openmp-proc-bind=" + echo " --openmp-proc-bind=" echo " Override logic for selecting OMP_PROC_BIND" - echo " --no-openmp-nested Set OMP_NESTED to false" + echo " --openmp-nested Set OMP_NESTED to true" + echo " --no-openmp-proc-bind Set OMP_PROC_BIND to false and unset OMP_PLACES" echo " --output-prefix=

Save the output to files of the form" echo " P.hpcbind.N, P.stdout.N and P.stderr.N where P is " echo " the prefix and N is the rank (no spaces)" echo " --output-mode= How console output should be handled." echo " Options are all, rank0, and none. Default: rank0" echo " --lstopo Show bindings in lstopo" + echo " --save-topology= Save the topology to the given xml file" + echo " --load-topology= Load a previously saved topology from an xml file" echo " -v|--verbose Print bindings and relevant environment variables" echo " -h|--help Show this message" echo "" @@ -189,7 +191,7 @@ HPCBIND_OPENMP_PLACES=${OMP_PLACES:-threads} declare -i HPCBIND_OPENMP_PROC_BIND=1 HPCBIND_OPENMP_FORCE_NUM_THREADS="" HPCBIND_OPENMP_FORCE_PROC_BIND="" -declare -i HPCBIND_OPENMP_NESTED=1 +declare -i HPCBIND_OPENMP_NESTED=0 declare -i HPCBIND_VERBOSE=0 declare -i HPCBIND_LSTOPO=0 @@ -197,6 +199,9 @@ declare -i HPCBIND_LSTOPO=0 HPCBIND_OUTPUT_PREFIX="" HPCBIND_OUTPUT_MODE="rank0" +HPCBIND_OUTPUT_TOPOLOGY="" +HPCBIND_INPUT_TOPOLOGY="" + declare -i HPCBIND_HAS_COMMAND=0 for i in "$@"; do @@ -276,10 +281,22 @@ for i in "$@"; do HPCBIND_OPENMP_NESTED=0 shift ;; + --openmp-nested) + HPCBIND_OPENMP_NESTED=1 + shift + ;; --output-prefix=*) HPCBIND_OUTPUT_PREFIX="${i#*=}" shift ;; + --save-topology=*) + HPCBIND_OUTPUT_TOPOLOGY="${i#*=}" + shift + ;; + --load-topology=*) + HPCBIND_INPUT_TOPOLOGY="${i#*=}" + shift + ;; --output-mode=*) HPCBIND_OUTPUT_MODE="${i#*=}" #convert to lower case @@ -327,24 +344,37 @@ elif [[ ${HPCBIND_QUEUE_RANK} -eq 0 ]]; then HPCBIND_TEE=1 fi +# Save the topology to the given xml file +if [[ "${HPCBIND_OUTPUT_TOPOLOGY}" != "" ]]; then + if [[ ${HPCBIND_QUEUE_RANK} -eq 0 ]]; then + lstopo-no-graphics "${HPCBIND_OUTPUT_TOPOLOGY}" + else + lstopo-no-graphics >/dev/null 2>&1 + fi +fi + +# Load the topology to the given xml file +if [[ "${HPCBIND_INPUT_TOPOLOGY}" != "" ]]; then + if [ -f ${HPCBIND_INPUT_TOPOLOGY} ]; then + export HWLOC_XMLFILE="${HPCBIND_INPUT_TOPOLOGY}" + export HWLOC_THISSYSTEM=1 + fi +fi if [[ "${HPCBIND_OUTPUT_PREFIX}" == "" ]]; then HPCBIND_LOG=/dev/null HPCBIND_ERR=/dev/null HPCBIND_OUT=/dev/null else - if [[ ${HPCBIND_QUEUE_SIZE} -gt 0 ]]; then - HPCBIND_STR_QUEUE_SIZE="${HPCBIND_QUEUE_SIZE}" - HPCBIND_STR_QUEUE_RANK=$(printf %0*d ${#HPCBIND_STR_QUEUE_SIZE} ${HPCBIND_QUEUE_RANK}) - - HPCBIND_LOG="${HPCBIND_OUTPUT_PREFIX}.hpcbind.${HPCBIND_STR_QUEUE_RANK}" - HPCBIND_ERR="${HPCBIND_OUTPUT_PREFIX}.stderr.${HPCBIND_STR_QUEUE_RANK}" - HPCBIND_OUT="${HPCBIND_OUTPUT_PREFIX}.stdout.${HPCBIND_STR_QUEUE_RANK}" - else - HPCBIND_LOG="${HPCBIND_OUTPUT_PREFIX}.hpcbind.${HPCBIND_QUEUE_RANK}" - HPCBIND_ERR="${HPCBIND_OUTPUT_PREFIX}.stderr.${HPCBIND_QUEUE_RANK}" - HPCBIND_OUT="${HPCBIND_OUTPUT_PREFIX}.stdout.${HPCBIND_QUEUE_RANK}" + if [[ ${HPCBIND_QUEUE_SIZE} -le 0 ]]; then + HPCBIND_QUEUE_SIZE=1 fi + HPCBIND_STR_QUEUE_SIZE="${HPCBIND_QUEUE_SIZE}" + HPCBIND_STR_QUEUE_RANK=$(printf %0*d ${#HPCBIND_STR_QUEUE_SIZE} ${HPCBIND_QUEUE_RANK}) + + HPCBIND_LOG="${HPCBIND_OUTPUT_PREFIX}.hpcbind.${HPCBIND_STR_QUEUE_RANK}" + HPCBIND_ERR="${HPCBIND_OUTPUT_PREFIX}.stderr.${HPCBIND_STR_QUEUE_RANK}" + HPCBIND_OUT="${HPCBIND_OUTPUT_PREFIX}.stdout.${HPCBIND_STR_QUEUE_RANK}" > ${HPCBIND_LOG} fi @@ -546,6 +576,8 @@ if [[ ${HPCBIND_TEE} -eq 0 || ${HPCBIND_VERBOSE} -eq 0 ]]; then hostname -s >> ${HPCBIND_LOG} echo "[HPCBIND]" >> ${HPCBIND_LOG} echo "${TMP_ENV}" | grep -E "^HPCBIND_" >> ${HPCBIND_LOG} + echo "[HWLOC]" >> ${HPCBIND_LOG} + echo "${TMP_ENV}" | grep -E "^HWLOC_" >> ${HPCBIND_LOG} echo "[CUDA]" >> ${HPCBIND_LOG} echo "${TMP_ENV}" | grep -E "^CUDA_" >> ${HPCBIND_LOG} echo "[OPENMP]" >> ${HPCBIND_LOG} @@ -568,6 +600,8 @@ else hostname -s > >(tee -a ${HPCBIND_LOG}) echo "[HPCBIND]" > >(tee -a ${HPCBIND_LOG}) echo "${TMP_ENV}" | grep -E "^HPCBIND_" > >(tee -a ${HPCBIND_LOG}) + echo "[HWLOC]" > >(tee -a ${HPCBIND_LOG}) + echo "${TMP_ENV}" | grep -E "^HWLOC_" > >(tee -a ${HPCBIND_LOG}) echo "[CUDA]" > >(tee -a ${HPCBIND_LOG}) echo "${TMP_ENV}" | grep -E "^CUDA_" > >(tee -a ${HPCBIND_LOG}) echo "[OPENMP]" > >(tee -a ${HPCBIND_LOG}) diff --git a/lib/kokkos/bin/nvcc_wrapper b/lib/kokkos/bin/nvcc_wrapper index d339da4fcd..94bc72854e 100755 --- a/lib/kokkos/bin/nvcc_wrapper +++ b/lib/kokkos/bin/nvcc_wrapper @@ -74,6 +74,9 @@ dry_run=0 host_only=0 host_only_args="" +# Just run version on host compiler +get_host_version=0 + # Enable workaround for CUDA 6.5 for pragma ident replace_pragma_ident=0 @@ -93,6 +96,9 @@ depfile_separate=0 depfile_output_arg="" depfile_target_arg="" +# Option to remove duplicate libraries and object files +remove_duplicate_link_files=0 + #echo "Arguments: $# $@" while [ $# -gt 0 ] @@ -106,10 +112,18 @@ do --host-only) host_only=1 ;; + #get the host version only + --host-version) + get_host_version=1 + ;; #replace '#pragma ident' with '#ident' this is needed to compile OpenMPI due to a configure script bug and a non standardized behaviour of pragma with macros --replace-pragma-ident) replace_pragma_ident=1 ;; + #remove duplicate link files + --remove-duplicate-link-files) + remove_duplicate_link_files=1 + ;; #handle source files to be compiled as cuda files *.cpp|*.cxx|*.cc|*.C|*.c++|*.cu) cpp_files="$cpp_files $1" @@ -124,7 +138,12 @@ do fi ;; #Handle shared args (valid for both nvcc and the host compiler) - -D*|-I*|-L*|-l*|-g|--help|--version|-E|-M|-shared) + -D*) + unescape_commas=`echo "$1" | sed -e 's/\\\,/,/g'` + arg=`printf "%q" $unescape_commas` + shared_args="$shared_args $arg" + ;; + -I*|-L*|-l*|-g|--help|--version|-E|-M|-shared|-w) shared_args="$shared_args $1" ;; #Handle compilation argument @@ -152,7 +171,7 @@ do shift ;; #Handle known nvcc args - -gencode*|--dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|--resource-usage|-Xptxas*) + --dryrun|--verbose|--keep|--keep-dir*|-G|--relocatable-device-code*|-lineinfo|-expt-extended-lambda|--resource-usage|-Xptxas*) cuda_args="$cuda_args $1" ;; #Handle more known nvcc args @@ -164,8 +183,11 @@ do cuda_args="$cuda_args $1 $2" shift ;; + -rdc=*|-maxrregcount*|--maxrregcount*) + cuda_args="$cuda_args $1" + ;; #Handle c++11 - --std=c++11|-std=c++11|--std=c++14|-std=c++14|--std=c++1z|-std=c++1z) + --std=c++11|-std=c++11|--std=c++14|-std=c++14|--std=c++1y|-std=c++1y|--std=c++17|-std=c++17|--std=c++1z|-std=c++1z) if [ $stdcxx_applied -eq 1 ]; then echo "nvcc_wrapper - *warning* you have set multiple optimization flags (-std=c++1* or --std=c++1*), only the first is used because nvcc can only accept a single std setting" else @@ -205,6 +227,15 @@ do fi shift ;; + #Handle -+ (same as -x c++, specifically used for xl compilers, but mutually exclusive with -x. So replace it with -x c++) + -+) + if [ $first_xcompiler_arg -eq 1 ]; then + xcompiler_args="-x,c++" + first_xcompiler_arg=0 + else + xcompiler_args="$xcompiler_args,-x,c++" + fi + ;; #Handle -ccbin (if its not set we can set it to a default value) -ccbin) cuda_args="$cuda_args $1 $2" @@ -212,18 +243,39 @@ do host_compiler=$2 shift ;; - #Handle -arch argument (if its not set use a default - -arch*) + + #Handle -arch argument (if its not set use a default) this is the version with = sign + -arch*|-gencode*) cuda_args="$cuda_args $1" arch_set=1 ;; + #Handle -code argument (if its not set use a default) this is the version with = sign + -code*) + cuda_args="$cuda_args $1" + ;; + #Handle -arch argument (if its not set use a default) this is the version without = sign + -arch|-gencode) + cuda_args="$cuda_args $1 $2" + arch_set=1 + shift + ;; + #Handle -code argument (if its not set use a default) this is the version without = sign + -code) + cuda_args="$cuda_args $1 $2" + shift + ;; #Handle -Xcudafe argument -Xcudafe) cuda_args="$cuda_args -Xcudafe $2" shift ;; + #Handle -Xlinker argument + -Xlinker) + xlinker_args="$xlinker_args -Xlinker $2" + shift + ;; #Handle args that should be sent to the linker - -Wl*) + -Wl,*) xlinker_args="$xlinker_args -Xlinker ${1:4:${#1}}" host_linker_args="$host_linker_args ${1:4:${#1}}" ;; @@ -256,6 +308,54 @@ do shift done +#Check if nvcc exists +if [ $host_only -ne 1 ]; then + var=$(which nvcc ) + if [ $? -gt 0 ]; then + echo "Could not find nvcc in PATH" + exit $? + fi +fi + + +# Only print host compiler version +if [ $get_host_version -eq 1 ]; then + $host_compiler --version + exit +fi + +#Remove duplicate object files +if [ $remove_duplicate_link_files -eq 1 ]; then +for obj in $object_files +do + object_files_reverse="$obj $object_files_reverse" +done + +object_files_reverse_clean="" +for obj in $object_files_reverse +do + exists=false + for obj2 in $object_files_reverse_clean + do + if [ "$obj" == "$obj2" ] + then + exists=true + echo "Exists: $obj" + fi + done + if [ "$exists" == "false" ] + then + object_files_reverse_clean="$object_files_reverse_clean $obj" + fi +done + +object_files="" +for obj in $object_files_reverse_clean +do + object_files="$obj $object_files" +done +fi + #Add default host compiler if necessary if [ $ccbin_set -ne 1 ]; then cuda_args="$cuda_args -ccbin $host_compiler" @@ -328,10 +428,19 @@ fi #Run compilation command if [ $host_only -eq 1 ]; then + if [ "$NVCC_WRAPPER_SHOW_COMMANDS_BEING_RUN" == "1" ] ; then + echo "$host_command" + fi $host_command elif [ -n "$nvcc_depfile_command" ]; then + if [ "$NVCC_WRAPPER_SHOW_COMMANDS_BEING_RUN" == "1" ] ; then + echo "$nvcc_command && $nvcc_depfile_command" + fi $nvcc_command && $nvcc_depfile_command else + if [ "$NVCC_WRAPPER_SHOW_COMMANDS_BEING_RUN" == "1" ] ; then + echo "$nvcc_command" + fi $nvcc_command fi error_code=$? diff --git a/lib/kokkos/cmake/kokkos_build.cmake b/lib/kokkos/cmake/kokkos_build.cmake index 94dd733ca3..8178483d01 100644 --- a/lib/kokkos/cmake/kokkos_build.cmake +++ b/lib/kokkos/cmake/kokkos_build.cmake @@ -235,3 +235,7 @@ install(FILES # Install the export set for use with the install-tree INSTALL(EXPORT KokkosTargets DESTINATION "${INSTALL_CMAKE_DIR}") + +# build and install pkgconfig file +CONFIGURE_FILE(core/src/kokkos.pc.in kokkos.pc @ONLY) +INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/kokkos.pc DESTINATION lib/pkgconfig) diff --git a/lib/kokkos/cmake/kokkos_functions.cmake b/lib/kokkos/cmake/kokkos_functions.cmake index c0c62ccb6a..bc490115af 100644 --- a/lib/kokkos/cmake/kokkos_functions.cmake +++ b/lib/kokkos/cmake/kokkos_functions.cmake @@ -47,7 +47,7 @@ function(set_kokkos_cxx_compiler) OUTPUT_VARIABLE INTERNAL_CXX_COMPILER_VERSION OUTPUT_STRIP_TRAILING_WHITESPACE) - string(REGEX MATCH "[0-9]+\.[0-9]+\.[0-9]+$" + string(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+$" INTERNAL_CXX_COMPILER_VERSION ${INTERNAL_CXX_COMPILER_VERSION}) endif() diff --git a/lib/kokkos/cmake/kokkos_options.cmake b/lib/kokkos/cmake/kokkos_options.cmake index 80a091bb98..be494e5df0 100644 --- a/lib/kokkos/cmake/kokkos_options.cmake +++ b/lib/kokkos/cmake/kokkos_options.cmake @@ -41,7 +41,6 @@ list(APPEND KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST foreach(opt ${KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST}) string(TOUPPER ${opt} OPT ) IF(DEFINED Kokkos_ENABLE_${opt}) - MESSAGE("Kokkos_ENABLE_${opt} is defined!") IF(DEFINED KOKKOS_ENABLE_${OPT}) IF(NOT ("${KOKKOS_ENABLE_${OPT}}" STREQUAL "${Kokkos_ENABLE_${opt}}")) IF(DEFINED KOKKOS_ENABLE_${OPT}_INTERNAL) @@ -59,7 +58,6 @@ foreach(opt ${KOKKOS_INTERNAL_ENABLE_OPTIONS_LIST}) ENDIF() ELSE() SET(KOKKOS_INTERNAL_ENABLE_${OPT}_DEFAULT ${Kokkos_ENABLE_${opt}}) - MESSAGE("set KOKKOS_INTERNAL_ENABLE_${OPT}_DEFAULT!") ENDIF() ENDIF() endforeach() @@ -81,6 +79,7 @@ list(APPEND KOKKOS_ARCH_LIST ARMv80 # (HOST) ARMv8.0 Compatible CPU ARMv81 # (HOST) ARMv8.1 Compatible CPU ARMv8-ThunderX # (HOST) ARMv8 Cavium ThunderX CPU + ARMv8-TX2 # (HOST) ARMv8 Cavium ThunderX2 CPU WSM # (HOST) Intel Westmere CPU SNB # (HOST) Intel Sandy/Ivy Bridge CPUs HSW # (HOST) Intel Haswell CPUs @@ -105,6 +104,7 @@ list(APPEND KOKKOS_ARCH_LIST Pascal61 # (GPU) NVIDIA Pascal generation CC 6.1 Volta70 # (GPU) NVIDIA Volta generation CC 7.0 Volta72 # (GPU) NVIDIA Volta generation CC 7.2 + Turing75 # (GPU) NVIDIA Turing generation CC 7.5 ) # List of possible device architectures. @@ -123,11 +123,18 @@ list(APPEND KOKKOS_DEVICES_LIST # List of possible TPLs for Kokkos # From Makefile.kokkos: Options: hwloc,librt,experimental_memkind set(KOKKOS_USE_TPLS_LIST) +if(APPLE) +list(APPEND KOKKOS_USE_TPLS_LIST + HWLOC # hwloc + MEMKIND # experimental_memkind + ) +else() list(APPEND KOKKOS_USE_TPLS_LIST HWLOC # hwloc LIBRT # librt MEMKIND # experimental_memkind ) +endif() # Map of cmake variables to Makefile variables set(KOKKOS_INTERNAL_HWLOC hwloc) set(KOKKOS_INTERNAL_LIBRT librt) @@ -172,6 +179,7 @@ set(KOKKOS_INTERNAL_LAMBDA enable_lambda) set(tmpr "\n ") string(REPLACE ";" ${tmpr} KOKKOS_INTERNAL_ARCH_DOCSTR "${KOKKOS_ARCH_LIST}") +set(KOKKOS_INTERNAL_ARCH_DOCSTR "${tmpr}${KOKKOS_INTERNAL_ARCH_DOCSTR}") # This would be useful, but we use Foo_ENABLE mechanisms #string(REPLACE ";" ${tmpr} KOKKOS_INTERNAL_DEVICES_DOCSTR "${KOKKOS_DEVICES_LIST}") #string(REPLACE ";" ${tmpr} KOKKOS_INTERNAL_USE_TPLS_DOCSTR "${KOKKOS_USE_TPLS_LIST}") @@ -269,7 +277,7 @@ set(KOKKOS_ENABLE_PROFILING_LOAD_PRINT ${KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_P set_kokkos_default_default(DEPRECATED_CODE ON) set(KOKKOS_ENABLE_DEPRECATED_CODE ${KOKKOS_INTERNAL_ENABLE_DEPRECATED_CODE_DEFAULT} CACHE BOOL "Enable deprecated code.") -set_kokkos_default_default(EXPLICIT_INSTANTIATION ON) +set_kokkos_default_default(EXPLICIT_INSTANTIATION OFF) set(KOKKOS_ENABLE_EXPLICIT_INSTANTIATION ${KOKKOS_INTERNAL_ENABLE_EXPLICIT_INSTANTIATION_DEFAULT} CACHE BOOL "Enable explicit template instantiation.") #------------------------------------------------------------------------------- diff --git a/lib/kokkos/cmake/kokkos_settings.cmake b/lib/kokkos/cmake/kokkos_settings.cmake index 58b30ba24d..387ced6d52 100644 --- a/lib/kokkos/cmake/kokkos_settings.cmake +++ b/lib/kokkos/cmake/kokkos_settings.cmake @@ -15,16 +15,16 @@ # Ensure that KOKKOS_ARCH is in the ARCH_LIST if (KOKKOS_ARCH MATCHES ",") - message("-- Detected a comma in: KOKKOS_ARCH=${KOKKOS_ARCH}") + message("-- Detected a comma in: KOKKOS_ARCH=`${KOKKOS_ARCH}`") message("-- Although we prefer KOKKOS_ARCH to be semicolon-delimited, we do allow") message("-- comma-delimited values for compatibility with scripts (see github.com/trilinos/Trilinos/issues/2330)") string(REPLACE "," ";" KOKKOS_ARCH "${KOKKOS_ARCH}") - message("-- Commas were changed to semicolons, now KOKKOS_ARCH=${KOKKOS_ARCH}") + message("-- Commas were changed to semicolons, now KOKKOS_ARCH=`${KOKKOS_ARCH}`") endif() foreach(arch ${KOKKOS_ARCH}) list(FIND KOKKOS_ARCH_LIST ${arch} indx) if (indx EQUAL -1) - message(FATAL_ERROR "${arch} is not an accepted value for KOKKOS_ARCH." + message(FATAL_ERROR "`${arch}` is not an accepted value in KOKKOS_ARCH=`${KOKKOS_ARCH}`." " Please pick from these choices: ${KOKKOS_INTERNAL_ARCH_DOCSTR}") endif () endforeach() @@ -130,7 +130,8 @@ string(REPLACE ";" ":" KOKKOS_INTERNAL_ADDTOPATH "${addpathl}") # Set the KOKKOS_SETTINGS String -- this is the primary communication with the # makefile configuration. See Makefile.kokkos -set(KOKKOS_SETTINGS KOKKOS_SRC_PATH=${KOKKOS_SRC_PATH}) +set(KOKKOS_SETTINGS KOKKOS_CMAKE=yes) +set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} KOKKOS_SRC_PATH=${KOKKOS_SRC_PATH}) set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} KOKKOS_PATH=${KOKKOS_PATH}) set(KOKKOS_SETTINGS ${KOKKOS_SETTINGS} KOKKOS_INSTALL_PATH=${CMAKE_INSTALL_PREFIX}) diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia index 15e6049afb..d94c38cbc6 100755 --- a/lib/kokkos/config/test_all_sandia +++ b/lib/kokkos/config/test_all_sandia @@ -241,17 +241,16 @@ elif [ "$MACHINE" = "white" ]; then BASE_MODULE_LIST="/" IBM_MODULE_LIST="/xl/" - CUDA_MODULE_LIST="/,gcc/5.4.0" - CUDA_MODULE_LIST2="/,gcc/6.3.0,ibm/xl/13.1.6" + CUDA_MODULE_LIST="/,gcc/6.4.0,ibm/xl/16.1.0" # Don't do pthread on white. GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" # Format: (compiler module-list build-list exe-name warning-flag) COMPILERS=("gcc/5.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" - "ibm/13.1.6 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" - "cuda/8.0.44 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/9.0.103 $CUDA_MODULE_LIST2 $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "gcc/6.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "ibm/16.1.0 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" + "cuda/9.0.103 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) if [ -z "$ARCH_FLAG" ]; then @@ -362,7 +361,7 @@ elif [ "$MACHINE" = "apollo" ]; then "gcc/5.3.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" - "clang/6.0 $CLANG_MODULE_LIST "Cuda_Pthread" clang++ $CUDA_WARNING_FLAGS" + "clang/6.0 $CLANG_MODULE_LIST "Cuda_Pthread,OpenMP" clang++ $CUDA_WARNING_FLAGS" "cuda/9.1 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) else diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 548e96d251..f6631a4149 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -96,6 +96,7 @@ template< class DataType , class Arg3Type = void> class DualView : public ViewTraits< DataType , Arg1Type , Arg2Type, Arg3Type > { +template< class , class , class , class > friend class DualView ; public: //! \name Typedefs for device types and various Kokkos::View specializations. //@{ @@ -182,8 +183,20 @@ public: //! \name Counters to keep track of changes ("modified" flags) //@{ - View modified_device; - View modified_host; +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE +protected: + // modified_flags[0] -> host + // modified_flags[1] -> device + typedef View t_modified_flags; + t_modified_flags modified_flags; + +public: +#else + typedef View t_modified_flags; + typedef View t_modified_flag; + t_modified_flags modified_flags; + t_modified_flag modified_host,modified_device; +#endif //@} //! \name Constructors @@ -194,10 +207,14 @@ public: /// Both device and host View objects are constructed using their /// default constructors. The "modified" flags are both initialized /// to "unmodified." - DualView () : - modified_device (View ("DualView::modified_device")), - modified_host (View ("DualView::modified_host")) - {} +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE + DualView () = default; +#else + DualView ():modified_flags (t_modified_flags("DualView::modified_flags")) { + modified_host = t_modified_flag(modified_flags,0); + modified_device = t_modified_flag(modified_flags,1); + } +#endif /// \brief Constructor that allocates View objects on both host and device. /// @@ -219,17 +236,24 @@ public: const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG) : d_view (label, n0, n1, n2, n3, n4, n5, n6, n7) , h_view (create_mirror_view (d_view)) // without UVM, host View mirrors - , modified_device (View ("DualView::modified_device")) - , modified_host (View ("DualView::modified_host")) - {} + , modified_flags (t_modified_flags("DualView::modified_flags")) + { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + modified_host = t_modified_flag(modified_flags,0); + modified_device = t_modified_flag(modified_flags,1); +#endif + } //! Copy constructor (shallow copy) template DualView (const DualView& src) : d_view (src.d_view), h_view (src.h_view), - modified_device (src.modified_device), - modified_host (src.modified_host) + modified_flags (src.modified_flags) +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + , modified_host(src.modified_host) + , modified_device(src.modified_device) +#endif {} //! Subview constructor @@ -241,8 +265,11 @@ public: ) : d_view( Kokkos::subview( src.d_view , arg0 , args ... ) ) , h_view( Kokkos::subview( src.h_view , arg0 , args ... ) ) - , modified_device (src.modified_device) - , modified_host (src.modified_host) + , modified_flags (src.modified_flags) +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + , modified_host(src.modified_host) + , modified_device(src.modified_device) +#endif {} /// \brief Create DualView from existing device and host View objects. @@ -258,8 +285,7 @@ public: DualView (const t_dev& d_view_, const t_host& h_view_) : d_view (d_view_), h_view (h_view_), - modified_device (View ("DualView::modified_device")), - modified_host (View ("DualView::modified_host")) + modified_flags (t_modified_flags("DualView::modified_flags")) { if ( int(d_view.rank) != int(h_view.rank) || d_view.extent(0) != h_view.extent(0) || @@ -281,6 +307,10 @@ public: d_view.span() != h_view.span() ) { Kokkos::Impl::throw_runtime_exception("DualView constructed with incompatible views"); } +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + modified_host = t_modified_flag(modified_flags,0); + modified_device = t_modified_flag(modified_flags,1); +#endif } //@} @@ -316,6 +346,30 @@ public: t_dev, t_host>::type& view () const { + #ifndef KOKKOS_ENABLE_DEPRECATED_CODE + constexpr bool device_is_memspace = std::is_same::value; + constexpr bool device_is_execspace = std::is_same::value; + constexpr bool device_exec_is_t_dev_exec = std::is_same::value; + constexpr bool device_mem_is_t_dev_mem = std::is_same::value; + constexpr bool device_exec_is_t_host_exec = std::is_same::value; + constexpr bool device_mem_is_t_host_mem = std::is_same::value; + constexpr bool device_is_t_host_device = std::is_same::value; + constexpr bool device_is_t_dev_device = std::is_same::value; + + static_assert( + device_is_t_dev_device || device_is_t_host_device || + (device_is_memspace && (device_mem_is_t_dev_mem || device_mem_is_t_host_mem) ) || + (device_is_execspace && (device_exec_is_t_dev_exec || device_exec_is_t_host_exec) ) || + ( + (!device_is_execspace && !device_is_memspace) && ( + (device_mem_is_t_dev_mem || device_mem_is_t_host_mem) || + (device_exec_is_t_dev_exec || device_exec_is_t_host_exec) + ) + ) + , + "Template parameter to .view() must exactly match one of the DualView's device types or one of the execution or memory spaces"); + #endif + return Impl::if_c< std::is_same< typename t_dev::memory_space, @@ -324,6 +378,72 @@ public: t_host >::select (d_view , h_view); } + KOKKOS_INLINE_FUNCTION + t_host view_host() const { + return h_view; + } + + KOKKOS_INLINE_FUNCTION + t_dev view_device() const { + return d_view; + } + + template + static int get_device_side() { + constexpr bool device_is_memspace = std::is_same::value; + constexpr bool device_is_execspace = std::is_same::value; + constexpr bool device_exec_is_t_dev_exec = std::is_same::value; + constexpr bool device_mem_is_t_dev_mem = std::is_same::value; + constexpr bool device_exec_is_t_host_exec = std::is_same::value; + constexpr bool device_mem_is_t_host_mem = std::is_same::value; + constexpr bool device_is_t_host_device = std::is_same::value; + constexpr bool device_is_t_dev_device = std::is_same::value; + + #ifndef KOKKOS_ENABLE_DEPRECATED_CODE + static_assert( + device_is_t_dev_device || device_is_t_host_device || + (device_is_memspace && (device_mem_is_t_dev_mem || device_mem_is_t_host_mem) ) || + (device_is_execspace && (device_exec_is_t_dev_exec || device_exec_is_t_host_exec) ) || + ( + (!device_is_execspace && !device_is_memspace) && ( + (device_mem_is_t_dev_mem || device_mem_is_t_host_mem) || + (device_exec_is_t_dev_exec || device_exec_is_t_host_exec) + ) + ) + , + "Template parameter to .sync() must exactly match one of the DualView's device types or one of the execution or memory spaces"); + #endif + + #ifndef KOKKOS_ENABLE_DEPRECATED_CODE + int dev = -1; + #else + int dev = 0; + #endif + if(device_is_t_dev_device) dev = 1; + else if(device_is_t_host_device) dev = 0; + else { + if(device_is_memspace) { + if(device_mem_is_t_dev_mem) dev = 1; + if(device_mem_is_t_host_mem) dev = 0; + if(device_mem_is_t_host_mem && device_mem_is_t_dev_mem) dev = -1; + } + if(device_is_execspace) { + if(device_exec_is_t_dev_exec) dev = 1; + if(device_exec_is_t_host_exec) dev = 0; + if(device_exec_is_t_host_exec && device_exec_is_t_dev_exec) dev = -1; + } + if(!device_is_execspace && !device_is_memspace) { + if(device_mem_is_t_dev_mem) dev = 1; + if(device_mem_is_t_host_mem) dev = 0; + if(device_mem_is_t_host_mem && device_mem_is_t_dev_mem) dev = -1; + if(device_exec_is_t_dev_exec) dev = 1; + if(device_exec_is_t_host_exec) dev = 0; + if(device_exec_is_t_host_exec && device_exec_is_t_dev_exec) dev = -1; + } + } + return dev; + } + /// \brief Update data on device or host only if data in the other /// space has been marked as modified. /// @@ -347,23 +467,20 @@ public: ( std::is_same< Device , int>::value) , int >::type& = 0) { - const unsigned int dev = - Impl::if_c< - std::is_same< - typename t_dev::memory_space, - typename Device::memory_space>::value , - unsigned int, - unsigned int>::select (1, 0); + if(modified_flags.data()==NULL) return; - if (dev) { // if Device is the same as DualView's device type - if ((modified_host () > 0) && (modified_host () >= modified_device ())) { + int dev = get_device_side(); + + if (dev == 1) { // if Device is the same as DualView's device type + if ((modified_flags(0) > 0) && (modified_flags(0) >= modified_flags(1))) { deep_copy (d_view, h_view); - modified_host() = modified_device() = 0; + modified_flags(0) = modified_flags(1) = 0; } - } else { // hopefully Device is the same as DualView's host type - if ((modified_device () > 0) && (modified_device () >= modified_host ())) { + } + if (dev == 0) { // hopefully Device is the same as DualView's host type + if ((modified_flags(1) > 0) && (modified_flags(1) >= modified_flags(0))) { deep_copy (h_view, d_view); - modified_host() = modified_device() = 0; + modified_flags(0) = modified_flags(1) = 0; } } if(std::is_same::value) { @@ -378,46 +495,71 @@ public: ( std::is_same< Device , int>::value) , int >::type& = 0 ) { - const unsigned int dev = - Impl::if_c< - std::is_same< - typename t_dev::memory_space, - typename Device::memory_space>::value, - unsigned int, - unsigned int>::select (1, 0); - if (dev) { // if Device is the same as DualView's device type - if ((modified_host () > 0) && (modified_host () >= modified_device ())) { + if(modified_flags.data()==NULL) return; + + int dev = get_device_side(); + + if (dev == 1) { // if Device is the same as DualView's device type + if ((modified_flags(0) > 0) && (modified_flags(0) >= modified_flags(1))) { Impl::throw_runtime_exception("Calling sync on a DualView with a const datatype."); } - } else { // hopefully Device is the same as DualView's host type - if ((modified_device () > 0) && (modified_device () >= modified_host ())) { + } + if (dev == 0){ // hopefully Device is the same as DualView's host type + if ((modified_flags(1) > 0) && (modified_flags(1) >= modified_flags(0))) { Impl::throw_runtime_exception("Calling sync on a DualView with a const datatype."); } } } + void sync_host() { + if( ! std::is_same< typename traits::data_type , typename traits::non_const_data_type>::value ) + Impl::throw_runtime_exception("Calling sync_host on a DualView with a const datatype."); + if(modified_flags.data()==NULL) return; + if(modified_flags(1) > modified_flags(0)) { + deep_copy (h_view, d_view); + modified_flags(1) = modified_flags(0) = 0; + } + } + + void sync_device() { + if( ! std::is_same< typename traits::data_type , typename traits::non_const_data_type>::value ) + Impl::throw_runtime_exception("Calling sync_device on a DualView with a const datatype."); + if(modified_flags.data()==NULL) return; + if(modified_flags(0) > modified_flags(1)) { + deep_copy (d_view, h_view); + modified_flags(1) = modified_flags(0) = 0; + } + } + template bool need_sync() const { - const unsigned int dev = - Impl::if_c< - std::is_same< - typename t_dev::memory_space, - typename Device::memory_space>::value , - unsigned int, - unsigned int>::select (1, 0); + if(modified_flags.data()==NULL) return false; + int dev = get_device_side(); - if (dev) { // if Device is the same as DualView's device type - if ((modified_host () > 0) && (modified_host () >= modified_device ())) { + if (dev == 1) { // if Device is the same as DualView's device type + if ((modified_flags(0) > 0) && (modified_flags(0) >= modified_flags(1))) { return true; } - } else { // hopefully Device is the same as DualView's host type - if ((modified_device () > 0) && (modified_device () >= modified_host ())) { + } + if (dev == 0){ // hopefully Device is the same as DualView's host type + if ((modified_flags(1) > 0) && (modified_flags(1) >= modified_flags(0))) { return true; } } return false; } + + inline bool need_sync_host() const { + if(modified_flags.data()==NULL) return false; + return modified_flags(0) void modify () { - const unsigned int dev = - Impl::if_c< - std::is_same< - typename t_dev::memory_space, - typename Device::memory_space>::value, - unsigned int, - unsigned int>::select (1, 0); + if(modified_flags.data()==NULL) return; + int dev = get_device_side(); - if (dev) { // if Device is the same as DualView's device type + if (dev == 1) { // if Device is the same as DualView's device type // Increment the device's modified count. - modified_device () = (modified_device () > modified_host () ? - modified_device () : modified_host ()) + 1; - } else { // hopefully Device is the same as DualView's host type + modified_flags(1) = (modified_flags(1) > modified_flags(0) ? + modified_flags(1) : modified_flags(0)) + 1; + } + if (dev == 0) { // hopefully Device is the same as DualView's host type // Increment the host's modified count. - modified_host () = (modified_device () > modified_host () ? - modified_device () : modified_host ()) + 1; + modified_flags(0) = (modified_flags(1) > modified_flags(0) ? + modified_flags(1) : modified_flags(0)) + 1; } #ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK - if (modified_host() && modified_device()) { + if (modified_flags(0) && modified_flags(1)) { std::string msg = "Kokkos::DualView::modify ERROR: "; msg += "Concurrent modification of host and device views "; msg += "in DualView \""; @@ -455,6 +593,45 @@ public: #endif } + inline void modify_host() { + if(modified_flags.data()!=NULL) { + modified_flags(0) = (modified_flags(1) > modified_flags(0) ? + modified_flags(1) : modified_flags(0)) + 1; + #ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK + if (modified_flags(0) && modified_flags(1)) { + std::string msg = "Kokkos::DualView::modify_host ERROR: "; + msg += "Concurrent modification of host and device views "; + msg += "in DualView \""; + msg += d_view.label(); + msg += "\"\n"; + Kokkos::abort(msg.c_str()); + } + #endif + } + } + + inline void modify_device() { + if(modified_flags.data()!=NULL) { + modified_flags(1) = (modified_flags(1) > modified_flags(0) ? + modified_flags(1) : modified_flags(0)) + 1; + #ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK + if (modified_flags(0) && modified_flags(1)) { + std::string msg = "Kokkos::DualView::modify_device ERROR: "; + msg += "Concurrent modification of host and device views "; + msg += "in DualView \""; + msg += d_view.label(); + msg += "\"\n"; + Kokkos::abort(msg.c_str()); + } + #endif + } + } + + inline void clear_sync_state() { + if(modified_flags.data()!=NULL) + modified_flags(1) = modified_flags(0) = 0; + } + //@} //! \name Methods for reallocating or resizing the View objects. //@{ @@ -476,7 +653,10 @@ public: h_view = create_mirror_view( d_view ); /* Reset dirty flags */ - modified_device() = modified_host() = 0; + if(modified_flags.data()==NULL) { + modified_flags = t_modified_flags("DualView::modified_flags"); + } else + modified_flags(1) = modified_flags(0) = 0; } /// \brief Resize both views, copying old contents into new if necessary. @@ -491,13 +671,16 @@ public: const size_t n5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , const size_t n6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG , const size_t n7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG ) { - if(modified_device() >= modified_host()) { + if(modified_flags.data()==NULL) { + modified_flags = t_modified_flags("DualView::modified_flags"); + } + if(modified_flags(1) >= modified_flags(0)) { /* Resize on Device */ ::Kokkos::resize(d_view,n0,n1,n2,n3,n4,n5,n6,n7); h_view = create_mirror_view( d_view ); /* Mark Device copy as modified */ - modified_device() = modified_device()+1; + modified_flags(1) = modified_flags(1)+1; } else { /* Realloc on Device */ @@ -525,7 +708,7 @@ public: d_view = create_mirror_view( typename t_dev::execution_space(), h_view ); /* Mark Host copy as modified */ - modified_host() = modified_host()+1; + modified_flags(0) = modified_flags(0)+1; } } @@ -649,13 +832,14 @@ void deep_copy (DualView dst, // trust me, this must not be a reference const DualView& src ) { - if (src.modified_device () >= src.modified_host ()) { - deep_copy (dst.d_view, src.d_view); - dst.template modify::device_type> (); - } else { + if ( src.need_sync_device() ) { deep_copy (dst.h_view, src.h_view); - dst.template modify::host_mirror_space> (); + dst.modify_host(); } + else { + deep_copy (dst.d_view, src.d_view); + dst.modify_device(); + } } template< class ExecutionSpace , @@ -666,12 +850,12 @@ deep_copy (const ExecutionSpace& exec , DualView dst, // trust me, this must not be a reference const DualView& src ) { - if (src.modified_device () >= src.modified_host ()) { - deep_copy (exec, dst.d_view, src.d_view); - dst.template modify::device_type> (); - } else { + if ( src.need_sync_device() ) { deep_copy (exec, dst.h_view, src.h_view); - dst.template modify::host_mirror_space> (); + dst.modify_host(); + } else { + deep_copy (exec, dst.d_view, src.d_view); + dst.modify_device(); } } diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index b30009a999..3f284e6a8d 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -64,7 +64,7 @@ namespace Impl { template struct DynRankDimTraits { - enum : size_t{unspecified =KOKKOS_INVALID_INDEX}; + enum : size_t{unspecified = KOKKOS_INVALID_INDEX}; // Compute the rank of the view from the nonzero dimension arguments. KOKKOS_INLINE_FUNCTION @@ -368,8 +368,8 @@ public: enum { is_assignable = is_assignable_value_type && is_assignable_layout }; - typedef ViewMapping< DstTraits , void > DstType ; - typedef ViewMapping< SrcTraits , void > SrcType ; + typedef ViewMapping< DstTraits , typename DstTraits::specialize > DstType ; + typedef ViewMapping< SrcTraits , typename SrcTraits::specialize > SrcType ; template < typename DT , typename ... DP , typename ST , typename ... SP > KOKKOS_INLINE_FUNCTION @@ -384,8 +384,8 @@ public: // Removed dimension checks... typedef typename DstType::offset_type dst_offset_type ; - dst.m_map.m_offset = dst_offset_type(std::integral_constant() , src.layout() ); //Check this for integer input1 for padding, etc - dst.m_map.m_handle = Kokkos::Impl::ViewDataHandle< DstTraits >::assign( src.m_map.m_handle , src.m_track ); + dst.m_map.m_impl_offset = dst_offset_type(std::integral_constant() , src.layout() ); //Check this for integer input1 for padding, etc + dst.m_map.m_impl_handle = Kokkos::Impl::ViewDataHandle< DstTraits >::assign( src.m_map.m_impl_handle , src.m_track ); dst.m_track.assign( src.m_track , DstTraits::is_managed ); dst.m_rank = src.Rank ; } @@ -432,7 +432,7 @@ public: private: - typedef Kokkos::Impl::ViewMapping< traits , void > map_type ; + typedef Kokkos::Impl::ViewMapping< traits , typename traits::specialize > map_type ; typedef Kokkos::Impl::SharedAllocationTracker track_type ; track_type m_track ; @@ -565,10 +565,14 @@ public: //---------------------------------------- // Allow specializations to query their specialized map - +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE KOKKOS_INLINE_FUNCTION - const Kokkos::Impl::ViewMapping< traits , void > & + const Kokkos::Impl::ViewMapping< traits , typename traits::specialize > & implementation_map() const { return m_map ; } +#endif + KOKKOS_INLINE_FUNCTION + const Kokkos::Impl::ViewMapping< traits , typename traits::specialize > & + impl_map() const { return m_map ; } //---------------------------------------- @@ -624,7 +628,7 @@ public: reference_type operator()() const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank(), m_track, m_map) ) - return implementation_map().reference(); + return impl_map().reference(); //return m_map.reference(0,0,0,0,0,0,0); } @@ -647,7 +651,7 @@ public: typename std::enable_if< !std::is_same::value && std::is_integral::value, reference_type>::type operator[](const iType & i0) const { -// auto map = implementation_map(); +// auto map = impl_map(); const size_t dim_scalar = m_map.dimension_scalar(); const size_t bytes = this->span() / dim_scalar; @@ -785,7 +789,7 @@ public: reference_type access() const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank(), m_track, m_map) ) - return implementation_map().reference(); + return impl_map().reference(); //return m_map.reference(0,0,0,0,0,0,0); } @@ -948,7 +952,7 @@ public: , m_rank(rhs.m_rank) { typedef typename DynRankView ::traits SrcTraits ; - typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , typename traits::specialize > Mapping ; static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" ); Mapping::assign( m_map , rhs.m_map , rhs.m_track ); } @@ -958,7 +962,7 @@ public: DynRankView & operator = (const DynRankView & rhs ) { typedef typename DynRankView ::traits SrcTraits ; - typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , typename traits::specialize > Mapping ; static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" ); Mapping::assign( m_map , rhs.m_map , rhs.m_track ); m_track.assign( rhs.m_track , traits::is_managed ); @@ -976,7 +980,7 @@ public: { typedef typename View::traits SrcTraits ; typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , Kokkos::Impl::ViewToDynRankViewTag > Mapping ; - static_assert( Mapping::is_assignable , "Incompatible DynRankView copy construction" ); + static_assert( Mapping::is_assignable , "Incompatible View to DynRankView copy construction" ); Mapping::assign( *this , rhs ); } @@ -1004,7 +1008,7 @@ public: //---------------------------------------- // Allocation according to allocation properties and array layout - // unused arg_layout dimensions must be set toKOKKOS_INVALID_INDEX so that rank deduction can properly take place + // unused arg_layout dimensions must be set to KOKKOS_INVALID_INDEX so that rank deduction can properly take place template< class ... P > explicit inline DynRankView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop @@ -1179,7 +1183,7 @@ public: : DynRankView( Kokkos::Impl::ViewCtorProp< std::string >( arg_label ) , typename traits::array_layout ( arg_N0 , arg_N1 , arg_N2 , arg_N3 , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) - ) + ) {} // For backward compatibility @@ -1189,8 +1193,7 @@ public: , const typename traits::array_layout & arg_layout ) : DynRankView( Kokkos::Impl::ViewCtorProp< std::string , Kokkos::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::WithoutInitializing ) - - , Impl::DynRankDimTraits::createLayout(arg_layout) + , arg_layout ) {} @@ -1205,7 +1208,9 @@ public: , const size_t arg_N6 =KOKKOS_INVALID_INDEX , const size_t arg_N7 =KOKKOS_INVALID_INDEX ) - : DynRankView(Kokkos::Impl::ViewCtorProp< std::string , Kokkos::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::WithoutInitializing ), arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6, arg_N7 ) + : DynRankView(Kokkos::Impl::ViewCtorProp< std::string , Kokkos::Impl::WithoutInitializing_t >( arg_prop.label , Kokkos::WithoutInitializing ) + , typename traits::array_layout(arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6, arg_N7) + ) {} //---------------------------------------- @@ -1427,7 +1432,7 @@ public: , Args ... args ) { - typedef ViewMapping< traits_type, void > DstType ; + typedef ViewMapping< traits_type, typename traits_type::specialize > DstType ; typedef typename std::conditional< (rank==0) , ViewDimension<> , typename std::conditional< (rank==1) , ViewDimension<0> @@ -1445,30 +1450,30 @@ public: ret_type dst ; const SubviewExtents< 7 , rank > extents = - ExtentGenerator< Args ... >::generator( src.m_map.m_offset.m_dim , args... ) ; + ExtentGenerator< Args ... >::generator( src.m_map.m_impl_offset.m_dim , args... ) ; - dst_offset_type tempdst( src.m_map.m_offset , extents ) ; + dst_offset_type tempdst( src.m_map.m_impl_offset , extents ) ; dst.m_track = src.m_track ; - dst.m_map.m_offset.m_dim.N0 = tempdst.m_dim.N0 ; - dst.m_map.m_offset.m_dim.N1 = tempdst.m_dim.N1 ; - dst.m_map.m_offset.m_dim.N2 = tempdst.m_dim.N2 ; - dst.m_map.m_offset.m_dim.N3 = tempdst.m_dim.N3 ; - dst.m_map.m_offset.m_dim.N4 = tempdst.m_dim.N4 ; - dst.m_map.m_offset.m_dim.N5 = tempdst.m_dim.N5 ; - dst.m_map.m_offset.m_dim.N6 = tempdst.m_dim.N6 ; + dst.m_map.m_impl_offset.m_dim.N0 = tempdst.m_dim.N0 ; + dst.m_map.m_impl_offset.m_dim.N1 = tempdst.m_dim.N1 ; + dst.m_map.m_impl_offset.m_dim.N2 = tempdst.m_dim.N2 ; + dst.m_map.m_impl_offset.m_dim.N3 = tempdst.m_dim.N3 ; + dst.m_map.m_impl_offset.m_dim.N4 = tempdst.m_dim.N4 ; + dst.m_map.m_impl_offset.m_dim.N5 = tempdst.m_dim.N5 ; + dst.m_map.m_impl_offset.m_dim.N6 = tempdst.m_dim.N6 ; - dst.m_map.m_offset.m_stride.S0 = tempdst.m_stride.S0 ; - dst.m_map.m_offset.m_stride.S1 = tempdst.m_stride.S1 ; - dst.m_map.m_offset.m_stride.S2 = tempdst.m_stride.S2 ; - dst.m_map.m_offset.m_stride.S3 = tempdst.m_stride.S3 ; - dst.m_map.m_offset.m_stride.S4 = tempdst.m_stride.S4 ; - dst.m_map.m_offset.m_stride.S5 = tempdst.m_stride.S5 ; - dst.m_map.m_offset.m_stride.S6 = tempdst.m_stride.S6 ; + dst.m_map.m_impl_offset.m_stride.S0 = tempdst.m_stride.S0 ; + dst.m_map.m_impl_offset.m_stride.S1 = tempdst.m_stride.S1 ; + dst.m_map.m_impl_offset.m_stride.S2 = tempdst.m_stride.S2 ; + dst.m_map.m_impl_offset.m_stride.S3 = tempdst.m_stride.S3 ; + dst.m_map.m_impl_offset.m_stride.S4 = tempdst.m_stride.S4 ; + dst.m_map.m_impl_offset.m_stride.S5 = tempdst.m_stride.S5 ; + dst.m_map.m_impl_offset.m_stride.S6 = tempdst.m_stride.S6 ; - dst.m_map.m_handle = dst_handle_type( src.m_map.m_handle + - src.m_map.m_offset( extents.domain_offset(0) + dst.m_map.m_impl_handle = dst_handle_type( src.m_map.m_impl_handle + + src.m_map.m_impl_offset( extents.domain_offset(0) , extents.domain_offset(1) , extents.domain_offset(2) , extents.domain_offset(3) @@ -1896,6 +1901,7 @@ inline typename DynRankView::HostMirror create_mirror( const DynRankView & src , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value && ! std::is_same< typename Kokkos::ViewTraits::array_layout , Kokkos::LayoutStride >::value >::type * = 0 @@ -1914,6 +1920,7 @@ inline typename DynRankView::HostMirror create_mirror( const DynRankView & src , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value && std::is_same< typename Kokkos::ViewTraits::array_layout , Kokkos::LayoutStride >::value >::type * = 0 @@ -1929,7 +1936,11 @@ create_mirror( const DynRankView & src // Create a mirror in a new space (specialization for different space) template -typename Impl::MirrorDRVType::view_type create_mirror(const Space& , const Kokkos::DynRankView & src) { +typename Impl::MirrorDRVType::view_type +create_mirror(const Space& , const Kokkos::DynRankView & src + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value + >::type * = 0) { return typename Impl::MirrorDRVType::view_type(src.label(), Impl::reconstructLayout(src.layout(), src.rank()) ); } @@ -1985,6 +1996,29 @@ create_mirror_view(const Space& , const Kokkos::DynRankView & src return typename Impl::MirrorDRViewType::view_type(src.label(), Impl::reconstructLayout(src.layout(), src.rank()) ); } +// Create a mirror view and deep_copy in a new space (specialization for same space) +template +typename Impl::MirrorDRViewType::view_type +create_mirror_view_and_copy(const Space& , const Kokkos::DynRankView & src + , std::string const& name = "" + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + (void)name; + return src; +} + +// Create a mirror view and deep_copy in a new space (specialization for different space) +template +typename Impl::MirrorDRViewType::view_type +create_mirror_view_and_copy(const Space& , const Kokkos::DynRankView & src + , std::string const& name = "" + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + using Mirror = typename Impl::MirrorDRViewType::view_type; + std::string label = name.empty() ? src.label() : name; + auto mirror = Mirror( Kokkos::ViewAllocateWithoutInitializing(label), Impl::reconstructLayout(src.layout(), src.rank()) ); + deep_copy(mirror, src); + return mirror; +} + } //end Kokkos diff --git a/lib/kokkos/containers/src/Kokkos_OffsetView.hpp b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp new file mode 100644 index 0000000000..b614764ee7 --- /dev/null +++ b/lib/kokkos/containers/src/Kokkos_OffsetView.hpp @@ -0,0 +1,1895 @@ +/* + * Kokkos_OffsetView.hpp + * + * Created on: Apr 23, 2018 + * Author: swbova + */ + +#ifndef KOKKOS_OFFSETVIEW_HPP_ +#define KOKKOS_OFFSETVIEW_HPP_ + + +#include + +#include + +namespace Kokkos { + + namespace Experimental { + //---------------------------------------------------------------------------- + //---------------------------------------------------------------------------- + + template< class DataType , class ... Properties > + class OffsetView ; + + template< class > struct is_offset_view : public std::false_type {}; + + template< class D, class ... P > + struct is_offset_view< OffsetView > : public std::true_type {}; + + template< class D, class ... P > + struct is_offset_view< const OffsetView > : public std::true_type {}; + +#define KOKKOS_INVALID_OFFSET int64_t(0) +#define KOKKOS_INVALID_INDEX_RANGE {KOKKOS_INVALID_OFFSET, KOKKOS_INVALID_OFFSET} + + template ::value && + std::is_signed::value, iType >::type = 0> + using IndexRange = Kokkos::Array; + + + using index_list_type = std::initializer_list; + + + // template ::value && + // std::is_signed::value, iType >::type = 0> using min_index_type = std::initializer_list; + + namespace Impl { + + template + struct GetOffsetViewTypeFromViewType { + + typedef OffsetView type; + + }; + + template< unsigned , class MapType, class BeginsType > + KOKKOS_INLINE_FUNCTION + bool offsetview_verify_operator_bounds( const MapType &, const BeginsType & ) + { return true ; } + + template< unsigned R , class MapType , class BeginsType, class iType , class ... Args > + KOKKOS_INLINE_FUNCTION + bool offsetview_verify_operator_bounds + ( const MapType & map + , const BeginsType & begins + , const iType & i + , Args ... args + ) + { + + const bool legalIndex = ( int64_t(i) >= begins[R] ) && + ( int64_t(i) <= int64_t(begins[R] + map.extent(R) - 1) ); + return legalIndex + && offsetview_verify_operator_bounds( map , begins, args ... ); + } + template< unsigned , class MapType, class BeginsType > + inline + void offsetview_error_operator_bounds( char * , int , const MapType & , const BeginsType &) + {} + + template< unsigned R , class MapType , class BeginsType , class iType , class ... Args > + inline + void offsetview_error_operator_bounds + ( char * buf + , int len + , const MapType & map + , const BeginsType begins + , const iType & i + , Args ... args + ) + { + const int64_t b = begins[R]; + const int64_t e = b + map.extent(R) - 1; + const int n = + snprintf(buf,len," %ld <= %ld <= %ld %c" + , static_cast(b) + , static_cast(i) + , static_cast(e) + , ( sizeof...(Args) ? ',' : ')' ) + ); + offsetview_error_operator_bounds(buf+n,len-n,map,begins,args...); + } + + template< class MemorySpace , class MapType , class BeginsType, class ... Args > + KOKKOS_INLINE_FUNCTION + void offsetview_verify_operator_bounds + ( Kokkos::Impl::SharedAllocationTracker const & tracker + , const MapType & map , const BeginsType & begins, Args ... args ) + { + if ( ! offsetview_verify_operator_bounds<0>( map , begins, args ... ) ) { +#if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) + enum { LEN = 1024 }; + char buffer[ LEN ]; + const std::string label = tracker.template get_label(); + int n = snprintf(buffer,LEN,"OffsetView bounds error of view labeled %s (",label.c_str()); + offsetview_error_operator_bounds<0>( buffer + n , LEN - n , map ,begins, args ... ); + Kokkos::Impl::throw_runtime_exception(std::string(buffer)); +#else + /* Check #1: is there a SharedAllocationRecord? + (we won't use it, but if its not there then there isn't + a corresponding SharedAllocationHeader containing a label). + This check should cover the case of Views that don't + have the Unmanaged trait but were initialized by pointer. */ + if (tracker.has_record()) { + Kokkos::Impl::operator_bounds_error_on_device( + map, Kokkos::Impl::has_printable_label_typedef()); + } else { + Kokkos::abort("OffsetView bounds error"); + } +#endif + } + } + +#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST + KOKKOS_INLINE_FUNCTION + void runtime_check_rank_host(const size_t rank_dynamic, const size_t rank, + const index_list_type minIndices, const std::string & label) + { + bool isBad = false; + std::string message = "Kokkos::Experimental::OffsetView ERROR: for OffsetView labeled '" + label + "':"; + if (rank_dynamic != rank) { + message += "The full rank must be the same as the dynamic rank. full rank = "; + message += std::to_string(rank) + " dynamic rank = " + std::to_string(rank_dynamic) + "\n"; + isBad = true; + } + + size_t numOffsets = 0; + for(size_t i = 0; i < minIndices.size(); ++i ){ + if( minIndices.begin()[i] != -KOKKOS_INVALID_OFFSET) numOffsets++; + } + if (numOffsets != rank_dynamic) { + message += "The number of offsets provided ( " + std::to_string(numOffsets) + + " ) must equal the dynamic rank ( " + std::to_string(rank_dynamic) + " )."; + isBad = true; + } + + if(isBad) Kokkos::abort(message.c_str()); + } +#endif + + KOKKOS_INLINE_FUNCTION + void runtime_check_rank_device(const size_t rank_dynamic, const size_t rank, + const index_list_type minIndices) + { + if (rank_dynamic != rank) { + Kokkos::abort("The full rank of an OffsetView must be the same as the dynamic rank."); + } + size_t numOffsets = 0; + for(size_t i = 0; i < minIndices.size(); ++i ){ + if( minIndices.begin()[i] != -KOKKOS_INVALID_OFFSET) numOffsets++; + } + if (numOffsets != rank) { + Kokkos::abort("The number of offsets provided to an OffsetView constructor must equal the dynamic rank."); + } + + } + } + + template< class DataType , class ... Properties > + class OffsetView : public ViewTraits< DataType , Properties ... > { + public: + + typedef ViewTraits< DataType , Properties ... > traits ; + + + + private: + + template< class , class ... > friend class OffsetView ; + template< class , class ... > friend class View ; //FIXME delete this line + template< class , class ... > friend class Kokkos::Impl::ViewMapping ; + + + typedef Kokkos::Impl::ViewMapping< traits , void > map_type ; + typedef Kokkos::Impl::SharedAllocationTracker track_type ; + public: + enum { Rank = map_type::Rank }; + typedef Kokkos::Array begins_type ; + + + template ::value, iType>::type = 0> + KOKKOS_INLINE_FUNCTION + int64_t begin(const iType dimension) const { + return dimension < Rank ? m_begins[dimension] : 0; + } + + KOKKOS_INLINE_FUNCTION + begins_type begins() const { return m_begins;} + + template ::value, iType>::type = 0> + KOKKOS_INLINE_FUNCTION + int64_t end(const iType dimension) const {return begin(dimension) + m_map.extent(dimension);} + + + private: + track_type m_track ; + map_type m_map ; + begins_type m_begins; + + public: + //---------------------------------------- + /** \brief Compatible view of array of scalar types */ + typedef OffsetView< typename traits::scalar_array_type , + typename traits::array_layout , + typename traits::device_type , + typename traits::memory_traits > + array_type ; + + /** \brief Compatible view of const data type */ + typedef OffsetView< typename traits::const_data_type , + typename traits::array_layout , + typename traits::device_type , + typename traits::memory_traits > + const_type ; + + /** \brief Compatible view of non-const data type */ + typedef OffsetView< typename traits::non_const_data_type , + typename traits::array_layout , + typename traits::device_type , + typename traits::memory_traits > + non_const_type ; + + /** \brief Compatible HostMirror view */ + typedef OffsetView< typename traits::non_const_data_type , + typename traits::array_layout , + typename traits::host_mirror_space > + HostMirror ; + + //---------------------------------------- + // Domain rank and extents + + /** \brief rank() to be implemented + */ + //KOKKOS_INLINE_FUNCTION + //static + //constexpr unsigned rank() { return map_type::Rank; } + + template< typename iType > + KOKKOS_INLINE_FUNCTION constexpr + typename std::enable_if< std::is_integral::value , size_t >::type + extent( const iType & r ) const + { return m_map.extent(r); } + + template< typename iType > + KOKKOS_INLINE_FUNCTION constexpr + typename std::enable_if< std::is_integral::value , int >::type + extent_int( const iType & r ) const + { return static_cast(m_map.extent(r)); } + + KOKKOS_INLINE_FUNCTION constexpr + typename traits::array_layout layout() const + { return m_map.layout(); } + + + KOKKOS_INLINE_FUNCTION constexpr size_t size() const { return m_map.dimension_0() * + m_map.dimension_1() * + m_map.dimension_2() * + m_map.dimension_3() * + m_map.dimension_4() * + m_map.dimension_5() * + m_map.dimension_6() * + m_map.dimension_7(); } + + KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_map.stride_0(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_map.stride_1(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_map.stride_2(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_map.stride_3(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_map.stride_4(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_map.stride_5(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_map.stride_6(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_map.stride_7(); } + + template< typename iType > + KOKKOS_INLINE_FUNCTION constexpr + typename std::enable_if< std::is_integral::value , size_t >::type + stride(iType r) const { + return (r == 0 ? m_map.stride_0() : + (r == 1 ? m_map.stride_1() : + (r == 2 ? m_map.stride_2() : + (r == 3 ? m_map.stride_3() : + (r == 4 ? m_map.stride_4() : + (r == 5 ? m_map.stride_5() : + (r == 6 ? m_map.stride_6() : + m_map.stride_7()))))))); + } + + template< typename iType > + KOKKOS_INLINE_FUNCTION void stride( iType * const s ) const { m_map.stride(s); } + + //---------------------------------------- + // Range span is the span which contains all members. + + typedef typename map_type::reference_type reference_type ; + typedef typename map_type::pointer_type pointer_type ; + + enum { reference_type_is_lvalue_reference = std::is_lvalue_reference< reference_type >::value }; + + KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_map.span(); } + KOKKOS_INLINE_FUNCTION bool span_is_contiguous() const { return m_map.span_is_contiguous(); } + KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const { return m_map.data(); } + + //---------------------------------------- + // Allow specializations to query their specialized map + + KOKKOS_INLINE_FUNCTION + const Kokkos::Impl::ViewMapping< traits , void > & + implementation_map() const { return m_map ; } + + //---------------------------------------- + + private: + + enum { + is_layout_left = std::is_same< typename traits::array_layout + , Kokkos::LayoutLeft >::value , + + is_layout_right = std::is_same< typename traits::array_layout + , Kokkos::LayoutRight >::value , + + is_layout_stride = std::is_same< typename traits::array_layout + , Kokkos::LayoutStride >::value , + + is_default_map = + std::is_same< typename traits::specialize , void >::value && + ( is_layout_left || is_layout_right || is_layout_stride ) + }; + + template< class Space , bool = Kokkos::Impl::MemorySpaceAccess< Space , typename traits::memory_space >::accessible > struct verify_space + { KOKKOS_FORCEINLINE_FUNCTION static void check() {} }; + + template< class Space > struct verify_space + { KOKKOS_FORCEINLINE_FUNCTION static void check() + { Kokkos::abort("Kokkos::View ERROR: attempt to access inaccessible memory space"); + }; + }; + +#if defined( KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK ) + +#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( ARG ) \ + OffsetView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check(); \ + Kokkos::Experimental::Impl::offsetview_verify_operator_bounds< typename traits::memory_space > ARG ; + +#else + +#define KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( ARG ) \ + OffsetView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check(); + +#endif + public: + + //------------------------------ + // Rank 0 operator() + + KOKKOS_FORCEINLINE_FUNCTION + reference_type + operator()() const + { + return m_map.reference(); + } + //------------------------------ + // Rank 1 operator() + + + template< typename I0> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0) const + { + + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0) ) + const size_t j0 = i0 - m_begins[0]; + return m_map.reference(j0); + } + + template< typename I0> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && ! is_layout_stride + ), reference_type >::type + operator()( const I0 & i0 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0) ) + const size_t j0 = i0 - m_begins[0]; + return m_map.m_impl_handle[ j0 ]; + } + + template< typename I0 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && is_layout_stride + ), reference_type >::type + operator()( const I0 & i0) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0) ) + const size_t j0 = i0 - m_begins[0]; + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * j0 ]; + } + //------------------------------ + // Rank 1 operator[] + + template< typename I0 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && ! is_default_map + ), reference_type >::type + operator[]( const I0 & i0 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0) ) + const size_t j0 = i0 - m_begins[0]; + return m_map.reference(j0); + } + + template< typename I0 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && ! is_layout_stride + ), reference_type >::type + operator[]( const I0 & i0 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0) ) + const size_t j0 = i0 - m_begins[0]; + return m_map.m_impl_handle[ j0 ]; + } + + template< typename I0 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && is_layout_stride + ), reference_type >::type + operator[]( const I0 & i0 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0) ) + const size_t j0 = i0 - m_begins[0]; + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * j0 ]; + } + + + //------------------------------ + // Rank 2 + + template< typename I0 , typename I1 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + return m_map.reference(j0,j1); + } + + template< typename I0 , typename I1 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_left && ( traits::rank_dynamic == 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + return m_map.m_impl_handle[ j0 + m_map.m_impl_offset.m_dim.N0 * j1 ]; + } + + template< typename I0 , typename I1> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_left && ( traits::rank_dynamic != 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + return m_map.m_impl_handle[ j0 + m_map.m_impl_offset.m_stride * j1 ]; + } + + template< typename I0 , typename I1 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_right && ( traits::rank_dynamic == 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + return m_map.m_impl_handle[ j1 + m_map.m_impl_offset.m_dim.N1 * j0 ]; + } + + template< typename I0 , typename I1 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_right && ( traits::rank_dynamic != 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + return m_map.m_impl_handle[ j1 + m_map.m_impl_offset.m_stride * j0 ]; + } + + template< typename I0 , typename I1> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_stride + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + return m_map.m_impl_handle[ j0 * m_map.m_impl_offset.m_stride.S0 + + j1 * m_map.m_impl_offset.m_stride.S1 ]; + } + + //------------------------------ + // Rank 3 + + template< typename I0 , typename I1 , typename I2 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 3 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1, i2) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + return m_map.m_impl_handle[ m_map.m_impl_offset(j0, j1, j2) ]; + } + + template< typename I0 , typename I1 , typename I2> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 3 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + return m_map.reference(j0, j1, j2); + } + + //------------------------------ + // Rank 4 + + template< typename I0 , typename I1 , typename I2 , typename I3> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 4 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1, i2, i3) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + return m_map.m_impl_handle[ m_map.m_impl_offset(j0,j1,j2,j3) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 4 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1, i2, i3) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + return m_map.reference(j0,j1,j2,j3); + } + + //------------------------------ + // Rank 5 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 5 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1, i2, i3, i4) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + return m_map.m_impl_handle[ m_map.m_impl_offset(j0, j1,j2, j3, j4) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 5 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map, m_begins, i0,i1, i2, i3, i4) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + return m_map.reference(j0,j1,j2,j3,j4); + } + + //------------------------------ + // Rank 6 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 6 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2, i3, i4, i5) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + const size_t j5 = i5 - m_begins[5]; + return m_map.m_impl_handle[ m_map.m_impl_offset(j0,j1,j2,j3,j4,j5) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 6 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2, i3, i4, i5) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + const size_t j5 = i5 - m_begins[5]; + return m_map.reference(j0,j1,j2,j3,j4,j5); + } + + //------------------------------ + // Rank 7 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 7 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2, i3, i4, i5, i6) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + const size_t j5 = i5 - m_begins[5]; + const size_t j6 = i6 - m_begins[6]; + return m_map.m_impl_handle[ m_map.m_impl_offset(j0,j1,j2,j3,j4,j5,j6) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 7 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2, i3, i4, i5, i6) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + const size_t j5 = i5 - m_begins[5]; + const size_t j6 = i6 - m_begins[6]; + return m_map.reference(j0,j1,j2,j3,j4,j5,j6); + } + + //------------------------------ + // Rank 8 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 , typename I7 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 8 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2, i3, i4, i5, i6, i7) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + const size_t j5 = i5 - m_begins[5]; + const size_t j6 = i6 - m_begins[6]; + const size_t j7 = i7 - m_begins[7]; + return m_map.m_impl_handle[ m_map.m_impl_offset(j0,j1,j2,j3,j4,j5,j6,j7) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 , typename I7> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 8 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 ) const + { + KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY( (m_track,m_map,m_begins, i0,i1, i2, i3, i4, i5, i6, i7) ) + const size_t j0 = i0 - m_begins[0]; + const size_t j1 = i1 - m_begins[1]; + const size_t j2 = i2 - m_begins[2]; + const size_t j3 = i3 - m_begins[3]; + const size_t j4 = i4 - m_begins[4]; + const size_t j5 = i5 - m_begins[5]; + const size_t j6 = i6 - m_begins[6]; + const size_t j7 = i7 - m_begins[7]; + return m_map.reference(j0,j1,j2,j3,j4,j5,j6,j7); + } + + +#undef KOKKOS_IMPL_OFFSETVIEW_OPERATOR_VERIFY + + //---------------------------------------- + // Standard destructor, constructors, and assignment operators + + KOKKOS_INLINE_FUNCTION + ~OffsetView() {} + + KOKKOS_INLINE_FUNCTION + OffsetView() : m_track(), m_map() { + + for(size_t i = 0; i < Rank; ++i) m_begins[i] = KOKKOS_INVALID_INDEX; + } + + KOKKOS_INLINE_FUNCTION + OffsetView( const OffsetView & rhs ) : m_track( rhs.m_track, traits::is_managed ), m_map( rhs.m_map ), + m_begins(rhs.m_begins) {} + + KOKKOS_INLINE_FUNCTION + OffsetView( OffsetView && rhs ) : m_track( std::move(rhs.m_track) ), + m_map( std::move(rhs.m_map)), m_begins(std::move(rhs.m_begins)) {} + + KOKKOS_INLINE_FUNCTION + OffsetView & operator = ( const OffsetView & rhs ) { + m_track = rhs.m_track ; + m_map = rhs.m_map ; + m_begins = rhs.m_begins; + return *this ; + } + + KOKKOS_INLINE_FUNCTION + OffsetView & operator = ( OffsetView && rhs ) { + m_track = std::move(rhs.m_track) ; + m_map = std::move(rhs.m_map) ; + m_begins = std::move(rhs.m_begins) ; + return *this ; + } + + //interoperability with View + private: + typedef View< typename traits::scalar_array_type , + typename traits::array_layout , + typename traits::device_type , + typename traits::memory_traits > view_type; + public: + + KOKKOS_INLINE_FUNCTION + view_type view() const { + + view_type v(m_track, m_map); + return v ; + } + + template + KOKKOS_INLINE_FUNCTION + OffsetView( const View & aview) : + m_track(aview.impl_track()), m_map(){ + + typedef typename OffsetView::traits SrcTraits ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + static_assert( Mapping::is_assignable , "Incompatible OffsetView copy construction" ); + Mapping::assign( m_map , aview.impl_map() , m_track ); + + for (int i = 0; i < aview.Rank; ++i) { + m_begins[i] = 0; + } + } + + template + KOKKOS_INLINE_FUNCTION + OffsetView( const View & aview + ,const index_list_type & minIndices) : + m_track(aview.impl_track()), m_map(){ + + typedef typename OffsetView::traits SrcTraits ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + static_assert( Mapping::is_assignable , "Incompatible OffsetView copy construction" ); + Mapping::assign( m_map , aview.impl_map() , m_track ); + +#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST + Kokkos::Experimental::Impl::runtime_check_rank_host(traits::rank_dynamic, Rank, minIndices, label()); +#else + Kokkos::Experimental::Impl::runtime_check_rank_device(traits::rank_dynamic, Rank, minIndices); + +#endif + + for (size_t i = 0; i < minIndices.size(); ++i) { + m_begins[i] = minIndices.begin()[i]; + } + } + template + KOKKOS_INLINE_FUNCTION + OffsetView( const View & aview + ,const begins_type & beg) : + m_track(aview.impl_track()), m_map(), m_begins(beg){ + + typedef typename OffsetView::traits SrcTraits ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + static_assert( Mapping::is_assignable , "Incompatible OffsetView copy construction" ); + Mapping::assign( m_map , aview.impl_map() , m_track ); + + + //#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST + // Kokkos::Experimental::Impl::runtime_check_rank_host(traits::rank_dynamic, Rank, minIndices, label()); + //#else + // Kokkos::Experimental::Impl::runtime_check_rank_device(traits::rank_dynamic, Rank, minIndices); + // + //#endif + + } + + // may assign unmanaged from managed. + + + template< class RT , class ... RP > + KOKKOS_INLINE_FUNCTION + OffsetView( const OffsetView & rhs ) + : m_track( rhs.m_track , traits::is_managed ) + , m_map() + , m_begins(rhs.m_begins) + { + typedef typename OffsetView::traits SrcTraits ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + static_assert( Mapping::is_assignable , "Incompatible OffsetView copy construction" ); + Mapping::assign( m_map , rhs.m_map , rhs.m_track ); //swb what about assign? + } + + + //---------------------------------------- + // Allocation tracking properties + KOKKOS_INLINE_FUNCTION + int use_count() const + { return m_track.use_count(); } + + inline + const std::string label() const + { return m_track.template get_label< typename traits::memory_space >(); } + + + template< typename Label> + explicit inline + OffsetView( const Label & arg_label + ,typename std::enable_if::value , const index_list_type >::type + range0 + ,const index_list_type range1 = KOKKOS_INVALID_INDEX_RANGE + ,const index_list_type range2 = KOKKOS_INVALID_INDEX_RANGE + ,const index_list_type range3 = KOKKOS_INVALID_INDEX_RANGE + ,const index_list_type range4 = KOKKOS_INVALID_INDEX_RANGE + ,const index_list_type range5 = KOKKOS_INVALID_INDEX_RANGE + ,const index_list_type range6 = KOKKOS_INVALID_INDEX_RANGE + ,const index_list_type range7 = KOKKOS_INVALID_INDEX_RANGE + + ) : OffsetView( Kokkos::Impl::ViewCtorProp< std::string >( arg_label ), + typename traits::array_layout + ( range0.begin()[1] - range0.begin()[0] + 1, range1.begin()[1] - range1.begin()[0] + 1 , + range2.begin()[1] - range2.begin()[0] + 1, range3.begin()[1] - range3.begin()[0] + 1, + range4.begin()[1] - range4.begin()[0] + 1, range5.begin()[1] - range5.begin()[0] + 1 , + range6.begin()[1] - range6.begin()[0] + 1, range7.begin()[1] - range7.begin()[0] + 1 ), + {range0.begin()[0], range1.begin()[0], range2.begin()[0], range3.begin()[0], range4.begin()[0], + range5.begin()[0], range6.begin()[0], range7.begin()[0] }) + { + + } + + + + template + explicit KOKKOS_INLINE_FUNCTION + OffsetView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop + ,typename std::enable_if< Kokkos::Impl::ViewCtorProp< P... >::has_pointer , typename traits::array_layout >::type const & arg_layout + ,const index_list_type minIndices + ) + : m_track() // No memory tracking + , m_map( arg_prop , arg_layout ) + { + + + for (size_t i = 0; i < minIndices.size(); ++i) { + m_begins[i] = minIndices.begin()[i]; + } + static_assert( + std::is_same< pointer_type + , typename Kokkos::Impl::ViewCtorProp< P... >::pointer_type + >::value , + "When constructing OffsetView to wrap user memory, you must supply matching pointer type" ); + } + + template + explicit inline + OffsetView( const Kokkos::Impl::ViewCtorProp< P ... > & arg_prop + , typename std::enable_if< ! Kokkos::Impl::ViewCtorProp< P... >::has_pointer , typename traits::array_layout>::type const & arg_layout + ,const index_list_type minIndices + ) + : m_track() + , m_map() + + { + + for(size_t i = 0; i < Rank; ++i) + m_begins[i] = minIndices.begin()[i]; + + // Append layout and spaces if not input + typedef Kokkos::Impl::ViewCtorProp< P ... > alloc_prop_input ; + + // use 'std::integral_constant' for non-types + // to avoid duplicate class error. + typedef Kokkos::Impl::ViewCtorProp + < P ..., typename std::conditional < alloc_prop_input::has_label + , std::integral_constant, typename std::string >::type + , typename std::conditional + < alloc_prop_input::has_memory_space + , std::integral_constant + , typename traits::device_type::memory_space + >::type + , typename std::conditional + < alloc_prop_input::has_execution_space + , std::integral_constant + , typename traits::device_type::execution_space + >::type + > alloc_prop ; + + static_assert( traits::is_managed + , "OffsetView allocation constructor requires managed memory" ); + + if ( alloc_prop::initialize && +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + ! alloc_prop::execution_space::is_initialized() +#else + ! alloc_prop::execution_space::impl_is_initialized() +#endif + ) { + // If initializing view data then + // the execution space must be initialized. + Kokkos::Impl::throw_runtime_exception("Constructing OffsetView and initializing data with uninitialized execution space"); + } + + // Copy the input allocation properties with possibly defaulted properties + alloc_prop prop( arg_prop ); + + //------------------------------------------------------------ +#if defined( KOKKOS_ENABLE_CUDA ) + // If allocating in CudaUVMSpace must fence before and after + // the allocation to protect against possible concurrent access + // on the CPU and the GPU. + // Fence using the trait's executon space (which will be Kokkos::Cuda) + // to avoid incomplete type errors from usng Kokkos::Cuda directly. + if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) { + traits::device_type::memory_space::execution_space::fence(); + } +#endif + //------------------------------------------------------------ + + Kokkos::Impl::SharedAllocationRecord<> * + record = m_map.allocate_shared( prop , arg_layout ); + + //------------------------------------------------------------ +#if defined( KOKKOS_ENABLE_CUDA ) + if ( std::is_same< Kokkos::CudaUVMSpace , typename traits::device_type::memory_space >::value ) { + traits::device_type::memory_space::execution_space::fence(); + } +#endif + //------------------------------------------------------------ + + // Setup and initialization complete, start tracking + m_track.assign_allocated_record_to_uninitialized( record ); + +#ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST + Kokkos::Experimental::Impl::runtime_check_rank_host(traits::rank_dynamic, Rank, minIndices, label()); +#else + Kokkos::Experimental::Impl::runtime_check_rank_device(traits::rank_dynamic, Rank, minIndices); + +#endif + + } + + + }; + + + + /** \brief Temporary free function rank() + * until rank() is implemented + * in the View + */ + template < typename D , class ... P > + KOKKOS_INLINE_FUNCTION + constexpr unsigned rank( const OffsetView & V ) { return V.Rank; } //Temporary until added to view + + //---------------------------------------------------------------------------- + //---------------------------------------------------------------------------- + namespace Impl { + + template< class T > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< std::is_integral::value, T>::type + shift_input(const T arg, const int64_t offset) + { + return arg - offset; + } + + KOKKOS_INLINE_FUNCTION + Kokkos::Impl::ALL_t + shift_input(const Kokkos::Impl::ALL_t arg, const int64_t offset) + { + return arg; + } + + template< class T > + KOKKOS_INLINE_FUNCTION + typename std::enable_if< std::is_integral::value, Kokkos::pair >::type + shift_input(const Kokkos::pair arg, const int64_t offset) + { + + return Kokkos::make_pair(arg.first - offset, arg.second - offset); + + } + template< class T > + inline + typename std::enable_if< std::is_integral::value, std::pair >::type + shift_input(const std::pair arg, const int64_t offset) + { + + return std::make_pair(arg.first - offset, arg.second - offset); + + } + + template + KOKKOS_INLINE_FUNCTION + void + map_arg_to_new_begin(const size_t i, + Kokkos::Array &subviewBegins, typename std::enable_if< N != 0, const Arg>::type shiftedArg, + const Arg arg, const A viewBegins, size_t & counter) { + + if( !std::is_integral::value) { + subviewBegins[counter] = shiftedArg == arg ? viewBegins[i] : 0; + counter++; + } + } + + template + KOKKOS_INLINE_FUNCTION + void + map_arg_to_new_begin(const size_t i, + Kokkos::Array &subviewBegins, typename std::enable_if< N == 0, const Arg>::type shiftedArg, + const Arg arg, const A viewBegins, size_t & counter) { + + } + + + template< class D, class ... P , class T > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T arg) { + + auto theView = src.view(); + auto begins = src.begins(); + + T shiftedArg = shift_input(arg, begins[0]); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T>::type::Rank; + + auto theSubview = Kokkos::subview( theView , shiftedArg); + + Kokkos::Array subviewBegins; + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg, arg, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + + } + + template< class D, class ... P , class T0, class T1 > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1 + >::type >::type + subview_offset(const Kokkos::Experimental::OffsetView< D, P... > & src, T0 arg0, T1 arg1) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + + auto theSubview = Kokkos::subview(theView , shiftedArg0, shiftedArg1); + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1>::type::Rank; + + Kokkos::Array subviewBegins; + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + + } + + template< class D, class ... P , class T0, class T1, class T2 > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1, T2 + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T0 arg0, T1 arg1, T2 arg2) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + T2 shiftedArg2 = shift_input(arg2, begins[2]); + + auto theSubview = Kokkos::subview( theView , shiftedArg0, shiftedArg1, shiftedArg2); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1, T2>::type::Rank; + + Kokkos::Array subviewBegins; + + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(2, subviewBegins, shiftedArg2, arg2, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1, T2 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + } + + template< class D, class ... P , class T0, class T1, class T2, class T3 > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1, T2, T3 + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T0 arg0, T1 arg1, T2 arg2, T3 arg3) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + T2 shiftedArg2 = shift_input(arg2, begins[2]); + T3 shiftedArg3 = shift_input(arg3, begins[3]); + + auto theSubview = Kokkos::subview( theView , shiftedArg0, shiftedArg1, shiftedArg2, shiftedArg3); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1, T2, T3>::type::Rank; + Kokkos::Array subviewBegins; + + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(2, subviewBegins, shiftedArg2, arg2, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(3, subviewBegins, shiftedArg3, arg3, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1, T2, T3 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + } + + template< class D, class ... P , class T0, class T1, class T2, class T3, class T4 > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1, T2, T3, T4 + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T0 arg0, T1 arg1, T2 arg2, T3 arg3, T4 arg4) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + T2 shiftedArg2 = shift_input(arg2, begins[2]); + T3 shiftedArg3 = shift_input(arg3, begins[3]); + T4 shiftedArg4 = shift_input(arg4, begins[4]); + + auto theSubview = Kokkos::subview( theView , shiftedArg0, shiftedArg1, shiftedArg2, shiftedArg3, shiftedArg4); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1, T2, T3, T4>::type::Rank; + Kokkos::Array subviewBegins; + + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(2, subviewBegins, shiftedArg2, arg2, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(3, subviewBegins, shiftedArg3, arg3, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(4, subviewBegins, shiftedArg4, arg4, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1, T2, T3, T4 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + } + + template< class D, class ... P , class T0, class T1, class T2, class T3, class T4, + class T5 > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1, T2, T3, T4, T5 + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T0 arg0, T1 arg1, T2 arg2, T3 arg3, T4 arg4, T5 arg5) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + T2 shiftedArg2 = shift_input(arg2, begins[2]); + T3 shiftedArg3 = shift_input(arg3, begins[3]); + T4 shiftedArg4 = shift_input(arg4, begins[4]); + T5 shiftedArg5 = shift_input(arg5, begins[5]); + + auto theSubview = Kokkos::subview( theView , shiftedArg0, shiftedArg1, shiftedArg2, shiftedArg3, shiftedArg4, shiftedArg5); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1, T2, T3, T4, T5>::type::Rank; + + Kokkos::Array subviewBegins; + + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(2, subviewBegins, shiftedArg2, arg2, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(3, subviewBegins, shiftedArg3, arg3, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(4, subviewBegins, shiftedArg4, arg4, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(5, subviewBegins, shiftedArg5, arg5, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1, T2, T3, T4, T5 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + } + template< class D, class ... P , class T0, class T1, class T2, class T3, class T4, + class T5, class T6> + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1, T2, T3, T4, T5, T6 + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T0 arg0, T1 arg1, T2 arg2, T3 arg3, T4 arg4, T5 arg5, + T6 arg6) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + T2 shiftedArg2 = shift_input(arg2, begins[2]); + T3 shiftedArg3 = shift_input(arg3, begins[3]); + T4 shiftedArg4 = shift_input(arg4, begins[4]); + T5 shiftedArg5 = shift_input(arg5, begins[5]); + T6 shiftedArg6 = shift_input(arg6, begins[6]); + + auto theSubview = Kokkos::subview( theView , shiftedArg0, shiftedArg1, shiftedArg2, shiftedArg3, shiftedArg4, shiftedArg5, + shiftedArg6); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1, T2, T3, T4, T5, T6>::type::Rank; + + Kokkos::Array subviewBegins; + + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(2, subviewBegins, shiftedArg2, arg2, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(3, subviewBegins, shiftedArg3, arg3, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(4, subviewBegins, shiftedArg4, arg4, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(5, subviewBegins, shiftedArg5, arg5, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(6, subviewBegins, shiftedArg6, arg6, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1, T2, T3, T4, T5, + T6 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + } + + template< class D, class ... P , class T0, class T1, class T2, class T3, class T4, + class T5, class T6, class T7> + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , T0, T1, T2, T3, T4, T5, T6, T7 + >::type >::type + subview_offset(const OffsetView< D, P... > & src, T0 arg0, T1 arg1, T2 arg2, T3 arg3, T4 arg4, T5 arg5, + T6 arg6, T7 arg7) { + + auto theView = src.view(); + auto begins = src.begins(); + + T0 shiftedArg0 = shift_input(arg0, begins[0]); + T1 shiftedArg1 = shift_input(arg1, begins[1]); + T2 shiftedArg2 = shift_input(arg2, begins[2]); + T3 shiftedArg3 = shift_input(arg3, begins[3]); + T4 shiftedArg4 = shift_input(arg4, begins[4]); + T5 shiftedArg5 = shift_input(arg5, begins[5]); + T6 shiftedArg6 = shift_input(arg6, begins[6]); + T7 shiftedArg7 = shift_input(arg7, begins[7]); + + auto theSubview = Kokkos::subview( theView , shiftedArg0, shiftedArg1, shiftedArg2, shiftedArg3, shiftedArg4, shiftedArg5, + shiftedArg6, shiftedArg7); + + constexpr size_t rank = Kokkos::Impl::ViewMapping + < void /* deduce subview type from source view traits */ + , ViewTraits< D , P... > + , T0, T1, T2, T3, T4, T5, T6, T7>::type::Rank; + + Kokkos::Array subviewBegins; + + size_t counter = 0; + Kokkos::Experimental::Impl::map_arg_to_new_begin(0, subviewBegins, shiftedArg0, arg0, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(1, subviewBegins, shiftedArg1, arg1, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(2, subviewBegins, shiftedArg2, arg2, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(3, subviewBegins, shiftedArg3, arg3, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(4, subviewBegins, shiftedArg4, arg4, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(5, subviewBegins, shiftedArg5, arg5, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(6, subviewBegins, shiftedArg6, arg6, begins, counter); + Kokkos::Experimental::Impl::map_arg_to_new_begin(7, subviewBegins, shiftedArg7, arg7, begins, counter); + + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType , T0, T1, T2, T3, T4, T5, + T6, T7 >::type >::type offsetView(theSubview, subviewBegins); + + return offsetView; + } + } + + template< class D, class ... P , class ... Args > + KOKKOS_INLINE_FUNCTION + typename Kokkos::Experimental::Impl::GetOffsetViewTypeFromViewType + , Args ... + >::type >::type + subview( const OffsetView< D, P... > & src , Args ... args ) + { + static_assert( OffsetView< D , P... >::Rank == sizeof...(Args) , + "subview requires one argument for each source OffsetView rank" ); + + + return Kokkos::Experimental::Impl::subview_offset(src, args...); + + + } + + } +} +//---------------------------------------------------------------------------- +//---------------------------------------------------------------------------- + +namespace Kokkos { + namespace Experimental { + template< class LT , class ... LP , class RT , class ... RP > + KOKKOS_INLINE_FUNCTION + bool operator == ( const OffsetView & lhs , + const OffsetView & rhs ) + { + // Same data, layout, dimensions + typedef ViewTraits lhs_traits ; + typedef ViewTraits rhs_traits ; + + return + std::is_same< typename lhs_traits::const_value_type , + typename rhs_traits::const_value_type >::value && + std::is_same< typename lhs_traits::array_layout , + typename rhs_traits::array_layout >::value && + std::is_same< typename lhs_traits::memory_space , + typename rhs_traits::memory_space >::value && + unsigned(lhs_traits::rank) == unsigned(rhs_traits::rank) && + lhs.data() == rhs.data() && + lhs.span() == rhs.span() && + lhs.extent(0) == rhs.extent(0) && + lhs.extent(1) == rhs.extent(1) && + lhs.extent(2) == rhs.extent(2) && + lhs.extent(3) == rhs.extent(3) && + lhs.extent(4) == rhs.extent(4) && + lhs.extent(5) == rhs.extent(5) && + lhs.extent(6) == rhs.extent(6) && + lhs.extent(7) == rhs.extent(7) && + lhs.begin(0) == rhs.begin(0) && + lhs.begin(1) == rhs.begin(1) && + lhs.begin(2) == rhs.begin(2) && + lhs.begin(3) == rhs.begin(3) && + lhs.begin(4) == rhs.begin(4) && + lhs.begin(5) == rhs.begin(5) && + lhs.begin(6) == rhs.begin(6) && + lhs.begin(7) == rhs.begin(7) + ; + } + + template< class LT , class ... LP , class RT , class ... RP > + KOKKOS_INLINE_FUNCTION + bool operator != ( const OffsetView & lhs , + const OffsetView & rhs ) + { + return ! ( operator==(lhs,rhs) ); + } + + template< class LT , class ... LP , class RT , class ... RP > + KOKKOS_INLINE_FUNCTION + bool operator == ( const View & lhs , + const OffsetView & rhs ) + { + // Same data, layout, dimensions + typedef ViewTraits lhs_traits ; + typedef ViewTraits rhs_traits ; + + return + std::is_same< typename lhs_traits::const_value_type , + typename rhs_traits::const_value_type >::value && + std::is_same< typename lhs_traits::array_layout , + typename rhs_traits::array_layout >::value && + std::is_same< typename lhs_traits::memory_space , + typename rhs_traits::memory_space >::value && + unsigned(lhs_traits::rank) == unsigned(rhs_traits::rank) && + lhs.data() == rhs.data() && + lhs.span() == rhs.span() && + lhs.extent(0) == rhs.extent(0) && + lhs.extent(1) == rhs.extent(1) && + lhs.extent(2) == rhs.extent(2) && + lhs.extent(3) == rhs.extent(3) && + lhs.extent(4) == rhs.extent(4) && + lhs.extent(5) == rhs.extent(5) && + lhs.extent(6) == rhs.extent(6) && + lhs.extent(7) == rhs.extent(7) + ; + } + + template< class LT , class ... LP , class RT , class ... RP > + KOKKOS_INLINE_FUNCTION + bool operator == ( const OffsetView & lhs , + const View & rhs ) + { return rhs == lhs;} + + } +} /* namespace Kokkos */ + +//---------------------------------------------------------------------------- +//---------------------------------------------------------------------------- + + +namespace Kokkos { + namespace Experimental { + template< class DT , class ... DP > + inline + void deep_copy + ( const OffsetView & dst + , typename ViewTraits::const_value_type & value + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value + >::type * = 0 ) + { + static_assert( + std::is_same< typename ViewTraits::non_const_value_type , + typename ViewTraits::value_type >::value + , "deep_copy requires non-const type" ); + + auto dstView = dst.view(); + Kokkos::deep_copy( dstView , value ); + + } + + template< class DT , class ... DP , class ST , class ... SP > + inline + void deep_copy + ( const OffsetView & dst + , const OffsetView & value + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value + >::type * = 0 ) + { + static_assert( + std::is_same< typename ViewTraits::value_type , + typename ViewTraits::non_const_value_type >::value + , "deep_copy requires matching non-const destination type" ); + + auto dstView = dst.view(); + Kokkos::deep_copy( dstView , value.view() ); + + } + template< class DT , class ... DP , class ST , class ... SP > + inline + void deep_copy + ( const OffsetView & dst + , const View & value + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value + >::type * = 0 ) + { + static_assert( + std::is_same< typename ViewTraits::value_type , + typename ViewTraits::non_const_value_type >::value + , "deep_copy requires matching non-const destination type" ); + + auto dstView = dst.view(); + Kokkos::deep_copy( dstView , value); + + } + + template< class DT , class ... DP , class ST , class ... SP > + inline + void deep_copy + ( const View & dst + , const OffsetView & value + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value + >::type * = 0 ) + { + static_assert( + std::is_same< typename ViewTraits::value_type , + typename ViewTraits::non_const_value_type >::value + , "deep_copy requires matching non-const destination type" ); + + Kokkos::deep_copy( dst , value.view() ); + + } + namespace Impl { + + // Deduce Mirror Types + template + struct MirrorOffsetViewType { + // The incoming view_type + typedef typename Kokkos::Experimental::OffsetView src_view_type; + // The memory space for the mirror view + typedef typename Space::memory_space memory_space; + // Check whether it is the same memory space + enum { is_same_memspace = std::is_same::value }; + // The array_layout + typedef typename src_view_type::array_layout array_layout; + // The data type (we probably want it non-const since otherwise we can't even deep_copy to it. + typedef typename src_view_type::non_const_data_type data_type; + // The destination view type if it is not the same memory space + typedef Kokkos::Experimental::OffsetView dest_view_type; + // If it is the same memory_space return the existsing view_type + // This will also keep the unmanaged trait if necessary + typedef typename std::conditional::type view_type; + }; + + template + struct MirrorOffsetType { + // The incoming view_type + typedef typename Kokkos::Experimental::OffsetView src_view_type; + // The memory space for the mirror view + typedef typename Space::memory_space memory_space; + // Check whether it is the same memory space + enum { is_same_memspace = std::is_same::value }; + // The array_layout + typedef typename src_view_type::array_layout array_layout; + // The data type (we probably want it non-const since otherwise we can't even deep_copy to it. + typedef typename src_view_type::non_const_data_type data_type; + // The destination view type if it is not the same memory space + typedef Kokkos::Experimental::OffsetView view_type; + }; + + } + + template< class T , class ... P > + inline + typename Kokkos::Experimental::OffsetView::HostMirror + create_mirror( const Kokkos::Experimental::OffsetView & src + , typename std::enable_if< + ! std::is_same< typename Kokkos::ViewTraits::array_layout + , Kokkos::LayoutStride >::value + >::type * = 0 + ) + { + typedef OffsetView src_type ; + typedef typename src_type::HostMirror dst_type ; + + return dst_type( Kokkos::Impl::ViewCtorProp< std::string >(std::string( src.label() ).append("_mirror") ), + typename Kokkos::ViewTraits::array_layout + ( src.extent(0), src.extent(1), src.extent(2), src.extent(3), src.extent(4), + src.extent(5), src.extent(6), src.extent(7) ), + { src.begin(0), src.begin(1), src.begin(2), src.begin(3), src.begin(4), + src.begin(5), src.begin(6), src.begin(7) }); + } + + template< class T , class ... P > + inline + typename Kokkos::Experimental::OffsetView::HostMirror + create_mirror( const Kokkos::Experimental::OffsetView & src + , typename std::enable_if< + std::is_same< typename Kokkos::ViewTraits::array_layout + , Kokkos::LayoutStride >::value + >::type * = 0 + ) + { + typedef OffsetView src_type ; + typedef typename src_type::HostMirror dst_type ; + + Kokkos::LayoutStride layout ; + + layout.dimension[0] = src.extent(0); + layout.dimension[1] = src.extent(1); + layout.dimension[2] = src.extent(2); + layout.dimension[3] = src.extent(3); + layout.dimension[4] = src.extent(4); + layout.dimension[5] = src.extent(5); + layout.dimension[6] = src.extent(6); + layout.dimension[7] = src.extent(7); + + layout.stride[0] = src.stride_0(); + layout.stride[1] = src.stride_1(); + layout.stride[2] = src.stride_2(); + layout.stride[3] = src.stride_3(); + layout.stride[4] = src.stride_4(); + layout.stride[5] = src.stride_5(); + layout.stride[6] = src.stride_6(); + layout.stride[7] = src.stride_7(); + + return dst_type( std::string( src.label() ).append("_mirror") , layout, + { src.begin(0), src.begin(1), src.begin(2), src.begin(3), src.begin(4), + src.begin(5), src.begin(6), src.begin(7) } ); + } + + + // Create a mirror in a new space (specialization for different space) + template + typename Kokkos::Experimental::Impl::MirrorOffsetType::view_type + create_mirror(const Space& , const Kokkos::Experimental::OffsetView & src) { + return typename Kokkos::Experimental::Impl::MirrorOffsetType::view_type(src.label(),src.layout(), + { src.begin(0), src.begin(1), src.begin(2), src.begin(3), src.begin(4), + src.begin(5), src.begin(6), src.begin(7) } ); + } + + + template< class T , class ... P > + inline + typename Kokkos::Experimental::OffsetView< T, P... >::HostMirror + create_mirror_view( const typename Kokkos::Experimental::OffsetView< T,P... > & src + , typename std::enable_if<( + std::is_same< typename Kokkos::Experimental::OffsetView::memory_space + , typename Kokkos::Experimental::OffsetView::HostMirror::memory_space + >::value + && + std::is_same< typename Kokkos::Experimental::OffsetView::data_type + , typename Kokkos::Experimental::OffsetView::HostMirror::data_type + >::value + )>::type * = 0 + ) + { + return src ; + } + + template< class T , class ... P > + inline + typename Kokkos::Experimental::OffsetView::HostMirror + create_mirror_view( const Kokkos::Experimental::OffsetView & src + , typename std::enable_if< ! ( + std::is_same< typename Kokkos::Experimental::OffsetView::memory_space + , typename Kokkos::Experimental::OffsetView::HostMirror::memory_space + >::value + && + std::is_same< typename Kokkos::Experimental::OffsetView::data_type + , typename Kokkos::Experimental::OffsetView::HostMirror::data_type + >::value + )>::type * = 0 + ) + { + return Kokkos::Experimental::create_mirror( src ); + } + + // Create a mirror view in a new space (specialization for same space) + template + typename Kokkos::Experimental::Impl::MirrorOffsetViewType::view_type + create_mirror_view(const Space& , const Kokkos::Experimental::OffsetView & src + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + return src; + } + + // Create a mirror view in a new space (specialization for different space) + template + typename Kokkos::Experimental::Impl::MirrorOffsetViewType::view_type + create_mirror_view(const Space& , const Kokkos::Experimental::OffsetView & src + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + return typename Kokkos::Experimental::Impl::MirrorOffsetViewType::view_type(src.label(),src.layout(), + { src.begin(0), src.begin(1), src.begin(2), src.begin(3), src.begin(4), + src.begin(5), src.begin(6), src.begin(7) } ); + } + // + // // Create a mirror view and deep_copy in a new space (specialization for same space) + // template + // typename Kokkos::Experimental::Impl::MirrorViewType::view_type + // create_mirror_view_and_copy(const Space& , const Kokkos::Experimental::OffsetView & src + // , std::string const& name = "" + // , typename std::enable_if::is_same_memspace>::type* = 0 ) { + // (void)name; + // return src; + // } + // + // // Create a mirror view and deep_copy in a new space (specialization for different space) + // template + // typename Kokkos::Experimental::Impl::MirrorViewType::view_type + // create_mirror_view_and_copy(const Space& , const Kokkos::Experimental::OffsetView & src + // , std::string const& name = "" + // , typename std::enable_if::is_same_memspace>::type* = 0 ) { + // using Mirror = typename Kokkos::Experimental::Impl::MirrorViewType::view_type; + // std::string label = name.empty() ? src.label() : name; + // auto mirror = Mirror(ViewAllocateWithoutInitializing(label), src.layout(), + // { src.begin(0), src.begin(1), src.begin(2), src.begin(3), src.begin(4), + // src.begin(5), src.begin(6), src.begin(7) }); + // deep_copy(mirror, src); + // return mirror; + // } + + } +} /* namespace Kokkos */ + + +//---------------------------------------------------------------------------- +//---------------------------------------------------------------------------- + + +#endif /* KOKKOS_OFFSETVIEW_HPP_ */ diff --git a/lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp b/lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp index c522d85c5b..f63ce4b880 100644 --- a/lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp +++ b/lib/kokkos/containers/src/Kokkos_StaticCrsGraph.hpp @@ -47,7 +47,9 @@ #include #include -#include +#include +#include +#include namespace Kokkos { diff --git a/lib/kokkos/containers/src/Kokkos_Vector.hpp b/lib/kokkos/containers/src/Kokkos_Vector.hpp index 8204ba776e..76c515941e 100644 --- a/lib/kokkos/containers/src/Kokkos_Vector.hpp +++ b/lib/kokkos/containers/src/Kokkos_Vector.hpp @@ -86,14 +86,13 @@ public: vector():DV() { _size = 0; _extra_storage = 1.1; - DV::modified_host() = 1; } vector(int n, Scalar val=Scalar()):DualView("Vector",size_t(n*(1.1))) { _size = n; _extra_storage = 1.1; - DV::modified_host() = 1; + DV::modified_flags(0) = 1; assign(n,val); } @@ -119,16 +118,16 @@ public: /* Assign value either on host or on device */ - if( DV::modified_host() >= DV::modified_device() ) { + if( DV::template need_sync() ) { set_functor_host f(DV::h_view,val); parallel_for(n,f); DV::t_host::execution_space::fence(); - DV::modified_host()++; + DV::template modify(); } else { set_functor f(DV::d_view,val); parallel_for(n,f); DV::t_dev::execution_space::fence(); - DV::modified_device()++; + DV::template modify(); } } @@ -137,7 +136,8 @@ public: } void push_back(Scalar val) { - DV::modified_host()++; + DV::template sync(); + DV::template modify(); if(_size == span()) { size_t new_size = _size*_extra_storage; if(new_size == _size) new_size++; @@ -247,10 +247,10 @@ public: } void on_host() { - DV::modified_host() = DV::modified_device() + 1; + DV::template modify(); } void on_device() { - DV::modified_device() = DV::modified_host() + 1; + DV::template modify(); } void set_overallocation(float extra) { diff --git a/lib/kokkos/containers/unit_tests/CMakeLists.txt b/lib/kokkos/containers/unit_tests/CMakeLists.txt index 3dbe79183a..0f94afec8c 100644 --- a/lib/kokkos/containers/unit_tests/CMakeLists.txt +++ b/lib/kokkos/containers/unit_tests/CMakeLists.txt @@ -23,6 +23,7 @@ TRIBITS_ADD_EXECUTABLE_AND_TEST( threads/TestThreads_DynRankViewAPI_rank12345.cpp threads/TestThreads_DynRankViewAPI_rank67.cpp threads/TestThreads_ErrorReporter.cpp + threads/TestThreads_OffsetView.cpp threads/TestThreads_ScatterView.cpp threads/TestThreads_StaticCrsGraph.cpp threads/TestThreads_UnorderedMap.cpp @@ -47,6 +48,7 @@ TRIBITS_ADD_EXECUTABLE_AND_TEST( serial/TestSerial_DynRankViewAPI_rank12345.cpp serial/TestSerial_DynRankViewAPI_rank67.cpp serial/TestSerial_ErrorReporter.cpp + serial/TestSerial_OffsetView.cpp serial/TestSerial_ScatterView.cpp serial/TestSerial_StaticCrsGraph.cpp serial/TestSerial_UnorderedMap.cpp @@ -71,6 +73,7 @@ TRIBITS_ADD_EXECUTABLE_AND_TEST( openmp/TestOpenMP_DynRankViewAPI_rank12345.cpp openmp/TestOpenMP_DynRankViewAPI_rank67.cpp openmp/TestOpenMP_ErrorReporter.cpp + openmp/TestOpenMP_OffsetView.cpp openmp/TestOpenMP_ScatterView.cpp openmp/TestOpenMP_StaticCrsGraph.cpp openmp/TestOpenMP_UnorderedMap.cpp @@ -95,6 +98,7 @@ TRIBITS_ADD_EXECUTABLE_AND_TEST( cuda/TestCuda_DynRankViewAPI_rank12345.cpp cuda/TestCuda_DynRankViewAPI_rank67.cpp cuda/TestCuda_ErrorReporter.cpp + cuda/TestCuda_OffsetView.cpp cuda/TestCuda_ScatterView.cpp cuda/TestCuda_StaticCrsGraph.cpp cuda/TestCuda_UnorderedMap.cpp diff --git a/lib/kokkos/containers/unit_tests/Makefile b/lib/kokkos/containers/unit_tests/Makefile index 52d5d61aa9..c0e5d2820c 100644 --- a/lib/kokkos/containers/unit_tests/Makefile +++ b/lib/kokkos/containers/unit_tests/Makefile @@ -39,6 +39,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA += TestCuda_DynRankViewAPI_rank12345.o OBJ_CUDA += TestCuda_DynRankViewAPI_rank67.o OBJ_CUDA += TestCuda_ErrorReporter.o + OBJ_CUDA += TestCuda_OffsetView.o OBJ_CUDA += TestCuda_ScatterView.o OBJ_CUDA += TestCuda_StaticCrsGraph.o OBJ_CUDA += TestCuda_UnorderedMap.o @@ -57,6 +58,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) OBJ_ROCM += TestROCm_DynRankViewAPI_rank12345.o OBJ_ROCM += TestROCm_DynRankViewAPI_rank67.o OBJ_ROCM += TestROCm_ErrorReporter.o + OBJ_ROCM += TestROCm_OffsetView.o OBJ_ROCM += TestROCm_ScatterView.o OBJ_ROCM += TestROCm_StaticCrsGraph.o OBJ_ROCM += TestROCm_UnorderedMap.o @@ -75,6 +77,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) OBJ_THREADS += TestThreads_DynRankViewAPI_rank12345.o OBJ_THREADS += TestThreads_DynRankViewAPI_rank67.o OBJ_THREADS += TestThreads_ErrorReporter.o + OBJ_THREADS += TestThreads_OffsetView.o OBJ_THREADS += TestThreads_ScatterView.o OBJ_THREADS += TestThreads_StaticCrsGraph.o OBJ_THREADS += TestThreads_UnorderedMap.o @@ -93,6 +96,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) OBJ_OPENMP += TestOpenMP_DynRankViewAPI_rank12345.o OBJ_OPENMP += TestOpenMP_DynRankViewAPI_rank67.o OBJ_OPENMP += TestOpenMP_ErrorReporter.o + OBJ_OPENMP += TestOpenMP_OffsetView.o OBJ_OPENMP += TestOpenMP_ScatterView.o OBJ_OPENMP += TestOpenMP_StaticCrsGraph.o OBJ_OPENMP += TestOpenMP_UnorderedMap.o @@ -111,6 +115,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) OBJ_SERIAL += TestSerial_DynRankViewAPI_rank12345.o OBJ_SERIAL += TestSerial_DynRankViewAPI_rank67.o OBJ_SERIAL += TestSerial_ErrorReporter.o + OBJ_SERIAL += TestSerial_OffsetView.o OBJ_SERIAL += TestSerial_ScatterView.o OBJ_SERIAL += TestSerial_StaticCrsGraph.o OBJ_SERIAL += TestSerial_UnorderedMap.o diff --git a/lib/kokkos/containers/unit_tests/TestDualView.hpp b/lib/kokkos/containers/unit_tests/TestDualView.hpp index cbff27cb39..767f93c093 100644 --- a/lib/kokkos/containers/unit_tests/TestDualView.hpp +++ b/lib/kokkos/containers/unit_tests/TestDualView.hpp @@ -101,13 +101,98 @@ namespace Impl { result = run_me< Kokkos::DualView >(size,3); } - }; + }; + + template < typename Scalar, class ViewType > + struct SumViewEntriesFunctor { + + typedef Scalar value_type; + + ViewType fv; + + SumViewEntriesFunctor ( const ViewType & fv_ ) : fv(fv_) {} + + KOKKOS_INLINE_FUNCTION + void operator() ( const int i , value_type & total ) const { + for ( size_t j = 0; j < fv.extent(1); ++j ) { + total += fv(i,j); + } + } + + }; + + + template + struct test_dual_view_deep_copy + { + typedef Scalar scalar_type; + typedef Device execution_space; + + template + void run_me() { + + const unsigned int n = 10; + const unsigned int m = 5; + const unsigned int sum_total = n * m; + + ViewType a("A",n,m); + ViewType b("B",n,m); + + Kokkos::deep_copy( a.d_view , 1 ); + + a.template modify(); + a.template sync(); + + // Check device view is initialized as expected + scalar_type a_d_sum = 0; + // Execute on the execution_space associated with t_dev's memory space + typedef typename ViewType::t_dev::memory_space::execution_space t_dev_exec_space; + Kokkos::parallel_reduce( Kokkos::RangePolicy(0,n), SumViewEntriesFunctor(a.d_view), a_d_sum ); + ASSERT_EQ(a_d_sum, sum_total); + + // Check host view is synced as expected + scalar_type a_h_sum = 0; + for ( size_t i = 0; i < a.h_view.extent(0); ++i ) + for ( size_t j = 0; j < a.h_view.extent(1); ++j ) { + a_h_sum += a.h_view(i,j); + } + + ASSERT_EQ(a_h_sum, sum_total); + + + // Test deep_copy + Kokkos::deep_copy( b, a ); + b.template sync(); + + // Perform same checks on b as done on a + // Check device view is initialized as expected + scalar_type b_d_sum = 0; + // Execute on the execution_space associated with t_dev's memory space + Kokkos::parallel_reduce( Kokkos::RangePolicy(0,n), SumViewEntriesFunctor(b.d_view), b_d_sum ); + ASSERT_EQ(b_d_sum, sum_total); + + // Check host view is synced as expected + scalar_type b_h_sum = 0; + for ( size_t i = 0; i < b.h_view.extent(0); ++i ) + for ( size_t j = 0; j < b.h_view.extent(1); ++j ) { + b_h_sum += b.h_view(i,j); + } + + ASSERT_EQ(b_h_sum, sum_total); + + } // end run_me + + test_dual_view_deep_copy() + { + run_me< Kokkos::DualView >(); + } + + }; } // namespace Impl - template void test_dualview_combinations(unsigned int size) { @@ -116,10 +201,21 @@ void test_dualview_combinations(unsigned int size) } +template +void test_dualview_deep_copy() +{ + Impl::test_dual_view_deep_copy (); +} + TEST_F( TEST_CATEGORY, dualview_combination) { test_dualview_combinations(10); } +TEST_F( TEST_CATEGORY, dualview_deep_copy) { + test_dualview_deep_copy(); + test_dualview_deep_copy(); +} + } // namespace Test diff --git a/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp b/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp index 8c073710e2..6684a55452 100644 --- a/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp +++ b/lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp @@ -729,6 +729,7 @@ public: static void run_tests() { run_test_resize_realloc(); run_test_mirror(); + run_test_mirror_and_copy(); run_test_scalar(); run_test(); run_test_const(); @@ -885,6 +886,69 @@ public: } } + static void run_test_mirror_and_copy() + { + // LayoutLeft + { + Kokkos::DynRankView< double, Kokkos::LayoutLeft, Kokkos::HostSpace > a_org( "A", 10 ); + a_org(5) = 42.0; + Kokkos::DynRankView< double, Kokkos::LayoutLeft, Kokkos::HostSpace > a_h = a_org; + auto a_h2 = Kokkos::create_mirror_view_and_copy( Kokkos::HostSpace(), a_h ); + auto a_d = Kokkos::create_mirror_view_and_copy( DeviceType(), a_h ); + auto a_h3 = Kokkos::create_mirror_view_and_copy( Kokkos::HostSpace(), a_d ); + + int equal_ptr_h_h2 = a_h.data() == a_h2.data() ? 1 : 0; + int equal_ptr_h_d = a_h.data() == a_d.data() ? 1 : 0; + int equal_ptr_h2_d = a_h2.data() == a_d.data() ? 1 : 0; + int equal_ptr_h3_d = a_h3.data() == a_d.data() ? 1 : 0; + + int is_same_memspace = std::is_same< Kokkos::HostSpace, typename DeviceType::memory_space >::value ? 1 : 0; + ASSERT_EQ( equal_ptr_h_h2, 1 ); + ASSERT_EQ( equal_ptr_h_d, is_same_memspace ); + ASSERT_EQ( equal_ptr_h2_d, is_same_memspace ); + ASSERT_EQ( equal_ptr_h3_d, is_same_memspace ); + + ASSERT_EQ( a_h.extent(0), a_h3.extent(0) ); + ASSERT_EQ( a_h.extent(0), a_h2.extent(0) ); + ASSERT_EQ( a_h.extent(0), a_d .extent(0) ); + ASSERT_EQ( a_h.extent(0), a_h3.extent(0) ); + ASSERT_EQ( a_h.rank(), a_org.rank() ); + ASSERT_EQ( a_h.rank(), a_h2.rank() ); + ASSERT_EQ( a_h.rank(), a_h3.rank() ); + ASSERT_EQ( a_h.rank(), a_d.rank() ); + ASSERT_EQ( a_org(5), a_h3(5) ); + } + // LayoutRight + { + Kokkos::DynRankView< double, Kokkos::LayoutRight, Kokkos::HostSpace > a_org( "A", 10 ); + a_org(5) = 42.0; + Kokkos::DynRankView< double, Kokkos::LayoutRight, Kokkos::HostSpace > a_h = a_org; + auto a_h2 = Kokkos::create_mirror_view_and_copy( Kokkos::HostSpace(), a_h ); + auto a_d = Kokkos::create_mirror_view_and_copy( DeviceType(), a_h ); + auto a_h3 = Kokkos::create_mirror_view_and_copy( Kokkos::HostSpace(), a_d ); + + int equal_ptr_h_h2 = a_h.data() == a_h2.data() ? 1 : 0; + int equal_ptr_h_d = a_h.data() == a_d.data() ? 1 : 0; + int equal_ptr_h2_d = a_h2.data() == a_d.data() ? 1 : 0; + int equal_ptr_h3_d = a_h3.data() == a_d.data() ? 1 : 0; + + int is_same_memspace = std::is_same< Kokkos::HostSpace, typename DeviceType::memory_space >::value ? 1 : 0; + ASSERT_EQ( equal_ptr_h_h2, 1 ); + ASSERT_EQ( equal_ptr_h_d, is_same_memspace ); + ASSERT_EQ( equal_ptr_h2_d, is_same_memspace ); + ASSERT_EQ( equal_ptr_h3_d, is_same_memspace ); + + ASSERT_EQ( a_h.extent(0), a_h3.extent(0) ); + ASSERT_EQ( a_h.extent(0), a_h2.extent(0) ); + ASSERT_EQ( a_h.extent(0), a_d .extent(0) ); + ASSERT_EQ( a_h.rank(), a_org.rank() ); + ASSERT_EQ( a_h.rank(), a_h2.rank() ); + ASSERT_EQ( a_h.rank(), a_h3.rank() ); + ASSERT_EQ( a_h.rank(), a_d.rank() ); + ASSERT_EQ( a_org(5), a_h3(5) ); + } + } + static void run_test_scalar() { typedef typename dView0::HostMirror hView0 ; //HostMirror of DynRankView is a DynRankView diff --git a/lib/kokkos/containers/unit_tests/TestOffsetView.hpp b/lib/kokkos/containers/unit_tests/TestOffsetView.hpp new file mode 100644 index 0000000000..6965199d45 --- /dev/null +++ b/lib/kokkos/containers/unit_tests/TestOffsetView.hpp @@ -0,0 +1,426 @@ +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER + +/* + * FIXME the OffsetView class is really not very well tested. + */ +#ifndef CONTAINERS_UNIT_TESTS_TESTOFFSETVIEW_HPP_ +#define CONTAINERS_UNIT_TESTS_TESTOFFSETVIEW_HPP_ + + + +#include +#include +#include +#include +#include +#include +#include + +using std::endl; +using std::cout; + +namespace Test{ + + template + void test_offsetview_construction(unsigned int size) + { + + typedef Kokkos::Experimental::OffsetView offset_view_type; + typedef Kokkos::View view_type; + + Kokkos::Experimental::index_list_type range0 = {-1, 3}; + Kokkos::Experimental::index_list_type range1 = {-2, 2}; + + offset_view_type ov("firstOV", range0, range1); + + ASSERT_EQ("firstOV", ov.label()); + ASSERT_EQ(2, ov.Rank); + + ASSERT_EQ(ov.begin(0), -1); + ASSERT_EQ(ov.end(0), 4); + + ASSERT_EQ(ov.begin(1), -2); + ASSERT_EQ(ov.end(1), 3); + + ASSERT_EQ(ov.extent(0), 5); + ASSERT_EQ(ov.extent(1), 5); + + const int ovmin0 = ov.begin(0); + const int ovend0 = ov.end(0); + const int ovmin1 = ov.begin(1); + const int ovend1 = ov.end(1); + +#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) + { + Kokkos::Experimental::OffsetView offsetV1("OneDOffsetView", range0); + + Kokkos::RangePolicy rangePolicy1(offsetV1.begin(0), offsetV1.end(0)); + Kokkos::parallel_for(rangePolicy1, KOKKOS_LAMBDA (const int i){ + offsetV1(i) = 1; + } + ); + Kokkos::fence(); + + int OVResult = 0; + Kokkos::parallel_reduce(rangePolicy1, KOKKOS_LAMBDA(const int i, int & updateMe){ + updateMe += offsetV1(i); + }, OVResult); + + Kokkos::fence(); + ASSERT_EQ(OVResult, offsetV1.end(0) - offsetV1.begin(0)) << "found wrong number of elements in OffsetView that was summed."; + + } + { //test deep copy of scalar const value into mirro + const int constVal = 6; + typename offset_view_type::HostMirror hostOffsetView = + Kokkos::Experimental::create_mirror_view(ov); + + Kokkos::Experimental::deep_copy(hostOffsetView, constVal); + + for(int i = hostOffsetView.begin(0); i < hostOffsetView.end(0); ++i) { + for(int j = hostOffsetView.begin(1); j < hostOffsetView.end(1); ++j) { + ASSERT_EQ(hostOffsetView(i,j), constVal) << "Bad data found in OffsetView"; + } + } + } + + typedef Kokkos::MDRangePolicy, Kokkos::IndexType > range_type; + typedef typename range_type::point_type point_type; + + range_type rangePolicy2D(point_type{ {ovmin0, ovmin1 } }, + point_type{ { ovend0, ovend1 } }); + + const int constValue = 9; + Kokkos::parallel_for(rangePolicy2D, KOKKOS_LAMBDA (const int i, const int j) { + ov(i,j) = constValue; + } + ); + + //test offsetview to offsetviewmirror deep copy + typename offset_view_type::HostMirror hostOffsetView = + Kokkos::Experimental::create_mirror_view(ov); + + Kokkos::Experimental::deep_copy(hostOffsetView, ov); + + for(int i = hostOffsetView.begin(0); i < hostOffsetView.end(0); ++i) { + for(int j = hostOffsetView.begin(1); j < hostOffsetView.end(1); ++j) { + ASSERT_EQ(hostOffsetView(i,j), constValue) << "Bad data found in OffsetView"; + } + } + + int OVResult = 0; + Kokkos::parallel_reduce(rangePolicy2D, KOKKOS_LAMBDA(const int i, const int j, int & updateMe){ + updateMe += ov(i, j); + }, OVResult); + + int answer = 0; + for(int i = ov.begin(0); i < ov.end(0); ++i) { + for(int j = ov.begin(1); j < ov.end(1); ++j) { + answer += constValue; + } + } + + ASSERT_EQ(OVResult, answer) << "Bad data found in OffsetView"; +#endif + + { + offset_view_type ovCopy(ov); + ASSERT_EQ(ovCopy==ov, true) << + "Copy constructor or equivalence operator broken"; + } + + { + offset_view_type ovAssigned = ov; + ASSERT_EQ(ovAssigned==ov, true) << + "Assignment operator or equivalence operator broken"; + } + + { //construct OffsetView from a View plus begins array + const int extent0 = 100; + const int extent1 = 200; + const int extent2 = 300; + Kokkos::View view3D("view3D", extent0, extent1, extent2); + + Kokkos::deep_copy(view3D, 1); + + Kokkos::Array begins = {{-10, -20, -30}}; + Kokkos::Experimental::OffsetView offsetView3D(view3D, begins); + + typedef Kokkos::MDRangePolicy, Kokkos::IndexType > range3_type; + typedef typename range3_type::point_type point3_type; + + range3_type rangePolicy3DZero(point3_type{ {0, 0, 0 } }, + point3_type{ { extent0, extent1, extent2 } }); + +#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) + int view3DSum = 0; + Kokkos::parallel_reduce(rangePolicy3DZero, KOKKOS_LAMBDA(const int i, const int j, int k, int & updateMe){ + updateMe += view3D(i, j, k); + }, view3DSum); + + range3_type rangePolicy3D(point3_type{ {begins[0], begins[1], begins[2] } }, + point3_type{ { begins[0] + extent0, begins[1] + extent1, begins[2] + extent2 } }); + int offsetView3DSum = 0; + + Kokkos::parallel_reduce(rangePolicy3D, KOKKOS_LAMBDA(const int i, const int j, int k, int & updateMe){ + updateMe += offsetView3D(i, j, k); + }, offsetView3DSum); + + ASSERT_EQ(view3DSum, offsetView3DSum) << "construction of OffsetView from View and begins array broken."; +#endif + } + view_type viewFromOV = ov.view(); + + ASSERT_EQ(viewFromOV == ov, true) << + "OffsetView::view() or equivalence operator View == OffsetView broken"; + + { + offset_view_type ovFromV(viewFromOV, {-1, -2}); + + ASSERT_EQ(ovFromV == viewFromOV , true) << + "Construction of OffsetView from View or equivalence operator OffsetView == View broken"; + } + { + offset_view_type ovFromV = viewFromOV; + ASSERT_EQ(ovFromV == viewFromOV , true) << + "Construction of OffsetView from View by assignment (implicit conversion) or equivalence operator OffsetView == View broken"; + } + + {// test offsetview to view deep copy + view_type aView("aView", ov.extent(0), ov.extent(1)); + Kokkos::Experimental::deep_copy(aView, ov); + +#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) + int sum = 0; + Kokkos::parallel_reduce(rangePolicy2D, KOKKOS_LAMBDA(const int i, const int j, int & updateMe){ + updateMe += ov(i, j) - aView(i- ov.begin(0), j-ov.begin(1)); + }, sum); + + ASSERT_EQ(sum, 0) << "deep_copy(view, offsetView) broken."; +#endif + } + + {// test view to offsetview deep copy + view_type aView("aView", ov.extent(0), ov.extent(1)); + + Kokkos::deep_copy(aView, 99); + Kokkos::Experimental::deep_copy(ov, aView); + + +#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) + int sum = 0; + Kokkos::parallel_reduce(rangePolicy2D, KOKKOS_LAMBDA(const int i, const int j, int & updateMe){ + updateMe += ov(i, j) - aView(i- ov.begin(0), j-ov.begin(1)); + }, sum); + + ASSERT_EQ(sum, 0) << "deep_copy(offsetView, view) broken."; +#endif + } + } + template + void test_offsetview_subview(unsigned int size) + { + {//test subview 1 + Kokkos::Experimental::OffsetView sliceMe("offsetToSlice", {-10, 20}); + { + auto offsetSubviewa = Kokkos::Experimental::subview(sliceMe, 0); + ASSERT_EQ(offsetSubviewa.Rank, 0) << "subview of offset is broken."; + } + + } + {//test subview 2 + Kokkos::Experimental::OffsetView sliceMe("offsetToSlice", {-10,20}, {-20,30}); + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(),-2); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, 0, Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + } + + + {//test subview rank 3 + + Kokkos::Experimental::OffsetView sliceMe("offsetToSlice", {-10,20}, {-20,30}, {-30,40}); + + //slice 1 + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe,Kokkos::ALL(),Kokkos::ALL(), 0); + ASSERT_EQ(offsetSubview.Rank, 2) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe,Kokkos::ALL(), 0,Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 2) << "subview of offset is broken."; + } + + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe,0, Kokkos::ALL(),Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 2) << "subview of offset is broken."; + + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe,0, Kokkos::ALL(), Kokkos::make_pair(-30, -21)); + ASSERT_EQ(offsetSubview.Rank, 2) << "subview of offset is broken."; + + ASSERT_EQ(offsetSubview.begin(0) , -20); + ASSERT_EQ(offsetSubview.end(0) , 31); + ASSERT_EQ(offsetSubview.begin(1) , 0); + ASSERT_EQ(offsetSubview.end(1) , 9); + +#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA) + typedef Kokkos::MDRangePolicy, Kokkos::IndexType > range_type; + typedef typename range_type::point_type point_type; + + const int b0 = offsetSubview.begin(0); + const int b1 = offsetSubview.begin(1); + + const int e0 = offsetSubview.end(0); + const int e1 = offsetSubview.end(1); + + range_type rangeP2D(point_type{ {b0, b1 } }, point_type{ { e0, e1} }); + + Kokkos::parallel_for(rangeP2D, KOKKOS_LAMBDA(const int i, const int j) { + offsetSubview(i,j) = 6; + } + ); + + int sum = 0; + Kokkos::parallel_reduce(rangeP2D, KOKKOS_LAMBDA(const int i, const int j, int & updateMe){ + updateMe += offsetSubview(i, j); + }, sum); + + ASSERT_EQ(sum, 6*(e0-b0)*(e1-b1)); +#endif + } + + // slice 2 + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(), 0, 0); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, 0, 0, Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, 0, Kokkos::ALL(), 0); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + } + + {//test subview rank 4 + + Kokkos::Experimental::OffsetView sliceMe("offsetToSlice", {-10,20}, {-20,30}, {-30,40}, {-40, 50}); + + //slice 1 + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(),Kokkos::ALL(), Kokkos::ALL(), 0); + ASSERT_EQ(offsetSubview.Rank, 3) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(), Kokkos::ALL(), 0, Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 3) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe ,Kokkos::ALL(), 0, Kokkos::ALL(),Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 3) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe , 0, Kokkos::ALL(), Kokkos::ALL(), Kokkos::ALL() ); + ASSERT_EQ(offsetSubview.Rank, 3) << "subview of offset is broken."; + } + + // slice 2 + auto offsetSubview2a = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(), Kokkos::ALL(), 0, 0); + ASSERT_EQ(offsetSubview2a.Rank, 2) << "subview of offset is broken."; + { + auto offsetSubview2b = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(), 0, Kokkos::ALL(), 0); + ASSERT_EQ(offsetSubview2b.Rank, 2) << "subview of offset is broken."; + } + { + auto offsetSubview2b = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(), 0, 0, Kokkos::ALL()); + ASSERT_EQ(offsetSubview2b.Rank, 2) << "subview of offset is broken."; + } + { + auto offsetSubview2b = Kokkos::Experimental::subview(sliceMe, 0, Kokkos::ALL(), 0, Kokkos::ALL()); + ASSERT_EQ(offsetSubview2b.Rank, 2) << "subview of offset is broken."; + } + { + auto offsetSubview2b = Kokkos::Experimental::subview(sliceMe, 0, 0, Kokkos::ALL(), Kokkos::ALL()); + ASSERT_EQ(offsetSubview2b.Rank, 2) << "subview of offset is broken."; + } + // slice 3 + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, Kokkos::ALL(), 0, 0, 0); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, 0, Kokkos::ALL(), 0, 0); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, 0, 0, Kokkos::ALL(), 0); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + { + auto offsetSubview = Kokkos::Experimental::subview(sliceMe, 0, 0, 0, Kokkos::ALL()); + ASSERT_EQ(offsetSubview.Rank, 1) << "subview of offset is broken."; + } + + } + + } + + TEST_F( TEST_CATEGORY, offsetview_construction) { + test_offsetview_construction(10); + } + TEST_F( TEST_CATEGORY, offsetview_subview) { + test_offsetview_subview(10); + } + +} // namespace Test + +#endif /* CONTAINERS_UNIT_TESTS_TESTOFFSETVIEW_HPP_ */ diff --git a/lib/kokkos/containers/unit_tests/TestScatterView.hpp b/lib/kokkos/containers/unit_tests/TestScatterView.hpp index 106d2cf98d..d402a91b9f 100644 --- a/lib/kokkos/containers/unit_tests/TestScatterView.hpp +++ b/lib/kokkos/containers/unit_tests/TestScatterView.hpp @@ -80,7 +80,9 @@ void test_scatter_view_config(int n) Kokkos::Experimental::contribute(original_view, scatter_view); } #if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) + Kokkos::fence(); auto host_view = Kokkos::create_mirror_view_and_copy(Kokkos::HostSpace(), original_view); + Kokkos::fence(); for (typename decltype(host_view)::size_type i = 0; i < host_view.extent(0); ++i) { auto val0 = host_view(i, 0); auto val1 = host_view(i, 1); @@ -111,9 +113,6 @@ struct TestDuplicatedScatterView { test_scatter_view_config(n); - test_scatter_view_config(n); } }; @@ -127,6 +126,16 @@ struct TestDuplicatedScatterView { }; #endif +#ifdef KOKKOS_ENABLE_ROCM +// disable duplicated instantiation with ROCm until +// UniqueToken can support it +template <> +struct TestDuplicatedScatterView { + TestDuplicatedScatterView(int) { + } +}; +#endif + template void test_scatter_view(int n) { @@ -142,16 +151,28 @@ void test_scatter_view(int n) Kokkos::Experimental::ScatterNonDuplicated, Kokkos::Experimental::ScatterNonAtomic>(n); } +#ifdef KOKKOS_ENABLE_SERIAL + if (!std::is_same::value) { +#endif test_scatter_view_config(n); +#ifdef KOKKOS_ENABLE_SERIAL + } +#endif TestDuplicatedScatterView duptest(n); } TEST_F( TEST_CATEGORY, scatterview) { +#ifndef KOKKOS_ENABLE_ROCM test_scatter_view(10); +#ifdef KOKKOS_ENABLE_DEBUG + test_scatter_view(100000); +#else test_scatter_view(10000000); +#endif +#endif } } // namespace Test diff --git a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp index 06d7ed8246..7ba307079f 100644 --- a/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp +++ b/lib/kokkos/containers/unit_tests/TestStaticCrsGraph.hpp @@ -46,6 +46,7 @@ #include #include +#include /*--------------------------------------------------------------------------*/ namespace Test { diff --git a/lib/kokkos/containers/unit_tests/cuda/TestCuda_OffsetView.cpp b/lib/kokkos/containers/unit_tests/cuda/TestCuda_OffsetView.cpp new file mode 100644 index 0000000000..546f6d603a --- /dev/null +++ b/lib/kokkos/containers/unit_tests/cuda/TestCuda_OffsetView.cpp @@ -0,0 +1,47 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/containers/unit_tests/openmp/TestOpenMP_OffsetView.cpp b/lib/kokkos/containers/unit_tests/openmp/TestOpenMP_OffsetView.cpp new file mode 100644 index 0000000000..169dae3212 --- /dev/null +++ b/lib/kokkos/containers/unit_tests/openmp/TestOpenMP_OffsetView.cpp @@ -0,0 +1,47 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/containers/unit_tests/rocm/TestROCm_Category.hpp b/lib/kokkos/containers/unit_tests/rocm/TestROCm_Category.hpp index 555ddd6bdf..d520bbc5a7 100644 --- a/lib/kokkos/containers/unit_tests/rocm/TestROCm_Category.hpp +++ b/lib/kokkos/containers/unit_tests/rocm/TestROCm_Category.hpp @@ -60,6 +60,6 @@ protected: } // namespace Test #define TEST_CATEGORY rocm -#define TEST_EXECSPACE Kokkos::ROCm +#define TEST_EXECSPACE Kokkos::Experimental::ROCm #endif diff --git a/lib/kokkos/containers/unit_tests/serial/TestSerial_OffsetView.cpp b/lib/kokkos/containers/unit_tests/serial/TestSerial_OffsetView.cpp new file mode 100644 index 0000000000..fadd748efb --- /dev/null +++ b/lib/kokkos/containers/unit_tests/serial/TestSerial_OffsetView.cpp @@ -0,0 +1,46 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/containers/unit_tests/threads/TestThreads_OffsetView.cpp b/lib/kokkos/containers/unit_tests/threads/TestThreads_OffsetView.cpp new file mode 100644 index 0000000000..d1eaa265e3 --- /dev/null +++ b/lib/kokkos/containers/unit_tests/threads/TestThreads_OffsetView.cpp @@ -0,0 +1,47 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/core/src/CMakeLists.txt b/lib/kokkos/core/src/CMakeLists.txt index eb02616703..ab7f3f55c7 100644 --- a/lib/kokkos/core/src/CMakeLists.txt +++ b/lib/kokkos/core/src/CMakeLists.txt @@ -108,3 +108,7 @@ else() endif() #----------------------------------------------------------------------------- + +# build and install pkgconfig file +CONFIGURE_FILE(kokkos.pc.in kokkos.pc @ONLY) +INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/kokkos.pc DESTINATION lib/pkgconfig) diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp index ada3f64fe1..c31b7f5b5d 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp @@ -208,7 +208,7 @@ struct CudaParallelLaunch< DriverType , const int shmem , const cudaStream_t stream = 0 ) { - if ( grid.x && ( block.x * block.y * block.z ) ) { + if ( (grid.x != 0) && ( ( block.x * block.y * block.z ) != 0 ) ) { if ( sizeof( Kokkos::Impl::CudaTraits::ConstantGlobalBufferType ) < sizeof( DriverType ) ) { @@ -264,7 +264,7 @@ struct CudaParallelLaunch< DriverType , const int shmem , const cudaStream_t stream = 0 ) { - if ( grid.x && ( block.x * block.y * block.z ) ) { + if ( (grid.x != 0) && ( ( block.x * block.y * block.z ) != 0 ) ) { if ( sizeof( Kokkos::Impl::CudaTraits::ConstantGlobalBufferType ) < sizeof( DriverType ) ) { @@ -321,7 +321,7 @@ struct CudaParallelLaunch< DriverType , const int shmem , const cudaStream_t stream = 0 ) { - if ( grid.x && ( block.x * block.y * block.z ) ) { + if ( (grid.x != 0) && ( ( block.x * block.y * block.z ) != 0 ) ) { if ( sizeof( Kokkos::Impl::CudaTraits::ConstantGlobalBufferType ) < sizeof( DriverType ) ) { @@ -370,7 +370,7 @@ struct CudaParallelLaunch< DriverType , const int shmem , const cudaStream_t stream = 0 ) { - if ( grid.x && ( block.x * block.y * block.z ) ) { + if ( (grid.x != 0) && ( ( block.x * block.y * block.z ) != 0 ) ) { if ( sizeof( Kokkos::Impl::CudaTraits::ConstantGlobalBufferType ) < sizeof( DriverType ) ) { diff --git a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp index 302cf13d47..e13744e327 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp @@ -453,6 +453,8 @@ SharedAllocationRecord( const Kokkos::CudaSpace & arg_space , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + // Set last element zero, in case c_str is too long + header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; // Copy to device memory Kokkos::Impl::DeepCopy( RecordBase::m_alloc_ptr , & header , sizeof(SharedAllocationHeader) ); @@ -491,6 +493,9 @@ SharedAllocationRecord( const Kokkos::CudaUVMSpace & arg_space , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + + // Set last element zero, in case c_str is too long + RecordBase::m_alloc_ptr->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; } SharedAllocationRecord< Kokkos::CudaHostPinnedSpace , void >:: @@ -525,6 +530,8 @@ SharedAllocationRecord( const Kokkos::CudaHostPinnedSpace & arg_space , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + // Set last element zero, in case c_str is too long + RecordBase::m_alloc_ptr->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; } //---------------------------------------------------------------------------- @@ -822,7 +829,8 @@ void* cuda_resize_scratch_space(std::int64_t bytes, bool force_shrink) { } if(bytes > current_size) { current_size = bytes; - ptr = Kokkos::kokkos_realloc(ptr,current_size); + Kokkos::kokkos_free(ptr); + ptr = Kokkos::kokkos_malloc("CudaSpace::ScratchMemory",current_size); } if((bytes < current_size) && (force_shrink)) { current_size = bytes; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp index 8249da6a80..4fd7a9c69e 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp @@ -561,7 +561,11 @@ void CudaInternal::initialize( int cuda_device_id , int stream_count ) } #endif + #ifdef KOKKOS_ENABLE_PRE_CUDA_10_DEPRECATION_API cudaThreadSetCacheConfig(cudaFuncCachePreferShared); + #else + cudaDeviceSetCacheConfig(cudaFuncCachePreferShared); + #endif // Init the array for used for arbitrarily sized atomics Impl::initialize_host_cuda_lock_arrays(); @@ -689,9 +693,13 @@ Cuda::size_type cuda_internal_multiprocessor_count() CudaSpace::size_type cuda_internal_maximum_concurrent_block_count() { + #if defined(KOKKOS_ARCH_KEPLER) + // Compute capability 3.0 through 3.7 + enum : int { max_resident_blocks_per_multiprocessor = 16 }; + #else // Compute capability 5.0 through 6.2 enum : int { max_resident_blocks_per_multiprocessor = 32 }; - + #endif return CudaInternal::singleton().m_multiProcCount * max_resident_blocks_per_multiprocessor ; }; diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp index 31f405dd84..145d93ed76 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp @@ -52,22 +52,22 @@ namespace Kokkos { namespace Impl { -template +template struct CudaGetMaxBlockSize; -template +template int cuda_get_max_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra_block, const size_t shmem_extra_thread) { - return CudaGetMaxBlockSize::get_block_size(f,vector_length, shmem_extra_block,shmem_extra_thread); + return CudaGetMaxBlockSize::get_block_size(f,vector_length, shmem_extra_block,shmem_extra_thread); } template -struct CudaGetMaxBlockSize { +struct CudaGetMaxBlockSize,true> { static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra_block, const size_t shmem_extra_thread) { int numBlocks; - int blockSize=32; + int blockSize=1024; int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); cudaOccupancyMaxActiveBlocksPerMultiprocessor( @@ -76,8 +76,9 @@ struct CudaGetMaxBlockSize { blockSize, sharedmem); - while (blockSize<1024 && numBlocks>0) { - blockSize*=2; + if(numBlocks>0) return blockSize; + while (blockSize>32 && numBlocks==0) { + blockSize/=2; sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); @@ -87,19 +88,30 @@ struct CudaGetMaxBlockSize { blockSize, sharedmem); } - if(numBlocks>0) return blockSize; - else return blockSize/2; + int blockSizeUpperBound = blockSize*2; + while (blockSize0) { + blockSize+=32; + sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_constant_memory, + blockSize, + sharedmem); + } + return blockSize - 32; } }; template -struct CudaGetMaxBlockSize { +struct CudaGetMaxBlockSize,false> { static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra_block, const size_t shmem_extra_thread) { int numBlocks; - int blockSize=32; - int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + unsigned int blockSize=1024; + unsigned int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); cudaOccupancyMaxActiveBlocksPerMultiprocessor( &numBlocks, @@ -107,8 +119,9 @@ struct CudaGetMaxBlockSize { blockSize, sharedmem); - while (blockSize<1024 && numBlocks>0) { - blockSize*=2; + if(numBlocks>0) return blockSize; + while (blockSize>32 && numBlocks==0) { + blockSize/=2; sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); @@ -118,24 +131,121 @@ struct CudaGetMaxBlockSize { blockSize, sharedmem); } - if(numBlocks>0) return blockSize; - else return blockSize/2; + unsigned int blockSizeUpperBound = blockSize*2; + while (blockSize0) { + blockSize+=32; + sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_local_memory, + blockSize, + sharedmem); + } + return blockSize - 32; + } +}; + +template +struct CudaGetMaxBlockSize,true> { + static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, + const size_t shmem_extra_block, const size_t shmem_extra_thread) { + int numBlocks = 0, oldNumBlocks = 0; + unsigned int blockSize=MaxThreadsPerBlock; + unsigned int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_constant_memory, + blockSize, + sharedmem); + + if(static_cast(numBlocks)>=MinBlocksPerSM) return blockSize; + + while (blockSize>32 && static_cast(numBlocks)::value( f , blockSize/vector_length ); + + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_constant_memory, + blockSize, + sharedmem); + } + unsigned int blockSizeUpperBound = (blockSize*2(numBlocks)>MinBlocksPerSM) { + blockSize+=32; + sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + oldNumBlocks = numBlocks; + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_constant_memory, + blockSize, + sharedmem); + } + if(static_cast(oldNumBlocks)>=MinBlocksPerSM) return blockSize - 32; + return -1; + } +}; + +template +struct CudaGetMaxBlockSize,false> { + static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, + const size_t shmem_extra_block, const size_t shmem_extra_thread) { + int numBlocks = 0, oldNumBlocks = 0; + unsigned int blockSize=MaxThreadsPerBlock; + int sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_local_memory, + blockSize, + sharedmem); + if(static_cast(numBlocks)>=MinBlocksPerSM) return blockSize; + + while (blockSize>32 && static_cast(numBlocks)::value( f , blockSize/vector_length ); + + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_local_memory, + blockSize, + sharedmem); + } + unsigned int blockSizeUpperBound = (blockSize*2(numBlocks)>=MinBlocksPerSM) { + blockSize+=32; + sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + oldNumBlocks = numBlocks; + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_local_memory, + blockSize, + sharedmem); + } + if(static_cast(oldNumBlocks)>=MinBlocksPerSM) return blockSize - 32; + return -1; } }; - -template +template struct CudaGetOptBlockSize; -template +template int cuda_get_opt_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra_block, const size_t shmem_extra_thread) { - return CudaGetOptBlockSize::get_block_size(f,vector_length,shmem_extra_block,shmem_extra_thread); + return CudaGetOptBlockSize::get_block_size(f,vector_length,shmem_extra_block,shmem_extra_thread); } template -struct CudaGetOptBlockSize { +struct CudaGetOptBlockSize,true> { static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra_block, const size_t shmem_extra_thread) { int blockSize=16; @@ -165,7 +275,7 @@ struct CudaGetOptBlockSize { }; template -struct CudaGetOptBlockSize { +struct CudaGetOptBlockSize,false> { static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, const size_t shmem_extra_block, const size_t shmem_extra_thread) { int blockSize=16; @@ -194,6 +304,75 @@ struct CudaGetOptBlockSize { } }; +template +struct CudaGetOptBlockSize,true> { + static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, + const size_t shmem_extra_block, const size_t shmem_extra_thread) { + int blockSize=16; + int numBlocks; + int sharedmem; + int maxOccupancy=0; + int bestBlockSize=0; + int max_threads_per_block = std::min(MaxThreadsPerBlock,cuda_internal_maximum_warp_count()*CudaTraits::WarpSize); + + while(blockSize < max_threads_per_block ) { + blockSize*=2; + + //calculate the occupancy with that optBlockSize and check whether its larger than the largest one found so far + sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_constant_memory, + blockSize, + sharedmem); + if(numBlocks >= int(MinBlocksPerSM) && blockSize<=int(MaxThreadsPerBlock)) { + if(maxOccupancy < numBlocks*blockSize) { + maxOccupancy = numBlocks*blockSize; + bestBlockSize = blockSize; + } + } + } + if(maxOccupancy > 0) + return bestBlockSize; + return -1; + } +}; + +template +struct CudaGetOptBlockSize,false> { + static int get_block_size(const typename DriverType::functor_type & f, const size_t vector_length, + const size_t shmem_extra_block, const size_t shmem_extra_thread) { + int blockSize=16; + int numBlocks; + int sharedmem; + int maxOccupancy=0; + int bestBlockSize=0; + int max_threads_per_block = std::min(MaxThreadsPerBlock,cuda_internal_maximum_warp_count()*CudaTraits::WarpSize); + + while(blockSize < max_threads_per_block ) { + blockSize*=2; + sharedmem = shmem_extra_block + shmem_extra_thread*(blockSize/vector_length) + + FunctorTeamShmemSize< typename DriverType::functor_type >::value( f , blockSize/vector_length ); + + cudaOccupancyMaxActiveBlocksPerMultiprocessor( + &numBlocks, + cuda_parallel_launch_local_memory, + blockSize, + sharedmem); + if(numBlocks >= int(MinBlocksPerSM) && blockSize<=int(MaxThreadsPerBlock)) { + if(maxOccupancy < numBlocks*blockSize) { + maxOccupancy = numBlocks*blockSize; + bestBlockSize = blockSize; + } + } + } + if(maxOccupancy > 0) + return bestBlockSize; + return -1; + } +}; + }} // namespace Kokkos::Impl #endif // KOKKOS_ENABLE_CUDA diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp index 80192bf338..8363a45662 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Locks.hpp @@ -148,6 +148,9 @@ namespace Kokkos { namespace Impl { namespace { static int lock_array_copied = 0; + inline int eliminate_warning_for_lock_array() { + return lock_array_copied; + } } } } diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp index eac4abac1b..665d0732a7 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp @@ -60,6 +60,7 @@ #include #include #include +#include #if defined(KOKKOS_ENABLE_PROFILING) #include @@ -114,6 +115,7 @@ public: //---------------------------------------- +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE template< class FunctorType > inline static int team_size_max( const FunctorType & functor ) @@ -131,7 +133,35 @@ public: return n ; } +#endif + template + int team_size_max( const FunctorType& f, const ParallelForTag& ) const { + typedef Impl::ParallelFor< FunctorType , TeamPolicy > closure_type; + int block_size = Kokkos::Impl::cuda_get_max_block_size< closure_type, typename traits::launch_bounds >( f ,(size_t) vector_length(), + (size_t) team_scratch_size(0) + 2*sizeof(double), (size_t) thread_scratch_size(0) + sizeof(double) ); + return block_size/vector_length(); + } + + template + int team_size_max( const FunctorType& f, const ParallelReduceTag& ) const { + typedef Impl::FunctorAnalysis functor_analysis_type; + typedef typename Impl::ParallelReduceReturnValue::reducer_type reducer_type; + typedef Impl::ParallelReduce< FunctorType , TeamPolicy, reducer_type > closure_type; + typedef Impl::FunctorValueTraits< FunctorType , typename traits::work_tag > functor_value_traits; + + int block_size = Kokkos::Impl::cuda_get_max_block_size< closure_type, typename traits::launch_bounds >( f ,(size_t) vector_length(), + (size_t) team_scratch_size(0) + 2*sizeof(double), (size_t) thread_scratch_size(0) + sizeof(double) + + ((functor_value_traits::StaticValueSize!=0)?0:functor_value_traits::value_size( f ))); + + // Currently we require Power-of-2 team size for reductions. + int p2 = 1; + while(p2<=block_size) p2*=2; + p2/=2; + return p2/vector_length(); + } + +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE template< class FunctorType > static int team_size_recommended( const FunctorType & functor ) { return team_size_max( functor ); } @@ -143,11 +173,41 @@ public: if(max<1) max = 1; return max; } +#endif + + template + int team_size_recommended( const FunctorType& f, const ParallelForTag& ) const { + typedef Impl::ParallelFor< FunctorType , TeamPolicy > closure_type; + int block_size = Kokkos::Impl::cuda_get_opt_block_size< closure_type, typename traits::launch_bounds >( f ,(size_t) vector_length(), + (size_t) team_scratch_size(0) + 2*sizeof(double), (size_t) thread_scratch_size(0) + sizeof(double)); + return block_size/vector_length(); + } + + template + int team_size_recommended( const FunctorType& f, const ParallelReduceTag& ) const { + typedef Impl::FunctorAnalysis functor_analysis_type; + typedef typename Impl::ParallelReduceReturnValue::reducer_type reducer_type; + typedef Impl::ParallelReduce< FunctorType , TeamPolicy, reducer_type > closure_type; + typedef Impl::FunctorValueTraits< FunctorType , typename traits::work_tag > functor_value_traits; + + int block_size = Kokkos::Impl::cuda_get_opt_block_size< closure_type, typename traits::launch_bounds >( f ,(size_t) vector_length(), + (size_t) team_scratch_size(0) + 2*sizeof(double), (size_t) thread_scratch_size(0) + sizeof(double) + + ((functor_value_traits::StaticValueSize!=0)?0:functor_value_traits::value_size( f ))); + return block_size/vector_length(); + } + inline static int vector_length_max() { return Impl::CudaTraits::WarpSize; } + inline static + int scratch_size_max(int level) + { return (level==0? + 1024*40: // 48kB is the max for CUDA, but we need some for team_member.reduce etc. + 20*1024*1024); // arbitrarily setting this to 20MB, for a Volta V100 that would give us about 3.2GB for 2 teams per SM + } + //---------------------------------------- inline int vector_length() const { return m_vector_length ; } @@ -419,7 +479,7 @@ public: void execute() const { const typename Policy::index_type nwork = m_policy.end() - m_policy.begin(); - const int block_size = Kokkos::Impl::cuda_get_opt_block_size< ParallelFor >( m_functor , 1, 0 , 0 ); + const int block_size = Kokkos::Impl::cuda_get_opt_block_size< ParallelFor, LaunchBounds>( m_functor , 1, 0 , 0 ); const dim3 block( 1 , block_size , 1); const dim3 grid( std::min( typename Policy::index_type(( nwork + block.y - 1 ) / block.y) , typename Policy::index_type(cuda_internal_maximum_grid_count()) ) , 1 , 1); @@ -465,6 +525,7 @@ public: inline void execute() const { + if(m_rp.m_num_tiles==0) return; const array_index_type maxblocks = static_cast(Kokkos::Impl::CudaTraits::UpperBoundGridCount); if ( RP::rank == 2 ) { @@ -625,7 +686,7 @@ public: typename Policy::member_type( kokkos_impl_cuda_shared_memory() , m_shmem_begin , m_shmem_size - , (void*) ( ((char*)m_scratch_ptr[1]) + threadid/(blockDim.x*blockDim.y) * m_scratch_size[1]) + , (void*) ( ((char*)m_scratch_ptr[1]) + ptrdiff_t(threadid/(blockDim.x*blockDim.y)) * m_scratch_size[1]) , m_scratch_size[1] , league_rank , m_league_size ) ); @@ -654,7 +715,7 @@ public: : m_functor( arg_functor ) , m_league_size( arg_policy.league_size() ) , m_team_size( 0 <= arg_policy.team_size() ? arg_policy.team_size() : - Kokkos::Impl::cuda_get_opt_block_size< ParallelFor >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() ) + Kokkos::Impl::cuda_get_opt_block_size< ParallelFor, LaunchBounds >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() ) , m_vector_size( arg_policy.vector_length() ) , m_shmem_begin( sizeof(double) * ( m_team_size + 2 ) ) , m_shmem_size( arg_policy.scratch_size(0,m_team_size) + FunctorTeamShmemSize< FunctorType >::value( m_functor , m_team_size ) ) @@ -670,7 +731,7 @@ public: } if ( int(m_team_size) > - int(Kokkos::Impl::cuda_get_max_block_size< ParallelFor > + int(Kokkos::Impl::cuda_get_max_block_size< ParallelFor, LaunchBounds > ( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length())) { Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelFor< Cuda > requested too large team size.")); } @@ -725,12 +786,13 @@ public: const Policy m_policy ; const ReducerType m_reducer ; const pointer_type m_result_ptr ; + const bool m_result_ptr_device_accessible ; size_type * m_scratch_space ; size_type * m_scratch_flags ; size_type * m_unified_space ; - // Shall we use the shfl based reduction or not (only use it for static sized types of more than 128bit - enum { UseShflReduction = ((sizeof(value_type)>2*sizeof(double)) && ValueTraits::StaticValueSize) }; + // Shall we use the shfl based reduction or not (only use it for static sized types of more than 128bit) + enum { UseShflReduction = false };//((sizeof(value_type)>2*sizeof(double)) && ValueTraits::StaticValueSize) }; // Some crutch to do function overloading private: typedef double DummyShflReductionType; @@ -752,12 +814,12 @@ public: __device__ inline void operator() () const { - run(Kokkos::Impl::if_c::select(1,1.0) ); +/* run(Kokkos::Impl::if_c::select(1,1.0) ); } __device__ inline void run(const DummySHMEMReductionType& ) const - { + {*/ const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(size_type) > word_count( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) / sizeof(size_type) ); @@ -786,7 +848,8 @@ public: // This is the final block with the final result at the final threads' location size_type * const shared = kokkos_impl_cuda_shared_memory() + ( blockDim.y - 1 ) * word_count.value ; - size_type * const global = m_unified_space ? m_unified_space : m_scratch_space ; + size_type * const global = m_result_ptr_device_accessible? reinterpret_cast(m_result_ptr) : + ( m_unified_space ? m_unified_space : m_scratch_space ); if ( threadIdx.y == 0 ) { Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTagFwd >::final( ReducerConditional::select(m_functor , m_reducer) , shared ); @@ -798,10 +861,9 @@ public: } } - __device__ inline +/* __device__ inline void run(const DummyShflReductionType&) const { - value_type value; ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , &value); // Number of blocks is bounded so that the reduction can be limited to two passes. @@ -832,7 +894,7 @@ public: *result = value; } } - } + }*/ // Determine block size constrained by shared memory: static inline @@ -863,16 +925,18 @@ public: CudaParallelLaunch< ParallelReduce, LaunchBounds >( *this, grid, block, shmem ); // copy to device and execute - Cuda::fence(); + if(!m_result_ptr_device_accessible) { + Cuda::fence(); - if ( m_result_ptr ) { - if ( m_unified_space ) { - const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) ); - for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; } - } - else { - const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); - DeepCopy( m_result_ptr , m_scratch_space , size ); + if ( m_result_ptr ) { + if ( m_unified_space ) { + const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) ); + for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; } + } + else { + const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); + DeepCopy( m_result_ptr , m_scratch_space , size ); + } } } } @@ -883,17 +947,18 @@ public: } } - template< class HostViewType > + template< class ViewType > ParallelReduce( const FunctorType & arg_functor , const Policy & arg_policy - , const HostViewType & arg_result + , const ViewType & arg_result , typename std::enable_if< - Kokkos::is_view< HostViewType >::value + Kokkos::is_view< ViewType >::value ,void*>::type = NULL) : m_functor( arg_functor ) , m_policy( arg_policy ) , m_reducer( InvalidType() ) , m_result_ptr( arg_result.data() ) + , m_result_ptr_device_accessible(MemorySpaceAccess< Kokkos::CudaSpace , typename ViewType::memory_space>::accessible ) , m_scratch_space( 0 ) , m_scratch_flags( 0 ) , m_unified_space( 0 ) @@ -906,6 +971,7 @@ public: , m_policy( arg_policy ) , m_reducer( reducer ) , m_result_ptr( reducer.view().data() ) + , m_result_ptr_device_accessible(MemorySpaceAccess< Kokkos::CudaSpace , typename ReducerType::result_view_type::memory_space>::accessible ) , m_scratch_space( 0 ) , m_scratch_flags( 0 ) , m_unified_space( 0 ) @@ -953,6 +1019,7 @@ public: const Policy m_policy ; // used for workrange and nwork const ReducerType m_reducer ; const pointer_type m_result_ptr ; + const bool m_result_ptr_device_accessible ; size_type * m_scratch_space ; size_type * m_scratch_flags ; size_type * m_unified_space ; @@ -960,7 +1027,7 @@ public: typedef typename Kokkos::Impl::Reduce::DeviceIterateTile DeviceIteratePattern; // Shall we use the shfl based reduction or not (only use it for static sized types of more than 128bit - enum { UseShflReduction = ((sizeof(value_type)>2*sizeof(double)) && ValueTraits::StaticValueSize) }; + enum { UseShflReduction = ((sizeof(value_type)>2*sizeof(double)) && (ValueTraits::StaticValueSize!=0)) }; // Some crutch to do function overloading private: typedef double DummyShflReductionType; @@ -978,12 +1045,12 @@ public: inline __device__ void operator() (void) const { - run(Kokkos::Impl::if_c::select(1,1.0) ); +/* run(Kokkos::Impl::if_c::select(1,1.0) ); } __device__ inline void run(const DummySHMEMReductionType& ) const - { + {*/ const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(size_type) > word_count( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) / sizeof(size_type) ); @@ -1007,7 +1074,8 @@ public: // This is the final block with the final result at the final threads' location size_type * const shared = kokkos_impl_cuda_shared_memory() + ( blockDim.y - 1 ) * word_count.value ; - size_type * const global = m_unified_space ? m_unified_space : m_scratch_space ; + size_type * const global = m_result_ptr_device_accessible? reinterpret_cast(m_result_ptr) : + ( m_unified_space ? m_unified_space : m_scratch_space ); if ( threadIdx.y == 0 ) { Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTagFwd >::final( ReducerConditional::select(m_functor , m_reducer) , shared ); @@ -1019,7 +1087,7 @@ public: } } - __device__ inline +/* __device__ inline void run(const DummyShflReductionType&) const { @@ -1051,7 +1119,7 @@ public: } } } - +*/ // Determine block size constrained by shared memory: static inline unsigned local_block_size( const FunctorType & f ) @@ -1089,16 +1157,18 @@ public: CudaParallelLaunch< ParallelReduce, LaunchBounds >( *this, grid, block, shmem ); // copy to device and execute - Cuda::fence(); + if(!m_result_ptr_device_accessible) { + Cuda::fence(); - if ( m_result_ptr ) { - if ( m_unified_space ) { - const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) ); - for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; } - } - else { - const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); - DeepCopy( m_result_ptr , m_scratch_space , size ); + if ( m_result_ptr ) { + if ( m_unified_space ) { + const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) ); + for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; } + } + else { + const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); + DeepCopy( m_result_ptr , m_scratch_space , size ); + } } } } @@ -1109,17 +1179,18 @@ public: } } - template< class HostViewType > + template< class ViewType > ParallelReduce( const FunctorType & arg_functor , const Policy & arg_policy - , const HostViewType & arg_result + , const ViewType & arg_result , typename std::enable_if< - Kokkos::is_view< HostViewType >::value + Kokkos::is_view< ViewType >::value ,void*>::type = NULL) : m_functor( arg_functor ) , m_policy( arg_policy ) , m_reducer( InvalidType() ) , m_result_ptr( arg_result.data() ) + , m_result_ptr_device_accessible(MemorySpaceAccess< Kokkos::CudaSpace , typename ViewType::memory_space>::accessible ) , m_scratch_space( 0 ) , m_scratch_flags( 0 ) , m_unified_space( 0 ) @@ -1132,6 +1203,7 @@ public: , m_policy( arg_policy ) , m_reducer( reducer ) , m_result_ptr( reducer.view().data() ) + , m_result_ptr_device_accessible(MemorySpaceAccess< Kokkos::CudaSpace , typename ReducerType::result_view_type::memory_space>::accessible ) , m_scratch_space( 0 ) , m_scratch_flags( 0 ) , m_unified_space( 0 ) @@ -1174,7 +1246,7 @@ public: typedef FunctorType functor_type ; typedef Cuda::size_type size_type ; - enum { UseShflReduction = (true && ValueTraits::StaticValueSize) }; + enum { UseShflReduction = (true && (ValueTraits::StaticValueSize!=0)) }; private: typedef double DummyShflReductionType; @@ -1191,6 +1263,7 @@ private: const FunctorType m_functor ; const ReducerType m_reducer ; const pointer_type m_result_ptr ; + const bool m_result_ptr_device_accessible ; size_type * m_scratch_space ; size_type * m_scratch_flags ; size_type * m_unified_space ; @@ -1264,7 +1337,7 @@ public: ( Member( kokkos_impl_cuda_shared_memory() + m_team_begin , m_shmem_begin , m_shmem_size - , (void*) ( ((char*)m_scratch_ptr[1]) + threadid/(blockDim.x*blockDim.y) * m_scratch_size[1]) + , (void*) ( ((char*)m_scratch_ptr[1]) + ptrdiff_t(threadid/(blockDim.x*blockDim.y)) * m_scratch_size[1]) , m_scratch_size[1] , league_rank , m_league_size ) @@ -1279,7 +1352,8 @@ public: // This is the final block with the final result at the final threads' location size_type * const shared = kokkos_impl_cuda_shared_memory() + ( blockDim.y - 1 ) * word_count.value ; - size_type * const global = m_unified_space ? m_unified_space : m_scratch_space ; + size_type * const global = m_result_ptr_device_accessible? reinterpret_cast(m_result_ptr) : + ( m_unified_space ? m_unified_space : m_scratch_space ); if ( threadIdx.y == 0 ) { Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTagFwd >::final( ReducerConditional::select(m_functor , m_reducer) , shared ); @@ -1305,19 +1379,25 @@ public: ( Member( kokkos_impl_cuda_shared_memory() + m_team_begin , m_shmem_begin , m_shmem_size - , (void*) ( ((char*)m_scratch_ptr[1]) + threadid/(blockDim.x*blockDim.y) * m_scratch_size[1]) + , (void*) ( ((char*)m_scratch_ptr[1]) + ptrdiff_t(threadid/(blockDim.x*blockDim.y)) * m_scratch_size[1]) , m_scratch_size[1] , league_rank , m_league_size ) , value ); } - pointer_type const result = (pointer_type) (m_unified_space ? m_unified_space : m_scratch_space) ; + pointer_type const result = m_result_ptr_device_accessible? m_result_ptr : + (pointer_type) ( m_unified_space ? m_unified_space : m_scratch_space ); value_type init; ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , &init); - if(Impl::cuda_inter_block_reduction - (value,init,ValueJoin(ReducerConditional::select(m_functor , m_reducer)),m_scratch_space,result,m_scratch_flags,blockDim.y)) { + if( + Impl::cuda_inter_block_reduction + (value,init,ValueJoin(ReducerConditional::select(m_functor , m_reducer)),m_scratch_space,result,m_scratch_flags,blockDim.y) + //This breaks a test + // Kokkos::Impl::CudaReductionsFunctor::scalar_inter_block_reduction(ReducerConditional::select(m_functor , m_reducer) , blockIdx.x , gridDim.x , + // kokkos_impl_cuda_shared_memory() , m_scratch_space , m_scratch_flags) + ) { const unsigned id = threadIdx.y*blockDim.x + threadIdx.x; if(id==0) { Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTagFwd >::final( ReducerConditional::select(m_functor , m_reducer) , (void*) &value ); @@ -1331,7 +1411,7 @@ public: { const int nwork = m_league_size * m_team_size ; if ( nwork ) { - const int block_count = UseShflReduction? std::min( m_league_size , size_type(1024) ) + const int block_count = UseShflReduction? std::min( m_league_size , size_type(1024*32) ) :std::min( m_league_size , m_team_size ); m_scratch_space = cuda_internal_scratch_space( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) * block_count ); @@ -1344,16 +1424,18 @@ public: CudaParallelLaunch< ParallelReduce, LaunchBounds >( *this, grid, block, shmem_size_total ); // copy to device and execute - Cuda::fence(); + if(!m_result_ptr_device_accessible) { + Cuda::fence(); - if ( m_result_ptr ) { - if ( m_unified_space ) { - const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) ); - for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; } - } - else { - const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); - DeepCopy( m_result_ptr, m_scratch_space, size ); + if ( m_result_ptr ) { + if ( m_unified_space ) { + const int count = ValueTraits::value_count( ReducerConditional::select(m_functor , m_reducer) ); + for ( int i = 0 ; i < count ; ++i ) { m_result_ptr[i] = pointer_type(m_unified_space)[i] ; } + } + else { + const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); + DeepCopy( m_result_ptr, m_scratch_space, size ); + } } } } @@ -1364,16 +1446,17 @@ public: } } - template< class HostViewType > + template< class ViewType > ParallelReduce( const FunctorType & arg_functor , const Policy & arg_policy - , const HostViewType & arg_result + , const ViewType & arg_result , typename std::enable_if< - Kokkos::is_view< HostViewType >::value + Kokkos::is_view< ViewType >::value ,void*>::type = NULL) : m_functor( arg_functor ) , m_reducer( InvalidType() ) , m_result_ptr( arg_result.data() ) + , m_result_ptr_device_accessible(MemorySpaceAccess< Kokkos::CudaSpace , typename ViewType::memory_space>::accessible ) , m_scratch_space( 0 ) , m_scratch_flags( 0 ) , m_unified_space( 0 ) @@ -1383,17 +1466,17 @@ public: , m_scratch_ptr{NULL,NULL} , m_scratch_size{ arg_policy.scratch_size(0,( 0 <= arg_policy.team_size() ? arg_policy.team_size() : - Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(), + Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce, LaunchBounds >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() ) ), arg_policy.scratch_size(1,( 0 <= arg_policy.team_size() ? arg_policy.team_size() : - Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(), + Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce, LaunchBounds >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() ) )} , m_league_size( arg_policy.league_size() ) , m_team_size( 0 <= arg_policy.team_size() ? arg_policy.team_size() : - Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(), + Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce, LaunchBounds >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() ) , m_vector_size( arg_policy.vector_length() ) @@ -1430,9 +1513,7 @@ public: Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too much L0 scratch memory")); } - if ( unsigned(m_team_size) > - unsigned(Kokkos::Impl::cuda_get_max_block_size< ParallelReduce > - ( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length())) { + if ( int(m_team_size) > arg_policy.team_size_max(m_functor,ParallelReduceTag()) ) { Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too large team size.")); } @@ -1444,6 +1525,7 @@ public: : m_functor( arg_functor ) , m_reducer( reducer ) , m_result_ptr( reducer.view().data() ) + , m_result_ptr_device_accessible(MemorySpaceAccess< Kokkos::CudaSpace , typename ReducerType::result_view_type::memory_space>::accessible ) , m_scratch_space( 0 ) , m_scratch_flags( 0 ) , m_unified_space( 0 ) @@ -1453,7 +1535,7 @@ public: , m_scratch_ptr{NULL,NULL} , m_league_size( arg_policy.league_size() ) , m_team_size( 0 <= arg_policy.team_size() ? arg_policy.team_size() : - Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce >( arg_functor , arg_policy.vector_length(), + Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce, LaunchBounds >( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length() ) , m_vector_size( arg_policy.vector_length() ) @@ -1486,10 +1568,7 @@ public: CudaTraits::SharedMemoryCapacity < shmem_size_total ) { Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > bad team size")); } - - if ( int(m_team_size) > - int(Kokkos::Impl::cuda_get_max_block_size< ParallelReduce > - ( arg_functor , arg_policy.vector_length(), arg_policy.team_scratch_size(0),arg_policy.thread_scratch_size(0) ) / arg_policy.vector_length())) { + if ( int(m_team_size) > arg_policy.team_size_max(m_functor,ParallelReduceTag()) ) { Kokkos::Impl::throw_runtime_exception(std::string("Kokkos::Impl::ParallelReduce< Cuda > requested too large team size.")); } @@ -1753,7 +1832,7 @@ public: // Occupancy calculator assumes whole block. m_team_size = - Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce > + Kokkos::Impl::cuda_get_opt_block_size< ParallelReduce, LaunchBounds > ( arg_functor , arg_policy.vector_length() , arg_policy.team_scratch_size(0) @@ -1970,7 +2049,9 @@ private: const WorkRange range( m_policy , blockIdx.x , gridDim.x ); for ( typename Policy::member_type iwork_base = range.begin(); iwork_base < range.end() ; iwork_base += blockDim.y ) { - + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned MASK=KOKKOS_IMPL_CUDA_ACTIVEMASK; + #endif const typename Policy::member_type iwork = iwork_base + threadIdx.y ; __syncthreads(); // Don't overwrite previous iteration values until they are used @@ -1981,7 +2062,11 @@ private: for ( unsigned i = threadIdx.y ; i < word_count.value ; ++i ) { shared_data[i + word_count.value] = shared_data[i] = shared_accum[i] ; } - + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + KOKKOS_IMPL_CUDA_SYNCWARP_MASK(MASK); + #else + KOKKOS_IMPL_CUDA_SYNCWARP; + #endif if ( CudaTraits::WarpSize < word_count.value ) { __syncthreads(); } // Protect against large scan values. // Call functor to accumulate inclusive scan value for this work item @@ -2189,6 +2274,9 @@ private: const WorkRange range( m_policy , blockIdx.x , gridDim.x ); for ( typename Policy::member_type iwork_base = range.begin(); iwork_base < range.end() ; iwork_base += blockDim.y ) { + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned MASK=KOKKOS_IMPL_CUDA_ACTIVEMASK; + #endif const typename Policy::member_type iwork = iwork_base + threadIdx.y ; @@ -2201,6 +2289,11 @@ private: shared_data[i + word_count.value] = shared_data[i] = shared_accum[i] ; } + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + KOKKOS_IMPL_CUDA_SYNCWARP_MASK(MASK); + #else + KOKKOS_IMPL_CUDA_SYNCWARP; + #endif if ( CudaTraits::WarpSize < word_count.value ) { __syncthreads(); } // Protect against large scan values. // Call functor to accumulate inclusive scan value for this work item diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp index 676ba38c6e..d09854c3a5 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp @@ -194,8 +194,9 @@ void cuda_shfl_up( T & out , T const & in , int delta , */ template< class ValueType , class JoinOp> -__device__ -inline void cuda_intra_warp_reduction( ValueType& result, +__device__ inline +typename std::enable_if< !Kokkos::is_reducer::value >::type +cuda_intra_warp_reduction( ValueType& result, const JoinOp& join, const uint32_t max_active_thread = blockDim.y) { @@ -214,8 +215,9 @@ inline void cuda_intra_warp_reduction( ValueType& result, } template< class ValueType , class JoinOp> -__device__ -inline void cuda_inter_warp_reduction( ValueType& value, +__device__ inline +typename std::enable_if< !Kokkos::is_reducer::value >::type +cuda_inter_warp_reduction( ValueType& value, const JoinOp& join, const int max_active_thread = blockDim.y) { @@ -247,8 +249,9 @@ inline void cuda_inter_warp_reduction( ValueType& value, } template< class ValueType , class JoinOp> -__device__ -inline void cuda_intra_block_reduction( ValueType& value, +__device__ inline +typename std::enable_if< !Kokkos::is_reducer::value >::type +cuda_intra_block_reduction( ValueType& value, const JoinOp& join, const int max_active_thread = blockDim.y) { cuda_intra_warp_reduction(value,join,max_active_thread); @@ -314,31 +317,52 @@ bool cuda_inter_block_reduction( typename FunctorValueTraits< FunctorType , ArgT if( id + 1 < int(gridDim.x) ) join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 2) { value_type tmp = Kokkos::shfl_down(value, 2,32); if( id + 2 < int(gridDim.x) ) join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 4) { value_type tmp = Kokkos::shfl_down(value, 4,32); if( id + 4 < int(gridDim.x) ) join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 8) { value_type tmp = Kokkos::shfl_down(value, 8,32); if( id + 8 < int(gridDim.x) ) join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 16) { value_type tmp = Kokkos::shfl_down(value, 16,32); if( id + 16 < int(gridDim.x) ) join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif } } //The last block has in its thread=0 the global reduction value through "value" @@ -478,31 +502,52 @@ cuda_inter_block_reduction( const ReducerType& reducer, if( id + 1 < int(gridDim.x) ) reducer.join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 2) { value_type tmp = Kokkos::shfl_down(value, 2,32); if( id + 2 < int(gridDim.x) ) reducer.join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 4) { value_type tmp = Kokkos::shfl_down(value, 4,32); if( id + 4 < int(gridDim.x) ) reducer.join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 8) { value_type tmp = Kokkos::shfl_down(value, 8,32); if( id + 8 < int(gridDim.x) ) reducer.join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif if (int(blockDim.x*blockDim.y) > 16) { value_type tmp = Kokkos::shfl_down(value, 16,32); if( id + 16 < int(gridDim.x) ) reducer.join(value, tmp); } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + active += KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else active += KOKKOS_IMPL_CUDA_BALLOT(1); +#endif } } @@ -513,6 +558,213 @@ cuda_inter_block_reduction( const ReducerType& reducer, #endif } +template +struct CudaReductionsFunctor; + +template +struct CudaReductionsFunctor { + typedef FunctorValueTraits< FunctorType , ArgTag > ValueTraits ; + typedef FunctorValueJoin< FunctorType , ArgTag > ValueJoin ; + typedef FunctorValueInit< FunctorType , ArgTag > ValueInit ; + typedef FunctorValueOps< FunctorType , ArgTag > ValueOps ; + typedef typename ValueTraits::pointer_type pointer_type ; + typedef typename ValueTraits::value_type Scalar; + + __device__ + static inline void scalar_intra_warp_reduction( + const FunctorType& functor, + Scalar value, // Contribution + const bool skip_vector, // Skip threads if Kokkos vector lanes are not part of the reduction + const int width, // How much of the warp participates + Scalar& result) + { + unsigned mask = width==32?0xffffffff:((1<=w && warp_id +struct CudaReductionsFunctor { + typedef FunctorValueTraits< FunctorType , ArgTag > ValueTraits ; + typedef FunctorValueJoin< FunctorType , ArgTag > ValueJoin ; + typedef FunctorValueInit< FunctorType , ArgTag > ValueInit ; + typedef FunctorValueOps< FunctorType , ArgTag > ValueOps ; + typedef typename ValueTraits::pointer_type pointer_type ; + typedef typename ValueTraits::value_type Scalar; + + __device__ + static inline void scalar_intra_warp_reduction( + const FunctorType& functor, + Scalar* value, // Contribution + const bool skip_vector, // Skip threads if Kokkos vector lanes are not part of the reduction + const int width) // How much of the warp participates + { +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned mask = width==32?0xffffffff:((1< __device__ -bool cuda_single_inter_block_reduce_scan( const FunctorType & functor , - const Cuda::size_type block_id , - const Cuda::size_type block_count , - Cuda::size_type * const shared_data , - Cuda::size_type * const global_data , - Cuda::size_type * const global_flags ) +bool cuda_single_inter_block_reduce_scan2( const FunctorType & functor , + const Cuda::size_type block_id , + const Cuda::size_type block_count , + Cuda::size_type * const shared_data , + Cuda::size_type * const global_data , + Cuda::size_type * const global_flags ) { typedef Cuda::size_type size_type ; typedef FunctorValueTraits< FunctorType , ArgTag > ValueTraits ; @@ -655,7 +925,6 @@ bool cuda_single_inter_block_reduce_scan( const FunctorType & functor , typedef FunctorValueOps< FunctorType , ArgTag > ValueOps ; typedef typename ValueTraits::pointer_type pointer_type ; - //typedef typename ValueTraits::reference_type reference_type ; // '__ffs' = position of the least significant bit set to 1. // 'blockDim.y' is guaranteed to be a power of two so this @@ -678,12 +947,7 @@ bool cuda_single_inter_block_reduce_scan( const FunctorType & functor , size_type * const shared = shared_data + word_count.value * BlockSizeMask ; size_type * const global = global_data + word_count.value * block_id ; -//#if (__CUDA_ARCH__ < 500) for ( int i = int(threadIdx.y) ; i < int(word_count.value) ; i += int(blockDim.y) ) { global[i] = shared[i] ; } -//#else -// for ( size_type i = 0 ; i < word_count.value ; i += 1 ) { global[i] = shared[i] ; } -//#endif - } // Contributing blocks note that their contribution has been completed via an atomic-increment flag @@ -725,6 +989,22 @@ bool cuda_single_inter_block_reduce_scan( const FunctorType & functor , return is_last_block ; } +template< bool DoScan , class FunctorType , class ArgTag > +__device__ +bool cuda_single_inter_block_reduce_scan( const FunctorType & functor , + const Cuda::size_type block_id , + const Cuda::size_type block_count , + Cuda::size_type * const shared_data , + Cuda::size_type * const global_data , + Cuda::size_type * const global_flags ) +{ + typedef FunctorValueTraits< FunctorType , ArgTag > ValueTraits ; + if(!DoScan && ValueTraits::StaticValueSize) + return Kokkos::Impl::CudaReductionsFunctor16)>::scalar_inter_block_reduction(functor,block_id,block_count,shared_data,global_data,global_flags); + else + return cuda_single_inter_block_reduce_scan2(functor, block_id, block_count, shared_data, global_data, global_flags); +} + // Size in bytes required for inter block reduce or scan template< bool DoScan , class FunctorType , class ArgTag > inline diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp index 73ec409b29..18271a5146 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_Team.hpp @@ -160,7 +160,7 @@ public: template KOKKOS_INLINE_FUNCTION - void team_broadcast( ValueType & val, const int& thread_id) const + void team_broadcast( ValueType & val, const int& thread_id ) const { #ifdef __CUDA_ARCH__ if ( 1 == blockDim.z ) { // team == block @@ -178,6 +178,29 @@ public: } #endif } + + template + KOKKOS_INLINE_FUNCTION + void team_broadcast( Closure const & f, ValueType & val, const int& thread_id ) const + { + #ifdef __CUDA_ARCH__ + f( val ); + + if ( 1 == blockDim.z ) { // team == block + __syncthreads(); + // Wait for shared data write until all threads arrive here + if ( threadIdx.x == 0u && threadIdx.y == (uint32_t)thread_id ) { + *((ValueType*) m_team_reduce) = val ; + } + __syncthreads(); // Wait for shared data read until root thread writes + val = *((ValueType*) m_team_reduce); + } + else { // team <= warp + ValueType tmp( val ); // input might not be a register variable + cuda_shfl( val, tmp, blockDim.x * thread_id, blockDim.x * blockDim.y ); + } + #endif + } //-------------------------------------------------------------------------- /**\brief Reduction across a team @@ -200,92 +223,7 @@ public: team_reduce( ReducerType const & reducer ) const noexcept { #ifdef __CUDA_ARCH__ - - typedef typename ReducerType::value_type value_type ; - - value_type tmp( reducer.reference() ); - - // reduce within the warp using shuffle - - const int wx = - ( threadIdx.x + blockDim.x * threadIdx.y ) & CudaTraits::WarpIndexMask ; - - for ( int i = CudaTraits::WarpSize ; (int)blockDim.x <= ( i >>= 1 ) ; ) { - - cuda_shfl_down( reducer.reference() , tmp , i , CudaTraits::WarpSize ); - - // Root of each vector lane reduces: - if ( 0 == threadIdx.x && wx < i ) { - reducer.join( tmp , reducer.reference() ); - } - } - - if ( 1 < blockDim.z ) { // team <= warp - // broadcast result from root vector lange of root thread - - cuda_shfl( reducer.reference() , tmp - , blockDim.x * threadIdx.y , CudaTraits::WarpSize ); - - } - else { // team == block - // Reduce across warps using shared memory - // Broadcast result within block - - // Number of warps, blockDim.y may not be power of two: - const int nw = ( blockDim.x * blockDim.y + CudaTraits::WarpIndexMask ) >> CudaTraits::WarpIndexShift ; - - // Warp index: - const int wy = ( blockDim.x * threadIdx.y ) >> CudaTraits::WarpIndexShift ; - - // Number of shared memory entries for the reduction: - int nsh = m_team_reduce_size / sizeof(value_type); - - // Using at most one entry per warp: - if ( nw < nsh ) nsh = nw ; - - __syncthreads(); // Wait before shared data write - - if ( 0 == wx && wy < nsh ) { - ((value_type*) m_team_reduce)[wy] = tmp ; - } - - // When more warps than shared entries: - for ( int i = nsh ; i < nw ; i += nsh ) { - - __syncthreads(); - - if ( 0 == wx && i <= wy ) { - const int k = wy - i ; - if ( k < nsh ) { - reducer.join( *((value_type*) m_team_reduce + k) , tmp ); - } - } - } - - __syncthreads(); - - // One warp performs the inter-warp reduction: - - if ( 0 == wy ) { - - // Start at power of two covering nsh - - for ( int i = 1 << ( 32 - __clz(nsh-1) ) ; ( i >>= 1 ) ; ) { - const int k = wx + i ; - if ( wx < i && k < nsh ) { - reducer.join( ((value_type*)m_team_reduce)[wx] - , ((value_type*)m_team_reduce)[k] ); - __threadfence_block(); - } - } - } - - __syncthreads(); // Wait for reduction - - // Broadcast result to all threads - reducer.reference() = *((value_type*)m_team_reduce); - } - + cuda_intra_block_reduction(reducer,blockDim.y); #endif /* #ifdef __CUDA_ARCH__ */ } @@ -352,7 +290,7 @@ public: // Intra vector lane shuffle reduction: typename ReducerType::value_type tmp ( reducer.reference() ); - unsigned mask = blockDim.x==32?0xffffffff:((1<>= 1 ) ; ) { cuda_shfl_down( reducer.reference() , tmp , i , blockDim.x , mask ); @@ -801,7 +739,11 @@ void parallel_for ; i += blockDim.x ) { closure(i); } + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK KOKKOS_IMPL_CUDA_SYNCWARP_MASK(blockDim.x==32?0xffffffff:((1<& , const FunctorType& lambda) { #ifdef __CUDA_ARCH__ if(threadIdx.x == 0) lambda(); + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK KOKKOS_IMPL_CUDA_SYNCWARP_MASK(blockDim.x==32?0xffffffff:((1<& , const FunctorType& lambda) { #ifdef __CUDA_ARCH__ if(threadIdx.x == 0 && threadIdx.y == 0) lambda(); + #ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK KOKKOS_IMPL_CUDA_SYNCWARP_MASK(blockDim.x==32?0xffffffff:((1<& , const FunctorType& lambda, ValueType& val) { #ifdef __CUDA_ARCH__ if(threadIdx.x == 0) lambda(val); - unsigned mask = blockDim.x==32?0xffffffff:((1<= 9000 ) && (!defined(KOKKOS_COMPILER_CLANG)) diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp index 11aa695f08..af2aff8b35 100644 --- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp +++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp @@ -279,6 +279,8 @@ public: KOKKOS_INLINE_FUNCTION static handle_type assign( value_type * arg_data_ptr, track_type const & arg_tracker ) { + if(arg_data_ptr == NULL) return handle_type(); + #if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) // Assignment of texture = non-texture requires creation of a texture object // which can only occur on the host. In addition, 'get_record' is only valid @@ -292,8 +294,7 @@ public: #if ! defined( KOKKOS_ENABLE_CUDA_LDG_INTRINSIC ) if ( 0 == r ) { - //Kokkos::abort("Cuda const random access View using Cuda texture memory requires Kokkos to allocate the View's memory"); - return handle_type(); + Kokkos::abort("Cuda const random access View using Cuda texture memory requires Kokkos to allocate the View's memory"); } #endif diff --git a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp index 976bdf05d3..fb0d6cde84 100644 --- a/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp +++ b/lib/kokkos/core/src/KokkosExp_MDRangePolicy.hpp @@ -46,6 +46,8 @@ #include +#include + #include #include #include @@ -63,13 +65,15 @@ namespace Kokkos { // ------------------------------------------------------------------ // - +// Moved to Kokkos_Layout.hpp for more general accessibility +/* enum class Iterate { Default, // Default for the device Left, // Left indices stride fastest Right, // Right indices stride fastest }; +*/ template struct default_outer_direction diff --git a/lib/kokkos/core/src/Kokkos_Array.hpp b/lib/kokkos/core/src/Kokkos_Array.hpp index c602b03538..8e5862fe9c 100644 --- a/lib/kokkos/core/src/Kokkos_Array.hpp +++ b/lib/kokkos/core/src/Kokkos_Array.hpp @@ -45,11 +45,13 @@ #define KOKKOS_ARRAY_HPP #include +#include #include #include #include #include +#include namespace Kokkos { @@ -132,6 +134,7 @@ public: KOKKOS_INLINE_FUNCTION static constexpr size_type size() { return N ; } KOKKOS_INLINE_FUNCTION static constexpr bool empty(){ return false ; } + KOKKOS_INLINE_FUNCTION constexpr size_type max_size() const { return N ; } template< typename iType > KOKKOS_INLINE_FUNCTION @@ -160,7 +163,7 @@ public: return & m_internal_implementation_private_member_data[0]; } - #ifdef KOKKOS_ROCM_CLANG_WORKAROUND + #ifdef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND // Do not default unless move and move-assignment are also defined KOKKOS_INLINE_FUNCTION ~Array() = default ; @@ -197,6 +200,7 @@ public: KOKKOS_INLINE_FUNCTION static constexpr size_type size() { return 0 ; } KOKKOS_INLINE_FUNCTION static constexpr bool empty() { return true ; } + KOKKOS_INLINE_FUNCTION constexpr size_type max_size() const { return 0 ; } template< typename iType > KOKKOS_INLINE_FUNCTION @@ -261,6 +265,7 @@ public: KOKKOS_INLINE_FUNCTION constexpr size_type size() const { return m_size ; } KOKKOS_INLINE_FUNCTION constexpr bool empty() const { return 0 != m_size ; } + KOKKOS_INLINE_FUNCTION constexpr size_type max_size() const { return m_size ; } template< typename iType > KOKKOS_INLINE_FUNCTION @@ -336,6 +341,7 @@ public: KOKKOS_INLINE_FUNCTION constexpr size_type size() const { return m_size ; } KOKKOS_INLINE_FUNCTION constexpr bool empty() const { return 0 != m_size ; } + KOKKOS_INLINE_FUNCTION constexpr size_type max_size() const { return m_size ; } template< typename iType > KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/core/src/Kokkos_Concepts.hpp b/lib/kokkos/core/src/Kokkos_Concepts.hpp index 2e2507b27d..117469b0a2 100644 --- a/lib/kokkos/core/src/Kokkos_Concepts.hpp +++ b/lib/kokkos/core/src/Kokkos_Concepts.hpp @@ -105,7 +105,10 @@ namespace Kokkos { template< typename T > struct is_ ## CONCEPT { \ private: \ template< typename , typename = std::true_type > struct have : std::false_type {}; \ - template< typename U > struct have::type> : std::true_type {}; \ + template< typename U > struct have::type, \ + typename std::remove_cv::type \ + >::type> : std::true_type {}; \ public: \ enum { value = is_ ## CONCEPT::template have::value }; \ }; diff --git a/lib/kokkos/core/src/Kokkos_CopyViews.hpp b/lib/kokkos/core/src/Kokkos_CopyViews.hpp index 31281bc315..31605c9d39 100644 --- a/lib/kokkos/core/src/Kokkos_CopyViews.hpp +++ b/lib/kokkos/core/src/Kokkos_CopyViews.hpp @@ -453,8 +453,9 @@ template { ViewTypeA a; ViewTypeB b; - - typedef Kokkos::Rank<2,ViewFillLayoutSelector::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<2,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -475,7 +476,9 @@ struct ViewCopy::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<3,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -496,7 +499,9 @@ struct ViewCopy::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<4,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -519,7 +524,9 @@ struct ViewCopy::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<5,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -542,7 +549,9 @@ struct ViewCopy::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<6,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -566,7 +575,9 @@ struct ViewCopy::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<6,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -590,7 +601,9 @@ struct ViewCopy::iterate,ViewFillLayoutSelector::iterate> iterate_type; + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::layout_iterate_type_selector::inner_iteration_pattern; + typedef Kokkos::Rank<6,outer_iteration_pattern,inner_iteration_pattern> iterate_type; typedef Kokkos::MDRangePolicy> policy_type; ViewCopy(const ViewTypeA& a_, const ViewTypeB& b_):a(a_),b(b_) { @@ -642,7 +655,9 @@ void view_copy(const DstType& dst, const SrcType& src) { int64_t strides[DstType::Rank+1]; dst.stride(strides); Kokkos::Iterate iterate; - if ( std::is_same::value ) { + if ( Kokkos::is_layouttiled::value ) { + iterate = Kokkos::layout_iterate_type_selector::outer_iteration_pattern; + } else if ( std::is_same::value ) { iterate = Kokkos::Iterate::Right; } else if ( std::is_same::value ) { iterate = Kokkos::Iterate::Left; @@ -1243,9 +1258,9 @@ void deep_copy ViewTypeFlat; ViewTypeFlat dst_flat(dst.data(),dst.size()); - if(dst.span() < std::numeric_limits::max()) + if(dst.span() < std::numeric_limits::max()) { Kokkos::Impl::ViewFill< ViewTypeFlat , Kokkos::LayoutRight, typename ViewType::execution_space, ViewTypeFlat::Rank, int >( dst_flat , value ); - else + } else Kokkos::Impl::ViewFill< ViewTypeFlat , Kokkos::LayoutRight, typename ViewType::execution_space, ViewTypeFlat::Rank, int64_t >( dst_flat , value ); Kokkos::fence(); return; @@ -1386,7 +1401,33 @@ void deep_copy typedef typename src_type::memory_space src_memory_space ; typedef typename dst_type::value_type dst_value_type ; typedef typename src_type::value_type src_value_type ; - if(dst.data() == NULL && src.data() == NULL) { + if(dst.data() == NULL || src.data() == NULL) { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + // do nothing +#else + // throw if dimension mismatch + if ( (src.extent(0) != dst.extent(0)) || + (src.extent(1) != dst.extent(1)) || + (src.extent(2) != dst.extent(2)) || + (src.extent(3) != dst.extent(3)) || + (src.extent(4) != dst.extent(4)) || + (src.extent(5) != dst.extent(5)) || + (src.extent(6) != dst.extent(6)) || + (src.extent(7) != dst.extent(7)) + ) { + std::string message("Deprecation Error: Kokkos::deep_copy extents of views don't match: "); + message += dst.label(); message += "("; + for(int r = 0; r::accessible }; - // Checking for Overlapping Views. dst_value_type* dst_start = dst.data(); dst_value_type* dst_end = dst.data() + dst.span(); @@ -1493,7 +1533,7 @@ void deep_copy Kokkos::fence(); } else { Kokkos::fence(); - Impl::view_copy(typename dst_type::uniform_runtime_nomemspace_type(dst),typename src_type::uniform_runtime_const_nomemspace_type(src)); + Impl::view_copy(dst, src); Kokkos::fence(); } } @@ -1632,7 +1672,33 @@ void deep_copy typedef typename dst_type::value_type dst_value_type ; typedef typename src_type::value_type src_value_type ; - if(dst.data() == NULL && src.data() == NULL) { + if(dst.data() == NULL || src.data() == NULL) { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + // do nothing +#else + // throw if dimension mismatch + if ( (src.extent(0) != dst.extent(0)) || + (src.extent(1) != dst.extent(1)) || + (src.extent(2) != dst.extent(2)) || + (src.extent(3) != dst.extent(3)) || + (src.extent(4) != dst.extent(4)) || + (src.extent(5) != dst.extent(5)) || + (src.extent(6) != dst.extent(6)) || + (src.extent(7) != dst.extent(7)) + ) { + std::string message("Deprecation Error: Kokkos::deep_copy extents of views don't match: "); + message += dst.label(); message += "("; + for(int r = 0; r & v , } } /* namespace Kokkos */ +//---------------------------------------------------------------------------- +//---------------------------------------------------------------------------- + +namespace Kokkos { +namespace Impl { + +// Deduce Mirror Types +template +struct MirrorViewType { + // The incoming view_type + typedef typename Kokkos::View src_view_type; + // The memory space for the mirror view + typedef typename Space::memory_space memory_space; + // Check whether it is the same memory space + enum { is_same_memspace = std::is_same::value }; + // The array_layout + typedef typename src_view_type::array_layout array_layout; + // The data type (we probably want it non-const since otherwise we can't even deep_copy to it. + typedef typename src_view_type::non_const_data_type data_type; + // The destination view type if it is not the same memory space + typedef Kokkos::View dest_view_type; + // If it is the same memory_space return the existsing view_type + // This will also keep the unmanaged trait if necessary + typedef typename std::conditional::type view_type; +}; + +template +struct MirrorType { + // The incoming view_type + typedef typename Kokkos::View src_view_type; + // The memory space for the mirror view + typedef typename Space::memory_space memory_space; + // Check whether it is the same memory space + enum { is_same_memspace = std::is_same::value }; + // The array_layout + typedef typename src_view_type::array_layout array_layout; + // The data type (we probably want it non-const since otherwise we can't even deep_copy to it. + typedef typename src_view_type::non_const_data_type data_type; + // The destination view type if it is not the same memory space + typedef Kokkos::View view_type; +}; + +} + +template< class T , class ... P > +inline +typename Kokkos::View::HostMirror +create_mirror( const Kokkos::View & src + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value && + ! std::is_same< typename Kokkos::ViewTraits::array_layout + , Kokkos::LayoutStride >::value + >::type * = 0 + ) +{ + typedef View src_type ; + typedef typename src_type::HostMirror dst_type ; + + return dst_type( std::string( src.label() ).append("_mirror") +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + , src.extent(0) + , src.extent(1) + , src.extent(2) + , src.extent(3) + , src.extent(4) + , src.extent(5) + , src.extent(6) + , src.extent(7) ); +#else + , src.rank_dynamic > 0 ? src.extent(0): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 1 ? src.extent(1): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 2 ? src.extent(2): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 3 ? src.extent(3): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 4 ? src.extent(4): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 5 ? src.extent(5): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 6 ? src.extent(6): KOKKOS_IMPL_CTOR_DEFAULT_ARG + , src.rank_dynamic > 7 ? src.extent(7): KOKKOS_IMPL_CTOR_DEFAULT_ARG ); +#endif +} + +template< class T , class ... P > +inline +typename Kokkos::View::HostMirror +create_mirror( const Kokkos::View & src + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value && + std::is_same< typename Kokkos::ViewTraits::array_layout + , Kokkos::LayoutStride >::value + >::type * = 0 + ) +{ + typedef View src_type ; + typedef typename src_type::HostMirror dst_type ; + + Kokkos::LayoutStride layout ; + + layout.dimension[0] = src.extent(0); + layout.dimension[1] = src.extent(1); + layout.dimension[2] = src.extent(2); + layout.dimension[3] = src.extent(3); + layout.dimension[4] = src.extent(4); + layout.dimension[5] = src.extent(5); + layout.dimension[6] = src.extent(6); + layout.dimension[7] = src.extent(7); + + layout.stride[0] = src.stride_0(); + layout.stride[1] = src.stride_1(); + layout.stride[2] = src.stride_2(); + layout.stride[3] = src.stride_3(); + layout.stride[4] = src.stride_4(); + layout.stride[5] = src.stride_5(); + layout.stride[6] = src.stride_6(); + layout.stride[7] = src.stride_7(); + + return dst_type( std::string( src.label() ).append("_mirror") , layout ); +} + + +// Create a mirror in a new space (specialization for different space) +template +typename Impl::MirrorType::view_type +create_mirror(const Space& , const Kokkos::View & src + , typename std::enable_if< + std::is_same< typename ViewTraits::specialize , void >::value + >::type * = 0) { + return typename Impl::MirrorType::view_type(src.label(),src.layout()); +} + +template< class T , class ... P > +inline +typename Kokkos::View::HostMirror +create_mirror_view( const Kokkos::View & src + , typename std::enable_if<( + std::is_same< typename Kokkos::View::memory_space + , typename Kokkos::View::HostMirror::memory_space + >::value + && + std::is_same< typename Kokkos::View::data_type + , typename Kokkos::View::HostMirror::data_type + >::value + )>::type * = 0 + ) +{ + return src ; +} + +template< class T , class ... P > +inline +typename Kokkos::View::HostMirror +create_mirror_view( const Kokkos::View & src + , typename std::enable_if< ! ( + std::is_same< typename Kokkos::View::memory_space + , typename Kokkos::View::HostMirror::memory_space + >::value + && + std::is_same< typename Kokkos::View::data_type + , typename Kokkos::View::HostMirror::data_type + >::value + )>::type * = 0 + ) +{ + return Kokkos::create_mirror( src ); +} + +// Create a mirror view in a new space (specialization for same space) +template +typename Impl::MirrorViewType::view_type +create_mirror_view(const Space& , const Kokkos::View & src + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + return src; +} + +// Create a mirror view in a new space (specialization for different space) +template +typename Impl::MirrorViewType::view_type +create_mirror_view(const Space& , const Kokkos::View & src + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + return typename Impl::MirrorViewType::view_type(src.label(),src.layout()); +} + +// Create a mirror view and deep_copy in a new space (specialization for same space) +template +typename Impl::MirrorViewType::view_type +create_mirror_view_and_copy(const Space& , const Kokkos::View & src + , std::string const& name = "" + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + (void)name; + return src; +} + +// Create a mirror view and deep_copy in a new space (specialization for different space) +template +typename Impl::MirrorViewType::view_type +create_mirror_view_and_copy(const Space& , const Kokkos::View & src + , std::string const& name = "" + , typename std::enable_if::is_same_memspace>::type* = 0 ) { + using Mirror = typename Impl::MirrorViewType::view_type; + std::string label = name.empty() ? src.label() : name; + auto mirror = Mirror(ViewAllocateWithoutInitializing(label), src.layout()); + deep_copy(mirror, src); + return mirror; +} + +} /* namespace Kokkos */ + + +//---------------------------------------------------------------------------- +//---------------------------------------------------------------------------- + #endif diff --git a/lib/kokkos/core/src/Kokkos_Crs.hpp b/lib/kokkos/core/src/Kokkos_Crs.hpp index 09b0d666a1..ccc3944d86 100644 --- a/lib/kokkos/core/src/Kokkos_Crs.hpp +++ b/lib/kokkos/core/src/Kokkos_Crs.hpp @@ -100,32 +100,27 @@ public: row_map_type row_map; entries_type entries; - //! Construct an empty view. - Crs() : row_map(), entries() {} - - //! Copy constructor (shallow copy). - Crs(const Crs& rhs) : row_map(rhs.row_map), entries(rhs.entries) - {} + /* + * Default Constructors, operators and destructor + */ + KOKKOS_FUNCTION Crs() = default; + KOKKOS_FUNCTION Crs(Crs const &) = default; + KOKKOS_FUNCTION Crs(Crs &&) = default; + KOKKOS_FUNCTION Crs& operator=(Crs const &) = default; + KOKKOS_FUNCTION Crs& operator=(Crs &&) = default; + KOKKOS_FUNCTION ~Crs() = default; + /** \brief Assign to a view of the rhs array. + * If the old view is the last view + * then allocated memory is deallocated. + */ template - Crs(const RowMapType& row_map_, const EntriesType& entries_) : row_map(row_map_), entries(entries_) - {} - - /** \brief Assign to a view of the rhs array. - * If the old view is the last view - * then allocated memory is deallocated. - */ - Crs& operator= (const Crs& rhs) { - row_map = rhs.row_map; - entries = rhs.entries; - return *this; + KOKKOS_INLINE_FUNCTION + Crs(const RowMapType& row_map_, const EntriesType& entries_) + : row_map(row_map_), entries(entries_) + { } - /** \brief Destroy this view of the array. - * If the last view then allocated memory is deallocated. - */ - ~Crs() {} - /** \brief Return number of rows in the graph */ KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp index a33e28fcd4..d4693b43c1 100644 --- a/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp +++ b/lib/kokkos/core/src/Kokkos_ExecPolicy.hpp @@ -57,6 +57,10 @@ namespace Kokkos { +struct ParallelForTag {}; +struct ParallelScanTag {}; +struct ParallelReduceTag {}; + struct ChunkSize { int value; ChunkSize(int value_):value(value_) {} @@ -320,6 +324,10 @@ public: template< class FunctorType > static int team_size_recommended( const FunctorType & , const int&); + + template + int team_size_recommended( const FunctorType & functor , const int vector_length); + //---------------------------------------- /** \brief Construct policy with the given instance of the execution space */ TeamPolicyInternal( const typename traits::execution_space & , int league_size_request , int team_size_request , int vector_length_request = 1 ); diff --git a/lib/kokkos/core/src/Kokkos_Layout.hpp b/lib/kokkos/core/src/Kokkos_Layout.hpp index b0f92d8cf1..43e117783b 100644 --- a/lib/kokkos/core/src/Kokkos_Layout.hpp +++ b/lib/kokkos/core/src/Kokkos_Layout.hpp @@ -76,6 +76,8 @@ struct LayoutLeft { size_t dimension[ ARRAY_LAYOUT_MAX_RANK ]; + enum { is_extent_constructible = true }; + LayoutLeft( LayoutLeft const & ) = default ; LayoutLeft( LayoutLeft && ) = default ; LayoutLeft & operator = ( LayoutLeft const & ) = default ; @@ -108,6 +110,8 @@ struct LayoutRight { size_t dimension[ ARRAY_LAYOUT_MAX_RANK ]; + enum { is_extent_constructible = true }; + LayoutRight( LayoutRight const & ) = default ; LayoutRight( LayoutRight && ) = default ; LayoutRight & operator = ( LayoutRight const & ) = default ; @@ -132,6 +136,8 @@ struct LayoutStride { size_t dimension[ ARRAY_LAYOUT_MAX_RANK ] ; size_t stride[ ARRAY_LAYOUT_MAX_RANK ] ; + enum { is_extent_constructible = false }; + LayoutStride( LayoutStride const & ) = default ; LayoutStride( LayoutStride && ) = default ; LayoutStride & operator = ( LayoutStride const & ) = default ; @@ -222,6 +228,8 @@ struct LayoutTileLeft { size_t dimension[ ARRAY_LAYOUT_MAX_RANK ] ; + enum { is_extent_constructible = true }; + LayoutTileLeft( LayoutTileLeft const & ) = default ; LayoutTileLeft( LayoutTileLeft && ) = default ; LayoutTileLeft & operator = ( LayoutTileLeft const & ) = default ; @@ -235,6 +243,144 @@ struct LayoutTileLeft { : dimension { argN0 , argN1 , argN2 , argN3 , argN4 , argN5 , argN6 , argN7 } {} }; + +////////////////////////////////////////////////////////////////////////////////////// + +enum class Iterate +{ + Default, + Left, // Left indices stride fastest + Right // Right indices stride fastest +}; + +// To check for LayoutTiled +// This is to hide extra compile-time 'identifier' info within the LayoutTiled class by not relying on template specialization to include the ArgN*'s +template < typename LayoutTiledCheck, class Enable = void > +struct is_layouttiled : std::false_type {}; + +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE +template < typename LayoutTiledCheck > +struct is_layouttiled< LayoutTiledCheck, typename std::enable_if::type > : std::true_type {}; + +namespace Experimental { + +/// LayoutTiled +// Must have Rank >= 2 +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, + unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 = 0, unsigned ArgN3 = 0, unsigned ArgN4 = 0, unsigned ArgN5 = 0, unsigned ArgN6 = 0, unsigned ArgN7 = 0, + bool IsPowerOfTwo = + ( Impl::is_integral_power_of_two(ArgN0) && + Impl::is_integral_power_of_two(ArgN1) && + (Impl::is_integral_power_of_two(ArgN2) || (ArgN2 == 0) ) && + (Impl::is_integral_power_of_two(ArgN3) || (ArgN3 == 0) ) && + (Impl::is_integral_power_of_two(ArgN4) || (ArgN4 == 0) ) && + (Impl::is_integral_power_of_two(ArgN5) || (ArgN5 == 0) ) && + (Impl::is_integral_power_of_two(ArgN6) || (ArgN6 == 0) ) && + (Impl::is_integral_power_of_two(ArgN7) || (ArgN7 == 0) ) + ) + > +struct LayoutTiled { + + static_assert( IsPowerOfTwo + , "LayoutTiled must be given power-of-two tile dimensions" ); + +#if 0 + static_assert( (Impl::is_integral_power_of_two(ArgN0) ) && + (Impl::is_integral_power_of_two(ArgN1) ) && + (Impl::is_integral_power_of_two(ArgN2) || (ArgN2 == 0) ) && + (Impl::is_integral_power_of_two(ArgN3) || (ArgN3 == 0) ) && + (Impl::is_integral_power_of_two(ArgN4) || (ArgN4 == 0) ) && + (Impl::is_integral_power_of_two(ArgN5) || (ArgN5 == 0) ) && + (Impl::is_integral_power_of_two(ArgN6) || (ArgN6 == 0) ) && + (Impl::is_integral_power_of_two(ArgN7) || (ArgN7 == 0) ) + , "LayoutTiled must be given power-of-two tile dimensions" ); +#endif + + typedef LayoutTiled array_layout ; + static constexpr Iterate outer_pattern = OuterP; + static constexpr Iterate inner_pattern = InnerP; + + enum { N0 = ArgN0 }; + enum { N1 = ArgN1 }; + enum { N2 = ArgN2 }; + enum { N3 = ArgN3 }; + enum { N4 = ArgN4 }; + enum { N5 = ArgN5 }; + enum { N6 = ArgN6 }; + enum { N7 = ArgN7 }; + + size_t dimension[ ARRAY_LAYOUT_MAX_RANK ] ; + + enum { is_extent_constructible = true }; + + LayoutTiled( LayoutTiled const & ) = default ; + LayoutTiled( LayoutTiled && ) = default ; + LayoutTiled & operator = ( LayoutTiled const & ) = default ; + LayoutTiled & operator = ( LayoutTiled && ) = default ; + + KOKKOS_INLINE_FUNCTION + explicit constexpr + LayoutTiled( size_t argN0 = 0 , size_t argN1 = 0 , size_t argN2 = 0 , size_t argN3 = 0 + , size_t argN4 = 0 , size_t argN5 = 0 , size_t argN6 = 0 , size_t argN7 = 0 + ) + : dimension { argN0 , argN1 , argN2 , argN3 , argN4 , argN5 , argN6 , argN7 } {} +}; + +} // namespace Experimental +#endif + + +// For use with view_copy +template < typename ... Layout > +struct layout_iterate_type_selector { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Default ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Default ; +}; + +template <> +struct layout_iterate_type_selector< Kokkos::LayoutRight > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Right ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Right ; +}; + +template <> +struct layout_iterate_type_selector< Kokkos::LayoutLeft > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Left ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Left ; +}; + +template <> +struct layout_iterate_type_selector< Kokkos::LayoutStride > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Default ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Default ; +}; + +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE +template < unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 , unsigned ArgN7 > +struct layout_iterate_type_selector< Kokkos::Experimental::LayoutTiled > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Left ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Left ; +}; + +template < unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 , unsigned ArgN7 > +struct layout_iterate_type_selector< Kokkos::Experimental::LayoutTiled > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Right ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Left ; +}; + +template < unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 , unsigned ArgN7 > +struct layout_iterate_type_selector< Kokkos::Experimental::LayoutTiled > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Left ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Right ; +}; + +template < unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 , unsigned ArgN7 > +struct layout_iterate_type_selector< Kokkos::Experimental::LayoutTiled > { + static const Kokkos::Iterate outer_iteration_pattern = Kokkos::Iterate::Right ; + static const Kokkos::Iterate inner_iteration_pattern = Kokkos::Iterate::Right ; +}; +#endif + } // namespace Kokkos #endif // #ifndef KOKKOS_LAYOUT_HPP diff --git a/lib/kokkos/core/src/Kokkos_Macros.hpp b/lib/kokkos/core/src/Kokkos_Macros.hpp index 0cd19d2237..10fc09423e 100644 --- a/lib/kokkos/core/src/Kokkos_Macros.hpp +++ b/lib/kokkos/core/src/Kokkos_Macros.hpp @@ -153,7 +153,7 @@ #else #define KOKKOS_LAMBDA [=]__host__ __device__ - #if defined( KOKKOS_ENABLE_CXX1Z ) + #if defined( KOKKOS_ENABLE_CXX17 ) || defined( KOKKOS_ENABLE_CXX20 ) #define KOKKOS_CLASS_LAMBDA [=,*this] __host__ __device__ #endif #endif @@ -170,6 +170,10 @@ // see https://github.com/kokkos/kokkos/issues/1470 #define KOKKOS_CUDA_9_DEFAULTED_BUG_WORKAROUND #endif + + #if ( 10000 > CUDA_VERSION ) + #define KOKKOS_ENABLE_PRE_CUDA_10_DEPRECATION_API + #endif #endif // #if defined( KOKKOS_ENABLE_CUDA ) && defined( __CUDACC__ ) //---------------------------------------------------------------------------- @@ -213,7 +217,7 @@ #define KOKKOS_LAMBDA [=] #endif -#if defined( KOKKOS_ENABLE_CXX1Z ) && !defined( KOKKOS_CLASS_LAMBDA ) +#if (defined( KOKKOS_ENABLE_CXX17 ) || defined( KOKKOS_ENABLE_CXX20) )&& !defined( KOKKOS_CLASS_LAMBDA ) #define KOKKOS_CLASS_LAMBDA [=,*this] #endif @@ -521,6 +525,9 @@ #if defined ( KOKKOS_ENABLE_CUDA ) #if ( 9000 <= CUDA_VERSION ) #define KOKKOS_IMPL_CUDA_VERSION_9_WORKAROUND + #if ( __CUDA_ARCH__ ) + #define KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + #endif #endif #endif diff --git a/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp b/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp index 7bed7aa3dc..06aaa6546e 100644 --- a/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp +++ b/lib/kokkos/core/src/Kokkos_Parallel_Reduce.hpp @@ -505,7 +505,7 @@ public: } KOKKOS_INLINE_FUNCTION - value_type& reference() { + value_type& reference() const { return *value; } @@ -559,7 +559,7 @@ public: } KOKKOS_INLINE_FUNCTION - value_type& reference() { + value_type& reference() const { return *value; } @@ -637,7 +637,7 @@ public: } KOKKOS_INLINE_FUNCTION - value_type& reference() { + value_type& reference() const { return *value; } @@ -727,7 +727,7 @@ public: } KOKKOS_INLINE_FUNCTION - value_type& reference() { + value_type& reference() const { return *value; } @@ -793,7 +793,7 @@ struct ParallelReduceReturnValue::value ) @@ -1002,7 +1002,8 @@ void parallel_reduce(const std::string& label, typename Impl::enable_if< Kokkos::Impl::is_execution_policy::value >::type * = 0) { - Impl::ParallelReduceAdaptor::execute(label,policy,functor,return_value); + ReturnType return_value_impl = return_value; + Impl::ParallelReduceAdaptor::execute(label,policy,functor,return_value_impl); } template< class PolicyType, class FunctorType, class ReturnType > @@ -1054,6 +1055,9 @@ void parallel_reduce(const std::string& label, , typename ValueTraits::pointer_type >::type value_type ; + static_assert(Impl::FunctorAnalysis:: + has_final_member_function,"Calling parallel_reduce without either return value or final function."); + typedef Kokkos::View< value_type , Kokkos::HostSpace , Kokkos::MemoryUnmanaged @@ -1076,6 +1080,9 @@ void parallel_reduce(const PolicyType& policy, , typename ValueTraits::pointer_type >::type value_type ; + static_assert(Impl::FunctorAnalysis:: + has_final_member_function,"Calling parallel_reduce without either return value or final function."); + typedef Kokkos::View< value_type , Kokkos::HostSpace , Kokkos::MemoryUnmanaged @@ -1096,6 +1103,9 @@ void parallel_reduce(const size_t& policy, , typename ValueTraits::pointer_type >::type value_type ; + static_assert(Impl::FunctorAnalysis,FunctorType>:: + has_final_member_function,"Calling parallel_reduce without either return value or final function."); + typedef Kokkos::View< value_type , Kokkos::HostSpace , Kokkos::MemoryUnmanaged @@ -1117,6 +1127,9 @@ void parallel_reduce(const std::string& label, , typename ValueTraits::pointer_type >::type value_type ; + static_assert(Impl::FunctorAnalysis,FunctorType>:: + has_final_member_function,"Calling parallel_reduce without either return value or final function."); + typedef Kokkos::View< value_type , Kokkos::HostSpace , Kokkos::MemoryUnmanaged diff --git a/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp b/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp index 4527dd4c14..86d803ccc9 100644 --- a/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp +++ b/lib/kokkos/core/src/Kokkos_ScratchSpace.hpp @@ -136,6 +136,55 @@ public: } } + + KOKKOS_INLINE_FUNCTION + void* get_shmem_aligned (const ptrdiff_t size, const ptrdiff_t alignment, int level = -1) const { + if(level == -1) + level = m_default_level; + if(level == 0) { + + char* previous = m_iter_L0; + const ptrdiff_t missalign = size_t(m_iter_L0)%alignment; + if(missalign) m_iter_L0 += alignment-missalign; + + void* tmp = m_iter_L0 + m_offset * size; + if (m_end_L0 < (m_iter_L0 += size * m_multiplier)) { + m_iter_L0 = previous; // put it back like it was + #ifdef KOKKOS_DEBUG + // mfh 23 Jun 2015: printf call consumes 25 registers + // in a CUDA build, so only print in debug mode. The + // function still returns NULL if not enough memory. + printf ("ScratchMemorySpace<...>::get_shmem: Failed to allocate " + "%ld byte(s); remaining capacity is %ld byte(s)\n", long(size), + long(m_end_L0-m_iter_L0)); + #endif // KOKKOS_DEBUG + tmp = 0; + } + return tmp; + } else { + + char* previous = m_iter_L1; + const ptrdiff_t missalign = size_t(m_iter_L1)%alignment; + if(missalign) m_iter_L1 += alignment-missalign; + + void* tmp = m_iter_L1 + m_offset * size; + if (m_end_L1 < (m_iter_L1 += size * m_multiplier)) { + m_iter_L1 = previous; // put it back like it was + #ifdef KOKKOS_DEBUG + // mfh 23 Jun 2015: printf call consumes 25 registers + // in a CUDA build, so only print in debug mode. The + // function still returns NULL if not enough memory. + printf ("ScratchMemorySpace<...>::get_shmem: Failed to allocate " + "%ld byte(s); remaining capacity is %ld byte(s)\n", long(size), + long(m_end_L1-m_iter_L1)); + #endif // KOKKOS_DEBUG + tmp = 0; + } + return tmp; + + } + } + template< typename IntType > KOKKOS_INLINE_FUNCTION ScratchMemorySpace( void * ptr_L0 , const IntType & size_L0 , void * ptr_L1 = NULL , const IntType & size_L1 = 0) diff --git a/lib/kokkos/core/src/Kokkos_Serial.hpp b/lib/kokkos/core/src/Kokkos_Serial.hpp index 911aba8922..01701e53a2 100644 --- a/lib/kokkos/core/src/Kokkos_Serial.hpp +++ b/lib/kokkos/core/src/Kokkos_Serial.hpp @@ -262,7 +262,7 @@ public: } //---------------------------------------- - +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE template< class FunctorType > static int team_size_max( const FunctorType & ) { return 1 ; } @@ -274,6 +274,16 @@ public: template< class FunctorType > static int team_size_recommended( const FunctorType & , const int& ) { return 1 ; } +#endif + + template + int team_size_max( const FunctorType&, const ParallelForTag& ) const { return 1 ; } + template + int team_size_max( const FunctorType&, const ParallelReduceTag& ) const { return 1 ; } + template + int team_size_recommended( const FunctorType&, const ParallelForTag& ) const { return 1 ; } + template + int team_size_recommended( const FunctorType&, const ParallelReduceTag& ) const { return 1 ; } //---------------------------------------- @@ -281,6 +291,16 @@ public: inline int league_size() const { return m_league_size ; } inline size_t scratch_size(const int& level, int = 0) const { return m_team_scratch_size[level] + m_thread_scratch_size[level]; } + inline static + int vector_length_max() + { return 1024; } // Use arbitrary large number, is meant as a vectorizable length + + inline static + int scratch_size_max(int level) + { return (level==0? + 1024*32: + 20*1024*1024); + } /** \brief Specify league size, request team size */ TeamPolicyInternal( execution_space & , int league_size_request diff --git a/lib/kokkos/core/src/Kokkos_TaskScheduler.hpp b/lib/kokkos/core/src/Kokkos_TaskScheduler.hpp index c3185853dc..5045e9cbbc 100644 --- a/lib/kokkos/core/src/Kokkos_TaskScheduler.hpp +++ b/lib/kokkos/core/src/Kokkos_TaskScheduler.hpp @@ -624,7 +624,6 @@ public: when_all( Future< A1 , A2 > const arg[] , int narg ) { using future_type = Future< execution_space > ; - using task_base = Kokkos::Impl::TaskBase< void , void , void > ; future_type f ; @@ -692,7 +691,6 @@ public: { using input_type = decltype( func(0) ); using future_type = Future< execution_space > ; - using task_base = Kokkos::Impl::TaskBase< void , void , void > ; static_assert( is_future< input_type >::value , "Functor must return a Kokkos::Future" ); diff --git a/lib/kokkos/core/src/Kokkos_View.hpp b/lib/kokkos/core/src/Kokkos_View.hpp index 70301884c3..754a0ab8c0 100644 --- a/lib/kokkos/core/src/Kokkos_View.hpp +++ b/lib/kokkos/core/src/Kokkos_View.hpp @@ -198,6 +198,7 @@ struct ViewTraits< void > typedef void HostMirrorSpace ; typedef void array_layout ; typedef void memory_traits ; + typedef void specialize ; }; template< class ... Prop > @@ -209,6 +210,7 @@ struct ViewTraits< void , void , Prop ... > typedef typename ViewTraits::HostMirrorSpace HostMirrorSpace ; typedef typename ViewTraits::array_layout array_layout ; typedef typename ViewTraits::memory_traits memory_traits ; + typedef typename ViewTraits::specialize specialize ; }; template< class ArrayLayout , class ... Prop > @@ -221,6 +223,7 @@ struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_array_layout::HostMirrorSpace HostMirrorSpace ; typedef ArrayLayout array_layout ; typedef typename ViewTraits::memory_traits memory_traits ; + typedef typename ViewTraits::specialize specialize ; }; template< class Space , class ... Prop > @@ -239,6 +242,7 @@ struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_space::value typedef typename Kokkos::Impl::HostMirror< Space >::Space HostMirrorSpace ; typedef typename execution_space::array_layout array_layout ; typedef typename ViewTraits::memory_traits memory_traits ; + typedef typename ViewTraits::specialize specialize ; }; template< class MemoryTraits , class ... Prop > @@ -257,6 +261,7 @@ struct ViewTraits< typename std::enable_if< Kokkos::Impl::is_memory_traits::value + ,typename prop::specialize + ,typename data_analysis::specialize>::type + specialize ; /* mapping specialization tag */ enum { rank = dimension::rank }; enum { rank_dynamic = dimension::rank_dynamic }; @@ -542,7 +552,7 @@ public: private: - typedef Kokkos::Impl::ViewMapping< traits , void > map_type ; + typedef Kokkos::Impl::ViewMapping< traits , typename traits::specialize > map_type ; typedef Kokkos::Impl::SharedAllocationTracker track_type ; track_type m_track ; @@ -608,13 +618,18 @@ public: template< typename iType > KOKKOS_INLINE_FUNCTION constexpr typename std::enable_if< std::is_integral::value , size_t >::type - extent( const iType & r ) const + extent( const iType & r ) const noexcept { return m_map.extent(r); } + static KOKKOS_INLINE_FUNCTION constexpr + size_t + static_extent( const unsigned r ) noexcept + { return map_type::static_extent(r); } + template< typename iType > KOKKOS_INLINE_FUNCTION constexpr typename std::enable_if< std::is_integral::value , int >::type - extent_int( const iType & r ) const + extent_int( const iType & r ) const noexcept { return static_cast(m_map.extent(r)); } KOKKOS_INLINE_FUNCTION constexpr @@ -707,10 +722,17 @@ public: //---------------------------------------- // Allow specializations to query their specialized map +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE KOKKOS_INLINE_FUNCTION - const Kokkos::Impl::ViewMapping< traits , void > & + const Kokkos::Impl::ViewMapping< traits , typename traits::specialize > & implementation_map() const { return m_map ; } - +#endif + KOKKOS_INLINE_FUNCTION + const Kokkos::Impl::ViewMapping< traits , typename traits::specialize > & + impl_map() const { return m_map ; } + KOKKOS_INLINE_FUNCTION + const Kokkos::Impl::SharedAllocationTracker & + impl_track() const { return m_track ; } //---------------------------------------- private: @@ -752,423 +774,421 @@ private: #endif public: - #ifdef KOKKOS_ENABLE_DEPRECATED_CODE - template< class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if<( Kokkos::Impl::are_integral::value - && ( 0 == Rank ) - ), reference_type >::type - operator()( Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,args...) ) - return m_map.reference(); - } + template< class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if<( Kokkos::Impl::are_integral::value + && ( 0 == Rank ) + ), reference_type >::type + operator()( Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,args...) ) + return m_map.reference(); + } - template< typename I0 - , class ... Args> - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 1 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0, - Args ... args) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) - return m_map.reference(i0); - } + template< typename I0 + , class ... Args> + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0, + Args ... args) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) + return m_map.reference(i0); + } - template< typename I0 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 1 == Rank ) - && is_default_map - && ! is_layout_stride - ), reference_type >::type - operator()( const I0 & i0 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) - return m_map.m_handle[ i0 ]; - } + template< typename I0 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && ! is_layout_stride + ), reference_type >::type + operator()( const I0 & i0 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) + return m_map.m_impl_handle[ i0 ]; + } - template< typename I0 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 1 == Rank ) - && is_default_map - && is_layout_stride - ), reference_type >::type - operator()( const I0 & i0 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) - return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ]; - } + template< typename I0 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && is_layout_stride + ), reference_type >::type + operator()( const I0 & i0 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * i0 ]; + } - //------------------------------ - // Rank 1 operator[] + //------------------------------ + // Rank 1 operator[] + + template< typename I0 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && ! is_default_map + ), reference_type >::type + operator[]( const I0 & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) + return m_map.reference(i0); + } template< typename I0 > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 1 == Rank ) - && ! is_default_map - ), reference_type >::type - operator[]( const I0 & i0 ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.reference(i0); - } + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && ! is_layout_stride + ), reference_type >::type + operator[]( const I0 & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) + return m_map.m_impl_handle[ i0 ]; + } - template< typename I0 > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 1 == Rank ) - && is_default_map - && ! is_layout_stride - ), reference_type >::type - operator[]( const I0 & i0 ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.m_handle[ i0 ]; - } + template< typename I0 > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 1 == Rank ) + && is_default_map + && is_layout_stride + ), reference_type >::type + operator[]( const I0 & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * i0 ]; + } - template< typename I0 > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 1 == Rank ) - && is_default_map - && is_layout_stride - ), reference_type >::type - operator[]( const I0 & i0 ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ]; - } + template< typename I0 , typename I1 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) + return m_map.reference(i0,i1); + } + + template< typename I0 , typename I1 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_left && ( traits::rank_dynamic == 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) + return m_map.m_impl_handle[ i0 + m_map.m_impl_offset.m_dim.N0 * i1 ]; + } + + template< typename I0 , typename I1 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_left && ( traits::rank_dynamic != 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) + return m_map.m_impl_handle[ i0 + m_map.m_impl_offset.m_stride * i1 ]; + } + + template< typename I0 , typename I1 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_right && ( traits::rank_dynamic == 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) + return m_map.m_impl_handle[ i1 + m_map.m_impl_offset.m_dim.N1 * i0 ]; + } + + template< typename I0 , typename I1 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_right && ( traits::rank_dynamic != 0 ) + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) + return m_map.m_impl_handle[ i1 + m_map.m_impl_offset.m_stride * i0 ]; + } + + template< typename I0 , typename I1 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 2 == Rank ) + && is_default_map + && is_layout_stride + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) + return m_map.m_impl_handle[ i0 * m_map.m_impl_offset.m_stride.S0 + + i1 * m_map.m_impl_offset.m_stride.S1 ]; + } + + //------------------------------ + // Rank 3 + + template< typename I0 , typename I1 , typename I2 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 3 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2) ]; + } + + template< typename I0 , typename I1 , typename I2 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 3 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,args...) ) + return m_map.reference(i0,i1,i2); + } + + //------------------------------ + // Rank 4 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 4 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 4 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,args...) ) + return m_map.reference(i0,i1,i2,i3); + } + + //------------------------------ + // Rank 5 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 5 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 5 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,args...) ) + return m_map.reference(i0,i1,i2,i3,i4); + } + + //------------------------------ + // Rank 6 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 6 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 6 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,args...) ) + return m_map.reference(i0,i1,i2,i3,i4,i5); + } + + //------------------------------ + // Rank 7 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 7 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5,i6) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 7 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,args...) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,i6); + } + + //------------------------------ + // Rank 8 + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 , typename I7 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 8 == Rank ) + && is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) ) + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; + } + + template< typename I0 , typename I1 , typename I2 , typename I3 + , typename I4 , typename I5 , typename I6 , typename I7 + , class ... Args > + KOKKOS_FORCEINLINE_FUNCTION + typename std::enable_if< + ( Kokkos::Impl::are_integral::value + && ( 8 == Rank ) + && ! is_default_map + ), reference_type >::type + operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 + , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 + , Args ... args ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,i6,i7); + } - template< typename I0 , typename I1 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 2 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.reference(i0,i1); - } - - template< typename I0 , typename I1 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 2 == Rank ) - && is_default_map - && is_layout_left && ( traits::rank_dynamic == 0 ) - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i0 + m_map.m_offset.m_dim.N0 * i1 ]; - } - - template< typename I0 , typename I1 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 2 == Rank ) - && is_default_map - && is_layout_left && ( traits::rank_dynamic != 0 ) - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i0 + m_map.m_offset.m_stride * i1 ]; - } - - template< typename I0 , typename I1 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 2 == Rank ) - && is_default_map - && is_layout_right && ( traits::rank_dynamic == 0 ) - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i1 + m_map.m_offset.m_dim.N1 * i0 ]; - } - - template< typename I0 , typename I1 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 2 == Rank ) - && is_default_map - && is_layout_right && ( traits::rank_dynamic != 0 ) - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i1 + m_map.m_offset.m_stride * i0 ]; - } - - template< typename I0 , typename I1 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 2 == Rank ) - && is_default_map - && is_layout_stride - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i0 * m_map.m_offset.m_stride.S0 + - i1 * m_map.m_offset.m_stride.S1 ]; - } - - //------------------------------ - // Rank 3 - - template< typename I0 , typename I1 , typename I2 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 3 == Rank ) - && is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2) ]; - } - - template< typename I0 , typename I1 , typename I2 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 3 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,args...) ) - return m_map.reference(i0,i1,i2); - } - - //------------------------------ - // Rank 4 - - template< typename I0 , typename I1 , typename I2 , typename I3 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 4 == Rank ) - && is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3) ]; - } - - template< typename I0 , typename I1 , typename I2 , typename I3 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 4 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,args...) ) - return m_map.reference(i0,i1,i2,i3); - } - - //------------------------------ - // Rank 5 - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 5 == Rank ) - && is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4) ]; - } - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 5 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,args...) ) - return m_map.reference(i0,i1,i2,i3,i4); - } - - //------------------------------ - // Rank 6 - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 , typename I5 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 6 == Rank ) - && is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 , const I5 & i5 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5) ]; - } - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 , typename I5 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 6 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 , const I5 & i5 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,args...) ) - return m_map.reference(i0,i1,i2,i3,i4,i5); - } - - //------------------------------ - // Rank 7 - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 , typename I5 , typename I6 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 7 == Rank ) - && is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 , const I5 & i5 , const I6 & i6 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6) ]; - } - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 , typename I5 , typename I6 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 7 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 , const I5 & i5 , const I6 & i6 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,args...) ) - return m_map.reference(i0,i1,i2,i3,i4,i5,i6); - } - - //------------------------------ - // Rank 8 - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 , typename I5 , typename I6 , typename I7 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 8 == Rank ) - && is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; - } - - template< typename I0 , typename I1 , typename I2 , typename I3 - , typename I4 , typename I5 , typename I6 , typename I7 - , class ... Args > - KOKKOS_FORCEINLINE_FUNCTION - typename std::enable_if< - ( Kokkos::Impl::are_integral::value - && ( 8 == Rank ) - && ! is_default_map - ), reference_type >::type - operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 - , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 - , Args ... args ) const - { - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) ) - return m_map.reference(i0,i1,i2,i3,i4,i5,i6,i7); - } - - - #else + #else //------------------------------ // Rank 0 operator() @@ -1206,7 +1226,7 @@ public: operator()( const I0 & i0 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.m_handle[ i0 ]; + return m_map.m_impl_handle[ i0 ]; } template< typename I0 > @@ -1220,7 +1240,7 @@ public: operator()( const I0 & i0) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ]; + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * i0 ]; } //------------------------------ // Rank 1 operator[] @@ -1249,7 +1269,7 @@ public: operator[]( const I0 & i0 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.m_handle[ i0 ]; + return m_map.m_impl_handle[ i0 ]; } template< typename I0 > @@ -1263,7 +1283,7 @@ public: operator[]( const I0 & i0 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0) ) - return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ]; + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * i0 ]; } @@ -1294,7 +1314,7 @@ public: operator()( const I0 & i0 , const I1 & i1) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1) ) - return m_map.m_handle[ i0 + m_map.m_offset.m_dim.N0 * i1 ]; + return m_map.m_impl_handle[ i0 + m_map.m_impl_offset.m_dim.N0 * i1 ]; } template< typename I0 , typename I1> @@ -1308,7 +1328,7 @@ public: operator()( const I0 & i0 , const I1 & i1) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1) ) - return m_map.m_handle[ i0 + m_map.m_offset.m_stride * i1 ]; + return m_map.m_impl_handle[ i0 + m_map.m_impl_offset.m_stride * i1 ]; } template< typename I0 , typename I1 > @@ -1322,7 +1342,7 @@ public: operator()( const I0 & i0 , const I1 & i1 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1) ) - return m_map.m_handle[ i1 + m_map.m_offset.m_dim.N1 * i0 ]; + return m_map.m_impl_handle[ i1 + m_map.m_impl_offset.m_dim.N1 * i0 ]; } template< typename I0 , typename I1 > @@ -1336,7 +1356,7 @@ public: operator()( const I0 & i0 , const I1 & i1 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1) ) - return m_map.m_handle[ i1 + m_map.m_offset.m_stride * i0 ]; + return m_map.m_impl_handle[ i1 + m_map.m_impl_offset.m_stride * i0 ]; } template< typename I0 , typename I1> @@ -1350,8 +1370,8 @@ public: operator()( const I0 & i0 , const I1 & i1 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1) ) - return m_map.m_handle[ i0 * m_map.m_offset.m_stride.S0 + - i1 * m_map.m_offset.m_stride.S1 ]; + return m_map.m_impl_handle[ i0 * m_map.m_impl_offset.m_stride.S0 + + i1 * m_map.m_impl_offset.m_stride.S1 ]; } //------------------------------ @@ -1367,7 +1387,7 @@ public: operator()( const I0 & i0 , const I1 & i1 , const I2 & i2) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2) ]; } template< typename I0 , typename I1 , typename I2> @@ -1396,7 +1416,7 @@ public: operator()( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 > @@ -1427,7 +1447,7 @@ public: , const I4 & i4 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1460,7 +1480,7 @@ public: , const I4 & i4 , const I5 & i5 ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1493,7 +1513,7 @@ public: , const I4 & i4 , const I5 & i5 , const I6 & i6) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5,i6) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1526,7 +1546,7 @@ public: , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,i7) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1545,7 +1565,6 @@ public: } #endif - template< class ... Args > KOKKOS_FORCEINLINE_FUNCTION typename std::enable_if<( Kokkos::Impl::are_integral::value @@ -1585,7 +1604,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) - return m_map.m_handle[ i0 ]; + return m_map.m_impl_handle[ i0 ]; } template< typename I0 @@ -1601,7 +1620,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,args...) ) - return m_map.m_handle[ m_map.m_offset.m_stride.S0 * i0 ]; + return m_map.m_impl_handle[ m_map.m_impl_offset.m_stride.S0 * i0 ]; } template< typename I0 , typename I1 @@ -1632,7 +1651,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i0 + m_map.m_offset.m_dim.N0 * i1 ]; + return m_map.m_impl_handle[ i0 + m_map.m_impl_offset.m_dim.N0 * i1 ]; } template< typename I0 , typename I1 @@ -1648,7 +1667,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i0 + m_map.m_offset.m_stride * i1 ]; + return m_map.m_impl_handle[ i0 + m_map.m_impl_offset.m_stride * i1 ]; } template< typename I0 , typename I1 @@ -1664,7 +1683,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i1 + m_map.m_offset.m_dim.N1 * i0 ]; + return m_map.m_impl_handle[ i1 + m_map.m_impl_offset.m_dim.N1 * i0 ]; } template< typename I0 , typename I1 @@ -1680,7 +1699,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i1 + m_map.m_offset.m_stride * i0 ]; + return m_map.m_impl_handle[ i1 + m_map.m_impl_offset.m_stride * i0 ]; } template< typename I0 , typename I1 @@ -1696,8 +1715,8 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,args...) ) - return m_map.m_handle[ i0 * m_map.m_offset.m_stride.S0 + - i1 * m_map.m_offset.m_stride.S1 ]; + return m_map.m_impl_handle[ i0 * m_map.m_impl_offset.m_stride.S0 + + i1 * m_map.m_impl_offset.m_stride.S1 ]; } //------------------------------ @@ -1715,7 +1734,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2) ]; } template< typename I0 , typename I1 , typename I2 @@ -1748,7 +1767,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1783,7 +1802,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1820,7 +1839,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1857,7 +1876,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5,i6) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1894,7 +1913,7 @@ public: , Args ... args ) const { KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (m_track,m_map,i0,i1,i2,i3,i4,i5,i6,i7,args...) ) - return m_map.m_handle[ m_map.m_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; + return m_map.m_impl_handle[ m_map.m_impl_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 @@ -1938,6 +1957,8 @@ public: KOKKOS_INLINE_FUNCTION View & operator = ( View && rhs ) { m_track = std::move(rhs.m_track) ; m_map = std::move(rhs.m_map) ; return *this ; } + + //---------------------------------------- // Compatible view copy constructor and assignment // may assign unmanaged from managed. @@ -1949,7 +1970,7 @@ public: , m_map() { typedef typename View::traits SrcTraits ; - typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , typename traits::specialize > Mapping ; static_assert( Mapping::is_assignable , "Incompatible View copy construction" ); Mapping::assign( m_map , rhs.m_map , rhs.m_track ); } @@ -1959,7 +1980,7 @@ public: View & operator = ( const View & rhs ) { typedef typename View::traits SrcTraits ; - typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , void > Mapping ; + typedef Kokkos::Impl::ViewMapping< traits , SrcTraits , typename traits::specialize > Mapping ; static_assert( Mapping::is_assignable , "Incompatible View copy assignment" ); Mapping::assign( m_map , rhs.m_map , rhs.m_track ); m_track.assign( rhs.m_track , traits::is_managed ); @@ -1986,7 +2007,7 @@ public: typedef typename Mapping::type DstType ; - static_assert( Kokkos::Impl::ViewMapping< traits , typename DstType::traits , void >::is_assignable + static_assert( Kokkos::Impl::ViewMapping< traits , typename DstType::traits , typename traits::specialize >::is_assignable , "Subview construction requires compatible view and subview arguments" ); Mapping::assign( m_map, src_view.m_map, arg0 , args... ); @@ -2206,7 +2227,8 @@ public: , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) ) { - + static_assert ( traits::array_layout::is_extent_constructible , "Layout is not extent constructible. A layout object should be passed too.\n" ); + #ifdef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST Impl::runtime_check_rank_host(traits::rank_dynamic, std::is_same::value, arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6, arg_N7, label()); @@ -2257,6 +2279,15 @@ public: #endif } + template + KOKKOS_INLINE_FUNCTION + View( const track_type & track, const Kokkos::Impl::ViewMapping< Traits , typename Traits::specialize > &map ) : + m_track(track), m_map() + { + typedef Kokkos::Impl::ViewMapping< traits , Traits , typename traits::specialize > Mapping ; + static_assert( Mapping::is_assignable , "Incompatible View copy construction" ); + Mapping::assign( m_map , map , track ); + } //---------------------------------------- // Memory span required to wrap these dimensions. @@ -2346,7 +2377,7 @@ public: static inline size_t shmem_size( typename traits::array_layout const& arg_layout ) { - return map_type::memory_span( arg_layout ); + return map_type::memory_span( arg_layout )+sizeof(typename traits::value_type); } explicit KOKKOS_INLINE_FUNCTION @@ -2354,7 +2385,7 @@ public: , const typename traits::array_layout & arg_layout ) : View( Impl::ViewCtorProp( reinterpret_cast( - arg_space.get_shmem( map_type::memory_span( arg_layout ) ) ) ) + arg_space.get_shmem_aligned( map_type::memory_span( arg_layout ), sizeof(typename traits::value_type) ) ) ) , arg_layout ) {} @@ -2370,11 +2401,11 @@ public: , const size_t arg_N7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG ) : View( Impl::ViewCtorProp( reinterpret_cast( - arg_space.get_shmem( + arg_space.get_shmem_aligned( map_type::memory_span( typename traits::array_layout ( arg_N0 , arg_N1 , arg_N2 , arg_N3 - , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) ) ) ) ) + , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) ), sizeof(typename traits::value_type) ) ) ) , typename traits::array_layout ( arg_N0 , arg_N1 , arg_N2 , arg_N3 , arg_N4 , arg_N5 , arg_N6 , arg_N7 ) @@ -2515,209 +2546,6 @@ void shared_allocation_tracking_enable() } /* namespace Impl */ } /* namespace Kokkos */ -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- - -namespace Kokkos { -namespace Impl { - -// Deduce Mirror Types -template -struct MirrorViewType { - // The incoming view_type - typedef typename Kokkos::View src_view_type; - // The memory space for the mirror view - typedef typename Space::memory_space memory_space; - // Check whether it is the same memory space - enum { is_same_memspace = std::is_same::value }; - // The array_layout - typedef typename src_view_type::array_layout array_layout; - // The data type (we probably want it non-const since otherwise we can't even deep_copy to it. - typedef typename src_view_type::non_const_data_type data_type; - // The destination view type if it is not the same memory space - typedef Kokkos::View dest_view_type; - // If it is the same memory_space return the existsing view_type - // This will also keep the unmanaged trait if necessary - typedef typename std::conditional::type view_type; -}; - -template -struct MirrorType { - // The incoming view_type - typedef typename Kokkos::View src_view_type; - // The memory space for the mirror view - typedef typename Space::memory_space memory_space; - // Check whether it is the same memory space - enum { is_same_memspace = std::is_same::value }; - // The array_layout - typedef typename src_view_type::array_layout array_layout; - // The data type (we probably want it non-const since otherwise we can't even deep_copy to it. - typedef typename src_view_type::non_const_data_type data_type; - // The destination view type if it is not the same memory space - typedef Kokkos::View view_type; -}; - -} - -template< class T , class ... P > -inline -typename Kokkos::View::HostMirror -create_mirror( const Kokkos::View & src - , typename std::enable_if< - ! std::is_same< typename Kokkos::ViewTraits::array_layout - , Kokkos::LayoutStride >::value - >::type * = 0 - ) -{ - typedef View src_type ; - typedef typename src_type::HostMirror dst_type ; - - return dst_type( std::string( src.label() ).append("_mirror") -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE - , src.extent(0) - , src.extent(1) - , src.extent(2) - , src.extent(3) - , src.extent(4) - , src.extent(5) - , src.extent(6) - , src.extent(7) ); -#else - , src.rank_dynamic > 0 ? src.extent(0): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 1 ? src.extent(1): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 2 ? src.extent(2): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 3 ? src.extent(3): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 4 ? src.extent(4): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 5 ? src.extent(5): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 6 ? src.extent(6): KOKKOS_IMPL_CTOR_DEFAULT_ARG - , src.rank_dynamic > 7 ? src.extent(7): KOKKOS_IMPL_CTOR_DEFAULT_ARG ); -#endif -} - -template< class T , class ... P > -inline -typename Kokkos::View::HostMirror -create_mirror( const Kokkos::View & src - , typename std::enable_if< - std::is_same< typename Kokkos::ViewTraits::array_layout - , Kokkos::LayoutStride >::value - >::type * = 0 - ) -{ - typedef View src_type ; - typedef typename src_type::HostMirror dst_type ; - - Kokkos::LayoutStride layout ; - - layout.dimension[0] = src.extent(0); - layout.dimension[1] = src.extent(1); - layout.dimension[2] = src.extent(2); - layout.dimension[3] = src.extent(3); - layout.dimension[4] = src.extent(4); - layout.dimension[5] = src.extent(5); - layout.dimension[6] = src.extent(6); - layout.dimension[7] = src.extent(7); - - layout.stride[0] = src.stride_0(); - layout.stride[1] = src.stride_1(); - layout.stride[2] = src.stride_2(); - layout.stride[3] = src.stride_3(); - layout.stride[4] = src.stride_4(); - layout.stride[5] = src.stride_5(); - layout.stride[6] = src.stride_6(); - layout.stride[7] = src.stride_7(); - - return dst_type( std::string( src.label() ).append("_mirror") , layout ); -} - - -// Create a mirror in a new space (specialization for different space) -template -typename Impl::MirrorType::view_type create_mirror(const Space& , const Kokkos::View & src) { - return typename Impl::MirrorType::view_type(src.label(),src.layout()); -} - -template< class T , class ... P > -inline -typename Kokkos::View::HostMirror -create_mirror_view( const Kokkos::View & src - , typename std::enable_if<( - std::is_same< typename Kokkos::View::memory_space - , typename Kokkos::View::HostMirror::memory_space - >::value - && - std::is_same< typename Kokkos::View::data_type - , typename Kokkos::View::HostMirror::data_type - >::value - )>::type * = 0 - ) -{ - return src ; -} - -template< class T , class ... P > -inline -typename Kokkos::View::HostMirror -create_mirror_view( const Kokkos::View & src - , typename std::enable_if< ! ( - std::is_same< typename Kokkos::View::memory_space - , typename Kokkos::View::HostMirror::memory_space - >::value - && - std::is_same< typename Kokkos::View::data_type - , typename Kokkos::View::HostMirror::data_type - >::value - )>::type * = 0 - ) -{ - return Kokkos::create_mirror( src ); -} - -// Create a mirror view in a new space (specialization for same space) -template -typename Impl::MirrorViewType::view_type -create_mirror_view(const Space& , const Kokkos::View & src - , typename std::enable_if::is_same_memspace>::type* = 0 ) { - return src; -} - -// Create a mirror view in a new space (specialization for different space) -template -typename Impl::MirrorViewType::view_type -create_mirror_view(const Space& , const Kokkos::View & src - , typename std::enable_if::is_same_memspace>::type* = 0 ) { - return typename Impl::MirrorViewType::view_type(src.label(),src.layout()); -} - -// Create a mirror view and deep_copy in a new space (specialization for same space) -template -typename Impl::MirrorViewType::view_type -create_mirror_view_and_copy(const Space& , const Kokkos::View & src - , std::string const& name = "" - , typename std::enable_if::is_same_memspace>::type* = 0 ) { - (void)name; - return src; -} - -// Create a mirror view and deep_copy in a new space (specialization for different space) -template -typename Impl::MirrorViewType::view_type -create_mirror_view_and_copy(const Space& , const Kokkos::View & src - , std::string const& name = "" - , typename std::enable_if::is_same_memspace>::type* = 0 ) { - using Mirror = typename Impl::MirrorViewType::view_type; - std::string label = name.empty() ? src.label() : name; - auto mirror = Mirror(ViewAllocateWithoutInitializing(label), src.layout()); - deep_copy(mirror, src); - return mirror; -} - -} /* namespace Kokkos */ - - //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/Makefile b/lib/kokkos/core/src/Makefile index 6ee5fec716..c2dbddf45e 100644 --- a/lib/kokkos/core/src/Makefile +++ b/lib/kokkos/core/src/Makefile @@ -16,6 +16,7 @@ endif CXXFLAGS ?= -O3 LINK ?= $(CXX) LDFLAGS ?= +CP = cp include $(KOKKOS_PATH)/Makefile.kokkos include $(KOKKOS_PATH)/core/src/Makefile.generate_header_lists @@ -50,7 +51,12 @@ ifeq ($(KOKKOS_OS),Linux) COPY_FLAG = -u endif ifeq ($(KOKKOS_OS),Darwin) - COPY_FLAG = + COPY_FLAG = + # If Homebrew coreutils is installed, its cp will have the -u option + ifneq ("$(wildcard /usr/local/opt/coreutils/libexec/gnubin/cp)","") + CP = /usr/local/opt/coreutils/libexec/gnubin/cp + COPY_FLAG = -u + endif endif ifeq ($(KOKKOS_DEBUG),"no") @@ -66,36 +72,38 @@ mkdir: mkdir -p $(PREFIX)/bin mkdir -p $(PREFIX)/include mkdir -p $(PREFIX)/lib + mkdir -p $(PREFIX)/lib/pkgconfig mkdir -p $(PREFIX)/include/impl copy-cuda: mkdir mkdir -p $(PREFIX)/include/Cuda - cp $(COPY_FLAG) $(KOKKOS_HEADERS_CUDA) $(PREFIX)/include/Cuda + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_CUDA) $(PREFIX)/include/Cuda copy-threads: mkdir mkdir -p $(PREFIX)/include/Threads - cp $(COPY_FLAG) $(KOKKOS_HEADERS_THREADS) $(PREFIX)/include/Threads + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_THREADS) $(PREFIX)/include/Threads copy-qthreads: mkdir mkdir -p $(PREFIX)/include/Qthreads - cp $(COPY_FLAG) $(KOKKOS_HEADERS_QTHREADS) $(PREFIX)/include/Qthreads + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_QTHREADS) $(PREFIX)/include/Qthreads copy-openmp: mkdir mkdir -p $(PREFIX)/include/OpenMP - cp $(COPY_FLAG) $(KOKKOS_HEADERS_OPENMP) $(PREFIX)/include/OpenMP + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_OPENMP) $(PREFIX)/include/OpenMP copy-rocm: mkdir mkdir -p $(PREFIX)/include/ROCm - cp $(COPY_FLAG) $(KOKKOS_HEADERS_ROCM) $(PREFIX)/include/ROCm + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_ROCM) $(PREFIX)/include/ROCm install: mkdir $(CONDITIONAL_COPIES) build-lib generate_build_settings - cp $(COPY_FLAG) $(NVCC_WRAPPER) $(PREFIX)/bin - cp $(COPY_FLAG) $(KOKKOS_HEADERS_INCLUDE) $(PREFIX)/include - cp $(COPY_FLAG) $(KOKKOS_HEADERS_INCLUDE_IMPL) $(PREFIX)/include/impl - cp $(COPY_FLAG) $(KOKKOS_MAKEFILE) $(PREFIX) - cp $(COPY_FLAG) $(KOKKOS_CMAKEFILE) $(PREFIX) - cp $(COPY_FLAG) libkokkos.a $(PREFIX)/lib - cp $(COPY_FLAG) $(KOKKOS_CONFIG_HEADER) $(PREFIX)/include + $(CP) $(COPY_FLAG) $(NVCC_WRAPPER) $(PREFIX)/bin + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_INCLUDE) $(PREFIX)/include + $(CP) $(COPY_FLAG) $(KOKKOS_HEADERS_INCLUDE_IMPL) $(PREFIX)/include/impl + $(CP) $(COPY_FLAG) $(KOKKOS_MAKEFILE) $(PREFIX) + $(CP) $(COPY_FLAG) $(KOKKOS_CMAKEFILE) $(PREFIX) + $(CP) $(COPY_FLAG) $(KOKKOS_PKGCONFIG) $(PREFIX)/lib/pkgconfig + $(CP) $(COPY_FLAG) libkokkos.a $(PREFIX)/lib + $(CP) $(COPY_FLAG) $(KOKKOS_CONFIG_HEADER) $(PREFIX)/include clean: kokkos-clean - rm -f $(KOKKOS_MAKEFILE) $(KOKKOS_CMAKEFILE) + rm -f $(KOKKOS_MAKEFILE) $(KOKKOS_CMAKEFILE) $(KOKKOS_PKGCONFIG) diff --git a/lib/kokkos/core/src/Makefile.generate_build_files b/lib/kokkos/core/src/Makefile.generate_build_files index 7e0c6351fe..cc856ee9a3 100644 --- a/lib/kokkos/core/src/Makefile.generate_build_files +++ b/lib/kokkos/core/src/Makefile.generate_build_files @@ -5,6 +5,7 @@ # These files are generated by this makefile KOKKOS_MAKEFILE=Makefile.kokkos KOKKOS_CMAKEFILE=kokkos_generated_settings.cmake +KOKKOS_PKGCONFIG=kokkos.pc ifeq ($(KOKKOS_DEBUG),"no") KOKKOS_DEBUG_CMAKE = OFF @@ -33,11 +34,29 @@ kokkos_append_var = $(call kokkos_appendvar_makefile,$1); $(call kokkos_appendva kokkos_append_var2 = $(call kokkos_appendvar2_makefile,$1); $(call kokkos_appendvar_cmakefile,$1,$2) kokkos_append_varval = $(call kokkos_appendval_makefile,$1,$2); $(call kokkos_appendval_cmakefile,$1,$2,$3) +kokkos_fixup_sed_impl = sed \ + -e 's|$(KOKKOS_PATH)/core/src|$(PREFIX)/include|g' \ + -e 's|$(KOKKOS_PATH)/containers/src|$(PREFIX)/include|g' \ + -e 's|$(KOKKOS_PATH)/algorithms/src|$(PREFIX)/include|g' \ + -e 's|-L$(PWD)|-L$(PREFIX)/lib|g' \ + -e 's|= libkokkos.a|= $(PREFIX)/lib/libkokkos.a|g' \ + -e 's|= $(KOKKOS_CONFIG_HEADER)|= $(PREFIX)/include/$(KOKKOS_CONFIG_HEADER)|g' $1 \ + > $1.tmp && mv -f $1.tmp $1 + +$(KOKKOS_PKGCONFIG): $(KOKKOS_PATH)/core/src/$(KOKKOS_PKGCONFIG).in + @sed -e 's|@CMAKE_INSTALL_PREFIX@|$(PREFIX)|g' \ + -e 's|@KOKKOS_CXXFLAGS@|$(patsubst -I%,,$(KOKKOS_CXXFLAGS))|g' \ + -e 's|@KOKKOS_EXTRA_LIBS_LIST@|$(KOKKOS_EXTRA_LIBS)|g' \ + -e 's|@KOKKOS_LINK_FLAGS@|$(KOKKOS_LINK_FLAGS)|g' \ + $< > $@ + +kokkos_fixup_sed = $(call kokkos_fixup_sed_impl,$(KOKKOS_MAKEFILE)); $(call kokkos_fixup_sed_impl,$(KOKKOS_CMAKEFILE)) + #This function should be used for variables whose values are different in GNU Make versus CMake, #especially lists which are delimited by commas in one case and semicolons in another kokkos_append_gmakevar = $(call kokkos_appendvar_makefile,$1); $(call kokkos_append_gmakevar_cmakefile,$1,$2) -generate_build_settings: $(KOKKOS_CONFIG_HEADER) +generate_build_settings: $(KOKKOS_CONFIG_HEADER) $(KOKKOS_PKGCONFIG) @rm -f $(KOKKOS_MAKEFILE) @rm -f $(KOKKOS_CMAKEFILE) @$(call kokkos_append_string, "#Global Settings used to generate this library") @@ -68,7 +87,6 @@ generate_build_settings: $(KOKKOS_CONFIG_HEADER) @$(call kokkos_append_var,KOKKOS_HEADERS_ROCM,'STRING "Kokkos headers ROCm list"') @$(call kokkos_append_var,KOKKOS_HEADERS_THREADS,'STRING "Kokkos headers Threads list"') @$(call kokkos_append_var,KOKKOS_HEADERS_QTHREADS,'STRING "Kokkos headers QThreads list"') - @$(call kokkos_append_var,KOKKOS_SRC,'STRING "Kokkos source list"') @$(call kokkos_append_string,"") @$(call kokkos_append_string,"#Variables used in application Makefiles") @$(call kokkos_append_var,KOKKOS_OS,'STRING ""') # This was not in original cmake gen @@ -94,19 +112,11 @@ generate_build_settings: $(KOKKOS_CONFIG_HEADER) @$(call kokkos_append_makefile,"#Fake kokkos-clean target") @$(call kokkos_append_makefile,"kokkos-clean:") @$(call kokkos_append_makefile,"") - @sed \ - -e 's|$(KOKKOS_PATH)/core/src|$(PREFIX)/include|g' \ - -e 's|$(KOKKOS_PATH)/containers/src|$(PREFIX)/include|g' \ - -e 's|$(KOKKOS_PATH)/algorithms/src|$(PREFIX)/include|g' \ - -e 's|-L$(PWD)|-L$(PREFIX)/lib|g' \ - -e 's|= libkokkos.a|= $(PREFIX)/lib/libkokkos.a|g' \ - -e 's|= $(KOKKOS_CONFIG_HEADER)|= $(PREFIX)/include/$(KOKKOS_CONFIG_HEADER)|g' $(KOKKOS_MAKEFILE) \ - > $(KOKKOS_MAKEFILE).tmp - @mv -f $(KOKKOS_MAKEFILE).tmp $(KOKKOS_MAKEFILE) + @$(call kokkos_fixup_sed) + @$(call kokkos_append_var,KOKKOS_SRC,'STRING "Kokkos source list"') @$(call kokkos_setvar_cmakefile,KOKKOS_CXX_FLAGS,$(KOKKOS_CXXFLAGS)) @$(call kokkos_setvar_cmakefile,KOKKOS_CPP_FLAGS,$(KOKKOS_CPPFLAGS)) @$(call kokkos_setvar_cmakefile,KOKKOS_LD_FLAGS,$(KOKKOS_LDFLAGS)) @$(call kokkos_setlist_cmakefile,KOKKOS_LIBS_LIST,$(KOKKOS_LIBS)) @$(call kokkos_setlist_cmakefile,KOKKOS_EXTRA_LIBS_LIST,$(KOKKOS_EXTRA_LIBS)) @$(call kokkos_setvar_cmakefile,KOKKOS_LINK_FLAGS,$(KOKKOS_LINK_FLAGS)) - diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp index 351f5f1ec2..2f2c768460 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Task.cpp @@ -103,8 +103,6 @@ public: void TaskQueueSpecialization< Kokkos::OpenMP >::execute ( TaskQueue< Kokkos::OpenMP > * const queue ) { - using execution_space = Kokkos::OpenMP ; - using queue_type = TaskQueue< execution_space > ; using task_root_type = TaskBase< void , void , void > ; using Member = Impl::HostThreadTeamMember< execution_space > ; @@ -213,8 +211,6 @@ void TaskQueueSpecialization< Kokkos::OpenMP >:: iff_single_thread_recursive_execute ( TaskQueue< Kokkos::OpenMP > * const queue ) { - using execution_space = Kokkos::OpenMP ; - using queue_type = TaskQueue< execution_space > ; using task_root_type = TaskBase< void , void , void > ; using Member = Impl::HostThreadTeamMember< execution_space > ; diff --git a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Team.hpp b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Team.hpp index b530dca10f..e8fbc467e0 100644 --- a/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Team.hpp +++ b/lib/kokkos/core/src/OpenMP/Kokkos_OpenMP_Team.hpp @@ -76,14 +76,11 @@ public: //---------------------------------------- +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE template< class FunctorType > inline static int team_size_max( const FunctorType & ) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE int pool_size = traits::execution_space::thread_pool_size(1); -#else - int pool_size = traits::execution_space::impl_thread_pool_size(1); -#endif int max_host_team_size = Impl::HostThreadTeamData::max_team_members; return pool_size + inline static + int team_size_recommended( const FunctorType &, const int& ) + { + return traits::execution_space::thread_pool_size(2); + } +#endif + + template + int team_size_max( const FunctorType&, const ParallelForTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + int pool_size = traits::execution_space::thread_pool_size(1); +#else + int pool_size = traits::execution_space::impl_thread_pool_size(1); +#endif + int max_host_team_size = Impl::HostThreadTeamData::max_team_members; + return pool_size + int team_size_max( const FunctorType&, const ParallelReduceTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + int pool_size = traits::execution_space::thread_pool_size(1); +#else + int pool_size = traits::execution_space::impl_thread_pool_size(1); +#endif + int max_host_team_size = Impl::HostThreadTeamData::max_team_members; + return pool_size + int team_size_recommended( const FunctorType&, const ParallelForTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + return traits::execution_space::thread_pool_size(2); +#else + return traits::execution_space::impl_thread_pool_size(2); +#endif + } + template + int team_size_recommended( const FunctorType&, const ParallelReduceTag& ) const { #ifdef KOKKOS_ENABLE_DEPRECATED_CODE return traits::execution_space::thread_pool_size(2); #else @@ -99,16 +137,17 @@ public: #endif } - template< class FunctorType > + inline static - int team_size_recommended( const FunctorType &, const int& ) - { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE - return traits::execution_space::thread_pool_size(2); -#else - return traits::execution_space::impl_thread_pool_size(2); -#endif - } + int vector_length_max() + { return 1024; } // Use arbitrary large number, is meant as a vectorizable length + + inline static + int scratch_size_max(int level) + { return (level==0? + 1024*32: // Roughly L1 size + 20*1024*1024); // Limit to keep compatibility with CUDA + } //---------------------------------------- diff --git a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp index 2d53670c8d..c7d4defad2 100644 --- a/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp +++ b/lib/kokkos/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp @@ -160,7 +160,8 @@ SharedAllocationRecord( const Kokkos::Experimental::OpenMPTargetSpace & arg_spac , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); - + // Set last element zero, in case c_str is too long + header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; //TODO DeepCopy // DeepCopy diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Config.hpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Config.hpp index 71643458b4..87840bb37b 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Config.hpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Config.hpp @@ -44,8 +44,8 @@ #ifndef GUARD_CORE_KOKKOS_ROCM_CONFIG_HPP #define GUARD_CORE_KOKKOS_ROCM_CONFIG_HPP -#ifndef KOKKOS_ROCM_HAS_WORKAROUNDS -#define KOKKOS_ROCM_HAS_WORKAROUNDS 1 +#ifndef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND +#define KOKKOS_IMPL_ROCM_CLANG_WORKAROUND 1 #endif #endif diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Exec.hpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Exec.hpp index 1c2bf303cf..205e6a2955 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Exec.hpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Exec.hpp @@ -55,14 +55,14 @@ namespace Impl { struct ROCmTraits { // TODO: determine if needed - enum { WavefrontSize = 64 /* 64 */ }; - enum { WorkgroupSize = 64 /* 64 */ }; - enum { WavefrontIndexMask = 0x001f /* Mask for warpindex */ }; - enum { WavefrontIndexShift = 5 /* WarpSize == 1 << WarpShift */ }; + enum { WavefrontSize = 64 /* 64 */ }; + enum { WorkgroupSize = 256 /* 256 */ }; + enum { WavefrontIndexMask = 0x003f /* Mask for wavefrontindex */ }; + enum { WavefrontIndexShift = 6 /* WavefrontSize == 1 << WavefrontShift */ }; - enum { SharedMemoryBanks = 32 /* Compute device 2.0 */ }; - enum { SharedMemoryCapacity = 0x0C000 /* 48k shared / 16k L1 Cache */ }; - enum { SharedMemoryUsage = 0x04000 /* 16k shared / 48k L1 Cache */ }; + enum { SharedMemoryBanks = 64 /* GCN */ }; + enum { SharedMemoryCapacity = 0x10000 /* 64k shared / 16k L1 Cache */ }; + enum { SharedMemoryUsage = 0x04000 /* 64k shared / 16k L1 Cache */ }; enum { UpperBoundExtentCount = 4294967295 /* Hard upper bound */ }; #if 0 @@ -84,6 +84,16 @@ size_t rocm_internal_maximum_workgroup_count(); size_t * rocm_internal_scratch_flags( const size_t size ); size_t * rocm_internal_scratch_space( const size_t size ); +// This pointer is the start of dynamic shared memory (LDS). +// Dynamic is at the end of LDS and it's size must be specified +// in a tile_block specification at kernel launch time. +template< typename T > +KOKKOS_INLINE_FUNCTION +T * kokkos_impl_rocm_shared_memory() +//{ return (T*) hc::get_group_segment_base_pointer() ; } +{ return (T*) hc::get_dynamic_group_segment_base_pointer() ; } + + } } // namespace Kokkos #define ROCM_SPACE_ATOMIC_MASK 0x1FFFF @@ -249,7 +259,6 @@ struct ROCmParallelLaunch< DriverType size_t bx = (grid.x > block.x)? block.x : grid.x; size_t by = (grid.y > block.y)? block.y : grid.y; size_t bz = (grid.z > block.z)? block.z : grid.z; - hc::parallel_for_each(ext.tile_with_dynamic(bz,by,bx,shmem), [=](const hc::index<3> & idx) [[hc]] diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Impl.cpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Impl.cpp index 3ae312647e..236042ccc2 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Impl.cpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Impl.cpp @@ -543,20 +543,13 @@ enum { sizeScratchGrain = sizeof(ScratchGrain) }; void rocmMemset( Kokkos::Experimental::ROCm::size_type * ptr , Kokkos::Experimental::ROCm::size_type value , Kokkos::Experimental::ROCm::size_type size) { char * mptr = (char * ) ptr; -#if 0 - parallel_for_each(hc::extent<1>(size), +/* parallel_for_each(hc::extent<1>(size), [=, &ptr] (hc::index<1> idx) __HC__ { int i = idx[0]; ptr[i] = value; - }).wait(); -#else - for (int i= 0; i Record ; + typedef Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::ROCmSpace , void > Record ; - Record * const r = Record::allocate( Kokkos::HostSpace() + Record * const r = Record::allocate( Kokkos::Experimental::ROCmSpace() , "InternalScratchFlags" , ( sizeScratchGrain * m_scratchFlagsCount ) ); @@ -590,9 +583,9 @@ ROCmInternal::scratch_space( const Kokkos::Experimental::ROCm::size_type size ) m_scratchSpaceCount = ( size + sizeScratchGrain - 1 ) / sizeScratchGrain ; - typedef Kokkos::Impl::SharedAllocationRecord< Kokkos::HostSpace , void > Record ; + typedef Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::ROCmSpace , void > Record ; - Record * const r = Record::allocate( Kokkos::HostSpace() + static Record * const r = Record::allocate( Kokkos::Experimental::ROCmSpace() , "InternalScratchSpace" , ( sizeScratchGrain * m_scratchSpaceCount ) ); @@ -616,7 +609,7 @@ void ROCmInternal::finalize() // scratch_lock_array_rocm_space_ptr(false); // threadid_lock_array_rocm_space_ptr(false); - typedef Kokkos::Impl::SharedAllocationRecord< HostSpace > RecordROCm ; + typedef Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::ROCmSpace > RecordROCm ; typedef Kokkos::Impl::SharedAllocationRecord< Kokkos::Experimental::ROCmHostPinnedSpace > RecordHost ; RecordROCm::decrement( RecordROCm::get_record( m_scratchFlags ) ); diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Parallel.hpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Parallel.hpp index 2978ae8f5f..edd1c12e45 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Parallel.hpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Parallel.hpp @@ -243,6 +243,15 @@ public: return(max); } + template< class FunctorType , class PatternTypeTag> + int team_size_max( const FunctorType& functor, PatternTypeTag) { + return 256/vector_length(); + } + template< class FunctorType , class PatternTypeTag> + int team_size_recommended( const FunctorType& functor, PatternTypeTag) { + return 128/vector_length(); + } + template KOKKOS_INLINE_FUNCTION int team_size(const F& f) const { return (m_team_size > 0) ? m_team_size : team_size_recommended(f); } KOKKOS_INLINE_FUNCTION int team_size() const { return (m_team_size > 0) ? m_team_size : Impl::get_max_tile_thread(); ; } @@ -261,6 +270,11 @@ public: return m_thread_scratch_size[level]; } + static int scratch_size_max(int level) { + return level==0 ? + 1024*40 : 1024*1204*20; + } + typedef Impl::ROCmTeamMember member_type; }; @@ -487,6 +501,7 @@ public: #endif } m_idx.barrier.wait(); + reducer.reference() = buffer[0]; } /** \brief Intra-team vector reduce @@ -541,19 +556,19 @@ public: } template< typename ReducerType > - KOKKOS_INLINE_FUNCTION static + KOKKOS_INLINE_FUNCTION typename std::enable_if< is_reducer< ReducerType >::value >::type - vector_reduce( ReducerType const & reducer ) + vector_reduce( ReducerType const & reducer ) const { #ifdef __HCC_ACCELERATOR__ - if(blockDim_x == 1) return; + if(m_vector_length == 1) return; // Intra vector lane shuffle reduction: typename ReducerType::value_type tmp ( reducer.reference() ); - for ( int i = blockDim_x ; ( i >>= 1 ) ; ) { - shfl_down( reducer.reference() , i , blockDim_x ); - if ( (int)threadIdx_x < i ) { reducer.join( tmp , reducer.reference() ); } + for ( int i = m_vector_length ; ( i >>= 1 ) ; ) { + reducer.reference() = shfl_down( tmp , i , m_vector_length ); + if ( (int)vector_rank() < i ) { reducer.join( tmp , reducer.reference() ); } } // Broadcast from root lane to all other lanes. @@ -561,7 +576,7 @@ public: // because floating point summation is not associative // and thus different threads could have different results. - shfl( reducer.reference() , 0 , blockDim_x ); + reducer.reference() = shfl( tmp , 0 , m_vector_length ); #endif } @@ -847,7 +862,7 @@ public: hc::extent< 1 > flat_extent( total_size ); - hc::tiled_extent< 1 > team_extent = flat_extent.tile(team_size*vector_length); + hc::tiled_extent< 1 > team_extent = flat_extent.tile(vector_length*team_size); hc::parallel_for_each( team_extent , [=](hc::tiled_index<1> idx) [[hc]] { rocm_invoke(f, typename Policy::member_type(idx, league_size, team_size, shared, shared_size, scratch_size0, scratch, scratch_size1,vector_length)); @@ -958,6 +973,176 @@ public: }; +//---------------------------------------------------------------------------- + +template< class FunctorType , class ReducerType, class... Traits > +class ParallelReduce< + FunctorType , Kokkos::MDRangePolicy< Traits... >, ReducerType, Kokkos::Experimental::ROCm > +{ +private: + typedef Kokkos::MDRangePolicy< Traits ... > Policy ; + using RP = Policy; + typedef typename Policy::array_index_type array_index_type; + typedef typename Policy::index_type index_type; + typedef typename Policy::work_tag WorkTag ; + typedef typename Policy::member_type Member ; + typedef typename Policy::launch_bounds LaunchBounds; + + typedef Kokkos::Impl::if_c< std::is_same::value, FunctorType, ReducerType> ReducerConditional; + typedef typename ReducerConditional::type ReducerTypeFwd; + typedef typename Kokkos::Impl::if_c< std::is_same::value, WorkTag, void>::type WorkTagFwd; + + typedef Kokkos::Impl::FunctorValueTraits< ReducerTypeFwd, WorkTagFwd > ValueTraits ; + typedef Kokkos::Impl::FunctorValueInit< ReducerTypeFwd, WorkTagFwd > ValueInit ; + typedef Kokkos::Impl::FunctorValueJoin< ReducerTypeFwd, WorkTagFwd > ValueJoin ; + + +public: + + typedef typename ValueTraits::pointer_type pointer_type ; + typedef typename ValueTraits::value_type value_type ; + typedef typename ValueTraits::reference_type reference_type ; + typedef FunctorType functor_type ; + typedef Kokkos::Experimental::ROCm::size_type size_type ; + + // Algorithmic constraints: blockSize is a power of two AND blockDim.y == blockDim.z == 1 + + const FunctorType m_functor ; + const Policy m_policy ; // used for workrange and nwork + const ReducerType m_reducer ; + const pointer_type m_result_ptr ; + value_type * m_scratch_space ; + size_type * m_scratch_flags ; + + typedef typename Kokkos::Impl::Reduce::DeviceIterateTile DeviceIteratePattern; + + KOKKOS_INLINE_FUNCTION + void exec_range( reference_type update ) const + { + Kokkos::Impl::Reduce::DeviceIterateTile(m_policy, m_functor, update).exec_range(); + } + + + KOKKOS_INLINE_FUNCTION + void operator()(void) const + { + run(); + } + + KOKKOS_INLINE_FUNCTION + void run( ) const + { + const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(value_type) > + word_count( (ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) )) / sizeof(value_type) ); + // pointer to shared data accounts for the reserved space at the start + value_type * const shared = kokkos_impl_rocm_shared_memory() + + 2*sizeof(uint64_t); + + { + reference_type value = + ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , shared + threadIdx_y * word_count.value ); + // Number of blocks is bounded so that the reduction can be limited to two passes. + // Each thread block is given an approximately equal amount of work to perform. + // Accumulate the values for this block. + // The accumulation ordering does not match the final pass, but is arithmatically equivalent. + + this-> exec_range( value ); + } + + // Reduce with final value at blockDim.y - 1 location. + // Problem: non power-of-two blockDim + + if ( rocm_single_inter_block_reduce_scan( + ReducerConditional::select(m_functor , m_reducer) , blockIdx_x , + gridDim_x , shared , m_scratch_space , m_scratch_flags ) ) { + + // This is the final block with the final result at the final threads' location + value_type * const tshared = shared + ( blockDim_y - 1 ) * word_count.value ; + value_type * const global = m_scratch_space ; + + if ( threadIdx_y == 0 ) { + Kokkos::Impl::FunctorFinal< ReducerTypeFwd , WorkTagFwd >::final( ReducerConditional::select(m_functor , m_reducer) , tshared ); +// for ( unsigned i = 0 ; i < word_count.value ; i+=blockDim_y ) { global[i] = tshared[i]; } + for ( unsigned i = 0 ; i < word_count.value ; i++ ) { global[i] = tshared[i]; } + } + } + } + + + + // Determine block size constrained by shared memory: + static inline + unsigned local_block_size( const FunctorType & f ) + { + unsigned n = ROCmTraits::WavefrontSize * 8 ; + while ( n && ROCmTraits::SharedMemoryCapacity < rocm_single_inter_block_reduce_scan_shmem( f , n ) ) { n >>= 1 ; } + return n ; + } + + inline + void execute() + { + const int nwork = m_policy.m_num_tiles; + if ( nwork ) { + int block_size = m_policy.m_prod_tile_dims; + // CONSTRAINT: Algorithm requires block_size >= product of tile dimensions + // Nearest power of two + int exponent_pow_two = std::ceil( std::log2((float)block_size) ); + block_size = 1<<(exponent_pow_two); + + m_scratch_space = (value_type*)rocm_internal_scratch_space( ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ) * block_size*nwork /* block_size == max block_count */ ); + m_scratch_flags = rocm_internal_scratch_flags( sizeof(size_type) ); + const dim3 block( 1 , block_size , 1 ); + // Required grid.x <= block.y + const dim3 grid( nwork, block_size , 1 ); + const int shmem = rocm_single_inter_block_reduce_scan_shmem( m_functor , block.y ); + + ROCmParallelLaunch< ParallelReduce, LaunchBounds >( *this, grid, block, shmem ); // copy to device and execute + + ROCM::fence(); + + if ( m_result_ptr ) { + const int size = ValueTraits::value_size( ReducerConditional::select(m_functor , m_reducer) ); + DeepCopy( m_result_ptr , m_scratch_space , size ); + } + } + else { + if (m_result_ptr) { + ValueInit::init( ReducerConditional::select(m_functor , m_reducer) , m_result_ptr ); + } + } + } + + + template< class HostViewType > + ParallelReduce( const FunctorType & arg_functor + , const Policy & arg_policy + , const HostViewType & arg_result + , typename std::enable_if< + Kokkos::is_view< HostViewType >::value + ,void*>::type = NULL) + : m_functor( arg_functor ) + , m_policy( arg_policy ) + , m_reducer( InvalidType() ) + , m_result_ptr( arg_result.data() ) + , m_scratch_space( 0 ) + , m_scratch_flags( 0 ) + {} + + ParallelReduce( const FunctorType & arg_functor + , const Policy & arg_policy + , const ReducerType & reducer) + : m_functor( arg_functor ) + , m_policy( arg_policy ) + , m_reducer( reducer ) + , m_result_ptr( reducer.view().data() ) + , m_scratch_space( 0 ) + , m_scratch_flags( 0 ) + {} + +}; +//---------------------------------------------------------------------------- + template< class FunctorType, class ReducerType, class... Traits > class ParallelReduce< FunctorType , Kokkos::TeamPolicy< Traits... >, ReducerType, Kokkos::Experimental::ROCm > @@ -992,8 +1177,14 @@ public: const int scratch_size0 = policy.scratch_size(0,team_size); const int scratch_size1 = policy.scratch_size(1,team_size); const int total_size = league_size * team_size ; - - if(total_size == 0) return; + + typedef Kokkos::Impl::FunctorValueInit< FunctorType, typename Policy::work_tag > ValueInit ; + if(total_size==0) { + if (result_view.data()) { + ValueInit::init( f , result_view.data() ); + } + return; + } const int reduce_size = ValueTraits::value_size( f ); const int shared_size = FunctorTeamShmemSize< FunctorType >::value( f , team_size ); @@ -1042,7 +1233,16 @@ public: const int vector_length = policy.vector_length(); const int total_size = league_size * team_size; - if(total_size == 0) return; + typedef Kokkos::Impl::FunctorValueInit< ReducerType, typename Policy::work_tag > ValueInit ; + typedef Kokkos::Impl::if_c< std::is_same::value, + FunctorType, ReducerType> ReducerConditional; + if(total_size==0) { + if (reducer.view().data()) { + ValueInit::init( ReducerConditional::select(f,reducer), + reducer.view().data() ); + } + return; + } const int reduce_size = ValueTraits::value_size( f ); const int shared_size = FunctorTeamShmemSize< FunctorType >::value( f , team_size ); @@ -1113,6 +1313,39 @@ public: //---------------------------------------- }; +template< class FunctorType , class ReturnType , class... Traits > +class ParallelScanWithTotal< FunctorType , Kokkos::RangePolicy< Traits... >, + ReturnType, Kokkos::Experimental::ROCm > +{ +private: + + typedef Kokkos::RangePolicy< Traits... > Policy; + typedef typename Policy::work_tag Tag; + typedef Kokkos::Impl::FunctorValueTraits< FunctorType, Tag> ValueTraits; + +public: + + //---------------------------------------- + + inline + ParallelScanWithTotal( const FunctorType & f + , const Policy & policy + , ReturnType & arg_returnvalue) + { + const auto len = policy.end()-policy.begin(); + + + if(len==0) return; + + scan_enqueue(len, f, arg_returnvalue, [](hc::tiled_index<1> idx, int, int) { return idx.global[0]; }); + } + + KOKKOS_INLINE_FUNCTION + void execute() const {} + + //---------------------------------------- +}; + template< class FunctorType , class... Traits> class ParallelScan< FunctorType , Kokkos::TeamPolicy< Traits... >, Kokkos::Experimental::ROCm > { @@ -1350,22 +1583,17 @@ void parallel_for(const Impl::TeamThreadRangeBoundariesStruct KOKKOS_INLINE_FUNCTION -void parallel_reduce(const Impl::TeamThreadRangeBoundariesStruct& loop_boundaries, +typename std::enable_if< ! Kokkos::is_reducer< ValueType >::value >::type +parallel_reduce(const Impl::TeamThreadRangeBoundariesStruct& loop_boundaries, const Lambda & lambda, ValueType& result) { - result = ValueType(); + Kokkos::Sum reducer(result); + reducer.init( reducer.reference() ); for( iType i = loop_boundaries.start; i < loop_boundaries.end; i+=loop_boundaries.increment) { - ValueType tmp = ValueType(); - lambda(i,tmp); - result+=tmp; + lambda(i,reducer.reference()); } - result = loop_boundaries.thread.team_reduce(result, - Impl::JoinAdd()); -// Impl::rocm_intra_workgroup_reduction( loop_boundaries.thread, result, -// Impl::JoinAdd()); -// Impl::rocm_inter_workgroup_reduction( loop_boundaries.thread, result, -// Impl::JoinAdd()); + loop_boundaries.thread.team_reduce(reducer); } /** \brief Inter-thread thread range parallel_reduce. Executes lambda(iType i, ValueType & val) for each i=0..N-1. @@ -1374,7 +1602,8 @@ void parallel_reduce(const Impl::TeamThreadRangeBoundariesStruct KOKKOS_INLINE_FUNCTION -void parallel_reduce(const Impl::TeamThreadRangeBoundariesStruct& loop_boundaries, +typename std::enable_if< Kokkos::is_reducer< ReducerType >::value >::type +parallel_reduce(const Impl::TeamThreadRangeBoundariesStruct& loop_boundaries, const Lambda & lambda, ReducerType const & reducer) { reducer.init( reducer.reference() ); @@ -1439,7 +1668,8 @@ void parallel_for(const Impl::ThreadVectorRangeBoundariesStruct KOKKOS_INLINE_FUNCTION -void parallel_reduce(const Impl::ThreadVectorRangeBoundariesStruct& +typename std::enable_if< !Kokkos::is_reducer< ValueType >::value >::type +parallel_reduce(const Impl::ThreadVectorRangeBoundariesStruct& loop_boundaries, const Lambda & lambda, ValueType& result) { result = ValueType(); @@ -1477,7 +1707,8 @@ void parallel_reduce(const Impl::ThreadVectorRangeBoundariesStruct KOKKOS_INLINE_FUNCTION -void parallel_reduce(const Impl::ThreadVectorRangeBoundariesStruct& +typename std::enable_if< Kokkos::is_reducer< ReducerType >::value >::type +parallel_reduce(const Impl::ThreadVectorRangeBoundariesStruct& loop_boundaries, const Lambda & lambda, ReducerType const & reducer) { reducer.init( reducer.reference() ); @@ -1523,86 +1754,46 @@ void parallel_scan(const Impl::ThreadVectorRangeBoundariesStruct ValueTraits ; typedef typename ValueTraits::value_type value_type ; - value_type scan_val = value_type(); -#if (__ROCM_ARCH__ >= 800) -// adopt the cuda vector shuffle method - const int VectorLength = loop_boundaries.increment; - int lid = loop_boundaries.thread.lindex(); - int vector_rank = lid%VectorLength; + value_type val = value_type(); + const int vector_length = loop_boundaries.thread.vector_length(); + const int vector_rank = loop_boundaries.thread.vector_rank(); - iType loop_bound = ((loop_boundaries.end+VectorLength-1)/VectorLength) * VectorLength; - value_type val ; - for(int _i = vector_rank; _i < loop_bound; _i += VectorLength) { - val = value_type(); - if(_i 1) { - const value_type tmp2 = shfl_up(tmp, 1,VectorLength); - if(vector_rank > 0) - tmp+=tmp2; - } - if(vector_rank == 1) - result_i = tmp; - if (VectorLength > 3) { - const value_type tmp2 = shfl_up(tmp, 2,VectorLength); - if(vector_rank > 1) - tmp+=tmp2; - } - if ((vector_rank >= 2) && - (vector_rank < 4)) - result_i = tmp; - if (VectorLength > 7) { - const value_type tmp2 = shfl_up(tmp, 4,VectorLength); - if(vector_rank > 3) - tmp+=tmp2; - } - if ((vector_rank >= 4) && - (vector_rank < 8)) - result_i = tmp; - if (VectorLength > 15) { - const value_type tmp2 = shfl_up(tmp, 8,VectorLength); - if(vector_rank > 7) - tmp+=tmp2; - } - if ((vector_rank >= 8) && - (vector_rank < 16)) - result_i = tmp; - if (VectorLength > 31) { - const value_type tmp2 = shfl_up(tmp, 16,VectorLength); - if(vector_rank > 15) - tmp+=tmp2; - } - if ((vector_rank >=16) && - (vector_rank < 32)) - result_i = tmp; - if (VectorLength > 63) { - const value_type tmp2 = shfl_up(tmp, 32,VectorLength); - if(vector_rank > 31) - tmp+=tmp2; + value_type val = 0 ; + + // First acquire per-lane contributions: + if ( i < loop_boundaries.end ) lambda( i , val , false ); + + value_type sval = val ; + + // Bottom up inclusive scan in triangular pattern + // where each thread is the root of a reduction tree + // from the zeroth "lane" to itself. + // [t] += [t-1] if t >= 1 + // [t] += [t-2] if t >= 2 + // [t] += [t-4] if t >= 4 + // ... + + for ( int j = 1 ; j < vector_length ; j <<= 1 ) { + value_type tmp = 0 ; + tmp = shfl_up(sval , j , vector_length ); + if ( j <= vector_rank ) { sval += tmp ; } } - if (vector_rank >= 32) - result_i = tmp; + // Include accumulation and remove value for exclusive scan: + val = accum + sval - val ; - val = scan_val + result_i - val; - scan_val += shfl(tmp,VectorLength-1,VectorLength); - if(_i #include #include - ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// namespace Kokkos { @@ -75,7 +74,7 @@ T& reduce_value(T* x, std::false_type) [[hc]] return *x; } -#if KOKKOS_ROCM_HAS_WORKAROUNDS +#ifdef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND struct always_true { template @@ -149,7 +148,7 @@ void reduce_enqueue( // Store the tile result in the global memory. if (local == 0) { -#if KOKKOS_ROCM_HAS_WORKAROUNDS +#ifdef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND // Workaround for assigning from LDS memory: std::copy should work // directly buffer.action_at(0, [&](T* x) @@ -158,7 +157,7 @@ void reduce_enqueue( // new ROCM 15 address space changes aren't implemented in std algorithms yet auto * src = reinterpret_cast(x); auto * dest = reinterpret_cast(result.data()+tile*output_length); - for(int i=0; i + KOKKOS_INLINE_FUNCTION + unsigned long operator () (volatile unsigned long * dest, OP &&op){ + unsigned long read,compare,val; + compare = *dest; + read = compare; + do { + compare = read; + val = op(compare); +#if __KALMAR_ACCELERATOR__ == 1 + hc::atomic_compare_exchange((uint64_t *)dest,&read,val); +#endif + } while (read != compare); + return val; + } +}; + + template + KOKKOS_INLINE_FUNCTION + unsigned long atomic_cas_op (volatile unsigned long * dest, OP &&op) { + ROCm_atomic_CAS cas_op; + return cas_op(dest, std::forward(op)); + } + + KOKKOS_INLINE_FUNCTION + unsigned long atomicInc (volatile unsigned long * dest, const unsigned long& val) { + return atomic_cas_op(dest, [=](unsigned long old){return ((old>=val)?0:(old+1));}); + } + + //---------------------------------------------------------------------------- template< typename T > @@ -375,18 +445,7 @@ bool rocm_inter_block_reduction( ROCmTeamMember& team, #endif } #endif -#if 0 -//---------------------------------------------------------------------------- -// See section B.17 of ROCm C Programming Guide Version 3.2 -// for discussion of -// __launch_bounds__(maxThreadsPerBlock,minBlocksPerMultiprocessor) -// function qualifier which could be used to improve performance. -//---------------------------------------------------------------------------- -// Maximize shared memory and minimize L1 cache: -// rocmFuncSetCacheConfig(MyKernel, rocmFuncCachePreferShared ); -// For 2.0 capability: 48 KB shared and 16 KB L1 -//---------------------------------------------------------------------------- //---------------------------------------------------------------------------- /* * Algorithmic constraints: @@ -406,87 +465,105 @@ void rocm_intra_block_reduce_scan( const FunctorType & functor , typedef typename ValueTraits::pointer_type pointer_type ; const unsigned value_count = ValueTraits::value_count( functor ); - const unsigned BlockSizeMask = team.team_size() - 1 ; + const unsigned BlockSizeMask = blockDim_y - 1 ; // Must have power of two thread count - if ( BlockSizeMask & team.team_size() ) { Kokkos::abort("ROCm::rocm_intra_block_scan requires power-of-two blockDim"); } + if ( BlockSizeMask & blockDim_y ) { Kokkos::abort("ROCm::rocm_intra_block_scan requires power-of-two blockDim"); } #define BLOCK_REDUCE_STEP( R , TD , S ) \ - if ( ! ( R & ((1<<(S+1))-1) ) ) { ValueJoin::join( functor , TD , (TD - (value_count<0; i-= 64) + ValueJoin::join( functor , base_data + (blockDim_y-1)*value_count + threadIdx_y , base_data + i*value_count + threadIdx_y ); + } + __syncthreads(); +#if 0 + const unsigned rtid_inter = ( threadIdx_y ^ BlockSizeMask ) << ROCmTraits::WavefrontIndexShift ; + + if ( rtid_inter < blockDim_y ) { - if ( rtid_inter < team.team_size() ) { const pointer_type tdata_inter = base_data + value_count * ( rtid_inter ^ BlockSizeMask ); +// +// remove these comments +// for rocm, we start with a block size of 64, so the 5 step is already done. +// The remaining steps are only done if block size is > 64, so we leave them +// in place until we tune blocksize for performance, then remove the ones +// that will never be used. +// if ( (1<<6) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,6) } +// if ( (1<<7) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,7) } +// if ( (1<<8) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,8) } +// if ( (1<<9) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,9) } - if ( (1<<5) < BlockSizeMask ) { BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,5) } - if ( (1<<6) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,6) } - if ( (1<<7) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,7) } - if ( (1<<8) < BlockSizeMask ) { __threadfence_block(); BLOCK_REDUCE_STEP(rtid_inter,tdata_inter,8) } if ( DoScan ) { - int n = ( rtid_inter & 32 ) ? 32 : ( - ( rtid_inter & 64 ) ? 64 : ( + int n = ( rtid_inter & 64 ) ? 64 : ( ( rtid_inter & 128 ) ? 128 : ( - ( rtid_inter & 256 ) ? 256 : 0 ))); + ( rtid_inter & 256 ) ? 256 : 0 )); - if ( ! ( rtid_inter + n < team.team_size() ) ) n = 0 ; + if ( ! ( rtid_inter + n < blockDim_y ) ) n = 0 ; __threadfence_block(); BLOCK_SCAN_STEP(tdata_inter,n,8) __threadfence_block(); BLOCK_SCAN_STEP(tdata_inter,n,7) __threadfence_block(); BLOCK_SCAN_STEP(tdata_inter,n,6) - __threadfence_block(); BLOCK_SCAN_STEP(tdata_inter,n,5) +// __threadfence_block(); BLOCK_SCAN_STEP(tdata_inter,n,5) } } +#endif } - team.team_barrier(); // Wait for inter-workgroup reduce-scan to complete + __syncthreads(); // Wait for inter-workgroup reduce-scan to complete if ( DoScan ) { int n = ( rtid_intra & 1 ) ? 1 : ( ( rtid_intra & 2 ) ? 2 : ( ( rtid_intra & 4 ) ? 4 : ( ( rtid_intra & 8 ) ? 8 : ( - ( rtid_intra & 16 ) ? 16 : 0 )))); + ( rtid_intra & 16 ) ? 16 : ( + ( rtid_intra & 32 ) ? 32 : 0 ))))); - if ( ! ( rtid_intra + n < team.team_size() ) ) n = 0 ; - #ifdef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND - BLOCK_SCAN_STEP(tdata_intra,n,4) team.team_barrier();//__threadfence_block(); - BLOCK_SCAN_STEP(tdata_intra,n,3) team.team_barrier();//__threadfence_block(); - BLOCK_SCAN_STEP(tdata_intra,n,2) team.team_barrier();//__threadfence_block(); - BLOCK_SCAN_STEP(tdata_intra,n,1) team.team_barrier();//__threadfence_block(); - BLOCK_SCAN_STEP(tdata_intra,n,0) team.team_barrier(); - #else - BLOCK_SCAN_STEP(tdata_intra,n,4) __threadfence_block(); + if ( ! ( rtid_intra + n < blockDim_y ) ) n = 0 ; + +// BLOCK_SCAN_STEP(tdata_intra,n,5) __threadfence_block(); +// BLOCK_SCAN_STEP(tdata_intra,n,4) __threadfence_block(); BLOCK_SCAN_STEP(tdata_intra,n,3) __threadfence_block(); BLOCK_SCAN_STEP(tdata_intra,n,2) __threadfence_block(); BLOCK_SCAN_STEP(tdata_intra,n,1) __threadfence_block(); BLOCK_SCAN_STEP(tdata_intra,n,0) __threadfence_block(); - #endif } #undef BLOCK_SCAN_STEP #undef BLOCK_REDUCE_STEP +#undef KOKKOS_IMPL_ROCM_SYNCWF } //---------------------------------------------------------------------------- @@ -497,16 +574,18 @@ void rocm_intra_block_reduce_scan( const FunctorType & functor , * * Global reduce result is in the last threads' 'shared_data' location. */ +using ROCM = Kokkos::Experimental::ROCm ; + template< bool DoScan , class FunctorType , class ArgTag > KOKKOS_INLINE_FUNCTION bool rocm_single_inter_block_reduce_scan( const FunctorType & functor , - const ROCm::size_type block_id , - const ROCm::size_type block_count , - ROCm::size_type * const shared_data , - ROCm::size_type * const global_data , - ROCm::size_type * const global_flags ) + const ROCM::size_type block_id , + const ROCM::size_type block_count , + typename FunctorValueTraits::value_type * const shared_data , + typename FunctorValueTraits::value_type * const global_data , + ROCM::size_type * const global_flags ) { - typedef ROCm::size_type size_type ; + typedef ROCM::size_type size_type ; typedef FunctorValueTraits< FunctorType , ArgTag > ValueTraits ; typedef FunctorValueJoin< FunctorType , ArgTag > ValueJoin ; typedef FunctorValueInit< FunctorType , ArgTag > ValueInit ; @@ -517,16 +596,17 @@ bool rocm_single_inter_block_reduce_scan( const FunctorType & functor , typedef typename ValueTraits::value_type value_type ; // '__ffs' = position of the least significant bit set to 1. - // 'team.team_size()' is guaranteed to be a power of two so this + // blockDim_y is guaranteed to be a power of two so this // is the integral shift value that can replace an integral divide. - const unsigned BlockSizeShift = __ffs( team.team_size() ) - 1 ; - const unsigned BlockSizeMask = team.team_size() - 1 ; + // const unsigned long BlockSizeShift = __ffs( blockDim_y ) - 1 ; + const unsigned long BlockSizeShift = __lastbit_u32_u32( blockDim_y ) ; + const unsigned long BlockSizeMask = blockDim_y - 1 ; // Must have power of two thread count - if ( BlockSizeMask & team.team_size() ) { Kokkos::abort("ROCm::rocm_single_inter_block_reduce_scan requires power-of-two blockDim"); } + if ( BlockSizeMask & blockDim_y ) { Kokkos::abort("ROCm::rocm_single_inter_block_reduce_scan requires power-of-two blockDim"); } - const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(size_type) > - word_count( ValueTraits::value_size( functor ) / sizeof(size_type) ); + const integral_nonzero_constant< size_type , ValueTraits::StaticValueSize / sizeof(value_type) > + word_count( ValueTraits::value_size( functor )/ sizeof(value_type) ); // Reduce the accumulation for the entire block. rocm_intra_block_reduce_scan( functor , pointer_type(shared_data) ); @@ -534,54 +614,47 @@ bool rocm_single_inter_block_reduce_scan( const FunctorType & functor , { // Write accumulation total to global scratch space. // Accumulation total is the last thread's data. - size_type * const shared = shared_data + word_count.value * BlockSizeMask ; - size_type * const global = global_data + word_count.value * block_id ; - -#if (__ROCM_ARCH__ < 500) - for ( size_type i = team.team_rank() ; i < word_count.value ; i += team.team_size() ) { global[i] = shared[i] ; } -#else - for ( size_type i = 0 ; i < word_count.value ; i += 1 ) { global[i] = shared[i] ; } -#endif + value_type * const shared = shared_data + + word_count.value * BlockSizeMask ; + value_type * const global = global_data + word_count.value * block_id ; + for ( int i = int(threadIdx_y) ; i < word_count.value ; i += blockDim_y ) { global[i] = shared[i] ; } } // Contributing blocks note that their contribution has been completed via an atomic-increment flag // If this block is not the last block to contribute to this group then the block is done. - team.team_barrier(); + const bool is_last_block = - ! team.team_reduce( team.team_rank() ? 0 : ( 1 + atomicInc( global_flags , block_count - 1 ) < block_count ) ,Impl::JoinAdd()); - + ! __syncthreads_or( threadIdx_y ? 0 : ( 1 + atomicInc( global_flags , block_count - 1 ) < block_count ) ); if ( is_last_block ) { - const size_type b = ( long(block_count) * long(team.team_rank()) ) >> BlockSizeShift ; - const size_type e = ( long(block_count) * long( team.team_rank() + 1 ) ) >> BlockSizeShift ; + const size_type b = ( long(block_count) * long(threadIdx_y )) >> BlockSizeShift ; + const size_type e = ( long(block_count) * long(threadIdx_y + 1 ) ) >> BlockSizeShift ; { - void * const shared_ptr = shared_data + word_count.value * team.team_rank() ; - reference_type shared_value = ValueInit::init( functor , shared_ptr ); + value_type * const shared_ptr = shared_data + word_count.value * threadIdx_y ; + ValueInit::init( functor , shared_ptr ); + for ( size_type i = b ; i < e ; ++i ) { ValueJoin::join( functor , shared_ptr , global_data + word_count.value * i ); } } - rocm_intra_block_reduce_scan( functor , pointer_type(shared_data) ); if ( DoScan ) { + value_type * const shared_value = shared_data + word_count.value * ( threadIdx_y ? threadIdx_y - 1 : blockDim_y ); - size_type * const shared_value = shared_data + word_count.value * ( team.team_rank() ? team.team_rank() - 1 : team.team_size() ); - - if ( ! team.team_rank() ) { ValueInit::init( functor , shared_value ); } + if ( ! threadIdx_y ) { ValueInit::init( functor , shared_value ); } // Join previous inclusive scan value to each member for ( size_type i = b ; i < e ; ++i ) { - size_type * const global_value = global_data + word_count.value * i ; + value_type * const global_value = global_data + word_count.value * i ; ValueJoin::join( functor , shared_value , global_value ); ValueOps ::copy( functor , global_value , shared_value ); } } } - return is_last_block ; } @@ -592,7 +665,6 @@ unsigned rocm_single_inter_block_reduce_scan_shmem( const FunctorType & functor { return ( BlockSize + 2 ) * Impl::FunctorValueTraits< FunctorType , ArgTag >::value_size( functor ); } -#endif } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Scan.hpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Scan.hpp index 9890598bc9..f24db42cee 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Scan.hpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Scan.hpp @@ -98,7 +98,7 @@ void scan_enqueue( { auto j = i + d - 1; auto k = i + d2 - 1; -// join(k, j); // no longer needed with ROCm 1.6 + ValueJoin::join(f, &buffer[k], &buffer[j]); } } @@ -116,7 +116,7 @@ void scan_enqueue( auto j = i + d - 1; auto k = i + d2 - 1; auto t = buffer[k]; -// join(k, j); // no longer needed with ROCm 1.6 + ValueJoin::join(f, &buffer[k], &buffer[j]); buffer[j] = t; } @@ -127,17 +127,13 @@ void scan_enqueue( }).wait(); copy(result,result_cpu.data()); -// The std::partial_sum was segfaulting, despite that this is cpu code. -// if(td.num_tiles>1) -// std::partial_sum(result_cpu.data(), result_cpu.data()+(td.num_tiles-1)*sizeof(value_type), result_cpu.data(), make_join_operator(f)); -// use this implementation instead. for(int i=1; i(len).tile(td.tile_size), [&,f,len,td](hc::tiled_index<1> t_idx) [[hc]] + size_t launch_len = (((len - 1) / td.tile_size) + 1) * td.tile_size; + hc::parallel_for_each(hc::extent<1>(launch_len).tile(td.tile_size), [&,f,len,td](hc::tiled_index<1> t_idx) [[hc]] { -// const auto local = t_idx.local[0]; const auto global = t_idx.global[0]; const auto tile = t_idx.tile[0]; @@ -145,13 +141,115 @@ void scan_enqueue( { auto final_state = scratch[global]; -// the join is locking up, at least with 1.6 - if (tile != 0) final_state += result[tile-1]; -// if (tile != 0) ValueJoin::join(f, &final_state, &result[tile-1]); + if (tile != 0) ValueJoin::join(f, &final_state, &result[tile-1]); rocm_invoke(f, transform_index(t_idx, td.tile_size, td.num_tiles), final_state, true); } }).wait(); } +template< class Tag, class ReturnType, class F, class TransformIndex> +void scan_enqueue( + const int len, + const F & f, + ReturnType & return_val, + TransformIndex transform_index) +{ + typedef Kokkos::Impl::FunctorValueTraits< F, Tag> ValueTraits; + typedef Kokkos::Impl::FunctorValueInit< F, Tag> ValueInit; + typedef Kokkos::Impl::FunctorValueJoin< F, Tag> ValueJoin; + typedef Kokkos::Impl::FunctorValueOps< F, Tag> ValueOps; + + typedef typename ValueTraits::value_type value_type; + typedef typename ValueTraits::pointer_type pointer_type; + typedef typename ValueTraits::reference_type reference_type; + + const auto td = get_tile_desc(len); + std::vector result_cpu(td.num_tiles); + hc::array result(td.num_tiles); + hc::array scratch(len); + std::vector total_cpu(1); + hc::array total(1); + + tile_for(td, [&,f,len,td](hc::tiled_index<1> t_idx, tile_buffer buffer) [[hc]] + { + const auto local = t_idx.local[0]; + const auto global = t_idx.global[0]; + const auto tile = t_idx.tile[0]; + + // Join tile buffer elements + const auto join = [&](std::size_t i, std::size_t j) + { + buffer.action_at(i, j, [&](value_type& x, const value_type& y) + { + ValueJoin::join(f, &x, &y); + }); + }; + + // Copy into tile + buffer.action_at(local, [&](value_type& state) + { + ValueInit::init(f, &state); + if (global < len) rocm_invoke(f, transform_index(t_idx, td.tile_size, td.num_tiles), state, false); + }); + t_idx.barrier.wait(); + // Up sweep phase + for(std::size_t d=1;d0;d/=2) + { + auto d2 = 2*d; + auto i = local*d2; + if(i(launch_len).tile(td.tile_size), [&,f,len,td](hc::tiled_index<1> t_idx) [[hc]] + { + const auto global = t_idx.global[0]; + const auto tile = t_idx.tile[0]; + + if (global < len) + { + auto final_state = scratch[global]; + + if (tile != 0) ValueJoin::join(f, &final_state, &result[tile-1]); + rocm_invoke(f, transform_index(t_idx, td.tile_size, td.num_tiles), final_state, true); + if(global==(len-1)) total[0] = final_state; + } + }).wait(); + copy(total,total_cpu.data()); + return_val = total_cpu[0]; +} + } // namespace Impl } // namespace Kokkos diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Space.cpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Space.cpp index 12f34373ce..2fe0c4192d 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Space.cpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Space.cpp @@ -362,6 +362,8 @@ SharedAllocationRecord( const Kokkos::Experimental::ROCmSpace & arg_space , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + // Set last element zero, in case c_str is too long + header.m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; // Copy to device memory Kokkos::Impl::DeepCopy( RecordBase::m_alloc_ptr , & header , sizeof(SharedAllocationHeader) ); @@ -399,6 +401,8 @@ SharedAllocationRecord( const Kokkos::Experimental::ROCmHostPinnedSpace & arg_sp , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + // Set last element zero, in case c_str is too long + RecordBase::m_alloc_ptr->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; } //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Tile.hpp b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Tile.hpp index db16db3f91..b4436ae156 100644 --- a/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Tile.hpp +++ b/lib/kokkos/core/src/ROCm/Kokkos_ROCm_Tile.hpp @@ -278,7 +278,7 @@ struct single_action void action_at(std::size_t i, Action a) [[hc]] { auto& value = static_cast(*this)[i]; -#if KOKKOS_ROCM_HAS_WORKAROUNDS +#ifdef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND T state = value; a(state); value = state; @@ -347,7 +347,7 @@ struct tile_buffer #if defined (ROCM15) a(value); #else -#if KOKKOS_ROCM_HAS_WORKAROUNDS +#ifdef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND if (m > get_max_tile_array_size()) return; T state[get_max_tile_array_size()]; // std::copy(value, value+m, state); @@ -372,7 +372,6 @@ struct tile_buffer #if defined (ROCM15) a(value); #else -//#if KOKKOS_ROCM_HAS_WORKAROUNDS if (m > get_max_tile_array_size()) return; T state[get_max_tile_array_size()]; // std::copy(value, value+m, state); diff --git a/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp b/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp index e63f868c59..e88abdba50 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_ThreadsTeam.hpp @@ -175,6 +175,27 @@ public: #endif } + template + KOKKOS_INLINE_FUNCTION + void team_broadcast(Closure const & f, ValueType& value, const int& thread_id) const + { +#if ! defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) + { } +#else + // Make sure there is enough scratch space: + typedef typename if_c< sizeof(ValueType) < TEAM_REDUCE_SIZE + , ValueType , void >::type type ; + f( value ); + if ( m_team_base ) { + type * const local_value = ((type*) m_team_base[0]->scratch_memory()); + if(team_rank() == thread_id) *local_value = value; + memory_fence(); + team_barrier(); + value = *local_value; + } +#endif + } + template< typename Type > KOKKOS_INLINE_FUNCTION typename std::enable_if< !Kokkos::is_reducer< Type >::value , Type>::type @@ -626,39 +647,77 @@ public: //---------------------------------------- +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE template< class FunctorType > inline static int team_size_max( const FunctorType & ) { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE - int pool_size = traits::execution_space::thread_pool_size(1); -#else - int pool_size = traits::execution_space::impl_thread_pool_size(1); -#endif - int max_host_team_size = Impl::HostThreadTeamData::max_team_members; - return pool_size - static int team_size_recommended( const FunctorType & ) - { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE - return traits::execution_space::thread_pool_size(2); -#else - return traits::execution_space::impl_thread_pool_size(2); -#endif - } - + inline static + int team_size_recommended( const FunctorType & ) + { + return traits::execution_space::thread_pool_size(2); + } template< class FunctorType > inline static int team_size_recommended( const FunctorType &, const int& ) - { -#ifdef KOKKOS_ENABLE_DEPRECATED_CODE - return traits::execution_space::thread_pool_size(2); -#else - return traits::execution_space::impl_thread_pool_size(2); + { + return traits::execution_space::thread_pool_size(2); + } #endif + + template + int team_size_max( const FunctorType&, const ParallelForTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + int pool_size = traits::execution_space::thread_pool_size(1); +#else + int pool_size = traits::execution_space::impl_thread_pool_size(1); +#endif + int max_host_team_size = Impl::HostThreadTeamData::max_team_members; + return pool_size + int team_size_max( const FunctorType&, const ParallelReduceTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + int pool_size = traits::execution_space::thread_pool_size(1); +#else + int pool_size = traits::execution_space::impl_thread_pool_size(1); +#endif + int max_host_team_size = Impl::HostThreadTeamData::max_team_members; + return pool_size + int team_size_recommended( const FunctorType&, const ParallelForTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + return traits::execution_space::thread_pool_size(2); +#else + return traits::execution_space::impl_thread_pool_size(2); +#endif + } + template + int team_size_recommended( const FunctorType&, const ParallelReduceTag& ) const { +#ifdef KOKKOS_ENABLE_DEPRECATED_CODE + return traits::execution_space::thread_pool_size(2); +#else + return traits::execution_space::impl_thread_pool_size(2); +#endif + } + + + inline static + int vector_length_max() + { return 1024; } // Use arbitrary large number, is meant as a vectorizable length + + inline static + int scratch_size_max(int level) + { return (level==0? + 1024*32: // Roughly L1 size + 20*1024*1024); // Limit to keep compatibility with CUDA } //---------------------------------------- diff --git a/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp b/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp index 6b3e206f6c..42269176ed 100644 --- a/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp +++ b/lib/kokkos/core/src/Threads/Kokkos_Threads_Parallel.hpp @@ -142,16 +142,15 @@ private: WorkRange range( self.m_policy , exec.pool_rank() , exec.pool_size() ); - exec.set_work_range(range.begin(),range.end(),self.m_policy.chunk_size()); + exec.set_work_range(range.begin()-self.m_policy.begin(),range.end()-self.m_policy.begin(),self.m_policy.chunk_size()); exec.reset_steal_target(); exec.barrier(); long work_index = exec.get_work_index(); while(work_index != -1) { - const Member begin = static_cast(work_index) * self.m_policy.chunk_size(); + const Member begin = static_cast(work_index) * self.m_policy.chunk_size()+self.m_policy.begin(); const Member end = begin + self.m_policy.chunk_size() < self.m_policy.end()?begin+self.m_policy.chunk_size():self.m_policy.end(); - ParallelFor::template exec_range< WorkTag > ( self.m_functor , begin , end ); work_index = exec.get_work_index(); @@ -470,14 +469,14 @@ private: const ParallelReduce & self = * ((const ParallelReduce *) arg ); const WorkRange range( self.m_policy, exec.pool_rank(), exec.pool_size() ); - exec.set_work_range(range.begin(),range.end(),self.m_policy.chunk_size()); + exec.set_work_range(range.begin()-self.m_policy.begin(),range.end()-self.m_policy.begin(),self.m_policy.chunk_size()); exec.reset_steal_target(); exec.barrier(); long work_index = exec.get_work_index(); reference_type update = ValueInit::init( ReducerConditional::select(self.m_functor , self.m_reducer) , exec.reduce_memory() ); while(work_index != -1) { - const Member begin = static_cast(work_index) * self.m_policy.chunk_size(); + const Member begin = static_cast(work_index) * self.m_policy.chunk_size() + self.m_policy.begin(); const Member end = begin + self.m_policy.chunk_size() < self.m_policy.end()?begin+self.m_policy.chunk_size():self.m_policy.end(); ParallelReduce::template exec_range< WorkTag > ( self.m_functor , begin , end diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_float_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int64_t_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_int_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_double_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_float_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int64_t_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank1.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank1.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank1.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank1.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank2.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank2.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank2.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank2.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank3.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank3.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank3.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank3.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank4.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank4.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank4.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank4.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank5.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank5.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank5.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank5.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank8.cpp b/lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank8.cpp similarity index 100% rename from lib/kokkos/core/src/eti/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank8.cpp rename to lib/kokkos/core/src/eti/ROCm/Kokkos_ROCm_ViewCopyETIInst_int_int_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/eti/ROCm/Makefile.eti_Experimental::ROCm b/lib/kokkos/core/src/eti/ROCm/Makefile.eti_Experimental::ROCm deleted file mode 100644 index 054360fd17..0000000000 --- a/lib/kokkos/core/src/eti/ROCm/Makefile.eti_Experimental::ROCm +++ /dev/null @@ -1,288 +0,0 @@ -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank1.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank2.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank3.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank4.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank5.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutLeft_Rank8.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank1.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank2.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank3.cpp -Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank4.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_Experimental::ROCm_ViewCopyETIInst_int_int_LayoutRight_Rank4.cpp - $(CXX) 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$(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank1.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank1.cpp +Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank2.cpp +Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank3.cpp +Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank4.cpp +Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank5.cpp +Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_ETI_PATH)/ROCm/Kokkos_ROCm_ViewCopyETIInst_int64_t_double_LayoutStride_Rank8.cpp diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp index ad115dd8ff..3d99b07568 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp @@ -107,7 +107,12 @@ T atomic_compare_exchange( volatile T * const dest , const T & compare , T return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif unsigned int done_active = 0; while (active!=done_active) { if(!done) { @@ -119,7 +124,11 @@ T atomic_compare_exchange( volatile T * const dest , const T & compare , done = 1; } } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,done); +#else done_active = KOKKOS_IMPL_CUDA_BALLOT(done); +#endif } return return_val; } @@ -299,6 +308,16 @@ T atomic_compare_exchange( volatile T * const dest_v, const T compare, const T v #endif #endif // !defined ROCM_ATOMICS +// dummy for non-CUDA Kokkos headers being processed by NVCC +#if defined(__CUDA_ARCH__) && !defined(KOKKOS_ENABLE_CUDA) +template +__inline__ __device__ +T atomic_compare_exchange(volatile T * const, const Kokkos::Impl::identity_t, const Kokkos::Impl::identity_t) +{ + return T(); +} +#endif + template KOKKOS_INLINE_FUNCTION bool atomic_compare_exchange_strong(volatile T* const dest, const T compare, const T val) diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp index 801a8091dd..6ccf35816b 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Exchange.hpp @@ -130,7 +130,12 @@ T atomic_exchange( volatile T * const dest , #endif int done = 0; +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif unsigned int done_active = 0; while (active!=done_active) { if(!done) { @@ -141,7 +146,11 @@ T atomic_exchange( volatile T * const dest , done = 1; } } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,done); +#else done_active = KOKKOS_IMPL_CUDA_BALLOT(done); +#endif } return return_val; } @@ -409,6 +418,23 @@ void atomic_assign( volatile T * const dest_v , const T val ) #endif #endif + +// dummy for non-CUDA Kokkos headers being processed by NVCC +#if defined(__CUDA_ARCH__) && !defined(KOKKOS_ENABLE_CUDA) +template +__inline__ __device__ +T atomic_exchange(volatile T * const, const Kokkos::Impl::identity_t) +{ + return T(); +} + +template < typename T > +__inline__ __device__ +void atomic_assign(volatile T * const, const Kokkos::Impl::identity_t) +{ +} +#endif + } // namespace Kokkos #endif diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp index 8249e709da..d6fab81133 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Add.hpp @@ -143,7 +143,12 @@ T atomic_fetch_add( volatile T * const dest , T return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif unsigned int done_active = 0; while (active!=done_active) { if(!done) { @@ -155,7 +160,12 @@ T atomic_fetch_add( volatile T * const dest , done = 1; } } + +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,done); +#else done_active = KOKKOS_IMPL_CUDA_BALLOT(done); +#endif } return return_val; } @@ -374,6 +384,15 @@ T atomic_fetch_add( volatile T * const dest_v , typename std::add_const::type #endif // !defined ROCM_ATOMICS //---------------------------------------------------------------------------- +// dummy for non-CUDA Kokkos headers being processed by NVCC +#if defined(__CUDA_ARCH__) && !defined(KOKKOS_ENABLE_CUDA) +template< typename T > +__inline__ __device__ +T atomic_fetch_add(volatile T* const, Kokkos::Impl::identity_t) { + return T(); +} +#endif + // Simpler version of atomic_fetch_add without the fetch template KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_And.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_And.hpp index 044cbdf79a..db0d97ca19 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_And.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_And.hpp @@ -149,6 +149,15 @@ T atomic_fetch_and( volatile T * const dest_v , const T val ) #endif //---------------------------------------------------------------------------- +// dummy for non-CUDA Kokkos headers being processed by NVCC +#if defined(__CUDA_ARCH__) && !defined(KOKKOS_ENABLE_CUDA) +template< typename T > +__inline__ __device__ +T atomic_fetch_and(volatile T* const, Kokkos::Impl::identity_t) { + return T(); +} +#endif + // Simpler version of atomic_fetch_and without the fetch template KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Or.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Or.hpp index 0b8cbb1d8c..d146ef3148 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Or.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Or.hpp @@ -149,6 +149,15 @@ T atomic_fetch_or( volatile T * const dest_v , const T val ) #endif //---------------------------------------------------------------------------- +// dummy for non-CUDA Kokkos headers being processed by NVCC +#if defined(__CUDA_ARCH__) && !defined(KOKKOS_ENABLE_CUDA) +template< typename T > +__inline__ __device__ +T atomic_fetch_or(volatile T* const, Kokkos::Impl::identity_t) { + return T(); +} +#endif + // Simpler version of atomic_fetch_or without the fetch template KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp index 3f58c55396..48dc8731ef 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Fetch_Sub.hpp @@ -135,7 +135,12 @@ T atomic_fetch_sub( volatile T * const dest , T return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif unsigned int done_active = 0; while (active!=done_active) { if(!done) { @@ -146,7 +151,11 @@ T atomic_fetch_sub( volatile T * const dest , done = 1; } } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,done); +#else done_active = KOKKOS_IMPL_CUDA_BALLOT(done); +#endif } return return_val; } @@ -295,6 +304,15 @@ T atomic_fetch_sub( volatile T * const dest_v , const T val ) #endif #endif // !defined ROCM_ATOMICS +// dummy for non-CUDA Kokkos headers being processed by NVCC +#if defined(__CUDA_ARCH__) && !defined(KOKKOS_ENABLE_CUDA) +template< typename T > +__inline__ __device__ +T atomic_fetch_sub(volatile T* const, Kokkos::Impl::identity_t) { + return T(); +} +#endif + // Simpler version of atomic_fetch_sub without the fetch template KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp index 6140d45896..a3a18166af 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp @@ -230,9 +230,6 @@ T atomic_fetch_oper( const Oper& op, volatile T * const dest , typename Kokkos::Impl::enable_if< ( sizeof(T) != 4 ) && ( sizeof(T) != 8 ) - #if defined(KOKKOS_ENABLE_ASM) && defined(KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST) - && ( sizeof(T) != 16 ) - #endif , const T >::type val ) { @@ -246,7 +243,12 @@ T atomic_fetch_oper( const Oper& op, volatile T * const dest , // This is a way to (hopefully) avoid dead lock in a warp T return_val; int done = 0; +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif unsigned int done_active = 0; while (active!=done_active) { if(!done) { @@ -257,7 +259,11 @@ T atomic_fetch_oper( const Oper& op, volatile T * const dest , done=1; } } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,done); +#else done_active = KOKKOS_IMPL_CUDA_BALLOT(done); +#endif } return return_val; #endif @@ -285,7 +291,12 @@ T atomic_oper_fetch( const Oper& op, volatile T * const dest , T return_val; // This is a way to (hopefully) avoid dead lock in a warp int done = 0; +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + unsigned int mask = KOKKOS_IMPL_CUDA_ACTIVEMASK; + unsigned int active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,1); +#else unsigned int active = KOKKOS_IMPL_CUDA_BALLOT(1); +#endif unsigned int done_active = 0; while (active!=done_active) { if(!done) { @@ -296,7 +307,11 @@ T atomic_oper_fetch( const Oper& op, volatile T * const dest , done=1; } } +#ifdef KOKKOS_IMPL_CUDA_SYNCWARP_NEEDS_MASK + done_active = KOKKOS_IMPL_CUDA_BALLOT_MASK(mask,done); +#else done_active = KOKKOS_IMPL_CUDA_BALLOT(done); +#endif } return return_val; #endif diff --git a/lib/kokkos/core/src/impl/Kokkos_Atomic_Windows.hpp b/lib/kokkos/core/src/impl/Kokkos_Atomic_Windows.hpp index eeec2d1f4b..b18134f40c 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Atomic_Windows.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Atomic_Windows.hpp @@ -45,13 +45,17 @@ #ifdef _WIN32 +#ifndef NOMINMAX #define NOMINMAX +#endif #include -#include +#include namespace Kokkos { namespace Impl { +#ifdef _MSC_VER _declspec(align(16)) +#endif struct cas128_t { LONGLONG lower; @@ -60,7 +64,11 @@ namespace Kokkos { bool operator != (const cas128_t& a) const { return (lower != a.lower) || upper != a.upper; } - }; + } +#ifdef __GNUC__ + __attribute__ ((aligned (16))) +#endif + ; } template < typename T > diff --git a/lib/kokkos/core/src/impl/Kokkos_Core.cpp b/lib/kokkos/core/src/impl/Kokkos_Core.cpp index 8184dad3ec..82fdee4399 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Core.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_Core.cpp @@ -49,6 +49,7 @@ #include #include #include +#include //---------------------------------------------------------------------------- @@ -70,7 +71,6 @@ bool is_unsigned_int(const char* str) } return true; } - void initialize_internal(const InitArguments& args) { // This is an experimental setting @@ -99,6 +99,7 @@ setenv("MEMKIND_HBW_NODES", "1", 0); if (use_gpu < 0 && ndevices >= 0) { auto local_rank_str = std::getenv("OMPI_COMM_WORLD_LOCAL_RANK"); //OpenMPI if (!local_rank_str) local_rank_str = std::getenv("MV2_COMM_WORLD_LOCAL_RANK"); //MVAPICH2 + if (!local_rank_str) local_rank_str = std::getenv("SLURM_LOCALID"); //SLURM if (local_rank_str) { auto local_rank = std::atoi(local_rank_str); use_gpu = local_rank % ndevices; @@ -532,6 +533,85 @@ void initialize(int& narg, char* arg[]) iarg++; } + //Read environment variables + char * endptr; + auto env_num_threads_str = std::getenv("KOKKOS_NUM_THREADS"); + if (env_num_threads_str!=nullptr) { + errno = 0; + auto env_num_threads = std::strtol(env_num_threads_str,&endptr,10); + if (endptr== env_num_threads_str) + Impl::throw_runtime_exception("Error: cannot convert KOKKOS_NUM_THREADS to an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if (errno == ERANGE) + Impl::throw_runtime_exception("Error: KOKKOS_NUM_THREADS out of range of representable values by an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if ((num_threads != -1)&&(env_num_threads!=num_threads)) + Impl::throw_runtime_exception("Error: expecting a match between --kokkos-threads and KOKKOS_NUM_THREADS if both are set. Raised by Kokkos::initialize(int narg, char* argc[])."); + else + num_threads = env_num_threads; + } + auto env_numa_str = std::getenv("KOKKOS_NUMA"); + if (env_numa_str!=nullptr) { + errno = 0; + auto env_numa = std::strtol(env_numa_str,&endptr,10); + if (endptr== env_numa_str) + Impl::throw_runtime_exception("Error: cannot convert KOKKOS_NUMA to an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if (errno == ERANGE) + Impl::throw_runtime_exception("Error: KOKKOS_NUMA out of range of representable values by an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if ((numa != -1)&&(env_numa!=numa)) + Impl::throw_runtime_exception("Error: expecting a match between --kokkos-numa and KOKKOS_NUMA if both are set. Raised by Kokkos::initialize(int narg, char* argc[])."); + else + numa = env_numa; + } + auto env_device_str = std::getenv("KOKKOS_DEVICE_ID"); + if (env_device_str!=nullptr) { + errno = 0; + auto env_device = std::strtol(env_device_str,&endptr,10); + if (endptr== env_device_str) + Impl::throw_runtime_exception("Error: cannot convert KOKKOS_DEVICE_ID to an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if (errno == ERANGE) + Impl::throw_runtime_exception("Error: KOKKOS_DEVICE_ID out of range of representable values by an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if ((device != -1)&&(env_device!=device)) + Impl::throw_runtime_exception("Error: expecting a match between --kokkos-device and KOKKOS_DEVICE_ID if both are set. Raised by Kokkos::initialize(int narg, char* argc[])."); + else + device = env_device; + } + auto env_ndevices_str = std::getenv("KOKKOS_NUM_DEVICES"); + if (env_ndevices_str!=nullptr) { + errno = 0; + auto env_ndevices = std::strtol(env_ndevices_str,&endptr,10); + if (endptr== env_ndevices_str) + Impl::throw_runtime_exception("Error: cannot convert KOKKOS_NUM_DEVICES to an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if (errno == ERANGE) + Impl::throw_runtime_exception("Error: KOKKOS_NUM_DEVICES out of range of representable values by an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if ((ndevices != -1)&&(env_ndevices!=ndevices)) + Impl::throw_runtime_exception("Error: expecting a match between --kokkos-ndevices and KOKKOS_NUM_DEVICES if both are set. Raised by Kokkos::initialize(int narg, char* argc[])."); + else + ndevices = env_ndevices; + //Skip device + auto env_skip_device_str = std::getenv("KOKKOS_SKIP_DEVICE"); + if (env_skip_device_str!=nullptr) { + errno = 0; + auto env_skip_device = std::strtol(env_skip_device_str,&endptr,10); + if (endptr== env_skip_device_str) + Impl::throw_runtime_exception("Error: cannot convert KOKKOS_SKIP_DEVICE to an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if (errno == ERANGE) + Impl::throw_runtime_exception("Error: KOKKOS_SKIP_DEVICE out of range of representable values by an integer. Raised by Kokkos::initialize(int narg, char* argc[])."); + if ((skip_device != 9999)&&(env_skip_device!=skip_device)) + Impl::throw_runtime_exception("Error: expecting a match between --kokkos-ndevices and KOKKOS_SKIP_DEVICE if both are set. Raised by Kokkos::initialize(int narg, char* argc[])."); + else + skip_device = env_skip_device; + } + } + char * env_disablewarnings_str = std::getenv("KOKKOS_DISABLE_WARNINGS"); + if (env_disablewarnings_str!=nullptr) { + std::string env_str (env_disablewarnings_str); // deep-copies string + for (char& c : env_str) { c = toupper (c); } + if ((env_str == "TRUE") || (env_str == "ON") || (env_str == "1")) + disable_warnings = true; + else + if (disable_warnings) + Impl::throw_runtime_exception("Error: expecting a match between --kokkos-disable-warnings and KOKKOS_DISABLE_WARNINGS if both are set. Raised by Kokkos::initialize(int narg, char* argc[])."); + } + InitArguments arguments; arguments.num_threads = num_threads; arguments.num_numa = numa; @@ -780,8 +860,20 @@ void print_configuration( std::ostream & out , const bool detail ) #else msg << "no" << std::endl; #endif - msg << " KOKKOS_ENABLE_CXX1Z: "; -#ifdef KOKKOS_ENABLE_CXX1Z + msg << " KOKKOS_ENABLE_CXX14: "; +#ifdef KOKKOS_ENABLE_CXX14 + msg << "yes" << std::endl; +#else + msg << "no" << std::endl; +#endif + msg << " KOKKOS_ENABLE_CXX17: "; +#ifdef KOKKOS_ENABLE_CXX17 + msg << "yes" << std::endl; +#else + msg << "no" << std::endl; +#endif + msg << " KOKKOS_ENABLE_CXX20: "; +#ifdef KOKKOS_ENABLE_CXX20 msg << "yes" << std::endl; #else msg << "no" << std::endl; diff --git a/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp b/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp index 699902e320..680e937db4 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_HBWSpace.cpp @@ -235,6 +235,8 @@ SharedAllocationRecord( const Kokkos::Experimental::HBWSpace & arg_space , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + // Set last element zero, in case c_str is too long + RecordBase::m_alloc_ptr->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; } //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp b/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp index da9ce6b9fb..d8cb7593bf 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp @@ -356,6 +356,8 @@ SharedAllocationRecord( const Kokkos::HostSpace & arg_space , arg_label.c_str() , SharedAllocationHeader::maximum_label_length ); + // Set last element zero, in case c_str is too long + RecordBase::m_alloc_ptr->m_label[SharedAllocationHeader::maximum_label_length - 1] = (char) 0; } //---------------------------------------------------------------------------- diff --git a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp index 558eef9e4a..fff48e87f6 100644 --- a/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_HostThreadTeam.hpp @@ -144,6 +144,30 @@ public: return m_team_rank == 0; } + + inline + bool team_rendezvous(const int source_team_rank) const noexcept + { + int * ptr = (int *)(m_team_scratch + m_team_rendezvous); + HostBarrier::split_arrive( ptr + , m_team_size + , m_team_rendezvous_step + ); + if (m_team_rank != source_team_rank) { + HostBarrier::wait( ptr + , m_team_size + , m_team_rendezvous_step + ); + } + else { + HostBarrier::split_master_wait( ptr + , m_team_size + , m_team_rendezvous_step + ); + } + + return (m_team_rank == source_team_rank); + } inline void team_rendezvous_release() const noexcept @@ -540,15 +564,16 @@ public: { if ( 1 < m_data.m_team_size ) { T volatile * const shared_value = (T*) m_data.team_reduce(); - + // Don't overwrite shared memory until all threads arrive - if ( m_data.team_rendezvous() ) { + if ( m_data.team_rendezvous(source_team_rank) ) { + // All threads have entered 'team_rendezvous' // only this thread returned from 'team_rendezvous' // with a return value of 'true' - *shared_value = value ; + *shared_value = value; m_data.team_rendezvous_release(); // This thread released all other threads from 'team_rendezvous' @@ -574,7 +599,7 @@ public: // Don't overwrite shared memory until all threads arrive - if ( m_data.team_rendezvous() ) { + if ( m_data.team_rendezvous(source_team_rank) ) { // All threads have entered 'team_rendezvous' // only this thread returned from 'team_rendezvous' diff --git a/lib/kokkos/core/src/impl/Kokkos_OldMacros.hpp b/lib/kokkos/core/src/impl/Kokkos_OldMacros.hpp index bad158c291..c3198c0f13 100644 --- a/lib/kokkos/core/src/impl/Kokkos_OldMacros.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_OldMacros.hpp @@ -142,18 +142,13 @@ #endif #endif -#ifdef KOKKOS_HAVE_CXX1Z + +#if defined(KOKKOS_HAVE_CXX1Z) || defined(KOKKOS_ENABLE_CXX17) #ifndef KOKKOS_ENABLE_CXX1Z #define KOKKOS_ENABLE_CXX1Z KOKKOS_HAVE_CXX1Z #endif #endif -#ifdef KOKKOS_HAVE_DEBUG -#ifndef KOKKOS_DEBUG -#define KOKKOS_DEBUG KOKKOS_HAVE_DEBUG -#endif -#endif - #ifdef KOKKOS_HAVE_DEFAULT_DEVICE_TYPE_CUDA #ifndef KOKKOS_ENABLE_DEFAULT_DEVICE_TYPE_CUDA #define KOKKOS_ENABLE_DEFAULT_DEVICE_TYPE_CUDA KOKKOS_HAVE_DEFAULT_DEVICE_TYPE_CUDA @@ -482,6 +477,12 @@ #define KOKKOS_HAVE_DEBUG 1 #endif +#ifdef KOKKOS_HAVE_DEBUG +#ifndef KOKKOS_DEBUG +#define KOKKOS_DEBUG KOKKOS_HAVE_DEBUG +#endif +#endif + #if (!defined(KOKKOS_HAVE_HWLOC)) && defined(KOKKOS_ENABLE_HWLOC) #define KOKKOS_HAVE_HWLOC 1 #endif diff --git a/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp b/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp index 7b85909ed5..d84a854622 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_Serial_Task.cpp @@ -60,10 +60,10 @@ template class TaskQueue< Kokkos::Serial > ; void TaskQueueSpecialization< Kokkos::Serial >::execute ( TaskQueue< Kokkos::Serial > * const queue ) { - using execution_space = Kokkos::Serial ; - using queue_type = TaskQueue< execution_space > ; + using exec_space = Kokkos::Serial ; + using tqs_queue_type = TaskQueue< exec_space > ; using task_root_type = TaskBase< void , void , void > ; - using Member = Impl::HostThreadTeamMember< execution_space > ; + using Member = Impl::HostThreadTeamMember< exec_space > ; task_root_type * const end = (task_root_type *) task_root_type::EndTag ; @@ -83,9 +83,9 @@ void TaskQueueSpecialization< Kokkos::Serial >::execute task_root_type * task = end ; - for ( int i = 0 ; i < queue_type::NumQueue && end == task ; ++i ) { + for ( int i = 0 ; i < tqs_queue_type::NumQueue && end == task ; ++i ) { for ( int j = 0 ; j < 2 && end == task ; ++j ) { - task = queue_type::pop_ready_task( & queue->m_ready[i][j] ); + task = tqs_queue_type::pop_ready_task( & queue->m_ready[i][j] ); } } @@ -120,10 +120,10 @@ void TaskQueueSpecialization< Kokkos::Serial > :: iff_single_thread_recursive_execute( TaskQueue< Kokkos::Serial > * const queue ) { - using execution_space = Kokkos::Serial ; - using queue_type = TaskQueue< execution_space > ; + using exec_space = Kokkos::Serial ; + using tqs_queue_type = TaskQueue< exec_space > ; using task_root_type = TaskBase< void , void , void > ; - using Member = Impl::HostThreadTeamMember< execution_space > ; + using Member = Impl::HostThreadTeamMember< exec_space > ; task_root_type * const end = (task_root_type *) task_root_type::EndTag ; @@ -139,9 +139,9 @@ void TaskQueueSpecialization< Kokkos::Serial > :: task = end ; - for ( int i = 0 ; i < queue_type::NumQueue && end == task ; ++i ) { + for ( int i = 0 ; i < tqs_queue_type::NumQueue && end == task ; ++i ) { for ( int j = 0 ; j < 2 && end == task ; ++j ) { - task = queue_type::pop_ready_task( & queue->m_ready[i][j] ); + task = tqs_queue_type::pop_ready_task( & queue->m_ready[i][j] ); } } diff --git a/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp b/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp index 868b31861a..611a32c4fe 100644 --- a/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_Utilities.hpp @@ -409,6 +409,9 @@ struct inclusive_scan_integer_sequence static constexpr value_type value = helper::value ; }; +template +using identity_t = T; + }} // namespace Kokkos::Impl diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp index 3c306ec94b..e1539d10b0 100644 --- a/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_ViewArray.hpp @@ -103,13 +103,7 @@ namespace Impl { /** \brief View mapping for non-specialized data type and standard layout */ template< class Traits > -class ViewMapping< Traits , - typename std::enable_if<( - std::is_same< typename Traits::specialize , Kokkos::Array<> >::value && - ( std::is_same< typename Traits::array_layout , Kokkos::LayoutLeft >::value || - std::is_same< typename Traits::array_layout , Kokkos::LayoutRight >::value || - std::is_same< typename Traits::array_layout , Kokkos::LayoutStride >::value ) - )>::type > +class ViewMapping< Traits , Kokkos::Array<> > { private: @@ -123,8 +117,8 @@ private: typedef typename Traits::value_type::pointer handle_type ; - handle_type m_handle ; - offset_type m_offset ; + handle_type m_impl_handle ; + offset_type m_impl_offset ; size_t m_stride ; typedef typename Traits::value_type::value_type scalar_type ; @@ -140,8 +134,8 @@ private: KOKKOS_INLINE_FUNCTION ViewMapping( const handle_type & arg_handle , const offset_type & arg_offset ) - : m_handle( arg_handle ) - , m_offset( arg_offset ) + : m_impl_handle( arg_handle ) + , m_impl_offset( arg_offset ) , m_stride( is_contiguous_reference ? 0 : arg_offset.span() ) {} @@ -154,44 +148,44 @@ public: template< typename iType > KOKKOS_INLINE_FUNCTION constexpr size_t extent( const iType & r ) const - { return m_offset.m_dim.extent(r); } + { return m_impl_offset.m_dim.extent(r); } KOKKOS_INLINE_FUNCTION constexpr typename Traits::array_layout layout() const - { return m_offset.layout(); } + { return m_impl_offset.layout(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_offset.dimension_0(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_offset.dimension_1(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_offset.dimension_2(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_offset.dimension_3(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_offset.dimension_4(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_offset.dimension_5(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_offset.dimension_6(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_offset.dimension_7(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_impl_offset.dimension_0(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_impl_offset.dimension_1(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_impl_offset.dimension_2(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_impl_offset.dimension_3(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_impl_offset.dimension_4(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_impl_offset.dimension_5(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_impl_offset.dimension_6(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_impl_offset.dimension_7(); } // Is a regular layout with uniform striding for each index. using is_regular = typename offset_type::is_regular ; - KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_offset.stride_0(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_offset.stride_1(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_offset.stride_2(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_offset.stride_3(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_offset.stride_4(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_offset.stride_5(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_offset.stride_6(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_offset.stride_7(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_impl_offset.stride_0(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_impl_offset.stride_1(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_impl_offset.stride_2(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_impl_offset.stride_3(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_impl_offset.stride_4(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_impl_offset.stride_5(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_impl_offset.stride_6(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_impl_offset.stride_7(); } //---------------------------------------- // Range span /** \brief Span of the mapped range */ KOKKOS_INLINE_FUNCTION constexpr size_t span() const - { return m_offset.span() * Array_N ; } + { return m_impl_offset.span() * Array_N ; } /** \brief Is the mapped range span contiguous */ KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const - { return m_offset.span_is_contiguous(); } + { return m_impl_offset.span_is_contiguous(); } typedef typename std::conditional< is_contiguous_reference , contiguous_reference , strided_reference >::type reference_type ; @@ -199,63 +193,63 @@ public: /** \brief If data references are lvalue_reference than can query pointer to memory */ KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const - { return m_handle ; } + { return m_impl_handle ; } //---------------------------------------- // The View class performs all rank and bounds checking before // calling these element reference methods. KOKKOS_FORCEINLINE_FUNCTION - reference_type reference() const { return reference_type( m_handle + 0 , Array_N , 0 ); } + reference_type reference() const { return reference_type( m_impl_handle + 0 , Array_N , 0 ); } template< typename I0 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 ) const - { return reference_type( m_handle + m_offset(i0) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 ) const - { return reference_type( m_handle + m_offset(i0,i1) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 , typename I2 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 ) const - { return reference_type( m_handle + m_offset(i0,i1,i2) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1,i2) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 , typename I2 , typename I3 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 ) const - { return reference_type( m_handle + m_offset(i0,i1,i2,i3) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1,i2,i3) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 ) const - { return reference_type( m_handle + m_offset(i0,i1,i2,i3,i4) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1,i2,i3,i4) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 , typename I5 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 , const I5 & i5 ) const - { return reference_type( m_handle + m_offset(i0,i1,i2,i3,i4,i5) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1,i2,i3,i4,i5) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 , typename I5 , typename I6 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 , const I5 & i5 , const I6 & i6 ) const - { return reference_type( m_handle + m_offset(i0,i1,i2,i3,i4,i5,i6) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1,i2,i3,i4,i5,i6) * Array_S , Array_N , m_stride ); } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 , typename I5 , typename I6 , typename I7 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 ) const - { return reference_type( m_handle + m_offset(i0,i1,i2,i3,i4,i5,i6,i7) * Array_S , Array_N , m_stride ); } + { return reference_type( m_impl_handle + m_impl_offset(i0,i1,i2,i3,i4,i5,i6,i7) * Array_S , Array_N , m_stride ); } //---------------------------------------- @@ -269,31 +263,31 @@ public: /** \brief Span, in bytes, of the referenced memory */ KOKKOS_INLINE_FUNCTION constexpr size_t memory_span() const { - return ( m_offset.span() * Array_N * MemorySpanSize + MemorySpanMask ) & ~size_t(MemorySpanMask); + return ( m_impl_offset.span() * Array_N * MemorySpanSize + MemorySpanMask ) & ~size_t(MemorySpanMask); } //---------------------------------------- KOKKOS_INLINE_FUNCTION ~ViewMapping() {} - KOKKOS_INLINE_FUNCTION ViewMapping() : m_handle(), m_offset(), m_stride(0) {} + KOKKOS_INLINE_FUNCTION ViewMapping() : m_impl_handle(), m_impl_offset(), m_stride(0) {} KOKKOS_INLINE_FUNCTION ViewMapping( const ViewMapping & rhs ) - : m_handle( rhs.m_handle ), m_offset( rhs.m_offset ), m_stride( rhs.m_stride ) {} + : m_impl_handle( rhs.m_impl_handle ), m_impl_offset( rhs.m_impl_offset ), m_stride( rhs.m_stride ) {} KOKKOS_INLINE_FUNCTION ViewMapping & operator = ( const ViewMapping & rhs ) - { m_handle = rhs.m_handle ; m_offset = rhs.m_offset ; m_stride = rhs.m_stride ; ; return *this ; } + { m_impl_handle = rhs.m_impl_handle ; m_impl_offset = rhs.m_impl_offset ; m_stride = rhs.m_stride ; ; return *this ; } KOKKOS_INLINE_FUNCTION ViewMapping( ViewMapping && rhs ) - : m_handle( rhs.m_handle ), m_offset( rhs.m_offset ), m_stride( rhs.m_stride ) {} + : m_impl_handle( rhs.m_impl_handle ), m_impl_offset( rhs.m_impl_offset ), m_stride( rhs.m_stride ) {} KOKKOS_INLINE_FUNCTION ViewMapping & operator = ( ViewMapping && rhs ) - { m_handle = rhs.m_handle ; m_offset = rhs.m_offset ; m_stride = rhs.m_stride ; return *this ; } + { m_impl_handle = rhs.m_impl_handle ; m_impl_offset = rhs.m_impl_offset ; m_stride = rhs.m_stride ; return *this ; } //---------------------------------------- template< class ... Args > KOKKOS_INLINE_FUNCTION ViewMapping( pointer_type ptr , Args ... args ) - : m_handle( ptr ) - , m_offset( std::integral_constant< unsigned , 0 >() , args... ) - , m_stride( m_offset.span() ) + : m_impl_handle( ptr ) + , m_impl_offset( std::integral_constant< unsigned , 0 >() , args... ) + , m_stride( m_impl_offset.span() ) {} //---------------------------------------- @@ -315,10 +309,10 @@ public: typedef std::integral_constant< unsigned , alloc_prop::allow_padding ? sizeof(scalar_type) : 0 > padding ; - m_offset = offset_type( padding(), arg_layout ); + m_impl_offset = offset_type( padding(), arg_layout ); const size_t alloc_size = - ( m_offset.span() * Array_N * MemorySpanSize + MemorySpanMask ) & ~size_t(MemorySpanMask); + ( m_impl_offset.span() * Array_N * MemorySpanSize + MemorySpanMask ) & ~size_t(MemorySpanMask); // Allocate memory from the memory space and create tracking record. record_type * const record = @@ -327,14 +321,14 @@ public: , alloc_size ); if ( alloc_size ) { - m_handle = + m_impl_handle = handle_type( reinterpret_cast< pointer_type >( record->data() ) ); if ( alloc_prop::initialize ) { // The functor constructs and destroys record->m_destroy = functor_type( ((Kokkos::Impl::ViewCtorProp const & )arg_prop).value - , (pointer_type) m_handle - , m_offset.span() * Array_N + , (pointer_type) m_impl_handle + , m_impl_offset.span() * Array_N ); record->m_destroy.construct_shared_allocation(); @@ -345,64 +339,6 @@ public: } }; -//---------------------------------------------------------------------------- -//---------------------------------------------------------------------------- -/** \brief Assign compatible default mappings */ - -template< class DstTraits , class SrcTraits > -class ViewMapping< DstTraits , SrcTraits , - typename std::enable_if<( - std::is_same< typename DstTraits::memory_space , typename SrcTraits::memory_space >::value - && - std::is_same< typename DstTraits::specialize , Kokkos::Array<> >::value - && - ( - std::is_same< typename DstTraits::array_layout , Kokkos::LayoutLeft >::value || - std::is_same< typename DstTraits::array_layout , Kokkos::LayoutRight >::value || - std::is_same< typename DstTraits::array_layout , Kokkos::LayoutStride >::value - ) - && - std::is_same< typename SrcTraits::specialize , Kokkos::Array<> >::value - && - ( - std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutLeft >::value || - std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutRight >::value || - std::is_same< typename SrcTraits::array_layout , Kokkos::LayoutStride >::value - ) - )>::type > -{ -public: - - enum { is_assignable = true }; - - typedef Kokkos::Impl::SharedAllocationTracker TrackType ; - typedef ViewMapping< DstTraits , void > DstType ; - typedef ViewMapping< SrcTraits , void > SrcType ; - - KOKKOS_INLINE_FUNCTION - static void assign( DstType & dst , const SrcType & src , const TrackType & src_track ) - { - static_assert( std::is_same< typename DstTraits::value_type , typename SrcTraits::value_type >::value || - std::is_same< typename DstTraits::value_type , typename SrcTraits::const_value_type >::value - , "View assignment must have same value type or const = non-const" ); - - static_assert( ViewDimensionAssignable< typename DstTraits::dimension , typename SrcTraits::dimension >::value - , "View assignment must have compatible dimensions" ); - - static_assert( std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value || - std::is_same< typename DstTraits::array_layout , Kokkos::LayoutStride >::value || - ( DstTraits::dimension::rank == 0 ) || - ( DstTraits::dimension::rank == 1 && DstTraits::dimension::rank_dynamic == 1 ) - , "View assignment must have compatible layout or have rank <= 1" ); - - typedef typename DstType::offset_type dst_offset_type ; - - dst.m_offset = dst_offset_type( src.m_offset ); - dst.m_handle = src.m_handle ; - dst.m_stride = src.m_stride ; - } -}; - /** \brief Assign Array to non-Array */ template< class DstTraits , class SrcTraits > @@ -436,7 +372,7 @@ public: typedef Kokkos::Impl::SharedAllocationTracker TrackType ; typedef ViewMapping< DstTraits , void > DstType ; - typedef ViewMapping< SrcTraits , void > SrcType ; + typedef ViewMapping< SrcTraits , Kokkos::Array<> > SrcType ; KOKKOS_INLINE_FUNCTION static void assign( DstType & dst , const SrcType & src , const TrackType & src_track ) @@ -448,7 +384,7 @@ public: // Array dimension becomes the last dimension. // Arguments beyond the destination rank are ignored. if ( src.span_is_contiguous() ) { // not padded - dst.m_offset = dst_offset_type( std::integral_constant() , + dst.m_impl_offset = dst_offset_type( std::integral_constant() , typename DstTraits::array_layout ( ( 0 < SrcType::Rank ? src.dimension_0() : SrcTraits::value_type::size() ) , ( 1 < SrcType::Rank ? src.dimension_1() : SrcTraits::value_type::size() ) @@ -463,7 +399,7 @@ public: else { // is padded typedef std::integral_constant padded ; - dst.m_offset = dst_offset_type( padded() , + dst.m_impl_offset = dst_offset_type( padded() , typename DstTraits::array_layout ( ( 0 < SrcType::Rank ? src.dimension_0() : SrcTraits::value_type::size() ) , ( 1 < SrcType::Rank ? src.dimension_1() : SrcTraits::value_type::size() ) @@ -476,10 +412,11 @@ public: ) ); } - dst.m_handle = src.m_handle ; + dst.m_impl_handle = src.m_impl_handle ; } }; + //---------------------------------------------------------------------------- //---------------------------------------------------------------------------- @@ -579,11 +516,11 @@ public: typedef typename DstType::handle_type dst_handle_type ; const SubviewExtents< SrcTraits::rank , rank > - extents( src.m_offset.m_dim , args... ); + extents( src.m_impl_offset.m_dim , args... ); - dst.m_offset = dst_offset_type( src.m_offset , extents ); - dst.m_handle = dst_handle_type( src.m_handle + - src.m_offset( extents.domain_offset(0) + dst.m_impl_offset = dst_offset_type( src.m_impl_offset , extents ); + dst.m_impl_handle = dst_handle_type( src.m_impl_handle + + src.m_impl_offset( extents.domain_offset(0) , extents.domain_offset(1) , extents.domain_offset(2) , extents.domain_offset(3) diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewLayoutTiled.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewLayoutTiled.hpp new file mode 100644 index 0000000000..a64101110f --- /dev/null +++ b/lib/kokkos/core/src/impl/Kokkos_ViewLayoutTiled.hpp @@ -0,0 +1,945 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#ifndef KOKKOS_EXPERIMENTAL_VIEWLAYOUTTILE_HPP +#define KOKKOS_EXPERIMENTAL_VIEWLAYOUTTILE_HPP + +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE + +#include +#include + +//---------------------------------------------------------------------------- +//---------------------------------------------------------------------------- + +namespace Kokkos { + +// View offset and mapping for tiled view's + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 , unsigned ArgN7 > +struct is_array_layout < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; + + +template< class L > +struct is_array_layout_tiled : public std::false_type {}; + +template < Kokkos::Iterate OuterP, Kokkos::Iterate InnerP, unsigned ArgN0 , unsigned ArgN1 , unsigned ArgN2 , unsigned ArgN3 , unsigned ArgN4 , unsigned ArgN5 , unsigned ArgN6 , unsigned ArgN7 , bool IsPowerTwo > +struct is_array_layout_tiled < Kokkos::Experimental::LayoutTiled > : public std::true_type {}; // Last template parameter "true" meaning this currently only supports powers-of-two + + +namespace Impl { + +template< class Dimension , class Layout > +struct ViewOffset< Dimension , Layout , + typename std::enable_if<( + ( Dimension::rank <= 8 ) + && + ( Dimension::rank >= 2 ) + && + is_array_layout< Layout >::value + && + is_array_layout_tiled< Layout >::value + )>::type > +{ +public: + +// enum { outer_pattern = Layout::outer_pattern }; +// enum { inner_pattern = Layout::inner_pattern }; + static constexpr Kokkos::Iterate outer_pattern = Layout::outer_pattern; + static constexpr Kokkos::Iterate inner_pattern = Layout::inner_pattern; + + enum { VORank = Dimension::rank }; + + enum { SHIFT_0 = Kokkos::Impl::integral_power_of_two(Layout::N0) }; + enum { SHIFT_1 = Kokkos::Impl::integral_power_of_two(Layout::N1) }; + enum { SHIFT_2 = Kokkos::Impl::integral_power_of_two(Layout::N2) }; + enum { SHIFT_3 = Kokkos::Impl::integral_power_of_two(Layout::N3) }; + enum { SHIFT_4 = Kokkos::Impl::integral_power_of_two(Layout::N4) }; + enum { SHIFT_5 = Kokkos::Impl::integral_power_of_two(Layout::N5) }; + enum { SHIFT_6 = Kokkos::Impl::integral_power_of_two(Layout::N6) }; + enum { SHIFT_7 = Kokkos::Impl::integral_power_of_two(Layout::N7) }; + enum { MASK_0 = Layout::N0 - 1 }; + enum { MASK_1 = Layout::N1 - 1 }; + enum { MASK_2 = Layout::N2 - 1 }; + enum { MASK_3 = Layout::N3 - 1 }; + enum { MASK_4 = Layout::N4 - 1 }; + enum { MASK_5 = Layout::N5 - 1 }; + enum { MASK_6 = Layout::N6 - 1 }; + enum { MASK_7 = Layout::N7 - 1 }; + + enum { SHIFT_2T = SHIFT_0 + SHIFT_1 }; + enum { SHIFT_3T = SHIFT_0 + SHIFT_1 + SHIFT_2 }; + enum { SHIFT_4T = SHIFT_0 + SHIFT_1 + SHIFT_2 + SHIFT_3 }; + enum { SHIFT_5T = SHIFT_0 + SHIFT_1 + SHIFT_2 + SHIFT_3 + SHIFT_4 }; + enum { SHIFT_6T = SHIFT_0 + SHIFT_1 + SHIFT_2 + SHIFT_3 + SHIFT_4 + SHIFT_5 }; + enum { SHIFT_7T = SHIFT_0 + SHIFT_1 + SHIFT_2 + SHIFT_3 + SHIFT_4 + SHIFT_5 + SHIFT_6 }; + enum { SHIFT_8T = SHIFT_0 + SHIFT_1 + SHIFT_2 + SHIFT_3 + SHIFT_4 + SHIFT_5 + SHIFT_6 + SHIFT_7 }; + + // Is an irregular layout that does not have uniform striding for each index. + using is_mapping_plugin = std::true_type ; + using is_regular = std::false_type ; + + typedef size_t size_type ; + typedef Dimension dimension_type ; + typedef Layout array_layout ; + + dimension_type m_dim ; + size_type m_tile_N0 ; // Num tiles dim 0 + size_type m_tile_N1 ; + size_type m_tile_N2 ; + size_type m_tile_N3 ; + size_type m_tile_N4 ; + size_type m_tile_N5 ; + size_type m_tile_N6 ; + size_type m_tile_N7 ; + + //---------------------------------------- + +#define DEBUG_OUTPUT_CHECK 0 + + // Rank 2 + template< typename I0 , typename I1 > + KOKKOS_INLINE_FUNCTION + size_type operator()( I0 const & i0 , I1 const & i1 ) const { + auto tile_offset = (outer_pattern == (Kokkos::Iterate::Left)) + ? ( ( (i0>>SHIFT_0) + m_tile_N0*((i1>>SHIFT_1)) ) << SHIFT_2T) + : ( ( (m_tile_N1*(i0>>SHIFT_0) + (i1>>SHIFT_1)) ) << SHIFT_2T) ; + // ( num_tiles[1] * ti0 + ti1 ) * FTD + + auto local_offset = (inner_pattern == (Kokkos::Iterate::Left)) + ? ( (i0 & MASK_0) + ((i1 & MASK_1)< + KOKKOS_INLINE_FUNCTION + ViewOffset( const ViewOffset< DimRHS , Kokkos::LayoutStride , void > & rhs ) + : m_dim( rhs.m_dim.N0 , rhs.m_dim.N1 , rhs.m_dim.N2 , rhs.m_dim.N3 + , rhs.m_dim.N4 , rhs.m_dim.N5 , rhs.m_dim.N6 , rhs.m_dim.N7 ) + , m_stride( rhs.stride_1() ) + { + if ( rhs.m_stride.S0 != 1 ) { + Kokkos::abort("Kokkos::Impl::ViewOffset assignment of LayoutLeft from LayoutStride requires stride == 1" ); + } + } + //---------------------------------------- // Subview construction // This subview must be 2 == rank and 2 == rank_dynamic @@ -1518,16 +1539,7 @@ struct ViewOffset< Dimension , Kokkos::LayoutRight ViewOffset( const ViewOffset< DimRHS , Kokkos::LayoutStride , void > & rhs ) : m_dim( rhs.m_dim.N0, 0, 0, 0, 0, 0, 0, 0 ) { - static_assert( - ( DimRHS::rank == 0 && - dimension_type::rank == 0 ) || - ( DimRHS::rank == 1 && - dimension_type::rank == 1 && - dimension_type::rank_dynamic == 1 ) - , "ViewOffset LayoutRight and LayoutString are only compatible when rank <= 1" ); - if ( rhs.m_stride.S0 != 1 ) { - Kokkos::abort("Kokkos::Impl::ViewOffset assignment of LayoutLeft/Right from LayoutStride requires stride == 1" ); - } + } //---------------------------------------- @@ -1771,6 +1783,23 @@ public: // Also requires equal static dimensions ... } + template< class DimRHS > + KOKKOS_INLINE_FUNCTION + ViewOffset( const ViewOffset< DimRHS , Kokkos::LayoutStride , void > & rhs ) + : m_dim( rhs.m_dim.N0 , rhs.m_dim.N1 , rhs.m_dim.N2 , rhs.m_dim.N3 + , rhs.m_dim.N4 , rhs.m_dim.N5 , rhs.m_dim.N6 , rhs.m_dim.N7 ) + , m_stride( rhs.stride_0() ) + { + if ( ((dimension_type::rank == 2)?rhs.m_stride.S1: + ((dimension_type::rank == 3)?rhs.m_stride.S2: + ((dimension_type::rank == 4)?rhs.m_stride.S3: + ((dimension_type::rank == 5)?rhs.m_stride.S4: + ((dimension_type::rank == 6)?rhs.m_stride.S5: + ((dimension_type::rank == 7)?rhs.m_stride.S6:rhs.m_stride.S7)))))) != 1 ){ + Kokkos::abort("Kokkos::Impl::ViewOffset assignment of LayoutRight from LayoutStride requires right-most stride == 1" ); + } + } + //---------------------------------------- // Subview construction // Last dimension must be non-zero @@ -2498,7 +2527,7 @@ struct ViewValueFunctor< ExecSpace , ValueType , false /* is_scalar */ > #if defined(KOKKOS_ENABLE_PROFILING) uint64_t kpID = 0; if(Kokkos::Profiling::profileLibraryLoaded()) { - Kokkos::Profiling::beginParallelFor("Kokkos::View::initialization", 0, &kpID); + Kokkos::Profiling::beginParallelFor((destroy ? "Kokkos::View::destruction" : "Kokkos::View::initialization"), 0, &kpID); } #endif const Kokkos::Impl::ParallelFor< ViewValueFunctor , PolicyType > @@ -2588,11 +2617,8 @@ class ViewMapping< Traits , , void >::is_mapping_plugin::value )>::type > { -private: - - template< class , class ... > friend class ViewMapping ; - template< class , class ... > friend class Kokkos::View ; +public: typedef ViewOffset< typename Traits::dimension , typename Traits::array_layout , void @@ -2600,13 +2626,17 @@ private: typedef typename ViewDataHandle< Traits >::handle_type handle_type ; - handle_type m_handle ; - offset_type m_offset ; + handle_type m_impl_handle ; + offset_type m_impl_offset ; + +private: + + template < class , class ...> friend class ViewMapping; KOKKOS_INLINE_FUNCTION ViewMapping( const handle_type & arg_handle , const offset_type & arg_offset ) - : m_handle( arg_handle ) - , m_offset( arg_offset ) + : m_impl_handle( arg_handle ) + , m_impl_offset( arg_offset ) {} public: @@ -2621,44 +2651,50 @@ public: template< typename iType > KOKKOS_INLINE_FUNCTION constexpr size_t extent( const iType & r ) const - { return m_offset.m_dim.extent(r); } + { return m_impl_offset.m_dim.extent(r); } + + static KOKKOS_INLINE_FUNCTION constexpr size_t static_extent( const unsigned r ) noexcept + { + using dim_type = typename offset_type::dimension_type; + return dim_type::static_extent(r); + } KOKKOS_INLINE_FUNCTION constexpr typename Traits::array_layout layout() const - { return m_offset.layout(); } + { return m_impl_offset.layout(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_offset.dimension_0(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_offset.dimension_1(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_offset.dimension_2(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_offset.dimension_3(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_offset.dimension_4(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_offset.dimension_5(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_offset.dimension_6(); } - KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_offset.dimension_7(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_0() const { return m_impl_offset.dimension_0(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_1() const { return m_impl_offset.dimension_1(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_2() const { return m_impl_offset.dimension_2(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_3() const { return m_impl_offset.dimension_3(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_4() const { return m_impl_offset.dimension_4(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_5() const { return m_impl_offset.dimension_5(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_6() const { return m_impl_offset.dimension_6(); } + KOKKOS_INLINE_FUNCTION constexpr size_t dimension_7() const { return m_impl_offset.dimension_7(); } // Is a regular layout with uniform striding for each index. using is_regular = typename offset_type::is_regular ; - KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_offset.stride_0(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_offset.stride_1(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_offset.stride_2(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_offset.stride_3(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_offset.stride_4(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_offset.stride_5(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_offset.stride_6(); } - KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_offset.stride_7(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_0() const { return m_impl_offset.stride_0(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_1() const { return m_impl_offset.stride_1(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_2() const { return m_impl_offset.stride_2(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_3() const { return m_impl_offset.stride_3(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_4() const { return m_impl_offset.stride_4(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_5() const { return m_impl_offset.stride_5(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_6() const { return m_impl_offset.stride_6(); } + KOKKOS_INLINE_FUNCTION constexpr size_t stride_7() const { return m_impl_offset.stride_7(); } template< typename iType > - KOKKOS_INLINE_FUNCTION void stride( iType * const s ) const { m_offset.stride(s); } + KOKKOS_INLINE_FUNCTION void stride( iType * const s ) const { m_impl_offset.stride(s); } //---------------------------------------- // Range span /** \brief Span of the mapped range */ - KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_offset.span(); } + KOKKOS_INLINE_FUNCTION constexpr size_t span() const { return m_impl_offset.span(); } /** \brief Is the mapped range span contiguous */ - KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const { return m_offset.span_is_contiguous(); } + KOKKOS_INLINE_FUNCTION constexpr bool span_is_contiguous() const { return m_impl_offset.span_is_contiguous(); } typedef typename ViewDataHandle< Traits >::return_type reference_type ; typedef typename Traits::value_type * pointer_type ; @@ -2666,7 +2702,7 @@ public: /** \brief Query raw pointer to memory */ KOKKOS_INLINE_FUNCTION constexpr pointer_type data() const { - return m_handle; + return m_impl_handle; } //---------------------------------------- @@ -2674,7 +2710,7 @@ public: // calling these element reference methods. KOKKOS_FORCEINLINE_FUNCTION - reference_type reference() const { return m_handle[0]; } + reference_type reference() const { return m_impl_handle[0]; } template< typename I0 > KOKKOS_FORCEINLINE_FUNCTION @@ -2682,7 +2718,7 @@ public: std::enable_if< std::is_integral::value && ! std::is_same< typename Traits::array_layout , Kokkos::LayoutStride >::value , reference_type >::type - reference( const I0 & i0 ) const { return m_handle[i0]; } + reference( const I0 & i0 ) const { return m_impl_handle[i0]; } template< typename I0 > KOKKOS_FORCEINLINE_FUNCTION @@ -2690,50 +2726,50 @@ public: std::enable_if< std::is_integral::value && std::is_same< typename Traits::array_layout , Kokkos::LayoutStride >::value , reference_type >::type - reference( const I0 & i0 ) const { return m_handle[ m_offset(i0) ]; } + reference( const I0 & i0 ) const { return m_impl_handle[ m_impl_offset(i0) ]; } template< typename I0 , typename I1 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 ) const - { return m_handle[ m_offset(i0,i1) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1) ]; } template< typename I0 , typename I1 , typename I2 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 ) const - { return m_handle[ m_offset(i0,i1,i2) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1,i2) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 ) const - { return m_handle[ m_offset(i0,i1,i2,i3) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1,i2,i3) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 ) const - { return m_handle[ m_offset(i0,i1,i2,i3,i4) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1,i2,i3,i4) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 , typename I5 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 , const I5 & i5 ) const - { return m_handle[ m_offset(i0,i1,i2,i3,i4,i5) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1,i2,i3,i4,i5) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 , typename I5 , typename I6 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 , const I5 & i5 , const I6 & i6 ) const - { return m_handle[ m_offset(i0,i1,i2,i3,i4,i5,i6) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1,i2,i3,i4,i5,i6) ]; } template< typename I0 , typename I1 , typename I2 , typename I3 , typename I4 , typename I5 , typename I6 , typename I7 > KOKKOS_FORCEINLINE_FUNCTION reference_type reference( const I0 & i0 , const I1 & i1 , const I2 & i2 , const I3 & i3 , const I4 & i4 , const I5 & i5 , const I6 & i6 , const I7 & i7 ) const - { return m_handle[ m_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; } + { return m_impl_handle[ m_impl_offset(i0,i1,i2,i3,i4,i5,i6,i7) ]; } //---------------------------------------- @@ -2747,22 +2783,22 @@ public: /** \brief Span, in bytes, of the referenced memory */ KOKKOS_INLINE_FUNCTION constexpr size_t memory_span() const { - return ( m_offset.span() * sizeof(typename Traits::value_type) + MemorySpanMask ) & ~size_t(MemorySpanMask); + return ( m_impl_offset.span() * sizeof(typename Traits::value_type) + MemorySpanMask ) & ~size_t(MemorySpanMask); } //---------------------------------------- KOKKOS_INLINE_FUNCTION ~ViewMapping() {} - KOKKOS_INLINE_FUNCTION ViewMapping() : m_handle(), m_offset() {} + KOKKOS_INLINE_FUNCTION ViewMapping() : m_impl_handle(), m_impl_offset() {} KOKKOS_INLINE_FUNCTION ViewMapping( const ViewMapping & rhs ) - : m_handle( rhs.m_handle ), m_offset( rhs.m_offset ) {} + : m_impl_handle( rhs.m_impl_handle ), m_impl_offset( rhs.m_impl_offset ) {} KOKKOS_INLINE_FUNCTION ViewMapping & operator = ( const ViewMapping & rhs ) - { m_handle = rhs.m_handle ; m_offset = rhs.m_offset ; return *this ; } + { m_impl_handle = rhs.m_impl_handle ; m_impl_offset = rhs.m_impl_offset ; return *this ; } KOKKOS_INLINE_FUNCTION ViewMapping( ViewMapping && rhs ) - : m_handle( rhs.m_handle ), m_offset( rhs.m_offset ) {} + : m_impl_handle( rhs.m_impl_handle ), m_impl_offset( rhs.m_impl_offset ) {} KOKKOS_INLINE_FUNCTION ViewMapping & operator = ( ViewMapping && rhs ) - { m_handle = rhs.m_handle ; m_offset = rhs.m_offset ; return *this ; } + { m_impl_handle = rhs.m_impl_handle ; m_impl_offset = rhs.m_impl_offset ; return *this ; } //---------------------------------------- @@ -2780,14 +2816,14 @@ public: ViewMapping( Kokkos::Impl::ViewCtorProp< P ... > const & arg_prop , typename Traits::array_layout const & arg_layout ) - : m_handle( ( (Kokkos::Impl::ViewCtorProp const &) arg_prop ).value ) - , m_offset( std::integral_constant< unsigned , 0 >() , arg_layout ) + : m_impl_handle( ( (Kokkos::Impl::ViewCtorProp const &) arg_prop ).value ) + , m_impl_offset( std::integral_constant< unsigned , 0 >() , arg_layout ) {} /**\brief Assign data */ KOKKOS_INLINE_FUNCTION void assign_data( pointer_type arg_ptr ) - { m_handle = handle_type( arg_ptr ); } + { m_impl_handle = handle_type( arg_ptr ); } //---------------------------------------- /* Allocate and construct mapped array. @@ -2815,10 +2851,10 @@ public: , alloc_prop::allow_padding ? sizeof(value_type) : 0 > padding ; - m_offset = offset_type( padding(), arg_layout ); + m_impl_offset = offset_type( padding(), arg_layout ); const size_t alloc_size = - ( m_offset.span() * MemorySpanSize + MemorySpanMask ) & ~size_t(MemorySpanMask); + ( m_impl_offset.span() * MemorySpanSize + MemorySpanMask ) & ~size_t(MemorySpanMask); // Create shared memory tracking record with allocate memory from the memory space record_type * const record = @@ -2829,7 +2865,7 @@ public: #ifdef KOKKOS_ENABLE_DEPRECATED_CODE if ( alloc_size ) { #endif - m_handle = handle_type( reinterpret_cast< pointer_type >( record->data() ) ); + m_impl_handle = handle_type( reinterpret_cast< pointer_type >( record->data() ) ); #ifdef KOKKOS_ENABLE_DEPRECATED_CODE } #endif @@ -2840,8 +2876,8 @@ public: // Assume destruction is only required when construction is requested. // The ViewValueFunctor has both value construction and destruction operators. record->m_destroy = functor_type( ( (Kokkos::Impl::ViewCtorProp const &) arg_prop).value - , (value_type *) m_handle - , m_offset.span() + , (value_type *) m_impl_handle + , m_impl_offset.span() ); // Construct values @@ -2859,16 +2895,17 @@ public: template< class DstTraits , class SrcTraits > class ViewMapping< DstTraits , SrcTraits , typename std::enable_if<( - /* default mappings */ + !(std::is_same::value) && //Added to have a new specialization for SrcType of LayoutStride + // default mappings std::is_same< typename DstTraits::specialize , void >::value && std::is_same< typename SrcTraits::specialize , void >::value && ( - /* same layout */ + // same layout std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value || - /* known layout */ + // known layout ( ( std::is_same< typename DstTraits::array_layout , Kokkos::LayoutLeft >::value || @@ -2968,8 +3005,127 @@ public: if(!assignable) Kokkos::abort("View Assignment: trying to assign runtime dimension to non matching compile time dimension."); } - dst.m_offset = dst_offset_type( src.m_offset ); - dst.m_handle = Kokkos::Impl::ViewDataHandle< DstTraits >::assign( src.m_handle , src_track ); + dst.m_impl_offset = dst_offset_type( src.m_impl_offset ); + dst.m_impl_handle = Kokkos::Impl::ViewDataHandle< DstTraits >::assign( src.m_impl_handle , src_track ); + } +}; + +//---------------------------------------------------------------------------- +//Create new specialization for SrcType of LayoutStride. Runtime check for compatible layout +template< class DstTraits , class SrcTraits > +class ViewMapping< DstTraits , SrcTraits , + typename std::enable_if<( + std::is_same< typename SrcTraits::array_layout, Kokkos::LayoutStride >::value + && + std::is_same< typename DstTraits::specialize , void >::value + && + std::is_same< typename SrcTraits::specialize , void >::value + && + ( + // same layout + std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value + || + // known layout + ( + std::is_same< typename DstTraits::array_layout , Kokkos::LayoutLeft >::value || + std::is_same< typename DstTraits::array_layout , Kokkos::LayoutRight >::value || + std::is_same< typename DstTraits::array_layout , Kokkos::LayoutStride >::value + ) + ) + )>::type > +{ +private: + + enum { is_assignable_space = + Kokkos::Impl::MemorySpaceAccess + < typename DstTraits::memory_space + , typename SrcTraits::memory_space >::assignable }; + + enum { is_assignable_value_type = + std::is_same< typename DstTraits::value_type + , typename SrcTraits::value_type >::value || + std::is_same< typename DstTraits::value_type + , typename SrcTraits::const_value_type >::value }; + + enum { is_assignable_dimension = + ViewDimensionAssignable< typename DstTraits::dimension + , typename SrcTraits::dimension >::value }; + +public: + + enum { is_assignable = is_assignable_space && + is_assignable_value_type && + is_assignable_dimension }; + + typedef Kokkos::Impl::SharedAllocationTracker TrackType ; + typedef ViewMapping< DstTraits , void > DstType ; + typedef ViewMapping< SrcTraits , void > SrcType ; + + KOKKOS_INLINE_FUNCTION + static bool assignable_layout_check(DstType & dst, const SrcType & src) //Runtime check + { + size_t strides[9]; + bool assignable = true; + src.stride(strides); + size_t exp_stride = 1; + if (std::is_same< typename DstTraits::array_layout, Kokkos::LayoutLeft >::value) { + for(int i=0; i0) exp_stride *= src.extent(i-1); + if (strides[i] != exp_stride){assignable=false;break;} + } + } + else if (std::is_same< typename DstTraits::array_layout, Kokkos::LayoutRight >::value) { + for(int i=src.Rank-1; i>=0; i--) { + if (i DstTraits::dimension::rank_dynamic && 1 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN0 == src.dimension_0() : true ) && + ( ( 2 > DstTraits::dimension::rank_dynamic && 2 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN1 == src.dimension_1() : true ) && + ( ( 3 > DstTraits::dimension::rank_dynamic && 3 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN2 == src.dimension_2() : true ) && + ( ( 4 > DstTraits::dimension::rank_dynamic && 4 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN3 == src.dimension_3() : true ) && + ( ( 5 > DstTraits::dimension::rank_dynamic && 5 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN4 == src.dimension_4() : true ) && + ( ( 6 > DstTraits::dimension::rank_dynamic && 6 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN5 == src.dimension_5() : true ) && + ( ( 7 > DstTraits::dimension::rank_dynamic && 7 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN6 == src.dimension_6() : true ) && + ( ( 8 > DstTraits::dimension::rank_dynamic && 8 <= SrcTraits::dimension::rank_dynamic ) ? + dst_dim::ArgN7 == src.dimension_7() : true ) + ; + if(!assignable) + Kokkos::abort("View Assignment: trying to assign runtime dimension to non matching compile time dimension."); + } + dst.m_impl_offset = dst_offset_type( src.m_impl_offset ); + dst.m_impl_handle = Kokkos::Impl::ViewDataHandle< DstTraits >::assign( src.m_impl_handle , src_track ); } }; @@ -3106,12 +3262,12 @@ public: typedef typename DstType::offset_type dst_offset_type ; const SubviewExtents< SrcTraits::rank , rank > - extents( src.m_offset.m_dim , args... ); + extents( src.m_impl_offset.m_dim , args... ); - dst.m_offset = dst_offset_type( src.m_offset , extents ); + dst.m_impl_offset = dst_offset_type( src.m_impl_offset , extents ); - dst.m_handle = ViewDataHandle< DstTraits >::assign(src.m_handle, - src.m_offset( extents.domain_offset(0) + dst.m_impl_handle = ViewDataHandle< DstTraits >::assign(src.m_impl_handle, + src.m_impl_offset( extents.domain_offset(0) , extents.domain_offset(1) , extents.domain_offset(2) , extents.domain_offset(3) @@ -3152,6 +3308,7 @@ bool view_verify_operator_bounds && view_verify_operator_bounds( map , args ... ); } + template< unsigned , class MapType > inline void view_error_operator_bounds( char * , int , const MapType & ) @@ -3176,6 +3333,7 @@ void view_error_operator_bounds view_error_operator_bounds(buf+n,len-n,map,args...); } + #if ! defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) /* Check #3: is the View managed as determined by the MemoryTraits? */ @@ -3275,6 +3433,8 @@ void view_verify_operator_bounds } } + + } /* namespace Impl */ } /* namespace Kokkos */ diff --git a/lib/kokkos/core/src/impl/Kokkos_ViewTile.hpp b/lib/kokkos/core/src/impl/Kokkos_ViewTile.hpp index 42bc8c2308..716b9ceca5 100644 --- a/lib/kokkos/core/src/impl/Kokkos_ViewTile.hpp +++ b/lib/kokkos/core/src/impl/Kokkos_ViewTile.hpp @@ -202,8 +202,8 @@ struct ViewMapping typedef typename src_map_type::offset_type src_offset_type ; dst = dst_map_type( - dst_handle_type( src.m_handle + - ( ( i_tile0 + src.m_offset.m_tile_N0 * i_tile1 ) << src_offset_type::SHIFT_T ) ) , + dst_handle_type( src.m_impl_handle + + ( ( i_tile0 + src.m_impl_offset.m_tile_N0 * i_tile1 ) << src_offset_type::SHIFT_T ) ) , dst_offset_type() ); } }; diff --git a/lib/kokkos/core/src/impl/Kokkos_hwloc.cpp b/lib/kokkos/core/src/impl/Kokkos_hwloc.cpp index 7dc8a53566..423944962b 100644 --- a/lib/kokkos/core/src/impl/Kokkos_hwloc.cpp +++ b/lib/kokkos/core/src/impl/Kokkos_hwloc.cpp @@ -336,11 +336,11 @@ Sentinel::Sentinel() const hwloc_obj_t core = hwloc_get_obj_by_type( s_hwloc_topology , HWLOC_OBJ_CORE , 0 ); - if ( hwloc_bitmap_intersects( s_process_binding , core->allowed_cpuset ) ) { + if ( hwloc_bitmap_intersects( s_process_binding , core->cpuset ) ) { hwloc_bitmap_t s_process_no_core_zero = hwloc_bitmap_alloc(); - hwloc_bitmap_andnot( s_process_no_core_zero , s_process_binding , core->allowed_cpuset ); + hwloc_bitmap_andnot( s_process_no_core_zero , s_process_binding , core->cpuset ); bool ok = 0 == hwloc_set_cpubind( s_hwloc_topology , s_process_no_core_zero , @@ -402,14 +402,14 @@ Sentinel::Sentinel() const hwloc_obj_t root = hwloc_get_obj_by_type( s_hwloc_topology , root_type , i ); - if ( hwloc_bitmap_intersects( s_process_binding , root->allowed_cpuset ) ) { + if ( hwloc_bitmap_intersects( s_process_binding , root->cpuset ) ) { ++root_count ; // Remember which root (NUMA) object the master thread is running on. // This will be logical NUMA rank #0 for this process. - if ( hwloc_bitmap_intersects( proc_cpuset_location, root->allowed_cpuset ) ) { + if ( hwloc_bitmap_intersects( proc_cpuset_location, root->cpuset ) ) { root_base = i ; } @@ -417,7 +417,7 @@ Sentinel::Sentinel() const unsigned max_core = hwloc_get_nbobjs_inside_cpuset_by_type( s_hwloc_topology , - root->allowed_cpuset , + root->cpuset , HWLOC_OBJ_CORE ); unsigned core_count = 0 ; @@ -426,7 +426,7 @@ Sentinel::Sentinel() const hwloc_obj_t core = hwloc_get_obj_inside_cpuset_by_type( s_hwloc_topology , - root->allowed_cpuset , + root->cpuset , HWLOC_OBJ_CORE , j ); // If process' cpuset intersects core's cpuset then process can access this core. @@ -438,13 +438,13 @@ Sentinel::Sentinel() // This assumes that it would be performance-detrimental // to spawn more than one MPI process per core and use nested threading. - if ( hwloc_bitmap_intersects( s_process_binding , core->allowed_cpuset ) ) { + if ( hwloc_bitmap_intersects( s_process_binding , core->cpuset ) ) { ++core_count ; const unsigned pu_count = hwloc_get_nbobjs_inside_cpuset_by_type( s_hwloc_topology , - core->allowed_cpuset , + core->cpuset , HWLOC_OBJ_PU ); if ( pu_per_core == 0 ) pu_per_core = pu_count ; @@ -480,11 +480,11 @@ Sentinel::Sentinel() const hwloc_obj_t root = hwloc_get_obj_by_type( s_hwloc_topology , root_type , root_rank ); - if ( hwloc_bitmap_intersects( s_process_binding , root->allowed_cpuset ) ) { + if ( hwloc_bitmap_intersects( s_process_binding , root->cpuset ) ) { const unsigned max_core = hwloc_get_nbobjs_inside_cpuset_by_type( s_hwloc_topology , - root->allowed_cpuset , + root->cpuset , HWLOC_OBJ_CORE ); unsigned core_count = 0 ; @@ -493,12 +493,12 @@ Sentinel::Sentinel() const hwloc_obj_t core = hwloc_get_obj_inside_cpuset_by_type( s_hwloc_topology , - root->allowed_cpuset , + root->cpuset , HWLOC_OBJ_CORE , j ); - if ( hwloc_bitmap_intersects( s_process_binding , core->allowed_cpuset ) ) { + if ( hwloc_bitmap_intersects( s_process_binding , core->cpuset ) ) { - s_core[ core_count + core_per_root * i ] = core->allowed_cpuset ; + s_core[ core_count + core_per_root * i ] = core->cpuset ; ++core_count ; } diff --git a/lib/kokkos/core/src/kokkos.pc.in b/lib/kokkos/core/src/kokkos.pc.in new file mode 100644 index 0000000000..f27b57c960 --- /dev/null +++ b/lib/kokkos/core/src/kokkos.pc.in @@ -0,0 +1,71 @@ +# +# Kokkos v. 2.0 +# Copyright (2014) Sandia Corporation +# +# Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +# the U.S. Government retains certain rights in this software. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: +# +# 1. Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# 2. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# 3. Neither the name of the Corporation nor the names of the +# contributors may be used to endorse or promote products derived from +# this software without specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# +# Questions? Contact Christian R. Trott (crtrott@sandia.gov) +# + +# Add the directory where kokkos.pc got installed to your PKG_CONFIG_PATH + +# Use this on commandline with: +# c++ `pkg-config --cflags --libs kokkos` -o myapp myapp.cpp + +# Use this in a Makefile: +# myapp: myapp.cpp +# $(CC) `pkg-config --cflags --libs kokkos` -o $@ $< + +# Use this in autotools: +# configure.ac: +# PKG_CHECK_MODULES([KOKKOS], [kokkos]) +# Makefile.am: +# myapp_CFLAGS = $(KOKKOS_CFLAGS) +# myapp_LDADD = $(KOKKOS_LIBS) + +# Use this in CMake: +# CMakeLists.txt: +# find_package(PkgConfig) +# pkg_check_modules(KOKKOS IMPORTED_TARGET kokkos) +# target_link_libraries( PkgConfig::KOKKOS) + +prefix=@CMAKE_INSTALL_PREFIX@ +libdir=${prefix}/lib +includedir=${prefix}/include + +Name: kokkos +Description: Kokkos C++ Performance Portability Programming EcoSystem +URL: https://github.com/kokkos +Version: +Requires: +Libs: -L${libdir} -lkokkos @KOKKOS_EXTRA_LIBS_LIST@ @KOKKOS_LINK_FLAGS@ +Libs.private: -lm +Cflags: -I${includedir} @KOKKOS_CXXFLAGS@ diff --git a/lib/kokkos/core/unit_test/CMakeLists.txt b/lib/kokkos/core/unit_test/CMakeLists.txt index 651abf04dd..fad4e1d45e 100644 --- a/lib/kokkos/core/unit_test/CMakeLists.txt +++ b/lib/kokkos/core/unit_test/CMakeLists.txt @@ -284,6 +284,7 @@ IF(Kokkos_ENABLE_Cuda) SOURCES UnitTestMainInit.cpp cuda/TestCudaHostPinned_SharedAlloc.cpp + cuda/TestCudaHostPinned_ViewCopy.cpp cuda/TestCudaHostPinned_ViewAPI_a.cpp cuda/TestCudaHostPinned_ViewAPI_b.cpp cuda/TestCudaHostPinned_ViewAPI_c.cpp @@ -293,6 +294,7 @@ IF(Kokkos_ENABLE_Cuda) cuda/TestCudaHostPinned_ViewMapping_b.cpp cuda/TestCudaHostPinned_ViewMapping_subview.cpp cuda/TestCudaUVM_SharedAlloc.cpp + cuda/TestCudaUVM_ViewCopy.cpp cuda/TestCudaUVM_ViewAPI_a.cpp cuda/TestCudaUVM_ViewAPI_b.cpp cuda/TestCudaUVM_ViewAPI_c.cpp diff --git a/lib/kokkos/core/unit_test/Makefile b/lib/kokkos/core/unit_test/Makefile index b50222e376..72832271c8 100644 --- a/lib/kokkos/core/unit_test/Makefile +++ b/lib/kokkos/core/unit_test/Makefile @@ -43,12 +43,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA += TestCuda_SharedAlloc.o TestCudaUVM_SharedAlloc.o TestCudaHostPinned_SharedAlloc.o OBJ_CUDA += TestCuda_RangePolicy.o OBJ_CUDA += TestCuda_ViewAPI_a.o TestCuda_ViewAPI_b.o TestCuda_ViewAPI_c.o TestCuda_ViewAPI_d.o TestCuda_ViewAPI_e.o - OBJ_CUDA += TestCuda_ViewMapping_a.o TestCuda_ViewMapping_b.o TestCuda_ViewMapping_subview.o - OBJ_CUDA += TestCudaUVM_ViewAPI_a.o TestCudaUVM_ViewAPI_b.o TestCudaUVM_ViewAPI_c.o TestCudaUVM_ViewAPI_d.o TestCudaUVM_ViewAPI_e.o + OBJ_CUDA += TestCuda_ViewMapping_a.o TestCuda_ViewMapping_b.o TestCuda_ViewMapping_subview.o TestCuda_ViewLayoutStrideAssignment.o + OBJ_CUDA += TestCudaUVM_ViewCopy.o TestCudaUVM_ViewAPI_a.o TestCudaUVM_ViewAPI_b.o TestCudaUVM_ViewAPI_c.o TestCudaUVM_ViewAPI_d.o TestCudaUVM_ViewAPI_e.o OBJ_CUDA += TestCudaUVM_ViewMapping_a.o TestCudaUVM_ViewMapping_b.o TestCudaUVM_ViewMapping_subview.o - OBJ_CUDA += TestCudaHostPinned_ViewAPI_a.o TestCudaHostPinned_ViewAPI_b.o TestCudaHostPinned_ViewAPI_c.o TestCudaHostPinned_ViewAPI_d.o TestCudaHostPinned_ViewAPI_e.o + OBJ_CUDA += TestCudaHostPinned_ViewCopy.o TestCudaHostPinned_ViewAPI_a.o TestCudaHostPinned_ViewAPI_b.o TestCudaHostPinned_ViewAPI_c.o TestCudaHostPinned_ViewAPI_d.o TestCudaHostPinned_ViewAPI_e.o OBJ_CUDA += TestCudaHostPinned_ViewMapping_a.o TestCudaHostPinned_ViewMapping_b.o TestCudaHostPinned_ViewMapping_subview.o - OBJ_CUDA += TestCuda_View_64bit.o + OBJ_CUDA += TestCuda_View_64bit.o OBJ_CUDA += TestCuda_ViewOfClass.o OBJ_CUDA += TestCuda_SubView_a.o TestCuda_SubView_b.o OBJ_CUDA += TestCuda_SubView_c01.o TestCuda_SubView_c02.o TestCuda_SubView_c03.o @@ -57,13 +57,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA += TestCuda_SubView_c10.o TestCuda_SubView_c11.o TestCuda_SubView_c12.o OBJ_CUDA += TestCuda_SubView_c13.o OBJ_CUDA += TestCuda_Reductions.o TestCuda_Scan.o + OBJ_CUDA += TestCuda_Reductions_DeviceView.o OBJ_CUDA += TestCuda_Reducers_a.o TestCuda_Reducers_b.o TestCuda_Reducers_c.o TestCuda_Reducers_d.o OBJ_CUDA += TestCuda_Complex.o OBJ_CUDA += TestCuda_AtomicOperations_int.o TestCuda_AtomicOperations_unsignedint.o TestCuda_AtomicOperations_longint.o OBJ_CUDA += TestCuda_AtomicOperations_unsignedlongint.o TestCuda_AtomicOperations_longlongint.o TestCuda_AtomicOperations_double.o TestCuda_AtomicOperations_float.o OBJ_CUDA += TestCuda_AtomicViews.o TestCuda_Atomics.o OBJ_CUDA += TestCuda_Team.o TestCuda_TeamScratch.o - OBJ_CUDA += TestCuda_TeamReductionScan.o + OBJ_CUDA += TestCuda_TeamReductionScan.o TestCuda_TeamTeamSize.o OBJ_CUDA += TestCuda_Other.o OBJ_CUDA += TestCuda_MDRange_a.o TestCuda_MDRange_b.o TestCuda_MDRange_c.o TestCuda_MDRange_d.o TestCuda_MDRange_e.o OBJ_CUDA += TestCuda_Crs.o @@ -84,13 +85,11 @@ ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) OBJ_ROCM += TestROCm_AtomicOperations_int.o TestROCm_AtomicOperations_unsignedint.o TestROCm_AtomicOperations_longint.o OBJ_ROCM += TestROCm_AtomicOperations_unsignedlongint.o TestROCm_AtomicOperations_longlongint.o TestROCm_AtomicOperations_double.o TestROCm_AtomicOperations_float.o OBJ_ROCM += TestROCm_Atomics.o -# complex failing OBJ_ROCM += TestROCm_AtomicViews.o OBJ_ROCM += TestROCm_Other.o -# Compiles but runtime Segfaults: -# OBJ_ROCM += TestROCm_MDRange_a.o TestROCm_MDRange_b.o TestROCm_MDRange_c.o TestROCm_MDRange_d.o TestROCm_MDRange_e.o -# rocm.memory_pool - OBJ_ROCM += TestROCm_Reductions.o + OBJ_ROCM += TestROCm_MDRange_a.o TestROCm_MDRange_b.o TestROCm_MDRange_c.o TestROCm_MDRange_d.o TestROCm_MDRange_e.o + OBJ_ROCM += TestROCm_MDRangeReduce_a.o TestROCm_MDRangeReduce_b.o TestROCm_MDRangeReduce_c.o TestROCm_MDRangeReduce_d.o TestROCm_MDRangeReduce_e.o + OBJ_ROCM += TestROCm_Reductions.o OBJ_ROCM += TestROCm_Reducers_a.o TestROCm_Reducers_b.o TestROCm_Reducers_c.o TestROCm_Reducers_d.o OBJ_ROCM += TestROCm_Scan.o OBJ_ROCM += TestROCm_SharedAlloc.o @@ -108,22 +107,22 @@ ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1) OBJ_ROCM += TestROCm_SubView_c10.o OBJ_ROCM += TestROCm_SubView_c11.o OBJ_ROCM += TestROCm_SubView_c12.o + OBJ_ROCM += TestROCm_SubView_c13.o OBJ_ROCM += TestROCm_Team.o -# compile fails / compiler segfaults - #OBJ_ROCM += TestROCm_TeamReductionScan.o -# compile fails - OBJ_ROCM += TestROCm_TeamScratch.o + OBJ_ROCM += TestROCm_TeamReductionScan.o + OBJ_ROCM += TestROCm_TeamScratch.o TestROCm_TeamTeamSize.o OBJ_ROCM += TestROCm_ViewAPI_a.o TestROCm_ViewAPI_b.o TestROCm_ViewAPI_c.o TestROCm_ViewAPI_d.o TestROCm_ViewAPI_e.o OBJ_ROCM += TestROCm_ViewMapping_a.o OBJ_ROCM += TestROCm_ViewMapping_b.o OBJ_ROCM += TestROCm_ViewMapping_subview.o - OBJ_ROCM += TestROCmHostPinned_ViewAPI_a.o TestROCmHostPinned_ViewAPI_b.o TestROCmHostPinned_ViewAPI_c.o TestROCmHostPinned_ViewAPI_d.o TestROCmHostPinned_ViewAPI_e.o + OBJ_ROCM += TestROCmHostPinned_ViewCopy.o TestROCmHostPinned_ViewAPI_a.o TestROCmHostPinned_ViewAPI_b.o TestROCmHostPinned_ViewAPI_c.o TestROCmHostPinned_ViewAPI_d.o TestROCmHostPinned_ViewAPI_e.o OBJ_ROCM += TestROCmHostPinned_View_64bit.o - OBJ_ROCM += TestROCmHostPinned_ViewMapping_a.o - OBJ_ROCM += TestROCmHostPinned_ViewMapping_b.o - OBJ_ROCM += TestROCmHostPinned_ViewMapping_subview.o + OBJ_ROCM += TestROCmHostPinned_ViewMapping_a.o + OBJ_ROCM += TestROCmHostPinned_ViewMapping_b.o + OBJ_ROCM += TestROCmHostPinned_ViewMapping_subview.o OBJ_ROCM += TestROCm_ViewOfClass.o - OBJ_ROCM += TestROCm_Spaces.o + OBJ_ROCM += TestROCm_Spaces.o + OBJ_ROCM += TestROCm_Crs.o TARGETS += KokkosCore_UnitTest_ROCm TEST_TARGETS += test-rocm @@ -137,7 +136,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) OBJ_THREADS += TestThreads_RangePolicy.o OBJ_THREADS += TestThreads_View_64bit.o OBJ_THREADS += TestThreads_ViewAPI_a.o TestThreads_ViewAPI_b.o TestThreads_ViewAPI_c.o TestThreads_ViewAPI_d.o TestThreads_ViewAPI_e.o - OBJ_THREADS += TestThreads_ViewMapping_a.o TestThreads_ViewMapping_b.o TestThreads_ViewMapping_subview.o + OBJ_THREADS += TestThreads_ViewMapping_a.o TestThreads_ViewMapping_b.o TestThreads_ViewMapping_subview.o TestThreads_ViewLayoutStrideAssignment.o OBJ_THREADS += TestThreads_ViewOfClass.o OBJ_THREADS += TestThreads_SubView_a.o TestThreads_SubView_b.o OBJ_THREADS += TestThreads_SubView_c01.o TestThreads_SubView_c02.o TestThreads_SubView_c03.o @@ -145,12 +144,13 @@ ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1) OBJ_THREADS += TestThreads_SubView_c07.o TestThreads_SubView_c08.o TestThreads_SubView_c09.o OBJ_THREADS += TestThreads_SubView_c10.o TestThreads_SubView_c11.o TestThreads_SubView_c12.o OBJ_THREADS += TestThreads_Reductions.o TestThreads_Scan.o + OBJ_THREADS += TestThreads_Reductions_DeviceView.o OBJ_THREADS += TestThreads_Reducers_a.o TestThreads_Reducers_b.o TestThreads_Reducers_c.o TestThreads_Reducers_d.o OBJ_THREADS += TestThreads_Complex.o OBJ_THREADS += TestThreads_AtomicOperations_int.o TestThreads_AtomicOperations_unsignedint.o TestThreads_AtomicOperations_longint.o OBJ_THREADS += TestThreads_AtomicOperations_unsignedlongint.o TestThreads_AtomicOperations_longlongint.o TestThreads_AtomicOperations_double.o TestThreads_AtomicOperations_float.o OBJ_THREADS += TestThreads_AtomicViews.o TestThreads_Atomics.o - OBJ_THREADS += TestThreads_Team.o TestThreads_TeamScratch.o + OBJ_THREADS += TestThreads_Team.o TestThreads_TeamScratch.o TestThreads_TeamTeamSize.o OBJ_THREADS += TestThreads_TeamReductionScan.o OBJ_THREADS += TestThreads_Other.o OBJ_THREADS += TestThreads_MDRange_a.o TestThreads_MDRange_b.o TestThreads_MDRange_c.o TestThreads_MDRange_d.o TestThreads_MDRange_e.o @@ -167,7 +167,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) OBJ_OPENMP += TestOpenMP_RangePolicy.o OBJ_OPENMP += TestOpenMP_View_64bit.o OBJ_OPENMP += TestOpenMP_ViewAPI_a.o TestOpenMP_ViewAPI_b.o TestOpenMP_ViewAPI_c.o TestOpenMP_ViewAPI_d.o TestOpenMP_ViewAPI_e.o - OBJ_OPENMP += TestOpenMP_ViewMapping_a.o TestOpenMP_ViewMapping_b.o TestOpenMP_ViewMapping_subview.o + OBJ_OPENMP += TestOpenMP_ViewMapping_a.o TestOpenMP_ViewMapping_b.o TestOpenMP_ViewMapping_subview.o TestOpenMP_ViewLayoutStrideAssignment.o OBJ_OPENMP += TestOpenMP_ViewOfClass.o OBJ_OPENMP += TestOpenMP_SubView_a.o TestOpenMP_SubView_b.o OBJ_OPENMP += TestOpenMP_SubView_c01.o TestOpenMP_SubView_c02.o TestOpenMP_SubView_c03.o @@ -176,13 +176,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) OBJ_OPENMP += TestOpenMP_SubView_c10.o TestOpenMP_SubView_c11.o TestOpenMP_SubView_c12.o OBJ_OPENMP += TestOpenMP_SubView_c13.o OBJ_OPENMP += TestOpenMP_Reductions.o TestOpenMP_Scan.o + OBJ_OPENMP += TestOpenMP_Reductions_DeviceView.o OBJ_OPENMP += TestOpenMP_Reducers_a.o TestOpenMP_Reducers_b.o TestOpenMP_Reducers_c.o TestOpenMP_Reducers_d.o OBJ_OPENMP += TestOpenMP_Complex.o OBJ_OPENMP += TestOpenMP_AtomicOperations_int.o TestOpenMP_AtomicOperations_unsignedint.o TestOpenMP_AtomicOperations_longint.o OBJ_OPENMP += TestOpenMP_AtomicOperations_unsignedlongint.o TestOpenMP_AtomicOperations_longlongint.o TestOpenMP_AtomicOperations_double.o TestOpenMP_AtomicOperations_float.o OBJ_OPENMP += TestOpenMP_AtomicViews.o TestOpenMP_Atomics.o OBJ_OPENMP += TestOpenMP_Team.o TestOpenMP_TeamScratch.o - OBJ_OPENMP += TestOpenMP_TeamReductionScan.o + OBJ_OPENMP += TestOpenMP_TeamReductionScan.o TestOpenMP_TeamTeamSize.o OBJ_OPENMP += TestOpenMP_Other.o OBJ_OPENMP += TestOpenMP_MDRange_a.o TestOpenMP_MDRange_b.o TestOpenMP_MDRange_c.o TestOpenMP_MDRange_d.o TestOpenMP_MDRange_e.o OBJ_OPENMP += TestOpenMP_Crs.o @@ -256,7 +257,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) OBJ_SERIAL += TestSerial_RangePolicy.o OBJ_SERIAL += TestSerial_View_64bit.o OBJ_SERIAL += TestSerial_ViewAPI_a.o TestSerial_ViewAPI_b.o TestSerial_ViewAPI_c.o TestSerial_ViewAPI_d.o TestSerial_ViewAPI_e.o - OBJ_SERIAL += TestSerial_ViewMapping_a.o TestSerial_ViewMapping_b.o TestSerial_ViewMapping_subview.o + OBJ_SERIAL += TestSerial_ViewMapping_a.o TestSerial_ViewMapping_b.o TestSerial_ViewMapping_subview.o TestSerial_ViewLayoutStrideAssignment.o OBJ_SERIAL += TestSerial_ViewOfClass.o OBJ_SERIAL += TestSerial_SubView_a.o TestSerial_SubView_b.o OBJ_SERIAL += TestSerial_SubView_c01.o TestSerial_SubView_c02.o TestSerial_SubView_c03.o @@ -265,13 +266,14 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) OBJ_SERIAL += TestSerial_SubView_c10.o TestSerial_SubView_c11.o TestSerial_SubView_c12.o OBJ_SERIAL += TestSerial_SubView_c13.o OBJ_SERIAL += TestSerial_Reductions.o TestSerial_Scan.o + OBJ_SERIAL += TestSerial_Reductions_DeviceView.o OBJ_SERIAL += TestSerial_Reducers_a.o TestSerial_Reducers_b.o TestSerial_Reducers_c.o TestSerial_Reducers_d.o OBJ_SERIAL += TestSerial_Complex.o OBJ_SERIAL += TestSerial_AtomicOperations_int.o TestSerial_AtomicOperations_unsignedint.o TestSerial_AtomicOperations_longint.o OBJ_SERIAL += TestSerial_AtomicOperations_unsignedlongint.o TestSerial_AtomicOperations_longlongint.o TestSerial_AtomicOperations_double.o TestSerial_AtomicOperations_float.o OBJ_SERIAL += TestSerial_AtomicViews.o TestSerial_Atomics.o OBJ_SERIAL += TestSerial_Team.o TestSerial_TeamScratch.o - OBJ_SERIAL += TestSerial_TeamReductionScan.o + OBJ_SERIAL += TestSerial_TeamReductionScan.o TestSerial_TeamTeamSize.o OBJ_SERIAL += TestSerial_Other.o #HCC_WORKAROUND ifneq ($(KOKKOS_INTERNAL_COMPILER_HCC), 1) diff --git a/lib/kokkos/core/unit_test/TestAtomic.hpp b/lib/kokkos/core/unit_test/TestAtomic.hpp index cf4bae5844..58b6325115 100644 --- a/lib/kokkos/core/unit_test/TestAtomic.hpp +++ b/lib/kokkos/core/unit_test/TestAtomic.hpp @@ -224,7 +224,8 @@ T AddLoop( int loop ) { struct AddFunctorReduce< T, execution_space > f_add_red; f_add_red.data = data; - Kokkos::parallel_reduce( loop, f_add_red ); + int dummy_result; + Kokkos::parallel_reduce( loop, f_add_red , dummy_result ); execution_space::fence(); return val; @@ -309,7 +310,8 @@ T CASLoop( int loop ) { struct CASFunctorReduce< T, execution_space > f_cas_red; f_cas_red.data = data; - Kokkos::parallel_reduce( loop, f_cas_red ); + int dummy_result; + Kokkos::parallel_reduce( loop, f_cas_red , dummy_result ); execution_space::fence(); return val; @@ -401,7 +403,8 @@ T ExchLoop( int loop ) { struct ExchFunctorReduce< T, execution_space > f_exch_red; f_exch_red.data = data; f_exch_red.data2 = data2; - Kokkos::parallel_reduce( loop, f_exch_red ); + int dummy_result; + Kokkos::parallel_reduce( loop, f_exch_red , dummy_result ); execution_space::fence(); return val; @@ -529,7 +532,7 @@ TEST_F( TEST_CATEGORY, atomics ) ASSERT_TRUE( ( TestAtomic::Loop< float, TEST_EXECSPACE >( 100, 3 ) ) ); #ifndef KOKKOS_ENABLE_OPENMPTARGET -#ifndef KOKKOS_ENABLE_ROCM +#ifndef KOKKOS_ENABLE_ROCM // ROCM doesn't yet support atomics for >64bit types ASSERT_TRUE( ( TestAtomic::Loop< Kokkos::complex, TEST_EXECSPACE >( 1, 1 ) ) ); ASSERT_TRUE( ( TestAtomic::Loop< Kokkos::complex, TEST_EXECSPACE >( 1, 2 ) ) ); ASSERT_TRUE( ( TestAtomic::Loop< Kokkos::complex, TEST_EXECSPACE >( 1, 3 ) ) ); diff --git a/lib/kokkos/core/unit_test/TestCXX11.hpp b/lib/kokkos/core/unit_test/TestCXX11.hpp index b6c34d2d4b..8a158e2667 100644 --- a/lib/kokkos/core/unit_test/TestCXX11.hpp +++ b/lib/kokkos/core/unit_test/TestCXX11.hpp @@ -216,7 +216,7 @@ template< class DeviceType, bool PWRTest > double ReduceTestFunctor() { typedef Kokkos::TeamPolicy< DeviceType > policy_type; typedef Kokkos::View< double**, DeviceType > view_type; - typedef Kokkos::View< double, typename view_type::host_mirror_space, Kokkos::MemoryUnmanaged > unmanaged_result; + typedef Kokkos::View< double, Kokkos::HostSpace, Kokkos::MemoryUnmanaged > unmanaged_result; view_type a( "A", 100, 5 ); typename view_type::HostMirror h_a = Kokkos::create_mirror_view( a ); @@ -244,7 +244,7 @@ template< class DeviceType, bool PWRTest > double ReduceTestLambda() { typedef Kokkos::TeamPolicy< DeviceType > policy_type; typedef Kokkos::View< double**, DeviceType > view_type; - typedef Kokkos::View< double, typename view_type::host_mirror_space, Kokkos::MemoryUnmanaged > unmanaged_result; + typedef Kokkos::View< double, Kokkos::HostSpace, Kokkos::MemoryUnmanaged > unmanaged_result; view_type a( "A", 100, 5 ); typename view_type::HostMirror h_a = Kokkos::create_mirror_view( a ); @@ -327,12 +327,18 @@ bool Test( int test ) { }; bool passed = true; - if ( res_functor != res_lambda ) { + auto a = res_functor; + auto b = res_lambda; + // use a tolerant comparison because functors and lambdas vectorize differently + // https://github.com/trilinos/Trilinos/issues/3233 + auto rel_err = (std::abs(b - a) / std::max(std::abs(a), std::abs(b))); + auto tol = 1e-14; + if (rel_err > tol) { passed = false; std::cout << "CXX11 ( test = '" - << testnames[test] << "' FAILED : " - << res_functor << " != " << res_lambda + << testnames[test] << "' FAILED : relative error " + << rel_err << " > tolerance " << tol << std::endl; } diff --git a/lib/kokkos/core/unit_test/TestComplex.hpp b/lib/kokkos/core/unit_test/TestComplex.hpp index fcaebe3c6e..f4343df0ce 100644 --- a/lib/kokkos/core/unit_test/TestComplex.hpp +++ b/lib/kokkos/core/unit_test/TestComplex.hpp @@ -71,7 +71,7 @@ struct TestComplexConstruction { ASSERT_FLOAT_EQ(h_results(7).real(),7.5); ASSERT_FLOAT_EQ(h_results(7).imag(),0.0); ASSERT_FLOAT_EQ(h_results(8).real(),double(8)); ASSERT_FLOAT_EQ(h_results(8).imag(),0.0); -#ifndef KOKKOS_ENABLE_ROCM +#ifndef KOKKOS_ENABLE_ROCM // Copy construction conversion between Kokkos::complex and std::complex doesn't compile Kokkos::complex a(1.5,2.5),b(3.25,5.25),r_kk; std::complex sa(a),sb(3.25,5.25),r; r = a; r_kk = a; ASSERT_FLOAT_EQ(r.real(),r_kk.real()); ASSERT_FLOAT_EQ(r.imag(),r_kk.imag()); diff --git a/lib/kokkos/core/unit_test/TestCrs.hpp b/lib/kokkos/core/unit_test/TestCrs.hpp index 77ea508b89..08087ae062 100644 --- a/lib/kokkos/core/unit_test/TestCrs.hpp +++ b/lib/kokkos/core/unit_test/TestCrs.hpp @@ -63,6 +63,86 @@ struct CountFillFunctor { } }; +/* RunUpdateCrsTest + * 4 test cases: + * 1. use member object version which is constructed directly using the copy constructor + * 2. excplicity copy construct in local variable + * 3. construct default and assign to input object + * 4. construct object from views + */ +template< class CrsType, class ExecSpace, class scalarType > +struct RunUpdateCrsTest { + + struct TestOne {}; + struct TestTwo {}; + struct TestThree {}; + struct TestFour {}; + + CrsType graph; + RunUpdateCrsTest( CrsType g_in ) : graph(g_in) + { + } + + void run_test(int nTest) { + switch (nTest) + { + case 1: + parallel_for ("TestCrs1", Kokkos::RangePolicy(0,graph.numRows()),*this); + break; + case 2: + parallel_for ("TestCrs2", Kokkos::RangePolicy(0,graph.numRows()),*this); + break; + case 3: + parallel_for ("TestCrs3", Kokkos::RangePolicy(0,graph.numRows()),*this); + break; + case 4: + parallel_for ("TestCrs4", Kokkos::RangePolicy(0,graph.numRows()),*this); + break; + default: + break; + } + } + + KOKKOS_INLINE_FUNCTION + void updateGraph(const CrsType & g_in, const scalarType row) const { + auto row_map = g_in.row_map; + auto entries = g_in.entries; + auto j_start = row_map(row); + auto j_end = row_map(row+1)-j_start; + for (scalarType j = 0; j < j_end; ++j) { + entries(j_start+j) = (j+1)*(j+1); + } + } + + // Test Crs class from class member + KOKKOS_INLINE_FUNCTION + void operator()(const TestOne &, const scalarType row) const { + updateGraph(graph, row); + } + + // Test Crs class from copy constructor (local_graph(graph) + KOKKOS_INLINE_FUNCTION + void operator()(const TestTwo &, const scalarType row) const { + CrsType local_graph(graph); + updateGraph(local_graph, row); + } + + // Test Crs class from default constructor assigned to function parameter + KOKKOS_INLINE_FUNCTION + void operator()(const TestThree &, const scalarType row) const { + CrsType local_graph; + local_graph = graph; + updateGraph(local_graph, row); + } + + // Test Crs class from local graph constructed from row_map and entities access on input parameter) + KOKKOS_INLINE_FUNCTION + void operator()(const TestFour &, const scalarType row) const { + CrsType local_graph(graph.row_map, graph.entries); + updateGraph(local_graph, row); + } +}; + template< class ExecSpace > void test_count_fill(std::int32_t nrows) { Kokkos::Crs graph; @@ -81,6 +161,38 @@ void test_count_fill(std::int32_t nrows) { } } +// Test Crs Constructor / assignment operation by +// using count and fill to create/populate initial graph, +// then use parallel_for with Crs directly to update content +// then verify results +template< class ExecSpace > +void test_constructor(std::int32_t nrows) { + + for (int nTest = 1; nTest < 5; nTest++) + { + typedef Kokkos::Crs crs_int32; + crs_int32 graph; + Kokkos::count_and_fill_crs(graph, nrows, CountFillFunctor()); + ASSERT_EQ(graph.numRows(), nrows); + + RunUpdateCrsTest crstest(graph); + crstest.run_test(nTest); + + auto row_map = Kokkos::create_mirror_view(graph.row_map); + Kokkos::deep_copy(row_map, graph.row_map); + auto entries = Kokkos::create_mirror_view(graph.entries); + Kokkos::deep_copy(entries, graph.entries); + + for (std::int32_t row = 0; row < nrows; ++row) { + auto n = (row % 4) + 1; + ASSERT_EQ(row_map(row + 1) - row_map(row), n); + for (std::int32_t j = 0; j < n; ++j) { + ASSERT_EQ(entries(row_map(row) + j), (j + 1)*(j+1)); + } + } + } +} + } // anonymous namespace TEST_F( TEST_CATEGORY, crs_count_fill ) @@ -95,4 +207,17 @@ TEST_F( TEST_CATEGORY, crs_count_fill ) test_count_fill(10000); } +TEST_F( TEST_CATEGORY, crs_copy_constructor ) +{ + test_constructor(0); + test_constructor(1); + test_constructor(2); + test_constructor(3); + test_constructor(13); + test_constructor(100); + test_constructor(1000); + test_constructor(10000); +} + + } // namespace Test diff --git a/lib/kokkos/core/unit_test/TestMDRange.hpp b/lib/kokkos/core/unit_test/TestMDRange.hpp index 9298983aa8..a382a20700 100644 --- a/lib/kokkos/core/unit_test/TestMDRange.hpp +++ b/lib/kokkos/core/unit_test/TestMDRange.hpp @@ -318,6 +318,24 @@ struct TestMDRange_2D { ASSERT_EQ( sum, 2 * (N0 - s0) * (N1 - s1) ); } + // Test with reducers - scalar + label + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<2>, Kokkos::IndexType > range_type; + int s0 = 1; + int s1 = 1; + range_type range( {{ s0, s1 }}, {{ N0, N1 }}, {{ 3, 3 }} ); + + TestMDRange_2D functor( N0, N1 ); + + parallel_for( "rank2-parfor-label", range, functor ); + + value_type sum = 0.0; + Kokkos::Sum< value_type > reducer_scalar( sum ); + + parallel_reduce( "rank2-reducer-label", range, functor, reducer_scalar ); + + ASSERT_EQ( sum, 2 * (N0 - s0) * (N1 - s1) ); + } // Test with reducers - scalar view { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<2>, Kokkos::IndexType > range_type; @@ -337,7 +355,31 @@ struct TestMDRange_2D { ASSERT_EQ( sum, 2 * N0 * N1 ); } + // Test Min reducer with lambda +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<2>, Kokkos::IndexType > range_type; + range_type range( {{ 1, 1 }}, {{ N0, N1 }}, {{ 3, 3 }} ); + Kokkos::View< double**, ExecSpace > v_in("v_in", N0, N1 ); + + parallel_for( "rank2-init-lambda", range, KOKKOS_LAMBDA ( const int i, const int j ) { + v_in( i , j ) = (i+1) * (j+1) ; + }); + + double min; + Kokkos::Min< double > reducer_scalar( min ); + + parallel_reduce( "rank2-min-reducer", range, KOKKOS_LAMBDA ( const int i, const int j, double& min_val ) { + min_val = fmin( v_in(i,j), min_val ); + } + , reducer_scalar); + + ASSERT_EQ( min, 4.0 ); + } +#endif +#endif // Tagged operator test { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<2, Iterate::Default, Iterate::Default >, Kokkos::IndexType, InitTag > range_type; @@ -858,6 +900,22 @@ struct TestMDRange_3D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 ); } + // Test with reducers - scalar + label + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<3>, Kokkos::IndexType > range_type; + range_type range( {{ 0, 0, 0 }}, {{ N0, N1, N2 }}, {{ 3, 3, 3 }} ); + + TestMDRange_3D functor( N0, N1, N2 ); + + parallel_for( "rank3-parfor-label", range, functor ); + + value_type sum = 0.0; + Kokkos::Sum< value_type > reducer_scalar( sum ); + + parallel_reduce( "rank3-reducer-label", range, functor, reducer_scalar ); + + ASSERT_EQ( sum, 2 * N0 * N1 * N2 ); + } // Test with reducers - scalar view { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<3>, Kokkos::IndexType > range_type; @@ -877,6 +935,36 @@ struct TestMDRange_3D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 ); } + // Test Min reducer with lambda +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<3>, Kokkos::IndexType > range_type; + + range_type range( {{ 1, 1, 1 }}, {{ N0, N1, N2 }}, {{ 3, 3, 3 }} ); + + Kokkos::View< double***, ExecSpace > v_in("v_in", N0, N1, N2 ); + + parallel_for( "rank3-init-lambda", range, KOKKOS_LAMBDA ( const int i, const int j, const int k ) { + v_in( i, j, k ) = (i+1) * (j+1) * (k+1) ; + }); + + double min; + + parallel_reduce("rank3-min-reducer", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, double& min_val ) { + min_val = (v_in(i,j,k) < min_val) ? v_in(i,j,k) : min_val; + } + , Kokkos::Min(min) ); + + if((N0-1)*(N1-1)*(N2-1)>0) + ASSERT_EQ( min, 8.0 ); + else { + double min_identity = Kokkos::reduction_identity::min(); + ASSERT_EQ( min, min_identity ); + } + } +#endif +#endif // Tagged operator test { @@ -1382,6 +1470,23 @@ struct TestMDRange_4D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 ); } + // Test with reducers - scalar + label + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<4>, Kokkos::IndexType > range_type; + range_type range( {{ 0, 0, 0, 0 }}, {{ N0, N1, N2, N3 }}, {{ 3, 3, 3, 3 }} ); + + TestMDRange_4D functor( N0, N1, N2, N3 ); + + parallel_for( "rank4-parfor-label", range, functor ); + + value_type sum = 0.0; + Kokkos::Sum< value_type > reducer_scalar( sum ); + + parallel_reduce( "rank4-reducer-label", range, functor, reducer_scalar ); + + ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 ); + } + // Test with reducers - scalar view { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<4>, Kokkos::IndexType > range_type; @@ -1402,6 +1507,32 @@ struct TestMDRange_4D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 ); } + // Test Min reducer with lambda +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<4>, Kokkos::IndexType > range_type; + + range_type range( {{ 1, 1, 1, 1 }}, {{ N0, N1, N2, N3 }}, {{ 3, 3, 3, 3 }} ); + + Kokkos::View< double****, ExecSpace > v_in("v_in", N0, N1, N2, N3 ); + + parallel_for( "rank4-init-lambda", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, const int l ) { + v_in( i, j, k, l ) = (i+1) * (j+1) * (k+1) * (l+1) ; + }); + + double min; + + parallel_reduce("rank4-min-reducer", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, const int l, double& min_val ) { + min_val = (v_in(i,j,k,l) < min_val) ? v_in(i,j,k,l) : min_val; + } + , Kokkos::Min(min) ); + + ASSERT_EQ( min, 16.0 ); + } +#endif +#endif + // Tagged operator test { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<4, Iterate::Default, Iterate::Default >, Kokkos::IndexType, InitTag > range_type; @@ -1926,6 +2057,23 @@ struct TestMDRange_5D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 * N4 ); } + // Test with reducers - scalar + label + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<5>, Kokkos::IndexType > range_type; + range_type range( {{ 0, 0, 0, 0, 0 }}, {{ N0, N1, N2, N3, N4 }}, {{ 3, 3, 3, 3, 3 }} ); + + TestMDRange_5D functor( N0, N1, N2, N3, N4 ); + + parallel_for( "rank5-parfor-label", range, functor ); + + value_type sum = 0.0; + Kokkos::Sum< value_type > reducer_scalar( sum ); + + parallel_reduce( "rank5-reducer-label", range, functor, reducer_scalar ); + + ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 * N4 ); + } + // Test with reducers - scalar view { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<5>, Kokkos::IndexType > range_type; @@ -1946,6 +2094,32 @@ struct TestMDRange_5D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 * N4 ); } + // Test Min reducer with lambda +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<5>, Kokkos::IndexType > range_type; + + range_type range( {{ 1, 1, 1, 1, 1 }}, {{ N0, N1, N2, N3, N4 }}, {{ 3, 3, 3, 2, 2 }} ); + + Kokkos::View< double*****, ExecSpace > v_in("v_in", N0, N1, N2, N3, N4 ); + + parallel_for( "rank5-init-lambda", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, const int l, const int m ) { + v_in( i, j, k, l, m ) = (i+1) * (j+1) * (k+1) * (l+1) * (m+1) ; + }); + + double min; + + parallel_reduce("rank5-min-reducer", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, const int l, const int m, double& min_val ) { + min_val = (v_in(i,j,k,l,m) < min_val) ? v_in(i,j,k,l,m) : min_val; + } + , Kokkos::Min(min) ); + + ASSERT_EQ( min, 32.0 ); + } +#endif +#endif + // Tagged operator test { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<5, Iterate::Default, Iterate::Default >, Kokkos::IndexType, InitTag > range_type; @@ -2401,6 +2575,23 @@ struct TestMDRange_6D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 * N4 * N5 ); } + // Test with reducers - scalar + label + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<6>, Kokkos::IndexType > range_type; + range_type range( {{ 0, 0, 0, 0, 0, 0 }}, {{ N0, N1, N2, N3, N4, N5 }}, {{ 3, 3, 3, 3, 3, 2 }} ); + + TestMDRange_6D functor( N0, N1, N2, N3, N4, N5 ); + + parallel_for( "rank6-parfor-label", range, functor ); + + value_type sum = 0.0; + Kokkos::Sum< value_type > reducer_scalar( sum ); + + parallel_reduce( "rank6-reducer-label", range, functor, reducer_scalar ); + + ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 * N4 * N5 ); + } + // Test with reducers - scalar view { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<6>, Kokkos::IndexType > range_type; @@ -2421,6 +2612,32 @@ struct TestMDRange_6D { ASSERT_EQ( sum, 2 * N0 * N1 * N2 * N3 * N4 * N5 ); } + // Test Min reducer with lambda +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + { + typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<6>, Kokkos::IndexType > range_type; + + range_type range( {{ 1, 1, 1, 1, 1, 1 }}, {{ N0, N1, N2, N3, N4, N5 }}, {{ 3, 3, 3, 2, 2, 1 }} ); + + Kokkos::View< double******, ExecSpace > v_in("v_in", N0, N1, N2, N3, N4, N5 ); + + parallel_for( "rank6-init-lambda", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, const int l, const int m, const int n ) { + v_in( i, j, k, l, m, n ) = (i+1) * (j+1) * (k+1) * (l+1) * (m+1) * (n+1) ; + }); + + double min; + + parallel_reduce("rank6-min-reducer", range, KOKKOS_LAMBDA ( const int i, const int j, const int k, const int l, const int m, const int n, double& min_val ) { + min_val = (v_in(i,j,k,l,m,n) < min_val) ? v_in(i,j,k,l,m,n) : min_val; + } + , Kokkos::Min(min) ); + + ASSERT_EQ( min, 64.0 ); + } +#endif +#endif + // Tagged operator test { typedef typename Kokkos::MDRangePolicy< ExecSpace, Kokkos::Rank<6, Iterate::Default, Iterate::Default >, Kokkos::IndexType, InitTag > range_type; diff --git a/lib/kokkos/core/unit_test/TestMDRange_a.hpp b/lib/kokkos/core/unit_test/TestMDRange_a.hpp index 5de5225eb8..308b3a3029 100644 --- a/lib/kokkos/core/unit_test/TestMDRange_a.hpp +++ b/lib/kokkos/core/unit_test/TestMDRange_a.hpp @@ -44,8 +44,12 @@ #include namespace Test { + TEST_F( TEST_CATEGORY , mdrange_5d ) { +#if !defined ( KOKKOS_ENABLE_ROCM ) // MDRange Reduce explicitly handled in its own cpp file TestMDRange_5D< TEST_EXECSPACE >::test_reduce5( 100, 10, 10, 10, 5 ); +#endif TestMDRange_5D< TEST_EXECSPACE >::test_for5( 100, 10, 10, 10, 5 ); } + } diff --git a/lib/kokkos/core/unit_test/TestMDRange_b.hpp b/lib/kokkos/core/unit_test/TestMDRange_b.hpp index 60ece56aab..e714f18395 100644 --- a/lib/kokkos/core/unit_test/TestMDRange_b.hpp +++ b/lib/kokkos/core/unit_test/TestMDRange_b.hpp @@ -45,10 +45,11 @@ namespace Test { - TEST_F( TEST_CATEGORY , mdrange_6d ) { TestMDRange_6D< TEST_EXECSPACE >::test_for6( 10, 10, 10, 10, 5, 5 ); +#if !defined( KOKKOS_ENABLE_ROCM ) // MDRange Reduce explicitly handled in its own cpp file TestMDRange_6D< TEST_EXECSPACE >::test_reduce6( 100, 10, 10, 10, 5, 5 ); +#endif } } diff --git a/lib/kokkos/core/unit_test/TestMDRange_c.hpp b/lib/kokkos/core/unit_test/TestMDRange_c.hpp index 029b1e2b1c..810e1d82bc 100644 --- a/lib/kokkos/core/unit_test/TestMDRange_c.hpp +++ b/lib/kokkos/core/unit_test/TestMDRange_c.hpp @@ -46,8 +46,10 @@ namespace Test { TEST_F( TEST_CATEGORY , mdrange_2d) { - TestMDRange_2D< TEST_EXECSPACE >::test_for2( 100, 100 ); +#if !defined( KOKKOS_ENABLE_ROCM ) // MDRange Reduce explicitly handled in its own cpp file TestMDRange_2D< TEST_EXECSPACE >::test_reduce2( 100, 100 ); +#endif + TestMDRange_2D< TEST_EXECSPACE >::test_for2( 100, 100 ); } TEST_F( TEST_CATEGORY , mdrange_array_reduce ) { diff --git a/lib/kokkos/core/unit_test/TestMDRange_d.hpp b/lib/kokkos/core/unit_test/TestMDRange_d.hpp index 240df9aec0..e25213a289 100644 --- a/lib/kokkos/core/unit_test/TestMDRange_d.hpp +++ b/lib/kokkos/core/unit_test/TestMDRange_d.hpp @@ -44,9 +44,14 @@ #include namespace Test { + TEST_F( TEST_CATEGORY , mdrange_3d) { + TestMDRange_3D< TEST_EXECSPACE >::test_for3( 1, 10, 100 ); TestMDRange_3D< TEST_EXECSPACE >::test_for3( 100, 10, 100 ); +#if !defined( KOKKOS_ENABLE_ROCM ) // MDRange Reduced explicitly handled in its own cpp file + TestMDRange_3D< TEST_EXECSPACE >::test_reduce3( 1, 10, 100 ); TestMDRange_3D< TEST_EXECSPACE >::test_reduce3( 100, 10, 100 ); +#endif } TEST_F( TEST_CATEGORY , mdrange_neg_idx ) { @@ -56,4 +61,5 @@ TEST_F( TEST_CATEGORY , mdrange_neg_idx ) { TestMDRange_5D_NegIdx< TEST_EXECSPACE >::test_5D_negidx( 128, 32, 8, 8, 4 ); TestMDRange_6D_NegIdx< TEST_EXECSPACE >::test_6D_negidx( 128, 32, 8, 8, 4, 2 ); } + } diff --git a/lib/kokkos/core/unit_test/TestMDRange_e.hpp b/lib/kokkos/core/unit_test/TestMDRange_e.hpp index 8162184c9b..a626725352 100644 --- a/lib/kokkos/core/unit_test/TestMDRange_e.hpp +++ b/lib/kokkos/core/unit_test/TestMDRange_e.hpp @@ -44,8 +44,12 @@ #include namespace Test { + TEST_F( TEST_CATEGORY , mdrange_4d ) { +#if !defined( KOKKOS_ENABLE_ROCM ) // MDRange Reduce explicitly handled in its own cpp file TestMDRange_4D< TEST_EXECSPACE >::test_reduce4( 100, 10, 10, 10 ); +#endif TestMDRange_4D< TEST_EXECSPACE >::test_for4( 100, 10, 10, 10 ); } + } diff --git a/lib/kokkos/core/unit_test/TestMemoryPool.hpp b/lib/kokkos/core/unit_test/TestMemoryPool.hpp index 9fb1d900f7..00079e02ee 100644 --- a/lib/kokkos/core/unit_test/TestMemoryPool.hpp +++ b/lib/kokkos/core/unit_test/TestMemoryPool.hpp @@ -626,7 +626,9 @@ TEST_F( TEST_CATEGORY, memory_pool ) TestMemoryPool::test_host_memory_pool_stats<>(); TestMemoryPool::test_memory_pool_v2< TEST_EXECSPACE >(false,false); TestMemoryPool::test_memory_pool_corners< TEST_EXECSPACE >(false,false); +#ifdef KOKKOS_ENABLE_LARGE_MEM_TESTS TestMemoryPool::test_memory_pool_huge< TEST_EXECSPACE >(); +#endif } } diff --git a/lib/kokkos/core/unit_test/TestRange.hpp b/lib/kokkos/core/unit_test/TestRange.hpp index bc0acfb21d..be878046cb 100644 --- a/lib/kokkos/core/unit_test/TestRange.hpp +++ b/lib/kokkos/core/unit_test/TestRange.hpp @@ -60,8 +60,11 @@ struct TestRange { struct VerifyInitTag {}; struct ResetTag {}; struct VerifyResetTag {}; + struct OffsetTag {}; + struct VerifyOffsetTag {}; - int N; + int N; + static const int offset = 13; TestRange( const size_t N_ ) : m_flags( Kokkos::ViewAllocateWithoutInitializing( "flags" ), N_ ), N(N_) {} @@ -117,6 +120,18 @@ struct TestRange { if ( int( 2 * i ) != host_flags( i ) ) ++error_count; } ASSERT_EQ( error_count, int( 0 ) ); + + Kokkos::parallel_for( Kokkos::RangePolicy< ExecSpace, ScheduleType, OffsetTag >( offset, N + offset ), *this ); + Kokkos::parallel_for( std::string("TestKernelFor"), Kokkos::RangePolicy( 0, N ), *this); + + Kokkos::deep_copy(host_flags, m_flags); + + error_count = 0; + for (int i = 0; i < N; ++i) { + if (i + offset != host_flags(i)) + ++error_count; + } + ASSERT_EQ(error_count, int(0)); } KOKKOS_INLINE_FUNCTION @@ -144,9 +159,19 @@ struct TestRange { } } - //---------------------------------------- + KOKKOS_INLINE_FUNCTION + void operator()(const OffsetTag &, const int i) const { + m_flags(i - offset) = i; + } - struct OffsetTag {}; + KOKKOS_INLINE_FUNCTION + void operator()(const VerifyOffsetTag &, const int i) const { + if (i + offset != m_flags(i)) { + printf("TestRange::test_for error at %d != %d\n", i + offset, m_flags(i)); + } + } + + //---------------------------------------- void test_reduce( ) { @@ -158,7 +183,7 @@ struct TestRange { // sum( 0 .. N-1 ) ASSERT_EQ( size_t( ( N - 1 ) * ( N ) / 2 ), size_t( total ) ); - Kokkos::parallel_reduce( Kokkos::RangePolicy< ExecSpace, ScheduleType, OffsetTag>( 0, N ), *this, total ); + Kokkos::parallel_reduce( Kokkos::RangePolicy< ExecSpace, ScheduleType, OffsetTag>( offset, N+offset ), *this, total ); // sum( 1 .. N ) ASSERT_EQ( size_t( ( N ) * ( N + 1 ) / 2 ), size_t( total ) ); } @@ -169,7 +194,7 @@ struct TestRange { KOKKOS_INLINE_FUNCTION void operator()( const OffsetTag &, const int i, value_type & update ) const - { update += 1 + m_flags( i ); } + { update += 1 + m_flags( i-offset ); } //---------------------------------------- diff --git a/lib/kokkos/core/unit_test/TestReduce.hpp b/lib/kokkos/core/unit_test/TestReduce.hpp index 5748df1f17..924d8eb45f 100644 --- a/lib/kokkos/core/unit_test/TestReduce.hpp +++ b/lib/kokkos/core/unit_test/TestReduce.hpp @@ -63,9 +63,11 @@ public: const size_type nwork; + KOKKOS_INLINE_FUNCTION ReduceFunctor( const size_type & arg_nwork ) : nwork( arg_nwork ) {} + KOKKOS_INLINE_FUNCTION ReduceFunctor( const ReduceFunctor & rhs ) : nwork( rhs.nwork ) {} @@ -102,6 +104,7 @@ class ReduceFunctorFinal : public ReduceFunctor< long, DeviceType > { public: typedef typename ReduceFunctor< long, DeviceType >::value_type value_type; + KOKKOS_INLINE_FUNCTION ReduceFunctorFinal( const size_t n ) : ReduceFunctor< long, DeviceType >( n ) {} diff --git a/lib/kokkos/core/unit_test/TestReduceDeviceView.hpp b/lib/kokkos/core/unit_test/TestReduceDeviceView.hpp new file mode 100644 index 0000000000..4f65166e37 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestReduceDeviceView.hpp @@ -0,0 +1,131 @@ +#include + +namespace Test { +namespace { + +struct TestIsAsynchFunctor { + Kokkos::View atomic_test; + TestIsAsynchFunctor(Kokkos::View atomic_test_):atomic_test(atomic_test_){} + + KOKKOS_INLINE_FUNCTION + void operator()(const int) const { + Kokkos::atomic_add(&atomic_test(),1.0); + } +}; + +template +void test_reduce_device_view(int64_t N, PolicyType policy, ReduceFunctor functor) { + + using ExecSpace = TEST_EXECSPACE; + + Kokkos::View result("Result"); + Kokkos::View atomic_test("Atomic"); + int64_t reducer_result, view_result, scalar_result; + + + Kokkos::Timer timer; + + // Establish whether execspace is asynchronous + Kokkos::parallel_for("Test::ReduceDeviceView::TestIsAsynch",Kokkos::RangePolicy(0,1000000), + TestIsAsynchFunctor(atomic_test)); + double time0 = timer.seconds(); + timer.reset(); + ExecSpace::execution_space::fence(); + double time_fence0 = timer.seconds(); + Kokkos::deep_copy(result,0); + timer.reset(); + bool is_async = time0(result)); + double time1 = timer.seconds(); + // Check whether it was asyncronous + timer.reset(); + ExecSpace::execution_space::fence(); + double time_fence1 = timer.seconds(); + Kokkos::deep_copy(reducer_result,result); + Kokkos::deep_copy(result,0); + ASSERT_EQ(N,reducer_result); + timer.reset(); + + + // Test View + Kokkos::parallel_reduce("Test::ReduceDeviceView::TestView",policy, functor, result); + double time2 = timer.seconds(); + // Check whether it was asyncronous + timer.reset(); + ExecSpace::execution_space::fence(); + double time_fence2 = timer.seconds(); + Kokkos::deep_copy(view_result,result); + Kokkos::deep_copy(result,0); + ASSERT_EQ(N,view_result); + timer.reset(); + + + // Test Scalar + Kokkos::parallel_reduce("Test::ReduceDeviceView::TestScalar",policy, functor, scalar_result); + double time3 = timer.seconds(); + + // Check whether it was asyncronous + timer.reset(); + ExecSpace::execution_space::fence(); + double time_fence3 = timer.seconds(); + + ASSERT_EQ(N,scalar_result); + if(is_async) { + ASSERT_TRUE(time1time_fence3); + } + } + +struct RangePolicyFunctor { + KOKKOS_INLINE_FUNCTION + void operator() (const int, int64_t& lsum) const { + lsum += 1; + } +}; + +struct MDRangePolicyFunctor { + KOKKOS_INLINE_FUNCTION + void operator() (const int, const int, const int, int64_t& lsum) const { + lsum += 1; + } +}; + +struct TeamPolicyFunctor { + int M; + TeamPolicyFunctor(int M_):M(M_){} + + KOKKOS_INLINE_FUNCTION + void operator() (const Kokkos::TeamPolicy::member_type& team, int64_t& lsum) const { + for(int i=team.team_rank(); i(0,N),RangePolicyFunctor()); +} + +TEST_F( TEST_CATEGORY, reduce_device_view_mdrange_policy ) +{ + int N=1000*1024*1024; + test_reduce_device_view(N,Kokkos::MDRangePolicy>({0,0,0},{1000,1024,1024}),MDRangePolicyFunctor()); +} + +TEST_F( TEST_CATEGORY, reduce_device_view_team_policy ) +{ + int N=1000*1024*1024; + test_reduce_device_view(N,Kokkos::TeamPolicy(1000*1024,Kokkos::AUTO),TeamPolicyFunctor(1024)); +} + +} // namespace Test + diff --git a/lib/kokkos/core/unit_test/TestReducers.hpp b/lib/kokkos/core/unit_test/TestReducers.hpp index 519e3a80f7..7270ea3375 100644 --- a/lib/kokkos/core/unit_test/TestReducers.hpp +++ b/lib/kokkos/core/unit_test/TestReducers.hpp @@ -477,7 +477,7 @@ struct TestReducers { int reference_loc = -1; for ( int i = 0; i < N; i++ ) { - h_values( i ) = (Scalar) ( rand() % 100000 ); + h_values( i ) = (Scalar) ( rand() % 100000 + 2 ); if ( h_values( i ) < reference_min ) { reference_min = h_values( i ); @@ -485,7 +485,7 @@ struct TestReducers { } else if ( h_values( i ) == reference_min ) { // Make min unique. - h_values( i ) += std::numeric_limits< Scalar >::epsilon(); + h_values( i ) += Scalar(1); } } Kokkos::deep_copy( values, h_values ); @@ -537,7 +537,7 @@ struct TestReducers { int reference_loc = -1; for ( int i = 0; i < N; i++ ) { - h_values( i ) = (Scalar) ( rand() % 100000 ); + h_values( i ) = (Scalar) ( rand() % 100000 + 2 ); if ( h_values( i ) > reference_max ) { reference_max = h_values( i ); @@ -545,7 +545,7 @@ struct TestReducers { } else if ( h_values( i ) == reference_max ) { // Make max unique. - h_values( i ) -= std::numeric_limits< Scalar >::epsilon(); + h_values( i ) -= Scalar(1); } } Kokkos::deep_copy( values, h_values ); @@ -599,7 +599,7 @@ struct TestReducers { int reference_maxloc = -1; for ( int i = 0; i < N; i++ ) { - h_values( i ) = (Scalar) ( rand() % 100000 ); + h_values( i ) = (Scalar) ( rand() % 100000 + 2); } for ( int i = 0; i < N; i++ ) { @@ -609,7 +609,7 @@ struct TestReducers { } else if ( h_values( i ) == reference_max ) { // Make max unique. - h_values( i ) -= std::numeric_limits< Scalar >::epsilon(); + h_values( i ) -= Scalar(1); } } @@ -620,7 +620,7 @@ struct TestReducers { } else if ( h_values( i ) == reference_min ) { // Make min unique. - h_values( i ) += std::numeric_limits< Scalar >::epsilon(); + h_values( i ) += Scalar(1); } } diff --git a/lib/kokkos/core/unit_test/TestScan.hpp b/lib/kokkos/core/unit_test/TestScan.hpp index 5700c21dc6..e021ed09f5 100644 --- a/lib/kokkos/core/unit_test/TestScan.hpp +++ b/lib/kokkos/core/unit_test/TestScan.hpp @@ -69,9 +69,9 @@ struct TestScan { const value_type answer = n & 1 ? ( n * ( ( n + 1 ) / 2 ) ) : ( ( n / 2 ) * ( n + 1 ) ); if ( answer != update ) { - errors()++; + int fail = errors()++; - if ( errors() < 20 ) { + if ( fail < 20 ) { printf( "TestScan(%d,%ld) != %ld\n", iwork, update, answer ); } } @@ -97,6 +97,7 @@ struct TestScan { long long int total = 0; Kokkos::parallel_scan( N, *this, total ); run_check( size_t( ( N+1 )*N/2 ), size_t( total ) ); + check_error(); } TestScan( const WorkSpec & Start , const WorkSpec & N ) @@ -108,6 +109,13 @@ struct TestScan { errors = errors_a; Kokkos::parallel_scan( exec_policy( Start , N ) , *this ); + check_error(); + } + + void check_error() { + int total_errors; + Kokkos::deep_copy(total_errors, errors); + ASSERT_EQ(total_errors,0); } static void test_range( const WorkSpec & begin, const WorkSpec & end ) diff --git a/lib/kokkos/core/unit_test/TestTeam.hpp b/lib/kokkos/core/unit_test/TestTeam.hpp index 2fe615a75a..487a4d581c 100644 --- a/lib/kokkos/core/unit_test/TestTeam.hpp +++ b/lib/kokkos/core/unit_test/TestTeam.hpp @@ -61,7 +61,7 @@ struct TestTeamPolicy { TestTeamPolicy( const size_t league_size ) : m_flags( Kokkos::ViewAllocateWithoutInitializing( "flags" ), - Kokkos::TeamPolicy< ScheduleType, ExecSpace >::team_size_max( *this ), + Kokkos::TeamPolicy< ScheduleType, ExecSpace >(1,1).team_size_max( *this, Kokkos::ParallelReduceTag() ), league_size ) {} struct VerifyInitTag {}; @@ -113,11 +113,14 @@ struct TestTeamPolicy { static void test_for( const size_t league_size ) { TestTeamPolicy functor( league_size ); + typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace > policy_type; + typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace, VerifyInitTag > policy_type_init; - const int team_size = Kokkos::TeamPolicy< ScheduleType, ExecSpace >::team_size_max( functor ); + const int team_size = policy_type(league_size,1).team_size_max( functor, Kokkos::ParallelForTag() ); + const int team_size_init = policy_type_init(league_size,1).team_size_max( functor, Kokkos::ParallelForTag() ); - Kokkos::parallel_for( Kokkos::TeamPolicy< ScheduleType, ExecSpace >( league_size, team_size ), functor ); - Kokkos::parallel_for( Kokkos::TeamPolicy< ScheduleType, ExecSpace, VerifyInitTag >( league_size, team_size ), functor ); + Kokkos::parallel_for( policy_type( league_size, team_size ), functor ); + Kokkos::parallel_for( policy_type_init( league_size, team_size_init ), functor ); test_small_league_size(); } @@ -142,15 +145,19 @@ struct TestTeamPolicy { { TestTeamPolicy functor( league_size ); - const int team_size = Kokkos::TeamPolicy< ScheduleType, ExecSpace >::team_size_max( functor ); + typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace > policy_type; + typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace, ReduceTag > policy_type_reduce; + + const int team_size = policy_type_reduce(league_size,1).team_size_max( functor, Kokkos::ParallelReduceTag() ); + const long N = team_size * league_size; long total = 0; - Kokkos::parallel_reduce( Kokkos::TeamPolicy< ScheduleType, ExecSpace >( league_size, team_size ), functor, total ); + Kokkos::parallel_reduce( policy_type( league_size, team_size ), functor, total ); ASSERT_EQ( size_t( ( N - 1 ) * ( N ) ) / 2, size_t( total ) ); - Kokkos::parallel_reduce( Kokkos::TeamPolicy< ScheduleType, ExecSpace, ReduceTag >( league_size, team_size ), functor, total ); + Kokkos::parallel_reduce( policy_type_reduce( league_size, team_size ), functor, total ); ASSERT_EQ( ( size_t( N ) * size_t( N + 1 ) ) / 2, size_t( total ) ); } }; @@ -177,8 +184,10 @@ public: const size_type nwork; + KOKKOS_INLINE_FUNCTION ReduceTeamFunctor( const size_type & arg_nwork ) : nwork( arg_nwork ) {} + KOKKOS_INLINE_FUNCTION ReduceTeamFunctor( const ReduceTeamFunctor & rhs ) : nwork( rhs.nwork ) {} KOKKOS_INLINE_FUNCTION @@ -244,10 +253,12 @@ public: const unsigned long nsum = nw % 2 ? nw * ( ( nw + 1 ) / 2 ) : ( nw / 2 ) * ( nw + 1 ); - const unsigned team_size = policy_type::team_size_recommended( functor_type( nwork ) ); + policy_type team_exec( nw, 1 ); + + const unsigned team_size = team_exec.team_size_recommended( functor_type( nwork ), Kokkos::ParallelReduceTag() ); const unsigned league_size = ( nwork + team_size - 1 ) / team_size; - policy_type team_exec( league_size, team_size ); + team_exec = policy_type( league_size, team_size ); for ( unsigned i = 0; i < Repeat; ++i ) { result_type tmp( & result[i] ); @@ -370,7 +381,8 @@ public: functor_type functor; - policy_type team_exec( nteam, policy_type::team_size_max( functor ) ); + policy_type team_exec( nteam, 1); + team_exec = policy_type(nteam, team_exec.team_size_max(functor, Kokkos::ParallelReduceTag())); for ( unsigned i = 0; i < Repeat; ++i ) { long int accum = 0; @@ -475,7 +487,8 @@ struct TestSharedTeam { typedef Test::SharedTeamFunctor Functor; typedef Kokkos::View< typename Functor::value_type, Kokkos::HostSpace, Kokkos::MemoryUnmanaged > result_type; - const size_t team_size = Kokkos::TeamPolicy< ScheduleType, ExecSpace >::team_size_max( Functor() ); + const size_t team_size = Kokkos::TeamPolicy< ScheduleType, ExecSpace >(8192, 1).team_size_max( Functor(), + Kokkos::ParallelReduceTag() ); Kokkos::TeamPolicy< ScheduleType, ExecSpace > team_exec( 8192 / team_size, team_size ); @@ -648,16 +661,20 @@ struct TestScratchTeam { typedef Kokkos::View< typename Functor::value_type, Kokkos::HostSpace, Kokkos::MemoryUnmanaged > result_type; typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace > p_type; - const size_t team_size = p_type::team_size_max( Functor() ); - - p_type team_exec( 8192 / team_size, team_size ); typename Functor::value_type error_count = 0; + int thread_scratch_size = Functor::shared_int_array_type::shmem_size( Functor::SHARED_THREAD_COUNT ); + + p_type team_exec = p_type(8192,1).set_scratch_size( 1, Kokkos::PerTeam( Functor::shared_int_array_type::shmem_size( Functor::SHARED_TEAM_COUNT ) ), + Kokkos::PerThread( thread_scratch_size + 3*sizeof(int))); + + const size_t team_size = team_exec.team_size_max( Functor(), Kokkos::ParallelReduceTag() ); + int team_scratch_size = Functor::shared_int_array_type::shmem_size( Functor::SHARED_TEAM_COUNT ) + Functor::shared_int_array_type::shmem_size( 3 * team_size ); - int thread_scratch_size = Functor::shared_int_array_type::shmem_size( Functor::SHARED_THREAD_COUNT ); + team_exec = p_type(8192 / team_size, team_size ); Kokkos::parallel_reduce( team_exec.set_scratch_size( 1, Kokkos::PerTeam( team_scratch_size ), Kokkos::PerThread( thread_scratch_size ) ), @@ -956,7 +973,7 @@ struct TestShmemSize { size_t size = view_type::shmem_size( d1, d2, d3 ); - ASSERT_EQ( size, d1 * d2 * d3 * sizeof( long ) ); + ASSERT_EQ( size, (d1 * d2 * d3 + 1)* sizeof( long ) ); test_layout_stride(); } @@ -973,3 +990,123 @@ struct TestShmemSize { }; } // namespace Test + +/*--------------------------------------------------------------------------*/ + +namespace Test { + +namespace { + +template< class ExecSpace, class ScheduleType > +struct TestTeamBroadcast { + typedef typename Kokkos::TeamPolicy< ScheduleType, ExecSpace >::member_type team_member; + + TestTeamBroadcast( const size_t league_size ) {} + + struct BroadcastTag {}; + + typedef long value_type; + + KOKKOS_INLINE_FUNCTION + void operator()( const team_member &teamMember, value_type &update ) const + { + int lid = teamMember.league_rank(); + int tid = teamMember.team_rank(); + int ts = teamMember.team_size(); + + value_type parUpdate = 0; + value_type value = tid * 3 + 1; + + teamMember.team_broadcast(value, lid%ts); + + Kokkos::parallel_reduce( Kokkos::TeamThreadRange( teamMember, ts ), [&] ( const int j, value_type &teamUpdate ) { + teamUpdate += value; + }, parUpdate ); + + if ( teamMember.team_rank() == 0 ) update += parUpdate; + } + + KOKKOS_INLINE_FUNCTION + void operator()( const BroadcastTag &, const team_member &teamMember, value_type &update ) const + { + int lid = teamMember.league_rank(); + int tid = teamMember.team_rank(); + int ts = teamMember.team_size(); + + value_type parUpdate = 0; + value_type value = tid * 3 + 1; + + teamMember.team_broadcast([&] (value_type & var) { var*=2; }, value, lid%ts); + + Kokkos::parallel_reduce( Kokkos::TeamThreadRange( teamMember, ts ), [&] ( const int j, value_type &teamUpdate ) { + teamUpdate += value; + }, parUpdate ); + + if ( teamMember.team_rank() == 0 ) update += parUpdate; + } + + static void test_teambroadcast( const size_t league_size ) + { + TestTeamBroadcast functor( league_size ); + + typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace > policy_type; + typedef Kokkos::TeamPolicy< ScheduleType, ExecSpace, BroadcastTag > policy_type_f; + + const int team_size = policy_type_f(league_size,1).team_size_max( functor, Kokkos::ParallelReduceTag() ); //printf("team_size=%d\n",team_size); + + //team_broadcast with value + long total = 0; + + Kokkos::parallel_reduce( policy_type( league_size, team_size ), functor, total ); + + value_type expected_result = 0; + for (unsigned int i=0; i +struct TestScratchAlignment { + struct TestScalar { + double x,y,z; + }; + TestScratchAlignment() { + test(true); + test(false); + } + typedef Kokkos::View ScratchView; + typedef Kokkos::View ScratchViewInt; + void test(bool allocate_small) { + int shmem_size = ScratchView::shmem_size(11); + if(allocate_small) shmem_size += ScratchViewInt::shmem_size(1); + Kokkos::parallel_for(Kokkos::TeamPolicy(1,1).set_scratch_size(0,Kokkos::PerTeam(shmem_size)), + KOKKOS_LAMBDA (const typename Kokkos::TeamPolicy::member_type& team) { + if(allocate_small) ScratchViewInt p(team.team_scratch(0),1); + ScratchView a(team.team_scratch(0),11); + if(ptrdiff_t(a.data())%sizeof(TestScalar)!=0) + Kokkos::abort("Error: invalid scratch view alignment\n"); + }); + Kokkos::fence(); + } +}; + +} // namespace + +} // namespace Test + +/*--------------------------------------------------------------------------*/ diff --git a/lib/kokkos/core/unit_test/TestTeamTeamSize.hpp b/lib/kokkos/core/unit_test/TestTeamTeamSize.hpp new file mode 100644 index 0000000000..f9d5add5d0 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestTeamTeamSize.hpp @@ -0,0 +1,146 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include +#include +#include + +#include + +namespace Test { + +namespace { + template + class MyArray { + public: + T values[N]; + KOKKOS_INLINE_FUNCTION + void operator+= (const MyArray& src) { for(int i=0; i + struct FunctorFor { + double static_array[S]; + KOKKOS_INLINE_FUNCTION + void operator() (const typename PolicyType::member_type& team) const { + } + }; + template + struct FunctorReduce { + double static_array[S]; + KOKKOS_INLINE_FUNCTION + void operator() (const typename PolicyType::member_type& team, MyArray& lval) const { + for(int j=0; j policy_type; +typedef Kokkos::TeamPolicy > policy_type_128_8; +typedef Kokkos::TeamPolicy > policy_type_1024_2; + +template +void test_team_policy_max_recommended_static_size(int scratch_size) { + PolicyType p = PolicyType(10000, Kokkos::AUTO, 4).set_scratch_size(0,Kokkos::PerTeam(scratch_size)); + int team_size_max_for = p.team_size_max(FunctorFor(),Kokkos::ParallelForTag()); + int team_size_rec_for = p.team_size_recommended(FunctorFor(),Kokkos::ParallelForTag()); + int team_size_max_reduce = p.team_size_max(FunctorReduce(),Kokkos::ParallelReduceTag()); + int team_size_rec_reduce = p.team_size_recommended(FunctorReduce(),Kokkos::ParallelReduceTag()); + + ASSERT_TRUE( team_size_max_for >= team_size_rec_for ); + ASSERT_TRUE( team_size_max_reduce >= team_size_rec_reduce ); + ASSERT_TRUE( team_size_max_for >= team_size_max_reduce ); + + Kokkos::parallel_for(PolicyType(10000, team_size_max_for, 4).set_scratch_size(0,Kokkos::PerTeam(scratch_size)), + FunctorFor()); + Kokkos::parallel_for(PolicyType(10000, team_size_rec_for, 4).set_scratch_size(0,Kokkos::PerTeam(scratch_size)), + FunctorFor()); + MyArray val; + Kokkos::parallel_reduce(PolicyType(10000, team_size_max_reduce, 4).set_scratch_size(0,Kokkos::PerTeam(scratch_size)), + FunctorReduce(),val); + Kokkos::parallel_reduce(PolicyType(10000, team_size_rec_reduce, 4).set_scratch_size(0,Kokkos::PerTeam(scratch_size)), + FunctorReduce(),val); + Kokkos::fence(); +} + +template +void test_team_policy_max_recommended(int scratch_size) { + test_team_policy_max_recommended_static_size(scratch_size); + test_team_policy_max_recommended_static_size(scratch_size); +} + +TEST_F( TEST_CATEGORY, team_policy_max_recommended ) +{ + int max_scratch_size = policy_type::scratch_size_max(0); + test_team_policy_max_recommended(0); + test_team_policy_max_recommended(max_scratch_size/3); + test_team_policy_max_recommended(max_scratch_size); + test_team_policy_max_recommended(0); + test_team_policy_max_recommended(max_scratch_size/3/8); + test_team_policy_max_recommended(max_scratch_size/8); + test_team_policy_max_recommended(0); + test_team_policy_max_recommended(max_scratch_size/3/2); + test_team_policy_max_recommended(max_scratch_size/2); + + test_team_policy_max_recommended(0); + test_team_policy_max_recommended(max_scratch_size/3); + test_team_policy_max_recommended(max_scratch_size); + test_team_policy_max_recommended(0); + test_team_policy_max_recommended(max_scratch_size/3/8); + test_team_policy_max_recommended(max_scratch_size/8); + test_team_policy_max_recommended(0); + test_team_policy_max_recommended(max_scratch_size/3/2); + test_team_policy_max_recommended(max_scratch_size/2); +} + + +} // namespace Test diff --git a/lib/kokkos/core/unit_test/TestTeamVector.hpp b/lib/kokkos/core/unit_test/TestTeamVector.hpp index 783fde600b..498d156db3 100644 --- a/lib/kokkos/core/unit_test/TestTeamVector.hpp +++ b/lib/kokkos/core/unit_test/TestTeamVector.hpp @@ -227,14 +227,13 @@ struct functor_team_for { functor_team_for( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { - typedef typename ExecutionSpace::scratch_memory_space shmem_space; - typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; - typedef typename shared_int::size_type size_type; - + typedef typename shmem_space::size_type size_type; const size_type shmemSize = team.team_size() * 13; shared_int values = shared_int( team.team_shmem(), shmemSize ); @@ -290,7 +289,9 @@ struct functor_team_reduce { functor_team_reduce( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { @@ -333,7 +334,9 @@ struct functor_team_reduce_reducer { functor_team_reduce_reducer( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { @@ -376,12 +379,12 @@ struct functor_team_vector_for { functor_team_vector_for( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { - typedef typename ExecutionSpace::scratch_memory_space shmem_space; - typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; typedef typename shared_int::size_type size_type; const size_type shmemSize = team.team_size() * 13; @@ -442,7 +445,9 @@ struct functor_team_vector_reduce { Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag; functor_team_vector_reduce( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { @@ -485,7 +490,9 @@ struct functor_team_vector_reduce_reducer { functor_team_vector_reduce_reducer( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { @@ -525,7 +532,11 @@ struct functor_vec_single { typedef ExecutionSpace execution_space; Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag; - functor_vec_single( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} + int nStart; + int nEnd; + + functor_vec_single( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_, const int start_, const int end_ ) : + flag( flag_ ), nStart(start_), nEnd(end_) {} KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { @@ -534,7 +545,7 @@ struct functor_vec_single { // inside a parallel_for and write to it. Scalar value = 0; - Kokkos::parallel_for( Kokkos::ThreadVectorRange( team, 0, 13 ), [&] ( int i ) + Kokkos::parallel_for( Kokkos::ThreadVectorRange( team, nStart, nEnd ), [&] ( int i ) { value = i; // This write is violating Kokkos semantics for nested parallelism. }); @@ -545,12 +556,12 @@ struct functor_vec_single { }, value ); Scalar value2 = 0; - Kokkos::parallel_reduce( Kokkos::ThreadVectorRange( team, 0, 13 ), [&] ( int i, Scalar & val ) + Kokkos::parallel_reduce( Kokkos::ThreadVectorRange( team, nStart, nEnd ), [&] ( int i, Scalar & val ) { val += value; }, value2 ); - if ( value2 != ( value * 13 ) ) { + if ( value2 != ( value * (nEnd-nStart) ) ) { printf( "FAILED vector_single broadcast %i %i %f %f\n", team.league_rank(), team.team_rank(), (double) value2, (double) value ); @@ -568,12 +579,12 @@ struct functor_vec_for { functor_vec_for( Kokkos::View< int, Kokkos::LayoutLeft, ExecutionSpace > flag_ ) : flag( flag_ ) {} - unsigned team_shmem_size( int team_size ) const { return team_size * 13 * sizeof( Scalar ) + 8; } + typedef typename ExecutionSpace::scratch_memory_space shmem_space; + typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; + unsigned team_shmem_size( int team_size ) const { return shared_int::shmem_size(team_size*13); } KOKKOS_INLINE_FUNCTION void operator()( typename policy_type::member_type team ) const { - typedef typename ExecutionSpace::scratch_memory_space shmem_space; - typedef Kokkos::View< Scalar*, shmem_space, Kokkos::MemoryUnmanaged > shared_int; shared_int values = shared_int( team.team_shmem(), team.team_size() * 13 ); @@ -739,23 +750,10 @@ bool test_scalar( int nteams, int team_size, int test ) { functor_vec_red< Scalar, ExecutionSpace >( d_flag ) ); } else if ( test == 1 ) { - // WORKAROUND ROCM/CUDA - #if defined(KOKKOS_ENABLE_CUDA) - #if defined(KOKKOS_IMPL_CUDA_CLANG_WORKAROUND) || defined(KOKKOS_ARCH_PASCAL) - if(!std::is_same::value) - #endif - #endif - #if defined(KOKKOS_ENABLE_ROCM) - if(!std::is_same::value) - #endif Kokkos::parallel_for( Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size, 8 ), functor_vec_red_reducer< Scalar, ExecutionSpace >( d_flag ) ); } else if ( test == 2 ) { - // WORKAROUND ROCM - #if defined(KOKKOS_ENABLE_ROCM) - if(!std::is_same::value) - #endif Kokkos::parallel_for( Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size, 8 ), functor_vec_scan< Scalar, ExecutionSpace >( d_flag ) ); } @@ -765,7 +763,7 @@ bool test_scalar( int nteams, int team_size, int test ) { } else if ( test == 4 ) { Kokkos::parallel_for( "B", Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size, 8 ), - functor_vec_single< Scalar, ExecutionSpace >( d_flag ) ); + functor_vec_single< Scalar, ExecutionSpace >( d_flag, 0, 13 ) ); } else if ( test == 5 ) { Kokkos::parallel_for( Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size ), @@ -776,10 +774,6 @@ bool test_scalar( int nteams, int team_size, int test ) { functor_team_reduce< Scalar, ExecutionSpace >( d_flag ) ); } else if ( test == 7 ) { - // WORKAROUND ROCM - #if defined(KOKKOS_ENABLE_ROCM) - if(!std::is_same::value) - #endif Kokkos::parallel_for( Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size ), functor_team_reduce_reducer< Scalar, ExecutionSpace >( d_flag ) ); } @@ -792,13 +786,13 @@ bool test_scalar( int nteams, int team_size, int test ) { functor_team_vector_reduce< Scalar, ExecutionSpace >( d_flag ) ); } else if ( test == 10 ) { - // WORKAROUND ROCM - #if defined(KOKKOS_ENABLE_ROCM) - if(!std::is_same::value) - #endif Kokkos::parallel_for( Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size, 8 ), functor_team_vector_reduce_reducer< Scalar, ExecutionSpace >( d_flag ) ); } + else if ( test == 11 ) { + Kokkos::parallel_for( "B", Kokkos::TeamPolicy< ExecutionSpace >( nteams, team_size, 8 ), + functor_vec_single< Scalar, ExecutionSpace >( d_flag, 4, 13 ) ); + } Kokkos::deep_copy( h_flag, d_flag ); @@ -946,6 +940,7 @@ TEST_F( TEST_CATEGORY, team_vector ) ASSERT_TRUE( ( TestTeamVector::Test< TEST_EXECSPACE >( 8 ) ) ); ASSERT_TRUE( ( TestTeamVector::Test< TEST_EXECSPACE >( 9 ) ) ); ASSERT_TRUE( ( TestTeamVector::Test< TEST_EXECSPACE >( 10 ) ) ); + ASSERT_TRUE( ( TestTeamVector::Test< TEST_EXECSPACE >( 11 ) ) ); } #endif @@ -955,28 +950,22 @@ TEST_F( TEST_CATEGORY, triple_nested_parallelism ) // With KOKKOS_DEBUG enabled, the functor uses too many registers to run // with a team size of 32 on GPUs, 16 is the max possible (at least on a K80 GPU) // See https://github.com/kokkos/kokkos/issues/1513 -#if defined(KOKKOS_DEBUG) && defined(KOKKOS_ENABLE_CUDA) +#if defined(KOKKOS_ENABLE_DEBUG) && defined(KOKKOS_ENABLE_CUDA) if (!std::is_same::value) { #endif #ifdef KOKKOS_ENABLE_ROCM // ROCm doesn't support TeamSize 32x32 - if (!std::is_same::value) { + if (!std::is_same::value) #endif TestTripleNestedReduce< double, TEST_EXECSPACE >( 8192, 2048, 32, 32 ); -#ifdef KOKKOS_ENABLE_ROCM - } -#endif TestTripleNestedReduce< double, TEST_EXECSPACE >( 8192, 2048, 32, 16 ); -#if defined(KOKKOS_DEBUG) && defined(KOKKOS_ENABLE_CUDA) +#if defined(KOKKOS_ENABLE_DEBUG) && defined(KOKKOS_ENABLE_CUDA) } #endif TestTripleNestedReduce< double, TEST_EXECSPACE >( 8192, 2048, 16, 16 ); #ifdef KOKKOS_ENABLE_ROCM // ROCm doesn't support team sizes not powers of two - if (!std::is_same::value) { + if (!std::is_same::value) #endif TestTripleNestedReduce< double, TEST_EXECSPACE >( 8192, 2048, 7, 16 ); -#ifdef KOKKOS_ENABLE_ROCM - } -#endif } #endif diff --git a/lib/kokkos/core/unit_test/TestViewAPI_a.hpp b/lib/kokkos/core/unit_test/TestViewAPI_a.hpp index efc9ab27b6..ba74331c51 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI_a.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI_a.hpp @@ -45,11 +45,9 @@ namespace Test { -#if !defined(KOKKOS_ENABLE_ROCM) TEST_F( TEST_CATEGORY, view_api_a ) { TestViewAPI< double, TEST_EXECSPACE >::run_test(); } -#endif } diff --git a/lib/kokkos/core/unit_test/TestViewAPI_b.hpp b/lib/kokkos/core/unit_test/TestViewAPI_b.hpp index e006dd9b60..03b41db516 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI_b.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI_b.hpp @@ -45,13 +45,11 @@ namespace Test { -#if !defined(KOKKOS_ENABLE_ROCM) TEST_F( TEST_CATEGORY, view_api_b ) { TestViewAPI< double, TEST_EXECSPACE >::run_test_view_operator_a(); TestViewAPI< double, TEST_EXECSPACE >::run_test_mirror(); TestViewAPI< double, TEST_EXECSPACE >::run_test_scalar(); } -#endif } diff --git a/lib/kokkos/core/unit_test/TestViewAPI_c.hpp b/lib/kokkos/core/unit_test/TestViewAPI_c.hpp index a0f03ff181..d34ae6340e 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI_c.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI_c.hpp @@ -45,12 +45,10 @@ namespace Test { -#if !defined(KOKKOS_ENABLE_ROCM) TEST_F( TEST_CATEGORY, view_api_c ) { TestViewAPI< double, TEST_EXECSPACE >::run_test_deep_copy_empty(); TestViewAPI< double, TEST_EXECSPACE >::run_test_view_operator_b(); } -#endif } diff --git a/lib/kokkos/core/unit_test/TestViewAPI_d.hpp b/lib/kokkos/core/unit_test/TestViewAPI_d.hpp index b984df98b4..38e10381f2 100644 --- a/lib/kokkos/core/unit_test/TestViewAPI_d.hpp +++ b/lib/kokkos/core/unit_test/TestViewAPI_d.hpp @@ -45,7 +45,6 @@ namespace Test { -#if !defined(KOKKOS_ENABLE_ROCM) TEST_F( TEST_CATEGORY, view_api_d ) { TestViewAPI< double, TEST_EXECSPACE >::run_test_const(); @@ -54,6 +53,5 @@ TEST_F( TEST_CATEGORY, view_api_d ) TestViewAPI< double, TEST_EXECSPACE >::run_test_vector(); TestViewAPI< double, TEST_EXECSPACE >::run_test_view_operator_c(); } -#endif } diff --git a/lib/kokkos/core/unit_test/TestViewCopy.hpp b/lib/kokkos/core/unit_test/TestViewCopy.hpp new file mode 100644 index 0000000000..ddcd0ae5ba --- /dev/null +++ b/lib/kokkos/core/unit_test/TestViewCopy.hpp @@ -0,0 +1,183 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include + +#include + +#include + +namespace Test { + +namespace { + +template < typename ExecSpace > +struct TestViewCopy { + + using InExecSpace = ExecSpace; + + static void test_view_copy(const int dim0, const int dim1, const int dim2) + { +#if defined( KOKKOS_ENABLE_CUDA ) || defined( KOKKOS_ENABLE_ROCM ) + // ExecSpace = CudaUVM, CudaHostPinned + // This test will fail at runtime with an illegal memory access if something goes wrong + // Test 1: deep_copy from host_mirror_space to ExecSpace and ExecSpace back to host_mirror_space + { + typedef Kokkos::View Rank4ViewType; + Rank4ViewType view_4; + view_4 = Rank4ViewType("view_4", dim0, dim1, dim2, dim2); + + typedef typename Kokkos::Impl::is_space::host_mirror_space::execution_space host_space_type; + Kokkos::View srcView("srcView", dim2, dim2); + + // Strided dst view + auto dstView = Kokkos::subview(view_4, 0, 0, Kokkos::ALL(), Kokkos::ALL()); + + // host_mirror_space to ExecSpace + Kokkos::deep_copy( dstView, srcView ); + Kokkos::fence(); + + // ExecSpace to host_mirror_space + Kokkos::deep_copy( srcView, dstView ); + Kokkos::fence(); + } + + // Test 2: deep_copy from Cuda to ExecSpace and ExecSpace back to Cuda + { + typedef Kokkos::View Rank4ViewType; + Rank4ViewType view_4; + view_4 = Rank4ViewType("view_4", dim0, dim1, dim2, dim2); + +#if defined( KOKKOS_ENABLE_CUDA ) + typedef typename std::conditional< + Kokkos::Impl::MemorySpaceAccess::accessible, + Kokkos::CudaSpace, + InExecSpace>::type space_type; +#endif +#if defined( KOKKOS_ENABLE_ROCM ) + typedef typename std::conditional< + Kokkos::Impl::MemorySpaceAccess::accessible, + Kokkos::ROCmSpace, + InExecSpace>::type space_type; +#endif + Kokkos::View srcView("srcView", dim2, dim2); + + // Strided dst view + auto dstView = Kokkos::subview(view_4, 0, 0, Kokkos::ALL(), Kokkos::ALL()); + + // Cuda to ExecSpace + Kokkos::deep_copy( dstView, srcView ); + Kokkos::fence(); + + // ExecSpace to Cuda + Kokkos::deep_copy( srcView, dstView ); + Kokkos::fence(); + } + + // Test 3: deep_copy from host_space to ExecSpace and ExecSpace back to host_space + { + typedef Kokkos::View Rank4ViewType; + Rank4ViewType view_4; + view_4 = Rank4ViewType("view_4", dim0, dim1, dim2, dim2); + + typedef Kokkos::HostSpace host_space_type; + Kokkos::View srcView("srcView", dim2, dim2); + + // Strided dst view + auto dstView = Kokkos::subview(view_4, 0, 0, Kokkos::ALL(), Kokkos::ALL()); + + // host_space to ExecSpace + Kokkos::deep_copy( dstView, srcView ); + Kokkos::fence(); + + // ExecSpace to host_space + Kokkos::deep_copy( srcView, dstView ); + Kokkos::fence(); + } +#endif + } // end test_view_copy + +}; // end struct + +} // namespace + +TEST_F( TEST_CATEGORY , view_copy_tests ) { + //Only include this file to be compiled with CudaUVM and CudaHostPinned + TestViewCopy< TEST_EXECSPACE >::test_view_copy(4,2,3); + TestViewCopy< TEST_EXECSPACE >::test_view_copy(4,2,0); +} + +TEST_F( TEST_CATEGORY , view_copy_degenerated ) { + //Only include this file to be compiled with CudaUVM and CudaHostPinned + Kokkos::View> v_um_def_1; + Kokkos::View> v_um_1( reinterpret_cast(-1), 0 ); + Kokkos::View v_m_def_1; + Kokkos::View v_m_1("v_m_1", 0); + + Kokkos::View> v_um_def_2; + Kokkos::View> v_um_2( reinterpret_cast(-1), 0 ); + Kokkos::View v_m_def_2; + Kokkos::View v_m_2("v_m_2", 0); + + Kokkos::deep_copy(v_um_def_1, v_um_def_2); + Kokkos::deep_copy(v_um_def_1, v_um_2); + Kokkos::deep_copy(v_um_def_1, v_m_def_2); + Kokkos::deep_copy(v_um_def_1, v_m_2); + + Kokkos::deep_copy(v_um_1, v_um_def_2); + Kokkos::deep_copy(v_um_1, v_um_2); + Kokkos::deep_copy(v_um_1, v_m_def_2); + Kokkos::deep_copy(v_um_1, v_m_2); + + Kokkos::deep_copy(v_m_def_1, v_um_def_2); + Kokkos::deep_copy(v_m_def_1, v_um_2); + Kokkos::deep_copy(v_m_def_1, v_m_def_2); + Kokkos::deep_copy(v_m_def_1, v_m_2); + + Kokkos::deep_copy(v_m_1, v_um_def_2); + Kokkos::deep_copy(v_m_1, v_um_2); + Kokkos::deep_copy(v_m_1, v_m_def_2); + Kokkos::deep_copy(v_m_1, v_m_2); +} + +} // namespace Test diff --git a/lib/kokkos/core/unit_test/TestViewLayoutStrideAssignment.hpp b/lib/kokkos/core/unit_test/TestViewLayoutStrideAssignment.hpp new file mode 100644 index 0000000000..3185fa5473 --- /dev/null +++ b/lib/kokkos/core/unit_test/TestViewLayoutStrideAssignment.hpp @@ -0,0 +1,740 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include + +#include +#include +#include +#include + +#include + +namespace Test { + +TEST_F( TEST_CATEGORY , view_layoutstride_left_to_layoutleft_assignment ) +{ + typedef TEST_EXECSPACE exec_space ; + + auto t = time(0); + srand(t);// Use current time as seed for random generator + printf("view_layoutstride_left_to_layoutleft_assignment: srand(%lu)\n",size_t(t)); + + { // Assignment of rank-1 LayoutLeft = LayoutStride + int ndims = 1; + int dims [] = {10}; + int order [] = {0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double*, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double*, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double*, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double**, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double**, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double***, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double***, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double****, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double****, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double*****, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double*****, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double******, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double******, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double*******, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double*******, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double********, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double********, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double*, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double*, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double**, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double**, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double***, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double***, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double****, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double****, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double*****, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double*****, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double******, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double******, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double*******, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double*******, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double********, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst = src; + + Kokkos::View< double********, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double*, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst; + + dst = src; + + Kokkos::View< double*, Kokkos::LayoutLeft, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double**, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-3 LayoutLeft = LayoutStride (LayoutRight compatible) + int ndims = 3; + int dims [] = {10,9,8}; + int order [] = {2,1,0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double***, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double***, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-4 LayoutLeft = LayoutStride (LayoutRight compatible) + int ndims = 4; + int dims [] = {10,9,8,7}; + int order [] = {3,2,1,0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double****, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double****, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-5 LayoutLeft = LayoutStride (LayoutRight compatible) + int ndims = 5; + int dims [] = {10,9,8,7,6}; + int order [] = {4,3,2,1,0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double*****, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double*****, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-6 LayoutLeft = LayoutStride (LayoutRight compatible) + int ndims = 6; + int dims [] = {10,9,8,7,6,5}; + int order [] = {5,4,3,2,1,0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double******, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double******, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-7 LayoutLeft = LayoutStride (LayoutRight compatible) + int ndims = 7; + int dims [] = {10,9,8,7,6,5,4}; + int order [] = {6,5,4,3,2,1,0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double*******, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double*******, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-8 LayoutLeft = LayoutStride (LayoutRight compatible) + int ndims = 8; + int dims [] = {10,9,8,7,6,5,4,3}; + int order [] = {7,6,5,4,3,2,1,0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double********, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double********, Kokkos::LayoutLeft, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + +} + +TEST_F( TEST_CATEGORY , view_layoutstride_left_to_layoutright_assignment ) +{ + typedef TEST_EXECSPACE exec_space ; + + auto t = time(0); + srand(t);// Use current time as seed for random generator + printf("view_layoutstride_left_to_layoutright_assignment: srand(%lu)\n",size_t(t)); + + { // Assignment of rank-1 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 1; + int dims [] = {10}; + int order [] = {0}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double*, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double*, Kokkos::LayoutStride, exec_space >::HostMirror h_src = Kokkos::create_mirror_view( src ); + + for(size_t i=0; i dst; + + dst = src; + + Kokkos::View< double*, Kokkos::LayoutRight, exec_space >::HostMirror h_dst = Kokkos::create_mirror_view( dst ); + + Kokkos::deep_copy( h_dst, dst ); + + bool test = true; + for(size_t i=0; i src("LayoutStride", layout); + + Kokkos::View< double**, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-3 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 3; + int dims [] = {10,9,8}; + int order [] = {0,1,2}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double***, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double***, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-4 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 4; + int dims [] = {10,9,8,7}; + int order [] = {0,1,2,3}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double****, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double****, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-5 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 5; + int dims [] = {10,9,8,7,6}; + int order [] = {0,1,2,3,4}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double*****, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double*****, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-6 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 6; + int dims [] = {10,9,8,7,6,5}; + int order [] = {0,1,2,3,4,5}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double******, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double******, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-7 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 7; + int dims [] = {10,9,8,7,6,5,4}; + int order [] = {0,1,2,3,4,5,6}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double*******, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double*******, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + { // Assignment of rank-8 LayoutRight = LayoutStride (LayoutLeft compatible) + int ndims = 8; + int dims [] = {10,9,8,7,6,5,4,3}; + int order [] = {0,1,2,3,4,5,6,7}; + Kokkos::LayoutStride layout = Kokkos::LayoutStride::order_dimensions(ndims, order, dims); + Kokkos::View< double********, Kokkos::LayoutStride, exec_space > src("LayoutStride", layout); + + Kokkos::View< double********, Kokkos::LayoutRight, exec_space > dst; + + ::testing::FLAGS_gtest_death_test_style = "threadsafe"; + ASSERT_DEATH({dst=src;}, "View assignment must have compatible layouts"); + } + +} + +} + diff --git a/lib/kokkos/core/unit_test/TestViewLayoutTiled.hpp b/lib/kokkos/core/unit_test/TestViewLayoutTiled.hpp new file mode 100644 index 0000000000..e765e8b06d --- /dev/null +++ b/lib/kokkos/core/unit_test/TestViewLayoutTiled.hpp @@ -0,0 +1,1215 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include + +#include + +#include +#include + +#include +#include + +namespace Test { + +#ifndef KOKKOS_ENABLE_DEPRECATED_CODE +namespace { + +template +struct TestViewLayoutTiled { + + typedef double Scalar; + + static constexpr int T0 = 2; + static constexpr int T1 = 4; + static constexpr int T2 = 4; + static constexpr int T3 = 2; + static constexpr int T4 = 2; + static constexpr int T5 = 2; + static constexpr int T6 = 2; + static constexpr int T7 = 2; + + // Rank 2 + typedef Kokkos::Experimental::LayoutTiled LayoutLL_2D_2x4; + typedef Kokkos::Experimental::LayoutTiled LayoutRL_2D_2x4; + typedef Kokkos::Experimental::LayoutTiled LayoutLR_2D_2x4; + typedef Kokkos::Experimental::LayoutTiled LayoutRR_2D_2x4; + + // Rank 3 + typedef Kokkos::Experimental::LayoutTiled LayoutLL_3D_2x4x4; + typedef Kokkos::Experimental::LayoutTiled LayoutRL_3D_2x4x4; + typedef Kokkos::Experimental::LayoutTiled LayoutLR_3D_2x4x4; + typedef Kokkos::Experimental::LayoutTiled LayoutRR_3D_2x4x4; + + // Rank 4 + typedef Kokkos::Experimental::LayoutTiled LayoutLL_4D_2x4x4x2; + typedef Kokkos::Experimental::LayoutTiled LayoutRL_4D_2x4x4x2; + typedef Kokkos::Experimental::LayoutTiled LayoutLR_4D_2x4x4x2; + typedef Kokkos::Experimental::LayoutTiled LayoutRR_4D_2x4x4x2; + + + static void test_view_layout_tiled_2d( const int N0, const int N1 ) + { +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + const int FT = T0*T1; + + const int NT0 = int( std::ceil( N0 / T0 ) ); + const int NT1 = int( std::ceil( N1 / T1 ) ); + // Test create_mirror_view, deep_copy + // Create LL View + { + typedef typename Kokkos::View< Scalar**, LayoutLL_2D_2x4, ExecSpace > ViewType; + ViewType v("v", N0, N1); + + typename ViewType::HostMirror hv = Kokkos::create_mirror_view(v); + + // Initialize host-view + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + hv(ti*T0 + i, tj*T1+j) = ( ti + tj*NT0 )*FT + ( i + j*T0 ); + } } + } } + + // copy to device + Kokkos::deep_copy(v, hv); + + Kokkos::MDRangePolicy< Kokkos::Rank<2, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, ExecSpace > mdrangepolicy( {0,0}, {NT0, NT1}, {T0,T1} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 2 LL", mdrangepolicy, + KOKKOS_LAMBDA (const int ti, const int tj) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( (ti*T0 + i < N0) && (tj*T1 + j < N1) ) { v(ti*T0 + i, tj*T1+j) += 1; } + } } + }); + + Kokkos::deep_copy(hv, v); + + long counter_subview = 0; + long counter_inc = 0; + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( hv, ti, tj ); + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j) != hv(ti*T0+i, tj*T1+j) ) { ++counter_subview; } + if ( tile_subview(i,j) != (( ti + tj*NT0 )*FT + ( i + j*T0 ) + 1 )) { ++counter_inc; } + } } + } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } + + // Create RL View + { + typedef typename Kokkos::View< Scalar**, LayoutRL_2D_2x4, ExecSpace > ViewType; + Kokkos::View< Scalar**, LayoutRL_2D_2x4, ExecSpace > v("v", N0, N1); + + typename ViewType::HostMirror hv = Kokkos::create_mirror_view(v); + + // Initialize host-view + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + hv(ti*T0 + i, tj*T1+j) = ( ti*NT1 + tj )*FT + ( i + j*T0 ); + } } + } } + + // copy to device + Kokkos::deep_copy(v, hv); + + Kokkos::MDRangePolicy< Kokkos::Rank<2, Kokkos::Iterate::Right, Kokkos::Iterate::Left>, ExecSpace > mdrangepolicy( {0,0}, {NT0, NT1}, {T0,T1} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 2 RL", mdrangepolicy, + KOKKOS_LAMBDA (const int ti, const int tj) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( (ti*T0 + i < N0) && (tj*T1 + j < N1) ) { v(ti*T0 + i, tj*T1+j) += 1; } + } } + }); + + Kokkos::deep_copy(hv, v); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + auto tile_subview = Kokkos::tile_subview( hv, ti, tj ); + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j) != hv(ti*T0+i, tj*T1+j) ) { ++counter_subview; } + if ( tile_subview(i,j) != (( ti*NT1 + tj )*FT + ( i + j*T0 ) + 1 )) { ++counter_inc; } + } } + } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create LR View + { + typedef typename Kokkos::View< Scalar**, LayoutLR_2D_2x4, ExecSpace > ViewType; + Kokkos::View< Scalar**, LayoutLR_2D_2x4, ExecSpace > v("v", N0, N1); + + typename ViewType::HostMirror hv = Kokkos::create_mirror_view(v); + + // Initialize host-view + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + hv(ti*T0 + i, tj*T1+j) = ( ti + tj*NT0 )*FT + ( i*T1 + j ); + } } + } } + + // copy to device + Kokkos::deep_copy(v, hv); + + Kokkos::MDRangePolicy< Kokkos::Rank<2, Kokkos::Iterate::Left, Kokkos::Iterate::Right>, ExecSpace > mdrangepolicy( {0,0}, {NT0, NT1}, {T0,T1} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 2 LR", mdrangepolicy, + KOKKOS_LAMBDA (const int ti, const int tj) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( (ti*T0 + i < N0) && (tj*T1 + j < N1) ) { v(ti*T0 + i, tj*T1+j) += 1; } + } } + }); + + Kokkos::deep_copy(hv, v); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( hv, ti, tj ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + if ( tile_subview(i,j) != hv(ti*T0+i, tj*T1+j) ) { ++counter_subview; } + if ( tile_subview(i,j) != ( ( ti + tj*NT0 )*FT + ( i*T1 + j ) + 1 ) ) { ++counter_inc; } + } } + } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create RR View + { + typedef typename Kokkos::View< Scalar**, LayoutRR_2D_2x4, ExecSpace > ViewType; + Kokkos::View< Scalar**, LayoutRR_2D_2x4, ExecSpace > v("v", N0, N1); + + typename ViewType::HostMirror hv = Kokkos::create_mirror_view(v); + + // Initialize host-view + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + hv(ti*T0 + i, tj*T1+j) = ( ti*NT1 + tj )*FT + ( i*T1 + j ); + } } + } } + + // copy to device + Kokkos::deep_copy(v, hv); + + Kokkos::MDRangePolicy< Kokkos::Rank<2, Kokkos::Iterate::Left, Kokkos::Iterate::Right>, ExecSpace > mdrangepolicy( {0,0}, {NT0, NT1}, {T0,T1} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 2 LR", mdrangepolicy, + KOKKOS_LAMBDA (const int ti, const int tj) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( (ti*T0 + i < N0) && (tj*T1 + j < N1) ) { v(ti*T0 + i, tj*T1+j) += 1; } + } } + }); + + Kokkos::deep_copy(hv, v); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + auto tile_subview = Kokkos::tile_subview( hv, ti, tj ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + if ( tile_subview(i,j) != hv(ti*T0+i, tj*T1+j) ) { ++counter_subview; } + if ( tile_subview(i,j) != ( ( ti*NT1 + tj )*FT + ( i*T1 + j ) + 1 ) ) { ++counter_inc; } + } } + } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope +#endif +#endif + } // end test_view_layout_tiled_2d + + + static void test_view_layout_tiled_3d( const int N0, const int N1, const int N2 ) + { +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + + const int FT = T0*T1*T2; + + const int NT0 = int( std::ceil( N0 / T0 ) ); + const int NT1 = int( std::ceil( N1 / T1 ) ); + const int NT2 = int( std::ceil( N2 / T2 ) ); + + // Create LL View + { + typedef Kokkos::View< Scalar***, LayoutLL_3D_2x4x4, ExecSpace > ViewType; + Kokkos::View< Scalar***, LayoutLL_3D_2x4x4, ExecSpace > dv("dv", N0, N1, N2); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti + tj*NT0 + tk*N0*N1 )*FT + ( i + j*T0 + k*T0*T1 ); + } } } + } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<3, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, ExecSpace > mdrangepolicy( {0,0,0}, {N0,N1,N2}, {T0,T1,T2} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 3 LL", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k) { + dv(i,j,k) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter_subview; } + if ( tile_subview(i,j,k) != ( ( ti + tj*NT0 + tk*N0*N1 )*FT + ( i + j*T0 + k*T0*T1 ) + 1 ) ) { ++counter_inc; } + } } } + } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create RL View + { + typedef Kokkos::View< Scalar***, LayoutRL_3D_2x4x4, ExecSpace > ViewType; + Kokkos::View< Scalar***, LayoutRL_3D_2x4x4, ExecSpace > dv("dv", N0, N1, N2); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i + j*T0 + k*T0*T1 ); + } } } + } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<3, Kokkos::Iterate::Right, Kokkos::Iterate::Left>, ExecSpace > mdrangepolicy( {0,0,0}, {N0,N1,N2}, {T0,T1,T2} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 3 RL", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k) { + dv(i,j,k) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter_subview; } + if ( tile_subview(i,j,k) != ( ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i + j*T0 + k*T0*T1 ) + 1 ) ) { ++counter_inc; } + } } } + } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create LR View + { + typedef Kokkos::View< Scalar***, LayoutLR_3D_2x4x4, ExecSpace > ViewType; + Kokkos::View< Scalar***, LayoutLR_3D_2x4x4, ExecSpace > dv("dv", N0, N1, N2); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti + tj*NT0 + tk*NT0*NT1 )*FT + ( i*T1*T2 + j*T2 + k ); + } } } + } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<3, Kokkos::Iterate::Left, Kokkos::Iterate::Right>, ExecSpace > mdrangepolicy( {0,0,0}, {N0,N1,N2}, {T0,T1,T2} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 3 LR", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k) { + dv(i,j,k) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter_subview; } + if ( tile_subview(i,j,k) != ( ( ti + tj*NT0 + tk*NT0*NT1 )*FT + ( i*T1*T2 + j*T2 + k ) + 1 ) ) { ++counter_inc; } + } } } + } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create RR View + { + typedef Kokkos::View< Scalar***, LayoutRR_3D_2x4x4, ExecSpace > ViewType; + Kokkos::View< Scalar***, LayoutRR_3D_2x4x4, ExecSpace > dv("dv", N0, N1, N2); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i*T1*T2 + j*T2 + k ); + } } } + } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<3, Kokkos::Iterate::Right, Kokkos::Iterate::Right>, ExecSpace > mdrangepolicy( {0,0,0}, {N0,N1,N2}, {T0,T1,T2} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 3 RR", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k) { + dv(i,j,k) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter_subview; } + if ( tile_subview(i,j,k) != ( ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i*T1*T2 + j*T2 + k ) + 1 ) ) { ++counter_inc; } + } } } + } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope +#endif +#endif + } // end test_view_layout_tiled_3d + + + static void test_view_layout_tiled_4d( const int N0, const int N1, const int N2, const int N3 ) + { +#if defined( KOKKOS_ENABLE_CXX11_DISPATCH_LAMBDA ) +#if !defined(KOKKOS_ENABLE_CUDA) || ( 8000 <= CUDA_VERSION ) + const int FT = T0*T1*T2*T3; + + const int NT0 = int( std::ceil( N0 / T0 ) ); + const int NT1 = int( std::ceil( N1 / T1 ) ); + const int NT2 = int( std::ceil( N2 / T2 ) ); + const int NT3 = int( std::ceil( N3 / T3 ) ); + + // Create LL View + { + typedef Kokkos::View< Scalar****, LayoutLL_4D_2x4x4x2, ExecSpace > ViewType; + Kokkos::View< Scalar****, LayoutLL_4D_2x4x4x2, ExecSpace > dv("dv", N0, N1, N2, N3); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti + tj*NT0 + tk*N0*N1 + tl*N0*N1*N2 )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ); + } } } } + } } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<4, Kokkos::Iterate::Left, Kokkos::Iterate::Left>, ExecSpace > mdrangepolicy( {0,0,0,0}, {N0,N1,N2,N3}, {T0,T1,T2,T3} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 4 LL", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k, const int l) { + dv(i,j,k,l) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter_subview; } + if ( tile_subview(i,j,k,l) != ( ( ti + tj*NT0 + tk*N0*N1 + tl*N0*N1*N2 )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ) + 1 ) ) { ++counter_inc; } + } } } } + } } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create RL View + { + typedef Kokkos::View< Scalar****, LayoutRL_4D_2x4x4x2, ExecSpace > ViewType; + Kokkos::View< Scalar****, LayoutRL_4D_2x4x4x2, ExecSpace > dv("dv", N0, N1, N2, N3); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti*NT1*NT2*N3 + tj*NT2*N3 + tk*N3 + tl )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ); + } } } } + } } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<4, Kokkos::Iterate::Right, Kokkos::Iterate::Left>, ExecSpace > mdrangepolicy( {0,0,0,0}, {N0,N1,N2,N3}, {T0,T1,T2,T3} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 4 RL", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k, const int l) { + dv(i,j,k,l) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter_subview; } + if ( tile_subview(i,j,k,l) != ( ( ti*NT1*NT2*N3 + tj*NT2*N3 + tk*N3 + tl )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ) + 1 ) ) { ++counter_inc; } + } } } } + } } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create LR View + { + typedef Kokkos::View< Scalar****, LayoutLR_4D_2x4x4x2, ExecSpace > ViewType; + Kokkos::View< Scalar****, LayoutLR_4D_2x4x4x2, ExecSpace > dv("dv", N0, N1, N2, N3); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti + tj*NT0 + tk*NT0*NT1 + tl*NT0*NT1*NT2 )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ); + } } } } + } } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<4, Kokkos::Iterate::Left, Kokkos::Iterate::Right>, ExecSpace > mdrangepolicy( {0,0,0,0}, {N0,N1,N2,N3}, {T0,T1,T2,T3} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 4 LR", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k, const int l) { + dv(i,j,k,l) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter_subview; } + if ( tile_subview(i,j,k,l) != ( ( ti + tj*NT0 + tk*NT0*NT1 + tl*NT0*NT1*NT2 )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ) + 1 ) ) { ++counter_inc; } + } } } } + } } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope + + // Create RR View + { + typedef Kokkos::View< Scalar****, LayoutRR_4D_2x4x4x2, ExecSpace > ViewType; + Kokkos::View< Scalar****, LayoutRR_4D_2x4x4x2, ExecSpace > dv("dv", N0, N1, N2, N3); + + typename ViewType::HostMirror v = Kokkos::create_mirror_view(dv); + + // Initialize on host + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti*NT1*NT2*NT3 + tj*NT2*NT3 + tk*NT3 + tl )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ); + } } } } + } } } } + + // copy to device + Kokkos::deep_copy(dv, v); + + Kokkos::MDRangePolicy< Kokkos::Rank<4, Kokkos::Iterate::Right, Kokkos::Iterate::Right>, ExecSpace > mdrangepolicy( {0,0,0,0}, {N0,N1,N2,N3}, {T0,T1,T2,T3} ); + + // iterate by tile + Kokkos::parallel_for( "ViewTile rank 4 RR", mdrangepolicy, + KOKKOS_LAMBDA (const int i, const int j, const int k, const int l) { + dv(i,j,k,l) += 1; + }); + + Kokkos::deep_copy(v, dv); + + long counter_subview = 0; + long counter_inc = 0; + + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter_subview; } + if ( tile_subview(i,j,k,l) != ( ( ti*NT1*NT2*NT3 + tj*NT2*NT3 + tk*NT3 + tl )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ) + 1 ) ) { ++counter_inc; } + } } } } + } } } } + ASSERT_EQ(counter_subview, long(0)); + ASSERT_EQ(counter_inc, long(0)); + } // end scope +#endif +#endif + } // end test_view_layout_tiled_4d + + + static void test_view_layout_tiled_subtile_2d( const int N0, const int N1 ) + { + const int FT = T0*T1; + + const int NT0 = int( std::ceil( N0 / T0 ) ); + const int NT1 = int( std::ceil( N1 / T1 ) ); + + // Counter to check for errors at the end + long counter[4] = {0}; + + // Create LL View + { + Kokkos::View< Scalar**, LayoutLL_2D_2x4, Kokkos::HostSpace > v("v", N0, N1); + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j) = ( ti + tj*NT0 )*FT + ( i + j*T0 ); + } } + } } + + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj ); + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j) != v(ti*T0+i, tj*T1+j) ) { ++counter[0]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1 = " << ti*T0 + i << "," << tj*T1 + j << std::endl; + std::cout << "ti,tj,i,j: " << ti << "," << tj << "," << i << "," << j << " v = " << v(ti*T0 + i, tj*T1+j) << " flat idx = " << ( ti + tj*NT0 )*FT + ( i + j*T0 ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j) << std::endl; +#endif + } } + } } + } // end scope + + // Create RL View + { + Kokkos::View< Scalar**, LayoutRL_2D_2x4, Kokkos::HostSpace > v("v", N0, N1); + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j) = ( ti*NT1 + tj )*FT + ( i + j*T0 ); + } } + } } + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj ); + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j) != v(ti*T0+i, tj*T1+j) ) { ++counter[1]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1 = " << ti*T0 + i << "," << tj*T1 + j << std::endl; + std::cout << "ti,tj,i,j: " << ti << "," << tj << "," << i << "," << j << " v = " << v(ti*T0 + i, tj*T1+j) << " flat idx = " << ( ti*NT1 + tj )*FT + ( i + j*T0 ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j) << std::endl; +#endif + } } + } } + } // end scope + + // Create LR View + { + Kokkos::View< Scalar**, LayoutLR_2D_2x4, Kokkos::HostSpace > v("v", N0, N1); + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + v(ti*T0 + i, tj*T1+j) = ( ti + tj*NT0 )*FT + ( i*T1 + j ); + } } + } } + + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + if ( tile_subview(i,j) != v(ti*T0+i, tj*T1+j) ) { ++counter[2]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1 = " << ti*T0 + i << "," << tj*T1 + j << std::endl; + std::cout << "ti,tj,i,j: " << ti << "," << tj << "," << i << "," << j << " v = " << v(ti*T0 + i, tj*T1+j) << " flat idx = " << ( ti + tj*NT0 )*FT + ( i*T1 + j ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j) << std::endl; +#endif + } } + } } + } // end scope + + // Create RR View + { + Kokkos::View< Scalar**, LayoutRR_2D_2x4, Kokkos::HostSpace > v("v", N0, N1); + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + v(ti*T0 + i, tj*T1+j) = ( ti*NT1 + tj )*FT + ( i*T1 + j ); + } } + } } + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + if ( tile_subview(i,j) != v(ti*T0+i, tj*T1+j) ) { ++counter[3]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1 = " << ti*T0 + i << "," << tj*T1 + j << std::endl; + std::cout << "ti,tj,i,j: " << ti << "," << tj << "," << i << "," << j << " v = " << v(ti*T0 + i, tj*T1+j) << " flat idx = " << ( ti*NT1 + tj )*FT + ( i*T1 + j ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } + } } + } // end scope + +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "subview_tile vs view errors:\n" + << " LL: " << counter[0] + << " RL: " << counter[1] + << " LR: " << counter[2] + << " RR: " << counter[3] + << std::endl; +#endif + + ASSERT_EQ(counter[0], long(0)); + ASSERT_EQ(counter[1], long(0)); + ASSERT_EQ(counter[2], long(0)); + ASSERT_EQ(counter[3], long(0)); + } // end test_view_layout_tiled_subtile_2d + + + static void test_view_layout_tiled_subtile_3d( const int N0, const int N1, const int N2 ) + { + + const int FT = T0*T1*T2; + + const int NT0 = int( std::ceil( N0 / T0 ) ); + const int NT1 = int( std::ceil( N1 / T1 ) ); + const int NT2 = int( std::ceil( N2 / T2 ) ); + + // Counter to check for errors at the end + long counter[4] = {0}; + // Create LL View + { + Kokkos::View< Scalar***, LayoutLL_3D_2x4x4, Kokkos::HostSpace > v("v", N0, N1, N2); + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti + tj*NT0 + tk*N0*N1 )*FT + ( i + j*T0 + k*T0*T1 ); + } } } + } } } + + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter[0]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << std::endl; + std::cout << "ti,tj,tk,i,j,k: " << ti << "," << tj << "," << tk << "," << i << "," << j << "," << k << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k) << " flat idx = " << ( ti + tj*NT0 + tk*N0*N1 )*FT + ( i + j*T0 + k*T0*T1 ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } + } } } + } // end scope + + // Create RL View + { + Kokkos::View< Scalar***, LayoutRL_3D_2x4x4, Kokkos::HostSpace > v("v", N0, N1, N2); + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i + j*T0 + k*T0*T1 ); + } } } + } } } + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter[1]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << std::endl; + std::cout << "ti,tj,tk,i,j,k: " << ti << "," << tj << "," << tk << "," << i << "," << j << "," << k << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k) << " flat idx = " << ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i + j*T0 + k*T0*T1 ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k) << std::endl; +#endif + } } } + } } } + } // end scope + + // Create LR View + { + Kokkos::View< Scalar***, LayoutLR_3D_2x4x4, Kokkos::HostSpace > v("v", N0, N1, N2); + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti + tj*NT0 + tk*NT0*NT1 )*FT + ( i*T1*T2 + j*T2 + k ); + } } } + } } } + + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter[2]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << std::endl; + std::cout << "ti,tj,tk,i,j,k: " << ti << "," << tj << "," << tk << "," << i << "," << j << "," << k << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k) << " flat idx = " << ( ti + tj*NT0 + tk*NT0*NT1 )*FT + ( i*T1*T2 + j*T2 + k ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } + } } } + } // end scope + + // Create RR View + { + Kokkos::View< Scalar***, LayoutRR_3D_2x4x4, Kokkos::HostSpace > v("v", N0, N1, N2); + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k) = ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i*T1*T2 + j*T2 + k ); + } } } + } } } + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + if ( tile_subview(i,j,k) != v(ti*T0+i, tj*T1+j, tk*T2+k) ) { ++counter[3]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << std::endl; + std::cout << "ti,tj,tk,i,j,k: " << ti << "," << tj << "," << tk << "," << i << "," << j << "," << k << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k) << " flat idx = " << ( ti*NT1*NT2 + tj*NT2 + tk )*FT + ( i*T1*T2 + j*T2 + k ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } + } } } + } // end scope + +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "subview_tile vs view errors:\n" + << " LL: " << counter[0] + << " RL: " << counter[1] + << " LR: " << counter[2] + << " RR: " << counter[3] + << std::endl; +#endif + + ASSERT_EQ(counter[0], long(0)); + ASSERT_EQ(counter[1], long(0)); + ASSERT_EQ(counter[2], long(0)); + ASSERT_EQ(counter[3], long(0)); + + } // end test_view_layout_tiled_subtile_3d + + + static void test_view_layout_tiled_subtile_4d( const int N0, const int N1, const int N2, const int N3 ) + { + const int FT = T0*T1*T2*T3; + + const int NT0 = int( std::ceil( N0 / T0 ) ); + const int NT1 = int( std::ceil( N1 / T1 ) ); + const int NT2 = int( std::ceil( N2 / T2 ) ); + const int NT3 = int( std::ceil( N3 / T3 ) ); + + // Counter to check for errors at the end + long counter[4] = {0}; + // Create LL View + { + Kokkos::View< Scalar****, LayoutLL_4D_2x4x4x2, Kokkos::HostSpace > v("v", N0, N1, N2, N3); + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti + tj*NT0 + tk*N0*N1 + tl*N0*N1*N2 )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ); + } } } } + } } } } + + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter[0]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2,idx3 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << "," << tl*T3 + l<< std::endl; + std::cout << "ti,tj,tk,tl: " << ti << "," << tj << "," << tk << "," << tl << "," + << " i,j,k,l: " << i << "," << j << "," << k << "," << l + << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) + << " flat idx = " << ( ti + tj*NT0 + tk*N0*N1 + tl*N0*N1*N2 )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k,l) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } } + } } } } + } // end scope + + // Create RL View + { + Kokkos::View< Scalar****, LayoutRL_4D_2x4x4x2, Kokkos::HostSpace > v("v", N0, N1, N2, N3); + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti*NT1*NT2*N3 + tj*NT2*N3 + tk*N3 + tl )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ); + } } } } + } } } } + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int l = 0; l < T3; ++l ) { + for ( int k = 0; k < T2; ++k ) { + for ( int j = 0; j < T1; ++j ) { + for ( int i = 0; i < T0; ++i ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter[1]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2,idx3 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << "," << tl*T3 + l<< std::endl; + std::cout << "ti,tj,tk,tl: " << ti << "," << tj << "," << tk << "," << tl << "," + << " i,j,k,l: " << i << "," << j << "," << k << "," << l + << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) + << " flat idx = " << ( ti*NT1*NT2*N3 + tj*NT2*N3 + tk*N3 + tl )*FT + ( i + j*T0 + k*T0*T1 + l*T0*T1*T2 ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k,l) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } } + } } } } + } // end scope + + // Create LR View + { + Kokkos::View< Scalar****, LayoutLR_4D_2x4x4x2, Kokkos::HostSpace > v("v", N0, N1, N2, N3); + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti + tj*NT0 + tk*NT0*NT1 + tl*NT0*NT1*NT2 )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ); + } } } } + } } } } + + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int ti = 0; ti < NT0; ++ti ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter[2]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2,idx3 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << "," << tl*T3 + l<< std::endl; + std::cout << "ti,tj,tk,tl: " << ti << "," << tj << "," << tk << "," << tl << "," + << " i,j,k,l: " << i << "," << j << "," << k << "," << l + << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) + << " flat idx = " << ( ti + tj*NT0 + tk*NT0*NT1 + tl*NT0*NT1*NT2 )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k,l) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } } + } } } } + } // end scope + + // Create RR View + { + Kokkos::View< Scalar****, LayoutRR_4D_2x4x4x2, Kokkos::HostSpace > v("v", N0, N1, N2, N3); + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) = ( ti*NT1*NT2*NT3 + tj*NT2*NT3 + tk*NT3 + tl )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ); + } } } } + } } } } + + for ( int ti = 0; ti < NT0; ++ti ) { + for ( int tj = 0; tj < NT1; ++tj ) { + for ( int tk = 0; tk < NT2; ++tk ) { + for ( int tl = 0; tl < NT3; ++tl ) { + auto tile_subview = Kokkos::tile_subview( v, ti, tj, tk, tl ); + for ( int i = 0; i < T0; ++i ) { + for ( int j = 0; j < T1; ++j ) { + for ( int k = 0; k < T2; ++k ) { + for ( int l = 0; l < T3; ++l ) { + if ( tile_subview(i,j,k,l) != v(ti*T0+i, tj*T1+j, tk*T2+k, tl*T3 + l) ) { ++counter[3]; } +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "idx0,idx1,idx2,idx3 = " << ti*T0 + i << "," << tj*T1 + j << "," << tk*T2 + k << "," << tl*T3 + l<< std::endl; + std::cout << "ti,tj,tk,tl: " << ti << "," << tj << "," << tk << "," << tl << "," + << " i,j,k,l: " << i << "," << j << "," << k << "," << l + << " v = " << v(ti*T0 + i, tj*T1+j, tk*T2 + k, tl*T3 + l) + << " flat idx = " << ( ti*NT1*NT2*NT3 + tj*NT2*NT3 + tk*NT3 + tl )*FT + ( i*T1*T2*T3 + j*T2*T3 + k*T3 + l ) << std::endl; + std::cout << "subview_tile output = " << tile_subview(i,j,k,l) << std::endl; + std::cout << "subview tile rank = " << Kokkos::rank(tile_subview) << std::endl; +#endif + } } } } + } } } } + } // end scope + +#ifdef KOKKOS_VERBOSE_LAYOUTTILED_OUTPUT + std::cout << "subview_tile vs view errors:\n" + << " LL: " << counter[0] + << " RL: " << counter[1] + << " LR: " << counter[2] + << " RR: " << counter[3] + << std::endl; +#endif + + ASSERT_EQ(counter[0], long(0)); + ASSERT_EQ(counter[1], long(0)); + ASSERT_EQ(counter[2], long(0)); + ASSERT_EQ(counter[3], long(0)); + + } // end test_view_layout_tiled_subtile_4d + +}; // end TestViewLayoutTiled struct + +} // namespace + +TEST_F( TEST_CATEGORY , view_layouttiled) { + // These two examples are iterating by tile, then within a tile - not by extents + // If N# is not a power of two, but want to iterate by tile then within a tile, need to check that mapped index is within extent + TestViewLayoutTiled< TEST_EXECSPACE >::test_view_layout_tiled_2d( 4, 12 ); + TestViewLayoutTiled< TEST_EXECSPACE >::test_view_layout_tiled_3d( 4, 12, 16 ); + TestViewLayoutTiled< TEST_EXECSPACE >::test_view_layout_tiled_4d( 4, 12, 16, 12 ); +} +TEST_F( TEST_CATEGORY , view_layouttiled_subtile) { + // These two examples are iterating by tile, then within a tile - not by extents + // If N# is not a power of two, but want to iterate by tile then within a tile, need to check that mapped index is within extent + TestViewLayoutTiled< TEST_EXECSPACE >::test_view_layout_tiled_subtile_2d( 4, 12 ); + TestViewLayoutTiled< TEST_EXECSPACE >::test_view_layout_tiled_subtile_3d( 4, 12, 16 ); + TestViewLayoutTiled< TEST_EXECSPACE >::test_view_layout_tiled_subtile_4d( 4, 12, 16, 12 ); +} +#endif +} // namespace Test diff --git a/lib/kokkos/core/unit_test/TestViewMapping_a.hpp b/lib/kokkos/core/unit_test/TestViewMapping_a.hpp index 365531cb6f..03d5e501b9 100644 --- a/lib/kokkos/core/unit_test/TestViewMapping_a.hpp +++ b/lib/kokkos/core/unit_test/TestViewMapping_a.hpp @@ -1245,5 +1245,12 @@ TEST_F( TEST_CATEGORY , view_mapping_operator ) test_view_mapping_operator< TEST_EXECSPACE >(); } +TEST_F( TEST_CATEGORY , static_extent ) +{ + using T = Kokkos::View; + ASSERT_EQ( T::static_extent(1), 2 ); + ASSERT_EQ( T::static_extent(2), 3 ); +} + } diff --git a/lib/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewCopy.cpp b/lib/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewCopy.cpp new file mode 100644 index 0000000000..3748592355 --- /dev/null +++ b/lib/kokkos/core/unit_test/cuda/TestCudaHostPinned_ViewCopy.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/cuda/TestCudaUVM_ViewCopy.cpp b/lib/kokkos/core/unit_test/cuda/TestCudaUVM_ViewCopy.cpp new file mode 100644 index 0000000000..b0ea67a1b5 --- /dev/null +++ b/lib/kokkos/core/unit_test/cuda/TestCudaUVM_ViewCopy.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_Other.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_Other.cpp index f63409da29..788e458eea 100644 --- a/lib/kokkos/core/unit_test/cuda/TestCuda_Other.cpp +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_Other.cpp @@ -50,3 +50,4 @@ #include #include +#include diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_Reductions_DeviceView.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_Reductions_DeviceView.cpp new file mode 100644 index 0000000000..5b34090149 --- /dev/null +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_Reductions_DeviceView.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp index f7bfdc6787..e871b3c0c0 100644 --- a/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_Spaces.cpp @@ -228,6 +228,10 @@ TEST_F( cuda, uvm ) } } +/* Removing UVM Allocs Test due to added time to complete overall unit test + * The issue verified with this unit test appears to no longer be an + * problem. Refer to github issue 1880 for more details + * TEST_F( cuda, uvm_num_allocs ) { // The max number of UVM allocations allowed is 65536. @@ -288,6 +292,7 @@ TEST_F( cuda, uvm_num_allocs ) #undef MAX_NUM_ALLOCS } +*/ template< class MemSpace, class ExecSpace > struct TestViewCudaAccessible { diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_Team.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_Team.cpp index c633585096..3740683450 100644 --- a/lib/kokkos/core/unit_test/cuda/TestCuda_Team.cpp +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_Team.cpp @@ -68,6 +68,22 @@ TEST_F( TEST_CATEGORY, team_reduce ) TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); } + +TEST_F( TEST_CATEGORY, team_broadcast ) +{ + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); +} + } #include diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_TeamScratch.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_TeamScratch.cpp index 879633b0c8..dcb6896b8f 100644 --- a/lib/kokkos/core/unit_test/cuda/TestCuda_TeamScratch.cpp +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_TeamScratch.cpp @@ -65,6 +65,10 @@ TEST_F( TEST_CATEGORY, team_lambda_shared_request ) TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); } + +TEST_F( TEST_CATEGORY, scratch_align) { + TestScratchAlignment< TEST_EXECSPACE >(); +} #endif #endif diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_TeamTeamSize.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_TeamTeamSize.cpp new file mode 100644 index 0000000000..7e61e0810b --- /dev/null +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_TeamTeamSize.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/cuda/TestCuda_ViewLayoutStrideAssignment.cpp b/lib/kokkos/core/unit_test/cuda/TestCuda_ViewLayoutStrideAssignment.cpp new file mode 100644 index 0000000000..2732cd4baa --- /dev/null +++ b/lib/kokkos/core/unit_test/cuda/TestCuda_ViewLayoutStrideAssignment.cpp @@ -0,0 +1,46 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_Other.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_Other.cpp index 566891bb35..0ddd67acf9 100644 --- a/lib/kokkos/core/unit_test/openmp/TestOpenMP_Other.cpp +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_Other.cpp @@ -50,6 +50,7 @@ #include #include +#include #include diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_Reductions_DeviceView.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_Reductions_DeviceView.cpp new file mode 100644 index 0000000000..99fe5842cb --- /dev/null +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_Reductions_DeviceView.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_Team.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_Team.cpp index 790ea9e6da..e5b900ac58 100644 --- a/lib/kokkos/core/unit_test/openmp/TestOpenMP_Team.cpp +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_Team.cpp @@ -68,6 +68,21 @@ TEST_F( TEST_CATEGORY, team_reduce ) TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); } + +TEST_F( TEST_CATEGORY, team_broadcast ) +{ + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); +} } #include diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamScratch.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamScratch.cpp index f57da139a6..64d7575339 100644 --- a/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamScratch.cpp +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamScratch.cpp @@ -65,6 +65,9 @@ TEST_F( TEST_CATEGORY, team_lambda_shared_request ) TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); } +TEST_F( TEST_CATEGORY, scratch_align) { + TestScratchAlignment< TEST_EXECSPACE >(); +} #endif #endif diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamTeamSize.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamTeamSize.cpp new file mode 100644 index 0000000000..a98728f02c --- /dev/null +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_TeamTeamSize.cpp @@ -0,0 +1,46 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewAPI_e.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewAPI_e.cpp index 4249b58e82..2e8134aac4 100644 --- a/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewAPI_e.cpp +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewAPI_e.cpp @@ -43,3 +43,4 @@ #include #include +#include diff --git a/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewLayoutStrideAssignment.cpp b/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewLayoutStrideAssignment.cpp new file mode 100644 index 0000000000..81b296d15d --- /dev/null +++ b/lib/kokkos/core/unit_test/openmp/TestOpenMP_ViewLayoutStrideAssignment.cpp @@ -0,0 +1,46 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCmHostPinned_ViewCopy.cpp b/lib/kokkos/core/unit_test/rocm/TestROCmHostPinned_ViewCopy.cpp new file mode 100644 index 0000000000..4636691d99 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCmHostPinned_ViewCopy.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_Crs.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_Crs.cpp new file mode 100644 index 0000000000..05a90da83b --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_Crs.cpp @@ -0,0 +1,47 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_a.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_a.cpp new file mode 100644 index 0000000000..23edcbcc31 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_a.cpp @@ -0,0 +1,54 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include +namespace Test { + +TEST_F( TEST_CATEGORY , mdrange_5d_reduce ) { + TestMDRange_5D< TEST_EXECSPACE >::test_reduce5( 100, 10, 10, 10, 5 ); +} + +} + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_b.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_b.cpp new file mode 100644 index 0000000000..5f02e893a9 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_b.cpp @@ -0,0 +1,54 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include +namespace Test { + +TEST_F( TEST_CATEGORY , mdrange_6d_reduce ) { + TestMDRange_6D< TEST_EXECSPACE >::test_reduce6( 10, 10, 10, 10, 10, 5 ); +} + +} + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_c.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_c.cpp new file mode 100644 index 0000000000..6a84962d16 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_c.cpp @@ -0,0 +1,54 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include +namespace Test { + +TEST_F( TEST_CATEGORY , mdrange_2d_reduce ) { + TestMDRange_2D< TEST_EXECSPACE >::test_reduce2( 100, 100 ); +} + +} + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_d.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_d.cpp new file mode 100644 index 0000000000..c6c6ba2918 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_d.cpp @@ -0,0 +1,54 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include +namespace Test { + +TEST_F( TEST_CATEGORY , mdrange_3d_reduce ) { + TestMDRange_3D< TEST_EXECSPACE >::test_reduce3( 100, 100, 5 ); +} + +} + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_e.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_e.cpp new file mode 100644 index 0000000000..6afd8b8ece --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_MDRangeReduce_e.cpp @@ -0,0 +1,54 @@ + +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include +namespace Test { + +TEST_F( TEST_CATEGORY , mdrange_4d_reduce ) { + TestMDRange_4D< TEST_EXECSPACE >::test_reduce4( 100, 100, 10, 5 ); +} + +} + diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_SubView_c13.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_SubView_c13.cpp new file mode 100644 index 0000000000..03b39972a3 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_SubView_c13.cpp @@ -0,0 +1,54 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + +namespace Test { + +TEST_F( TEST_CATEGORY, view_test_unmanaged_subview_reset ) +{ + TestViewSubview::test_unmanaged_subview_reset< TEST_EXECSPACE >(); +} + +} // namespace Test diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_TeamReductionScan.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_TeamReductionScan.cpp index e1025f1baa..57887450e2 100644 --- a/lib/kokkos/core/unit_test/rocm/TestROCm_TeamReductionScan.cpp +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_TeamReductionScan.cpp @@ -46,7 +46,6 @@ namespace Test { -#if !defined(KOKKOS_ROCM_CLANG_WORKAROUND) TEST_F( TEST_CATEGORY, team_scan ) { TestScanTeam< TEST_EXECSPACE, Kokkos::Schedule >( 0 ); @@ -56,7 +55,6 @@ TEST_F( TEST_CATEGORY, team_scan ) TestScanTeam< TEST_EXECSPACE, Kokkos::Schedule >( 10000 ); TestScanTeam< TEST_EXECSPACE, Kokkos::Schedule >( 10000 ); } -#endif TEST_F( TEST_CATEGORY, team_long_reduce ) { diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_TeamScratch.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_TeamScratch.cpp index 1968ab31ea..c7255919d9 100644 --- a/lib/kokkos/core/unit_test/rocm/TestROCm_TeamScratch.cpp +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_TeamScratch.cpp @@ -65,6 +65,10 @@ TEST_F( TEST_CATEGORY, team_lambda_shared_request ) TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); } + +TEST_F( TEST_CATEGORY, scratch_align) { + TestScratchAlignment< TEST_EXECSPACE >(); +} #endif #endif diff --git a/lib/kokkos/core/unit_test/rocm/TestROCm_TeamTeamSize.cpp b/lib/kokkos/core/unit_test/rocm/TestROCm_TeamTeamSize.cpp new file mode 100644 index 0000000000..583e01fcb6 --- /dev/null +++ b/lib/kokkos/core/unit_test/rocm/TestROCm_TeamTeamSize.cpp @@ -0,0 +1,49 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +// Doesn't work right now due to bug with static sized array member + +//#include +//#ifndef KOKKOS_IMPL_ROCM_CLANG_WORKAROUND +//#include +//#endif diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_Other.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_Other.cpp index 0c3bae3774..26a218c5c1 100644 --- a/lib/kokkos/core/unit_test/serial/TestSerial_Other.cpp +++ b/lib/kokkos/core/unit_test/serial/TestSerial_Other.cpp @@ -50,3 +50,4 @@ #include #include +#include diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_Reductions_DeviceView.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_Reductions_DeviceView.cpp new file mode 100644 index 0000000000..1c20670c28 --- /dev/null +++ b/lib/kokkos/core/unit_test/serial/TestSerial_Reductions_DeviceView.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_Team.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_Team.cpp index 619cb727ac..47d02f7001 100644 --- a/lib/kokkos/core/unit_test/serial/TestSerial_Team.cpp +++ b/lib/kokkos/core/unit_test/serial/TestSerial_Team.cpp @@ -68,6 +68,21 @@ TEST_F( TEST_CATEGORY, team_reduce ) TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); } + +TEST_F( TEST_CATEGORY, team_broadcast ) +{ + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); +} } #include diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_TeamScratch.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_TeamScratch.cpp index 963908c92d..029999ab72 100644 --- a/lib/kokkos/core/unit_test/serial/TestSerial_TeamScratch.cpp +++ b/lib/kokkos/core/unit_test/serial/TestSerial_TeamScratch.cpp @@ -65,6 +65,10 @@ TEST_F( TEST_CATEGORY, team_lambda_shared_request ) TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); } + +TEST_F( TEST_CATEGORY, scratch_align) { + TestScratchAlignment< TEST_EXECSPACE >(); +} #endif #endif diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_TeamTeamSize.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_TeamTeamSize.cpp new file mode 100644 index 0000000000..53451b30c9 --- /dev/null +++ b/lib/kokkos/core/unit_test/serial/TestSerial_TeamTeamSize.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_ViewAPI_e.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_ViewAPI_e.cpp index 9f0e765aba..5082729789 100644 --- a/lib/kokkos/core/unit_test/serial/TestSerial_ViewAPI_e.cpp +++ b/lib/kokkos/core/unit_test/serial/TestSerial_ViewAPI_e.cpp @@ -43,3 +43,5 @@ #include #include +#include + diff --git a/lib/kokkos/core/unit_test/serial/TestSerial_ViewLayoutStrideAssignment.cpp b/lib/kokkos/core/unit_test/serial/TestSerial_ViewLayoutStrideAssignment.cpp new file mode 100644 index 0000000000..64c5b642d8 --- /dev/null +++ b/lib/kokkos/core/unit_test/serial/TestSerial_ViewLayoutStrideAssignment.cpp @@ -0,0 +1,46 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/core/unit_test/standalone/Makefile b/lib/kokkos/core/unit_test/standalone/Makefile new file mode 100644 index 0000000000..f8a75616c5 --- /dev/null +++ b/lib/kokkos/core/unit_test/standalone/Makefile @@ -0,0 +1,55 @@ +KOKKOS_DEVICES=Cuda +KOKKOS_CUDA_OPTIONS=enable_lambda +KOKKOS_ARCH = "SNB,Kepler35" + +MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) + +ifndef KOKKOS_PATH + KOKKOS_PATH = $(MAKEFILE_PATH)../../../ +endif + +SRC = $(wildcard $(MAKEFILE_PATH)*.cpp) +HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp) +HEADERS = $(wildcard $(MAKEFILE_PATH)/../*.hpp) + +vpath %.cpp $(sort $(dir $(SRC))) + +default: build + echo "Start Build" + +ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper +EXE = test.cuda +else +CXX = g++ +EXE = test.host +endif + +CXXFLAGS ?= -O3 -g +override CXXFLAGS += -I$(MAKEFILE_PATH) -I$(KOKKOS_PATH)/core/unit_test -I$(KOKKOS_PATH)/tpls/gtest -DTESTFILE=$(TESTFILE) +#SRC += $(KOKKOS_PATH)/tpls/gtest/gtest/gtest-all.cc + +DEPFLAGS = -M +LINK = ${CXX} +LINKFLAGS = + +OBJ = $(notdir $(SRC:.cpp=.o)) +LIB = + +include $(KOKKOS_PATH)/Makefile.kokkos + +build: $(EXE) + +$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) gtest-all.o + $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) gtest-all.o -o $(EXE) + +clean: kokkos-clean + rm -f *.o *.cuda *.host + +# Compilation rules + +%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS) + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@) + +gtest-all.o:$(KOKKOS_PATH)/tpls/gtest/gtest/gtest-all.cc + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $(KOKKOS_PATH)/tpls/gtest/gtest/gtest-all.cc diff --git a/lib/kokkos/core/unit_test/standalone/UnitTestMainInit.cpp b/lib/kokkos/core/unit_test/standalone/UnitTestMainInit.cpp new file mode 100644 index 0000000000..2db51658cd --- /dev/null +++ b/lib/kokkos/core/unit_test/standalone/UnitTestMainInit.cpp @@ -0,0 +1,71 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + +#include + +#ifdef KOKKOS_ENABLE_ROCM +#include +#endif +#ifdef KOKKOS_ENABLE_CUDA +#include +#endif +#ifdef KOKKOS_ENABLE_OPENMP +#include +#endif +#ifdef KOKKOS_ENABLE_THREADS +#include +#endif + +#include + +int main( int argc, char *argv[] ) { + Kokkos::initialize(argc,argv); + ::testing::InitGoogleTest( &argc, argv ); + + int result = RUN_ALL_TESTS(); + Kokkos::finalize(); + return result; +} diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_Other.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_Other.cpp index a0c8b41597..13786aa4a6 100644 --- a/lib/kokkos/core/unit_test/threads/TestThreads_Other.cpp +++ b/lib/kokkos/core/unit_test/threads/TestThreads_Other.cpp @@ -50,3 +50,4 @@ #include #include +#include diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_Reductions_DeviceView.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_Reductions_DeviceView.cpp new file mode 100644 index 0000000000..28f4b7d579 --- /dev/null +++ b/lib/kokkos/core/unit_test/threads/TestThreads_Reductions_DeviceView.cpp @@ -0,0 +1,45 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_Team.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_Team.cpp index b87c1f77d3..63d2509355 100644 --- a/lib/kokkos/core/unit_test/threads/TestThreads_Team.cpp +++ b/lib/kokkos/core/unit_test/threads/TestThreads_Team.cpp @@ -68,6 +68,21 @@ TEST_F( TEST_CATEGORY, team_reduce ) TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); TestTeamPolicy< TEST_EXECSPACE, Kokkos::Schedule >::test_reduce( 1000 ); } + +TEST_F( TEST_CATEGORY, team_broadcast ) +{ + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 0 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 2 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 16 ); + + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); + TestTeamBroadcast< TEST_EXECSPACE, Kokkos::Schedule >::test_teambroadcast( 1000 ); +} } #include diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_TeamScratch.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_TeamScratch.cpp index c07fae77c3..d171195798 100644 --- a/lib/kokkos/core/unit_test/threads/TestThreads_TeamScratch.cpp +++ b/lib/kokkos/core/unit_test/threads/TestThreads_TeamScratch.cpp @@ -65,6 +65,10 @@ TEST_F( TEST_CATEGORY, team_lambda_shared_request ) TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); TestLambdaSharedTeam< Kokkos::HostSpace, TEST_EXECSPACE, Kokkos::Schedule >(); } + +TEST_F( TEST_CATEGORY, scratch_align) { + TestScratchAlignment< TEST_EXECSPACE >(); +} #endif #endif diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_TeamTeamSize.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_TeamTeamSize.cpp new file mode 100644 index 0000000000..b1cf4ec875 --- /dev/null +++ b/lib/kokkos/core/unit_test/threads/TestThreads_TeamTeamSize.cpp @@ -0,0 +1,47 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + + diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_ViewAPI_e.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_ViewAPI_e.cpp index 2d9b17bc3e..616a923496 100644 --- a/lib/kokkos/core/unit_test/threads/TestThreads_ViewAPI_e.cpp +++ b/lib/kokkos/core/unit_test/threads/TestThreads_ViewAPI_e.cpp @@ -43,3 +43,4 @@ #include #include +#include diff --git a/lib/kokkos/core/unit_test/threads/TestThreads_ViewLayoutStrideAssignment.cpp b/lib/kokkos/core/unit_test/threads/TestThreads_ViewLayoutStrideAssignment.cpp new file mode 100644 index 0000000000..5ddd07108b --- /dev/null +++ b/lib/kokkos/core/unit_test/threads/TestThreads_ViewLayoutStrideAssignment.cpp @@ -0,0 +1,46 @@ +/* +//@HEADER +// ************************************************************************ +// +// Kokkos v. 2.0 +// Copyright (2014) Sandia Corporation +// +// Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, +// the U.S. Government retains certain rights in this software. +// +// Redistribution and use in source and binary forms, with or without +// modification, are permitted provided that the following conditions are +// met: +// +// 1. Redistributions of source code must retain the above copyright +// notice, this list of conditions and the following disclaimer. +// +// 2. Redistributions in binary form must reproduce the above copyright +// notice, this list of conditions and the following disclaimer in the +// documentation and/or other materials provided with the distribution. +// +// 3. Neither the name of the Corporation nor the names of the +// contributors may be used to endorse or promote products derived from +// this software without specific prior written permission. +// +// THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY +// EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +// PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE +// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, +// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR +// PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +// LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING +// NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +// SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +// +// Questions? Contact Christian R. Trott (crtrott@sandia.gov) +// +// ************************************************************************ +//@HEADER +*/ + +#include +#include + diff --git a/lib/kokkos/doc/kokkos-promotion.txt b/lib/kokkos/doc/kokkos-promotion.txt index 5a1306eccf..0aede5f328 100644 --- a/lib/kokkos/doc/kokkos-promotion.txt +++ b/lib/kokkos/doc/kokkos-promotion.txt @@ -149,7 +149,9 @@ Step 5: This step can be done on any SEMS machine (e.g. kokkos-dev). Actually, t git clone -b kokkos-develop git@github.com:trilinos/Trilinos.git TRILINOS_PATH=$PWD/Trilinos - 5.2. Snapshot Kokkos into Trilinos - this requires python/2.7.9 and that both Trilinos and Kokkos be clean - no untracked or modified files. Run the following outside of the Kokkos and Trilinos source trees. + 5.2. Snapshot Kokkos into Trilinos - this requires python/2.7.9 and that both Trilinos and Kokkos be clean - no untracked or modified files. Run the following outside of the Kokkos and Trilinos source trees. + + * Use the master branch of Kokkos for this. module load sems-python/2.7.9 python $KOKKOS_PATH/scripts/snapshot.py $KOKKOS_PATH $TRILINOS_PATH/packages @@ -173,20 +175,22 @@ Step 5: This step can be done on any SEMS machine (e.g. kokkos-dev). Actually, t ## KokkosKernels Changelog - 5.4. Run checkin-test to push to trilinos using the CI build modules (gcc/4.9.3) - - cd $TRILINOS_PATH - mkdir CHECKIN - cd CHECKIN - nohup ../cmake/std/sems/checkin-test-sems.sh --do-all --push & - - Although Trilinos has experimental Pull Request testing, it is not good enough to replace the checkin script yet. + 5.4. Wait for Trilinos Autotester results 5.5. If there are failures, fix and backtrack. Otherwise, go to next step // -------------------------------------------------------------------------------- // -Step 6: Push Kokkos master to GitHub (requires Owner permission). +Step 6: Push Kokkos master and develop to GitHub (requires Owner permission). + 6.1. Master branch: cd KOKKOS_PATH + git checkout master git push --follow-tags origin master + + 6.2. Develop branch: First merge (--no-ff) master back into develop + cd KOKKOS_PATH + git checkout develop + git merge --no-ff maseter + git push origin develop + diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp index ff3002e645..e8c1550fc6 100644 --- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp +++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/01_thread_teams/thread_teams.cpp @@ -81,13 +81,22 @@ int main(int narg, char* args[]) { Kokkos::initialize(narg,args); // Launch 12 teams of the maximum number of threads per team - const team_policy policy( 12 , team_policy::team_size_max( hello_world() ) ); - - int sum = 0; - Kokkos::parallel_reduce( policy , hello_world() , sum ); + const int team_size_max = team_policy(1,1).team_size_max(hello_world(), Kokkos::ParallelReduceTag()); + const team_policy policy_a( 12 , team_size_max ); - // The result will be 12*team_policy::team_size_max( hello_world()) - printf("Result %i\n",sum); + int sum = 0; + Kokkos::parallel_reduce( policy_a , hello_world() , sum ); + + // The result will be 12*team_size_max + printf("Result A: %i == %i\n",sum, team_size_max*12); + + // In practice it is often better to let Kokkos decide on the team_size + const team_policy policy_b( 12 , Kokkos::AUTO ); + + Kokkos::parallel_reduce( policy_b , hello_world() , sum ); + // The result will be 12*policy_b.team_size_recommended( hello_world(), Kokkos::ParallelReduceTag()) + const int team_size_recommended = policy_b.team_size_recommended( hello_world(), Kokkos::ParallelReduceTag()); + printf("Result B: %i %i\n",sum, team_size_recommended*12); Kokkos::finalize(); } diff --git a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp index 721aab2d3e..bbb1000e90 100644 --- a/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp +++ b/lib/kokkos/example/tutorial/Hierarchical_Parallelism/02_nested_parallel_for/nested_parallel_for.cpp @@ -79,7 +79,8 @@ int main(int narg, char* args[]) { Kokkos::initialize(narg,args); // Launch 3 teams of the maximum number of threads per team - const team_policy policy( 3 , team_policy::team_size_max( hello_world() ) ); + const int team_size_max = team_policy(3,1).team_size_max( hello_world(), Kokkos::ParallelReduceTag()); + const team_policy policy( 3 , team_size_max ); int sum = 0; Kokkos::parallel_reduce( policy , hello_world() , sum ); diff --git a/lib/kokkos/example/virtual_functions/Makefile b/lib/kokkos/example/virtual_functions/Makefile new file mode 100644 index 0000000000..06186786c2 --- /dev/null +++ b/lib/kokkos/example/virtual_functions/Makefile @@ -0,0 +1,55 @@ +KOKKOS_DEVICES=Cuda +KOKKOS_CUDA_OPTIONS=enable_lambda +KOKKOS_ARCH = "SNB,Kepler35" + +#KOKKOS_DEVICES=OpenMP +#KOKKOS_CUDA_OPTIONS=enable_lambda +#KOKKOS_ARCH = "SNB" + +MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST)))) + +ifndef KOKKOS_PATH + KOKKOS_PATH = $(MAKEFILE_PATH)../.. +endif + +SRC = $(wildcard $(MAKEFILE_PATH)*.cpp) +HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp) + +vpath %.cpp $(sort $(dir $(SRC))) + +default: build + echo "Start Build" + +LINKFLAGS = +ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper +EXE = virtual.cuda +override LINKFLAGS += --remove-duplicate-link-files +else +CXX = g++ +EXE = virtual.host +endif + +CXXFLAGS ?= -O3 -g +override CXXFLAGS += -I$(MAKEFILE_PATH) + +DEPFLAGS = -M +LINK = ${CXX} + +OBJ = $(notdir $(SRC:.cpp=.o)) +LIB = + +include $(KOKKOS_PATH)/Makefile.kokkos + +build: $(EXE) + +$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) + $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) + +clean: kokkos-clean + rm -f *.o *.cuda *.host + +# Compilation rules + +%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS) + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@) diff --git a/lib/kokkos/example/virtual_functions/classes.cpp b/lib/kokkos/example/virtual_functions/classes.cpp new file mode 100644 index 0000000000..1b9d7cb385 --- /dev/null +++ b/lib/kokkos/example/virtual_functions/classes.cpp @@ -0,0 +1,26 @@ +#include + +KOKKOS_FUNCTION +Foo::Foo() { + val = 0; +} + +KOKKOS_FUNCTION +Foo_1::Foo_1() { + val = 1; +} + +KOKKOS_FUNCTION +int Foo_1::value() { + return val; +} + +KOKKOS_FUNCTION +Foo_2::Foo_2() { + val = 2; +} + +KOKKOS_FUNCTION +int Foo_2::value() { + return val; +} diff --git a/lib/kokkos/example/virtual_functions/classes.hpp b/lib/kokkos/example/virtual_functions/classes.hpp new file mode 100644 index 0000000000..362c473ce6 --- /dev/null +++ b/lib/kokkos/example/virtual_functions/classes.hpp @@ -0,0 +1,39 @@ +#ifndef KOKKOS_EXAMPLE_VIRTUAL_FUNCTIONS_CLASSES_HPP +#define KOKKOS_EXAMPLE_VIRTUAL_FUNCTIONS_CLASSES_HPP + +#include + +class Foo { + protected: + int val; + public: + KOKKOS_FUNCTION + Foo(); + + KOKKOS_FUNCTION + virtual int value() { return 0; }; + + KOKKOS_FUNCTION + virtual ~Foo() {} +}; + +class Foo_1: public Foo { + public: + KOKKOS_FUNCTION + Foo_1(); + + KOKKOS_FUNCTION + int value(); +}; + +class Foo_2: public Foo { + public: + KOKKOS_FUNCTION + Foo_2(); + + KOKKOS_FUNCTION + int value(); +}; + +#endif //KOKKOS_EXAMPLE_VIRTUAL_FUNCTIONS_CLASSES_HPP + diff --git a/lib/kokkos/example/virtual_functions/main.cpp b/lib/kokkos/example/virtual_functions/main.cpp new file mode 100644 index 0000000000..a16e0cf73f --- /dev/null +++ b/lib/kokkos/example/virtual_functions/main.cpp @@ -0,0 +1,36 @@ +#include + +int main(int argc, char* argv[]) { + Kokkos::initialize(argc,argv); + + { + Foo* f_1 = (Foo*) Kokkos::kokkos_malloc(sizeof(Foo_1)); + Foo* f_2 = (Foo*) Kokkos::kokkos_malloc(sizeof(Foo_2)); + + Kokkos::parallel_for("CreateObjects",1, KOKKOS_LAMBDA (const int&) { + new ((Foo_1*)f_1) Foo_1(); + new ((Foo_2*)f_2) Foo_2(); + }); + + int value_1,value_2; + Kokkos::parallel_reduce("CheckValues",1, KOKKOS_LAMBDA (const int&, int& lsum) { + lsum = f_1->value(); + },value_1); + + Kokkos::parallel_reduce("CheckValues",1, KOKKOS_LAMBDA (const int&, int& lsum) { + lsum = f_2->value(); + },value_2); + + printf("Values: %i %i\n",value_1,value_2); + + Kokkos::parallel_for("DestroyObjects",1, KOKKOS_LAMBDA (const int&) { + f_1->~Foo(); + f_2->~Foo(); + }); + + Kokkos::kokkos_free(f_1); + Kokkos::kokkos_free(f_2); + } + + Kokkos::finalize(); +} diff --git a/lib/kokkos/generate_makefile.bash b/lib/kokkos/generate_makefile.bash index 4225e5b2de..f3c4f16238 100755 --- a/lib/kokkos/generate_makefile.bash +++ b/lib/kokkos/generate_makefile.bash @@ -68,6 +68,9 @@ do --cxxflags*) CXXFLAGS="${key#*=}" ;; + --cxxstandard*) + KOKKOS_CXX_STANDARD="${key#*=}" + ;; --ldflags*) LDFLAGS="${key#*=}" ;; @@ -97,12 +100,21 @@ do echo "Invalid compiler by --compiler command: '${COMPILER}'" exit fi + # ... valid compiler, ensure absolute path set + WCOMPATH=`which $COMPILER` + COMPDIR=`dirname $WCOMPATH` + COMPNAME=`basename $WCOMPATH` + COMPILER=${COMPDIR}/${COMPNAME} ;; --with-options*) KOKKOS_OPT="${key#*=}" ;; + --gcc-toolchain*) + KOKKOS_GCC_TOOLCHAIN="${key#*=}" + ;; --help) echo "Kokkos configure options:" + echo "" echo "--kokkos-path=/Path/To/Kokkos: Path to the Kokkos root directory." echo "--qthreads-path=/Path/To/Qthreads: Path to Qthreads install directory." echo " Overrides path given by --with-qthreads." @@ -118,6 +130,7 @@ do echo "--arch=[OPT]: Set target architectures. Options are:" echo " [AMD]" echo " AMDAVX = AMD CPU" + echo " EPYC = AMD EPYC Zen-Core CPU" echo " [ARM]" echo " ARMv80 = ARMv8.0 Compatible CPU" echo " ARMv81 = ARMv8.1 Compatible CPU" @@ -156,6 +169,8 @@ do echo " build. This will still set certain required" echo " flags via KOKKOS_CXXFLAGS (such as -fopenmp," echo " --std=c++11, etc.)." + echo "--cxxstandard=[FLAGS] Overwrite KOKKOS_CXX_STANDARD for library build and test" + echo " c++11 (default), c++14, c++17, c++1y, c++1z, c++2a" echo "--ldflags=[FLAGS] Overwrite LDFLAGS for library build and test" echo " build. This will still set certain required" echo " flags via KOKKOS_LDFLAGS (such as -fopenmp," @@ -171,6 +186,7 @@ do echo " " echo "--with-cuda-options=[OPT]: Additional options to CUDA:" echo " force_uvm, use_ldg, enable_lambda, rdc" + echo "--gcc-toolchain=/Path/To/GccRoot: Set the gcc toolchain to use with clang (e.g. /usr)" echo "--make-j=[NUM]: DEPRECATED: call make with appropriate" echo " -j flag" exit 0 @@ -195,7 +211,7 @@ else fi if [ "${KOKKOS_PATH}" = "${PWD}" ] || [ "${KOKKOS_PATH}" = "${PWD}/" ]; then - echo "Running generate_makefile.sh in the Kokkos root directory is not allowed" + echo "Running generate_makefile.bash in the Kokkos root directory is not allowed" exit fi @@ -204,8 +220,13 @@ KOKKOS_SRC_PATH=${KOKKOS_PATH} KOKKOS_SETTINGS="KOKKOS_SRC_PATH=${KOKKOS_SRC_PATH}" #KOKKOS_SETTINGS="KOKKOS_PATH=${KOKKOS_PATH}" +# The double [[ ]] in the elif branch is not a typo if [ ${#COMPILER} -gt 0 ]; then KOKKOS_SETTINGS="${KOKKOS_SETTINGS} CXX=${COMPILER}" +elif + [ ${#COMPILER} -eq 0 ] && [[ ${KOKKOS_DEVICES} =~ .*Cuda.* ]]; then + COMPILER="${KOKKOS_PATH}/bin/nvcc_wrapper" + KOKKOS_SETTINGS="${KOKKOS_SETTINGS} CXX=${COMPILER}" fi if [ ${#KOKKOS_DEVICES} -gt 0 ]; then @@ -228,6 +249,10 @@ if [ ${#CXXFLAGS} -gt 0 ]; then KOKKOS_SETTINGS="${KOKKOS_SETTINGS} CXXFLAGS=\"${CXXFLAGS}\"" fi +if [ ${#KOKKOS_CXX_STANDARD} -gt 0 ]; then + KOKKOS_SETTINGS="${KOKKOS_SETTINGS} KOKKOS_CXX_STANDARD=\"${KOKKOS_CXX_STANDARD}\"" +fi + if [ ${#LDFLAGS} -gt 0 ]; then KOKKOS_SETTINGS="${KOKKOS_SETTINGS} LDFLAGS=\"${LDFLAGS}\"" fi @@ -265,6 +290,10 @@ if [ ${#KOKKOS_CUDA_OPT} -gt 0 ]; then KOKKOS_SETTINGS="${KOKKOS_SETTINGS} KOKKOS_CUDA_OPTIONS=${KOKKOS_CUDA_OPT}" fi +if [ ${#KOKKOS_GCC_TOOLCHAIN} -gt 0 ]; then + KOKKOS_SETTINGS="${KOKKOS_SETTINGS} KOKKOS_INTERNAL_GCC_TOOLCHAIN=${KOKKOS_GCC_TOOLCHAIN}" +fi + KOKKOS_SETTINGS_NO_KOKKOS_PATH="${KOKKOS_SETTINGS}" KOKKOS_TEST_INSTALL_PATH="${PWD}/install" @@ -276,7 +305,7 @@ fi mkdir -p install gen_makefile=Makefile.kokkos -echo "#Makefile to satisfy existens of target kokkos-clean before installing the library" > install/${gen_makefile} +echo "#Makefile to satisfy existence of target kokkos-clean before installing the library" > install/${gen_makefile} echo "kokkos-clean:" >> install/${gen_makefile} echo "" >> install/${gen_makefile} mkdir -p core diff --git a/lib/kokkos/master_history.txt b/lib/kokkos/master_history.txt index fe90cc2960..777f080c49 100644 --- a/lib/kokkos/master_history.txt +++ b/lib/kokkos/master_history.txt @@ -14,3 +14,5 @@ tag: 2.04.11 date: 10:28:2017 master: 54a1330a develop: ed36c017 tag: 2.5.00 date: 12:15:2017 master: dfe685f4 develop: ec7ad6d8 tag: 2.6.00 date: 03:07:2018 master: 62e760fa develop: d1ba7d71 tag: 2.7.00 date: 05:24:2018 master: e01945d0 develop: 2d13f608 +tag: 2.7.24 date: 11:04:2018 master: d3a94192 develop: 7a06fc81 +tag: 2.8.00 date: 02:05:2019 master: 34931a36 develop: d1659d1d diff --git a/lib/kokkos/scripts/eti/generate_view_copy_cpp_files_write b/lib/kokkos/scripts/eti/generate_view_copy_cpp_files_write index ffe2a593b9..45208e76b0 100755 --- a/lib/kokkos/scripts/eti/generate_view_copy_cpp_files_write +++ b/lib/kokkos/scripts/eti/generate_view_copy_cpp_files_write @@ -19,8 +19,8 @@ echo "KOKKOS_IMPL_VIEWCOPY_ETI_DECL(${SCALAR_TYPE}${RANK_STARS},${LAYOUT_TYPE},L echo "KOKKOS_IMPL_VIEWFILL_ETI_DECL(${SCALAR_TYPE}${RANK_STARS},${LAYOUT_TYPE},KOKKOS_IMPL_VIEWCOPY_ETI_AVAIL_EXECSPACE,${INDEX_TYPE})" >> common/Kokkos_ViewFillCopyETIDecl_Macros.hpp -FileName=${EXECUTION_SPACE_DIR}/Kokkos_${EXECUTION_SPACE}_ViewCopyETIInst_${INDEX_TYPE}_${SCALAR_TYPE}_${LAYOUT_TYPE}_Rank${RANK}.cpp -ObjectName=Kokkos_${EXECUTION_SPACE}_ViewCopyETIInst_${INDEX_TYPE}_${SCALAR_TYPE}_${LAYOUT_TYPE}_Rank${RANK}.o +FileName=${EXECUTION_SPACE_DIR}/Kokkos_${EXECUTION_SPACE_DIR}_ViewCopyETIInst_${INDEX_TYPE}_${SCALAR_TYPE}_${LAYOUT_TYPE}_Rank${RANK}.cpp +ObjectName=Kokkos_${EXECUTION_SPACE_DIR}_ViewCopyETIInst_${INDEX_TYPE}_${SCALAR_TYPE}_${LAYOUT_TYPE}_Rank${RANK}.o cp ${SCRIPT_PATH}/../../LICENSE ${FileName} @@ -37,5 +37,5 @@ echo "" >> ${FileName} echo "}" >> ${FileName} echo "}" >> ${FileName} -echo "${ObjectName}: \$(KOKKOS_CPP_DEPENDS) \$(KOKKOS_ETI_PATH)/${FileName}" >> ${EXECUTION_SPACE_DIR}/Makefile.eti_${EXECUTION_SPACE} -echo -e "\t\$(CXX) \$(KOKKOS_CPPFLAGS) \$(KOKKOS_CXXFLAGS) \$(CXXFLAGS) -c \$(KOKKOS_ETI_PATH)/${FileName}" >> ${EXECUTION_SPACE_DIR}/Makefile.eti_${EXECUTION_SPACE} +echo "${ObjectName}: \$(KOKKOS_CPP_DEPENDS) \$(KOKKOS_ETI_PATH)/${FileName}" >> ${EXECUTION_SPACE_DIR}/Makefile.eti_${EXECUTION_SPACE_DIR} +echo -e "\t\$(CXX) \$(KOKKOS_CPPFLAGS) \$(KOKKOS_CXXFLAGS) \$(CXXFLAGS) -c \$(KOKKOS_ETI_PATH)/${FileName}" >> ${EXECUTION_SPACE_DIR}/Makefile.eti_${EXECUTION_SPACE_DIR} diff --git a/lib/kokkos/scripts/testing_scripts/test_all_sandia b/lib/kokkos/scripts/testing_scripts/test_all_sandia new file mode 100755 index 0000000000..d34d04b7ce --- /dev/null +++ b/lib/kokkos/scripts/testing_scripts/test_all_sandia @@ -0,0 +1,811 @@ +#!/bin/bash -e + +# +# Global config +# + +set -o pipefail + +# Determine current machine. + +MACHINE="" +HOSTNAME=$(hostname) +PROCESSOR=`uname -p` + +if [[ "$HOSTNAME" =~ (white|ride).* ]]; then + MACHINE=white + module load git +fi + +if [[ "$HOSTNAME" =~ .*bowman.* ]]; then + MACHINE=bowman + module load git +fi + +if [[ "$HOSTNAME" == *blake* ]]; then # Warning: very generic name + MACHINE=blake + module load git +fi + +if [[ "$HOSTNAME" == apollo\.* ]]; then + MACHINE=apollo + module load git +fi + +if [[ "$HOSTNAME" == mayer\.* ]]; then + MACHINE=mayer +# module load git +fi +if [[ "$HOSTNAME" == cn* ]]; then # Warning: very generic name + MACHINE=mayer +fi + +if [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then + if [[ "$MACHINE" = "" ]]; then + MACHINE=sems + module load sems-git + fi +fi + +if [[ "$MACHINE" = "" ]]; then + echo "Unrecognized machine" >&2 + exit 1 +fi + +echo "Running on machine: $MACHINE" + +GCC_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial" +IBM_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" +ARM_GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" +INTEL_BUILD_LIST="OpenMP,Pthread,Serial,OpenMP_Serial,Pthread_Serial" +CLANG_BUILD_LIST="Pthread,Serial,Pthread_Serial" +CUDA_BUILD_LIST="Cuda_OpenMP,Cuda_Pthread,Cuda_Serial" +CUDA_IBM_BUILD_LIST="Cuda_OpenMP,Cuda_Serial" + +GCC_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wignored-qualifiers,-Wempty-body,-Wclobbered,-Wuninitialized" +IBM_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Wsign-compare,-Wtype-limits,-Wuninitialized" +CLANG_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" +INTEL_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" +CUDA_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Werror,-Wsign-compare,-Wtype-limits,-Wuninitialized" +#CUDA_WARNING_FLAGS="-Wall,-Wshadow,-pedantic,-Wsign-compare,-Wtype-limits,-Wuninitialized" +PGI_WARNING_FLAGS="" + +# Default. Machine specific can override. +DEBUG=False +ARGS="" +CUSTOM_BUILD_LIST="" +QTHREADS_PATH="" +DRYRUN=False +BUILD_ONLY=False +declare -i NUM_JOBS_TO_RUN_IN_PARALLEL=1 +TEST_SCRIPT=False +SKIP_HWLOC=False +SPOT_CHECK=False + +PRINT_HELP=False +OPT_FLAG="" +CXX_FLAGS_EXTRA="" +LD_FLAGS_EXTRA="" +KOKKOS_OPTIONS="" + +CXX_STANDARD="c++11" + +# +# Handle arguments. +# + +while [[ $# > 0 ]] +do + key="$1" + + case $key in + --kokkos-path*) + KOKKOS_PATH="${key#*=}" + ;; + --qthreads-path*) + QTHREADS_PATH="${key#*=}" + ;; + --build-list*) + CUSTOM_BUILD_LIST="${key#*=}" + ;; + --debug*) + DEBUG=True + ;; + --build-only*) + BUILD_ONLY=True + ;; + --test-script*) + TEST_SCRIPT=True + ;; + --skip-hwloc*) + SKIP_HWLOC=True + ;; + --num*) + NUM_JOBS_TO_RUN_IN_PARALLEL="${key#*=}" + ;; + --dry-run*) + DRYRUN=True + ;; + --spot-check*) + SPOT_CHECK=True + ;; + --arch*) + ARCH_FLAG="--arch=${key#*=}" + ;; + --opt-flag*) + OPT_FLAG="${key#*=}" + ;; + --with-cuda-options*) + KOKKOS_CUDA_OPTIONS="--with-cuda-options=${key#*=}" + ;; + --with-options*) + KOKKOS_OPTIONS="--with-options=${key#*=}" + ;; + --cxxflags-extra*) + CXX_FLAGS_EXTRA="${key#*=}" + ;; + --cxxstandard*) + CXX_STANDARD="${key#*=}" + ;; + --ldflags-extra*) + LD_FLAGS_EXTRA="${key#*=}" + ;; + --help*) + PRINT_HELP=True + ;; + *) + # args, just append + ARGS="$ARGS $1" + ;; + esac + + shift +done + +SCRIPT_KOKKOS_ROOT=$( cd "$( dirname "$0" )" && cd ../.. && pwd ) + +# Set kokkos path. +if [ -z "$KOKKOS_PATH" ]; then + KOKKOS_PATH=$SCRIPT_KOKKOS_ROOT +else + # Ensure KOKKOS_PATH is abs path. + KOKKOS_PATH=$( cd $KOKKOS_PATH && pwd ) +fi + +UNCOMMITTED=`cd ${KOKKOS_PATH}; git status --porcelain 2>/dev/null` +if ! [ -z "$UNCOMMITTED" ]; then + echo "WARNING!! THE FOLLOWING CHANGES ARE UNCOMMITTED!! :" + echo "$UNCOMMITTED" + echo "" +fi + +GITSTATUS=`cd ${KOKKOS_PATH}; git log -n 1 --format=oneline` +echo "Repository Status: " ${GITSTATUS} +echo "" +echo "" + +# +# Machine specific config. +# + +if [ "$MACHINE" = "sems" ]; then + source /projects/sems/modulefiles/utils/sems-modules-init.sh + + BASE_MODULE_LIST="sems-env,kokkos-env,kokkos-hwloc/1.10.1/base,sems-/" + CUDA_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/4.8.4,kokkos-hwloc/1.10.1/base" + CUDA8_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" + + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="" + fi + + if [ "$SPOT_CHECK" = "True" ]; then + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/5.3.0 $BASE_MODULE_LIST "OpenMP" g++ $GCC_WARNING_FLAGS" + "gcc/7.3.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" + "intel/17.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" + "clang/4.0.1 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" + "cuda/8.0.44 $CUDA8_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + ) + else + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/4.9.3 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/5.3.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/6.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/7.3.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "intel/15.0.2 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "intel/16.0.3 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "intel/17.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/3.7.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/3.8.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/3.9.0 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/4.0.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA8_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + ) + fi +elif [ "$MACHINE" = "white" ]; then + source /etc/profile.d/modules.sh + SKIP_HWLOC=True + export SLURM_TASKS_PER_NODE=32 + + BASE_MODULE_LIST="/" + IBM_MODULE_LIST="/xl/,gcc/7.2.0" + CUDA_MODULE_LIST="/,gcc/7.2.0,ibm/xl/16.1.0" + CUDA10_MODULE_LIST="/,gcc/7.4.0,ibm/xl/16.1.0" + + # Don't do pthread on white. + GCC_BUILD_LIST="OpenMP,Serial,OpenMP_Serial" + + if [ "$SPOT_CHECK" = "True" ]; then + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/6.4.0 $BASE_MODULE_LIST "OpenMP_Serial" g++ $GCC_WARNING_FLAGS" + "gcc/7.2.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "ibm/16.1.0 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" + "cuda/9.2.88 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + ) + else + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/6.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/7.2.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "ibm/16.1.0 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" + "ibm/16.1.1 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" + "cuda/9.2.88 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/10.0.130 $CUDA10_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + ) + fi + + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="--arch=Power8,Kepler37" + fi + +elif [ "$MACHINE" = "bowman" ]; then + source /etc/profile.d/modules.sh + SKIP_HWLOC=True + export SLURM_TASKS_PER_NODE=32 + + BASE_MODULE_LIST="/compilers/" + + OLD_INTEL_BUILD_LIST="Pthread,Serial,Pthread_Serial" + + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("intel/16.4.258 $BASE_MODULE_LIST $OLD_INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "intel/17.2.174 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "intel/18.2.199 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + ) + + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="--arch=KNL" + fi + +elif [ "$MACHINE" = "mayer" ]; then + SKIP_HWLOC=True + export SLURM_TASKS_PER_NODE=96 + + BASE_MODULE_LIST="/" + ARM_MODULE_LIST="/compilers/" + + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/7.2.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "arm/18.4.0 $ARM_MODULE_LIST $ARM_GCC_BUILD_LIST armclang++ $CLANG_WARNING_FLAGS") + + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="--arch=ARMv8-TX2" + fi + +elif [ "$MACHINE" = "blake" ]; then + source /etc/profile.d/modules.sh + SKIP_HWLOC=True + export SLURM_TASKS_PER_NODE=32 + + BASE_MODULE_LIST="/" + BASE_MODULE_LIST_INTEL="/compilers/" + + if [ "$SPOT_CHECK" = "True" ]; then + + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("intel/18.1.163 $BASE_MODULE_LIST_INTEL $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "gcc/7.2.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "pgi/17.10.0 $BASE_MODULE_LIST $GCC_BUILD_LIST pgc++ $PGI_WARNING_FLAGS" + ) + else + COMPILERS=("intel/18.1.163 $BASE_MODULE_LIST_INTEL $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "gcc/4.9.3 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/5.5.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/6.4.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/7.2.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/8.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "pgi/17.10.0 $BASE_MODULE_LIST $GCC_BUILD_LIST pgc++ $PGI_WARNING_FLAGS" + ) + + fi + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="--arch=SKX" + fi + +elif [ "$MACHINE" = "apollo" ]; then + source /projects/sems/modulefiles/utils/sems-modules-init.sh + module use /home/projects/modulefiles/local/x86-64 + module load kokkos-env + + module load sems-git + module load sems-tex + module load sems-cmake/3.5.2 + module load sems-gdb + + SKIP_HWLOC=True + + BASE_MODULE_LIST="sems-env,kokkos-env,sems-/,kokkos-hwloc/1.10.1/base" + CUDA_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/4.8.4,kokkos-hwloc/1.10.1/base" + CUDA8_MODULE_LIST="sems-env,kokkos-env,kokkos-/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" + CUDA10_MODULE_LIST="sems-env,kokkos-env,/,sems-gcc/5.3.0,kokkos-hwloc/1.10.1/base" + + CLANG_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,cuda/9.0.69" + CLANG7_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,cuda/9.1" + NVCC_MODULE_LIST="sems-env,kokkos-env,sems-git,sems-cmake/3.5.2,/,sems-gcc/5.3.0" + + BUILD_LIST_CUDA_NVCC="Cuda_Serial,Cuda_OpenMP" + BUILD_LIST_CUDA_CLANG="Cuda_Serial,Cuda_Pthread" + BUILD_LIST_CLANG="Serial,Pthread,OpenMP" + + if [ "$SPOT_CHECK" = "True" ]; then + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("gcc/4.8.4 $BASE_MODULE_LIST "OpenMP,Pthread" g++ $GCC_WARNING_FLAGS" + "gcc/5.3.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" + "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" + "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" + "clang/6.0 $CLANG_MODULE_LIST "Cuda_Pthread,OpenMP" clang++ $CUDA_WARNING_FLAGS" + "cuda/9.1 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + ) + else + # Format: (compiler module-list build-list exe-name warning-flag) + COMPILERS=("cuda/9.1 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/10.0 $CUDA10_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "clang/6.0 $CLANG_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" + "clang/7.0 $CLANG7_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" + "clang/3.9.0 $CLANG_MODULE_LIST $BUILD_LIST_CLANG clang++ $CLANG_WARNING_FLAGS" + "gcc/4.8.4 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/4.9.3 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/5.3.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "gcc/6.1.0 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" + "intel/15.0.2 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "intel/17.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" + "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + ) + fi + + if [ -z "$ARCH_FLAG" ]; then + ARCH_FLAG="--arch=SNB,Volta70" + fi + +else + echo "Unhandled machine $MACHINE" >&2 + exit 1 +fi + +export OMP_NUM_THREADS=8 +export OMP_PROC_BIND=spread +export OMP_PLACES=cores + +declare -i NUM_RESULTS_TO_KEEP=7 + +RESULT_ROOT_PREFIX=TestAll + +if [ "$PRINT_HELP" = "True" ]; then + echo "test_all_sandia :" + echo "--kokkos-path=/Path/To/Kokkos: Path to the Kokkos root directory" + echo " Defaults to root repo containing this script" + echo "--debug: Run tests in debug. Defaults to False" + echo "--test-script: Test this script, not Kokkos" + echo "--skip-hwloc: Do not do hwloc tests" + echo "--num=N: Number of jobs to run in parallel" + echo "--spot-check: Minimal test set to issue pull request" + echo "--dry-run: Just print what would be executed" + echo "--build-only: Just do builds, don't run anything" + echo "--opt-flag=FLAG: Optimization flag (default: -O3)" + echo "--cxxflags-extra=FLAGS: Extra flags to be added to CXX_FLAGS" + echo "--ldflags-extra=FLAGS: Extra flags to be added to LD_FLAGS" + echo "--arch=ARCHITECTURE: overwrite architecture flags" + echo "--with-cuda-options=OPT: set KOKKOS_CUDA_OPTIONS" + echo "--build-list=BUILD,BUILD,BUILD..." + echo " Provide a comma-separated list of builds instead of running all builds" + echo " Valid items:" + echo " OpenMP, Pthread, Qthreads, Serial, OpenMP_Serial, Pthread_Serial" + echo " Qthreads_Serial, Cuda_OpenMP, Cuda_Pthread, Cuda_Serial" + echo "" + + echo "ARGS: list of expressions matching compilers to test" + echo " supported compilers sems" + for COMPILER_DATA in "${COMPILERS[@]}"; do + ARR=($COMPILER_DATA) + COMPILER=${ARR[0]} + echo " $COMPILER" + done + echo "" + + echo "Examples:" + echo " Run all tests" + echo " % test_all_sandia" + echo "" + echo " Run all gcc tests" + echo " % test_all_sandia gcc" + echo "" + echo " Run all gcc/4.8.4 and all intel tests" + echo " % test_all_sandia gcc/4.8.4 intel" + echo "" + echo " Run all tests in debug" + echo " % test_all_sandia --debug" + echo "" + echo " Run gcc/4.8.4 and only do OpenMP and OpenMP_Serial builds" + echo " % test_all_sandia gcc/4.8.4 --build-list=OpenMP,OpenMP_Serial" + echo "" + echo "If you want to kill the tests, do:" + echo " hit ctrl-z" + echo " % kill -9 %1" + echo + exit 0 +fi + +# Set build type. +if [ "$DEBUG" = "True" ]; then + BUILD_TYPE=debug +else + BUILD_TYPE=release +fi + +# If no args provided, do all compilers. +if [ -z "$ARGS" ]; then + ARGS='?' +fi + +# Process args to figure out which compilers to test. +COMPILERS_TO_TEST="" + +for ARG in $ARGS; do + for COMPILER_DATA in "${COMPILERS[@]}"; do + ARR=($COMPILER_DATA) + COMPILER=${ARR[0]} + + if [[ "$COMPILER" = $ARG* ]]; then + if [[ "$COMPILERS_TO_TEST" != *${COMPILER}* ]]; then + COMPILERS_TO_TEST="$COMPILERS_TO_TEST $COMPILER" + else + echo "Tried to add $COMPILER twice" + fi + fi + done +done + +# Check if Qthreads build requested. +HAVE_QTHREADS_BUILD="False" +if [ -n "$CUSTOM_BUILD_LIST" ]; then + if [[ "$CUSTOM_BUILD_LIST" = *Qthreads* ]]; then + HAVE_QTHREADS_BUILD="True" + fi +else + for COMPILER_DATA in "${COMPILERS[@]}"; do + ARR=($COMPILER_DATA) + BUILD_LIST=${ARR[2]} + if [[ "$BUILD_LIST" = *Qthreads* ]]; then + HAVE_QTHREADS_BUILD="True" + fi + done +fi + +# Ensure Qthreads path is set if Qthreads build is requested. +if [ "$HAVE_QTHREADS_BUILD" = "True" ]; then + if [ -z "$QTHREADS_PATH" ]; then + echo "Need to supply Qthreads path (--qthreads-path) when testing Qthreads backend." >&2 + exit 1 + else + # Strip trailing slashes from path. + QTHREADS_PATH=$(echo $QTHREADS_PATH | sed 's/\/*$//') + fi +fi + +# +# Functions. +# + +# get_compiler_name +get_compiler_name() { + echo $1 | cut -d/ -f1 +} + +# get_compiler_version +get_compiler_version() { + echo $1 | cut -d/ -f2 +} + +# Do not call directly. +get_compiler_data() { + local compiler=$1 + local item=$2 + local compiler_name=$(get_compiler_name $compiler) + local compiler_vers=$(get_compiler_version $compiler) + + local compiler_data + for compiler_data in "${COMPILERS[@]}" ; do + local arr=($compiler_data) + + if [ "$compiler" = "${arr[0]}" ]; then + echo "${arr[$item]}" | tr , ' ' | sed -e "s//$compiler_name/g" -e "s//$compiler_vers/g" + return 0 + fi + done + + # Not found. + echo "Unreconized compiler $compiler" >&2 + exit 1 +} + +# +# For all getters, usage: +# + +get_compiler_modules() { + get_compiler_data $1 1 +} + +get_compiler_build_list() { + get_compiler_data $1 2 +} + +get_compiler_exe_name() { + get_compiler_data $1 3 +} + +get_compiler_warning_flags() { + get_compiler_data $1 4 +} + +run_cmd() { + echo "RUNNING: $*" + if [ "$DRYRUN" != "True" ]; then + eval "$* 2>&1" + fi +} + +# report_and_log_test_results +report_and_log_test_result() { + # Use sane var names. + local success=$1; local desc=$2; local comment=$3; + + if [ "$success" = "0" ]; then + echo " PASSED $desc" + echo $comment > $PASSED_DIR/$desc + else + # For failures, comment should be the name of the phase that failed. + echo " FAILED $desc" >&2 + echo $comment > $FAILED_DIR/$desc + cat ${desc}.${comment}.log + fi +} + +setup_env() { + local compiler=$1 + local compiler_modules=$(get_compiler_modules $compiler) + + module purge + + local mod + for mod in $compiler_modules; do + echo "Loading module $mod" + module load $mod 2>&1 + # It is ridiculously hard to check for the success of a loaded + # module. Module does not return error codes and piping to grep + # causes module to run in a subshell. + module list 2>&1 | grep "$mod" >& /dev/null || return 1 + done + + return 0 +} + +# single_build_and_test +single_build_and_test() { + # Use sane var names. + local compiler=$1; local build=$2; local build_type=$3; + + # Set up env. + mkdir -p $ROOT_DIR/$compiler/"${build}-$build_type" + cd $ROOT_DIR/$compiler/"${build}-$build_type" + local desc=$(echo "${compiler}-${build}-${build_type}" | sed 's:/:-:g') + setup_env $compiler >& ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; } + + # Set up flags. + local compiler_warning_flags=$(get_compiler_warning_flags $compiler) + local compiler_exe=$(get_compiler_exe_name $compiler) + + if [[ "$build_type" = hwloc* ]]; then + local extra_args=--with-hwloc=$(dirname $(dirname $(which hwloc-info))) + fi + + if [[ "$build" = *Qthreads* ]]; then + if [[ "$build_type" = hwloc* ]]; then + local extra_args="$extra_args --qthreads-path=${QTHREADS_PATH}_hwloc" + else + local extra_args="$extra_args --qthreads-path=$QTHREADS_PATH" + fi + fi + + if [[ "$OPT_FLAG" = "" ]]; then + OPT_FLAG="-O3" + fi + + if [[ "$build_type" = *debug* ]]; then + local extra_args="$extra_args --debug" + local cxxflags="-g $compiler_warning_flags" + local ldflags="-g" + else + local cxxflags="$OPT_FLAG $compiler_warning_flags" + local ldflags="${OPT_FLAG}" + fi + + local cxxflags="${cxxflags} ${CXX_FLAGS_EXTRA}" + local ldflags="${ldflags} ${LD_FLAGS_EXTRA}" + + local cxx_standard="${CXX_STANDARD}" + + if [[ "$KOKKOS_CUDA_OPTIONS" != "" ]]; then + local extra_args="$extra_args $KOKKOS_CUDA_OPTIONS" + fi + if [[ "$KOKKOS_OPTIONS" != "" ]]; then + local extra_args="$extra_args $KOKKOS_OPTIONS" + else + local extra_args="$extra_args --with-options=enable_large_mem_tests" + fi + + echo " Starting job $desc" + + local comment="no_comment" + + if [ "$TEST_SCRIPT" = "True" ]; then + local rand=$[ 1 + $[ RANDOM % 10 ]] + sleep $rand + + if [ $rand -gt 5 ]; then + run_cmd ls fake_problem >& ${desc}.configure.log || { report_and_log_test_result 1 $desc configure && return 0; } + fi + else + run_cmd ${KOKKOS_PATH}/generate_makefile.bash --with-devices=$build $ARCH_FLAG --compiler=$(which $compiler_exe) --cxxflags=\"$cxxflags\" --cxxstandard=\"$cxx_standard\" --ldflags=\"$ldflags\" $extra_args &>> ${desc}.configure.log || { report_and_log_test_result 1 ${desc} configure && return 0; } + local -i build_start_time=$(date +%s) + run_cmd make -j 48 build-test >& ${desc}.build.log || { report_and_log_test_result 1 ${desc} build && return 0; } + local -i build_end_time=$(date +%s) + comment="build_time=$(($build_end_time-$build_start_time))" + + if [[ "$BUILD_ONLY" == False ]]; then + run_cmd make test >& ${desc}.test.log || { report_and_log_test_result 1 ${desc} test && return 0; } + local -i run_end_time=$(date +%s) + comment="$comment run_time=$(($run_end_time-$build_end_time))" + fi + fi + + report_and_log_test_result 0 $desc "$comment" + + return 0 +} + +# wait_for_jobs +wait_for_jobs() { + local -i max_jobs=$1 + local -i num_active_jobs=$(jobs | wc -l) + while [ $num_active_jobs -ge $max_jobs ] + do + sleep 1 + num_active_jobs=$(jobs | wc -l) + jobs >& /dev/null + done +} + +# run_in_background +run_in_background() { + local compiler=$1 + + local -i num_jobs=$NUM_JOBS_TO_RUN_IN_PARALLEL + # Don't override command line input. + # if [[ "$BUILD_ONLY" == True ]]; then + # num_jobs=8 + # else + if [[ "$compiler" == cuda* ]]; then + num_jobs=1 + fi + if [[ "$compiler" == clang ]]; then + num_jobs=1 + fi + # fi + wait_for_jobs $num_jobs + + single_build_and_test $* & +} + +# build_and_test_all +build_and_test_all() { + # Get compiler data. + local compiler=$1 + if [ -z "$CUSTOM_BUILD_LIST" ]; then + local compiler_build_list=$(get_compiler_build_list $compiler) + else + local compiler_build_list=$(echo "$CUSTOM_BUILD_LIST" | tr , ' ') + fi + + # Do builds. + local build + for build in $compiler_build_list + do + run_in_background $compiler $build $BUILD_TYPE + + # If not cuda, do a hwloc test too. + if [[ "$compiler" != cuda* && "$SKIP_HWLOC" == False ]]; then + run_in_background $compiler $build "hwloc-$BUILD_TYPE" + fi + done + + return 0 +} + +get_test_root_dir() { + local existing_results=$(find . -maxdepth 1 -name "$RESULT_ROOT_PREFIX*" | sort) + local -i num_existing_results=$(echo $existing_results | tr ' ' '\n' | wc -l) + local -i num_to_delete=${num_existing_results}-${NUM_RESULTS_TO_KEEP} + + if [ $num_to_delete -gt 0 ]; then + /bin/rm -rf $(echo $existing_results | tr ' ' '\n' | head -n $num_to_delete) + fi + + echo $(pwd)/${RESULT_ROOT_PREFIX}_$(date +"%Y-%m-%d_%H.%M.%S") +} + +wait_summarize_and_exit() { + wait_for_jobs 1 + + echo "#######################################################" + echo "PASSED TESTS" + echo "#######################################################" + + local passed_test + for passed_test in $(\ls -1 $PASSED_DIR | sort) + do + echo $passed_test $(cat $PASSED_DIR/$passed_test) + done + + local -i rv=0 + if [ "$(ls -A $FAILED_DIR)" ]; then + echo "#######################################################" + echo "FAILED TESTS" + echo "#######################################################" + + local failed_test + for failed_test in $(\ls -1 $FAILED_DIR | sort) + do + echo $failed_test "("$(cat $FAILED_DIR/$failed_test)" failed)" + rv=$rv+1 + done + fi + + exit $rv +} + +# +# Main. +# + +ROOT_DIR=$(get_test_root_dir) +mkdir -p $ROOT_DIR +cd $ROOT_DIR + +PASSED_DIR=$ROOT_DIR/results/passed +FAILED_DIR=$ROOT_DIR/results/failed +mkdir -p $PASSED_DIR +mkdir -p $FAILED_DIR + +echo "Going to test compilers: " $COMPILERS_TO_TEST +for COMPILER in $COMPILERS_TO_TEST; do + echo "Testing compiler $COMPILER" + build_and_test_all $COMPILER +done + +wait_summarize_and_exit diff --git a/lib/kokkos/scripts/trilinos-integration/shepard_jenkins_run_script_pthread_intel b/lib/kokkos/scripts/trilinos-integration/blake_jenkins_run_script_pthread_intel similarity index 82% rename from lib/kokkos/scripts/trilinos-integration/shepard_jenkins_run_script_pthread_intel rename to lib/kokkos/scripts/trilinos-integration/blake_jenkins_run_script_pthread_intel index 3b2c725517..df370509a7 100755 --- a/lib/kokkos/scripts/trilinos-integration/shepard_jenkins_run_script_pthread_intel +++ b/lib/kokkos/scripts/trilinos-integration/blake_jenkins_run_script_pthread_intel @@ -1,6 +1,8 @@ #!/bin/bash -el ulimit -c 0 -module load devpack/openmpi/2.1.1/intel/17.4.196/cuda/none +module load devpack/20171203/openmpi/2.1.2/intel/18.1.163 +# Trilinos now requires cmake version >= 3.10.0 +module swap cmake/3.9.0 cmake/3.10.2 KOKKOS_BRANCH=$1 TRILINOS_UPDATE_BRANCH=$2 @@ -28,8 +30,9 @@ export JENKINS_DO_PTHREAD=ON export JENKINS_DO_SERIAL=OFF export JENKINS_DO_COMPLEX=OFF -export JENKINS_ARCH_CXX_FLAG="-xCORE-AVX2 -mkl" -export JENKINS_ARCH_C_FLAG="-xCORE-AVX2 -mkl" +export JENKINS_ARCH=SKX +export JENKINS_ARCH_CXX_FLAG="-xCORE-AVX512 -mkl" +export JENKINS_ARCH_C_FLAG="-xCORE-AVX512 -mkl" export BLAS_LIBRARIES="-mkl;${MKLROOT}/lib/intel64/libmkl_intel_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_thread.a;${MKLROOT}/lib/intel64/libmkl_core.a" export LAPACK_LIBRARIES=${BLAS_LIBRARIES} @@ -37,7 +40,7 @@ export JENKINS_DO_TESTS=ON export JENKINS_DO_EXAMPLES=ON export JENKINS_DO_SHARED=ON -export QUEUE=haswell +export QUEUE=blake module load python diff --git a/lib/kokkos/scripts/trilinos-integration/shepard_jenkins_run_script_serial_intel b/lib/kokkos/scripts/trilinos-integration/blake_jenkins_run_script_serial_intel similarity index 82% rename from lib/kokkos/scripts/trilinos-integration/shepard_jenkins_run_script_serial_intel rename to lib/kokkos/scripts/trilinos-integration/blake_jenkins_run_script_serial_intel index 9ce936ae26..04f1378cec 100755 --- a/lib/kokkos/scripts/trilinos-integration/shepard_jenkins_run_script_serial_intel +++ b/lib/kokkos/scripts/trilinos-integration/blake_jenkins_run_script_serial_intel @@ -1,6 +1,8 @@ #!/bin/bash -el ulimit -c 0 -module load devpack/openmpi/2.1.1/intel/17.4.196/cuda/none +module load devpack/20171203/openmpi/2.1.2/intel/18.1.163 +# Trilinos now requires cmake version >= 3.10.0 +module swap cmake/3.9.0 cmake/3.10.2 KOKKOS_BRANCH=$1 TRILINOS_UPDATE_BRANCH=$2 @@ -28,8 +30,9 @@ export JENKINS_DO_PTHREAD=OFF export JENKINS_DO_SERIAL=ON export JENKINS_DO_COMPLEX=ON -export JENKINS_ARCH_CXX_FLAG="-xCORE-AVX2 -mkl" -export JENKINS_ARCH_C_FLAG="-xCORE-AVX2 -mkl" +export JENKINS_ARCH=SKX +export JENKINS_ARCH_CXX_FLAG="-xCORE-AVX512 -mkl" +export JENKINS_ARCH_C_FLAG="-xCORE-AVX512 -mkl" export BLAS_LIBRARIES="-mkl;${MKLROOT}/lib/intel64/libmkl_intel_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_thread.a;${MKLROOT}/lib/intel64/libmkl_core.a" export LAPACK_LIBRARIES=${BLAS_LIBRARIES} @@ -37,7 +40,7 @@ export JENKINS_DO_TESTS=ON export JENKINS_DO_EXAMPLES=ON export JENKINS_DO_SHARED=ON -export QUEUE=haswell +export QUEUE=blake module load python diff --git a/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_cuda b/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_cuda index 2716767fe5..98900c3c9b 100755 --- a/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_cuda +++ b/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_cuda @@ -20,7 +20,10 @@ then TRILINOS_PRISTINE_BRANCH=develop fi -module load devpack/openmpi/1.10.4/gcc/5.4.0/cuda/8.0.44 +module load devpack/20180521/openmpi/2.1.2/gcc/7.2.0/cuda/9.2.88 +module swap openblas/0.2.20/gcc/7.2.0 netlib/3.8.0/gcc/7.2.0 +# Trilinos now requires cmake version >= 3.10.0 +module swap cmake/3.9.6 cmake/3.12.3 export OMP_NUM_THREADS=8 export JENKINS_DO_CUDA=ON export JENKINS_DO_OPENMP=OFF @@ -28,6 +31,7 @@ export JENKINS_DO_PTHREAD=OFF export JENKINS_DO_SERIAL=ON export JENKINS_DO_COMPLEX=OFF +export JENKINS_ARCH="Power8,Kepler37" export JENKINS_ARCH_CXX_FLAG="-mcpu=power8 -arch=sm_37" export JENKINS_ARCH_C_FLAG="-mcpu=power8" export BLAS_LIBRARIES="${BLAS_ROOT}/lib/libblas.a;gfortran;gomp" diff --git a/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_omp b/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_omp index ff1086507c..9c5244cd35 100755 --- a/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_omp +++ b/lib/kokkos/scripts/trilinos-integration/white_run_jenkins_script_omp @@ -20,7 +20,10 @@ then TRILINOS_PRISTINE_BRANCH=develop fi -module load devpack/openmpi/1.10.4/gcc/5.4.0/cuda/8.0.44 +module load devpack/20180521/openmpi/2.1.2/gcc/7.2.0/cuda/9.2.88 +module swap openblas/0.2.20/gcc/7.2.0 netlib/3.8.0/gcc/7.2.0 +# Trilinos now requires cmake version >= 3.10.0 +module swap cmake/3.9.6 cmake/3.12.3 export OMP_NUM_THREADS=8 export JENKINS_DO_CUDA=OFF export JENKINS_DO_OPENMP=ON @@ -28,6 +31,7 @@ export JENKINS_DO_PTHREAD=OFF export JENKINS_DO_SERIAL=OFF export JENKINS_DO_COMPLEX=OFF +export JENKINS_ARCH="Power8" export JENKINS_ARCH_CXX_FLAG="-mcpu=power8" export JENKINS_ARCH_C_FLAG="-mcpu=power8" export BLAS_LIBRARIES="${BLAS_ROOT}/lib/libblas.a;gfortran;gomp" diff --git a/lib/latte/Install.py b/lib/latte/Install.py index 1e1f3040c2..25c12aeb40 100644 --- a/lib/latte/Install.py +++ b/lib/latte/Install.py @@ -1,14 +1,35 @@ #!/usr/bin/env python -# Install.py tool to download, unpack, build, and link to the LATTE library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to download, unpack, build, and link to the LATTE library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,subprocess,hashlib +import sys, os, subprocess, shutil, tarfile +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = '1.2.1' +suffix = 'gfortran' + +# known checksums for different LATTE versions. used to validate the download. +checksums = { \ + '1.1.0' : '533635721ee222d0ed2925a18fb5b294', \ + '1.2.0' : '68bf0db879da5e068a71281020239ae7', \ + '1.2.1' : '85ac414fdada2d04619c8f936344df14', \ + } # help message -help = """ +HELP = """ Syntax from src dir: make lib-latte args="-b" or: make lib-latte args="-p /usr/local/latte" or: make lib-latte args="-m gfortran" @@ -19,190 +40,99 @@ Syntax from lib dir: python Install.py -b or: python Install.py -m gfortran or: python Install.py -v 1.2.1 -b -specify one or more options, order does not matter - - -b = download and build the LATTE library - -p = specify folder of existing LATTE installation - -m = copy Makefile.lammps.suffix to Makefile.lammps - -v = set version of LATTE library to download and set up (default = 1.2.1) - Example: make lib-latte args="-b -m gfortran" # download/build in lib/latte make lib-latte args="-p $HOME/latte" # use existing LATTE installation """ -# settings -version = '1.2.1' +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the LATTE library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing LATTE installation") +parser.add_argument("-m", "--machine", choices=['gfortran', 'ifort', 'linalg', 'serial', 'mpi'], + help="suffix of a Makefile.lammps.* file used for linking LAMMPS with this library") +parser.add_argument("-v", "--version", default=version, + help="set version of LATTE to download and build (default: %s)" % version) -# known checksums for different LATTE versions. used to validate the download. -checksums = { \ - '1.1.0' : '533635721ee222d0ed2925a18fb5b294', \ - '1.2.0' : '68bf0db879da5e068a71281020239ae7', \ - '1.2.1' : '85ac414fdada2d04619c8f936344df14', \ - } +args = parser.parse_args() -# print error message or help +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +homepath = fullpath(".") -# expand to full path name -# process leading '~' or relative path +buildflag = args.build +pathflag = args.path is not None +version = args.version +suffixflag = args.machine is not None +suffix = args.machine -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) - -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) - - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program - else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file - - return None - -def geturl(url,fname): - success = False - - if which('curl') != None: - cmd = 'curl -L -o "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling curl failed with: %s" % e.output.decode('UTF-8')) - - if not success and which('wget') != None: - cmd = 'wget -O "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling wget failed with: %s" % e.output.decode('UTF-8')) - - if not success: - error("Failed to download source code with 'curl' or 'wget'") - return - -def checkmd5sum(md5sum,fname): - with open(fname,'rb') as fh: - m = hashlib.md5() - while True: - data = fh.read(81920) - if not data: - break - m.update(data) - fh.close() - return m.hexdigest() == md5sum - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -homepath = "." - -buildflag = False -pathflag = False -suffixflag = False -linkflag = True - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-p": - if iarg+2 > nargs: error() - lattedir = fullpath(args[iarg+1]) - pathflag = True - iarg += 2 - elif args[iarg] == "-b": - buildflag = True - iarg += 1 - elif args[iarg] == "-m": - if iarg+2 > nargs: error() - suffix = args[iarg+1] - suffixflag = True - iarg += 2 - elif args[iarg] == "-v": - if iarg+2 > nargs: error() - version = args[iarg+1] - iarg += 2 - else: error() +if pathflag: + lattedir = args.path + if not os.path.isdir(lattedir): + sys.exit("LATTE path %s does not exist" % lattedir) + lattedir = fullpath(lattedir) homedir = "LATTE-%s" % version -if (buildflag and pathflag): - error("Cannot use -b and -p flag at the same time") - if buildflag: url = "https://github.com/lanl/LATTE/archive/v%s.tar.gz" % version lattepath = fullpath(homepath) - lattedir = "%s/%s" % (lattepath,homedir) - -if pathflag: - if not os.path.isdir(lattedir): error("LATTE path does not exist") + lattedir = os.path.join(lattepath, homedir) # download and unpack LATTE tarball if buildflag: print("Downloading LATTE ...") - geturl(url,"LATTE.tar.gz") + geturl(url, "LATTE.tar.gz") # verify downloaded archive integrity via md5 checksum, if known. if version in checksums: - if not checkmd5sum(checksums[version],'LATTE.tar.gz'): - error("Checksum for LATTE library does not match") + if not checkmd5sum(checksums[version], 'LATTE.tar.gz'): + sys.exit("Checksum for LATTE library does not match") print("Unpacking LATTE ...") if os.path.exists(lattedir): - cmd = 'rm -rf "%s"' % lattedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'cd "%s"; tar zxvf LATTE.tar.gz' % lattepath - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.remove("%s/LATTE.tar.gz" % lattepath) + shutil.rmtree(lattedir) + if tarfile.is_tarfile('LATTE.tar.gz'): + tgz = tarfile.open('LATTE.tar.gz') + tgz.extractall() + os.remove('LATTE.tar.gz') + else: + sys.exit("File LATTE.tar.gz is not a supported archive") -# build LATTE - -if buildflag: + # build LATTE print("Building LATTE ...") cmd = 'cd "%s"; make' % lattedir - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - print(txt.decode('UTF-8')) + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + sys.exit("Make failed with:\n %s" % e.output.decode('UTF-8')) # create 3 links in lib/latte to LATTE dirs -# do this -b or -p is set -if buildflag or pathflag: - print("Creating links to LATTE files") - if os.path.isfile("includelink") or os.path.islink("includelink"): - os.remove("includelink") - if os.path.isfile("liblink") or os.path.islink("liblink"): - os.remove("liblink") - if os.path.isfile("filelink.o") or os.path.islink("filelink.o"): - os.remove("filelink.o") - cmd = 'ln -s "%s/src" includelink' % lattedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "%s" liblink' % lattedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "%s/src/latte_c_bind.o" filelink.o' % lattedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print("Creating links to LATTE files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") +if os.path.isfile("filelink.o") or os.path.islink("filelink.o"): + os.remove("filelink.o") +os.symlink(os.path.join(lattedir, 'src'), 'includelink') +os.symlink(lattedir, 'liblink') +os.symlink(os.path.join(lattedir, 'src', 'latte_c_bind.o'), 'filelink.o') # copy Makefile.lammps.suffix to Makefile.lammps -if suffixflag: +if suffixflag or not os.path.exists("Makefile.lammps"): + if suffix is None: + suffix = 'gfortran' print("Creating Makefile.lammps") if os.path.exists("Makefile.lammps.%s" % suffix): - cmd = 'cp Makefile.lammps.%s Makefile.lammps' % suffix - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + shutil.copyfile("Makefile.lammps.%s" % suffix, 'Makefile.lammps') diff --git a/lib/meam/.depend b/lib/meam/.depend deleted file mode 100644 index 0945fba47a..0000000000 --- a/lib/meam/.depend +++ /dev/null @@ -1,9 +0,0 @@ -# dependencies. needed for parallel make -$(DIR)meam_data.o: meam_data.F -$(DIR)meam_cleanup.o: meam_cleanup.F $(DIR)meam_data.o -$(DIR)meam_dens_final.o: meam_dens_final.F $(DIR)meam_data.o -$(DIR)meam_dens_init.o: meam_dens_init.F $(DIR)meam_data.o -$(DIR)meam_force.o: meam_force.F $(DIR)meam_data.o -$(DIR)meam_setup_done.o: meam_setup_done.F $(DIR)meam_data.o -$(DIR)meam_setup_global.o: meam_setup_global.F $(DIR)meam_data.o -$(DIR)meam_setup_param.o: meam_setup_param.F $(DIR)meam_data.o diff --git a/lib/meam/.gitignore b/lib/meam/.gitignore deleted file mode 100644 index 63a7748cf4..0000000000 --- a/lib/meam/.gitignore +++ /dev/null @@ -1 +0,0 @@ -*.mod diff --git a/lib/meam/Install.py b/lib/meam/Install.py deleted file mode 120000 index ffe709d44c..0000000000 --- a/lib/meam/Install.py +++ /dev/null @@ -1 +0,0 @@ -../Install.py \ No newline at end of file diff --git a/lib/meam/Makefile.g95 b/lib/meam/Makefile.g95 deleted file mode 100644 index 91371441bd..0000000000 --- a/lib/meam/Makefile.g95 +++ /dev/null @@ -1,57 +0,0 @@ -# * -# *_________________________________________________________________________* -# * MEAM: MODEFIED EMBEDDED ATOM METHOD * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * AUTHORS: Greg Wagner, Sandia National Laboratories * -# * CONTACT: gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.gfortran - -# ------ FILES ------ - -SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F - -FILES = $(SRC) Makefile - -# ------ DEFINITIONS ------ - -LIB = libmeam.a -OBJ = $(SRC:.F=.o) fm_exp.o - -# ------ SETTINGS ------ - -F90 = g95 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F - $(F90) $(F90FLAGS) -c $< - -%.o:%.c - $(CC) $(F90FLAGS) -c $< - -include .depend -# ------ CLEAN ------ - -clean: - -rm *.o *.mod *~ $(LIB) - -tar: - -tar -cvf ../MEAM.tar $(FILES) diff --git a/lib/meam/Makefile.gfortran b/lib/meam/Makefile.gfortran deleted file mode 100644 index 509e4cebc3..0000000000 --- a/lib/meam/Makefile.gfortran +++ /dev/null @@ -1,61 +0,0 @@ -# * -# *_________________________________________________________________________* -# * MEAM: MODEFIED EMBEDDED ATOM METHOD * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * AUTHORS: Greg Wagner, Sandia National Laboratories * -# * CONTACT: gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.gfortran - -# ------ FILES ------ - -SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F - -FILES = $(SRC) Makefile - -# ------ DEFINITIONS ------ - -LIB = libmeam.a -OBJ = $(SRC:.F=.o) fm_exp.o - -# ------ SETTINGS ------ - -F90 = gfortran -CC = gcc -F90FLAGS = -O3 -fPIC -ffast-math -ftree-vectorize -fexpensive-optimizations -fno-second-underscore -g -#F90FLAGS = -O -ARCHIVE = ar -ARCHFLAG = -rc -LINK = g++ -LINKFLAGS = -O -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F - $(F90) $(F90FLAGS) -c $< - -%.o:%.c - $(CC) $(F90FLAGS) -c $< - -include .depend -# ------ CLEAN ------ - -clean: - -rm *.o *.mod *~ $(LIB) - -tar: - -tar -cvf ../MEAM.tar $(FILES) diff --git a/lib/meam/Makefile.ifort b/lib/meam/Makefile.ifort deleted file mode 100644 index cd3bca9882..0000000000 --- a/lib/meam/Makefile.ifort +++ /dev/null @@ -1,57 +0,0 @@ -# * -# *_________________________________________________________________________* -# * MEAM: MODEFIED EMBEDDED ATOM METHOD * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * AUTHORS: Greg Wagner, Sandia National Laboratories * -# * CONTACT: gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.ifort - -# ------ FILES ------ - -SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F - -FILES = $(SRC) Makefile - -# ------ DEFINITIONS ------ - -LIB = libmeam.a -OBJ = $(SRC:.F=.o) fm_exp.o - -# ------ SETTINGS ------ - -F90 = ifort -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F - $(F90) $(F90FLAGS) -c $< - -%.o:%.c - $(CC) $(F90FLAGS) -c $< - -include .depend -# ------ CLEAN ------ - -clean: - -rm *.o *.mod *~ $(LIB) - -tar: - -tar -cvf ../MEAM.tar $(FILES) diff --git a/lib/meam/Makefile.lammps.gfortran b/lib/meam/Makefile.lammps.gfortran deleted file mode 100644 index fa62c997dc..0000000000 --- a/lib/meam/Makefile.lammps.gfortran +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -meam_SYSINC = -meam_SYSLIB = -lgfortran -meam_SYSPATH = diff --git a/lib/meam/Makefile.lammps.glory b/lib/meam/Makefile.lammps.glory deleted file mode 100644 index 153e699b72..0000000000 --- a/lib/meam/Makefile.lammps.glory +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -meam_SYSINC = -meam_SYSLIB = -lifcore -lsvml -lompstub -limf -meam_SYSPATH = -L/opt/intel-11.1.046/lib/intel64 diff --git a/lib/meam/Makefile.lammps.ifort b/lib/meam/Makefile.lammps.ifort deleted file mode 100644 index bd4d98f929..0000000000 --- a/lib/meam/Makefile.lammps.ifort +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -meam_SYSINC = -meam_SYSLIB = -lifcore -lsvml -lompstub -limf -meam_SYSPATH = -L/opt/intel/fce/10.0.023/lib diff --git a/lib/meam/Makefile.mpi b/lib/meam/Makefile.mpi deleted file mode 100644 index fd3dbde555..0000000000 --- a/lib/meam/Makefile.mpi +++ /dev/null @@ -1,61 +0,0 @@ -# * -# *_________________________________________________________________________* -# * MEAM: MODEFIED EMBEDDED ATOM METHOD * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * AUTHORS: Greg Wagner, Sandia National Laboratories * -# * CONTACT: gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.empty - -# ------ FILES ------ - -SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F - -FILES = $(SRC) Makefile - -# ------ DEFINITIONS ------ - -LIB = libmeam.a -OBJ = $(SRC:.F=.o) fm_exp.o - -# ------ SETTINGS ------ - -F90 = mpifort -CC = mpicc -F90FLAGS = -O3 -fPIC -#F90FLAGS = -O -ARCHIVE = ar -ARCHFLAG = -rc -LINK = mpicxx -LINKFLAGS = -O -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F - $(F90) $(F90FLAGS) -c $< - -%.o:%.c - $(CC) $(F90FLAGS) -c $< - -include .depend -# ------ CLEAN ------ - -clean: - -rm *.o *.mod *~ $(LIB) - -tar: - -tar -cvf ../MEAM.tar $(FILES) diff --git a/lib/meam/Makefile.pgf90 b/lib/meam/Makefile.pgf90 deleted file mode 100644 index 32ce909f48..0000000000 --- a/lib/meam/Makefile.pgf90 +++ /dev/null @@ -1,57 +0,0 @@ -# * -# *_________________________________________________________________________* -# * MEAM: MODEFIED EMBEDDED ATOM METHOD * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * AUTHORS: Greg Wagner, Sandia National Laboratories * -# * CONTACT: gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.pgf90 - -# ------ FILES ------ - -SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F - -FILES = $(SRC) Makefile - -# ------ DEFINITIONS ------ - -LIB = libmeam.a -OBJ = $(SRC:.F=.o) fm_exp.o - -# ------ SETTINGS ------ - -F90 = pgf90 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F - $(F90) $(F90FLAGS) -c $< - -%.o:%.c - $(CC) $(F90FLAGS) -c $< - -include .depend -# ------ CLEAN ------ - -clean: - -rm *.o *.mod *~ $(LIB) - -tar: - -tar -cvf ../MEAM.tar $(FILES) diff --git a/lib/meam/Makefile.serial b/lib/meam/Makefile.serial deleted file mode 120000 index c52fbcb986..0000000000 --- a/lib/meam/Makefile.serial +++ /dev/null @@ -1 +0,0 @@ -Makefile.gfortran \ No newline at end of file diff --git a/lib/meam/Makefile.tbird b/lib/meam/Makefile.tbird deleted file mode 100644 index 7253d8305b..0000000000 --- a/lib/meam/Makefile.tbird +++ /dev/null @@ -1,59 +0,0 @@ -# * -# *_________________________________________________________________________* -# * MEAM: MODEFIED EMBEDDED ATOM METHOD * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * AUTHORS: Greg Wagner, Sandia National Laboratories * -# * CONTACT: gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.glory - -# ------ FILES ------ - -SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F - -FILES = $(SRC) Makefile - -# ------ DEFINITIONS ------ - -LIB = libmeam.a -OBJ = $(SRC:.F=.o) fm_exp.o - -# ------ SETTINGS ------ - -F90 = mpif90 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -LINK = g++ -LINKFLAGS = -O -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F - $(F90) $(F90FLAGS) -c $< - -%.o:%.c - $(CC) $(F90FLAGS) -c $< - -include .depend -# ------ CLEAN ------ - -clean: - -rm *.o *.mod *~ $(LIB) - -tar: - -tar -cvf ../MEAM.tar $(FILES) diff --git a/lib/meam/README b/lib/meam/README deleted file mode 100644 index b3111c1317..0000000000 --- a/lib/meam/README +++ /dev/null @@ -1,51 +0,0 @@ -MEAM (modified embedded atom method) library - -Greg Wagner, Sandia National Labs -gjwagne at sandia.gov -Jan 2007 - -This library is in implementation of the MEAM potential, specifically -designed to work with LAMMPS. - -------------------------------------------------- - -This directory has source files to build a library that LAMMPS -links against when using the MEAM package. - -This library must be built with a F90 compiler, before LAMMPS is -built, so LAMMPS can link against it. - -You can type "make lib-meam" from the src directory to see help on how -to build this library via make commands, or you can do the same thing -by typing "python Install.py" from within this directory, or you can -do it manually by following the instructions below. - -Build the library using one of the provided Makefile.* files or create -your own, specific to your compiler and system. For example: - -make -f Makefile.gfortran - -When you are done building this library, two files should -exist in this directory: - -libmeam.a the library LAMMPS will link against -Makefile.lammps settings the LAMMPS Makefile will import - -Makefile.lammps is created by the make command, by copying one of the -Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the -Makefile.* files. - -IMPORTANT: You must examine the final Makefile.lammps to insure it is -correct for your system, else the LAMMPS build will likely fail. - -Makefile.lammps has settings for 3 variables: - -user-meam_SYSINC = leave blank for this package -user-meam_SYSLIB = auxiliary F90 libs needed to link a F90 lib with - a C++ program (LAMMPS) via a C++ compiler -user-meam_SYSPATH = path(s) to where those libraries are - -Because you have a F90 compiler on your system, you should have these -libraries. But you will have to figure out which ones are needed and -where they are. Examples of common configurations are in the -Makefile.lammps.* files. diff --git a/lib/meam/fm_exp.c b/lib/meam/fm_exp.c deleted file mode 100644 index 26d23b2e24..0000000000 --- a/lib/meam/fm_exp.c +++ /dev/null @@ -1,133 +0,0 @@ -/* - Copyright (c) 2012,2013 Axel Kohlmeyer - All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions - are met: - - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - * Neither the name of the nor the - names of its contributors may be used to endorse or promote products - derived from this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL BE LIABLE FOR ANY -DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND -ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF -THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. -*/ - -/* faster versions of 2**x, e**x, and 10**x in single and double precision. - * - * Based on the Cephes math library 2.8 - */ - -#include -#include - -/* internal definitions for the fastermath library */ - -/* IEEE 754 double precision floating point data manipulation */ -typedef union -{ - double f; - uint64_t u; - struct {int32_t i0,i1;}; -} udi_t; -#define FM_DOUBLE_BIAS 1023 -#define FM_DOUBLE_EMASK 2146435072 -#define FM_DOUBLE_MBITS 20 -#define FM_DOUBLE_MMASK 1048575 -#define FM_DOUBLE_EZERO 1072693248 - -/* generate 2**num in floating point by bitshifting */ -#define FM_DOUBLE_INIT_EXP(var,num) \ - var.i0 = 0; \ - var.i1 = (((int) num) + FM_DOUBLE_BIAS) << 20 - -/* double precision constants */ -#define FM_DOUBLE_LOG2OFE 1.4426950408889634074 -#define FM_DOUBLE_LOGEOF2 6.9314718055994530942e-1 -#define FM_DOUBLE_LOG2OF10 3.32192809488736234789 -#define FM_DOUBLE_LOG10OF2 3.0102999566398119521e-1 -#define FM_DOUBLE_LOG10OFE 4.3429448190325182765e-1 -#define FM_DOUBLE_SQRT2 1.41421356237309504880 -#define FM_DOUBLE_SQRTH 0.70710678118654752440 - -/* optimizer friendly implementation of exp2(x). - * - * strategy: - * - * split argument into an integer part and a fraction: - * ipart = floor(x+0.5); - * fpart = x - ipart; - * - * compute exp2(ipart) from setting the ieee754 exponent - * compute exp2(fpart) using a pade' approximation for x in [-0.5;0.5[ - * - * the result becomes: exp2(x) = exp2(ipart) * exp2(fpart) - */ - -static const double fm_exp2_q[] = { -/* 1.00000000000000000000e0, */ - 2.33184211722314911771e2, - 4.36821166879210612817e3 -}; -static const double fm_exp2_p[] = { - 2.30933477057345225087e-2, - 2.02020656693165307700e1, - 1.51390680115615096133e3 -}; - -static double fm_exp2(double x) -{ - double ipart, fpart, px, qx; - udi_t epart; - - ipart = floor(x+0.5); - fpart = x - ipart; - FM_DOUBLE_INIT_EXP(epart,ipart); - - x = fpart*fpart; - - px = fm_exp2_p[0]; - px = px*x + fm_exp2_p[1]; - qx = x + fm_exp2_q[0]; - px = px*x + fm_exp2_p[2]; - qx = qx*x + fm_exp2_q[1]; - - px = px * fpart; - - x = 1.0 + 2.0*(px/(qx-px)); - return epart.f*x; -} - -double fm_exp_(double *x) -{ -#if defined(__BYTE_ORDER__) -#if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__ - return fm_exp2(FM_DOUBLE_LOG2OFE * (*x)); -#endif -#endif - return exp(*x); -} - -/* - * Local Variables: - * mode: c - * compile-command: "make -C .." - * c-basic-offset: 4 - * fill-column: 76 - * indent-tabs-mode: nil - * End: - */ diff --git a/lib/meam/meam_cleanup.F b/lib/meam/meam_cleanup.F deleted file mode 100644 index dce0c6469e..0000000000 --- a/lib/meam/meam_cleanup.F +++ /dev/null @@ -1,26 +0,0 @@ -c Declaration in pair_meam.h: -c -c void meam_cleanup() -c -c Call from PairMEAM destructor -c -c meam_cleanup() -c - - subroutine meam_cleanup - use meam_data - implicit none - - integer dealloc_error - - deallocate(phir,STAT=dealloc_error) - deallocate(phirar,STAT=dealloc_error) - deallocate(phirar1,STAT=dealloc_error) - deallocate(phirar2,STAT=dealloc_error) - deallocate(phirar3,STAT=dealloc_error) - deallocate(phirar4,STAT=dealloc_error) - deallocate(phirar5,STAT=dealloc_error) - deallocate(phirar6,STAT=dealloc_error) - - return - end diff --git a/lib/meam/meam_data.F b/lib/meam/meam_data.F deleted file mode 100644 index 719963bd59..0000000000 --- a/lib/meam/meam_data.F +++ /dev/null @@ -1,87 +0,0 @@ - - module meam_data - - integer, parameter :: maxelt = 5 - real*8 , external :: fm_exp - -c cutforce = force cutoff -c cutforcesq = force cutoff squared - - real*8 cutforce,cutforcesq - -c Ec_meam = cohesive energy -c re_meam = nearest-neighbor distance -c Omega_meam = atomic volume -c B_meam = bulk modulus -c Z_meam = number of first neighbors for reference structure -c ielt_meam = atomic number of element -c A_meam = adjustable parameter -c alpha_meam = sqrt(9*Omega*B/Ec) -c rho0_meam = density scaling parameter -c delta_meam = heat of formation for alloys -c beta[0-3]_meam = electron density constants -c t[0-3]_meam = coefficients on densities in Gamma computation -c rho_ref_meam = background density for reference structure -c ibar_meam(i) = selection parameter for Gamma function for elt i, -c lattce_meam(i,j) = lattce configuration for elt i or alloy (i,j) -c neltypes = maximum number of element type defined -c eltind = index number of pair (similar to Voigt notation; ij = ji) -c phir = pair potential function array -c phirar[1-6] = spline coeffs -c attrac_meam = attraction parameter in Rose energy -c repuls_meam = repulsion parameter in Rose energy -c nn2_meam = 1 if second nearest neighbors are to be computed, else 0 -c zbl_meam = 1 if zbl potential for small r to be use, else 0 -c emb_lin_neg = 1 if linear embedding function for rhob to be used, else 0 -c bkgd_dyn = 1 if reference densities follows Dynamo, else 0 -c Cmin_meam, Cmax_meam = min and max values in screening cutoff -c rc_meam = cutoff distance for meam -c delr_meam = cutoff region for meam -c ebound_meam = factor giving maximum boundary of sceen fcn ellipse -c augt1 = flag for whether t1 coefficient should be augmented -c ialloy = flag for newer alloy formulation (as in dynamo code) -c mix_ref_t = flag to recover "old" way of computing t in reference config -c erose_form = selection parameter for form of E_rose function -c gsmooth_factor = factor determining length of G smoothing region -c vind[23]D = Voight notation index maps for 2 and 3D -c v2D,v3D = array of factors to apply for Voight notation - -c nr,dr = pair function discretization parameters -c nrar,rdrar = spline coeff array parameters - - real*8 Ec_meam(maxelt,maxelt),re_meam(maxelt,maxelt) - real*8 Omega_meam(maxelt),Z_meam(maxelt) - real*8 A_meam(maxelt),alpha_meam(maxelt,maxelt),rho0_meam(maxelt) - real*8 delta_meam(maxelt,maxelt) - real*8 beta0_meam(maxelt),beta1_meam(maxelt) - real*8 beta2_meam(maxelt),beta3_meam(maxelt) - real*8 t0_meam(maxelt),t1_meam(maxelt) - real*8 t2_meam(maxelt),t3_meam(maxelt) - real*8 rho_ref_meam(maxelt) - integer ibar_meam(maxelt),ielt_meam(maxelt) - character*3 lattce_meam(maxelt,maxelt) - integer nn2_meam(maxelt,maxelt) - integer zbl_meam(maxelt,maxelt) - integer eltind(maxelt,maxelt) - integer neltypes - - real*8, allocatable :: phir(:,:) - - real*8, allocatable :: phirar(:,:),phirar1(:,:),phirar2(:,:), - $ phirar3(:,:),phirar4(:,:),phirar5(:,:),phirar6(:,:) - - real*8 attrac_meam(maxelt,maxelt),repuls_meam(maxelt,maxelt) - - real*8 Cmin_meam(maxelt,maxelt,maxelt) - real*8 Cmax_meam(maxelt,maxelt,maxelt) - real*8 rc_meam,delr_meam,ebound_meam(maxelt,maxelt) - integer augt1, ialloy, mix_ref_t, erose_form - integer emb_lin_neg, bkgd_dyn - real*8 gsmooth_factor - integer vind2D(3,3),vind3D(3,3,3) - integer v2D(6),v3D(10) - - integer nr,nrar - real*8 dr,rdrar - - end module diff --git a/lib/meam/meam_dens_final.F b/lib/meam/meam_dens_final.F deleted file mode 100644 index 098b00f296..0000000000 --- a/lib/meam/meam_dens_final.F +++ /dev/null @@ -1,296 +0,0 @@ -c Extern "C" declaration has the form: -c -c void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *, -c int *, int *, int *, -c double *, double *, double *, double *, double *, double *, -c double *, double *, double *, double *, double *, double *, -c double *, double *, double *, double *, double *, int *); -c -c Call from pair_meam.cpp has the form: -c -c meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom, -c &eng_vdwl,eatom,ntype,type,fmap, -c &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0], -c &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1, -c dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag); -c - - subroutine meam_dens_final(nlocal, nmax, - $ eflag_either, eflag_global, eflag_atom, eng_vdwl, eatom, - $ ntype, type, fmap, - $ Arho1, Arho2, Arho2b, Arho3, Arho3b, t_ave, tsq_ave, - $ Gamma, dGamma1, dGamma2, dGamma3, - $ rho, rho0, rho1, rho2, rho3, fp, errorflag) - - use meam_data - implicit none - - integer nlocal, nmax, eflag_either, eflag_global, eflag_atom - integer ntype, type, fmap - real*8 eng_vdwl, eatom, Arho1, Arho2 - real*8 Arho2b, Arho3, Arho3b - real*8 t_ave, tsq_ave - real*8 Gamma, dGamma1, dGamma2, dGamma3 - real*8 rho, rho0, rho1, rho2, rho3 - real*8 fp - integer errorflag - - dimension eatom(nmax) - dimension type(nmax), fmap(ntype) - dimension Arho1(3,nmax), Arho2(6,nmax), Arho2b(nmax) - dimension Arho3(10,nmax), Arho3b(3,nmax), t_ave(3,nmax) - dimension tsq_ave(3,nmax) - dimension Gamma(nmax), dGamma1(nmax), dGamma2(nmax) - dimension dGamma3(nmax), rho(nmax), rho0(nmax) - dimension rho1(nmax), rho2(nmax), rho3(nmax) - dimension fp(nmax) - - integer i, elti - integer m - real*8 rhob, G, dG, Gbar, dGbar, gam, shp(3), shpi(3), Z - real*8 B, denom, rho_bkgd - -c Complete the calculation of density - - do i = 1,nlocal - - elti = fmap(type(i)) - if (elti.gt.0) then - rho1(i) = 0.d0 - rho2(i) = -1.d0/3.d0*Arho2b(i)*Arho2b(i) - rho3(i) = 0.d0 - do m = 1,3 - rho1(i) = rho1(i) + Arho1(m,i)*Arho1(m,i) - rho3(i) = rho3(i) - 3.d0/5.d0*Arho3b(m,i)*Arho3b(m,i) - enddo - do m = 1,6 - rho2(i) = rho2(i) + v2D(m)*Arho2(m,i)*Arho2(m,i) - enddo - do m = 1,10 - rho3(i) = rho3(i) + v3D(m)*Arho3(m,i)*Arho3(m,i) - enddo - - if( rho0(i) .gt. 0.0 ) then - if (ialloy.eq.1) then - if (tsq_ave(1,i) .ne. 0.0d0) then - t_ave(1,i) = t_ave(1,i)/tsq_ave(1,i) - else - t_ave(1,i) = 0.0d0 - endif - if (tsq_ave(2,i) .ne. 0.0d0) then - t_ave(2,i) = t_ave(2,i)/tsq_ave(2,i) - else - t_ave(2,i) = 0.0d0 - endif - if (tsq_ave(3,i) .ne. 0.0d0) then - t_ave(3,i) = t_ave(3,i)/tsq_ave(3,i) - else - t_ave(3,i) = 0.0d0 - endif - else if (ialloy.eq.2) then - t_ave(1,i) = t1_meam(elti) - t_ave(2,i) = t2_meam(elti) - t_ave(3,i) = t3_meam(elti) - else - t_ave(1,i) = t_ave(1,i)/rho0(i) - t_ave(2,i) = t_ave(2,i)/rho0(i) - t_ave(3,i) = t_ave(3,i)/rho0(i) - endif - endif - - Gamma(i) = t_ave(1,i)*rho1(i) - $ + t_ave(2,i)*rho2(i) + t_ave(3,i)*rho3(i) - - if( rho0(i) .gt. 0.0 ) then - Gamma(i) = Gamma(i)/(rho0(i)*rho0(i)) - end if - - Z = Z_meam(elti) - - call G_gam(Gamma(i),ibar_meam(elti), - $ gsmooth_factor,G,errorflag) - if (errorflag.ne.0) return - call get_shpfcn(shp,lattce_meam(elti,elti)) - if (ibar_meam(elti).le.0) then - Gbar = 1.d0 - dGbar = 0.d0 - else - if (mix_ref_t.eq.1) then - gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2) - $ +t_ave(3,i)*shp(3))/(Z*Z) - else - gam = (t1_meam(elti)*shp(1)+t2_meam(elti)*shp(2) - $ +t3_meam(elti)*shp(3))/(Z*Z) - endif - call G_gam(gam,ibar_meam(elti),gsmooth_factor, - $ Gbar,errorflag) - endif - rho(i) = rho0(i) * G - - if (mix_ref_t.eq.1) then - if (ibar_meam(elti).le.0) then - Gbar = 1.d0 - dGbar = 0.d0 - else - gam = (t_ave(1,i)*shp(1)+t_ave(2,i)*shp(2) - $ +t_ave(3,i)*shp(3))/(Z*Z) - call dG_gam(gam,ibar_meam(elti),gsmooth_factor, - $ Gbar,dGbar) - endif - rho_bkgd = rho0_meam(elti)*Z*Gbar - else - if (bkgd_dyn.eq.1) then - rho_bkgd = rho0_meam(elti)*Z - else - rho_bkgd = rho_ref_meam(elti) - endif - endif - rhob = rho(i)/rho_bkgd - denom = 1.d0/rho_bkgd - - call dG_gam(Gamma(i),ibar_meam(elti),gsmooth_factor,G,dG) - - dGamma1(i) = (G - 2*dG*Gamma(i))*denom - - if( rho0(i) .ne. 0.d0 ) then - dGamma2(i) = (dG/rho0(i))*denom - else - dGamma2(i) = 0.d0 - end if - -c dGamma3 is nonzero only if we are using the "mixed" rule for -c computing t in the reference system (which is not correct, but -c included for backward compatibility - if (mix_ref_t.eq.1) then - dGamma3(i) = rho0(i)*G*dGbar/(Gbar*Z*Z)*denom - else - dGamma3(i) = 0.0 - endif - - B = A_meam(elti)*Ec_meam(elti,elti) - - if( rhob .ne. 0.d0 ) then - if (emb_lin_neg.eq.1 .and. rhob.le.0) then - fp(i) = -B - else - fp(i) = B*(log(rhob)+1.d0) - endif - if (eflag_either.ne.0) then - if (eflag_global.ne.0) then - if (emb_lin_neg.eq.1 .and. rhob.le.0) then - eng_vdwl = eng_vdwl - B*rhob - else - eng_vdwl = eng_vdwl + B*rhob*log(rhob) - endif - endif - if (eflag_atom.ne.0) then - if (emb_lin_neg.eq.1 .and. rhob.le.0) then - eatom(i) = eatom(i) - B*rhob - else - eatom(i) = eatom(i) + B*rhob*log(rhob) - endif - endif - endif - else - if (emb_lin_neg.eq.1) then - fp(i) = -B - else - fp(i) = B - endif - endif - endif - enddo - - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine G_gam(Gamma,ibar,gsmooth_factor,G,errorflag) -c Compute G(Gamma) based on selection flag ibar: -c 0 => G = sqrt(1+Gamma) -c 1 => G = exp(Gamma/2) -c 2 => not implemented -c 3 => G = 2/(1+exp(-Gamma)) -c 4 => G = sqrt(1+Gamma) -c -5 => G = +-sqrt(abs(1+Gamma)) - use meam_data , only: fm_exp - implicit none - real*8 Gamma,G - real*8 gsmooth_factor, gsmooth_switchpoint - integer ibar, errorflag - if (ibar.eq.0.or.ibar.eq.4) then - gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor+1) - if (Gamma.lt.gsmooth_switchpoint) then -c e.g. gsmooth_factor is 99, then: -c gsmooth_switchpoint = -0.99 -c G = 0.01*(-0.99/Gamma)**99 - G = 1/(gsmooth_factor+1) - $ *(gsmooth_switchpoint/Gamma)**gsmooth_factor - G = sqrt(G) - else - G = sqrt(1.d0+Gamma) - endif - else if (ibar.eq.1) then - G = fm_exp(Gamma/2.d0) - else if (ibar.eq.3) then - G = 2.d0/(1.d0+exp(-Gamma)) - else if (ibar.eq.-5) then - if ((1.d0+Gamma).ge.0) then - G = sqrt(1.d0+Gamma) - else - G = -sqrt(-1.d0-Gamma) - endif - else - errorflag = 1 - endif - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine dG_gam(Gamma,ibar,gsmooth_factor,G,dG) -c Compute G(Gamma) and dG(gamma) based on selection flag ibar: -c 0 => G = sqrt(1+Gamma) -c 1 => G = fm_exp(Gamma/2) -c 2 => not implemented -c 3 => G = 2/(1+fm_exp(-Gamma)) -c 4 => G = sqrt(1+Gamma) -c -5 => G = +-sqrt(abs(1+Gamma)) - use meam_data , only: fm_exp - real*8 Gamma,G,dG - real*8 gsmooth_factor, gsmooth_switchpoint - integer ibar - if (ibar.eq.0.or.ibar.eq.4) then - gsmooth_switchpoint = -gsmooth_factor / (gsmooth_factor+1) - if (Gamma.lt.gsmooth_switchpoint) then -c e.g. gsmooth_factor is 99, then: -c gsmooth_switchpoint = -0.99 -c G = 0.01*(-0.99/Gamma)**99 - G = 1/(gsmooth_factor+1) - $ *(gsmooth_switchpoint/Gamma)**gsmooth_factor - G = sqrt(G) - dG = -gsmooth_factor*G/(2.0*Gamma) - else - G = sqrt(1.d0+Gamma) - dG = 1.d0/(2.d0*G) - endif - else if (ibar.eq.1) then - G = fm_exp(Gamma/2.d0) - dG = G/2.d0 - else if (ibar.eq.3) then - G = 2.d0/(1.d0+fm_exp(-Gamma)) - dG = G*(2.d0-G)/2 - else if (ibar.eq.-5) then - if ((1.d0+Gamma).ge.0) then - G = sqrt(1.d0+Gamma) - dG = 1.d0/(2.d0*G) - else - G = -sqrt(-1.d0-Gamma) - dG = -1.d0/(2.d0*G) - endif - endif - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc diff --git a/lib/meam/meam_dens_init.F b/lib/meam/meam_dens_init.F deleted file mode 100644 index 2ca2558135..0000000000 --- a/lib/meam/meam_dens_init.F +++ /dev/null @@ -1,564 +0,0 @@ -c Extern "C" declaration has the form: -c -c void meam_dens_init_(int *, int *, int *, double *, int *, int *, int *, double *, -c int *, int *, int *, int *, -c double *, double *, double *, double *, double *, double *, -c double *, double *, double *, double *, double *, int *); -c -c -c Call from pair_meam.cpp has the form: -c -c meam_dens_init_(&i,&nmax,ntype,type,fmap,&x[0][0], -c &numneigh[i],firstneigh[i],&numneigh_full[i],firstneigh_full[i], -c &scrfcn[offset],&dscrfcn[offset],&fcpair[offset], -c rho0,&arho1[0][0],&arho2[0][0],arho2b, -c &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],&errorflag); -c - - subroutine meam_dens_init(i, nmax, - $ ntype, type, fmap, x, - $ numneigh, firstneigh, - $ numneigh_full, firstneigh_full, - $ scrfcn, dscrfcn, fcpair, rho0, arho1, arho2, arho2b, - $ arho3, arho3b, t_ave, tsq_ave, errorflag) - - use meam_data - implicit none - - integer i, nmax, ntype, type, fmap - real*8 x - integer numneigh, firstneigh, numneigh_full, firstneigh_full - real*8 scrfcn, dscrfcn, fcpair - real*8 rho0, arho1, arho2 - real*8 arho2b, arho3, arho3b, t_ave, tsq_ave - integer errorflag - integer j,jn - - dimension x(3,nmax) - dimension type(nmax), fmap(ntype) - dimension firstneigh(numneigh), firstneigh_full(numneigh_full) - dimension scrfcn(numneigh), dscrfcn(numneigh), fcpair(numneigh) - dimension rho0(nmax), arho1(3,nmax), arho2(6,nmax) - dimension arho2b(nmax), arho3(10,nmax), arho3b(3,nmax) - dimension t_ave(3,nmax), tsq_ave(3,nmax) - - errorflag = 0 - -c Compute screening function and derivatives - call getscreen(i, nmax, scrfcn, dscrfcn, fcpair, x, - $ numneigh, firstneigh, - $ numneigh_full, firstneigh_full, - $ ntype, type, fmap) - -c Calculate intermediate density terms to be communicated - call calc_rho1(i, nmax, ntype, type, fmap, x, - $ numneigh, firstneigh, - $ scrfcn, fcpair, rho0, arho1, arho2, arho2b, - $ arho3, arho3b, t_ave, tsq_ave) - - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine getscreen(i, nmax, scrfcn, dscrfcn, fcpair, x, - $ numneigh, firstneigh, - $ numneigh_full, firstneigh_full, - $ ntype, type, fmap) - - use meam_data - implicit none - - integer i, nmax - real*8 scrfcn, dscrfcn, fcpair, x - integer numneigh, firstneigh, numneigh_full, firstneigh_full - integer ntype, type, fmap - - dimension scrfcn(numneigh), dscrfcn(numneigh) - dimension fcpair(numneigh), x(3,nmax) - dimension firstneigh(numneigh), firstneigh_full(numneigh_full) - dimension type(nmax), fmap(ntype) - - integer jn,j,kn,k - integer elti,eltj,eltk - real*8 xitmp,yitmp,zitmp,delxij,delyij,delzij,rij2,rij - real*8 xjtmp,yjtmp,zjtmp,delxik,delyik,delzik,rik2,rik - real*8 xktmp,yktmp,zktmp,delxjk,delyjk,delzjk,rjk2,rjk - real*8 xik,xjk,sij,fcij,sfcij,dfcij,sikj,dfikj,cikj - real*8 Cmin,Cmax,delc,ebound,rbound,a,coef1,coef2 - real*8 coef1a,coef1b,coef2a,coef2b - real*8 dcikj - real*8 dC1a,dC1b,dC2a,dC2b - real*8 rnorm,fc,dfc,drinv - - drinv = 1.d0/delr_meam - elti = fmap(type(i)) - - if (elti.gt.0) then - - xitmp = x(1,i) - yitmp = x(2,i) - zitmp = x(3,i) - - do jn = 1,numneigh - j = firstneigh(jn) - - eltj = fmap(type(j)) - if (eltj.gt.0) then - -c First compute screening function itself, sij - xjtmp = x(1,j) - yjtmp = x(2,j) - zjtmp = x(3,j) - delxij = xjtmp - xitmp - delyij = yjtmp - yitmp - delzij = zjtmp - zitmp - rij2 = delxij*delxij + delyij*delyij + delzij*delzij - rij = sqrt(rij2) - if (rij.gt.rc_meam) then - fcij = 0.0 - dfcij = 0.d0 - sij = 0.d0 - else - rnorm = (rc_meam-rij)*drinv - call screen(i, j, nmax, x, rij2, sij, - $ numneigh_full, firstneigh_full, ntype, type, fmap) - call dfcut(rnorm,fc,dfc) - fcij = fc - dfcij = dfc*drinv - endif - -c Now compute derivatives - dscrfcn(jn) = 0.d0 - sfcij = sij*fcij - if (sfcij.eq.0.d0.or.sfcij.eq.1.d0) goto 100 - rbound = ebound_meam(elti,eltj) * rij2 - do kn = 1,numneigh_full - k = firstneigh_full(kn) - if (k.eq.j) goto 10 - eltk = fmap(type(k)) - if (eltk.eq.0) goto 10 - xktmp = x(1,k) - yktmp = x(2,k) - zktmp = x(3,k) - delxjk = xktmp - xjtmp - delyjk = yktmp - yjtmp - delzjk = zktmp - zjtmp - rjk2 = delxjk*delxjk + delyjk*delyjk + delzjk*delzjk - if (rjk2.gt.rbound) goto 10 - delxik = xktmp - xitmp - delyik = yktmp - yitmp - delzik = zktmp - zitmp - rik2 = delxik*delxik + delyik*delyik + delzik*delzik - if (rik2.gt.rbound) goto 10 - xik = rik2/rij2 - xjk = rjk2/rij2 - a = 1 - (xik-xjk)*(xik-xjk) -c if a < 0, then ellipse equation doesn't describe this case and -c atom k can't possibly screen i-j - if (a.le.0.d0) goto 10 - cikj = (2.d0*(xik+xjk) + a - 2.d0)/a - Cmax = Cmax_meam(elti,eltj,eltk) - Cmin = Cmin_meam(elti,eltj,eltk) - if (cikj.ge.Cmax) then - goto 10 -c Note that cikj may be slightly negative (within numerical -c tolerance) if atoms are colinear, so don't reject that case here -c (other negative cikj cases were handled by the test on "a" above) -c Note that we never have 0 ebound*rijsq, atom k is definitely outside the ellipse - rbound = ebound_meam(elti,eltj)*rijsq - - do nk = 1,numneigh_full - k = firstneigh_full(nk) - eltk = fmap(type(k)) - if (k.eq.j) goto 10 - delxjk = x(1,k) - x(1,j) - delyjk = x(2,k) - x(2,j) - delzjk = x(3,k) - x(3,j) - rjksq = delxjk*delxjk + delyjk*delyjk + delzjk*delzjk - if (rjksq.gt.rbound) goto 10 - delxik = x(1,k) - x(1,i) - delyik = x(2,k) - x(2,i) - delzik = x(3,k) - x(3,i) - riksq = delxik*delxik + delyik*delyik + delzik*delzik - if (riksq.gt.rbound) goto 10 - xik = riksq/rijsq - xjk = rjksq/rijsq - a = 1 - (xik-xjk)*(xik-xjk) -c if a < 0, then ellipse equation doesn't describe this case and -c atom k can't possibly screen i-j - if (a.le.0.d0) goto 10 - cikj = (2.d0*(xik+xjk) + a - 2.d0)/a - Cmax = Cmax_meam(elti,eltj,eltk) - Cmin = Cmin_meam(elti,eltj,eltk) - if (cikj.ge.Cmax) then - goto 10 -c note that cikj may be slightly negative (within numerical -c tolerance) if atoms are colinear, so don't reject that case here -c (other negative cikj cases were handled by the test on "a" above) - else if (cikj.le.Cmin) then - sij = 0.d0 - goto 20 - else - delc = Cmax - Cmin - cikj = (cikj-Cmin)/delc - call fcut(cikj,sikj) - endif - sij = sij * sikj - 10 continue - enddo - - 20 continue - - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine dsij(i,j,k,jn,nmax,numneigh,rij2,dsij1,dsij2, - $ ntype,type,fmap,x,scrfcn,fcpair) -c Inputs: i,j,k = id's of 3 atom triplet -c jn = id of i-j pair -c rij2 = squared distance between i and j -c Outputs: dsij1 = deriv. of sij w.r.t. rik -c dsij2 = deriv. of sij w.r.t. rjk - use meam_data - implicit none - integer i,j,k,jn,nmax,numneigh - integer elti,eltj,eltk - real*8 rij2,rik2,rjk2,dsij1,dsij2 - integer ntype, type, fmap - real*8 x, scrfcn, fcpair - - dimension type(nmax), fmap(ntype) - dimension x(3,nmax), scrfcn(numneigh), fcpair(numneigh) - - real*8 dxik,dyik,dzik - real*8 dxjk,dyjk,dzjk - real*8 rbound,delc,sij,xik,xjk,cikj,sikj,dfc,a - real*8 Cmax,Cmin,dCikj1,dCikj2 - - sij = scrfcn(jn)*fcpair(jn) - elti = fmap(type(i)) - eltj = fmap(type(j)) - eltk = fmap(type(k)) - Cmax = Cmax_meam(elti,eltj,eltk) - Cmin = Cmin_meam(elti,eltj,eltk) - - dsij1 = 0.d0 - dsij2 = 0.d0 - if ((sij.ne.0.d0).and.(sij.ne.1.d0)) then - rbound = rij2*ebound_meam(elti,eltj) - delc = Cmax-Cmin - dxjk = x(1,k) - x(1,j) - dyjk = x(2,k) - x(2,j) - dzjk = x(3,k) - x(3,j) - rjk2 = dxjk*dxjk + dyjk*dyjk + dzjk*dzjk - if (rjk2.le.rbound) then - dxik = x(1,k) - x(1,i) - dyik = x(2,k) - x(2,i) - dzik = x(3,k) - x(3,i) - rik2 = dxik*dxik + dyik*dyik + dzik*dzik - if (rik2.le.rbound) then - xik = rik2/rij2 - xjk = rjk2/rij2 - a = 1 - (xik-xjk)*(xik-xjk) - if (a.ne.0.d0) then - cikj = (2.d0*(xik+xjk) + a - 2.d0)/a - if (cikj.ge.Cmin.and.cikj.le.Cmax) then - cikj = (cikj-Cmin)/delc - call dfcut(cikj,sikj,dfc) - call dCfunc2(rij2,rik2,rjk2,dCikj1,dCikj2) - a = sij/delc*dfc/sikj - dsij1 = a*dCikj1 - dsij2 = a*dCikj2 - endif - endif - endif - endif - endif - - return - end - - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine fcut(xi,fc) -c cutoff function - implicit none - real*8 xi,fc - real*8 a - if (xi.ge.1.d0) then - fc = 1.d0 - else if (xi.le.0.d0) then - fc = 0.d0 - else - a = 1.d0-xi - a = a*a - a = a*a - a = 1.d0-a - fc = a*a -c fc = xi - endif - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine dfcut(xi,fc,dfc) -c cutoff function and its derivative - implicit none - real*8 xi,fc,dfc,a,a3,a4 - if (xi.ge.1.d0) then - fc = 1.d0 - dfc = 0.d0 - else if (xi.le.0.d0) then - fc = 0.d0 - dfc = 0.d0 - else - a = 1.d0-xi - a3 = a*a*a - a4 = a*a3 - fc = (1.d0-a4)**2 - dfc = 8*(1.d0-a4)*a3 -c fc = xi -c dfc = 1.d0 - endif - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine dCfunc(rij2,rik2,rjk2,dCikj) -c Inputs: rij,rij2,rik2,rjk2 -c Outputs: dCikj = derivative of Cikj w.r.t. rij - implicit none - real*8 rij2,rik2,rjk2,dCikj - real*8 rij4,a,b,denom - - rij4 = rij2*rij2 - a = rik2-rjk2 - b = rik2+rjk2 - denom = rij4 - a*a - denom = denom*denom - dCikj = -4*(-2*rij2*a*a + rij4*b + a*a*b)/denom - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - subroutine dCfunc2(rij2,rik2,rjk2,dCikj1,dCikj2) -c Inputs: rij,rij2,rik2,rjk2 -c Outputs: dCikj1 = derivative of Cikj w.r.t. rik -c dCikj2 = derivative of Cikj w.r.t. rjk - implicit none - real*8 rij2,rik2,rjk2,dCikj1,dCikj2 - real*8 rij4,rik4,rjk4,a,b,denom - - rij4 = rij2*rij2 - rik4 = rik2*rik2 - rjk4 = rjk2*rjk2 - a = rik2-rjk2 - b = rik2+rjk2 - denom = rij4 - a*a - denom = denom*denom - dCikj1 = 4*rij2*(rij4 + rik4 + 2*rik2*rjk2 - 3*rjk4 - 2*rij2*a)/ - $ denom - dCikj2 = 4*rij2*(rij4 - 3*rik4 + 2*rik2*rjk2 + rjk4 + 2*rij2*a)/ - $ denom - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc - - - - diff --git a/lib/meam/meam_force.F b/lib/meam/meam_force.F deleted file mode 100644 index 1297eb2170..0000000000 --- a/lib/meam/meam_force.F +++ /dev/null @@ -1,608 +0,0 @@ -c Extern "C" declaration has the form: -c -c void meam_force_(int *, int *, int *, double *, int *, int *, int *, double *, -c int *, int *, int *, int *, double *, double *, -c double *, double *, double *, double *, double *, double *, -c double *, double *, double *, double *, double *, double *, -c double *, double *, double *, double *, double *, double *, int *); -c -c Call from pair_meam.cpp has the form: -c -c meam_force_(&i,&nmax,&eflag_either,&eflag_global,&eflag_atom,&vflag_atom, -c &eng_vdwl,eatom,&ntype,type,fmap,&x[0][0], -c &numneigh[i],firstneigh[i],&numneigh_full[i],firstneigh_full[i], -c &scrfcn[offset],&dscrfcn[offset],&fcpair[offset], -c dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop, -c &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0], -c &t_ave[0][0],&tsq_ave[0][0],&f[0][0],&vatom[0][0],&errorflag); -c - - subroutine meam_force(i, nmax, - $ eflag_either, eflag_global, eflag_atom, vflag_atom, - $ eng_vdwl, eatom, ntype, type, fmap, x, - $ numneigh, firstneigh, numneigh_full, firstneigh_full, - $ scrfcn, dscrfcn, fcpair, - $ dGamma1, dGamma2, dGamma3, rho0, rho1, rho2, rho3, fp, - $ Arho1, Arho2, Arho2b, Arho3, Arho3b, t_ave, tsq_ave, f, - $ vatom, errorflag) - - use meam_data - implicit none - - integer eflag_either, eflag_global, eflag_atom, vflag_atom - integer nmax, ntype, type, fmap - real*8 eng_vdwl, eatom, x - integer numneigh, firstneigh, numneigh_full, firstneigh_full - real*8 scrfcn, dscrfcn, fcpair - real*8 dGamma1, dGamma2, dGamma3 - real*8 rho0, rho1, rho2, rho3, fp - real*8 Arho1, Arho2, Arho2b - real*8 Arho3, Arho3b - real*8 t_ave, tsq_ave, f, vatom - integer errorflag - - dimension eatom(nmax) - dimension type(nmax), fmap(ntype) - dimension x(3,nmax) - dimension firstneigh(numneigh), firstneigh_full(numneigh_full) - dimension scrfcn(numneigh), dscrfcn(numneigh), fcpair(numneigh) - dimension dGamma1(nmax), dGamma2(nmax), dGamma3(nmax) - dimension rho0(nmax), rho1(nmax), rho2(nmax), rho3(nmax), fp(nmax) - dimension Arho1(3,nmax), Arho2(6,nmax), Arho2b(nmax) - dimension Arho3(10,nmax), Arho3b(3,nmax) - dimension t_ave(3,nmax), tsq_ave(3,nmax), f(3,nmax), vatom(6,nmax) - - integer i,j,jn,k,kn,kk,m,n,p,q - integer nv2,nv3,elti,eltj,eltk,ind - real*8 xitmp,yitmp,zitmp,delij(3),delref(3),rij2,rij,rij3 - real*8 delik(3),deljk(3),v(6),fi(3),fj(3) - real*8 Eu,astar,astarp,third,sixth - real*8 pp,phiforce,dUdrij,dUdsij,dUdrijm(3),force,forcem - real*8 B,r,recip,phi,phip,rhop,a - real*8 sij,fcij,dfcij,ds(3) - real*8 a0,a1,a1i,a1j,a2,a2i,a2j - real*8 a3i,a3j,a3i1,a3i2,a3j1,a3j2 - real*8 G,dG,Gbar,dGbar,gam,shpi(3),shpj(3),Z,denom - real*8 ai,aj,ro0i,ro0j,invrei,invrej - real*8 b0,rhoa0j,drhoa0j,rhoa0i,drhoa0i - real*8 b1,rhoa1j,drhoa1j,rhoa1i,drhoa1i - real*8 b2,rhoa2j,drhoa2j,rhoa2i,drhoa2i - real*8 a3,a3a,b3,rhoa3j,drhoa3j,rhoa3i,drhoa3i - real*8 drho0dr1,drho0dr2,drho0ds1,drho0ds2 - real*8 drho1dr1,drho1dr2,drho1ds1,drho1ds2 - real*8 drho1drm1(3),drho1drm2(3) - real*8 drho2dr1,drho2dr2,drho2ds1,drho2ds2 - real*8 drho2drm1(3),drho2drm2(3) - real*8 drho3dr1,drho3dr2,drho3ds1,drho3ds2 - real*8 drho3drm1(3),drho3drm2(3) - real*8 dt1dr1,dt1dr2,dt1ds1,dt1ds2 - real*8 dt2dr1,dt2dr2,dt2ds1,dt2ds2 - real*8 dt3dr1,dt3dr2,dt3ds1,dt3ds2 - real*8 drhodr1,drhodr2,drhods1,drhods2,drhodrm1(3),drhodrm2(3) - real*8 arg,arg1,arg2 - real*8 arg1i1,arg1j1,arg1i2,arg1j2,arg2i2,arg2j2 - real*8 arg1i3,arg1j3,arg2i3,arg2j3,arg3i3,arg3j3 - real*8 dsij1,dsij2,force1,force2 - real*8 t1i,t2i,t3i,t1j,t2j,t3j - - errorflag = 0 - third = 1.0/3.0 - sixth = 1.0/6.0 - -c Compute forces atom i - - elti = fmap(type(i)) - - if (elti.gt.0) then - xitmp = x(1,i) - yitmp = x(2,i) - zitmp = x(3,i) - -c Treat each pair - do jn = 1,numneigh - - j = firstneigh(jn) - eltj = fmap(type(j)) - - if (scrfcn(jn).ne.0.d0.and.eltj.gt.0) then - - sij = scrfcn(jn)*fcpair(jn) - delij(1) = x(1,j) - xitmp - delij(2) = x(2,j) - yitmp - delij(3) = x(3,j) - zitmp - rij2 = delij(1)*delij(1) + delij(2)*delij(2) - $ + delij(3)*delij(3) - if (rij2.lt.cutforcesq) then - rij = sqrt(rij2) - r = rij - -c Compute phi and phip - ind = eltind(elti,eltj) - pp = rij*rdrar + 1.0D0 - kk = pp - kk = min(kk,nrar-1) - pp = pp - kk - pp = min(pp,1.0D0) - phi = ((phirar3(kk,ind)*pp + phirar2(kk,ind))*pp - $ + phirar1(kk,ind))*pp + phirar(kk,ind) - phip = (phirar6(kk,ind)*pp + phirar5(kk,ind))*pp - $ + phirar4(kk,ind) - recip = 1.0d0/r - - if (eflag_either.ne.0) then - if (eflag_global.ne.0) eng_vdwl = eng_vdwl + phi*sij - if (eflag_atom.ne.0) then - eatom(i) = eatom(i) + 0.5*phi*sij - eatom(j) = eatom(j) + 0.5*phi*sij - endif - endif - -c write(1,*) "force_meamf: phi: ",phi -c write(1,*) "force_meamf: phip: ",phip - -c Compute pair densities and derivatives - invrei = 1.d0/re_meam(elti,elti) - ai = rij*invrei - 1.d0 - ro0i = rho0_meam(elti) - rhoa0i = ro0i*fm_exp(-beta0_meam(elti)*ai) - drhoa0i = -beta0_meam(elti)*invrei*rhoa0i - rhoa1i = ro0i*fm_exp(-beta1_meam(elti)*ai) - drhoa1i = -beta1_meam(elti)*invrei*rhoa1i - rhoa2i = ro0i*fm_exp(-beta2_meam(elti)*ai) - drhoa2i = -beta2_meam(elti)*invrei*rhoa2i - rhoa3i = ro0i*fm_exp(-beta3_meam(elti)*ai) - drhoa3i = -beta3_meam(elti)*invrei*rhoa3i - - if (elti.ne.eltj) then - invrej = 1.d0/re_meam(eltj,eltj) - aj = rij*invrej - 1.d0 - ro0j = rho0_meam(eltj) - rhoa0j = ro0j*fm_exp(-beta0_meam(eltj)*aj) - drhoa0j = -beta0_meam(eltj)*invrej*rhoa0j - rhoa1j = ro0j*fm_exp(-beta1_meam(eltj)*aj) - drhoa1j = -beta1_meam(eltj)*invrej*rhoa1j - rhoa2j = ro0j*fm_exp(-beta2_meam(eltj)*aj) - drhoa2j = -beta2_meam(eltj)*invrej*rhoa2j - rhoa3j = ro0j*fm_exp(-beta3_meam(eltj)*aj) - drhoa3j = -beta3_meam(eltj)*invrej*rhoa3j - else - rhoa0j = rhoa0i - drhoa0j = drhoa0i - rhoa1j = rhoa1i - drhoa1j = drhoa1i - rhoa2j = rhoa2i - drhoa2j = drhoa2i - rhoa3j = rhoa3i - drhoa3j = drhoa3i - endif - - if (ialloy.eq.1) then - rhoa1j = rhoa1j * t1_meam(eltj) - rhoa2j = rhoa2j * t2_meam(eltj) - rhoa3j = rhoa3j * t3_meam(eltj) - rhoa1i = rhoa1i * t1_meam(elti) - rhoa2i = rhoa2i * t2_meam(elti) - rhoa3i = rhoa3i * t3_meam(elti) - drhoa1j = drhoa1j * t1_meam(eltj) - drhoa2j = drhoa2j * t2_meam(eltj) - drhoa3j = drhoa3j * t3_meam(eltj) - drhoa1i = drhoa1i * t1_meam(elti) - drhoa2i = drhoa2i * t2_meam(elti) - drhoa3i = drhoa3i * t3_meam(elti) - endif - - nv2 = 1 - nv3 = 1 - arg1i1 = 0.d0 - arg1j1 = 0.d0 - arg1i2 = 0.d0 - arg1j2 = 0.d0 - arg1i3 = 0.d0 - arg1j3 = 0.d0 - arg3i3 = 0.d0 - arg3j3 = 0.d0 - do n = 1,3 - do p = n,3 - do q = p,3 - arg = delij(n)*delij(p)*delij(q)*v3D(nv3) - arg1i3 = arg1i3 + Arho3(nv3,i)*arg - arg1j3 = arg1j3 - Arho3(nv3,j)*arg - nv3 = nv3+1 - enddo - arg = delij(n)*delij(p)*v2D(nv2) - arg1i2 = arg1i2 + Arho2(nv2,i)*arg - arg1j2 = arg1j2 + Arho2(nv2,j)*arg - nv2 = nv2+1 - enddo - arg1i1 = arg1i1 + Arho1(n,i)*delij(n) - arg1j1 = arg1j1 - Arho1(n,j)*delij(n) - arg3i3 = arg3i3 + Arho3b(n,i)*delij(n) - arg3j3 = arg3j3 - Arho3b(n,j)*delij(n) - enddo - -c rho0 terms - drho0dr1 = drhoa0j * sij - drho0dr2 = drhoa0i * sij - -c rho1 terms - a1 = 2*sij/rij - drho1dr1 = a1*(drhoa1j-rhoa1j/rij)*arg1i1 - drho1dr2 = a1*(drhoa1i-rhoa1i/rij)*arg1j1 - a1 = 2.d0*sij/rij - do m = 1,3 - drho1drm1(m) = a1*rhoa1j*Arho1(m,i) - drho1drm2(m) = -a1*rhoa1i*Arho1(m,j) - enddo - -c rho2 terms - a2 = 2*sij/rij2 - drho2dr1 = a2*(drhoa2j - 2*rhoa2j/rij)*arg1i2 - $ - 2.d0/3.d0*Arho2b(i)*drhoa2j*sij - drho2dr2 = a2*(drhoa2i - 2*rhoa2i/rij)*arg1j2 - $ - 2.d0/3.d0*Arho2b(j)*drhoa2i*sij - a2 = 4*sij/rij2 - do m = 1,3 - drho2drm1(m) = 0.d0 - drho2drm2(m) = 0.d0 - do n = 1,3 - drho2drm1(m) = drho2drm1(m) - $ + Arho2(vind2D(m,n),i)*delij(n) - drho2drm2(m) = drho2drm2(m) - $ - Arho2(vind2D(m,n),j)*delij(n) - enddo - drho2drm1(m) = a2*rhoa2j*drho2drm1(m) - drho2drm2(m) = -a2*rhoa2i*drho2drm2(m) - enddo - -c rho3 terms - rij3 = rij*rij2 - a3 = 2*sij/rij3 - a3a = 6.d0/5.d0*sij/rij - drho3dr1 = a3*(drhoa3j - 3*rhoa3j/rij)*arg1i3 - $ - a3a*(drhoa3j - rhoa3j/rij)*arg3i3 - drho3dr2 = a3*(drhoa3i - 3*rhoa3i/rij)*arg1j3 - $ - a3a*(drhoa3i - rhoa3i/rij)*arg3j3 - a3 = 6*sij/rij3 - a3a = 6*sij/(5*rij) - do m = 1,3 - drho3drm1(m) = 0.d0 - drho3drm2(m) = 0.d0 - nv2 = 1 - do n = 1,3 - do p = n,3 - arg = delij(n)*delij(p)*v2D(nv2) - drho3drm1(m) = drho3drm1(m) - $ + Arho3(vind3D(m,n,p),i)*arg - drho3drm2(m) = drho3drm2(m) - $ + Arho3(vind3D(m,n,p),j)*arg - nv2 = nv2 + 1 - enddo - enddo - drho3drm1(m) = (a3*drho3drm1(m) - a3a*Arho3b(m,i)) - $ *rhoa3j - drho3drm2(m) = (-a3*drho3drm2(m) + a3a*Arho3b(m,j)) - $ *rhoa3i - enddo - -c Compute derivatives of weighting functions t wrt rij - t1i = t_ave(1,i) - t2i = t_ave(2,i) - t3i = t_ave(3,i) - t1j = t_ave(1,j) - t2j = t_ave(2,j) - t3j = t_ave(3,j) - - if (ialloy.eq.1) then - - a1i = 0.d0 - a1j = 0.d0 - a2i = 0.d0 - a2j = 0.d0 - a3i = 0.d0 - a3j = 0.d0 - if ( tsq_ave(1,i) .ne. 0.d0 ) then - a1i = drhoa0j*sij/tsq_ave(1,i) - endif - if ( tsq_ave(1,j) .ne. 0.d0 ) then - a1j = drhoa0i*sij/tsq_ave(1,j) - endif - if ( tsq_ave(2,i) .ne. 0.d0 ) then - a2i = drhoa0j*sij/tsq_ave(2,i) - endif - if ( tsq_ave(2,j) .ne. 0.d0 ) then - a2j = drhoa0i*sij/tsq_ave(2,j) - endif - if ( tsq_ave(3,i) .ne. 0.d0 ) then - a3i = drhoa0j*sij/tsq_ave(3,i) - endif - if ( tsq_ave(3,j) .ne. 0.d0 ) then - a3j = drhoa0i*sij/tsq_ave(3,j) - endif - - dt1dr1 = a1i*(t1_meam(eltj)-t1i*t1_meam(eltj)**2) - dt1dr2 = a1j*(t1_meam(elti)-t1j*t1_meam(elti)**2) - dt2dr1 = a2i*(t2_meam(eltj)-t2i*t2_meam(eltj)**2) - dt2dr2 = a2j*(t2_meam(elti)-t2j*t2_meam(elti)**2) - dt3dr1 = a3i*(t3_meam(eltj)-t3i*t3_meam(eltj)**2) - dt3dr2 = a3j*(t3_meam(elti)-t3j*t3_meam(elti)**2) - - else if (ialloy.eq.2) then - - dt1dr1 = 0.d0 - dt1dr2 = 0.d0 - dt2dr1 = 0.d0 - dt2dr2 = 0.d0 - dt3dr1 = 0.d0 - dt3dr2 = 0.d0 - - else - - ai = 0.d0 - if( rho0(i) .ne. 0.d0 ) then - ai = drhoa0j*sij/rho0(i) - end if - aj = 0.d0 - if( rho0(j) .ne. 0.d0 ) then - aj = drhoa0i*sij/rho0(j) - end if - - dt1dr1 = ai*(t1_meam(eltj)-t1i) - dt1dr2 = aj*(t1_meam(elti)-t1j) - dt2dr1 = ai*(t2_meam(eltj)-t2i) - dt2dr2 = aj*(t2_meam(elti)-t2j) - dt3dr1 = ai*(t3_meam(eltj)-t3i) - dt3dr2 = aj*(t3_meam(elti)-t3j) - - endif - -c Compute derivatives of total density wrt rij, sij and rij(3) - call get_shpfcn(shpi,lattce_meam(elti,elti)) - call get_shpfcn(shpj,lattce_meam(eltj,eltj)) - drhodr1 = dGamma1(i)*drho0dr1 - $ + dGamma2(i)* - $ (dt1dr1*rho1(i)+t1i*drho1dr1 - $ + dt2dr1*rho2(i)+t2i*drho2dr1 - $ + dt3dr1*rho3(i)+t3i*drho3dr1) - $ - dGamma3(i)* - $ (shpi(1)*dt1dr1+shpi(2)*dt2dr1+shpi(3)*dt3dr1) - drhodr2 = dGamma1(j)*drho0dr2 - $ + dGamma2(j)* - $ (dt1dr2*rho1(j)+t1j*drho1dr2 - $ + dt2dr2*rho2(j)+t2j*drho2dr2 - $ + dt3dr2*rho3(j)+t3j*drho3dr2) - $ - dGamma3(j)* - $ (shpj(1)*dt1dr2+shpj(2)*dt2dr2+shpj(3)*dt3dr2) - do m = 1,3 - drhodrm1(m) = 0.d0 - drhodrm2(m) = 0.d0 - drhodrm1(m) = dGamma2(i)* - $ (t1i*drho1drm1(m) - $ + t2i*drho2drm1(m) - $ + t3i*drho3drm1(m)) - drhodrm2(m) = dGamma2(j)* - $ (t1j*drho1drm2(m) - $ + t2j*drho2drm2(m) - $ + t3j*drho3drm2(m)) - enddo - -c Compute derivatives wrt sij, but only if necessary - if (dscrfcn(jn).ne.0.d0) then - drho0ds1 = rhoa0j - drho0ds2 = rhoa0i - a1 = 2.d0/rij - drho1ds1 = a1*rhoa1j*arg1i1 - drho1ds2 = a1*rhoa1i*arg1j1 - a2 = 2.d0/rij2 - drho2ds1 = a2*rhoa2j*arg1i2 - $ - 2.d0/3.d0*Arho2b(i)*rhoa2j - drho2ds2 = a2*rhoa2i*arg1j2 - $ - 2.d0/3.d0*Arho2b(j)*rhoa2i - a3 = 2.d0/rij3 - a3a = 6.d0/(5.d0*rij) - drho3ds1 = a3*rhoa3j*arg1i3 - a3a*rhoa3j*arg3i3 - drho3ds2 = a3*rhoa3i*arg1j3 - a3a*rhoa3i*arg3j3 - - if (ialloy.eq.1) then - - a1i = 0.d0 - a1j = 0.d0 - a2i = 0.d0 - a2j = 0.d0 - a3i = 0.d0 - a3j = 0.d0 - if ( tsq_ave(1,i) .ne. 0.d0 ) then - a1i = rhoa0j/tsq_ave(1,i) - endif - if ( tsq_ave(1,j) .ne. 0.d0 ) then - a1j = rhoa0i/tsq_ave(1,j) - endif - if ( tsq_ave(2,i) .ne. 0.d0 ) then - a2i = rhoa0j/tsq_ave(2,i) - endif - if ( tsq_ave(2,j) .ne. 0.d0 ) then - a2j = rhoa0i/tsq_ave(2,j) - endif - if ( tsq_ave(3,i) .ne. 0.d0 ) then - a3i = rhoa0j/tsq_ave(3,i) - endif - if ( tsq_ave(3,j) .ne. 0.d0 ) then - a3j = rhoa0i/tsq_ave(3,j) - endif - - dt1ds1 = a1i*(t1_meam(eltj)-t1i*t1_meam(eltj)**2) - dt1ds2 = a1j*(t1_meam(elti)-t1j*t1_meam(elti)**2) - dt2ds1 = a2i*(t2_meam(eltj)-t2i*t2_meam(eltj)**2) - dt2ds2 = a2j*(t2_meam(elti)-t2j*t2_meam(elti)**2) - dt3ds1 = a3i*(t3_meam(eltj)-t3i*t3_meam(eltj)**2) - dt3ds2 = a3j*(t3_meam(elti)-t3j*t3_meam(elti)**2) - - else if (ialloy.eq.2) then - - dt1ds1 = 0.d0 - dt1ds2 = 0.d0 - dt2ds1 = 0.d0 - dt2ds2 = 0.d0 - dt3ds1 = 0.d0 - dt3ds2 = 0.d0 - - else - - ai = 0.d0 - if( rho0(i) .ne. 0.d0 ) then - ai = rhoa0j/rho0(i) - end if - aj = 0.d0 - if( rho0(j) .ne. 0.d0 ) then - aj = rhoa0i/rho0(j) - end if - - dt1ds1 = ai*(t1_meam(eltj)-t1i) - dt1ds2 = aj*(t1_meam(elti)-t1j) - dt2ds1 = ai*(t2_meam(eltj)-t2i) - dt2ds2 = aj*(t2_meam(elti)-t2j) - dt3ds1 = ai*(t3_meam(eltj)-t3i) - dt3ds2 = aj*(t3_meam(elti)-t3j) - - endif - - drhods1 = dGamma1(i)*drho0ds1 - $ + dGamma2(i)* - $ (dt1ds1*rho1(i)+t1i*drho1ds1 - $ + dt2ds1*rho2(i)+t2i*drho2ds1 - $ + dt3ds1*rho3(i)+t3i*drho3ds1) - $ - dGamma3(i)* - $ (shpi(1)*dt1ds1+shpi(2)*dt2ds1+shpi(3)*dt3ds1) - drhods2 = dGamma1(j)*drho0ds2 - $ + dGamma2(j)* - $ (dt1ds2*rho1(j)+t1j*drho1ds2 - $ + dt2ds2*rho2(j)+t2j*drho2ds2 - $ + dt3ds2*rho3(j)+t3j*drho3ds2) - $ - dGamma3(j)* - $ (shpj(1)*dt1ds2+shpj(2)*dt2ds2+shpj(3)*dt3ds2) - endif - -c Compute derivatives of energy wrt rij, sij and rij(3) - dUdrij = phip*sij - $ + fp(i)*drhodr1 + fp(j)*drhodr2 - dUdsij = 0.d0 - if (dscrfcn(jn).ne.0.d0) then - dUdsij = phi - $ + fp(i)*drhods1 + fp(j)*drhods2 - endif - do m = 1,3 - dUdrijm(m) = fp(i)*drhodrm1(m) + fp(j)*drhodrm2(m) - enddo - -c Add the part of the force due to dUdrij and dUdsij - - force = dUdrij*recip + dUdsij*dscrfcn(jn) - do m = 1,3 - forcem = delij(m)*force + dUdrijm(m) - f(m,i) = f(m,i) + forcem - f(m,j) = f(m,j) - forcem - enddo - -c Tabulate per-atom virial as symmetrized stress tensor - - if (vflag_atom.ne.0) then - fi(1) = delij(1)*force + dUdrijm(1) - fi(2) = delij(2)*force + dUdrijm(2) - fi(3) = delij(3)*force + dUdrijm(3) - v(1) = -0.5 * (delij(1) * fi(1)) - v(2) = -0.5 * (delij(2) * fi(2)) - v(3) = -0.5 * (delij(3) * fi(3)) - v(4) = -0.25 * (delij(1)*fi(2) + delij(2)*fi(1)) - v(5) = -0.25 * (delij(1)*fi(3) + delij(3)*fi(1)) - v(6) = -0.25 * (delij(2)*fi(3) + delij(3)*fi(2)) - - vatom(1,i) = vatom(1,i) + v(1) - vatom(2,i) = vatom(2,i) + v(2) - vatom(3,i) = vatom(3,i) + v(3) - vatom(4,i) = vatom(4,i) + v(4) - vatom(5,i) = vatom(5,i) + v(5) - vatom(6,i) = vatom(6,i) + v(6) - vatom(1,j) = vatom(1,j) + v(1) - vatom(2,j) = vatom(2,j) + v(2) - vatom(3,j) = vatom(3,j) + v(3) - vatom(4,j) = vatom(4,j) + v(4) - vatom(5,j) = vatom(5,j) + v(5) - vatom(6,j) = vatom(6,j) + v(6) - endif - -c Now compute forces on other atoms k due to change in sij - - if (sij.eq.0.d0.or.sij.eq.1.d0) goto 100 - do kn = 1,numneigh_full - k = firstneigh_full(kn) - eltk = fmap(type(k)) - if (k.ne.j.and.eltk.gt.0) then - call dsij(i,j,k,jn,nmax,numneigh,rij2,dsij1,dsij2, - $ ntype,type,fmap,x,scrfcn,fcpair) - if (dsij1.ne.0.d0.or.dsij2.ne.0.d0) then - force1 = dUdsij*dsij1 - force2 = dUdsij*dsij2 - do m = 1,3 - delik(m) = x(m,k) - x(m,i) - deljk(m) = x(m,k) - x(m,j) - enddo - do m = 1,3 - f(m,i) = f(m,i) + force1*delik(m) - f(m,j) = f(m,j) + force2*deljk(m) - f(m,k) = f(m,k) - force1*delik(m) - $ - force2*deljk(m) - enddo - -c Tabulate per-atom virial as symmetrized stress tensor - - if (vflag_atom.ne.0) then - fi(1) = force1*delik(1) - fi(2) = force1*delik(2) - fi(3) = force1*delik(3) - fj(1) = force2*deljk(1) - fj(2) = force2*deljk(2) - fj(3) = force2*deljk(3) - v(1) = -third * (delik(1)*fi(1) + deljk(1)*fj(1)) - v(2) = -third * (delik(2)*fi(2) + deljk(2)*fj(2)) - v(3) = -third * (delik(3)*fi(3) + deljk(3)*fj(3)) - v(4) = -sixth * (delik(1)*fi(2) + deljk(1)*fj(2) + - $ delik(2)*fi(1) + deljk(2)*fj(1)) - v(5) = -sixth * (delik(1)*fi(3) + deljk(1)*fj(3) + - $ delik(3)*fi(1) + deljk(3)*fj(1)) - v(6) = -sixth * (delik(2)*fi(3) + deljk(2)*fj(3) + - $ delik(3)*fi(2) + deljk(3)*fj(2)) - - vatom(1,i) = vatom(1,i) + v(1) - vatom(2,i) = vatom(2,i) + v(2) - vatom(3,i) = vatom(3,i) + v(3) - vatom(4,i) = vatom(4,i) + v(4) - vatom(5,i) = vatom(5,i) + v(5) - vatom(6,i) = vatom(6,i) + v(6) - vatom(1,j) = vatom(1,j) + v(1) - vatom(2,j) = vatom(2,j) + v(2) - vatom(3,j) = vatom(3,j) + v(3) - vatom(4,j) = vatom(4,j) + v(4) - vatom(5,j) = vatom(5,j) + v(5) - vatom(6,j) = vatom(6,j) + v(6) - vatom(1,k) = vatom(1,k) + v(1) - vatom(2,k) = vatom(2,k) + v(2) - vatom(3,k) = vatom(3,k) + v(3) - vatom(4,k) = vatom(4,k) + v(4) - vatom(5,k) = vatom(5,k) + v(5) - vatom(6,k) = vatom(6,k) + v(6) - endif - - endif - endif -c end of k loop - enddo - endif - 100 continue - endif -c end of j loop - enddo - -c else if elti=0, this is not a meam atom - endif - - return - end diff --git a/lib/meam/meam_setup_done.F b/lib/meam/meam_setup_done.F deleted file mode 100644 index c94bce8b44..0000000000 --- a/lib/meam/meam_setup_done.F +++ /dev/null @@ -1,1041 +0,0 @@ -c Declaration in pair_meam.h: -c -c void meam_setup_done(double *) -c -c Call from pair_meam.cpp: -c -c meam_setup_done(&cutmax) -c - - subroutine meam_setup_done(cutmax) - use meam_data - implicit none - - real*8 cutmax - - integer nv2, nv3, m, n, p - -c Force cutoff - cutforce = rc_meam - cutforcesq = cutforce*cutforce - -c Pass cutoff back to calling program - cutmax = cutforce - -c Augment t1 term - t1_meam(:) = t1_meam(:) + augt1 * 3.d0/5.d0 * t3_meam(:) - -c Compute off-diagonal alloy parameters - call alloyparams - -c indices and factors for Voight notation - nv2 = 1 - nv3 = 1 - do m = 1,3 - do n = m,3 - vind2D(m,n) = nv2 - vind2D(n,m) = nv2 - nv2 = nv2+1 - do p = n,3 - vind3D(m,n,p) = nv3 - vind3D(m,p,n) = nv3 - vind3D(n,m,p) = nv3 - vind3D(n,p,m) = nv3 - vind3D(p,m,n) = nv3 - vind3D(p,n,m) = nv3 - nv3 = nv3+1 - enddo - enddo - enddo - - v2D(1) = 1 - v2D(2) = 2 - v2D(3) = 2 - v2D(4) = 1 - v2D(5) = 2 - v2D(6) = 1 - - v3D(1) = 1 - v3D(2) = 3 - v3D(3) = 3 - v3D(4) = 3 - v3D(5) = 6 - v3D(6) = 3 - v3D(7) = 1 - v3D(8) = 3 - v3D(9) = 3 - v3D(10) = 1 - - nv2 = 1 - do m = 1,neltypes - do n = m,neltypes - eltind(m,n) = nv2 - eltind(n,m) = nv2 - nv2 = nv2+1 - enddo - enddo - -c Compute background densities for reference structure - call compute_reference_density - -c Compute pair potentials and setup arrays for interpolation - nr = 1000 - dr = 1.1*rc_meam/nr - call compute_pair_meam - - return - end - -cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc -c Fill off-diagonal alloy parameters - subroutine alloyparams - use meam_data - implicit none - integer i,j,k - real*8 eb - -c Loop over pairs - do i = 1,neltypes - do j = 1,neltypes -c Treat off-diagonal pairs -c If i>j, set all equal to ij, set equal to the iebound, -c atom k definitely lies outside the screening function ellipse (so -c there is no need to calculate its effects). Here, compute it for all -c triplets (i,j,k) so that ebound(i,j) is the maximized over k - do i = 1,neltypes - do j = 1,neltypes - do k = 1,neltypes - eb = (Cmax_meam(i,j,k)*Cmax_meam(i,j,k)) - $ /(4.d0*(Cmax_meam(i,j,k)-1.d0)) - ebound_meam(i,j) = max(ebound_meam(i,j),eb) - enddo - enddo - enddo - - return - end - -c----------------------------------------------------------------------- -c compute MEAM pair potential for each pair of element types -c - - subroutine compute_pair_meam - use meam_data - implicit none - - real*8 r, temp - integer j,a,b,nv2 - real*8 astar,frac,phizbl - integer n,nmax,Z1,Z2 - real*8 arat,rarat,scrn,scrn2 - real*8 phiaa,phibb,phitmp - real*8 C,s111,s112,s221,S11,S22 - - real*8, external :: phi_meam - real*8, external :: zbl - real*8, external :: compute_phi - -c check for previously allocated arrays and free them - if(allocated(phir)) deallocate(phir) - if(allocated(phirar)) deallocate(phirar) - if(allocated(phirar1)) deallocate(phirar1) - if(allocated(phirar2)) deallocate(phirar2) - if(allocated(phirar3)) deallocate(phirar3) - if(allocated(phirar4)) deallocate(phirar4) - if(allocated(phirar5)) deallocate(phirar5) - if(allocated(phirar6)) deallocate(phirar6) - -c allocate memory for array that defines the potential - allocate(phir(nr,(neltypes*(neltypes+1))/2)) - -c allocate coeff memory - - allocate(phirar(nr,(neltypes*(neltypes+1))/2)) - allocate(phirar1(nr,(neltypes*(neltypes+1))/2)) - allocate(phirar2(nr,(neltypes*(neltypes+1))/2)) - allocate(phirar3(nr,(neltypes*(neltypes+1))/2)) - allocate(phirar4(nr,(neltypes*(neltypes+1))/2)) - allocate(phirar5(nr,(neltypes*(neltypes+1))/2)) - allocate(phirar6(nr,(neltypes*(neltypes+1))/2)) - -c loop over pairs of element types - nv2 = 0 - do a = 1,neltypes - do b = a,neltypes - nv2 = nv2 + 1 - -c loop over r values and compute - do j = 1,nr - - r = (j-1)*dr - - phir(j,nv2) = phi_meam(r,a,b) - -c if using second-nearest neighbor, solve recursive problem -c (see Lee and Baskes, PRB 62(13):8564 eqn.(21)) - if (nn2_meam(a,b).eq.1) then - call get_Zij(Z1,lattce_meam(a,b)) - call get_Zij2(Z2,arat,scrn,lattce_meam(a,b), - $ Cmin_meam(a,a,b),Cmax_meam(a,a,b)) - -c The B1, B2, and L12 cases with NN2 have a trick to them; we need to -c compute the contributions from second nearest neighbors, like a-a -c pairs, but need to include NN2 contributions to those pairs as -c well. - if (lattce_meam(a,b).eq.'b1'.or. - $ lattce_meam(a,b).eq.'b2'.or. - $ lattce_meam(a,b).eq.'l12'.or. - $ lattce_meam(a,b).eq.'dia') then - rarat = r*arat - -c phi_aa - phiaa = phi_meam(rarat,a,a) - call get_Zij(Z1,lattce_meam(a,a)) - call get_Zij2(Z2,arat,scrn,lattce_meam(a,a), - $ Cmin_meam(a,a,a),Cmax_meam(a,a,a)) - nmax = 10 - if (scrn.gt.0.0) then - do n = 1,nmax - phiaa = phiaa + - $ (-Z2*scrn/Z1)**n * phi_meam(rarat*arat**n,a,a) - enddo - endif - -c phi_bb - phibb = phi_meam(rarat,b,b) - call get_Zij(Z1,lattce_meam(b,b)) - call get_Zij2(Z2,arat,scrn,lattce_meam(b,b), - $ Cmin_meam(b,b,b),Cmax_meam(b,b,b)) - nmax = 10 - if (scrn.gt.0.0) then - do n = 1,nmax - phibb = phibb + - $ (-Z2*scrn/Z1)**n * phi_meam(rarat*arat**n,b,b) - enddo - endif - - if (lattce_meam(a,b).eq.'b1'. - $ or.lattce_meam(a,b).eq.'b2'. - $ or.lattce_meam(a,b).eq.'dia') then -c Add contributions to the B1 or B2 potential - call get_Zij(Z1,lattce_meam(a,b)) - call get_Zij2(Z2,arat,scrn,lattce_meam(a,b), - $ Cmin_meam(a,a,b),Cmax_meam(a,a,b)) - phir(j,nv2) = phir(j,nv2) - - $ Z2*scrn/(2*Z1) * phiaa - call get_Zij2(Z2,arat,scrn2,lattce_meam(a,b), - $ Cmin_meam(b,b,a),Cmax_meam(b,b,a)) - phir(j,nv2) = phir(j,nv2) - - $ Z2*scrn2/(2*Z1) * phibb - - else if (lattce_meam(a,b).eq.'l12') then -c The L12 case has one last trick; we have to be careful to compute -c the correct screening between 2nd-neighbor pairs. 1-1 -c second-neighbor pairs are screened by 2 type 1 atoms and two type -c 2 atoms. 2-2 second-neighbor pairs are screened by 4 type 1 -c atoms. - C = 1.d0 - call get_sijk(C,a,a,a,s111) - call get_sijk(C,a,a,b,s112) - call get_sijk(C,b,b,a,s221) - S11 = s111 * s111 * s112 * s112 - S22 = s221**4 - phir(j,nv2) = phir(j,nv2) - - $ 0.75*S11*phiaa - 0.25*S22*phibb - - endif - - else - nmax = 10 - do n = 1,nmax - phir(j,nv2) = phir(j,nv2) + - $ (-Z2*scrn/Z1)**n * phi_meam(r*arat**n,a,b) - enddo - endif - - endif - -c For Zbl potential: -c if astar <= -3 -c potential is zbl potential -c else if -3 < astar < -1 -c potential is linear combination with zbl potential -c endif - if (zbl_meam(a,b).eq.1) then - astar = alpha_meam(a,b) * (r/re_meam(a,b) - 1.d0) - if (astar.le.-3.d0) then - phir(j,nv2) = zbl(r,ielt_meam(a),ielt_meam(b)) - else if (astar.gt.-3.d0.and.astar.lt.-1.d0) then - call fcut(1-(astar+1.d0)/(-3.d0+1.d0),frac) - phizbl = zbl(r,ielt_meam(a),ielt_meam(b)) - phir(j,nv2) = frac*phir(j,nv2) + (1-frac)*phizbl - endif - endif - - enddo - -c call interpolation - call interpolate_meam(nv2) - - enddo - enddo - - return - end - - -c----------------------------------------------------------------------c -c Compute MEAM pair potential for distance r, element types a and b -c - real*8 recursive function phi_meam(r,a,b)result(phi_m) - use meam_data - implicit none - - - integer a,b - real*8 r - real*8 a1,a2,a12 - real*8 t11av,t21av,t31av,t12av,t22av,t32av - real*8 G1,G2,s1(3),s2(3),s12(3),rho0_1,rho0_2 - real*8 Gam1,Gam2,Z1,Z2 - real*8 rhobar1,rhobar2,F1,F2 - real*8 rhoa01,rhoa11,rhoa21,rhoa31 - real*8 rhoa02,rhoa12,rhoa22,rhoa32 - real*8 rho01,rho11,rho21,rho31 - real*8 rho02,rho12,rho22,rho32 - real*8 scalfac,phiaa,phibb - real*8 Eu - real*8 arat,scrn,scrn2 - integer Z12, errorflag - integer n,nmax,Z1nn,Z2nn - character*3 latta,lattb - real*8 rho_bkgd1, rho_bkgd2 - - real*8, external :: erose - -c Equation numbers below refer to: -c I. Huang et.al., Modelling simul. Mater. Sci. Eng. 3:615 - -c get number of neighbors in the reference structure -c Nref(i,j) = # of i's neighbors of type j - call get_Zij(Z12,lattce_meam(a,b)) - - call get_densref(r,a,b,rho01,rho11,rho21,rho31, - $ rho02,rho12,rho22,rho32) - -c if densities are too small, numerical problems may result; just return zero - if (rho01.le.1e-14.and.rho02.le.1e-14) then - phi_m = 0.0 - return - endif - -c calculate average weighting factors for the reference structure - if (lattce_meam(a,b).eq.'c11') then - if (ialloy.eq.2) then - t11av = t1_meam(a) - t12av = t1_meam(b) - t21av = t2_meam(a) - t22av = t2_meam(b) - t31av = t3_meam(a) - t32av = t3_meam(b) - else - scalfac = 1.0/(rho01+rho02) - t11av = scalfac*(t1_meam(a)*rho01 + t1_meam(b)*rho02) - t12av = t11av - t21av = scalfac*(t2_meam(a)*rho01 + t2_meam(b)*rho02) - t22av = t21av - t31av = scalfac*(t3_meam(a)*rho01 + t3_meam(b)*rho02) - t32av = t31av - endif - else -c average weighting factors for the reference structure, eqn. I.8 - call get_tavref(t11av,t21av,t31av,t12av,t22av,t32av, - $ t1_meam(a),t2_meam(a),t3_meam(a), - $ t1_meam(b),t2_meam(b),t3_meam(b), - $ r,a,b,lattce_meam(a,b)) - endif - -c for c11b structure, calculate background electron densities - if (lattce_meam(a,b).eq.'c11') then - latta = lattce_meam(a,a) - if (latta.eq.'dia') then - rhobar1 = ((Z12/2)*(rho02+rho01))**2 + - $ t11av*(rho12-rho11)**2 + - $ t21av/6.0*(rho22+rho21)**2 + - $ 121.0/40.*t31av*(rho32-rho31)**2 - rhobar1 = sqrt(rhobar1) - rhobar2 = (Z12*rho01)**2 + 2.0/3.0*t21av*rho21**2 - rhobar2 = sqrt(rhobar2) - else - rhobar2 = ((Z12/2)*(rho01+rho02))**2 + - $ t12av*(rho11-rho12)**2 + - $ t22av/6.0*(rho21+rho22)**2 + - $ 121.0/40.*t32av*(rho31-rho32)**2 - rhobar2 = sqrt(rhobar2) - rhobar1 = (Z12*rho02)**2 + 2.0/3.0*t22av*rho22**2 - rhobar1 = sqrt(rhobar1) - endif - else -c for other structures, use formalism developed in Huang's paper -c -c composition-dependent scaling, equation I.7 -c If using mixing rule for t, apply to reference structure; else -c use precomputed values - if (mix_ref_t.eq.1) then - Z1 = Z_meam(a) - Z2 = Z_meam(b) - if (ibar_meam(a).le.0) then - G1 = 1.d0 - else - call get_shpfcn(s1,lattce_meam(a,a)) - Gam1 = (s1(1)*t11av+s1(2)*t21av+s1(3)*t31av)/(Z1*Z1) - call G_gam(Gam1,ibar_meam(a),gsmooth_factor,G1,errorflag) - endif - if (ibar_meam(b).le.0) then - G2 = 1.d0 - else - call get_shpfcn(s2,lattce_meam(b,b)) - Gam2 = (s2(1)*t12av+s2(2)*t22av+s2(3)*t32av)/(Z2*Z2) - call G_gam(Gam2,ibar_meam(b),gsmooth_factor,G2,errorflag) - endif - rho0_1 = rho0_meam(a)*Z1*G1 - rho0_2 = rho0_meam(b)*Z2*G2 - endif - Gam1 = (t11av*rho11+t21av*rho21+t31av*rho31) - if (rho01 < 1.0d-14) then - Gam1 = 0.0d0 - else - Gam1 = Gam1/(rho01*rho01) - endif - Gam2 = (t12av*rho12+t22av*rho22+t32av*rho32) - if (rho02 < 1.0d-14) then - Gam2 = 0.0d0 - else - Gam2 = Gam2/(rho02*rho02) - endif - call G_gam(Gam1,ibar_meam(a),gsmooth_factor,G1,errorflag) - call G_gam(Gam2,ibar_meam(b),gsmooth_factor,G2,errorflag) - if (mix_ref_t.eq.1) then - rho_bkgd1 = rho0_1 - rho_bkgd2 = rho0_2 - else - if (bkgd_dyn.eq.1) then - rho_bkgd1 = rho0_meam(a)*Z_meam(a) - rho_bkgd2 = rho0_meam(b)*Z_meam(b) - else - rho_bkgd1 = rho_ref_meam(a) - rho_bkgd2 = rho_ref_meam(b) - endif - endif - rhobar1 = rho01/rho_bkgd1*G1 - rhobar2 = rho02/rho_bkgd2*G2 - - endif - -c compute embedding functions, eqn I.5 - if (rhobar1.eq.0.d0) then - F1 = 0.d0 - else - if (emb_lin_neg.eq.1 .and. rhobar1.le.0) then - F1 = -A_meam(a)*Ec_meam(a,a)*rhobar1 - else - F1 = A_meam(a)*Ec_meam(a,a)*rhobar1*log(rhobar1) - endif - endif - if (rhobar2.eq.0.d0) then - F2 = 0.d0 - else - if (emb_lin_neg.eq.1 .and. rhobar2.le.0) then - F2 = -A_meam(b)*Ec_meam(b,b)*rhobar2 - else - F2 = A_meam(b)*Ec_meam(b,b)*rhobar2*log(rhobar2) - endif - endif - -c compute Rose function, I.16 - Eu = erose(r,re_meam(a,b),alpha_meam(a,b), - $ Ec_meam(a,b),repuls_meam(a,b),attrac_meam(a,b),erose_form) - -c calculate the pair energy - if (lattce_meam(a,b).eq.'c11') then - latta = lattce_meam(a,a) - if (latta.eq.'dia') then - phiaa = phi_meam(r,a,a) - phi_m = (3*Eu - F2 - 2*F1 - 5*phiaa)/Z12 - else - phibb = phi_meam(r,b,b) - phi_m = (3*Eu - F1 - 2*F2 - 5*phibb)/Z12 - endif - else if (lattce_meam(a,b).eq.'l12') then - phiaa = phi_meam(r,a,a) -c account for second neighbor a-a potential here... - call get_Zij(Z1nn,lattce_meam(a,a)) - call get_Zij2(Z2nn,arat,scrn,lattce_meam(a,a), - $ Cmin_meam(a,a,a),Cmax_meam(a,a,a)) - nmax = 10 - if (scrn.gt.0.0) then - do n = 1,nmax - phiaa = phiaa + - $ (-Z2nn*scrn/Z1nn)**n * phi_meam(r*arat**n,a,a) - enddo - endif - phi_m = Eu/3. - F1/4. - F2/12. - phiaa - else -c -c potential is computed from Rose function and embedding energy - phi_m = (2*Eu - F1 - F2)/Z12 -c - endif - -c if r = 0, just return 0 - if (r.eq.0.d0) then - phi_m = 0.d0 - endif - - return - end - -c----------------------------------------------------------------------c -c Compute background density for reference structure of each element - subroutine compute_reference_density - use meam_data - implicit none - - integer a,Z,Z2,errorflag - real*8 gam,Gbar,shp(3) - real*8 rho0,rho0_2nn,arat,scrn - -c loop over element types - do a = 1,neltypes - - Z = Z_meam(a) - if (ibar_meam(a).le.0) then - Gbar = 1.d0 - else - call get_shpfcn(shp,lattce_meam(a,a)) - gam = (t1_meam(a)*shp(1)+t2_meam(a)*shp(2) - $ +t3_meam(a)*shp(3))/(Z*Z) - call G_gam(gam,ibar_meam(a),gsmooth_factor, - $ Gbar,errorflag) - endif - -c The zeroth order density in the reference structure, with -c equilibrium spacing, is just the number of first neighbors times -c the rho0_meam coefficient... - rho0 = rho0_meam(a)*Z - -c ...unless we have unscreened second neighbors, in which case we -c add on the contribution from those (accounting for partial -c screening) - if (nn2_meam(a,a).eq.1) then - call get_Zij2(Z2,arat,scrn,lattce_meam(a,a), - $ Cmin_meam(a,a,a),Cmax_meam(a,a,a)) - rho0_2nn = rho0_meam(a)*fm_exp(-beta0_meam(a)*(arat-1)) - rho0 = rho0 + Z2*rho0_2nn*scrn - endif - - rho_ref_meam(a) = rho0*Gbar - - enddo - - return - end - -c----------------------------------------------------------------------c -c Shape factors for various configurations - subroutine get_shpfcn(s,latt) - implicit none - real*8 s(3) - character*3 latt - if (latt.eq.'fcc'.or.latt.eq.'bcc'. - $ or.latt.eq.'b1'.or.latt.eq.'b2') then - s(1) = 0.d0 - s(2) = 0.d0 - s(3) = 0.d0 - else if (latt.eq.'hcp') then - s(1) = 0.d0 - s(2) = 0.d0 - s(3) = 1.d0/3.d0 - else if (latt.eq.'dia') then - s(1) = 0.d0 - s(2) = 0.d0 - s(3) = 32.d0/9.d0 - else if (latt.eq.'dim') then - s(1) = 1.d0 - s(2) = 2.d0/3.d0 -c s(3) = 1.d0 - s(3) = 0.4d0 - else - s(1) = 0.0 -c call error('Lattice not defined in get_shpfcn.') - endif - return - end -c------------------------------------------------------------------------------c -c Average weighting factors for the reference structure - subroutine get_tavref(t11av,t21av,t31av,t12av,t22av,t32av, - $ t11,t21,t31,t12,t22,t32, - $ r,a,b,latt) - use meam_data - implicit none - real*8 t11av,t21av,t31av,t12av,t22av,t32av - real*8 t11,t21,t31,t12,t22,t32,r - integer a,b - character*3 latt - real*8 rhoa01,rhoa02,a1,a2,rho01,rho02 - -c For ialloy = 2, no averaging is done - if (ialloy.eq.2) then - t11av = t11 - t21av = t21 - t31av = t31 - t12av = t12 - t22av = t22 - t32av = t32 - else - if (latt.eq.'fcc'.or.latt.eq.'bcc'.or.latt.eq.'dia' - $ .or.latt.eq.'hcp'.or.latt.eq.'b1' - $ .or.latt.eq.'dim'.or.latt.eq.'b2') then -c all neighbors are of the opposite type - t11av = t12 - t21av = t22 - t31av = t32 - t12av = t11 - t22av = t21 - t32av = t31 - else - a1 = r/re_meam(a,a) - 1.d0 - a2 = r/re_meam(b,b) - 1.d0 - rhoa01 = rho0_meam(a)*fm_exp(-beta0_meam(a)*a1) - rhoa02 = rho0_meam(b)*fm_exp(-beta0_meam(b)*a2) - if (latt.eq.'l12') then - rho01 = 8*rhoa01 + 4*rhoa02 - t11av = (8*t11*rhoa01 + 4*t12*rhoa02)/rho01 - t12av = t11 - t21av = (8*t21*rhoa01 + 4*t22*rhoa02)/rho01 - t22av = t21 - t31av = (8*t31*rhoa01 + 4*t32*rhoa02)/rho01 - t32av = t31 - else -c call error('Lattice not defined in get_tavref.') - endif - endif - endif - return - end -c------------------------------------------------------------------------------c -c Number of neighbors for the reference structure - subroutine get_Zij(Zij,latt) - implicit none - integer Zij - character*3 latt - if (latt.eq.'fcc') then - Zij = 12 - else if (latt.eq.'bcc') then - Zij = 8 - else if (latt.eq.'hcp') then - Zij = 12 - else if (latt.eq.'b1') then - Zij = 6 - else if (latt.eq.'dia') then - Zij = 4 - else if (latt.eq.'dim') then - Zij = 1 - else if (latt.eq.'c11') then - Zij = 10 - else if (latt.eq.'l12') then - Zij = 12 - else if (latt.eq.'b2') then - Zij = 8 - else -c call error('Lattice not defined in get_Zij.') - endif - return - end - -c------------------------------------------------------------------------------c -c Zij2 = number of second neighbors, a = distance ratio R1/R2, and S = second -c neighbor screening function for lattice type "latt" - - subroutine get_Zij2(Zij2,a,S,latt,cmin,cmax) - implicit none - integer Zij2 - real*8 a,S,cmin,cmax - character*3 latt - real*8 rratio,C,x,sijk - integer numscr - - if (latt.eq.'bcc') then - Zij2 = 6 - a = 2.d0/sqrt(3.d0) - numscr = 4 - else if (latt.eq.'fcc') then - Zij2 = 6 - a = sqrt(2.d0) - numscr = 4 - else if (latt.eq.'dia') then - Zij2 = 12 - a = sqrt(8.d0/3.d0) - numscr = 1 - if (cmin.lt.0.500001) then -c call error('can not do 2NN MEAM for dia') - endif - else if (latt.eq.'hcp') then - Zij2 = 6 - a = sqrt(2.d0) - numscr = 4 - else if (latt.eq.'b1') then - Zij2 = 12 - a = sqrt(2.d0) - numscr = 2 - else if (latt.eq.'l12') then - Zij2 = 6 - a = sqrt(2.d0) - numscr = 4 - else if (latt.eq.'b2') then - Zij2 = 6 - a = 2.d0/sqrt(3.d0) - numscr = 4 - else if (latt.eq.'dim') then -c this really shouldn't be allowed; make sure screening is zero - Zij2 = 0 - a = 1 - S = 0 - return - else -c call error('Lattice not defined in get_Zij2.') - endif - -c Compute screening for each first neighbor - C = 4.d0/(a*a) - 1.d0 - x = (C-cmin)/(cmax-cmin) - call fcut(x,sijk) -c There are numscr first neighbors screening the second neighbors - S = sijk**numscr - - return - end - - -c------------------------------------------------------------------------------c - subroutine get_sijk(C,i,j,k,sijk) - use meam_data - implicit none - real*8 C,sijk - integer i,j,k - real*8 x - x = (C-Cmin_meam(i,j,k))/(Cmax_meam(i,j,k)-Cmin_meam(i,j,k)) - call fcut(x,sijk) - return - end - -c------------------------------------------------------------------------------c -c Calculate density functions, assuming reference configuration - subroutine get_densref(r,a,b,rho01,rho11,rho21,rho31, - $ rho02,rho12,rho22,rho32) - use meam_data - implicit none - real*8 r,rho01,rho11,rho21,rho31,rho02,rho12,rho22,rho32 - real*8 a1,a2 - real*8 rhoa01,rhoa11,rhoa21,rhoa31,rhoa02,rhoa12,rhoa22,rhoa32 - real*8 s(3) - character*3 lat - integer a,b - integer Zij1nn,Zij2nn - real*8 rhoa01nn,rhoa02nn - real*8 arat,scrn,denom - real*8 C,s111,s112,s221,S11,S22 - - a1 = r/re_meam(a,a) - 1.d0 - a2 = r/re_meam(b,b) - 1.d0 - - rhoa01 = rho0_meam(a)*fm_exp(-beta0_meam(a)*a1) - rhoa11 = rho0_meam(a)*fm_exp(-beta1_meam(a)*a1) - rhoa21 = rho0_meam(a)*fm_exp(-beta2_meam(a)*a1) - rhoa31 = rho0_meam(a)*fm_exp(-beta3_meam(a)*a1) - rhoa02 = rho0_meam(b)*fm_exp(-beta0_meam(b)*a2) - rhoa12 = rho0_meam(b)*fm_exp(-beta1_meam(b)*a2) - rhoa22 = rho0_meam(b)*fm_exp(-beta2_meam(b)*a2) - rhoa32 = rho0_meam(b)*fm_exp(-beta3_meam(b)*a2) - - lat = lattce_meam(a,b) - - rho11 = 0.d0 - rho21 = 0.d0 - rho31 = 0.d0 - rho12 = 0.d0 - rho22 = 0.d0 - rho32 = 0.d0 - - call get_Zij(Zij1nn,lat) - - if (lat.eq.'fcc') then - rho01 = 12.d0*rhoa02 - rho02 = 12.d0*rhoa01 - else if (lat.eq.'bcc') then - rho01 = 8.d0*rhoa02 - rho02 = 8.d0*rhoa01 - else if (lat.eq.'b1') then - rho01 = 6*rhoa02 - rho02 = 6*rhoa01 - else if (lat.eq.'dia') then - rho01 = 4*rhoa02 - rho02 = 4*rhoa01 - rho31 = 32.d0/9.d0*rhoa32*rhoa32 - rho32 = 32.d0/9.d0*rhoa31*rhoa31 - else if (lat.eq.'hcp') then - rho01 = 12*rhoa02 - rho02 = 12*rhoa01 - rho31 = 1.d0/3.d0*rhoa32*rhoa32 - rho32 = 1.d0/3.d0*rhoa31*rhoa31 - else if (lat.eq.'dim') then - call get_shpfcn(s,'dim') - rho01 = rhoa02 - rho02 = rhoa01 - rho11 = s(1)*rhoa12*rhoa12 - rho12 = s(1)*rhoa11*rhoa11 - rho21 = s(2)*rhoa22*rhoa22 - rho22 = s(2)*rhoa21*rhoa21 - rho31 = s(3)*rhoa32*rhoa32 - rho32 = s(3)*rhoa31*rhoa31 - else if (lat.eq.'c11') then - rho01 = rhoa01 - rho02 = rhoa02 - rho11 = rhoa11 - rho12 = rhoa12 - rho21 = rhoa21 - rho22 = rhoa22 - rho31 = rhoa31 - rho32 = rhoa32 - else if (lat.eq.'l12') then - rho01 = 8*rhoa01 + 4*rhoa02 - rho02 = 12*rhoa01 - if (ialloy.eq.1) then - rho21 = 8./3.*(rhoa21*t2_meam(a)-rhoa22*t2_meam(b))**2 - denom = 8*rhoa01*t2_meam(a)**2 + 4*rhoa02*t2_meam(b)**2 - if (denom.gt.0.) then - rho21 = rho21/denom * rho01 - endif - else - rho21 = 8./3.*(rhoa21-rhoa22)*(rhoa21-rhoa22) - endif - else if (lat.eq.'b2') then - rho01 = 8.d0*rhoa02 - rho02 = 8.d0*rhoa01 - else -c call error('Lattice not defined in get_densref.') - endif - - if (nn2_meam(a,b).eq.1) then - - call get_Zij2(Zij2nn,arat,scrn,lat, - $ Cmin_meam(a,a,b),Cmax_meam(a,a,b)) - - a1 = arat*r/re_meam(a,a) - 1.d0 - a2 = arat*r/re_meam(b,b) - 1.d0 - - rhoa01nn = rho0_meam(a)*fm_exp(-beta0_meam(a)*a1) - rhoa02nn = rho0_meam(b)*fm_exp(-beta0_meam(b)*a2) - - if (lat.eq.'l12') then -c As usual, L12 thinks it's special; we need to be careful computing -c the screening functions - C = 1.d0 - call get_sijk(C,a,a,a,s111) - call get_sijk(C,a,a,b,s112) - call get_sijk(C,b,b,a,s221) - S11 = s111 * s111 * s112 * s112 - S22 = s221**4 - rho01 = rho01 + 6*S11*rhoa01nn - rho02 = rho02 + 6*S22*rhoa02nn - - else -c For other cases, assume that second neighbor is of same type, -c first neighbor may be of different type - - rho01 = rho01 + Zij2nn*scrn*rhoa01nn - -c Assume Zij2nn and arat don't depend on order, but scrn might - call get_Zij2(Zij2nn,arat,scrn,lat, - $ Cmin_meam(b,b,a),Cmax_meam(b,b,a)) - rho02 = rho02 + Zij2nn*scrn*rhoa02nn - - endif - - endif - - return - end - -c--------------------------------------------------------------------- -c Compute ZBL potential -c - real*8 function zbl(r,z1,z2) - use meam_data , only : fm_exp - implicit none - integer i,z1,z2 - real*8 r,c,d,a,azero,cc,x - dimension c(4),d(4) - data c /0.028171,0.28022,0.50986,0.18175/ - data d /0.20162,0.40290,0.94229,3.1998/ - data azero /0.4685/ - data cc /14.3997/ -c azero = (9pi^2/128)^1/3 (0.529) Angstroms - a = azero/(z1**0.23+z2**0.23) - zbl = 0.0 - x = r/a - do i=1,4 - zbl = zbl + c(i)*fm_exp(-d(i)*x) - enddo - if (r.gt.0.d0) zbl = zbl*z1*z2/r*cc - return - end - -c--------------------------------------------------------------------- -c Compute Rose energy function, I.16 -c - real*8 function erose(r,re,alpha,Ec,repuls,attrac,form) - use meam_data , only : fm_exp - implicit none - real*8 r,re,alpha,Ec,repuls,attrac,astar,a3 - integer form - - erose = 0.d0 - - if (r.gt.0.d0) then - astar = alpha * (r/re - 1.d0) - a3 = 0.d0 - if (astar.ge.0) then - a3 = attrac - else if (astar.lt.0) then - a3 = repuls - endif - if (form.eq.1) then - erose = -Ec*(1+astar+(-attrac+repuls/r)* - $ (astar**3))*fm_exp(-astar) - else if (form.eq.2) then - erose = -Ec * (1 +astar + a3*(astar**3))*fm_exp(-astar) - else - erose = -Ec * (1+ astar + a3*(astar**3)/(r/re))*fm_exp(-astar) - endif - endif - - return - end - -c ----------------------------------------------------------------------- - - subroutine interpolate_meam(ind) - use meam_data - implicit none - - integer j,ind - real*8 drar - -c map to coefficient space - - nrar = nr - drar = dr - rdrar = 1.0D0/drar - -c phir interp - do j = 1,nrar - phirar(j,ind) = phir(j,ind) - enddo - - phirar1(1,ind) = phirar(2,ind)-phirar(1,ind) - phirar1(2,ind) = 0.5D0*(phirar(3,ind)-phirar(1,ind)) - phirar1(nrar-1,ind) = 0.5D0*(phirar(nrar,ind) - $ -phirar(nrar-2,ind)) - phirar1(nrar,ind) = 0.0D0 - do j = 3,nrar-2 - phirar1(j,ind) = ((phirar(j-2,ind)-phirar(j+2,ind)) + - $ 8.0D0*(phirar(j+1,ind)-phirar(j-1,ind)))/12. - enddo - - do j = 1,nrar-1 - phirar2(j,ind) = 3.0D0*(phirar(j+1,ind)-phirar(j,ind)) - - $ 2.0D0*phirar1(j,ind) - phirar1(j+1,ind) - phirar3(j,ind) = phirar1(j,ind) + phirar1(j+1,ind) - - $ 2.0D0*(phirar(j+1,ind)-phirar(j,ind)) - enddo - phirar2(nrar,ind) = 0.0D0 - phirar3(nrar,ind) = 0.0D0 - - do j = 1,nrar - phirar4(j,ind) = phirar1(j,ind)/drar - phirar5(j,ind) = 2.0D0*phirar2(j,ind)/drar - phirar6(j,ind) = 3.0D0*phirar3(j,ind)/drar - enddo - - end - -c--------------------------------------------------------------------- -c Compute Rose energy function, I.16 -c - real*8 function compute_phi(rij, elti, eltj) - use meam_data - implicit none - - real*8 rij, pp - integer elti, eltj, ind, kk - - ind = eltind(elti, eltj) - pp = rij*rdrar + 1.0D0 - kk = pp - kk = min(kk,nrar-1) - pp = pp - kk - pp = min(pp,1.0D0) - compute_phi = ((phirar3(kk,ind)*pp + phirar2(kk,ind))*pp - $ + phirar1(kk,ind))*pp + phirar(kk,ind) - - return - end diff --git a/lib/meam/meam_setup_global.F b/lib/meam/meam_setup_global.F deleted file mode 100644 index d11dec5a4a..0000000000 --- a/lib/meam/meam_setup_global.F +++ /dev/null @@ -1,111 +0,0 @@ -c -c declaration in pair_meam.h: -c -c void meam_setup_global(int *, int *, double *, int *, double *, double *, -c double *, double *, double *, double *, double *, -c double *, double *, double *, double *, double *, -c double *, double *, int *); -c -c call in pair_meam.cpp: -c -c meam_setup_global(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3, -c alat,esub,asub,t0,t1,t2,t3,rozero,ibar); -c -c - - subroutine meam_setup_global(nelt, lat, z, ielement, atwt, alpha, - $ b0, b1, b2, b3, alat, esub, asub, - $ t0, t1, t2, t3, rozero, ibar) - - use meam_data - implicit none - - integer nelt, lat, ielement, ibar - real*8 z, atwt, alpha, b0, b1, b2, b3 - real*8 alat, esub, asub, t0, t1, t2, t3 - real*8 rozero - - dimension lat(nelt), ielement(nelt), ibar(nelt) - dimension z(nelt), atwt(nelt), alpha(nelt) - dimension b0(nelt), b1(nelt), b2(nelt), b3(nelt) - dimension alat(nelt), esub(nelt), asub(nelt) - dimension t0(nelt), t1(nelt), t2(nelt), t3(nelt), rozero(nelt) - - integer i - real*8 tmplat(maxelt) - - neltypes = nelt - - do i = 1,nelt - - if (lat(i).eq.0) then - lattce_meam(i,i) = 'fcc' - else if (lat(i).eq.1) then - lattce_meam(i,i) = 'bcc' - else if (lat(i).eq.2) then - lattce_meam(i,i) = 'hcp' - else if (lat(i).eq.3) then - lattce_meam(i,i) = 'dim' - else if (lat(i).eq.4) then - lattce_meam(i,i) = 'dia' - else -c unknown - endif - - Z_meam(i) = z(i) - ielt_meam(i) = ielement(i) - alpha_meam(i,i) = alpha(i) - beta0_meam(i) = b0(i) - beta1_meam(i) = b1(i) - beta2_meam(i) = b2(i) - beta3_meam(i) = b3(i) - tmplat(i) = alat(i) - Ec_meam(i,i) = esub(i) - A_meam(i) = asub(i) - t0_meam(i) = t0(i) - t1_meam(i) = t1(i) - t2_meam(i) = t2(i) - t3_meam(i) = t3(i) - rho0_meam(i) = rozero(i) - ibar_meam(i) = ibar(i) - - if (lattce_meam(i,i).eq.'fcc') then - re_meam(i,i) = tmplat(i)/sqrt(2.d0) - elseif (lattce_meam(i,i).eq.'bcc') then - re_meam(i,i) = tmplat(i)*sqrt(3.d0)/2.d0 - elseif (lattce_meam(i,i).eq.'hcp') then - re_meam(i,i) = tmplat(i) - elseif (lattce_meam(i,i).eq.'dim') then - re_meam(i,i) = tmplat(i) - elseif (lattce_meam(i,i).eq.'dia') then - re_meam(i,i) = tmplat(i)*sqrt(3.d0)/4.d0 - else -c error - endif - - enddo - - -c Set some defaults - rc_meam = 4.0 - delr_meam = 0.1 - attrac_meam(:,:) = 0.0 - repuls_meam(:,:) = 0.0 - Cmax_meam(:,:,:) = 2.8 - Cmin_meam(:,:,:) = 2.0 - ebound_meam(:,:) = (2.8d0**2)/(4.d0*(2.8d0-1.d0)) - delta_meam(:,:) = 0.0 - nn2_meam(:,:) = 0 - zbl_meam(:,:) = 1 - gsmooth_factor = 99.0 - augt1 = 1 - ialloy = 0 - mix_ref_t = 0 - emb_lin_neg = 0 - bkgd_dyn = 0 - erose_form = 0 - - return - end - - diff --git a/lib/meam/meam_setup_param.F b/lib/meam/meam_setup_param.F deleted file mode 100644 index cfe7430285..0000000000 --- a/lib/meam/meam_setup_param.F +++ /dev/null @@ -1,204 +0,0 @@ -c -c do a sanity check on index parameters - subroutine meam_checkindex(num,lim,nidx,idx,ierr) - implicit none - integer i,num,lim,nidx,idx(3),ierr - - ierr = 0 - if (nidx.lt.num) then - ierr = 2 - return - endif - - do i=1,num - if ((idx(i).lt.1).or.(idx(i).gt.lim)) then - ierr = 3 - return - endif - enddo - end - -c -c Declaration in pair_meam.h: -c -c void meam_setup_param(int *, double *, int *, int *, int *); -c -c Call in pair_meam.cpp -c -c meam_setup_param(&which,&value,&nindex,index,&errorflag); -c -c -c -c The "which" argument corresponds to the index of the "keyword" array -c in pair_meam.cpp: -c -c 0 = Ec_meam -c 1 = alpha_meam -c 2 = rho0_meam -c 3 = delta_meam -c 4 = lattce_meam -c 5 = attrac_meam -c 6 = repuls_meam -c 7 = nn2_meam -c 8 = Cmin_meam -c 9 = Cmax_meam -c 10 = rc_meam -c 11 = delr_meam -c 12 = augt1 -c 13 = gsmooth_factor -c 14 = re_meam -c 15 = ialloy -c 16 = mixture_ref_t -c 17 = erose_form -c 18 = zbl_meam -c 19 = emb_lin_neg -c 20 = bkgd_dyn - - subroutine meam_setup_param(which, value, nindex, - $ index, errorflag) - - use meam_data - implicit none - - integer which, nindex, index(3), errorflag - real*8 value - integer i1, i2 - - errorflag = 0 - -c 0 = Ec_meam - if (which.eq.0) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - Ec_meam(index(1),index(2)) = value - -c 1 = alpha_meam - else if (which.eq.1) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - alpha_meam(index(1),index(2)) = value - -c 2 = rho0_meam - else if (which.eq.2) then - call meam_checkindex(1,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - rho0_meam(index(1)) = value - -c 3 = delta_meam - else if (which.eq.3) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - delta_meam(index(1),index(2)) = value - -c 4 = lattce_meam - else if (which.eq.4) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - if (value.eq.0) then - lattce_meam(index(1),index(2)) = "fcc" - else if (value.eq.1) then - lattce_meam(index(1),index(2)) = "bcc" - else if (value.eq.2) then - lattce_meam(index(1),index(2)) = "hcp" - else if (value.eq.3) then - lattce_meam(index(1),index(2)) = "dim" - else if (value.eq.4) then - lattce_meam(index(1),index(2)) = "dia" - else if (value.eq.5) then - lattce_meam(index(1),index(2)) = 'b1' - else if (value.eq.6) then - lattce_meam(index(1),index(2)) = 'c11' - else if (value.eq.7) then - lattce_meam(index(1),index(2)) = 'l12' - else if (value.eq.8) then - lattce_meam(index(1),index(2)) = 'b2' - endif - -c 5 = attrac_meam - else if (which.eq.5) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - attrac_meam(index(1),index(2)) = value - -c 6 = repuls_meam - else if (which.eq.6) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - repuls_meam(index(1),index(2)) = value - -c 7 = nn2_meam - else if (which.eq.7) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - i1 = min(index(1),index(2)) - i2 = max(index(1),index(2)) - nn2_meam(i1,i2) = value - -c 8 = Cmin_meam - else if (which.eq.8) then - call meam_checkindex(3,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - Cmin_meam(index(1),index(2),index(3)) = value - -c 9 = Cmax_meam - else if (which.eq.9) then - call meam_checkindex(3,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - Cmax_meam(index(1),index(2),index(3)) = value - -c 10 = rc_meam - else if (which.eq.10) then - rc_meam = value - -c 11 = delr_meam - else if (which.eq.11) then - delr_meam = value - -c 12 = augt1 - else if (which.eq.12) then - augt1 = value - -c 13 = gsmooth - else if (which.eq.13) then - gsmooth_factor = value - -c 14 = re_meam - else if (which.eq.14) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - re_meam(index(1),index(2)) = value - -c 15 = ialloy - else if (which.eq.15) then - ialloy = value - -c 16 = mixture_ref_t - else if (which.eq.16) then - mix_ref_t = value - -c 17 = erose_form - else if (which.eq.17) then - erose_form = value - -c 18 = zbl_meam - else if (which.eq.18) then - call meam_checkindex(2,maxelt,nindex,index,errorflag) - if (errorflag.ne.0) return - i1 = min(index(1),index(2)) - i2 = max(index(1),index(2)) - zbl_meam(i1,i2) = value - -c 19 = emb_lin_neg - else if (which.eq.19) then - emb_lin_neg = value - -c 20 = bkgd_dyn - else if (which.eq.20) then - bkgd_dyn = value - - else - errorflag = 1 - endif - - return - end diff --git a/lib/message/Install.py b/lib/message/Install.py index d3f31c986f..829d58b5f8 100644 --- a/lib/message/Install.py +++ b/lib/message/Install.py @@ -1,118 +1,84 @@ #!/usr/bin/env python -# Install.py tool to build the CSlib library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to build the CSlib library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,subprocess +import sys, os, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import fullpath + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") # help message -help = """ +HELP = """ Syntax from src dir: make lib-message args="-m" or: make lib-message args="-s -z" Syntax from lib dir: python Install.py -m or: python Install.py -s -z -specify zero or more options, order does not matter - - -m = parallel build of CSlib library - -s = serial build of CSlib library - -z = build CSlib library with ZMQ socket support, default = no ZMQ support - Example: make lib-message args="-m -z" # build parallel CSlib with ZMQ support make lib-message args="-s" # build serial CSlib with no ZMQ support """ -# print error message or help +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-m", "--mpi", action="store_true", + help="parallel build of CSlib with MPI") +pgroup.add_argument("-s", "--serial", action="store_true", + help="serial build of CSlib") +parser.add_argument("-z", "--zmq", default=False, action="store_true", + help="build CSlib with ZMQ socket support, default ()") -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +args = parser.parse_args() -# expand to full path name -# process leading '~' or relative path +# print help message and exit, if neither build nor path options are given +if not args.mpi and not args.serial: + parser.print_help() + sys.exit(HELP) -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) - -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) - - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program - else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file - - return None - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -mpiflag = False -serialflag = False -zmqflag = False - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-m": - mpiflag = True - iarg += 1 - elif args[iarg] == "-s": - serialflag = True - iarg += 1 - elif args[iarg] == "-z": - zmqflag = True - iarg += 1 - else: error() - -if (not mpiflag and not serialflag): - error("Must use either -m or -s flag") - -if (mpiflag and serialflag): - error("Cannot use -m and -s flag at the same time") +mpiflag = args.mpi +serialflag = args.serial +zmqflag = args.zmq # build CSlib # copy resulting lib to cslib/src/libmessage.a # copy appropriate Makefile.lammps.* to Makefile.lammps print("Building CSlib ...") -srcdir = fullpath("./cslib/src") +srcdir = fullpath(os.path.join("cslib", "src")) if mpiflag and zmqflag: - cmd = "cd %s; make lib_parallel" % srcdir + cmd = "make -C %s lib_parallel" % srcdir elif mpiflag and not zmqflag: - cmd = "cd %s; make lib_parallel zmq=no" % srcdir + cmd = "make -C %s lib_parallel zmq=no" % srcdir elif not mpiflag and zmqflag: - cmd = "cd %s; make lib_serial" % srcdir + cmd = "make -C %s lib_serial" % srcdir elif not mpiflag and not zmqflag: - cmd = "cd %s; make lib_serial zmq=no" % srcdir - -print(cmd) -txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) -print(txt.decode('UTF-8')) + cmd = "make -C %s lib_serial zmq=no" % srcdir -if mpiflag: cmd = "cd %s; cp libcsmpi.a libmessage.a" % srcdir -else: cmd = "cd %s; cp libcsnompi.a libmessage.a" % srcdir print(cmd) -txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) -print(txt.decode('UTF-8')) +try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) +except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) -if zmqflag: cmd = "cp Makefile.lammps.zmq Makefile.lammps" -else: cmd = "cp Makefile.lammps.nozmq Makefile.lammps" -print(cmd) -txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) -print(txt.decode('UTF-8')) +slb = os.path.join(srcdir, "libcsnompi.a") +if mpiflag: + slb = os.path.join(srcdir, "libcsmpi.a") +shutil.copyfile(slb, os.path.join(srcdir, "libmessage.a")) + +smk = "Makefile.lammps.nozmq" +if zmqflag: + smk = "Makefile.lammps.zmq" +shutil.copyfile(smk, "Makefile.lammps") +print("Using %s for Makefile.lammps" % smk) diff --git a/lib/message/cslib/src/msg.cpp b/lib/message/cslib/src/msg.cpp index c67e4a5c8c..da22c81850 100644 --- a/lib/message/cslib/src/msg.cpp +++ b/lib/message/cslib/src/msg.cpp @@ -13,9 +13,9 @@ ------------------------------------------------------------------------- */ #include -#include -#include -#include +#include +#include +#include #include "msg.h" @@ -23,7 +23,7 @@ using namespace CSLIB_NS; /* ---------------------------------------------------------------------- */ -Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld) +Msg::Msg(int csflag, const void * /* ptr */, MPI_Comm cworld) { world = cworld; MPI_Comm_rank(world,&me); @@ -34,7 +34,7 @@ Msg::Msg(int csflag, const void *ptr, MPI_Comm cworld) /* ---------------------------------------------------------------------- */ -Msg::Msg(int csflag, const void *ptr) +Msg::Msg(int csflag, const void * /* ptr */) { world = 0; me = 0; @@ -57,7 +57,7 @@ void Msg::init(int csflag) /* ---------------------------------------------------------------------- */ void Msg::allocate(int nheader, int &maxheader, int *&header, - int nbuf, int &maxbuf, char *&buf) + int nbuf, int &maxbuf, char *&buf) { if (nheader > maxheader) { sfree(header); diff --git a/lib/mscg/.gitignore b/lib/mscg/.gitignore index 7d45bcb60a..6c9a531977 100644 --- a/lib/mscg/.gitignore +++ b/lib/mscg/.gitignore @@ -1,4 +1,4 @@ # files to ignore /liblink /includelink -/MSCG-release-master +/MSCG-release-* diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py index ec70f13f6e..9d18b7c083 100644 --- a/lib/mscg/Install.py +++ b/lib/mscg/Install.py @@ -1,187 +1,142 @@ #!/usr/bin/env python -# Install.py tool to download, unpack, build, and link to the MS-CG library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to download, unpack, build, and link to the MS-CG library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,subprocess +import sys, os, subprocess, shutil, tarfile +from argparse import ArgumentParser -# help message +sys.path.append('..') +from install_helpers import fullpath, geturl -help = """ -Syntax from src dir: make lib-mscg args="-p [path] -m [suffix]" - or: make lib-mscg args="-b -m [suffix]" -Syntax from lib dir: python Install.py -p [path] -m [suffix] -Syntax from lib dir: python Install.py -b -m [suffix] - -specify one or more options, order does not matter - - -b = download and build MS-CG library - -p = specify folder of existing MS-CG installation - -m = machine suffix specifies which src/Make/Makefile.suffix to use - default suffix = g++_simple - -Example: - -make lib-mscg args="-b -m serial " # download/build in lib/mscg/MSCG-release-master with settings compatible with "make serial" -make lib-mscg args="-b -m mpi " # download/build in lib/mscg/MSCG-release-master with settings compatible with "make mpi" -make lib-mscg args="-p /usr/local/mscg-release " # use existing MS-CG installation in /usr/local/mscg-release -""" +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = "1.7.3.1" +machine = "g++_simple" + +# help message + +HELP = """ +Syntax from src dir: make lib-mscg args="-p [path] -m [suffix] -v [version]" + or: make lib-mscg args="-b -m [suffix]" +Syntax from lib dir: python Install.py -p [path] -m [suffix] -v [version] +Syntax from lib dir: python Install.py -b -m [suffix] + +Example: + +make lib-mscg args="-b -m serial " # download/build in lib/mscg/MSCG-release with settings compatible with "make serial" +make lib-mscg args="-b -m mpi " # download/build in lib/mscg/MSCG-release with settings compatible with "make mpi" +make lib-mscg args="-p /usr/local/mscg-release " # use existing MS-CG installation in /usr/local/mscg-release +""" + +# known checksums for different MSCG versions. used to validate the download. +checksums = { \ + '1.7.3.1' : '8c45e269ee13f60b303edd7823866a91', \ + } + +# parse and process arguments + +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the MSCG library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing MSCG installation") +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), + help="set version of MSCG to download and build (default: %s)" % version) +parser.add_argument("-m", "--machine", default=machine, choices=['mpi', 'serial', 'g++_simple', 'intel_simple', 'lapack', 'mac'], + help="set machine suffix specifies which src/Make/Makefile.suffix to use. (default: %s)" % machine) + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) + +buildflag = args.build +pathflag = args.path is not None +mscgpath = args.path +msuffix = args.machine +mscgver = args.version # settings -mscgver = "1.7.3.1" url = "https://github.com/uchicago-voth/MSCG-release/archive/%s.tar.gz" % mscgver -tarfile = "MS-CG-%s.tar.gz" % mscgver +tarname = "MS-CG-%s.tar.gz" % mscgver tardir = "MSCG-release-%s" % mscgver -# print error message or help +homepath = fullpath('.') +homedir = os.path.join(homepath, tardir) -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() - -# expand to full path name -# process leading '~' or relative path - -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) - -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) - - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program - else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file - - return None - -def geturl(url,fname): - success = False - - if which('curl') != None: - cmd = 'curl -L -o "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling curl failed with: %s" % e.output.decode('UTF-8')) - - if not success and which('wget') != None: - cmd = 'wget -O "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling wget failed with: %s" % e.output.decode('UTF-8')) - - if not success: - error("Failed to download source code with 'curl' or 'wget'") - return - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -homepath = "." -homedir = tardir - -buildflag = False -pathflag = False -linkflag = True -msuffix = "g++_simple" - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-p": - if iarg+2 > nargs: error() - mscgpath = fullpath(args[iarg+1]) - pathflag = True - iarg += 2 - elif args[iarg] == "-m": - if iarg+2 > nargs: error() - msuffix = args[iarg+1] - iarg += 2 - elif args[iarg] == "-b": - buildflag = True - iarg += 1 - else: error() - -homepath = fullpath(homepath) -homedir = "%s/%s" % (homepath,homedir) - -if (pathflag): - if not os.path.isdir(mscgpath): error("MS-CG path does not exist") - homedir = mscgpath - -if (buildflag and pathflag): - error("Cannot use -b and -p flag at the same time") - -if (not buildflag and not pathflag): - error("Have to use either -b or -p flag") +if pathflag: + if not os.path.isdir(mscgpath): + sys.exit("MS-CG path %s does not exist" % mscgpath) + homedir = fullpath(mscgpath) # download and unpack MS-CG tarfile if buildflag: print("Downloading MS-CG ...") - geturl(url,"%s/%s" % (homepath,tarfile)) + tarname = os.path.join(homepath, tarname) + geturl(url, tarname) print("Unpacking MS-CG tarfile ...") - if os.path.exists("%s/%s" % (homepath,tardir)): - cmd = 'rm -rf "%s/%s"' % (homepath,tardir) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarfile) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.remove("%s/%s" % (homepath,tarfile)) + + if os.path.exists(os.path.join(homepath, tardir)): + shutil.rmtree(os.path.join(homepath, tardir)) + + if tarfile.is_tarfile(tarname): + tgz = tarfile.open(tarname) + tgz.extractall(path=homepath) + os.remove(tarname) + else: + sys.exit("File %s is not a supported archive", tarname) + if os.path.basename(homedir) != tardir: if os.path.exists(homedir): - cmd = 'rm -rf "%s"' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.rename("%s/%s" % (homepath,tardir),homedir) + shutil.rmtree(homedir) + os.rename(os.path.join(homepath, tardir), homedir) # build MS-CG if buildflag: print("Building MS-CG ...") - if os.path.exists("%s/src/Make/Makefile.%s" % (homedir,msuffix)): - cmd = 'cd "%s/src"; cp Make/Makefile.%s .; make -f Makefile.%s' % \ - (homedir,msuffix,msuffix) + mkf = "Makefile.%s" % msuffix + mkp = os.path.join(homedir, 'src', 'Make', mkf) + if os.path.exists(mkp): + shutil.copyfile(mkp, os.path.join(homedir, 'src', mkf)) elif os.path.exists("Makefile.%s" % msuffix): - cmd = 'cd "%s/src"; cp ../../Makefile.%s .; make -f Makefile.%s' % \ - (homedir,msuffix,msuffix) + shutil.copyfile("Makefile.%s" % msuffix, os.path.join(homedir, 'src', mkf)) else: - error("Cannot find Makefile.%s" % msuffix) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - print(txt.decode('UTF-8')) + sys.exit("Cannot find Makefile.%s" % msuffix) + try: + cmd = 'make -C %s -f Makefile.%s' % (os.path.join(homedir, 'src'), msuffix) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + if not os.path.exists("Makefile.lammps"): print("Creating Makefile.lammps") if os.path.exists("Makefile.lammps.%s" % msuffix): - cmd = 'cp Makefile.lammps.%s Makefile.lammps' % msuffix + shutil.copyfile('Makefile.lammps.%s' % msuffix, 'Makefile.lammps') else: - cmd = 'cp Makefile.lammps.default Makefile.lammps' - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + shutil.copyfile('Makefile.lammps.default', 'Makefile.lammps') else: print("Makefile.lammps exists. Please check its settings") # create 2 links in lib/mscg to MS-CG src dir -if linkflag: - print("Creating links to MS-CG include and lib files") - if os.path.isfile("includelink") or os.path.islink("includelink"): - os.remove("includelink") - if os.path.isfile("liblink") or os.path.islink("liblink"): - os.remove("liblink") - cmd = 'ln -s "%s/src" includelink' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "%s/src" liblink' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print("Creating links to MS-CG include and lib files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") +os.symlink(os.path.join(homedir, 'src'), 'includelink') +os.symlink(os.path.join(homedir, 'src'), 'liblink') diff --git a/lib/plumed/.gitignore b/lib/plumed/.gitignore new file mode 100644 index 0000000000..d79d6d4413 --- /dev/null +++ b/lib/plumed/.gitignore @@ -0,0 +1,4 @@ +/plumed2* +/includelink +/liblink +/plumed-* diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py new file mode 100644 index 0000000000..70296b35d3 --- /dev/null +++ b/lib/plumed/Install.py @@ -0,0 +1,135 @@ +#!/usr/bin/env python + +""" +Install.py tool to download, unpack, build, and link to the plumed2 library +used to automate the steps described in the README file in this dir +""" + +from __future__ import print_function +import sys, os, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import get_cpus, fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = "2.4.4" +mode = "static" + +# help message + +HELP = """ +Syntax from src dir: make lib-plumed args="-b" + or: make lib-plumed args="-b -v 2.4.3" + or: make lib-plumed args="-p /usr/local/plumed2 -m shared" + +Syntax from lib dir: python Install.py -b -v 2.4.3 + or: python Install.py -b + or: python Install.py -p /usr/local/plumed2 -m shared + +Example: + +make lib-plumed args="-b" # download/build in lib/plumed/plumed2 +make lib-plumed args="-p $HOME/plumed2 -m shared" # use existing Plumed2 installation in $HOME/plumed2 +""" + +# known checksums for different PLUMED versions. used to validate the download. +checksums = { \ + '2.4.2' : '88188743a6e03ef076e5377d03ebb0e7', \ + '2.4.3' : 'b1be7c48971627febc11c61b70767fc5', \ + '2.4.4' : '71ed465bdc7c2059e282dbda8d564e71', \ + '2.5.0' : '6224cd089493661e19ceacccd35cf911', \ + } + +# parse and process arguments + +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the plumed2 library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing plumed2 installation") +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), + help="set version of plumed to download and build (default: %s)" % version) +parser.add_argument("-m", "--mode", default=mode, choices=['static', 'shared', 'runtime'], + help="set plumed linkage mode: static (default), shared, or runtime") + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) + +buildflag = args.build +pathflag = args.path is not None +plumedpath = args.path + +homepath = fullpath('.') +homedir = "%s/plumed2" % (homepath) + +if pathflag: + if not os.path.isdir(plumedpath): + sys.exit("Plumed2 path %s does not exist" % plumedpath) + homedir = fullpath(plumedpath) + +# download and unpack plumed2 tarball + +if buildflag: + url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version, version) + filename = "plumed-src-%s.tar.gz" %version + print("Downloading plumed ...") + geturl(url, filename) + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], filename): + sys.exit("Checksum for plumed2 library does not match") + + print("Unpacking plumed2 source tarball ...") + if os.path.exists("%s/plumed-%s" % (homepath, version)): + shutil.rmtree("%s/plumed-%s" % (homepath, version)) + if os.path.exists(homedir): + shutil.rmtree(homedir) + cmd = 'cd "%s"; tar -xzvf %s' % (homepath, filename) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + os.remove(os.path.join(homepath, filename)) + + # build plumed + print("Building plumed ...") + n_cpus = get_cpus() + cmd = 'cd %s/plumed-%s; ./configure --prefix=%s --enable-modules=all --enable-static-patch ; make -j%d ; make install' % (homepath, version, homedir, n_cpus) + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) + +# create 2 links in lib/plumed to plumed2 installation dir + +print("Creating links to plumed2 include and lib files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") +os.symlink(os.path.join(homedir, 'include'), 'includelink') +libpath = os.path.join(homedir, 'lib64') +if not os.path.exists(libpath): + libpath = os.path.join(homedir, 'lib') +os.symlink(libpath, 'liblink') +if os.path.isfile("Makefile.lammps.%s" % mode): + print("Creating Makefile.lammps") + plumedinc = os.path.join('liblink', 'plumed', 'src', 'lib', 'Plumed.inc.' + mode) + lines1 = open(plumedinc, 'r').readlines() + lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines() + fp = open("Makefile.lammps", 'w') + fp.write(os.path.join("PLUMED_LIBDIR=", homedir, "lib\n")) + for line in lines1: + fp.write(line) + for line in lines2: + fp.write(line) + fp.close() diff --git a/lib/plumed/Makefile.lammps.runtime b/lib/plumed/Makefile.lammps.runtime new file mode 100644 index 0000000000..b8c8636940 --- /dev/null +++ b/lib/plumed/Makefile.lammps.runtime @@ -0,0 +1,5 @@ +# Settings that the LAMMPS build will import when this package library is used + +plumed_SYSINC = -D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=$(PLUMED_LIBDIR)/libplumedKernel.so +plumed_SYSLIB = $(PLUMED_LOAD) -rdynamic +plumed_SYSPATH = diff --git a/lib/meam/Makefile.lammps.empty b/lib/plumed/Makefile.lammps.shared similarity index 54% rename from lib/meam/Makefile.lammps.empty rename to lib/plumed/Makefile.lammps.shared index 10394b68ad..860202a6f2 100644 --- a/lib/meam/Makefile.lammps.empty +++ b/lib/plumed/Makefile.lammps.shared @@ -1,5 +1,5 @@ # Settings that the LAMMPS build will import when this package library is used -meam_SYSINC = -meam_SYSLIB = -meam_SYSPATH = +plumed_SYSINC = +plumed_SYSLIB = $(PLUMED_LOAD) +plumed_SYSPATH = diff --git a/lib/plumed/Makefile.lammps.static b/lib/plumed/Makefile.lammps.static new file mode 100644 index 0000000000..2ca0858610 --- /dev/null +++ b/lib/plumed/Makefile.lammps.static @@ -0,0 +1,7 @@ +# Settings that the LAMMPS build will import when this package library is used + +# Use statically linked C++ interface to plumed + +plumed_SYSINC = -D__PLUMED_WRAPPER_CXX=1 +plumed_SYSLIB = $(PLUMED_LOAD) +plumed_SYSPATH = diff --git a/lib/plumed/README b/lib/plumed/README new file mode 100644 index 0000000000..fb8ef29ff3 --- /dev/null +++ b/lib/plumed/README @@ -0,0 +1,56 @@ +This directory contains links to the PLUMED library which is required +to use the PLUMED package and its fix plumed command in a +LAMMPS input script. PLUMED should only be downloaded into this directory if +you wish to statically link the library. If you wish to link PLUMED as +a dynamic library (as we recommend) then you can compile and build PLUMED +separately to LAMMPS. To use PLUMED in conjuction with LAMMPS you then simply +need to ensure that the PLUMED library is in your path at runtime. + +More info about the PLUMED library can be found at http://www.plumed.org. + +You can type "make lib-plumed" from the src directory to see help on +how to download, build and statically link PLUMED via make commands, or you can +do the same thing by typing "python Install.py" from within this +directory. Alternatively you can download and build PLUMED manually by following the instructions +below. + +----------------- + +Instructions: + +1. Download PLUMED either as a tarball from + http://www.plumed.org/get-it + or clone it using git clone https://github.com/plumed/plumed2.git. + If you download the tarball + unpack it in unpack it in this /lib/plumed directory. + Similarly if you clone it clone it to the /lib/plumed + directory. + +2. Compile PLUMED from within its home directory. In the + simplest cases this be done by issuing the commands + % ./configure + % make + More detailed instructions can be found at + http://plumed.github.io/doc-master/user-doc/html/_installation.html + +3. There is no need to install PLUMED if you only wish + to use it from LAMMPS. You should thus only run + make install if you want to use PLUMED as a stand-alone + code or from some other code. To install it you can + run the following commands: + a) install under the default /usr/local + % sudo make install + b) install under a user-writeable location by first + changing the PREFIX variable when running the + configure command file, then + % make install + +----------------- + +When these steps are complete you can build LAMMPS +with the PLUMED package installed: + +% cd lammps/src +% make yes-user-plumed +% make mpi (or whatever target you wish) + diff --git a/lib/poems/POEMSChain.h b/lib/poems/POEMSChain.h index 7dc143a9d9..9f0db59333 100644 --- a/lib/poems/POEMSChain.h +++ b/lib/poems/POEMSChain.h @@ -31,6 +31,7 @@ struct POEMSChain{ { delete childChains(i); } + listOfNodes.DeleteValues(); } //void printTreeStructure(int tabs); //void getTreeAsList(List * temp); diff --git a/lib/poems/SystemProcessor.h b/lib/poems/SystemProcessor.h index 9ef511f997..3be168c34d 100644 --- a/lib/poems/SystemProcessor.h +++ b/lib/poems/SystemProcessor.h @@ -40,7 +40,9 @@ struct POEMSNode { class SystemProcessor{ private: Tree nodes; -// List forDeletion; + static void POEMSNodeDelete_cb(void *node) { + delete (POEMSNode *) node; + } List headsOfSystems; List > ringsInSystem; POEMSNode * findSingleLink(TreeNode * aNode); @@ -65,6 +67,8 @@ public: }; SystemProcessor::SystemProcessor(void){ + // register callback for deleting auxiliary data from tree nodes. + nodes.SetDeleteAuxData(&POEMSNodeDelete_cb); } void SystemProcessor::processArray(int** links, int numLinks) diff --git a/lib/poems/poemstree.h b/lib/poems/poemstree.h index 889de313f8..8f8e80ab66 100644 --- a/lib/poems/poemstree.h +++ b/lib/poems/poemstree.h @@ -40,6 +40,9 @@ protected: // used by the copy constructor and assignment operator TreeNode *CopyTree(TreeNode *t); + // callback function to delete aux data + void (*DeleteAuxData)(void *); + // used by insert and delete method to re-establish // the avl conditions after a node is added or deleted // from a subtree @@ -72,7 +75,13 @@ public: // standard list handling methods void * Find(int& item); - void * GetAuxData(int item) { return (void *)(FindNode(item, root)->GetAuxData());} + void * GetAuxData(int item) { + return (void *)(FindNode(item, root)->GetAuxData()); + } + void SetDeleteAuxData(void (*callback)(void *)) { + DeleteAuxData = callback; + } + void Insert(const int& item, const int& data, void * AuxData = NULL); void Delete(const int& item); void AVLInsert(TreeNode* &tree, TreeNode* newNode, int &reviseBalanceFactor); @@ -90,6 +99,7 @@ Tree::Tree(void) root = 0; current = 0; size = 0; + DeleteAuxData = NULL; } @@ -569,14 +579,19 @@ TreeNode *Tree::CopyTree(TreeNode *t) // the tree and delete each node as the vist operation void Tree::DeleteTree(TreeNode *t) { - if (t != NULL) - { - DeleteTree(t->Left()); - DeleteTree(t->Right()); - if (t->GetAuxData() != NULL) - delete (TreeNode *) t->GetAuxData(); - FreeTreeNode(t); - } + if (t != NULL) { + DeleteTree(t->Left()); + DeleteTree(t->Right()); + void *aux = t->GetAuxData(); + if (aux != NULL) { + if (DeleteAuxData != NULL) { + (*DeleteAuxData)(aux); + } else { + delete (TreeNode *) aux; + } + } + FreeTreeNode(t); + } } // call the function DeleteTree to deallocate the nodes. then diff --git a/lib/pylint.rc b/lib/pylint.rc new file mode 100644 index 0000000000..99ff478343 --- /dev/null +++ b/lib/pylint.rc @@ -0,0 +1,564 @@ +# pylint configuration for checking Install.py files in the lib folder and its subdirs + +[MASTER] + +# A comma-separated list of package or module names from where C extensions may +# be loaded. Extensions are loading into the active Python interpreter and may +# run arbitrary code. +extension-pkg-whitelist= + +# Add files or directories to the blacklist. They should be base names, not +# paths. +ignore=CVS + +# Add files or directories matching the regex patterns to the blacklist. The +# regex matches against base names, not paths. +ignore-patterns= + +# Python code to execute, usually for sys.path manipulation such as +# pygtk.require(). +init-hook=sys.path.append('..') + +# Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the +# number of processors available to use. +jobs=1 + +# Control the amount of potential inferred values when inferring a single +# object. This can help the performance when dealing with large functions or +# complex, nested conditions. +limit-inference-results=100 + +# List of plugins (as comma separated values of python modules names) to load, +# usually to register additional checkers. +load-plugins= + +# Pickle collected data for later comparisons. +persistent=yes + +# Specify a configuration file. +#rcfile= + +# When enabled, pylint would attempt to guess common misconfiguration and emit +# user-friendly hints instead of false-positive error messages. +suggestion-mode=yes + +# Allow loading of arbitrary C extensions. Extensions are imported into the +# active Python interpreter and may run arbitrary code. +unsafe-load-any-extension=no + + +[MESSAGES CONTROL] + +# Only show warnings with the listed confidence levels. Leave empty to show +# all. Valid levels: HIGH, INFERENCE, INFERENCE_FAILURE, UNDEFINED. +confidence= + +# Disable the message, report, category or checker with the given id(s). You +# can either give multiple identifiers separated by comma (,) or put this +# option multiple times (only on the command line, not in the configuration +# file where it should appear only once). You can also use "--disable=all" to +# disable everything first and then reenable specific checks. For example, if +# you want to run only the similarities checker, you can use "--disable=all +# --enable=similarities". If you want to run only the classes checker, but have +# no Warning level messages displayed, use "--disable=all --enable=classes +# --disable=W". +disable=print-statement, + parameter-unpacking, + unpacking-in-except, + old-raise-syntax, + backtick, + long-suffix, + old-ne-operator, + old-octal-literal, + import-star-module-level, + non-ascii-bytes-literal, + raw-checker-failed, + bad-inline-option, + locally-disabled, + locally-enabled, + file-ignored, + suppressed-message, + useless-suppression, + deprecated-pragma, + use-symbolic-message-instead, + apply-builtin, + basestring-builtin, + buffer-builtin, + cmp-builtin, + coerce-builtin, + execfile-builtin, + file-builtin, + long-builtin, + raw_input-builtin, + reduce-builtin, + standarderror-builtin, + unicode-builtin, + xrange-builtin, + coerce-method, + delslice-method, + getslice-method, + setslice-method, + no-absolute-import, + old-division, + dict-iter-method, + dict-view-method, + next-method-called, + metaclass-assignment, + indexing-exception, + raising-string, + reload-builtin, + oct-method, + hex-method, + nonzero-method, + cmp-method, + input-builtin, + round-builtin, + intern-builtin, + unichr-builtin, + map-builtin-not-iterating, + zip-builtin-not-iterating, + range-builtin-not-iterating, + filter-builtin-not-iterating, + using-cmp-argument, + eq-without-hash, + div-method, + idiv-method, + rdiv-method, + exception-message-attribute, + invalid-str-codec, + sys-max-int, + bad-python3-import, + deprecated-string-function, + deprecated-str-translate-call, + deprecated-itertools-function, + deprecated-types-field, + next-method-defined, + dict-items-not-iterating, + dict-keys-not-iterating, + dict-values-not-iterating, + deprecated-operator-function, + deprecated-urllib-function, + xreadlines-attribute, + deprecated-sys-function, + exception-escape, + comprehension-escape, + invalid-name, + bad-indentation, + multiple-imports, + line-too-long + +# Enable the message, report, category or checker with the given id(s). You can +# either give multiple identifier separated by comma (,) or put this option +# multiple time (only on the command line, not in the configuration file where +# it should appear only once). See also the "--disable" option for examples. +enable=c-extension-no-member + + +[REPORTS] + +# Python expression which should return a note less than 10 (10 is the highest +# note). You have access to the variables errors warning, statement which +# respectively contain the number of errors / warnings messages and the total +# number of statements analyzed. This is used by the global evaluation report +# (RP0004). +evaluation=10.0 - ((float(5 * error + warning + refactor + convention) / statement) * 10) + +# Template used to display messages. This is a python new-style format string +# used to format the message information. See doc for all details. +#msg-template= + +# Set the output format. Available formats are text, parseable, colorized, json +# and msvs (visual studio). You can also give a reporter class, e.g. +# mypackage.mymodule.MyReporterClass. +output-format=text + +# Tells whether to display a full report or only the messages. +reports=no + +# Activate the evaluation score. +score=yes + + +[REFACTORING] + +# Maximum number of nested blocks for function / method body +max-nested-blocks=5 + +# Complete name of functions that never returns. When checking for +# inconsistent-return-statements if a never returning function is called then +# it will be considered as an explicit return statement and no message will be +# printed. +never-returning-functions=sys.exit + + +[FORMAT] + +# Expected format of line ending, e.g. empty (any line ending), LF or CRLF. +expected-line-ending-format= + +# Regexp for a line that is allowed to be longer than the limit. +ignore-long-lines=^\s*(# )??$ + +# Number of spaces of indent required inside a hanging or continued line. +indent-after-paren=4 + +# String used as indentation unit. This is usually " " (4 spaces) or "\t" (1 +# tab). +indent-string=' ' + +# Maximum number of characters on a single line. +max-line-length=100 + +# Maximum number of lines in a module. +max-module-lines=1000 + +# List of optional constructs for which whitespace checking is disabled. `dict- +# separator` is used to allow tabulation in dicts, etc.: {1 : 1,\n222: 2}. +# `trailing-comma` allows a space between comma and closing bracket: (a, ). +# `empty-line` allows space-only lines. +no-space-check=trailing-comma, + dict-separator + +# Allow the body of a class to be on the same line as the declaration if body +# contains single statement. +single-line-class-stmt=no + +# Allow the body of an if to be on the same line as the test if there is no +# else. +single-line-if-stmt=no + + +[VARIABLES] + +# List of additional names supposed to be defined in builtins. Remember that +# you should avoid to define new builtins when possible. +additional-builtins= + +# Tells whether unused global variables should be treated as a violation. +allow-global-unused-variables=yes + +# List of strings which can identify a callback function by name. A callback +# name must start or end with one of those strings. +callbacks=cb_, + _cb + +# A regular expression matching the name of dummy variables (i.e. expected to +# not be used). +dummy-variables-rgx=_+$|(_[a-zA-Z0-9_]*[a-zA-Z0-9]+?$)|dummy|^ignored_|^unused_ + +# Argument names that match this expression will be ignored. Default to name +# with leading underscore. +ignored-argument-names=_.*|^ignored_|^unused_ + +# Tells whether we should check for unused import in __init__ files. +init-import=no + +# List of qualified module names which can have objects that can redefine +# builtins. +redefining-builtins-modules=six.moves,past.builtins,future.builtins,builtins,io + + +[SIMILARITIES] + +# Ignore comments when computing similarities. +ignore-comments=yes + +# Ignore docstrings when computing similarities. +ignore-docstrings=yes + +# Ignore imports when computing similarities. +ignore-imports=no + +# Minimum lines number of a similarity. +min-similarity-lines=4 + + +[SPELLING] + +# Limits count of emitted suggestions for spelling mistakes. +max-spelling-suggestions=4 + +# Spelling dictionary name. Available dictionaries: none. To make it working +# install python-enchant package.. +spelling-dict= + +# List of comma separated words that should not be checked. +spelling-ignore-words= + +# A path to a file that contains private dictionary; one word per line. +spelling-private-dict-file= + +# Tells whether to store unknown words to indicated private dictionary in +# --spelling-private-dict-file option instead of raising a message. +spelling-store-unknown-words=no + + +[LOGGING] + +# Logging modules to check that the string format arguments are in logging +# function parameter format. +logging-modules=logging + + +[MISCELLANEOUS] + +# List of note tags to take in consideration, separated by a comma. +notes=FIXME, + XXX, + TODO + + +[TYPECHECK] + +# List of decorators that produce context managers, such as +# contextlib.contextmanager. Add to this list to register other decorators that +# produce valid context managers. +contextmanager-decorators=contextlib.contextmanager + +# List of members which are set dynamically and missed by pylint inference +# system, and so shouldn't trigger E1101 when accessed. Python regular +# expressions are accepted. +generated-members= + +# Tells whether missing members accessed in mixin class should be ignored. A +# mixin class is detected if its name ends with "mixin" (case insensitive). +ignore-mixin-members=yes + +# Tells whether to warn about missing members when the owner of the attribute +# is inferred to be None. +ignore-none=yes + +# This flag controls whether pylint should warn about no-member and similar +# checks whenever an opaque object is returned when inferring. The inference +# can return multiple potential results while evaluating a Python object, but +# some branches might not be evaluated, which results in partial inference. In +# that case, it might be useful to still emit no-member and other checks for +# the rest of the inferred objects. +ignore-on-opaque-inference=yes + +# List of class names for which member attributes should not be checked (useful +# for classes with dynamically set attributes). This supports the use of +# qualified names. +ignored-classes=optparse.Values,thread._local,_thread._local + +# List of module names for which member attributes should not be checked +# (useful for modules/projects where namespaces are manipulated during runtime +# and thus existing member attributes cannot be deduced by static analysis. It +# supports qualified module names, as well as Unix pattern matching. +ignored-modules= + +# Show a hint with possible names when a member name was not found. The aspect +# of finding the hint is based on edit distance. +missing-member-hint=yes + +# The minimum edit distance a name should have in order to be considered a +# similar match for a missing member name. +missing-member-hint-distance=1 + +# The total number of similar names that should be taken in consideration when +# showing a hint for a missing member. +missing-member-max-choices=1 + + +[BASIC] + +# Naming style matching correct argument names. +argument-naming-style=snake_case + +# Regular expression matching correct argument names. Overrides argument- +# naming-style. +#argument-rgx= + +# Naming style matching correct attribute names. +attr-naming-style=snake_case + +# Regular expression matching correct attribute names. Overrides attr-naming- +# style. +#attr-rgx= + +# Bad variable names which should always be refused, separated by a comma. +bad-names=foo, + bar, + baz, + toto, + tutu, + tata + +# Naming style matching correct class attribute names. +class-attribute-naming-style=any + +# Regular expression matching correct class attribute names. Overrides class- +# attribute-naming-style. +#class-attribute-rgx= + +# Naming style matching correct class names. +class-naming-style=PascalCase + +# Regular expression matching correct class names. Overrides class-naming- +# style. +#class-rgx= + +# Naming style matching correct constant names. +const-naming-style=UPPER_CASE + +# Regular expression matching correct constant names. Overrides const-naming- +# style. +#const-rgx= + +# Minimum line length for functions/classes that require docstrings, shorter +# ones are exempt. +docstring-min-length=-1 + +# Naming style matching correct function names. +function-naming-style=snake_case + +# Regular expression matching correct function names. Overrides function- +# naming-style. +#function-rgx= + +# Good variable names which should always be accepted, separated by a comma. +good-names=i, + j, + k, + ex, + Run, + _ + +# Include a hint for the correct naming format with invalid-name. +include-naming-hint=no + +# Naming style matching correct inline iteration names. +inlinevar-naming-style=any + +# Regular expression matching correct inline iteration names. Overrides +# inlinevar-naming-style. +#inlinevar-rgx= + +# Naming style matching correct method names. +method-naming-style=snake_case + +# Regular expression matching correct method names. Overrides method-naming- +# style. +#method-rgx= + +# Naming style matching correct module names. +module-naming-style=snake_case + +# Regular expression matching correct module names. Overrides module-naming- +# style. +#module-rgx= + +# Colon-delimited sets of names that determine each other's naming style when +# the name regexes allow several styles. +name-group= + +# Regular expression which should only match function or class names that do +# not require a docstring. +no-docstring-rgx=^_ + +# List of decorators that produce properties, such as abc.abstractproperty. Add +# to this list to register other decorators that produce valid properties. +# These decorators are taken in consideration only for invalid-name. +property-classes=abc.abstractproperty + +# Naming style matching correct variable names. +variable-naming-style=snake_case + +# Regular expression matching correct variable names. Overrides variable- +# naming-style. +#variable-rgx= + + +[IMPORTS] + +# Allow wildcard imports from modules that define __all__. +allow-wildcard-with-all=no + +# Analyse import fallback blocks. This can be used to support both Python 2 and +# 3 compatible code, which means that the block might have code that exists +# only in one or another interpreter, leading to false positives when analysed. +analyse-fallback-blocks=no + +# Deprecated modules which should not be used, separated by a comma. +deprecated-modules=optparse,tkinter.tix + +# Create a graph of external dependencies in the given file (report RP0402 must +# not be disabled). +ext-import-graph= + +# Create a graph of every (i.e. internal and external) dependencies in the +# given file (report RP0402 must not be disabled). +import-graph= + +# Create a graph of internal dependencies in the given file (report RP0402 must +# not be disabled). +int-import-graph= + +# Force import order to recognize a module as part of the standard +# compatibility libraries. +known-standard-library= + +# Force import order to recognize a module as part of a third party library. +known-third-party=enchant + + +[DESIGN] + +# Maximum number of arguments for function / method. +max-args=5 + +# Maximum number of attributes for a class (see R0902). +max-attributes=7 + +# Maximum number of boolean expressions in an if statement. +max-bool-expr=5 + +# Maximum number of branch for function / method body. +max-branches=12 + +# Maximum number of locals for function / method body. +max-locals=15 + +# Maximum number of parents for a class (see R0901). +max-parents=7 + +# Maximum number of public methods for a class (see R0904). +max-public-methods=20 + +# Maximum number of return / yield for function / method body. +max-returns=6 + +# Maximum number of statements in function / method body. +max-statements=50 + +# Minimum number of public methods for a class (see R0903). +min-public-methods=2 + + +[CLASSES] + +# List of method names used to declare (i.e. assign) instance attributes. +defining-attr-methods=__init__, + __new__, + setUp + +# List of member names, which should be excluded from the protected access +# warning. +exclude-protected=_asdict, + _fields, + _replace, + _source, + _make + +# List of valid names for the first argument in a class method. +valid-classmethod-first-arg=cls + +# List of valid names for the first argument in a metaclass class method. +valid-metaclass-classmethod-first-arg=cls + + +[EXCEPTIONS] + +# Exceptions that will emit a warning when being caught. Defaults to +# "Exception". +overgeneral-exceptions=Exception diff --git a/lib/reax/Install.py b/lib/reax/Install.py deleted file mode 120000 index ffe709d44c..0000000000 --- a/lib/reax/Install.py +++ /dev/null @@ -1 +0,0 @@ -../Install.py \ No newline at end of file diff --git a/lib/reax/Makefile.g95 b/lib/reax/Makefile.g95 deleted file mode 100644 index 55c40daa00..0000000000 --- a/lib/reax/Makefile.g95 +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.gfortran - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = g95 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/Makefile.gfortran b/lib/reax/Makefile.gfortran deleted file mode 100644 index ab42301688..0000000000 --- a/lib/reax/Makefile.gfortran +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.gfortran - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = gfortran -F90FLAGS = -O3 -fPIC -fno-second-underscore -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/Makefile.ifort b/lib/reax/Makefile.ifort deleted file mode 100644 index 1760cb9c6a..0000000000 --- a/lib/reax/Makefile.ifort +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.ifort - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = ifort -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/Makefile.lammps.empty b/lib/reax/Makefile.lammps.empty deleted file mode 100644 index 758755f3c8..0000000000 --- a/lib/reax/Makefile.lammps.empty +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -reax_SYSINC = -reax_SYSLIB = -reax_SYSPATH = diff --git a/lib/reax/Makefile.lammps.gfortran b/lib/reax/Makefile.lammps.gfortran deleted file mode 100644 index f5da63bc38..0000000000 --- a/lib/reax/Makefile.lammps.gfortran +++ /dev/null @@ -1,5 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -reax_SYSINC = -reax_SYSLIB = -lgfortran -reax_SYSPATH = diff --git a/lib/reax/Makefile.lammps.ifort b/lib/reax/Makefile.lammps.ifort deleted file mode 100644 index 69ac12606d..0000000000 --- a/lib/reax/Makefile.lammps.ifort +++ /dev/null @@ -1,6 +0,0 @@ -# Settings that the LAMMPS build will import when this package library is used - -reax_SYSINC = -reax_SYSLIB = -lifcore -reax_SYSPATH = - diff --git a/lib/reax/Makefile.mpi b/lib/reax/Makefile.mpi deleted file mode 100644 index 142f7e9bc6..0000000000 --- a/lib/reax/Makefile.mpi +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.empty - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = mpifort -F90FLAGS = -O3 -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/Makefile.pgf90 b/lib/reax/Makefile.pgf90 deleted file mode 100644 index dfc17eca11..0000000000 --- a/lib/reax/Makefile.pgf90 +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.pgf90 - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = pgf90 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/Makefile.redsky b/lib/reax/Makefile.redsky deleted file mode 100644 index f51a15d1f1..0000000000 --- a/lib/reax/Makefile.redsky +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.ifort - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = mpif90 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/Makefile.serial b/lib/reax/Makefile.serial deleted file mode 120000 index c52fbcb986..0000000000 --- a/lib/reax/Makefile.serial +++ /dev/null @@ -1 +0,0 @@ -Makefile.gfortran \ No newline at end of file diff --git a/lib/reax/Makefile.tbird b/lib/reax/Makefile.tbird deleted file mode 100644 index f51a15d1f1..0000000000 --- a/lib/reax/Makefile.tbird +++ /dev/null @@ -1,51 +0,0 @@ -# * -# *_________________________________________________________________________* -# * Fortran Library for Reactive Force Field * -# * DESCRIPTION: SEE READ-ME * -# * FILE NAME: Makefile * -# * CONTRIBUTING AUTHORS: Hansohl Cho(MIT), Aidan Thompson(SNL) * -# * and Greg Wagner(SNL) * -# * CONTACT: hansohl@mit.edu, athompson@sandia.gov, gjwagne@sandia.gov * -# *_________________________________________________________________________*/ - -SHELL = /bin/sh - -# which file will be copied to Makefile.lammps - -EXTRAMAKE = Makefile.lammps.ifort - -# ------ FILES ------ - -SRC = reax_connect.F reax_inout.F reax_lammps.F reax_poten.F reax_reac.F reax_charges.F - -HEADERFILES = reax_defs.h *.blk - -# ------ DEFINITIONS ------ - -LIB = libreax.a -OBJ = $(SRC:.F=.o) - -# ------ SETTINGS ------ - -F90 = mpif90 -F90FLAGS = -O -fPIC -ARCHIVE = ar -ARCHFLAG = -rc -USRLIB = -SYSLIB = - -# ------ MAKE PROCEDURE ------ - -lib: $(OBJ) - $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) - @cp $(EXTRAMAKE) Makefile.lammps - -# ------ COMPILE RULES ------ - -%.o:%.F $(HEADERFILES) - $(F90) $(F90FLAGS) -c $< - -# ------ CLEAN ------ - -clean: - -rm *.o $(LIB) diff --git a/lib/reax/README b/lib/reax/README deleted file mode 100644 index f21a470618..0000000000 --- a/lib/reax/README +++ /dev/null @@ -1,78 +0,0 @@ -ReaxFF library - -Aidan Thompson, Sandia National Labs -athomps at sandia.gov -Jan 2008 - -This library is an implementation of the ReaxFF potential, -specifically designed to work with LAMMPS. It is derived from Adri van -Duin's original serial code, with intervening incarnations in CMDF and -GRASP. - -------------------------------------------------- - -This directory has source files to build a library that LAMMPS -links against when using the REAX package. - -This library must be built with a F90 compiler, before LAMMPS is -built, so LAMMPS can link against it. - -You can type "make lib-reax" from the src directory to see help on how -to build this library via make commands, or you can do the same thing -by typing "python Install.py" from within this directory, or you can -do it manually by following the instructions below. - -Build the library using one of the provided Makefile.* files or create -your own, specific to your compiler and system. For example: - -make -f Makefile.gfortran - -When you are done building this library, two files should -exist in this directory: - -libreax.a the library LAMMPS will link against -Makefile.lammps settings the LAMMPS Makefile will import - -Makefile.lammps is created by the make command, by copying one of the -Makefile.lammps.* files. See the EXTRAMAKE setting at the top of the -Makefile.* files. - -IMPORTANT: You must examine the final Makefile.lammps to insure it is -correct for your system, else the LAMMPS build will likely fail. - -Makefile.lammps has settings for 3 variables: - -user-reax_SYSINC = leave blank for this package -user-reax_SYSLIB = auxiliary F90 libs needed to link a F90 lib with - a C++ program (LAMMPS) via a C++ compiler -user-reax_SYSPATH = path(s) to where those libraries are - -Because you have a F90 compiler on your system, you should have these -libraries. But you will have to figure out which ones are needed and -where they are. Examples of common configurations are in the -Makefile.lammps.* files. - -------------------------------------------------- - -Additional build notes: - -The include file reax_defs.h is used by both the ReaxFF library source -files and the LAMMPS pair_reax.cpp source file (in package src/REAX). -It contains dimensions of statically-allocated arrays created by the -ReaxFF library. The size of these arrays must be set small enough to -avoid exceeding the available machine memory, and large enough to fit -the actual data generated by ReaxFF. If you change the values in -reax_defs.h, you must first rebuild the library and then rebuild -LAMMPS. - -This library is called by functions in pair_reax.cpp. The C++ to -FORTRAN function calls in pair_reax.cpp assume that FORTRAN object -names are converted to C object names by appending an underscore -character. This is generally the case, but on machines that do not -conform to this convention, you will need to modify either the C++ -code or your compiler settings. The name conversion is handled by the -preprocessor macro called FORTRAN in the file pair_reax_fortran.h, -which is included by pair_reax.cpp. Different definitions of this -macro can be obtained by adding a machine-specific macro definition to -the CCFLAGS variable in your your LAMMPS Makefile e.g. -D_IBM. See -pair_reax_fortran.h for more info. diff --git a/lib/reax/cbka.blk b/lib/reax/cbka.blk deleted file mode 100644 index 4dbe0a36c6..0000000000 --- a/lib/reax/cbka.blk +++ /dev/null @@ -1,116 +0,0 @@ -#include "reax_defs.h" - implicit real*8 (a-h,o-z),integer(i-n) - parameter (nneighmax=NNEIGHMAXDEF) - parameter (nat=NATDEF) !Max number of atoms - parameter (nattot=NATTOTDEF) !Max number of global atoms - parameter (nsort=NSORTDEF) !Max number of atom types - parameter (mbond=MBONDDEF) !Max number of bonds connected to one atom - parameter (na1mx3=3*nat) !3*max number of atoms - parameter (navib=NAVIBDEF) !for 2nd derivatives - parameter (nbotym=NBOTYMDEF) !Max number of bond types - parameter (nvatym=NVATYMDEF) !Max number of valency angle types - parameter (ntotym=NTOTYMDEF) !Max number of torsion angle types - parameter (nhbtym=NHBTYMDEF) !Max number of hydrogen bond types - parameter (nodmtym=NODMTYMDEF) !Max number of off-diagonal Morse types - parameter (nboallmax=NBOALLMAXDEF) !Max number of all bonds - parameter (nbomax=NBOMAXDEF) !Max number of bonds - parameter (nhbmax=NHBMAXDEF) !Max number of hydrogen bonds - parameter (nvamax=NVAMAXDEF) !Max number of valency angles - parameter (nopmax=NOPMAXDEF) !Max number of out of plane angles - parameter (ntomax=NTOMAXDEF) !Max number of torsion angles - parameter (npamax=NPAMAXDEF) !Max number of general parameters in force field - parameter (nmolmax=NMOLMAXDEF) !Max number of molecules in system - parameter (nmolset=NMOLSETDEF) !Max number of molecules in training set - parameter (mrestra=MRESTRADEF) !Max number of restraints - parameter (mtreg=MTREGDEF) !Max number of temperature regimes - parameter (mtzone=MTZONEDEF) !Max number of temperature zones - parameter (mvreg=MVREGDEF) !Max number of volume regimes - parameter (mvzone=MVZONEDEF) !Max number of volume zones - parameter (mereg=MEREGDEF) !Max number of electric field regimes - parameter (mezone=MEZONEDEF) !Max number of electric field zones - character*1 qr,qrset,qresi2 - character*2 qaset,qadd - character*3 qresi1 - character*5 qlabel,qffty,qbgfaxes,qbgfsgn,qresi3 - character*20 qkeyw - character*25 qfile - character*40 qffield,qformat,qstrana2 - character*60 qremark,qremset,qmolset - character*200 qstrana1 - common - $/cbka/ dhbdc(nhbmax,3,3),cp(nat,3), - $ cadd(nat,3),d2(3*navib,3*navib), - $ veladd(3,nat), - $ aold(3,nat),dic(3,nat),pvdw1(nsort,nsort), - $ pvdw2(nsort,nsort),angimp(nat,6), - $ yt(na1mx3),pt(na1mx3),gi(na1mx3),enmolset(nmolset), - $ ai(na1mx3),bi(na1mx3),yi(na1mx3),pn(na1mx3),tbo(nat), - $ chgbgf(nattot), - $ abo2(nat),bor4(nat),bos(nbomax), - $ eldef(nat),vradic(nat), - $ vmo2(nat), - $ ro(nbomax),dbondr(nbomax), - $ dbosidr(nbomax),thgo(nopmax), - $ elmol(nmolmax), - $ elaf(nsort),vpq(nsort), - $ rvdw(nsort),alf(nsort),eps(nsort),chat(nsort), - $ rcore(nsort,nsort),ecore(nsort,nsort),acore(nsort,nsort), - $ vlp2(nsort), - $ valp2(nsort),vincr(nsort), - $ vval3(nsort), - $ vuncor(nbotym), - $ vop(nsort), - $ sigqeq(nsort), - $ rrcha(mrestra), - $ rmstra3(mrestra), - $ rmcha(mrestra), - $ rtcha(mrestra),rvcha(mrestra), - $ v2bo(ntotym),v3bo(ntotym), - $ eel,fctor,elr, - $ presx2,presy2,presz2, - $ tset2, - $ enmol,formol,vvol,tpnrad, - $ delvib, - $ taut2,tincr,xmasmd, - $ gdicmax,parc1,parc2,sumelec, - $ xinh,fsnh,vqnh,snh,ham,errnh,sumhe, - $ swa,swb2,swc0,swc1,swc2,swc3,swc4,swc5,swc6, - $ swc7,plr,endpo2,ccpar, - $ c4,estrmin,endpo,accincr, - $ endpoold,xadd,yadd,zadd,addist,taddmol, - $ Hug_E0, Hug_P0, Hug_V0, xImpVcm, shock_vel, - $ shock_z_sep - common - $/cbka/ - $ ioop(nopmax,9),ifreqset(nmolset), - $ ijk(nat,4),icgeopt(nmolset), - $ irap(50),irdo(50,2), - $ ityadd(nat), - $ nmoloo(nat),iradic(nat),idef(nsort),nasort(nsort), - $ ibgr1(nattot),ibgr2(nattot),idupc(6), - $ imolsta(nat), - $ ncent2(nbomax),irads,nrdd,nrddf,nbiolab,nuge, - $ nbon2,npar,nodmty,ngnh,irac,nincrop, - $ nboty,mdstep, - $ nreac, - $ nbonop,icelo2, - $ iaddfreq,iveladd,invt, - $ noop,ndtau, - $ nelc3,nfc,nsav2,nmmax,ibh2, - $ nmmaxold,nfcold,icellold,imodfile, - $ icelo2old,inmov1,inmov2,nchaold,naa,nadattempt, - $ nequi,iadj, - $ ntest,nmm, - $ nmolo5o,nradcount,nmollset,iflga, - $ iperiod,ibgfversion,iremark,iconne, - $ kx,ky,kz,iexco,iruid,ibity,nvlist, - $ ityrad,iredo,iexx,iexy,iexz,ncellopt, - $ ndata2,nprob,nit,i5758,ingeo,nmoloold,itemp, - $ icgeo,ishock_type,isymm, - $ qadd(nat),qlabel(nattot),qffty(nattot),qresi1(nattot), - $ qresi2(nattot),qresi3(nattot), - $ qremark(20),qformat(20),qr,qffield, - $ qstrana1,qstrana2,qmolset(nmolset) -*********************************************************************** - - diff --git a/lib/reax/cbkabo.blk b/lib/reax/cbkabo.blk deleted file mode 100644 index 957651d002..0000000000 --- a/lib/reax/cbkabo.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbkabo/ abo(nat) - - diff --git a/lib/reax/cbkatomcoord.blk b/lib/reax/cbkatomcoord.blk deleted file mode 100644 index 711fab85a0..0000000000 --- a/lib/reax/cbkatomcoord.blk +++ /dev/null @@ -1,3 +0,0 @@ - common - $/cbkatomcoord/ id(nat,3),xmasat(nat),vel(3,nat),accel(3,nat) - diff --git a/lib/reax/cbkbo.blk b/lib/reax/cbkbo.blk deleted file mode 100644 index 4c7a552c73..0000000000 --- a/lib/reax/cbkbo.blk +++ /dev/null @@ -1,3 +0,0 @@ - common - $/cbkbo/ bo(nbomax) - diff --git a/lib/reax/cbkboncor.blk b/lib/reax/cbkboncor.blk deleted file mode 100644 index 96d89e3a7e..0000000000 --- a/lib/reax/cbkboncor.blk +++ /dev/null @@ -1,5 +0,0 @@ - common - $/cbkboncor/ dbosindc(nbomax,3,2*mbond+2),dbosidc(nbomax,3,2), - $ bo131(nsort),bo132(nsort),bo133(nsort), - $ ovc(nbotym),v13cor(nbotym) - diff --git a/lib/reax/cbkbopi.blk b/lib/reax/cbkbopi.blk deleted file mode 100644 index c58ba31306..0000000000 --- a/lib/reax/cbkbopi.blk +++ /dev/null @@ -1,3 +0,0 @@ - common - $/cbkbopi/ bopi(nbomax) - diff --git a/lib/reax/cbkbopi2.blk b/lib/reax/cbkbopi2.blk deleted file mode 100644 index f150895b05..0000000000 --- a/lib/reax/cbkbopi2.blk +++ /dev/null @@ -1,3 +0,0 @@ - common - $/cbkbopi2/ bopi2(nbomax) - diff --git a/lib/reax/cbkbosi.blk b/lib/reax/cbkbosi.blk deleted file mode 100644 index 27a73ce884..0000000000 --- a/lib/reax/cbkbosi.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbkbosi/ bosi(nbomax) - - diff --git a/lib/reax/cbkc.blk b/lib/reax/cbkc.blk deleted file mode 100644 index 2a2519eb2e..0000000000 --- a/lib/reax/cbkc.blk +++ /dev/null @@ -1,5 +0,0 @@ - common - $/cbkc/ c(nat,3),cglobal(nattot,3),itag(nat), - $chgglobal(nattot) - - diff --git a/lib/reax/cbkch.blk b/lib/reax/cbkch.blk deleted file mode 100644 index e3199934be..0000000000 --- a/lib/reax/cbkch.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbkch/ ch(nat) - - diff --git a/lib/reax/cbkcha.blk b/lib/reax/cbkcha.blk deleted file mode 100644 index 3bcc218711..0000000000 --- a/lib/reax/cbkcha.blk +++ /dev/null @@ -1,5 +0,0 @@ - common - $/cbkcha/ ech,syscha,chisys - $ vfieldx,vfieldy,vfieldz,nmcharge,ioldchg - - diff --git a/lib/reax/cbkcharmol.blk b/lib/reax/cbkcharmol.blk deleted file mode 100644 index 4ffeaf7d28..0000000000 --- a/lib/reax/cbkcharmol.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbkcharmol/ vmcha(nmolmax), - $ iat1mc(nmolmax),iat2mc(nmolmax) - diff --git a/lib/reax/cbkchb.blk b/lib/reax/cbkchb.blk deleted file mode 100644 index b725afb662..0000000000 --- a/lib/reax/cbkchb.blk +++ /dev/null @@ -1,3 +0,0 @@ - common - $/cbkchb/ chi(nsort),eta(nsort),gam(nsort) - diff --git a/lib/reax/cbkconst.blk b/lib/reax/cbkconst.blk deleted file mode 100644 index e23dbbf20f..0000000000 --- a/lib/reax/cbkconst.blk +++ /dev/null @@ -1,5 +0,0 @@ - - common - $/cbkconst/ dgrrdn,one,half,three,zero,caljou,rgasc,xjouca - $ convmd - diff --git a/lib/reax/cbkcovbon.blk b/lib/reax/cbkcovbon.blk deleted file mode 100644 index b37545c152..0000000000 --- a/lib/reax/cbkcovbon.blk +++ /dev/null @@ -1,7 +0,0 @@ - - - common - $/cbkcovbon/ de2(nbotym),de3(nbotym),psi(nbotym), - $ psp(nbotym), - $ ltripstaball - diff --git a/lib/reax/cbkd.blk b/lib/reax/cbkd.blk deleted file mode 100644 index 4baf7f350e..0000000000 --- a/lib/reax/cbkd.blk +++ /dev/null @@ -1,7 +0,0 @@ - integer Lvirial,Latomvirial - - common - $/cbkd/ d(3,nat),estrain(nat) - - common - $/cbkvirial/ atomvirial(6,nat),virial(6),Lvirial,Latomvirial diff --git a/lib/reax/cbkdbodc.blk b/lib/reax/cbkdbodc.blk deleted file mode 100644 index a3c9722554..0000000000 --- a/lib/reax/cbkdbodc.blk +++ /dev/null @@ -1,3 +0,0 @@ - common - $/cbkdbodc/ dbodc(nbomax,3,2) - diff --git a/lib/reax/cbkdbopi2ndc.blk b/lib/reax/cbkdbopi2ndc.blk deleted file mode 100644 index 94fde9fd07..0000000000 --- a/lib/reax/cbkdbopi2ndc.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - - common - $/cbkdbopi2ndc/ dbopi2ndc(nbomax,3,2*mbond+2) - diff --git a/lib/reax/cbkdbopidc.blk b/lib/reax/cbkdbopidc.blk deleted file mode 100644 index 559c6a77a1..0000000000 --- a/lib/reax/cbkdbopidc.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/dbopidc/ dbopi2dc(nbomax,3,2),dbopidc(nbomax,3,2) - diff --git a/lib/reax/cbkdbopindc.blk b/lib/reax/cbkdbopindc.blk deleted file mode 100644 index 96285f7c86..0000000000 --- a/lib/reax/cbkdbopindc.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - - common - $/dbopindc/ dbopindc(nbomax,3,2*mbond+2) - diff --git a/lib/reax/cbkdcell.blk b/lib/reax/cbkdcell.blk deleted file mode 100644 index c3f22240a6..0000000000 --- a/lib/reax/cbkdcell.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbkdcell/ dcell(3,nat,27) - diff --git a/lib/reax/cbkdhdc.blk b/lib/reax/cbkdhdc.blk deleted file mode 100644 index e5e4638f28..0000000000 --- a/lib/reax/cbkdhdc.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbkdhdc/ dhdc(nvamax,3,3) - diff --git a/lib/reax/cbkdistan.blk b/lib/reax/cbkdistan.blk deleted file mode 100644 index d752173f24..0000000000 --- a/lib/reax/cbkdistan.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbkdistan/ axis(3),aaxh,baxh,caxh,iortho - - diff --git a/lib/reax/cbkdrdc.blk b/lib/reax/cbkdrdc.blk deleted file mode 100644 index 1d5615440e..0000000000 --- a/lib/reax/cbkdrdc.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbkdrdc/ drdc(nbomax,3,2) - diff --git a/lib/reax/cbkefield.blk b/lib/reax/cbkefield.blk deleted file mode 100644 index 7991f4b98e..0000000000 --- a/lib/reax/cbkefield.blk +++ /dev/null @@ -1,4 +0,0 @@ - - common - $/cbkefield/ efix,efiy,efiz,c1 - diff --git a/lib/reax/cbkenergies.blk b/lib/reax/cbkenergies.blk deleted file mode 100644 index e0220e88ef..0000000000 --- a/lib/reax/cbkenergies.blk +++ /dev/null @@ -1,7 +0,0 @@ - - common - $/cbkenergies/ eb,eoop,epen,estrc,deda(3),pressu, - $ efi,elp,emol,ea,eres,et,eradbo, - $ ev,eco,ecoa,ehb,sw,ew,ep,ekin - - diff --git a/lib/reax/cbkeregime.blk b/lib/reax/cbkeregime.blk deleted file mode 100644 index 198862e5f1..0000000000 --- a/lib/reax/cbkeregime.blk +++ /dev/null @@ -1,5 +0,0 @@ - character*5 qetype - common - $/cbkeregime/ qetype(mereg,mezone),nnereg(mereg),nerc, - $ ereg(mereg,mezone),nitec(mereg) - diff --git a/lib/reax/cbkff.blk b/lib/reax/cbkff.blk deleted file mode 100644 index 36ffceea0c..0000000000 --- a/lib/reax/cbkff.blk +++ /dev/null @@ -1,9 +0,0 @@ - character*2 qas - common - $/cbkff/ gamcco(nsort,nsort),vpar(npamax),vovun(nsort), - $ stlp(nsort),aval(nsort),vlp1(nsort), - $ vover(nbotym),valp1(nsort), - $ vka(nvatym),qas(nsort),amas(nsort),e1(nbotym), - $ valf(nsort),de1(nbotym),swb,nvs(nvatym,3),nso,nvaty - - diff --git a/lib/reax/cbkfftorang.blk b/lib/reax/cbkfftorang.blk deleted file mode 100644 index 4154e5565d..0000000000 --- a/lib/reax/cbkfftorang.blk +++ /dev/null @@ -1,8 +0,0 @@ - - - - - common - $/cbkfftorang/ v4(ntotym),vconj(ntotym), - $ v1(ntotym),v2(ntotym),v3(ntotym) - diff --git a/lib/reax/cbkh.blk b/lib/reax/cbkh.blk deleted file mode 100644 index 7be7c5d7b3..0000000000 --- a/lib/reax/cbkh.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbkh/ h(nvamax) - diff --git a/lib/reax/cbkhbond.blk b/lib/reax/cbkhbond.blk deleted file mode 100644 index 7a071ef096..0000000000 --- a/lib/reax/cbkhbond.blk +++ /dev/null @@ -1,5 +0,0 @@ - - common - - $/cbkhbond/ hhb(nhbmax) - diff --git a/lib/reax/cbkia.blk b/lib/reax/cbkia.blk deleted file mode 100644 index f7ada0e8fd..0000000000 --- a/lib/reax/cbkia.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - - common - $/cbkia/ ia(nat,mbond+3),iag(nat,mbond+3) - diff --git a/lib/reax/cbkidbo.blk b/lib/reax/cbkidbo.blk deleted file mode 100644 index cc3fb49331..0000000000 --- a/lib/reax/cbkidbo.blk +++ /dev/null @@ -1,7 +0,0 @@ - - - - common - $/cbkidbo/ idbo(nbomax,2*mbond+2),dbondc(nbomax,3,2*mbond+2), - $ idbo1(nbomax) - diff --git a/lib/reax/cbkimove.blk b/lib/reax/cbkimove.blk deleted file mode 100644 index e65bd01e43..0000000000 --- a/lib/reax/cbkimove.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - common - $/cbkimove/ imove(nattot) - - diff --git a/lib/reax/cbkinit.blk b/lib/reax/cbkinit.blk deleted file mode 100644 index 45ac3396a0..0000000000 --- a/lib/reax/cbkinit.blk +++ /dev/null @@ -1,6 +0,0 @@ - - character*40 qruid - common - $/cbkinit/ tsetor,nzero,none,ntwo,nthree,qruid,systime, - $ ustime,two,pi,avognr,axiss(3),pset,rdndgr - diff --git a/lib/reax/cbklonpar.blk b/lib/reax/cbklonpar.blk deleted file mode 100644 index 016888f286..0000000000 --- a/lib/reax/cbklonpar.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbklonpar/ vlp(nat),dvlpdsbo(nat) - diff --git a/lib/reax/cbkmolec.blk b/lib/reax/cbkmolec.blk deleted file mode 100644 index 847ae44edb..0000000000 --- a/lib/reax/cbkmolec.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - - common - $/cbkmolec/ nmolat2(nmolmax,nat),elmol2(nmolmax) - diff --git a/lib/reax/cbknmolat.blk b/lib/reax/cbknmolat.blk deleted file mode 100644 index a89f0f677c..0000000000 --- a/lib/reax/cbknmolat.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - - common - $/cbknmolat/ nmolat(nmolmax,nat) - diff --git a/lib/reax/cbknonbon.blk b/lib/reax/cbknonbon.blk deleted file mode 100644 index c0ec0feaa1..0000000000 --- a/lib/reax/cbknonbon.blk +++ /dev/null @@ -1,6 +0,0 @@ - - - common - $/cbknonbon/ gamwco(nsort,nsort),sw1,p3co(nsort,nsort), - $ p2co(nsort,nsort),p1co(nsort,nsort) - diff --git a/lib/reax/cbknubon2.blk b/lib/reax/cbknubon2.blk deleted file mode 100644 index ecc7eafd47..0000000000 --- a/lib/reax/cbknubon2.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbknubon2/ nubon1(nat,mbond), nubon2(nat,mbond) - diff --git a/lib/reax/cbknvlbo.blk b/lib/reax/cbknvlbo.blk deleted file mode 100644 index b9a3791811..0000000000 --- a/lib/reax/cbknvlbo.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbknvlbo/ nvlbo(nneighmax*nat) - - diff --git a/lib/reax/cbknvlown.blk b/lib/reax/cbknvlown.blk deleted file mode 100644 index d51ce5531f..0000000000 --- a/lib/reax/cbknvlown.blk +++ /dev/null @@ -1,2 +0,0 @@ - common - $/cbknvlown/ nvlown(nneighmax*nat) diff --git a/lib/reax/cbkpairs.blk b/lib/reax/cbkpairs.blk deleted file mode 100644 index 028b0f2fac..0000000000 --- a/lib/reax/cbkpairs.blk +++ /dev/null @@ -1,4 +0,0 @@ - common - $/cbkpairs/ nvl1(nneighmax*nat),nvl2(nneighmax*nat),nvpair,nvlself - - diff --git a/lib/reax/cbkpres.blk b/lib/reax/cbkpres.blk deleted file mode 100644 index bf14b380c4..0000000000 --- a/lib/reax/cbkpres.blk +++ /dev/null @@ -1,4 +0,0 @@ - - common - $/cbkpres/ presx,presy,presz - diff --git a/lib/reax/cbkqa.blk b/lib/reax/cbkqa.blk deleted file mode 100644 index 63e88e7411..0000000000 --- a/lib/reax/cbkqa.blk +++ /dev/null @@ -1,5 +0,0 @@ - character*2 qa - common - $/cbkqa/ qa(nattot) - - diff --git a/lib/reax/cbkrbo.blk b/lib/reax/cbkrbo.blk deleted file mode 100644 index e9b99f008a..0000000000 --- a/lib/reax/cbkrbo.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbkrbo/ rbo(nbomax),ibsym(nbomax),ib(nbomax,3) - diff --git a/lib/reax/cbkrestr.blk b/lib/reax/cbkrestr.blk deleted file mode 100644 index 15169677e4..0000000000 --- a/lib/reax/cbkrestr.blk +++ /dev/null @@ -1,12 +0,0 @@ - common - $/cbkrestr/ vkrv(mrestra),vrstra(mrestra),vkr2v(mrestra), - $ dismacen(mrestra),rmstra1(mrestra), - $ rrstra(mrestra),vkrst2(mrestra), - $ rmstra2(mrestra),rmstrax(mrestra),rmstray(mrestra), - $ rmstraz(mrestra),cmo(nat,3),vmo1(nat),trstra(mrestra), - $ vkrt(mrestra),vkr2t(mrestra),vkrstr(mrestra), - $ irstrav(mrestra,3),irstra(mrestra,2),itend(mrestra), - $ irstram(mrestra,5),itstart(mrestra),irstrat(mrestra,4), - $ imorph - - diff --git a/lib/reax/cbksrtbon1.blk b/lib/reax/cbksrtbon1.blk deleted file mode 100644 index 9a4d425e18..0000000000 --- a/lib/reax/cbksrtbon1.blk +++ /dev/null @@ -1,13 +0,0 @@ - character*60 qmol - common - $/cbksrtbon1/ dbodr(nbomax),dbopidr(nbomax), - $ dbopi2dr(nbomax), - $ rob1(nsort,nsort),rob2(nsort,nsort), - $ rob3(nsort,nsort), - $ rat(nsort),rapt(nsort),vnq(nsort),bom(nbotym), - $ pdp(nbotym),ptp(nbotym),pdo(nbotym), - $ popi(nbotym),bop1(nbotym),bop2(nbotym),cutoff, - $ nbs(nbotym,2), - $ nsbma2,nsbmax,nboty2,nbonall,qfile(nmolset),qmol - - diff --git a/lib/reax/cbksrthb.blk b/lib/reax/cbksrthb.blk deleted file mode 100644 index ad035f6c05..0000000000 --- a/lib/reax/cbksrthb.blk +++ /dev/null @@ -1,10 +0,0 @@ - - - common - $/cbksrthb/ vhb1(nhbtym),vhb2(nhbtym),rhb(nhbtym), - $ dehb(nhbtym),ihb(nhbmax,8),nhb, - $ nphb(nsort),nhbs(nhbtym,3),nhbty,hbcut, - $ lhbnew - - - diff --git a/lib/reax/cbktorang.blk b/lib/reax/cbktorang.blk deleted file mode 100644 index 3e8c94fd5f..0000000000 --- a/lib/reax/cbktorang.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbktorang/ dargtdc(ntomax,3,4),thg(ntomax) - diff --git a/lib/reax/cbktorsion.blk b/lib/reax/cbktorsion.blk deleted file mode 100644 index 30f984b7df..0000000000 --- a/lib/reax/cbktorsion.blk +++ /dev/null @@ -1,7 +0,0 @@ - - - - common - $/cbktorsion/ nts(ntotym,4),ntoty,ntor,it(ntomax,11) - - diff --git a/lib/reax/cbktregime.blk b/lib/reax/cbktregime.blk deleted file mode 100644 index 06df64e192..0000000000 --- a/lib/reax/cbktregime.blk +++ /dev/null @@ -1,8 +0,0 @@ - common - $/cbktregime/ dttreg(mtreg,mtzone),tdamptreg(mtreg,mtzone), - $ ia1treg(mtreg,mtzone),ia2treg(mtreg,mtzone), - $ tsettreg(mtreg,mtzone),nntreg(mtreg),ittc(mtreg), - $ nittc(mtreg),ifieldz,ifieldx,ifieldy, - $ nrestra,nrestram,nrestrat,nrestrav,ntrc - - diff --git a/lib/reax/cbkvalence.blk b/lib/reax/cbkvalence.blk deleted file mode 100644 index 3e7bee9b60..0000000000 --- a/lib/reax/cbkvalence.blk +++ /dev/null @@ -1,5 +0,0 @@ - - - common - $/cbkvalence/ nval,iv(nvamax,6) - diff --git a/lib/reax/cbkvregime.blk b/lib/reax/cbkvregime.blk deleted file mode 100644 index ed2f5a45e6..0000000000 --- a/lib/reax/cbkvregime.blk +++ /dev/null @@ -1,7 +0,0 @@ - character*5 qvtype - common - $/cbkvregime/ ivsca(mvreg,mvzone),dvvreg(mvreg,mvzone), - $ nnvreg(mvreg),invrc,nitvc(mvreg), - $ qvtype(mvreg,mvzone) - - diff --git a/lib/reax/cellcoord.blk b/lib/reax/cellcoord.blk deleted file mode 100644 index 3cbee22656..0000000000 --- a/lib/reax/cellcoord.blk +++ /dev/null @@ -1,4 +0,0 @@ - - common - $/cellcoord/ tm11,tm21,tm31,tm22,tm32,tm33,angle(3),angles(3) - diff --git a/lib/reax/control.blk b/lib/reax/control.blk deleted file mode 100644 index 4e84f85b9e..0000000000 --- a/lib/reax/control.blk +++ /dev/null @@ -1,12 +0,0 @@ - common - $/control/ vrange,cutof2,cutof3,vlbora,tstep,range,taut,volcha, - $ axis1,axis2,axis3,taup, - $ icpres,nmethod,noutpt,inpt,napp,ianaly,ncha2, - $ nrand,ntscale,itstep,ndebug,icentr,itrout, - $ nchaudixmolo,itrans,nsav, - $ nrep1,ncontrol,nhop2,nsav3,ngeofor,ifreq, - $ nprevrun,maxstp,nvel,nsurp,ncons, - $ ncha,icell,imolde,nchaud -********************************************************************************* - - diff --git a/lib/reax/opt.blk b/lib/reax/opt.blk deleted file mode 100644 index c72df23d5c..0000000000 --- a/lib/reax/opt.blk +++ /dev/null @@ -1,23 +0,0 @@ - parameter (maxdat=5000) - parameter (maxmdat=2500) - parameter (maxkop=2500) - character*80 qff - character*60 qmdat - character*100 qdatid - character*2 qas2 - common - $/opt/ fpar(7,nvatym,40),datopt(maxdat),caldat(maxdat), - $ compdat(maxdat),weightdat(maxdat), - $ devi(maxdat),vkop(maxkop),devkop(maxkop),sdy(3), - $ valpar,valnew,change,vchange, - $ molin(maxmdat,nsort), - $ iboo(nbotym,2),idmo(nodmtym,2),ivao(nvatym,5), - $ itoo(ntotym,7),ihbo(nhbtym,5),iheada(maxmdat), - $ ndatm(maxmdat),iheada2(maxmdat),ichn(3), - $ ikop1(maxkop),ikop2(maxkop),idat(maxdat),mu1(maxkop), - $ mu2(maxkop), - $ ndata,imam,iopt,iheatf,nkop,iagain, - $ qdatid(maxdat),qmdat(maxmdat),qff(250),qas2(nsort) -*********************************************************************** - - diff --git a/lib/reax/reax_charges.F b/lib/reax/reax_charges.F deleted file mode 100644 index 5815501a29..0000000000 --- a/lib/reax/reax_charges.F +++ /dev/null @@ -1,85 +0,0 @@ -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -************************************************************************ - - subroutine taper(r,r2) - -************************************************************************ -#include "cbka.blk" -#include "cbkconst.blk" -#include "cbkenergies.blk" -#include "cbkinit.blk" -#include "cbknonbon.blk" -************************************************************************ -* * -* Taper function for Coulomb interaction * -* * -************************************************************************ - r3=r2*r - SW=SWC7*R3*R3*R+SWC6*R3*R3+SWC5*R3*R2+SWC4*R2*R2+SWC3*R3+SWC2*R2+ - $SWC1*R+SWC0 - SW1=7.0D0*SWC7*R3*R3+6.0D0*SWC6*R3*R2+5.0D0*SWC5*R2*R2+ - $4.0D0*SWC4*R3+THREE*SWC3*R2+TWO*SWC2*R+SWC1 - return - end -************************************************************************ -************************************************************************ - - subroutine tap7th - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkff.blk" -#include "cbkh.blk" -#include "control.blk" - -************************************************************************ -* * -* 7th order taper function setup * -* * -************************************************************************ -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In tap7th' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - D1=SWB-SWA - D7=D1**7.0D0 - SWA2=SWA*SWA - SWA3=SWA2*SWA - SWB2=SWB*SWB - SWB3=SWB2*SWB - -************************************************************************ -* 7th order taper function * -************************************************************************ - - SWC7= 20.0D0/D7 - SWC6= -70.0D0*(SWA+SWB)/D7 - SWC5= 84.0D0*(SWA2+3.0D0*SWA*SWB+SWB2)/D7 - SWC4= -35.0D0*(SWA3+9.0D0*SWA2*SWB+9.0D0*SWA*SWB2+SWB3)/D7 - SWC3= 140.0D0*(SWA3*SWB+3.0D0*SWA2*SWB2+SWA*SWB3)/D7 - SWC2=-210.0D0*(SWA3*SWB2+SWA2*SWB3)/D7 - SWC1= 140.0D0*SWA3*SWB3/D7 - SWC0=(-35.0D0*SWA3*SWB2*SWB2+21.0D0*SWA2*SWB3*SWB2- - $7.0D0*SWA*SWB3*SWB3+SWB3*SWB3*SWB)/D7 - - return - END diff --git a/lib/reax/reax_connect.F b/lib/reax/reax_connect.F deleted file mode 100644 index e77875124f..0000000000 --- a/lib/reax/reax_connect.F +++ /dev/null @@ -1,1547 +0,0 @@ -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -********************************************************************** - - subroutine srtatom - -********************************************************************** -#include "cbka.blk" -#include "cbkatomcoord.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkqa.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" -********************************************************************** -* * -* Determine atom types in system * -* * -********************************************************************** -* Requires the following variables -* ndebug - opt.blk; determines whether to debug or not; everywhere -* xmasmd - cbka.blk; some sort of atmoic mass?; srtatom, reac.f -* molin - opt.blk; keeps info on?; srtatom -* nso - cbka.blk; number of atoms?; srtatom, inout.f -* nprob - cbka.blk; does?; connect.f, inout.f, reac.f -* nasort - cbka.blk; a sorting array; srtatom -* ia - cbka.blk; atom numbers?; poten.f, inout.f, connect.f, charges.f -* iag - cbka.blk; ; connect.f, inout.f, poten.f, reac.f -* xmasat - cbka.blk; does?; srtatom, reac.f -* amas - cbka.blk; ? ; srtatom, ffinpt, molanal, ovcor -* qa - cbka.blk; some sort of error statement variable?; srtatom, srtbon1, inout.f, radbo -* -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In srtatom' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - xmasmd=0.0 - do i1=1,nso - molin(nprob,i1)=0 - nasort(i1)=0 - end do - do i1=1,na - ia(i1,1)=0 - iag(i1,1)=0 - do i2=1,nso - if (qa(i1).eq.qas(i2)) then - ia(i1,1)=i2 - iag(i1,1)=i2 - molin(nprob,i2)=molin(nprob,i2)+1 - xmasat(i1)=amas(i2) - xmasmd=xmasmd+amas(i2) - nasort(i2)=nasort(i2)+1 - end if - end do - if (ia(i1,1).eq.0) then - write (*,*)'Unknown atom type: ',qa(i1) - stop 'Unknown atom type' - end if - end do - - return - end -********************************************************************** -********************************************************************** - - subroutine molec - -********************************************************************** -#include "cbka.blk" -#include "cbkdcell.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkmolec.blk" -#include "cbknmolat.blk" -#include "control.blk" -#include "small.blk" - dimension nmolo2(nat),iseen(nmolmax),isee2(nmolmax) -********************************************************************** -* * -* Determine changes in molecules * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In molec' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - npreac=0 - - do i1=1,nmolo - natmol=0 - do i2=1,na - if (ia(i2,3+mbond).eq.i1) then - natmol=natmol+1 - nmolat(i1,natmol+1)=i2 - end if - end do - nmolat(i1,1)=natmol - end do - - if (nmolo5.lt.nmolo5o) nradcount=0 !reset reaction counter - do i1=1,nmolo5 - natmol=0 - do i2=1,na - if (iag(i2,3+mbond).eq.i1) then - natmol=natmol+1 - nmolat2(i1,natmol+1)=i2 - end if - end do - nmolat2(i1,1)=natmol - end do - nmolo5o=nmolo5 - - do i1=nmolo+1,nmoloold - do i2=1,nmolat(i1,1) - nmolat(i1,1+i2)=0 - end do - nmolat(i1,1)=0 - end do - - do i1=1,nmolo - elmol(i1)=0.0 - do i2=1,nmolat(i1,1) - ihu=nmolat(i1,i2+1) - ity=ia(ihu,1) - elmol(i1)=elmol(i1)+stlp(ity) - end do - end do - - do i1=1,nmolo5 - elmol2(i1)=0.0 - do i2=1,nmolat2(i1,1) - ihu=nmolat2(i1,i2+1) - ity=iag(ihu,1) - elmol2(i1)=elmol2(i1)+stlp(ity) - end do - end do - - return - end -********************************************************************** -********************************************************************** - - subroutine dista2 (n1,n2,dista,dx,dy,dz) - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -********************************************************************** -* * -* Determine interatomic distances * -* * -********************************************************************** -c$$$* if (ndebug.eq.1) then -c$$$C* open (65,file='fort.65',status='unknown',access='append') -c$$$* write (65,*) 'In dista2' -c$$$* call timer(65) -c$$$* close (65) -c$$$* end if - - dx=c(n1,1)-c(n2,1) - dy=c(n1,2)-c(n2,2) - dz=c(n1,3)-c(n2,3) - dista=sqrt(dx*dx+dy*dy+dz*dz) - - return - end -********************************************************************** -********************************************************************** - - subroutine srtbon1(lprune,lhb,hbcut_in,lhbnew_in,ltripstaball_in) - -********************************************************************** -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkbo.blk" -#include "cbkbosi.blk" -#include "cbkbopi.blk" -#include "cbkbopi2.blk" -#include "cbkc.blk" -#include "cbkch.blk" -#include "cbkconst.blk" -#include "cbkdbopidc.blk" -#include "cbkdrdc.blk" -#include "cbkia.blk" -#include "cbknubon2.blk" -#include "cbknvlbo.blk" -#include "cbkpairs.blk" -#include "cbknvlown.blk" -#include "cbkqa.blk" -#include "cbkrbo.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" -#include "cbkdbodc.blk" -#include "cbksrtbon1.blk" -#include "cbkff.blk" -#include "cbksrthb.blk" -#include "cbkcovbon.blk" - logical found - integer nboncol(nboallmax) - integer iball(nboallmax,3) - -********************************************************************** -* * -* Determine connections within the molecule * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In srtbon1' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - -c Transfer hbcut, lhbnew, and ltripstaball from C++ calling function - hbcut = hbcut_in - lhbnew = lhbnew_in - ltripstaball = ltripstaball_in - - do i1=1,na - abo(i1)=0.0d0 - end do - nbonall=0 - nbon2=0 - nsbmax=0 - nsbma2=0 - - if (imolde.eq.0) then - - nmolo=0 - nmolo5=0 - end if - if (imolde.eq.0) then - do i1=1,na - do i2=2,mbond+3 - ia(i1,i2)=0 - iag(i1,i2)=0 - end do - end do - - else - - do i1=1,na - do i2=2,mbond+2 - ia(i1,i2)=0 - iag(i1,i2)=0 - end do - end do - - end if - - do i1=1,na - do i2=1,mbond - nubon1(i1,i2)=0 - nubon2(i1,i2)=0 - end do - end do - -* First detect all bonds and create preliminary list - - do 11 ivl=1,nvpair - if (nvlbo(ivl).eq.0) goto 11 !not in bond order range - i1=nvl1(ivl) - i2=nvl2(ivl) - call dista2(i1,i2,dis,dxm,dym,dzm) - ih1=ia(i1,1) - ih2=ia(i2,1) - disdx=dxm/dis - disdy=dym/dis - disdz=dzm/dis - itype=0 - if (ih1.gt.ih2) then - ih1=ia(i2,1) - ih2=ia(i1,1) - end if - do i3=1,nboty2 - if (ih1.eq.nbs(i3,1).and.ih2.eq.nbs(i3,2)) itype=i3 - end do - if (itype.eq.0.and.rat(ih1).gt.zero.and.rat(ih2).gt.zero) then -c$$$ call mdsav(1,qfile(nprob)) - write (*,*)qa(i1),'-',qa(i2),'Fatal: Unknown bond in molecule' - stop - end if - - rhulp=dis/rob1(ih1,ih2) - -********************************************************************** -* * -* Determine bond orders * -* * -********************************************************************** - rh2=zero - rh2p=zero - rh2pp=zero - ehulp=zero - ehulpp=zero - ehulppp=zero - if (rapt(ih1).gt.zero.and.rapt(ih2).gt.zero) then - rhulp2=dis/rob2(ih1,ih2) - rh2p=rhulp2**ptp(itype) - ehulpp=exp(pdp(itype)*rh2p) - end if - if (vnq(ih1).gt.zero.and.vnq(ih2).gt.zero) then - rhulp3=dis/rob3(ih1,ih2) - rh2pp=rhulp3**popi(itype) - ehulppp=exp(pdo(itype)*rh2pp) - end if - - if (rat(ih1).gt.zero.and.rat(ih2).gt.zero) then - rh2=rhulp**bop2(itype) - ehulp=(1.0+cutoff)*exp(bop1(itype)*rh2) - end if - - bor=ehulp+ehulpp+ehulppp - - j1=i1 - j2=i2 - -********************************************************************** -* * -* Determine bond orders * -* * -********************************************************************** - if (bor.gt.cutoff) then - nbonall=nbonall+1 - if (nbonall.gt.nboallmax) then - write (6,*)'nbonall = ',nbonall, - $ ' reax_defs.h::NBOALLMAXDEF = ',NBOALLMAXDEF, - $ ' after',ivl, ' of ',nvpair,' pairs completed.' - stop 'Too many bonds; maybe wrong cell parameters.' - end if - iball(nbonall,1)=itype - iball(nbonall,2)=j1 - iball(nbonall,3)=j2 - - ia(i1,2)=ia(i1,2)+1 - if (ia(i1,2).gt.mbond) then - write (6,*)'ia(i1,2) = ',ia(i1,2), - $ ' reax_defs.h::MBONDDEF = ',MBONDDEF, - $ ' after',ivl, ' of ',nvpair,' pairs completed.' - stop 'Too many bonds on atom. Increase MBONDDEF' - end if - - if (i1.ne.i2) then - ia(i2,2)=ia(i2,2)+1 - if (ia(i2,2).gt.mbond) then - write (6,*)'ia(i1,2) = ',ia(i1,2), - $ ' reax_defs.h::MBONDDEF = ',MBONDDEF, - $ ' after',ivl, ' of ',nvpair,' pairs completed.' - stop 'Too many bonds on atom. Increase MBONDDEF' - end if - endif - - ia(i1,ia(i1,2)+2)=i2 - ia(i2,ia(i2,2)+2)=i1 - if (abs(de1(iball(nbonall,1))).gt.-0.01) then - nubon2(i1,ia(i1,2))=nbonall - nubon2(i2,ia(i2,2))=nbonall - else - nbonall=nbonall-1 !Inorganics - end if - end if - 11 continue - -********************************************************************** -* * -* lprune controls level of bond-pruning performed to increase * -* performance. For correct results, it should be set to 4. * -* However, making it smaller can speed up * -* force calculation and may not have a big effect on forces. * -* Setting it to 0 turns off pruning, useful for debugging. * -* * -********************************************************************** -********************************************************************* -* * -* lhb controls whether or not to unprune ghost bonds that * -* may possibly form ghost hydrogen bonds. * -* Setting it to 1 causes unpruning, and so is the safe option. * -* If lprune = 0, then pruning is not used, results are exact * -* and lhb has no effect. * -* * -********************************************************************** - if (lprune .gt. 0) then -********************************************************************** -* * -* Eliminate bonds that are not in 1-6 interaction * -* with local atom, or closer. * -* Need additional sweep to catch possible hydrogen bonds * -* * -********************************************************************** - - ntmp0 = 0 - ntmp1 = 0 - ntmp2 = 0 - ntmp3 = 0 - ntmp4 = 0 - ntmp5 = 0 - ntmp6 = 0 - ntmphb = 0 - -* color 1 are bonds with two local atoms -* color 2 are bonds with one local atom -* color 3 are bonds adjacent to bond with one local atom - - do i1 = 1,nbonall - if (iball(i1,2).le.na_local) then - if (iball(i1,3).le.na_local) then - nboncol(i1) = 1 - ntmp1 = ntmp1+1 - else - nboncol(i1) = 2 - ntmp2 = ntmp2+1 - endif - else if (iball(i1,3).le.na_local) then - nboncol(i1) = 2 - ntmp2 = ntmp2+1 - else - nboncol(i1) = 0 - endif - end do - - if (lprune .ge. 3) then - do i1 = 1,nbonall - if (nboncol(i1).eq.2) then - if (iball(i1,2).le.na_local) then - i3=iball(i1,3) - else - i3=iball(i1,2) - endif - - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.0) then - nboncol(i5)=3 - ntmp3 = ntmp3+1 - endif - end do - endif - end do - endif -* color 4 bonds are part of a 1-4 interaction with local atom - - if (lprune .ge. 4) then - do i1 = 1,nbonall - if (nboncol(i1).eq.3) then -* One end definitely has a bond of color 2 -* Find it and color bonds on other end 4 - i3=iball(i1,2) - i3b=0 - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.2) then - i3b=iball(i1,3) - endif - end do - - if (i3b.eq.0) then - i3=iball(i1,3) - i3b=0 - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.2) then - i3b=iball(i1,2) - endif - end do - endif - - if (i3b.eq.0) then - stop 'Could not find color 2 from color 3 bond' - endif - - do i4 = 1,ia(i3b,2) - i5=nubon2(i3b,i4) - if (nboncol(i5).eq.0) then - nboncol(i5)=4 - ntmp4 = ntmp4+1 - endif - end do - - endif - end do - endif - -* color 5 bonds are part of a 1-5 interaction with local atom - - if (lprune .ge. 5) then - do i1 = 1,nbonall - if (nboncol(i1).eq.4) then -* One end definitely has a bond of color 3 -* Find it and color bonds on other end 5 - i3=iball(i1,2) - i3b=0 - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.3) then - i3b=iball(i1,3) - endif - end do - - if (i3b.eq.0) then - i3=iball(i1,3) - i3b=0 - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.3) then - i3b=iball(i1,2) - endif - end do - endif - - if (i3b.eq.0) then - stop 'Could not find color 3 from color 4 bond' - endif - - do i4 = 1,ia(i3b,2) - i5=nubon2(i3b,i4) - if (nboncol(i5).eq.0) then - nboncol(i5)=5 - ntmp5 = ntmp5+1 - endif - end do - - endif - end do - endif - -* color 6 bonds are part of a 1-6 interaction with local atom - - if (lprune .ge. 6) then - do i1 = 1,nbonall - if (nboncol(i1).eq.5) then -* One end definitely has a bond of color 4 -* Find it and color bonds on other end 6 - i3=iball(i1,2) - i3b=0 - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.4) then - i3b=iball(i1,3) - endif - end do - - if (i3b.eq.0) then - i3=iball(i1,3) - i3b=0 - do i4 = 1,ia(i3,2) - i5=nubon2(i3,i4) - if (nboncol(i5).eq.4) then - i3b=iball(i1,2) - endif - end do - endif - - if (i3b.eq.0) then - stop 'Could not find color 4 from color 5 bond' - endif - - do i4 = 1,ia(i3b,2) - i5=nubon2(i3b,i4) - if (nboncol(i5).eq.0) then - nboncol(i5)=6 - ntmp6 = ntmp6+1 - endif - end do - - endif - end do - endif - -* Catch all the possible hydrogen bonds -* This section replicates the logic used in srthb() - if (lhb .eq. 1) then -c Outer loop must be Verlet list, because ia() does not store Verlet entries, -c but it does store bond entries in nubon2() - do ivl=1,nvpair !Use Verlet-list to find donor-acceptor pairs - - j1=nvl1(ivl) - j2=nvl2(ivl) - ihhb1=nphb(ia(j1,1)) - ihhb2=nphb(ia(j2,1)) - - if (ihhb1.gt.ihhb2) then !Make j1 donor(H) atom and j2 acceptor(O) atom - j2=nvl1(ivl) - j1=nvl2(ivl) - ihhb1=nphb(ia(j1,1)) - ihhb2=nphb(ia(j2,1)) - end if - -* Only need to compute bonds where j1 is local - if (j1 .le. na_local) then - - if (ihhb1.eq.1.and.ihhb2.eq.2) then - call dista2(j1,j2,dishb,dxm,dym,dzm) - if (dishb.lt.hbcut) then - do i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom - if (nboncol(nubon2(j1,i23)).eq.0) then - j3=ia(j1,2+i23) - if (nphb(ia(j3,1)).eq.2.and.j3.ne.j2) then - nboncol(nubon2(j1,i23))=-1 - ntmphb = ntmphb+1 - endif - endif - end do - end if - end if - end if - end do - end if - -* Compact the list, removing all uncolored bonds - - nbon = 0 - do i1 = 1,nbonall - if (nboncol(i1).eq.0) then - ntmp0=ntmp0+1 - else - nbon = nbon+1 - - if (nbon.gt.nbomax) then - write (6,*)nbon,nbomax - write (6,*)'nbon = ',nbon,' reax_defs.h::NBOMAXDEF = ', - $ NBOMAXDEF,' after',i1, ' of ',nbonall, - $ ' initial bonds completed.' - stop 'Too many pruned bonds; increase NBOMAXDEF' - end if - - - ib(nbon,1) = iball(i1,1) - ib(nbon,2) = iball(i1,2) - ib(nbon,3) = iball(i1,3) - endif - end do - -********************************************************************** -* * -* Do not perform ghost-bond pruning * -* * -********************************************************************** - - else - - nbon = 0 - do i1 = 1,nbonall - nbon = nbon+1 - - if (nbon.gt.nbomax) then - write (6,*)nbon,nbomax - write (6,*)'nbon = ',nbon,' reax_defs.h::NBOMAXDEF = ', - $ NBOMAXDEF,' after',i1, ' of ',nbonall, - $ ' initial bonds completed.' - stop 'Too many pruned bonds; increase NBOMAXDEF' - end if - - ib(nbon,1) = iball(i1,1) - ib(nbon,2) = iball(i1,2) - ib(nbon,3) = iball(i1,3) - end do - - endif - - do i1=1,na - do i2=2,mbond+2 - ia(i1,i2)=0 - iag(i1,i2)=0 - end do - end do - -* Generate full set of bond data structures - - do 10 i0 = 1,nbon - i1 = ib(i0,2) - i2 = ib(i0,3) - call dista2(i1,i2,dis,dxm,dym,dzm) -* do 10 i1=1,na-1 -* do 10 i2=i1+1,na -* call dista2(i1,i2,dis,dxm,dym,dzm) - ih1=ia(i1,1) - ih2=ia(i2,1) -* if (dis.gt.5.0*rob) goto 10 - disdx=dxm/dis - disdy=dym/dis - disdz=dzm/dis - itype=0 - if (ih1.gt.ih2) then - ih1=ia(i2,1) - ih2=ia(i1,1) - end if - do i3=1,nboty2 - if (ih1.eq.nbs(i3,1).and.ih2.eq.nbs(i3,2)) itype=i3 - end do - if (itype.eq.0.and.rat(ih1).gt.zero.and.rat(ih2).gt.zero) then -c$$$ call mdsav(1,qfile(nprob)) - write (*,*)qa(i1),'-',qa(i2),'Fatal: Unknown bond in molecule' - stop - end if - - rhulp=dis/rob1(ih1,ih2) - -********************************************************************** -* * -* Determine bond orders * -* * -********************************************************************** - rh2=zero - rh2p=zero - rh2pp=zero - ehulp=zero - ehulpp=zero - ehulppp=zero - if (rapt(ih1).gt.zero.and.rapt(ih2).gt.zero) then - rhulp2=dis/rob2(ih1,ih2) - rh2p=rhulp2**ptp(itype) - ehulpp=exp(pdp(itype)*rh2p) - end if - if (vnq(ih1).gt.zero.and.vnq(ih2).gt.zero) then - rhulp3=dis/rob3(ih1,ih2) - rh2pp=rhulp3**popi(itype) - ehulppp=exp(pdo(itype)*rh2pp) - end if - - if (rat(ih1).gt.zero.and.rat(ih2).gt.zero) then - rh2=rhulp**bop2(itype) - ehulp=(1.0+cutoff)*exp(bop1(itype)*rh2) - end if - - bor=ehulp+ehulpp+ehulppp - borsi=ehulp - borpi=ehulpp - borpi2=ehulppp - dbordrob=bop2(itype)*bop1(itype)*rh2*(1.0/dis)*ehulp+ - $ptp(itype)*pdp(itype)*rh2p*(1.0/dis)*ehulpp+ - $popi(itype)*pdo(itype)*rh2pp*(1.0/dis)*ehulppp - dborsidrob=bop2(itype)*bop1(itype)*rh2*(1.0/dis)*ehulp - dborpidrob=ptp(itype)*pdp(itype)*rh2p*(1.0/dis)*ehulpp - dborpi2drob=popi(itype)*pdo(itype)*rh2pp*(1.0/dis)*ehulppp - - nbon2=nbon2+1 - j1=i1 - j2=i2 - -********************************************************************** -* * -* Determine bond orders * -* * -********************************************************************** - ib(i0,1)=itype - ib(i0,2)=j1 - ib(i0,3)=j2 - ibsym(i0)=ivl - drdc(i0,1,1)=disdx - drdc(i0,2,1)=disdy - drdc(i0,3,1)=disdz - drdc(i0,1,2)=-disdx - drdc(i0,2,2)=-disdy - drdc(i0,3,2)=-disdz - abo(i1)=abo(i1)+bor-cutoff - if (i1.ne.i2) abo(i2)=abo(i2)+bor-cutoff - bo(i0)=bor-cutoff - bos(i0)=bor-cutoff - bosi(i0)=borsi-cutoff - bopi(i0)=borpi - bopi2(i0)=borpi2 - rbo(i0)=dis - dbodr(i0)=dbordrob -* dbosidr(i0)=dborsidrob - dbopidr(i0)=dborpidrob - dbopi2dr(i0)=dborpi2drob - dbodc(i0,1,1)=dbodr(i0)*drdc(i0,1,1) - dbodc(i0,2,1)=dbodr(i0)*drdc(i0,2,1) - dbodc(i0,3,1)=dbodr(i0)*drdc(i0,3,1) - dbodc(i0,1,2)=dbodr(i0)*drdc(i0,1,2) - dbodc(i0,2,2)=dbodr(i0)*drdc(i0,2,2) - dbodc(i0,3,2)=dbodr(i0)*drdc(i0,3,2) -* dbosidc(i0,1,1)=dbosidr(i0)*drdc(i0,1,1) -* dbosidc(i0,2,1)=dbosidr(i0)*drdc(i0,2,1) -* dbosidc(i0,3,1)=dbosidr(i0)*drdc(i0,3,1) -* dbosidc(i0,1,2)=dbosidr(i0)*drdc(i0,1,2) -* dbosidc(i0,2,2)=dbosidr(i0)*drdc(i0,2,2) -* dbosidc(i0,3,2)=dbosidr(i0)*drdc(i0,3,2) - dbopidc(i0,1,1)=dbopidr(i0)*drdc(i0,1,1) - dbopidc(i0,2,1)=dbopidr(i0)*drdc(i0,2,1) - dbopidc(i0,3,1)=dbopidr(i0)*drdc(i0,3,1) - dbopidc(i0,1,2)=dbopidr(i0)*drdc(i0,1,2) - dbopidc(i0,2,2)=dbopidr(i0)*drdc(i0,2,2) - dbopidc(i0,3,2)=dbopidr(i0)*drdc(i0,3,2) - dbopi2dc(i0,1,1)=dbopi2dr(i0)*drdc(i0,1,1) - dbopi2dc(i0,2,1)=dbopi2dr(i0)*drdc(i0,2,1) - dbopi2dc(i0,3,1)=dbopi2dr(i0)*drdc(i0,3,1) - dbopi2dc(i0,1,2)=dbopi2dr(i0)*drdc(i0,1,2) - dbopi2dc(i0,2,2)=dbopi2dr(i0)*drdc(i0,2,2) - dbopi2dc(i0,3,2)=dbopi2dr(i0)*drdc(i0,3,2) - ia(i1,2)=ia(i1,2)+1 - if (i1.ne.i2) ia(i2,2)=ia(i2,2)+1 - ia(i1,ia(i1,2)+2)=i2 - ia(i2,ia(i2,2)+2)=i1 - if (ia(i1,2).gt.nsbma2) nsbma2=ia(i1,2) - if (ia(i2,2).gt.nsbma2) nsbma2=ia(i2,2) - if (bor.gt.cutof3) then - iag(i1,2)=iag(i1,2)+1 - iag(i2,2)=iag(i2,2)+1 - iag(i1,iag(i1,2)+2)=i2 - iag(i2,iag(i2,2)+2)=i1 - nubon1(i1,iag(i1,2))=i0 - nubon1(i2,iag(i2,2))=i0 - if (iag(i1,2).gt.nsbmax) nsbmax=iag(i1,2) - if (iag(i2,2).gt.nsbmax) nsbmax=iag(i2,2) - end if - nubon2(i1,ia(i1,2))=i0 - nubon2(i2,ia(i2,2))=i0 - - 10 continue - -********************************************************************** -* * -* Sort molecules * -* * -********************************************************************** - imolde = 1 - if (imolde.eq.1) return !fixed molecular definitions - - FOUND=.FALSE. - DO 31 K1=1,NA - IF (IA(K1,3+mbond).EQ.0) FOUND=.TRUE. - 31 IF (IA(K1,3+mbond).GT.NMOLO) NMOLO=IA(K1,3+mbond) - IF (.NOT.FOUND) GOTO 32 -************************************************************************ -* * -* Molecule numbers are assigned. No restrictions are made for the * -* sequence of the numbers in the connection table. * -* * -************************************************************************ - N3=1 - 34 N2=N3 - NMOLO=NMOLO+1 - if (nmolo.gt.nmolmax) then - write (*,*)nmolmax - write (*,*)'Too many molecules in system; increase nmolmax' - write (*,*)'nmolmax = ',nmolmax - write (*,*)'nmolo = ',nmolo - write (*,*)'n2 = ',n2 - stop 'Too many molecules in system' - end if - IA(N2,3+mbond)=NMOLO - 37 FOUND=.FALSE. - DO 36 N1=N2+1,NA - IF (IA(N1,3+mbond).NE.0) GOTO 36 - DO 35 L=1,mbond - IF (IA(N1,l+2).EQ.0) GOTO 36 - IF (IA(IA(N1,l+2),3+mbond).EQ.NMOLO) THEN - FOUND=.TRUE. - IA(N1,3+mbond)=NMOLO - GOTO 36 - ENDIF - 35 CONTINUE - 36 CONTINUE - IF (FOUND) GOTO 37 - DO 33 N3=N2+1,NA - 33 IF (IA(N3,3+mbond).EQ.0) GOTO 34 -************************************************************************ -* * -* The assigned or input molecule numbers are checked for their * -* consistency. * -* * -************************************************************************ - 32 FOUND=.FALSE. - DO 42 N1=1,NA - DO 41 L=1,mbond - IF (IA(N1,L+2).EQ.0) GOTO 42 - IF (IA(IA(N1,L+2),3+mbond).NE.IA(N1,3+mbond)) THEN - FOUND=.TRUE. - ENDIF - 41 CONTINUE - 42 CONTINUE - IF (FOUND) THEN - write (7,1000)NA,qmol - do i1=1,NA - write (7,1100)i1,ia(i1,1),(ia(i1,2+i2),i2=1,nsbmax), - $ia(i1,3+mbond) - end do - write (7,*)tm11,tm22,tm33,angle(1),angle(2),angle(3) - STOP' Mol.nrs. not consistent; maybe wrong cell parameters' - end if -********************************************************************** -* * -* Sort molecules again * -* This sort is on iag, enforces bond order cutoff * -* * -********************************************************************** - FOUND=.FALSE. - DO 61 K1=1,NA - IF (IAG(K1,3+mbond).EQ.0) FOUND=.TRUE. - 61 IF (IAG(K1,3+mbond).GT.NMOLO5) NMOLO5=IAG(K1,3+mbond) - IF (.NOT.FOUND) GOTO 62 -************************************************************************ -* * -* Molecule numbers are assigned. No restrictions are made for the * -* sequence of the numbers in the connection table. * -* * -************************************************************************ - N3=1 - 64 N2=N3 - NMOLO5=NMOLO5+1 - if (nmolo5.gt.nmolmax) stop 'Too many molecules in system' - IAG(N2,3+mbond)=NMOLO5 - 67 FOUND=.FALSE. - DO 66 N1=N2+1,NA - IF (IAG(N1,3+mbond).NE.0) GOTO 66 - DO 65 L=1,mbond - IF (IAG(N1,l+2).EQ.0) GOTO 66 - IF (IAG(IAG(N1,l+2),3+mbond).EQ.NMOLO5) THEN - FOUND=.TRUE. - IAG(N1,3+mbond)=NMOLO5 - GOTO 66 - ENDIF - 65 CONTINUE - 66 CONTINUE - IF (FOUND) GOTO 67 - DO 63 N3=N2+1,NA - 63 IF (IAG(N3,3+mbond).EQ.0) GOTO 64 -************************************************************************ -* * -* The assigned or input molecule numbers are checked for their * -* consistency. * -* * -************************************************************************ - 62 FOUND=.FALSE. - DO 72 N1=1,NA - DO 71 L=1,mbond - IF (IAG(N1,L+2).EQ.0) GOTO 72 - IF (IAG(IAG(N1,L+2),3+mbond).NE.IAG(N1,3+mbond)) THEN - FOUND=.TRUE. - ENDIF - 71 CONTINUE - 72 CONTINUE - IF (FOUND) THEN - write (7,1000)NA,qmol - do i1=1,NA - write (7,1100)i1,iag(i1,1),(iag(i1,2+i2),i2=1,nsbmax), - $iag(i1,3+mbond) - end do - write (7,*)tm11,tm22,tm33,angle(1),angle(2),angle(3) - STOP' Mol.nrs. not consistent; maybe wrong cell parameters' - ENDIF - -********************************************************************** -* * -* Format part * -* * -********************************************************************** - 1000 format (i3,2x,a60) - 1100 format (8i3) - end -********************************************************************** -********************************************************************** - - subroutine srtang - -********************************************************************** -#include "cbka.blk" -#include "cbkbo.blk" -#include "cbknubon2.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkrbo.blk" -#include "cbkvalence.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" - - dimension a(3),b(3),j(3) - dimension ityva(100) - -********************************************************************** -* * -* Find valency angles in molecule * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In srtang' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - nval=0 - if (nvaty.eq.0) return - do iindexatom=1,na - inumbonds=ia(iindexatom,2) - do jindexbond=1,inumbonds-1 - jindexbondlist = nubon2(iindexatom,jindexbond) - if (bo(jindexbondlist).lt.cutof2) goto 51 - k4=ib(jindexbondlist,2) - k5=ib(jindexbondlist,3) - do kindexbond=jindexbond+1,inumbonds - kindexbondlist = nubon2(iindexatom,kindexbond) - iju=0 - if (bo(kindexbondlist).lt.cutof2) goto 50 - if (bo(jindexbondlist)*bo(kindexbondlist).lt.0.001) goto 50 - k7=ib(kindexbondlist,2) - k8=ib(kindexbondlist,3) - -* Exclude angles that have no local atoms. -* Angles with non-local center atom are not needed for angle -* energies, but are needed to construct torsions. - if ( k4 .le. na_local .or. - $ k5 .le. na_local .or. - $ k7 .le. na_local .or. - $ k8 .le. na_local) then - - if (k4.eq.k7.and.k5.eq.k8.and.k4.ne.k8.and.k5.ne.k7) then - nval=nval+1 - iv(nval,2)=k5 - iv(nval,3)=k4 - iv(nval,4)=k8 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - nval=nval+1 - iv(nval,2)=k4 - iv(nval,3)=k5 - iv(nval,4)=k7 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - iju=2 - write(6,*) 'Aaaah!' - end if - if (iju.eq.2) goto 50 - - if (k4.eq.k8.and.k5.eq.k7.and.k4.ne.k7.and.k5.ne.k8) then - nval=nval+1 - iv(nval,2)=k5 - iv(nval,3)=k4 - iv(nval,4)=k7 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - nval=nval+1 - iv(nval,2)=k4 - iv(nval,3)=k5 - iv(nval,4)=k8 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - iju=2 - write(6,*) 'Aaaah!' - end if - if (iju.eq.2) goto 50 - - if (k4.eq.k7) then - nval=nval+1 - iv(nval,2)=k5 - iv(nval,3)=k4 - iv(nval,4)=k8 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - iju=1 - end if - if (iju.eq.1) goto 50 - - if (k4.eq.k8) then - nval=nval+1 - iv(nval,2)=k5 - iv(nval,3)=k4 - iv(nval,4)=k7 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - iju=1 - end if - if (iju.eq.1) goto 50 - - if (k5.eq.k7) then - nval=nval+1 - iv(nval,2)=k4 - iv(nval,3)=k5 - iv(nval,4)=k8 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - iju=1 - end if - if (iju.eq.1) goto 50 - - if (k5.eq.k8) then - nval=nval+1 - iv(nval,2)=k4 - iv(nval,3)=k5 - iv(nval,4)=k7 - iv(nval,5)=jindexbondlist - iv(nval,6)=kindexbondlist - iju=1 - end if - if (iju.eq.1) goto 50 - - write (6,*)'nval = ',nval, - $ ' after',iindexatom, ' of ',na,' atoms completed.' - stop 'Adjacent bonds did not make an angle' - - endif - - 50 continue - - if (nval.gt.nvamax) then - write (6,*)'nval = ',nval,' reax_defs.h::NVAMAXDEF = ', - $ NVAMAXDEF, - $ ' after',iindexatom, ' of ',na,' atoms completed.' - stop 'Too many valency angles. Increase NVAMAXDEF' - endif - - if (iju.gt.0) then -********************************************************************** -* * -* Determine force field types of angles * -* * -********************************************************************** - ityva(1)=0 - ih1=ia(iv(nval,2),1) - ih2=ia(iv(nval,3),1) - ih3=ia(iv(nval,4),1) - if (ih3.lt.ih1) then - ih3=ia(iv(nval,2),1) - ih2=ia(iv(nval,3),1) - ih1=ia(iv(nval,4),1) - end if - - nfound=0 - do i3=1,nvaty - if (ih1.eq.nvs(i3,1).and.ih2.eq.nvs(i3,2).and. - $ih3.eq.nvs(i3,3)) then - nfound=nfound+1 - ityva(nfound)=i3 - end if - end do - - if (ityva(1).eq.0.or.abs(vka(ityva(1))).lt.0.001) then !Valence angle does not exist in force field;ignore - nval=nval-1 - ihul=0 - else - iv(nval,1)=ityva(1) - ihul=1 - - do i3=1,nfound-1 !Found multiple angles of the same type - nval=nval+1 - iv(nval,1)=ityva(i3+1) - do i4=2,6 - iv(nval,i4)=iv(nval-1,i4) - end do - - end do - - end if - - if (iju.eq.2) then - ityva(1)=0 - ih1=ia(iv(nval-ihul,2),1) - ih2=ia(iv(nval-ihul,3),1) - ih3=ia(iv(nval-ihul,4),1) - if (ih3.lt.ih1) then - ih3=ia(iv(nval-ihul,2),1) - ih2=ia(iv(nval-ihul,3),1) - ih1=ia(iv(nval-ihul,4),1) - end if - - nfound=0 - do i3=1,nvaty - if (ih1.eq.nvs(i3,1).and.ih2.eq.nvs(i3,2).and. - $ih3.eq.nvs(i3,3)) then - nfound=nfound+1 - ityva(nfound)=i3 - end if - end do - - if (ityva(1).eq.0.or.abs(vka(ityva(1))).lt.0.001) then !Valence angle does not exist in force field;ignore - if (ihul.eq.1) then - do i3=1,6 - iv(nval-1,i3)=iv(nval,i3) - end do - end if - nval=nval-1 - else - iv(nval-ihul,1)=ityva(1) - - do i3=1,nfound-1 !Found multiple angles of the same type - nval=nval+1 - iv(nval,1)=ityva(i3+1) - do i4=2,6 - iv(nval,i4)=iv(nval-1,i4) - end do - - end do - - end if - - end if - - end if - - end do - 51 continue - end do - end do - - nbonop=0 - - return - end -********************************************************************** -********************************************************************** - - subroutine srttor - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkbo.blk" -#include "cbkrbo.blk" -#include "cbkia.blk" -#include "cbktorsion.blk" -#include "cbkvalence.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" -#include "cbknubon2.blk" -********************************************************************** -* * -* Find torsion angles in molecule * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$ open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In srttor' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - ntor=0 - if (ntoty.eq.0) return - do 61 i1=1,nbon - k2=ib(i1,2) - k3=ib(i1,3) -c Only compute interaction if both atoms local -c are local or else flip a coin - if (k2 .gt. na_local) go to 61 - if (k3 .gt. na_local) then - if (itag(k2) .lt. itag(k3)) go to 61 - if (itag(k2) .eq. itag(k3)) then - if(c(k2,3) .gt. c(k3,3)) go to 61 - if(c(k2,3) .eq. c(k3,3) .and. - $ c(k2,2) .gt. c(k3,2)) go to 61 - if(c(k2,3) .eq. c(k3,3) .and. - $ c(k2,2) .eq. c(k3,2) .and. - $ c(k2,1) .gt. c(k3,1)) go to 61 - endif - endif - - iob1=ia(k2,2) - iob2=ia(k3,2) - do 60 i2=1,iob1 !Atoms connected to k2 - k4=ia(k2,2+i2) - ibo2=nubon2(k2,i2) - do 60 i3=1,iob2 !Atoms connected to k3 - k5=ia(k3,2+i3) - ibo3=nubon2(k3,i3) - bopr=bo(i1)*bo(ibo2)*bo(ibo3) - if (bopr.gt.cutof2.and.k2.ne.k5.and.k3.ne.k4.and.k4.ne.k5) then - - ntor=ntor+1 - it(ntor,2)=k4 - it(ntor,3)=k2 - it(ntor,4)=k3 - it(ntor,5)=k5 - it(ntor,6)=ibo2 - it(ntor,7)=i1 - it(ntor,8)=ibo3 - -********************************************************************** -* * -* Determine force field types of torsion angles * -* * -********************************************************************** - ity=0 - ih1=ia(it(ntor,2),1) - ih2=ia(it(ntor,3),1) - ih3=ia(it(ntor,4),1) - ih4=ia(it(ntor,5),1) - - if (ih2.gt.ih3) then - ih1=ia(it(ntor,5),1) - ih2=ia(it(ntor,4),1) - ih3=ia(it(ntor,3),1) - ih4=ia(it(ntor,2),1) - end if - - if (ih2.eq.ih3.and.ih4.lt.ih1) then - ih1=ia(it(ntor,5),1) - ih2=ia(it(ntor,4),1) - ih3=ia(it(ntor,3),1) - ih4=ia(it(ntor,2),1) - end if - - do i4=1,ntoty - if (ih1.eq.nts(i4,1).and.ih2.eq.nts(i4,2).and.ih3.eq.nts(i4,3) - $.and.ih4.eq.nts(i4,4)) ity=i4 - end do - - if (ity.eq.0) then - do i4=1,ntoty - if (nts(i4,1).eq.0.and.ih2.eq.nts(i4,2).and.ih3.eq.nts(i4,3) - $.and.nts(i4,4).eq.0) ity=i4 - end do - end if - - if (ity.eq.0) then - ntor=ntor-1 !Torsion angle does not exist in force field: ignore - else - it(ntor,1)=ity - end if - - end if - - 60 continue - 61 continue - - if (ntor.gt.ntomax) stop 'Too many torsion angles' -* do i1=1,ntor -* write (41,'(20i4)')i1,it(i1,1),it(i1,2),it(i1,3), -* $it(i1,4),it(i1,5),it(i1,6),it(i1,7),it(i1,8) -* end do - - return - end -********************************************************************** -********************************************************************** - - subroutine srtoop - -********************************************************************** -#include "cbka.blk" -#include "cbkbo.blk" -#include "cbkrbo.blk" -#include "cbkvalence.blk" -#include "control.blk" -#include "small.blk" -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In srtoop' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -********************************************************************** -* * -* Find out of plane angles in molecule * -* * -********************************************************************** - noop=0 - do i1=1,nval - k2=iv(i1,2) - k3=iv(i1,3) - k4=iv(i1,4) - k5=iv(i1,5) - k6=iv(i1,6) - do i2=1,nbon - k7=ib(i2,2) - k8=ib(i2,3) - if (bo(i2).gt.cutof2) then - if (k7.eq.k3.and.k8.ne.k4.and.k8.ne.k2) then - noop=noop+1 - ioop(noop,2)=k8 - ioop(noop,3)=k3 - ioop(noop,4)=k2 - ioop(noop,5)=k4 - ioop(noop,6)=i2 - ioop(noop,7)=iv(i1,5) - ioop(noop,8)=iv(i1,6) - ioop(noop,9)=i1 - end if - if (k8.eq.k3.and.k7.ne.k4.and.k7.ne.k2) then - noop=noop+1 - ioop(noop,2)=k7 - ioop(noop,3)=k3 - ioop(noop,4)=k2 - ioop(noop,5)=k4 - ioop(noop,6)=i2 - ioop(noop,7)=iv(i1,5) - ioop(noop,8)=iv(i1,6) - ioop(noop,9)=i1 - end if - end if - end do - end do - - do i1=1,noop - call caltor(ioop(i1,2),ioop(i1,3),ioop(i1,4),ioop(i1,5),hoop) - end do - -********************************************************************** - return - end -********************************************************************** - -********************************************************************** - - subroutine srthb - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkbo.blk" -#include "cbkconst.blk" -#include "cbkia.blk" -#include "cbkrbo.blk" -#include "cbksrthb.blk" -#include "control.blk" -#include "small.blk" -#include "cbkpairs.blk" -#include "cbknvlown.blk" -#include "cbknubon2.blk" -********************************************************************** -* * -* Find hydrogen bonds in molecule * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$ open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In srthb' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - nhb=0 -********************************************************************** -* * -* Locate donor/acceptor bonds * -* * -********************************************************************** -c Outer loop must be Verlet list, because ia() does not store Verlet entries, -c but it does store bond entries in nubon2() -c -c The problem with using the nvlown ownership criterion -c is that it would require that we unprune every bond that is within -c certain distance, as well as its first and second neighbor bonds. -c -c For the ownership criterion based on H atom location no unpruning is required. -c Apparently lprune=4 is sufficient here, implying that we need to capture first and -c second neighbor bonds of the O-H bond, and of course we need to include all hydrogen -c bond partners within hbcut. -c - - do 20 ivl=1,nvpair !Use Verlet-list to find donor-acceptor pairs - - j1=nvl1(ivl) - j2=nvl2(ivl) - ity1=ia(j1,1) - ity2=ia(j2,1) - ihhb1=nphb(ia(j1,1)) - ihhb2=nphb(ia(j2,1)) - - if (ihhb1.gt.ihhb2) then !Make j1 donor(H) atom and j2 acceptor(O) atom - j2=nvl1(ivl) - j1=nvl2(ivl) - ity1=ia(j1,1) - ity2=ia(j2,1) - ihhb1=nphb(ia(j1,1)) - ihhb2=nphb(ia(j2,1)) - end if - -* Only need to compute bonds where j1 is local - if (j1 .le. na_local) then - - if (ihhb1.eq.1.and.ihhb2.eq.2) then - call dista2(j1,j2,dishb,dxm,dym,dzm) - if (dishb.lt.hbcut) then - do 10 i23=1,ia(j1,2) !Search for acceptor atoms bound to donor atom - j3=ia(j1,2+i23) - ity3=ia(j3,1) - nbohb=nubon2(j1,i23) - if (nphb(ity3).eq.2.and.j3.ne.j2.and.bo(nbohb).gt.0.01) then -********************************************************************** -* * -* Accept hydrogen bond and find hydrogen bond type * -* * -********************************************************************** - nhb=nhb+1 - - if (nhb.gt.nhbmax) then - write (*,*)nhb,nhbmax - write (*,*)'Maximum number of hydrogen bonds exceeded' - stop 'Maximum number of hydrogen bonds exceeded' - end if - - ihb(nhb,1)=0 - - do i3=1,nhbty - if (ity3.eq.nhbs(i3,1).and.ity1.eq.nhbs(i3,2).and.ity2.eq. - $nhbs(i3,3)) ihb(nhb,1)=i3 - end do - - if (ihb(nhb,1).eq.0) then !Hydrogen bond not in force field - nhb=nhb-1 -* write (*,*)'Warning: added hydrogen bond ',ity3,ity1,ity2 -* nhbty=nhbty+1 -* nhbs(nhbty,1)=ity3 -* nhbs(nhbty,2)=ity1 -* nhbs(nhbty,3)=ity2 -* rhb(nhbty)=2.70 -* dehb(nhbty)=zero -* vhb1(nhbty)=5.0 -* vhb2(nhbty)=20.0 -* ihb(nhb,1)=nhbty - end if - - ihb(nhb,2)=j3 - ihb(nhb,3)=j1 - ihb(nhb,4)=j2 - ihb(nhb,5)=nbohb - ihb(nhb,6)=k1 - ihb(nhb,7)=k2 - ihb(nhb,8)=k3 -* write (64,*)nhb,ihb(nhb,1),j3,j1,j2,nbohb,k1,k2,k3,bo(nbohb), -* $dishb - - end if - - 10 continue - - end if - end if - end if - 20 end do - -* stop 'end in srthb' - return - end -********************************************************************** diff --git a/lib/reax/reax_defs.h b/lib/reax/reax_defs.h deleted file mode 100644 index e28533fa9b..0000000000 --- a/lib/reax/reax_defs.h +++ /dev/null @@ -1,70 +0,0 @@ -#define PORTABLECOMMENTFLAG -#ifndef PORTABLECOMMENTFLAG -// This is just a way to have portable comments -// for both C++ and FORTRAN preprocessing. - /* ///:EOH~ */ - /* */ - /* This file contains array dimension parameters for all the main */ - /* ReaxFF data structures, some of which need to be directly accessed */ - /* by Grasp C++ functions. If they are set too small, the calculation */ - /* will run out of allocated memory. If they are set too big, the machine */ - /* will not be able to allocate enough memory. */ - /* */ - - /* NNEIGHMAXDEF = Max number of neighbors / NATDEF */ - /* NATDEF = Max number of atoms */ - /* NATTOTDEF = Max number of global atoms */ - /* NSORTDEF = Max number of atom types */ - /* MBONDDEF = Max number of bonds connected to one atom */ - /* NAVIBDEF = for 2nd derivatives */ - /* NBOTYMDEF = Max number of bond types */ - /* NVATYMDEF = Max number of valency angle types */ - /* NTOTYMDEF = Max number of torsion angle types */ - /* NHBTYMDEF = Max number of hydrogen bond types */ - /* NODMTYMDEF = Max number of off-diagonal Morse types */ - /* NBOALLMAXDEF = Max number of all bonds */ - /* NBOMAXDEF = Max number of bonds */ - /* NHBMAXDEF = Max number of hydrogen bonds */ - /* NVAMAXDEF = Max number of valency angles */ - /* NOPMAXDEF = Max number of out of plane angles */ - /* NTOMAXDEF = Max number of torsion angles */ - /* NPAMAXDEF = Max number of general parameters in force field */ - /* NMOLMAXDEF = Max number of molecules in system */ - /* NMOLSETDEF = Max number of molecules in training set */ - /* MRESTRADEF = Max number of restraints */ - /* MTREGDEF = Max number of temperature regimes */ - /* MTZONEDEF = Max number of temperature zones */ - /* MVREGDEF = Max number of volume regimes */ - /* MVZONEDEF = Max number of volume zones */ - /* MEREGDEF = Max number of electric field regimes */ - /* MEZONEDEF = Max number of electric field zones */ -#endif - -#define NNEIGHMAXDEF 120 -#define NATDEF 40000 -#define NATTOTDEF 39744 -#define NSORTDEF 20 -#define MBONDDEF 20 -#define NAVIBDEF 50 -#define NBOTYMDEF 200 -#define NVATYMDEF 200 -#define NTOTYMDEF 200 -#define NHBTYMDEF 200 -#define NODMTYMDEF 20 -#define NBOALLMAXDEF 180000 -#define NBOMAXDEF 90000 -#define NHBMAXDEF 400000 -#define NVAMAXDEF 300000 -#define NOPMAXDEF 00010 -#define NTOMAXDEF 65000 -#define NPAMAXDEF 50 -#define NMOLMAXDEF 2000 -#define NMOLSETDEF 1500 -#define MRESTRADEF 100 -#define MTREGDEF 100 -#define MTZONEDEF 5 -#define MVREGDEF 100 -#define MVZONEDEF 6 -#define MEREGDEF 100 -#define MEZONEDEF 3 - diff --git a/lib/reax/reax_inout.F b/lib/reax/reax_inout.F deleted file mode 100644 index 944400a968..0000000000 --- a/lib/reax/reax_inout.F +++ /dev/null @@ -1,3870 +0,0 @@ -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -********************************************************************** - - subroutine ffinpt - -********************************************************************** -#include "cbka.blk" -#include "cbkboncor.blk" -#include "cbkconst.blk" -#include "cbkcovbon.blk" -#include "cbkff.blk" -#include "cbkfftorang.blk" -#include "cbknonbon.blk" -#include "cbksrthb.blk" -#include "cbktorsion.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "valang.blk" -#include "cbksrtbon1.blk" -#include "cbkchb.blk" - dimension rcore2(nsort),ecore2(nsort),acore2(nsort) -********************************************************************** -* * -* Read in force field * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In ffinpt' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - open (4,file='ffield.reax',status='old') - rewind (4) - iline=0 - read (4,'(a40)',end=990,err=990)qffield - iline=iline+1 -********************************************************************** -* * -* Read in general force field parameters * -* * -********************************************************************** - read (4,1100,end=990,err=990)npar - iline=iline+1 - do i1=1,npar - read (4,1300,end=990,err=990)vpar(i1) - iline=iline+1 - end do - cutoff=0.01*vpar(30) - swa=vpar(12) - if (abs(swa).gt.0.01) write (*,*) - $'Warning: non-zero value for lower Taper-radius cutoff' - swb=vpar(13) - if (swb.lt.zero) stop - $'Negative value for upper Taper-radius cutoff' - if (swb.lt.5.0) write (*,*) - $'Warning: very low value for upper Taper-radius cutoff:',swb -********************************************************************** -* * -* Read in atom type data * -* * -********************************************************************** - read (4,1100,end=990,err=990) nso - iline=iline+1 - read (4,*,end=990,err=990) - iline=iline+1 - read (4,*,end=990,err=990) - iline=iline+1 - read (4,*,end=990,err=990) - iline=iline+1 - if (nso.gt.nsort) stop 'Maximum number of atom types exceeded' - do i1=1,nso - read (4,1200,end=990,err=990)qas(i1),rat(i1),aval(i1),amas(i1), - $rvdw(i1),eps(i1),gam(i1),rapt(i1),stlp(i1) - iline=iline+1 - read (4,1250,end=990,err=990)alf(i1),vop(i1),valf(i1), - $valp1(i1),valp2(i1),chi(i1),eta(i1),vnphb - iline=iline+1 - read (4,1250,end=990,err=990)vnq(i1),vlp1(i1),vincr(i1), - $bo131(i1),bo132(i1),bo133(i1),sigqeq(i1),default - iline=iline+1 - read (4,1250,end=990,err=990)vovun(i1),vval1(i1),vrom, - $vval3(i1),vval4(i1),rcore2(i1),ecore2(i1),acore2(i1) - iline=iline+1 - idef(i1)=int(default) - nphb(i1)=int(vnphb) - end do -********************************************************************** -* * -* Calculate van der Waals and Coulomb pair-parameters * -* * -********************************************************************** - do i1=1,nso - do i2=1,nso - rcore(i1,i2)=sqrt(rcore2(i1)*rcore2(i2)) - ecore(i1,i2)=sqrt(ecore2(i1)*ecore2(i2)) - acore(i1,i2)=sqrt(acore2(i1)*acore2(i2)) - p1co(i1,i2)=sqrt(4.0*rvdw(i1)*rvdw(i2)) - p2co(i1,i2)=sqrt(eps(i1)*eps(i2)) - p3co(i1,i2)=sqrt(alf(i1)*alf(i2)) - gamwh=sqrt(vop(i1)*vop(i2)) - gamwco(i1,i2)=1.0/gamwh**vpar(29) - gamch=sqrt(gam(i1)*gam(i2)) - gamcco(i1,i2)=1.0/gamch**3 - rob1(i1,i2)=0.50*(rat(i1)+rat(i2)) - rob2(i1,i2)=0.50*(rapt(i1)+rapt(i2)) - rob3(i1,i2)=0.50*(vnq(i1)+vnq(i2)) - end do - end do -********************************************************************** -* * -* Read in bond type data * -* * -********************************************************************** - read (4,1100,end=990,err=990)nboty - iline=iline+1 - read (4,*,end=990,err=990) - iline=iline+1 - if (2*nboty.gt.nbotym) stop 'Maximum nr. of bond types exceeded' - ih=0 - do i1=1,nboty - ih=ih+1 - read (4,1400,end=990,err=990)nbs(ih,1),nbs(ih,2),de1(ih), - $de2(ih),de3(ih),psi(ih),pdo(ih),v13cor(ih),popi(ih),vover(ih) - iline=iline+1 - read (4,1450,end=990,err=990)psp(ih),pdp(ih),ptp(ih), - $bom(ih),bop1(ih),bop2(ih),ovc(ih),vuncor(ih) - iline=iline+1 - if (nbs(ih,1).ne.nbs(ih,2)) then - ih=ih+1 - nbs(ih,1)=nbs(ih-1,2) - nbs(ih,2)=nbs(ih-1,1) - de1(ih)=de1(ih-1) - de2(ih)=de2(ih-1) - de3(ih)=de3(ih-1) - psi(ih)=psi(ih-1) - pdo(ih)=pdo(ih-1) - v13cor(ih)=v13cor(ih-1) - vover(ih)=vover(ih-1) - psp(ih)=psp(ih-1) - pdp(ih)=pdp(ih-1) - ptp(ih)=ptp(ih-1) - bop1(ih)=bop1(ih-1) - bop2(ih)=bop2(ih-1) -* bop3(ih)=bop3(ih-1) -* bop4(ih)=bop4(ih-1) - bom(ih)=bom(ih-1) - popi(ih)=popi(ih-1) - ovc(ih)=ovc(ih-1) - end if - end do - nboty2=ih -********************************************************************** -* * -* Read in off-diagonal parameters * -* * -********************************************************************** - read (4,1100,end=990,err=990)nodmty - iline=iline+1 - if (nodmty.gt.nodmtym) - $stop 'Maximum nr. of off-diagonal Morse types exceeded' - ih=0 - do i1=1,nodmty - ih=ih+1 - read (4,1400,end=990,err=990)nodm1,nodm2,deodmh,rodmh,godmh, - $rsig,rpi,rpi2 - iline=iline+1 - if (rsig.gt.zero) rob1(nodm1,nodm2)=rsig - if (rsig.gt.zero) rob1(nodm2,nodm1)=rsig - if (rpi.gt.zero) rob2(nodm1,nodm2)=rpi - if (rpi.gt.zero) rob2(nodm2,nodm1)=rpi - if (rpi2.gt.zero) rob3(nodm1,nodm2)=rpi2 - if (rpi2.gt.zero) rob3(nodm2,nodm1)=rpi2 - if (rodmh.gt.zero) p1co(nodm1,nodm2)=2.0*rodmh - if (rodmh.gt.zero) p1co(nodm2,nodm1)=2.0*rodmh - if (deodmh.gt.zero) p2co(nodm1,nodm2)=deodmh - if (deodmh.gt.zero) p2co(nodm2,nodm1)=deodmh - if (godmh.gt.zero) p3co(nodm1,nodm2)=godmh - if (godmh.gt.zero) p3co(nodm2,nodm1)=godmh - end do -********************************************************************** -* * -* Read in valency angle and conjugation type data * -* * -********************************************************************** - read (4,1100,end=990,err=990)nvaty - iline=iline+1 - if (nvaty.gt.nvatym) - $stop 'Maximum nr. of valency angle types exceeded' - do i1=1,nvaty - read (4,1500,end=990,err=990)nvs(i1,1),nvs(i1,2), - $nvs(i1,3),th0(i1),vka(i1),vka3(i1),vka8(i1),vkac(i1),vkap(i1), - $vval2(i1) - iline=iline+1 - end do -********************************************************************** -* * -* Read in torsion angle type data * -* * -********************************************************************** - read (4,1100,end=990,err=990)ntoty - iline=iline+1 - if (ntoty.gt.ntotym) - $stop 'Maximum nr. of torsion angle types exceeded' - do i1=1,ntoty - read (4,1600,end=990,err=990)nts(i1,1),nts(i1,2),nts(i1,3), - $nts(i1,4),v1(i1), - $v2(i1),v3(i1),v4(i1),vconj(i1),v2bo(i1),v3bo(i1) - iline=iline+1 - end do -********************************************************************** -* * -* Read in hydrogen bond type data * -* * -********************************************************************** - read (4,1100,end=990,err=990)nhbty - iline=iline+1 - if (nhbty.gt.nhbtym) - $stop 'Maximum nr. of hydrogen bond types exceeded' - do i1=1,nhbty - read (4,1500,end=990,err=990)nhbs(i1,1),nhbs(i1,2), - $nhbs(i1,3),rhb(i1),dehb(i1),vhb1(i1),vhb2(i1) - iline=iline+1 - end do -********************************************************************** -* * -* Calculate vdWaals interaction parameters * -* * -********************************************************************** - do i1=1,nso - do i2=1,nso - rr=(rvdw(i1)+rvdw(i2)) - rr2=rr*rr - eps2=sqrt(eps(i1)*eps(i2)) - rr6=rr2*rr2*rr2 - pvdw1(i1,i2)=eps2*rr6*rr6 - pvdw1(i2,i1)=eps2*rr6*rr6 - pvdw2(i1,i2)=2.0*eps2*rr6 - pvdw2(i2,i1)=2.0*eps2*rr6 - end do - end do -********************************************************************** -* * -* Error part * -* * -********************************************************************** - goto 999 - 990 write (*,*)'Error or end-of-file reading unit 4 on line:',iline - stop - 999 continue - close(4) -********************************************************************** -* * -* Format part * -* * -********************************************************************** - 1100 format (i3,2x,a2,3x,3d22.15) - 1200 format (1x,a2,10f9.4) - 1250 format (3x,10f9.4) - 1300 format (f10.4) - 1400 format (2i3,8f9.4) - 1450 format (6x,8f9.4) - 1500 format (3i3,7f9.4) - 1600 format (4i3,7f9.4) - return - end -********************************************************************** -*********************************************************************** - - subroutine mdsav(node) - -*********************************************************************** -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkatomcoord.blk" -#include "cbkbo.blk" -#include "cbkc.blk" -#include "cbkch.blk" -#include "cbkconst.blk" -#include "cbkdistan.blk" -#include "cbkenergies.blk" -#include "cbkia.blk" -#include "cbkinit.blk" -#include "cbklonpar.blk" -#include "cbknubon2.blk" -#include "cbkqa.blk" -#include "cbktregime.blk" -#include "cbksrtbon1.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" - - dimension idum(mbond+3),bodum(mbond+3),qat2(2) - character*25 qfileh - character*33 qfile2 - character*4 qext - character*6 qmdfi - character *7 var - character *3 qat2,pepname - character *1 qrtemp -************************************************************************ -* * -* Save coordinates, velocities and accelerations of MD-system * -* * -************************************************************************ -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In mdsav' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - -************************************************************************ -c -c This is just for test purposes -c -************************************************************************ -c$$$ write(6,*) '***************************' -c$$$ write(6,*) 'mdsav node number is ',node -c$$$ write(6,*) '***************************' - return - - - qfileh='Unknown' - qmdfi='moldyn' - pepname=' ' - ipeptide=0 - if (ni.eq.2) qmdfi='molsav' - - if (iopt.eq.0) then - - do i1=1,mbond+3 - idum(i1)=nzero - bodum(i1)=zero - end do -C if (napp.eq.1) -C $open (7,file='fort.7',status='unknown',access='append') - if (napp.ne.1) - $open (7,file='fort.7',status='unknown') - nsbmaxh=5*((nsbmax/5)+1) - write (7,100)na,qmol,mdstep,nsbmaxh - if (nbiolab.eq.1) write (67,101)na,qmol - do i1=1,na - bosum=0.0 - do i3=1,nsbmax - if (iag(i1,2+i3).gt.0) bosum=bosum+bo(nubon1(i1,i3)) - end do - if (nsbmax.lt.5) then - write (7,200)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)), - $(idum(i2),i2=1,5-iag(i1,2)), - $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)), - $(bodum(i2),i2=1,5-iag(i1,2)),abo(i1),vlp(i1),ch(i1) - if (nbiolab.eq.1) then !Delphi-connection table output - write (67,201)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)) - end if - else if (nsbmax.lt.10) then - write (7,210)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)), - $(idum(i2),i2=1,10-iag(i1,2)), - $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)), - $(bodum(i2),i2=1,10-iag(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbmax.lt.15) then - write (7,220)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)), - $(idum(i2),i2=1,15-iag(i1,2)), - $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)), - $(bodum(i2),i2=1,15-iag(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbmax.lt.20) then - write (7,230)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)), - $(idum(i2),i2=1,20-iag(i1,2)), - $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)), - $(bodum(i2),i2=1,20-iag(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbmax.lt.25) then - write (7,240)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)), - $(idum(i2),i2=1,25-iag(i1,2)), - $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)), - $(bodum(i2),i2=1,25-iag(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbmax.gt.25) then - write (7,250)i1,iag(i1,1),(iag(i1,2+i2),i2=1,iag(i1,2)), - $(idum(i2),i2=1,35-iag(i1,2)), - $iag(i1,3+mbond),(bo(nubon1(i1,i2)),i2=1,iag(i1,2)), - $(bodum(i2),i2=1,35-iag(i1,2)),abo(i1),vlp(i1),ch(i1) - end if - end do - boss=zero - vlps=0.0 -C if (napp.eq.1) -C $open (8,file='fort.8',status='unknown',access='append') - if (napp.ne.1) - $open (8,file='fort.8',status='unknown') - nsbmaxh=5*((nsbma2/5)+1) - write (8,100)na,qmol,mdstep,nsbmaxh - chsum=0.0 - do i1=1,na - bosum=0.0 - do i3=1,nsbma2 - if (ia(i1,2+i3).gt.0) bosum=bosum+bo(nubon2(i1,i3)) - end do - if (nsbma2.lt.5) then - write (8,200)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)), - $(idum(i2),i2=1,5-ia(i1,2)), - $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)), - $(bodum(i2),i2=1,5-ia(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbma2.lt.10) then - write (8,210)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)), - $(idum(i2),i2=1,10-ia(i1,2)), - $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)), - $(bodum(i2),i2=1,10-ia(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbma2.lt.15) then - write (8,220)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)), - $(idum(i2),i2=1,15-ia(i1,2)), - $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)), - $(bodum(i2),i2=1,15-ia(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbma2.lt.20) then - write (8,230)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)), - $(idum(i2),i2=1,20-ia(i1,2)), - $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)), - $(bodum(i2),i2=1,20-ia(i1,2)),abo(i1),vlp(i1),ch(i1) - else if (nsbma2.lt.25) then - write (8,240)i1,ia(i1,1),(ia(i1,2+i2),i2=1,ia(i1,2)), - $(idum(i2),i2=1,25-ia(i1,2)), - $ia(i1,3+mbond),(bo(nubon2(i1,i2)),i2=1,ia(i1,2)), - $(bodum(i2),i2=1,25-ia(i1,2)),abo(i1),vlp(i1),ch(i1) - end if - boss=boss+bosum/2.0 - vlps=vlps+vlp(i1) - chsum=chsum+ch(i1) - end do - write (7,*)2.0*boss,vlps,2.0*boss+2.0*vlps,chsum - close(8) - close(7) - - end if - - if (noutpt.eq.0) then - write (var,'(f7.4)')float(mdstep/nsav)/1d4 - if (ni.eq.0) open (unit=67,file=qmdfi//var(3:7), - $status='unknown') - write (67,300)qmol - do i1=1,na - write (67,400)i1,qa(i1),(c(i1,i2),i2=1,3) - end do - write (67,*) - close(67) - end if - - if (noutpt.eq.2) then -C open (88,file='moldyn.bgf',status='unknown',access='append') - call writebgf(88) - close (88) - end if - - if ((ni.eq.1.and.iopt.eq.0).or.(ni.eq.1.and.iopt.eq.1.and. - $iflga.eq.1)) then - qrtemp=qr - if (qr.eq.'I') qr='C' - if (qfileh.eq.' ') then - write (*,*)'Warning: no file name given; use Unknown' - qfileh='Unknown' - end if - qfile2=qfileh - if (imodfile.eq.0) then - istart=1 - qstrana1(1:25)=qfileh - call stranal(istart,iend,vout,iout,1) - qfile2=qfileh(istart:iend-1)//".geo" - end if - call writegeo(98) - - if (imodfile.eq.1.or.iopt.eq.0) then - open (88,file=qfile2,status='unknown') - call writegeo(88) - close (88) - end if - - qr=qrtemp - - if (iopt.eq.0) then - - do i1=1,na - write (56,410) i1,ch(i1) - write (55,410) i1,chgbgf(i1) - end do -********************************************************************** -* * -* Write .pdb output file * -* * -********************************************************************** - open (unit=47,file='output.pdb',status='unknown') - do i1=1,na - write (47,412)'ATOM ',i1,qa(i1),pepname,ipeptide,c(i1,1), - $c(i1,2),c(i1,3),1.0,2.2,qa(i1) - end do - write (47,*) 'TER' - write (47,*) 'END' - close (47) - - if (nsurp.eq.0) then - if (kx.gt.0.or.ky.gt.0.or.kz.gt.0) then - qrtemp=qr -********************************************************************** -* * -* Write crystal structure including periodic images * -* * -********************************************************************** -* mux=(1+kx+kx) -* muy=(1+ky+ky) -* muz=(1+kz+kz) -* qr='F' -* write (86,'(2x,a1,1x,a60)')qr,qmol -* qr=qrtemp -* write (86,'(3f10.4)')mux*axiss(1),muy*axiss(2),muz*axiss(3) -* write (86,'(3f10.4)')angle(1),angle(2),angle(3) -* do i1=1,na -* write (86,'(i4,1x,a2,3x,3d22.15)')i1,qa(i1),(c(i1,i2),i2=1,3) -* end do -* nhulp=na+1 -* do k1=-kx,kx -* do k2=-ky,ky -* do k3=-kz,kz -* if (k1.ne.0.or.k2.ne.0.or.k3.ne.0) then -* do i1=1,na -* cx=c(i1,1)+k1*tm11 -* cy=c(i1,2)+k1*tm21+k2*tm22 -* cz=c(i1,3)+k1*tm31+k2*tm32+k3*tm33 -* write (86,'(i4,1x,a2,3x,3d22.15)')nhulp,qa(i1),cx,cy,cz -* nhulp=nhulp+1 -* end do -* end if -* end do -* end do -* end do -* write (86,*) -********************************************************************** -* * -* Write crystal structure with extra unit cells * -* * -********************************************************************** - mux=1+iexx - muy=1+iexy - muz=1+iexz - qr='F' - write (85,'(2x,a1,1x,a60)')qr,qmol - qr=qrtemp - write (85,'(3f10.4)')mux*axiss(1),muy*axiss(2),muz*axiss(3) - write (85,'(3f10.4)')angle(1),angle(2),angle(3) - do i1=1,na - write (85,'(i4,1x,a2,3x,3d22.15)')i1,qa(i1),(c(i1,i2),i2=1,3) - end do - nhulp=na+1 - do k1=0,iexx - do k2=0,iexy - do k3=0,iexz - if (k1.ne.0.or.k2.ne.0.or.k3.ne.0) then - do i1=1,na - cx=c(i1,1)+k1*tm11 - cy=c(i1,2)+k1*tm21+k2*tm22 - cz=c(i1,3)+k1*tm31+k2*tm32+k3*tm33 - write (85,'(i4,1x,a2,3x,3d22.15)')nhulp,qa(i1),cx,cy,cz - nhulp=nhulp+1 - end do - end if - end do - end do - end do - write (85,*) - - end if - end if - end if - - end if - - if (ni.eq.0.or.ni.eq.2) then -********************************************************************** -* * -* Write ASCII trajectory file * -* * -********************************************************************** - if (ni.eq.0) open(unit=66,file=qmdfi//'.vel',status='unknown') - if (ni.eq.2) then - write (var,'(f7.4)')float(mdstep/nsav3)/1d4 - open (unit=66,file=qmdfi//var(3:7),status='unknown') - end if - write (66,500)axis(1),axis(2),axis(3) - write (66,550)angle(1),angle(2),angle(3) - write (66,600)na,((c(i,j),j=1,3),qlabel(i),i=1,na) - write (66,700)((vel(j,i),j=1,3),i=1,na) - write (66,800)((accel(j,i),j=1,3),i=1,na) - write (66,900)((aold(j,i),j=1,3),i=1,na) - write (66,1000)tempmd - write (66,1050) - close (66) - end if - if (ni.ne.2.and.iopt.eq.0) then - -C open (unit=68,file='xmolout',status='unknown',access='append') - write (68,1200)na - write (68,1300)qmol,mdstep+nit+nprevrun,estrc, - $axis(1),axis(2),axis(3),angle(1),angle(2),angle(3) - do i1=1,na - if (ixmolo.eq.0) write (68,1400)qa(i1),(c(i1,i2),i2=1,3) - if (ixmolo.eq.1) write (68,1400)qa(i1),(c(i1,i2),i2=1,3), - $(vel(i2,i1)/1e+10,i2=1,3),iag(i1,3+mbond) - if (ixmolo.eq.2) write (68,1401)qa(i1),(c(i1,i2),i2=1,3), - $iag(i1,3+mbond) - end do - close (68) - - if (itrout.ne.0) then -C open (unit=69,file='xmolout2',status='unknown',access='append') - write (69,1200)na - write (69,1300)qmol,mdstep+nit+nprevrun,estrc, - $axis(1),axis(2),axis(3),angle(1),angle(2),angle(3) - do i1=1,na - if (ixmolo.eq.0) write (69,1400)qa(i1),(cp(i1,i2),i2=1,3) - if (ixmolo.eq.1) write (69,1400)qa(i1),(cp(i1,i2),i2=1,3), - $(vel(i2,i1)/1e+10,i2=1,3),iag(i1,3+mbond) - if (ixmolo.eq.2) write (68,1401)qa(i1),(c(i1,i2),i2=1,3), - $iag(i1,3+mbond) - end do - close (69) - end if - - call molanal - end if -********************************************************************** -* * -* Generate BIOGRAF output-file * -* * -********************************************************************** - if ((ni.eq.1.and.iopt.eq.0).or.(ni.eq.1.and.iopt.eq.1.and. - $iflga.eq.1)) then - - if (qfileh.eq.' ') then - write (*,*)'Warning: no file name given; use Unknown' - qfileh='Unknown' - end if - qfile2=qfileh - if (imodfile.eq.0) then - istart=1 - qstrana1(1:25)=qfileh - call stranal(istart,iend,vout,iout,1) - qfile2=qfileh(istart:iend-1)//".bgf" - end if - call writebgf(90) - - if (imodfile.eq.1.or.iopt.eq.0) then - open (88,file=qfile2,status='unknown') - call writebgf(88) - close (88) - end if - - end if - - return -********************************************************************** -* * -* Format part * -* * -********************************************************************** - 100 format (i4,1x,a40,'Iteration:',i8,' #Bonds:',i4) - 101 format (i3,2x,a40) - 200 format (8i4,8f7.3) - 201 format (8i3) - 210 format (13i4,13f7.3) - 220 format (18i4,18f7.3) - 230 format (23i4,23f7.3) - 240 format (28i4,28f7.3) - 250 format (38i4,38f7.3) - 300 format (2x,a1,1x,a60) - 301 format (2x,a1,1x,f6.2,a60) - 302 format (2x,a1,1x,2f6.2,a60) - 310 format (2x,a1,1x,a60) - 320 format (3f10.4) - 400 format (i4,1x,a2,3x,3(d21.14,1x),1x,a5,1x,i5) - 410 format (i4,f12.6) - 412 format(A6,I5,1x,A2,3x,A3,2x,i4,4x,3f8.3,f6.2,f6.2,4x,2x,A6) - 500 format (1x,'Lattice parameters:',/(3f15.8)) - 550 format (3f15.8) - 600 format (i4,1x,'Atom coordinates (Angstrom):',/ - $(3d24.15,1x,a5)) - 700 format (1x,'Atom velocities (Angstrom/s):',/(3d24.15)) - 800 format (1x,'Atom accelerations (Angstrom/s**2):',/(3d24.15)) - 900 format (1x,'Previous atom accelerations:',/(3d24.15)) - 1000 format (1x,'MD-temperature (K):',/(1d24.15)) - 1050 format (1x,'Connections, bond orders and lone pairs:') - 1100 format (8i3,8f8.4) - 1200 format (i4) - 1300 format (a40,i6,f12.4,6f7.2) - 1400 format (a2,3f10.5,3f15.5,i6) - 1401 format (a2,3f10.5,i6) - 1500 format ('BIOGRF',i4) - 1600 format ('XTLGRF',i4) - 1700 format ('DESCRP ',a60) - 1800 format ('REMARK ',a60) - 1900 format ('FFIELD ',a40) - 2000 format ('RUTYPE ',a40) - 2100 format ('CRYSTX ',6f11.5) - 2200 format ('CELLS ',6i5) - 2300 format ('# At1 At2 R12 Force1 Force2 ', - $'dR12/dIteration(MD only)') - 2400 format ('BOND RESTRAINT ',2i4,f8.4,f8.2,f8.5,f10.7) - 2500 format ('# At1 At2 At3 Angle Force1 Force2', - $' dAngle/dIteration (MD only)') - 2600 format ('ANGLE RESTRAINT ',3i4,2f8.2,f8.4,f9.6) - 2700 format ('# At1 At2 At3 At3 Angle Force1 ', - $'Force2 dAngle/dIteration (MD only)') - 2800 format ('TORSION RESTRAINT ',4i4,2f8.2,f8.4,f9.6) - 2900 format ('FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,', - $'3f10.5,1x,a5,i3,i2,1x,f8.5)') - 3000 format ('HETATM',1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x, - $a5,i3,i2,1x,f8.5) - 3100 format ('FORMAT CONECT (a6,12i6)') - 3200 format ('CONECT',12i6) - 3300 format ('UNIT ENERGY kcal') - 3400 format ('ENERGY',5x,f14.6) - 3500 format ('END') - end - -************************************************************************ -************************************************************************ - - subroutine readc - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkcha.blk" -#include "cbkconst.blk" -#include "cbkdistan.blk" -#include "cbkinit.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" - - character*6 qident - character*20 qhulp -* dimension qident(100) -************************************************************************ -* * -* Read control file * -* * -************************************************************************ -c$$$c if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$c write (65,*) 'In readc' -c$$$c call timer(65) -c$$$c close (65) -c$$$c end if - if (mdstep.gt.0.or.nit.gt.0) nmmsav=nmm -************************************************************************ -* * -* Set default values * -* * -************************************************************************ - nreac=0 - axis1=200.0d0 - axis2=200.0d0 - axis3=200.0d0 - cutof2=0.001d0 - cutof3=0.300d0 - tsetor=298.0d0 - tset2=298.0d0 - pset=0.0d0 - tincr=0.0d0 - tstep=0.5d0 -* swa=0.0 !Moved to force field -* swb=12.5 !Moved to force field - taut=2.5d0 - taut2=2.5d0 - ndtau=50000 - taup=500.0d0 - vqnd=100.0d0 - errnh=1.0d0 - range=2.5d0 - maxstp=1000 - nequi=0 - nmethod=3 - ncha=3 - ncha2=1 - nchaud=1 - nvlist=25 - nrep1=5 - nsav=50 - icheck=0 - ivels=0 - itfix=0 - ncontrol=25 - noutpt=0 - napp=0 - nsurp=0 - ncons=2 - nrand=0 - nmm=0 - endpo=1.0d0 - endpo2=1.0d0 - nfc=50 - nsav2=50 - nmmax=50 - i5758=0 - parc1=1.0d0 - parc2=0.001d0 - icell=0 - ingeo=1 - ccpar=1.0005d0 - icelo2=0 - nrdd=0 - nrddf=200000 - nbiolab=0 -c ngeofor=0 - nincrop=0 - accerr=2.50d0 - vrange=2.50d0 - vlbora=5.00d0 - nsav3=1000 - nhop2=25 - nprevrun=0 - ndebug=0 - volcha=10.00d0 - ixmolo=0 - inpt=0 - iconne=0 - imolde=0 - ianaly=0 - icentr=0 - itrans=0 - itrout=0 - tpnrad=300.0d0 - ityrad=3 - iexx=1 - iexy=1 - iexz=1 - syscha=0.00d0 - inmov1=0 - inmov2=0 - vfield=0.00d0 - itstep=0 - ifreq=0 - isymm=1 - icpres=0 - delvib=0.0001d0 -c shock variables - shock_vel = 2.d0 ! impact velocity for shock simulations (nm/ps) - shock_z_sep = 10.0d0 ! separation z value to apply initial velocities in shocks - ishock_type = 0.0d0 ! shock type. 0: simple impact; 1: compressing c axis -c Hugoniostat variables - Hug_E0 = 0.d0 ! Reference energy - Hug_P0 = 0.d0 ! Reference pressure - Hug_V0 = 0.d0 ! Reference volume -c Shear flow simulations for viscosity - xImpVcm = 1.d0 ! velocity applied in shear simulations (in nm/ps), left half mover at -xImpVcm and right at +xImpVcm -c$$$************************************************************************ -c$$$* * -c$$$* Read control-file * -c$$$* * -c$$$************************************************************************ -c$$$ open (10,file='control',status='old') -c$$$ 10 read (10,'(a20)',end=20,err=30)qhulp -c$$$ if (qhulp(1:1).eq.'#') goto 10 -c$$$ read (qhulp,*,err=30)vhulp -c$$$ read (qhulp,'(8x,a6)',err=30)qident -c$$$ if (qident.eq.'Hug_V0') Hug_P0=vhulp -c$$$ if (qident.eq.'Hug_P0') Hug_V0=vhulp -c$$$ if (qident.eq.'Hug_E0') Hug_E0=vhulp -c$$$ if (qident.eq.'shea_v') xImpVcm=vhulp -c$$$ if (qident.eq.'shok_t') ishock_type=int(vhulp) -c$$$ if (qident.eq.'shok_z') shock_z_sep=vhulp -c$$$ if (qident.eq.'shok_v') shock_vel=vhulp -c$$$ if (qident.eq.'nreac') nreac=int(vhulp) -c$$$ if (qident.eq.'axis1') axis1=vhulp -c$$$ if (qident.eq.'axis2') axis2=vhulp -c$$$ if (qident.eq.'axis3') axis3=vhulp -c$$$ if (qident.eq.'cutof2') cutof2=vhulp -c$$$ if (qident.eq.'cutof3') cutof3=vhulp -c$$$ if (qident.eq.'mdtemp') tsetor=vhulp -c$$$ if (qident.eq.'mdtem2') tset2=vhulp -c$$$ if (qident.eq.'mdpres') pset=vhulp*0.001 -c$$$ if (qident.eq.'tincr') tincr=vhulp -c$$$ if (qident.eq.'tstep') tstep=vhulp -c$$$* if (qident.eq.'lowtap') swa=vhulp !Moved to force field -c$$$* if (qident.eq.'uptap') swb=vhulp !Moved to force field -c$$$ if (qident.eq.'tdamp1') taut=vhulp -c$$$ if (qident.eq.'tdamp2') taut2=vhulp -c$$$ if (qident.eq.'ntdamp') ndtau=int(vhulp) -c$$$ if (qident.eq.'pdamp1') taup=vhulp -c$$$ if (qident.eq.'tdhoov') vqnd=vhulp -c$$$ if (qident.eq.'achoov') errnh=vhulp/100.0 -c$$$ if (qident.eq.'range') range=vhulp -c$$$ if (qident.eq.'nmdit') maxstp=int(vhulp) -c$$$ if (qident.eq.'nmdeqi') nequi=int(vhulp) -c$$$ if (qident.eq.'imdmet') nmethod=int(vhulp) -c$$$ if (qident.eq.'icharg') ncha=int(vhulp) - nchaold=ncha -c$$$ if (qident.eq.'ichaen') ncha2=int(vhulp) -c$$$ if (qident.eq.'ichupd') nchaud=int(vhulp) -c$$$ if (qident.eq.'iout1') nrep1=int(vhulp) -c$$$ if (qident.eq.'iout2') nsav=int(vhulp) -c$$$ if (qident.eq.'icheck') ntest=int(vhulp) -c$$$ if (qident.eq.'ivels') nvel=int(vhulp) -c$$$ if (qident.eq.'itfix') ntscale=int(vhulp) -c$$$ if (qident.eq.'irecon') ncontrol=int(vhulp) -c$$$ if (qident.eq.'iout3') noutpt=int(vhulp) -c$$$ if (qident.eq.'iappen') napp=int(vhulp) -c$$$ if (qident.eq.'isurpr') nsurp=int(vhulp) -c$$$ if (qident.eq.'itdmet') ncons=int(vhulp) -c$$$ if (qident.eq.'iravel') nrand=int(vhulp) -c$$$ if (qident.eq.'imetho') nmm=int(vhulp) -c$$$ if (qident.eq.'endmm') endpo=vhulp - endpoold=endpo -c$$$ if (qident.eq.'endmd') endpo2=vhulp -c$$$ if (qident.eq.'imaxmo') nfc=int(vhulp) - nfcold=nfc -c$$$ if (qident.eq.'iout4') nsav2=int(vhulp) -c$$$ if (qident.eq.'imaxit') nmmax=int(vhulp) - nmmaxold=nmmax -c$$$ if (qident.eq.'iout5') i5758=int(vhulp) -c$$$ if (qident.eq.'parsca') parc1=vhulp -c$$$ if (qident.eq.'parext') parc2=vhulp -c$$$ if (qident.eq.'icelop') icell=int(vhulp) - icellold=icell -c$$$ if (qident.eq.'igeopt') ingeo=int(vhulp) -c$$$ if (qident.eq.'celopt') ccpar=vhulp -c$$$ if (qident.eq.'icelo2') icelo2=int(vhulp) - icelo2old=icelo2 -c$$$ if (qident.eq.'ideve1') nrdd=int(vhulp) -c$$$ if (qident.eq.'ideve2') nrddf=int(vhulp) -c$$$ if (qident.eq.'ibiola') nbiolab=int(vhulp) -c$$$c if (qident.eq.'igeofo') ngeofor=int(vhulp) -c$$$ if (qident.eq.'iincop') nincrop=int(vhulp) -c$$$ if (qident.eq.'accerr') accincr=vhulp -c$$$ if (qident.eq.'iout6') nsav3=int(vhulp) -c$$$ if (qident.eq.'irten') nhop2=int(vhulp) -c$$$ if (qident.eq.'npreit') nprevrun=int(vhulp) -c$$$ if (qident.eq.'idebug') ndebug=int(vhulp) -c$$$ if (qident.eq.'volcha') volcha=vhulp -c$$$ if (qident.eq.'ixmolo') ixmolo=int(vhulp) -c$$$ if (qident.eq.'inpt') inpt=int(vhulp) -c$$$ if (qident.eq.'iconne') iconne=int(vhulp) -c$$$ if (qident.eq.'imolde') imolde=int(vhulp) -c$$$ if (qident.eq.'ianaly') ianaly=int(vhulp) -c$$$ if (qident.eq.'icentr') icentr=int(vhulp) -c$$$ if (qident.eq.'itrans') itrans=int(vhulp) -c$$$ if (qident.eq.'itrout') itrout=int(vhulp) -c$$$ if (qident.eq.'nvlist') nvlist=int(vhulp) -c$$$ if (qident.eq.'vrange') vrange=vhulp -c$$$ if (qident.eq.'vlbora') vlbora=vhulp -c$$$ if (qident.eq.'tpnrad') tpnrad=vhulp -c$$$ if (qident.eq.'ityrad') ityrad=int(vhulp) -c$$$ if (qident.eq.'iexx') iexx=int(vhulp) -c$$$ if (qident.eq.'iexy') iexy=int(vhulp) -c$$$ if (qident.eq.'iexz') iexz=int(vhulp) -c$$$ if (qident.eq.'syscha') syscha=vhulp -c$$$ if (qident.eq.'inmov1') inmov1=int(vhulp) -c$$$ if (qident.eq.'inmov2') inmov2=int(vhulp) -c$$$ if (qident.eq.'itstep') itstep=int(vhulp) -c$$$ if (qident.eq.'ifreq') ifreq=int(vhulp) -c$$$ if (qident.eq.'isymm') isymm=int(vhulp) -c$$$ if (qident.eq.'icpres') icpres=int(vhulp) -c$$$ if (qident.eq.'delvib') delvib=vhulp -c$$$ goto 10 -c$$$ 20 continue - close (10) - axis(1)=axis1 - axis(2)=axis2 - axis(3)=axis3 - if (axiss(1).gt.zero) then - axis(1)=axiss(1) - axis(2)=axiss(2) - axis(3)=axiss(3) - end if - if (tincr.lt.0.0001.and.tincr.gt.-0.0001) tset=tsetor - iequi=1 - if (nequi.gt.0) iequi=0 - if (iopt.eq.1.and.napp.eq.1) then - stop 'No fort.7 and fort.8 append with iopt=1 !' - end if - if (mdstep.gt.0.or.nit.gt.0) nmm=nmmsav - if (mdstep.gt.0.and.itstep.eq.1) then - tstepmax=tstep - tstep=tstep*(tsetor/tempmd) - if (tstep.gt.tstepmax) tstep=tstepmax - end if - tstep=1.0d-15*tstep - taus=taut - taut=1.0d-15*taut - taut2=1.0d-15*taut2 - taup=1.0d-15*taup - ts2=tstep/2.0 - ts22=tstep*ts2 - return - 30 continue - write (*,*)'Error reading control-file' - stop 'Error reading control-file' -************************************************************************ -* * -* Format part * -* * -************************************************************************ - 1050 format (f7.3) - 1055 format (f7.4) - 1056 format (f9.4) - 1060 format (i8) - 1070 format (f7.5) - end -************************************************************************ -************************************************************************ - - subroutine staint - -************************************************************************ -#include "cbka.blk" -#include "cbkdcell.blk" -#include "cbkqa.blk" -#include "control.blk" -#include "small.blk" -#include "cbkc.blk" -#include "cbkconst.blk" - dimension bvt(nat,4) -************************************************************************ -* * -* Generate cartesian coordinates from internal coordinate input * -* * -************************************************************************ -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In staint' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - k=0 - 10 read (3,1200,end=20,err=20)(ijk(k+1,k1),k1=1,3),k2,qa(k+1), - $bvt(k+1,3),bvt(k+1,2),bvt(k+1,1) - qlabel(k+1)=qa(k+1) - qresi1(k+1)=' ' - qresi2(k+1)=' ' - qresi3(k+1)=' ' - qffty(k+1)=' ' - if (k2.ne.k+1) then - write (*,*)'Wrong order in internal coordinates at atom:',k2 - goto 20 -* stop 'Wrong order in internal coordinates' - end if - k=k+1 - if (k.gt.nat) then - write (*,*)na,nat - stop 'Maximum number of atoms exceeded' - end if - goto 10 - 20 continue - na=k - -************************************************************************ -* * -* CALCULATION OF CARTESIAN COORDINATES FROM INTERNAL COORDINAATES * -* * -************************************************************************ - - 12 C(1,1)=ZERO - C(1,2)=ZERO - C(1,3)=ZERO - C(2,1)=BVT(2,1) - C(2,2)=ZERO - C(2,3)=ZERO - HR=(BVT(3,2)-90.0D0)*DGRRDN - C(3,1)=C(2,1)+BVT(3,1)*SIN(HR) - C(3,2)=BVT(3,1)*COS(HR) - C(3,3)=ZERO - DO 32 K1=4,NA - J=IJK(K1,2) - KB=K1-1 - XH=C(J,1) - YH=C(J,2) - ZH=C(J,3) - DO 13 K2=1,KB - C(K2,1)=C(K2,1)-XH - C(K2,2)=C(K2,2)-YH - C(K2,3)=C(K2,3)-ZH - DO 13 K3=1,3 - 13 IF (ABS(C(K2,K3)).LT.1.0D-15) C(K2,K3)=1.0D-15 - K=IJK(K1,3) - P2=C(K,2)*C(K,2)+C(K,3)*C(K,3) - IF (P2.NE.ZERO) THEN - P=SQRT(P2) - Q=SQRT(C(K,1)*C(K,1)+P2) - SA=C(K,2)/P - CA=C(K,3)/P - SB=-C(K,1)/Q - CB=P/Q - ELSE - SA=ZERO - CA=ONE - SB=ONE - CB=ZERO - ENDIF - DO 16 K2=1,KB - AZ=C(K2,1) - BZ=C(K2,2) - C(K2,1)=AZ*CB+BZ*SB*SA+C(K2,3)*SB*CA - C(K2,2)=BZ*CA-C(K2,3)*SA - 16 C(K2,3)=-AZ*SB+BZ*CB*SA+C(K2,3)*CB*CA - IF (C(K,3).LE.ZERO) THEN - DO 17 K2=1,KB - 17 C(K2,3)=-C(K2,3) - ENDIF - I=IJK(K1,1) - IF (1.0D5*ABS(C(I,1)).LE.ABS(C(I,2))) THEN - T1=HALF*PI - ELSE - YX=ABS(C(I,2)/C(I,1)) - T1=ATAN(YX) - ENDIF - IF (C(I,1).GE.ZERO.AND.C(I,2).LT.ZERO) T1=TWO*PI-T1 - IF (C(I,1).LT.ZERO.AND.C(I,2).GE.ZERO) T1=PI-T1 - IF (C(I,1).LT.ZERO.AND.C(I,2).LT.ZERO) T1=T1+PI - DO 31 K2=1,KB - IF (C(K2,1).EQ.ZERO.AND.C(K2,2).EQ.ZERO) GOTO 31 - IF (1.0D5*ABS(C(K2,1)).LT.ABS(C(K2,2))) THEN - T2=HALF*PI - ELSE - YX=ABS(C(K2,2)/C(K2,1)) - T2=ATAN(YX) - ENDIF - IF (C(K2,1).GE.ZERO.AND.C(K2,2).LT.ZERO) T2=TWO*PI-T2 - IF (C(K2,1).LT.ZERO.AND.C(K2,2).GE.ZERO) T2=PI-T2 - IF (C(K2,1).LT.ZERO.AND.C(K2,2).LT.ZERO) T2=T2+PI - T3=T2-T1 - IF (T3.LT.ZERO)T3=T3+TWO*PI - RZ=SQRT(C(K2,1)*C(K2,1)+C(K2,2)*C(K2,2)) - C(K2,1)=RZ*COS(T3) - C(K2,2)=RZ*SIN(T3) - 31 CONTINUE - HR=(BVT(K1,2)-90.0D0)*DGRRDN - HT=BVT(K1,3)*DGRRDN - CHR=COS(HR) - C(K1,1)=BVT(K1,1)*CHR*COS(HT) - C(K1,2)=BVT(K1,1)*CHR*SIN(HT) - 32 C(K1,3)=C(IJK(K1,3),3)+BVT(K1,1)*SIN(HR) - - return - 1200 FORMAT(4I3,1X,A2,3F10.5,4X,I1,F10.5) - end -************************************************************************ -************************************************************************ - - subroutine outint - -************************************************************************ -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkbo.blk" -#include "cbkconst.blk" -#include "cbkia.blk" -#include "cbkinit.blk" -#include "cbknubon2.blk" -#include "cbkqa.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "small.blk" -#include "cbksrtbon1.blk" -************************************************************************ -* * -* Output internal coordinates * -* * -************************************************************************ - dimension dvdc(3,3),dargdc(3,3) -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In outint' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - write (91,50)qmol - open (82,file='output.MOP',status='unknown') - write (82,*) - write (82,'(a40)')qmol - write (82,*) - close (82) - -* IF (NMOLO.GT.1) THEN -* WRITE(6,*)' OUTPUT INTERNAL COORDINATES NOT POSSIBLE FOR ', -* $'CALCULATION ON MORE THAN ONE MOLECULE' -* RETURN -* END IF - -************************************************************************ -* * -* Output of internal coordinates. * -* First 3 atoms of other input file. * -* * -************************************************************************ - N1=1 - N2=2 - N3=3 -C open (82,file='output.MOP',status='unknown',access='append') - write(91,100)N1,qa(n1) - write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n1), - $zero,nzero,zero,nzero,zero,nzero,nzero,nzero,nzero - call dista2(n1,n2,rr,dx,dy,dz) - write(91,200)N1,N2,qa(n2),RR - write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n2), - $rr,none,zero,nzero,zero,nzero,n1,nzero,nzero - close (82) - - call dista2(n2,n3,rr,dx,dy,dz) - hv=zero - call calvalres(n1,n2,n3,arg,hv,dvdc,dargdc) - WRITE(91,300)N1,N2,N3,qa(n3),rdndgr*HV,RR -C open (82,file='output.MOP',status='unknown',access='append') - write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(n3), - $rr,none,rdndgr*hv,none,zero,nzero,n2,n1,nzero - close (82) - - naih=3 - - do i1=naih+1,na - bomax=zero - j1=0 - do i2=1,ia(i1,2) - iob=ia(i1,2+i2) - ncubo=nubon2(i1,i2) - if (bo(ncubo).gt.bomax.and.iob.lt.i1) then - bomax=bo(ncubo) - j1=iob - end if - end do - if (j1.eq.0) j1=i1-1 - call dista2(j1,i1,rr,dx,dy,dz) - - bomax=zero - j2=0 - do i2=1,ia(j1,2) - iob=ia(j2,2+i2) - ncubo=nubon2(j1,i2) - if (bo(ncubo).gt.bomax.and.iob.lt.i1.and. - $abo(iob).gt.bo(ncubo)+0.2) then - bomax=bo(ncubo) - j2=iob - end if - end do - if (j2.eq.0) j2=i1-2 - if (j2.eq.j1) j2=j2+1 - - call calvalres(j2,j1,i1,arg,hh,dvdc,dargdc) - - bomax=zero - j3=0 - do i2=1,ia(j2,2) - iob=ia(j2,2+i2) - ncubo=nubon2(j2,i2) - if (bo(ncubo).gt.bomax.and.iob.lt.i1.and.iob.ne.j1) then - bomax=bo(ncubo) - j3=iob - end if - end do - if (j3.eq.0) j3=i1-3 - if (j3.eq.j2.and.j3.ne.j1-1) j3=j3+1 - if (j3.eq.j2.and.j3.ne.j1-2) j3=j3+2 - if (j3.eq.j1.and.j3.ne.j2-1) j3=j3+1 - if (j3.eq.j1.and.j3.ne.j2-2) j3=j3+2 - - call caltor(j3,j2,j1,i1,ht) - - write(91,400)j3,j2,j1,i1,qa(i1),ht,rdndgr*hh,rr -C open (82,file='output.MOP',status='unknown',access='append') - write(82,'(2x,a2,f12.6,i3,f12.6,i3,f12.6,i3,1x,3i4)')qa(i1), - $rr,none,rdndgr*hh,none,ht,none,j1,j2,j3 - close (82) - end do - - close(82) - return - 50 format (' I',2x,a60) - 100 FORMAT(9X,I3,1x,a2) - 200 FORMAT(6X,2I3,1x,a2,20X,F10.5) - 300 FORMAT(3X,3I3,1x,a2,10X,2F10.5) - 400 FORMAT(4I3,1x,a2,3F10.5) - - end -************************************************************************ -************************************************************************ - - subroutine outres - -************************************************************************ -#include "cbka.blk" -#include "cbkbo.blk" -#include "cbkch.blk" -#include "cbkd.blk" -#include "cbkenergies.blk" -#include "cbkh.blk" -#include "cbkimove.blk" -#include "cbkrbo.blk" -#include "cbktorang.blk" -#include "cbktorsion.blk" -#include "cbktregime.blk" -#include "cbkvalence.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" -#include "cbkinit.blk" - -************************************************************************ -* * -* Output molecular data * -* * -************************************************************************ - dimension isort(100),iad1(100),iad2(100),iad3(100),iad4(100) - character*60 qm2 -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In outres' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - read (9,100,end=50)idata,qm2 -* if (qm2.ne.qmol) then -* write (*,*)'Wrong molecule in outres-file' -* write (*,*)qmol -* write (*,*)qm2 -* return -* end if - do 25 i1=1,idata - read (9,200)isort(i1),iad1(i1),iad2(i1),iad3(i1),iad4(i1) - ndata2=ndata2+1 - - if (isort(i1).eq.1) then -* do i2=1,nbon -* if (ib(i2,2).eq.iad1(i1).and.ib(i2,3).eq.iad2(i1)) then -* if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),rbo(i2) -* caldat(ndata2)=rbo(i2) -* end if -* end do - call dista2(iad1(i1),iad2(i1),dish,dx,dy,dz) - write (81,*)iad1(i1),iad2(i1),dish - caldat(ndata2)=dish - end if - - if (isort(i1).eq.2) then - do i2=1,nval - if (iv(i2,2).eq.iad1(i1).and.iv(i2,3).eq.iad2(i1).and. - $iv(i2,4).eq.iad3(i1)) then - if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1), - $iad3(i1),h(i2)*rdndgr - caldat(ndata2)=h(i2)*rdndgr - end if - end do - end if - - if (isort(i1).eq.3) then - do i2=1,ntor - if (it(i2,2).eq.iad1(i1).and.it(i2,3).eq.iad2(i1).and. - $it(i2,4).eq.iad3(i1).and.it(i2,5).eq.iad4(i1)) then - if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),iad3(i1),iad4(i1), - $abs(thg(i2)) - caldat(ndata2)=abs(thg(i2)) - end if - end do - end if - - if (isort(i1).eq.4) then - if (iopt.ne.1) write (81,*)estrmin - caldat(ndata2)=estrmin - end if - - if (isort(i1).eq.5) then - if (iopt.ne.1) write (81,*)estrmin - caldat(ndata2)=estrmin - end if - - if (isort(i1).eq.6) then - if (iopt.ne.1) write (81,*)iad1(i1),axiss(iad1(i1)) - caldat(ndata2)=axiss(iad1(i1)) - end if - - if (isort(i1).eq.7) then - if (iopt.ne.1) write (81,*)eco - caldat(ndata2)=eco - end if - - if (isort(i1).eq.8) then - do i2=1,nbon - if (ib(i2,2).eq.iad1(i1).and.ib(i2,3).eq.iad2(i1)) then - if (iopt.ne.1) write (81,*)iad1(i1),iad2(i1),bo(i2) - caldat(ndata2)=bo(i2) - end if - end do - end if - - if (isort(i1).eq.9) then - if (iopt.ne.1) write (81,*)ch(iad1(i1)) - caldat(ndata2)=ch(iad1(i1)) - end if - - if (isort(i1).eq.10) then - rmsg=0.0 - nmovh=0 - do i2=1,na - do i3=1,3 - rmsg=rmsg+imove(i2)*d(i3,i2)*d(i3,i2) - nmovh=nmovh+imove(i2) - end do - end do - rmsg=sqrt(rmsg/float(nmovh*3)) - - if (iopt.ne.1) write (81,*)rmsg - caldat(ndata2)=rmsg - end if - - if (isort(i1).eq.11) then - if (iopt.ne.1) write (81,*)1000.0*pressu - caldat(ndata2)=1000.0*pressu - end if - - 25 continue - - 50 return -************************************************************************ -* * -* Format part * -* * -************************************************************************ - 100 format (i3,a60) - 200 format (5i3) - end -************************************************************************ -************************************************************************ - - subroutine readgeo - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkdistan.blk" -#include "cbkinit.blk" -#include "cbkqa.blk" -#include "cbksrtbon1.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" - character*80 qromb - character*25 qfileh -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readgeo' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - if (ngeofor.eq.-1) return - -********************************************************************** -* * -* Read in system geometry * -* * -********************************************************************** - if (ngeofor.eq.0) then - call readdelphi (qfileh,iend,naold) - namov=na - end if - - if (ngeofor.eq.1) then - call readbgf(iend,naold) - end if - - - - if (ngeofor.eq.2) then -********************************************************************** -* * -* Read in free format (xmol) geometry * -* * -********************************************************************** - qr='1' - read (3,'(i6)')na - namov=na - read (3,'(a60)')qmol - do i1=1,na - read (3,'(a80)')qromb - ifirstchar=80 - do i2=1,80 - if (qromb(i2:i2).ne.' '.and.i2.lt.ifirstchar) ifirstchar=i2 - end do - read (qromb(ifirstchar:80),'(a2)')qa(i1) - read (qromb(ifirstchar+2:80),*)c(i1,1),c(i1,2),c(i1,3) - qlabel(i1)=qa(i1) - qresi1(i1)=' ' - qresi2(i1)=' ' - qresi3(i1)=' ' - qffty(i1)=' ' - end do - ibity=1 - axiss(1)=-1.0 - end if - - - if (ngeofor.eq.3) then -********************************************************************** -* * -* Read in ChemDraw CC1-file * -* * -********************************************************************** - qr='1' - read (3,*)na - namov=na - read (3,'(a60)')qmol - do i1=1,na - read (3,'(2x,a2,5x,3f12.6)')qa(i1),c(i1,1),c(i1,2),c(i1,3) - end do - end if - - if (ngeofor.eq.4) then -********************************************************************** -* * -* Read in .pdb-format * -* * -********************************************************************** - qr='C' - call readpdb(iendf) - namov=na - ibity=1 - axiss(1)=-1.0 - qfile(nprob)=qmol - if (iendf.eq.1) stop 'End-of-file while reading in .pdb' - end if - -********************************************************************** -* * -* Set up periodic system * -* * -********************************************************************** - axis(1)=axiss(1) - axis(2)=axiss(2) - axis(3)=axiss(3) - angle(1)=angles(1) - angle(2)=angles(2) - angle(3)=angles(3) - if (axiss(1).lt.zero) then - axis(1)=axis1 - axis(2)=axis2 - axis(3)=axis3 - angle(1)=90.0 - angle(2)=90.0 - angle(3)=90.0 - end if - halfa=angle(1)*dgrrdn - hbeta=angle(2)*dgrrdn - hgamma=angle(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axis(1)*sinbet*sinphi - tm21=axis(1)*sinbet*cosphi - tm31=axis(1)*cosbet - tm22=axis(2)*sinalf - tm32=axis(2)*cosalf - tm33=axis(3) - - return - end -************************************************************************ -************************************************************************ - - subroutine readdelphi (qfileh,iend,naold) - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkdcell.blk" -#include "cbkdistan.blk" -#include "cbkff.blk" -#include "cbkh.blk" -#include "cbkinit.blk" -#include "cbkqa.blk" -#include "cbkrestr.blk" -#include "cbksrtbon1.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" - character*25 qfileh -********************************************************************** -* * -* Read in geometries in Delphi-format (xyz) * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readdelphi' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - if (imodfile.eq.1) then - open (3,file=qfileh,status='old') - end if - nmmax=nmmaxold - nfc=nfcold - ibity=1 - iredo=1 - endpo=endpoold - icell=icellold - icelo2=icelo2old - iend=0 - read (3,1000,end=900)qr,qmol -********************************************************************** -* * -* Read in restraint information (optional) * -* * -********************************************************************** - if (qr.eq.'R'.or.qr.eq.'P'.or.qr.eq.'X') then - qmol=qmol(7:60) - qmolset(nuge)=qmol - read (18,1070,end=4,err=4) nrestra - do i1=1,nrestra - read (18,1090)irstra(i1,1),irstra(i1,2),rrstra(i1),vkrstr(i1), - $vkrst2(i1),rrcha(i1) - end do - 4 continue - end if -********************************************************************** -* * -* Read in torsion restraint information (optional) * -* * -********************************************************************** - if (qr.eq.'T'.or.qr.eq.'X') then - if (qr.eq.'T') then - qmol=qmol(7:60) - qmolset(nuge)=qmol - end if - read (28,1070,end=6,err=6) nrestrat - do i1=1,nrestrat - read (28,1091)irstrat(i1,1),irstrat(i1,2),irstrat(i1,3), - $irstrat(i1,4),trstra(i1),vkrt(i1),vkr2t(i1),rtcha(i1) - end do - 6 continue - end if -********************************************************************** -* * -* Read in valency angle restraint information (optional) * -* * -********************************************************************** - if (qr.eq.'V') then - qmol=qmol(7:60) - qmolset(nuge)=qmol - read (38,1070,end=7,err=7) nrestrav - do i1=1,nrestrav - read (38,1092)irstrav(i1,1),irstrav(i1,2),irstrav(i1,3), - $vrstra(i1),vkrv(i1),vkr2v(i1) - end do - 7 continue - end if -********************************************************************** -* * -* Read in geometry * -* * -********************************************************************** - ibh2=0 - iequi=1 - iexco=0 - if (nequi.gt.0) iequi=0 - axiss(1)=-1.0 - - if (qr.eq.'O'.or.qr.eq.'L') stop 'Not xyz-format' - - if (qr.eq.'I') then !Delphi internal coordinates - if (nsurp.ge.2) stop 'Int.coordinates only with 1 gemetry' - call staint - goto 20 - end if - - if (qr.eq.'B') then !Previous geometry with volume reduction - read (3,*) - vred=(1.0-0.01*volcha)**(0.33333) - iexco=1 - na=naold - do i1=1,3 - qmol=qmol - axiss(i1)=vred*axis(i1) - angles(i1)=angle(i1) - do i2=1,na - c(i2,i1)=vred*c(i2,i1) - end do - end do - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - ibity=2 - - goto 20 - end if - - if (qr.eq.'S') then !Previous geometry with volume expansion - read (3,*) - vexp=(1.0+0.01*volcha)**(0.33333) - na=naold - iexco=1 - do i1=1,3 - qmol=qmol - axiss(i1)=vexp*axis(i1) - angles(i1)=angle(i1) - do i2=1,na - c(i2,i1)=vexp*c(i2,i1) - end do - end do - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - ibity=2 - - goto 20 - end if - - if (qr.eq.'F'.or.qr.eq.'Y'.or.qr.eq.'3'.or.qr.eq.'5'. - $or.qr.eq.'P') then - kx=0 - ky=0 - kz=0 - ibity=2 - read(3,1005)axiss(1),axiss(2),axiss(3) - read(3,1005)angles(1),angles(2),angles(3) - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - - end if - - if (qr.eq.'M'.or.qr.eq.'A') then - nmmsav=nmm - nmm=2 - end if - - if (qr.eq.'A') nmm=1 - - if (qr.eq.'D') then - endpo=endpo/25 - nmmax=nmmax*5 - qruid='HIGH PRECISION' - end if - - if (qr.eq.'H') then - nmmax=nmmax/10 - qruid='LOW PRECISION' - end if - - if (qr.eq.'1'.or.qr.eq.'5') then - nmm=1 - nmmax=1 - qruid='SINGLE POINT' - end if - - if (qr.eq.'Y') then - icell=0 - qruid='NO CELL OPT' - end if - - 10 read (3,1100,end=20,err=20)ir,qa(na+1),(c(na+1,i2),i2=1,3) - qlabel(na+1)=qa(na+1) - qresi1(na+1)=' ' - qresi2(na+1)=' ' - qresi3(na+1)=' ' - qffty(na+1)=' ' - if (ir.eq.0) goto 20 - na=na+1 - - if (na.gt.nat) then - write (*,*)'Maximum number of atom exceeded ',na,nat - stop 'Maximum number of atoms exceeded' - end if - - goto 10 - 20 continue - - if (imodfile.eq.1) close (3) - - return - 900 iend=1 - return - 1000 format (2x,a1,1x,a60) - 1005 format (3f10.4) - 1070 format (i3) - 1090 format (2i4,2f8.4,f8.6,f10.8) - 1091 format (4i4,2f8.4,3f8.6) - 1092 format (3i4,2f8.4,2f8.6) - 1100 format (i4,1x,a2,3x,3d22.15,1x,a5,1x,i5) - end -************************************************************************ -************************************************************************ - - subroutine readbgf(iendf,naold) - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkcha.blk" -#include "cbkcharmol.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkdcell.blk" -#include "cbkdistan.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkh.blk" -#include "cbkimove.blk" -#include "cbkinit.blk" -#include "cbkqa.blk" -#include "cbkrestr.blk" -#include "cbksrtbon1.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" - character*80 qromb - character*2 qrom - character*5 quen - character*5 qlabhulp - character*25 qfileh - character*200 qhulp -********************************************************************** -* * -* Read in BIOGRAF-geometry * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readbgf' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - iendf=0 - ienread=0 - iredo=0 - qremark(1)=' ' - enmol=zero - formol=zero -c$$$ if (imodfile.eq.1) then -c$$$ open (3,file=qfileh,status='old') -c$$$ end if - open (3,file='fort.3',status='old') - read (3,'(a40)',end=900)qromb - ibity=0 - if (qromb(1:6).eq.'BIOGRF') ibity=1 - if (qromb(1:6).eq.'XTLGRF') ibity=2 - if (ibity.eq.0) then - write (*,*)qromb(1:6) - stop 'Unknown Biograf-file' - end if - read (qromb,'(6x,i4)')ibgfversion - if (ibity.eq.1) qr='C' - if (ibity.eq.2) qr='F' - iremark=0 - iformat=0 - iline=0 - iexco=0 - iruid=1 - vvol=1.0 - nmcharge=0 - nmmax=nmmaxold - nfc=nfcold - ncha=nchaold - endpo=endpoold - icell=icellold - icelo2=icelo2old - axiss(1)=-1.0 - - 30 read (3,'(a200)',end=46,err=40)qhulp - qstrana1(1:200)=qhulp - iline=iline+1 - irecog=0 - - if (qhulp(1:6).eq.'DESCRP') then - read (qhulp,'(7x,a40)',end=46,err=46)qmol - irecog=1 - end if - - if (qhulp(1:6).eq.'REMARK') then - if (iremark.lt.20) iremark=iremark+1 - read (qhulp,'(7x,a40)',end=46,err=46)qremark(iremark) - irecog=1 - end if - - if (qhulp(1:6).eq.'FORMAT') then - if (iformat.lt.20) iformat=iformat+1 - read(qhulp,'(7x,a40)',end=46,err=46)qformat(iformat) - irecog=1 - end if - - if (qhulp(1:7).eq.'VCHANGE') then - read (qhulp(8:60),*)vvol - vred=(1.0+(vvol-1.0))**(0.33333333) - iexco=1 - na=naold - qmol=qmol - do i1=1,3 - axiss(i1)=vred*axis(i1) - angles(i1)=angle(i1) - do i2=1,na - cglobal(i2,i1)=vred*cglobal(i2,i1) - end do - end do - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - ibity=2 - irecog=1 - end if - - if (qhulp(1:7).eq.'VCHANGX') then - read (qhulp(8:60),*)vvol - vred=vvol - iexco=1 - na=naold - qmol=qmol - do i1=1,3 - axiss(i1)=axis(i1) - angles(i1)=angle(i1) - do i2=1,na - cglobal(i2,i1)=cglobal(i2,i1) - end do - end do - - axiss(1)=vred*axiss(1) - do i2=1,na - cglobal(i2,1)=vred*cglobal(i2,1) - end do - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - ibity=2 - irecog=1 - end if - - if (qhulp(1:7).eq.'VCHANGY') then - read (qhulp(8:60),*)vvol - vred=vvol - iexco=1 - na=naold - qmol=qmol - do i1=1,3 - axiss(i1)=axis(i1) - angles(i1)=angle(i1) - do i2=1,na - cglobal(i2,i1)=cglobal(i2,i1) - end do - end do - - axiss(2)=vred*axiss(2) - do i2=1,na - cglobal(i2,2)=vred*cglobal(i2,2) - end do - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - ibity=2 - irecog=1 - end if - - if (qhulp(1:7).eq.'VCHANGZ') then - read (qhulp(8:60),*)vvol - vred=vvol - iexco=1 - na=naold - qmol=qmol - - do i1=1,3 - axiss(i1)=axis(i1) - angles(i1)=angle(i1) - do i2=1,na - cglobal(i2,i1)=cglobal(i2,i1) - end do - end do - - axiss(3)=vred*axiss(3) - do i2=1,na - cglobal(i2,3)=vred*cglobal(i2,3) - end do - - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - ibity=2 - irecog=1 - end if - - if (qhulp(1:6).eq.'CRYSTX') then - read (qhulp,'(8x,6f11.5)',end=46,err=46)axiss(1), - $axiss(2),axiss(3),angles(1),angles(2),angles(3) - kx=0 - ky=0 - kz=0 - halfa=angles(1)*dgrrdn - hbeta=angles(2)*dgrrdn - hgamma=angles(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axiss(1)*sinbet*sinphi - tm21=axiss(1)*sinbet*cosphi - tm31=axiss(1)*cosbet - tm22=axiss(2)*sinalf - tm32=axiss(2)*cosalf - tm33=axiss(3) - kx=int(2.0*swb/tm11) - ky=int(2.0*swb/tm22) - kz=int(2.0*swb/tm33) - qr='F' - if (nmmax.eq.1.and.nmmaxold.gt.1) qr='5' - if (icell.eq.0.and.icellold.gt.0) qr='Y' - ibity=2 - irecog=1 - end if - - if (qhulp(1:6).eq.'PERIOD') then - read (qhulp,'(7x,i3)',end=46,err=46)iperiod - irecog=1 - end if - - if (qhulp(1:4).eq.'AXES') then - read (qhulp,'(7x,a3)',end=46,err=46)qbgfaxes - irecog=1 - end if - - if (qhulp(1:6).eq.'SGNAME') then - read (qhulp,'(7x,a3)',end=46,err=46)qbgfsgn - irecog=1 - end if - -* if (qhulp(1:5).eq.'CELLS') then -* read (qhulp,'(7x,*)',end=40,err=40)kx,ky,kz -* irecog=1 -* end if - - if (qhulp(1:6).eq.'HETATM') then - if (ibgfversion.lt.400) then - read (qhulp, - $'(7x,i5,1x,a5,1x,a3,1x,a1,1x,a5,3f10.5,1x,a5,i3,i2,1x,f8.5)' - $,end=40,err=40) - $ir,qlabel(na+1),qresi1(na+1),qresi2(na+1),qresi3(na+1), - $cglobal(na+1,1),cglobal(na+1,2), - $cglobal(na+1,3),qffty(na+1),ibgr1(na+1),ibgr2(na+1), - $chgglobal(na+1) - else - stop 'Unsupported Biograf-version' - end if - qlabhulp=qlabel(na+1) - if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:5) - if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:4) - if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:3) - if (qlabhulp(1:1).eq.'C ') qa(na+1)='C ' - if (qlabhulp(1:2).eq.'Ca') qa(na+1)='Ca' - if (qlabhulp(1:2).eq.'Cl') qa(na+1)='Cl' - if (qlabhulp(1:2).eq.'Cu') qa(na+1)='Cu' - if (qlabhulp(1:2).eq.'Co') qa(na+1)='Co' - if (qlabhulp(1:1).eq.'H ') qa(na+1)='H ' - if (qlabhulp(1:2).eq.'He') qa(na+1)='He' - if (qlabhulp(1:1).eq.'N ') qa(na+1)='N ' - if (qlabhulp(1:2).eq.'Ni') qa(na+1)='Ni' - if (qlabhulp(1:1).eq.'O ') qa(na+1)='O ' - if (qlabhulp(1:1).eq.'B ') qa(na+1)='B ' - if (qlabhulp(1:1).eq.'F ') qa(na+1)='F ' - if (qlabhulp(1:2).eq.'Fe') qa(na+1)='Fe' - if (qlabhulp(1:1).eq.'P ') qa(na+1)='P ' - if (qlabhulp(1:1).eq.'S ') qa(na+1)='S ' - if (qlabhulp(1:1).eq.'Y ') qa(na+1)='Y ' - if (qlabhulp(1:2).eq.'Al ') qa(na+1)='Al' - if (qlabhulp(1:2).eq.'Au ') qa(na+1)='Au' - if (qlabhulp(1:2).eq.'Si') qa(na+1)='Si' - if (qlabhulp(1:2).eq.'Pt') qa(na+1)='Pt' - if (qlabhulp(1:2).eq.'Mo') qa(na+1)='Mo' - if (qlabhulp(1:2).eq.'Mg') qa(na+1)='Mg' - if (qlabhulp(1:2).eq.'Ar') qa(na+1)='Ar' - if (qlabhulp(1:2).eq.'Zr') qa(na+1)='Zr' - if (qlabhulp(1:2).eq.'Ti') qa(na+1)='Ti' - if (qlabhulp(1:2).eq.'Ru') qa(na+1)='Ru' - if (qlabhulp(1:2).eq.'Ba') qa(na+1)='Ba' - if (qlabhulp(1:2).eq.'Bi') qa(na+1)='Bi' - if (qlabhulp(1:2).eq.'Li') qa(na+1)='Li' - if (qlabhulp(1:2).eq.'V ') qa(na+1)='V ' - if (qlabhulp(1:2).eq.'X ') qa(na+1)='X ' - na=na+1 - if (na.gt.nattot) then - write (*,*)'Number of atoms:read ',na - write (*,*)'Maximum number of atoms: ',nattot - stop - $'Maximum number of atoms exceeded; increase nattot in cbka.blk' - end if - irecog=1 - end if - - if (qhulp(1:6).eq.'RUTYPE') then !run-type identifiers - irecrun=0 - read (qhulp,'(7x,a40)',end=46,err=46)qruid - - if (qruid(1:10).eq.'NORMAL RUN') then - iruid=0 - irecrun=1 - end if - - if (qruid(1:14).eq.'HIGH PRECISION') then - endpo=endpo/25 - nmmax=nmmax*5 - qr='D' - iruid=1 - irecrun=1 - end if - - if (qruid(1:13).eq.'LOW PRECISION') then - nmmax=nmmax/10 - qr='H' - iruid=1 - irecrun=1 - end if - - if (qruid(1:12).eq.'SINGLE POINT') then - iruid=1 - nmmax=1 - qr='1' - if (ibity.eq.2) qr='5' - irecrun=1 - end if - - if (qruid(1:11).eq.'NO CELL OPT') then - iruid=1 - icell=0 - if (ibity.eq.2) qr='Y' - irecrun=1 - end if - - if (qruid(1:8).eq.'CELL OPT') then - iruid=1 - icell=1 - iexco=0 !Override from VCHANGE - read (qruid,'(8x,i6)',end=46,err=46)ncellopt - if (ncellopt.eq.2) icell=2 !cell optimisation during energy minimisation - if (ncellopt.eq.3) icelo2=4 !c/a optimisation - if (ncellopt.eq.4) icelo2=1 !only a optimisation - if (ncellopt.eq.5) icelo2=2 !only b optimisation - if (ncellopt.eq.6) icelo2=3 !only c optimisation - if (ncellopt.eq.7) then - icelo2=4 !c/a optimisation - icell=2 !cell optimisation during energy minimisation - end if - if (ibity.eq.2) qr='F' - irecrun=1 - end if - - if (qruid(1:6).eq.'MAXMOV') then - iruid=1 - read (qruid,'(6x,i6)',end=46,err=46)nfc - irecrun=1 - end if - - if (qruid(1:4).eq.'REDO') then - iruid=1 - read (qruid,'(4x,i6)',end=46,err=46)iredo - irecrun=1 - end if - - if (qruid(1:5).eq.'MAXIT') then - iruid=1 - read (qruid,'(6x,i6)',end=46,err=46)nmmax - if (qruid(14:18).eq.'ENDPO') then - read (qruid,'(18x,f6.3)',end=46,err=46)endpo - end if - irecrun=1 - end if - if (qruid(1:5).eq.'ENDPO') then - iruid=1 - read (qruid,'(6x,f6.3)',end=46,err=46)endpo - irecrun=1 - end if - - if (qruid(1:9).eq.'CHARGEMET') then - iruid=1 - read (qruid,'(9x,i6)',end=46,err=46)ncha - irecrun=1 - end if - - if (irecrun.eq.0) then - write (*,*)'Warning: ignored RUTYPE identifier ',qruid(1:12) - end if - - irecog=1 - end if - - if (qhulp(1:14).eq.'BOND RESTRAINT') then - nrestra=nrestra+1 - istart=15 - call stranal(istart,iend,vout,iout,1) - irstra(nrestra,1)=iout - istart=iend - call stranal(istart,iend,vout,iout,1) - irstra(nrestra,2)=iout - istart=iend - call stranal(istart,iend,vout,iout,1) - rrstra(nrestra)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - vkrstr(nrestra)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - vkrst2(nrestra)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - rrcha(nrestra)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - itstart(nrestra)=iout - istart=iend - call stranal(istart,iend,vout,iout,1) - itend(nrestra)=iout - istart=iend -* read (qhulp,'(15x,2i4,f8.4,f8.2,f8.5,f10.7)',end=46,err=46) -* $irstra(nrestra,1),irstra(nrestra,2),rrstra(nrestra), -* $vkrstr(nrestra),vkrst2(nrestra),rrcha(nrestra) - qr='R' - irecog=1 - end if - - if (qhulp(1:15).eq.'ANGLE RESTRAINT') then - nrestrav=nrestrav+1 - read (qhulp,'(16x,3i4,2f8.2,f8.4,f9.6)',end=46,err=46) - $irstrav(nrestrav,1),irstrav(nrestrav,2),irstrav(nrestrav,3), - $vrstra(nrestrav),vkrv(nrestrav),vkr2v(nrestrav), - $rvcha(nrestrav) - qr='V' - irecog=1 - end if - - if (qhulp(1:17).eq.'TORSION RESTRAINT') then - nrestrat=nrestrat+1 - read (qhulp,'(18x,4i4,2f8.2,f8.4,f9.6)',end=46,err=46) - $irstrat(nrestrat,1),irstrat(nrestrat,2),irstrat(nrestrat,3), - $irstrat(nrestrat,4),trstra(nrestrat),vkrt(nrestrat), - $vkr2t(nrestrat),rtcha(nrestrat) - qr='T' - irecog=1 - end if - - if (qhulp(1:16).eq.'MASCEN RESTRAINT') then - nrestram=nrestram+1 - istart=17 - call stranal(istart,iend,vout,iout,1) - istart=iend - irstram(nrestram,1)=0 - if (qstrana2.eq.'x') irstram(nrestram,1)=1 - if (qstrana2.eq.'y') irstram(nrestram,1)=2 - if (qstrana2.eq.'z') irstram(nrestram,1)=3 - if (qstrana2.eq.'p') irstram(nrestram,1)=4 !fixed center of mass - if (irstram(nrestram,1).eq.0) - $stop 'Error in mass centre restraint' - call stranal(istart,iend,vout,iout,1) - istart=iend - irstram(nrestram,2)=iout - call stranal(istart,iend,vout,iout,1) - istart=iend - irstram(nrestram,3)=iout - call stranal(istart,iend,vout,iout,1) - istart=iend - rmstra1(nrestram)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - if (irstram(nrestram,1).le.3) irstram(nrestram,4)=iout - if (irstram(nrestram,1).eq.4) rmstra2(nrestram)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - if (irstram(nrestram,1).le.3) irstram(nrestram,5)=iout - if (irstram(nrestram,1).eq.4) rmstra3(nrestram)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - if (irstram(nrestram,1).le.3) rmstra2(nrestram)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - if (irstram(nrestram,1).le.3) rmstra3(nrestram)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - if (irstram(nrestram,1).le.3) rmcha(nrestram)=vout - irecog=1 - end if - - if (qhulp(1:9).eq.'MOLCHARGE') then - nmcharge=nmcharge+1 - istart=10 - call stranal(istart,iend,vout,iout,1) - istart=iend - iat1mc(nmcharge)=iout - call stranal(istart,iend,vout,iout,1) - istart=iend - iat2mc(nmcharge)=iout - call stranal(istart,iend,vout,iout,1) - istart=iend - vmcha(nmcharge)=vout - irecog=1 - end if - - if (qhulp(1:8).eq.'FIXATOMS') then - istart=9 - call stranal(istart,iend,vout,iout,1) - if1=iout - istart=iend - call stranal(istart,iend,vout,iout,1) - if2=iout - do i12=if1,if2 - imove(i12)=0 - end do - irecog=1 - end if - - if (qhulp(1:11).eq.'UNIT ENERGY') then - eenconv=zero - read (qhulp,'(14x,a5)',end=46,err=46)quen - if (quen.eq.'eV') eenconv=23.0408 - if (quen.eq.'EV') eenconv=23.0408 - if (quen.eq.'ev') eenconv=23.0408 - if (quen.eq.'h') eenconv=627.5 - if (quen.eq.'H') eenconv=627.5 - if (quen.eq.'kcal') eenconv=1.0 - if (quen.eq.'kCal') eenconv=1.0 - if (quen.eq.'KCAL') eenconv=1.0 - if (eenconv.eq.zero) then - write (*,*)quen,': unknown energy unit; assuming kcal/mol' - eenconv=1.0 - end if - irecog=1 - end if - - if (qhulp(1:6).eq.'ENERGY') then - read (qhulp(7:80),*,end=46,err=46)enmol - ienread=1 - irecog=1 - end if - - if (qhulp(1:6).eq.'GEOUPD') then - icgeopt(nprob)=0 - icgeo=0 - irecog=1 - end if - - if (qhulp(1:9).eq.'NO GEOUPD') then - icgeopt(nprob)=1 - icgeo=1 - irecog=1 - end if - - if (qhulp(1:9).eq.'FREQUENCY') then - ifreqset(nprob)=1 - ifreq=1 - irecog=1 - end if - -* if (qhulp(1:5).eq.'FORCE') then -* read (qhulp(6:80),*,end=46,err=46)formol -* ienread=1 -* irecog=1 -* end if - - if (qhulp(1:6).eq.'FFIELD') goto 30 - if (qhulp(1:6).eq.'CONECT') goto 30 - if (qhulp(1:5).eq.'ORDER') goto 30 - if (qhulp(1:1).eq.'#') goto 30 - if (qhulp(1:3).eq.'END') goto 45 - - if (irecog.eq.0) then - write (*,*)'Warning: ignored line starting with: ',qhulp(1:10) - end if - - goto 30 - - 40 write (*,*)'Error on line ',iline+1,' of Biograf-input' - stop - 45 read (3,*,err=46,end=46) - 46 continue - if (ienread.eq.1) then - if (eenconv.eq.zero) then - write (*,*)'No energy unit given; assuming kcal/mol' - eenconv=1.0 - end if - enmol=enmol*eenconv !Convert energies to kcal/mol - end if - - namov=0 !calculate number of moving atoms - do i1=1,na - if (imove(i1).eq.1) namov=namov+1 - end do - - if (imodfile.eq.1) close (3) - return - 900 iendf=1 - return - end -************************************************************************ -************************************************************************ - - subroutine readpdb (iendf) - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkqa.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" -#include "cbksrtbon1.blk" - character*200 qhulp -********************************************************************** -* * -* Read in .pdb-geometry * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readpdb' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - iendf=1 - qmol='pdb_in' - 5 read (3,'(a200)',end=10,err=900) qhulp - qstrana1(1:200)=qhulp - istart=1 - call stranal(istart,iend,vout,iout,1) - istart=iend - - if (qstrana2(1:6).eq.'HEADER') then - call stranal(istart,iend,vout,iout,1) - istart=iend - qmol=qstrana2(1:20) - end if - - if (qstrana2(1:6).eq.'HETATM'.or.qstrana2(1:4).eq.'ATOM') then - call stranal(istart,iend,vout,iout,1) - istart=iend - call stranal(istart,iend,vout,iout,1) - istart=iend - qa(na+1)=qstrana2(1:2) - call stranal(istart,iend,vout,iout,1) - istart=iend - call stranal(istart,iend,vout,iout,1) - istart=iend - call stranal(istart,iend,vout,iout,1) - istart=iend - c(na+1,1)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - c(na+1,2)=vout - call stranal(istart,iend,vout,iout,1) - istart=iend - c(na+1,3)=vout - na=na+1 - end if - - if (qstrana2(1:3).eq.'END'.or.qstrana2(2:4).eq.'END') then - iendf=0 - goto 10 - end if - - goto 5 - 10 continue - return - 900 write (*,*)'Error reading in .pdb-format' - stop 'Error reading in .pdb-format' - end -************************************************************************ -************************************************************************ - - subroutine readtreg - -************************************************************************ -#include "cbka.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "small.blk" - dimension isumattreg(mtreg) - character*200 qrom -********************************************************************** -* * -* Read in temperature regime * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readtreg' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - ntrc=0 - open (19,file='tregime.in',status='old',err=60) - 10 read (19,'(a200)',end=50,err=900)qrom - qstrana1(1:200)=qrom - if (qrom(1:1).eq.'#') goto 10 - istart=1 - ntrc=ntrc+1 - if (ntrc.gt.mtreg) then - write (*,*)'Too many temperature regimes in tregime.in;', - $' inrease mtreg in cbka.blk' - stop 'Too many temperature regimes in tregime.in' - end if - call stranal(istart,iend,vout,iout,1) - nittc(ntrc)=iout - istart=iend - - if (ntrc.gt.1) then - if (nittc(ntrc).lt.nittc(ntrc-1)) then - ntrc=ntrc-1 - write (*,*)'Warning: wrong order or empty line in tregime.in' - write (*,*)'Ignored lines below iteration:',nittc(ntrc) - goto 50 - end if - end if - - call stranal(istart,iend,vout,iout,1) - nntreg(ntrc)=iout - if (nntreg(ntrc).gt.mtzone) then - write (*,*)'Too many temperature zones in tregime.in;', - $' inrease mtzone in cbka.blk' - stop 'Too many temperature zones in tregime.in' - end if - istart=iend - isumattreg(ntrc)=0 - do i1=1,nntreg(ntrc) - call stranal(istart,iend,vout,iout,1) - ia1treg(ntrc,i1)=iout - istart=iend - call stranal(istart,iend,vout,iout,1) - ia2treg(ntrc,i1)=iout - istart=iend - isumattreg(ntrc)=isumattreg(ntrc)+1+ia2treg(ntrc,i1)- - $ia1treg(ntrc,i1) - call stranal(istart,iend,vout,iout,1) - tsettreg(ntrc,i1)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - tdamptreg(ntrc,i1)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - dttreg(ntrc,i1)=vout - istart=iend - end do - goto 10 - 50 continue - close (19) - 60 continue -********************************************************************** -* * -* Check consistency temperature programs in tregime.in * -* * -********************************************************************** - if (ntrc.gt.0) then - do i1=1,ntrc - if (isumattreg(i1).ne.na) then - write (*,*)'Inconsistency in temperature regime nr.',i1 - write (*,*)'Number of atoms defined in tregime.in:', - $isumattreg(i1) - write (*,*)'Number of atoms in system:',na - stop 'Inconsistency in tregime.in' - end if - end do - end if - - return - 900 stop 'Error reading tregime.in' - end -************************************************************************ -************************************************************************ - - subroutine readvreg - -************************************************************************ -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkvregime.blk" -#include "control.blk" - character*200 qrom -********************************************************************** -* * -* Read in volume regime * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readvreg' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - nvrc=0 - open (19,file='vregime.in',status='old',err=60) - 10 read (19,'(a200)',end=50,err=900)qrom - qstrana1(1:200)=qrom - if (qrom(1:1).eq.'#') goto 10 - istart=1 - nvrc=nvrc+1 - if (nvrc.gt.mvreg) then - write (*,*)'Too many volume regimes in vregime.in;', - $' inrease mvreg in cbka.blk' - stop 'Too many volume regimes in vregime.in' - end if - - call stranal(istart,iend,vout,iout,1) - nitvc(nvrc)=iout - istart=iend - - if (nvrc.gt.1) then - if (nitvc(nvrc).lt.nitvc(nvrc-1)) then - nvrc=nvrc-1 - write (*,*)'Warning: wrong order or empty line in vregime.in' - write (*,*)'Ignored lines below iteration:',nitvc(nvrc) - goto 50 - end if - end if - - call stranal(istart,iend,vout,iout,1) - nnvreg(nvrc)=iout - if (nnvreg(nvrc).gt.mvzone) then - write (*,*)'Too many volume regimes in vregime.in;', - $' inrease mvzone in cbka.blk' - stop 'Too many volume zones in vregime.in' - end if - istart=iend - do i1=1,nnvreg(nvrc) - call stranal(istart,iend,vout,iout,1) - if (qstrana2(1:1).ne.'a'.and.qstrana2(1:1).ne.'b'.and. - $qstrana2(1:1).ne.'c'.and.qstrana2(1:4).ne.'alfa'.and. - $qstrana2(1:4).ne.'beta'.and.qstrana2(1:5).ne.'gamma') then - write (*,*)qstrana2 - write (*,*)'Invalid cell parameter type in vregime.in ;', - $' use a,b,c,alfa,beta or gamma' - stop 'Invalid cell parameter type in vregime.in' - end if - qvtype(nvrc,i1)=qstrana2 - istart=iend - call stranal(istart,iend,vout,iout,1) - dvvreg(nvrc,i1)=vout - istart=iend - call stranal(istart,iend,vout,iout,1) - ivsca(nvrc,i1)=1 - if (qstrana2(1:1).eq.'n') ivsca(nvrc,i1)=0 - istart=iend - end do - goto 10 - 50 continue - close (19) - 60 continue - return - 900 stop 'Error reading vregime.in' - end -************************************************************************ -************************************************************************ - - subroutine readereg - -************************************************************************ -#include "cbka.blk" -#include "cbkeregime.blk" -#include "control.blk" - character*200 qrom -********************************************************************** -* * -* Read in electric field regime * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readereg' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - nerc=0 - open (19,file='eregime.in',status='old',err=60) - 10 read (19,'(a200)',end=50,err=900)qrom - qstrana1(1:200)=qrom - if (qrom(1:1).eq.'#') goto 10 - istart=1 - nerc=nerc+1 - if (nerc.gt.mereg) then - write (*,*)'Too many electric field regimes in eregime.in;', - $' inrease mereg in cbka.blk' - stop 'Too many electric field regimes in eregime.in' - end if - call stranal(istart,iend,vout,iout,1) - nitec(nerc)=iout - - if (nerc.gt.1) then - if (nitec(nerc).lt.nitec(nerc-1)) then - nerc=nerc-1 - write (*,*)'Warning: wrong order or empty line in eregime.in' - write (*,*)'Ignored lines below iteration:',nitec(nerc) - goto 50 - end if - end if - - istart=iend - call stranal(istart,iend,vout,iout,1) - nnereg(nerc)=iout - if (nnereg(nerc).gt.mezone) then - write (*,*)'Too many electric field zones in eregime.in;', - $' inrease mezone in cbka.blk' - stop 'Too many electric field zones in vregime.in' - end if - istart=iend - do i1=1,nnereg(nerc) - call stranal(istart,iend,vout,iout,1) - if (qstrana2(1:1).ne.'x'.and.qstrana2(1:1).ne.'y'.and. - $qstrana2(1:1).ne.'z') then - write (*,*)qstrana2 - write (*,*)'Invalid field direction in eregime.in ;', - $' use x,y or z' - stop 'Invalid field direction in eregime.in' - end if - qetype(nerc,i1)=qstrana2 - istart=iend - call stranal(istart,iend,vout,iout,1) - ereg(nerc,i1)=vout - istart=iend - end do - goto 10 - 50 continue - close (19) - 60 continue - return - 900 stop 'Error reading vregime.in' - end -************************************************************************ -************************************************************************ - - subroutine readaddmol - -************************************************************************ -#include "cbka.blk" -#include "cbkatomcoord.blk" -#include "cbkc.blk" -#include "cbkff.blk" -#include "cbkh.blk" -#include "control.blk" - character*80 qromb - character*200 qhulp - character*5 qlabhulp -********************************************************************** -* * -* Read in molecule coordinates. This molecule will be added to * -* the system at regular intervals * -* Accepts only .bgf-format * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readaddmol' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -********************************************************************** -* * -* Set default values * -* * -********************************************************************** - iaddfreq=-1 !frequency of molecule addition; <0: no addition - xadd=-9000.0 !x-coordinate for added molecule; <-5000.0: random - yadd=-9000.0 !y-coordinate for added molecule; <-5000.0: random - zadd=-9000.0 !z-coordinate for added molecule; <-5000.0: random - iveladd=1 !1: random initial velocities; 2: read in velocities - !from addmol.vel - addist=-1.00 !Minimum distance between added molecule and rest - !of system. < 0.0: do not check - nadattempt=10 !Number of attempts at adding the molecule - taddmol=-1.0 !Temperature added molecule. <0.0: system temperature - open (19,file='addmol.bgf',status='old',err=60) - read (19,'(a40)',end=900,err=900)qromb - if (qromb(1:6).ne.'BIOGRF') then - write (*,*)'addmol.bgf should start with BIOGRF' - stop 'addmol.bgf should start with BIOGRF' - end if - naa=0 - iline=0 - 30 read (19,'(a200)',end=900,err=900)qhulp - irecog=0 - iline=iline+1 - - if (qhulp(1:6).eq.'DESCRP') then - irecog=1 - end if - - if (qhulp(1:6).eq.'FORMAT') then - irecog=1 - end if - - if (qhulp(1:6).eq.'REMARK') then - irecog=1 - end if - - if (qhulp(1:6).eq.'HETATM') then - irecog=1 - read (qhulp,'(7x,i5,1x,a5,1x,3x,1x,1x,1x,5x,3f10.5)' - $,end=900,err=900) - $ir,qlabhulp,cadd(naa+1,1),cadd(naa+1,2),cadd(naa+1,3) - if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:5) - if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:4) - if (qlabhulp(1:1).eq.' ') qlabhulp=qlabhulp(2:3) - if (qlabhulp(1:1).eq.'C ') qadd(naa+1)='C ' - if (qlabhulp(1:2).eq.'Ca') qadd(naa+1)='Ca' - if (qlabhulp(1:2).eq.'Cl') qadd(naa+1)='Cl' - if (qlabhulp(1:2).eq.'Cu') qadd(naa+1)='Cu' - if (qlabhulp(1:2).eq.'Co') qadd(naa+1)='Co' - if (qlabhulp(1:1).eq.'H ') qadd(naa+1)='H ' - if (qlabhulp(1:2).eq.'He') qadd(naa+1)='He' - if (qlabhulp(1:1).eq.'N ') qadd(naa+1)='N ' - if (qlabhulp(1:2).eq.'Ni') qadd(naa+1)='Ni' - if (qlabhulp(1:1).eq.'O ') qadd(naa+1)='O ' - if (qlabhulp(1:1).eq.'B ') qadd(naa+1)='B ' - if (qlabhulp(1:1).eq.'F ') qadd(naa+1)='F ' - if (qlabhulp(1:2).eq.'Fe') qadd(naa+1)='Fe' - if (qlabhulp(1:1).eq.'P ') qadd(naa+1)='P ' - if (qlabhulp(1:1).eq.'S ') qadd(naa+1)='S ' - if (qlabhulp(1:1).eq.'Y ') qadd(naa+1)='Y ' - if (qlabhulp(1:2).eq.'Al') qadd(naa+1)='Al' - if (qlabhulp(1:2).eq.'Au') qadd(naa+1)='Au' - if (qlabhulp(1:2).eq.'Si') qadd(naa+1)='Si' - if (qlabhulp(1:2).eq.'Pt') qadd(naa+1)='Pt' - if (qlabhulp(1:2).eq.'Mo') qadd(naa+1)='Mo' - if (qlabhulp(1:2).eq.'Mg') qadd(naa+1)='Mg' - if (qlabhulp(1:2).eq.'Ar') qadd(naa+1)='Ar' - if (qlabhulp(1:2).eq.'Zr') qadd(naa+1)='Zr' - if (qlabhulp(1:2).eq.'Ba') qadd(naa+1)='Ba' - if (qlabhulp(1:2).eq.'X ') qadd(naa+1)='X ' - ityadd(naa+1)=0 - do i1=1,nso !Find force field type - if (qadd(naa+1).eq.qas(i1)) ityadd(naa+1)=i1 - end do - if (ityadd(naa+1).eq.0) then - write (*,*) 'Unknown atom type:',qadd(naa+1) - stop 'Unknown atom type' - end if - naa=naa+1 - end if - - if (qhulp(1:7).eq.'FREQADD') then - irecog=1 - read (qhulp,'(8x,i6)',end=900,err=900) iaddfreq - end if - - if (qhulp(1:6).eq.'VELADD') then - irecog=1 - read (qhulp,'(8x,i6)',end=900,err=900) iveladd - end if - - if (qhulp(1:6).eq.'STARTX') then - irecog=1 - read (qhulp,'(7x,f8.2)',end=900,err=900) xadd - end if - - if (qhulp(1:6).eq.'STARTY') then - irecog=1 - read (qhulp,'(7x,f8.2)',end=900,err=900) yadd - end if - - if (qhulp(1:6).eq.'STARTZ') then - irecog=1 - read (qhulp,'(7x,f8.2)',end=900,err=900) zadd - end if - - if (qhulp(1:6).eq.'ADDIST') then - irecog=1 - read (qhulp,'(7x,f8.2)',end=900,err=900) addist - end if - - if (qhulp(1:8).eq.'NATTEMPT') then - irecog=1 - read (qhulp,'(9x,i6)',end=900,err=900) nadattempt - end if - - if (qhulp(1:7).eq.'TADDMOL') then - irecog=1 - read (qhulp,'(8x,f8.2)',end=900,err=900) taddmol - end if - - if (qhulp(1:6).eq.'FFIELD') goto 30 - if (qhulp(1:6).eq.'CONECT') goto 30 - if (qhulp(1:5).eq.'ORDER') goto 30 - if (qhulp(1:1).eq.'#') goto 30 - if (qhulp(1:3).eq.'END') goto 45 - - if (irecog.eq.0) then - write (*,*)'Warning: ignored line starting with: ',qhulp(1:10) - end if - - goto 30 - - 45 continue - close (19) - if (iveladd.eq.2) then - open (19,file='addmol.vel',status='old',err=800) - read (19,*) - read (19,'(3d24.15)',err=850,end=850) - $((veladd(j,i),j=1,3),i=1,naa) - close (19) - end if -************************************************************************ -* * -* Place molecule at origin * -* * -************************************************************************ - ccx=0.0 - ccy=0.0 - ccz=0.0 - do i1=1,naa - ccx=ccx+cadd(i1,1)/float(naa) - ccy=ccy+cadd(i1,2)/float(naa) - ccz=ccz+cadd(i1,3)/float(naa) - end do - do i1=1,naa - cadd(i1,1)=cadd(i1,1)-ccx - cadd(i1,2)=cadd(i1,2)-ccy - cadd(i1,3)=cadd(i1,3)-ccz - end do - - 60 continue - return - 800 stop 'Error opening addmol.vel' - 850 stop 'Error or end of file reading addmol.vel' - 900 write (*,*)'Error or end-of-file reading addmol.bgf on line:', - $iline - return - end -************************************************************************ -********************************************************************** - - subroutine writegeo(nunit1) - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkqa.blk" -#include "cbkrestr.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" -#include "cbksrtbon1.blk" -#include "cbkinit.blk" -********************************************************************** -* * -* Copy new geometries to unit nunit1 * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In writegeo' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - if (axiss(1).lt.zero) then - if (nrestra.eq.0.and.nrestrat.eq.0.and. - $nrestrav.eq.0) - $write (nunit1,300)qr,qmol - if (nrestra.gt.0) write (nunit1,301)qr, - $rrstra(1),qmol - if (nrestrav.gt.0) write (nunit1,301)qr, - $vrstra(1),qmol - if (nrestrat.gt.0) write (nunit1,301)qr, - $trstra(1),qmol - else - write (nunit1,310)qr,qmol - write (nunit1,320)axiss(1),axiss(2),axiss(3) - write (nunit1,320)angles(1),angles(2),angles(3) - end if - do i1=1,na - if (nbiolab.ne.1) write (nunit1,400)i1,qa(i1),(c(i1,i2),i2=1,3) - if (nbiolab.eq.1) write (nunit1,401)i1,qa(i1),(c(i1,i2),i2=1,3) !Delphi-format - end do - if (nbiolab.ne.1) write (nunit1,*) - - return - - 300 format (2x,a1,1x,a60) - 301 format (2x,a1,1x,f6.2,a60) - 310 format (2x,a1,1x,a60) - 320 format (3f10.4) - 400 format (i4,1x,a2,3x,3(d21.14,1x),1x,a5,1x,i5) - 401 format (i3,2x,a2,3x,3(d21.14,1x),1x,a5,1x,i5) - end -********************************************************************** -********************************************************************** - - subroutine writebgf(nunit1) - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkcha.blk" -#include "cbkcharmol.blk" -#include "cbkconst.blk" -#include "cbkenergies.blk" -#include "cbkia.blk" -#include "cbkimove.blk" -#include "cbkinit.blk" -#include "cbkqa.blk" -#include "cbkrestr.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "cbksrtbon1.blk" -#include "small.blk" - - dimension qdir(3) - character*2 qt - character*1 qdir -********************************************************************** -* * -* Copy new Biograf-geometries to unit nunit1 * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In newbgf' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - irom=1 - qdir(1)='x' - qdir(2)='y' - qdir(3)='z' - ibgfversion=200 - if (ibity.eq.1) write (nunit1,1500)ibgfversion - if (ibity.eq.2) write (nunit1,1600)ibgfversion -* if (qr.ne.'F'.and.qr.ne.'5'.and.qr.ne.'Y') -* $write (nunit1,1500)ibgfversion -* if (qr.eq.'F'.or.qr.eq.'5'.or.qr.eq.'Y') -* $write (nunit1,1600)ibgfversion - write (nunit1,1700)qmol -* write (nunit1,1700)qkeyw(nprob) - do i1=1,iremark - write (nunit1,1800)qremark(i1) - end do - qruid='NORMAL RUN' - if (iruid.eq.0) then - write (nunit1,2000) - else - if (abs(endpo-endpoold).gt.1e-5) write (nunit1,2010)endpo - if (nmmax.ne.nmmaxold) write (nunit1,2020)nmmax - if (nfc.ne.nfcold) write (nunit1,2030)nfc - if (ncha.ne.nchaold) write (nunit1,2036)ncha - if (iredo.gt.1) write (nunit1,2035)iredo - if (icell.ne.icellold) then - if (icell.eq.0) write (nunit1,2033) - if (icell.gt.0) write (nunit1,2034)ncellopt - end if - end if - if (iexco.ne.0.and.nsurp.gt.0) then - write (nunit1,2040)vvol - write (nunit1,3500) - write (nunit1,*) - return - end if - if (nmcharge.gt.0) then - do i3=1,nmcharge - write (nunit1,2050)iat1mc(i3),iat2mc(i3),vmcha(i3) - end do - end if - - ims=0 - do i1=1,na - if (ims.eq.0.and.imove(i1).eq.0) then - if1=i1 - ims=1 - end if - if (ims.eq.1.and.imove(i1).eq.1) then - write (nunit1,2060)if1,i1-1 - ims=0 - end if - end do - if (ims.eq.1) then - write (nunit1,2060)if1,na - end if - -* if (qr.eq.'F'.or.qr.eq.'5'.or.qr.eq.'Y') - if (ibity.eq.2) - $write (nunit1,2100)axiss(1),axiss(2),axiss(3),angles(1), - $angles(2),angles(3) - - if (nrestra.gt.0) write (nunit1,2300) - do i2=1,nrestra - write (nunit1,2400) - $irstra(i2,1),irstra(i2,2),rrstra(i2), - $vkrstr(i2),vkrst2(i2),rrcha(i2),itstart(i2),itend(i2) - end do - - if (nrestrav.gt.0) write (nunit1,2500) - do i2=1,nrestrav - write (nunit1,2600) - $irstrav(i2,1),irstrav(i2,2),irstrav(i2,3), - $vrstra(i2),vkrv(i2),vkr2v(i2),zero - end do - - if (nrestrat.gt.0) write (nunit1,2700) - do i2=1,nrestrat - write (nunit1,2800) - $irstrat(i2,1),irstrat(i2,2),irstrat(i2,3), - $irstrat(i2,4),trstra(i2),vkrt(i2), - $vkr2t(i2),zero - end do - - if (nrestram.gt.0) write (nunit1,2810) - do i2=1,nrestram - write (nunit1,2820) - $qdir(irstram(i2,1)),irstram(i2,2),irstram(i2,3), - $rmstra1(i2),irstram(i2,4),irstram(i2,5),rmstra2(i2), - $rmstra3(i2),rmcha(i2) - end do - - if (icgeo.eq.0.and.ingeo.eq.0) write (nunit1,2830) - if (icgeo.eq.1.and.ingeo.eq.1) write (nunit1,2840) - if (ifreq.eq.1) write (nunit1,2850) - write (nunit1,2900) - do i2=1,na - write (nunit1,3000)i2,qa(i2),c(i2,1),c(i2,2),c(i2,3), - $qa(i2),irom,irom,chgbgf(i2) - end do - write (nunit1,3100) - if (nsurp.lt.2) then - do i1=1,na - write (nunit1,3200)i1,(iag(i1,2+i2),i2=1,iag(i1,2)) - end do - write (nunit1,3300) - write (nunit1,3400)estrc - end if - - write (nunit1,3500) - write (nunit1,*) - - return - 1500 format ('BIOGRF',i4) - 1600 format ('XTLGRF',i4) - 1700 format ('DESCRP ',a60) - 1800 format ('REMARK ',a60) - 1900 format ('FFIELD ',a40) - 2000 format ('RUTYPE NORMAL RUN') - 2010 format ('RUTYPE ENDPO',f6.3) - 2020 format ('RUTYPE MAXIT',i6) - 2030 format ('RUTYPE MAXMOV',i6) - 2033 format ('RUTYPE NO CELL OPT') - 2034 format ('RUTYPE CELL OPT',i6) - 2035 format ('RUTYPE REDO',i6) - 2036 format ('RUTYPE CHARGEMET',i6) - 2040 format ('VCHANGE',f8.4) - 2050 format ('MOLCHARGE',2i4,f6.2) - 2060 format ('FIXATOMS',2i6) - 2100 format ('CRYSTX ',6f11.5) - 2200 format ('CELLS ',6i5) - 2300 format ('# At1 At2 R12 Force1 Force2 ', - $'dR12/dIter(MD) Start (MD) End (MD)') - 2400 format ('BOND RESTRAINT ',2i4,f8.4,f8.2,f8.4,1x,f10.7,2i8) - 2500 format ('# At1 At2 At3 Angle Force1 Force2', - $' dAngle/dIteration (MD only)') - 2600 format ('ANGLE RESTRAINT ',3i4,2f8.2,f8.4,f9.6) - 2700 format ('# At1 At2 At3 At3 Angle Force1 ', - $'Force2 dAngle/dIteration (MD only)') - 2800 format ('TORSION RESTRAINT ',4i4,2f8.2,f8.4,f9.6) - 2810 format ('# x/y/z At1 At2 R At3 At4 Force1', - $' Force2 dR/dIteration (MD only)') - 2820 format ('MASCEN RESTRAINT ',a1,1x,2i4,f8.2,2i4,2f8.2,f9.6) - 2830 format ('GEOUPD') - 2840 format ('NO GEOUPD') - 2850 format ('FREQUENCY') - 2900 format ('FORMAT ATOM (a6,1x,i5,1x,a5,1x,a3,1x,a1,1x,a5,', - $'3f10.5,1x,a5,i3,i2,1x,f8.5)') - 3000 format ('HETATM',1x,i5,1x,a2,3x,1x,3x,1x,1x,1x,5x,3f10.5,1x, - $a5,i3,i2,1x,f8.5) - 3100 format ('FORMAT CONECT (a6,12i6)') - 3200 format ('CONECT',12i6) - 3300 format ('UNIT ENERGY kcal') - 3400 format ('ENERGY',5x,f14.6) - 3500 format ('END') - - end -********************************************************************** -********************************************************************** - - subroutine writeen(tottime,sum1,sdev,sdeva,sum12,sumt,sump, - $sumtt,tmax,eaver,eav2,eav3,etot2,ediff) -********************************************************************** -#include "cbka.blk" -#include "cbkcha.blk" -#include "cbkenergies.blk" -#include "cbkrestr.blk" -#include "cbktorang.blk" -#include "cbktorsion.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "small.blk" - - dimension disres(mrestra) -********************************************************************** -* * -* Write out MD statistics to units 71,73 and 76 * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In writeen' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - if (nrep1.gt.1) - $sdev=sqrt((sum12-sum1*sum1/float(nrep1))/float(nrep1-1)) - eavn=eaver/float(mdstep) - if (mdstep.gt.1) - $sdeva=sqrt((eav3-eav2*eav2/float(mdstep))/float(mdstep-1)) -C open (71,file='fort.71',status='unknown',access='append') -C open (73,file='fort.73',status='unknown',access='append') - write (71,'(i8,2i4,1x,19(f10.2,1x))')mdstep+nprevrun,nmolo, - $nmolo5,estrc,ekin,estrc+ekin,tempmd,sum1/float(nrep1),eavn, - $sumt/float(nrep1),tmax,sump/float(nrep1),sdev,sdeva,tset, - $tstep*1d+15,rmsg,tottime - write (73,'(i8,1x,14(f10.2,1x))')mdstep+nprevrun,eb,ea,elp, - $emol,ev,ecoa,ehb,et,eco,ew,ep,ech,efi - close (71) - close (73) - - if ((sumt/float(nrep1)).gt.tset) then - if (invt.eq.0) write (*,*)'Switched to NVT in iteration',mdstep - invt=1 - end if - -C if (nrestra.gt.0.or.nrestrat.gt.0) -C $open (76,file='fort.76',status='unknown',access='append') - - if (nrestra.gt.0) then - do i2=1,nrestra - call dista2(irstra(i2,1),irstra(i2,2),disres(i2),dx,dy,dz) - end do -C open (76,file='fort.76',status='unknown',access='append') - write (76,'(i8,1x,40f12.4)')mdstep,eres,estrc, - $(rrstra(i2),disres(i2),i2=1,nrestra) - end if - - if (nrestrat.gt.0) then -C open (76,file='fort.76',status='unknown',access='append') - do i2=1,nrestrat - do i3=1,ntor - ih1=irstrat(i2,1) - ih2=irstrat(i2,2) - ih3=irstrat(i2,3) - ih4=irstrat(i2,4) - if (ih1.eq.it(i3,2).and.ih2.eq.it(i3,3).and.ih3.eq.it(i3,4) - $.and.ih4.eq.it(i3,5)) ittr=i3 - end do - write (76,'(i8,1x,40f12.4)')mdstep,eres, - $trstra(i2),thg(ittr) - end do - end if - - if (nrestra.gt.0.or.nrestrat.gt.0) close(76) - - if (nrestram.gt.0) then -C open (76,file='fort.76',status='unknown',access='append') - do i2=1,nrestram - write (76,'(2i8,1x,20f12.4)')mdstep,i2,eres,rmstra1(i2), - $dismacen(i2) - end do - close (76) - end if - - return - end -********************************************************************** -************************************************************************ - - subroutine molanal - -************************************************************************ -#include "cbka.blk" -#include "cbkbo.blk" -#include "cbkconst.blk" -#include "cbkdcell.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkrbo.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" -#include "cbksrtbon1.blk" - dimension iam(nat,mbond+3),nmolata(nmolmax,nat) - dimension molfra(nmolmax,nsort),ndup(nmolmax) - character*40 qmolan1 - character*100 qmolan - logical found -************************************************************************ -* * -* Analyse and output molecular fragments * -* * -************************************************************************ -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In molanal' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - do i1=1,nmolmax - do i2=1,nsort - molfra(i1,i2)=0 - end do - ndup(i1)=1 - end do - - do i1=1,na - do i2=1,mbond+3 - iam(i1,i2)=0 - end do - end do -************************************************************************ -* * -* Create connection table based on corrected bond orders * -* * -************************************************************************ - do i1=1,nbon - if (bo(i1).gt.cutof3) then - j1=ib(i1,2) - j2=ib(i1,3) - iam(j1,2)=iam(j1,2)+1 - iam(j1,2+iam(j1,2))=j2 - iam(j2,2)=iam(j2,2)+1 - iam(j2,2+iam(j2,2))=j1 - end if - end do -********************************************************************** -* * -* Find molecules * -* * -********************************************************************** - nmolo6=0 - found=.FALSE. - DO 61 k1=1,na - IF (iam(K1,3+mbond).EQ.0) found=.TRUE. - 61 IF (iam(K1,3+mbond).GT.nmolo6) nmolo6=iam(K1,3+mbond) - IF (.NOT.FOUND) GOTO 62 -************************************************************************ -* * -* Molecule numbers are assigned. No restrictions are made for the * -* sequence of the numbers in the connection table. * -* * -************************************************************************ - N3=1 - 64 N2=N3 - nmolo6=nmolo6+1 - if (nmolo6.gt.nmolmax) stop 'Too many molecules in system' - iam(N2,3+mbond)=nmolo6 - 67 FOUND=.FALSE. - DO 66 N1=N2+1,na - IF (iam(N1,3+mbond).NE.0) GOTO 66 - DO 65 L=1,mbond - IF (iam(N1,l+2).EQ.0) GOTO 66 - IF (iam(iam(N1,l+2),3+mbond).EQ.nmolo6) THEN - FOUND=.TRUE. - iam(N1,3+mbond)=nmolo6 - GOTO 66 - ENDIF - 65 CONTINUE - 66 CONTINUE - IF (FOUND) GOTO 67 - DO 63 N3=N2+1,NA - 63 if (iam(N3,3+mbond).eq.0) goto 64 -************************************************************************ -* * -* The assigned or input molecule numbers are checked for their * -* consistency. * -* * -************************************************************************ - 62 FOUND=.FALSE. - DO 72 N1=1,NA - DO 71 L=1,mbond - IF (iam(N1,L+2).EQ.0) GOTO 72 - IF (iam(iam(N1,L+2),3+mbond).NE.iam(N1,3+mbond)) THEN - FOUND=.TRUE. - ENDIF - 71 CONTINUE - 72 CONTINUE - IF (FOUND) THEN - write (7,'(i4,a40)')na,qmol - do i1=1,na - write (7,'(40i4)')i1,iam(i1,1),(iam(i1,2+i2),i2=1,nsbmax), - $iam(i1,3+mbond) - end do - STOP' Mol.nrs. not consistent; maybe wrong cell parameters' - ENDIF - - do i1=1,nmolo6 - natmol=0 - do i2=1,na - if (iam(i2,3+mbond).eq.i1) then - natmol=natmol+1 - nmolata(i1,natmol+1)=i2 - end if - end do - nmolata(i1,1)=natmol - end do -************************************************************************ -* * -* Analyze molecules * -* * -************************************************************************ - do i1=1,nmolo6 - do i2=1,nmolata(i1,1) - i3=nmolata(i1,1+i2) - ityp=ia(i3,1) - molfra(i1,ityp)=molfra(i1,ityp)+1 - end do - end do - - do i1=1,nmolo6 - isee=0 - do i2=1,nmolo6 - isee2=1 - do i3=1,nso - if (molfra(i1,i3).ne.molfra(i2,i3)) isee2=0 - end do - if (isee2.eq.1.and.i1.gt.i2.and.isee.eq.0) then !molecule type already exists - ndup(i2)=ndup(i2)+1 - ndup(i1)=0 - isee=1 - end if - - end do - end do - -C open (45,file='molfra.out',status='unknown',access='append') - if (mdstep.eq.0) write (45,100)cutof3 - write (45,110) - ntotmol=0 - ntotat=0 - vtotmass=zero - do i1=1,nmolo6 - if (ndup(i1).gt.0) then -* write (45,110)i1,(molfra(i1,i2),i2=1,nso),ndup(i1) - ntotmol=ntotmol+ndup(i1) - qmolan=' ' - qmolan1=' ' - istart=-4 - ihulp=0 - vmass=zero - do i2=1,nso - vmass=vmass+molfra(i1,i2)*amas(i2) - ntotat=ntotat+molfra(i1,i2)*ndup(i1) - if (molfra(i1,i2).gt.0) then - istart=istart+6 - iend=istart+5 - if (molfra(i1,i2).gt.1) then - write (qmolan(istart:iend),'(a2,i3)')qas(i2),molfra(i1,i2) - else - write (qmolan(istart:iend-2),'(a2)')qas(i2) - end if - end if - end do - ihulp=1 - do i2=1,iend - if (qmolan(i2:i2).ne.' ') then - qmolan1(ihulp:ihulp)=qmolan(i2:i2) - ihulp=ihulp+1 - end if - end do - -* write (45,120)ndup(i1),qmolan(1:iend),vmass - write (45,120)mdstep,ndup(i1),qmolan1,vmass - vtotmass=vtotmass+ndup(i1)*vmass - end if - end do - write (45,*)'Total number of molecules:',ntotmol - write (45,*)'Total number of atoms:',ntotat - write (45,*)'Total system mass:',vtotmass - close (45) - return - 100 format('Bond order cutoff:',f6.4) - 110 format('Iteration Freq. Molecular formula',15x,'Molecular mass') - 120 format(i8,i4,' x ',a35,f10.4) - end -************************************************************************ -************************************************************************ - - subroutine stranal(istart,iend,vout,iout,icheck) - -************************************************************************ -#include "cbka.blk" -#include "cbkconst.blk" -#include "opt.blk" - - character*1 qchar - dimension qchar(5) -********************************************************************** -* * -* Analyze string for special characters; find words in string * -* * -********************************************************************** - qchar(1)=' ' - qchar(2)='/' - - ifound1=0 - do i1=istart,200 - ifound2=0 - do i2=1,icheck - - if (qstrana1(i1:i1).eq.qchar(i2)) then - ifound2=1 - if (ifound1.eq.1) then !End of word - iend=i1 - goto 10 - end if - - end if - - end do - - if (ifound2.eq.0.and.ifound1.eq.0) then !Start of word - istart2=i1 - ifound1=1 - end if - - end do - - 10 continue - qstrana2=' ' - vout=zero - iout=0 - - if (ifound1.eq.1) then - qstrana2=qstrana1(istart2:iend-1) - istart=istart2 - vout=zero - read (qstrana2,*,end=20,err=20) vout - 20 iout=int(vout) - end if - - return - end -************************************************************************ -********************************************************************** - - subroutine dipmom(naold,dpmm,xdip,ydip,zdip,xdir,ydir,zdir) - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkch.blk" -#include "cbkconst.blk" -#include "control.blk" -#include "small.blk" -********************************************************************** -* * -* Calculate and output dipole moment * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In dipmom' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -************************************************************************ -* * -* CONVERSION FACTOR TO DEBYE UNITS IS CALCULATED * -* THE CALCULATION IS INITIALIZED * -* * -************************************************************************ - - ELCHG=1.60217733D-19 ! [C] = [As] - CLIGHT=2.99792458D8 ! [m/s] - DBCONV=ONE/(CLIGHT*ELCHG*1.0D11) - - CHCPX=ZERO - CHCPY=ZERO - CHCPZ=ZERO - CHCMX=ZERO - CHCMY=ZERO - CHCMZ=ZERO - XDIP=ZERO - YDIP=ZERO - ZDIP=ZERO - XGRD=ZERO - YGRD=ZERO - ZGRD=ZERO -************************************************************************ -* * -* CALCULATION OF MAGNITUDE AND CENTRES OF POSITIVE AND NEGATIVE * -* CHARGES * -* * -************************************************************************ - - if (na.eq.0) na=naold - CHRG=ZERO - DO 4 K1=1,NA - CHK1=CH(K1) - IF (CHK1.EQ.ZERO) GOTO 4 - IF (CHK1.LT.ZERO) GOTO 3 - CHRG=CHRG+CHK1 - CHCPX=CHCPX+CHK1*C(K1,1) - CHCPY=CHCPY+CHK1*C(K1,2) - CHCPZ=CHCPZ+CHK1*C(K1,3) - GOTO 4 - 3 CHCMX=CHCMX-CHK1*C(K1,1) - CHCMY=CHCMY-CHK1*C(K1,2) - CHCMZ=CHCMZ-CHK1*C(K1,3) - 4 CONTINUE - -************************************************************************ -* * -* CALCULATION OF DISTANCE BETWEEN CENTRES AND OF DIPOLE MOMENT * -* IN DEBIJE UNITS * -* * -************************************************************************ - - CHDSTX=CHCPX-CHCMX - CHDSTY=CHCPY-CHCMY - CHDSTZ=CHCPZ-CHCMZ - DPMM=SQRT(CHDSTX*CHDSTX+CHDSTY*CHDSTY+CHDSTZ*CHDSTZ)/DBCONV - IF(DPMM.LT.1.0D-4)RETURN - XDIP=HALF*(CHCPX+CHCMX)/CHRG - YDIP=HALF*(CHCPY+CHCMY)/CHRG - ZDIP=HALF*(CHCPZ+CHCMZ)/CHRG - GRTST=MAX(CHDSTX,CHDSTY,CHDSTZ) - XDIR=-CHDSTX/GRTST - YDIR=-CHDSTY/GRTST - ZDIR=-CHDSTZ/GRTST - open (64,file='dipole.out',status='unknown') - write (64,100)dpmm,xdip,ydip,zdip,xdir,ydir,zdir - close (64) - - 100 format ('Dipole moment (Debye):',f12.4,' Location:',3f12.4, - $' Direction (-side):',3f12.4) - return - end -************************************************************************ -********************************************************************** - - subroutine readtraj(ivels) - -********************************************************************** -#include "cbka.blk" -#include "cbkatomcoord.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkdistan.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" -#include "cbkinit.blk" -********************************************************************** -* * -* Read in trajectory file * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In readtraj' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - open(unit=66,file='moldyn.vel',status='old',err=10) - ivels=1 - read (66,*) - read (66,100)aaxis,baxis,caxis - read (66,100)angles(1),angles(2),angles(3) - if (qr.eq.'F'.or.qr.eq.'P'.or.ngeofor.eq.1) then - axis(1)=aaxis - axis(2)=baxis - axis(3)=caxis - axiss(1)=axis(1) - axiss(2)=axis(2) - axiss(3)=axis(3) - angle(1)=angles(1) - angle(2)=angles(2) - angle(3)=angles(3) - halfa=angle(1)*dgrrdn - hbeta=angle(2)*dgrrdn - hgamma=angle(3)*dgrrdn - sinalf=sin(halfa) - cosalf=cos(halfa) - sinbet=sin(hbeta) - cosbet=cos(hbeta) - cosphi=(cos(hgamma)-cosalf*cosbet)/(sinalf*sinbet) - if (cosphi.gt.1.0) cosphi=1.0 - sinphi=sqrt(one-cosphi*cosphi) - tm11=axis(1)*sinbet*sinphi - tm21=axis(1)*sinbet*cosphi - tm31=axis(1)*cosbet - tm22=axis(2)*sinalf - tm32=axis(2)*cosalf - tm33=axis(3) - end if - if (aaxis.ne.axis(1).or.baxis.ne.axis(2).or.caxis.ne.axis(3)) - $stop 'Wrong cell parameters in moldyn.vel' - read (66,200)nan - if (nan.ne.na) stop 'Wrong number of atoms in moldyn.vel-file' - if (nbiolab.eq.1) write (*,*)'Warning: using labels in vels-file' - read (66,250)((c(i,j),j=1,3),qlabel(i),i=1,na) - read (66,*) - read (66,300)((vel(j,i),j=1,3),i=1,na) - read (66,*) - read (66,300)((accel(j,i),j=1,3),i=1,na) - read (66,*) - read (66,300,end=10,err=10)((aold(j,i),j=1,3),i=1,na) - read (66,*) - read (66,300,end=10,err=10)tempmd - read (66,*) - read (66,350,end=10,err=10)nsbma2 - 10 continue -********************************************************************** -* * -* Format part * -* * -********************************************************************** - 100 format(3d15.8) - 200 format(i4) - 250 format(3d24.15,1x,a5) - 300 format(3d24.15) - 350 format(i3) - 400 format (8i3,8f8.4) - return - end -********************************************************************** diff --git a/lib/reax/reax_lammps.F b/lib/reax/reax_lammps.F deleted file mode 100644 index 116e88827d..0000000000 --- a/lib/reax/reax_lammps.F +++ /dev/null @@ -1,392 +0,0 @@ -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -********************************************************************** - - subroutine getswb(swb_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbkff.blk" - real*8 swb_tmp - -********************************************************************** -* * -* Report the value of swb * -* * -********************************************************************** - - swb_tmp = swb - - return - end - -********************************************************************** - - subroutine getswa(swa_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbkff.blk" - real*8 swa_tmp - -********************************************************************** -* * -* Report the value of swa * -* * -********************************************************************** - - swa_tmp = swa - - return - end - -********************************************************************** - - subroutine getvrange(vrange_tmp) - -********************************************************************** -#include "cbka.blk" -#include "control.blk" - real*8 vrange_tmp - -********************************************************************** -* * -* Report the value of vrange * -* * -********************************************************************** - - vrange_tmp = vrange - - return - end - -********************************************************************** - - subroutine getnvlist(nvlist_tmp) - -********************************************************************** -#include "cbka.blk" - integer nvlist_tmp - -********************************************************************** -* * -* Report the value of nvlist * -* * -********************************************************************** - - nvlist_tmp = nvlist - - return - end - -********************************************************************** - - subroutine getvlbora(vlbora_tmp) - -********************************************************************** -#include "cbka.blk" -#include "control.blk" - real*8 vlbora_tmp - -********************************************************************** -* * -* Report the value of vlbora * -* * -********************************************************************** - - vlbora_tmp = vlbora - - return - end - -********************************************************************** - - subroutine getnval(nval_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbkvalence.blk" - integer nval_tmp - -********************************************************************** -* * -* Report the value of nval * -* * -********************************************************************** - - nval_tmp = nval - - return - end - -********************************************************************** - - subroutine getntor(ntor_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbktorsion.blk" - integer ntor_tmp - -********************************************************************** -* * -* Report the value of ntor * -* * -********************************************************************** - - ntor_tmp = ntor - - return - end - - -********************************************************************** - - subroutine getnhb(nhb_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbksrthb.blk" - integer nhb_tmp - -********************************************************************** -* * -* Report the value of nhb * -* * -********************************************************************** - - nhb_tmp = nhb - - return - end - - -********************************************************************** - - subroutine getnbonall(nbonall_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbksrtbon1.blk" - integer nbonall_tmp - -********************************************************************** -* * -* Report the value of nbonall * -* * -********************************************************************** - - nbonall_tmp = nbonall - - return - end - - -********************************************************************** - - subroutine getnneighmax(nneighmax_tmp) - -********************************************************************** -#include "cbka.blk" - integer nneighmax_tmp - -********************************************************************** -* * -* Report the value of nneighmax * -* * -********************************************************************** - - nneighmax_tmp = nneighmax - - return - end - -********************************************************************** - - subroutine getnat(nat_tmp) - -********************************************************************** -#include "cbka.blk" - integer nat_tmp - -********************************************************************** -* * -* Report the value of nat * -* * -********************************************************************** - - nat_tmp = nat - - return - end - -********************************************************************** - - subroutine getnattot(nattot_tmp) - -********************************************************************** -#include "cbka.blk" - integer nattot_tmp - -********************************************************************** -* * -* Report the value of nattot * -* * -********************************************************************** - - nattot_tmp = nattot - - return - end - -********************************************************************** - - subroutine getnsort(nsort_tmp) - -********************************************************************** -#include "cbka.blk" - integer nsort_tmp - -********************************************************************** -* * -* Report the value of nsort * -* * -********************************************************************** - - nsort_tmp = nsort - - return - end - -********************************************************************** - - subroutine getmbond(mbond_tmp) - -********************************************************************** -#include "cbka.blk" - integer mbond_tmp - -********************************************************************** -* * -* Report the value of mbond * -* * -********************************************************************** - - mbond_tmp = mbond - - return - end - -********************************************************************** - - subroutine getnso(nso_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbkff.blk" - integer nso_tmp - -********************************************************************** -* * -* Report the value of nso * -* * -********************************************************************** - - nso_tmp = nso - - return - end - - -********************************************************************** - - subroutine setngeofor(ngeofor_tmp) - -********************************************************************** -#include "cbka.blk" -#include "control.blk" - integer ngeofor_tmp - -********************************************************************** -* * -* Set value of ngeofor -* * -********************************************************************** - - ngeofor = ngeofor_tmp - return - end - -********************************************************************** - - subroutine getnsbmax(nsbmax_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbksrtbon1.blk" - integer nsbmax_tmp - -********************************************************************** -* * -* Report the value of nsbmax * -* * -********************************************************************** - - nsbmax_tmp = nsbmax - - return - end - -********************************************************************** - - subroutine getnsbma2(nsbma2_tmp) - -********************************************************************** -#include "cbka.blk" -#include "cbksrtbon1.blk" - integer nsbma2_tmp - -********************************************************************** -* * -* Report the value of nsbma2 * -* * -********************************************************************** - - nsbma2_tmp = nsbma2 - - return - end - -********************************************************************** - - subroutine getcutof3(cutof3_tmp) - -********************************************************************** -#include "cbka.blk" -#include "control.blk" - real*8 cutof3_tmp - -********************************************************************** -* * -* Report the value of cutof3 * -* * -********************************************************************** - - cutof3_tmp = cutof3 - - return - end - diff --git a/lib/reax/reax_poten.F b/lib/reax/reax_poten.F deleted file mode 100644 index 2228f8546b..0000000000 --- a/lib/reax/reax_poten.F +++ /dev/null @@ -1,3985 +0,0 @@ -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -******************************************************************** - - subroutine calval - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkdhdc.blk" -#include "cbkdrdc.blk" -#include "cbkh.blk" -#include "cbkrbo.blk" -#include "cbkvalence.blk" -#include "cellcoord.blk" -#include "control.blk" - dimension a(3),b(3),j(3),dradc(3,3),drbdc(3,3),dtdc(3,3), - $dargdc(3,3),dndc(3,3),dadc(3),dbdc(3) -********************************************************************** -* * -* Calculate valency angles and their derivatives to cartesian * -* coordinates * -* Valency angle energies are calculated in valang * -* * -********************************************************************** -********************************************************************** -* Description of variables used in this routine. -* -* ndebug: stored in cbka.blk; control-parameter -* third: local variable -* twothird: local variable -* dadc(3): local array; stores derivative distance to cartesians -* dbdc(3): local array; stores derivative distance to cartesians -* i1: local do-loop counter -* i2: local do-loop counter -* k1: local do-loop counter -* k2: local do-loop counter -* dradc(3,3): local array; stores derivatives bond lengths to -* cartesians -* drbdc(3,3): local array; stores derivatives bond lengths to -* cartesians -* nval: stored in cbka.blk; number of valence angles -* ity: local integer; atom type -* iv(nvalmax,6): stored in cbka.blk; valence angle identifiers -* j(3): local integer array; stores valence angle atom numbers -* la: local integer: stores bond numbers in valence angle -* lb: local integer: stores bond numbers in valence angle -* ivl1: local integer; stores symmetric copy number of bond -* ivl2: local integer; stores symmetric copy number of bond -* ibsym(nbomax): stored in cbka.blk; symmetric copy number of bond -* isign1: local integer; -1 or 1 -* isign2: local integer; -1 or 1 -* rla: local variable; stores bond length for bond la -* rlb: local variable; stores bond length for bond lb -* rbo(nbomax): stored in cbka.blk; stores bond lengths -* ix1,iy1,iz1,ix2,iy2,iz2: local integers; periodic cell shifts -* a(3): local variable; distance in x,y and z-direction between atoms -* b(3): local variable; distance in x,y and z-direction between atoms -* c(nat,3): stored in cbka.blk; cartesian coordinate array -* tm11,tm21,tm22,tm31,tm32,tm33: stored in cbka.blk; periodic cell -* matrix -* poem: local variable; product of bond lengths -* tel: local variable; cross-product of x,y and z-interatomic -* distances -* arg: local variable; cosine of angle between bonds a and b -* arg2: local variable; square of arg -* s1ma22: local variable; used to check whether angle gets to 180 -* degrees -* s1ma2: local variable; square root of s1ma22 -* hl: local variable; angle (in radians) between bonds a and b -* h(nvamax): stored in cbka.blk; angle (in radians) between bonds a -* and b -* ib(nbomax,3): stored in cbka.blk: bond distance identifiers -* drdc(nbomax,3,2): stored in cbka.blk; derivatives bond distances -* to cartesian coordinates -* dndc(3,3): local variable; temporary storage for calculating -* derivatives of valence angle to cartesians -* dtdc(3,3): local variable; temporary storage for calculating -* derivatives of valence angle to cartesians -* dargdc(3,3): local variable; temporary storage for calculating -* derivatives of valence angle to cartesians -* dhdc(nvamax,3,3): stored in cbka.blk; derivatives of valence angle -* to cartesians -* -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In calval' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - - third=1.0/3.0 - twothird=2.0/3.0 - dadc(1)=-1.0 - dadc(2)=1.0 - dadc(3)=0.0 - dbdc(1)=0.0 - dbdc(2)=1.0 - dbdc(3)=-1.0 - do k1=1,3 - do k2=1,3 - dradc(k1,k2)=0.0 - drbdc(k1,k2)=0.0 - end do - end do - if (nval.eq.0) return - - do 10 i1=1,nval - ity=iv(i1,1) - j(1)=iv(i1,2) - j(2)=iv(i1,3) - j(3)=iv(i1,4) -********************************************************************** -* * -* Determine valency angle * -* * -********************************************************************** - la=iv(i1,5) - lb=iv(i1,6) - ivl1=ibsym(la) - ivl2=ibsym(lb) - isign1=1 - isign2=1 - rla=rbo(la) - rlb=rbo(lb) - - call dista2(j(2),j(1),dis,a(1),a(2),a(3)) - call dista2(j(2),j(3),dis,b(1),b(2),b(3)) - - poem=rla*rlb - tel=a(1)*b(1)+a(2)*b(2)+a(3)*b(3) - arg=tel/poem - arg2=arg*arg - s1ma22=1.0-arg2 - if (s1ma22.lt.1.0d-10) s1ma22=1.0d-10 - s1ma2=sqrt(s1ma22) - if (arg.gt.1.0) arg=1.0 - if (arg.lt.-1.0) arg=-1.0 - hl=acos(arg) - h(i1)=hl -********************************************************************** -* * -* Calculate derivative valency angle to cartesian coordinates * -* * -********************************************************************** - if (j(1).eq.ib(la,2)) then - do k1=1,3 - dradc(k1,1)=drdc(la,k1,1) - dradc(k1,2)=drdc(la,k1,2) - end do - else - do k1=1,3 - dradc(k1,1)=drdc(la,k1,2) - dradc(k1,2)=drdc(la,k1,1) - end do - end if - if (j(2).eq.ib(lb,2)) then - do k1=1,3 - drbdc(k1,2)=drdc(lb,k1,1) - drbdc(k1,3)=drdc(lb,k1,2) - end do - else - do k1=1,3 - drbdc(k1,2)=drdc(lb,k1,2) - drbdc(k1,3)=drdc(lb,k1,1) - end do - end if - do k1=1,3 - do k2=1,3 - dndc(k1,k2)=rla*drbdc(k1,k2)+rlb*dradc(k1,k2) - dtdc(k1,k2)=a(k1)*dbdc(k2)+b(k1)*dadc(k2) - dargdc(k1,k2)=(dtdc(k1,k2)-arg*dndc(k1,k2))/poem - dhdc(i1,k1,k2)=-dargdc(k1,k2)/s1ma2 - end do - end do - - 10 continue - - return - end -********************************************************************** -********************************************************************** - - subroutine boncor - -********************************************************************** -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkc.blk" -#include "cbkbo.blk" -#include "cbkboncor.blk" -#include "cbkbosi.blk" -#include "cbkbopi.blk" -#include "cbkbopi2.blk" -#include "cbkconst.blk" -#include "cbkdbopi2ndc.blk" -#include "cbkdbopidc.blk" -#include "cbkdbopindc.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbknubon2.blk" -#include "cbkrbo.blk" -#include "control.blk" -#include "small.blk" -#include "cbkdbodc.blk" -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In boncor' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -********************************************************************** -* * -* Correction for overcoordination and 1-3 bond orders * -* * -********************************************************************** -********************************************************************** -* Description of variables used in this routine. -* -* ndebug: stored in cbka.blk; control-parameter -* i1: local do-loop counter -* i2: local do-loop counter -* k1: local do-loop counter -* k2: local do-loop counter -* nbon: stored in cbka.blk; number of bonds in system -* ibt: local integer; stores bond type -* ib(nbomax,3): stored in cbka.blk: bond distance identifiers -* j1: local integer; stores atom number 1st atom in bond -* j2: local integer; stores atom number 2nd atom in bond -* ovc(nbotym): stored in cbka.blk: force field parameter for -* overcoordination correction -* v13cor(nbotym): stored in cbka.blk: force field parameter for -* 1-3 bond order correction -* idbo1(nbomax): stored in cbka.blk; number of atoms in the -* derivative of the bond order -* idbo(nbomax,2*mbond): stored in cbka.blk; atom numbers of the -* atoms in the derivative of the bond order -* dbondc(nbomax,3,2*mbond): stored in cbka.blk; derivative of -* corrected total bond orders to cartesians -* dbosindc(nbomax,3,2*mbond): stored in cbka.blk; derivative of -* corrected sigma bond orders to cartesians -* dbopindc(nbomax,3,2*mbond): stored in cbka.blk; derivative of -* corrected pi bond orders to cartesians -* dbopi2ndc(nbomax,3,2*mbond): stored in cbka.blk; derivative of -* corrected double pi bond orders to cartesians -* dbodc(nbomax,3,2): stored in cbka.blk; derivative of -* uncorrected total bond orders to cartesians -* dbosidc(nbomax,3,2): stored in cbka.blk; derivative of -* uncorrected sigma bond orders to cartesians -* dbopidc(nbomax,3,2): stored in cbka.blk; derivative of -* uncorrected pi bond orders to cartesians -* dbopi2dc(nbomax,3,2): stored in cbka.blk; derivative of -* uncorrected double pi bond orders to cartesians -* boo: local variable; storage of uncorrected total bond order -* bo(nbomax): stored in cbka.blk; total bond order -* bopi(nbomax): stored in cbka.blk; pi bond order -* bopi2(nbomax): stored in cbka.blk; double pi bond order -* bopio: local variable; storage of uncorrected pi bond order -* bopi2o: local variable; storage of uncorrected double pi bond order -* iti: local integer; atom type first atom in bond -* itj: local integer; atom type second atom in bond -* ia(nat,mbond+3): stored in cbka.blk; connection table without bond -* order cutoff -* aboi: local variable: total bond order around atom i -* aboj: local variable: total bond order around atom j -* abo(nat): stored in cbka.blk; total bond order around atoms -* vp131: local variable; force field cross-term -* vp132: local variable; force field cross-term -* vp133: local variable; force field cross-term -* bo131(nsort): stored in cbka.blk; force field parameter for 1-3 -* bond order correction -* bo132(nsort): stored in cbka.blk; force field parameter for 1-3 -* bond order correction -* bo133(nsort): stored in cbka.blk; force field parameter for 1-3 -* bond order correction -* corrtot:local variable; total correction on bond order -* dbodsboi1: local variable; derivative of bond order to sum of bond -* orders around atom i -* dbodsboj1: local variable; derivative of bond order to sum of bond -* orders around atom j -* ovi: local variable; overcoordination on atom i -* ovj: local variable; overcoordination on atom j -* aval(nat): stored in cbka.blk; nr. of valence electrons on atom -* exphu1: local variable; stores exponential -* exphu2: local variable; stores exponential -* exp11: local variable; stores exponential -* exp21: local variable; stores exponential -* vpar(npamax): stored in cbka.blk: general parameters -* exphu12: local variable; stores sum of exponential -* ovcor: local variable; temporary storage for BO/ovcor corr. -* huli: local variable; temporary storage for BO/ovcor corr. -* hulj: local variable; temporary storage for BO/ovcor corr. -* corr1: local variable; temporary storage for BO/ovcor corr. -* corr2: local variable; temporary storage for BO/ovcor corr. -* dbodsboi2: local variable; derivative of 1-3 BO correction to sum -* of bond orders around atom i -* dbodsboj2: local variable; derivative of 1-3 BO correction to sum -* of bond orders around atom i -* bocor1: local variable; 1-3 bond order correction -* bocor2: local variable; 1-3 bond order correction -* ovi2: local variable; overcoordination on atom i with reference to -* total number of electrons on atom i, including lone -* pairs -* ovj2: local variable; overcoordination on atom j with reference to -* total number of electrons on atom j, including lone -* pairs -* valf(nsort): stored in cbka.blk; total number of electrons on -* atom, including lone pairs -* cor1: local variable; temporary storage for BO/1-3 bond corr. -* cor2: local variable; temporary storage for BO/1-3 bond corr. -* exphu3: local variable; storage exponential -* exphu4: local variable; storage exponential -* corrtot2: local variable; square of corrtot -* dbodboo: local variable; derivative of corrected total bond order to -* uncorrected bond order -* dbopidbopio: local variable; derivative of corrected pi bond order -* to uncorrected pi bond order -* dbopidboo: local variable; derivative of corrected pi bond order -* to uncorrected total bond order -* dbopi2dbopi2o: local variable; derivative of corrected double pi bond order -* to uncorrected double pi bond order -* dbopi2dboo: local variable; derivative of corrected double pi bond order -* to uncorrected total bond order -* dbodsboit: local variable; derivative of total bond order to sum -* of bond orders around atom i -* dbodsbojt: local variable; derivative of total bond order to sum -* of bond orders around atom j -* vhui: local variable; temporary storage -* vhuj: local variable; temporary storage -* dbopidsboit: local variable; derivative of pi bond order to sum -* of bond orders around atom i -* dbopidsbojt: local variable; derivative of pi bond order to sum -* of bond orders around atom j -* dbopi2dsboit: local variable; derivative of pi bond order to sum -* of bond orders around atom i -* dbopi2dsbojt: local variable; derivative of pi bond order to sum -* of bond orders around atom j -* nco: local integer; counter for number of atoms in derivative -* ihl: local integer; helps to access right dbodc-term -* nubon2(nat,mbond): stored in cbka.blk; stored bond number as a -* function of atom number and connection number -* iob: local integer; atom number of second atom in bond -* ncubo: local integer; stores number of current bond -* na: stored in cbka.blk: number of atoms in system -* zero: stored in cbka.blk: value 0.00 -* -********************************************************************** - do 10 i1=1,nbon - ibt=ib(i1,1) - j1=ib(i1,2) - j2=ib(i1,3) - if (ovc(ibt).lt.0.001.and.v13cor(ibt).lt.0.001) then - idbo1(i1)=2 - idbo(i1,1)=j1 - idbo(i1,2)=j2 - do k1=1,3 - dbondc(i1,k1,1)=dbodc(i1,k1,1) - dbondc(i1,k1,2)=dbodc(i1,k1,2) - dbosindc(i1,k1,1)=dbosidc(i1,k1,1) - dbosindc(i1,k1,2)=dbosidc(i1,k1,2) - dbopindc(i1,k1,1)=dbopidc(i1,k1,1) - dbopindc(i1,k1,2)=dbopidc(i1,k1,2) - dbopi2ndc(i1,k1,1)=dbopi2dc(i1,k1,1) - dbopi2ndc(i1,k1,2)=dbopi2dc(i1,k1,2) - end do - goto 10 - end if - boo=bo(i1) - bopio=bopi(i1) - bopi2o=bopi2(i1) - iti=ia(j1,1) - itj=ia(j2,1) - aboi=abo(j1) - aboj=abo(j2) - vp131=sqrt(bo131(iti)*bo131(itj)) - vp132=sqrt(bo132(iti)*bo132(itj)) - vp133=sqrt(bo133(iti)*bo133(itj)) - corrtot=1.0 - dbodsboi1=zero - dbodsboj1=zero - if (ovc(ibt).gt.0.001) then - ovi=aboi-aval(iti) - ovj=aboj-aval(itj) - -********************************************************************** -* * -* Correction for overcoordination * -* * -********************************************************************** - exphu1=exp(-vpar(2)*ovi) - exphu2=exp(-vpar(2)*ovj) - exp11=exp(-vpar(1)*ovi) - exp21=exp(-vpar(1)*ovj) - exphu12=(exphu1+exphu2) - ovcor=-(1.0/vpar(2))*log(0.50*exphu12) -* huli=((1.0/ovc(ibt))*aval(iti)+exp11+exp21) -* hulj=((1.0/ovc(ibt))*aval(itj)+exp11+exp21) - huli=aval(iti)+exp11+exp21 - hulj=aval(itj)+exp11+exp21 - corr1=huli/(huli+ovcor) - corr2=hulj/(hulj+ovcor) - corrtot=0.50*(corr1+corr2) - - dbodsboi1=0.50*(-vpar(1)*exp11/(huli+ovcor)- - $(corr1/(huli+ovcor))* - $(-vpar(1)*exp11+exphu1/exphu12)-vpar(1)*exp11/(hulj+ovcor)- - $(corr2/(hulj+ovcor))*(-vpar(1)*exp11+exphu1/exphu12)) - dbodsboj1=0.50*(-vpar(1)*exp21/(huli+ovcor)- - $(corr1/(huli+ovcor))* - $(-vpar(1)*exp21+exphu2/exphu12)-vpar(1)*exp21/(hulj+ovcor)- - $(corr2/(hulj+ovcor))*(-vpar(1)*exp21+exphu2/exphu12)) - end if -********************************************************************** -* * -* Correction for 1-3 bond orders * -* * -********************************************************************** - dbodsboi2=zero - dbodsboj2=zero - bocor1=1.0 - bocor2=1.0 - if (v13cor(ibt).gt.0.001) then - ovi2=aboi-vval3(iti) !Modification for metal surfaces - ovj2=aboj-vval3(itj) -* ovi2=aboi-valf(iti) -* ovj2=aboj-valf(itj) -* ovi2=aboi-aval(iti) -* ovj2=aboj-aval(itj) - cor1=vp131*boo*boo-ovi2 - cor2=vp131*boo*boo-ovj2 -* exphu3=v13cor(ibt)*exp(-vp132*cor1+vp133) -* exphu4=v13cor(ibt)*exp(-vp132*cor2+vp133) - exphu3=exp(-vp132*cor1+vp133) - exphu4=exp(-vp132*cor2+vp133) - bocor1=1.0/(1.0+exphu3) - bocor2=1.0/(1.0+exphu4) - dbodsboi2=-bocor1*bocor1*bocor2*vp132*exphu3 - dbodsboj2=-bocor1*bocor2*bocor2*vp132*exphu4 - end if - - bo(i1)=boo*corrtot*bocor1*bocor2 - if (bo(i1).lt.1e-10) bo(i1)=zero - corrtot2=corrtot*corrtot - bopi(i1)=bopio*corrtot2*bocor1*bocor2 - bopi2(i1)=bopi2o*corrtot2*bocor1*bocor2 - if (bopi(i1).lt.1e-10) bopi(i1)=zero - if (bopi2(i1).lt.1e-10) bopi2(i1)=zero - - dbodboo=corrtot*bocor1*bocor2+corrtot* - $bocor1*bocor1*bocor2*boo*vp132*vp131*2.0*boo*exphu3+ - $corrtot*bocor1*bocor2*bocor2*boo* - $vp132*vp131*exphu4*2.0*boo - - dbopidbopio=corrtot2*bocor1*bocor2 - - dbopidboo=corrtot2* - $bocor1*bocor1*bocor2*boo*vp132*vp131*2.0*bopio*exphu3+ - $corrtot2*bocor1*bocor2*bocor2*boo* - $vp132*vp131*exphu4*2.0*bopio - - dbopi2dbopi2o=corrtot2*bocor1*bocor2 - - dbopi2dboo=corrtot2* - $bocor1*bocor1*bocor2*boo*vp132*vp131*2.0*bopi2o*exphu3+ - $corrtot2*bocor1*bocor2*bocor2*boo* - $vp132*vp131*exphu4*2.0*bopi2o - - dbodsboit=boo*dbodsboi1*bocor1*bocor2+boo*corrtot*dbodsboi2 - dbodsbojt=boo*dbodsboj1*bocor1*bocor2+boo*corrtot*dbodsboj2 - - vhui=2.0*corrtot*dbodsboi1*bocor1*bocor2+corrtot2*dbodsboi2 - vhuj=2.0*corrtot*dbodsboj1*bocor1*bocor2+corrtot2*dbodsboj2 - dbopidsboit=bopio*vhui - dbopidsbojt=bopio*vhuj - - dbopi2dsboit=bopi2o*vhui - dbopi2dsbojt=bopi2o*vhuj - -********************************************************************** -* * -* Calculate bond order derivatives * -* * -********************************************************************** - idbo1(i1)=2+ia(j1,2)+ia(j2,2) - idbo(i1,1)=j1 - idbo(i1,2)=j2 - nco=0 - do k1=1,3 - dbondc(i1,k1,1)=dbodc(i1,k1,1)*dbodboo - dbondc(i1,k1,2)=dbodc(i1,k1,2)*dbodboo -* dbosindc(i1,k1,1)=dbosidc(i1,k1,1)*dbosidboo -* dbosindc(i1,k1,2)=dbosidc(i1,k1,2)*dbosidboo - dbopindc(i1,k1,1)=dbopidc(i1,k1,1)*dbopidbopio+ - $dbodc(i1,k1,1)*dbopidboo - dbopindc(i1,k1,2)=dbopidc(i1,k1,2)*dbopidbopio+ - $dbodc(i1,k1,2)*dbopidboo - dbopi2ndc(i1,k1,1)=dbopi2dc(i1,k1,1)*dbopi2dbopi2o+ - $dbodc(i1,k1,1)*dbopi2dboo - dbopi2ndc(i1,k1,2)=dbopi2dc(i1,k1,2)*dbopi2dbopi2o+ - $dbodc(i1,k1,2)*dbopi2dboo - end do - do i2=1,ia(j1,2) - ihl=0 - iob=ia(j1,2+i2) - if (iob.lt.j1) ihl=1 - ncubo=nubon2(j1,i2) - idbo(i1,2+nco+1)=iob - do k1=1,3 - dbondc(i1,k1,1)=dbondc(i1,k1,1)+dbodc(ncubo,k1,1+ihl)*dbodsboit - dbondc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbodsboit - -* dbosindc(i1,k1,1)=dbosindc(i1,k1,1)+ -* $dbodc(ncubo,k1,1+ihl)*dbosidsboit -* dbosindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbosidsboit - - dbopindc(i1,k1,1)=dbopindc(i1,k1,1)+ - $dbodc(ncubo,k1,1+ihl)*dbopidsboit - dbopindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopidsboit - - dbopi2ndc(i1,k1,1)=dbopi2ndc(i1,k1,1)+ - $dbodc(ncubo,k1,1+ihl)*dbopi2dsboit - dbopi2ndc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopi2dsboit - - end do - nco=nco+1 - end do - do i2=1,ia(j2,2) - ihl=0 - iob=ia(j2,2+i2) - if (iob.lt.j2) ihl=1 - ncubo=nubon2(j2,i2) - idbo(i1,2+nco+1)=iob - do k1=1,3 - - dbondc(i1,k1,2)=dbondc(i1,k1,2)+dbodc(ncubo,k1,1+ihl)*dbodsbojt - dbondc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbodsbojt - -* dbosindc(i1,k1,2)=dbosindc(i1,k1,2)+ -* $dbodc(ncubo,k1,1+ihl)*dbosidsbojt -* dbosindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbosidsbojt - - dbopindc(i1,k1,2)=dbopindc(i1,k1,2)+ - $dbodc(ncubo,k1,1+ihl)*dbopidsbojt - dbopindc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopidsbojt - - dbopi2ndc(i1,k1,2)=dbopi2ndc(i1,k1,2)+ - $dbodc(ncubo,k1,1+ihl)*dbopi2dsbojt - dbopi2ndc(i1,k1,2+nco+1)=dbodc(ncubo,k1,2-ihl)*dbopi2dsbojt - - end do - nco=nco+1 - end do - - 10 continue - - do i1=1,na - abo(i1)=zero - end do -* do i1=1,na -* do i2=1,ia(i1,2) -* iob=ia(i1,2+i2) -* ncubo=nubon2(i1,i2) -* abo(i1)=abo(i1)+bo(ncubo) -* end do -* end do - do i1=1,nbon - j1=ib(i1,2) - j2=ib(i1,3) - abo(j1)=abo(j1)+bo(i1) - if (j1.ne.j2) abo(j2)=abo(j2)+bo(i1) - end do - - 15 continue - return - end -********************************************************************** -********************************************************************** - - subroutine lonpar - -********************************************************************** -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkconst.blk" -#include "cbkc.blk" -#include "cbkd.blk" -#include "cbkdcell.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbklonpar.blk" -#include "cbknubon2.blk" -#include "control.blk" -#include "small.blk" - dimension virial_tmp(3,3),virialsym(6) -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In lonpar' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -********************************************************************** -* * -* Calculate lone pair energy and first derivatives * -* * -********************************************************************** - elp=zero - do i1=1,na -********************************************************************** -* * -* Determine number of lone pairs on atoms -* * -********************************************************************** - ity=ia(i1,1) - voptlp=0.50*(stlp(ity)-aval(ity)) - vlp(i1)=zero - vund=abo(i1)-stlp(ity) - vlph=2.0*int(vund/2.0) - vlpex=vund-vlph - vp16h=vpar(16)-1.0 - - expvlp=exp(-vpar(16)*(2.0+vlpex)*(2.0+vlpex)) - dvlpdsbo(i1)=-vpar(16)*2.0*(2.0+vlpex)*expvlp - vlp(i1)=expvlp-int(vund/2.0) -* expvlp=exp(-vpar(16)*(2.0+vlpex)) -* dvlpdsbo(i1)=-vpar(16)*expvlp -* expvlp=exp(-6.0*((-0.50*vlpex)**vpar(16))) -* vlp(i1)=(1.0-expvlp)-int(vund/2.0) -* dvlpdsbo(i1)=-0.5*6.0*vpar(16)*((-0.5*vlpex)**vp16h)* -* $expvlp -********************************************************************** -* * -* Calculate lone pair energy * -* * -********************************************************************** - if (i1 .le. na_local) then - - diffvlp=voptlp-vlp(i1) - exphu1=exp(-75.0*diffvlp) - hulp1=1.0/(1.0+exphu1) - elph=vlp1(ity)*diffvlp*hulp1 -* elph=vlp1(ity)*diffvlp - delpdvlp=-vlp1(ity)*hulp1-vlp1(ity)*diffvlp*hulp1*hulp1* - $75.0*exphu1 - - elp=elp+elph - estrain(i1)=estrain(i1)+elph !atom energy - - delpdsbo=delpdvlp*dvlpdsbo(i1) -********************************************************************** -* * -* Calculate first derivative of lone pair energy to * -* cartesian coordinates * -* * -********************************************************************** - do i3=1,ia(i1,2) - iob=ia(i1,2+i3) - ncubo=nubon2(i1,i3) - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = delpdsbo*dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - endif - - end do - endif - - end do - - return - end -********************************************************************** -********************************************************************** - - subroutine covbon - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkabo.blk" -#include "cbkbo.blk" -#include "cbkbosi.blk" -#include "cbkbopi.blk" -#include "cbkbopi2.blk" -#include "cbkconst.blk" -#include "cbkcovbon.blk" -#include "cbkd.blk" -#include "cbkdbopi2ndc.blk" -#include "cbkdbopindc.blk" -#include "cbkdcell.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbknubon2.blk" -#include "cbkqa.blk" -#include "cbkrbo.blk" -#include "control.blk" -#include "small.blk" - dimension virial_tmp(3,3),virialsym(6) -********************************************************************** -* * -* Calculate bond energy and first derivatives * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In covbon' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - eb=0.0d0 - if (nbon.eq.0) return -********************************************************************** -* * -* Calculate bond energies * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write(65,*) 'Bond forces' -c$$$ write(65,*) 'nbon = ',nbon -c$$$ endif - - do 20 i1=1,nbon - - boa=bo(i1) -* if (boa.lt.cutof2) goto 20 - j1=ib(i1,2) - j2=ib(i1,3) - -c Only compute interaction if both atoms -c are local or else flip a coin - if (j1 .gt. na_local) go to 20 - if (j2 .gt. na_local) then - if (itag(j1) .lt. itag(j2)) go to 20 - if (itag(j1) .eq. itag(j2)) then - if(c(j1,3) .gt. c(j2,3)) go to 20 - if(c(j1,3) .eq. c(j2,3) .and. - $ c(j1,2) .gt. c(j2,2)) go to 20 - if(c(j1,3) .eq. c(j2,3) .and. - $ c(j1,2) .eq. c(j2,2) .and. - $ c(j1,1) .gt. c(j2,1)) go to 20 - endif - endif - vsymm=1.0 - if (j1.eq.j2) vsymm=0.5 - - bopia=bopi(i1) - bopi2a=bopi2(i1) - bosia=boa-bopia-bopi2a - if (bosia.lt.zero) bosia=zero - it1=ia(j1,1) - it2=ia(j2,1) - ibt=ib(i1,1) - de1h=vsymm*de1(ibt) - de2h=vsymm*de2(ibt) - de3h=vsymm*de3(ibt) - - bopo1=bosia**psp(ibt) - exphu1=exp(psi(ibt)*(1.0-bopo1)) - ebh=-de1h*bosia*exphu1-de2h*bopia-de3h*bopi2a - - debdbo=-de1h*exphu1+de1h*exphu1*psp(ibt)*psi(ibt)*bopo1 - debdbopi=-de2h - debdbopi2=-de3h - - eb=eb+ebh - estrain(j1)=estrain(j1)+0.50*ebh !1st atom energy - estrain(j2)=estrain(j2)+0.50*ebh !2nd atom energy - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(i1) - ihu=idbo(i1,i2) - do k1=1,3 - ftmp = debdbo*(dbondc(i1,k1,i2)-dbopindc(i1,k1,i2)- - $dbopi2ndc(i1,k1,i2))+ - $debdbopi*dbopindc(i1,k1,i2)+ - $debdbopi2*dbopi2ndc(i1,k1,i2) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(i1) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(i1) - ihu=idbo(i1,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - -********************************************************************** -* * -* Stabilisation terminal triple bond in CO * -* * -********************************************************************** - if (boa.lt.1.00) goto 20 -* Stabilization for all triple bonds (not just for CO) in ReaxFF combustion FF - if (ltripstaball.eq.1 .or. - $ (qa(j1).eq.'C '.and.qa(j2).eq.'O ').or. - $ (qa(j1).eq.'O '.and.qa(j2).eq.'C ')) then - - ba=(boa-2.50)*(boa-2.50) - exphu=exp(-vpar(8)*ba) - oboa=abo(j1)-boa - obob=abo(j2)-boa - exphua1=exp(-vpar(4)*oboa) - exphub1=exp(-vpar(4)*obob) - ovoab=abo(j1)-aval(it1)+abo(j2)-aval(it2) - exphuov=exp(vpar(5)*ovoab) - hulpov=1.0/(1.0+25.0*exphuov) - - estriph=vpar(11)*exphu*hulpov*(exphua1+exphub1) - - eb=eb+estriph - estrain(j1)=estrain(j1)+0.50*estriph !1st atom energy - estrain(j2)=estrain(j2)+0.50*estriph !2nd atom energy - - decobdbo=vpar(4)*vpar(11)*exphu*hulpov*(exphua1+exphub1) - $-2.0*vpar(11)*vpar(8)*(boa-2.50)*hulpov*exphu* - $(exphua1+exphub1) - decobdboua=-25.0*vpar(5)*vpar(11)*exphu*exphuov*hulpov*hulpov* - $(exphua1+exphub1)-vpar(11)*exphu*vpar(4)*hulpov*exphua1 - decobdboub=-25.0*vpar(5)*vpar(11)*exphu*exphuov*hulpov*hulpov* - $(exphua1+exphub1)-vpar(11)*exphu*vpar(4)*hulpov*exphub1 - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(i1) - ihu=idbo(i1,i2) - do k1=1,3 - ftmp = decobdbo*dbondc(i1,k1,i2) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(i1) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(i1) - ihu=idbo(i1,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - do i3=1,ia(j1,2) - iob=ia(j1,2+i3) - ncubo=nubon2(j1,i3) - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = decobdboua*dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - end do - - do i3=1,ia(j2,2) - iob=ia(j2,2+i3) - ncubo=nubon2(j2,i3) - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = decobdboub*dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - end do - - endif - - 20 continue - - return - end -********************************************************************** -********************************************************************** - - subroutine ovcor - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkabo.blk" -#include "cbkbo.blk" -#include "cbkbopi.blk" -#include "cbkbopi2.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkdbopi2ndc.blk" -#include "cbkdbopindc.blk" -#include "cbkdcell.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbklonpar.blk" -#include "cbknubon2.blk" -#include "cbkrbo.blk" -#include "control.blk" -#include "small.blk" -********************************************************************** -* * -* Calculate atom energy * -* Correction for over- and undercoordinated atoms * -* * -********************************************************************** - dimension vlptemp(nat) - dimension virial_tmp(3,3),virialsym(6) -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In ovcor' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - do i1=1,na - ity1=ia(i1,1) - vlptemp(i1)=vlp(i1) - if (amas(ity1).gt.21.0) vlptemp(i1)=0.50*(stlp(ity1)-aval(ity1)) !Only for 1st-row elements - end do - 25 ea=zero - eaot=zero - eaut=zero - epen=0.0 - - do 30 i1=1,na_local - ity1=ia(i1,1) - dfvl=1.0 - if (amas(ity1).gt.21.0) dfvl=0.0 !Only for 1st-row elements -********************************************************************** -* * -* Calculate overcoordination energy * -* Valency is corrected for lone pairs * -* * -********************************************************************** - - voptlp=0.50*(stlp(ity1)-aval(ity1)) - diffvlph=dfvl*(voptlp-vlptemp(i1)) -********************************************************************** -* * -* Determine coordination neighboring atoms * -* * -********************************************************************** - sumov=0.0 - sumov2=0.0 - do i3=1,ia(i1,2) - iat2=ia(i1,2+i3) - ity2=ia(iat2,1) - ncubo=nubon2(i1,i3) - if (bo(ncubo).gt.0.0) then - ibt=ib(ncubo,1) - voptlp2=0.50*(stlp(ity2)-aval(ity2)) - diffvlp2=dfvl*(voptlp2-vlptemp(iat2)) - sumov=sumov+(bopi(ncubo)+bopi2(ncubo))* - $(abo(iat2)-aval(ity2)-diffvlp2) - sumov2=sumov2+vover(ibt)*de1(ibt)*bo(ncubo) - endif - end do - - exphu1=exp(vpar(32)*sumov) - vho=1.0/(1.0+vpar(33)*exphu1) - diffvlp=diffvlph*vho - - vov1=abo(i1)-aval(ity1)-diffvlp - dvov1dsumov=diffvlph*vpar(32)*vpar(33)*vho*vho*exphu1 - exphuo=exp(vovun(ity1)*vov1) - hulpo=1.0/(1.0+exphuo) - - hulpp=(1.0/(vov1+aval(ity1)+1e-8)) - - eah=sumov2*hulpp*hulpo*vov1 - deadvov1=-sumov2*hulpp*hulpp*vov1*hulpo+ - $sumov2*hulpp*hulpo-sumov2*hulpp*vov1*vovun(ity1)* - $hulpo*hulpo*exphuo - - ea=ea+eah - estrain(i1)=estrain(i1)+eah !atom energy -********************************************************************** -* * -* Calculate first derivative of overcoordination energy to * -* cartesian coordinates * -* * -********************************************************************** - do i3=1,ia(i1,2) - iob=ia(i1,2+i3) - ncubo=nubon2(i1,i3) - if (bo(ncubo).gt.0.0) then - ibt=ib(ncubo,1) - deadbo=vover(ibt)*de1(ibt)*hulpp*hulpo*vov1 - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = deadvov1*(1.0+dfvl*vho*dvlpdsbo(i1))* - $dbondc(ncubo,k1,i4)+deadbo*dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - do i2=1,ia(i1,2) - - iat2=ia(i1,2+i2) - ity2=ia(iat2,1) - nbosa=nubon2(i1,i2) - if (bo(nbosa).gt.0.0) then - deadvov2=deadvov1*dvov1dsumov*(bopi(nbosa)+bopi2(nbosa)) - - voptlp2=0.50*(stlp(ity2)-aval(ity2)) - diffvlp2=dfvl*(voptlp2-vlptemp(iat2)) - deadpibo=deadvov1*dvov1dsumov*(abo(iat2)-aval(ity2)-diffvlp2) - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(nbosa) - ihu=idbo(nbosa,i4) - do k1=1,3 - ftmp = deadpibo*(dbopindc(nbosa,k1,i4)+ - $dbopi2ndc(nbosa,k1,i4)) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(nbosa) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(nbosa) - ihu=idbo(nbosa,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - endif - - do i3=1,ia(iat2,2) - iob=ia(iat2,2+i3) - ncubo=nubon2(iat2,i3) - if (bo(ncubo).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = deadvov2*(1.0+dfvl*dvlpdsbo(iat2))* - $dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - endif - - end do - -********************************************************************** -* * -* Calculate undercoordination energy * -* * -********************************************************************** - if (valp1(ity1).lt.zero) goto 30 !skip undercoordination - exphu2=exp(vpar(10)*sumov) - vuhu1=1.0+vpar(9)*exphu2 - hulpu2=1.0/vuhu1 - - exphu3=-exp(vpar(7)*vov1) - hulpu3=-(1.0+exphu3) - - dise2=valp1(ity1) - exphuu=exp(-vovun(ity1)*vov1) - hulpu=1.0/(1.0+exphuu) - eahu=dise2*hulpu*hulpu2*hulpu3 - deaudvov1=dise2*hulpu2*vovun(ity1)*hulpu*hulpu*exphuu*hulpu3- - $dise2*hulpu*hulpu2*vpar(7)*exphu3 - - ea=ea+eahu - estrain(i1)=estrain(i1)+eahu !atom energy - - deaudsumov=-dise2*hulpu*vpar(9)*vpar(10)*hulpu3*exphu2* - $hulpu2*hulpu2 - -********************************************************************** -* * -* Calculate first derivative of atom energy to cartesian * -* coordinates * -* * -********************************************************************** - - do i3=1,ia(i1,2) - iob=ia(i1,2+i3) - ncubo=nubon2(i1,i3) - if (bo(ncubo).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = deaudvov1*(1.0+dfvl*vho*dvlpdsbo(i1))* - $dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - do i2=1,ia(i1,2) - - iat2=ia(i1,2+i2) - ity2=ia(iat2,1) - nbosa=nubon2(i1,i2) - if (bo(nbosa).gt.0.0) then - deadvov2=(deaudsumov+dvov1dsumov*deaudvov1)* - $(bopi(nbosa)+bopi2(nbosa)) - - voptlp2=0.50*(stlp(ity2)-aval(ity2)) - diffvlp2=dfvl*(voptlp2-vlptemp(iat2)) - deadpibo1=(dvov1dsumov*deaudvov1+deaudsumov)* - $(abo(iat2)-aval(ity2)-diffvlp2) - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(nbosa) - ihu=idbo(nbosa,i4) - do k1=1,3 - ftmp = deadpibo1* - $(dbopindc(nbosa,k1,i4)+dbopi2ndc(nbosa,k1,i4)) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(nbosa) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(nbosa) - ihu=idbo(nbosa,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - do i3=1,ia(iat2,2) - iob=ia(iat2,2+i3) - ncubo=nubon2(iat2,i3) - if (bo(ncubo).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = deadvov2*(1.0+dfvl*dvlpdsbo(iat2))* - $dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - endif - - end do - - - 30 continue - -********************************************************************** -* * -* Calculate correction for C2 * -* * -********************************************************************** - if (abs(vpar(6)).gt.0.001) then - do 40 i1=1,na_local - ity1=ia(i1,1) - vov4=abo(i1)-aval(ity1) - - do i2=1,ia(i1,2) - iat2=ia(i1,2+i2) - nbohu=nubon2(i1,i2) - if (bo(nbohu).gt.0.0) then - - ibt=ib(nbohu,1) - elph=zero - deahu2dbo=zero - deahu2dsbo=zero - vov3=bo(nbohu)-vov4-0.040*(vov4**4) - if (vov3.gt.3.0) then - elph=vpar(6)*(vov3-3.0)*(vov3-3.0) - deahu2dbo=2.0*vpar(6)*(vov3-3.0) - deahu2dsbo=2.0*vpar(6)*(vov3-3.0)*(-1.0- - $0.16*(vov4**3)) - end if - - elp=elp+elph - estrain(i1)=estrain(i1)+elph !atom energy - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(nbohu) - ihu=idbo(nbohu,i3) - do k1=1,3 - ftmp = deahu2dbo*dbondc(nbohu,k1,i3) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(nbohu) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(nbohu) - ihu=idbo(nbohu,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - do i3=1,ia(i1,2) - iob=ia(i1,2+i3) - ncubo=nubon2(i1,i3) - if (bo(ncubo).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = deahu2dsbo*dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - end if - end do - - end if - end do - - 40 continue - end if - - return - end -********************************************************************** -********************************************************************** - - subroutine molen - -********************************************************************** -#include "cbka.blk" -#include "cbkbo.blk" -#include "cbkconst.blk" -#include "cbkc.blk" -#include "cbkd.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbknmolat.blk" -#include "cbknubon2.blk" -#include "control.blk" -#include "small.blk" - dimension virial_tmp(3,3),virialsym(6) -********************************************************************** -* * -* Calculate molecular energy and first derivatives * -* Only used to prevent creating virtual electrons * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In molen' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - emol=zero - return - do i1=1,nmolo - - enelm=0.0 - do i2=1,na - if (ia(i2,3+mbond).eq.i1) then - it1=ia(i2,1) - enelm=enelm+aval(it1) - end if - end do - - na1m=nmolat(i1,1) - - enelm=2*int(enelm*0.50) -* enelm=elmol(i1) - bomsum=zero - do i2=1,na1m - ihu=nmolat(i1,i2+1) - do i3=1,ia(ihu,2) - ihu2=nubon2(ihu,i3) - bomsum=bomsum+bo(ihu2) - end do - end do - diff=(bomsum-enelm) - exphu=exp(-vpar(37)*diff) - exphu2=1.0/(1.0+15.0*exphu) - emolh=zero - demoldsbo=zero - emolh=vpar(38)*exphu2 - emol=emol+emolh - demoldsbo=vpar(38)*vpar(37)*15.0*exphu2*exphu2*exphu - - do i2=1,na1m - ihu1=nmolat(i1,i2+1) - do i3=1,ia(ihu1,2) - iob=ia(ihu1,2+i3) - ncubo=nubon2(ihu1,i3) - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - do k1=1,3 - ftmp = demoldsbo*dbondc(ncubo,k1,i4) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i4=1,idbo1(ncubo) - ihu=idbo(ncubo,i4) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - end do - end do - - - end do - - - return - end -********************************************************************** -********************************************************************** - - subroutine valang - -********************************************************************** -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkbo.blk" -#include "cbkbopi.blk" -#include "cbkbopi2.blk" -#include "cbkconst.blk" -#include "cbkc.blk" -#include "cbkd.blk" -#include "cbkdbopi2ndc.blk" -#include "cbkdbopindc.blk" -#include "cbkdcell.blk" -#include "cbkdhdc.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkh.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbklonpar.blk" -#include "cbknubon2.blk" -#include "cbkvalence.blk" -#include "control.blk" -#include "valang.blk" -#include "small.blk" - dimension j(3) - dimension virial_tmp(3,3),virialsym(6) -********************************************************************** -* * -* Calculate valency angle energies and first derivatives * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In valang' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -* eco=0.0 - ev=0.0 - ecoa=0.0 - if (nval.eq.0) return - - do 10 i1=1,nval - ity=iv(i1,1) - j(1)=iv(i1,2) - j(2)=iv(i1,3) - j(3)=iv(i1,4) - - if (j(2) .le. na_local) then - - la=iv(i1,5) - lb=iv(i1,6) - boa=bo(la)-cutof2 - bob=bo(lb)-cutof2 - if (boa.lt.zero.or.bob.lt.zero) goto 10 - - hl=h(i1) ! Calculated earlier in routine calval -********************************************************************** -* * -* Calculate valency angle energy * -* * -********************************************************************** - nbocen=ia(j(2),2) - sbo2=0.0 - vmbo=1.0 - - do i2=1,nbocen - ibv=nubon2(j(2),i2) - if (bo(ibv).gt.0.0) then - vmbo=vmbo*exp(-bo(ibv)**8) - sbo2=sbo2+bopi(ibv)+bopi2(ibv) - endif - end do - - ity2=ia(j(2),1) -* exbo=abo(j(2))-stlp(ia(j(2),1)) - exbo=abo(j(2))-valf(ity2) -* if (exbo.gt.zero) exbo=zero -* expov=exp(vka8(ity)*exbo) -* expov2=exp(-vpar(13)*exbo) -* htov1=2.0+expov2 -* htov2=1.0+expov+expov2 -* evboadj=htov1/htov2 - evboadj=1.0 - expun=exp(-vkac(ity)*exbo) - expun2=exp(vpar(15)*exbo) - htun1=2.0+expun2 - htun2=1.0+expun+expun2 - evboadj2=vval4(ity2)-(vval4(ity2)-1.0)*htun1/htun2 -********************************************************************** -* * -* Calculate number of lone pairs * -* * -********************************************************************** - dsbo2dvlp=(1.0-vmbo) - vlpadj=zero - exlp1=abo(j(2))-stlp(ia(j(2),1)) - exlp2=2.0*int(exlp1/2.0) - exlp=exlp1-exlp2 - if (exlp.lt.zero) then -* expvlp=exp(-vpar(16)*(2.0+exlp)*(2.0+exlp)) -* vlpadj=expvlp-int(exlp1/2.0) -* dsbo2dvlp=(1.0-vmbo)*(1.0-vpar(34)*2.0* -* $(2.0+exlp)*vpar(16)*expvlp) - vlpadj=vlp(j(2)) - dsbo2dvlp=(1.0-vmbo)*(1.0+vpar(34)*dvlpdsbo(j(2))) - end if - - sbo2=sbo2+(1.0-vmbo)*(-exbo-vpar(34)*vlpadj) - dsbo2dvmbo=exbo+vpar(34)*vlpadj - - sbo2h=sbo2 - powv=vpar(17) - if (sbo2.le.0.0) sbo2h=0.0 - if (sbo2.gt.0.0.and.sbo2.le.1.0) sbo2h=sbo2**powv - if (sbo2.gt.1.0.and.sbo2.lt.2.0) sbo2h=2.0-(2.0-sbo2)**powv - if (sbo2.gt.2.0) sbo2h=2.0 - thba=th0(ity) - expsbo=exp(-vpar(18)*(2.0-sbo2h)) - thetao=180.0-thba*(1.0-expsbo) - - thetao=thetao*dgrrdn - thdif=(thetao-hl) - thdi2=thdif*thdif - dthsbo=dgrrdn*thba*vpar(18)*expsbo - if (sbo2.lt.0.0) dthsbo=zero - if (sbo2.gt.0.0.and.sbo2.le.1.0) - $dthsbo=powv*(sbo2**(powv-1.0))*dgrrdn*thba*vpar(18)*expsbo - if (sbo2.gt.1.0.and.sbo2.lt.2.0) - $dthsbo=powv*((2.0-sbo2)**(powv-1.0))*dgrrdn*thba*vpar(18)*expsbo - if (sbo2.gt.2.0) dthsbo=zero - - exphu=vka(ity)*exp(-vka3(ity)*thdi2) - exphu2=vka(ity)-exphu - if (vka(ity).lt.zero) exphu2=exphu2-vka(ity) !To avoid linear Me-H-Me angles (6/6/06) - boap=boa**vval2(ity) - boap2=boa**(vval2(ity)-1.0) - bobp=bob**vval2(ity) - bobp2=bob**(vval2(ity)-1.0) - exa=exp(-vval1(ity2)*boap) - exb=exp(-vval1(ity2)*bobp) - dexadboa=vval2(ity)*vval1(ity2)*exa*boap2 - dexbdbob=vval2(ity)*vval1(ity2)*exb*bobp2 - exa2=(1.0-exa) - exb2=(1.0-exb) - - evh=evboadj2*evboadj*exa2*exb2*exphu2 - devdlb=evboadj2*evboadj*dexbdbob*exa2*exphu2 - devdla=evboadj2*evboadj*dexadboa*exb2*exphu2 - devdsbo=2.0*evboadj2*evboadj*dthsbo*exa2*exb2* - $vka3(ity)*thdif*exphu - devdh=-2.0*evboadj2*evboadj*exa2*exb2*vka3(ity)*thdif*exphu - - devdsbo2= - $evboadj*exa2*exb2*exphu2*(vval4(ity2)-1.0)*(-vpar(15)*expun2/htun2 - $+htun1*(vpar(15)*expun2-vkac(ity)*expun)/(htun2*htun2)) - -* devdsbo2=-evboadj2*exa2*exb2*exphu2*(vpar(13)*expov2/htov2+ -* $htov1*(vka8(ity)*expov-vpar(13)*expov2)/(htov2*htov2))+ -* $evboadj*exa2*exb2*exphu2*(vpar(14)-1.0)*(-vpar(15)*expun2/htun2 -* $+htun1*(vpar(15)*expun2-vkac(ity)*expun)/(htun2*htun2)) - - if (j(2) .le. na_local) then - ev=ev+evh - estrain(j(2))=estrain(j(2))+evh !central atom energy - endif - -* write (64,'(4i8,18f8.2)')mdstep,j(1),j(2),j(3),sbo2,sbo2h, -* $thetao*rdndgr,hl*rdndgr,bo(la),bo(lb),bopi(la), -* $vlp(j(2)),exbo,vlpadj,vmbo,evh,ev,vka(ity) -********************************************************************** -* * -* Calculate penalty for two double bonds in valency angle * -* * -********************************************************************** - exbo=abo(j(2))-aval(ia(j(2),1)) - expov=exp(vpar(22)*exbo) - expov2=exp(-vpar(21)*exbo) - htov1=2.0+expov2 - htov2=1.0+expov+expov2 - ecsboadj=htov1/htov2 - exphu1=exp(-vpar(20)*(boa-2.0)*(boa-2.0)) - exphu2=exp(-vpar(20)*(bob-2.0)*(bob-2.0)) - - epenh=vkap(ity)*ecsboadj*exphu1*exphu2 - estrain(j(2))=estrain(j(2))+epenh - epen=epen+epenh - decoadboa=-2.0*vpar(20)*epenh*(boa-2.0) - decoadbob=-2.0*vpar(20)*epenh*(bob-2.0) - - decdsbo2=-vkap(ity)*exphu1*exphu2*(vpar(21)*expov2/htov2+htov1* - $(vpar(22)*expov-vpar(21)*expov2)/(htov2*htov2)) -********************************************************************** -* * -* Calculate valency angle conjugation energy * -* * -********************************************************************** - unda=abo(j(1))-boa -* ovb=abo(j(2))-valf(ia(j(2),1)) - ovb=abo(j(2))-vval3(ia(j(2),1)) !Modification for Ru 7/6/2004 - - undc=abo(j(3))-bob - ba=(boa-1.50)*(boa-1.50) - bb=(bob-1.50)*(bob-1.50) - exphua=exp(-vpar(31)*ba) - exphub=exp(-vpar(31)*bb) - exphuua=exp(-vpar(39)*unda*unda) - exphuob=exp(vpar(3)*ovb) - exphuuc=exp(-vpar(39)*undc*undc) - hulpob=1.0/(1.0+exphuob) - ecoah=vka8(ity)*exphua*exphub*exphuua*exphuuc*hulpob - decodbola=-2.0*vka8(ity)*(boa-1.50)*vpar(31)*exphua*exphub - $*exphuua*exphuuc*hulpob+vpar(39)*vka8(ity)*exphua*exphub* - $exphuua*exphuuc*hulpob*2.0*unda - decodbolb=-2.0*vka8(ity)*(bob-1.50)*vpar(31)*exphua*exphub - $*exphuua*exphuuc*hulpob+vpar(39)*vka8(ity)*exphua*exphub* - $exphuua*exphuuc*hulpob*2.0*undc - decodboua=-2.0*unda*vka8(ity)*vpar(39)*exphua*exphub - $*exphuua*exphuuc*hulpob - decodbouc=-2.0*undc*vka8(ity)*vpar(39)*exphua*exphub - $*exphuua*exphuuc*hulpob - decodboob=-vka8(ity)*exphua*exphub*exphuua*exphuuc*hulpob* - $hulpob*vpar(3)*exphuob -* decodboob=zero -* decodboua=zero -* decodbouc=zero - - ecoa=ecoa+ecoah - estrain(j(2))=estrain(j(2))+ecoah !central atom energy - -********************************************************************** -* * -* Calculate derivative valency energy to cartesian coordinates * -* * -********************************************************************** - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do k1=1,3 - do k2=1,3 - ftmp = devdh*dhdc(i1,k1,k2) - d(k1,j(k2))=d(k1,j(k2))+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(j(k2),k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/3 - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do k2=1,3 - ihu=j(k2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(la) - ihu=idbo(la,i2) - do k1=1,3 - ftmp = (devdla+decoadboa+decodbola)* - $dbondc(la,k1,i2) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(la) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(la) - ihu=idbo(la,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(lb) - ihu=idbo(lb,i2) - do k1=1,3 - ftmp = (devdlb+decoadbob+decodbolb)* - $dbondc(lb,k1,i2) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(lb) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(lb) - ihu=idbo(lb,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - do i2=1,nbocen - j5=ia(j(2),2+i2) - ibv=nubon2(j(2),i2) - if (bo(ibv).gt.0.0) then - dvmbodbo=-vmbo*8.0*bo(ibv)**7 - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - do k1=1,3 - ftmp = (-dsbo2dvlp*devdsbo+devdsbo2+decdsbo2 - $+dvmbodbo*dsbo2dvmbo*devdsbo)* - $dbondc(ibv,k1,i3)+devdsbo*(dbopindc(ibv,k1,i3)+ - $dbopi2ndc(ibv,k1,i3)) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ibv) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - do i2=1,ia(j(1),2) - j5=ia(j(1),2+i2) - ibv=nubon2(j(1),i2) - if (bo(ibv).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - do k1=1,3 - ftmp = decodboua*dbondc(ibv,k1,i3) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ibv) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - do i2=1,ia(j(2),2) - j5=ia(j(2),2+i2) - ibv=nubon2(j(2),i2) - if (bo(ibv).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - do k1=1,3 - ftmp = decodboob*dbondc(ibv,k1,i3) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ibv) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - do i2=1,ia(j(3),2) - j5=ia(j(3),2+i2) - ibv=nubon2(j(3),i2) - if (bo(ibv).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - do k1=1,3 - ftmp = decodbouc*dbondc(ibv,k1,i3) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ibv) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(ibv) - ihu=idbo(ibv,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - endif - - 10 continue - - return - end -********************************************************************** -********************************************************************** - - subroutine hbond - -********************************************************************** -#include "cbka.blk" -#include "cbkbo.blk" -#include "cbkconst.blk" -#include "cbkc.blk" -#include "cbkd.blk" -#include "cbkdcell.blk" -#include "cbkenergies.blk" -#include "cbkidbo.blk" -#include "cbksrthb.blk" -#include "control.blk" -#include "cbkhbond.blk" -#include "small.blk" - dimension drda(3),j(3),dvdc(3,3),dargdc(3,3) - dimension virial_tmp(3,3),virialsym(6) -********************************************************************** -* * -* Calculate hydrogen bond energies and first derivatives * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In hbond' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - ehb=zero - do 10 i1=1,nhb - ityhb=ihb(i1,1) - j(1)=ihb(i1,2) - j(2)=ihb(i1,3) - j(3)=ihb(i1,4) - la=ihb(i1,5) - boa=bo(la) - call dista2(j(2),j(3),rda,dxm,dym,dzm) - drda(1)=dxm/rda - drda(2)=dym/rda - drda(3)=dzm/rda - call calvalhb(j(1),j(2),j(3),ix,iy,iz,arg,hhb(i1),dvdc,dargdc) - rhu1=rhb(ityhb)/rda - rhu2=rda/rhb(ityhb) - sinhu=sin(hhb(i1)/2.0) - sin2=sinhu*sinhu - exphu1=exp(-vhb1(ityhb)*boa) - exphu2=exp(-vhb2(ityhb)*(rhu1+rhu2-2.0)) - if (lhbnew .eq. 0) then - ehbh=(1.0-exphu1)*dehb(ityhb)*exphu2*sin2*sin2*sin2*sin2 - else - ehbh=(1.0-exphu1)*dehb(ityhb)*exphu2*sin2*sin2 - endif - ehb=ehb+ehbh - estrain(j(2))=estrain(j(2))+ehbh !2nd atom energy - -********************************************************************** -* * -* Calculate first derivatives * -* * -********************************************************************** - if (lhbnew .eq. 0) then - dehbdbo=vhb1(ityhb)*exphu1*dehb(ityhb)*exphu2*sin2*sin2* - $ sin2*sin2 - dehbdv=(1.0-exphu1)*dehb(ityhb)*exphu2* - $ 4.0*sin2*sin2*sin2*sinhu*cos(hhb(i1)/2.0) - dehbdrda=(1.0-exphu1)*dehb(ityhb)*sin2*sin2*sin2*sin2* - $ vhb2(ityhb)*(rhb(ityhb)/(rda*rda)-1.0/rhb(ityhb))*exphu2 - else - dehbdbo=vhb1(ityhb)*exphu1*dehb(ityhb)*exphu2*sin2*sin2 - dehbdv=(1.0-exphu1)*dehb(ityhb)*exphu2* - $ 2.0*sin2*sinhu*cos(hhb(i1)/2.0) - dehbdrda=(1.0-exphu1)*dehb(ityhb)*sin2*sin2* - $ vhb2(ityhb)*(rhb(ityhb)/(rda*rda)-1.0/rhb(ityhb))*exphu2 - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do k1=1,3 - ftmp = dehbdrda*drda(k1) - d(k1,j(2))=d(k1,j(2))+ftmp - d(k1,j(3))=d(k1,j(3))-ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ - $ ftmp*c(j(2),k1p)-ftmp*c(j(3),k1p) - end do - endif - - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/2 - do k1 = 1,6 - vtmp = virialsym(k1)*frac - ihu = j(2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - ihu = j(3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do k1=1,3 - do k2=1,3 - ftmp = dehbdv*dvdc(k1,k2) - d(k1,j(k2))=d(k1,j(k2))+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(j(k2),k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/3 - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do k2=1,3 - ihu=j(k2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(la) - ihu=idbo(la,i2) - do k1=1,3 - ftmp = dehbdbo*dbondc(la,k1,i2) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(la) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(la) - ihu=idbo(la,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - 10 continue - return - end - -********************************************************************** -********************************************************************** - - subroutine torang - -********************************************************************** -#include "cbka.blk" -#include "cbkabo.blk" -#include "cbkbo.blk" -#include "cbkbopi.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkdbopindc.blk" -#include "cbkdcell.blk" -#include "cbkdhdc.blk" -#include "cbkdrdc.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkfftorang.blk" -#include "cbkh.blk" -#include "cbkia.blk" -#include "cbkidbo.blk" -#include "cbkinit.blk" -#include "cbknubon2.blk" -#include "cbkrbo.blk" -#include "cbktorang.blk" -#include "cbktorsion.blk" -#include "cbktregime.blk" -#include "cbkvalence.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" - - DIMENSION A(3),DRDA(3),DADC(4),DRADC(3,4),DRBDC(3,4), - $DRCDC(3,4),DHDDC(3,4),DHEDC(3,4),DRVDC(3,4),DTDC(3,4), - $DNDC(3,4) - dimension j(4),dh1rdc(3,3),dh2rdc(3,3),dargdc(3,3) - dimension virial_tmp(3,3),virialsym(6) -********************************************************************** -* * -* Calculate torsion angle energies and first derivatives * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In torang' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - do k1=1,3 - do k2=1,4 - dhddc(k1,k2)=0.0 - dhedc(k1,k2)=0.0 - dradc(k1,k2)=0.0 - drbdc(k1,k2)=0.0 - drcdc(k1,k2)=0.0 - end do - end do - et=0.0 - eth12=0.0 - eco=0.0 - dadc(1)=1.0 - dadc(2)=0.0 - dadc(3)=0.0 - dadc(4)=-1.0 - if (ntor.eq.0) return - - do 10 i1=1,ntor - j(1)=it(i1,2) - j(2)=it(i1,3) - j(3)=it(i1,4) - j(4)=it(i1,5) - - ity=it(i1,1) - la=it(i1,6) - lb=it(i1,7) - lc=it(i1,8) - call calvalres(j(1),j(2),j(3),arg1,ht1,dh1rdc,dargdc) - call calvalres(j(2),j(3),j(4),arg2,ht2,dh2rdc,dargdc) - boa=bo(la)-cutof2 - bob=bo(lb)-cutof2 - boc=bo(lc)-cutof2 - if (boa.lt.zero.or.bob.lt.zero.or.boc.lt.zero) - $goto 10 - r42=0.0 - ivl1=ibsym(la) - ivl2=ibsym(lb) - ivl3=ibsym(lc) - isign1=1 - isign2=1 - isign3=1 - rla=rbo(la) - rlb=rbo(lb) - - call dista2(j(1),j(4),r4,a(1),a(2),a(3)) -********************************************************************** -* * -* Determine torsion angle * -* * -********************************************************************** - d142=r4*r4 - rla=rbo(la) - rlb=rbo(lb) - rlc=rbo(lc) - coshd=cos(ht1) - coshe=cos(ht2) - sinhd=sin(ht1) - sinhe=sin(ht2) - poem=2.0*rla*rlc*sinhd*sinhe - poem2=poem*poem - tel=rla*rla+rlb*rlb+rlc*rlc-d142-2.0*(rla*rlb*coshd-rla*rlc* - $coshd*coshe+rlb*rlc*coshe) - if (poem.lt.1e-20) poem=1e-20 - arg=tel/poem - if (arg.gt.1.0) arg=1.0 - if (arg.lt.-1.0) arg=-1.0 - arg2=arg*arg - thg(i1)=acos(arg)*rdndgr - k1=j(1) - k2=j(2) - k3=j(3) - k4=j(4) - call dista2(k3,k2,dis,x3,y3,z3) - y32z32=y3*y3+z3*z3 - wort1=sqrt(y32z32)+1e-6 - wort2=sqrt(y32z32+x3*x3)+1e-6 -* if (wort1.lt.1e-6) wort1=1e-6 -* if (wort2.lt.1e-6) wort2=1e-6 - sinalf=y3/wort1 - cosalf=z3/wort1 - sinbet=x3/wort2 - cosbet=wort1/wort2 - call dista2(k1,k2,dis,x1,y1,z1) - x1=x1*cosbet-y1*sinalf*sinbet-z1*cosalf*sinbet - y1=y1*cosalf-z1*sinalf - wort3=sqrt(x1*x1+y1*y1)+1e-6 -* if (wort3.lt.1e-6) wort3=1e-6 - singam=y1/wort3 - cosgam=x1/wort3 - call dista2(k4,k2,dis,x4,y4,z4) - x4=x4*cosbet-y4*sinalf*sinbet-z4*cosalf*sinbet - y4=y4*cosalf-z4*sinalf - y4=x4*singam-y4*cosgam - if (y4.gt.0.0) thg(i1)=-thg(i1) - if (thg(i1).lt.-179.999999d0) thg(i1)=-179.999999d0 - if (thg(i1).gt.179.999999d0) thg(i1)=179.999999d0 - th2=thg(i1)*dgrrdn -********************************************************************** -* * -* Calculate torsion angle energy * -* * -********************************************************************** - exbo1=abo(j(2))-valf(ia(j(2),1)) - exbo2=abo(j(3))-valf(ia(j(3),1)) - htovt=exbo1+exbo2 - expov=exp(vpar(26)*htovt) - expov2=exp(-vpar(25)*(htovt)) - htov1=2.0+expov2 - htov2=1.0+expov+expov2 - etboadj=htov1/htov2 - - btb2=bopi(lb)-1.0+etboadj - bo2t=1.0-btb2 - bo2p=bo2t*bo2t - bocor2=exp(v4(ity)*bo2p) - - hsin=sinhd*sinhe - ethhulp=0.50*v1(ity)*(1.0+arg)+v2(ity)*bocor2*(1.0-arg2)+ - $v3(ity)*(0.50+2.0*arg2*arg-1.50*arg) - - exphua=exp(-vpar(24)*boa) - exphub=exp(-vpar(24)*bob) - exphuc=exp(-vpar(24)*boc) - bocor4=(1.0-exphua)*(1.0-exphub)*(1.0-exphuc) - eth=hsin*ethhulp*bocor4 - - detdar=hsin*bocor4*(0.50*v1(ity)-2.0*v2(ity)*bocor2*arg+ - $v3(ity)*(6.0*arg2-1.5d0)) - detdhd=coshd*sinhe*bocor4*ethhulp - detdhe=sinhd*coshe*bocor4*ethhulp - - detdboa=vpar(24)*exphua*(1.0-exphub)*(1.0-exphuc)*ethhulp*hsin - detdbopib=-bocor4*2.0*v4(ity)*v2(ity)* - $bo2t*bocor2*(1.0-arg2)*hsin - detdbob=vpar(24)*exphub*(1.0-exphua)* - $(1.0-exphuc)*ethhulp*hsin - detdboc=vpar(24)*exphuc*(1.0-exphua)* - $(1.0-exphub)*ethhulp*hsin - - detdsbo1=-(detdbopib)* - $(vpar(25)*expov2/htov2+htov1* - $(vpar(26)*expov-vpar(25)*expov2)/(htov2*htov2)) - - et=et+eth - estrain(j(2))=estrain(j(2))+0.50*eth !2nd atom energy - estrain(j(3))=estrain(j(3))+0.50*eth !3rd atom energy - -********************************************************************** -* * -* Calculate conjugation energy * -* * -********************************************************************** - ba=(boa-1.50)*(boa-1.50) - bb=(bob-1.50)*(bob-1.50) - bc=(boc-1.50)*(boc-1.50) - exphua1=exp(-vpar(28)*ba) - exphub1=exp(-vpar(28)*bb) - exphuc1=exp(-vpar(28)*bc) - sbo=exphua1*exphub1*exphuc1 - dbohua=-2.0*(boa-1.50)*vpar(28)*exphua1*exphub1*exphuc1 - dbohub=-2.0*(bob-1.50)*vpar(28)*exphua1*exphub1*exphuc1 - dbohuc=-2.0*(boc-1.50)*vpar(28)*exphua1*exphub1*exphuc1 - arghu0=(arg2-1.0)*sinhd*sinhe - ehulp=vconj(ity)*(arghu0+1.0) - ecoh=ehulp*sbo - decodar=sbo*vconj(ity)*2.0*arg*sinhd*sinhe - decodbola=dbohua*ehulp - decodbolb=dbohub*ehulp - decodbolc=dbohuc*ehulp - decodhd=coshd*sinhe*vconj(ity)*sbo*(arg2-1.0) - decodhe=coshe*sinhd*vconj(ity)*sbo*(arg2-1.0) - - eco=eco+ecoh - estrain(j(2))=estrain(j(2))+0.50*ecoh !2nd atom energy - estrain(j(3))=estrain(j(3))+0.50*ecoh !3rd atom energy - - 1 continue -********************************************************************** -* * -* Calculate derivative torsion angle and conjugation energy * -* to cartesian coordinates * -* * -********************************************************************** - SINTH=SIN(THG(i1)*DGRRDN) - IF (SINTH.GE.0.0.AND.SINTH.LT.1.0D-10) SINTH=1.0D-10 - IF (SINTH.LT.0.0.AND.SINTH.GT.-1.0D-10) SINTH=-1.0D-10 - IF (j(1).EQ.IB(LA,2)) THEN - DO K1=1,3 - DRADC(K1,1)=DRDC(LA,K1,1) - DRADC(K1,2)=DRDC(LA,K1,2) - end do - ELSE - DO K1=1,3 - DRADC(K1,1)=DRDC(LA,K1,2) - DRADC(K1,2)=DRDC(LA,K1,1) - end do - ENDIF - IF (j(2).EQ.IB(LB,2)) THEN - DO K1=1,3 - DRBDC(K1,2)=DRDC(LB,K1,1) - DRBDC(K1,3)=DRDC(LB,K1,2) - end do - ELSE - DO K1=1,3 - DRBDC(K1,2)=DRDC(LB,K1,2) - DRBDC(K1,3)=DRDC(LB,K1,1) - end do - ENDIF - IF (j(3).EQ.IB(LC,2)) THEN - DO K1=1,3 - DRCDC(K1,3)=DRDC(LC,K1,1) - DRCDC(K1,4)=DRDC(LC,K1,2) - end do - ELSE - DO K1=1,3 - DRCDC(K1,3)=DRDC(LC,K1,2) - DRCDC(K1,4)=DRDC(LC,K1,1) - end do - ENDIF - - do k1=1,3 - dhddc(1,k1)=dh1rdc(1,k1) - dhddc(2,k1)=dh1rdc(2,k1) - dhddc(3,k1)=dh1rdc(3,k1) - dhedc(1,k1+1)=dh2rdc(1,k1) - dhedc(2,k1+1)=dh2rdc(2,k1) - dhedc(3,k1+1)=dh2rdc(3,k1) - end do - -********************************************************************** -* write (64,*)j(1),j(2),j(3),j(4) -* do k1=1,3 -* write (64,'(10f12.4)')(dh1rdc(k1,k2),k2=1,3), -* $(dhdc(ld,k1,k2),k2=1,3),(dhddc(k1,k2),k2=1,4) -* write (64,'(10f12.4)')(dh2rdc(k1,k2),k2=1,3), -* $(dhdc(le,k1,k2),k2=1,3),(dhedc(k1,k2),k2=1,4) -* end do -* write (64,*) -********************************************************************** - HTRA=RLA+COSHD*(RLC*COSHE-RLB) - HTRB=RLB-RLA*COSHD-RLC*COSHE - HTRC=RLC+COSHE*(RLA*COSHD-RLB) - HTHD=RLA*SINHD*(RLB-RLC*COSHE) - HTHE=RLC*SINHE*(RLB-RLA*COSHD) - HNRA=RLC*SINHD*SINHE - HNRC=RLA*SINHD*SINHE - HNHD=RLA*RLC*COSHD*SINHE - HNHE=RLA*RLC*SINHD*COSHE - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - DO K1=1,3 - DRDA(K1)=A(K1)/R4 - DO K2=1,4 - DRVDC(K1,K2)=DRDA(K1)*DADC(K2) - DTDC(K1,K2)=2.0*(DRADC(K1,K2)*HTRA+DRBDC(K1,K2)*HTRB+DRCDC(K1,K2 - $)*HTRC-DRVDC(K1,K2)*R4+DHDDC(K1,K2)*HTHD+DHEDC(K1,K2)*HTHE) - DNDC(K1,K2)=2.0*(DRADC(K1,K2)*HNRA+DRCDC(K1,K2)*HNRC+DHDDC(K1,K2 - $)*HNHD+DHEDC(K1,K2)*HNHE) - DARGTDC(i1,K1,K2)=(DTDC(K1,K2)-ARG*DNDC(K1,K2))/POEM - - ftmp = DARGTDC(i1,K1,K2)*detdar+ - $dargtdc(i1,k1,k2)*decodar+(detdhd+decodhd)*dhddc(k1,k2)+ - $(detdhe+decodhe)*dhedc(k1,k2) - D(K1,J(K2))=D(K1,J(K2))+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(j(k2),k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/4 - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do k2=1,4 - ihu=j(k2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(la) - ihu=idbo(la,i2) - do k1=1,3 - ftmp = dbondc(la,k1,i2)*(detdboa+decodbola) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(la) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(la) - ihu=idbo(la,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(lb) - ihu=idbo(lb,i2) - do k1=1,3 - ftmp = dbondc(lb,k1,i2)*(detdbob+decodbolb) - $ +dbopindc(lb,k1,i2)*detdbopib - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(lb) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(lb) - ihu=idbo(lb,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i2=1,idbo1(lc) - ihu=idbo(lc,i2) - do k1=1,3 - ftmp = dbondc(lc,k1,i2)*(detdboc+decodbolc) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(lc) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i2=1,idbo1(lc) - ihu=idbo(lc,i2) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - do i2=1,ia(j(2),2) - iob=ia(j(2),2+i2) - ncubo=nubon2(j(2),i2) - if (bo(ncubo).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(ncubo) - ihu=idbo(ncubo,i3) - do k1=1,3 - ftmp = detdsbo1*dbondc(ncubo,k1,i3) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(ncubo) - ihu=idbo(ncubo,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - do i2=1,ia(j(3),2) - iob=ia(j(3),2+i2) - ncubo=nubon2(j(3),i2) - if (bo(ncubo).gt.0.0) then - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do i3=1,idbo1(ncubo) - ihu=idbo(ncubo,i3) - do k1=1,3 - ftmp = detdsbo1*dbondc(ncubo,k1,i3) - d(k1,ihu)=d(k1,ihu)+ftmp - - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k1,k1p)=virial_tmp(k1,k1p)+ftmp*c(ihu,k1p) - end do - endif - - end do - end do - - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/idbo1(ncubo) - do k1 = 1,6 - vtmp = virialsym(k1)*frac - do i3=1,idbo1(ncubo) - ihu=idbo(ncubo,i3) - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - end do - endif - - endif - - endif - end do - - 10 continue - - return - end -********************************************************************** -********************************************************************** - - subroutine nonbon - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkch.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkdcell.blk" -#include "cbkenergies.blk" -#include "cbkff.blk" -#include "cbkia.blk" -#include "cbknonbon.blk" -#include "cbkpairs.blk" -#include "cbknvlown.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" - - dimension a(3),da(6) - dimension virial_tmp(3,3),virialsym(6) -********************************************************************** -* * -* Calculate vdWaals and Coulomb energies and derivatives * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In nonbon' -c$$$ call timer(65) -c$$$ end if - - ew=0.0 - ep=0.0 - - c1c=332.0638 - third=one/three - fothird=4.0/3.0 - twothird=2.0/3.0 - h15=(vpar(29)-1.0)/vpar(29) - - nptmp=0 - nstmp=0 - do 10 ivl=1,nvpair-nvlself -c Use precomputed midpoint criterion to decide if interaction is owned. - if (nvlown(ivl).eq.1) then - - i1=nvl1(ivl) - i2=nvl2(ivl) - - call dista2(i1,i2,rr,a(1),a(2),a(3)) - if (rr.gt.swb.or.rr.lt.0.001) goto 10 - - ity1=ia(i1,1) - ity2=ia(i2,1) - imol1=iag(i1,3+mbond) - imol2=iag(i2,3+mbond) - rr2=rr*rr - - sw=1.0 - sw1=0.0 - call taper(rr,rr2) -********************************************************************** -* * -* Calculate vdWaals energy * -* * -********************************************************************** - p1=p1co(ity1,ity2) - p2=p2co(ity1,ity2) - p3=p3co(ity1,ity2) - hulpw=(rr**vpar(29)+gamwco(ity1,ity2)) - rrw=hulpw**(1.0/vpar(29)) - h1=exp(p3*(1.0-rrw/p1)) - h2=exp(0.50*p3*(1.0-rrw/p1)) - - ewh=p2*(h1-2.0*h2) - rrhuw=rr**(vpar(29)-1.0) - dewdr=(p2*p3/p1)*(h2-h1)*rrhuw*(hulpw**(-h15)) - -********************************************************************** -* * -* Calculate Coulomb energy * -* * -********************************************************************** - q1q2=ch(i1)*ch(i2) - hulp1=(rr2*rr+gamcco(ity1,ity2)) - eph=c1c*q1q2/(hulp1**third) - depdr=-c1c*q1q2*rr2/(hulp1**fothird) -********************************************************************** -* * -* Taper correction * -* * -********************************************************************** - ephtap=eph*sw - depdrtap=depdr*sw+eph*sw1 - ewhtap=ewh*sw - dewdrtap=dewdr*sw+ewh*sw1 - -* write (64,*)i1,i2,p1,p2,p3,gamwco(ity1,ity2),vpar(29),ewh,ew - ew=ew+ewhtap - ep=ep+ephtap - estrain(i1)=estrain(i1)+0.50*(ewhtap+ephtap) !1st atom energy - estrain(i2)=estrain(i2)+0.50*(ewhtap+ephtap) !2nd atom energy - -********************************************************************** -* * -* Calculate derivatives vdWaals energy to cartesian * -* coordinates * -* * -********************************************************************** - - if (Lvirial.eq.1) then - do k1=1,3 - do k2=1,3 - virial_tmp(k1,k2) = 0.0 - end do - end do - endif - - do k4=1,3 - ftmp = (dewdrtap+depdrtap)*(a(k4)/rr) - d(k4,i1)=d(k4,i1)+ftmp - d(k4,i2)=d(k4,i2)-ftmp - if (Lvirial.eq.1) then - do k1p=1,3 - virial_tmp(k4,k1p)=virial_tmp(k4,k1p)+ - $ ftmp*c(i1,k1p)-ftmp*c(i2,k1p) - end do - endif - end do - - if (Lvirial.eq.1) then - virialsym(1) = virial_tmp(1,1) - virialsym(2) = virial_tmp(2,2) - virialsym(3) = virial_tmp(3,3) - virialsym(4) = virial_tmp(1,2) - virialsym(5) = virial_tmp(1,3) - virialsym(6) = virial_tmp(2,3) - do k1 = 1,6 - virial(k1) = virial(k1) + virialsym(k1) - end do - - if (Latomvirial.eq.1) then - frac = 1.0d0/2 - do k1 = 1,6 - vtmp = virialsym(k1)*frac - ihu=i1 - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - ihu=i2 - atomvirial(k1,ihu) = atomvirial(k1,ihu) + vtmp - end do - endif - - endif - - endif - - 10 continue - - return - end - -********************************************************************** -********************************************************************** - - subroutine efield - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkch.blk" -#include "cbkcha.blk" -#include "cbkd.blk" -#include "cbkefield.blk" -#include "cbkenergies.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "small.blk" -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In efield' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -********************************************************************** -* * -* Electric field * -* * -********************************************************************** - efi=0.0 - efix=0.0 - efiy=0.0 - efiz=0.0 - c1c=332.0638 !Coulomb energy conversion - c1=23.02 !conversion from kcal to eV - - if (ifieldx.eq.1) then - do i1=1,na - efih=vfieldx*c1*c1c*ch(i1)*c(i1,1) - efix=efix+efih - estrain(i1)=estrain(i1)+efih !atom energy - - defidc=c1*c1c*vfieldx*ch(i1) - d(1,i1)=d(1,i1)+defidc - end do - end if - - if (ifieldy.eq.1) then - do i1=1,na - efih=vfieldy*c1*c1c*ch(i1)*c(i1,2) - efiy=efiy+efih - estrain(i1)=estrain(i1)+efih !atom energy - - defidc=c1*c1c*vfieldy*ch(i1) - d(2,i1)=d(2,i1)+defidc - end do - end if - - if (ifieldz.eq.1) then - do i1=1,na - efih=vfieldz*c1*c1c*ch(i1)*c(i1,3) - efiz=efiz+efih - estrain(i1)=estrain(i1)+efih !atom energy - - defidc=c1*c1c*vfieldz*ch(i1) - d(3,i1)=d(3,i1)+defidc - end do - end if - - efi=efix+efiy+efiz - return - end -********************************************************************** -********************************************************************** - - subroutine restraint - -********************************************************************** -#include "cbka.blk" -#include "cbkatomcoord.blk" -#include "cbkc.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkenergies.blk" -#include "cbkrestr.blk" -#include "cbktorang.blk" -#include "cbktorsion.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "small.blk" -#include "cbkinit.blk" - dimension drda(3),j(4),dhrdc(3,3),dargdc(3,3) -********************************************************************** -* * -* Calculate distance restraint energy * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In restraint' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - do i1=1,nrestra - ih1=irstra(i1,1) - ih2=irstra(i1,2) - if (itend(i1).eq.0.or.(mdstep.gt.itstart(i1).and.mdstep.lt. - $itend(i1))) then - call dista2(ih1,ih2,rr,dx,dy,dz) - diffr=rr-rrstra(i1) -* diffr=rrstra(i1) - exphu=exp(-vkrst2(i1)*(diffr*diffr)) - erh=vkrstr(i1)*(1.0-exphu) - deresdr=2.0*vkrst2(i1)*diffr*vkrstr(i1)*exphu -* deresdr=-2.0*vkrst2(i1)*diffr*vkrstr(i1)*exphu - eres=eres+erh - drda(1)=dx/rr - drda(2)=dy/rr - drda(3)=dz/rr - do k1=1,3 - d(k1,ih1)=d(k1,ih1)+deresdr*drda(k1) - d(k1,ih2)=d(k1,ih2)-deresdr*drda(k1) - end do - end if - end do - -********************************************************************** -* * -* Calculate angle restraint energy * -* * -********************************************************************** - do i1=1,nrestrav - j(1)=irstrav(i1,1) - j(2)=irstrav(i1,2) - j(3)=irstrav(i1,3) - ittr=0 -* do i2=1,nval -* if (j(1).eq.iv(i2,2).and.j(2).eq.iv(i2,3).and.j(3).eq.iv(i2,4)) -* $ittr=i2 -* end do -* if (ittr.eq.0) stop 'Wrong valence angle restraint' - call calvalres(j(1),j(2),j(3),arg,hr,dhrdc,dargdc) - vaval=hr*rdndgr - diffv=-(vaval-vrstra(i1))*dgrrdn - exphu=exp(-vkr2v(i1)*(diffv*diffv)) - erh=vkrv(i1)*(1.0-exphu) - deresdv=-2.0*vkr2v(i1)*diffv*vkrv(i1)*exphu - eres=eres+erh - do k1=1,3 - do k2=1,3 - d(k1,j(k2))=d(k1,j(k2))+deresdv*dhrdc(k1,k2) - end do - end do - - end do - -********************************************************************** -* * -* Calculate torsion restraint energy * -* * -********************************************************************** - do i1=1,nrestrat - j(1)=irstrat(i1,1) - j(2)=irstrat(i1,2) - j(3)=irstrat(i1,3) - j(4)=irstrat(i1,4) - ittr=0 - do i2=1,ntor - if (j(1).eq.it(i2,2).and.j(2).eq.it(i2,3).and.j(3).eq.it(i2,4) - $.and.j(4).eq.it(i2,5)) ittr=i2 - if (j(4).eq.it(i2,2).and.j(3).eq.it(i2,3).and.j(2).eq.it(i2,4) - $.and.j(1).eq.it(i2,5)) ittr=i2 - end do - if (ittr.eq.0) then - write (*,*)'Wrong torsion restraint' - write (*,*)i1,j(1),j(2),j(3),j(4) - stop 'Wrong torsion restraint' - end if - vtor=thg(ittr) - difft=-(vtor-trstra(i1))*dgrrdn - exphu=exp(-vkr2t(i1)*(difft*difft)) - erh=vkrt(i1)*(1.0-exphu) - deresdt=2.0*vkr2t(i1)*difft*vkrt(i1)*exphu - if (vtor.lt.zero) deresdt=-deresdt - eres=eres+erh - do k1=1,3 - do k2=1,4 - d(k1,j(k2))=d(k1,j(k2))+deresdt*dargtdc(ittr,k1,k2) - end do - end do - - end do -********************************************************************** -* * -* Calculate mass centre restraint energy * -* * -********************************************************************** - do i1=1,nrestram - j1=irstram(i1,2) - j2=irstram(i1,3) - j3=irstram(i1,4) - j4=irstram(i1,5) - kdir=irstram(i1,1) - cmx1=0.0 - cmy1=0.0 - cmz1=0.0 - cmx2=0.0 - cmy2=0.0 - cmz2=0.0 - summas1=0.0 - summas2=0.0 - do i2=j1,j2 - cmx1=cmx1+c(i2,1)*xmasat(i2) - cmy1=cmy1+c(i2,2)*xmasat(i2) - cmz1=cmz1+c(i2,3)*xmasat(i2) - summas1=summas1+xmasat(i2) - end do - cmx1=cmx1/summas1 - cmy1=cmy1/summas1 - cmz1=cmz1/summas1 - if (mdstep.lt.2) then - rmstrax(i1)=cmx1 - rmstray(i1)=cmy1 - rmstraz(i1)=cmz1 - end if - if (kdir.le.3) then - do i2=j3,j4 - cmx2=cmx2+c(i2,1)*xmasat(i2) - cmy2=cmy2+c(i2,2)*xmasat(i2) - cmz2=cmz2+c(i2,3)*xmasat(i2) - summas2=summas2+xmasat(i2) - end do - cmx2=cmx2/summas2 - cmy2=cmy2/summas2 - cmz2=cmz2/summas2 - end if - if (kdir.eq.1) dist=cmx1-cmx2 - if (kdir.eq.2) dist=cmy1-cmy2 - if (kdir.eq.3) dist=cmz1-cmz2 - if (kdir.eq.4) then - distx=cmx1-rmstrax(i1) - disty=cmy1-rmstray(i1) - distz=cmz1-rmstraz(i1) - dist=sqrt(distx*distx+disty*disty+distz*distz) - end if - dismacen(i1)=dist - dist=dist-rmstra1(i1) - erh=rmstra2(i1)*dist*dist - deresdr=2.0*dist*rmstra2(i1) -* exphu=exp(-rmstra3(i1)*(dist*dist)) -* erh=rmstra2(i1)*(1.0-exphu) -* deresdr=2.0*rmstra3(i1)*dist*rmstra2(i1)*exphu - eres=eres+erh - if (kdir.le.3) then - do i2=j1,j2 - d(kdir,i2)=d(kdir,i2)+deresdr*xmasat(i2)/summas1 - end do - do i2=j3,j4 - d(kdir,i2)=d(kdir,i2)-deresdr*xmasat(i2)/summas2 - end do - end if - if (kdir.eq.4.and.mdstep.gt.5) then - do i2=j1,j2 - d(1,i2)=d(1,i2)+deresdr*(distx/dist)*(xmasat(i2)/summas1) - d(2,i2)=d(2,i2)+deresdr*(disty/dist)*(xmasat(i2)/summas1) - d(3,i2)=d(3,i2)+deresdr*(distz/dist)*(xmasat(i2)/summas1) - end do - end if - end do -********************************************************************** -* * -* Calculate morphing energy * -* * -********************************************************************** - if (imorph.eq.1) then - distot=zero - do i1=1,na - dmx=c(i1,1)-cmo(i1,1) - dmy=c(i1,2)-cmo(i1,2) - dmz=c(i1,3)-cmo(i1,3) - dism=sqrt(dmx*dmx+dmy*dmy+dmz*dmz) - distot=distot+dism -* exphu=exp(-vmo2(i1)*(dism*dism)) -* erh=vmo1(i1)*(1.0-exphu) - erh=vmo1(i1)*dism - eres=eres+erh -* deresddis=2.0*vmo2(i1)*dism*vmo1(i1)*exphu - deresddis=vmo1(i1) - drda1=dmx/dism - drda2=dmy/dism - drda3=dmz/dism - d(1,i1)=d(1,i1)+deresddis*drda1 - d(2,i1)=d(2,i1)+deresddis*drda2 - d(3,i1)=d(3,i1)+deresddis*drda3 - end do - - end if - - - return - end -********************************************************************** -******************************************************************** - - subroutine calvalres (ja1,ja2,ja3,arg,hr,dhrdc,dargdc) - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" - dimension a(3),b(3),j(3),dradc(3,3),drbdc(3,3),dtdc(3,3), - $dargdc(3,3),dndc(3,3),dadc(3),dbdc(3),dhrdc(3,3) -********************************************************************** -* * -* Calculate valency angles and their derivatives to cartesian * -* coordinates for restraint calculations * -* * -********************************************************************** -c$$$* if (ndebug.eq.1) then -c$$$C* open (65,file='fort.65',status='unknown',access='append') -c$$$* write (65,*) 'In calvalres' -c$$$* call timer(65) -c$$$* close (65) -c$$$* end if - - dadc(1)=-1.0 - dadc(2)=1.0 - dadc(3)=0.0 - dbdc(1)=0.0 - dbdc(2)=1.0 - dbdc(3)=-1.0 - do k1=1,3 - do k2=1,3 - dradc(k1,k2)=0.0 - drbdc(k1,k2)=0.0 - end do - end do -********************************************************************** -* * -* Determine valency angle * -* * -********************************************************************** - call dista2(ja1,ja2,rla,dx1,dy1,dz1) - call dista2(ja2,ja3,rlb,dx2,dy2,dz2) - - a(1)=-dx1 - a(2)=-dy1 - a(3)=-dz1 - b(1)=dx2 - b(2)=dy2 - b(3)=dz2 - poem=rla*rlb - tel=a(1)*b(1)+a(2)*b(2)+a(3)*b(3) - arg=tel/poem - arg2=arg*arg - s1ma22=1.0-arg2 - if (s1ma22.lt.1.0d-10) s1ma22=1.0d-10 - s1ma2=sqrt(s1ma22) - if (arg.gt.1.0) arg=1.0 - if (arg.lt.-1.0) arg=-1.0 - hr=acos(arg) -********************************************************************** -* * -* Calculate derivative valency angle to cartesian coordinates * -* * -********************************************************************** - do k1=1,3 - dradc(k1,1)=-a(k1)/rla - dradc(k1,2)=a(k1)/rla - end do - - do k1=1,3 - drbdc(k1,2)=b(k1)/rlb - drbdc(k1,3)=-b(k1)/rlb - end do - - do k1=1,3 - do k2=1,3 - dndc(k1,k2)=rla*drbdc(k1,k2)+rlb*dradc(k1,k2) - dtdc(k1,k2)=a(k1)*dbdc(k2)+b(k1)*dadc(k2) - dargdc(k1,k2)=(dtdc(k1,k2)-arg*dndc(k1,k2))/poem - dhrdc(k1,k2)=-dargdc(k1,k2)/s1ma2 - end do - end do - - 10 continue - - return - end -********************************************************************** -******************************************************************** - - subroutine calvalhb (ja1,ja2,ja3,ix,iy,iz,arg,hr,dhrdc,dargdc) - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" - dimension a(3),b(3),j(3),dradc(3,3),drbdc(3,3),dtdc(3,3), - $dargdc(3,3),dndc(3,3),dadc(3),dbdc(3),dhrdc(3,3) -********************************************************************** -* * -* Calculate valency angles and their derivatives to cartesian * -* coordinates for hydrogen bond calculations * -* * -********************************************************************** -c$$$* if (ndebug.eq.1) then -c$$$* open (65,file='fort.65',status='unknown',access='append') -c$$$* write (65,*) 'In calvalhb' -c$$$* call timer(65) -c$$$* close (65) -c$$$* end if - - dadc(1)=-1.0 - dadc(2)=1.0 - dadc(3)=0.0 - dbdc(1)=0.0 - dbdc(2)=1.0 - dbdc(3)=-1.0 - do k1=1,3 - do k2=1,3 - dradc(k1,k2)=0.0 - drbdc(k1,k2)=0.0 - end do - end do -********************************************************************** -* * -* Determine valency angle * -* * -********************************************************************** - call dista2(ja1,ja2,rla,dx1,dy1,dz1) - call dista2(ja2,ja3,rlb,dx2,dy2,dz2) - - a(1)=-dx1 - a(2)=-dy1 - a(3)=-dz1 - b(1)=dx2 - b(2)=dy2 - b(3)=dz2 - poem=rla*rlb - tel=a(1)*b(1)+a(2)*b(2)+a(3)*b(3) - arg=tel/poem - arg2=arg*arg - s1ma22=1.0-arg2 - if (s1ma22.lt.1.0d-10) s1ma22=1.0d-10 - s1ma2=sqrt(s1ma22) - if (arg.gt.1.0) arg=1.0 - if (arg.lt.-1.0) arg=-1.0 - hr=acos(arg) -********************************************************************** -* * -* Calculate derivative valency angle to cartesian coordinates * -* * -********************************************************************** - do k1=1,3 - dradc(k1,1)=-a(k1)/rla - dradc(k1,2)=a(k1)/rla - end do - - do k1=1,3 - drbdc(k1,2)=b(k1)/rlb - drbdc(k1,3)=-b(k1)/rlb - end do - - do k1=1,3 - do k2=1,3 - dndc(k1,k2)=rla*drbdc(k1,k2)+rlb*dradc(k1,k2) - dtdc(k1,k2)=a(k1)*dbdc(k2)+b(k1)*dadc(k2) - dargdc(k1,k2)=(dtdc(k1,k2)-arg*dndc(k1,k2))/poem - dhrdc(k1,k2)=-dargdc(k1,k2)/s1ma2 - end do - end do - - 10 continue - - return - end -********************************************************************** -********************************************************************** - - subroutine caltor(ja1,ja2,ja3,ja4,ht) - -********************************************************************** -#include "cbka.blk" -#include "cbkenergies.blk" -#include "cbktregime.blk" -#include "control.blk" -#include "cbkinit.blk" - DIMENSION A(3),DRDA(3),DADC(4),DRADC(3,4),DRBDC(3,4), - $DRCDC(3,4),DHDDC(3,4),DHEDC(3,4),DRVDC(3,4),DTDC(3,4), - $DNDC(3,4) - dimension j(4),dvdc1(3,3),dargdc1(3,3),dvdc2(3,3),dargdc2(3,3) -********************************************************************** -* * -* Calculate torsion angle (for internal coordinates output) * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In caltor' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - do k1=1,3 - do k2=1,4 - dhddc(k1,k2)=0.0 - dhedc(k1,k2)=0.0 - dradc(k1,k2)=0.0 - drbdc(k1,k2)=0.0 - drcdc(k1,k2)=0.0 - end do - end do - et=0.0 - eco=0.0 - dadc(1)=1.0 - dadc(2)=0.0 - dadc(3)=0.0 - dadc(4)=-1.0 - call dista2(ja1,ja2,rla,dx1,dy1,dz1) - call dista2(ja2,ja3,rlb,dx2,dy2,dz2) - call dista2(ja3,ja4,rlc,dx2,dy2,dz2) - call dista2(ja1,ja4,r4,dx2,dy2,dz2) - call calvalres(ja1,ja2,ja3,arg1,h1,dvdc1,dargdc1) - call calvalres(ja2,ja3,ja4,arg2,h2,dvdc2,dargdc2) -********************************************************************** -* * -* Determine torsion angle * -* * -********************************************************************** - d142=r4*r4 - coshd=cos(h1) - coshe=cos(h2) - sinhd=sin(h1) - sinhe=sin(h2) - poem=2.0*rla*rlc*sinhd*sinhe - poem2=poem*poem - tel=rla*rla+rlb*rlb+rlc*rlc-d142-2.0*(rla*rlb*coshd-rla*rlc* - $coshd*coshe+rlb*rlc*coshe) - arg=tel/poem - if (arg.gt.1.0) arg=1.0 - if (arg.lt.-1.0) arg=-1.0 - arg2=arg*arg - ht=acos(arg)*rdndgr - k1=ja1 - k2=ja2 - k3=ja3 - k4=ja4 - call dista2(k3,k2,dis,x3,y3,z3) - y32z32=y3*y3+z3*z3 - wort1=sqrt(y32z32)+1e-6 - wort2=sqrt(y32z32+x3*x3)+1e-6 - sinalf=y3/wort1 - cosalf=z3/wort1 - sinbet=x3/wort2 - cosbet=wort1/wort2 - call dista2(k1,k2,dis,x1,y1,z1) - x1=x1*cosbet-y1*sinalf*sinbet-z1*cosalf*sinbet - y1=y1*cosalf-z1*sinalf - wort3=sqrt(x1*x1+y1*y1)+1e-6 - singam=y1/wort3 - cosgam=x1/wort3 - call dista2(k4,k2,dis,x4,y4,z4) - x4=x4*cosbet-y4*sinalf*sinbet-z4*cosalf*sinbet - y4=y4*cosalf-z4*sinalf - y4=x4*singam-y4*cosgam - if (y4.gt.0.0) ht=-ht - if (ht.lt.-179.999999d0) ht=-179.999999d0 - if (ht.gt.179.999999d0) ht=179.999999d0 - - return - end -********************************************************************** diff --git a/lib/reax/reax_reac.F b/lib/reax/reax_reac.F deleted file mode 100644 index 73c625d7f1..0000000000 --- a/lib/reax/reax_reac.F +++ /dev/null @@ -1,312 +0,0 @@ -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -********************************************************************** -* * -* REAXFF Reactive force field program * -* * -* Developed and written by Adri van Duin, duin@wag.caltech.edu * -* * -* Copyright (c) 2001-2010 California Institute of Technology * -* * -* This is an open-source program. Feel free to modify its * -* contents. Please keep me informed of any useful modification * -* or addition that you made. Please do not distribute this * -* program to others; if people are interested in obtaining * -* a copy of this program let them contact me first. * -* * -********************************************************************** -********************************************************************** - - subroutine encalc - -********************************************************************** -#include "cbka.blk" -#include "cbkc.blk" -#include "cbkcha.blk" -#include "cbkconst.blk" -#include "cbkd.blk" -#include "cbkdcell.blk" -#include "cbkenergies.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "small.blk" -********************************************************************** -* * -* Calculate energy and first derivatives * -* * -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In encalc' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if - estrc=0.0 - do i1=1,na - do i2=1,3 - d(i2,i1)=0.0 - estrain(i1)=0.0 - end do - end do - eb=zero - ea=zero - elp=zero - emol=zero - ev=zero - ehb=zero - ecoa=zero - epen=zero - et=zero - eco=zero - eres=zero - eradbo=zero - efi=zero - - if(Lvirial.eq.1) then - do k1 = 1,6 - virial(k1) = zero - end do - endif - - if (Latomvirial.eq.1) then - do i1=1,na - do i2=1,6 - atomvirial(i2,i1)=0.0 - end do - end do - endif - - call boncor - call lonpar - call covbon - call ovcor - - call srtang !Determine valency angles - call srttor !Determine torsion angles -* call srtoop !Determine out of plane angles - call srthb !Determine hydrogen bonds - - call calval - call valang - -* call oopang - - call torang - call hbond - !print *, 'called hbond' - !print *, nchaud - - call nonbon - call efield - - call restraint - -c -c Use this to print out fort.73-style energies -c It only works correctly in serial mode -c -c write (6,'(i8,1x,14(f21.10,1x))')mdstep+nprevrun,eb,ea,elp, -c $emol,ev+epen,ecoa,ehb,et,eco,ew,ep,ech,efi - - estrc=eb+ea+elp+ev+ecoa+emol+epen+et+ehb+eco+ew+ep+ncha2*ech+efi - if (estrc.gt.zero) return - if (estrc.le.zero) then - goto 10 - else - write (*,*)mdstep - write (92,*)eb,ea,elp,ev,ecoa,emol,epen,eoop,et,eco,ew, - $ep,ech,eres,eradbo - stop 'Energy not a number' - end if - - 10 continue - return - end -********************************************************************** -********************************************************************** - - subroutine reaxinit - -********************************************************************** -#include "cbka.blk" -#include "cbkatomcoord.blk" -#include "cbkc.blk" -#include "cbkcha.blk" -#include "cbkconst.blk" -#include "cbkdcell.blk" -#include "cbkdistan.blk" -#include "cbkenergies.blk" -#include "cbkia.blk" -#include "cbkimove.blk" -#include "cbkinit.blk" -#include "cbktregime.blk" -#include "cellcoord.blk" -#include "control.blk" -#include "opt.blk" -#include "small.blk" -********************************************************************** -c$$$ if (ndebug.eq.1) then -c$$$C open (65,file='fort.65',status='unknown',access='append') -c$$$ write (65,*) 'In init' -c$$$ call timer(65) -c$$$ close (65) -c$$$ end if -********************************************************************** -* * -* Initialize variables * -* * -********************************************************************** - convmd=4.184*1.0d26 - pi=3.14159265 - avognr=6.0221367d23 - rdndgr=180.0/pi - dgrrdn=1.0/rdndgr - rgasc=8.314510 - caljou=4.184 - xjouca=1.0/caljou - ech=zero - zero=0.0 - one=1.0 - two=2.0 - three=3.0 - half=one/two - nzero=0 - none=1 - ntwo=2 - nthree=3 - invt=0 - ndata2=0 - iheatf=0 - nradcount=0 - itemp=1 - xinh=zero - ifieldx=0 - ifieldy=0 - ifieldz=0 - mdstep=0 - kx=0 - ky=0 - kz=0 - nit=0 - nbon=0 - angle(1)=90.0 - angle(2)=90.0 - angle(3)=90.0 - axiss(1)=zero - axiss(2)=zero - axiss(3)=zero - do i1=1,nat - id(i1,1)=0 - id(i1,2)=0 - id(i1,3)=0 - end do - icgeo=0 - sumhe=zero - ustime=zero - systime=zero - vpmax=zero - vpmin=zero - dseed=0 - iagain=0 - do i1=1,nat - do i2=1,mbond+3 - ia(i1,i2)=0 - iag(i1,i2)=0 - end do - end do - - ioldchg=0 - na=0 - nrestra=0 - nrestrav=0 - nrestrat=0 - nrestram=0 - tset=tsetor - tm11=axis(1) - tm21=zero - tm31=zero - tm22=axis(2) - tm32=zero - tm33=axis(3) - qruid='NORMAL RUN' -c$$$ do i1=1,nat -c$$$ imove(i1)=1 -c$$$ end do - -********************************************************************** -* * -* Write file headers * -* * -********************************************************************** -Cc open (71,file='fort.71',status='unknown',access='append') -c write (71,10) -c close (71) -Cc open (73,file='fort.73',status='unknown',access='append') -c write (73,20) -c close (73) -c if (ntrc.gt.0) then -Cc open (75,file='fort.75',status='unknown',access='append') -c write (75,30) -c close (75) -c end if -c if (nmethod.eq.4) then -Cc open (59,file='fort.59',status='unknown',access='append') -c write (59,40) -c close (59) -c end if - - return -********************************************************************** -* * -* Format part * -* * -********************************************************************** - 10 format (' Iter. Nmol Epot Ekin Etot ', - $' T(K) Eaver(block) Eaver(total) Taver Tmax ', - $' Pres(MPa) sdev(Epot) sdev(Eaver) Tset Timestep', - $' RMSG Totaltime') - 20 format (' Iter. Ebond Eatom Elp Emol', - $' Eval Ecoa Ehbo Etors Econj', - $' Evdw Ecoul Echarge Efield') - 30 format (' Iter. Tsys Tzone1 Tset1 Tzone2 Tset2') - 40 format (' Iter. a b c px', - $'(MPa) py(MPa) pz(MPa) pset(MPa) Volume ') - end -********************************************************************** -************************************************************************ - -c subroutine timer(nunit) - -************************************************************************ -c#include "cbka.blk" -c#include "cbkinit.blk" -c real timear -c real tarray(2) -c#ifdef _IBM -c call dtime_(tarray,timear) -c#else -c call dtime(tarray,timear) -c#endif - -c ustime=ustime+tarray(1) -c systime=systime+tarray(2) -c write (nunit,100)ustime,systime,ustime+systime -c return -c 100 format ('User time:',f20.4,' System time:',f20.4, -c $' Total time:',f20.4) -c end -************************************************************************ -************************************************************************ diff --git a/lib/reax/small.blk b/lib/reax/small.blk deleted file mode 100644 index 9ec66b6e17..0000000000 --- a/lib/reax/small.blk +++ /dev/null @@ -1,5 +0,0 @@ - common - $/rsmall/ tset,dseed,tempmd,ts2,ts22,nmolo,nmolo5,nbon,na,namov, - $ na_local - - diff --git a/lib/reax/valang.blk b/lib/reax/valang.blk deleted file mode 100644 index c4b0027b8a..0000000000 --- a/lib/reax/valang.blk +++ /dev/null @@ -1,9 +0,0 @@ - - - - common - $/cbkvalang/ vval1(nsort),vval2(nvatym), - $ vval4(nsort),vkac(nvatym),vkap(nvatym), - $ vka3(nvatym),vka8(nvatym),th0(nvatym) - - diff --git a/lib/scafacos/.gitignore b/lib/scafacos/.gitignore new file mode 100644 index 0000000000..2752e713ed --- /dev/null +++ b/lib/scafacos/.gitignore @@ -0,0 +1,4 @@ +/scafacos* +/includelink +/liblink +/build diff --git a/lib/scafacos/Install.py b/lib/scafacos/Install.py index d23e8a3686..8044215d47 100644 --- a/lib/scafacos/Install.py +++ b/lib/scafacos/Install.py @@ -1,165 +1,122 @@ #!/usr/bin/env python -# Install.py tool to download, unpack, build, and link to the Scafacos library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to download, unpack, build, and link to the ScaFaCoS library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,subprocess +import sys, os, subprocess, shutil, tarfile +from argparse import ArgumentParser -# help message +sys.path.append('..') +from install_helpers import fullpath, geturl, get_cpus, checkmd5sum -help = """ +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = "1.0.1" +url = "https://github.com/scafacos/scafacos/releases/download/v%s/scafacos-%s.tar.gz" % (version, version) + +# known checksums for different ScaFaCoS versions. used to validate the download. +checksums = { \ + '1.0.1' : 'bd46d74e3296bd8a444d731bb10c1738' \ + } + +# extra help message + +HELP = """ Syntax from src dir: make lib-scafacos args="-b" or: make lib-scafacos args="-p /usr/local/scafacos" Syntax from lib dir: python Install.py -b or: python Install.py -p /usr/local/scafacos -specify zero or more options, order does not matter - - -b = download and build the Scafacos library - -p = specify folder of existing Scafacos installation - - always creates includelink, liblink to Scafacos dirs - Example: make lib-scafacos args="-b" # download/build in lib/scafacos/scafacos -make lib-scafacos args="-p $HOME/scafacos" # use existing Scafacos installation in $HOME +make lib-scafacos args="-p $HOME/scafacos" # use existing ScaFaCoS installation in $HOME """ -# settings +# parse and process arguments -version = "scafacos-1.0.1" -url = "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" -#url = "https://gigamove.rz.rwth-aachen.de/d/id/CTzyApN76MXMJ6/dd/100" % version +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the ScaFaCoS library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing ScaFaCoS installation") +parser.add_argument("-v", "--version", default=version, + help="set version of ScaFaCoS to download and build (default: %s)" % version) -# print error message or help +args = parser.parse_args() -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) -# expand to full path name -# process leading '~' or relative path +buildflag = args.build +pathflag = args.path is not None +version = args.version -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) +homepath = fullpath(".") +scafacospath = os.path.join(homepath, "scafacos-%s" % version) -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) +if pathflag: + scafacospath = args.path + if not os.path.isdir(os.path.join(scafacospath, "include")): + sys.exit("ScaFaCoS include path for %s does not exist" % scafacospath) + if (not os.path.isdir(os.path.join(scafacospath, "lib64"))) \ + and (not os.path.isdir(os.path.join(scafacospath, "lib"))): + sys.exit("ScaFaCoS lib path for %s does not exist" % scafacospath) + scafacospath = fullpath(scafacospath) - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program +# download and unpack ScaFaCoS tarball + +if buildflag: + print("Downloading ScaFaCoS ...") + geturl(url, "%s/scafacos-%s.tar.gz" % (homepath, version)) + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], '%s/scafacos-%s.tar.gz' % (homepath, version)): + sys.exit("Checksum for ScaFaCoS library does not match") + + print("Unpacking ScaFaCoS tarball ...") + if os.path.exists(scafacospath): + shutil.rmtree(scafacospath) + tarname = os.path.join(homepath, "%s.tar.gz" % scafacospath) + if tarfile.is_tarfile(tarname): + tgz = tarfile.open(tarname) + tgz.extractall(path=homepath) + os.remove(tarname) else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file + sys.exit("File %s is not a supported archive" % tarname) - return None + # build ScaFaCoS + print("Building ScaFaCoS ...") + n_cpu = get_cpus() + cmd = 'cd "%s"; ./configure --prefix="%s" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77=; make -j%d; make install' % (scafacospath, os.path.join(homepath, 'build'), n_cpu) + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + sys.exit("Make failed with:\n %s" % e.output.decode('UTF-8')) -def geturl(url,fname): - success = False - - if which('curl') != None: - cmd = 'curl -L -o "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling curl failed with: %s" % e.output.decode('UTF-8')) - - if not success and which('wget') != None: - cmd = 'wget -O "%s" %s' % (fname,url) - print("Wget command: %s" % cmd) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling wget failed with: %s" % e.output.decode('UTF-8')) - - if not success: - error("Failed to download source code with 'curl' or 'wget'") - return - -# parse args - -args = sys.argv[1:] -nargs = len(args) - -homepath = "." - -buildflag = True -pathflag = False -linkflag = True - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-v": - if iarg+2 > nargs: error() - version = args[iarg+1] - iarg += 2 - elif args[iarg] == "-p": - if iarg+2 > nargs: error() - scafacospath = fullpath(args[iarg+1]) - pathflag = True - iarg += 2 - elif args[iarg] == "-b": - buildflag = True - iarg += 1 - else: error() - -homepath = fullpath(homepath) -homedir = "%s/%s" % (homepath,version) - -if (pathflag): - if not os.path.isdir(scafacospath): error("Scafacos path does not exist") - homedir =scafacospath - -if (buildflag and pathflag): - error("Cannot use -b and -p flag at the same time") - -# download and unpack Scafacos tarball +# create 2 links in lib/scafacos to ScaFaCoS include/lib dirs +print("Creating links to ScaFaCoS include and lib files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") if buildflag: - print("Downloading Scafacos ...") - geturl(url,"%s/%s.tar.gz" % (homepath,version)) - - print("Unpacking Scafacos tarball ...") - if os.path.exists("%s/%s" % (homepath,version)): - cmd = 'rm -rf "%s/%s"' % (homepath,version) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.remove("%s/%s.tar.gz" % (homepath,version)) - if os.path.basename(homedir) != version: - if os.path.exists(homedir): - cmd = 'rm -rf "%s"' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.rename("%s/%s" % (homepath,version),homedir) - -# build Scafacos - -if buildflag: - print("Building Scafacos ...") - cmd = 'cd "%s"; ./configure --prefix="`pwd`/build" --disable-doc --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m --with-internal-fftw --with-internal-pfft --with-internal-pnfft CC=mpicc FC=mpif90 CXX=mpicxx F77= > log.txt; make -j; make install' % homedir - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - print(txt.decode('UTF-8')) - -# create 2 links in lib/scafacos to Scafacos include/lib dirs - -if linkflag: - print("Creating links to Scafacos include and lib files") - if os.path.isfile("includelink") or os.path.islink("includelink"): - os.remove("includelink") - if os.path.isfile("liblink") or os.path.islink("liblink"): - os.remove("liblink") - cmd = 'ln -s "%s/build/include" includelink' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "%s/build/lib" liblink' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + os.symlink(os.path.join(homepath, 'build', 'include'), 'includelink') + os.symlink(os.path.join(homepath, 'build', 'lib'), 'liblink') +else: + os.symlink(os.path.join(scafacospath, 'include'), 'includelink') + if os.path.isdir(os.path.join(scafacospath, "lib64")): + os.symlink(os.path.join(scafacospath, 'lib64'), 'liblink') + else: + os.symlink(os.path.join(scafacospath, 'lib'), 'liblink') diff --git a/lib/smd/Install.py b/lib/smd/Install.py index 9247cb449b..1829b9c236 100644 --- a/lib/smd/Install.py +++ b/lib/smd/Install.py @@ -1,14 +1,36 @@ #!/usr/bin/env python -# Install.py tool to download, unpack, and point to the Eigen library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to download, unpack, and point to the Eigen library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,glob,subprocess +import sys, os, glob, shutil, tarfile +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = '3.3.7' +tarball = "eigen.tar.gz" + +# known checksums for different Eigen versions. used to validate the download. +checksums = { \ + '3.3.4' : '1a47e78efe365a97de0c022d127607c3', \ + '3.3.5' : 'ee48cafede2f51fe33984ff5c9f48026', \ + '3.3.6' : 'd1be14064b50310b0eb2b49e402c64d7', \ + '3.3.7' : 'f2a417d083fe8ca4b8ed2bc613d20f07' \ +} # help message -help = """ +HELP = """ Syntax from src dir: make lib-smd args="-b" or: make lib-smd args="-p /usr/include/eigen3" @@ -16,143 +38,77 @@ Syntax from lib dir: python Install.py -b or: python Install.py -p /usr/include/eigen3" or: python Install.py -v 3.3.4 -b -specify one or more options, order does not matter - - -b = download and unpack/configure the Eigen library - -p = specify folder holding an existing installation of Eigen - -v = set version of Eigen library to download and set up (default = 3.3.4) - - Example: make lib-smd args="-b" # download/build in default lib/smd/eigen-eigen-* make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 """ -# settings +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the Eigen3 library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing Eigen installation") +parser.add_argument("-v", "--version", default=version, + help="set version of Eigen to download and build (default: %s)" % version) -version = '3.3.4' -tarball = "eigen.tar.gz" +args = parser.parse_args() -# print error message or help +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +homepath = fullpath(".") +eigenpath = os.path.join(homepath, "eigen3") -# expand to full path name -# process leading '~' or relative path +buildflag = args.build +pathflag = args.path is not None +version = args.version -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) - -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) - - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program - else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file - - return None - -def geturl(url,fname): - success = False - - if which('curl') != None: - cmd = 'curl -L -o "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling curl failed with: %s" % e.output.decode('UTF-8')) - - if not success and which('wget') != None: - cmd = 'wget -O "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling wget failed with: %s" % e.output.decode('UTF-8')) - - if not success: - error("Failed to download source code with 'curl' or 'wget'") - return - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -homepath = "." -homedir = "eigen3" - -buildflag = False -pathflag = False -linkflag = True - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-v": - if iarg+2 > nargs: error() - version = args[iarg+1] - iarg += 2 - elif args[iarg] == "-p": - if iarg+2 > nargs: error() - eigenpath = fullpath(args[iarg+1]) - pathflag = True - iarg += 2 - elif args[iarg] == "-b": - buildflag = True - iarg += 1 - else: error() - -homepath = fullpath(homepath) - -if (pathflag): - if not os.path.isdir(eigenpath): error("Eigen path does not exist") - -if (buildflag and pathflag): - error("Cannot use -b and -p flag at the same time") - -if (not buildflag and not pathflag): - error("Have to use either -b or -p flag") +if pathflag: + eigenpath = args.path + if not os.path.isdir(eigenpath): + sys.exit("Eigen path %s does not exist" % eigenpath) + eigenpath = fullpath(eigenpath) # download and unpack Eigen tarball # use glob to find name of dir it unpacks to if buildflag: print("Downloading Eigen ...") + eigentar = os.path.join(homepath, tarball) url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version - geturl(url,"%s/%s" % (homepath,tarball)) + geturl(url, eigentar) - print("Unpacking Eigen tarball ...") - edir = glob.glob("%s/eigen-eigen-*" % homepath) + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + print("checking version %s\n" % version) + if not checkmd5sum(checksums[version], eigentar): + sys.exit("Checksum for Eigen library does not match") + + + print("Cleaning up old folders ...") + edir = glob.glob(os.path.join(homepath, "eigen-eigen-*")) + edir.append(eigenpath) for one in edir: if os.path.isdir(one): - subprocess.check_output('rm -rf "%s"' % one,stderr=subprocess.STDOUT,shell=True) - cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarball) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - edir = glob.glob("%s/eigen-eigen-*" % homepath) - os.rename(edir[0],"%s/%s" % (homepath,homedir)) - os.remove(tarball) + shutil.rmtree(one) + + print("Unpacking Eigen tarball ...") + if tarfile.is_tarfile(eigentar): + tgz = tarfile.open(eigentar) + tgz.extractall(path=homepath) + os.remove(eigentar) + else: + sys.exit("File %s is not a supported archive" % eigentar) + edir = glob.glob(os.path.join(homepath, "eigen-eigen-*")) + os.rename(edir[0], eigenpath) # create link in lib/smd to Eigen src dir -if linkflag: - print("Creating link to Eigen files") - if os.path.isfile("includelink") or os.path.islink("includelink"): - os.remove("includelink") - if pathflag: linkdir = eigenpath - else: linkdir = "%s/%s" % (homepath,homedir) - cmd = 'ln -s "%s" includelink' % linkdir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print("Creating link to Eigen include folder") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +linkdir = eigenpath +os.symlink(linkdir, 'includelink') diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py index f40eb53bc6..6a95637720 100644 --- a/lib/voronoi/Install.py +++ b/lib/voronoi/Install.py @@ -1,169 +1,121 @@ #!/usr/bin/env python -# Install.py tool to download, unpack, build, and link to the Voro++ library -# used to automate the steps described in the README file in this dir +""" +Install.py tool to download, unpack, build, and link to the Voro++ library +used to automate the steps described in the README file in this dir +""" from __future__ import print_function -import sys,os,re,subprocess +import sys, os, subprocess, shutil, tarfile +from argparse import ArgumentParser -# help message +sys.path.append('..') +from install_helpers import fullpath, geturl, checkmd5sum -help = """ +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +version = "voro++-0.4.6" +url = "https://download.lammps.org/thirdparty/%s.tar.gz" % version + +# known checksums for different Voro++ versions. used to validate the download. +checksums = { \ + 'voro++-0.4.6' : '2338b824c3b7b25590e18e8df5d68af9' \ + } + +# extra help message + +HELP = """ Syntax from src dir: make lib-voronoi args="-b" or: make lib-voronoi args="-p /usr/local/voro++-0.4.6" or: make lib-voronoi args="-b -v voro++-0.4.6" + Syntax from lib dir: python Install.py -b -v voro++-0.4.6 or: python Install.py -b or: python Install.py -p /usr/local/voro++-0.4.6 -specify one or more options, order does not matter - - -b = download and build the Voro++ library - -p = specify folder of existing Voro++ installation - -v = set version of Voro++ to download and build (default voro++-0.4.6) - Example: make lib-voronoi args="-b" # download/build in lib/voronoi/voro++-0.4.6 make lib-voronoi args="-p $HOME/voro++-0.4.6" # use existing Voro++ installation in $HOME/voro++-0.4.6 """ -# settings +# parse and process arguments -version = "voro++-0.4.6" -url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build the Voro++ library") +pgroup.add_argument("-p", "--path", + help="specify folder of existing Voro++ installation") +parser.add_argument("-v", "--version", default=version, + help="set version of Voro++ to download and build (default: %s)" % version) -# print error message or help +args = parser.parse_args() -def error(str=None): - if not str: print(help) - else: print("ERROR",str) - sys.exit() +# print help message and exit, if neither build nor path options are given +if not args.build and not args.path: + parser.print_help() + sys.exit(HELP) -# expand to full path name -# process leading '~' or relative path +buildflag = args.build +pathflag = args.path is not None +voropath = args.path -def fullpath(path): - return os.path.abspath(os.path.expanduser(path)) +homepath = fullpath(".") +homedir = os.path.join(homepath, version) -def which(program): - def is_exe(fpath): - return os.path.isfile(fpath) and os.access(fpath, os.X_OK) - - fpath, fname = os.path.split(program) - if fpath: - if is_exe(program): - return program - else: - for path in os.environ["PATH"].split(os.pathsep): - path = path.strip('"') - exe_file = os.path.join(path, program) - if is_exe(exe_file): - return exe_file - - return None - -def geturl(url,fname): - success = False - - if which('curl') != None: - cmd = 'curl -L -o "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling curl failed with: %s" % e.output.decode('UTF-8')) - - if not success and which('wget') != None: - cmd = 'wget -O "%s" %s' % (fname,url) - try: - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - success = True - except subprocess.CalledProcessError as e: - print("Calling wget failed with: %s" % e.output.decode('UTF-8')) - - if not success: - error("Failed to download source code with 'curl' or 'wget'") - return - -# parse args - -args = sys.argv[1:] -nargs = len(args) -if nargs == 0: error() - -homepath = "." -homedir = version - -buildflag = False -pathflag = False -linkflag = True - -iarg = 0 -while iarg < nargs: - if args[iarg] == "-v": - if iarg+2 > nargs: error() - version = args[iarg+1] - iarg += 2 - elif args[iarg] == "-p": - if iarg+2 > nargs: error() - voropath = fullpath(args[iarg+1]) - pathflag = True - iarg += 2 - elif args[iarg] == "-b": - buildflag = True - iarg += 1 - else: error() - -homepath = fullpath(homepath) -homedir = "%s/%s" % (homepath,version) - -if (pathflag): - if not os.path.isdir(voropath): error("Voro++ path does not exist") - homedir = voropath - -if (buildflag and pathflag): - error("Cannot use -b and -p flag at the same time") - -if (not buildflag and not pathflag): - error("Have to use either -b or -p flag") +if pathflag: + if not os.path.isdir(voropath): + sys.exit("Voro++ path %s does not exist" % voropath) + homedir = fullpath(voropath) # download and unpack Voro++ tarball if buildflag: print("Downloading Voro++ ...") - geturl(url,"%s/%s.tar.gz" % (homepath,version)) + vorotar = os.path.join(homepath, version) + '.tar.gz' + geturl(url, vorotar) + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], vorotar): + sys.exit("Checksum for Voro++ library does not match") print("Unpacking Voro++ tarball ...") - if os.path.exists("%s/%s" % (homepath,version)): - cmd = 'rm -rf "%s/%s"' % (homepath,version) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version) - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.remove("%s/%s.tar.gz" % (homepath,version)) + srcpath = os.path.join(homepath, version) + if os.path.exists(srcpath): + shutil.rmtree(srcpath) + if tarfile.is_tarfile(vorotar): + tgz = tarfile.open(vorotar) + tgz.extractall(path=homepath) + os.remove(vorotar) + else: + sys.exit("File %s is not a supported archive" % vorotar) if os.path.basename(homedir) != version: if os.path.exists(homedir): - cmd = 'rm -rf "%s"' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - os.rename("%s/%s" % (homepath,version),homedir) + shutil.rmtree(homedir) + os.rename(srcpath, homedir) # build Voro++ if buildflag: print("Building Voro++ ...") cmd = 'cd "%s"; make CXX=g++ CFLAGS="-fPIC -O3"' % homedir - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - print(txt.decode('UTF-8')) + try: + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + print(txt.decode('UTF-8')) + except subprocess.CalledProcessError as e: + print("Make failed with:\n %s" % e.output.decode('UTF-8')) + sys.exit(1) # create 2 links in lib/voronoi to Voro++ src dir -if linkflag: - print("Creating links to Voro++ include and lib files") - if os.path.isfile("includelink") or os.path.islink("includelink"): - os.remove("includelink") - if os.path.isfile("liblink") or os.path.islink("liblink"): - os.remove("liblink") - cmd = 'ln -s "%s/src" includelink' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - cmd = 'ln -s "%s/src" liblink' % homedir - subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) +print("Creating links to Voro++ include and lib files") +if os.path.isfile("includelink") or os.path.islink("includelink"): + os.remove("includelink") +if os.path.isfile("liblink") or os.path.islink("liblink"): + os.remove("liblink") +os.symlink(os.path.join(homedir, 'src'), 'includelink') +os.symlink(os.path.join(homedir, 'src'), 'liblink') diff --git a/potentials/CC.Lebedeva b/potentials/CC.Lebedeva new file mode 100644 index 0000000000..930f7b4328 --- /dev/null +++ b/potentials/CC.Lebedeva @@ -0,0 +1,14 @@ +# Lebedeva Potential. Original values from Lebedeva. May be played with ;) +# +# Cite as: Irina V. Lebedeva, Andrey A. Knizhnik, Andrey M. Popov, Yurii E. Lozovik, Boris V. Potapkin, +# Modeling of graphene-based NEMS +# Physica E 44 (6), 949 (2012) +# https://doi.org/10.1016/j.physe.2011.07.018 +# +# Parameters must be in this order as here, otherwise their values may be changed. +# The last one, S, is convenient for scaling the potential amplitude. S is a multiplication factor for A, B, C +# A B C z0 alpha D1 D2 lambda1 lambda2 S +# These are values according to Levedeva et al +#C C 10.510 11.6523.34 35.883 3.34 4.16 -0.86232 0.10049 0.48703 0.46445 1.0 +# These are values by Z. Koziol et al.: https://arxiv.org/abs/1803.05162 +C C 14.558 21.204 1.8 3.198 4.16 -0.862 0.10049 0.6 0.4 1.0 diff --git a/potentials/Mo_Chen_PRM2017.snap b/potentials/Mo_Chen_PRM2017.snap index 579315b3dd..05d642358e 100644 --- a/potentials/Mo_Chen_PRM2017.snap +++ b/potentials/Mo_Chen_PRM2017.snap @@ -1,6 +1,7 @@ + # DATE: 2017-09-18 CONTRIBUTOR: Chi Chen CITATION: C. Chen, Z. Deng, R. Tran, H. Tang, I.-H. Chu, S. P. Ong, "Accurate force field for molybdenum by machine learning large materials data" Physical Review Materials 1, 04 3603 (2017) # Generated by Materials Virtual Lab # Definition of SNAP potential. pair_style snap -pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo Mo_Chen_PRM2017.snapparam Mo +pair_coeff * * Mo_Chen_PRM2017.snapcoeff Mo_Chen_PRM2017.snapparam Mo diff --git a/potentials/Ta06A.snap b/potentials/Ta06A.snap index 43ce31fdcc..d9feae0b46 100644 --- a/potentials/Ta06A.snap +++ b/potentials/Ta06A.snap @@ -2,7 +2,7 @@ # Definition of SNAP potential Ta_Cand06A # Assumes 1 LAMMPS atom type - + variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 73 @@ -13,5 +13,5 @@ pair_style hybrid/overlay & zbl ${zblcutinner} ${zblcutouter} & snap pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap Ta06A.snapcoeff Ta Ta06A.snapparam Ta +pair_coeff * * snap Ta06A.snapcoeff Ta06A.snapparam Ta diff --git a/potentials/Ta06A.snapparam b/potentials/Ta06A.snapparam index 0627253341..283629d658 100644 --- a/potentials/Ta06A.snapparam +++ b/potentials/Ta06A.snapparam @@ -8,7 +8,8 @@ twojmax 6 # optional -gamma 1 rfac0 0.99363 rmin0 0 diagonalstyle 3 +bzeroflag 0 +quadraticflag 0 diff --git a/potentials/W_2940_2017_2.snap b/potentials/W_2940_2017_2.snap index 51eee41a0a..93c2bf866a 100644 --- a/potentials/W_2940_2017_2.snap +++ b/potentials/W_2940_2017_2.snap @@ -5,12 +5,12 @@ variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay & zbl ${zblcutinner} ${zblcutouter} & snap pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W +pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W #Nomenclature on the snap files are Element_DakotaID_Year_Month diff --git a/potentials/W_2940_2017_2.snapparam b/potentials/W_2940_2017_2.snapparam index e0b20005e6..27ab61a266 100644 --- a/potentials/W_2940_2017_2.snapparam +++ b/potentials/W_2940_2017_2.snapparam @@ -6,7 +6,8 @@ twojmax 8 # optional -gamma 1 rfac0 0.99363 rmin0 0 diagonalstyle 3 +bzeroflag 0 +quadraticflag 0 diff --git a/potentials/W_2940_2017_2_He_JW2013.snap b/potentials/W_2940_2017_2_He_JW2013.snap index ff0827c138..7eb4f65401 100644 --- a/potentials/W_2940_2017_2_He_JW2013.snap +++ b/potentials/W_2940_2017_2_He_JW2013.snap @@ -5,11 +5,11 @@ variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 -pair_coeff 1 1 zbl ${zblz} ${zblz} -pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL +pair_coeff 1 1 zbl ${zblz} ${zblz} +pair_coeff * * snap W_2940_2017_2.snapcoeff W_2940_2017_2.snapparam W NULL pair_coeff 2 2 table 1 He_He_JW2013.table HeHe pair_coeff 1 2 table 2 W_He_JW2013.table WHe #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here diff --git a/python/lammps.py b/python/lammps.py index 598e4c506f..9b3790f2db 100644 --- a/python/lammps.py +++ b/python/lammps.py @@ -85,14 +85,19 @@ class lammps(object): # fall back to loading with a relative path, # typically requires LD_LIBRARY_PATH to be set appropriately + if any([f.startswith('liblammps') and f.endswith('.dylib') for f in os.listdir(modpath)]): + lib_ext = ".dylib" + else: + lib_ext = ".so" + if not self.lib: try: - if not name: self.lib = CDLL(join(modpath,"liblammps.so"),RTLD_GLOBAL) - else: self.lib = CDLL(join(modpath,"liblammps_%s.so" % name), + if not name: self.lib = CDLL(join(modpath,"liblammps" + lib_ext),RTLD_GLOBAL) + else: self.lib = CDLL(join(modpath,"liblammps_%s" % name + lib_ext), RTLD_GLOBAL) except: - if not name: self.lib = CDLL("liblammps.so",RTLD_GLOBAL) - else: self.lib = CDLL("liblammps_%s.so" % name,RTLD_GLOBAL) + if not name: self.lib = CDLL("liblammps" + lib_ext,RTLD_GLOBAL) + else: self.lib = CDLL("liblammps_%s" % name + lib_ext,RTLD_GLOBAL) # define ctypes API for each library method # NOTE: should add one of these for each lib function @@ -265,7 +270,7 @@ class lammps(object): def extract_setting(self, name): if name: name = name.encode() - self.lib.lammps_extract_atom.restype = c_int + self.lib.lammps_extract_setting.restype = c_int return int(self.lib.lammps_extract_setting(self.lmp,name)) # extract global info @@ -986,7 +991,7 @@ class PyLammps(object): elif line.startswith("Dihedrals"): parts = self._split_values(line) system['ndihedrals'] = int(self._get_pair(parts[0])[1]) - system['nangletypes'] = int(self._get_pair(parts[1])[1]) + system['ndihedraltypes'] = int(self._get_pair(parts[1])[1]) system['dihedral_style'] = self._get_pair(parts[2])[1] elif line.startswith("Impropers"): parts = self._split_values(line) diff --git a/src/.gitignore b/src/.gitignore index 4f517af3af..27f4f8a64c 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -6,6 +6,7 @@ /style_*.h /lmpinstalledpkgs.h +/lmpgitversion.h /*_gpu.h /*_gpu.cpp @@ -25,6 +26,11 @@ /*_ssa.h /*_ssa.cpp +/kim_query.cpp +/kim_query.h +/pair_kim.cpp +/pair_kim.h + /kokkos.cpp /kokkos.h /kokkos_type.h @@ -59,6 +65,8 @@ /colvarproxy_lammps_version.h /fix_colvars.cpp /fix_colvars.h +/fix_plumed.cpp +/fix_plumed.h /dump_molfile.cpp /dump_molfile.h /molfile_interface.cpp @@ -223,6 +231,10 @@ /atom_vec_template.h /body_nparticle.cpp /body_nparticle.h +/body_rounded_polygon.cpp +/body_rounded_polygon.h +/body_rounded_polyhedron.cpp +/body_rounded_polyhedron.h /bond_class2.cpp /bond_class2.h /bond_fene.cpp @@ -307,8 +319,12 @@ /compute_pressure_cylinder.h /compute_pressure_grem.cpp /compute_pressure_grem.h +/compute_ptm_atom.cpp +/compute_ptm_atom.h /compute_rigid_local.cpp /compute_rigid_local.h +/compute_smd_triangle_vertices.cpp +/compute_smd_triangle_vertices.h /compute_spec_atom.cpp /compute_spec_atom.h /compute_stress_mop.cpp @@ -419,6 +435,8 @@ /fix_bond_react.h /fix_bond_swap.cpp /fix_bond_swap.h +/fix_client_md.cpp +/fix_client_md.h /fix_cmap.cpp /fix_cmap.h /fix_deposit.cpp @@ -443,6 +461,8 @@ /fix_ehex.h /fix_event.cpp /fix_event.h +/fix_event_hyper.cpp +/fix_event_hyper.h /fix_event_prd.cpp /fix_event_prd.h /fix_event_tad.cpp @@ -461,6 +481,12 @@ /fix_gpu.h /fix_grem.cpp /fix_grem.h +/fix_hyper.cpp +/fix_hyper.h +/fix_hyper_global.cpp +/fix_hyper_global.h +/fix_hyper_local.cpp +/fix_hyper_local.h /fix_imd.cpp /fix_imd.h /fix_ipi.cpp @@ -485,6 +511,8 @@ /fix_load_report.h /fix_meso.cpp /fix_meso.h +/fix_meso_move.cpp +/fix_meso_move.h /fix_meso_stationary.cpp /fix_meso_stationary.h /fix_mscg.cpp @@ -561,8 +589,6 @@ /fix_qeq_reax.h /fix_qmmm.cpp /fix_qmmm.h -/fix_reax_bonds.cpp -/fix_reax_bonds.h /fix_reaxc.cpp /fix_reaxc.h /fix_reaxc_bonds.cpp @@ -573,6 +599,8 @@ /fix_rhok.h /fix_rigid.cpp /fix_rigid.h +/fix_rigid_meso.cpp +/fix_rigid_meso.h /fix_rigid_nh.cpp /fix_rigid_nh.h /fix_rigid_nph.cpp @@ -620,6 +648,10 @@ /fix_ttm.h /fix_tune_kspace.cpp /fix_tune_kspace.h +/fix_wall_body_polygon.cpp +/fix_wall_body_polygon.h +/fix_wall_body_polyhedron.cpp +/fix_wall_body_polyhedron.h /fix_wall_colloid.cpp /fix_wall_colloid.h /fix_wall_ees.cpp @@ -641,6 +673,8 @@ /group_ndx.h /ndx_group.cpp /ndx_group.h +/hyper.cpp +/hyper.h /improper_class2.cpp /improper_class2.h /improper_cossq.cpp @@ -665,6 +699,8 @@ /lj_sdk_common.h /math_complex.h /math_vector.h +/message.cpp +/message.h /mgpt_*.cpp /mgpt_*.h /msm.cpp @@ -682,8 +718,14 @@ /pair_airebo.h /pair_airebo_morse.cpp /pair_airebo_morse.h -/pair_body.cpp -/pair_body.h +/pair_atm.cpp +/pair_atm.h +/pair_body_nparticle.cpp +/pair_body_nparticle.h +/pair_body_rounded_polygon.cpp +/pair_body_rounded_polygon.h +/pair_body_rounded_polyhedron.cpp +/pair_body_rounded_polyhedron.h /pair_bop.cpp /pair_bop.h /pair_born_coul_long.cpp @@ -781,8 +823,6 @@ /pair_hbond_dreiding_morse.h /pair_ilp_graphene_hbn.cpp /pair_ilp_graphene_hbn.h -/pair_kim.cpp -/pair_kim.h /pair_kolmogorov_crespi_full.cpp /pair_kolmogorov_crespi_full.h /pair_kolmogorov_crespi_z.cpp @@ -892,15 +932,14 @@ /pair_peri_ves.h /pair_quip.cpp /pair_quip.h -/pair_reax.cpp -/pair_reax.h -/pair_reax_fortran.h /pair_reaxc.cpp /pair_reaxc.h /pair_rebo.cpp /pair_rebo.h /pair_resquared.cpp /pair_resquared.h +/pair_sdpd_taitwater_isothermal.cpp +/pair_sdpd_taitwater_isothermal.h /pair_sph_heatconduction.cpp /pair_sph_heatconduction.h /pair_sph_idealgas.cpp @@ -1020,6 +1059,14 @@ /remap_wrap.h /restart_mpiio.cpp /restart_mpiio.h +/scafacos.cpp +/scafacos.h +/server.cpp +/server.h +/server_mc.cpp +/server_mc.h +/server_md.cpp +/server_md.h /smd_kernels.h /smd_material_models.cpp /smd_material_models.h diff --git a/src/ASPHERE/pair_gayberne.cpp b/src/ASPHERE/pair_gayberne.cpp index 857541957e..3d4ed3f183 100644 --- a/src/ASPHERE/pair_gayberne.cpp +++ b/src/ASPHERE/pair_gayberne.cpp @@ -94,8 +94,7 @@ void PairGayBerne::compute(int eflag, int vflag) double *iquat,*jquat; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); AtomVecEllipsoid::Bonus *bonus = avec->bonus; int *ellipsoid = atom->ellipsoid; diff --git a/src/ASPHERE/pair_line_lj.cpp b/src/ASPHERE/pair_line_lj.cpp index 963ff985c4..4873b44dc4 100644 --- a/src/ASPHERE/pair_line_lj.cpp +++ b/src/ASPHERE/pair_line_lj.cpp @@ -77,8 +77,7 @@ void PairLineLJ::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/ASPHERE/pair_resquared.cpp b/src/ASPHERE/pair_resquared.cpp index c477b1b8cf..b100a5f184 100644 --- a/src/ASPHERE/pair_resquared.cpp +++ b/src/ASPHERE/pair_resquared.cpp @@ -85,8 +85,7 @@ void PairRESquared::compute(int eflag, int vflag) RE2Vars wi,wj; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/ASPHERE/pair_tri_lj.cpp b/src/ASPHERE/pair_tri_lj.cpp index 142caf3764..cefd73f976 100644 --- a/src/ASPHERE/pair_tri_lj.cpp +++ b/src/ASPHERE/pair_tri_lj.cpp @@ -77,8 +77,7 @@ void PairTriLJ::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); AtomVecTri::Bonus *bonus = avec->bonus; double **x = atom->x; diff --git a/src/BODY/body_rounded_polygon.cpp b/src/BODY/body_rounded_polygon.cpp index 00a09c912d..d352c789d7 100644 --- a/src/BODY/body_rounded_polygon.cpp +++ b/src/BODY/body_rounded_polygon.cpp @@ -170,7 +170,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, // nentries = number of double entries to be read from Body section: // 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius - int nentries = 6 + 3*nsub + 1; + int nentries = 6 + 3*nsub + 1; if (ndouble != nentries) error->one(FLERR,"Incorrect # of floating-point values in " "Bodies section of data file"); @@ -279,7 +279,7 @@ void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble, bonus->dvalue[k] = 0; *(&bonus->dvalue[k]+1) = 1; k += 2; - } + } erad = sqrt(erad2); bonus->dvalue[k] = erad; @@ -341,7 +341,7 @@ double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble, double maxrad = 0.0; double delta[3]; - int offset = 6; + int offset = 6; for (int i = 0; i < nsub; i++) { delta[0] = dfile[offset]; delta[1] = dfile[offset+1]; @@ -350,9 +350,9 @@ double BodyRoundedPolygon::radius_body(int /*ninteger*/, int ndouble, onerad = MathExtra::len3(delta); maxrad = MAX(maxrad,onerad); } - + // add in radius of rounded corners - + return maxrad + 0.5*dfile[offset]; } @@ -401,7 +401,7 @@ int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/, AtomVecBody::Bonus *bonus = &avec->bonus[ibonus]; int n = bonus->ivalue[0]; - + if (n == 1) { for (int i = 0; i < n; i++) { imflag[i] = SPHERE; @@ -418,7 +418,7 @@ int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/, } } else { - + // first end pt of each line for (int i = 0; i < n; i++) { @@ -436,7 +436,7 @@ int BodyRoundedPolygon::image(int ibonus, double flag1, double /*flag2*/, } // second end pt of each line - + for (int i = 0; i < n; i++) { j = i+1; if (j == n) j = 0; diff --git a/src/BODY/body_rounded_polyhedron.cpp b/src/BODY/body_rounded_polyhedron.cpp index 0e2ebbed83..99a380a932 100644 --- a/src/BODY/body_rounded_polyhedron.cpp +++ b/src/BODY/body_rounded_polyhedron.cpp @@ -132,7 +132,7 @@ double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus) int nvertices = bonus->ivalue[0]; if (nvertices == 1 || nvertices == 2) return *(bonus->dvalue+3*nsub(bonus)+2); - return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + + return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + MAX_FACE_SIZE*nfaces(bonus)); } @@ -143,7 +143,7 @@ double BodyRoundedPolyhedron::rounded_radius(struct AtomVecBody::Bonus *bonus) int nvertices = bonus->ivalue[0]; if (nvertices == 1 || nvertices == 2) return *(bonus->dvalue+3*nsub(bonus)+2+1); - return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + + return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) + MAX_FACE_SIZE*nfaces(bonus)+1); } @@ -207,7 +207,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, // nsub == 1 || nsub == 2 || nsub == 3: // 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius // nsub > 3: - // 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges + + // 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges + // 3*nfaces + 1 for rounded radius int nedges,nentries; @@ -327,7 +327,7 @@ void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble, bonus->dvalue[k] = 0; *(&bonus->dvalue[k]+1) = 1; k += 2; - } + } erad = sqrt(erad2); bonus->dvalue[k] = erad; @@ -407,7 +407,7 @@ double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble, double maxrad = 0.0; double delta[3]; - int offset = 6; + int offset = 6; for (int i = 0; i < nsub; i++) { delta[0] = dfile[offset]; delta[1] = dfile[offset+1]; @@ -420,7 +420,7 @@ double BodyRoundedPolyhedron::radius_body(int /*ninteger*/, int ndouble, if (nsub > 2) offset += (2*nedges+MAX_FACE_SIZE*nfac); // add in radius of rounded corners - + return maxrad + 0.5*dfile[offset]; } diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp index 3f8c08b6bd..221937461b 100644 --- a/src/BODY/fix_wall_body_polygon.cpp +++ b/src/BODY/fix_wall_body_polygon.cpp @@ -206,7 +206,7 @@ void FixWallBodyPolygon::setup(int vflag) void FixWallBodyPolygon::post_force(int /*vflag*/) { - double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos; + double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,wall_pos; int i,ni,npi,ifirst,nei,iefirst,side; double facc[3]; @@ -263,7 +263,7 @@ void FixWallBodyPolygon::post_force(int /*vflag*/) } ndiscrete = nedge = 0; - for (i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) dnum[i] = ednum[i] = 0; for (i = 0; i < nlocal; i++) { @@ -316,7 +316,6 @@ void FixWallBodyPolygon::post_force(int /*vflag*/) nei = ednum[i]; iefirst = edfirst[i]; eradi = enclosing_radius[i]; - rradi = rounded_radius[i]; // reset vertex and edge forces @@ -332,14 +331,14 @@ void FixWallBodyPolygon::post_force(int /*vflag*/) edge[iefirst+ni][4] = 0; } - int interact, num_contacts, done; + int num_contacts, done; double delta_a, delta_ua, j_a; Contact contact_list[MAX_CONTACTS]; num_contacts = 0; facc[0] = facc[1] = facc[2] = 0; - interact = vertex_against_wall(i, wall_pos, x, f, torque, side, - contact_list, num_contacts, facc); + vertex_against_wall(i, wall_pos, x, f, torque, side, + contact_list, num_contacts, facc); if (num_contacts >= 2) { @@ -475,12 +474,11 @@ int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos, Contact* contact_list, int &num_contacts, double* /*facc*/) { int ni, npi, ifirst, interact; - double xpi[3], eradi, rradi; + double xpi[3], rradi; double fx, fy, fz; npi = dnum[i]; ifirst = dfirst[i]; - eradi = enclosing_radius[i]; rradi = rounded_radius[i]; interact = 0; @@ -675,7 +673,7 @@ void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a, AtomVecBody::Bonus *bonus; ibody = contact.ibody; - + // compute the velocity of the vertex in the space-fixed frame ibonus = atom->body[ibody]; diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp index 9504e256b4..24a9e51dad 100644 --- a/src/BODY/fix_wall_body_polyhedron.cpp +++ b/src/BODY/fix_wall_body_polyhedron.cpp @@ -102,7 +102,7 @@ FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg) if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG; else hi = force->numeric(FLERR,arg[iarg+2]); iarg += 3; - } + } // check for trailing keyword/values @@ -213,8 +213,8 @@ void FixWallBodyPolyhedron::setup(int vflag) void FixWallBodyPolyhedron::post_force(int /*vflag*/) { - double vwall[3],dx,dy,dz,del1,del2,rsq,eradi,rradi,wall_pos; - int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side; + double vwall[3],dx,dy,dz,del1,del2,rsq,wall_pos; + int i,ni,npi,ifirst,nei,iefirst,side; double facc[3]; // set position of wall to initial settings and velocity to 0.0 @@ -274,7 +274,7 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/) } ndiscrete = nedge = nface = 0; - for (i = 0; i < nlocal; i++) + for (i = 0; i < nlocal; i++) dnum[i] = ednum[i] = facnum[i] = 0; for (i = 0; i < nlocal; i++) { @@ -320,7 +320,7 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/) wall_pos = whi; side = ZHI; } - } + } rsq = dx*dx + dy*dy + dz*dz; if (rsq > radius[i]*radius[i]) continue; @@ -330,10 +330,6 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/) ifirst = dfirst[i]; nei = ednum[i]; iefirst = edfirst[i]; - nfi = facnum[i]; - iffirst = facfirst[i]; - eradi = enclosing_radius[i]; - rradi = rounded_radius[i]; if (npi == 1) { sphere_against_wall(i, wall_pos, side, vwall, x, v, f, angmom, torque); @@ -356,13 +352,13 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/) edge[iefirst+ni][5] = 0; } - int interact, num_contacts; + int num_contacts; Contact contact_list[MAX_CONTACTS]; num_contacts = 0; facc[0] = facc[1] = facc[2] = 0; - interact = edge_against_wall(i, wall_pos, side, vwall, x, f, torque, - contact_list, num_contacts, facc); + edge_against_wall(i, wall_pos, side, vwall, x, f, torque, + contact_list, num_contacts, facc); } // group bit } @@ -502,7 +498,7 @@ int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos, hi[0] = x[i][0]; hi[1] = x[i][1]; hi[2] = wall_pos; - } + } distance(hi, x[i], d); @@ -536,7 +532,7 @@ int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos, Output: contact_list = list of contacts between i and the wall num_contacts = number of contacts between i's vertices and the wall - Return: + Return: number of contacts of the edge to the wall (0, 1 or 2) ---------------------------------------------------------------------- */ @@ -544,7 +540,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos, int side, double* vwall, double** x, double** /*f*/, double** /*torque*/, Contact* /*contact_list*/, int &/*num_contacts*/, double* /*facc*/) { - int ni, nei, mode, contact; + int ni, nei, contact; double rradi; nei = ednum[i]; @@ -555,8 +551,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos, // loop through body i's edges for (ni = 0; ni < nei; ni++) - mode = compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall, - contact); + compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall, contact); return contact; } @@ -578,7 +573,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos, ------------------------------------------------------------------------- */ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index, - double *xmi, double rounded_radius_i, double wall_pos, + double *xmi, double rounded_radius_i, double wall_pos, int /*side*/, double* vwall, int &contact) { int mode,ifirst,iefirst,npi1,npi2; @@ -623,7 +618,7 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index, hi[0] = xpi1[0]; hi[1] = xpi1[1]; hi[2] = wall_pos; - } + } distance(hi, xpi1, d1); @@ -658,7 +653,7 @@ int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index, hi[0] = xpi2[0]; hi[1] = xpi2[1]; hi[2] = wall_pos; - } + } distance(hi, xpi2, d2); @@ -790,7 +785,7 @@ void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a, AtomVecBody::Bonus *bonus; ibody = contact.ibody; - + // compute the velocity of the vertex in the space-fixed frame ibonus = atom->body[ibody]; diff --git a/src/BODY/fix_wall_body_polyhedron.h b/src/BODY/fix_wall_body_polyhedron.h index ff7b7ca7cf..7479f79e23 100644 --- a/src/BODY/fix_wall_body_polyhedron.h +++ b/src/BODY/fix_wall_body_polyhedron.h @@ -90,7 +90,7 @@ class FixWallBodyPolyhedron : public Fix { double rounded_radius_i, double wall_pos, int side, double* vwall, int &contact); double contact_separation(const Contact& c1, const Contact& c2); - void contact_forces(int ibody, double j_a, double *xi, double *xj, + void contact_forces(int ibody, double j_a, double *xi, double *xj, double delx, double dely, double delz, double fx, double fy, double fz, double** x, double** v, double** angmom, double** f, double** torque, double* vwall); diff --git a/src/BODY/pair_body_nparticle.cpp b/src/BODY/pair_body_nparticle.cpp index 80b45beb4e..f2eb2aa520 100644 --- a/src/BODY/pair_body_nparticle.cpp +++ b/src/BODY/pair_body_nparticle.cpp @@ -77,8 +77,7 @@ void PairBodyNparticle::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp index 6a176f1083..69495ea57f 100644 --- a/src/BODY/pair_body_rounded_polygon.cpp +++ b/src/BODY/pair_body_rounded_polygon.cpp @@ -107,12 +107,11 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) int nei,nej,iefirst,jefirst; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl; double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij; - double xi[3],xj[3],facc[3]; + double facc[3]; int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; @@ -275,9 +274,9 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) // scale the force at both contacts - contact_forces(contact_list[m], j_a, x, v, angmom, f, torque, + contact_forces(contact_list[m], j_a, x, v, angmom, f, torque, evdwl, facc); - contact_forces(contact_list[n], j_a, x, v, angmom, f, torque, + contact_forces(contact_list[n], j_a, x, v, angmom, f, torque, evdwl, facc); done = 1; @@ -288,15 +287,15 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag) "xv = %f %f %f; xe = %f %f %f\n", m, contact_list[m].vertex, contact_list[m].ibody, contact_list[m].edge, contact_list[m].jbody, - contact_list[m].xv[0], contact_list[m].xv[1], - contact_list[m].xv[2], contact_list[m].xe[0], + contact_list[m].xv[0], contact_list[m].xv[1], + contact_list[m].xv[2], contact_list[m].xe[0], contact_list[m].xe[1], contact_list[m].xe[2]); printf(" %d: vertex %d of body %d and edge %d of body %d; " "xv = %f %f %f; xe = %f %f %f\n", n, contact_list[n].vertex, contact_list[n].ibody, contact_list[n].edge, contact_list[n].jbody, - contact_list[n].xv[0], contact_list[n].xv[1], - contact_list[n].xv[2], contact_list[n].xe[0], + contact_list[n].xv[0], contact_list[n].xv[1], + contact_list[n].xv[2], contact_list[n].xe[0], contact_list[n].xe[1], contact_list[n].xe[2]); #endif @@ -420,7 +419,7 @@ void PairBodyRoundedPolygon::coeff(int narg, char **arg) void PairBodyRoundedPolygon::init_style() { avec = (AtomVecBody *) atom->style_match("body"); - if (!avec) + if (!avec) error->all(FLERR,"Pair body/rounded/polygon requires atom style body"); if (strcmp(avec->bptr->style,"rounded/polygon") != 0) error->all(FLERR,"Pair body/rounded/polygon requires " @@ -501,7 +500,7 @@ void PairBodyRoundedPolygon::init_style() if (dnum[i] == 0) body2space(i); eradi = enclosing_radius[i]; if (eradi > merad[itype]) merad[itype] = eradi; - } else + } else merad[itype] = 0; } @@ -669,7 +668,7 @@ void PairBodyRoundedPolygon::sphere_against_sphere(int i, int j, f[i][0] += fx; f[i][1] += fy; f[i][2] += fz; - + if (newton_pair || j < nlocal) { f[j][0] -= fx; f[j][1] -= fy; @@ -860,7 +859,7 @@ int PairBodyRoundedPolygon::vertex_against_edge(int i, int j, #ifdef _CONVEX_POLYGON // done with the edges from body j, - // given that vertex ni interacts with only one vertex + // given that vertex ni interacts with only one vertex // from one edge of body j break; #endif @@ -1124,7 +1123,7 @@ int PairBodyRoundedPolygon::compute_distance_to_vertex(int ibody, mode = EDGE; if (d < contact_dist + EPSILON) contact = 1; - + } else { // t < 0 || t > 1: closer to either vertices of the edge if (t < 0) { diff --git a/src/BODY/pair_body_rounded_polyhedron.cpp b/src/BODY/pair_body_rounded_polyhedron.cpp index eea2aa3724..60f6df3582 100644 --- a/src/BODY/pair_body_rounded_polyhedron.cpp +++ b/src/BODY/pair_body_rounded_polyhedron.cpp @@ -127,8 +127,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; @@ -283,7 +282,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) // check interaction between i's edges and j' faces #ifdef _POLYHEDRON_DEBUG printf("INTERACTION between edges of %d vs. faces of %d:\n", i, j); - #endif + #endif interact = edge_against_face(i, j, itype, jtype, x, contact_list, num_contacts, evdwl, facc); @@ -297,7 +296,7 @@ void PairBodyRoundedPolyhedron::compute(int eflag, int vflag) // check interaction between i's edges and j' edges #ifdef _POLYHEDRON_DEBUG printf("INTERACTION between edges of %d vs. edges of %d:\n", i, j); - #endif + #endif interact = edge_against_edge(i, j, itype, jtype, x, contact_list, num_contacts, evdwl, facc); @@ -478,7 +477,7 @@ void PairBodyRoundedPolyhedron::init_style() if (dnum[i] == 0) body2space(i); eradi = enclosing_radius[i]; if (eradi > merad[itype]) merad[itype] = eradi; - } else + } else merad[itype] = 0; } @@ -630,7 +629,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody, vr3 = v[ibody][2] - v[jbody][2]; // normal component - + rsqinv = 1.0/rsq; vnnr = vr1*delx + vr2*dely + vr3*delz; vn1 = delx*vnnr * rsqinv; @@ -664,7 +663,7 @@ void PairBodyRoundedPolyhedron::sphere_against_sphere(int ibody, int jbody, f[ibody][0] += fx; f[ibody][1] += fy; f[ibody][2] += fz; - + if (newton_pair || jbody < nlocal) { f[jbody][0] -= fx; f[jbody][1] -= fy; @@ -797,7 +796,7 @@ void PairBodyRoundedPolyhedron::sphere_against_edge(int ibody, int jbody, fn[1] = -c_n * vn2; fn[2] = -c_n * vn3; - // tangential friction term at contact, + // tangential friction term at contact, // excluding the tangential deformation term ft[0] = -c_t * vt1; @@ -873,7 +872,7 @@ void PairBodyRoundedPolyhedron::sphere_against_face(int ibody, int jbody, xi3[2] = x[ibody][2] + discrete[ifirst+npi3][2]; // find the normal unit vector of the face - + MathExtra::sub3(xi2, xi1, ui); MathExtra::sub3(xi3, xi1, vi); MathExtra::cross3(ui, vi, n); @@ -1076,7 +1075,7 @@ int PairBodyRoundedPolyhedron::edge_against_face(int ibody, int jbody, itype, jtype, cut_inner, contact_list, num_contacts, energy, facc); - } + } } // end for looping through the edges of body i @@ -1171,7 +1170,7 @@ int PairBodyRoundedPolyhedron::interaction_edge_to_edge(int ibody, printf(" edge npi1 = %d (%f %f %f); npi2 = %d (%f %f %f) vs." " edge npj1 = %d (%f %f %f); npj2 = %d (%f %f %f): " "t1 = %f; t2 = %f; r = %f; dot = %f\n", - npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2], + npi1, xi1[0], xi1[1], xi1[2], npi2, xi2[0], xi2[1], xi2[2], npj1, xpj1[0], xpj1[1], xpj1[2], npj2, xpj2[0], xpj2[1], xpj2[2], t1, t2, r, dot); #endif @@ -1276,7 +1275,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, xi3[2] = xmi[2] + discrete[ifirst+npi3][2]; // find the normal unit vector of the face, ensure it point outward of the body - + MathExtra::sub3(xi2, xi1, ui); MathExtra::sub3(xi3, xi1, vi); MathExtra::cross3(ui, vi, n); @@ -1305,7 +1304,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, xpj2[1] = xmj[1] + discrete[jfirst+npj2][1]; xpj2[2] = xmj[2] + discrete[jfirst+npj2][2]; - // no interaction if two ends of the edge + // no interaction if two ends of the edge // are on the same side with the COM wrt the face if (opposite_sides(n, xi1, xmi, xpj1) == 0 && @@ -1340,9 +1339,9 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, int jflag = 1; #ifdef _POLYHEDRON_DEBUG - if (interact == EF_SAME_SIDE_OF_FACE) + if (interact == EF_SAME_SIDE_OF_FACE) printf(" - same side of face\n"); - else if (interact == EF_PARALLEL) + else if (interact == EF_PARALLEL) printf(" - parallel\n"); printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n", xi1[0], xi1[1], xi1[2], xi2[0], xi2[1], xi2[2], xi3[0], xi3[1], xi3[2]); @@ -1387,9 +1386,9 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, } else { num_outside++; } - } + } - // xpj2 is in the interaction zone + // xpj2 is in the interaction zone // and its projection on the face is inside the triangle // compute vertex-face interaction and accumulate force/torque to both bodies @@ -1401,7 +1400,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, jflag, energy, facc); #ifdef _POLYHEDRON_DEBUG printf(" - compute pair force between vertex %d from edge %d of body %d " - "with face %d of body %d: d2 = %f\n", + "with face %d of body %d: d2 = %f\n", npj2, edge_index, jbody, face_index, ibody, d2); #endif @@ -1448,7 +1447,7 @@ int PairBodyRoundedPolyhedron::interaction_face_to_edge(int ibody, // compute interaction between the edge with the three edges of the face #ifdef _POLYHEDRON_DEBUG - printf(" - intersect outside triangle\n"); + printf(" - intersect outside triangle\n"); printf(" - compute pair force between edge %d of body %d " "with face %d of body %d\n", edge_index, jbody, face_index, ibody); printf(" face: xi1 (%f %f %f) xi2 (%f %f %f) xi3 (%f %f %f)\n", @@ -1693,7 +1692,7 @@ void PairBodyRoundedPolyhedron::rescale_cohesive_forces(double** x, xc[0] /= (double)num_unique_contacts; xc[1] /= (double)num_unique_contacts; xc[2] /= (double)num_unique_contacts; - + contact_area = 0.0; for (int m = 0; m < num_contacts; m++) { if (contact_list[m].unique == 0) continue; @@ -1847,12 +1846,12 @@ int PairBodyRoundedPolyhedron::edge_face_intersect(double* x1, double* x2, if (t < 0 || t > 1) { interact = EF_SAME_SIDE_OF_FACE; } else { - if (inside == 1) + if (inside == 1) interact = EF_INTERSECT_INSIDE; else interact = EF_INTERSECT_OUTSIDE; } - + return interact; } @@ -1998,7 +1997,7 @@ void PairBodyRoundedPolyhedron::project_pt_plane(const double* q, q_proj[2] = q[2] + n[2] * t; // check if the projection point is inside the triangle - // exclude the edges and vertices + // exclude the edges and vertices // edge-sphere and sphere-sphere interactions are handled separately inside = 0; @@ -2022,7 +2021,7 @@ void PairBodyRoundedPolyhedron::project_pt_line(const double* q, MathExtra::sub3(xi2, xi1, u); MathExtra::norm3(u); MathExtra::sub3(q, xi1, v); - + s = MathExtra::dot3(u, v); h[0] = xi1[0] + s * u[0]; h[1] = xi1[1] + s * u[1]; @@ -2039,13 +2038,13 @@ void PairBodyRoundedPolyhedron::project_pt_line(const double* q, t = (h[2] - xi1[2])/(xi2[2] - xi1[2]); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- compute the shortest distance between two edges (line segments) x1, x2: two endpoints of the first edge x3, x4: two endpoints of the second edge - h1: the end point of the shortest segment perpendicular to both edges + h1: the end point of the shortest segment perpendicular to both edges on the line (x1;x2) - h2: the end point of the shortest segment perpendicular to both edges + h2: the end point of the shortest segment perpendicular to both edges on the line (x3;x4) t1: fraction of h1 in the segment (x1,x2) t2: fraction of h2 in the segment (x3,x4) @@ -2080,7 +2079,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, double s1,s2,x13[3],x23[3],x13h[3]; double t13,t23,t31,t41,x31[3],x41[3]; t13=t23=t31=t41=0.0; - + MathExtra::sub3(x1,x3,x13); // x13 = x1 - x3 MathExtra::sub3(x2,x3,x23); // x23 = x2 - x3 @@ -2089,7 +2088,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, x13h[1] = x13[1] - s1*v[1]; x13h[2] = x13[2] - s1*v[2]; r = MathExtra::len3(x13h); - + // x13 is the projection of x1 on x3-x4 x13[0] = x3[0] + s1*v[0]; @@ -2102,7 +2101,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, x23[0] = x3[0] + s2*v[0]; x23[1] = x3[1] + s2*v[1]; x23[2] = x3[2] + s2*v[2]; - + // find the fraction of the projection points on the edges if (fabs(x4[0] - x3[0]) > 0) @@ -2177,8 +2176,8 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, h1[0] = (x1[0]+x2[0])/2; h1[1] = (x1[1]+x2[1])/2; h1[2] = (x1[2]+x2[2])/2; - h2[0] = (x13[0]+x23[0])/2; - h2[1] = (x13[1]+x23[1])/2; + h2[0] = (x13[0]+x23[0])/2; + h2[1] = (x13[1]+x23[1])/2; h2[2] = (x13[2]+x23[2])/2; t1 = 0.5; t2 = (t13+t23)/2; @@ -2216,8 +2215,8 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, h1[0] = (x31[0]+x41[0])/2; h1[1] = (x31[1]+x41[1])/2; h1[2] = (x31[2]+x41[2])/2; - h2[0] = (x3[0]+x4[0])/2; - h2[1] = (x3[1]+x4[1])/2; + h2[0] = (x3[0]+x4[0])/2; + h2[1] = (x3[1]+x4[1])/2; h2[2] = (x3[2]+x4[2])/2; t1 = (t31+t41)/2; t2 = 0.5; @@ -2225,7 +2224,7 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, n2++; } } - } + } // if n1 == 0 and n2 == 0 at this point, // which means no overlapping segments bt two parallel edges, @@ -2233,10 +2232,10 @@ void PairBodyRoundedPolyhedron::distance_bt_edges(const double* x1, return; - } + } // find the vector n perpendicular to both edges - + MathExtra::cross3(u, v, n); MathExtra::norm3(n); @@ -2326,7 +2325,7 @@ double PairBodyRoundedPolyhedron::contact_separation(const Contact& c1, find the number of unique contacts ------------------------------------------------------------------------- */ -void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list, +void PairBodyRoundedPolyhedron::find_unique_contacts(Contact* contact_list, int& num_contacts) { int n = num_contacts; diff --git a/src/BODY/pair_body_rounded_polyhedron.h b/src/BODY/pair_body_rounded_polyhedron.h index 71c04ff966..369f394c50 100644 --- a/src/BODY/pair_body_rounded_polyhedron.h +++ b/src/BODY/pair_body_rounded_polyhedron.h @@ -155,13 +155,13 @@ class PairBodyRoundedPolyhedron : public Pair { int& inside_a, int& inside_b); // helper functions int opposite_sides(double* n, double* x0, double* a, double* b); - void project_pt_plane(const double* q, const double* p, + void project_pt_plane(const double* q, const double* p, const double* n, double* q_proj, double &d); - void project_pt_plane(const double* q, const double* x1, const double* x2, + void project_pt_plane(const double* q, const double* x1, const double* x2, const double* x3, double* q_proj, double &d, int& inside); void project_pt_line(const double* q, const double* xi1, const double* xi2, double* h, double& d, double& t); - void inside_polygon(int ibody, int face_index, double* xmi, + void inside_polygon(int ibody, int face_index, double* xmi, const double* q1, const double* q2, int& inside1, int& inside2); void distance_bt_edges(const double* x1, const double* x2, diff --git a/src/CLASS2/angle_class2.cpp b/src/CLASS2/angle_class2.cpp index 24f41bfd58..d550767e5e 100644 --- a/src/CLASS2/angle_class2.cpp +++ b/src/CLASS2/angle_class2.cpp @@ -78,8 +78,7 @@ void AngleClass2::compute(int eflag, int vflag) double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CLASS2/bond_class2.cpp b/src/CLASS2/bond_class2.cpp index af20313e0a..26c4e63a4d 100644 --- a/src/CLASS2/bond_class2.cpp +++ b/src/CLASS2/bond_class2.cpp @@ -56,8 +56,7 @@ void BondClass2::compute(int eflag, int vflag) double rsq,r,dr,dr2,dr3,dr4,de_bond; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CLASS2/dihedral_class2.cpp b/src/CLASS2/dihedral_class2.cpp index c6360dd846..c471b1f353 100644 --- a/src/CLASS2/dihedral_class2.cpp +++ b/src/CLASS2/dihedral_class2.cpp @@ -118,8 +118,7 @@ void DihedralClass2::compute(int eflag, int vflag) double fabcd[4][3]; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CLASS2/improper_class2.cpp b/src/CLASS2/improper_class2.cpp index 77f594af9d..ccb81aebd9 100644 --- a/src/CLASS2/improper_class2.cpp +++ b/src/CLASS2/improper_class2.cpp @@ -90,8 +90,7 @@ void ImproperClass2::compute(int eflag, int vflag) double fabcd[4][3]; eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); for (i = 0; i < 3; i++) for (j = 0; j < 4; j++) diff --git a/src/CLASS2/pair_lj_class2.cpp b/src/CLASS2/pair_lj_class2.cpp index 6451921dc5..f2eef55290 100644 --- a/src/CLASS2/pair_lj_class2.cpp +++ b/src/CLASS2/pair_lj_class2.cpp @@ -14,6 +14,7 @@ #include #include #include +#include #include "pair_lj_class2.h" #include "atom.h" #include "comm.h" @@ -37,20 +38,20 @@ PairLJClass2::PairLJClass2(LAMMPS *lmp) : Pair(lmp) PairLJClass2::~PairLJClass2() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(cut); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(offset); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); } } @@ -64,8 +65,7 @@ void PairLJClass2::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -394,3 +394,13 @@ double PairLJClass2::single(int /*i*/, int /*j*/, int itype, int jtype, double r offset[itype][jtype]; return factor_lj*philj; } + +/* ---------------------------------------------------------------------- */ + +void *PairLJClass2::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + return NULL; +} diff --git a/src/CLASS2/pair_lj_class2.h b/src/CLASS2/pair_lj_class2.h index 4a89ce2a3f..02a1f44ff7 100644 --- a/src/CLASS2/pair_lj_class2.h +++ b/src/CLASS2/pair_lj_class2.h @@ -39,6 +39,7 @@ class PairLJClass2 : public Pair { void write_data(FILE *); void write_data_all(FILE *); double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); protected: double cut_global; diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index 5cd5ad0e32..dafa83c8fd 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -14,6 +14,7 @@ #include #include #include +#include #include "pair_lj_class2_coul_cut.h" #include "atom.h" #include "comm.h" @@ -38,23 +39,23 @@ PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp) PairLJClass2CoulCut::~PairLJClass2CoulCut() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(cut_coul); - memory->destroy(cut_coulsq); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(offset); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(cut_coul); + memory->destroy(cut_coulsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); } } @@ -69,8 +70,7 @@ void PairLJClass2CoulCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -216,7 +216,9 @@ void PairLJClass2CoulCut::settings(int narg, char **arg) void PairLJClass2CoulCut::coeff(int narg, char **arg) { - if (narg < 4 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -466,3 +468,16 @@ double PairLJClass2CoulCut::single(int i, int j, int itype, int jtype, return eng; } + +/* ---------------------------------------------------------------------- */ + +void *PairLJClass2CoulCut::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + return NULL; +} + diff --git a/src/CLASS2/pair_lj_class2_coul_cut.h b/src/CLASS2/pair_lj_class2_coul_cut.h index 9b9c654ec6..f33502e23a 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.h +++ b/src/CLASS2/pair_lj_class2_coul_cut.h @@ -40,6 +40,7 @@ class PairLJClass2CoulCut : public Pair { void write_data(FILE *); void write_data_all(FILE *); double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); protected: double cut_lj_global,cut_coul_global; diff --git a/src/CLASS2/pair_lj_class2_coul_long.cpp b/src/CLASS2/pair_lj_class2_coul_long.cpp index bf892bc894..85fe0152e2 100644 --- a/src/CLASS2/pair_lj_class2_coul_long.cpp +++ b/src/CLASS2/pair_lj_class2_coul_long.cpp @@ -50,21 +50,21 @@ PairLJClass2CoulLong::PairLJClass2CoulLong(LAMMPS *lmp) : Pair(lmp) PairLJClass2CoulLong::~PairLJClass2CoulLong() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(offset); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); } if (ftable) free_tables(); } @@ -82,8 +82,7 @@ void PairLJClass2CoulLong::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -252,8 +251,9 @@ void PairLJClass2CoulLong::settings(int narg, char **arg) void PairLJClass2CoulLong::coeff(int narg, char **arg) { - if (narg < 4 || narg > 6) + if (narg < 4 || narg > 5) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); int ilo,ihi,jlo,jhi; @@ -549,5 +549,8 @@ void *PairLJClass2CoulLong::extract(const char *str, int &dim) { dim = 0; if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; return NULL; } diff --git a/src/COLLOID/pair_brownian.cpp b/src/COLLOID/pair_brownian.cpp index e532c06c86..aefa96b1fb 100644 --- a/src/COLLOID/pair_brownian.cpp +++ b/src/COLLOID/pair_brownian.cpp @@ -80,8 +80,7 @@ void PairBrownian::compute(int eflag, int vflag) double rsq,r,h_sep,radi; int *ilist,*jlist,*numneigh,**firstneigh; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/COLLOID/pair_brownian_poly.cpp b/src/COLLOID/pair_brownian_poly.cpp index c6d5def2fa..389ae084b7 100644 --- a/src/COLLOID/pair_brownian_poly.cpp +++ b/src/COLLOID/pair_brownian_poly.cpp @@ -66,8 +66,7 @@ void PairBrownianPoly::compute(int eflag, int vflag) double rsq,r,h_sep,beta0,beta1,radi,radj; int *ilist,*jlist,*numneigh,**firstneigh; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/COLLOID/pair_colloid.cpp b/src/COLLOID/pair_colloid.cpp index c16dbf41af..04c35a7c00 100644 --- a/src/COLLOID/pair_colloid.cpp +++ b/src/COLLOID/pair_colloid.cpp @@ -78,8 +78,7 @@ void PairColloid::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/COLLOID/pair_lubricate.cpp b/src/COLLOID/pair_lubricate.cpp index de53d91818..4e629bd442 100644 --- a/src/COLLOID/pair_lubricate.cpp +++ b/src/COLLOID/pair_lubricate.cpp @@ -88,8 +88,7 @@ void PairLubricate::compute(int eflag, int vflag) double vxmu2f = force->vxmu2f; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; diff --git a/src/COLLOID/pair_lubricateU.cpp b/src/COLLOID/pair_lubricateU.cpp index 35fe33c84e..3ea3d4fe4a 100644 --- a/src/COLLOID/pair_lubricateU.cpp +++ b/src/COLLOID/pair_lubricateU.cpp @@ -116,8 +116,7 @@ void PairLubricateU::compute(int eflag, int vflag) int nghost = atom->nghost; int nall = nlocal + nghost; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // skip compute() if called from integrate::setup() // this is b/c do not want compute() to update velocities twice on a restart diff --git a/src/COLLOID/pair_lubricateU_poly.cpp b/src/COLLOID/pair_lubricateU_poly.cpp index 90ac848d26..4fec95dcd8 100644 --- a/src/COLLOID/pair_lubricateU_poly.cpp +++ b/src/COLLOID/pair_lubricateU_poly.cpp @@ -78,8 +78,7 @@ void PairLubricateUPoly::compute(int eflag, int vflag) double **f = atom->f; double **torque = atom->torque; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // grow per-atom arrays if necessary // need to be atom->nmax in length diff --git a/src/COLLOID/pair_lubricate_poly.cpp b/src/COLLOID/pair_lubricate_poly.cpp index 5e52933364..ffbe7fce3c 100644 --- a/src/COLLOID/pair_lubricate_poly.cpp +++ b/src/COLLOID/pair_lubricate_poly.cpp @@ -72,8 +72,7 @@ void PairLubricatePoly::compute(int eflag, int vflag) double vxmu2f = force->vxmu2f; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; diff --git a/src/COLLOID/pair_yukawa_colloid.cpp b/src/COLLOID/pair_yukawa_colloid.cpp index d21bc43524..ab7d088508 100644 --- a/src/COLLOID/pair_yukawa_colloid.cpp +++ b/src/COLLOID/pair_yukawa_colloid.cpp @@ -46,8 +46,7 @@ void PairYukawaColloid::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_born_coul_dsf_cs.cpp b/src/CORESHELL/pair_born_coul_dsf_cs.cpp index 549c7c0348..f4d7447ade 100644 --- a/src/CORESHELL/pair_born_coul_dsf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_dsf_cs.cpp @@ -57,8 +57,7 @@ void PairBornCoulDSFCS::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_born_coul_long_cs.cpp b/src/CORESHELL/pair_born_coul_long_cs.cpp index 76f6eb387d..a19f8c34a8 100644 --- a/src/CORESHELL/pair_born_coul_long_cs.cpp +++ b/src/CORESHELL/pair_born_coul_long_cs.cpp @@ -68,8 +68,7 @@ void PairBornCoulLongCS::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_born_coul_wolf_cs.cpp b/src/CORESHELL/pair_born_coul_wolf_cs.cpp index 84179ce50a..7b52c28664 100644 --- a/src/CORESHELL/pair_born_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_born_coul_wolf_cs.cpp @@ -53,8 +53,7 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag) double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_buck_coul_long_cs.cpp b/src/CORESHELL/pair_buck_coul_long_cs.cpp index ea072d44a1..8df91f39a3 100644 --- a/src/CORESHELL/pair_buck_coul_long_cs.cpp +++ b/src/CORESHELL/pair_buck_coul_long_cs.cpp @@ -68,8 +68,7 @@ void PairBuckCoulLongCS::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_coul_long_cs.cpp b/src/CORESHELL/pair_coul_long_cs.cpp index b214653841..c8c8387d6d 100644 --- a/src/CORESHELL/pair_coul_long_cs.cpp +++ b/src/CORESHELL/pair_coul_long_cs.cpp @@ -69,8 +69,7 @@ void PairCoulLongCS::compute(int eflag, int vflag) double rsq; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_coul_wolf_cs.cpp b/src/CORESHELL/pair_coul_wolf_cs.cpp index b50f14833e..36e037bfc8 100644 --- a/src/CORESHELL/pair_coul_wolf_cs.cpp +++ b/src/CORESHELL/pair_coul_wolf_cs.cpp @@ -53,8 +53,7 @@ void PairCoulWolfCS::compute(int eflag, int vflag) double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp index 8caefc0e66..56c75f0f5d 100644 --- a/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp +++ b/src/CORESHELL/pair_lj_cut_coul_long_cs.cpp @@ -74,8 +74,7 @@ void PairLJCutCoulLongCS::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -399,8 +398,7 @@ void PairLJCutCoulLongCS::compute_outer(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp index 6af9b45724..18b78c55e0 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp @@ -69,8 +69,7 @@ void PairLJCutDipoleCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/DIPOLE/pair_lj_cut_dipole_long.cpp b/src/DIPOLE/pair_lj_cut_dipole_long.cpp index 817a120e3d..0806d1ee73 100644 --- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp @@ -90,8 +90,7 @@ void PairLJCutDipoleLong::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/DIPOLE/pair_lj_long_dipole_long.cpp b/src/DIPOLE/pair_lj_long_dipole_long.cpp index 21fc035854..fbdc47a15b 100644 --- a/src/DIPOLE/pair_lj_long_dipole_long.cpp +++ b/src/DIPOLE/pair_lj_long_dipole_long.cpp @@ -405,8 +405,7 @@ void PairLJLongDipoleLong::compute(int eflag, int vflag) double evdwl,ecoul,fpair; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x, *x0 = x[0]; double **mu = atom->mu, *mu0 = mu[0], *imu, *jmu; diff --git a/src/Depend.sh b/src/Depend.sh index a3f4e49667..b7ee740c52 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -107,6 +107,7 @@ fi if (test $1 = "RIGID") then depend USER-OMP + depend USER-SDPD fi if (test $1 = "SNAP") then diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 268a741032..0d5b4334c9 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -30,6 +30,7 @@ #include "neighbor.h" #include "citeme.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -221,12 +222,11 @@ void FixGPU::init() // hybrid cannot be used with force/neigh option if (_gpu_mode == GPU_NEIGH || _gpu_mode == GPU_HYB_NEIGH) - if (force->pair_match("hybrid",1) != NULL || - force->pair_match("hybrid/overlay",1) != NULL) + if (force->pair_match("^hybrid",0) != NULL) error->all(FLERR,"Cannot use pair hybrid with GPU neighbor list builds"); + if (_particle_split < 0) - if (force->pair_match("hybrid",1) != NULL || - force->pair_match("hybrid/overlay",1) != NULL) + if (force->pair_match("^hybrid",0) != NULL) error->all(FLERR,"GPU split param must be positive " "for hybrid pair styles"); @@ -243,21 +243,16 @@ void FixGPU::init() // make sure fdotr virial is not accumulated multiple times - if (force->pair_match("hybrid",1) != NULL) { + if (force->pair_match("^hybrid",0) != NULL) { PairHybrid *hybrid = (PairHybrid *) force->pair; for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i],"/gpu")==NULL) - force->pair->no_virial_fdotr_compute = 1; - } else if (force->pair_match("hybrid/overlay",1) != NULL) { - PairHybridOverlay *hybrid = (PairHybridOverlay *) force->pair; - for (int i = 0; i < hybrid->nstyles; i++) - if (strstr(hybrid->keywords[i],"/gpu")==NULL) + if (!utils::strmatch(hybrid->keywords[i],"/gpu$")) force->pair->no_virial_fdotr_compute = 1; } // rRESPA support - if (strstr(update->integrate_style,"respa")) + if (utils::strmatch(update->integrate_style,"^respa")) _nlevels_respa = ((Respa *) update->integrate)->nlevels; } @@ -288,7 +283,7 @@ void FixGPU::min_setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixGPU::post_force(int vflag) +void FixGPU::post_force(int /* vflag */) { if (!force->pair) return; @@ -320,7 +315,7 @@ void FixGPU::min_post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixGPU::post_force_respa(int vflag, int ilevel, int iloop) +void FixGPU::post_force_respa(int vflag, int /* ilevel */, int /* iloop */) { post_force(vflag); } diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp index f929dd437f..9f76975ef1 100644 --- a/src/GPU/pair_beck_gpu.cpp +++ b/src/GPU/pair_beck_gpu.cpp @@ -84,8 +84,7 @@ PairBeckGPU::~PairBeckGPU() void PairBeckGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -171,8 +170,9 @@ double PairBeckGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairBeckGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairBeckGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r5,force_beck,factor_lj; diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp index 13cf5f643a..291ad8ad1f 100644 --- a/src/GPU/pair_born_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp @@ -106,8 +106,7 @@ PairBornCoulLongCSGPU::~PairBornCoulLongCSGPU() void PairBornCoulLongCSGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -212,8 +211,8 @@ double PairBornCoulLongCSGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairBornCoulLongCSGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itable,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp index c3c3fee40c..eb204691c7 100644 --- a/src/GPU/pair_born_coul_long_gpu.cpp +++ b/src/GPU/pair_born_coul_long_gpu.cpp @@ -101,8 +101,7 @@ PairBornCoulLongGPU::~PairBornCoulLongGPU() void PairBornCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -207,8 +206,8 @@ double PairBornCoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairBornCoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp index 90ddf825a9..4877a442b5 100644 --- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp @@ -94,8 +94,7 @@ PairBornCoulWolfCSGPU::~PairBornCoulWolfCSGPU() void PairBornCoulWolfCSGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -193,9 +192,9 @@ double PairBornCoulWolfCSGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairBornCoulWolfCSGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) { +void PairBornCoulWolfCSGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair; double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp index df1922d76a..851174988b 100644 --- a/src/GPU/pair_born_coul_wolf_gpu.cpp +++ b/src/GPU/pair_born_coul_wolf_gpu.cpp @@ -92,8 +92,7 @@ PairBornCoulWolfGPU::~PairBornCoulWolfGPU() void PairBornCoulWolfGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -191,9 +190,9 @@ double PairBornCoulWolfGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) { +void PairBornCoulWolfGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair; double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj; diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp index 92a7a85997..253d2d7282 100644 --- a/src/GPU/pair_born_gpu.cpp +++ b/src/GPU/pair_born_gpu.cpp @@ -87,8 +87,7 @@ PairBornGPU::~PairBornGPU() void PairBornGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -185,8 +184,9 @@ double PairBornGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairBornGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairBornGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r2inv,r6inv,forceborn,factor_lj; diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp index 6396e301e3..ed602f9cab 100644 --- a/src/GPU/pair_buck_coul_cut_gpu.cpp +++ b/src/GPU/pair_buck_coul_cut_gpu.cpp @@ -88,8 +88,7 @@ PairBuckCoulCutGPU::~PairBuckCoulCutGPU() void PairBuckCoulCutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -179,9 +178,9 @@ double PairBuckCoulCutGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) { +void PairBuckCoulCutGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair; double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj; diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp index 73821cee8a..d6b9e53282 100644 --- a/src/GPU/pair_buck_coul_long_gpu.cpp +++ b/src/GPU/pair_buck_coul_long_gpu.cpp @@ -97,8 +97,7 @@ PairBuckCoulLongGPU::~PairBuckCoulLongGPU() void PairBuckCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -201,8 +200,8 @@ double PairBuckCoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp index 20302e4f1a..8c85407e6e 100644 --- a/src/GPU/pair_buck_gpu.cpp +++ b/src/GPU/pair_buck_gpu.cpp @@ -85,8 +85,7 @@ PairBuckGPU::~PairBuckGPU() void PairBuckGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -182,8 +181,8 @@ double PairBuckGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairBuckGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r2inv,r6inv,forcebuck,factor_lj; diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp index 7bbac32ed3..0ee8708b5b 100644 --- a/src/GPU/pair_colloid_gpu.cpp +++ b/src/GPU/pair_colloid_gpu.cpp @@ -85,8 +85,7 @@ PairColloidGPU::~PairColloidGPU() void PairColloidGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -184,8 +183,9 @@ double PairColloidGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) +void PairColloidGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp index d5d9b10abb..fb50c446b1 100644 --- a/src/GPU/pair_coul_cut_gpu.cpp +++ b/src/GPU/pair_coul_cut_gpu.cpp @@ -85,8 +85,7 @@ PairCoulCutGPU::~PairCoulCutGPU() void PairCoulCutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -186,9 +185,9 @@ double PairCoulCutGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) +void PairCoulCutGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp index 9fd28bf9c5..ec771a9935 100644 --- a/src/GPU/pair_coul_debye_gpu.cpp +++ b/src/GPU/pair_coul_debye_gpu.cpp @@ -86,8 +86,7 @@ PairCoulDebyeGPU::~PairCoulDebyeGPU() void PairCoulDebyeGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -189,8 +188,8 @@ double PairCoulDebyeGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairCoulDebyeGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, - int *numneigh, int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp index 75168c3cd9..1753b8a91c 100644 --- a/src/GPU/pair_coul_dsf_gpu.cpp +++ b/src/GPU/pair_coul_dsf_gpu.cpp @@ -97,8 +97,7 @@ PairCoulDSFGPU::~PairCoulDSFGPU() void PairCoulDSFGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -196,9 +195,9 @@ double PairCoulDSFGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) +void PairCoulDSFGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp index cbb9c73ceb..6ca00d6361 100644 --- a/src/GPU/pair_coul_long_cs_gpu.cpp +++ b/src/GPU/pair_coul_long_cs_gpu.cpp @@ -99,8 +99,7 @@ PairCoulLongCSGPU::~PairCoulLongCSGPU() void PairCoulLongCSGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -153,7 +152,7 @@ void PairCoulLongCSGPU::init_style() for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { - double cut = init_one(i,j); + init_one(i,j); } } } @@ -208,8 +207,8 @@ double PairCoulLongCSGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairCoulLongCSGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itable,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp index 2f12e41b0c..f75d10b6dd 100644 --- a/src/GPU/pair_coul_long_gpu.cpp +++ b/src/GPU/pair_coul_long_gpu.cpp @@ -94,8 +94,7 @@ PairCoulLongGPU::~PairCoulLongGPU() void PairCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -148,7 +147,7 @@ void PairCoulLongGPU::init_style() for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) { - double cut = init_one(i,j); + init_one(i,j); } } } @@ -203,8 +202,8 @@ double PairCoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairCoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair; diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp index 293a82ffa9..b1e45fbecd 100644 --- a/src/GPU/pair_dpd_gpu.cpp +++ b/src/GPU/pair_dpd_gpu.cpp @@ -225,8 +225,7 @@ PairDPDGPU::~PairDPDGPU() void PairDPDGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -319,8 +318,8 @@ double PairDPDGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairDPDGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairDPDGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double vxtmp,vytmp,vztmp,delvx,delvy,delvz; diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp index bf02570f43..0693a27344 100644 --- a/src/GPU/pair_dpd_tstat_gpu.cpp +++ b/src/GPU/pair_dpd_tstat_gpu.cpp @@ -228,8 +228,7 @@ PairDPDTstatGPU::~PairDPDTstatGPU() void PairDPDTstatGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // adjust sigma if target T is changing @@ -336,8 +335,9 @@ double PairDPDTstatGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairDPDTstatGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairDPDTstatGPU::cpu_compute(int start, int inum, int /* eflag */, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,fpair; double vxtmp,vytmp,vztmp,delvx,delvy,delvz; diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp index 11af562f15..9b3412d3d1 100644 --- a/src/GPU/pair_eam_alloy_gpu.cpp +++ b/src/GPU/pair_eam_alloy_gpu.cpp @@ -29,6 +29,8 @@ #include "neigh_request.h" #include "gpu_extra.h" #include "domain.h" +#include "utils.h" + using namespace LAMMPS_NS; @@ -92,8 +94,7 @@ double PairEAMAlloyGPU::memory_usage() void PairEAMAlloyGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // compute density on each atom on GPU @@ -192,8 +193,8 @@ void PairEAMAlloyGPU::init_style() /* ---------------------------------------------------------------------- */ double PairEAMAlloyGPU::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, - double &fforce) + double rsq, double /* factor_coul */, + double /* factor_lj */, double &fforce) { int m; double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; @@ -235,7 +236,7 @@ double PairEAMAlloyGPU::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ int PairEAMAlloyGPU::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag,int *pbc) + int /* pbc_flag */, int * /* pbc */) { int i,j,m; @@ -374,10 +375,10 @@ void PairEAMAlloyGPU::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -402,7 +403,7 @@ void PairEAMAlloyGPU::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -422,7 +423,7 @@ void PairEAMAlloyGPU::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fptr); + utils::sfgets(FLERR,line,MAXLINE,fptr,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp index ef8dd09e23..11ef28af3e 100644 --- a/src/GPU/pair_eam_fs_gpu.cpp +++ b/src/GPU/pair_eam_fs_gpu.cpp @@ -92,8 +92,7 @@ double PairEAMFSGPU::memory_usage() void PairEAMFSGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // compute density on each atom on GPU @@ -192,8 +191,8 @@ void PairEAMFSGPU::init_style() /* ---------------------------------------------------------------------- */ double PairEAMFSGPU::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, - double &fforce) + double rsq, double /* factor_coul */, + double /* factor_lj */, double &fforce) { int m; double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; @@ -235,7 +234,7 @@ double PairEAMFSGPU::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ int PairEAMFSGPU::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag,int *pbc) + int /* pbc_flag */, int * /* pbc */) { int i,j,m; diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp index e2eb9daced..4788a72417 100644 --- a/src/GPU/pair_eam_gpu.cpp +++ b/src/GPU/pair_eam_gpu.cpp @@ -95,8 +95,7 @@ double PairEAMGPU::memory_usage() void PairEAMGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // compute density on each atom on GPU @@ -195,8 +194,8 @@ void PairEAMGPU::init_style() /* ---------------------------------------------------------------------- */ double PairEAMGPU::single(int i, int j, int itype, int jtype, - double rsq, double factor_coul, double factor_lj, - double &fforce) + double rsq, double /* factor_coul */, + double /* factor_lj */, double &fforce) { int m; double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip; @@ -238,7 +237,7 @@ double PairEAMGPU::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ int PairEAMGPU::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag,int *pbc) + int /* pbc_flag */, int * /* pbc */) { int i,j,m; diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp index f99a10a680..c596a9d644 100644 --- a/src/GPU/pair_gauss_gpu.cpp +++ b/src/GPU/pair_gauss_gpu.cpp @@ -82,8 +82,7 @@ PairGaussGPU::~PairGaussGPU() void PairGaussGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -178,7 +177,7 @@ double PairGaussGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int vflag, +void PairGaussGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp index 8bd5eb073f..4ed2750e57 100644 --- a/src/GPU/pair_gayberne_gpu.cpp +++ b/src/GPU/pair_gayberne_gpu.cpp @@ -92,8 +92,7 @@ PairGayBerneGPU::~PairGayBerneGPU() void PairGayBerneGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -221,8 +220,9 @@ double PairGayBerneGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) +void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj; diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp index 800f13ef60..5bc30c809d 100644 --- a/src/GPU/pair_lj96_cut_gpu.cpp +++ b/src/GPU/pair_lj96_cut_gpu.cpp @@ -82,8 +82,7 @@ PairLJ96CutGPU::~PairLJ96CutGPU() void PairLJ96CutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -171,8 +170,9 @@ double PairLJ96CutGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) +void PairLJ96CutGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp index 8c806053d4..134295c69f 100644 --- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp @@ -99,8 +99,7 @@ PairLJCharmmCoulLongGPU::~PairLJCharmmCoulLongGPU() void PairLJCharmmCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -151,11 +150,10 @@ void PairLJCharmmCoulLongGPU::init_style() // Repeat cutsq calculation because done after call to init_style - double cut; for (int i = 1; i <= atom->ntypes; i++) { for (int j = i; j <= atom->ntypes; j++) { if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) - cut = init_one(i,j); + init_one(i,j); } } @@ -219,7 +217,7 @@ double PairLJCharmmCoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, + int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp index 214ff306db..fdffb06a8d 100644 --- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp @@ -96,8 +96,7 @@ PairLJClass2CoulLongGPU::~PairLJClass2CoulLongGPU() void PairLJClass2CoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -197,8 +196,8 @@ double PairLJClass2CoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJClass2CoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp index 61b0a8caf1..bbb9168169 100644 --- a/src/GPU/pair_lj_class2_gpu.cpp +++ b/src/GPU/pair_lj_class2_gpu.cpp @@ -81,8 +81,7 @@ PairLJClass2GPU::~PairLJClass2GPU() void PairLJClass2GPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -168,8 +167,9 @@ double PairLJClass2GPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) +void PairLJClass2GPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp index 366c33191b..95eee6ae8f 100644 --- a/src/GPU/pair_lj_cubic_gpu.cpp +++ b/src/GPU/pair_lj_cubic_gpu.cpp @@ -86,8 +86,7 @@ PairLJCubicGPU::~PairLJCubicGPU() void PairLJCubicGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -174,8 +173,9 @@ double PairLJCubicGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJCubicGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairLJCubicGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r2inv,r6inv,forcelj,factor_lj; diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp index baafcd2d62..69fefbcdea 100644 --- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp @@ -87,8 +87,7 @@ PairLJCutCoulCutGPU::~PairLJCutCoulCutGPU() void PairLJCutCoulCutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -180,9 +179,9 @@ double PairLJCutCoulCutGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) +void PairLJCutCoulCutGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp index 662375da2c..de86c58647 100644 --- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp @@ -89,8 +89,7 @@ ljcd_gpu_clear(); void PairLJCutCoulDebyeGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -184,7 +183,7 @@ double PairLJCutCoulDebyeGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJCutCoulDebyeGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, + int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp index c8e68140a1..87eac52749 100644 --- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp @@ -98,8 +98,7 @@ PairLJCutCoulDSFGPU::~PairLJCutCoulDSFGPU() void PairLJCutCoulDSFGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -198,9 +197,9 @@ double PairLJCutCoulDSFGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, - int **firstneigh) +void PairLJCutCoulDSFGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp index 3cccb898cc..c854dab83d 100644 --- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp @@ -99,8 +99,7 @@ PairLJCutCoulLongGPU::~PairLJCutCoulLongGPU() void PairLJCutCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -215,8 +214,8 @@ double PairLJCutCoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJCutCoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp index 04ffe245b2..f87dc0ec91 100644 --- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp +++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp @@ -88,8 +88,7 @@ PairLJCutCoulMSMGPU::~PairLJCutCoulMSMGPU() void PairLJCutCoulMSMGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -192,8 +191,9 @@ double PairLJCutCoulMSMGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; double fraction,table; diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp index 1f4528cb88..d2c925d950 100644 --- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp @@ -89,8 +89,7 @@ PairLJCutDipoleCutGPU::~PairLJCutDipoleCutGPU() void PairLJCutDipoleCutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -199,8 +198,7 @@ void PairLJCutDipoleCutGPU::cpu_compute(int start, int inum, int eflag, int vfla int *jlist; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp index 870dc8ba6d..774ff2fae4 100644 --- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp +++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp @@ -100,8 +100,7 @@ PairLJCutDipoleLongGPU::~PairLJCutDipoleLongGPU() void PairLJCutDipoleLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -216,7 +215,7 @@ void PairLJCutDipoleLongGPU::cpu_compute(int start, int inum, int eflag, int vfl double qtmp,xtmp,ytmp,ztmp,delx,dely,delz; double rsq,r,rinv,r2inv,r6inv; double forcecoulx,forcecouly,forcecoulz,fforce; - double tixcoul,tiycoul,tizcoul,tjxcoul,tjycoul,tjzcoul; + double tixcoul,tiycoul,tizcoul; double fx,fy,fz,fdx,fdy,fdz,fax,fay,faz; double pdotp,pidotr,pjdotr,pre1,pre2,pre3; double grij,expm2,t,erfc; @@ -228,8 +227,7 @@ void PairLJCutDipoleLongGPU::cpu_compute(int start, int inum, int eflag, int vfl int *jlist; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -378,14 +376,9 @@ void PairLJCutDipoleLongGPU::cpu_compute(int start, int inum, int eflag, int vfl tixcoul = mu[i][1]*(zdiz + zaiz) - mu[i][2]*(zdiy + zaiy); tiycoul = mu[i][2]*(zdix + zaix) - mu[i][0]*(zdiz + zaiz); tizcoul = mu[i][0]*(zdiy + zaiy) - mu[i][1]*(zdix + zaix); - tjxcoul = mu[j][1]*(zdjz + zajz) - mu[j][2]*(zdjy + zajy); - tjycoul = mu[j][2]*(zdjx + zajx) - mu[j][0]*(zdjz + zajz); - tjzcoul = mu[j][0]*(zdjy + zajy) - mu[j][1]*(zdjx + zajx); - } else { forcecoulx = forcecouly = forcecoulz = 0.0; tixcoul = tiycoul = tizcoul = 0.0; - tjxcoul = tjycoul = tjzcoul = 0.0; } // LJ interaction diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp index af654bcc5d..6dde9689f7 100644 --- a/src/GPU/pair_lj_cut_gpu.cpp +++ b/src/GPU/pair_lj_cut_gpu.cpp @@ -86,8 +86,7 @@ PairLJCutGPU::~PairLJCutGPU() void PairLJCutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -184,7 +183,7 @@ double PairLJCutGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int vflag, +void PairLJCutGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp index 49e8be5879..31f4fd651c 100644 --- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp @@ -99,8 +99,7 @@ PairLJExpandCoulLongGPU::~PairLJExpandCoulLongGPU() void PairLJExpandCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -215,8 +214,8 @@ double PairLJExpandCoulLongGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJExpandCoulLongGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp index f0a9f67b10..a2e1cf54e3 100644 --- a/src/GPU/pair_lj_expand_gpu.cpp +++ b/src/GPU/pair_lj_expand_gpu.cpp @@ -85,8 +85,7 @@ PairLJExpandGPU::~PairLJExpandGPU() void PairLJExpandGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -181,8 +180,9 @@ double PairLJExpandGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) +void PairLJExpandGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp index f200679829..e03f4b2e50 100644 --- a/src/GPU/pair_lj_gromacs_gpu.cpp +++ b/src/GPU/pair_lj_gromacs_gpu.cpp @@ -87,8 +87,7 @@ PairLJGromacsGPU::~PairLJGromacsGPU() void PairLJGromacsGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -177,7 +176,7 @@ double PairLJGromacsGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairLJGromacsGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, + int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp index 4dbd8874d6..f5029df5dc 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp @@ -102,8 +102,7 @@ PairLJSDKCoulLongGPU::~PairLJSDKCoulLongGPU() void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp index 84d224a8c4..4797a34408 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_sdk_gpu.cpp @@ -87,8 +87,7 @@ PairLJSDKGPU::~PairLJSDKGPU() void PairLJSDKGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp index a5ebb1dbc1..dd25a70eee 100644 --- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp +++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp @@ -88,8 +88,7 @@ PairLJSFDipoleSFGPU::~PairLJSFDipoleSFGPU() void PairLJSFDipoleSFGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -202,8 +201,7 @@ void PairLJSFDipoleSFGPU::cpu_compute(int start, int inum, int eflag, int vflag, int *jlist; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp index 5919b05466..838d28033f 100644 --- a/src/GPU/pair_mie_cut_gpu.cpp +++ b/src/GPU/pair_mie_cut_gpu.cpp @@ -83,8 +83,7 @@ PairMIECutGPU::~PairMIECutGPU() void PairMIECutGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -172,8 +171,8 @@ double PairMIECutGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairMIECutGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairMIECutGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r2inv,rgamR,rgamA,forcemie,factor_mie; diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp index 81ea7c818a..1f94643e3a 100644 --- a/src/GPU/pair_morse_gpu.cpp +++ b/src/GPU/pair_morse_gpu.cpp @@ -81,8 +81,7 @@ PairMorseGPU::~PairMorseGPU() void PairMorseGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -168,7 +167,7 @@ double PairMorseGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairMorseGPU::cpu_compute(int start, int inum, int eflag, int vflag, +void PairMorseGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp index 34bd0ec22f..5e90f788bf 100644 --- a/src/GPU/pair_resquared_gpu.cpp +++ b/src/GPU/pair_resquared_gpu.cpp @@ -94,8 +94,7 @@ PairRESquaredGPU::~PairRESquaredGPU() void PairRESquaredGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -219,8 +218,9 @@ double PairRESquaredGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) +void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag, + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj; diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp index cc0ea72633..42adb02553 100644 --- a/src/GPU/pair_soft_gpu.cpp +++ b/src/GPU/pair_soft_gpu.cpp @@ -86,8 +86,7 @@ PairSoftGPU::~PairSoftGPU() void PairSoftGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -182,8 +181,8 @@ double PairSoftGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairSoftGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairSoftGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double r,rsq,arg,factor_lj; diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp index 5368bee959..0cc858e57d 100644 --- a/src/GPU/pair_sw_gpu.cpp +++ b/src/GPU/pair_sw_gpu.cpp @@ -93,8 +93,7 @@ PairSWGPU::~PairSWGPU() void PairSWGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp index c5aef996db..a0b6562e5e 100644 --- a/src/GPU/pair_table_gpu.cpp +++ b/src/GPU/pair_table_gpu.cpp @@ -89,8 +89,7 @@ PairTableGPU::~PairTableGPU() void PairTableGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -246,7 +245,7 @@ double PairTableGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag, +void PairTableGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype,itable; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp index 535b56163e..cd0c5e6693 100644 --- a/src/GPU/pair_tersoff_gpu.cpp +++ b/src/GPU/pair_tersoff_gpu.cpp @@ -97,8 +97,7 @@ PairTersoffGPU::~PairTersoffGPU() void PairTersoffGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp index f8b6c50db5..fd55ddc6e6 100644 --- a/src/GPU/pair_tersoff_mod_gpu.cpp +++ b/src/GPU/pair_tersoff_mod_gpu.cpp @@ -90,8 +90,7 @@ PairTersoffMODGPU::~PairTersoffMODGPU() void PairTersoffMODGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp index b45503d759..d3828962e2 100644 --- a/src/GPU/pair_tersoff_zbl_gpu.cpp +++ b/src/GPU/pair_tersoff_zbl_gpu.cpp @@ -98,8 +98,7 @@ PairTersoffZBLGPU::~PairTersoffZBLGPU() void PairTersoffZBLGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp index 40e8df3323..31422b0f4d 100644 --- a/src/GPU/pair_ufm_gpu.cpp +++ b/src/GPU/pair_ufm_gpu.cpp @@ -88,8 +88,7 @@ PairUFMGPU::~PairUFMGPU() void PairUFMGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -186,8 +185,8 @@ double PairUFMGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairUFMGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairUFMGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,expuf,factor_lj; diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp index 00dbac5f1e..b496359b8a 100644 --- a/src/GPU/pair_vashishta_gpu.cpp +++ b/src/GPU/pair_vashishta_gpu.cpp @@ -94,8 +94,7 @@ PairVashishtaGPU::~PairVashishtaGPU() void PairVashishtaGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -151,7 +150,7 @@ void PairVashishtaGPU::init_style() if (force->newton_pair != 0) error->all(FLERR,"Pair style vashishta/gpu requires newton pair off"); - double *cutsq, *r0, *r0eps, *gamma, *eta; + double *cutsq, *r0, *gamma, *eta; double *lam1inv, *lam4inv, *zizj, *mbigd; double *dvrc, *big6w, *heta, *bigh; double *bigw, *c0, *costheta, *bigb; diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp index 0332e5f755..3645f392a2 100644 --- a/src/GPU/pair_yukawa_colloid_gpu.cpp +++ b/src/GPU/pair_yukawa_colloid_gpu.cpp @@ -84,8 +84,7 @@ PairYukawaColloidGPU::~PairYukawaColloidGPU() void PairYukawaColloidGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -179,8 +178,8 @@ double PairYukawaColloidGPU::memory_usage() /* ---------------------------------------------------------------------- */ void PairYukawaColloidGPU::cpu_compute(int start, int inum, int eflag, - int vflag, int *ilist, int *numneigh, - int **firstneigh) { + int /* vflag */, int *ilist, + int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,radi,radj; double r,rsq,rinv,screening,forceyukawa,factor; diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp index dda4250f07..90317fea34 100644 --- a/src/GPU/pair_yukawa_gpu.cpp +++ b/src/GPU/pair_yukawa_gpu.cpp @@ -83,8 +83,7 @@ PairYukawaGPU::~PairYukawaGPU() void PairYukawaGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -170,8 +169,8 @@ double PairYukawaGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int vflag, - int *ilist, int *numneigh, int **firstneigh) { +void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, + int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; double rsq,r2inv,r,rinv,screening,forceyukawa,factor; diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp index daca79c8e3..99471cbe90 100644 --- a/src/GPU/pair_zbl_gpu.cpp +++ b/src/GPU/pair_zbl_gpu.cpp @@ -86,8 +86,7 @@ PairZBLGPU::~PairZBLGPU() void PairZBLGPU::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int nall = atom->nlocal + atom->nghost; int inum, host_start; @@ -177,7 +176,7 @@ double PairZBLGPU::memory_usage() /* ---------------------------------------------------------------------- */ -void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int vflag, +void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */, int *ilist, int *numneigh, int **firstneigh) { int i,j,ii,jj,jnum,itype,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; diff --git a/src/GPU/pppm_gpu.cpp b/src/GPU/pppm_gpu.cpp index 4b460b1280..1bb1a39703 100644 --- a/src/GPU/pppm_gpu.cpp +++ b/src/GPU/pppm_gpu.cpp @@ -199,9 +199,7 @@ void PPPMGPU::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // If need per-atom energies/virials, allocate per-atom arrays here // so that particle map on host can be done concurrently with GPU calculations diff --git a/src/GRANULAR/pair_gran_hertz_history.cpp b/src/GRANULAR/pair_gran_hertz_history.cpp index d1f3c7bbe1..728491c17a 100644 --- a/src/GRANULAR/pair_gran_hertz_history.cpp +++ b/src/GRANULAR/pair_gran_hertz_history.cpp @@ -55,8 +55,7 @@ void PairGranHertzHistory::compute(int eflag, int vflag) int *touch,**firsttouch; double *shear,*allshear,**firstshear; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int shearupdate = 1; if (update->setupflag) shearupdate = 0; diff --git a/src/GRANULAR/pair_gran_hooke.cpp b/src/GRANULAR/pair_gran_hooke.cpp index 5244396ead..cfcc2743ba 100644 --- a/src/GRANULAR/pair_gran_hooke.cpp +++ b/src/GRANULAR/pair_gran_hooke.cpp @@ -51,8 +51,7 @@ void PairGranHooke::compute(int eflag, int vflag) double fn,fs,ft,fs1,fs2,fs3; int *ilist,*jlist,*numneigh,**firstneigh; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // update rigid body info for owned & ghost atoms if using FixRigid masses // body[i] = which body atom I is in, -1 if none diff --git a/src/GRANULAR/pair_gran_hooke_history.cpp b/src/GRANULAR/pair_gran_hooke_history.cpp index 83f75c221d..cec825316c 100644 --- a/src/GRANULAR/pair_gran_hooke_history.cpp +++ b/src/GRANULAR/pair_gran_hooke_history.cpp @@ -98,8 +98,7 @@ void PairGranHookeHistory::compute(int eflag, int vflag) int *touch,**firsttouch; double *shear,*allshear,**firstshear; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int shearupdate = 1; if (update->setupflag) shearupdate = 0; diff --git a/src/KIM/README b/src/KIM/README index 496db92cf2..a69206596f 100644 --- a/src/KIM/README +++ b/src/KIM/README @@ -26,5 +26,4 @@ library you can test it using an input file from the examples dir: ./lmp_serial < lammps/examples/kim/in.kim.lj -This pair_style was written by Valeriu Smirichinski and Ryan -S. Elliott (U Minn). +This pair_style was written by Ryan S. Elliott (U Minn). diff --git a/src/KIM/kim_query.cpp b/src/KIM/kim_query.cpp new file mode 100644 index 0000000000..2e1f752dc1 --- /dev/null +++ b/src/KIM/kim_query.cpp @@ -0,0 +1,235 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-v2-2.0.0 (and newer) package +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "kim_query.h" +#include "comm.h" +#include "error.h" +#include "input.h" +#include "variable.h" + +#include +#include + +using namespace LAMMPS_NS; + +#if defined(LMP_KIM_CURL) + +struct WriteBuf { + char *dataptr; + size_t sizeleft; +}; + +static char *do_query(char *, int, char **, int, MPI_Comm); +static size_t write_callback(void *, size_t, size_t, void *); + +#endif + +/* ---------------------------------------------------------------------- */ + +void KimQuery::command(int narg, char **arg) +{ + char *varname, *function, *value; + + if (narg < 2) error->all(FLERR,"Illegal kim_query command"); + + varname = arg[0]; + function = arg[1]; + +#if defined(LMP_KIM_CURL) + + value = do_query(function, narg-2, arg+2, comm->me, world); + + // check for valid result + // on error the content of "value" is a '\0' byte + // as the first element, and then the error message + // that was returned by the web server + + if (0 == strlen(value)) { + char errmsg[512]; + + sprintf(errmsg,"OpenKIM query failed: %s",value+1); + error->all(FLERR,errmsg); + } + + char **varcmd = new char*[3]; + varcmd[0] = varname; + varcmd[1] = (char *) "string"; + varcmd[2] = value; + + input->variable->set(3,varcmd); + + delete[] varcmd; + delete[] value; +#else + error->all(FLERR,"Cannot use 'kim_query' command when KIM package " + "is compiled without support for libcurl"); +#endif +} + +#if defined(LMP_KIM_CURL) + +// copy data to the user provided data structure, optionally in increments + +size_t write_callback(void *data, size_t size, size_t nmemb, void *userp) +{ + struct WriteBuf *buf = (struct WriteBuf *)userp; + size_t buffer_size = size*nmemb; + + // copy chunks into the buffer for as long as there is space left + if (buf->sizeleft) { + size_t copy_this_much = buf->sizeleft; + if (copy_this_much > buffer_size) + copy_this_much = buffer_size; + memcpy(buf->dataptr, data, copy_this_much); + + buf->dataptr += copy_this_much; + buf->sizeleft -= copy_this_much; + return copy_this_much; + } + return 0; // done +} + +char *do_query(char *qfunction, int narg, char **arg, int rank, MPI_Comm comm) +{ + char value[512], *retval; + + // run the web query from rank 0 only + + if (rank == 0) { + CURL *handle; + CURLcode res; + + // set up and clear receive buffer + + struct WriteBuf buf; + buf.dataptr = value; + buf.sizeleft = 511; + memset(value,0,512); + + // create curl web query instance + curl_global_init(CURL_GLOBAL_DEFAULT); + handle = curl_easy_init(); + + if (handle) { + std::string url("https://query.openkim.org/api/"); + url += qfunction; + + std::string query(arg[0]); + for (int i=1; i < narg; ++i) { + query += '&'; + query += arg[i]; + } + +#if LMP_DEBUG_CURL + curl_easy_setopt(handle, CURLOPT_VERBOSE, 1L); +#endif + +#if defined(LMP_NO_SSL_CHECK) + // disable verifying SSL certificate and host name + curl_easy_setopt(handle, CURLOPT_SSL_VERIFYPEER, 0L); + curl_easy_setopt(handle, CURLOPT_SSL_VERIFYHOST, 0L); +#endif + + curl_easy_setopt(handle, CURLOPT_URL, url.c_str()); + curl_easy_setopt(handle, CURLOPT_FOLLOWLOCATION, 1L); + curl_easy_setopt(handle, CURLOPT_POSTFIELDS, query.c_str()); + + curl_easy_setopt(handle, CURLOPT_WRITEFUNCTION,write_callback); + curl_easy_setopt(handle, CURLOPT_WRITEDATA,&buf); + + // perform OpenKIM query and check for errors + res = curl_easy_perform(handle); + if (res != CURLE_OK) { + // on error we return an "empty" string but add error message after it + value[0]= '\0'; + strcpy(value+1,curl_easy_strerror(res)); + } + curl_easy_cleanup(handle); + } + curl_global_cleanup(); + } + MPI_Bcast(value, 512, MPI_CHAR, 0, comm); + + // we must make a proper copy of the query, as the stack allocation + // for "value" will go out of scope. a valid query has a '[' as + // the first character. skip over it (and the last character ']', too) + // an error messages starts with a '\0' character. copy that and + // the remaining string, as that is the error message. + + if (value[0] == '[') { + int len = strlen(value)-1; + retval = new char[len]; + value[len] = '\0'; + strcpy(retval,value+1); + } else if (value[0] == '\0') { + int len = strlen(value+1)+2; + retval = new char[len]; + retval[0] = '\0'; + strcpy(retval+1,value+1); + } else { + // unknown response type. we should not get here. + // copy response without modifications. + int len = strlen(value)+1; + retval = new char[len]; + strcpy(retval,value); + } + return retval; +} +#endif diff --git a/src/KIM/kim_query.h b/src/KIM/kim_query.h new file mode 100644 index 0000000000..ed5a7c88f3 --- /dev/null +++ b/src/KIM/kim_query.h @@ -0,0 +1,85 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Axel Kohlmeyer (Temple U), + Ryan S. Elliott (UMN) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-v2-2.0.0 (and newer) package +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(kim_query,KimQuery) + +#else + +#ifndef LMP_KIM_QUERY_H +#define LMP_KIM_QUERY_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class KimQuery : protected Pointers { + public: + KimQuery(class LAMMPS *lmp) : Pointers(lmp) {}; + void command(int, char **); + +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + + +*/ diff --git a/src/KIM/pair_kim.cpp b/src/KIM/pair_kim.cpp index fe638214ba..84842f87cc 100644 --- a/src/KIM/pair_kim.cpp +++ b/src/KIM/pair_kim.cpp @@ -12,14 +12,45 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Ryan S. Elliott, - Valeriu Smirichinski, - Ellad Tadmor + Contributing authors: Ryan S. Elliott (UMinn) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the openkim-api-v1.5.0 package and for use with - the kim-api-v1.6.0 (and newer) package + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-v2-2.0.0 (and newer) package ------------------------------------------------------------------------- */ #include @@ -38,17 +69,6 @@ #include "domain.h" #include "error.h" -// includes from KIM -#include "KIM_API.h" -#include "KIM_API_status.h" - -#ifndef KIM_API_VERSION_MAJOR -// support v1.5.0 -#define KIM_API_VERSION_MAJOR 1 -#define KIM_API_VERSION_MINOR 5 -#define KIM_API_VERSION_PATCH 0 -#endif - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ @@ -57,44 +77,47 @@ PairKIM::PairKIM(LAMMPS *lmp) : Pair(lmp), settings_call_count(0), init_style_call_count(0), - kim_modelname(0), - lmps_map_species_to_unique(0), - lmps_unique_elements(0), + kim_modelname(NULL), + lmps_map_species_to_unique(NULL), + lmps_unique_elements(NULL), lmps_num_unique_elements(0), lmps_units(METAL), - pkim(0), - kim_ind_coordinates(-1), - kim_ind_numberOfParticles(-1), - kim_ind_numberContributingParticles(-1), - kim_ind_numberOfSpecies(-1), - kim_ind_particleSpecies(-1), - kim_ind_get_neigh(-1), - kim_ind_neighObject(-1), - kim_ind_cutoff(-1), - kim_ind_energy(-1), - kim_ind_particleEnergy(-1), - kim_ind_forces(-1), - kim_ind_virial(-1), - kim_ind_particleVirial(-1), - kim_particle_codes(0), + lengthUnit(KIM_LENGTH_UNIT_unused), + energyUnit(KIM_ENERGY_UNIT_unused), + chargeUnit(KIM_CHARGE_UNIT_unused), + temperatureUnit(KIM_TEMPERATURE_UNIT_unused), + timeUnit(KIM_TIME_UNIT_unused), + pkim(NULL), + pargs(NULL), + kim_model_support_for_energy(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_forces(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_particleEnergy(KIM_SUPPORT_STATUS_notSupported), + kim_model_support_for_particleVirial(KIM_SUPPORT_STATUS_notSupported), lmps_local_tot_num_atoms(0), - kim_global_cutoff(0.0), + kim_global_influence_distance(0.0), + kim_number_of_neighbor_lists(0), + kim_cutoff_values(NULL), + modelWillNotRequestNeighborsOfNoncontributingParticles(NULL), + neighborLists(NULL), + kim_particle_codes(NULL), lmps_maxalloc(0), - kim_particleSpecies(0), - lmps_force_tmp(0), - lmps_stripped_neigh_list(0), - kim_iterator_position(0), - Rij(0) + kim_particleSpecies(NULL), + kim_particleContributing(NULL), + lmps_stripped_neigh_list(NULL), + lmps_stripped_neigh_ptr(NULL) { // Initialize Pair data members to appropriate values single_enable = 0; // We do not provide the Single() function restartinfo = 0; // We do not write any restart info one_coeff = 1; // We only allow one coeff * * call + // set to 1, regardless use of fdotr, to avoid ev_set()'s futzing with + // vflag_global + no_virial_fdotr_compute = 1; // BEGIN: initial values that determine the KIM state // (used by kim_free(), etc.) - kim_model_init_ok = false; kim_init_ok = false; + kim_particle_codes_ok = false; // END return; @@ -113,10 +136,23 @@ PairKIM::~PairKIM() delete [] lmps_unique_elements[i]; delete [] lmps_unique_elements; + if (kim_particle_codes_ok) + { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } + // clean up local memory used to support KIM interface memory->destroy(kim_particleSpecies); - memory->destroy(lmps_force_tmp); + memory->destroy(kim_particleContributing); memory->destroy(lmps_stripped_neigh_list); + // clean up lmps_stripped_neigh_ptr + if (lmps_stripped_neigh_ptr) + { + delete [] lmps_stripped_neigh_ptr; + lmps_stripped_neigh_ptr = 0; + } // clean up allocated memory for standard Pair class usage // also, we allocate lmps_map_species_to_uniuqe in the allocate() function @@ -126,8 +162,12 @@ PairKIM::~PairKIM() delete [] lmps_map_species_to_unique; } - // clean up Rij array - memory->destroy(Rij); + // clean up neighborlist pointers + if (neighborLists) + { + delete [] neighborLists; + neighborLists = 0; + } // clean up KIM interface (if necessary) kim_free(); @@ -135,30 +175,49 @@ PairKIM::~PairKIM() return; } +/* ---------------------------------------------------------------------- */ +void PairKIM::set_contributing() +{ + int const nall = atom->nlocal + atom->nghost; + for (int i = 0; i < nall; ++i) + { + kim_particleContributing[i] = ( (i < atom->nlocal) ? 1 : 0 ); + } +} + /* ---------------------------------------------------------------------- */ void PairKIM::compute(int eflag , int vflag) { int kimerror; - if (eflag || vflag) - ev_setup(eflag,vflag); - else - ev_unset(); + ev_init(eflag,vflag); - // grow kim_particleSpecies array if necessary + // grow kim_particleSpecies and kim_particleContributing array if necessary // needs to be atom->nmax in length if (atom->nmax > lmps_maxalloc) { memory->destroy(kim_particleSpecies); - memory->destroy(lmps_force_tmp); + memory->destroy(kim_particleContributing); lmps_maxalloc = atom->nmax; - memory->create(kim_particleSpecies,lmps_maxalloc,"pair:kim_particleSpecies"); - memory->create(lmps_force_tmp,lmps_maxalloc,3,"pair:lmps_force_tmp"); + memory->create(kim_particleSpecies,lmps_maxalloc, + "pair:kim_particleSpecies"); + int kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, + KIM_COMPUTE_ARGUMENT_NAME_particleSpeciesCodes, + kim_particleSpecies); + memory->create(kim_particleContributing,lmps_maxalloc, + "pair:kim_particleContributing"); + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerInteger( + pargs, + KIM_COMPUTE_ARGUMENT_NAME_particleContributing, + kim_particleContributing); + if (kimerror) + error->all( + FLERR, + "Unable to set KIM particle species codes and/or contributing"); } // kim_particleSpecies = KIM atom species for each LAMMPS atom - // set ielement to valid 0 if lmps_map_species_to_unique[] stores an un-used -1 int *species = atom->type; int nall = atom->nlocal + atom->nghost; @@ -166,57 +225,38 @@ void PairKIM::compute(int eflag , int vflag) for (int i = 0; i < nall; i++) { ielement = lmps_map_species_to_unique[species[i]]; - ielement = MAX(ielement,0); - // @@ this (above line) provides bogus info - // @@ (when lmps_map_species_to_unique[species[i]]==-1) to KIM, but - // @@ I guess this only happens when lmps_hybrid==true, - // @@ and we are sure that iterator mode will - // @@ not use these atoms.... (?) kim_particleSpecies[i] = kim_particle_codes[ielement]; } - // pass current atom pointers to KIM - set_volatiles(); + // Set kim contributing flags + set_contributing(); - pkim->setm_compute_by_index(&kimerror,3*3, - kim_ind_particleEnergy, eflag_atom, - (int) kim_model_has_particleEnergy, - kim_ind_particleVirial, vflag_atom, - (int) kim_model_has_particleVirial, - kim_ind_virial, vflag_global!=0, - no_virial_fdotr_compute); - kim_error(__LINE__,"setm_compute_by_index",kimerror); + // pass current atom pointers to KIM + set_argument_pointers(); + + // set number of particles + lmps_local_tot_num_atoms = (int) nall; // compute via KIM model - kimerror = pkim->model_compute(); - kim_error(__LINE__,"PairKIM::pkim->model_compute() error",kimerror); - // assemble force and particleVirial if needed - if (!lmps_using_newton) comm->reverse_comm_pair(this); + kimerror = KIM_Model_Compute(pkim, pargs); + if (kimerror) error->all(FLERR,"KIM Compute returned error"); - // sum lmps_force_tmp to f if running in hybrid mode - if (lmps_hybrid) { - double **f = atom->f; - for (int i = 0; i < nall; i++) { - f[i][0] += lmps_force_tmp[i][0]; - f[i][1] += lmps_force_tmp[i][1]; - f[i][2] += lmps_force_tmp[i][2]; - } + // compute virial before reverse comm! + if (vflag_global) + { + virial_fdotr_compute(); } - if ((no_virial_fdotr_compute == 1) && (vflag_global)) - { // flip sign and order of virial if KIM is computing it - for (int i = 0; i < 3; ++i) virial[i] = -1.0*virial[i]; - double tmp = virial[3]; - virial[3] = -virial[5]; - virial[4] = -virial[4]; - virial[5] = -tmp; - } - else - { // compute virial via LAMMPS fdotr mechanism - if (vflag_fdotr) virial_fdotr_compute(); + // if newton is off, perform reverse comm + if (!lmps_using_newton) + { + comm->reverse_comm_pair(this); } - if ((kim_model_has_particleVirial) && (vflag_atom)) + if ((vflag_atom) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported) + ) { // flip sign and order of virial if KIM is computing it double tmp; for (int i = 0; i < nall; ++i) @@ -267,10 +307,20 @@ void PairKIM::settings(int narg, char **arg) ++settings_call_count; init_style_call_count = 0; - if (narg < 2) error->all(FLERR,"Illegal pair_style command"); - // arg[0] is the virial handling option: "LAMMPSvirial" or "KIMvirial" - // arg[1] is the KIM Model name - // arg[2] is the print-kim-file flag: 0/1 do-not/do print (default 0) + if (narg != 1) + { + if ((narg > 0) && ((0 == strcmp("KIMvirial", arg[0])) || + (0 == strcmp("LAMMPSvirial", arg[0])))) + { + error->all(FLERR,"'KIMvirial' or 'LAMMPSvirial' not supported with " + "kim-api-v2."); + } + else + error->all(FLERR,"Illegal pair_style command"); + } + // arg[0] is the KIM Model name + + lmps_using_molecular = (atom->molecular > 0); // ensure we are in a clean state for KIM (needed on repeated call) // first time called will do nothing... @@ -288,39 +338,18 @@ void PairKIM::settings(int narg, char **arg) // set lmps_* bool flags set_lmps_flags(); - // set virial handling - if (strcmp(arg[0],"LAMMPSvirial") == 0) - { - no_virial_fdotr_compute = 0; - } - else if (strcmp(arg[0],"KIMvirial") == 0) - { - no_virial_fdotr_compute = 1; - } - else - { - error->all(FLERR,"Unrecognized virial argument in pair_style command"); - } - // set KIM Model name - int nmlen = strlen(arg[1]); + int nmlen = strlen(arg[0]); if (kim_modelname != 0) { delete [] kim_modelname; kim_modelname = 0; } kim_modelname = new char[nmlen+1]; - strcpy(kim_modelname, arg[1]); + strcpy(kim_modelname, arg[0]); - // set print_kim_file - if ((2 == narg) || ('0' == *(arg[2]))) - { - print_kim_file = false; - } - else - { - print_kim_file = true; - } + // initialize KIM Model + kim_init(); return; } @@ -341,13 +370,19 @@ void PairKIM::coeff(int narg, char **arg) if (narg != 2 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); + // insure I,J args are * * + + if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + int ilo,ihi,jlo,jhi; force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); // read args that map atom species to KIM elements // lmps_map_species_to_unique[i] = - // which element the Ith atom type is, -1 if NULL + // which element the Ith atom type is // lmps_num_unique_elements = # of unique elements // lmps_unique_elements = list of element names @@ -360,23 +395,20 @@ void PairKIM::coeff(int narg, char **arg) lmps_unique_elements = new char*[atom->ntypes]; for (i = 0; i < atom->ntypes; i++) lmps_unique_elements[i] = 0; + + // Assume all species arguments are valid + // errors will be detected by below lmps_num_unique_elements = 0; for (i = 2; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - if (!lmps_hybrid) - error->all(FLERR,"Invalid args for non-hybrid pair coefficients"); - lmps_map_species_to_unique[i-1] = -1; - continue; - } - for (j = 0; j < lmps_num_unique_elements; j++) - if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; - lmps_map_species_to_unique[i-1] = j; - if (j == lmps_num_unique_elements) { - n = strlen(arg[i]) + 1; - lmps_unique_elements[j] = new char[n]; - strcpy(lmps_unique_elements[j],arg[i]); - lmps_num_unique_elements++; - } + for (j = 0; j < lmps_num_unique_elements; j++) + if (strcmp(arg[i],lmps_unique_elements[j]) == 0) break; + lmps_map_species_to_unique[i-1] = j; + if (j == lmps_num_unique_elements) { + n = strlen(arg[i]) + 1; + lmps_unique_elements[j] = new char[n]; + strcpy(lmps_unique_elements[j],arg[i]); + lmps_num_unique_elements++; + } } int count = 0; @@ -392,6 +424,35 @@ void PairKIM::coeff(int narg, char **arg) if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); + // setup mapping between LAMMPS unique elements and KIM species codes + if (kim_particle_codes_ok) + { + delete [] kim_particle_codes; + kim_particle_codes = NULL; + kim_particle_codes_ok = false; + } + kim_particle_codes = new int[lmps_num_unique_elements]; + kim_particle_codes_ok = true; + for(int i = 0; i < lmps_num_unique_elements; i++){ + int kimerror; + int supported; + int code; + kimerror = KIM_Model_GetSpeciesSupportAndCode( + pkim, + KIM_SpeciesName_FromString(lmps_unique_elements[i]), + &supported, + &code); + if (supported) + kim_particle_codes[i] = code; + else + { + std::stringstream msg; + msg << "create_kim_particle_codes: symbol not found: " + << lmps_unique_elements[i]; + error->all(FLERR, msg.str().c_str()); + } + } + return; } @@ -408,58 +469,64 @@ void PairKIM::init_style() error->all(FLERR,"PairKIM only works with 3D problems"); int kimerror; - // KIM and Model initialization (only once) - // also sets kim_ind_* and kim_* bool flags - if (!kim_init_ok) - { - kim_init(); - kimerror = pkim->model_init(); - if (kimerror != KIM_STATUS_OK) - kim_error(__LINE__, "KIM API:model_init() failed", kimerror); - else - { - kim_model_init_ok = true; - // allocate enough memory to ensure we are safe - // (by using neighbor->oneatom) - if (kim_model_using_Rij) - memory->create(Rij,3*(neighbor->oneatom),"pair:Rij"); + // setup lmps_stripped_neigh_list for neighbors of one atom, if needed + if (lmps_using_molecular) { + memory->destroy(lmps_stripped_neigh_list); + memory->create(lmps_stripped_neigh_list, + kim_number_of_neighbor_lists*neighbor->oneatom, + "pair:lmps_stripped_neigh_list"); + delete [] lmps_stripped_neigh_ptr; + lmps_stripped_neigh_ptr = new int*[kim_number_of_neighbor_lists]; + for (int i = 0; i < kim_number_of_neighbor_lists; ++i) + { + lmps_stripped_neigh_ptr[i] + = &(lmps_stripped_neigh_list[(i-1)*(neighbor->oneatom)]); } + } - // request none, half, or full neighbor list - // depending on KIM model requirement + // make sure comm_reverse expects (at most) 9 values when newton is off + if (!lmps_using_newton) comm_reverse_off = 9; - int irequest = neighbor->request(this,instance_me); - if (kim_model_using_cluster) + // request full neighbor + for (int i = 0; i < kim_number_of_neighbor_lists; ++i) { - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 0; - } - else - { - // make sure comm_reverse expects (at most) 9 values when newton is off - if (!lmps_using_newton) comm_reverse_off = 9; + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->id = i; + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; - if (kim_model_using_half) - { - neighbor->requests[irequest]->half = 1; - neighbor->requests[irequest]->full = 0; - // make sure half lists also include local-ghost pairs - if (lmps_using_newton) neighbor->requests[irequest]->newton = 2; - } - else - { - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; - // make sure full lists also include local-ghost pairs - if (lmps_using_newton) neighbor->requests[irequest]->newton = 0; - } + if (modelWillNotRequestNeighborsOfNoncontributingParticles[i]) + { + neighbor->requests[irequest]->ghost = 0; + } + else + { + neighbor->requests[irequest]->ghost = 1; + + } + // always want all owned/ghost pairs + neighbor->requests[irequest]->newton = 2; + // set cutoff + neighbor->requests[irequest]->cut = 1; + neighbor->requests[irequest]->cutoff + = kim_cutoff_values[i] + neighbor->skin; } return; } +/* ---------------------------------------------------------------------- + neighbor callback to inform pair style of neighbor list to use + half or full +------------------------------------------------------------------------- */ + +void PairKIM::init_list(int id, NeighList *ptr) +{ + neighborLists[id] = ptr; +} + /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ @@ -471,22 +538,7 @@ double PairKIM::init_one(int i, int j) if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - return kim_global_cutoff; -} - -/* ---------------------------------------------------------------------- */ - -void PairKIM::reinit() -{ - // This is called by fix-adapt - - // Call parent class implementation - Pair::reinit(); - - // Then reinit KIM model - int kimerror; - kimerror = pkim->model_reinit(); - kim_error(__LINE__,"model_reinit unsuccessful", kimerror); + return kim_global_influence_distance; } /* ---------------------------------------------------------------------- */ @@ -495,13 +547,16 @@ int PairKIM::pack_reverse_comm(int n, int first, double *buf) { int i,m,last; double *fp; - if (lmps_hybrid) fp = &(lmps_force_tmp[0][0]); - else fp = &(atom->f[0][0]); + fp = &(atom->f[0][0]); m = 0; last = first + n; - if ((kim_model_has_forces) && ((vflag_atom == 0) || - (!kim_model_has_particleVirial))) + if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + ((vflag_atom == 0) || + KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported))) { for (i = first; i < last; i++) { @@ -511,8 +566,11 @@ int PairKIM::pack_reverse_comm(int n, int first, double *buf) } return m; } - else if ((kim_model_has_forces) && (vflag_atom == 1) && - (kim_model_has_particleVirial)) + else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { double *va=&(vatom[0][0]); for (i = first; i < last; i++) @@ -530,8 +588,12 @@ int PairKIM::pack_reverse_comm(int n, int first, double *buf) } return m; } - else if ((!kim_model_has_forces) && (vflag_atom == 1) && - (kim_model_has_particleVirial)) + else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { double *va=&(vatom[0][0]); for (i = first; i < last; i++) @@ -555,12 +617,15 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) { int i,j,m; double *fp; - if (lmps_hybrid) fp = &(lmps_force_tmp[0][0]); - else fp = &(atom->f[0][0]); + fp = &(atom->f[0][0]); m = 0; - if ((kim_model_has_forces) && ((vflag_atom == 0) || - (!kim_model_has_particleVirial))) + if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + ((vflag_atom == 0) || + KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported))) { for (i = 0; i < n; i++) { @@ -570,8 +635,12 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) fp[3*j+2]+= buf[m++]; } } - else if ((kim_model_has_forces) && (vflag_atom == 1) && - (kim_model_has_particleVirial)) + else if (KIM_SupportStatus_NotEqual(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { double *va=&(vatom[0][0]); for (i = 0; i < n; i++) @@ -589,8 +658,12 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) va[j*6+5]+=buf[m++]; } } - else if ((!kim_model_has_forces) && (vflag_atom == 1) && - (kim_model_has_particleVirial)) + else if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported) + && + (vflag_atom == 1) && + KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) { double *va=&(vatom[0][0]); for (i = 0; i < n; i++) @@ -616,7 +689,7 @@ void PairKIM::unpack_reverse_comm(int n, int *list, double *buf) double PairKIM::memory_usage() { - double bytes = lmps_maxalloc * sizeof(int); + double bytes = 2 * lmps_maxalloc * sizeof(int); return bytes; } @@ -624,45 +697,30 @@ double PairKIM::memory_usage() KIM-specific interface ------------------------------------------------------------------------- */ -void PairKIM::kim_error(int ln, const char* msg, int errcode) +int PairKIM::get_neigh(void const * const dataObject, + int const numberOfNeighborLists, + double const * const cutoffs, + int const neighborListIndex, int const particleNumber, + int * const numberOfNeighbors, + int const ** const neighborsOfParticle) { - if (errcode == KIM_STATUS_OK) return; - KIM_API_model::report_error(ln,(char *) __FILE__, (char *) msg,errcode); - error->all(__FILE__,ln,"Internal KIM error"); + PairKIM const * const Model + = reinterpret_cast(dataObject); - return; -} - -/* ---------------------------------------------------------------------- */ - -int PairKIM::get_neigh(void **kimmdl,int *mode,int *request, - int *atom, int *numnei, int **nei1atom, double **pRij) -{ - KIM_API_model *pkim = (KIM_API_model *) *kimmdl; - - int kimerror; - PairKIM *self = (PairKIM *) pkim->get_sim_buffer(&kimerror); - - if (self->kim_model_using_Rij) { - *pRij = &(self->Rij[0]); - } else { - *pRij = 0; + if (numberOfNeighborLists != Model->kim_number_of_neighbor_lists) + return true; + for (int i = 0; i < numberOfNeighborLists; ++i) + { + if (Model->kim_cutoff_values[i] < cutoffs[i]) return true; } + // neighborListIndex and particleNumber are validated by KIM API - // subvert KIM api by using direct access to self->list - // - // get neighObj from KIM API obj - // NeighList * neiobj = (NeighList * ) - // (*pkim).get_data_by_index(self->kim_ind_neighObject, &kimerror); - NeighList * neiobj = self->list; + // initialize numNeigh + *numberOfNeighbors = 0; - // subvert KIM api by using direct acces to self->lmps_local_tot_num_atoms - // - //int * pnAtoms = (int *) - // (*pkim).get_data_by_index(self->kim_ind_numberOfParticles, &kimerror); - //int nAtoms = *pnAtoms; - int nAtoms = self->lmps_local_tot_num_atoms; + NeighList * neiobj = Model->neighborLists[neighborListIndex]; + int nAtoms = Model->lmps_local_tot_num_atoms; int j, jj, inum, *ilist, *numneigh, **firstneigh; inum = neiobj->inum; //# of I atoms neighbors are stored for @@ -670,97 +728,22 @@ int PairKIM::get_neigh(void **kimmdl,int *mode,int *request, numneigh = neiobj->numneigh; // # of J neighbors for each I atom firstneigh = neiobj->firstneigh; // ptr to 1st J int value of each I atom - if (*mode==0){ //iterator mode - if (*request==1) { //increment iterator - if (self->kim_iterator_position < inum) { - *atom = ilist[self->kim_iterator_position]; - *numnei = numneigh[*atom]; + *numberOfNeighbors = numneigh[particleNumber]; - // strip off neighbor mask for molecular systems - if (!self->lmps_using_molecular) - *nei1atom = firstneigh[*atom]; - else - { - int n = *numnei; - int *ptr = firstneigh[*atom]; - int *lmps_stripped_neigh_list = self->lmps_stripped_neigh_list; - for (int i = 0; i < n; i++) - lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; - *nei1atom = lmps_stripped_neigh_list; - } - - // set Rij if needed - if (self->kim_model_using_Rij) { - double* x = (double *) - (*pkim).get_data_by_index(self->kim_ind_coordinates, - &kimerror); - for (jj=0; jj < *numnei; jj++) { - int i = *atom; - j = (*nei1atom)[jj]; - self->Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0]; - self->Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1]; - self->Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2]; - } - } - - // increment iterator - self->kim_iterator_position++; - - return KIM_STATUS_OK; //successful increment - } else if (self->kim_iterator_position == inum) { - *numnei = 0; - return KIM_STATUS_NEIGH_ITER_PAST_END; //reached end by iterator - } else if (self->kim_iterator_position > inum || inum < 0){ - self->error->one(FLERR, "KIM neighbor iterator exceeded range"); - } - } else if (*request == 0){ //restart iterator - self->kim_iterator_position = 0; - *numnei = 0; - return KIM_STATUS_NEIGH_ITER_INIT_OK; //succsesful restart - } - } else if (*mode == 1){//locator mode - //... - if (*request < inum) { - *atom = *request; - *numnei = numneigh[*atom]; - - // strip off neighbor mask for molecular systems - if (!self->lmps_using_molecular) - *nei1atom = firstneigh[*atom]; - else - { - int n = *numnei; - int *ptr = firstneigh[*atom]; - int *lmps_stripped_neigh_list = self->lmps_stripped_neigh_list; - for (int i = 0; i < n; i++) - lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; - *nei1atom = lmps_stripped_neigh_list; - } - - // set Rij if needed - if (self->kim_model_using_Rij){ - double* x = (double *) - (*pkim).get_data_by_index(self->kim_ind_coordinates, &kimerror); - for(int jj=0; jj < *numnei; jj++){ - int i = *atom; - int j = (*nei1atom)[jj]; - self->Rij[jj*3 +0] = -x[i*3+0] + x[j*3+0]; - self->Rij[jj*3 +1] = -x[i*3+1] + x[j*3+1]; - self->Rij[jj*3 +2] = -x[i*3+2] + x[j*3+2]; - } - } - return KIM_STATUS_OK; //successful end - } - else if (*request >= nAtoms || inum < 0) - return KIM_STATUS_NEIGH_INVALID_REQUEST; - else if (*request >= inum) { - *atom = *request; - *numnei = 0; - return KIM_STATUS_OK; //successfull but no neighbors in the list - } - } else return KIM_STATUS_NEIGH_INVALID_MODE; //invalid mode - - return -16; //should not get here: unspecified error + // strip off neighbor mask for molecular systems + if (!Model->lmps_using_molecular) + *neighborsOfParticle = firstneigh[particleNumber]; + else + { + int n = *numberOfNeighbors; + int *ptr = firstneigh[particleNumber]; + int *lmps_stripped_neigh_list + = Model->lmps_stripped_neigh_ptr[neighborListIndex]; + for (int i = 0; i < n; i++) + lmps_stripped_neigh_list[i] = *(ptr++) & NEIGHMASK; + *neighborsOfParticle = lmps_stripped_neigh_list; + } + return false; } /* ---------------------------------------------------------------------- */ @@ -769,27 +752,15 @@ void PairKIM::kim_free() { int kimerror; - if (kim_model_init_ok) - { - kimerror = pkim->model_destroy(); - kim_model_init_ok = false; - } if (kim_init_ok) { - pkim->free(&kimerror); - kim_init_ok = false; - } - if (pkim != 0) - { - delete pkim; - pkim = 0; - } - if (kim_particle_codes_ok) - { - delete [] kim_particle_codes; - kim_particle_codes = 0; - kim_particle_codes_ok = false; + int kimerror = KIM_Model_ComputeArgumentsDestroy(pkim, &pargs); + if (kimerror) + error->all(FLERR,"Unable to destroy Compute Arguments Object"); + + KIM_Model_Destroy(&pkim); } + kim_init_ok = false; return; } @@ -800,182 +771,165 @@ void PairKIM::kim_init() { int kimerror; - // + // initialize KIM model + int requestedUnitsAccepted; + kimerror = KIM_Model_Create( + KIM_NUMBERING_zeroBased, + lengthUnit, energyUnit, chargeUnit, temperatureUnit, timeUnit, + kim_modelname, + &requestedUnitsAccepted, + &pkim); + if (kimerror) + error->all(FLERR,"KIM ModelCreate failed"); + else { + if (!requestedUnitsAccepted) { + error->all(FLERR,"KIM Model did not accept the requested unit system"); + } + + // check that the model does not require unknown capabilities + kimerror = check_for_routine_compatibility(); + if (kimerror) + { + error->all(FLERR, + "KIM Model requires unknown Routines. Unable to proceed."); + } + + kimerror = KIM_Model_ComputeArgumentsCreate(pkim, &pargs); + if (kimerror) + { + KIM_Model_Destroy(&pkim); + error->all(FLERR,"KIM ComputeArgumentsCreate failed"); + } + else + { + kim_init_ok = true; + } + } // determine KIM Model capabilities (used in this function below) set_kim_model_has_flags(); - // create appropriate KIM descriptor file - char* test_descriptor_string = 0; - // allocate memory for test_descriptor_string and write descriptor file - write_descriptor(&test_descriptor_string); - // print descriptor - if (print_kim_file) + KIM_Model_GetInfluenceDistance(pkim, &kim_global_influence_distance); + KIM_Model_GetNeighborListPointers( + pkim, + &kim_number_of_neighbor_lists, + &kim_cutoff_values, + &modelWillNotRequestNeighborsOfNoncontributingParticles); + if (neighborLists) { - error->message(FLERR, test_descriptor_string); + delete [] neighborLists; + neighborLists = 0; } + neighborLists = new NeighList*[kim_number_of_neighbor_lists]; - // initialize KIM model - pkim = new KIM_API_model(); - kimerror = pkim->string_init(test_descriptor_string, kim_modelname); - if (kimerror != KIM_STATUS_OK) - kim_error(__LINE__,"KIM initialization failed", kimerror); - else - { - kim_init_ok = true; - delete [] test_descriptor_string; - test_descriptor_string = 0; - } + kimerror = KIM_ComputeArguments_SetArgumentPointerInteger(pargs, + KIM_COMPUTE_ARGUMENT_NAME_numberOfParticles, + &lmps_local_tot_num_atoms); + if (KIM_SupportStatus_NotEqual(kim_model_support_for_energy, + KIM_SUPPORT_STATUS_notSupported)) + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble(pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialEnergy, + &(eng_vdwl)); - // determine kim_model_using_* true/false values - // - // check for half or full list - kim_model_using_half = (pkim->is_half_neighbors(&kimerror)); - // - const char* NBC_method; - kimerror = pkim->get_NBC_method(&NBC_method); - kim_error(__LINE__,"NBC method not set",kimerror); - // check for CLUSTER mode - kim_model_using_cluster = (strcmp(NBC_method,"CLUSTER")==0); - // check if Rij needed for get_neigh - kim_model_using_Rij = ((strcmp(NBC_method,"NEIGH_RVEC_H")==0) || - (strcmp(NBC_method,"NEIGH_RVEC_F")==0)); + kimerror = KIM_ComputeArguments_SetCallbackPointer(pargs, + KIM_COMPUTE_CALLBACK_NAME_GetNeighborList, + KIM_LANGUAGE_NAME_cpp, + reinterpret_cast(get_neigh), + reinterpret_cast(this)); - // get correct index of each variable in kim_api object - pkim->getm_index(&kimerror, 3*13, - "coordinates", &kim_ind_coordinates, 1, - "cutoff", &kim_ind_cutoff, 1, - "numberOfParticles", &kim_ind_numberOfParticles, 1, -#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5 - "numberParticleTypes", &kim_ind_numberOfSpecies, 1, - "particleTypes", &kim_ind_particleSpecies, 1, -#else - "numberOfSpecies", &kim_ind_numberOfSpecies, 1, - "particleSpecies", &kim_ind_particleSpecies, 1, -#endif - "numberContributingParticles", &kim_ind_numberContributingParticles, - kim_model_using_half, - "particleEnergy", &kim_ind_particleEnergy, - (int) kim_model_has_particleEnergy, - "energy", &kim_ind_energy, (int) kim_model_has_energy, - "forces", &kim_ind_forces, (int) kim_model_has_forces, - "neighObject", &kim_ind_neighObject, (int) !kim_model_using_cluster, - "get_neigh", &kim_ind_get_neigh, (int) !kim_model_using_cluster, - "particleVirial", &kim_ind_particleVirial, - (int) kim_model_has_particleVirial, - "virial", &kim_ind_virial, no_virial_fdotr_compute); - kim_error(__LINE__,"getm_index",kimerror); - - // setup mapping between LAMMPS unique elements and KIM species codes - kim_particle_codes = new int[lmps_num_unique_elements]; - kim_particle_codes_ok = true; - for(int i = 0; i < lmps_num_unique_elements; i++){ - int kimerror; - kim_particle_codes[i] - = pkim->get_species_code(lmps_unique_elements[i], &kimerror); - kim_error(__LINE__, "create_kim_particle_codes: symbol not found ", - kimerror); - } - - // set pointer values in KIM API object that will not change during run - set_statics(); + if (kimerror) + error->all(FLERR,"Unable to register KIM pointers"); return; } /* ---------------------------------------------------------------------- */ -void PairKIM::set_statics() +void PairKIM::set_argument_pointers() { - // set total number of atoms - lmps_local_tot_num_atoms = (int) (atom->nghost + atom->nlocal); + int kimerror; + kimerror = KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, KIM_COMPUTE_ARGUMENT_NAME_coordinates, &(atom->x[0][0])); - int kimerror; - pkim->setm_data_by_index(&kimerror, 4*6, - kim_ind_numberOfSpecies, 1, (void *) &(atom->ntypes), 1, - kim_ind_cutoff, 1, (void *) &(kim_global_cutoff), 1, - kim_ind_numberOfParticles, 1, (void *) &lmps_local_tot_num_atoms, 1, - kim_ind_numberContributingParticles, 1, (void *) &(atom->nlocal), - (int) kim_model_using_half, - kim_ind_energy, 1, (void *) &(eng_vdwl), (int) kim_model_has_energy, - kim_ind_virial, 1, (void *) &(virial[0]), no_virial_fdotr_compute); - kim_error(__LINE__, "setm_data_by_index", kimerror); - if (!kim_model_using_cluster) - { - kimerror = pkim->set_method_by_index(kim_ind_get_neigh, 1, - (func_ptr) &get_neigh); - kim_error(__LINE__, "set_method_by_index", kimerror); - } + // Set KIM pointer appropriately for particalEnergy + if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, + KIM_SUPPORT_STATUS_required) + && (eflag_atom != 1)) + { + // reallocate per-atom energy array if necessary + if (atom->nmax > maxeatom) + { + maxeatom = atom->nmax; + memory->destroy(eatom); + memory->create(eatom,comm->nthreads*maxeatom,"pair:eatom"); + } + } + if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, + KIM_SUPPORT_STATUS_optional) + && (eflag_atom != 1)) + { + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, + reinterpret_cast(NULL)); + } + else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleEnergy, + KIM_SUPPORT_STATUS_notSupported)) + { + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, eatom); + } - pkim->set_sim_buffer((void *)this, &kimerror); - kim_error(__LINE__, "set_sim_buffer", kimerror); + // Set KIM pointer appropriately for forces + if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported)) + { + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialForces, + reinterpret_cast(NULL)); + } + else + { + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, KIM_COMPUTE_ARGUMENT_NAME_partialForces, &(atom->f[0][0])); + } - return; -} + // Set KIM pointer appropriately for particleVirial + if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_required) + && (vflag_atom != 1)) + { + // reallocate per-atom virial array if necessary + if (atom->nmax > maxeatom) + { + maxvatom = atom->nmax; + memory->destroy(vatom); + memory->create(vatom,comm->nthreads*maxvatom,6,"pair:vatom"); + } + } + if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_optional) + && (vflag_atom != 1)) + { + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial, + reinterpret_cast(NULL)); + } + else if (KIM_SupportStatus_NotEqual(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) + { + kimerror = kimerror || KIM_ComputeArguments_SetArgumentPointerDouble( + pargs, KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy, &(vatom[0][0])); + } -/* ---------------------------------------------------------------------- */ + if (kimerror) + { + error->all(FLERR,"Unable to set KIM argument pointers"); + } -void PairKIM::set_volatiles() -{ - int kimerror; - lmps_local_tot_num_atoms = (int) (atom->nghost + atom->nlocal); - intptr_t nall = (intptr_t) lmps_local_tot_num_atoms; - - pkim->setm_data_by_index(&kimerror, 4*2, - kim_ind_coordinates, 3*nall, (void*) &(atom->x[0][0]), 1, - kim_ind_particleSpecies, nall, (void*) kim_particleSpecies, 1); - kim_error(__LINE__, "setm_data_by_index", kimerror); - - if (kim_model_has_particleEnergy && (eflag_atom == 1)) - { - kimerror = pkim->set_data_by_index(kim_ind_particleEnergy, nall, - (void*) eatom); - kim_error(__LINE__, "set_data_by_index", kimerror); - } - - if (kim_model_has_particleVirial && (vflag_atom == 1)) - { - kimerror = pkim->set_data_by_index(kim_ind_particleVirial, 6*nall, - (void*) &(vatom[0][0])); - kim_error(__LINE__, "set_data_by_index", kimerror); - } - - if (kim_model_has_forces) - { - if (lmps_hybrid) - kimerror = pkim->set_data_by_index(kim_ind_forces, nall*3, - (void*) &(lmps_force_tmp[0][0])); - else - kimerror = pkim->set_data_by_index(kim_ind_forces, nall*3, - (void*) &(atom->f[0][0])); - kim_error(__LINE__, "setm_data_by_index", kimerror); - } - - // subvert the KIM api by direct access to this->list in get_neigh - // - //if (!kim_model_using_cluster) - // kimerror = pkim->set_data_by_index(kim_ind_neighObject, 1, - // (void*) this->list); - - if (kim_model_has_particleVirial) - { - if(vflag_atom != 1) { - pkim->set_compute_by_index(kim_ind_particleVirial, KIM_COMPUTE_FALSE, - &kimerror); - } else { - pkim->set_compute_by_index(kim_ind_particleVirial, KIM_COMPUTE_TRUE, - &kimerror); - } - } - - if (no_virial_fdotr_compute == 1) - { - pkim->set_compute_by_index(kim_ind_virial, - ((vflag_global != 1) ? KIM_COMPUTE_FALSE : KIM_COMPUTE_TRUE), - &kimerror); - } - - return; + return; } /* ---------------------------------------------------------------------- */ @@ -985,432 +939,183 @@ void PairKIM::set_lmps_flags() // determint if newton is on or off lmps_using_newton = (force->newton_pair == 1); - // setup lmps_stripped_neigh_list for neighbors of one atom, if needed - lmps_using_molecular = (atom->molecular > 0); - if (lmps_using_molecular) { - memory->destroy(lmps_stripped_neigh_list); - memory->create(lmps_stripped_neigh_list,neighbor->oneatom, - "pair:lmps_stripped_neigh_list"); + // determine if running with pair hybrid + if (force->pair_match("hybrid",0)) + { + error->all(FLERR,"pair_kim does not support hybrid"); } - // determine if running with pair hybrid - lmps_hybrid = (force->pair_match("hybrid",0)); - - // support cluster mode if everything is just right - lmps_support_cluster = ((domain->xperiodic == 0 && - domain->yperiodic == 0 && - domain->zperiodic == 0 - ) - && - (comm->nprocs == 1) - ); - // determine unit system and set lmps_units flag - if ((strcmp(update->unit_style,"real")==0)) - lmps_units = REAL; - else if ((strcmp(update->unit_style,"metal")==0)) - lmps_units = METAL; - else if ((strcmp(update->unit_style,"si")==0)) - lmps_units = SI; - else if ((strcmp(update->unit_style,"cgs")==0)) - lmps_units = CGS; - else if ((strcmp(update->unit_style,"electron")==0)) - lmps_units = ELECTRON; - else if ((strcmp(update->unit_style,"lj")==0)) - error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); - else - error->all(FLERR,"Unknown unit_style"); + if ((strcmp(update->unit_style,"real")==0)) { + lmps_units = REAL; + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_kcal_mol; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(update->unit_style,"metal")==0)) { + lmps_units = METAL; + lengthUnit = KIM_LENGTH_UNIT_A; + energyUnit = KIM_ENERGY_UNIT_eV; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_ps; + } else if ((strcmp(update->unit_style,"si")==0)) { + lmps_units = SI; + lengthUnit = KIM_LENGTH_UNIT_m; + energyUnit = KIM_ENERGY_UNIT_J; + chargeUnit = KIM_CHARGE_UNIT_C; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(update->unit_style,"cgs")==0)) { + lmps_units = CGS; + lengthUnit = KIM_LENGTH_UNIT_cm; + energyUnit = KIM_ENERGY_UNIT_erg; + chargeUnit = KIM_CHARGE_UNIT_statC; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_s; + } else if ((strcmp(update->unit_style,"electron")==0)) { + lmps_units = ELECTRON; + lengthUnit = KIM_LENGTH_UNIT_Bohr; + energyUnit = KIM_ENERGY_UNIT_Hartree; + chargeUnit = KIM_CHARGE_UNIT_e; + temperatureUnit = KIM_TEMPERATURE_UNIT_K; + timeUnit = KIM_TIME_UNIT_fs; + } else if ((strcmp(update->unit_style,"lj")==0)) { + error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models"); + } else { + error->all(FLERR,"Unknown unit_style"); + } return; } /* ---------------------------------------------------------------------- */ +int PairKIM::check_for_routine_compatibility() +{ + /* Check that we know about all required routines */ + int numberOfModelRoutineNames; + KIM_MODEL_ROUTINE_NAME_GetNumberOfModelRoutineNames( + &numberOfModelRoutineNames); + for (int i = 0; i < numberOfModelRoutineNames; ++i) + { + KIM_ModelRoutineName modelRoutineName; + KIM_MODEL_ROUTINE_NAME_GetModelRoutineName(i, &modelRoutineName); + + int present; + int required; + int error = KIM_Model_IsRoutinePresent( + pkim, modelRoutineName, &present, &required); + if (error) { return true; } + + if ((present == true) && (required == true)) + { + if (!(KIM_ModelRoutineName_Equal(modelRoutineName, + KIM_MODEL_ROUTINE_NAME_Create) + || KIM_ModelRoutineName_Equal( + modelRoutineName, + KIM_MODEL_ROUTINE_NAME_ComputeArgumentsCreate) + || KIM_ModelRoutineName_Equal(modelRoutineName, + KIM_MODEL_ROUTINE_NAME_Compute) + || KIM_ModelRoutineName_Equal(modelRoutineName, + KIM_MODEL_ROUTINE_NAME_Refresh) + || KIM_ModelRoutineName_Equal( + modelRoutineName, + KIM_MODEL_ROUTINE_NAME_ComputeArgumentsDestroy) + || KIM_ModelRoutineName_Equal(modelRoutineName, + KIM_MODEL_ROUTINE_NAME_Destroy))) + { return true; } + } + } + + /* everything is good */ + return false; +} + +/* ---------------------------------------------------------------------- */ + void PairKIM::set_kim_model_has_flags() { - KIM_API_model mdl; - - int kimerror; - - // get KIM API object representing the KIM Model only - kimerror = mdl.model_info(kim_modelname); - kim_error(__LINE__,"KIM initialization failed", kimerror); - - // determine if the KIM Model can compute the total energy - mdl.get_index((char*) "energy", &kimerror); - kim_model_has_energy = (kimerror == KIM_STATUS_OK); - if (!kim_model_has_energy) - error->warning(FLERR,"KIM Model does not provide `energy'; " - "Potential energy will be zero"); - - // determine if the KIM Model can compute the forces - mdl.get_index((char*) "forces", &kimerror); - kim_model_has_forces = (kimerror == KIM_STATUS_OK); - if (!kim_model_has_forces) - error->warning(FLERR,"KIM Model does not provide `forces'; " - "Forces will be zero"); - - // determine if the KIM Model can compute the particleEnergy - mdl.get_index((char*) "particleEnergy", &kimerror); - kim_model_has_particleEnergy = (kimerror == KIM_STATUS_OK); - if (!kim_model_has_particleEnergy) - error->warning(FLERR,"KIM Model does not provide `particleEnergy'; " - "energy per atom will be zero"); - - // determine if the KIM Model can compute the particleVerial - mdl.get_index((char*) "particleVirial", &kimerror); - kim_model_has_particleVirial = (kimerror == KIM_STATUS_OK); - mdl.get_index((char*) "process_dEdr", &kimerror); - kim_model_has_particleVirial = kim_model_has_particleVirial || - (kimerror == KIM_STATUS_OK); - if (!kim_model_has_particleVirial) - error->warning(FLERR,"KIM Model does not provide `particleVirial'; " - "virial per atom will be zero"); - - // tear down KIM API object - mdl.free(&kimerror); - // now destructor will do the remaining tear down for mdl - - return; -} - -/* ---------------------------------------------------------------------- */ - -void PairKIM::write_descriptor(char** test_descriptor_string) -{ - // allocate memory - if (*test_descriptor_string != 0) - error->all(FLERR, "Test_descriptor_string already allocated"); - // assuming 75 lines at 100 characters each (should be plenty) - *test_descriptor_string = new char[100*75]; - // initialize - strcpy(*test_descriptor_string, ""); - - // Write Test name and units - strcat(*test_descriptor_string, - "#\n" - "# BEGINNING OF KIM DESCRIPTOR FILE\n" - "#\n" - "# This file is automatically generated from LAMMPS pair_style " - "kim command\n"); - strcat(*test_descriptor_string, - "\n" - "# The call number is (pair_style).(init_style): "); - char tmp_num[100]; - sprintf(tmp_num, "%i.%i\n", settings_call_count, init_style_call_count); - strcat(*test_descriptor_string, tmp_num); - strcat(*test_descriptor_string, - "#\n" - "\n" -#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSION_MINOR == 5 -#else - "KIM_API_Version := 1.6.0\n\n" -#endif - "# Base units\n"); - switch (lmps_units) - { - case REAL: - strcat(*test_descriptor_string, - "Unit_length := A\n" - "Unit_energy := kcal/mol\n" - "Unit_charge := e\n" - "Unit_temperature := K\n" - "Unit_time := fs\n\n"); - break; - case METAL: - strcat(*test_descriptor_string, - "Unit_length := A\n" - "Unit_energy := eV\n" - "Unit_charge := e\n" - "Unit_temperature := K\n" - "Unit_time := ps\n\n"); - break; - case SI: - strcat(*test_descriptor_string, - "Unit_length := m\n" - "Unit_energy := J\n" - "Unit_charge := C\n" - "Unit_temperature := K\n" - "Unit_time := s\n\n"); - break; - case CGS: - strcat(*test_descriptor_string, - "Unit_length := cm\n" - "Unit_energy := erg\n" - "Unit_charge := statC\n" - "Unit_temperature := K\n" - "Unit_time := s\n\n"); - break; - case ELECTRON: - strcat(*test_descriptor_string, - "Unit_length := Bohr\n" - "Unit_energy := Hartree\n" - "Unit_charge := e\n" - "Unit_temperature := K\n" - "Unit_time := fs\n\n"); - break; - } - - // Write Supported species section - strcat(*test_descriptor_string, - "\n" -#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5 - "SUPPORTED_ATOM/PARTICLES_TYPES:\n" -#else - "PARTICLE_SPECIES:\n" -#endif - "# Symbol/name Type code\n"); - int code=1; - char* tmp_line = 0; - tmp_line = new char[100]; - for (int i=0; i < lmps_num_unique_elements; i++){ - sprintf(tmp_line, "%-24s%-16s%-3i\n", lmps_unique_elements[i], - "spec", code++); - strcat(*test_descriptor_string, tmp_line); - } - delete [] tmp_line; - tmp_line = 0; - strcat(*test_descriptor_string, "\n"); - - // Write conventions section - strcat(*test_descriptor_string, - "\n" - "CONVENTIONS:\n" - "# Name Type\n" - "ZeroBasedLists flag\n"); - // can use iterator or locator neighbor mode, unless in hybrid mode - if (lmps_hybrid) - strcat(*test_descriptor_string, - "Neigh_IterAccess flag\n"); - else - strcat(*test_descriptor_string, - "Neigh_BothAccess flag\n\n"); - - strcat(*test_descriptor_string, - "NEIGH_PURE_H flag\n" - "NEIGH_PURE_F flag\n" - "NEIGH_RVEC_H flag\n" - "NEIGH_RVEC_F flag\n"); - // @@ add code for MI_OPBC_? support ???? - if (lmps_support_cluster) - { - strcat(*test_descriptor_string, - "CLUSTER flag\n\n"); - } - else - { - strcat(*test_descriptor_string, "\n"); - } - - // Write input section - strcat(*test_descriptor_string, - "\n" - "MODEL_INPUT:\n" - "# Name Type Unit Shape\n" - "numberOfParticles integer none []\n" - "numberContributingParticles integer none []\n" -#if KIM_API_VERSION_MAJOR == 1 && KIM_API_VERSON_MINOR == 5 - "numberParticleTypes integer none []\n" - "particleTypes integer none " -#else - "numberOfSpecies integer none []\n" - "particleSpecies integer none " -#endif - "[numberOfParticles]\n" - "coordinates double length " - "[numberOfParticles,3]\n" - "neighObject pointer none []\n" - "get_neigh method none []\n"); - - // Write output section - strcat(*test_descriptor_string, - "\n" - "MODEL_OUPUT:\n" - "# Name Type Unit Shape\n" - "compute method none []\n" - "destroy method none []\n" - "cutoff double length []\n"); - if (!kim_model_has_energy) strcat(*test_descriptor_string,"# "); - strcat(*test_descriptor_string, - "energy double energy []\n"); - if (!kim_model_has_forces) strcat(*test_descriptor_string, "# "); - strcat(*test_descriptor_string, - "forces double force " - "[numberOfParticles,3]\n"); - if (!kim_model_has_particleEnergy) strcat(*test_descriptor_string, "# "); - strcat(*test_descriptor_string, - "particleEnergy double energy " - "[numberOfParticles]\n"); - if (no_virial_fdotr_compute != 1) strcat(*test_descriptor_string, "# "); - strcat(*test_descriptor_string, - "virial double energy [6]\n"); - if (!kim_model_has_particleVirial) strcat(*test_descriptor_string, "# "); - strcat(*test_descriptor_string, - "particleVirial double energy " - "[numberOfParticles,6]\n" - "\n"); - strcat(*test_descriptor_string, - "#\n" - "# END OF KIM DESCRIPTOR FILE\n" - "#\n"); - - return; -} - -void *PairKIM::extract(const char *str, int &dim) -{ - void *paramData; - int kimerror=0; - int ier; - int dummyint; - int isIndexed = 0; - const int MAXLINE = 1024; - int rank; - int validParam = 0; - int numParams; - int *speciesIndex = new int[MAXLINE]; - char *paramStr = new char[MAXLINE]; - char *paramName; - char *indexStr; - char message[MAXLINE]; - int offset; - double* paramPtr; - - // set dim to 0, we will always deal with scalars to circumvent lammps species - // indexing - dim = 0; - - // copy the input str into paramStr for parsing - strcpy(paramStr, str); - // get the name of the parameter (whatever is before ":") - paramName = strtok(paramStr, ":"); - if (0 == strcmp(paramName, str)) - paramName = (char*) str; - else - isIndexed = 1; - - // parse the rest of the string into tokens deliminated by "," and convert - // them to integers, saving them into speciesIndex - int count = -1; - if (isIndexed == 1) + int numberOfComputeArgumentNames; + KIM_COMPUTE_ARGUMENT_NAME_GetNumberOfComputeArgumentNames( + &numberOfComputeArgumentNames); + for (int i = 0; i < numberOfComputeArgumentNames; ++i) { - while((indexStr = strtok(NULL, ",")) != NULL) + KIM_ComputeArgumentName computeArgumentName; + int kimerror = KIM_COMPUTE_ARGUMENT_NAME_GetComputeArgumentName( + i, &computeArgumentName); + KIM_SupportStatus supportStatus; + kimerror = KIM_ComputeArguments_GetArgumentSupportStatus( + pargs, computeArgumentName, &supportStatus); + + if (KIM_ComputeArgumentName_Equal(computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialEnergy) + ) + kim_model_support_for_energy = supportStatus; + else if (KIM_ComputeArgumentName_Equal( + computeArgumentName, KIM_COMPUTE_ARGUMENT_NAME_partialForces) + ) + kim_model_support_for_forces = supportStatus; + else if + (KIM_ComputeArgumentName_Equal( + computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleEnergy)\ + ) + kim_model_support_for_particleEnergy = supportStatus; + else if + (KIM_ComputeArgumentName_Equal( + computeArgumentName, + KIM_COMPUTE_ARGUMENT_NAME_partialParticleVirial) + ) + kim_model_support_for_particleVirial = supportStatus; + else if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required) + ) { - count++; - ier = sscanf(indexStr, "%d", &speciesIndex[count]); - if (ier != 1) - { - ier = -1; - break; - } + std::stringstream msg; + msg << "KIM Model requires unsupported compute argument: " + << KIM_ComputeArgumentName_ToString(computeArgumentName); + error->all(FLERR, msg.str().c_str()); } } - if (ier == -1) - { - delete [] speciesIndex, speciesIndex = 0; - delete [] paramStr, paramStr = 0; - kim_error(__LINE__,"error in PairKIM::extract(), invalid parameter-indicie format", KIM_STATUS_FAIL); - } - // check to make sure that the requested parameter is a valid free parameter + if (KIM_SupportStatus_Equal(kim_model_support_for_energy, + KIM_SUPPORT_STATUS_notSupported)) + error->warning(FLERR,"KIM Model does not provide `partialEnergy'; " + "Potential energy will be zero"); - kimerror = pkim->get_num_params(&numParams, &dummyint); - kim_error(__LINE__, "get_num_free_params", kimerror); - char **freeParamNames = new char*[numParams]; - for (int k = 0; k < numParams; k++) + if (KIM_SupportStatus_Equal(kim_model_support_for_forces, + KIM_SUPPORT_STATUS_notSupported)) + error->warning(FLERR,"KIM Model does not provide `partialForce'; " + "Forces will be zero"); + + if (KIM_SupportStatus_Equal(kim_model_support_for_particleEnergy, + KIM_SUPPORT_STATUS_notSupported)) + error->warning(FLERR,"KIM Model does not provide `partialParticleEnergy'; " + "energy per atom will be zero"); + + if (KIM_SupportStatus_Equal(kim_model_support_for_particleVirial, + KIM_SUPPORT_STATUS_notSupported)) + error->warning(FLERR,"KIM Model does not provide `partialParticleVirial'; " + "virial per atom will be zero"); + + int numberOfComputeCallbackNames; + KIM_COMPUTE_CALLBACK_NAME_GetNumberOfComputeCallbackNames( + &numberOfComputeCallbackNames); + for (int i = 0; i < numberOfComputeCallbackNames; ++i) { - kimerror = pkim->get_free_parameter(k, (const char**) &freeParamNames[k]); - kim_error(__LINE__, "get_free_parameter", kimerror); - if (0 == strcmp(paramName, freeParamNames[k])) + KIM_ComputeCallbackName computeCallbackName; + int kimerror = KIM_COMPUTE_CALLBACK_NAME_GetComputeCallbackName( + i, &computeCallbackName); + KIM_SupportStatus supportStatus; + kimerror = KIM_ComputeArguments_GetCallbackSupportStatus( + pargs, computeCallbackName, &supportStatus); + + if (KIM_SupportStatus_Equal(supportStatus, KIM_SUPPORT_STATUS_required)) { - validParam = 1; - break; + error->all(FLERR,"KIM Model requires unsupported compute callback"); } } - delete [] freeParamNames, freeParamNames = 0; - if (validParam == 0) - { - sprintf(message, "Invalid parameter to adapt: \"%s\" is not a FREE_PARAM", paramName); - delete [] speciesIndex, speciesIndex = 0; - delete [] paramStr, paramStr = 0; - kim_error(__LINE__, message, KIM_STATUS_FAIL); - } - // get the parameter arry from pkim object - paramData = pkim->get_data(paramName, &kimerror); - if (kimerror == KIM_STATUS_FAIL) - { - delete [] speciesIndex, speciesIndex = 0; - delete [] paramStr, paramStr = 0; - } - kim_error(__LINE__,"get_data",kimerror); - - // get rank and shape of parameter - rank = (*pkim).get_rank(paramName, &kimerror); - if (kimerror == KIM_STATUS_FAIL) - { - delete [] speciesIndex, speciesIndex = 0; - delete [] paramStr, paramStr = 0; - } - kim_error(__LINE__,"get_rank",kimerror); - - int *shape = new int[MAXLINE]; - dummyint = (*pkim).get_shape(paramName, shape, &kimerror); - if (kimerror == KIM_STATUS_FAIL) - { - delete [] speciesIndex, speciesIndex = 0; - delete [] paramStr, paramStr = 0; - delete [] shape, shape = 0; - } - kim_error(__LINE__,"get_shape",kimerror); - - delete [] paramStr, paramStr = 0; - // check that number of inputs is rank, and that input indicies are less than - // their respective dimensions in shape - if ((count+1) != rank) - { - sprintf(message, "Number of input indicies not equal to rank of specified parameter (%d)", rank); - kimerror = KIM_STATUS_FAIL; - delete [] speciesIndex, speciesIndex = 0; - delete [] shape, shape = 0; - kim_error(__LINE__,message, kimerror); - } - if (isIndexed == 1) - { - for (int i=0; i <= count; i++) - { - if (shape[i] <= speciesIndex[i] || speciesIndex[i] < 0) - { - kimerror = KIM_STATUS_FAIL; - break; - } - } - } - delete [] shape, shape = 0; - if (kimerror == KIM_STATUS_FAIL) - { - sprintf(message, "One or more parameter indicies out of bounds"); - delete [] speciesIndex, speciesIndex = 0; - kim_error(__LINE__, message, kimerror); - } - - // Cast it to a double - paramPtr = static_cast(paramData); - - // If it is indexed (not just a scalar for the whole model), then get pointer - // corresponding to specified indicies by calculating the adress offset using - // specified indicies and the shape - if (isIndexed == 1) - { - offset = 0; - for (int i = 0; i < (rank-1); i++) - { - offset = (offset + speciesIndex[i]) * shape[i+1]; - } - offset = offset + speciesIndex[(rank - 1)]; - paramPtr = (paramPtr + offset); - } - delete [] speciesIndex, speciesIndex = 0; - - return ((void*) paramPtr); + return; } diff --git a/src/KIM/pair_kim.h b/src/KIM/pair_kim.h index fb4cda8af9..a6f882347d 100644 --- a/src/KIM/pair_kim.h +++ b/src/KIM/pair_kim.h @@ -12,14 +12,45 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing authors: Ryan S. Elliott, - Valeriu Smirichinski, - Ellad Tadmor (U Minn) + Contributing authors: Ryan S. Elliott (UMinn) ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Designed for use with the openkim-api-v1.5.0 package and for use with - the kim-api-v1.6.0 (and newer) package + This program is free software; you can redistribute it and/or modify it + under the terms of the GNU General Public License as published by the Free + Software Foundation; either version 2 of the License, or (at your option) + any later version. + + This program is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for + more details. + + You should have received a copy of the GNU General Public License along with + this program; if not, see . + + Linking LAMMPS statically or dynamically with other modules is making a + combined work based on LAMMPS. Thus, the terms and conditions of the GNU + General Public License cover the whole combination. + + In addition, as a special exception, the copyright holders of LAMMPS give + you permission to combine LAMMPS with free software programs or libraries + that are released under the GNU LGPL and with code included in the standard + release of the "kim-api" under the CDDL (or modified versions of such code, + with unchanged license). You may copy and distribute such a system following + the terms of the GNU GPL for LAMMPS and the licenses of the other code + concerned, provided that you include the source code of that other code + when and as the GNU GPL requires distribution of source code. + + Note that people who make modified versions of LAMMPS are not obligated to + grant this special exception for their modified versions; it is their choice + whether to do so. The GNU General Public License gives permission to release + a modified version without this exception; this exception also makes it + possible to release a modified version which carries forward this exception. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Designed for use with the kim-api-v2-2.0.0 (and newer) package ------------------------------------------------------------------------- */ #ifdef PAIR_CLASS @@ -34,6 +65,10 @@ PairStyle(kim,PairKIM) // includes from KIM & LAMMPS class KIM_API_model; #include "pair.h" +extern "C" { +#include "KIM_SimulatorHeaders.h" +} +#include namespace LAMMPS_NS { @@ -48,14 +83,13 @@ namespace LAMMPS_NS { virtual void settings(int, char**); virtual void coeff(int, char**); virtual void init_style(); + virtual void init_list(int id, NeighList *ptr); virtual double init_one(int, int); - virtual void reinit(); virtual int pack_reverse_comm(int, int, double*); virtual void unpack_reverse_comm(int, int*, double*); virtual double memory_usage(); - void *extract(const char *, int &); - private: + protected: // (nearly) all bool flags are not initialized in constructor, but set // explicitly in the indicated function. All other data members are // initialized in constructor @@ -64,12 +98,11 @@ namespace LAMMPS_NS { // values set in settings() char* kim_modelname; - bool print_kim_file; // values set in coeff() // values set in allocate(), called by coeff() - void allocate(); + virtual void allocate(); int* lmps_map_species_to_unique; // values set in coeff(), after calling allocate() @@ -80,74 +113,59 @@ namespace LAMMPS_NS { // values set in set_lmps_flags(), called from init_style() bool lmps_using_newton; bool lmps_using_molecular; - bool lmps_hybrid; // true if running with pair hybrid - bool lmps_support_cluster; // true if running in mode compat. - // with CLUSTER enum unit_sys {REAL, METAL, SI, CGS, ELECTRON}; unit_sys lmps_units; + KIM_LengthUnit lengthUnit; + KIM_EnergyUnit energyUnit; + KIM_ChargeUnit chargeUnit; + KIM_TemperatureUnit temperatureUnit; + KIM_TimeUnit timeUnit; + + KIM_Model * pkim; + KIM_ComputeArguments * pargs; // values set in set_kim_model_has_flags(), called by kim_init() - KIM_API_model* pkim; - bool kim_model_has_energy; - bool kim_model_has_forces; - bool kim_model_has_particleEnergy; - bool kim_model_has_particleVirial; + KIM_SupportStatus kim_model_support_for_energy; + KIM_SupportStatus kim_model_support_for_forces; + KIM_SupportStatus kim_model_support_for_particleEnergy; + KIM_SupportStatus kim_model_support_for_particleVirial; - // values set in kim_init(), after call to string_init(_) + // values set in kim_init() bool kim_init_ok; - bool kim_model_using_half; - bool kim_model_using_cluster; - bool kim_model_using_Rij; - int kim_ind_coordinates; - int kim_ind_numberOfParticles; - int kim_ind_numberContributingParticles; - int kim_ind_numberOfSpecies; - int kim_ind_particleSpecies; - int kim_ind_get_neigh; - int kim_ind_neighObject; - int kim_ind_cutoff; - int kim_ind_energy; - int kim_ind_particleEnergy; - int kim_ind_forces; - int kim_ind_virial; - int kim_ind_particleVirial; + int lmps_local_tot_num_atoms; + double kim_global_influence_distance; // KIM Model cutoff value + int kim_number_of_neighbor_lists; + double const * kim_cutoff_values; + int const * modelWillNotRequestNeighborsOfNoncontributingParticles; + class NeighList ** neighborLists; - // values set in init_style(), after calling pkim->model_init() - bool kim_model_init_ok; + // values set in init_style() bool kim_particle_codes_ok; int *kim_particle_codes; - // values set in set_statics(), called at end of kim_init(), - // then again in set_volatiles(), called in compute() - int lmps_local_tot_num_atoms; - double kim_global_cutoff; // KIM Model cutoff value - // values set in compute() int lmps_maxalloc; // max allocated memory value int* kim_particleSpecies; // array of KIM particle species - double** lmps_force_tmp; // temp storage for f, when running in - // hybrid mode needed to avoid resetting - // f to zero in each object + int* kim_particleContributing; // array of KIM particle contributing int* lmps_stripped_neigh_list; // neighbors of one atom, used when LAMMPS // is in molecular mode - - // values used in get_neigh() - int kim_iterator_position; //get_neigh iterator current position - double *Rij; + int** lmps_stripped_neigh_ptr; // pointer into lists // KIM specific helper functions - void kim_error(int, const char *, int); - void kim_init(); - void kim_free(); - void set_statics(); - void set_volatiles(); - void set_lmps_flags(); - void set_kim_model_has_flags(); - void write_descriptor(char** test_descriptor_string); + virtual void set_contributing(); + virtual void kim_init(); + virtual void kim_free(); + virtual void set_argument_pointers(); + virtual void set_lmps_flags(); + virtual void set_kim_model_has_flags(); + virtual int check_for_routine_compatibility(); // static methods used as callbacks from KIM - static int get_neigh(void** kimmdl, int* mode, int* request, - int* atom, int* numnei, int** nei1atom, - double** pRij); + static int get_neigh( + void const * const dataObject, + int const numberOfCutoffs, double const * const cutoffs, + int const neighborListIndex, int const particleNumber, + int * const numberOfNeighbors, + int const ** const neighborsOfParticle); }; } @@ -156,81 +174,92 @@ namespace LAMMPS_NS { /* ERROR/WARNING messages: -E: Illegal ... command +E: Unable to set KIM particle species codes and/or contributing -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. +A low-level kim-api error has occurred. -E: Unrecognized virial argument in pair_style command +E: KIM Compute returned error -Only two options are supported: LAMMPSvirial and KIMvirial +The KIM model was unable, for some reason, to complete the computation. + +E: 'KIMvirial' or 'LAMMPSvirial' not supported with kim-api-v2. + +"KIMvirial or "LAMMPSvirial" found on the pair_style line. These keys are not supported kim-api-v2. (The virial computation is always performed by LAMMPS.) Please remove these keys, make sure the KIM model you are using supports kim-api-v2, and rerun. + +E: Illegal pair_style command + +Self-explanatory. E: Incorrect args for pair coefficients -Self-explanatory. Check the input script or data file. +Self-explanatory. -E: Invalid args for non-hybrid pair coefficients +E: create_kim_particle_codes: symbol not found: XX -"NULL" is only supported in pair_coeff calls when using pair hybrid +The KIM model specified does not support the atomic species symbol E: PairKIM only works with 3D problems -This is a current limitation. +Self-explanatory. E: All pair coeffs are not set -All pair coefficients must be set in the data file or by the -pair_coeff command before running a simulation. +Self-explanatory. -E: KIM neighbor iterator exceeded range +E: Unable to destroy Compute Arguments Object -This should not happen. It likely indicates a bug -in the KIM implementation of the interatomic potential -where it is requesting neighbors incorrectly. +A low-level kim-api error has occurred. -E: LAMMPS unit_style lj not supported by KIM models +E: KIM ModelCreate failed -Self-explanatory. Check the input script or data file. +The kim-api was not able to create a model object for the specified model. -E: Unknown unit_style +E: KIM Model did not accept the requested unit system -Self-explanatory. Check the input script or data file. +The KIM Model does not support the specified LAMMPS unit system -W: KIM Model does not provide `energy'; Potential energy will be zero +E: KIM ComputeArgumentsCreate failed -UNDOCUMENTED +A low-level kim-api error has occurred. -W: KIM Model does not provide `forces'; Forces will be zero +E: Unable to register KIM pointers -UNDOCUMENTED +A low-level kim-api error has occurred. -W: KIM Model does not provide `particleEnergy'; energy per atom will be zero +E: Unable to set KIM argument pointers -UNDOCUMENTED +A low-level kim-api error has occurred. -W: KIM Model does not provide `particleVirial'; virial per atom will be zero - -UNDOCUMENTED - -E: Test_descriptor_string already allocated - -This is an internal error. Contact the developers. - -U: KIM Model does not provide 'energy'; Potential energy will be zero +E: pair_kim does not support hybrid Self-explanatory. -U: KIM Model does not provide 'forces'; Forces will be zero +E: LAMMPS unit_style lj not suppored by KIM models Self-explanatory. -U: KIM Model does not provide 'particleEnergy'; energy per atom will be zero +E: KIM Model requires unsupported compute argument: XXX + +A low-level kim-api error has occurred. + +W: KIM Model does not provide `partialEnergy'; Potential energy will be zero Self-explanatory. -U: KIM Model does not provide 'particleVirial'; virial per atom will be zero +W: KIM Model does not provide `partialForce'; Forces will be zero Self-explanatory. +W: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero + +Self-explanatory. + +W: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero + +Self-explanatory. + +E: KIM Model requires unsupported compute callback + +A low-level kim-api error has occurred. + */ diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 321fa34ad7..7c465128d8 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -49,6 +49,8 @@ action angle_charmm_kokkos.cpp angle_charmm.cpp action angle_charmm_kokkos.h angle_charmm.h action angle_class2_kokkos.cpp angle_class2.cpp action angle_class2_kokkos.h angle_class2.h +action angle_cosine_kokkos.cpp angle_cosine.cpp +action angle_cosine_kokkos.h angle_cosine.h action angle_harmonic_kokkos.cpp angle_harmonic.cpp action angle_harmonic_kokkos.h angle_harmonic.h action atom_kokkos.cpp diff --git a/src/KOKKOS/angle_charmm_kokkos.cpp b/src/KOKKOS/angle_charmm_kokkos.cpp index 7a83e0d654..0f46c958d6 100644 --- a/src/KOKKOS/angle_charmm_kokkos.cpp +++ b/src/KOKKOS/angle_charmm_kokkos.cpp @@ -64,8 +64,7 @@ void AngleCharmmKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -447,7 +446,7 @@ void AngleCharmmKokkos::ev_tally(EV_FLOAT &ev, const int i, const in namespace LAMMPS_NS { template class AngleCharmmKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class AngleCharmmKokkos; #endif } diff --git a/src/KOKKOS/angle_class2_kokkos.cpp b/src/KOKKOS/angle_class2_kokkos.cpp index 289753a3ee..836714764d 100644 --- a/src/KOKKOS/angle_class2_kokkos.cpp +++ b/src/KOKKOS/angle_class2_kokkos.cpp @@ -64,8 +64,7 @@ void AngleClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -598,7 +597,7 @@ void AngleClass2Kokkos::ev_tally(EV_FLOAT &ev, const int i, const in namespace LAMMPS_NS { template class AngleClass2Kokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class AngleClass2Kokkos; #endif } diff --git a/src/KOKKOS/angle_cosine_kokkos.cpp b/src/KOKKOS/angle_cosine_kokkos.cpp new file mode 100644 index 0000000000..4a4866948f --- /dev/null +++ b/src/KOKKOS/angle_cosine_kokkos.cpp @@ -0,0 +1,393 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Stan Moore (SNL) +------------------------------------------------------------------------- */ + +#include +#include +#include "angle_cosine_kokkos.h" +#include "atom_kokkos.h" +#include "neighbor_kokkos.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "math_const.h" +#include "memory_kokkos.h" +#include "error.h" +#include "atom_masks.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +template +AngleCosineKokkos::AngleCosineKokkos(LAMMPS *lmp) : AngleCosine(lmp) +{ + atomKK = (AtomKokkos *) atom; + neighborKK = (NeighborKokkos *) neighbor; + execution_space = ExecutionSpaceFromDevice::space; + datamask_read = X_MASK | F_MASK | ENERGY_MASK | VIRIAL_MASK; + datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK; +} + +/* ---------------------------------------------------------------------- */ + +template +AngleCosineKokkos::~AngleCosineKokkos() +{ + if (!copymode) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->destroy_kokkos(k_vatom,vatom); + } +} + +/* ---------------------------------------------------------------------- */ + +template +void AngleCosineKokkos::compute(int eflag_in, int vflag_in) +{ + eflag = eflag_in; + vflag = vflag_in; + + ev_init(eflag,vflag,0); + + // reallocate per-atom arrays if necessary + + if (eflag_atom) { + memoryKK->destroy_kokkos(k_eatom,eatom); + memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom"); + d_eatom = k_eatom.template view(); + } + if (vflag_atom) { + memoryKK->destroy_kokkos(k_vatom,vatom); + memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom"); + d_vatom = k_vatom.template view(); + } + + //atomKK->sync(execution_space,datamask_read); + k_k.template sync(); + // if (eflag || vflag) atomKK->modified(execution_space,datamask_modify); + // else atomKK->modified(execution_space,F_MASK); + + x = atomKK->k_x.template view(); + f = atomKK->k_f.template view(); + neighborKK->k_anglelist.template sync(); + anglelist = neighborKK->k_anglelist.template view(); + int nanglelist = neighborKK->nanglelist; + nlocal = atom->nlocal; + newton_bond = force->newton_bond; + + copymode = 1; + + // loop over neighbors of my atoms + + EV_FLOAT ev; + + if (evflag) { + if (newton_bond) { + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,nanglelist),*this,ev); + } else { + Kokkos::parallel_reduce(Kokkos::RangePolicy >(0,nanglelist),*this,ev); + } + } else { + if (newton_bond) { + Kokkos::parallel_for(Kokkos::RangePolicy >(0,nanglelist),*this); + } else { + Kokkos::parallel_for(Kokkos::RangePolicy >(0,nanglelist),*this); + } + } + + if (eflag_global) energy += ev.evdwl; + if (vflag_global) { + virial[0] += ev.v[0]; + virial[1] += ev.v[1]; + virial[2] += ev.v[2]; + virial[3] += ev.v[3]; + virial[4] += ev.v[4]; + virial[5] += ev.v[5]; + } + + if (eflag_atom) { + k_eatom.template modify(); + k_eatom.template sync(); + } + + if (vflag_atom) { + k_vatom.template modify(); + k_vatom.template sync(); + } + + copymode = 0; +} + +template +template +KOKKOS_INLINE_FUNCTION +void AngleCosineKokkos::operator()(TagAngleCosineCompute, const int &n, EV_FLOAT& ev) const { + + // The f array is atomic + Kokkos::View > a_f = f; + + const int i1 = anglelist(n,0); + const int i2 = anglelist(n,1); + const int i3 = anglelist(n,2); + const int type = anglelist(n,3); + + // 1st bond + + const F_FLOAT delx1 = x(i1,0) - x(i2,0); + const F_FLOAT dely1 = x(i1,1) - x(i2,1); + const F_FLOAT delz1 = x(i1,2) - x(i2,2); + + const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + const F_FLOAT r1 = sqrt(rsq1); + + // 2nd bond + + const F_FLOAT delx2 = x(i3,0) - x(i2,0); + const F_FLOAT dely2 = x(i3,1) - x(i2,1); + const F_FLOAT delz2 = x(i3,2) - x(i2,2); + + const F_FLOAT rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + const F_FLOAT r2 = sqrt(rsq2); + + // c = cosine of angle + + F_FLOAT c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + // force & energy + + F_FLOAT eangle = 0.0; + if (eflag) eangle = d_k[type]*(1.0+c); + + const F_FLOAT a = d_k[type]; + const F_FLOAT a11 = a*c / rsq1; + const F_FLOAT a12 = -a / (r1*r2); + const F_FLOAT a22 = a*c / rsq2; + + F_FLOAT f1[3],f3[3]; + f1[0] = a11*delx1 + a12*delx2; + f1[1] = a11*dely1 + a12*dely2; + f1[2] = a11*delz1 + a12*delz2; + f3[0] = a22*delx2 + a12*delx1; + f3[1] = a22*dely2 + a12*dely1; + f3[2] = a22*delz2 + a12*delz1; + + // apply force to each of 3 atoms + + if (NEWTON_BOND || i1 < nlocal) { + a_f(i1,0) += f1[0]; + a_f(i1,1) += f1[1]; + a_f(i1,2) += f1[2]; + } + + if (NEWTON_BOND || i2 < nlocal) { + a_f(i2,0) -= f1[0] + f3[0]; + a_f(i2,1) -= f1[1] + f3[1]; + a_f(i2,2) -= f1[2] + f3[2]; + } + + if (NEWTON_BOND || i3 < nlocal) { + a_f(i3,0) += f3[0]; + a_f(i3,1) += f3[1]; + a_f(i3,2) += f3[2]; + } + + if (EVFLAG) ev_tally(ev,i1,i2,i3,eangle,f1,f3, + delx1,dely1,delz1,delx2,dely2,delz2); +} + +template +template +KOKKOS_INLINE_FUNCTION +void AngleCosineKokkos::operator()(TagAngleCosineCompute, const int &n) const { + EV_FLOAT ev; + this->template operator()(TagAngleCosineCompute(), n, ev); +} + +/* ---------------------------------------------------------------------- */ + +template +void AngleCosineKokkos::allocate() +{ + AngleCosine::allocate(); + + int n = atom->nangletypes; + k_k = typename ArrayTypes::tdual_ffloat_1d("AngleCosine::k",n+1); + d_k = k_k.template view(); +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more types +------------------------------------------------------------------------- */ + +template +void AngleCosineKokkos::coeff(int narg, char **arg) +{ + AngleCosine::coeff(narg, arg); + + int n = atom->nangletypes; + for (int i = 1; i <= n; i++) + k_k.h_view[i] = k[i]; + + k_k.template modify(); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +template +void AngleCosineKokkos::read_restart(FILE *fp) +{ + AngleCosine::read_restart(fp); + + int n = atom->nangletypes; + for (int i = 1; i <= n; i++) + k_k.h_view[i] = k[i]; + + k_k.template modify(); +} + +/* ---------------------------------------------------------------------- + tally energy and virial into global and per-atom accumulators + virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3 +------------------------------------------------------------------------- */ + +template +//template +KOKKOS_INLINE_FUNCTION +void AngleCosineKokkos::ev_tally(EV_FLOAT &ev, const int i, const int j, const int k, + F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3, + const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1, + const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const +{ + E_FLOAT eanglethird; + F_FLOAT v[6]; + + // The eatom and vatom arrays are atomic + Kokkos::View > v_eatom = k_eatom.template view(); + Kokkos::View > v_vatom = k_vatom.template view(); + + if (eflag_either) { + if (eflag_global) { + if (newton_bond) ev.evdwl += eangle; + else { + eanglethird = THIRD*eangle; + + if (i < nlocal) ev.evdwl += eanglethird; + if (j < nlocal) ev.evdwl += eanglethird; + if (k < nlocal) ev.evdwl += eanglethird; + } + } + if (eflag_atom) { + eanglethird = THIRD*eangle; + + if (newton_bond || i < nlocal) v_eatom[i] += eanglethird; + if (newton_bond || j < nlocal) v_eatom[j] += eanglethird; + if (newton_bond || k < nlocal) v_eatom[k] += eanglethird; + } + } + + if (vflag_either) { + v[0] = delx1*f1[0] + delx2*f3[0]; + v[1] = dely1*f1[1] + dely2*f3[1]; + v[2] = delz1*f1[2] + delz2*f3[2]; + v[3] = delx1*f1[1] + delx2*f3[1]; + v[4] = delx1*f1[2] + delx2*f3[2]; + v[5] = dely1*f1[2] + dely2*f3[2]; + + if (vflag_global) { + if (newton_bond) { + ev.v[0] += v[0]; + ev.v[1] += v[1]; + ev.v[2] += v[2]; + ev.v[3] += v[3]; + ev.v[4] += v[4]; + ev.v[5] += v[5]; + } else { + if (i < nlocal) { + ev.v[0] += THIRD*v[0]; + ev.v[1] += THIRD*v[1]; + ev.v[2] += THIRD*v[2]; + ev.v[3] += THIRD*v[3]; + ev.v[4] += THIRD*v[4]; + ev.v[5] += THIRD*v[5]; + } + if (j < nlocal) { + ev.v[0] += THIRD*v[0]; + ev.v[1] += THIRD*v[1]; + ev.v[2] += THIRD*v[2]; + ev.v[3] += THIRD*v[3]; + ev.v[4] += THIRD*v[4]; + ev.v[5] += THIRD*v[5]; + } + if (k < nlocal) { + ev.v[0] += THIRD*v[0]; + + ev.v[1] += THIRD*v[1]; + ev.v[2] += THIRD*v[2]; + ev.v[3] += THIRD*v[3]; + ev.v[4] += THIRD*v[4]; + ev.v[5] += THIRD*v[5]; + } + } + } + + if (vflag_atom) { + if (newton_bond || i < nlocal) { + v_vatom(i,0) += THIRD*v[0]; + v_vatom(i,1) += THIRD*v[1]; + v_vatom(i,2) += THIRD*v[2]; + v_vatom(i,3) += THIRD*v[3]; + v_vatom(i,4) += THIRD*v[4]; + v_vatom(i,5) += THIRD*v[5]; + } + if (newton_bond || j < nlocal) { + v_vatom(j,0) += THIRD*v[0]; + v_vatom(j,1) += THIRD*v[1]; + v_vatom(j,2) += THIRD*v[2]; + v_vatom(j,3) += THIRD*v[3]; + v_vatom(j,4) += THIRD*v[4]; + v_vatom(j,5) += THIRD*v[5]; + } + if (newton_bond || k < nlocal) { + v_vatom(k,0) += THIRD*v[0]; + v_vatom(k,1) += THIRD*v[1]; + v_vatom(k,2) += THIRD*v[2]; + v_vatom(k,3) += THIRD*v[3]; + v_vatom(k,4) += THIRD*v[4]; + v_vatom(k,5) += THIRD*v[5]; + + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +namespace LAMMPS_NS { +template class AngleCosineKokkos; +#ifdef KOKKOS_ENABLE_CUDA +template class AngleCosineKokkos; +#endif +} + diff --git a/src/KOKKOS/angle_cosine_kokkos.h b/src/KOKKOS/angle_cosine_kokkos.h new file mode 100644 index 0000000000..8ea6719814 --- /dev/null +++ b/src/KOKKOS/angle_cosine_kokkos.h @@ -0,0 +1,90 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ANGLE_CLASS + +AngleStyle(cosine/kk,AngleCosineKokkos) +AngleStyle(cosine/kk/device,AngleCosineKokkos) +AngleStyle(cosine/kk/host,AngleCosineKokkos) + +#else + +#ifndef LMP_ANGLE_COSINE_KOKKOS_H +#define LMP_ANGLE_COSINE_KOKKOS_H + +#include "angle_cosine.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +template +struct TagAngleCosineCompute{}; + +template +class AngleCosineKokkos : public AngleCosine { + + public: + typedef DeviceType device_type; + typedef EV_FLOAT value_type; + + AngleCosineKokkos(class LAMMPS *); + virtual ~AngleCosineKokkos(); + void compute(int, int); + void coeff(int, char **); + void read_restart(FILE *); + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagAngleCosineCompute, const int&, EV_FLOAT&) const; + + template + KOKKOS_INLINE_FUNCTION + void operator()(TagAngleCosineCompute, const int&) const; + + //template + KOKKOS_INLINE_FUNCTION + void ev_tally(EV_FLOAT &ev, const int i, const int j, const int k, + F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3, + const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1, + const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const; + + protected: + + class NeighborKokkos *neighborKK; + + typename ArrayTypes::t_x_array_randomread x; + typename ArrayTypes::t_f_array f; + typename ArrayTypes::t_int_2d anglelist; + + typename ArrayTypes::tdual_efloat_1d k_eatom; + typename ArrayTypes::tdual_virial_array k_vatom; + typename ArrayTypes::t_efloat_1d d_eatom; + typename ArrayTypes::t_virial_array d_vatom; + + int nlocal,newton_bond; + int eflag,vflag; + + typename ArrayTypes::tdual_ffloat_1d k_k; + typename ArrayTypes::t_ffloat_1d d_k; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/KOKKOS/angle_harmonic_kokkos.cpp b/src/KOKKOS/angle_harmonic_kokkos.cpp index 250397c8e3..dbe705800c 100644 --- a/src/KOKKOS/angle_harmonic_kokkos.cpp +++ b/src/KOKKOS/angle_harmonic_kokkos.cpp @@ -64,8 +64,7 @@ void AngleHarmonicKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -405,7 +404,7 @@ void AngleHarmonicKokkos::ev_tally(EV_FLOAT &ev, const int i, const namespace LAMMPS_NS { template class AngleHarmonicKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class AngleHarmonicKokkos; #endif } diff --git a/src/KOKKOS/atom_vec_kokkos.h b/src/KOKKOS/atom_vec_kokkos.h index efe55c47ad..58f21b9cd4 100644 --- a/src/KOKKOS/atom_vec_kokkos.h +++ b/src/KOKKOS/atom_vec_kokkos.h @@ -125,7 +125,7 @@ class AtomVecKokkos : public AtomVec { size_t buffer_size; void* buffer; - #ifdef KOKKOS_HAVE_CUDA + #ifdef KOKKOS_ENABLE_CUDA template Kokkos::View::type, Kokkos::MemoryTraits > mirror_type; if (buffer_size == 0) { - buffer = Kokkos::kokkos_malloc(src.capacity()); - buffer_size = src.capacity(); - } else if (buffer_size < src.capacity()) { - buffer = Kokkos::kokkos_realloc(buffer,src.capacity()); - buffer_size = src.capacity(); + buffer = Kokkos::kokkos_malloc(src.span()); + buffer_size = src.span(); + } else if (buffer_size < src.span()) { + buffer = Kokkos::kokkos_realloc(buffer,src.span()); + buffer_size = src.span(); } return mirror_type( buffer , src.extent(0) , @@ -157,7 +157,7 @@ class AtomVecKokkos : public AtomVec { } template - void perform_async_copy(const ViewType& src, unsigned int space) { + void perform_async_copy(ViewType& src, unsigned int space) { typedef Kokkos::View::type, Kokkos::MemoryTraits > mirror_type; if (buffer_size == 0) { - buffer = Kokkos::kokkos_malloc(src.capacity()*sizeof(typename ViewType::value_type)); - buffer_size = src.capacity(); - } else if (buffer_size < src.capacity()) { - buffer = Kokkos::kokkos_realloc(buffer,src.capacity()*sizeof(typename ViewType::value_type)); - buffer_size = src.capacity(); + buffer = Kokkos::kokkos_malloc(src.span()*sizeof(typename ViewType::value_type)); + buffer_size = src.span(); + } else if (buffer_size < src.span()) { + buffer = Kokkos::kokkos_realloc(buffer,src.span()*sizeof(typename ViewType::value_type)); + buffer_size = src.span(); } mirror_type tmp_view( (typename ViewType::value_type*)buffer , src.extent(0) , @@ -183,11 +183,11 @@ class AtomVecKokkos : public AtomVec { if(space == Device) { Kokkos::deep_copy(LMPHostType(),tmp_view,src.h_view), Kokkos::deep_copy(LMPHostType(),src.d_view,tmp_view); - src.modified_device() = src.modified_host(); + src.clear_sync_state(); } else { Kokkos::deep_copy(LMPHostType(),tmp_view,src.d_view), Kokkos::deep_copy(LMPHostType(),src.h_view,tmp_view); - src.modified_device() = src.modified_host(); + src.clear_sync_state(); } } #else diff --git a/src/KOKKOS/atom_vec_sphere_kokkos.cpp b/src/KOKKOS/atom_vec_sphere_kokkos.cpp index 3dfbc5efdc..f05e8d09df 100644 --- a/src/KOKKOS/atom_vec_sphere_kokkos.cpp +++ b/src/KOKKOS/atom_vec_sphere_kokkos.cpp @@ -792,7 +792,7 @@ int AtomVecSphereKokkos::pack_comm_self( const int &n, const DAT::tdual_int_2d &list, const int &iswap, const int nfirst, const int &pbc_flag, const int* const pbc) { // Fallback to AtomVecKokkos if radvary == 0 - if (radvary == 0) + if (radvary == 0) return AtomVecKokkos::pack_comm_self(n,list,iswap,nfirst,pbc_flag,pbc); if(commKK->forward_comm_on_host) { sync(Host,X_MASK|RADIUS_MASK|RMASS_MASK); @@ -1462,7 +1462,7 @@ struct AtomVecSphereKokkos_PackBorder { const int maxsend = (buf.extent(0)*buf.extent(1))/elements; _buf = typename ArrayTypes::t_xfloat_2d_um(buf.data(),maxsend,elements); } - + KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { const int j = _list(_iswap,i); diff --git a/src/KOKKOS/bond_class2_kokkos.cpp b/src/KOKKOS/bond_class2_kokkos.cpp index cb625f06c1..798fb41c92 100644 --- a/src/KOKKOS/bond_class2_kokkos.cpp +++ b/src/KOKKOS/bond_class2_kokkos.cpp @@ -60,8 +60,7 @@ void BondClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -366,7 +365,7 @@ void BondClass2Kokkos::ev_tally(EV_FLOAT &ev, const int &i, const in namespace LAMMPS_NS { template class BondClass2Kokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class BondClass2Kokkos; #endif } diff --git a/src/KOKKOS/bond_fene_kokkos.cpp b/src/KOKKOS/bond_fene_kokkos.cpp index 4342223f7e..b5cdc1a05a 100644 --- a/src/KOKKOS/bond_fene_kokkos.cpp +++ b/src/KOKKOS/bond_fene_kokkos.cpp @@ -69,8 +69,7 @@ void BondFENEKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -401,7 +400,7 @@ void BondFENEKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int namespace LAMMPS_NS { template class BondFENEKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class BondFENEKokkos; #endif } diff --git a/src/KOKKOS/bond_harmonic_kokkos.cpp b/src/KOKKOS/bond_harmonic_kokkos.cpp index 35b957ffd3..51a9fa4389 100644 --- a/src/KOKKOS/bond_harmonic_kokkos.cpp +++ b/src/KOKKOS/bond_harmonic_kokkos.cpp @@ -61,8 +61,7 @@ void BondHarmonicKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -340,7 +339,7 @@ void BondHarmonicKokkos::ev_tally(EV_FLOAT &ev, const int &i, const namespace LAMMPS_NS { template class BondHarmonicKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class BondHarmonicKokkos; #endif } diff --git a/src/KOKKOS/comm_kokkos.cpp b/src/KOKKOS/comm_kokkos.cpp index f40156aabc..1d31c07180 100644 --- a/src/KOKKOS/comm_kokkos.cpp +++ b/src/KOKKOS/comm_kokkos.cpp @@ -210,7 +210,7 @@ void CommKokkos::forward_comm_device(int dummy) space,X_MASK); } } else if (ghost_velocity) { - if (size_forward_recv[iswap]) { + if (size_forward_recv[iswap]) { MPI_Irecv(k_buf_recv.view().data(), size_forward_recv[iswap],MPI_DOUBLE, recvproc[iswap],0,world,&request); diff --git a/src/KOKKOS/compute_temp_kokkos.cpp b/src/KOKKOS/compute_temp_kokkos.cpp index d94c6e76b5..7b76f54f57 100644 --- a/src/KOKKOS/compute_temp_kokkos.cpp +++ b/src/KOKKOS/compute_temp_kokkos.cpp @@ -153,7 +153,7 @@ void ComputeTempKokkos::operator()(TagComputeTempVector, cons namespace LAMMPS_NS { template class ComputeTempKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class ComputeTempKokkos; #endif } diff --git a/src/KOKKOS/dihedral_charmm_kokkos.cpp b/src/KOKKOS/dihedral_charmm_kokkos.cpp index 9e25dda894..61ddcc425a 100644 --- a/src/KOKKOS/dihedral_charmm_kokkos.cpp +++ b/src/KOKKOS/dihedral_charmm_kokkos.cpp @@ -69,8 +69,7 @@ void DihedralCharmmKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // insure pair->ev_tally() will use 1-4 virial contribution @@ -786,7 +785,7 @@ void DihedralCharmmKokkos::ev_tally(EVM_FLOAT &evm, const int i, con namespace LAMMPS_NS { template class DihedralCharmmKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class DihedralCharmmKokkos; #endif } diff --git a/src/KOKKOS/dihedral_class2_kokkos.cpp b/src/KOKKOS/dihedral_class2_kokkos.cpp index de1d9c5458..98436bc696 100644 --- a/src/KOKKOS/dihedral_class2_kokkos.cpp +++ b/src/KOKKOS/dihedral_class2_kokkos.cpp @@ -69,8 +69,7 @@ void DihedralClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1127,7 +1126,7 @@ void DihedralClass2Kokkos::ev_tally(EV_FLOAT &ev, const int i1, cons namespace LAMMPS_NS { template class DihedralClass2Kokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class DihedralClass2Kokkos; #endif } diff --git a/src/KOKKOS/dihedral_opls_kokkos.cpp b/src/KOKKOS/dihedral_opls_kokkos.cpp index 3f34c2f5f3..f50dea2c36 100644 --- a/src/KOKKOS/dihedral_opls_kokkos.cpp +++ b/src/KOKKOS/dihedral_opls_kokkos.cpp @@ -69,8 +69,7 @@ void DihedralOPLSKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -536,7 +535,7 @@ void DihedralOPLSKokkos::ev_tally(EV_FLOAT &ev, const int i1, const namespace LAMMPS_NS { template class DihedralOPLSKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class DihedralOPLSKokkos; #endif } diff --git a/src/KOKKOS/fix_dpd_energy_kokkos.cpp b/src/KOKKOS/fix_dpd_energy_kokkos.cpp index b12c6a476e..d092cb4802 100644 --- a/src/KOKKOS/fix_dpd_energy_kokkos.cpp +++ b/src/KOKKOS/fix_dpd_energy_kokkos.cpp @@ -90,7 +90,7 @@ void FixDPDenergyKokkos::final_integrate() namespace LAMMPS_NS { template class FixDPDenergyKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixDPDenergyKokkos; #endif } diff --git a/src/KOKKOS/fix_enforce2d_kokkos.cpp b/src/KOKKOS/fix_enforce2d_kokkos.cpp index 26075b269c..346e440f55 100644 --- a/src/KOKKOS/fix_enforce2d_kokkos.cpp +++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp @@ -56,13 +56,13 @@ void FixEnforce2DKokkos::post_force(int vflag) v = atomKK->k_v.view(); f = atomKK->k_f.view(); - if( atomKK->omega_flag ) + if (atomKK->omega_flag) omega = atomKK->k_omega.view(); - if( atomKK->angmom_flag ) + if (atomKK->angmom_flag) angmom = atomKK->k_angmom.view(); - if( atomKK->torque_flag ) + if (atomKK->torque_flag) torque = atomKK->k_torque.view(); @@ -72,9 +72,9 @@ void FixEnforce2DKokkos::post_force(int vflag) if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst; int flag_mask = 0; - if( atomKK->omega_flag ) flag_mask |= 1; - if( atomKK->angmom_flag ) flag_mask |= 2; - if( atomKK->torque_flag ) flag_mask |= 4; + if (atomKK->omega_flag) flag_mask |= 1; + if (atomKK->angmom_flag) flag_mask |= 2; + if (atomKK->torque_flag) flag_mask |= 4; copymode = 1; switch( flag_mask ){ @@ -162,7 +162,7 @@ void FixEnforce2DKokkos::post_force_item( int i ) const namespace LAMMPS_NS { template class FixEnforce2DKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixEnforce2DKokkos; #endif } diff --git a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp index 39f612ec46..2f730d1193 100644 --- a/src/KOKKOS/fix_eos_table_rx_kokkos.cpp +++ b/src/KOKKOS/fix_eos_table_rx_kokkos.cpp @@ -563,7 +563,7 @@ void FixEOStableRXKokkos::create_kokkos_tables() namespace LAMMPS_NS { template class FixEOStableRXKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixEOStableRXKokkos; #endif } diff --git a/src/KOKKOS/fix_freeze_kokkos.cpp b/src/KOKKOS/fix_freeze_kokkos.cpp index b87ec86f8f..fb0c3841e6 100644 --- a/src/KOKKOS/fix_freeze_kokkos.cpp +++ b/src/KOKKOS/fix_freeze_kokkos.cpp @@ -75,7 +75,7 @@ void FixFreezeKokkos::post_force(int vflag) OriginalForce original; Kokkos::parallel_reduce(nlocal, *this, original); copymode = 0; - + foriginal[0] = original.values[0]; foriginal[1] = original.values[1]; foriginal[2] = original.values[2]; @@ -118,7 +118,7 @@ void FixFreezeKokkos::operator()(const int i, OriginalForce &origina namespace LAMMPS_NS { template class FixFreezeKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixFreezeKokkos; #endif } diff --git a/src/KOKKOS/fix_freeze_kokkos.h b/src/KOKKOS/fix_freeze_kokkos.h index 193e011995..3b5bc8e437 100644 --- a/src/KOKKOS/fix_freeze_kokkos.h +++ b/src/KOKKOS/fix_freeze_kokkos.h @@ -26,7 +26,7 @@ FixStyle(freeze/kk/host,FixFreezeKokkos) #include "kokkos_type.h" namespace LAMMPS_NS { - + template class FixFreezeKokkos : public FixFreeze { public: @@ -66,7 +66,7 @@ class FixFreezeKokkos : public FixFreeze { KOKKOS_INLINE_FUNCTION void operator()(const int i, OriginalForce &original) const; - + private: typename ArrayTypes::t_f_array f; typename ArrayTypes::t_f_array torque; diff --git a/src/KOKKOS/fix_gravity_kokkos.cpp b/src/KOKKOS/fix_gravity_kokkos.cpp index 2aff7af56c..5d3b4f62fb 100644 --- a/src/KOKKOS/fix_gravity_kokkos.cpp +++ b/src/KOKKOS/fix_gravity_kokkos.cpp @@ -115,7 +115,7 @@ void FixGravityKokkos::operator()(TagFixGravityMass, const int i, do namespace LAMMPS_NS { template class FixGravityKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixGravityKokkos; #endif } diff --git a/src/KOKKOS/fix_gravity_kokkos.h b/src/KOKKOS/fix_gravity_kokkos.h index cc487a0e2d..9aa9ef803f 100644 --- a/src/KOKKOS/fix_gravity_kokkos.h +++ b/src/KOKKOS/fix_gravity_kokkos.h @@ -50,7 +50,7 @@ class FixGravityKokkos : public FixGravity { typename ArrayTypes::t_int_1d type; typename ArrayTypes::t_int_1d mask; }; - + } // namespace LAMMPS_NS #endif // LMP_FIX_GRAVITY_KOKKOS_H diff --git a/src/KOKKOS/fix_langevin_kokkos.cpp b/src/KOKKOS/fix_langevin_kokkos.cpp index 8c403d3325..0947fee693 100644 --- a/src/KOKKOS/fix_langevin_kokkos.cpp +++ b/src/KOKKOS/fix_langevin_kokkos.cpp @@ -195,8 +195,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else{ + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -204,8 +203,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -214,8 +212,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -223,8 +220,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else{ + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -234,8 +230,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -243,8 +238,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -253,8 +247,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -262,8 +255,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -274,8 +266,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -283,8 +274,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -293,8 +283,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -302,8 +291,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -313,8 +301,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -322,8 +309,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -332,8 +318,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -341,8 +326,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -354,8 +338,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -363,8 +346,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -373,8 +355,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -382,8 +363,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -393,8 +373,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -402,8 +381,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -412,8 +390,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -421,8 +398,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -433,8 +409,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -442,8 +417,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -452,8 +426,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -461,8 +434,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -472,8 +444,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -481,8 +452,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -491,8 +461,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -500,8 +469,7 @@ void FixLangevinKokkos::post_force(int vflag) if (zeroflag) { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_reduce(nlocal,post_functor,s_fsum); - } - else { + } else { FixLangevinKokkosPostForceFunctor post_functor(this); Kokkos::parallel_for(nlocal,post_functor); } @@ -578,7 +546,7 @@ FSUM FixLangevinKokkos::post_force_item(int i) const if (v(i,0) == 0.0) fran[0] = 0.0; if (v(i,1) == 0.0) fran[1] = 0.0; if (v(i,2) == 0.0) fran[2] = 0.0; - }else{ + } else { fdrag[0] = gamma1*v(i,0); fdrag[1] = gamma1*v(i,1); fdrag[2] = gamma1*v(i,2); @@ -806,7 +774,7 @@ void FixLangevinKokkos::cleanup_copy() namespace LAMMPS_NS { template class FixLangevinKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixLangevinKokkos; #endif } diff --git a/src/KOKKOS/fix_momentum_kokkos.cpp b/src/KOKKOS/fix_momentum_kokkos.cpp index 493dffc3d9..38500531ca 100644 --- a/src/KOKKOS/fix_momentum_kokkos.cpp +++ b/src/KOKKOS/fix_momentum_kokkos.cpp @@ -199,7 +199,7 @@ void FixMomentumKokkos::end_of_step() namespace LAMMPS_NS { template class FixMomentumKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixMomentumKokkos; #endif } diff --git a/src/KOKKOS/fix_neigh_history_kokkos.cpp b/src/KOKKOS/fix_neigh_history_kokkos.cpp index d481c20818..5f53950fe6 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.cpp +++ b/src/KOKKOS/fix_neigh_history_kokkos.cpp @@ -77,7 +77,7 @@ template void FixNeighHistoryKokkos::pre_exchange() { copymode = 1; - + h_resize() = 1; while (h_resize() > 0) { FixNeighHistoryKokkosZeroPartnerCountFunctor zero(this); @@ -156,7 +156,7 @@ template void FixNeighHistoryKokkos::post_neighbor() { tag = atomKK->k_tag.view(); - + int inum = pair->list->inum; NeighListKokkos* k_list = static_cast*>(pair->list); d_numneigh = k_list->d_numneigh; @@ -179,7 +179,7 @@ void FixNeighHistoryKokkos::post_neighbor() } copymode = 1; - + FixNeighHistoryKokkosPostNeighborFunctor f(this); Kokkos::parallel_for(inum,f); @@ -251,7 +251,7 @@ void FixNeighHistoryKokkos::grow_arrays(int nmax) k_npartner.template sync(); // force reallocation on host k_partner.template sync(); k_valuepartner.template sync(); - + memoryKK->grow_kokkos(k_npartner,npartner,nmax,"neighbor_history:npartner"); memoryKK->grow_kokkos(k_partner,partner,nmax,maxpartner,"neighbor_history:partner"); memoryKK->grow_kokkos(k_valuepartner,valuepartner,nmax,dnum*maxpartner,"neighbor_history:valuepartner"); @@ -329,7 +329,7 @@ int FixNeighHistoryKokkos::unpack_exchange(int nlocal, double *buf) namespace LAMMPS_NS { template class FixNeighHistoryKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNeighHistoryKokkos; #endif } diff --git a/src/KOKKOS/fix_neigh_history_kokkos.h b/src/KOKKOS/fix_neigh_history_kokkos.h index d5bb1c3971..ba594a567f 100644 --- a/src/KOKKOS/fix_neigh_history_kokkos.h +++ b/src/KOKKOS/fix_neigh_history_kokkos.h @@ -61,11 +61,11 @@ class FixNeighHistoryKokkos : public FixNeighHistory { typename ArrayTypes::t_neighbors_2d d_neighbors; typename ArrayTypes::t_int_1d_randomread d_ilist; typename ArrayTypes::t_int_1d_randomread d_numneigh; - + typename ArrayTypes::t_tagint_1d tag; typename ArrayTypes::t_int_1d d_npartner; typename ArrayTypes::t_tagint_2d d_partner; - typename ArrayTypes::t_float_2d d_valuepartner; + typename ArrayTypes::t_float_2d d_valuepartner; typename ArrayTypes::t_int_scalar d_resize; typename ArrayTypes::t_int_scalar h_resize; diff --git a/src/KOKKOS/fix_nh_kokkos.cpp b/src/KOKKOS/fix_nh_kokkos.cpp index 42d421e92e..ba6e8919ea 100644 --- a/src/KOKKOS/fix_nh_kokkos.cpp +++ b/src/KOKKOS/fix_nh_kokkos.cpp @@ -269,7 +269,10 @@ void FixNHKokkos::final_integrate() //atomKK->sync(pressure->execution_space,pressure->datamask_read); //atomKK->modified(pressure->execution_space,pressure->datamask_modify); if (pstyle == ISO) pressure->compute_scalar(); - else pressure->compute_vector(); + else { + temperature->compute_vector(); + pressure->compute_vector(); + } couple(); pressure->addstep(update->ntimestep+1); } @@ -730,7 +733,7 @@ void FixNHKokkos::pre_exchange() namespace LAMMPS_NS { template class FixNHKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNHKokkos; #endif } diff --git a/src/KOKKOS/fix_nph_kokkos.cpp b/src/KOKKOS/fix_nph_kokkos.cpp index ed825ad9ee..c5072e6ae9 100644 --- a/src/KOKKOS/fix_nph_kokkos.cpp +++ b/src/KOKKOS/fix_nph_kokkos.cpp @@ -71,7 +71,7 @@ FixNPHKokkos::FixNPHKokkos(LAMMPS *lmp, int narg, char **arg) : namespace LAMMPS_NS { template class FixNPHKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNPHKokkos; #endif } diff --git a/src/KOKKOS/fix_npt_kokkos.cpp b/src/KOKKOS/fix_npt_kokkos.cpp index b33e733aee..c488c8e4f3 100644 --- a/src/KOKKOS/fix_npt_kokkos.cpp +++ b/src/KOKKOS/fix_npt_kokkos.cpp @@ -71,7 +71,7 @@ FixNPTKokkos::FixNPTKokkos(LAMMPS *lmp, int narg, char **arg) : namespace LAMMPS_NS { template class FixNPTKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNPTKokkos; #endif } diff --git a/src/KOKKOS/fix_nve_kokkos.cpp b/src/KOKKOS/fix_nve_kokkos.cpp index 621f16f420..052bf411d6 100644 --- a/src/KOKKOS/fix_nve_kokkos.cpp +++ b/src/KOKKOS/fix_nve_kokkos.cpp @@ -172,7 +172,7 @@ void FixNVEKokkos::cleanup_copy() namespace LAMMPS_NS { template class FixNVEKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNVEKokkos; #endif } diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.cpp b/src/KOKKOS/fix_nve_sphere_kokkos.cpp index d636f56b20..95945a858f 100644 --- a/src/KOKKOS/fix_nve_sphere_kokkos.cpp +++ b/src/KOKKOS/fix_nve_sphere_kokkos.cpp @@ -75,7 +75,7 @@ void FixNVESphereKokkos::initial_integrate(int vflag) int nlocal = atom->nlocal; if (igroup == atom->firstgroup) nlocal = atom->nfirst; - FixNVESphereKokkosInitialIntegrateFunctor f(this); + FixNVESphereKokkosInitialIntegrateFunctor f(this); Kokkos::parallel_for(nlocal,f); } @@ -95,7 +95,7 @@ void FixNVESphereKokkos::initial_integrate_item(const int i) const x(i,0) += dtv * v(i,0); x(i,1) += dtv * v(i,1); x(i,2) += dtv * v(i,2); - + const double dtirotate = dtfrotate / (radius(i)*radius(i)*rmass(i)); omega(i,0) += dtirotate * torque(i,0); omega(i,1) += dtirotate * torque(i,1); @@ -139,7 +139,7 @@ void FixNVESphereKokkos::final_integrate_item(const int i) const v(i,0) += dtfm * f(i,0); v(i,1) += dtfm * f(i,1); v(i,2) += dtfm * f(i,2); - + const double dtirotate = dtfrotate / (radius(i)*radius(i)*rmass(i)); omega(i,0) += dtirotate * torque(i,0); omega(i,1) += dtirotate * torque(i,1); @@ -149,7 +149,7 @@ void FixNVESphereKokkos::final_integrate_item(const int i) const namespace LAMMPS_NS { template class FixNVESphereKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNVESphereKokkos; #endif } diff --git a/src/KOKKOS/fix_nve_sphere_kokkos.h b/src/KOKKOS/fix_nve_sphere_kokkos.h index 382e530319..87a1835eb7 100644 --- a/src/KOKKOS/fix_nve_sphere_kokkos.h +++ b/src/KOKKOS/fix_nve_sphere_kokkos.h @@ -26,7 +26,7 @@ FixStyle(nve/sphere/kk/host,FixNVESphereKokkos) #include "kokkos_type.h" namespace LAMMPS_NS { - + template class FixNVESphereKokkos : public FixNVESphere { public: @@ -36,7 +36,7 @@ class FixNVESphereKokkos : public FixNVESphere { void init(); void initial_integrate(int); void final_integrate(); - + KOKKOS_INLINE_FUNCTION void initial_integrate_item(const int i) const; KOKKOS_INLINE_FUNCTION diff --git a/src/KOKKOS/fix_nvt_kokkos.cpp b/src/KOKKOS/fix_nvt_kokkos.cpp index 8b2d936274..4db42a62fb 100644 --- a/src/KOKKOS/fix_nvt_kokkos.cpp +++ b/src/KOKKOS/fix_nvt_kokkos.cpp @@ -52,7 +52,7 @@ FixNVTKokkos::FixNVTKokkos(LAMMPS *lmp, int narg, char **arg) : namespace LAMMPS_NS { template class FixNVTKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixNVTKokkos; #endif } diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.cpp b/src/KOKKOS/fix_qeq_reax_kokkos.cpp index 578afd2077..9969ab7257 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.cpp +++ b/src/KOKKOS/fix_qeq_reax_kokkos.cpp @@ -1115,7 +1115,7 @@ int FixQEqReaxKokkos::pack_forward_comm(int n, int *list, double *bu { int m; - if( pack_flag == 1) + if (pack_flag == 1) for(m = 0; m < n; m++) buf[m] = h_d[list[m]]; else if( pack_flag == 2 ) for(m = 0; m < n; m++) buf[m] = h_s[list[m]]; @@ -1134,7 +1134,7 @@ void FixQEqReaxKokkos::unpack_forward_comm(int n, int first, double { int i, m; - if( pack_flag == 1) + if (pack_flag == 1) for(m = 0, i = first; m < n; m++, i++) h_d[i] = buf[m]; else if( pack_flag == 2) for(m = 0, i = first; m < n; m++, i++) h_s[i] = buf[m]; @@ -1266,7 +1266,7 @@ int FixQEqReaxKokkos::unpack_exchange(int nlocal, double *buf) namespace LAMMPS_NS { template class FixQEqReaxKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixQEqReaxKokkos; #endif } diff --git a/src/KOKKOS/fix_rx_kokkos.cpp b/src/KOKKOS/fix_rx_kokkos.cpp index f636f6454d..80333e1e9b 100644 --- a/src/KOKKOS/fix_rx_kokkos.cpp +++ b/src/KOKKOS/fix_rx_kokkos.cpp @@ -2276,7 +2276,7 @@ void FixRxKokkos::unpack_reverse_comm(int n, int *list, double *buf) namespace LAMMPS_NS { template class FixRxKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixRxKokkos; #endif } diff --git a/src/KOKKOS/fix_setforce_kokkos.cpp b/src/KOKKOS/fix_setforce_kokkos.cpp index 5150c71249..5d15b88d76 100644 --- a/src/KOKKOS/fix_setforce_kokkos.cpp +++ b/src/KOKKOS/fix_setforce_kokkos.cpp @@ -184,7 +184,7 @@ void FixSetForceKokkos::operator()(TagFixSetForceNonConstant, const namespace LAMMPS_NS { template class FixSetForceKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixSetForceKokkos; #endif } diff --git a/src/KOKKOS/fix_shardlow_kokkos.cpp b/src/KOKKOS/fix_shardlow_kokkos.cpp index 99e51ebe38..968f877abd 100644 --- a/src/KOKKOS/fix_shardlow_kokkos.cpp +++ b/src/KOKKOS/fix_shardlow_kokkos.cpp @@ -808,7 +808,7 @@ double FixShardlowKokkos::memory_usage() namespace LAMMPS_NS { template class FixShardlowKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixShardlowKokkos; #endif } diff --git a/src/KOKKOS/fix_wall_lj93_kokkos.cpp b/src/KOKKOS/fix_wall_lj93_kokkos.cpp index 3aaa45f8a8..5dbb054175 100644 --- a/src/KOKKOS/fix_wall_lj93_kokkos.cpp +++ b/src/KOKKOS/fix_wall_lj93_kokkos.cpp @@ -98,7 +98,7 @@ void FixWallLJ93Kokkos::wall_particle_item(int i, value_type ewall) namespace LAMMPS_NS { template class FixWallLJ93Kokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixWallLJ93Kokkos; #endif } diff --git a/src/KOKKOS/fix_wall_reflect_kokkos.cpp b/src/KOKKOS/fix_wall_reflect_kokkos.cpp index 2516ac6577..75a5c1a81e 100644 --- a/src/KOKKOS/fix_wall_reflect_kokkos.cpp +++ b/src/KOKKOS/fix_wall_reflect_kokkos.cpp @@ -107,7 +107,7 @@ void FixWallReflectKokkos::operator()(TagFixWallReflectPostIntegrate namespace LAMMPS_NS { template class FixWallReflectKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class FixWallReflectKokkos; #endif } diff --git a/src/KOKKOS/gridcomm_kokkos.cpp b/src/KOKKOS/gridcomm_kokkos.cpp index 64a9d6992f..14b84a5733 100644 --- a/src/KOKKOS/gridcomm_kokkos.cpp +++ b/src/KOKKOS/gridcomm_kokkos.cpp @@ -652,7 +652,7 @@ double GridCommKokkos::memory_usage() namespace LAMMPS_NS { template class GridCommKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class GridCommKokkos; #endif } diff --git a/src/KOKKOS/improper_class2_kokkos.cpp b/src/KOKKOS/improper_class2_kokkos.cpp index 2a7e8076d4..ad32e6da4e 100644 --- a/src/KOKKOS/improper_class2_kokkos.cpp +++ b/src/KOKKOS/improper_class2_kokkos.cpp @@ -71,8 +71,7 @@ void ImproperClass2Kokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1134,7 +1133,7 @@ void ImproperClass2Kokkos::ev_tally(EV_FLOAT &ev, const int i1, cons namespace LAMMPS_NS { template class ImproperClass2Kokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class ImproperClass2Kokkos; #endif } diff --git a/src/KOKKOS/improper_harmonic_kokkos.cpp b/src/KOKKOS/improper_harmonic_kokkos.cpp index b364d0b0c7..bb397a2c2f 100644 --- a/src/KOKKOS/improper_harmonic_kokkos.cpp +++ b/src/KOKKOS/improper_harmonic_kokkos.cpp @@ -71,8 +71,7 @@ void ImproperHarmonicKokkos::compute(int eflag_in, int vflag_in) eflag = eflag_in; vflag = vflag_in; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -484,7 +483,7 @@ void ImproperHarmonicKokkos::ev_tally(EV_FLOAT &ev, const int i1, co namespace LAMMPS_NS { template class ImproperHarmonicKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class ImproperHarmonicKokkos; #endif } diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 9973b5a688..295fddc6e7 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -26,7 +26,7 @@ #include "error.h" #include "memory_kokkos.h" -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA // for detecting GPU-direct support: // the function int have_gpu_direct() @@ -55,7 +55,7 @@ GPU_DIRECT_UNKNOWN GPU_DIRECT_UNKNOWN #endif -#endif // KOKKOS_HAVE_CUDA +#endif // KOKKOS_ENABLE_CUDA using namespace LAMMPS_NS; @@ -92,7 +92,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } else if (strcmp(arg[iarg],"g") == 0 || strcmp(arg[iarg],"gpus") == 0) { -#ifndef KOKKOS_HAVE_CUDA +#ifndef KOKKOS_ENABLE_CUDA error->all(FLERR,"GPUs are requested but Kokkos has not been compiled for CUDA"); #endif if (iarg+2 > narg) error->all(FLERR,"Invalid Kokkos command-line args"); @@ -142,7 +142,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) if (logfile) fprintf(logfile," will use up to %d GPU(s) per node\n",ngpu); } -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA if (ngpu <= 0) error->all(FLERR,"Kokkos has been compiled for CUDA but no GPUs are requested"); @@ -166,7 +166,7 @@ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) } #endif -#ifndef KOKKOS_HAVE_SERIAL +#ifndef KOKKOS_ENABLE_SERIAL if (num_threads == 1) error->warning(FLERR,"When using a single thread, the Kokkos Serial backend " "(i.e. Makefile.kokkos_mpi_only) gives better performance " diff --git a/src/KOKKOS/kokkos.h b/src/KOKKOS/kokkos.h index e1e17a425a..cd429d5c1c 100644 --- a/src/KOKKOS/kokkos.h +++ b/src/KOKKOS/kokkos.h @@ -46,10 +46,10 @@ class KokkosLMP : protected Pointers { int need_dup() { int value = 0; - + if (neighflag == HALFTHREAD) value = NeedDup::value; - + return value; } diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index b88c92ff73..ff96684edc 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -24,7 +24,7 @@ enum{FULL=1u,HALFTHREAD=2u,HALF=4u,N2=8u}; -#if defined(KOKKOS_HAVE_CXX11) +#if defined(KOKKOS_ENABLE_CXX11) #undef ISFINITE #define ISFINITE(x) std::isfinite(x) #endif @@ -201,7 +201,7 @@ template<> struct ExecutionSpaceFromDevice { static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Host; }; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template<> struct ExecutionSpaceFromDevice { static const LAMMPS_NS::ExecutionSpace space = LAMMPS_NS::Device; @@ -776,7 +776,7 @@ typedef tdual_int_64::t_dev_um t_int_64_um; }; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template <> struct ArrayTypes { @@ -1074,7 +1074,7 @@ void memset_kokkos (ViewType &view) { #ifndef KOKKOS_USING_DEPRECATED_VIEW Kokkos::parallel_for(view.span()*sizeof(typename ViewType::value_type)/4, f); #else - Kokkos::parallel_for(view.capacity()*sizeof(typename ViewType::value_type)/4, f); + Kokkos::parallel_for(view.span()*sizeof(typename ViewType::value_type)/4, f); #endif ViewType::execution_space::fence(); } @@ -1087,12 +1087,12 @@ struct params_lj_coul { F_FLOAT cut_ljsq,cut_coulsq,lj1,lj2,lj3,lj4,offset; }; -#if defined(KOKKOS_HAVE_CXX11) +#if defined(KOKKOS_ENABLE_CXX11) #undef ISFINITE #define ISFINITE(x) std::isfinite(x) #endif -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA #define LAMMPS_LAMBDA [=] __device__ #else #define LAMMPS_LAMBDA [=] diff --git a/src/KOKKOS/nbin_kokkos.cpp b/src/KOKKOS/nbin_kokkos.cpp index c35c349675..090519a5a8 100644 --- a/src/KOKKOS/nbin_kokkos.cpp +++ b/src/KOKKOS/nbin_kokkos.cpp @@ -146,7 +146,7 @@ void NBinKokkos::binatomsItem(const int &i) const namespace LAMMPS_NS { template class NBinKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NBinKokkos; #endif } diff --git a/src/KOKKOS/nbin_ssa_kokkos.cpp b/src/KOKKOS/nbin_ssa_kokkos.cpp index d040ee2c83..ecf0e08535 100644 --- a/src/KOKKOS/nbin_ssa_kokkos.cpp +++ b/src/KOKKOS/nbin_ssa_kokkos.cpp @@ -301,7 +301,7 @@ void NBinSSAKokkos::sortBin( namespace LAMMPS_NS { template class NBinSSAKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NBinSSAKokkos; #endif } diff --git a/src/KOKKOS/neigh_bond_kokkos.cpp b/src/KOKKOS/neigh_bond_kokkos.cpp index 615dc94ee2..05a6fd605c 100644 --- a/src/KOKKOS/neigh_bond_kokkos.cpp +++ b/src/KOKKOS/neigh_bond_kokkos.cpp @@ -1301,7 +1301,7 @@ void NeighBondKokkos::update_domain_variables() namespace LAMMPS_NS { template class NeighBondKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NeighBondKokkos; #endif } diff --git a/src/KOKKOS/neigh_list_kokkos.cpp b/src/KOKKOS/neigh_list_kokkos.cpp index 93cf0af937..1c78fe3a68 100644 --- a/src/KOKKOS/neigh_list_kokkos.cpp +++ b/src/KOKKOS/neigh_list_kokkos.cpp @@ -53,7 +53,7 @@ void NeighListKokkos::grow(int nmax) namespace LAMMPS_NS { template class NeighListKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NeighListKokkos; #endif } diff --git a/src/KOKKOS/npair_copy_kokkos.cpp b/src/KOKKOS/npair_copy_kokkos.cpp index 8702816033..7dde05745c 100644 --- a/src/KOKKOS/npair_copy_kokkos.cpp +++ b/src/KOKKOS/npair_copy_kokkos.cpp @@ -53,7 +53,7 @@ void NPairCopyKokkos::build(NeighList *list) namespace LAMMPS_NS { template class NPairCopyKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NPairCopyKokkos; #endif } diff --git a/src/KOKKOS/npair_halffull_kokkos.cpp b/src/KOKKOS/npair_halffull_kokkos.cpp index 67481985da..cc8f663ef2 100644 --- a/src/KOKKOS/npair_halffull_kokkos.cpp +++ b/src/KOKKOS/npair_halffull_kokkos.cpp @@ -121,7 +121,7 @@ void NPairHalffullKokkos::operator()(TagNPairHalffullCompute, namespace LAMMPS_NS { template class NPairHalffullKokkos; template class NPairHalffullKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NPairHalffullKokkos; template class NPairHalffullKokkos; #endif diff --git a/src/KOKKOS/npair_kokkos.cpp b/src/KOKKOS/npair_kokkos.cpp index 6f75e6cabc..5e1b7b0414 100644 --- a/src/KOKKOS/npair_kokkos.cpp +++ b/src/KOKKOS/npair_kokkos.cpp @@ -187,7 +187,7 @@ void NPairKokkos::build(NeighList *list_) Kokkos::deep_copy(data.resize, data.h_resize); Kokkos::deep_copy(data.new_maxneighs, data.h_new_maxneighs); -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA #define BINS_PER_BLOCK 2 const int factor = atoms_per_bin<64?2:1; Kokkos::TeamPolicy config((mbins+factor-1)/factor,atoms_per_bin*factor); @@ -202,7 +202,7 @@ void NPairKokkos::build(NeighList *list_) if (newton_pair) { if (SIZE) { NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA if (ExecutionSpaceFromDevice::space == Device) Kokkos::parallel_for(config, f); else @@ -212,7 +212,7 @@ void NPairKokkos::build(NeighList *list_) #endif } else { NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA if (ExecutionSpaceFromDevice::space == Device) Kokkos::parallel_for(config, f); else @@ -224,7 +224,7 @@ void NPairKokkos::build(NeighList *list_) } else { if (SIZE) { NPairKokkosBuildFunctorSize f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA if (ExecutionSpaceFromDevice::space == Device) Kokkos::parallel_for(config, f); else @@ -234,7 +234,7 @@ void NPairKokkos::build(NeighList *list_) #endif } else { NPairKokkosBuildFunctor f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor); -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA if (ExecutionSpaceFromDevice::space == Device) Kokkos::parallel_for(config, f); else @@ -383,7 +383,7 @@ void NeighborKokkosExecute:: if (which == 0){ if(n:: if (which == 0){ if(n:: /* ---------------------------------------------------------------------- */ -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA extern __shared__ X_FLOAT sharedmem[]; /* ---------------------------------------------------------------------- */ @@ -567,7 +567,7 @@ void NeighborKokkosExecute::build_ItemCuda(typename Kokkos::TeamPoli if (which == 0){ if(n::build_ItemCuda(typename Kokkos::TeamPoli if (which == 0){ if(n:: if (which == 0){ if(n:: /* ---------------------------------------------------------------------- */ -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template template __device__ inline void NeighborKokkosExecute::build_ItemSizeCuda(typename Kokkos::TeamPolicy::member_type dev) const @@ -1093,7 +1093,7 @@ template class NPairKokkos; template class NPairKokkos; template class NPairKokkos; template class NPairKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NPairKokkos; template class NPairKokkos; template class NPairKokkos; diff --git a/src/KOKKOS/npair_kokkos.h b/src/KOKKOS/npair_kokkos.h index 970e40c9fc..62138bd524 100644 --- a/src/KOKKOS/npair_kokkos.h +++ b/src/KOKKOS/npair_kokkos.h @@ -311,7 +311,7 @@ class NeighborKokkosExecute KOKKOS_FUNCTION void build_ItemSize(const int &i) const; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template __device__ inline void build_ItemCuda(typename Kokkos::TeamPolicy::member_type dev) const; @@ -388,7 +388,7 @@ struct NPairKokkosBuildFunctor { void operator() (const int & i) const { c.template build_Item(i); } -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA __device__ inline void operator() (typename Kokkos::TeamPolicy::member_type dev) const { @@ -449,7 +449,7 @@ struct NPairKokkosBuildFunctorSize { c.template build_ItemSize(i); } -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA __device__ inline void operator() (typename Kokkos::TeamPolicy::member_type dev) const { c.template build_ItemSizeCuda(dev); diff --git a/src/KOKKOS/npair_skip_kokkos.cpp b/src/KOKKOS/npair_skip_kokkos.cpp index c537afaa6b..e614e624c9 100644 --- a/src/KOKKOS/npair_skip_kokkos.cpp +++ b/src/KOKKOS/npair_skip_kokkos.cpp @@ -151,7 +151,7 @@ void NPairSkipKokkos::operator()(TagNPairSkipCountLocal, const int & namespace LAMMPS_NS { template class NPairSkipKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NPairSkipKokkos; #endif } diff --git a/src/KOKKOS/npair_ssa_kokkos.cpp b/src/KOKKOS/npair_ssa_kokkos.cpp index ba941b8e54..5234c4e6d2 100644 --- a/src/KOKKOS/npair_ssa_kokkos.cpp +++ b/src/KOKKOS/npair_ssa_kokkos.cpp @@ -588,7 +588,7 @@ void NPairSSAKokkosExecute::build_locals_onePhase(const bool firstTr if (which == 0){ if(n::build_ghosts_onePhase(int workPhase) con if (which == 0){ if(n::build_ghosts_onePhase(int workPhase) con namespace LAMMPS_NS { template class NPairSSAKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class NPairSSAKokkos; #endif } diff --git a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp index 9c12d2c978..57ac3a9c57 100644 --- a/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_cut_kokkos.cpp @@ -92,8 +92,7 @@ void PairBuckCoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -360,7 +359,7 @@ double PairBuckCoulCutKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairBuckCoulCutKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairBuckCoulCutKokkos; #endif } diff --git a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp index 4978d3d7fc..349c4c0601 100644 --- a/src/KOKKOS/pair_buck_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_buck_coul_long_kokkos.cpp @@ -111,8 +111,7 @@ void PairBuckCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -522,7 +521,7 @@ double PairBuckCoulLongKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairBuckCoulLongKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairBuckCoulLongKokkos; #endif } diff --git a/src/KOKKOS/pair_buck_kokkos.cpp b/src/KOKKOS/pair_buck_kokkos.cpp index 8785700186..02c02c986e 100644 --- a/src/KOKKOS/pair_buck_kokkos.cpp +++ b/src/KOKKOS/pair_buck_kokkos.cpp @@ -81,8 +81,7 @@ void PairBuckKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -274,7 +273,7 @@ double PairBuckKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairBuckKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairBuckKokkos; #endif } diff --git a/src/KOKKOS/pair_coul_cut_kokkos.cpp b/src/KOKKOS/pair_coul_cut_kokkos.cpp index b6e36d4f0d..54ba0b63ce 100644 --- a/src/KOKKOS/pair_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_coul_cut_kokkos.cpp @@ -80,8 +80,7 @@ void PairCoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -280,7 +279,7 @@ double PairCoulCutKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairCoulCutKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairCoulCutKokkos; #endif } diff --git a/src/KOKKOS/pair_coul_debye_kokkos.cpp b/src/KOKKOS/pair_coul_debye_kokkos.cpp index 5d15be7d76..8966e30394 100644 --- a/src/KOKKOS/pair_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_coul_debye_kokkos.cpp @@ -87,8 +87,7 @@ void PairCoulDebyeKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -323,7 +322,7 @@ double PairCoulDebyeKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairCoulDebyeKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairCoulDebyeKokkos; #endif } diff --git a/src/KOKKOS/pair_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_coul_dsf_kokkos.cpp index a714f665f7..748fed71a7 100644 --- a/src/KOKKOS/pair_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_dsf_kokkos.cpp @@ -80,8 +80,7 @@ void PairCoulDSFKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -422,7 +421,7 @@ int PairCoulDSFKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairCoulDSFKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairCoulDSFKokkos; #endif } diff --git a/src/KOKKOS/pair_coul_long_kokkos.cpp b/src/KOKKOS/pair_coul_long_kokkos.cpp index 1e8c6c5f4e..a21cb050ff 100644 --- a/src/KOKKOS/pair_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_coul_long_kokkos.cpp @@ -104,8 +104,7 @@ void PairCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -471,7 +470,7 @@ double PairCoulLongKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairCoulLongKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairCoulLongKokkos; #endif } diff --git a/src/KOKKOS/pair_coul_wolf_kokkos.cpp b/src/KOKKOS/pair_coul_wolf_kokkos.cpp index 2bff824c3d..20391d9530 100644 --- a/src/KOKKOS/pair_coul_wolf_kokkos.cpp +++ b/src/KOKKOS/pair_coul_wolf_kokkos.cpp @@ -75,8 +75,7 @@ void PairCoulWolfKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -424,7 +423,7 @@ int PairCoulWolfKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairCoulWolfKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairCoulWolfKokkos; #endif } diff --git a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp index 3282c9da1e..a44ef1790e 100644 --- a/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp +++ b/src/KOKKOS/pair_dpd_fdt_energy_kokkos.cpp @@ -165,8 +165,7 @@ void PairDPDfdtEnergyKokkos::compute(int eflag_in, int vflag_in) vflag = vflag_in; if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -795,7 +794,7 @@ int PairDPDfdtEnergyKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairDPDfdtEnergyKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairDPDfdtEnergyKokkos; #endif } diff --git a/src/KOKKOS/pair_eam_alloy_kokkos.cpp b/src/KOKKOS/pair_eam_alloy_kokkos.cpp index e198ddb85a..b580f00ed0 100644 --- a/src/KOKKOS/pair_eam_alloy_kokkos.cpp +++ b/src/KOKKOS/pair_eam_alloy_kokkos.cpp @@ -74,8 +74,7 @@ void PairEAMAlloyKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1199,7 +1198,7 @@ void PairEAMAlloyKokkos::file2array_alloy() namespace LAMMPS_NS { template class PairEAMAlloyKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairEAMAlloyKokkos; #endif } diff --git a/src/KOKKOS/pair_eam_fs_kokkos.cpp b/src/KOKKOS/pair_eam_fs_kokkos.cpp index f5e4445db3..1b1ec5c31e 100644 --- a/src/KOKKOS/pair_eam_fs_kokkos.cpp +++ b/src/KOKKOS/pair_eam_fs_kokkos.cpp @@ -74,8 +74,7 @@ void PairEAMFSKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1208,7 +1207,7 @@ void PairEAMFSKokkos::file2array_fs() namespace LAMMPS_NS { template class PairEAMFSKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairEAMFSKokkos; #endif } diff --git a/src/KOKKOS/pair_eam_kokkos.cpp b/src/KOKKOS/pair_eam_kokkos.cpp index 6ef3d99ac3..d423f2c927 100644 --- a/src/KOKKOS/pair_eam_kokkos.cpp +++ b/src/KOKKOS/pair_eam_kokkos.cpp @@ -68,8 +68,7 @@ void PairEAMKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -899,7 +898,7 @@ void PairEAMKokkos::ev_tally(EV_FLOAT &ev, const int &i, const int & namespace LAMMPS_NS { template class PairEAMKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairEAMKokkos; #endif } diff --git a/src/KOKKOS/pair_exp6_rx_kokkos.cpp b/src/KOKKOS/pair_exp6_rx_kokkos.cpp index f38feea5f4..fa10c6d30f 100644 --- a/src/KOKKOS/pair_exp6_rx_kokkos.cpp +++ b/src/KOKKOS/pair_exp6_rx_kokkos.cpp @@ -147,8 +147,7 @@ void PairExp6rxKokkos::compute(int eflag_in, int vflag_in) vflag = vflag_in; if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -232,7 +231,7 @@ void PairExp6rxKokkos::compute(int eflag_in, int vflag_in) } else Kokkos::parallel_for(Kokkos::RangePolicy(0,np_total),*this); -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA Kokkos::parallel_for(Kokkos::RangePolicy(0,np_total),*this); #else int errorFlag = 0; @@ -277,7 +276,7 @@ void PairExp6rxKokkos::compute(int eflag_in, int vflag_in) EV_FLOAT ev; -#ifdef KOKKOS_HAVE_CUDA // Use atomics +#ifdef KOKKOS_ENABLE_CUDA // Use atomics if (neighflag == HALF) { if (newton_pair) { @@ -814,7 +813,7 @@ void PairExp6rxKokkos::operator()(TagPairExp6rxComputeNoAtomics unique_token_type; unique_token_type unique_token; @@ -1156,7 +1155,7 @@ void PairExp6rxKokkos::operator()(TagPairExp6rxComputeNoAtomics::vectorized_operator(const int &ii, EV_FLOAT& Kokkos::View::value> > a_uCGnew = uCGnew; int tid = 0; -#ifndef KOKKOS_HAVE_CUDA +#ifndef KOKKOS_ENABLE_CUDA typedef Kokkos::Experimental::UniqueToken< DeviceType, Kokkos::Experimental::UniqueTokenScope::Global> unique_token_type; unique_token_type unique_token; @@ -1623,7 +1622,7 @@ void PairExp6rxKokkos::vectorized_operator(const int &ii, EV_FLOAT& t_uCGnew(tid,i) += uCGnew_i; } -#ifndef KOKKOS_HAVE_CUDA +#ifndef KOKKOS_ENABLE_CUDA unique_token.release(tid); #endif } @@ -2128,7 +2127,7 @@ void partition_range( const int begin, const int end, int &thread_begin, int &th /* ---------------------------------------------------------------------- */ -#ifndef KOKKOS_HAVE_CUDA +#ifndef KOKKOS_ENABLE_CUDA template template void PairExp6rxKokkos::getMixingWeightsVect(const int np_total, int errorFlag, @@ -2654,7 +2653,7 @@ int PairExp6rxKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairExp6rxKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairExp6rxKokkos; #endif } diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp index cd8beed583..068580b525 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.cpp @@ -111,8 +111,7 @@ void PairGranHookeHistoryKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); int shearupdate = 1; if (update->setupflag) shearupdate = 0; @@ -331,7 +330,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC const LMP_FLOAT imass = rmass[i]; const LMP_FLOAT irad = radius[i]; const int jnum = d_numneigh_touch[i]; - + F_FLOAT fx_i = 0.0; F_FLOAT fy_i = 0.0; F_FLOAT fz_i = 0.0; @@ -343,7 +342,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC for (int jj = 0; jj < jnum; jj++) { const int m = d_neighbors_touch(i, jj); const int j = d_neighbors(i, m) & NEIGHMASK; - + const X_FLOAT delx = xtmp - x(j,0); const X_FLOAT dely = ytmp - x(j,1); const X_FLOAT delz = ztmp - x(j,2); @@ -363,16 +362,16 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC V_FLOAT vr1 = v(i,0) - v(j,0); V_FLOAT vr2 = v(i,1) - v(j,1); V_FLOAT vr3 = v(i,2) - v(j,2); - + // normal component V_FLOAT vnnr = vr1*delx + vr2*dely + vr3*delz; V_FLOAT vn1 = delx*vnnr * rsqinv; V_FLOAT vn2 = dely*vnnr * rsqinv; V_FLOAT vn3 = delz*vnnr * rsqinv; - + // tangential component - + V_FLOAT vt1 = vr1 - vn1; V_FLOAT vt2 = vr2 - vn2; V_FLOAT vt3 = vr3 - vn3; @@ -467,7 +466,7 @@ void PairGranHookeHistoryKokkos::operator()(TagPairGranHookeHistoryC torquex_i -= irad*tor1; torquey_i -= irad*tor2; torquez_i -= irad*tor3; - + if (NEWTON_PAIR || j < nlocal) { a_f(j,0) -= fx; a_f(j,1) -= fy; @@ -550,7 +549,7 @@ void PairGranHookeHistoryKokkos::ev_tally_xyz_atom(EV_FLOAT &ev, int F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const { - Kokkos::View::value> > v_vatom = k_vatom.view(); + Kokkos::View::value> > v_vatom = k_vatom.view(); F_FLOAT v[6]; @@ -581,7 +580,7 @@ void PairGranHookeHistoryKokkos::ev_tally_xyz_atom(EV_FLOAT &ev, int namespace LAMMPS_NS { template class PairGranHookeHistoryKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairGranHookeHistoryKokkos; #endif } diff --git a/src/KOKKOS/pair_gran_hooke_history_kokkos.h b/src/KOKKOS/pair_gran_hooke_history_kokkos.h index 822b9203a4..8d1778e091 100644 --- a/src/KOKKOS/pair_gran_hooke_history_kokkos.h +++ b/src/KOKKOS/pair_gran_hooke_history_kokkos.h @@ -30,7 +30,7 @@ namespace LAMMPS_NS { template class FixNeighHistoryKokkos; - + template struct TagPairGranHookeHistoryCompute {}; @@ -68,7 +68,7 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { void ev_tally_xyz_atom(EV_FLOAT &ev, int i, int j, F_FLOAT fx, F_FLOAT fy, F_FLOAT fz, X_FLOAT delx, X_FLOAT dely, X_FLOAT delz) const; - + protected: typename AT::t_x_array_randomread x; typename AT::t_x_array c_x; @@ -96,7 +96,7 @@ class PairGranHookeHistoryKokkos : public PairGranHookeHistory { typename AT::t_neighbors_2d d_neighbors_touch; typename AT::t_int_1d d_numneigh_touch; - + int newton_pair; double special_lj[4]; diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp index 03ad77c34a..00df4a8f3c 100644 --- a/src/KOKKOS/pair_hybrid_kokkos.cpp +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -78,9 +78,7 @@ void PairHybridKokkos::compute(int eflag, int vflag) if (no_virial_fdotr_compute && vflag % 4 == 2) vflag = 1 + vflag/4 * 4; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // check if global component of incoming vflag = 2 // if so, reset vflag passed to substyle as if it were 0 diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp index d0d290d1f1..510740112a 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_implicit_kokkos.cpp @@ -112,8 +112,7 @@ void PairLJCharmmCoulCharmmImplicitKokkos::compute(int eflag_in, int if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -528,7 +527,7 @@ double PairLJCharmmCoulCharmmImplicitKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCharmmCoulCharmmImplicitKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCharmmCoulCharmmImplicitKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp index 2203dfa2a0..51c96354f9 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_charmm_kokkos.cpp @@ -112,8 +112,7 @@ void PairLJCharmmCoulCharmmKokkos::compute(int eflag_in, int vflag_i if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -529,7 +528,7 @@ double PairLJCharmmCoulCharmmKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCharmmCoulCharmmKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCharmmCoulCharmmKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp index e1ecfbac3c..22faa98935 100644 --- a/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_charmm_coul_long_kokkos.cpp @@ -112,8 +112,7 @@ void PairLJCharmmCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -536,7 +535,7 @@ double PairLJCharmmCoulLongKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCharmmCoulLongKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCharmmCoulLongKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp index abd0183e21..60d480188b 100644 --- a/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_cut_kokkos.cpp @@ -89,8 +89,7 @@ void PairLJClass2CoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -364,7 +363,7 @@ double PairLJClass2CoulCutKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJClass2CoulCutKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJClass2CoulCutKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp index 5f850689d4..4c8aea8e92 100644 --- a/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_coul_long_kokkos.cpp @@ -97,8 +97,7 @@ void PairLJClass2CoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -517,7 +516,7 @@ double PairLJClass2CoulLongKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJClass2CoulLongKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJClass2CoulLongKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_class2_kokkos.cpp b/src/KOKKOS/pair_lj_class2_kokkos.cpp index 063753f1f8..dd42baa4e0 100644 --- a/src/KOKKOS/pair_lj_class2_kokkos.cpp +++ b/src/KOKKOS/pair_lj_class2_kokkos.cpp @@ -89,8 +89,7 @@ void PairLJClass2Kokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -292,7 +291,7 @@ double PairLJClass2Kokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJClass2Kokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJClass2Kokkos; #endif } diff --git a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp index a2067f8cf9..cb5ab96871 100644 --- a/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp @@ -89,8 +89,7 @@ void PairLJCutCoulCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -357,7 +356,7 @@ double PairLJCutCoulCutKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCutCoulCutKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCutCoulCutKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp index 277f1f658c..800092a09b 100644 --- a/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_debye_kokkos.cpp @@ -93,8 +93,7 @@ void PairLJCutCoulDebyeKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -386,7 +385,7 @@ double PairLJCutCoulDebyeKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCutCoulDebyeKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCutCoulDebyeKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp index 165bd97276..f793485b47 100644 --- a/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_dsf_kokkos.cpp @@ -101,8 +101,7 @@ void PairLJCutCoulDSFKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -377,7 +376,7 @@ double PairLJCutCoulDSFKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCutCoulDSFKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCutCoulDSFKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp index d02e83eb11..02150586f4 100644 --- a/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp @@ -101,8 +101,7 @@ void PairLJCutCoulLongKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -515,7 +514,7 @@ double PairLJCutCoulLongKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCutCoulLongKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCutCoulLongKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_cut_kokkos.cpp b/src/KOKKOS/pair_lj_cut_kokkos.cpp index daaab8d29e..4ba8c00f88 100644 --- a/src/KOKKOS/pair_lj_cut_kokkos.cpp +++ b/src/KOKKOS/pair_lj_cut_kokkos.cpp @@ -89,8 +89,7 @@ void PairLJCutKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -289,7 +288,7 @@ double PairLJCutKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJCutKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJCutKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_expand_kokkos.cpp b/src/KOKKOS/pair_lj_expand_kokkos.cpp index 55c8b200ef..5ea6c9e438 100644 --- a/src/KOKKOS/pair_lj_expand_kokkos.cpp +++ b/src/KOKKOS/pair_lj_expand_kokkos.cpp @@ -88,8 +88,7 @@ void PairLJExpandKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -297,7 +296,7 @@ double PairLJExpandKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJExpandKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJExpandKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp index b7fb5acccb..2421d059da 100644 --- a/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_coul_gromacs_kokkos.cpp @@ -103,8 +103,7 @@ void PairLJGromacsCoulGromacsKokkos::compute(int eflag_in, int vflag if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -516,7 +515,7 @@ double PairLJGromacsCoulGromacsKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJGromacsCoulGromacsKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJGromacsCoulGromacsKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp index 5d2725ccdd..09a0261ae1 100644 --- a/src/KOKKOS/pair_lj_gromacs_kokkos.cpp +++ b/src/KOKKOS/pair_lj_gromacs_kokkos.cpp @@ -100,8 +100,7 @@ void PairLJGromacsKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -348,7 +347,7 @@ double PairLJGromacsKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJGromacsKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJGromacsKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_sdk_kokkos.cpp index 8f719582fa..c2375fa7a8 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_sdk_kokkos.cpp @@ -88,8 +88,7 @@ void PairLJSDKKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -326,7 +325,7 @@ double PairLJSDKKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairLJSDKKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairLJSDKKokkos; #endif } diff --git a/src/KOKKOS/pair_morse_kokkos.cpp b/src/KOKKOS/pair_morse_kokkos.cpp index 97c5f9be84..b308330ead 100644 --- a/src/KOKKOS/pair_morse_kokkos.cpp +++ b/src/KOKKOS/pair_morse_kokkos.cpp @@ -93,8 +93,7 @@ void PairMorseKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -303,7 +302,7 @@ double PairMorseKokkos::init_one(int i, int j) namespace LAMMPS_NS { template class PairMorseKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairMorseKokkos; #endif } diff --git a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp index a6af26cb0f..7d17ac3f43 100644 --- a/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp +++ b/src/KOKKOS/pair_multi_lucy_rx_kokkos.cpp @@ -148,8 +148,7 @@ void PairMultiLucyRXKokkos::compute_style(int eflag_in, int vflag_in vflag = vflag_in; if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -993,7 +992,7 @@ void PairMultiLucyRXKokkos::settings(int narg, char **arg) namespace LAMMPS_NS { template class PairMultiLucyRXKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairMultiLucyRXKokkos; #endif } diff --git a/src/KOKKOS/pair_reaxc_kokkos.cpp b/src/KOKKOS/pair_reaxc_kokkos.cpp index 46ecddfd83..c6ee50c6ac 100644 --- a/src/KOKKOS/pair_reaxc_kokkos.cpp +++ b/src/KOKKOS/pair_reaxc_kokkos.cpp @@ -530,9 +530,7 @@ int PairReaxCKokkos::Init_Lookup_Tables() Natural_Cubic_Spline( &h[1], &fCEclmb[1], &(LR[i][j].CEclmb[1]), control->tabulate+1, world ); - }// else{ - // LR[i][j].n = 0; - //}// + } } free(h); free(fh); @@ -556,7 +554,7 @@ void PairReaxCKokkos::Deallocate_Lookup_Tables() for( i = 0; i <= ntypes; ++i ) { for( j = i; j <= ntypes; ++j ) - if( LR[i][j].n ) { + if (LR[i][j].n) { sfree( LR[i][j].y, "LR[i,j].y" ); sfree( LR[i][j].H, "LR[i,j].H" ); sfree( LR[i][j].vdW, "LR[i,j].vdW" ); @@ -622,7 +620,7 @@ void PairReaxCKokkos::LR_vdW_Coulomb( int i, int j, double r_ij, LR_ lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } - else{ // no shielding + else { // no shielding exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); @@ -679,8 +677,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); atomKK->sync(execution_space,datamask_read); k_params_sing.template sync(); @@ -854,7 +851,7 @@ void PairReaxCKokkos::compute(int eflag_in, int vflag_in) //dup_Cdbo = Kokkos::Experimental::create_scatter_view(d_Cdbo); //dup_Cdbopi = Kokkos::Experimental::create_scatter_view(d_Cdbopi); //dup_Cdbopi2 = Kokkos::Experimental::create_scatter_view(d_Cdbopi2); - } else { + } else { ndup_CdDelta = Kokkos::Experimental::create_scatter_view(d_CdDelta); //ndup_Cdbo = Kokkos::Experimental::create_scatter_view(d_Cdbo); //ndup_Cdbopi = Kokkos::Experimental::create_scatter_view(d_Cdbopi); @@ -1319,7 +1316,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTabulatedLJCoulomb::allocate_array() d_CdDelta = typename AT::t_ffloat_1d("reax/c/kk:CdDelta",nmax); d_sum_ovun = typename AT::t_ffloat_2d_dl("reax/c/kk:sum_ovun",nmax,3); - // FixReaxCSpecies - if (fixspecies_flag) { - memoryKK->destroy_kokkos(k_tmpid,tmpid); - memoryKK->destroy_kokkos(k_tmpbo,tmpbo); - memoryKK->create_kokkos(k_tmpid,tmpid,nmax,MAXSPECBOND,"pair:tmpid"); - memoryKK->create_kokkos(k_tmpbo,tmpbo,nmax,MAXSPECBOND,"pair:tmpbo"); - } - // FixReaxCBonds d_abo = typename AT::t_ffloat_2d("reax/c/kk:abo",nmax,maxbo); d_neighid = typename AT::t_tagint_2d("reax/c/kk:neighid",nmax,maxbo); @@ -1536,7 +1525,7 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsFull, const int & // hbond list if (i < nlocal && cut_hbsq > 0.0 && (ihb == 1 || ihb == 2) && rsq <= cut_hbsq) { jhb = paramssing(jtype).p_hbond; - if( ihb == 1 && jhb == 2) { + if (ihb == 1 && jhb == 2) { const int jj_index = hb_index - hb_first_i; if (jj_index >= maxhb) { d_resize_hb() = 1; @@ -1704,7 +1693,7 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf, // hbond list if (i < nlocal && cut_hbsq > 0.0 && (ihb == 1 || ihb == 2) && rsq <= cut_hbsq) { jhb = paramssing(jtype).p_hbond; - if( ihb == 1 && jhb == 2) { + if (ihb == 1 && jhb == 2) { if (NEIGHFLAG == HALF) { j_index = hb_first_i + d_hb_num[i]; d_hb_num[i]++; @@ -1927,7 +1916,7 @@ void PairReaxCKokkos::operator()(PairReaxBuildListsHalf_LessAtomics< // hbond list if (i < nlocal && cut_hbsq > 0.0 && (ihb == 1 || ihb == 2) && rsq <= cut_hbsq) { jhb = paramssing(jtype).p_hbond; - if( ihb == 1 && jhb == 2) { + if (ihb == 1 && jhb == 2) { if (NEIGHFLAG == HALF) { j_index = hb_first_i + d_hb_num[i]; d_hb_num[i]++; @@ -2290,7 +2279,7 @@ void PairReaxCKokkos::operator()(PairReaxBondOrder3, const int &ii) const F_FLOAT Clp = 2.0 * gp[15] * explp1 * (2.0 + vlpex); d_dDelta_lp[i] = Clp; - if( paramssing(itype).mass > 21.0 ) { + if (paramssing(itype).mass > 21.0) { nlp_temp = 0.5 * (paramssing(itype).valency_e - paramssing(itype).valency); d_Delta_lp_temp[i] = paramssing(itype).nlp_opt - nlp_temp; } else { @@ -2569,10 +2558,10 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular= 0.0 ){ + if (vlpex >= 0.0) { vlpadj = 0.0; dSBO2 = prod_SBO - 1.0; - } else{ + } else { vlpadj = nlp; dSBO2 = (prod_SBO - 1.0) * (1.0 - p_val8 * d_dDelta_lp[i]); } @@ -2580,13 +2569,13 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular 0.0 && SBO <= 1.0 ) { + } else if (SBO > 0.0 && SBO <= 1.0) { SBO2 = pow( SBO, p_val9 ); CSBO2 = p_val9 * pow( SBO, p_val9 - 1.0 ); - } else if( SBO > 1.0 && SBO < 2.0 ) { + } else if (SBO > 1.0 && SBO < 2.0) { SBO2 = 2.0 - pow( 2.0-SBO, p_val9 ); CSBO2 = p_val9 * pow( 2.0 - SBO, p_val9 - 1.0 ); } else { @@ -2642,8 +2631,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular 1.0 ) cos_theta = 1.0; - if( cos_theta < -1.0 ) cos_theta = -1.0; + if (cos_theta > 1.0) cos_theta = 1.0; + if (cos_theta < -1.0) cos_theta = -1.0; theta = acos(cos_theta); const F_FLOAT inv_dists = 1.0 / (rij * rik); @@ -2684,7 +2673,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeAngular= 0 ) + if (p_val1 >= 0) expval12theta = p_val1 * (1.0 - expval2theta); else // To avoid linear Me-H-Me angles (6/6/06) expval12theta = p_val1 * -expval2theta; @@ -2912,8 +2901,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion 1.0 ) cos_ijk = 1.0; - if( cos_ijk < -1.0 ) cos_ijk = -1.0; + if (cos_ijk > 1.0) cos_ijk = 1.0; + if (cos_ijk < -1.0) cos_ijk = -1.0; theta_ijk = acos(cos_ijk); // dcos_ijk @@ -2927,7 +2916,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion= 0 && sin_ijk <= 1e-10 ) + if (sin_ijk >= 0 && sin_ijk <= 1e-10) tan_ijk_i = cos_ijk / 1e-10; else if( sin_ijk <= 0 && sin_ijk >= -1e-10 ) tan_ijk_i = -cos_ijk / 1e-10; @@ -2954,8 +2943,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion 1.0 ) cos_jil = 1.0; - if( cos_jil < -1.0 ) cos_jil = -1.0; + if (cos_jil > 1.0) cos_jil = 1.0; + if (cos_jil < -1.0) cos_jil = -1.0; theta_jil = acos(cos_jil); // dcos_jil @@ -2970,7 +2959,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion= 0 && sin_jil <= 1e-10 ) + if (sin_jil >= 0 && sin_jil <= 1e-10) tan_jil_i = cos_jil / 1e-10; else if( sin_jil <= 0 && sin_jil >= -1e-10 ) tan_jil_i = -cos_jil / 1e-10; @@ -3010,21 +2999,21 @@ void PairReaxCKokkos::operator()(PairReaxComputeTorsion 1.0 ) arg = 1.0; - if( arg < -1.0 ) arg = -1.0; + if (arg > 1.0) arg = 1.0; + if (arg < -1.0) arg = -1.0; F_FLOAT sin_ijk_rnd = sin_ijk; F_FLOAT sin_jil_rnd = sin_jil; - if( sin_ijk >= 0 && sin_ijk <= 1e-10 ) sin_ijk_rnd = 1e-10; + if (sin_ijk >= 0 && sin_ijk <= 1e-10) sin_ijk_rnd = 1e-10; else if( sin_ijk <= 0 && sin_ijk >= -1e-10 ) sin_ijk_rnd = -1e-10; - if( sin_jil >= 0 && sin_jil <= 1e-10 ) sin_jil_rnd = 1e-10; + if (sin_jil >= 0 && sin_jil <= 1e-10) sin_jil_rnd = 1e-10; else if( sin_jil <= 0 && sin_jil >= -1e-10 ) sin_jil_rnd = -1e-10; // dcos_omega_di @@ -3198,7 +3187,7 @@ void PairReaxCKokkos::operator()(PairReaxComputeHydrogen::operator()(PairReaxComputeHydrogen= HB_THRESHOLD ) { + if (paramssing(jtype).p_hbond == 2 && bo_ij >= HB_THRESHOLD) { hblist[top] = jj; top ++; } @@ -3258,8 +3247,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeHydrogen 1.0 ) cos_theta = 1.0; - if( cos_theta < -1.0 ) cos_theta = -1.0; + if (cos_theta > 1.0) cos_theta = 1.0; + if (cos_theta < -1.0) cos_theta = -1.0; theta = acos(cos_theta); const F_FLOAT inv_dists = 1.0 / (rij * rik); @@ -3477,8 +3466,8 @@ void PairReaxCKokkos::operator()(PairReaxComputeBond1= 1.00 ) { - if( gp[37] == 2 || (imass == 12.0000 && jmass == 15.9990) || + if (BO_i >= 1.00) { + if (gp[37] == 2 || (imass == 12.0000 && jmass == 15.9990) || (jmass == 12.0000 && imass == 15.9990) ) { const F_FLOAT exphu = exp(-gp[7] * SQR(BO_i - 2.50) ); const F_FLOAT exphua1 = exp(-gp[3] * (d_total_bo[i]-BO_i)); @@ -4239,6 +4228,14 @@ void PairReaxCKokkos::pack_bond_buffer_item(int i, int &j, const boo template void PairReaxCKokkos::FindBondSpecies() { + + if (nmax > k_tmpid.extent(0)) { + memoryKK->destroy_kokkos(k_tmpid,tmpid); + memoryKK->destroy_kokkos(k_tmpbo,tmpbo); + memoryKK->create_kokkos(k_tmpid,tmpid,nmax,MAXSPECBOND,"pair:tmpid"); + memoryKK->create_kokkos(k_tmpbo,tmpbo,nmax,MAXSPECBOND,"pair:tmpbo"); + } + copymode = 1; Kokkos::parallel_for(Kokkos::RangePolicy(0,nmax),*this); @@ -4294,7 +4291,7 @@ void PairReaxCKokkos::operator()(PairReaxFindBondSpecies, const int } template class PairReaxCKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairReaxCKokkos; #endif } diff --git a/src/KOKKOS/pair_snap_kokkos.cpp b/src/KOKKOS/pair_snap_kokkos.cpp index 32510721d3..76d6aa5462 100644 --- a/src/KOKKOS/pair_snap_kokkos.cpp +++ b/src/KOKKOS/pair_snap_kokkos.cpp @@ -16,7 +16,7 @@ namespace LAMMPS_NS { template class PairSNAPKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairSNAPKokkos; #endif } diff --git a/src/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h index c452042cfe..569783f926 100644 --- a/src/KOKKOS/pair_snap_kokkos_impl.h +++ b/src/KOKKOS/pair_snap_kokkos_impl.h @@ -137,8 +137,7 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -256,7 +255,6 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) if (vflag_fdotr) pair_virial_fdotr_compute(this); - if (eflag_atom) { k_eatom.template modify(); k_eatom.template sync(); @@ -275,8 +273,8 @@ void PairSNAPKokkos::compute(int eflag_in, int vflag_in) // free duplicated memory if (need_dup) { - dup_f = decltype(dup_f)(); - dup_vatom = decltype(dup_vatom)(); + dup_f = decltype(dup_f)(); + dup_vatom = decltype(dup_vatom)(); } } @@ -453,6 +451,13 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const //t4 += timer.seconds(); timer.reset(); team.team_barrier(); + if (quadraticflag) { + my_sna.compute_bi(team); + team.team_barrier(); + my_sna.copy_bi2bvec(team); + team.team_barrier(); + } + // for neighbors of I within cutoff: // compute dUi/drj and dBi/drj // Fij = dEi/dRj = -dEi/dRi => add to Fi, subtract from Fj @@ -472,10 +477,6 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const my_sna.compute_dbidrj(team); //t7 += timer2.seconds(); timer2.reset(); my_sna.copy_dbi2dbvec(team); - if (quadraticflag) { - my_sna.compute_bi(team); - my_sna.copy_bi2bvec(team); - } Kokkos::single(Kokkos::PerThread(team), [&] (){ F_FLOAT fij[3]; @@ -536,10 +537,10 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const a_f(j,1) -= fij[1]; a_f(j,2) -= fij[2]; - // tally per-atom virial contribution + // tally global and per-atom virial contribution if (EVFLAG) { - if (vflag) { + if (vflag_either) { v_tally_xyz(ev,i,j, fij[0],fij[1],fij[2], -my_sna.rij(jj,0),-my_sna.rij(jj,1), @@ -554,11 +555,13 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const // tally energy contribution if (EVFLAG) { - if (eflag) { + if (eflag_either) { if (!quadraticflag) { my_sna.compute_bi(team); + team.team_barrier(); my_sna.copy_bi2bvec(team); + team.team_barrier(); } // E = beta.B + 0.5*B^t.alpha.B @@ -566,14 +569,15 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const // coeff[k] = alpha_ii or // coeff[k] = alpha_ij = alpha_ji, j != i - if (team.team_rank() == 0) - Kokkos::single(Kokkos::PerThread(team), [&] () { + Kokkos::single(Kokkos::PerTeam(team), [&] () { - // evdwl = energy of atom I, sum over coeffs_k * Bi_k + // evdwl = energy of atom I, sum over coeffs_k * Bi_k - double evdwl = d_coeffi[0]; + double evdwl = d_coeffi[0]; + + // linear contributions + // could use thread vector range on this loop - // linear contributions for (int k = 1; k <= ncoeff; k++) evdwl += d_coeffi[k]*my_sna.bvec[k-1]; @@ -589,11 +593,10 @@ void PairSNAPKokkos::operator() (TagPairSNAP,const } } } -// ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0); - if (eflag_either) { - if (eflag_global) ev.evdwl += evdwl; - if (eflag_atom) d_eatom[i] += evdwl; - } + + //ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0); + if (eflag_global) ev.evdwl += evdwl; + if (eflag_atom) d_eatom[i] += evdwl; }); } } diff --git a/src/KOKKOS/pair_sw_kokkos.cpp b/src/KOKKOS/pair_sw_kokkos.cpp index 5452d2293f..da4737a2c1 100644 --- a/src/KOKKOS/pair_sw_kokkos.cpp +++ b/src/KOKKOS/pair_sw_kokkos.cpp @@ -80,8 +80,7 @@ void PairSWKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -972,7 +971,7 @@ void PairSWKokkos::ev_tally3_atom(EV_FLOAT &ev, const int &i, namespace LAMMPS_NS { template class PairSWKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairSWKokkos; #endif } diff --git a/src/KOKKOS/pair_table_kokkos.cpp b/src/KOKKOS/pair_table_kokkos.cpp index b72df04c5f..737d600d1e 100644 --- a/src/KOKKOS/pair_table_kokkos.cpp +++ b/src/KOKKOS/pair_table_kokkos.cpp @@ -86,8 +86,7 @@ void PairTableKokkos::compute_style(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -550,7 +549,7 @@ void PairTableKokkos::cleanup_copy() { namespace LAMMPS_NS { template class PairTableKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairTableKokkos; #endif diff --git a/src/KOKKOS/pair_table_rx_kokkos.cpp b/src/KOKKOS/pair_table_rx_kokkos.cpp index 30ca54986b..ec7a2ffb94 100644 --- a/src/KOKKOS/pair_table_rx_kokkos.cpp +++ b/src/KOKKOS/pair_table_rx_kokkos.cpp @@ -619,8 +619,7 @@ void PairTableRXKokkos::compute_style(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); if (eflag_atom) { memoryKK->destroy_kokkos(k_eatom,eatom); @@ -1301,7 +1300,7 @@ void PairTableRXKokkos::cleanup_copy() { namespace LAMMPS_NS { template class PairTableRXKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairTableRXKokkos; #endif diff --git a/src/KOKKOS/pair_tersoff_kokkos.cpp b/src/KOKKOS/pair_tersoff_kokkos.cpp index c3e1494d0b..9252e3de52 100644 --- a/src/KOKKOS/pair_tersoff_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_kokkos.cpp @@ -164,8 +164,7 @@ void PairTersoffKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1289,7 +1288,7 @@ int PairTersoffKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairTersoffKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairTersoffKokkos; #endif } diff --git a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp index 61493794ba..585074b128 100644 --- a/src/KOKKOS/pair_tersoff_mod_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_mod_kokkos.cpp @@ -164,8 +164,7 @@ void PairTersoffMODKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1292,7 +1291,7 @@ int PairTersoffMODKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairTersoffMODKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairTersoffMODKokkos; #endif } diff --git a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp index f51da2afde..e1e2211ab5 100644 --- a/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_tersoff_zbl_kokkos.cpp @@ -178,8 +178,7 @@ void PairTersoffZBLKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -1386,7 +1385,7 @@ int PairTersoffZBLKokkos::sbmask(const int& j) const { namespace LAMMPS_NS { template class PairTersoffZBLKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairTersoffZBLKokkos; #endif } diff --git a/src/KOKKOS/pair_vashishta_kokkos.cpp b/src/KOKKOS/pair_vashishta_kokkos.cpp index 3d4bd22a3c..4a1f291b17 100644 --- a/src/KOKKOS/pair_vashishta_kokkos.cpp +++ b/src/KOKKOS/pair_vashishta_kokkos.cpp @@ -79,8 +79,7 @@ void PairVashishtaKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -947,7 +946,7 @@ void PairVashishtaKokkos::ev_tally3_atom(EV_FLOAT &ev, const int &i, namespace LAMMPS_NS { template class PairVashishtaKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairVashishtaKokkos; #endif } diff --git a/src/KOKKOS/pair_yukawa_kokkos.cpp b/src/KOKKOS/pair_yukawa_kokkos.cpp index 8fc2fda120..27e18533a2 100644 --- a/src/KOKKOS/pair_yukawa_kokkos.cpp +++ b/src/KOKKOS/pair_yukawa_kokkos.cpp @@ -177,8 +177,7 @@ void PairYukawaKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -295,7 +294,7 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, namespace LAMMPS_NS { template class PairYukawaKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairYukawaKokkos; #endif } diff --git a/src/KOKKOS/pair_zbl_kokkos.cpp b/src/KOKKOS/pair_zbl_kokkos.cpp index f57d5eaad0..06c84e5189 100644 --- a/src/KOKKOS/pair_zbl_kokkos.cpp +++ b/src/KOKKOS/pair_zbl_kokkos.cpp @@ -129,8 +129,7 @@ void PairZBLKokkos::compute(int eflag_in, int vflag_in) if (neighflag == FULL) no_virial_fdotr_compute = 1; - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag,0); // reallocate per-atom arrays if necessary @@ -433,7 +432,7 @@ void PairZBLKokkos::cleanup_copy() { namespace LAMMPS_NS { template class PairZBLKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PairZBLKokkos; #endif } diff --git a/src/KOKKOS/pppm_kokkos.cpp b/src/KOKKOS/pppm_kokkos.cpp index 5ec454f783..c233ca6264 100644 --- a/src/KOKKOS/pppm_kokkos.cpp +++ b/src/KOKKOS/pppm_kokkos.cpp @@ -202,7 +202,7 @@ void PPPMKokkos::init() if (!atomKK->q_flag) error->all(FLERR,"Kspace style requires atomKK attribute q"); if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM"); + error->all(FLERR,"Cannot use non-periodic boundaries with PPPM"); if (slabflag) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -371,7 +371,7 @@ void PPPMKokkos::setup() // perform some checks to avoid illegal boundaries with read_data if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM"); + error->all(FLERR,"Cannot use non-periodic boundaries with PPPM"); if (slabflag) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -615,8 +615,7 @@ void PPPMKokkos::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag,0); - else evflag = evflag_atom = eflag_global = vflag_global = + ev_init(eflag,vflag,0); eflag_atom = vflag_atom = 0; // reallocate per-atom arrays if necessary @@ -1648,7 +1647,7 @@ void PPPMKokkos::make_rho() nlocal = atomKK->nlocal; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA copymode = 1; Kokkos::parallel_for(Kokkos::RangePolicy(0,nlocal),*this); copymode = 0; @@ -3121,7 +3120,7 @@ double PPPMKokkos::memory_usage() namespace LAMMPS_NS { template class PPPMKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class PPPMKokkos; #endif } diff --git a/src/KOKKOS/pppm_kokkos.h b/src/KOKKOS/pppm_kokkos.h index db5b8f7ae6..21896eb714 100644 --- a/src/KOKKOS/pppm_kokkos.h +++ b/src/KOKKOS/pppm_kokkos.h @@ -454,7 +454,7 @@ E: Kspace style requires atomKK attribute q UNDOCUMENTED -E: Cannot use nonperiodic boundaries with PPPM +E: Cannot use non-periodic boundaries with PPPM For kspace style pppm, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a diff --git a/src/KOKKOS/rand_pool_wrap_kokkos.h b/src/KOKKOS/rand_pool_wrap_kokkos.h index 12255a8a62..c1461c5216 100644 --- a/src/KOKKOS/rand_pool_wrap_kokkos.h +++ b/src/KOKKOS/rand_pool_wrap_kokkos.h @@ -50,7 +50,7 @@ class RandPoolWrap : protected Pointers { KOKKOS_INLINE_FUNCTION RandWrap get_state() const { -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA error->all(FLERR,"Cannot use Marsaglia RNG with GPUs"); #endif diff --git a/src/KOKKOS/region_block_kokkos.cpp b/src/KOKKOS/region_block_kokkos.cpp index 8ff6e8937d..730ef81466 100644 --- a/src/KOKKOS/region_block_kokkos.cpp +++ b/src/KOKKOS/region_block_kokkos.cpp @@ -167,7 +167,7 @@ void RegBlockKokkos::rotate(double &x, double &y, double &z, double namespace LAMMPS_NS { template class RegBlockKokkos; -#ifdef KOKKOS_HAVE_CUDA +#ifdef KOKKOS_ENABLE_CUDA template class RegBlockKokkos; #endif } diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h index 25561fef5d..6a19c57829 100644 --- a/src/KOKKOS/sna_kokkos_impl.h +++ b/src/KOKKOS/sna_kokkos_impl.h @@ -327,29 +327,40 @@ void SNAKokkos::compute_bi(const typename Kokkos::TeamPolicy::compute_bi(const typename Kokkos::TeamPolicy::create_team_scratch_arrays(const typename Kokkos::Te uarraytot_i_a = uarraytot_i = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim); zarray_r = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim); zarray_i = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim); + bvec = Kokkos::View(team.team_scratch(1),ncoeff); + barray = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim); rij = t_sna_2d(team.team_scratch(1),nmax,3); rcutij = t_sna_1d(team.team_scratch(1),nmax); @@ -1046,6 +1061,8 @@ T_INT SNAKokkos::size_team_scratch_arrays() { size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarraytot_i_a size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_r size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_i + size += Kokkos::View::shmem_size(ncoeff); // bvec + size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray size += t_sna_2d::shmem_size(nmax,3); // rij size += t_sna_1d::shmem_size(nmax); // rcutij @@ -1062,8 +1079,6 @@ KOKKOS_INLINE_FUNCTION void SNAKokkos::create_thread_scratch_arrays(const typename Kokkos::TeamPolicy::member_type& team) { int jdim = twojmax + 1; - bvec = Kokkos::View(team.thread_scratch(1),ncoeff); - barray = t_sna_3d(team.thread_scratch(1),jdim,jdim,jdim); dbvec = Kokkos::View(team.thread_scratch(1),ncoeff); dbarray = t_sna_4d(team.thread_scratch(1),jdim,jdim,jdim); @@ -1079,8 +1094,6 @@ inline T_INT SNAKokkos::size_thread_scratch_arrays() { T_INT size = 0; int jdim = twojmax + 1; - size += Kokkos::View::shmem_size(ncoeff); // bvec - size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray size += Kokkos::View::shmem_size(ncoeff); // dbvec size += t_sna_4d::shmem_size(jdim,jdim,jdim); // dbarray diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index f56e6015d0..d75a7e491f 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -537,7 +537,7 @@ void VerletKokkos::run(int n) Kokkos::deep_copy(LMPHostType(),f_merge_copy,atomKK->k_f.h_view); Kokkos::parallel_for(atomKK->k_f.extent(0), ForceAdder(atomKK->k_f.d_view,f_merge_copy)); - atomKK->k_f.modified_host() = 0; // special case + atomKK->k_f.clear_sync_state(); // special case atomKK->k_f.modify(); } @@ -585,8 +585,8 @@ void VerletKokkos::force_clear() { if (external_force_clear) return; - atomKK->k_f.modified_host() = 0; // ignore host forces/torques since device views - atomKK->k_torque.modified_host() = 0; // will be cleared below + atomKK->k_f.clear_sync_state(); // ignore host forces/torques since device views + atomKK->k_torque.clear_sync_state(); // will be cleared below // clear force on all particles // if either newton flag is set, also include ghosts diff --git a/src/KSPACE/ewald.cpp b/src/KSPACE/ewald.cpp index c9c10ab738..ccbb3ed708 100644 --- a/src/KSPACE/ewald.cpp +++ b/src/KSPACE/ewald.cpp @@ -72,7 +72,7 @@ void Ewald::settings(int narg, char **arg) if (narg != 1) error->all(FLERR,"Illegal kspace_style ewald command"); accuracy_relative = fabs(force->numeric(FLERR,arg[0])); -} +} /* ---------------------------------------------------------------------- free all memory @@ -105,7 +105,7 @@ void Ewald::init() if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with Ewald"); + error->all(FLERR,"Cannot use non-periodic boundaries with Ewald"); if (slabflag) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -365,9 +365,7 @@ void Ewald::compute(int eflag, int vflag) // set energy/virial flags - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // if atom count has changed, update qsum and qsqsum diff --git a/src/KSPACE/ewald.h b/src/KSPACE/ewald.h index 7d520b3ab0..ef7ff05675 100644 --- a/src/KSPACE/ewald.h +++ b/src/KSPACE/ewald.h @@ -99,7 +99,7 @@ E: Kspace style requires atom attribute q The atom style defined does not have these attributes. -E: Cannot use nonperiodic boundaries with Ewald +E: Cannot use non-periodic boundaries with Ewald For kspace style ewald, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index 0ff8acff6e..0603d68eb2 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -100,7 +100,7 @@ void EwaldDisp::init() if (domain->dimension == 2) error->all(FLERR,"Cannot use EwaldDisp with 2d simulation"); if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldDisp"); + error->all(FLERR,"Cannot use non-periodic boundaries with EwaldDisp"); if (slabflag == 1) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -688,8 +688,7 @@ void EwaldDisp::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (!peratom_allocate_flag && (eflag_atom || vflag_atom)) { allocate_peratom(); diff --git a/src/KSPACE/ewald_disp.h b/src/KSPACE/ewald_disp.h index a8dfb5bb20..77b03a1ff7 100644 --- a/src/KSPACE/ewald_disp.h +++ b/src/KSPACE/ewald_disp.h @@ -108,7 +108,7 @@ E: Cannot use EwaldDisp with 2d simulation This is a current restriction of this command. -E: Cannot use nonperiodic boundaries with EwaldDisp +E: Cannot use non-periodic boundaries with EwaldDisp For kspace style ewald/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d diff --git a/src/KSPACE/fix_tune_kspace.cpp b/src/KSPACE/fix_tune_kspace.cpp index a3ac5e1e83..3e90988cba 100644 --- a/src/KSPACE/fix_tune_kspace.cpp +++ b/src/KSPACE/fix_tune_kspace.cpp @@ -89,6 +89,14 @@ void FixTuneKspace::init() error->all(FLERR,"Cannot use fix tune/kspace without a kspace style"); if (!force->pair) error->all(FLERR,"Cannot use fix tune/kspace without a pair style"); + if (strncmp(force->pair_style,"hybrid",6) == 0) + error->all(FLERR,"Cannot use fix tune/kspace with a hybrid pair style"); + if (force->kspace->dispersionflag) + error->all(FLERR,"Cannot use fix tune/kspace with long-range dispersion"); + if (force->kspace->tip4pflag) + error->all(FLERR,"Cannot use fix tune/kspace with TIP4P water"); + if (force->kspace->dipoleflag) + error->all(FLERR,"Cannot use fix tune/kspace with dipole long-range solver"); double old_acc = force->kspace->accuracy/force->kspace->two_charge_force; char old_acc_str[12]; diff --git a/src/KSPACE/msm.cpp b/src/KSPACE/msm.cpp index ed4abcf077..d7cc3f6876 100644 --- a/src/KSPACE/msm.cpp +++ b/src/KSPACE/msm.cpp @@ -454,9 +454,7 @@ void MSM::compute(int eflag, int vflag) // set energy/virial flags - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = eflag_either = vflag_either = 0; + ev_init(eflag,vflag); if (scalar_pressure_flag && vflag_either) { if (vflag_atom) @@ -533,7 +531,7 @@ void MSM::compute(int eflag, int vflag) restriction(n); } - // compute direct interation for top grid level for nonperiodic + // compute direct interation for top grid level for non-periodic // and for second from top grid level for periodic if (active_flag[levels-1]) { @@ -1120,7 +1118,7 @@ void MSM::set_grid_global() if (nx_msm[0] >= OFFSET || ny_msm[0] >= OFFSET || nz_msm[0] >= OFFSET) error->all(FLERR,"MSM grid is too large"); - // compute number of extra grid points needed for nonperiodic boundary conditions + // compute number of extra grid points needed for non-periodic boundary conditions if (domain->nonperiodic) { alpha[0] = -(order/2 - 1); @@ -1254,7 +1252,7 @@ void MSM::set_grid_local() nzlo_out[n] = nlo - order; nzhi_out[n] = nhi + MAX(order,nzhi_direct); - // add extra grid points for nonperiodic boundary conditions + // add extra grid points for non-periodic boundary conditions if (domain->nonperiodic) { diff --git a/src/KSPACE/msm_cg.cpp b/src/KSPACE/msm_cg.cpp index 1139ce4957..c7896db50c 100644 --- a/src/KSPACE/msm_cg.cpp +++ b/src/KSPACE/msm_cg.cpp @@ -90,9 +90,7 @@ void MSMCG::compute(int eflag, int vflag) // set energy/virial flags - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = eflag_either = vflag_either = 0; + ev_init(eflag,vflag); // invoke allocate_peratom() if needed for first time @@ -199,7 +197,7 @@ void MSMCG::compute(int eflag, int vflag) } - // compute direct interation for top grid level for nonperiodic + // compute direct interation for top grid level for non-periodic // and for second from top grid level for periodic if (active_flag[levels-1]) { diff --git a/src/KSPACE/pair_born_coul_long.cpp b/src/KSPACE/pair_born_coul_long.cpp index d55a5a3afe..f12f5779d9 100644 --- a/src/KSPACE/pair_born_coul_long.cpp +++ b/src/KSPACE/pair_born_coul_long.cpp @@ -87,8 +87,7 @@ void PairBornCoulLong::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_born_coul_msm.cpp b/src/KSPACE/pair_born_coul_msm.cpp index 775d26df95..eaa1c116c1 100644 --- a/src/KSPACE/pair_born_coul_msm.cpp +++ b/src/KSPACE/pair_born_coul_msm.cpp @@ -82,8 +82,7 @@ void PairBornCoulMSM::compute(int eflag, int vflag) } evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_buck_coul_long.cpp b/src/KSPACE/pair_buck_coul_long.cpp index a37e4ab4e9..0a1ec88da5 100644 --- a/src/KSPACE/pair_buck_coul_long.cpp +++ b/src/KSPACE/pair_buck_coul_long.cpp @@ -50,23 +50,23 @@ PairBuckCoulLong::PairBuckCoulLong(LAMMPS *lmp) : Pair(lmp) PairBuckCoulLong::~PairBuckCoulLong() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(a); - memory->destroy(rho); - memory->destroy(c); - memory->destroy(rhoinv); - memory->destroy(buck1); - memory->destroy(buck2); - memory->destroy(offset); - } - if (ftable) free_tables(); + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(a); + memory->destroy(rho); + memory->destroy(c); + memory->destroy(rhoinv); + memory->destroy(buck1); + memory->destroy(buck2); + memory->destroy(offset); } + if (ftable) free_tables(); } /* ---------------------------------------------------------------------- */ @@ -82,8 +82,7 @@ void PairBuckCoulLong::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_buck_coul_msm.cpp b/src/KSPACE/pair_buck_coul_msm.cpp index fc72f1a4d6..257d1b661f 100644 --- a/src/KSPACE/pair_buck_coul_msm.cpp +++ b/src/KSPACE/pair_buck_coul_msm.cpp @@ -79,8 +79,7 @@ void PairBuckCoulMSM::compute(int eflag, int vflag) } evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_buck_long_coul_long.cpp b/src/KSPACE/pair_buck_long_coul_long.cpp index d5bb7b6c5b..c7a4a4b2f6 100644 --- a/src/KSPACE/pair_buck_long_coul_long.cpp +++ b/src/KSPACE/pair_buck_long_coul_long.cpp @@ -445,8 +445,7 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag) double evdwl,ecoul,fpair; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x, *x0 = x[0]; double **f = atom->f, *f0 = f[0], *fi = f0; @@ -785,8 +784,7 @@ void PairBuckLongCoulLong::compute_outer(int eflag, int vflag) { double evdwl,ecoul,fpair,fvirial; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x, *x0 = x[0]; double **f = atom->f, *f0 = f[0], *fi = f0; diff --git a/src/KSPACE/pair_coul_long.cpp b/src/KSPACE/pair_coul_long.cpp index 8db5979b39..ae268b9857 100644 --- a/src/KSPACE/pair_coul_long.cpp +++ b/src/KSPACE/pair_coul_long.cpp @@ -55,15 +55,15 @@ PairCoulLong::PairCoulLong(LAMMPS *lmp) : Pair(lmp) PairCoulLong::~PairCoulLong() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(scale); - } - if (ftable) free_tables(); + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(scale); } + if (ftable) free_tables(); } /* ---------------------------------------------------------------------- */ @@ -79,8 +79,7 @@ void PairCoulLong::compute(int eflag, int vflag) double rsq; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_coul_msm.cpp b/src/KSPACE/pair_coul_msm.cpp index ab59dfa4c1..960505142c 100644 --- a/src/KSPACE/pair_coul_msm.cpp +++ b/src/KSPACE/pair_coul_msm.cpp @@ -67,8 +67,7 @@ void PairCoulMSM::compute(int eflag, int vflag) } ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_lj_charmm_coul_long.cpp b/src/KSPACE/pair_lj_charmm_coul_long.cpp index 749d9657aa..b40eab244b 100644 --- a/src/KSPACE/pair_lj_charmm_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_long.cpp @@ -59,27 +59,27 @@ PairLJCharmmCoulLong::PairLJCharmmCoulLong(LAMMPS *lmp) : Pair(lmp) PairLJCharmmCoulLong::~PairLJCharmmCoulLong() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(eps14); - memory->destroy(sigma14); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(lj14_1); - memory->destroy(lj14_2); - memory->destroy(lj14_3); - memory->destroy(lj14_4); - memory->destroy(offset); - } - if (ftable) free_tables(); + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(eps14); + memory->destroy(sigma14); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(lj14_1); + memory->destroy(lj14_2); + memory->destroy(lj14_3); + memory->destroy(lj14_4); + memory->destroy(offset); } + if (ftable) free_tables(); } /* ---------------------------------------------------------------------- */ @@ -96,8 +96,7 @@ void PairLJCharmmCoulLong::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -404,8 +403,7 @@ void PairLJCharmmCoulLong::compute_outer(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_lj_charmm_coul_msm.cpp b/src/KSPACE/pair_lj_charmm_coul_msm.cpp index aecadcf127..72a8e340bc 100644 --- a/src/KSPACE/pair_lj_charmm_coul_msm.cpp +++ b/src/KSPACE/pair_lj_charmm_coul_msm.cpp @@ -87,8 +87,7 @@ void PairLJCharmmCoulMSM::compute(int eflag, int vflag) } evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -265,8 +264,7 @@ void PairLJCharmmCoulMSM::compute_outer(int eflag, int vflag) "for rRESPA with kspace_style MSM"); evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp index 614980117e..4aecc8453a 100644 --- a/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp +++ b/src/KSPACE/pair_lj_charmmfsw_coul_long.cpp @@ -77,27 +77,6 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp) PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(eps14); - memory->destroy(sigma14); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(lj14_1); - memory->destroy(lj14_2); - memory->destroy(lj14_3); - memory->destroy(lj14_4); - } - if (ftable) free_tables(); - } - // switch qqr2e back from CHARMM value to LAMMPS value if (update && strcmp(update->unit_style,"real") == 0) { @@ -106,6 +85,27 @@ PairLJCharmmfswCoulLong::~PairLJCharmmfswCoulLong() " conversion constant"); force->qqr2e = force->qqr2e_lammps_real; } + + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(eps14); + memory->destroy(sigma14); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(lj14_1); + memory->destroy(lj14_2); + memory->destroy(lj14_3); + memory->destroy(lj14_4); + } + if (ftable) free_tables(); } /* ---------------------------------------------------------------------- */ @@ -121,8 +121,7 @@ void PairLJCharmmfswCoulLong::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -452,8 +451,7 @@ void PairLJCharmmfswCoulLong::compute_outer(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_lj_cut_coul_long.cpp b/src/KSPACE/pair_lj_cut_coul_long.cpp index c9530fe157..fde7fa8e35 100644 --- a/src/KSPACE/pair_lj_cut_coul_long.cpp +++ b/src/KSPACE/pair_lj_cut_coul_long.cpp @@ -90,8 +90,7 @@ void PairLJCutCoulLong::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -397,8 +396,7 @@ void PairLJCutCoulLong::compute_outer(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_lj_cut_coul_msm.cpp b/src/KSPACE/pair_lj_cut_coul_msm.cpp index 78c364bd6a..c2e566a117 100644 --- a/src/KSPACE/pair_lj_cut_coul_msm.cpp +++ b/src/KSPACE/pair_lj_cut_coul_msm.cpp @@ -87,8 +87,7 @@ void PairLJCutCoulMSM::compute(int eflag, int vflag) } evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -252,8 +251,7 @@ void PairLJCutCoulMSM::compute_outer(int eflag, int vflag) "for rRESPA with kspace_style MSM"); evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/KSPACE/pair_lj_cut_tip4p_long.cpp b/src/KSPACE/pair_lj_cut_tip4p_long.cpp index d622a83b39..f5889fd520 100644 --- a/src/KSPACE/pair_lj_cut_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_cut_tip4p_long.cpp @@ -94,8 +94,7 @@ void PairLJCutTIP4PLong::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/KSPACE/pair_lj_long_coul_long.cpp b/src/KSPACE/pair_lj_long_coul_long.cpp index 2de527ab39..493866a895 100644 --- a/src/KSPACE/pair_lj_long_coul_long.cpp +++ b/src/KSPACE/pair_lj_long_coul_long.cpp @@ -441,8 +441,7 @@ void PairLJLongCoulLong::compute(int eflag, int vflag) { double evdwl,ecoul,fpair; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x, *x0 = x[0]; double **f = atom->f, *f0 = f[0], *fi = f0; @@ -778,8 +777,7 @@ void PairLJLongCoulLong::compute_outer(int eflag, int vflag) { double evdwl,ecoul,fvirial,fpair; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x, *x0 = x[0]; double **f = atom->f, *f0 = f[0], *fi = f0; diff --git a/src/KSPACE/pair_lj_long_tip4p_long.cpp b/src/KSPACE/pair_lj_long_tip4p_long.cpp index a571e30fc3..3137b9d79a 100644 --- a/src/KSPACE/pair_lj_long_tip4p_long.cpp +++ b/src/KSPACE/pair_lj_long_tip4p_long.cpp @@ -92,8 +92,7 @@ void PairLJLongTIP4PLong::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred @@ -1004,8 +1003,7 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag) int respa_flag; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/KSPACE/pair_tip4p_long.cpp b/src/KSPACE/pair_tip4p_long.cpp index ac428d483a..9419fdf196 100644 --- a/src/KSPACE/pair_tip4p_long.cpp +++ b/src/KSPACE/pair_tip4p_long.cpp @@ -90,8 +90,7 @@ void PairTIP4PLong::compute(int eflag, int vflag) double rsq; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/KSPACE/pppm.cpp b/src/KSPACE/pppm.cpp index 57e030f255..773305bb5e 100644 --- a/src/KSPACE/pppm.cpp +++ b/src/KSPACE/pppm.cpp @@ -214,7 +214,7 @@ void PPPM::init() if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM"); + error->all(FLERR,"Cannot use non-periodic boundaries with PPPM"); if (slabflag) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -411,7 +411,7 @@ void PPPM::setup() // perform some checks to avoid illegal boundaries with read_data if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with PPPM"); + error->all(FLERR,"Cannot use non-periodic boundaries with PPPM"); if (slabflag) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -630,9 +630,7 @@ void PPPM::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) { allocate_peratom(); diff --git a/src/KSPACE/pppm.h b/src/KSPACE/pppm.h index 20ba7c3ff1..c9190d9fca 100644 --- a/src/KSPACE/pppm.h +++ b/src/KSPACE/pppm.h @@ -235,7 +235,7 @@ E: Kspace style requires atom attribute q The atom style defined does not have these attributes. -E: Cannot use nonperiodic boundaries with PPPM +E: Cannot use non-periodic boundaries with PPPM For kspace style pppm, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d slab with a diff --git a/src/KSPACE/pppm_cg.cpp b/src/KSPACE/pppm_cg.cpp index fa73588363..3285dba21c 100644 --- a/src/KSPACE/pppm_cg.cpp +++ b/src/KSPACE/pppm_cg.cpp @@ -88,9 +88,7 @@ void PPPMCG::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) { allocate_peratom(); diff --git a/src/KSPACE/pppm_disp.cpp b/src/KSPACE/pppm_disp.cpp index 9fcfb7d769..45dce0895b 100644 --- a/src/KSPACE/pppm_disp.cpp +++ b/src/KSPACE/pppm_disp.cpp @@ -269,7 +269,7 @@ void PPPMDisp::init() "comm_style brick"); if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp"); + error->all(FLERR,"Cannot use non-periodic boundaries with PPPMDisp"); if (slabflag == 1) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -657,7 +657,7 @@ void PPPMDisp::setup() { if (slabflag == 0 && domain->nonperiodic > 0) - error->all(FLERR,"Cannot use nonperiodic boundaries with PPPMDisp"); + error->all(FLERR,"Cannot use non-periodic boundaries with PPPMDisp"); if (slabflag == 1) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) @@ -928,9 +928,7 @@ void PPPMDisp::compute(int eflag, int vflag) int i; // convert atoms from box to lamda coords - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) { allocate_peratom(); diff --git a/src/KSPACE/pppm_disp.h b/src/KSPACE/pppm_disp.h index 8a3fb700e6..ccbeb60f3c 100644 --- a/src/KSPACE/pppm_disp.h +++ b/src/KSPACE/pppm_disp.h @@ -390,7 +390,7 @@ E: PPPMDisp can only currently be used with comm_style brick This is a current restriction in LAMMPS. -E: Cannot use nonperiodic boundaries with PPPMDisp +E: Cannot use non-periodic boundaries with PPPMDisp For kspace style pppm/disp, all 3 dimensions must have periodic boundaries unless you use the kspace_modify command to define a 2d @@ -489,7 +489,7 @@ Self-explanatory. E: KSpace accuracy too large to estimate G vector -Reduce the accuracy request or specify gwald explicitly +Reduce the accuracy request or specify gewald explicitly via the kspace_modify command. E: Could not compute grid size for Coulomb interaction diff --git a/src/KSPACE/pppm_stagger.cpp b/src/KSPACE/pppm_stagger.cpp index ca369cf260..a5ed6de626 100644 --- a/src/KSPACE/pppm_stagger.cpp +++ b/src/KSPACE/pppm_stagger.cpp @@ -124,9 +124,7 @@ void PPPMStagger::compute(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) { allocate_peratom(); diff --git a/src/LATTE/fix_latte.cpp b/src/LATTE/fix_latte.cpp index a89be57bed..645b298e09 100644 --- a/src/LATTE/fix_latte.cpp +++ b/src/LATTE/fix_latte.cpp @@ -239,8 +239,7 @@ void FixLatte::pre_reverse(int eflag, int /*vflag*/) void FixLatte::post_force(int vflag) { int eflag = eflag_caller; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // compute Coulombic potential = pe[i]/q[i] // invoke compute pe/atom @@ -299,7 +298,7 @@ void FixLatte::post_force(int vflag) if (coulomb) forces = &flatte[0][0]; else forces = &atom->f[0][0]; int maxiter = -1; - + latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy, &domain->xz,&domain->yz,forces,&maxiter,&latte_energy, &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); diff --git a/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl b/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl index 0f5087618b..9f29e9a87e 100644 --- a/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl +++ b/src/MAKE/MACHINES/Makefile.aarch64_arm_openmpi_armpl @@ -1,121 +1,121 @@ -# g++_openmpi = OpenMPI with compiler set to GNU g++ - -SHELL = /bin/sh - -# --------------------------------------------------------------------- -# compiler/linker settings -# specify flags and libraries needed for your compiler - -#export OMPI_CXX = armclang++ -CC = mpicxx -CCFLAGS = -O3 -mcpu=native -SHFLAGS = -fPIC -DEPFLAGS = -M - -LINK = mpicxx -LINKFLAGS = -g -O -LIB = -SIZE = size - -ARCHIVE = ar -ARFLAGS = -rc -SHLIBFLAGS = -shared - -# --------------------------------------------------------------------- -# LAMMPS-specific settings, all OPTIONAL -# specify settings for LAMMPS features you will use -# if you change any -D setting, do full re-compile after "make clean" - -# LAMMPS ifdef settings -# see possible settings in Section 2.2 (step 4) of manual - -LMP_INC = -DLAMMPS_GZIP - -# MPI library -# see discussion in Section 2.2 (step 5) of manual -# MPI wrapper compiler/linker can provide this info -# can point to dummy MPI library in src/STUBS as in Makefile.serial -# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts -# INC = path for mpi.h, MPI compiler settings -# PATH = path for MPI library -# LIB = name of MPI library - -MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -MPI_PATH = -MPI_LIB = - -# FFT library -# see discussion in Section 2.2 (step 6) of manaul -# can be left blank to use provided KISS FFT library -# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings -# PATH = path for FFT library -# LIB = name of FFT library - -FFT_INC = -DFFT_FFTW -FFT_PATH = -L$(ARMPL_LIBRARIES) -FFT_LIB = -larmpl_lp64 - -# JPEG and/or PNG library -# see discussion in Section 2.2 (step 7) of manual -# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC -# INC = path(s) for jpeglib.h and/or png.h -# PATH = path(s) for JPEG library and/or PNG library -# LIB = name(s) of JPEG library and/or PNG library - -JPG_INC = -JPG_PATH = -JPG_LIB = - -# --------------------------------------------------------------------- -# build rules and dependencies -# do not edit this section - -include Makefile.package.settings -include Makefile.package - -EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) -EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) -EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) -EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) -EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) - -# Path to src files - -vpath %.cpp .. -vpath %.h .. - -# Link target - -$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) - $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) - $(SIZE) $(EXE) - -# Library targets - -lib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) - -shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ - $(OBJ) $(EXTRA_LIB) $(LIB) - -# Compilation rules - -%.o:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -%.d:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ - -%.o:%.cu $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -# Individual dependencies - -depend : fastdep.exe $(SRC) - @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 - -fastdep.exe: ../DEPEND/fastdep.c - cc -O -o $@ $< - -sinclude .depend +# g++_openmpi = OpenMPI with compiler set to GNU g++ + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +#export OMPI_CXX = armclang++ +CC = mpicxx +CCFLAGS = -O3 -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -g -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl b/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl index c303a97e17..6397118357 100644 --- a/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl +++ b/src/MAKE/MACHINES/Makefile.aarch64_arm_serial_armpl @@ -1,120 +1,120 @@ -# arm_serial = Arm armclang compiler, no MPI - -SHELL = /bin/sh - -# --------------------------------------------------------------------- -# compiler/linker settings -# specify flags and libraries needed for your compiler - -CC = armclang++ -CCFLAGS = -O3 -mcpu=native -SHFLAGS = -fPIC -DEPFLAGS = -M - -LINK = armclang++ -LINKFLAGS = -g -O -LIB = -SIZE = size - -ARCHIVE = ar -ARFLAGS = -rc -SHLIBFLAGS = -shared - -# --------------------------------------------------------------------- -# LAMMPS-specific settings, all OPTIONAL -# specify settings for LAMMPS features you will use -# if you change any -D setting, do full re-compile after "make clean" - -# LAMMPS ifdef settings -# see possible settings in Section 2.2 (step 4) of manual - -LMP_INC = -DLAMMPS_GZIP - -# MPI library -# see discussion in Section 2.2 (step 5) of manual -# MPI wrapper compiler/linker can provide this info -# can point to dummy MPI library in src/STUBS as in Makefile.serial -# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts -# INC = path for mpi.h, MPI compiler settings -# PATH = path for MPI library -# LIB = name of MPI library - -MPI_INC = -I../STUBS -MPI_PATH = -L../STUBS -MPI_LIB = -lmpi_stubs - -# FFT library -# see discussion in Section 2.2 (step 6) of manaul -# can be left blank to use provided KISS FFT library -# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings -# PATH = path for FFT library -# LIB = name of FFT library - -FFT_INC = -DFFT_FFTW -FFT_PATH = -L$(ARMPL_LIBRARIES) -FFT_LIB = -larmpl_lp64 - -# JPEG and/or PNG library -# see discussion in Section 2.2 (step 7) of manual -# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC -# INC = path(s) for jpeglib.h and/or png.h -# PATH = path(s) for JPEG library and/or PNG library -# LIB = name(s) of JPEG library and/or PNG library - -JPG_INC = -JPG_PATH = -JPG_LIB = - -# --------------------------------------------------------------------- -# build rules and dependencies -# do not edit this section - -include Makefile.package.settings -include Makefile.package - -EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) -EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) -EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) -EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) -EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) - -# Path to src files - -vpath %.cpp .. -vpath %.h .. - -# Link target - -$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) - $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) - $(SIZE) $(EXE) - -# Library targets - -lib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) - -shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ - $(OBJ) $(EXTRA_LIB) $(LIB) - -# Compilation rules - -%.o:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -%.d:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ - -%.o:%.cu $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -# Individual dependencies - -depend : fastdep.exe $(SRC) - @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 - -fastdep.exe: ../DEPEND/fastdep.c - cc -O -o $@ $< - -sinclude .depend +# arm_serial = Arm armclang compiler, no MPI + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = armclang++ +CCFLAGS = -O3 -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = armclang++ +LINKFLAGS = -g -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl b/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl index b3cc1f48a3..933c97cba4 100644 --- a/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl +++ b/src/MAKE/MACHINES/Makefile.aarch64_g++_openmpi_armpl @@ -1,121 +1,121 @@ -# g++_openmpi = OpenMPI with compiler set to GNU g++ - -SHELL = /bin/sh - -# --------------------------------------------------------------------- -# compiler/linker settings -# specify flags and libraries needed for your compiler - -export OMPI_CXX = g++ -CC = mpicxx -CCFLAGS = -O3 -march=native -mcpu=native -SHFLAGS = -fPIC -DEPFLAGS = -M - -LINK = mpicxx -LINKFLAGS = -O -LIB = -SIZE = size - -ARCHIVE = ar -ARFLAGS = -rc -SHLIBFLAGS = -shared - -# --------------------------------------------------------------------- -# LAMMPS-specific settings, all OPTIONAL -# specify settings for LAMMPS features you will use -# if you change any -D setting, do full re-compile after "make clean" - -# LAMMPS ifdef settings -# see possible settings in Section 2.2 (step 4) of manual - -LMP_INC = -DLAMMPS_GZIP - -# MPI library -# see discussion in Section 2.2 (step 5) of manual -# MPI wrapper compiler/linker can provide this info -# can point to dummy MPI library in src/STUBS as in Makefile.serial -# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts -# INC = path for mpi.h, MPI compiler settings -# PATH = path for MPI library -# LIB = name of MPI library - -MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -MPI_PATH = -MPI_LIB = - -# FFT library -# see discussion in Section 2.2 (step 6) of manaul -# can be left blank to use provided KISS FFT library -# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings -# PATH = path for FFT library -# LIB = name of FFT library - -FFT_INC = -DFFT_FFTW -FFT_PATH = -L$(ARMPL_LIBRARIES) -FFT_LIB = -larmpl_lp64 - -# JPEG and/or PNG library -# see discussion in Section 2.2 (step 7) of manual -# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC -# INC = path(s) for jpeglib.h and/or png.h -# PATH = path(s) for JPEG library and/or PNG library -# LIB = name(s) of JPEG library and/or PNG library - -JPG_INC = -JPG_PATH = -JPG_LIB = - -# --------------------------------------------------------------------- -# build rules and dependencies -# do not edit this section - -include Makefile.package.settings -include Makefile.package - -EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) -EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) -EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) -EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) -EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) - -# Path to src files - -vpath %.cpp .. -vpath %.h .. - -# Link target - -$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) - $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) - $(SIZE) $(EXE) - -# Library targets - -lib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) - -shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ - $(OBJ) $(EXTRA_LIB) $(LIB) - -# Compilation rules - -%.o:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -%.d:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ - -%.o:%.cu $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -# Individual dependencies - -depend : fastdep.exe $(SRC) - @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 - -fastdep.exe: ../DEPEND/fastdep.c - cc -O -o $@ $< - -sinclude .depend +# g++_openmpi = OpenMPI with compiler set to GNU g++ + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +export OMPI_CXX = g++ +CC = mpicxx +CCFLAGS = -O3 -march=native -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = mpicxx +LINKFLAGS = -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 +MPI_PATH = +MPI_LIB = + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl b/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl index 45c0bb162b..e7f1a81f3b 100644 --- a/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl +++ b/src/MAKE/MACHINES/Makefile.aarch64_g++_serial_armpl @@ -1,120 +1,120 @@ -# g++_serial = GNU g++ compiler, no MPI - -SHELL = /bin/sh - -# --------------------------------------------------------------------- -# compiler/linker settings -# specify flags and libraries needed for your compiler - -CC = g++ -CCFLAGS = -O3 -march=native -mcpu=native -SHFLAGS = -fPIC -DEPFLAGS = -M - -LINK = g++ -LINKFLAGS = -O -LIB = -SIZE = size - -ARCHIVE = ar -ARFLAGS = -rc -SHLIBFLAGS = -shared - -# --------------------------------------------------------------------- -# LAMMPS-specific settings, all OPTIONAL -# specify settings for LAMMPS features you will use -# if you change any -D setting, do full re-compile after "make clean" - -# LAMMPS ifdef settings -# see possible settings in Section 2.2 (step 4) of manual - -LMP_INC = -DLAMMPS_GZIP - -# MPI library -# see discussion in Section 2.2 (step 5) of manual -# MPI wrapper compiler/linker can provide this info -# can point to dummy MPI library in src/STUBS as in Makefile.serial -# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts -# INC = path for mpi.h, MPI compiler settings -# PATH = path for MPI library -# LIB = name of MPI library - -MPI_INC = -I../STUBS -MPI_PATH = -L../STUBS -MPI_LIB = -lmpi_stubs - -# FFT library -# see discussion in Section 2.2 (step 6) of manaul -# can be left blank to use provided KISS FFT library -# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings -# PATH = path for FFT library -# LIB = name of FFT library - -FFT_INC = -DFFT_FFTW -FFT_PATH = -L$(ARMPL_LIBRARIES) -FFT_LIB = -larmpl_lp64 - -# JPEG and/or PNG library -# see discussion in Section 2.2 (step 7) of manual -# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC -# INC = path(s) for jpeglib.h and/or png.h -# PATH = path(s) for JPEG library and/or PNG library -# LIB = name(s) of JPEG library and/or PNG library - -JPG_INC = -JPG_PATH = -JPG_LIB = - -# --------------------------------------------------------------------- -# build rules and dependencies -# do not edit this section - -include Makefile.package.settings -include Makefile.package - -EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) -EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) -EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) -EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) -EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) - -# Path to src files - -vpath %.cpp .. -vpath %.h .. - -# Link target - -$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) - $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) - $(SIZE) $(EXE) - -# Library targets - -lib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) - -shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ - $(OBJ) $(EXTRA_LIB) $(LIB) - -# Compilation rules - -%.o:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -%.d:%.cpp $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ - -%.o:%.cu $(EXTRA_CPP_DEPENDS) - $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< - -# Individual dependencies - -depend : fastdep.exe $(SRC) - @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 - -fastdep.exe: ../DEPEND/fastdep.c - cc -O -o $@ $< - -sinclude .depend +# g++_serial = GNU g++ compiler, no MPI + +SHELL = /bin/sh + +# --------------------------------------------------------------------- +# compiler/linker settings +# specify flags and libraries needed for your compiler + +CC = g++ +CCFLAGS = -O3 -march=native -mcpu=native +SHFLAGS = -fPIC +DEPFLAGS = -M + +LINK = g++ +LINKFLAGS = -O +LIB = +SIZE = size + +ARCHIVE = ar +ARFLAGS = -rc +SHLIBFLAGS = -shared + +# --------------------------------------------------------------------- +# LAMMPS-specific settings, all OPTIONAL +# specify settings for LAMMPS features you will use +# if you change any -D setting, do full re-compile after "make clean" + +# LAMMPS ifdef settings +# see possible settings in Section 2.2 (step 4) of manual + +LMP_INC = -DLAMMPS_GZIP + +# MPI library +# see discussion in Section 2.2 (step 5) of manual +# MPI wrapper compiler/linker can provide this info +# can point to dummy MPI library in src/STUBS as in Makefile.serial +# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts +# INC = path for mpi.h, MPI compiler settings +# PATH = path for MPI library +# LIB = name of MPI library + +MPI_INC = -I../STUBS +MPI_PATH = -L../STUBS +MPI_LIB = -lmpi_stubs + +# FFT library +# see discussion in Section 2.2 (step 6) of manaul +# can be left blank to use provided KISS FFT library +# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings +# PATH = path for FFT library +# LIB = name of FFT library + +FFT_INC = -DFFT_FFTW +FFT_PATH = -L$(ARMPL_LIBRARIES) +FFT_LIB = -larmpl_lp64 + +# JPEG and/or PNG library +# see discussion in Section 2.2 (step 7) of manual +# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC +# INC = path(s) for jpeglib.h and/or png.h +# PATH = path(s) for JPEG library and/or PNG library +# LIB = name(s) of JPEG library and/or PNG library + +JPG_INC = +JPG_PATH = +JPG_LIB = + +# --------------------------------------------------------------------- +# build rules and dependencies +# do not edit this section + +include Makefile.package.settings +include Makefile.package + +EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC) +EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH) +EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB) +EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS) +EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS) + +# Path to src files + +vpath %.cpp .. +vpath %.h .. + +# Link target + +$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS) + $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE) + $(SIZE) $(EXE) + +# Library targets + +lib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ) + +shlib: $(OBJ) $(EXTRA_LINK_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \ + $(OBJ) $(EXTRA_LIB) $(LIB) + +# Compilation rules + +%.o:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +%.d:%.cpp $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@ + +%.o:%.cu $(EXTRA_CPP_DEPENDS) + $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $< + +# Individual dependencies + +depend : fastdep.exe $(SRC) + @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1 + +fastdep.exe: ../DEPEND/fastdep.c + cc -O -o $@ $< + +sinclude .depend diff --git a/src/MAKE/MACHINES/Makefile.cori2 b/src/MAKE/MACHINES/Makefile.cori2 old mode 100755 new mode 100644 diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 7146ee9d65..5019e7711a 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -33,6 +33,8 @@ #include "update.h" #include "memory.h" #include "error.h" +#include "utils.h" + using namespace LAMMPS_NS; using namespace FixConst; @@ -121,12 +123,12 @@ void FixQEQComb::init() if (!atom->q_flag) error->all(FLERR,"Fix qeq/comb requires atom attribute q"); - comb = (PairComb *) force->pair_match("comb",1); - comb3 = (PairComb3 *) force->pair_match("comb3",1); + comb = (PairComb *) force->pair_match("^comb",0); + comb3 = (PairComb3 *) force->pair_match("^comb3",0); if (comb == NULL && comb3 == NULL) error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb"); - if (strstr(update->integrate_style,"respa")) { + if (utils::strmatch(update->integrate_style,"^respa")) { ilevel_respa = ((Respa *) update->integrate)->nlevels-1; if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa); } diff --git a/src/MANYBODY/pair_adp.cpp b/src/MANYBODY/pair_adp.cpp index 7b48522e84..68511b8709 100644 --- a/src/MANYBODY/pair_adp.cpp +++ b/src/MANYBODY/pair_adp.cpp @@ -28,6 +28,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -132,8 +133,7 @@ void PairADP::compute(int eflag, int vflag) double sumlamxx,sumlamyy,sumlamzz,sumlamyz,sumlamxz,sumlamxy; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // grow local arrays if necessary // need to be atom->nmax in length @@ -561,10 +561,10 @@ void PairADP::read_file(char *filename) int n; if (me == 0) { - fgets(line,MAXLINE,fp); - fgets(line,MAXLINE,fp); - fgets(line,MAXLINE,fp); - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); @@ -589,7 +589,7 @@ void PairADP::read_file(char *filename) delete [] words; if (me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); sscanf(line,"%d %lg %d %lg %lg", &file->nrho,&file->drho,&file->nr,&file->dr,&file->cut); } @@ -613,32 +613,32 @@ void PairADP::read_file(char *filename) int i,j,tmp; for (i = 0; i < file->nelements; i++) { if (me == 0) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); sscanf(line,"%d %lg",&tmp,&file->mass[i]); } MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world); - if (me == 0) grab(fp,file->nrho,&file->frho[i][1]); + if (me == 0) grab(fp,filename,file->nrho,&file->frho[i][1]); MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world); - if (me == 0) grab(fp,file->nr,&file->rhor[i][1]); + if (me == 0) grab(fp,filename,file->nr,&file->rhor[i][1]); MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world); } for (i = 0; i < file->nelements; i++) for (j = 0; j <= i; j++) { - if (me == 0) grab(fp,file->nr,&file->z2r[i][j][1]); + if (me == 0) grab(fp,filename,file->nr,&file->z2r[i][j][1]); MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world); } for (i = 0; i < file->nelements; i++) for (j = 0; j <= i; j++) { - if (me == 0) grab(fp,file->nr,&file->u2r[i][j][1]); + if (me == 0) grab(fp,filename,file->nr,&file->u2r[i][j][1]); MPI_Bcast(&file->u2r[i][j][1],file->nr,MPI_DOUBLE,0,world); } for (i = 0; i < file->nelements; i++) for (j = 0; j <= i; j++) { - if (me == 0) grab(fp,file->nr,&file->w2r[i][j][1]); + if (me == 0) grab(fp,filename,file->nr,&file->w2r[i][j][1]); MPI_Bcast(&file->w2r[i][j][1],file->nr,MPI_DOUBLE,0,world); } @@ -918,14 +918,14 @@ void PairADP::interpolate(int n, double delta, double *f, double **spline) only called by proc 0 ------------------------------------------------------------------------- */ -void PairADP::grab(FILE *fp, int n, double *list) +void PairADP::grab(FILE *fp, char *filename, int n, double *list) { char *ptr; char line[MAXLINE]; int i = 0; while (i < n) { - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,filename,error); ptr = strtok(line," \t\n\r\f"); list[i++] = atof(ptr); while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr); diff --git a/src/MANYBODY/pair_adp.h b/src/MANYBODY/pair_adp.h index e4f8275639..360e910c2a 100644 --- a/src/MANYBODY/pair_adp.h +++ b/src/MANYBODY/pair_adp.h @@ -82,7 +82,7 @@ class PairADP : public Pair { void allocate(); void array2spline(); void interpolate(int, double, double *, double **); - void grab(FILE *, int, double *); + void grab(FILE *, char *, int, double *); void read_file(char *); void file2array(); diff --git a/src/MANYBODY/pair_airebo.cpp b/src/MANYBODY/pair_airebo.cpp index 067eb1634f..4502bd9a82 100644 --- a/src/MANYBODY/pair_airebo.cpp +++ b/src/MANYBODY/pair_airebo.cpp @@ -38,6 +38,7 @@ #include "math_special.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -107,8 +108,7 @@ PairAIREBO::~PairAIREBO() void PairAIREBO::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); pvector[0] = pvector[1] = pvector[2] = 0.0; REBO_neigh(); @@ -2116,7 +2116,7 @@ but of the vector r_ij. */ -double PairAIREBO::bondorderLJ(int i, int j, double /*rij_mod*/[3], double rijmag_mod, +double PairAIREBO::bondorderLJ(int i, int j, double /* rij_mod */[3], double rijmag_mod, double VA, double rij[3], double rijmag, double **f, int vflag_atom) { @@ -3368,8 +3368,12 @@ void PairAIREBO::read_file(char *filename) // read file on proc 0 + int cerror = 0; + int numpar = 0; + FILE *fp = NULL; + if (me == 0) { - FILE *fp = force->open_potential(filename); + fp = force->open_potential(filename); if (fp == NULL) { char str[128]; if (morseflag) @@ -3382,296 +3386,402 @@ void PairAIREBO::read_file(char *filename) // skip initial comment lines while (1) { - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); if (s[0] != '#') break; } // read parameters - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmin_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmin_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmin_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmax_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmax_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmax_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmaxp_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmaxp_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcmaxp_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&smin); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Nmin); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Nmax); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&NCmin); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&NCmax); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Q_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Q_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Q_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&alpha_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&alpha_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&alpha_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&A_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&A_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&A_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_CC1); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_CC2); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_CC3); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_CH1); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_CH2); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_CH3); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_HH1); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_HH2); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&BIJc_HH3); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_CC1); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_CC2); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_CC3); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_CH1); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_CH2); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_CH3); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_HH1); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_HH2); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Beta_HH3); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rho_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rho_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rho_HH); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmin_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmin_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmin_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmax_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmax_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmax_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmaxp_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmaxp_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcmaxp_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&smin)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Nmin)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Nmax)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&NCmin)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&NCmax)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Q_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Q_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Q_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&alpha_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&alpha_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&alpha_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&A_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&A_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&A_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_CC1)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_CC2)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_CC3)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_CH1)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_CH2)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_CH3)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_HH1)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_HH2)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&BIJc_HH3)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_CC1)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_CC2)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_CC3)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_CH1)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_CH2)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_CH3)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_HH1)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_HH2)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Beta_HH3)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rho_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rho_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rho_HH)) ++cerror; // LJ parameters - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcLJmin_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcLJmin_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcLJmin_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcLJmax_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcLJmax_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&rcLJmax_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&bLJmin_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&bLJmin_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&bLJmin_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&bLJmax_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&bLJmax_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&bLJmax_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilon_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilon_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilon_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&sigma_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&sigma_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&sigma_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilonT_CCCC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilonT_CCCH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilonT_HCCH); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcLJmin_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcLJmin_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcLJmin_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcLJmax_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcLJmax_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&rcLJmax_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&bLJmin_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&bLJmin_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&bLJmin_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&bLJmax_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&bLJmax_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&bLJmax_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilon_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilon_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilon_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&sigma_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&sigma_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&sigma_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilonT_CCCC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilonT_CCCH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilonT_HCCH)) ++cerror; if (morseflag) { // lines for reading in MORSE parameters from CH.airebo_m file - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilonM_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilonM_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&epsilonM_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&alphaM_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&alphaM_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&alphaM_HH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&reqM_CC); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&reqM_CH); - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&reqM_HH); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilonM_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilonM_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&epsilonM_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&alphaM_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&alphaM_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&alphaM_HH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&reqM_CC)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&reqM_CH)) ++cerror; + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&reqM_HH)) ++cerror; } + + } + + // check for errors parsing global parameters + MPI_Bcast(&cerror,1,MPI_INT,0,world); + if (cerror > 0) { + char msg[128]; + snprintf(msg,128,"Could not parse %d of %d parameters from file %s", + cerror,numpar,filename); + error->all(FLERR,msg); + } + cerror = numpar = 0; + + if (me == 0) { + // gC spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); // number-1 = # of domains for the spline - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit; i++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&gCdom[i]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&gCdom[i])) ++cerror; } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < limit-1; i++) { for (j = 0; j < 6; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&gC1[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&gC1[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < limit-1; i++) { for (j = 0; j < 6; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&gC2[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&gC2[i][j])) ++cerror; } } // gH spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit; i++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&gHdom[i]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&gHdom[i])) ++cerror; } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < limit-1; i++) { for (j = 0; j < 6; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&gH[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&gH[i][j])) ++cerror; } } // pCC spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit/2; i++) { for (j = 0; j < limit/2; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&pCCdom[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&pCCdom[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < (int) pCCdom[0][1]; i++) { for (j = 0; j < (int) pCCdom[1][1]; j++) { for (k = 0; k < 16; k++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&pCC[i][j][k]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&pCC[i][j][k])) ++cerror; } } } // pCH spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit/2; i++) { for (j = 0; j < limit/2; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&pCHdom[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&pCHdom[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < (int) pCHdom[0][1]; i++) { for (j = 0; j < (int) pCHdom[1][1]; j++) { for (k = 0; k < 16; k++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&pCH[i][j][k]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&pCH[i][j][k])) ++cerror; } } } // piCC cpline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit/2; i++) { for (j = 0; j < limit/3; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&piCCdom[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&piCCdom[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < (int) piCCdom[0][1]; i++) { for (j = 0; j < (int) piCCdom[1][1]; j++) { for (k = 0; k < (int) piCCdom[2][1]; k++) { for (l = 0; l < 64; l = l+1) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&piCC[i][j][k][l]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&piCC[i][j][k][l])) ++cerror; } } } @@ -3679,27 +3789,30 @@ void PairAIREBO::read_file(char *filename) // piCH spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit/2; i++) { for (j = 0; j < limit/3; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&piCHdom[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&piCHdom[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < (int) piCHdom[0][1]; i++) { for (j = 0; j < (int) piCHdom[1][1]; j++) { for (k = 0; k < (int) piCHdom[2][1]; k++) { for (l = 0; l < 64; l = l+1) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&piCH[i][j][k][l]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&piCH[i][j][k][l])) ++cerror; } } } @@ -3707,27 +3820,30 @@ void PairAIREBO::read_file(char *filename) // piHH spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit/2; i++) { for (j = 0; j < limit/3; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&piHHdom[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&piHHdom[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < (int) piHHdom[0][1]; i++) { for (j = 0; j < (int) piHHdom[1][1]; j++) { for (k = 0; k < (int) piHHdom[2][1]; k++) { for (l = 0; l < 64; l = l+1) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&piHH[i][j][k][l]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&piHH[i][j][k][l])) ++cerror; } } } @@ -3735,27 +3851,30 @@ void PairAIREBO::read_file(char *filename) // Tij spline - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); - fgets(s,MAXLINE,fp); - sscanf(s,"%d",&limit); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%d",&limit)) ++cerror; for (i = 0; i < limit/2; i++) { for (j = 0; j < limit/3; j++) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Tijdom[i][j]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Tijdom[i][j])) ++cerror; } } - fgets(s,MAXLINE,fp); + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); for (i = 0; i < (int) Tijdom[0][1]; i++) { for (j = 0; j < (int) Tijdom[1][1]; j++) { for (k = 0; k < (int) Tijdom[2][1]; k++) { for (l = 0; l < 64; l = l+1) { - fgets(s,MAXLINE,fp); - sscanf(s,"%lg",&Tijc[i][j][k][l]); + ++numpar; + utils::sfgets(FLERR,s,MAXLINE,fp,filename,error); + if (1 != sscanf(s,"%lg",&Tijc[i][j][k][l])) ++cerror; } } } @@ -3763,6 +3882,16 @@ void PairAIREBO::read_file(char *filename) fclose(fp); } + + // check for errors parsing spline data + + MPI_Bcast(&cerror,1,MPI_INT,0,world); + if (cerror > 0) { + char msg[128]; + snprintf(msg,128,"Could not parse %d of %d spline data from file %s", + cerror,numpar,filename); + error->all(FLERR,msg); + } // store read-in values in arrays diff --git a/src/MANYBODY/pair_atm.cpp b/src/MANYBODY/pair_atm.cpp index a6e52faeba..c157e0763c 100644 --- a/src/MANYBODY/pair_atm.cpp +++ b/src/MANYBODY/pair_atm.cpp @@ -82,8 +82,7 @@ void PairATM::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -272,7 +271,7 @@ double PairATM::init_one(int i, int j) int ntypes = atom->ntypes; for (int k = j; k <= ntypes; k++) - nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] = + nu[i][k][j] = nu[j][i][k] = nu[j][k][i] = nu[k][i][j] = nu[k][j][i] = nu[i][j][k]; return cut_global; @@ -290,8 +289,8 @@ void PairATM::write_restart(FILE *fp) for (i = 1; i <= atom->ntypes; i++) { for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) - for (k = j; k <= atom->ntypes; k++) + if (setflag[i][j]) + for (k = j; k <= atom->ntypes; k++) fwrite(&nu[i][j][k],sizeof(double),1,fp); } } @@ -361,12 +360,12 @@ void PairATM::interaction_ddd(double nu, double r6, rrk = rjk[0]*rik[0] + rjk[1]*rik[1] + rjk[2]*rik[2]; rrr = 5.0*rri*rrj*rrk; for (int i = 0; i < 3; i++) { - fj[i] = rrj*(rrk - rri)*rik[i] - - (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] + + fj[i] = rrj*(rrk - rri)*rik[i] - + (rrk*rri - rjk2*rik2 + rrr/rij2) * rij[i] + (rrk*rri - rik2*rij2 + rrr/rjk2) * rjk[i]; fj[i] *= 3.0*r5inv; - fk[i] = rrk*(rri + rrj)*rij[i] + - (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] + + fk[i] = rrk*(rri + rrj)*rij[i] + + (rri*rrj + rik2*rij2 - rrr/rjk2) * rjk[i] + (rri*rrj + rij2*rjk2 - rrr/rik2) * rik[i]; fk[i] *= 3.0*r5inv; } diff --git a/src/MANYBODY/pair_atm.h b/src/MANYBODY/pair_atm.h index 70883a81c7..8a9d38ec3b 100644 --- a/src/MANYBODY/pair_atm.h +++ b/src/MANYBODY/pair_atm.h @@ -43,7 +43,7 @@ class PairATM : public Pair { double ***nu; void allocate(); - void interaction_ddd(double, double, double, double, double, double *, + void interaction_ddd(double, double, double, double, double, double *, double *, double *, double *, double *, int, double &); }; diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp index ca0f229068..ac157e071c 100644 --- a/src/MANYBODY/pair_bop.cpp +++ b/src/MANYBODY/pair_bop.cpp @@ -297,8 +297,7 @@ void PairBOP::compute(int eflag, int vflag) ilist = list->ilist; firstneigh = list->firstneigh; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // BOP Neighbor lists must be updated every timestep maxnall=nall; @@ -4988,7 +4987,7 @@ void PairBOP::read_table(char *filename) fgets(s,MAXLINE,fp); nws=0; ws=1; - for(j=0;jme == 0 && screen) fprintf(screen, + if (comm->me == 0 && screen) fprintf(screen, " PairComb3: Found C: reading additional library file\n"); read_lib(); cflag = 1; @@ -922,7 +922,7 @@ void PairComb3::Short_neigh() icontrol = params[iparam_ij].jelementgp; - if( icontrol == 1) + if (icontrol == 1) xcctmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross; if (icontrol == 2) xchtmp[i] += comb_fc(rr1,¶ms[iparam_ij]) * params[iparam_ij].pcross; @@ -987,8 +987,7 @@ void PairComb3::compute(int eflag, int vflag) evdwl = eng_tmp = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); // Build short range neighbor list Short_neigh(); @@ -1250,7 +1249,7 @@ void PairComb3::compute(int eflag, int vflag) // torsion: i-j-k-l: apply to all C-C bonds - if( params[iparam_ij].tor_flag != 0 ) { + if (params[iparam_ij].tor_flag != 0) { srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2)); srmu = sqrt(1.0-srmu*srmu); @@ -1382,7 +1381,7 @@ void PairComb3::compute(int eflag, int vflag) } // torsion and radical: apply to all C-C bonds - if( params[iparam_ijk].tor_flag != 0 && fabs(ptorr)>1.0e-8) { + if (params[iparam_ijk].tor_flag != 0 && fabs(ptorr)>1.0e-8) { srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2)); srmu = sqrt(1.0-srmu*srmu); @@ -2578,7 +2577,7 @@ void PairComb3::tables() rvdw[1][inty] = params[iparam_ij].vsig * 0.950; // radius check: outer radius vs. sigma - if( rvdw[0][inty] > rvdw[1][inty] ) + if (rvdw[0][inty] > rvdw[1][inty]) error->all(FLERR,"Error in vdw spline: inner radius > outer radius"); rrc[0] = rvdw[1][inty]; diff --git a/src/MANYBODY/pair_eam.cpp b/src/MANYBODY/pair_eam.cpp index f4b4901075..b7957349b6 100644 --- a/src/MANYBODY/pair_eam.cpp +++ b/src/MANYBODY/pair_eam.cpp @@ -142,8 +142,7 @@ void PairEAM::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // grow energy and fp arrays if necessary // need to be atom->nmax in length diff --git a/src/MANYBODY/pair_eam_cd.cpp b/src/MANYBODY/pair_eam_cd.cpp index 8db1b6dd9a..c111c6d950 100644 --- a/src/MANYBODY/pair_eam_cd.cpp +++ b/src/MANYBODY/pair_eam_cd.cpp @@ -73,8 +73,7 @@ void PairEAMCD::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // Grow per-atom arrays if necessary diff --git a/src/MANYBODY/pair_eim.cpp b/src/MANYBODY/pair_eim.cpp index b0fa1b1eef..f1c028ef38 100644 --- a/src/MANYBODY/pair_eim.cpp +++ b/src/MANYBODY/pair_eim.cpp @@ -113,8 +113,7 @@ void PairEIM::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); // grow energy array if necessary diff --git a/src/MANYBODY/pair_gw.cpp b/src/MANYBODY/pair_gw.cpp index f2d3b67eb0..e4b74f7a29 100644 --- a/src/MANYBODY/pair_gw.cpp +++ b/src/MANYBODY/pair_gw.cpp @@ -87,8 +87,7 @@ void PairGW::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -521,7 +520,7 @@ void PairGW::setup_params() for (m = 0; m < nparams; m++) { if (i == params[m].ielement && j == params[m].jelement && k == params[m].kelement) { - if (n >= 0) + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); n = m; } diff --git a/src/MANYBODY/pair_lcbop.cpp b/src/MANYBODY/pair_lcbop.cpp index 88477e48f3..05cdea8055 100644 --- a/src/MANYBODY/pair_lcbop.cpp +++ b/src/MANYBODY/pair_lcbop.cpp @@ -87,8 +87,7 @@ PairLCBOP::~PairLCBOP() void PairLCBOP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); SR_neigh(); FSR(eflag,vflag); @@ -122,7 +121,7 @@ void PairLCBOP::allocate() ------------------------------------------------------------------------- */ void PairLCBOP::settings(int narg, char **/*arg*/) { - if( narg != 0 ) error->all(FLERR,"Illegal pair_style command"); + if (narg != 0 ) error->all(FLERR,"Illegal pair_style command"); } /* ---------------------------------------------------------------------- @@ -402,7 +401,7 @@ void PairLCBOP::FSR(int eflag, int /*vflag*/) r_sq = delx*delx + dely*dely + delz*delz; rijmag = sqrt(r_sq); f_c_ij = f_c( rijmag,r_1,r_2,&df_c_ij ); - if( f_c_ij <= TOL ) continue; + if (f_c_ij <= TOL) continue; VR = A*exp(-alpha*rijmag); dVRdi = -alpha*VR; @@ -502,10 +501,10 @@ void PairLCBOP::FLR(int eflag, int /*vflag*/) df_c_ij = -df_c_ij; // derivative may be inherited from previous call, see f_c_LR definition f_c_ij *= f_c_LR( rijmag, r_1_LR, r_2_LR, &df_c_ij ); - if( f_c_ij <= TOL ) continue; + if (f_c_ij <= TOL) continue; V = dVdi = 0; - if( rijmag r_1*r_1 ) { // && riksq < r_2*r_2, if second condition not fulfilled neighbor would not be in the list + if (riksq > r_1*r_1) { // && riksq < r_2*r_2, if second condition not fulfilled neighbor would not be in the list double rikmag = sqrt(riksq); double df_c_ik; f_c( rikmag, r_1, r_2, &df_c_ik ); @@ -598,7 +597,7 @@ void PairLCBOP::FMij( int i, int j, double factor, double **f, int vflag_atom ) double Fx = 1-f_c_LR(Nki, 2,3,&dF); dF = -dF; - if( df_c_ik > TOL ) { + if (df_c_ik > TOL) { double factor2 = factor*df_c_ik*Fx; // F = factor2*(-grad rikmag) // grad_i rikmag = \vec{rik} /rikmag @@ -613,7 +612,7 @@ void PairLCBOP::FMij( int i, int j, double factor, double **f, int vflag_atom ) if (vflag_atom) v_tally2(atomi,atomk,fpair,rik); } - if( dF > TOL ) { + if (dF > TOL) { double factor2 = factor*f_c_ik*dF; FNij( atomk, atomi, factor2, f, vflag_atom ); } @@ -676,12 +675,12 @@ double PairLCBOP::bondorder(int i, int j, double rij[3], double num_Nconj = ( Nij+1 )*( Nji+1 )*( Nij_el+Nji_el ) - 4*( Nij+Nji+2); double den_Nconj = Nij*( 3-Nij )*( Nji+1 ) + Nji*( 3-Nji )*( Nij+1 ) + eps; Nconj = num_Nconj / den_Nconj; - if( Nconj <= 0 ) { + if (Nconj <= 0) { Nconj = 0; dNconj_dNij = 0; dNconj_dNji = 0; dNconj_dNel = 0; - } else if( Nconj >= 1 ) { + } else if (Nconj >= 1) { Nconj = 1; dNconj_dNij = 0; dNconj_dNji = 0; @@ -703,21 +702,21 @@ double PairLCBOP::bondorder(int i, int j, double rij[3], Fij_conj = F_conj( Nij, Nji, Nconj, &dF_dNij, &dF_dNji, &dF_dNconj ); /*forces for Nij*/ - if( 3-Nij > TOL ) { + if (3-Nij > TOL) { double factor = -VA*0.5*( dF_dNij + dF_dNconj*( dNconj_dNij + dNconj_dNel*dNij_el_dNij ) ); FNij( i, j, factor, f, vflag_atom ); } /*forces for Nji*/ - if( 3-Nji > TOL ) { + if (3-Nji > TOL) { double factor = -VA*0.5*( dF_dNji + dF_dNconj*( dNconj_dNji + dNconj_dNel*dNji_el_dNji ) ); FNij( j, i, factor, f, vflag_atom ); } /*forces for Mij*/ - if( 3-Mij > TOL ) { + if (3-Mij > TOL) { double factor = -VA*0.5*( dF_dNconj*dNconj_dNel*dNij_el_dMij ); FMij( i, j, factor, f, vflag_atom ); } - if( 3-Mji > TOL ) { + if (3-Mji > TOL) { double factor = -VA*0.5*( dF_dNconj*dNconj_dNel*dNji_el_dMji ); FMij( j, i, factor, f, vflag_atom ); } @@ -900,14 +899,14 @@ double PairLCBOP::gSpline( double x, double *dgdc ) { /* ---------------------------------------------------------------------- */ double PairLCBOP::hSpline( double x, double *dhdx ) { - if( x < -d ) { + if (x < -d) { double z = kappa*( x+d ); double y = pow(z, 10.0); double w = pow( 1+y, -0.1 ); *dhdx = kappa*L*w/(1+y); return L*( 1 + z*w ); } - if( x > d ) { + if (x > d) { *dhdx = R_1; return R_0 + R_1*( x-d ); } @@ -941,13 +940,13 @@ double PairLCBOP::F_conj( double N_ij, double N_ji, double N_conj_ij, double *dF double dF_0_dx = 0, dF_0_dy = 0; double dF_1_dx = 0, dF_1_dy = 0; double l, r; - if( N_conj_ij < 1 ) { + if (N_conj_ij < 1) { l = (1-y)* (1-x); r = ( f0.f_00 + x* x* f0.f_x_10 + y* y* f0.f_y_01 ); F_0 += l*r; dF_0_dx += -(1-y)*r +l*2*x* f0.f_x_10; dF_0_dy += -(1-x)*r +l*2*y* f0.f_y_01; l = (1-y)* x; r = ( f0.f_10 + (1-x)*(1-x)*f0.f_x_00 + y* y* f0.f_y_11 ); F_0 += l*r; dF_0_dx += (1-y)*r -l*2*(1-x)*f0.f_x_00; dF_0_dy += -x* r +l*2*y* f0.f_y_11; l = y* (1-x); r = ( f0.f_01 + x* x* f0.f_x_11 + (1-y)*(1-y)*f0.f_y_00 ); F_0 += l*r; dF_0_dx += -y* r +l*2*x* f0.f_x_11; dF_0_dy += (1-x)*r -l*2*(1-y)*f0.f_y_00; l = y* x; r = ( f0.f_11 + (1-x)*(1-x)*f0.f_x_01 + (1-y)*(1-y)*f0.f_y_10 ); F_0 += l*r; dF_0_dx += y* r -l*2*(1-x)*f0.f_x_01; dF_0_dy += x* r -l*2*(1-y)*f0.f_y_10; } - if( N_conj_ij > 0 ) { + if (N_conj_ij > 0) { l = (1-y)* (1-x); r = ( f0.f_00 + x* x* f1.f_x_10 + y* y* f1.f_y_01 ); F_1 += l*r; dF_1_dx += -(1-y)*r +l*2*x* f1.f_x_10; dF_1_dy += -(1-x)*r +l*2*y* f1.f_y_01; l = (1-y)* x; r = ( f1.f_10 + (1-x)*(1-x)*f1.f_x_00 + y* y* f1.f_y_11 ); F_1 += l*r; dF_1_dx += (1-y)*r -l*2*(1-x)*f1.f_x_00; dF_1_dy += -x* r +l*2*y* f1.f_y_11; l = y* (1-x); r = ( f1.f_01 + x* x* f1.f_x_11 + (1-y)*(1-y)*f1.f_y_00 ); F_1 += l*r; dF_1_dx += -y* r +l*2*x* f1.f_x_11; dF_1_dy += (1-x)*r -l*2*(1-y)*f1.f_y_00; diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index ce449e4890..a61b403459 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -87,8 +87,7 @@ void PairNb3bHarmonic::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MANYBODY/pair_polymorphic.cpp b/src/MANYBODY/pair_polymorphic.cpp index 41c5892d4e..d3aca4e889 100644 --- a/src/MANYBODY/pair_polymorphic.cpp +++ b/src/MANYBODY/pair_polymorphic.cpp @@ -117,8 +117,7 @@ void PairPolymorphic::compute(int eflag, int vflag) double emb; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MANYBODY/pair_sw.cpp b/src/MANYBODY/pair_sw.cpp index 91e11b3d26..5a148fb152 100644 --- a/src/MANYBODY/pair_sw.cpp +++ b/src/MANYBODY/pair_sw.cpp @@ -91,8 +91,7 @@ void PairSW::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MANYBODY/pair_tersoff.cpp b/src/MANYBODY/pair_tersoff.cpp index 54101aef9e..213b1037bb 100644 --- a/src/MANYBODY/pair_tersoff.cpp +++ b/src/MANYBODY/pair_tersoff.cpp @@ -93,8 +93,7 @@ void PairTersoff::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MANYBODY/pair_vashishta.cpp b/src/MANYBODY/pair_vashishta.cpp index b4c3086ca8..3d4b1d900e 100644 --- a/src/MANYBODY/pair_vashishta.cpp +++ b/src/MANYBODY/pair_vashishta.cpp @@ -93,8 +93,7 @@ void PairVashishta::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MANYBODY/pair_vashishta_table.cpp b/src/MANYBODY/pair_vashishta_table.cpp index 1055db99fa..d4eaa59f1a 100644 --- a/src/MANYBODY/pair_vashishta_table.cpp +++ b/src/MANYBODY/pair_vashishta_table.cpp @@ -64,8 +64,7 @@ void PairVashishtaTable::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index b40ce6a1b3..f1664e3540 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -46,9 +46,8 @@ #include "thermo.h" #include "output.h" #include "neighbor.h" -#include +#include "utils.h" -using namespace std; using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -406,6 +405,8 @@ FixGCMC::~FixGCMC() memory->destroy(local_gas_list); memory->destroy(molcoords); + memory->destroy(molq); + memory->destroy(molimage); delete [] idrigid; delete [] idshake; @@ -476,8 +477,8 @@ void FixGCMC::init() if ((force->kspace) || (force->pair == NULL) || (force->pair->single_enable == 0) || - (force->pair_match("hybrid",0)) || - (force->pair_match("eam",0)) || + (force->pair_match("^hybrid",0)) || + (force->pair_match("^eam",0)) || (force->pair->tail_flag) ) { full_flag = true; diff --git a/src/MEAM/README b/src/MEAM/README deleted file mode 100644 index 2f2bf275fb..0000000000 --- a/src/MEAM/README +++ /dev/null @@ -1,11 +0,0 @@ -This package implements the MEAM potential as a LAMMPS pair style. - -This package uses an external library in lib/meam which must be -compiled before making LAMMPS. See the lib/meam/README file and the -LAMMPS manual for information on building LAMMPS with external -libraries. The settings in the Makefile.lammps file in that directory -must be correct for LAMMPS to build correctly with this package -installed. - -The person who created the MEAM library and this pair style is Greg -Wagner (while at Sandia, now at Northwestern U). diff --git a/src/MEAM/pair_meam.cpp b/src/MEAM/pair_meam.cpp deleted file mode 100644 index 38e8e97810..0000000000 --- a/src/MEAM/pair_meam.cpp +++ /dev/null @@ -1,949 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Greg Wagner (SNL) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_meam.h" -#include "atom.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -#define MAXLINE 1024 - -enum{FCC,BCC,HCP,DIM,DIAMOND,B1,C11,L12,B2}; -static const int nkeywords = 21; -static const char *keywords[] = { - "Ec","alpha","rho0","delta","lattce", - "attrac","repuls","nn2","Cmin","Cmax","rc","delr", - "augt1","gsmooth_factor","re","ialloy", - "mixture_ref_t","erose_form","zbl", - "emb_lin_neg","bkgd_dyn"}; - -/* ---------------------------------------------------------------------- */ - -PairMEAM::PairMEAM(LAMMPS *lmp) : Pair(lmp) -{ - if (comm->me == 0) - error->warning(FLERR,"THE pair_style meam COMMAND IS OBSOLETE AND " - "WILL BE REMOVED VERY SOON. PLEASE USE meam/c"); - - single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; - - nmax = 0; - rho = rho0 = rho1 = rho2 = rho3 = frhop = NULL; - gamma = dgamma1 = dgamma2 = dgamma3 = arho2b = NULL; - arho1 = arho2 = arho3 = arho3b = t_ave = tsq_ave = NULL; - - maxneigh = 0; - allocated = 0; - scrfcn = dscrfcn = fcpair = NULL; - - nelements = 0; - elements = NULL; - mass = NULL; - - // set comm size needed by this Pair - - comm_forward = 38; - comm_reverse = 30; -} - -/* ---------------------------------------------------------------------- - free all arrays - check if allocated, since class can be destructed when incomplete -------------------------------------------------------------------------- */ - -PairMEAM::~PairMEAM() -{ - meam_cleanup_(); - - memory->destroy(rho); - memory->destroy(rho0); - memory->destroy(rho1); - memory->destroy(rho2); - memory->destroy(rho3); - memory->destroy(frhop); - memory->destroy(gamma); - memory->destroy(dgamma1); - memory->destroy(dgamma2); - memory->destroy(dgamma3); - memory->destroy(arho2b); - - memory->destroy(arho1); - memory->destroy(arho2); - memory->destroy(arho3); - memory->destroy(arho3b); - memory->destroy(t_ave); - memory->destroy(tsq_ave); - - memory->destroy(scrfcn); - memory->destroy(dscrfcn); - memory->destroy(fcpair); - - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - delete [] mass; - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - delete [] map; - delete [] fmap; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairMEAM::compute(int eflag, int vflag) -{ - int i,j,ii,n,inum_half,errorflag; - int *ilist_half,*numneigh_half,**firstneigh_half; - int *numneigh_full,**firstneigh_full; - - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; - - // grow local arrays if necessary - - if (atom->nmax > nmax) { - memory->destroy(rho); - memory->destroy(rho0); - memory->destroy(rho1); - memory->destroy(rho2); - memory->destroy(rho3); - memory->destroy(frhop); - memory->destroy(gamma); - memory->destroy(dgamma1); - memory->destroy(dgamma2); - memory->destroy(dgamma3); - memory->destroy(arho2b); - memory->destroy(arho1); - memory->destroy(arho2); - memory->destroy(arho3); - memory->destroy(arho3b); - memory->destroy(t_ave); - memory->destroy(tsq_ave); - - nmax = atom->nmax; - - memory->create(rho,nmax,"pair:rho"); - memory->create(rho0,nmax,"pair:rho0"); - memory->create(rho1,nmax,"pair:rho1"); - memory->create(rho2,nmax,"pair:rho2"); - memory->create(rho3,nmax,"pair:rho3"); - memory->create(frhop,nmax,"pair:frhop"); - memory->create(gamma,nmax,"pair:gamma"); - memory->create(dgamma1,nmax,"pair:dgamma1"); - memory->create(dgamma2,nmax,"pair:dgamma2"); - memory->create(dgamma3,nmax,"pair:dgamma3"); - memory->create(arho2b,nmax,"pair:arho2b"); - memory->create(arho1,nmax,3,"pair:arho1"); - memory->create(arho2,nmax,6,"pair:arho2"); - memory->create(arho3,nmax,10,"pair:arho3"); - memory->create(arho3b,nmax,3,"pair:arho3b"); - memory->create(t_ave,nmax,3,"pair:t_ave"); - memory->create(tsq_ave,nmax,3,"pair:tsq_ave"); - } - - // neighbor list info - - inum_half = listhalf->inum; - ilist_half = listhalf->ilist; - numneigh_half = listhalf->numneigh; - firstneigh_half = listhalf->firstneigh; - numneigh_full = listfull->numneigh; - firstneigh_full = listfull->firstneigh; - - // strip neighbor lists of any special bond flags before using with MEAM - // necessary before doing neigh_f2c and neigh_c2f conversions each step - - if (neighbor->ago == 0) { - neigh_strip(inum_half,ilist_half,numneigh_half,firstneigh_half); - neigh_strip(inum_half,ilist_half,numneigh_full,firstneigh_full); - } - - // check size of scrfcn based on half neighbor list - - int nlocal = atom->nlocal; - int nall = nlocal + atom->nghost; - - n = 0; - for (ii = 0; ii < inum_half; ii++) n += numneigh_half[ilist_half[ii]]; - - if (n > maxneigh) { - memory->destroy(scrfcn); - memory->destroy(dscrfcn); - memory->destroy(fcpair); - maxneigh = n; - memory->create(scrfcn,maxneigh,"pair:scrfcn"); - memory->create(dscrfcn,maxneigh,"pair:dscrfcn"); - memory->create(fcpair,maxneigh,"pair:fcpair"); - } - - // zero out local arrays - - for (i = 0; i < nall; i++) { - rho0[i] = 0.0; - arho2b[i] = 0.0; - arho1[i][0] = arho1[i][1] = arho1[i][2] = 0.0; - for (j = 0; j < 6; j++) arho2[i][j] = 0.0; - for (j = 0; j < 10; j++) arho3[i][j] = 0.0; - arho3b[i][0] = arho3b[i][1] = arho3b[i][2] = 0.0; - t_ave[i][0] = t_ave[i][1] = t_ave[i][2] = 0.0; - tsq_ave[i][0] = tsq_ave[i][1] = tsq_ave[i][2] = 0.0; - } - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int ntype = atom->ntypes; - - // change neighbor list indices to Fortran indexing - - neigh_c2f(inum_half,ilist_half,numneigh_half,firstneigh_half); - neigh_c2f(inum_half,ilist_half,numneigh_full,firstneigh_full); - - // 3 stages of MEAM calculation - // loop over my atoms followed by communication - - int ifort; - int offset = 0; - errorflag = 0; - - for (ii = 0; ii < inum_half; ii++) { - i = ilist_half[ii]; - ifort = i+1; - meam_dens_init_(&ifort,&nmax,&ntype,type,fmap,&x[0][0], - &numneigh_half[i],firstneigh_half[i], - &numneigh_full[i],firstneigh_full[i], - &scrfcn[offset],&dscrfcn[offset],&fcpair[offset], - rho0,&arho1[0][0],&arho2[0][0],arho2b, - &arho3[0][0],&arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0], - &errorflag); - if (errorflag) { - char str[128]; - sprintf(str,"MEAM library error %d",errorflag); - error->one(FLERR,str); - } - offset += numneigh_half[i]; - } - - comm->reverse_comm_pair(this); - - meam_dens_final_(&nlocal,&nmax,&eflag_either,&eflag_global,&eflag_atom, - &eng_vdwl,eatom,&ntype,type,fmap, - &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0], - &arho3b[0][0],&t_ave[0][0],&tsq_ave[0][0],gamma,dgamma1, - dgamma2,dgamma3,rho,rho0,rho1,rho2,rho3,frhop,&errorflag); - if (errorflag) { - char str[128]; - sprintf(str,"MEAM library error %d",errorflag); - error->one(FLERR,str); - } - - comm->forward_comm_pair(this); - - offset = 0; - - // vptr is first value in vatom if it will be used by meam_force() - // else vatom may not exist, so pass dummy ptr - - double *vptr; - if (vflag_atom) vptr = &vatom[0][0]; - else vptr = &cutmax; - - for (ii = 0; ii < inum_half; ii++) { - i = ilist_half[ii]; - ifort = i+1; - meam_force_(&ifort,&nmax,&eflag_either,&eflag_global,&eflag_atom, - &vflag_atom,&eng_vdwl,eatom,&ntype,type,fmap,&x[0][0], - &numneigh_half[i],firstneigh_half[i], - &numneigh_full[i],firstneigh_full[i], - &scrfcn[offset],&dscrfcn[offset],&fcpair[offset], - dgamma1,dgamma2,dgamma3,rho0,rho1,rho2,rho3,frhop, - &arho1[0][0],&arho2[0][0],arho2b,&arho3[0][0],&arho3b[0][0], - &t_ave[0][0],&tsq_ave[0][0],&f[0][0],vptr,&errorflag); - if (errorflag) { - char str[128]; - sprintf(str,"MEAM library error %d",errorflag); - error->one(FLERR,str); - } - offset += numneigh_half[i]; - } - - // change neighbor list indices back to C indexing - - neigh_f2c(inum_half,ilist_half,numneigh_half,firstneigh_half); - neigh_f2c(inum_half,ilist_half,numneigh_full,firstneigh_full); - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- */ - -void PairMEAM::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - map = new int[n+1]; - fmap = new int[n]; -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairMEAM::settings(int narg, char **/*arg*/) -{ - if (narg != 0) error->all(FLERR,"Illegal pair_style command"); -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairMEAM::coeff(int narg, char **arg) -{ - int i,j,m,n; - - if (!allocated) allocate(); - - if (narg < 6) error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read MEAM element names between 2 filenames - // nelements = # of MEAM elements - // elements = list of unique element names - - if (nelements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - delete [] mass; - } - nelements = narg - 4 - atom->ntypes; - if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); - elements = new char*[nelements]; - mass = new double[nelements]; - - for (i = 0; i < nelements; i++) { - n = strlen(arg[i+3]) + 1; - elements[i] = new char[n]; - strcpy(elements[i],arg[i+3]); - } - - // read MEAM library and parameter files - // pass all parameters to MEAM package - // tell MEAM package that setup is done - - read_files(arg[2],arg[2+nelements+1]); - meam_setup_done_(&cutmax); - - // read args that map atom types to MEAM elements - // map[i] = which element the Ith atom type is, -1 if not mapped - - for (i = 4 + nelements; i < narg; i++) { - m = i - (4+nelements) + 1; - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - if (j < nelements) map[m] = j; - else if (strcmp(arg[i],"NULL") == 0) map[m] = -1; - else error->all(FLERR,"Incorrect args for pair coefficients"); - } - - // clear setflag since coeff() called once with I,J = * * - - n = atom->ntypes; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - // set setflag i,j for type pairs where both are mapped to elements - // set mass for i,i in atom class - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - if (i == j) atom->set_mass(FLERR,i,mass[map[i]]); - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairMEAM::init_style() -{ - if (force->newton_pair == 0) - error->all(FLERR,"Pair style MEAM requires newton pair on"); - - // need full and half neighbor list - - int irequest_full = neighbor->request(this,instance_me); - neighbor->requests[irequest_full]->id = 1; - neighbor->requests[irequest_full]->half = 0; - neighbor->requests[irequest_full]->full = 1; - int irequest_half = neighbor->request(this,instance_me); - neighbor->requests[irequest_half]->id = 2; - - // setup Fortran-style mapping array needed by MEAM package - // fmap is indexed from 1:ntypes by Fortran and stores a Fortran index - // if type I is not a MEAM atom, fmap stores a 0 - - for (int i = 1; i <= atom->ntypes; i++) fmap[i-1] = map[i] + 1; -} - -/* ---------------------------------------------------------------------- - neighbor callback to inform pair style of neighbor list to use - half or full -------------------------------------------------------------------------- */ - -void PairMEAM::init_list(int id, NeighList *ptr) -{ - if (id == 1) listfull = ptr; - else if (id == 2) listhalf = ptr; -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairMEAM::init_one(int /*i*/, int /*j*/) -{ - return cutmax; -} - -/* ---------------------------------------------------------------------- */ - -void PairMEAM::read_files(char *globalfile, char *userfile) -{ - // open global meamf file on proc 0 - - FILE *fp; - if (comm->me == 0) { - fp = force->open_potential(globalfile); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open MEAM potential file %s",globalfile); - error->one(FLERR,str); - } - } - - // allocate parameter arrays - - int params_per_line = 19; - - int *lat = new int[nelements]; - int *ielement = new int[nelements]; - int *ibar = new int[nelements]; - double *z = new double[nelements]; - double *atwt = new double[nelements]; - double *alpha = new double[nelements]; - double *b0 = new double[nelements]; - double *b1 = new double[nelements]; - double *b2 = new double[nelements]; - double *b3 = new double[nelements]; - double *alat = new double[nelements]; - double *esub = new double[nelements]; - double *asub = new double[nelements]; - double *t0 = new double[nelements]; - double *t1 = new double[nelements]; - double *t2 = new double[nelements]; - double *t3 = new double[nelements]; - double *rozero = new double[nelements]; - - bool *found = new bool[nelements]; - for (int i = 0; i < nelements; i++) found[i] = false; - - // read each set of params from global MEAM file - // one set of params can span multiple lines - // store params if element name is in element list - // if element name appears multiple times, only store 1st entry - - int i,n,nwords; - char **words = new char*[params_per_line+1]; - char line[MAXLINE],*ptr; - int eof = 0; - - int nset = 0; - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - - // strip comment, skip line if blank - - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); - if (nwords == 0) continue; - - // concatenate additional lines until have params_per_line words - - while (nwords < params_per_line) { - n = strlen(line); - if (comm->me == 0) { - ptr = fgets(&line[n],MAXLINE-n,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); - } - - if (nwords != params_per_line) - error->all(FLERR,"Incorrect format in MEAM potential file"); - - // words = ptrs to all words in line - // strip single and double quotes from words - - nwords = 0; - words[nwords++] = strtok(line,"' \t\n\r\f"); - while ((words[nwords++] = strtok(NULL,"' \t\n\r\f"))) continue; - - // skip if element name isn't in element list - - for (i = 0; i < nelements; i++) - if (strcmp(words[0],elements[i]) == 0) break; - if (i >= nelements) continue; - - // skip if element already appeared - - if (found[i] == true) continue; - found[i] = true; - - // map lat string to an integer - - if (strcmp(words[1],"fcc") == 0) lat[i] = FCC; - else if (strcmp(words[1],"bcc") == 0) lat[i] = BCC; - else if (strcmp(words[1],"hcp") == 0) lat[i] = HCP; - else if (strcmp(words[1],"dim") == 0) lat[i] = DIM; - else if (strcmp(words[1],"dia") == 0) lat[i] = DIAMOND; - else error->all(FLERR,"Unrecognized lattice type in MEAM file 1"); - - // store parameters - - z[i] = atof(words[2]); - ielement[i] = atoi(words[3]); - atwt[i] = atof(words[4]); - alpha[i] = atof(words[5]); - b0[i] = atof(words[6]); - b1[i] = atof(words[7]); - b2[i] = atof(words[8]); - b3[i] = atof(words[9]); - alat[i] = atof(words[10]); - esub[i] = atof(words[11]); - asub[i] = atof(words[12]); - t0[i] = atof(words[13]); - t1[i] = atof(words[14]); - t2[i] = atof(words[15]); - t3[i] = atof(words[16]); - rozero[i] = atof(words[17]); - ibar[i] = atoi(words[18]); - - nset++; - } - - // error if didn't find all elements in file - - if (nset != nelements) - error->all(FLERR,"Did not find all elements in MEAM library file"); - - // pass element parameters to MEAM package - - meam_setup_global_(&nelements,lat,z,ielement,atwt,alpha,b0,b1,b2,b3, - alat,esub,asub,t0,t1,t2,t3,rozero,ibar); - - // set element masses - - for (i = 0; i < nelements; i++) mass[i] = atwt[i]; - - // clean-up memory - - delete [] words; - - delete [] lat; - delete [] ielement; - delete [] ibar; - delete [] z; - delete [] atwt; - delete [] alpha; - delete [] b0; - delete [] b1; - delete [] b2; - delete [] b3; - delete [] alat; - delete [] esub; - delete [] asub; - delete [] t0; - delete [] t1; - delete [] t2; - delete [] t3; - delete [] rozero; - delete [] found; - - // done if user param file is NULL - - if (strcmp(userfile,"NULL") == 0) return; - - // open user param file on proc 0 - - if (comm->me == 0) { - fp = force->open_potential(userfile); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open MEAM potential file %s",userfile); - error->one(FLERR,str); - } - } - - // read settings - // pass them one at a time to MEAM package - // match strings to list of corresponding ints - - int which; - double value; - int nindex,index[3]; - int maxparams = 6; - char **params = new char*[maxparams]; - int nparams; - - eof = 0; - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - - // strip comment, skip line if blank - - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nparams = atom->count_words(line); - if (nparams == 0) continue; - - // words = ptrs to all words in line - - nparams = 0; - params[nparams++] = strtok(line,"=(), '\t\n\r\f"); - while (nparams < maxparams && - (params[nparams++] = strtok(NULL,"=(), '\t\n\r\f"))) - continue; - nparams--; - - for (which = 0; which < nkeywords; which++) - if (strcmp(params[0],keywords[which]) == 0) break; - if (which == nkeywords) { - char str[128]; - snprintf(str,128,"Keyword %s in MEAM parameter file not recognized", - params[0]); - error->all(FLERR,str); - } - nindex = nparams - 2; - for (i = 0; i < nindex; i++) index[i] = atoi(params[i+1]); - - // map lattce_meam value to an integer - - if (which == 4) { - if (strcmp(params[nparams-1],"fcc") == 0) value = FCC; - else if (strcmp(params[nparams-1],"bcc") == 0) value = BCC; - else if (strcmp(params[nparams-1],"hcp") == 0) value = HCP; - else if (strcmp(params[nparams-1],"dim") == 0) value = DIM; - else if (strcmp(params[nparams-1],"dia") == 0) value = DIAMOND; - else if (strcmp(params[nparams-1],"b1") == 0) value = B1; - else if (strcmp(params[nparams-1],"c11") == 0) value = C11; - else if (strcmp(params[nparams-1],"l12") == 0) value = L12; - else if (strcmp(params[nparams-1],"b2") == 0) value = B2; - else error->all(FLERR,"Unrecognized lattice type in MEAM file 2"); - } - else value = atof(params[nparams-1]); - - // pass single setting to MEAM package - - int errorflag = 0; - meam_setup_param_(&which,&value,&nindex,index,&errorflag); - if (errorflag) { - char str[128]; - sprintf(str,"MEAM library error %d",errorflag); - error->all(FLERR,str); - } - } - - delete [] params; -} - -/* ---------------------------------------------------------------------- */ - -int PairMEAM::pack_forward_comm(int n, int *list, double *buf, - int /*pbc_flag*/, int * /*pbc*/) -{ - int i,j,k,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = rho0[j]; - buf[m++] = rho1[j]; - buf[m++] = rho2[j]; - buf[m++] = rho3[j]; - buf[m++] = frhop[j]; - buf[m++] = gamma[j]; - buf[m++] = dgamma1[j]; - buf[m++] = dgamma2[j]; - buf[m++] = dgamma3[j]; - buf[m++] = arho2b[j]; - buf[m++] = arho1[j][0]; - buf[m++] = arho1[j][1]; - buf[m++] = arho1[j][2]; - buf[m++] = arho2[j][0]; - buf[m++] = arho2[j][1]; - buf[m++] = arho2[j][2]; - buf[m++] = arho2[j][3]; - buf[m++] = arho2[j][4]; - buf[m++] = arho2[j][5]; - for (k = 0; k < 10; k++) buf[m++] = arho3[j][k]; - buf[m++] = arho3b[j][0]; - buf[m++] = arho3b[j][1]; - buf[m++] = arho3b[j][2]; - buf[m++] = t_ave[j][0]; - buf[m++] = t_ave[j][1]; - buf[m++] = t_ave[j][2]; - buf[m++] = tsq_ave[j][0]; - buf[m++] = tsq_ave[j][1]; - buf[m++] = tsq_ave[j][2]; - } - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairMEAM::unpack_forward_comm(int n, int first, double *buf) -{ - int i,k,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - rho0[i] = buf[m++]; - rho1[i] = buf[m++]; - rho2[i] = buf[m++]; - rho3[i] = buf[m++]; - frhop[i] = buf[m++]; - gamma[i] = buf[m++]; - dgamma1[i] = buf[m++]; - dgamma2[i] = buf[m++]; - dgamma3[i] = buf[m++]; - arho2b[i] = buf[m++]; - arho1[i][0] = buf[m++]; - arho1[i][1] = buf[m++]; - arho1[i][2] = buf[m++]; - arho2[i][0] = buf[m++]; - arho2[i][1] = buf[m++]; - arho2[i][2] = buf[m++]; - arho2[i][3] = buf[m++]; - arho2[i][4] = buf[m++]; - arho2[i][5] = buf[m++]; - for (k = 0; k < 10; k++) arho3[i][k] = buf[m++]; - arho3b[i][0] = buf[m++]; - arho3b[i][1] = buf[m++]; - arho3b[i][2] = buf[m++]; - t_ave[i][0] = buf[m++]; - t_ave[i][1] = buf[m++]; - t_ave[i][2] = buf[m++]; - tsq_ave[i][0] = buf[m++]; - tsq_ave[i][1] = buf[m++]; - tsq_ave[i][2] = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -int PairMEAM::pack_reverse_comm(int n, int first, double *buf) -{ - int i,k,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) { - buf[m++] = rho0[i]; - buf[m++] = arho2b[i]; - buf[m++] = arho1[i][0]; - buf[m++] = arho1[i][1]; - buf[m++] = arho1[i][2]; - buf[m++] = arho2[i][0]; - buf[m++] = arho2[i][1]; - buf[m++] = arho2[i][2]; - buf[m++] = arho2[i][3]; - buf[m++] = arho2[i][4]; - buf[m++] = arho2[i][5]; - for (k = 0; k < 10; k++) buf[m++] = arho3[i][k]; - buf[m++] = arho3b[i][0]; - buf[m++] = arho3b[i][1]; - buf[m++] = arho3b[i][2]; - buf[m++] = t_ave[i][0]; - buf[m++] = t_ave[i][1]; - buf[m++] = t_ave[i][2]; - buf[m++] = tsq_ave[i][0]; - buf[m++] = tsq_ave[i][1]; - buf[m++] = tsq_ave[i][2]; - } - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairMEAM::unpack_reverse_comm(int n, int *list, double *buf) -{ - int i,j,k,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - rho0[j] += buf[m++]; - arho2b[j] += buf[m++]; - arho1[j][0] += buf[m++]; - arho1[j][1] += buf[m++]; - arho1[j][2] += buf[m++]; - arho2[j][0] += buf[m++]; - arho2[j][1] += buf[m++]; - arho2[j][2] += buf[m++]; - arho2[j][3] += buf[m++]; - arho2[j][4] += buf[m++]; - arho2[j][5] += buf[m++]; - for (k = 0; k < 10; k++) arho3[j][k] += buf[m++]; - arho3b[j][0] += buf[m++]; - arho3b[j][1] += buf[m++]; - arho3b[j][2] += buf[m++]; - t_ave[j][0] += buf[m++]; - t_ave[j][1] += buf[m++]; - t_ave[j][2] += buf[m++]; - tsq_ave[j][0] += buf[m++]; - tsq_ave[j][1] += buf[m++]; - tsq_ave[j][2] += buf[m++]; - } -} - -/* ---------------------------------------------------------------------- - memory usage of local atom-based arrays -------------------------------------------------------------------------- */ - -double PairMEAM::memory_usage() -{ - double bytes = 11 * nmax * sizeof(double); - bytes += (3 + 6 + 10 + 3 + 3 + 3) * nmax * sizeof(double); - bytes += 3 * maxneigh * sizeof(double); - return bytes; -} - -/* ---------------------------------------------------------------------- - strip special bond flags from neighbor list entries - are not used with MEAM - need to do here so Fortran lib doesn't see them - done once per reneighbor so that neigh_f2c and neigh_c2f don't see them -------------------------------------------------------------------------- */ - -void PairMEAM::neigh_strip(int inum, int *ilist, - int *numneigh, int **firstneigh) -{ - int i,j,ii,jnum; - int *jlist; - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - for (j = 0; j < jnum; j++) jlist[j] &= NEIGHMASK; - } -} - -/* ---------------------------------------------------------------------- - toggle neighbor list indices between zero- and one-based values - needed for access by MEAM Fortran library -------------------------------------------------------------------------- */ - -void PairMEAM::neigh_f2c(int inum, int *ilist, int *numneigh, int **firstneigh) -{ - int i,j,ii,jnum; - int *jlist; - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - for (j = 0; j < jnum; j++) jlist[j]--; - } -} - -void PairMEAM::neigh_c2f(int inum, int *ilist, int *numneigh, int **firstneigh) -{ - int i,j,ii,jnum; - int *jlist; - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - for (j = 0; j < jnum; j++) jlist[j]++; - } -} diff --git a/src/MEAM/pair_meam.h b/src/MEAM/pair_meam.h deleted file mode 100644 index 24aec1c3ed..0000000000 --- a/src/MEAM/pair_meam.h +++ /dev/null @@ -1,159 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(meam,PairMEAM) - -#else - -#ifndef LMP_PAIR_MEAM_H -#define LMP_PAIR_MEAM_H - -extern "C" { - void meam_setup_global_(int *, int *, double *, int *, double *, double *, - double *, double *, double *, double *, double *, - double *, double *, double *, double *, double *, - double *, double *, int *); - void meam_setup_param_(int *, double *, int *, int *, int *); - void meam_setup_done_(double *); - - void meam_dens_init_(int *, int *, int *, int *, int *, - double *, int *, int *, int *, int *, - double *, double *, double *, double *, - double *, double *, - double *, double *, double *, double *, double *, - int *); - - void meam_dens_final_(int *, int *, int *, int *, int *, double *, double *, - int *, int *, int *, - double *, double *, double *, double *, - double *, double *, double *, - double *, double *, double *, double *, - double *, double *, - double *, double *, double *, double *, int *); - - void meam_force_(int *, int *, int *, int *, int *, int *, - double *, double *, int *, int *, int *, - double *, int *, int *, int *, int *, double *, double *, - double *, double *, double *, double *, double *, double *, - double *, double *, double *, double *, double *, double *, - double *, double *, double *, double *, double *, double *, int *); - - void meam_cleanup_(); -} - - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairMEAM : public Pair { - public: - PairMEAM(class LAMMPS *); - ~PairMEAM(); - void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - void init_style(); - void init_list(int, class NeighList *); - double init_one(int, int); - - int pack_forward_comm(int, int *, double *, int, int *); - void unpack_forward_comm(int, int, double *); - int pack_reverse_comm(int, int, double *); - void unpack_reverse_comm(int, int *, double *); - double memory_usage(); - - private: - double cutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - double *mass; // mass of each element - - int *map; // mapping from atom types to elements - int *fmap; // Fortran version of map array for MEAM lib - - int maxneigh; - double *scrfcn,*dscrfcn,*fcpair; - - int nmax; - double *rho,*rho0,*rho1,*rho2,*rho3,*frhop; - double *gamma,*dgamma1,*dgamma2,*dgamma3,*arho2b; - double **arho1,**arho2,**arho3,**arho3b,**t_ave,**tsq_ave; - - void allocate(); - void read_files(char *, char *); - void neigh_strip(int, int *, int *, int **); - void neigh_f2c(int, int *, int *, int **); - void neigh_c2f(int, int *, int *, int **); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -W: The pair_style meam command is unsupported. Please use pair_style meam/c instead - -UNDOCUMENTED - -E: MEAM library error %d - -A call to the MEAM Fortran library returned an error. - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -E: Pair style MEAM requires newton pair on - -See the newton command. This is a restriction to use the MEAM -potential. - -E: Cannot open MEAM potential file %s - -The specified MEAM potential file cannot be opened. Check that the -path and name are correct. - -E: Incorrect format in MEAM potential file - -Incorrect number of words per line in the potential file. - -E: Unrecognized lattice type in MEAM file 1 - -The lattice type in an entry of the MEAM library file is not -valid. - -E: Did not find all elements in MEAM library file - -The requested elements were not found in the MEAM file. - -E: Keyword %s in MEAM parameter file not recognized - -Self-explanatory. - -E: Unrecognized lattice type in MEAM file 2 - -The lattice type in an entry of the MEAM parameter file is not -valid. - -*/ diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp index aca5cd41f9..9c1bfcc796 100644 --- a/src/MESSAGE/fix_client_md.cpp +++ b/src/MESSAGE/fix_client_md.cpp @@ -40,11 +40,11 @@ enum{FORCES=1,ENERGY,PRESSURE,ERROR}; FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { - if (lmp->clientserver != 1) + if (lmp->clientserver != 1) error->all(FLERR,"Fix client/md requires LAMMPS be running as a client"); if (!atom->map_style) error->all(FLERR,"Fix client/md requires atom map"); - if (sizeof(tagint) != 4) + if (sizeof(tagint) != 4) error->all(FLERR,"Fix client/md requires 4-byte atom IDs"); if (strcmp(update->unit_style,"real") == 0) units = REAL; @@ -306,7 +306,7 @@ void FixClientMD::receive_fev(int vflag) } eng = econvert * cs->unpack_double(ENERGY); - + if (vflag) { double *v = (double *) cs->unpack(PRESSURE); diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp index 329ce1fbd9..e9bff7d38a 100644 --- a/src/MESSAGE/message.cpp +++ b/src/MESSAGE/message.cpp @@ -51,13 +51,13 @@ void Message::command(int narg, char **arg) strcmp(arg[2],"mpi/two") == 0) { if (narg != 4) error->all(FLERR,"Illegal message command"); lmp->cslib = new CSlib(clientserver-1,arg[2],arg[3],&world); - + } else if (strcmp(arg[2],"mpi/one") == 0) { if (narg != 3) error->all(FLERR,"Illegal message command"); - if (!lmp->cscomm) + if (!lmp->cscomm) error->all(FLERR,"Message mpi/one mode, but -mpi cmdline arg not used"); lmp->cslib = new CSlib(clientserver-1,arg[2],&lmp->cscomm,&world); - + } else error->all(FLERR,"Illegal message command"); // perform initial handshake between client and server @@ -75,16 +75,16 @@ void Message::command(int narg, char **arg) int *fieldID,*fieldtype,*fieldlen; int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake"); - + } else { int nfield; int *fieldID,*fieldtype,*fieldlen; int msgID = cs->recv(nfield,fieldID,fieldtype,fieldlen); if (msgID != 0) error->one(FLERR,"Bad initial client/server handshake"); char *pstr = cs->unpack_string(1); - if (strcmp(pstr,arg[1]) != 0) + if (strcmp(pstr,arg[1]) != 0) error->one(FLERR,"Mismatch in client/server protocol"); - + cs->send(0,0); } } diff --git a/src/MESSAGE/server_mc.cpp b/src/MESSAGE/server_mc.cpp index 8a7344e86b..8e9a297912 100644 --- a/src/MESSAGE/server_mc.cpp +++ b/src/MESSAGE/server_mc.cpp @@ -128,7 +128,7 @@ void ServerMC::loop() update->nsteps = nsteps; update->firststep = update->ntimestep; update->laststep = update->ntimestep + nsteps; - + update->integrate->setup(1); update->integrate->run(nsteps); diff --git a/src/MESSAGE/server_md.cpp b/src/MESSAGE/server_md.cpp index aa771b7d46..8debd3a987 100644 --- a/src/MESSAGE/server_md.cpp +++ b/src/MESSAGE/server_md.cpp @@ -100,7 +100,7 @@ void ServerMD::loop() if (msgID < 0) break; // SETUP receive at beginning of each run - // required fields: DIM, PERIODICTY, ORIGIN, BOX, + // required fields: DIM, PERIODICTY, ORIGIN, BOX, // NATOMS, NTYPES, TYPES, COORDS // optional fields: others in enum above @@ -152,7 +152,7 @@ void ServerMD::loop() } else error->all(FLERR,"Server md setup field unknown"); } - if (dim == 0 || !periodicity || !origin || !box || + if (dim == 0 || !periodicity || !origin || !box || natoms < 0 || ntypes < 0 || !types || !coords) error->all(FLERR,"Required server md setup field not received"); @@ -164,8 +164,8 @@ void ServerMD::loop() // reset box, global and local // reset proc decomposition - - if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && + + if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && domain->triclinic == 0) error->all(FLERR,"Server md is not initialized for a triclinic box"); @@ -194,7 +194,7 @@ void ServerMD::loop() int ntotal; MPI_Allreduce(&atom->nlocal,&ntotal,1,MPI_INT,MPI_SUM,world); - if (ntotal != natoms) + if (ntotal != natoms) error->all(FLERR,"Server md atom count does not match client"); atom->map_init(); @@ -247,7 +247,7 @@ void ServerMD::loop() // reset global/local box like FixDeform at end_of_step() if (origin && box) { - if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && + if ((box[3] != 0.0 || box[6] != 0.0 || box[7] != 0.0) && domain->triclinic == 0) error->all(FLERR,"Server md is not initialized for a triclinic box"); box_change(origin,box); @@ -348,7 +348,7 @@ void ServerMD::send_fev(int msgID) CSlib *cs = (CSlib *) lmp->cslib; cs->send(msgID,3); - + double *forces = NULL; if (atom->nlocal) { if (units != REAL) forces = &atom->f[0][0]; @@ -370,7 +370,7 @@ void ServerMD::send_fev(int msgID) MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world); engall *= econvert; cs->pack_double(ENERGY,engall); - + double v[6],vall[6]; for (int i = 0; i < 6; i++) v[i] = force->pair->virial[i]; diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index 4e15581377..170103b0d0 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -199,7 +199,7 @@ void FixTTM::init() if (domain->dimension == 2) error->all(FLERR,"Cannot use fix ttm with 2d simulation"); if (domain->nonperiodic != 0) - error->all(FLERR,"Cannot use nonperiodic boundares with fix ttm"); + error->all(FLERR,"Cannot use non-periodic boundares with fix ttm"); if (domain->triclinic) error->all(FLERR,"Cannot use fix ttm with triclinic box"); diff --git a/src/MISC/fix_ttm.h b/src/MISC/fix_ttm.h index 57d18bcb3a..9fbae2a418 100644 --- a/src/MISC/fix_ttm.h +++ b/src/MISC/fix_ttm.h @@ -130,7 +130,7 @@ E: Cannot use fix ttm with 2d simulation This is a current restriction of this fix due to the grid it creates. -E: Cannot use nonperiodic boundares with fix ttm +E: Cannot use non-periodic boundares with fix ttm This fix requires a fully periodic simulation box. diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp index ce077a7a04..124832b63e 100644 --- a/src/MISC/pair_nm_cut.cpp +++ b/src/MISC/pair_nm_cut.cpp @@ -70,8 +70,7 @@ void PairNMCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -274,14 +273,6 @@ double PairNMCut::init_one(int i, int j) } MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); - double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]); - double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]); - double p1 = 1-nn[i][j]; - double p2 = 1-mm[i][j]; - - double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); - double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); - double cut3 = cut[i][j]*cut[i][j]*cut[i][j]; ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut3 * (pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3)); diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp index b807bc972b..6a09d579b7 100644 --- a/src/MISC/pair_nm_cut_coul_cut.cpp +++ b/src/MISC/pair_nm_cut_coul_cut.cpp @@ -74,8 +74,7 @@ void PairNMCutCoulCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -324,14 +323,6 @@ double PairNMCutCoulCut::init_one(int i, int j) } MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); - double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]); - double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]); - double p1 = 1-nn[i][j]; - double p2 = 1-mm[i][j]; - - double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); - double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); - double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 * (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3)); diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp index 325f3da003..af21f02881 100644 --- a/src/MISC/pair_nm_cut_coul_long.cpp +++ b/src/MISC/pair_nm_cut_coul_long.cpp @@ -90,8 +90,7 @@ void PairNMCutCoulLong::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -371,14 +370,6 @@ double PairNMCutCoulLong::init_one(int i, int j) } MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); - double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]); - double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]); - double p1 = 1-nn[i][j]; - double p2 = 1-mm[i][j]; - - double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]); - double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]); - double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 * (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3)); diff --git a/src/MISC/xdr_compat.cpp b/src/MISC/xdr_compat.cpp index 0f4d73cdd9..2d8d0ce7e5 100644 --- a/src/MISC/xdr_compat.cpp +++ b/src/MISC/xdr_compat.cpp @@ -70,7 +70,7 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x) static xdr_uint32_t xdr_htonl(xdr_uint32_t x) { short s=0x0F00; - if( *((char *)&s)==(char)0x0F) { + if (*((char *)&s)==(char)0x0F) { /* bigendian, do nothing */ return x; } else { @@ -82,7 +82,7 @@ static xdr_uint32_t xdr_htonl(xdr_uint32_t x) static xdr_uint32_t xdr_ntohl(xdr_uint32_t x) { short s=0x0F00; - if( *((char *)&s)==(char)0x0F) { + if (*((char *)&s)==(char)0x0F) { /* bigendian, do nothing */ return x; } else { diff --git a/src/MOLECULE/angle_charmm.cpp b/src/MOLECULE/angle_charmm.cpp index 3608601c1f..efd1c682f7 100644 --- a/src/MOLECULE/angle_charmm.cpp +++ b/src/MOLECULE/angle_charmm.cpp @@ -61,8 +61,7 @@ void AngleCharmm::compute(int eflag, int vflag) double delxUB,delyUB,delzUB,rsqUB,rUB,dr,rk,forceUB; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/angle_cosine.cpp b/src/MOLECULE/angle_cosine.cpp index 7fb7ce4c27..6e1b9fa2fb 100644 --- a/src/MOLECULE/angle_cosine.cpp +++ b/src/MOLECULE/angle_cosine.cpp @@ -36,7 +36,7 @@ AngleCosine::AngleCosine(LAMMPS *lmp) : Angle(lmp) {} AngleCosine::~AngleCosine() { - if (allocated) { + if (allocated && !copymode) { memory->destroy(setflag); memory->destroy(k); } @@ -52,8 +52,7 @@ void AngleCosine::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/angle_cosine.h b/src/MOLECULE/angle_cosine.h index ac50a67468..f2406bc5dd 100644 --- a/src/MOLECULE/angle_cosine.h +++ b/src/MOLECULE/angle_cosine.h @@ -30,17 +30,17 @@ class AngleCosine : public Angle { AngleCosine(class LAMMPS *); virtual ~AngleCosine(); virtual void compute(int, int); - void coeff(int, char **); + virtual void coeff(int, char **); double equilibrium_angle(int); void write_restart(FILE *); - void read_restart(FILE *); + virtual void read_restart(FILE *); void write_data(FILE *); double single(int, int, int, int); protected: double *k; - void allocate(); + virtual void allocate(); }; } diff --git a/src/MOLECULE/angle_cosine_delta.cpp b/src/MOLECULE/angle_cosine_delta.cpp index 6f4f5c20d7..eca10970f2 100644 --- a/src/MOLECULE/angle_cosine_delta.cpp +++ b/src/MOLECULE/angle_cosine_delta.cpp @@ -44,8 +44,7 @@ void AngleCosineDelta::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,a,cot,a11,a12,a22,b11,b12,b22,c0,s0,s; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/angle_cosine_periodic.cpp b/src/MOLECULE/angle_cosine_periodic.cpp index e8dd970b3b..cb0a26871a 100644 --- a/src/MOLECULE/angle_cosine_periodic.cpp +++ b/src/MOLECULE/angle_cosine_periodic.cpp @@ -61,8 +61,7 @@ void AngleCosinePeriodic::compute(int eflag, int vflag) double tn,tn_1,tn_2,un,un_1,un_2; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/angle_cosine_squared.cpp b/src/MOLECULE/angle_cosine_squared.cpp index c83ba90a60..28d63344a4 100644 --- a/src/MOLECULE/angle_cosine_squared.cpp +++ b/src/MOLECULE/angle_cosine_squared.cpp @@ -62,8 +62,7 @@ void AngleCosineSquared::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index d28afd76d6..48b493d9b2 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -58,8 +58,7 @@ void AngleHarmonic::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/angle_table.cpp b/src/MOLECULE/angle_table.cpp index 2867865497..7dd56ffb76 100644 --- a/src/MOLECULE/angle_table.cpp +++ b/src/MOLECULE/angle_table.cpp @@ -27,6 +27,7 @@ #include "math_const.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -71,8 +72,7 @@ void AngleTable::compute(int eflag, int vflag) double theta,u,mdu; //mdu: minus du, -du/dx=f eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -381,17 +381,18 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword) if (strspn(line," \t\n") == strlen(line)) continue; // blank line if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + if (strcmp(word,keyword) == 0) break; // matching keyword + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->afile,tb->ninput,"angle:afile"); memory->create(tb->efile,tb->ninput,"angle:efile"); @@ -399,15 +400,24 @@ void AngleTable::read_table(Table *tb, char *file, char *keyword) // read a,e,f table values from file - int itmp; - fgets(line,MAXLINE,fp); + int cerror = 0; + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) { - fgets(line,MAXLINE,fp); - sscanf(line,"%d %lg %lg %lg", - &itmp,&tb->afile[i],&tb->efile[i],&tb->ffile[i]); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + if (3 != sscanf(line,"%*d %lg %lg %lg", + &tb->afile[i],&tb->efile[i],&tb->ffile[i])) ++cerror; } fclose(fp); + + // warn if data was read incompletely, e.g. columns were missing + + if (cerror) { + char str[128]; + sprintf(str,"%d of %d lines in table were incomplete or could not be" + " parsed completely",cerror,tb->ninput); + error->warning(FLERR,str); + } } /* ---------------------------------------------------------------------- diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp index 6e903a936e..cdd3f02505 100644 --- a/src/MOLECULE/atom_vec_molecular.cpp +++ b/src/MOLECULE/atom_vec_molecular.cpp @@ -677,33 +677,33 @@ int AtomVecMolecular::unpack_exchange(double *buf) num_bond[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_bond[nlocal]; k++) { bond_type[nlocal][k] = (int) ubuf(buf[m++]).i; - bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i; + bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i; } num_angle[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_angle[nlocal]; k++) { angle_type[nlocal][k] = (int) ubuf(buf[m++]).i; - angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i; - angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i; - angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i; + angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i; + angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i; + angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i; } num_dihedral[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_dihedral[nlocal]; k++) { dihedral_type[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom1[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom2[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom3[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom4[nlocal][k] = (int) ubuf(buf[m++]).i; + dihedral_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i; + dihedral_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i; + dihedral_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i; + dihedral_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i; } num_improper[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_improper[nlocal]; k++) { improper_type[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom1[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom2[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom3[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom4[nlocal][k] = (int) ubuf(buf[m++]).i; + improper_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i; + improper_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i; + improper_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i; + improper_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i; } nspecial[nlocal][0] = (int) ubuf(buf[m++]).i; @@ -840,33 +840,33 @@ int AtomVecMolecular::unpack_restart(double *buf) num_bond[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_bond[nlocal]; k++) { bond_type[nlocal][k] = (int) ubuf(buf[m++]).i; - bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i; + bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i; } num_angle[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_angle[nlocal]; k++) { angle_type[nlocal][k] = (int) ubuf(buf[m++]).i; - angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i; - angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i; - angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i; + angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i; + angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i; + angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i; } num_dihedral[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_dihedral[nlocal]; k++) { dihedral_type[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom1[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom2[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom3[nlocal][k] = (int) ubuf(buf[m++]).i; - dihedral_atom4[nlocal][k] = (int) ubuf(buf[m++]).i; + dihedral_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i; + dihedral_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i; + dihedral_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i; + dihedral_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i; } num_improper[nlocal] = (int) ubuf(buf[m++]).i; for (k = 0; k < num_improper[nlocal]; k++) { improper_type[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom1[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom2[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom3[nlocal][k] = (int) ubuf(buf[m++]).i; - improper_atom4[nlocal][k] = (int) ubuf(buf[m++]).i; + improper_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i; + improper_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i; + improper_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i; + improper_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i; } nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0; diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 671290b0ad..c023a7e81e 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -54,8 +54,7 @@ void BondFENE::compute(int eflag, int vflag) double rsq,r0sq,rlogarg,sr2,sr6; ebond = sr6 = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/bond_fene_expand.cpp b/src/MOLECULE/bond_fene_expand.cpp index 3e191683fb..b1bfdc6a1b 100644 --- a/src/MOLECULE/bond_fene_expand.cpp +++ b/src/MOLECULE/bond_fene_expand.cpp @@ -56,8 +56,7 @@ void BondFENEExpand::compute(int eflag, int vflag) double r,rshift,rshiftsq; ebond = sr6 = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/bond_gromos.cpp b/src/MOLECULE/bond_gromos.cpp index 279f4fb2d4..f65adeb2cb 100644 --- a/src/MOLECULE/bond_gromos.cpp +++ b/src/MOLECULE/bond_gromos.cpp @@ -55,8 +55,7 @@ void BondGromos::compute(int eflag, int vflag) double delx,dely,delz,ebond,fbond; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -204,7 +203,7 @@ double BondGromos::single(int type, double rsq, int /*i*/, int /*j*/, void *BondGromos::extract( char *str, int &dim ) { dim = 1; - if( strcmp(str,"kappa")==0) return (void*) k; - if( strcmp(str,"r0")==0) return (void*) r0; + if (strcmp(str,"kappa")==0) return (void*) k; + if (strcmp(str,"r0")==0) return (void*) r0; return NULL; } diff --git a/src/MOLECULE/bond_harmonic.cpp b/src/MOLECULE/bond_harmonic.cpp index f795610b37..cb8434ce6e 100644 --- a/src/MOLECULE/bond_harmonic.cpp +++ b/src/MOLECULE/bond_harmonic.cpp @@ -52,8 +52,7 @@ void BondHarmonic::compute(int eflag, int vflag) double rsq,r,dr,rk; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -207,8 +206,8 @@ double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/, void *BondHarmonic::extract( char *str, int &dim ) { dim = 1; - if( strcmp(str,"kappa")==0) return (void*) k; - if( strcmp(str,"r0")==0) return (void*) r0; + if (strcmp(str,"kappa")==0) return (void*) k; + if (strcmp(str,"r0")==0) return (void*) r0; return NULL; } diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index 06af28f2b0..91dd2dbc49 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -53,8 +53,7 @@ void BondMorse::compute(int eflag, int vflag) double rsq,r,dr,ralpha; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/bond_nonlinear.cpp b/src/MOLECULE/bond_nonlinear.cpp index 645b081779..9999ead47f 100644 --- a/src/MOLECULE/bond_nonlinear.cpp +++ b/src/MOLECULE/bond_nonlinear.cpp @@ -49,8 +49,7 @@ void BondNonlinear::compute(int eflag, int vflag) double rsq,r,dr,drsq,lamdasq,denom,denomsq; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/bond_quartic.cpp b/src/MOLECULE/bond_quartic.cpp index f200030d6c..895202ff00 100644 --- a/src/MOLECULE/bond_quartic.cpp +++ b/src/MOLECULE/bond_quartic.cpp @@ -60,8 +60,7 @@ void BondQuartic::compute(int eflag, int vflag) double r,rsq,dr,r2,ra,rb,sr2,sr6; ebond = evdwl = sr6 = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/MOLECULE/bond_table.cpp b/src/MOLECULE/bond_table.cpp index 392904149d..94e843eb65 100644 --- a/src/MOLECULE/bond_table.cpp +++ b/src/MOLECULE/bond_table.cpp @@ -26,6 +26,7 @@ #include "force.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -67,8 +68,7 @@ void BondTable::compute(int eflag, int vflag) double u,mdu; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -310,17 +310,18 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + if (strcmp(word,keyword) == 0) break; // matching keyword + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"bond:rfile"); memory->create(tb->efile,tb->ninput,"bond:efile"); @@ -328,16 +329,15 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) // read r,e,f table values from file - int itmp; int cerror = 0; int r0idx = -1; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) { if (NULL == fgets(line,MAXLINE,fp)) error->one(FLERR,"Premature end of file in bond table"); - if (4 != sscanf(line,"%d %lg %lg %lg", - &itmp,&tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror; + if (3 != sscanf(line,"%*d %lg %lg %lg", + &tb->rfile[i],&tb->efile[i],&tb->ffile[i])) ++cerror; if (tb->efile[i] < emin) { emin = tb->efile[i]; r0idx = i; @@ -369,8 +369,6 @@ void BondTable::read_table(Table *tb, char *file, char *keyword) fright = - (enext-e) / (rnext-r); if (f < fleft && f < fright) ferror++; if (f > fleft && f > fright) ferror++; - //printf("Values %d: %g %g %g\n",i,r,e,f); - //printf(" secant %d %d %g: %g %g %g\n",i,ferror,r,fleft,fright,f); } if (ferror) { diff --git a/src/MOLECULE/dihedral_charmm.cpp b/src/MOLECULE/dihedral_charmm.cpp index 2372fae38b..68c62eb4fd 100644 --- a/src/MOLECULE/dihedral_charmm.cpp +++ b/src/MOLECULE/dihedral_charmm.cpp @@ -76,8 +76,7 @@ void DihedralCharmm::compute(int eflag, int vflag) double forcecoul,forcelj,fpair,ecoul,evdwl; edihedral = evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/MOLECULE/dihedral_charmmfsw.cpp b/src/MOLECULE/dihedral_charmmfsw.cpp index 99a5333620..f65d01e9ed 100644 --- a/src/MOLECULE/dihedral_charmmfsw.cpp +++ b/src/MOLECULE/dihedral_charmmfsw.cpp @@ -79,8 +79,7 @@ void DihedralCharmmfsw::compute(int eflag, int vflag) double forcecoul,forcelj,fpair,ecoul,evdwl; edihedral = evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/MOLECULE/dihedral_harmonic.cpp b/src/MOLECULE/dihedral_harmonic.cpp index cb122f4bc2..ddb94dc571 100644 --- a/src/MOLECULE/dihedral_harmonic.cpp +++ b/src/MOLECULE/dihedral_harmonic.cpp @@ -67,8 +67,7 @@ void DihedralHarmonic::compute(int eflag, int vflag) double c,s,p,sx2,sy2,sz2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/dihedral_helix.cpp b/src/MOLECULE/dihedral_helix.cpp index ae23b77951..d19731c097 100644 --- a/src/MOLECULE/dihedral_helix.cpp +++ b/src/MOLECULE/dihedral_helix.cpp @@ -39,7 +39,10 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -DihedralHelix::DihedralHelix(LAMMPS *lmp) : Dihedral(lmp) {} +DihedralHelix::DihedralHelix(LAMMPS *lmp) : Dihedral(lmp) +{ + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -67,8 +70,7 @@ void DihedralHelix::compute(int eflag, int vflag) double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index f6461abb6e..04e7bbb627 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -34,7 +34,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *lmp) : Dihedral(lmp) {} +DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *lmp) : Dihedral(lmp) +{ + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -64,8 +67,7 @@ void DihedralMultiHarmonic::compute(int eflag, int vflag) double s2,sin2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index b5103413b2..293245e411 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -67,8 +67,7 @@ void DihedralOPLS::compute(int eflag, int vflag) double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp index a889a8d0db..3395c7ef14 100644 --- a/src/MOLECULE/fix_cmap.cpp +++ b/src/MOLECULE/fix_cmap.cpp @@ -341,8 +341,7 @@ void FixCMAP::post_force(int vflag) ecmap = 0.0; int eflag = eflag_caller; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); for (n = 0; n < ncrosstermlist; n++) { i1 = crosstermlist[n][0]; @@ -943,7 +942,7 @@ double FixCMAP::dihedral_angle_atan2(double fx, double fy, double fz, { // calculate the dihedral angle - double angle, arg1, arg2; + double angle = 0.0, arg1, arg2; arg1 = absg*(fx*bx+fy*by+fz*bz); arg2 = ax*bx+ay*by+az*bz; diff --git a/src/MOLECULE/improper_cvff.cpp b/src/MOLECULE/improper_cvff.cpp index 641eea74a8..01e9729e80 100644 --- a/src/MOLECULE/improper_cvff.cpp +++ b/src/MOLECULE/improper_cvff.cpp @@ -61,8 +61,7 @@ void ImproperCvff::compute(int eflag, int vflag) double a33,a12,a13,a23,sx2,sy2,sz2; eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/improper_harmonic.cpp b/src/MOLECULE/improper_harmonic.cpp index 091bd46316..c5421fffdb 100644 --- a/src/MOLECULE/improper_harmonic.cpp +++ b/src/MOLECULE/improper_harmonic.cpp @@ -61,8 +61,7 @@ void ImproperHarmonic::compute(int eflag, int vflag) double sx2,sy2,sz2; eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp index 31d7cba54d..3de46df0f3 100644 --- a/src/MOLECULE/improper_umbrella.cpp +++ b/src/MOLECULE/improper_umbrella.cpp @@ -65,8 +65,7 @@ void ImproperUmbrella::compute(int eflag, int vflag) double ax,ay,az,ra2,rh2,ra,rh,rar,rhr,arx,ary,arz,hrx,hry,hrz; eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -189,17 +188,17 @@ void ImproperUmbrella::compute(int eflag, int vflag) dahy = ary-c*hry; dahz = arz-c*hrz; - f2[0] = (dhay*vb1z - dhaz*vb1y)*rar; - f2[1] = (dhaz*vb1x - dhax*vb1z)*rar; - f2[2] = (dhax*vb1y - dhay*vb1x)*rar; + f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a; + f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a; + f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a; - f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar; - f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar; - f3[2] = (-dhax*vb2y + dhay*vb2x)*rar; + f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a; + f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a; + f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a; - f4[0] = dahx*rhr; - f4[1] = dahy*rhr; - f4[2] = dahz*rhr; + f4[0] = dahx*rhr*a; + f4[1] = dahy*rhr*a; + f4[2] = dahz*rhr*a; f1[0] = -(f2[0] + f3[0] + f4[0]); f1[1] = -(f2[1] + f3[1] + f4[1]); @@ -208,27 +207,27 @@ void ImproperUmbrella::compute(int eflag, int vflag) // apply force to each of 4 atoms if (newton_bond || i1 < nlocal) { - f[i1][0] += f1[0]*a; - f[i1][1] += f1[1]*a; - f[i1][2] += f1[2]*a; + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; } if (newton_bond || i2 < nlocal) { - f[i2][0] += f3[0]*a; - f[i2][1] += f3[1]*a; - f[i2][2] += f3[2]*a; + f[i2][0] += f3[0]; + f[i2][1] += f3[1]; + f[i2][2] += f3[2]; } if (newton_bond || i3 < nlocal) { - f[i3][0] += f2[0]*a; - f[i3][1] += f2[1]*a; - f[i3][2] += f2[2]*a; + f[i3][0] += f2[0]; + f[i3][1] += f2[1]; + f[i3][2] += f2[2]; } if (newton_bond || i4 < nlocal) { - f[i4][0] += f4[0]*a; - f[i4][1] += f4[1]*a; - f[i4][2] += f4[2]*a; + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; } if (evflag) { @@ -247,7 +246,7 @@ void ImproperUmbrella::compute(int eflag, int vflag) vb3y = x[i4][1] - x[i3][1]; vb3z = x[i4][2] - x[i3][2]; - ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4, + ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f2,f4, vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); } } diff --git a/src/MOLECULE/pair_hbond_dreiding_lj.cpp b/src/MOLECULE/pair_hbond_dreiding_lj.cpp index c0c885d4d4..ddc1110081 100644 --- a/src/MOLECULE/pair_hbond_dreiding_lj.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_lj.cpp @@ -91,8 +91,7 @@ void PairHbondDreidingLJ::compute(int eflag, int vflag) tagint *klist; evdwl = ehbond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/pair_hbond_dreiding_morse.cpp b/src/MOLECULE/pair_hbond_dreiding_morse.cpp index f464d2c621..055f0ed46b 100644 --- a/src/MOLECULE/pair_hbond_dreiding_morse.cpp +++ b/src/MOLECULE/pair_hbond_dreiding_morse.cpp @@ -61,8 +61,7 @@ void PairHbondDreidingMorse::compute(int eflag, int vflag) tagint *klist; evdwl = ehbond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp index 688c675815..af4611e014 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm.cpp @@ -43,8 +43,9 @@ PairLJCharmmCoulCharmm::PairLJCharmmCoulCharmm(LAMMPS *lmp) : Pair(lmp) PairLJCharmmCoulCharmm::~PairLJCharmmCoulCharmm() { - if (!copymode) { - if (allocated) { + if (copymode) return; + + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); @@ -60,7 +61,6 @@ PairLJCharmmCoulCharmm::~PairLJCharmmCoulCharmm() memory->destroy(lj14_2); memory->destroy(lj14_3); memory->destroy(lj14_4); - } } } @@ -75,8 +75,7 @@ void PairLJCharmmCoulCharmm::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp index 6c083a49b0..d68d5e8f6d 100644 --- a/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp +++ b/src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.cpp @@ -39,8 +39,7 @@ void PairLJCharmmCoulCharmmImplicit::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index 4b9147c169..0e1cbd85a5 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -62,26 +62,6 @@ PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) : PairLJCharmmfswCoulCharmmfsh::~PairLJCharmmfswCoulCharmmfsh() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(eps14); - memory->destroy(sigma14); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(lj14_1); - memory->destroy(lj14_2); - memory->destroy(lj14_3); - memory->destroy(lj14_4); - } - } - // switch qqr2e back from CHARMM value to LAMMPS value if (update && strcmp(update->unit_style,"real") == 0) { @@ -90,6 +70,26 @@ PairLJCharmmfswCoulCharmmfsh::~PairLJCharmmfswCoulCharmmfsh() " conversion constant"); force->qqr2e = force->qqr2e_lammps_real; } + + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(eps14); + memory->destroy(sigma14); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(lj14_1); + memory->destroy(lj14_2); + memory->destroy(lj14_3); + memory->destroy(lj14_4); + } } /* ---------------------------------------------------------------------- */ @@ -103,8 +103,7 @@ void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp index 92dead8435..2b3d2c60f5 100644 --- a/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp +++ b/src/MOLECULE/pair_lj_cut_tip4p_cut.cpp @@ -91,8 +91,7 @@ void PairLJCutTIP4PCut::compute(int eflag, int vflag) double *x1,*x2,*xH1,*xH2; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/MOLECULE/pair_tip4p_cut.cpp b/src/MOLECULE/pair_tip4p_cut.cpp index 79dd79b180..e6fb9aab99 100644 --- a/src/MOLECULE/pair_tip4p_cut.cpp +++ b/src/MOLECULE/pair_tip4p_cut.cpp @@ -79,8 +79,7 @@ void PairTIP4PCut::compute(int eflag, int vflag) double *x1,*x2,*xH1,*xH2; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/Makefile b/src/Makefile index 7d31c81c75..f1030ae08f 100644 --- a/src/Makefile +++ b/src/Makefile @@ -13,12 +13,13 @@ ARLIB = liblammps_$@.a SHLIB = liblammps_$@.so ARLINK = liblammps.a SHLINK = liblammps.so +TMPNAME= tmp_$@_name OBJDIR = Obj_$@ OBJSHDIR = Obj_shared_$@ SRC = $(wildcard *.cpp) -INC = $(filter-out lmpinstalledpkgs.h,$(wildcard *.h)) +INC = $(filter-out lmpinstalledpkgs.h lmpgitversion.h,$(wildcard *.h)) OBJ = $(SRC:.cpp=.o) SRCLIB = $(filter-out main.cpp,$(SRC)) @@ -53,29 +54,30 @@ endif # PACKEXT = subset that require an external (downloaded) library PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \ - granular kim kokkos kspace latte manybody mc meam message misc \ + granular kim kokkos kspace latte manybody mc message misc \ molecule mpiio mscg opt peri poems \ - python qeq reax replica rigid shock snap spin srd voronoi + python qeq replica rigid shock snap spin srd voronoi -PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ +PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \ user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-meso \ user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-ptm user-qmmm user-qtb \ - user-quip user-reaxc user-scafacos user-smd user-smtbq \ - user-sph user-tally user-uef user-vtk + user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ + user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \ + user-sdpd user-sph user-tally user-uef user-vtk user-yaff -PACKLIB = compress gpu kim kokkos latte meam message mpiio mscg poems \ - python reax voronoi \ - user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ - user-netcdf user-qmmm user-quip user-scafacos user-smd user-vtk +PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ + python voronoi \ + user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ + user-netcdf user-plumed user-qmmm user-quip user-scafacos \ + user-smd user-vtk PACKSYS = compress mpiio python user-lb -PACKINT = gpu kokkos meam message poems reax user-atc user-awpmd user-colvars +PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars PACKEXT = kim latte mscg voronoi \ - user-h5md user-molfile user-netcdf user-qmmm user-quip \ + user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) @@ -153,17 +155,42 @@ help: lmpinstalledpkgs.h: $(SRC) $(INC) @echo 'Gathering installed package information (may take a little while)' - @echo '#ifndef LMP_INSTALLED_PKGS_H' > lmpinstalledpkgs.tmp - @echo '#define LMP_INSTALLED_PKGS_H' >> lmpinstalledpkgs.tmp - @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> lmpinstalledpkgs.tmp + @echo '#ifndef LMP_INSTALLED_PKGS_H' > ${TMPNAME}.lmpinstalled + @echo '#define LMP_INSTALLED_PKGS_H' >> ${TMPNAME}.lmpinstalled + @echo 'const char * LAMMPS_NS::LAMMPS::installed_packages[] = {' >> ${TMPNAME}.lmpinstalled @for p in $(PACKAGEUC) $(PACKUSERUC); do info=$$($(SHELL) Package.sh $$p installed); \ - [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> lmpinstalledpkgs.tmp || :; done - @echo ' NULL };' >> lmpinstalledpkgs.tmp - @echo '#endif' >> lmpinstalledpkgs.tmp + [ -n "$$info" ] && echo "\"$$info\"" | sed -e 's/".*package \(.*\)"/"\1",/' >> ${TMPNAME}.lmpinstalled || :; done + @echo ' NULL };' >> ${TMPNAME}.lmpinstalled + @echo '#endif' >> ${TMPNAME}.lmpinstalled @if [ -f lmpinstalledpkgs.h ]; \ - then test "`diff --brief lmpinstalledpkgs.tmp lmpinstalledpkgs.h`" != "" && \ - mv lmpinstalledpkgs.tmp lmpinstalledpkgs.h || rm lmpinstalledpkgs.tmp ; \ - else mv lmpinstalledpkgs.tmp lmpinstalledpkgs.h ; fi + then test "`diff --brief ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h`" != "" && \ + mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h || rm ${TMPNAME}.lmpinstalled ; \ + else mv ${TMPNAME}.lmpinstalled lmpinstalledpkgs.h ; fi + +gitversion: + @echo 'Gathering git version information' + @echo '#ifndef LMP_GIT_VERSION_H' > ${TMPNAME}.lmpgitversion + @echo '#define LMP_GIT_VERSION_H' >> ${TMPNAME}.lmpgitversion + @if (type git && test -e ../.git ) >> /dev/null 2>> /dev/null ; then \ + git='true'; \ + commit=$$(git rev-parse HEAD); \ + branch=$$(git rev-parse --abbrev-ref HEAD); \ + describe=$$(git describe --dirty=-modified); \ + else \ + git='false' ; \ + commit='(unknown)' ; \ + branch='(unknown)' ; \ + describe='(unknown)' ; \ + fi ; \ + echo "const bool LAMMPS_NS::LAMMPS::has_git_info = $${git};" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_commit[] = \"$${commit}\";" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_branch[] = \"$${branch}\";" >> ${TMPNAME}.lmpgitversion ; \ + echo "const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"$${describe}\";" >> ${TMPNAME}.lmpgitversion + @echo '#endif' >> ${TMPNAME}.lmpgitversion + @if [ -f lmpgitversion.h ]; \ + then test "`diff --brief ${TMPNAME}.lmpgitversion lmpgitversion.h`" != "" && \ + mv ${TMPNAME}.lmpgitversion lmpgitversion.h || rm ${TMPNAME}.lmpgitversion ; \ + else mv ${TMPNAME}.lmpgitversion lmpgitversion.h ; fi # Build LAMMPS in one of 4 modes # exe = exe with static compile in Obj_machine (default) @@ -178,7 +205,7 @@ lmpinstalledpkgs.h: $(SRC) $(INC) -f MAKE/MACHINES/Makefile.$@ -o -f MAKE/MINE/Makefile.$@ @if [ ! -d $(objdir) ]; then mkdir $(objdir); fi @$(SHELL) Make.sh style - @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h + @$(MAKE) $(MFLAGS) lmpinstalledpkgs.h gitversion @echo 'Compiling LAMMPS for machine $@' @if [ -f MAKE/MACHINES/Makefile.$@ ]; \ then cp MAKE/MACHINES/Makefile.$@ $(objdir)/Makefile; fi diff --git a/src/OPT/pair_eam_opt.cpp b/src/OPT/pair_eam_opt.cpp index 5345d7f8d6..fc2b6731ee 100644 --- a/src/OPT/pair_eam_opt.cpp +++ b/src/OPT/pair_eam_opt.cpp @@ -38,8 +38,7 @@ PairEAMOpt::PairEAMOpt(LAMMPS *lmp) : PairEAM(lmp) {} void PairEAMOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/OPT/pair_lj_charmm_coul_long_opt.cpp b/src/OPT/pair_lj_charmm_coul_long_opt.cpp index 43f4ba7f5a..d80d3d1ec4 100644 --- a/src/OPT/pair_lj_charmm_coul_long_opt.cpp +++ b/src/OPT/pair_lj_charmm_coul_long_opt.cpp @@ -44,8 +44,7 @@ PairLJCharmmCoulLongOpt::PairLJCharmmCoulLongOpt(LAMMPS *lmp) : void PairLJCharmmCoulLongOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/OPT/pair_lj_cut_coul_long_opt.cpp b/src/OPT/pair_lj_cut_coul_long_opt.cpp index 98683a67a4..a25010cf1f 100644 --- a/src/OPT/pair_lj_cut_coul_long_opt.cpp +++ b/src/OPT/pair_lj_cut_coul_long_opt.cpp @@ -38,8 +38,7 @@ PairLJCutCoulLongOpt::PairLJCutCoulLongOpt(LAMMPS *lmp) : PairLJCutCoulLong(lmp) void PairLJCutCoulLongOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (!ncoultablebits) { if (evflag) { diff --git a/src/OPT/pair_lj_cut_opt.cpp b/src/OPT/pair_lj_cut_opt.cpp index ed35178c1f..c6684461be 100644 --- a/src/OPT/pair_lj_cut_opt.cpp +++ b/src/OPT/pair_lj_cut_opt.cpp @@ -34,8 +34,7 @@ PairLJCutOpt::PairLJCutOpt(LAMMPS *lmp) : PairLJCut(lmp) {} void PairLJCutOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp index 4842cc4fc0..92facca43e 100644 --- a/src/OPT/pair_lj_cut_tip4p_long_opt.cpp +++ b/src/OPT/pair_lj_cut_tip4p_long_opt.cpp @@ -53,8 +53,7 @@ PairLJCutTIP4PLongOpt::PairLJCutTIP4PLongOpt(LAMMPS *lmp) : void PairLJCutTIP4PLongOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/OPT/pair_lj_long_coul_long_opt.cpp b/src/OPT/pair_lj_long_coul_long_opt.cpp index 6bd1e8cb96..243b64391f 100644 --- a/src/OPT/pair_lj_long_coul_long_opt.cpp +++ b/src/OPT/pair_lj_long_coul_long_opt.cpp @@ -44,8 +44,7 @@ PairLJLongCoulLongOpt::PairLJLongCoulLongOpt(LAMMPS *lmp) : PairLJLongCoulLong(l void PairLJLongCoulLongOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6); if (order6) { @@ -290,8 +289,7 @@ void PairLJLongCoulLongOpt::compute(int eflag, int vflag) void PairLJLongCoulLongOpt::compute_outer(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int order1 = ewald_order&(1<<1), order6 = ewald_order&(1<<6); if (order6) { diff --git a/src/OPT/pair_morse_opt.cpp b/src/OPT/pair_morse_opt.cpp index 6299136f46..c9c6bba355 100644 --- a/src/OPT/pair_morse_opt.cpp +++ b/src/OPT/pair_morse_opt.cpp @@ -35,8 +35,7 @@ PairMorseOpt::PairMorseOpt(LAMMPS *lmp) : PairMorse(lmp) {} void PairMorseOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/OPT/pair_ufm_opt.cpp b/src/OPT/pair_ufm_opt.cpp index 85c76d624d..f463dac3f1 100644 --- a/src/OPT/pair_ufm_opt.cpp +++ b/src/OPT/pair_ufm_opt.cpp @@ -34,8 +34,7 @@ PairUFMOpt::PairUFMOpt(LAMMPS *lmp) : PairUFM(lmp) {} void PairUFMOpt::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/PERI/pair_peri_eps.cpp b/src/PERI/pair_peri_eps.cpp index 76267426c6..c00495ba4d 100644 --- a/src/PERI/pair_peri_eps.cpp +++ b/src/PERI/pair_peri_eps.cpp @@ -96,8 +96,7 @@ void PairPeriEPS::compute(int eflag, int vflag) double d_ij,delta,stretch; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); double **f = atom->f; double **x = atom->x; diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp index 383b91c6f5..f0418c8c8d 100644 --- a/src/PERI/pair_peri_lps.cpp +++ b/src/PERI/pair_peri_lps.cpp @@ -93,8 +93,7 @@ void PairPeriLPS::compute(int eflag, int vflag) double d_ij,delta,stretch; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); double **f = atom->f; double **x = atom->x; diff --git a/src/PERI/pair_peri_pmb.cpp b/src/PERI/pair_peri_pmb.cpp index 772e47f2d6..ad2f3fb7c7 100644 --- a/src/PERI/pair_peri_pmb.cpp +++ b/src/PERI/pair_peri_pmb.cpp @@ -84,8 +84,7 @@ void PairPeriPMB::compute(int eflag, int vflag) double d_ij,delta,stretch; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **f = atom->f; double **x = atom->x; diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp index 7590077f0e..24a9f92a97 100644 --- a/src/PERI/pair_peri_ves.cpp +++ b/src/PERI/pair_peri_ves.cpp @@ -98,8 +98,7 @@ void PairPeriVES::compute(int eflag, int vflag) double d_ij,delta,stretch; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); double **f = atom->f; double **x = atom->x; diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp index f345d52aab..41cfcede34 100644 --- a/src/POEMS/fix_poems.cpp +++ b/src/POEMS/fix_poems.cpp @@ -366,7 +366,7 @@ void FixPOEMS::init() int pflag = 0; for (i = 0; i < modify->nfix; i++) { if (strcmp(modify->fix[i]->style,"poems") == 0) pflag = 1; - if (pflag && (modify->fmask[i] & POST_FORCE) && + if (pflag && (modify->fmask[i] & POST_FORCE) && !modify->fix[i]->rigid_flag) { char str[128]; snprintf(str,128,"Fix %s alters forces after fix poems",modify->fix[i]->id); @@ -748,19 +748,9 @@ void FixPOEMS::initial_integrate(int vflag) /* ---------------------------------------------------------------------- */ -void FixPOEMS::post_force(int vflag) +void FixPOEMS::post_force(int /* vflag */) { if (earlyflag) compute_forces_and_torques(); - - /* - for (int ibody = 0; ibody < nbody; ibody++) { - if (ibody == 0) { - printf("PFF %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]); - printf("PFT %d %g %g %g\n",ibody, - torque[ibody][0],torque[ibody][1],torque[ibody][2]); - } - } - */ } /* ---------------------------------------------------------------------- @@ -850,7 +840,7 @@ void FixPOEMS::final_integrate() /* ---------------------------------------------------------------------- */ -void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop) +void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -862,14 +852,14 @@ void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop) /* ---------------------------------------------------------------------- */ -void FixPOEMS::post_force_respa(int vflag, int ilevel, int iloop) +void FixPOEMS::post_force_respa(int vflag, int ilevel, int /* iloop */) { if (ilevel == nlevels_respa-1) post_force(vflag); } /* ---------------------------------------------------------------------- */ -void FixPOEMS::final_integrate_respa(int ilevel, int iloop) +void FixPOEMS::final_integrate_respa(int ilevel, int /* iloop */) { dtf = 0.5 * step_respa[ilevel] * force->ftm2v; final_integrate(); @@ -949,7 +939,7 @@ int FixPOEMS::dof(int igroup) thus this routine does nothing for now ------------------------------------------------------------------------- */ -void FixPOEMS::deform(int flag) {} +void FixPOEMS::deform(int /* flag */) {} /* ---------------------------------------------------------------------- */ @@ -1607,7 +1597,7 @@ void FixPOEMS::grow_arrays(int nmax) copy values within local atom-based arrays ------------------------------------------------------------------------- */ -void FixPOEMS::copy_arrays(int i, int j, int delflag) +void FixPOEMS::copy_arrays(int i, int j, int /* delflag */) { natom2body[j] = natom2body[i]; for (int k = 0; k < natom2body[j]; k++) atom2body[j][k] = atom2body[i][k]; diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 199dd94f3d..280c2d91e2 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -24,7 +24,7 @@ #include "update.h" #include "respa.h" #include "error.h" -#include "python.h" +#include "lmppython.h" #include "python_compat.h" using namespace LAMMPS_NS; diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index b330ab7945..ec21dbeadd 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -25,7 +25,7 @@ #include "force.h" #include "memory.h" #include "neigh_list.h" -#include "python.h" +#include "lmppython.h" #include "error.h" #include "python_compat.h" diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index 223129f7d6..2148fc67b8 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -26,7 +26,7 @@ #include "memory.h" #include "update.h" #include "neigh_list.h" -#include "python.h" +#include "lmppython.h" #include "error.h" #include "python_compat.h" @@ -82,8 +82,7 @@ void PairPython::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -401,9 +400,9 @@ double PairPython::init_one(int, int) /* ---------------------------------------------------------------------- */ -double PairPython::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, - double &fforce) +double PairPython::single(int /* i */, int /* j */, int itype, int jtype, + double rsq, double /* factor_coul */, + double factor_lj, double &fforce) { // with hybrid/overlay we might get called for skipped types if (skip_types[itype] || skip_types[jtype]) { diff --git a/src/PYTHON/python_impl.cpp b/src/PYTHON/python_impl.cpp index cc5edaf3f5..aaa4f74c69 100644 --- a/src/PYTHON/python_impl.cpp +++ b/src/PYTHON/python_impl.cpp @@ -16,7 +16,7 @@ ------------------------------------------------------------------------- */ #include -#include "python.h" +#include "lmppython.h" #include "force.h" #include "input.h" #include "variable.h" diff --git a/src/Purge.list b/src/Purge.list index 6cfc580c25..59c35efca5 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -24,6 +24,21 @@ style_nstencil.h style_ntopo.h # other auto-generated files lmpinstalledpkgs.h +lmpgitversion.h +# renamed on 7 January 2019 +pair_lebedeva.cpp +pair_lebedeva.h +# removed on 12 December 2018 +pair_reax.cpp +pair_reax.h +pair_reax_fortran.h +fix_reax_bonds.cpp +fix_reax_bonds.h +pair_meam.cpp +pair_meam.h +# removed on 27 September 2018 +pair_nb3b_harmonic_omp.h +pair_nb3b_harmonic_omp.cpp # renamed on 25 September 2018 compute_smd_triangle_mesh_vertices.h compute_smd_triangle_mesh_vertices.cpp diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index 49e0a6d423..0ab010b7bb 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -100,6 +100,7 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : q1 = NULL; q2 = NULL; streitz_flag = 0; + reax_flag = 0; qv = NULL; comm_forward = comm_reverse = 1; @@ -117,6 +118,8 @@ FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[7],"coul/streitz") == 0) { streitz_flag = 1; + } else if (strcmp(arg[7],"reax/c") == 0) { + reax_flag = 1; } else { read_file(arg[7]); } @@ -138,7 +141,7 @@ FixQEq::~FixQEq() memory->destroy(shld); - if (!streitz_flag) { + if (!streitz_flag && !reax_flag) { memory->destroy(chi); memory->destroy(eta); memory->destroy(gamma); @@ -475,7 +478,7 @@ int FixQEq::pack_forward_comm(int n, int *list, double *buf, { int m; - if( pack_flag == 1) + if (pack_flag == 1) for(m = 0; m < n; m++) buf[m] = d[list[m]]; else if( pack_flag == 2 ) for(m = 0; m < n; m++) buf[m] = s[list[m]]; @@ -493,7 +496,7 @@ void FixQEq::unpack_forward_comm(int n, int first, double *buf) { int i, m; - if( pack_flag == 1) + if (pack_flag == 1) for(m = 0, i = first; m < n; m++, i++) d[i] = buf[m]; else if( pack_flag == 2) for(m = 0, i = first; m < n; m++, i++) s[i] = buf[m]; diff --git a/src/QEQ/fix_qeq.h b/src/QEQ/fix_qeq.h index 2a022d28a9..9a3087840b 100644 --- a/src/QEQ/fix_qeq.h +++ b/src/QEQ/fix_qeq.h @@ -70,7 +70,7 @@ class FixQEq : public Fix { double *chi,*eta,*gamma,*zeta,*zcore; // qeq parameters double *chizj; double **shld; - int streitz_flag; + int streitz_flag, reax_flag; bigint ngroup; diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index f496c7e6c0..ba88f4f1c3 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -103,7 +103,7 @@ void FixQEqDynamic::pre_force(int /*vflag*/) if (update->ntimestep % nevery) return; - if( atom->nmax > nmax ) reallocate_storage(); + if (atom->nmax > nmax) reallocate_storage(); inum = list->inum; ilist = list->ilist; @@ -251,7 +251,7 @@ int FixQEqDynamic::pack_forward_comm(int n, int *list, double *buf, { int m=0; - if( pack_flag == 1 ) + if (pack_flag == 1) for(m = 0; m < n; m++) buf[m] = atom->q[list[m]]; else if( pack_flag == 2 ) for(m = 0; m < n; m++) buf[m] = qf[list[m]]; @@ -265,7 +265,7 @@ void FixQEqDynamic::unpack_forward_comm(int n, int first, double *buf) { int i, m; - if( pack_flag == 1) + if (pack_flag == 1) for(m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m]; else if( pack_flag == 2) for(m = 0, i = first; m < n; m++, i++) qf[i] = buf[m]; diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index 83c9907f1b..1e3686f99c 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -122,7 +122,7 @@ void FixQEqFire::pre_force(int /*vflag*/) if (ntimestep % nevery) return; - if( atom->nmax > nmax ) reallocate_storage(); + if (atom->nmax > nmax) reallocate_storage(); inum = list->inum; ilist = list->ilist; @@ -315,7 +315,7 @@ int FixQEqFire::pack_forward_comm(int n, int *list, double *buf, { int m = 0; - if( pack_flag == 1 ) + if (pack_flag == 1) for(m = 0; m < n; m++) buf[m] = atom->q[list[m]]; else if( pack_flag == 2 ) for(m = 0; m < n; m++) buf[m] = qf[list[m]]; @@ -329,7 +329,7 @@ void FixQEqFire::unpack_forward_comm(int n, int first, double *buf) { int i, m; - if( pack_flag == 1) + if (pack_flag == 1) for(m = 0, i = first; m < n; m++, i++) atom->q[i] = buf[m]; else if( pack_flag == 2) for(m = 0, i = first; m < n; m++, i++) qf[i] = buf[m]; diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index db2d800c06..9517343974 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -73,9 +73,9 @@ void FixQEqPoint::pre_force(int /*vflag*/) nlocal = atom->nlocal; - if( atom->nmax > nmax ) reallocate_storage(); + if (atom->nmax > nmax) reallocate_storage(); - if( nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE ) + if (nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE) reallocate_matrix(); init_matvec(); diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 88cd1ab3ad..a74eee7d29 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -29,6 +29,7 @@ #include "update.h" #include "force.h" #include "group.h" +#include "pair.h" #include "kspace.h" #include "respa.h" #include "memory.h" @@ -39,7 +40,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ FixQEqShielded::FixQEqShielded(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) {} + FixQEq(lmp, narg, arg) { + if (reax_flag) extract_reax(); +} /* ---------------------------------------------------------------------- */ @@ -73,6 +76,22 @@ void FixQEqShielded::init() } +/* ---------------------------------------------------------------------- */ + +void FixQEqShielded::extract_reax() +{ + Pair *pair = force->pair_match("reax/c",1); + if (pair == NULL) error->all(FLERR,"No pair reax/c for fix qeq/shielded"); + int tmp; + chi = (double *) pair->extract("chi",tmp); + eta = (double *) pair->extract("eta",tmp); + gamma = (double *) pair->extract("gamma",tmp); + if (chi == NULL || eta == NULL || gamma == NULL) + error->all(FLERR, + "Fix qeq/slater could not extract params from pair reax/c"); +} + + /* ---------------------------------------------------------------------- */ void FixQEqShielded::init_shielding() @@ -117,9 +136,9 @@ void FixQEqShielded::pre_force(int /*vflag*/) nlocal = atom->nlocal; - if( atom->nmax > nmax ) reallocate_storage(); + if (atom->nmax > nmax) reallocate_storage(); - if( nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE ) + if (nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE) reallocate_matrix(); init_matvec(); diff --git a/src/QEQ/fix_qeq_shielded.h b/src/QEQ/fix_qeq_shielded.h index f9e1e0172e..dfdea2b719 100644 --- a/src/QEQ/fix_qeq_shielded.h +++ b/src/QEQ/fix_qeq_shielded.h @@ -32,6 +32,7 @@ class FixQEqShielded : public FixQEq { void pre_force(int); private: + void extract_reax(); void init_shielding(); void init_matvec(); void compute_H(); diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 81fdc73241..3443a519a2 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -114,9 +114,9 @@ void FixQEqSlater::pre_force(int /*vflag*/) nlocal = atom->nlocal; nall = atom->nlocal + atom->nghost; - if( atom->nmax > nmax ) reallocate_storage(); + if (atom->nmax > nmax) reallocate_storage(); - if( nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE ) + if (nlocal > n_cap*DANGER_ZONE || m_fill > m_cap*DANGER_ZONE) reallocate_matrix(); init_matvec(); diff --git a/src/REAX/Install.sh b/src/REAX/Install.sh deleted file mode 100755 index bf8c8dbca2..0000000000 --- a/src/REAX/Install.sh +++ /dev/null @@ -1,67 +0,0 @@ -# Install/unInstall package files in LAMMPS -# mode = 0/1/2 for uninstall/install/update - -mode=$1 - -# arg1 = file, arg2 = file it depends on - -# enforce using portable C locale -LC_ALL=C -export LC_ALL - -action () { - if (test $mode = 0) then - rm -f ../$1 - elif (! cmp -s $1 ../$1) then - if (test -z "$2" || test -e ../$2) then - cp $1 .. - if (test $mode = 2) then - echo " updating src/$1" - fi - fi - elif (test -n "$2") then - if (test ! -e ../$2) then - rm -f ../$1 - fi - fi -} - -# all package files with no dependencies - -for file in *.cpp *.h; do - test -f ${file} && action $file -done - -# edit 2 Makefile.package files to include/exclude package info - -if (test $1 = 1) then - - if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*reax[^ \t]* //' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/reax |' ../Makefile.package - sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/reax |' ../Makefile.package - sed -i -e 's|^PKG_LIB =[ \t]*|&-lreax |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(reax_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(reax_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(reax_SYSPATH) |' ../Makefile.package - fi - - if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*reax.*$/d' ../Makefile.package.settings - # multiline form needed for BSD sed on Macs - sed -i -e '4 i \ -include ..\/..\/lib\/reax\/Makefile.lammps -' ../Makefile.package.settings - fi - -elif (test $1 = 0) then - - if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*reax[^ \t]* //' ../Makefile.package - fi - - if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*reax.*$/d' ../Makefile.package.settings - fi - -fi diff --git a/src/REAX/fix_reax_bonds.cpp b/src/REAX/fix_reax_bonds.cpp deleted file mode 100644 index c6c1d309ee..0000000000 --- a/src/REAX/fix_reax_bonds.cpp +++ /dev/null @@ -1,267 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Aidan Thompson (Sandia) -------------------------------------------------------------------------- */ - -#ifdef LAMMPS_BIGBIG -#error LAMMPS_BIGBIG is not supported by the REAX package -#endif - -#include -#include -#include "fix_reax_bonds.h" -#include "pair_reax_fortran.h" -#include "atom.h" -#include "update.h" -#include "force.h" -#include "modify.h" -#include "compute.h" -#include "input.h" -#include "variable.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; -using namespace FixConst; - -/* ---------------------------------------------------------------------- */ - -FixReaxBonds::FixReaxBonds(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg) -{ - if (narg < 5) error->all(FLERR,"Illegal fix reax/bonds command"); - - MPI_Comm_rank(world,&me); - - nevery = force->inumeric(FLERR,arg[3]); - if (nevery < 1) error->all(FLERR,"Illegal fix reax/bonds command"); - - if (me == 0) { - char *suffix = strrchr(arg[4],'.'); - if (suffix && strcmp(suffix,".gz") == 0) { -#ifdef LAMMPS_GZIP - char gzip[128]; - snprintf(gzip,128,"gzip -6 > %s",arg[4]); -#ifdef _WIN32 - fp = _popen(gzip,"wb"); -#else - fp = popen(gzip,"w"); -#endif -#else - error->one(FLERR,"Cannot open gzipped file"); -#endif - } else fp = fopen(arg[4],"w"); - - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open fix reax/bonds file %s",arg[4]); - error->one(FLERR,str); - } - } -} - -/* ---------------------------------------------------------------------- */ - -FixReaxBonds::~FixReaxBonds() -{ - if (me == 0) fclose(fp); -} - -/* ---------------------------------------------------------------------- */ - -int FixReaxBonds::setmask() -{ - int mask = 0; - mask |= END_OF_STEP; - return mask; -} - -/* ---------------------------------------------------------------------- - perform initial write -------------------------------------------------------------------------- */ - -void FixReaxBonds::setup(int vflag) -{ - end_of_step(); -} - -/* ---------------------------------------------------------------------- */ - -void FixReaxBonds::init() -{ - // insure ReaxFF is defined - - if (force->pair_match("reax",1) == NULL) - error->all(FLERR,"Cannot use fix reax/bonds without pair_style reax"); -} - -/* ---------------------------------------------------------------------- */ - -void FixReaxBonds::end_of_step() -{ - OutputReaxBonds(update->ntimestep,fp); - if (me == 0) fflush(fp); -} - -/* ---------------------------------------------------------------------- */ - -void FixReaxBonds::OutputReaxBonds(bigint ntimestep, FILE *fp) -{ - int nparticles,nparticles_tot,nbuf,nbuf_local,most,j; - int ii,jn,mbond,numbonds,nsbmax,nsbmax_most; - int nprocs,nlocal_tmp,itmp; - int k,kk,jj,jbufknum; - double cutof3; - double *buf; - MPI_Request irequest; - - MPI_Comm_size(world,&nprocs); - - nparticles = atom->nlocal; - nparticles_tot = static_cast (atom->natoms); - - jn = ReaxParams::nat; - mbond = ReaxParams::mbond; - FORTRAN(getnsbmax,GETNSBMAX)(&nsbmax); - FORTRAN(getcutof3,GETCUTOF3)(&cutof3); - MPI_Allreduce(&nparticles,&most,1,MPI_INT,MPI_MAX,world); - MPI_Allreduce(&nsbmax,&nsbmax_most,1,MPI_INT,MPI_MAX,world); - - if (me == 0) { - fprintf(fp,"# Timestep " BIGINT_FORMAT " \n",ntimestep); - fprintf(fp,"# \n"); - fprintf(fp,"# Number of particles %d \n",nparticles_tot); - fprintf(fp,"# \n"); - fprintf(fp,"# Max number of bonds per atom %d with " - "coarse bond order cutoff %5.3f \n", - nsbmax_most,cutof3); - fprintf(fp,"# Particle connection table and bond orders \n"); - fprintf(fp,"# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q \n"); - } - - // allocate a temporary buffer for the snapshot info - // big enough for largest number of atoms on any one proc - // nbuf_local = size of local buffer for table of atom bonds - - nbuf = 1+(2*nsbmax_most+7)*most; - memory->create(buf,nbuf,"reax/bonds:buf"); - - j = 0; - buf[j++] = nparticles; - for (int iparticle=0;iparticletag[iparticle]; //atom tag - buf[j++] = FORTRAN(cbkia,CBKIA).iag[iparticle]; //atom type - jbufknum = j++; - numbonds = FORTRAN(cbkia,CBKIA).iag[iparticle+jn]; - - // connection table based on coarse bond order cutoff (> cutof3) - - kk = 0; - for (k=0;k cutof3) { - kk++; - jj = FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(k+2)]; - buf[j++] = FORTRAN(cbkc,CBKC).itag[jj-1]; - } - } - buf[jbufknum] = kk; //no.bonds - buf[j++]=FORTRAN(cbkia,CBKIA).iag[iparticle+jn*(mbond+2)]; //molec.id - - // bond orders (> cutof3) - - kk = 0; - for (k=0;k cutof3) { - kk++; - buf[j++] = FORTRAN(cbkbo,CBKBO).bo[ii-1]; - } - } - - // atom bond order (abo), no. of lone pairs (vlp), charge (ch) - - buf[j++] = FORTRAN(cbkabo,CBKABO).abo[iparticle]; - buf[j++] = FORTRAN(cbklonpar,CBKLONPAR).vlp[iparticle]; - buf[j++] = atom->q[iparticle]; - } - nbuf_local = j-1; - - // node 0 pings each node, receives their buffer, writes to file - // all other nodes wait for ping, send buffer to node 0 - - if (me == 0) { - for (int inode = 0; inode nsbmax_most) - error->one(FLERR,"Fix reax/bonds numbonds > nsbmax_most"); - - // print connection table - - for (k=0;kdestroy(buf); -} - -/* ---------------------------------------------------------------------- */ - -int FixReaxBonds::nint(const double &r) -{ - int i = 0; - if (r>0.0) i = static_cast(r+0.5); - else if (r<0.0) i = static_cast(r-0.5); - return i; -} diff --git a/src/REAX/pair_reax.cpp b/src/REAX/pair_reax.cpp deleted file mode 100644 index a430380711..0000000000 --- a/src/REAX/pair_reax.cpp +++ /dev/null @@ -1,1067 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing authors: Aidan Thompson (Sandia, athomps@sandia.gov) - Hansohl Cho (MIT, hansohl@mit.edu) - LAMMPS implementation of the Reactive Force Field (ReaxFF) is based on - Aidan Thompson's GRASP code - (General Reactive Atomistic Simulation Program) - and Ardi Van Duin's original ReaxFF code -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include -#include "pair_reax.h" -#include "pair_reax_fortran.h" -#include "atom.h" -#include "update.h" -#include "force.h" -#include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -#define SMALL 0.0001 - -/* ---------------------------------------------------------------------- */ - -PairREAX::PairREAX(LAMMPS *lmp) : Pair(lmp) -{ - if (comm->me == 0) - error->warning(FLERR,"THE pair_style reax COMMAND IS OBSOLETE AND " - "WILL BE REMOVED VERY SOON. PLEASE USE reax/c"); - - single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; - no_virial_fdotr_compute = 1; - - nextra = 14; - pvector = new double[nextra]; - - cutmax = 0.0; - hbcut = 6.0; - ihbnew = 1; - itripstaball = 1; - iprune = 4; - ihb = 1; - chpot = 0; - - nmax = 0; - arow_ptr = NULL; - ch = NULL; - elcvec = NULL; - rcg = NULL; - wcg = NULL; - pcg = NULL; - poldcg = NULL; - qcg = NULL; - - matmax = 0; - aval = NULL; - acol_ind = NULL; - - comm_forward = 1; - comm_reverse = 1; - - precision = 1.0e-6; -} - -/* ---------------------------------------------------------------------- - free all arrays - check if allocated, since class can be destructed when incomplete -------------------------------------------------------------------------- */ - -PairREAX::~PairREAX() -{ - delete [] pvector; - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - for (int i = 1; i <= atom->ntypes; i++) - delete [] param_list[i].params; - delete [] param_list; - - delete [] map; - } - - memory->destroy(arow_ptr); - memory->destroy(ch); - memory->destroy(elcvec); - memory->destroy(rcg); - memory->destroy(wcg); - memory->destroy(pcg); - memory->destroy(poldcg); - memory->destroy(qcg); - - memory->destroy(aval); - memory->destroy(acol_ind); -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::compute(int eflag, int vflag) -{ - int i,j; - double evdwl,ecoul; - double energy_charge_equilibration; - - evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else ev_unset(); - - if (vflag_global) FORTRAN(cbkvirial, CBKVIRIAL).Lvirial = 1; - else FORTRAN(cbkvirial, CBKVIRIAL).Lvirial = 0; - - if (vflag_atom) FORTRAN(cbkvirial, CBKVIRIAL).Latomvirial = 1; - else FORTRAN(cbkvirial, CBKVIRIAL).Latomvirial = 0; - - // reallocate charge equilibration and CG arrays if necessary - - if (atom->nmax > nmax) { - memory->destroy(rcg); - memory->destroy(wcg); - memory->destroy(pcg); - memory->destroy(poldcg); - memory->destroy(qcg); - - nmax = atom->nmax; - int n = nmax+1; - - memory->create(arow_ptr,n,"reax:arow_ptr"); - memory->create(ch,n,"reax:ch"); - memory->create(elcvec,n,"reax:elcvec"); - memory->create(rcg,n,"reax:rcg"); - memory->create(wcg,n,"reax:wcg"); - memory->create(pcg,n,"reax:pcg"); - memory->create(poldcg,n,"reax:poldcg"); - memory->create(qcg,n,"reax:qcg"); - } - - // calculate the atomic charge distribution - - compute_charge(energy_charge_equilibration); - - // transfer LAMMPS positions and neighbor lists to REAX - - write_reax_positions(); - write_reax_vlist(); - - // determine whether this bond is owned by the processor or not - - FORTRAN(srtbon1, SRTBON1)(&iprune, &ihb, &hbcut, &ihbnew, &itripstaball); - - // communicate local atomic bond order to ghost atomic bond order - - packflag = 0; - comm->forward_comm_pair(this); - - FORTRAN(molec, MOLEC)(); - FORTRAN(encalc, ENCALC)(); - FORTRAN(mdsav, MDSAV)(&comm->me); - - // read forces from ReaxFF Fortran - - read_reax_forces(); - - // extract global and per-atom energy from ReaxFF Fortran - // compute_charge already contributed to eatom - - if (eflag_global) { - evdwl += FORTRAN(cbkenergies, CBKENERGIES).eb; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).ea; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).elp; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).emol; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).ev; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).epen; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).ecoa; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).ehb; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).et; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).eco; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).ew; - evdwl += FORTRAN(cbkenergies, CBKENERGIES).efi; - - ecoul += FORTRAN(cbkenergies, CBKENERGIES).ep; - ecoul += energy_charge_equilibration; - - eng_vdwl += evdwl; - eng_coul += ecoul; - - // Store the different parts of the energy - // in a list for output by compute pair command - - pvector[0] = FORTRAN(cbkenergies, CBKENERGIES).eb; - pvector[1] = FORTRAN(cbkenergies, CBKENERGIES).ea; - pvector[2] = FORTRAN(cbkenergies, CBKENERGIES).elp; - pvector[3] = FORTRAN(cbkenergies, CBKENERGIES).emol; - pvector[4] = FORTRAN(cbkenergies, CBKENERGIES).ev; - pvector[5] = FORTRAN(cbkenergies, CBKENERGIES).epen; - pvector[6] = FORTRAN(cbkenergies, CBKENERGIES).ecoa; - pvector[7] = FORTRAN(cbkenergies, CBKENERGIES).ehb; - pvector[8] = FORTRAN(cbkenergies, CBKENERGIES).et; - pvector[9] = FORTRAN(cbkenergies, CBKENERGIES).eco; - pvector[10] = FORTRAN(cbkenergies, CBKENERGIES).ew; - pvector[11] = FORTRAN(cbkenergies, CBKENERGIES).ep; - pvector[12] = FORTRAN(cbkenergies, CBKENERGIES).efi; - pvector[13] = energy_charge_equilibration; - - } - - if (eflag_atom) { - int ntotal = atom->nlocal + atom->nghost; - for (i = 0; i < ntotal; i++) - eatom[i] += FORTRAN(cbkd,CBKD).estrain[i]; - } - - // extract global and per-atom virial from ReaxFF Fortran - - if (vflag_global) { - virial[0] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[0]; - virial[1] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[1]; - virial[2] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[2]; - virial[3] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[3]; - virial[4] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[4]; - virial[5] = -FORTRAN(cbkvirial, CBKVIRIAL).virial[5]; - } - - if (vflag_atom) { - int ntotal = atom->nlocal + atom->nghost; - j = 0; - for (i = 0; i < ntotal; i++) { - vatom[i][0] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+0]; - vatom[i][1] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+1]; - vatom[i][2] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+2]; - vatom[i][3] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+3]; - vatom[i][4] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+4]; - vatom[i][5] = -FORTRAN(cbkvirial, CBKVIRIAL).atomvirial[j+5]; - j += 6; - } - } -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::write_reax_positions() -{ - int j, jx, jy, jz, jia; - - double **x = atom->x; - double *q = atom->q; - int *type = atom->type; - int *tag = atom->tag; - int nlocal = atom->nlocal; - int nghost = atom->nghost; - - FORTRAN(rsmall, RSMALL).na = nlocal+nghost; - FORTRAN(rsmall, RSMALL).na_local = nlocal; - - if (nlocal+nghost > ReaxParams::nat) - error->one(FLERR,"Reax_defs.h setting for NATDEF is too small"); - - jx = 0; - jy = ReaxParams::nat; - jz = 2*ReaxParams::nat; - jia = 0; - - j = 0; - for (int i = 0; i < nlocal+nghost; i++, j++) { - FORTRAN(cbkc, CBKC).c[j+jx] = x[i][0]; - FORTRAN(cbkc, CBKC).c[j+jy] = x[i][1]; - FORTRAN(cbkc, CBKC).c[j+jz] = x[i][2]; - FORTRAN(cbkch, CBKCH).ch[j] = q[i]; - FORTRAN(cbkia, CBKIA).ia[j+jia] = map[type[i]]; - FORTRAN(cbkia, CBKIA).iag[j+jia] = map[type[i]]; - FORTRAN(cbkc, CBKC).itag[j] = tag[i]; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::write_reax_vlist() -{ - int ii, jj, i, j, iii, jjj; - double xitmp, yitmp, zitmp; - double xjtmp, yjtmp, zjtmp; - int itag,jtag; - int nvpair, nvlself, nvpairmax; - int nbond; - int inum,jnum; - int *ilist,*jlist,*numneigh,**firstneigh; - double delr2; - double delx, dely, delz; - - double **x = atom->x; - int *tag = atom->tag; - int nlocal = atom->nlocal; - int nghost = atom->nghost; - - nvpairmax = ReaxParams::nneighmax * ReaxParams::nat; - - nvpair = 0; - nvlself =0; - nbond = 0; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xitmp = x[i][0]; - yitmp = x[i][1]; - zitmp = x[i][2]; - itag = tag[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - xjtmp = x[j][0]; - yjtmp = x[j][1]; - zjtmp = x[j][2]; - jtag = tag[j]; - - delx = xitmp - xjtmp; - dely = yitmp - yjtmp; - delz = zitmp - zjtmp; - - delr2 = delx*delx+dely*dely+delz*delz; - - if (delr2 <= rcutvsq) { - if (i < j) { - iii = i+1; - jjj = j+1; - } else { - iii = j+1; - jjj = i+1; - } - if (nvpair >= nvpairmax) - error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small"); - - FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii; - FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj; - FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0; - - if (delr2 <= rcutbsq) { - FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1; - nbond++; - } - - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0; - - if (j < nlocal) - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1; - else if (itag < jtag) - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1; - else if (itag == jtag) { - if (delz > SMALL) - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1; - else if (fabs(delz) < SMALL) { - if (dely > SMALL) - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1; - else if (fabs(dely) < SMALL && delx > SMALL) - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 1; - } - } - nvpair++; - } - } - } - - int ntotal = nlocal + nghost; - - for (int i = nlocal; i < ntotal; i++) { - xitmp = x[i][0]; - yitmp = x[i][1]; - zitmp = x[i][2]; - itag = tag[i]; - - for (int j = i+1; j < ntotal; j++) { - xjtmp = x[j][0]; - yjtmp = x[j][1]; - zjtmp = x[j][2]; - jtag = tag[j]; - - delx = xitmp - xjtmp; - dely = yitmp - yjtmp; - delz = zitmp - zjtmp; - - delr2 = delx*delx+dely*dely+delz*delz; - - // don't need to check the double count since i < j in the ghost region - - if (delr2 <= rcutvsq) { - iii = i+1; - jjj = j+1; - - if (nvpair >= nvpairmax) - error->one(FLERR,"Reax_defs.h setting for NNEIGHMAXDEF is too small"); - - FORTRAN(cbkpairs, CBKPAIRS).nvl1[nvpair] = iii; - FORTRAN(cbkpairs, CBKPAIRS).nvl2[nvpair] = jjj; - FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 0; - - if (delr2 <= rcutbsq) { - FORTRAN(cbknvlbo, CBKNVLBO).nvlbo[nvpair] = 1; - nbond++; - } - - FORTRAN(cbknvlown, CBKNVLOWN).nvlown[nvpair] = 0; - nvpair++; - } - } - } - - FORTRAN(cbkpairs, CBKPAIRS).nvpair = nvpair; - FORTRAN(cbkpairs, CBKPAIRS).nvlself = nvlself; -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::read_reax_forces() -{ - double ftmp[3]; - - double **f = atom->f; - int ntotal = atom->nlocal + atom->nghost; - - int j = 0; - for (int i = 0; i < ntotal; i++) { - ftmp[0] = -FORTRAN(cbkd, CBKD).d[j]; - ftmp[1] = -FORTRAN(cbkd, CBKD).d[j+1]; - ftmp[2] = -FORTRAN(cbkd, CBKD).d[j+2]; - f[i][0] = ftmp[0]; - f[i][1] = ftmp[1]; - f[i][2] = ftmp[2]; - j += 3; - } -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - param_list = new ff_params[n+1]; - for (int i = 1; i <= n; i++) - param_list[i].params = new double[5]; - - map = new int[n+1]; -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairREAX::settings(int narg, char **arg) -{ - if (narg != 0 && narg !=4) error->all(FLERR,"Illegal pair_style command"); - - if (narg == 4) { - hbcut = force->numeric(FLERR,arg[0]); - ihbnew = static_cast (force->numeric(FLERR,arg[1])); - itripstaball = static_cast (force->numeric(FLERR,arg[2])); - precision = force->numeric(FLERR,arg[3]); - - if (hbcut <= 0.0 || - (ihbnew != 0 && ihbnew != 1) || - (itripstaball != 0 && itripstaball != 1) || - precision <= 0.0) - error->all(FLERR,"Illegal pair_style command"); - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairREAX::coeff(int narg, char **arg) -{ - if (!allocated) allocate(); - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure I,J args are * * - - if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // insure filename is ffield.reax - - if (strcmp(arg[2],"ffield.reax") != 0) - error->all(FLERR,"Incorrect args for pair coefficients"); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if NULL - // NOTE: for now throw an error if NULL is used to disallow use with hybrid - // qEq matrix solver needs to be modified to exclude atoms - - for (int i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - error->all(FLERR,"Cannot currently use pair reax with pair hybrid"); - continue; - } - map[i-2] = force->inumeric(FLERR,arg[i]); - } - - int n = atom->ntypes; - - int count = 0; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairREAX::init_style() -{ - if (atom->tag_enable == 0) - error->all(FLERR,"Pair style reax requires atom IDs"); - if (force->newton_pair == 0) - error->all(FLERR,"Pair style reax requires newton pair on"); - if (!atom->q_flag) - error->all(FLERR,"Pair style reax requires atom attribute q"); - if (strcmp(update->unit_style,"real") != 0 && comm->me == 0) - error->warning(FLERR,"Not using real units with pair reax"); - - int irequest = neighbor->request(this,instance_me); - neighbor->requests[irequest]->newton = 2; - - FORTRAN(readc, READC)(); - FORTRAN(reaxinit, REAXINIT)(); - FORTRAN(ffinpt, FFINPT)(); - FORTRAN(tap7th, TAP7TH)(); - - // turn off read_in by fort.3 in REAX Fortran - - int ngeofor_tmp = -1; - FORTRAN(setngeofor, SETNGEOFOR)(&ngeofor_tmp); - if (comm->me == 0) FORTRAN(readgeo, READGEO)(); - - // initial setup for cutoff radius of VLIST and BLIST in ReaxFF - - double vlbora; - - FORTRAN(getswb, GETSWB)(&swb); - cutmax=MAX(swb, hbcut); - rcutvsq=cutmax*cutmax; - FORTRAN(getvlbora, GETVLBORA)(&vlbora); - rcutbsq=vlbora*vlbora; - - // parameters for charge equilibration from ReaxFF input, fort.4 - // verify that no LAMMPS type to REAX type mapping was invalid - - int nelements; - FORTRAN(getnso, GETNSO)(&nelements); - - FORTRAN(getswa, GETSWA)(&swa); - double chi, eta, gamma; - for (int itype = 1; itype <= atom->ntypes; itype++) { - if (map[itype] < 1 || map[itype] > nelements) - error->all(FLERR,"Invalid REAX atom type"); - chi = FORTRAN(cbkchb, CBKCHB).chi[map[itype]-1]; - eta = FORTRAN(cbkchb, CBKCHB).eta[map[itype]-1]; - gamma = FORTRAN(cbkchb, CBKCHB).gam[map[itype]-1]; - param_list[itype].np = 5; - param_list[itype].rcutsq = cutmax; - param_list[itype].params[0] = chi; - param_list[itype].params[1] = eta; - param_list[itype].params[2] = gamma; - param_list[itype].params[3] = swa; - param_list[itype].params[4] = swb; - } - - taper_setup(); -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairREAX::init_one(int i, int j) -{ - return cutmax; -} - -/* ---------------------------------------------------------------------- */ - -int PairREAX::pack_forward_comm(int n, int *list, double *buf, - int pbc_flag, int *pbc) -{ - int i,j,m; - - m = 0; - - if (packflag == 0) { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = FORTRAN(cbkabo, CBKABO).abo[j]; - } - - } else { - for (i = 0; i < n; i++) { - j = list[i]; - buf[m++] = wcg[j]; - } - } - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::unpack_forward_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - - if (packflag == 0) { - for (i = first; i < last; i++) - FORTRAN(cbkabo, CBKABO).abo[i] = buf[m++]; - - } else { - for (i = first; i < last; i++) - wcg[i] = buf[m++]; - } -} - -/* ---------------------------------------------------------------------- */ - -int PairREAX::pack_reverse_comm(int n, int first, double *buf) -{ - int i,m,last; - - m = 0; - last = first + n; - for (i = first; i < last; i++) - buf[m++] = wcg[i]; - - return m; -} - -/* ---------------------------------------------------------------------- */ - -void PairREAX::unpack_reverse_comm(int n, int *list, double *buf) -{ - int i,j,m; - - m = 0; - for (i = 0; i < n; i++) { - j = list[i]; - wcg[j] += buf[m++]; - } -} - -/* ---------------------------------------------------------------------- - charge equilibration routines -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- */ - -void PairREAX::taper_setup() -{ - double swb2,swa2,swb3,swa3,d1,d7; - - d1=swb-swa; - d7=pow(d1,7.0); - swa2=swa*swa; - swa3=swa2*swa; - swb2=swb*swb; - swb3=swb2*swb; - - swc7= 20.0e0/d7; - swc6= -70.0e0*(swa+swb)/d7; - swc5= 84.0e0*(swa2+3.0e0*swa*swb+swb2)/d7; - swc4= -35.0e0*(swa3+9.0e0*swa2*swb+9.0e0*swa*swb2+swb3)/d7; - swc3= 140.0e0*(swa3*swb+3.0e0*swa2*swb2+swa*swb3)/d7; - swc2=-210.0e0*(swa3*swb2+swa2*swb3)/d7; - swc1= 140.0e0*swa3*swb3/d7; - swc0=(-35.0e0*swa3*swb2*swb2+21.0e0*swa2*swb3*swb2- - 7.0e0*swa*swb3*swb3+swb3*swb3*swb)/d7; -} - -/* ---------------------------------------------------------------------- */ - -double PairREAX::taper_E(const double &r, const double &r2) -{ - double r3=r2*r; - return swc7*r3*r3*r+swc6*r3*r3+swc5*r3*r2+swc4*r2*r2+swc3*r3+swc2*r2+ - swc1*r+swc0; -} - -/* ---------------------------------------------------------------------- */ - -double PairREAX::taper_F(const double &r, const double &r2) -{ - double r3=r2*r; - return 7.0e0*swc7*r3*r3+6.0e0*swc6*r3*r2+5.0e0*swc5*r2*r2+ - 4.0e0*swc4*r3+3.0e0*swc3*r2+2.0e0*swc2*r+swc1; -} - -/* ---------------------------------------------------------------------- - compute current charge distributions based on the charge equilibration -------------------------------------------------------------------------- */ - -void PairREAX::compute_charge(double &energy_charge_equilibration) -{ - double xitmp, yitmp, zitmp; - double xjtmp, yjtmp, zjtmp; - int itype, jtype, itag, jtag; - int ii, jj, i, j; - double delr2, delr_norm, gamt, hulp1, hulp2; - double delx, dely, delz; - double qsum,qi; - int nmatentries; - double sw; - int inum,jnum; - int *ilist,*jlist,*numneigh,**firstneigh; - - double **x = atom->x; - double *q = atom->q; - int *type = atom->type; - int *tag = atom->tag; - - int nlocal = atom->nlocal; - int nghost = atom->nghost; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // realloc neighbor based arrays if necessary - - int numneigh_total = 0; - for (ii = 0; ii < inum; ii++) - numneigh_total += numneigh[ilist[ii]]; - - if (numneigh_total + 2*nlocal > matmax) { - memory->destroy(aval); - memory->destroy(acol_ind); - matmax = numneigh_total + 2*nlocal; - memory->create(aval,matmax,"reax:aval"); - memory->create(acol_ind,matmax,"reax:acol_ind"); - } - - // build linear system - - nmatentries = 0; - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xitmp = x[i][0]; - yitmp = x[i][1]; - zitmp = x[i][2]; - itype = type[i]; - itag = tag[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - arow_ptr[i] = nmatentries; - aval[nmatentries] = 2.0*param_list[itype].params[1]; - acol_ind[nmatentries] = i; - nmatentries++; - - aval[nmatentries] = 1.0; - acol_ind[nmatentries] = nlocal + nghost; - nmatentries++; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - - xjtmp = x[j][0]; - yjtmp = x[j][1]; - zjtmp = x[j][2]; - jtype = type[j]; - jtag = tag[j]; - - delx = xitmp - xjtmp; - dely = yitmp - yjtmp; - delz = zitmp - zjtmp; - - delr2 = delx*delx+dely*dely+delz*delz; - - // avoid counting local-ghost pair twice since - // ReaxFF uses half neigh list with newton off - - if (j >= nlocal) { - if (itag > jtag) { - if ((itag+jtag) % 2 == 0) continue; - } else if (itag < jtag) { - if ((itag+jtag) % 2 == 1) continue; - } else { - if (zjtmp < zitmp) continue; - if (zjtmp == zitmp && yjtmp < yitmp) continue; - if (zjtmp == zitmp && yjtmp == yitmp && xjtmp < xitmp) continue; - } - } - - // rcutvsq = cutmax*cutmax, in ReaxFF - - if (delr2 <= rcutvsq) { - gamt = sqrt(param_list[itype].params[2]*param_list[jtype].params[2]); - delr_norm = sqrt(delr2); - sw = taper_E(delr_norm, delr2); - hulp1=(delr_norm*delr2+(1.0/(gamt*gamt*gamt))); - hulp2=sw*14.40/cbrt(hulp1); - aval[nmatentries] = hulp2; - acol_ind[nmatentries] = j; - nmatentries++; - } - } - } - - // in this case, we don't use Midpoint method - // so, we don't need to consider ghost-ghost interactions - // but, need to fill the arow_ptr[] arrays for the ghost atoms - - for (i = nlocal; i < nlocal+nghost; i++) - arow_ptr[i] = nmatentries; - arow_ptr[nlocal+nghost] = nmatentries; - - // add rhs matentries to linear system - - for (ii =0; iireverse_comm_pair(this); - comm->forward_comm_pair(this); - - MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world); - w[n-1] = sumtmp; - rho_old = one; - - for (iter = 1; iter < maxiter; iter++) { - rho = 0.0; - for (int i=0; i 1) { - beta = rho/rho_old; - for (int i = 0; ireverse_comm_pair(this); - comm->forward_comm_pair(this); - - MPI_Allreduce(&w[n-1], &sumtmp, 1, MPI_DOUBLE, MPI_SUM, world); - w[n-1] = sumtmp; - - for (int i=0; i Fortran calling syntax -// It defines the FORTRAN macro for converting variable and function -// names from FORTRAN to C. Different compilers do this in different -// ways. The default is add an underscore to the lower case string. -// Other definitions of the macro can be invoked by defining the -// corresponding macro at compile time using -D e.g. -D_IBM - -// CONS(a,b) should return ab, the concatenation of its arguments. -// If compiler is using strict ISO C standards, the ## works. -// Otherwise try the old /**/ trick and test. -// If that fails, you will need to figure out -// a definition for the FORTRAN macro that works on your machine. - -#if __STDC__ -#define CONS(a,b) a##b -#elif defined(_IBM) -#define CONS(a,b) a##b -#else -#define CONS(a,b) a/**/b -#warning "The following declaration is a test of the CONS macro" -#warning "If it fails, pair_reax_fortran.h must be modified by hand" -static int my_apples_my_oranges = 1; -static int my_applesoroanges = CONS(my_apples,_my_oranges); -#endif - - -#ifdef _IBM -#define FORTRAN(lcname,ucname) lcname -#endif - -#ifdef _F2C_LINUX -#define FORTRAN(lcname,ucname) CONS(lcname,__) -#endif - -#ifndef FORTRAN -#define FORTRAN(lcname,ucname) CONS(lcname,_) -#endif - -// hard-wired array sizes set in Fortran library -// accesses include file from Fortran library - -#include "reax_defs.h" - -class ReaxParams { - public: - enum {nneighmax=NNEIGHMAXDEF, - nat=NATDEF, - nattot=NATTOTDEF, - nsort=NSORTDEF, - mbond=MBONDDEF, - nbomax=NBOMAXDEF, - }; -}; - -// data structures corresponding to values in Fortran library - -extern "C" struct { - double abo[ReaxParams::nat]; -} FORTRAN(cbkabo,CBKABO); - -extern "C" struct { - double bo[ReaxParams::nbomax]; -} FORTRAN(cbkbo,CBKBO); - -extern "C" struct { - double c[3*ReaxParams::nat]; double cglobal[3*ReaxParams::nattot]; - int itag[ReaxParams::nat]; -} FORTRAN(cbkc,CBKC); - -extern "C" struct { -double ch[ReaxParams::nat]; -} FORTRAN(cbkch,CBKCH); - -extern "C" struct { - double chi[ReaxParams::nsort]; - double eta[ReaxParams::nsort]; - double gam[ReaxParams::nsort]; -} FORTRAN(cbkchb,CBKCHB); - -extern "C" struct { - double d[3*ReaxParams::nat]; double estrain[ReaxParams::nat]; -} FORTRAN(cbkd,CBKD); - -extern "C" struct { - double atomvirial[6*ReaxParams::nat]; - double virial[6]; - int Lvirial; - int Latomvirial; -} FORTRAN(cbkvirial,CBKVIRIAL); - -extern "C" struct { - int ia[ReaxParams::nat*(ReaxParams::mbond+3)]; - int iag[ReaxParams::nat*(ReaxParams::mbond+3)]; -} FORTRAN(cbkia,CBKIA); - -extern "C" struct { - double vlp[ReaxParams::nat]; - double dvlpdsbo[ReaxParams::nat]; -} FORTRAN(cbklonpar,CBKLONPAR); - -extern "C" struct { - int nubon1[ReaxParams::nat*(ReaxParams::mbond)]; - int nubon2[ReaxParams::nat*(ReaxParams::mbond)]; -} FORTRAN(cbknubon2,CBKNUBON2); - -extern "C" struct { - int nvl1[ReaxParams::nneighmax * ReaxParams::nat]; - int nvl2[ReaxParams::nneighmax * ReaxParams::nat]; - int nvpair; - int nvlself; -} FORTRAN(cbkpairs,CBKPAIRS); - -extern "C" struct { - int nvlbo[ReaxParams::nneighmax * ReaxParams::nat]; -} FORTRAN(cbknvlbo,CBKNVLBO); - -extern "C" struct { - int nvlown[ReaxParams::nneighmax * ReaxParams::nat]; -} FORTRAN(cbknvlown,CBKNVLOWN); - -extern "C" struct { - char qa[20*ReaxParams::nattot+10]; -} FORTRAN(cbkqa,CBKQA); - -extern "C" struct { - double eb; - double eoop; - double epen; - double estrc; - double deda[3]; - double pressu; - double efi; - double elp; - double emol; - double ea; - double eres; - double et; - double eradbo; - double ev; - double eco; - double ecoa; - double ehb; - double sw; - double ew; - double ep; - double ekin; -} FORTRAN(cbkenergies,CBKENERGIES); - -extern "C" struct { - double tset; - double dseed; - double tempmd; - double ts2; - double ts22; - int nmolo; - int nmolo5; - int nbon; - int na; - int namov; - int na_local; -} FORTRAN(rsmall,RSMALL); - -// external routines provided by Fortran library - -extern "C" void FORTRAN(readc,READC)(); -extern "C" void FORTRAN(reaxinit,REAXINIT)(); -extern "C" void FORTRAN(ffinpt,FFINPT)(); -extern "C" void FORTRAN(tap7th,TAP7TH)(); -extern "C" void FORTRAN(taper,TAPER)(double*,double*); -extern "C" void FORTRAN(readgeo,READGEO)(); -extern "C" void FORTRAN(srtatom,SRTATOM)(); -extern "C" void FORTRAN(vlist,VLIST) (); -extern "C" void FORTRAN(srtbon1,SRTBON1)(int*,int*,double*,int*,int*); -extern "C" void FORTRAN(molec,MOLEC)(); -extern "C" void FORTRAN(encalc,ENCALC)(); -extern "C" void FORTRAN(getswb,GETSWB)(double*); -extern "C" void FORTRAN(getswa,GETSWA)(double*); -extern "C" void FORTRAN(getvrange,GET_VRANGE)(double*); -extern "C" void FORTRAN(getnvlist,GET_NVLIST)(int*); -extern "C" void FORTRAN(getvlbora,GETVLBORA)(double*); -extern "C" void FORTRAN(cgsolve,CGSOLVE) - (int*,double*,int*,double*,double*,int*); -extern "C" void FORTRAN(getnval,GETNVAL)(int*); -extern "C" void FORTRAN(getntor,GETNTOR)(int*); -extern "C" void FORTRAN(getnhb,GETNHB)(int*); -extern "C" void FORTRAN(getnbonall,GETNBONALL)(int*); -extern "C" void FORTRAN(getnneighmax,GETNNEIGHMAX)(int*); -extern "C" void FORTRAN(getnat,GETNAT)(int*); -extern "C" void FORTRAN(getnattot,GETNATTOT)(int*); -extern "C" void FORTRAN(getnsort,GETNSORT)(int*); -extern "C" void FORTRAN(getmbond,GETMBOND)(int*); -extern "C" void FORTRAN(getnso,GETNSO)(int*); -extern "C" void FORTRAN(setngeofor,SETNGEOFOR)(int*); -extern "C" void FORTRAN(mdsav,MDSAV)(int*); -extern "C" void FORTRAN(getnsbmax,GETNSBMAX)(int*); -extern "C" void FORTRAN(getnsbma2,GETNSBMA2)(int*); -extern "C" void FORTRAN(getcutof3,GETCUTOF3)(double*); diff --git a/src/REPLICA/fix_event_hyper.cpp b/src/REPLICA/fix_event_hyper.cpp new file mode 100644 index 0000000000..eae1ad021d --- /dev/null +++ b/src/REPLICA/fix_event_hyper.cpp @@ -0,0 +1,95 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_event_hyper.h" +#include "atom.h" +#include "update.h" +#include "domain.h" +#include "neighbor.h" +#include "comm.h" +#include "universe.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixEventHyper::FixEventHyper(LAMMPS *lmp, int narg, char **arg) : + FixEvent(lmp, narg, arg) +{ + if (narg != 3) error->all(FLERR,"Illegal fix event command"); + + restart_global = 1; + + event_number = 0; + event_timestep = update->ntimestep; + clock = 0; +} + +/* ---------------------------------------------------------------------- + save current atom coords as an event (via call to base class) + called when an event occurs in some replica + set event_timestep = when event occurred in a particular replica + update clock = elapsed time since last event, across all replicas +------------------------------------------------------------------------- */ + +void FixEventHyper::store_event_hyper(bigint ntimestep, int delta_clock) +{ + store_event(); + event_timestep = ntimestep; + clock += delta_clock; + event_number++; +} + +/* ---------------------------------------------------------------------- + pack entire state of Fix into one write +------------------------------------------------------------------------- */ + +void FixEventHyper::write_restart(FILE *fp) +{ + int n = 0; + double list[6]; + list[n++] = event_number; + list[n++] = event_timestep; + list[n++] = clock; + list[n++] = replica_number; + list[n++] = correlated_event; + list[n++] = ncoincident; + + if (comm->me == 0) { + int size = n * sizeof(double); + fwrite(&size,sizeof(int),1,fp); + fwrite(list,sizeof(double),n,fp); + } +} + +/* ---------------------------------------------------------------------- + use state info from restart file to restart the Fix +------------------------------------------------------------------------- */ + +void FixEventHyper::restart(char *buf) +{ + int n = 0; + double *list = (double *) buf; + + event_number = static_cast (list[n++]); + event_timestep = static_cast (list[n++]); + clock = static_cast (list[n++]); + replica_number = static_cast (list[n++]); + correlated_event = static_cast (list[n++]); + ncoincident = static_cast (list[n++]); +} diff --git a/src/REPLICA/fix_event_hyper.h b/src/REPLICA/fix_event_hyper.h new file mode 100644 index 0000000000..4c5d4a93ee --- /dev/null +++ b/src/REPLICA/fix_event_hyper.h @@ -0,0 +1,60 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(EVENT/HYPER,FixEventHyper) + +#else + +#ifndef LMP_FIX_EVENT_HYPER_H +#define LMP_FIX_EVENT_HYPER_H + +#include "fix_event.h" + +namespace LAMMPS_NS { + +class FixEventHyper : public FixEvent { + public: + int event_number; // event counter + bigint event_timestep; // timestep of last event on any replica + bigint clock; // total elapsed timesteps across all replicas + int replica_number; // replica where last event occured + int correlated_event; // 1 if last event was correlated, 0 otherwise + int ncoincident; // # of simultaneous events on different replicas + + FixEventHyper(class LAMMPS *, int, char **); + ~FixEventHyper() {} + + void write_restart(FILE *); + void restart(char *); + + // methods specific to FixEventHyper, invoked by hyper + + void store_event_hyper(bigint, int); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/REPLICA/fix_hyper.cpp b/src/REPLICA/fix_hyper.cpp new file mode 100644 index 0000000000..c86c00ad45 --- /dev/null +++ b/src/REPLICA/fix_hyper.cpp @@ -0,0 +1,36 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "fix_hyper.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +FixHyper::FixHyper(LAMMPS *lmp, int narg, char **arg) + : Fix(lmp, narg, arg), hyperflag(0) {} + +/* ---------------------------------------------------------------------- + extract hyper flag setting for all Fixes that perform hyperdynamics +------------------------------------------------------------------------- */ + +void *FixHyper::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"hyperflag") == 0) { + return &hyperflag; + } + return NULL; +} + diff --git a/src/REPLICA/fix_hyper.h b/src/REPLICA/fix_hyper.h new file mode 100644 index 0000000000..7cb6cadf8f --- /dev/null +++ b/src/REPLICA/fix_hyper.h @@ -0,0 +1,43 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_FIX_HYPER_H +#define LMP_FIX_HYPER_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixHyper : public Fix { + public: + FixHyper(class LAMMPS *, int, char **); + virtual ~FixHyper() {} + void *extract(const char *, int &); + + // must be provided by child class + + virtual void init_hyper() = 0; + virtual void build_bond_list(int) = 0; + virtual double query(int) = 0; + + protected: + int hyperflag; +}; + +} + +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/REPLICA/fix_hyper_global.cpp b/src/REPLICA/fix_hyper_global.cpp new file mode 100644 index 0000000000..6924fe2d93 --- /dev/null +++ b/src/REPLICA/fix_hyper_global.cpp @@ -0,0 +1,563 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "fix_hyper_global.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "domain.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "modify.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define DELTABOND 16384 +#define VECLEN 5 + +// possible enhancements +// should there be a virial contribution from boosted bond? +// allow newton off? + +/* ---------------------------------------------------------------------- */ + +FixHyperGlobal::FixHyperGlobal(LAMMPS *lmp, int narg, char **arg) : + FixHyper(lmp, narg, arg), blist(NULL), xold(NULL), tagold(NULL) +{ + if (atom->map_style == 0) + error->all(FLERR,"Fix hyper/global command requires atom map"); + + if (narg != 7) error->all(FLERR,"Illegal fix hyper/global command"); + + hyperflag = 1; + scalar_flag = 1; + vector_flag = 1; + size_vector = 12; + global_freq = 1; + extscalar = 0; + extvector = 0; + + cutbond = force->numeric(FLERR,arg[3]); + qfactor = force->numeric(FLERR,arg[4]); + vmax = force->numeric(FLERR,arg[5]); + tequil = force->numeric(FLERR,arg[6]); + + if (cutbond < 0.0 || qfactor <= 0.0 || vmax < 0.0 || tequil <= 0.0) + error->all(FLERR,"Illegal fix hyper/global command"); + + invqfactorsq = 1.0 / (qfactor*qfactor); + cutbondsq = cutbond*cutbond; + beta = 1.0 / (force->boltz * tequil); + + maxbond = 0; + nblocal = 0; + blist = NULL; + + maxold = 0; + xold = NULL; + tagold = NULL; + old2now = NULL; + + me = comm->me; + firstflag = 1; + bcastflag = 0; + for (int i = 0; i < VECLEN; i++) outvec[i] = 0.0; + + nevent = 0; + nevent_atom = 0; + t_hyper = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +FixHyperGlobal::~FixHyperGlobal() +{ + memory->sfree(blist); + memory->destroy(xold); + memory->destroy(tagold); + memory->destroy(old2now); +} + +/* ---------------------------------------------------------------------- */ + +int FixHyperGlobal::setmask() +{ + int mask = 0; + mask |= PRE_NEIGHBOR; + mask |= PRE_REVERSE; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::init_hyper() +{ + maxdriftsq = 0.0; + maxbondlen = 0.0; + nobias = 0; + negstrain = 0; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::init() +{ + if (force->newton_pair == 0) + error->all(FLERR,"Hyper global requires newton pair on"); + + if (atom->molecular && me == 0) + error->warning(FLERR,"Hyper global for molecular systems " + "requires care in defining hyperdynamic bonds"); + + dt = update->dt; + + // need an occasional half neighbor list + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->fix = 1; + neighbor->requests[irequest]->occasional = 1; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::init_list(int /* id */, NeighList *ptr) +{ + list = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::setup_pre_neighbor() +{ + pre_neighbor(); +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::setup_pre_reverse(int eflag, int vflag) +{ + // no increment in these quantities when pre-run forces are calculated + + int nobias_hold = nobias; + int negstrain_hold = negstrain; + double t_hyper_hold = t_hyper; + + pre_reverse(eflag,vflag); + + nobias = nobias_hold; + negstrain = negstrain_hold; + t_hyper = t_hyper_hold; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::pre_neighbor() +{ + int i,m,iold,jold,ilocal,jlocal; + // double distsq; + + // reset local indices for owned bond atoms, since atoms have migrated + // must be done after ghost atoms are setup via comm->borders() + // first time this is done for a particular I or J atom: + // use tagold and xold from when bonds were created + // atom->map() finds atom ID if it exists, owned index if possible + // closest current I or J atoms to old I may now be ghost atoms + // closest_image() returns the ghost atom index in that case + // also compute max drift of any atom in a bond + // drift = displacement from quenched coord while event has not yet occured + // NOTE: drift calc is now done in bond_build(), between 2 quenched states + + for (i = 0; i < nall_old; i++) old2now[i] = -1; + + double **x = atom->x; + + for (m = 0; m < nblocal; m++) { + iold = blist[m].iold; + jold = blist[m].jold; + ilocal = old2now[iold]; + jlocal = old2now[jold]; + + if (ilocal < 0) { + ilocal = atom->map(tagold[iold]); + ilocal = domain->closest_image(xold[iold],ilocal); + if (ilocal < 0) + error->one(FLERR,"Fix hyper/global bond atom not found"); + old2now[iold] = ilocal; + //distsq = MathExtra::distsq3(x[ilocal],xold[iold]); + //maxdriftsq = MAX(distsq,maxdriftsq); + } + if (jlocal < 0) { + jlocal = atom->map(tagold[jold]); + jlocal = domain->closest_image(xold[iold],jlocal); // closest to iold + if (jlocal < 0) + error->one(FLERR,"Fix hyper/global bond atom not found"); + old2now[jold] = jlocal; + //distsq = MathExtra::distsq3(x[jlocal],xold[jold]); + //maxdriftsq = MAX(distsq,maxdriftsq); + } + + blist[m].i = ilocal; + blist[m].j = jlocal; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::pre_reverse(int /* eflag */, int /* vflag */) +{ + int i,j,m,imax,jmax; + double delx,dely,delz; + double r,r0,estrain,rmax,r0max,dt_boost; + double ebias,vbias,fbias,fbiasr; + + // compute current strain of each owned bond + // emax = maximum abs value of strain of any bond I own + // imax,jmax = local indices of my 2 atoms in that bond + // rmax,r0max = current and relaxed lengths of that bond + + double **x = atom->x; + double emax = 0.0; + + for (m = 0; m < nblocal; m++) { + i = blist[m].i; + j = blist[m].j; + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + r = sqrt(delx*delx + dely*dely + delz*delz); + maxbondlen = MAX(r,maxbondlen); + r0 = blist[m].r0; + estrain = fabs(r-r0) / r0; + + if (estrain > emax) { + emax = estrain; + rmax = r; + r0max = r0; + imax = i; + jmax = j; + } + } + + // perform Allreduce() on pairme = double/int pair + // finds max strain and what proc owns it + // owner = proc that owns that bond + + pairme.value = emax; + pairme.proc = me; + MPI_Allreduce(&pairme,&pairall,1,MPI_DOUBLE_INT,MPI_MAXLOC,world); + owner = pairall.proc; + + bcastflag = 1; + + // all procs acquire t_hyper from owner proc + // MPI_Bcast call by owner proc is below + + for (int i = 0; i < VECLEN; i++) outvec[i] = 0.0; + + if (owner != me) { + MPI_Bcast(&t_hyper,1,MPI_DOUBLE,owner,world); + return; + } + + // I own the bond with max absolute value of strain + // compute bias force on atoms imax,jmax if strain < q, else zero + // Ebias = current strain = (r-r0) / r0 + // Vbias = bias potential = Vmax (1 - Ebias^2/q^2) + // Fbias = bias force as function of strain + // = -dVbias/dEbias = 2 Vmax Ebias / q^2 + // Fix = x component of force on atom I + // = Fbias dEbias/dr dr/dxi, dEbias/dr = 1/r0, dr/dxi = delx/r + // dt_boost = time boost factor = exp(Vbias/kT) + + double **f = atom->f; + + vbias = fbias = 0.0; + dt_boost = 1.0; + + if (emax < qfactor) { + ebias = (rmax-r0max) / r0max; + vbias = vmax * (1.0 - ebias*ebias*invqfactorsq); + fbias = 2.0 * vmax * ebias * invqfactorsq; + dt_boost = exp(beta*vbias); + + delx = x[imax][0] - x[jmax][0]; + dely = x[imax][1] - x[jmax][1]; + delz = x[imax][2] - x[jmax][2]; + + fbiasr = fbias / r0max / rmax; + f[imax][0] += delx*fbiasr; + f[imax][1] += dely*fbiasr; + f[imax][2] += delz*fbiasr; + + f[jmax][0] -= delx*fbiasr; + f[jmax][1] -= dely*fbiasr; + f[jmax][2] -= delz*fbiasr; + + if (ebias < 0.0) negstrain++; + + } else nobias++; + + // output quantities + + outvec[0] = vbias; + outvec[1] = dt_boost; + outvec[2] = emax; + outvec[3] = atom->tag[imax]; + outvec[4] = atom->tag[jmax]; + + t_hyper += dt_boost*dt; + MPI_Bcast(&t_hyper,1,MPI_DOUBLE,owner,world); +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperGlobal::build_bond_list(int natom) +{ + int i,j,m,ii,jj,iold,jold,ilocal,jlocal,inum,jnum; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq,distsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + if (natom) { + nevent++; + nevent_atom += natom; + } + + // compute max distance any bond atom has moved between 2 quenched states + // xold[iold] = last quenched coord for iold + // x[ilocal] = current quenched coord for same atom + + double **x = atom->x; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + for (m = 0; m < nblocal; m++) { + iold = blist[m].iold; + ilocal = atom->map(tagold[iold]); + ilocal = domain->closest_image(xold[iold],ilocal); + distsq = MathExtra::distsq3(x[ilocal],xold[iold]); + maxdriftsq = MAX(distsq,maxdriftsq); + jold = blist[m].jold; + jlocal = atom->map(tagold[jold]); + jlocal = domain->closest_image(xold[iold],jlocal); + distsq = MathExtra::distsq3(x[jlocal],xold[jold]); + maxdriftsq = MAX(distsq,maxdriftsq); + } + + // trigger neighbor list build + + neighbor->build_one(list); + + // identify bonds assigned to each owned atom + // do not create a bond between two non-group atoms + + int *mask = atom->mask; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + nblocal = 0; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + // skip if neither atom I or J are in fix group + + if (!(mask[i] & groupbit) && !(mask[j] & groupbit)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutbondsq) { + if (nblocal == maxbond) grow_bond(); + blist[nblocal].i = i; + blist[nblocal].j = j; + blist[nblocal].iold = i; + blist[nblocal].jold = j; + blist[nblocal].r0 = sqrt(rsq); + nblocal++; + } + } + } + + // store per-atom quantities for owned+ghost atoms at time of bond creation + // nall_old = value of nall at time bonds are built + + tagint *tag = atom->tag; + + if (nall > maxold) { + memory->destroy(xold); + memory->destroy(tagold); + memory->destroy(old2now); + maxold = atom->nmax; + memory->create(xold,maxold,3,"hyper/global:xold"); + memory->create(tagold,maxold,"hyper/global:tagold"); + memory->create(old2now,maxold,"hyper/global:old2now"); + } + + memcpy(&xold[0][0],&x[0][0],3*nall*sizeof(double)); + for (i = 0; i < nall; i++) tagold[i] = tag[i]; + + nlocal_old = nlocal; + nall_old = nall; +} + +/* ---------------------------------------------------------------------- + grow bond list by a chunk +------------------------------------------------------------------------- */ + +void FixHyperGlobal::grow_bond() +{ + if (maxbond + DELTABOND > MAXSMALLINT) + error->one(FLERR,"Fix hyper/global bond count is too big"); + maxbond += DELTABOND; + blist = (OneBond *) + memory->srealloc(blist,maxbond*sizeof(OneBond),"hyper/global:blist"); +} + +/* ---------------------------------------------------------------------- */ + +double FixHyperGlobal::compute_scalar() +{ + if (bcastflag) { + MPI_Bcast(outvec,VECLEN,MPI_DOUBLE,owner,world); + bcastflag = 0; + } + return outvec[0]; +} + +/* ---------------------------------------------------------------------- */ + +double FixHyperGlobal::compute_vector(int i) +{ + if (bcastflag) { + MPI_Bcast(outvec,VECLEN,MPI_DOUBLE,owner,world); + bcastflag = 0; + } + + // 12 vector outputs returned for i = 0-11 + + // i = 0 = boost factor on this step + // i = 1 = max strain of any bond on this step (positive or negative) + // i = 2 = ID of atom I in max-strain bond on this step + // i = 3 = ID of atom J in max-strain bond on this step + // i = 4 = ave bonds/atom on this step + + // i = 5 = fraction of steps where bond has no bias during this run + // i = 6 = fraction of steps where bond has negative strain during this run + // i = 7 = max drift distance of any atom during this run + // i = 8 = max bond length during this run + + // i = 9 = cummulative hyper time since fix created + // i = 10 = cummulative # of event timesteps since fix created + // i = 11 = cummulative # of atoms in events since fix created + + if (i == 0) return outvec[1]; + if (i == 1) return outvec[2]; + if (i == 2) return outvec[3]; + if (i == 3) return outvec[4]; + + if (i == 4) { + bigint mybonds = nblocal; + bigint allbonds; + MPI_Allreduce(&mybonds,&allbonds,1,MPI_LMP_BIGINT,MPI_SUM,world); + return 2.0*allbonds/atom->natoms; + } + + if (i == 5) { + if (update->ntimestep == update->firststep) return 0.0; + int allnobias; + MPI_Allreduce(&nobias,&allnobias,1,MPI_INT,MPI_SUM,world); + return 1.0*allnobias / (update->ntimestep - update->firststep); + } + + if (i == 6) { + if (update->ntimestep == update->firststep) return 0.0; + int allnegstrain; + MPI_Allreduce(&negstrain,&allnegstrain,1,MPI_INT,MPI_SUM,world); + return 1.0*allnegstrain / (update->ntimestep - update->firststep); + } + + if (i == 7) { + double alldriftsq; + MPI_Allreduce(&maxdriftsq,&alldriftsq,1,MPI_DOUBLE,MPI_MAX,world); + return sqrt(alldriftsq); + } + + if (i == 8) { + double allbondlen; + MPI_Allreduce(&maxbondlen,&allbondlen,1,MPI_DOUBLE,MPI_MAX,world); + return allbondlen; + } + + if (i == 9) return t_hyper; + if (i == 10) return (double) nevent; + if (i == 11) return (double) nevent_atom; + + return 0.0; +} + +/* ---------------------------------------------------------------------- + wrapper on compute_vector() + used by hyper.cpp to call FixHyper +------------------------------------------------------------------------- */ + +double FixHyperGlobal::query(int i) +{ + if (i == 1) return compute_vector(9); // cummulative hyper time + if (i == 2) return compute_vector(10); // nevent + if (i == 3) return compute_vector(11); // nevent_atom + if (i == 4) return compute_vector(4); // ave bonds/atom + if (i == 5) return compute_vector(7); // maxdrift + if (i == 6) return compute_vector(8); // maxbondlen + if (i == 7) return compute_vector(5); // fraction with zero bias + if (i == 8) return compute_vector(6); // fraction with negative strain + + error->all(FLERR,"Invalid query to fix hyper/global"); + + return 0.0; +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double FixHyperGlobal::memory_usage() +{ + double bytes = maxbond * sizeof(OneBond); // blist + return bytes; +} diff --git a/src/REPLICA/fix_hyper_global.h b/src/REPLICA/fix_hyper_global.h new file mode 100644 index 0000000000..a62f80b54a --- /dev/null +++ b/src/REPLICA/fix_hyper_global.h @@ -0,0 +1,114 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(hyper/global,FixHyperGlobal) + +#else + +#ifndef LMP_FIX_HYPER_GLOBAL_H +#define LMP_FIX_HYPER_GLOBAL_H + +#include "fix_hyper.h" + +namespace LAMMPS_NS { + +class FixHyperGlobal : public FixHyper { + public: + FixHyperGlobal(class LAMMPS *, int, char **); + ~FixHyperGlobal(); + int setmask(); + void init(); + void init_list(int, class NeighList *); + void setup_pre_neighbor(); + void setup_pre_reverse(int, int); + void pre_neighbor(); + void pre_reverse(int, int); + double compute_scalar(); + double compute_vector(int); + double query(int); + + double memory_usage(); + + // extra methods visible to callers + + void init_hyper(); + void build_bond_list(int); + + private: + int me; + double cutbond,qfactor,vmax,tequil; + + int firstflag,bcastflag,owner,nevent,nevent_atom; + double cutbondsq,beta,dt,t_hyper,invqfactorsq; + double outvec[5]; // same as VECLEN in *.cpp + double maxbondlen; // max length of any bond + double maxdriftsq; // max distance any atom drifts from original pos + int nobias; // # of steps when bias = 0, b/c bond too long + int negstrain; // # of steps when biased bond has negative strain + + class NeighList *list; + + // list of my owned bonds + // persists on a proc from one event until the next + + int maxbond; // allocated size of blist + + struct OneBond { // single IJ bond, atom I is owner + int i,j; // current local indices of 2 bond atoms + int iold,jold; // local indices when bonds were formed + double r0; // relaxed bond length + }; + + OneBond *blist; // list of owned bonds + int nblocal; // # of owned bonds + + // coords and IDs of owned+ghost atoms when bonds were formed + // persists on a proc from one event until the next + + int nlocal_old; // nlocal for old atoms + int nall_old; // nlocal+nghost for old atoms + int maxold; // allocated size of old atoms + + double **xold; // coords of atoms when bonds were formed + tagint *tagold; // IDs of atoms when bonds were forme + int *old2now; // o2n[i] = current local index of old atom I + + // MPI data struct for finding bond with max strain via Allreduce + + struct Two { + double value; + int proc; + }; + Two pairme,pairall; + + // internal methods + + void grow_bond(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp new file mode 100644 index 0000000000..dc7a0b94b9 --- /dev/null +++ b/src/REPLICA/fix_hyper_local.cpp @@ -0,0 +1,1573 @@ + /* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU Gene +#include +#include +#include +#include "fix_hyper_local.h" +#include "atom.h" +#include "update.h" +#include "force.h" +#include "pair.h" +#include "domain.h" +#include "comm.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "neigh_list.h" +#include "modify.h" +#include "math_extra.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define DELTABOND 16384 +#define DELTABIAS 16 +#define COEFFINIT 1.0 +#define FCCBONDS 12 +#define BIG 1.0e20 + +enum{STRAIN,STRAINDOMAIN,BIASFLAG,BIASCOEFF}; +enum{IGNORE,WARN,ERROR}; + +/* ---------------------------------------------------------------------- */ + +FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) : + FixHyper(lmp, narg, arg), blist(NULL), biascoeff(NULL), numbond(NULL), + maxhalf(NULL), eligible(NULL), maxhalfstrain(NULL), old2now(NULL), + tagold(NULL), xold(NULL), maxstrain(NULL), maxstrain_domain(NULL), + biasflag(NULL), bias(NULL), cpage(NULL), clist(NULL), numcoeff(NULL) +{ + // error checks + + if (atom->map_style == 0) + error->all(FLERR,"Fix hyper/local command requires atom map"); + + // parse args + + if (narg < 10) error->all(FLERR,"Illegal fix hyper/local command"); + + hyperflag = 2; + scalar_flag = 1; + vector_flag = 1; + size_vector = 21; + local_flag = 1; + size_local_rows = 0; + size_local_cols = 0; + local_freq = 1; + + global_freq = 1; + extscalar = 0; + extvector = 0; + + cutbond = force->numeric(FLERR,arg[3]); + qfactor = force->numeric(FLERR,arg[4]); + vmax = force->numeric(FLERR,arg[5]); + tequil = force->numeric(FLERR,arg[6]); + dcut = force->numeric(FLERR,arg[7]); + alpha_user = force->numeric(FLERR,arg[8]); + boost_target = force->numeric(FLERR,arg[9]); + + if (cutbond < 0.0 || qfactor < 0.0 || vmax < 0.0 || + tequil <= 0.0 || dcut <= 0.0 || alpha_user <= 0.0 || boost_target < 1.0) + error->all(FLERR,"Illegal fix hyper/local command"); + + invqfactorsq = 1.0 / (qfactor*qfactor); + cutbondsq = cutbond*cutbond; + dcutsq = dcut*dcut; + beta = 1.0 / (force->boltz * tequil); + + // optional args + + checkghost = 0; + checkbias = 0; + + int iarg = 10; + while (iarg < narg) { + if (strcmp(arg[iarg],"check/ghost") == 0) { + checkghost = 1; + iarg++; + } else if (strcmp(arg[iarg],"check/bias") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal fix hyper/local command"); + checkbias = 1; + checkbias_every = force->inumeric(FLERR,arg[iarg+1]); + if (strcmp(arg[iarg+2],"error") == 0) checkbias_flag = ERROR; + else if (strcmp(arg[iarg+2],"warn") == 0) checkbias_flag = WARN; + else if (strcmp(arg[iarg+2],"ignore") == 0) checkbias_flag = IGNORE; + else error->all(FLERR,"Illegal fix hyper/local command"); + iarg += 3; + } else error->all(FLERR,"Illegal fix hyper/local command"); + } + + // per-atom data structs + + maxbond = nblocal = 0; + blist = NULL; + biascoeff = NULL; + allbonds = 0; + + maxatom = 0; + maxstrain = NULL; + maxstrain_domain = NULL; + biasflag = NULL; + + maxlocal = nlocal_old = 0; + numbond = NULL; + maxhalf = NULL; + eligible = NULL; + maxhalfstrain = NULL; + + maxall = nall_old = 0; + xold = NULL; + tagold = NULL; + old2now = NULL; + + nbias = maxbias = 0; + bias = NULL; + + // data structs for persisting bias coeffs when bond list is reformed + // maxbondperatom = max # of bonds any atom is part of + // FCCBONDS = 12 is a good estimate for fcc lattices + // will be reset in build_bond() if necessary + + maxcoeff = 0; + maxbondperatom = FCCBONDS; + numcoeff = NULL; + clist = NULL; + cpage = new MyPage; + cpage->init(maxbondperatom,1024*maxbondperatom,1); + + // set comm sizes needed by this fix + // reverse = 2 is for sending atom index + value, though total likely < 1 + // reverse comm for bias coeffs has variable size, so not tallied here + + comm_forward = 1; + comm_reverse = 2; + + me = comm->me; + firstflag = 1; + + sumbiascoeff = 0.0; + avebiascoeff = 0.0; + + starttime = update->ntimestep; + nostrainyet = 1; + nnewbond = 0; + nevent = 0; + nevent_atom = 0; + mybias = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +FixHyperLocal::~FixHyperLocal() +{ + memory->destroy(blist); + memory->destroy(biascoeff); + + memory->destroy(maxstrain); + memory->destroy(maxstrain_domain); + memory->destroy(biasflag); + + memory->destroy(numbond); + memory->destroy(maxhalf); + memory->destroy(eligible); + memory->destroy(maxhalfstrain); + + memory->destroy(xold); + memory->destroy(tagold); + memory->destroy(old2now); + + memory->destroy(bias); + + memory->destroy(numcoeff); + memory->sfree(clist); + delete cpage; +} + +/* ---------------------------------------------------------------------- */ + +int FixHyperLocal::setmask() +{ + int mask = 0; + mask |= PRE_NEIGHBOR; + mask |= PRE_REVERSE; + mask |= MIN_PRE_NEIGHBOR; + mask |= THERMO_ENERGY; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::init_hyper() +{ + ghost_toofar = 0; + checkbias_count = 0; + maxdriftsq = 0.0; + maxbondlen = 0.0; + avebiascoeff = 0.0; + minbiascoeff = BIG; + maxbiascoeff = 0.0; + nbias_running = 0; + nobias_running = 0; + negstrain_running = 0; + rmaxever = 0.0; + rmaxeverbig = 0.0; + + nbondbuild = 0; + time_bondbuild = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::init() +{ + // for newton off, bond force bias will not be applied correctly + // for bonds that straddle 2 procs + // warn if molecular system, since near-neighbors may not appear in neigh list + // user should not be including bonded atoms as hyper "bonds" + + if (force->newton_pair == 0) + error->all(FLERR,"Hyper local requires newton pair on"); + + if (atom->molecular && me == 0) + error->warning(FLERR,"Hyper local for molecular systems " + "requires care in defining hyperdynamic bonds"); + + // cutghost = communication cutoff as calculated by Neighbor and Comm + // error if cutghost is smaller than Dcut + // warn if no drift distance added to cutghost + + if (firstflag) { + double cutghost; + if (force->pair) + cutghost = MAX(force->pair->cutforce+neighbor->skin,comm->cutghostuser); + else + cutghost = comm->cutghostuser; + + if (cutghost < dcut) + error->all(FLERR,"Fix hyper/local domain cutoff exceeds ghost atom range - " + "use comm_modify cutoff command"); + if (cutghost < dcut+cutbond/2.0 && me == 0) + error->warning(FLERR,"Fix hyper/local ghost atom range " + "may not allow for atom drift between events"); + } + + alpha = update->dt / alpha_user; + + // need occasional full neighbor list with cutoff = Dcut + // used for finding maxstrain of neighbor bonds out to Dcut + // do not need to include neigh skin in cutoff, + // b/c this list will be built every time build_bond() is called + // NOTE: what if pair style list cutoff > Dcut + // or what if neigh skin is huge? + + int irequest_full = neighbor->request(this,instance_me); + neighbor->requests[irequest_full]->id = 1; + neighbor->requests[irequest_full]->pair = 0; + neighbor->requests[irequest_full]->fix = 1; + neighbor->requests[irequest_full]->half = 0; + neighbor->requests[irequest_full]->full = 1; + neighbor->requests[irequest_full]->cut = 1; + neighbor->requests[irequest_full]->cutoff = dcut; + neighbor->requests[irequest_full]->occasional = 1; + + // also need occasional half neighbor list derived from pair style + // used for building local bond list + // no specified cutoff, should be longer than cutbond + // this list will also be built (or derived/copied) + // every time build_bond() is called + + int irequest_half = neighbor->request(this,instance_me); + neighbor->requests[irequest_half]->id = 2; + neighbor->requests[irequest_half]->pair = 0; + neighbor->requests[irequest_half]->fix = 1; + neighbor->requests[irequest_half]->occasional = 1; + + // extra timing output + + //timefirst = timesecond = timethird = timefourth = timefifth = + // timesixth = timeseventh = timetotal = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::init_list(int id, NeighList *ptr) +{ + if (id == 1) listfull = ptr; + else if (id == 2) listhalf = ptr; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::setup_pre_neighbor() +{ + // called for dynamics and minimization + + pre_neighbor(); +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::setup_pre_reverse(int eflag, int vflag) +{ + // only called for dynamics, not minimization + // setupflag prevents boostostat update of bias coeffs in setup + // also prevents increments of nbias_running, nobias_running, + // negstrain_running, sumbiascoeff + + setupflag = 1; + pre_reverse(eflag,vflag); + setupflag = 0; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::pre_neighbor() +{ + int i,m,iold,jold,ilocal,jlocal; + // double distsq; + + // reset local indices for owned bond atoms, since atoms have migrated + // must be done after ghost atoms are setup via comm->borders() + // first time this is done for a particular I or J atom: + // use tagold and xold from when bonds were created + // atom->map() finds atom ID if it exists, owned index if possible + // closest current I or J atoms to old I may now be ghost atoms + // closest_image() returns the ghost atom index in that case + // also compute max drift of any atom in a bond + // drift = displacement from quenched coord while event has not yet occured + // NOTE: drift calc is now done in bond_build(), between 2 quenched states + + for (i = 0; i < nall_old; i++) old2now[i] = -1; + + double **x = atom->x; + + for (m = 0; m < nblocal; m++) { + iold = blist[m].iold; + jold = blist[m].jold; + ilocal = old2now[iold]; + jlocal = old2now[jold]; + + if (ilocal < 0) { + ilocal = atom->map(tagold[iold]); + ilocal = domain->closest_image(xold[iold],ilocal); + if (ilocal < 0) + error->one(FLERR,"Fix hyper/local bond atom not found"); + old2now[iold] = ilocal; + //distsq = MathExtra::distsq3(x[ilocal],xold[iold]); + //maxdriftsq = MAX(distsq,maxdriftsq); + } + if (jlocal < 0) { + jlocal = atom->map(tagold[jold]); + jlocal = domain->closest_image(xold[iold],jlocal); // close to I atom + if (jlocal < 0) + error->one(FLERR,"Fix hyper/local bond atom not found"); + old2now[jold] = jlocal; + //distsq = MathExtra::distsq3(x[jlocal],xold[jold]); + //maxdriftsq = MAX(distsq,maxdriftsq); + } + + blist[m].i = ilocal; + blist[m].j = jlocal; + } + + // set remaining old2now values to point to current local atom indices + // if old2now >= 0, already set by bond loop above + // only necessary for tagold entries > 0 + // because if tagold = 0, atom is not active in Dcut neighbor list + // must be done after atoms migrate and ghost atoms setup via comm->borders() + // does not matter which atom (owned or ghost) that atom->map() finds + // b/c old2now is only used to access maxstrain() or biasflag() + // which will be identical for every copy of the same atom ID + + for (iold = 0; iold < nall_old; iold++) { + if (old2now[iold] >= 0) continue; + if (tagold[iold] == 0) continue; + ilocal = atom->map(tagold[iold]); + old2now[iold] = ilocal; + if (ilocal < 0) ghost_toofar++; + } +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */) +{ + int i,j,m,ii,jj,inum,jnum,iold,jold,ibond,nbond,ijhalf,ncount; + double xtmp,ytmp,ztmp,delx,dely,delz; + double r,r0,estrain,emax,ebias,vbias,fbias,fbiasr; + double halfstrain,selfstrain; + int *ilist,*jlist,*numneigh,**firstneigh; + + //double time1,time2,time3,time4,time5,time6,time7,time8; + //time1 = MPI_Wtime(); + + nostrainyet = 0; + + // reallocate per-atom maxstrain and biasflag vectors if necessary + + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (maxatom < nall) { + memory->destroy(maxstrain); + memory->destroy(maxstrain_domain); + if (checkbias) memory->destroy(biasflag); + maxatom = atom->nmax; + memory->create(maxstrain,maxatom,"hyper/local:maxstrain"); + memory->create(maxstrain_domain,maxatom,"hyper/local:maxstrain_domain"); + if (checkbias) memory->create(biasflag,maxatom,"hyper/local:biasflag"); + } + + // one max strain bond per old owned atom is eligible for biasing + + for (iold = 0; iold < nlocal_old; iold++) eligible[iold] = 1; + + // ------------------------------------------------------------- + // stage 1: + // maxstrain[i] = max abs value of strain of any bond atom I is part of + // reverse/forward comm so know it for all current owned and ghost atoms + // ------------------------------------------------------------- + + // compute estrain = current abs value strain of each owned bond + // blist = bondlist from last event + // mark atom I ineligible if it has no bonds + // also store: + // maxhalf = which owned bond is maxstrain for each old atom I + // maxhalfstrain = abs value strain of that bond for each old atom I + + for (i = 0; i < nall; i++) maxstrain[i] = 0.0; + + double **x = atom->x; + + m = 0; + for (iold = 0; iold < nlocal_old; iold++) { + nbond = numbond[iold]; + if (!nbond) { + eligible[iold] = 0; + continue; + } + halfstrain = 0.0; + for (ibond = 0; ibond < nbond; ibond++) { + i = blist[m].i; + j = blist[m].j; + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + r = sqrt(delx*delx + dely*dely + delz*delz); + maxbondlen = MAX(r,maxbondlen); + r0 = blist[m].r0; + estrain = fabs(r-r0) / r0; + maxstrain[i] = MAX(maxstrain[i],estrain); + maxstrain[j] = MAX(maxstrain[j],estrain); + if (estrain > halfstrain) { + halfstrain = estrain; + ijhalf = m; + } + m++; + } + maxhalf[iold] = ijhalf; + maxhalfstrain[iold] = halfstrain; + } + + //time2 = MPI_Wtime(); + + // reverse comm acquires maxstrain of all current owned atoms + // needed b/c only saw half the bonds of each atom + // also needed b/c bond list may refer to old owned atoms that are now ghost + // forward comm acquires maxstrain of all current ghost atoms + + commflag = STRAIN; + comm->reverse_comm_fix(this); + comm->forward_comm_fix(this); + + //time3 = MPI_Wtime(); + + // ------------------------------------------------------------- + // stage 2: + // maxstrain_domain[i] = maxstrain of atom I and all its J neighs out to Dcut + // reverse/forward comm so know it for all current owned and ghost atoms + // ------------------------------------------------------------- + + // use full Dcut neighbor list to check maxstrain of all neighbor atoms + // neighlist is from last event + // has old indices for I,J (reneighboring may have occurred) + // use old2now[] to convert to current indices + // if J is unknown (drifted ghost), + // assume it was part of an event and its strain = qfactor + // mark atom I ineligible for biasing if: + // its maxhalfstrain < maxstrain (J atom owns the IJ bond) + // its maxstrain < maxstrain_domain + // ncount > 1 (break tie by making all atoms with tie value ineligible) + // if ncount > 1, also flip sign of maxstrain_domain for atom I + + for (i = 0; i < nall; i++) maxstrain_domain[i] = 0.0; + + inum = listfull->inum; + ilist = listfull->ilist; + numneigh = listfull->numneigh; + firstneigh = listfull->firstneigh; + + double rmax = rmaxever; + double rmaxbig = rmaxeverbig; + double *sublo = domain->sublo; + double *subhi = domain->subhi; + + // first two lines of outer loop should be identical to this: + // for (iold = 0; iold < nlocal_old; iold++) + + for (ii = 0; ii < inum; ii++) { + iold = ilist[ii]; + if (eligible[iold] == 0) continue; + jlist = firstneigh[iold]; + jnum = numneigh[iold]; + + // I or J may be ghost atoms + // will always know I b/c atoms do not drift that far + // but may no longer know J if hops outside cutghost + // in that case, assume it performed an event, its strain = qfactor + // this assumes cutghost is sufficiently longer than Dcut + + i = old2now[iold]; + emax = selfstrain = maxstrain[i]; + ncount = 0; + + for (jj = 0; jj < jnum; jj++) { + jold = jlist[jj]; + j = old2now[jold]; + + // special case for missing (drifted) J atom + + if (j < 0) { + emax = MAX(emax,qfactor); + if (selfstrain == qfactor) ncount++; + continue; + } + + emax = MAX(emax,maxstrain[j]); + if (selfstrain == maxstrain[j]) ncount++; + + // optional diagnostic + // tally largest distance from subbox that a ghost atom is (rmaxbig) + // and the largest distance if strain < qfactor (rmax) + + if (checkghost) { + if (j >= nlocal) { + if (x[j][0] < sublo[0]) rmaxbig = MAX(rmaxbig,sublo[0]-x[j][0]); + if (x[j][1] < sublo[1]) rmaxbig = MAX(rmaxbig,sublo[1]-x[j][1]); + if (x[j][2] < sublo[2]) rmaxbig = MAX(rmaxbig,sublo[2]-x[j][2]); + if (x[j][0] > subhi[0]) rmaxbig = MAX(rmaxbig,x[j][0]-subhi[0]); + if (x[j][1] > subhi[1]) rmaxbig = MAX(rmaxbig,x[j][1]-subhi[1]); + if (x[j][2] > subhi[2]) rmaxbig = MAX(rmaxbig,x[j][2]-subhi[2]); + if (maxstrain[j] < qfactor) { + if (x[j][0] < sublo[0]) rmax = MAX(rmax,sublo[0]-x[j][0]); + if (x[j][1] < sublo[1]) rmax = MAX(rmax,sublo[1]-x[j][1]); + if (x[j][2] < sublo[2]) rmax = MAX(rmax,sublo[2]-x[j][2]); + if (x[j][0] > subhi[0]) rmax = MAX(rmax,x[j][0]-subhi[0]); + if (x[j][1] > subhi[1]) rmax = MAX(rmax,x[j][1]-subhi[1]); + if (x[j][2] > subhi[2]) rmax = MAX(rmax,x[j][2]-subhi[2]); + } + } + } + } + + if (maxhalfstrain[iold] < selfstrain) eligible[iold] = 0; + if (selfstrain < emax) eligible[iold] = 0; + else if (ncount > 1) { + eligible[iold] = 0; + emax = -emax; + } + maxstrain_domain[i] = emax; + } + + //time4 = MPI_Wtime(); + + // reverse comm to acquire maxstrain_domain from ghost atoms + // needed b/c neigh list may refer to old owned atoms that are now ghost + // forward comm acquires maxstrain_domain of all current ghost atoms + + commflag = STRAINDOMAIN; + comm->reverse_comm_fix(this); + comm->forward_comm_fix(this); + + //time5 = MPI_Wtime(); + + // ------------------------------------------------------------- + // stage 3: + // create bias = list of Nbias biased bonds this proc owns + // ------------------------------------------------------------- + + // identify biased bonds and add to bias list + // bias the I,J maxhalf bond of atom I only if all these conditions hold: + // maxstrain[i] = maxstrain_domain[i] (checked in stage 2) + // maxstrain[j] = maxstrain_domain[j] (checked here) + // I is not part of an I,J bond with > strain owned by some J (checked in 2) + // no ties with other maxstrain bonds in atom I's domain (chedcked in 2) + + nbias = 0; + for (iold = 0; iold < nlocal_old; iold++) { + if (eligible[iold] == 0) continue; + j = blist[maxhalf[iold]].j; + if (maxstrain[j] != maxstrain_domain[j]) continue; + if (nbias == maxbias) { + maxbias += DELTABIAS; + memory->grow(bias,maxbias,"hyper/local:bias"); + } + bias[nbias++] = maxhalf[iold]; + } + + //time6 = MPI_Wtime(); + + // ------------------------------------------------------------- + // stage 4: + // apply bias force to bonds with locally max strain + // ------------------------------------------------------------- + + double **f = atom->f; + + int nobias = 0; + int negstrain = 0; + mybias = 0.0; + + for (int ibias = 0; ibias < nbias; ibias++) { + m = bias[ibias]; + i = blist[m].i; + j = blist[m].j; + + if (maxstrain[i] >= qfactor) { + nobias++; + continue; + } + + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + r = sqrt(delx*delx + dely*dely + delz*delz); + r0 = blist[m].r0; + ebias = (r-r0) / r0; + vbias = biascoeff[m] * vmax * (1.0 - ebias*ebias*invqfactorsq); + fbias = biascoeff[m] * 2.0 * vmax * ebias * invqfactorsq; + + fbiasr = fbias / r0 / r; + f[i][0] += delx*fbiasr; + f[i][1] += dely*fbiasr; + f[i][2] += delz*fbiasr; + + f[j][0] -= delx*fbiasr; + f[j][1] -= dely*fbiasr; + f[j][2] -= delz*fbiasr; + + if (ebias < 0.0) negstrain++; + mybias += vbias; + } + + //time7 = MPI_Wtime(); + + // ------------------------------------------------------------- + // apply boostostat to bias coeffs of all bonds I own + // ------------------------------------------------------------- + + // no boostostat update when pre_reverse called from setup() + // nbias_running, nobias_running, negstrain_running only incremented + // on run steps + + if (setupflag) return; + nbias_running += nbias; + nobias_running += nobias; + negstrain_running += negstrain; + + // loop over bonds I own to adjust bias coeff + // delta in boost coeff is function of maxboost_domain vs target boost + // maxboost_domain is function of two maxstrain_domains for I,J + + double emaxi,emaxj,maxboost_domain,bc; + double mybiascoeff = 0.0; + + for (m = 0; m < nblocal; m++) { + i = blist[m].i; + j = blist[m].j; + emaxi = maxstrain_domain[i]; + emaxj = maxstrain_domain[j]; + emax = MAX(emaxi,emaxj); + if (emax < qfactor) vbias = vmax * (1.0 - emax*emax*invqfactorsq); + else vbias = 0.0; + + maxboost_domain = exp(beta * biascoeff[m]*vbias); + biascoeff[m] -= alpha * (maxboost_domain-boost_target) / boost_target; + + // stats + + bc = biascoeff[m]; + mybiascoeff += bc; + minbiascoeff = MIN(minbiascoeff,bc); + maxbiascoeff = MAX(maxbiascoeff,bc); + } + + // ------------------------------------------------------------- + // diagnostics, some optional + // ------------------------------------------------------------- + + MPI_Allreduce(&mybiascoeff,&sumbiascoeff,1,MPI_DOUBLE,MPI_SUM,world); + if (allbonds) avebiascoeff += sumbiascoeff/allbonds; + + // if requested, monitor ghost distance from processor sub-boxes + + if (checkghost) { + double rmax2[2],rmax2all[2]; + rmax2[0] = rmax; + rmax2[1] = rmaxbig; + MPI_Allreduce(&rmax2,&rmax2all,2,MPI_DOUBLE,MPI_MAX,world); + rmaxever = rmax2all[0]; + rmaxeverbig = rmax2all[1]; + } + + // if requsted, check for any biased bonds that are too close to each other + // keep a running count for output + // requires 2 additional local comm operations + + if (checkbias && update->ntimestep % checkbias_every == 0) { + + // mark each atom in a biased bond with ID of partner + // this may mark some ghost atoms + + for (i = 0; i < nall; i++) biasflag[i] = 0; + + tagint *tag = atom->tag; + + for (int ibias = 0; ibias < nbias; ibias++) { + m = bias[ibias]; + i = blist[m].i; + j = blist[m].j; + biasflag[i] = tag[j]; + biasflag[j] = tag[i]; + } + + // reverse comm to acquire biasflag from ghost atoms + // forward comm to set biasflag for all ghost atoms + + commflag = BIASFLAG; + comm->reverse_comm_fix(this); + comm->forward_comm_fix(this); + + // loop over Dcut full neighbor list + // I and J may be ghost atoms + // only continue if I is a biased atom + // if J is unknown (drifted ghost) just ignore + // if J is biased and is not bonded to I, then flag as too close + + for (ii = 0; ii < inum; ii++) { + iold = ilist[ii]; + i = old2now[iold]; + if (biasflag[i] == 0) continue; + + jlist = firstneigh[iold]; + jnum = numneigh[iold]; + + for (jj = 0; jj < jnum; jj++) { + jold = jlist[jj]; + j = old2now[jold]; + if (j < 0) continue; + if (biasflag[j] && biasflag[j] != tag[i]) checkbias_count++; + } + } + + if (checkbias_flag != IGNORE) { + int allcount; + MPI_Allreduce(&checkbias_count,&allcount,1,MPI_INT,MPI_SUM,world); + if (allcount) { + char str[128]; + sprintf(str,"Fix hyper/local biased bonds too close: " + "cumulative atom count %d",allcount); + if (checkbias_flag == WARN) { + if (me == 0) error->warning(FLERR,str); + } else error->all(FLERR,str); + } + } + } +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::min_pre_neighbor() +{ + pre_neighbor(); +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::build_bond_list(int natom) +{ + int i,j,ii,jj,m,n,iold,jold,ilocal,jlocal,inum,jnum,nbond; + tagint itag,jtag; + double xtmp,ytmp,ztmp,delx,dely,delz,rsq,distsq,oldcoeff; + int *ilist,*jlist,*numneigh,**firstneigh; + + double time1,time2; + time1 = MPI_Wtime(); + + if (natom) { + nevent++; + nevent_atom += natom; + } + + // compute max distance any bond atom has moved between 2 quenched states + // xold[iold] = last quenched coord for iold + // x[ilocal] = current quenched coord for same atom + // use of old2now calculates distsq only once per atom + + double **x = atom->x; + + for (i = 0; i < nall_old; i++) old2now[i] = -1; + + for (m = 0; m < nblocal; m++) { + iold = blist[m].iold; + if (old2now[iold] < 0) { + ilocal = atom->map(tagold[iold]); + ilocal = domain->closest_image(xold[iold],ilocal); + if (ilocal < 0) error->one(FLERR,"Fix hyper/local bond atom not found"); + old2now[iold] = ilocal; + distsq = MathExtra::distsq3(x[ilocal],xold[iold]); + maxdriftsq = MAX(distsq,maxdriftsq); + } + jold = blist[m].jold; + if (old2now[jold] < 0) { + jold = blist[m].jold; + jlocal = atom->map(tagold[jold]); + jlocal = domain->closest_image(xold[iold],jlocal); // close to I atom + if (jlocal < 0) error->one(FLERR,"Fix hyper/local bond atom not found"); + old2now[jold] = jlocal; + distsq = MathExtra::distsq3(x[jlocal],xold[jold]); + maxdriftsq = MAX(distsq,maxdriftsq); + } + } + + // store old bond coeffs so can persist them in new blist + // while loop allows growing value of maxbondperatom + // will loop at most 2 times, stops when maxbondperatom is large enough + // requires reverse comm, no forward comm: + // b/c new coeff list is stored only by current owned atoms + + tagint *tag = atom->tag; + int nlocal = atom->nlocal; + int nall = nlocal + atom->nghost; + + if (maxcoeff < nall) { + memory->destroy(numcoeff); + memory->sfree(clist); + maxcoeff = atom->nmax; + memory->create(numcoeff,maxcoeff,"hyper/local:numcoeff"); + clist = (OneCoeff **) memory->smalloc(maxcoeff*sizeof(OneCoeff *), + "hyper/local:clist"); + } + + while (1) { + if (firstflag) break; + for (i = 0; i < nall; i++) numcoeff[i] = 0; + for (i = 0; i < nall; i++) clist[i] = NULL; + cpage->reset(); + + for (m = 0; m < nblocal; m++) { + i = blist[m].i; + j = blist[m].j; + + if (numcoeff[i] == 0) clist[i] = cpage->get(maxbondperatom); + if (numcoeff[j] == 0) clist[j] = cpage->get(maxbondperatom); + + if (numcoeff[i] < maxbondperatom) { + clist[i][numcoeff[i]].biascoeff = biascoeff[m]; + clist[i][numcoeff[i]].tag = tag[j]; + } + numcoeff[i]++; + + if (numcoeff[j] < maxbondperatom) { + clist[j][numcoeff[j]].biascoeff = biascoeff[m]; + clist[j][numcoeff[j]].tag = tag[i]; + } + numcoeff[j]++; + } + + int mymax = 0; + for (i = 0; i < nall; i++) mymax = MAX(mymax,numcoeff[i]); + int maxcoeffall; + MPI_Allreduce(&mymax,&maxcoeffall,1,MPI_INT,MPI_MAX,world); + + if (maxcoeffall > maxbondperatom) { + maxbondperatom = maxcoeffall; + cpage->init(maxbondperatom,1024*maxbondperatom,1); + continue; + } + + commflag = BIASCOEFF; + comm->reverse_comm_fix_variable(this); + + mymax = 0; + for (i = 0; i < nall; i++) mymax = MAX(mymax,numcoeff[i]); + MPI_Allreduce(&mymax,&maxcoeffall,1,MPI_INT,MPI_MAX,world); + if (maxcoeffall <= maxbondperatom) break; + + maxbondperatom = maxcoeffall; + cpage->init(maxbondperatom,1024*maxbondperatom,1); + } + + // reallocate vectors that are maxlocal and maxall length if necessary + + if (nlocal > maxlocal) { + memory->destroy(eligible); + memory->destroy(numbond); + memory->destroy(maxhalf); + memory->destroy(maxhalfstrain); + maxlocal = nlocal; + memory->create(eligible,maxlocal,"hyper/local:eligible"); + memory->create(numbond,maxlocal,"hyper/local:numbond"); + memory->create(maxhalf,maxlocal,"hyper/local:maxhalf"); + memory->create(maxhalfstrain,maxlocal,"hyper/local:maxhalfstrain"); + } + + if (nall > maxall) { + memory->destroy(xold); + memory->destroy(tagold); + memory->destroy(old2now); + maxall = atom->nmax; + memory->create(xold,maxall,3,"hyper/local:xold"); + memory->create(tagold,maxall,"hyper/local:tagold"); + memory->create(old2now,maxall,"hyper/local:old2now"); + } + + // nlocal_old = value of nlocal at time bonds are built + // nall_old = value of nall at time bonds are built + // archive current atom coords in xold + // tagold will be set to non-zero below for accessed atoms + // numbond will be set below + + nlocal_old = nlocal; + nall_old = nall; + + memcpy(&xold[0][0],&x[0][0],3*nall*sizeof(double)); + for (i = 0; i < nall; i++) tagold[i] = 0; + for (i = 0; i < nlocal; i++) numbond[i] = 0; + + // trigger neighbor list builds for both lists + // insure the I loops in both are from 1 to nlocal + + neighbor->build_one(listfull); + neighbor->build_one(listhalf); + + if (listfull->inum != nlocal || listhalf->inum != nlocal) + error->one(FLERR,"Invalid neighbor list in fix hyper/local bond build"); + + // set tagold = 1 for all J atoms used in full neighbor list + // tagold remains 0 for unused atoms, skipped in pre_neighbor + + inum = listfull->inum; + ilist = listfull->ilist; + numneigh = listfull->numneigh; + firstneigh = listfull->firstneigh; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + tagold[i] = tag[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + tagold[j] = tag[j]; + } + } + + // identify bonds assigned to each owned atom + // do not create a bond between two non-group atoms + + int *mask = atom->mask; + + inum = listhalf->inum; + ilist = listhalf->ilist; + numneigh = listhalf->numneigh; + firstneigh = listhalf->firstneigh; + + nblocal = 0; + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + + itag = tag[i]; + tagold[i] = tag[i]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + nbond = 0; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + jtag = tag[j]; + tagold[j] = jtag; + + // skip if neither atom I or J are in fix group + + if (!(mask[i] & groupbit) && !(mask[j] & groupbit)) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq < cutbondsq) { + nbond++; + + if (nblocal == maxbond) grow_bond(); + blist[nblocal].i = i; + blist[nblocal].j = j; + blist[nblocal].iold = i; + blist[nblocal].jold = j; + blist[nblocal].r0 = sqrt(rsq); + + // set biascoeff to old coeff for same I,J pair or to default + + if (firstflag) oldcoeff = 0.0; + else { + oldcoeff = 0.0; + jtag = tag[j]; + n = numcoeff[i]; + for (m = 0; m < n; m++) { + if (clist[i][m].tag == jtag) { + oldcoeff = clist[i][m].biascoeff; + break; + } + } + } + + if (oldcoeff > 0.0) biascoeff[nblocal] = oldcoeff; + else { + biascoeff[nblocal] = COEFFINIT; + nnewbond++; + } + + nblocal++; + } + } + + numbond[i] = nbond; + } + + // this fix allows access to biascoeffs as local data + + size_local_rows = nblocal; + + // allbonds = total # of bonds in system + + bigint bondcount = nblocal; + MPI_Allreduce(&bondcount,&allbonds,1,MPI_LMP_BIGINT,MPI_SUM,world); + + time2 = MPI_Wtime(); + + if (firstflag) nnewbond = 0; + else { + time_bondbuild += time2-time1; + nbondbuild++; + } + firstflag = 0; +} + +/* ---------------------------------------------------------------------- */ + +int FixHyperLocal::pack_forward_comm(int n, int *list, double *buf, + int /* pbc_flag */, int * /* pbc */) +{ + int i,j,m; + + m = 0; + + // STRAIN + // pack maxstrain vector + // must send to all ghosts out to Dcut + + if (commflag == STRAIN) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = maxstrain[j]; + } + + // STRAINDOMAIN + // pack maxstrain_domain vector + // could just send to nearby ghosts in bonds + // don't see easy way to determine precisely which atoms that is + + } else if (commflag == STRAINDOMAIN) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = maxstrain_domain[j]; + } + + // BIASFLAG + // pack biasflag vector + // must send to all ghosts out to Dcut + + } else if (commflag == BIASFLAG) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = ubuf(biasflag[j]).d; + } + } + + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::unpack_forward_comm(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + // STRAIN + // unpack maxstrain vector + + if (commflag == STRAIN) { + for (i = first; i < last; i++) { + maxstrain[i] = buf[m++]; + } + + // STRAINREGION + // unpack maxstrain_domain vector + + } else if (commflag == STRAINDOMAIN) { + for (i = first; i < last; i++) { + maxstrain_domain[i] = buf[m++]; + } + + // BIASFLAG + // unpack biasflag vector + + } else if (commflag == BIASFLAG) { + for (i = first; i < last; i++) { + biasflag[i] = (tagint) ubuf(buf[m++]).i; + } + } +} + +/* ---------------------------------------------------------------------- */ + +int FixHyperLocal::pack_reverse_comm(int n, int first, double *buf) +{ + int i,j,m,last; + + m = 0; + last = first + n; + + // STRAIN + // pack maxstrain vector + // only pack for nonzero values + + if (commflag == STRAIN) { + int nonzero = 0; + m++; // placeholder for count of atoms + for (i = first; i < last; i++) { + if (maxstrain[i] == 0.0) continue; + nonzero++; + buf[m++] = ubuf(i-first).d; // which atom is next + buf[m++] = maxstrain[i]; // value + } + buf[0] = ubuf(nonzero).d; + + // STRAINDOMAIN + // pack maxstrain_domain vector + // only pack for nonzero values + + } else if (commflag == STRAINDOMAIN) { + int nonzero = 0; + m++; // placeholder for count of atoms + for (i = first; i < last; i++) { + if (maxstrain_domain[i] == 0.0) continue; + nonzero++; + buf[m++] = ubuf(i-first).d; // which atom is next + buf[m++] = maxstrain_domain[i]; // value + } + buf[0] = ubuf(nonzero).d; + + // BIASFLAG + // pack biasflag vector + // could just pack for nonzero values, like STRAIN and STRAINDOMAIN + + } else if (commflag == BIASFLAG) { + for (i = first; i < last; i++) { + buf[m++] = ubuf(biasflag[i]).d; + } + + // BIASCOEFF + // pack list of biascoeffs + // only pack for atoms with nonzero # of bias coeffs + // this will skip majority of ghost atoms + + } else if (commflag == BIASCOEFF) { + int ncoeff; + int nonzero = 0; + m++; // placeholder for count of atoms + for (i = first; i < last; i++) { + if (numcoeff[i] == 0) continue; + nonzero++; + ncoeff = numcoeff[i]; + buf[m++] = ubuf(i-first).d; // which atom is next + buf[m++] = ubuf(ncoeff).d; // # of bias coeffs + for (j = 0; j < ncoeff; j++) { + buf[m++] = clist[i][j].biascoeff; + buf[m++] = ubuf(clist[i][j].tag).d; + } + } + buf[0] = ubuf(nonzero).d; + } + + return m; +} + +/* ---------------------------------------------------------------------- + callback by comm->reverse_comm_fix_variable() in build_bond() + same logic as BIASCOEFF option in pack_reverse_comm() + m = returned size of message +------------------------------------------------------------------------- */ + +int FixHyperLocal::pack_reverse_comm_size(int n, int first) +{ + int last = first + n; + int m = 1; + for (int i = first; i < last; i++) { + if (numcoeff[i]) m += 2 + 2*numcoeff[i]; + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +void FixHyperLocal::unpack_reverse_comm(int n, int *list, double *buf) +{ + int i,j,k,m; + + // return if n = 0 + // b/c if there are no atoms (n = 0), the message will not have + // been sent by Comm::reverse_comm_fix() or reverse_comm_fix_variable() + // so must not read nonzero from first buf location (would be zero anyway) + + if (n == 0) return; + + // STRAIN + // unpack maxstrain vector + // nonzero # of entries, each has offset to which atom in receiver's list + // use MAX, b/c want maximum abs value strain for each atom's bonds + + m = 0; + + if (commflag == STRAIN) { + int offset; + int nonzero = (int) ubuf(buf[m++]).i; // # of atoms with values + + for (int iatom = 0; iatom < nonzero; iatom++) { + offset = (int) ubuf(buf[m++]).i; // offset into list for which atom + j = list[offset]; + maxstrain[j] = MAX(maxstrain[j],buf[m]); + m++; + } + + // STRAINDOMAIN + // unpack maxstrain_domain vector + // use MAX, b/c want maximum abs value strain for each atom's domain + // could also use SUM, b/c exactly one ghost or owned value is non-zero + + } else if (commflag == STRAINDOMAIN) { + int offset; + int nonzero = (int) ubuf(buf[m++]).i; // # of atoms with values + for (int iatom = 0; iatom < nonzero; iatom++) { + offset = (int) ubuf(buf[m++]).i; // offset into list for which atom + j = list[offset]; + maxstrain_domain[j] = MAX(maxstrain_domain[j],buf[m]); + m++; + } + + // BIASFLAG + // unpack biasflag vector + + } else if (commflag == BIASFLAG) { + for (i = 0; i < n; i++) { + j = list[i]; + biasflag[j] = (tagint) ubuf(buf[m++]).i; + } + + // BIASCOEFF + // unpack list of biascoeffs + // nonzero # of entries, each has offset to which atom in receiver's list + // protect against overflow of clist vector + // if that happens, caller will re-setup cpage and reverse comm again + + } else if (commflag == BIASCOEFF) { + int offset,ncoeff; + int nonzero = (int) ubuf(buf[m++]).i; // # of atoms with coeffs + for (int iatom = 0; iatom < nonzero; iatom++) { + offset = (int) ubuf(buf[m++]).i; // offset into list for which atom + j = list[offset]; + ncoeff = (int) ubuf(buf[m++]).i; // # of bias coeffs + for (k = 0; k < ncoeff; k++) { + if (numcoeff[j] == 0) clist[j] = cpage->get(maxbondperatom); + if (numcoeff[j] < maxbondperatom) { + clist[j][numcoeff[j]].biascoeff = buf[m++]; + clist[j][numcoeff[j]].tag = (tagint) ubuf(buf[m++]).i; + } else m += 2; + numcoeff[j]++; + } + } + } +} + +/* ---------------------------------------------------------------------- + grow bond list and bias coeff vector by a chunk +------------------------------------------------------------------------- */ + +void FixHyperLocal::grow_bond() +{ + if (maxbond + DELTABOND > MAXSMALLINT) + error->one(FLERR,"Fix hyper/local bond count is too big"); + maxbond += DELTABOND; + blist = (OneBond *) + memory->srealloc(blist,maxbond*sizeof(OneBond),"hyper/local:blist"); + memory->grow(biascoeff,maxbond,"hyper/local:biascoeff"); + vector_local = biascoeff; +} + +/* ---------------------------------------------------------------------- */ + +double FixHyperLocal::compute_scalar() +{ + double allbias; + MPI_Allreduce(&mybias,&allbias,1,MPI_DOUBLE,MPI_SUM,world); + return allbias; +} + +/* ---------------------------------------------------------------------- */ + +double FixHyperLocal::compute_vector(int i) +{ + // 21 vector outputs returned for i = 0-20 + + // i = 0 = # of biased bonds on this step + // i = 1 = max strain of any bond on this step + // i = 2 = average bias coeff for all bonds on this step + // i = 3 = ave bonds/atom on this step + // i = 4 = ave neighbor bonds/bond on this step + + // i = 5 = max bond length during this run + // i = 6 = average # of biased bonds/step during this run + // i = 7 = fraction of biased bonds with no bias during this run + // i = 8 = fraction of biased bonds with negative strain during this run + // i = 9 = average bias coeff for all bonds during this run + // i = 10 = min bias coeff for any bond during this run + // i = 11 = max bias coeff for any bond during this run + + // i = 12 = max drift distance of any atom during this run + // i = 13 = max distance from proc subbox of any ghost atom with + // maxstrain < qfactor during this run + // i = 14 = max distance from proc subbox of any ghost atom with + // any maxstrain during this run + // i = 15 = count of ghost atoms that could not be found + // on reneighbor steps during this run + // i = 16 = count of bias overlaps (< Dcut) found during this run + + // i = 17 = cumulative hyper time since fix created + // i = 18 = cumulative # of event timesteps since fix created + // i = 19 = cumulative # of atoms in events since fix created + // i = 20 = cumulative # of new bonds formed since fix created + + if (i == 0) { + int nbiasall; + MPI_Allreduce(&nbias,&nbiasall,1,MPI_INT,MPI_SUM,world); + return (double) nbiasall; + } + + if (i == 1) { + if (nostrainyet) return 0.0; + int nlocal = atom->nlocal; + double emax = 0.0; + for (int j = 0; j < nlocal; j++) + emax = MAX(emax,maxstrain[j]); + double eall; + MPI_Allreduce(&emax,&eall,1,MPI_DOUBLE,MPI_MAX,world); + return eall; + } + + if (i == 2) { + if (allbonds) return sumbiascoeff/allbonds; + return 1.0; + } + + if (i == 3) { + return 2.0*allbonds/atom->natoms; + } + + if (i == 4) { + const int nlocal = atom->nlocal; + bigint allneigh,thisneigh; + thisneigh = listfull->ipage->ndatum; + MPI_Allreduce(&thisneigh,&allneigh,1,MPI_LMP_BIGINT,MPI_SUM,world); + const double natoms = atom->natoms; + const double neighsperatom = static_cast(allneigh)/natoms; + const double bondsperatom = static_cast(allbonds)/natoms; + return neighsperatom * bondsperatom; + } + + if (i == 5) { + double allbondlen; + MPI_Allreduce(&maxbondlen,&allbondlen,1,MPI_DOUBLE,MPI_MAX,world); + return allbondlen; + } + + if (i == 6) { + if (update->ntimestep == update->firststep) return 0.0; + int allbias_running; + MPI_Allreduce(&nbias_running,&allbias_running,1,MPI_INT,MPI_SUM,world); + return 1.0*allbias_running / (update->ntimestep - update->firststep); + } + + if (i == 7) { + int allbias_running,allnobias_running; + MPI_Allreduce(&nbias_running,&allbias_running,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&nobias_running,&allnobias_running,1,MPI_INT,MPI_SUM,world); + if (allbias_running) return 1.0*allnobias_running / allbias_running; + return 0.0; + } + + if (i == 8) { + int allbias_running,allnegstrain_running; + MPI_Allreduce(&nbias_running,&allbias_running,1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(&negstrain_running,&allnegstrain_running,1,MPI_INT, + MPI_SUM,world); + if (allbias_running) return 1.0*allnegstrain_running / allbias_running; + return 0.0; + } + + if (i == 9) { + if (update->ntimestep == update->firststep) return 0.0; + return avebiascoeff / (update->ntimestep - update->firststep); + } + + if (i == 10) { + double biascoeff; + MPI_Allreduce(&minbiascoeff,&biascoeff,1,MPI_DOUBLE,MPI_MIN,world); + return biascoeff; + } + + if (i == 11) { + double biascoeff; + MPI_Allreduce(&maxbiascoeff,&biascoeff,1,MPI_DOUBLE,MPI_MAX,world); + return biascoeff; + } + + if (i == 12) { + double alldriftsq; + MPI_Allreduce(&maxdriftsq,&alldriftsq,1,MPI_DOUBLE,MPI_MAX,world); + return (double) sqrt(alldriftsq); + } + + if (i == 13) return rmaxever; + if (i == 14) return rmaxeverbig; + + if (i == 15) { + int allghost_toofar; + MPI_Allreduce(&ghost_toofar,&allghost_toofar,1,MPI_INT,MPI_SUM,world); + return 1.0*allghost_toofar; + } + + if (i == 16) { + int allclose; + MPI_Allreduce(&checkbias_count,&allclose,1,MPI_INT,MPI_SUM,world); + return 1.0*allclose; + } + + if (i == 17) { + return boost_target * update->dt * (update->ntimestep - starttime); + } + + if (i == 18) return (double) nevent; + if (i == 19) return (double) nevent_atom; + + if (i == 20) { + int allnewbond; + MPI_Allreduce(&nnewbond,&allnewbond,1,MPI_INT,MPI_SUM,world); + return (double) allnewbond; + } + + return 0.0; +} + +/* ---------------------------------------------------------------------- + wrapper on compute_vector() + used by hyper.cpp to call FixHyper +------------------------------------------------------------------------- */ + +double FixHyperLocal::query(int i) +{ + if (i == 1) return compute_vector(17); // cummulative hyper time + if (i == 2) return compute_vector(18); // nevent + if (i == 3) return compute_vector(19); // nevent_atom + if (i == 4) return compute_vector(3); // ave bonds/atom + if (i == 5) return compute_vector(12); // maxdrift + if (i == 6) return compute_vector(5); // maxbondlen + if (i == 7) return compute_vector(7); // fraction with zero bias + if (i == 8) return compute_vector(8); // fraction with negative strain + + // unique to local hyper + + if (i == 9) return compute_vector(20); // number of new bonds + if (i == 10) return 1.0*maxbondperatom; // max bonds/atom + if (i == 11) return compute_vector(6); // ave # of biased bonds/step + if (i == 12) return compute_vector(9); // ave bias coeff over all bonds + if (i == 13) return compute_vector(10); // min bias cooef for any bond + if (i == 14) return compute_vector(11); // max bias cooef for any bond + if (i == 15) return compute_vector(4); // neighbor bonds/bond + if (i == 16) return compute_vector(2); // ave bias coeff now + if (i == 17) return time_bondbuild; // CPU time for build_bond calls + if (i == 18) return rmaxever; // ghost atom distance for < maxstrain + if (i == 19) return rmaxeverbig; // ghost atom distance for any strain + if (i == 20) return compute_vector(15); // count of ghost atoms not found + if (i == 21) return compute_vector(16); // count of bias overlaps + + error->all(FLERR,"Invalid query to fix hyper/local"); + + return 0.0; +} + +/* ---------------------------------------------------------------------- + memory usage of per-atom and per-bond data structs +------------------------------------------------------------------------- */ + +double FixHyperLocal::memory_usage() +{ + double bytes = maxbond * sizeof(OneBond); // blist + bytes = maxbond * sizeof(double); // per-bond bias coeffs + bytes += 3*maxlocal * sizeof(int); // numbond,maxhalf,eligible + bytes += maxlocal * sizeof(double); // maxhalfstrain + bytes += maxall * sizeof(int); // old2now + bytes += maxall * sizeof(tagint); // tagold + bytes += 3*maxall * sizeof(double); // xold + bytes += 2*maxall * sizeof(double); // maxstrain,maxstrain_domain + if (checkbias) bytes += maxall * sizeof(tagint); // biasflag + bytes += maxcoeff * sizeof(int); // numcoeff + bytes += maxcoeff * sizeof(OneCoeff *); // clist + bytes += maxlocal*maxbondperatom * sizeof(OneCoeff); // cpage estimate + return bytes; +} diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h new file mode 100644 index 0000000000..6f13acb606 --- /dev/null +++ b/src/REPLICA/fix_hyper_local.h @@ -0,0 +1,201 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(hyper/local,FixHyperLocal) + +#else + +#ifndef LMP_FIX_HYPER_LOCAL_H +#define LMP_FIX_HYPER_LOCAL_H + +#include "fix_hyper.h" +#include "my_page.h" + +namespace LAMMPS_NS { + +class FixHyperLocal : public FixHyper { + public: + FixHyperLocal(class LAMMPS *, int, char **); + ~FixHyperLocal(); + int setmask(); + void init(); + void init_list(int, class NeighList *); + void setup_pre_neighbor(); + void setup_pre_reverse(int, int); + void pre_neighbor(); + void pre_reverse(int, int); + void min_pre_neighbor(); + double compute_scalar(); + double compute_vector(int); + double query(int); + + int pack_forward_comm(int, int *, double *, int, int *); + void unpack_forward_comm(int, int, double *); + int pack_reverse_comm(int, int, double *); + int pack_reverse_comm_size(int, int); + void unpack_reverse_comm(int, int *, double *); + + double memory_usage(); + + // extra methods visible to callers + + void init_hyper(); + void build_bond_list(int); + + private: + int me; + + // inputs and derived quantities + + double cutbond,qfactor,vmax,tequil,dcut; + double alpha_user; // timescale to apply boostostat (time units) + double alpha; // unitless dt/alpha_user + double boost_target; // target value of boost + int checkghost,checkbias; // flags for optional stats + + double cutbondsq,dcutsq; + double beta,invqfactorsq; + + // flags + + int setupflag; // 1 during setup, 0 during run + int firstflag; // set for first time bond_build takes place + int nostrainyet; // 1 until maxstrain is first compute + bigint starttime; // timestep when this fix was invoked + int commflag; // flag for communication mode + + // stats + + int nbondbuild; // # of rebuilds of bond list + double time_bondbuild; // CPU time for bond builds + + bigint allbonds; // current total # of bonds + int nnewbond; // running tally of # of new bonds created + int maxbondperatom; // max # of bonds any atom ever has + int nevent; // # of events that trigger bond rebuild + int nevent_atom; // # of atoms that experienced an event + + int nbias_running; // running count of biased bonds + int nobias_running; // ditto for bonds with bias = 0, b/c too long + int negstrain_running; // ditto for bonds with negative strain + + double mybias; // sum of bias potentials for biased bonds + double maxbondlen; // cummulative max length of any bond + double maxdriftsq; // max distance any bond atom drifts from quenched x + + double sumbiascoeff; // sum of all bond bias coeffs at each timestep + double avebiascoeff; // cummulative sumbiascoeff/allbonds across steps + double minbiascoeff; // cummulative min bias coeff for any bond + double maxbiascoeff; // cummulative max bias coeff for any bond + + double rmaxever,rmaxeverbig; + int ghost_toofar; // # of ghost atoms not found in Dcut neigh list + + int checkbias_every,checkbias_flag,checkbias_count; + + // 2 neighbor lists + + class NeighList *listfull; // full neigh list up to Dcut distance + class NeighList *listhalf; // half neigh list up to pair distance + // both created only when bonds are rebuilt + + // list of my owned bonds and bias coeffs + // persists on a proc from one event until the next + + struct OneBond { // single IJ bond, atom I is owner + int i,j; // current local indices of 2 bond atoms + int iold,jold; // local indices when bonds were formed + double r0; // relaxed bond length + }; + + OneBond *blist; // list of owned bonds + double *biascoeff; // biasing coefficient Cij for each bond + int nblocal; // # of owned bonds + int maxbond; // allocated size of blist + + // old data from last timestep bonds were formed + // persists on a proc from one event until the next + // first set of vectors are maxlocal in length + // second set of vectors are maxall in length + + int nlocal_old; // nlocal for old atoms + int nall_old; // nlocal+nghost for old atoms + int maxlocal; // allocated size of old local atom vecs + int maxall; // allocated size of old all atom vecs + + int *numbond; // # of bonds owned by old owned atoms + int *maxhalf; // bond index for maxstrain bond of old atoms + int *eligible; // 0/1 flag for bias on one of old atom's bonds + double *maxhalfstrain; // strain value for maxstrain bond of old atoms + + int *old2now; // o2n[i] = current local index of old atom I + // may be -1 if ghost atom has drifted + tagint *tagold; // IDs of atoms when bonds were formed + // 0 if a ghost atom is not in Dcut neigh list + double **xold; // coords of atoms when bonds were formed + + // vectors used to find maxstrain bonds within a local domain + + int maxatom; // size of these vectors, nlocal + nghost + + double *maxstrain; // max-strain of any bond atom I is part of + // for owned and ghost atoms + double *maxstrain_domain; // max-strain of any neighbor atom J of atom I + // for owned and ghost atoms + tagint *biasflag; // atoms in biased bonds marked with bond partner + // for owned and ghost atoms + + // list of biased bonds this proc owns + + int maxbias; // allocated size of bias list + int nbias; // # of biased bonds I own + int *bias; // index of biased bonds in my bond list + + // data structs for persisting bias coeffs when bond list is reformed + + struct OneCoeff { + double biascoeff; + tagint tag; + }; + + MyPage *cpage; // pages of OneCoeff datums for clist + OneCoeff **clist; // ptrs to vectors of bias coeffs for each atom + int *numcoeff; // # of bias coeffs per atom (one per bond) + int maxcoeff; // allocate sized of clist and numcoeff + + // extra timers + + //double timefirst,timesecond,timethird,timefourth; + //double timefifth,timesixth,timeseventh,timetotal; + + // private methods + + void grow_bond(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +*/ diff --git a/src/REPLICA/fix_neb.cpp b/src/REPLICA/fix_neb.cpp index dc86c70956..e1b1e46a53 100644 --- a/src/REPLICA/fix_neb.cpp +++ b/src/REPLICA/fix_neb.cpp @@ -302,7 +302,7 @@ void FixNEB::min_post_force(int /*vflag*/) int procFirst; procFirst=universe->root_proc[0]; MPI_Bcast(&vIni,1,MPI_DOUBLE,procFirst,uworld); - }else { + } else { if (me == 0) MPI_Bcast(&vIni,1,MPI_DOUBLE,0,rootworld); diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp new file mode 100644 index 0000000000..5d820b2e27 --- /dev/null +++ b/src/REPLICA/hyper.cpp @@ -0,0 +1,494 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "hyper.h" +#include "update.h" +#include "atom.h" +#include "domain.h" +#include "region.h" +#include "integrate.h" +#include "min.h" +#include "force.h" +#include "neighbor.h" +#include "modify.h" +#include "compute_event_displace.h" +#include "fix_hyper.h" +#include "fix_event_hyper.h" +#include "output.h" +#include "dump.h" +#include "finish.h" +#include "timer.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +enum{NOHYPER,GLOBAL,LOCAL}; + +/* ---------------------------------------------------------------------- */ + +Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp), dumplist(NULL) {} + +/* ---------------------------------------------------------------------- + perform hyperdynamics simulation +------------------------------------------------------------------------- */ + +void Hyper::command(int narg, char **arg) +{ + MPI_Comm_rank(world,&me); + MPI_Comm_size(world,&nprocs); + + // error checks + + if (domain->box_exist == 0) + error->all(FLERR,"Hyper command before simulation box is defined"); + + if (narg < 4) error->all(FLERR,"Illegal hyper command"); + + int nsteps = force->inumeric(FLERR,arg[0]); + t_event = force->inumeric(FLERR,arg[1]); + + char *id_fix = new char[strlen(arg[2])+1]; + strcpy(id_fix,arg[2]); + + char *id_compute = new char[strlen(arg[3])+1]; + strcpy(id_compute,arg[3]); + + options(narg-4,&arg[4]); + + // total # of timesteps must be multiple of t_event + + if (t_event <= 0) + error->all(FLERR,"Invalid t_event in hyper command"); + if (nsteps % t_event) + error->all(FLERR,"Hyper nsteps must be multiple of t_event"); + if (rebond < 0) + error->all(FLERR,"Invalid rebond in hyper command"); + if (rebond && rebond % t_event) + error->all(FLERR,"Hyper rebond must be multiple of t_event"); + + // FixHyper class performs global or local hyperdynamics + + int hyperenable,hyperstyle; + + if (strcmp(id_fix,"NULL") == 0) { + hyperenable = 0; + hyperstyle = NOHYPER; + } else { + int ifix = modify->find_fix(id_fix); + if (ifix < 0) error->all(FLERR,"Could not find fix ID for hyper"); + fix_hyper = (FixHyper *) modify->fix[ifix]; + int dim; + int *hyperflag = (int *) fix_hyper->extract("hyperflag",dim); + if (hyperflag == NULL || *hyperflag == 0) + error->all(FLERR,"Hyper fix is not a valid hyperdynamics fix"); + if (*hyperflag == 1) hyperstyle = GLOBAL; + if (*hyperflag == 2) hyperstyle = LOCAL; + hyperenable = 1; + } + + // create FixEventHyper class to store event and pre-quench states + + char **args = new char*[3]; + args[0] = (char *) "hyper_event"; + args[1] = (char *) "all"; + args[2] = (char *) "EVENT/HYPER"; + modify->add_fix(3,args); + fix_event = (FixEventHyper *) modify->fix[modify->nfix-1]; + delete [] args; + + // create Finish for timing output + + finish = new Finish(lmp); + + // assign FixEventHyper to event-detection compute + // necessary so it will know atom coords at last event + + int icompute = modify->find_compute(id_compute); + if (icompute < 0) error->all(FLERR,"Could not find compute ID for hyper"); + compute_event = (ComputeEventDisplace *) modify->compute[icompute]; + compute_event->reset_extra_compute_fix("hyper_event"); + + // reset reneighboring criteria since will perform minimizations + + neigh_every = neighbor->every; + neigh_delay = neighbor->delay; + neigh_dist_check = neighbor->dist_check; + + if (neigh_every != 1 || neigh_delay != 0 || neigh_dist_check != 1) { + if (me == 0) + error->warning(FLERR,"Resetting reneighboring criteria during hyper"); + } + + neighbor->every = 1; + neighbor->delay = 0; + neighbor->dist_check = 1; + + // initialize hyper as if one long dynamics run + + update->whichflag = 1; + update->nsteps = nsteps; + update->beginstep = update->firststep = update->ntimestep; + update->endstep = update->laststep = update->firststep + nsteps; + if (update->laststep < 0) + error->all(FLERR,"Too many timesteps"); + + lmp->init(); + + // init minimizer settings and minimizer itself + + update->etol = etol; + update->ftol = ftol; + update->max_eval = maxeval; + + // cannot use hyper with a changing box + // removing this restriction would require saving/restoring box params + + if (domain->box_change) + error->all(FLERR,"Cannot use hyper with a changing box"); + + // cannot use hyper with time-dependent fixes or regions + + for (int i = 0; i < modify->nfix; i++) + if (modify->fix[i]->time_depend) + error->all(FLERR,"Cannot use hyper with a time-dependent fix defined"); + + for (int i = 0; i < domain->nregion; i++) + if (domain->regions[i]->dynamic_check()) + error->all(FLERR,"Cannot use hyper with a time-dependent region defined"); + + // perform hyperdynamics simulation + + timer->init(); + timer->barrier_start(); + time_start = timer->get_wall(Timer::TOTAL); + + nbuild = ndanger = 0; + time_dynamics = time_quench = 0.0; + + if (hyperenable) fix_hyper->init_hyper(); + + // perform initial minimization and bond list creation + + int nevent = 0; + int nevent_atoms = 0; + + fix_event->store_state_quench(); + quench(1); + if (dumpflag) + for (int idump = 0; idump < ndump; idump++) + output->dump[dumplist[idump]]->write(); + fix_event->store_event(); + if (hyperenable) fix_hyper->build_bond_list(0); + fix_event->restore_state_quench(); + + // reset stats and timers to skip HD setup + + nbuild = ndanger = 0; + time_dynamics = time_quench = 0.0; + + timer->barrier_start(); + time_start = timer->get_wall(Timer::TOTAL); + + // main loop: dynamics, store state, quench, check event, restore state + + int ecount; + int istep = 0; + + while (istep < nsteps) { + dynamics(t_event,time_dynamics); + fix_event->store_state_quench(); + quench(0); + + ecount = compute_event->all_events(); + + if (ecount) { + nevent++; + nevent_atoms += ecount; + + if (dumpflag) + for (int idump = 0; idump < ndump; idump++) + output->dump[dumplist[idump]]->write(); + fix_event->store_event(); + if (hyperenable) fix_hyper->build_bond_list(ecount); + + } else if (rebond && update->ntimestep % rebond == 0) { + fix_event->store_event(); + if (hyperenable) fix_hyper->build_bond_list(ecount); + } + + fix_event->restore_state_quench(); + istep = update->ntimestep - update->beginstep; + } + + nsteps = update->ntimestep - update->beginstep; + + // set total timers and counters so Finish() will process them + + timer->set_wall(Timer::TOTAL,time_start); + timer->barrier_stop(); + + timer->set_wall(Timer::DYNAMICS,time_dynamics); + timer->set_wall(Timer::QUENCH,time_quench); + + neighbor->ncalls = nbuild; + neighbor->ndanger = ndanger; + + update->nsteps = nsteps; + + if (me == 0) { + if (screen) fprintf(screen,"Final hyper stats ...\n\n"); + if (logfile) fprintf(logfile,"Final hyper stats ...\n\n"); + } + + // subset of quantities also available in fix hyper output + + int nevent_running = 0; + int nevent_atoms_running = 0; + double t_hyper = 0.0; + double avebonds = 0.0; + double maxdrift = 0.0; + double maxbondlen = 0.0; + double fraczero = 1.0; + double fracneg = 1.0; + + double nnewbond,avenbias,avebiascoeff,minbiascoeff,maxbiascoeff; + double maxbondperatom,neighbondperbond,avebiasnow; + double tbondbuild,rmaxever,rmaxeverbig,allghost_toofar; + double lostbond,lostbondcoeff,biasoverlap; + + if (hyperenable) { + t_hyper = fix_hyper->query(1); + nevent_running = fix_hyper->query(2); + nevent_atoms_running = fix_hyper->query(3); + avebonds = fix_hyper->query(4); + maxdrift = fix_hyper->query(5); + maxbondlen = fix_hyper->query(6); + fraczero = fix_hyper->query(7); + fracneg = fix_hyper->query(8); + + if (hyperstyle == LOCAL) { + nnewbond = fix_hyper->query(9); + maxbondperatom = fix_hyper->query(10); + avenbias = fix_hyper->query(11); + avebiascoeff = fix_hyper->query(12); + minbiascoeff = fix_hyper->query(13); + maxbiascoeff = fix_hyper->query(14); + neighbondperbond = fix_hyper->query(15); + avebiasnow = fix_hyper->query(16); + tbondbuild = fix_hyper->query(17); + rmaxever = fix_hyper->query(18); + rmaxeverbig = fix_hyper->query(19); + allghost_toofar = fix_hyper->query(20); + biasoverlap = fix_hyper->query(21); + } + } + + if (me == 0) { + FILE *out; + for (int iout = 0; iout < 2; iout++) { + if (iout == 0) out = screen; + if (iout == 1) out = logfile; + if (!out) continue; + fprintf(out,"Cummulative quantities for fix hyper:\n"); + fprintf(out," hyper time = %g\n",t_hyper); + fprintf(out," time boost factor = %g\n",t_hyper/(nsteps*update->dt)); + fprintf(out," event timesteps = %d\n",nevent_running); + fprintf(out," # of atoms in events = %d\n",nevent_atoms_running); + fprintf(out,"Quantities for this hyper run:\n"); + fprintf(out," event timesteps = %d\n",nevent); + fprintf(out," # of atoms in events = %d\n",nevent_atoms); + fprintf(out," max length of any bond = %g\n",maxbondlen); + fprintf(out," max drift distance of any atom = %g\n",maxdrift); + fprintf(out," fraction of biased bonds with zero bias = %g\n",fraczero); + fprintf(out," fraction of biased bonds with negative strain = %g\n", + fracneg); + fprintf(out,"Current quantities:\n"); + fprintf(out," ave bonds/atom = %g\n",avebonds); + + if (hyperstyle == LOCAL) { + fprintf(out,"Cummulative quantities specific to fix hyper/local:\n"); + fprintf(out," # of new bonds formed = %g\n",nnewbond); + fprintf(out," max bonds/atom = %g\n",maxbondperatom); + fprintf(out,"Quantities for this hyper run specific to " + "fix hyper/local:\n"); + fprintf(out," ave biased bonds/step = %g\n",avenbias); + fprintf(out," ave bias coeff of all bonds = %g\n",avebiascoeff); + fprintf(out," min bias coeff of any bond = %g\n",minbiascoeff); + fprintf(out," max bias coeff of any bond = %g\n",maxbiascoeff); + fprintf(out," max dist from my subbox of any " + "non-maxstrain bond ghost atom = %g\n",rmaxever); + fprintf(out," max dist from my box of any bond ghost atom = %g\n", + rmaxeverbig); + fprintf(out," count of bond ghost neighbors " + "not found on reneighbor steps = %g\n",allghost_toofar); + fprintf(out," bias overlaps = %g\n",biasoverlap); + fprintf(out," CPU time for bond builds = %g\n",tbondbuild); + fprintf(out,"Current quantities specific to fix hyper/local:\n"); + fprintf(out," neighbor bonds/bond = %g\n",neighbondperbond); + fprintf(out," ave boost coeff for all bonds = %g\n",avebiasnow); + } + fprintf(out,"\n"); + } + } + + // timing stats + + finish->end(4); + + update->whichflag = 0; + update->firststep = update->laststep = 0; + update->beginstep = update->endstep = 0; + + // reset reneighboring criteria + + neighbor->every = neigh_every; + neighbor->delay = neigh_delay; + neighbor->dist_check = neigh_dist_check; + + delete [] id_fix; + delete [] id_compute; + memory->destroy(dumplist); + delete finish; + modify->delete_fix("hyper_event"); + + compute_event->reset_extra_compute_fix(NULL); +} + +/* ---------------------------------------------------------------------- + short dynamics run +------------------------------------------------------------------------- */ + +void Hyper::dynamics(int nsteps, double & /* time_category */) +{ + update->whichflag = 1; + update->nsteps = nsteps; + + // full init works + // need to try partial init or setup + + lmp->init(); + update->integrate->setup(0); + // this may be needed if don't do full init + //modify->addstep_compute_all(update->ntimestep); + bigint ncalls = neighbor->ncalls; + + timer->barrier_start(); + update->integrate->run(nsteps); + timer->barrier_stop(); + time_dynamics += timer->get_wall(Timer::TOTAL); + + nbuild += neighbor->ncalls - ncalls; + ndanger += neighbor->ndanger; + + update->integrate->cleanup(); + finish->end(0); +} + +/* ---------------------------------------------------------------------- + quench minimization + flag = 1 to trigger output of memory in setup() call +------------------------------------------------------------------------- */ + +void Hyper::quench(int flag) +{ + bigint ntimestep_hold = update->ntimestep; + bigint endstep_hold = update->endstep; + + // need to change whichflag so that minimize->setup() calling + // modify->setup() will call fix->min_setup() + + update->whichflag = 2; + update->nsteps = maxiter; + update->endstep = update->laststep = update->firststep + maxiter; + if (update->laststep < 0) + error->all(FLERR,"Too many iterations"); + update->restrict_output = 1; + + // full init works + + lmp->init(); + update->minimize->setup(flag); + + // partial init does not work + + //modify->addstep_compute_all(update->ntimestep); + //update->minimize->setup_minimal(1); + + timer->barrier_start(); + update->minimize->run(maxiter); + timer->barrier_stop(); + time_quench += timer->get_wall(Timer::TOTAL); + + update->minimize->cleanup(); + finish->end(0); + + // reset timestep as if quench did not occur + // clear timestep storage from computes, since now invalid + + update->restrict_output = 0; + update->ntimestep = ntimestep_hold; + update->endstep = update->laststep = endstep_hold; + for (int i = 0; i < modify->ncompute; i++) + if (modify->compute[i]->timeflag) modify->compute[i]->clearstep(); +} + +/* ---------------------------------------------------------------------- + parse optional parameters at end of hyper input line +------------------------------------------------------------------------- */ + +void Hyper::options(int narg, char **arg) +{ + // set defaults + + etol = 1.0e-4; + ftol = 1.0e-4; + maxiter = 40; + maxeval = 50; + dumpflag = 0; + ndump = 0; + dumplist = NULL; + rebond = 0; + + int iarg = 0; + while (iarg < narg) { + if (strcmp(arg[iarg],"min") == 0) { + if (iarg+5 > narg) error->all(FLERR,"Illegal hyper command"); + etol = force->numeric(FLERR,arg[iarg+1]); + ftol = force->numeric(FLERR,arg[iarg+2]); + maxiter = force->inumeric(FLERR,arg[iarg+3]); + maxeval = force->inumeric(FLERR,arg[iarg+4]); + if (maxiter < 0) error->all(FLERR,"Illegal hyper command"); + iarg += 5; + + } else if (strcmp(arg[iarg],"dump") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal hyper command"); + dumpflag = 1; + int idump = output->find_dump(arg[iarg+1]); + if (idump < 0) + error->all(FLERR,"Dump ID in hyper command does not exist"); + memory->grow(dumplist,ndump+1,"hyper:dumplist"); + dumplist[ndump++] = idump; + iarg += 2; + + } else if (strcmp(arg[iarg],"rebond") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal hyper command"); + rebond = force->inumeric(FLERR,arg[iarg+1]); + iarg += 2; + + } else error->all(FLERR,"Illegal hyper command"); + } +} diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h new file mode 100644 index 0000000000..1b05172bcf --- /dev/null +++ b/src/REPLICA/hyper.h @@ -0,0 +1,65 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(hyper,Hyper) + +#else + +#ifndef LMP_HYPER_H +#define LMP_HYPER_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Hyper : protected Pointers { + public: + Hyper(class LAMMPS *); + ~Hyper() {} + void command(int, char **); + + private: + int me,nprocs; + int t_event; + double etol,ftol; + int maxiter,maxeval; + int stepmode,dumpflag,ndump,rebond; + int *dumplist; + + int neigh_every,neigh_delay,neigh_dist_check; + int quench_reneighbor; + bigint nbuild,ndanger; + + double time_dynamics,time_quench; + double time_start; + + class FixHyper *fix_hyper; + class FixEventHyper *fix_event; + class ComputeEventDisplace *compute_event; + class Finish *finish; + + void dynamics(int, double &); + void quench(int flag); + void options(int, char **); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/REPLICA/verlet_split.cpp b/src/REPLICA/verlet_split.cpp index 05ea0877ab..7042fc6993 100644 --- a/src/REPLICA/verlet_split.cpp +++ b/src/REPLICA/verlet_split.cpp @@ -223,7 +223,7 @@ void VerletSplit::init() if (!force->kspace && comm->me == 0) error->warning(FLERR,"No Kspace calculation with verlet/split"); - if (force->kspace_match("tip4p",0)) tip4p_flag = 1; + if (force->kspace_match("/tip4p",0)) tip4p_flag = 1; else tip4p_flag = 0; // currently TIP4P does not work with verlet/split, so generate error diff --git a/src/RIGID/fix_ehex.h b/src/RIGID/fix_ehex.h index b606330f11..e29ddac135 100644 --- a/src/RIGID/fix_ehex.h +++ b/src/RIGID/fix_ehex.h @@ -75,7 +75,7 @@ class FixEHEX : public Fix { /* ERROR/WARNING messages: -E: Illegal fix ehex command: wrong number of parameters +E: Illegal fix ehex command: wrong number of parameters UNDOCUMENTED @@ -87,11 +87,11 @@ E: Region ID for fix ehex does not exist Self-explanatory. -E: Illegal fix ehex keyword +E: Illegal fix ehex keyword UNDOCUMENTED -E: You can only use the keyword 'com' together with the keyword 'constrain' +E: You can only use the keyword 'com' together with the keyword 'constrain' UNDOCUMENTED diff --git a/src/RIGID/fix_rattle.h b/src/RIGID/fix_rattle.h index a0405bbdcc..48edaef379 100644 --- a/src/RIGID/fix_rattle.h +++ b/src/RIGID/fix_rattle.h @@ -79,7 +79,7 @@ class FixRattle : public FixShake { /* ERROR/WARNING messages: -W: Fix rattle should come after all other integration fixes +W: Fix rattle should come after all other integration fixes UNDOCUMENTED @@ -88,15 +88,15 @@ E: Rattle determinant = 0.0 The determinant of the matrix being solved for a single cluster specified by the fix rattle command is numerically invalid. -E: Rattle failed +E: Rattle failed UNDOCUMENTED -E: Coordinate constraints are not satisfied up to desired tolerance +E: Coordinate constraints are not satisfied up to desired tolerance UNDOCUMENTED -E: Velocity constraints are not satisfied up to desired tolerance +E: Velocity constraints are not satisfied up to desired tolerance UNDOCUMENTED diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 39c49ca1c4..8fa43b89ce 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -174,7 +174,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) : MPI_Allreduce(&vmin,&minval,1,MPI_INT,MPI_MIN,world); molecule = new tagint[nlocal]; for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit) + if (mask[i] & groupbit) molecule[i] = (tagint)((tagint)value[i] - minval + 1); delete[] value; } else error->all(FLERR,"Unsupported fix rigid custom property"); @@ -727,7 +727,7 @@ void FixRigid::init() int rflag = 0; for (i = 0; i < modify->nfix; i++) { if (modify->fix[i]->rigid_flag) rflag = 1; - if (rflag && (modify->fmask[i] & POST_FORCE) && + if (rflag && (modify->fmask[i] & POST_FORCE) && !modify->fix[i]->rigid_flag) { char str[128]; snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id); @@ -2639,7 +2639,7 @@ int FixRigid::modify_param(int narg, char **arg) else error->all(FLERR,"Illegal fix_modify command"); // reset fix mask - // must do here and not in init, + // must do here and not in init, // since modify.cpp::init() uses fix masks before calling fix::init() for (int i = 0; i < modify->nfix; i++) diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 44e1870e0a..fb185d7702 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -566,7 +566,7 @@ void FixRigidSmall::init() int rflag = 0; for (i = 0; i < modify->nfix; i++) { if (modify->fix[i]->rigid_flag) rflag = 1; - if (rflag && (modify->fmask[i] & POST_FORCE) && + if (rflag && (modify->fmask[i] & POST_FORCE) && !modify->fix[i]->rigid_flag) { char str[128]; snprintf(str,128,"Fix %s alters forces after fix rigid",modify->fix[i]->id); @@ -3430,7 +3430,7 @@ int FixRigidSmall::modify_param(int narg, char **arg) else error->all(FLERR,"Illegal fix_modify command"); // reset fix mask - // must do here and not in init, + // must do here and not in init, // since modify.cpp::init() uses fix masks before calling fix::init() for (int i = 0; i < modify->nfix; i++) diff --git a/src/SNAP/pair_snap.cpp b/src/SNAP/pair_snap.cpp index 9f4c6bf5e2..8b547e6e73 100644 --- a/src/SNAP/pair_snap.cpp +++ b/src/SNAP/pair_snap.cpp @@ -176,8 +176,7 @@ void PairSNAP::compute_regular(int eflag, int vflag) int *jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -486,8 +485,7 @@ void PairSNAP::compute_optimized(int eflag, int vflag) #pragma omp master #endif { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); } #if defined(_OPENMP) @@ -1416,11 +1414,7 @@ void PairSNAP::settings(int narg, char **arg) void PairSNAP::coeff(int narg, char **arg) { - // read SNAP element names between 2 filenames - // nelements = # of SNAP elements - // elements = list of unique element names - - if (narg < 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); if (nelements) { @@ -1432,30 +1426,17 @@ void PairSNAP::coeff(int narg, char **arg) memory->destroy(coeffelem); } - nelements = narg - 4 - atom->ntypes; - if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients"); - char* type1 = arg[0]; char* type2 = arg[1]; char* coefffilename = arg[2]; - char** elemlist = &arg[3]; - char* paramfilename = arg[3+nelements]; - char** elemtypes = &arg[4+nelements]; + char* paramfilename = arg[3]; + char** elemtypes = &arg[4]; // insure I,J args are * * if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0) error->all(FLERR,"Incorrect args for pair coefficients"); - elements = new char*[nelements]; - - for (int i = 0; i < nelements; i++) { - char* elemname = elemlist[i]; - int n = strlen(elemname) + 1; - elements[i] = new char[n]; - strcpy(elements[i],elemname); - } - // read snapcoeff and snapparam files read_files(coefffilename,paramfilename); @@ -1631,22 +1612,19 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) iword = 1; words[iword] = strtok(NULL,"' \t\n\r\f"); - int nelemfile = atoi(words[0]); + nelements = atoi(words[0]); ncoeffall = atoi(words[1]); - // Set up element lists + // set up element lists + elements = new char*[nelements]; memory->create(radelem,nelements,"pair:radelem"); memory->create(wjelem,nelements,"pair:wjelem"); memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem"); - int *found = new int[nelements]; - for (int ielem = 0; ielem < nelements; ielem++) - found[ielem] = 0; + // Loop over nelements blocks in the SNAP coefficient file - // Loop over elements in the SNAP coefficient file - - for (int ielemfile = 0; ielemfile < nelemfile; ielemfile++) { + for (int ielem = 0; ielem < nelements; ielem++) { if (comm->me == 0) { ptr = fgets(line,MAXLINE,fpcoeff); @@ -1673,33 +1651,12 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) words[iword] = strtok(NULL,"' \t\n\r\f"); char* elemtmp = words[0]; - double radtmp = atof(words[1]); - double wjtmp = atof(words[2]); + int n = strlen(elemtmp) + 1; + elements[ielem] = new char[n]; + strcpy(elements[ielem],elemtmp); - // skip if element name isn't in element list - - int ielem; - for (ielem = 0; ielem < nelements; ielem++) - if (strcmp(elemtmp,elements[ielem]) == 0) break; - if (ielem == nelements) { - if (comm->me == 0) - for (int icoeff = 0; icoeff < ncoeffall; icoeff++) - ptr = fgets(line,MAXLINE,fpcoeff); - continue; - } - - // skip if element already appeared - - if (found[ielem]) { - if (comm->me == 0) - for (int icoeff = 0; icoeff < ncoeffall; icoeff++) - ptr = fgets(line,MAXLINE,fpcoeff); - continue; - } - - found[ielem] = 1; - radelem[ielem] = radtmp; - wjelem[ielem] = wjtmp; + radelem[ielem] = atof(words[1]); + wjelem[ielem] = atof(words[2]); if (comm->me == 0) { @@ -1821,7 +1778,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) if (rcutfacflag == 0 || twojmaxflag == 0) error->all(FLERR,"Incorrect SNAP parameter file"); - delete[] found; } /* ---------------------------------------------------------------------- diff --git a/src/SNAP/pair_snap.h b/src/SNAP/pair_snap.h index d39cb0f8d4..1fa065755c 100644 --- a/src/SNAP/pair_snap.h +++ b/src/SNAP/pair_snap.h @@ -173,4 +173,8 @@ E: Incorrect format in SNAP parameter file Incorrect number of words per line in the parameter file. +E: Did not find all elements in SNAP coefficient file. + +One or more elements listed in the pair_coeff command were not found in the coefficient file. + */ diff --git a/src/SPIN/README b/src/SPIN/README index e371e39767..53e456bacb 100644 --- a/src/SPIN/README +++ b/src/SPIN/README @@ -9,6 +9,7 @@ atom in the system * implementing magnetic pair interactions and magnetic forces * thermostating and applying a transverse damping to the magnetic spins * computing and outputing magnetic quantities +* minimizing the energy or total torque of a magnetic system The different options provided by this package are explained in the LAMMPS documentation. diff --git a/src/SPIN/compute_spin.cpp b/src/SPIN/compute_spin.cpp index dc16190c98..0a881e1de6 100644 --- a/src/SPIN/compute_spin.cpp +++ b/src/SPIN/compute_spin.cpp @@ -84,7 +84,7 @@ void ComputeSpin::compute_vector() invoked_vector = update->ntimestep; - countsp = countsptot = 0.0; + countsp = countsptot = 0.0; mag[0] = mag[1] = mag[2] = mag[3] = 0.0; magtot[0] = magtot[1] = magtot[2] = magtot[3] = 0.0; magenergy = magenergytot = 0.0; @@ -96,7 +96,7 @@ void ComputeSpin::compute_vector() double **sp = atom->sp; double **fm = atom->fm; double tx,ty,tz; - + int nlocal = atom->nlocal; // compute total magnetization and magnetic energy @@ -105,16 +105,16 @@ void ComputeSpin::compute_vector() for (i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { if (atom->sp_flag) { - mag[0] += sp[i][0]; - mag[1] += sp[i][1]; - mag[2] += sp[i][2]; - magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]); + mag[0] += sp[i][0]; + mag[1] += sp[i][1]; + mag[2] += sp[i][2]; + magenergy -= (sp[i][0]*fm[i][0] + sp[i][1]*fm[i][1] + sp[i][2]*fm[i][2]); tx = sp[i][1]*fm[i][2]-sp[i][2]*fm[i][1]; ty = sp[i][2]*fm[i][0]-sp[i][0]*fm[i][2]; tz = sp[i][0]*fm[i][1]-sp[i][1]*fm[i][0]; tempnum += tx*tx+ty*ty+tz*tz; - tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2]; - countsp++; + tempdenom += sp[i][0]*fm[i][0]+fm[i][1]*sp[i][1]+sp[i][2]*fm[i][2]; + countsp++; } } else error->all(FLERR,"Compute compute/spin requires atom/spin style"); diff --git a/src/SPIN/fix_langevin_spin.cpp b/src/SPIN/fix_langevin_spin.cpp index 55b4d8dfec..ec6f719a77 100644 --- a/src/SPIN/fix_langevin_spin.cpp +++ b/src/SPIN/fix_langevin_spin.cpp @@ -131,8 +131,8 @@ void FixLangevinSpin::init() gil_factor = 1.0/(1.0+(alpha_t)*(alpha_t)); dts = update->dt; - double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) - double kb = force->boltz; // eV/K + double hbar = force->hplanck/MY_2PI; // eV/(rad.THz) + double kb = force->boltz; // eV/K D = (MY_2PI*alpha_t*gil_factor*kb*temp); D /= (hbar*dts); sigma = sqrt(2.0*D); @@ -158,7 +158,7 @@ void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3]) double cpx = fmi[1]*spi[2] - fmi[2]*spi[1]; double cpy = fmi[2]*spi[0] - fmi[0]*spi[2]; double cpz = fmi[0]*spi[1] - fmi[1]*spi[0]; - + // adding the transverse damping fmi[0] -= alpha_t*cpx; diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 7d96aca6d4..8d549ed64a 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -183,7 +183,7 @@ void FixNVESpin::init() npairs = pair->instance_total; for (int i = 0; ipair_match("spin",0,i)) { - npairspin ++; + npairspin ++; } } } @@ -203,8 +203,8 @@ void FixNVESpin::init() } else if (npairspin > 1) { for (int i = 0; ipair_match("spin",0,i)) { - spin_pairs[count] = (PairSpin *) force->pair_match("spin",0,i); - count++; + spin_pairs[count] = (PairSpin *) force->pair_match("spin",0,i); + count++; } } } @@ -264,8 +264,8 @@ void FixNVESpin::init() void FixNVESpin::initial_integrate(int /*vflag*/) { double dtfm; - - double **x = atom->x; + + double **x = atom->x; double **v = atom->v; double **f = atom->f; double *rmass = atom->rmass; @@ -291,32 +291,32 @@ void FixNVESpin::initial_integrate(int /*vflag*/) // update half s for all atoms - if (sector_flag) { // sectoring seq. update - for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal + if (sector_flag) { // sectoring seq. update + for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal comm->forward_comm(); int i = stack_foot[j]; while (i >= 0) { ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = forward_stacks[i]; + AdvanceSingleSpin(i); + i = forward_stacks[i]; } } - for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal + for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal comm->forward_comm(); int i = stack_head[j]; while (i >= 0) { ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = backward_stacks[i]; + AdvanceSingleSpin(i); + i = backward_stacks[i]; } } - } else if (sector_flag == 0) { // serial seq. update - comm->forward_comm(); // comm. positions of ghost atoms - for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal + } else if (sector_flag == 0) { // serial seq. update + comm->forward_comm(); // comm. positions of ghost atoms + for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal ComputeInteractionsSpin(i); AdvanceSingleSpin(i); } - for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal + for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal ComputeInteractionsSpin(i); AdvanceSingleSpin(i); } @@ -336,32 +336,32 @@ void FixNVESpin::initial_integrate(int /*vflag*/) // update half s for all particles - if (sector_flag) { // sectoring seq. update - for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal + if (sector_flag) { // sectoring seq. update + for (int j = 0; j < nsectors; j++) { // advance quarter s for nlocal comm->forward_comm(); int i = stack_foot[j]; while (i >= 0) { ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = forward_stacks[i]; + AdvanceSingleSpin(i); + i = forward_stacks[i]; } } - for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal + for (int j = nsectors-1; j >= 0; j--) { // advance quarter s for nlocal comm->forward_comm(); int i = stack_head[j]; while (i >= 0) { ComputeInteractionsSpin(i); - AdvanceSingleSpin(i); - i = backward_stacks[i]; + AdvanceSingleSpin(i); + i = backward_stacks[i]; } } - } else if (sector_flag == 0) { // serial seq. update - comm->forward_comm(); // comm. positions of ghost atoms - for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal-1 + } else if (sector_flag == 0) { // serial seq. update + comm->forward_comm(); // comm. positions of ghost atoms + for (int i = 0; i < nlocal; i++){ // advance quarter s for nlocal-1 ComputeInteractionsSpin(i); AdvanceSingleSpin(i); } - for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal-1 + for (int i = nlocal-1; i >= 0; i--){ // advance quarter s for nlocal-1 ComputeInteractionsSpin(i); AdvanceSingleSpin(i); } @@ -384,10 +384,10 @@ void FixNVESpin::setup_pre_neighbor() void FixNVESpin::pre_neighbor() { - double **x = atom->x; + double **x = atom->x; int nlocal = atom->nlocal; - if (nlocal_max < nlocal) { // grow linked lists if necessary + if (nlocal_max < nlocal) { // grow linked lists if necessary nlocal_max = nlocal; backward_stacks = memory->grow(backward_stacks,nlocal_max,"NVE/spin:backward_stacks"); forward_stacks = memory->grow(forward_stacks,nlocal_max,"NVE/spin:forward_stacks"); @@ -399,7 +399,7 @@ void FixNVESpin::pre_neighbor() } int nseci; - for (int j = 0; j < nsectors; j++) { // stacking backward order + for (int j = 0; j < nsectors; j++) { // stacking backward order for (int i = 0; i < nlocal; i++) { nseci = coords2sector(x[i]); if (j != nseci) continue; @@ -407,7 +407,7 @@ void FixNVESpin::pre_neighbor() stack_head[j] = i; } } - for (int j = nsectors-1; j >= 0; j--) { // stacking forward order + for (int j = nsectors-1; j >= 0; j--) { // stacking forward order for (int i = nlocal-1; i >= 0; i--) { nseci = coords2sector(x[i]); if (j != nseci) continue; @@ -453,11 +453,11 @@ void FixNVESpin::ComputeInteractionsSpin(int i) // update langevin damping and random force - if (maglangevin_flag) { // mag. langevin - if (tdamp_flag) { // transverse damping + if (maglangevin_flag) { // mag. langevin + if (tdamp_flag) { // transverse damping locklangevinspin->add_tdamping(spi,fmi); } - if (temp_flag) { // spin temperature + if (temp_flag) { // spin temperature locklangevinspin->add_temperature(fmi); } } @@ -567,7 +567,7 @@ void FixNVESpin::AdvanceSingleSpin(int i) g[0] = g[1] = g[2] = 0.0; fm2 = (fm[i][0]*fm[i][0])+(fm[i][1]*fm[i][1])+(fm[i][2]*fm[i][2]); energy = (sp[i][0]*fm[i][0])+(sp[i][1]*fm[i][1])+(sp[i][2]*fm[i][2]); - dts2 = dts*dts; + dts2 = dts*dts; cp[0] = fm[i][1]*sp[i][2]-fm[i][2]*sp[i][1]; cp[1] = fm[i][2]*sp[i][0]-fm[i][0]*sp[i][2]; @@ -576,18 +576,18 @@ void FixNVESpin::AdvanceSingleSpin(int i) g[0] = sp[i][0]+cp[0]*dts; g[1] = sp[i][1]+cp[1]*dts; g[2] = sp[i][2]+cp[2]*dts; - + g[0] += (fm[i][0]*energy-0.5*sp[i][0]*fm2)*0.5*dts2; g[1] += (fm[i][1]*energy-0.5*sp[i][1]*fm2)*0.5*dts2; g[2] += (fm[i][2]*energy-0.5*sp[i][2]*fm2)*0.5*dts2; - + g[0] /= (1+0.25*fm2*dts2); g[1] /= (1+0.25*fm2*dts2); g[2] /= (1+0.25*fm2*dts2); - + sp[i][0] = g[0]; sp[i][1] = g[1]; - sp[i][2] = g[2]; + sp[i][2] = g[2]; // renormalization (check if necessary) @@ -616,9 +616,9 @@ void FixNVESpin::AdvanceSingleSpin(int i) /* ---------------------------------------------------------------------- */ void FixNVESpin::final_integrate() -{ +{ double dtfm; - + double **v = atom->v; double **f = atom->f; double *rmass = atom->rmass; diff --git a/src/SPIN/fix_precession_spin.cpp b/src/SPIN/fix_precession_spin.cpp index d3edb3ae8a..9ee691c227 100644 --- a/src/SPIN/fix_precession_spin.cpp +++ b/src/SPIN/fix_precession_spin.cpp @@ -115,6 +115,7 @@ int FixPrecessionSpin::setmask() { int mask = 0; mask |= POST_FORCE; + mask |= MIN_POST_FORCE; mask |= THERMO_ENERGY; mask |= POST_FORCE_RESPA; return mask; @@ -169,8 +170,16 @@ void FixPrecessionSpin::setup(int vflag) /* ---------------------------------------------------------------------- */ -void FixPrecessionSpin::post_force(int /*vflag*/) +void FixPrecessionSpin::min_setup(int vflag) { + post_force(vflag); +} + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::post_force(int /* vflag */) +{ + // update mag field with time (potential improvement) if (varflag != CONSTANT) { @@ -200,7 +209,7 @@ void FixPrecessionSpin::post_force(int /*vflag*/) if (aniso_flag) { // compute magnetic anisotropy compute_anisotropy(spi,fmi); - emag -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + emag -= 0.5*(spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); } fm[i][0] += fmi[0]; @@ -228,9 +237,9 @@ void FixPrecessionSpin::compute_single_precession(int i, double spi[3], double f void FixPrecessionSpin::compute_zeeman(int i, double fmi[3]) { double **sp = atom->sp; - fmi[0] -= sp[i][3]*hx; - fmi[1] -= sp[i][3]*hy; - fmi[2] -= sp[i][3]*hz; + fmi[0] += sp[i][3]*hx; + fmi[1] += sp[i][3]*hy; + fmi[2] += sp[i][3]*hz; } /* ---------------------------------------------------------------------- */ @@ -280,3 +289,10 @@ double FixPrecessionSpin::compute_scalar() } return emag_all; } + +/* ---------------------------------------------------------------------- */ + +void FixPrecessionSpin::min_post_force(int vflag) +{ + post_force(vflag); +} diff --git a/src/SPIN/fix_precession_spin.h b/src/SPIN/fix_precession_spin.h index 53ae4ba124..1db4d32ae9 100644 --- a/src/SPIN/fix_precession_spin.h +++ b/src/SPIN/fix_precession_spin.h @@ -33,8 +33,10 @@ class FixPrecessionSpin : public Fix { int setmask(); void init(); void setup(int); - virtual void post_force(int); - virtual void post_force_respa(int, int, int); + void min_setup(int); + void post_force(int); + void post_force_respa(int, int, int); + void min_post_force(int); double compute_scalar(); int zeeman_flag, aniso_flag; diff --git a/src/SPIN/min_spin.cpp b/src/SPIN/min_spin.cpp new file mode 100644 index 0000000000..2bddc110e7 --- /dev/null +++ b/src/SPIN/min_spin.cpp @@ -0,0 +1,333 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + + Please cite the related publication: +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "min_spin.h" +#include "universe.h" +#include "atom.h" +#include "force.h" +#include "update.h" +#include "output.h" +#include "timer.h" +#include "error.h" +#include "modify.h" +#include "math_special.h" +#include "math_const.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +// EPS_ENERGY = minimum normalization for energy tolerance + +#define EPS_ENERGY 1.0e-8 + +#define DELAYSTEP 5 + +/* ---------------------------------------------------------------------- */ + +MinSpin::MinSpin(LAMMPS *lmp) : Min(lmp) {} + +/* ---------------------------------------------------------------------- */ + +void MinSpin::init() +{ + alpha_damp = 1.0; + discrete_factor = 10.0; + + Min::init(); + + dts = dt = update->dt; + last_negative = update->ntimestep; +} + +/* ---------------------------------------------------------------------- */ + +void MinSpin::setup_style() +{ + double **v = atom->v; + int nlocal = atom->nlocal; + + // check if the atom/spin style is defined + + if (!atom->sp_flag) + error->all(FLERR,"min/spin requires atom/spin style"); + + for (int i = 0; i < nlocal; i++) + v[i][0] = v[i][1] = v[i][2] = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +int MinSpin::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"alpha_damp") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + alpha_damp = force->numeric(FLERR,arg[1]); + return 2; + } + if (strcmp(arg[0],"discrete_factor") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + discrete_factor = force->numeric(FLERR,arg[1]); + return 2; + } + return 0; +} + +/* ---------------------------------------------------------------------- + set current vector lengths and pointers + called after atoms have migrated +------------------------------------------------------------------------- */ + +void MinSpin::reset_vectors() +{ + // atomic dof + + // size sp is 4N vector + nvec = 4 * atom->nlocal; + if (nvec) spvec = atom->sp[0]; + + nvec = 3 * atom->nlocal; + if (nvec) fmvec = atom->fm[0]; + + if (nvec) xvec = atom->x[0]; + if (nvec) fvec = atom->f[0]; +} + +/* ---------------------------------------------------------------------- + minimization via damped spin dynamics +------------------------------------------------------------------------- */ + +int MinSpin::iterate(int maxiter) +{ + bigint ntimestep; + double fmdotfm; + int flag,flagall; + + for (int iter = 0; iter < maxiter; iter++) { + + if (timer->check_timeout(niter)) + return TIMEOUT; + + ntimestep = ++update->ntimestep; + niter++; + + // optimize timestep accross processes / replicas + // need a force calculation for timestep optimization + + energy_force(0); + dts = evaluate_dt(); + + // apply damped precessional dynamics to the spins + + advance_spins(dts); + + eprevious = ecurrent; + ecurrent = energy_force(0); + neval++; + + //// energy tolerance criterion + //// only check after DELAYSTEP elapsed since velocties reset to 0 + //// sync across replicas if running multi-replica minimization + + if (update->etol > 0.0 && ntimestep-last_negative > DELAYSTEP) { + if (update->multireplica == 0) { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + return ETOL; + } else { + if (fabs(ecurrent-eprevious) < + update->etol * 0.5*(fabs(ecurrent) + fabs(eprevious) + EPS_ENERGY)) + flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return ETOL; + } + } + + // magnetic torque tolerance criterion + // sync across replicas if running multi-replica minimization + + if (update->ftol > 0.0) { + fmdotfm = fmnorm_sqr(); + if (update->multireplica == 0) { + if (fmdotfm < update->ftol*update->ftol) return FTOL; + } else { + if (fmdotfm < update->ftol*update->ftol) flag = 0; + else flag = 1; + MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,universe->uworld); + if (flagall == 0) return FTOL; + } + } + + // output for thermo, dump, restart files + + if (output->next == ntimestep) { + timer->stamp(); + output->write(ntimestep); + timer->stamp(Timer::OUTPUT); + } + } + + return MAXITER; +} + +/* ---------------------------------------------------------------------- + evaluate max timestep +---------------------------------------------------------------------- */ + +double MinSpin::evaluate_dt() +{ + double dtmax; + double fmsq; + double fmaxsqone,fmaxsqloc,fmaxsqall; + int nlocal = atom->nlocal; + double **fm = atom->fm; + + // finding max fm on this proc. + + fmsq = fmaxsqone = fmaxsqloc = fmaxsqall = 0.0; + for (int i = 0; i < nlocal; i++) { + fmsq = fm[i][0]*fm[i][0]+fm[i][1]*fm[i][1]+fm[i][2]*fm[i][2]; + fmaxsqone = MAX(fmaxsqone,fmsq); + } + + // finding max fm on this replica + + fmaxsqloc = fmaxsqone; + MPI_Allreduce(&fmaxsqone,&fmaxsqloc,1,MPI_DOUBLE,MPI_MAX,world); + + // finding max fm over all replicas, if necessary + // this communicator would be invalid for multiprocess replicas + + fmaxsqall = fmaxsqloc; + if (update->multireplica == 1) { + fmaxsqall = fmaxsqloc; + MPI_Allreduce(&fmaxsqloc,&fmaxsqall,1,MPI_DOUBLE,MPI_MAX,universe->uworld); + } + + if (fmaxsqall == 0.0) + error->all(FLERR,"Incorrect fmaxsqall calculation"); + + // define max timestep by dividing by the + // inverse of max frequency by discrete_factor + + dtmax = MY_2PI/(discrete_factor*sqrt(fmaxsqall)); + + return dtmax; +} + +/* ---------------------------------------------------------------------- + geometric damped advance of spins +---------------------------------------------------------------------- */ + +void MinSpin::advance_spins(double dts) +{ + int nlocal = atom->nlocal; + double **sp = atom->sp; + double **fm = atom->fm; + double tdampx,tdampy,tdampz; + double msq,scale,fm2,energy,dts2; + double cp[3],g[3]; + + dts2 = dts*dts; + + // loop on all spins on proc. + + for (int i = 0; i < nlocal; i++) { + + // calc. damping torque + + tdampx = -alpha_damp*(fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]); + tdampy = -alpha_damp*(fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]); + tdampz = -alpha_damp*(fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]); + + // apply advance algorithm (geometric, norm preserving) + + fm2 = (tdampx*tdampx+tdampy*tdampy+tdampz*tdampz); + energy = (sp[i][0]*tdampx)+(sp[i][1]*tdampy)+(sp[i][2]*tdampz); + + cp[0] = tdampy*sp[i][2]-tdampz*sp[i][1]; + cp[1] = tdampz*sp[i][0]-tdampx*sp[i][2]; + cp[2] = tdampx*sp[i][1]-tdampy*sp[i][0]; + + g[0] = sp[i][0]+cp[0]*dts; + g[1] = sp[i][1]+cp[1]*dts; + g[2] = sp[i][2]+cp[2]*dts; + + g[0] += (tdampx*energy-0.5*sp[i][0]*fm2)*0.5*dts2; + g[1] += (tdampy*energy-0.5*sp[i][1]*fm2)*0.5*dts2; + g[2] += (tdampz*energy-0.5*sp[i][2]*fm2)*0.5*dts2; + + g[0] /= (1+0.25*fm2*dts2); + g[1] /= (1+0.25*fm2*dts2); + g[2] /= (1+0.25*fm2*dts2); + + sp[i][0] = g[0]; + sp[i][1] = g[1]; + sp[i][2] = g[2]; + + // renormalization (check if necessary) + + msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2]; + scale = 1.0/sqrt(msq); + sp[i][0] *= scale; + sp[i][1] *= scale; + sp[i][2] *= scale; + + // no comm. to atoms with same tag + // because no need for simplecticity + } +} + +/* ---------------------------------------------------------------------- + compute and return ||mag. torque||_2^2 +------------------------------------------------------------------------- */ + +double MinSpin::fmnorm_sqr() +{ + int nlocal = atom->nlocal; + double tx,ty,tz; + double **sp = atom->sp; + double **fm = atom->fm; + + // calc. magnetic torques + + double local_norm2_sqr = 0.0; + for (int i = 0; i < nlocal; i++) { + tx = (fm[i][1]*sp[i][2] - fm[i][2]*sp[i][1]); + ty = (fm[i][2]*sp[i][0] - fm[i][0]*sp[i][2]); + tz = (fm[i][0]*sp[i][1] - fm[i][1]*sp[i][0]); + + local_norm2_sqr += tx*tx + ty*ty + tz*tz; + } + + // no extra atom calc. for spins + + if (nextra_atom) + error->all(FLERR,"extra atom option not available yet"); + + double norm2_sqr = 0.0; + MPI_Allreduce(&local_norm2_sqr,&norm2_sqr,1,MPI_DOUBLE,MPI_SUM,world); + + return norm2_sqr; +} + diff --git a/src/SPIN/min_spin.h b/src/SPIN/min_spin.h new file mode 100644 index 0000000000..224d205000 --- /dev/null +++ b/src/SPIN/min_spin.h @@ -0,0 +1,59 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef MINIMIZE_CLASS + +MinimizeStyle(spin,MinSpin) + +#else + +#ifndef LMP_MIN_SPIN_H +#define LMP_MIN_SPIN_H + +#include "min.h" + +namespace LAMMPS_NS { + +class MinSpin : public Min { + public: + MinSpin(class LAMMPS *); + ~MinSpin() {} + void init(); + void setup_style(); + int modify_param(int, char **); + void reset_vectors(); + int iterate(int); + double evaluate_dt(); + void advance_spins(double); + double fmnorm_sqr(); + + private: + + // global and spin timesteps + + double dt; + double dts; + + double alpha_damp; // damping for spin minimization + double discrete_factor; // factor for spin timestep evaluation + + double *spvec; // variables for atomic dof, as 1d vector + double *fmvec; // variables for atomic dof, as 1d vector + + bigint last_negative; +}; + +} + +#endif +#endif diff --git a/src/SPIN/pair_spin_dmi.cpp b/src/SPIN/pair_spin_dmi.cpp index 6f8114042e..d0506e972d 100644 --- a/src/SPIN/pair_spin_dmi.cpp +++ b/src/SPIN/pair_spin_dmi.cpp @@ -173,8 +173,8 @@ void PairSpinDmi::init_style() if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; ifix++; } - if (ifix == modify->nfix) - error->all(FLERR,"pair/spin style requires nve/spin"); + if ((ifix == modify->nfix) && (comm->me == 0)) + error->warning(FLERR,"Using pair/spin style without nve/spin"); // get the lattice_flag from nve/spin @@ -233,13 +233,12 @@ void PairSpinDmi::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; int *type = atom->type; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; @@ -296,32 +295,32 @@ void PairSpinDmi::compute(int eflag, int vflag) // compute dmi interaction if (rsq <= local_cut2) { - compute_dmi(i,j,eij,fmi,spj); - if (lattice_flag) { - compute_dmi_mech(i,j,rsq,eij,fi,spi,spj); - } + compute_dmi(i,j,eij,fmi,spj); + if (lattice_flag) { + compute_dmi_mech(i,j,rsq,eij,fi,spi,spj); + } } - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { - evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); - evdwl *= hbar; + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); } } @@ -329,7 +328,9 @@ void PairSpinDmi::compute(int eflag, int vflag) } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + update the pair interactions fmi acting on the spin ii +------------------------------------------------------------------------- */ void PairSpinDmi::compute_single_pair(int ii, double fmi[3]) { @@ -341,52 +342,76 @@ void PairSpinDmi::compute_single_pair(int ii, double fmi[3]) double delx,dely,delz; double spj[3]; - int i,j,jnum,itype,jtype; - int *ilist,*jlist,*numneigh,**firstneigh; + int j,jnum,itype,jtype,ntypes; + int k,locflag; + int *jlist,*numneigh,**firstneigh; double rsq, inorm; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - i = ilist[ii]; - itype = type[i]; - - xi[0] = x[i][0]; - xi[1] = x[i][1]; - xi[2] = x[i][2]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (int jj = 0; jj < jnum; jj++) { - - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - - delx = xi[0] - x[j][0]; - dely = xi[1] - x[j][1]; - delz = xi[2] - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - inorm = 1.0/sqrt(rsq); - eij[0] = -inorm*delx; - eij[1] = -inorm*dely; - eij[2] = -inorm*delz; - - local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype]; - - if (rsq <= local_cut2) { - compute_dmi(i,j,eij,fmi,spj); - } + // check if interaction applies to type of ii + itype = type[ii]; + ntypes = atom->ntypes; + locflag = 0; + k = 1; + while (k <= ntypes) { + if (k <= itype) { + if (setflag[k][itype] == 1) { + locflag =1; + break; + } + k++; + } else if (k > itype) { + if (setflag[itype][k] == 1) { + locflag =1; + break; + } + k++; + } else error->all(FLERR,"Wrong type number"); } + // if interaction applies to type ii, + // locflag = 1 and compute pair interaction + + //i = ilist[ii]; + if (locflag == 1) { + + xi[0] = x[ii][0]; + xi[1] = x[ii][1]; + xi[2] = x[ii][2]; + + jlist = firstneigh[ii]; + jnum = numneigh[ii]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + local_cut2 = cut_spin_dmi[itype][jtype]*cut_spin_dmi[itype][jtype]; + + if (rsq <= local_cut2) { + compute_dmi(ii,j,eij,fmi,spj); + } + } + } } /* ---------------------------------------------------------------------- @@ -397,7 +422,7 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double { int *type = atom->type; int itype, jtype; - double dmix, dmiy, dmiz; + double dmix, dmiy, dmiz; itype = type[i]; jtype = type[j]; @@ -414,12 +439,12 @@ void PairSpinDmi::compute_dmi(int i, int j, double eij[3], double fmi[3], double compute the mechanical force due to the dmi interaction between atom i and atom j ------------------------------------------------------------------------- */ -void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3], +void PairSpinDmi::compute_dmi_mech(int i, int j, double rsq, double /*eij*/[3], double fi[3], double spi[3], double spj[3]) { int *type = atom->type; int itype, jtype; - double dmix,dmiy,dmiz; + double dmix,dmiy,dmiz; itype = type[i]; jtype = type[j]; double csx,csy,csz,cdmx,cdmy,cdmz,irij; @@ -484,7 +509,7 @@ void PairSpinDmi::write_restart(FILE *fp) for (j = i; j <= atom->ntypes; j++) { fwrite(&setflag[i][j],sizeof(int),1,fp); if (setflag[i][j]) { - fwrite(&DM[i][j],sizeof(double),1,fp); + fwrite(&DM[i][j],sizeof(double),1,fp); fwrite(&v_dmx[i][j],sizeof(double),1,fp); fwrite(&v_dmy[i][j],sizeof(double),1,fp); fwrite(&v_dmz[i][j],sizeof(double),1,fp); diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp index cc074bb97d..cb3242c711 100644 --- a/src/SPIN/pair_spin_exchange.cpp +++ b/src/SPIN/pair_spin_exchange.cpp @@ -97,7 +97,7 @@ void PairSpinExchange::settings(int narg, char **arg) } /* ---------------------------------------------------------------------- - set coeffs for one or more type spin pairs (only one for now) + set coeffs for one or more type spin pairs ------------------------------------------------------------------------- */ void PairSpinExchange::coeff(int narg, char **arg) @@ -134,7 +134,7 @@ void PairSpinExchange::coeff(int narg, char **arg) count++; } } - + if (count == 0) error->all(FLERR,"Incorrect args in pair_style command"); } @@ -160,8 +160,8 @@ void PairSpinExchange::init_style() if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; ifix++; } - if (ifix == modify->nfix) - error->all(FLERR,"pair/spin style requires nve/spin"); + if ((ifix == modify->nfix) && (comm->me == 0)) + error->warning(FLERR,"Using pair/spin style without nve/spin"); // get the lattice_flag from nve/spin @@ -218,13 +218,12 @@ void PairSpinExchange::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; double **fm = atom->fm; - double **sp = atom->sp; + double **sp = atom->sp; int *type = atom->type; int nlocal = atom->nlocal; int newton_pair = force->newton_pair; @@ -279,32 +278,32 @@ void PairSpinExchange::compute(int eflag, int vflag) // compute exchange interaction if (rsq <= local_cut2) { - compute_exchange(i,j,rsq,fmi,spj); + compute_exchange(i,j,rsq,fmi,spj); if (lattice_flag) { - compute_exchange_mech(i,j,rsq,eij,fi,spi,spj); - } + compute_exchange_mech(i,j,rsq,eij,fi,spi,spj); + } } - f[i][0] += fi[0]; - f[i][1] += fi[1]; + f[i][0] += fi[0]; + f[i][1] += fi[1]; f[i][2] += fi[2]; - fm[i][0] += fmi[0]; - fm[i][1] += fmi[1]; + fm[i][0] += fmi[0]; + fm[i][1] += fmi[1]; fm[i][2] += fmi[2]; if (newton_pair || j < nlocal) { - f[j][0] -= fi[0]; - f[j][1] -= fi[1]; + f[j][0] -= fi[0]; + f[j][1] -= fi[1]; f[j][2] -= fi[2]; } if (eflag) { - evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); - evdwl *= hbar; + evdwl -= (spi[0]*fmi[0] + spi[1]*fmi[1] + spi[2]*fmi[2]); + evdwl *= hbar; } else evdwl = 0.0; if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair, - evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); + evdwl,ecoul,fi[0],fi[1],fi[2],delx,dely,delz); } } @@ -318,55 +317,78 @@ void PairSpinExchange::compute(int eflag, int vflag) void PairSpinExchange::compute_single_pair(int ii, double fmi[3]) { - int *type = atom->type; double **x = atom->x; double **sp = atom->sp; double local_cut2; - double xi[3], rij[3]; + double xi[3]; double delx,dely,delz; double spj[3]; - int i,j,jnum,itype,jtype; - int *ilist,*jlist,*numneigh,**firstneigh; + int j,jnum,itype,jtype,ntypes; + int k,locflag; + int *jlist,*numneigh,**firstneigh; double rsq; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - i = ilist[ii]; - itype = type[i]; + // check if interaction applies to type of ii - xi[0] = x[i][0]; - xi[1] = x[i][1]; - xi[2] = x[i][2]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (int jj = 0; jj < jnum; jj++) { - - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype]; - - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - - delx = xi[0] - x[j][0]; - dely = xi[1] - x[j][1]; - delz = xi[2] - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - - if (rsq <= local_cut2) { - compute_exchange(i,j,rsq,fmi,spj); - } + itype = type[ii]; + ntypes = atom->ntypes; + locflag = 0; + k = 1; + while (k <= ntypes) { + if (k <= itype) { + if (setflag[k][itype] == 1) { + locflag =1; + break; + } + k++; + } else if (k > itype) { + if (setflag[itype][k] == 1) { + locflag =1; + break; + } + k++; + } else error->all(FLERR,"Wrong type number"); } + // if interaction applies to type ii, + // locflag = 1 and compute pair interaction + + if (locflag == 1) { + + xi[0] = x[ii][0]; + xi[1] = x[ii][1]; + xi[2] = x[ii][2]; + + jlist = firstneigh[ii]; + jnum = numneigh[ii]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + local_cut2 = cut_spin_exchange[itype][jtype]*cut_spin_exchange[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + + if (rsq <= local_cut2) { + compute_exchange(ii,j,rsq,fmi,spj); + } + } + } } /* ---------------------------------------------------------------------- @@ -395,7 +417,7 @@ void PairSpinExchange::compute_exchange(int i, int j, double rsq, double fmi[3], compute the mechanical force due to the exchange interaction between atom i and atom j ------------------------------------------------------------------------- */ -void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3], +void PairSpinExchange::compute_exchange_mech(int i, int j, double rsq, double eij[3], double fi[3], double spi[3], double spj[3]) { int *type = atom->type; @@ -528,3 +550,4 @@ void PairSpinExchange::read_restart_settings(FILE *fp) MPI_Bcast(&mix_flag,1,MPI_INT,0,world); } + diff --git a/src/SPIN/pair_spin_magelec.cpp b/src/SPIN/pair_spin_magelec.cpp index 570c995754..6ff003521d 100644 --- a/src/SPIN/pair_spin_magelec.cpp +++ b/src/SPIN/pair_spin_magelec.cpp @@ -142,7 +142,6 @@ void PairSpinMagelec::coeff(int narg, char **arg) } if (count == 0) error->all(FLERR,"Incorrect args in pair_style command"); - } /* ---------------------------------------------------------------------- @@ -167,8 +166,8 @@ void PairSpinMagelec::init_style() if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; ifix++; } - if (ifix == modify->nfix) - error->all(FLERR,"pair/spin style requires nve/spin"); + if ((ifix == modify->nfix) && (comm->me == 0)) + error->warning(FLERR,"Using pair/spin style without nve/spin"); // get the lattice_flag from nve/spin @@ -226,8 +225,7 @@ void PairSpinMagelec::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -287,7 +285,7 @@ void PairSpinMagelec::compute(int eflag, int vflag) // compute me interaction if (rsq <= local_cut2) { - compute_magelec(i,j,rsq,eij,fmi,spj); + compute_magelec(i,j,eij,fmi,spj); if (lattice_flag) { compute_magelec_mech(i,j,fi,spi,spj); } @@ -320,7 +318,9 @@ void PairSpinMagelec::compute(int eflag, int vflag) } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + update the pair interactions fmi acting on the spin ii +------------------------------------------------------------------------- */ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3]) { @@ -332,55 +332,79 @@ void PairSpinMagelec::compute_single_pair(int ii, double fmi[3]) double delx,dely,delz; double spj[3]; - int i,j,jnum,itype,jtype; - int *ilist,*jlist,*numneigh,**firstneigh; + int j,jnum,itype,jtype,ntypes; + int k,locflag; + int *jlist,*numneigh,**firstneigh; double rsq, inorm; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - i = ilist[ii]; - itype = type[i]; + // check if interaction applies to type of ii - xi[0] = x[i][0]; - xi[1] = x[i][1]; - xi[2] = x[i][2]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (int jj = 0; jj < jnum; jj++) { - - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype]; - - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - - delx = xi[0] - x[j][0]; - dely = xi[1] - x[j][1]; - delz = xi[2] - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - inorm = 1.0/sqrt(rsq); - eij[0] = -inorm*delx; - eij[1] = -inorm*dely; - eij[2] = -inorm*delz; - - if (rsq <= local_cut2) { - compute_magelec(i,j,rsq,eij,fmi,spj); - } + itype = type[ii]; + ntypes = atom->ntypes; + locflag = 0; + k = 1; + while (k <= ntypes) { + if (k <= itype) { + if (setflag[k][itype] == 1) { + locflag =1; + break; + } + k++; + } else if (k > itype) { + if (setflag[itype][k] == 1) { + locflag =1; + break; + } + k++; + } else error->all(FLERR,"Wrong type number"); } + // if interaction applies to type ii, + // locflag = 1 and compute pair interaction + + if (locflag == 1) { + + xi[0] = x[ii][0]; + xi[1] = x[ii][1]; + xi[2] = x[ii][2]; + + jlist = firstneigh[ii]; + jnum = numneigh[ii]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + local_cut2 = cut_spin_magelec[itype][jtype]*cut_spin_magelec[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + delx = xi[0] - x[j][0]; + dely = xi[1] - x[j][1]; + delz = xi[2] - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + inorm = 1.0/sqrt(rsq); + eij[0] = -inorm*delx; + eij[1] = -inorm*dely; + eij[2] = -inorm*delz; + + if (rsq <= local_cut2) { + compute_magelec(ii,j,eij,fmi,spj); + } + } + } } /* ---------------------------------------------------------------------- */ -void PairSpinMagelec::compute_magelec(int i, int j, double /*rsq*/, double eij[3], double fmi[3], double spj[3]) +void PairSpinMagelec::compute_magelec(int i, int j, double eij[3], double fmi[3], double spj[3]) { int *type = atom->type; int itype, jtype; diff --git a/src/SPIN/pair_spin_magelec.h b/src/SPIN/pair_spin_magelec.h index ce13476271..5e72a4c35e 100644 --- a/src/SPIN/pair_spin_magelec.h +++ b/src/SPIN/pair_spin_magelec.h @@ -37,7 +37,7 @@ class PairSpinMagelec : public PairSpin { void compute(int, int); void compute_single_pair(int, double *); - void compute_magelec(int, int, double, double *, double *, double *); + void compute_magelec(int, int, double *, double *, double *); void compute_magelec_mech(int, int, double *, double *, double *); void write_restart(FILE *); diff --git a/src/SPIN/pair_spin_neel.cpp b/src/SPIN/pair_spin_neel.cpp index 55f537cf4f..a39d6f3461 100644 --- a/src/SPIN/pair_spin_neel.cpp +++ b/src/SPIN/pair_spin_neel.cpp @@ -173,8 +173,8 @@ void PairSpinNeel::init_style() if (strcmp(modify->fix[ifix]->style,"nve/spin") == 0) break; ifix++; } - if (ifix == modify->nfix) - error->all(FLERR,"pair/spin style requires nve/spin"); + if ((ifix == modify->nfix) && (comm->me == 0)) + error->warning(FLERR,"Using pair/spin style without nve/spin"); // get the lattice_flag from nve/spin @@ -232,8 +232,7 @@ void PairSpinNeel::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -330,7 +329,9 @@ void PairSpinNeel::compute(int eflag, int vflag) } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + update the pair interactions fmi acting on the spin ii +------------------------------------------------------------------------- */ void PairSpinNeel::compute_single_pair(int ii, double fmi[3]) { @@ -342,57 +343,81 @@ void PairSpinNeel::compute_single_pair(int ii, double fmi[3]) double xi[3], rij[3], eij[3]; double spi[3], spj[3]; - int i,j,jnum,itype,jtype; - int *ilist,*jlist,*numneigh,**firstneigh; + int j,jnum,itype,jtype,ntypes; + int k,locflag; + int *jlist,*numneigh,**firstneigh; double rsq, inorm; - ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - i = ilist[ii]; - itype = type[i]; + // check if interaction applies to type of ii - spi[0] = sp[i][0]; - spi[1] = sp[i][1]; - spi[2] = sp[i][2]; - - xi[0] = x[i][0]; - xi[1] = x[i][1]; - xi[2] = x[i][2]; - - eij[0] = eij[1] = eij[2] = 0.0; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (int jj = 0; jj < jnum; jj++) { - - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - - local_cut2 = cut_spin_neel[itype][jtype]*cut_spin_neel[itype][jtype]; - - spj[0] = sp[j][0]; - spj[1] = sp[j][1]; - spj[2] = sp[j][2]; - - rij[0] = x[j][0] - xi[0]; - rij[1] = x[j][1] - xi[1]; - rij[2] = x[j][2] - xi[2]; - rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; - inorm = 1.0/sqrt(rsq); - eij[0] = inorm*rij[0]; - eij[1] = inorm*rij[1]; - eij[2] = inorm*rij[2]; - - if (rsq <= local_cut2) { - compute_neel(i,j,rsq,eij,fmi,spi,spj); - } + itype = type[ii]; + ntypes = atom->ntypes; + locflag = 0; + k = 1; + while (k <= ntypes) { + if (k <= itype) { + if (setflag[k][itype] == 1) { + locflag =1; + break; + } + k++; + } else if (k > itype) { + if (setflag[itype][k] == 1) { + locflag =1; + break; + } + k++; + } else error->all(FLERR,"Wrong type number"); } + // if interaction applies to type ii, + // locflag = 1 and compute pair interaction + + if (locflag == 1) { + + spi[0] = sp[ii][0]; + spi[1] = sp[ii][1]; + spi[2] = sp[ii][2]; + + xi[0] = x[ii][0]; + xi[1] = x[ii][1]; + xi[2] = x[ii][2]; + + eij[0] = eij[1] = eij[2] = 0.0; + + jlist = firstneigh[ii]; + jnum = numneigh[ii]; + + for (int jj = 0; jj < jnum; jj++) { + + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + local_cut2 = cut_spin_neel[itype][jtype]*cut_spin_neel[itype][jtype]; + + spj[0] = sp[j][0]; + spj[1] = sp[j][1]; + spj[2] = sp[j][2]; + + rij[0] = x[j][0] - xi[0]; + rij[1] = x[j][1] - xi[1]; + rij[2] = x[j][2] - xi[2]; + rsq = rij[0]*rij[0] + rij[1]*rij[1] + rij[2]*rij[2]; + inorm = 1.0/sqrt(rsq); + eij[0] = inorm*rij[0]; + eij[1] = inorm*rij[1]; + eij[2] = inorm*rij[2]; + + if (rsq <= local_cut2) { + compute_neel(ii,j,rsq,eij,fmi,spi,spj); + } + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/SRD/fix_srd.cpp b/src/SRD/fix_srd.cpp index 186f51e06a..d87d2b5e56 100644 --- a/src/SRD/fix_srd.cpp +++ b/src/SRD/fix_srd.cpp @@ -1348,7 +1348,7 @@ void FixSRD::collisions_single() atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1); if (insideflag == INSIDE_ERROR) error->one(FLERR,str); error->warning(FLERR,str); - } else{ + } else { sprintf(str, "SRD particle " TAGINT_FORMAT " started " "inside wall %d on step " BIGINT_FORMAT " bounce %d", @@ -1507,7 +1507,7 @@ void FixSRD::collisions_multi() atom->tag[i],atom->tag[j],update->ntimestep,ibounce+1); if (insideflag == INSIDE_ERROR) error->one(FLERR,str); error->warning(FLERR,str); - } else{ + } else { sprintf(str, "SRD particle " TAGINT_FORMAT " started " "inside wall %d on step " BIGINT_FORMAT " bounce %d", diff --git a/src/SRD/fix_srd.h b/src/SRD/fix_srd.h index e14652e526..b86b3d9f9b 100644 --- a/src/SRD/fix_srd.h +++ b/src/SRD/fix_srd.h @@ -373,7 +373,7 @@ This may indicate a problem with your simulation parameters. E: Big particle in fix srd cannot be point particle -Big particles must be extended spheriods or ellipsoids. +Big particles must be extended spheroids or ellipsoids. E: Cannot use lines with fix srd unless overlap is set diff --git a/src/STUBS/mpi.c b/src/STUBS/mpi.c index 281a12a4e7..053108fee8 100644 --- a/src/STUBS/mpi.c +++ b/src/STUBS/mpi.c @@ -463,8 +463,8 @@ int MPI_Allreduce(void *sendbuf, void *recvbuf, int count, /* copy values from data1 to data2 */ int MPI_Reduce(void *sendbuf, void *recvbuf, int count, - MPI_Datatype datatype, MPI_Op op, - int root, MPI_Comm comm) + MPI_Datatype datatype, MPI_Op op, + int root, MPI_Comm comm) { int n = count * stubtypesize(datatype); @@ -550,8 +550,8 @@ int MPI_Gather(void *sendbuf, int sendcount, MPI_Datatype sendtype, /* copy values from data1 to data2 */ int MPI_Gatherv(void *sendbuf, int sendcount, MPI_Datatype sendtype, - void *recvbuf, int *recvcounts, int *displs, - MPI_Datatype recvtype, int root, MPI_Comm comm) + void *recvbuf, int *recvcounts, int *displs, + MPI_Datatype recvtype, int root, MPI_Comm comm) { int n = sendcount * stubtypesize(sendtype); @@ -581,8 +581,8 @@ int MPI_Scatter(void *sendbuf, int sendcount, MPI_Datatype sendtype, /* copy values from data1 to data2 */ int MPI_Scatterv(void *sendbuf, int *sendcounts, int *displs, - MPI_Datatype sendtype, void *recvbuf, int recvcount, - MPI_Datatype recvtype, int root, MPI_Comm comm) + MPI_Datatype sendtype, void *recvbuf, int recvcount, + MPI_Datatype recvtype, int root, MPI_Comm comm) { int n = recvcount * stubtypesize(recvtype); diff --git a/src/USER-ADIOS/Install.sh b/src/USER-ADIOS/Install.sh new file mode 100644 index 0000000000..434df14f60 --- /dev/null +++ b/src/USER-ADIOS/Install.sh @@ -0,0 +1,93 @@ +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +for file in *.cpp *.h; do + action $file +done + +# edit 2 Makefile.package files to include/exclude package info + +if (test $1 = 1) then + + CONFIGSCRIPT=none + if ( test `which adios2-config 2>> /dev/null` ) then + CONFIGSCRIPT=adios2-config + elif ( ! test -z "$ADIOS2_DIR" ) then + if ( test `which $ADIOS2_DIR/bin/adios2-config` ) then + CONFIGSCRIPT=$ADIOS2_DIR/bin/adios2-config + else + echo "ERROR: ADIOS2_DIR environment variable is set but" \ + "\$ADIOS2_DIR/bin/adios2-config does not exist" + fi + elif ( ! test -z "$ADIOS_DIR" ) then + if ( test `which $ADIOS_DIR/bin/adios2-config` ) then + CONFIGSCRIPT=$ADIOS_DIR/bin/adios2-config + else + echo "ERROR: ADIOS_DIR environment variable is set but" \ + "\$ADIOS_DIR/bin/adios2-config does not exist" + fi + else + echo "ERROR: ADIOS2_DIR environment variable must point to ADIOS 2.x" \ + "installation directory or adios2-config should be in PATH" + fi + + if [ "$CONFIGSCRIPT" != "none" ]; then + ADIOS2_INC=`$CONFIGSCRIPT --cxx-flags` + ADIOS2_LIB=`$CONFIGSCRIPT --cxx-libs` + + echo "adios_SYSINC=${ADIOS2_INC} +adios_SYSLIB=${ADIOS2_LIB} +" > Makefile.lammps + + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*adios[^ \t]* //g' ../Makefile.package + sed -i -e '/^adios_SYS.*$/d' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(adios_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(adios_SYSLIB) |' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ../USER-ADIOS/Makefile.lammps +' ../Makefile.package.settings + fi + fi + +elif (test $1 = 0) then + + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*adios[^ \t]* //g' ../Makefile.package + sed -i -e '/^adios_SYS.*$/d' ../Makefile.package + fi + + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*ADIOS.*$/d' ../Makefile.package.settings + fi + + rm -f Makefile.lammps + +fi diff --git a/src/USER-ADIOS/README b/src/USER-ADIOS/README new file mode 100644 index 0000000000..49717a741f --- /dev/null +++ b/src/USER-ADIOS/README @@ -0,0 +1,16 @@ +This package provides the adios dump and restart styles. + +See the doc page for the "dump adios" and "restart adios" commands. +These styles require having ADIOS 2.x itself installed on your system. + +Configure LAMMPS with CMake + a. set the environment variable + ADIOS2_DIR + to the ADIOS 2.x installation path + b. use the cmake option + -D PKG_USER-ADIOS=yes + +The person who created this package is Norbert Podhorszki (Oak Ridge National Laboratory); +If you need help, please submit a ticket at the OLCF ticket user support mentioning his name in the ticket. +https://www.olcf.ornl.gov/support/submit-ticket + diff --git a/src/USER-ADIOS/dump_atom_adios.cpp b/src/USER-ADIOS/dump_atom_adios.cpp new file mode 100644 index 0000000000..55d6c5fbf9 --- /dev/null +++ b/src/USER-ADIOS/dump_atom_adios.cpp @@ -0,0 +1,339 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Norbert Podhorszki (ORNL) +------------------------------------------------------------------------- */ + +#include "dump_atom_adios.h" +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "memory.h" +#include "universe.h" +#include "update.h" +#include + +#include "adios2.h" + +using namespace LAMMPS_NS; + +#define MAX_TEXT_HEADER_SIZE 4096 +#define DUMP_BUF_CHUNK_SIZE 16384 +#define DUMP_BUF_INCREMENT_SIZE 4096 + +namespace LAMMPS_NS +{ +class DumpAtomADIOSInternal +{ + +public: + DumpAtomADIOSInternal(){}; + ~DumpAtomADIOSInternal() = default; + + // name of adios group, referrable in adios2_config.xml + const std::string ioName = "atom"; + adios2::ADIOS *ad = nullptr; // adios object + adios2::IO io; // adios group of variables and attributes in this dump + adios2::Engine fh; // adios file/stream handle object + // one ADIOS output variable we need to change every step + adios2::Variable varAtoms; +}; +} + +/* ---------------------------------------------------------------------- */ + +DumpAtomADIOS::DumpAtomADIOS(LAMMPS *lmp, int narg, char **arg) +: DumpAtom(lmp, narg, arg) +{ + internal = new DumpAtomADIOSInternal(); + internal->ad = + new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON); +} + +/* ---------------------------------------------------------------------- */ + +DumpAtomADIOS::~DumpAtomADIOS() +{ + if (internal->fh) { + internal->fh.Close(); + } + delete internal->ad; + delete internal; +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtomADIOS::openfile() +{ + if (multifile) { + // if one file per timestep, replace '*' with current timestep + char *filestar = strdup(filename); + char *filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar, '*'); + *ptr = '\0'; + if (padflag == 0) + snprintf(filecurrent, sizeof(filecurrent), "%s" BIGINT_FORMAT "%s", + filestar, update->ntimestep, ptr + 1); + else { + char bif[8], pad[16]; + strcpy(bif, BIGINT_FORMAT); + snprintf(pad, sizeof(pad), "%%s%%0%d%s%%s", padflag, &bif[1]); + snprintf(filecurrent, sizeof(filecurrent), pad, filestar, + update->ntimestep, ptr + 1); + } + internal->fh = + internal->io.Open(filecurrent, adios2::Mode::Write, world); + if (!internal->fh) { + char str[128]; + snprintf(str, sizeof(str), "Cannot open dump file %s", filecurrent); + error->one(FLERR, str); + } + free(filestar); + delete[] filecurrent; + } else { + if (!singlefile_opened) { + internal->fh = + internal->io.Open(filename, adios2::Mode::Write, world); + if (!internal->fh) { + char str[128]; + snprintf(str, sizeof(str), "Cannot open dump file %s", + filename); + error->one(FLERR, str); + } + singlefile_opened = 1; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtomADIOS::write() +{ + if (domain->triclinic == 0) { + boxxlo = domain->boxlo[0]; + boxxhi = domain->boxhi[0]; + boxylo = domain->boxlo[1]; + boxyhi = domain->boxhi[1]; + boxzlo = domain->boxlo[2]; + boxzhi = domain->boxhi[2]; + } else { + boxxlo = domain->boxlo_bound[0]; + boxxhi = domain->boxhi_bound[0]; + boxylo = domain->boxlo_bound[1]; + boxyhi = domain->boxhi_bound[1]; + boxzlo = domain->boxlo_bound[2]; + boxzhi = domain->boxhi_bound[2]; + boxxy = domain->xy; + boxxz = domain->xz; + boxyz = domain->yz; + } + + // nme = # of dump lines this proc contributes to dump + + nme = count(); + + // ntotal = total # of atoms in snapshot + // atomOffset = sum of # of atoms up to this proc (exclusive prefix sum) + + bigint bnme = nme; + MPI_Allreduce(&bnme, &ntotal, 1, MPI_LMP_BIGINT, MPI_SUM, world); + + bigint atomOffset; // sum of all atoms on processes 0..me-1 + MPI_Scan(&bnme, &atomOffset, 1, MPI_LMP_BIGINT, MPI_SUM, world); + atomOffset -= nme; // exclusive prefix sum needed + + // Now we know the global size and the local subset size and offset + // of the atoms table + size_t nAtomsGlobal = static_cast(ntotal); + size_t startRow = static_cast(atomOffset); + size_t nAtomsLocal = static_cast(nme); + size_t nColumns = static_cast(size_one); + internal->varAtoms.SetShape({nAtomsGlobal, nColumns}); + internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}}); + + // insure buf is sized for packing + // adios does not limit per-process data size so nme*size_one is not + // constrained to int + // if sorting on IDs also request ID list from pack() + // sort buf as needed + + if (nme > maxbuf) { + maxbuf = nme; + memory->destroy(buf); + memory->create(buf, (maxbuf * size_one), "dump:buf"); + } + if (sort_flag && sortcol == 0 && nme > maxids) { + maxids = nme; + memory->destroy(ids); + memory->create(ids, maxids, "dump:ids"); + } + + if (sort_flag && sortcol == 0) + pack(ids); + else + pack(NULL); + if (sort_flag) + sort(); + + openfile(); + internal->fh.BeginStep(); + // write info on data as scalars (by me==0) + if (me == 0) { + internal->fh.Put("ntimestep", update->ntimestep); + internal->fh.Put("nprocs", nprocs); + + internal->fh.Put("boxxlo", boxxlo); + internal->fh.Put("boxxhi", boxxhi); + internal->fh.Put("boxylo", boxylo); + internal->fh.Put("boxyhi", boxyhi); + internal->fh.Put("boxzlo", boxzlo); + internal->fh.Put("boxzhi", boxzhi); + + if (domain->triclinic) { + internal->fh.Put("boxxy", boxxy); + internal->fh.Put("boxxz", boxxz); + internal->fh.Put("boxyz", boxyz); + } + } + // Everyone needs to write scalar variables that are used as dimensions and + // offsets of arrays + internal->fh.Put("natoms", ntotal); + internal->fh.Put("ncolumns", size_one); + internal->fh.Put("nme", bnme); + internal->fh.Put("offset", atomOffset); + // now write the atoms + internal->fh.Put(internal->varAtoms, buf); + internal->fh.EndStep(); // I/O will happen now... + + if (multifile) { + internal->fh.Close(); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpAtomADIOS::init_style() +{ + if (image_flag == 0) + size_one = 5; + else + size_one = 8; + + // setup boundary string + + domain->boundary_string(boundstr); + + // remove % from filename since ADIOS always writes a global file with + // data/metadata + int len = strlen(filename); + char *ptr = strchr(filename, '%'); + if (ptr) { + *ptr = '\0'; + char *s = new char[len - 1]; + snprintf(s, sizeof(s), "%s%s", filename, ptr + 1); + strncpy(filename, s, len); + } + + // setup column string + + if (scale_flag == 0 && image_flag == 0) + columns = (char *)"id type x y z"; + else if (scale_flag == 0 && image_flag == 1) + columns = (char *)"id type x y z ix iy iz"; + else if (scale_flag == 1 && image_flag == 0) + columns = (char *)"id type xs ys zs"; + else if (scale_flag == 1 && image_flag == 1) + columns = (char *)"id type xs ys zs ix iy iz"; + + // setup function ptrs + + if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 0) + pack_choice = &DumpAtomADIOS::pack_scale_noimage; + else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 0) + pack_choice = &DumpAtomADIOS::pack_scale_image; + else if (scale_flag == 1 && image_flag == 0 && domain->triclinic == 1) + pack_choice = &DumpAtomADIOS::pack_scale_noimage_triclinic; + else if (scale_flag == 1 && image_flag == 1 && domain->triclinic == 1) + pack_choice = &DumpAtomADIOS::pack_scale_image_triclinic; + else if (scale_flag == 0 && image_flag == 0) + pack_choice = &DumpAtomADIOS::pack_noscale_noimage; + else if (scale_flag == 0 && image_flag == 1) + pack_choice = &DumpAtomADIOS::pack_noscale_image; + + /* Define the group of variables for the atom style here since it's a fixed + * set */ + internal->io = internal->ad->DeclareIO(internal->ioName); + if (!internal->io.InConfigFile()) { + // if not defined by user, we can change the default settings + // BPFile is the default writer + internal->io.SetEngine("BPFile"); + int num_aggregators = multiproc; + if (num_aggregators == 0) + num_aggregators = 1; + char nstreams[128]; + snprintf(nstreams, sizeof(nstreams), "%d", num_aggregators); + internal->io.SetParameters({{"substreams", nstreams}}); + if (me == 0 && screen) + fprintf( + screen, + "ADIOS method for %s is n-to-m (aggregation with %s writers)\n", + filename, nstreams); + } + + internal->io.DefineVariable("ntimestep"); + internal->io.DefineVariable("natoms"); + + internal->io.DefineVariable("nprocs"); + internal->io.DefineVariable("ncolumns"); + + internal->io.DefineVariable("boxxlo"); + internal->io.DefineVariable("boxxhi"); + internal->io.DefineVariable("boxylo"); + internal->io.DefineVariable("boxyhi"); + internal->io.DefineVariable("boxzlo"); + internal->io.DefineVariable("boxzhi"); + + internal->io.DefineVariable("boxxy"); + internal->io.DefineVariable("boxxz"); + internal->io.DefineVariable("boxyz"); + + internal->io.DefineAttribute("triclinic", domain->triclinic); + internal->io.DefineAttribute("scaled", scale_flag); + internal->io.DefineAttribute("image", image_flag); + + int *boundaryptr = reinterpret_cast(domain->boundary); + internal->io.DefineAttribute("boundary", boundaryptr, 6); + + internal->io.DefineAttribute("columns", columns); + internal->io.DefineAttribute("boundarystr", boundstr); + internal->io.DefineAttribute("LAMMPS/dump_style", "atom"); + internal->io.DefineAttribute("LAMMPS/version", + universe->version); + internal->io.DefineAttribute("LAMMPS/num_ver", + universe->num_ver); + + internal->io.DefineVariable( + "nme", {adios2::LocalValueDim}); // local dimension variable + internal->io.DefineVariable( + "offset", {adios2::LocalValueDim}); // local dimension variable + + // atom table size is not known at the moment + // it will be correctly defined at the moment of write + size_t UnknownSizeYet = 1; + size_t nColumns = static_cast(size_one); + internal->varAtoms = internal->io.DefineVariable( + "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, + {UnknownSizeYet, nColumns}); +} diff --git a/src/USER-ADIOS/dump_atom_adios.h b/src/USER-ADIOS/dump_atom_adios.h new file mode 100644 index 0000000000..dc6bc519bb --- /dev/null +++ b/src/USER-ADIOS/dump_atom_adios.h @@ -0,0 +1,62 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DUMP_CLASS +// clang-format off +DumpStyle(atom/adios, DumpAtomADIOS) +// clang-format on +#else + +#ifndef LMP_DUMP_ATOM_ADIOS_H +#define LMP_DUMP_ATOM_ADIOS_H + +#include "dump_atom.h" + +namespace LAMMPS_NS +{ + +class DumpAtomADIOSInternal; + +class DumpAtomADIOS : public DumpAtom +{ + +public: + DumpAtomADIOS(class LAMMPS *, int, char **); + virtual ~DumpAtomADIOS(); + +protected: + virtual void openfile(); + virtual void write(); + virtual void init_style(); + +private: + DumpAtomADIOSInternal *internal; +}; +} + +#endif +#endif + + /* ERROR/WARNING messages: + + E: Cannot open dump file %s + + The output file for the dump command cannot be opened. Check that the + path and name are correct. + + E: Too much per-proc info for dump + + Number of local atoms times number of columns must fit in a 32-bit + integer for dump. + + */ diff --git a/src/USER-ADIOS/dump_custom_adios.cpp b/src/USER-ADIOS/dump_custom_adios.cpp new file mode 100644 index 0000000000..67f3deeb64 --- /dev/null +++ b/src/USER-ADIOS/dump_custom_adios.cpp @@ -0,0 +1,435 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Norbert Podhorszki (ORNL) +------------------------------------------------------------------------- */ + +#include "dump_custom_adios.h" +#include "atom.h" +#include "compute.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" +#include "input.h" +#include "memory.h" +#include "modify.h" +#include "region.h" +#include "universe.h" +#include "update.h" +#include "variable.h" +#include +#include + +#include "adios2.h" + +using namespace LAMMPS_NS; + +#define MAX_TEXT_HEADER_SIZE 4096 +#define DUMP_BUF_CHUNK_SIZE 16384 +#define DUMP_BUF_INCREMENT_SIZE 4096 + +enum { + ID, + MOL, + TYPE, + ELEMENT, + MASS, + X, + Y, + Z, + XS, + YS, + ZS, + XSTRI, + YSTRI, + ZSTRI, + XU, + YU, + ZU, + XUTRI, + YUTRI, + ZUTRI, + XSU, + YSU, + ZSU, + XSUTRI, + YSUTRI, + ZSUTRI, + IX, + IY, + IZ, + VX, + VY, + VZ, + FX, + FY, + FZ, + Q, + MUX, + MUY, + MUZ, + MU, + RADIUS, + DIAMETER, + OMEGAX, + OMEGAY, + OMEGAZ, + ANGMOMX, + ANGMOMY, + ANGMOMZ, + TQX, + TQY, + TQZ, + SPIN, + ERADIUS, + ERVEL, + ERFORCE, + COMPUTE, + FIX, + VARIABLE +}; +enum { LT, LE, GT, GE, EQ, NEQ }; +enum { INT, DOUBLE, STRING, BIGINT }; // same as in DumpCustom + +namespace LAMMPS_NS +{ +class DumpCustomADIOSInternal +{ + +public: + DumpCustomADIOSInternal(){}; + ~DumpCustomADIOSInternal() = default; + + // name of adios group, referrable in adios2_config.xml + const std::string ioName = "custom"; + adios2::ADIOS *ad = nullptr; // adios object + adios2::IO io; // adios group of variables and attributes in this dump + adios2::Engine fh; // adios file/stream handle object + // one ADIOS output variable we need to change every step + adios2::Variable varAtoms; + // list of column names for the atom table + // (individual list of 'columns' string) + std::vector columnNames; +}; +} + +/* ---------------------------------------------------------------------- */ + +DumpCustomADIOS::DumpCustomADIOS(LAMMPS *lmp, int narg, char **arg) +: DumpCustom(lmp, narg, arg) +{ + internal = new DumpCustomADIOSInternal(); + internal->ad = + new adios2::ADIOS("adios2_config.xml", world, adios2::DebugON); + + // if (screen) fprintf(screen, "DumpCustomADIOS constructor: nvariable=%d + // id_variable=%p, variables=%p, nfield=%d, earg=%p\n", nvariable, + // id_variable, variable, nfield, earg); + internal->columnNames.reserve(nfield); + for (int i = 0; i < nfield; ++i) { + internal->columnNames.push_back(earg[i]); + // if (screen) fprintf(screen, "earg[%d] = '%s'\n", i, earg[i]); + } +} + +/* ---------------------------------------------------------------------- */ + +DumpCustomADIOS::~DumpCustomADIOS() +{ + internal->columnNames.clear(); + if (internal->fh) { + internal->fh.Close(); + } + delete internal->ad; + delete internal; +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustomADIOS::openfile() +{ + if (multifile) { + // if one file per timestep, replace '*' with current timestep + char *filestar = strdup(filename); + char *filecurrent = new char[strlen(filestar) + 16]; + char *ptr = strchr(filestar, '*'); + *ptr = '\0'; + if (padflag == 0) + sprintf(filecurrent, "%s" BIGINT_FORMAT "%s", filestar, + update->ntimestep, ptr + 1); + else { + char bif[8], pad[16]; + strcpy(bif, BIGINT_FORMAT); + sprintf(pad, "%%s%%0%d%s%%s", padflag, &bif[1]); + sprintf(filecurrent, pad, filestar, update->ntimestep, ptr + 1); + } + internal->fh = + internal->io.Open(filecurrent, adios2::Mode::Write, world); + if (!internal->fh) { + char str[128]; + sprintf(str, "Cannot open dump file %s", filecurrent); + error->one(FLERR, str); + } + free(filestar); + delete[] filecurrent; + } else { + if (!singlefile_opened) { + internal->fh = + internal->io.Open(filename, adios2::Mode::Write, world); + if (!internal->fh) { + char str[128]; + sprintf(str, "Cannot open dump file %s", filename); + error->one(FLERR, str); + } + singlefile_opened = 1; + } + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustomADIOS::write() +{ + if (domain->triclinic == 0) { + boxxlo = domain->boxlo[0]; + boxxhi = domain->boxhi[0]; + boxylo = domain->boxlo[1]; + boxyhi = domain->boxhi[1]; + boxzlo = domain->boxlo[2]; + boxzhi = domain->boxhi[2]; + } else { + boxxlo = domain->boxlo_bound[0]; + boxxhi = domain->boxhi_bound[0]; + boxylo = domain->boxlo_bound[1]; + boxyhi = domain->boxhi_bound[1]; + boxzlo = domain->boxlo_bound[2]; + boxzhi = domain->boxhi_bound[2]; + boxxy = domain->xy; + boxxz = domain->xz; + boxyz = domain->yz; + } + + // nme = # of dump lines this proc contributes to dump + + nme = count(); + + // ntotal = total # of atoms in snapshot + // atomOffset = sum of # of atoms up to this proc (exclusive prefix sum) + + bigint bnme = nme; + MPI_Allreduce(&bnme, &ntotal, 1, MPI_LMP_BIGINT, MPI_SUM, world); + + bigint atomOffset; // sum of all atoms on processes 0..me-1 + MPI_Scan(&bnme, &atomOffset, 1, MPI_LMP_BIGINT, MPI_SUM, world); + atomOffset -= nme; // exclusive prefix sum needed + + // Now we know the global size and the local subset size and offset + // of the atoms table + size_t nAtomsGlobal = static_cast(ntotal); + size_t startRow = static_cast(atomOffset); + size_t nAtomsLocal = static_cast(nme); + size_t nColumns = static_cast(size_one); + internal->varAtoms.SetShape({nAtomsGlobal, nColumns}); + internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}}); + + // insure filewriter proc can receive everyone's info + // limit nmax*size_one to int since used as arg in MPI_Rsend() below + // pack my data into buf + // if sorting on IDs also request ID list from pack() + // sort buf as needed + + if (nme > maxbuf) { + if ((bigint)nme * size_one > MAXSMALLINT) + error->all(FLERR, "Too much per-proc info for dump"); + maxbuf = nme; + memory->destroy(buf); + memory->create(buf, (maxbuf * size_one), "dump:buf"); + } + if (sort_flag && sortcol == 0 && nme > maxids) { + maxids = nme; + memory->destroy(ids); + memory->create(ids, maxids, "dump:ids"); + } + + if (sort_flag && sortcol == 0) + pack(ids); + else + pack(NULL); + if (sort_flag) + sort(); + + openfile(); + internal->fh.BeginStep(); + // write info on data as scalars (by me==0) + if (me == 0) { + internal->fh.Put("ntimestep", update->ntimestep); + internal->fh.Put("nprocs", nprocs); + + internal->fh.Put("boxxlo", boxxlo); + internal->fh.Put("boxxhi", boxxhi); + internal->fh.Put("boxylo", boxylo); + internal->fh.Put("boxyhi", boxyhi); + internal->fh.Put("boxzlo", boxzlo); + internal->fh.Put("boxzhi", boxzhi); + + if (domain->triclinic) { + internal->fh.Put("boxxy", boxxy); + internal->fh.Put("boxxz", boxxz); + internal->fh.Put("boxyz", boxyz); + } + } + // Everyone needs to write scalar variables that are used as dimensions and + // offsets of arrays + internal->fh.Put("natoms", ntotal); + internal->fh.Put("ncolumns", size_one); + internal->fh.Put("nme", bnme); + internal->fh.Put("offset", atomOffset); + // now write the atoms + internal->fh.Put("atoms", buf); + internal->fh.EndStep(); // I/O will happen now... + + if (multifile) { + internal->fh.Close(); + } +} + +/* ---------------------------------------------------------------------- */ + +void DumpCustomADIOS::init_style() +{ + + // setup boundary string + + domain->boundary_string(boundstr); + + // remove % from filename since ADIOS always writes a global file with + // data/metadata + int len = strlen(filename); + char *ptr = strchr(filename, '%'); + if (ptr) { + *ptr = '\0'; + char *s = new char[len - 1]; + sprintf(s, "%s%s", filename, ptr + 1); + strncpy(filename, s, len); + } + + /* The next four loops are copied from dump_custom_mpiio, but nothing is + * done with them. + * It is unclear why we need them here. + * For metadata, variable[] will be written out as an ADIOS attribute if + * nvariable>0 + */ + // find current ptr for each compute,fix,variable + // check that fix frequency is acceptable + int icompute; + for (int i = 0; i < ncompute; i++) { + icompute = modify->find_compute(id_compute[i]); + if (icompute < 0) + error->all(FLERR, "Could not find dump custom compute ID"); + compute[i] = modify->compute[icompute]; + } + + int ifix; + for (int i = 0; i < nfix; i++) { + ifix = modify->find_fix(id_fix[i]); + if (ifix < 0) + error->all(FLERR, "Could not find dump custom fix ID"); + fix[i] = modify->fix[ifix]; + if (nevery % modify->fix[ifix]->peratom_freq) + error->all(FLERR, + "Dump custom and fix not computed at compatible times"); + } + + int ivariable; + for (int i = 0; i < nvariable; i++) { + ivariable = input->variable->find(id_variable[i]); + if (ivariable < 0) + error->all(FLERR, "Could not find dump custom variable name"); + variable[i] = ivariable; + } + + // set index and check validity of region + if (iregion >= 0) { + iregion = domain->find_region(idregion); + if (iregion == -1) + error->all(FLERR, "Region ID for dump custom does not exist"); + } + + /* Define the group of variables for the atom style here since it's a fixed + * set */ + internal->io = internal->ad->DeclareIO(internal->ioName); + if (!internal->io.InConfigFile()) { + // if not defined by user, we can change the default settings + // BPFile is the default writer + internal->io.SetEngine("BPFile"); + int num_aggregators = multiproc; + if (num_aggregators == 0) + num_aggregators = 1; + char nstreams[128]; + sprintf(nstreams, "%d", num_aggregators); + internal->io.SetParameters({{"substreams", nstreams}}); + if (me == 0 && screen) + fprintf( + screen, + "ADIOS method for %s is n-to-m (aggregation with %s writers)\n", + filename, nstreams); + } + + internal->io.DefineVariable("ntimestep"); + internal->io.DefineVariable("natoms"); + + internal->io.DefineVariable("nprocs"); + internal->io.DefineVariable("ncolumns"); + + internal->io.DefineVariable("boxxlo"); + internal->io.DefineVariable("boxxhi"); + internal->io.DefineVariable("boxylo"); + internal->io.DefineVariable("boxyhi"); + internal->io.DefineVariable("boxzlo"); + internal->io.DefineVariable("boxzhi"); + + internal->io.DefineVariable("boxxy"); + internal->io.DefineVariable("boxxz"); + internal->io.DefineVariable("boxyz"); + + internal->io.DefineAttribute("triclinic", domain->triclinic); + + int *boundaryptr = reinterpret_cast(domain->boundary); + internal->io.DefineAttribute("boundary", boundaryptr, 6); + + size_t nColumns = static_cast(size_one); + internal->io.DefineAttribute( + "columns", internal->columnNames.data(), nColumns); + internal->io.DefineAttribute("columnstr", columns); + internal->io.DefineAttribute("boundarystr", boundstr); + internal->io.DefineAttribute("LAMMPS/dump_style", "atom"); + internal->io.DefineAttribute("LAMMPS/version", + universe->version); + internal->io.DefineAttribute("LAMMPS/num_ver", + universe->num_ver); + + internal->io.DefineVariable( + "nme", {adios2::LocalValueDim}); // local dimension variable + internal->io.DefineVariable( + "offset", {adios2::LocalValueDim}); // local dimension variable + + // atom table size is not known at the moment + // it will be correctly defined at the moment of write + size_t UnknownSizeYet = 1; + internal->varAtoms = internal->io.DefineVariable( + "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, + {UnknownSizeYet, nColumns}); +} diff --git a/src/USER-ADIOS/dump_custom_adios.h b/src/USER-ADIOS/dump_custom_adios.h new file mode 100644 index 0000000000..d5d41eb8c7 --- /dev/null +++ b/src/USER-ADIOS/dump_custom_adios.h @@ -0,0 +1,87 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef DUMP_CLASS +// clang-format off +DumpStyle(custom/adios, DumpCustomADIOS) +// clang-format on +#else + +#ifndef LMP_DUMP_CUSTOM_ADIOS_H +#define LMP_DUMP_CUSTOM_ADIOS_H + +#include "dump_custom.h" + +namespace LAMMPS_NS +{ + +class DumpCustomADIOSInternal; + +class DumpCustomADIOS : public DumpCustom +{ +public: + DumpCustomADIOS(class LAMMPS *, int, char **); + virtual ~DumpCustomADIOS(); + +protected: + virtual void openfile(); + virtual void write(); + virtual void init_style(); + +private: + DumpCustomADIOSInternal *internal; +}; +} + +#endif +#endif + + /* ERROR/WARNING messages: + + E: Cannot open dump file %s + + The output file for the dump command cannot be opened. Check that the + path and name are correct. + + E: Too much per-proc info for dump + + Number of local atoms times number of columns must fit in a 32-bit + integer for dump. + + E: Dump_modify format string is too short + + There are more fields to be dumped in a line of output than your + format string specifies. + + E: Could not find dump custom compute ID + + Self-explanatory. + + E: Could not find dump custom fix ID + + Self-explanatory. + + E: Dump custom and fix not computed at compatible times + + The fix must produce per-atom quantities on timesteps that dump custom + needs them. + + E: Could not find dump custom variable name + + Self-explanatory. + + E: Region ID for dump custom does not exist + + Self-explanatory. + + */ diff --git a/src/USER-AWPMD/pair_awpmd_cut.cpp b/src/USER-AWPMD/pair_awpmd_cut.cpp index 2dcb3e6296..1b7bf35c28 100644 --- a/src/USER-AWPMD/pair_awpmd_cut.cpp +++ b/src/USER-AWPMD/pair_awpmd_cut.cpp @@ -108,10 +108,7 @@ void PairAWPMDCut::compute(int eflag, int vflag) // pvector = [KE, Pauli, ecoul, radial_restraint] for (int i=0; i<4; i++) pvector[i] = 0.0; - if (eflag || vflag) - ev_setup(eflag,vflag); - else - evflag = vflag_fdotr = 0; //?? + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -274,13 +271,12 @@ void PairAWPMDCut::compute(int eflag, int vflag) int i = ilist[ii]; if(gmap[i]<0) // this particle was filtered out continue; - if(spin[i]==0){ // this is an ion, copying forces + if (spin[i]==0) { // this is an ion, copying forces int ion=gmap[i]; f[i][0]=fi[ion][0]; f[i][0]=fi[ion][1]; f[i][0]=fi[ion][2]; - } - else { // electron + } else { // electron int iel=gmap[i]; int s=spin[i] >0 ? 0 : 1; wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce+3*i),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce+2*i)); @@ -304,12 +300,11 @@ void PairAWPMDCut::compute(int eflag, int vflag) if (eflag_atom) { // transfer per-atom energies here for (int i = 0; i < ntot; i++) { - if(gmap[i]<0) // this particle was filtered out + if (gmap[i]<0) // this particle was filtered out continue; - if(spin[i]==0){ + if (spin[i]==0) { eatom[i]=wpmd->Eiep[gmap[i]]+wpmd->Eiip[gmap[i]]; - } - else { + } else { int s=spin[i] >0 ? 0 : 1; eatom[i]=wpmd->Eep[s][gmap[i]]+wpmd->Eeip[s][gmap[i]]+wpmd->Eeep[s][gmap[i]]+wpmd->Ewp[s][gmap[i]]; } @@ -474,9 +469,9 @@ void PairAWPMDCut::coeff(int narg, char **arg) if(cut_global<0) cut_global=half_box_length; - if (!allocated) + if (!allocated) { allocate(); - else{ + } else { int i,j; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp index bf11b1d6ba..7bdb8933e3 100644 --- a/src/USER-BOCS/fix_bocs.cpp +++ b/src/USER-BOCS/fix_bocs.cpp @@ -697,6 +697,11 @@ int FixBocs::read_F_table( char *filename, int p_basis_type ) "of %d in read_F_table",p_basis_type); error->all(FLERR,errmsg); } + // cleanup + for (i = 0; i < N_columns; ++i) { + free(data[i]); + } + free(data); return n_entries; } diff --git a/src/USER-CGDNA/README b/src/USER-CGDNA/README index d71f3b7a43..8e3f16372c 100644 --- a/src/USER-CGDNA/README +++ b/src/USER-CGDNA/README @@ -74,10 +74,10 @@ pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp: - corresponding pair styles in oxDNA2 (see [3]) + corresponding pair styles in oxDNA2 (see [3]) pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone - sites + sites ** Fixes provided by this package: diff --git a/src/USER-CGDNA/bond_oxdna_fene.cpp b/src/USER-CGDNA/bond_oxdna_fene.cpp index 34a25a9b5a..8271668e3f 100644 --- a/src/USER-CGDNA/bond_oxdna_fene.cpp +++ b/src/USER-CGDNA/bond_oxdna_fene.cpp @@ -96,8 +96,7 @@ void BondOxdnaFene::compute(int eflag, int vflag) int newton_bond = force->newton_bond; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); // loop over FENE bonds diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp index d31890ea52..f54197aea7 100644 --- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp @@ -64,6 +64,7 @@ PairOxdna2Coaxstk::~PairOxdna2Coaxstk() memory->destroy(cut_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); + memory->destroy(cutsq_cxst_hc); memory->destroy(a_cxst1); memory->destroy(theta_cxst1_0); @@ -103,9 +104,9 @@ PairOxdna2Coaxstk::~PairOxdna2Coaxstk() void PairOxdna2Coaxstk::compute(int eflag, int vflag) { - double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment; + double delf[3],delta[3],deltb[3]; // force, torque increment; double evdwl,fpair,finc,tpair,factor_lj; - double v1tmp[3],v2tmp[3],v3tmp[3]; + double v1tmp[3]; double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss; double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st; double theta1,theta1p,t1dir[3],cost1; @@ -114,12 +115,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag) double theta6,theta6p,t6dir[3],cost6; double cosphi3; - double gamma,gammacub,rinv_ss_cub,fac; - double aybx,azbx,rax,ray,raz,rbx; - double dcdr,dcdrbx; - double dcdaxbx,dcdaybx,dcdazbx; - double dcdrax,dcdray,dcdraz; - // distances COM-backbone site, COM-stacking site double d_cs=-0.4, d_cst=+0.34; // vectors COM-backbone site, COM-stacking site in lab frame @@ -149,8 +144,7 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag) double df2,df4f6t1,df4t4,df4t5,df4t6,rsint; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); anum = list->inum; alist = list->ilist; diff --git a/src/USER-CGDNA/pair_oxdna2_dh.cpp b/src/USER-CGDNA/pair_oxdna2_dh.cpp index da6e1f8bbd..10e7121427 100644 --- a/src/USER-CGDNA/pair_oxdna2_dh.cpp +++ b/src/USER-CGDNA/pair_oxdna2_dh.cpp @@ -114,8 +114,7 @@ void PairOxdna2Dh::compute(int eflag, int vflag) int a,b,ia,ib,anum,bnum,atype,btype; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); anum = list->inum; alist = list->ilist; diff --git a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp index ca03bcb35c..6d3061620d 100644 --- a/src/USER-CGDNA/pair_oxdna_coaxstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_coaxstk.cpp @@ -64,6 +64,7 @@ PairOxdnaCoaxstk::~PairOxdnaCoaxstk() memory->destroy(cut_cxst_hc); memory->destroy(b_cxst_lo); memory->destroy(b_cxst_hi); + memory->destroy(cutsq_cxst_hc); memory->destroy(a_cxst1); memory->destroy(theta_cxst1_0); @@ -155,8 +156,7 @@ void PairOxdnaCoaxstk::compute(int eflag, int vflag) double df2,df4t1,df4t4,df4t5,df4t6,df5c3,rsint; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); anum = list->inum; alist = list->ilist; diff --git a/src/USER-CGDNA/pair_oxdna_excv.cpp b/src/USER-CGDNA/pair_oxdna_excv.cpp index 719a63b5f4..82af5ed1c7 100644 --- a/src/USER-CGDNA/pair_oxdna_excv.cpp +++ b/src/USER-CGDNA/pair_oxdna_excv.cpp @@ -144,8 +144,7 @@ void PairOxdnaExcv::compute(int eflag, int vflag) int a,b,ia,ib,anum,bnum,atype,btype; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); anum = list->inum; alist = list->ilist; diff --git a/src/USER-CGDNA/pair_oxdna_hbond.cpp b/src/USER-CGDNA/pair_oxdna_hbond.cpp index cb9f61bd7e..d2aa236a05 100644 --- a/src/USER-CGDNA/pair_oxdna_hbond.cpp +++ b/src/USER-CGDNA/pair_oxdna_hbond.cpp @@ -74,6 +74,7 @@ PairOxdnaHbond::~PairOxdnaHbond() memory->destroy(b_hb_lo); memory->destroy(b_hb_hi); memory->destroy(shift_hb); + memory->destroy(cutsq_hb_hc); memory->destroy(a_hb1); memory->destroy(theta_hb1_0); @@ -160,8 +161,7 @@ void PairOxdnaHbond::compute(int eflag, int vflag) double df1,df4t1,df4t4,df4t2,df4t3,df4t7,df4t8; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); anum = list->inum; alist = list->ilist; diff --git a/src/USER-CGDNA/pair_oxdna_stk.cpp b/src/USER-CGDNA/pair_oxdna_stk.cpp index f713e4d27c..4cbc0317dd 100644 --- a/src/USER-CGDNA/pair_oxdna_stk.cpp +++ b/src/USER-CGDNA/pair_oxdna_stk.cpp @@ -154,8 +154,7 @@ void PairOxdnaStk::compute(int eflag, int vflag) double tptofp; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // loop over stacking interaction neighours using bond topology diff --git a/src/USER-CGDNA/pair_oxdna_xstk.cpp b/src/USER-CGDNA/pair_oxdna_xstk.cpp index c4c23bf2c9..071886556c 100644 --- a/src/USER-CGDNA/pair_oxdna_xstk.cpp +++ b/src/USER-CGDNA/pair_oxdna_xstk.cpp @@ -64,6 +64,7 @@ PairOxdnaXstk::~PairOxdnaXstk() memory->destroy(cut_xst_hc); memory->destroy(b_xst_lo); memory->destroy(b_xst_hi); + memory->destroy(cutsq_xst_hc); memory->destroy(a_xst1); memory->destroy(theta_xst1_0); @@ -152,8 +153,7 @@ void PairOxdnaXstk::compute(int eflag, int vflag) double df2,df4t1,df4t4,df4t2,df4t3,df4t7,df4t8,rsint; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); anum = list->inum; alist = list->ilist; diff --git a/src/USER-CGSDK/angle_sdk.cpp b/src/USER-CGSDK/angle_sdk.cpp index 6b8245b491..823c725e07 100644 --- a/src/USER-CGSDK/angle_sdk.cpp +++ b/src/USER-CGSDK/angle_sdk.cpp @@ -68,8 +68,7 @@ void AngleSDK::compute(int eflag, int vflag) double rsq1,rsq2,rsq3,r1,r2,c,s,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-CGSDK/pair_lj_sdk.cpp b/src/USER-CGSDK/pair_lj_sdk.cpp index 3404beb58a..7dd6c04436 100644 --- a/src/USER-CGSDK/pair_lj_sdk.cpp +++ b/src/USER-CGSDK/pair_lj_sdk.cpp @@ -78,9 +78,7 @@ PairLJSDK::~PairLJSDK() void PairLJSDK::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp index c51235518b..33a1659df9 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_long.cpp @@ -90,9 +90,7 @@ PairLJSDKCoulLong::~PairLJSDKCoulLong() void PairLJSDKCoulLong::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp index c4882fdbdb..d26f8efcdc 100644 --- a/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp +++ b/src/USER-CGSDK/pair_lj_sdk_coul_msm.cpp @@ -57,9 +57,7 @@ void PairLJSDKCoulMSM::compute(int eflag, int vflag) if (force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' with Pair style"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (evflag) { if (eflag) { diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp index 450c250ffa..858336c9d5 100644 --- a/src/USER-COLVARS/group_ndx.cpp +++ b/src/USER-COLVARS/group_ndx.cpp @@ -50,7 +50,7 @@ static int cmptagint(const void *p1, const void *p2) static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me, int np, MPI_Comm world, FILE *screen, FILE *logfile) { - char fmt[8]; + char fmt[16]; tagint *sendlist, *recvlist; bigint num = group->count(gid); int lnum, cols; @@ -73,7 +73,7 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me, ++i; j /= 10; } - sprintf(fmt,"%%%dd ", i); + snprintf(fmt,16,"%%%dd ", i); cols = 80 / (i+1); } diff --git a/src/USER-DIFFRACTION/compute_saed.cpp b/src/USER-DIFFRACTION/compute_saed.cpp index 3d09955275..dcafe57ba8 100644 --- a/src/USER-DIFFRACTION/compute_saed.cpp +++ b/src/USER-DIFFRACTION/compute_saed.cpp @@ -281,7 +281,7 @@ ComputeSAED::~ComputeSAED() { memory->destroy(vector); memory->destroy(store_tmp); - delete ztype; + delete[] ztype; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DIFFRACTION/compute_xrd.cpp b/src/USER-DIFFRACTION/compute_xrd.cpp index 4d5cccdc50..d6b7549272 100644 --- a/src/USER-DIFFRACTION/compute_xrd.cpp +++ b/src/USER-DIFFRACTION/compute_xrd.cpp @@ -247,7 +247,7 @@ ComputeXRD::~ComputeXRD() { memory->destroy(array); memory->destroy(store_tmp); - delete ztype; + delete[] ztype; } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-DIFFRACTION/fix_saed_vtk.cpp b/src/USER-DIFFRACTION/fix_saed_vtk.cpp index 882c13bc3e..4d9af66818 100644 --- a/src/USER-DIFFRACTION/fix_saed_vtk.cpp +++ b/src/USER-DIFFRACTION/fix_saed_vtk.cpp @@ -287,6 +287,8 @@ FixSAEDVTK::FixSAEDVTK(LAMMPS *lmp, int narg, char **arg) : FixSAEDVTK::~FixSAEDVTK() { delete [] extlist; + delete [] filename; + delete [] ids; memory->destroy(vector); memory->destroy(vector_total); if (fp && me == 0) fclose(fp); diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp index 97668471c8..cb8349786f 100644 --- a/src/USER-DPD/fix_rx.cpp +++ b/src/USER-DPD/fix_rx.cpp @@ -758,8 +758,10 @@ void FixRX::pre_force(int /*vflag*/) memory->create( diagnosticCounterPerODE[FuncSum], nlocal, "FixRX::diagnosticCounterPerODE"); } - //#pragma omp parallel \ - // reduction(+: nSteps, nIters, nFuncs, nFails ) +#if 0 + #pragma omp parallel \ + reduction(+: nSteps, nIters, nFuncs, nFails ) +#endif { double *rwork = new double[8*nspecies]; diff --git a/src/USER-DPD/nbin_ssa.cpp b/src/USER-DPD/nbin_ssa.cpp index 4c57a8e70f..dcd434cb4a 100644 --- a/src/USER-DPD/nbin_ssa.cpp +++ b/src/USER-DPD/nbin_ssa.cpp @@ -147,12 +147,12 @@ int NBinSSA::coord2ssaAIR(const double *x) if(iz < 0){ return -1; } else if(iz == 0){ - if( iy<0 ) return -1; // bottom left/middle/right - if( (iy==0) && (ix<0) ) return -1; // left atoms - if( (iy==0) && (ix==0) ) return 0; // Locally owned atoms - if( (iy==0) && (ix>0) ) return 2; // Right atoms - if( (iy>0) && (ix==0) ) return 1; // Top-middle atoms - if( (iy>0) && (ix!=0) ) return 3; // Top-right and top-left atoms + if (iy<0) return -1; // bottom left/middle/right + if ((iy==0) && (ix<0) ) return -1; // left atoms + if ((iy==0) && (ix==0)) return 0; // Locally owned atoms + if ((iy==0) && (ix>0) ) return 2; // Right atoms + if ((iy>0) && (ix==0)) return 1; // Top-middle atoms + if ((iy>0) && (ix!=0)) return 3; // Top-right and top-left atoms } else { // iz > 0 if((ix==0) && (iy==0)) return 4; // Back atoms if((ix==0) && (iy!=0)) return 5; // Top-back and bottom-back atoms diff --git a/src/USER-DPD/pair_dpd_fdt.cpp b/src/USER-DPD/pair_dpd_fdt.cpp index 12e6d9f257..07ef8190f0 100644 --- a/src/USER-DPD/pair_dpd_fdt.cpp +++ b/src/USER-DPD/pair_dpd_fdt.cpp @@ -76,8 +76,7 @@ void PairDPDfdt::compute(int eflag, int vflag) double gamma_ij; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; diff --git a/src/USER-DPD/pair_dpd_fdt_energy.cpp b/src/USER-DPD/pair_dpd_fdt_energy.cpp index 42c23e3ad2..12e6989c00 100644 --- a/src/USER-DPD/pair_dpd_fdt_energy.cpp +++ b/src/USER-DPD/pair_dpd_fdt_energy.cpp @@ -85,8 +85,7 @@ void PairDPDfdtEnergy::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; diff --git a/src/USER-DPD/pair_exp6_rx.cpp b/src/USER-DPD/pair_exp6_rx.cpp index 0251f019c5..13521b52b1 100644 --- a/src/USER-DPD/pair_exp6_rx.cpp +++ b/src/USER-DPD/pair_exp6_rx.cpp @@ -121,8 +121,7 @@ void PairExp6rx::compute(int eflag, int vflag) evdwlOld = 0.0; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-DPD/pair_multi_lucy.cpp b/src/USER-DPD/pair_multi_lucy.cpp index 19a4a02f0b..ffc1562f88 100644 --- a/src/USER-DPD/pair_multi_lucy.cpp +++ b/src/USER-DPD/pair_multi_lucy.cpp @@ -95,8 +95,7 @@ void PairMultiLucy::compute(int eflag, int vflag) int tlm1 = tablength - 1; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-DPD/pair_multi_lucy_rx.cpp b/src/USER-DPD/pair_multi_lucy_rx.cpp index f3ad86eb2f..801e8ff039 100644 --- a/src/USER-DPD/pair_multi_lucy_rx.cpp +++ b/src/USER-DPD/pair_multi_lucy_rx.cpp @@ -111,8 +111,7 @@ void PairMultiLucyRX::compute(int eflag, int vflag) evdwlOld = 0.0; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-DPD/pair_table_rx.cpp b/src/USER-DPD/pair_table_rx.cpp index 1e7bc440d1..f2d0d7b1fb 100644 --- a/src/USER-DPD/pair_table_rx.cpp +++ b/src/USER-DPD/pair_table_rx.cpp @@ -78,8 +78,7 @@ void PairTableRX::compute(int eflag, int vflag) evdwlOld = 0.0; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp index ce5d3a92a9..1ebe4a4c2d 100644 --- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp +++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp @@ -98,8 +98,7 @@ void PairLJCutTholeLong::compute(int eflag, int vflag) int di_closest; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -683,7 +682,7 @@ void *PairLJCutTholeLong::extract(const char *str, int &dim) { dim = 0; if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; - dim = 6; + dim = 2; if (strcmp(str,"epsilon") == 0) return (void *) epsilon; if (strcmp(str,"sigma") == 0) return (void *) sigma; if (strcmp(str,"scale") == 0) return (void *) scale; diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp index 6901ad1f2d..1bb75af825 100644 --- a/src/USER-DRUDE/pair_thole.cpp +++ b/src/USER-DRUDE/pair_thole.cpp @@ -64,8 +64,7 @@ void PairThole::compute(int eflag, int vflag) double dcoul,asr,exp_asr; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -414,7 +413,7 @@ double PairThole::single(int i, int j, int itype, int jtype, void *PairThole::extract(const char *str, int &dim) { - dim = 4; + dim = 2; if (strcmp(str,"scale") == 0) return (void *) scale; if (strcmp(str,"polar") == 0) return (void *) polar; if (strcmp(str,"thole") == 0) return (void *) thole; diff --git a/src/USER-EFF/fix_nvt_sllod_eff.cpp b/src/USER-EFF/fix_nvt_sllod_eff.cpp index 13cb34048c..ed2274dcf9 100644 --- a/src/USER-EFF/fix_nvt_sllod_eff.cpp +++ b/src/USER-EFF/fix_nvt_sllod_eff.cpp @@ -75,7 +75,7 @@ void FixNVTSllodEff::init() int i; for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"deform") == 0) { + if (strncmp(modify->fix[i]->style,"deform",6) == 0) { if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP) error->all(FLERR,"Using fix nvt/sllod/eff with inconsistent fix deform " "remap option"); diff --git a/src/USER-EFF/pair_eff_cut.cpp b/src/USER-EFF/pair_eff_cut.cpp index b4e9011e33..f566922ef7 100644 --- a/src/USER-EFF/pair_eff_cut.cpp +++ b/src/USER-EFF/pair_eff_cut.cpp @@ -81,8 +81,7 @@ void PairEffCut::compute(int eflag, int vflag) // pvector = [KE, Pauli, ecoul, radial_restraint] for (i=0; i<4; i++) pvector[i] = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-FEP/Install.sh b/src/USER-FEP/Install.sh index 09c2024ad2..c6e7a53aa1 100755 --- a/src/USER-FEP/Install.sh +++ b/src/USER-FEP/Install.sh @@ -50,4 +50,10 @@ action pair_morse_soft.cpp action pair_morse_soft.h action pair_tip4p_long_soft.cpp pppm_tip4p.cpp action pair_tip4p_long_soft.h pppm_tip4p.cpp +action pair_lj_class2_soft.cpp +action pair_lj_class2_soft.h +action pair_lj_class2_coul_cut_soft.cpp +action pair_lj_class2_coul_cut_soft.h +action pair_lj_class2_coul_long_soft.cpp pppm.cpp +action pair_lj_class2_coul_long_soft.h pppm.cpp diff --git a/src/USER-FEP/README b/src/USER-FEP/README index 8c942a90d8..90e58f9e82 100644 --- a/src/USER-FEP/README +++ b/src/USER-FEP/README @@ -16,3 +16,7 @@ Pair style morse/soft was contributed by Stefan Paquay, s.paquay at tue.nl Applied Physics/Theory of Polymers and Soft Matter, Eindhoven University of Technology (TU/e), The Netherlands Contact him in case of problems with this pair style. + +Pair styles lj/class2/soft were contributed by Evangelos Voyiatzis at +Technical University of Darmstadt (e.voyiatzis at theo.chemie.tu-darmstadt.de) +Contact him in case of problems with these pair styles. diff --git a/src/USER-FEP/pair_coul_cut_soft.cpp b/src/USER-FEP/pair_coul_cut_soft.cpp index 529ffe6b09..86a6d02819 100644 --- a/src/USER-FEP/pair_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_coul_cut_soft.cpp @@ -60,8 +60,7 @@ void PairCoulCutSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-FEP/pair_coul_long_soft.cpp b/src/USER-FEP/pair_coul_long_soft.cpp index e45dbe72d6..9d3ffc0da1 100644 --- a/src/USER-FEP/pair_coul_long_soft.cpp +++ b/src/USER-FEP/pair_coul_long_soft.cpp @@ -78,8 +78,7 @@ void PairCoulLongSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp index 34758b159b..ac6f1e6384 100644 --- a/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp @@ -92,8 +92,7 @@ void PairLJCharmmCoulLongSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -415,8 +414,7 @@ void PairLJCharmmCoulLongSoft::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp new file mode 100644 index 0000000000..ae79515488 --- /dev/null +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.cpp @@ -0,0 +1,518 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lj_class2_coul_cut_soft.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairLJClass2CoulCutSoft::PairLJClass2CoulCutSoft(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJClass2CoulCutSoft::~PairLJClass2CoulCutSoft() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(cut_coul); + memory->destroy(cut_coulsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double rsq,forcecoul,forcelj; + double factor_coul,factor_lj; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + + if (rsq < cut_coulsq[itype][jtype]) { + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0); + r4sig6 = rsq*rsq / lj2[itype][jtype]; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2)); + } else forcelj = 0.0; + + fpair = factor_coul*forcecoul + factor_lj*forcelj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq[itype][jtype]) + ecoul = factor_coul * qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0); + evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - + offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(cut_coul,n+1,n+1,"pair:cut_coul"); + memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lambda,n+1,n+1,"pair:lambda"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::settings(int narg, char **arg) +{ + if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + alphac = force->numeric(FLERR,arg[2]); + + cut_lj_global = force->numeric(FLERR,arg[3]); + if (narg == 4) cut_coul_global = cut_lj_global; + else cut_coul_global = force->numeric(FLERR,arg[4]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut_lj[i][j] = cut_lj_global; + cut_coul[i][j] = cut_coul_global; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 7) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + if (sigma_one <= 0.0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + double cut_lj_one = cut_lj_global; + double cut_coul_one = cut_coul_global; + if (narg >= 6) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[5]); + if (narg == 7) cut_coul_one = force->numeric(FLERR,arg[6]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + cut_lj[i][j] = cut_lj_one; + lambda[i][j] = lambda_one; + cut_coul[i][j] = cut_coul_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style lj/class2/coul/cut/soft requires atom attribute q"); + + neighbor->request(this,instance_me); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJClass2CoulCutSoft::init_one(int i, int j) +{ + // always mix epsilon,sigma via sixthpower rules + // mix distance via user-defined rule + + if (setflag[i][j] == 0) { + epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) * + pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) / + (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0)); + sigma[i][j] = + pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]); + } + + double cut = MAX(cut_lj[i][j],cut_coul[i][j]); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j]; + + lj1[i][j] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + if (offset_flag && (cut_lj[i][j] > 0.0)) { + double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0); + offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0*pow(denlj,-1.5) - 3.0*pow(denlj,-1.0)); + } else offset[i][j] = 0.0; + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + cut_ljsq[j][i] = cut_ljsq[i][j]; + cut_coulsq[j][i] = cut_coulsq[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + offset[j][i] = offset[i][j]; + + // compute I,J contribution to long-range tail correction + // count total # of atoms of type I and J via Allreduce + + if (tail_flag) { + int *type = atom->type; + int nlocal = atom->nlocal; + + double count[2],all[2]; + count[0] = count[1] = 0.0; + for (int k = 0; k < nlocal; k++) { + if (type[k] == i) count[0] += 1.0; + if (type[k] == j) count[1] += 1.0; + } + MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); + + double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j]; + double sig6 = sig3*sig3; + double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + double rc6 = rc3*rc3; + // the tail and pressure corrections are not exact but approximate + etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] * + sig6 * (sig3 - 3.0*rc3) / (3.0*rc6); + ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] * + sig6 * (sig3 - 2.0*rc3) / rc6; + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&lambda[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + fwrite(&cut_coul[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&lambda[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + fread(&cut_coul[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,fp); + fwrite(&alphac,sizeof(double),1,fp); + + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + fread(&alphac,sizeof(double),1,fp); + + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); + + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulCutSoft::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJClass2CoulCutSoft::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double forcecoul,forcelj,phicoul,philj; + double denc, denlj, r4sig6; + + if (rsq < cut_coulsq[itype][jtype]) { + denc = sqrt(lj4[itype][jtype] + rsq); + forcecoul = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / + (denc*denc*denc); + } else forcecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + fforce = factor_coul*forcecoul + factor_lj*forcelj; + + double eng = 0.0; + if (rsq < cut_coulsq[itype][jtype]) { + phicoul = force->qqrd2e *lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; + eng += factor_coul*phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + philj = lj1[itype][jtype] * epsilon[itype][jtype] * + (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - offset[itype][jtype]; + eng += factor_lj*philj; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJClass2CoulCutSoft::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"lambda") == 0) return (void *) lambda; + return NULL; +} diff --git a/src/USER-FEP/pair_lj_class2_coul_cut_soft.h b/src/USER-FEP/pair_lj_class2_coul_cut_soft.h new file mode 100644 index 0000000000..d4d8c264b5 --- /dev/null +++ b/src/USER-FEP/pair_lj_class2_coul_cut_soft.h @@ -0,0 +1,81 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/class2/coul/cut/soft,PairLJClass2CoulCutSoft) + +#else + +#ifndef LMP_PAIR_LJ_CLASS2_COUL_CUT_SOFT_H +#define LMP_PAIR_LJ_CLASS2_COUL_CUT_SOFT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJClass2CoulCutSoft : public Pair { + public: + PairLJClass2CoulCutSoft(class LAMMPS *); + virtual ~PairLJClass2CoulCutSoft(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_lj_global,cut_coul_global; + double **cut_lj,**cut_ljsq; + double **cut_coul,**cut_coulsq; + double **epsilon,**sigma, **lambda; + double nlambda, alphalj, alphac; + double **lj1,**lj2,**lj3,**lj4,**offset; + + virtual void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style lj/class2/coul/cut/soft requires atom attribute q + +The atom style defined does not have this attribute. + +E: Pair lj/class2/coul/cut/soft different lambda values in mix + +The value of lambda has to be the same for I J pairs. + +*/ diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp new file mode 100644 index 0000000000..6410f83fa1 --- /dev/null +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.cpp @@ -0,0 +1,542 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lj_class2_coul_long_soft.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairLJClass2CoulLongSoft::PairLJClass2CoulLongSoft(LAMMPS *lmp) : Pair(lmp) +{ + ewaldflag = pppmflag = 1; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJClass2CoulLongSoft::~PairLJClass2CoulLongSoft() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double fraction; + double rsq,r,forcecoul,forcelj; + double grij,expm2,prefactor,t,erfc; + double factor_coul,factor_lj; + double denc, denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + denc = sqrt(lj4[itype][jtype] + rsq); + prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / (denc*denc*denc); + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2)); + } else forcelj = 0.0; + + fpair = forcecoul + factor_lj*forcelj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_coulsq) { + prefactor = qqrd2e * lj1[itype][jtype] * qtmp*q[j] / denc; + ecoul = prefactor*erfc; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - + offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lambda,n+1,n+1,"pair:lambda"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::settings(int narg, char **arg) +{ + if (narg < 4 || narg > 5) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + alphac = force->numeric(FLERR,arg[2]); + + cut_lj_global = force->numeric(FLERR,arg[3]); + if (narg == 4) cut_coul = cut_lj_global; + else cut_coul = force->numeric(FLERR,arg[4]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + if (sigma_one <= 0.0) + error->all(FLERR,"Incorrect args for pair coefficients"); + + double cut_lj_one = cut_lj_global; + if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + lambda[i][j] = lambda_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::init_style() +{ + if (!atom->q_flag) + error->all(FLERR, + "Pair style lj/class2/coul/long/soft requires atom attribute q"); + + neighbor->request(this,instance_me); + + cut_coulsq = cut_coul * cut_coul; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJClass2CoulLongSoft::init_one(int i, int j) +{ + // always mix epsilon,sigma via sixthpower rules + // mix distance via user-defined rule + + if (setflag[i][j] == 0) { + epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) * + pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) / + (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0)); + sigma[i][j] = + pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/class2/coul/long/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + } + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + lj1[i][j] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + lj4[i][j] = alphac * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + if (offset_flag && (cut_lj[i][j] > 0.0)) { + double denlj = lj3[i][j] + pow(cut_lj[i][j] / sigma[i][j], 6.0); + offset[i][j] = epsilon[i][j] * (2.0*pow(denlj,-1.5) - 3.0*pow(denlj,-1.0)); + } else offset[i][j] = 0.0; + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + cut_ljsq[j][i] = cut_ljsq[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + offset[j][i] = offset[i][j]; + + // compute I,J contribution to long-range tail correction + // count total # of atoms of type I and J via Allreduce + + if (tail_flag) { + int *type = atom->type; + int nlocal = atom->nlocal; + + double count[2],all[2]; + count[0] = count[1] = 0.0; + for (int k = 0; k < nlocal; k++) { + if (type[k] == i) count[0] += 1.0; + if (type[k] == j) count[1] += 1.0; + } + MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); + + double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j]; + double sig6 = sig3*sig3; + double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j]; + double rc6 = rc3*rc3; + etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] * + sig6 * (sig3 - 3.0*rc3) / (3.0*rc6); + ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] * + sig6 * (sig3 - 2.0*rc3) / rc6; + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&lambda[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&lambda[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,fp); + fwrite(&alphac,sizeof(double),1,fp); + + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + fread(&alphac,sizeof(double),1,fp); + + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphac,1,MPI_DOUBLE,0,world); + + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJClass2CoulLongSoft::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJClass2CoulLongSoft::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double denc,r,denlj,r4sig6,grij,expm2,t,erfc,prefactor; + double fraction,forcecoul,forcelj,phicoul,philj; + + if (rsq < cut_coulsq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + denc = sqrt(lj4[itype][jtype] + rsq); + prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / + (denc*denc*denc); + forcecoul = prefactor * (erfc + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + fforce = forcecoul + factor_lj*forcelj; + + double eng = 0.0; + if (rsq < cut_coulsq) { + prefactor = force->qqrd2e * lj1[itype][jtype] * atom->q[i]*atom->q[j] / denc; + phicoul = prefactor*erfc; + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + if (rsq < cut_ljsq[itype][jtype]) { + philj = lj1[itype][jtype] * epsilon[itype][jtype] * + (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - offset[itype][jtype]; + eng += factor_lj*philj; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJClass2CoulLongSoft::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"lambda") == 0) return (void *) lambda; + return NULL; +} diff --git a/src/USER-FEP/pair_lj_class2_coul_long_soft.h b/src/USER-FEP/pair_lj_class2_coul_long_soft.h new file mode 100644 index 0000000000..c334ef19df --- /dev/null +++ b/src/USER-FEP/pair_lj_class2_coul_long_soft.h @@ -0,0 +1,82 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/class2/coul/long/soft,PairLJClass2CoulLongSoft) + +#else + +#ifndef LMP_PAIR_LJ_CLASS2_COUL_LONG_SOFT_H +#define LMP_PAIR_LJ_CLASS2_COUL_LONG_SOFT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJClass2CoulLongSoft : public Pair { + public: + PairLJClass2CoulLongSoft(class LAMMPS *); + virtual ~PairLJClass2CoulLongSoft(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_restart_settings(FILE *); + void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_lj_global; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **epsilon,**sigma, **lambda; + double nlambda, alphalj, alphac; + double **lj1,**lj2,**lj3,**lj4,**offset; + double g_ewald; + + virtual void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style lj/class2/coul/long/soft requires atom attribute q + +The atom style defined does not have this attribute. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +*/ diff --git a/src/USER-FEP/pair_lj_class2_soft.cpp b/src/USER-FEP/pair_lj_class2_soft.cpp new file mode 100644 index 0000000000..d22cd53883 --- /dev/null +++ b/src/USER-FEP/pair_lj_class2_soft.cpp @@ -0,0 +1,435 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lj_class2_soft.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairLJClass2Soft::PairLJClass2Soft(LAMMPS *lmp) : Pair(lmp) +{ + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLJClass2Soft::~PairLJClass2Soft() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lambda); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJClass2Soft::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,forcelj,factor_lj; + double denlj, r4sig6; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0); + r4sig6 = rsq*rsq / lj2[itype][jtype]; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (18.0*r4sig6*pow(denlj, -2.5) - 18.0*r4sig6*pow(denlj, -2)); + fpair = factor_lj*forcelj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + denlj = lj3[itype][jtype] + pow(rsq, 3) * pow(sigma[itype][jtype], -6.0); + evdwl = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - + offset[itype][jtype]; + evdwl *= factor_lj; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lambda,n+1,n+1,"pair:lambda"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::settings(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Illegal pair_style command"); + + nlambda = force->numeric(FLERR,arg[0]); + alphalj = force->numeric(FLERR,arg[1]); + + cut_global = force->numeric(FLERR,arg[2]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double lambda_one = force->numeric(FLERR,arg[4]); + if (sigma_one <= 0.0) error->all(FLERR,"Incorrect args for pair coefficients"); + + double cut_one = cut_global; + if (narg == 6) cut_one = force->numeric(FLERR,arg[5]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + lambda[i][j] = lambda_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJClass2Soft::init_one(int i, int j) +{ + // always mix epsilon,sigma via sixthpower rules + // mix distance via user-defined rule + + if (setflag[i][j] == 0) { + epsilon[i][j] = 2.0 * sqrt(epsilon[i][i]*epsilon[j][j]) * + pow(sigma[i][i],3.0) * pow(sigma[j][j],3.0) / + (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0)); + sigma[i][j] = + pow((0.5 * (pow(sigma[i][i],6.0) + pow(sigma[j][j],6.0))),1.0/6.0); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/class2/coul/cut/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + lj1[i][j] = pow(lambda[i][j], nlambda); + lj2[i][j] = pow(sigma[i][j], 6.0); + lj3[i][j] = alphalj * (1.0 - lambda[i][j])*(1.0 - lambda[i][j]); + + if (offset_flag && (cut[i][j] > 0.0)) { + double denlj = lj3[i][j] + pow(cut[i][j] / sigma[i][j], 6.0); + offset[i][j] = lj1[i][j] * epsilon[i][j] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj); + } else offset[i][j] = 0.0; + + epsilon[j][i] = epsilon[i][j]; + sigma[j][i] = sigma[i][j]; + lambda[j][i] = lambda[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + offset[j][i] = offset[i][j]; + + // compute I,J contribution to long-range tail correction + // count total # of atoms of type I and J via Allreduce + + if (tail_flag) { + int *type = atom->type; + int nlocal = atom->nlocal; + + double count[2],all[2]; + count[0] = count[1] = 0.0; + for (int k = 0; k < nlocal; k++) { + if (type[k] == i) count[0] += 1.0; + if (type[k] == j) count[1] += 1.0; + } + MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); + + double sig3 = sigma[i][j]*sigma[i][j]*sigma[i][j]; + double sig6 = sig3*sig3; + double rc3 = cut[i][j]*cut[i][j]*cut[i][j]; + double rc6 = rc3*rc3; + // check the following expressions for etail_lj & ptail_ij they are not correct ! + etail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] * + sig6 * (sig3 - 3.0*rc3) / (3.0*rc6); + ptail_ij = 2.0*MY_PI*all[0]*all[1]*lj1[i][j] *epsilon[i][j] * + sig6 * (sig3 - 2.0*rc3) / rc6; + } + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&lambda[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&lambda[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&lambda[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::write_restart_settings(FILE *fp) +{ + fwrite(&nlambda,sizeof(double),1,fp); + fwrite(&alphalj,sizeof(double),1,fp); + fwrite(&cut_global,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&nlambda,sizeof(double),1,fp); + fread(&alphalj,sizeof(double),1,fp); + fread(&cut_global,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&nlambda,1,MPI_DOUBLE,0,world); + MPI_Bcast(&alphalj,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],lambda[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJClass2Soft::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j], + lambda[i][j],cut[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJClass2Soft::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, + double &fforce) +{ + double forcelj,philj; + double r4sig6, denlj; + + if (rsq < cutsq[itype][jtype]) { + r4sig6 = rsq*rsq / lj2[itype][jtype]; + denlj = lj3[itype][jtype] + rsq*r4sig6; + forcelj = lj1[itype][jtype] * epsilon[itype][jtype] * + (18.0*r4sig6/(denlj*denlj*sqrt(denlj)) - 18.0*r4sig6/(denlj*denlj)); + } else forcelj = 0.0; + fforce = factor_lj*forcelj; + + if (rsq < cutsq[itype][jtype]) { + denlj = lj3[itype][jtype] + rsq*rsq*rsq / lj2[itype][jtype]; + philj = lj1[itype][jtype] * epsilon[itype][jtype] * (2.0/(denlj*sqrt(denlj)) - 3.0/denlj) - + offset[itype][jtype]; + } else philj = 0.0; + + return factor_lj*philj; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJClass2Soft::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"lambda") == 0) return (void *) lambda; + return NULL; +} diff --git a/src/USER-FEP/pair_lj_class2_soft.h b/src/USER-FEP/pair_lj_class2_soft.h new file mode 100644 index 0000000000..ef031a1911 --- /dev/null +++ b/src/USER-FEP/pair_lj_class2_soft.h @@ -0,0 +1,69 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/class2/soft,PairLJClass2Soft) + +#else + +#ifndef LMP_PAIR_LJ_CLASS2_SOFT_H +#define LMP_PAIR_LJ_CLASS2_SOFT_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJClass2Soft : public Pair { + public: + PairLJClass2Soft(class LAMMPS *); + virtual ~PairLJClass2Soft(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + virtual double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + void *extract(const char *, int &); + + protected: + double cut_global; + double **cut; + double **epsilon, **sigma, **lambda; + double nlambda, alphalj; + double **lj1,**lj2,**lj3,**offset; + + virtual void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: +E: Illegal ... command +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients +Self-explanatory. Check the input script or data file. + +E: Pair lj/cut/soft different lambda values in mix +The value of lambda has to be the same for I J pairs. + +*/ diff --git a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp index fc887fbec5..35c9162dbc 100644 --- a/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp @@ -73,8 +73,7 @@ void PairLJCutCoulCutSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp index a9032ab4d7..79253d2b9c 100644 --- a/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_coul_long_soft.cpp @@ -89,8 +89,7 @@ void PairLJCutCoulLongSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -390,8 +389,7 @@ void PairLJCutCoulLongSoft::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-FEP/pair_lj_cut_soft.cpp b/src/USER-FEP/pair_lj_cut_soft.cpp index a33445f6f8..4192d6546b 100644 --- a/src/USER-FEP/pair_lj_cut_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_soft.cpp @@ -77,8 +77,7 @@ void PairLJCutSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -323,8 +322,7 @@ void PairLJCutSoft::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -566,6 +564,9 @@ double PairLJCutSoft::init_one(int i, int j) epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], sigma[i][i],sigma[j][j]); sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); + if (lambda[i][i] != lambda[j][j]) + error->all(FLERR,"Pair lj/cut/soft different lambda values in mix"); + lambda[i][j] = lambda[i][i]; cut[i][j] = mix_distance(cut[i][i],cut[j][j]); } diff --git a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp index 8653800ee6..8ac28f9fa9 100644 --- a/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_lj_cut_tip4p_long_soft.cpp @@ -92,8 +92,7 @@ void PairLJCutTIP4PLongSoft::compute(int eflag, int vflag) double rsq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/USER-FEP/pair_morse_soft.cpp b/src/USER-FEP/pair_morse_soft.cpp index 965d570863..21f616a082 100644 --- a/src/USER-FEP/pair_morse_soft.cpp +++ b/src/USER-FEP/pair_morse_soft.cpp @@ -53,8 +53,7 @@ void PairMorseSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -116,7 +115,7 @@ void PairMorseSoft::compute(int eflag, int vflag) // Force computation: fpair = 3.0*a*B*dexp3*s1 + 2.0*a*D*(dexp2 - dexp); fpair /= r; - }else{ + } else { llf = MathSpecial::powint( l / shift_range, nlambda ); phi = V0 + B*dexp3; phi *= llf; @@ -124,7 +123,7 @@ void PairMorseSoft::compute(int eflag, int vflag) // Force computation: if (r == 0.0){ fpair = 0.0; - }else{ + } else { fpair = 3.0*a*B*dexp3 + 2.0*a*D*(dexp2 - dexp); fpair *= llf / r; } @@ -234,7 +233,8 @@ void PairMorseSoft::settings(int narg, char **arg) double PairMorseSoft::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) + error->all(FLERR,"All pair coeffs are not set"); morse1[i][j] = 2.0*d0[i][j]*alpha[i][j]; @@ -259,8 +259,7 @@ double PairMorseSoft::init_one(int i, int j) if (l >= shift_range){ s1 = (l - 1.0) / (shift_range - 1.0); offset[i][j] = V0 + B*dexp3 * s1; - - }else{ + } else { llf = MathSpecial::powint( l / shift_range, nlambda ); offset[i][j] = V0 + B*dexp3; offset[i][j] *= llf; @@ -392,7 +391,7 @@ double PairMorseSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double // Force computation: fforce = 3.0*a*B*dexp3*s1 + 2.0*a*D*(dexp2 - dexp); fforce /= r; - }else{ + } else { llf = MathSpecial::powint( l / shift_range, nlambda ); phi = V0 + B*dexp3; phi *= llf; @@ -400,7 +399,7 @@ double PairMorseSoft::single(int /*i*/, int /*j*/, int itype, int jtype, double // Force computation: if (r == 0.0){ fforce = 0.0; - }else{ + } else { fforce = 3.0*a*B*dexp3 + 2.0*a*D*(dexp2 - dexp); fforce *= llf / r; } diff --git a/src/USER-FEP/pair_tip4p_long_soft.cpp b/src/USER-FEP/pair_tip4p_long_soft.cpp index 5e8c5000f8..9b6a6841fe 100644 --- a/src/USER-FEP/pair_tip4p_long_soft.cpp +++ b/src/USER-FEP/pair_tip4p_long_soft.cpp @@ -91,8 +91,7 @@ void PairTIP4PLongSoft::compute(int eflag, int vflag) double rsq; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh & newsite if necessary // initialize hneigh[0] to -1 on steps when reneighboring occurred diff --git a/src/USER-H5MD/dump_h5md.cpp b/src/USER-H5MD/dump_h5md.cpp index 393871ae0b..af77258780 100644 --- a/src/USER-H5MD/dump_h5md.cpp +++ b/src/USER-H5MD/dump_h5md.cpp @@ -346,7 +346,7 @@ void DumpH5MD::openfile() /* ---------------------------------------------------------------------- */ -void DumpH5MD::write_header(bigint nbig) +void DumpH5MD::write_header(bigint /* nbig */) { return; } diff --git a/src/USER-INTEL/TEST/in.intel.water b/src/USER-INTEL/TEST/in.intel.water index 0643def19e..8bf91f487e 100644 --- a/src/USER-INTEL/TEST/in.intel.water +++ b/src/USER-INTEL/TEST/in.intel.water @@ -1,47 +1,47 @@ -# Coarse-grain water simulation using Stillinger-Weber - -variable N index on # Newton Setting -variable w index 10 # Warmup Timesteps -variable t index 2600 # Main Run Timesteps -variable m index 1 # Main Run Timestep Multiplier -variable n index 0 # Use NUMA Mapping for Multi-Node -variable p index 0 # Use Power Measurement - -variable x index 4 -variable y index 2 -variable z index 2 -variable rr equal floor($t*$m) - -newton $N -if "$n > 0" then "processors * * * grid numa" - -units real -atom_style atomic - -read_data mW_32k_cube.data -reset_timestep 0 -replicate $x $y $z - -pair_style sw -pair_coeff * * mW.sw mW - -mass 1 18.015 #g/mol -group mW type 1 - -neighbor 2 bin #Angstroms -neigh_modify every 1 delay 4 - -fix 1 all nvt temp 300.0 300.0 1000.0 - -velocity all zero linear - -timestep 10 #femtoseconds - -thermo_modify norm yes - -thermo 1000 - -if "$p > 0" then "run_style verlet/power" - -if "$w > 0" then "run $w" -run ${rr} +# Coarse-grain water simulation using Stillinger-Weber + +variable N index on # Newton Setting +variable w index 10 # Warmup Timesteps +variable t index 2600 # Main Run Timesteps +variable m index 1 # Main Run Timestep Multiplier +variable n index 0 # Use NUMA Mapping for Multi-Node +variable p index 0 # Use Power Measurement + +variable x index 4 +variable y index 2 +variable z index 2 +variable rr equal floor($t*$m) + +newton $N +if "$n > 0" then "processors * * * grid numa" + +units real +atom_style atomic + +read_data mW_32k_cube.data +reset_timestep 0 +replicate $x $y $z + +pair_style sw +pair_coeff * * mW.sw mW + +mass 1 18.015 #g/mol +group mW type 1 + +neighbor 2 bin #Angstroms +neigh_modify every 1 delay 4 + +fix 1 all nvt temp 300.0 300.0 1000.0 + +velocity all zero linear + +timestep 10 #femtoseconds + +thermo_modify norm yes + +thermo 1000 + +if "$p > 0" then "run_style verlet/power" + +if "$w > 0" then "run $w" +run ${rr} diff --git a/src/USER-INTEL/angle_charmm_intel.cpp b/src/USER-INTEL/angle_charmm_intel.cpp index f2542fc0c7..c5ada951a5 100644 --- a/src/USER-INTEL/angle_charmm_intel.cpp +++ b/src/USER-INTEL/angle_charmm_intel.cpp @@ -78,8 +78,7 @@ void AngleCharmmIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/angle_harmonic_intel.cpp b/src/USER-INTEL/angle_harmonic_intel.cpp index 6d8901a5ee..aae6fcf0a2 100644 --- a/src/USER-INTEL/angle_harmonic_intel.cpp +++ b/src/USER-INTEL/angle_harmonic_intel.cpp @@ -78,8 +78,7 @@ void AngleHarmonicIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/bond_fene_intel.cpp b/src/USER-INTEL/bond_fene_intel.cpp index bff3722a44..bd8bc94c18 100644 --- a/src/USER-INTEL/bond_fene_intel.cpp +++ b/src/USER-INTEL/bond_fene_intel.cpp @@ -74,8 +74,7 @@ void BondFENEIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/bond_harmonic_intel.cpp b/src/USER-INTEL/bond_harmonic_intel.cpp index 65894efa05..4424b868eb 100644 --- a/src/USER-INTEL/bond_harmonic_intel.cpp +++ b/src/USER-INTEL/bond_harmonic_intel.cpp @@ -74,8 +74,7 @@ void BondHarmonicIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/dihedral_charmm_intel.cpp b/src/USER-INTEL/dihedral_charmm_intel.cpp index c9237e7309..4f4b091300 100644 --- a/src/USER-INTEL/dihedral_charmm_intel.cpp +++ b/src/USER-INTEL/dihedral_charmm_intel.cpp @@ -84,9 +84,7 @@ void DihedralCharmmIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/USER-INTEL/dihedral_fourier_intel.cpp b/src/USER-INTEL/dihedral_fourier_intel.cpp index 6ccc165c61..030d371e44 100644 --- a/src/USER-INTEL/dihedral_fourier_intel.cpp +++ b/src/USER-INTEL/dihedral_fourier_intel.cpp @@ -73,9 +73,7 @@ void DihedralFourierIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/dihedral_harmonic_intel.cpp b/src/USER-INTEL/dihedral_harmonic_intel.cpp index ae5eb914e7..d84db4f4ac 100644 --- a/src/USER-INTEL/dihedral_harmonic_intel.cpp +++ b/src/USER-INTEL/dihedral_harmonic_intel.cpp @@ -73,9 +73,7 @@ void DihedralHarmonicIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/dihedral_opls_intel.cpp b/src/USER-INTEL/dihedral_opls_intel.cpp index 7a60b62cae..eae796974b 100644 --- a/src/USER-INTEL/dihedral_opls_intel.cpp +++ b/src/USER-INTEL/dihedral_opls_intel.cpp @@ -77,9 +77,7 @@ void DihedralOPLSIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/fix_intel.cpp b/src/USER-INTEL/fix_intel.cpp index b305590729..67bf33e751 100644 --- a/src/USER-INTEL/fix_intel.cpp +++ b/src/USER-INTEL/fix_intel.cpp @@ -456,7 +456,7 @@ void FixIntel::pair_init_check(const bool cdmessage) " exclusions with Intel"); } #endif - + int need_tag = 0; if (atom->molecular) need_tag = 1; diff --git a/src/USER-INTEL/fix_intel.h b/src/USER-INTEL/fix_intel.h index a01ed18bfe..3810b57355 100644 --- a/src/USER-INTEL/fix_intel.h +++ b/src/USER-INTEL/fix_intel.h @@ -83,7 +83,7 @@ class FixIntel : public Fix { } inline void set_reduce_flag() { if (_nthreads > 1) _need_reduce = 1; } inline int lrt() { - if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1) + if (force->kspace_match("pppm/intel", 0) && update->whichflag == 1) return _lrt; else return 0; } @@ -104,7 +104,7 @@ class FixIntel : public Fix { int _pair_intel_count, _pair_hybrid_flag; // These should be removed in subsequent update w/ simpler hybrid arch int _pair_hybrid_zero, _hybrid_nonpair, _zero_master; - + public: inline int* get_overflow_flag() { return _overflow_flag; } inline int* get_off_overflow_flag() { return _off_overflow_flag; } @@ -215,7 +215,7 @@ class FixIntel : public Fix { _alignvar(double _stopwatch_offload_pair[1],64); void _sync_main_arrays(const int prereverse); - + template void reduce_results(ft * _noalias const f_in); @@ -512,13 +512,13 @@ issues. Please use 14.0.1.106 or 15.1.133 or later. E: Currently, cannot offload more than one intel style with hybrid. -Currently, when using offload, hybrid pair styles can only use the intel +Currently, when using offload, hybrid pair styles can only use the intel suffix for one of the pair styles. E: Cannot yet use hybrid styles with Intel offload. The hybrid pair style configuration is not yet supported when using offload -within the Intel package. Support is limited to hybrid/overlay or a hybrid +within the Intel package. Support is limited to hybrid/overlay or a hybrid style that does not require a skip list. W: Leaving a core/node free can improve performance for offload @@ -564,7 +564,7 @@ atoms throughout the simulation. E: Intel package requires fdotr virial with newton on. This error can occur with a hybrid pair style that mixes styles that are -incompatible with the newton pair setting turned on. Try turning the +incompatible with the newton pair setting turned on. Try turning the newton pair setting off. E: Add -DLMP_INTEL_NBOR_COMPAT to build for special_bond exclusions with Intel diff --git a/src/USER-INTEL/fix_nvt_sllod_intel.cpp b/src/USER-INTEL/fix_nvt_sllod_intel.cpp index ad7e1384f0..f5a5dabfb1 100644 --- a/src/USER-INTEL/fix_nvt_sllod_intel.cpp +++ b/src/USER-INTEL/fix_nvt_sllod_intel.cpp @@ -76,7 +76,7 @@ void FixNVTSllodIntel::init() int i; for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"deform") == 0) { + if (strncmp(modify->fix[i]->style,"deform",6) == 0) { if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP) error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform " "remap option"); diff --git a/src/USER-INTEL/improper_cvff_intel.cpp b/src/USER-INTEL/improper_cvff_intel.cpp index 03bd134b40..de316250c0 100644 --- a/src/USER-INTEL/improper_cvff_intel.cpp +++ b/src/USER-INTEL/improper_cvff_intel.cpp @@ -83,8 +83,7 @@ void ImproperCvffIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/improper_harmonic_intel.cpp b/src/USER-INTEL/improper_harmonic_intel.cpp index 167095150e..846c3cfbf9 100644 --- a/src/USER-INTEL/improper_harmonic_intel.cpp +++ b/src/USER-INTEL/improper_harmonic_intel.cpp @@ -84,8 +84,7 @@ void ImproperHarmonicIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); if (evflag) { if (vflag && !eflag) { diff --git a/src/USER-INTEL/intel_buffers.cpp b/src/USER-INTEL/intel_buffers.cpp index b7026f90b7..c0995b6a9c 100644 --- a/src/USER-INTEL/intel_buffers.cpp +++ b/src/USER-INTEL/intel_buffers.cpp @@ -255,7 +255,7 @@ void IntelBuffers::free_list_local() #endif lmp->memory->destroy(cnumneigh); } - + #ifdef _LMP_INTEL_OFFLOAD if (_off_map_ilist != NULL) { const int * ilist = _off_map_ilist; @@ -295,7 +295,7 @@ void IntelBuffers::grow_data3(NeighList *list, { const int size = list->get_maxlocal(); int list_num; - for (list_num = 0; list_num < _n_list_ptrs; list_num++) + for (list_num = 0; list_num < _n_list_ptrs; list_num++) if (_neigh_list_ptrs[list_num].list_ptr == (void*)list) break; if (list_num == _n_list_ptrs) { if (_n_list_ptrs == _max_list_ptrs) { diff --git a/src/USER-INTEL/intel_intrinsics_airebo.h b/src/USER-INTEL/intel_intrinsics_airebo.h index b20f9c8ad1..2b55b41ad1 100644 --- a/src/USER-INTEL/intel_intrinsics_airebo.h +++ b/src/USER-INTEL/intel_intrinsics_airebo.h @@ -1027,7 +1027,7 @@ VEC_INLINE inline __m256 _mm256_compress_ps(__m256 mask, __m256 a) { _mm256_store_ps(a_buf, a); int k = 0; for (int i = 0; i < 8; i++) { - if (mask[i]) { + if (mask_buf[i]) { dst_buf[k++] = a_buf[i]; } } @@ -1052,7 +1052,7 @@ VEC_INLINE inline __m256 _mm256_expand_ps(__m256 mask, __m256 a) { _mm256_store_ps(a_buf, a); int k = 0; for (int i = 0; i < 8; i++) { - if (mask[i]) { + if (mask_buf[i]) { dst_buf[i] = a_buf[k++]; } } diff --git a/src/USER-INTEL/intel_preprocess.h b/src/USER-INTEL/intel_preprocess.h index 178a20c6e1..2515e47c52 100644 --- a/src/USER-INTEL/intel_preprocess.h +++ b/src/USER-INTEL/intel_preprocess.h @@ -146,7 +146,7 @@ enum {TIME_PACK, TIME_HOST_NEIGHBOR, TIME_HOST_PAIR, TIME_OFFLOAD_NEIGHBOR, } #else - + #define IP_PRE_edge_align(n, esize) \ #endif diff --git a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp index 5149b26f2f..db4b0c50a4 100644 --- a/src/USER-INTEL/npair_full_bin_ghost_intel.cpp +++ b/src/USER-INTEL/npair_full_bin_ghost_intel.cpp @@ -482,7 +482,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, #endif } } - + #ifndef _LMP_INTEL_OFFLOAD if (exclude) { int alln = n; @@ -515,7 +515,7 @@ void NPairFullBinGhostIntel::fbi(const int offload, NeighList * list, } } #endif - + int ns = n - maxnbors; int alln = n; atombin[i] = ns; diff --git a/src/USER-INTEL/npair_halffull_newton_intel.cpp b/src/USER-INTEL/npair_halffull_newton_intel.cpp index 93a1a97923..8248f2257a 100644 --- a/src/USER-INTEL/npair_halffull_newton_intel.cpp +++ b/src/USER-INTEL/npair_halffull_newton_intel.cpp @@ -61,7 +61,7 @@ void NPairHalffullNewtonIntel::build_t(NeighList *list, const int * _noalias const numneigh_full = list->listfull->numneigh; const int ** _noalias const firstneigh_full = (const int ** const)list->listfull->firstneigh; - + #if defined(_OPENMP) #pragma omp parallel #endif @@ -148,7 +148,7 @@ void NPairHalffullNewtonIntel::build_t3(NeighList *list, int *numhalf) const int * _noalias const numneigh_full = numhalf; const int ** _noalias const firstneigh_full = (const int ** const)list->listfull->firstneigh; - + int packthreads = 1; if (comm->nthreads > INTEL_HTHREADS) packthreads = comm->nthreads; diff --git a/src/USER-INTEL/npair_intel.cpp b/src/USER-INTEL/npair_intel.cpp index a1c0785d4c..e20c437cb7 100644 --- a/src/USER-INTEL/npair_intel.cpp +++ b/src/USER-INTEL/npair_intel.cpp @@ -72,7 +72,7 @@ void NPairIntel::copy_cutsq_info(IntelBuffers *buffers) { if (cutneighghostsq) use_ghost_cut = 1; buffers->set_ntypes(tp1, use_ghost_cut); - + flt_t **cutneighsqb = buffers->get_cutneighsq(); for (int i = 1; i <= atom->ntypes; i++) for (int j = 1; j <= atom->ntypes; j++) @@ -116,7 +116,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, #ifdef _LMP_INTEL_OFFLOAD if (offload_noghost && offload) nall_t = atom->nlocal; #endif - + const int pack_width = _fix->nbor_pack_width(); const ATOM_T * _noalias const x = buffers->get_x(); @@ -146,7 +146,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, int ** _noalias const firstneigh = list->firstneigh; int * _noalias const numneigh = list->numneigh; int * _noalias const cnumneigh = buffers->cnumneigh(); - + const int nstencil = this->nstencil; const int * _noalias const stencil = this->stencil; const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0]; @@ -204,7 +204,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } } const int special_bound = sb; - + #ifdef _LMP_INTEL_OFFLOAD const int * _noalias const binhead = this->binhead; const int * _noalias const bins = this->bins; @@ -547,7 +547,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, j = -j - 1; } else ofind_special(which, special, nspecial, i, tag[j]); - + if (which) { j = j ^ (which << SBBITS); if (which < special_bound) addme = 0; @@ -562,7 +562,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, if (THREE) { alln = n2; n2 = pack_offset + maxnbors; - + #if defined(LMP_SIMD_COMPILER) #pragma vector aligned #ifdef LMP_INTEL_NBOR_COMPAT @@ -592,7 +592,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, } } } - + #ifndef _LMP_INTEL_OFFLOAD if (exclude) { neighptr2 = neighptr; @@ -643,7 +643,7 @@ void NPairIntel::bin_newton(const int offload, NeighList *list, n += pack_width; } #endif - + for (int u = pack_offset + maxnbors; u < n2; u++) { #ifdef LMP_INTEL_3BODY_FAST neighptr[n] = neighptr2[u]; diff --git a/src/USER-INTEL/npair_intel.h b/src/USER-INTEL/npair_intel.h index e47687abea..6d4e01462f 100644 --- a/src/USER-INTEL/npair_intel.h +++ b/src/USER-INTEL/npair_intel.h @@ -76,7 +76,7 @@ class NPairIntel : public NPair { NPairIntel(class LAMMPS *); ~NPairIntel(); virtual void copy_neighbor_info(); - + #ifdef _LMP_INTEL_OFFLOAD void grow_stencil(); #endif @@ -86,7 +86,7 @@ class NPairIntel : public NPair { template void copy_cutsq_info(IntelBuffers *); - + template void bin_newton(const int, NeighList *, IntelBuffers *, const int, const int, const int offload_end = 0); diff --git a/src/USER-INTEL/npair_skip_intel.cpp b/src/USER-INTEL/npair_skip_intel.cpp index 3d2463a0b9..fa202d5da1 100644 --- a/src/USER-INTEL/npair_skip_intel.cpp +++ b/src/USER-INTEL/npair_skip_intel.cpp @@ -109,7 +109,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, int my_inum = ifrom; _inum_starts[tid] = ifrom; - + // loop over parent full list for (int ii = ifrom; ii < ito; ii++) { const int i = ilist_skip[ii]; @@ -131,7 +131,7 @@ void NPairSkipIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, const int j = joriginal & NEIGHMASK; if (!ijskip[itype][type[j]]) neighptr[n++] = joriginal; } - numhalf[my_inum] = n; + numhalf[my_inum] = n; for (int jj = jnumhalf; jj < jnum; jj++) { const int joriginal = jlist[jj]; diff --git a/src/USER-INTEL/npair_skip_intel.h b/src/USER-INTEL/npair_skip_intel.h index e3277708d5..6bb3dfa5d0 100644 --- a/src/USER-INTEL/npair_skip_intel.h +++ b/src/USER-INTEL/npair_skip_intel.h @@ -46,7 +46,7 @@ class NPairSkipIntel : public NPair { ~NPairSkipIntel(); virtual void copy_neighbor_info(); void build(class NeighList *); - + protected: FixIntel *_fix; int *_inum_starts, *_inum_counts, *_full_props; diff --git a/src/USER-INTEL/pair_airebo_intel.cpp b/src/USER-INTEL/pair_airebo_intel.cpp index 198f8798fa..f330e3ec86 100644 --- a/src/USER-INTEL/pair_airebo_intel.cpp +++ b/src/USER-INTEL/pair_airebo_intel.cpp @@ -292,8 +292,7 @@ template void PairAIREBOIntel::compute( int eflag, int vflag, IntelBuffers * buffers ) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); pvector[0] = pvector[1] = pvector[2] = 0.0; const int inum = list->inum; diff --git a/src/USER-INTEL/pair_airebo_intel.h b/src/USER-INTEL/pair_airebo_intel.h index 8a319536de..95e054fc0f 100644 --- a/src/USER-INTEL/pair_airebo_intel.h +++ b/src/USER-INTEL/pair_airebo_intel.h @@ -110,7 +110,7 @@ path and name are correct. E: Cannot yet use airebo/intel with hybrid. Pair style airebo/intel cannot currently be used as part of a hybrid -pair style (with the exception of hybrid/overlay). +pair style (with the exception of hybrid/overlay). */ diff --git a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp index 3954d559e1..3f2d64fb93 100644 --- a/src/USER-INTEL/pair_buck_coul_cut_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_cut_intel.cpp @@ -73,9 +73,7 @@ void PairBuckCoulCutIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -204,7 +202,7 @@ void PairBuckCoulCutIntel::eval(const int offload, const int vflag, acc_t oevdwl, oecoul, ov0, ov1, ov2, ov3, ov4, ov5; if (EFLAG || vflag) oevdwl = oecoul = ov0 = ov1 = ov2 = ov3 = ov4 = ov5 = (acc_t)0; - if (NEWTON_PAIR == 0 && inum != nlocal) + if (NEWTON_PAIR == 0 && inum != nlocal) memset(f_start, 0, f_stride * sizeof(FORCE_T)); // loop over neighbors of my atoms diff --git a/src/USER-INTEL/pair_buck_coul_long_intel.cpp b/src/USER-INTEL/pair_buck_coul_long_intel.cpp index 059413c3d9..2ddcd55663 100644 --- a/src/USER-INTEL/pair_buck_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_buck_coul_long_intel.cpp @@ -73,9 +73,7 @@ void PairBuckCoulLongIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_buck_intel.cpp b/src/USER-INTEL/pair_buck_intel.cpp index 0e0bd0f56f..34af3462e2 100644 --- a/src/USER-INTEL/pair_buck_intel.cpp +++ b/src/USER-INTEL/pair_buck_intel.cpp @@ -66,9 +66,7 @@ void PairBuckIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_dpd_intel.cpp b/src/USER-INTEL/pair_dpd_intel.cpp index 9baa64e8e0..016f3b5ca0 100644 --- a/src/USER-INTEL/pair_dpd_intel.cpp +++ b/src/USER-INTEL/pair_dpd_intel.cpp @@ -82,9 +82,7 @@ void PairDPDIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag, vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); const int inum = list->inum; const int nthreads = comm->nthreads; @@ -521,7 +519,7 @@ void PairDPDIntel::pack_force_const(ForceConst &fc, } } if (mytypes > 1 || atom->molecular) _onetype = 0; - + for (int i = 0; i < 4; i++) { fc.special_lj[i] = force->special_lj[i]; fc.special_lj[0] = 1.0; diff --git a/src/USER-INTEL/pair_eam_intel.cpp b/src/USER-INTEL/pair_eam_intel.cpp index 95d0272d33..7f4806c87c 100644 --- a/src/USER-INTEL/pair_eam_intel.cpp +++ b/src/USER-INTEL/pair_eam_intel.cpp @@ -78,9 +78,7 @@ void PairEAMIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag, vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_gayberne_intel.cpp b/src/USER-INTEL/pair_gayberne_intel.cpp index 51524355d5..1d9ee7d4cd 100644 --- a/src/USER-INTEL/pair_gayberne_intel.cpp +++ b/src/USER-INTEL/pair_gayberne_intel.cpp @@ -72,9 +72,7 @@ void PairGayBerneIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag, vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); const int inum = list->inum; const int nall = atom->nlocal + atom->nghost; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp index 0b6ac3ffa5..9689c0bf50 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_charmm_intel.cpp @@ -66,9 +66,7 @@ void PairLJCharmmCoulCharmmIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp index 753a9afdd9..8de4ced549 100644 --- a/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp @@ -70,9 +70,7 @@ void PairLJCharmmCoulLongIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp index 35ed9061ce..8ad1823d97 100644 --- a/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp @@ -71,9 +71,7 @@ void PairLJCutCoulLongIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_lj_cut_intel.cpp b/src/USER-INTEL/pair_lj_cut_intel.cpp index 94133a7f47..74dae7e096 100644 --- a/src/USER-INTEL/pair_lj_cut_intel.cpp +++ b/src/USER-INTEL/pair_lj_cut_intel.cpp @@ -62,9 +62,7 @@ void PairLJCutIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag, vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_sw_intel.cpp b/src/USER-INTEL/pair_sw_intel.cpp index 9e00516087..8482895fb6 100644 --- a/src/USER-INTEL/pair_sw_intel.cpp +++ b/src/USER-INTEL/pair_sw_intel.cpp @@ -95,9 +95,7 @@ void PairSWIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag, vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pair_tersoff_intel.cpp b/src/USER-INTEL/pair_tersoff_intel.cpp index 5d4c5f2cb6..668cb0cf33 100644 --- a/src/USER-INTEL/pair_tersoff_intel.cpp +++ b/src/USER-INTEL/pair_tersoff_intel.cpp @@ -107,9 +107,7 @@ void PairTersoffIntel::compute(int eflag, int vflag, IntelBuffers *buffers, const ForceConst &fc) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int inum = list->inum; const int nthreads = comm->nthreads; diff --git a/src/USER-INTEL/pppm_disp_intel.cpp b/src/USER-INTEL/pppm_disp_intel.cpp index 795fe1a47d..9d075c78a1 100644 --- a/src/USER-INTEL/pppm_disp_intel.cpp +++ b/src/USER-INTEL/pppm_disp_intel.cpp @@ -174,9 +174,7 @@ void PPPMDispIntel::compute(int eflag, int vflag) int i; // convert atoms from box to lamda coords - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) { allocate_peratom(); diff --git a/src/USER-INTEL/pppm_intel.cpp b/src/USER-INTEL/pppm_intel.cpp index f3fa8dd15d..e3d1e7d4aa 100644 --- a/src/USER-INTEL/pppm_intel.cpp +++ b/src/USER-INTEL/pppm_intel.cpp @@ -161,9 +161,7 @@ void PPPMIntel::compute_first(int eflag, int vflag) // set energy/virial flags // invoke allocate_peratom() if needed for first time - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); if (evflag_atom && !peratom_allocate_flag) { allocate_peratom(); @@ -586,7 +584,7 @@ void PPPMIntel::fieldforce_ik(IntelBuffers *buffers) if (force->newton_pair) zl += atom->nghost; memset(f, 0, zl * sizeof(FORCE_T)); } - + #if defined(_OPENMP) #pragma omp parallel default(none) \ shared(nlocal, nthr) if(!_use_lrt) @@ -737,7 +735,7 @@ void PPPMIntel::fieldforce_ad(IntelBuffers *buffers) if (force->newton_pair) zl += atom->nghost; memset(f, 0, zl * sizeof(FORCE_T)); } - + #if defined(_OPENMP) #pragma omp parallel default(none) \ shared(nlocal, nthr) if(!_use_lrt) diff --git a/src/USER-INTEL/verlet_lrt_intel.cpp b/src/USER-INTEL/verlet_lrt_intel.cpp index 5dd0da1939..2b28eea3a2 100644 --- a/src/USER-INTEL/verlet_lrt_intel.cpp +++ b/src/USER-INTEL/verlet_lrt_intel.cpp @@ -66,7 +66,7 @@ void VerletLRTIntel::init() { Verlet::init(); - _intel_kspace = (PPPMIntel*)(force->kspace_match("pppm/intel", 0)); + _intel_kspace = (PPPMIntel*)(force->kspace_match("^pppm/intel", 0)); #ifndef LMP_INTEL_USELRT error->all(FLERR, diff --git a/src/USER-LB/fix_lb_fluid.cpp b/src/USER-LB/fix_lb_fluid.cpp index fecd6f2b25..6f1dfc9982 100644 --- a/src/USER-LB/fix_lb_fluid.cpp +++ b/src/USER-LB/fix_lb_fluid.cpp @@ -231,7 +231,7 @@ a z wall velocity without implementing fixed BCs in z"); initializeLB = &FixLbFluid::initializeLB15; equilibriumdist = &FixLbFluid::equilibriumdist15; update_full = &FixLbFluid::update_full15; - }else{ + } else { initializeLB = &FixLbFluid::initializeLB19; equilibriumdist = &FixLbFluid::equilibriumdist19; update_full = &FixLbFluid::update_full19; @@ -379,7 +379,7 @@ a z wall velocity without implementing fixed BCs in z"); char str[128]; if(setdx == 1){ sprintf(str,"Using a lattice-Boltzmann grid of %i by %i by %i total grid points. To change, use the dx keyword",Nbx,Nby,Nbz); - }else{ + } else { sprintf(str,"Using a lattice-Boltzmann grid of %i by %i by %i total grid points.",Nbx,Nby,Nbz); } error->message(FLERR,str); @@ -544,7 +544,7 @@ FixLbFluid::~FixLbFluid() if(setGamma == 1){ delete [] Gamma; - }else{ + } else { delete [] NodeArea; } } @@ -841,7 +841,7 @@ void FixLbFluid::calc_fluidforce(void) if(mask[i] & groupbit){ if(trilinear_stencil==1) { trilinear_interpolation(i); - }else{ + } else { peskin_interpolation(i); } @@ -1017,37 +1017,37 @@ void FixLbFluid::peskin_interpolation(int i) for(ii=-1; ii<3; ii++){ rsq=(-dx1+ii)*(-dx1+ii); - if(rsq>=4) + if(rsq>=4) { weightx=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } for(jj=-1; jj<3; jj++){ rsq=(-dy1+jj)*(-dy1+jj); - if(rsq>=4) + if(rsq>=4) { weighty=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } for(kk=-1; kk<3; kk++){ rsq=(-dz1+kk)*(-dz1+kk); - if(rsq>=4) + if(rsq>=4) { weightz=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } @@ -1090,8 +1090,7 @@ require more frequent neighborlist rebuilds"); massone = massone/dm_lb; gammavalue = 2.0*(mnode*massone)*dtoverdtcollision/(mnode+massone); - } - else{ + } else { gammavalue = Gamma[type[i]]; } @@ -1219,7 +1218,7 @@ require more frequent neighborlist rebuilds"); massone = massone/dm_lb; gammavalue = 2.0*(mnode*massone)*dtoverdtcollision/(mnode+massone); - }else{ + } else { gammavalue = Gamma[type[i]]; } @@ -1350,7 +1349,7 @@ void FixLbFluid::rescale(void) for(int i=0; i<= atom->ntypes; i++){ NodeArea[i] = NodeArea[i]/dx_lb/dx_lb; } - }else{ + } else { for(int i=0; i<= atom->ntypes; i++){ Gamma[i] = Gamma[i]*dt_lb/dm_lb; } @@ -1388,11 +1387,11 @@ satisfy the Courant condition.\n"); noisefactor = 1.0; if(a_0 <= 0.333333333333333){ K_0 = 5.17*(0.333333333333333 - a_0); - }else{ + } else { K_0 = 2.57*(a_0 - 0.333333333333333); } dtoverdtcollision = dt_lb*6.0*viscosity/densityinit_real/dx_lb/dx_lb; - }else if(typeLB==2){ + } else if(typeLB==2){ expminusdtovertau=exp(-1.0/tau); Dcoeff=(1.0-(1.0-expminusdtovertau)*tau); namp = 2.0*kB*T/3.; @@ -1821,7 +1820,7 @@ void FixLbFluid::initialize_feq(void) // If using the standary LB integrator, do not need to send feqn. if(typeLB == 1){ numrequests = 4; - }else{ + } else { numrequests = 8; } @@ -1888,7 +1887,7 @@ void FixLbFluid::initialize_feq(void) feqoldn[i][j][k][p] = feqn[i][j][k][p]; } } - }else{ + } else { step = 1; read_restartfile(); @@ -2020,7 +2019,7 @@ void FixLbFluid::equilibriumdist15(int xstart, int xend, int ystart, int yend, i (u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox); Pyz = kappa_lb*drhoy*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)* (u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy); - }else if(typeLB==2){ + } else if(typeLB==2){ Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+tau*(1.0/3.0-dPdrho)* (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz); Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+tau*(1.0/3.0-dPdrho)* @@ -2198,7 +2197,7 @@ void FixLbFluid::equilibriumdist19(int xstart, int xend, int ystart, int yend, i (u_lb[i][j][k][0]*drhoz+u_lb[i][j][k][2]*drhox); Pyz = kappa_lb*drhoy*drhoz+(tau-0.5)*(1.0/3.0-dPdrho)* (u_lb[i][j][k][1]*drhoz+u_lb[i][j][k][2]*drhoy); - }else if(typeLB==2){ + } else if(typeLB==2){ Pxx = p0 + kappa_lb*(drhox*drhox - 0.5*grs)+tau*(1.0/3.0-dPdrho)* (3.0*u_lb[i][j][k][0]*drhox+u_lb[i][j][k][1]*drhoy+u_lb[i][j][k][2]*drhoz); Pyy = p0 + kappa_lb*(drhoy*drhoy - 0.5*grs)+tau*(1.0/3.0-dPdrho)* @@ -2489,7 +2488,7 @@ void FixLbFluid::update_periodic(int xstart, int xend, int ystart, int yend, int fnew[i][j][k][m] = f_lb[imod][jmod][kmod][m] + (feq[imod][jmod][kmod][m]-f_lb[imod][jmod][kmod][m])/tau; } - }else if(typeLB==2){ + } else if(typeLB==2){ for(m=0; mperiodicity[2]==0){ if(comm->myloc[2]==comm->procgrid[2]-1){ kstart=comm->myloc[2]*(subNbz-3); - }else{ + } else { kstart=comm->myloc[2]*(subNbz-2); } - }else{ + } else { kstart=comm->myloc[2]*(subNbz-2); } iend=istart+subNbx-2; @@ -2659,7 +2658,7 @@ void FixLbFluid::update_full15(void) //-------------------------------------------------------------------------- if(typeLB == 1){ numrequests = 4; - }else{ + } else { numrequests = 8; } @@ -2719,7 +2718,7 @@ void FixLbFluid::update_full15(void) if(typeLB==1){ update_periodic(1,subNbx-1,1,subNby-1,1,2); update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1); - }else if(typeLB==2){ + } else if(typeLB==2){ if(comm->myloc[2]==0){ for(i=1; imyloc[2]==comm->procgrid[2]-1){ @@ -2836,8 +2835,7 @@ void FixLbFluid::update_full15(void) } } } - } - else{ + } else { update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1); } } @@ -2866,8 +2864,7 @@ void FixLbFluid::update_full15(void) if(typeLB == 1){ fnew[i][j][k][5]=fnew[i][j][k-1][6]; tmp1=fnew[i][j][k-1][11]+fnew[i][j][k-1][12]+fnew[i][j][k-1][13]+fnew[i][j][k-1][14]; - } - else{ + } else { fnew[i][j][k][5]=fnew[i][j][k-1][6] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k+1][5]; tmp1=fnew[i][j][k-1][11]+fnew[i][j][k-1][12]+fnew[i][j][k-1][13]+fnew[i][j][k-1][14] + (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j-1][k+1][7] + feqn[i+1][j-1][k+1][8] + @@ -2908,8 +2905,7 @@ void FixLbFluid::update_full15(void) if(typeLB == 1){ fnew[i][j][k][6]=fnew[i][j][k+1][5]; tmp1=fnew[i][j][k+1][7]+fnew[i][j][k+1][8]+fnew[i][j][k+1][9]+fnew[i][j][k+1][10]; - } - else{ + } else { fnew[i][j][k][6]=fnew[i][j][k+1][5] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k-1][6]; tmp1=fnew[i][j][k+1][7]+fnew[i][j][k+1][8]+fnew[i][j][k+1][9]+fnew[i][j][k+1][10] + (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j-1][k-1][11] + feqn[i+1][j-1][k-1][12] + @@ -2941,7 +2937,7 @@ void FixLbFluid::update_full15(void) //-------------------------------------------------------------------------- // Periodic z boundary conditions. //-------------------------------------------------------------------------- - }else { + } else { for(i=0; imyloc[2]==0){ for(i=1; imyloc[2]==comm->procgrid[2]-1){ @@ -3193,8 +3189,7 @@ void FixLbFluid::update_full19(void) } } } - } - else{ + } else { update_periodic(1,subNbx-1,1,subNby-1,subNbz-2,subNbz-1); } } @@ -3224,8 +3219,7 @@ void FixLbFluid::update_full19(void) if(typeLB == 1){ fnew[i][j][k][5]=fnew[i][j][k-1][6]; tmp1=fnew[i][j][k-1][12]+fnew[i][j][k-1][14]+fnew[i][j][k-1][16]+fnew[i][j][k-1][18]; - } - else{ + } else { fnew[i][j][k][5]=fnew[i][j][k-1][6] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k+1][5]; tmp1=fnew[i][j][k-1][12]+fnew[i][j][k-1][14]+fnew[i][j][k-1][16]+fnew[i][j][k-1][18] + (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j][k+1][11] + feqn[i+1][j][k+1][13] + @@ -3261,8 +3255,7 @@ void FixLbFluid::update_full19(void) if(typeLB == 1){ fnew[i][j][k][6]=fnew[i][j][k+1][5]; tmp1=fnew[i][j][k+1][11]+fnew[i][j][k+1][13]+fnew[i][j][k+1][15]+fnew[i][j][k+1][17]; - } - else{ + } else { fnew[i][j][k][6]=fnew[i][j][k+1][5] + (0.5-Dcoeff*(tau+0.5))*feqn[i][j][k-1][6]; tmp1=fnew[i][j][k+1][11]+fnew[i][j][k+1][13]+fnew[i][j][k+1][15]+fnew[i][j][k+1][17] + (0.5-Dcoeff*(tau+0.5))*(feqn[i-1][j][k-1][12] + feqn[i+1][j][k-1][14] + @@ -3290,7 +3283,7 @@ void FixLbFluid::update_full19(void) //-------------------------------------------------------------------------- // Periodic z boundary conditions. //-------------------------------------------------------------------------- - }else { + } else { for(i=0; iftm2v/Gamma_MD[type[i]])*expminusdttimesgamma + f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0]; v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma + @@ -195,7 +195,7 @@ void FixLbPC::initial_integrate(int /*vflag*/) { v[i][0] += f[i][0]*dtfm; v[i][1] += f[i][1]*dtfm; v[i][2] += f[i][2]*dtfm; - }else{ + } else { v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma + f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0]; v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma + @@ -234,7 +234,7 @@ void FixLbPC::final_integrate() v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm; v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm; v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm; - }else{ + } else { v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv; v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv; v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv; @@ -255,7 +255,7 @@ void FixLbPC::final_integrate() v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm; v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm; v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm; - }else{ + } else { v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv; v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv; v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv; @@ -387,37 +387,37 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf) for(ii=-1; ii<3; ii++){ rsq=(-dx1+ii)*(-dx1+ii); - if(rsq>=4) + if(rsq>=4) { weightx=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } for(jj=-1; jj<3; jj++){ rsq=(-dy1+jj)*(-dy1+jj); - if(rsq>=4) + if(rsq>=4) { weighty=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } for(kk=-1; kk<3; kk++){ rsq=(-dz1+kk)*(-dz1+kk); - if(rsq>=4) + if(rsq>=4) { weightz=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } @@ -438,7 +438,7 @@ int FixLbPC::unpack_exchange(int nlocal, double *buf) } } } - }else{ + } else { FfP[0] = (1.-dx1)*(1.-dy1)*(1.-dz1); FfP[1] = (1.-dx1)*(1.-dy1)*dz1; FfP[2] = (1.-dx1)*dy1*(1.-dz1); diff --git a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp index 2601539727..83dc751631 100644 --- a/src/USER-LB/fix_lb_rigid_pc_sphere.cpp +++ b/src/USER-LB/fix_lb_rigid_pc_sphere.cpp @@ -178,7 +178,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) : delete [] igroups; - }else error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command"); + } else error->all(FLERR,"Illegal fix lb/rigid/pc/sphere command"); // error check on nbody @@ -328,7 +328,7 @@ FixLbRigidPCSphere::FixLbRigidPCSphere(LAMMPS *lmp, int narg, char **arg) : MPI_Allreduce(ncount,nrigid,nbody,MPI_INT,MPI_SUM,world); //count the number of atoms in the shell. - if(inner_nodes == 1){ + if (inner_nodes == 1) { int *mask = atom->mask; for(ibody=0; ibodybitmask[igroupinner])) error->one(FLERR,"the inner nodes specified in lb/rigid/pc/sphere should not be included in the lb/fluid fix"); } - }else{ + } else { for(int j=0; jone(FLERR,"use the innerNodes keyword in the lb/rigid/pc/sphere fix for atoms which do not interact with the lb/fluid"); @@ -536,7 +536,7 @@ void FixLbRigidPCSphere::init() if(!(mask[i] & group->bitmask[igroupinner])){ sum[ibody][4] += massone; } - }else{ + } else { sum[ibody][4] += massone; } } @@ -581,7 +581,7 @@ void FixLbRigidPCSphere::init() sum[ibody][0] += dx*dx + dy*dy + dz*dz; sum[ibody][1] += Gamma[type[i]]; } - }else{ + } else { ibody = body[i]; xbox = (image[i] & IMGMASK) - IMGMAX; @@ -619,7 +619,7 @@ void FixLbRigidPCSphere::init() if(Gamma_MD[ibody]*dt_lb/dm_lb - Gamma[type[i]] > eps) error->one(FLERR,"All atoms in a rigid body must have the same gamma value"); } - }else{ + } else { ibody = body[i]; if(Gamma_MD[ibody]*dt_lb/dm_lb - Gamma[type[i]] > eps) @@ -798,7 +798,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag) sum[ibody][1] += up[i][1]*massone; sum[ibody][2] += up[i][2]*massone; } - }else{ + } else { sum[ibody][0] += up[i][0]*massone; sum[ibody][1] += up[i][1]*massone; sum[ibody][2] += up[i][2]*massone; @@ -841,7 +841,7 @@ void FixLbRigidPCSphere::initial_integrate(int vflag) sum[ibody][4] += -Gamma_MD[ibody]*(v[i][1]-up[i][1]); sum[ibody][5] += -Gamma_MD[ibody]*(v[i][2]-up[i][2]); } - }else{ + } else { sum[ibody][0] += Gamma_MD[ibody]*(dy * ((up[i][2]-vcm[ibody][2])) - dz * ((up[i][1]-vcm[ibody][1]))); sum[ibody][1] += Gamma_MD[ibody]*(dz * ((up[i][0]-vcm[ibody][0])) - @@ -1054,7 +1054,7 @@ void FixLbRigidPCSphere::final_integrate() sum[ibody][5] += Gamma_MD[ibody]*(dx * ((up[i][1]-vcm[ibody][1])) - dy * ((up[i][0]-vcm[ibody][0]))); } - }else{ + } else { sum[ibody][0] += up[i][0]*massone; sum[ibody][1] += up[i][1]*massone; sum[ibody][2] += up[i][2]*massone; @@ -1336,8 +1336,9 @@ void FixLbRigidPCSphere::pre_neighbor() original = imagebody[ibody]; domain->remap(xcm[ibody],imagebody[ibody]); - if (original == imagebody[ibody]) remapflag[ibody][3] = 0; - else { + if (original == imagebody[ibody]) { + remapflag[ibody][3] = 0; + } else { oldimage = original & IMGMASK; newimage = imagebody[ibody] & IMGMASK; remapflag[ibody][0] = newimage - oldimage; @@ -1608,37 +1609,37 @@ double FixLbRigidPCSphere::compute_array(int i, int j) for(ii=-1; ii<3; ii++){ rsq=(-dx1+ii)*(-dx1+ii); - if(rsq>=4) + if(rsq>=4) { weightx=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } for(jj=-1; jj<3; jj++){ rsq=(-dy1+jj)*(-dy1+jj); - if(rsq>=4) + if(rsq>=4) { weighty=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } for(kk=-1; kk<3; kk++){ rsq=(-dz1+kk)*(-dz1+kk); - if(rsq>=4) + if(rsq>=4) { weightz=0.0; - else{ + } else { r=sqrt(rsq); if(rsq>1){ weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.; - } else{ + } else { weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.; } } @@ -1659,7 +1660,7 @@ double FixLbRigidPCSphere::compute_array(int i, int j) } } } - }else{ + } else { FfP[0] = (1.-dx1)*(1.-dy1)*(1.-dz1); FfP[1] = (1.-dx1)*(1.-dy1)*dz1; FfP[2] = (1.-dx1)*dy1*(1.-dz1); diff --git a/src/USER-MANIFOLD/fix_manifoldforce.cpp b/src/USER-MANIFOLD/fix_manifoldforce.cpp index 4e717ce556..00293bfec7 100644 --- a/src/USER-MANIFOLD/fix_manifoldforce.cpp +++ b/src/USER-MANIFOLD/fix_manifoldforce.cpp @@ -53,14 +53,14 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : // Command is given as // fix manifoldforce manifold_name manifold_args - if( narg < 5 ){ + if (narg < 5) { error->all(FLERR,"Illegal fix manifoldforce! No manifold given"); } const char *m_name = arg[3]; ptr_m = create_manifold(m_name,lmp,narg,arg); // Construct manifold from factory: - if( !ptr_m ){ + if (!ptr_m) { char msg[2048]; snprintf(msg,2048,"Manifold pointer for manifold '%s' was NULL for some reason", arg[3]); error->all(FLERR,msg); @@ -70,7 +70,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : // After constructing the manifold, you can safely make // room for the parameters nvars = ptr_m->nparams(); - if( narg < nvars+4 ){ + if (narg < nvars+4) { char msg[2048]; sprintf(msg,"Manifold %s needs at least %d argument(s)!", m_name, nvars); @@ -78,7 +78,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : } ptr_m->params = new double[nvars]; - if( ptr_m->params == NULL ){ + if (ptr_m->params == NULL) { error->all(FLERR,"Parameter pointer was NULL!"); } @@ -89,7 +89,7 @@ FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) : double *params = ptr_m->params; for( int i = 0; i < nvars; ++i ){ - if( was_var( arg[i+4] ) ) + if (was_var( arg[i+4] )) error->all(FLERR,"Equal-style variables not allowed with fix manifoldforce"); // Use force->numeric to trigger an error if arg is not a number. diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp index 3c6c70f6df..794a324f03 100644 --- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp @@ -84,8 +84,8 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, int error_on_unknown_keyword ) : Fix(lmp,narg,arg) { - if( lmp->citeme) lmp->citeme->add(cite_fix_nve_manifold_rattle); - if( narg < 6 ) error->all(FLERR, "Illegal fix nve/manifold/rattle command"); + if (lmp->citeme) lmp->citeme->add(cite_fix_nve_manifold_rattle); + if (narg < 6 ) error->all(FLERR, "Illegal fix nve/manifold/rattle command"); // Set all bits/settings: time_integrate = 1; @@ -101,7 +101,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, max_iter = force->numeric( FLERR, arg[4] ); ptr_m = create_manifold(arg[5], lmp, narg, arg); - if( !ptr_m ){ + if (!ptr_m) { error->all(FLERR,"Error creating manifold pointer"); } @@ -111,12 +111,12 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, tstyle = new int[nvars]; is_var = new int[nvars]; - if( !tstrs || !tvars || !tstyle || !is_var ){ + if (!tstrs || !tvars || !tstyle || !is_var) { error->all(FLERR, "Error creating manifold arg arrays"); } // Check if you have enough args: - if( 6 + nvars > narg ){ + if (6 + nvars > narg) { char msg[2048]; sprintf(msg, "Not enough args for manifold %s, %d expected but got %d\n", ptr_m->id(), nvars, narg - 6); @@ -125,22 +125,22 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, // Loop over manifold args: for( int i = 0; i < nvars; ++i ){ int len = 0, offset = 0; - if( was_var( arg[i+6] ) ){ + if (was_var( arg[i+6] )) { len = strlen(arg[i+6]) - 1; // -1 because -2 for v_, +1 for \0. is_var[i] = 1; offset = 2; - }else{ + } else { force->numeric(FLERR,arg[i+6]); // Check if legal number. len = strlen( arg[i+6] ) + 1; // +1 for \0. is_var[i] = 0; } tstrs[i] = new char[len]; - if( tstrs[i] == NULL ) error->all(FLERR,"Error allocating space for args."); + if (tstrs[i] == NULL ) error->all(FLERR,"Error allocating space for args."); strcpy( tstrs[i], arg[i+6] + offset ); } ptr_m->params = new double[nvars]; - if( !ptr_m->params ) error->all(FLERR,"Failed to allocate params!"); + if (!ptr_m->params ) error->all(FLERR,"Failed to allocate params!"); for( int i = 0; i < nvars; ++i ){ // If param i was variable type, it will be set later... ptr_m->params[i] = is_var[i] ? 0.0 : force->numeric( FLERR, arg[i+6] ); @@ -151,19 +151,19 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, // Loop over rest of args: int argi = 6 + nvars; while( argi < narg ){ - if( strcmp(arg[argi], "every") == 0 ){ + if (strcmp(arg[argi], "every") == 0) { nevery = force->inumeric(FLERR,arg[argi+1]); next_output = update->ntimestep + nevery; - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"Outputing every %d steps, next is %d\n", nevery, next_output); } argi += 2; - }else if( error_on_unknown_keyword ){ + } else if (error_on_unknown_keyword) { char msg[2048]; sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]); error->all(FLERR, msg); - }else{ + } else { argi += 1; } } @@ -175,16 +175,16 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg, ---------------------------------------------------------------------------*/ FixNVEManifoldRattle::~FixNVEManifoldRattle() { - if( tstrs ){ + if (tstrs) { for( int i = 0; i < nvars; ++i ){ delete [] tstrs[i]; } delete [] tstrs; } - if( tvars ) delete [] tvars; - if( tstyle ) delete [] tstyle; - if( is_var ) delete [] is_var; + if (tvars ) delete [] tvars; + if (tstyle) delete [] tstyle; + if (is_var) delete [] is_var; } @@ -204,7 +204,7 @@ void FixNVEManifoldRattle::reset_dt() void FixNVEManifoldRattle::print_stats( const char *header ) { double n = stats.natoms; - if( n > 0 ){ + if (n > 0) { stats.x_iters_per_atom += stats.x_iters / n; stats.v_iters_per_atom += stats.v_iters / n; } @@ -223,7 +223,7 @@ void FixNVEManifoldRattle::print_stats( const char *header ) stats.v_iters_per_atom = stats.v_iters = 0; - if( me == 0 ){ + if (me == 0) { double inv_tdiff = 1.0/( static_cast(ntimestep) - stats.last_out ); stats.last_out = ntimestep; @@ -245,9 +245,9 @@ void FixNVEManifoldRattle::print_stats( const char *header ) ---------------------------------------------------------------------------*/ int FixNVEManifoldRattle::was_var( const char *str ) { - if( strlen(str) > 2 ){ + if (strlen(str) > 2) { return (str[0] == 'v') && (str[1] == '_'); - }else{ + } else { return 0; } } @@ -261,7 +261,7 @@ int FixNVEManifoldRattle::setmask() int mask = 0; mask |= INITIAL_INTEGRATE; mask |= FINAL_INTEGRATE; - if( nevery > 0 ) mask |= END_OF_STEP; + if (nevery > 0) mask |= END_OF_STEP; return mask; } @@ -284,18 +284,18 @@ void FixNVEManifoldRattle::update_var_params() double *ptr_params = ptr_m->params; for( int i = 0; i < nvars; ++i ){ - if( is_var[i] ){ + if (is_var[i]) { tvars[i] = input->variable->find(tstrs[i]); - if( tvars[i] < 0 ){ + if (tvars[i] < 0) { error->all(FLERR, "Variable name for fix nve/manifold/rattle does not exist"); } - if( input->variable->equalstyle(tvars[i]) ){ + if (input->variable->equalstyle(tvars[i])) { tstyle[i] = EQUAL; double new_val = input->variable->compute_equal(tvars[i]); ptr_params[i] = new_val; - }else{ + } else { error->all(FLERR, "Variable for fix nve/manifold/rattle is invalid style"); } @@ -322,7 +322,7 @@ int FixNVEManifoldRattle::dof(int /*igroup*/) // Make sure that, if there is just no or one atom, no dofs are subtracted, // since for the first atom already 3 dofs are subtracted because of the // centre of mass corrections: - if( dofs <= 1 ) dofs = 0; + if (dofs <= 1) dofs = 0; stats.dofs_removed = dofs; return dofs; @@ -369,7 +369,7 @@ void FixNVEManifoldRattle::final_integrate() void FixNVEManifoldRattle::end_of_step() { if (nevery && (update->ntimestep == next_output)){ - if( comm->me == 0 ){ + if (comm->me == 0) { print_stats( "nve/manifold/rattle" ); next_output += nevery; } @@ -415,7 +415,7 @@ void FixNVEManifoldRattle::nve_x_rattle(int igroup, int groupbit) } } - if( nevery > 0 ){ + if (nevery > 0) { // Count ALL atoms this fix works on: MPI_Allreduce(&natoms,&stats.natoms,1,MPI_INT,MPI_SUM,world); } @@ -549,7 +549,7 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v, res = infnorm<4>(R); ++iters; - if( (res < tolerance) || (iters >= max_iter) ) break; + if ((res < tolerance) || (iters >= max_iter)) break; // Update nn and g. gg = ptr_m->g(x); @@ -557,7 +557,7 @@ void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v, // gg = ptr_m->g(x); } - if( iters >= max_iter && res > tolerance ){ + if (iters >= max_iter && res > tolerance) { char msg[2048]; sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n", tagi, x[0], x[1], x[2], res, iters); @@ -650,7 +650,7 @@ void FixNVEManifoldRattle::rattle_manifold_v(double *v, double *f, ++iters; }while( (res > tolerance) && (iters < max_iter) ); - if( iters >= max_iter && res >= tolerance ){ + if (iters >= max_iter && res >= tolerance) { char msg[2048]; sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n", tagi, x[0], x[1], x[2], res, iters); diff --git a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp index 2a204d2048..a4eed66336 100644 --- a/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp +++ b/src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp @@ -86,7 +86,7 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, { if (lmp->citeme) lmp->citeme->add(cite_fix_nvt_manifold_rattle); - if( narg < 6 ) error->all(FLERR,"Illegal fix nvt/manifold/rattle command"); + if (narg < 6 ) error->all(FLERR,"Illegal fix nvt/manifold/rattle command"); // Set all bits/settings: dof_flag = 1; @@ -104,8 +104,8 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, int argi = 6 + ptr_m->nparams(); while( argi < narg ) { - if( strcmp( arg[argi], "temp") == 0 ){ - if( argi+3 >= narg ) + if (strcmp( arg[argi], "temp") == 0) { + if (argi+3 >= narg) error->all(FLERR,"Keyword 'temp' needs 3 arguments"); t_start = force->numeric(FLERR, arg[argi+1]); @@ -115,26 +115,26 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, got_temp = 1; argi += 4; - }else if( strcmp( arg[argi], "tchain" ) == 0 ){ - if( argi+1 >= narg ) + } else if (strcmp( arg[argi], "tchain" ) == 0) { + if (argi+1 >= narg) error->all(FLERR,"Keyword 'tchain' needs 1 argument"); mtchain = force->inumeric(FLERR, arg[argi+1]); argi += 2; - }else if( error_on_unknown_keyword ){ + } else if (error_on_unknown_keyword) { char msg[2048]; sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]); error->all(FLERR, msg); - }else{ + } else { argi += 1; } } reset_dt(); - if( !got_temp ) error->all(FLERR,"Fix nvt/manifold/rattle needs 'temp'!"); + if (!got_temp ) error->all(FLERR,"Fix nvt/manifold/rattle needs 'temp'!"); - if( t_period < 0.0 ){ + if (t_period < 0.0) { error->all(FLERR,"Fix nvt/manifold/rattle damping parameter must be > 0.0"); } @@ -153,12 +153,12 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, modify->add_compute(3,newarg); delete [] newarg; int icompute = modify->find_compute(id_temp); - if( icompute < 0 ){ + if (icompute < 0) { error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle " "does not exist"); } temperature = modify->compute[icompute]; - if( temperature->tempbias ) which = BIAS; + if (temperature->tempbias) which = BIAS; else which = NOBIAS; // Set t_freq from t_period @@ -184,13 +184,13 @@ FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg, FixNVTManifoldRattle::~FixNVTManifoldRattle() { // Deallocate heap-allocated objects. - if( eta ) delete[] eta; - if( eta_dot ) delete[] eta_dot; - if( eta_dotdot ) delete[] eta_dotdot; - if( eta_mass ) delete[] eta_mass; + if (eta) delete[] eta; + if (eta_dot) delete[] eta_dot; + if (eta_dotdot) delete[] eta_dotdot; + if (eta_mass) delete[] eta_mass; modify->delete_compute(id_temp); - if( id_temp ) delete[] id_temp; + if (id_temp) delete[] id_temp; } @@ -201,7 +201,7 @@ int FixNVTManifoldRattle::setmask() int mask = 0; mask |= INITIAL_INTEGRATE; mask |= FINAL_INTEGRATE; - if( nevery > 0 ) mask |= END_OF_STEP; + if (nevery > 0) mask |= END_OF_STEP; return mask; } @@ -217,12 +217,12 @@ void FixNVTManifoldRattle::init() update_var_params(); int icompute = modify->find_compute(id_temp); - if( icompute < 0 ){ + if (icompute < 0) { error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle " "does not exist"); } temperature = modify->compute[icompute]; - if( temperature->tempbias ) which = BIAS; + if (temperature->tempbias) which = BIAS; else which = NOBIAS; } @@ -279,9 +279,9 @@ void FixNVTManifoldRattle::nhc_temp_integrate() eta_mass[ich] = boltz * t_target * inv_t_freq2; } - if( eta_mass[0] > 0.0 ){ + if (eta_mass[0] > 0.0) { eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0]; - }else{ + } else { eta_dotdot[0] = 0; } @@ -300,7 +300,7 @@ void FixNVTManifoldRattle::nhc_temp_integrate() factor_eta = exp(-dthalf*eta_dot[0]); - if( factor_eta == 0 ){ + if (factor_eta == 0) { char msg[2048]; sprintf(msg, "WTF, factor_eta is 0! dthalf = %f, eta_dot[0] = %f", dthalf, eta_dot[0]); @@ -312,9 +312,9 @@ void FixNVTManifoldRattle::nhc_temp_integrate() t_current *= factor_eta*factor_eta; kecurrent = tdof * boltz * t_current; - if( eta_mass[0] > 0.0 ){ + if (eta_mass[0] > 0.0) { eta_dotdot[0] = (kecurrent - ke_target) / eta_mass[0]; - }else{ + } else { eta_dotdot[0] = 0.0; } @@ -341,22 +341,22 @@ void FixNVTManifoldRattle::nh_v_temp() double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; - if( igroup == atom->firstgroup) nlocal = atom->nfirst; + if (igroup == atom->firstgroup) nlocal = atom->nfirst; - if( which == NOBIAS ){ + if (which == NOBIAS) { for( int i = 0; i < nlocal; ++i ){ - if( mask[i] & groupbit ){ + if (mask[i] & groupbit) { v[i][0] *= factor_eta; v[i][1] *= factor_eta; v[i][2] *= factor_eta; } } - }else if( which == BIAS ){ + } else if (which == BIAS) { for( int i = 0; i < nlocal; ++i ){ - if( mask[i] & groupbit ){ + if (mask[i] & groupbit) { temperature->remove_bias(i,v[i]); v[i][0] *= factor_eta; v[i][1] *= factor_eta; diff --git a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp index 4df4c833d3..6fe8e3453c 100644 --- a/src/USER-MANIFOLD/manifold_cylinder_dent.cpp +++ b/src/USER-MANIFOLD/manifold_cylinder_dent.cpp @@ -17,11 +17,11 @@ double manifold_cylinder_dent::g( const double *x ) { double l = params[1], R = params[0], a = params[2]; double r2 = x[1]*x[1] + x[0]*x[0]; - if( fabs(x[2]) < 0.5*l ){ + if (fabs(x[2]) < 0.5*l) { double k = MathConst::MY_2PI / l; double c = R - 0.5*a*( 1.0 + cos(k*x[2]) ); return c*c - r2; - }else{ + } else { return R*R - r2; } } @@ -30,13 +30,13 @@ double manifold_cylinder_dent::g( const double *x ) void manifold_cylinder_dent::n( const double *x, double *n ) { double l = params[1], R = params[0], a = params[2]; - if( fabs(x[2]) < 0.5*l ){ + if (fabs(x[2]) < 0.5*l) { double k = MathConst::MY_2PI / l; double c = R - 0.5*a*(1.0 + cos(k*x[2])); n[0] = -2*x[0]; n[1] = -2*x[1]; n[2] = c*a*k*sin(k*x[2]); - }else{ + } else { n[0] = -2*x[0]; n[1] = -2*x[1]; n[2] = 0.0; diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp index b95162740b..b9b7ae7279 100644 --- a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp +++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp @@ -42,15 +42,15 @@ public: void test() { - if( fabs( x(0) - x0 ) > 1e-8 ) err->one(FLERR, "x0 wrong"); - if( fabs( x(1) - x1 ) > 1e-8 ) err->one(FLERR, "x1 wrong"); - if( fabs( y(0) - y0 ) > 1e-8 ) err->one(FLERR, "y0 wrong"); - if( fabs( y(1) - y1 ) > 1e-8 ) err->one(FLERR, "y1 wrong"); + if (fabs( x(0) - x0 ) > 1e-8 ) err->one(FLERR, "x0 wrong"); + if (fabs( x(1) - x1 ) > 1e-8 ) err->one(FLERR, "x1 wrong"); + if (fabs( y(0) - y0 ) > 1e-8 ) err->one(FLERR, "y0 wrong"); + if (fabs( y(1) - y1 ) > 1e-8 ) err->one(FLERR, "y1 wrong"); } double get_t_from_x( double xx ) const { - if( xx < x0 || xx > x1 ){ + if (xx < x0 || xx > x1) { char msg[2048]; sprintf(msg, "x ( %g ) out of bounds [%g, %g]", xx, x0, x1 ); err->one(FLERR, msg); @@ -72,7 +72,7 @@ public: ff = x(t) - xx; ffp = xp(t); double res = ff; - if( fabs( res ) < tol ){ + if (fabs( res ) < tol) { return t; } } @@ -139,8 +139,8 @@ manifold_gaussian_bump::manifold_gaussian_bump(class LAMMPS* lmp, manifold_gaussian_bump::~manifold_gaussian_bump() { - if( lut_z ) delete lut_z; - if( lut_zp ) delete lut_zp; + if (lut_z ) delete lut_z; + if (lut_zp) delete lut_zp; } @@ -157,13 +157,13 @@ double manifold_gaussian_bump::g( const double *x ) xf[2] = 0.0; double x2 = dot(xf,xf); - if( x2 < rc12 ){ + if (x2 < rc12) { return x[2] - gaussian_bump_x2( x2 ); - }else if( x2 < rc22 ){ + } else if (x2 < rc22) { double rr = sqrt( x2 ); double z_taper_func = lut_get_z( rr ); return x[2] - z_taper_func; - }else{ + } else { return x[2]; } } @@ -178,12 +178,12 @@ void manifold_gaussian_bump::n( const double *x, double *nn ) double x2 = dot(xf,xf); - if( x2 < rc12 ){ + if (x2 < rc12) { double factor = gaussian_bump_x2(x2); factor /= (ll*ll); nn[0] = factor * x[0]; nn[1] = factor * x[1]; - }else if( x2 < rc22 ){ + } else if (x2 < rc22) { double rr = sqrt( x2 ); double zp_taper_func = lut_get_zp( rr ); @@ -193,7 +193,7 @@ void manifold_gaussian_bump::n( const double *x, double *nn ) nn[0] = der_part * x[0]; nn[1] = der_part * x[1]; - }else{ + } else { nn[0] = nn[1] = 0.0; } } @@ -207,14 +207,14 @@ double manifold_gaussian_bump::g_and_n( const double *x, double *nn ) nn[2] = 1.0; double x2 = dot(xf,xf); - if( x2 < rc12 ){ + if (x2 < rc12) { double gb = gaussian_bump_x2(x2); double factor = gb / (ll*ll); nn[0] = factor * x[0]; nn[1] = factor * x[1]; return x[2] - gb; - }else if( x2 < rc22 ){ + } else if (x2 < rc22) { double z_taper_func, zp_taper_func; double rr = sqrt( x2 ); lut_get_z_and_zp( rr, z_taper_func, zp_taper_func ); @@ -226,7 +226,7 @@ double manifold_gaussian_bump::g_and_n( const double *x, double *nn ) nn[1] = der_part * x[1]; return x[2] - z_taper_func; - }else{ + } else { nn[0] = nn[1] = 0.0; return x[2]; } @@ -349,7 +349,7 @@ void manifold_gaussian_bump::lut_get_z_and_zp( double rr, double &zz, void manifold_gaussian_bump::test_lut() { double x[3], nn[3]; - if( comm->me != 0 ) return; + if (comm->me != 0) return; FILE *fp = fopen( "test_lut_gaussian.dat", "w" ); double dx = 0.1; @@ -360,11 +360,11 @@ void manifold_gaussian_bump::test_lut() double gg = g( x ); n( x, nn ); double taper_z; - if( xx <= rc1 ){ + if (xx <= rc1) { taper_z = gaussian_bump(xx); - }else if( xx < rc2 ){ + } else if (xx < rc2) { taper_z = lut_get_z( xx ); - }else{ + } else { taper_z = 0.0; } fprintf( fp, "%g %g %g %g %g %g %g\n", xx, gaussian_bump(xx), taper_z, diff --git a/src/USER-MANIFOLD/manifold_spine.cpp b/src/USER-MANIFOLD/manifold_spine.cpp index 0ca4c67002..9641f53885 100644 --- a/src/USER-MANIFOLD/manifold_spine.cpp +++ b/src/USER-MANIFOLD/manifold_spine.cpp @@ -45,10 +45,10 @@ double manifold_spine::g_and_n( const double *x, double *nn ) double AMs, AMc; double dazc, dAMs; - if( x[2] > 0 ){ + if (x[2] > 0) { BB = B; cc = c; - }else{ + } else { BB = B2; cc = 1.0; } @@ -94,10 +94,10 @@ void manifold_spine::n( const double *x, double *nn ) double AMs, AMc; double dazc, dAMs; - if( x[2] > 0 ){ + if (x[2] > 0) { BB = B; cc = c; - }else{ + } else { BB = B2; cc = 1.0; } @@ -138,10 +138,10 @@ double manifold_spine::g( const double *x ) double c2, As, azc, Apart; double AMs; - if( x[2] > 0 ){ + if (x[2] > 0) { BB = B; cc = c; - }else{ + } else { BB = B2; cc = 1.0; } diff --git a/src/USER-MANIFOLD/manifold_thylakoid.cpp b/src/USER-MANIFOLD/manifold_thylakoid.cpp index 93cf60ad03..530e0a876d 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid.cpp @@ -46,7 +46,7 @@ void manifold_thylakoid::post_param_init() LB = params[1]; lB = params[2]; - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"My params are now: lT = %f, LT = %f, pad = %f, " "wB = %f, LB = %f, lB = %f\n", lT, LT, pad, wB, LB, lB ); fprintf(screen,"Calling init_domains() from post_param_init().\n"); @@ -57,7 +57,7 @@ void manifold_thylakoid::post_param_init() void manifold_thylakoid::checkup() { - if( comm->me == 0 ){ + if (comm->me == 0 ) { fprintf(screen,"This is checkup of thylakoid %p\n", this); fprintf(screen,"I have %ld parts. They are:\n", parts.size()); for( int i = 0; i < parts.size(); ++i ){ @@ -85,9 +85,9 @@ double manifold_thylakoid::g( const double *x ) error->one(FLERR,msg); } double con_val = p->g(x); - if( std::isfinite(con_val) ){ + if (std::isfinite(con_val)) { return con_val; - }else{ + } else { char msg[2048]; sprintf(msg,"Error, thyla_part of type %d returned %f as constraint val!", p->type, con_val); @@ -107,9 +107,9 @@ void manifold_thylakoid::n( const double *x, double *n ) error->one(FLERR,msg); } p->n(x,n); - if( std::isfinite(n[0]) && std::isfinite(n[1]) && std::isfinite(n[2]) ){ + if (std::isfinite(n[0]) && std::isfinite(n[1]) && std::isfinite(n[2])) { return; - }else{ + } else { char msg[2048]; sprintf(msg,"Error, thyla_part of type %d returned (%f,%f,%f) as gradient!", p->type, n[0], n[1], n[2]); @@ -122,8 +122,8 @@ thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_fla for( std::size_t i = 0; i < parts.size(); ++i ){ thyla_part *p = parts[i]; - if( is_in_domain(p,x) ){ - if( idx != NULL ) *idx = i; + if (is_in_domain(p,x)) { + if (idx != NULL) *idx = i; return p; } } @@ -140,7 +140,7 @@ thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int * /*err_fla void manifold_thylakoid::init_domains() { - if( wB + 2*lB > LT ){ + if (wB + 2*lB > LT) { char msg[2048]; sprintf(msg,"LT = %f not large enough to accomodate bridge with " "wB = %f and lB = %f! %f > %f\n", LT, wB, lB, wB + 2*lB, LT); @@ -152,19 +152,19 @@ void manifold_thylakoid::init_domains() y0 = -( 0.5*LT + lT + pad ); z0 = -15; #ifdef MANIFOLD_THYLAKOID_DEBUG - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"x0, y0, z0 = %f, %f, %f\n",x0,y0,z0); } #endif // MANIFOLD_THYLAKOID_DEBUG #ifndef USE_PHONY_LAMMPS - if( x0 < domain->boxlo[0] ){ + if (x0 < domain->boxlo[0]) { char msg[2048]; sprintf(msg,"Thylakoid expects xlo of at most %f, but found %f", x0, domain->boxlo[0]); error->one(FLERR,msg); } - if( y0 < domain->boxlo[1] ){ + if (y0 < domain->boxlo[1]) { char msg[2048]; sprintf(msg,"Thylakoid expects ylo of at most %f, but found %f", y0, domain->boxlo[1]); @@ -243,7 +243,7 @@ void manifold_thylakoid::init_domains() // double X0, double R0, double R, double s, #ifdef MANIFOLD_THYLAKOID_DEBUG - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"x0, r0, R = %f, %f, %f\n", bl.pt[0], rB, lB); } #endif // MANIFOLD_THYLAKOID_DEBUG @@ -266,7 +266,7 @@ void manifold_thylakoid::init_domains() // double X0, double R0, double R, double s, #ifdef MANIFOLD_THYLAKOID_DEBUG - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"x0, r0, R = %f, %f, %f\n", br.pt[0], rB, lB); } #endif // MANIFOLD_THYLAKOID_DEBUG @@ -293,7 +293,7 @@ void manifold_thylakoid::init_domains() p = make_cyl_part( 0, 1, 1, bc.pt, rB ); set_domain( p, bc.lo, bc.hi ); #ifdef MANIFOLD_THYLAKOID_DEBUG - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"Cylinder lives on [ %f x %f ] x [ %f x %f ] x [ %f x %f]\n", bc.lo[0], bc.hi[0], bc.lo[1], bc.hi[1], bc.lo[2], bc.hi[2]); } @@ -405,7 +405,7 @@ void manifold_thylakoid::init_domains() parts.push_back(p); // Check if this plane lines up with bl: - if( fabs(plr.pt[0] - bl.pt[0] + lB) > 1e-8 ){ + if (fabs(plr.pt[0] - bl.pt[0] + lB) > 1e-8) { char msg[2048]; sprintf(msg,"Origins of plane left right and bridge left misaligned! %f != %f!\n", plr.pt[0], bl.pt[0] - lB ); @@ -458,7 +458,7 @@ void manifold_thylakoid::init_domains() set_domain(p, prr.lo, prr.hi); parts.push_back(p); - if( fabs(prr.pt[0] - br.pt[0] - lB) > 1e-8 ){ + if (fabs(prr.pt[0] - br.pt[0] - lB) > 1e-8) { char msg[2048]; sprintf(msg,"Origins of plane left right and bridge left misaligned! %f != %f!\n", prr.pt[0], br.pt[0] + lB); @@ -467,7 +467,7 @@ void manifold_thylakoid::init_domains() // For debugging, print the domains and coms: #ifdef MANIFOLD_THYLAKOID_DEBUG - if( comm->me == 0 ){ + if (comm->me == 0) { FILE *fp_doms = fopen("test_doms.dat","w"); FILE *fp_coms = fopen("test_coms.dat","w"); print_part_data(fp_doms, fp_coms); @@ -482,20 +482,20 @@ void manifold_thylakoid::set_domain( thyla_part *p, const std::vector &l const std::vector &hi ) { #ifdef MANIFOLD_THYLAKOID_DEBUG - if( comm->me == 0 ){ + if (comm->me == 0) { fprintf(screen,"Adding part with domain [%f, %f] x [%f, %f] x [%f, %f]\n", lo[0],hi[0],lo[1],hi[1],lo[2],hi[2] ); } #endif // MANIFOLD_THYLAKOID_DEBUG - if( lo[0] >= hi[0] ){ + if (lo[0] >= hi[0]) { char msg[2048]; sprintf(msg,"xlo >= xhi (%f >= %f)",lo[0],hi[0]); error->one(FLERR,msg); - }else if( lo[1] >= hi[1] ){ + } else if (lo[1] >= hi[1]) { char msg[2048]; sprintf(msg,"ylo >= yhi (%f >= %f)",lo[1],hi[1]); error->one(FLERR,msg); - }else if( lo[2] >= hi[2] ){ + } else if (lo[2] >= hi[2]) { char msg[2048]; sprintf(msg,"zlo >= zhi (%f >= %f)",lo[2],hi[2]); error->one(FLERR,msg); @@ -515,11 +515,11 @@ int manifold_thylakoid::is_in_domain( thyla_part *part, const double *x ) (x[1] >= part->ylo) && (x[1] <= part->yhi) && (x[2] >= part->zlo) && (x[2] <= part->zhi); - if( !domain_ok ) return false; + if (!domain_ok) return false; // From here on out, domain is ok. - if( part->type == thyla_part::THYLA_TYPE_CYL_TO_PLANE ){ + if (part->type == thyla_part::THYLA_TYPE_CYL_TO_PLANE) { double R0 = part->params[1]; double R = part->params[2]; @@ -530,13 +530,13 @@ int manifold_thylakoid::is_in_domain( thyla_part *part, const double *x ) double RR2 = RR*RR; - if( dist2 < RR2 ){ + if (dist2 < RR2) { return true; - }else{ + } else { // Domain was ok, but radius not. return false; } - }else{ + } else { return true; } } diff --git a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp index 4c4297f822..1c6b4dd06a 100644 --- a/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp +++ b/src/USER-MANIFOLD/manifold_thylakoid_shared.cpp @@ -33,12 +33,12 @@ thyla_part::thyla_part( int type, double *args, double xlo, double ylo, double z params[4] = args[4]; // y0 params[5] = args[5]; // z0 params[6] = args[6]; // R - if( (args[0] != 0.0) && (args[1] != 0.0) && (args[2] != 0.0) ){ + if ((args[0] != 0.0) && (args[1] != 0.0) && (args[2] != 0.0)) { err_flag = -1; return; } // The others should be 1. - if( (args[0] != 1.0) && (args[0] != 0.0) && + if ( (args[0] != 1.0) && (args[0] != 0.0) && (args[1] != 1.0) && (args[1] != 0.0) && (args[2] != 1.0) && (args[2] != 0.0) ){ err_flag = -1; diff --git a/src/USER-MANIFOLD/manifold_torus.cpp b/src/USER-MANIFOLD/manifold_torus.cpp index 0b4ca24370..4806af5213 100644 --- a/src/USER-MANIFOLD/manifold_torus.cpp +++ b/src/USER-MANIFOLD/manifold_torus.cpp @@ -14,7 +14,7 @@ double manifold_torus::g( const double *x ) { double R = params[0]; double r = params[1]; - if( R < r ){ + if (R < r) { error->all(FLERR,"Large radius < small radius!"); } @@ -27,7 +27,7 @@ void manifold_torus::n( const double *x, double *n ) { double R = params[0]; double r = params[1]; - if( R < r ){ + if (R < r) { error->all(FLERR,"Large radius < small radius!"); } diff --git a/src/USER-MEAMC/meam_impl.cpp b/src/USER-MEAMC/meam_impl.cpp index d4a47a4f48..b099ead8d5 100644 --- a/src/USER-MEAMC/meam_impl.cpp +++ b/src/USER-MEAMC/meam_impl.cpp @@ -34,12 +34,12 @@ MEAM::MEAM(Memory* mem) maxneigh = 0; scrfcn = dscrfcn = fcpair = NULL; - + neltypes = 0; for (int i = 0; i < maxelt; i++) { - Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] = - beta1_meam[i]= beta2_meam[i] = beta3_meam[i] = - t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] = + Omega_meam[i] = Z_meam[i] = A_meam[i] = rho0_meam[i] = beta0_meam[i] = + beta1_meam[i]= beta2_meam[i] = beta3_meam[i] = + t0_meam[i] = t1_meam[i] = t2_meam[i] = t3_meam[i] = rho_ref_meam[i] = ibar_meam[i] = ielt_meam[i] = 0.0; for (int j = 0; j < maxelt; j++) { lattce_meam[i][j] = FCC; diff --git a/src/USER-MEAMC/pair_meamc.cpp b/src/USER-MEAMC/pair_meamc.cpp index b74416a46d..3a934694bf 100644 --- a/src/USER-MEAMC/pair_meamc.cpp +++ b/src/USER-MEAMC/pair_meamc.cpp @@ -93,9 +93,7 @@ void PairMEAMC::compute(int eflag, int vflag) int *ilist_half,*numneigh_half,**firstneigh_half; int *numneigh_full,**firstneigh_full; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // neighbor list info diff --git a/src/USER-MEAMC/pair_meamc.h b/src/USER-MEAMC/pair_meamc.h index 476a70dd04..a006e70bdb 100644 --- a/src/USER-MEAMC/pair_meamc.h +++ b/src/USER-MEAMC/pair_meamc.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS PairStyle(meam/c,PairMEAMC) +PairStyle(meam,PairMEAMC) #else diff --git a/src/USER-MESO/pair_edpd.cpp b/src/USER-MESO/pair_edpd.cpp index 5ed63a2a8b..e428b02822 100644 --- a/src/USER-MESO/pair_edpd.cpp +++ b/src/USER-MESO/pair_edpd.cpp @@ -99,8 +99,7 @@ PairEDPD::~PairEDPD() void PairEDPD::compute(int eflag, int vflag) { double evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; @@ -191,7 +190,7 @@ void PairEDPD::compute(int eflag, int vflag) // heat transfer double dQc,dQd,dQr; - if( r < cutT[itype][jtype]) { + if (r < cutT[itype][jtype]) { double wrT = 1.0 - r/cutT[itype][jtype]; wrT = MAX(0.0,MIN(1.0,wrT)); wrT = pow(wrT, 0.5*powerT[itype][jtype]); diff --git a/src/USER-MESO/pair_mdpd.cpp b/src/USER-MESO/pair_mdpd.cpp index f9acd3dbe1..4102499d46 100644 --- a/src/USER-MESO/pair_mdpd.cpp +++ b/src/USER-MESO/pair_mdpd.cpp @@ -88,8 +88,7 @@ void PairMDPD::compute(int eflag, int vflag) double rhoi, rhoj; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; diff --git a/src/USER-MESO/pair_mdpd_rhosum.cpp b/src/USER-MESO/pair_mdpd_rhosum.cpp index 806a63f898..2fd238088c 100644 --- a/src/USER-MESO/pair_mdpd_rhosum.cpp +++ b/src/USER-MESO/pair_mdpd_rhosum.cpp @@ -84,10 +84,7 @@ void PairMDPDRhoSum::compute(int eflag, int vflag) { // neighbor list variables int inum, *ilist, *numneigh, **firstneigh; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **x = atom->x; double *rho = atom->rho; diff --git a/src/USER-MESO/pair_tdpd.cpp b/src/USER-MESO/pair_tdpd.cpp index 821d8c0486..7df9d6d163 100644 --- a/src/USER-MESO/pair_tdpd.cpp +++ b/src/USER-MESO/pair_tdpd.cpp @@ -91,8 +91,7 @@ PairTDPD::~PairTDPD() void PairTDPD::compute(int eflag, int vflag) { double evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; @@ -161,7 +160,7 @@ void PairTDPD::compute(int eflag, int vflag) f[i][2] += delz*fpair; // chemical concentration transport - if( r < cutcc[itype][jtype]) { + if (r < cutcc[itype][jtype]) { for(int k=0; knewton_pair; double e_s,e_p,e_t,e_q; diff --git a/src/USER-MISC/README b/src/USER-MISC/README index cf948df233..13e406d42f 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -71,6 +71,7 @@ pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 +pair_style lebedeva/z, Zbigniew Koziol (National Center for Nuclear Research), softquake at gmail dot com, 4 Jan 19 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 diff --git a/src/USER-MISC/angle_cosine_shift.cpp b/src/USER-MISC/angle_cosine_shift.cpp index a361db4970..18c87c81e3 100644 --- a/src/USER-MISC/angle_cosine_shift.cpp +++ b/src/USER-MISC/angle_cosine_shift.cpp @@ -62,8 +62,7 @@ void AngleCosineShift::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,s,cps,kcos,ksin,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/angle_cosine_shift_exp.cpp b/src/USER-MISC/angle_cosine_shift_exp.cpp index c87c73171a..8c6282de20 100644 --- a/src/USER-MISC/angle_cosine_shift_exp.cpp +++ b/src/USER-MISC/angle_cosine_shift_exp.cpp @@ -72,8 +72,7 @@ void AngleCosineShiftExp::compute(int eflag, int vflag) double exp2,aa,uumin,cccpsss,cssmscc; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/angle_dipole.cpp b/src/USER-MISC/angle_dipole.cpp index c4186da472..781da46869 100644 --- a/src/USER-MISC/angle_dipole.cpp +++ b/src/USER-MISC/angle_dipole.cpp @@ -59,8 +59,7 @@ void AngleDipole::compute(int eflag, int vflag) double r,cosGamma,deltaGamma,kdg,rmu; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; // position vector double **mu = atom->mu; // point-dipole components and moment magnitude diff --git a/src/USER-MISC/angle_fourier.cpp b/src/USER-MISC/angle_fourier.cpp index e6cc1f1a7e..8f5074ff5d 100644 --- a/src/USER-MISC/angle_fourier.cpp +++ b/src/USER-MISC/angle_fourier.cpp @@ -67,8 +67,7 @@ void AngleFourier::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,c2,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/angle_fourier_simple.cpp b/src/USER-MISC/angle_fourier_simple.cpp index 8464fe815c..615556bbe7 100644 --- a/src/USER-MISC/angle_fourier_simple.cpp +++ b/src/USER-MISC/angle_fourier_simple.cpp @@ -65,8 +65,7 @@ void AngleFourierSimple::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,cn,th,nth,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/angle_quartic.cpp b/src/USER-MISC/angle_quartic.cpp index 356f2df5d4..21a96100aa 100644 --- a/src/USER-MISC/angle_quartic.cpp +++ b/src/USER-MISC/angle_quartic.cpp @@ -61,8 +61,7 @@ void AngleQuartic::compute(int eflag, int vflag) double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/bond_harmonic_shift.cpp b/src/USER-MISC/bond_harmonic_shift.cpp index b34f71e888..c7e4444cce 100644 --- a/src/USER-MISC/bond_harmonic_shift.cpp +++ b/src/USER-MISC/bond_harmonic_shift.cpp @@ -53,8 +53,7 @@ void BondHarmonicShift::compute(int eflag, int vflag) double rsq,r,dr,rk; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/bond_harmonic_shift_cut.cpp b/src/USER-MISC/bond_harmonic_shift_cut.cpp index a58df70878..5b396f5d72 100644 --- a/src/USER-MISC/bond_harmonic_shift_cut.cpp +++ b/src/USER-MISC/bond_harmonic_shift_cut.cpp @@ -53,8 +53,7 @@ void BondHarmonicShiftCut::compute(int eflag, int vflag) double rsq,r,dr,rk; ebond = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp index 4946bc437e..0367d7fe6d 100644 --- a/src/USER-MISC/compute_entropy_atom.cpp +++ b/src/USER-MISC/compute_entropy_atom.cpp @@ -65,6 +65,7 @@ ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) : if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom" " command; cutoff must be positive"); + cutoff2 = 0.; avg_flag = 0; local_flag = 0; @@ -137,15 +138,20 @@ void ComputeEntropyAtom::init() if (count > 1 && comm->me == 0) error->warning(FLERR,"More than one compute entropy/atom"); - // need a full neighbor list with neighbors of the ghost atoms - + // Request neighbor list int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->pair = 0; neighbor->requests[irequest]->compute = 1; neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; neighbor->requests[irequest]->occasional = 0; - neighbor->requests[irequest]->ghost = 1; + if (avg_flag) { + // need a full neighbor list with neighbors of the ghost atoms + neighbor->requests[irequest]->ghost = 1; + } else { + // need a full neighbor list + neighbor->requests[irequest]->ghost = 0; + } } diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp index e63dff507f..cb2a0b9713 100644 --- a/src/USER-MISC/compute_stress_mop.cpp +++ b/src/USER-MISC/compute_stress_mop.cpp @@ -70,7 +70,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[4],"center")==0) { pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]); } else pos = force->numeric(FLERR,arg[4]); - + if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) { pos1 = pos + domain->prd[dir]; } else { @@ -118,7 +118,7 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) : if (pos >domain->boxhi[dir] || pos boxlo[dir]) error->all(FLERR, "Plane for compute stress/mop is out of bounds"); - + // Initialize some variables values_local = values_global = vector = NULL; @@ -168,13 +168,13 @@ void ComputeStressMop::init() // Timestep Value dt = update->dt; - + // Error check - + // Compute stress/mop requires fixed simulation box if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) error->all(FLERR, "Compute stress/mop requires a fixed simulation box"); - + // This compute requires a pair style with pair_single method implemented if (force->pair == NULL) @@ -210,7 +210,7 @@ void ComputeStressMop::init() /* ---------------------------------------------------------------------- */ -void ComputeStressMop::init_list(int id, NeighList *ptr) +void ComputeStressMop::init_list(int /* id */, NeighList *ptr) { list = ptr; } @@ -246,12 +246,13 @@ void ComputeStressMop::compute_vector() void ComputeStressMop::compute_pairs() { - int i,j,m,n,ii,jj,inum,jnum,itype,jtype; + int i,j,m,ii,jj,inum,jnum,itype,jtype; double delx,dely,delz; - double rsq,eng,fpair,factor_coul,factor_lj; + double rsq,fpair,factor_coul,factor_lj; int *ilist,*jlist,*numneigh,**firstneigh; double *mass = atom->mass; + double *rmass = atom->rmass; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -363,8 +364,7 @@ void ComputeStressMop::compute_pairs() // counts local particles transfers across the plane if (which[m] == KIN || which[m] == TOTAL){ - double vcm[3]; - double masstotal,sgn; + double sgn; for (int i = 0; i < nlocal; i++){ @@ -389,9 +389,15 @@ void ComputeStressMop::compute_pairs() fi[2] = atom->f[i][2]; //coordinates at t-dt (based on Velocity-Verlet alg.) - xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; - xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; - xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + if (rmass) { + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/rmass[i]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/rmass[i]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/rmass[i]*dt*dt*ftm2v; + } else { + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + } // because LAMMPS does not put atoms back in the box // at each timestep, must check atoms going through the @@ -407,9 +413,15 @@ void ComputeStressMop::compute_pairs() //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.) double vcross[3]; - vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt; - vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt; - vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt; + if (rmass) { + vcross[0] = vi[0]-fi[0]/rmass[i]/2*ftm2v*dt; + vcross[1] = vi[1]-fi[1]/rmass[i]/2*ftm2v*dt; + vcross[2] = vi[2]-fi[2]/rmass[i]/2*ftm2v*dt; + } else { + vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt; + vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt; + vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt; + } values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v; values_local[m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v; diff --git a/src/USER-MISC/compute_stress_mop.h b/src/USER-MISC/compute_stress_mop.h index 2047d1d54f..07bb774148 100644 --- a/src/USER-MISC/compute_stress_mop.h +++ b/src/USER-MISC/compute_stress_mop.h @@ -56,47 +56,47 @@ namespace LAMMPS_NS { #endif /* ERROR/WARNING messages: - + E: Illegal ... command - + Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. - + E: Compute stress/mop incompatible with simulation dimension - + Compute stress/mop only works with 3D simulations. - + E: Compute stress/mop incompatible with triclinic simulation box - + Self-explanatory. - + E: Compute stress/mop requires a fixed simulation box - + Compute stress/mop is not compatible with any change of volume or shape or boundary conditions of the simulation box. - + E: No pair style is defined for compute stress/mop - + Self-explanatory. Compute stress/mop requires the definition of a pair style. - + E: Pair style does not support compute stress/mop - + The pair style does not have a single() function, so it can not be invoked by compute stress/mop. - + W: compute stress/mop does not account for bond potentials - + W: compute stress/mop does not account for angle potentials - + W: compute stress/mop does not account for dihedral potentials - + W: compute stress/mop does not account for improper potentials - + W: compute stress/mop does not account for kspace contributions - + Compute stress/mop only accounts for pairwise additive interactions for the computation of local stress tensor components. - + */ diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp index 02ad3ea453..5499a37a46 100644 --- a/src/USER-MISC/compute_stress_mop_profile.cpp +++ b/src/USER-MISC/compute_stress_mop_profile.cpp @@ -168,20 +168,20 @@ void ComputeStressMopProfile::init() // timestep Value dt = update->dt; - + // Error check // Compute stress/mop/profile requires fixed simulation box - + if (domain->box_change_size || domain->box_change_shape || domain->deform_flag) error->all(FLERR, "Compute stress/mop/profile requires a fixed simulation box"); - + //This compute requires a pair style with pair_single method implemented if (force->pair == NULL) error->all(FLERR,"No pair style is defined for compute stress/mop/profile"); if (force->pair->single_enable == 0) error->all(FLERR,"Pair style does not support compute stress/mop/profile"); - + // Warnings if (me==0){ @@ -211,7 +211,7 @@ void ComputeStressMopProfile::init() /* ---------------------------------------------------------------------- */ -void ComputeStressMopProfile::init_list(int id, NeighList *ptr) +void ComputeStressMopProfile::init_list(int /* id */, NeighList *ptr) { list = ptr; } @@ -232,7 +232,7 @@ void ComputeStressMopProfile::compute_array() MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues, MPI_DOUBLE,MPI_SUM,world); - int ibin,m,mo; + int ibin,m,mo; for (ibin=0; ibinmass; + double *rmass = atom->rmass; int *type = atom->type; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -385,8 +386,7 @@ void ComputeStressMopProfile::compute_pairs() if (which[m] == KIN || which[m] == TOTAL){ - double vcm[3]; - double masstotal,sgn; + double sgn; for (int i = 0; i < nlocal; i++){ @@ -412,9 +412,15 @@ void ComputeStressMopProfile::compute_pairs() fi[2] = atom->f[i][2]; //coordinates at t-dt (based on Velocity-Verlet alg.) - xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; - xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; - xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + if (rmass) { + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/rmass[i]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/rmass[i]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/rmass[i]*dt*dt*ftm2v; + } else { + xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v; + xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v; + xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v; + } for (ibin=0;ibinboxlo; boxhi = domain->boxhi; - prd = domain->prd; if (originflag == LOWER) origin = boxlo[dir]; else if (originflag == UPPER) origin = boxhi[dir]; diff --git a/src/USER-MISC/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h index 648d86cc7f..d86237b0bd 100644 --- a/src/USER-MISC/compute_stress_mop_profile.h +++ b/src/USER-MISC/compute_stress_mop_profile.h @@ -50,7 +50,6 @@ namespace LAMMPS_NS { double **coord,**coordp; double **values_local,**values_global; - int ndim; double dt,nktv2p,ftm2v; double area; class NeighList *list; @@ -71,43 +70,43 @@ namespace LAMMPS_NS { command-line option when running LAMMPS to see the offending line. E: Compute stress/mop/profile incompatible with simulation dimension - + Compute stress/mop/profile only works with 3D simulations. - + E: Compute stress/mop/profile incompatible with triclinic simulation box - + Self-explanatory. - + E: Compute stress/mop/profile requires a fixed simulation box - + Compute stress/mop/profile is not compatible with any change of volume or shape or boundary conditions of the simulation box. - + E: No pair style is defined for compute stress/mop/profile - + Self-explanatory. Compute stress/mop/profile requires the definition of a pair style. - + E: Pair style does not support compute stress/mop/profile - + The pair style does not have a single() function, so it can not be invoked by compute stress/mop/profile. - + E: Origin of bins for compute stress/mop/profile is out of bounds - + Self-explanatory. - + W: compute stress/mop/profile does not account for bond potentials - + W: compute stress/mop/profile does not account for angle potentials - + W: compute stress/mop/profile does not account for dihedral potentials - + W: compute stress/mop/profile does not account for improper potentials - + W: compute stress/mop/profile does not account for kspace contributions - + Compute stress/mop/profile only accounts for pairwise additive interactions for the computation of local stress tensor components. - + */ diff --git a/src/USER-MISC/dihedral_cosine_shift_exp.cpp b/src/USER-MISC/dihedral_cosine_shift_exp.cpp index 82da173f8e..c411ea8150 100644 --- a/src/USER-MISC/dihedral_cosine_shift_exp.cpp +++ b/src/USER-MISC/dihedral_cosine_shift_exp.cpp @@ -36,7 +36,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -DihedralCosineShiftExp::DihedralCosineShiftExp(LAMMPS *lmp) : Dihedral(lmp) {} +DihedralCosineShiftExp::DihedralCosineShiftExp(LAMMPS *lmp) : Dihedral(lmp) +{ + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -68,8 +71,7 @@ void DihedralCosineShiftExp::compute(int eflag, int vflag) double cccpsss,cssmscc,exp2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/dihedral_fourier.cpp b/src/USER-MISC/dihedral_fourier.cpp index 7c405ee28c..af86259c01 100644 --- a/src/USER-MISC/dihedral_fourier.cpp +++ b/src/USER-MISC/dihedral_fourier.cpp @@ -79,8 +79,7 @@ void DihedralFourier::compute(int eflag, int vflag) double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz; double c,s,p_,sx2,sy2,sz2; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/dihedral_nharmonic.cpp b/src/USER-MISC/dihedral_nharmonic.cpp index f8e8850680..ea2b76f415 100644 --- a/src/USER-MISC/dihedral_nharmonic.cpp +++ b/src/USER-MISC/dihedral_nharmonic.cpp @@ -35,7 +35,8 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp) { +DihedralNHarmonic::DihedralNHarmonic(LAMMPS *lmp) : Dihedral(lmp) +{ writedata = 1; } @@ -66,8 +67,7 @@ void DihedralNHarmonic::compute(int eflag, int vflag) double s2,sin2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/dihedral_quadratic.cpp b/src/USER-MISC/dihedral_quadratic.cpp index 1b64b52faf..8436e73c5c 100644 --- a/src/USER-MISC/dihedral_quadratic.cpp +++ b/src/USER-MISC/dihedral_quadratic.cpp @@ -38,7 +38,10 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -DihedralQuadratic::DihedralQuadratic(LAMMPS *lmp) : Dihedral(lmp) {} +DihedralQuadratic::DihedralQuadratic(LAMMPS *lmp) : Dihedral(lmp) +{ + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -65,8 +68,7 @@ void DihedralQuadratic::compute(int eflag, int vflag) double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/dihedral_spherical.cpp b/src/USER-MISC/dihedral_spherical.cpp index 77fa885b7a..3b30121551 100644 --- a/src/USER-MISC/dihedral_spherical.cpp +++ b/src/USER-MISC/dihedral_spherical.cpp @@ -41,7 +41,10 @@ using namespace MathExtra; /* ---------------------------------------------------------------------- */ -DihedralSpherical::DihedralSpherical(LAMMPS *lmp) : Dihedral(lmp) {} +DihedralSpherical::DihedralSpherical(LAMMPS *lmp) : Dihedral(lmp) +{ + writedata = 1; +} /* ---------------------------------------------------------------------- */ @@ -213,8 +216,7 @@ void DihedralSpherical::compute(int eflag, int vflag) // perp34on23[d] = v34[d] - proj34on23[d] edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); for (n = 0; n < ndihedrallist; n++) { @@ -817,10 +819,11 @@ void DihedralSpherical::write_data(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) { fprintf(fp,"%d %d ", i , nterms[i]); for (int j = 0; j < nterms[i]; j++) { - fprintf(fp, "%g %g %g %g %g %g %g %g %g ", - phi_mult[i][j], phi_shift[i][j], phi_offset[i][j], - theta1_mult[i][j], theta1_shift[i][j], theta1_offset[i][j], - theta2_mult[i][j], theta2_shift[i][j], theta2_offset[i][j]); + fprintf(fp, "%g %g %g %g %g %g %g %g %g %g ", Ccoeff[i][j], + phi_mult[i][j], phi_shift[i][j]*180.0/MY_PI, phi_offset[i][j], + theta1_mult[i][j], theta1_shift[i][j]*180.0/MY_PI, + theta1_offset[i][j], theta2_mult[i][j], + theta2_shift[i][j]*180.0/MY_PI, theta2_offset[i][j]); } fprintf(fp,"\n"); } diff --git a/src/USER-MISC/dihedral_table.cpp b/src/USER-MISC/dihedral_table.cpp index f84814cc5e..a97ae3649f 100644 --- a/src/USER-MISC/dihedral_table.cpp +++ b/src/USER-MISC/dihedral_table.cpp @@ -35,6 +35,7 @@ #include "memory.h" #include "error.h" #include "dihedral_table.h" +#include "utils.h" #include "math_const.h" #include "math_extra.h" @@ -51,7 +52,7 @@ using namespace MathExtra; // ------------------------------------------------------------------------ // ------------------------------------------------------------------- -// --------- The function was stolen verbatim from the --------- +// --------- The function was taken verbatim from the --------- // --------- GNU Scientific Library (GSL, version 1.15) --------- // ------------------------------------------------------------------- @@ -548,8 +549,7 @@ void DihedralTable::compute(int eflag, int vflag) edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); for (n = 0; n < ndihedrallist; n++) { @@ -1090,18 +1090,18 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + if (strcmp(word,keyword) == 0) break; // matching keyword + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->phifile,tb->ninput,"dihedral:phifile"); memory->create(tb->efile,tb->ninput,"dihedral:efile"); @@ -1111,9 +1111,8 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) int itmp; for (int i = 0; i < tb->ninput; i++) { - // Read the next line. Make sure the file is long enough. - if (! fgets(line,MAXLINE,fp)) - error->one(FLERR, "Dihedral table does not contain enough entries."); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + // Skip blank lines and delete text following a '#' character char *pe = strchr(line, '#'); if (pe != NULL) *pe = '\0'; //terminate string at '#' character @@ -1123,15 +1122,10 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) if (*pc != '\0') { //If line is not a blank line stringstream line_ss(line); if (tb->f_unspecified) { - //sscanf(line,"%d %lg %lg", - // &itmp,&tb->phifile[i],&tb->efile[i]); line_ss >> itmp; line_ss >> tb->phifile[i]; line_ss >> tb->efile[i]; - } - else { - //sscanf(line,"%d %lg %lg %lg", - // &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]); + } else { line_ss >> itmp; line_ss >> tb->phifile[i]; line_ss >> tb->efile[i]; @@ -1145,8 +1139,7 @@ void DihedralTable::read_table(Table *tb, char *file, char *keyword) err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n"; error->one(FLERR, err_msg.str().c_str()); } - } - else //if it is a blank line, then skip it. + } else //if it is a blank line, then skip it. i--; } //for (int i = 0; (i < tb->ninput) && fp; i++) { diff --git a/src/USER-MISC/dihedral_table_cut.cpp b/src/USER-MISC/dihedral_table_cut.cpp index 7345bcdad1..18a645cd75 100644 --- a/src/USER-MISC/dihedral_table_cut.cpp +++ b/src/USER-MISC/dihedral_table_cut.cpp @@ -37,6 +37,7 @@ #include "math_extra.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -45,7 +46,7 @@ using namespace MathExtra; static const char cite_dihedral_tablecut[] = - "dihedral_style tablecut command:\n\n" + "dihedral_style table/cut command:\n\n" "@Article{Salerno17,\n" " author = {K. M. Salerno and N. Bernstein},\n" " title = {Persistence Length, End-to-End Distance, and Structure of Coarse-Grained Polymers},\n" @@ -66,7 +67,7 @@ static const char cite_dihedral_tablecut[] = // ------------------------------------------------------------------------ // ------------------------------------------------------------------- -// --------- The function was stolen verbatim from the --------- +// --------- The function was taken verbatim from the --------- // --------- GNU Scientific Library (GSL, version 1.15) --------- // ------------------------------------------------------------------- @@ -424,17 +425,6 @@ DihedralTableCut::DihedralTableCut(LAMMPS *lmp) : Dihedral(lmp) DihedralTableCut::~DihedralTableCut() { if (allocated) { - memory->destroy(setflag); - memory->destroy(setflag_d); - memory->destroy(setflag_aat); - - memory->destroy(k1); - memory->destroy(k2); - memory->destroy(k3); - memory->destroy(phi1); - memory->destroy(phi2); - memory->destroy(phi3); - memory->destroy(aat_k); memory->destroy(aat_theta0_1); memory->destroy(aat_theta0_2); @@ -454,7 +444,7 @@ DihedralTableCut::~DihedralTableCut() void DihedralTableCut::compute(int eflag, int vflag) { - + int i1,i2,i3,i4,i,j,k,n,type; double edihedral; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm; @@ -471,8 +461,7 @@ void DihedralTableCut::compute(int eflag, int vflag) double fabcd[4][3]; edihedral = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -704,12 +693,12 @@ void DihedralTableCut::compute(int eflag, int vflag) double gptt = 0; if ( acos(costh12) > aat_theta0_1[type]) { - gt *= 1-da1*da1/dtheta/dtheta; + gt *= 1-da1*da1/dtheta/dtheta; gpt = -aat_k[type]*2*da1/dtheta/dtheta; } if ( acos(costh23) > aat_theta0_1[type]) { - gtt *= 1-da2*da2/dtheta/dtheta; + gtt *= 1-da2*da2/dtheta/dtheta; gptt = -aat_k[type]*2*da2/dtheta/dtheta; } @@ -717,7 +706,7 @@ void DihedralTableCut::compute(int eflag, int vflag) for (i = 0; i < 4; i++) for (j = 0; j < 3; j++) - fabcd[i][j] -= - gt*gtt*fpphi*dphidr[i][j] + fabcd[i][j] -= - gt*gtt*fpphi*dphidr[i][j] - gt*gptt*fphi*dthetadr[1][i][j] + gpt*gtt*fphi*dthetadr[0][i][j]; // apply force to each of 4 atoms @@ -760,27 +749,15 @@ void DihedralTableCut::allocate() allocated = 1; int n = atom->ndihedraltypes; - memory->create(k1,n+1,"dihedral:k1"); - memory->create(k2,n+1,"dihedral:k2"); - memory->create(k3,n+1,"dihedral:k3"); - memory->create(phi1,n+1,"dihedral:phi1"); - memory->create(phi2,n+1,"dihedral:phi2"); - memory->create(phi3,n+1,"dihedral:phi3"); - memory->create(aat_k,n+1,"dihedral:aat_k"); memory->create(aat_theta0_1,n+1,"dihedral:aat_theta0_1"); memory->create(aat_theta0_2,n+1,"dihedral:aat_theta0_2"); - memory->create(setflag,n+1,"dihedral:setflag"); - memory->create(setflag_d,n+1,"dihedral:setflag_d"); - memory->create(setflag_aat,n+1,"dihedral:setflag_aat"); - memory->create(tabindex,n+1,"dihedral:tabindex"); - //memory->create(phi0,n+1,"dihedral:phi0"); <-equilibrium angles not supported memory->create(setflag,n+1,"dihedral:setflag"); for (int i = 1; i <= n; i++) - setflag[i] = setflag_d[i] = setflag_aat[i] = 0; + setflag[i] = 0; } void DihedralTableCut::settings(int narg, char **arg) @@ -823,9 +800,6 @@ void DihedralTableCut::coeff(int narg, char **arg) int ilo,ihi; force->bounds(FLERR,arg[0],atom->ndihedraltypes,ilo,ihi); - int count = 0; - - double k_one = force->numeric(FLERR,arg[2]); double theta0_1_one = force->numeric(FLERR,arg[3]); double theta0_2_one = force->numeric(FLERR,arg[4]); @@ -836,8 +810,6 @@ void DihedralTableCut::coeff(int narg, char **arg) aat_k[i] = k_one; aat_theta0_1[i] = theta0_1_one/180.0 * MY_PI; aat_theta0_2[i] = theta0_2_one/180.0 * MY_PI; - setflag_aat[i] = 1; - count++; } int me; @@ -997,8 +969,7 @@ void DihedralTableCut::coeff(int narg, char **arg) // To be nice and report something, I do the same thing here.) cyc_splintD(tb->phi, tb->e, tb->e2, tablength, MY_2PI,phi); f = -dU_dphi; - } - else + } else // Otherwise we calculated the tb->f[] array. Report its contents. f = tb->f[i]; if (tb->use_degrees) { @@ -1014,9 +985,8 @@ void DihedralTableCut::coeff(int narg, char **arg) } // if (me == 0) // store ptr to table in tabindex - count = 0; - for (int i = ilo; i <= ihi; i++) - { + int count = 0; + for (int i = ilo; i <= ihi; i++) { tabindex[i] = ntables; //phi0[i] = tb->phi0; <- equilibrium dihedral angles not supported setflag[i] = 1; @@ -1024,12 +994,7 @@ void DihedralTableCut::coeff(int narg, char **arg) } ntables++; - if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients"); - - for (int i = ilo; i <= ihi; i++) - if (setflag_d[i] == 1 && setflag_aat[i] == 1 ) - setflag[i] = 1; } /* ---------------------------------------------------------------------- @@ -1040,16 +1005,6 @@ void DihedralTableCut::write_restart(FILE *fp) { fwrite(&tabstyle,sizeof(int),1,fp); fwrite(&tablength,sizeof(int),1,fp); - fwrite(&k1[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&k2[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&k3[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&phi1[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&phi2[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&phi3[1],sizeof(double),atom->ndihedraltypes,fp); - - fwrite(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp); - fwrite(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp); } /* ---------------------------------------------------------------------- @@ -1063,33 +1018,10 @@ void DihedralTableCut::read_restart(FILE *fp) if (comm->me == 0) { fread(&tabstyle,sizeof(int),1,fp); fread(&tablength,sizeof(int),1,fp); - fread(&k1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&k3[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi2[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&phi3[1],sizeof(double),atom->ndihedraltypes,fp); - - fread(&aat_k[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&aat_theta0_1[1],sizeof(double),atom->ndihedraltypes,fp); - fread(&aat_theta0_2[1],sizeof(double),atom->ndihedraltypes,fp); } - MPI_Bcast(&k1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&k2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&k3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&phi1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&phi2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&phi3[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - - MPI_Bcast(&aat_k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&aat_theta0_1[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); - MPI_Bcast(&aat_theta0_2[1],atom->ndihedraltypes,MPI_DOUBLE,0,world); MPI_Bcast(&tabstyle,1,MPI_INT,0,world); MPI_Bcast(&tablength,1,MPI_INT,0,world); - - allocate(); - for (int i = 1; i <= atom->ndihedraltypes; i++) setflag[i] = 1; } /* ---------------------------------------------------------------------- */ @@ -1151,17 +1083,17 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->phifile,tb->ninput,"dihedral:phifile"); memory->create(tb->efile,tb->ninput,"dihedral:efile"); @@ -1172,8 +1104,8 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) int itmp; for (int i = 0; i < tb->ninput; i++) { // Read the next line. Make sure the file is long enough. - if (! fgets(line,MAXLINE,fp)) - error->one(FLERR, "Dihedral table does not contain enough entries."); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + // Skip blank lines and delete text following a '#' character char *pe = strchr(line, '#'); if (pe != NULL) *pe = '\0'; //terminate string at '#' character @@ -1183,15 +1115,10 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) if (*pc != '\0') { //If line is not a blank line stringstream line_ss(line); if (tb->f_unspecified) { - //sscanf(line,"%d %lg %lg", - // &itmp,&tb->phifile[i],&tb->efile[i]); line_ss >> itmp; line_ss >> tb->phifile[i]; line_ss >> tb->efile[i]; - } - else { - //sscanf(line,"%d %lg %lg %lg", - // &itmp,&tb->phifile[i],&tb->efile[i],&tb->ffile[i]); + } else { line_ss >> itmp; line_ss >> tb->phifile[i]; line_ss >> tb->efile[i]; @@ -1205,8 +1132,7 @@ void DihedralTableCut::read_table(Table *tb, char *file, char *keyword) err_msg << "\n (This sometimes occurs if users forget to specify the \"NOF\" option.)\n"; error->one(FLERR, err_msg.str().c_str()); } - } - else //if it is a blank line, then skip it. + } else //if it is a blank line, then skip it. i--; } //for (int i = 0; (i < tb->ninput) && fp; i++) { @@ -1479,22 +1405,3 @@ void DihedralTableCut::bcast_table(Table *tb) } - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void DihedralTableCut::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ndihedraltypes; i++) - fprintf(fp,"%d %g %g %g %g %g %g\n",i, - k1[i],phi1[i]*180.0/MY_PI, - k2[i],phi2[i]*180.0/MY_PI, - k3[i],phi3[i]*180.0/MY_PI); - - fprintf(fp,"\nAngleAngleTorsion Coeffs\n\n"); - for (int i = 1; i <= atom->ndihedraltypes; i++) - fprintf(fp,"%d %g %g %g\n",i,aat_k[i], - aat_theta0_1[i]*180.0/MY_PI,aat_theta0_2[i]*180.0/MY_PI); - -} diff --git a/src/USER-MISC/dihedral_table_cut.h b/src/USER-MISC/dihedral_table_cut.h index d01903c88b..dd645bedda 100644 --- a/src/USER-MISC/dihedral_table_cut.h +++ b/src/USER-MISC/dihedral_table_cut.h @@ -20,7 +20,6 @@ DihedralStyle(table/cut,DihedralTableCut) #ifndef LMP_DIHEDRAL_TABLE_CUT_H #define LMP_DIHEDRAL_TABLE_CUT_H -#include #include "dihedral.h" namespace LAMMPS_NS { @@ -34,26 +33,18 @@ class DihedralTableCut : public Dihedral { void coeff(int, char **); void write_restart(FILE *); void read_restart(FILE *); - void write_data(FILE *); - double single(int type, int i1, int i2, int i3, int i4); protected: - double *k1,*k2,*k3; - double *phi1,*phi2,*phi3; double *aat_k,*aat_theta0_1,*aat_theta0_2; - int *setflag_d; - int *setflag_aat; void allocate(); int tabstyle,tablength; - // double *phi0; <- equilibrium angles not supported char *checkU_fname; char *checkF_fname; struct Table { int ninput; - //double phi0; <-equilibrium angles not supported int f_unspecified; // boolean (but MPI does not like type "bool") int use_degrees; // boolean (but MPI does not like type "bool") double *phifile,*efile,*ffile; diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp index 5c9f478a65..dc52d94b14 100644 --- a/src/USER-MISC/fix_ave_correlate_long.cpp +++ b/src/USER-MISC/fix_ave_correlate_long.cpp @@ -307,7 +307,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg): for (int i=0;i 0) { t[jm] = j; for (int i=0;i0) { t[jm] = j * pow((double)m, k); for (int i=0;i -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2]; if (i==0) ++ncorrelation[k][j]; @@ -620,7 +620,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const int k){ } } else { int ind2=ind1-dmin; - for (int j=dmin;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2]; @@ -661,7 +661,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB, unsigned int ind1=insertindex[k]; if (k==0) { int ind2=ind1; - for (int j=0;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2]; if (i==0) ++ncorrelation[k][j]; @@ -672,7 +672,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB, } else { int ind2=ind1-dmin; - for (int j=dmin;j -1e10) { correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2]; @@ -743,7 +743,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) { list[n++] = last_accumulated_step; for (int i=0;i (list[n++]); if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators) - || (pin!=p) || (min!=m)) + || (pin!=(int)p) || (min!=(int)m)) error->all(FLERR,"Fix ave/correlate/long: restart and input data are different"); for (int i=0;i(list[n++]); naccumulator[i] = static_cast (list[n++]); insertindex[i] = static_cast (list[n++]); diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h index 5b38f454ea..548a0e7183 100644 --- a/src/USER-MISC/fix_ave_correlate_long.h +++ b/src/USER-MISC/fix_ave_correlate_long.h @@ -52,7 +52,7 @@ class FixAveCorrelateLong : public Fix { unsigned int *insertindex; int numcorrelators; // Recommended 20 - int p; // Points per correlator (recommended 16) + unsigned int p; // Points per correlator (recommended 16) unsigned int m; // Num points for average (recommended 2; p mod m = 0) unsigned int dmin; // Min distance between ponts for correlators k>0; dmin=p/m diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp index a7b85e92d3..5d624ad7f4 100644 --- a/src/USER-MISC/fix_bond_react.cpp +++ b/src/USER-MISC/fix_bond_react.cpp @@ -58,7 +58,8 @@ static const char cite_fix_bond_react[] = #define BIG 1.0e20 #define DELTA 16 #define MAXLINE 256 -#define MAXGUESS 20 +#define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm +#define MAXCONARGS 5 // max # of arguments for any type of constraint // various statuses of superimpose algorithm: // ACCEPT: site successfully matched to pre-reacted template @@ -161,10 +162,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol"); memory->create(reacted_mol,nreacts,"bond/react:reacted_mol"); memory->create(fraction,nreacts,"bond/react:fraction"); + memory->create(max_rxn,nreacts,"bond/react:max_rxn"); + memory->create(nlocalskips,nreacts,"bond/react:nlocalskips"); + memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips"); memory->create(seed,nreacts,"bond/react:seed"); memory->create(limit_duration,nreacts,"bond/react:limit_duration"); memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag"); memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag"); + memory->create(nconstraints,nreacts,"bond/react:nconstraints"); + memory->create(constraints,nreacts,MAXCONARGS,"bond/react:constraints"); memory->create(iatomtype,nreacts,"bond/react:iatomtype"); memory->create(jatomtype,nreacts,"bond/react:jatomtype"); memory->create(ibonding,nreacts,"bond/react:ibonding"); @@ -179,8 +185,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : for (int i = 0; i < nreacts; i++) { fraction[i] = 1; seed[i] = 12345; + max_rxn[i] = INT_MAX; stabilize_steps_flag[i] = 0; update_edges_flag[i] = 0; + nconstraints[i] = 0; // set default limit duration to 60 timesteps limit_duration[i] = 60; reaction_count[i] = 0; @@ -244,6 +252,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: " "probability seed must be positive"); iarg += 3; + } else if (strcmp(arg[iarg],"max_rxn") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " + "'max_rxn' has too few arguments"); + max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]); + if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: " + "'max_rxn' cannot be negative"); + iarg += 2; } else if (strcmp(arg[iarg],"stabilize_steps") == 0) { if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword " "used without stabilization keyword"); @@ -255,7 +270,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : } else if (strcmp(arg[iarg],"update_edges") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: " "'update_edges' has too few arguments"); - if (strcmp(arg[iarg+1],"charges") == 0) update_edges_flag[rxn] = 1; + if (strcmp(arg[iarg+1],"none") == 0) update_edges_flag[rxn] = 0; + else if (strcmp(arg[iarg+1],"charges") == 0) update_edges_flag[rxn] = 1; + else if (strcmp(arg[iarg+1],"custom") == 0) update_edges_flag[rxn] = 2; + else error->all(FLERR,"Illegal value for 'update_edges' keyword'"); iarg += 2; } else error->all(FLERR,"Illegal fix bond/react command: unknown keyword"); } @@ -271,15 +289,24 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : memory->create(reverse_equiv,max_natoms,2,nreacts,"bond/react:reverse_equiv"); memory->create(edge,max_natoms,nreacts,"bond/react:edge"); memory->create(landlocked_atoms,max_natoms,nreacts,"bond/react:landlocked_atoms"); + memory->create(custom_edges,max_natoms,nreacts,"bond/react:custom_edges"); + memory->create(delete_atoms,max_natoms,nreacts,"bond/react:delete_atoms"); for (int j = 0; j < nreacts; j++) - for (int i = 0; i < max_natoms; i++) edge[i][j] = 0; + for (int i = 0; i < max_natoms; i++) { + edge[i][j] = 0; + if (update_edges_flag[j] == 1) custom_edges[i][j] = 1; + else custom_edges[i][j] = 0; + delete_atoms[i][j] = 0; + } - // read all superimpose files afterward + // read all map files afterward for (int i = 0; i < nreacts; i++) { open(files[i]); onemol = atom->molecules[unreacted_mol[i]]; twomol = atom->molecules[reacted_mol[i]]; + onemol->check_attributes(0); + twomol->check_attributes(0); if (onemol->natoms != twomol->natoms) error->all(FLERR,"Post-reacted template must contain the same " "number of atoms as the pre-reacted template"); @@ -367,9 +394,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : FixBondReact::~FixBondReact() { - // unregister callbacks to this fix from Atom class - atom->delete_callback(id,0); - for (int i = 0; i < nreacts; i++) { delete random[i]; } @@ -384,6 +408,9 @@ FixBondReact::~FixBondReact() memory->destroy(edge); memory->destroy(equivalences); memory->destroy(reverse_equiv); + memory->destroy(landlocked_atoms); + memory->destroy(custom_edges); + memory->destroy(delete_atoms); memory->destroy(nevery); memory->destroy(cutsq); @@ -391,6 +418,9 @@ FixBondReact::~FixBondReact() memory->destroy(reacted_mol); memory->destroy(fraction); memory->destroy(seed); + memory->destroy(max_rxn); + memory->destroy(nlocalskips); + memory->destroy(nghostlyskips); memory->destroy(limit_duration); memory->destroy(stabilize_steps_flag); memory->destroy(update_edges_flag); @@ -420,7 +450,6 @@ FixBondReact::~FixBondReact() memory->destroy(restore); memory->destroy(glove); memory->destroy(pioneers); - memory->destroy(landlocked_atoms); memory->destroy(local_mega_glove); memory->destroy(ghostly_mega_glove); } @@ -428,22 +457,32 @@ FixBondReact::~FixBondReact() memory->destroy(global_mega_glove); if (stabilization_flag == 1) { - delete [] exclude_group; - // check nfix in case all fixes have already been deleted - if (id_fix1 == NULL && modify->nfix) modify->delete_fix(id_fix1); + if (id_fix1 && modify->nfix) modify->delete_fix(id_fix1); delete [] id_fix1; - if (id_fix3 == NULL && modify->nfix) modify->delete_fix(id_fix3); + if (id_fix3 && modify->nfix) modify->delete_fix(id_fix3); delete [] id_fix3; } - if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2); + if (id_fix2 && modify->nfix) modify->delete_fix(id_fix2); delete [] id_fix2; delete [] statted_id; delete [] guess_branch; delete [] pioneer_count; + + char **newarg; + newarg = new char*[2]; + newarg[0] = master_group; + newarg[1] = (char *) "delete"; + group->assign(2,newarg); + if (stabilization_flag == 1) { + newarg[0] = exclude_group; + group->assign(2,newarg); + delete [] exclude_group; + } + delete [] newarg; } /* ---------------------------------------------------------------------- */ @@ -663,6 +702,8 @@ void FixBondReact::post_integrate() reaction_count[i] = 0; local_rxn_count[i] = 0; ghostly_rxn_count[i] = 0; + nlocalskips[i] = 0; + nghostlyskips[i] = 0; } if (nevery_check) { @@ -734,6 +775,7 @@ void FixBondReact::post_integrate() int j; for (rxnID = 0; rxnID < nreacts; rxnID++) { + if (max_rxn[rxnID] <= reaction_count_total[rxnID]) continue; for (int ii = 0; ii < nall; ii++) { partner[ii] = 0; finalpartner[ii] = 0; @@ -930,6 +972,7 @@ void FixBondReact::far_partner() delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; + domain->minimum_image(delx,dely,delz); // ghost location fix rsq = delx*delx + dely*dely + delz*delz; if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) { @@ -989,13 +1032,24 @@ void FixBondReact::close_partner() rsq = delx*delx + dely*dely + delz*delz; if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) continue; - if (rsq > distsq[i1][0]) { - partner[i1] = tag[i2]; - distsq[i1][0] = rsq; - } - if (rsq > distsq[i2][0]) { - partner[i2] = tag[i1]; - distsq[i2][0] = rsq; + if (closeneigh[rxnID] == 0) { + if (rsq > distsq[i1][0]) { + partner[i1] = tag[i2]; + distsq[i1][0] = rsq; + } + if (rsq > distsq[i2][0]) { + partner[i2] = tag[i1]; + distsq[i2][0] = rsq; + } + } else { + if (rsq < distsq[i1][1]) { + partner[i1] = tag[i2]; + distsq[i1][1] = rsq; + } + if (rsq < distsq[i2][1]) { + partner[i2] = tag[i1]; + distsq[i2][1] = rsq; + } } } } @@ -1111,7 +1165,7 @@ void FixBondReact::superimpose_algorithm() } } - if (status == ACCEPT) { // reaction site found successfully! + if (status == ACCEPT && check_constraints()) { // reaction site found successfully! glove_ghostcheck(); } hang_catch++; @@ -1131,14 +1185,49 @@ void FixBondReact::superimpose_algorithm() MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world); - for (int i = 0; i < nreacts; i++) - reaction_count_total[i] += reaction_count[i]; - - // this assumes compute_vector is called from process 0 - // ...so doesn't bother to bcast ghostly_rxn_count if (me == 0) for (int i = 0; i < nreacts; i++) - reaction_count_total[i] += ghostly_rxn_count[i]; + reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i]; + + MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world); + + // check if we overstepped our reaction limit + for (int i = 0; i < nreacts; i++) { + if (reaction_count_total[i] > max_rxn[i]) { + // let's randomly choose rxns to skip, unbiasedly from local and ghostly + int *local_rxncounts; + int *all_localskips; + memory->create(local_rxncounts,nprocs,"bond/react:local_rxncounts"); + memory->create(all_localskips,nprocs,"bond/react:all_localskips"); + MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world); + if (me == 0) { + int overstep = reaction_count_total[i] - max_rxn[i]; + int delta_rxn = reaction_count[i] + ghostly_rxn_count[i]; + int *rxn_by_proc; + memory->create(rxn_by_proc,delta_rxn,"bond/react:rxn_by_proc"); + for (int j = 0; j < delta_rxn; j++) + rxn_by_proc[j] = -1; // corresponds to ghostly + int itemp = 0; + for (int j = 0; j < nprocs; j++) + for (int k = 0; k < local_rxn_count[j]; k++) + rxn_by_proc[itemp++] = j; + std::random_shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn]); + for (int j = 0; j < nprocs; j++) + all_localskips[j] = 0; + nghostlyskips[i] = 0; + for (int j = 0; j < overstep; j++) { + if (rxn_by_proc[j] == -1) nghostlyskips[i]++; + else all_localskips[rxn_by_proc[j]]++; + } + memory->destroy(rxn_by_proc); + } + reaction_count_total[i] = max_rxn[i]; + MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world); + MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world); + memory->destroy(local_rxncounts); + memory->destroy(all_localskips); + } + } // this updates topology next step next_reneighbor = update->ntimestep; @@ -1515,6 +1604,32 @@ void FixBondReact::ring_check() } } +/* ---------------------------------------------------------------------- +evaluate constraints: return 0 if any aren't satisfied +------------------------------------------------------------------------- */ + +int FixBondReact::check_constraints() +{ + tagint atom1,atom2; + double delx,dely,delz,rsq; + + double **x = atom->x; + + for (int i = 0; i < nconstraints[rxnID]; i++) { + if (constraints[rxnID][0] == 0) { // 'distance' type + atom1 = atom->map(glove[(int) constraints[rxnID][1]-1][1]); + atom2 = atom->map(glove[(int) constraints[rxnID][2]-1][1]); + delx = x[atom1][0] - x[atom2][0]; + dely = x[atom1][1] - x[atom2][1]; + delz = x[atom1][2] - x[atom2][2]; + domain->minimum_image(delx,dely,delz); // ghost location fix + rsq = delx*delx + dely*dely + delz*delz; + if (rsq < constraints[rxnID][3] || rsq > constraints[rxnID][4]) return 0; + } + } + return 1; +} + /* ---------------------------------------------------------------------- Get xspecials for current molecule templates ------------------------------------------------------------------------- */ @@ -1641,6 +1756,18 @@ void FixBondReact::find_landlocked_atoms(int myrxn) } } + // additionally, if a deleted atom is bonded to an atom that is not deleted, bad + for (int i = 0; i < onemol->natoms; i++) { + if (delete_atoms[i][myrxn] == 1) { + int ii = reverse_equiv[i][1][myrxn] - 1; + for (int j = 0; j < twomol_nxspecial[ii][0]; j++) { + if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) { + error->one(FLERR,"A deleted atom cannot remain bonded to an atom that is not deleted"); + } + } + } + } + // also, if atoms change number of bonds, but aren't landlocked, that could be bad if (me == 0) for (int i = 0; i < twomol->natoms; i++) { @@ -1854,8 +1981,11 @@ void FixBondReact::limit_bond(int limit_bond_mode) int index1 = atom->find_custom("limit_tags",flag); int *i_limit_tags = atom->ivector[index1]; - int index2 = atom->find_custom(statted_id,flag); - int *i_statted_tags = atom->ivector[index2]; + int *i_statted_tags; + if (stabilization_flag == 1) { + int index2 = atom->find_custom(statted_id,flag); + i_statted_tags = atom->ivector[index2]; + } int index3 = atom->find_custom("react_tags",flag); int *i_react_tags = atom->ivector[index3]; @@ -1863,7 +1993,7 @@ void FixBondReact::limit_bond(int limit_bond_mode) for (int i = 0; i < temp_limit_num; i++) { // update->ntimestep could be 0. so add 1 throughout i_limit_tags[atom->map(temp_limit_glove[i])] = update->ntimestep + 1; - i_statted_tags[atom->map(temp_limit_glove[i])] = 0; + if (stabilization_flag == 1) i_statted_tags[atom->map(temp_limit_glove[i])] = 0; i_react_tags[atom->map(temp_limit_glove[i])] = rxnID; } @@ -1884,8 +2014,11 @@ void FixBondReact::unlimit_bond() int index1 = atom->find_custom("limit_tags",flag); int *i_limit_tags = atom->ivector[index1]; - int index2 = atom->find_custom(statted_id,flag); - int *i_statted_tags = atom->ivector[index2]; + int *i_statted_tags; + if (stabilization_flag == 1) { + int index2 = atom->find_custom(statted_id,flag); + i_statted_tags = atom->ivector[index2]; + } int index3 = atom->find_custom("react_tags",flag); int *i_react_tags = atom->ivector[index3]; @@ -1895,7 +2028,7 @@ void FixBondReact::unlimit_bond() // first '1': indexing offset, second '1': for next step if (i_limit_tags[i] != 0 && (update->ntimestep + 1 - i_limit_tags[i]) > limit_duration[i_react_tags[i]]) { // + 1 i_limit_tags[i] = 0; - i_statted_tags[i] = 1; + if (stabilization_flag == 1) i_statted_tags[i] = 1; i_react_tags[i] = 0; } } @@ -1916,19 +2049,19 @@ void FixBondReact::glove_ghostcheck() // 'ghosts of another' indication taken from comm->sendlist int ghostly = 0; - if (comm->style == 0) { - for (int i = 0; i < onemol->natoms; i++) { - int ilocal = atom->map(glove[i][1]); - if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { - ghostly = 1; - break; + #if !defined(MPI_STUBS) + if (comm->style == 0) { + for (int i = 0; i < onemol->natoms; i++) { + int ilocal = atom->map(glove[i][1]); + if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) { + ghostly = 1; + break; + } } - } - } else { - #if !defined(MPI_STUBS) + } else { ghostly = 1; - #endif - } + } + #endif if (ghostly == 1) { ghostly_mega_glove[0][ghostly_num_mega] = rxnID; @@ -2038,6 +2171,13 @@ void FixBondReact::update_everything() tagint **bond_atom = atom->bond_atom; int *num_bond = atom->num_bond; + // used when deleting atoms + int ndel,ndelone; + int *mark = new int[nlocal]; + for (int i = 0; i < nlocal; i++) mark[i] = 0; + tagint *tag = atom->tag; + AtomVec *avec = atom->avec; + // update atom->nbonds, etc. // TODO: correctly tally with 'newton off' int delta_bonds = 0; @@ -2056,18 +2196,39 @@ void FixBondReact::update_everything() memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove"); for (int pass = 0; pass < 2; pass++) { - + update_num_mega = 0; + int *iskip = new int[nreacts]; + for (int i = 0; i < nreacts; i++) iskip[i] = 0; if (pass == 0) { - update_num_mega = local_num_mega; - for (int i = 0; i < update_num_mega; i++) { + for (int i = 0; i < local_num_mega; i++) { + rxnID = local_mega_glove[0][i]; + // reactions already shuffled from dedup procedure, so can skip first N + if (iskip[rxnID]++ < nlocalskips[rxnID]) continue; for (int j = 0; j < max_natoms+1; j++) - update_mega_glove[j][i] = local_mega_glove[j][i]; + update_mega_glove[j][update_num_mega] = local_mega_glove[j][i]; + update_num_mega++; } } else if (pass == 1) { - update_num_mega = global_megasize; for (int i = 0; i < global_megasize; i++) { + rxnID = global_mega_glove[0][i]; + // reactions already shuffled from dedup procedure, so can skip first N + if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue; for (int j = 0; j < max_natoms+1; j++) - update_mega_glove[j][i] = global_mega_glove[j][i]; + update_mega_glove[j][update_num_mega] = global_mega_glove[j][i]; + update_num_mega++; + } + } + delete [] iskip; + + // mark to-delete atoms + for (int i = 0; i < update_num_mega; i++) { + rxnID = update_mega_glove[0][i]; + onemol = atom->molecules[unreacted_mol[rxnID]]; + for (int j = 0; j < onemol->natoms; j++) { + int iatom = atom->map(update_mega_glove[j+1][i]); + if (delete_atoms[j][rxnID] == 1 && iatom >= 0 && iatom < nlocal) { + mark[iatom] = 1; + } } } @@ -2077,7 +2238,7 @@ void FixBondReact::update_everything() twomol = atom->molecules[reacted_mol[rxnID]]; for (int j = 0; j < twomol->natoms; j++) { int jj = equivalences[j][1][rxnID]-1; - if ((landlocked_atoms[j][rxnID] == 1 || update_edges_flag[rxnID] == 1) && + if ((landlocked_atoms[j][rxnID] == 1 || custom_edges[jj][rxnID] == 1) && atom->map(update_mega_glove[jj+1][i]) >= 0 && atom->map(update_mega_glove[jj+1][i]) < nlocal) { type[atom->map(update_mega_glove[jj+1][i])] = twomol->type[j]; @@ -2471,6 +2632,59 @@ void FixBondReact::update_everything() memory->destroy(update_mega_glove); + // delete atoms. taken from fix_evaporate. but don't think it needs to be in pre_exchange + // loop in reverse order to avoid copying marked atoms + ndel = ndelone = 0; + for (int i = atom->nlocal-1; i >= 0; i--) { + if (mark[i] == 1) { + avec->copy(atom->nlocal-1,i,1); + atom->nlocal--; + ndelone++; + + if (atom->avec->bonds_allow) { + if (force->newton_bond) delta_bonds += atom->num_bond[i]; + else { + for (int j = 0; j < atom->num_bond[i]; j++) { + if (tag[i] < atom->bond_atom[i][j]) delta_bonds++; + } + } + } + if (atom->avec->angles_allow) { + if (force->newton_bond) delta_angle += atom->num_angle[i]; + else { + for (int j = 0; j < atom->num_angle[i]; j++) { + int m = atom->map(atom->angle_atom2[i][j]); + if (m >= 0 && m < nlocal) delta_angle++; + } + } + } + if (atom->avec->dihedrals_allow) { + if (force->newton_bond) delta_dihed += atom->num_dihedral[i]; + else { + for (int j = 0; j < atom->num_dihedral[i]; j++) { + int m = atom->map(atom->dihedral_atom2[i][j]); + if (m >= 0 && m < nlocal) delta_dihed++; + } + } + } + if (atom->avec->impropers_allow) { + if (force->newton_bond) delta_imprp += atom->num_improper[i]; + else { + for (int j = 0; j < atom->num_improper[i]; j++) { + int m = atom->map(atom->improper_atom2[i][j]); + if (m >= 0 && m < nlocal) delta_imprp++; + } + } + } + } + } + delete [] mark; + + MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world); + + atom->natoms -= ndel; + // done deleting atoms + // something to think about: this could done much more concisely if // all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG @@ -2520,6 +2734,9 @@ void FixBondReact::read(int myrxn) if (strstr(line,"edgeIDs")) sscanf(line,"%d",&nedge); else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent); + else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom); + else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); + else if (strstr(line,"constraints")) sscanf(line,"%d",&nconstraints[myrxn]); else break; } @@ -2532,7 +2749,7 @@ void FixBondReact::read(int myrxn) // loop over sections of superimpose file - int equivflag = 0, edgeflag = 0, bondflag = 0; + int equivflag = 0, edgeflag = 0, bondflag = 0, customedgesflag = 0; while (strlen(keyword)) { if (strcmp(keyword,"BondingIDs") == 0) { bondflag = 1; @@ -2546,6 +2763,13 @@ void FixBondReact::read(int myrxn) } else if (strcmp(keyword,"Equivalences") == 0) { equivflag = 1; Equivalences(line, myrxn); + } else if (strcmp(keyword,"Custom Edges") == 0) { + customedgesflag = 1; + CustomEdges(line, myrxn); + } else if (strcmp(keyword,"DeleteIDs") == 0) { + DeleteAtoms(line, myrxn); + } else if (strcmp(keyword,"Constraints") == 0) { + Constraints(line, myrxn); } else error->one(FLERR,"Unknown section in superimpose file"); parse_keyword(1,line,keyword); @@ -2555,6 +2779,12 @@ void FixBondReact::read(int myrxn) // error check if (bondflag == 0 || equivflag == 0) error->all(FLERR,"Superimpose file missing BondingIDs or Equivalences section\n"); + + if (update_edges_flag[myrxn] == 2 && customedgesflag == 0) + error->all(FLERR,"Map file must have a Custom Edges section when using 'update_edges custom'\n"); + + if (update_edges_flag[myrxn] != 2 && customedgesflag == 1) + error->all(FLERR,"Specify 'update_edges custom' to include Custom Edges section in map file\n"); } void FixBondReact::EdgeIDs(char *line, int myrxn) @@ -2585,6 +2815,57 @@ void FixBondReact::Equivalences(char *line, int myrxn) } } +void FixBondReact::CustomEdges(char *line, int myrxn) +{ + // 0 for 'none', 1 for 'charges' + + int tmp; + int n = MAX(strlen("none"),strlen("charges")) + 1; + char *edgemode = new char[n]; + for (int i = 0; i < ncustom; i++) { + readline(line); + sscanf(line,"%d %s",&tmp,edgemode); + if (strcmp(edgemode,"none") == 0) + custom_edges[tmp-1][myrxn] = 0; + else if (strcmp(edgemode,"charges") == 0) + custom_edges[tmp-1][myrxn] = 1; + else + error->one(FLERR,"Illegal value in 'Custom Edges' section of map file"); + } + delete [] edgemode; +} + +void FixBondReact::DeleteAtoms(char *line, int myrxn) +{ + int tmp; + for (int i = 0; i < ndelete; i++) { + readline(line); + sscanf(line,"%d",&tmp); + delete_atoms[tmp-1][myrxn] = 1; + } +} + +void FixBondReact::Constraints(char *line, int myrxn) +{ + double tmp[MAXCONARGS]; + int n = strlen("distance") + 1; + char *constraint_type = new char[n]; + for (int i = 0; i < nconstraints[myrxn]; i++) { + readline(line); + sscanf(line,"%s",constraint_type); + if (strcmp(constraint_type,"distance") == 0) { + constraints[myrxn][0] = 0; // 0 = 'distance' ...maybe use another enum eventually + sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]); + constraints[myrxn][1] = tmp[0]; + constraints[myrxn][2] = tmp[1]; + constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance + constraints[myrxn][4] = tmp[3]*tmp[3]; + } else + error->one(FLERR,"Illegal constraint type in 'Constraints' section of map file"); + } + delete [] constraint_type; +} + void FixBondReact::open(char *file) { fp = fopen(file,"r"); @@ -2767,7 +3048,7 @@ int FixBondReact::pack_reverse_comm(int n, int first, double *buf) for (i = first; i < last; i++) { buf[m++] = ubuf(partner[i]).d; - if (closeneigh[rxnID] < 0) + if (closeneigh[rxnID] != 0) buf[m++] = distsq[i][1]; else buf[m++] = distsq[i][0]; @@ -2786,11 +3067,11 @@ void FixBondReact::unpack_reverse_comm(int n, int *list, double *buf) if (commflag != 1) { for (i = 0; i < n; i++) { j = list[i]; - if (closeneigh[rxnID] < 0) + if (closeneigh[rxnID] != 0) if (buf[m+1] < distsq[j][1]) { partner[j] = (tagint) ubuf(buf[m++]).i; distsq[j][1] = buf[m++]; - } else m += 2; + } else m += 2; else if (buf[m+1] > distsq[j][0]) { partner[j] = (tagint) ubuf(buf[m++]).i; diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h index ca1f3bd20c..74d53b8f21 100644 --- a/src/USER-MISC/fix_bond_react.h +++ b/src/USER-MISC/fix_bond_react.h @@ -55,11 +55,14 @@ class FixBondReact : public Fix { int *iatomtype,*jatomtype; int *seed; double **cutsq,*fraction; + int *max_rxn,*nlocalskips,*nghostlyskips; tagint lastcheck; int stabilization_flag; int custom_exclude_flag; int *stabilize_steps_flag; int *update_edges_flag; + int *nconstraints; + double **constraints; int status; int *groupbits; @@ -101,7 +104,7 @@ class FixBondReact : public Fix { int *ibonding,*jbonding; int *closeneigh; // indicates if bonding atoms of a rxn are 1-2, 1-3, or 1-4 neighbors - int nedge,nequivalent; // number of edge, equivalent atoms in mapping file + int nedge,nequivalent,ncustom,ndelete; // number of edge, equivalent, custom atoms in mapping file int attempted_rxn; // there was an attempt! int *local_rxn_count; int *ghostly_rxn_count; @@ -115,6 +118,8 @@ class FixBondReact : public Fix { int ***equivalences; // relation between pre- and post-reacted templates int ***reverse_equiv; // re-ordered equivalences int **landlocked_atoms; // all atoms at least three bonds away from edge atoms + int **custom_edges; // atoms in molecule templates with incorrect valences + int **delete_atoms; // atoms in pre-reacted templates to delete int **nxspecial,**onemol_nxspecial,**twomol_nxspecial; // full number of 1-4 neighbors tagint **xspecial,**onemol_xspecial,**twomol_xspecial; // full 1-4 neighbor list @@ -136,6 +141,9 @@ class FixBondReact : public Fix { void read(int); void EdgeIDs(char *,int); void Equivalences(char *,int); + void CustomEdges(char *,int); + void DeleteAtoms(char *,int); + void Constraints(char *,int); void make_a_guess (); void neighbor_loop(); @@ -143,6 +151,7 @@ class FixBondReact : public Fix { void crosscheck_the_neighbor(); void inner_crosscheck_loop(); void ring_check(); + int check_constraints(); void open(char *); void readline(char *); diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp index e2fb0166a2..9ab113aeaa 100644 --- a/src/USER-MISC/fix_ffl.cpp +++ b/src/USER-MISC/fix_ffl.cpp @@ -108,8 +108,6 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : } t_target=t_start; - const double kT = t_target * force->boltz / force->mvv2e; - // initialize Marsaglia RNG with processor-unique seed // NB: this means runs will not be the same with different numbers of processors @@ -138,6 +136,9 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) : FixFFL::~FixFFL() { delete random; + atom->delete_callback(id,0); + atom->delete_callback(id,1); + memory->destroy(sqrt_m); memory->destroy(ffl_tmp1); memory->destroy(ffl_tmp2); @@ -298,7 +299,7 @@ void FixFFL::ffl_integrate() { } -void FixFFL::initial_integrate(int vflag) { +void FixFFL::initial_integrate(int /* vflag */) { double dtfm; // update v and x of atoms in group @@ -391,7 +392,7 @@ void FixFFL::final_integrate() { } /* ---------------------------------------------------------------------- */ -void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) { +void FixFFL::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; @@ -406,7 +407,7 @@ void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) { } } -void FixFFL::final_integrate_respa(int ilevel, int iloop) { +void FixFFL::final_integrate_respa(int ilevel, int /* iloop */) { dtv = step_respa[ilevel]; dtf = 0.5 * step_respa[ilevel] * force->ftm2v; diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp index 56ab2b3df9..f6cc1c435f 100644 --- a/src/USER-MISC/fix_filter_corotate.cpp +++ b/src/USER-MISC/fix_filter_corotate.cpp @@ -217,7 +217,6 @@ FixFilterCorotate::~FixFilterCorotate() memory->destroy(dn2dx); memory->destroy(dn3dx); - atom->delete_callback(id,2); atom->delete_callback(id,0); // delete locally stored arrays @@ -592,14 +591,13 @@ void FixFilterCorotate::pre_neighbor() double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]); int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2])); - if (fabs(signum)!= 1) + if (abs(signum) != 1) error->all(FLERR,"Wrong orientation in cluster of size 4" "in fix filter/corotate!"); clist_q0[i][8] *= signum; clist_q0[i][11] *= signum; - } else if (N == 5) - { + } else if (N == 5) { oxy = atom->map(shake_atom[m][0]); atom1 = atom->map(shake_atom[m][1]); atom2 = atom->map(shake_atom[m][2]); @@ -666,14 +664,12 @@ void FixFilterCorotate::pre_neighbor() double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]); int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2])); - if (fabs(signum)!= 1) + if (abs(signum)!= 1) error->all(FLERR,"Wrong orientation in cluster of size 5" "in fix filter/corotate!"); clist_q0[i][8] *= signum; clist_q0[i][11] *= signum; - } - else - { + } else { error->all(FLERR,"Fix filter/corotate cluster with size > 5" "not yet configured..."); } diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp index 78d63b79a8..6a6e71ebaa 100644 --- a/src/USER-MISC/fix_rhok.cpp +++ b/src/USER-MISC/fix_rhok.cpp @@ -52,7 +52,7 @@ FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ) if (lmp->citeme) lmp->citeme->add(cite_fix_rhok); // Check arguments - if( inArgc != 8 ) + if (inArgc != 8) error->all(FLERR,"Illegal fix rhoKUmbrella command" ); // Set up fix flags @@ -104,7 +104,7 @@ void FixRhok::init() { // RESPA boilerplate - if( strcmp( update->integrate_style, "respa" ) == 0 ) + if (strcmp( update->integrate_style, "respa" ) == 0) mNLevelsRESPA = ((Respa *) update->integrate)->nlevels; // Count the number of affected particles @@ -112,7 +112,7 @@ FixRhok::init() int *mask = atom->mask; int nlocal = atom->nlocal; for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU - if( mask[i] & groupbit ) { // ...only those affected by this fix + if (mask[i] & groupbit) { // ...only those affected by this fix nThisLocal++; } } @@ -125,7 +125,7 @@ FixRhok::init() void FixRhok::setup( int inVFlag ) { - if( strcmp( update->integrate_style, "verlet" ) == 0 ) + if (strcmp( update->integrate_style, "verlet" ) == 0) post_force( inVFlag ); else { @@ -157,7 +157,7 @@ FixRhok::post_force( int /*inVFlag*/ ) mRhoKLocal[1] = 0.0; for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU - if( mask[i] & groupbit ) { // ...only those affected by this fix + if (mask[i] & groupbit) { // ...only those affected by this fix // rho_k = sum_i exp( - i k.r_i ) mRhoKLocal[0] += cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] ); @@ -180,7 +180,7 @@ FixRhok::post_force( int /*inVFlag*/ ) + mRhoKGlobal[1]*mRhoKGlobal[1] ); for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU - if( mask[i] & groupbit ) { // ...only those affected by this fix + if (mask[i] & groupbit) { // ...only those affected by this fix // Calculate forces // U = kappa/2 ( |rho_k| - rho_k^0 )^2 @@ -208,7 +208,7 @@ FixRhok::post_force( int /*inVFlag*/ ) void FixRhok::post_force_respa( int inVFlag, int inILevel, int /*inILoop*/ ) { - if( inILevel == mNLevelsRESPA - 1 ) + if (inILevel == mNLevelsRESPA - 1) post_force( inVFlag ); } @@ -233,7 +233,7 @@ FixRhok::compute_scalar() double FixRhok::compute_vector( int inI ) { - if( inI == 0 ) + if (inI == 0) return mRhoKGlobal[0]; // Real part else if( inI == 1 ) return mRhoKGlobal[1]; // Imagniary part diff --git a/src/USER-MISC/fix_ttm_mod.cpp b/src/USER-MISC/fix_ttm_mod.cpp index a423b510e5..a34c2eb42f 100644 --- a/src/USER-MISC/fix_ttm_mod.cpp +++ b/src/USER-MISC/fix_ttm_mod.cpp @@ -325,7 +325,7 @@ void FixTTMMod::init() if (domain->dimension == 2) error->all(FLERR,"Cannot use fix ttm/mod with 2d simulation"); if (domain->nonperiodic != 0) - error->all(FLERR,"Cannot use nonperiodic boundares with fix ttm/mod"); + error->all(FLERR,"Cannot use non-periodic boundares with fix ttm/mod"); if (domain->triclinic) error->all(FLERR,"Cannot use fix ttm/mod with triclinic box"); // set force prefactors @@ -346,9 +346,9 @@ void FixTTMMod::init() void FixTTMMod::setup(int vflag) { - if (strstr(update->integrate_style,"verlet")) + if (strstr(update->integrate_style,"verlet")) { post_force_setup(vflag); - else { + } else { ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); post_force_respa_setup(vflag,nlevels_respa-1,0); ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); @@ -428,8 +428,7 @@ void FixTTMMod::post_force(int /*vflag*/) flangevin[i][1] -= pres_factor/ionic_density/dy*(C_iu*T_iu-C_i*T_i); flangevin[i][2] -= pres_factor/ionic_density/dz*(C_if*T_if-C_i*T_i); } - } - else{ + } else { flangevin[i][0] -= pres_factor/ionic_density/dx*(C_ir*T_ir-C_i*T_i); flangevin[i][1] -= pres_factor/ionic_density/dy*(C_iu*T_iu-C_i*T_i); flangevin[i][2] -= pres_factor/ionic_density/dz*(C_if*T_if-C_i*T_i); diff --git a/src/USER-MISC/improper_cossq.cpp b/src/USER-MISC/improper_cossq.cpp index 2483840e42..c8eb0808fb 100644 --- a/src/USER-MISC/improper_cossq.cpp +++ b/src/USER-MISC/improper_cossq.cpp @@ -63,8 +63,7 @@ void ImproperCossq::compute(int eflag, int vflag) eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/improper_distance.cpp b/src/USER-MISC/improper_distance.cpp index 2edf37ec5c..50babcc84e 100644 --- a/src/USER-MISC/improper_distance.cpp +++ b/src/USER-MISC/improper_distance.cpp @@ -67,8 +67,7 @@ void ImproperDistance::compute(int eflag, int vflag) double domega,a; eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp index 11478d08ea..288d888d12 100644 --- a/src/USER-MISC/improper_fourier.cpp +++ b/src/USER-MISC/improper_fourier.cpp @@ -59,8 +59,7 @@ void ImproperFourier::compute(int eflag, int vflag) int i1,i2,i3,i4,n,type; double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; int **improperlist = neighbor->improperlist; @@ -206,17 +205,17 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int dahy = ary-c*hry; dahz = arz-c*hrz; - f2[0] = (dhay*vb1z - dhaz*vb1y)*rar; - f2[1] = (dhaz*vb1x - dhax*vb1z)*rar; - f2[2] = (dhax*vb1y - dhay*vb1x)*rar; + f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a; + f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a; + f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a; - f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar; - f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar; - f3[2] = (-dhax*vb2y + dhay*vb2x)*rar; + f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a; + f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a; + f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a; - f4[0] = dahx*rhr; - f4[1] = dahy*rhr; - f4[2] = dahz*rhr; + f4[0] = dahx*rhr*a; + f4[1] = dahy*rhr*a; + f4[2] = dahz*rhr*a; f1[0] = -(f2[0] + f3[0] + f4[0]); f1[1] = -(f2[1] + f3[1] + f4[1]); @@ -225,32 +224,32 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int // apply force to each of 4 atoms if (newton_bond || i1 < nlocal) { - f[i1][0] += f1[0]*a; - f[i1][1] += f1[1]*a; - f[i1][2] += f1[2]*a; + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; } if (newton_bond || i2 < nlocal) { - f[i2][0] += f3[0]*a; - f[i2][1] += f3[1]*a; - f[i2][2] += f3[2]*a; + f[i2][0] += f3[0]; + f[i2][1] += f3[1]; + f[i2][2] += f3[2]; } if (newton_bond || i3 < nlocal) { - f[i3][0] += f2[0]*a; - f[i3][1] += f2[1]*a; - f[i3][2] += f2[2]*a; + f[i3][0] += f2[0]; + f[i3][1] += f2[1]; + f[i3][2] += f2[2]; } if (newton_bond || i4 < nlocal) { - f[i4][0] += f4[0]*a; - f[i4][1] += f4[1]*a; - f[i4][2] += f4[2]*a; + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; } if (evflag) - ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4, - vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z); + ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f2,f4, + -vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z); } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/improper_ring.cpp b/src/USER-MISC/improper_ring.cpp index 70124b2ed1..36ba73af0f 100644 --- a/src/USER-MISC/improper_ring.cpp +++ b/src/USER-MISC/improper_ring.cpp @@ -95,8 +95,7 @@ void ImproperRing::compute(int eflag, int vflag) double cjiji, ckjji, ckjkj, fix, fiy, fiz, fjx, fjy, fjz, fkx, fky, fkz; eimproper = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); /* References to simulation data. */ double **x = atom->x; diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp index 0277969d15..21a6f1deee 100644 --- a/src/USER-MISC/pair_agni.cpp +++ b/src/USER-MISC/pair_agni.cpp @@ -136,8 +136,7 @@ void PairAGNI::compute(int eflag, int vflag) double rsq; int *ilist,*jlist,*numneigh,**firstneigh; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_buck_mdf.cpp b/src/USER-MISC/pair_buck_mdf.cpp index 61d32892fc..b5e81417ee 100644 --- a/src/USER-MISC/pair_buck_mdf.cpp +++ b/src/USER-MISC/pair_buck_mdf.cpp @@ -68,8 +68,7 @@ void PairBuckMDF::compute(int eflag, int vflag) double dp, d, tt, dt, dd; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -427,7 +426,7 @@ double PairBuckMDF::single(int /*i*/, int /*j*/, int itype, int jtype, void *PairBuckMDF::extract(const char *str, int &dim) { dim = 2; - if (strcmp(str,"aparm") == 0) return (void *) a; - if (strcmp(str,"cparm") == 0) return (void *) c; + if (strcmp(str,"a") == 0) return (void *) a; + if (strcmp(str,"c") == 0) return (void *) c; return NULL; } diff --git a/src/USER-MISC/pair_coul_diel.cpp b/src/USER-MISC/pair_coul_diel.cpp index 0154e89731..a86921d296 100644 --- a/src/USER-MISC/pair_coul_diel.cpp +++ b/src/USER-MISC/pair_coul_diel.cpp @@ -58,8 +58,7 @@ void PairCoulDiel::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_coul_shield.cpp b/src/USER-MISC/pair_coul_shield.cpp index 11df975c19..f74dcfe7d8 100644 --- a/src/USER-MISC/pair_coul_shield.cpp +++ b/src/USER-MISC/pair_coul_shield.cpp @@ -64,8 +64,7 @@ void PairCoulShield::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_edip.cpp b/src/USER-MISC/pair_edip.cpp index 491268567f..0b5220fdfd 100644 --- a/src/USER-MISC/pair_edip.cpp +++ b/src/USER-MISC/pair_edip.cpp @@ -149,8 +149,7 @@ void PairEDIP::compute(int eflag, int vflag) double potential2B_factor; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_edip_multi.cpp b/src/USER-MISC/pair_edip_multi.cpp index f56650d2f6..ab48fbaa73 100644 --- a/src/USER-MISC/pair_edip_multi.cpp +++ b/src/USER-MISC/pair_edip_multi.cpp @@ -118,8 +118,7 @@ void PairEDIPMulti::compute(int eflag, int vflag) // vflag != 0 means compute virial contributions in this step evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_extep.cpp b/src/USER-MISC/pair_extep.cpp index 1e7d17f040..132b857dde 100644 --- a/src/USER-MISC/pair_extep.cpp +++ b/src/USER-MISC/pair_extep.cpp @@ -190,8 +190,7 @@ void PairExTeP::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); SR_neigh(); @@ -1075,10 +1074,10 @@ void PairExTeP::costheta_d(double *rij_hat, double rij, // initialize spline for F_corr (based on PairLCBOP::F_conj) void PairExTeP::spline_init() { - for ( size_t iel=0; ielntypes; iel++) { - for ( size_t jel=0; jelntypes; jel++) { - for ( size_t N_ij=0; N_ij<4; N_ij++ ) { - for ( size_t N_ji=0; N_ji<4; N_ji++ ) { + for ( int iel=0; ielntypes; iel++) { + for ( int jel=0; jelntypes; jel++) { + for ( int N_ij=0; N_ij<4; N_ij++ ) { + for ( int N_ji=0; N_ji<4; N_ji++ ) { TF_corr_param &f = F_corr_param[iel][jel][N_ij][N_ji]; // corner points for each spline function @@ -1150,8 +1149,8 @@ double PairExTeP::F_corr(int iel, int jel, double Ndij, double Ndji, double *dFN // compute F_XY - size_t Ndij_int = static_cast( floor( Ndij ) ); - size_t Ndji_int = static_cast( floor( Ndji ) ); + int Ndij_int = static_cast( floor( Ndij ) ); + int Ndji_int = static_cast( floor( Ndji ) ); double x = Ndij - Ndij_int; double y = Ndji - Ndji_int; TF_corr_param &f = F_corr_param[iel][jel][Ndij_int][Ndji_int]; diff --git a/src/USER-MISC/pair_gauss_cut.cpp b/src/USER-MISC/pair_gauss_cut.cpp index a000eff028..24d0b191d8 100644 --- a/src/USER-MISC/pair_gauss_cut.cpp +++ b/src/USER-MISC/pair_gauss_cut.cpp @@ -69,8 +69,7 @@ void PairGaussCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_ilp_graphene_hbn.cpp b/src/USER-MISC/pair_ilp_graphene_hbn.cpp index f613f0aff0..d1b8a3be38 100644 --- a/src/USER-MISC/pair_ilp_graphene_hbn.cpp +++ b/src/USER-MISC/pair_ilp_graphene_hbn.cpp @@ -46,7 +46,6 @@ using namespace LAMMPS_NS; PairILPGrapheneHBN::PairILPGrapheneHBN(LAMMPS *lmp) : Pair(lmp) { - writedata = 1; restartinfo = 0; // initialize element to parameter maps @@ -118,8 +117,7 @@ void PairILPGrapheneHBN::compute(int eflag, int vflag) int *ILP_neighs_i,*ILP_neighs_j; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp index 2f868ae418..289ed19bd3 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_full.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_full.cpp @@ -46,8 +46,6 @@ using namespace LAMMPS_NS; PairKolmogorovCrespiFull::PairKolmogorovCrespiFull(LAMMPS *lmp) : Pair(lmp) { - writedata = 1; - // initialize element to parameter maps nelements = 0; elements = NULL; @@ -117,8 +115,7 @@ void PairKolmogorovCrespiFull::compute(int eflag, int vflag) int *KC_neighs_i,*KC_neighs_j; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp index b39b9fdb72..dcea990a3b 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.cpp +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.cpp @@ -1,442 +1,441 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Jaap Kroes (Radboud Universiteit) - e-mail: jaapkroes at gmail dot com - based on previous versions by Merel van Wijk and by Marco Raguzzoni - - This is a simplified version of the potential described in - [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] - The simplification is that all normals are taken along the z-direction -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_kolmogorov_crespi_z.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -#define MAXLINE 1024 -#define DELTA 4 - -/* ---------------------------------------------------------------------- */ - -PairKolmogorovCrespiZ::PairKolmogorovCrespiZ(LAMMPS *lmp) : Pair(lmp) -{ - writedata = 1; - restartinfo = 0; - - // initialize element to parameter maps - nelements = 0; - elements = NULL; - nparams = maxparam = 0; - params = NULL; - elem2param = NULL; - map = NULL; - - // always compute energy offset - offset_flag = 1; -} - -/* ---------------------------------------------------------------------- */ - -PairKolmogorovCrespiZ::~PairKolmogorovCrespiZ() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(cut); - memory->destroy(offset); - } - - if (elements) - for (int i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - memory->destroy(params); - memory->destroy(elem2param); - if (allocated) delete [] map; -} - -/* ---------------------------------------------------------------------- */ - -void PairKolmogorovCrespiZ::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair, fpair1; - double rsq,r,rhosq,exp1,exp2,r6,r8; - double frho,sumC,sumC2,sumCff,fsum,rdsq; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; - jtype = type[j]; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - // rho^2 = r^2 - (n,r) = r^2 - z^2 - rhosq = delx*delx + dely*dely; - rsq = rhosq + delz*delz; - - if (rsq < cutsq[itype][jtype]) { - - int iparam_ij = elem2param[map[itype]][map[jtype]]; - Param& p = params[iparam_ij]; - - r = sqrt(rsq); - r6 = rsq*rsq*rsq; - r8 = r6*rsq; - rdsq = rhosq*p.delta2inv; // (rho/delta)^2 - - // store exponents - exp1 = exp(-p.lambda*(r-p.z0)); - exp2 = exp(-rdsq); - - // note that f(rho_ij) equals f(rho_ji) as normals are all along z - sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq; - sumC2 = (2*p.C2+4*p.C4*rdsq)*p.delta2inv; - frho = exp2*sumC; - sumCff = p.C + 2*frho; - - // derivatives - fpair = -6.0*p.A*p.z06/r8+p.lambda*exp1/r*sumCff; - fpair1 = exp1*exp2*(4.0*p.delta2inv*sumC-2.0*sumC2); - fsum = fpair + fpair1; - - f[i][0] += delx*fsum; - f[i][1] += dely*fsum; - // fi_z does not contain contributions from df/dr - // because rho_ij does not depend on z_i or z_j - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fsum; - f[j][1] -= dely*fsum; - f[j][2] -= delz*fpair; - } - - if (eflag) { - evdwl = -p.A*p.z06/r6+ exp1*sumCff - offset[itype][jtype]; - } - - if (evflag){ - ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0, - fsum,fsum,fpair,delx,dely,delz); - } - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairKolmogorovCrespiZ::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(offset,n+1,n+1,"pair:offset"); - map = new int[atom->ntypes+1]; -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairKolmogorovCrespiZ::settings(int narg, char **arg) -{ - if (narg != 1) error->all(FLERR,"Illegal pair_style command"); - if (strcmp(force->pair_style,"hybrid/overlay")!=0) - error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); - - cut_global = force->numeric(FLERR,arg[0]); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) - if (setflag[i][j]) cut[i][j] = cut_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairKolmogorovCrespiZ::coeff(int narg, char **arg) -{ - int i,j,n; - - if (narg != 3 + atom->ntypes) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - // read args that map atom types to elements in potential file - // map[i] = which element the Ith atom type is, -1 if NULL - // nelements = # of unique elements - // elements = list of element names - - if (elements) { - for (i = 0; i < nelements; i++) delete [] elements[i]; - delete [] elements; - } - elements = new char*[atom->ntypes]; - for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; - - nelements = 0; - for (i = 3; i < narg; i++) { - if (strcmp(arg[i],"NULL") == 0) { - map[i-2] = -1; - continue; - } - for (j = 0; j < nelements; j++) - if (strcmp(arg[i],elements[j]) == 0) break; - map[i-2] = j; - if (j == nelements) { - n = strlen(arg[i]) + 1; - elements[j] = new char[n]; - strcpy(elements[j],arg[i]); - nelements++; - } - } - - - read_file(arg[2]); - - double cut_one = cut_global; - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairKolmogorovCrespiZ::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - if (offset_flag && (cut[i][j] > 0.0)) { - int iparam_ij = elem2param[map[i]][map[j]]; - Param& p = params[iparam_ij]; - offset[i][j] = -p.A*pow(p.z0/cut[i][j],6); - } else offset[i][j] = 0.0; - offset[j][i] = offset[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - read Kolmogorov-Crespi potential file -------------------------------------------------------------------------- */ - -void PairKolmogorovCrespiZ::read_file(char *filename) -{ - int params_per_line = 11; - char **words = new char*[params_per_line+1]; - memory->sfree(params); - params = NULL; - nparams = maxparam = 0; - - // open file on proc 0 - - FILE *fp; - if (comm->me == 0) { - fp = force->open_potential(filename); - if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open KC potential file %s",filename); - error->one(FLERR,str); - } - } - - // read each line out of file, skipping blank lines or leading '#' - // store line of params if all 3 element tags are in element list - - int i,j,n,m,nwords,ielement,jelement; - char line[MAXLINE],*ptr; - int eof = 0; - - while (1) { - if (comm->me == 0) { - ptr = fgets(line,MAXLINE,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - - // strip comment, skip line if blank - - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); - if (nwords == 0) continue; - - // concatenate additional lines until have params_per_line words - - while (nwords < params_per_line) { - n = strlen(line); - if (comm->me == 0) { - ptr = fgets(&line[n],MAXLINE-n,fp); - if (ptr == NULL) { - eof = 1; - fclose(fp); - } else n = strlen(line) + 1; - } - MPI_Bcast(&eof,1,MPI_INT,0,world); - if (eof) break; - MPI_Bcast(&n,1,MPI_INT,0,world); - MPI_Bcast(line,n,MPI_CHAR,0,world); - if ((ptr = strchr(line,'#'))) *ptr = '\0'; - nwords = atom->count_words(line); - } - - if (nwords != params_per_line) - error->all(FLERR,"Insufficient format in KC potential file"); - - // words = ptrs to all words in line - - nwords = 0; - words[nwords++] = strtok(line," \t\n\r\f"); - while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; - - // ielement,jelement = 1st args - // if these 2 args are in element list, then parse this line - // else skip to next line (continue) - - for (ielement = 0; ielement < nelements; ielement++) - if (strcmp(words[0],elements[ielement]) == 0) break; - if (ielement == nelements) continue; - for (jelement = 0; jelement < nelements; jelement++) - if (strcmp(words[1],elements[jelement]) == 0) break; - if (jelement == nelements) continue; - - // load up parameter settings and error check their values - - if (nparams == maxparam) { - maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), - "pair:params"); - } - - params[nparams].ielement = ielement; - params[nparams].jelement = jelement; - params[nparams].z0 = atof(words[2]); - params[nparams].C0 = atof(words[3]); - params[nparams].C2 = atof(words[4]); - params[nparams].C4 = atof(words[5]); - params[nparams].C = atof(words[6]); - params[nparams].delta = atof(words[7]); - params[nparams].lambda = atof(words[8]); - params[nparams].A = atof(words[9]); - // S provides a convenient scaling of all energies - params[nparams].S = atof(words[10]); - - // energies in meV further scaled by S - double meV = 1.0e-3*params[nparams].S; - params[nparams].C *= meV; - params[nparams].A *= meV; - params[nparams].C0 *= meV; - params[nparams].C2 *= meV; - params[nparams].C4 *= meV; - - // precompute some quantities - params[nparams].delta2inv = pow(params[nparams].delta,-2); - params[nparams].z06 = pow(params[nparams].z0,6); - - nparams++; - if(nparams >= pow(atom->ntypes,3)) break; - } - memory->destroy(elem2param); - memory->create(elem2param,nelements,nelements,"pair:elem2param"); - for (i = 0; i < nelements; i++) { - for (j = 0; j < nelements; j++) { - n = -1; - for (m = 0; m < nparams; m++) { - if (i == params[m].ielement && j == params[m].jelement) { - if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); - n = m; - } - } - if (n < 0) error->all(FLERR,"Potential file is missing an entry"); - elem2param[i][j] = n; - } - } - delete [] words; -} - -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Jaap Kroes (Radboud Universiteit) + e-mail: jaapkroes at gmail dot com + based on previous versions by Merel van Wijk and by Marco Raguzzoni + + This is a simplified version of the potential described in + [Kolmogorov & Crespi, Phys. Rev. B 71, 235415 (2005)] + The simplification is that all normals are taken along the z-direction +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_kolmogorov_crespi_z.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 +#define DELTA 4 + +/* ---------------------------------------------------------------------- */ + +PairKolmogorovCrespiZ::PairKolmogorovCrespiZ(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + restartinfo = 0; + + // initialize element to parameter maps + nelements = 0; + elements = NULL; + nparams = maxparam = 0; + params = NULL; + elem2param = NULL; + map = NULL; + + // always compute energy offset + offset_flag = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairKolmogorovCrespiZ::~PairKolmogorovCrespiZ() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + memory->destroy(offset); + } + + if (elements) + for (int i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + memory->destroy(params); + memory->destroy(elem2param); + if (allocated) delete [] map; +} + +/* ---------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair, fpair1; + double rsq,r,rhosq,exp1,exp2,r6,r8; + double frho,sumC,sumC2,sumCff,fsum,rdsq; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + // rho^2 = r^2 - (n,r) = r^2 - z^2 + rhosq = delx*delx + dely*dely; + rsq = rhosq + delz*delz; + + if (rsq < cutsq[itype][jtype]) { + + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; + + r = sqrt(rsq); + r6 = rsq*rsq*rsq; + r8 = r6*rsq; + rdsq = rhosq*p.delta2inv; // (rho/delta)^2 + + // store exponents + exp1 = exp(-p.lambda*(r-p.z0)); + exp2 = exp(-rdsq); + + // note that f(rho_ij) equals f(rho_ji) as normals are all along z + sumC = p.C0+p.C2*rdsq+p.C4*rdsq*rdsq; + sumC2 = (2*p.C2+4*p.C4*rdsq)*p.delta2inv; + frho = exp2*sumC; + sumCff = p.C + 2*frho; + + // derivatives + fpair = -6.0*p.A*p.z06/r8+p.lambda*exp1/r*sumCff; + fpair1 = exp1*exp2*(4.0*p.delta2inv*sumC-2.0*sumC2); + fsum = fpair + fpair1; + + f[i][0] += delx*fsum; + f[i][1] += dely*fsum; + // fi_z does not contain contributions from df/dr + // because rho_ij does not depend on z_i or z_j + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fsum; + f[j][1] -= dely*fsum; + f[j][2] -= delz*fpair; + } + + if (eflag) { + evdwl = -p.A*p.z06/r6+ exp1*sumCff - offset[itype][jtype]; + } + + if (evflag){ + ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0, + fsum,fsum,fpair,delx,dely,delz); + } + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(offset,n+1,n+1,"pair:offset"); + map = new int[atom->ntypes+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + if (strcmp(force->pair_style,"hybrid/overlay")!=0) + error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); + + cut_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::coeff(int narg, char **arg) +{ + int i,j,n; + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names + + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; + + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } + + + read_file(arg[2]); + + double cut_one = cut_global; + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairKolmogorovCrespiZ::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + if (offset_flag && (cut[i][j] > 0.0)) { + int iparam_ij = elem2param[map[i]][map[j]]; + Param& p = params[iparam_ij]; + offset[i][j] = -p.A*pow(p.z0/cut[i][j],6); + } else offset[i][j] = 0.0; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + read Kolmogorov-Crespi potential file +------------------------------------------------------------------------- */ + +void PairKolmogorovCrespiZ::read_file(char *filename) +{ + int params_per_line = 11; + char **words = new char*[params_per_line+1]; + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; + + // open file on proc 0 + + FILE *fp; + if (comm->me == 0) { + fp = force->open_potential(filename); + if (fp == NULL) { + char str[128]; + snprintf(str,128,"Cannot open KC potential file %s",filename); + error->one(FLERR,str); + } + } + + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list + + int i,j,n,m,nwords,ielement,jelement; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + } + + if (nwords != params_per_line) + error->all(FLERR,"Insufficient format in KC potential file"); + + // words = ptrs to all words in line + + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; + + // ielement,jelement = 1st args + // if these 2 args are in element list, then parse this line + // else skip to next line (continue) + + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].z0 = atof(words[2]); + params[nparams].C0 = atof(words[3]); + params[nparams].C2 = atof(words[4]); + params[nparams].C4 = atof(words[5]); + params[nparams].C = atof(words[6]); + params[nparams].delta = atof(words[7]); + params[nparams].lambda = atof(words[8]); + params[nparams].A = atof(words[9]); + // S provides a convenient scaling of all energies + params[nparams].S = atof(words[10]); + + // energies in meV further scaled by S + double meV = 1.0e-3*params[nparams].S; + params[nparams].C *= meV; + params[nparams].A *= meV; + params[nparams].C0 *= meV; + params[nparams].C2 *= meV; + params[nparams].C4 *= meV; + + // precompute some quantities + params[nparams].delta2inv = pow(params[nparams].delta,-2); + params[nparams].z06 = pow(params[nparams].z0,6); + + nparams++; + if(nparams >= pow(atom->ntypes,3)) break; + } + memory->destroy(elem2param); + memory->create(elem2param,nelements,nelements,"pair:elem2param"); + for (i = 0; i < nelements; i++) { + for (j = 0; j < nelements; j++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = m; + } + } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + elem2param[i][j] = n; + } + } + delete [] words; +} + +/* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_kolmogorov_crespi_z.h b/src/USER-MISC/pair_kolmogorov_crespi_z.h index caa5dac868..1a90fdfa0b 100644 --- a/src/USER-MISC/pair_kolmogorov_crespi_z.h +++ b/src/USER-MISC/pair_kolmogorov_crespi_z.h @@ -1,83 +1,83 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef PAIR_CLASS - -PairStyle(kolmogorov/crespi/z,PairKolmogorovCrespiZ) - -#else - -#ifndef LMP_PAIR_KolmogorovCrespiZ_H -#define LMP_PAIR_KolmogorovCrespiZ_H - -#include "pair.h" - -namespace LAMMPS_NS { - -class PairKolmogorovCrespiZ : public Pair { - public: - PairKolmogorovCrespiZ(class LAMMPS *); - virtual ~PairKolmogorovCrespiZ(); - - virtual void compute(int, int); - void settings(int, char **); - void coeff(int, char **); - double init_one(int, int); - - protected: - int me; - - struct Param { - double z0,C0,C2,C4,C,delta,lambda,A,S; - double delta2inv,z06; - int ielement,jelement; - }; - Param *params; // parameter set for I-J interactions - char **elements; // names of unique elements - int **elem2param; // mapping from element pairs to parameters - int *map; // mapping from atom types to elements - int nelements; // # of unique elements - int nparams; // # of stored parameter sets - int maxparam; // max # of parameter sets - - double cut_global; - double **cut; - double **offset; - void read_file( char * ); - void allocate(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -E: Incorrect args for pair coefficients - -Self-explanatory. Check the input script or data file. - -E: All pair coeffs are not set - -All pair coefficients must be set in the data file or by the -pair_coeff command before running a simulation. - -*/ - +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(kolmogorov/crespi/z,PairKolmogorovCrespiZ) + +#else + +#ifndef LMP_PAIR_KolmogorovCrespiZ_H +#define LMP_PAIR_KolmogorovCrespiZ_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairKolmogorovCrespiZ : public Pair { + public: + PairKolmogorovCrespiZ(class LAMMPS *); + virtual ~PairKolmogorovCrespiZ(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + + protected: + int me; + + struct Param { + double z0,C0,C2,C4,C,delta,lambda,A,S; + double delta2inv,z06; + int ielement,jelement; + }; + Param *params; // parameter set for I-J interactions + char **elements; // names of unique elements + int **elem2param; // mapping from element pairs to parameters + int *map; // mapping from atom types to elements + int nelements; // # of unique elements + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + + double cut_global; + double **cut; + double **offset; + void read_file( char * ); + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ + diff --git a/src/USER-MISC/pair_lebedeva_z.cpp b/src/USER-MISC/pair_lebedeva_z.cpp new file mode 100644 index 0000000000..0ab22e04c1 --- /dev/null +++ b/src/USER-MISC/pair_lebedeva_z.cpp @@ -0,0 +1,434 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Zbigniew Koziol + (National Center for Nuclear Research, Poland) + e-mail: softquake at gmail dot com + Writing this was based on C code of Kolmogorov-Crespi potential + of Jaap Kroes and others. + + This is potential described in + [Lebedeva et al., Physica E, 44(6), 949-954, 2012.] +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lebedeva_z.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define MAXLINE 1024 +#define DELTA 4 + +/* ---------------------------------------------------------------------- */ + +PairLebedevaZ::PairLebedevaZ(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 0; + + // initialize element to parameter maps + nelements = 0; + elements = NULL; + nparams = maxparam = 0; + params = NULL; + elem2param = NULL; + map = NULL; + + // always compute energy offset + offset_flag = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairLebedevaZ::~PairLebedevaZ() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(cut); + memory->destroy(offset); + } + + if (elements) + for (int i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + memory->destroy(params); + memory->destroy(elem2param); + if (allocated) delete [] map; +} + +/* ---------------------------------------------------------------------- */ + +void PairLebedevaZ::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,der; + double rsq,r,rhosq,exp1,exp2,exp3,r6,r8; + double sumD,Ulm,fxy,fz; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + jtype = type[j]; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + // rho^2 = r^2 - z^2 + rhosq = delx*delx + dely*dely; + rsq = rhosq + delz*delz; + + if (rsq < cutsq[itype][jtype]) { + + int iparam_ij = elem2param[map[itype]][map[jtype]]; + Param& p = params[iparam_ij]; + + r = sqrt(rsq); + r6 = rsq*rsq*rsq; + r8 = r6*rsq; + + // store exponents + exp1 = exp(-p.alpha*(r-p.z0)); + exp2 = exp(-p.lambda1*rhosq); + exp3 = exp(-p.lambda2*(delz*delz-p.z02)); + sumD = 1+p.D1*rhosq+p.D2*rhosq*rhosq; + Ulm = -p.A*p.z06/r6+ p.B*exp1+p.C*sumD*exp2*exp3; + + // derivatives + fpair = -6.0*p.A*p.z06/r8+p.B*p.alpha*exp1/r; // used for x,y,z + der = p.D1+2*p.D2*rhosq-p.lambda1*sumD; // used for x,y + fxy = fpair - 2*p.C*exp2*exp3*der; + fz = fpair + 2*p.C*p.lambda2*sumD*exp2*exp3; + + f[i][0] += delx*fxy; + f[i][1] += dely*fxy; + f[i][2] += delz*fz; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fxy; + f[j][1] -= dely*fxy; + f[j][2] -= delz*fz; + } + + if (eflag) { + evdwl = Ulm - offset[itype][jtype]; + } + + if (evflag){ + ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0, + -fxy,-fxy,-fz,delx,dely,delz); + } + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLebedevaZ::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(offset,n+1,n+1,"pair:offset"); + map = new int[atom->ntypes+1]; +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLebedevaZ::settings(int narg, char **arg) +{ + if (narg != 1) error->all(FLERR,"Illegal pair_style command"); + if (strcmp(force->pair_style,"hybrid/overlay")!=0) + error->all(FLERR,"ERROR: requires hybrid/overlay pair_style"); + + cut_global = force->numeric(FLERR,arg[0]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLebedevaZ::coeff(int narg, char **arg) +{ + int i,j,n; + + if (narg != 3 + atom->ntypes) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + // read args that map atom types to elements in potential file + // map[i] = which element the Ith atom type is, -1 if NULL + // nelements = # of unique elements + // elements = list of element names + + if (elements) { + for (i = 0; i < nelements; i++) delete [] elements[i]; + delete [] elements; + } + elements = new char*[atom->ntypes]; + for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; + + nelements = 0; + for (i = 3; i < narg; i++) { + if (strcmp(arg[i],"NULL") == 0) { + map[i-2] = -1; + continue; + } + for (j = 0; j < nelements; j++) + if (strcmp(arg[i],elements[j]) == 0) break; + map[i-2] = j; + if (j == nelements) { + n = strlen(arg[i]) + 1; + elements[j] = new char[n]; + strcpy(elements[j],arg[i]); + nelements++; + } + } + + + read_file(arg[2]); + + double cut_one = cut_global; + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLebedevaZ::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + if (offset_flag && (cut[i][j] > 0.0)) { + int iparam_ij = elem2param[map[i]][map[j]]; + Param& p = params[iparam_ij]; + offset[i][j] = -p.A*pow(p.z0/cut[i][j],6); + } else offset[i][j] = 0.0; + offset[j][i] = offset[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + read Lebedeva potential file +------------------------------------------------------------------------- */ + +void PairLebedevaZ::read_file(char *filename) +{ + int params_per_line = 12; + char **words = new char*[params_per_line+1]; + memory->sfree(params); + params = NULL; + nparams = maxparam = 0; + + // open file on proc 0 + + FILE *fp; + if (comm->me == 0) { + fp = force->open_potential(filename); + if (fp == NULL) { + char str[128]; + sprintf(str,"Cannot open Lebedeva potential file %s",filename); + error->one(FLERR,str); + } + } + + // read each line out of file, skipping blank lines or leading '#' + // store line of params if all 3 element tags are in element list + + int i,j,n,m,nwords,ielement,jelement; + char line[MAXLINE],*ptr; + int eof = 0; + + while (1) { + if (comm->me == 0) { + ptr = fgets(line,MAXLINE,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + + // strip comment, skip line if blank + + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + if (nwords == 0) continue; + + // concatenate additional lines until have params_per_line words + + while (nwords < params_per_line) { + n = strlen(line); + if (comm->me == 0) { + ptr = fgets(&line[n],MAXLINE-n,fp); + if (ptr == NULL) { + eof = 1; + fclose(fp); + } else n = strlen(line) + 1; + } + MPI_Bcast(&eof,1,MPI_INT,0,world); + if (eof) break; + MPI_Bcast(&n,1,MPI_INT,0,world); + MPI_Bcast(line,n,MPI_CHAR,0,world); + if ((ptr = strchr(line,'#'))) *ptr = '\0'; + nwords = atom->count_words(line); + } + + if (nwords != params_per_line) + error->all(FLERR,"Insufficient format in Lebedeva potential file"); + + // words = ptrs to all words in line + + nwords = 0; + words[nwords++] = strtok(line," \t\n\r\f"); + while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; + + // ielement,jelement = 1st args + // if these 2 args are in element list, then parse this line + // else skip to next line (continue) + + for (ielement = 0; ielement < nelements; ielement++) + if (strcmp(words[0],elements[ielement]) == 0) break; + if (ielement == nelements) continue; + for (jelement = 0; jelement < nelements; jelement++) + if (strcmp(words[1],elements[jelement]) == 0) break; + if (jelement == nelements) continue; + + // load up parameter settings and error check their values + + if (nparams == maxparam) { + maxparam += DELTA; + params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + "pair:params"); + } + params[nparams].ielement = ielement; + params[nparams].jelement = jelement; + params[nparams].A = atof(words[2]); + params[nparams].B = atof(words[3]); + params[nparams].C = atof(words[4]); + params[nparams].z0 = atof(words[5]); + params[nparams].alpha = atof(words[6]); + params[nparams].D1 = atof(words[7]); + params[nparams].D2 = atof(words[8]); + params[nparams].lambda1 = atof(words[9]); + params[nparams].lambda2 = atof(words[10]); + // S provides a convenient scaling of all energies + params[nparams].S = atof(words[11]); + + // energies in meV further scaled by S + double meV = 1.0e-3*params[nparams].S; + params[nparams].A *= meV; + params[nparams].B *= meV; + params[nparams].C *= meV; + + // precompute some quantities. That speeds up later process + params[nparams].z02 = pow(params[nparams].z0,2); + params[nparams].z06 = pow(params[nparams].z0,6); + + nparams++; + if(nparams >= pow(atom->ntypes,3)) break; + } + memory->destroy(elem2param); + memory->create(elem2param,nelements,nelements,"pair:elem2param"); + for (i = 0; i < nelements; i++) { + for (j = 0; j < nelements; j++) { + n = -1; + for (m = 0; m < nparams; m++) { + if (i == params[m].ielement && j == params[m].jelement) { + if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); + n = m; + } + } + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + elem2param[i][j] = n; + } + } + delete [] words; +} + +/* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/pair_lebedeva_z.h b/src/USER-MISC/pair_lebedeva_z.h new file mode 100644 index 0000000000..e221087a0a --- /dev/null +++ b/src/USER-MISC/pair_lebedeva_z.h @@ -0,0 +1,83 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lebedeva/z,PairLebedevaZ) + +#else + +#ifndef LMP_PAIR_LEBEDEVA_Z_H +#define LMP_PAIR_LEBEDEVA_Z_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLebedevaZ : public Pair { + public: + PairLebedevaZ(class LAMMPS *); + virtual ~PairLebedevaZ(); + + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + double init_one(int, int); + + protected: + int me; + + struct Param { + double z0,A,B,C,alpha,D1,D2,lambda1,lambda2,S; + double z02,z06; + int ielement,jelement; + }; + Param *params; // parameter set for I-J interactions + char **elements; // names of unique elements + int **elem2param; // mapping from element pairs to parameters + int *map; // mapping from atom types to elements + int nelements; // # of unique elements + int nparams; // # of stored parameter sets + int maxparam; // max # of parameter sets + + double cut_global; + double **cut; + double **offset; + void read_file( char * ); + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +*/ + diff --git a/src/USER-MISC/pair_lennard_mdf.cpp b/src/USER-MISC/pair_lennard_mdf.cpp index 45d0da4d83..b51639e80e 100644 --- a/src/USER-MISC/pair_lennard_mdf.cpp +++ b/src/USER-MISC/pair_lennard_mdf.cpp @@ -65,8 +65,7 @@ void PairLJ_AB_MDF::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -389,7 +388,7 @@ double PairLJ_AB_MDF::single(int /*i*/, int /*j*/, int itype, int jtype, void *PairLJ_AB_MDF::extract(const char *str, int &dim) { dim = 2; - if (strcmp(str,"aparm") == 0) return (void *) aparm; - if (strcmp(str,"bparm") == 0) return (void *) bparm; + if (strcmp(str,"a") == 0) return (void *) aparm; + if (strcmp(str,"b") == 0) return (void *) bparm; return NULL; } diff --git a/src/USER-MISC/pair_list.cpp b/src/USER-MISC/pair_list.cpp index aaeb586c1d..562a60aa99 100644 --- a/src/USER-MISC/pair_list.cpp +++ b/src/USER-MISC/pair_list.cpp @@ -80,9 +80,7 @@ PairList::~PairList() void PairList::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = - vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int newton_pair = force->newton_pair; diff --git a/src/USER-MISC/pair_lj_expand_coul_long.cpp b/src/USER-MISC/pair_lj_expand_coul_long.cpp index 79a3c2a497..fe21538f2d 100644 --- a/src/USER-MISC/pair_lj_expand_coul_long.cpp +++ b/src/USER-MISC/pair_lj_expand_coul_long.cpp @@ -91,8 +91,7 @@ void PairLJExpandCoulLong::compute(int eflag, int vflag) double rsq,rshift,rshiftsq,rshift2inv; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -412,8 +411,7 @@ void PairLJExpandCoulLong::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_lj_mdf.cpp b/src/USER-MISC/pair_lj_mdf.cpp index 891239016b..ca0118ffb0 100644 --- a/src/USER-MISC/pair_lj_mdf.cpp +++ b/src/USER-MISC/pair_lj_mdf.cpp @@ -1,395 +1,394 @@ - -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Paolo Raiteri (Curtin University) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_lj_mdf.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "error.h" - -using namespace LAMMPS_NS; - -/* ---------------------------------------------------------------------- */ - -PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {} - -/* ---------------------------------------------------------------------- */ - -PairLJMDF::~PairLJMDF() -{ - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut); - memory->destroy(cut_inner); - memory->destroy(cut_inner_sq); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - } -} - -/* ---------------------------------------------------------------------- */ - -void PairLJMDF::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; - double rsq,r2inv,r6inv,forcelj,factor_lj; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_lj = force->special_lj; - int newton_pair = force->newton_pair; - double rr, d, dd, tt, dt, dp, philj; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - - if (rsq > cut_inner_sq[itype][jtype]) { - philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - - rr = sqrt(rsq); - dp = (cut[itype][jtype] - cut_inner[itype][jtype]); - d = (rr-cut_inner[itype][jtype]) / dp; - dd = 1.-d; -// taperig function - mdf style - tt = (1. + 3.*d + 6.*d*d)*dd*dd*dd; -// minus the derivative of the tapering function - dt = 30.* d*d * dd*dd * rr / dp; - - forcelj = forcelj*tt + philj*dt; - } else { - tt = 1; - } - fpair = factor_lj*forcelj*r2inv; - - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - - if (eflag) { - evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); - if (rsq > cut_inner_sq[itype][jtype]) evdwl *= tt; - - evdwl *= factor_lj; - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,0.0,fpair,delx,dely,delz); - } - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairLJMDF::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(cut,n+1,n+1,"pair:cut"); - memory->create(cut_inner,n+1,n+1,"pair:cut_inner"); - memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq"); - memory->create(epsilon,n+1,n+1,"pair:epsilon"); - memory->create(sigma,n+1,n+1,"pair:sigma"); - memory->create(lj1,n+1,n+1,"pair:lj1"); - memory->create(lj2,n+1,n+1,"pair:lj2"); - memory->create(lj3,n+1,n+1,"pair:lj3"); - memory->create(lj4,n+1,n+1,"pair:lj4"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairLJMDF::settings(int narg, char **arg) -{ - if (narg != 2) error->all(FLERR,"Illegal pair_style command"); - - cut_inner_global = force->numeric(FLERR,arg[0]); - cut_global = force->numeric(FLERR,arg[1]); - - if (cut_inner_global <= 0.0 || cut_inner_global > cut_global) - error->all(FLERR,"Illegal pair_style command"); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) - if (setflag[i][j]) { - cut_inner[i][j] = cut_inner_global; - cut[i][j] = cut_global; - } - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairLJMDF::coeff(int narg, char **arg) -{ - if (narg != 4 && narg != 6) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - double epsilon_one = force->numeric(FLERR,arg[2]); - double sigma_one = force->numeric(FLERR,arg[3]); - - double cut_inner_one = cut_inner_global; - double cut_one = cut_global; - if (narg == 6) { - cut_inner_one = force->numeric(FLERR,arg[4]); - cut_one = force->numeric(FLERR,arg[5]); - } - if (cut_inner_global <= 0.0 || cut_inner_global > cut_global) - error->all(FLERR,"Illegal pair_style command"); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - epsilon[i][j] = epsilon_one; - sigma[i][j] = sigma_one; - cut_inner[i][j] = cut_inner_one; - cut[i][j] = cut_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairLJMDF::init_one(int i, int j) -{ - if (setflag[i][j] == 0) { - epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], - sigma[i][i],sigma[j][j]); - sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); - cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]); - cut[i][j] = mix_distance(cut[i][i],cut[j][j]); - } - - cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j]; - lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); - lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); - - cut[j][i] = cut[i][j]; // BUG FIX - cut_inner[j][i] = cut_inner[i][j]; - cut_inner_sq[j][i] = cut_inner_sq[i][j]; - lj1[j][i] = lj1[i][j]; - lj2[j][i] = lj2[i][j]; - lj3[j][i] = lj3[i][j]; - lj4[j][i] = lj4[i][j]; - - return cut[i][j]; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJMDF::write_restart(FILE *fp) -{ - write_restart_settings(fp); - - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&epsilon[i][j],sizeof(double),1,fp); - fwrite(&sigma[i][j],sizeof(double),1,fp); - fwrite(&cut_inner[i][j],sizeof(double),1,fp); - fwrite(&cut[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairLJMDF::read_restart(FILE *fp) -{ - read_restart_settings(fp); - allocate(); - - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); - } - MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairLJMDF::write_restart_settings(FILE *fp) -{ - fwrite(&mix_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairLJMDF::read_restart_settings(FILE *fp) -{ - int me = comm->me; - if (me == 0) { - fread(&mix_flag,sizeof(int),1,fp); - } - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- */ - -double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype, - double rsq, - double /*factor_coul*/, double factor_lj, - double &fforce) -{ - double r2inv,r6inv,forcelj,philj; - double rr, dp, d, tt, dt, dd; - - r2inv = 1.0/rsq; - r6inv = r2inv*r2inv*r2inv; - - philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); - forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); - - if (rsq > cut_inner_sq[itype][jtype]) { - - rr = sqrt(rsq); - dp = (cut[itype][jtype] - cut_inner[itype][jtype]); - d = (rr - cut_inner[itype][jtype]) / dp; - dd = 1-d; - tt = (1. + 3.*d + 6.*d*d)* dd*dd*dd; - dt = 30.* d*d * dd*dd * rr / dp; - - forcelj = forcelj*tt + philj*dt; - philj *= tt; - } - - fforce = factor_lj*forcelj*r2inv; - - return factor_lj*philj; -} - -/* ---------------------------------------------------------------------- */ - -void *PairLJMDF::extract(const char *str, int &dim) -{ - dim = 2; - if (strcmp(str,"epsilon") == 0) return (void *) epsilon; - if (strcmp(str,"sigma") == 0) return (void *) sigma; - return NULL; -} + +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Paolo Raiteri (Curtin University) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lj_mdf.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairLJMDF::PairLJMDF(LAMMPS *lmp) : Pair(lmp) {} + +/* ---------------------------------------------------------------------- */ + +PairLJMDF::~PairLJMDF() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut); + memory->destroy(cut_inner); + memory->destroy(cut_inner_sq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairLJMDF::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; + double rsq,r2inv,r6inv,forcelj,factor_lj; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double rr, d, dd, tt, dt, dp, philj; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + + if (rsq > cut_inner_sq[itype][jtype]) { + philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); + + rr = sqrt(rsq); + dp = (cut[itype][jtype] - cut_inner[itype][jtype]); + d = (rr-cut_inner[itype][jtype]) / dp; + dd = 1.-d; +// taperig function - mdf style + tt = (1. + 3.*d + 6.*d*d)*dd*dd*dd; +// minus the derivative of the tapering function + dt = 30.* d*d * dd*dd * rr / dp; + + forcelj = forcelj*tt + philj*dt; + } else { + tt = 1; + } + fpair = factor_lj*forcelj*r2inv; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]); + if (rsq > cut_inner_sq[itype][jtype]) evdwl *= tt; + + evdwl *= factor_lj; + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,0.0,fpair,delx,dely,delz); + } + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJMDF::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut,n+1,n+1,"pair:cut"); + memory->create(cut_inner,n+1,n+1,"pair:cut_inner"); + memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJMDF::settings(int narg, char **arg) +{ + if (narg != 2) error->all(FLERR,"Illegal pair_style command"); + + cut_inner_global = force->numeric(FLERR,arg[0]); + cut_global = force->numeric(FLERR,arg[1]); + + if (cut_inner_global <= 0.0 || cut_inner_global > cut_global) + error->all(FLERR,"Illegal pair_style command"); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) { + cut_inner[i][j] = cut_inner_global; + cut[i][j] = cut_global; + } + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJMDF::coeff(int narg, char **arg) +{ + if (narg != 4 && narg != 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + + double cut_inner_one = cut_inner_global; + double cut_one = cut_global; + if (narg == 6) { + cut_inner_one = force->numeric(FLERR,arg[4]); + cut_one = force->numeric(FLERR,arg[5]); + } + if (cut_inner_global <= 0.0 || cut_inner_global > cut_global) + error->all(FLERR,"Illegal pair_style command"); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + cut_inner[i][j] = cut_inner_one; + cut[i][j] = cut_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJMDF::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], + sigma[i][i],sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); + cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]); + cut[i][j] = mix_distance(cut[i][i],cut[j][j]); + } + + cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[i][j]; + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + + cut[j][i] = cut[i][j]; // BUG FIX + cut_inner[j][i] = cut_inner[i][j]; + cut_inner_sq[j][i] = cut_inner_sq[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + + return cut[i][j]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJMDF::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&cut_inner[i][j],sizeof(double),1,fp); + fwrite(&cut[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJMDF::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&cut_inner[i][j],sizeof(double),1,fp); + fread(&cut[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJMDF::write_restart_settings(FILE *fp) +{ + fwrite(&mix_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJMDF::read_restart_settings(FILE *fp) +{ + int me = comm->me; + if (me == 0) { + fread(&mix_flag,sizeof(int),1,fp); + } + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJMDF::single(int /*i*/, int /*j*/, int itype, int jtype, + double rsq, + double /*factor_coul*/, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,forcelj,philj; + double rr, dp, d, tt, dt, dd; + + r2inv = 1.0/rsq; + r6inv = r2inv*r2inv*r2inv; + + philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]); + forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]); + + if (rsq > cut_inner_sq[itype][jtype]) { + + rr = sqrt(rsq); + dp = (cut[itype][jtype] - cut_inner[itype][jtype]); + d = (rr - cut_inner[itype][jtype]) / dp; + dd = 1-d; + tt = (1. + 3.*d + 6.*d*d)* dd*dd*dd; + dt = 30.* d*d * dd*dd * rr / dp; + + forcelj = forcelj*tt + philj*dt; + philj *= tt; + } + + fforce = factor_lj*forcelj*r2inv; + + return factor_lj*philj; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJMDF::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + return NULL; +} diff --git a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp index 523b2ca71a..af7d23370d 100644 --- a/src/USER-MISC/pair_lj_sf_dipole_sf.cpp +++ b/src/USER-MISC/pair_lj_sf_dipole_sf.cpp @@ -79,8 +79,7 @@ void PairLJSFDipoleSF::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_meam_spline.cpp b/src/USER-MISC/pair_meam_spline.cpp index 0300e2c7a2..f09919ce0f 100644 --- a/src/USER-MISC/pair_meam_spline.cpp +++ b/src/USER-MISC/pair_meam_spline.cpp @@ -103,12 +103,7 @@ void PairMEAMSpline::compute(int eflag, int vflag) double* const * const forces = atom->f; const int ntypes = atom->ntypes; - if (eflag || vflag) { - ev_setup(eflag, vflag); - } else { - evflag = vflag_fdotr = eflag_global = 0; - vflag_global = eflag_atom = vflag_atom = 0; - } + ev_init(eflag, vflag); // Grow per-atom array if necessary diff --git a/src/USER-MISC/pair_meam_sw_spline.cpp b/src/USER-MISC/pair_meam_sw_spline.cpp index e17c13865d..af1e8788bd 100644 --- a/src/USER-MISC/pair_meam_sw_spline.cpp +++ b/src/USER-MISC/pair_meam_sw_spline.cpp @@ -85,9 +85,7 @@ PairMEAMSWSpline::~PairMEAMSWSpline() void PairMEAMSWSpline::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag, vflag); - else evflag = vflag_fdotr = - eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag, vflag); double cutforcesq = cutoff*cutoff; diff --git a/src/USER-MISC/pair_momb.cpp b/src/USER-MISC/pair_momb.cpp index 927181ebf6..1716149a98 100644 --- a/src/USER-MISC/pair_momb.cpp +++ b/src/USER-MISC/pair_momb.cpp @@ -81,8 +81,7 @@ void PairMomb::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_morse_smooth_linear.cpp b/src/USER-MISC/pair_morse_smooth_linear.cpp index a88e7a1a27..7c7973f830 100644 --- a/src/USER-MISC/pair_morse_smooth_linear.cpp +++ b/src/USER-MISC/pair_morse_smooth_linear.cpp @@ -60,8 +60,7 @@ void PairMorseSmoothLinear::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MISC/pair_srp.cpp b/src/USER-MISC/pair_srp.cpp index 7297b545f9..01deaf0fbe 100644 --- a/src/USER-MISC/pair_srp.cpp +++ b/src/USER-MISC/pair_srp.cpp @@ -68,6 +68,7 @@ static int srp_instance = 0; PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp) { writedata = 1; + single_enable = 0; if (lmp->citeme) lmp->citeme->add(cite_srp); @@ -142,10 +143,7 @@ void PairSRP::compute(int eflag, int vflag) { // setup energy and virial - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **x = atom->x; double **f = atom->f; @@ -196,7 +194,7 @@ void PairSRP::compute(int eflag, int vflag) j = jlist[jj]; // enforce 1-2 exclusions - if( (sbmask(j) & exclude) ) + if ((sbmask(j) & exclude)) continue; j &= NEIGHMASK; @@ -257,8 +255,7 @@ void PairSRP::compute(int eflag, int vflag) } } } - } - else{ + } else { // using min distance option for (ii = 0; ii < inum; ii++) { @@ -274,7 +271,7 @@ void PairSRP::compute(int eflag, int vflag) j = jlist[jj]; // enforce 1-2 exclusions - if( (sbmask(j) & exclude) ) + if ((sbmask(j) & exclude)) continue; j &= NEIGHMASK; @@ -360,9 +357,9 @@ void PairSRP::settings(int narg, char **arg) cut_global = force->numeric(FLERR,arg[0]); // wildcard - if (strcmp(arg[1],"*") == 0) + if (strcmp(arg[1],"*") == 0) { btype = 0; - else { + } else { btype = force->inumeric(FLERR,arg[1]); if ((btype > atom->nbondtypes) || (btype <= 0)) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-MISC/pair_tersoff_table.cpp b/src/USER-MISC/pair_tersoff_table.cpp index d1044cc336..e0985d1dce 100644 --- a/src/USER-MISC/pair_tersoff_table.cpp +++ b/src/USER-MISC/pair_tersoff_table.cpp @@ -117,8 +117,7 @@ void PairTersoffTable::compute(int eflag, int vflag) double evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp index c821c9d883..e8e6f279de 100644 --- a/src/USER-MOFFF/angle_class2_p6.cpp +++ b/src/USER-MOFFF/angle_class2_p6.cpp @@ -79,8 +79,7 @@ void AngleClass2P6::compute(int eflag, int vflag) double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22; eangle = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -429,7 +428,7 @@ void AngleClass2P6::read_restart(FILE *fp) void AngleClass2P6::write_data(FILE *fp) { for (int i = 1; i <= atom->nangletypes; i++) - fprintf(fp,"%d %g %g %g %g\n", + fprintf(fp,"%d %g %g %g %g %g %g\n", i,theta0[i]/MY_PI*180.0,k2[i],k3[i],k4[i],k5[i],k6[i]); fprintf(fp,"\nBondBond Coeffs\n\n"); diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp index 3f87aeb757..3829d2b8dc 100644 --- a/src/USER-MOFFF/angle_cosine_buck6d.cpp +++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp @@ -69,8 +69,7 @@ void AngleCosineBuck6d::compute(int eflag, int vflag) double rcu,rqu,sme,smf; eangle = evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-3 virial contribution @@ -353,7 +352,7 @@ void AngleCosineBuck6d::read_restart(FILE *fp) void AngleCosineBuck6d::write_data(FILE *fp) { for (int i = 1; i <= atom->nangletypes; i++) { - fprintf(fp,"%d %g %d %d\n",i,k[i],multiplicity[i],th0[i]); + fprintf(fp,"%d %g %d %g\n",i,k[i],multiplicity[i],th0[i]); } } diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp index 9608d58054..3f1e61e54a 100644 --- a/src/USER-MOFFF/improper_inversion_harmonic.cpp +++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp @@ -66,8 +66,7 @@ void ImproperInversionHarmonic::compute(int eflag, int vflag) double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z; double rrvb1,rrvb2,rrvb3,rr2vb1,rr2vb2,rr2vb3; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; int **improperlist = neighbor->improperlist; @@ -241,8 +240,8 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2, f[i4][2] += f4[2]; } - double rb3x, rb3y, rb3z; - if (evflag) + if (evflag) { + double rb3x, rb3y, rb3z; rb3x = vb1x - vb2x; rb3y = vb1y - vb2y; @@ -252,6 +251,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2, vb3x,vb3y,vb3z, vb2x,vb2y,vb2z, rb3x,rb3y,rb3z); + } } /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp index f434d03858..282bb0c58f 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp @@ -1,590 +1,589 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Hendrik Heenen (Technical University of Munich) - and Rochus Schmid (Ruhr-Universitaet Bochum) - References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) - Fennell and Gezelter, JCP 124, 234104 (2006) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_buck6d_coul_gauss_dsf.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "math_const.h" -#include "error.h" -#include "math_special.h" - -using namespace LAMMPS_NS; -using namespace MathConst; - -/* ---------------------------------------------------------------------- */ - -PairBuck6dCoulGaussDSF::PairBuck6dCoulGaussDSF(LAMMPS *lmp) : Pair(lmp) -{ - single_enable = 1; - writedata = 1; -} - -/* ---------------------------------------------------------------------- */ - -PairBuck6dCoulGaussDSF::~PairBuck6dCoulGaussDSF() -{ - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(alpha_ij); - memory->destroy(f_shift_ij); - memory->destroy(e_shift_ij); - memory->destroy(buck6d1); - memory->destroy(buck6d2); - memory->destroy(buck6d3); - memory->destroy(buck6d4); - memory->destroy(c0); - memory->destroy(c1); - memory->destroy(c2); - memory->destroy(c3); - memory->destroy(c4); - memory->destroy(c5); - memory->destroy(rsmooth_sq); - memory->destroy(offset); - } - } -} - -/* ---------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj; - double term1,term2,term3,term4,term5; - double rcu,rqu,sme,smf,ebuck6d; - double prefactor,erfcc,erfcd,t,arg; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_lj = force->special_lj; - double *special_coul = force->special_coul; - int newton_pair = force->newton_pair; - double qqrd2e = force->qqrd2e; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - qtmp = q[i]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - factor_coul = special_coul[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - r2inv = 1.0/rsq; - r = sqrt(rsq); - - if (rsq < cut_ljsq[itype][jtype]) { - r6inv = r2inv*r2inv*r2inv; - r14inv = r6inv*r6inv*r2inv; - rexp = exp(-r*buck6d2[itype][jtype]); - term1 = buck6d3[itype][jtype]*r6inv; - term2 = buck6d4[itype][jtype]*r14inv; - term3 = term2*term2; - term4 = 1.0/(1.0 + term2); - term5 = 1.0/(1.0 + 2.0*term2 + term3); - forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; - forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); - ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; - - // smoothing term - if (rsq > rsmooth_sq[itype][jtype]) { - rcu = r*rsq; - rqu = rsq*rsq; - sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + - c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; - smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + - 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; - // forcebuck6d is -dE/dr*r - forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r - ebuck6d *= sme; - } - } else forcebuck6d = 0.0; - - if (rsq < cut_coulsq) { - prefactor = qqrd2e*qtmp*q[j]/r; - - //below: parametrization for erfcc = erf(alpha_ij[itype][jtype]*r); - arg = alpha_ij[itype][jtype]*r; - erfcd = MathSpecial::expmsq(arg); - erfcc = 1 - (MathSpecial::my_erfcx(arg) * erfcd); - - forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) + - r*f_shift_ij[itype][jtype]) * r; - - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; - } else forcecoul = 0.0; - - fpair = (forcecoul + factor_lj*forcebuck6d) * r2inv; - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - - if (eflag) { - if (rsq < cut_ljsq[itype][jtype]) { - evdwl = ebuck6d - offset[itype][jtype]; - evdwl *= factor_lj; - } else evdwl = 0.0; - - if (rsq < cut_coulsq) { - ecoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] - - rsq*f_shift_ij[itype][jtype]); - if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; - } else ecoul = 0.0; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,ecoul,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); - memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); - memory->create(alpha_ij,n+1,n+1,"pair:alpha_ij"); - memory->create(f_shift_ij,n+1,n+1,"pair:f_shift_ij"); - memory->create(e_shift_ij,n+1,n+1,"pair:e_shift_ij"); - memory->create(buck6d1,n+1,n+1,"pair:buck6d1"); - memory->create(buck6d2,n+1,n+1,"pair:buck6d2"); - memory->create(buck6d3,n+1,n+1,"pair:buck6d3"); - memory->create(buck6d4,n+1,n+1,"pair:buck6d4"); - memory->create(c0,n+1,n+1,"pair:c0"); - memory->create(c1,n+1,n+1,"pair:c1"); - memory->create(c2,n+1,n+1,"pair:c2"); - memory->create(c3,n+1,n+1,"pair:c3"); - memory->create(c4,n+1,n+1,"pair:c4"); - memory->create(c5,n+1,n+1,"pair:c5"); - memory->create(rsmooth_sq,n+1,n+1,"pair:rsmooth_sq"); - memory->create(offset,n+1,n+1,"pair:offset"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::settings(int narg, char **arg) -{ - if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); - - vdwl_smooth = force->numeric(FLERR,arg[0]); - - cut_lj_global = force->numeric(FLERR,arg[1]); - if (narg == 2) cut_coul = cut_lj_global; - else cut_coul = force->numeric(FLERR,arg[2]); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i+1; j <= atom->ntypes; j++) - if (setflag[i][j]) - cut_lj[i][j] = cut_lj_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::coeff(int narg, char **arg) -{ - if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - double buck6d1_one = force->numeric(FLERR,arg[2]); - double buck6d2_one = force->numeric(FLERR,arg[3]); - double buck6d3_one = force->numeric(FLERR,arg[4]); - double buck6d4_one = force->numeric(FLERR,arg[5]); - double alpha_one = force->numeric(FLERR,arg[6]); - - double cut_lj_one = cut_lj_global; - if (narg == 8) cut_lj_one = force->numeric(FLERR,arg[7]); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - buck6d1[i][j] = buck6d1_one; - buck6d2[i][j] = buck6d2_one; - buck6d3[i][j] = buck6d3_one; - buck6d4[i][j] = buck6d4_one; - alpha_ij[i][j] = alpha_one; - cut_lj[i][j] = cut_lj_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::init_style() -{ - if (!atom->q_flag) - error->all(FLERR,"Pair style buck6d/coul/dsf requires atom attribute q"); - - neighbor->request(this,instance_me); - - cut_coulsq = cut_coul * cut_coul; -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairBuck6dCoulGaussDSF::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - double cut = MAX(cut_lj[i][j],cut_coul); - cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; - - //calculation of smoothing coefficients c0-c5 - c0[i][j] = c1[i][j] = c2[i][j] = c3[i][j] = c4[i][j] = c5[i][j] = 0.0; - rsmooth_sq[i][j] = cut_ljsq[i][j]; - if (vdwl_smooth < 1.0) { - double rsm = vdwl_smooth * cut_lj[i][j]; - double rsm_sq = rsm * rsm; - double denom = pow((cut_lj[i][j]-rsm),5.0); - c0[i][j] = cut_lj[i][j]*cut_ljsq[i][j]*(cut_ljsq[i][j]- - 5.0*cut_lj[i][j]*rsm+10.0*rsm_sq)/denom; - c1[i][j] = -30.0*(cut_ljsq[i][j]*rsm_sq)/denom; - c2[i][j] = 30.0*(cut_ljsq[i][j]*rsm + cut_lj[i][j]*rsm_sq)/denom; - c3[i][j] = -10.0*(cut_ljsq[i][j] + 4.0*cut_lj[i][j]*rsm + rsm_sq)/denom; - c4[i][j] = 15.0*(cut_lj[i][j]+rsm)/denom; - c5[i][j] = -6.0/denom; - rsmooth_sq[i][j] = rsm_sq; - } - - // if offset_flag, shift is only invoked if there is not already smoothing - if (offset_flag && vdwl_smooth >= 1.0) { - double term1 = buck6d3[i][j]/pow(cut_lj[i][j],6.0); - double term4 = 1.0/(1.0 + (buck6d4[i][j]/pow(cut_lj[i][j],14.0))); - double rexp = exp(-cut_lj[i][j]*buck6d2[i][j]); - offset[i][j] = buck6d1[i][j]*rexp - term1*term4; - } else offset[i][j] = 0.0; - - double erfcd_c = exp(-alpha_ij[i][j]*alpha_ij[i][j]*cut_coul*cut_coul); - double erfcc_c = erf(alpha_ij[i][j]*cut_coul); - f_shift_ij[i][j] = -erfcc_c/cut_coulsq + 2.0/MY_PIS*alpha_ij[i][j]*erfcd_c/cut_coul; - e_shift_ij[i][j] = erfcc_c/cut_coul - f_shift_ij[i][j]*cut_coul; - - cut_ljsq[j][i] = cut_ljsq[i][j]; - alpha_ij[j][i] = alpha_ij[i][j]; - f_shift_ij[j][i] = f_shift_ij[i][j]; - e_shift_ij[j][i] = e_shift_ij[i][j]; - buck6d1[j][i] = buck6d1[i][j]; - buck6d2[j][i] = buck6d2[i][j]; - buck6d3[j][i] = buck6d3[i][j]; - buck6d4[j][i] = buck6d4[i][j]; - c0[j][i] = c0[i][j]; - c1[j][i] = c1[i][j]; - c2[j][i] = c2[i][j]; - c3[j][i] = c3[i][j]; - c4[j][i] = c4[i][j]; - c5[j][i] = c5[i][j]; - rsmooth_sq[j][i] = rsmooth_sq[i][j]; - offset[j][i] = offset[i][j]; - - return cut; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::write_restart(FILE *fp) -{ - write_restart_settings(fp); - - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&buck6d1[i][j],sizeof(double),1,fp); - fwrite(&buck6d2[i][j],sizeof(double),1,fp); - fwrite(&buck6d3[i][j],sizeof(double),1,fp); - fwrite(&buck6d4[i][j],sizeof(double),1,fp); - fwrite(&alpha_ij[i][j],sizeof(double),1,fp); - fwrite(&cut_lj[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::read_restart(FILE *fp) -{ - read_restart_settings(fp); - allocate(); - - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - fread(&buck6d1[i][j],sizeof(double),1,fp); - fread(&buck6d2[i][j],sizeof(double),1,fp); - fread(&buck6d3[i][j],sizeof(double),1,fp); - fread(&buck6d4[i][j],sizeof(double),1,fp); - fread(&alpha_ij[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - } - MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&buck6d3[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&buck6d4[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&alpha_ij[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::write_restart_settings(FILE *fp) -{ - fwrite(&vdwl_smooth,sizeof(double),1,fp); - fwrite(&cut_lj_global,sizeof(double),1,fp); - fwrite(&cut_coul,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); - fwrite(&tail_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - fread(&vdwl_smooth,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - } - MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); - MPI_Bcast(&offset_flag,1,MPI_INT,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); - MPI_Bcast(&tail_flag,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g %g %g\n",i, - buck6d1[i][i],buck6d2[i][i],buck6d3[i][i], - buck6d4[i][i],alpha_ij[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussDSF::write_data_all(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j, - buck6d1[i][j],buck6d2[i][j],buck6d3[i][j], - buck6d4[i][j],alpha_ij[i][j],cut_lj[i][j]); -} -/* ---------------------------------------------------------------------- */ - -double PairBuck6dCoulGaussDSF::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double r,r2inv,r6inv,r14inv,rexp,term1,term2,term3,term4,term5; - double rcu,rqu,sme,smf; - double erfcc,erfcd,prefactor,arg; - double forcecoul,forcebuck6d,ebuck6d,phicoul,phibuck6d; - - r2inv = 1.0/rsq; - r = sqrt(rsq); - if (rsq < cut_ljsq[itype][jtype]) { - r6inv = r2inv*r2inv*r2inv; - r14inv = r6inv*r6inv*r2inv; - rexp = exp(-r*buck6d2[itype][jtype]); - term1 = buck6d3[itype][jtype]*r6inv; - term2 = buck6d4[itype][jtype]*r14inv; - term3 = term2*term2; - term4 = 1.0/(1.0 + term2); - term5 = 1.0/(1.0 + 2.0*term2 + term3); - forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; - forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); - ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; - // smoothing term - if (rsq > rsmooth_sq[itype][jtype]) { - rcu = r*rsq; - rqu = rsq*rsq; - sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + - c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; - smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + - 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; - // forcebuck6d is -dE/dr*r - forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r - ebuck6d *= sme; - } - } else forcebuck6d = 0.0; - - if (rsq < cut_coulsq) { - prefactor = factor_coul * force->qqrd2e * atom->q[i] * atom->q[j] / r; - arg = alpha_ij[itype][jtype]*r; - erfcd = MathSpecial::expmsq(arg); - erfcc = 1 - (MathSpecial::my_erfcx(arg) * erfcd); - forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) + - r*f_shift_ij[itype][jtype]) * r; - } else forcecoul = 0.0; - - fforce = (forcecoul + factor_lj*forcebuck6d) * r2inv; - - double eng = 0.0; - if (rsq < cut_ljsq[itype][jtype]) { - phibuck6d = ebuck6d - offset[itype][jtype]; - eng += factor_lj*phibuck6d; - } - - if (rsq < cut_coulsq) { - phicoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] - - rsq*f_shift_ij[itype][jtype]); - eng += phicoul; - } - - return eng; -} - -/* ---------------------------------------------------------------------- */ - -void *PairBuck6dCoulGaussDSF::extract(const char *str, int &dim) -{ - dim = 2; - if (strcmp(str,"cut_ljsq") == 0) return (void *) cut_ljsq; - if (strcmp(str,"buck6d1") == 0) return (void *) buck6d1; - if (strcmp(str,"buck6d2") == 0) return (void *) buck6d2; - if (strcmp(str,"buck6d3") == 0) return (void *) buck6d3; - if (strcmp(str,"buck6d4") == 0) return (void *) buck6d4; - if (strcmp(str,"rsmooth_sq") == 0) return (void *) rsmooth_sq; - if (strcmp(str,"c0") == 0) return (void *) c0; - if (strcmp(str,"c1") == 0) return (void *) c1; - if (strcmp(str,"c2") == 0) return (void *) c2; - if (strcmp(str,"c3") == 0) return (void *) c3; - if (strcmp(str,"c4") == 0) return (void *) c4; - if (strcmp(str,"c5") == 0) return (void *) c5; - if (strcmp(str,"offset") == 0) return (void *) offset; - - if (strcmp(str,"cut_coul") == 0) { - dim = 0; - return (void *) &cut_coul; - } - return NULL; -} +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hendrik Heenen (Technical University of Munich) + and Rochus Schmid (Ruhr-Universitaet Bochum) + References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) + Fennell and Gezelter, JCP 124, 234104 (2006) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_buck6d_coul_gauss_dsf.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "math_const.h" +#include "error.h" +#include "math_special.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +/* ---------------------------------------------------------------------- */ + +PairBuck6dCoulGaussDSF::PairBuck6dCoulGaussDSF(LAMMPS *lmp) : Pair(lmp) +{ + single_enable = 1; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairBuck6dCoulGaussDSF::~PairBuck6dCoulGaussDSF() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(alpha_ij); + memory->destroy(f_shift_ij); + memory->destroy(e_shift_ij); + memory->destroy(buck6d1); + memory->destroy(buck6d2); + memory->destroy(buck6d3); + memory->destroy(buck6d4); + memory->destroy(c0); + memory->destroy(c1); + memory->destroy(c2); + memory->destroy(c3); + memory->destroy(c4); + memory->destroy(c5); + memory->destroy(rsmooth_sq); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj; + double term1,term2,term3,term4,term5; + double rcu,rqu,sme,smf,ebuck6d; + double prefactor,erfcc,erfcd,arg; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + double *special_coul = force->special_coul; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + r = sqrt(rsq); + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r14inv = r6inv*r6inv*r2inv; + rexp = exp(-r*buck6d2[itype][jtype]); + term1 = buck6d3[itype][jtype]*r6inv; + term2 = buck6d4[itype][jtype]*r14inv; + term3 = term2*term2; + term4 = 1.0/(1.0 + term2); + term5 = 1.0/(1.0 + 2.0*term2 + term3); + forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; + forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); + ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; + + // smoothing term + if (rsq > rsmooth_sq[itype][jtype]) { + rcu = r*rsq; + rqu = rsq*rsq; + sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + + c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; + smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + + 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; + // forcebuck6d is -dE/dr*r + forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r + ebuck6d *= sme; + } + } else forcebuck6d = 0.0; + + if (rsq < cut_coulsq) { + prefactor = qqrd2e*qtmp*q[j]/r; + + //below: parametrization for erfcc = erf(alpha_ij[itype][jtype]*r); + arg = alpha_ij[itype][jtype]*r; + erfcd = MathSpecial::expmsq(arg); + erfcc = 1 - (MathSpecial::my_erfcx(arg) * erfcd); + + forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) + + r*f_shift_ij[itype][jtype]) * r; + + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else forcecoul = 0.0; + + fpair = (forcecoul + factor_lj*forcebuck6d) * r2inv; + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = ebuck6d - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + + if (rsq < cut_coulsq) { + ecoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] - + rsq*f_shift_ij[itype][jtype]); + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(alpha_ij,n+1,n+1,"pair:alpha_ij"); + memory->create(f_shift_ij,n+1,n+1,"pair:f_shift_ij"); + memory->create(e_shift_ij,n+1,n+1,"pair:e_shift_ij"); + memory->create(buck6d1,n+1,n+1,"pair:buck6d1"); + memory->create(buck6d2,n+1,n+1,"pair:buck6d2"); + memory->create(buck6d3,n+1,n+1,"pair:buck6d3"); + memory->create(buck6d4,n+1,n+1,"pair:buck6d4"); + memory->create(c0,n+1,n+1,"pair:c0"); + memory->create(c1,n+1,n+1,"pair:c1"); + memory->create(c2,n+1,n+1,"pair:c2"); + memory->create(c3,n+1,n+1,"pair:c3"); + memory->create(c4,n+1,n+1,"pair:c4"); + memory->create(c5,n+1,n+1,"pair:c5"); + memory->create(rsmooth_sq,n+1,n+1,"pair:rsmooth_sq"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::settings(int narg, char **arg) +{ + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + + vdwl_smooth = force->numeric(FLERR,arg[0]); + + cut_lj_global = force->numeric(FLERR,arg[1]); + if (narg == 2) cut_coul = cut_lj_global; + else cut_coul = force->numeric(FLERR,arg[2]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) + cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double buck6d1_one = force->numeric(FLERR,arg[2]); + double buck6d2_one = force->numeric(FLERR,arg[3]); + double buck6d3_one = force->numeric(FLERR,arg[4]); + double buck6d4_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + + double cut_lj_one = cut_lj_global; + if (narg == 8) cut_lj_one = force->numeric(FLERR,arg[7]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + buck6d1[i][j] = buck6d1_one; + buck6d2[i][j] = buck6d2_one; + buck6d3[i][j] = buck6d3_one; + buck6d4[i][j] = buck6d4_one; + alpha_ij[i][j] = alpha_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style buck6d/coul/dsf requires atom attribute q"); + + neighbor->request(this,instance_me); + + cut_coulsq = cut_coul * cut_coul; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBuck6dCoulGaussDSF::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + //calculation of smoothing coefficients c0-c5 + c0[i][j] = c1[i][j] = c2[i][j] = c3[i][j] = c4[i][j] = c5[i][j] = 0.0; + rsmooth_sq[i][j] = cut_ljsq[i][j]; + if (vdwl_smooth < 1.0) { + double rsm = vdwl_smooth * cut_lj[i][j]; + double rsm_sq = rsm * rsm; + double denom = pow((cut_lj[i][j]-rsm),5.0); + c0[i][j] = cut_lj[i][j]*cut_ljsq[i][j]*(cut_ljsq[i][j]- + 5.0*cut_lj[i][j]*rsm+10.0*rsm_sq)/denom; + c1[i][j] = -30.0*(cut_ljsq[i][j]*rsm_sq)/denom; + c2[i][j] = 30.0*(cut_ljsq[i][j]*rsm + cut_lj[i][j]*rsm_sq)/denom; + c3[i][j] = -10.0*(cut_ljsq[i][j] + 4.0*cut_lj[i][j]*rsm + rsm_sq)/denom; + c4[i][j] = 15.0*(cut_lj[i][j]+rsm)/denom; + c5[i][j] = -6.0/denom; + rsmooth_sq[i][j] = rsm_sq; + } + + // if offset_flag, shift is only invoked if there is not already smoothing + if (offset_flag && vdwl_smooth >= 1.0) { + double term1 = buck6d3[i][j]/pow(cut_lj[i][j],6.0); + double term4 = 1.0/(1.0 + (buck6d4[i][j]/pow(cut_lj[i][j],14.0))); + double rexp = exp(-cut_lj[i][j]*buck6d2[i][j]); + offset[i][j] = buck6d1[i][j]*rexp - term1*term4; + } else offset[i][j] = 0.0; + + double erfcd_c = exp(-alpha_ij[i][j]*alpha_ij[i][j]*cut_coul*cut_coul); + double erfcc_c = erf(alpha_ij[i][j]*cut_coul); + f_shift_ij[i][j] = -erfcc_c/cut_coulsq + 2.0/MY_PIS*alpha_ij[i][j]*erfcd_c/cut_coul; + e_shift_ij[i][j] = erfcc_c/cut_coul - f_shift_ij[i][j]*cut_coul; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + alpha_ij[j][i] = alpha_ij[i][j]; + f_shift_ij[j][i] = f_shift_ij[i][j]; + e_shift_ij[j][i] = e_shift_ij[i][j]; + buck6d1[j][i] = buck6d1[i][j]; + buck6d2[j][i] = buck6d2[i][j]; + buck6d3[j][i] = buck6d3[i][j]; + buck6d4[j][i] = buck6d4[i][j]; + c0[j][i] = c0[i][j]; + c1[j][i] = c1[i][j]; + c2[j][i] = c2[i][j]; + c3[j][i] = c3[i][j]; + c4[j][i] = c4[i][j]; + c5[j][i] = c5[i][j]; + rsmooth_sq[j][i] = rsmooth_sq[i][j]; + offset[j][i] = offset[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&buck6d1[i][j],sizeof(double),1,fp); + fwrite(&buck6d2[i][j],sizeof(double),1,fp); + fwrite(&buck6d3[i][j],sizeof(double),1,fp); + fwrite(&buck6d4[i][j],sizeof(double),1,fp); + fwrite(&alpha_ij[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&buck6d1[i][j],sizeof(double),1,fp); + fread(&buck6d2[i][j],sizeof(double),1,fp); + fread(&buck6d3[i][j],sizeof(double),1,fp); + fread(&buck6d4[i][j],sizeof(double),1,fp); + fread(&alpha_ij[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&buck6d3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&buck6d4[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&alpha_ij[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::write_restart_settings(FILE *fp) +{ + fwrite(&vdwl_smooth,sizeof(double),1,fp); + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&vdwl_smooth,sizeof(double),1,fp); + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i, + buck6d1[i][i],buck6d2[i][i],buck6d3[i][i], + buck6d4[i][i],alpha_ij[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussDSF::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j, + buck6d1[i][j],buck6d2[i][j],buck6d3[i][j], + buck6d4[i][j],alpha_ij[i][j],cut_lj[i][j]); +} +/* ---------------------------------------------------------------------- */ + +double PairBuck6dCoulGaussDSF::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r,r2inv,r6inv,r14inv,rexp,term1,term2,term3,term4,term5; + double rcu,rqu,sme,smf; + double erfcc,erfcd,prefactor,arg; + double forcecoul,forcebuck6d,ebuck6d,phicoul,phibuck6d; + + r2inv = 1.0/rsq; + r = sqrt(rsq); + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r14inv = r6inv*r6inv*r2inv; + rexp = exp(-r*buck6d2[itype][jtype]); + term1 = buck6d3[itype][jtype]*r6inv; + term2 = buck6d4[itype][jtype]*r14inv; + term3 = term2*term2; + term4 = 1.0/(1.0 + term2); + term5 = 1.0/(1.0 + 2.0*term2 + term3); + forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; + forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); + ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; + // smoothing term + if (rsq > rsmooth_sq[itype][jtype]) { + rcu = r*rsq; + rqu = rsq*rsq; + sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + + c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; + smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + + 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; + // forcebuck6d is -dE/dr*r + forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r + ebuck6d *= sme; + } + } else forcebuck6d = 0.0; + + if (rsq < cut_coulsq) { + prefactor = factor_coul * force->qqrd2e * atom->q[i] * atom->q[j] / r; + arg = alpha_ij[itype][jtype]*r; + erfcd = MathSpecial::expmsq(arg); + erfcc = 1 - (MathSpecial::my_erfcx(arg) * erfcd); + forcecoul = prefactor * ((erfcc/r) - (2.0/MY_PIS*alpha_ij[itype][jtype]*erfcd) + + r*f_shift_ij[itype][jtype]) * r; + } else forcecoul = 0.0; + + fforce = (forcecoul + factor_lj*forcebuck6d) * r2inv; + + double eng = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + phibuck6d = ebuck6d - offset[itype][jtype]; + eng += factor_lj*phibuck6d; + } + + if (rsq < cut_coulsq) { + phicoul = prefactor * (erfcc - r*e_shift_ij[itype][jtype] - + rsq*f_shift_ij[itype][jtype]); + eng += phicoul; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairBuck6dCoulGaussDSF::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"cut_ljsq") == 0) return (void *) cut_ljsq; + if (strcmp(str,"buck6d1") == 0) return (void *) buck6d1; + if (strcmp(str,"buck6d2") == 0) return (void *) buck6d2; + if (strcmp(str,"buck6d3") == 0) return (void *) buck6d3; + if (strcmp(str,"buck6d4") == 0) return (void *) buck6d4; + if (strcmp(str,"rsmooth_sq") == 0) return (void *) rsmooth_sq; + if (strcmp(str,"c0") == 0) return (void *) c0; + if (strcmp(str,"c1") == 0) return (void *) c1; + if (strcmp(str,"c2") == 0) return (void *) c2; + if (strcmp(str,"c3") == 0) return (void *) c3; + if (strcmp(str,"c4") == 0) return (void *) c4; + if (strcmp(str,"c5") == 0) return (void *) c5; + if (strcmp(str,"offset") == 0) return (void *) offset; + + if (strcmp(str,"cut_coul") == 0) { + dim = 0; + return (void *) &cut_coul; + } + return NULL; +} diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp index 9902896d18..d6a4121d21 100644 --- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp +++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp @@ -1,646 +1,645 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -/* ---------------------------------------------------------------------- - Contributing author: Hendrik Heenen (Technical University of Munich) - and Rochus Schmid (Ruhr-Universitaet Bochum) - References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) -------------------------------------------------------------------------- */ - -#include -#include -#include -#include -#include "pair_buck6d_coul_gauss_long.h" -#include "atom.h" -#include "comm.h" -#include "force.h" -#include "kspace.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "memory.h" -#include "math_const.h" -#include "error.h" -#include "math_special.h" - -using namespace LAMMPS_NS; -using namespace MathConst; - -#define EWALD_F 1.12837917 - -/* ---------------------------------------------------------------------- */ - -PairBuck6dCoulGaussLong::PairBuck6dCoulGaussLong(LAMMPS *lmp) : Pair(lmp) -{ - ewaldflag = pppmflag = 1; - single_enable = 1; - writedata = 1; -} - -/* ---------------------------------------------------------------------- */ - -PairBuck6dCoulGaussLong::~PairBuck6dCoulGaussLong() -{ - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(alpha_ij); - memory->destroy(buck6d1); - memory->destroy(buck6d2); - memory->destroy(buck6d3); - memory->destroy(buck6d4); - memory->destroy(c0); - memory->destroy(c1); - memory->destroy(c2); - memory->destroy(c3); - memory->destroy(c4); - memory->destroy(c5); - memory->destroy(rsmooth_sq); - memory->destroy(offset); - } - } -} - -/* ---------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::compute(int eflag, int vflag) -{ - int i,j,ii,jj,inum,jnum,itype,jtype; - double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; - double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj; - double grij,expm2,erf; - double term1,term2,term3,term4,term5; - double rcu,rqu,sme,smf,ebuck6d,ealpha; - double prefactor,erfa,expa,t,arg,falpha; - int *ilist,*jlist,*numneigh,**firstneigh; - - evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; - - double **x = atom->x; - double **f = atom->f; - double *q = atom->q; - int *type = atom->type; - int nlocal = atom->nlocal; - double *special_lj = force->special_lj; - double *special_coul = force->special_coul; - int newton_pair = force->newton_pair; - double qqrd2e = force->qqrd2e; - - inum = list->inum; - ilist = list->ilist; - numneigh = list->numneigh; - firstneigh = list->firstneigh; - - // loop over neighbors of my atoms - - for (ii = 0; ii < inum; ii++) { - i = ilist[ii]; - qtmp = q[i]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - itype = type[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - factor_lj = special_lj[sbmask(j)]; - factor_coul = special_coul[sbmask(j)]; - j &= NEIGHMASK; - - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - jtype = type[j]; - - if (rsq < cutsq[itype][jtype]) { - r2inv = 1.0/rsq; - r = sqrt(rsq); - - if (rsq < cut_ljsq[itype][jtype]) { - r6inv = r2inv*r2inv*r2inv; - r14inv = r6inv*r6inv*r2inv; - rexp = exp(-r*buck6d2[itype][jtype]); - term1 = buck6d3[itype][jtype]*r6inv; - term2 = buck6d4[itype][jtype]*r14inv; - term3 = term2*term2; - term4 = 1.0/(1.0 + term2); - term5 = 1.0/(1.0 + 2.0*term2 + term3); - forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; - forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); - ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; - - // smoothing term - if (rsq > rsmooth_sq[itype][jtype]) { - rcu = r*rsq; - rqu = rsq*rsq; - sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + - c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; - smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + - 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; - // forcebuck6d is -dE/dr*r - forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; - ebuck6d *= sme; - } - } else forcebuck6d = 0.0; - - if (rsq < cut_coulsq) { - // long range - real space - grij = g_ewald * r; - expm2 = MathSpecial::expmsq(grij); - erf = 1 - (MathSpecial::my_erfcx(grij) * expm2); - - // gaussian for 1/r alpha_ij contribution - arg = alpha_ij[itype][jtype]*r; - expa = MathSpecial::expmsq(arg); - erfa = 1 - (MathSpecial::my_erfcx(arg) * expa); - - prefactor = qqrd2e*qtmp*q[j]/r; - falpha = erfa - EWALD_F*arg*expa; - forcecoul = prefactor * (falpha - erf + EWALD_F*grij*expm2); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*falpha; - - // (q*q/r) * (gauss(alpha_ij) - gauss(alpha_long) - ealpha = prefactor * (erfa-erf); - // smoothing term - NOTE: ingnored in special_bonds correction - // since likely rsmooth_sq_c >> d(special) - if (rsq > rsmooth_sq_c) { - rcu = r*rsq; - rqu = rsq*rsq; - sme = c5_c*rqu*r + c4_c*rqu + c3_c*rcu + c2_c*rsq + c1_c*r + c0_c; - smf = 5.0*c5_c*rqu + 4.0*c4_c*rcu + 3.0*c3_c*rsq + 2.0*c2_c*r + c1_c; - forcecoul = forcecoul*sme - ealpha*smf*r; - ealpha *= sme; - } - } else forcecoul = 0.0; - - - fpair = (forcecoul + factor_lj*forcebuck6d) * r2inv; - f[i][0] += delx*fpair; - f[i][1] += dely*fpair; - f[i][2] += delz*fpair; - if (newton_pair || j < nlocal) { - f[j][0] -= delx*fpair; - f[j][1] -= dely*fpair; - f[j][2] -= delz*fpair; - } - - if (eflag) { - if (rsq < cut_ljsq[itype][jtype]) { - evdwl = ebuck6d - offset[itype][jtype]; - evdwl *= factor_lj; - } else evdwl = 0.0; - - if (rsq < cut_coulsq) { - ecoul = ealpha; - if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*erfa; - } else ecoul = 0.0; - } - - if (evflag) ev_tally(i,j,nlocal,newton_pair, - evdwl,ecoul,fpair,delx,dely,delz); - } - } - } - - if (vflag_fdotr) virial_fdotr_compute(); -} - -/* ---------------------------------------------------------------------- - allocate all arrays -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::allocate() -{ - allocated = 1; - int n = atom->ntypes; - - memory->create(setflag,n+1,n+1,"pair:setflag"); - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - setflag[i][j] = 0; - - memory->create(cutsq,n+1,n+1,"pair:cutsq"); - - memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); - memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); - memory->create(alpha_ij,n+1,n+1,"pair:alpha_ij"); - memory->create(buck6d1,n+1,n+1,"pair:buck6d1"); - memory->create(buck6d2,n+1,n+1,"pair:buck6d2"); - memory->create(buck6d3,n+1,n+1,"pair:buck6d3"); - memory->create(buck6d4,n+1,n+1,"pair:buck6d4"); - memory->create(c0,n+1,n+1,"pair:c0"); - memory->create(c1,n+1,n+1,"pair:c1"); - memory->create(c2,n+1,n+1,"pair:c2"); - memory->create(c3,n+1,n+1,"pair:c3"); - memory->create(c4,n+1,n+1,"pair:c4"); - memory->create(c5,n+1,n+1,"pair:c5"); - memory->create(rsmooth_sq,n+1,n+1,"pair:rsmooth_sq"); - memory->create(offset,n+1,n+1,"pair:offset"); -} - -/* ---------------------------------------------------------------------- - global settings -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::settings(int narg, char **arg) -{ - if (narg < 3 || narg > 4) error->all(FLERR,"Illegal pair_style command"); - - vdwl_smooth = force->numeric(FLERR,arg[0]); - coul_smooth = force->numeric(FLERR,arg[1]); - - cut_lj_global = force->numeric(FLERR,arg[2]); - if (narg == 3) cut_coul = cut_lj_global; - else cut_coul = force->numeric(FLERR,arg[3]); - - // reset cutoffs that have been explicitly set - - if (allocated) { - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i+1; j <= atom->ntypes; j++) - if (setflag[i][j]) - cut_lj[i][j] = cut_lj_global; - } -} - -/* ---------------------------------------------------------------------- - set coeffs for one or more type pairs -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::coeff(int narg, char **arg) -{ - if (narg < 7 || narg > 8) - error->all(FLERR,"Incorrect args for pair coefficients"); - if (!allocated) allocate(); - - int ilo,ihi,jlo,jhi; - force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); - force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); - - double buck6d1_one = force->numeric(FLERR,arg[2]); - double buck6d2_one = force->numeric(FLERR,arg[3]); - double buck6d3_one = force->numeric(FLERR,arg[4]); - double buck6d4_one = force->numeric(FLERR,arg[5]); - double alpha_one = force->numeric(FLERR,arg[6]); - - double cut_lj_one = cut_lj_global; - if (narg == 8) cut_lj_one = force->numeric(FLERR,arg[7]); - - int count = 0; - for (int i = ilo; i <= ihi; i++) { - for (int j = MAX(jlo,i); j <= jhi; j++) { - buck6d1[i][j] = buck6d1_one; - buck6d2[i][j] = buck6d2_one; - buck6d3[i][j] = buck6d3_one; - buck6d4[i][j] = buck6d4_one; - alpha_ij[i][j] = alpha_one; - cut_lj[i][j] = cut_lj_one; - setflag[i][j] = 1; - count++; - } - } - - if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); -} - -/* ---------------------------------------------------------------------- - init specific to this pair style -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::init_style() -{ - if (!atom->q_flag) - error->all(FLERR,"Pair style buck6d/coul/dsf requires atom attribute q"); - - // insure use of KSpace long-range solver, set g_ewald - - if (force->kspace == NULL) - error->all(FLERR,"Pair style requires a KSpace style"); - g_ewald = force->kspace->g_ewald; - - neighbor->request(this,instance_me); - - cut_coulsq = cut_coul * cut_coul; - - //calculation of smoothing coefficients c0_c-c5_c for coulomb smoothing - c0_c = c1_c = c2_c = c3_c = c4_c = c5_c = 0.0; - rsmooth_sq_c = cut_coulsq; - if (coul_smooth < 1.0) { - double rsm = coul_smooth * cut_coul; - double rsm_sq = rsm * rsm; - double denom = pow((cut_coul-rsm),5.0); - c0_c = cut_coul*cut_coulsq*(cut_coulsq- - 5.0*cut_coul*rsm+10.0*rsm_sq)/denom; - c1_c = -30.0*(cut_coulsq*rsm_sq)/denom; - c2_c = 30.0*(cut_coulsq*rsm + cut_coul*rsm_sq)/denom; - c3_c = -10.0*(cut_coulsq + 4.0*cut_coul*rsm + rsm_sq)/denom; - c4_c = 15.0*(cut_coul+rsm)/denom; - c5_c = -6.0/denom; - rsmooth_sq_c = rsm_sq; - } -} - -/* ---------------------------------------------------------------------- - init for one type pair i,j and corresponding j,i -------------------------------------------------------------------------- */ - -double PairBuck6dCoulGaussLong::init_one(int i, int j) -{ - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); - - double cut = MAX(cut_lj[i][j],cut_coul); - cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; - - //calculation of smoothing coefficients c0-c5 - c0[i][j] = c1[i][j] = c2[i][j] = c3[i][j] = c4[i][j] = c5[i][j] = 0.0; - rsmooth_sq[i][j] = cut_ljsq[i][j]; - if (vdwl_smooth < 1.0) { - double rsm = vdwl_smooth * cut_lj[i][j]; - double rsm_sq = rsm * rsm; - double denom = pow((cut_lj[i][j]-rsm),5.0); - c0[i][j] = cut_lj[i][j]*cut_ljsq[i][j]*(cut_ljsq[i][j]- - 5.0*cut_lj[i][j]*rsm+10.0*rsm_sq)/denom; - c1[i][j] = -30.0*(cut_ljsq[i][j]*rsm_sq)/denom; - c2[i][j] = 30.0*(cut_ljsq[i][j]*rsm + cut_lj[i][j]*rsm_sq)/denom; - c3[i][j] = -10.0*(cut_ljsq[i][j] + 4.0*cut_lj[i][j]*rsm + rsm_sq)/denom; - c4[i][j] = 15.0*(cut_lj[i][j]+rsm)/denom; - c5[i][j] = -6.0/denom; - rsmooth_sq[i][j] = rsm_sq; - } - - // if offset_flag, shift is only invoked if there is not already smoothing - if (offset_flag && vdwl_smooth >= 1.0) { - double term1 = buck6d3[i][j]/pow(cut_lj[i][j],6.0); - double term4 = 1.0/(1.0 + (buck6d4[i][j]/pow(cut_lj[i][j],14.0))); - double rexp = exp(-cut_lj[i][j]*buck6d2[i][j]); - offset[i][j] = buck6d1[i][j]*rexp - term1*term4; - } else offset[i][j] = 0.0; - - cut_ljsq[j][i] = cut_ljsq[i][j]; - alpha_ij[j][i] = alpha_ij[i][j]; - buck6d1[j][i] = buck6d1[i][j]; - buck6d2[j][i] = buck6d2[i][j]; - buck6d3[j][i] = buck6d3[i][j]; - buck6d4[j][i] = buck6d4[i][j]; - c0[j][i] = c0[i][j]; - c1[j][i] = c1[i][j]; - c2[j][i] = c2[i][j]; - c3[j][i] = c3[i][j]; - c4[j][i] = c4[i][j]; - c5[j][i] = c5[i][j]; - rsmooth_sq[j][i] = rsmooth_sq[i][j]; - offset[j][i] = offset[i][j]; - - return cut; -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::write_restart(FILE *fp) -{ - write_restart_settings(fp); - - int i,j; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - fwrite(&setflag[i][j],sizeof(int),1,fp); - if (setflag[i][j]) { - fwrite(&buck6d1[i][j],sizeof(double),1,fp); - fwrite(&buck6d2[i][j],sizeof(double),1,fp); - fwrite(&buck6d3[i][j],sizeof(double),1,fp); - fwrite(&buck6d4[i][j],sizeof(double),1,fp); - fwrite(&alpha_ij[i][j],sizeof(double),1,fp); - fwrite(&cut_lj[i][j],sizeof(double),1,fp); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::read_restart(FILE *fp) -{ - read_restart_settings(fp); - allocate(); - - int i,j; - int me = comm->me; - for (i = 1; i <= atom->ntypes; i++) - for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); - MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); - if (setflag[i][j]) { - if (me == 0) { - fread(&buck6d1[i][j],sizeof(double),1,fp); - fread(&buck6d2[i][j],sizeof(double),1,fp); - fread(&buck6d3[i][j],sizeof(double),1,fp); - fread(&buck6d4[i][j],sizeof(double),1,fp); - fread(&alpha_ij[i][j],sizeof(double),1,fp); - fread(&cut_lj[i][j],sizeof(double),1,fp); - } - MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&buck6d3[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&buck6d4[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&alpha_ij[i][j],1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); - } - } -} - -/* ---------------------------------------------------------------------- - proc 0 writes to restart file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::write_restart_settings(FILE *fp) -{ - fwrite(&vdwl_smooth,sizeof(double),1,fp); - fwrite(&coul_smooth,sizeof(double),1,fp); - fwrite(&cut_lj_global,sizeof(double),1,fp); - fwrite(&cut_coul,sizeof(double),1,fp); - fwrite(&offset_flag,sizeof(int),1,fp); - fwrite(&mix_flag,sizeof(int),1,fp); - fwrite(&tail_flag,sizeof(int),1,fp); -} - -/* ---------------------------------------------------------------------- - proc 0 reads from restart file, bcasts -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::read_restart_settings(FILE *fp) -{ - if (comm->me == 0) { - fread(&vdwl_smooth,sizeof(double),1,fp); - fread(&coul_smooth,sizeof(double),1,fp); - fread(&cut_lj_global,sizeof(double),1,fp); - fread(&cut_coul,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); - fread(&tail_flag,sizeof(int),1,fp); - } - MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world); - MPI_Bcast(&coul_smooth,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); - MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); - MPI_Bcast(&offset_flag,1,MPI_INT,0,world); - MPI_Bcast(&mix_flag,1,MPI_INT,0,world); - MPI_Bcast(&tail_flag,1,MPI_INT,0,world); -} - -/* ---------------------------------------------------------------------- - proc 0 writes to data file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::write_data(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - fprintf(fp,"%d %g %g %g %g %g\n",i, - buck6d1[i][i],buck6d2[i][i],buck6d3[i][i], - buck6d4[i][i],alpha_ij[i][i]); -} - -/* ---------------------------------------------------------------------- - proc 0 writes all pairs to data file -------------------------------------------------------------------------- */ - -void PairBuck6dCoulGaussLong::write_data_all(FILE *fp) -{ - for (int i = 1; i <= atom->ntypes; i++) - for (int j = i; j <= atom->ntypes; j++) - fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j, - buck6d1[i][j],buck6d2[i][j],buck6d3[i][j], - buck6d4[i][j],alpha_ij[i][j],cut_lj[i][j]); -} -/* ---------------------------------------------------------------------- */ - -double PairBuck6dCoulGaussLong::single(int i, int j, int itype, int jtype, double rsq, - double factor_coul, double factor_lj, - double &fforce) -{ - double r,r2inv,r6inv,r14inv,rexp,term1,term2,term3,term4,term5; - double rcu,rqu,sme,smf; - double erfa,expa,prefactor,arg,falpha,ealpha; - double grij,expm2,erf; - double forcecoul,forcebuck6d,ebuck6d,phicoul,phibuck6d; - - r2inv = 1.0/rsq; - r = sqrt(rsq); - if (rsq < cut_ljsq[itype][jtype]) { - r6inv = r2inv*r2inv*r2inv; - r14inv = r6inv*r6inv*r2inv; - rexp = exp(-r*buck6d2[itype][jtype]); - term1 = buck6d3[itype][jtype]*r6inv; - term2 = buck6d4[itype][jtype]*r14inv; - term3 = term2*term2; - term4 = 1.0/(1.0 + term2); - term5 = 1.0/(1.0 + 2.0*term2 + term3); - forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; - forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); - ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; - // smoothing term - if (rsq > rsmooth_sq[itype][jtype]) { - rcu = r*rsq; - rqu = rsq*rsq; - sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + - c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; - smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + - 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; - // forcebuck6d is -dE/dr*r - forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r - ebuck6d *= sme; - } - } else forcebuck6d = 0.0; - - if (rsq < cut_coulsq) { - // long range - real space - grij = g_ewald * r; - expm2 = MathSpecial::expmsq(grij); - erf = 1 - (MathSpecial::my_erfcx(grij) * expm2); - - // gaussian for 1/r alpha_ij contribution - arg = alpha_ij[itype][jtype]*r; - expa = MathSpecial::expmsq(arg); - erfa = 1 - (MathSpecial::my_erfcx(arg) * expa); - - prefactor = force->qqrd2e * atom->q[i] * atom->q[j] / r; - falpha = erfa - EWALD_F*arg*expa; - forcecoul = prefactor * (falpha - erf + EWALD_F*grij*expm2); - if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*falpha; - - ealpha = prefactor * (erfa-erf); - // smoothing term - if (rsq > rsmooth_sq_c) { - rcu = r*rsq; - rqu = rsq*rsq; - sme = c5_c*rqu*r + c4_c*rqu + c3_c*rcu + c2_c*rsq + c1_c*r + c0_c; - smf = 5.0*c5_c*rqu + 4.0*c4_c*rcu + 3.0*c3_c*rsq + 2.0*c2_c*r + c1_c; - forcecoul = forcecoul*sme - ealpha*smf*r; - ealpha *= sme; - } - } else forcecoul = 0.0; - - fforce = (forcecoul + factor_lj*forcebuck6d) * r2inv; - - double eng = 0.0; - if (rsq < cut_ljsq[itype][jtype]) { - phibuck6d = ebuck6d - offset[itype][jtype]; - eng += factor_lj*phibuck6d; - } - - if (rsq < cut_coulsq) { - phicoul = ealpha; - if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor*erfa; - eng += phicoul; - } - - return eng; -} - -/* ---------------------------------------------------------------------- */ - -void *PairBuck6dCoulGaussLong::extract(const char *str, int &dim) -{ - dim = 2; - if (strcmp(str,"cut_ljsq") == 0) return (void *) cut_ljsq; - if (strcmp(str,"buck6d1") == 0) return (void *) buck6d1; - if (strcmp(str,"buck6d2") == 0) return (void *) buck6d2; - if (strcmp(str,"buck6d3") == 0) return (void *) buck6d3; - if (strcmp(str,"buck6d4") == 0) return (void *) buck6d4; - if (strcmp(str,"rsmooth_sq") == 0) return (void *) rsmooth_sq; - if (strcmp(str,"c0") == 0) return (void *) c0; - if (strcmp(str,"c1") == 0) return (void *) c1; - if (strcmp(str,"c2") == 0) return (void *) c2; - if (strcmp(str,"c3") == 0) return (void *) c3; - if (strcmp(str,"c4") == 0) return (void *) c4; - if (strcmp(str,"c5") == 0) return (void *) c5; - if (strcmp(str,"offset") == 0) return (void *) offset; - - if (strcmp(str,"cut_coul") == 0) { - dim = 0; - return (void *) &cut_coul; - } - return NULL; -} +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Hendrik Heenen (Technical University of Munich) + and Rochus Schmid (Ruhr-Universitaet Bochum) + References: Bureekaew and Schmid, Phys. Status Solidi B 250, 1128 (2013) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_buck6d_coul_gauss_long.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "memory.h" +#include "math_const.h" +#include "error.h" +#include "math_special.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EWALD_F 1.12837917 + +/* ---------------------------------------------------------------------- */ + +PairBuck6dCoulGaussLong::PairBuck6dCoulGaussLong(LAMMPS *lmp) : Pair(lmp) +{ + ewaldflag = pppmflag = 1; + single_enable = 1; + writedata = 1; +} + +/* ---------------------------------------------------------------------- */ + +PairBuck6dCoulGaussLong::~PairBuck6dCoulGaussLong() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(alpha_ij); + memory->destroy(buck6d1); + memory->destroy(buck6d2); + memory->destroy(buck6d3); + memory->destroy(buck6d4); + memory->destroy(c0); + memory->destroy(c1); + memory->destroy(c2); + memory->destroy(c3); + memory->destroy(c4); + memory->destroy(c5); + memory->destroy(rsmooth_sq); + memory->destroy(offset); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::compute(int eflag, int vflag) +{ + int i,j,ii,jj,inum,jnum,itype,jtype; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj; + double grij,expm2,erf; + double term1,term2,term3,term4,term5; + double rcu,rqu,sme,smf,ebuck6d,ealpha; + double prefactor,erfa,expa,arg,falpha; + int *ilist,*jlist,*numneigh,**firstneigh; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_lj = force->special_lj; + double *special_coul = force->special_coul; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + r = sqrt(rsq); + + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r14inv = r6inv*r6inv*r2inv; + rexp = exp(-r*buck6d2[itype][jtype]); + term1 = buck6d3[itype][jtype]*r6inv; + term2 = buck6d4[itype][jtype]*r14inv; + term3 = term2*term2; + term4 = 1.0/(1.0 + term2); + term5 = 1.0/(1.0 + 2.0*term2 + term3); + forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; + forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); + ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; + + // smoothing term + if (rsq > rsmooth_sq[itype][jtype]) { + rcu = r*rsq; + rqu = rsq*rsq; + sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + + c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; + smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + + 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; + // forcebuck6d is -dE/dr*r + forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; + ebuck6d *= sme; + } + } else forcebuck6d = 0.0; + + if (rsq < cut_coulsq) { + // long range - real space + grij = g_ewald * r; + expm2 = MathSpecial::expmsq(grij); + erf = 1 - (MathSpecial::my_erfcx(grij) * expm2); + + // gaussian for 1/r alpha_ij contribution + arg = alpha_ij[itype][jtype]*r; + expa = MathSpecial::expmsq(arg); + erfa = 1 - (MathSpecial::my_erfcx(arg) * expa); + + prefactor = qqrd2e*qtmp*q[j]/r; + falpha = erfa - EWALD_F*arg*expa; + forcecoul = prefactor * (falpha - erf + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*falpha; + + // (q*q/r) * (gauss(alpha_ij) - gauss(alpha_long) + ealpha = prefactor * (erfa-erf); + // smoothing term - NOTE: ingnored in special_bonds correction + // since likely rsmooth_sq_c >> d(special) + if (rsq > rsmooth_sq_c) { + rcu = r*rsq; + rqu = rsq*rsq; + sme = c5_c*rqu*r + c4_c*rqu + c3_c*rcu + c2_c*rsq + c1_c*r + c0_c; + smf = 5.0*c5_c*rqu + 4.0*c4_c*rcu + 3.0*c3_c*rsq + 2.0*c2_c*r + c1_c; + forcecoul = forcecoul*sme - ealpha*smf*r; + ealpha *= sme; + } + } else forcecoul = 0.0; + + + fpair = (forcecoul + factor_lj*forcebuck6d) * r2inv; + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (eflag) { + if (rsq < cut_ljsq[itype][jtype]) { + evdwl = ebuck6d - offset[itype][jtype]; + evdwl *= factor_lj; + } else evdwl = 0.0; + + if (rsq < cut_coulsq) { + ecoul = ealpha; + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor*erfa; + } else ecoul = 0.0; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(alpha_ij,n+1,n+1,"pair:alpha_ij"); + memory->create(buck6d1,n+1,n+1,"pair:buck6d1"); + memory->create(buck6d2,n+1,n+1,"pair:buck6d2"); + memory->create(buck6d3,n+1,n+1,"pair:buck6d3"); + memory->create(buck6d4,n+1,n+1,"pair:buck6d4"); + memory->create(c0,n+1,n+1,"pair:c0"); + memory->create(c1,n+1,n+1,"pair:c1"); + memory->create(c2,n+1,n+1,"pair:c2"); + memory->create(c3,n+1,n+1,"pair:c3"); + memory->create(c4,n+1,n+1,"pair:c4"); + memory->create(c5,n+1,n+1,"pair:c5"); + memory->create(rsmooth_sq,n+1,n+1,"pair:rsmooth_sq"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::settings(int narg, char **arg) +{ + if (narg < 3 || narg > 4) error->all(FLERR,"Illegal pair_style command"); + + vdwl_smooth = force->numeric(FLERR,arg[0]); + coul_smooth = force->numeric(FLERR,arg[1]); + + cut_lj_global = force->numeric(FLERR,arg[2]); + if (narg == 3) cut_coul = cut_lj_global; + else cut_coul = force->numeric(FLERR,arg[3]); + + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i+1; j <= atom->ntypes; j++) + if (setflag[i][j]) + cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::coeff(int narg, char **arg) +{ + if (narg < 7 || narg > 8) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double buck6d1_one = force->numeric(FLERR,arg[2]); + double buck6d2_one = force->numeric(FLERR,arg[3]); + double buck6d3_one = force->numeric(FLERR,arg[4]); + double buck6d4_one = force->numeric(FLERR,arg[5]); + double alpha_one = force->numeric(FLERR,arg[6]); + + double cut_lj_one = cut_lj_global; + if (narg == 8) cut_lj_one = force->numeric(FLERR,arg[7]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + buck6d1[i][j] = buck6d1_one; + buck6d2[i][j] = buck6d2_one; + buck6d3[i][j] = buck6d3_one; + buck6d4[i][j] = buck6d4_one; + alpha_ij[i][j] = alpha_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style buck6d/coul/dsf requires atom attribute q"); + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + + neighbor->request(this,instance_me); + + cut_coulsq = cut_coul * cut_coul; + + //calculation of smoothing coefficients c0_c-c5_c for coulomb smoothing + c0_c = c1_c = c2_c = c3_c = c4_c = c5_c = 0.0; + rsmooth_sq_c = cut_coulsq; + if (coul_smooth < 1.0) { + double rsm = coul_smooth * cut_coul; + double rsm_sq = rsm * rsm; + double denom = pow((cut_coul-rsm),5.0); + c0_c = cut_coul*cut_coulsq*(cut_coulsq- + 5.0*cut_coul*rsm+10.0*rsm_sq)/denom; + c1_c = -30.0*(cut_coulsq*rsm_sq)/denom; + c2_c = 30.0*(cut_coulsq*rsm + cut_coul*rsm_sq)/denom; + c3_c = -10.0*(cut_coulsq + 4.0*cut_coul*rsm + rsm_sq)/denom; + c4_c = 15.0*(cut_coul+rsm)/denom; + c5_c = -6.0/denom; + rsmooth_sq_c = rsm_sq; + } +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairBuck6dCoulGaussLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + + double cut = MAX(cut_lj[i][j],cut_coul); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + + //calculation of smoothing coefficients c0-c5 + c0[i][j] = c1[i][j] = c2[i][j] = c3[i][j] = c4[i][j] = c5[i][j] = 0.0; + rsmooth_sq[i][j] = cut_ljsq[i][j]; + if (vdwl_smooth < 1.0) { + double rsm = vdwl_smooth * cut_lj[i][j]; + double rsm_sq = rsm * rsm; + double denom = pow((cut_lj[i][j]-rsm),5.0); + c0[i][j] = cut_lj[i][j]*cut_ljsq[i][j]*(cut_ljsq[i][j]- + 5.0*cut_lj[i][j]*rsm+10.0*rsm_sq)/denom; + c1[i][j] = -30.0*(cut_ljsq[i][j]*rsm_sq)/denom; + c2[i][j] = 30.0*(cut_ljsq[i][j]*rsm + cut_lj[i][j]*rsm_sq)/denom; + c3[i][j] = -10.0*(cut_ljsq[i][j] + 4.0*cut_lj[i][j]*rsm + rsm_sq)/denom; + c4[i][j] = 15.0*(cut_lj[i][j]+rsm)/denom; + c5[i][j] = -6.0/denom; + rsmooth_sq[i][j] = rsm_sq; + } + + // if offset_flag, shift is only invoked if there is not already smoothing + if (offset_flag && vdwl_smooth >= 1.0) { + double term1 = buck6d3[i][j]/pow(cut_lj[i][j],6.0); + double term4 = 1.0/(1.0 + (buck6d4[i][j]/pow(cut_lj[i][j],14.0))); + double rexp = exp(-cut_lj[i][j]*buck6d2[i][j]); + offset[i][j] = buck6d1[i][j]*rexp - term1*term4; + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + alpha_ij[j][i] = alpha_ij[i][j]; + buck6d1[j][i] = buck6d1[i][j]; + buck6d2[j][i] = buck6d2[i][j]; + buck6d3[j][i] = buck6d3[i][j]; + buck6d4[j][i] = buck6d4[i][j]; + c0[j][i] = c0[i][j]; + c1[j][i] = c1[i][j]; + c2[j][i] = c2[i][j]; + c3[j][i] = c3[i][j]; + c4[j][i] = c4[i][j]; + c5[j][i] = c5[i][j]; + rsmooth_sq[j][i] = rsmooth_sq[i][j]; + offset[j][i] = offset[i][j]; + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&buck6d1[i][j],sizeof(double),1,fp); + fwrite(&buck6d2[i][j],sizeof(double),1,fp); + fwrite(&buck6d3[i][j],sizeof(double),1,fp); + fwrite(&buck6d4[i][j],sizeof(double),1,fp); + fwrite(&alpha_ij[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::read_restart(FILE *fp) +{ + read_restart_settings(fp); + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&buck6d1[i][j],sizeof(double),1,fp); + fread(&buck6d2[i][j],sizeof(double),1,fp); + fread(&buck6d3[i][j],sizeof(double),1,fp); + fread(&buck6d4[i][j],sizeof(double),1,fp); + fread(&alpha_ij[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&buck6d1[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&buck6d2[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&buck6d3[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&buck6d4[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&alpha_ij[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::write_restart_settings(FILE *fp) +{ + fwrite(&vdwl_smooth,sizeof(double),1,fp); + fwrite(&coul_smooth,sizeof(double),1,fp); + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&vdwl_smooth,sizeof(double),1,fp); + fread(&coul_smooth,sizeof(double),1,fp); + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + } + MPI_Bcast(&vdwl_smooth,1,MPI_DOUBLE,0,world); + MPI_Bcast(&coul_smooth,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g %g %g\n",i, + buck6d1[i][i],buck6d2[i][i],buck6d3[i][i], + buck6d4[i][i],alpha_ij[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairBuck6dCoulGaussLong::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g %g %g\n",i,j, + buck6d1[i][j],buck6d2[i][j],buck6d3[i][j], + buck6d4[i][j],alpha_ij[i][j],cut_lj[i][j]); +} +/* ---------------------------------------------------------------------- */ + +double PairBuck6dCoulGaussLong::single(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r,r2inv,r6inv,r14inv,rexp,term1,term2,term3,term4,term5; + double rcu,rqu,sme,smf; + double erfa,expa,prefactor,arg,falpha,ealpha; + double grij,expm2,erf; + double forcecoul,forcebuck6d,ebuck6d,phicoul,phibuck6d; + + r2inv = 1.0/rsq; + r = sqrt(rsq); + if (rsq < cut_ljsq[itype][jtype]) { + r6inv = r2inv*r2inv*r2inv; + r14inv = r6inv*r6inv*r2inv; + rexp = exp(-r*buck6d2[itype][jtype]); + term1 = buck6d3[itype][jtype]*r6inv; + term2 = buck6d4[itype][jtype]*r14inv; + term3 = term2*term2; + term4 = 1.0/(1.0 + term2); + term5 = 1.0/(1.0 + 2.0*term2 + term3); + forcebuck6d = buck6d1[itype][jtype]*buck6d2[itype][jtype]*r*rexp; + forcebuck6d -= term1*(6.0*term4 - term5*14.0*term2); + ebuck6d = buck6d1[itype][jtype]*rexp - term1*term4; + // smoothing term + if (rsq > rsmooth_sq[itype][jtype]) { + rcu = r*rsq; + rqu = rsq*rsq; + sme = c5[itype][jtype]*rqu*r + c4[itype][jtype]*rqu + c3[itype][jtype]*rcu + + c2[itype][jtype]*rsq + c1[itype][jtype]*r + c0[itype][jtype]; + smf = 5.0*c5[itype][jtype]*rqu + 4.0*c4[itype][jtype]*rcu + + 3.0*c3[itype][jtype]*rsq + 2.0*c2[itype][jtype]*r + c1[itype][jtype]; + // forcebuck6d is -dE/dr*r + forcebuck6d = forcebuck6d*sme - ebuck6d*smf*r; //RS was here: changed this from +E*smf to -E*smf*r + ebuck6d *= sme; + } + } else forcebuck6d = 0.0; + + if (rsq < cut_coulsq) { + // long range - real space + grij = g_ewald * r; + expm2 = MathSpecial::expmsq(grij); + erf = 1 - (MathSpecial::my_erfcx(grij) * expm2); + + // gaussian for 1/r alpha_ij contribution + arg = alpha_ij[itype][jtype]*r; + expa = MathSpecial::expmsq(arg); + erfa = 1 - (MathSpecial::my_erfcx(arg) * expa); + + prefactor = force->qqrd2e * atom->q[i] * atom->q[j] / r; + falpha = erfa - EWALD_F*arg*expa; + forcecoul = prefactor * (falpha - erf + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor*falpha; + + ealpha = prefactor * (erfa-erf); + // smoothing term + if (rsq > rsmooth_sq_c) { + rcu = r*rsq; + rqu = rsq*rsq; + sme = c5_c*rqu*r + c4_c*rqu + c3_c*rcu + c2_c*rsq + c1_c*r + c0_c; + smf = 5.0*c5_c*rqu + 4.0*c4_c*rcu + 3.0*c3_c*rsq + 2.0*c2_c*r + c1_c; + forcecoul = forcecoul*sme - ealpha*smf*r; + ealpha *= sme; + } + } else forcecoul = 0.0; + + fforce = (forcecoul + factor_lj*forcebuck6d) * r2inv; + + double eng = 0.0; + if (rsq < cut_ljsq[itype][jtype]) { + phibuck6d = ebuck6d - offset[itype][jtype]; + eng += factor_lj*phibuck6d; + } + + if (rsq < cut_coulsq) { + phicoul = ealpha; + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor*erfa; + eng += phicoul; + } + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairBuck6dCoulGaussLong::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"cut_ljsq") == 0) return (void *) cut_ljsq; + if (strcmp(str,"buck6d1") == 0) return (void *) buck6d1; + if (strcmp(str,"buck6d2") == 0) return (void *) buck6d2; + if (strcmp(str,"buck6d3") == 0) return (void *) buck6d3; + if (strcmp(str,"buck6d4") == 0) return (void *) buck6d4; + if (strcmp(str,"rsmooth_sq") == 0) return (void *) rsmooth_sq; + if (strcmp(str,"c0") == 0) return (void *) c0; + if (strcmp(str,"c1") == 0) return (void *) c1; + if (strcmp(str,"c2") == 0) return (void *) c2; + if (strcmp(str,"c3") == 0) return (void *) c3; + if (strcmp(str,"c4") == 0) return (void *) c4; + if (strcmp(str,"c5") == 0) return (void *) c5; + if (strcmp(str,"offset") == 0) return (void *) offset; + + if (strcmp(str,"cut_coul") == 0) { + dim = 0; + return (void *) &cut_coul; + } + return NULL; +} diff --git a/src/USER-MOLFILE/reader_molfile.cpp b/src/USER-MOLFILE/reader_molfile.cpp index 8e49f56d5c..bbbe65959e 100644 --- a/src/USER-MOLFILE/reader_molfile.cpp +++ b/src/USER-MOLFILE/reader_molfile.cpp @@ -197,7 +197,7 @@ void ReaderMolfile::skip() bigint ReaderMolfile::read_header(double box[3][3], int &triclinic, int fieldinfo, int nfield, - int *fieldtype, char **fieldlabel, + int *fieldtype, char ** /* fieldlabel */, int scaleflag, int wrapflag, int &fieldflag, int &xflag, int &yflag, int &zflag) { diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp index c08bc89d04..f297ef45eb 100644 --- a/src/USER-NETCDF/dump_netcdf.cpp +++ b/src/USER-NETCDF/dump_netcdf.cpp @@ -281,6 +281,9 @@ void DumpNetCDF::openfile() // get total number of atoms ntotalgr = group->count(igroup); + for (int i = 0; i < DUMP_NC_MAX_DIMS; i++) { + vector_dim[i] = -1; + } if (filewriter) { if (append_flag && !multifile && access(filecurrent, F_OK) != -1) { @@ -294,9 +297,6 @@ void DumpNetCDF::openfile() // dimensions NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR ); - NCERRX( nc_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim), - NC_SPATIAL_STR ); - NCERRX( nc_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR ); NCERRX( nc_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR ); NCERRX( nc_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim), NC_CELL_SPATIAL_STR ); @@ -304,6 +304,26 @@ void DumpNetCDF::openfile() NC_CELL_ANGULAR_STR ); NCERRX( nc_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR ); + for (int i = 0; i < n_perat; i++) { + int dims = perat[i].dims; + if (vector_dim[dims] < 0) { + char dimstr[1024]; + if (dims == 3) { + strcpy(dimstr, NC_SPATIAL_STR); + } + else if (dims == 6) { + strcpy(dimstr, NC_VOIGT_STR); + } + else { + sprintf(dimstr, "vec%i", dims); + } + if (dims != 1) { + NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]), + dimstr ); + } + } + } + // default variables NCERRX( nc_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var), NC_SPATIAL_STR ); @@ -320,7 +340,6 @@ void DumpNetCDF::openfile() NCERRX( nc_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var), NC_CELL_ANGLES_STR); - // variables specified in the input file for (int i = 0; i < n_perat; i++) { NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var), perat[i].name ); @@ -359,10 +378,6 @@ void DumpNetCDF::openfile() // dimensions NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim), NC_FRAME_STR ); - NCERRX( nc_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim), - NC_SPATIAL_STR ); - NCERRX( nc_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim), - NC_VOIGT_STR ); NCERRX( nc_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim), NC_ATOM_STR ); NCERRX( nc_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim), @@ -372,13 +387,33 @@ void DumpNetCDF::openfile() NCERRX( nc_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), NC_LABEL_STR ); + for (int i = 0; i < n_perat; i++) { + int dims = perat[i].dims; + if (vector_dim[dims] < 0) { + char dimstr[1024]; + if (dims == 3) { + strcpy(dimstr, NC_SPATIAL_STR); + } + else if (dims == 6) { + strcpy(dimstr, NC_VOIGT_STR); + } + else { + sprintf(dimstr, "vec%i", dims); + } + if (dims != 1) { + NCERRX( nc_def_dim(ncid, dimstr, dims, &vector_dim[dims]), + dimstr ); + } + } + } + // default variables - dims[0] = spatial_dim; + dims[0] = vector_dim[3]; NCERRX( nc_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var), NC_SPATIAL_STR ); NCERRX( nc_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims, &cell_spatial_var), NC_CELL_SPATIAL_STR ); - dims[0] = spatial_dim; + dims[0] = vector_dim[3]; dims[1] = label_dim; NCERRX( nc_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, &cell_angular_var), NC_CELL_ANGULAR_STR ); @@ -400,7 +435,7 @@ void DumpNetCDF::openfile() // variables specified in the input file dims[0] = frame_dim; dims[1] = atom_dim; - dims[2] = spatial_dim; + dims[2] = vector_dim[3]; for (int i = 0; i < n_perat; i++) { nc_type xtype; @@ -419,53 +454,27 @@ void DumpNetCDF::openfile() if (perat[i].constant) { // this quantity will only be written once - if (perat[i].dims == 6) { - // this is a tensor in Voigt notation - dims[2] = Voigt_dim; - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1, - &perat[i].var), perat[i].name ); - } - else if (perat[i].dims == 3) { - // this is a vector, we need to store x-, y- and z-coordinates - dims[2] = spatial_dim; - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1, - &perat[i].var), perat[i].name ); - } - else if (perat[i].dims == 1) { + if (perat[i].dims == 1) { NCERRX( nc_def_var(ncid, perat[i].name, xtype, 1, dims+1, - &perat[i].var), perat[i].name ); + &perat[i].var), perat[i].name ); } else { - char errstr[1024]; - sprintf(errstr, "%i dimensions for '%s'. Not sure how to write " - "this to the NetCDF trajectory file.", perat[i].dims, - perat[i].name); - error->all(FLERR,errstr); + // this is a vector + dims[1] = vector_dim[perat[i].dims]; + NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1, + &perat[i].var), perat[i].name ); } } else { - if (perat[i].dims == 6) { - // this is a tensor in Voigt notation - dims[2] = Voigt_dim; - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims, - &perat[i].var), perat[i].name ); - } - else if (perat[i].dims == 3) { - // this is a vector, we need to store x-, y- and z-coordinates - dims[2] = spatial_dim; - NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims, - &perat[i].var), perat[i].name ); - } - else if (perat[i].dims == 1) { + if (perat[i].dims == 1) { NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims, &perat[i].var), perat[i].name ); } else { - char errstr[1024]; - sprintf(errstr, "%i dimensions for '%s'. Not sure how to write " - "this to the NetCDF trajectory file.", perat[i].dims, - perat[i].name); - error->all(FLERR,errstr); + // this is a vector + dims[2] = vector_dim[perat[i].dims]; + NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims, + &perat[i].var), perat[i].name ); } } } @@ -785,7 +794,7 @@ void DumpNetCDF::write_header(bigint n) cell_angles[2] = acos(cosgamma)*180.0/MY_PI; } - // Recent AMBER conventions say that nonperiodic boundaries should have + // Recent AMBER conventions say that non-periodic boundaries should have // 'cell_lengths' set to zero. for (int dim = 0; dim < 3; dim++) { if (!domain->periodicity[dim]) diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/USER-NETCDF/dump_netcdf.h index f97fd58409..f74e95be38 100644 --- a/src/USER-NETCDF/dump_netcdf.h +++ b/src/USER-NETCDF/dump_netcdf.h @@ -72,8 +72,7 @@ class DumpNetCDF : public DumpCustom { int ncid; int frame_dim; - int spatial_dim; - int Voigt_dim; + int vector_dim[DUMP_NC_MAX_DIMS]; int atom_dim; int cell_spatial_dim; int cell_angular_dim; diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp index 0a292d4721..026a6eaa3a 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp +++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp @@ -278,6 +278,9 @@ void DumpNetCDFMPIIO::openfile() // get total number of atoms ntotalgr = group->count(igroup); + for (int i = 0; i < DUMP_NC_MPIIO_MAX_DIMS; i++) { + vector_dim[i] = -1; + } if (append_flag && !multifile && access(filecurrent, F_OK) != -1) { // Fixme! Perform checks if dimensions and variables conform with @@ -294,9 +297,6 @@ void DumpNetCDFMPIIO::openfile() // dimensions NCERRX( ncmpi_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR ); - NCERRX( ncmpi_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim), - NC_SPATIAL_STR ); - NCERRX( ncmpi_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR ); NCERRX( ncmpi_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR ); NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim), NC_CELL_SPATIAL_STR ); @@ -304,6 +304,26 @@ void DumpNetCDFMPIIO::openfile() NC_CELL_ANGULAR_STR ); NCERRX( ncmpi_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR ); + for (int i = 0; i < n_perat; i++) { + int dims = perat[i].dims; + if (vector_dim[dims] < 0) { + char dimstr[1024]; + if (dims == 3) { + strcpy(dimstr, NC_SPATIAL_STR); + } + else if (dims == 6) { + strcpy(dimstr, NC_VOIGT_STR); + } + else { + sprintf(dimstr, "vec%i", dims); + } + if (dims != 1) { + NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dims]), + dimstr ); + } + } + } + // default variables NCERRX( ncmpi_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var), NC_SPATIAL_STR ); @@ -358,10 +378,6 @@ void DumpNetCDFMPIIO::openfile() // dimensions NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim), NC_FRAME_STR ); - NCERRX( ncmpi_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim), - NC_SPATIAL_STR ); - NCERRX( ncmpi_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim), - NC_VOIGT_STR ); NCERRX( ncmpi_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim), NC_ATOM_STR ); NCERRX( ncmpi_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim), @@ -371,13 +387,33 @@ void DumpNetCDFMPIIO::openfile() NCERRX( ncmpi_def_dim(ncid, NC_LABEL_STR, 10, &label_dim), NC_LABEL_STR ); + for (int i = 0; i < n_perat; i++) { + int dims = perat[i].dims; + if (vector_dim[dims] < 0) { + char dimstr[1024]; + if (dims == 3) { + strcpy(dimstr, NC_SPATIAL_STR); + } + else if (dims == 6) { + strcpy(dimstr, NC_VOIGT_STR); + } + else { + sprintf(dimstr, "vec%i", dims); + } + if (dims != 1) { + NCERRX( ncmpi_def_dim(ncid, dimstr, dims, &vector_dim[dims]), + dimstr ); + } + } + } + // default variables - dims[0] = spatial_dim; + dims[0] = vector_dim[3]; NCERRX( ncmpi_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var), NC_SPATIAL_STR ); NCERRX( ncmpi_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims, &cell_spatial_var), NC_CELL_SPATIAL_STR ); - dims[0] = spatial_dim; + dims[0] = vector_dim[3]; dims[1] = label_dim; NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims, &cell_angular_var), NC_CELL_ANGULAR_STR ); @@ -399,7 +435,7 @@ void DumpNetCDFMPIIO::openfile() // variables specified in the input file dims[0] = frame_dim; dims[1] = atom_dim; - dims[2] = spatial_dim; + dims[2] = vector_dim[3]; for (int i = 0; i < n_perat; i++) { nc_type xtype; @@ -416,28 +452,15 @@ void DumpNetCDFMPIIO::openfile() xtype = NC_FLOAT; } - if (perat[i].dims == 6) { - // this is a tensor in Voigt notation - dims[2] = Voigt_dim; - NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims, - &perat[i].var), perat[i].name ); - } - else if (perat[i].dims == 3) { - // this is a vector, we need to store x-, y- and z-coordinates - dims[2] = spatial_dim; - NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims, - &perat[i].var), perat[i].name ); - } - else if (perat[i].dims == 1) { + if (perat[i].dims == 1) { NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 2, dims, &perat[i].var), perat[i].name ); } else { - char errstr[1024]; - sprintf(errstr, "%i dimensions for '%s'. Not sure how to write " - "this to the NetCDF trajectory file.", perat[i].dims, - perat[i].name); - error->all(FLERR,errstr); + // this is a vector + dims[2] = vector_dim[perat[i].dims]; + NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims, + &perat[i].var), perat[i].name ); } } @@ -803,7 +826,7 @@ void DumpNetCDFMPIIO::write_time_and_cell() cell_angles[2] = acos(cosgamma)*180.0/MY_PI; } - // Recent AMBER conventions say that nonperiodic boundaries should have + // Recent AMBER conventions say that non-periodic boundaries should have // 'cell_lengths' set to zero. for (int dim = 0; dim < 3; dim++) { if (!domain->periodicity[dim]) diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/USER-NETCDF/dump_netcdf_mpiio.h index 330fa46c04..98ccb87927 100644 --- a/src/USER-NETCDF/dump_netcdf_mpiio.h +++ b/src/USER-NETCDF/dump_netcdf_mpiio.h @@ -71,8 +71,7 @@ class DumpNetCDFMPIIO : public DumpCustom { int ncid; int frame_dim; - int spatial_dim; - int Voigt_dim; + int vector_dim[DUMP_NC_MPIIO_MAX_DIMS]; int atom_dim; int cell_spatial_dim; int cell_angular_dim; diff --git a/src/USER-OMP/angle_charmm_omp.cpp b/src/USER-OMP/angle_charmm_omp.cpp index 1f24438df3..118ba00226 100644 --- a/src/USER-OMP/angle_charmm_omp.cpp +++ b/src/USER-OMP/angle_charmm_omp.cpp @@ -44,10 +44,7 @@ using namespace MathConst; void AngleCharmmOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_class2_omp.cpp b/src/USER-OMP/angle_class2_omp.cpp index bd13e20bcc..e072d136e1 100644 --- a/src/USER-OMP/angle_class2_omp.cpp +++ b/src/USER-OMP/angle_class2_omp.cpp @@ -44,10 +44,7 @@ AngleClass2OMP::AngleClass2OMP(class LAMMPS *lmp) void AngleClass2OMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_cosine_delta_omp.cpp b/src/USER-OMP/angle_cosine_delta_omp.cpp index b3bb3e1f8a..a6dfb20433 100644 --- a/src/USER-OMP/angle_cosine_delta_omp.cpp +++ b/src/USER-OMP/angle_cosine_delta_omp.cpp @@ -44,10 +44,7 @@ AngleCosineDeltaOMP::AngleCosineDeltaOMP(class LAMMPS *lmp) void AngleCosineDeltaOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_cosine_omp.cpp b/src/USER-OMP/angle_cosine_omp.cpp index 04b3870bc4..9097c8569c 100644 --- a/src/USER-OMP/angle_cosine_omp.cpp +++ b/src/USER-OMP/angle_cosine_omp.cpp @@ -44,10 +44,7 @@ AngleCosineOMP::AngleCosineOMP(class LAMMPS *lmp) void AngleCosineOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_cosine_periodic_omp.cpp b/src/USER-OMP/angle_cosine_periodic_omp.cpp index 8060ebec7b..3fcea7ad1d 100644 --- a/src/USER-OMP/angle_cosine_periodic_omp.cpp +++ b/src/USER-OMP/angle_cosine_periodic_omp.cpp @@ -46,10 +46,7 @@ AngleCosinePeriodicOMP::AngleCosinePeriodicOMP(class LAMMPS *lmp) void AngleCosinePeriodicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp index 3e00681ec9..6bd2feb023 100644 --- a/src/USER-OMP/angle_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_exp_omp.cpp @@ -44,10 +44,7 @@ AngleCosineShiftExpOMP::AngleCosineShiftExpOMP(class LAMMPS *lmp) void AngleCosineShiftExpOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_cosine_shift_omp.cpp b/src/USER-OMP/angle_cosine_shift_omp.cpp index 0ab3df4359..56486faac1 100644 --- a/src/USER-OMP/angle_cosine_shift_omp.cpp +++ b/src/USER-OMP/angle_cosine_shift_omp.cpp @@ -44,10 +44,7 @@ AngleCosineShiftOMP::AngleCosineShiftOMP(class LAMMPS *lmp) void AngleCosineShiftOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_cosine_squared_omp.cpp b/src/USER-OMP/angle_cosine_squared_omp.cpp index a1b1ffdf1a..6dd2a3bb3b 100644 --- a/src/USER-OMP/angle_cosine_squared_omp.cpp +++ b/src/USER-OMP/angle_cosine_squared_omp.cpp @@ -44,10 +44,7 @@ AngleCosineSquaredOMP::AngleCosineSquaredOMP(class LAMMPS *lmp) void AngleCosineSquaredOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_dipole_omp.cpp b/src/USER-OMP/angle_dipole_omp.cpp index 92a5ba092e..da2e819ee2 100644 --- a/src/USER-OMP/angle_dipole_omp.cpp +++ b/src/USER-OMP/angle_dipole_omp.cpp @@ -45,10 +45,7 @@ AngleDipoleOMP::AngleDipoleOMP(class LAMMPS *lmp) void AngleDipoleOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); if (!force->newton_bond) error->all(FLERR,"'newton' flag for bonded interactions must be 'on'"); diff --git a/src/USER-OMP/angle_fourier_omp.cpp b/src/USER-OMP/angle_fourier_omp.cpp index dfc713c372..b2f9b47e05 100644 --- a/src/USER-OMP/angle_fourier_omp.cpp +++ b/src/USER-OMP/angle_fourier_omp.cpp @@ -44,10 +44,7 @@ AngleFourierOMP::AngleFourierOMP(class LAMMPS *lmp) void AngleFourierOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_fourier_simple_omp.cpp b/src/USER-OMP/angle_fourier_simple_omp.cpp index dea7a88723..93532a30e5 100644 --- a/src/USER-OMP/angle_fourier_simple_omp.cpp +++ b/src/USER-OMP/angle_fourier_simple_omp.cpp @@ -44,10 +44,7 @@ AngleFourierSimpleOMP::AngleFourierSimpleOMP(class LAMMPS *lmp) void AngleFourierSimpleOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_harmonic_omp.cpp b/src/USER-OMP/angle_harmonic_omp.cpp index 0a71e5c9dd..824b254287 100644 --- a/src/USER-OMP/angle_harmonic_omp.cpp +++ b/src/USER-OMP/angle_harmonic_omp.cpp @@ -44,10 +44,7 @@ AngleHarmonicOMP::AngleHarmonicOMP(class LAMMPS *lmp) void AngleHarmonicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_quartic_omp.cpp b/src/USER-OMP/angle_quartic_omp.cpp index 97a9b14f1d..fff08ddb39 100644 --- a/src/USER-OMP/angle_quartic_omp.cpp +++ b/src/USER-OMP/angle_quartic_omp.cpp @@ -44,10 +44,7 @@ AngleQuarticOMP::AngleQuarticOMP(class LAMMPS *lmp) void AngleQuarticOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_sdk_omp.cpp b/src/USER-OMP/angle_sdk_omp.cpp index 9383a9af83..e8c762092c 100644 --- a/src/USER-OMP/angle_sdk_omp.cpp +++ b/src/USER-OMP/angle_sdk_omp.cpp @@ -46,10 +46,7 @@ AngleSDKOMP::AngleSDKOMP(class LAMMPS *lmp) void AngleSDKOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/angle_table_omp.cpp b/src/USER-OMP/angle_table_omp.cpp index c3d2307489..d9d80b744d 100644 --- a/src/USER-OMP/angle_table_omp.cpp +++ b/src/USER-OMP/angle_table_omp.cpp @@ -44,10 +44,7 @@ AngleTableOMP::AngleTableOMP(class LAMMPS *lmp) void AngleTableOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_class2_omp.cpp b/src/USER-OMP/bond_class2_omp.cpp index 1f9bcaa320..fdd73c20b0 100644 --- a/src/USER-OMP/bond_class2_omp.cpp +++ b/src/USER-OMP/bond_class2_omp.cpp @@ -40,10 +40,7 @@ BondClass2OMP::BondClass2OMP(class LAMMPS *lmp) void BondClass2OMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_fene_expand_omp.cpp b/src/USER-OMP/bond_fene_expand_omp.cpp index d002d454dd..a8eec11760 100644 --- a/src/USER-OMP/bond_fene_expand_omp.cpp +++ b/src/USER-OMP/bond_fene_expand_omp.cpp @@ -41,10 +41,7 @@ BondFENEExpandOMP::BondFENEExpandOMP(class LAMMPS *lmp) void BondFENEExpandOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_fene_omp.cpp b/src/USER-OMP/bond_fene_omp.cpp index ba958e1d6f..be7dcd4b49 100644 --- a/src/USER-OMP/bond_fene_omp.cpp +++ b/src/USER-OMP/bond_fene_omp.cpp @@ -41,10 +41,7 @@ BondFENEOMP::BondFENEOMP(class LAMMPS *lmp) void BondFENEOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_gromos_omp.cpp b/src/USER-OMP/bond_gromos_omp.cpp index bcfde436d5..8f0926c0e9 100644 --- a/src/USER-OMP/bond_gromos_omp.cpp +++ b/src/USER-OMP/bond_gromos_omp.cpp @@ -39,10 +39,7 @@ BondGromosOMP::BondGromosOMP(class LAMMPS *lmp) void BondGromosOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_harmonic_omp.cpp b/src/USER-OMP/bond_harmonic_omp.cpp index 46a93cbbdd..a3bb69c53c 100644 --- a/src/USER-OMP/bond_harmonic_omp.cpp +++ b/src/USER-OMP/bond_harmonic_omp.cpp @@ -39,10 +39,7 @@ BondHarmonicOMP::BondHarmonicOMP(class LAMMPS *lmp) void BondHarmonicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp index 5f39bb1b64..5c16e27a32 100644 --- a/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_cut_omp.cpp @@ -39,10 +39,7 @@ BondHarmonicShiftCutOMP::BondHarmonicShiftCutOMP(class LAMMPS *lmp) void BondHarmonicShiftCutOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_harmonic_shift_omp.cpp b/src/USER-OMP/bond_harmonic_shift_omp.cpp index 8c260bfc9b..39e957c137 100644 --- a/src/USER-OMP/bond_harmonic_shift_omp.cpp +++ b/src/USER-OMP/bond_harmonic_shift_omp.cpp @@ -39,10 +39,7 @@ BondHarmonicShiftOMP::BondHarmonicShiftOMP(class LAMMPS *lmp) void BondHarmonicShiftOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_morse_omp.cpp b/src/USER-OMP/bond_morse_omp.cpp index 0c3cded71a..c0203de0d6 100644 --- a/src/USER-OMP/bond_morse_omp.cpp +++ b/src/USER-OMP/bond_morse_omp.cpp @@ -39,10 +39,7 @@ BondMorseOMP::BondMorseOMP(class LAMMPS *lmp) void BondMorseOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_nonlinear_omp.cpp b/src/USER-OMP/bond_nonlinear_omp.cpp index cdc70eac8d..8fa3daf8ab 100644 --- a/src/USER-OMP/bond_nonlinear_omp.cpp +++ b/src/USER-OMP/bond_nonlinear_omp.cpp @@ -39,10 +39,7 @@ BondNonlinearOMP::BondNonlinearOMP(class LAMMPS *lmp) void BondNonlinearOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/bond_quartic_omp.cpp b/src/USER-OMP/bond_quartic_omp.cpp index b2b1696bb4..fd0ccaf79d 100644 --- a/src/USER-OMP/bond_quartic_omp.cpp +++ b/src/USER-OMP/bond_quartic_omp.cpp @@ -40,10 +40,7 @@ BondQuarticOMP::BondQuarticOMP(class LAMMPS *lmp) void BondQuarticOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/USER-OMP/bond_table_omp.cpp b/src/USER-OMP/bond_table_omp.cpp index 71dc237496..1616988385 100644 --- a/src/USER-OMP/bond_table_omp.cpp +++ b/src/USER-OMP/bond_table_omp.cpp @@ -39,10 +39,7 @@ BondTableOMP::BondTableOMP(class LAMMPS *lmp) void BondTableOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_charmm_omp.cpp b/src/USER-OMP/dihedral_charmm_omp.cpp index 1bed449774..b09863613e 100644 --- a/src/USER-OMP/dihedral_charmm_omp.cpp +++ b/src/USER-OMP/dihedral_charmm_omp.cpp @@ -45,10 +45,7 @@ DihedralCharmmOMP::DihedralCharmmOMP(class LAMMPS *lmp) void DihedralCharmmOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); // insure pair->ev_tally() will use 1-4 virial contribution diff --git a/src/USER-OMP/dihedral_class2_omp.cpp b/src/USER-OMP/dihedral_class2_omp.cpp index c7ae1572c7..03ac9d9bab 100644 --- a/src/USER-OMP/dihedral_class2_omp.cpp +++ b/src/USER-OMP/dihedral_class2_omp.cpp @@ -43,10 +43,7 @@ DihedralClass2OMP::DihedralClass2OMP(class LAMMPS *lmp) void DihedralClass2OMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp index c43b990028..c64cad9fc3 100644 --- a/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp +++ b/src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp @@ -43,10 +43,7 @@ DihedralCosineShiftExpOMP::DihedralCosineShiftExpOMP(class LAMMPS *lmp) void DihedralCosineShiftExpOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_fourier_omp.cpp b/src/USER-OMP/dihedral_fourier_omp.cpp index 319acb0beb..94bdae3795 100644 --- a/src/USER-OMP/dihedral_fourier_omp.cpp +++ b/src/USER-OMP/dihedral_fourier_omp.cpp @@ -44,10 +44,7 @@ DihedralFourierOMP::DihedralFourierOMP(class LAMMPS *lmp) void DihedralFourierOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_harmonic_omp.cpp b/src/USER-OMP/dihedral_harmonic_omp.cpp index bb659cf262..10ccbd3d9f 100644 --- a/src/USER-OMP/dihedral_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_harmonic_omp.cpp @@ -43,10 +43,7 @@ DihedralHarmonicOMP::DihedralHarmonicOMP(class LAMMPS *lmp) void DihedralHarmonicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_helix_omp.cpp b/src/USER-OMP/dihedral_helix_omp.cpp index e40f084e54..8c8e29cac0 100644 --- a/src/USER-OMP/dihedral_helix_omp.cpp +++ b/src/USER-OMP/dihedral_helix_omp.cpp @@ -46,10 +46,7 @@ DihedralHelixOMP::DihedralHelixOMP(class LAMMPS *lmp) void DihedralHelixOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp index e10fc7b94a..38961e1746 100644 --- a/src/USER-OMP/dihedral_multi_harmonic_omp.cpp +++ b/src/USER-OMP/dihedral_multi_harmonic_omp.cpp @@ -43,10 +43,7 @@ DihedralMultiHarmonicOMP::DihedralMultiHarmonicOMP(class LAMMPS *lmp) void DihedralMultiHarmonicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_nharmonic_omp.cpp b/src/USER-OMP/dihedral_nharmonic_omp.cpp index ad758fc892..e74238265d 100644 --- a/src/USER-OMP/dihedral_nharmonic_omp.cpp +++ b/src/USER-OMP/dihedral_nharmonic_omp.cpp @@ -43,10 +43,7 @@ DihedralNHarmonicOMP::DihedralNHarmonicOMP(class LAMMPS *lmp) void DihedralNHarmonicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_opls_omp.cpp b/src/USER-OMP/dihedral_opls_omp.cpp index 53fddf51cb..64eaffe6fe 100644 --- a/src/USER-OMP/dihedral_opls_omp.cpp +++ b/src/USER-OMP/dihedral_opls_omp.cpp @@ -44,10 +44,7 @@ DihedralOPLSOMP::DihedralOPLSOMP(class LAMMPS *lmp) void DihedralOPLSOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_quadratic_omp.cpp b/src/USER-OMP/dihedral_quadratic_omp.cpp index f6110cd505..8df622b847 100644 --- a/src/USER-OMP/dihedral_quadratic_omp.cpp +++ b/src/USER-OMP/dihedral_quadratic_omp.cpp @@ -44,10 +44,7 @@ DihedralQuadraticOMP::DihedralQuadraticOMP(class LAMMPS *lmp) void DihedralQuadraticOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/dihedral_table_omp.cpp b/src/USER-OMP/dihedral_table_omp.cpp index 1457f7b2bf..792ee90c26 100644 --- a/src/USER-OMP/dihedral_table_omp.cpp +++ b/src/USER-OMP/dihedral_table_omp.cpp @@ -111,10 +111,7 @@ DihedralTableOMP::DihedralTableOMP(class LAMMPS *lmp) void DihedralTableOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/ewald_omp.cpp b/src/USER-OMP/ewald_omp.cpp index 1fece5c31b..b56fc25142 100644 --- a/src/USER-OMP/ewald_omp.cpp +++ b/src/USER-OMP/ewald_omp.cpp @@ -61,9 +61,7 @@ void EwaldOMP::compute(int eflag, int vflag) { // set energy/virial flags - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // extend size of per-atom arrays if necessary diff --git a/src/USER-OMP/fix_gravity_omp.cpp b/src/USER-OMP/fix_gravity_omp.cpp index ef1a07aa5a..eae918ec52 100644 --- a/src/USER-OMP/fix_gravity_omp.cpp +++ b/src/USER-OMP/fix_gravity_omp.cpp @@ -42,7 +42,7 @@ FixGravityOMP::FixGravityOMP(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -void FixGravityOMP::post_force(int vflag) +void FixGravityOMP::post_force(int /* vflag */) { // update gravity due to variables @@ -106,7 +106,7 @@ void FixGravityOMP::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixGravityOMP::post_force_respa(int vflag, int ilevel, int iloop) +void FixGravityOMP::post_force_respa(int vflag, int ilevel, int /* iloop */) { if (ilevel == ilevel_respa) post_force(vflag); } diff --git a/src/USER-OMP/fix_nphug_omp.cpp b/src/USER-OMP/fix_nphug_omp.cpp deleted file mode 100644 index a2ed8eb7aa..0000000000 --- a/src/USER-OMP/fix_nphug_omp.cpp +++ /dev/null @@ -1,460 +0,0 @@ -/* ---------------------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#include -#include -#include -#include "fix_nphug_omp.h" -#include "modify.h" -#include "error.h" -#include "update.h" -#include "compute.h" -#include "force.h" -#include "domain.h" -#include "group.h" -#include "memory.h" -#include "comm.h" - -using namespace LAMMPS_NS; -using namespace FixConst; - -enum{ISO,ANISO,TRICLINIC}; // same as fix_nh.cpp - -/* ---------------------------------------------------------------------- */ - -FixNPHugOMP::FixNPHugOMP(LAMMPS *lmp, int narg, char **arg) : - FixNHOMP(lmp, narg, arg), pe(NULL), id_pe(NULL) -{ - - // Prevent masses from being updated every timestep - - eta_mass_flag = 0; - omega_mass_flag = 0; - etap_mass_flag = 0; - - // extend vector of base-class computes - - size_vector += 3; - - // turn off deviatoric flag and remove strain energy from vector - - deviatoric_flag = 0; - size_vector -= 1; - - // use initial state as reference state - - v0_set = p0_set = e0_set = 0; - - // check pressure settings - - if (p_start[0] != p_stop[0] || - p_start[1] != p_stop[1] || - p_start[2] != p_stop[2]) - error->all(FLERR,"Pstart and Pstop must have the same value"); - - // uniaxial = 0 means hydrostatic compression - // uniaxial = 1 means uniaxial compression - // in x, y, or z (idir = 0, 1, or 2) - - // isotropic hydrostatic compression - - if (pstyle == ISO) { - uniaxial = 0; - - // anisotropic compression - - } else if (pstyle == ANISO) { - - // anisotropic hydrostatic compression - - if (p_start[0] == p_start[1] && - p_start[0] == p_start[2] ) - uniaxial = 0; - - // uniaxial compression - - else if (p_flag[0] == 1 && p_flag[1] == 0 - && p_flag[2] == 0) { - uniaxial = 1; - idir = 0; - } else if (p_flag[0] == 0 && p_flag[1] == 1 - && p_flag[2] == 0) { - uniaxial = 1; - idir = 1; - } else if (p_flag[0] == 0 && p_flag[1] == 0 - && p_flag[2] == 1) { - uniaxial = 1; - idir = 2; - - } else error->all(FLERR,"Specified target stress must be uniaxial or hydrostatic"); - - // triclinic hydrostatic compression - - } else if (pstyle == TRICLINIC) { - - if (p_start[0] == p_start[1] && - p_start[0] == p_start[2] && - p_start[3] == 0.0 && - p_start[4] == 0.0 && - p_start[5] == 0.0 ) - uniaxial = 0; - - else error->all(FLERR,"For triclinic deformation, specified target stress must be hydrostatic"); - } - - if (!tstat_flag) - error->all(FLERR,"Temperature control must be used with fix nphug/omp"); - if (!pstat_flag) - error->all(FLERR,"Pressure control must be used with fix nphug/omp"); - - // create a new compute temp style - // id = fix-ID + temp - // compute group = all since pressure is always global (group all) - // and thus its KE/temperature contribution should use group all - - int n = strlen(id) + 6; - id_temp = new char[n]; - strcpy(id_temp,id); - strcat(id_temp,"_temp"); - - char **newarg = new char*[3]; - newarg[0] = id_temp; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "temp"; - - modify->add_compute(3,newarg); - delete [] newarg; - tcomputeflag = 1; - - // create a new compute pressure style - // id = fix-ID + press, compute group = all - // pass id_temp as 4th arg to pressure constructor - - n = strlen(id) + 7; - id_press = new char[n]; - strcpy(id_press,id); - strcat(id_press,"_press"); - - newarg = new char*[4]; - newarg[0] = id_press; - newarg[1] = (char *) "all"; - newarg[2] = (char *) "pressure"; - newarg[3] = id_temp; - modify->add_compute(4,newarg); - delete [] newarg; - pcomputeflag = 1; - - // create a new compute potential energy compute - - n = strlen(id) + 4; - id_pe = new char[n]; - strcpy(id_pe,id); - strcat(id_pe,"_pe"); - - newarg = new char*[3]; - newarg[0] = id_pe; - newarg[1] = (char*)"all"; - newarg[2] = (char*)"pe"; - modify->add_compute(3,newarg); - delete [] newarg; - peflag = 1; -} - -/* ---------------------------------------------------------------------- */ - -FixNPHugOMP::~FixNPHugOMP() -{ - - // temp and press computes handled by base class - // delete pe compute - - if (peflag) modify->delete_compute(id_pe); - delete [] id_pe; - -} - -/* ---------------------------------------------------------------------- */ - -void FixNPHugOMP::init() -{ - // Call base class init() - - FixNHOMP::init(); - - // set pe ptr - - int icompute = modify->find_compute(id_pe); - if (icompute < 0) - error->all(FLERR,"Potential energy ID for fix nvt/nph/npt does not exist"); - pe = modify->compute[icompute]; -} - - -/* ---------------------------------------------------------------------- - compute initial state before integrator starts -------------------------------------------------------------------------- */ - -void FixNPHugOMP::setup(int vflag) -{ - FixNHOMP::setup(vflag); - - if ( v0_set == 0 ) { - v0 = compute_vol(); - v0_set = 1; - } - - if ( p0_set == 0 ) { - p0_set = 1; - if (uniaxial == 1) - p0 = p_current[idir]; - else - p0 = (p_current[0]+p_current[1]+p_current[2])/3.0; - } - - if ( e0_set == 0 ) { - e0 = compute_etotal(); - e0_set = 1; - } - - double masstot = group->mass(igroup); - rho0 = nktv2p*force->mvv2e*masstot/v0; - - t_target = 0.01; - - pe->addstep(update->ntimestep+1); -} - -/* ---------------------------------------------------------------------- - compute target temperature and kinetic energy ------------------------------------------------------------------------*/ - -void FixNPHugOMP::compute_temp_target() -{ - t_target = t_current + compute_hugoniot(); - ke_target = tdof * boltz * t_target; - pe->addstep(update->ntimestep+1); -} - -/* ---------------------------------------------------------------------- */ - -double FixNPHugOMP::compute_etotal() -{ - double epot,ekin,etot; - epot = pe->compute_scalar(); - if (thermo_energy) epot -= compute_scalar(); - ekin = temperature->compute_scalar(); - ekin *= 0.5 * tdof * force->boltz; - etot = epot+ekin; - return etot; -} - -/* ---------------------------------------------------------------------- */ - -double FixNPHugOMP::compute_vol() -{ - if (domain->dimension == 3) - return domain->xprd * domain->yprd * domain->zprd; - else - return domain->xprd * domain->yprd; -} - -/* ---------------------------------------------------------------------- - Computes the deviation of the current point - from the Hugoniot in temperature units. -------------------------------------------------------------------------- */ - -double FixNPHugOMP::compute_hugoniot() -{ - double v,e,p; - double dhugo; - - e = compute_etotal(); - - temperature->compute_vector(); - - - if (uniaxial == 1) { - pressure->compute_vector(); - p = pressure->vector[idir]; - } else - p = pressure->compute_scalar(); - - v = compute_vol(); - - dhugo = (0.5 * (p + p0 ) * ( v0 - v)) / - force->nktv2p + e0 - e; - - dhugo /= tdof * boltz; - - return dhugo; -} - -/* ---------------------------------------------------------------------- - Compute shock velocity is distance/time units -------------------------------------------------------------------------- */ - -double FixNPHugOMP::compute_us() -{ - double v,p; - double eps,us; - - temperature->compute_vector(); - - if (uniaxial == 1) { - pressure->compute_vector(); - p = pressure->vector[idir]; - } else - p = pressure->compute_scalar(); - - v = compute_vol(); - - // Us^2 = (p-p0)/(rho0*eps) - - eps = 1.0 - v/v0; - if (eps < 1.0e-10) us = 0.0; - else if (p < p0) us = 0.0; - else us = sqrt((p-p0)/(rho0*eps)); - - return us; -} - -/* ---------------------------------------------------------------------- - Compute particle velocity is distance/time units -------------------------------------------------------------------------- */ - -double FixNPHugOMP::compute_up() -{ - double v; - double eps,us,up; - - v = compute_vol(); - us = compute_us(); - - // u = eps*Us - - eps = 1.0 - v/v0; - up = us*eps; - - return up; -} - -// look for index in local class -// if index not found, look in base class - -double FixNPHugOMP::compute_vector(int n) -{ - int ilen; - - // n = 0: Hugoniot energy difference (temperature units) - - ilen = 1; - if (n < ilen) return compute_hugoniot(); - n -= ilen; - - // n = 1: Shock velocity - - ilen = 1; - if (n < ilen) return compute_us(); - n -= ilen; - - // n = 2: Particle velocity - - ilen = 1; - if (n < ilen) return compute_up(); - n -= ilen; - - // index not found, look in base class - - return FixNHOMP::compute_vector(n); -} - -/* ---------------------------------------------------------------------- - pack restart data -------------------------------------------------------------------------- */ - -int FixNPHugOMP::pack_restart_data(double *list) -{ - int n = 0; - - list[n++] = e0; - list[n++] = v0; - list[n++] = p0; - - // call the base class function - - n += FixNHOMP::pack_restart_data(list+n); - - return n; -} - -/* ---------------------------------------------------------------------- - calculate the number of data to be packed -------------------------------------------------------------------------- */ - -int FixNPHugOMP::size_restart_global() -{ - int nsize = 3; - - // call the base class function - - nsize += FixNHOMP::size_restart_global(); - - return nsize; -} - -/* ---------------------------------------------------------------------- - use state info from restart file to restart the Fix -------------------------------------------------------------------------- */ - -void FixNPHugOMP::restart(char *buf) -{ - int n = 0; - double *list = (double *) buf; - e0 = list[n++]; - v0 = list[n++]; - p0 = list[n++]; - - e0_set = 1; - v0_set = 1; - p0_set = 1; - - // call the base class function - - buf += n*sizeof(double); - FixNHOMP::restart(buf); - -} - -/* ---------------------------------------------------------------------- */ - -int FixNPHugOMP::modify_param(int narg, char **arg) -{ - if (strcmp(arg[0],"e0") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix nphug/omp command"); - e0 = force->numeric(FLERR,arg[1]); - e0_set = 1; - return 2; - } else if (strcmp(arg[0],"v0") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix nphug/omp command"); - v0 = force->numeric(FLERR,arg[1]); - v0_set = 1; - return 2; - } else if (strcmp(arg[0],"p0") == 0) { - if (narg < 2) error->all(FLERR,"Illegal fix nphug/omp command"); - p0 = force->numeric(FLERR,arg[1]); - p0_set = 1; - return 2; - } - - return 0; -} diff --git a/src/USER-OMP/fix_nphug_omp.h b/src/USER-OMP/fix_nphug_omp.h deleted file mode 100644 index 4a4db63440..0000000000 --- a/src/USER-OMP/fix_nphug_omp.h +++ /dev/null @@ -1,98 +0,0 @@ -/* -*- c++ -*- ---------------------------------------------------------- - LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator - http://lammps.sandia.gov, Sandia National Laboratories - Steve Plimpton, sjplimp@sandia.gov - - Copyright (2003) Sandia Corporation. Under the terms of Contract - DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed under - the GNU General Public License. - - See the README file in the top-level LAMMPS directory. -------------------------------------------------------------------------- */ - -#ifdef FIX_CLASS - -FixStyle(nphug/omp,FixNPHugOMP) - -#else - -#ifndef LMP_FIX_NPHUG_OMP_H -#define LMP_FIX_NPHUG_OMP_H - -#include "fix_nh_omp.h" - -namespace LAMMPS_NS { - -class FixNPHugOMP : public FixNHOMP { - public: - FixNPHugOMP(class LAMMPS *, int, char **); - virtual ~FixNPHugOMP(); - - virtual void init(); - virtual void setup(int); - virtual int modify_param(int, char **); - virtual int pack_restart_data(double *); // pack restart data - virtual void restart(char *); - - private: - class Compute *pe; // PE compute pointer - - void compute_temp_target(); - double compute_vector(int); - double compute_etotal(); - double compute_vol(); - double compute_hugoniot(); - double compute_us(); - double compute_up(); - - char *id_pe; - int peflag; - int v0_set,p0_set,e0_set; - double v0,p0,e0,rho0; - int idir; - int uniaxial; - - int size_restart_global(); -}; - -} - -#endif -#endif - -/* ERROR/WARNING messages: - -E: Pstart and Pstop must have the same value - -Self-explanatory. - -E: Specified target stress must be uniaxial or hydrostatic - -Self-explanatory. - -E: For triclinic deformation, specified target stress must be hydrostatic - -Triclinic pressure control is allowed using the tri keyword, but -non-hydrostatic pressure control can not be used in this case. - -E: Temperature control must be used with fix nphug - -The temp keyword must be provided. - -E: Pressure control must be used with fix nphug - -A pressure control keyword (iso, aniso, tri, x, y, or z) must be -provided. - -E: Potential energy ID for fix nvt/nph/npt does not exist - -A compute for potential energy must be defined. - -E: Illegal ... command - -Self-explanatory. Check the input script syntax and compare to the -documentation for the command. You can use -echo screen as a -command-line option when running LAMMPS to see the offending line. - -*/ diff --git a/src/USER-OMP/fix_nve_omp.cpp b/src/USER-OMP/fix_nve_omp.cpp index 9e132aa539..c61ad7155c 100644 --- a/src/USER-OMP/fix_nve_omp.cpp +++ b/src/USER-OMP/fix_nve_omp.cpp @@ -29,7 +29,7 @@ FixNVEOMP::FixNVEOMP(LAMMPS *lmp, int narg, char **arg) : allow for both per-type and per-atom mass ------------------------------------------------------------------------- */ -void FixNVEOMP::initial_integrate(int vflag) +void FixNVEOMP::initial_integrate(int /* vflag */) { // update v and x of atoms in group diff --git a/src/USER-OMP/fix_nve_sphere_omp.cpp b/src/USER-OMP/fix_nve_sphere_omp.cpp index dd13e58d7c..2286120bee 100644 --- a/src/USER-OMP/fix_nve_sphere_omp.cpp +++ b/src/USER-OMP/fix_nve_sphere_omp.cpp @@ -37,7 +37,7 @@ enum{NODLM,DLM}; /* ---------------------------------------------------------------------- */ -void FixNVESphereOMP::initial_integrate(int vflag) +void FixNVESphereOMP::initial_integrate(int /* vflag */) { double * const * const x = atom->x; double * const * const v = atom->v; diff --git a/src/USER-OMP/fix_nvt_sllod_omp.cpp b/src/USER-OMP/fix_nvt_sllod_omp.cpp index 6ef1188d53..e439647c12 100644 --- a/src/USER-OMP/fix_nvt_sllod_omp.cpp +++ b/src/USER-OMP/fix_nvt_sllod_omp.cpp @@ -82,7 +82,7 @@ void FixNVTSllodOMP::init() int i; for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"deform") == 0) { + if (strncmp(modify->fix[i]->style,"deform",6) == 0) { if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP) error->all(FLERR,"Using fix nvt/sllod/omp with inconsistent fix " "deform remap option"); diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp index 8be54caada..a4587b1c14 100644 --- a/src/USER-OMP/fix_omp.cpp +++ b/src/USER-OMP/fix_omp.cpp @@ -80,7 +80,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg) if (nthreads < 1) error->all(FLERR,"Illegal number of OpenMP threads requested"); +#if defined(_OPENMP) int reset_thr = 0; +#endif if (nthreads != comm->nthreads) { #if defined(_OPENMP) reset_thr = 1; diff --git a/src/USER-OMP/fix_qeq_comb_omp.cpp b/src/USER-OMP/fix_qeq_comb_omp.cpp index b898fe3fe4..2f0a90a790 100644 --- a/src/USER-OMP/fix_qeq_comb_omp.cpp +++ b/src/USER-OMP/fix_qeq_comb_omp.cpp @@ -73,7 +73,7 @@ void FixQEQCombOMP::init() /* ---------------------------------------------------------------------- */ -void FixQEQCombOMP::post_force(int vflag) +void FixQEQCombOMP::post_force(int /* vflag */) { int i,ii,iloop,loopmax,inum,*ilist; double heatpq,qmass,dtq,dtq2; diff --git a/src/USER-OMP/fix_qeq_reax_omp.cpp b/src/USER-OMP/fix_qeq_reax_omp.cpp index a9ffb32d90..45da91305d 100644 --- a/src/USER-OMP/fix_qeq_reax_omp.cpp +++ b/src/USER-OMP/fix_qeq_reax_omp.cpp @@ -275,7 +275,7 @@ void FixQEqReaxOMP::init_storage() /* ---------------------------------------------------------------------- */ -void FixQEqReaxOMP::pre_force(int vflag) +void FixQEqReaxOMP::pre_force(int /* vflag */) { #ifdef OMP_TIMING diff --git a/src/USER-OMP/fix_wall_gran_omp.cpp b/src/USER-OMP/fix_wall_gran_omp.cpp index d45e748b6a..f015135385 100644 --- a/src/USER-OMP/fix_wall_gran_omp.cpp +++ b/src/USER-OMP/fix_wall_gran_omp.cpp @@ -37,7 +37,7 @@ FixWallGranOMP::FixWallGranOMP(LAMMPS *lmp, int narg, char **arg) : /* ---------------------------------------------------------------------- */ -void FixWallGranOMP::post_force(int vflag) +void FixWallGranOMP::post_force(int /* vflag */) { double vwall[3]; @@ -48,7 +48,7 @@ void FixWallGranOMP::post_force(int vflag) if (neighbor->ago == 0 && fix_rigid) { int tmp; - const int * const body = (const int * const) fix_rigid->extract("body",tmp); + const int * const body = (const int *) fix_rigid->extract("body",tmp); double *mass_body = (double *) fix_rigid->extract("masstotal",tmp); if (atom->nmax > nmax) { memory->destroy(mass_rigid); @@ -180,7 +180,7 @@ void FixWallGranOMP::post_force(int vflag) /* ---------------------------------------------------------------------- */ -void FixWallGranOMP::post_force_respa(int vflag, int ilevel, int iloop) +void FixWallGranOMP::post_force_respa(int vflag, int ilevel, int /* iloop */) { if (ilevel == nlevels_respa-1) post_force(vflag); } diff --git a/src/USER-OMP/hack_openmp_for_pgi.sh b/src/USER-OMP/hack_openmp_for_pgi.sh deleted file mode 100755 index a076fd1fcb..0000000000 --- a/src/USER-OMP/hack_openmp_for_pgi.sh +++ /dev/null @@ -1,8 +0,0 @@ -#!/bin/sh - -for f in *.h *.cpp -do \ - sed -e '/#pragma omp/s/^\(.*default\)(none)\(.*\)$/\1(shared)\2/' \ - -e '/#pragma omp/s/shared([a-z0-9,_]\+)//' \ - -i.bak $f -done diff --git a/src/USER-OMP/hack_openmp_for_pgi_gcc9.sh b/src/USER-OMP/hack_openmp_for_pgi_gcc9.sh new file mode 100755 index 0000000000..6f9f30cedd --- /dev/null +++ b/src/USER-OMP/hack_openmp_for_pgi_gcc9.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +# convert default(none) directives for OpenMP pragmas to default(shared) and remove shared() directive +# this allows compiling OpenMP pragmas in LAMMPS with compilers that don't support default(none) properly +# or require backward incompatible OpenMP 4 and OpenMP 5 semantics + +for f in *.h *.cpp +do \ + sed -e '/#pragma omp/s/^\(.*default\)(none)\(.*\)$/\1(shared)\2/' \ + -e '/#pragma omp/s/shared([a-z0-9,_]\+)//' \ + -i.bak $f +done diff --git a/src/USER-OMP/improper_class2_omp.cpp b/src/USER-OMP/improper_class2_omp.cpp index 7184cbeb69..c2b493f425 100644 --- a/src/USER-OMP/improper_class2_omp.cpp +++ b/src/USER-OMP/improper_class2_omp.cpp @@ -43,10 +43,7 @@ ImproperClass2OMP::ImproperClass2OMP(class LAMMPS *lmp) void ImproperClass2OMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/improper_cossq_omp.cpp b/src/USER-OMP/improper_cossq_omp.cpp index 022cfa6adf..3b328e5b78 100644 --- a/src/USER-OMP/improper_cossq_omp.cpp +++ b/src/USER-OMP/improper_cossq_omp.cpp @@ -43,10 +43,7 @@ ImproperCossqOMP::ImproperCossqOMP(class LAMMPS *lmp) void ImproperCossqOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/improper_cvff_omp.cpp b/src/USER-OMP/improper_cvff_omp.cpp index 78c5a55e05..fe1fc45bec 100644 --- a/src/USER-OMP/improper_cvff_omp.cpp +++ b/src/USER-OMP/improper_cvff_omp.cpp @@ -43,10 +43,7 @@ ImproperCvffOMP::ImproperCvffOMP(class LAMMPS *lmp) void ImproperCvffOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp index aed04003a5..b5af428cb9 100644 --- a/src/USER-OMP/improper_fourier_omp.cpp +++ b/src/USER-OMP/improper_fourier_omp.cpp @@ -43,10 +43,7 @@ ImproperFourierOMP::ImproperFourierOMP(class LAMMPS *lmp) void ImproperFourierOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; @@ -239,17 +236,17 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2, dahy = ary-c*hry; dahz = arz-c*hrz; - f2[0] = (dhay*vb1z - dhaz*vb1y)*rar; - f2[1] = (dhaz*vb1x - dhax*vb1z)*rar; - f2[2] = (dhax*vb1y - dhay*vb1x)*rar; + f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a; + f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a; + f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a; - f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar; - f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar; - f3[2] = (-dhax*vb2y + dhay*vb2x)*rar; + f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a; + f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a; + f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a; - f4[0] = dahx*rhr; - f4[1] = dahy*rhr; - f4[2] = dahz*rhr; + f4[0] = dahx*rhr*a; + f4[1] = dahy*rhr*a; + f4[2] = dahz*rhr*a; f1[0] = -(f2[0] + f3[0] + f4[0]); f1[1] = -(f2[1] + f3[1] + f4[1]); @@ -258,30 +255,31 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2, // apply force to each of 4 atoms if (NEWTON_BOND || i1 < nlocal) { - f[i1][0] += f1[0]*a; - f[i1][1] += f1[1]*a; - f[i1][2] += f1[2]*a; + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; } if (NEWTON_BOND || i2 < nlocal) { - f[i2][0] += f3[0]*a; - f[i2][1] += f3[1]*a; - f[i2][2] += f3[2]*a; + f[i2][0] += f3[0]; + f[i2][1] += f3[1]; + f[i2][2] += f3[2]; } if (NEWTON_BOND || i3 < nlocal) { - f[i3][0] += f2[0]*a; - f[i3][1] += f2[1]*a; - f[i3][2] += f2[2]*a; + f[i3][0] += f2[0]; + f[i3][1] += f2[1]; + f[i3][2] += f2[2]; } if (NEWTON_BOND || i4 < nlocal) { - f[i4][0] += f4[0]*a; - f[i4][1] += f4[1]*a; - f[i4][2] += f4[2]*a; + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; } if (EVFLAG) - ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4, - vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr); + ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4, + -vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z,thr); + } diff --git a/src/USER-OMP/improper_harmonic_omp.cpp b/src/USER-OMP/improper_harmonic_omp.cpp index 3f1895142d..6e02d0968e 100644 --- a/src/USER-OMP/improper_harmonic_omp.cpp +++ b/src/USER-OMP/improper_harmonic_omp.cpp @@ -43,10 +43,7 @@ ImproperHarmonicOMP::ImproperHarmonicOMP(class LAMMPS *lmp) void ImproperHarmonicOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/improper_ring_omp.cpp b/src/USER-OMP/improper_ring_omp.cpp index 7970de3839..e198b99337 100644 --- a/src/USER-OMP/improper_ring_omp.cpp +++ b/src/USER-OMP/improper_ring_omp.cpp @@ -45,10 +45,7 @@ ImproperRingOMP::ImproperRingOMP(class LAMMPS *lmp) void ImproperRingOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp index dc11f24a4d..ceaca35074 100644 --- a/src/USER-OMP/improper_umbrella_omp.cpp +++ b/src/USER-OMP/improper_umbrella_omp.cpp @@ -43,10 +43,7 @@ ImproperUmbrellaOMP::ImproperUmbrellaOMP(class LAMMPS *lmp) void ImproperUmbrellaOMP::compute(int eflag, int vflag) { - - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; @@ -212,17 +209,17 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr) dahy = ary-c*hry; dahz = arz-c*hrz; - f2[0] = (dhay*vb1z - dhaz*vb1y)*rar; - f2[1] = (dhaz*vb1x - dhax*vb1z)*rar; - f2[2] = (dhax*vb1y - dhay*vb1x)*rar; + f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a; + f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a; + f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a; - f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar; - f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar; - f3[2] = (-dhax*vb2y + dhay*vb2x)*rar; + f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a; + f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a; + f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a; - f4[0] = dahx*rhr; - f4[1] = dahy*rhr; - f4[2] = dahz*rhr; + f4[0] = dahx*rhr*a; + f4[1] = dahy*rhr*a; + f4[2] = dahz*rhr*a; f1[0] = -(f2[0] + f3[0] + f4[0]); f1[1] = -(f2[1] + f3[1] + f4[1]); @@ -231,27 +228,27 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr) // apply force to each of 4 atoms if (NEWTON_BOND || i1 < nlocal) { - f[i1].x += f1[0]*a; - f[i1].y += f1[1]*a; - f[i1].z += f1[2]*a; + f[i1].x += f1[0]; + f[i1].y += f1[1]; + f[i1].z += f1[2]; } if (NEWTON_BOND || i2 < nlocal) { - f[i2].x += f3[0]*a; - f[i2].y += f3[1]*a; - f[i2].z += f3[2]*a; + f[i2].x += f3[0]; + f[i2].y += f3[1]; + f[i2].z += f3[2]; } if (NEWTON_BOND || i3 < nlocal) { - f[i3].x += f2[0]*a; - f[i3].y += f2[1]*a; - f[i3].z += f2[2]*a; + f[i3].x += f2[0]; + f[i3].y += f2[1]; + f[i3].z += f2[2]; } if (NEWTON_BOND || i4 < nlocal) { - f[i4].x += f4[0]*a; - f[i4].y += f4[1]*a; - f[i4].z += f4[2]*a; + f[i4].x += f4[0]; + f[i4].y += f4[1]; + f[i4].z += f4[2]; } if (EVFLAG) { @@ -270,7 +267,7 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr) vb3y = x[i4].y - x[i3].y; vb3z = x[i4].z - x[i3].z; - ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4, + ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4, vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr); } } diff --git a/src/USER-OMP/msm_cg_omp.cpp b/src/USER-OMP/msm_cg_omp.cpp index eaff373742..8a920e05d5 100644 --- a/src/USER-OMP/msm_cg_omp.cpp +++ b/src/USER-OMP/msm_cg_omp.cpp @@ -90,9 +90,7 @@ void MSMCGOMP::compute(int eflag, int vflag) // set energy/virial flags - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = eflag_either = vflag_either = 0; + ev_init(eflag,vflag); // invoke allocate_peratom() if needed for first time @@ -199,7 +197,7 @@ void MSMCGOMP::compute(int eflag, int vflag) } - // compute direct interation for top grid level for nonperiodic + // compute direct interation for top grid level for non-periodic // and for second from top grid level for periodic if (active_flag[levels-1]) { diff --git a/src/USER-OMP/pair_adp_omp.cpp b/src/USER-OMP/pair_adp_omp.cpp index 264169773b..645d697994 100644 --- a/src/USER-OMP/pair_adp_omp.cpp +++ b/src/USER-OMP/pair_adp_omp.cpp @@ -39,9 +39,7 @@ PairADPOMP::PairADPOMP(LAMMPS *lmp) : void PairADPOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_agni_omp.cpp b/src/USER-OMP/pair_agni_omp.cpp index e8f003ea88..854bcbebf3 100644 --- a/src/USER-OMP/pair_agni_omp.cpp +++ b/src/USER-OMP/pair_agni_omp.cpp @@ -42,9 +42,7 @@ PairAGNIOMP::PairAGNIOMP(LAMMPS *lmp) : void PairAGNIOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_airebo_omp.cpp b/src/USER-OMP/pair_airebo_omp.cpp index 8decda7cab..bed6c81ee4 100644 --- a/src/USER-OMP/pair_airebo_omp.cpp +++ b/src/USER-OMP/pair_airebo_omp.cpp @@ -49,9 +49,7 @@ void PairAIREBOOMP::compute(int eflag, int vflag) { double pv0=0.0,pv1=0.0,pv2=0.0; - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); REBO_neigh_thr(); @@ -1869,7 +1867,7 @@ there probably also need to be performed here. */ -double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij_mod[3], double rijmag_mod, +double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double /* rij_mod */[3], double rijmag_mod, double VA, double rij[3], double rijmag, int vflag_atom, ThrData * const thr) { diff --git a/src/USER-OMP/pair_beck_omp.cpp b/src/USER-OMP/pair_beck_omp.cpp index 1494ec2987..90c3777932 100644 --- a/src/USER-OMP/pair_beck_omp.cpp +++ b/src/USER-OMP/pair_beck_omp.cpp @@ -38,9 +38,7 @@ PairBeckOMP::PairBeckOMP(LAMMPS *lmp) : void PairBeckOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_born_coul_long_omp.cpp b/src/USER-OMP/pair_born_coul_long_omp.cpp index f198184406..a5df8f8182 100644 --- a/src/USER-OMP/pair_born_coul_long_omp.cpp +++ b/src/USER-OMP/pair_born_coul_long_omp.cpp @@ -44,9 +44,7 @@ PairBornCoulLongOMP::PairBornCoulLongOMP(LAMMPS *lmp) : void PairBornCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_born_coul_msm_omp.cpp b/src/USER-OMP/pair_born_coul_msm_omp.cpp index 1b4757359f..ad1e5e63cd 100644 --- a/src/USER-OMP/pair_born_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_born_coul_msm_omp.cpp @@ -41,9 +41,7 @@ void PairBornCoulMSMOMP::compute(int eflag, int vflag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' " "with OMP MSM Pair styles"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_born_coul_wolf_omp.cpp b/src/USER-OMP/pair_born_coul_wolf_omp.cpp index 7904181ba5..567eddc9cb 100644 --- a/src/USER-OMP/pair_born_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_born_coul_wolf_omp.cpp @@ -38,9 +38,7 @@ PairBornCoulWolfOMP::PairBornCoulWolfOMP(LAMMPS *lmp) : void PairBornCoulWolfOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_born_omp.cpp b/src/USER-OMP/pair_born_omp.cpp index f75d4b9f35..fce2013745 100644 --- a/src/USER-OMP/pair_born_omp.cpp +++ b/src/USER-OMP/pair_born_omp.cpp @@ -36,9 +36,7 @@ PairBornOMP::PairBornOMP(LAMMPS *lmp) : void PairBornOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_brownian_omp.cpp b/src/USER-OMP/pair_brownian_omp.cpp index b1af821bba..cef9fb0955 100644 --- a/src/USER-OMP/pair_brownian_omp.cpp +++ b/src/USER-OMP/pair_brownian_omp.cpp @@ -68,9 +68,7 @@ PairBrownianOMP::~PairBrownianOMP() void PairBrownianOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int inum = list->inum; diff --git a/src/USER-OMP/pair_brownian_poly_omp.cpp b/src/USER-OMP/pair_brownian_poly_omp.cpp index 2e677ed535..239a820242 100644 --- a/src/USER-OMP/pair_brownian_poly_omp.cpp +++ b/src/USER-OMP/pair_brownian_poly_omp.cpp @@ -68,9 +68,7 @@ PairBrownianPolyOMP::~PairBrownianPolyOMP() void PairBrownianPolyOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int inum = list->inum; diff --git a/src/USER-OMP/pair_buck_coul_cut_omp.cpp b/src/USER-OMP/pair_buck_coul_cut_omp.cpp index 8fa6be06b2..b9b77dc2b6 100644 --- a/src/USER-OMP/pair_buck_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_cut_omp.cpp @@ -36,9 +36,7 @@ PairBuckCoulCutOMP::PairBuckCoulCutOMP(LAMMPS *lmp) : void PairBuckCoulCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_buck_coul_long_omp.cpp b/src/USER-OMP/pair_buck_coul_long_omp.cpp index 4d30eb3e82..951ba0688c 100644 --- a/src/USER-OMP/pair_buck_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_long_omp.cpp @@ -44,9 +44,7 @@ PairBuckCoulLongOMP::PairBuckCoulLongOMP(LAMMPS *lmp) : void PairBuckCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_buck_coul_msm_omp.cpp b/src/USER-OMP/pair_buck_coul_msm_omp.cpp index a8bca36394..6226191627 100644 --- a/src/USER-OMP/pair_buck_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_buck_coul_msm_omp.cpp @@ -41,9 +41,7 @@ void PairBuckCoulMSMOMP::compute(int eflag, int vflag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' " "with OMP MSM Pair styles"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp index acb95ab76c..20d380a464 100644 --- a/src/USER-OMP/pair_buck_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_buck_long_coul_long_omp.cpp @@ -46,9 +46,8 @@ PairBuckLongCoulLongOMP::PairBuckLongCoulLongOMP(LAMMPS *lmp) : void PairBuckLongCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); + const int order1 = ewald_order&(1<<1); const int order6 = ewald_order&(1<<6); diff --git a/src/USER-OMP/pair_buck_omp.cpp b/src/USER-OMP/pair_buck_omp.cpp index f3fa32a5ea..cc7e81b9c5 100644 --- a/src/USER-OMP/pair_buck_omp.cpp +++ b/src/USER-OMP/pair_buck_omp.cpp @@ -36,9 +36,7 @@ PairBuckOMP::PairBuckOMP(LAMMPS *lmp) : void PairBuckOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_colloid_omp.cpp b/src/USER-OMP/pair_colloid_omp.cpp index 536b7644bd..64613cb31d 100644 --- a/src/USER-OMP/pair_colloid_omp.cpp +++ b/src/USER-OMP/pair_colloid_omp.cpp @@ -39,9 +39,7 @@ PairColloidOMP::PairColloidOMP(LAMMPS *lmp) : void PairColloidOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_comb_omp.cpp b/src/USER-OMP/pair_comb_omp.cpp index 8a77ab955f..be641dd0b9 100644 --- a/src/USER-OMP/pair_comb_omp.cpp +++ b/src/USER-OMP/pair_comb_omp.cpp @@ -41,9 +41,7 @@ PairCombOMP::PairCombOMP(LAMMPS *lmp) : void PairCombOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_cut_omp.cpp b/src/USER-OMP/pair_coul_cut_omp.cpp index b9ac72421e..056daf210a 100644 --- a/src/USER-OMP/pair_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_omp.cpp @@ -36,9 +36,7 @@ PairCoulCutOMP::PairCoulCutOMP(LAMMPS *lmp) : void PairCoulCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_coul_cut_soft_omp.cpp index c7e8c5e560..70997da62b 100644 --- a/src/USER-OMP/pair_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_cut_soft_omp.cpp @@ -36,9 +36,7 @@ PairCoulCutSoftOMP::PairCoulCutSoftOMP(LAMMPS *lmp) : void PairCoulCutSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_debye_omp.cpp b/src/USER-OMP/pair_coul_debye_omp.cpp index cb7a9025ce..d202e314bf 100644 --- a/src/USER-OMP/pair_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_coul_debye_omp.cpp @@ -36,9 +36,7 @@ PairCoulDebyeOMP::PairCoulDebyeOMP(LAMMPS *lmp) : void PairCoulDebyeOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_diel_omp.cpp b/src/USER-OMP/pair_coul_diel_omp.cpp index c75e36b55e..f2bb6a46bf 100644 --- a/src/USER-OMP/pair_coul_diel_omp.cpp +++ b/src/USER-OMP/pair_coul_diel_omp.cpp @@ -36,9 +36,7 @@ PairCoulDielOMP::PairCoulDielOMP(LAMMPS *lmp) : void PairCoulDielOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_dsf_omp.cpp b/src/USER-OMP/pair_coul_dsf_omp.cpp index 740e3242ad..217fb844c3 100644 --- a/src/USER-OMP/pair_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_coul_dsf_omp.cpp @@ -46,9 +46,7 @@ PairCoulDSFOMP::PairCoulDSFOMP(LAMMPS *lmp) : void PairCoulDSFOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_long_omp.cpp b/src/USER-OMP/pair_coul_long_omp.cpp index eb74bb9615..1e3170c73c 100644 --- a/src/USER-OMP/pair_coul_long_omp.cpp +++ b/src/USER-OMP/pair_coul_long_omp.cpp @@ -45,9 +45,7 @@ PairCoulLongOMP::PairCoulLongOMP(LAMMPS *lmp) : void PairCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_long_soft_omp.cpp b/src/USER-OMP/pair_coul_long_soft_omp.cpp index 4e65483a17..dd1fc1030d 100644 --- a/src/USER-OMP/pair_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_coul_long_soft_omp.cpp @@ -44,9 +44,7 @@ PairCoulLongSoftOMP::PairCoulLongSoftOMP(LAMMPS *lmp) : void PairCoulLongSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_msm_omp.cpp b/src/USER-OMP/pair_coul_msm_omp.cpp index f4bc279532..9b50b86954 100644 --- a/src/USER-OMP/pair_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_coul_msm_omp.cpp @@ -42,9 +42,7 @@ void PairCoulMSMOMP::compute(int eflag, int vflag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' with " "OMP MSM Pair styles"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_coul_wolf_omp.cpp b/src/USER-OMP/pair_coul_wolf_omp.cpp index bc86cdbf5d..0913a2b188 100644 --- a/src/USER-OMP/pair_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_coul_wolf_omp.cpp @@ -38,9 +38,7 @@ PairCoulWolfOMP::PairCoulWolfOMP(LAMMPS *lmp) : void PairCoulWolfOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_dpd_omp.cpp b/src/USER-OMP/pair_dpd_omp.cpp index 29b5568def..77db3d9183 100644 --- a/src/USER-OMP/pair_dpd_omp.cpp +++ b/src/USER-OMP/pair_dpd_omp.cpp @@ -55,9 +55,7 @@ PairDPDOMP::~PairDPDOMP() void PairDPDOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int inum = list->inum; diff --git a/src/USER-OMP/pair_dpd_tstat_omp.cpp b/src/USER-OMP/pair_dpd_tstat_omp.cpp index 0a9e96fa0c..d7233a16c5 100644 --- a/src/USER-OMP/pair_dpd_tstat_omp.cpp +++ b/src/USER-OMP/pair_dpd_tstat_omp.cpp @@ -55,9 +55,7 @@ PairDPDTstatOMP::~PairDPDTstatOMP() void PairDPDTstatOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int inum = list->inum; diff --git a/src/USER-OMP/pair_eam_cd_omp.cpp b/src/USER-OMP/pair_eam_cd_omp.cpp index 68c01c83d2..51b83f3bf5 100644 --- a/src/USER-OMP/pair_eam_cd_omp.cpp +++ b/src/USER-OMP/pair_eam_cd_omp.cpp @@ -55,9 +55,7 @@ PairEAMCDOMP::PairEAMCDOMP(LAMMPS *lmp, int _cdeamVersion) : void PairEAMCDOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_eam_omp.cpp b/src/USER-OMP/pair_eam_omp.cpp index 492ff79769..99417f27da 100644 --- a/src/USER-OMP/pair_eam_omp.cpp +++ b/src/USER-OMP/pair_eam_omp.cpp @@ -39,9 +39,7 @@ PairEAMOMP::PairEAMOMP(LAMMPS *lmp) : void PairEAMOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_edip_omp.cpp b/src/USER-OMP/pair_edip_omp.cpp index 3392160d92..144d893c1c 100644 --- a/src/USER-OMP/pair_edip_omp.cpp +++ b/src/USER-OMP/pair_edip_omp.cpp @@ -43,9 +43,7 @@ PairEDIPOMP::PairEDIPOMP(LAMMPS *lmp) : void PairEDIPOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_eim_omp.cpp b/src/USER-OMP/pair_eim_omp.cpp index 6a3e0bc529..2ecd6f8ec7 100644 --- a/src/USER-OMP/pair_eim_omp.cpp +++ b/src/USER-OMP/pair_eim_omp.cpp @@ -39,9 +39,7 @@ PairEIMOMP::PairEIMOMP(LAMMPS *lmp) : void PairEIMOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_gauss_cut_omp.cpp b/src/USER-OMP/pair_gauss_cut_omp.cpp index 9a41dcc87e..928312240b 100644 --- a/src/USER-OMP/pair_gauss_cut_omp.cpp +++ b/src/USER-OMP/pair_gauss_cut_omp.cpp @@ -36,9 +36,7 @@ PairGaussCutOMP::PairGaussCutOMP(LAMMPS *lmp) : void PairGaussCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_gauss_omp.cpp b/src/USER-OMP/pair_gauss_omp.cpp index 059c77c677..159f1c3e31 100644 --- a/src/USER-OMP/pair_gauss_omp.cpp +++ b/src/USER-OMP/pair_gauss_omp.cpp @@ -37,9 +37,7 @@ PairGaussOMP::PairGaussOMP(LAMMPS *lmp) : void PairGaussOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_gayberne_omp.cpp b/src/USER-OMP/pair_gayberne_omp.cpp index 5b0ff67afe..cfa05745ff 100644 --- a/src/USER-OMP/pair_gayberne_omp.cpp +++ b/src/USER-OMP/pair_gayberne_omp.cpp @@ -38,9 +38,7 @@ PairGayBerneOMP::PairGayBerneOMP(LAMMPS *lmp) : void PairGayBerneOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_gran_hertz_history_omp.cpp b/src/USER-OMP/pair_gran_hertz_history_omp.cpp index 9854b8f9ff..271c70e9b9 100644 --- a/src/USER-OMP/pair_gran_hertz_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hertz_history_omp.cpp @@ -40,9 +40,7 @@ PairGranHertzHistoryOMP::PairGranHertzHistoryOMP(LAMMPS *lmp) : void PairGranHertzHistoryOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_gran_hooke_history_omp.cpp b/src/USER-OMP/pair_gran_hooke_history_omp.cpp index 2327fc815a..9a0e8aab76 100644 --- a/src/USER-OMP/pair_gran_hooke_history_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_history_omp.cpp @@ -41,9 +41,7 @@ PairGranHookeHistoryOMP::PairGranHookeHistoryOMP(LAMMPS *lmp) : void PairGranHookeHistoryOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int shearupdate = (update->setupflag) ? 0 : 1; diff --git a/src/USER-OMP/pair_gran_hooke_omp.cpp b/src/USER-OMP/pair_gran_hooke_omp.cpp index 876fe9c4de..d226ceaa14 100644 --- a/src/USER-OMP/pair_gran_hooke_omp.cpp +++ b/src/USER-OMP/pair_gran_hooke_omp.cpp @@ -38,9 +38,7 @@ PairGranHookeOMP::PairGranHookeOMP(LAMMPS *lmp) : void PairGranHookeOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp index ec9da78b16..ea56ff51b5 100644 --- a/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp @@ -57,9 +57,7 @@ PairHbondDreidingLJOMP::~PairHbondDreidingLJOMP() void PairHbondDreidingLJOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp index 4965be43b8..1cff2de3b2 100644 --- a/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp +++ b/src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp @@ -57,9 +57,7 @@ PairHbondDreidingMorseOMP::~PairHbondDreidingMorseOMP() void PairHbondDreidingMorseOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj96_cut_omp.cpp b/src/USER-OMP/pair_lj96_cut_omp.cpp index 1cca674369..9ba8e09a54 100644 --- a/src/USER-OMP/pair_lj96_cut_omp.cpp +++ b/src/USER-OMP/pair_lj96_cut_omp.cpp @@ -37,9 +37,7 @@ PairLJ96CutOMP::PairLJ96CutOMP(LAMMPS *lmp) : void PairLJ96CutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp index 2f72f3851e..3dc9b77c0f 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp @@ -36,9 +36,7 @@ PairLJCharmmCoulCharmmImplicitOMP::PairLJCharmmCoulCharmmImplicitOMP(LAMMPS *lmp void PairLJCharmmCoulCharmmImplicitOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp index b61a80a178..f9230996f0 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp @@ -36,9 +36,7 @@ PairLJCharmmCoulCharmmOMP::PairLJCharmmCoulCharmmOMP(LAMMPS *lmp) : void PairLJCharmmCoulCharmmOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp index 5351ab9aea..4bdaa3519f 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp @@ -37,9 +37,7 @@ PairLJCharmmCoulLongOMP::PairLJCharmmCoulLongOMP(LAMMPS *lmp) : void PairLJCharmmCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp index ea5d739e49..1f6daf052c 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_long_soft_omp.cpp @@ -37,9 +37,7 @@ PairLJCharmmCoulLongSoftOMP::PairLJCharmmCoulLongSoftOMP(LAMMPS *lmp) : void PairLJCharmmCoulLongSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp index 3baa9597a8..eab62d919e 100644 --- a/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp @@ -42,9 +42,7 @@ void PairLJCharmmCoulMSMOMP::compute(int eflag, int vflag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' " "with OMP MSM Pair styles"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp index 38390918c7..b9ffad134b 100644 --- a/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp @@ -36,9 +36,7 @@ PairLJClass2CoulCutOMP::PairLJClass2CoulCutOMP(LAMMPS *lmp) : void PairLJClass2CoulCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp index f47672c9bc..e5995363ad 100644 --- a/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_coul_long_omp.cpp @@ -44,9 +44,7 @@ PairLJClass2CoulLongOMP::PairLJClass2CoulLongOMP(LAMMPS *lmp) : void PairLJClass2CoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_class2_omp.cpp b/src/USER-OMP/pair_lj_class2_omp.cpp index 7ab4626c3e..67715572ae 100644 --- a/src/USER-OMP/pair_lj_class2_omp.cpp +++ b/src/USER-OMP/pair_lj_class2_omp.cpp @@ -36,9 +36,7 @@ PairLJClass2OMP::PairLJClass2OMP(LAMMPS *lmp) : void PairLJClass2OMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cubic_omp.cpp b/src/USER-OMP/pair_lj_cubic_omp.cpp index 3e8adb33b8..5fa4f92f45 100644 --- a/src/USER-OMP/pair_lj_cubic_omp.cpp +++ b/src/USER-OMP/pair_lj_cubic_omp.cpp @@ -37,9 +37,7 @@ PairLJCubicOMP::PairLJCubicOMP(LAMMPS *lmp) : void PairLJCubicOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp index ea560a09bf..69cc2d3042 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp @@ -36,9 +36,7 @@ PairLJCutCoulCutOMP::PairLJCutCoulCutOMP(LAMMPS *lmp) : void PairLJCutCoulCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp index 4ef12bb1bb..5dfa414bd4 100644 --- a/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_cut_soft_omp.cpp @@ -36,9 +36,7 @@ PairLJCutCoulCutSoftOMP::PairLJCutCoulCutSoftOMP(LAMMPS *lmp) : void PairLJCutCoulCutSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp index 9163e98edd..4644e565a7 100644 --- a/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp @@ -36,9 +36,7 @@ PairLJCutCoulDebyeOMP::PairLJCutCoulDebyeOMP(LAMMPS *lmp) : void PairLJCutCoulDebyeOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp index 9d9c098f87..13d877ec07 100644 --- a/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_dsf_omp.cpp @@ -46,9 +46,7 @@ PairLJCutCoulDSFOMP::PairLJCutCoulDSFOMP(LAMMPS *lmp) : void PairLJCutCoulDSFOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp index d2eaae4ca4..d4fe5fd2a7 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_omp.cpp @@ -45,9 +45,7 @@ PairLJCutCoulLongOMP::PairLJCutCoulLongOMP(LAMMPS *lmp) : void PairLJCutCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp index 725bfe4724..4a0ef73f60 100644 --- a/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_long_soft_omp.cpp @@ -45,9 +45,7 @@ PairLJCutCoulLongSoftOMP::PairLJCutCoulLongSoftOMP(LAMMPS *lmp) : void PairLJCutCoulLongSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp index 234204af93..4c34b73622 100644 --- a/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp @@ -42,9 +42,7 @@ void PairLJCutCoulMSMOMP::compute(int eflag, int vflag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' " "with OMP MSM Pair styles"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp index 36ef9d54f9..052be0a2fa 100644 --- a/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_coul_wolf_omp.cpp @@ -38,9 +38,7 @@ PairLJCutCoulWolfOMP::PairLJCutCoulWolfOMP(LAMMPS *lmp) : void PairLJCutCoulWolfOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp index d4145d9835..55359db3be 100644 --- a/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp @@ -36,9 +36,7 @@ PairLJCutDipoleCutOMP::PairLJCutDipoleCutOMP(LAMMPS *lmp) : void PairLJCutDipoleCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_omp.cpp index 319257b56b..34068185d2 100644 --- a/src/USER-OMP/pair_lj_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_omp.cpp @@ -37,9 +37,7 @@ PairLJCutOMP::PairLJCutOMP(LAMMPS *lmp) : void PairLJCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_soft_omp.cpp index 7698f19b95..9bbe58146c 100644 --- a/src/USER-OMP/pair_lj_cut_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_soft_omp.cpp @@ -37,9 +37,7 @@ PairLJCutSoftOMP::PairLJCutSoftOMP(LAMMPS *lmp) : void PairLJCutSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp index 536d5bcb86..85cab4fe7b 100644 --- a/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_thole_long_omp.cpp @@ -57,9 +57,7 @@ PairLJCutTholeLongOMP::PairLJCutTholeLongOMP(LAMMPS *lmp) : void PairLJCutTholeLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp index 619e970bb0..288724cd77 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_cut_omp.cpp @@ -62,8 +62,7 @@ PairLJCutTIP4PCutOMP::~PairLJCutTIP4PCutOMP() void PairLJCutTIP4PCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp index ca8f450dc6..e2c1da1a89 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_omp.cpp @@ -62,8 +62,7 @@ PairLJCutTIP4PLongOMP::~PairLJCutTIP4PLongOMP() void PairLJCutTIP4PLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp index 80b17fba96..6baba8aec4 100644 --- a/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp +++ b/src/USER-OMP/pair_lj_cut_tip4p_long_soft_omp.cpp @@ -62,8 +62,7 @@ PairLJCutTIP4PLongSoftOMP::~PairLJCutTIP4PLongSoftOMP() void PairLJCutTIP4PLongSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_lj_expand_omp.cpp b/src/USER-OMP/pair_lj_expand_omp.cpp index 064ea97809..6c6ddb045e 100644 --- a/src/USER-OMP/pair_lj_expand_omp.cpp +++ b/src/USER-OMP/pair_lj_expand_omp.cpp @@ -36,9 +36,7 @@ PairLJExpandOMP::PairLJExpandOMP(LAMMPS *lmp) : void PairLJExpandOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp index c87f369d11..77c5bc0da0 100644 --- a/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp @@ -36,9 +36,7 @@ PairLJGromacsCoulGromacsOMP::PairLJGromacsCoulGromacsOMP(LAMMPS *lmp) : void PairLJGromacsCoulGromacsOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_gromacs_omp.cpp b/src/USER-OMP/pair_lj_gromacs_omp.cpp index 1d7cec5eef..15bcb08eed 100644 --- a/src/USER-OMP/pair_lj_gromacs_omp.cpp +++ b/src/USER-OMP/pair_lj_gromacs_omp.cpp @@ -36,9 +36,7 @@ PairLJGromacsOMP::PairLJGromacsOMP(LAMMPS *lmp) : void PairLJGromacsOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp index 391840285b..c9edc087b6 100644 --- a/src/USER-OMP/pair_lj_long_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_coul_long_omp.cpp @@ -46,9 +46,8 @@ PairLJLongCoulLongOMP::PairLJLongCoulLongOMP(LAMMPS *lmp) : void PairLJLongCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); + const int order1 = ewald_order&(1<<1); const int order6 = ewald_order&(1<<6); diff --git a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp index 19278d19bb..6d7c5b5638 100644 --- a/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp @@ -63,9 +63,7 @@ PairLJLongTIP4PLongOMP::~PairLJLongTIP4PLongOMP() void PairLJLongTIP4PLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // reallocate hneigh_thr & newsite_thr if necessary // initialize hneigh_thr[0] to -1 on steps when reneighboring occured diff --git a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp index c87f26204e..16c87d5ed4 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_long_omp.cpp @@ -38,9 +38,7 @@ PairLJSDKCoulLongOMP::PairLJSDKCoulLongOMP(LAMMPS *lmp) : void PairLJSDKCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp index 8ff0cfe921..1002cc193e 100644 --- a/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp @@ -44,9 +44,7 @@ void PairLJSDKCoulMSMOMP::compute(int eflag, int vflag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' " "with OMP MSM Pair styles"); - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_sdk_omp.cpp b/src/USER-OMP/pair_lj_sdk_omp.cpp index e107399316..1e64973cbb 100644 --- a/src/USER-OMP/pair_lj_sdk_omp.cpp +++ b/src/USER-OMP/pair_lj_sdk_omp.cpp @@ -40,9 +40,7 @@ PairLJSDKOMP::PairLJSDKOMP(LAMMPS *lmp) : void PairLJSDKOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp index 250f6ff272..aea22fc4df 100644 --- a/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp +++ b/src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp @@ -36,9 +36,7 @@ PairLJSFDipoleSFOMP::PairLJSFDipoleSFOMP(LAMMPS *lmp) : void PairLJSFDipoleSFOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp index b06de641f5..420c55b0ed 100644 --- a/src/USER-OMP/pair_lj_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_linear_omp.cpp @@ -36,9 +36,7 @@ PairLJSmoothLinearOMP::PairLJSmoothLinearOMP(LAMMPS *lmp) : void PairLJSmoothLinearOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lj_smooth_omp.cpp b/src/USER-OMP/pair_lj_smooth_omp.cpp index 36935616bf..d61dc19ff1 100644 --- a/src/USER-OMP/pair_lj_smooth_omp.cpp +++ b/src/USER-OMP/pair_lj_smooth_omp.cpp @@ -36,9 +36,7 @@ PairLJSmoothOMP::PairLJSmoothOMP(LAMMPS *lmp) : void PairLJSmoothOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lubricate_omp.cpp b/src/USER-OMP/pair_lubricate_omp.cpp index a7f9fc65b5..132dbc575e 100644 --- a/src/USER-OMP/pair_lubricate_omp.cpp +++ b/src/USER-OMP/pair_lubricate_omp.cpp @@ -54,9 +54,7 @@ PairLubricateOMP::~PairLubricateOMP() void PairLubricateOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_lubricate_poly_omp.cpp b/src/USER-OMP/pair_lubricate_poly_omp.cpp index 3f0ef1dba6..3a5f03364d 100644 --- a/src/USER-OMP/pair_lubricate_poly_omp.cpp +++ b/src/USER-OMP/pair_lubricate_poly_omp.cpp @@ -54,9 +54,7 @@ PairLubricatePolyOMP::~PairLubricatePolyOMP() void PairLubricatePolyOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_meam_spline_omp.cpp b/src/USER-OMP/pair_meam_spline_omp.cpp index dfc3b978a2..e9307c8666 100644 --- a/src/USER-OMP/pair_meam_spline_omp.cpp +++ b/src/USER-OMP/pair_meam_spline_omp.cpp @@ -39,9 +39,7 @@ PairMEAMSplineOMP::PairMEAMSplineOMP(LAMMPS *lmp) : void PairMEAMSplineOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_morse_omp.cpp b/src/USER-OMP/pair_morse_omp.cpp index 922b67b463..bf57019f11 100644 --- a/src/USER-OMP/pair_morse_omp.cpp +++ b/src/USER-OMP/pair_morse_omp.cpp @@ -36,9 +36,7 @@ PairMorseOMP::PairMorseOMP(LAMMPS *lmp) : void PairMorseOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp index 61cef69c37..5ba6acb439 100644 --- a/src/USER-OMP/pair_morse_smooth_linear_omp.cpp +++ b/src/USER-OMP/pair_morse_smooth_linear_omp.cpp @@ -40,9 +40,7 @@ PairMorseSmoothLinearOMP::PairMorseSmoothLinearOMP(LAMMPS *lmp) : void PairMorseSmoothLinearOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp index fcbf5dbabb..d62b4e5c62 100644 --- a/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_cut_omp.cpp @@ -36,9 +36,7 @@ PairNMCutCoulCutOMP::PairNMCutCoulCutOMP(LAMMPS *lmp) : void PairNMCutCoulCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp index b31387dbfe..a8696c74a1 100644 --- a/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_coul_long_omp.cpp @@ -44,9 +44,7 @@ PairNMCutCoulLongOMP::PairNMCutCoulLongOMP(LAMMPS *lmp) : void PairNMCutCoulLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_nm_cut_omp.cpp b/src/USER-OMP/pair_nm_cut_omp.cpp index 79cd046311..9304b10ef0 100644 --- a/src/USER-OMP/pair_nm_cut_omp.cpp +++ b/src/USER-OMP/pair_nm_cut_omp.cpp @@ -36,9 +36,7 @@ PairNMCutOMP::PairNMCutOMP(LAMMPS *lmp) : void PairNMCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_peri_lps_omp.cpp b/src/USER-OMP/pair_peri_lps_omp.cpp index 7b174face7..61db45363e 100644 --- a/src/USER-OMP/pair_peri_lps_omp.cpp +++ b/src/USER-OMP/pair_peri_lps_omp.cpp @@ -45,9 +45,7 @@ PairPeriLPSOMP::PairPeriLPSOMP(LAMMPS *lmp) : void PairPeriLPSOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_peri_pmb_omp.cpp b/src/USER-OMP/pair_peri_pmb_omp.cpp index 8199d8aa47..b1816e4052 100644 --- a/src/USER-OMP/pair_peri_pmb_omp.cpp +++ b/src/USER-OMP/pair_peri_pmb_omp.cpp @@ -43,9 +43,7 @@ PairPeriPMBOMP::PairPeriPMBOMP(LAMMPS *lmp) : void PairPeriPMBOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_reaxc_omp.cpp b/src/USER-OMP/pair_reaxc_omp.cpp index d4448ad868..7f2db420bf 100644 --- a/src/USER-OMP/pair_reaxc_omp.cpp +++ b/src/USER-OMP/pair_reaxc_omp.cpp @@ -191,8 +191,7 @@ void PairReaxCOMP::compute(int eflag, int vflag) int *num_hbonds = fix_reax->num_hbonds; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else ev_unset(); + ev_init(eflag,vflag); if (vflag_global) control->virial = 1; else control->virial = 0; @@ -205,7 +204,7 @@ void PairReaxCOMP::compute(int eflag, int vflag) system->big_box.box_norms[0] = 0; system->big_box.box_norms[1] = 0; system->big_box.box_norms[2] = 0; - if( comm->me == 0 ) t_start = MPI_Wtime(); + if (comm->me == 0 ) t_start = MPI_Wtime(); // setup data structures setup(); @@ -218,7 +217,7 @@ void PairReaxCOMP::compute(int eflag, int vflag) write_reax_lists(); // timing for filling in the reax lists - if( comm->me == 0 ) { + if (comm->me == 0) { t_end = MPI_Wtime(); data->timing.nbrs = t_end - t_start; } @@ -582,7 +581,7 @@ int PairReaxCOMP::write_reax_lists() /* ---------------------------------------------------------------------- */ -void PairReaxCOMP::read_reax_forces(int vflag) +void PairReaxCOMP::read_reax_forces(int /* vflag */) { #if defined(_OPENMP) #pragma omp parallel for schedule(static) default(shared) diff --git a/src/USER-OMP/pair_rebo_omp.cpp b/src/USER-OMP/pair_rebo_omp.cpp index 9a1ce8e11b..2b58b45b53 100644 --- a/src/USER-OMP/pair_rebo_omp.cpp +++ b/src/USER-OMP/pair_rebo_omp.cpp @@ -24,7 +24,7 @@ PairREBOOMP::PairREBOOMP(LAMMPS *lmp) : PairAIREBOOMP(lmp) {} global settings ------------------------------------------------------------------------- */ -void PairREBOOMP::settings(int narg, char **arg) +void PairREBOOMP::settings(int narg, char ** /* arg */) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); diff --git a/src/USER-OMP/pair_resquared_omp.cpp b/src/USER-OMP/pair_resquared_omp.cpp index 1736e794f5..d9e0059a9f 100644 --- a/src/USER-OMP/pair_resquared_omp.cpp +++ b/src/USER-OMP/pair_resquared_omp.cpp @@ -38,9 +38,7 @@ PairRESquaredOMP::PairRESquaredOMP(LAMMPS *lmp) : void PairRESquaredOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_soft_omp.cpp b/src/USER-OMP/pair_soft_omp.cpp index a860ad97d9..eb151bc0df 100644 --- a/src/USER-OMP/pair_soft_omp.cpp +++ b/src/USER-OMP/pair_soft_omp.cpp @@ -40,9 +40,7 @@ PairSoftOMP::PairSoftOMP(LAMMPS *lmp) : void PairSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_sw_omp.cpp b/src/USER-OMP/pair_sw_omp.cpp index e323fc4c37..745b3a1f04 100644 --- a/src/USER-OMP/pair_sw_omp.cpp +++ b/src/USER-OMP/pair_sw_omp.cpp @@ -37,9 +37,7 @@ PairSWOMP::PairSWOMP(LAMMPS *lmp) : void PairSWOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_table_omp.cpp b/src/USER-OMP/pair_table_omp.cpp index d27456e1b5..b55817e75c 100644 --- a/src/USER-OMP/pair_table_omp.cpp +++ b/src/USER-OMP/pair_table_omp.cpp @@ -37,9 +37,7 @@ PairTableOMP::PairTableOMP(LAMMPS *lmp) : void PairTableOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp index fad077ca12..a11bd87640 100644 --- a/src/USER-OMP/pair_tersoff_mod_c_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_c_omp.cpp @@ -36,9 +36,7 @@ PairTersoffMODCOMP::PairTersoffMODCOMP(LAMMPS *lmp) : void PairTersoffMODCOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_tersoff_mod_omp.cpp b/src/USER-OMP/pair_tersoff_mod_omp.cpp index 04e54c6e69..da22110c1c 100644 --- a/src/USER-OMP/pair_tersoff_mod_omp.cpp +++ b/src/USER-OMP/pair_tersoff_mod_omp.cpp @@ -36,9 +36,7 @@ PairTersoffMODOMP::PairTersoffMODOMP(LAMMPS *lmp) : void PairTersoffMODOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_tersoff_omp.cpp b/src/USER-OMP/pair_tersoff_omp.cpp index a5afdc7509..661f15d64d 100644 --- a/src/USER-OMP/pair_tersoff_omp.cpp +++ b/src/USER-OMP/pair_tersoff_omp.cpp @@ -37,9 +37,7 @@ PairTersoffOMP::PairTersoffOMP(LAMMPS *lmp) : void PairTersoffOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_tersoff_table_omp.cpp b/src/USER-OMP/pair_tersoff_table_omp.cpp index de045f9c62..7e83814f95 100644 --- a/src/USER-OMP/pair_tersoff_table_omp.cpp +++ b/src/USER-OMP/pair_tersoff_table_omp.cpp @@ -61,9 +61,7 @@ PairTersoffTableOMP::~PairTersoffTableOMP() void PairTersoffTableOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_tip4p_cut_omp.cpp b/src/USER-OMP/pair_tip4p_cut_omp.cpp index 85589cf043..1900ed4394 100644 --- a/src/USER-OMP/pair_tip4p_cut_omp.cpp +++ b/src/USER-OMP/pair_tip4p_cut_omp.cpp @@ -62,8 +62,7 @@ PairTIP4PCutOMP::~PairTIP4PCutOMP() void PairTIP4PCutOMP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_tip4p_long_omp.cpp b/src/USER-OMP/pair_tip4p_long_omp.cpp index c6c4bfe5fc..ee65937c46 100644 --- a/src/USER-OMP/pair_tip4p_long_omp.cpp +++ b/src/USER-OMP/pair_tip4p_long_omp.cpp @@ -62,8 +62,7 @@ PairTIP4PLongOMP::~PairTIP4PLongOMP() void PairTIP4PLongOMP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp index 7e9d3b6dff..adb984a2cd 100644 --- a/src/USER-OMP/pair_tip4p_long_soft_omp.cpp +++ b/src/USER-OMP/pair_tip4p_long_soft_omp.cpp @@ -62,8 +62,7 @@ PairTIP4PLongSoftOMP::~PairTIP4PLongSoftOMP() void PairTIP4PLongSoftOMP::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nlocal = atom->nlocal; const int nall = nlocal + atom->nghost; diff --git a/src/USER-OMP/pair_ufm_omp.cpp b/src/USER-OMP/pair_ufm_omp.cpp index ff258b5b3b..08d8cc15f9 100644 --- a/src/USER-OMP/pair_ufm_omp.cpp +++ b/src/USER-OMP/pair_ufm_omp.cpp @@ -38,9 +38,7 @@ PairUFMOMP::PairUFMOMP(LAMMPS *lmp) : void PairUFMOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_vashishta_omp.cpp b/src/USER-OMP/pair_vashishta_omp.cpp index 194a3e2d86..28104013f0 100644 --- a/src/USER-OMP/pair_vashishta_omp.cpp +++ b/src/USER-OMP/pair_vashishta_omp.cpp @@ -37,9 +37,7 @@ PairVashishtaOMP::PairVashishtaOMP(LAMMPS *lmp) : void PairVashishtaOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_vashishta_table_omp.cpp b/src/USER-OMP/pair_vashishta_table_omp.cpp index e0d96d8bb6..b044902ebe 100644 --- a/src/USER-OMP/pair_vashishta_table_omp.cpp +++ b/src/USER-OMP/pair_vashishta_table_omp.cpp @@ -37,9 +37,7 @@ PairVashishtaTableOMP::PairVashishtaTableOMP(LAMMPS *lmp) : void PairVashishtaTableOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_yukawa_colloid_omp.cpp b/src/USER-OMP/pair_yukawa_colloid_omp.cpp index c1d2133a1c..86314ce7b8 100644 --- a/src/USER-OMP/pair_yukawa_colloid_omp.cpp +++ b/src/USER-OMP/pair_yukawa_colloid_omp.cpp @@ -36,9 +36,7 @@ PairYukawaColloidOMP::PairYukawaColloidOMP(LAMMPS *lmp) : void PairYukawaColloidOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_yukawa_omp.cpp b/src/USER-OMP/pair_yukawa_omp.cpp index cbfd627f97..add81e9b04 100644 --- a/src/USER-OMP/pair_yukawa_omp.cpp +++ b/src/USER-OMP/pair_yukawa_omp.cpp @@ -36,9 +36,7 @@ PairYukawaOMP::PairYukawaOMP(LAMMPS *lmp) : void PairYukawaOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/pair_zbl_omp.cpp b/src/USER-OMP/pair_zbl_omp.cpp index 788679434b..f6856c4fa0 100644 --- a/src/USER-OMP/pair_zbl_omp.cpp +++ b/src/USER-OMP/pair_zbl_omp.cpp @@ -37,9 +37,7 @@ PairZBLOMP::PairZBLOMP(LAMMPS *lmp) : void PairZBLOMP::compute(int eflag, int vflag) { - if (eflag || vflag) { - ev_setup(eflag,vflag); - } else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); const int nall = atom->nlocal + atom->nghost; const int nthreads = comm->nthreads; diff --git a/src/USER-OMP/reaxc_bond_orders_omp.cpp b/src/USER-OMP/reaxc_bond_orders_omp.cpp index 8b78a3aa55..33780f5e3f 100644 --- a/src/USER-OMP/reaxc_bond_orders_omp.cpp +++ b/src/USER-OMP/reaxc_bond_orders_omp.cpp @@ -113,7 +113,7 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj, rvec_Add(workspace->forceReduction[reductionOffset+i],temp ); - if( system->pair_ptr->vflag_atom) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fi_tmp, -1.0, temp); rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x ); @@ -147,7 +147,7 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj, rvec_Add(workspace->forceReduction[reductionOffset+j],temp ); - if( system->pair_ptr->vflag_atom) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fj_tmp, -1.0, temp); rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x ); @@ -171,7 +171,7 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj, rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); - if( system->pair_ptr->vflag_atom ) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fk_tmp, -1.0, temp); rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); @@ -201,7 +201,7 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj, rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); - if( system->pair_ptr->vflag_atom ) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fk_tmp, -1.0, temp); rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); @@ -220,7 +220,8 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj, /* ---------------------------------------------------------------------- */ -void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_data *data, +void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, + simulation_data * /* data */, storage *workspace, reax_list **lists ) { reax_list *bonds = (*lists) + BONDS; bond_data *nbr_j, *nbr_k; @@ -312,7 +313,7 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_ rvec_Add(workspace->forceReduction[reductionOffset+k],temp ); /* pressure */ - if( k != i ) { + if (k != i) { ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i) rvec_iMultiply( ext_press, rel_box, temp ); rvec_Add( workspace->my_ext_pressReduction[tid], ext_press ); @@ -343,9 +344,9 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_ /* ---------------------------------------------------------------------- */ -int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut, +int BOp_OMP( storage * /* workspace */, reax_list *bonds, double bo_cut, int i, int btop_i, far_neighbor_data *nbr_pj, - single_body_parameters *sbp_i, single_body_parameters *sbp_j, + single_body_parameters * /* sbp_i */, single_body_parameters * /* sbp_j */, two_body_parameters *twbp, int btop_j, double C12, double C34, double C56, double BO, double BO_s, double BO_pi, double BO_pi2) { int j; @@ -419,8 +420,8 @@ int BOp_OMP( storage *workspace, reax_list *bonds, double bo_cut, /* ---------------------------------------------------------------------- */ -void BOOMP( reax_system *system, control_params *control, simulation_data *data, - storage *workspace, reax_list **lists, output_controls *out_control ) +void BOOMP( reax_system *system, control_params * /* control */, simulation_data * /* data */, + storage *workspace, reax_list **lists, output_controls * /* out_control */) { #ifdef OMP_TIMING double endTimeBase, startTimeBase; @@ -489,10 +490,10 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data, if(type_j < 0) continue; bo_ij = &( bonds->select.bond_list[pj].bo_data ); - if( i < j || workspace->bond_mark[j] > 3) { + if (i < j || workspace->bond_mark[j] > 3) { twbp = &( system->reax_param.tbp[type_i][type_j] ); - if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) { + if (twbp->ovc < 0.001 && twbp->v13cor < 0.001) { bo_ij->C1dbo = 1.000000; bo_ij->C2dbo = 0.000000; bo_ij->C3dbo = 0.000000; @@ -514,7 +515,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data, Deltap_boc_j = workspace->Deltap_boc[j]; /* on page 1 */ - if( twbp->ovc >= 0.001 ) { + if (twbp->ovc >= 0.001) { /* Correction for overcoordination */ exp_p1i = exp( -p_boc1 * Deltap_i ); exp_p2i = exp( -p_boc2 * Deltap_i ); @@ -555,7 +556,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data, Cf1_ij = Cf1_ji = 0.0; } - if( twbp->v13cor >= 0.001 ) { + if (twbp->v13cor >= 0.001) { /* Correction for 1-3 bond orders */ exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) - Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5); @@ -606,13 +607,13 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data, } /* neglect bonds that are < 1e-10 */ - if( bo_ij->BO < 1e-10 ) + if (bo_ij->BO < 1e-10) bo_ij->BO = 0.0; - if( bo_ij->BO_s < 1e-10 ) + if (bo_ij->BO_s < 1e-10) bo_ij->BO_s = 0.0; - if( bo_ij->BO_pi < 1e-10 ) + if (bo_ij->BO_pi < 1e-10) bo_ij->BO_pi = 0.0; - if( bo_ij->BO_pi2 < 1e-10 ) + if (bo_ij->BO_pi2 < 1e-10) bo_ij->BO_pi2 = 0.0; workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO @@ -653,7 +654,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data, type_j = system->my_atoms[j].type; if(type_j < 0) continue; - if( i < j || workspace->bond_mark[j] > 3) { + if (i < j || workspace->bond_mark[j] > 3) { // Computed in previous for-loop } else { /* We only need to update bond orders from bo_ji @@ -704,7 +705,7 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data, workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]); workspace->dDelta_lp[j] = workspace->Clp[j]; - if( sbp_j->mass > 21.0 ) { + if (sbp_j->mass > 21.0) { workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency); workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; workspace->dDelta_lp_temp[j] = 0.; diff --git a/src/USER-OMP/reaxc_bonds_omp.cpp b/src/USER-OMP/reaxc_bonds_omp.cpp index 0ccb4d8f99..5160c6f55d 100644 --- a/src/USER-OMP/reaxc_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_bonds_omp.cpp @@ -42,9 +42,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -void BondsOMP( reax_system *system, control_params *control, +void BondsOMP( reax_system *system, control_params * /* control */, simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control ) + output_controls * /* out_control */) { #ifdef OMP_TIMING double endTimeBase, startTimeBase; @@ -99,9 +99,9 @@ void BondsOMP( reax_system *system, control_params *control, for (pj = start_i; pj < end_i; ++pj) { j = bonds->select.bond_list[pj].nbr; - if( system->my_atoms[i].orig_id > system->my_atoms[j].orig_id ) continue; + if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id) continue; - if( system->my_atoms[i].orig_id == system->my_atoms[j].orig_id ) { + if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) { if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue; if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue; diff --git a/src/USER-OMP/reaxc_forces_omp.cpp b/src/USER-OMP/reaxc_forces_omp.cpp index 01e58c4fd3..80741a46a8 100644 --- a/src/USER-OMP/reaxc_forces_omp.cpp +++ b/src/USER-OMP/reaxc_forces_omp.cpp @@ -64,7 +64,7 @@ void Init_Force_FunctionsOMP( control_params *control ) Interaction_Functions[2] = Atom_EnergyOMP; //Dummy_Interaction; Interaction_Functions[3] = Valence_AnglesOMP; //Dummy_Interaction; Interaction_Functions[4] = Torsion_AnglesOMP; //Dummy_Interaction; - if( control->hbond_cut > 0 ) + if (control->hbond_cut > 0) Interaction_Functions[5] = Hydrogen_BondsOMP; else Interaction_Functions[5] = Dummy_Interaction; Interaction_Functions[6] = Dummy_Interaction; //empty @@ -79,7 +79,7 @@ void Init_Force_FunctionsOMP( control_params *control ) void Compute_Bonded_ForcesOMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control, - MPI_Comm comm ) + MPI_Comm /* comm */) { int i; @@ -105,7 +105,7 @@ void Compute_Bonded_ForcesOMP( reax_system *system, control_params *control, void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, reax_list **lists, output_controls *out_control, - MPI_Comm comm ) + MPI_Comm /* comm */) { /* van der Waals and Coulomb interactions */ #ifdef OMP_TIMING @@ -113,7 +113,7 @@ void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control, startTimeBase = MPI_Wtime(); #endif - if( control->tabulate == 0 ) + if (control->tabulate == 0) vdW_Coulomb_Energy_OMP( system, control, data, workspace, lists, out_control ); else @@ -133,7 +133,7 @@ void Compute_NonBonded_ForcesOMP( reax_system *system, control_params *control, Saves enormous time & space! */ void Compute_Total_ForceOMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, mpi_datatypes *mpi_data ) + reax_list **lists, mpi_datatypes * /* mpi_data */) { #ifdef OMP_TIMING double startTimeBase,endTimeBase; @@ -262,7 +262,7 @@ void Compute_Total_ForceOMP( reax_system *system, control_params *control, /* ---------------------------------------------------------------------- */ -void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lists, +void Validate_ListsOMP( reax_system *system, storage * /*workspace */, reax_list **lists, int step, int n, int N, int numH, MPI_Comm comm ) { int i, comp, Hindex; @@ -275,7 +275,7 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis { /* bond list */ - if( N > 0 ) { + if (N > 0) { bonds = *lists + BONDS; #if defined(_OPENMP) @@ -284,11 +284,11 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis for( i = 0; i < N; ++i ) { system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); - if( i < N-1 ) + if (i < N-1) comp = Start_Index(i+1, bonds); else comp = bonds->num_intrs; - if( End_Index(i, bonds) > comp ) { + if (End_Index(i, bonds) > comp) { fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", step, i, End_Index(i,bonds), comp ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -298,7 +298,7 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis /* hbonds list */ - if( numH > 0 ) { + if (numH > 0) { hbonds = *lists + HBONDS; #if defined(_OPENMP) @@ -306,15 +306,15 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis #endif for( i = 0; i < n; ++i ) { Hindex = system->my_atoms[i].Hindex; - if( Hindex > -1 ) { + if (Hindex > -1) { system->my_atoms[i].num_hbonds = (int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS )); - if( Hindex < numH-1 ) + if (Hindex < numH-1) comp = Start_Index(Hindex+1, hbonds); else comp = hbonds->num_intrs; - if( End_Index(Hindex, hbonds) > comp ) { + if (End_Index(Hindex, hbonds) > comp) { fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", step, Hindex, End_Index(Hindex,hbonds), comp ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -329,7 +329,7 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control, + reax_list **lists, output_controls * /* out_control */, MPI_Comm comm ) { #ifdef OMP_TIMING double startTimeBase, endTimeBase; @@ -402,7 +402,7 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, // #pragma omp critical // { // btop_i = End_Index(i, bonds); -// if( BOp(workspace, bonds, control->bo_cut, i, btop_i, nbr_pj, sbp_i, sbp_j, twbp) ) { +// if (BOp(workspace, bonds, control->bo_cut, i, btop_i, nbr_pj, sbp_i, sbp_j, twbp)) { // num_bonds++; // btop_i++; // Set_End_Index(i, btop_i, bonds); @@ -418,19 +418,19 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control, double BO, BO_s, BO_pi, BO_pi2; double bo_cut = control->bo_cut; - if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) { + if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 ); BO_s = (1.0 + bo_cut) * exp( C12 ); } else BO_s = C12 = 0.0; - if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) { + if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 ); BO_pi = exp( C34 ); } else BO_pi = C34 = 0.0; - if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) { + if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 ); BO_pi2= exp( C56 ); } diff --git a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp index 4c0a4c269e..7acf26262e 100644 --- a/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp +++ b/src/USER-OMP/reaxc_hydrogen_bonds_omp.cpp @@ -45,7 +45,7 @@ using namespace LAMMPS_NS; void Hydrogen_BondsOMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) + reax_list **lists, output_controls * /* out_control */) { #ifdef OMP_TIMING double endTimeBase, startTimeBase; @@ -110,7 +110,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control, // for( j = 0; j < system->n; ++j ) for( j = ifrom; j < ito; ++j ) { /* j has to be of type H */ - if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) { + if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) { /*set j's variables */ type_j = system->my_atoms[j].type; start_j = Start_Index(j, bonds); @@ -146,7 +146,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control, pbond_ij = &( bonds->select.bond_list[pi] ); i = pbond_ij->nbr; - if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) { + if (system->my_atoms[i].orig_id != system->my_atoms[k].orig_id) { bo_ij = &(pbond_ij->bo_data); type_i = system->my_atoms[i].type; if(type_i < 0) continue; @@ -179,7 +179,7 @@ void Hydrogen_BondsOMP( reax_system *system, control_params *control, /* hydrogen bond forces */ bo_ij->Cdbo += CEhb1; // dbo term - if( control->virial == 0 ) { + if (control->virial == 0) { // dcos terms rvec_ScaledAdd(workspace->forceReduction[reductionOffset+i], +CEhb2, dcos_theta_di ); rvec_ScaledAdd(workspace->forceReduction[reductionOffset+j], +CEhb2, dcos_theta_dj ); diff --git a/src/USER-OMP/reaxc_init_md_omp.cpp b/src/USER-OMP/reaxc_init_md_omp.cpp index 68d39d4f80..bd15b3b9df 100644 --- a/src/USER-OMP/reaxc_init_md_omp.cpp +++ b/src/USER-OMP/reaxc_init_md_omp.cpp @@ -48,8 +48,8 @@ extern int Init_Workspace(reax_system*, control_params*, storage*, MPI_Comm, cha /* ---------------------------------------------------------------------- */ int Init_ListsOMP( reax_system *system, control_params *control, - simulation_data *data, storage *workspace, reax_list **lists, - mpi_datatypes *mpi_data, char *msg ) + simulation_data * /* data */, storage * /* workspace */, + reax_list **lists, mpi_datatypes *mpi_data, char * /* msg */) { int i, total_hbonds, total_bonds, bond_cap, num_3body, cap_3body, Htop; int *hb_top, *bond_top; @@ -65,7 +65,7 @@ int Init_ListsOMP( reax_system *system, control_params *control, Estimate_Storages( system, control, lists, &Htop, hb_top, bond_top, &num_3body, comm ); - if( control->hbond_cut > 0 ) { + if (control->hbond_cut > 0) { /* init H indexes */ total_hbonds = 0; for( i = 0; i < system->n; ++i ) { @@ -127,7 +127,7 @@ void InitializeOMP( reax_system *system, control_params *control, char msg[MAX_STR]; - if( Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE ) { + if (Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE) { fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n", system->my_rank ); fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n", @@ -135,22 +135,22 @@ void InitializeOMP( reax_system *system, control_params *control, MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_System(system, control, msg) == FAILURE ){ + if (Init_System(system, control, msg) == FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: system could not be initialized! terminating.\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Simulation_Data( system, control, data, msg ) == FAILURE ) { + if (Init_Simulation_Data( system, control, data, msg ) == FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) == - FAILURE ) { + if (Init_Workspace( system, control, workspace, mpi_data->world, msg ) == + FAILURE) { fprintf( stderr, "p%d:init_workspace: not enough memory\n", system->my_rank ); fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n", @@ -158,23 +158,23 @@ void InitializeOMP( reax_system *system, control_params *control, MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_ListsOMP( system, control, data, workspace, lists, mpi_data, msg ) == - FAILURE ) { + if (Init_ListsOMP( system, control, data, workspace, lists, mpi_data, msg ) == + FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: system could not be initialized! terminating.\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) { + if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: could not open output files! terminating...\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( control->tabulate ) { - if( Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE ) { + if (control->tabulate) { + if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n", system->my_rank ); diff --git a/src/USER-OMP/reaxc_multi_body_omp.cpp b/src/USER-OMP/reaxc_multi_body_omp.cpp index fc4982ca9f..7552e7a733 100644 --- a/src/USER-OMP/reaxc_multi_body_omp.cpp +++ b/src/USER-OMP/reaxc_multi_body_omp.cpp @@ -42,9 +42,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -void Atom_EnergyOMP( reax_system *system, control_params *control, +void Atom_EnergyOMP( reax_system *system, control_params * /* control */, simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control ) + output_controls * /* out_control */) { #ifdef OMP_TIMING double endTimeBase, startTimeBase; @@ -128,24 +128,24 @@ void Atom_EnergyOMP( reax_system *system, control_params *control, if(numbonds > 0) workspace->CdDelta[i] += CElp; // lp - 1st term /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, i, system->n, 1, e_lp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); /* correction for C2 */ - if( p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C") ) + if (p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C")) for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) { j = bonds->select.bond_list[pj].nbr; type_j = system->my_atoms[j].type; if(type_j < 0) continue; - if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) { + if (!strcmp( system->reax_param.sbp[type_j].name, "C" )) { twbp = &( system->reax_param.tbp[type_i][type_j]); bo_ij = &( bonds->select.bond_list[pj].bo_data ); Di = workspace->Delta[i]; vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.); - if( vov3 > 3. ) { + if (vov3 > 3.) { total_Elp += e_lph = p_lp3 * SQR(vov3-3.0); deahu2dbo = 2.*p_lp3*(vov3 - 3.); @@ -155,7 +155,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control, workspace->CdDelta[i] += deahu2dsbo; /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, i, j, system->n, 1, e_lph, 0.0, 0.0, 0.0, 0.0, 0.0, thr); } @@ -172,7 +172,7 @@ void Atom_EnergyOMP( reax_system *system, control_params *control, sbp_i = &(system->reax_param.sbp[ type_i ]); /* over-coordination energy */ - if( sbp_i->mass > 21.0 ) + if (sbp_i->mass > 21.0) dfvl = 0.0; else dfvl = 1.0; // only for 1st-row elements diff --git a/src/USER-OMP/reaxc_nonbonded_omp.cpp b/src/USER-OMP/reaxc_nonbonded_omp.cpp index 552783e41c..41b1474791 100644 --- a/src/USER-OMP/reaxc_nonbonded_omp.cpp +++ b/src/USER-OMP/reaxc_nonbonded_omp.cpp @@ -47,8 +47,8 @@ using namespace LAMMPS_NS; void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) { - + reax_list **lists, output_controls * /* out_control */ ) +{ int natoms = system->n; reax_list *far_nbrs = (*lists) + FAR_NBRS; double p_vdW1 = system->reax_param.gp.l[28]; @@ -162,7 +162,7 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control, CEvd = dTap * e_vdW - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } - else{ // no shielding + else { // no shielding exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); @@ -208,7 +208,7 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control, ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; /* tally into per-atom energy */ - if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { + if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { pe_vdw = Tap * (e_vdW + e_core + e_lg); rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); @@ -218,12 +218,11 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control, delij[0], delij[1], delij[2], thr); } - if( control->virial == 0 ) { + if (control->virial == 0) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->forceReduction[reductionOffset+j], +(CEvd + CEclmb), nbr_pj->dvec ); - } - else { /* NPT, iNPT or sNPT */ + } else { /* NPT, iNPT or sNPT */ /* for pressure coupling, terms not related to bond order derivatives are added directly into pressure vector/tensor */ @@ -254,7 +253,7 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control, void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *control, simulation_data *data, storage *workspace, reax_list **lists, - output_controls *out_control ) { + output_controls * /* out_control */) { double SMALL = 0.0001; int natoms = system->n; @@ -328,7 +327,7 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro /* Cubic Spline Interpolation */ r = (int)(r_ij * t->inv_dx); - if( r == 0 ) ++r; + if (r == 0) ++r; base = (double)(r+1) * t->dx; dif = r_ij - base; @@ -350,7 +349,7 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; /* tally into per-atom energy */ - if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { + if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); f_tmp = -(CEvd + CEclmb); @@ -358,12 +357,11 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro f_tmp, delij[0], delij[1], delij[2], thr); } - if( control->virial == 0 ) { + if (control->virial == 0) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->forceReduction[froffset+j], +(CEvd + CEclmb), nbr_pj->dvec ); - } - else { // NPT, iNPT or sNPT + } else { // NPT, iNPT or sNPT /* for pressure coupling, terms not related to bond order derivatives are added directly into pressure vector/tensor */ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); diff --git a/src/USER-OMP/reaxc_torsion_angles_omp.cpp b/src/USER-OMP/reaxc_torsion_angles_omp.cpp index 94a06bf1f9..d290dc264f 100644 --- a/src/USER-OMP/reaxc_torsion_angles_omp.cpp +++ b/src/USER-OMP/reaxc_torsion_angles_omp.cpp @@ -198,7 +198,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control, sin_ijk = sin( theta_ijk ); cos_ijk = cos( theta_ijk ); //tan_ijk_i = 1. / tan( theta_ijk ); - if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) tan_ijk_i = cos_ijk / MIN_SINE; else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) tan_ijk_i = cos_ijk / -MIN_SINE; @@ -237,7 +237,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control, sin_jkl = sin( theta_jkl ); cos_jkl = cos( theta_jkl ); //tan_jkl_i = 1. / tan( theta_jkl ); - if( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) + if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) tan_jkl_i = cos_jkl / MIN_SINE; else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) tan_jkl_i = cos_jkl / -MIN_SINE; @@ -338,7 +338,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control, //bo_kl->Cdbo += (CEtors6 + CEconj3); bo_kl->CdboReduction[tid] += (CEtors6 + CEconj3); - if( control->virial == 0 ) { + if (control->virial == 0) { /* dcos_theta_ijk */ rvec_ScaledAdd( workspace->f[j], CEtors7 + CEconj4, p_ijk->dcos_dj ); @@ -417,7 +417,7 @@ void Torsion_AnglesOMP( reax_system *system, control_params *control, } /* tally into per-atom virials */ - if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { + if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { // acquire vectors rvec_ScaledSum( delil, 1., system->my_atoms[l].x, diff --git a/src/USER-OMP/reaxc_valence_angles_omp.cpp b/src/USER-OMP/reaxc_valence_angles_omp.cpp index 6765c091b9..4164d39cab 100644 --- a/src/USER-OMP/reaxc_valence_angles_omp.cpp +++ b/src/USER-OMP/reaxc_valence_angles_omp.cpp @@ -100,7 +100,7 @@ void Calculate_dCos_ThetaOMP( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_ played by j which sits in the middle of the other two. */ void Valence_AnglesOMP( reax_system *system, control_params *control, simulation_data *data, storage *workspace, - reax_list **lists, output_controls *out_control ) + reax_list **lists, output_controls * /* out_control */) { #ifdef OMP_TIMING @@ -308,11 +308,10 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, } // modifications to match Adri's code - 09/01/09 - if( workspace->vlpex[j] >= 0 ){ + if (workspace->vlpex[j] >= 0) { vlpadj = 0; dSBO2 = prod_SBO - 1; - } - else{ + } else { vlpadj = workspace->nlp[j]; dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); } @@ -320,13 +319,13 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj ); - if( SBO <= 0 ) + if (SBO <= 0) SBO2 = 0, CSBO2 = 0; - else if( SBO > 0 && SBO <= 1 ) { + else if (SBO > 0 && SBO <= 1) { SBO2 = pow( SBO, p_val9 ); CSBO2 = p_val9 * pow( SBO, p_val9 - 1 ); } - else if( SBO > 1 && SBO < 2 ) { + else if (SBO > 1 && SBO < 2) { SBO2 = 2 - pow( 2-SBO, p_val9 ); CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 ); } @@ -399,7 +398,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, p_ijk->theta = theta; sin_theta = sin( theta ); - if( sin_theta < 1.0e-5 ) + if (sin_theta < 1.0e-5) sin_theta = 1.0e-5; ++my_offset; // add this to the list of 3-body interactions @@ -413,7 +412,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, for (cnt = 0; cnt < thbh->cnt; ++cnt) { - if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) { + if (fabs(thbh->prm[cnt].p_val1) > 0.001) { thbp = &( thbh->prm[cnt] ); /* ANGLE ENERGY */ @@ -537,14 +536,13 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, bo_jt->Cdbopi2 += CEval5; } - if( control->virial == 0 ) { + if (control->virial == 0) { rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); rvec_ScaledAdd( workspace->forceReduction[reductionOffset+i], CEval8, p_ijk->dcos_di ); rvec_ScaledAdd( workspace->forceReduction[reductionOffset+k], CEval8, p_ijk->dcos_dk ); - } - else { + } else { /* terms not related to bond order derivatives are added directly into forces and pressure vector/tensor */ rvec_Scale( force, CEval8, p_ijk->dcos_di ); @@ -563,7 +561,7 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, } /* tally into per-atom virials */ - if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { + if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { /* Acquire vectors */ rvec_ScaledSum( delij, 1., system->my_atoms[i].x, @@ -577,10 +575,10 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, eng_tmp = e_ang + e_pen + e_coa; - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) pair_reax_ptr->ev_tally_thr_proxy(system->pair_ptr, j, j, system->N, 1, eng_tmp, 0.0, 0.0, 0.0, 0.0, 0.0, thr); - if( system->pair_ptr->vflag_atom) + if (system->pair_ptr->vflag_atom) // NEED TO MAKE AN OMP VERSION OF THIS CALL! system->pair_ptr->v_tally3( i, j, k, fi_tmp, fk_tmp, delij, delkj); } @@ -600,9 +598,9 @@ void Valence_AnglesOMP( reax_system *system, control_params *control, data->my_en.e_pen = total_Epen; data->my_en.e_coa = total_Ecoa; - if( num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE ) { + if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { workspace->realloc.num_3body = num_thb_intrs * TWICE; - if( num_thb_intrs > thb_intrs->num_intrs ) { + if (num_thb_intrs > thb_intrs->num_intrs) { fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d", data->step, num_thb_intrs, thb_intrs->num_intrs ); MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY ); diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h index 0821f8cea0..87d921290e 100644 --- a/src/USER-OMP/thr_omp.h +++ b/src/USER-OMP/thr_omp.h @@ -185,6 +185,7 @@ static inline void loop_setup_thr(int &ifrom, int &ito, int &tid, tid = 0; ifrom = 0; ito = inum; + nthreads = 1; #endif } diff --git a/src/USER-PHONON/Install.sh b/src/USER-PHONON/Install.sh index 3428415443..a73f529cfa 100755 --- a/src/USER-PHONON/Install.sh +++ b/src/USER-PHONON/Install.sh @@ -40,3 +40,7 @@ fi action fix_phonon.cpp fft3d_wrap.h action fix_phonon.h fft3d_wrap.h +action dynamical_matrix.cpp +action dynamical_matrix.h +action third_order.cpp +action third_order.h diff --git a/src/USER-PHONON/README b/src/USER-PHONON/README index 2212eaaebd..b554eacd5e 100644 --- a/src/USER-PHONON/README +++ b/src/USER-PHONON/README @@ -1,19 +1,23 @@ This package contains a fix phonon command that calculates dynamical -matrices, which can then be used to compute phonon dispersion -relations, directly from molecular dynamics simulations. +matrices from finite temperature MD simulations, which can then be +used to compute phonon dispersion relations, directly from molecular +dynamics simulations. -See the doc page for the fix phonon command for detailed usage -instructions. +It also contains a command to compute the dynamical matrix at +pre-optimized positions through finite differences. + +See the doc page for the fix phonon command or the dynamical_matrix +command for detailed usage instructions. Use of this package requires building LAMMPS with FFT suppport, as described in doc/Section_start.html. -There are example scripts for using this package in +There are example scripts for using commands in this package in examples/USER/phonon. There is an auxiliary post-processing tool in tools/phonon that will compute phonon frequencies and dispersion relations from the dynamical -matrices output by this command. +matrices output by the fix phonon command. There is also an alternative code, dump2phonon, available which enables one to use the functions of fix-phonon by reading in atom-style dump @@ -21,6 +25,10 @@ files of lammps (which can be converted from the trajectories of any other MD code): https://github.com/lingtikong/dump2phonon -The person who created this package is Ling-Ti Kong (konglt at +The person who created fix phonon is Ling-Ti Kong (konglt at sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly if you have questions. + +The person who created the dynamical_matrix command is Charlie Sievers +(charliesievers at cox.net) at UC Davis. Contact him directly if you +have questions about his code. diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp new file mode 100644 index 0000000000..d94bd11a80 --- /dev/null +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -0,0 +1,573 @@ +// +// Created by charlie sievers on 6/21/18. +// + +#include +#include +#include "dynamical_matrix.h" +#include "atom.h" +#include "modify.h" +#include "domain.h" +#include "comm.h" +#include "group.h" +#include "force.h" +#include "math_extra.h" +#include "memory.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "update.h" +#include "neighbor.h" +#include "pair.h" +#include "timer.h" +#include "finish.h" +#include + + +using namespace LAMMPS_NS; +enum{REGULAR,ESKM}; + +/* ---------------------------------------------------------------------- */ + +DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(NULL) +{ + external_force_clear = 1; +} + +/* ---------------------------------------------------------------------- */ + +DynamicalMatrix::~DynamicalMatrix() +{ + if (fp && me == 0) fclose(fp); + memory->destroy(groupmap); + fp = NULL; +} + +/* ---------------------------------------------------------------------- + setup without output or one-time post-init setup + flag = 0 = just force calculation + flag = 1 = reneighbor and force calculation +------------------------------------------------------------------------- */ + +void DynamicalMatrix::setup() +{ + // setup domain, communication and neighboring + // acquire ghosts + // build neighbor lists + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + domain->reset_box(); + comm->setup(); + if (neighbor->style) neighbor->setup_bins(); + comm->exchange(); + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost); + domain->image_check(); + domain->box_too_small_check(); + neighbor->build(1); + neighbor->ncalls = 0; + neighbor->every = 2; // build every this many steps + neighbor->delay = 1; + neighbor->ago = 0; + neighbor->ndanger = 0; + + // compute all forces + external_force_clear = 0; + eflag=0; + vflag=0; + update_force(); + + //if all then skip communication groupmap population + if (gcount == atom->natoms) + for (bigint i=0; inatoms; i++) + groupmap[i] = i; + else + create_groupmap(); +} + +/* ---------------------------------------------------------------------- */ + +void DynamicalMatrix::command(int narg, char **arg) +{ + MPI_Comm_rank(world,&me); + + if (domain->box_exist == 0) + error->all(FLERR,"Dynamical_matrix command before simulation box is defined"); + if (narg < 2) error->all(FLERR,"Illegal dynamical_matrix command"); + + lmp->init(); + + // orthogonal vs triclinic simulation box + + triclinic = domain->triclinic; + + if (force->pair && force->pair->compute_flag) pair_compute_flag = 1; + else pair_compute_flag = 0; + if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1; + else kspace_compute_flag = 0; + + // group and style + + igroup = group->find(arg[0]); + if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID"); + groupbit = group->bitmask[igroup]; + gcount = group->count(igroup); + dynlen = (gcount)*3; + memory->create(groupmap,atom->natoms,"total_group_map:totalgm"); + update->setupflag = 1; + + int style = -1; + if (strcmp(arg[1],"regular") == 0) style = REGULAR; + else if (strcmp(arg[1],"eskm") == 0) style = ESKM; + else error->all(FLERR,"Illegal Dynamical Matrix command"); + del = force->numeric(FLERR, arg[2]); + + // set option defaults + + binaryflag = 0; + scaleflag = 0; + compressed = 0; + file_flag = 0; + file_opened = 0; + conversion = 1; + + // read options from end of input line + if (style == REGULAR) options(narg-3,&arg[3]); //COME BACK + else if (style == ESKM) options(narg-3,&arg[3]); //COME BACK + else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n"); + + if (atom->map_style == 0) + error->all(FLERR,"Dynamical_matrix command requires an atom map, see atom_modify"); + + // move atoms by 3-vector or specified variable(s) + + if (style == REGULAR) { + setup(); + timer->init(); + timer->barrier_start(); + calculateMatrix(); + timer->barrier_stop(); + } + + if (style == ESKM) { + setup(); + convert_units(update->unit_style); + conversion = conv_energy/conv_distance/conv_mass; + timer->init(); + timer->barrier_start(); + calculateMatrix(); + timer->barrier_stop(); + } + + Finish finish(lmp); + finish.end(1); +} + +/* ---------------------------------------------------------------------- + parse optional parameters +------------------------------------------------------------------------- */ + +void DynamicalMatrix::options(int narg, char **arg) +{ + if (narg < 0) error->all(FLERR,"Illegal dynamical_matrix command"); + int iarg = 0; + const char* filename = "dynmat.dyn"; + while (iarg < narg) { + if (strcmp(arg[iarg],"binary") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal dynamical_matrix command"); + if (strcmp(arg[iarg+1],"gzip") == 0) { + compressed = 1; + } + else if (strcmp(arg[iarg+1],"yes") == 0) { + binaryflag = 1; + } + iarg += 2; + } + else if (strcmp(arg[iarg],"file") == 0) { + if (iarg+2 > narg) error->all(FLERR, "Illegal dynamical_matrix command"); + filename = arg[iarg + 1]; + file_flag = 1; + iarg += 2; + } else error->all(FLERR,"Illegal dynamical_matrix command"); + } + if (file_flag == 1) { + openfile(filename); + } +} + +/* ---------------------------------------------------------------------- + generic opening of a file + ASCII or binary or gzipped + some derived classes override this function +------------------------------------------------------------------------- */ + +void DynamicalMatrix::openfile(const char* filename) +{ + // if file already opened, return + //if (me!=0) return; + if (file_opened) return; + + if (compressed) { +#ifdef LAMMPS_GZIP + char gzip[128]; + sprintf(gzip,"gzip -6 > %s",filename); +#ifdef _WIN32 + fp = _popen(gzip,"wb"); +#else + fp = popen(gzip,"w"); +#endif +#else + error->one(FLERR,"Cannot open gzipped file"); +#endif + } else if (binaryflag) { + fp = fopen(filename,"wb"); + } else { + fp = fopen(filename,"w"); + } + + if (fp == NULL) error->one(FLERR,"Cannot open dump file"); + + file_opened = 1; +} + +/* ---------------------------------------------------------------------- + create dynamical matrix +------------------------------------------------------------------------- */ + +void DynamicalMatrix::calculateMatrix() +{ + int local_idx; // local index + int local_jdx; // second local index + int nlocal = atom->nlocal; + bigint natoms = atom->natoms; + int *type = atom->type; + bigint *gm = groupmap; + double imass; // dynamical matrix element + double *m = atom->mass; + double **f = atom->f; + + double **dynmat = new double*[3]; + for (int i=0; i<3; i++) + dynmat[i] = new double[dynlen]; + + double **fdynmat = new double*[3]; + for (int i=0; i<3; i++) + fdynmat[i] = new double[dynlen]; + + //initialize dynmat to all zeros + dynmat_clear(dynmat); + + if (comm->me == 0 && screen) { + fprintf(screen,"Calculating Dynamical Matrix ...\n"); + fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms); + fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount); + fprintf(screen," Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) ); + } + + // emit dynlen rows of dimalpha*dynlen*dimbeta elements + + update->nsteps = 0; + int prog = 0; + for (bigint i=1; i<=natoms; i++){ + local_idx = atom->map(i); + if (gm[i-1] < 0) + continue; + for (bigint alpha=0; alpha<3; alpha++){ + displace_atom(local_idx, alpha, 1); + update_force(); + for (bigint j=1; j<=natoms; j++){ + local_jdx = atom->map(j); + if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal + && gm[j-1] >= 0){ + for (int beta=0; beta<3; beta++){ + dynmat[alpha][gm[j-1]*3+beta] -= f[local_jdx][beta]; + } + } + } + displace_atom(local_idx,alpha,-2); + update_force(); + for (bigint j=1; j<=natoms; j++){ + local_jdx = atom->map(j); + if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal + && gm[j-1] >= 0){ + for (bigint beta=0; beta<3; beta++){ + if (atom->rmass_flag == 1) + imass = sqrt(m[local_idx] * m[local_jdx]); + else + imass = sqrt(m[type[local_idx]] * m[type[local_jdx]]); + dynmat[alpha][gm[j-1]*3+beta] -= -f[local_jdx][beta]; + dynmat[alpha][gm[j-1]*3+beta] /= (2 * del * imass); + dynmat[alpha][gm[j-1]*3+beta] *= conversion; + } + } + } + displace_atom(local_idx,alpha,1); + } + for (int k=0; k<3; k++) + MPI_Reduce(dynmat[k],fdynmat[k],dynlen,MPI_DOUBLE,MPI_SUM,0,world); + if (me == 0) + writeMatrix(fdynmat); + dynmat_clear(dynmat); + if (comm->me == 0 && screen) { + int p = 10 * gm[i-1] / gcount; + if (p > prog) { + prog = p; + fprintf(screen," %d%%",p*10); + fflush(screen); + } + } + } + if (comm->me == 0 && screen) fprintf(screen,"\n"); + + for (int i=0; i < 3; i++) + delete [] dynmat[i]; + delete [] dynmat; + + for (int i=0; i < 3; i++) + delete [] fdynmat[i]; + delete [] fdynmat; + + if (screen && me ==0 ) fprintf(screen,"Finished Calculating Dynamical Matrix\n"); +} + +/* ---------------------------------------------------------------------- + write dynamical matrix +------------------------------------------------------------------------- */ + +void DynamicalMatrix::writeMatrix(double **dynmat) +{ + if (me != 0 || !fp) + return; + + clearerr(fp); + if (binaryflag) { + for (int i=0; i<3; i++) + fwrite(dynmat[i], sizeof(double), dynlen, fp); + if (ferror(fp)) + error->one(FLERR, "Error writing to binary file"); + } else { + for (int i = 0; i < 3; i++) { + for (bigint j = 0; j < dynlen; j++) { + if ((j+1)%3==0) fprintf(fp, "%4.8f\n", dynmat[i][j]); + else fprintf(fp, "%4.8f ",dynmat[i][j]); + } + } + if (ferror(fp)) + error->one(FLERR,"Error writing to file"); + } +} + +/* ---------------------------------------------------------------------- + Displace atoms + ---------------------------------------------------------------------- */ + +void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude) +{ + if (local_idx < 0) return; + + double **x = atom->x; + int *sametag = atom->sametag; + int j = local_idx; + + x[local_idx][direction] += del*magnitude; + + while (sametag[j] >= 0){ + j = sametag[j]; + x[j][direction] += del*magnitude; + } +} + + +/* ---------------------------------------------------------------------- + evaluate potential energy and forces + may migrate atoms due to reneighboring + return new energy, which should include nextra_global dof + return negative gradient stored in atom->f + return negative gradient for nextra_global dof in fextra +------------------------------------------------------------------------- */ + +void DynamicalMatrix::update_force() +{ + force_clear(); + + if (pair_compute_flag) { + force->pair->compute(eflag,vflag); + timer->stamp(Timer::PAIR); + } + if (atom->molecular) { + if (force->bond) force->bond->compute(eflag,vflag); + if (force->angle) force->angle->compute(eflag,vflag); + if (force->dihedral) force->dihedral->compute(eflag,vflag); + if (force->improper) force->improper->compute(eflag,vflag); + timer->stamp(Timer::BOND); + } + if (kspace_compute_flag) { + force->kspace->compute(eflag,vflag); + timer->stamp(Timer::KSPACE); + } + if (force->newton) { + comm->reverse_comm(); + timer->stamp(Timer::COMM); + } + ++ update->nsteps; +} + +/* ---------------------------------------------------------------------- + clear force on own & ghost atoms + clear other arrays as needed +------------------------------------------------------------------------- */ + +void DynamicalMatrix::force_clear() +{ + if (external_force_clear) return; + + // clear global force array + // if either newton flag is set, also include ghosts + + size_t nbytes = sizeof(double) * atom->nlocal; + if (force->newton) nbytes += sizeof(double) * atom->nghost; + + if (nbytes) { + memset(&atom->f[0][0],0,3*nbytes); + } +} + +/* ---------------------------------------------------------------------- + clear dynmat needed +------------------------------------------------------------------------- */ + +void DynamicalMatrix::dynmat_clear(double **dynmat) +{ + + size_t nbytes = sizeof(double) * dynlen; + + if (nbytes) { + for (int i=0; i<3; i++) + memset(&dynmat[i][0],0,nbytes); + } +} + +/* ---------------------------------------------------------------------- */ + +void DynamicalMatrix::convert_units(const char *style) +{ + // physical constants from: + // http://physics.nist.gov/cuu/Constants/Table/allascii.txt + // using thermochemical calorie = 4.184 J + + if (strcmp(style,"lj") == 0) { + error->all(FLERR,"Conversion Not Set"); + //conversion = 1; // lj -> 10 J/mol + + } else if (strcmp(style,"real") == 0) { + conv_energy = 418.4; // kcal/mol -> 10 J/mol + conv_mass = 1; // g/mol -> g/mol + conv_distance = 1; // angstrom -> angstrom + + } else if (strcmp(style,"metal") == 0) { + conv_energy = 9648.5; // eV -> 10 J/mol + conv_mass = 1; // g/mol -> g/mol + conv_distance = 1; // angstrom -> angstrom + + } else if (strcmp(style,"si") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float"); + conv_energy = 6.022E22; // J -> 10 J/mol + conv_mass = 6.022E26; // kg -> g/mol + conv_distance = 1E-10; // meter -> angstrom + + } else if (strcmp(style,"cgs") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Multiplication by Large Float"); + conv_energy = 6.022E12; // Erg -> 10 J/mol + conv_mass = 6.022E23; // g -> g/mol + conv_distance = 1E-7; // centimeter -> angstrom + + } else if (strcmp(style,"electron") == 0) { + conv_energy = 262550; // Hartree -> 10 J/mol + conv_mass = 1; // amu -> g/mol + conv_distance = 0.529177249; // bohr -> angstrom + + } else if (strcmp(style,"micro") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion"); + conv_energy = 6.022E10; // picogram-micrometer^2/microsecond^2 -> 10 J/mol + conv_mass = 6.022E11; // pg -> g/mol + conv_distance = 1E-4; // micrometer -> angstrom + + } else if (strcmp(style,"nano") == 0) { + if (comm->me) error->warning(FLERR,"Conversion Warning: Untested Conversion"); + conv_energy = 6.022E4; // attogram-nanometer^2/nanosecond^2 -> 10 J/mol + conv_mass = 6.022E5; // ag -> g/mol + conv_distance = 0.1; // angstrom -> angstrom + + } else error->all(FLERR,"Units Type Conversion Not Found"); + +} + +/* ---------------------------------------------------------------------- */ + +void DynamicalMatrix::create_groupmap() +{ + //Create a group map which maps atom order onto group + // groupmap[global atom index-1] = output column/row + + int local_idx; // local index + int gid = 0; //group index + int nlocal = atom->nlocal; + int *mask = atom->mask; + bigint natoms = atom->natoms; + int *recv = new int[comm->nprocs]; + int *displs = new int[comm->nprocs]; + bigint *temp_groupmap = new bigint[natoms]; + + //find number of local atoms in the group (final_gid) + for (bigint i=1; i<=natoms; i++){ + local_idx = atom->map(i); + if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit) + gid += 1; // gid at the end of loop is final_Gid + } + //create an array of length final_gid + bigint *sub_groupmap = new bigint[gid]; + + gid = 0; + //create a map between global atom id and group atom id for each proc + for (bigint i=1; i<=natoms; i++){ + local_idx = atom->map(i); + if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){ + sub_groupmap[gid] = i; + gid += 1; + } + } + + //populate arrays for Allgatherv + for (int i=0; inprocs; i++){ + recv[i] = 0; + } + recv[comm->me] = gid; + MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world); + for (int i=0; inprocs; i++){ + recv[i]=displs[i]; + if (i>0) displs[i] = displs[i-1]+recv[i-1]; + else displs[i] = 0; + } + + //combine subgroup maps into total temporary groupmap + MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world); + std::sort(temp_groupmap,temp_groupmap+gcount); + + //populate member groupmap based on temp groupmap + bigint j = 0; + for (bigint i=1; i<=natoms; i++){ + // flag groupmap contents that are in temp_groupmap + if (j < gcount && i == temp_groupmap[j]) + groupmap[i-1] = j++; + else + groupmap[i-1] = -1; + } + + //free that memory! + delete[] recv; + delete[] displs; + delete[] sub_groupmap; + delete[] temp_groupmap; +} diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/USER-PHONON/dynamical_matrix.h new file mode 100644 index 0000000000..8ff11044ea --- /dev/null +++ b/src/USER-PHONON/dynamical_matrix.h @@ -0,0 +1,74 @@ +// +// Created by charlie sievers on 6/21/18. +// + +#ifdef COMMAND_CLASS + +CommandStyle(dynamical_matrix,DynamicalMatrix) + +#else + +#ifndef LMP_DYNAMICAL_MATRIX_H +#define LMP_DYNAMICAL_MATRIX_H + +#include "pointers.h" + +namespace LAMMPS_NS { + + class DynamicalMatrix : protected Pointers { + public: + DynamicalMatrix(class LAMMPS *); + virtual ~DynamicalMatrix(); + void command(int, char **); + void setup(); + + protected: + int eflag,vflag; // flags for energy/virial computation + int external_force_clear; // clear forces locally or externally + + + int triclinic; // 0 if domain is orthog, 1 if triclinic + int pairflag; + + int pair_compute_flag; // 0 if pair->compute is skipped + int kspace_compute_flag; // 0 if kspace->compute is skipped + + int nvec; // local atomic dof = length of xvec + + void update_force(); + void force_clear(); + virtual void openfile(const char* filename); + + private: + void options(int, char **); + void calculateMatrix(); + void dynmat_clear(double **dynmat); + void create_groupmap(); + void writeMatrix(double **dynmat); + void convert_units(const char *style); + void displace_atom(int local_idx, int direction, int magnitude); + + double conversion; + double conv_energy; + double conv_distance; + double conv_mass; + double del; + int igroup,groupbit; + bigint gcount; // number of atoms in group + bigint dynlen; // rank of dynamical matrix + int scaleflag; + int me; + bigint *groupmap; + + int compressed; // 1 if dump file is written compressed, 0 no + int binaryflag; // 1 if dump file is written binary, 0 no + int file_opened; // 1 if openfile method has been called, 0 no + int file_flag; // 1 custom file name, 0 dynmat.dat + + FILE *fp; + }; +} + + +#endif //LMP_DYNAMICAL_MATRIX_H +#endif diff --git a/src/MEAM/Install.sh b/src/USER-PLUMED/Install.sh similarity index 59% rename from src/MEAM/Install.sh rename to src/USER-PLUMED/Install.sh index 7bfc76c0e2..f879d42feb 100755 --- a/src/MEAM/Install.sh +++ b/src/USER-PLUMED/Install.sh @@ -37,31 +37,29 @@ done if (test $1 = 1) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*meam[^ \t]* //' ../Makefile.package - sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/meam |' ../Makefile.package - sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/meam |' ../Makefile.package - sed -i -e 's|^PKG_LIB =[ \t]*|&-lmeam |' ../Makefile.package - sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(meam_SYSINC) |' ../Makefile.package - sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(meam_SYSLIB) |' ../Makefile.package - sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(meam_SYSPATH) |' ../Makefile.package + sed -i -e 's/[^ \t]*plumed[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/plumed/includelink |' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(plumed_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(plumed_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(plumed_SYSPATH) |' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*meam.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings # multiline form needed for BSD sed on Macs sed -i -e '4 i \ -include ..\/..\/lib\/meam\/Makefile.lammps +include ..\/..\/lib\/plumed\/Makefile.lammps ' ../Makefile.package.settings fi elif (test $1 = 0) then if (test -e ../Makefile.package) then - sed -i -e 's/[^ \t]*meam[^ \t]* //' ../Makefile.package + sed -i -e 's/[^ \t]*plumed[^ \t]* //' ../Makefile.package fi if (test -e ../Makefile.package.settings) then - sed -i -e '/^include.*meam.*$/d' ../Makefile.package.settings + sed -i -e '/^include.*plumed.*$/d' ../Makefile.package.settings fi fi diff --git a/src/USER-PLUMED/README b/src/USER-PLUMED/README new file mode 100644 index 0000000000..11ca0a7281 --- /dev/null +++ b/src/USER-PLUMED/README @@ -0,0 +1,70 @@ +This package implements the "fix plumed" command, which can be used +in a LAMMPS input script. + +The fix allows enhanced sampling methods such as umbrella sampling and +metadynamics to be used. Furthermore, PLUMED can be used to perform a +wide range of analyses on trajectories on the fly as they are generated. + +The package uses the "PLUMED" library, whose source code is not included +in the LAMMPS source code distribution. The files in the USER-PLUMED package +folder implement an interface between LAMMPS and PLUMED, that are written +and maintained by Gareth Tribello (gareth.tribello@gmail.com). + +PLUMED must instead be downloaded and compiled separately to LAMMPS. This building +and compiling of PLUMED can be done before or after the building of LAMMPS as LAMMPS +can call PLUMED as a dynamic library. There is also the possibility to link PLUEMD +statically. In this case a copy of PLUMED must be downloaded into the lib/plumed +directory. This copy of PLUMED will then always be linked into the code at compile +time. + +However you decide to link PLUMED (statically or dynamically) you must run the command: + +make yes-user-plumed + +before compiling LAMMPS in order to enable the module. In addition, if you have chosen to +link PLUMED dynamically you must ensure that PLUMED is in your +PATH when running a LAMMPS calculation that takes advantage of PLUMED. If +PLUMED is linked as a runtime library and if PLUMED is not in the PATH an error will be returned whenever LAMMPS encounters +the fix plumed command in its input. To be clear, however, a LAMMPS executable that was dynamically linked with PLUMED will run +even if PLUMED is not in the path if as long as the input does not contain a fix +plumed command. + +If you wish to statically link PLUMED you must download PLUMED to the /lib/plumed directory before compiling LAMMPS. You can +download a tar ball into that directory or you can clone the plumed2 repository from github there. Once you have created a +directory containing a distribution of PLUMED within /lib/plumed you then must build PLUMED within that directory by issuing +the usual commands. It is worth noting that we have provided a script that will download and build PLUMED for you with +a minimal set of options. To run this script you need to issue the following command: + +make lib-plumed args="-b" + +in the src directory. + +More info about the PLUMED library can be found at: + +www.plumed.org + +and in the reference articles: + +PLUMED2: New feathers for an old bird +G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, +Comp. Phys. Comm 185, 604 (2014) +https://doi.org/10.1016/j.cpc.2013.09.018 + +PLUMED: a portable plugin for free energy calculations with molecular dynamics +M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R.A. Broglia and M. Parrinello +Comp. Phys. Comm. 180, 1961 (2009) +https://doi.org/10.1016/j.cpc.2009.05.011 + +Instructions explaining how to use PLUMED and LAMMPS in tandem can be found on the PLUMED website, which also gives +numerous example scripts for PLUMED as well as citations to articles that dcoment the various methods that are +implemented within PLUMED. + +There are also example scripts for using this package in the folder +examples/USER/plumed, as well as on the GitHub page for PLUMED. + +Please contact Gareth Tribello (gareth.tribello@gmail.com) for questions +regarding this package. + +--------------------------------- + +Version: 2016-12-22 diff --git a/src/USER-PLUMED/fix_plumed.cpp b/src/USER-PLUMED/fix_plumed.cpp new file mode 100644 index 0000000000..635d08c573 --- /dev/null +++ b/src/USER-PLUMED/fix_plumed.cpp @@ -0,0 +1,576 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing authors: Gareth Tribello (Queens U, Belfast) + Pablo Piaggi (EPFL) +------------------------------------------------------------------------- */ + +#include +#include +#include + +#include "atom.h" +#include "comm.h" +#include "update.h" +#include "force.h" +#include "respa.h" +#include "domain.h" +#include "error.h" +#include "group.h" +#include "fix_plumed.h" +#include "universe.h" +#include "compute.h" +#include "modify.h" +#include "pair.h" + +#include "plumed/wrapper/Plumed.h" + +#if defined(__PLUMED_DEFAULT_KERNEL) +#define PLUMED_QUOTE_DIRECT(name) #name +#define PLUMED_QUOTE(macro) PLUMED_QUOTE_DIRECT(macro) +static char plumed_default_kernel[] = "PLUMED_KERNEL=" PLUMED_QUOTE(__PLUMED_DEFAULT_KERNEL); +#endif + +/* -------------------------------------------------------------------- */ + +using namespace LAMMPS_NS; +using namespace FixConst; + +#define INVOKED_SCALAR 1 + +FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + p(NULL), nlocal(0), gatindex(NULL), masses(NULL), charges(NULL), + id_pe(NULL), id_press(NULL) +{ + + if (!atom->tag_enable) + error->all(FLERR,"Fix plumed requires atom tags"); + + if (atom->tag_consecutive() == 0) + error->all(FLERR,"Fix plumed requires consecutive atom IDs"); + + if (igroup != 0 && comm->me == 0) + error->warning(FLERR,"Fix group for fix plumed is not 'all'. " + "Group will be ignored."); + +#if defined(__PLUMED_DEFAULT_KERNEL) + if (getenv("PLUMED_KERNEL") == NULL) + putenv(plumed_default_kernel); +#endif + + p=new PLMD::Plumed; + + // Check API version + + int api_version; + p->cmd("getApiVersion",&api_version); + if (api_version > 6) + error->all(FLERR,"Incompatible API version for PLUMED in fix plumed"); + + // If the -partition option is activated then enable + // inter-partition communication + + if (universe->existflag == 1) { + int me; + MPI_Comm inter_comm; + MPI_Comm_rank(world,&me); + + // Change MPI_COMM_WORLD to universe->uworld which seems more appropriate + + MPI_Comm_split(universe->uworld,me,0,&inter_comm); + p->cmd("GREX setMPIIntracomm",&world); + if (me == 0) { + // The inter-partition communicator is only defined for the root in + // each partition (a.k.a. world). This is due to the way in which + // it is defined inside plumed. + p->cmd("GREX setMPIIntercomm",&inter_comm); + } + p->cmd("GREX init",NULL); + } + + // The general communicator is independent of the existence of partitions, + // if there are partitions, world is defined within each partition, + // whereas if partitions are not defined then world is equal to + // MPI_COMM_WORLD. + + p->cmd("setMPIComm",&world); + + // Set up units + // LAMMPS units wrt kj/mol - nm - ps + // Set up units + + if(strcmp(update->unit_style,"lj") == 0) { + // LAMMPS units lj + p->cmd("setNaturalUnits"); + } else { + + // Conversion factor from LAMMPS energy units to kJ/mol (units of PLUMED) + + double energyUnits=1.0; + + // LAMMPS units real :: kcal/mol; + + if (strcmp(update->unit_style,"real") == 0) { + energyUnits=4.184; + + // LAMMPS units metal :: eV; + + } else if (strcmp(update->unit_style,"metal") == 0) { + energyUnits=96.48530749925792; + + // LAMMPS units si :: Joule; + + } else if (strcmp(update->unit_style,"si") == 0) { + energyUnits=0.001; + + // LAMMPS units cgs :: erg; + + } else if (strcmp(update->unit_style,"cgs") == 0) { + energyUnits=6.0221418e13; + + // LAMMPS units electron :: Hartree; + + } else if (strcmp(update->unit_style,"electron") == 0) { + energyUnits=2625.5257; + + } else error->all(FLERR,"Fix plumed cannot handle your choice of units"); + + // Conversion factor from LAMMPS length units to nm (units of PLUMED) + + double lengthUnits=0.1/force->angstrom; + + // Conversion factor from LAMMPS time unit to ps (units of PLUMED) + + double timeUnits=0.001/force->femtosecond; + + p->cmd("setMDEnergyUnits",&energyUnits); + p->cmd("setMDLengthUnits",&lengthUnits); + p->cmd("setMDTimeUnits",&timeUnits); + } + + // Read fix parameters: + + int next=0; + for (int i=3;iexistflag == 1) { + // Each replica writes an independent log file + // with suffix equal to the replica id + char str_num[32], logFile[1024]; + sprintf(str_num,".%d",universe->iworld); + strncpy(logFile,arg[i],1024-32); + strcat(logFile,str_num); + p->cmd("setLogFile",logFile); + next=0; + } else { + // partition option not used + p->cmd("setLogFile",arg[i]); + next=0; + } + } else if (!strcmp(arg[i],"plumedfile")) { + next=2; + } else if (next==2) { + p->cmd("setPlumedDat",arg[i]); + next=0; + } else error->all(FLERR,"Syntax error - use 'fix plumed " + "plumedfile plumed.dat outfile plumed.out' "); + } + if (next==1) error->all(FLERR,"missing argument for outfile option"); + if (next==2) error->all(FLERR,"missing argument for plumedfile option"); + + p->cmd("setMDEngine","LAMMPS"); + + if (atom->natoms > MAXSMALLINT) + error->all(FLERR,"Fix plumed can only handle up to 2.1 billion atoms"); + + natoms=int(atom->natoms); + p->cmd("setNatoms",&natoms); + + double dt=update->dt; + p->cmd("setTimestep",&dt); + + virial_flag=1; + thermo_virial=1; + scalar_flag = 1; + + // This is the real initialization: + + p->cmd("init"); + + // Define compute to calculate potential energy + + id_pe = new char[8]; + strcpy(id_pe,"plmd_pe"); + char **newarg = new char*[3]; + newarg[0] = id_pe; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pe"; + modify->add_compute(3,newarg); + delete [] newarg; + int ipe = modify->find_compute(id_pe); + c_pe = modify->compute[ipe]; + + // Define compute to calculate pressure tensor + + id_press = new char[11]; + strcpy(id_press,"plmd_press"); + newarg = new char*[5]; + newarg[0] = id_press; + newarg[1] = (char *) "all"; + newarg[2] = (char *) "pressure"; + newarg[3] = (char *) "NULL"; + newarg[4] = (char *) "virial"; + modify->add_compute(5,newarg); + delete [] newarg; + int ipress = modify->find_compute(id_press); + c_press = modify->compute[ipress]; + + for (int i = 0; i < modify->nfix; i++) { + const char * const check_style = modify->fix[i]->style; + + // There must be only one + + if (strcmp(check_style,"plumed") == 0) + error->all(FLERR,"There must be only one instance of fix plumed"); + + // Avoid conflict with fixes that define internal pressure computes. + // See comment in the setup method + + if ((strncmp(check_style,"nph",3) == 0) || + (strncmp(check_style,"npt",3) == 0) || + (strncmp(check_style,"rigid/nph",9) == 0) || + (strncmp(check_style,"rigid/npt",9) == 0) || + (strncmp(check_style,"msst",4) == 0) || + (strncmp(check_style,"nphug",5) == 0) || + (strncmp(check_style,"ipi",3) == 0) || + (strncmp(check_style,"press/berendsen",15) == 0) || + (strncmp(check_style,"qbmsst",6) == 0)) + error->all(FLERR,"Fix plumed must be defined before any other fixes, " + "that compute pressure internally"); + } +} + +FixPlumed::~FixPlumed() +{ + delete p; + modify->delete_compute(id_pe); + modify->delete_compute(id_press); + delete[] id_pe; + delete[] id_press; + delete[] masses; + delete[] charges; + delete[] gatindex; +} + +int FixPlumed::setmask() +{ + // set with a bitmask how and when apply the force from plumed + int mask = 0; + mask |= POST_FORCE; + mask |= THERMO_ENERGY; + mask |= POST_FORCE_RESPA; + mask |= MIN_POST_FORCE; + return mask; +} + +void FixPlumed::init() +{ + if (strcmp(update->integrate_style,"respa") == 0) + nlevels_respa = ((Respa *) update->integrate)->nlevels; + + // This avoids nan pressure if compute_pressure is called + // in a setup method + + for (int i=0;i<6;i++) virial[i] = 0.; +} + +void FixPlumed::setup(int vflag) +{ + // Here there is a crucial issue connected to constant pressure + // simulations. The fix_nh will call the compute_pressure inside + // the setup method, that is executed once and for all at the + // beginning of the simulation. Since our fix has a contribution + // to the virial, when this happens the variable virial must have + // been calculated. In other words, the setup method of fix_plumed + // has to be executed first. This creates a race condition with the + // setup method of fix_nh. This is why in the constructor I check if + // nh fixes have already been called. + if (strcmp(update->integrate_style,"verlet") == 0) + post_force(vflag); + else { + ((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1); + post_force_respa(vflag,nlevels_respa-1,0); + ((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1); + } +} + +void FixPlumed::min_setup(int vflag) +{ + // This has to be checked. + // For instance it might have problems with fix_box_relax + post_force(vflag); +} + +void FixPlumed::post_force(int /* vflag */) +{ + + int update_gatindex=0; + + if (natoms != int(atom->natoms)) + error->all(FLERR,"Fix plumed does not support simulations with varying " + "numbers of atoms"); + + // Try to find out if the domain decomposition has been updated: + + if (nlocal != atom->nlocal) { + + if (charges) delete [] charges; + if (masses) delete [] masses; + if (gatindex) delete [] gatindex; + + nlocal=atom->nlocal; + gatindex=new int [nlocal]; + masses=new double [nlocal]; + charges=new double [nlocal]; + update_gatindex=1; + + } else { + + for (int i=0;itag[i]-1) { + update_gatindex=1; + break; + } + } + } + MPI_Allreduce(MPI_IN_PLACE,&update_gatindex,1,MPI_INT,MPI_SUM,world); + + // In case it has been updated, rebuild the local mass/charges array + // and tell plumed about the change: + + if (update_gatindex) { + for (int i=0;itag[i]-1; + // Get masses + if (atom->rmass_flag) { + for (int i=0;irmass[i]; + } else { + for (int i=0;imass[atom->type[i]]; + } + // Get charges + if (atom->q_flag) { + for (int i=0;iq[i]; + } else { + for (int i=0;icmd("setAtomsNlocal",&nlocal); + p->cmd("setAtomsGatindex",gatindex); + } + + + // set up local virial/box. plumed uses full 3x3 matrices + double plmd_virial[3][3]; + for (int i=0;i<3;i++) for (int j=0;j<3;j++) plmd_virial[i][j]=0.0; + double box[3][3]; + for (int i=0;i<3;i++) for (int j=0;j<3;j++) box[i][j]=0.0; + box[0][0]=domain->h[0]; + box[1][1]=domain->h[1]; + box[2][2]=domain->h[2]; + box[2][1]=domain->h[3]; + box[2][0]=domain->h[4]; + box[1][0]=domain->h[5]; + + // Make initial of virial of this fix zero + // The following line is very important, otherwise + // the compute pressure will include + for (int i=0;i<6;++i) virial[i] = 0.; + + // local variable with timestep: + if (update->ntimestep > MAXSMALLINT) + error->all(FLERR,"Fix plumed can only handle up to 2.1 billion timesteps"); + int step=int(update->ntimestep); + + // pass all pointers to plumed: + p->cmd("setStep",&step); + p->cmd("setPositions",&atom->x[0][0]); + p->cmd("setBox",&box[0][0]); + p->cmd("setForces",&atom->f[0][0]); + p->cmd("setMasses",&masses[0]); + p->cmd("setCharges",&charges[0]); + p->cmd("getBias",&bias); + + // Pass virial to plumed + // If energy is needed plmd_virial is equal to Lammps' virial + // If energy is not needed plmd_virial is initialized to zero + // In the first case the virial will be rescaled and an extra term will be added + // In the latter case only an extra term will be added + p->cmd("setVirial",&plmd_virial[0][0]); + p->cmd("prepareCalc"); + + plumedNeedsEnergy=0; + p->cmd("isEnergyNeeded",&plumedNeedsEnergy); + + // Pass potential energy and virial if needed + double *virial_lmp; + if (plumedNeedsEnergy) { + // Error if tail corrections are included + if (force->pair && force->pair->tail_flag && comm->me == 0) + error->warning(FLERR,"Tail corrections to the pair potential included." + " The energy cannot be biased correctly in this case." + " Remove the tail corrections by removing the" + " command: pair_modify tail yes"); + + // compute the potential energy + double pot_energy = 0.; + c_pe->compute_scalar(); + pot_energy = c_pe->scalar; + + // Divide energy by number of processes + // Plumed wants it this way + int nprocs; + MPI_Comm_size(world,&nprocs); + pot_energy /= nprocs; + p->cmd("setEnergy",&pot_energy); + + // Compute pressure due to the virial (no kinetic energy term!) + c_press->compute_vector(); + virial_lmp = c_press->vector; + + // Check if pressure is finite + if (!std::isfinite(virial_lmp[0]) || !std::isfinite(virial_lmp[1]) + || !std::isfinite(virial_lmp[2]) || !std::isfinite(virial_lmp[3]) + || !std::isfinite(virial_lmp[4]) || !std::isfinite(virial_lmp[5])) + error->all(FLERR,"Non-numeric virial - Plumed cannot work with that"); + + // Convert pressure to virial per number of MPI processes + // From now on all virials are divided by the number of MPI processes + + double nktv2p = force->nktv2p; + double inv_volume; + if (domain->dimension == 3) { + inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd); + } else { + inv_volume = 1.0 / (domain->xprd * domain->yprd); + } + for (int i=0;i<6;i++) virial_lmp[i] /= (inv_volume * nktv2p * nprocs); + // Convert virial from lammps to plumed representation + plmd_virial[0][0]=-virial_lmp[0]; + plmd_virial[1][1]=-virial_lmp[1]; + plmd_virial[2][2]=-virial_lmp[2]; + plmd_virial[0][1]=-virial_lmp[3]; + plmd_virial[0][2]=-virial_lmp[4]; + plmd_virial[1][2]=-virial_lmp[5]; + } + // do the real calculation: + p->cmd("performCalc"); + + // retransform virial to lammps representation and assign it to this + // fix's virial. If the energy is biased, Plumed is giving back the full + // virial and therefore we have to subtract the initial virial i.e. virial_lmp. + // The vector virial contains only the contribution added by plumed. + // The calculation of the pressure will be done by a compute pressure + // and will include this contribution. + if (plumedNeedsEnergy) { + virial[0] = -plmd_virial[0][0]-virial_lmp[0]; + virial[1] = -plmd_virial[1][1]-virial_lmp[1]; + virial[2] = -plmd_virial[2][2]-virial_lmp[2]; + virial[3] = -plmd_virial[0][1]-virial_lmp[3]; + virial[4] = -plmd_virial[0][2]-virial_lmp[4]; + virial[5] = -plmd_virial[1][2]-virial_lmp[5]; + } else { + virial[0] = -plmd_virial[0][0]; + virial[1] = -plmd_virial[1][1]; + virial[2] = -plmd_virial[2][2]; + virial[3] = -plmd_virial[0][1]; + virial[4] = -plmd_virial[0][2]; + virial[5] = -plmd_virial[1][2]; + } + + // Ask for the computes in the next time step + // such that the virial and energy are tallied. + // This should be changed to something that triggers the + // calculation only if plumed needs it. + c_pe->addstep(update->ntimestep+1); + c_press->addstep(update->ntimestep+1); +} + +void FixPlumed::post_force_respa(int vflag, int ilevel, int /* iloop */) +{ + if (ilevel == nlevels_respa-1) post_force(vflag); +} + +void FixPlumed::min_post_force(int vflag) +{ + post_force(vflag); +} + +void FixPlumed::reset_dt() +{ + error->all(FLERR,"Cannot change the time step when fix plumed is active"); +} + +double FixPlumed::compute_scalar() +{ + return bias; +} + +int FixPlumed::modify_param(int narg, char **arg) +{ + if (strcmp(arg[0],"pe") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + modify->delete_compute(id_pe); + delete[] id_pe; + int n = strlen(arg[1]) + 1; + id_pe = new char[n]; + strcpy(id_pe,arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) error->all(FLERR,"Could not find fix_modify potential energy ID"); + c_pe = modify->compute[icompute]; + + if (c_pe->peflag == 0) + error->all(FLERR,"Fix_modify plmd_pe ID does not compute potential energy"); + if (c_pe->igroup != 0 && comm->me == 0) + error->warning(FLERR,"Potential for fix PLUMED is not for group all"); + + return 2; + + } else if (strcmp(arg[0],"press") == 0) { + if (narg < 2) error->all(FLERR,"Illegal fix_modify command"); + modify->delete_compute(id_press); + delete[] id_press; + int n = strlen(arg[1]) + 1; + id_press = new char[n]; + strcpy(id_press,arg[1]); + + int icompute = modify->find_compute(arg[1]); + if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID"); + c_press = modify->compute[icompute]; + + if (c_press->pressflag == 0) + error->all(FLERR,"Fix_modify pressure ID does not compute pressure"); + if (c_press->igroup != 0 && comm->me == 0) + error->warning(FLERR,"Virial for fix PLUMED is not for group all"); + + return 2; + } + return 0; +} + +double FixPlumed::memory_usage() +{ + return double((8+8+4)*atom->nlocal); +} diff --git a/src/USER-PLUMED/fix_plumed.h b/src/USER-PLUMED/fix_plumed.h new file mode 100644 index 0000000000..e20633fadc --- /dev/null +++ b/src/USER-PLUMED/fix_plumed.h @@ -0,0 +1,68 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(plumed,FixPlumed) + +#else + +#ifndef LMP_FIX_PLUMED_H +#define LMP_FIX_PLUMED_H + +#include "fix.h" + +// forward declaration +namespace PLMD { + class Plumed; +} + +namespace LAMMPS_NS { + +class FixPlumed : public Fix { + public: + FixPlumed(class LAMMPS *, int, char **); + ~FixPlumed(); + int setmask(); + void init(); + void setup(int); + void min_setup(int); + void post_force(int); + void post_force_respa(int, int, int); + void min_post_force(int); + double compute_scalar(); + void reset_dt(); + int modify_param(int narg, char **arg); + double memory_usage(); + + private: + + PLMD::Plumed *p; // pointer to plumed object + int nlocal; // number of atoms local to this process + int natoms; // total number of atoms + int *gatindex; // array of atom indexes local to this process + double *masses; // array of masses for local atoms + double *charges; // array of charges for local atoms + int nlevels_respa; // this is something to enable respa + double bias; // output bias potential + class Compute *c_pe; // Compute for the energy + class Compute *c_press; // Compute for the pressure + int plumedNeedsEnergy; // Flag to trigger calculation of the + // energy and virial + char *id_pe, *id_press; // ID for potential energy and pressure compute +}; + +}; + +#endif +#endif diff --git a/src/USER-PTM/README b/src/USER-PTM/README new file mode 100644 index 0000000000..d661fa5ac5 --- /dev/null +++ b/src/USER-PTM/README @@ -0,0 +1,27 @@ + +This package provides the compute ptm/atom command for LAMMPS which implements the +Polyhedral Template Matching algorithm for analysis of molecular dynamics simulation data + +The method is currently (Fall 2018) included in OVITO, LAMMPS, and ASAP. + +OVITO PTM documentation: http://www.ovito.org/manual/particles.modifiers.polyhedral_template_matching.html + +LAMMPS PTM documentation: http://lammps.sandia.gov/doc/compute_ptm_atom.html + +ASAP PTM documentation: http://wiki.fysik.dtu.dk/asap/Local%20crystalline%20order + + +If you use PTM in a publication, please reference: + +Peter Mahler Larsen and Søren Schmidt and Jakob Schiøtz +Robust structural identification via polyhedral template matching +Modelling Simul. Mater. Sci. Eng. 24 (2016) 055007 + +Article available at: +http://stacks.iop.org/0965-0393/24/i=5/a=055007 + +Preprint available at: +http://arxiv.org/abs/1603.05143 + + +Contact email: pmla@mit.edu diff --git a/src/USER-PTM/compute_ptm_atom.cpp b/src/USER-PTM/compute_ptm_atom.cpp index eb0138de26..41e6540b97 100644 --- a/src/USER-PTM/compute_ptm_atom.cpp +++ b/src/USER-PTM/compute_ptm_atom.cpp @@ -3,9 +3,9 @@ http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov - Copyright (2003) Sandia Corporation. Under the terms of Contract + Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains - certain rights in this software. This software is distributed + certain rights in this software. This software is distributed under the GNU General Public License. @@ -20,6 +20,7 @@ under #include #include #include +#include #include "atom.h" #include "comm.h" @@ -36,10 +37,9 @@ under #include "ptm_functions.h" -#define MAX_NEIGHBORS 30 #define NUM_COLUMNS 7 -#define UNKNOWN 0 -#define OTHER 8 +#define PTM_LAMMPS_UNKNOWN -1 +#define PTM_LAMMPS_OTHER 0 using namespace LAMMPS_NS; @@ -69,7 +69,9 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) char *ptr = structures; const char *strings[] = {"fcc", "hcp", "bcc", "ico", "sc", - "dcub", "dhex", "all", "default"}; + "dcub", "dhex", "graphene", "all", "default"}; + int num_strings = sizeof(strings) / sizeof(const char*); + int32_t flags[] = { PTM_CHECK_FCC, PTM_CHECK_HCP, @@ -78,6 +80,7 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) PTM_CHECK_SC, PTM_CHECK_DCUB, PTM_CHECK_DHEX, + PTM_CHECK_GRAPHENE, PTM_CHECK_ALL, PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_BCC | PTM_CHECK_ICO}; @@ -85,7 +88,7 @@ ComputePTMAtom::ComputePTMAtom(LAMMPS *lmp, int narg, char **arg) while (*ptr != '\0') { bool found = false; - for (int i = 0; i < 9; i++) { + for (int i = 0; i < num_strings; i++) { int len = strlen(strings[i]); if (strncmp(ptr, strings[i], len) == 0) { input_flags |= flags[i]; @@ -152,10 +155,21 @@ void ComputePTMAtom::init() { /* ---------------------------------------------------------------------- */ -void ComputePTMAtom::init_list(int id, NeighList *ptr) { list = ptr; } +void ComputePTMAtom::init_list(int /* id */, NeighList *ptr) { list = ptr; } /* ---------------------------------------------------------------------- */ +typedef struct +{ + double **x; + int *numneigh; + int **firstneigh; + int *ilist; + int nlocal; + +} ptmnbrdata_t; + + typedef struct { int index; double d; @@ -165,38 +179,59 @@ static bool sorthelper_compare(ptmnbr_t const &a, ptmnbr_t const &b) { return a.d < b.d; } -static int get_neighbors(double *pos, int jnum, int *jlist, double **x, - double (*nbr)[3]) { +static int get_neighbours(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3]) +{ + ptmnbrdata_t* data = (ptmnbrdata_t*)vdata; - ptmnbr_t *nbr_order = new ptmnbr_t[jnum]; + double **x = data->x; + double *pos = x[atom_index]; + + int *jlist = NULL; + int jnum = 0; + if (atom_index < data->nlocal) { + jlist = data->firstneigh[atom_index]; + jnum = data->numneigh[atom_index]; + } + else { + jlist = data->firstneigh[central_index]; + jnum = data->numneigh[central_index]; + } + + std::vector nbr_order; for (int jj = 0; jj < jnum; jj++) { int j = jlist[jj]; j &= NEIGHMASK; + if (j == atom_index) + continue; double dx = pos[0] - x[j][0]; double dy = pos[1] - x[j][1]; double dz = pos[2] - x[j][2]; double rsq = dx * dx + dy * dy + dz * dz; - nbr_order[jj].index = j; - nbr_order[jj].d = rsq; + ptmnbr_t nbr = {j, rsq}; + nbr_order.push_back(nbr); } - std::sort(nbr_order, nbr_order + jnum, &sorthelper_compare); - int num_nbrs = std::min(MAX_NEIGHBORS, jnum); + std::sort(nbr_order.begin(), nbr_order.end(), &sorthelper_compare); + int num_nbrs = std::min(num - 1, (int)nbr_order.size()); - nbr[0][0] = nbr[0][1] = nbr[0][2] = 0; + nbr_pos[0][0] = nbr_pos[0][1] = nbr_pos[0][2] = 0; + nbr_indices[0] = atom_index; + numbers[0] = 0; for (int jj = 0; jj < num_nbrs; jj++) { int j = nbr_order[jj].index; - nbr[jj + 1][0] = x[j][0] - pos[0]; - nbr[jj + 1][1] = x[j][1] - pos[1]; - nbr[jj + 1][2] = x[j][2] - pos[2]; + nbr_pos[jj + 1][0] = x[j][0] - pos[0]; + nbr_pos[jj + 1][1] = x[j][1] - pos[1]; + nbr_pos[jj + 1][2] = x[j][2] - pos[2]; + + nbr_indices[jj + 1] = j; + numbers[jj + 1] = 0; } - delete[] nbr_order; - return num_nbrs; + return num_nbrs + 1; } void ComputePTMAtom::compute_peratom() { @@ -228,51 +263,29 @@ void ComputePTMAtom::compute_peratom() { double **x = atom->x; int *mask = atom->mask; - int nlocal = atom->nlocal; + ptmnbrdata_t nbrlist = {x, numneigh, firstneigh, ilist, atom->nlocal}; for (int ii = 0; ii < inum; ii++) { int i = ilist[ii]; - output[i][0] = UNKNOWN; + output[i][0] = PTM_LAMMPS_UNKNOWN; if (!(mask[i] & groupbit)) continue; - double *pos = x[i]; - - int *jlist = firstneigh[i]; int jnum = numneigh[i]; if (jnum <= 0) continue; - // get neighbours ordered by increasing distance - double nbr[MAX_NEIGHBORS + 1][3]; - int num_nbrs = get_neighbors(pos, jnum, jlist, x, nbr); - - // check that we have enough neighbours for the desired structure types - int32_t flags = 0; - if (num_nbrs >= PTM_NUM_NBRS_SC && (input_flags & PTM_CHECK_SC)) - flags |= PTM_CHECK_SC; - if (num_nbrs >= PTM_NUM_NBRS_FCC && (input_flags & PTM_CHECK_FCC)) - flags |= PTM_CHECK_FCC; - if (num_nbrs >= PTM_NUM_NBRS_HCP && (input_flags & PTM_CHECK_HCP)) - flags |= PTM_CHECK_HCP; - if (num_nbrs >= PTM_NUM_NBRS_ICO && (input_flags & PTM_CHECK_ICO)) - flags |= PTM_CHECK_ICO; - if (num_nbrs >= PTM_NUM_NBRS_BCC && (input_flags & PTM_CHECK_BCC)) - flags |= PTM_CHECK_BCC; - if (num_nbrs >= PTM_NUM_NBRS_DCUB && (input_flags & PTM_CHECK_DCUB)) - flags |= PTM_CHECK_DCUB; - if (num_nbrs >= PTM_NUM_NBRS_DHEX && (input_flags & PTM_CHECK_DHEX)) - flags |= PTM_CHECK_DHEX; // now run PTM - int8_t mapping[MAX_NEIGHBORS + 1]; int32_t type, alloy_type; - double scale, rmsd, interatomic_distance, lattice_constant; - double q[4], F[9], F_res[3], U[9], P[9]; - ptm_index(local_handle, flags, num_nbrs + 1, nbr, NULL, true, &type, - &alloy_type, &scale, &rmsd, q, F, F_res, U, P, mapping, - &interatomic_distance, &lattice_constant); + double scale, rmsd, interatomic_distance; + double q[4]; + bool standard_orientations = false; + ptm_index(local_handle, i, get_neighbours, (void*)&nbrlist, + input_flags, standard_orientations, + &type, &alloy_type, &scale, &rmsd, q, + NULL, NULL, NULL, NULL, &interatomic_distance, NULL, NULL); if (rmsd > rmsd_threshold) { type = PTM_MATCH_NONE; @@ -280,8 +293,10 @@ void ComputePTMAtom::compute_peratom() { // printf("%d type=%d rmsd=%f\n", i, type, rmsd); - if (type == PTM_MATCH_NONE) - type = OTHER; + if (type == PTM_MATCH_NONE) { + type = PTM_LAMMPS_OTHER; + rmsd = INFINITY; + } output[i][0] = type; output[i][1] = rmsd; diff --git a/src/USER-PTM/compute_ptm_atom.h b/src/USER-PTM/compute_ptm_atom.h index 5c10e0c443..586d7a44cd 100644 --- a/src/USER-PTM/compute_ptm_atom.h +++ b/src/USER-PTM/compute_ptm_atom.h @@ -35,7 +35,7 @@ class ComputePTMAtom : public Compute { private: int nmax; - int32_t input_flags; + smallint input_flags; double rmsd_threshold; class NeighList *list; double **output; diff --git a/src/USER-PTM/ptm_alloy_types.cpp b/src/USER-PTM/ptm_alloy_types.cpp index 151de3e5b8..b6b94a3733 100644 --- a/src/USER-PTM/ptm_alloy_types.cpp +++ b/src/USER-PTM/ptm_alloy_types.cpp @@ -1,3 +1,12 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include #include "ptm_constants.h" #include "ptm_initialize_data.h" @@ -6,98 +15,107 @@ namespace ptm { #define NUM_ALLOY_TYPES 3 static uint32_t typedata[NUM_ALLOY_TYPES][3] = { - {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x000001fe}, - {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x0000001e}, - {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe}, + {PTM_MATCH_FCC, PTM_ALLOY_L10, 0x00000db6}, + {PTM_MATCH_FCC, PTM_ALLOY_L12_CU, 0x00000492}, + {PTM_MATCH_FCC, PTM_ALLOY_L12_AU, 0x00001ffe}, }; static bool test_pure(int num_nbrs, int32_t* numbers) { - for (int i=1;inum_nbrs+1;i++) - binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; + int8_t binary[PTM_MAX_POINTS]; + for (int i=0;inum_nbrs+1;i++) + binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; - for (int i=1;inum_nbrs+1;i++) - if (binary[i] != binary[0]) - return false; + for (int i=num_inner+1;inum_nbrs+1;i++) + if (binary[i] != binary[0]) + return false; - return true; + return true; } static int32_t canonical_alloy_representation(const refdata_t* ref, int8_t* mapping, int32_t* numbers) { - int8_t binary[PTM_MAX_POINTS]; - for (int i=0;inum_nbrs+1;i++) - binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; + int8_t binary[PTM_MAX_POINTS]; + for (int i=0;inum_nbrs+1;i++) + binary[i] = numbers[mapping[i]] == numbers[0] ? 0 : 1; - int8_t temp[PTM_MAX_POINTS]; - uint32_t best = 0xFFFFFFFF; - for (int j=0;jnum_mappings;j++) - { - for (int i=0;inum_nbrs+1;i++) - temp[ref->mapping[j][i]] = binary[i]; + int8_t temp[PTM_MAX_POINTS]; + uint32_t best = 0xFFFFFFFF; + for (int j=0;jnum_mappings;j++) + { + for (int i=0;inum_nbrs+1;i++) + temp[ref->mapping[j][i]] = binary[i]; - uint32_t code = 0; - for (int i=0;inum_nbrs+1;i++) - code |= (temp[i] << i); + uint32_t code = 0; + for (int i=0;inum_nbrs+1;i++) + code |= (temp[i] << i); - best = std::min(best, code); - } + best = std::min(best, code); + } - return best; + return best; } int32_t find_alloy_type(const refdata_t* ref, int8_t* mapping, int32_t* numbers) { - if (test_pure(ref->num_nbrs, numbers)) - return PTM_ALLOY_PURE; + for (int i=0;inum_nbrs+1;i++) + if (numbers[i] == -1) + return PTM_ALLOY_NONE; - if (!test_binary(ref->num_nbrs, numbers)) - return PTM_ALLOY_NONE; + if (test_pure(ref->num_nbrs, numbers)) + return PTM_ALLOY_PURE; - uint32_t code = canonical_alloy_representation(ref, mapping, numbers); - for (int i=0;itype == typedata[i][0] && code == typedata[i][2]) - return typedata[i][1]; + if (!test_binary(ref->num_nbrs, numbers)) + return PTM_ALLOY_NONE; - if (ref->type == PTM_MATCH_BCC) - if (test_shell_structure(ref, mapping, numbers, 8)) - return PTM_ALLOY_B2; + uint32_t code = canonical_alloy_representation(ref, mapping, numbers); + for (int i=0;itype == typedata[i][0] && code == typedata[i][2]) + return typedata[i][1]; - if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX) - if (test_shell_structure(ref, mapping, numbers, 4)) - return PTM_ALLOY_SIC; + if (ref->type == PTM_MATCH_BCC) + if (test_shell_structure(ref, mapping, numbers, 8)) + return PTM_ALLOY_B2; - return PTM_ALLOY_NONE; + if (ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX) + if (test_shell_structure(ref, mapping, numbers, 4)) + return PTM_ALLOY_SIC; + + + if (ref->type == PTM_MATCH_GRAPHENE) + if (test_shell_structure(ref, mapping, numbers, 3)) + return PTM_ALLOY_BN; + + return PTM_ALLOY_NONE; } } diff --git a/src/USER-PTM/ptm_alloy_types.h b/src/USER-PTM/ptm_alloy_types.h index 559e0a7490..e51ec1dd01 100644 --- a/src/USER-PTM/ptm_alloy_types.h +++ b/src/USER-PTM/ptm_alloy_types.h @@ -1,3 +1,12 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_ALLOY_TYPES_H #define PTM_ALLOY_TYPES_H diff --git a/src/USER-PTM/ptm_alt_templates.h b/src/USER-PTM/ptm_alt_templates.h new file mode 100644 index 0000000000..6a348315bf --- /dev/null +++ b/src/USER-PTM/ptm_alt_templates.h @@ -0,0 +1,127 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +#ifndef PTM_ALT_TEMPLATES_H +#define PTM_ALT_TEMPLATES_H + +#include + + +const double ptm_template_hcp_alt1[PTM_NUM_POINTS_HCP][3] = { + { 0, 0, 0 }, + { 1, 0, 0 }, + { -0.5, -sqrt(3)/2, 0 }, + { -0.5, -sqrt(3)/6, -sqrt(6)/3 }, + { 0, sqrt(3)/3, -sqrt(6)/3 }, + { 0.5, -sqrt(3)/6, -sqrt(6)/3 }, + { -1, 0, 0 }, + { -0.5, sqrt(3)/2, 0 }, + { 0.5, sqrt(3)/2, 0 }, + { 0.5, -sqrt(3)/2, 0 }, + { 0.5, -sqrt(3)/6, sqrt(6)/3 }, + { 0, sqrt(3)/3, sqrt(6)/3 }, + { -0.5, -sqrt(3)/6, sqrt(6)/3 }, +}; + +const double ptm_template_dcub_alt1[PTM_NUM_POINTS_DCUB][3] = { + { 0, 0, 0 }, + { 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) }, + { 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) }, + { -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) }, + { -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) }, + { 0, -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 }, + { -8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) }, + { 0, -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) }, + { -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 }, + { -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 }, + { -8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) }, + { 0, 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) }, +}; + +const double ptm_template_dhex_alt1[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, 0, 4*sqrt(3)/(sqrt(3)+6*sqrt(2)) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, +}; + +const double ptm_template_dhex_alt2[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, 0, -4*sqrt(3)/(sqrt(3)+6*sqrt(2)) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, +}; + +const double ptm_template_dhex_alt3[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, 0, -4*sqrt(3)/(sqrt(3)+6*sqrt(2)) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 0, 8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, +}; + + +const double ptm_template_graphene_alt1[PTM_NUM_POINTS_GRAPHENE][3] = { + { 0, 0, 0 }, + { 3*sqrt(3)/22-9./11, -3./22+3*sqrt(3)/11, 0 }, + { 9./11-3*sqrt(3)/22, -3./22+3*sqrt(3)/11, 0 }, + { 0, -6*sqrt(3)/11+3./11, 0 }, + { -18./11+3*sqrt(3)/11, 0, 0 }, + { 3*sqrt(3)/22-9./11, -9./22+9*sqrt(3)/11, 0 }, + { 9./11-3*sqrt(3)/22, -9./22+9*sqrt(3)/11, 0 }, + { -3*sqrt(3)/11+18./11, 0, 0 }, + { 9./11-3*sqrt(3)/22, -9*sqrt(3)/11+9./22, 0 }, + { 3*sqrt(3)/22-9./11, -9*sqrt(3)/11+9./22, 0 }, +}; + +#endif + diff --git a/src/USER-PTM/ptm_canonical_coloured.cpp b/src/USER-PTM/ptm_canonical_coloured.cpp index ade8f23b15..86c3f90b3b 100644 --- a/src/USER-PTM/ptm_canonical_coloured.cpp +++ b/src/USER-PTM/ptm_canonical_coloured.cpp @@ -1,4 +1,13 @@ -#include +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +#include #include #include #include "ptm_graph_tools.h" @@ -8,162 +17,162 @@ namespace ptm { static bool weinberg_coloured(int num_nodes, int num_edges, int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS], int8_t* colours, int8_t* best_code, int8_t* canonical_labelling, int a, int b) { - bool m[PTM_MAX_NBRS][PTM_MAX_NBRS]; - memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS); + bool m[PTM_MAX_NBRS][PTM_MAX_NBRS]; + memset(m, 0, sizeof(bool) * PTM_MAX_NBRS * PTM_MAX_NBRS); - int8_t index[PTM_MAX_NBRS]; - memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS); + int8_t index[PTM_MAX_NBRS]; + memset(index, -1, sizeof(int8_t) * PTM_MAX_NBRS); - int n = 0; - index[a] = colours[a] * num_nodes + n++; - if (index[a] > best_code[0]) - return false; + int n = 0; + index[a] = colours[a] * num_nodes + n++; + if (index[a] > best_code[0]) + return false; - bool winning = false; - if (index[a] < best_code[0]) - { - best_code[0] = index[a]; - winning = true; - } + bool winning = false; + if (index[a] < best_code[0]) + { + best_code[0] = index[a]; + winning = true; + } - int c = -1; - for (int it=1;it<2*num_edges;it++) - { - bool newvertex = index[b] == -1; + int c = -1; + for (int it=1;it<2*num_edges;it++) + { + bool newvertex = index[b] == -1; - if (newvertex) - index[b] = colours[b] * num_nodes + n++; + if (newvertex) + index[b] = colours[b] * num_nodes + n++; - if (!winning && index[b] > best_code[it]) - return false; + if (!winning && index[b] > best_code[it]) + return false; - if (winning || index[b] < best_code[it]) - { - winning = true; - best_code[it] = index[b]; - } + if (winning || index[b] < best_code[it]) + { + winning = true; + best_code[it] = index[b]; + } - if (newvertex) - { - //When a new vertex is reached, take the right-most edge - //relative to the edge on which the vertex is reached. + if (newvertex) + { + //When a new vertex is reached, take the right-most edge + //relative to the edge on which the vertex is reached. - c = common[a][b]; - } - else if (m[b][a] == false) - { - //When an old vertex is reached on a new path, go back - //in the opposite direction. + c = common[a][b]; + } + else if (m[b][a] == false) + { + //When an old vertex is reached on a new path, go back + //in the opposite direction. - c = a; - } - else - { - //When an old vertex is reached on an old path, leave the - //vertex on the right-most edge that has not previously - //been traversed in that direction. + c = a; + } + else + { + //When an old vertex is reached on an old path, leave the + //vertex on the right-most edge that has not previously + //been traversed in that direction. - c = common[a][b]; - while (m[b][c] == true) - c = common[c][b]; - } + c = common[a][b]; + while (m[b][c] == true) + c = common[c][b]; + } - m[a][b] = true; - a = b; - b = c; - } + m[a][b] = true; + a = b; + b = c; + } - if (winning) - { - memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes); - return true; - } + if (winning) + { + memcpy(canonical_labelling, index, sizeof(int8_t) * num_nodes); + return true; + } - return false; + return false; } int canonical_form_coloured(int num_facets, int8_t facets[][3], int num_nodes, int8_t* degree, int8_t* colours, int8_t* canonical_labelling, int8_t* best_code, uint64_t* p_hash) { - int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}}; - int num_edges = 3 * num_facets / 2; - if (!build_facet_map(num_facets, facets, common)) - return -1; + int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS] = {{0}}; + int num_edges = 3 * num_facets / 2; + if (!build_facet_map(num_facets, facets, common)) + return -1; - memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES); + memset(best_code, SCHAR_MAX, sizeof(int8_t) * 2 * PTM_MAX_EDGES); - bool equal = true; - for (int i = 1;i=0;i--) - canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1; - canonical_labelling[0] = 0; + for (int i = num_nodes-1;i>=0;i--) + canonical_labelling[i+1] = (canonical_labelling[i] % num_nodes) + 1; + canonical_labelling[0] = 0; - uint64_t hash = 0; - for (int i = 0;i<2 * num_edges;i++) - { - uint64_t e = best_code[i]; - e += i % 8; - e &= 0xF; - e <<= (4 * i) % 64; - hash ^= e; - } + uint64_t hash = 0; + for (int i = 0;i<2 * num_edges;i++) + { + uint64_t e = best_code[i]; + e += i % 8; + e &= 0xF; + e <<= (4 * i) % 64; + hash ^= e; + } - *p_hash = hash; - return PTM_NO_ERROR; + *p_hash = hash; + return PTM_NO_ERROR; } } diff --git a/src/USER-PTM/ptm_canonical_coloured.h b/src/USER-PTM/ptm_canonical_coloured.h index f8e2a7af5d..3ba2daebcd 100644 --- a/src/USER-PTM/ptm_canonical_coloured.h +++ b/src/USER-PTM/ptm_canonical_coloured.h @@ -1,3 +1,12 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_CANONICAL_COLOURED_H #define PTM_CANONICAL_COLOURED_H diff --git a/src/USER-PTM/ptm_constants.h b/src/USER-PTM/ptm_constants.h index f868f51e84..c3882f622c 100644 --- a/src/USER-PTM/ptm_constants.h +++ b/src/USER-PTM/ptm_constants.h @@ -1,45 +1,59 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_CONSTANTS_H #define PTM_CONSTANTS_H +#include + //------------------------------------ // definitions //------------------------------------ -#define PTM_NO_ERROR 0 +#define PTM_NO_ERROR 0 -#define PTM_CHECK_FCC (1 << 0) -#define PTM_CHECK_HCP (1 << 1) -#define PTM_CHECK_BCC (1 << 2) -#define PTM_CHECK_ICO (1 << 3) -#define PTM_CHECK_SC (1 << 4) -#define PTM_CHECK_DCUB (1 << 5) -#define PTM_CHECK_DHEX (1 << 6) -#define PTM_CHECK_NONDIAMOND (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) -#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX) +#define PTM_CHECK_FCC (1 << 0) +#define PTM_CHECK_HCP (1 << 1) +#define PTM_CHECK_BCC (1 << 2) +#define PTM_CHECK_ICO (1 << 3) +#define PTM_CHECK_SC (1 << 4) +#define PTM_CHECK_DCUB (1 << 5) +#define PTM_CHECK_DHEX (1 << 6) +#define PTM_CHECK_GRAPHENE (1 << 7) +#define PTM_CHECK_DEFAULT (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC) +#define PTM_CHECK_ALL (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC | PTM_CHECK_DCUB | PTM_CHECK_DHEX | PTM_CHECK_GRAPHENE) -#define PTM_MATCH_NONE 0 -#define PTM_MATCH_FCC 1 -#define PTM_MATCH_HCP 2 -#define PTM_MATCH_BCC 3 -#define PTM_MATCH_ICO 4 -#define PTM_MATCH_SC 5 -#define PTM_MATCH_DCUB 6 -#define PTM_MATCH_DHEX 7 +#define PTM_MATCH_NONE 0 +#define PTM_MATCH_FCC 1 +#define PTM_MATCH_HCP 2 +#define PTM_MATCH_BCC 3 +#define PTM_MATCH_ICO 4 +#define PTM_MATCH_SC 5 +#define PTM_MATCH_DCUB 6 +#define PTM_MATCH_DHEX 7 +#define PTM_MATCH_GRAPHENE 8 -#define PTM_ALLOY_NONE 0 -#define PTM_ALLOY_PURE 1 -#define PTM_ALLOY_L10 2 -#define PTM_ALLOY_L12_CU 3 -#define PTM_ALLOY_L12_AU 4 -#define PTM_ALLOY_B2 5 -#define PTM_ALLOY_SIC 6 +#define PTM_ALLOY_NONE 0 +#define PTM_ALLOY_PURE 1 +#define PTM_ALLOY_L10 2 +#define PTM_ALLOY_L12_CU 3 +#define PTM_ALLOY_L12_AU 4 +#define PTM_ALLOY_B2 5 +#define PTM_ALLOY_SIC 6 +#define PTM_ALLOY_BN 7 -#define PTM_MAX_INPUT_POINTS 35 -#define PTM_MAX_NBRS 16 -#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) -#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 -#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 +#define PTM_MAX_INPUT_POINTS 19 +#define PTM_MAX_NBRS 16 +#define PTM_MAX_POINTS (PTM_MAX_NBRS + 1) +#define PTM_MAX_FACETS 28 //2 * PTM_MAX_NBRS - 4 +#define PTM_MAX_EDGES 42 //3 * PTM_MAX_NBRS - 6 //------------------------------------ @@ -52,16 +66,18 @@ #define PTM_NUM_NBRS_SC 6 #define PTM_NUM_NBRS_DCUB 16 #define PTM_NUM_NBRS_DHEX 16 +#define PTM_NUM_NBRS_GRAPHENE 9 #define PTM_NUM_POINTS_FCC (PTM_NUM_NBRS_FCC + 1) #define PTM_NUM_POINTS_HCP (PTM_NUM_NBRS_HCP + 1) #define PTM_NUM_POINTS_BCC (PTM_NUM_NBRS_BCC + 1) #define PTM_NUM_POINTS_ICO (PTM_NUM_NBRS_ICO + 1) #define PTM_NUM_POINTS_SC (PTM_NUM_NBRS_SC + 1) -#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1) -#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) +#define PTM_NUM_POINTS_DCUB (PTM_NUM_NBRS_DCUB + 1) +#define PTM_NUM_POINTS_DHEX (PTM_NUM_NBRS_DHEX + 1) +#define PTM_NUM_POINTS_GRAPHENE (PTM_NUM_NBRS_GRAPHENE + 1) -const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX}; +const int ptm_num_nbrs[9] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS_BCC, PTM_NUM_NBRS_ICO, PTM_NUM_NBRS_SC, PTM_NUM_NBRS_DCUB, PTM_NUM_NBRS_DHEX, PTM_NUM_NBRS_GRAPHENE}; //------------------------------------ // template structures @@ -69,106 +85,134 @@ const int ptm_num_nbrs[8] = {0, PTM_NUM_NBRS_FCC, PTM_NUM_NBRS_HCP, PTM_NUM_NBRS //these point sets have barycentre {0, 0, 0} and are scaled such that the mean neighbour distance is 1 -const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { { 0. , 0. , 0. }, - { 0. , 0.707106781187, 0.707106781187 }, - { 0. , -0.707106781187, -0.707106781187 }, - { 0. , 0.707106781187, -0.707106781187 }, - { 0. , -0.707106781187, 0.707106781187 }, - { 0.707106781187, 0. , 0.707106781187 }, - { -0.707106781187, 0. , -0.707106781187 }, - { 0.707106781187, 0. , -0.707106781187 }, - { -0.707106781187, 0. , 0.707106781187 }, - { 0.707106781187, 0.707106781187, 0. }, - { -0.707106781187, -0.707106781187, 0. }, - { 0.707106781187, -0.707106781187, 0. }, - { -0.707106781187, 0.707106781187, 0. } }; +const double ptm_template_fcc[PTM_NUM_POINTS_FCC][3] = { + { 0, 0, 0 }, + { sqrt(2)/2, sqrt(2)/2, 0 }, + { 0, sqrt(2)/2, sqrt(2)/2 }, + { sqrt(2)/2, 0, sqrt(2)/2 }, + { -sqrt(2)/2, -sqrt(2)/2, 0 }, + { 0, -sqrt(2)/2, -sqrt(2)/2 }, + { -sqrt(2)/2, 0, -sqrt(2)/2 }, + { -sqrt(2)/2, sqrt(2)/2, 0 }, + { 0, -sqrt(2)/2, sqrt(2)/2 }, + { -sqrt(2)/2, 0, sqrt(2)/2 }, + { sqrt(2)/2, -sqrt(2)/2, 0 }, + { 0, sqrt(2)/2, -sqrt(2)/2 }, + { sqrt(2)/2, 0, -sqrt(2)/2 }, +}; -const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { { 0. , 0. , 0. }, - { 0.707106781186, 0. , 0.707106781186 }, - { -0.235702260395, -0.942809041583, -0.235702260395 }, - { 0.707106781186, 0.707106781186, 0. }, - { -0.235702260395, -0.235702260395, -0.942809041583 }, - { 0. , 0.707106781186, 0.707106781186 }, - { -0.942809041583, -0.235702260395, -0.235702260395 }, - { -0.707106781186, 0.707106781186, 0. }, - { 0. , 0.707106781186, -0.707106781186 }, - { 0.707106781186, 0. , -0.707106781186 }, - { 0.707106781186, -0.707106781186, 0. }, - { -0.707106781186, 0. , 0.707106781186 }, - { 0. , -0.707106781186, 0.707106781186 } }; +const double ptm_template_hcp[PTM_NUM_POINTS_HCP][3] = { + { 0, 0, 0 }, + { 0.5, -sqrt(3)/2, 0 }, + { -1, 0, 0 }, + { -0.5, sqrt(3)/6, -sqrt(6)/3 }, + { 0.5, sqrt(3)/6, -sqrt(6)/3 }, + { 0, -sqrt(3)/3, -sqrt(6)/3 }, + { -0.5, sqrt(3)/2, 0 }, + { 0.5, sqrt(3)/2, 0 }, + { 1, 0, 0 }, + { -0.5, -sqrt(3)/2, 0 }, + { 0, -sqrt(3)/3, sqrt(6)/3 }, + { 0.5, sqrt(3)/6, sqrt(6)/3 }, + { -0.5, sqrt(3)/6, sqrt(6)/3 }, +}; -const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { { 0. , 0. , 0. }, - { -0.541451884327, -0.541451884327, -0.541451884327 }, - { 0.541451884327, 0.541451884327, 0.541451884327 }, - { 0.541451884327, -0.541451884327, -0.541451884327 }, - { -0.541451884327, 0.541451884327, 0.541451884327 }, - { -0.541451884327, 0.541451884327, -0.541451884327 }, - { 0.541451884327, -0.541451884327, 0.541451884327 }, - { -0.541451884327, -0.541451884327, 0.541451884327 }, - { 0.541451884327, 0.541451884327, -0.541451884327 }, - { 0. , 0. , -1.082903768655 }, - { 0. , 0. , 1.082903768655 }, - { 0. , -1.082903768655, 0. }, - { 0. , 1.082903768655, 0. }, - { -1.082903768655, 0. , 0. }, - { 1.082903768655, 0. , 0. } }; +const double ptm_template_bcc[PTM_NUM_POINTS_BCC][3] = { + { 0, 0, 0 }, + { 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2 }, + { 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2 }, + { 7*sqrt(3)/3-7./2, 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3 }, + { 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2 }, + { 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2 }, + { 7./2-7*sqrt(3)/3, 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3 }, + { 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3 }, + { 7*sqrt(3)/3-7./2, 7./2-7*sqrt(3)/3, 7./2-7*sqrt(3)/3 }, + { 14*sqrt(3)/3-7, 0, 0 }, + { 7-14*sqrt(3)/3, 0, 0 }, + { 0, 14*sqrt(3)/3-7, 0 }, + { 0, 7-14*sqrt(3)/3, 0 }, + { 0, 0, 14*sqrt(3)/3-7 }, + { 0, 0, 7-14*sqrt(3)/3 }, +}; -const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { { 0. , 0. , 0. }, - { 0. , 0.525731112119, 0.850650808352 }, - { 0. , -0.525731112119, -0.850650808352 }, - { 0. , 0.525731112119, -0.850650808352 }, - { 0. , -0.525731112119, 0.850650808352 }, - { -0.525731112119, -0.850650808352, 0. }, - { 0.525731112119, 0.850650808352, 0. }, - { 0.525731112119, -0.850650808352, 0. }, - { -0.525731112119, 0.850650808352, 0. }, - { -0.850650808352, 0. , -0.525731112119 }, - { 0.850650808352, 0. , 0.525731112119 }, - { 0.850650808352, 0. , -0.525731112119 }, - { -0.850650808352, 0. , 0.525731112119 } }; +const double ptm_template_ico[PTM_NUM_POINTS_ICO][3] = { + { 0, 0, 0 }, + { 0, 0, 1 }, + { 0, 0, -1 }, + { -sqrt((5-sqrt(5))/10), (5+sqrt(5))/10, -sqrt(5)/5 }, + { sqrt((5-sqrt(5))/10), -(5+sqrt(5))/10, sqrt(5)/5 }, + { 0, -2*sqrt(5)/5, -sqrt(5)/5 }, + { 0, 2*sqrt(5)/5, sqrt(5)/5 }, + { sqrt((5+sqrt(5))/10), -(5-sqrt(5))/10, -sqrt(5)/5 }, + { -sqrt((5+sqrt(5))/10), (5-sqrt(5))/10, sqrt(5)/5 }, + { -sqrt((5+sqrt(5))/10), -(5-sqrt(5))/10, -sqrt(5)/5 }, + { sqrt((5+sqrt(5))/10), (5-sqrt(5))/10, sqrt(5)/5 }, + { sqrt((5-sqrt(5))/10), (5+sqrt(5))/10, -sqrt(5)/5 }, + { -sqrt((5-sqrt(5))/10), -(5+sqrt(5))/10, sqrt(5)/5 }, +}; -const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { { 0. , 0. , 0. }, - { 0. , 0. , -1. }, - { 0. , 0. , 1. }, - { 0. , -1. , 0. }, - { 0. , 1. , 0. }, - { -1. , 0. , 0. }, - { 1. , 0. , 0. } }; +const double ptm_template_sc[PTM_NUM_POINTS_SC][3] = { + { 0, 0, 0 }, + { 0, 0, -1 }, + { 0, 0, 1 }, + { 0, -1, 0 }, + { 0, 1, 0 }, + { -1, 0, 0 }, + { 1, 0, 0 }, +}; -const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { { 0. , 0. , 0. }, - { -0.391491627053, 0.391491627053, 0.391491627053 }, - { -0.391491627053, -0.391491627053, -0.391491627053 }, - { 0.391491627053, -0.391491627053, 0.391491627053 }, - { 0.391491627053, 0.391491627053, -0.391491627053 }, - { -0.782983254107, 0. , 0.782983254107 }, - { -0.782983254107, 0.782983254107, 0. }, - { 0. , 0.782983254107, 0.782983254107 }, - { -0.782983254107, -0.782983254107, 0. }, - { -0.782983254107, 0. , -0.782983254107 }, - { 0. , -0.782983254107, -0.782983254107 }, - { 0. , -0.782983254107, 0.782983254107 }, - { 0.782983254107, -0.782983254107, 0. }, - { 0.782983254107, 0. , 0.782983254107 }, - { 0. , 0.782983254107, -0.782983254107 }, - { 0.782983254107, 0. , -0.782983254107 }, - { 0.782983254107, 0.782983254107, 0. } }; +const double ptm_template_dcub[PTM_NUM_POINTS_DCUB][3] = { + { 0, 0, 0 }, + { 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) }, + { 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) }, + { -4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)) }, + { -4/(sqrt(3)+6*sqrt(2)), 4/(sqrt(3)+6*sqrt(2)), -4/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, 8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) }, + { 0, -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) }, + { 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 }, + { 8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) }, + { -8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)) }, + { -8/(sqrt(3)+6*sqrt(2)), 0, 8/(sqrt(3)+6*sqrt(2)) }, + { -8/(sqrt(3)+6*sqrt(2)), 0, -8/(sqrt(3)+6*sqrt(2)) }, + { -8/(sqrt(3)+6*sqrt(2)), 8/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, 8/(sqrt(3)+6*sqrt(2)), -8/(sqrt(3)+6*sqrt(2)) }, +}; + +const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { + { 0, 0, 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -4*sqrt(3)/(3*sqrt(3)+18*sqrt(2)) }, + { 0, 0, 4*sqrt(3)/(sqrt(3)+6*sqrt(2)) }, + { -8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), -4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), -16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(sqrt(3)+6*sqrt(2)), 0 }, + { 8*sqrt(2)/(sqrt(3)+6*sqrt(2)), 0, 0 }, + { 0, -8*sqrt(6)/(3*sqrt(3)+18*sqrt(2)), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { 4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, + { -4*sqrt(2)/(sqrt(3)+6*sqrt(2)), 4*sqrt(6)/(3*(sqrt(3)+6*sqrt(2))), 16*sqrt(3)/(3*(sqrt(3)+6*sqrt(2))) }, +}; + +const double ptm_template_graphene[PTM_NUM_POINTS_GRAPHENE][3] = { + { 0, 0, 0 }, + { 0, -3./11+6*sqrt(3)/11, 0 }, + { -3*sqrt(3)/22+9./11, -3*sqrt(3)/11+3./22, 0 }, + { -9./11+3*sqrt(3)/22, -3*sqrt(3)/11+3./22, 0 }, + { -9./11+3*sqrt(3)/22, -9./22+9*sqrt(3)/11, 0 }, + { -3*sqrt(3)/22+9./11, -9./22+9*sqrt(3)/11, 0 }, + { -3*sqrt(3)/11+18./11, 0, 0 }, + { -3*sqrt(3)/22+9./11, -9*sqrt(3)/11+9./22, 0 }, + { -9./11+3*sqrt(3)/22, -9*sqrt(3)/11+9./22, 0 }, + { -18./11+3*sqrt(3)/11, 0, 0 }, +}; -const double ptm_template_dhex[PTM_NUM_POINTS_DHEX][3] = { { 0. , 0. , 0. }, - { -0.391491627053, -0.391491627053, -0.391491627053 }, - { 0.391491627053, -0.391491627053, 0.391491627053 }, - { -0.391491627053, 0.391491627053, 0.391491627053 }, - { 0.391491627053, 0.391491627053, -0.391491627053 }, - { -0.260994418036, -1.043977672142, -0.260994418036 }, - { -1.043977672142, -0.260994418036, -0.260994418036 }, - { -0.260994418036, -0.260994418036, -1.043977672142 }, - { 0.782983254107, 0. , 0.782983254107 }, - { 0.782983254107, -0.782983254107, 0. }, - { 0. , -0.782983254107, 0.782983254107 }, - { 0. , 0.782983254107, 0.782983254107 }, - { -0.782983254107, 0.782983254107, 0. }, - { -0.782983254107, 0. , 0.782983254107 }, - { 0.782983254107, 0.782983254107, 0. }, - { 0. , 0.782983254107, -0.782983254107 }, - { 0.782983254107, 0. , -0.782983254107 } }; #endif diff --git a/src/USER-PTM/ptm_convex_hull_incremental.cpp b/src/USER-PTM/ptm_convex_hull_incremental.cpp index 7c79fd371a..45643ec515 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.cpp +++ b/src/USER-PTM/ptm_convex_hull_incremental.cpp @@ -1,6 +1,15 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include #include -#include +#include #include #include #include "ptm_convex_hull_incremental.h" @@ -15,351 +24,351 @@ namespace ptm { static double norm_squared(double* p) { - double x = p[0]; - double y = p[1]; - double z = p[2]; + double x = p[0]; + double y = p[1]; + double z = p[2]; - return x*x + y*y + z*z; + return x*x + y*y + z*z; } static double dot_product(const double* a, const double* b) { - return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; + return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; } static void cross_product(double* a, double* b, double* c) { - c[0] = a[1] * b[2] - a[2] * b[1]; - c[1] = a[2] * b[0] - a[0] * b[2]; - c[2] = a[0] * b[1] - a[1] * b[0]; + c[0] = a[1] * b[2] - a[2] * b[1]; + c[1] = a[2] * b[0] - a[0] * b[2]; + c[2] = a[0] * b[1] - a[1] * b[0]; } static void calculate_plane_normal(const double (*points)[3], int a, int b, int c, double* plane_normal) { - double u[3] = { points[b][0] - points[a][0], - points[b][1] - points[a][1], - points[b][2] - points[a][2] }; + double u[3] = { points[b][0] - points[a][0], + points[b][1] - points[a][1], + points[b][2] - points[a][2] }; - double v[3] = { points[c][0] - points[a][0], - points[c][1] - points[a][1], - points[c][2] - points[a][2] }; + double v[3] = { points[c][0] - points[a][0], + points[c][1] - points[a][1], + points[c][2] - points[a][2] }; - cross_product(u, v, plane_normal); - double norm = sqrt(norm_squared(plane_normal)); - plane_normal[0] /= norm; - plane_normal[1] /= norm; - plane_normal[2] /= norm; + cross_product(u, v, plane_normal); + double norm = sqrt(norm_squared(plane_normal)); + plane_normal[0] /= norm; + plane_normal[1] /= norm; + plane_normal[2] /= norm; } static double point_plane_distance(const double* w, const double* plane_point, const double* plane_cross) { - return plane_cross[0] * (plane_point[0] - w[0]) - + plane_cross[1] * (plane_point[1] - w[1]) - + plane_cross[2] * (plane_point[2] - w[2]); + return plane_cross[0] * (plane_point[0] - w[0]) + + plane_cross[1] * (plane_point[1] - w[1]) + + plane_cross[2] * (plane_point[2] - w[2]); } static bool calc_max_extent(int num_points, const double (*points)[3], int* min_index, int* max_index) { - for (int j=0;j<3;j++) - { - double dmin = DBL_MAX, dmax = -DBL_MAX; - int imin = 0, imax = 0; + for (int j=0;j<3;j++) + { + double dmin = DBL_MAX, dmax = -DBL_MAX; + int imin = 0, imax = 0; - for (int i = 0;i dmax) - { - dmax = d; - imax = i; - } - } + for (int i = 0;i dmax) + { + dmax = d; + imax = i; + } + } - if (imin == imax) - return false; //degenerate point set + if (imin == imax) + return false; //degenerate point set - min_index[j] = imin; - max_index[j] = imax; - } + min_index[j] = imin; + max_index[j] = imax; + } - return true; + return true; } static bool find_third_point(int num_points, const double (*points)[3], int a, int b, int* p_c) { - const double* x1 = points[a]; - const double* x2 = points[b]; + const double* x1 = points[a]; + const double* x2 = points[b]; - double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]}; - double ns_x2x1 = norm_squared(x2x1); + double x2x1[3] = {x2[0] - x1[0], x2[1] - x1[1], x2[2] - x1[2]}; + double ns_x2x1 = norm_squared(x2x1); - int bi = -1; - double max_dist = 0.0; - for (int i = 0;i max_dist) - { - max_dist = dist; - bi = i; - } - } + if (dist > max_dist) + { + max_dist = dist; + bi = i; + } + } - *p_c = bi; - return max_dist > TOLERANCE; + *p_c = bi; + return max_dist > TOLERANCE; } static bool find_fourth_point(int num_points, const double (*points)[3], int a, int b, int c, int* p_d) { - double plane_normal[3]; - calculate_plane_normal(points, a, b, c, plane_normal); + double plane_normal[3]; + calculate_plane_normal(points, a, b, c, plane_normal); - int bi = -1; - double max_dist = 0.0; - for (int i = 0;i max_dist) - { - max_dist = dist; - bi = i; - } - } + const double* x0 = points[i]; + double dist = fabs(point_plane_distance(x0, points[a], plane_normal)); + if (dist > max_dist) + { + max_dist = dist; + bi = i; + } + } - *p_d = bi; - return max_dist > TOLERANCE; + *p_d = bi; + return max_dist > TOLERANCE; } static int initial_simplex(int num_points, const double (*points)[3], int* initial_vertices) { - int min_index[3] = {0}; - int max_index[3] = {0}; - if (!calc_max_extent(num_points, points, min_index, max_index)) - return -1; + int min_index[3] = {0}; + int max_index[3] = {0}; + if (!calc_max_extent(num_points, points, min_index, max_index)) + return -1; - int bi = -1; - double max_dist = 0.0; - for (int i = 0;i<3;i++) - { - int a = min_index[i], b = max_index[i]; - double delta[3] = { points[a][0] - points[b][0], - points[a][1] - points[b][1], - points[a][2] - points[b][2] }; - double dist = norm_squared(delta); - if (dist > max_dist) - { - bi = i; - max_dist = dist; - } - } + int bi = -1; + double max_dist = 0.0; + for (int i = 0;i<3;i++) + { + int a = min_index[i], b = max_index[i]; + double delta[3] = { points[a][0] - points[b][0], + points[a][1] - points[b][1], + points[a][2] - points[b][2] }; + double dist = norm_squared(delta); + if (dist > max_dist) + { + bi = i; + max_dist = dist; + } + } - //first two points are (a, b) - int a = min_index[bi], b = max_index[bi], c = -1, d = -1; + //first two points are (a, b) + int a = min_index[bi], b = max_index[bi], c = -1, d = -1; - if (!find_third_point(num_points, points, a, b, &c)) - return -2; + if (!find_third_point(num_points, points, a, b, &c)) + return -2; - if (!find_fourth_point(num_points, points, a, b, c, &d)) - return -3; + if (!find_fourth_point(num_points, points, a, b, c, &d)) + return -3; - initial_vertices[0] = a; - initial_vertices[1] = b; - initial_vertices[2] = c; - initial_vertices[3] = d; - return 0; + initial_vertices[0] = a; + initial_vertices[1] = b; + initial_vertices[2] = c; + initial_vertices[3] = d; + return 0; } static bool visible(const double* w, const double* plane_point, const double* plane_normal) { - return point_plane_distance(w, plane_point, plane_normal) > 0; + return point_plane_distance(w, plane_point, plane_normal) > 0; } void add_facet(const double (*points)[3], int a, int b, int c, int8_t* facet, double* plane_normal, double* barycentre) { - calculate_plane_normal(points, a, b, c, plane_normal); - if (visible(barycentre, points[a], plane_normal)) - { - plane_normal[0] = -plane_normal[0]; - plane_normal[1] = -plane_normal[1]; - plane_normal[2] = -plane_normal[2]; + calculate_plane_normal(points, a, b, c, plane_normal); + if (visible(barycentre, points[a], plane_normal)) + { + plane_normal[0] = -plane_normal[0]; + plane_normal[1] = -plane_normal[1]; + plane_normal[2] = -plane_normal[2]; - facet[0] = b; - facet[1] = a; - facet[2] = c; - } - else - { - facet[0] = a; - facet[1] = b; - facet[2] = c; - } + facet[0] = b; + facet[1] = a; + facet[2] = c; + } + else + { + facet[0] = a; + facet[1] = b; + facet[2] = c; + } } static int initialize_convex_hull(int num_points, const double (*points)[3], int8_t facets[][3], double plane_normal[][3], bool* processed, int* initial_vertices, double* barycentre) { - memset(processed, 0, PTM_MAX_POINTS * sizeof(bool)); - memset(barycentre, 0, 3 * sizeof(double)); - int ret = initial_simplex(num_points, points, initial_vertices); - if (ret != 0) - return ret; + memset(processed, 0, PTM_MAX_POINTS * sizeof(bool)); + memset(barycentre, 0, 3 * sizeof(double)); + int ret = initial_simplex(num_points, points, initial_vertices); + if (ret != 0) + return ret; - for (int i = 0;i<4;i++) - { - int a = initial_vertices[i]; - processed[a] = true; + for (int i = 0;i<4;i++) + { + int a = initial_vertices[i]; + processed[a] = true; - barycentre[0] += points[a][0]; - barycentre[1] += points[a][1]; - barycentre[2] += points[a][2]; - } - barycentre[0] /= 4; - barycentre[1] /= 4; - barycentre[2] /= 4; + barycentre[0] += points[a][0]; + barycentre[1] += points[a][1]; + barycentre[2] += points[a][2]; + } + barycentre[0] /= 4; + barycentre[1] /= 4; + barycentre[2] /= 4; - add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre); - add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre); - add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre); - add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre); - return 0; + add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[2], facets[0], plane_normal[0], barycentre); + add_facet(points, initial_vertices[0], initial_vertices[1], initial_vertices[3], facets[1], plane_normal[1], barycentre); + add_facet(points, initial_vertices[0], initial_vertices[2], initial_vertices[3], facets[2], plane_normal[2], barycentre); + add_facet(points, initial_vertices[1], initial_vertices[2], initial_vertices[3], facets[3], plane_normal[3], barycentre); + return 0; } int get_convex_hull(int num_points, const double (*points)[3], convexhull_t* ch, int8_t simplex[][3]) { - assert( num_points == PTM_NUM_POINTS_FCC - || num_points == PTM_NUM_POINTS_HCP - || num_points == PTM_NUM_POINTS_BCC - || num_points == PTM_NUM_POINTS_ICO - || num_points == PTM_NUM_POINTS_SC - || num_points == PTM_NUM_POINTS_DCUB - || num_points == PTM_NUM_POINTS_DHEX); + assert( num_points == PTM_NUM_POINTS_FCC + || num_points == PTM_NUM_POINTS_HCP + || num_points == PTM_NUM_POINTS_BCC + || num_points == PTM_NUM_POINTS_ICO + || num_points == PTM_NUM_POINTS_SC + || num_points == PTM_NUM_POINTS_DCUB + || num_points == PTM_NUM_POINTS_DHEX); - int ret = 0; - int num_prev = ch->num_prev; - ch->num_prev = num_points; - if (!ch->ok || 0) - { - ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre); - if (ret != 0) - return ret; + int ret = 0; + int num_prev = ch->num_prev; + ch->num_prev = num_points; + if (!ch->ok || 0) + { + ret = initialize_convex_hull(num_points, points, ch->facets, ch->plane_normal, ch->processed, ch->initial_vertices, ch->barycentre); + if (ret != 0) + return ret; - ch->num_facets = 4; - num_prev = 0; - } + ch->num_facets = 4; + num_prev = 0; + } - for (int i = num_prev;iprocessed[i]) - continue; - ch->processed[i] = true; + for (int i = num_prev;iprocessed[i]) + continue; + ch->processed[i] = true; - int num_to_add = 0; - int8_t to_add[PTM_MAX_FACETS][3]; - int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS]; - memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS); - for (int j = 0;jnum_facets;j++) - { - int a = ch->facets[j][0]; - int b = ch->facets[j][1]; - int c = ch->facets[j][2]; + int num_to_add = 0; + int8_t to_add[PTM_MAX_FACETS][3]; + int8_t edge_visible[PTM_MAX_POINTS][PTM_MAX_POINTS]; + memset(edge_visible, 0, sizeof(int8_t) * PTM_MAX_POINTS * PTM_MAX_POINTS); + for (int j = 0;jnum_facets;j++) + { + int a = ch->facets[j][0]; + int b = ch->facets[j][1]; + int c = ch->facets[j][2]; - int u = 0, v = 0, w = 0; + int u = 0, v = 0, w = 0; - double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]); - bool vis = distance > TOLERANCE; - if (vis) - { - u = edge_visible[a][b] |= VISIBLE; - edge_visible[b][a] |= VISIBLE; + double distance = point_plane_distance(points[i], points[a], ch->plane_normal[j]); + bool vis = distance > TOLERANCE; + if (vis) + { + u = edge_visible[a][b] |= VISIBLE; + edge_visible[b][a] |= VISIBLE; - v = edge_visible[b][c] |= VISIBLE; - edge_visible[c][b] |= VISIBLE; + v = edge_visible[b][c] |= VISIBLE; + edge_visible[c][b] |= VISIBLE; - w = edge_visible[c][a] |= VISIBLE; - edge_visible[a][c] |= VISIBLE; + w = edge_visible[c][a] |= VISIBLE; + edge_visible[a][c] |= VISIBLE; - memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t)); - memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double)); - ch->num_facets--; - j--; - } - else - { - u = edge_visible[a][b] |= INVISIBLE; - edge_visible[b][a] |= INVISIBLE; + memcpy(ch->facets[j], ch->facets[ch->num_facets-1], 3 * sizeof(int8_t)); + memcpy(ch->plane_normal[j], ch->plane_normal[ch->num_facets-1], 3 * sizeof(double)); + ch->num_facets--; + j--; + } + else + { + u = edge_visible[a][b] |= INVISIBLE; + edge_visible[b][a] |= INVISIBLE; - v = edge_visible[b][c] |= INVISIBLE; - edge_visible[c][b] |= INVISIBLE; + v = edge_visible[b][c] |= INVISIBLE; + edge_visible[c][b] |= INVISIBLE; - w = edge_visible[c][a] |= INVISIBLE; - edge_visible[a][c] |= INVISIBLE; - } + w = edge_visible[c][a] |= INVISIBLE; + edge_visible[a][c] |= INVISIBLE; + } - if (u == BOTH) - { - to_add[num_to_add][0] = i; - to_add[num_to_add][1] = a; - to_add[num_to_add][2] = b; - num_to_add++; - } + if (u == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = a; + to_add[num_to_add][2] = b; + num_to_add++; + } - if (v == BOTH) - { - to_add[num_to_add][0] = i; - to_add[num_to_add][1] = b; - to_add[num_to_add][2] = c; - num_to_add++; - } + if (v == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = b; + to_add[num_to_add][2] = c; + num_to_add++; + } - if (w == BOTH) - { - to_add[num_to_add][0] = i; - to_add[num_to_add][1] = c; - to_add[num_to_add][2] = a; - num_to_add++; - } - } + if (w == BOTH) + { + to_add[num_to_add][0] = i; + to_add[num_to_add][1] = c; + to_add[num_to_add][2] = a; + num_to_add++; + } + } - for (int j = 0;jnum_facets >= PTM_MAX_FACETS) - return -4; + for (int j = 0;jnum_facets >= PTM_MAX_FACETS) + return -4; - add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++; - } - } + add_facet(points, to_add[j][0], to_add[j][1], to_add[j][2], ch->facets[ch->num_facets], ch->plane_normal[ch->num_facets], ch->barycentre); ch->num_facets++; + } + } - for (int i=0;inum_facets;i++) - { - int a = ch->facets[i][0]; - int b = ch->facets[i][1]; - int c = ch->facets[i][2]; - if (a == 0 || b == 0 || c == 0) - return 1; //central atom contained in convex hull + for (int i=0;inum_facets;i++) + { + int a = ch->facets[i][0]; + int b = ch->facets[i][1]; + int c = ch->facets[i][2]; + if (a == 0 || b == 0 || c == 0) + return 1; //central atom contained in convex hull - simplex[i][0] = a - 1; - simplex[i][1] = b - 1; - simplex[i][2] = c - 1; - } + simplex[i][0] = a - 1; + simplex[i][1] = b - 1; + simplex[i][2] = c - 1; + } - return ret; + return ret; } } diff --git a/src/USER-PTM/ptm_convex_hull_incremental.h b/src/USER-PTM/ptm_convex_hull_incremental.h index 6474723907..1d51ae4dec 100644 --- a/src/USER-PTM/ptm_convex_hull_incremental.h +++ b/src/USER-PTM/ptm_convex_hull_incremental.h @@ -1,3 +1,12 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_CONVEX_HULL_INCREMENTAL_H #define PTM_CONVEX_HULL_INCREMENTAL_H @@ -10,14 +19,14 @@ namespace ptm { typedef struct { - int8_t facets[PTM_MAX_FACETS][3]; - double plane_normal[PTM_MAX_FACETS][3]; - bool processed[PTM_MAX_POINTS]; - int initial_vertices[4]; - double barycentre[3]; - int num_facets; - int num_prev; - bool ok; + int8_t facets[PTM_MAX_FACETS][3]; + double plane_normal[PTM_MAX_FACETS][3]; + bool processed[PTM_MAX_POINTS]; + int initial_vertices[4]; + double barycentre[3]; + int num_facets; + int num_prev; + bool ok; } convexhull_t; diff --git a/src/USER-PTM/ptm_deformation_gradient.cpp b/src/USER-PTM/ptm_deformation_gradient.cpp index fc851920a6..2715c21aab 100644 --- a/src/USER-PTM/ptm_deformation_gradient.cpp +++ b/src/USER-PTM/ptm_deformation_gradient.cpp @@ -1,39 +1,48 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include "ptm_deformation_gradient.h" namespace ptm { void calculate_deformation_gradient(int num_points, const double (*ideal_points)[3], int8_t* mapping, double (*normalized)[3], const double (*penrose)[3], double* F, double* res) { - for (int i = 0;i<3;i++) - { - for (int j = 0;j<3;j++) - { - double acc = 0.0; - for (int k = 0;k +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +#include #include #include "ptm_graph_tools.h" #include "ptm_constants.h" @@ -8,48 +17,48 @@ namespace ptm { bool build_facet_map(int num_facets, int8_t facets[][3], int8_t common[PTM_MAX_NBRS][PTM_MAX_NBRS]) { - memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS); + memset(common, -1, sizeof(int8_t) * PTM_MAX_NBRS * PTM_MAX_NBRS); - for (int i = 0;i -#include -#include -#include -#include -#include -#include -#include "ptm_convex_hull_incremental.h" -#include "ptm_graph_data.h" -#include "ptm_deformation_gradient.h" +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include "ptm_alloy_types.h" +#include "ptm_constants.h" +#include "ptm_convex_hull_incremental.h" +#include "ptm_deformation_gradient.h" +#include "ptm_functions.h" +#include "ptm_graph_data.h" +#include "ptm_initialize_data.h" #include "ptm_neighbour_ordering.h" #include "ptm_normalize_vertices.h" -#include "ptm_quat.h" #include "ptm_polar.h" -#include "ptm_initialize_data.h" +#include "ptm_quat.h" #include "ptm_structure_matcher.h" -#include "ptm_functions.h" -#include "ptm_constants.h" +#include +#include +#include +#include +#include +#include +#include +static double calculate_interatomic_distance(int type, double scale) { + assert(type >= 1 && type <= 8); -//todo: verify that c == norm(template[1]) -static double calculate_interatomic_distance(int type, double scale) -{ - assert(type >= 1 && type <= 7); - double c[8] = {0, 1, 1, (7. - 3.5 * sqrt(3)), 1, 1, sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3))}; - return c[type] / scale; + // these values should be equal to norm(template[1]) + double c[9] = {0, + 1, + 1, + (7. - 3.5 * sqrt(3)), + 1, + 1, + sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), + sqrt(3) * 4. / (6 * sqrt(2) + sqrt(3)), + -3. / 11 + 6 * sqrt(3) / 11}; + return c[type] / scale; } -static double calculate_lattice_constant(int type, double interatomic_distance) -{ - assert(type >= 1 && type <= 7); - double c[8] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), 1, 4 / sqrt(3), 4 / sqrt(3)}; - return c[type] * interatomic_distance; +static double calculate_lattice_constant(int type, + double interatomic_distance) { + assert(type >= 1 && type <= 8); + double c[9] = {0, 2 / sqrt(2), 2 / sqrt(2), 2. / sqrt(3), 2 / sqrt(2), + 1, 4 / sqrt(3), 4 / sqrt(3), sqrt(3)}; + return c[type] * interatomic_distance; } -static int rotate_into_fundamental_zone(int type, double* q) -{ - if (type == PTM_MATCH_SC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_FCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_BCC) return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); - if (type == PTM_MATCH_ICO) return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q); - if (type == PTM_MATCH_HCP) return ptm::rotate_quaternion_into_hcp_fundamental_zone(q); - if (type == PTM_MATCH_DCUB) return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q); - if (type == PTM_MATCH_DHEX) return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); - return -1; +static int rotate_into_fundamental_zone(int type, + bool output_conventional_orientation, + double *q) { + if (type == PTM_MATCH_SC) + return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_FCC) + return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_BCC) + return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + if (type == PTM_MATCH_ICO) + return ptm::rotate_quaternion_into_icosahedral_fundamental_zone(q); + + if (type == PTM_MATCH_HCP || type == PTM_MATCH_GRAPHENE) { + if (output_conventional_orientation) { + return ptm::rotate_quaternion_into_hcp_conventional_fundamental_zone(q); + } else { + return ptm::rotate_quaternion_into_hcp_fundamental_zone(q); + } + } + + if (type == PTM_MATCH_DCUB) { + if (output_conventional_orientation) { + return ptm::rotate_quaternion_into_cubic_fundamental_zone(q); + } else { + return ptm::rotate_quaternion_into_diamond_cubic_fundamental_zone(q); + } + } + + if (type == PTM_MATCH_DHEX) { + if (output_conventional_orientation) { + return ptm::rotate_quaternion_into_hcp_conventional_fundamental_zone(q); + } else { + return ptm::rotate_quaternion_into_diamond_hexagonal_fundamental_zone(q); + } + } + + return -1; } -static void order_points(ptm_local_handle_t local_handle, int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, - int8_t* ordering, double (*points)[3], int32_t* numbers) -{ - if (topological_ordering) - { - double normalized_points[PTM_MAX_INPUT_POINTS][3]; - ptm::normalize_vertices(num_points, unpermuted_points, normalized_points); - int ret = ptm::calculate_neighbour_ordering((void*)local_handle, num_points, (const double (*)[3])normalized_points, ordering); - if (ret != 0) - topological_ordering = false; - } +static void output_data(ptm::result_t *res, double (*points)[3], + int32_t *numbers, size_t *ordering, + bool output_conventional_orientation, int32_t *p_type, + int32_t *p_alloy_type, double *p_scale, double *p_rmsd, + double *q, double *F, double *F_res, double *U, + double *P, double *p_interatomic_distance, + double *p_lattice_constant, size_t *output_indices) { + const ptm::refdata_t *ref = res->ref_struct; + if (ref == NULL) + return; - if (!topological_ordering) - for (int i=0;itype; + if (p_alloy_type != NULL) + *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers); - for (int i=0;itype, + output_conventional_orientation, res->q); + //todo: return if bi == -1 + if (bi != -1) + { + if (output_conventional_orientation & (ref->type == PTM_MATCH_HCP || ref->type == PTM_MATCH_GRAPHENE || ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)) + { + for (int i = 0; i < ref->num_nbrs + 1; i++) + temp[ref->mapping_conventional[bi][i]] = res->mapping[i]; + } + else + { + for (int i = 0; i < ref->num_nbrs + 1; i++) + temp[ref->mapping[bi][i]] = res->mapping[i]; + } + } - if (unpermuted_numbers != NULL) - numbers[i] = unpermuted_numbers[ordering[i]]; - } + memcpy(res->mapping, temp, (ref->num_nbrs + 1) * sizeof(int8_t)); + + if (F != NULL && F_res != NULL) { + double scaled_points[PTM_MAX_INPUT_POINTS][3]; + + ptm::subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); + for (int i = 0; i < ref->num_nbrs + 1; i++) { + scaled_points[i][0] *= res->scale; + scaled_points[i][1] *= res->scale; + scaled_points[i][2] *= res->scale; + } + + const double (*ref_template)[3] = ref->points; + const double (*ref_penrose)[3] = ref->penrose; + if (output_conventional_orientation & (ref->type == PTM_MATCH_HCP || ref->type == PTM_MATCH_GRAPHENE || ref->type == PTM_MATCH_DCUB || ref->type == PTM_MATCH_DHEX)) + { + if (ref->template_indices[bi] == 1) + { + ref_template = ref->points_alt1; + ref_penrose = ref->penrose_alt1; + } + else if (ref->template_indices[bi] == 2) + { + ref_template = ref->points_alt2; + ref_penrose = ref->penrose_alt2; + } + else if (ref->template_indices[bi] == 3) + { + ref_template = ref->points_alt3; + ref_penrose = ref->penrose_alt3; + } + } + + ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref_template, + res->mapping, scaled_points, ref_penrose, + F, F_res); + if (ref->type == PTM_MATCH_GRAPHENE) // hack for pseudo-2d structures + F[8] = 1; + + if (P != NULL && U != NULL) + ptm::polar_decomposition_3x3(F, false, U, P); + } + + if (output_indices != NULL) + for (int i = 0; i < ref->num_nbrs + 1; i++) + output_indices[i] = ordering[res->mapping[i]]; + + double interatomic_distance = + calculate_interatomic_distance(ref->type, res->scale); + double lattice_constant = + calculate_lattice_constant(ref->type, interatomic_distance); + + if (p_interatomic_distance != NULL) + *p_interatomic_distance = interatomic_distance; + + if (p_lattice_constant != NULL) + *p_lattice_constant = lattice_constant; + + *p_rmsd = res->rmsd; + *p_scale = res->scale; + memcpy(q, res->q, 4 * sizeof(double)); } -static void output_data(ptm::result_t* res, int num_points, int32_t* unpermuted_numbers, double (*points)[3], int32_t* numbers, int8_t* ordering, - int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, - double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) -{ - *p_type = PTM_MATCH_NONE; - if (p_alloy_type != NULL) - *p_alloy_type = PTM_ALLOY_NONE; - - if (mapping != NULL) - memset(mapping, -1, num_points * sizeof(int8_t)); - - const ptm::refdata_t* ref = res->ref_struct; - if (ref == NULL) - return; - - *p_type = ref->type; - if (p_alloy_type != NULL && unpermuted_numbers != NULL) - *p_alloy_type = ptm::find_alloy_type(ref, res->mapping, numbers); - - int bi = rotate_into_fundamental_zone(ref->type, res->q); - int8_t temp[PTM_MAX_POINTS]; - for (int i=0;inum_nbrs+1;i++) - temp[ref->mapping[bi][i]] = res->mapping[i]; - - memcpy(res->mapping, temp, (ref->num_nbrs+1) * sizeof(int8_t)); - - if (F != NULL && F_res != NULL) - { - double scaled_points[PTM_MAX_INPUT_POINTS][3]; - - ptm::subtract_barycentre(ref->num_nbrs + 1, points, scaled_points); - for (int i = 0;inum_nbrs + 1;i++) - { - scaled_points[i][0] *= res->scale; - scaled_points[i][1] *= res->scale; - scaled_points[i][2] *= res->scale; - } - ptm::calculate_deformation_gradient(ref->num_nbrs + 1, ref->points, res->mapping, scaled_points, ref->penrose, F, F_res); - - if (P != NULL && U != NULL) - ptm::polar_decomposition_3x3(F, false, U, P); - } - - if (mapping != NULL) - for (int i=0;inum_nbrs + 1;i++) - mapping[i] = ordering[res->mapping[i]]; - - double interatomic_distance = calculate_interatomic_distance(ref->type, res->scale); - double lattice_constant = calculate_lattice_constant(ref->type, interatomic_distance); - - if (p_interatomic_distance != NULL) - *p_interatomic_distance = interatomic_distance; - - if (p_lattice_constant != NULL) - *p_lattice_constant = lattice_constant; - - *p_rmsd = res->rmsd; - *p_scale = res->scale; - memcpy(q, res->q, 4 * sizeof(double)); -} - - extern bool ptm_initialized; -int ptm_index( ptm_local_handle_t local_handle, int32_t flags, - int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, bool topological_ordering, - int32_t* p_type, int32_t* p_alloy_type, double* p_scale, double* p_rmsd, double* q, double* F, double* F_res, - double* U, double* P, int8_t* mapping, double* p_interatomic_distance, double* p_lattice_constant) -{ - assert(ptm_initialized); - assert(num_points <= PTM_MAX_INPUT_POINTS); +int ptm_index(ptm_local_handle_t local_handle, size_t atom_index, + int(get_neighbours)(void *vdata, size_t central_index, size_t atom_index, int num, + size_t *nbr_indices, int32_t *numbers, + double (*nbr_pos)[3]), + void *nbrlist, int32_t flags, + bool output_conventional_orientation, int32_t *p_type, + int32_t *p_alloy_type, double *p_scale, double *p_rmsd, double *q, + double *F, double *F_res, double *U, double *P, + double *p_interatomic_distance, double *p_lattice_constant, + size_t *output_indices) { + assert(ptm_initialized); - if (flags & PTM_CHECK_SC) - assert(num_points >= PTM_NUM_POINTS_SC); + int ret = 0; + ptm::result_t res; + res.ref_struct = NULL; + res.rmsd = INFINITY; - if (flags & PTM_CHECK_BCC) - assert(num_points >= PTM_NUM_POINTS_BCC); + size_t ordering[PTM_MAX_INPUT_POINTS]; + int32_t numbers[PTM_MAX_INPUT_POINTS]; + double points[PTM_MAX_INPUT_POINTS][3]; - if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) - assert(num_points >= PTM_NUM_POINTS_FCC); + size_t dordering[PTM_MAX_INPUT_POINTS]; + int32_t dnumbers[PTM_MAX_INPUT_POINTS]; + double dpoints[PTM_MAX_INPUT_POINTS][3]; - if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) - assert(num_points >= PTM_NUM_POINTS_DCUB); + size_t gordering[PTM_MAX_INPUT_POINTS]; + int32_t gnumbers[PTM_MAX_INPUT_POINTS]; + double gpoints[PTM_MAX_INPUT_POINTS][3]; - int ret = 0; - ptm::result_t res; - res.ref_struct = NULL; - res.rmsd = INFINITY; + ptm::convexhull_t ch; + double ch_points[PTM_MAX_INPUT_POINTS][3]; + int num_lpoints = 0; - int8_t ordering[PTM_MAX_INPUT_POINTS]; - double points[PTM_MAX_POINTS][3]; - int32_t numbers[PTM_MAX_POINTS]; + if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | + PTM_CHECK_BCC)) { + int min_points = PTM_NUM_POINTS_SC; + if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) + min_points = PTM_NUM_POINTS_FCC; + if (flags & PTM_CHECK_BCC) + min_points = PTM_NUM_POINTS_BCC; - int8_t dordering[PTM_MAX_INPUT_POINTS]; - double dpoints[PTM_MAX_POINTS][3]; - int32_t dnumbers[PTM_MAX_POINTS]; + num_lpoints = ptm::calculate_neighbour_ordering( + local_handle, atom_index, min_points, get_neighbours, nbrlist, false, + ordering, points, numbers); + if (num_lpoints >= min_points) { + ptm::normalize_vertices(num_lpoints, points, ch_points); + ch.ok = false; - ptm::convexhull_t ch; - double ch_points[PTM_MAX_INPUT_POINTS][3]; + if (flags & PTM_CHECK_SC) + ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res); - if (flags & (PTM_CHECK_SC | PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO | PTM_CHECK_BCC)) - { - int num_lpoints = std::min(std::min(PTM_MAX_POINTS, 20), num_points); - order_points(local_handle, num_lpoints, unpermuted_points, unpermuted_numbers, topological_ordering, ordering, points, numbers); - ptm::normalize_vertices(num_lpoints, points, ch_points); - ch.ok = false; + if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) + ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); - if (flags & PTM_CHECK_SC) - ret = match_general(&ptm::structure_sc, ch_points, points, &ch, &res); + if (flags & PTM_CHECK_BCC) + ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res); + } + } - if (flags & (PTM_CHECK_FCC | PTM_CHECK_HCP | PTM_CHECK_ICO)) - ret = match_fcc_hcp_ico(ch_points, points, flags, &ch, &res); + if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) { + const int num_inner = 4, num_outer = 3, max_snbrs = 12; + ret = ptm::calculate_two_shell_neighbour_ordering( + (void *)local_handle, atom_index, get_neighbours, nbrlist, num_inner, + num_outer, max_snbrs, false, dordering, dpoints, dnumbers); + if (ret == 0) { + ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); + ch.ok = false; - if (flags & PTM_CHECK_BCC) - ret = match_general(&ptm::structure_bcc, ch_points, points, &ch, &res); - } + ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); + } + } - if (flags & (PTM_CHECK_DCUB | PTM_CHECK_DHEX)) - { - ret = ptm::calculate_diamond_neighbour_ordering(num_points, unpermuted_points, unpermuted_numbers, dordering, dpoints, dnumbers); - if (ret == 0) - { - ptm::normalize_vertices(PTM_NUM_NBRS_DCUB + 1, dpoints, ch_points); - ch.ok = false; + if (flags & PTM_CHECK_GRAPHENE) { + const int num_inner = 3, num_outer = 2, max_snbrs = 12; + ret = ptm::calculate_two_shell_neighbour_ordering( + (void *)local_handle, atom_index, get_neighbours, nbrlist, num_inner, + num_outer, max_snbrs, true, gordering, gpoints, gnumbers); + if (ret == 0) { + ret = match_graphene(gpoints, &res); + } + } - ret = match_dcub_dhex(ch_points, dpoints, flags, &ch, &res); - } - } + *p_type = PTM_MATCH_NONE; + if (p_alloy_type != NULL) + *p_alloy_type = PTM_ALLOY_NONE; - if (res.ref_struct != NULL && (res.ref_struct->type == PTM_MATCH_DCUB || res.ref_struct->type == PTM_MATCH_DHEX)) - { - output_data( &res, num_points, unpermuted_numbers, dpoints, dnumbers, dordering, - p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, - U, P, mapping, p_interatomic_distance, p_lattice_constant); - } - else - { - output_data( &res, num_points, unpermuted_numbers, points, numbers, ordering, - p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, - U, P, mapping, p_interatomic_distance, p_lattice_constant); - } + if (output_indices != NULL) + memset(output_indices, -1, PTM_MAX_INPUT_POINTS * sizeof(size_t)); - return PTM_NO_ERROR; + if (res.ref_struct == NULL) + return PTM_NO_ERROR; + + if (res.ref_struct->type == PTM_MATCH_DCUB || + res.ref_struct->type == PTM_MATCH_DHEX) { + output_data(&res, dpoints, dnumbers, dordering, + output_conventional_orientation, p_type, p_alloy_type, p_scale, + p_rmsd, q, F, F_res, U, P, p_interatomic_distance, + p_lattice_constant, output_indices); + } else if (res.ref_struct->type == PTM_MATCH_GRAPHENE) { + output_data(&res, gpoints, gnumbers, gordering, + output_conventional_orientation, p_type, p_alloy_type, p_scale, + p_rmsd, q, F, F_res, U, P, p_interatomic_distance, + p_lattice_constant, output_indices); + } else { + output_data(&res, points, numbers, ordering, output_conventional_orientation, + p_type, p_alloy_type, p_scale, p_rmsd, q, F, F_res, U, P, + p_interatomic_distance, p_lattice_constant, output_indices); + } + + return PTM_NO_ERROR; } - diff --git a/src/USER-PTM/ptm_initialize_data.cpp b/src/USER-PTM/ptm_initialize_data.cpp index 8d96e2a2b7..49dc6f2323 100644 --- a/src/USER-PTM/ptm_initialize_data.cpp +++ b/src/USER-PTM/ptm_initialize_data.cpp @@ -1,6 +1,15 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include #include -#include +#include #include #include #include @@ -10,62 +19,62 @@ static void make_facets_clockwise(int num_facets, int8_t (*facets)[3], const double (*points)[3]) { - double plane_normal[3]; - double origin[3] = {0, 0, 0}; + double plane_normal[3]; + double origin[3] = {0, 0, 0}; - for (int i = 0;inum_graphs;i++) - { - int8_t code[2 * PTM_MAX_EDGES]; - int8_t degree[PTM_MAX_NBRS]; - int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); - assert(_max_degree <= s->max_degree); + for (int i = 0;inum_graphs;i++) + { + int8_t code[2 * PTM_MAX_EDGES]; + int8_t degree[PTM_MAX_NBRS]; + int _max_degree = ptm::graph_degree(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree); + assert(_max_degree <= s->max_degree); - make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); - int ret = ptm::canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); - if (ret != 0) - return ret; - } + make_facets_clockwise(s->num_facets, s->graphs[i].facets, &s->points[1]); + int ret = ptm::canonical_form_coloured(s->num_facets, s->graphs[i].facets, s->num_nbrs, degree, colours, s->graphs[i].canonical_labelling, (int8_t*)&code[0], &s->graphs[i].hash); + if (ret != 0) + return ret; + } - return PTM_NO_ERROR; + return PTM_NO_ERROR; } bool ptm_initialized = false; int ptm_initialize_global() { - if (ptm_initialized) - return PTM_NO_ERROR; + if (ptm_initialized) + return PTM_NO_ERROR; - int8_t colours[PTM_MAX_POINTS] = {0}; - int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t dcolours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - int ret = initialize_graphs(&ptm::structure_sc, colours); - ret |= initialize_graphs(&ptm::structure_fcc, colours); - ret |= initialize_graphs(&ptm::structure_hcp, colours); - ret |= initialize_graphs(&ptm::structure_ico, colours); - ret |= initialize_graphs(&ptm::structure_bcc, colours); - ret |= initialize_graphs(&ptm::structure_dcub, dcolours); - ret |= initialize_graphs(&ptm::structure_dhex, dcolours); + int ret = initialize_graphs(&ptm::structure_sc, colours); + ret |= initialize_graphs(&ptm::structure_fcc, colours); + ret |= initialize_graphs(&ptm::structure_hcp, colours); + ret |= initialize_graphs(&ptm::structure_ico, colours); + ret |= initialize_graphs(&ptm::structure_bcc, colours); + ret |= initialize_graphs(&ptm::structure_dcub, dcolours); + ret |= initialize_graphs(&ptm::structure_dhex, dcolours); - if (ret == PTM_NO_ERROR) - ptm_initialized = true; + if (ret == PTM_NO_ERROR) + ptm_initialized = true; - return ret; + return ret; } ptm_local_handle_t ptm_initialize_local() { - assert(ptm_initialized); - return (ptm_local_handle_t)ptm::voronoi_initialize_local(); + assert(ptm_initialized); + return (ptm_local_handle_t)ptm::voronoi_initialize_local(); } void ptm_uninitialize_local(ptm_local_handle_t ptr) { - ptm::voronoi_uninitialize_local(ptr); + ptm::voronoi_uninitialize_local(ptr); } diff --git a/src/USER-PTM/ptm_initialize_data.h b/src/USER-PTM/ptm_initialize_data.h index 5374fbf7d0..20c9921962 100644 --- a/src/USER-PTM/ptm_initialize_data.h +++ b/src/USER-PTM/ptm_initialize_data.h @@ -1,3 +1,12 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_INITIALIZE_DATA_H #define PTM_INITIALIZE_DATA_H @@ -9,34 +18,193 @@ #include "ptm_neighbour_ordering.h" #include "ptm_canonical_coloured.h" #include "ptm_convex_hull_incremental.h" +#include "ptm_alt_templates.h" namespace ptm { typedef struct { - int type; - int num_nbrs; - int num_facets; - int max_degree; - int num_graphs; - int num_mappings; - graph_t* graphs; - const double (*points)[3]; - const double (*penrose)[3]; - const int8_t (*mapping)[PTM_MAX_POINTS]; + int type; + int num_nbrs; + int num_facets; + int max_degree; + int num_graphs; + graph_t* graphs; + const double (*points)[3]; + const double (*points_alt1)[3]; + const double (*points_alt2)[3]; + const double (*points_alt3)[3]; + const double (*penrose)[3]; + const double (*penrose_alt1)[3]; + const double (*penrose_alt2)[3]; + const double (*penrose_alt3)[3]; + int num_mappings; + const int8_t (*mapping)[PTM_MAX_POINTS]; + const int8_t (*mapping_conventional)[PTM_MAX_POINTS]; + const int8_t *template_indices; } refdata_t; -//refdata_t structure_sc = { .type = PTM_MATCH_SC, .num_nbrs = 6, .num_facets = 8, .max_degree = 4, .num_graphs = NUM_SC_GRAPHS, .graphs = graphs_sc, .points = ptm_template_sc, .penrose = penrose_sc , .mapping = mapping_sc }; -const refdata_t structure_sc = { PTM_MATCH_SC, 6, 8, 4, NUM_SC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_sc, ptm_template_sc, penrose_sc, mapping_sc }; -const refdata_t structure_fcc = { PTM_MATCH_FCC, 12, 20, 6, NUM_FCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_fcc, ptm_template_fcc, penrose_fcc, mapping_fcc }; -const refdata_t structure_hcp = { PTM_MATCH_HCP, 12, 20, 6, NUM_HCP_GRAPHS, NUM_HEX_MAPPINGS, graphs_hcp, ptm_template_hcp, penrose_hcp, mapping_hcp }; -const refdata_t structure_ico = { PTM_MATCH_ICO, 12, 20, 6, NUM_ICO_GRAPHS, NUM_ICO_MAPPINGS, graphs_ico, ptm_template_ico, penrose_ico, mapping_ico }; -const refdata_t structure_bcc = { PTM_MATCH_BCC, 14, 24, 8, NUM_BCC_GRAPHS, NUM_CUBIC_MAPPINGS, graphs_bcc, ptm_template_bcc, penrose_bcc, mapping_bcc }; -const refdata_t structure_dcub = { PTM_MATCH_DCUB, 16, 28, 8, NUM_DCUB_GRAPHS, NUM_DCUB_MAPPINGS, graphs_dcub, ptm_template_dcub, penrose_dcub, mapping_dcub }; -const refdata_t structure_dhex = { PTM_MATCH_DHEX, 16, 28, 8, NUM_DHEX_GRAPHS, NUM_DHEX_MAPPINGS, graphs_dhex, ptm_template_dhex, penrose_dhex, mapping_dhex }; +const refdata_t structure_sc = { PTM_MATCH_SC, //.type + 6, //.num_nbrs + 8, //.num_facets + 4, //.max_degree + NUM_SC_GRAPHS, //.num_graphs + graphs_sc, //.graphs + ptm_template_sc, //.points + NULL, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_sc, //.penrose + NULL, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + NUM_CUBIC_MAPPINGS, //.num_mappings + mapping_sc, //.mapping + NULL, //.mapping_conventional + NULL, //.template_indices + }; +const refdata_t structure_fcc = { PTM_MATCH_FCC, //.type + 12, //.num_nbrs + 20, //.num_facets + 6, //.max_degree + NUM_FCC_GRAPHS, //.num_graphs + graphs_fcc, //.graphs + ptm_template_fcc, //.points + NULL, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_fcc, //.penrose + NULL, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + NUM_CUBIC_MAPPINGS, //.num_mappings + mapping_fcc, //.mapping + NULL, //.mapping_conventional + NULL, //.template_indices + }; + +const refdata_t structure_hcp = { PTM_MATCH_HCP, //.type + 12, //.num_nbrs + 20, //.num_facets + 6, //.max_degree + NUM_HCP_GRAPHS, //.num_graphs + graphs_hcp, //.graphs + ptm_template_hcp, //.points + ptm_template_hcp_alt1, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_hcp, //.penrose + penrose_hcp_alt1, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + NUM_HEX_MAPPINGS, //.num_mappings + mapping_hcp, //.mapping + mapping_hcp_conventional, //.mapping_conventional + template_indices_hcp, //.template_indices + }; + +const refdata_t structure_ico = { PTM_MATCH_ICO, //.type + 12, //.num_nbrs + 20, //.num_facets + 6, //.max_degree + NUM_ICO_GRAPHS, //.num_graphs + graphs_ico, //.graphs + ptm_template_ico, //.points + NULL, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_ico, //.penrose + NULL, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + NUM_ICO_MAPPINGS, //.num_mappings + mapping_ico, //.mapping + NULL, //.mapping_conventional + NULL, //.template_indices + }; + +const refdata_t structure_bcc = { PTM_MATCH_BCC, //.type + 14, //.num_nbrs + 24, //.num_facets + 8, //.max_degree + NUM_BCC_GRAPHS, //.num_graphs + graphs_bcc, //.graphs + ptm_template_bcc, //.points + NULL, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_bcc, //.penrose + NULL, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + NUM_CUBIC_MAPPINGS, //.num_mappings + mapping_bcc, //.mapping + NULL, //.mapping_conventional + NULL, //.template_indices + }; + +const refdata_t structure_dcub = { PTM_MATCH_DCUB, //.type + 16, //.num_nbrs + 28, //.num_facets + 8, //.max_degree + NUM_DCUB_GRAPHS, //.num_graphs + graphs_dcub, //.graphs + ptm_template_dcub, //.points + ptm_template_dcub_alt1, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_dcub, //.penrose + penrose_dcub_alt1, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + NUM_DCUB_MAPPINGS, //.num_mappings + mapping_dcub, //.mapping + mapping_dcub_conventional, //.mapping_conventional + template_indices_dcub, //.template_indices + }; + +const refdata_t structure_dhex = { PTM_MATCH_DHEX, //.type + 16, //.num_nbrs + 28, //.num_facets + 8, //.max_degree + NUM_DHEX_GRAPHS, //.num_graphs + graphs_dhex, //.graphs + ptm_template_dhex, //.points + ptm_template_dhex_alt1, //.points_alt1 + ptm_template_dhex_alt2, //.points_alt2 + ptm_template_dhex_alt3, //.points_alt3 + penrose_dhex, //.penrose + penrose_dhex_alt1, //.penrose_alt1 + penrose_dhex_alt2, //.penrose_alt2 + penrose_dhex_alt3, //.penrose_alt3 + NUM_DHEX_MAPPINGS, //.num_mappings + mapping_dhex, //.mapping + mapping_dhex_conventional, //.mapping_conventional + template_indices_dhex, //.template_indices + }; + +const refdata_t structure_graphene = { PTM_MATCH_GRAPHENE, //.type + 9, //.num_nbrs + -1, //.num_facets + -1, //.max_degree + -1, //.num_graphs + NULL, //.graphs + ptm_template_graphene, //.points + ptm_template_graphene_alt1, //.points_alt1 + NULL, //.points_alt2 + NULL, //.points_alt3 + penrose_graphene, //.penrose + penrose_graphene_alt1, //.penrose_alt1 + NULL, //.penrose_alt2 + NULL, //.penrose_alt3 + -1, //.num_mappings + mapping_graphene, //.mapping + mapping_graphene_conventional, //.mapping_conventional + template_indices_graphene, //.template_indices + }; } #ifdef __cplusplus diff --git a/src/USER-PTM/ptm_neighbour_ordering.cpp b/src/USER-PTM/ptm_neighbour_ordering.cpp index d5948b9dc6..cb72a43711 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.cpp +++ b/src/USER-PTM/ptm_neighbour_ordering.cpp @@ -1,205 +1,399 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +//todo: normalize vertices + #include #include #include #include #include +#include #include "ptm_constants.h" #include "ptm_voronoi_cell.h" #include "ptm_neighbour_ordering.h" +#include "ptm_normalize_vertices.h" namespace ptm { typedef struct { - double area; - double dist; - int index; + double area; + double dist; + int index; + int inner; + int32_t number; + double offset[3]; } sorthelper_t; +typedef struct +{ + size_t index; + int32_t number; + double area; + double offset[3]; + +} solidnbr_t; + static bool sorthelper_compare(sorthelper_t const& a, sorthelper_t const& b) { - if (a.area > b.area) - return true; + if (a.area > b.area) + return true; - if (a.area < b.area) - return false; + if (a.area < b.area) + return false; - if (a.dist < b.dist) - return true; + if (a.dist < b.dist) + return true; - return false; + return false; +} + +static double dot_product(double* a, double* b) +{ + return a[0] * b[0] + a[1] * b[1] + a[2] * b[2]; +} + +static void cross_product(double* a, double* b, double* c) +{ + c[0] = a[1] * b[2] - a[2] * b[1]; + c[1] = a[2] * b[0] - a[0] * b[2]; + c[2] = a[0] * b[1] - a[1] * b[0]; +} + +static double calculate_solid_angle(double* R1, double* R2, double* R3) //norms of R1-R3 must be 1 +{ + double R2R3[3]; + cross_product(R2, R3, R2R3); + double numerator = dot_product(R1, R2R3); + + double r1r2 = dot_product(R1, R2); + double r2r3 = dot_product(R2, R3); + double r3r1 = dot_product(R3, R1); + + double denominator = 1 + r1r2 + r3r1 + r2r3; + return fabs(2 * atan2(numerator, denominator)); } //todo: change voronoi code to return errors rather than exiting -static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, ptm_voro::voronoicell_neighbor* v, std::vector& nbr_indices, std::vector& face_areas) +static int calculate_voronoi_face_areas(int num_points, const double (*_points)[3], double* normsq, double max_norm, ptm_voro::voronoicell_neighbor* v, bool calc_solid_angles, + std::vector& nbr_indices, std::vector& face_areas) { - const double k = 1000 * max_norm; //todo: reduce this constant - v->init(-k,k,-k,k,-k,k); + const double k = 10 * max_norm; + v->init(-k,k,-k,k,-k,k); - for (int i=1;inplane(x,y,z,normsq[i],i); - } + for (int i=1;inplane(x,y,z,normsq[i],i); + } - v->neighbors(nbr_indices); - v->face_areas(face_areas); - return 0; + v->neighbors(nbr_indices); + +//v->face_areas(face_areas); + if (!calc_solid_angles) + { + v->face_areas(face_areas); + return 0; + } + else + { + std::vector face_vertices; + std::vector vertices; + + v->face_vertices(face_vertices); + v->vertices(0, 0, 0, vertices); + + size_t num_vertices = vertices.size() / 3; + for (size_t i=0;inumber_of_faces(); + +#ifdef DEBUG + printf("number of voronoi faces: %d\n", num_faces); +#endif + +//std::vector solids(face_areas.size()+1); + + size_t c = 0; + for (int current_face=0;current_face 0) + { + double solid_angle = 0; + int u = face_vertices[c]; + int v = face_vertices[c+1]; + for (int i=2;i nbr_indices(num_points + 6); - std::vector face_areas(num_points + 6); - int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, nbr_indices, face_areas); - if (ret != 0) - return ret; + max_norm = sqrt(max_norm); - double areas[PTM_MAX_INPUT_POINTS]; - memset(areas, 0, num_points * sizeof(double)); - areas[0] = INFINITY; - for (size_t i=0;i 0) - areas[index] = face_areas[i]; - } + std::vector nbr_indices(num_points + 6); + std::vector face_areas(num_points + 6); + int ret = calculate_voronoi_face_areas(num_points, points, normsq, max_norm, voronoi_handle, calc_solid_angles, nbr_indices, face_areas); + if (ret != 0) + return ret; - sorthelper_t data[PTM_MAX_INPUT_POINTS]; - for (int i=0;i 0) + areas[index] = face_areas[i]; + } - std::sort(data, data + num_points, &sorthelper_compare); + for (int i=0;i claimed; + claimed.insert(atom_index); + for (int i=0;i= 3) - continue; + //---------------------------------------------- + size_t inner_nbr_indices[MAX_SNBRS + 1]; + int32_t inner_nbr_numbers[MAX_SNBRS + 1]; + double inner_nbr_pos[MAX_SNBRS + 1][3]; + int num_points = get_neighbours(nbrlist, atom_index, inner_index, max_snbrs + 1, inner_nbr_indices, inner_nbr_numbers, inner_nbr_pos); + if (num_points < num_inner + 1) + return -1; - ordering[1 + 4 + 3 * p + counts[p]] = q; - counts[p]++; - index++; - num_found++; - if (num_found >= 12) - break; - } + solidnbr_t inner_solid[MAX_SNBRS]; + ret = find_diamond_neighbours(_voronoi_handle, num_points, inner_nbr_pos, inner_nbr_indices, inner_nbr_numbers, max_snbrs, calc_solid_angles, inner_solid); + if (ret != 0) + return ret; + //---------------------------------------------- - if (num_found != 12) - return -1; + int n = std::min(6, num_points); + for (int j=0;j= num_outer || already_claimed) + continue; + + nbr_indices[1 + num_inner + num_outer * inner + counts[inner]] = nbr_atom_index; + numbers[1 + num_inner + num_outer * inner + counts[inner]] = data[i].number; + memcpy(points[1 + num_inner + num_outer * inner + counts[inner]], &data[i].offset, 3 * sizeof(double)); + claimed.insert(nbr_atom_index); + + counts[inner]++; + num_found++; + if (num_found >= num_inner * num_outer) + break; + } + + if (num_found != num_inner * num_outer) + return -1; + + return 0; } } diff --git a/src/USER-PTM/ptm_neighbour_ordering.h b/src/USER-PTM/ptm_neighbour_ordering.h index 78bf4d533b..2a619880bb 100644 --- a/src/USER-PTM/ptm_neighbour_ordering.h +++ b/src/USER-PTM/ptm_neighbour_ordering.h @@ -1,14 +1,27 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_NEIGHBOUR_ORDERING_H #define PTM_NEIGHBOUR_ORDERING_H -#include +#include +#include namespace ptm { -int calculate_neighbour_ordering(void* voronoi_handle, int num_points, const double (*_points)[3], int8_t* ordering); +int calculate_neighbour_ordering( void* _voronoi_handle, size_t atom_index, int min_points, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, + double (*nbr_pos)[3]), void* nbrlist, bool calc_solid_angles, + size_t* nbr_indices, double (*points)[3], int32_t* numbers); -int calculate_diamond_neighbour_ordering( int num_points, double (*unpermuted_points)[3], int32_t* unpermuted_numbers, - int8_t* ordering, double (*points)[3], int32_t* numbers); +int calculate_two_shell_neighbour_ordering( void* _voronoi_handle, size_t atom_index, int (get_neighbours)(void* vdata, size_t central_index, size_t atom_index, int num, size_t* nbr_indices, int32_t* numbers, double (*nbr_pos)[3]), void* nbrlist, + int num_inner, int num_outer, int max_snbrs, bool calc_solid_angles, + size_t* nbr_indices, double (*points)[3], int32_t* numbers); void* voronoi_initialize_local(); void voronoi_uninitialize_local(void* ptr); diff --git a/src/USER-PTM/ptm_normalize_vertices.cpp b/src/USER-PTM/ptm_normalize_vertices.cpp index 22e3c1e670..8817e9faaf 100644 --- a/src/USER-PTM/ptm_normalize_vertices.cpp +++ b/src/USER-PTM/ptm_normalize_vertices.cpp @@ -1,57 +1,66 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include namespace ptm { void subtract_barycentre(int num, double (*points)[3], double (*normalized)[3]) { - //calculate barycentre - double sum[3] = {0, 0, 0}; - for (int i=0;i nor the names of its contributors may be used to - * endorse or promote products derived from this software without specific prior written - * permission. + * endorse or promote products derived from this software without specific prior written + * permission. * * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT @@ -63,279 +63,278 @@ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. * - * Source: started anew. + * Source: started anew. * * Change History: - * 2009/04/13 Started source - * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr - * If trying all rows of the adjoint still gives too small - * qsqr, then just return identity matrix. (DLT) - * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct() - * invalid mem access - * 2011/02/21 Made CenterCoords use weights - * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h - * Also changed some functions to static - * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error - * 2012/07/26 minor changes to comments and main.c, more info (v.1.4) + * 2009/04/13 Started source + * 2010/03/28 Modified FastCalcRMSDAndRotation() to handle tiny qsqr + * If trying all rows of the adjoint still gives too small + * qsqr, then just return identity matrix. (DLT) + * 2010/06/30 Fixed prob in assigning A[9] = 0 in InnerProduct() + * invalid mem access + * 2011/02/21 Made CenterCoords use weights + * 2011/05/02 Finally changed CenterCoords declaration in qcprot.h + * Also changed some functions to static + * 2011/07/08 put in fabs() to fix taking sqrt of small neg numbers, fp error + * 2012/07/26 minor changes to comments and main.c, more info (v.1.4) * * 2016/05/29 QCP method adapted for polar decomposition of a 3x3 matrix, - * for use in Polyhedral Template Matching. - * + * for use in Polyhedral Template Matching. + * ******************************************************************************/ #include #include -#include +#include #include "ptm_quat.h" -#include "ptm_polar.h" namespace ptm { static void matmul_3x3(double* A, double* x, double* b) { - b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6]; - b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6]; - b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6]; + b[0] = A[0] * x[0] + A[1] * x[3] + A[2] * x[6]; + b[3] = A[3] * x[0] + A[4] * x[3] + A[5] * x[6]; + b[6] = A[6] * x[0] + A[7] * x[3] + A[8] * x[6]; - b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7]; - b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7]; - b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7]; + b[1] = A[0] * x[1] + A[1] * x[4] + A[2] * x[7]; + b[4] = A[3] * x[1] + A[4] * x[4] + A[5] * x[7]; + b[7] = A[6] * x[1] + A[7] * x[4] + A[8] * x[7]; - b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8]; - b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8]; - b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8]; + b[2] = A[0] * x[2] + A[1] * x[5] + A[2] * x[8]; + b[5] = A[3] * x[2] + A[4] * x[5] + A[5] * x[8]; + b[8] = A[6] * x[2] + A[7] * x[5] + A[8] * x[8]; } static double matrix_determinant_3x3(double* A) { - return A[0] * (A[4]*A[8] - A[5]*A[7]) - - A[1] * (A[3]*A[8] - A[5]*A[6]) - + A[2] * (A[3]*A[7] - A[4]*A[6]); + return A[0] * (A[4]*A[8] - A[5]*A[7]) + - A[1] * (A[3]*A[8] - A[5]*A[6]) + + A[2] * (A[3]*A[7] - A[4]*A[6]); } static void flip_matrix(double* A) { - for (int i=0;i<9;i++) - A[i] = -A[i]; + for (int i=0;i<9;i++) + A[i] = -A[i]; } static bool optimal_quaternion(double* A, bool polar, double E0, double* p_nrmsdsq, double* qopt) { - const double evecprec = 1e-6; - const double evalprec = 1e-11; + const double evecprec = 1e-6; + const double evalprec = 1e-11; - double Sxx = A[0], Sxy = A[1], Sxz = A[2], - Syx = A[3], Syy = A[4], Syz = A[5], - Szx = A[6], Szy = A[7], Szz = A[8]; + double Sxx = A[0], Sxy = A[1], Sxz = A[2], + Syx = A[3], Syy = A[4], Syz = A[5], + Szx = A[6], Szy = A[7], Szz = A[8]; - double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz, - Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz, - Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx; + double Sxx2 = Sxx * Sxx, Syy2 = Syy * Syy, Szz2 = Szz * Szz, + Sxy2 = Sxy * Sxy, Syz2 = Syz * Syz, Sxz2 = Sxz * Sxz, + Syx2 = Syx * Syx, Szy2 = Szy * Szy, Szx2 = Szx * Szx; - double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2; + double fnorm_squared = Sxx2 + Syy2 + Szz2 + Sxy2 + Syz2 + Sxz2 + Syx2 + Szy2 + Szx2; - double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz); - double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2; - double SxzpSzx = Sxz + Szx; - double SyzpSzy = Syz + Szy; - double SxypSyx = Sxy + Syx; - double SyzmSzy = Syz - Szy; - double SxzmSzx = Sxz - Szx; - double SxymSyx = Sxy - Syx; - double SxxpSyy = Sxx + Syy; - double SxxmSyy = Sxx - Syy; - double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2; + double SyzSzymSyySzz2 = 2.0 * (Syz * Szy - Syy * Szz); + double Sxx2Syy2Szz2Syz2Szy2 = Syy2 + Szz2 - Sxx2 + Syz2 + Szy2; + double SxzpSzx = Sxz + Szx; + double SyzpSzy = Syz + Szy; + double SxypSyx = Sxy + Syx; + double SyzmSzy = Syz - Szy; + double SxzmSzx = Sxz - Szx; + double SxymSyx = Sxy - Syx; + double SxxpSyy = Sxx + Syy; + double SxxmSyy = Sxx - Syy; + double Sxy2Sxz2Syx2Szx2 = Sxy2 + Sxz2 - Syx2 - Szx2; - double C[3]; - C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 - + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2) - + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz)) - + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz)) - + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz)) - + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz)); + double C[3]; + C[0] = Sxy2Sxz2Syx2Szx2 * Sxy2Sxz2Syx2Szx2 + + (Sxx2Syy2Szz2Syz2Szy2 + SyzSzymSyySzz2) * (Sxx2Syy2Szz2Syz2Szy2 - SyzSzymSyySzz2) + + (-(SxzpSzx)*(SyzmSzy)+(SxymSyx)*(SxxmSyy-Szz)) * (-(SxzmSzx)*(SyzpSzy)+(SxymSyx)*(SxxmSyy+Szz)) + + (-(SxzpSzx)*(SyzpSzy)-(SxypSyx)*(SxxpSyy-Szz)) * (-(SxzmSzx)*(SyzmSzy)-(SxypSyx)*(SxxpSyy+Szz)) + + (+(SxypSyx)*(SyzpSzy)+(SxzpSzx)*(SxxmSyy+Szz)) * (-(SxymSyx)*(SyzmSzy)+(SxzpSzx)*(SxxpSyy+Szz)) + + (+(SxypSyx)*(SyzmSzy)+(SxzmSzx)*(SxxmSyy-Szz)) * (-(SxymSyx)*(SyzpSzy)+(SxzmSzx)*(SxxpSyy-Szz)); - C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz); - C[2] = -2.0 * fnorm_squared; + C[1] = 8.0 * (Sxx*Syz*Szy + Syy*Szx*Sxz + Szz*Sxy*Syx - Sxx*Syy*Szz - Syz*Szx*Sxy - Szy*Syx*Sxz); + C[2] = -2.0 * fnorm_squared; - //Newton-Raphson - double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0; - if (mxEigenV > evalprec) - { - for (int i=0;i<50;i++) - { - double oldg = mxEigenV; - double x2 = mxEigenV*mxEigenV; - double b = (x2 + C[2])*mxEigenV; - double a = b + C[1]; - double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a)); - mxEigenV -= delta; - if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV)) - break; - } - } - else - { - mxEigenV = 0.0; - } + //Newton-Raphson + double mxEigenV = polar ? sqrt(3 * fnorm_squared) : E0; + if (mxEigenV > evalprec) + { + for (int i=0;i<50;i++) + { + double oldg = mxEigenV; + double x2 = mxEigenV*mxEigenV; + double b = (x2 + C[2])*mxEigenV; + double a = b + C[1]; + double delta = ((a * mxEigenV + C[0]) / (2 * x2 * mxEigenV + b + a)); + mxEigenV -= delta; + if (fabs(mxEigenV - oldg) < fabs(evalprec * mxEigenV)) + break; + } + } + else + { + mxEigenV = 0.0; + } - (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV)); + (*p_nrmsdsq) = std::max(0.0, 2.0 * (E0 - mxEigenV)); - double a11 = SxxpSyy + Szz - mxEigenV; - double a12 = SyzmSzy; - double a13 = -SxzmSzx; - double a14 = SxymSyx; + double a11 = SxxpSyy + Szz - mxEigenV; + double a12 = SyzmSzy; + double a13 = -SxzmSzx; + double a14 = SxymSyx; - double a21 = SyzmSzy; - double a22 = SxxmSyy - Szz -mxEigenV; - double a23 = SxypSyx; - double a24 = SxzpSzx; + double a21 = SyzmSzy; + double a22 = SxxmSyy - Szz -mxEigenV; + double a23 = SxypSyx; + double a24 = SxzpSzx; - double a31 = a13; - double a32 = a23; - double a33 = Syy - Sxx - Szz - mxEigenV; - double a34 = SyzpSzy; + double a31 = a13; + double a32 = a23; + double a33 = Syy - Sxx - Szz - mxEigenV; + double a34 = SyzpSzy; - double a41 = a14; - double a42 = a24; - double a43 = a34; - double a44 = Szz - SxxpSyy - mxEigenV; + double a41 = a14; + double a42 = a24; + double a43 = a34; + double a44 = Szz - SxxpSyy - mxEigenV; - double a3344_4334 = a33 * a44 - a43 * a34; - double a3244_4234 = a32 * a44 - a42 * a34; - double a3243_4233 = a32 * a43 - a42 * a33; - double a3143_4133 = a31 * a43 - a41 * a33; - double a3144_4134 = a31 * a44 - a41 * a34; - double a3142_4132 = a31 * a42 - a41 * a32; - double a1324_1423 = a13 * a24 - a14 * a23; - double a1224_1422 = a12 * a24 - a14 * a22; - double a1223_1322 = a12 * a23 - a13 * a22; - double a1124_1421 = a11 * a24 - a14 * a21; - double a1123_1321 = a11 * a23 - a13 * a21; - double a1122_1221 = a11 * a22 - a12 * a21; + double a3344_4334 = a33 * a44 - a43 * a34; + double a3244_4234 = a32 * a44 - a42 * a34; + double a3243_4233 = a32 * a43 - a42 * a33; + double a3143_4133 = a31 * a43 - a41 * a33; + double a3144_4134 = a31 * a44 - a41 * a34; + double a3142_4132 = a31 * a42 - a41 * a32; + double a1324_1423 = a13 * a24 - a14 * a23; + double a1224_1422 = a12 * a24 - a14 * a22; + double a1223_1322 = a12 * a23 - a13 * a22; + double a1124_1421 = a11 * a24 - a14 * a21; + double a1123_1321 = a11 * a23 - a13 * a21; + double a1122_1221 = a11 * a22 - a12 * a21; - double q[4][4]; - q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233; - q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133; - q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132; - q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132; + double q[4][4]; + q[0][0] = a12 * a3344_4334 - a13 * a3244_4234 + a14 * a3243_4233; + q[0][1] = -a11 * a3344_4334 + a13 * a3144_4134 - a14 * a3143_4133; + q[0][2] = a11 * a3244_4234 - a12 * a3144_4134 + a14 * a3142_4132; + q[0][3] = -a11 * a3243_4233 + a12 * a3143_4133 - a13 * a3142_4132; - q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233; - q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133; - q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132; - q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132; + q[1][0] = a22 * a3344_4334 - a23 * a3244_4234 + a24 * a3243_4233; + q[1][1] = -a21 * a3344_4334 + a23 * a3144_4134 - a24 * a3143_4133; + q[1][2] = a21 * a3244_4234 - a22 * a3144_4134 + a24 * a3142_4132; + q[1][3] = -a21 * a3243_4233 + a22 * a3143_4133 - a23 * a3142_4132; - q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322; - q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321; - q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221; - q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221; + q[2][0] = a32 * a1324_1423 - a33 * a1224_1422 + a34 * a1223_1322; + q[2][1] = -a31 * a1324_1423 + a33 * a1124_1421 - a34 * a1123_1321; + q[2][2] = a31 * a1224_1422 - a32 * a1124_1421 + a34 * a1122_1221; + q[2][3] = -a31 * a1223_1322 + a32 * a1123_1321 - a33 * a1122_1221; - q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322; - q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321; - q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221; - q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221; + q[3][0] = a42 * a1324_1423 - a43 * a1224_1422 + a44 * a1223_1322; + q[3][1] = -a41 * a1324_1423 + a43 * a1124_1421 - a44 * a1123_1321; + q[3][2] = a41 * a1224_1422 - a42 * a1124_1421 + a44 * a1122_1221; + q[3][3] = -a41 * a1223_1322 + a42 * a1123_1321 - a43 * a1122_1221; - double qsqr[4]; - for (int i=0;i<4;i++) - qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3]; + double qsqr[4]; + for (int i=0;i<4;i++) + qsqr[i] = q[i][0]*q[i][0] + q[i][1]*q[i][1] + q[i][2]*q[i][2] + q[i][3]*q[i][3]; - int bi = 0; - double max = 0; - for (int i=0;i<4;i++) - { - if (qsqr[i] > max) - { - bi = i; - max = qsqr[i]; - } - } + int bi = 0; + double max = 0; + for (int i=0;i<4;i++) + { + if (qsqr[i] > max) + { + bi = i; + max = qsqr[i]; + } + } - bool too_small = false; - if (qsqr[bi] < evecprec) - { - //if qsqr is still too small, return the identity rotation. - q[bi][0] = 1; - q[bi][1] = 0; - q[bi][2] = 0; - q[bi][3] = 0; - too_small = true; - } - else - { - double normq = sqrt(qsqr[bi]); - q[bi][0] /= normq; - q[bi][1] /= normq; - q[bi][2] /= normq; - q[bi][3] /= normq; - } + bool too_small = false; + if (qsqr[bi] < evecprec) + { + //if qsqr is still too small, return the identity rotation. + q[bi][0] = 1; + q[bi][1] = 0; + q[bi][2] = 0; + q[bi][3] = 0; + too_small = true; + } + else + { + double normq = sqrt(qsqr[bi]); + q[bi][0] /= normq; + q[bi][1] /= normq; + q[bi][2] /= normq; + q[bi][3] /= normq; + } - memcpy(qopt, q[bi], 4 * sizeof(double)); - return !too_small; + memcpy(qopt, q[bi], 4 * sizeof(double)); + return !too_small; } int polar_decomposition_3x3(double* _A, bool right_sided, double* U, double* P) { - double A[9]; - memcpy(A, _A, 9 * sizeof(double)); + double A[9]; + memcpy(A, _A, 9 * sizeof(double)); - double det = matrix_determinant_3x3(A); - if (det < 0) - flip_matrix(A); + double det = matrix_determinant_3x3(A); + if (det < 0) + flip_matrix(A); - double q[4]; - double nrmsdsq = 0; - optimal_quaternion(A, true, -1, &nrmsdsq, q); - q[0] = -q[0]; - quaternion_to_rotation_matrix(q, U); + double q[4]; + double nrmsdsq = 0; + optimal_quaternion(A, true, -1, &nrmsdsq, q); + q[0] = -q[0]; + quaternion_to_rotation_matrix(q, U); - if (det < 0) - flip_matrix(U); + if (det < 0) + flip_matrix(U); - double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]}; + double UT[9] = {U[0], U[3], U[6], U[1], U[4], U[7], U[2], U[5], U[8]}; - if (right_sided) - matmul_3x3(UT, _A, P); - else - matmul_3x3(_A, UT, P); + if (right_sided) + matmul_3x3(UT, _A, P); + else + matmul_3x3(_A, UT, P); - return 0; + return 0; } void InnerProduct(double *A, int num, const double (*coords1)[3], double (*coords2)[3], int8_t* permutation) { - A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0; + A[0] = A[1] = A[2] = A[3] = A[4] = A[5] = A[6] = A[7] = A[8] = 0.0; - for (int i = 0; i < num; ++i) - { - double x1 = coords1[i][0]; - double y1 = coords1[i][1]; - double z1 = coords1[i][2]; + for (int i = 0; i < num; ++i) + { + double x1 = coords1[i][0]; + double y1 = coords1[i][1]; + double z1 = coords1[i][2]; - double x2 = coords2[permutation[i]][0]; - double y2 = coords2[permutation[i]][1]; - double z2 = coords2[permutation[i]][2]; + double x2 = coords2[permutation[i]][0]; + double y2 = coords2[permutation[i]][1]; + double z2 = coords2[permutation[i]][2]; - A[0] += x1 * x2; - A[1] += x1 * y2; - A[2] += x1 * z2; + A[0] += x1 * x2; + A[1] += x1 * y2; + A[2] += x1 * z2; - A[3] += y1 * x2; - A[4] += y1 * y2; - A[5] += y1 * z2; + A[3] += y1 * x2; + A[4] += y1 * y2; + A[5] += y1 * z2; - A[6] += z1 * x2; - A[7] += z1 * y2; - A[8] += z1 * z2; - } + A[6] += z1 * x2; + A[7] += z1 * y2; + A[8] += z1 * z2; + } } int FastCalcRMSDAndRotation(double *A, double E0, double *p_nrmsdsq, double *q, double* U) { - optimal_quaternion(A, false, E0, p_nrmsdsq, q); - quaternion_to_rotation_matrix(q, U); - return 0; + optimal_quaternion(A, false, E0, p_nrmsdsq, q); + quaternion_to_rotation_matrix(q, U); + return 0; } } diff --git a/src/USER-PTM/ptm_polar.h b/src/USER-PTM/ptm_polar.h index e1980f974a..e03963048b 100644 --- a/src/USER-PTM/ptm_polar.h +++ b/src/USER-PTM/ptm_polar.h @@ -1,9 +1,17 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_POLAR_H #define PTM_POLAR_H #include #include -#include namespace ptm { diff --git a/src/USER-PTM/ptm_quat.cpp b/src/USER-PTM/ptm_quat.cpp index 376cc74901..4a93499b3a 100644 --- a/src/USER-PTM/ptm_quat.cpp +++ b/src/USER-PTM/ptm_quat.cpp @@ -1,399 +1,339 @@ -#include +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + +#include #include #include +#include namespace ptm { #define SIGN(x) (x >= 0 ? 1 : -1) -#define MIN(X, Y) (((X) < (Y)) ? (X) : (Y)) -#define MAX(X, Y) (((X) > (Y)) ? (X) : (Y)) -#define SQRT_2 1.4142135623730951454746218587388284504414 -#define HALF_SQRT_2 0.7071067811865474617150084668537601828575 +const double generator_cubic[24][4] = { + { 1, 0, 0, 0 }, + { sqrt(2)/2, sqrt(2)/2, 0, 0 }, + { sqrt(2)/2, 0, sqrt(2)/2, 0 }, + { sqrt(2)/2, 0, 0, sqrt(2)/2 }, + { sqrt(2)/2, 0, 0, -sqrt(2)/2 }, + { sqrt(2)/2, 0, -sqrt(2)/2, 0 }, + { sqrt(2)/2, -sqrt(2)/2, -0, -0 }, + { 0.5, 0.5, 0.5, 0.5 }, + { 0.5, 0.5, 0.5, -0.5 }, + { 0.5, 0.5, -0.5, 0.5 }, + { 0.5, 0.5, -0.5, -0.5 }, + { 0.5, -0.5, 0.5, 0.5 }, + { 0.5, -0.5, 0.5, -0.5 }, + { 0.5, -0.5, -0.5, 0.5 }, + { 0.5, -0.5, -0.5, -0.5 }, + { 0, 1, 0, 0 }, + { 0, sqrt(2)/2, sqrt(2)/2, 0 }, + { 0, sqrt(2)/2, 0, sqrt(2)/2 }, + { 0, sqrt(2)/2, 0, -sqrt(2)/2 }, + { 0, sqrt(2)/2, -sqrt(2)/2, 0 }, + { 0, 0, 1, 0 }, + { 0, 0, sqrt(2)/2, sqrt(2)/2 }, + { 0, 0, sqrt(2)/2, -sqrt(2)/2 }, + { 0, 0, 0, 1 }, +}; -#define PHI 1.6180339887498949025257388711906969547272 -#define HALF_PHI 0.8090169943749474512628694355953484773636 +const double generator_diamond_cubic[12][4] = { + { 1, 0, 0, 0 }, + { 0.5, 0.5, 0.5, 0.5 }, + { 0.5, 0.5, 0.5, -0.5 }, + { 0.5, 0.5, -0.5, 0.5 }, + { 0.5, 0.5, -0.5, -0.5 }, + { 0.5, -0.5, 0.5, 0.5 }, + { 0.5, -0.5, 0.5, -0.5 }, + { 0.5, -0.5, -0.5, 0.5 }, + { 0.5, -0.5, -0.5, -0.5 }, + { 0, 1, 0, 0 }, + { 0, 0, 1, 0 }, + { 0, 0, 0, 1 }, +}; -#define INV_PHI 0.6180339887498947915034364086750429123640 -#define HALF_INV_PHI 0.3090169943749473957517182043375214561820 - -#define SQRT_5_ 2.23606797749978969640917366873127623544061835961152572427089 -#define SQRT_2_3 0.8164965809277260344600790631375275552273 -#define SQRT_1_6 0.4082482904638630172300395315687637776136 +const double generator_hcp[6][4] = { + { 1, 0, 0, 0 }, + { 0.5, 0, 0, sqrt(3)/2 }, + { 0.5, 0, 0, -sqrt(3)/2 }, + { 0, sqrt(3)/2, 0.5, 0 }, + { 0, sqrt(3)/2, -0.5, 0 }, + { 0, 0, 1, 0 }, +}; -double generator_cubic[24][4] = { {1, 0, 0, 0 }, - {0, 1, 0, 0 }, - {0, 0, 1, 0 }, - {0, 0, 0, 1 }, - {0.5, 0.5, 0.5, 0.5 }, - {0.5, 0.5, -0.5, 0.5 }, - {0.5, -0.5, 0.5, 0.5 }, - {0.5, -0.5, -0.5, 0.5 }, - {-0.5, 0.5, 0.5, 0.5 }, - {-0.5, 0.5, -0.5, 0.5 }, - {-0.5, -0.5, 0.5, 0.5 }, - {-0.5, -0.5, -0.5, 0.5 }, - {HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, - {HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, - {HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, - {-HALF_SQRT_2, HALF_SQRT_2, 0, 0 }, - {-HALF_SQRT_2, 0, HALF_SQRT_2, 0 }, - {-HALF_SQRT_2, 0, 0, HALF_SQRT_2 }, - {0, HALF_SQRT_2, HALF_SQRT_2, 0 }, - {0, HALF_SQRT_2, 0, HALF_SQRT_2 }, - {0, 0, HALF_SQRT_2, HALF_SQRT_2 }, - {0, -HALF_SQRT_2, HALF_SQRT_2, 0 }, - {0, -HALF_SQRT_2, 0, HALF_SQRT_2 }, - {0, 0, -HALF_SQRT_2, HALF_SQRT_2 } }; +const double generator_hcp_conventional[12][4] = { + { 1, 0, 0, 0 }, + { sqrt(3)/2, 0, 0, 0.5 }, + { sqrt(3)/2, 0, 0, -0.5 }, + { 0.5, 0, 0, sqrt(3)/2 }, + { 0.5, 0, 0, -sqrt(3)/2 }, + { 0, 1, 0, 0 }, + { 0, sqrt(3)/2, 0.5, 0 }, + { 0, sqrt(3)/2, -0.5, 0 }, + { 0, 0.5, sqrt(3)/2, 0 }, + { 0, 0.5, -sqrt(3)/2, 0 }, + { 0, 0, 1, 0 }, + { 0, 0, 0, 1 }, +}; -double generator_diamond_cubic[12][4] = { {1, 0, 0, 0 }, - {0, 1, 0, 0 }, - {0, 0, 1, 0 }, - {0, 0, 0, 1 }, - {0.5, 0.5, 0.5, 0.5 }, - {0.5, 0.5, -0.5, 0.5 }, - {0.5, -0.5, 0.5, 0.5 }, - {0.5, -0.5, -0.5, 0.5 }, - {-0.5, 0.5, 0.5, 0.5 }, - {-0.5, 0.5, -0.5, 0.5 }, - {-0.5, -0.5, 0.5, 0.5 }, - {-0.5, -0.5, -0.5, 0.5 } }; +const double generator_diamond_hexagonal[3][4] = { + { 1, 0, 0, 0 }, + { 0.5, 0, 0, sqrt(3)/2 }, + { 0.5, 0, 0, -sqrt(3)/2 }, +}; -double generator_hcp[6][4] = { {1, 0, 0, 0}, - {0.5, 0.5, 0.5, 0.5}, - {0.5, -0.5, -0.5, -0.5}, - {0, SQRT_2_3, -SQRT_1_6, -SQRT_1_6}, - {0, SQRT_1_6, -SQRT_2_3, SQRT_1_6}, - {0, SQRT_1_6, SQRT_1_6, -SQRT_2_3} }; +const double generator_icosahedral[60][4] = { + { 1, 0, 0, 0 }, + { (1+sqrt(5))/4, 0.5, sqrt(25-10*sqrt(5))/10, sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, 0.5, -sqrt(25-10*sqrt(5))/10, -sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, 1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, -sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, 1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, 0, sqrt(50-10*sqrt(5))/10, sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, 0, 0, sqrt(5./8-sqrt(5)/8) }, + { (1+sqrt(5))/4, 0, 0, -sqrt(5./8-sqrt(5)/8) }, + { (1+sqrt(5))/4, 0, -sqrt(50-10*sqrt(5))/10, -sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, -1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, -sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, -1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, -0.5, sqrt(25-10*sqrt(5))/10, sqrt(50-10*sqrt(5))/20 }, + { (1+sqrt(5))/4, -0.5, -sqrt(25-10*sqrt(5))/10, -sqrt(50-10*sqrt(5))/20 }, + { 0.5, (1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, -sqrt(25-10*sqrt(5))/10 }, + { 0.5, (1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, sqrt(25-10*sqrt(5))/10 }, + { 0.5, 0.5, sqrt((5+2*sqrt(5))/20), sqrt(25-10*sqrt(5))/10 }, + { 0.5, 0.5, sqrt(25-10*sqrt(5))/10, -sqrt((5+2*sqrt(5))/20) }, + { 0.5, 0.5, -sqrt(25-10*sqrt(5))/10, sqrt((5+2*sqrt(5))/20) }, + { 0.5, 0.5, -sqrt((5+2*sqrt(5))/20), -sqrt(25-10*sqrt(5))/10 }, + { 0.5, 1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, sqrt((5+2*sqrt(5))/20) }, + { 0.5, 1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, -sqrt((5+2*sqrt(5))/20) }, + { 0.5, 0, sqrt((5+sqrt(5))/10), -sqrt(25-10*sqrt(5))/10 }, + { 0.5, 0, sqrt(50-10*sqrt(5))/10, -sqrt((5+2*sqrt(5))/20) }, + { 0.5, 0, -sqrt(50-10*sqrt(5))/10, sqrt((5+2*sqrt(5))/20) }, + { 0.5, 0, -sqrt((5+sqrt(5))/10), sqrt(25-10*sqrt(5))/10 }, + { 0.5, -1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, sqrt((5+2*sqrt(5))/20) }, + { 0.5, -1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, -sqrt((5+2*sqrt(5))/20) }, + { 0.5, -0.5, sqrt((5+2*sqrt(5))/20), sqrt(25-10*sqrt(5))/10 }, + { 0.5, -0.5, sqrt(25-10*sqrt(5))/10, -sqrt((5+2*sqrt(5))/20) }, + { 0.5, -0.5, -sqrt(25-10*sqrt(5))/10, sqrt((5+2*sqrt(5))/20) }, + { 0.5, -0.5, -sqrt((5+2*sqrt(5))/20), -sqrt(25-10*sqrt(5))/10 }, + { 0.5, -(1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, -sqrt(25-10*sqrt(5))/10 }, + { 0.5, -(1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, sqrt(25-10*sqrt(5))/10 }, + { 1/(1+sqrt(5)), (1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), (1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, -sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), 0.5, sqrt((5+2*sqrt(5))/20), -sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), 0.5, -sqrt((5+2*sqrt(5))/20), sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), 0, sqrt((5+sqrt(5))/10), sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), 0, 0, sqrt(1-1/(2*sqrt(5)+6)) }, + { 1/(1+sqrt(5)), 0, 0, -sqrt(1-1/(2*sqrt(5)+6)) }, + { 1/(1+sqrt(5)), 0, -sqrt((5+sqrt(5))/10), -sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), -0.5, sqrt((5+2*sqrt(5))/20), -sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), -0.5, -sqrt((5+2*sqrt(5))/20), sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), -(1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, sqrt(10*sqrt(5)+50)/20 }, + { 1/(1+sqrt(5)), -(1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, -sqrt(10*sqrt(5)+50)/20 }, + { 0, 1, 0, 0 }, + { 0, (1+sqrt(5))/4, sqrt(5./8-sqrt(5)/8), 0 }, + { 0, (1+sqrt(5))/4, sqrt(50-10*sqrt(5))/20, -sqrt(50-10*sqrt(5))/10 }, + { 0, (1+sqrt(5))/4, -sqrt(50-10*sqrt(5))/20, sqrt(50-10*sqrt(5))/10 }, + { 0, (1+sqrt(5))/4, -sqrt(5./8-sqrt(5)/8), 0 }, + { 0, 0.5, sqrt((5+2*sqrt(5))/20), sqrt(50-10*sqrt(5))/10 }, + { 0, 0.5, sqrt(25-10*sqrt(5))/10, sqrt((5+sqrt(5))/10) }, + { 0, 0.5, -sqrt(25-10*sqrt(5))/10, -sqrt((5+sqrt(5))/10) }, + { 0, 0.5, -sqrt((5+2*sqrt(5))/20), -sqrt(50-10*sqrt(5))/10 }, + { 0, 1/(1+sqrt(5)), sqrt(1-1/(2*sqrt(5)+6)), 0 }, + { 0, 1/(1+sqrt(5)), sqrt(10*sqrt(5)+50)/20, -sqrt((5+sqrt(5))/10) }, + { 0, 1/(1+sqrt(5)), -sqrt(10*sqrt(5)+50)/20, sqrt((5+sqrt(5))/10) }, + { 0, 1/(1+sqrt(5)), -sqrt(1-1/(2*sqrt(5)+6)), 0 }, + { 0, 0, sqrt((5+sqrt(5))/10), -sqrt(50-10*sqrt(5))/10 }, + { 0, 0, sqrt(50-10*sqrt(5))/10, sqrt((5+sqrt(5))/10) }, +}; -double generator_diamond_hexagonal[3][4] = { {1, 0, 0, 0}, - {0.5, 0.5, 0.5, 0.5}, - {0.5, -0.5, -0.5, -0.5} }; - -double generator_icosahedral[60][4] = { {1, 0, 0, 0}, - {HALF_PHI, -HALF_INV_PHI, -0.5, 0}, - {HALF_PHI, 0, -HALF_INV_PHI, -0.5}, - {HALF_PHI, -0.5, 0, -HALF_INV_PHI}, - {HALF_PHI, HALF_INV_PHI, -0.5, 0}, - {HALF_PHI, 0, HALF_INV_PHI, -0.5}, - {HALF_PHI, -0.5, 0, HALF_INV_PHI}, - {HALF_PHI, 0.5, 0, -HALF_INV_PHI}, - {HALF_PHI, 0, -HALF_INV_PHI, 0.5}, - {HALF_PHI, -HALF_INV_PHI, 0.5, 0}, - {HALF_PHI, 0, HALF_INV_PHI, 0.5}, - {HALF_PHI, HALF_INV_PHI, 0.5, 0}, - {HALF_PHI, 0.5, 0, HALF_INV_PHI}, - {0.5, HALF_PHI, -HALF_INV_PHI, 0}, - {0.5, HALF_PHI, HALF_INV_PHI, 0}, - {0.5, 0.5, 0.5, 0.5}, - {0.5, 0.5, 0.5, -0.5}, - {0.5, 0.5, -0.5, 0.5}, - {0.5, 0.5, -0.5, -0.5}, - {0.5, HALF_INV_PHI, 0, HALF_PHI}, - {0.5, HALF_INV_PHI, 0, -HALF_PHI}, - {0.5, 0, HALF_PHI, -HALF_INV_PHI}, - {0.5, 0, HALF_PHI, HALF_INV_PHI}, - {0.5, 0, -HALF_PHI, -HALF_INV_PHI}, - {0.5, 0, -HALF_PHI, HALF_INV_PHI}, - {0.5, -HALF_INV_PHI, 0, HALF_PHI}, - {0.5, -HALF_INV_PHI, 0, -HALF_PHI}, - {0.5, -0.5, 0.5, 0.5}, - {0.5, -0.5, 0.5, -0.5}, - {0.5, -0.5, -0.5, 0.5}, - {0.5, -0.5, -0.5, -0.5}, - {0.5, -HALF_PHI, -HALF_INV_PHI, 0}, - {0.5, -HALF_PHI, HALF_INV_PHI, 0}, - {HALF_INV_PHI, -HALF_PHI, 0, -0.5}, - {HALF_INV_PHI, 0, -0.5, -HALF_PHI}, - {HALF_INV_PHI, -0.5, -HALF_PHI, 0}, - {HALF_INV_PHI, 0, 0.5, -HALF_PHI}, - {HALF_INV_PHI, -HALF_PHI, 0, 0.5}, - {HALF_INV_PHI, 0.5, -HALF_PHI, 0}, - {HALF_INV_PHI, HALF_PHI, 0, -0.5}, - {HALF_INV_PHI, -0.5, HALF_PHI, 0}, - {HALF_INV_PHI, 0, -0.5, HALF_PHI}, - {HALF_INV_PHI, HALF_PHI, 0, 0.5}, - {HALF_INV_PHI, 0, 0.5, HALF_PHI}, - {HALF_INV_PHI, 0.5, HALF_PHI, 0}, - {0, 1, 0, 0}, - {0, HALF_PHI, -0.5, HALF_INV_PHI}, - {0, HALF_PHI, -0.5, -HALF_INV_PHI}, - {0, HALF_PHI, 0.5, HALF_INV_PHI}, - {0, HALF_PHI, 0.5, -HALF_INV_PHI}, - {0, 0.5, HALF_INV_PHI, -HALF_PHI}, - {0, 0.5, HALF_INV_PHI, HALF_PHI}, - {0, 0.5, -HALF_INV_PHI, -HALF_PHI}, - {0, 0.5, -HALF_INV_PHI, HALF_PHI}, - {0, HALF_INV_PHI, -HALF_PHI, 0.5}, - {0, HALF_INV_PHI, -HALF_PHI, -0.5}, - {0, HALF_INV_PHI, HALF_PHI, 0.5}, - {0, HALF_INV_PHI, HALF_PHI, -0.5}, - {0, 0, 1, 0}, - {0, 0, 0, 1} }; static void quat_rot(double* r, double* a, double* b) { - b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]); - b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]); - b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]); - b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]); + b[0] = (r[0] * a[0] - r[1] * a[1] - r[2] * a[2] - r[3] * a[3]); + b[1] = (r[0] * a[1] + r[1] * a[0] + r[2] * a[3] - r[3] * a[2]); + b[2] = (r[0] * a[2] - r[1] * a[3] + r[2] * a[0] + r[3] * a[1]); + b[3] = (r[0] * a[3] + r[1] * a[2] - r[2] * a[1] + r[3] * a[0]); } -static int rotate_quaternion_into_fundamental_zone(int num_generators, double (*generator)[4], double* q) +static int rotate_quaternion_into_fundamental_zone(int num_generators, const double (*generator)[4], double* q) { - double max = 0.0; - int i = 0, bi = -1; - for (i=0;i max) - { - max = t; - bi = i; - } - } + double max = 0.0; + int i = 0, bi = -1; + for (i=0;i max) + { + max = t; + bi = i; + } + } - double f[4]; - quat_rot(q, generator[bi], f); - memcpy(q, &f, 4 * sizeof(double)); - if (q[0] < 0) - { - q[0] = -q[0]; - q[1] = -q[1]; - q[2] = -q[2]; - q[3] = -q[3]; - } + double f[4]; + quat_rot(q, (double*)generator[bi], f); + memcpy(q, &f, 4 * sizeof(double)); + if (q[0] < 0) + { + q[0] = -q[0]; + q[1] = -q[1]; + q[2] = -q[2]; + q[3] = -q[3]; + } - return bi; + return bi; } int rotate_quaternion_into_cubic_fundamental_zone(double* q) { - return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q); + return rotate_quaternion_into_fundamental_zone(24, generator_cubic, q); } int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q) { - return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q); + return rotate_quaternion_into_fundamental_zone(12, generator_diamond_cubic, q); } int rotate_quaternion_into_icosahedral_fundamental_zone(double* q) { - return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q); + return rotate_quaternion_into_fundamental_zone(60, generator_icosahedral, q); } int rotate_quaternion_into_hcp_fundamental_zone(double* q) { - return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q); + return rotate_quaternion_into_fundamental_zone(6, generator_hcp, q); +} + +int rotate_quaternion_into_hcp_conventional_fundamental_zone(double* q) +{ + return rotate_quaternion_into_fundamental_zone(12, generator_hcp_conventional, q); } int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q) { - return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q); + return rotate_quaternion_into_fundamental_zone(3, generator_diamond_hexagonal, q); } double quat_dot(double* a, double* b) { - return a[0] * b[0] - + a[1] * b[1] - + a[2] * b[2] - + a[3] * b[3]; + return a[0] * b[0] + + a[1] * b[1] + + a[2] * b[2] + + a[3] * b[3]; } double quat_size(double* q) { - return sqrt(quat_dot(q, q)); + return sqrt(quat_dot(q, q)); } void normalize_quaternion(double* q) { - double size = quat_size(q); + double size = quat_size(q); - q[0] /= size; - q[1] /= size; - q[2] /= size; - q[3] /= size; -} - -void rotation_matrix_to_quaternion(double* u, double* q) -{ - double r11 = u[0]; - double r12 = u[1]; - double r13 = u[2]; - double r21 = u[3]; - double r22 = u[4]; - double r23 = u[5]; - double r31 = u[6]; - double r32 = u[7]; - double r33 = u[8]; - - q[0] = (1.0 + r11 + r22 + r33) / 4.0; - q[1] = (1.0 + r11 - r22 - r33) / 4.0; - q[2] = (1.0 - r11 + r22 - r33) / 4.0; - q[3] = (1.0 - r11 - r22 + r33) / 4.0; - - q[0] = sqrt(MAX(0, q[0])); - q[1] = sqrt(MAX(0, q[1])); - q[2] = sqrt(MAX(0, q[2])); - q[3] = sqrt(MAX(0, q[3])); - - double m0 = MAX(q[0], q[1]); - double m1 = MAX(q[2], q[3]); - double max = MAX(m0, m1); - - int i = 0; - for (i=0;i<4;i++) - if (q[i] == max) - break; - - if (i == 0) - { - q[1] *= SIGN(r32 - r23); - q[2] *= SIGN(r13 - r31); - q[3] *= SIGN(r21 - r12); - } - else if (i == 1) - { - q[0] *= SIGN(r32 - r23); - q[2] *= SIGN(r21 + r12); - q[3] *= SIGN(r13 + r31); - } - else if (i == 2) - { - q[0] *= SIGN(r13 - r31); - q[1] *= SIGN(r21 + r12); - q[3] *= SIGN(r32 + r23); - } - else if (i == 3) - { - q[0] *= SIGN(r21 - r12); - q[1] *= SIGN(r31 + r13); - q[2] *= SIGN(r32 + r23); - } - - normalize_quaternion(q); + q[0] /= size; + q[1] /= size; + q[2] /= size; + q[3] /= size; } void quaternion_to_rotation_matrix(double* q, double* u) { - double a = q[0]; - double b = q[1]; - double c = q[2]; - double d = q[3]; + double a = q[0]; + double b = q[1]; + double c = q[2]; + double d = q[3]; - u[0] = a*a + b*b - c*c - d*d; - u[1] = 2*b*c - 2*a*d; - u[2] = 2*b*d + 2*a*c; + u[0] = a*a + b*b - c*c - d*d; + u[1] = 2*b*c - 2*a*d; + u[2] = 2*b*d + 2*a*c; - u[3] = 2*b*c + 2*a*d; - u[4] = a*a - b*b + c*c - d*d; - u[5] = 2*c*d - 2*a*b; + u[3] = 2*b*c + 2*a*d; + u[4] = a*a - b*b + c*c - d*d; + u[5] = 2*c*d - 2*a*b; - u[6] = 2*b*d - 2*a*c; - u[7] = 2*c*d + 2*a*b; - u[8] = a*a - b*b - c*c + d*d; + u[6] = 2*b*d - 2*a*c; + u[7] = 2*c*d + 2*a*b; + u[8] = a*a - b*b - c*c + d*d; +} + +void rotation_matrix_to_quaternion(double* u, double* q) +{ + double r11 = u[0]; + double r12 = u[1]; + double r13 = u[2]; + double r21 = u[3]; + double r22 = u[4]; + double r23 = u[5]; + double r31 = u[6]; + double r32 = u[7]; + double r33 = u[8]; + + q[0] = (1.0 + r11 + r22 + r33) / 4.0; + q[1] = (1.0 + r11 - r22 - r33) / 4.0; + q[2] = (1.0 - r11 + r22 - r33) / 4.0; + q[3] = (1.0 - r11 - r22 + r33) / 4.0; + + q[0] = sqrt(std::max(0., q[0])); + q[1] = sqrt(std::max(0., q[1])); + q[2] = sqrt(std::max(0., q[2])); + q[3] = sqrt(std::max(0., q[3])); + + double m0 = std::max(q[0], q[1]); + double m1 = std::max(q[2], q[3]); + double max = std::max(m0, m1); + + int i = 0; + for (i=0;i<4;i++) + if (q[i] == max) + break; + + if (i == 0) + { + q[1] *= SIGN(r32 - r23); + q[2] *= SIGN(r13 - r31); + q[3] *= SIGN(r21 - r12); + } + else if (i == 1) + { + q[0] *= SIGN(r32 - r23); + q[2] *= SIGN(r21 + r12); + q[3] *= SIGN(r13 + r31); + } + else if (i == 2) + { + q[0] *= SIGN(r13 - r31); + q[1] *= SIGN(r21 + r12); + q[3] *= SIGN(r32 + r23); + } + else if (i == 3) + { + q[0] *= SIGN(r21 - r12); + q[1] *= SIGN(r31 + r13); + q[2] *= SIGN(r32 + r23); + } + + normalize_quaternion(q); } double quat_quick_misorientation(double* q1, double* q2) { - double t = quat_dot(q1, q2); - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; + double t = quat_dot(q1, q2); + t = std::min(1., std::max(-1., t)); + return 2 * t * t - 1; } double quat_misorientation(double* q1, double* q2) { - return acos(quat_quick_misorientation(q1, q2)); -} - - -double quat_quick_disorientation_cubic(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_cubic_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_cubic(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_cubic(q0, q1)); -} - -double quat_quick_disorientation_diamond_cubic(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_diamond_cubic_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_diamond_cubic(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_diamond_cubic(q0, q1)); -} - -double quat_quick_disorientation_hcp(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_hcp_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_hcp(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_hcp(q0, q1)); -} - -double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_diamond_hexagonal_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_diamond_hexagonal(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_diamond_hexagonal(q0, q1)); -} - -double quat_quick_disorientation_icosahedral(double* q0, double* q1) -{ - double qrot[4]; - double qinv[4] = {q0[0], -q0[1], -q0[2], -q0[3]}; - quat_rot(qinv, q1, qrot); - - rotate_quaternion_into_icosahedral_fundamental_zone(qrot); - double t = qrot[0]; - t = MIN(1, MAX(-1, t)); - return 2 * t * t - 1; -} - -double quat_disorientation_icosahedral(double* q0, double* q1) -{ - return acos(quat_quick_disorientation_icosahedral(q0, q1)); + return acos(quat_quick_misorientation(q1, q2)); } } diff --git a/src/USER-PTM/ptm_quat.h b/src/USER-PTM/ptm_quat.h index 74caa2c62c..6f4d88920e 100644 --- a/src/USER-PTM/ptm_quat.h +++ b/src/USER-PTM/ptm_quat.h @@ -1,3 +1,12 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #ifndef PTM_QUAT_H #define PTM_QUAT_H @@ -7,26 +16,15 @@ int rotate_quaternion_into_cubic_fundamental_zone(double* q); int rotate_quaternion_into_diamond_cubic_fundamental_zone(double* q); int rotate_quaternion_into_icosahedral_fundamental_zone(double* q); int rotate_quaternion_into_hcp_fundamental_zone(double* q); +int rotate_quaternion_into_hcp_conventional_fundamental_zone(double* q); int rotate_quaternion_into_diamond_hexagonal_fundamental_zone(double* q); void normalize_quaternion(double* q); void quaternion_to_rotation_matrix(double* q, double* U); void rotation_matrix_to_quaternion(double* u, double* q); double quat_dot(double* a, double* b); -double quat_quick_misorientation(double* q1, double* q2); double quat_misorientation(double* q1, double* q2); -double quat_quick_disorientation_cubic(double* q0, double* q1); -double quat_disorientation_cubic(double* q0, double* q1); -double quat_quick_disorientation_diamond_cubic(double* q0, double* q1); -double quat_disorientation_diamond_cubic(double* q0, double* q1); -double quat_quick_disorientation_hcp(double* q0, double* q1); -double quat_disorientation_hcp(double* q0, double* q1); -double quat_quick_disorientation_diamond_hexagonal(double* q0, double* q1); -double quat_disorientation_diamond_hexagonal(double* q0, double* q1); -double quat_quick_disorientation_icosahedral(double* q0, double* q1); -double quat_disorientation_icosahedral(double* q0, double* q1); - } #endif diff --git a/src/USER-PTM/ptm_structure_matcher.cpp b/src/USER-PTM/ptm_structure_matcher.cpp index a86b3670ce..d50676a3c1 100644 --- a/src/USER-PTM/ptm_structure_matcher.cpp +++ b/src/USER-PTM/ptm_structure_matcher.cpp @@ -1,6 +1,15 @@ +/*Copyright (c) 2016 PM Larsen + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +*/ + #include #include -#include +#include #include #include #include @@ -18,280 +27,349 @@ namespace ptm { static double calc_rmsd(int num_points, const double (*ideal_points)[3], double (*normalized)[3], int8_t* mapping, - double G1, double G2, double E0, double* q, double* p_scale) + double G1, double G2, double E0, double* q, double* p_scale) { - double A0[9]; - InnerProduct(A0, num_points, ideal_points, normalized, mapping); + double A0[9]; + InnerProduct(A0, num_points, ideal_points, normalized, mapping); - double nrmsdsq, rot[9]; - FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot); + double nrmsdsq, rot[9]; + FastCalcRMSDAndRotation(A0, E0, &nrmsdsq, q, rot); - double k0 = 0; - for (int i=0;inum_nbrs + 1; - const double (*ideal_points)[3] = s->points; - int8_t inverse_labelling[PTM_MAX_POINTS]; - int8_t mapping[PTM_MAX_POINTS]; + int num_points = s->num_nbrs + 1; + const double (*ideal_points)[3] = s->points; + int8_t inverse_labelling[PTM_MAX_POINTS]; + int8_t mapping[PTM_MAX_POINTS]; - for (int i=0; inum_graphs;i++) - { - if (hash != s->graphs[i].hash) - continue; + for (int i = 0;inum_graphs;i++) + { + if (hash != s->graphs[i].hash) + continue; - graph_t* gref = &s->graphs[i]; - for (int j = 0;jnum_automorphisms;j++) - { - for (int k=0;kautomorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ]; + graph_t* gref = &s->graphs[i]; + for (int j = 0;jnum_automorphisms;j++) + { + for (int k=0;kautomorphism_index + j][k]] = inverse_labelling[ gref->canonical_labelling[k] ]; - double q[4], scale = 0; - double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale); - if (rmsd < res->rmsd) - { - res->rmsd = rmsd; - res->scale = scale; - res->ref_struct = s; - memcpy(res->q, q, 4 * sizeof(double)); - memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); - } - } - } + double q[4], scale = 0; + double rmsd = calc_rmsd(num_points, ideal_points, normalized, mapping, G1, G2, E0, q, &scale); + if (rmsd < res->rmsd) + { + res->rmsd = rmsd; + res->scale = scale; + res->ref_struct = s; + memcpy(res->q, q, 4 * sizeof(double)); + memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); + } + } + } } int match_general(const refdata_t* s, double (*ch_points)[3], double (*points)[3], convexhull_t* ch, result_t* res) { - int8_t degree[PTM_MAX_NBRS]; - int8_t facets[PTM_MAX_FACETS][3]; + int8_t degree[PTM_MAX_NBRS]; + int8_t facets[PTM_MAX_FACETS][3]; - int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); - ch->ok = ret >= 0; - if (ret != 0) - return PTM_NO_ERROR; + int ret = get_convex_hull(s->num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; - if (ch->num_facets != s->num_facets) - return PTM_NO_ERROR; //incorrect number of facets in convex hull + if (ch->num_facets != s->num_facets) + return PTM_NO_ERROR; //incorrect number of facets in convex hull - int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree); - if (max_degree > s->max_degree) - return PTM_NO_ERROR; + int max_degree = graph_degree(s->num_facets, facets, s->num_nbrs, degree); + if (max_degree > s->max_degree) + return PTM_NO_ERROR; - if (s->type == PTM_MATCH_SC) - for (int i = 0;inum_nbrs;i++) - if (degree[i] != 4) - return PTM_NO_ERROR; + if (s->type == PTM_MATCH_SC) + for (int i = 0;inum_nbrs;i++) + if (degree[i] != 4) + return PTM_NO_ERROR; - double normalized[PTM_MAX_POINTS][3]; - subtract_barycentre(s->num_nbrs + 1, points, normalized); + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(s->num_nbrs + 1, points, normalized); - int8_t code[2 * PTM_MAX_EDGES]; - int8_t colours[PTM_MAX_POINTS] = {0}; - int8_t canonical_labelling[PTM_MAX_POINTS]; - uint64_t hash = 0; - ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); - if (ret != PTM_NO_ERROR) - return ret; + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(s->num_facets, facets, s->num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; - check_graphs(s, hash, canonical_labelling, normalized, res); - return PTM_NO_ERROR; + check_graphs(s, hash, canonical_labelling, normalized, res); + return PTM_NO_ERROR; } int match_fcc_hcp_ico(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) { - int num_nbrs = structure_fcc.num_nbrs; - int num_facets = structure_fcc.num_facets; - int max_degree = structure_fcc.max_degree; + int num_nbrs = structure_fcc.num_nbrs; + int num_facets = structure_fcc.num_facets; + int max_degree = structure_fcc.max_degree; - int8_t degree[PTM_MAX_NBRS]; - int8_t facets[PTM_MAX_FACETS][3]; + int8_t degree[PTM_MAX_NBRS]; + int8_t facets[PTM_MAX_FACETS][3]; - int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); - ch->ok = ret >= 0; - if (ret != 0) - return PTM_NO_ERROR; + int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; - if (ch->num_facets != num_facets) - return PTM_NO_ERROR; //incorrect number of facets in convex hull + if (ch->num_facets != num_facets) + return PTM_NO_ERROR; //incorrect number of facets in convex hull - int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); - if (_max_degree > max_degree) - return PTM_NO_ERROR; + int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; - double normalized[PTM_MAX_POINTS][3]; - subtract_barycentre(num_nbrs + 1, points, normalized); + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_nbrs + 1, points, normalized); - int8_t code[2 * PTM_MAX_EDGES]; - int8_t colours[PTM_MAX_POINTS] = {0}; - int8_t canonical_labelling[PTM_MAX_POINTS]; - uint64_t hash = 0; - ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); - if (ret != PTM_NO_ERROR) - return ret; + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; - if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res); - if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res); - if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res); - return PTM_NO_ERROR; + if (flags & PTM_CHECK_FCC) check_graphs(&structure_fcc, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_HCP) check_graphs(&structure_hcp, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_ICO) check_graphs(&structure_ico, hash, canonical_labelling, normalized, res); + return PTM_NO_ERROR; } int match_dcub_dhex(double (*ch_points)[3], double (*points)[3], int32_t flags, convexhull_t* ch, result_t* res) { - int num_nbrs = structure_dcub.num_nbrs; - int num_facets = structure_fcc.num_facets; - int max_degree = structure_dcub.max_degree; + int num_nbrs = structure_dcub.num_nbrs; + int num_facets = structure_fcc.num_facets; + int max_degree = structure_dcub.max_degree; - int8_t facets[PTM_MAX_FACETS][3]; - int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); - ch->ok = ret >= 0; - if (ret != 0) - return PTM_NO_ERROR; + int8_t facets[PTM_MAX_FACETS][3]; + int ret = get_convex_hull(num_nbrs + 1, (const double (*)[3])ch_points, ch, facets); + ch->ok = ret >= 0; + if (ret != 0) + return PTM_NO_ERROR; - //check for facets with multiple inner atoms - bool inverted[4] = {false, false, false, false}; - for (int i=0;inum_facets;i++) - { - int n = 0; - for (int j=0;j<3;j++) - { - if (facets[i][j] <= 3) - { - inverted[facets[i][j]] = true; - n++; - } - } - if (n > 1) - return PTM_NO_ERROR; - } + //check for facets with multiple inner atoms + bool inverted[4] = {false, false, false, false}; + for (int i=0;inum_facets;i++) + { + int n = 0; + for (int j=0;j<3;j++) + { + if (facets[i][j] <= 3) + { + inverted[facets[i][j]] = true; + n++; + } + } + if (n > 1) + return PTM_NO_ERROR; + } - int num_inverted = 0; - for (int i=0;i<4;i++) - num_inverted += inverted[i] ? 1 : 0; + int num_inverted = 0; + for (int i=0;i<4;i++) + num_inverted += inverted[i] ? 1 : 0; - if (ch->num_facets != num_facets + 2 * num_inverted) - return PTM_NO_ERROR; //incorrect number of facets in convex hull + if (ch->num_facets != num_facets + 2 * num_inverted) + return PTM_NO_ERROR; //incorrect number of facets in convex hull - int8_t degree[PTM_MAX_NBRS]; - int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); - if (_max_degree > max_degree) - return PTM_NO_ERROR; + int8_t degree[PTM_MAX_NBRS]; + int _max_degree = graph_degree(num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; - int num_found = 0; - int8_t toadd[4][3]; - for (int i=0;inum_facets;i++) - { - int a = facets[i][0]; - int b = facets[i][1]; - int c = facets[i][2]; - if (a <= 3 || b <= 3 || c <= 3) - continue; + int num_found = 0; + int8_t toadd[4][3]; + for (int i=0;inum_facets;i++) + { + int a = facets[i][0]; + int b = facets[i][1]; + int c = facets[i][2]; + if (a <= 3 || b <= 3 || c <= 3) + continue; - int i0 = (a - 4) / 3; - int i1 = (b - 4) / 3; - int i2 = (c - 4) / 3; + int i0 = (a - 4) / 3; + int i1 = (b - 4) / 3; + int i2 = (c - 4) / 3; - if (i0 == i1 && i0 == i2) - { - if (num_found + num_inverted >= 4) - return PTM_NO_ERROR; + if (i0 == i1 && i0 == i2) + { + if (num_found + num_inverted >= 4) + return PTM_NO_ERROR; - toadd[num_found][0] = a; - toadd[num_found][1] = b; - toadd[num_found][2] = c; - num_found++; + toadd[num_found][0] = a; + toadd[num_found][1] = b; + toadd[num_found][2] = c; + num_found++; - memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t)); - ch->num_facets--; - i--; - } - } + memcpy(&facets[i], &facets[ch->num_facets - 1], 3 * sizeof(int8_t)); + ch->num_facets--; + i--; + } + } - if (num_found + num_inverted != 4) - return PTM_NO_ERROR; + if (num_found + num_inverted != 4) + return PTM_NO_ERROR; - for (int i=0;inum_facets][0] = i0; - facets[ch->num_facets][1] = b; - facets[ch->num_facets][2] = c; - ch->num_facets++; + facets[ch->num_facets][0] = i0; + facets[ch->num_facets][1] = b; + facets[ch->num_facets][2] = c; + ch->num_facets++; - facets[ch->num_facets][0] = a; - facets[ch->num_facets][1] = i0; - facets[ch->num_facets][2] = c; - ch->num_facets++; + facets[ch->num_facets][0] = a; + facets[ch->num_facets][1] = i0; + facets[ch->num_facets][2] = c; + ch->num_facets++; - facets[ch->num_facets][0] = a; - facets[ch->num_facets][1] = b; - facets[ch->num_facets][2] = i0; - ch->num_facets++; - } + facets[ch->num_facets][0] = a; + facets[ch->num_facets][1] = b; + facets[ch->num_facets][2] = i0; + ch->num_facets++; + } - _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree); - if (_max_degree > max_degree) - return PTM_NO_ERROR; + _max_degree = graph_degree(ch->num_facets, facets, num_nbrs, degree); + if (_max_degree > max_degree) + return PTM_NO_ERROR; - double normalized[PTM_MAX_POINTS][3]; - subtract_barycentre(num_nbrs + 1, points, normalized); + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_nbrs + 1, points, normalized); - int8_t code[2 * PTM_MAX_EDGES]; - int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; - int8_t canonical_labelling[PTM_MAX_POINTS]; - uint64_t hash = 0; - ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); - if (ret != PTM_NO_ERROR) - return ret; + int8_t code[2 * PTM_MAX_EDGES]; + int8_t colours[PTM_MAX_POINTS] = {1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0}; + int8_t canonical_labelling[PTM_MAX_POINTS]; + uint64_t hash = 0; + ret = canonical_form_coloured(ch->num_facets, facets, num_nbrs, degree, colours, canonical_labelling, &code[0], &hash); + if (ret != PTM_NO_ERROR) + return ret; - if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res); - if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_DCUB) check_graphs(&structure_dcub, hash, canonical_labelling, normalized, res); + if (flags & PTM_CHECK_DHEX) check_graphs(&structure_dhex, hash, canonical_labelling, normalized, res); - return PTM_NO_ERROR; + return PTM_NO_ERROR; +} + + +static void check_graphs_graphene( const refdata_t* s, + int num_points, + const double (*ideal_points)[3], + double (*normalized)[3], + int8_t* mapping, + result_t* res) +{ + double G1 = 0, G2 = 0; + for (int i=0;irmsd) + { + res->rmsd = rmsd; + res->scale = scale; + res->ref_struct = s; + memcpy(res->q, q, 4 * sizeof(double)); + memcpy(res->mapping, mapping, sizeof(int8_t) * num_points); + } +} + +int match_graphene(double (*points)[3], result_t* res) +{ + int num_nbrs = structure_graphene.num_nbrs; + int num_points = num_nbrs + 1; + const double (*ideal_points)[3] = structure_graphene.points; + + double normalized[PTM_MAX_POINTS][3]; + subtract_barycentre(num_points, points, normalized); + + int8_t mapping[PTM_MAX_POINTS]; + for (int i=0;i=0;i--) if(mem[i]>0) delete [] mep[i]; - delete [] marg; - delete [] ds2;delete [] ds; - delete [] mep;delete [] mec; - delete [] mem;delete [] pts; - delete [] nu;delete [] ed; + for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mep[i]; + delete [] marg; + delete [] ds2;delete [] ds; + delete [] mep;delete [] mec; + delete [] mem;delete [] pts; + delete [] nu;delete [] ed; } /** Ensures that enough memory is allocated prior to carrying out a copy. @@ -61,9 +103,9 @@ voronoicell_base::~voronoicell_base() { * \param[in] vb a pointered to the class to be copied. */ template void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) { - while(current_vertex_ordercurrent_vertex_order) add_memory_vorder(vc); - for(int i=0;imec[i]) add_memory(vc,i,ds2); - while(current_verticesp) add_memory_vertices(vc); + while(current_vertex_ordercurrent_vertex_order) add_memory_vorder(vc); + for(int i=0;imec[i]) add_memory(vc,i,ds2); + while(current_verticesp) add_memory_vertices(vc); } /** Increases the memory storage for a particular vertex order, by increasing @@ -79,50 +121,50 @@ void voronoicell_base::check_memory_for_copy(vc_class &vc,voronoicell_base* vb) * \param[in] i the order of the vertex memory to be increased. */ template void voronoicell_base::add_memory(vc_class &vc,int i,int *stackp2) { - int s=(i<<1)+1; - if(mem[i]==0) { - vc.n_allocate(i,init_n_vertices); - mep[i]=new int[init_n_vertices*s]; - mem[i]=init_n_vertices; + int s=(i<<1)+1; + if(mem[i]==0) { + vc.n_allocate(i,init_n_vertices); + mep[i]=new int[init_n_vertices*s]; + mem[i]=init_n_vertices; #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Order %d vertex memory created\n",i); + fprintf(stderr,"Order %d vertex memory created\n",i); #endif - } else { - int j=0,k,*l; - mem[i]<<=1; - if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); + } else { + int j=0,k,*l; + mem[i]<<=1; + if(mem[i]>max_n_vertices) voro_fatal_error("Point memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]); + fprintf(stderr,"Order %d vertex memory scaled up to %d\n",i,mem[i]); #endif - l=new int[s*mem[i]]; - int m=0; - vc.n_allocate_aux1(i); - while(j=0) { - ed[k]=l+j; - vc.n_set_to_aux1_offset(k,m); - } else { - int *dsp; - for(dsp=ds2;dsp=0) { + ed[k]=l+j; + vc.n_set_to_aux1_offset(k,m); + } else { + int *dsp; + for(dsp=ds2;dsp=3 - fputs("Relocated dangling pointer",stderr); + fputs("Relocated dangling pointer",stderr); #endif - } - for(k=0;kmax_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); + int i=(current_vertices<<1),j,**pp,*pnu; + if(i>max_vertices) voro_fatal_error("Vertex memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Vertex memory scaled up to %d\n",i); + fprintf(stderr,"Vertex memory scaled up to %d\n",i); #endif - double *ppts; - pp=new int*[i]; - for(j=0;j void voronoicell_base::add_memory_vorder(vc_class &vc) { - int i=(current_vertex_order<<1),j,*p1,**p2; - if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); + int i=(current_vertex_order<<1),j,*p1,**p2; + if(i>max_vertex_order) voro_fatal_error("Vertex order memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Vertex order memory scaled up to %d\n",i); + fprintf(stderr,"Vertex order memory scaled up to %d\n",i); #endif - p1=new int[i]; - for(j=0;jmax_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); + current_delete_size<<=1; + if(current_delete_size>max_delete_size) voro_fatal_error("Delete stack 1 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size); + fprintf(stderr,"Delete stack 1 memory scaled up to %d\n",current_delete_size); #endif - int *dsn=new int[current_delete_size],*dsnp=dsn,*dsp=ds; - while(dspmax_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); + current_delete2_size<<=1; + if(current_delete2_size>max_delete2_size) voro_fatal_error("Delete stack 2 memory allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size); + fprintf(stderr,"Delete stack 2 memory scaled up to %d\n",current_delete2_size); #endif - int *dsn=new int[current_delete2_size],*dsnp=dsn,*dsp=ds2; - while(dsp inline bool voronoicell_base::search_for_outside_edge(vc_class &vc,int &up) { - int i,lp,lw,*j(ds2),*stackp2(ds2); - double l; - *(stackp2++)=up; - while(j inline void voronoicell_base::add_to_stack(vc_class &vc,int lp,int *&stackp2) { - for(int *k(ds2);k bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id) { - int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp; - int us=0,ls=0,qs,iqs,cs,uw,qw,lw; - int *edp,*edd; - double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false; + int count=0,i,j,k,lp=up,cp,qp,rp,*stackp(ds),*stackp2(ds2),*dsp; + int us=0,ls=0,qs,iqs,cs,uw,qw,lw; + int *edp,*edd; + double u,l,r,q;bool complicated_setup=false,new_double_edge=false,double_edge=false; - // Initialize the safe testing routine - n_marg=0;px=x;py=y;pz=z;prsq=rsq; + // Initialize the safe testing routine + n_marg=0;px=x;py=y;pz=z;prsq=rsq; - // Test approximately sqrt(n)/4 points for their proximity to the plane - // and keep the one which is closest - uw=m_test(up,u); + // Test approximately sqrt(n)/4 points for their proximity to the plane + // and keep the one which is closest + uw=m_test(up,u); - // Starting from an initial guess, we now move from vertex to vertex, - // to try and find an edge which intersects the cutting plane, - // or a vertex which is on the plane - try { - if(uw==1) { + // Starting from an initial guess, we now move from vertex to vertex, + // to try and find an edge which intersects the cutting plane, + // or a vertex which is on the plane + try { + if(uw==1) { - // The test point is inside the cutting plane. - us=0; - do { - lp=ed[up][us]; - lw=m_test(lp,l); - if(l=p) throw true; - u=l;up=lp; - for(us=0;us=p) throw true; + u=l;up=lp; + for(us=0;us=p) throw true; - u=q;up=qp; - for(us=0;us=p) throw true; + u=q;up=qp; + for(us=0;us=1 - fputs("Bailed out of convex calculation\n",stderr); + fputs("Bailed out of convex calculation\n",stderr); #endif - qw=1;lw=0; - for(qp=0;qp=current_vertex_order) add_memory_vorder(vc); - if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); - vc.n_set_pointer(p,nu[p]); - ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; - ed[p][nu[p]<<1]=p; + // Add memory for the new vertex if needed, and + // initialize + while (nu[p]>=current_vertex_order) add_memory_vorder(vc); + if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); + vc.n_set_pointer(p,nu[p]); + ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; + ed[p][nu[p]<<1]=p; - // Copy the edges of the original vertex into the new - // one. Delete the edges of the original vertex, and - // update the relational table. - us=cycle_down(i,up); - while(i=current_vertex_order) add_memory_vorder(vc); - if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); + // Add memory to store the vertex if it doesn't exist + // already + k=1; + while(nu[p]>=current_vertex_order) add_memory_vorder(vc); + if(mec[nu[p]]==mem[nu[p]]) add_memory(vc,nu[p],stackp2); - // Copy the edges of the original vertex into the new - // one. Delete the edges of the original vertex, and - // update the relational table. - vc.n_set_pointer(p,nu[p]); - ed[p]=mep[nu[p]]+((nu[p]<<1)+1)*mec[nu[p]]++; - ed[p][nu[p]<<1]=p; - us=i++; - while(i0) k+=nu[j]; - } else { - if(j>0) { + // If we're heading into the final part of the + // new facet, then we never worry about the + // duplicate edge calculation. + new_double_edge=false; + if(j>0) k+=nu[j]; + } else { + if(j>0) { - // This vertex was visited before, so - // count those vertices to the ones we - // already have. - k+=nu[j]; + // This vertex was visited before, so + // count those vertices to the ones we + // already have. + k+=nu[j]; - // The only time when we might make a - // duplicate edge is if the point we're - // going to move to next is also a - // marginal point, so test for that - // first. - if(lw==0) { + // The only time when we might make a + // duplicate edge is if the point we're + // going to move to next is also a + // marginal point, so test for that + // first. + if(lw==0) { - // Now see whether this marginal point - // has been visited before. - i=-ed[lp][nu[lp]<<1]; - if(i>0) { + // Now see whether this marginal point + // has been visited before. + i=-ed[lp][nu[lp]<<1]; + if(i>0) { - // Now see if the last edge of that other - // marginal point actually ends up here. - if(ed[i][nu[i]-1]==j) { - new_double_edge=true; - k-=1; - } else new_double_edge=false; - } else { + // Now see if the last edge of that other + // marginal point actually ends up here. + if(ed[i][nu[i]-1]==j) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } else { - // That marginal point hasn't been visited - // before, so we probably don't have to worry - // about duplicate edges, except in the - // case when that's the way into the end - // of the facet, because that way always creates - // an edge. - if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) { - new_double_edge=true; - k-=1; - } else new_double_edge=false; - } - } else new_double_edge=false; - } else { + // That marginal point hasn't been visited + // before, so we probably don't have to worry + // about duplicate edges, except in the + // case when that's the way into the end + // of the facet, because that way always creates + // an edge. + if(j==rp&&lp==up&&ed[qp][nu[qp]+qs]==us) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } + } else new_double_edge=false; + } else { - // The vertex hasn't been visited - // before, but let's see if it's - // marginal - if(lw==0) { + // The vertex hasn't been visited + // before, but let's see if it's + // marginal + if(lw==0) { - // If it is, we need to check - // for the case that it's a - // small branch, and that we're - // heading right back to where - // we came from - i=-ed[lp][nu[lp]<<1]; - if(i==cp) { - new_double_edge=true; - k-=1; - } else new_double_edge=false; - } else new_double_edge=false; - } - } + // If it is, we need to check + // for the case that it's a + // small branch, and that we're + // heading right back to where + // we came from + i=-ed[lp][nu[lp]<<1]; + if(i==cp) { + new_double_edge=true; + k-=1; + } else new_double_edge=false; + } else new_double_edge=false; + } + } - // k now holds the number of edges of the new vertex - // we are forming. Add memory for it if it doesn't exist - // already. - while(k>=current_vertex_order) add_memory_vorder(vc); - if(mec[k]==mem[k]) add_memory(vc,k,stackp2); + // k now holds the number of edges of the new vertex + // we are forming. Add memory for it if it doesn't exist + // already. + while(k>=current_vertex_order) add_memory_vorder(vc); + if(mec[k]==mem[k]) add_memory(vc,k,stackp2); - // Now create a new vertex with order k, or augment - // the existing one - if(j>0) { + // Now create a new vertex with order k, or augment + // the existing one + if(j>0) { - // If we're augmenting a vertex but we don't - // actually need any more edges, just skip this - // routine to avoid memory confusion - if(nu[j]!=k) { - // Allocate memory and copy the edges - // of the previous instance into it - vc.n_set_aux1(k); - edp=mep[k]+((k<<1)+1)*mec[k]++; - i=0; - while(ids) { - --p; - while(ed[p][nu[p]]==-1) { - j=nu[p]; - edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]); - while(edpds) { + --p; + while(ed[p][nu[p]]==-1) { + j=nu[p]; + edp=ed[p];edd=(mep[j]+((j<<1)+1)*--mec[j]); + while(edp0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR); + // Check for any vertices of zero order + if(*mec>0) voro_fatal_error("Zero order vertex formed",VOROPP_INTERNAL_ERROR); - // Collapse any order 2 vertices and exit - return collapse_order2(vc); + // Collapse any order 2 vertices and exit + return collapse_order2(vc); } /** During the creation of a new facet in the plane routine, it is possible @@ -1035,58 +1078,58 @@ bool voronoicell_base::nplane(vc_class &vc,double x,double y,double z,double rsq * was successful. */ template inline bool voronoicell_base::collapse_order2(vc_class &vc) { - if(!collapse_order1(vc)) return false; - int a,b,i,j,k,l; - while(mec[2]>0) { + if(!collapse_order1(vc)) return false; + int a,b,i,j,k,l; + while(mec[2]>0) { - // Pick a order 2 vertex and read in its edges - i=--mec[2]; - j=mep[2][5*i];k=mep[2][5*i+1]; - if(j==k) { + // Pick a order 2 vertex and read in its edges + i=--mec[2]; + j=mep[2][5*i];k=mep[2][5*i+1]; + if(j==k) { #if VOROPP_VERBOSE >=1 - fputs("Order two vertex joins itself",stderr); + fputs("Order two vertex joins itself",stderr); #endif - return false; - } + return false; + } - // Scan the edges of j to see if joins k - for(l=0;l inline bool voronoicell_base::collapse_order1(vc_class &vc) { - int i,j,k; - while(mec[1]>0) { - up=0; + int i,j,k; + while(mec[1]>0) { + up=0; #if VOROPP_VERBOSE >=1 - fputs("Order one collapse\n",stderr); + fputs("Order one collapse\n",stderr); #endif - i=--mec[1]; - j=mep[1][3*i];k=mep[1][3*i+1]; - i=mep[1][3*i+2]; - if(!delete_connection(vc,j,k,false)) return false; - --p; - if(up==i) up=0; - if(p!=i) { - if(up==p) up=i; - pts[3*i]=pts[3*p]; - pts[3*i+1]=pts[3*p+1]; - pts[3*i+2]=pts[3*p+2]; - for(k=0;k inline bool voronoicell_base::delete_connection(vc_class &vc,int j,int k,bool hand) { - int q=hand?k:cycle_up(k,j); - int i=nu[j]-1,l,*edp,*edd,m; + int q=hand?k:cycle_up(k,j); + int i=nu[j]-1,l,*edp,*edd,m; #if VOROPP_VERBOSE >=1 - if(i<1) { - fputs("Zero order vertex formed\n",stderr); - return false; - } + if(i<1) { + fputs("Zero order vertex formed\n",stderr); + return false; + } #endif - if(mec[i]==mem[i]) add_memory(vc,i,ds2); - vc.n_set_aux1(i); - for(l=0;l &v) { - double area; - v.clear(); - int i,j,k,l,m,n; - double ux,uy,uz,vx,vy,vz,wx,wy,wz; - for(i=1;i=0) { - area=0; - ed[i][j]=-1-k; - l=cycle_up(ed[i][nu[i]+j],k); - m=ed[k][l];ed[k][l]=-1-m; - while(m!=i) { - n=cycle_up(ed[k][nu[k]+l],m); - ux=pts[3*k]-pts[3*i]; - uy=pts[3*k+1]-pts[3*i+1]; - uz=pts[3*k+2]-pts[3*i+2]; - vx=pts[3*m]-pts[3*i]; - vy=pts[3*m+1]-pts[3*i+1]; - vz=pts[3*m+2]-pts[3*i+2]; - wx=uy*vz-uz*vy; - wy=uz*vx-ux*vz; - wz=ux*vy-uy*vx; - area+=sqrt(wx*wx+wy*wy+wz*wz); - k=m;l=n; - m=ed[k][l];ed[k][l]=-1-m; - } - v.push_back(0.125*area); - } - } - reset_edges(); + double area; + v.clear(); + int i,j,k,l,m,n; + double ux,uy,uz,vx,vy,vz,wx,wy,wz; + for(i=1;i=0) { + area=0; + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + m=ed[k][l];ed[k][l]=-1-m; + while(m!=i) { + n=cycle_up(ed[k][nu[k]+l],m); + ux=pts[3*k]-pts[3*i]; + uy=pts[3*k+1]-pts[3*i+1]; + uz=pts[3*k+2]-pts[3*i+2]; + vx=pts[3*m]-pts[3*i]; + vy=pts[3*m+1]-pts[3*i+1]; + vz=pts[3*m+2]-pts[3*i+2]; + wx=uy*vz-uz*vy; + wy=uz*vx-ux*vz; + wz=ux*vy-uy*vx; + area+=sqrt(wx*wx+wy*wy+wz*wz); + k=m;l=n; + m=ed[k][l];ed[k][l]=-1-m; + } + v.push_back(0.125*area); + } + } + reset_edges(); } /** Several routines in the class that gather cell-based statistics internally @@ -1215,11 +1258,11 @@ void voronoicell_base::face_areas(std::vector &v) { * should have already been flipped to negative, and it bails out with an * internal error if it encounters a positive edge. */ inline void voronoicell_base::reset_edges() { - int i,j; - for(i=0;i=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR); - ed[i][j]=-1-ed[i][j]; - } + int i,j; + for(i=0;i=0) voro_fatal_error("Edge reset routine found a previously untested edge",VOROPP_INTERNAL_ERROR); + ed[i][j]=-1-ed[i][j]; + } } /** Checks to see if a given vertex is inside, outside or within the test @@ -1233,16 +1276,16 @@ inline void voronoicell_base::reset_edges() { * \return -1 if the point is inside the plane, 1 if the point is outside the * plane, or 0 if the point is within the plane. */ inline int voronoicell_base::m_test(int n,double &ans) { - double *pp=pts+n+(n<<1); - ans=*(pp++)*px; - ans+=*(pp++)*py; - ans+=*pp*pz-prsq; - if(ans<-tolerance2) { - return -1; - } else if(ans>tolerance2) { - return 1; - } - return check_marginal(n,ans); + double *pp=pts+n+(n<<1); + ans=*(pp++)*px; + ans+=*(pp++)*py; + ans+=*pp*pz-prsq; + if(ans<-tolerance2) { + return -1; + } else if(ans>tolerance2) { + return 1; + } + return check_marginal(n,ans); } /** Checks to see if a given vertex is inside, outside or within the test @@ -1258,23 +1301,23 @@ inline int voronoicell_base::m_test(int n,double &ans) { * \return -1 if the point is inside the plane, 1 if the point is outside the * plane, or 0 if the point is within the plane. */ int voronoicell_base::check_marginal(int n,double &ans) { - int i; - for(i=0;imax_marginal) - voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); + int i; + for(i=0;imax_marginal) + voro_fatal_error("Marginal case buffer allocation exceeded absolute maximum",VOROPP_MEMORY_ERROR); #if VOROPP_VERBOSE >=2 - fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i); + fprintf(stderr,"Marginal cases buffer scaled up to %d\n",i); #endif - int *pmarg=new int[current_marginal]; - for(int j=0;jtolerance?1:(ans<-tolerance?-1:0); - return marg[n_marg-1]; + int *pmarg=new int[current_marginal]; + for(int j=0;jtolerance?1:(ans<-tolerance?-1:0); + return marg[n_marg-1]; } /** This initializes the class to be a rectangular box. It calls the base class @@ -1285,79 +1328,144 @@ int voronoicell_base::check_marginal(int n,double &ans) { * \param[in] (ymin,ymax) the minimum and maximum y coordinates. * \param[in] (zmin,zmax) the minimum and maximum z coordinates. */ void voronoicell_neighbor::init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax) { - init_base(xmin,xmax,ymin,ymax,zmin,zmax); - int *q=mne[3]; - *q=-5;q[1]=-3;q[2]=-1; - q[3]=-5;q[4]=-2;q[5]=-3; - q[6]=-5;q[7]=-1;q[8]=-4; - q[9]=-5;q[10]=-4;q[11]=-2; - q[12]=-6;q[13]=-1;q[14]=-3; - q[15]=-6;q[16]=-3;q[17]=-2; - q[18]=-6;q[19]=-4;q[20]=-1; - q[21]=-6;q[22]=-2;q[23]=-4; - *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9; - ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21; + init_base(xmin,xmax,ymin,ymax,zmin,zmax); + int *q=mne[3]; + *q=-5;q[1]=-3;q[2]=-1; + q[3]=-5;q[4]=-2;q[5]=-3; + q[6]=-5;q[7]=-1;q[8]=-4; + q[9]=-5;q[10]=-4;q[11]=-2; + q[12]=-6;q[13]=-1;q[14]=-3; + q[15]=-6;q[16]=-3;q[17]=-2; + q[18]=-6;q[19]=-4;q[20]=-1; + q[21]=-6;q[22]=-2;q[23]=-4; + *ne=q;ne[1]=q+3;ne[2]=q+6;ne[3]=q+9; + ne[4]=q+12;ne[5]=q+15;ne[6]=q+18;ne[7]=q+21; } /** This routine checks to make sure the neighbor information of each face is * consistent. */ void voronoicell_neighbor::check_facets() { - int i,j,k,l,m,q; - for(i=1;i=0) { - ed[i][j]=-1-k; - q=ne[i][j]; - l=cycle_up(ed[i][nu[i]+j],k); - do { - m=ed[k][l]; - ed[k][l]=-1-m; - if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q); - l=cycle_up(ed[k][nu[k]+l],m); - k=m; - } while (k!=i); - } - } - reset_edges(); + int i,j,k,l,m,q; + for(i=1;i=0) { + ed[i][j]=-1-k; + q=ne[i][j]; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + if(ne[k][l]!=q) fprintf(stderr,"Facet error at (%d,%d)=%d, started from (%d,%d)=%d\n",k,l,ne[k][l],i,j,q); + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + } + } + reset_edges(); } /** The class constructor allocates memory for storing neighbor information. */ voronoicell_neighbor::voronoicell_neighbor() { - int i; - mne=new int*[current_vertex_order]; - ne=new int*[current_vertices]; - for(i=0;i<3;i++) mne[i]=new int[init_n_vertices*i]; - mne[3]=new int[init_3_vertices*3]; - for(i=4;i=0;i--) if(mem[i]>0) delete [] mne[i]; - delete [] mne; - delete [] ne; + for(int i=current_vertex_order-1;i>=0;i--) if(mem[i]>0) delete [] mne[i]; + delete [] mne; + delete [] ne; } /** Computes a vector list of neighbors. */ void voronoicell_neighbor::neighbors(std::vector &v) { - v.clear(); - int i,j,k,l,m; - for(i=1;i=0) { - v.push_back(ne[i][j]); - ed[i][j]=-1-k; - l=cycle_up(ed[i][nu[i]+j],k); - do { - m=ed[k][l]; - ed[k][l]=-1-m; - l=cycle_up(ed[k][nu[k]+l],m); - k=m; - } while (k!=i); - } - } - reset_edges(); + v.clear(); + int i,j,k,l,m; + for(i=1;i=0) { + v.push_back(ne[i][j]); + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + } + } + reset_edges(); +} + +/** Returns the number of faces of a computed Voronoi cell. + * \return The number of faces. */ +int voronoicell_base::number_of_faces() { + int i,j,k,l,m,s=0; + for(i=1;i=0) { + s++; + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + do { + m=ed[k][l]; + ed[k][l]=-1-m; + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + + } + } + reset_edges(); + return s; +} + +/** Returns a vector of the vertex vectors in the global coordinate system. + * \param[out] v the vector to store the results in. + * \param[in] (x,y,z) the position vector of the particle in the global + * coordinate system. */ +void voronoicell_base::vertices(double x,double y,double z,std::vector &v) { + v.resize(3*p); + double *ptsp=pts; + for(int i=0;i<3*p;i+=3) { + v[i]=x+*(ptsp++)*0.5; + v[i+1]=y+*(ptsp++)*0.5; + v[i+2]=z+*(ptsp++)*0.5; + } +} + +/** For each face, this routine outputs a bracketed sequence of numbers + * containing a list of all the vertices that make up that face. + * \param[out] v the vector to store the results in. */ +void voronoicell_base::face_vertices(std::vector &v) { + int i,j,k,l,m,vp(0),vn; + v.clear(); + for(i=1;i=0) { + v.push_back(0); + v.push_back(i); + ed[i][j]=-1-k; + l=cycle_up(ed[i][nu[i]+j],k); + do { + v.push_back(k); + m=ed[k][l]; + ed[k][l]=-1-m; + l=cycle_up(ed[k][nu[k]+l],m); + k=m; + } while (k!=i); + vn=v.size(); + v[vp]=vn-vp-1; + vp=vn; + } + } + reset_edges(); } // Explicit instantiation diff --git a/src/USER-PTM/ptm_voronoi_cell.h b/src/USER-PTM/ptm_voronoi_cell.h index e0284bc56f..eb091dd36b 100644 --- a/src/USER-PTM/ptm_voronoi_cell.h +++ b/src/USER-PTM/ptm_voronoi_cell.h @@ -1,3 +1,46 @@ +/* +Voro++ Copyright (c) 2008, The Regents of the University of California, through +Lawrence Berkeley National Laboratory (subject to receipt of any required +approvals from the U.S. Dept. of Energy). All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +(1) Redistributions of source code must retain the above copyright notice, this +list of conditions and the following disclaimer. + +(2) Redistributions in binary form must reproduce the above copyright notice, +this list of conditions and the following disclaimer in the documentation +and/or other materials provided with the distribution. + +(3) Neither the name of the University of California, Lawrence Berkeley +National Laboratory, U.S. Dept. of Energy nor the names of its contributors may +be used to endorse or promote products derived from this software without +specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR +ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES +(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; +LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON +ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS +SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +You are under no obligation whatsoever to provide any bug fixes, patches, or +upgrades to the features, functionality or performance of the source code +("Enhancements") to anyone; however, if you choose to make your Enhancements +available either publicly, or directly to Lawrence Berkeley National +Laboratory, without imposing a separate written license agreement for such +Enhancements, then you hereby grant the following license: a non-exclusive, +royalty-free perpetual license to install, use, modify, prepare derivative +works, incorporate into other computer software, distribute, and sublicense +such enhancements or derivative works thereof, in binary and source code form. +*/ + + // Voro++, a 3D cell-based Voronoi library // // Author : Chris H. Rycroft (LBL / UC Berkeley) @@ -33,180 +76,180 @@ namespace ptm_voro { * voronoicell and voronoicell_neighbor classes, which extend it based on * whether neighboring particle ID information needs to be tracked. */ class voronoicell_base { - public: - /** This holds the current size of the arrays ed and nu, which - * hold the vertex information. If more vertices are created - * than can fit in this array, then it is dynamically extended - * using the add_memory_vertices routine. */ - int current_vertices; - /** This holds the current maximum allowed order of a vertex, - * which sets the size of the mem, mep, and mec arrays. If a - * vertex is created with more vertices than this, the arrays - * are dynamically extended using the add_memory_vorder routine. - */ - int current_vertex_order; - /** This sets the size of the main delete stack. */ - int current_delete_size; - /** This sets the size of the auxiliary delete stack. */ - int current_delete2_size; - /** This sets the total number of vertices in the current cell. - */ - int p; - /** This is the index of particular point in the cell, which is - * used to start the tracing routines for plane intersection - * and cutting. These routines will work starting from any - * point, but it's often most efficient to start from the last - * point considered, since in many cases, the cell construction - * algorithm may consider many planes with similar vectors - * concurrently. */ - int up; - /** This is a two dimensional array that holds information - * about the edge connections of the vertices that make up the - * cell. The two dimensional array is not allocated in the - * usual method. To account for the fact the different vertices - * have different orders, and thus require different amounts of - * storage, the elements of ed[i] point to one-dimensional - * arrays in the mep[] array of different sizes. - * - * More specifically, if vertex i has order m, then ed[i] - * points to a one-dimensional array in mep[m] that has 2*m+1 - * entries. The first m elements hold the neighboring edges, so - * that the jth edge of vertex i is held in ed[i][j]. The next - * m elements hold a table of relations which is redundant but - * helps speed up the computation. It satisfies the relation - * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back - * pointer, so that ed[i+2*m]=i. The back pointers are used - * when rearranging the memory. */ - int **ed; - /** This array holds the order of the vertices in the Voronoi - * cell. This array is dynamically allocated, with its current - * size held by current_vertices. */ - int *nu; - /** This in an array with size 3*current_vertices for holding - * the positions of the vertices. */ - double *pts; - voronoicell_base(); - virtual ~voronoicell_base(); - void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); - void init_octahedron_base(double l); - void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3); - void translate(double x,double y,double z); - double volume(); - double max_radius_squared(); - double total_edge_distance(); - double surface_area(); - void centroid(double &cx,double &cy,double &cz); - int number_of_faces(); - int number_of_edges(); - void vertex_orders(std::vector &v); - void vertices(std::vector &v); - void vertices(double x,double y,double z,std::vector &v); - void face_areas(std::vector &v); - void face_orders(std::vector &v); - void face_freq_table(std::vector &v); - void face_vertices(std::vector &v); - void face_perimeters(std::vector &v); - void normals(std::vector &v); - template - bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id); - bool plane_intersects(double x,double y,double z,double rsq); - bool plane_intersects_guess(double x,double y,double z,double rsq); - void construct_relations(); - void check_relations(); - void check_duplicates(); - /** Returns a list of IDs of neighboring particles - * corresponding to each face. - * \param[out] v a reference to a vector in which to return the - * results. If no neighbor information is - * available, a blank vector is returned. */ - virtual void neighbors(std::vector &v) {v.clear();} - /** This a virtual function that is overridden by a routine to - * print the neighboring particle IDs for a given vertex. By - * default, when no neighbor information is available, the - * routine does nothing. - * \param[in] i the vertex to consider. */ - /** This is a simple inline function for picking out the index - * of the next edge counterclockwise at the current vertex. - * \param[in] a the index of an edge of the current vertex. - * \param[in] p the number of the vertex. - * \return 0 if a=nu[p]-1, or a+1 otherwise. */ - inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;} - /** This is a simple inline function for picking out the index - * of the next edge clockwise from the current vertex. - * \param[in] a the index of an edge of the current vertex. - * \param[in] p the number of the vertex. - * \return nu[p]-1 if a=0, or a-1 otherwise. */ - inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;} - protected: - /** This a one dimensional array that holds the current sizes - * of the memory allocations for them mep array.*/ - int *mem; - /** This is a one dimensional array that holds the current - * number of vertices of order p that are stored in the mep[p] - * array. */ - int *mec; - /** This is a two dimensional array for holding the information - * about the edges of the Voronoi cell. mep[p] is a - * one-dimensional array for holding the edge information about - * all vertices of order p, with each vertex holding 2*p+1 - * integers of information. The total number of vertices held - * on mep[p] is stored in mem[p]. If the space runs out, the - * code allocates more using the add_memory() routine. */ - int **mep; - inline void reset_edges(); - template - void check_memory_for_copy(vc_class &vc,voronoicell_base* vb); - void copy(voronoicell_base* vb); - private: - /** This is the delete stack, used to store the vertices which - * are going to be deleted during the plane cutting procedure. - */ - int *ds,*stacke; - /** This is the auxiliary delete stack, which has size set by - * current_delete2_size. */ - int *ds2,*stacke2; - /** This stores the current memory allocation for the marginal - * cases. */ - int current_marginal; - /** This stores the total number of marginal points which are - * currently in the buffer. */ - int n_marg; - /** This array contains a list of the marginal points, and also - * the outcomes of the marginal tests. */ - int *marg; - /** The x coordinate of the normal vector to the test plane. */ - double px; - /** The y coordinate of the normal vector to the test plane. */ - double py; - /** The z coordinate of the normal vector to the test plane. */ - double pz; - /** The magnitude of the normal vector to the test plane. */ - double prsq; - template - void add_memory(vc_class &vc,int i,int *stackp2); - template - void add_memory_vertices(vc_class &vc); - template - void add_memory_vorder(vc_class &vc); - void add_memory_ds(int *&stackp); - void add_memory_ds2(int *&stackp2); - template - inline bool collapse_order1(vc_class &vc); - template - inline bool collapse_order2(vc_class &vc); - template - inline bool delete_connection(vc_class &vc,int j,int k,bool hand); - template - inline bool search_for_outside_edge(vc_class &vc,int &up); - template - inline void add_to_stack(vc_class &vc,int lp,int *&stackp2); - inline bool plane_intersects_track(double x,double y,double z,double rs,double g); - inline void normals_search(std::vector &v,int i,int j,int k); - inline bool search_edge(int l,int &m,int &k); - inline int m_test(int n,double &ans); - int check_marginal(int n,double &ans); - friend class voronoicell; - friend class voronoicell_neighbor; + public: + /** This holds the current size of the arrays ed and nu, which + * hold the vertex information. If more vertices are created + * than can fit in this array, then it is dynamically extended + * using the add_memory_vertices routine. */ + int current_vertices; + /** This holds the current maximum allowed order of a vertex, + * which sets the size of the mem, mep, and mec arrays. If a + * vertex is created with more vertices than this, the arrays + * are dynamically extended using the add_memory_vorder routine. + */ + int current_vertex_order; + /** This sets the size of the main delete stack. */ + int current_delete_size; + /** This sets the size of the auxiliary delete stack. */ + int current_delete2_size; + /** This sets the total number of vertices in the current cell. + */ + int p; + /** This is the index of particular point in the cell, which is + * used to start the tracing routines for plane intersection + * and cutting. These routines will work starting from any + * point, but it's often most efficient to start from the last + * point considered, since in many cases, the cell construction + * algorithm may consider many planes with similar vectors + * concurrently. */ + int up; + /** This is a two dimensional array that holds information + * about the edge connections of the vertices that make up the + * cell. The two dimensional array is not allocated in the + * usual method. To account for the fact the different vertices + * have different orders, and thus require different amounts of + * storage, the elements of ed[i] point to one-dimensional + * arrays in the mep[] array of different sizes. + * + * More specifically, if vertex i has order m, then ed[i] + * points to a one-dimensional array in mep[m] that has 2*m+1 + * entries. The first m elements hold the neighboring edges, so + * that the jth edge of vertex i is held in ed[i][j]. The next + * m elements hold a table of relations which is redundant but + * helps speed up the computation. It satisfies the relation + * ed[ed[i][j]][ed[i][m+j]]=i. The final entry holds a back + * pointer, so that ed[i+2*m]=i. The back pointers are used + * when rearranging the memory. */ + int **ed; + /** This array holds the order of the vertices in the Voronoi + * cell. This array is dynamically allocated, with its current + * size held by current_vertices. */ + int *nu; + /** This in an array with size 3*current_vertices for holding + * the positions of the vertices. */ + double *pts; + voronoicell_base(); + virtual ~voronoicell_base(); + void init_base(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); + void init_octahedron_base(double l); + void init_tetrahedron_base(double x0,double y0,double z0,double x1,double y1,double z1,double x2,double y2,double z2,double x3,double y3,double z3); + void translate(double x,double y,double z); + double volume(); + double max_radius_squared(); + double total_edge_distance(); + double surface_area(); + void centroid(double &cx,double &cy,double &cz); + int number_of_faces(); + int number_of_edges(); + void vertex_orders(std::vector &v); + void vertices(std::vector &v); + void vertices(double x,double y,double z,std::vector &v); + void face_areas(std::vector &v); + void face_orders(std::vector &v); + void face_freq_table(std::vector &v); + void face_vertices(std::vector &v); + void face_perimeters(std::vector &v); + void normals(std::vector &v); + template + bool nplane(vc_class &vc,double x,double y,double z,double rsq,int p_id); + bool plane_intersects(double x,double y,double z,double rsq); + bool plane_intersects_guess(double x,double y,double z,double rsq); + void construct_relations(); + void check_relations(); + void check_duplicates(); + /** Returns a list of IDs of neighboring particles + * corresponding to each face. + * \param[out] v a reference to a vector in which to return the + * results. If no neighbor information is + * available, a blank vector is returned. */ + virtual void neighbors(std::vector &v) {v.clear();} + /** This a virtual function that is overridden by a routine to + * print the neighboring particle IDs for a given vertex. By + * default, when no neighbor information is available, the + * routine does nothing. + * \param[in] i the vertex to consider. */ + /** This is a simple inline function for picking out the index + * of the next edge counterclockwise at the current vertex. + * \param[in] a the index of an edge of the current vertex. + * \param[in] p the number of the vertex. + * \return 0 if a=nu[p]-1, or a+1 otherwise. */ + inline int cycle_up(int a,int p) {return a==nu[p]-1?0:a+1;} + /** This is a simple inline function for picking out the index + * of the next edge clockwise from the current vertex. + * \param[in] a the index of an edge of the current vertex. + * \param[in] p the number of the vertex. + * \return nu[p]-1 if a=0, or a-1 otherwise. */ + inline int cycle_down(int a,int p) {return a==0?nu[p]-1:a-1;} + protected: + /** This a one dimensional array that holds the current sizes + * of the memory allocations for them mep array.*/ + int *mem; + /** This is a one dimensional array that holds the current + * number of vertices of order p that are stored in the mep[p] + * array. */ + int *mec; + /** This is a two dimensional array for holding the information + * about the edges of the Voronoi cell. mep[p] is a + * one-dimensional array for holding the edge information about + * all vertices of order p, with each vertex holding 2*p+1 + * integers of information. The total number of vertices held + * on mep[p] is stored in mem[p]. If the space runs out, the + * code allocates more using the add_memory() routine. */ + int **mep; + inline void reset_edges(); + template + void check_memory_for_copy(vc_class &vc,voronoicell_base* vb); + void copy(voronoicell_base* vb); + private: + /** This is the delete stack, used to store the vertices which + * are going to be deleted during the plane cutting procedure. + */ + int *ds,*stacke; + /** This is the auxiliary delete stack, which has size set by + * current_delete2_size. */ + int *ds2,*stacke2; + /** This stores the current memory allocation for the marginal + * cases. */ + int current_marginal; + /** This stores the total number of marginal points which are + * currently in the buffer. */ + int n_marg; + /** This array contains a list of the marginal points, and also + * the outcomes of the marginal tests. */ + int *marg; + /** The x coordinate of the normal vector to the test plane. */ + double px; + /** The y coordinate of the normal vector to the test plane. */ + double py; + /** The z coordinate of the normal vector to the test plane. */ + double pz; + /** The magnitude of the normal vector to the test plane. */ + double prsq; + template + void add_memory(vc_class &vc,int i,int *stackp2); + template + void add_memory_vertices(vc_class &vc); + template + void add_memory_vorder(vc_class &vc); + void add_memory_ds(int *&stackp); + void add_memory_ds2(int *&stackp2); + template + inline bool collapse_order1(vc_class &vc); + template + inline bool collapse_order2(vc_class &vc); + template + inline bool delete_connection(vc_class &vc,int j,int k,bool hand); + template + inline bool search_for_outside_edge(vc_class &vc,int &up); + template + inline void add_to_stack(vc_class &vc,int lp,int *&stackp2); + inline bool plane_intersects_track(double x,double y,double z,double rs,double g); + inline void normals_search(std::vector &v,int i,int j,int k); + inline bool search_edge(int l,int &m,int &k); + inline int m_test(int n,double &ans); + int check_marginal(int n,double &ans); + friend class voronoicell; + friend class voronoicell_neighbor; }; /** \brief Extension of the voronoicell_base class to represent a Voronoi cell @@ -217,105 +260,105 @@ class voronoicell_base { * It contains additional data structures mne and ne for storing this * information. */ class voronoicell_neighbor : public voronoicell_base { - public: - using voronoicell_base::nplane; - /** This two dimensional array holds the neighbor information - * associated with each vertex. mne[p] is a one dimensional - * array which holds all of the neighbor information for - * vertices of order p. */ - int **mne; - /** This is a two dimensional array that holds the neighbor - * information associated with each vertex. ne[i] points to a - * one-dimensional array in mne[nu[i]]. ne[i][j] holds the - * neighbor information associated with the jth edge of vertex - * i. It is set to the ID number of the plane that made the - * face that is clockwise from the jth edge. */ - int **ne; - voronoicell_neighbor(); - ~voronoicell_neighbor(); - void operator=(voronoicell_neighbor &c); - /** Cuts the Voronoi cell by a particle whose center is at a - * separation of (x,y,z) from the cell center. The value of rsq - * should be initially set to \f$x^2+y^2+z^2\f$. - * \param[in] (x,y,z) the normal vector to the plane. - * \param[in] rsq the distance along this vector of the plane. - * \param[in] p_id the plane ID (for neighbor tracking only). - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool nplane(double x,double y,double z,double rsq,int p_id) { - return nplane(*this,x,y,z,rsq,p_id); - } - /** This routine calculates the modulus squared of the vector - * before passing it to the main nplane() routine with full - * arguments. - * \param[in] (x,y,z) the vector to cut the cell by. - * \param[in] p_id the plane ID (for neighbor tracking only). - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool nplane(double x,double y,double z,int p_id) { - double rsq=x*x+y*y+z*z; - return nplane(*this,x,y,z,rsq,p_id); - } - /** This version of the plane routine just makes up the plane - * ID to be zero. It will only be referenced if neighbor - * tracking is enabled. - * \param[in] (x,y,z) the vector to cut the cell by. - * \param[in] rsq the modulus squared of the vector. - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool plane(double x,double y,double z,double rsq) { - return nplane(*this,x,y,z,rsq,0); - } - /** Cuts a Voronoi cell using the influence of a particle at - * (x,y,z), first calculating the modulus squared of this - * vector before passing it to the main nplane() routine. Zero - * is supplied as the plane ID, which will be ignored unless - * neighbor tracking is enabled. - * \param[in] (x,y,z) the vector to cut the cell by. - * \return False if the plane cut deleted the cell entirely, - * true otherwise. */ - inline bool plane(double x,double y,double z) { - double rsq=x*x+y*y+z*z; - return nplane(*this,x,y,z,rsq,0); - } - void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); - void check_facets(); - virtual void neighbors(std::vector &v); + public: + using voronoicell_base::nplane; + /** This two dimensional array holds the neighbor information + * associated with each vertex. mne[p] is a one dimensional + * array which holds all of the neighbor information for + * vertices of order p. */ + int **mne; + /** This is a two dimensional array that holds the neighbor + * information associated with each vertex. ne[i] points to a + * one-dimensional array in mne[nu[i]]. ne[i][j] holds the + * neighbor information associated with the jth edge of vertex + * i. It is set to the ID number of the plane that made the + * face that is clockwise from the jth edge. */ + int **ne; + voronoicell_neighbor(); + ~voronoicell_neighbor(); + void operator=(voronoicell_neighbor &c); + /** Cuts the Voronoi cell by a particle whose center is at a + * separation of (x,y,z) from the cell center. The value of rsq + * should be initially set to \f$x^2+y^2+z^2\f$. + * \param[in] (x,y,z) the normal vector to the plane. + * \param[in] rsq the distance along this vector of the plane. + * \param[in] p_id the plane ID (for neighbor tracking only). + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool nplane(double x,double y,double z,double rsq,int p_id) { + return nplane(*this,x,y,z,rsq,p_id); + } + /** This routine calculates the modulus squared of the vector + * before passing it to the main nplane() routine with full + * arguments. + * \param[in] (x,y,z) the vector to cut the cell by. + * \param[in] p_id the plane ID (for neighbor tracking only). + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool nplane(double x,double y,double z,int p_id) { + double rsq=x*x+y*y+z*z; + return nplane(*this,x,y,z,rsq,p_id); + } + /** This version of the plane routine just makes up the plane + * ID to be zero. It will only be referenced if neighbor + * tracking is enabled. + * \param[in] (x,y,z) the vector to cut the cell by. + * \param[in] rsq the modulus squared of the vector. + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool plane(double x,double y,double z,double rsq) { + return nplane(*this,x,y,z,rsq,0); + } + /** Cuts a Voronoi cell using the influence of a particle at + * (x,y,z), first calculating the modulus squared of this + * vector before passing it to the main nplane() routine. Zero + * is supplied as the plane ID, which will be ignored unless + * neighbor tracking is enabled. + * \param[in] (x,y,z) the vector to cut the cell by. + * \return False if the plane cut deleted the cell entirely, + * true otherwise. */ + inline bool plane(double x,double y,double z) { + double rsq=x*x+y*y+z*z; + return nplane(*this,x,y,z,rsq,0); + } + void init(double xmin,double xmax,double ymin,double ymax,double zmin,double zmax); + void check_facets(); + virtual void neighbors(std::vector &v); - private: - int *paux1; - int *paux2; - inline void n_allocate(int i,int m) {mne[i]=new int[m*i];} - inline void n_add_memory_vertices(int i) { - int **pp=new int*[i]; - for(int j=0;jinum; ilist = list->ilist; @@ -252,7 +251,7 @@ void PairQUIP::coeff(int narg, char **arg) } } - if( narg != (4+n) ) { + if (narg != (4+n)) { char str[1024]; sprintf(str,"Number of arguments %d is not correct, it should be %d", narg, 4+n); error->all(FLERR,str); @@ -271,7 +270,7 @@ void PairQUIP::coeff(int narg, char **arg) for (int i = 4; i < narg; i++) { - if( 0 == sscanf(arg[i],"%d",&map[i-4])) { + if (0 == sscanf(arg[i],"%d",&map[i-4])) { char str[1024]; sprintf(str,"Incorrect atomic number %s at position %d",arg[i],i); error->all(FLERR,str); diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp index 6f0b93235f..b37c8fff83 100644 --- a/src/USER-REAXC/fix_qeq_reax.cpp +++ b/src/USER-REAXC/fix_qeq_reax.cpp @@ -126,14 +126,12 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) : reaxc = NULL; reaxc = (PairReaxC *) force->pair_match("reax/c",0); - if (reaxc) { - s_hist = t_hist = NULL; - grow_arrays(atom->nmax); - atom->add_callback(0); - for (int i = 0; i < atom->nmax; i++) - for (int j = 0; j < nprev; ++j) - s_hist[i][j] = t_hist[i][j] = 0; - } + s_hist = t_hist = NULL; + grow_arrays(atom->nmax); + atom->add_callback(0); + for (int i = 0; i < atom->nmax; i++) + for (int j = 0; j < nprev; ++j) + s_hist[i][j] = t_hist[i][j] = 0; } /* ---------------------------------------------------------------------- */ @@ -557,17 +555,11 @@ void FixQEqReax::init_matvec() b_s[i] = -chi[ atom->type[i] ]; b_t[i] = -1.0; - /* linear extrapolation for s & t from previous solutions */ - //s[i] = 2 * s_hist[i][0] - s_hist[i][1]; - //t[i] = 2 * t_hist[i][0] - t_hist[i][1]; - /* quadratic extrapolation for s & t from previous solutions */ - //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] ); t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1]); /* cubic extrapolation for s & t from previous solutions */ s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]); - //t[i] = 4*(t_hist[i][0]+t_hist[i][2])-(6*t_hist[i][1]+t_hist[i][3]); } } @@ -615,6 +607,7 @@ void FixQEqReax::compute_H() for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; + j &= NEIGHMASK; dx = x[j][0] - x[i][0]; dy = x[j][1] - x[i][1]; diff --git a/src/USER-REAXC/fix_reaxc.cpp b/src/USER-REAXC/fix_reaxc.cpp index c470173663..361733f3ca 100644 --- a/src/USER-REAXC/fix_reaxc.cpp +++ b/src/USER-REAXC/fix_reaxc.cpp @@ -41,17 +41,15 @@ FixReaxC::FixReaxC(LAMMPS *lmp,int narg, char **arg) : { // perform initial allocation of atom-based arrays // register with atom class - + + oldnmax = 0; num_bonds = NULL; num_hbonds = NULL; grow_arrays(atom->nmax); atom->add_callback(0); // initialize arrays to MIN so atom migration is OK the 1st time - - int nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) - num_bonds[i] = num_hbonds[i] = MIN_REAX_BONDS; + // it is done in grow_arrays() now // set comm sizes needed by this fix @@ -99,6 +97,11 @@ void FixReaxC::grow_arrays(int nmax) { memory->grow(num_bonds,nmax,"reaxc:num_bonds"); memory->grow(num_hbonds,nmax,"reaxc:num_hbonds"); + for (int i = oldnmax; i < nmax; i++) { + num_hbonds[i] = MIN_REAX_HBONDS; + num_bonds[i] = MIN_REAX_BONDS; + } + oldnmax = nmax; } /* ---------------------------------------------------------------------- diff --git a/src/USER-REAXC/fix_reaxc.h b/src/USER-REAXC/fix_reaxc.h index 0e173f5ece..6a37002847 100644 --- a/src/USER-REAXC/fix_reaxc.h +++ b/src/USER-REAXC/fix_reaxc.h @@ -56,6 +56,7 @@ class FixReaxC : public Fix { int maxhbonds; // max # of Hbonds for any atom int *num_bonds; // # of bonds for each atom int *num_hbonds; // # of Hbonds for each atom + int oldnmax; // arrays' size before growing }; } diff --git a/src/USER-REAXC/pair_reaxc.cpp b/src/USER-REAXC/pair_reaxc.cpp index 85bd8471b4..b9d488d8cf 100644 --- a/src/USER-REAXC/pair_reaxc.cpp +++ b/src/USER-REAXC/pair_reaxc.cpp @@ -137,9 +137,9 @@ PairReaxC::~PairReaxC() // deallocate reax data-structures - if( control->tabulate ) Deallocate_Lookup_Tables( system ); + if (control->tabulate ) Deallocate_Lookup_Tables( system); - if( control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world ); + if (control->hbond_cut > 0 ) Delete_List( lists+HBONDS, world); Delete_List( lists+BONDS, world ); Delete_List( lists+THREE_BODIES, world ); Delete_List( lists+FAR_NBRS, world ); @@ -157,7 +157,7 @@ PairReaxC::~PairReaxC() memory->destroy( mpi_data ); // deallocate interface storage - if( allocated ) { + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); memory->destroy(cutghost); @@ -361,7 +361,8 @@ void PairReaxC::init_style( ) int iqeq; for (iqeq = 0; iqeq < modify->nfix; iqeq++) - if (strstr(modify->fix[iqeq]->style,"qeq/reax")) break; + if (strstr(modify->fix[iqeq]->style,"qeq/reax") + || strstr(modify->fix[iqeq]->style,"qeq/shielded")) break; if (iqeq == modify->nfix && qeqflag == 1) error->all(FLERR,"Pair reax/c requires use of fix qeq/reax"); @@ -496,8 +497,7 @@ void PairReaxC::compute(int eflag, int vflag) int *num_hbonds = fix_reax->num_hbonds; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else ev_unset(); + ev_init(eflag,vflag); if (vflag_global) control->virial = 1; else control->virial = 0; @@ -510,7 +510,7 @@ void PairReaxC::compute(int eflag, int vflag) system->big_box.box_norms[0] = 0; system->big_box.box_norms[1] = 0; system->big_box.box_norms[2] = 0; - if( comm->me == 0 ) t_start = MPI_Wtime(); + if (comm->me == 0 ) t_start = MPI_Wtime(); // setup data structures @@ -519,7 +519,7 @@ void PairReaxC::compute(int eflag, int vflag) Reset( system, control, data, workspace, &lists, world ); workspace->realloc.num_far = write_reax_lists(); // timing for filling in the reax lists - if( comm->me == 0 ) { + if (comm->me == 0) { t_end = MPI_Wtime(); data->timing.nbrs = t_end - t_start; } @@ -683,7 +683,7 @@ int PairReaxC::estimate_reax_lists() j &= NEIGHMASK; get_distance( x[j], x[i], &d_sqr, &dvec ); - if( d_sqr <= SQR(control->nonb_cut) ) + if (d_sqr <= SQR(control->nonb_cut)) ++num_nbrs; } } @@ -735,7 +735,7 @@ int PairReaxC::write_reax_lists() j &= NEIGHMASK; get_distance( x[j], x[i], &d_sqr, &dvec ); - if( d_sqr <= (cutoff_sqr) ){ + if (d_sqr <= (cutoff_sqr)) { dist[j] = sqrt( d_sqr ); set_far_nbr( &far_list[num_nbrs], j, dist[j], dvec ); ++num_nbrs; diff --git a/src/USER-REAXC/reaxc_allocate.cpp b/src/USER-REAXC/reaxc_allocate.cpp index c6c103b6f4..700e68514c 100644 --- a/src/USER-REAXC/reaxc_allocate.cpp +++ b/src/USER-REAXC/reaxc_allocate.cpp @@ -122,7 +122,7 @@ void DeAllocate_Workspace( control_params * /*control*/, storage *workspace ) { int i; - if( !workspace->allocated ) + if (!workspace->allocated) return; workspace->allocated = 0; @@ -338,13 +338,13 @@ static int Reallocate_HBonds_List( reax_system *system, reax_list *hbonds, total_hbonds = 0; for( i = 0; i < system->n; ++i ) - if( (system->my_atoms[i].Hindex) >= 0 ) { + if ((system->my_atoms[i].Hindex) >= 0) { total_hbonds += system->my_atoms[i].num_hbonds; } total_hbonds = (int)(MAX( total_hbonds*saferzone, mincap*MIN_HBONDS )); Delete_List( hbonds, comm ); - if( !Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds, comm ) ) { + if (!Make_List( system->Hcap, total_hbonds, TYP_HBOND, hbonds, comm )) { fprintf( stderr, "not enough space for hbonds list. terminating!\n" ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); } @@ -429,10 +429,10 @@ void ReAllocate( reax_system *system, control_params *control, system->total_cap = MAX( (int)(system->N * safezone), mincap ); } - if( Nflag ) { + if (Nflag) { /* system */ ret = Allocate_System( system, system->local_cap, system->total_cap, msg ); - if( ret != SUCCESS ) { + if (ret != SUCCESS) { fprintf( stderr, "not enough space for atom_list: total_cap=%d", system->total_cap ); fprintf( stderr, "terminating...\n" ); @@ -443,7 +443,7 @@ void ReAllocate( reax_system *system, control_params *control, DeAllocate_Workspace( control, workspace ); ret = Allocate_Workspace( system, control, workspace, system->local_cap, system->total_cap, comm, msg ); - if( ret != SUCCESS ) { + if (ret != SUCCESS) { fprintf( stderr, "no space for workspace: local_cap=%d total_cap=%d", system->local_cap, system->total_cap ); fprintf( stderr, "terminating...\n" ); @@ -454,11 +454,11 @@ void ReAllocate( reax_system *system, control_params *control, renbr = (data->step - data->prev_steps) % control->reneighbor == 0; /* far neighbors */ - if( renbr ) { + if (renbr) { far_nbrs = *lists + FAR_NBRS; - if( Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE ) { - if( realloc->num_far > far_nbrs->num_intrs ) { + if (Nflag || realloc->num_far >= far_nbrs->num_intrs * DANGER_ZONE) { + if (realloc->num_far > far_nbrs->num_intrs) { fprintf( stderr, "step%d-ran out of space on far_nbrs: top=%d, max=%d", data->step, realloc->num_far, far_nbrs->num_intrs ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -473,7 +473,7 @@ void ReAllocate( reax_system *system, control_params *control, } /* hydrogen bonds list */ - if( control->hbond_cut > 0 ) { + if (control->hbond_cut > 0) { Hflag = 0; if( system->numH >= DANGER_ZONE * system->Hcap || (0 && system->numH <= LOOSE_ZONE * system->Hcap) ) { @@ -481,7 +481,7 @@ void ReAllocate( reax_system *system, control_params *control, system->Hcap = int(MAX( system->numH * saferzone, mincap )); } - if( Hflag || realloc->hbonds ) { + if (Hflag || realloc->hbonds) { ret = Reallocate_HBonds_List( system, (*lists)+HBONDS, comm ); realloc->hbonds = 0; } @@ -489,7 +489,7 @@ void ReAllocate( reax_system *system, control_params *control, /* bonds list */ num_bonds = est_3body = -1; - if( Nflag || realloc->bonds ){ + if (Nflag || realloc->bonds) { Reallocate_Bonds_List( system, (*lists)+BONDS, &num_bonds, &est_3body, comm ); realloc->bonds = 0; @@ -497,10 +497,10 @@ void ReAllocate( reax_system *system, control_params *control, } /* 3-body list */ - if( realloc->num_3body > 0 ) { + if (realloc->num_3body > 0) { Delete_List( (*lists)+THREE_BODIES, comm ); - if( num_bonds == -1 ) + if (num_bonds == -1) num_bonds = ((*lists)+BONDS)->num_intrs; realloc->num_3body = (int)(MAX(realloc->num_3body*safezone, MIN_3BODIES)); diff --git a/src/USER-REAXC/reaxc_bond_orders.cpp b/src/USER-REAXC/reaxc_bond_orders.cpp index 572d27526c..1ed58a0bfd 100644 --- a/src/USER-REAXC/reaxc_bond_orders.cpp +++ b/src/USER-REAXC/reaxc_bond_orders.cpp @@ -110,7 +110,7 @@ void Add_dBond_to_Forces_NPT( int i, int pj, simulation_data *data, /* force */ rvec_Add( workspace->f[k], temp ); /* pressure */ - if( k != i ) { + if (k != i) { ivec_Sum( rel_box, nbr_k->rel_box, nbr_j->rel_box ); //rel_box(k, i) rvec_iMultiply( ext_press, rel_box, temp ); rvec_Add( data->my_ext_press, ext_press ); @@ -189,7 +189,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj, rvec_ScaledAdd( temp, coef.C3dbopi2, workspace->dDeltap_self[i] ); rvec_Add( workspace->f[i], temp ); - if( system->pair_ptr->vflag_atom) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fi_tmp, -1.0, temp); rvec_ScaledSum( delij, 1., system->my_atoms[i].x,-1., system->my_atoms[j].x ); system->pair_ptr->v_tally(i,fi_tmp,delij); @@ -208,7 +208,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj, rvec_ScaledAdd( temp, coef.C4dbopi2, workspace->dDeltap_self[j]); rvec_Add( workspace->f[j], temp ); - if( system->pair_ptr->vflag_atom) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fj_tmp, -1.0, temp); rvec_ScaledSum( delji, 1., system->my_atoms[j].x,-1., system->my_atoms[i].x ); system->pair_ptr->v_tally(j,fj_tmp,delji); @@ -225,7 +225,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj, rvec_ScaledAdd( temp, -coef.C3dbopi2, nbr_k->bo_data.dBOp); rvec_Add( workspace->f[k], temp ); - if( system->pair_ptr->vflag_atom ) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fk_tmp, -1.0, temp); rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); system->pair_ptr->v_tally(k,fk_tmp,delki); @@ -245,7 +245,7 @@ void Add_dBond_to_Forces( reax_system *system, int i, int pj, rvec_ScaledAdd( temp, -coef.C4dbopi2, nbr_k->bo_data.dBOp); rvec_Add( workspace->f[k], temp ); - if( system->pair_ptr->vflag_atom ) { + if (system->pair_ptr->vflag_atom) { rvec_Scale(fk_tmp, -1.0, temp); rvec_ScaledSum(delki,1.,system->my_atoms[k].x,-1.,system->my_atoms[i].x); system->pair_ptr->v_tally(k,fk_tmp,delki); @@ -271,19 +271,19 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut, j = nbr_pj->nbr; r2 = SQR(nbr_pj->d); - if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0 ) { + if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { C12 = twbp->p_bo1 * pow( nbr_pj->d / twbp->r_s, twbp->p_bo2 ); BO_s = (1.0 + bo_cut) * exp( C12 ); } else BO_s = C12 = 0.0; - if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0 ) { + if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { C34 = twbp->p_bo3 * pow( nbr_pj->d / twbp->r_p, twbp->p_bo4 ); BO_pi = exp( C34 ); } else BO_pi = C34 = 0.0; - if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0 ) { + if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { C56 = twbp->p_bo5 * pow( nbr_pj->d / twbp->r_pp, twbp->p_bo6 ); BO_pi2= exp( C56 ); } @@ -292,7 +292,7 @@ int BOp( storage *workspace, reax_list *bonds, double bo_cut, /* Initially BO values are the uncorrected ones, page 1 */ BO = BO_s + BO_pi + BO_pi2; - if( BO >= bo_cut ) { + if (BO >= bo_cut) { /****** bonds i-j and j-i ******/ ibond = &( bonds->select.bond_list[btop_i] ); btop_j = End_Index( j, bonds ); @@ -410,10 +410,10 @@ void BO( reax_system *system, control_params * /*control*/, simulation_data * /* bo_ij = &( bonds->select.bond_list[pj].bo_data ); // fprintf( stderr, "\tj:%d - ubo: %8.3f\n", j+1, bo_ij->BO ); - if( i < j || workspace->bond_mark[j] > 3 ) { + if (i < j || workspace->bond_mark[j] > 3) { twbp = &( system->reax_param.tbp[type_i][type_j] ); - if( twbp->ovc < 0.001 && twbp->v13cor < 0.001 ) { + if (twbp->ovc < 0.001 && twbp->v13cor < 0.001) { bo_ij->C1dbo = 1.000000; bo_ij->C2dbo = 0.000000; bo_ij->C3dbo = 0.000000; @@ -435,7 +435,7 @@ void BO( reax_system *system, control_params * /*control*/, simulation_data * /* Deltap_boc_j = workspace->Deltap_boc[j]; /* on page 1 */ - if( twbp->ovc >= 0.001 ) { + if (twbp->ovc >= 0.001) { /* Correction for overcoordination */ exp_p1i = exp( -p_boc1 * Deltap_i ); exp_p2i = exp( -p_boc2 * Deltap_i ); @@ -475,7 +475,7 @@ void BO( reax_system *system, control_params * /*control*/, simulation_data * /* Cf1_ij = Cf1_ji = 0.0; } - if( twbp->v13cor >= 0.001 ) { + if (twbp->v13cor >= 0.001) { /* Correction for 1-3 bond orders */ exp_f4 =exp(-(twbp->p_boc4 * SQR( bo_ij->BO ) - Deltap_boc_i) * twbp->p_boc3 + twbp->p_boc5); @@ -527,13 +527,13 @@ void BO( reax_system *system, control_params * /*control*/, simulation_data * /* } /* neglect bonds that are < 1e-10 */ - if( bo_ij->BO < 1e-10 ) + if (bo_ij->BO < 1e-10) bo_ij->BO = 0.0; - if( bo_ij->BO_s < 1e-10 ) + if (bo_ij->BO_s < 1e-10) bo_ij->BO_s = 0.0; - if( bo_ij->BO_pi < 1e-10 ) + if (bo_ij->BO_pi < 1e-10) bo_ij->BO_pi = 0.0; - if( bo_ij->BO_pi2 < 1e-10 ) + if (bo_ij->BO_pi2 < 1e-10) bo_ij->BO_pi2 = 0.0; workspace->total_bond_order[i] += bo_ij->BO; //now keeps total_BO @@ -576,7 +576,7 @@ void BO( reax_system *system, control_params * /*control*/, simulation_data * /* workspace->Clp[j] = 2.0 * p_lp1 * explp1 * (2.0 + workspace->vlpex[j]); workspace->dDelta_lp[j] = workspace->Clp[j]; - if( sbp_j->mass > 21.0 ) { + if (sbp_j->mass > 21.0) { workspace->nlp_temp[j] = 0.5 * (sbp_j->valency_e - sbp_j->valency); workspace->Delta_lp_temp[j] = sbp_j->nlp_opt - workspace->nlp_temp[j]; workspace->dDelta_lp_temp[j] = 0.; diff --git a/src/USER-REAXC/reaxc_bonds.cpp b/src/USER-REAXC/reaxc_bonds.cpp index 6fde18e5c2..48fb872324 100644 --- a/src/USER-REAXC/reaxc_bonds.cpp +++ b/src/USER-REAXC/reaxc_bonds.cpp @@ -62,9 +62,9 @@ void Bonds( reax_system *system, control_params * /*control*/, for( pj = start_i; pj < end_i; ++pj ) { j = bonds->select.bond_list[pj].nbr; - if( system->my_atoms[i].orig_id > system->my_atoms[j].orig_id ) + if (system->my_atoms[i].orig_id > system->my_atoms[j].orig_id) continue; - if( system->my_atoms[i].orig_id == system->my_atoms[j].orig_id ) { + if (system->my_atoms[i].orig_id == system->my_atoms[j].orig_id) { if (system->my_atoms[j].x[2] < system->my_atoms[i].x[2]) continue; if (system->my_atoms[j].x[2] == system->my_atoms[i].x[2] && system->my_atoms[j].x[1] < system->my_atoms[i].x[1]) continue; @@ -95,7 +95,7 @@ void Bonds( reax_system *system, control_params * /*control*/, -twbp->De_pp * bo_ij->BO_pi2; /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(i,j,natoms,1,ebond,0.0,0.0,0.0,0.0,0.0); /* calculate derivatives of Bond Orders */ @@ -104,7 +104,7 @@ void Bonds( reax_system *system, control_params * /*control*/, bo_ij->Cdbopi2 -= (CEbo + twbp->De_pp); /* Stabilisation terminal triple bond */ - if( bo_ij->BO >= 1.00 ) { + if (bo_ij->BO >= 1.00) { if( gp37 == 2 || (sbp_i->mass == 12.0000 && sbp_j->mass == 15.9990) || (sbp_j->mass == 12.0000 && sbp_i->mass == 15.9990) ) { @@ -125,7 +125,7 @@ void Bonds( reax_system *system, control_params * /*control*/, (gp3*exphub1 + 25.0*gp4*exphuov*hulpov*(exphua1+exphub1)); /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(i,j,natoms,1,estriph,0.0,0.0,0.0,0.0,0.0); bo_ij->Cdbo += decobdbo; diff --git a/src/USER-REAXC/reaxc_control.cpp b/src/USER-REAXC/reaxc_control.cpp index 11a89020b8..dd2b5a32ad 100644 --- a/src/USER-REAXC/reaxc_control.cpp +++ b/src/USER-REAXC/reaxc_control.cpp @@ -118,16 +118,16 @@ char Read_Control_File( char *control_file, control_params* control, fgets( s, MAX_LINE, fp ); Tokenize( s, &tmp ); - if( strcmp(tmp[0], "simulation_name") == 0 ) { + if (strcmp(tmp[0], "simulation_name") == 0) { strcpy( control->sim_name, tmp[1] ); } - else if( strcmp(tmp[0], "ensemble_type") == 0 ) { + else if (strcmp(tmp[0], "ensemble_type") == 0) { ival = atoi(tmp[1]); control->ensemble = ival; - if( ival == iNPT || ival ==sNPT || ival == NPT ) + if (ival == iNPT || ival ==sNPT || ival == NPT) control->virial = 1; } - else if( strcmp(tmp[0], "nsteps") == 0 ) { + else if (strcmp(tmp[0], "nsteps") == 0) { ival = atoi(tmp[1]); control->nsteps = ival; } @@ -135,7 +135,7 @@ char Read_Control_File( char *control_file, control_params* control, val = atof(tmp[1]); control->dt = val * 1.e-3; // convert dt from fs to ps! } - else if( strcmp(tmp[0], "proc_by_dim") == 0 ) { + else if (strcmp(tmp[0], "proc_by_dim") == 0) { ival = atoi(tmp[1]); control->procs_by_dim[0] = ival; ival = atoi(tmp[2]); @@ -146,220 +146,220 @@ char Read_Control_File( char *control_file, control_params* control, control->nprocs = control->procs_by_dim[0]*control->procs_by_dim[1]* control->procs_by_dim[2]; } - else if( strcmp(tmp[0], "random_vel") == 0 ) { + else if (strcmp(tmp[0], "random_vel") == 0) { ival = atoi(tmp[1]); control->random_vel = ival; } - else if( strcmp(tmp[0], "restart_format") == 0 ) { + else if (strcmp(tmp[0], "restart_format") == 0) { ival = atoi(tmp[1]); out_control->restart_format = ival; } - else if( strcmp(tmp[0], "restart_freq") == 0 ) { + else if (strcmp(tmp[0], "restart_freq") == 0) { ival = atoi(tmp[1]); out_control->restart_freq = ival; } - else if( strcmp(tmp[0], "reposition_atoms") == 0 ) { + else if (strcmp(tmp[0], "reposition_atoms") == 0) { ival = atoi(tmp[1]); control->reposition_atoms = ival; } - else if( strcmp(tmp[0], "restrict_bonds") == 0 ) { + else if (strcmp(tmp[0], "restrict_bonds") == 0) { ival = atoi( tmp[1] ); control->restrict_bonds = ival; } - else if( strcmp(tmp[0], "remove_CoM_vel") == 0 ) { + else if (strcmp(tmp[0], "remove_CoM_vel") == 0) { ival = atoi(tmp[1]); control->remove_CoM_vel = ival; } - else if( strcmp(tmp[0], "debug_level") == 0 ) { + else if (strcmp(tmp[0], "debug_level") == 0) { ival = atoi(tmp[1]); out_control->debug_level = ival; } - else if( strcmp(tmp[0], "energy_update_freq") == 0 ) { + else if (strcmp(tmp[0], "energy_update_freq") == 0) { ival = atoi(tmp[1]); out_control->energy_update_freq = ival; } - else if( strcmp(tmp[0], "reneighbor") == 0 ) { + else if (strcmp(tmp[0], "reneighbor") == 0) { ival = atoi( tmp[1] ); control->reneighbor = ival; } - else if( strcmp(tmp[0], "vlist_buffer") == 0 ) { + else if (strcmp(tmp[0], "vlist_buffer") == 0) { val = atof(tmp[1]); control->vlist_cut= val + control->nonb_cut; } - else if( strcmp(tmp[0], "nbrhood_cutoff") == 0 ) { + else if (strcmp(tmp[0], "nbrhood_cutoff") == 0) { val = atof(tmp[1]); control->bond_cut = val; } - else if( strcmp(tmp[0], "bond_graph_cutoff") == 0 ) { + else if (strcmp(tmp[0], "bond_graph_cutoff") == 0) { val = atof(tmp[1]); control->bg_cut = val; } - else if( strcmp(tmp[0], "thb_cutoff") == 0 ) { + else if (strcmp(tmp[0], "thb_cutoff") == 0) { val = atof(tmp[1]); control->thb_cut = val; } - else if( strcmp(tmp[0], "thb_cutoff_sq") == 0 ) { + else if (strcmp(tmp[0], "thb_cutoff_sq") == 0) { val = atof(tmp[1]); control->thb_cutsq = val; } - else if( strcmp(tmp[0], "hbond_cutoff") == 0 ) { + else if (strcmp(tmp[0], "hbond_cutoff") == 0) { val = atof( tmp[1] ); control->hbond_cut = val; } - else if( strcmp(tmp[0], "ghost_cutoff") == 0 ) { + else if (strcmp(tmp[0], "ghost_cutoff") == 0) { val = atof(tmp[1]); control->user_ghost_cut = val; } - else if( strcmp(tmp[0], "tabulate_long_range") == 0 ) { + else if (strcmp(tmp[0], "tabulate_long_range") == 0) { ival = atoi( tmp[1] ); control->tabulate = ival; } - else if( strcmp(tmp[0], "qeq_freq") == 0 ) { + else if (strcmp(tmp[0], "qeq_freq") == 0) { ival = atoi( tmp[1] ); control->qeq_freq = ival; } - else if( strcmp(tmp[0], "q_err") == 0 ) { + else if (strcmp(tmp[0], "q_err") == 0) { val = atof( tmp[1] ); control->q_err = val; } - else if( strcmp(tmp[0], "ilu_refactor") == 0 ) { + else if (strcmp(tmp[0], "ilu_refactor") == 0) { ival = atoi( tmp[1] ); control->refactor = ival; } - else if( strcmp(tmp[0], "ilu_droptol") == 0 ) { + else if (strcmp(tmp[0], "ilu_droptol") == 0) { val = atof( tmp[1] ); control->droptol = val; } - else if( strcmp(tmp[0], "temp_init") == 0 ) { + else if (strcmp(tmp[0], "temp_init") == 0) { val = atof(tmp[1]); control->T_init = val; - if( control->T_init < 0.1 ) + if (control->T_init < 0.1) control->T_init = 0.1; } - else if( strcmp(tmp[0], "temp_final") == 0 ) { + else if (strcmp(tmp[0], "temp_final") == 0) { val = atof(tmp[1]); control->T_final = val; - if( control->T_final < 0.1 ) + if (control->T_final < 0.1) control->T_final = 0.1; } - else if( strcmp(tmp[0], "t_mass") == 0 ) { + else if (strcmp(tmp[0], "t_mass") == 0) { val = atof(tmp[1]); control->Tau_T = val * 1.e-3; // convert t_mass from fs to ps } - else if( strcmp(tmp[0], "t_mode") == 0 ) { + else if (strcmp(tmp[0], "t_mode") == 0) { ival = atoi(tmp[1]); control->T_mode = ival; } - else if( strcmp(tmp[0], "t_rate") == 0 ) { + else if (strcmp(tmp[0], "t_rate") == 0) { val = atof(tmp[1]); control->T_rate = val; } - else if( strcmp(tmp[0], "t_freq") == 0 ) { + else if (strcmp(tmp[0], "t_freq") == 0) { val = atof(tmp[1]); control->T_freq = val; } - else if( strcmp(tmp[0], "pressure") == 0 ) { - if( control->ensemble == iNPT ) { + else if (strcmp(tmp[0], "pressure") == 0) { + if (control->ensemble == iNPT) { control->P[0] = control->P[1] = control->P[2] = atof(tmp[1]); } - else if( control->ensemble == sNPT ) { + else if (control->ensemble == sNPT) { control->P[0] = atof(tmp[1]); control->P[1] = atof(tmp[2]); control->P[2] = atof(tmp[3]); } } - else if( strcmp(tmp[0], "p_mass") == 0 ) { + else if (strcmp(tmp[0], "p_mass") == 0) { // convert p_mass from fs to ps - if( control->ensemble == iNPT ) { + if (control->ensemble == iNPT) { control->Tau_P[0] = control->Tau_P[1] = control->Tau_P[2] = atof(tmp[1]) * 1.e-3; } - else if( control->ensemble == sNPT ) { + else if (control->ensemble == sNPT) { control->Tau_P[0] = atof(tmp[1]) * 1.e-3; control->Tau_P[1] = atof(tmp[2]) * 1.e-3; control->Tau_P[2] = atof(tmp[3]) * 1.e-3; } } - else if( strcmp(tmp[0], "pt_mass") == 0 ) { + else if (strcmp(tmp[0], "pt_mass") == 0) { val = atof(tmp[1]); control->Tau_PT[0] = control->Tau_PT[1] = control->Tau_PT[2] = val * 1.e-3; // convert pt_mass from fs to ps } - else if( strcmp(tmp[0], "compress") == 0 ) { + else if (strcmp(tmp[0], "compress") == 0) { val = atof(tmp[1]); control->compressibility = val; } - else if( strcmp(tmp[0], "press_mode") == 0 ) { + else if (strcmp(tmp[0], "press_mode") == 0) { ival = atoi(tmp[1]); control->press_mode = ival; } - else if( strcmp(tmp[0], "geo_format") == 0 ) { + else if (strcmp(tmp[0], "geo_format") == 0) { ival = atoi( tmp[1] ); control->geo_format = ival; } - else if( strcmp(tmp[0], "write_freq") == 0 ) { + else if (strcmp(tmp[0], "write_freq") == 0) { ival = atoi(tmp[1]); out_control->write_steps = ival; } - else if( strcmp(tmp[0], "traj_compress") == 0 ) { + else if (strcmp(tmp[0], "traj_compress") == 0) { ival = atoi(tmp[1]); out_control->traj_compress = ival; } - else if( strcmp(tmp[0], "traj_method") == 0 ) { + else if (strcmp(tmp[0], "traj_method") == 0) { ival = atoi(tmp[1]); out_control->traj_method = ival; } - else if( strcmp(tmp[0], "traj_title") == 0 ) { + else if (strcmp(tmp[0], "traj_title") == 0) { strcpy( out_control->traj_title, tmp[1] ); } - else if( strcmp(tmp[0], "atom_info") == 0 ) { + else if (strcmp(tmp[0], "atom_info") == 0) { ival = atoi(tmp[1]); out_control->atom_info += ival * 4; } - else if( strcmp(tmp[0], "atom_velocities") == 0 ) { + else if (strcmp(tmp[0], "atom_velocities") == 0) { ival = atoi(tmp[1]); out_control->atom_info += ival * 2; } - else if( strcmp(tmp[0], "atom_forces") == 0 ) { + else if (strcmp(tmp[0], "atom_forces") == 0) { ival = atoi(tmp[1]); out_control->atom_info += ival * 1; } - else if( strcmp(tmp[0], "bond_info") == 0 ) { + else if (strcmp(tmp[0], "bond_info") == 0) { ival = atoi(tmp[1]); out_control->bond_info = ival; } - else if( strcmp(tmp[0], "angle_info") == 0 ) { + else if (strcmp(tmp[0], "angle_info") == 0) { ival = atoi(tmp[1]); out_control->angle_info = ival; } - else if( strcmp(tmp[0], "molecular_analysis") == 0 ) { + else if (strcmp(tmp[0], "molecular_analysis") == 0) { ival = atoi(tmp[1]); control->molecular_analysis = ival; } - else if( strcmp(tmp[0], "ignore") == 0 ) { + else if (strcmp(tmp[0], "ignore") == 0) { control->num_ignored = atoi(tmp[1]); for( i = 0; i < control->num_ignored; ++i ) control->ignore[atoi(tmp[i+2])] = 1; } - else if( strcmp(tmp[0], "dipole_anal") == 0 ) { + else if (strcmp(tmp[0], "dipole_anal") == 0) { ival = atoi(tmp[1]); control->dipole_anal = ival; } - else if( strcmp(tmp[0], "freq_dipole_anal") == 0 ) { + else if (strcmp(tmp[0], "freq_dipole_anal") == 0) { ival = atoi(tmp[1]); control->freq_dipole_anal = ival; } - else if( strcmp(tmp[0], "diffusion_coef") == 0 ) { + else if (strcmp(tmp[0], "diffusion_coef") == 0) { ival = atoi(tmp[1]); control->diffusion_coef = ival; } - else if( strcmp(tmp[0], "freq_diffusion_coef") == 0 ) { + else if (strcmp(tmp[0], "freq_diffusion_coef") == 0) { ival = atoi(tmp[1]); control->freq_diffusion_coef = ival; } - else if( strcmp(tmp[0], "restrict_type") == 0 ) { + else if (strcmp(tmp[0], "restrict_type") == 0) { ival = atoi(tmp[1]); control->restrict_type = ival; } @@ -370,7 +370,7 @@ char Read_Control_File( char *control_file, control_params* control, } /* determine target T */ - if( control->T_mode == 0 ) + if (control->T_mode == 0) control->T = control->T_final; else control->T = control->T_init; diff --git a/src/USER-REAXC/reaxc_ffield.cpp b/src/USER-REAXC/reaxc_ffield.cpp index 7932e9cbd8..dd8f12f9d2 100644 --- a/src/USER-REAXC/reaxc_ffield.cpp +++ b/src/USER-REAXC/reaxc_ffield.cpp @@ -258,9 +258,9 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, val = atof(tmp[1]); reax->sbp[i].lgre = val; } - if( reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01 ){ // Inner-wall - if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals - if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3 ) { + if (reax->sbp[i].rcore2>0.01 && reax->sbp[i].acore2>0.01) { // Inner-wall + if (reax->sbp[i].gamma_w>0.5) { // Shielding vdWaals + if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 3) { if (errorflag && (me == 0)) fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \ "Force field parameters for element %s\n" \ @@ -270,12 +270,11 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, "Keeping vdWaals-setting for earlier atoms.\n", reax->sbp[i].name ); errorflag = 0; - } else{ + } else { reax->gp.vdw_type = 3; } - } - else { // No shielding vdWaals parameters present - if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2 ) { + } else { // No shielding vdWaals parameters present + if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 2) { if (me == 0) fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \ "Force field parameters for element %s\n" \ @@ -288,10 +287,9 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, reax->gp.vdw_type = 2; } } - } - else{ // No Inner wall parameters present - if( reax->sbp[i].gamma_w>0.5 ){ // Shielding vdWaals - if( reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1 ) { + } else { // No Inner wall parameters present + if (reax->sbp[i].gamma_w>0.5) { // Shielding vdWaals + if (reax->gp.vdw_type != 0 && reax->gp.vdw_type != 1) { if (me == 0) fprintf( stderr, "Warning: inconsistent vdWaals-parameters\n" \ "Force field parameters for element %s\n" \ @@ -642,9 +640,8 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, reax->fbp[j][k][m][n].prm[0].p_cot1 = val; reax->fbp[n][m][k][j].prm[0].p_cot1 = val; } - } - else { /* This means the entry is of the form 0-X-Y-0 */ - if( k < reax->num_atom_types && m < reax->num_atom_types ) + } else { /* This means the entry is of the form 0-X-Y-0 */ + if (k < reax->num_atom_types && m < reax->num_atom_types) for( p = 0; p < reax->num_atom_types; p++ ) for( o = 0; o < reax->num_atom_types; o++ ) { reax->fbp[p][k][m][o].cnt = 1; @@ -690,7 +687,7 @@ char Read_Force_Field( FILE *fp, reax_interaction *reax, m = atoi(tmp[2]) - 1; - if( j < reax->num_atom_types && m < reax->num_atom_types ) { + if (j < reax->num_atom_types && m < reax->num_atom_types) { val = atof(tmp[3]); reax->hbp[j][k][m].r0_hb = val; diff --git a/src/USER-REAXC/reaxc_forces.cpp b/src/USER-REAXC/reaxc_forces.cpp index dfcc9fd4ae..19b3cc4975 100644 --- a/src/USER-REAXC/reaxc_forces.cpp +++ b/src/USER-REAXC/reaxc_forces.cpp @@ -55,7 +55,7 @@ void Init_Force_Functions( control_params *control ) Interaction_Functions[2] = Atom_Energy; //Dummy_Interaction; Interaction_Functions[3] = Valence_Angles; //Dummy_Interaction; Interaction_Functions[4] = Torsion_Angles; //Dummy_Interaction; - if( control->hbond_cut > 0 ) + if (control->hbond_cut > 0) Interaction_Functions[5] = Hydrogen_Bonds; else Interaction_Functions[5] = Dummy_Interaction; Interaction_Functions[6] = Dummy_Interaction; //empty @@ -87,7 +87,7 @@ void Compute_NonBonded_Forces( reax_system *system, control_params *control, { /* van der Waals and Coulomb interactions */ - if( control->tabulate == 0 ) + if (control->tabulate == 0) vdW_Coulomb_Energy( system, control, data, workspace, lists, out_control ); else @@ -105,8 +105,8 @@ void Compute_Total_Force( reax_system *system, control_params *control, for( i = 0; i < system->N; ++i ) for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) - if( i < bonds->select.bond_list[pj].nbr ) { - if( control->virial == 0 ) + if (i < bonds->select.bond_list[pj].nbr) { + if (control->virial == 0) Add_dBond_to_Forces( system, i, pj, workspace, lists ); else Add_dBond_to_Forces_NPT( i, pj, data, workspace, lists ); @@ -123,17 +123,17 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l double saferzone = system->saferzone; /* bond list */ - if( N > 0 ) { + if (N > 0) { bonds = *lists + BONDS; for( i = 0; i < N; ++i ) { system->my_atoms[i].num_bonds = MAX(Num_Entries(i,bonds)*2, MIN_BONDS); - if( i < N-1 ) + if (i < N-1) comp = Start_Index(i+1, bonds); else comp = bonds->num_intrs; - if( End_Index(i, bonds) > comp ) { + if (End_Index(i, bonds) > comp) { fprintf( stderr, "step%d-bondchk failed: i=%d end(i)=%d str(i+1)=%d\n", step, i, End_Index(i,bonds), comp ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -143,12 +143,12 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l /* hbonds list */ - if( numH > 0 ) { + if (numH > 0) { hbonds = *lists + HBONDS; for( i = 0; i < N; ++i ) { Hindex = system->my_atoms[i].Hindex; - if( Hindex > -1 ) { + if (Hindex > -1) { system->my_atoms[i].num_hbonds = (int)(MAX( Num_Entries(Hindex, hbonds)*saferzone, MIN_HBONDS )); @@ -156,11 +156,11 @@ void Validate_Lists( reax_system *system, storage * /*workspace*/, reax_list **l //(Start_Index(i+1,hbonds)-Start_Index(i,hbonds))*0.90/*DANGER_ZONE*/){ // workspace->realloc.hbonds = 1; - if( Hindex < numH-1 ) + if (Hindex < numH-1) comp = Start_Index(Hindex+1, hbonds); else comp = hbonds->num_intrs; - if( End_Index(Hindex, hbonds) > comp ) { + if (End_Index(Hindex, hbonds) > comp) { fprintf(stderr,"step%d-hbondchk failed: H=%d end(H)=%d str(H+1)=%d\n", step, Hindex, End_Index(Hindex,hbonds), comp ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -212,20 +212,19 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, btop_i = End_Index( i, bonds ); sbp_i = &(system->reax_param.sbp[type_i]); - if( i < system->n ) { + if (i < system->n) { local = 1; cutoff = MAX( control->hbond_cut, control->bond_cut ); - } - else { + } else { local = 0; cutoff = control->bond_cut; } ihb = -1; ihb_top = -1; - if( local && control->hbond_cut > 0 ) { + if (local && control->hbond_cut > 0) { ihb = sbp_i->p_hbond; - if( ihb == 1 ) + if (ihb == 1) ihb_top = End_Index( atom_i->Hindex, hbonds ); else ihb_top = -1; } @@ -236,45 +235,43 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, j = nbr_pj->nbr; atom_j = &(system->my_atoms[j]); - if( renbr ) { - if( nbr_pj->d <= cutoff ) + if (renbr) { + if (nbr_pj->d <= cutoff) flag = 1; else flag = 0; - } - else{ + } else { nbr_pj->dvec[0] = atom_j->x[0] - atom_i->x[0]; nbr_pj->dvec[1] = atom_j->x[1] - atom_i->x[1]; nbr_pj->dvec[2] = atom_j->x[2] - atom_i->x[2]; nbr_pj->d = rvec_Norm_Sqr( nbr_pj->dvec ); - if( nbr_pj->d <= SQR(cutoff) ) { + if (nbr_pj->d <= SQR(cutoff)) { nbr_pj->d = sqrt(nbr_pj->d); flag = 1; - } - else { + } else { flag = 0; } } - if( flag ) { + if (flag) { type_j = atom_j->type; if (type_j < 0) continue; sbp_j = &(system->reax_param.sbp[type_j]); twbp = &(system->reax_param.tbp[type_i][type_j]); - if( local ) { + if (local) { /* hydrogen bond lists */ - if( control->hbond_cut > 0 && (ihb==1 || ihb==2) && + if (control->hbond_cut > 0 && (ihb==1 || ihb==2) && nbr_pj->d <= control->hbond_cut ) { // fprintf( stderr, "%d %d\n", atom1, atom2 ); jhb = sbp_j->p_hbond; - if( ihb == 1 && jhb == 2 ) { + if (ihb == 1 && jhb == 2) { hbonds->select.hbond_list[ihb_top].nbr = j; hbonds->select.hbond_list[ihb_top].scl = 1; hbonds->select.hbond_list[ihb_top].ptr = nbr_pj; ++ihb_top; ++num_hbonds; } - else if( j < system->n && ihb == 2 && jhb == 1 ) { + else if (j < system->n && ihb == 2 && jhb == 1) { jhb_top = End_Index( atom_j->Hindex, hbonds ); hbonds->select.hbond_list[jhb_top].nbr = i; hbonds->select.hbond_list[jhb_top].scl = -1; @@ -285,16 +282,16 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, } } - if( //(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) && + if (//(workspace->bond_mark[i] < 3 || workspace->bond_mark[j] < 3) && nbr_pj->d <= control->bond_cut && BOp( workspace, bonds, control->bo_cut, i , btop_i, nbr_pj, sbp_i, sbp_j, twbp ) ) { num_bonds += 2; ++btop_i; - if( workspace->bond_mark[j] > workspace->bond_mark[i] + 1 ) + if (workspace->bond_mark[j] > workspace->bond_mark[i] + 1) workspace->bond_mark[j] = workspace->bond_mark[i] + 1; - else if( workspace->bond_mark[i] > workspace->bond_mark[j] + 1 ) { + else if (workspace->bond_mark[i] > workspace->bond_mark[j] + 1) { workspace->bond_mark[i] = workspace->bond_mark[j] + 1; } } @@ -302,7 +299,7 @@ void Init_Forces_noQEq( reax_system *system, control_params *control, } Set_End_Index( i, btop_i, bonds ); - if( local && ihb == 1 ) + if (local && ihb == 1) Set_End_Index( atom_i->Hindex, ihb_top, hbonds ); } @@ -352,13 +349,12 @@ void Estimate_Storages( reax_system *system, control_params *control, end_i = End_Index(i, far_nbrs); sbp_i = &(system->reax_param.sbp[type_i]); - if( i < system->n ) { + if (i < system->n) { local = 1; cutoff = control->nonb_cut; ++(*Htop); ihb = sbp_i->p_hbond; - } - else { + } else { local = 0; cutoff = control->bond_cut; ihb = -1; @@ -376,15 +372,15 @@ void Estimate_Storages( reax_system *system, control_params *control, sbp_j = &(system->reax_param.sbp[type_j]); twbp = &(system->reax_param.tbp[type_i][type_j]); - if( local ) { - if( j < system->n || atom_i->orig_id < atom_j->orig_id ) //tryQEq ||1 + if (local) { + if (j < system->n || atom_i->orig_id < atom_j->orig_id) //tryQEq ||1 ++(*Htop); /* hydrogen bond lists */ - if( control->hbond_cut > 0.1 && (ihb==1 || ihb==2) && + if (control->hbond_cut > 0.1 && (ihb==1 || ihb==2) && nbr_pj->d <= control->hbond_cut ) { jhb = sbp_j->p_hbond; - if( ihb == 1 && jhb == 2 ) + if (ihb == 1 && jhb == 2) ++hb_top[i]; else if( j < system->n && ihb == 2 && jhb == 1 ) ++hb_top[j]; @@ -392,20 +388,20 @@ void Estimate_Storages( reax_system *system, control_params *control, } /* uncorrected bond orders */ - if( nbr_pj->d <= control->bond_cut ) { - if( sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { + if (nbr_pj->d <= control->bond_cut) { + if (sbp_i->r_s > 0.0 && sbp_j->r_s > 0.0) { C12 = twbp->p_bo1 * pow( r_ij / twbp->r_s, twbp->p_bo2 ); BO_s = (1.0 + control->bo_cut) * exp( C12 ); } else BO_s = C12 = 0.0; - if( sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { + if (sbp_i->r_pi > 0.0 && sbp_j->r_pi > 0.0) { C34 = twbp->p_bo3 * pow( r_ij / twbp->r_p, twbp->p_bo4 ); BO_pi = exp( C34 ); } else BO_pi = C34 = 0.0; - if( sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { + if (sbp_i->r_pi_pi > 0.0 && sbp_j->r_pi_pi > 0.0) { C56 = twbp->p_bo5 * pow( r_ij / twbp->r_pp, twbp->p_bo6 ); BO_pi2= exp( C56 ); } @@ -414,7 +410,7 @@ void Estimate_Storages( reax_system *system, control_params *control, /* Initially BO values are the uncorrected ones, page 1 */ BO = BO_s + BO_pi + BO_pi2; - if( BO >= control->bo_cut ) { + if (BO >= control->bo_cut) { ++bond_top[i]; ++bond_top[j]; } diff --git a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp index 6442dd47e9..be34df7571 100644 --- a/src/USER-REAXC/reaxc_hydrogen_bonds.cpp +++ b/src/USER-REAXC/reaxc_hydrogen_bonds.cpp @@ -63,7 +63,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control, hbond_list = hbonds->select.hbond_list; for( j = 0; j < system->n; ++j ) - if( system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1 ) { + if (system->reax_param.sbp[system->my_atoms[j].type].p_hbond == 1) { type_j = system->my_atoms[j].type; start_j = Start_Index(j, bonds); end_j = End_Index(j, bonds); @@ -98,7 +98,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control, pbond_ij = &( bonds->select.bond_list[pi] ); i = pbond_ij->nbr; - if( system->my_atoms[i].orig_id != system->my_atoms[k].orig_id ) { + if (system->my_atoms[i].orig_id != system->my_atoms[k].orig_id) { bo_ij = &(pbond_ij->bo_data); type_i = system->my_atoms[i].type; if (type_i < 0) continue; @@ -133,7 +133,7 @@ void Hydrogen_Bonds( reax_system *system, control_params *control, /* hydrogen bond forces */ bo_ij->Cdbo += CEhb1; // dbo term - if( control->virial == 0 ) { + if (control->virial == 0) { // dcos terms rvec_ScaledAdd( workspace->f[i], +CEhb2, dcos_theta_di ); rvec_ScaledAdd( workspace->f[j], +CEhb2, dcos_theta_dj ); diff --git a/src/USER-REAXC/reaxc_init_md.cpp b/src/USER-REAXC/reaxc_init_md.cpp index 88fb9cf17f..5901b76326 100644 --- a/src/USER-REAXC/reaxc_init_md.cpp +++ b/src/USER-REAXC/reaxc_init_md.cpp @@ -52,7 +52,7 @@ int Init_System( reax_system *system, control_params *control, char * /*msg*/ ) /* estimate numH and Hcap */ system->numH = 0; - if( control->hbond_cut > 0 ) + if (control->hbond_cut > 0) for( i = 0; i < system->n; ++i ) { atom = &(system->my_atoms[i]); if (system->reax_param.sbp[ atom->type ].p_hbond == 1 && atom->type >= 0) @@ -71,7 +71,7 @@ int Init_Simulation_Data( reax_system *system, control_params *control, Reset_Simulation_Data( data, control->virial ); /* initialize the timer(s) */ - if( system->my_rank == MASTER_NODE ) { + if (system->my_rank == MASTER_NODE) { data->timing.start = Get_Time( ); } @@ -89,10 +89,10 @@ void Init_Taper( control_params *control, storage *workspace, MPI_Comm comm ) swa = control->nonb_low; swb = control->nonb_cut; - if( fabs( swa ) > 0.01 ) + if (fabs( swa ) > 0.01) fprintf( stderr, "Warning: non-zero lower Taper-radius cutoff\n" ); - if( swb < 0 ) { + if (swb < 0) { fprintf( stderr, "Negative upper Taper-radius cutoff\n" ); MPI_Abort( comm, INVALID_INPUT ); } @@ -125,7 +125,7 @@ int Init_Workspace( reax_system *system, control_params *control, ret = Allocate_Workspace( system, control, workspace, system->local_cap, system->total_cap, comm, msg ); - if( ret != SUCCESS ) + if (ret != SUCCESS) return ret; memset( &(workspace->realloc), 0, sizeof(reallocate_data) ); @@ -168,7 +168,7 @@ int Init_Lists( reax_system *system, control_params *control, Estimate_Storages( system, control, lists, &Htop, hb_top, bond_top, &num_3body, comm ); - if( control->hbond_cut > 0 ) { + if (control->hbond_cut > 0) { /* init H indexes */ total_hbonds = 0; for( i = 0; i < system->n; ++i ) { @@ -219,7 +219,7 @@ void Initialize( reax_system *system, control_params *control, char msg[MAX_STR]; - if( Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE ) { + if (Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE) { fprintf( stderr, "p%d: init_mpi_datatypes: could not create datatypes\n", system->my_rank ); fprintf( stderr, "p%d: mpi_data couldn't be initialized! terminating.\n", @@ -227,22 +227,22 @@ void Initialize( reax_system *system, control_params *control, MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_System(system, control, msg) == FAILURE ){ + if (Init_System(system, control, msg) == FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: system could not be initialized! terminating.\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Simulation_Data( system, control, data, msg ) == FAILURE ) { + if (Init_Simulation_Data( system, control, data, msg ) == FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: sim_data couldn't be initialized! terminating.\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Workspace( system, control, workspace, mpi_data->world, msg ) == - FAILURE ) { + if (Init_Workspace( system, control, workspace, mpi_data->world, msg ) == + FAILURE) { fprintf( stderr, "p%d:init_workspace: not enough memory\n", system->my_rank ); fprintf( stderr, "p%d:workspace couldn't be initialized! terminating.\n", @@ -250,23 +250,23 @@ void Initialize( reax_system *system, control_params *control, MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) == - FAILURE ) { + if (Init_Lists( system, control, data, workspace, lists, mpi_data, msg ) == + FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: system could not be initialized! terminating.\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) { + if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: could not open output files! terminating...\n", system->my_rank ); MPI_Abort( mpi_data->world, CANNOT_INITIALIZE ); } - if( control->tabulate ) { - if( Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE ) { + if (control->tabulate) { + if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) { fprintf( stderr, "p%d: %s\n", system->my_rank, msg ); fprintf( stderr, "p%d: couldn't create lookup table! terminating.\n", system->my_rank ); diff --git a/src/USER-REAXC/reaxc_io_tools.cpp b/src/USER-REAXC/reaxc_io_tools.cpp index b63fee2309..f71fcbec8e 100644 --- a/src/USER-REAXC/reaxc_io_tools.cpp +++ b/src/USER-REAXC/reaxc_io_tools.cpp @@ -38,22 +38,22 @@ int Init_Output_Files( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes *mpi_data, char *msg ) { - char temp[MAX_STR]; + char temp[MAX_STR+8]; int ret; - if( out_control->write_steps > 0 ){ + if (out_control->write_steps > 0) { ret = Init_Traj( system, control, out_control, mpi_data, msg ); - if( ret == FAILURE ) + if (ret == FAILURE) return ret; } - if( system->my_rank == MASTER_NODE ) { + if (system->my_rank == MASTER_NODE) { /* These files are written only by the master node */ - if( out_control->energy_update_freq > 0 ) { + if (out_control->energy_update_freq > 0) { /* init potentials file */ sprintf( temp, "%s.pot", control->sim_name ); - if( (out_control->pot = fopen( temp, "w" )) != NULL ) { + if ((out_control->pot = fopen( temp, "w" )) != NULL) { fflush( out_control->pot ); } else { @@ -69,7 +69,7 @@ int Init_Output_Files( reax_system *system, control_params *control, control->ensemble == iNPT || control->ensemble == sNPT ) { sprintf( temp, "%s.prs", control->sim_name ); - if( (out_control->prs = fopen( temp, "w" )) != NULL ) { + if ((out_control->prs = fopen( temp, "w" )) != NULL) { fprintf(out_control->prs,"%8s%13s%13s%13s%13s%13s%13s%13s\n", "step", "Pint/norm[x]", "Pint/norm[y]", "Pint/norm[z]", "Pext/Ptot[x]", "Pext/Ptot[y]", "Pext/Ptot[z]", "Pkin/V" ); @@ -90,11 +90,11 @@ int Init_Output_Files( reax_system *system, control_params *control, int Close_Output_Files( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes * /*mpi_data*/ ) { - if( out_control->write_steps > 0 ) + if (out_control->write_steps > 0) End_Traj( system->my_rank, out_control ); - if( system->my_rank == MASTER_NODE ) { - if( out_control->energy_update_freq > 0 ) { + if (system->my_rank == MASTER_NODE) { + if (out_control->energy_update_freq > 0) { fclose( out_control->pot ); } @@ -124,7 +124,7 @@ void Output_Results( reax_system *system, control_params *control, out_control->energy_update_freq > 0 && data->step % out_control->energy_update_freq == 0 ) { - if( control->virial ){ + if (control->virial) { fprintf( out_control->prs, "%8d%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f%13.6f\n", data->step, diff --git a/src/USER-REAXC/reaxc_list.cpp b/src/USER-REAXC/reaxc_list.cpp index c15ba7927c..8a3bb9d322 100644 --- a/src/USER-REAXC/reaxc_list.cpp +++ b/src/USER-REAXC/reaxc_list.cpp @@ -97,7 +97,7 @@ int Make_List(int n, int num_intrs, int type, reax_list *l, MPI_Comm comm) void Delete_List( reax_list *l, MPI_Comm comm ) { - if( l->allocated == 0 ) + if (l->allocated == 0) return; l->allocated = 0; diff --git a/src/USER-REAXC/reaxc_lookup.cpp b/src/USER-REAXC/reaxc_lookup.cpp index 918099a631..92945ebdb5 100644 --- a/src/USER-REAXC/reaxc_lookup.cpp +++ b/src/USER-REAXC/reaxc_lookup.cpp @@ -198,9 +198,9 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, MPI_INT, MPI_SUM, mpi_data->world ); for( i = 0; i < num_atom_types; ++i ) { - if( aggregated[i] ) { + if (aggregated[i]) { for( j = i; j < num_atom_types; ++j ) { - if( aggregated[j] ) { + if (aggregated[j]) { LR[i][j].xmin = 0; LR[i][j].xmax = control->nonb_cut; LR[i][j].n = control->tabulate + 2; @@ -264,7 +264,7 @@ int Init_Lookup_Tables( reax_system *system, control_params *control, Natural_Cubic_Spline( &h[1], &fCEclmb[1], &(LR[i][j].CEclmb[1]), control->tabulate+1, comm ); - } else{ + } else { LR[i][j].n = 0; } } @@ -290,7 +290,7 @@ void Deallocate_Lookup_Tables( reax_system *system ) for( i = 0; i < ntypes; ++i ) { for( j = i; j < ntypes; ++j ) - if( LR[i][j].n ) { + if (LR[i][j].n) { sfree( LR[i][j].y, "LR[i,j].y" ); sfree( LR[i][j].H, "LR[i,j].H" ); sfree( LR[i][j].vdW, "LR[i,j].vdW" ); diff --git a/src/USER-REAXC/reaxc_multi_body.cpp b/src/USER-REAXC/reaxc_multi_body.cpp index 360a9431cf..f7d72a2678 100644 --- a/src/USER-REAXC/reaxc_multi_body.cpp +++ b/src/USER-REAXC/reaxc_multi_body.cpp @@ -91,23 +91,23 @@ void Atom_Energy( reax_system *system, control_params *control, workspace->CdDelta[i] += CElp; // lp - 1st term /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(i,i,system->n,1,e_lp,0.0,0.0,0.0,0.0,0.0); /* correction for C2 */ - if( p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C") ) + if (p_lp3 > 0.001 && !strcmp(system->reax_param.sbp[type_i].name, "C")) for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) { j = bonds->select.bond_list[pj].nbr; type_j = system->my_atoms[j].type; if (type_j < 0) continue; - if( !strcmp( system->reax_param.sbp[type_j].name, "C" ) ) { + if (!strcmp( system->reax_param.sbp[type_j].name, "C" )) { twbp = &( system->reax_param.tbp[type_i][type_j]); bo_ij = &( bonds->select.bond_list[pj].bo_data ); Di = workspace->Delta[i]; vov3 = bo_ij->BO - Di - 0.040*pow(Di, 4.); - if( vov3 > 3. ) { + if (vov3 > 3.) { data->my_en.e_lp += e_lph = p_lp3 * SQR(vov3-3.0); deahu2dbo = 2.*p_lp3*(vov3 - 3.); @@ -117,7 +117,7 @@ void Atom_Energy( reax_system *system, control_params *control, workspace->CdDelta[i] += deahu2dsbo; /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(i,j,system->n,1,e_lph,0.0,0.0,0.0,0.0,0.0); } @@ -132,7 +132,7 @@ void Atom_Energy( reax_system *system, control_params *control, sbp_i = &(system->reax_param.sbp[ type_i ]); /* over-coordination energy */ - if( sbp_i->mass > 21.0 ) + if (sbp_i->mass > 21.0) dfvl = 0.0; else dfvl = 1.0; // only for 1st-row elements @@ -201,7 +201,7 @@ void Atom_Energy( reax_system *system, control_params *control, p_ovun4 * exp_ovun1 * SQR(inv_exp_ovun1) + CEunder2; /* tally into per-atom energy */ - if( system->pair_ptr->evflag) { + if (system->pair_ptr->evflag) { eng_tmp = e_ov; if (numbonds > 0 || control->enobondsflag) eng_tmp += e_un; diff --git a/src/USER-REAXC/reaxc_nonbonded.cpp b/src/USER-REAXC/reaxc_nonbonded.cpp index b44632ec29..c13bc0d89f 100644 --- a/src/USER-REAXC/reaxc_nonbonded.cpp +++ b/src/USER-REAXC/reaxc_nonbonded.cpp @@ -127,7 +127,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control, CEvd = dTap * e_vdW - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } - else{ // no shielding + else { // no shielding exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); @@ -172,7 +172,7 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control, ( dTap - Tap * r_ij / dr3gamij_1 ) / dr3gamij_3; /* tally into per-atom energy */ - if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { + if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { pe_vdw = Tap * (e_vdW + e_core + e_lg); rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); @@ -181,11 +181,10 @@ void vdW_Coulomb_Energy( reax_system *system, control_params *control, f_tmp,delij[0],delij[1],delij[2]); } - if( control->virial == 0 ) { + if (control->virial == 0) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); - } - else { /* NPT, iNPT or sNPT */ + } else { /* NPT, iNPT or sNPT */ rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[i], -1., temp ); @@ -264,7 +263,7 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, /* Cubic Spline Interpolation */ r = (int)(r_ij * t->inv_dx); - if( r == 0 ) ++r; + if (r == 0) ++r; base = (double)(r+1) * t->dx; dif = r_ij - base; @@ -286,7 +285,7 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, CEclmb *= system->my_atoms[i].q * system->my_atoms[j].q; /* tally into per-atom energy */ - if( system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { + if (system->pair_ptr->evflag || system->pair_ptr->vflag_atom) { rvec_ScaledSum( delij, 1., system->my_atoms[i].x, -1., system->my_atoms[j].x ); f_tmp = -(CEvd + CEclmb); @@ -294,11 +293,10 @@ void Tabulated_vdW_Coulomb_Energy( reax_system *system,control_params *control, f_tmp,delij[0],delij[1],delij[2]); } - if( control->virial == 0 ) { + if (control->virial == 0) { rvec_ScaledAdd( workspace->f[i], -(CEvd + CEclmb), nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[j], +(CEvd + CEclmb), nbr_pj->dvec ); - } - else { // NPT, iNPT or sNPT + } else { // NPT, iNPT or sNPT rvec_Scale( temp, CEvd + CEclmb, nbr_pj->dvec ); rvec_ScaledAdd( workspace->f[i], -1., temp ); @@ -332,7 +330,7 @@ void Compute_Polarization_Energy( reax_system *system, simulation_data *data ) data->my_en.e_pol += en_tmp; /* tally into per-atom energy */ - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(i,i,system->n,1,0.0,en_tmp,0.0,0.0,0.0,0.0); } } @@ -388,7 +386,7 @@ void LR_vdW_Coulomb( reax_system *system, storage *workspace, lr->CEvd = dTap * twbp->D * (exp1 - 2.0 * exp2) - Tap * twbp->D * (twbp->alpha / twbp->r_vdW) * (exp1 - exp2) * dfn13; } - else{ // no shielding + else { // no shielding exp1 = exp( twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); exp2 = exp( 0.5 * twbp->alpha * (1.0 - r_ij / twbp->r_vdW) ); diff --git a/src/USER-REAXC/reaxc_reset_tools.cpp b/src/USER-REAXC/reaxc_reset_tools.cpp index 1b16f10aee..80faed1e9f 100644 --- a/src/USER-REAXC/reaxc_reset_tools.cpp +++ b/src/USER-REAXC/reaxc_reset_tools.cpp @@ -36,11 +36,11 @@ void Reset_Atoms( reax_system* system, control_params *control ) reax_atom *atom; system->numH = 0; - if( control->hbond_cut > 0 ) + if (control->hbond_cut > 0) for( i = 0; i < system->n; ++i ) { atom = &(system->my_atoms[i]); if (atom->type < 0) continue; - if( system->reax_param.sbp[ atom->type ].p_hbond == 1 ) + if (system->reax_param.sbp[ atom->type ].p_hbond == 1) atom->Hindex = system->numH++; else atom->Hindex = -1; } @@ -127,7 +127,7 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, reax_list *bonds, *hbonds; /* bonds list */ - if( system->N > 0 ){ + if (system->N > 0) { bonds = (*lists) + BONDS; total_bonds = 0; @@ -139,9 +139,9 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, } /* is reallocation needed? */ - if( total_bonds >= bonds->num_intrs * DANGER_ZONE ) { + if (total_bonds >= bonds->num_intrs * DANGER_ZONE) { workspace->realloc.bonds = 1; - if( total_bonds >= bonds->num_intrs ) { + if (total_bonds >= bonds->num_intrs) { fprintf(stderr, "p%d: not enough space for bonds! total=%d allocated=%d\n", system->my_rank, total_bonds, bonds->num_intrs ); @@ -150,14 +150,14 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, } } - if( control->hbond_cut > 0 && system->numH > 0 ) { + if (control->hbond_cut > 0 && system->numH > 0) { hbonds = (*lists) + HBONDS; total_hbonds = 0; /* reset start-end indexes */ for( i = 0; i < system->n; ++i ) { Hindex = system->my_atoms[i].Hindex; - if( Hindex > -1 ) { + if (Hindex > -1) { Set_Start_Index( Hindex, total_hbonds, hbonds ); Set_End_Index( Hindex, total_hbonds, hbonds ); total_hbonds += system->my_atoms[i].num_hbonds; @@ -165,9 +165,9 @@ void Reset_Neighbor_Lists( reax_system *system, control_params *control, } /* is reallocation needed? */ - if( total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/ ) { + if (total_hbonds >= hbonds->num_intrs * 0.90/*DANGER_ZONE*/) { workspace->realloc.hbonds = 1; - if( total_hbonds >= hbonds->num_intrs ) { + if (total_hbonds >= hbonds->num_intrs) { fprintf(stderr, "p%d: not enough space for hbonds! total=%d allocated=%d\n", system->my_rank, total_hbonds, hbonds->num_intrs ); diff --git a/src/USER-REAXC/reaxc_system_props.cpp b/src/USER-REAXC/reaxc_system_props.cpp index 54eeb6da1e..5024feffcf 100644 --- a/src/USER-REAXC/reaxc_system_props.cpp +++ b/src/USER-REAXC/reaxc_system_props.cpp @@ -60,7 +60,7 @@ void Compute_System_Energy( reax_system *system, simulation_data *data, data->my_en.e_tot = data->my_en.e_pot + E_CONV * data->my_en.e_kin; - if( system->my_rank == MASTER_NODE ) { + if (system->my_rank == MASTER_NODE) { data->sys_en.e_bond = sys_en[0]; data->sys_en.e_ov = sys_en[1]; data->sys_en.e_un = sys_en[2]; diff --git a/src/USER-REAXC/reaxc_tool_box.cpp b/src/USER-REAXC/reaxc_tool_box.cpp index 4fc6796efe..9e662e7a45 100644 --- a/src/USER-REAXC/reaxc_tool_box.cpp +++ b/src/USER-REAXC/reaxc_tool_box.cpp @@ -43,7 +43,7 @@ int Tokenize( char* s, char*** tok ) char *word; int count=0; - strncpy( test, s, MAX_LINE ); + strncpy( test, s, MAX_LINE-1); for( word = strtok(test, sep); word; word = strtok(NULL, sep) ) { strncpy( (*tok)[count], word, MAX_LINE ); @@ -58,7 +58,7 @@ void *smalloc( rc_bigint n, const char *name, MPI_Comm comm ) { void *ptr; - if( n <= 0 ) { + if (n <= 0) { fprintf( stderr, "WARNING: trying to allocate %ld bytes for array %s. ", n, name ); fprintf( stderr, "returning NULL.\n" ); @@ -66,7 +66,7 @@ void *smalloc( rc_bigint n, const char *name, MPI_Comm comm ) } ptr = malloc( n ); - if( ptr == NULL ) { + if (ptr == NULL) { fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s", n, name ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -81,14 +81,14 @@ void *scalloc( rc_bigint n, rc_bigint size, const char *name, MPI_Comm comm ) { void *ptr; - if( n <= 0 ) { + if (n <= 0) { fprintf( stderr, "WARNING: trying to allocate %ld elements for array %s. ", n, name ); fprintf( stderr, "returning NULL.\n" ); return NULL; } - if( size <= 0 ) { + if (size <= 0) { fprintf( stderr, "WARNING: elements size for array %s is %ld. ", name, size ); fprintf( stderr, "returning NULL.\n" ); @@ -96,7 +96,7 @@ void *scalloc( rc_bigint n, rc_bigint size, const char *name, MPI_Comm comm ) } ptr = calloc( n, size ); - if( ptr == NULL ) { + if (ptr == NULL) { fprintf( stderr, "ERROR: failed to allocate %ld bytes for array %s", n*size, name ); MPI_Abort( comm, INSUFFICIENT_MEMORY ); @@ -109,7 +109,7 @@ void *scalloc( rc_bigint n, rc_bigint size, const char *name, MPI_Comm comm ) /* safe free */ void sfree( void *ptr, const char *name ) { - if( ptr == NULL ) { + if (ptr == NULL) { fprintf( stderr, "WARNING: trying to free the already NULL pointer %s!\n", name ); return; diff --git a/src/USER-REAXC/reaxc_torsion_angles.cpp b/src/USER-REAXC/reaxc_torsion_angles.cpp index 2abfbde61d..ed76368d68 100644 --- a/src/USER-REAXC/reaxc_torsion_angles.cpp +++ b/src/USER-REAXC/reaxc_torsion_angles.cpp @@ -74,19 +74,19 @@ double Calculate_Omega( rvec dvec_ij, double r_ij, hnhe = r_ij * r_kl * sin_ijk * cos_jkl; poem = 2.0 * r_ij * r_kl * sin_ijk * sin_jkl; - if( poem < 1e-20 ) poem = 1e-20; + if (poem < 1e-20) poem = 1e-20; tel = SQR( r_ij ) + SQR( r_jk ) + SQR( r_kl ) - SQR( r_li ) - 2.0 * ( r_ij * r_jk * cos_ijk - r_ij * r_kl * cos_ijk * cos_jkl + r_jk * r_kl * cos_jkl ); arg = tel / poem; - if( arg > 1.0 ) arg = 1.0; - if( arg < -1.0 ) arg = -1.0; + if (arg > 1.0) arg = 1.0; + if (arg < -1.0) arg = -1.0; - if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) sin_ijk = MIN_SINE; + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) sin_ijk = MIN_SINE; else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) sin_ijk = -MIN_SINE; - if( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) sin_jkl = MIN_SINE; + if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) sin_jkl = MIN_SINE; else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) sin_jkl = -MIN_SINE; // dcos_omega_di @@ -181,9 +181,9 @@ void Torsion_Angles( reax_system *system, control_params *control, bo_jk = &( pbond_jk->bo_data ); BOA_jk = bo_jk->BO - control->thb_cut; - if( system->my_atoms[j].orig_id > system->my_atoms[k].orig_id ) + if (system->my_atoms[j].orig_id > system->my_atoms[k].orig_id) continue; - if( system->my_atoms[j].orig_id == system->my_atoms[k].orig_id ) { + if (system->my_atoms[j].orig_id == system->my_atoms[k].orig_id) { if (system->my_atoms[k].x[2] < system->my_atoms[j].x[2]) continue; if (system->my_atoms[k].x[2] == system->my_atoms[j].x[2] && system->my_atoms[k].x[1] < system->my_atoms[j].x[1]) continue; @@ -192,10 +192,10 @@ void Torsion_Angles( reax_system *system, control_params *control, system->my_atoms[k].x[0] < system->my_atoms[j].x[0]) continue; } - if( bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs) ) { + if (bo_jk->BO > control->thb_cut/*0*/ && Num_Entries(pk, thb_intrs)) { pj = pbond_jk->sym_index; // pj points to j on k's list - if( Num_Entries(pj, thb_intrs) ) { + if (Num_Entries(pj, thb_intrs)) { type_k = system->my_atoms[k].type; Delta_k = workspace->Delta_boc[k]; r_jk = pbond_jk->d; @@ -218,7 +218,7 @@ void Torsion_Angles( reax_system *system, control_params *control, pbond_ij = &( bonds->select.bond_list[pij] ); bo_ij = &( pbond_ij->bo_data ); - if( bo_ij->BO > control->thb_cut/*0*/ ) { + if (bo_ij->BO > control->thb_cut/*0*/) { i = p_ijk->thb; type_i = system->my_atoms[i].type; r_ij = pbond_ij->d; @@ -228,7 +228,7 @@ void Torsion_Angles( reax_system *system, control_params *control, sin_ijk = sin( theta_ijk ); cos_ijk = cos( theta_ijk ); //tan_ijk_i = 1. / tan( theta_ijk ); - if( sin_ijk >= 0 && sin_ijk <= MIN_SINE ) + if (sin_ijk >= 0 && sin_ijk <= MIN_SINE) tan_ijk_i = cos_ijk / MIN_SINE; else if( sin_ijk <= 0 && sin_ijk >= -MIN_SINE ) tan_ijk_i = cos_ijk / -MIN_SINE; @@ -260,7 +260,7 @@ void Torsion_Angles( reax_system *system, control_params *control, sin_jkl = sin( theta_jkl ); cos_jkl = cos( theta_jkl ); //tan_jkl_i = 1. / tan( theta_jkl ); - if( sin_jkl >= 0 && sin_jkl <= MIN_SINE ) + if (sin_jkl >= 0 && sin_jkl <= MIN_SINE) tan_jkl_i = cos_jkl / MIN_SINE; else if( sin_jkl <= 0 && sin_jkl >= -MIN_SINE ) tan_jkl_i = cos_jkl / -MIN_SINE; @@ -357,7 +357,7 @@ void Torsion_Angles( reax_system *system, control_params *control, bo_jk->Cdbo += (CEtors5 + CEconj2); bo_kl->Cdbo += (CEtors6 + CEconj3); - if( control->virial == 0 ) { + if (control->virial == 0) { /* dcos_theta_ijk */ rvec_ScaledAdd( workspace->f[i], CEtors7 + CEconj4, p_ijk->dcos_dk ); @@ -438,7 +438,7 @@ void Torsion_Angles( reax_system *system, control_params *control, } /* tally into per-atom virials */ - if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { + if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { // acquire vectors rvec_ScaledSum( delil, 1., system->my_atoms[l].x, @@ -463,9 +463,9 @@ void Torsion_Angles( reax_system *system, control_params *control, // tally eng_tmp = e_tor + e_con; - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(j,k,natoms,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); - if( system->pair_ptr->vflag_atom) + if (system->pair_ptr->vflag_atom) system->pair_ptr->v_tally4(i,j,k,l,fi_tmp,fj_tmp,fk_tmp,delil,deljl,delkl); } } // pl check ends diff --git a/src/USER-REAXC/reaxc_traj.cpp b/src/USER-REAXC/reaxc_traj.cpp index c1f3e8ae8f..54d8b3219c 100644 --- a/src/USER-REAXC/reaxc_traj.cpp +++ b/src/USER-REAXC/reaxc_traj.cpp @@ -32,12 +32,12 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space, MPI_Comm comm ) { - if( out_control->buffer_len > 0 ) + if (out_control->buffer_len > 0) free( out_control->buffer ); out_control->buffer_len = (int)(req_space*SAFE_ZONE); out_control->buffer = (char*) malloc(out_control->buffer_len*sizeof(char)); - if( out_control->buffer == NULL ) { + if (out_control->buffer == NULL) { fprintf( stderr, "insufficient memory for required buffer size %d. terminating!\n", (int) (req_space*SAFE_ZONE) ); @@ -51,7 +51,7 @@ int Reallocate_Output_Buffer( output_controls *out_control, int req_space, void Write_Skip_Line( output_controls *out_control, mpi_datatypes * /*mpi_data*/, int my_rank, int skip, int num_section ) { - if( my_rank == MASTER_NODE ) + if (my_rank == MASTER_NODE) fprintf( out_control->strj, INT2_LINE, "chars_to_skip_section:", skip, num_section ); } @@ -82,11 +82,11 @@ int Write_Header( reax_system *system, control_params *control, num_hdr_lines = NUM_HEADER_LINES; my_hdr_lines = num_hdr_lines * ( system->my_rank == MASTER_NODE ); buffer_req = my_hdr_lines * HEADER_LINE_LEN; - if( buffer_req > out_control->buffer_len * DANGER_ZONE ) + if (buffer_req > out_control->buffer_len * DANGER_ZONE) Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); /* only the master node writes into trajectory header */ - if( system->my_rank == MASTER_NODE ) { + if (system->my_rank == MASTER_NODE) { /* clear the contents of line & buffer */ out_control->line[0] = 0; out_control->buffer[0] = 0; @@ -252,7 +252,7 @@ int Write_Header( reax_system *system, control_params *control, } /* dump out the buffer */ - if( system->my_rank == MASTER_NODE ) + if (system->my_rank == MASTER_NODE) fprintf( out_control->strj, "%s", out_control->buffer ); return SUCCESS; @@ -273,11 +273,11 @@ int Write_Init_Desc( reax_system *system, control_params * /*control*/, Write_Skip_Line( out_control, mpi_data, me, system->bigN * INIT_DESC_LEN, system->bigN ); - if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE ) + if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) buffer_req = system->bigN * INIT_DESC_LEN + 1; else buffer_req = system->n * INIT_DESC_LEN + 1; - if( buffer_req > out_control->buffer_len * DANGER_ZONE ) + if (buffer_req > out_control->buffer_len * DANGER_ZONE) Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); out_control->line[0] = 0; @@ -291,13 +291,13 @@ int Write_Init_Desc( reax_system *system, control_params * /*control*/, out_control->line, INIT_DESC_LEN+1 ); } - if( me != MASTER_NODE ) + if (me != MASTER_NODE) { MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, np * INIT_DESCS + me, mpi_data->world ); - else{ + } else { buffer_len = system->n * INIT_DESC_LEN; for( i = 0; i < np; ++i ) - if( i != MASTER_NODE ) { + if (i != MASTER_NODE) { MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, MPI_CHAR, i, np*INIT_DESCS+i, mpi_data->world, &status ); MPI_Get_count( &status, MPI_CHAR, &cnt ); @@ -315,7 +315,7 @@ int Init_Traj( reax_system *system, control_params *control, output_controls *out_control, mpi_datatypes *mpi_data, char *msg ) { - char fname[MAX_STR]; + char fname[MAX_STR+8]; int atom_line_len[ NR_OPT_ATOM ] = { 0, 0, 0, 0, ATOM_BASIC_LEN, ATOM_wV_LEN, ATOM_wF_LEN, ATOM_FULL_LEN }; @@ -341,11 +341,10 @@ int Init_Traj( reax_system *system, control_params *control, out_control->buffer = NULL; /* write trajectory header and atom info, if applicable */ - if( out_control->traj_method == REG_TRAJ) { - if( system->my_rank == MASTER_NODE ) + if (out_control->traj_method == REG_TRAJ) { + if (system->my_rank == MASTER_NODE) out_control->strj = fopen( fname, "w" ); - } - else { + } else { strcpy( msg, "init_traj: unknown trajectory option" ); return FAILURE; } @@ -367,11 +366,11 @@ int Write_Frame_Header( reax_system *system, control_params *control, num_frm_hdr_lines = 22; my_frm_hdr_lines = num_frm_hdr_lines * ( me == MASTER_NODE ); buffer_req = my_frm_hdr_lines * HEADER_LINE_LEN; - if( buffer_req > out_control->buffer_len * DANGER_ZONE ) + if (buffer_req > out_control->buffer_len * DANGER_ZONE) Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); /* only the master node writes into trajectory header */ - if( me == MASTER_NODE ) { + if (me == MASTER_NODE) { /* clear the contents of line & buffer */ out_control->line[0] = 0; out_control->buffer[0] = 0; @@ -474,7 +473,7 @@ int Write_Frame_Header( reax_system *system, control_params *control, } /* dump out the buffer */ - if( system->my_rank == MASTER_NODE ) + if (system->my_rank == MASTER_NODE) fprintf( out_control->strj, "%s", out_control->buffer ); return SUCCESS; @@ -496,11 +495,11 @@ int Write_Atoms( reax_system *system, control_params * /*control*/, Write_Skip_Line( out_control, mpi_data, me, system->bigN*line_len, system->bigN ); - if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE ) + if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) buffer_req = system->bigN * line_len + 1; else buffer_req = system->n * line_len + 1; - if( buffer_req > out_control->buffer_len * DANGER_ZONE ) + if (buffer_req > out_control->buffer_len * DANGER_ZONE) Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); /* fill in buffer */ @@ -540,13 +539,13 @@ int Write_Atoms( reax_system *system, control_params * /*control*/, strncpy( out_control->buffer + i*line_len, out_control->line, line_len+1 ); } - if( me != MASTER_NODE ) + if (me != MASTER_NODE) { MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, np*ATOM_LINES+me, mpi_data->world ); - else{ + } else { buffer_len = system->n * line_len; for( i = 0; i < np; ++i ) - if( i != MASTER_NODE ) { + if (i != MASTER_NODE) { MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, MPI_CHAR, i, np*ATOM_LINES+i, mpi_data->world, &status ); MPI_Get_count( &status, MPI_CHAR, &cnt ); @@ -588,11 +587,11 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds, Write_Skip_Line( out_control, mpi_data, me, num_bonds*line_len, num_bonds ); - if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE ) + if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) buffer_req = num_bonds * line_len + 1; else buffer_req = my_bonds * line_len + 1; - if( buffer_req > out_control->buffer_len * DANGER_ZONE ) + if (buffer_req > out_control->buffer_len * DANGER_ZONE) Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); /* fill in the buffer */ @@ -630,13 +629,13 @@ int Write_Bonds(reax_system *system, control_params *control, reax_list *bonds, } } - if( me != MASTER_NODE ) + if (me != MASTER_NODE) { MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, np*BOND_LINES+me, mpi_data->world ); - else{ + } else { buffer_len = my_bonds * line_len; for( i = 0; i < np; ++i ) - if( i != MASTER_NODE ) { + if (i != MASTER_NODE) { MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, MPI_CHAR, i, np*BOND_LINES+i, mpi_data->world, &status ); MPI_Get_count( &status, MPI_CHAR, &cnt ); @@ -672,7 +671,7 @@ int Write_Angles( reax_system *system, control_params *control, bo_ij = &(bonds->select.bond_list[pi]); i = bo_ij->nbr; - if( bo_ij->bo_data.BO >= control->bg_cut ) // physical j&i bond + if (bo_ij->bo_data.BO >= control->bg_cut) // physical j&i bond for( pk = Start_Index( pi, thb_intrs ); pk < End_Index( pi, thb_intrs ); ++pk ) { angle_ijk = &(thb_intrs->select.three_body_list[pk]); @@ -689,11 +688,11 @@ int Write_Angles( reax_system *system, control_params *control, Write_Skip_Line( out_control, mpi_data, me, num_angles*line_len, num_angles ); - if( out_control->traj_method == REG_TRAJ && me == MASTER_NODE ) + if (out_control->traj_method == REG_TRAJ && me == MASTER_NODE) buffer_req = num_angles * line_len + 1; else buffer_req = my_angles * line_len + 1; - if( buffer_req > out_control->buffer_len * DANGER_ZONE ) + if (buffer_req > out_control->buffer_len * DANGER_ZONE) Reallocate_Output_Buffer( out_control, buffer_req, mpi_data->world ); /* fill in the buffer */ @@ -705,7 +704,7 @@ int Write_Angles( reax_system *system, control_params *control, bo_ij = &(bonds->select.bond_list[pi]); i = bo_ij->nbr; - if( bo_ij->bo_data.BO >= control->bg_cut ) // physical j&i bond + if (bo_ij->bo_data.BO >= control->bg_cut) // physical j&i bond for( pk = Start_Index( pi, thb_intrs ); pk < End_Index( pi, thb_intrs ); ++pk ) { angle_ijk = &(thb_intrs->select.three_body_list[pk]); @@ -725,13 +724,13 @@ int Write_Angles( reax_system *system, control_params *control, } } - if( me != MASTER_NODE ) + if (me != MASTER_NODE) { MPI_Send( out_control->buffer, buffer_req-1, MPI_CHAR, MASTER_NODE, np*ANGLE_LINES+me, mpi_data->world ); - else{ + } else { buffer_len = my_angles * line_len; for( i = 0; i < np; ++i ) - if( i != MASTER_NODE ) { + if (i != MASTER_NODE) { MPI_Recv( out_control->buffer + buffer_len, buffer_req - buffer_len, MPI_CHAR, i, np*ANGLE_LINES+i, mpi_data->world, &status ); MPI_Get_count( &status, MPI_CHAR, &cnt ); @@ -751,13 +750,13 @@ int Append_Frame( reax_system *system, control_params *control, { Write_Frame_Header( system, control, data, out_control, mpi_data ); - if( out_control->write_atoms ) + if (out_control->write_atoms) Write_Atoms( system, control, out_control, mpi_data ); - if( out_control->write_bonds ) + if (out_control->write_bonds) Write_Bonds( system, control, (*lists + BONDS), out_control, mpi_data ); - if( out_control->write_angles ) + if (out_control->write_angles) Write_Angles( system, control, (*lists + BONDS), (*lists + THREE_BODIES), out_control, mpi_data ); @@ -767,7 +766,7 @@ int Append_Frame( reax_system *system, control_params *control, int End_Traj( int my_rank, output_controls *out_control ) { - if( my_rank == MASTER_NODE ) + if (my_rank == MASTER_NODE) fclose( out_control->strj ); free( out_control->buffer ); diff --git a/src/USER-REAXC/reaxc_valence_angles.cpp b/src/USER-REAXC/reaxc_valence_angles.cpp index 118735fbbd..af1f1f8003 100644 --- a/src/USER-REAXC/reaxc_valence_angles.cpp +++ b/src/USER-REAXC/reaxc_valence_angles.cpp @@ -44,8 +44,8 @@ void Calculate_Theta( rvec dvec_ji, double d_ji, rvec dvec_jk, double d_jk, double *theta, double *cos_theta ) { (*cos_theta) = Dot( dvec_ji, dvec_jk, 3 ) / ( d_ji * d_jk ); - if( *cos_theta > 1. ) *cos_theta = 1.0; - if( *cos_theta < -1. ) *cos_theta = -1.0; + if (*cos_theta > 1.) *cos_theta = 1.0; + if (*cos_theta < -1.) *cos_theta = -1.0; (*theta) = acos( *cos_theta ); } @@ -140,11 +140,10 @@ void Valence_Angles( reax_system *system, control_params *control, prod_SBO *= exp( -temp ); } - if( workspace->vlpex[j] >= 0 ){ + if (workspace->vlpex[j] >= 0) { vlpadj = 0; dSBO2 = prod_SBO - 1; - } - else{ + } else { vlpadj = workspace->nlp[j]; dSBO2 = (prod_SBO - 1) * (1 - p_val8 * workspace->dDelta_lp[j]); } @@ -152,13 +151,13 @@ void Valence_Angles( reax_system *system, control_params *control, SBO = SBOp + (1 - prod_SBO) * (-workspace->Delta_boc[j] - p_val8 * vlpadj); dSBO1 = -8 * prod_SBO * ( workspace->Delta_boc[j] + p_val8 * vlpadj ); - if( SBO <= 0 ) + if (SBO <= 0) SBO2 = 0, CSBO2 = 0; - else if( SBO > 0 && SBO <= 1 ) { + else if (SBO > 0 && SBO <= 1) { SBO2 = pow( SBO, p_val9 ); CSBO2 = p_val9 * pow( SBO, p_val9 - 1 ); } - else if( SBO > 1 && SBO < 2 ) { + else if (SBO > 1 && SBO < 2) { SBO2 = 2 - pow( 2-SBO, p_val9 ); CSBO2 = p_val9 * pow( 2 - SBO, p_val9 - 1 ); } @@ -184,7 +183,7 @@ void Valence_Angles( reax_system *system, control_params *control, end_pk = End_Index( pk, thb_intrs ); for( t = start_pk; t < end_pk; ++t ) - if( thb_intrs->select.three_body_list[t].thb == i ) { + if (thb_intrs->select.three_body_list[t].thb == i) { p_ijk = &(thb_intrs->select.three_body_list[num_thb_intrs] ); p_kji = &(thb_intrs->select.three_body_list[t]); @@ -221,20 +220,20 @@ void Valence_Angles( reax_system *system, control_params *control, p_ijk->theta = theta; sin_theta = sin( theta ); - if( sin_theta < 1.0e-5 ) + if (sin_theta < 1.0e-5) sin_theta = 1.0e-5; ++num_thb_intrs; - if( (j < system->n) && (BOA_jk > 0.0) && + if ((j < system->n) && (BOA_jk > 0.0) && (bo_ij->BO > control->thb_cut) && (bo_jk->BO > control->thb_cut) && (bo_ij->BO * bo_jk->BO > control->thb_cutsq) ) { thbh = &( system->reax_param.thbp[ type_i ][ type_j ][ type_k ] ); for( cnt = 0; cnt < thbh->cnt; ++cnt ) { - if( fabs(thbh->prm[cnt].p_val1) > 0.001 ) { + if (fabs(thbh->prm[cnt].p_val1) > 0.001) { thbp = &( thbh->prm[cnt] ); /* ANGLE ENERGY */ @@ -264,7 +263,7 @@ void Valence_Angles( reax_system *system, control_params *control, theta_0 = DEG2RAD( theta_0 ); expval2theta = exp( -p_val2 * SQR(theta_0 - theta) ); - if( p_val1 >= 0 ) + if (p_val1 >= 0) expval12theta = p_val1 * (1.0 - expval2theta); else // To avoid linear Me-H-Me angles (6/6/06) expval12theta = p_val1 * -expval2theta; @@ -355,12 +354,11 @@ void Valence_Angles( reax_system *system, control_params *control, bo_jt->Cdbopi2 += CEval5; } - if( control->virial == 0 ) { + if (control->virial == 0) { rvec_ScaledAdd( workspace->f[i], CEval8, p_ijk->dcos_di ); rvec_ScaledAdd( workspace->f[j], CEval8, p_ijk->dcos_dj ); rvec_ScaledAdd( workspace->f[k], CEval8, p_ijk->dcos_dk ); - } - else { + } else { rvec_Scale( force, CEval8, p_ijk->dcos_di ); rvec_Add( workspace->f[i], force ); rvec_iMultiply( ext_press, pbond_ij->rel_box, force ); @@ -375,7 +373,7 @@ void Valence_Angles( reax_system *system, control_params *control, } /* tally into per-atom virials */ - if( system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { + if (system->pair_ptr->vflag_atom || system->pair_ptr->evflag) { /* Acquire vectors */ rvec_ScaledSum( delij, 1., system->my_atoms[i].x, @@ -389,9 +387,9 @@ void Valence_Angles( reax_system *system, control_params *control, eng_tmp = e_ang + e_pen + e_coa; - if( system->pair_ptr->evflag) + if (system->pair_ptr->evflag) system->pair_ptr->ev_tally(j,j,system->N,1,eng_tmp,0.0,0.0,0.0,0.0,0.0); - if( system->pair_ptr->vflag_atom) + if (system->pair_ptr->vflag_atom) system->pair_ptr->v_tally3(i,j,k,fi_tmp,fk_tmp,delij,delkj); } } @@ -404,9 +402,9 @@ void Valence_Angles( reax_system *system, control_params *control, } } - if( num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE ) { + if (num_thb_intrs >= thb_intrs->num_intrs * DANGER_ZONE) { workspace->realloc.num_3body = num_thb_intrs; - if( num_thb_intrs > thb_intrs->num_intrs ) { + if (num_thb_intrs > thb_intrs->num_intrs) { fprintf( stderr, "step%d-ran out of space on angle_list: top=%d, max=%d", data->step, num_thb_intrs, thb_intrs->num_intrs ); MPI_Abort( MPI_COMM_WORLD, INSUFFICIENT_MEMORY ); diff --git a/src/USER-REAXC/reaxc_vector.cpp b/src/USER-REAXC/reaxc_vector.cpp index 977b17a6dc..b54d329ce9 100644 --- a/src/USER-REAXC/reaxc_vector.cpp +++ b/src/USER-REAXC/reaxc_vector.cpp @@ -105,7 +105,7 @@ void rtensor_MatVec( rvec ret, rtensor m, rvec v ) int i; rvec temp; - if( ret == v ) + if (ret == v) { for( i = 0; i < 3; ++i ) temp[i] = m[i][0] * v[0] + m[i][1] * v[1] + m[i][2] * v[2]; diff --git a/src/USER-SCAFACOS/scafacos.cpp b/src/USER-SCAFACOS/scafacos.cpp index 482a5586c7..497442fbe8 100644 --- a/src/USER-SCAFACOS/scafacos.cpp +++ b/src/USER-SCAFACOS/scafacos.cpp @@ -65,10 +65,10 @@ void Scafacos::settings(int narg, char **arg) if (strcmp(method,"fmm") == 0) { tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; fmm_tuning_flag = 0; - } else if (strcmp(method,"p3m") == 0 || - strcmp(method,"p2nfft") == 0 || + } else if (strcmp(method,"p3m") == 0 || + strcmp(method,"p2nfft") == 0 || strcmp(method,"ewald") == 0) { - tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; } else if (strcmp(method,"direct") == 0) { ; // direct summation has no tolerance type } else { @@ -100,7 +100,13 @@ void Scafacos::init() if (logfile && me == 0) fprintf(logfile, "Setting up ScaFaCoS with solver %s ...\n",method); - if (!atom->q_flag) + if ((strcmp(method,"p3m") == 0) && (me == 0)) + error->warning(FLERR,"Virial computation for P3M not available"); + + if ((strcmp(method,"ewald") == 0) && (me == 0)) + error->warning(FLERR,"Virial computation for Ewald not available"); + + if (!atom->q_flag) error->all(FLERR,"Kspace style requires atom attribute q"); if (domain->dimension == 2) @@ -112,7 +118,7 @@ void Scafacos::init() if (atom->natoms > INT_MAX && sizeof(int) != 8) error->all(FLERR,"Scafacos atom count exceeds 2B"); - if (atom->molecular > 0) + if (atom->molecular > 0) error->all(FLERR, "Cannot use Scafacos with molecular charged systems yet"); @@ -140,11 +146,10 @@ void Scafacos::init() } double **x = atom->x; - double *q = atom->q; + double *q = atom->q; int nlocal = atom->nlocal; - if (strcmp(method,"fmm") == 0) - { + if (strcmp(method,"fmm") == 0) { if (fmm_tuning_flag == 1) fcs_fmm_set_internal_tuning((FCS)fcs,FCS_FMM_INHOMOGENOUS_SYSTEM); else @@ -152,8 +157,7 @@ void Scafacos::init() } // for the FMM at least one particle is required per process - if (strcmp(method,"fmm") == 0) - { + if (strcmp(method,"fmm") == 0) { int empty = (nlocal==0)?1:0; MPI_Allreduce(MPI_IN_PLACE,&empty,1,MPI_INT,MPI_SUM,world); if (empty > 0) @@ -164,7 +168,7 @@ void Scafacos::init() result = fcs_tune((FCS)fcs,nlocal,&x[0][0],q); check_result((void*)&result); - // more useful here, since the parameters should be tuned now + // more useful here, since the parameters should be tuned now if (me == 0) fcs_print_parameters((FCS)fcs); } @@ -193,13 +197,8 @@ void Scafacos::compute(int eflag, int vflag) fcs_set_redistribute((FCS)fcs,0); } - if (eflag || vflag) ev_setup(eflag,vflag); - else - { - eflag_atom = 0; - vflag_global = 0; - } - + ev_init(eflag,vflag); + // grow xpbc, epot, efield if necessary if (nlocal > maxatom || maxatom == 0) { @@ -212,11 +211,15 @@ void Scafacos::compute(int eflag, int vflag) memory->create(efield,maxatom,3,"scafacos:efield"); } - if (vflag_global) - { - fcs_set_compute_virial((FCS)fcs,1); - //if (strcmp(method,"p3m") == 0) - // error->all(FLERR,"ScaFaCoS p3m does not support computation of virial"); + if (vflag_global) { + + // for P3M or Ewald we cannot compute the virial. skip it. + + if ((strcmp(method,"p3m") != 0) + && (strcmp(method,"ewald") != 0)) { + result = fcs_set_compute_virial((FCS)fcs,1); + check_result((void*)&result); + } } // pack coords into xpbc and apply PBC @@ -230,6 +233,7 @@ void Scafacos::compute(int eflag, int vflag) j += 3; } } + // if simulation box has changed, call fcs_tune() if (box_has_changed()) { @@ -245,15 +249,22 @@ void Scafacos::compute(int eflag, int vflag) // extract virial - if (vflag_global) - { - fcs_get_virial((FCS)fcs,virial_int); - virial[0] = virial_int[0]; - virial[1] = virial_int[1]; - virial[2] = virial_int[2]; - virial[3] = virial_int[4]; - virial[4] = virial_int[5]; - virial[5] = virial_int[8]; + if (vflag_global) { + + // for P3M or Ewald we cannot compute the virial. skip it. + + if ((strcmp(method,"p3m") != 0) + && (strcmp(method,"ewald") != 0)) { + result = fcs_get_virial((FCS)fcs,virial_int); + check_result((void*)&result); + + virial[0] = virial_int[0]; + virial[1] = virial_int[1]; + virial[2] = virial_int[2]; + virial[3] = virial_int[4]; + virial[4] = virial_int[5]; + virial[5] = virial_int[8]; + } } // apply Efield to each particle @@ -270,7 +281,7 @@ void Scafacos::compute(int eflag, int vflag) f[i][1] += qone * efield[i][1]; f[i][2] += qone * efield[i][2]; myeng += 0.5 * qone * epot[i]; - } + } if (eflag_atom) { for (int i = 0; i < nlocal; i++) @@ -296,50 +307,50 @@ int Scafacos::modify_param(int narg, char **arg) if (narg < 3) error->all(FLERR, "Illegal kspace_modify command (tolerance)"); if (strcmp(arg[2],"energy") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY; else if (strcmp(arg[2],"energy_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; + tolerance_type = FCS_TOLERANCE_TYPE_ENERGY_REL; else if (strcmp(arg[2],"field") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD; + tolerance_type = FCS_TOLERANCE_TYPE_FIELD; else if (strcmp(arg[2],"field_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; + tolerance_type = FCS_TOLERANCE_TYPE_FIELD_REL; else if (strcmp(arg[2],"potential") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL; else if (strcmp(arg[2],"potential_rel") == 0) - tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; + tolerance_type = FCS_TOLERANCE_TYPE_POTENTIAL_REL; else error->all(FLERR, "Illegal kspace_modify command (tolerance argument)"); // check if method is compatatible to chosen tolerance type if( ( - strcmp(method,"fmm") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && + strcmp(method,"fmm") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_ENERGY && tolerance_type != FCS_TOLERANCE_TYPE_ENERGY_REL - ) - ) || - ( - strcmp(method,"p2nfft") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_FIELD && - tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL - ) - ) || - ( - strcmp(method,"p3m") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_FIELD - ) - ) || - ( - strcmp(method,"ewald") == 0 && - ( - tolerance_type != FCS_TOLERANCE_TYPE_FIELD ) - ) + ) || + ( + strcmp(method,"p2nfft") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD && + tolerance_type != FCS_TOLERANCE_TYPE_POTENTIAL + ) + ) || + ( + strcmp(method,"p3m") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD + ) + ) || + ( + strcmp(method,"ewald") == 0 && + ( + tolerance_type != FCS_TOLERANCE_TYPE_FIELD + ) + ) ) error->all(FLERR,"Illegal kspace_modify command \ - (invalid tolerance / method combination)"); + (invalid tolerance / method combination)"); return 3; } @@ -375,7 +386,7 @@ double Scafacos::memory_usage() } /* ---------------------------------------------------------------------- - setup of ScaFaCoS handle with common parameters + setup of ScaFaCoS handle with common parameters ------------------------------------------------------------------------- */ void Scafacos::setup_handle() @@ -443,7 +454,7 @@ bool Scafacos::box_has_changed() int *periodicity = domain->periodicity; double *prd = domain->prd; - bool changed = + bool changed = (periodicity[0] != old_periodicity[0]) || (periodicity[1] != old_periodicity[1]) || (periodicity[2] != old_periodicity[2]) || @@ -462,14 +473,14 @@ bool Scafacos::box_has_changed() check ScaFaCoS result for error condition ------------------------------------------------------------------------- */ -void Scafacos::check_result(void* result_p) +void Scafacos::check_result(void* result_p) { FCSResult result = *(FCSResult*)result_p; if (!result) return; std::stringstream ss; - ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n" + ss << "ScaFaCoS: " << fcs_result_get_function(result) << "\n" << fcs_result_get_message(result) << "\n"; fcs_result_destroy(result); std::string err_msg = ss.str(); @@ -477,4 +488,4 @@ void Scafacos::check_result(void* result_p) error->one(FLERR,str); } - + diff --git a/src/USER-SDPD/Install.sh b/src/USER-SDPD/Install.sh new file mode 100644 index 0000000000..cc4af1c038 --- /dev/null +++ b/src/USER-SDPD/Install.sh @@ -0,0 +1,37 @@ +# Install/Uninstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# package files without dependencies +action pair_sdpd_taitwater_isothermal.h +action pair_sdpd_taitwater_isothermal.cpp +action fix_meso_move.h +action fix_meso_move.cpp + +# package files with dependencies +action fix_rigid_meso.h fix_rigid.h +action fix_rigid_meso.cpp fix_rigid.h diff --git a/src/USER-SDPD/README b/src/USER-SDPD/README new file mode 100644 index 0000000000..88ece7ddbf --- /dev/null +++ b/src/USER-SDPD/README @@ -0,0 +1,13 @@ +This package implements the Smoothed Dissipative Particle Dynamics (SDPD) +method for modelling fluids at mesoscale and diffusion of colloids. +Currently it adds pair style sdpd/taitwater/isothermal for modelling water +at isothermal conditions using the Tait equation of state. +It also adds fix meso/move command to move mesoscopic SPH/SDPD particles with +prescribed velocity and fix rigid/meso command to integrate rigid bodies +composed of mesoscopic SPH/SDPD particles. + +Creator of this package is: + +Morteza Jalalvand +Institute for Advanced Studies in Basic Sciences +jalalvand.m AT gmail DOT com diff --git a/src/USER-SDPD/fix_meso_move.cpp b/src/USER-SDPD/fix_meso_move.cpp new file mode 100644 index 0000000000..85b08a2af7 --- /dev/null +++ b/src/USER-SDPD/fix_meso_move.cpp @@ -0,0 +1,997 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: + Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com +------------------------------------------------------------------------- */ + +#include +#include +#include "fix_meso_move.h" +#include "atom.h" +#include "group.h" +#include "update.h" +#include "modify.h" +#include "force.h" +#include "domain.h" +#include "lattice.h" +#include "comm.h" +#include "input.h" +#include "variable.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +enum{LINEAR,WIGGLE,ROTATE,VARIABLE}; +enum{EQUAL,ATOM}; + +/* ---------------------------------------------------------------------- */ + +FixMesoMove::FixMesoMove (LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + xvarstr(NULL), yvarstr(NULL), zvarstr(NULL), + vxvarstr(NULL), vyvarstr(NULL), vzvarstr(NULL), + xoriginal(NULL), displace(NULL), velocity(NULL) { + if ((atom->e_flag != 1) || (atom->rho_flag != 1)) + error->all(FLERR, + "fix meso/move command requires atom_style with both energy and density"); + + if (narg < 4) error->all(FLERR,"Illegal fix meso/move command"); + + restart_global = 1; + restart_peratom = 1; + peratom_flag = 1; + size_peratom_cols = 3; + peratom_freq = 1; + time_integrate = 1; + create_attribute = 1; + displaceflag = 0; + velocityflag = 0; + maxatom = 0; + + // parse args + + int iarg; + + if (strcmp(arg[3],"linear") == 0) { + if (narg < 7) error->all(FLERR,"Illegal fix meso/move command"); + iarg = 7; + mstyle = LINEAR; + if (strcmp(arg[4],"NULL") == 0) vxflag = 0; + else { + vxflag = 1; + vx = force->numeric(FLERR,arg[4]); + } + if (strcmp(arg[5],"NULL") == 0) vyflag = 0; + else { + vyflag = 1; + vy = force->numeric(FLERR,arg[5]); + } + if (strcmp(arg[6],"NULL") == 0) vzflag = 0; + else { + vzflag = 1; + vz = force->numeric(FLERR,arg[6]); + } + + } else if (strcmp(arg[3],"wiggle") == 0) { + if (narg < 8) error->all(FLERR,"Illegal fix meso/move command"); + iarg = 8; + mstyle = WIGGLE; + if (strcmp(arg[4],"NULL") == 0) axflag = 0; + else { + axflag = 1; + ax = force->numeric(FLERR,arg[4]); + } + if (strcmp(arg[5],"NULL") == 0) ayflag = 0; + else { + ayflag = 1; + ay = force->numeric(FLERR,arg[5]); + } + if (strcmp(arg[6],"NULL") == 0) azflag = 0; + else { + azflag = 1; + az = force->numeric(FLERR,arg[6]); + } + period = force->numeric(FLERR,arg[7]); + if (period <= 0.0) error->all(FLERR,"Illegal fix meso/move command"); + + } else if (strcmp(arg[3],"rotate") == 0) { + if (narg < 11) error->all(FLERR,"Illegal fix meso/move command"); + iarg = 11; + mstyle = ROTATE; + point[0] = force->numeric(FLERR,arg[4]); + point[1] = force->numeric(FLERR,arg[5]); + point[2] = force->numeric(FLERR,arg[6]); + axis[0] = force->numeric(FLERR,arg[7]); + axis[1] = force->numeric(FLERR,arg[8]); + axis[2] = force->numeric(FLERR,arg[9]); + period = force->numeric(FLERR,arg[10]); + if (period <= 0.0) error->all(FLERR,"Illegal fix meso/move command"); + + } else if (strcmp(arg[3],"variable") == 0) { + if (narg < 10) error->all(FLERR,"Illegal fix meso/move command"); + iarg = 10; + mstyle = VARIABLE; + if (strcmp(arg[4],"NULL") == 0) xvarstr = NULL; + else if (strstr(arg[4],"v_") == arg[4]) { + int n = strlen(&arg[4][2]) + 1; + xvarstr = new char[n]; + strcpy(xvarstr,&arg[4][2]); + } else error->all(FLERR,"Illegal fix meso/move command"); + if (strcmp(arg[5],"NULL") == 0) yvarstr = NULL; + else if (strstr(arg[5],"v_") == arg[5]) { + int n = strlen(&arg[5][2]) + 1; + yvarstr = new char[n]; + strcpy(yvarstr,&arg[5][2]); + } else error->all(FLERR,"Illegal fix meso/move command"); + if (strcmp(arg[6],"NULL") == 0) zvarstr = NULL; + else if (strstr(arg[6],"v_") == arg[6]) { + int n = strlen(&arg[6][2]) + 1; + zvarstr = new char[n]; + strcpy(zvarstr,&arg[6][2]); + } else error->all(FLERR,"Illegal fix meso/move command"); + if (strcmp(arg[7],"NULL") == 0) vxvarstr = NULL; + else if (strstr(arg[7],"v_") == arg[7]) { + int n = strlen(&arg[7][2]) + 1; + vxvarstr = new char[n]; + strcpy(vxvarstr,&arg[7][2]); + } else error->all(FLERR,"Illegal fix meso/move command"); + if (strcmp(arg[8],"NULL") == 0) vyvarstr = NULL; + else if (strstr(arg[8],"v_") == arg[8]) { + int n = strlen(&arg[8][2]) + 1; + vyvarstr = new char[n]; + strcpy(vyvarstr,&arg[8][2]); + } else error->all(FLERR,"Illegal fix meso/move command"); + if (strcmp(arg[9],"NULL") == 0) vzvarstr = NULL; + else if (strstr(arg[9],"v_") == arg[9]) { + int n = strlen(&arg[9][2]) + 1; + vzvarstr = new char[n]; + strcpy(vzvarstr,&arg[9][2]); + } else error->all(FLERR,"Illegal fix meso/move command"); + + } else error->all(FLERR,"Illegal fix meso/move command"); + + // optional args + + int scaleflag = 1; + + while (iarg < narg) { + if (strcmp(arg[iarg],"units") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix meso/move command"); + if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0; + else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1; + else error->all(FLERR,"Illegal fix meso/move command"); + iarg += 2; + } else error->all(FLERR,"Illegal fix meso/move command"); + } + + // error checks and warnings + + if (domain->dimension == 2) { + if (mstyle == LINEAR && vzflag && vz != 0.0) + error->all(FLERR,"Fix meso/move cannot set linear z motion for 2d problem"); + if (mstyle == WIGGLE && azflag && az != 0.0) + error->all(FLERR,"Fix meso/move cannot set wiggle z motion for 2d problem"); + if (mstyle == ROTATE && (axis[0] != 0.0 || axis[1] != 0.0)) + error->all(FLERR, "Fix meso/move cannot rotate aroung non z-axis for 2d problem"); + if (mstyle == VARIABLE && (zvarstr || vzvarstr)) + error->all(FLERR, "Fix meso/move cannot define z or vz variable for 2d problem"); + } + + // setup scaling and apply scaling factors to velocity & amplitude + + if ((mstyle == LINEAR || mstyle == WIGGLE || mstyle == ROTATE) && + scaleflag) { + double xscale = domain->lattice->xlattice; + double yscale = domain->lattice->ylattice; + double zscale = domain->lattice->zlattice; + + if (mstyle == LINEAR) { + if (vxflag) vx *= xscale; + if (vyflag) vy *= yscale; + if (vzflag) vz *= zscale; + } else if (mstyle == WIGGLE) { + if (axflag) ax *= xscale; + if (ayflag) ay *= yscale; + if (azflag) az *= zscale; + } else if (mstyle == ROTATE) { + point[0] *= xscale; + point[1] *= yscale; + point[2] *= zscale; + } + } + + // set omega_rotate from period + + if (mstyle == WIGGLE || mstyle == ROTATE) omega_rotate = MY_2PI / period; + + // runit = unit vector along rotation axis + + if (mstyle == ROTATE) { + double len = sqrt(axis[0]*axis[0] + axis[1]*axis[1] + axis[2]*axis[2]); + if (len == 0.0) + error->all(FLERR,"Zero length rotation vector with fix meso/move"); + runit[0] = axis[0]/len; + runit[1] = axis[1]/len; + runit[2] = axis[2]/len; + } + + // perform initial allocation of atom-based array + // register with Atom class + + grow_arrays(atom->nmax); + atom->add_callback(0); + atom->add_callback(1); + + displace = velocity = NULL; + + // xoriginal = initial unwrapped positions of atoms + + double **x = atom->x; + imageint *image = atom->image; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]); + else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0; + } + + time_origin = update->ntimestep; +} + +/* ---------------------------------------------------------------------- */ + +FixMesoMove::~FixMesoMove () { + // unregister callbacks to this fix from Atom class + + atom->delete_callback(id,0); + atom->delete_callback(id,1); + + // delete locally stored arrays + + memory->destroy(xoriginal); + memory->destroy(displace); + memory->destroy(velocity); + + delete [] xvarstr; + delete [] yvarstr; + delete [] zvarstr; + delete [] vxvarstr; + delete [] vyvarstr; + delete [] vzvarstr; +} + +/* ---------------------------------------------------------------------- */ + +int FixMesoMove::setmask () { + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= PRE_FORCE; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixMesoMove::init () { + dt = update->dt; + dtv = update->dt; + dtf = 0.5 * update->dt * force->ftm2v; + + // set indices and style of all variables + + displaceflag = velocityflag = 0; + + if (mstyle == VARIABLE) { + if (xvarstr) { + xvar = input->variable->find(xvarstr); + if (xvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist"); + if (input->variable->equalstyle(xvar)) xvarstyle = EQUAL; + else if (input->variable->atomstyle(xvar)) xvarstyle = ATOM; + else error->all(FLERR,"Variable for fix meso/move is invalid style"); + } + if (yvarstr) { + yvar = input->variable->find(yvarstr); + if (yvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist"); + if (input->variable->equalstyle(yvar)) yvarstyle = EQUAL; + else if (input->variable->atomstyle(yvar)) yvarstyle = ATOM; + else error->all(FLERR,"Variable for fix meso/move is invalid style"); + } + if (zvarstr) { + zvar = input->variable->find(zvarstr); + if (zvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist"); + if (input->variable->equalstyle(zvar)) zvarstyle = EQUAL; + else if (input->variable->atomstyle(zvar)) zvarstyle = ATOM; + else error->all(FLERR,"Variable for fix meso/move is invalid style"); + } + if (vxvarstr) { + vxvar = input->variable->find(vxvarstr); + if (vxvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist"); + if (input->variable->equalstyle(vxvar)) vxvarstyle = EQUAL; + else if (input->variable->atomstyle(vxvar)) vxvarstyle = ATOM; + else error->all(FLERR,"Variable for fix meso/move is invalid style"); + } + if (vyvarstr) { + vyvar = input->variable->find(vyvarstr); + if (vyvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist"); + if (input->variable->equalstyle(vyvar)) vyvarstyle = EQUAL; + else if (input->variable->atomstyle(vyvar)) vyvarstyle = ATOM; + else error->all(FLERR,"Variable for fix meso/move is invalid style"); + } + if (vzvarstr) { + vzvar = input->variable->find(vzvarstr); + if (vzvar < 0) error->all(FLERR, "Variable name for fix meso/move does not exist"); + if (input->variable->equalstyle(vzvar)) vzvarstyle = EQUAL; + else if (input->variable->atomstyle(vzvar)) vzvarstyle = ATOM; + else error->all(FLERR,"Variable for fix meso/move is invalid style"); + } + + if (xvarstr && xvarstyle == ATOM) displaceflag = 1; + if (yvarstr && yvarstyle == ATOM) displaceflag = 1; + if (zvarstr && zvarstyle == ATOM) displaceflag = 1; + if (vxvarstr && vxvarstyle == ATOM) velocityflag = 1; + if (vyvarstr && vyvarstyle == ATOM) velocityflag = 1; + if (vzvarstr && vzvarstyle == ATOM) velocityflag = 1; + } + + maxatom = atom->nmax; + memory->destroy(displace); + memory->destroy(velocity); + if (displaceflag) memory->create(displace,maxatom,3,"move:displace"); + else displace = NULL; + if (velocityflag) memory->create(velocity,maxatom,3,"move:velocity"); + else velocity = NULL; +} + +void FixMesoMove::setup_pre_force (int /*vflag*/) { + // set vest equal to v + double **v = atom->v; + double **vest = atom->vest; + int *mask = atom->mask; + int nlocal = atom->nlocal; + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + vest[i][0] = v[i][0]; + vest[i][1] = v[i][1]; + vest[i][2] = v[i][2]; + } + } +} + +/* ---------------------------------------------------------------------- + set x,v of particles +------------------------------------------------------------------------- */ + +void FixMesoMove::initial_integrate (int /*vflag*/) { + double ddotr,dx,dy,dz; + double dtfm; + double xold[3],a[3],b[3],c[3],d[3],disp[3],disp_next[3]; + + double delta = (update->ntimestep - time_origin) * dt; + double delta_next = (update->ntimestep - time_origin + 1) * dt; + + double **x = atom->x; + double **v = atom->v; + double **vest = atom->vest; + double *rho = atom->rho; + double *drho = atom->drho; + double *e = atom->e; + double *de = atom->de; + double **f = atom->f; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int rmass_flag = atom->rmass_flag; + + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + + // for linear: X = X0 + V*dt + + if (mstyle == LINEAR) { + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + xold[0] = x[i][0]; + xold[1] = x[i][1]; + xold[2] = x[i][2]; + + e[i] += dtf * de[i]; // half-step update of particle internal energy + rho[i] += dtf * drho[i]; // ... and density + + if (vxflag) { + vest[i][0] = v[i][0] = vx; + x[i][0] = xoriginal[i][0] + vx*delta; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0]; + v[i][0] += dtfm * f[i][0]; + x[i][0] += dtv * v[i][0]; + } + + if (vyflag) { + vest[i][1] = v[i][1] = vy; + x[i][1] = xoriginal[i][1] + vy*delta; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1]; + v[i][1] += dtfm * f[i][1]; + x[i][1] += dtv * v[i][1]; + } + + if (vzflag) { + vest[i][2] = v[i][2] = vz; + x[i][2] = xoriginal[i][2] + vz*delta; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2]; + v[i][2] += dtfm * f[i][2]; + x[i][2] += dtv * v[i][2]; + } + + domain->remap_near(x[i],xold); + } + } + + // for wiggle: X = X0 + A sin(w*dt) + + } else if (mstyle == WIGGLE) { + double arg = omega_rotate * delta; + double arg_next = omega_rotate * delta_next; + double sine = sin(arg); + double cosine = cos(arg); + double cosine_next = cos(arg_next); + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + xold[0] = x[i][0]; + xold[1] = x[i][1]; + xold[2] = x[i][2]; + + e[i] += dtf * de[i]; // half-step update of particle internal energy + rho[i] += dtf * drho[i]; // ... and density + + if (axflag) { + v[i][0] = ax*omega_rotate*cosine; + vest[i][0] = ax*omega_rotate*cosine_next; + x[i][0] = xoriginal[i][0] + ax*sine; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0]; + v[i][0] += dtfm * f[i][0]; + x[i][0] += dtv * v[i][0]; + } + + if (ayflag) { + v[i][1] = ay*omega_rotate*cosine; + vest[i][1] = ay*omega_rotate*cosine_next; + x[i][1] = xoriginal[i][1] + ay*sine; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1]; + v[i][1] += dtfm * f[i][1]; + x[i][1] += dtv * v[i][1]; + } + + if (azflag) { + v[i][2] = az*omega_rotate*cosine; + vest[i][2] = az*omega_rotate*cosine_next; + x[i][2] = xoriginal[i][2] + az*sine; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2]; + v[i][2] += dtfm * f[i][2]; + x[i][2] += dtv * v[i][2]; + } + + domain->remap_near(x[i],xold); + } + } + + // for rotate by right-hand rule around omega: + // P = point = vector = point of rotation + // R = vector = axis of rotation + // w = omega of rotation (from period) + // X0 = xoriginal = initial coord of atom + // R0 = runit = unit vector for R + // D = X0 - P = vector from P to X0 + // C = (D dot R0) R0 = projection of atom coord onto R line + // A = D - C = vector from R line to X0 + // B = R0 cross A = vector perp to A in plane of rotation + // A,B define plane of circular rotation around R line + // X = P + C + A cos(w*dt) + B sin(w*dt) + // V = w R0 cross (A cos(w*dt) + B sin(w*dt)) + + } else if (mstyle == ROTATE) { + double arg = omega_rotate * delta; + double arg_next = omega_rotate * delta_next; + double sine = sin(arg); + double cosine = cos(arg); + double sine_next = sin(arg_next); + double cosine_next = cos(arg_next); + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + xold[0] = x[i][0]; + xold[1] = x[i][1]; + xold[2] = x[i][2]; + + e[i] += dtf * de[i]; // half-step update of particle internal energy + rho[i] += dtf * drho[i]; // ... and density + + d[0] = xoriginal[i][0] - point[0]; + d[1] = xoriginal[i][1] - point[1]; + d[2] = xoriginal[i][2] - point[2]; + ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2]; + c[0] = ddotr*runit[0]; + c[1] = ddotr*runit[1]; + c[2] = ddotr*runit[2]; + a[0] = d[0] - c[0]; + a[1] = d[1] - c[1]; + a[2] = d[2] - c[2]; + b[0] = runit[1]*a[2] - runit[2]*a[1]; + b[1] = runit[2]*a[0] - runit[0]*a[2]; + b[2] = runit[0]*a[1] - runit[1]*a[0]; + disp[0] = a[0]*cosine + b[0]*sine; + disp[1] = a[1]*cosine + b[1]*sine; + disp[2] = a[2]*cosine + b[2]*sine; + disp_next[0] = a[0]*cosine_next + b[0]*sine_next; + disp_next[1] = a[1]*cosine_next + b[1]*sine_next; + disp_next[2] = a[2]*cosine_next + b[2]*sine_next; + + x[i][0] = point[0] + c[0] + disp[0]; + x[i][1] = point[1] + c[1] + disp[1]; + x[i][2] = point[2] + c[2] + disp[2]; + v[i][0] = omega_rotate * (runit[1]*disp[2] - runit[2]*disp[1]); + v[i][1] = omega_rotate * (runit[2]*disp[0] - runit[0]*disp[2]); + v[i][2] = omega_rotate * (runit[0]*disp[1] - runit[1]*disp[0]); + vest[i][0] = omega_rotate * (runit[1]*disp_next[2] - runit[2]*disp_next[1]); + vest[i][1] = omega_rotate * (runit[2]*disp_next[0] - runit[0]*disp_next[2]); + vest[i][2] = omega_rotate * (runit[0]*disp_next[1] - runit[1]*disp_next[0]); + + domain->remap_near(x[i],xold); + } + } + + // for variable: compute x,v from variables + + } else if (mstyle == VARIABLE) { + + // reallocate displace and velocity arrays as necessary + + if ((displaceflag || velocityflag) && atom->nmax > maxatom) { + maxatom = atom->nmax; + if (displaceflag) { + memory->destroy(displace); + memory->create(displace,maxatom,3,"move:displace"); + } + if (velocityflag) { + memory->destroy(velocity); + memory->create(velocity,maxatom,3,"move:velocity"); + } + } + + // pre-compute variable values, wrap with clear/add + + modify->clearstep_compute(); + + if (xvarstr) { + if (xvarstyle == EQUAL) dx = input->variable->compute_equal(xvar); + else input->variable->compute_atom(xvar,igroup,&displace[0][0],3,0); + } + if (yvarstr) { + if (yvarstyle == EQUAL) dy = input->variable->compute_equal(yvar); + else input->variable->compute_atom(yvar,igroup,&displace[0][1],3,0); + } + if (zvarstr) { + if (zvarstyle == EQUAL) dz = input->variable->compute_equal(zvar); + else input->variable->compute_atom(zvar,igroup,&displace[0][2],3,0); + } + if (vxvarstr) { + if (vxvarstyle == EQUAL) vx = input->variable->compute_equal(vxvar); + else input->variable->compute_atom(vxvar,igroup,&velocity[0][0],3,0); + } + if (vyvarstr) { + if (vyvarstyle == EQUAL) vy = input->variable->compute_equal(vyvar); + else input->variable->compute_atom(vyvar,igroup,&velocity[0][1],3,0); + } + if (vzvarstr) { + if (vzvarstyle == EQUAL) vz = input->variable->compute_equal(vzvar); + else input->variable->compute_atom(vzvar,igroup,&velocity[0][2],3,0); + } + + modify->addstep_compute(update->ntimestep + 1); + + // update x,v + // vest (velocity in next step) could be different from v in the next + // step, but this is the best we could do + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + xold[0] = x[i][0]; + xold[1] = x[i][1]; + xold[2] = x[i][2]; + + if (xvarstr && vxvarstr) { + if (vxvarstyle == EQUAL) { + vest[i][0] = 2*vx - v[i][0]; + v[i][0] = vx; + } + else { + vest[i][0] = 2*velocity[i][0] - v[i][0]; + v[i][0] = velocity[i][0]; + } + if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx; + else x[i][0] = xoriginal[i][0] + displace[i][0]; + } else if (xvarstr) { + if (xvarstyle == EQUAL) x[i][0] = xoriginal[i][0] + dx; + else x[i][0] = xoriginal[i][0] + displace[i][0]; + } else if (vxvarstr) { + if (vxvarstyle == EQUAL) { + vest[i][0] = 2*vx - v[i][0]; + v[i][0] = vx; + } + else { + vest[i][0] = 2*velocity[i][0] - v[i][0]; + v[i][0] = velocity[i][0]; + } + x[i][0] += dtv * v[i][0]; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0]; + v[i][0] += dtfm * f[i][0]; + x[i][0] += dtv * v[i][0]; + } + + if (yvarstr && vyvarstr) { + if (vyvarstyle == EQUAL) { + vest[i][1] = 2*vy - v[i][1]; + v[i][1] = vy; + } + else { + vest[i][1] = 2*velocity[i][1] - v[i][1]; + v[i][1] = velocity[i][1]; + } + if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy; + else x[i][1] = xoriginal[i][1] + displace[i][1]; + } else if (yvarstr) { + if (yvarstyle == EQUAL) x[i][1] = xoriginal[i][1] + dy; + else x[i][1] = xoriginal[i][1] + displace[i][1]; + } else if (vyvarstr) { + if (vyvarstyle == EQUAL) { + vest[i][1] = 2*vy - v[i][1]; + v[i][1] = vy; + } + else { + vest[i][1] = 2*velocity[i][1] - v[i][1]; + v[i][1] = velocity[i][1]; + } + x[i][1] += dtv * v[i][1]; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1]; + v[i][1] += dtfm * f[i][1]; + x[i][1] += dtv * v[i][1]; + } + + if (zvarstr && vzvarstr) { + if (vzvarstyle == EQUAL) { + vest[i][2] = 2*vz - v[i][2]; + v[i][2] = vz; + } + else { + vest[i][2] = 2*velocity[i][2] - v[i][2]; + v[i][2] = velocity[i][2]; + } + if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz; + else x[i][2] = xoriginal[i][2] + displace[i][2]; + } else if (zvarstr) { + if (zvarstyle == EQUAL) x[i][2] = xoriginal[i][2] + dz; + else x[i][2] = xoriginal[i][2] + displace[i][2]; + } else if (vzvarstr) { + if (vzvarstyle == EQUAL) { + vest[i][2] = 2*vz - v[i][2]; + v[i][2] = vz; + } + else { + vest[i][2] = 2*velocity[i][2] - v[i][2]; + v[i][2] = velocity[i][2]; + } + x[i][2] += dtv * v[i][2]; + } else { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2]; + v[i][2] += dtfm * f[i][2]; + x[i][2] += dtv * v[i][2]; + } + + domain->remap_near(x[i],xold); + } + } + } +} + +/* ---------------------------------------------------------------------- + final NVE of particles with NULL components +------------------------------------------------------------------------- */ + +void FixMesoMove::final_integrate () { + double dtfm; + + int xflag = 1; + if (mstyle == LINEAR && vxflag) xflag = 0; + else if (mstyle == WIGGLE && axflag) xflag = 0; + else if (mstyle == ROTATE) xflag = 0; + else if (mstyle == VARIABLE && (xvarstr || vxvarstr)) xflag = 0; + + int yflag = 1; + if (mstyle == LINEAR && vyflag) yflag = 0; + else if (mstyle == WIGGLE && ayflag) yflag = 0; + else if (mstyle == ROTATE) yflag = 0; + else if (mstyle == VARIABLE && (yvarstr || vyvarstr)) yflag = 0; + + int zflag = 1; + if (mstyle == LINEAR && vzflag) zflag = 0; + else if (mstyle == WIGGLE && azflag) zflag = 0; + else if (mstyle == ROTATE) zflag = 0; + else if (mstyle == VARIABLE && (zvarstr || vzvarstr)) zflag = 0; + + double **v = atom->v; + double **f = atom->f; + double *e = atom->e; + double *de = atom->de; + double *rho = atom->rho; + double *drho = atom->drho; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int *mask = atom->mask; + int nlocal = atom->nlocal; + int rmass_flag = atom->rmass_flag; + + if (igroup == atom->firstgroup) + nlocal = atom->nfirst; + + for (int i = 0; i < nlocal; i++) { + if (mask[i] & groupbit) { + e[i] += dtf * de[i]; + rho[i] += dtf * drho[i]; + + if (xflag) { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + v[i][0] += dtfm * f[i][0]; + } + + if (yflag) { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + v[i][1] += dtfm * f[i][1]; + } + + if (zflag) { + dtfm = rmass_flag ? dtf / rmass[i] : dtf / mass[type[i]]; + v[i][2] += dtfm * f[i][2]; + } + } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based array +------------------------------------------------------------------------- */ + +double FixMesoMove::memory_usage () { + double bytes = atom->nmax*3 * sizeof(double); + if (displaceflag) bytes += atom->nmax*3 * sizeof(double); + if (velocityflag) bytes += atom->nmax*3 * sizeof(double); + return bytes; +} + +/* ---------------------------------------------------------------------- + pack entire state of Fix into one write +------------------------------------------------------------------------- */ + +void FixMesoMove::write_restart (FILE *fp) { + int n = 0; + double list[1]; + list[n++] = time_origin; + + if (comm->me == 0) { + int size = n * sizeof(double); + fwrite(&size,sizeof(int),1,fp); + fwrite(list,sizeof(double),n,fp); + } +} + +/* ---------------------------------------------------------------------- + use state info from restart file to restart the Fix +------------------------------------------------------------------------- */ + +void FixMesoMove::restart (char *buf) { + int n = 0; + double *list = (double *) buf; + + time_origin = static_cast (list[n++]); +} + +/* ---------------------------------------------------------------------- + allocate atom-based array +------------------------------------------------------------------------- */ + +void FixMesoMove::grow_arrays (int nmax) { + memory->grow(xoriginal,nmax,3,"move:xoriginal"); + array_atom = xoriginal; +} + +/* ---------------------------------------------------------------------- + copy values within local atom-based array +------------------------------------------------------------------------- */ + +void FixMesoMove::copy_arrays (int i, int j, int /*delflag*/) { + xoriginal[j][0] = xoriginal[i][0]; + xoriginal[j][1] = xoriginal[i][1]; + xoriginal[j][2] = xoriginal[i][2]; +} + +/* ---------------------------------------------------------------------- + initialize one atom's array values, called when atom is created +------------------------------------------------------------------------- */ + +void FixMesoMove::set_arrays (int i) { + double **x = atom->x; + imageint *image = atom->image; + int *mask = atom->mask; + + // particle not in group + + if (!(mask[i] & groupbit)) { + xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0; + return; + } + + // current time still equal fix creation time + + if (update->ntimestep == time_origin) { + domain->unmap(x[i],image[i],xoriginal[i]); + return; + } + + // backup particle to time_origin + + if (mstyle == VARIABLE) + error->all(FLERR,"Cannot add atoms to fix meso/move variable"); + + domain->unmap(x[i],image[i],xoriginal[i]); + double delta = (update->ntimestep - time_origin) * update->dt; + + if (mstyle == LINEAR) { + if (vxflag) xoriginal[i][0] -= vx * delta; + if (vyflag) xoriginal[i][1] -= vy * delta; + if (vzflag) xoriginal[i][2] -= vz * delta; + } else if (mstyle == WIGGLE) { + double arg = omega_rotate * delta; + double sine = sin(arg); + if (axflag) xoriginal[i][0] -= ax*sine; + if (ayflag) xoriginal[i][1] -= ay*sine; + if (azflag) xoriginal[i][2] -= az*sine; + } else if (mstyle == ROTATE) { + double a[3],b[3],c[3],d[3],disp[3],ddotr; + double arg = - omega_rotate * delta; + double sine = sin(arg); + double cosine = cos(arg); + d[0] = x[i][0] - point[0]; + d[1] = x[i][1] - point[1]; + d[2] = x[i][2] - point[2]; + ddotr = d[0]*runit[0] + d[1]*runit[1] + d[2]*runit[2]; + c[0] = ddotr*runit[0]; + c[1] = ddotr*runit[1]; + c[2] = ddotr*runit[2]; + + a[0] = d[0] - c[0]; + a[1] = d[1] - c[1]; + a[2] = d[2] - c[2]; + b[0] = runit[1]*a[2] - runit[2]*a[1]; + b[1] = runit[2]*a[0] - runit[0]*a[2]; + b[2] = runit[0]*a[1] - runit[1]*a[0]; + disp[0] = a[0]*cosine + b[0]*sine; + disp[1] = a[1]*cosine + b[1]*sine; + disp[2] = a[2]*cosine + b[2]*sine; + + xoriginal[i][0] = point[0] + c[0] + disp[0]; + xoriginal[i][1] = point[1] + c[1] + disp[1]; + xoriginal[i][2] = point[2] + c[2] + disp[2]; + } +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based array for exchange with another proc +------------------------------------------------------------------------- */ + +int FixMesoMove::pack_exchange (int i, double *buf) { + buf[0] = xoriginal[i][0]; + buf[1] = xoriginal[i][1]; + buf[2] = xoriginal[i][2]; + return 3; +} + +/* ---------------------------------------------------------------------- + unpack values in local atom-based array from exchange with another proc +------------------------------------------------------------------------- */ + +int FixMesoMove::unpack_exchange (int nlocal, double *buf) { + xoriginal[nlocal][0] = buf[0]; + xoriginal[nlocal][1] = buf[1]; + xoriginal[nlocal][2] = buf[2]; + return 3; +} + +/* ---------------------------------------------------------------------- + pack values in local atom-based arrays for restart file +------------------------------------------------------------------------- */ + +int FixMesoMove::pack_restart (int i, double *buf) { + buf[0] = 4; + buf[1] = xoriginal[i][0]; + buf[2] = xoriginal[i][1]; + buf[3] = xoriginal[i][2]; + return 4; +} + +/* ---------------------------------------------------------------------- + unpack values from atom->extra array to restart the fix +------------------------------------------------------------------------- */ + +void FixMesoMove::unpack_restart (int nlocal, int nth) { + double **extra = atom->extra; + + // skip to Nth set of extra values + + int m = 0; + for (int i = 0; i < nth; i++) m += static_cast (extra[nlocal][m]); + m++; + + xoriginal[nlocal][0] = extra[nlocal][m++]; + xoriginal[nlocal][1] = extra[nlocal][m++]; + xoriginal[nlocal][2] = extra[nlocal][m++]; +} + +/* ---------------------------------------------------------------------- + maxsize of any atom's restart data +------------------------------------------------------------------------- */ + +int FixMesoMove::maxsize_restart () { + return 4; +} + +/* ---------------------------------------------------------------------- + size of atom nlocal's restart data +------------------------------------------------------------------------- */ + +int FixMesoMove::size_restart (int /* nlocal */) { + return 4; +} + +/* ---------------------------------------------------------------------- */ + +void FixMesoMove::reset_dt () { + error->all(FLERR,"Resetting timestep size is not allowed with fix meso/move"); +} diff --git a/src/USER-SDPD/fix_meso_move.h b/src/USER-SDPD/fix_meso_move.h new file mode 100644 index 0000000000..a5e213ba81 --- /dev/null +++ b/src/USER-SDPD/fix_meso_move.h @@ -0,0 +1,127 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(meso/move,FixMesoMove) + +#else + +#ifndef LMP_FIX_MESO_MOVE_H +#define LMP_FIX_MESO_MOVE_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixMesoMove : public Fix { + public: + FixMesoMove (class LAMMPS *, int, char **); + ~FixMesoMove (); + int setmask (); + void init (); + void setup_pre_force (int); + void initial_integrate (int); + void final_integrate (); + + double memory_usage (); + void write_restart (FILE *); + void restart (char *); + void grow_arrays (int); + void copy_arrays (int, int, int); + void set_arrays (int); + int pack_exchange (int, double *); + int unpack_exchange (int, double *); + int pack_restart (int, double *); + void unpack_restart (int, int); + int maxsize_restart (); + int size_restart (int); + + void reset_dt (); + + private: + char *xvarstr,*yvarstr,*zvarstr,*vxvarstr,*vyvarstr,*vzvarstr; + int mstyle; + int vxflag,vyflag,vzflag,axflag,ayflag,azflag; + double vx,vy,vz,ax,ay,az; + double period,omega_rotate; + double point[3],axis[3],runit[3]; + double dt,dtv,dtf; + int xvar,yvar,zvar,vxvar,vyvar,vzvar; + int xvarstyle,yvarstyle,zvarstyle,vxvarstyle,vyvarstyle,vzvarstyle; + int time_origin; + + double **xoriginal; // original coords of atoms + int displaceflag,velocityflag; + int maxatom; + double **displace,**velocity; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Fix meso/move cannot set linear z motion for 2d problem + +Self-explanatory. + +E: Fix meso/move cannot set wiggle z motion for 2d problem + +Self-explanatory. + +E: Fix meso/move cannot rotate aroung non z-axis for 2d problem + +Self-explanatory. + +E: Fix meso/move cannot define z or vz variable for 2d problem + +Self-explanatory. + +W: Fix meso/move does not update angular momentum + +Atoms store this quantity, but fix meso/move does not (yet) update it. + +W: Fix meso/move does not update quaternions + +Atoms store this quantity, but fix meso/move does not (yet) update it. + +E: Zero length rotation vector with fix meso/move + +Self-explanatory. + +E: Variable name for fix meso/move does not exist + +Self-explanatory. + +E: Variable for fix meso/move is invalid style + +Only equal-style variables can be used. + +E: Cannot add atoms to fix meso/move variable + +Atoms can not be added afterwards to this fix option. + +E: Resetting timestep size is not allowed with fix meso/move + +This is because fix meso/move is moving atoms based on elapsed time. + +*/ diff --git a/src/USER-SDPD/fix_rigid_meso.cpp b/src/USER-SDPD/fix_rigid_meso.cpp new file mode 100644 index 0000000000..49c9ca8614 --- /dev/null +++ b/src/USER-SDPD/fix_rigid_meso.cpp @@ -0,0 +1,500 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Tony Sheh (U Michigan), Trung Dac Nguyen (U Michigan) + references: Kamberaj et al., J. Chem. Phys. 122, 224114 (2005) + Miller et al., J Chem Phys. 116, 8649-8659 (2002) +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: + Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com + + This is an extension of fix/rigid/nve to SPH/SDPD particles + You can see the original copyright notice of fix/rigid authors above + Note that the Kamberaj paper was related to the nvt variant + and all codes relevant to that has been removed +------------------------------------------------------------------------- */ + +#include +#include "fix_rigid_meso.h" +#include "math_extra.h" +#include "atom.h" +#include "compute.h" +#include "domain.h" +#include "update.h" +#include "modify.h" +#include "group.h" +#include "force.h" +#include "output.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixRigidMeso::FixRigidMeso (LAMMPS *lmp, int narg, char **arg) : +FixRigid (lmp, narg, arg) { + scalar_flag = 0; + size_array_cols = 28; + if ((atom->e_flag != 1) || (atom->rho_flag != 1)) + error->all (FLERR, "fix rigid/meso command requires atom_style with" + " both energy and density"); + + if (langflag || tstat_flag) + error->all (FLERR,"Can not use thermostat with fix rigid/meso"); + + if (pstat_flag) + error->all (FLERR,"Can not use barostat with fix rigid/meso"); + + // memory allocation and initialization + + memory->create(conjqm,nbody,4,"rigid_nh:conjqm"); +} + +/* ---------------------------------------------------------------------- */ + +FixRigidMeso::~FixRigidMeso () { + memory->destroy(conjqm); +} + +/* ---------------------------------------------------------------------- */ + +int FixRigidMeso::setmask () { + int mask = 0; + mask |= INITIAL_INTEGRATE; + mask |= FINAL_INTEGRATE; + mask |= PRE_NEIGHBOR; + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixRigidMeso::setup (int vflag) { + FixRigid::setup(vflag); + + double mbody[3]; + for (int ibody = 0; ibody < nbody; ibody++) { + MathExtra::transpose_matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody], + angmom[ibody],mbody); + MathExtra::quatvec (quat[ibody],mbody,conjqm[ibody]); + conjqm[ibody][0] *= 2.0; + conjqm[ibody][1] *= 2.0; + conjqm[ibody][2] *= 2.0; + conjqm[ibody][3] *= 2.0; + } +} + +/* ---------------------------------------------------------------------- + perform preforce velocity Verlet integration + see Kamberaj paper for step references +------------------------------------------------------------------------- */ + +void FixRigidMeso::initial_integrate (int vflag) { + double dtfm,mbody[3],tbody[3],fquat[4]; + double dtf2 = dtf * 2.0; + + // update xcm, vcm, quat, conjqm and angmom + + for (int ibody = 0; ibody < nbody; ibody++) { + + // step 1.1 - update vcm by 1/2 step + + dtfm = dtf / masstotal[ibody]; + vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0]; + vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1]; + vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2]; + + // step 1.2 - update xcm by full step + + xcm[ibody][0] += dtv * vcm[ibody][0]; + xcm[ibody][1] += dtv * vcm[ibody][1]; + xcm[ibody][2] += dtv * vcm[ibody][2]; + + // step 1.3 - apply torque (body coords) to quaternion momentum + + torque[ibody][0] *= tflag[ibody][0]; + torque[ibody][1] *= tflag[ibody][1]; + torque[ibody][2] *= tflag[ibody][2]; + + MathExtra::transpose_matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody], + torque[ibody],tbody); + MathExtra::quatvec (quat[ibody],tbody,fquat); + + conjqm[ibody][0] += dtf2 * fquat[0]; + conjqm[ibody][1] += dtf2 * fquat[1]; + conjqm[ibody][2] += dtf2 * fquat[2]; + conjqm[ibody][3] += dtf2 * fquat[3]; + + // step 1.4 to 1.13 - use no_squish rotate to update p and q + + MathExtra::no_squish_rotate (3,conjqm[ibody],quat[ibody],inertia[ibody],dtq); + MathExtra::no_squish_rotate (2,conjqm[ibody],quat[ibody],inertia[ibody],dtq); + MathExtra::no_squish_rotate (1,conjqm[ibody],quat[ibody],inertia[ibody],dtv); + MathExtra::no_squish_rotate (2,conjqm[ibody],quat[ibody],inertia[ibody],dtq); + MathExtra::no_squish_rotate (3,conjqm[ibody],quat[ibody],inertia[ibody],dtq); + + // update exyz_space + // transform p back to angmom + // update angular velocity + + MathExtra::q_to_exyz (quat[ibody],ex_space[ibody],ey_space[ibody], + ez_space[ibody]); + MathExtra::invquatvec (quat[ibody],conjqm[ibody],mbody); + MathExtra::matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody], + mbody,angmom[ibody]); + + angmom[ibody][0] *= 0.5; + angmom[ibody][1] *= 0.5; + angmom[ibody][2] *= 0.5; + + MathExtra::angmom_to_omega (angmom[ibody],ex_space[ibody],ey_space[ibody], + ez_space[ibody],inertia[ibody],omega[ibody]); + } + + // virial setup before call to set_xv + + if (vflag) v_setup(vflag); + else evflag = 0; + + // set coords/orient and velocity/rotation of atoms in rigid bodies + // from quarternion and omega + + set_xv(); +} + +/* ---------------------------------------------------------------------- */ + +void FixRigidMeso::final_integrate () { + int ibody; + double dtfm; + double mbody[3],tbody[3],fquat[4]; + + double dtf2 = dtf * 2.0; + + // late calculation of forces and torques (if requested) + + if (!earlyflag) compute_forces_and_torques(); + + // update vcm and angmom + // fflag,tflag = 0 for some dimensions in 2d + + for (ibody = 0; ibody < nbody; ibody++) { + + // update vcm by 1/2 step + + dtfm = dtf / masstotal[ibody]; + + vcm[ibody][0] += dtfm * fcm[ibody][0] * fflag[ibody][0]; + vcm[ibody][1] += dtfm * fcm[ibody][1] * fflag[ibody][1]; + vcm[ibody][2] += dtfm * fcm[ibody][2] * fflag[ibody][2]; + + // update conjqm, then transform to angmom, set velocity again + // virial is already setup from initial_integrate + + torque[ibody][0] *= tflag[ibody][0]; + torque[ibody][1] *= tflag[ibody][1]; + torque[ibody][2] *= tflag[ibody][2]; + + MathExtra::transpose_matvec (ex_space[ibody],ey_space[ibody], + ez_space[ibody],torque[ibody],tbody); + MathExtra::quatvec (quat[ibody],tbody,fquat); + + conjqm[ibody][0] += dtf2 * fquat[0]; + conjqm[ibody][1] += dtf2 * fquat[1]; + conjqm[ibody][2] += dtf2 * fquat[2]; + conjqm[ibody][3] += dtf2 * fquat[3]; + + MathExtra::invquatvec (quat[ibody],conjqm[ibody],mbody); + MathExtra::matvec (ex_space[ibody],ey_space[ibody],ez_space[ibody], + mbody,angmom[ibody]); + + angmom[ibody][0] *= 0.5; + angmom[ibody][1] *= 0.5; + angmom[ibody][2] *= 0.5; + + MathExtra::angmom_to_omega (angmom[ibody],ex_space[ibody],ey_space[ibody], + ez_space[ibody],inertia[ibody],omega[ibody]); + } + + // set velocity/rotation of atoms in rigid bodies + // virial is already setup from initial_integrate + + set_v(); +} + +/* ---------------------------------------------------------------------- + set space-frame coords and velocity of each atom in each rigid body + set orientation and rotation of extended particles + x = Q displace + Xcm, mapped back to periodic box + v = Vcm + (W cross (x - Xcm)) +------------------------------------------------------------------------- */ + +void FixRigidMeso::set_xv () { + int ibody; + int xbox,ybox,zbox; + double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone; + double xy,xz,yz; + double vr[6]; + + double **x = atom->x; + double **v = atom->v; + double **vest = atom->vest; + double **f = atom->f; + double *e = atom->e; + double *de = atom->de; + double *rho = atom->rho; + double *drho = atom->drho; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int nlocal = atom->nlocal; + + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + + if (triclinic) { + xy = domain->xy; + xz = domain->xz; + yz = domain->yz; + } + + // set x and v of each atom + + for (int i = 0; i < nlocal; i++) { + if (body[i] < 0) continue; + + // half-step update of particle internal energy and density + e[i] += dtf * de[i]; + rho[i] += dtf * drho[i]; + + ibody = body[i]; + + xbox = (xcmimage[i] & IMGMASK) - IMGMAX; + ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX; + + // save old positions and velocities for virial + + if (evflag) { + if (triclinic == 0) { + x0 = x[i][0] + xbox*xprd; + x1 = x[i][1] + ybox*yprd; + x2 = x[i][2] + zbox*zprd; + } else { + x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz; + x1 = x[i][1] + ybox*yprd + zbox*yz; + x2 = x[i][2] + zbox*zprd; + } + } + + v0 = v[i][0]; + v1 = v[i][1]; + v2 = v[i][2]; + + // x = displacement from center-of-mass, based on body orientation + // v = vcm + omega around center-of-mass + // vest = 2*v - v_old + + MathExtra::matvec (ex_space[ibody],ey_space[ibody], + ez_space[ibody],displace[i],x[i]); + + v[i][0] = omega[ibody][1]*x[i][2] - omega[ibody][2]*x[i][1] + + vcm[ibody][0]; + v[i][1] = omega[ibody][2]*x[i][0] - omega[ibody][0]*x[i][2] + + vcm[ibody][1]; + v[i][2] = omega[ibody][0]*x[i][1] - omega[ibody][1]*x[i][0] + + vcm[ibody][2]; + + vest[i][0] = 2*v[i][0] - v0; + vest[i][1] = 2*v[i][1] - v1; + vest[i][2] = 2*v[i][2] - v2; + + // add center of mass to displacement + // map back into periodic box via xbox,ybox,zbox + // for triclinic, add in box tilt factors as well + + if (triclinic == 0) { + x[i][0] += xcm[ibody][0] - xbox*xprd; + x[i][1] += xcm[ibody][1] - ybox*yprd; + x[i][2] += xcm[ibody][2] - zbox*zprd; + } else { + x[i][0] += xcm[ibody][0] - xbox*xprd - ybox*xy - zbox*xz; + x[i][1] += xcm[ibody][1] - ybox*yprd - zbox*yz; + x[i][2] += xcm[ibody][2] - zbox*zprd; + } + + // virial = unwrapped coords dotted into body constraint force + // body constraint force = implied force due to v change minus f external + // assume f does not include forces internal to body + // 1/2 factor b/c final_integrate contributes other half + // assume per-atom contribution is due to constraint force on that atom + + if (evflag) { + if (rmass) massone = rmass[i]; + else massone = mass[type[i]]; + fc0 = massone*(v[i][0] - v0)/dtf - f[i][0]; + fc1 = massone*(v[i][1] - v1)/dtf - f[i][1]; + fc2 = massone*(v[i][2] - v2)/dtf - f[i][2]; + + vr[0] = 0.5*x0*fc0; + vr[1] = 0.5*x1*fc1; + vr[2] = 0.5*x2*fc2; + vr[3] = 0.5*x0*fc1; + vr[4] = 0.5*x0*fc2; + vr[5] = 0.5*x1*fc2; + + v_tally(1,&i,1.0,vr); + } + } + + // set orientation, omega, angmom of each extended particle + + if (extended) { + // TBD + } +} + +/* ---------------------------------------------------------------------- + set space-frame velocity of each atom in a rigid body + set omega and angmom of extended particles + v = Vcm + (W cross (x - Xcm)) +------------------------------------------------------------------------- */ + +void FixRigidMeso::set_v () { + int xbox,ybox,zbox; + double x0,x1,x2,v0,v1,v2,fc0,fc1,fc2,massone; + double xy,xz,yz; + double delta[3],vr[6]; + + double **x = atom->x; + double **v = atom->v; + double **f = atom->f; + double *e = atom->e; + double *de = atom->de; + double *rho = atom->rho; + double *drho = atom->drho; + double *rmass = atom->rmass; + double *mass = atom->mass; + int *type = atom->type; + int nlocal = atom->nlocal; + + double xprd = domain->xprd; + double yprd = domain->yprd; + double zprd = domain->zprd; + if (triclinic) { + xy = domain->xy; + xz = domain->xz; + yz = domain->yz; + } + + // set v of each atom + + for (int i = 0; i < nlocal; i++) { + if (body[i] < 0) continue; + + // half-step update of particle internal energy and density + e[i] += dtf * de[i]; + rho[i] += dtf * drho[i]; + + const int ibody = body[i]; + + MathExtra::matvec (ex_space[ibody],ey_space[ibody], + ez_space[ibody],displace[i],delta); + + // save old velocities for virial + + if (evflag) { + v0 = v[i][0]; + v1 = v[i][1]; + v2 = v[i][2]; + } + + v[i][0] = omega[ibody][1]*delta[2] - omega[ibody][2]*delta[1] + + vcm[ibody][0]; + v[i][1] = omega[ibody][2]*delta[0] - omega[ibody][0]*delta[2] + + vcm[ibody][1]; + v[i][2] = omega[ibody][0]*delta[1] - omega[ibody][1]*delta[0] + + vcm[ibody][2]; + + // virial = unwrapped coords dotted into body constraint force + // body constraint force = implied force due to v change minus f external + // assume f does not include forces internal to body + // 1/2 factor b/c initial_integrate contributes other half + // assume per-atom contribution is due to constraint force on that atom + + if (evflag) { + if (rmass) massone = rmass[i]; + else massone = mass[type[i]]; + fc0 = massone*(v[i][0] - v0)/dtf - f[i][0]; + fc1 = massone*(v[i][1] - v1)/dtf - f[i][1]; + fc2 = massone*(v[i][2] - v2)/dtf - f[i][2]; + + xbox = (xcmimage[i] & IMGMASK) - IMGMAX; + ybox = (xcmimage[i] >> IMGBITS & IMGMASK) - IMGMAX; + zbox = (xcmimage[i] >> IMG2BITS) - IMGMAX; + + if (triclinic == 0) { + x0 = x[i][0] + xbox*xprd; + x1 = x[i][1] + ybox*yprd; + x2 = x[i][2] + zbox*zprd; + } else { + x0 = x[i][0] + xbox*xprd + ybox*xy + zbox*xz; + x1 = x[i][1] + ybox*yprd + zbox*yz; + x2 = x[i][2] + zbox*zprd; + } + + vr[0] = 0.5*x0*fc0; + vr[1] = 0.5*x1*fc1; + vr[2] = 0.5*x2*fc2; + vr[3] = 0.5*x0*fc1; + vr[4] = 0.5*x0*fc2; + vr[5] = 0.5*x1*fc2; + + v_tally(1,&i,1.0,vr); + } + } + + // set omega, angmom of each extended particle + + if (extended) { + // TBD + } +} + +/* ---------------------------------------------------------------------- + return attributes of a rigid body + 19 values per body + xcm = 0,1,2; vcm = 3,4,5; fcm = 6,7,8; + quat = 9,10,11,12; omega = 13,14,15; torque = 16,17,18; + inertia = 19,20,21; angmom = 22,23,24; + image = 25,26,27 +------------------------------------------------------------------------- */ + +double FixRigidMeso::compute_array (int i, int j) { + if (j < 3) return xcm[i][j]; + if (j < 6) return vcm[i][j-3]; + if (j < 9) return fcm[i][j-6]; + if (j < 13) return quat[i][j-9]; + if (j < 16) return omega[i][j-13]; + if (j < 19) return torque[i][j-16]; + if (j < 22) return inertia[i][j-19]; + if (j < 25) return angmom[i][j-22]; + if (j == 25) return (imagebody[i] & IMGMASK) - IMGMAX; + if (j == 26) return (imagebody[i] >> IMGBITS & IMGMASK) - IMGMAX; + return (imagebody[i] >> IMG2BITS) - IMGMAX; +} diff --git a/src/REAX/fix_reax_bonds.h b/src/USER-SDPD/fix_rigid_meso.h similarity index 55% rename from src/REAX/fix_reax_bonds.h rename to src/USER-SDPD/fix_rigid_meso.h index 03bad1ef16..6945e3c144 100644 --- a/src/REAX/fix_reax_bonds.h +++ b/src/USER-SDPD/fix_rigid_meso.h @@ -13,34 +13,32 @@ #ifdef FIX_CLASS -FixStyle(reax/bonds,FixReaxBonds) +FixStyle(rigid/meso,FixRigidMeso) #else -#ifndef LMP_FIX_REAX_BONDS_H -#define LMP_FIX_REAX_BONDS_H +#ifndef LMP_FIX_RIGID_MESO_H +#define LMP_FIX_RIGID_MESO_H -#include -#include "fix.h" +#include "fix_rigid.h" namespace LAMMPS_NS { -class FixReaxBonds : public Fix { +class FixRigidMeso : public FixRigid { public: - FixReaxBonds(class LAMMPS *, int, char **); - ~FixReaxBonds(); - int setmask(); - void init(); - void setup(int); - void end_of_step(); + FixRigidMeso (class LAMMPS *, int, char **); + ~FixRigidMeso (); + int setmask (); + void setup (int); + void initial_integrate (int); + void final_integrate (); + double compute_scalar () { return 0.0; } + double compute_array (int, int); - private: - int me; - int nfreq; - FILE *fp; - - void OutputReaxBonds(bigint, FILE*); - int nint(const double&); + protected: + void set_xv (); + void set_v (); + double **conjqm; // conjugate quaternion momentum }; } @@ -50,28 +48,22 @@ class FixReaxBonds : public Fix { /* ERROR/WARNING messages: +E: fix rigid/meso command requires atom_style with both energy and density + +You should use atom_style meso with this fix + +E: Can not use thermostat with fix rigid/meso + +Self-explanatory + +E: Can not use barostat with fix rigid/meso + +Self-explanatory + E: Illegal ... command Self-explanatory. Check the input script syntax and compare to the documentation for the command. You can use -echo screen as a command-line option when running LAMMPS to see the offending line. -E: Cannot open gzipped file - -UNDOCUMENTED - -E: Cannot open fix reax/bonds file %s - -The output file for the fix reax/bonds command cannot be opened. -Check that the path and name are correct. - -E: Cannot use fix reax/bonds without pair_style reax - -Self-explanatory. - -E: Fix reax/bonds numbonds > nsbmax_most - -The limit of the number of bonds expected by the ReaxFF force field -was exceeded. - */ diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp new file mode 100644 index 0000000000..db80debe51 --- /dev/null +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.cpp @@ -0,0 +1,313 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + ------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: + Morteza Jalalvand (IASBS) jalalvand.m AT gmail.com + + references: Espanol and Revenga, Phys Rev E 67, 026705 (2003) +------------------------------------------------------------------------- */ + +#include +#include +#include "pair_sdpd_taitwater_isothermal.h" +#include "atom.h" +#include "force.h" +#include "comm.h" +#include "neigh_list.h" +#include "memory.h" +#include "error.h" +#include "domain.h" +#include "update.h" +#ifndef USE_ZEST +#include "random_mars.h" +#endif + +using namespace LAMMPS_NS; + +static const double sqrt_2_inv = std::sqrt(0.5); + +/* ---------------------------------------------------------------------- */ + +PairSDPDTaitwaterIsothermal::PairSDPDTaitwaterIsothermal (LAMMPS *lmp) +: Pair (lmp) { + restartinfo = 0; + single_enable =0; +} + +/* ---------------------------------------------------------------------- */ + +PairSDPDTaitwaterIsothermal::~PairSDPDTaitwaterIsothermal () { + if (allocated) { + memory->destroy (setflag); + memory->destroy (cutsq); + + memory->destroy (cut); + memory->destroy (rho0); + memory->destroy (soundspeed); + memory->destroy (B); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairSDPDTaitwaterIsothermal::compute (int eflag, int vflag) { + int i, j, ii, jj, inum, jnum, itype, jtype; + double xtmp, ytmp, ztmp, delx, dely, delz, fpair; + + int *ilist, *jlist, *numneigh, **firstneigh; + double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc; + double h, ih, ihsq, velx, vely, velz; + double rsq, tmp, wfd, delVdotDelR; + double prefactor, wiener[3][3], f_random[3]; + + ev_init(eflag, vflag); + + double **v = atom->vest; + double **x = atom->x; + double **f = atom->f; + double *rho = atom->rho; + double *mass = atom->mass; + double *drho = atom->drho; + int *type = atom->type; + int nlocal = atom->nlocal; + int newton_pair = force->newton_pair; + int dimension = domain->dimension; + double dtinv = 1.0 / update->dt; + double kBoltzmann = force->boltz; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + vxtmp = v[i][0]; + vytmp = v[i][1]; + vztmp = v[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + imass = mass[itype]; + + // compute pressure of atom i with Tait EOS + tmp = rho[i] / rho0[itype]; + fi = tmp * tmp * tmp; + fi = B[itype] * (fi * fi * tmp - 1.0) / (rho[i] * rho[i]); + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + jtype = type[j]; + jmass = mass[jtype]; + + if (rsq < cutsq[itype][jtype]) { + h = cut[itype][jtype]; + ih = 1.0 / h; + ihsq = ih * ih; + + double r = sqrt (rsq); + wfd = h - r; + if (dimension == 3) { + // Lucy Kernel, 3d + // Note that wfd, the derivative of the weight function with respect to r, + // is lacking a factor of r. + // The missing factor of r is recovered by + // (1) using delV . delX instead of delV . (delX/r) and + // (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair + wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih; + } else { + // Lucy Kernel, 2d + wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq; + } + + // compute pressure of atom j with Tait EOS + tmp = rho[j] / rho0[jtype]; + fj = tmp * tmp * tmp; + fj = B[jtype] * (fj * fj * tmp - 1.0) / (rho[j] * rho[j]); + + velx=vxtmp - v[j][0]; + vely=vytmp - v[j][1]; + velz=vztmp - v[j][2]; + + // dot product of velocity delta and distance vector + delVdotDelR = delx * velx + dely * vely + delz * velz; + + // Espanol Viscosity (Espanol, 2003) + + fvisc = (5. / 3.) * viscosity * imass * jmass * wfd / (rho[i]*rho[j]); + + // total pair force + fpair = -imass * jmass * (fi + fj) * wfd; + + // random force calculation + // independent increments of a Wiener process matrix +#ifdef USE_ZEST + wiener[0][0] = gaussian (generator); + wiener[1][1] = gaussian (generator); + wiener[2][2] = gaussian (generator); + + wiener[0][1] = wiener[1][0] = sqrt_2_inv * gaussian (generator); + wiener[0][2] = wiener[2][0] = sqrt_2_inv * gaussian (generator); + wiener[1][2] = wiener[2][1] = sqrt_2_inv * gaussian (generator); +#else + wiener[0][0] = random->gaussian (); + wiener[1][1] = random->gaussian (); + wiener[2][2] = random->gaussian (); + + wiener[0][1] = wiener[1][0] = sqrt_2_inv * random->gaussian (); + wiener[0][2] = wiener[2][0] = sqrt_2_inv * random->gaussian (); + wiener[1][2] = wiener[2][1] = sqrt_2_inv * random->gaussian (); +#endif + + prefactor = sqrt (-4. * kBoltzmann*temperature * fvisc * dtinv) / r; + + f_random[0] = prefactor * (wiener[0][0]*delx + wiener[0][1]*dely + wiener[0][2]*delz); + f_random[1] = prefactor * (wiener[1][0]*delx + wiener[1][1]*dely + wiener[1][2]*delz); + f_random[2] = prefactor * (wiener[2][0]*delx + wiener[2][1]*dely + wiener[2][2]*delz); + + f[i][0] += delx * fpair + (velx + delx * delVdotDelR / rsq) * fvisc + f_random[0]; + f[i][1] += dely * fpair + (vely + dely * delVdotDelR / rsq) * fvisc + f_random[1]; + f[i][2] += delz * fpair + (velz + delz * delVdotDelR / rsq) * fvisc + f_random[2]; + + // and change in density + drho[i] += jmass * delVdotDelR * wfd; + + if (newton_pair || j < nlocal) { + f[j][0] -= delx * fpair + (velx + delx * delVdotDelR / rsq) * fvisc + f_random[0]; + f[j][1] -= dely * fpair + (vely + dely * delVdotDelR / rsq) * fvisc + f_random[1]; + f[j][2] -= delz * fpair + (velz + delz * delVdotDelR / rsq) * fvisc + f_random[2]; + drho[j] += imass * delVdotDelR * wfd; + } + + if (evflag) + ev_tally (i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute (); +} + +/* ---------------------------------------------------------------------- + allocate all arrays + ------------------------------------------------------------------------- */ + +void PairSDPDTaitwaterIsothermal::allocate () { + allocated = 1; + int n = atom->ntypes; + + memory->create (setflag, n + 1, n + 1, "pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create (cutsq, n + 1, n + 1, "pair:cutsq"); + + memory->create (rho0, n + 1, "pair:rho0"); + memory->create (soundspeed, n + 1, "pair:soundspeed"); + memory->create (B, n + 1, "pair:B"); + memory->create (cut, n + 1, n + 1, "pair:cut"); +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairSDPDTaitwaterIsothermal::settings (int narg, char **arg) { + if (narg != 2 && narg != 3) + error->all (FLERR, "Illegal number of arguments for " + "pair_style sdpd/taitwater/morris/isothermal"); + + temperature = force->numeric (FLERR, arg[0]); + viscosity = force->numeric (FLERR, arg[1]); + + if (temperature <= 0) error->all (FLERR, "Temperature must be positive"); + if (viscosity <= 0) error->all (FLERR, "Viscosity must be positive"); + + // seed is immune to underflow/overflow because it is unsigned + seed = comm->nprocs + comm->me + atom->nlocal; + if (narg == 3) seed += force->inumeric (FLERR, arg[2]); +#ifdef USE_ZEST + generator.seed (seed); +#else + random = new RanMars (lmp, seed); +#endif +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs + ------------------------------------------------------------------------- */ + +void PairSDPDTaitwaterIsothermal::coeff (int narg, char **arg) { + if (narg != 5) + error->all (FLERR, "Incorrect args for pair_style " + "sph/taitwater/morris coefficients"); + + if (!allocated) allocate(); + + int ilo, ihi, jlo, jhi; + force->bounds (FLERR, arg[0], atom->ntypes, ilo, ihi); + force->bounds (FLERR, arg[1], atom->ntypes, jlo, jhi); + + double rho0_one = force->numeric (FLERR,arg[2]); + double soundspeed_one = force->numeric (FLERR,arg[3]); + double cut_one = force->numeric (FLERR,arg[4]); + double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0; + + if (rho0_one <= 0) error->all (FLERR, "Density must be positive"); + if (soundspeed_one <= 0) error->all (FLERR, "Sound speed must be positive"); + if (cut_one <= 0) error->all (FLERR, "Cutoff must be positive"); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + rho0[i] = rho0_one; + soundspeed[i] = soundspeed_one; + B[i] = B_one; + for (int j = MAX(jlo,i); j <= jhi; j++) { + cut[i][j] = cut_one; + + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) + error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i + ------------------------------------------------------------------------- */ + +double PairSDPDTaitwaterIsothermal::init_one (int i, int j) { + if (setflag[i][j] == 0) + error->all(FLERR,"Not all pair sph/taitwater/morris coeffs are set"); + + cut[j][i] = cut[i][j]; + + return cut[i][j]; +} + diff --git a/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h new file mode 100644 index 0000000000..caaa0759d0 --- /dev/null +++ b/src/USER-SDPD/pair_sdpd_taitwater_isothermal.h @@ -0,0 +1,59 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(sdpd/taitwater/isothermal,PairSDPDTaitwaterIsothermal) + +#else + +#ifndef LMP_PAIR_SDPD_TAITWATER_MORRIS_ISOTHERMAL_H +#define LMP_PAIR_SDPD_TAITWATER_MORRIS_ISOTHERMAL_H + +#include "pair.h" +#ifdef USE_ZEST +#include +#include "zest.hpp" +#endif + +namespace LAMMPS_NS { + +class PairSDPDTaitwaterIsothermal : public Pair { + public: + PairSDPDTaitwaterIsothermal (class LAMMPS *); + virtual ~PairSDPDTaitwaterIsothermal (); + virtual void compute (int, int); + void settings (int, char **); + void coeff (int, char **); + virtual double init_one (int, int); + + protected: + double viscosity, temperature; + double *rho0, *soundspeed, *B; + double **cut; + + void allocate (); + + unsigned int seed; +#ifdef USE_ZEST + std::mt19937_64 generator; + Ziggurat gaussian; +#else + class RanMars *random; +#endif +}; + +} + +#endif +#endif diff --git a/src/USER-SMD/pair_smd_hertz.cpp b/src/USER-SMD/pair_smd_hertz.cpp index 13f48e995e..541be9f05c 100644 --- a/src/USER-SMD/pair_smd_hertz.cpp +++ b/src/USER-SMD/pair_smd_hertz.cpp @@ -87,10 +87,7 @@ void PairHertz::compute(int eflag, int vflag) { double *rmass = atom->rmass; evdwl = 0.0; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **f = atom->f; double **x = atom->x; diff --git a/src/USER-SMD/pair_smd_tlsph.cpp b/src/USER-SMD/pair_smd_tlsph.cpp index ab6b7d2785..ac67a3279a 100644 --- a/src/USER-SMD/pair_smd_tlsph.cpp +++ b/src/USER-SMD/pair_smd_tlsph.cpp @@ -448,10 +448,7 @@ void PairTlsph::ComputeForces(int eflag, int vflag) { Matrix3d eye; eye.setIdentity(); - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); /* * iterate over pairs of particles i, j and assign forces using PK1 stress tensor diff --git a/src/USER-SMD/pair_smd_triangulated_surface.cpp b/src/USER-SMD/pair_smd_triangulated_surface.cpp index e40c876ec3..d3a4983379 100644 --- a/src/USER-SMD/pair_smd_triangulated_surface.cpp +++ b/src/USER-SMD/pair_smd_triangulated_surface.cpp @@ -96,10 +96,7 @@ void PairTriSurf::compute(int eflag, int vflag) { Vector2d w2d, rhs; evdwl = 0.0; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); tagint *mol = atom->molecule; double **f = atom->f; diff --git a/src/USER-SMD/pair_smd_ulsph.cpp b/src/USER-SMD/pair_smd_ulsph.cpp index 50af6e2356..2c4a2de989 100644 --- a/src/USER-SMD/pair_smd_ulsph.cpp +++ b/src/USER-SMD/pair_smd_ulsph.cpp @@ -386,10 +386,7 @@ void PairULSPH::compute(int eflag, int vflag) { int k; SelfAdjointEigenSolver < Matrix3d > es; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); if (atom->nmax > nmax) { //printf("... allocating in compute with nmax = %d\n", atom->nmax); diff --git a/src/USER-SMTBQ/README b/src/USER-SMTBQ/README index 74b621eef1..e778c65be2 100644 --- a/src/USER-SMTBQ/README +++ b/src/USER-SMTBQ/README @@ -2,9 +2,11 @@ This package implements the Second Moment Tight Binding - QEq (SMTB-Q) potential for the description of ionocovalent bonds in oxides. Authors: Nicolas Salles, Emile Maras, Olivier Politano, Robert Tetot -at LAAS-CNRS in France. +at ICB, Universite de Bourgogne and ICMMO, Universite Paris-Sud. -Contact emails: lammps@u-bourgogne.fr, nsalles@laas.fr +Contact emails: lammps@u-bourgogne.fr, nsalles33@gmail.com + +This package is occasionally maintained. See the doc page for the pair_style smtbq command to get started. diff --git a/src/USER-SMTBQ/pair_smtbq.cpp b/src/USER-SMTBQ/pair_smtbq.cpp index c2690dc864..ba7f8eb88c 100644 --- a/src/USER-SMTBQ/pair_smtbq.cpp +++ b/src/USER-SMTBQ/pair_smtbq.cpp @@ -42,6 +42,7 @@ #include #include #include +#include #include "pair_smtbq.h" #include "atom.h" #include "comm.h" @@ -122,7 +123,6 @@ PairSMTBQ::PairSMTBQ(LAMMPS *lmp) : Pair(lmp) sbcov = NULL; coord = NULL; sbmet = NULL; - chimet = NULL; ecov = NULL; potmad = NULL; @@ -187,6 +187,16 @@ PairSMTBQ::~PairSMTBQ() memory->destroy(potqn); memory->destroy(dpotqn); + memory->destroy(fafbOxOxSurf); + memory->destroy(dfafbOxOxSurf); + memory->destroy(fafbTiOxSurf); + memory->destroy(dfafbTiOxSurf); + + memory->destroy(fafbOxOxBB); + memory->destroy(dfafbOxOxBB); + memory->destroy(fafbTiOxBB); + memory->destroy(dfafbTiOxBB); + memory->destroy(ecov); memory->destroy(sbcov); memory->destroy(coord); @@ -199,7 +209,6 @@ PairSMTBQ::~PairSMTBQ() memory->destroy(potmad); memory->destroy(potself); memory->destroy(potcov); - memory->destroy(chimet); memory->destroy(nvsm); memory->destroy(vsm);; @@ -242,7 +251,7 @@ void PairSMTBQ::allocate() global settings ------------------------------------------------------------------------- */ -void PairSMTBQ::settings(int narg, char **/*arg*/) +void PairSMTBQ::settings(int narg, char ** /* arg */) { if (narg > 0) error->all(FLERR,"Illegal pair_style command"); } @@ -394,7 +403,13 @@ void PairSMTBQ::read_file(char *file) verbose = 1; verbose = 0; - // open file on all processors + coordOxBB = 0.0; + coordOxBulk = 0.0; + coordOxSurf = 0.0; + ROxBB = 0.0; + ROxSurf = 0.0; + + // open file on all processors FILE *fp; fp = force->open_potential(file); if ( fp == NULL ) { @@ -444,14 +459,12 @@ void PairSMTBQ::read_file(char *file) // load up parameter settings and error check their values - if (nparams == maxparam) { - maxparam += DELTA; - params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), + nparams = maxparam = num_atom_types; + params = (Param *) memory->create(params,maxparam*sizeof(Param), "pair:params"); - maxintparam += m; - intparams = (Intparam *) memory->srealloc(intparams,(maxintparam+1)*sizeof(Intparam), + maxintparam = m; + intparams = (Intparam *) memory->create(intparams,(maxintparam+1)*sizeof(Intparam), "pair:intparams"); - } for (i=0; i < num_atom_types; i++) params[i].nom = (char*) malloc(sizeof(char)*3); @@ -828,7 +841,8 @@ void PairSMTBQ::read_file(char *file) } //A adapter au STO - ncov = min((params[0].sto)*(params[0].n0),(params[1].sto)*(params[1].n0)); + for (i=1,ncov=params[0].sto*params[0].n0; i < nparams; ++i) + ncov = min(ncov,(params[1].sto)*(params[1].n0)); if (verbose) printf (" Parametre ncov = %f\n",ncov); if (verbose) printf (" ********************************************* \n"); @@ -859,7 +873,6 @@ void PairSMTBQ::compute(int eflag, int vflag) memory->destroy(sbcov); memory->destroy(coord); memory->destroy(sbmet); - memory->destroy(chimet); memory->destroy(flag_QEq); memory->destroy(qf); memory->destroy(q1); @@ -875,7 +888,6 @@ void PairSMTBQ::compute(int eflag, int vflag) memory->create(sbcov,nmax,"pair:sbcov"); memory->create(coord,nmax,"pair:coord"); memory->create(sbmet,nmax,"pair:sbmet"); - memory->create(chimet,nmax,"pair:chimet"); memory->create(flag_QEq,nmax,"pair:flag_QEq"); memory->create(qf,nmax,"pair:qf"); memory->create(q1,nmax,"pair:q1"); @@ -887,8 +899,7 @@ void PairSMTBQ::compute(int eflag, int vflag) evdwl = ecoul = ecovtot = ErepOO = ErepMO = Eion = 0.0; Eself = 0.0; - if (eflag || vflag) { ev_setup(eflag,vflag); } - else { evflag = vflag_fdotr = vflag_atom = 0; } + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -1312,10 +1323,7 @@ void PairSMTBQ::tabqeq() memory->create(sbcov,nmax,"pair:sbcov"); memory->create(coord,nmax,"pair:coord"); memory->create(sbmet,nmax,"pair:sbmet"); - memory->create(chimet,nmax,"pair:chimet"); - // memory->create(nvsm,nmax,"pair:nvsm"); - // memory->create(vsm,nmax,nmax,"pair:vsm"); memory->create(flag_QEq,nmax,"pair:flag_QEq"); memory->create(qf,nmax,"pair:qf"); @@ -2529,10 +2537,10 @@ void PairSMTBQ::Charge() // --------------------------- - double enegtotall[nteam+1],enegchkall[nteam+1],enegmaxall[nteam+1],qtota[nteam+1],qtotc[nteam+1]; - double qtotcll[nteam+1],qtotall[nteam+1]; - double sigmaa[nteam+1],sigmac[nteam+1],sigmaall[nteam+1],sigmacll[nteam+1]; - int end[nteam+1], nQEq[nteam+1],nQEqc[nteam+1],nQEqa[nteam+1]; + std::vector enegtotall(nteam+1),enegchkall(nteam+1),enegmaxall(nteam+1); + std::vector qtotcll(nteam+1),qtotall(nteam+1),qtota(nteam+1),qtotc(nteam+1); + std::vector sigmaa(nteam+1),sigmac(nteam+1),sigmaall(nteam+1),sigmacll(nteam+1); + std::vector end(nteam+1), nQEq(nteam+1),nQEqc(nteam+1),nQEqa(nteam+1); iloop = 0; @@ -2543,9 +2551,7 @@ void PairSMTBQ::Charge() dtq = 0.0006; // 0.0006 dtq2 = 0.5*dtq*dtq/qmass; - double enegchk[nteam+1]; - double enegtot[nteam+1]; - double enegmax[nteam+1]; + std::vector enegchk(nteam+1),enegtot(nteam+1),enegmax(nteam+1); @@ -2570,12 +2576,12 @@ void PairSMTBQ::Charge() if (itype == 0) { qtota[gp] += q[i]; nQEqa[gp] += 1; } } - MPI_Allreduce(nQEq,nQEqall,nteam+1,MPI_INT,MPI_SUM,world); - MPI_Allreduce(nQEqc,nQEqcall,nteam+1,MPI_INT,MPI_SUM,world); - MPI_Allreduce(nQEqa,nQEqaall,nteam+1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(nQEq.data(),nQEqall,nteam+1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(nQEqc.data(),nQEqcall,nteam+1,MPI_INT,MPI_SUM,world); + MPI_Allreduce(nQEqa.data(),nQEqaall,nteam+1,MPI_INT,MPI_SUM,world); - MPI_Allreduce(qtotc,qtotcll,nteam+1,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(qtota,qtotall,nteam+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(qtotc.data(),qtotcll.data(),nteam+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(qtota.data(),qtotall.data(),nteam+1,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&qtot,&qtotll,1,MPI_DOUBLE,MPI_SUM,world); @@ -2667,7 +2673,8 @@ void PairSMTBQ::Charge() gp = flag_QEq[i]; qf[i] = 0.0; - qf[i] = potself[i]+potmad[i]+potcov[i]+chimet[i] ; + // AK: chimet is not set anywhere + qf[i] = potself[i]+potmad[i]+potcov[i]; // +chimet[i]; Transf[gp] += qf[i]; } @@ -2694,8 +2701,8 @@ void PairSMTBQ::Charge() } // Boucle local - MPI_Allreduce(enegchk,enegchkall,nteam+1,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(enegmax,enegmaxall,nteam+1,MPI_DOUBLE,MPI_MAX,world); + MPI_Allreduce(enegchk.data(),enegchkall.data(),nteam+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(enegmax.data(),enegmaxall.data(),nteam+1,MPI_DOUBLE,MPI_MAX,world); for (gp = 0; gp < nteam+1; gp++) { @@ -2783,8 +2790,8 @@ void PairSMTBQ::Charge() if (itype == 1) sigmac[gp] += (q[i]-TransfAll[gp+cluster])*(q[i]-TransfAll[gp+cluster]); } - MPI_Allreduce(sigmaa,sigmaall,nteam+1,MPI_DOUBLE,MPI_SUM,world); - MPI_Allreduce(sigmac,sigmacll,nteam+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sigmaa.data(),sigmaall.data(),nteam+1,MPI_DOUBLE,MPI_SUM,world); + MPI_Allreduce(sigmac.data(),sigmacll.data(),nteam+1,MPI_DOUBLE,MPI_SUM,world); for (gp = 1; gp < nteam+1; gp++) { sigmaall[gp] = sqrt(sigmaall[gp]/static_cast(nQEqaall[gp])) ; @@ -2886,11 +2893,12 @@ void PairSMTBQ::groupSurface_QEq() void PairSMTBQ::groupQEqAllParallel_QEq() { int ii,i,jj,j,kk,k,itype,jtype,ktype,jnum,m,gp,zz,z,kgp; - int iproc,team_elt[10][nproc],team_QEq[10][nproc][5]; + int iproc; // ,team_elt[10][nproc],team_QEq[10][nproc][5]; + int **team_elt,***team_QEq; int *ilist,*jlist,*numneigh,**firstneigh,ngp,igp; double delr[3],xtmp,ytmp,ztmp,rsq; int **flag_gp, *nelt, **tab_gp; - int QEq,QEqall[nproc]; + int QEq,*QEqall; double **x = atom->x; int *type = atom->type; @@ -2918,6 +2926,9 @@ void PairSMTBQ::groupQEqAllParallel_QEq() memory->create(nelt,nall,"pair:nelt"); memory->create(tab_gp,10,nall,"pair:flag_gp"); + memory->create(team_elt,10,nproc,"pair:team_elt"); + memory->create(team_QEq,10,nproc,5,"pair:team_QEq"); + memory->create(QEqall,nproc,"pair:QEqall"); for (i = 0; i < nall ; i++) { flag_QEq[i] = 0; } for (i = 0; i < 10*nproc; i++) { @@ -2993,6 +3004,9 @@ void PairSMTBQ::groupQEqAllParallel_QEq() memory->destroy(tab_gp); memory->destroy(nelt); + memory->destroy(team_elt); + memory->destroy(team_QEq); + memory->destroy(QEqall); return; } // ::::::::::::::::::::::::::::::::::::::::::::::::::::::: @@ -3330,6 +3344,9 @@ void PairSMTBQ::groupQEqAllParallel_QEq() memory->destroy(tab_gp); memory->destroy(nelt); + memory->destroy(team_elt); + memory->destroy(team_QEq); + memory->destroy(QEqall); } /* ---------------------------------------------------------------------- */ @@ -3337,7 +3354,8 @@ void PairSMTBQ::groupQEqAllParallel_QEq() void PairSMTBQ::Init_charge(int * /*nQEq*/, int * /*nQEqa*/, int * /*nQEqc*/) { int ii,i,gp,itype; - int *ilist,test[nteam],init[nteam]; + int *ilist; + std::vector test(cluster),init(cluster); double bound,tot,totll; int inum = list->inum; @@ -3367,7 +3385,8 @@ void PairSMTBQ::Init_charge(int * /*nQEq*/, int * /*nQEqa*/, int * /*nQEqc*/) } } - MPI_Allreduce(test,init,nteam+1,MPI_INT,MPI_SUM,world); + // TODO + MPI_Allreduce(test.data(),init.data(),cluster,MPI_INT,MPI_SUM,world); // On fait que sur les atomes hybrides!!! // ---------------------------------------- diff --git a/src/USER-SMTBQ/pair_smtbq.h b/src/USER-SMTBQ/pair_smtbq.h index ac8ed70ac0..05e4b67242 100644 --- a/src/USER-SMTBQ/pair_smtbq.h +++ b/src/USER-SMTBQ/pair_smtbq.h @@ -90,7 +90,7 @@ protected: double coordOxBulk,coordOxSurf,ROxSurf,coordOxBB,ROxBB; // Covalent interaction - double *ecov, *potmad, *potself, *potcov, *chimet; + double *ecov, *potmad, *potself, *potcov; //, *chimet; double **tabsmb,**dtabsmb, **tabsmr, **dtabsmr, *sbcov, *sbmet; double ncov; diff --git a/src/USER-SPH/pair_sph_heatconduction.cpp b/src/USER-SPH/pair_sph_heatconduction.cpp index 4a8990d6fd..bafa26be89 100644 --- a/src/USER-SPH/pair_sph_heatconduction.cpp +++ b/src/USER-SPH/pair_sph_heatconduction.cpp @@ -52,10 +52,7 @@ void PairSPHHeatConduction::compute(int eflag, int vflag) { double imass, jmass, h, ih, ihsq; double rsq, wfd, D, deltaE; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **x = atom->x; double *e = atom->e; @@ -158,7 +155,7 @@ void PairSPHHeatConduction::allocate() { void PairSPHHeatConduction::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, - "Illegal number of setting arguments for pair_style sph/heatconduction"); + "Illegal number of arguments for pair_style sph/heatconduction"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SPH/pair_sph_idealgas.cpp b/src/USER-SPH/pair_sph_idealgas.cpp index 32b3e61233..db5ec964bc 100644 --- a/src/USER-SPH/pair_sph_idealgas.cpp +++ b/src/USER-SPH/pair_sph_idealgas.cpp @@ -53,10 +53,7 @@ void PairSPHIdealGas::compute(int eflag, int vflag) { double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq; double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **v = atom->vest; double **x = atom->x; @@ -200,7 +197,7 @@ void PairSPHIdealGas::allocate() { void PairSPHIdealGas::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, - "Illegal number of setting arguments for pair_style sph/idealgas"); + "Illegal number of arguments for pair_style sph/idealgas"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SPH/pair_sph_lj.cpp b/src/USER-SPH/pair_sph_lj.cpp index c382833baf..7d315c975c 100644 --- a/src/USER-SPH/pair_sph_lj.cpp +++ b/src/USER-SPH/pair_sph_lj.cpp @@ -53,10 +53,7 @@ void PairSPHLJ::compute(int eflag, int vflag) { double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, ihcub; double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj, lrc; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **v = atom->vest; double **x = atom->x; @@ -207,7 +204,7 @@ void PairSPHLJ::allocate() { void PairSPHLJ::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, - "Illegal number of setting arguments for pair_style sph/lj"); + "Illegal number of arguments for pair_style sph/lj"); } /* ---------------------------------------------------------------------- diff --git a/src/USER-SPH/pair_sph_rhosum.cpp b/src/USER-SPH/pair_sph_rhosum.cpp index 7a3c78efd0..842dddc744 100644 --- a/src/USER-SPH/pair_sph_rhosum.cpp +++ b/src/USER-SPH/pair_sph_rhosum.cpp @@ -72,10 +72,7 @@ void PairSPHRhoSum::compute(int eflag, int vflag) { // neighbor list variables int inum, *ilist, *numneigh, **firstneigh; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **x = atom->x; double *rho = atom->rho; @@ -228,7 +225,7 @@ void PairSPHRhoSum::allocate() { void PairSPHRhoSum::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR, - "Illegal number of setting arguments for pair_style sph/rhosum"); + "Illegal number of arguments for pair_style sph/rhosum"); nstep = force->inumeric(FLERR,arg[0]); } diff --git a/src/USER-SPH/pair_sph_taitwater.cpp b/src/USER-SPH/pair_sph_taitwater.cpp index 42b318f2c9..cf3c0e914b 100644 --- a/src/USER-SPH/pair_sph_taitwater.cpp +++ b/src/USER-SPH/pair_sph_taitwater.cpp @@ -29,7 +29,7 @@ using namespace LAMMPS_NS; PairSPHTaitwater::PairSPHTaitwater(LAMMPS *lmp) : Pair(lmp) { restartinfo = 0; - + single_enable = 0; first = 1; } @@ -58,10 +58,7 @@ void PairSPHTaitwater::compute(int eflag, int vflag) { double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq; double rsq, tmp, wfd, delVdotDelR, mu, deltaE; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **v = atom->vest; double **x = atom->x; @@ -228,7 +225,7 @@ void PairSPHTaitwater::allocate() { void PairSPHTaitwater::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, - "Illegal number of setting arguments for pair_style sph/taitwater"); + "Illegal number of arguments for pair_style sph/taitwater"); } /* ---------------------------------------------------------------------- @@ -282,7 +279,7 @@ void PairSPHTaitwater::coeff(int narg, char **arg) { double PairSPHTaitwater::init_one(int i, int j) { if (setflag[i][j] == 0) { - error->all(FLERR,"Not all pair sph/taitwater coeffs are set"); + error->all(FLERR,"All pair sph/taitwater coeffs are set"); } cut[j][i] = cut[i][j]; @@ -291,11 +288,3 @@ double PairSPHTaitwater::init_one(int i, int j) { return cut[i][j]; } -/* ---------------------------------------------------------------------- */ - -double PairSPHTaitwater::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, - double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { - fforce = 0.0; - - return 0.0; -} diff --git a/src/USER-SPH/pair_sph_taitwater.h b/src/USER-SPH/pair_sph_taitwater.h index adcca80b22..ea4cfd8b26 100644 --- a/src/USER-SPH/pair_sph_taitwater.h +++ b/src/USER-SPH/pair_sph_taitwater.h @@ -32,7 +32,6 @@ class PairSPHTaitwater : public Pair { void settings(int, char **); void coeff(int, char **); virtual double init_one(int, int); - virtual double single(int, int, int, int, double, double, double, double &); protected: double *rho0, *soundspeed, *B; diff --git a/src/USER-SPH/pair_sph_taitwater_morris.cpp b/src/USER-SPH/pair_sph_taitwater_morris.cpp index 8012895af8..5cbaa5959f 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.cpp +++ b/src/USER-SPH/pair_sph_taitwater_morris.cpp @@ -30,6 +30,7 @@ PairSPHTaitwaterMorris::PairSPHTaitwaterMorris(LAMMPS *lmp) : Pair(lmp) { restartinfo = 0; first = 1; + single_enable = 0; } /* ---------------------------------------------------------------------- */ @@ -57,10 +58,7 @@ void PairSPHTaitwaterMorris::compute(int eflag, int vflag) { double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, velx, vely, velz; double rsq, tmp, wfd, delVdotDelR, deltaE; - if (eflag || vflag) - ev_setup(eflag, vflag); - else - evflag = vflag_fdotr = 0; + ev_init(eflag, vflag); double **v = atom->vest; double **x = atom->x; @@ -228,7 +226,7 @@ void PairSPHTaitwaterMorris::allocate() { void PairSPHTaitwaterMorris::settings(int narg, char **/*arg*/) { if (narg != 0) error->all(FLERR, - "Illegal number of setting arguments for pair_style sph/taitwater/morris"); + "Illegal number of arguments for pair_style sph/taitwater/morris"); } /* ---------------------------------------------------------------------- @@ -278,7 +276,7 @@ void PairSPHTaitwaterMorris::coeff(int narg, char **arg) { double PairSPHTaitwaterMorris::init_one(int i, int j) { if (setflag[i][j] == 0) { - error->all(FLERR,"Not all pair sph/taitwater/morris coeffs are not set"); + error->all(FLERR,"All pair sph/taitwater/morris coeffs are not set"); } cut[j][i] = cut[i][j]; @@ -287,11 +285,3 @@ double PairSPHTaitwaterMorris::init_one(int i, int j) { return cut[i][j]; } -/* ---------------------------------------------------------------------- */ - -double PairSPHTaitwaterMorris::single(int /*i*/, int /*j*/, int /*itype*/, int /*jtype*/, - double /*rsq*/, double /*factor_coul*/, double /*factor_lj*/, double &fforce) { - fforce = 0.0; - - return 0.0; -} diff --git a/src/USER-SPH/pair_sph_taitwater_morris.h b/src/USER-SPH/pair_sph_taitwater_morris.h index 0a66e0ebaf..2736e347e1 100644 --- a/src/USER-SPH/pair_sph_taitwater_morris.h +++ b/src/USER-SPH/pair_sph_taitwater_morris.h @@ -32,7 +32,6 @@ class PairSPHTaitwaterMorris : public Pair { void settings(int, char **); void coeff(int, char **); virtual double init_one(int, int); - virtual double single(int, int, int, int, double, double, double, double &); protected: double *rho0, *soundspeed, *B; diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp index a2e6cb291e..75d4ee8895 100644 --- a/src/USER-UEF/uef_utils.cpp +++ b/src/USER-UEF/uef_utils.cpp @@ -150,7 +150,7 @@ void UEFBox::step_deform(const double ex, const double ey) theta[0] +=winv[0][0]*ex + winv[0][1]*ey; theta[1] +=winv[1][0]*ex + winv[1][1]*ey; - // deformation of the box. reduce() needs to be called regularly or + // deformation of the box. reduce() needs to be called regularly or // calculation will become unstable double eps[3]; @@ -169,7 +169,7 @@ void UEFBox::step_deform(const double ex, const double ey) ------------------------------------------------------------------------- */ bool UEFBox::reduce() { - // determine how many times to apply the automorphisms and find new theta + // determine how many times to apply the automorphisms and find new theta // values int f1 = round(theta[0]); @@ -184,7 +184,7 @@ bool UEFBox::reduce() for (int j=0;j<3;j++) r0[k][j]=r[k][j]; - // this modifies the old change basis matrix to handle the case where the + // this modifies the old change basis matrix to handle the case where the // automorphism transforms the box but the reduced basis doesn't change // (r0 should still equal r at the end) @@ -417,7 +417,7 @@ void make_unique(double b[3][3], int r[3][3], int ri[3][3]) if (fabs(b[0][0]) < fabs(b[0][1])) { col_swap(b,0,1); col_swap(r,0,1); - col_swap(ri,0,1); + col_swap(ri,0,1); } if (fabs(b[0][0]) < fabs(b[0][2])) { col_swap(b,0,2); @@ -433,7 +433,7 @@ void make_unique(double b[3][3], int r[3][3], int ri[3][3]) if (b[0][0] < 0) { neg_col(b,0); neg_col(r,0); - neg_col(ri,0); + neg_col(ri,0); } if (b[1][1] < 0) { neg_col(b,1); @@ -442,8 +442,8 @@ void make_unique(double b[3][3], int r[3][3], int ri[3][3]) } if (det(b) < 0) { neg_col(b,2); - neg_col(r,2); - neg_col(ri,2); + neg_col(r,2); + neg_col(ri,2); } } }} diff --git a/src/USER-UEF/uef_utils.h b/src/USER-UEF/uef_utils.h index 0a1cfcc9b2..5936d4f6bd 100644 --- a/src/USER-UEF/uef_utils.h +++ b/src/USER-UEF/uef_utils.h @@ -103,7 +103,6 @@ bool mat_same(T x1[3][3], T x2[3][3]) template void transpose(T m[3][3]) { - T t[3][3]; for (int k=0;k<3;k++) for (int j=k+1;j<3;j++) { T x = m[k][j]; diff --git a/src/USER-VTK/dump_vtk.cpp b/src/USER-VTK/dump_vtk.cpp index edbc647a81..88e95dd338 100644 --- a/src/USER-VTK/dump_vtk.cpp +++ b/src/USER-VTK/dump_vtk.cpp @@ -93,10 +93,10 @@ enum{VTK,VTP,VTU,PVTP,PVTU}; // file formats #define ONEFIELD 32 #define DELTA 1048576 -#if VTK_MAJOR_VERSION >= 7 -#define InsertNextTupleValue InsertNextTypedTuple -#elif VTK_MAJOR_VERSION > 8 +#if (VTK_MAJOR_VERSION < 5) || (VTK_MAJOR_VERSION > 8) #error This code has only been tested with VTK 5, 6, 7, and 8 +#elif VTK_MAJOR_VERSION > 6 +#define InsertNextTupleValue InsertNextTypedTuple #endif /* ---------------------------------------------------------------------- */ diff --git a/src/USER-YAFF/README b/src/USER-YAFF/README new file mode 100644 index 0000000000..4fabe67390 --- /dev/null +++ b/src/USER-YAFF/README @@ -0,0 +1,8 @@ +This package implements the styles that are needed to use typical force fields +generated by QuickFF for the simulation of metal-organic frameworks. The +QuickFF methodology is detailed in following papers: + Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) http://dx.doi.org/10.1002/jcc.23877 + Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) http://dx.doi.org/10.1002/jcc.25173 +The corresponding software package can be found on http://molmod.github.io/QuickFF + + diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp new file mode 100644 index 0000000000..2e6731f494 --- /dev/null +++ b/src/USER-YAFF/angle_cross.cpp @@ -0,0 +1,343 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "angle_cross.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +AngleCross::AngleCross(LAMMPS *lmp) : Angle(lmp) {} + +/* ---------------------------------------------------------------------- */ + +AngleCross::~AngleCross() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(kss); + memory->destroy(kbs0); + memory->destroy(kbs1); + memory->destroy(r00); + memory->destroy(r01); + memory->destroy(theta0); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCross::compute(int eflag, int vflag) +{ + int i1,i2,i3,n,type; + double delx1,dely1,delz1,delx2,dely2,delz2; + double eangle,f1[3],f3[3]; + double dtheta; + double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22; + double rsq1,rsq2,r1,r2,c,s,b1,b2; + double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22; + + eangle = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int **anglelist = neighbor->anglelist; + int nanglelist = neighbor->nanglelist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nanglelist; n++) { + i1 = anglelist[n][0]; + i2 = anglelist[n][1]; + i3 = anglelist[n][2]; + type = anglelist[n][3]; + + // 1st bond + + delx1 = x[i1][0] - x[i2][0]; + dely1 = x[i1][1] - x[i2][1]; + delz1 = x[i1][2] - x[i2][2]; + + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + // 2nd bond + + delx2 = x[i3][0] - x[i2][0]; + dely2 = x[i3][1] - x[i2][1]; + delz2 = x[i3][2] - x[i2][2]; + + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); + + // angle (cos and sin) + + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + s = 1.0/s; + + // force & energy for bond-bond term + dr1 = r1 - r00[type]; + dr2 = r2 - r01[type]; + tk1 = kss[type] * dr1; + tk2 = kss[type] * dr2; + + f1[0] = -delx1*tk2/r1; + f1[1] = -dely1*tk2/r1; + f1[2] = -delz1*tk2/r1; + + f3[0] = -delx2*tk1/r2; + f3[1] = -dely2*tk1/r2; + f3[2] = -delz2*tk1/r2; + + if (eflag) eangle = kss[type]*dr1*dr2; + + // force & energy for bond-angle term + dtheta = acos(c) - theta0[type]; + + aa1 = s * dr1 * kbs0[type]; + aa2 = s * dr2 * kbs1[type]; + + aa11 = aa1 * c / rsq1; + aa12 = -aa1 / (r1 * r2); + aa21 = aa2 * c / rsq1; + aa22 = -aa2 / (r1 * r2); + + vx11 = (aa11 * delx1) + (aa12 * delx2); + vx12 = (aa21 * delx1) + (aa22 * delx2); + vy11 = (aa11 * dely1) + (aa12 * dely2); + vy12 = (aa21 * dely1) + (aa22 * dely2); + vz11 = (aa11 * delz1) + (aa12 * delz2); + vz12 = (aa21 * delz1) + (aa22 * delz2); + + aa11 = aa1 * c / rsq2; + aa21 = aa2 * c / rsq2; + + vx21 = (aa11 * delx2) + (aa12 * delx1); + vx22 = (aa21 * delx2) + (aa22 * delx1); + vy21 = (aa11 * dely2) + (aa12 * dely1); + vy22 = (aa21 * dely2) + (aa22 * dely1); + vz21 = (aa11 * delz2) + (aa12 * delz1); + vz22 = (aa21 * delz2) + (aa22 * delz1); + + b1 = kbs0[type] * dtheta / r1; + b2 = kbs1[type] * dtheta / r2; + + f1[0] -= vx11 + b1*delx1 + vx12; + f1[1] -= vy11 + b1*dely1 + vy12; + f1[2] -= vz11 + b1*delz1 + vz12; + + f3[0] -= vx21 + b2*delx2 + vx22; + f3[1] -= vy21 + b2*dely2 + vy22; + f3[2] -= vz21 + b2*delz2 + vz22; + + if (eflag) eangle += kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta; + + // apply force to each of 3 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= f1[0] + f3[0]; + f[i2][1] -= f1[1] + f3[1]; + f[i2][2] -= f1[2] + f3[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3, + delx1,dely1,delz1,delx2,dely2,delz2); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleCross::allocate() +{ + allocated = 1; + int n = atom->nangletypes; + + memory->create(kss,n+1,"angle:kss"); + memory->create(kbs0,n+1,"angle:kbs0"); + memory->create(kbs1,n+1,"angle:kbs1"); + memory->create(r00,n+1,"angle:r00"); + memory->create(r01,n+1,"angle:r01"); + memory->create(theta0,n+1,"angle:theta0"); + memory->create(setflag,n+1,"angle:setflag"); + + for (int i = 1; i <= n; i++) + setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs +------------------------------------------------------------------------- */ + +void AngleCross::coeff(int narg, char **arg) +{ + if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi); + + int count = 0; + + double kss_one = force->numeric(FLERR,arg[1]); + double kbs0_one = force->numeric(FLERR,arg[2]); + double kbs1_one = force->numeric(FLERR,arg[3]); + double r0_one = force->numeric(FLERR,arg[4]); + double r1_one = force->numeric(FLERR,arg[5]); + double theta0_one = force->numeric(FLERR,arg[6]); + + for (int i = ilo; i <= ihi; i++) { + kss[i] = kss_one; + kbs0[i] = kbs0_one; + kbs1[i] = kbs1_one; + r00[i] = r0_one; + r01[i] = r1_one; + // Convert theta0 from degrees to radians + theta0[i] = theta0_one*MY_PI/180.0; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); +} + +/* ---------------------------------------------------------------------- */ + +double AngleCross::equilibrium_angle(int i) +{ + return theta0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleCross::write_restart(FILE *fp) +{ + fwrite(&kss[1],sizeof(double),atom->nangletypes,fp); + fwrite(&kbs0[1],sizeof(double),atom->nangletypes,fp); + fwrite(&kbs1[1],sizeof(double),atom->nangletypes,fp); + fwrite(&r00[1],sizeof(double),atom->nangletypes,fp); + fwrite(&r01[1],sizeof(double),atom->nangletypes,fp); + fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleCross::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&kss[1],sizeof(double),atom->nangletypes,fp); + fread(&kbs0[1],sizeof(double),atom->nangletypes,fp); + fread(&kbs1[1],sizeof(double),atom->nangletypes,fp); + fread(&r00[1],sizeof(double),atom->nangletypes,fp); + fread(&r01[1],sizeof(double),atom->nangletypes,fp); + fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + } + + MPI_Bcast(&kss[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&kbs0[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&kbs1[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r00[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r01[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void AngleCross::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nangletypes; i++) + fprintf(fp,"%d %g %g %g %g %g %g\n", + i,kss[i],kbs0[i],kbs1[i],r00[i],r01[i],theta0[i]/MY_PI*180.0); +} + +/* ---------------------------------------------------------------------- */ + +double AngleCross::single(int type, int i1, int i2, int i3) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + + double c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + double s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + s = 1.0/s; + + double dtheta = acos(c) - theta0[type]; + double dr1 = r1 - r00[type]; + double dr2 = r2 - r01[type]; + double energy = kss[type]*dr1*dr2+kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta; + return energy; +} diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h new file mode 100644 index 0000000000..7709c10414 --- /dev/null +++ b/src/USER-YAFF/angle_cross.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ANGLE_CLASS + +AngleStyle(cross,AngleCross) + +#else + +#ifndef LMP_ANGLE_CROSS_H +#define LMP_ANGLE_CROSS_H + +#include +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleCross : public Angle { + public: + AngleCross(class LAMMPS *); + virtual ~AngleCross(); + virtual void compute(int, int); + void coeff(int, char **); + double equilibrium_angle(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + double single(int, int, int, int); + + protected: + double *kss,*kbs0,*kbs1,*r00,*r01,*theta0; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args for angle coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp new file mode 100644 index 0000000000..53cb11b5df --- /dev/null +++ b/src/USER-YAFF/angle_mm3.cpp @@ -0,0 +1,285 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "angle_mm3.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +AngleMM3::AngleMM3(LAMMPS *lmp) : Angle(lmp) {} + +/* ---------------------------------------------------------------------- */ + +AngleMM3::~AngleMM3() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(theta0); + memory->destroy(k2); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleMM3::compute(int eflag, int vflag) +{ + int i1,i2,i3,n,type; + double delx1,dely1,delz1,delx2,dely2,delz2; + double eangle,f1[3],f3[3]; + double dtheta,dtheta2,dtheta3,dtheta4,de_angle; + double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22; + + eangle = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int **anglelist = neighbor->anglelist; + int nanglelist = neighbor->nanglelist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nanglelist; n++) { + i1 = anglelist[n][0]; + i2 = anglelist[n][1]; + i3 = anglelist[n][2]; + type = anglelist[n][3]; + + // 1st bond + + delx1 = x[i1][0] - x[i2][0]; + dely1 = x[i1][1] - x[i2][1]; + delz1 = x[i1][2] - x[i2][2]; + + rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1; + r1 = sqrt(rsq1); + + // 2nd bond + + delx2 = x[i3][0] - x[i2][0]; + dely2 = x[i3][1] - x[i2][1]; + delz2 = x[i3][2] - x[i2][2]; + + rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2; + r2 = sqrt(rsq2); + + // angle (cos and sin) + + c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + s = 1.0/s; + + // force & energy for angle term + + dtheta = acos(c) - theta0[type]; + dtheta2 = dtheta*dtheta; + dtheta3 = dtheta2*dtheta; + dtheta4 = dtheta3*dtheta; + // MM3 angle term, taking into account that dtheta is expressed in rad + de_angle = 2.0*k2[type]*dtheta*(1.0-1.203211*dtheta+0.367674*dtheta2-0.3239159*dtheta3+0.711270*dtheta4); + + a = -de_angle*s; + a11 = a*c / rsq1; + a12 = -a / (r1*r2); + a22 = a*c / rsq2; + + f1[0] = a11*delx1 + a12*delx2; + f1[1] = a11*dely1 + a12*dely2; + f1[2] = a11*delz1 + a12*delz2; + + f3[0] = a22*delx2 + a12*delx1; + f3[1] = a22*dely2 + a12*dely1; + f3[2] = a22*delz2 + a12*delz1; + // MM3 angle term, taking into account that dtheta is expressed in rad + if (eflag) eangle = k2[type]*dtheta2*(1.0-0.802141*dtheta+0.183837*dtheta2-0.131664*dtheta3+0.237090*dtheta4); + + // apply force to each of 3 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= f1[0] + f3[0]; + f[i2][1] -= f1[1] + f3[1]; + f[i2][2] -= f1[2] + f3[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3, + delx1,dely1,delz1,delx2,dely2,delz2); + } +} + +/* ---------------------------------------------------------------------- */ + +void AngleMM3::allocate() +{ + allocated = 1; + int n = atom->nangletypes; + + memory->create(setflag,n+1,"angle:setflag"); + memory->create(k2,n+1,"angle:k2"); + memory->create(theta0,n+1,"angle:theta0"); + for (int i = 1; i <= n; i++) + setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs + else -> Angle coeffs +------------------------------------------------------------------------- */ + +void AngleMM3::coeff(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi); + + int count = 0; + + double k2_one = force->numeric(FLERR,arg[1]); + double theta0_one = force->numeric(FLERR,arg[2]); + + // convert theta0 from degrees to radians + + for (int i = ilo; i <= ihi; i++) { + k2[i] = k2_one; + theta0[i] = theta0_one/180.0 * MY_PI; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients"); + +} + +/* ---------------------------------------------------------------------- */ + +double AngleMM3::equilibrium_angle(int i) +{ + return theta0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void AngleMM3::write_restart(FILE *fp) +{ + fwrite(&k2[1],sizeof(double),atom->nangletypes,fp); + fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void AngleMM3::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k2[1],sizeof(double),atom->nangletypes,fp); + fread(&theta0[1],sizeof(double),atom->nangletypes,fp); + } + + MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world); + MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void AngleMM3::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nangletypes; i++) + fprintf(fp,"%d %g %g\n", + i,k2[i],theta0[i]/MY_PI*180.0); +} + +/* ---------------------------------------------------------------------- */ + +double AngleMM3::single(int type, int i1, int i2, int i3) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + + double c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + double s = sqrt(1.0 - c*c); + if (s < SMALL) s = SMALL; + s = 1.0/s; + + double dtheta = acos(c) - theta0[type]; + double dtheta2 = dtheta*dtheta; + double dtheta3 = dtheta2*dtheta; + double dtheta4 = dtheta3*dtheta; + + double energy = k2[type]*dtheta2*(1.0-0.802141*dtheta+0.183837*dtheta2-0.131664*dtheta3+0.237090*dtheta4); + + return energy; +} diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h new file mode 100644 index 0000000000..2d19b4d1b4 --- /dev/null +++ b/src/USER-YAFF/angle_mm3.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ANGLE_CLASS + +AngleStyle(mm3,AngleMM3) + +#else + +#ifndef LMP_ANGLE_MM3_H +#define LMP_ANGLE_MM3_H + +#include +#include "angle.h" + +namespace LAMMPS_NS { + +class AngleMM3 : public Angle { + public: + AngleMM3(class LAMMPS *); + virtual ~AngleMM3(); + virtual void compute(int, int); + void coeff(int, char **); + double equilibrium_angle(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + double single(int, int, int, int); + + protected: + double *theta0,*k2; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args for angle coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp new file mode 100644 index 0000000000..ee1ebcdd61 --- /dev/null +++ b/src/USER-YAFF/bond_mm3.cpp @@ -0,0 +1,220 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande +------------------------------------------------------------------------- */ + +#include +#include +#include "bond_mm3.h" +#include "atom.h" +#include "neighbor.h" +#include "domain.h" +#include "comm.h" +#include "force.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +BondMM3::BondMM3(LAMMPS *lmp) : Bond(lmp) {} + +/* ---------------------------------------------------------------------- */ + +BondMM3::~BondMM3() +{ + if (copymode) return; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(r0); + memory->destroy(k2); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondMM3::compute(int eflag, int vflag) +{ + int i1,i2,n,type; + double delx,dely,delz,ebond,fbond; + double rsq,r,dr,dr2,de_bond,K3,K4; + + ebond = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int **bondlist = neighbor->bondlist; + int nbondlist = neighbor->nbondlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + /* + E = K(r-r0)^2 [1-2.55*(r-r0)+(7/12)*2.55^(2)*(r-r0)^2] + with -2.55 in angstrom^(-1) and (7/12)*2.55^(2) in angstrom^(-2) + These prefactors are converted here to the correct units + */ + K3 = -2.55/force->angstrom; + K4 = 7.0/12.0*2.55*2.55/force->angstrom/force->angstrom; + + for (n = 0; n < nbondlist; n++) { + i1 = bondlist[n][0]; + i2 = bondlist[n][1]; + type = bondlist[n][2]; + + delx = x[i1][0] - x[i2][0]; + dely = x[i1][1] - x[i2][1]; + delz = x[i1][2] - x[i2][2]; + + rsq = delx*delx + dely*dely + delz*delz; + r = sqrt(rsq); + dr = r - r0[type]; + dr2 = dr*dr; + + // force & energy + + de_bond = 2.0*k2[type]*dr*(1.0 + 1.5*K3*dr + 2.0*K4*dr2); + if (r > 0.0) fbond = -de_bond/r; + else fbond = 0.0; + + if (eflag) ebond = k2[type]*dr2*(1.0+K3*dr+K4*dr2); + + // apply force to each of 2 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += delx*fbond; + f[i1][1] += dely*fbond; + f[i1][2] += delz*fbond; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] -= delx*fbond; + f[i2][1] -= dely*fbond; + f[i2][2] -= delz*fbond; + } + + if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz); + } +} + +/* ---------------------------------------------------------------------- */ + +void BondMM3::allocate() +{ + allocated = 1; + int n = atom->nbondtypes; + + memory->create(r0,n+1,"bond:r0"); + memory->create(k2,n+1,"bond:k2"); + + memory->create(setflag,n+1,"bond:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs from one line in input script or data file +------------------------------------------------------------------------- */ + +void BondMM3::coeff(int narg, char **arg) +{ + if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(FLERR,arg[0],atom->nbondtypes,ilo,ihi); + + double k2_one = force->numeric(FLERR,arg[1]); + double r0_one = force->numeric(FLERR,arg[2]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k2[i] = k2_one; + r0[i] = r0_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients"); +} + +/* ---------------------------------------------------------------------- + return an equilbrium bond length +------------------------------------------------------------------------- */ + +double BondMM3::equilibrium_distance(int i) +{ + return r0[i]; +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void BondMM3::write_restart(FILE *fp) +{ + fwrite(&k2[1],sizeof(double),atom->nbondtypes,fp); + fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void BondMM3::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k2[1],sizeof(double),atom->nbondtypes,fp); + fread(&r0[1],sizeof(double),atom->nbondtypes,fp); + } + MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world); + MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void BondMM3::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->nbondtypes; i++) + fprintf(fp,"%d %g %g\n",i,k2[i],r0[i]); +} + +/* ---------------------------------------------------------------------- */ + +double BondMM3::single(int type, double rsq, + int /* i */, int /* j */, double &fforce) +{ + /* + E = K(r-r0)^2 [1-2.55*(r-r0)+(7/12)*2.55^(2)*(r-r0)^2] + with -2.55 in angstrom^(-1) and (7/12)*2.55^(2) in angstrom^(-2) + These prefactors are converted here to the correct units + */ + double K3 = -2.55/force->angstrom; + double K4 = 7.0/12.0*2.55*2.55/force->angstrom/force->angstrom; + double r = sqrt(rsq); + double dr = r - r0[type]; + double dr2 = dr*dr; + double de_bond = 2.0*k2[type]*dr*(1.0 + 1.5*K3*dr + 2.0*K4*dr2); + if (r > 0.0) fforce = -de_bond/r; + else fforce = 0.0; + return k2[type]*dr2*(1.0+K3*dr+K4*dr2); +} diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h new file mode 100644 index 0000000000..9711d89529 --- /dev/null +++ b/src/USER-YAFF/bond_mm3.h @@ -0,0 +1,57 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef BOND_CLASS + +BondStyle(mm3,BondMM3) + +#else + +#ifndef LMP_BOND_MM3_H +#define LMP_BOND_MM3_H + +#include +#include "bond.h" + +namespace LAMMPS_NS { + +class BondMM3 : public Bond { + public: + BondMM3(class LAMMPS *); + virtual ~BondMM3(); + virtual void compute(int, int); + void coeff(int, char **); + double equilibrium_distance(int); + void write_restart(FILE *); + void read_restart(FILE *); + void write_data(FILE *); + double single(int, double, int, int, double &); + + protected: + double *r0,*k2; + + void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args for bond coefficients + +Self-explanatory. Check the input script or data file. + +*/ diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp new file mode 100644 index 0000000000..b45087a9ab --- /dev/null +++ b/src/USER-YAFF/improper_distharm.cpp @@ -0,0 +1,268 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande, heavily based on the + improper_distance code by Paolo Raiteri (Curtin University) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "improper_distharm.h" +#include "atom.h" +#include "comm.h" +#include "neighbor.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define TOLERANCE 0.05 +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +ImproperDistHarm::ImproperDistHarm(LAMMPS *lmp) : Improper(lmp) {} + +/* ---------------------------------------------------------------------- */ + +ImproperDistHarm::~ImproperDistHarm() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(chi); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperDistHarm::compute(int eflag, int vflag) +{ + int i1,i2,i3,i4,n,type; + double xab, yab, zab; // bond 1-2 + double xac, yac, zac; // bond 1-3 + double xad, yad, zad; // bond 1-4 + double xbc, ybc, zbc; // bond 2-3 + double xbd, ybd, zbd; // bond 2-4 + double xcd, ycd, zcd; // bond 3-4 + double xna, yna, zna, rna; // normal + double da; + + double eimproper,f1[3],f2[3],f3[3],f4[3]; + double domega,a; + + eimproper = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int **improperlist = neighbor->improperlist; + int nimproperlist = neighbor->nimproperlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nimproperlist; n++) { + i1 = improperlist[n][0]; + i2 = improperlist[n][1]; + i3 = improperlist[n][2]; + i4 = improperlist[n][3]; + type = improperlist[n][4]; + + // geometry of 4-body + // 4 is the central atom + // 1-2-3 are ment to be equivalent + // I need the bonds between 2-3 and 3-4 to get the plane normal + // Then I need the bond 1-4 to project it onto the normal to the plane + + // bond 1->2 + xab = x[i2][0] - x[i1][0]; + yab = x[i2][1] - x[i1][1]; + zab = x[i2][2] - x[i1][2]; + domain->minimum_image(xab,yab,zab); + + // bond 1->3 + xac = x[i3][0] - x[i1][0]; + yac = x[i3][1] - x[i1][1]; + zac = x[i3][2] - x[i1][2]; + domain->minimum_image(xac,yac,zac); + + // bond 1->4 + xad = x[i4][0] - x[i1][0]; + yad = x[i4][1] - x[i1][1]; + zad = x[i4][2] - x[i1][2]; + domain->minimum_image(xad,yad,zad); + + // bond 2-3 + xbc = x[i3][0] - x[i2][0]; + ybc = x[i3][1] - x[i2][1]; + zbc = x[i3][2] - x[i2][2]; + domain->minimum_image(xbc,ybc,zbc); + + // bond 2-4 + xbd = x[i4][0] - x[i2][0]; + ybd = x[i4][1] - x[i2][1]; + zbd = x[i4][2] - x[i2][2]; + domain->minimum_image(xbd,ybd,zbd); + + // bond 3-4 + xcd = x[i4][0] - x[i3][0]; + ycd = x[i4][1] - x[i3][1]; + zcd = x[i4][2] - x[i3][2]; + domain->minimum_image(xcd,ycd,zcd); + + xna = ybc*zcd - zbc*ycd; + yna = -(xbc*zcd - zbc*xcd); + zna = xbc*ycd - ybc*xcd; + rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna); + xna *= rna; + yna *= rna; + zna *= rna; + + da = -(xna*xad + yna*yad + zna*zad); + + + domega = k[type]*(da - chi[type])*(da - chi[type]); + a = 2.0* k[type]*(da - chi[type]); + + if (eflag) eimproper = domega; + + f1[0] = a*( -xna); + f1[1] = a*( -yna); + f1[2] = a*( -zna); + f4[0] = a*( xna); + f4[1] = a*( yna); + f4[2] = a*( zna); + + f2[0] = a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd); + f2[1] = a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd); + f2[2] = a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd); + + f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd); + f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd); + f3[2] = - a*( xad*ycd - yad*xcd )*rna - a*da*rna*( xna*ycd - yna*xcd); + + f3[0] += -a*( yad*zbc - zad*ybc )*rna - a*da*rna*( yna*zbc - zna*ybc); + f3[1] += -a*( zad*xbc - xad*zbc )*rna - a*da*rna*( zna*xbc - xna*zbc); + f3[2] += -a*( xad*ybc - yad*xbc )*rna - a*da*rna*( xna*ybc - yna*xbc); + f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc); + f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc); + f4[2] += a*( xad*ybc - yad*xbc )*rna + a*da*rna*( xna*ybc - yna*xbc); + + // apply force to each of 4 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] += f2[0]; + f[i2][1] += f2[1]; + f[i2][2] += f2[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (newton_bond || i4 < nlocal) { + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; + } + + if (evflag) + ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f2,f3,f4, + xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperDistHarm::allocate() +{ + allocated = 1; + int n = atom->nimpropertypes; + + memory->create(k,n+1,"improper:k"); + memory->create(chi,n+1,"improper:chi"); + + memory->create(setflag,n+1,"improper:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +void ImproperDistHarm::coeff(int narg, char **arg) +{ +// if (which > 0) return; + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(FLERR,arg[0],atom->nimpropertypes,ilo,ihi); + + double k_one = force->numeric(FLERR,arg[1]); + double chi_one = force->numeric(FLERR,arg[2]); + + // convert chi from degrees to radians + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = k_one; + //chi[i] = chi_one/180.0 * PI; + chi[i] = chi_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void ImproperDistHarm::write_restart(FILE *fp) +{ + fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp); + fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void ImproperDistHarm::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k[1],sizeof(double),atom->nimpropertypes,fp); + fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + } + MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); + MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; +} diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h new file mode 100644 index 0000000000..b8b9ae780e --- /dev/null +++ b/src/USER-YAFF/improper_distharm.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef IMPROPER_CLASS + +ImproperStyle(distharm,ImproperDistHarm) + +#else + +#ifndef LMP_IMPROPER_DISTHARM_H +#define LMP_IMPROPER_DISTHARM_H + +#include +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperDistHarm : public Improper { + public: + ImproperDistHarm(class LAMMPS *); + ~ImproperDistHarm(); + void compute(int, int); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + + private: + double *k,*chi; + + void allocate(); +}; + +} + +#endif +#endif + diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp new file mode 100644 index 0000000000..ae702820cb --- /dev/null +++ b/src/USER-YAFF/improper_sqdistharm.cpp @@ -0,0 +1,268 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande, heavily based on the + improper_distance code by Paolo Raiteri (Curtin University) +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "improper_sqdistharm.h" +#include "atom.h" +#include "comm.h" +#include "neighbor.h" +#include "domain.h" +#include "force.h" +#include "update.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define TOLERANCE 0.05 +#define SMALL 0.001 + +/* ---------------------------------------------------------------------- */ + +ImproperSQDistHarm::ImproperSQDistHarm(LAMMPS *lmp) : Improper(lmp) {} + +/* ---------------------------------------------------------------------- */ + +ImproperSQDistHarm::~ImproperSQDistHarm() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(k); + memory->destroy(chi); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperSQDistHarm::compute(int eflag, int vflag) +{ + int i1,i2,i3,i4,n,type; + double xab, yab, zab; // bond 1-2 + double xac, yac, zac; // bond 1-3 + double xad, yad, zad; // bond 1-4 + double xbc, ybc, zbc; // bond 2-3 + double xbd, ybd, zbd; // bond 2-4 + double xcd, ycd, zcd; // bond 3-4 + double xna, yna, zna, rna; // normal + double da; + + double eimproper,f1[3],f2[3],f3[3],f4[3]; + double domega,a; + + eimproper = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + int **improperlist = neighbor->improperlist; + int nimproperlist = neighbor->nimproperlist; + int nlocal = atom->nlocal; + int newton_bond = force->newton_bond; + + for (n = 0; n < nimproperlist; n++) { + i1 = improperlist[n][0]; + i2 = improperlist[n][1]; + i3 = improperlist[n][2]; + i4 = improperlist[n][3]; + type = improperlist[n][4]; + + // geometry of 4-body + // 4 is the central atom + // 1-2-3 are ment to be equivalent + // I need the bonds between 2-3 and 3-4 to get the plane normal + // Then I need the bond 1-4 to project it onto the normal to the plane + + // bond 1->2 + xab = x[i2][0] - x[i1][0]; + yab = x[i2][1] - x[i1][1]; + zab = x[i2][2] - x[i1][2]; + domain->minimum_image(xab,yab,zab); + + // bond 1->3 + xac = x[i3][0] - x[i1][0]; + yac = x[i3][1] - x[i1][1]; + zac = x[i3][2] - x[i1][2]; + domain->minimum_image(xac,yac,zac); + + // bond 1->4 + xad = x[i4][0] - x[i1][0]; + yad = x[i4][1] - x[i1][1]; + zad = x[i4][2] - x[i1][2]; + domain->minimum_image(xad,yad,zad); + + // bond 2-3 + xbc = x[i3][0] - x[i2][0]; + ybc = x[i3][1] - x[i2][1]; + zbc = x[i3][2] - x[i2][2]; + domain->minimum_image(xbc,ybc,zbc); + + // bond 2-4 + xbd = x[i4][0] - x[i2][0]; + ybd = x[i4][1] - x[i2][1]; + zbd = x[i4][2] - x[i2][2]; + domain->minimum_image(xbd,ybd,zbd); + + // bond 3-4 + xcd = x[i4][0] - x[i3][0]; + ycd = x[i4][1] - x[i3][1]; + zcd = x[i4][2] - x[i3][2]; + domain->minimum_image(xcd,ycd,zcd); + + xna = ybc*zcd - zbc*ycd; + yna = -(xbc*zcd - zbc*xcd); + zna = xbc*ycd - ybc*xcd; + rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna); + xna *= rna; + yna *= rna; + zna *= rna; + + da = -(xna*xad + yna*yad + zna*zad); + + domega = k[type]*(da*da - chi[type])*(da*da - chi[type]); + a = 4.0 * da* k[type]*(da*da - chi[type]); + + if (eflag) eimproper = domega; + + f1[0] = a*( -xna); + f1[1] = a*( -yna); + f1[2] = a*( -zna); + f4[0] = a*( xna); + f4[1] = a*( yna); + f4[2] = a*( zna); + + f2[0] = a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd); + f2[1] = a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd); + f2[2] = a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd); + + f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd); + f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd); + f3[2] = - a*( xad*ycd - yad*xcd )*rna - a*da*rna*( xna*ycd - yna*xcd); + + f3[0] += -a*( yad*zbc - zad*ybc )*rna - a*da*rna*( yna*zbc - zna*ybc); + f3[1] += -a*( zad*xbc - xad*zbc )*rna - a*da*rna*( zna*xbc - xna*zbc); + f3[2] += -a*( xad*ybc - yad*xbc )*rna - a*da*rna*( xna*ybc - yna*xbc); + f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc); + f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc); + f4[2] += a*( xad*ybc - yad*xbc )*rna + a*da*rna*( xna*ybc - yna*xbc); + + + // apply force to each of 4 atoms + + if (newton_bond || i1 < nlocal) { + f[i1][0] += f1[0]; + f[i1][1] += f1[1]; + f[i1][2] += f1[2]; + } + + if (newton_bond || i2 < nlocal) { + f[i2][0] += f2[0]; + f[i2][1] += f2[1]; + f[i2][2] += f2[2]; + } + + if (newton_bond || i3 < nlocal) { + f[i3][0] += f3[0]; + f[i3][1] += f3[1]; + f[i3][2] += f3[2]; + } + + if (newton_bond || i4 < nlocal) { + f[i4][0] += f4[0]; + f[i4][1] += f4[1]; + f[i4][2] += f4[2]; + } + + if (evflag) + ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f2,f3,f4, + xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac); + } +} + +/* ---------------------------------------------------------------------- */ + +void ImproperSQDistHarm::allocate() +{ + allocated = 1; + int n = atom->nimpropertypes; + + memory->create(k,n+1,"improper:k"); + memory->create(chi,n+1,"improper:chi"); + + memory->create(setflag,n+1,"improper:setflag"); + for (int i = 1; i <= n; i++) setflag[i] = 0; +} + +/* ---------------------------------------------------------------------- + set coeffs for one type +------------------------------------------------------------------------- */ + +void ImproperSQDistHarm::coeff(int narg, char **arg) +{ +// if (which > 0) return; + if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients"); + if (!allocated) allocate(); + + int ilo,ihi; + force->bounds(FLERR,arg[0],atom->nimpropertypes,ilo,ihi); + + double k_one = force->numeric(FLERR,arg[1]); + double chi_one = force->numeric(FLERR,arg[2]); + + // convert chi from degrees to radians + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + k[i] = k_one; + //chi[i] = chi_one/180.0 * PI; + chi[i] = chi_one; + setflag[i] = 1; + count++; + } + + if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients"); +} + +/* ---------------------------------------------------------------------- + proc 0 writes out coeffs to restart file +------------------------------------------------------------------------- */ + +void ImproperSQDistHarm::write_restart(FILE *fp) +{ + fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp); + fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads coeffs from restart file, bcasts them +------------------------------------------------------------------------- */ + +void ImproperSQDistHarm::read_restart(FILE *fp) +{ + allocate(); + + if (comm->me == 0) { + fread(&k[1],sizeof(double),atom->nimpropertypes,fp); + fread(&chi[1],sizeof(double),atom->nimpropertypes,fp); + } + MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world); + MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world); + + for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1; +} diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h new file mode 100644 index 0000000000..301b5066cb --- /dev/null +++ b/src/USER-YAFF/improper_sqdistharm.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef IMPROPER_CLASS + +ImproperStyle(sqdistharm,ImproperSQDistHarm) + +#else + +#ifndef LMP_IMPROPER_SQDISTHARM_H +#define LMP_IMPROPER_SQDISTHARM_H + +#include +#include "improper.h" + +namespace LAMMPS_NS { + +class ImproperSQDistHarm : public Improper { + public: + ImproperSQDistHarm(class LAMMPS *); + ~ImproperSQDistHarm(); + void compute(int, int); + void coeff(int, char **); + void write_restart(FILE *); + void read_restart(FILE *); + + private: + double *k,*chi; + + void allocate(); +}; + +} + +#endif +#endif + diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp new file mode 100644 index 0000000000..f37dcc3ed1 --- /dev/null +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp @@ -0,0 +1,710 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_lj_switch3_coulgauss_long.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairLJSwitch3CoulGaussLong::PairLJSwitch3CoulGaussLong(LAMMPS *lmp) : Pair(lmp) +{ + ewaldflag = pppmflag = 1; + respa_enable = 1; + writedata = 1; + ftable = NULL; + qdist = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +PairLJSwitch3CoulGaussLong::~PairLJSwitch3CoulGaussLong() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(gamma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } + if (ftable) free_tables(); +} + +/* ---------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag) +{ + int i,ii,j,jj,inum,jnum,itype,jtype,itable; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double fraction,table; + double r,r2inv,r6inv,forcecoul,forcecoul2,forcelj,factor_coul,factor_lj,tr,ftr,trx; + double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2; + int *ilist,*jlist,*numneigh,**firstneigh; + double rsq; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + union_int_float_t rsq_lookup; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else { + rsq_lookup.f = rsq; + itable = rsq_lookup.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = qtmp*q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = qtmp*q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + // Lennard-Jones potential + r = sqrt(rsq); + r6inv = r2inv*r2inv*r2inv; + forcelj = r6inv*(12.0*lj3[itype][jtype]*r6inv - 6.0*lj4[itype][jtype]); + // Correction for Gaussian radii + if (lj2[itype][jtype]==0.0) { + // This means a point charge is considerd, so the correction is zero + expn2 = 0.0; + erfc2 = 0.0; + forcecoul2 = 0.0; + } + else { + rrij = lj2[itype][jtype]*r; + expn2 = exp(-rrij*rrij); + erfc2 = erfc(rrij); + prefactor2 = -qqrd2e*qtmp*q[j]/r; + forcecoul2 = prefactor2*(erfc2+EWALD_F*rrij*expn2); + } + } else forcelj = 0.0; + + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) + ecoul = prefactor*erfc1; + else { + table = etable[itable] + fraction*detable[itable]; + ecoul = qtmp*q[j] * table; + } + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + ecoul += prefactor2*erfc2*factor_coul; + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - + offset[itype][jtype]; + } else evdwl = 0.0; + + // Truncation, see Yaff Switch33 + if (truncw>0) { + if (rsq < cut_ljsq[itype][jtype]) { + if (r>cut_lj[itype][jtype]-truncw) { + trx = (cut_lj[itype][jtype]-r)*truncwi; + tr = trx*trx*(3.0-2.0*trx); + ftr = 6.0*trx*(1.0-trx)*r*truncwi; + forcelj = forcelj*tr + evdwl*ftr; + evdwl *= tr; + } + } + } + + fpair = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv; + evdwl *= factor_lj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg) +{ + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + + cut_lj_global = force->numeric(FLERR,arg[0]); + if (narg == 2) { + cut_coul = cut_lj_global; + truncw = force->numeric(FLERR,arg[1]); + } + else { + cut_coul = force->numeric(FLERR,arg[1]); + truncw = force->numeric(FLERR,arg[2]); + } + if (truncw>0.0) truncwi = 1.0/truncw; + else truncwi = 0.0; + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double gamma_one = force->numeric(FLERR,arg[4]); + + double cut_lj_one = cut_lj_global; + if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + gamma[i][j] = gamma_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style lj/switch3/coulgauss/long requires atom attribute q"); + + // request regular or rRESPA neighbor list + + int irequest; + int respa = 0; + + if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + } + + irequest = neighbor->request(this,instance_me); + + if (respa >= 1) { + neighbor->requests[irequest]->respaouter = 1; + neighbor->requests[irequest]->respainner = 1; + } + if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; + + cut_coulsq = cut_coul * cut_coul; + + // set rRESPA cutoffs + + if (strstr(update->integrate_style,"respa") && + ((Respa *) update->integrate)->level_inner >= 0) + cut_respa = ((Respa *) update->integrate)->cutoff; + else cut_respa = NULL; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + + // setup force tables + + if (ncoultablebits) init_tables(cut_coul,cut_respa); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairLJSwitch3CoulGaussLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j], + sigma[i][i],sigma[j][j]); + sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]); + gamma[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]); + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + } + + double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + if (gamma[i][i]==0.0 && gamma[j][j]==0.0) lj2[i][j] = 0.0; + else lj2[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]); + lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0); + lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0); + + if (offset_flag && (cut_lj[i][j] > 0.0)) { + // Truncation is active, so offset is zero, except if truncw==0.0 + if (truncw==0.0) { + double r = cut_lj[i][j]; + double r2inv = 1.0/(r*r); + double r6inv = r2inv*r2inv*r2inv; + double r12inv = r6inv*r6inv; + offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv; + } + else {offset[i][j] = 0.0;} + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + cut_lj[j][i] = cut_lj[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + offset[j][i] = offset[i][j]; + + // check interior rRESPA cutoff + + if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3]) + error->all(FLERR,"Pair cutoff < Respa interior cutoff"); + + // compute I,J contribution to long-range tail correction + // count total # of atoms of type I and J via Allreduce + + if (tail_flag) { + int *type = atom->type; + int nlocal = atom->nlocal; + + double count[2],all[2]; + count[0] = count[1] = 0.0; + for (int k = 0; k < nlocal; k++) { + if (type[k] == i) count[0] += 1.0; + if (type[k] == j) count[1] += 1.0; + } + MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); + + double cg = epsilon[i][j]; + double cg1 = cut_lj[i][j]; + double cg3 = sigma[i][j]; + if (truncw > 0.0) { + double cg5 = truncw; + double t1 = pow(cg1, 0.2e1); + double t2 = t1 * cg1; + double t3 = t1 * t1; + double t4 = t3 * t2; + double t5 = -cg1 + cg5; + double t6 = t5 * t5; + double t8 = t6 * t6; + double t9 = t8 * t6 * t5; + double t10 = t4 * t9; + double t11 = log(-t5); + double t14 = log(cg1); + double t19 = pow(cg5, 0.2e1); + double t20 = t19 * t19; + double t21 = t20 * t19; + double t24 = pow(cg3, 0.2e1); + double t25 = t24 * t24; + double t26 = t25 * t24; + double t29 = t20 * cg5; + double t35 = t3 * t3; + double t41 = t19 * cg5; + double t58 = t21 * t3 * t1 - t21 * t26 / 0.84e2 - 0.6e1 * t29 * t4 + t29 * cg1 * t26 / 0.18e2 + 0.15e2 * t20 * t35 - t20 * t1 * t26 / 0.9e1 - 0.20e2 * t41 * t35 * cg1 + t41 * t2 * t26 / 0.9e1 + 0.15e2 * t19 * t35 * t1 - t19 * t3 * t26 / 0.18e2 - 0.6e1 * t35 * t2 * cg5 + t35 * t3; + double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9; + etail_ij = 2.0*MY_PI*all[0]*all[1]*t71; + ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71; + } + else { + double t1 = pow(cg3, 0.2e1); + double t2 = t1 * t1; + double t3 = t2 * t1; + double t5 = pow(cg1, 0.2e1); + double t6 = t5 * t5; + double t10 = t6 * t6; + double t16 = -0.4e1 / 0.9e1 * t3 * cg * (0.3e1 * t6 * t5 - t3) / t10 / cg1; + t1 = pow(cg3, 0.2e1); + t2 = t1 * t1; + t3 = t2 * t1; + t5 = pow(cg1, 0.2e1); + t6 = t5 * t5; + double t11 = t6 * t6; + double t17 = 0.8e1 / 0.3e1 * t3 * cg * (0.3e1 * t6 * t5 - 0.2e1 * t3) / t11 / cg1; + etail_ij = 2.0*MY_PI*all[0]*all[1]*t16; + ptail_ij = -2.0/3.0*MY_PI*all[0]*all[1]*t17; + } + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&gamma[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::write_restart_settings(FILE *fp) +{ + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&truncw,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); + fwrite(&ncoultablebits,sizeof(int),1,fp); + fwrite(&tabinner,sizeof(double),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&truncw,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + fread(&ncoultablebits,sizeof(int),1,fp); + fread(&tabinner,sizeof(double),1,fp); + } + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&truncw,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); + MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world); + MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],gamma[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairLJSwitch3CoulGaussLong::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],gamma[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; + double fraction,table,forcecoul,forcecoul2,forcelj,phicoul; + double rrij,expn2,erfc2,expb,ecoul,evdwl,trx,tr,ftr; + + int itable; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else { + union_int_float_t rsq_lookup_single; + rsq_lookup_single.f = rsq; + itable = rsq_lookup_single.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = atom->q[i]*atom->q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = atom->q[i]*atom->q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r = sqrt(rsq); + r6inv = r2inv*r2inv*r2inv; + rrij = lj2[itype][jtype] * r; + if (rrij==0.0) { + expn2 = 0.0; + erfc2 = 0.0; + } + else { + expn2 = exp(-rrij*rrij); + erfc2 = erfc(rrij); + } + prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); + forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv; + } else forcelj = 0.0; + + double eng = 0.0; + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) + phicoul = prefactor*erfc1; + else { + table = etable[itable] + fraction*detable[itable]; + phicoul = atom->q[i]*atom->q[j] * table; + } + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + + if (rsq < cut_ljsq[itype][jtype]) { + ecoul += prefactor2*erfc2*factor_coul; + evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) - + offset[itype][jtype]; + } else evdwl = 0.0; + + // Truncation, see Yaff Switch3 + if (truncw>0) { + if (rsq < cut_ljsq[itype][jtype]) { + if (r>cut_lj[itype][jtype]-truncw) { + trx = (cut_lj[itype][jtype]-r)*truncwi; + tr = trx*trx*(3.0-2.0*trx); + ftr = 6.0*trx*(1.0-trx)*r*truncwi; + forcelj = forcelj*tr + evdwl*ftr; + evdwl *= tr; + } + } + } + eng += evdwl*factor_lj; + fforce = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv; + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairLJSwitch3CoulGaussLong::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"gamma") == 0) return (void *) gamma; + return NULL; +} diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h new file mode 100644 index 0000000000..75686d55a2 --- /dev/null +++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h @@ -0,0 +1,91 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(lj/switch3/coulgauss/long,PairLJSwitch3CoulGaussLong) + +#else + +#ifndef LMP_PAIR_LJ_SWITCH3_COULGAUSS_LONG_H +#define LMP_PAIR_LJ_SWITCH3_COULGAUSS_LONG_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairLJSwitch3CoulGaussLong : public Pair { + + public: + PairLJSwitch3CoulGaussLong(class LAMMPS *); + virtual ~PairLJSwitch3CoulGaussLong(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + + virtual void *extract(const char *, int &); + + protected: + double cut_lj_global; + double truncw, truncwi; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **epsilon,**sigma,**gamma; + double **lj1,**lj2,**lj3,**lj4,**offset; + double *cut_respa; + double qdist; // TIP4P distance from O site to negative charge + double g_ewald; + + virtual void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style lj/switch3/coulgauss/long requires atom attribute q + +The atom style defined does not have this attribute. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +E: Pair cutoff < Respa interior cutoff + +One or more pairwise cutoffs are too short to use with the specified +rRESPA cutoffs. + +*/ diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp new file mode 100644 index 0000000000..931ed1d116 --- /dev/null +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp @@ -0,0 +1,711 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Steven Vandenbrande +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_mm3_switch3_coulgauss_long.h" +#include "atom.h" +#include "comm.h" +#include "force.h" +#include "kspace.h" +#include "update.h" +#include "integrate.h" +#include "respa.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define EWALD_F 1.12837917 +#define EWALD_P 0.3275911 +#define A1 0.254829592 +#define A2 -0.284496736 +#define A3 1.421413741 +#define A4 -1.453152027 +#define A5 1.061405429 + +/* ---------------------------------------------------------------------- */ + +PairMM3Switch3CoulGaussLong::PairMM3Switch3CoulGaussLong(LAMMPS *lmp) : Pair(lmp) +{ + ewaldflag = pppmflag = 1; + respa_enable = 1; + writedata = 1; + ftable = NULL; + qdist = 0.0; +} + +/* ---------------------------------------------------------------------- */ + +PairMM3Switch3CoulGaussLong::~PairMM3Switch3CoulGaussLong() +{ + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(gamma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); + } + if (ftable) free_tables(); +} + +/* ---------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag) +{ + int i,ii,j,jj,inum,jnum,itype,jtype,itable; + double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; + double fraction,table; + double r,r2inv,r6inv,forcecoul,forcecoul2,forcelj,factor_coul,factor_lj,tr,ftr,trx; + double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2,expb; + int *ilist,*jlist,*numneigh,**firstneigh; + double rsq; + + evdwl = ecoul = 0.0; + ev_init(eflag,vflag); + + double **x = atom->x; + double **f = atom->f; + double *q = atom->q; + int *type = atom->type; + int nlocal = atom->nlocal; + double *special_coul = force->special_coul; + double *special_lj = force->special_lj; + int newton_pair = force->newton_pair; + double qqrd2e = force->qqrd2e; + union_int_float_t rsq_lookup; + + inum = list->inum; + ilist = list->ilist; + numneigh = list->numneigh; + firstneigh = list->firstneigh; + + // loop over neighbors of my atoms + for (ii = 0; ii < inum; ii++) { + i = ilist[ii]; + qtmp = q[i]; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + itype = type[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + factor_lj = special_lj[sbmask(j)]; + factor_coul = special_coul[sbmask(j)]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx*delx + dely*dely + delz*delz; + jtype = type[j]; + + if (rsq < cutsq[itype][jtype]) { + r2inv = 1.0/rsq; + + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = qqrd2e * qtmp*q[j]/r; + forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else { + rsq_lookup.f = rsq; + itable = rsq_lookup.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = qtmp*q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = qtmp*q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + // Repulsive exponential part + r = sqrt(rsq); + expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r); + forcelj = expb*lj1[itype][jtype]*r; + // Attractive r^-6 part + r6inv = r2inv*r2inv*r2inv; + forcelj -= 6.0*lj4[itype][jtype]*r6inv; + // Correction for Gaussian radii + if (lj2[itype][jtype]==0.0) { + // This means a point charge is considered, so the correction is zero + expn2 = 0.0; + erfc2 = 0.0; + forcecoul2 = 0.0; + } + else { + rrij = lj2[itype][jtype]*r; + expn2 = exp(-rrij*rrij); + erfc2 = erfc(rrij); + prefactor2 = -qqrd2e*qtmp*q[j]/r; + forcecoul2 = prefactor2*(erfc2+EWALD_F*rrij*expn2); + } + } else forcelj = 0.0; + + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) + ecoul = prefactor*erfc1; + else { + table = etable[itable] + fraction*detable[itable]; + ecoul = qtmp*q[j] * table; + } + if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor; + } else ecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + ecoul += prefactor2*erfc2*factor_coul; + evdwl = expb-lj4[itype][jtype]*r6inv-offset[itype][jtype]; + } else evdwl = 0.0; + + // Truncation, see Yaff Switch3 + if (truncw>0) { + if (rsq < cut_ljsq[itype][jtype]) { + if (r>cut_lj[itype][jtype]-truncw) { + trx = (cut_lj[itype][jtype]-r)*truncwi; + tr = trx*trx*(3.0-2.0*trx); + ftr = 6.0*trx*(1.0-trx)*r*truncwi; + forcelj = forcelj*tr + evdwl*ftr; + evdwl *= tr; + } + } + } + + fpair = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv; + evdwl *= factor_lj; + + f[i][0] += delx*fpair; + f[i][1] += dely*fpair; + f[i][2] += delz*fpair; + if (newton_pair || j < nlocal) { + f[j][0] -= delx*fpair; + f[j][1] -= dely*fpair; + f[j][2] -= delz*fpair; + } + + if (evflag) ev_tally(i,j,nlocal,newton_pair, + evdwl,ecoul,fpair,delx,dely,delz); + } + } + } + + if (vflag_fdotr) virial_fdotr_compute(); +} + + +/* ---------------------------------------------------------------------- + allocate all arrays +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::allocate() +{ + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag,n+1,n+1,"pair:setflag"); + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + setflag[i][j] = 0; + + memory->create(cutsq,n+1,n+1,"pair:cutsq"); + + memory->create(cut_lj,n+1,n+1,"pair:cut_lj"); + memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq"); + memory->create(epsilon,n+1,n+1,"pair:epsilon"); + memory->create(sigma,n+1,n+1,"pair:sigma"); + memory->create(gamma,n+1,n+1,"pair:gamma"); + memory->create(lj1,n+1,n+1,"pair:lj1"); + memory->create(lj2,n+1,n+1,"pair:lj2"); + memory->create(lj3,n+1,n+1,"pair:lj3"); + memory->create(lj4,n+1,n+1,"pair:lj4"); + memory->create(offset,n+1,n+1,"pair:offset"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg) +{ + if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command"); + + cut_lj_global = force->numeric(FLERR,arg[0]); + if (narg == 2) { + cut_coul = cut_lj_global; + truncw = force->numeric(FLERR,arg[1]); + } + else { + cut_coul = force->numeric(FLERR,arg[1]); + truncw = force->numeric(FLERR,arg[2]); + } + if (truncw>0.0) truncwi = 1.0/truncw; + else truncwi = 0.0; + // reset cutoffs that have been explicitly set + + if (allocated) { + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) + if (setflag[i][j]) cut_lj[i][j] = cut_lj_global; + } +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::coeff(int narg, char **arg) +{ + if (narg < 5 || narg > 6) + error->all(FLERR,"Incorrect args for pair coefficients"); + if (!allocated) allocate(); + + int ilo,ihi,jlo,jhi; + force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi); + force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi); + + double epsilon_one = force->numeric(FLERR,arg[2]); + double sigma_one = force->numeric(FLERR,arg[3]); + double gamma_one = force->numeric(FLERR,arg[4]); + + double cut_lj_one = cut_lj_global; + if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]); + + int count = 0; + for (int i = ilo; i <= ihi; i++) { + for (int j = MAX(jlo,i); j <= jhi; j++) { + epsilon[i][j] = epsilon_one; + sigma[i][j] = sigma_one; + gamma[i][j] = gamma_one; + cut_lj[i][j] = cut_lj_one; + setflag[i][j] = 1; + count++; + } + } + + if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::init_style() +{ + if (!atom->q_flag) + error->all(FLERR,"Pair style mm3/switch3/coulgauss/long requires atom attribute q"); + + // request regular or rRESPA neighbor list + + int irequest; + int respa = 0; + + if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) { + if (((Respa *) update->integrate)->level_inner >= 0) respa = 1; + if (((Respa *) update->integrate)->level_middle >= 0) respa = 2; + } + + irequest = neighbor->request(this,instance_me); + + if (respa >= 1) { + neighbor->requests[irequest]->respaouter = 1; + neighbor->requests[irequest]->respainner = 1; + } + if (respa == 2) neighbor->requests[irequest]->respamiddle = 1; + + cut_coulsq = cut_coul * cut_coul; + + // set rRESPA cutoffs + + if (strstr(update->integrate_style,"respa") && + ((Respa *) update->integrate)->level_inner >= 0) + cut_respa = ((Respa *) update->integrate)->cutoff; + else cut_respa = NULL; + + // insure use of KSpace long-range solver, set g_ewald + + if (force->kspace == NULL) + error->all(FLERR,"Pair style requires a KSpace style"); + g_ewald = force->kspace->g_ewald; + + // setup force tables + + if (ncoultablebits) init_tables(cut_coul,cut_respa); +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairMM3Switch3CoulGaussLong::init_one(int i, int j) +{ + if (setflag[i][j] == 0) { + epsilon[i][j] = sqrt(epsilon[i][i]*epsilon[j][j]); + sigma[i][j] = 0.5*(sigma[i][i] + sigma[j][j]); + gamma[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]); + cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]); + } + + double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist); + cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j]; + lj1[i][j] = 12.0 / (2.0*sigma[i][j]); + if (gamma[i][i]==0.0 && gamma[j][j]==0.0) lj2[i][j] = 0.0; + else lj2[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]); + lj3[i][j] = 1.84e5 * epsilon[i][j]; + lj4[i][j] = 2.25 * epsilon[i][j] * pow(2.0*sigma[i][j],6.0); + + if (offset_flag && (cut_lj[i][j] > 0.0)) { + // Truncation is active, so offset is zero, except if truncw==0.0 + if (truncw==0.0) { + double r = cut_lj[i][j]; + double r2inv = 1.0/(r*r); + double r6inv = r2inv*r2inv*r2inv; + double expb = lj3[i][j]*exp(-lj1[i][j]*r); + offset[i][j] = expb-lj4[i][j]*r6inv; + } + else {offset[i][j] = 0.0;} + } else offset[i][j] = 0.0; + + cut_ljsq[j][i] = cut_ljsq[i][j]; + cut_lj[j][i] = cut_lj[i][j]; + lj1[j][i] = lj1[i][j]; + lj2[j][i] = lj2[i][j]; + lj3[j][i] = lj3[i][j]; + lj4[j][i] = lj4[i][j]; + offset[j][i] = offset[i][j]; + + // check interior rRESPA cutoff + + if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3]) + error->all(FLERR,"Pair cutoff < Respa interior cutoff"); + + // compute I,J contribution to long-range tail correction + // count total # of atoms of type I and J via Allreduce + + if (tail_flag) { + int *type = atom->type; + int nlocal = atom->nlocal; + + double count[2],all[2]; + count[0] = count[1] = 0.0; + for (int k = 0; k < nlocal; k++) { + if (type[k] == i) count[0] += 1.0; + if (type[k] == j) count[1] += 1.0; + } + MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world); + + double cg = epsilon[i][j]; + double cg1 = cut_lj[i][j]; + double cg3 = 2.0*sigma[i][j];//Mind the factor 2 here!!! + if (truncw > 0.0) { + double cg5 = truncw; + double t1 = pow(cg3, 0.2e1); + double t2 = t1 * cg3; + double t3 = 0.5e1 / 0.216e3 * t2; + double t5 = cg1 / 0.9e1; + double t8 = -cg1 + cg5; + double t14 = t8 * t8; + double t17 = 0.1e1 / cg3; + double t20 = exp(0.12e2 * t17 * cg5); + double t30 = pow(cg1, 0.2e1); + double t36 = exp(-0.12e2 * t17 * cg1); + double t37 = pow(cg5, 0.2e1); + double t39 = 0.1e1 / t37 / cg5; + double t43 = cg1 * t8; + double t44 = log(-t8); + double t47 = log(cg1); + double t54 = t1 * t1; + double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39); + etail_ij = 2.0*MY_PI*all[0]*all[1]*t64; + ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64; + } + else { + double t2 = pow(cg3, 0.2e1); + double t3 = t2 * t2; + double t7 = 0.12e2 / cg3 * cg1; + double t8 = exp(t7); + double t11 = pow(cg1, 0.2e1); + double t12 = t11 * t11; + double t17 = t11 * cg1; + double t21 = exp(-t7); + double t27 = -0.9259259259e-2 * cg3 * cg * (0.81e2 * t3 * cg3 * t8 - 0.1656000e7 * t12 * cg1 - 0.276000e6 * cg3 * t12 - 0.23000e5 * t2 * t17) * t21 / t17; + double t1 = pow(cg3, 0.2e1); + t2 = t1 * t1; + double t6 = 0.12e2 / cg3 * cg1; + t7 = exp(t6); + double t10 = pow(cg1, 0.2e1); + t11 = t10 * t10; + double t19 = t10 * cg1; + double t25 = exp(-t6); + double t29 = 0.5555555556e-1 * cg * (0.81e2 * t2 * t1 * t7 - 0.3312000e7 * t11 * t10 - 0.828000e6 * cg3 * t11 * cg1 - 0.138000e6 * t1 * t11 - 0.11500e5 * t19 * t1 * cg3) * t25 / t19; + etail_ij = 2.0*MY_PI*all[0]*all[1]*t27; + ptail_ij = -2.0/3.0*MY_PI*all[0]*all[1]*t29; + } + } + + return cut; +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::write_restart(FILE *fp) +{ + write_restart_settings(fp); + + int i,j; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + fwrite(&setflag[i][j],sizeof(int),1,fp); + if (setflag[i][j]) { + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&gamma[i][j],sizeof(double),1,fp); + fwrite(&cut_lj[i][j],sizeof(double),1,fp); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::read_restart(FILE *fp) +{ + read_restart_settings(fp); + + allocate(); + + int i,j; + int me = comm->me; + for (i = 1; i <= atom->ntypes; i++) + for (j = i; j <= atom->ntypes; j++) { + if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); + if (setflag[i][j]) { + if (me == 0) { + fread(&epsilon[i][j],sizeof(double),1,fp); + fread(&sigma[i][j],sizeof(double),1,fp); + fread(&gamma[i][j],sizeof(double),1,fp); + fread(&cut_lj[i][j],sizeof(double),1,fp); + } + MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world); + } + } +} + +/* ---------------------------------------------------------------------- + proc 0 writes to restart file +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::write_restart_settings(FILE *fp) +{ + fwrite(&cut_lj_global,sizeof(double),1,fp); + fwrite(&cut_coul,sizeof(double),1,fp); + fwrite(&truncw,sizeof(double),1,fp); + fwrite(&offset_flag,sizeof(int),1,fp); + fwrite(&mix_flag,sizeof(int),1,fp); + fwrite(&tail_flag,sizeof(int),1,fp); + fwrite(&ncoultablebits,sizeof(int),1,fp); + fwrite(&tabinner,sizeof(double),1,fp); +} + +/* ---------------------------------------------------------------------- + proc 0 reads from restart file, bcasts +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::read_restart_settings(FILE *fp) +{ + if (comm->me == 0) { + fread(&cut_lj_global,sizeof(double),1,fp); + fread(&cut_coul,sizeof(double),1,fp); + fread(&truncw,sizeof(double),1,fp); + fread(&offset_flag,sizeof(int),1,fp); + fread(&mix_flag,sizeof(int),1,fp); + fread(&tail_flag,sizeof(int),1,fp); + fread(&ncoultablebits,sizeof(int),1,fp); + fread(&tabinner,sizeof(double),1,fp); + } + printf("Reading from restart, trunc = %f\n",truncw); + MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world); + MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world); + MPI_Bcast(&truncw,1,MPI_DOUBLE,0,world); + MPI_Bcast(&offset_flag,1,MPI_INT,0,world); + MPI_Bcast(&mix_flag,1,MPI_INT,0,world); + MPI_Bcast(&tail_flag,1,MPI_INT,0,world); + MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world); + MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world); +} + + +/* ---------------------------------------------------------------------- + proc 0 writes to data file +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::write_data(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],gamma[i][i]); +} + +/* ---------------------------------------------------------------------- + proc 0 writes all pairs to data file +------------------------------------------------------------------------- */ + +void PairMM3Switch3CoulGaussLong::write_data_all(FILE *fp) +{ + for (int i = 1; i <= atom->ntypes; i++) + for (int j = i; j <= atom->ntypes; j++) + fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],gamma[i][j],cut_lj[i][j]); +} + +/* ---------------------------------------------------------------------- */ + +double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype, + double rsq, + double factor_coul, double factor_lj, + double &fforce) +{ + double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2; + double fraction,table,forcecoul,forcecoul2,forcelj,phicoul; + double expb,rrij,expn2,erfc2,ecoul,evdwl,trx,tr,ftr; + + int itable; + + r2inv = 1.0/rsq; + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) { + r = sqrt(rsq); + grij = g_ewald * r; + expm2 = exp(-grij*grij); + t = 1.0 / (1.0 + EWALD_P*grij); + erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2; + prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2); + if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor; + } else { + union_int_float_t rsq_lookup_single; + rsq_lookup_single.f = rsq; + itable = rsq_lookup_single.i & ncoulmask; + itable >>= ncoulshiftbits; + fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable]; + table = ftable[itable] + fraction*dftable[itable]; + forcecoul = atom->q[i]*atom->q[j] * table; + if (factor_coul < 1.0) { + table = ctable[itable] + fraction*dctable[itable]; + prefactor = atom->q[i]*atom->q[j] * table; + forcecoul -= (1.0-factor_coul)*prefactor; + } + } + } else forcecoul = 0.0; + + if (rsq < cut_ljsq[itype][jtype]) { + r = sqrt(rsq); + r6inv = r2inv*r2inv*r2inv; + expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r); + rrij = lj2[itype][jtype] * r; + if (rrij==0.0) { + expn2 = 0.0; + erfc2 = 0.0; + } + else { + expn2 = exp(-rrij*rrij); + erfc2 = erfc(rrij); + } + prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r; + forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2); + forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv; + } else forcelj = 0.0; + + double eng = 0.0; + if (rsq < cut_coulsq) { + if (!ncoultablebits || rsq <= tabinnersq) + phicoul = prefactor*erfc1; + else { + table = etable[itable] + fraction*detable[itable]; + phicoul = atom->q[i]*atom->q[j] * table; + } + if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor; + eng += phicoul; + } + + if (rsq < cut_ljsq[itype][jtype]) { + ecoul += prefactor2*erfc2*factor_coul; + evdwl = expb-lj4[itype][jtype]*r6inv-offset[itype][jtype]; + } else evdwl = 0.0; + + // Truncation, see Yaff Switch3 + if (truncw>0) { + if (rsq < cut_ljsq[itype][jtype]) { + if (r>cut_lj[itype][jtype]-truncw) { + trx = (cut_lj[itype][jtype]-r)*truncwi; + tr = trx*trx*(3.0-2.0*trx); + ftr = 6.0*trx*(1.0-trx)*r*truncwi; + forcelj = forcelj*tr + evdwl*ftr; + evdwl *= tr; + } + } + } + eng += evdwl*factor_lj; + fforce = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv; + + return eng; +} + +/* ---------------------------------------------------------------------- */ + +void *PairMM3Switch3CoulGaussLong::extract(const char *str, int &dim) +{ + dim = 0; + if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul; + dim = 2; + if (strcmp(str,"epsilon") == 0) return (void *) epsilon; + if (strcmp(str,"sigma") == 0) return (void *) sigma; + if (strcmp(str,"gamma") == 0) return (void *) gamma; + return NULL; +} diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h new file mode 100644 index 0000000000..35ae6c7995 --- /dev/null +++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h @@ -0,0 +1,91 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS + +PairStyle(mm3/switch3/coulgauss/long,PairMM3Switch3CoulGaussLong) + +#else + +#ifndef LMP_PAIR_MM3_SWITCH3_COULGAUSS_LONG_H +#define LMP_PAIR_MM3_SWITCH3_COULGAUSS_LONG_H + +#include "pair.h" + +namespace LAMMPS_NS { + +class PairMM3Switch3CoulGaussLong : public Pair { + + public: + PairMM3Switch3CoulGaussLong(class LAMMPS *); + virtual ~PairMM3Switch3CoulGaussLong(); + virtual void compute(int, int); + virtual void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + virtual double init_one(int, int); + void write_restart(FILE *); + void read_restart(FILE *); + virtual void write_restart_settings(FILE *); + virtual void read_restart_settings(FILE *); + void write_data(FILE *); + void write_data_all(FILE *); + virtual double single(int, int, int, int, double, double, double, double &); + + virtual void *extract(const char *, int &); + + protected: + double cut_lj_global; + double truncw, truncwi; + double **cut_lj,**cut_ljsq; + double cut_coul,cut_coulsq; + double **epsilon,**sigma,**gamma; + double **lj1,**lj2,**lj3,**lj4,**offset; + double *cut_respa; + double qdist; // TIP4P distance from O site to negative charge + double g_ewald; + + virtual void allocate(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair style mm3/switch3/coulgauss/long requires atom attribute q + +The atom style defined does not have this attribute. + +E: Pair style requires a KSpace style + +No kspace style is defined. + +E: Pair cutoff < Respa interior cutoff + +One or more pairwise cutoffs are too short to use with the specified +rRESPA cutoffs. + +*/ diff --git a/src/VORONOI/compute_voronoi_atom.cpp b/src/VORONOI/compute_voronoi_atom.cpp index 621e29ff4b..f884530fd9 100644 --- a/src/VORONOI/compute_voronoi_atom.cpp +++ b/src/VORONOI/compute_voronoi_atom.cpp @@ -90,7 +90,7 @@ ComputeVoronoi::ComputeVoronoi(LAMMPS *lmp, int narg, char **arg) : else if (strcmp(arg[iarg], "surface") == 0) { if (iarg + 2 > narg) error->all(FLERR,"Illegal compute voronoi/atom command"); // group all is a special case where we just skip group testing - if(strcmp(arg[iarg+1], "all") == 0) { + if (strcmp(arg[iarg+1], "all") == 0) { surface = VOROSURF_ALL; } else { sgroup = group->find(arg[iarg+1]); @@ -266,7 +266,7 @@ void ComputeVoronoi::buildCells() double **x = atom->x; // setup bounds for voro++ domain for orthogonal and triclinic simulation boxes - if( domain->triclinic ) { + if (domain->triclinic) { // triclinic box: embed parallelepiped into orthogonal voro++ domain // cutghost is in lamda coordinates for triclinic boxes, use subxx_lamda @@ -356,7 +356,7 @@ void ComputeVoronoi::buildCells() // pass coordinates for local and ghost atoms to voro++ for (i = 0; i < nall; i++) { - if( !onlyGroup || (mask[i] & groupbit) ) + if (!onlyGroup || (mask[i] & groupbit)) con_poly->put(i,x[i][0],x[i][1],x[i][2],rfield[i]); } } else { @@ -374,7 +374,7 @@ void ComputeVoronoi::buildCells() // pass coordinates for local and ghost atoms to voro++ for (i = 0; i < nall; i++) - if( !onlyGroup || (mask[i] & groupbit) ) + if (!onlyGroup || (mask[i] & groupbit)) con_mono->put(i,x[i][0],x[i][1],x[i][2]); } } @@ -625,7 +625,7 @@ double ComputeVoronoi::memory_usage() void ComputeVoronoi::compute_vector() { invoked_vector = update->ntimestep; - if( invoked_peratom < invoked_vector ) compute_peratom(); + if (invoked_peratom < invoked_vector) compute_peratom(); for( int i=0; intimestep; - if( invoked_peratom < invoked_local ) compute_peratom(); + if (invoked_peratom < invoked_local) compute_peratom(); } /* ---------------------------------------------------------------------- */ diff --git a/src/angle.h b/src/angle.h index 0247fa0ff8..3d8371242e 100644 --- a/src/angle.h +++ b/src/angle.h @@ -58,6 +58,10 @@ class Angle : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; + void ev_init(int eflag, int vflag, int alloc = 1) { + if (eflag||vflag) ev_setup(eflag, vflag, alloc); + else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0; + } void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, int, double, double *, double *, double, double, double, double, double, double); diff --git a/src/angle_deprecated.cpp b/src/angle_deprecated.cpp index 66efbfacbc..b5af217b7b 100644 --- a/src/angle_deprecated.cpp +++ b/src/angle_deprecated.cpp @@ -52,6 +52,6 @@ void AngleDeprecated::settings(int, char **) writemsg(lmp,"\nAngle style 'DEPRECATED' is a dummy style\n\n",0); } -} +} diff --git a/src/angle_hybrid.cpp b/src/angle_hybrid.cpp index c29eaac2ae..6afa7413b2 100644 --- a/src/angle_hybrid.cpp +++ b/src/angle_hybrid.cpp @@ -103,8 +103,7 @@ void AngleHybrid::compute(int eflag, int vflag) // set neighbor->anglelist to sub-style anglelist before call // accumulate sub-style global/peratom energy/virial in hybrid - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); for (m = 0; m < nstyles; m++) { neighbor->nanglelist = nanglelist[m]; diff --git a/src/angle_zero.cpp b/src/angle_zero.cpp index d7b7c9cdb5..6eb127fa58 100644 --- a/src/angle_zero.cpp +++ b/src/angle_zero.cpp @@ -47,8 +47,7 @@ AngleZero::~AngleZero() void AngleZero::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/atom.cpp b/src/atom.cpp index 95f5406d95..34ea253751 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -58,6 +58,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp) natoms = 0; nlocal = nghost = nmax = 0; ntypes = 0; + nellipsoids = nlines = ntris = nbodies = 0; nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0; nbonds = nangles = ndihedrals = nimpropers = 0; @@ -738,6 +739,45 @@ int Atom::tag_consecutive() return 1; } +/* ---------------------------------------------------------------------- + check that bonus data settings are valid + error if number of atoms with ellipsoid/line/tri/body flags + are consistent with global setting. +------------------------------------------------------------------------- */ + +void Atom::bonus_check() +{ + bigint local_ellipsoids = 0, local_lines = 0, local_tris = 0; + bigint local_bodies = 0, num_global; + + for (int i = 0; i < nlocal; ++i) { + if (ellipsoid && (ellipsoid[i] >=0)) ++local_ellipsoids; + if (line && (line[i] >=0)) ++local_lines; + if (tri && (tri[i] >=0)) ++local_tris; + if (body && (body[i] >=0)) ++local_bodies; + } + + MPI_Allreduce(&local_ellipsoids,&num_global,1,MPI_LMP_BIGINT,MPI_SUM,world); + if (nellipsoids != num_global) + error->all(FLERR,"Inconsistent 'ellipsoids' header value and number of " + "atoms with enabled ellipsoid flags"); + + MPI_Allreduce(&local_lines,&num_global,1,MPI_LMP_BIGINT,MPI_SUM,world); + if (nlines != num_global) + error->all(FLERR,"Inconsistent 'lines' header value and number of " + "atoms with enabled line flags"); + + MPI_Allreduce(&local_tris,&num_global,1,MPI_LMP_BIGINT,MPI_SUM,world); + if (ntris != num_global) + error->all(FLERR,"Inconsistent 'tris' header value and number of " + "atoms with enabled tri flags"); + + MPI_Allreduce(&local_bodies,&num_global,1,MPI_LMP_BIGINT,MPI_SUM,world); + if (nbodies != num_global) + error->all(FLERR,"Inconsistent 'bodies' header value and number of " + "atoms with enabled body flags"); +} + /* ---------------------------------------------------------------------- count and return words in a single line make copy of line before using strtok so as not to change line @@ -1884,11 +1924,19 @@ void Atom::setup_sort_bins() // user setting if explicitly set // default = 1/2 of neighbor cutoff // check if neighbor cutoff = 0.0 + // and in that case, disable sorting - double binsize; + double binsize = 0.0; if (userbinsize > 0.0) binsize = userbinsize; - else binsize = 0.5 * neighbor->cutneighmax; - if (binsize == 0.0) error->all(FLERR,"Atom sorting has bin size = 0.0"); + else if (neighbor->cutneighmax > 0.0) binsize = 0.5 * neighbor->cutneighmax; + + if ((binsize == 0.0) && (sortfreq > 0)) { + sortfreq = 0; + if (comm->me == 0) + error->warning(FLERR,"No pairwise cutoff or binsize set. " + "Atom sorting therefore disabled."); + return; + } double bininv = 1.0/binsize; @@ -2036,9 +2084,7 @@ void Atom::delete_callback(const char *id, int flag) { if (id == NULL) return; - int ifix; - for (ifix = 0; ifix < modify->nfix; ifix++) - if (strcmp(id,modify->fix[ifix]->id) == 0) break; + int ifix = modify->find_fix(id); // compact the list of callbacks @@ -2046,6 +2092,8 @@ void Atom::delete_callback(const char *id, int flag) int match; for (match = 0; match < nextra_grow; match++) if (extra_grow[match] == ifix) break; + if ((nextra_grow == 0) || (match == nextra_grow)) + error->all(FLERR,"Trying to delete non-existent Atom::grow() callback"); for (int i = match; i < nextra_grow-1; i++) extra_grow[i] = extra_grow[i+1]; nextra_grow--; @@ -2054,6 +2102,8 @@ void Atom::delete_callback(const char *id, int flag) int match; for (match = 0; match < nextra_restart; match++) if (extra_restart[match] == ifix) break; + if ((nextra_restart == 0) || (match == nextra_restart)) + error->all(FLERR,"Trying to delete non-existent Atom::restart() callback"); for (int i = match; i < nextra_restart-1; i++) extra_restart[i] = extra_restart[i+1]; nextra_restart--; @@ -2062,6 +2112,8 @@ void Atom::delete_callback(const char *id, int flag) int match; for (match = 0; match < nextra_border; match++) if (extra_border[match] == ifix) break; + if ((nextra_border == 0) || (match == nextra_border)) + error->all(FLERR,"Trying to delete non-existent Atom::border() callback"); for (int i = match; i < nextra_border-1; i++) extra_border[i] = extra_border[i+1]; nextra_border--; @@ -2278,7 +2330,7 @@ int Atom::memcheck(const char *str) return 0; } - if (strlen(memstr) + n >= memlength) { + if ((int)strlen(memstr) + n >= memlength) { memlength += DELTA_MEMSTR; memory->grow(memstr,memlength,"atom:memstr"); } diff --git a/src/atom.h b/src/atom.h index 7e003dff5e..b2a657cf1a 100644 --- a/src/atom.h +++ b/src/atom.h @@ -34,6 +34,10 @@ class Atom : protected Pointers { int tag_enable; // 0/1 if atom ID tags are defined int molecular; // 0 = atomic, 1 = standard molecular system, // 2 = molecule template system + bigint nellipsoids; // number of ellipsoids + bigint nlines; // number of lines + bigint ntris; // number of triangles + bigint nbodies; // number of bodies bigint nbonds,nangles,ndihedrals,nimpropers; int ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes; @@ -233,6 +237,8 @@ class Atom : protected Pointers { void tag_extend(); int tag_consecutive(); + void bonus_check(); + int parse_data(const char *); int count_words(const char *); int count_words(const char *, char *); @@ -496,12 +502,6 @@ E: Atom sort did not operate correctly This is an internal LAMMPS error. Please report it to the developers. -E: Atom sorting has bin size = 0.0 - -The neighbor cutoff is being used as the bin size, but it is zero. -Thus you must explicitly list a bin size in the atom_modify sort -command or turn off sorting. - E: Too many atom sorting bins This is likely due to an immense simulation box that has blown up diff --git a/src/atom_vec_body.cpp b/src/atom_vec_body.cpp index 5a277627ee..893a4c7dc4 100644 --- a/src/atom_vec_body.cpp +++ b/src/atom_vec_body.cpp @@ -1286,7 +1286,7 @@ void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values) body[nlocal] = atoi(values[2]); if (body[nlocal] == 0) body[nlocal] = -1; else if (body[nlocal] == 1) body[nlocal] = 0; - else error->one(FLERR,"Invalid atom type in Atoms section of data file"); + else error->one(FLERR,"Invalid bodyflag in Atoms section of data file"); rmass[nlocal] = atof(values[3]); if (rmass[nlocal] <= 0.0) diff --git a/src/atom_vec_body.h b/src/atom_vec_body.h index 3244b0f64d..7cc052b6c5 100644 --- a/src/atom_vec_body.h +++ b/src/atom_vec_body.h @@ -92,6 +92,8 @@ class AtomVecBody : public AtomVec { double radius_body(int, int, int *, double *); void set_quat(int, double *); + int nlocal_bonus; + private: tagint *tag; int *type,*mask; @@ -102,7 +104,7 @@ class AtomVecBody : public AtomVec { double **angmom,**torque; int *body; - int nlocal_bonus,nghost_bonus,nmax_bonus; + int nghost_bonus,nmax_bonus; int intdoubleratio; // sizeof(double) / sizeof(int) MyPoolChunk *icp; diff --git a/src/atom_vec_ellipsoid.cpp b/src/atom_vec_ellipsoid.cpp index c569f89a09..2bf3f683d0 100644 --- a/src/atom_vec_ellipsoid.cpp +++ b/src/atom_vec_ellipsoid.cpp @@ -1148,7 +1148,7 @@ void AtomVecEllipsoid::data_atom(double *coord, imageint imagetmp, ellipsoid[nlocal] = atoi(values[2]); if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1; else if (ellipsoid[nlocal] == 1) ellipsoid[nlocal] = 0; - else error->one(FLERR,"Invalid atom type in Atoms section of data file"); + else error->one(FLERR,"Invalid ellipsoidflag in Atoms section of data file"); rmass[nlocal] = atof(values[3]); if (rmass[nlocal] <= 0.0) diff --git a/src/atom_vec_ellipsoid.h b/src/atom_vec_ellipsoid.h index 6beb68b176..d71859624e 100644 --- a/src/atom_vec_ellipsoid.h +++ b/src/atom_vec_ellipsoid.h @@ -83,6 +83,8 @@ class AtomVecEllipsoid : public AtomVec { void set_shape(int, double, double, double); + int nlocal_bonus; + private: tagint *tag; int *type,*mask; @@ -92,7 +94,7 @@ class AtomVecEllipsoid : public AtomVec { double **angmom,**torque; int *ellipsoid; - int nlocal_bonus,nghost_bonus,nmax_bonus; + int nghost_bonus,nmax_bonus; void grow_bonus(); void copy_bonus(int, int); diff --git a/src/atom_vec_line.cpp b/src/atom_vec_line.cpp index 9babfe3735..020b622c93 100644 --- a/src/atom_vec_line.cpp +++ b/src/atom_vec_line.cpp @@ -1044,7 +1044,7 @@ void AtomVecLine::data_atom(double *coord, imageint imagetmp, char **values) line[nlocal] = atoi(values[3]); if (line[nlocal] == 0) line[nlocal] = -1; else if (line[nlocal] == 1) line[nlocal] = 0; - else error->one(FLERR,"Invalid atom type in Atoms section of data file"); + else error->one(FLERR,"Invalid lineflag in Atoms section of data file"); rmass[nlocal] = atof(values[4]); if (rmass[nlocal] <= 0.0) diff --git a/src/atom_vec_line.h b/src/atom_vec_line.h index 7f07532fa4..6c8701cfc2 100644 --- a/src/atom_vec_line.h +++ b/src/atom_vec_line.h @@ -83,6 +83,8 @@ class AtomVecLine : public AtomVec { void set_length(int, double); + int nlocal_bonus; + private: tagint *tag; int *type,*mask; @@ -93,7 +95,7 @@ class AtomVecLine : public AtomVec { double **omega,**torque; int *line; - int nlocal_bonus,nghost_bonus,nmax_bonus; + int nghost_bonus,nmax_bonus; void grow_bonus(); void copy_bonus(int, int); diff --git a/src/atom_vec_tri.cpp b/src/atom_vec_tri.cpp index 2c31b95cfe..8fbe0a92dc 100644 --- a/src/atom_vec_tri.cpp +++ b/src/atom_vec_tri.cpp @@ -1443,7 +1443,7 @@ void AtomVecTri::data_atom(double *coord, imageint imagetmp, char **values) tri[nlocal] = atoi(values[3]); if (tri[nlocal] == 0) tri[nlocal] = -1; else if (tri[nlocal] == 1) tri[nlocal] = 0; - else error->one(FLERR,"Invalid atom type in Atoms section of data file"); + else error->one(FLERR,"Invalid triflag in Atoms section of data file"); rmass[nlocal] = atof(values[4]); if (rmass[nlocal] <= 0.0) diff --git a/src/atom_vec_tri.h b/src/atom_vec_tri.h index 390efc7c10..81b4c1ada9 100644 --- a/src/atom_vec_tri.h +++ b/src/atom_vec_tri.h @@ -85,6 +85,8 @@ class AtomVecTri : public AtomVec { void set_equilateral(int, double); + int nlocal_bonus; + private: tagint *tag; int *type,*mask; @@ -95,7 +97,7 @@ class AtomVecTri : public AtomVec { double **omega,**angmom,**torque; int *tri; - int nlocal_bonus,nghost_bonus,nmax_bonus; + int nghost_bonus,nmax_bonus; void grow_bonus(); void copy_bonus(int, int); diff --git a/src/bond.h b/src/bond.h index 9c353a1a6d..8fb7040832 100644 --- a/src/bond.h +++ b/src/bond.h @@ -64,6 +64,10 @@ class Bond : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; + void ev_init(int eflag, int vflag, int alloc = 1) { + if (eflag||vflag) ev_setup(eflag, vflag, alloc); + else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0; + } void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, double, double, double, double, double); }; diff --git a/src/bond_deprecated.cpp b/src/bond_deprecated.cpp index e7d91df7b5..567b1a4d00 100644 --- a/src/bond_deprecated.cpp +++ b/src/bond_deprecated.cpp @@ -52,6 +52,6 @@ void BondDeprecated::settings(int, char **) writemsg(lmp,"\nBond style 'DEPRECATED' is a dummy style\n\n",0); } -} +} diff --git a/src/bond_hybrid.cpp b/src/bond_hybrid.cpp index c3a71ee71c..65609b4b6e 100644 --- a/src/bond_hybrid.cpp +++ b/src/bond_hybrid.cpp @@ -33,6 +33,7 @@ BondHybrid::BondHybrid(LAMMPS *lmp) : Bond(lmp) { writedata = 0; nstyles = 0; + has_quartic = -1; } /* ---------------------------------------------------------------------- */ @@ -102,8 +103,7 @@ void BondHybrid::compute(int eflag, int vflag) // set neighbor->bondlist to sub-style bondlist before call // accumulate sub-style global/peratom energy/virial in hybrid - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); for (m = 0; m < nstyles; m++) { neighbor->nbondlist = nbondlist[m]; @@ -171,6 +171,7 @@ void BondHybrid::settings(int narg, char **arg) delete [] styles; for (int i = 0; i < nstyles; i++) delete [] keywords[i]; delete [] keywords; + has_quartic = -1; } if (allocated) { @@ -214,14 +215,23 @@ void BondHybrid::settings(int narg, char **arg) i = 0; while (i < narg) { + for (m = 0; m < nstyles; m++) if (strcmp(arg[i],keywords[m]) == 0) error->all(FLERR,"Bond style hybrid cannot use same bond style twice"); + if (strcmp(arg[i],"hybrid") == 0) error->all(FLERR,"Bond style hybrid cannot have hybrid as an argument"); + if (strcmp(arg[i],"none") == 0) error->all(FLERR,"Bond style hybrid cannot have none as an argument"); + // register index of quartic bond type, + // so that bond type 0 can be mapped to it + + if (strncmp(arg[i],"quartic",7) == 0) + has_quartic = m; + styles[nstyles] = force->new_bond(arg[i],1,dummy); force->store_style(keywords[nstyles],arg[i],0); @@ -283,6 +293,12 @@ void BondHybrid::init_style() { for (int m = 0; m < nstyles; m++) if (styles[m]) styles[m]->init_style(); + + // bond style quartic will set broken bonds to bond type 0, so we need + // to create an entry for it in the bond type to sub-style map + + if (has_quartic >= 0) + map[0] = has_quartic; } /* ---------------------------------------------------------------------- diff --git a/src/bond_hybrid.h b/src/bond_hybrid.h index a385a2e3f8..e51d467ac1 100644 --- a/src/bond_hybrid.h +++ b/src/bond_hybrid.h @@ -47,7 +47,7 @@ class BondHybrid : public Bond { private: int *map; // which style each bond type points to - + int has_quartic; // which style, if any is a quartic bond style int *nbondlist; // # of bonds in sub-style bondlists int *maxbond; // max # of bonds sub-style lists can store int ***bondlist; // bondlist for each sub-style diff --git a/src/bond_zero.cpp b/src/bond_zero.cpp index 9fcf300b21..0847cf9e6b 100644 --- a/src/bond_zero.cpp +++ b/src/bond_zero.cpp @@ -45,8 +45,7 @@ BondZero::~BondZero() void BondZero::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/change_box.cpp b/src/change_box.cpp index 93dff387c4..b7d3cb245f 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -272,7 +272,7 @@ void ChangeBox::command(int narg, char **arg) if (domain->dimension == 2 && domain->zperiodic == 0) error->all(FLERR, "Cannot change box z boundary to " - "nonperiodic for a 2d simulation"); + "non-periodic for a 2d simulation"); domain->set_initial_box(); domain->set_global_box(); domain->set_local_box(); diff --git a/src/change_box.h b/src/change_box.h index d9152b7fb0..d8a057f9a6 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -97,7 +97,7 @@ E: Cannot change box tilt factors for orthogonal box Cannot use tilt factors unless the simulation box is non-orthogonal. -E: Cannot change box z boundary to nonperiodic for a 2d simulation +E: Cannot change box z boundary to non-periodic for a 2d simulation Self-explanatory. diff --git a/src/comm_brick.cpp b/src/comm_brick.cpp index bf7f3e2f8f..330551aaed 100644 --- a/src/comm_brick.cpp +++ b/src/comm_brick.cpp @@ -1069,6 +1069,7 @@ void CommBrick::reverse_comm_fix_variable(Fix *fix) MPI_Sendrecv(&nsend,1,MPI_INT,recvproc[iswap],0, &nrecv,1,MPI_INT,sendproc[iswap],0,world, MPI_STATUS_IGNORE); + if (sendnum[iswap]) { if (nrecv > maxrecv) grow_recv(nrecv); MPI_Irecv(buf_recv,maxrecv,MPI_DOUBLE,sendproc[iswap],0, diff --git a/src/compute_adf.cpp b/src/compute_adf.cpp index 885a051b5b..e9f9ba2b6f 100644 --- a/src/compute_adf.cpp +++ b/src/compute_adf.cpp @@ -45,7 +45,7 @@ enum{DEGREE, RADIAN, COSINE}; ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), - ilo(NULL), ihi(NULL), jlo(NULL), jhi(NULL), klo(NULL), khi(NULL), + ilo(NULL), ihi(NULL), jlo(NULL), jhi(NULL), klo(NULL), khi(NULL), hist(NULL), histall(NULL), rcutinnerj(NULL), rcutinnerk(NULL), rcutouterj(NULL), rcutouterk(NULL), @@ -53,7 +53,7 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : iatomcount(NULL), iatomcountall(NULL), iatomflag(NULL), maxjatom(NULL), maxkatom(NULL), numjatom(NULL), numkatom(NULL), - neighjatom(NULL),neighkatom(NULL), + neighjatom(NULL),neighkatom(NULL), jatomflag(NULL), katomflag(NULL), maxjkatom(NULL), numjkatom(NULL), neighjkatom(NULL), bothjkatom(NULL), delrjkatom(NULL) @@ -99,7 +99,7 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : if (!nargtriple) ntriples = 1; else { - if (nargtriple % nargsperadf) + if (nargtriple % nargsperadf) error->all(FLERR,"Illegal compute adf command"); ntriples = nargtriple/nargsperadf; } @@ -140,8 +140,8 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[m],ihi[m]); force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[m],jhi[m]); force->bounds(FLERR,arg[iarg+2],atom->ntypes,klo[m],khi[m]); - if (ilo[m] > ihi[m] || - jlo[m] > jhi[m] || + if (ilo[m] > ihi[m] || + jlo[m] > jhi[m] || klo[m] > khi[m]) error->all(FLERR,"Illegal compute adf command"); rcutinnerj[m] = force->numeric(FLERR,arg[iarg+3]); @@ -157,7 +157,7 @@ ComputeADF::ComputeADF(LAMMPS *lmp, int narg, char **arg) : } // identify central atom types - + int i,j,k; for (int m = 0; m < ntriples; m++) { @@ -311,13 +311,13 @@ void ComputeADF::init() int x0; if (ordinate_style == DEGREE) { - deltax = MY_PI / nbin * rad2deg; - deltaxinv = nbin / MY_PI; + deltax = MY_PI / nbin * rad2deg; + deltaxinv = nbin / MY_PI; x0 = 0.0; } else if (ordinate_style == RADIAN) { deltax = MY_PI / nbin; - deltaxinv = nbin / MY_PI; + deltaxinv = nbin / MY_PI; x0 = 0.0; } else if (ordinate_style == COSINE) { @@ -392,7 +392,7 @@ void ComputeADF::compute_array() // tally the ADFs // all three atoms i, j, and k must be in fix group // tally I,J,K triple only if I is central atom - // and J,K matches unordered neighbor types (JJ,KK) + // and J,K matches unordered neighbor types (JJ,KK) double **x = atom->x; int *type = atom->type; @@ -422,22 +422,22 @@ void ComputeADF::compute_array() numkatom[m] = 0; numjkatom[m] = 0; } - + for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; factor_lj = special_lj[sbmask(j)]; factor_coul = special_coul[sbmask(j)]; j &= NEIGHMASK; - + // if both weighting factors are 0, skip this pair // could be 0 and still be in neigh list for long-range Coulombics // want consistency with non-charged triples which wouldn't be in list - + if (factor_lj == 0.0 && factor_coul == 0.0) continue; - + if (!(mask[j] & groupbit)) continue; jtype = type[j]; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2]; @@ -451,8 +451,8 @@ void ComputeADF::compute_array() if (!iatomflag[m][itype]) continue; int jflag = 0; - if (jatomflag[m][jtype] && - rsq >= rcutinnerj[m]*rcutinnerj[m] && + if (jatomflag[m][jtype] && + rsq >= rcutinnerj[m]*rcutinnerj[m] && rsq <= rcutouterj[m]*rcutouterj[m]) { jflag = 1; jatom = numjatom[m]++; @@ -462,10 +462,10 @@ void ComputeADF::compute_array() memory->grow(neighjatom[m],maxjatom[m],"adf:neighjatom"); } } - + int kflag = 0; - if (katomflag[m][jtype] && - rsq >= rcutinnerk[m]*rcutinnerk[m] && + if (katomflag[m][jtype] && + rsq >= rcutinnerk[m]*rcutinnerk[m] && rsq <= rcutouterk[m]*rcutouterk[m]) { kflag = 1; katom = numkatom[m]++; @@ -492,7 +492,7 @@ void ComputeADF::compute_array() memory->grow(delrjkatom[m],maxjkatom[m],4,"adf:delrjkatom"); } - // indicate if atom in both lists + // indicate if atom in both lists if (jflag && kflag) bothjkatom[m][jk] = 1; @@ -558,7 +558,7 @@ void ComputeADF::compute_array() // copy into output array for (m = 0; m < ntriples; m++) { - + double count = 0; for (ibin = 0; ibin < nbin; ibin++) count += histall[m][ibin]; diff --git a/src/compute_adf.h b/src/compute_adf.h index 4c9e13707b..a7983b7173 100644 --- a/src/compute_adf.h +++ b/src/compute_adf.h @@ -45,7 +45,7 @@ class ComputeADF : public Compute { double *rcutouterj, *rcutouterk; // list of outer cutoffs class NeighList *list; // full neighbor list - + int *iatomcount; // local number of central atoms int *iatomcountall; // total number of central atoms int **iatomflag; // 1 if type is central atom in ADF diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index cf5c9e808d..641784fe03 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -53,7 +53,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : bstyle = new int[nvalues]; vstr = new char*[nvalues]; vvar = new int[nvalues]; - + nvalues = 0; tflag = 0; nvar = 0; @@ -78,7 +78,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : setflag = 0; tstr = NULL; - + while (iarg < narg) { if (strcmp(arg[iarg],"set") == 0) { setflag = 1; @@ -114,7 +114,7 @@ ComputeAngleLocal::ComputeAngleLocal(LAMMPS *lmp, int narg, char **arg) : if (!input->variable->internalstyle(tvar)) error->all(FLERR,"Variable for compute angle/local is invalid style"); } - } else if (setflag) + } else if (setflag) error->all(FLERR,"Compute angle/local set with no variable"); // initialize output @@ -289,7 +289,7 @@ int ComputeAngleLocal::compute_angles(int flag) if (nvalues == 1) ptr = &vlocal[m]; else ptr = alocal[m]; - + if (nvar) { ivar = 0; if (tstr) input->variable->internal_set(tvar,theta); diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 72ce2b5f8d..adbbde1a0c 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -55,7 +55,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : bstyle = new int[nvalues]; vstr = new char*[nvalues]; vvar = new int[nvalues]; - + nvalues = 0; nvar = 0; @@ -82,7 +82,7 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : setflag = 0; dstr = NULL; - + while (iarg < narg) { if (strcmp(arg[iarg],"set") == 0) { setflag = 1; @@ -117,10 +117,10 @@ ComputeBondLocal::ComputeBondLocal(LAMMPS *lmp, int narg, char **arg) : if (!input->variable->internalstyle(dvar)) error->all(FLERR,"Variable for compute bond/local is invalid style"); } - } else if (setflag) + } else if (setflag) error->all(FLERR,"Compute bond/local set with no variable"); - + // set singleflag if need to call bond->single() // set velflag if compute any quantities based on velocities diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp index ddad7eb62f..61b653b375 100644 --- a/src/compute_chunk_atom.cpp +++ b/src/compute_chunk_atom.cpp @@ -66,7 +66,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) : // chunk style and its args - int iarg; + int iarg = 0; binflag = 0; ncoord = 0; @@ -248,7 +248,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else if (strcmp(arg[iarg],"bound") == 0) { if (iarg+4 > narg) error->all(FLERR,"Illegal compute chunk/atom command"); - int idim; + int idim = 0; if (strcmp(arg[iarg+1],"x") == 0) idim = 0; else if (strcmp(arg[iarg+1],"y") == 0) idim = 1; else if (strcmp(arg[iarg+1],"z") == 0) idim = 2; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index c5fd27b0c1..36fad5cca1 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -117,7 +117,7 @@ ComputeChunkSpreadAtom(LAMMPS *lmp, int narg, char **arg) : "does not exist"); char *ptr = strstr(modify->compute[icompute]->style,"/chunk"); - if (!ptr || (ptr != modify->compute[icompute]->style + + if (!ptr || (ptr != modify->compute[icompute]->style + strlen(modify->compute[icompute]->style) - strlen("/chunk"))) error->all(FLERR,"Compute for compute chunk/spread/atom " "does not calculate per-chunk values"); diff --git a/src/compute_dihedral_local.cpp b/src/compute_dihedral_local.cpp index 919081236c..9e18d03f9f 100644 --- a/src/compute_dihedral_local.cpp +++ b/src/compute_dihedral_local.cpp @@ -56,7 +56,7 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : bstyle = new int[nvalues]; vstr = new char*[nvalues]; vvar = new int[nvalues]; - + nvalues = 0; nvar = 0; @@ -77,11 +77,11 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : setflag = 0; pstr = NULL; - + while (iarg < narg) { if (strcmp(arg[iarg],"set") == 0) { setflag = 1; - if (iarg+3 > narg) + if (iarg+3 > narg) error->all(FLERR,"Illegal compute dihedral/local command"); if (strcmp(arg[iarg+1],"phi") == 0) { delete [] pstr; @@ -115,7 +115,7 @@ ComputeDihedralLocal::ComputeDihedralLocal(LAMMPS *lmp, int narg, char **arg) : if (!input->variable->internalstyle(pvar)) error->all(FLERR,"Variable for compute dihedral/local is invalid style"); } - } else if (setflag) + } else if (setflag) error->all(FLERR,"Compute dihedral/local set with no variable"); // initialize output @@ -295,17 +295,17 @@ int ComputeDihedralLocal::compute_dihedrals(int flag) if (rasq > 0) ra2inv = 1.0/rasq; if (rbsq > 0) rb2inv = 1.0/rbsq; rabinv = sqrt(ra2inv*rb2inv); - + c = (ax*bx + ay*by + az*bz)*rabinv; s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z); - + if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; phi = atan2(s,c); if (nvalues == 1) ptr = &vlocal[m]; else ptr = alocal[m]; - + if (nvar) { ivar = 0; if (pstr) input->variable->internal_set(pvar,phi); diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h index d5f6a64183..5c50a66e96 100644 --- a/src/compute_dihedral_local.h +++ b/src/compute_dihedral_local.h @@ -33,7 +33,7 @@ class ComputeDihedralLocal : public Compute { double memory_usage(); private: - int nvalues,nvar,ncount,setflag,tflag; + int nvalues,nvar,ncount,setflag; int pvar; int *bstyle,*vvar; diff --git a/src/compute_displace_atom.cpp b/src/compute_displace_atom.cpp index 0b6b40b62a..d8f279058e 100644 --- a/src/compute_displace_atom.cpp +++ b/src/compute_displace_atom.cpp @@ -48,7 +48,7 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) : int iarg = 3; while (iarg < narg) { if (strcmp(arg[iarg],"refresh") == 0) { - if (iarg+2 > narg) + if (iarg+2 > narg) error->all(FLERR,"Illegal compute displace/atom command"); refreshflag = 1; delete [] rvar; @@ -63,7 +63,7 @@ ComputeDisplaceAtom::ComputeDisplaceAtom(LAMMPS *lmp, int narg, char **arg) : if (refreshflag) { ivar = input->variable->find(rvar); - if (ivar < 0) + if (ivar < 0) error->all(FLERR,"Variable name for compute displace/atom does not exist"); if (input->variable->atomstyle(ivar) == 0) error->all(FLERR,"Compute displace/atom variable " diff --git a/src/compute_group_group.cpp b/src/compute_group_group.cpp index 51f84b020d..e55f679b2e 100644 --- a/src/compute_group_group.cpp +++ b/src/compute_group_group.cpp @@ -33,6 +33,7 @@ #include "comm.h" #include "domain.h" #include "math_const.h" +#include "utils.h" using namespace LAMMPS_NS; using namespace MathConst; @@ -124,7 +125,8 @@ void ComputeGroupGroup::init() if (pairflag && force->pair == NULL) error->all(FLERR,"No pair style defined for compute group/group"); - if (force->pair_match("hybrid",0) == NULL && force->pair->single_enable == 0) + if (force->pair_match("^hybrid",0) == NULL + && force->pair->single_enable == 0) error->all(FLERR,"Pair style does not support compute group/group"); // error if Kspace style does not compute group/group interactions diff --git a/src/compute_rdf.cpp b/src/compute_rdf.cpp index 0809cc8b8e..d49485b4ea 100644 --- a/src/compute_rdf.cpp +++ b/src/compute_rdf.cpp @@ -77,7 +77,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) : // pairwise args if (nargpair == 0) npairs = 1; - else { + else { if (nargpair % 2) error->all(FLERR,"Illegal compute rdf command"); npairs = nargpair/2; } diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index e3c3c5b70a..16dc84628a 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -30,8 +30,8 @@ using namespace LAMMPS_NS; -enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ReduceRegion -enum{X,V,F,COMPUTE,FIX,VARIABLE}; +enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ComputeReduceRegion +enum{UNKNOWN=-1,X,V,F,COMPUTE,FIX,VARIABLE}; enum{PERATOM,LOCAL}; #define INVOKED_VECTOR 2 @@ -92,6 +92,10 @@ ComputeReduce::ComputeReduce(LAMMPS *lmp, int narg, char **arg) : flavor = new int[nargnew]; ids = new char*[nargnew]; value2index = new int[nargnew]; + for (int i=0; i < nargnew; ++i) { + which[i] = argindex[i] = flavor[i] = value2index[i] = UNKNOWN; + ids[i] = NULL; + } nvalues = 0; iarg = 0; @@ -345,7 +349,7 @@ void ComputeReduce::init() error->all(FLERR,"Variable name for compute reduce does not exist"); value2index[m] = ivariable; - } else value2index[m] = -1; + } else value2index[m] = UNKNOWN; } // set index and check validity of region @@ -468,8 +472,16 @@ double ComputeReduce::compute_one(int m, int flag) index = -1; int vidx = value2index[m]; - int aidx = argindex[m]; + // initialization in case it has not yet been run, e.g. when + // the compute was invoked right after it has been created + + if (vidx == UNKNOWN) { + init(); + vidx = value2index[m]; + } + + int aidx = argindex[m]; int *mask = atom->mask; int nlocal = atom->nlocal; diff --git a/src/compute_reduce_chunk.cpp b/src/compute_reduce_chunk.cpp index beebc5f411..f31672ef74 100644 --- a/src/compute_reduce_chunk.cpp +++ b/src/compute_reduce_chunk.cpp @@ -28,7 +28,7 @@ using namespace LAMMPS_NS; enum{SUM,MINN,MAXX}; -enum{COMPUTE,FIX,VARIABLE}; +enum{UNKNOWN=-1,COMPUTE,FIX,VARIABLE}; #define INVOKED_PERATOM 8 @@ -51,7 +51,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : init_chunk(); // mode - + if (strcmp(arg[4],"sum") == 0) mode = SUM; else if (strcmp(arg[4],"min") == 0) mode = MINN; else if (strcmp(arg[4],"max") == 0) mode = MAXX; @@ -74,6 +74,10 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : argindex = new int[nargnew]; ids = new char*[nargnew]; value2index = new int[nargnew]; + for (int i=0; i < nargnew; ++i) { + which[i] = argindex[i] = value2index[i] = UNKNOWN; + ids[i] = NULL; + } nvalues = 0; iarg = 0; @@ -118,51 +122,51 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : } // error check - + for (int i = 0; i < nvalues; i++) { if (which[i] == COMPUTE) { int icompute = modify->find_compute(ids[i]); if (icompute < 0) - error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); + error->all(FLERR,"Compute ID for compute reduce/chunk does not exist"); if (!modify->compute[icompute]->peratom_flag) - error->all(FLERR,"Compute reduce/chunk compute does not " - "calculate per-atom values"); + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate per-atom values"); if (argindex[i] == 0 && - modify->compute[icompute]->size_peratom_cols != 0) - error->all(FLERR,"Compute reduce/chunk compute does not " - "calculate a per-atom vector"); + modify->compute[icompute]->size_peratom_cols != 0) + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate a per-atom vector"); if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) - error->all(FLERR,"Compute reduce/chunk compute does not " - "calculate a per-atom array"); - if (argindex[i] && + error->all(FLERR,"Compute reduce/chunk compute does not " + "calculate a per-atom array"); + if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom_cols) - error->all(FLERR, - "Compute reduce/chunk compute array is accessed out-of-range"); - + error->all(FLERR, + "Compute reduce/chunk compute array is accessed out-of-range"); + } else if (which[i] == FIX) { int ifix = modify->find_fix(ids[i]); if (ifix < 0) - error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); + error->all(FLERR,"Fix ID for compute reduce/chunk does not exist"); if (!modify->fix[ifix]->peratom_flag) - error->all(FLERR,"Compute reduce/chunk fix does not " - "calculate per-atom values"); + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate per-atom values"); if (argindex[i] == 0 && - modify->fix[ifix]->size_peratom_cols != 0) - error->all(FLERR,"Compute reduce/chunk fix does not " - "calculate a per-atom vector"); + modify->fix[ifix]->size_peratom_cols != 0) + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate a per-atom vector"); if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) - error->all(FLERR,"Compute reduce/chunk fix does not " - "calculate a per-atom array"); + error->all(FLERR,"Compute reduce/chunk fix does not " + "calculate a per-atom array"); if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) - error->all(FLERR,"Compute reduce/chunk fix array is " + error->all(FLERR,"Compute reduce/chunk fix array is " "accessed out-of-range"); - + } else if (which[i] == VARIABLE) { int ivariable = input->variable->find(ids[i]); if (ivariable < 0) - error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); + error->all(FLERR,"Variable name for compute reduce/chunk does not exist"); if (input->variable->atomstyle(ivariable) == 0) - error->all(FLERR,"Compute reduce/chunk variable is " + error->all(FLERR,"Compute reduce/chunk variable is " "not atom-style variable"); } } @@ -181,7 +185,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : } // setup - + if (mode == SUM) initvalue = 0.0; else if (mode == MINN) initvalue = BIG; else if (mode == MAXX) initvalue = -BIG; @@ -199,7 +203,7 @@ ComputeReduceChunk::ComputeReduceChunk(LAMMPS *lmp, int narg, char **arg) : ComputeReduceChunk::~ComputeReduceChunk() { delete [] idchunk; - + delete [] which; delete [] argindex; for (int m = 0; m < nvalues; m++) delete [] ids[m]; @@ -210,7 +214,7 @@ ComputeReduceChunk::~ComputeReduceChunk() memory->destroy(vglobal); memory->destroy(alocal); memory->destroy(aglobal); - + memory->destroy(varatom); } @@ -284,11 +288,11 @@ void ComputeReduceChunk::compute_vector() } // perform local reduction of single peratom value - + compute_one(0,vlocal,1); - + // reduce the per-chunk values across all procs - + if (mode == SUM) MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_SUM,world); else if (mode == MINN) @@ -296,7 +300,7 @@ void ComputeReduceChunk::compute_vector() else if (mode == MAXX) MPI_Allreduce(vlocal,vglobal,nchunk,MPI_DOUBLE,MPI_MAX,world); } - + /* ---------------------------------------------------------------------- */ void ComputeReduceChunk::compute_array() @@ -324,11 +328,11 @@ void ComputeReduceChunk::compute_array() } // perform local reduction of all peratom values - + for (int m = 0; m < nvalues; m++) compute_one(m,&alocal[0][m],nvalues); // reduce the per-chunk values across all procs - + if (mode == SUM) MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, MPI_DOUBLE,MPI_SUM,world); @@ -339,13 +343,13 @@ void ComputeReduceChunk::compute_array() MPI_Allreduce(&alocal[0][0],&aglobal[0][0],nchunk*nvalues, MPI_DOUBLE,MPI_MAX,world); } - + /* ---------------------------------------------------------------------- */ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) { // initialize per-chunk values in accumulation vector - + for (int i = 0; i < nchunk; i += nstride) vchunk[i] = initvalue; // loop over my atoms @@ -354,10 +358,19 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) int *mask = atom->mask; int nlocal = atom->nlocal; - int index; + int index = -1; + int vidx = value2index[m]; + + // initialization in case it has not yet been run, e.g. when + // the compute was invoked right after it has been created + + if (vidx == UNKNOWN) { + init(); + vidx = value2index[m]; + } if (which[m] == COMPUTE) { - Compute *compute = modify->compute[value2index[m]]; + Compute *compute = modify->compute[vidx]; if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); @@ -367,26 +380,26 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) if (argindex[m] == 0) { double *vcompute = compute->vector_atom; for (int i = 0; i < nlocal; i++) { - if (!(mask[i] & groupbit)) continue; - index = ichunk[i]-1; - if (index < 0) continue; - combine(vchunk[index*nstride],vcompute[i]); + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],vcompute[i]); } } else { double **acompute = compute->array_atom; int argindexm1 = argindex[m] - 1; for (int i = 0; i < nlocal; i++) { - if (!(mask[i] & groupbit)) continue; - index = ichunk[i]-1; - if (index < 0) continue; - combine(vchunk[index*nstride],acompute[i][argindexm1]); + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],acompute[i][argindexm1]); } } - + // access fix fields, check if fix frequency is a match } else if (which[m] == FIX) { - Fix *fix = modify->fix[value2index[m]]; + Fix *fix = modify->fix[vidx]; if (update->ntimestep % fix->peratom_freq) error->all(FLERR,"Fix used in compute reduce/chunk not " "computed at compatible time"); @@ -394,19 +407,19 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) if (argindex[m] == 0) { double *vfix = fix->vector_atom; for (int i = 0; i < nlocal; i++) { - if (!(mask[i] & groupbit)) continue; - index = ichunk[i]-1; - if (index < 0) continue; - combine(vchunk[index*nstride],vfix[i]); + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],vfix[i]); } } else { double **afix = fix->array_atom; int argindexm1 = argindex[m] - 1; for (int i = 0; i < nlocal; i++) { - if (!(mask[i] & groupbit)) continue; - index = ichunk[i]-1; - if (index < 0) continue; - combine(vchunk[index*nstride],afix[i][argindexm1]); + if (!(mask[i] & groupbit)) continue; + index = ichunk[i]-1; + if (index < 0) continue; + combine(vchunk[index*nstride],afix[i][argindexm1]); } } @@ -419,7 +432,7 @@ void ComputeReduceChunk::compute_one(int m, double *vchunk, int nstride) memory->create(varatom,maxatom,"reduce/chunk:varatom"); } - input->variable->compute_atom(value2index[m],igroup,varatom,1,0); + input->variable->compute_atom(vidx,igroup,varatom,1,0); for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; index = ichunk[i]-1; diff --git a/src/compute_reduce_chunk.h b/src/compute_reduce_chunk.h index ac556907b7..525bb0c7a7 100644 --- a/src/compute_reduce_chunk.h +++ b/src/compute_reduce_chunk.h @@ -52,7 +52,7 @@ class ComputeReduceChunk : public Compute { double *vlocal,*vglobal; double **alocal,**aglobal; double *varatom; - + class ComputeChunkAtom *cchunk; int *ichunk; diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp index 77cd6371c6..8e91a299e8 100644 --- a/src/compute_reduce_region.cpp +++ b/src/compute_reduce_region.cpp @@ -28,8 +28,8 @@ using namespace LAMMPS_NS; -enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ComputeReduce -enum{X,V,F,COMPUTE,FIX,VARIABLE}; +enum{SUM,SUMSQ,MINN,MAXX,AVE,AVESQ}; // also in ComputeReduce +enum{UNKNOWN=-1,X,V,F,COMPUTE,FIX,VARIABLE}; enum{PERATOM,LOCAL}; #define INVOKED_VECTOR 2 @@ -70,6 +70,14 @@ double ComputeReduceRegion::compute_one(int m, int flag) int nlocal = atom->nlocal; int n = value2index[m]; + + // initialization in case it has not yet been run, + // e.g. when invoked + if (n == UNKNOWN) { + init(); + n = value2index[m]; + } + int j = argindex[m]; double one = 0.0; diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 383c60f1cd..cb0da42970 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -68,6 +68,7 @@ void CreateAtoms::command(int narg, char **arg) if (strcmp(arg[1],"box") == 0) { style = BOX; iarg = 2; + nregion = -1; } else if (strcmp(arg[1],"region") == 0) { style = REGION; if (narg < 3) error->all(FLERR,"Illegal create_atoms command"); @@ -576,11 +577,11 @@ void CreateAtoms::add_single() if (triclinic) { domain->x2lamda(xone,lamda); if (remapflag) { - if (domain->xperiodic && (lamda[0] < 0.0 || lamda[0] >= 1.0)) + if (domain->xperiodic && (lamda[0] < 0.0 || lamda[0] >= 1.0)) lamda[0] = 0.0; - if (domain->yperiodic && (lamda[1] < 0.0 || lamda[1] >= 1.0)) + if (domain->yperiodic && (lamda[1] < 0.0 || lamda[1] >= 1.0)) lamda[1] = 0.0; - if (domain->zperiodic && (lamda[2] < 0.0 || lamda[2] >= 1.0)) + if (domain->zperiodic && (lamda[2] < 0.0 || lamda[2] >= 1.0)) lamda[2] = 0.0; } coord = lamda; @@ -704,10 +705,31 @@ void CreateAtoms::add_lattice() bboxlo[2] = domain->sublo[2]; bboxhi[2] = domain->subhi[2]; } else domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi); + // narrow down the subbox by the bounding box of the given region, if available. + // for small regions in large boxes, this can result in a significant speedup + + if ((style == REGION) && domain->regions[nregion]->bboxflag) { + + const double rxmin = domain->regions[nregion]->extent_xlo; + const double rxmax = domain->regions[nregion]->extent_xhi; + const double rymin = domain->regions[nregion]->extent_ylo; + const double rymax = domain->regions[nregion]->extent_yhi; + const double rzmin = domain->regions[nregion]->extent_zlo; + const double rzmax = domain->regions[nregion]->extent_zhi; + + if (rxmin > bboxlo[0]) bboxlo[0] = (rxmin > bboxhi[0]) ? bboxhi[0] : rxmin; + if (rxmax < bboxhi[0]) bboxhi[0] = (rxmax < bboxlo[0]) ? bboxlo[0] : rxmax; + if (rymin > bboxlo[1]) bboxlo[1] = (rymin > bboxhi[1]) ? bboxhi[1] : rymin; + if (rymax < bboxhi[1]) bboxhi[1] = (rymax < bboxlo[1]) ? bboxlo[1] : rymax; + if (rzmin > bboxlo[2]) bboxlo[2] = (rzmin > bboxhi[2]) ? bboxhi[2] : rzmin; + if (rzmax < bboxhi[2]) bboxhi[2] = (rzmax < bboxlo[2]) ? bboxlo[2] : rzmax; + } + double xmin,ymin,zmin,xmax,ymax,zmax; xmin = ymin = zmin = BIG; xmax = ymax = zmax = -BIG; + // convert to lattice coordinates and set bounding box domain->lattice->bbox(1,bboxlo[0],bboxlo[1],bboxlo[2], xmin,ymin,zmin,xmax,ymax,zmax); domain->lattice->bbox(1,bboxhi[0],bboxlo[1],bboxlo[2], @@ -751,15 +773,32 @@ void CreateAtoms::add_lattice() // convert lattice coords to box coords // add atom or molecule (on each basis point) if it meets all criteria - double **basis = domain->lattice->basis; - double x[3],lamda[3]; - double *coord; + const double * const * const basis = domain->lattice->basis; + + // rough estimate of total time used for create atoms. + // one inner loop takes about 25ns on a typical desktop CPU core in 2019 + double testimate = 2.5e-8/3600.0; // convert seconds to hours + testimate *= static_cast(khi-klo+1); + testimate *= static_cast(jhi-jlo+1); + testimate *= static_cast(ihi-ilo+1); + testimate *= static_cast(nbasis); + double maxestimate = 0.0; + MPI_Reduce(&testimate,&maxestimate,1,MPI_DOUBLE,MPI_MAX,0,world); + + if ((comm->me == 0) && (maxestimate > 0.01)) { + if (screen) fprintf(screen,"WARNING: create_atoms will take " + "approx. %.2f hours to complete\n",maxestimate); + if (logfile) fprintf(logfile,"WARNING: create_atoms will take " + "approx. %.2f hours to complete\n",maxestimate); + } int i,j,k,m; - for (k = klo; k <= khi; k++) - for (j = jlo; j <= jhi; j++) - for (i = ilo; i <= ihi; i++) + for (k = klo; k <= khi; k++) { + for (j = jlo; j <= jhi; j++) { + for (i = ilo; i <= ihi; i++) { for (m = 0; m < nbasis; m++) { + double *coord; + double x[3],lamda[3]; x[0] = i + basis[m][0]; x[1] = j + basis[m][1]; @@ -794,8 +833,12 @@ void CreateAtoms::add_lattice() if (mode == ATOM) atom->avec->create_atom(basistype[m],x); else add_molecule(x); } + } + } + } } + /* ---------------------------------------------------------------------- add a randomly rotated molecule with its center at center if quat_user set, perform requested rotation diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 751c4746ba..e19b565554 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -54,7 +54,7 @@ void CreateBonds::command(int narg, char **arg) int style; - int iarg; + int iarg = 0; if (strcmp(arg[0],"many") == 0) { style = MANY; if (narg != 6) error->all(FLERR,"Illegal create_bonds command"); diff --git a/src/create_box.h b/src/create_box.h index 2d94b80d82..740769b4de 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -47,7 +47,7 @@ E: Cannot create_box after simulation box is defined A simulation box can only be defined once. -E: Cannot run 2d simulation with nonperiodic Z dimension +E: Cannot run 2d simulation with non-periodic Z dimension Use the boundary command to make the z dimension periodic in order to run a 2d simulation. diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index e26ecad5f3..41df167f07 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -16,6 +16,10 @@ #include "delete_atoms.h" #include "atom.h" #include "atom_vec.h" +#include "atom_vec_ellipsoid.h" +#include "atom_vec_line.h" +#include "atom_vec_tri.h" +#include "atom_vec_body.h" #include "molecule.h" #include "comm.h" #include "domain.h" @@ -68,7 +72,7 @@ void DeleteAtoms::command(int narg, char **arg) if (allflag) { int igroup = group->find("all"); - if ((igroup >= 0) && + if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup])) error->warning(FLERR,"Attempting to delete atoms in rigid bodies"); } else { @@ -121,11 +125,39 @@ void DeleteAtoms::command(int narg, char **arg) } // reset atom->natoms and also topology counts - // reset atom->map if it exists - // set nghost to 0 so old ghosts of deleted atoms won't be mapped bigint nblocal = atom->nlocal; MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); + + // reset bonus data counts + + AtomVecEllipsoid *avec_ellipsoid = + (AtomVecEllipsoid *) atom->style_match("ellipsoid"); + AtomVecLine *avec_line = (AtomVecLine *) atom->style_match("line"); + AtomVecTri *avec_tri = (AtomVecTri *) atom->style_match("tri"); + AtomVecBody *avec_body = (AtomVecBody *) atom->style_match("body"); + bigint nlocal_bonus; + + if (atom->nellipsoids > 0) { + nlocal_bonus = avec_ellipsoid->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + if (atom->nlines > 0) { + nlocal_bonus = avec_line->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->nlines,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + if (atom->ntris > 0) { + nlocal_bonus = avec_tri->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->ntris,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + if (atom->nbodies > 0) { + nlocal_bonus = avec_body->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->nbodies,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + + // reset atom->map if it exists + // set nghost to 0 so old ghosts of deleted atoms won't be mapped + if (atom->map_style) { atom->nghost = 0; atom->map_init(); diff --git a/src/dihedral.h b/src/dihedral.h index 627104871b..f1b42008bf 100644 --- a/src/dihedral.h +++ b/src/dihedral.h @@ -56,6 +56,10 @@ class Dihedral : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; + void ev_init(int eflag, int vflag, int alloc = 1) { + if (eflag||vflag) ev_setup(eflag, vflag, alloc); + else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0; + } void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, int, int, double, double *, double *, double *, double, double, double, diff --git a/src/dihedral_deprecated.cpp b/src/dihedral_deprecated.cpp index 138d0971a8..70888ca76d 100644 --- a/src/dihedral_deprecated.cpp +++ b/src/dihedral_deprecated.cpp @@ -52,6 +52,6 @@ void DihedralDeprecated::settings(int, char **) writemsg(lmp,"\nDihedral style 'DEPRECATED' is a dummy style\n\n",0); } -} +} diff --git a/src/dihedral_hybrid.cpp b/src/dihedral_hybrid.cpp index b9107ac874..f3e4823d53 100644 --- a/src/dihedral_hybrid.cpp +++ b/src/dihedral_hybrid.cpp @@ -104,8 +104,7 @@ void DihedralHybrid::compute(int eflag, int vflag) // set neighbor->dihedrallist to sub-style dihedrallist before call // accumulate sub-style global/peratom energy/virial in hybrid - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); for (m = 0; m < nstyles; m++) { neighbor->ndihedrallist = ndihedrallist[m]; diff --git a/src/dihedral_zero.cpp b/src/dihedral_zero.cpp index 46facdb6db..8145d5f32d 100644 --- a/src/dihedral_zero.cpp +++ b/src/dihedral_zero.cpp @@ -44,8 +44,7 @@ DihedralZero::~DihedralZero() void DihedralZero::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index 04088bec8c..7b29b1d3d5 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -118,7 +118,7 @@ void DisplaceAtoms::command(int narg, char **arg) if (style == RAMP) { - int d_dim; + int d_dim = 0; if (strcmp(arg[2],"x") == 0) d_dim = 0; else if (strcmp(arg[2],"y") == 0) d_dim = 1; else if (strcmp(arg[2],"z") == 0) d_dim = 2; @@ -136,7 +136,7 @@ void DisplaceAtoms::command(int narg, char **arg) d_hi = zscale*force->numeric(FLERR,arg[4]); } - int coord_dim; + int coord_dim = 0; if (strcmp(arg[5],"x") == 0) coord_dim = 0; else if (strcmp(arg[5],"y") == 0) coord_dim = 1; else if (strcmp(arg[5],"z") == 0) coord_dim = 2; diff --git a/src/dump.cpp b/src/dump.cpp index 7cd80dcf71..8fa07a9cb2 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -423,7 +423,12 @@ void Dump::write() atom->x = xpbc; atom->v = vpbc; atom->image = imagepbc; + + // for triclinic, PBC is applied in lamda coordinates + + if (domain->triclinic) domain->x2lamda(nlocal); domain->pbc(); + if (domain->triclinic) domain->lamda2x(nlocal); } // pack my data into buf diff --git a/src/dump_image.cpp b/src/dump_image.cpp index a488f65161..0d63d2e4cb 100644 --- a/src/dump_image.cpp +++ b/src/dump_image.cpp @@ -1290,7 +1290,7 @@ int DumpImage::modify_param(int narg, char **arg) if (strcmp(arg[0],"amap") == 0) { if (narg < 6) error->all(FLERR,"Illegal dump_modify command"); if (strlen(arg[3]) != 2) error->all(FLERR,"Illegal dump_modify command"); - int factor; + int factor = 0; if (arg[3][0] == 's') factor = 1; else if (arg[3][0] == 'c') factor = 2; else if (arg[3][0] == 'd') factor = 3; diff --git a/src/finish.cpp b/src/finish.cpp index f35fb7e3a5..9ad8b44927 100644 --- a/src/finish.cpp +++ b/src/finish.cpp @@ -35,6 +35,7 @@ #include "output.h" #include "memory.h" #include "error.h" +#include "utils.h" #ifdef LMP_USER_OMP #include "modify.h" @@ -101,7 +102,7 @@ void Finish::end(int flag) if (update->whichflag == 1 && strncmp(update->integrate_style,"verlet/split",12) == 0 && universe->iworld == 1) neighflag = 0; - if (force->kspace && force->kspace_match("pppm",0) + if (force->kspace && force->kspace_match("^pppm",0) && force->kspace->fftbench) fftflag = 1; } if (flag == 2) prdflag = timeflag = histoflag = neighflag = 1; diff --git a/src/fix.h b/src/fix.h index 21dfc955a8..7eaff38bd3 100644 --- a/src/fix.h +++ b/src/fix.h @@ -223,6 +223,10 @@ class Fix : protected Pointers { int dynamic; // recount atoms for temperature computes + void ev_init(int eflag, int vflag) { + if (eflag||vflag) ev_setup(eflag, vflag); + else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0; + } void ev_setup(int, int); void ev_tally(int, int *, double, double, double *); void v_setup(int); diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index a5bf8db557..d60fe7af14 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -32,7 +32,7 @@ using namespace FixConst; enum{X,V,F,COMPUTE,FIX,VARIABLE}; enum{ONE,RUNNING}; enum{SCALAR,VECTOR,WINDOW}; -enum{GLOBAL,PERATOM,LOCAL}; +enum{DEFAULT,GLOBAL,PERATOM,LOCAL}; enum{IGNORE,END,EXTRA}; #define INVOKED_SCALAR 1 @@ -46,8 +46,10 @@ enum{IGNORE,END,EXTRA}; FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - nvalues(0), which(NULL), argindex(NULL), value2index(NULL), ids(NULL), fp(NULL), stats_list(NULL), - bin(NULL), bin_total(NULL), bin_all(NULL), bin_list(NULL), coord(NULL), vector(NULL) + nvalues(0), which(NULL), argindex(NULL), value2index(NULL), + ids(NULL), fp(NULL), stats_list(NULL), + bin(NULL), bin_total(NULL), bin_all(NULL), bin_list(NULL), + coord(NULL), vector(NULL) { if (narg < 10) error->all(FLERR,"Illegal fix ave/histo command"); @@ -188,9 +190,8 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : memory->sfree(earg); } - // setup and error check - // kind = inputs are all global, or all per-atom, or all local - // for fix inputs, check that fix frequency is acceptable + // check input args for kind consistency + // all inputs must all be global, per-atom, or local if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) error->all(FLERR,"Illegal fix ave/histo command"); @@ -201,40 +202,65 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : if (ave != RUNNING && overwrite) error->all(FLERR,"Illegal fix ave/histo command"); - int kindflag; + int kindglobal,kindperatom,kindlocal; + for (int i = 0; i < nvalues; i++) { - if (which[i] == X || which[i] == V || which[i] == F) kindflag = PERATOM; - else if (which[i] == COMPUTE) { + kindglobal = kindperatom = kindlocal = 0; + + if (which[i] == X || which[i] == V || which[i] == F) { + kindperatom = 1; + + } else if (which[i] == COMPUTE) { int c_id = modify->find_compute(ids[i]); if (c_id < 0) error->all(FLERR,"Fix ave/histo input is invalid compute"); Compute *compute = modify->compute[c_id]; + // computes can produce multiple kinds of output if (compute->scalar_flag || compute->vector_flag || compute->array_flag) - kindflag = GLOBAL; - else if (compute->peratom_flag) kindflag = PERATOM; - else if (compute->local_flag) kindflag = LOCAL; - else error->all(FLERR,"Fix ave/histo input is invalid compute"); + kindglobal = 1; + if (compute->peratom_flag) kindperatom = 1; + if (compute->local_flag) kindlocal = 1; + } else if (which[i] == FIX) { int f_id = modify->find_fix(ids[i]); if (f_id < 0) error->all(FLERR,"Fix ave/histo input is invalid fix"); Fix *fix = modify->fix[f_id]; + // fixes can produce multiple kinds of output if (fix->scalar_flag || fix->vector_flag || fix->array_flag) - kindflag = GLOBAL; - else if (fix->peratom_flag) kindflag = PERATOM; - else if (fix->local_flag) kindflag = LOCAL; - else error->all(FLERR,"Fix ave/histo input is invalid fix"); + kindglobal = 1; + if (fix->peratom_flag) kindperatom = 1; + if (fix->local_flag) kindlocal = 1; + } else if (which[i] == VARIABLE) { int ivariable = input->variable->find(ids[i]); - if (ivariable < 0) error->all(FLERR,"Fix ave/histo input is invalid variable"); - if (input->variable->equalstyle(ivariable)) kindflag = GLOBAL; - else if (input->variable->atomstyle(ivariable)) kindflag = PERATOM; - else error->all(FLERR,"Fix ave/histo input is invalid variable"); + if (ivariable < 0) + error->all(FLERR,"Fix ave/histo input is invalid variable"); + // variables only produce one kind of output + if (input->variable->equalstyle(ivariable)) kindglobal = 1; + else if (input->variable->atomstyle(ivariable)) kindperatom = 1; + else error->all(FLERR,"Fix ave/histo input is invalid kind of variable"); + } + + if (kind == DEFAULT) { + if (kindglobal + kindperatom + kindlocal > 1) + error->all(FLERR,"Fix ave/histo input kind is ambiguous"); + if (kindglobal) kind = GLOBAL; + if (kindperatom) kind = PERATOM; + if (kindlocal) kind = LOCAL; + } else if (kind == GLOBAL) { + if (!kindglobal) + error->all(FLERR,"Fix ave/histo input kind is invalid"); + } else if (kind == PERATOM) { + if (!kindperatom) + error->all(FLERR,"Fix ave/histo input kind is invalid"); + } else if (kind == LOCAL) { + if (!kindlocal) + error->all(FLERR,"Fix ave/histo input kind is invalid"); } - if (i == 0) kind = kindflag; - else if (kindflag != kind) - error->all(FLERR, - "Fix ave/histo inputs are not all global, peratom, or local"); } + // more error checks + // for fix inputs, check that fix frequency is acceptable + if (kind == PERATOM && mode == SCALAR) error->all(FLERR, "Fix ave/histo cannot input per-atom values in scalar mode"); @@ -919,6 +945,7 @@ void FixAveHisto::options(int iarg, int narg, char **arg) // option defaults fp = NULL; + kind = DEFAULT; ave = ONE; startstep = 0; mode = SCALAR; @@ -942,6 +969,13 @@ void FixAveHisto::options(int iarg, int narg, char **arg) } } iarg += 2; + } else if (strcmp(arg[iarg],"kind") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); + if (strcmp(arg[iarg+1],"global") == 0) kind = GLOBAL; + else if (strcmp(arg[iarg+1],"peratom") == 0) kind = PERATOM; + else if (strcmp(arg[iarg+1],"local") == 0) kind = LOCAL; + else error->all(FLERR,"Illegal fix ave/histo command"); + iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp index c960c310f6..909ead3e2a 100644 --- a/src/fix_deform.cpp +++ b/src/fix_deform.cpp @@ -802,7 +802,7 @@ void FixDeform::end_of_step() // tilt_target can be large positive or large negative value // add/subtract box lengths until tilt_target is closest to current value - int idenom; + int idenom = 0; if (i == 5) idenom = 0; else if (i == 4) idenom = 0; else if (i == 3) idenom = 1; diff --git a/src/fix_external.cpp b/src/fix_external.cpp index 5ac9206e7f..b1ffa65e49 100644 --- a/src/fix_external.cpp +++ b/src/fix_external.cpp @@ -141,8 +141,7 @@ void FixExternal::post_force(int vflag) bigint ntimestep = update->ntimestep; int eflag = eflag_caller; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); // invoke the callback in driver program // it will fill fexternal with forces diff --git a/src/fix_group.cpp b/src/fix_group.cpp index 0980ff5456..8a332bed95 100644 --- a/src/fix_group.cpp +++ b/src/fix_group.cpp @@ -205,7 +205,7 @@ void FixGroup::set_group() // invoke atom-style variable if defined // set post_integrate flag to 1, then unset after - // this is for any compute to check if it needs to + // this is for any compute to check if it needs to // operate differently due to invocation this early in timestep // e.g. perform ghost comm update due to atoms having just moved diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp index d829982274..36ea47daf6 100644 --- a/src/fix_langevin.cpp +++ b/src/fix_langevin.cpp @@ -177,8 +177,6 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) : } } - if (tallyflag && zeroflag && comm->me == 0) - error->warning(FLERR,"Energy tally does not account for 'zero yes'"); } /* ---------------------------------------------------------------------- */ @@ -605,6 +603,11 @@ void FixLangevin::post_force_untemplated f[i][0] -= fsumall[0]; f[i][1] -= fsumall[1]; f[i][2] -= fsumall[2]; + if (Tp_TALLY) { + flangevin[i][0] -= fsumall[0]; + flangevin[i][1] -= fsumall[1]; + flangevin[i][2] -= fsumall[2]; + } } } } diff --git a/src/fix_langevin.h b/src/fix_langevin.h index 2883ac9ea2..024e7a9539 100644 --- a/src/fix_langevin.h +++ b/src/fix_langevin.h @@ -104,12 +104,6 @@ E: Fix langevin period must be > 0.0 The time window for temperature relaxation must be > 0 -W: Energy tally does not account for 'zero yes' - -The energy removed by using the 'zero yes' flag is not accounted -for in the energy tally and thus energy conservation cannot be -monitored in this case. - E: Fix langevin omega requires atom style sphere Self-explanatory. diff --git a/src/fix_move.cpp b/src/fix_move.cpp index 2f9fb0ebaa..0a5f506ab2 100644 --- a/src/fix_move.cpp +++ b/src/fix_move.cpp @@ -68,7 +68,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) : // parse args - int iarg; + int iarg = 0; if (strcmp(arg[3],"linear") == 0) { if (narg < 7) error->all(FLERR,"Illegal fix move command"); diff --git a/src/fix_nh.cpp b/src/fix_nh.cpp index a1a562f2bb..deca0ad83d 100644 --- a/src/fix_nh.cpp +++ b/src/fix_nh.cpp @@ -904,9 +904,16 @@ void FixNH::final_integrate() t_current = temperature->compute_scalar(); tdof = temperature->dof; + // need to recompute pressure to account for change in KE + // t_current is up-to-date, but compute_temperature is not + // compute appropriately coupled elements of mvv_current + if (pstat_flag) { if (pstyle == ISO) pressure->compute_scalar(); - else pressure->compute_vector(); + else { + temperature->compute_vector(); + pressure->compute_vector(); + } couple(); pressure->addstep(update->ntimestep+1); } @@ -1871,7 +1878,8 @@ void FixNH::nhc_press_integrate() } } - lkt_press = pdof * kt; + if (pstyle == ISO) lkt_press = kt; + else lkt_press = pdof * kt; etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0]; double ncfac = 1.0/nc_pchain; diff --git a/src/fix_nvt_sllod.cpp b/src/fix_nvt_sllod.cpp index 012d67c318..c7d23364a7 100644 --- a/src/fix_nvt_sllod.cpp +++ b/src/fix_nvt_sllod.cpp @@ -80,7 +80,7 @@ void FixNVTSllod::init() int i; for (i = 0; i < modify->nfix; i++) - if (strcmp(modify->fix[i]->style,"deform") == 0) { + if (strncmp(modify->fix[i]->style,"deform",6) == 0) { if (((FixDeform *) modify->fix[i])->remapflag != Domain::V_REMAP) error->all(FLERR,"Using fix nvt/sllod with inconsistent fix deform " "remap option"); diff --git a/src/fix_restrain.cpp b/src/fix_restrain.cpp index bb09116374..08485d65b3 100644 --- a/src/fix_restrain.cpp +++ b/src/fix_restrain.cpp @@ -191,7 +191,7 @@ void FixRestrain::min_setup(int vflag) void FixRestrain::post_force(int /*vflag*/) { energy = 0.0; - + ebond = 0.0; eangle = 0.0; edihed = 0.0; @@ -658,7 +658,7 @@ double FixRestrain::compute_vector(int n) } else if (n == 1) { MPI_Allreduce(&eangle,&eangle_all,1,MPI_DOUBLE,MPI_SUM,world); return eangle_all; - } else if (n == 2) { + } else if (n == 2) { MPI_Allreduce(&edihed,&edihed_all,1,MPI_DOUBLE,MPI_SUM,world); return edihed_all; } else { diff --git a/src/force.cpp b/src/force.cpp index 2bfd809451..7ff5096ee4 100644 --- a/src/force.cpp +++ b/src/force.cpp @@ -35,6 +35,7 @@ #include "group.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -287,26 +288,13 @@ Pair *Force::pair_match(const char *word, int exact, int nsub) int iwhich,count; if (exact && strcmp(pair_style,word) == 0) return pair; - else if (!exact && strstr(pair_style,word)) return pair; - - else if (strstr(pair_style,"hybrid/overlay")) { - PairHybridOverlay *hybrid = (PairHybridOverlay *) pair; - count = 0; - for (int i = 0; i < hybrid->nstyles; i++) - if ((exact && strcmp(hybrid->keywords[i],word) == 0) || - (!exact && strstr(hybrid->keywords[i],word))) { - iwhich = i; - count++; - if (nsub == count) return hybrid->styles[iwhich]; - } - if (count == 1) return hybrid->styles[iwhich]; - - } else if (strstr(pair_style,"hybrid")) { + else if (!exact && utils::strmatch(pair_style,word)) return pair; + else if (utils::strmatch(pair_style,"^hybrid")) { PairHybrid *hybrid = (PairHybrid *) pair; count = 0; for (int i = 0; i < hybrid->nstyles; i++) if ((exact && strcmp(hybrid->keywords[i],word) == 0) || - (!exact && strstr(hybrid->keywords[i],word))) { + (!exact && utils::strmatch(hybrid->keywords[i],word))) { iwhich = i; count++; if (nsub == count) return hybrid->styles[iwhich]; @@ -327,7 +315,7 @@ char *Force::pair_match_ptr(Pair *ptr) { if (ptr == pair) return pair_style; - if (strstr(pair_style,"hybrid")) { + if (utils::strmatch(pair_style,"^hybrid")) { PairHybrid *hybrid = (PairHybrid *) pair; for (int i = 0; i < hybrid->nstyles; i++) if (ptr == hybrid->styles[i]) return hybrid->keywords[i]; @@ -741,7 +729,7 @@ KSpace *Force::kspace_creator(LAMMPS *lmp) KSpace *Force::kspace_match(const char *word, int exact) { if (exact && strcmp(kspace_style,word) == 0) return kspace; - else if (!exact && strstr(kspace_style,word)) return kspace; + else if (!exact && utils::strmatch(kspace_style,word)) return kspace; return NULL; } @@ -934,20 +922,21 @@ void Force::boundsbig(const char *file, int line, char *str, double Force::numeric(const char *file, int line, char *str) { - if (!str) - error->all(file,line,"Expected floating point parameter " - "in input script or data file"); - int n = strlen(str); + int n = 0; + + if (str) n = strlen(str); if (n == 0) - error->all(file,line,"Expected floating point parameter " - "in input script or data file"); + error->all(file,line,"Expected floating point parameter instead of" + " NULL or empty string in input script or data file"); for (int i = 0; i < n; i++) { if (isdigit(str[i])) continue; if (str[i] == '-' || str[i] == '+' || str[i] == '.') continue; if (str[i] == 'e' || str[i] == 'E') continue; - error->all(file,line,"Expected floating point parameter " - "in input script or data file"); + char msg[256]; + snprintf(msg,256,"Expected floating point parameter instead of " + "'%s' in input script or data file",str); + error->all(file,line,msg); } return atof(str); @@ -961,18 +950,19 @@ double Force::numeric(const char *file, int line, char *str) int Force::inumeric(const char *file, int line, char *str) { - if (!str) - error->all(file,line, - "Expected integer parameter in input script or data file"); - int n = strlen(str); + int n = 0; + + if (str) n = strlen(str); if (n == 0) - error->all(file,line, - "Expected integer parameter in input script or data file"); + error->all(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); for (int i = 0; i < n; i++) { if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue; - error->all(file,line, - "Expected integer parameter in input script or data file"); + char msg[256]; + snprintf(msg,256,"Expected integer parameter instead of " + "'%s' in input script or data file",str); + error->all(file,line,msg); } return atoi(str); @@ -986,18 +976,19 @@ int Force::inumeric(const char *file, int line, char *str) bigint Force::bnumeric(const char *file, int line, char *str) { - if (!str) - error->all(file,line, - "Expected integer parameter in input script or data file"); - int n = strlen(str); + int n = 0; + + if (str) n = strlen(str); if (n == 0) - error->all(file,line, - "Expected integer parameter in input script or data file"); + error->all(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); for (int i = 0; i < n; i++) { if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue; - error->all(file,line, - "Expected integer parameter in input script or data file"); + char msg[256]; + snprintf(msg,256,"Expected integer parameter instead of " + "'%s' in input script or data file",str); + error->all(file,line,msg); } return ATOBIGINT(str); @@ -1011,18 +1002,19 @@ bigint Force::bnumeric(const char *file, int line, char *str) tagint Force::tnumeric(const char *file, int line, char *str) { - if (!str) - error->all(file,line, - "Expected integer parameter in input script or data file"); - int n = strlen(str); + int n = 0; + + if (str) n = strlen(str); if (n == 0) - error->all(file,line, - "Expected integer parameter in input script or data file"); + error->all(file,line,"Expected integer parameter instead of " + "NULL or empty string in input script or data file"); for (int i = 0; i < n; i++) { if (isdigit(str[i]) || str[i] == '-' || str[i] == '+') continue; - error->all(file,line, - "Expected integer parameter in input script or data file"); + char msg[256]; + snprintf(msg,256,"Expected integer parameter instead of " + "'%s' in input script or data file",str); + error->all(file,line,msg); } return ATOTAGINT(str); diff --git a/src/group.cpp b/src/group.cpp index 3bc3f3d7bf..6c19af8bc6 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -207,6 +207,12 @@ void Group::assign(int narg, char **arg) else if (strcmp(arg[1],"molecule") == 0) category = MOLECULE; else if (strcmp(arg[1],"id") == 0) category = ID; + if ((category == MOLECULE) && (!atom->molecular)) + error->all(FLERR,"Group command requires atom attribute molecule"); + + if ((category == ID) && (!atom->tag_enable)) + error->all(FLERR,"Group command requires atom IDs"); + // args = logical condition if (narg > 3 && @@ -362,10 +368,13 @@ void Group::assign(int narg, char **arg) } else if (strcmp(arg[1],"include") == 0) { if (narg != 3) error->all(FLERR,"Illegal group command"); - if (strcmp(arg[2],"molecule") != 0) - error->all(FLERR,"Illegal group command"); + if (strcmp(arg[2],"molecule") == 0) { + if (!atom->molecular) + error->all(FLERR,"Group command requires atom attribute molecule"); - add_molecules(igroup,bit); + add_molecules(igroup,bit); + + } else error->all(FLERR,"Illegal group command"); // style = subtract diff --git a/src/improper.h b/src/improper.h index adcf6d29c8..d940b43a13 100644 --- a/src/improper.h +++ b/src/improper.h @@ -56,6 +56,10 @@ class Improper : protected Pointers { int vflag_either,vflag_global,vflag_atom; int maxeatom,maxvatom; + void ev_init(int eflag, int vflag, int alloc = 1) { + if (eflag||vflag) ev_setup(eflag, vflag, alloc); + else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0; + } void ev_setup(int, int, int alloc = 1); void ev_tally(int, int, int, int, int, int, double, double *, double *, double *, double, double, double, diff --git a/src/improper_deprecated.cpp b/src/improper_deprecated.cpp index e03fd785a7..6f4d08764f 100644 --- a/src/improper_deprecated.cpp +++ b/src/improper_deprecated.cpp @@ -52,6 +52,6 @@ void ImproperDeprecated::settings(int, char **) writemsg(lmp,"\nImproper style 'DEPRECATED' is a dummy style\n\n",0); } -} +} diff --git a/src/improper_hybrid.cpp b/src/improper_hybrid.cpp index 3c17e42eaf..5fdcb42a96 100644 --- a/src/improper_hybrid.cpp +++ b/src/improper_hybrid.cpp @@ -104,8 +104,7 @@ void ImproperHybrid::compute(int eflag, int vflag) // set neighbor->improperlist to sub-style improperlist before call // accumulate sub-style global/peratom energy/virial in hybrid - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); for (m = 0; m < nstyles; m++) { neighbor->nimproperlist = nimproperlist[m]; diff --git a/src/improper_zero.cpp b/src/improper_zero.cpp index 8a1fa529c6..747dd57919 100644 --- a/src/improper_zero.cpp +++ b/src/improper_zero.cpp @@ -44,8 +44,7 @@ ImproperZero::~ImproperZero() void ImproperZero::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); } /* ---------------------------------------------------------------------- */ diff --git a/src/info.cpp b/src/info.cpp index 672ce72b74..3d8a8d7b9e 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -260,13 +260,27 @@ void Info::command(int narg, char **arg) fprintf(out,"Printed on %s\n",ctime(&now)); if (flags & CONFIG) { - fprintf(out,"\nLAMMPS version: %s / %s\n\n", - universe->version, universe->num_ver); + if (lmp->has_git_info) { + fprintf(out,"\nLAMMPS version: %s / %s\nGit info: %s / %s / %s\n\n", + universe->version, universe->num_ver,lmp->git_branch, + lmp->git_descriptor,lmp->git_commit); + } else { + fprintf(out,"\nLAMMPS version: %s / %s\n\n", + universe->version, universe->num_ver); + } + const char *infobuf = get_os_info(); + fprintf(out,"OS information: %s\n\n",infobuf); + delete[] infobuf; + fprintf(out,"sizeof(smallint): %3d-bit\n",(int)sizeof(smallint)*8); fprintf(out,"sizeof(imageint): %3d-bit\n",(int)sizeof(imageint)*8); fprintf(out,"sizeof(tagint): %3d-bit\n",(int)sizeof(tagint)*8); fprintf(out,"sizeof(bigint): %3d-bit\n",(int)sizeof(bigint)*8); + infobuf = get_compiler_info(); + fprintf(out,"\nCompiler: %s with %s\n",infobuf,get_openmp_info()); + delete[] infobuf; + fputs("\nActive compile time flags:\n\n",out); if (has_gzip_support()) fputs("-DLAMMPS_GZIP\n",out); if (has_png_support()) fputs("-DLAMMPS_PNG\n",out); @@ -274,6 +288,14 @@ void Info::command(int narg, char **arg) if (has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",out); if (has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",out); +#if defined(LAMMPS_BIGBIG) + fputs("-DLAMMPS_BIGBIG\n",out); +#elif defined(LAMMPS_SMALLBIG) + fputs("-DLAMMPS_SMALLBIG\n",out); +#else // defined(LAMMPS_SMALLSMALL) + fputs("-DLAMMPS_SMALLSMALL\n",out); +#endif + const char *pkg; int ncword, ncline = 0; @@ -288,44 +310,6 @@ void Info::command(int narg, char **arg) ncline += ncword + 1; } fputs("\n",out); - -#if defined(_WIN32) - DWORD fullversion,majorv,minorv,buildv=0; - - fullversion = GetVersion(); - majorv = (DWORD) (LOBYTE(LOWORD(fullversion))); - minorv = (DWORD) (HIBYTE(LOWORD(fullversion))); - if (fullversion < 0x80000000) - buildv = (DWORD) (HIWORD(fullversion)); - - SYSTEM_INFO si; - GetSystemInfo(&si); - - const char *machine; - switch (si.wProcessorArchitecture) { - case PROCESSOR_ARCHITECTURE_AMD64: - machine = (const char *) "x86_64"; - break; - case PROCESSOR_ARCHITECTURE_ARM: - machine = (const char *) "arm"; - break; - case PROCESSOR_ARCHITECTURE_IA64: - machine = (const char *) "ia64"; - break; - case PROCESSOR_ARCHITECTURE_INTEL: - machine = (const char *) "i386"; - break; - default: - machine = (const char *) "(unknown)"; - } - fprintf(out,"\nOS information: Windows %d.%d (%d) on %s\n", - majorv,minorv,buildv,machine); -#else - struct utsname ut; - uname(&ut); - fprintf(out,"\nOS information: %s %s on %s\n", - ut.sysname, ut.release, ut.machine); -#endif } if (flags & MEMORY) { @@ -553,6 +537,12 @@ void Info::command(int narg, char **arg) fprintf(out,"Region[%3d]: %s, style = %s, side = %s\n", i, regs[i]->id, regs[i]->style, regs[i]->interior ? "in" : "out"); + if (regs[i]->bboxflag) + fprintf(out," Boundary: lo %g %g %g hi %g %g %g\n", + regs[i]->extent_xlo, regs[i]->extent_ylo, + regs[i]->extent_zlo, regs[i]->extent_xhi, + regs[i]->extent_yhi, regs[i]->extent_zhi); + else fprintf(out," No Boundary\n"); } } @@ -1103,6 +1093,103 @@ bool Info::has_package(const char * package_name) { return false; } +/* ---------------------------------------------------------------------- */ +#define _INFOBUF_SIZE 256 + +char *Info::get_os_info() +{ + char *buf = new char[_INFOBUF_SIZE]; + +#if defined(_WIN32) + DWORD fullversion,majorv,minorv,buildv=0; + + fullversion = GetVersion(); + majorv = (DWORD) (LOBYTE(LOWORD(fullversion))); + minorv = (DWORD) (HIBYTE(LOWORD(fullversion))); + if (fullversion < 0x80000000) + buildv = (DWORD) (HIWORD(fullversion)); + + SYSTEM_INFO si; + GetSystemInfo(&si); + + const char *machine; + switch (si.wProcessorArchitecture) { + case PROCESSOR_ARCHITECTURE_AMD64: + machine = (const char *) "x86_64"; + break; + case PROCESSOR_ARCHITECTURE_ARM: + machine = (const char *) "arm"; + break; + case PROCESSOR_ARCHITECTURE_IA64: + machine = (const char *) "ia64"; + break; + case PROCESSOR_ARCHITECTURE_INTEL: + machine = (const char *) "i386"; + break; + default: + machine = (const char *) "(unknown)"; + } + snprintf(buf,_INFOBUF_SIZE,"Windows %d.%d (%d) on %s", + majorv,minorv,buildv,machine); +#else + struct utsname ut; + uname(&ut); + snprintf(buf,_INFOBUF_SIZE,"%s %s on %s", + ut.sysname, ut.release, ut.machine); +#endif + return buf; +} + +char *Info::get_compiler_info() +{ + char *buf = new char[_INFOBUF_SIZE]; +#if __clang__ + snprintf(buf,_INFOBUF_SIZE,"Clang C++ %s", __VERSION__); +#elif __INTEL_COMPILER + snprintf(buf,_INFOBUF_SIZE,"Intel C++ %s", __VERSION__); +#elif __GNUC__ + snprintf(buf,_INFOBUF_SIZE,"GNU C++ %s", __VERSION__); +#else + snprintf(buf,_INFOBUF_SIZE,"(Unknown)"); +#endif + return buf; +} + +const char *Info::get_openmp_info() +{ + +#if !defined(_OPENMP) + return (const char *)"OpenMP not enabled"; +#else + +// Supported OpenMP version corresponds to the release date of the +// specifications as posted at https://www.openmp.org/specifications/ + +#if _OPENMP > 201811 + return (const char *)"OpenMP newer than version 5.0"; +#elif _OPENMP == 201811 + return (const char *)"OpenMP 5.0"; +#elif _OPENMP == 201611 + return (const char *)"OpenMP 5.0 preview 1"; +#elif _OPENMP == 201511 + return (const char *)"OpenMP 4.5"; +#elif _OPENMP == 201307 + return (const char *)"OpenMP 4.0"; +#elif _OPENMP == 201107 + return (const char *)"OpenMP 3.1"; +#elif _OPENMP == 200805 + return (const char *)"OpenMP 3.0"; +#elif _OPENMP == 200505 + return (const char *)"OpenMP 2.5"; +#elif _OPENMP == 200203 + return (const char *)"OpenMP 2.0"; +#else + return (const char *)"unknown OpenMP version"; +#endif + +#endif +} + /* ---------------------------------------------------------------------- */ char **Info::get_variable_names(int &num) { diff --git a/src/info.h b/src/info.h index 058400df78..ff8f15676d 100644 --- a/src/info.h +++ b/src/info.h @@ -40,6 +40,10 @@ class Info : protected Pointers { static bool has_exceptions(); static bool has_package(const char * package_name); + static char *get_os_info(); + static char *get_compiler_info(); + static const char *get_openmp_info(); + char **get_variable_names(int &num); private: diff --git a/src/input.cpp b/src/input.cpp index f9dd1ec314..f88c8ca0c0 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -429,14 +429,14 @@ char *Input::nextword(char *str, char **next) start += 3; *next = stop+3; if (**next && !isspace(**next)) - error->all(FLERR,"Input line quote not followed by whitespace"); + error->all(FLERR,"Input line quote not followed by white-space"); } else if (*start == '"' || *start == '\'') { stop = strchr(&start[1],*start); if (!stop) error->all(FLERR,"Unbalanced quotes in input line"); start++; *next = stop+1; if (**next && !isspace(**next)) - error->all(FLERR,"Input line quote not followed by whitespace"); + error->all(FLERR,"Input line quote not followed by white-space"); } else { stop = &start[strcspn(start," \t\n\v\f\r")]; if (*stop == '\0') *next = stop; @@ -1138,7 +1138,7 @@ void Input::partition() { if (narg < 3) error->all(FLERR,"Illegal partition command"); - int yesflag; + int yesflag = 0; if (strcmp(arg[0],"yes") == 0) yesflag = 1; else if (strcmp(arg[0],"no") == 0) yesflag = 0; else error->all(FLERR,"Illegal partition command"); diff --git a/src/input.h b/src/input.h index be320a41ec..47ad7779f1 100644 --- a/src/input.h +++ b/src/input.h @@ -173,9 +173,9 @@ E: Unbalanced quotes in input line No matching end double quote was found following a leading double quote. -E: Input line quote not followed by whitespace +E: Input line quote not followed by white-space -An end quote must be followed by whitespace. +An end quote must be followed by white-space. E: Invalid variable name @@ -337,7 +337,7 @@ after a read_data, read_restart, or create_box command. E: Package command after simulation box is defined -The package command cannot be used afer a read_data, read_restart, or +The package command cannot be used after a read_data, read_restart, or create_box command. E: Package gpu command without GPU package installed diff --git a/src/kspace.cpp b/src/kspace.cpp index 25491cd964..0144ea59a3 100644 --- a/src/kspace.cpp +++ b/src/kspace.cpp @@ -168,9 +168,7 @@ void KSpace::triclinic_check() void KSpace::compute_dummy(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = evflag_atom = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); } /* ---------------------------------------------------------------------- diff --git a/src/kspace.h b/src/kspace.h index f29659d0e8..2345cebf24 100644 --- a/src/kspace.h +++ b/src/kspace.h @@ -194,6 +194,10 @@ class KSpace : protected Pointers { int kx_ewald,ky_ewald,kz_ewald; // kspace settings for Ewald sum void pair_check(); + void ev_init(int eflag, int vflag, int alloc = 1) { + if (eflag||vflag) ev_setup(eflag, vflag, alloc); + else evflag = eflag_either = eflag_global = eflag_atom = vflag_either = vflag_global = vflag_atom = 0; + } void ev_setup(int, int, int alloc = 1); double estimate_table_accuracy(double, double); }; diff --git a/src/lammps.cpp b/src/lammps.cpp index 699efe37a3..2b3f001b09 100644 --- a/src/lammps.cpp +++ b/src/lammps.cpp @@ -46,12 +46,13 @@ #include "accelerator_kokkos.h" #include "accelerator_omp.h" #include "timer.h" -#include "python.h" +#include "lmppython.h" #include "version.h" #include "memory.h" #include "error.h" #include "lmpinstalledpkgs.h" +#include "lmpgitversion.h" using namespace LAMMPS_NS; @@ -65,13 +66,15 @@ static void print_style(FILE *fp, const char *str, int &pos); input is allocated at end after MPI info is setup ------------------------------------------------------------------------- */ -LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) +LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) : + memory(NULL), error(NULL), universe(NULL), input(NULL), atom(NULL), + update(NULL), neighbor(NULL), comm(NULL), domain(NULL), force(NULL), + modify(NULL), group(NULL), output(NULL), timer(NULL), kokkos(NULL), + atomKK(NULL), memoryKK(NULL), python(NULL), citeme(NULL) { memory = new Memory(this); error = new Error(this); universe = new Universe(this,communicator); - output = NULL; - python = NULL; clientserver = 0; cslib = NULL; @@ -413,7 +416,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) } } - if (universe->me == 0) { + if ((universe->me == 0) && !helpflag) { if (screen) fprintf(screen,"LAMMPS (%s)\n",universe->version); if (logfile) fprintf(logfile,"LAMMPS (%s)\n",universe->version); } @@ -487,7 +490,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) // screen and logfile messages for universe and world - if (universe->me == 0) { + if ((universe->me == 0) && (!helpflag)) { if (universe->uscreen) { fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version); fprintf(universe->uscreen,"Running on %d partitions of processors\n", @@ -500,7 +503,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) } } - if (me == 0) { + if ((me == 0) && (!helpflag)) { if (screen) { fprintf(screen,"LAMMPS (%s)\n",universe->version); fprintf(screen,"Processor partition = %d\n",universe->iworld); @@ -585,16 +588,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) memory->destroy(plast); } - // allocate top-level classes - - create(); - post_create(); - // if helpflag set, print help and quit with "success" status + // otherwise allocate top level classes. if (helpflag) { if (universe->me == 0 && screen) help(); error->done(0); + } else { + create(); + post_create(); } // if either restart conversion option was used, invoke 2 commands and quit @@ -760,26 +762,27 @@ void LAMMPS::post_create() // check that KOKKOS package classes were instantiated // check that GPU, INTEL, USER-OMP fixes were compiled with LAMMPS - if (!suffix_enable) return; + if (suffix_enable) { - if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU")) - error->all(FLERR,"Using suffix gpu without GPU package installed"); - if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL")) - error->all(FLERR,"Using suffix intel without USER-INTEL package installed"); - if (strcmp(suffix,"kk") == 0 && - (kokkos == NULL || kokkos->kokkos_exists == 0)) - error->all(FLERR,"Using suffix kk without KOKKOS package enabled"); - if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP")) - error->all(FLERR,"Using suffix omp without USER-OMP package installed"); + if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU")) + error->all(FLERR,"Using suffix gpu without GPU package installed"); + if (strcmp(suffix,"intel") == 0 && !modify->check_package("INTEL")) + error->all(FLERR,"Using suffix intel without USER-INTEL package installed"); + if (strcmp(suffix,"kk") == 0 && + (kokkos == NULL || kokkos->kokkos_exists == 0)) + error->all(FLERR,"Using suffix kk without KOKKOS package enabled"); + if (strcmp(suffix,"omp") == 0 && !modify->check_package("OMP")) + error->all(FLERR,"Using suffix omp without USER-OMP package installed"); - if (strcmp(suffix,"gpu") == 0) input->one("package gpu 1"); - if (strcmp(suffix,"intel") == 0) input->one("package intel 1"); - if (strcmp(suffix,"omp") == 0) input->one("package omp 0"); + if (strcmp(suffix,"gpu") == 0) input->one("package gpu 1"); + if (strcmp(suffix,"intel") == 0) input->one("package intel 1"); + if (strcmp(suffix,"omp") == 0) input->one("package omp 0"); - if (suffix2) { - if (strcmp(suffix2,"gpu") == 0) input->one("package gpu 1"); - if (strcmp(suffix2,"intel") == 0) input->one("package intel 1"); - if (strcmp(suffix2,"omp") == 0) input->one("package omp 0"); + if (suffix2) { + if (strcmp(suffix2,"gpu") == 0) input->one("package gpu 1"); + if (strcmp(suffix2,"intel") == 0) input->one("package intel 1"); + if (strcmp(suffix2,"omp") == 0) input->one("package omp 0"); + } } // invoke any command-line package commands @@ -896,9 +899,14 @@ void LAMMPS::help() // general help message about command line and flags + if (has_git_info) { + fprintf(fp,"\nLarge-scale Atomic/Molecular Massively Parallel Simulator - " + LAMMPS_VERSION "\nGit info (%s / %s)\n\n",git_branch, git_descriptor); + } else { + fprintf(fp,"\nLarge-scale Atomic/Molecular Massively Parallel Simulator - " + LAMMPS_VERSION "\n\n"); + } fprintf(fp, - "\nLarge-scale Atomic/Molecular Massively Parallel Simulator - " - LAMMPS_VERSION "\n\n" "Usage example: %s -var t 300 -echo screen -in in.alloy\n\n" "List of command line options supported by this LAMMPS executable:\n\n" "-echo none/screen/log/both : echoing of input script (-e)\n" @@ -1080,12 +1088,32 @@ void LAMMPS::print_config(FILE *fp) const char *pkg; int ncword, ncline = 0; + char *infobuf = Info::get_os_info(); + fprintf(fp,"OS: %s\n\n",infobuf); + delete[] infobuf; + + infobuf = Info::get_compiler_info(); + fprintf(fp,"Compiler: %s with %s\n\n",infobuf,Info::get_openmp_info()); + delete[] infobuf; + fputs("Active compile time flags:\n\n",fp); if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp); if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp); if (Info::has_jpeg_support()) fputs("-DLAMMPS_JPEG\n",fp); if (Info::has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",fp); if (Info::has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",fp); +#if defined(LAMMPS_BIGBIG) + fputs("-DLAMMPS_BIGBIG\n",fp); +#elif defined(LAMMPS_SMALLBIG) + fputs("-DLAMMPS_SMALLBIG\n",fp); +#else // defined(LAMMPS_SMALLSMALL) + fputs("-DLAMMPS_SMALLSMALL\n",fp); +#endif + fprintf(fp,"\nsizeof(smallint): %3d-bit\n",(int)sizeof(smallint)*8); + fprintf(fp,"sizeof(imageint): %3d-bit\n",(int)sizeof(imageint)*8); + fprintf(fp,"sizeof(tagint): %3d-bit\n",(int)sizeof(tagint)*8); + fprintf(fp,"sizeof(bigint): %3d-bit\n",(int)sizeof(bigint)*8); + fputs("\nInstalled packages:\n\n",fp); for (int i = 0; NULL != (pkg = installed_packages[i]); ++i) { diff --git a/src/lammps.h b/src/lammps.h index 5ccef3026e..2e052e5ed2 100644 --- a/src/lammps.h +++ b/src/lammps.h @@ -65,6 +65,11 @@ class LAMMPS { static const char * installed_packages[]; + static const bool has_git_info; + static const char git_commit[]; + static const char git_branch[]; + static const char git_descriptor[]; + LAMMPS(int, char **, MPI_Comm); ~LAMMPS(); void create(); @@ -170,7 +175,7 @@ The size of the MPI datatype does not match the size of a bigint. E: Small to big integers are not sized correctly -This error occurs whenthe sizes of smallint, imageint, tagint, bigint, +This error occurs when the sizes of smallint, imageint, tagint, bigint, as defined in src/lmptype.h are not what is expected. Contact the developers if this occurs. diff --git a/src/library.cpp b/src/library.cpp index a46689da09..d8c55159a2 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -957,7 +957,7 @@ void lammps_gather_atoms_concat(void *ptr, char *name, } // perform MPI_Allgatherv on each proc's chunk of Nlocal atoms - + int nprocs = lmp->comm->nprocs; int *recvcounts,*displs; @@ -1078,7 +1078,7 @@ void lammps_gather_atoms_subset(void *ptr, char *name, LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE - { + { int i,j,m,offset; tagint id; @@ -1319,9 +1319,9 @@ void lammps_scatter_atoms(void *ptr, char *name, ------------------------------------------------------------------------- */ void lammps_scatter_atoms_subset(void *ptr, char *name, - int type, int count, + int type, int count, int ndata, int *ids, void *data) -{ +{ LAMMPS *lmp = (LAMMPS *) ptr; BEGIN_CAPTURE @@ -1363,9 +1363,11 @@ void lammps_scatter_atoms_subset(void *ptr, char *name, int *dptr = (int *) data; if (count == 1) { - for (i = 0; i < ndata; i++) - if ((m = lmp->atom->map(i+1)) >= 0) + for (i = 0; i < ndata; i++) { + id = ids[i]; + if ((m = lmp->atom->map(id)) >= 0) vector[m] = dptr[i]; + } } else if (imgpack) { for (i = 0; i < ndata; i++) { diff --git a/src/python.cpp b/src/lmppython.cpp similarity index 99% rename from src/python.cpp rename to src/lmppython.cpp index e32e2a161c..7c6a490c24 100644 --- a/src/python.cpp +++ b/src/lmppython.cpp @@ -11,7 +11,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "python.h" +#include "lmppython.h" #include "error.h" using namespace LAMMPS_NS; diff --git a/src/python.h b/src/lmppython.h similarity index 100% rename from src/python.h rename to src/lmppython.h diff --git a/src/lmpwindows.h b/src/lmpwindows.h index ae2a545717..546fa62535 100644 --- a/src/lmpwindows.h +++ b/src/lmpwindows.h @@ -4,6 +4,7 @@ #endif #include #include +#include // LAMMPS uses usleep with 100 ms arguments, no microsecond precision needed #if !defined(__MINGW32__) #include "sleep.h" @@ -15,6 +16,7 @@ #define ATOBIGINT _atoi64 #define pclose _pclose +#define strdup _strdup // the following functions ared defined to get rid of // 'ambiguous call to overloaded function' error in VSS for mismathched type arguments diff --git a/src/memory.h b/src/memory.h index 20ea426f90..df942387fa 100644 --- a/src/memory.h +++ b/src/memory.h @@ -436,6 +436,53 @@ class Memory : protected Pointers { const char *name) {fail(name); return NULL;} +/* ---------------------------------------------------------------------- + grow or shrink 1st dim of a 4d array + last 3 dims must stay the same + ------------------------------------------------------------------------- */ + + template + TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, int n4, + const char *name) + { + if (array == NULL) return create(array, n1, n2, n3, n4, name); + + bigint nbytes = ((bigint) sizeof(TYPE)) * n1*n2*n3*n4; + TYPE *data = (TYPE *)srealloc(array[0][0][0], nbytes, name); + nbytes = ((bigint) sizeof(TYPE *)) * n1*n2*n3; + TYPE **cube = (TYPE **)srealloc(array[0][0], nbytes, name); + nbytes = ((bigint) sizeof(TYPE **)) * n1*n2; + TYPE ***plane = (TYPE ***)srealloc(array[0], nbytes, name); + nbytes = ((bigint) sizeof(TYPE ***)) * n1; + array = (TYPE ****)srealloc(array, nbytes, name); + + int i, j, k; + bigint m1, m2; + bigint n = 0; + for (i = 0; i < n1; i++) { + m2 = ((bigint)i) * n2; + array[i] = &plane[m2]; + for (j = 0; j < n2; j++) { + m1 = ((bigint)i) * n2 + j; + m2 = ((bigint)i) * n2*n3 + j*n3; + plane[m1] = &cube[m2]; + for (k = 0; k < n3; k++) { + m1 = ((bigint)i) * n2*n3 + j*n3 + k; + cube[m1] = &data[n]; + n += n4; + } + } + } + return array; + } + + template + TYPE *****grow(TYPE *****&array, int n1, int n2, int n3, int n4, + const char *name) + { + fail(name); return NULL; + } + /* ---------------------------------------------------------------------- destroy a 4d array ------------------------------------------------------------------------- */ diff --git a/src/min.cpp b/src/min.cpp index cd9253f8d3..2a42a444a0 100644 --- a/src/min.cpp +++ b/src/min.cpp @@ -655,7 +655,11 @@ void Min::modify_params(int narg, char **arg) else if (strcmp(arg[iarg+1],"forcezero") == 0) linestyle = 2; else error->all(FLERR,"Illegal min_modify command"); iarg += 2; - } else error->all(FLERR,"Illegal min_modify command"); + } else { + int n = modify_param(narg-iarg,&arg[iarg]); + if (n == 0) error->all(FLERR,"Illegal fix_modify command"); + iarg += n; + } } } diff --git a/src/min.h b/src/min.h index 92da97c664..a63254231c 100644 --- a/src/min.h +++ b/src/min.h @@ -38,6 +38,7 @@ class Min : protected Pointers { int request(class Pair *, int, double); virtual bigint memory_usage() {return 0;} void modify_params(int, char **); + virtual int modify_param(int, char **) {return 0;} double fnorm_sqr(); double fnorm_inf(); diff --git a/src/pair.cpp b/src/pair.cpp index f76bb54c36..0cd0c78971 100644 --- a/src/pair.cpp +++ b/src/pair.cpp @@ -72,6 +72,9 @@ Pair::Pair(LAMMPS *lmp) : Pointers(lmp) single_extra = 0; svector = NULL; + setflag = NULL; + cutsq = NULL; + ewaldflag = pppmflag = msmflag = dispersionflag = tip4pflag = dipoleflag = 0; reinitflag = 1; @@ -151,13 +154,13 @@ void Pair::modify_params(int narg, char **arg) } else if (strcmp(arg[iarg],"table") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command"); ncoultablebits = force->inumeric(FLERR,arg[iarg+1]); - if (ncoultablebits > sizeof(float)*CHAR_BIT) + if (ncoultablebits > (int)sizeof(float)*CHAR_BIT) error->all(FLERR,"Too many total bits for bitmapped lookup table"); iarg += 2; } else if (strcmp(arg[iarg],"table/disp") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command"); ndisptablebits = force->inumeric(FLERR,arg[iarg+1]); - if (ndisptablebits > sizeof(float)*CHAR_BIT) + if (ndisptablebits > (int)sizeof(float)*CHAR_BIT) error->all(FLERR,"Too many total bits for bitmapped lookup table"); iarg += 2; } else if (strcmp(arg[iarg],"tabinner") == 0) { @@ -195,7 +198,7 @@ void Pair::init() if (tail_flag && domain->dimension == 2) error->all(FLERR,"Cannot use pair tail corrections with 2d simulations"); if (tail_flag && domain->nonperiodic && comm->me == 0) - error->warning(FLERR,"Using pair tail corrections with nonperiodic system"); + error->warning(FLERR,"Using pair tail corrections with non-periodic system"); if (!compute_flag && tail_flag && comm->me == 0) error->warning(FLERR,"Using pair tail corrections with " "pair_modify compute no"); @@ -688,8 +691,7 @@ double Pair::mix_distance(double sig1, double sig2) void Pair::compute_dummy(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); } /* ---------------------------------------------------------------------- */ @@ -1619,7 +1621,7 @@ void Pair::write_file(int narg, char **arg) eamfp[0] = eamfp[1] = 0.0; double *eamfp_hold; - Pair *epair = force->pair_match("eam",0); + Pair *epair = force->pair_match("^eam",0); if (epair) epair->swap_eam(eamfp,&eamfp_hold); // if atom style defines charge, swap in dummy q vec @@ -1695,7 +1697,7 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits, if (sizeof(int) != sizeof(float)) error->all(FLERR,"Bitmapped lookup tables require int/float be same size"); - if (ntablebits > sizeof(float)*CHAR_BIT) + if (ntablebits > (int)sizeof(float)*CHAR_BIT) error->all(FLERR,"Too many total bits for bitmapped lookup table"); if (inner >= outer) @@ -1719,7 +1721,7 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits, int nmantbits = ntablebits - nexpbits; - if (nexpbits > sizeof(float)*CHAR_BIT - FLT_MANT_DIG) + if (nexpbits > (int)sizeof(float)*CHAR_BIT - FLT_MANT_DIG) error->all(FLERR,"Too many exponent bits for lookup table"); if (nmantbits+1 > FLT_MANT_DIG) error->all(FLERR,"Too many mantissa bits for lookup table"); diff --git a/src/pair.h b/src/pair.h index a9506480be..2d955816df 100644 --- a/src/pair.h +++ b/src/pair.h @@ -224,6 +224,10 @@ class Pair : protected Pointers { int copymode; // if set, do not deallocate during destruction // required when classes are used as functors by Kokkos + void ev_init(int eflag, int vflag, int alloc = 1) { + if (eflag||vflag) ev_setup(eflag, vflag, alloc); + else ev_unset(); + } virtual void ev_setup(int, int, int alloc = 1); void ev_unset(); void ev_tally_full(int, double, double, double, double, double, double); @@ -278,7 +282,7 @@ E: Cannot use pair tail corrections with 2d simulations The correction factors are only currently defined for 3d systems. -W: Using pair tail corrections with nonperiodic system +W: Using pair tail corrections with non-periodic system This is probably a bogus thing to do, since tail corrections are computed by integrating the density of a periodic system out to diff --git a/src/pair_beck.cpp b/src/pair_beck.cpp index d9c0fb902c..17731ebf0b 100644 --- a/src/pair_beck.cpp +++ b/src/pair_beck.cpp @@ -63,8 +63,7 @@ void PairBeck::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_born.cpp b/src/pair_born.cpp index 1a1db9dd90..78434c91f8 100644 --- a/src/pair_born.cpp +++ b/src/pair_born.cpp @@ -71,8 +71,7 @@ void PairBorn::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_born_coul_dsf.cpp b/src/pair_born_coul_dsf.cpp index be7f41ca2b..2e565897b5 100644 --- a/src/pair_born_coul_dsf.cpp +++ b/src/pair_born_coul_dsf.cpp @@ -77,8 +77,7 @@ void PairBornCoulDSF::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_born_coul_wolf.cpp b/src/pair_born_coul_wolf.cpp index 22dcfa9f2d..3bb0e39e57 100644 --- a/src/pair_born_coul_wolf.cpp +++ b/src/pair_born_coul_wolf.cpp @@ -76,8 +76,7 @@ void PairBornCoulWolf::compute(int eflag, int vflag) double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_buck.cpp b/src/pair_buck.cpp index 8b6d79234b..a3cf1a38d6 100644 --- a/src/pair_buck.cpp +++ b/src/pair_buck.cpp @@ -66,8 +66,7 @@ void PairBuck::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 7eecb62121..094797694c 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -42,7 +42,9 @@ PairBuckCoulCut::PairBuckCoulCut(LAMMPS *lmp) : Pair(lmp) PairBuckCoulCut::~PairBuckCoulCut() { - if (!copymode) { + if (copymode) return; + + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); @@ -71,8 +73,7 @@ void PairBuckCoulCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 8741abdb89..e7c0e0aabb 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -53,8 +53,7 @@ void PairCoulCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 432a015598..c8afdabb93 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -40,8 +40,7 @@ void PairCoulDebye::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_coul_dsf.cpp b/src/pair_coul_dsf.cpp index 8cd5f7fece..e487ff171c 100644 --- a/src/pair_coul_dsf.cpp +++ b/src/pair_coul_dsf.cpp @@ -68,8 +68,7 @@ void PairCoulDSF::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_coul_streitz.cpp b/src/pair_coul_streitz.cpp index 920770ed7f..244dccda12 100644 --- a/src/pair_coul_streitz.cpp +++ b/src/pair_coul_streitz.cpp @@ -412,8 +412,7 @@ void PairCoulStreitz::compute(int eflag, int vflag) ci_jfi = ci_fifj = dci_jfi = dci_fifj = 0.0; forcecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = vflag_atom = 0; + ev_init(eflag,vflag); inum = list->inum; ilist = list->ilist; diff --git a/src/pair_coul_wolf.cpp b/src/pair_coul_wolf.cpp index 762491166e..dbf21b8bee 100644 --- a/src/pair_coul_wolf.cpp +++ b/src/pair_coul_wolf.cpp @@ -64,8 +64,7 @@ void PairCoulWolf::compute(int eflag, int vflag) double erfcc,erfcd,v_sh,dvdrr,e_self,e_shift,f_shift,qisq; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_deprecated.cpp b/src/pair_deprecated.cpp index 20b5c9775b..0b1342fb2d 100644 --- a/src/pair_deprecated.cpp +++ b/src/pair_deprecated.cpp @@ -48,10 +48,13 @@ void PairDeprecated::settings(int, char **) my_style = hybrid->keywords[hybrid->nstyles]; } + if (strcmp(my_style,"reax") == 0) { + writemsg(lmp,"\nPair style 'reax' has been removed from LAMMPS " + "after the 12 December 2018 version\n\n",1); + } + if (strcmp(my_style,"DEPRECATED") == 0) { writemsg(lmp,"\nPair style 'DEPRECATED' is a dummy style\n\n",0); } -} - - +} diff --git a/src/pair_deprecated.h b/src/pair_deprecated.h index 29d6efffaf..029ec5e6d4 100644 --- a/src/pair_deprecated.h +++ b/src/pair_deprecated.h @@ -14,6 +14,7 @@ #ifdef PAIR_CLASS PairStyle(DEPRECATED,PairDeprecated) +PairStyle(reax,PairDeprecated) #else diff --git a/src/pair_dpd.cpp b/src/pair_dpd.cpp index 5c5fc4254b..914b4aee17 100644 --- a/src/pair_dpd.cpp +++ b/src/pair_dpd.cpp @@ -70,8 +70,7 @@ void PairDPD::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **v = atom->v; diff --git a/src/pair_dpd_tstat.cpp b/src/pair_dpd_tstat.cpp index f2c0b157ea..1207c954eb 100644 --- a/src/pair_dpd_tstat.cpp +++ b/src/pair_dpd_tstat.cpp @@ -43,8 +43,7 @@ void PairDPDTstat::compute(int eflag, int vflag) double rsq,r,rinv,dot,wd,randnum,factor_dpd; int *ilist,*jlist,*numneigh,**firstneigh; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); // adjust sigma if target T is changing diff --git a/src/pair_gauss.cpp b/src/pair_gauss.cpp index 426389753b..2d157d6cac 100644 --- a/src/pair_gauss.cpp +++ b/src/pair_gauss.cpp @@ -68,8 +68,7 @@ void PairGauss::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); int occ = 0; double **x = atom->x; diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 2b2304718c..a1a6c81195 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -1,3 +1,4 @@ + /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories @@ -45,7 +46,7 @@ PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp), PairHybrid::~PairHybrid() { - if (nstyles) { + if (nstyles > 0) { for (int m = 0; m < nstyles; m++) { delete styles[m]; delete [] keywords[m]; @@ -95,9 +96,7 @@ void PairHybrid::compute(int eflag, int vflag) if (no_virial_fdotr_compute && vflag % 4 == 2) vflag = 1 + vflag/4 * 4; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = eflag_global = vflag_global = - eflag_atom = vflag_atom = 0; + ev_init(eflag,vflag); // check if global component of incoming vflag = 2 // if so, reset vflag passed to substyle as if it were 0 @@ -243,11 +242,18 @@ void PairHybrid::settings(int narg, char **arg) // delete old lists, since cannot just change settings - if (nstyles) { - for (int m = 0; m < nstyles; m++) delete styles[m]; - delete [] styles; - for (int m = 0; m < nstyles; m++) delete [] keywords[m]; - delete [] keywords; + if (nstyles > 0) { + for (int m = 0; m < nstyles; m++) { + delete styles[m]; + delete [] keywords[m]; + if (special_lj[m]) delete [] special_lj[m]; + if (special_coul[m]) delete [] special_coul[m]; + } + delete[] styles; + delete[] keywords; + delete[] multiple; + delete[] special_lj; + delete[] special_coul; } if (allocated) { @@ -670,6 +676,12 @@ void PairHybrid::read_restart(FILE *fp) // allocate list of sub-styles + delete[] styles; + delete[] keywords; + delete[] multiple; + delete[] special_lj; + delete[] special_coul; + styles = new Pair*[nstyles]; keywords = new char*[nstyles]; multiple = new int[nstyles]; diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 457eba0e79..cefe9b87e0 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -73,8 +73,7 @@ void PairLJ96Cut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -308,8 +307,7 @@ void PairLJ96Cut::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_cubic.cpp b/src/pair_lj_cubic.cpp index 770caa6359..fdbfca608f 100644 --- a/src/pair_lj_cubic.cpp +++ b/src/pair_lj_cubic.cpp @@ -67,8 +67,7 @@ void PairLJCubic::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_cut.cpp b/src/pair_lj_cut.cpp index 13a546f5a5..2a0fcde3a5 100644 --- a/src/pair_lj_cut.cpp +++ b/src/pair_lj_cut.cpp @@ -73,8 +73,7 @@ void PairLJCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -305,8 +304,7 @@ void PairLJCut::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index 15c06ab36a..6f2ba75309 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -67,8 +67,7 @@ void PairLJCutCoulCut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_cut_coul_debye.cpp b/src/pair_lj_cut_coul_debye.cpp index dfd866ca7a..cc6e92b2e3 100644 --- a/src/pair_lj_cut_coul_debye.cpp +++ b/src/pair_lj_cut_coul_debye.cpp @@ -37,8 +37,7 @@ void PairLJCutCoulDebye::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_cut_coul_dsf.cpp b/src/pair_lj_cut_coul_dsf.cpp index a49af13fb2..f114a5851f 100644 --- a/src/pair_lj_cut_coul_dsf.cpp +++ b/src/pair_lj_cut_coul_dsf.cpp @@ -52,21 +52,21 @@ PairLJCutCoulDSF::PairLJCutCoulDSF(LAMMPS *lmp) : Pair(lmp) PairLJCutCoulDSF::~PairLJCutCoulDSF() { - if (!copymode) { - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); + if (copymode) return; - memory->destroy(cut_lj); - memory->destroy(cut_ljsq); - memory->destroy(epsilon); - memory->destroy(sigma); - memory->destroy(lj1); - memory->destroy(lj2); - memory->destroy(lj3); - memory->destroy(lj4); - memory->destroy(offset); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + + memory->destroy(cut_lj); + memory->destroy(cut_ljsq); + memory->destroy(epsilon); + memory->destroy(sigma); + memory->destroy(lj1); + memory->destroy(lj2); + memory->destroy(lj3); + memory->destroy(lj4); + memory->destroy(offset); } } @@ -81,8 +81,7 @@ void PairLJCutCoulDSF::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_cut_coul_wolf.cpp b/src/pair_lj_cut_coul_wolf.cpp index fc8a858ce1..2f796ded12 100644 --- a/src/pair_lj_cut_coul_wolf.cpp +++ b/src/pair_lj_cut_coul_wolf.cpp @@ -77,8 +77,7 @@ void PairLJCutCoulWolf::compute(int eflag, int vflag) evdwl = 0.0; ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_expand.cpp b/src/pair_lj_expand.cpp index 9aa58b3b88..d5c0a40f2d 100644 --- a/src/pair_lj_expand.cpp +++ b/src/pair_lj_expand.cpp @@ -38,8 +38,9 @@ PairLJExpand::PairLJExpand(LAMMPS *lmp) : Pair(lmp) PairLJExpand::~PairLJExpand() { - if (!copymode) { - if (allocated) { + if (copymode) return; + + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); @@ -52,7 +53,6 @@ PairLJExpand::~PairLJExpand() memory->destroy(lj3); memory->destroy(lj4); memory->destroy(offset); - } } } @@ -67,8 +67,7 @@ void PairLJExpand::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_gromacs.cpp b/src/pair_lj_gromacs.cpp index 495e96c368..1fdaefebe9 100644 --- a/src/pair_lj_gromacs.cpp +++ b/src/pair_lj_gromacs.cpp @@ -41,8 +41,9 @@ PairLJGromacs::PairLJGromacs(LAMMPS *lmp) : Pair(lmp) PairLJGromacs::~PairLJGromacs() { - if (!copymode) { - if (allocated) { + if (copymode) return; + + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); @@ -60,7 +61,6 @@ PairLJGromacs::~PairLJGromacs() memory->destroy(ljsw3); memory->destroy(ljsw4); memory->destroy(ljsw5); - } } } @@ -75,8 +75,7 @@ void PairLJGromacs::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_gromacs_coul_gromacs.cpp b/src/pair_lj_gromacs_coul_gromacs.cpp index 414bfea92a..28dc8ec79b 100644 --- a/src/pair_lj_gromacs_coul_gromacs.cpp +++ b/src/pair_lj_gromacs_coul_gromacs.cpp @@ -41,8 +41,9 @@ PairLJGromacsCoulGromacs::PairLJGromacsCoulGromacs(LAMMPS *lmp) : Pair(lmp) PairLJGromacsCoulGromacs::~PairLJGromacsCoulGromacs() { - if (!copymode) { - if (allocated) { + if (copymode) return; + + if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); @@ -57,7 +58,6 @@ PairLJGromacsCoulGromacs::~PairLJGromacsCoulGromacs() memory->destroy(ljsw3); memory->destroy(ljsw4); memory->destroy(ljsw5); - } } } @@ -72,8 +72,7 @@ void PairLJGromacsCoulGromacs::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = ecoul = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_smooth.cpp b/src/pair_lj_smooth.cpp index a12046bb3b..ecacadbffa 100644 --- a/src/pair_lj_smooth.cpp +++ b/src/pair_lj_smooth.cpp @@ -72,8 +72,7 @@ void PairLJSmooth::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_lj_smooth_linear.cpp b/src/pair_lj_smooth_linear.cpp index 4cf8d6d3db..370caeddf7 100644 --- a/src/pair_lj_smooth_linear.cpp +++ b/src/pair_lj_smooth_linear.cpp @@ -62,8 +62,7 @@ void PairLJSmoothLinear::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_mie_cut.cpp b/src/pair_mie_cut.cpp index c1e1c1ff50..231832dc48 100644 --- a/src/pair_mie_cut.cpp +++ b/src/pair_mie_cut.cpp @@ -75,8 +75,7 @@ void PairMIECut::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -310,8 +309,7 @@ void PairMIECut::compute_outer(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index c1031343e1..dca1834c14 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -59,8 +59,7 @@ void PairMorse::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_soft.cpp b/src/pair_soft.cpp index d1c51ac600..7602f7b925 100644 --- a/src/pair_soft.cpp +++ b/src/pair_soft.cpp @@ -58,8 +58,7 @@ void PairSoft::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_table.cpp b/src/pair_table.cpp index 0d692caccb..cf9e5c3bfb 100644 --- a/src/pair_table.cpp +++ b/src/pair_table.cpp @@ -26,6 +26,7 @@ #include "neigh_list.h" #include "memory.h" #include "error.h" +#include "utils.h" using namespace LAMMPS_NS; @@ -73,8 +74,7 @@ void PairTable::compute(int eflag, int vflag) int tlm1 = tablength - 1; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; @@ -361,9 +361,9 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) FILE *fp = force->open_potential(file); if (fp == NULL) { - char str[128]; - snprintf(str,128,"Cannot open file %s",file); - error->one(FLERR,str); + std::string str("Cannot open file "); + str += file; + error->one(FLERR,str.c_str()); } // loop until section found with matching keyword @@ -374,17 +374,18 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line if (line[0] == '#') continue; // comment char *word = strtok(line," \t\n\r"); - if (strcmp(word,keyword) == 0) break; // matching keyword - fgets(line,MAXLINE,fp); // no match, skip section + if (strcmp(word,keyword) == 0) break; // matching keyword + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); // no match, skip section param_extract(tb,line); - fgets(line,MAXLINE,fp); - for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); + for (int i = 0; i < tb->ninput; i++) + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); } // read args on 2nd line of section // allocate table arrays for file values - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); param_extract(tb,line); memory->create(tb->rfile,tb->ninput,"pair:rfile"); memory->create(tb->efile,tb->ninput,"pair:efile"); @@ -412,7 +413,7 @@ void PairTable::read_table(Table *tb, char *file, char *keyword) int rerror = 0; int cerror = 0; - fgets(line,MAXLINE,fp); + utils::sfgets(FLERR,line,MAXLINE,fp,file,error); for (int i = 0; i < tb->ninput; i++) { if (NULL == fgets(line,MAXLINE,fp)) error->one(FLERR,"Premature end of file in pair table"); diff --git a/src/pair_ufm.cpp b/src/pair_ufm.cpp index a9f076f504..226fb6e7d9 100644 --- a/src/pair_ufm.cpp +++ b/src/pair_ufm.cpp @@ -74,8 +74,7 @@ void PairUFM::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_yukawa.cpp b/src/pair_yukawa.cpp index af520fd3da..913afbd5a1 100644 --- a/src/pair_yukawa.cpp +++ b/src/pair_yukawa.cpp @@ -55,8 +55,7 @@ void PairYukawa::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_zbl.cpp b/src/pair_zbl.cpp index f23a1e5d56..254a82ea64 100644 --- a/src/pair_zbl.cpp +++ b/src/pair_zbl.cpp @@ -78,8 +78,7 @@ void PairZBL::compute(int eflag, int vflag) int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); double **x = atom->x; double **f = atom->f; diff --git a/src/pair_zero.cpp b/src/pair_zero.cpp index d423e196af..143808f598 100644 --- a/src/pair_zero.cpp +++ b/src/pair_zero.cpp @@ -50,8 +50,7 @@ PairZero::~PairZero() void PairZero::compute(int eflag, int vflag) { - if (eflag || vflag) ev_setup(eflag,vflag); - else evflag = vflag_fdotr = 0; + ev_init(eflag,vflag); if (vflag_fdotr) virial_fdotr_compute(); } diff --git a/src/read_data.cpp b/src/read_data.cpp index 26c406c1d6..2f4484010b 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -396,7 +396,8 @@ void ReadData::command(int narg, char **arg) // values in this data file - natoms = ntypes = 0; + natoms = 0; + ntypes = 0; nbonds = nangles = ndihedrals = nimpropers = 0; nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0; @@ -872,9 +873,9 @@ void ReadData::command(int narg, char **arg) if (domain->nonperiodic == 2) { if (domain->triclinic) domain->x2lamda(atom->nlocal); domain->reset_box(); - comm->init(); - comm->exchange(); - if (atom->map_style) atom->map_set(); + Irregular *irregular = new Irregular(lmp); + irregular->migrate_atoms(1); + delete irregular; if (domain->triclinic) domain->lamda2x(atom->nlocal); bigint natoms; @@ -993,18 +994,29 @@ void ReadData::header(int firstpass) if (!avec_ellipsoid) error->all(FLERR,"No ellipsoids allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&nellipsoids); + if (addflag == NONE) atom->nellipsoids = nellipsoids; + else if (firstpass) atom->nellipsoids += nellipsoids; + } else if (strstr(line,"lines")) { if (!avec_line) error->all(FLERR,"No lines allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&nlines); + if (addflag == NONE) atom->nlines = nlines; + else if (firstpass) atom->nlines += nlines; + } else if (strstr(line,"triangles")) { if (!avec_tri) error->all(FLERR,"No triangles allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&ntris); + if (addflag == NONE) atom->ntris = ntris; + else if (firstpass) atom->ntris += ntris; + } else if (strstr(line,"bodies")) { if (!avec_body) error->all(FLERR,"No bodies allowed with this atom style"); sscanf(line,BIGINT_FORMAT,&nbodies); + if (addflag == NONE) atom->nbodies = nbodies; + else if (firstpass) atom->nbodies += nbodies; } else if (strstr(line,"bonds")) { sscanf(line,BIGINT_FORMAT,&nbonds); @@ -1084,6 +1096,10 @@ void ReadData::header(int firstpass) // error check on total system size if (atom->natoms < 0 || atom->natoms >= MAXBIGINT || + atom->nellipsoids < 0 || atom->nellipsoids >= MAXBIGINT || + atom->nlines < 0 || atom->nlines >= MAXBIGINT || + atom->ntris < 0 || atom->ntris >= MAXBIGINT || + atom->nbodies < 0 || atom->nbodies >= MAXBIGINT || atom->nbonds < 0 || atom->nbonds >= MAXBIGINT || atom->nangles < 0 || atom->nangles >= MAXBIGINT || atom->ndihedrals < 0 || atom->ndihedrals >= MAXBIGINT || @@ -1174,6 +1190,10 @@ void ReadData::atoms() atom->tag_check(); + // check that bonus data has been reserved as needed + + atom->bonus_check(); + // create global mapping of atoms if (atom->map_style) { @@ -1248,7 +1268,7 @@ void ReadData::bonds(int firstpass) int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); - for (int i = 0; i < nlocal; i++) count[i] = 0; + memset(count,0,nlocal*sizeof(int)); } // read and process bonds @@ -1331,7 +1351,7 @@ void ReadData::angles(int firstpass) int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); - for (int i = 0; i < nlocal; i++) count[i] = 0; + memset(count,0,nlocal*sizeof(int)); } // read and process angles @@ -1414,7 +1434,7 @@ void ReadData::dihedrals(int firstpass) int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); - for (int i = 0; i < nlocal; i++) count[i] = 0; + memset(count,0,nlocal*sizeof(int)); } // read and process dihedrals @@ -1435,7 +1455,7 @@ void ReadData::dihedrals(int firstpass) if (firstpass) { int max = 0; - for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]); + for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]); int maxall; MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world); if (addflag == NONE) maxall += atom->extra_dihedral_per_atom; @@ -1497,7 +1517,7 @@ void ReadData::impropers(int firstpass) int *count = NULL; if (firstpass) { memory->create(count,nlocal,"read_data:count"); - for (int i = 0; i < nlocal; i++) count[i] = 0; + memset(count,0,nlocal*sizeof(int)); } // read and process impropers @@ -1963,7 +1983,7 @@ void ReadData::parse_keyword(int first) } while (eof == 0 && done == 0) { int blank = strspn(line," \t\n\r"); - if ((blank == strlen(line)) || (line[blank] == '#')) { + if ((blank == (int)strlen(line)) || (line[blank] == '#')) { if (fgets(line,MAXLINE,fp) == NULL) eof = 1; } else done = 1; } diff --git a/src/read_data.h b/src/read_data.h index 9dce8cfcf5..7d011c710a 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -160,7 +160,7 @@ E: Fix ID for read_data does not exist Self-explanatory. -E: Cannot run 2d simulation with nonperiodic Z dimension +E: Cannot run 2d simulation with non-periodic Z dimension Use the boundary command to make the z dimension periodic in order to run a 2d simulation. diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 30934f123b..551cc63c9e 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -43,8 +43,7 @@ using namespace LAMMPS_NS; -#define CHUNK 1024 -#define EPSILON 1.0e-6 +#define CHUNK 16384 // also in reader_native.cpp @@ -65,17 +64,21 @@ ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp) nfile = 0; files = NULL; + nnew = maxnew = 0; nfield = 0; fieldtype = NULL; fieldlabel = NULL; fields = NULL; + buf = NULL; int n = strlen("native") + 1; readerstyle = new char[n]; strcpy(readerstyle,"native"); - reader = NULL; - fp = NULL; + nreader = 0; + readers = NULL; + nsnapatoms = NULL; + clustercomm = MPI_COMM_NULL; } /* ---------------------------------------------------------------------- */ @@ -90,7 +93,13 @@ ReadDump::~ReadDump() delete [] readerstyle; memory->destroy(fields); - delete reader; + memory->destroy(buf); + + for (int i = 0; i < nreader; i++) delete readers[i]; + delete [] readers; + delete [] nsnapatoms; + + MPI_Comm_free(&clustercomm); } /* ---------------------------------------------------------------------- */ @@ -134,13 +143,20 @@ void ReadDump::command(int narg, char **arg) bigint natoms_prev = atom->natoms; atoms(); - if (me == 0) reader->close_file(); + if (filereader) + for (int i = 0; i < nreader; i++) + readers[i]->close_file(); // print out stats - bigint npurge_all,nreplace_all,ntrim_all,nadd_all; + bigint nsnap_all,npurge_all,nreplace_all,ntrim_all,nadd_all; + + bigint tmp = 0; + if (filereader) + for (int i = 0; i < nreader; i++) + tmp += nsnapatoms[i]; + MPI_Allreduce(&tmp,&nsnap_all,1,MPI_LMP_BIGINT,MPI_SUM,world); - bigint tmp; tmp = npurge; MPI_Allreduce(&tmp,&npurge_all,1,MPI_LMP_BIGINT,MPI_SUM,world); tmp = nreplace; @@ -155,7 +171,7 @@ void ReadDump::command(int narg, char **arg) if (me == 0) { if (screen) { fprintf(screen," " BIGINT_FORMAT " atoms before read\n",natoms_prev); - fprintf(screen," " BIGINT_FORMAT " atoms in snapshot\n",nsnapatoms); + fprintf(screen," " BIGINT_FORMAT " atoms in snapshot\n",nsnap_all); fprintf(screen," " BIGINT_FORMAT " atoms purged\n",npurge_all); fprintf(screen," " BIGINT_FORMAT " atoms replaced\n",nreplace_all); fprintf(screen," " BIGINT_FORMAT " atoms trimmed\n",ntrim_all); @@ -164,7 +180,7 @@ void ReadDump::command(int narg, char **arg) } if (logfile) { fprintf(logfile," " BIGINT_FORMAT " atoms before read\n",natoms_prev); - fprintf(logfile," " BIGINT_FORMAT " atoms in snapshot\n",nsnapatoms); + fprintf(logfile," " BIGINT_FORMAT " atoms in snapshot\n",nsnap_all); fprintf(logfile," " BIGINT_FORMAT " atoms purged\n",npurge_all); fprintf(logfile," " BIGINT_FORMAT " atoms replaced\n",nreplace_all); fprintf(logfile," " BIGINT_FORMAT " atoms trimmed\n",ntrim_all); @@ -181,10 +197,22 @@ void ReadDump::store_files(int nstr, char **str) nfile = nstr; files = new char*[nfile]; + // either all or none of files must have '%' wild-card + for (int i = 0; i < nfile; i++) { int n = strlen(str[i]) + 1; files[i] = new char[n]; strcpy(files[i],str[i]); + + if (i == 0) { + if (strchr(files[i],'%')) multiproc = 1; + else multiproc = 0; + } else { + if (multiproc && !strchr(files[i],'%')) + error->all(FLERR,"All read_dump files must be serial or parallel"); + if (!multiproc && strchr(files[i],'%')) + error->all(FLERR,"All read_dump files must be serial or parallel"); + } } } @@ -192,18 +220,47 @@ void ReadDump::store_files(int nstr, char **str) void ReadDump::setup_reader(int narg, char **arg) { - // allocate snapshot field buffer + // setup serial or parallel file reading + // multiproc = 0: only one file to read from, only proc 0 is a reader + // multiproc_nfile >= nprocs: every proc reads one or more files + // multiproc_nfile < nprocs: multiproc_nfile readers, create clusters + // see read_dump.h for explanation of these variables - memory->create(fields,CHUNK,nfield,"read_dump:fields"); + if (multiproc == 0) { + nreader = 1; + firstfile = -1; + MPI_Comm_dup(world,&clustercomm); + } else if (multiproc_nfile >= nprocs) { + firstfile = static_cast ((bigint) me * multiproc_nfile/nprocs); + int lastfile = static_cast ((bigint) (me+1) * multiproc_nfile/nprocs); + nreader = lastfile - firstfile; + MPI_Comm_split(world,me,0,&clustercomm); + } else if (multiproc_nfile < nprocs) { + nreader = 1; + int icluster = static_cast ((bigint) me * multiproc_nfile/nprocs); + firstfile = icluster; + MPI_Comm_split(world,icluster,0,&clustercomm); + } - // create reader class + MPI_Comm_rank(clustercomm,&me_cluster); + MPI_Comm_size(clustercomm,&nprocs_cluster); + if (me_cluster == 0) filereader = 1; + else filereader = 0; + + readers = new Reader*[nreader]; + nsnapatoms = new bigint[nreader]; + + // create Nreader reader classes per reader // match readerstyle to options in style_reader.h if (0) return; // dummy line to enable else-if macro expansion #define READER_CLASS #define ReaderStyle(key,Class) \ - else if (strcmp(readerstyle,#key) == 0) reader = new Class(lmp); + else if (strcmp(readerstyle,#key) == 0) { \ + for (int i = 0; i < nreader; i++) \ + readers[i] = new Class(lmp); \ + } #include "style_reader.h" #undef READER_CLASS @@ -211,9 +268,11 @@ void ReadDump::setup_reader(int narg, char **arg) else error->all(FLERR,"Unknown dump reader style"); - // pass any arguments to reader + // pass any arguments to readers - if (narg > 0) reader->settings(narg,arg); + if (narg > 0 && filereader) + for (int i = 0; i < nreader; i++) + readers[i]->settings(narg,arg); } /* ---------------------------------------------------------------------- @@ -228,6 +287,8 @@ bigint ReadDump::seek(bigint nrequest, int exact) int ifile,eofflag; bigint ntimestep; + // proc 0 finds the timestep in its first reader + if (me == 0) { // exit file loop when dump timestep >= nrequest @@ -235,24 +296,75 @@ bigint ReadDump::seek(bigint nrequest, int exact) for (ifile = 0; ifile < nfile; ifile++) { ntimestep = -1; - reader->open_file(files[ifile]); + if (multiproc) { + char *ptr = strchr(files[ifile],'%'); + char *multiname = new char[strlen(files[ifile]) + 16]; + *ptr = '\0'; + sprintf(multiname,"%s%d%s",files[ifile],0,ptr+1); + *ptr = '%'; + readers[0]->open_file(multiname); + delete [] multiname; + } else readers[0]->open_file(files[ifile]); + while (1) { - eofflag = reader->read_time(ntimestep); + eofflag = readers[0]->read_time(ntimestep); if (eofflag) break; if (ntimestep >= nrequest) break; - reader->skip(); + readers[0]->skip(); } + if (ntimestep >= nrequest) break; - reader->close_file(); + readers[0]->close_file(); } currentfile = ifile; if (ntimestep < nrequest) ntimestep = -1; if (exact && ntimestep != nrequest) ntimestep = -1; - if (ntimestep < 0) reader->close_file(); } + // proc 0 broadcasts timestep and currentfile to all procs + MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world); + MPI_Bcast(¤tfile,1,MPI_INT,0,world); + + // if ntimestep < 0: + // all filereader procs close all their files and return + + if (ntimestep < 0) { + if (filereader) + for (int i = 0; i < nreader; i++) + readers[i]->close_file(); + return ntimestep; + } + + // for multiproc mode: + // all filereader procs search for same ntimestep in currentfile + + if (multiproc && filereader) { + for (int i = 0; i < nreader; i++) { + if (me == 0 && i == 0) continue; // proc 0, reader 0 already found it + char *ptr = strchr(files[currentfile],'%'); + char *multiname = new char[strlen(files[currentfile]) + 16]; + *ptr = '\0'; + sprintf(multiname,"%s%d%s",files[currentfile],firstfile+i,ptr+1); + *ptr = '%'; + readers[i]->open_file(multiname); + delete [] multiname; + + bigint step; + while (1) { + eofflag = readers[i]->read_time(step); + if (eofflag) break; + if (step == ntimestep) break; + readers[i]->skip(); + } + + if (eofflag) + error->one(FLERR,"Read dump parallel files " + "do not all have same timestep"); + } + } + return ntimestep; } @@ -270,6 +382,8 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip) int ifile,eofflag; bigint ntimestep; + // proc 0 finds the timestep in its first reader + if (me == 0) { // exit file loop when dump timestep matches all criteria @@ -279,19 +393,34 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip) for (ifile = currentfile; ifile < nfile; ifile++) { ntimestep = -1; - if (ifile != currentfile) reader->open_file(files[ifile]); + if (ifile != currentfile) { + if (multiproc) { + char *ptr = strchr(files[ifile],'%'); + char *multiname = new char[strlen(files[ifile]) + 16]; + *ptr = '\0'; + sprintf(multiname,"%s%d%s",files[ifile],0,ptr+1); + *ptr = '%'; + readers[0]->open_file(multiname); + delete [] multiname; + } else readers[0]->open_file(files[ifile]); + } + while (1) { - eofflag = reader->read_time(ntimestep); + eofflag = readers[0]->read_time(ntimestep); + if (eofflag) break; + if (ntimestep > nlast) break; + if (ntimestep <= ncurrent) { + readers[0]->skip(); + continue; + } if (iskip == nskip) iskip = 0; iskip++; - if (eofflag) break; - if (ntimestep <= ncurrent) break; - if (ntimestep > nlast) break; - if (nevery && ntimestep % nevery) reader->skip(); - else if (iskip < nskip) reader->skip(); + if (nevery && ntimestep % nevery) readers[0]->skip(); + else if (iskip < nskip) readers[0]->skip(); else break; } - if (eofflag) reader->close_file(); + + if (eofflag) readers[0]->close_file(); else break; } @@ -299,10 +428,50 @@ bigint ReadDump::next(bigint ncurrent, bigint nlast, int nevery, int nskip) if (eofflag) ntimestep = -1; if (ntimestep <= ncurrent) ntimestep = -1; if (ntimestep > nlast) ntimestep = -1; - if (ntimestep < 0) reader->close_file(); } + // proc 0 broadcasts timestep and currentfile to all procs + MPI_Bcast(&ntimestep,1,MPI_LMP_BIGINT,0,world); + MPI_Bcast(¤tfile,1,MPI_INT,0,world); + + // if ntimestep < 0: + // all filereader procs close all their files and return + + if (ntimestep < 0) { + for (int i = 0; i < nreader; i++) + readers[i]->close_file(); + return ntimestep; + } + + // for multiproc mode: + // all filereader procs search for same ntimestep in currentfile + + if (multiproc && filereader) { + for (int i = 0; i < nreader; i++) { + if (me == 0 && i == 0) continue; + char *ptr = strchr(files[currentfile],'%'); + char *multiname = new char[strlen(files[currentfile]) + 16]; + *ptr = '\0'; + sprintf(multiname,"%s%d%s",files[currentfile],firstfile+i,ptr+1); + *ptr = '%'; + readers[i]->open_file(multiname); + delete [] multiname; + + bigint step; + while (1) { + eofflag = readers[i]->read_time(step); + if (eofflag) break; + if (step == ntimestep) break; + readers[i]->skip(); + } + + if (eofflag) + error->one(FLERR,"Read dump parallel files " + "do not all have same timestep"); + } + } + return ntimestep; } @@ -316,15 +485,17 @@ void ReadDump::header(int fieldinfo) int triclinic_snap; int fieldflag,xflag,yflag,zflag; - if (me == 0) - nsnapatoms = reader->read_header(box,triclinic_snap, - fieldinfo,nfield,fieldtype,fieldlabel, - scaleflag,wrapflag,fieldflag, - xflag,yflag,zflag); + if (filereader) { + for (int i = 0; i < nreader; i++) + nsnapatoms[i] = readers[i]->read_header(box,triclinic_snap,fieldinfo, + nfield,fieldtype,fieldlabel, + scaleflag,wrapflag,fieldflag, + xflag,yflag,zflag); + } - MPI_Bcast(&nsnapatoms,1,MPI_LMP_BIGINT,0,world); - MPI_Bcast(&triclinic_snap,1,MPI_INT,0,world); - MPI_Bcast(&box[0][0],9,MPI_DOUBLE,0,world); + MPI_Bcast(nsnapatoms,nreader,MPI_LMP_BIGINT,0,clustercomm); + MPI_Bcast(&triclinic_snap,1,MPI_INT,0,clustercomm); + MPI_Bcast(&box[0][0],9,MPI_DOUBLE,0,clustercomm); // local copy of snapshot box parameters // used in xfield,yfield,zfield when converting dump atom to absolute coords @@ -358,10 +529,10 @@ void ReadDump::header(int fieldinfo) if (!fieldinfo) return; - MPI_Bcast(&fieldflag,1,MPI_INT,0,world); - MPI_Bcast(&xflag,1,MPI_INT,0,world); - MPI_Bcast(&yflag,1,MPI_INT,0,world); - MPI_Bcast(&zflag,1,MPI_INT,0,world); + MPI_Bcast(&fieldflag,1,MPI_INT,0,clustercomm); + MPI_Bcast(&xflag,1,MPI_INT,0,clustercomm); + MPI_Bcast(&yflag,1,MPI_INT,0,clustercomm); + MPI_Bcast(&zflag,1,MPI_INT,0,clustercomm); // error check on current vs new box and fields // triclinic_snap < 0 means no box info in file @@ -430,7 +601,9 @@ void ReadDump::header(int fieldinfo) } } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + read and process one snapshot of atoms +------------------------------------------------------------------------- */ void ReadDump::atoms() { @@ -447,8 +620,23 @@ void ReadDump::atoms() atom->natoms = 0; } - // to match existing atoms to dump atoms: + // read all the snapshot atoms into fields + // each proc will own an arbitrary subset of atoms + + read_atoms(); + + // migrate old owned atoms to new procs based on atom IDs + // not necessary if purged all old atoms or if only 1 proc + + if (!purgeflag && nprocs > 1) migrate_old_atoms(); + + // migrate new snapshot atoms to same new procs based on atom IDs + // not necessary if purged all old atoms or if only 1 proc + + if (!purgeflag && nprocs > 1) migrate_new_atoms(); + // must build map if not a molecular system + // this will be needed to match new atoms to old atoms int mapflag = 0; if (atom->map_style == 0) { @@ -457,52 +645,14 @@ void ReadDump::atoms() atom->map_set(); } - // uflag[i] = 1 for each owned atom appearing in dump - // ucflag = similar flag for each chunk atom, used in process_atoms() + // each proc now owns both old and new info for same subset of atoms + // update each local atom with new info - int nlocal = atom->nlocal; - memory->create(uflag,nlocal,"read_dump:uflag"); - for (int i = 0; i < nlocal; i++) uflag[i] = 0; - memory->create(ucflag,CHUNK,"read_dump:ucflag"); - memory->create(ucflag_all,CHUNK,"read_dump:ucflag"); + process_atoms(); - // read, broadcast, and process atoms from snapshot in chunks + // check that atom IDs are valid - addproc = -1; - - int nchunk; - bigint nread = 0; - while (nread < nsnapatoms) { - nchunk = MIN(nsnapatoms-nread,CHUNK); - if (me == 0) reader->read_atoms(nchunk,nfield,fields); - MPI_Bcast(&fields[0][0],nchunk*nfield,MPI_DOUBLE,0,world); - process_atoms(nchunk); - nread += nchunk; - } - - // if addflag = YESADD, assign IDs to new snapshot atoms - - if (addflag == YESADD) { - bigint nblocal = atom->nlocal; - MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); - if (atom->natoms < 0 || atom->natoms >= MAXBIGINT) - error->all(FLERR,"Too many total atoms"); - if (atom->tag_enable) atom->tag_extend(); - } - - // if trimflag set, delete atoms not replaced by snapshot atoms - - if (trimflag) { - delete_atoms(); - bigint nblocal = atom->nlocal; - MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); - } - - // can now delete uflag arrays - - memory->destroy(uflag); - memory->destroy(ucflag); - memory->destroy(ucflag_all); + atom->tag_check(); // delete atom map if created it above // else reinitialize map for current atoms @@ -543,209 +693,152 @@ void ReadDump::atoms() domain->set_local_box(); } - // move atoms back inside simulation box and to new processors - // use remap() instead of pbc() in case atoms moved a long distance - // adjust image flags of all atoms (old and new) based on current box - // use irregular() in case atoms moved a long distance + // migrate atoms to their new owing proc, based on atom coords - double **x = atom->x; - imageint *image = atom->image; - nlocal = atom->nlocal; - for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); - - if (triclinic) domain->x2lamda(atom->nlocal); - domain->reset_box(); - Irregular *irregular = new Irregular(lmp); - irregular->migrate_atoms(1); - delete irregular; - if (triclinic) domain->lamda2x(atom->nlocal); - - // check that atom IDs are valid - - atom->tag_check(); + migrate_atoms_by_coords(); } /* ---------------------------------------------------------------------- - process arg list for dump file fields and optional keywords + read all the snapshot atoms into fields + done in different ways for multiproc no/yes and # of procs < or >= nprocs + nnew = # of snapshot atoms this proc stores ------------------------------------------------------------------------- */ -int ReadDump::fields_and_keywords(int narg, char **arg) +void ReadDump::read_atoms() { - // per-field vectors, leave space for ID and TYPE + int count,nread,nsend,nrecv,otherproc; + bigint nsnap,ntotal,ofirst,olast,rfirst,rlast,lo,hi; + MPI_Request request; + MPI_Status status; - fieldtype = new int[narg+2]; - fieldlabel = new char*[narg+2]; + // one reader per cluster of procs + // each reading proc reads one file and splits data across cluster + // cluster can be all procs or a subset - // add id and type fields as needed - // scan ahead to see if "add yes/keep" keyword/value is used - // requires extra "type" field from from dump file + if (!multiproc || multiproc_nfile < nprocs) { + nsnap = nsnapatoms[0]; - int iarg; - for (iarg = 0; iarg < narg; iarg++) - if (strcmp(arg[iarg],"add") == 0) - if (iarg < narg-1 && (strcmp(arg[iarg+1],"yes") == 0 || - strcmp(arg[iarg+1],"keep") == 0)) break; + if (filereader) { + if (!buf) memory->create(buf,CHUNK,nfield,"read_dump:buf"); - nfield = 0; - fieldtype[nfield++] = ID; - if (iarg < narg) fieldtype[nfield++] = TYPE; + otherproc = 0; + ofirst = (bigint) otherproc * nsnap/nprocs_cluster; + olast = (bigint) (otherproc+1) * nsnap/nprocs_cluster; + if (olast-ofirst > MAXSMALLINT) + error->one(FLERR,"Read dump snapshot is too large for a proc"); + nnew = static_cast (olast - ofirst); - // parse fields + if (nnew > maxnew || maxnew == 0) { + memory->destroy(fields); + maxnew = MAX(nnew,1); // avoid NULL ptr + memory->create(fields,maxnew,nfield,"read_dump:fields"); + } - iarg = 0; - while (iarg < narg) { - int type = whichtype(arg[iarg]); - if (type < 0) break; - if (type == Q && !atom->q_flag) - error->all(FLERR,"Read dump of atom property that isn't allocated"); - fieldtype[nfield++] = type; - iarg++; - } + ntotal = 0; + while (ntotal < nsnap) { + nread = MIN(CHUNK,nsnap-ntotal); + readers[0]->read_atoms(nread,nfield,buf); + rfirst = ntotal; + rlast = ntotal + nread; - // check for no fields + nsend = 0; + while (nsend < nread) { + lo = MAX(ofirst,rfirst); + hi = MIN(olast,rlast); + if (otherproc) // send to otherproc or copy to self + MPI_Send(&buf[nsend][0],(hi-lo)*nfield,MPI_DOUBLE, + otherproc,0,clustercomm); + else + memcpy(&fields[rfirst][0],&buf[nsend][0], + (hi-lo)*nfield*sizeof(double)); + nsend += hi-lo; + if (hi == olast) { + otherproc++; + ofirst = (bigint) otherproc * nsnap/nprocs_cluster; + olast = (bigint) (otherproc+1) * nsnap/nprocs_cluster; + } + } - if (fieldtype[nfield-1] == ID || fieldtype[nfield-1] == TYPE) - error->all(FLERR,"Illegal read_dump command"); + ntotal += nread; + } - if (dimension == 2) { - for (int i = 0; i < nfield; i++) - if (fieldtype[i] == Z || fieldtype[i] == VZ || - fieldtype[i] == IZ || fieldtype[i] == FZ) - error->all(FLERR,"Illegal read_dump command"); - } + } else { + ofirst = (bigint) me_cluster * nsnap/nprocs_cluster; + olast = (bigint) (me_cluster+1) * nsnap/nprocs_cluster; + if (olast-ofirst > MAXSMALLINT) + error->one(FLERR,"Read dump snapshot is too large for a proc"); + nnew = static_cast (olast - ofirst); + if (nnew > maxnew || maxnew == 0) { + memory->destroy(fields); + maxnew = MAX(nnew,1); // avoid NULL ptr + memory->create(fields,maxnew,nfield,"read_dump:fields"); + } - for (int i = 0; i < nfield; i++) - for (int j = i+1; j < nfield; j++) - if (fieldtype[i] == fieldtype[j]) - error->all(FLERR,"Duplicate fields in read_dump command"); + nrecv = 0; + while (nrecv < nnew) { + MPI_Irecv(&fields[nrecv][0],(nnew-nrecv)*nfield,MPI_DOUBLE,0,0, + clustercomm,&request); + MPI_Wait(&request,&status); + MPI_Get_count(&status,MPI_DOUBLE,&count); + nrecv += count/nfield; + } + } - // parse optional args + // every proc is a filereader, reads one or more files + // each proc keeps all data it reads, no communication required - boxflag = 1; - replaceflag = 1; - purgeflag = 0; - trimflag = 0; - addflag = NOADD; - for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL; - scaleflag = 0; - wrapflag = 1; + } else if (multiproc_nfile >= nprocs) { + bigint sum = 0; + for (int i = 0; i < nreader; i++) + sum += nsnapatoms[i]; + if (sum > MAXSMALLINT) + error->one(FLERR,"Read dump snapshot is too large for a proc"); + nnew = static_cast (sum); + if (nnew > maxnew || maxnew == 0) { + memory->destroy(fields); + maxnew = MAX(nnew,1); // avoid NULL ptr + memory->create(fields,maxnew,nfield,"read_dump:fields"); + } - while (iarg < narg) { - if (strcmp(arg[iarg],"box") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) boxflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) boxflag = 0; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"replace") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) replaceflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) replaceflag = 0; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"purge") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) purgeflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) purgeflag = 0; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"trim") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) trimflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) trimflag = 0; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"add") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) addflag = YESADD; - else if (strcmp(arg[iarg+1],"no") == 0) addflag = NOADD; - else if (strcmp(arg[iarg+1],"keep") == 0) addflag = KEEPADD; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"label") == 0) { - if (iarg+3 > narg) error->all(FLERR,"Illegal read_dump command"); - int type = whichtype(arg[iarg+1]); - int i; - for (i = 0; i < nfield; i++) - if (type == fieldtype[i]) break; - if (i == nfield) error->all(FLERR,"Illegal read_dump command"); - int n = strlen(arg[iarg+2]) + 1; - fieldlabel[i] = new char[n]; - strcpy(fieldlabel[i],arg[iarg+2]); - iarg += 3; - } else if (strcmp(arg[iarg],"scaled") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"wrapped") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - if (strcmp(arg[iarg+1],"yes") == 0) wrapflag = 1; - else if (strcmp(arg[iarg+1],"no") == 0) wrapflag = 0; - else error->all(FLERR,"Illegal read_dump command"); - iarg += 2; - } else if (strcmp(arg[iarg],"format") == 0) { - if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); - delete [] readerstyle; - int n = strlen(arg[iarg+1]) + 1; - readerstyle = new char[n]; - strcpy(readerstyle,arg[iarg+1]); - iarg += 2; - break; - } else error->all(FLERR,"Illegal read_dump command"); - } - - if (purgeflag && (replaceflag || trimflag)) - error->all(FLERR,"If read_dump purges it cannot replace or trim"); - if (addflag == KEEPADD && atom->tag_enable == 0) - error->all(FLERR,"Read_dump cannot use 'add keep' without atom IDs"); - - return narg-iarg; + nnew = 0; + for (int i = 0; i < nreader; i++) { + nsnap = nsnapatoms[i]; + ntotal = 0; + while (ntotal < nsnap) { + nread = MIN(CHUNK,nsnap-ntotal); + readers[i]->read_atoms(nread,nfield,&fields[nnew+ntotal]); + ntotal += nread; + } + nnew += nsnap; + } + } } /* ---------------------------------------------------------------------- - check if str is a field argument - if yes, return index of which - if not, return -1 -------------------------------------------------------------------------- */ - -int ReadDump::whichtype(char *str) -{ - int type = -1; - if (strcmp(str,"id") == 0) type = ID; - else if (strcmp(str,"type") == 0) type = TYPE; - else if (strcmp(str,"x") == 0) type = X; - else if (strcmp(str,"y") == 0) type = Y; - else if (strcmp(str,"z") == 0) type = Z; - else if (strcmp(str,"vx") == 0) type = VX; - else if (strcmp(str,"vy") == 0) type = VY; - else if (strcmp(str,"vz") == 0) type = VZ; - else if (strcmp(str,"q") == 0) type = Q; - else if (strcmp(str,"ix") == 0) type = IX; - else if (strcmp(str,"iy") == 0) type = IY; - else if (strcmp(str,"iz") == 0) type = IZ; - else if (strcmp(str,"fx") == 0) type = FX; - else if (strcmp(str,"fy") == 0) type = FY; - else if (strcmp(str,"fz") == 0) type = FZ; - return type; -} - -/* ---------------------------------------------------------------------- - process each of N atoms in chunk read from dump file + update info for each old atom I own based on snapshot info if in replace mode and atom ID matches current atom, overwrite atom info with fields from dump file - if in add mode and atom ID does not match any current atom, - create new atom with dump file field values, - and assign to a proc in round-robin manner - use round-robin method, b/c atom coords may not be inside simulation box + if in add mode and atom ID does not match any old atom, + create new atom with dump file field values ------------------------------------------------------------------------- */ -void ReadDump::process_atoms(int n) +void ReadDump::process_atoms() { int i,m,ifield,itype; int xbox,ybox,zbox; tagint mtag; + int *updateflag,*newflag; + + // updateflag[i] = flag for old atoms, 1 if updated, else 0 + // newflag[i] = flag for new atoms, 0 if used to update old atom, else 1 + + int nlocal = atom->nlocal; + memory->create(updateflag,nlocal,"read_dump:updateflag"); + for (int i = 0; i < nlocal; i++) updateflag[i] = 0; + memory->create(newflag,nnew,"read_dump:newflag"); + for (int i = 0; i < nnew; i++) newflag[i] = 1; + + // loop over new atoms double **x = atom->x; double **v = atom->v; @@ -753,11 +846,9 @@ void ReadDump::process_atoms(int n) double **f = atom->f; tagint *tag = atom->tag; imageint *image = atom->image; - int nlocal = atom->nlocal; tagint map_tag_max = atom->map_tag_max; - for (i = 0; i < n; i++) { - ucflag[i] = 0; + for (i = 0; i < nnew; i++) { // check if new atom matches one I own // setting m = -1 forces new atom not to match @@ -769,8 +860,8 @@ void ReadDump::process_atoms(int n) else m = -1; if (m < 0 || m >= nlocal) continue; - ucflag[i] = 1; - uflag[m] = 1; + updateflag[m] = 1; + newflag[i] = 0; if (replaceflag) { nreplace++; @@ -838,12 +929,39 @@ void ReadDump::process_atoms(int n) } } - // create any atoms in chunk that no processor owned - // add atoms in round-robin sequence on processors - // cannot do it geometrically b/c dump coords may not be in simulation box - // check that dump file snapshot has atom type field + // if trimflag set, delete atoms not updated by snapshot atoms - if (addflag == NOADD) return; + if (trimflag) { + AtomVec *avec = atom->avec; + + int i = 0; + while (i < nlocal) { + if (!updateflag[i]) { + avec->copy(nlocal-1,i,1); + updateflag[i] = updateflag[nlocal-1]; + nlocal--; + ntrim++; + } else i++; + } + + atom->nlocal = nlocal; + bigint nblocal = atom->nlocal; + MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + + // done if cannot add new atoms + + if (addflag == NOADD) { + memory->destroy(updateflag); + memory->destroy(newflag); + return; + } + + // ---------------------------------------------------- + // create new atoms for dump file atoms with ID that matches no old atom + // ---------------------------------------------------- + + // first check that dump file snapshot has atom type field int tflag = 0; for (ifield = 0; ifield < nfield; ifield++) @@ -851,19 +969,11 @@ void ReadDump::process_atoms(int n) if (!tflag) error->all(FLERR,"Cannot add atoms if dump file does not store atom type"); - MPI_Allreduce(ucflag,ucflag_all,n,MPI_INT,MPI_SUM,world); - int nlocal_previous = atom->nlocal; double one[3]; - for (i = 0; i < n; i++) { - if (ucflag_all[i]) continue; - - // each processor adds every Pth atom - - addproc++; - if (addproc == nprocs) addproc = 0; - if (addproc != me) continue; + for (i = 0; i < nnew; i++) { + if (!newflag[i]) continue; // create type and coord fields from dump file // coord = 0.0 unless corresponding dump file field was specified @@ -932,7 +1042,7 @@ void ReadDump::process_atoms(int n) break; } - // replace image flag in case changed by ix,iy,iz fields + // reset image flag in case changed by ix,iy,iz fields image[m] = ((imageint) (xbox + IMGMAX) & IMGMASK) | (((imageint) (ybox + IMGMAX) & IMGMASK) << IMGBITS) | @@ -940,31 +1050,287 @@ void ReadDump::process_atoms(int n) } } + // if addflag = YESADD or KEEPADD, update total atom count + + if (addflag == YESADD || addflag == KEEPADD) { + bigint nblocal = atom->nlocal; + MPI_Allreduce(&nblocal,&atom->natoms,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + + // if addflag = YESADD, + // assign consistent IDs to new snapshot atoms across all procs + + if (addflag == YESADD) { + if (atom->natoms < 0 || atom->natoms >= MAXBIGINT) + error->all(FLERR,"Too many total atoms"); + if (atom->tag_enable) atom->tag_extend(); + } + // init per-atom fix/compute/variable values for created atoms atom->data_fix_compute_variable(nlocal_previous,atom->nlocal); + + // free allocated vectors + + memory->destroy(updateflag); + memory->destroy(newflag); } /* ---------------------------------------------------------------------- - delete atoms not flagged as replaced by dump atoms + migrate old atoms to new procs based on atom IDs + use migrate_atoms() with explicit processor assignments ------------------------------------------------------------------------- */ -void ReadDump::delete_atoms() +void ReadDump::migrate_old_atoms() { - AtomVec *avec = atom->avec; + tagint *tag = atom->tag; int nlocal = atom->nlocal; - int i = 0; - while (i < nlocal) { - if (uflag[i] == 0) { - avec->copy(nlocal-1,i,1); - uflag[i] = uflag[nlocal-1]; - nlocal--; - ntrim++; - } else i++; + int *procassign; + memory->create(procassign,nlocal,"read_dump:procassign"); + for (int i = 0; i < nlocal; i++) + procassign[i] = tag[i] % nprocs; + + Irregular *irregular = new Irregular(lmp); + irregular->migrate_atoms(1,1,procassign); + delete irregular; + + memory->destroy(procassign); +} + +/* ---------------------------------------------------------------------- + migrate new atoms to same new procs based on atom IDs +------------------------------------------------------------------------- */ + +void ReadDump::migrate_new_atoms() +{ + tagint mtag; + int *procassign; + double **newfields; + + memory->create(procassign,nnew,"read_dump:procassign"); + for (int i = 0; i < nnew; i++) { + mtag = static_cast (fields[i][0]); + procassign[i] = mtag % nprocs; } - atom->nlocal = nlocal; + Irregular *irregular = new Irregular(lmp); + int nrecv = irregular->create_data(nnew,procassign,1); + int newmaxnew = MAX(nrecv,maxnew); + newmaxnew = MAX(newmaxnew,1); // avoid NULL ptr + memory->create(newfields,newmaxnew,nfield,"read_dump:newfields"); + irregular->exchange_data((char *) &fields[0][0],nfield*sizeof(double), + (char *) &newfields[0][0]); + irregular->destroy_data(); + delete irregular; + + memory->destroy(fields); + memory->destroy(procassign); + + // point fields at newfields + + fields = newfields; + maxnew = newmaxnew; + nnew = nrecv; +} + +/* ---------------------------------------------------------------------- + migrate final atoms to new procs based on atom coords + use migrate_atoms() with implicit processor assignments based on atom coords + move atoms back inside simulation box and to new processors + use remap() instead of pbc() in case atoms moved a long distance + adjust image flags of all atoms (old and new) based on current box +------------------------------------------------------------------------- */ + +void ReadDump::migrate_atoms_by_coords() +{ + double **x = atom->x; + imageint *image = atom->image; + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]); + + if (triclinic) domain->x2lamda(atom->nlocal); + domain->reset_box(); + Irregular *irregular = new Irregular(lmp); + irregular->migrate_atoms(1); + delete irregular; + if (triclinic) domain->lamda2x(atom->nlocal); +} + +/* ---------------------------------------------------------------------- + process arg list for dump file fields and optional keywords +------------------------------------------------------------------------- */ + +int ReadDump::fields_and_keywords(int narg, char **arg) +{ + // per-field vectors, leave space for ID and TYPE + + fieldtype = new int[narg+2]; + fieldlabel = new char*[narg+2]; + + // add id and type fields as needed + // scan ahead to see if "add yes/keep" keyword/value is used + // requires extra "type" field from from dump file + + int iarg; + for (iarg = 0; iarg < narg; iarg++) + if (strcmp(arg[iarg],"add") == 0) + if (iarg < narg-1 && (strcmp(arg[iarg+1],"yes") == 0 || + strcmp(arg[iarg+1],"keep") == 0)) break; + + nfield = 0; + fieldtype[nfield++] = ID; + if (iarg < narg) fieldtype[nfield++] = TYPE; + + // parse fields + + iarg = 0; + while (iarg < narg) { + int type = whichtype(arg[iarg]); + if (type < 0) break; + if (type == Q && !atom->q_flag) + error->all(FLERR,"Read dump of atom property that isn't allocated"); + fieldtype[nfield++] = type; + iarg++; + } + + // check for no fields + + if (fieldtype[nfield-1] == ID || fieldtype[nfield-1] == TYPE) + error->all(FLERR,"Illegal read_dump command"); + + if (dimension == 2) { + for (int i = 0; i < nfield; i++) + if (fieldtype[i] == Z || fieldtype[i] == VZ || + fieldtype[i] == IZ || fieldtype[i] == FZ) + error->all(FLERR,"Illegal read_dump command"); + } + + for (int i = 0; i < nfield; i++) + for (int j = i+1; j < nfield; j++) + if (fieldtype[i] == fieldtype[j]) + error->all(FLERR,"Duplicate fields in read_dump command"); + + // parse optional args + + multiproc_nfile = 0; + boxflag = 1; + replaceflag = 1; + purgeflag = 0; + trimflag = 0; + addflag = NOADD; + for (int i = 0; i < nfield; i++) fieldlabel[i] = NULL; + scaleflag = 0; + wrapflag = 1; + + while (iarg < narg) { + if (strcmp(arg[iarg],"nfile") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + multiproc_nfile = force->inumeric(FLERR,arg[iarg+1]); + iarg += 2; + } else if (strcmp(arg[iarg],"box") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) boxflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) boxflag = 0; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"replace") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) replaceflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) replaceflag = 0; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"purge") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) purgeflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) purgeflag = 0; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"trim") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) trimflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) trimflag = 0; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"add") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) addflag = YESADD; + else if (strcmp(arg[iarg+1],"no") == 0) addflag = NOADD; + else if (strcmp(arg[iarg+1],"keep") == 0) addflag = KEEPADD; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"label") == 0) { + if (iarg+3 > narg) error->all(FLERR,"Illegal read_dump command"); + int type = whichtype(arg[iarg+1]); + int i; + for (i = 0; i < nfield; i++) + if (type == fieldtype[i]) break; + if (i == nfield) error->all(FLERR,"Illegal read_dump command"); + int n = strlen(arg[iarg+2]) + 1; + fieldlabel[i] = new char[n]; + strcpy(fieldlabel[i],arg[iarg+2]); + iarg += 3; + } else if (strcmp(arg[iarg],"scaled") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) scaleflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) scaleflag = 0; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"wrapped") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + if (strcmp(arg[iarg+1],"yes") == 0) wrapflag = 1; + else if (strcmp(arg[iarg+1],"no") == 0) wrapflag = 0; + else error->all(FLERR,"Illegal read_dump command"); + iarg += 2; + } else if (strcmp(arg[iarg],"format") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal read_dump command"); + delete [] readerstyle; + int n = strlen(arg[iarg+1]) + 1; + readerstyle = new char[n]; + strcpy(readerstyle,arg[iarg+1]); + iarg += 2; + break; + } else error->all(FLERR,"Illegal read_dump command"); + } + + if (multiproc == 0 && multiproc_nfile) + error->all(FLERR,"Dump file is not a multi-proc file"); + if (multiproc && multiproc_nfile == 0) + error->all(FLERR,"Dump file is a multi-proc file"); + + if (purgeflag && (replaceflag || trimflag)) + error->all(FLERR,"If read_dump purges it cannot replace or trim"); + if (addflag == KEEPADD && atom->tag_enable == 0) + error->all(FLERR,"Read_dump cannot use 'add keep' without atom IDs"); + + return narg-iarg; +} + +/* ---------------------------------------------------------------------- + check if str is a field argument + if yes, return index of which + if not, return -1 +------------------------------------------------------------------------- */ + +int ReadDump::whichtype(char *str) +{ + int type = -1; + if (strcmp(str,"id") == 0) type = ID; + else if (strcmp(str,"type") == 0) type = TYPE; + else if (strcmp(str,"x") == 0) type = X; + else if (strcmp(str,"y") == 0) type = Y; + else if (strcmp(str,"z") == 0) type = Z; + else if (strcmp(str,"vx") == 0) type = VX; + else if (strcmp(str,"vy") == 0) type = VY; + else if (strcmp(str,"vz") == 0) type = VZ; + else if (strcmp(str,"q") == 0) type = Q; + else if (strcmp(str,"ix") == 0) type = IX; + else if (strcmp(str,"iy") == 0) type = IY; + else if (strcmp(str,"iz") == 0) type = IZ; + else if (strcmp(str,"fx") == 0) type = FX; + else if (strcmp(str,"fy") == 0) type = FY; + else if (strcmp(str,"fz") == 0) type = FZ; + return type; } /* ---------------------------------------------------------------------- diff --git a/src/read_dump.h b/src/read_dump.h index eb70b99808..73cb0a8995 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -22,6 +22,7 @@ CommandStyle(read_dump,ReadDump) #ifndef LMP_READ_DUMP_H #define LMP_READ_DUMP_H +#include #include #include "pointers.h" @@ -43,15 +44,26 @@ class ReadDump : protected Pointers { private: int me,nprocs; - FILE *fp; - int dimension; + char **files; // list of input dump files to process + int nfile; // # of dump files to process (each may be parallel) + int currentfile; // current open file (0 to nfile-1) + + MPI_Comm clustercomm; // comm for proc cluster that reads/shares a file + int me_cluster,nprocs_cluster; // proc ID and count for my read cluster + + int multiproc; // 0 = each dump file is a single file + // 1 = each dump file is parallel (multiple files) + int multiproc_nfile; // number of parallel files in one dump file + + int nreader; // # of parallel dump files read by my cluster + int firstfile; // index of 1st dump file my cluster reads + // (0 to multiproc_nfile-1) + int filereader; // 1 if this proc reads from a dump file(s) + + int dimension; // same as in Domain int triclinic; - int nfile; // # of dump files to process - char **files; // list of file names - int currentfile; // currently open file - int boxflag; // overwrite simulation with dump file box params int replaceflag,addflag; // flags for processing dump snapshot atoms int trimflag,purgeflag; @@ -59,10 +71,13 @@ private: int wrapflag; // user 0/1 if dump file coords are unwrapped/wrapped char *readerstyle; // style of dump files to read + int nnew; // # of dump file atoms this proc owns int nfield; // # of fields to extract from dump file int *fieldtype; // type of each field = X,VY,IZ,etc char **fieldlabel; // user specified label for field double **fields; // per-atom field values + int maxnew; // allocation size of fields array + double **buf; // read buffer int scaled; // 0/1 if dump file coords are unscaled/scaled int wrapped; // 0/1 if dump file coords are unwrapped/wrapped @@ -71,20 +86,26 @@ private: double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz; // dump snapshot box params double xprd,yprd,zprd; - bigint nsnapatoms; // # of atoms in dump file shapshot + bigint *nsnapatoms; // # of atoms in one snapshot from + // one (parallel) dump file + // nreader-length vector b/c a reader proc + // may read from multiple parallel dump files int npurge,nreplace,ntrim,nadd; // stats on processed atoms - int addproc; // proc that should add next atom int yindex,zindex; // field index for Y,Z coords - int *uflag; // set to 1 if snapshot atom matches owned atom - int *ucflag,*ucflag_all; // set to 1 if snapshot chunk atom was processed + class Reader **readers; // class that reads a dump file + // nreader-length list of readers if proc reads + // from multiple parallel dump files - class Reader *reader; // class that reads dump file + void read_atoms(); + void process_atoms(); + void migrate_old_atoms(); + void migrate_new_atoms(); + void migrate_atoms_by_coords(); + void setup_multiproc(); int whichtype(char *); - void process_atoms(int); - void delete_atoms(); double xfield(int, int); double yfield(int, int); diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 252c48d251..73dc37f4cb 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -627,7 +627,7 @@ void ReadRestart::file_search(char *infile, char *outfile) if ((ptr = strstr(&ep->d_name[nbegin],end)) == NULL) continue; if (strlen(end) == 0) ptr = ep->d_name + strlen(ep->d_name); *ptr = '\0'; - if (strlen(&ep->d_name[nbegin]) < n) { + if ((int)strlen(&ep->d_name[nbegin]) < n) { strcpy(middle,&ep->d_name[nbegin]); if (ATOBIGINT(middle) > maxnum) maxnum = ATOBIGINT(middle); } @@ -715,7 +715,7 @@ void ReadRestart::header(int incompatible) domain->dimension = dimension; if (domain->dimension == 2 && domain->zperiodic == 0) error->all(FLERR, - "Cannot run 2d simulation with nonperiodic Z dimension"); + "Cannot run 2d simulation with non-periodic Z dimension"); // read nprocs from restart file, warn if different @@ -924,11 +924,13 @@ void ReadRestart::header(int incompatible) atom->extra_dihedral_per_atom = read_int(); } else if (flag == EXTRA_IMPROPER_PER_ATOM) { atom->extra_improper_per_atom = read_int(); - } else if (flag == EXTRA_SPECIAL_PER_ATOM) { - force->special_extra = read_int(); } else if (flag == ATOM_MAXSPECIAL) { atom->maxspecial = read_int(); + // for backward compatibility + } else if (flag == EXTRA_SPECIAL_PER_ATOM) { + force->special_extra = read_int(); + } else error->all(FLERR,"Invalid flag in header section of restart file"); flag = read_int(); diff --git a/src/read_restart.h b/src/read_restart.h index 8d2547fb10..23d6ec3fba 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -31,11 +31,13 @@ class ReadRestart : protected Pointers { void command(int, char **); private: - int me,nprocs,nprocs_file,multiproc_file; + int me,nprocs; FILE *fp; - int multiproc; // 0 = proc 0 writes for all - // else # of procs writing files + int multiproc; // 0 = restart file is a single file + // 1 = restart file is parallel (multiple files) + int multiproc_file; // # of parallel files in restart + int nprocs_file; // total # of procs that wrote restart file // MPI-IO values @@ -141,7 +143,7 @@ E: Bigint setting in lmptype.h is not compatible Format of bigint stored in restart file is not consistent with LAMMPS version you are running. See the settings in src/lmptype.h -E: Cannot run 2d simulation with nonperiodic Z dimension +E: Cannot run 2d simulation with non-periodic Z dimension Use the boundary command to make the z dimension periodic in order to run a 2d simulation. diff --git a/src/reader.cpp b/src/reader.cpp index 22a21812e6..cf344b37b3 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -18,6 +18,8 @@ using namespace LAMMPS_NS; +// only proc 0 calls methods of this class, except for constructor/destructor + /* ---------------------------------------------------------------------- */ Reader::Reader(LAMMPS *lmp) : Pointers(lmp) diff --git a/src/region.cpp b/src/region.cpp index c52c0181aa..6b49a2819b 100644 --- a/src/region.cpp +++ b/src/region.cpp @@ -174,8 +174,7 @@ int Region::surface(double x, double y, double z, double cutoff) if (!openflag) { if (interior) ncontact = surface_interior(xnear,cutoff); else ncontact = surface_exterior(xnear,cutoff); - } - else{ + } else { // one of surface_int/ext() will return 0 // so no need to worry about offset of contact indices ncontact = surface_exterior(xnear,cutoff) + surface_interior(xnear,cutoff); diff --git a/src/region_block.cpp b/src/region_block.cpp index eeca132378..e55c481189 100644 --- a/src/region_block.cpp +++ b/src/region_block.cpp @@ -308,7 +308,7 @@ int RegBlock::surface_exterior(double *x, double cutoff) // could be edge or corner pt of block // do not add contact point if r >= cutoff - if (!openflag){ + if (!openflag) { if (x[0] < xlo) xp = xlo; else if (x[0] > xhi) xp = xhi; else xp = x[0]; @@ -318,13 +318,12 @@ int RegBlock::surface_exterior(double *x, double cutoff) if (x[2] < zlo) zp = zlo; else if (x[2] > zhi) zp = zhi; else zp = x[2]; - } - else{ + } else { mindist = BIG; for (int i = 0; i < 6; i++){ if (open_faces[i]) continue; dist = find_closest_point(i,x,xc,yc,zc); - if (dist < mindist){ + if (dist < mindist) { xp = xc; yp = yc; zp = zc; diff --git a/src/region_cylinder.cpp b/src/region_cylinder.cpp index 0b15a3644d..7709c57aab 100644 --- a/src/region_cylinder.cpp +++ b/src/region_cylinder.cpp @@ -30,7 +30,7 @@ enum{CONSTANT,VARIABLE}; /* ---------------------------------------------------------------------- */ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) : - Region(lmp, narg, arg), rstr(NULL) + Region(lmp, narg, arg), c1str(NULL), c2str(NULL), rstr(NULL) { options(narg-8,&arg[8]); @@ -44,17 +44,76 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) : axis = arg[2][0]; if (axis == 'x') { - c1 = yscale*force->numeric(FLERR,arg[3]); - c2 = zscale*force->numeric(FLERR,arg[4]); + if (strstr(arg[3],"v_") == arg[3]) { + int n = strlen(arg[3]+2) + 1; + c1str = new char[n]; + strcpy(c1str,arg[3]+2); + c1 = 0.0; + c1style = VARIABLE; + varshape = 1; + } else { + c1 = yscale*force->numeric(FLERR,arg[3]); + c1style = CONSTANT; + } + if (strstr(arg[4],"v_") == arg[4]) { + int n = strlen(arg[4]+2) + 1; + c2str = new char[n]; + strcpy(c2str,arg[4]+2); + c2 = 0.0; + c2style = VARIABLE; + varshape = 1; + } else { + c2 = zscale*force->numeric(FLERR,arg[4]); + c2style = CONSTANT; + } } else if (axis == 'y') { - c1 = xscale*force->numeric(FLERR,arg[3]); - c2 = zscale*force->numeric(FLERR,arg[4]); + if (strstr(arg[3],"v_") == arg[3]) { + int n = strlen(arg[3]+2) + 1; + c1str = new char[n]; + strcpy(c1str,arg[3]+2); + c1 = 0.0; + c1style = VARIABLE; + varshape = 1; + } else { + c1 = xscale*force->numeric(FLERR,arg[3]); + c1style = CONSTANT; + } + if (strstr(arg[4],"v_") == arg[4]) { + int n = strlen(arg[4]+2) + 1; + c2str = new char[n]; + strcpy(c2str,arg[4]+2); + c2 = 0.0; + c2style = VARIABLE; + varshape = 1; + } else { + c2 = zscale*force->numeric(FLERR,arg[4]); + c2style = CONSTANT; + } } else if (axis == 'z') { - c1 = xscale*force->numeric(FLERR,arg[3]); - c2 = yscale*force->numeric(FLERR,arg[4]); + if (strstr(arg[3],"v_") == arg[3]) { + int n = strlen(arg[3]+2) + 1; + c1str = new char[n]; + strcpy(c1str,arg[3]+2); + c1 = 0.0; + c1style = VARIABLE; + varshape = 1; + } else { + c1 = xscale*force->numeric(FLERR,arg[3]); + c1style = CONSTANT; + } + if (strstr(arg[4],"v_") == arg[4]) { + int n = strlen(arg[4]+2) + 1; + c2str = new char[n]; + strcpy(c2str,arg[4]+2); + c2 = 0.0; + c2style = VARIABLE; + varshape = 1; + } else { + c2 = yscale*force->numeric(FLERR,arg[4]); + c2style = CONSTANT; + } } - rstr = NULL; if (strstr(arg[5],"v_") == arg[5]) { int n = strlen(&arg[5][2]) + 1; rstr = new char[n]; @@ -62,8 +121,6 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) : radius = 0.0; rstyle = VARIABLE; varshape = 1; - variable_check(); - shape_update(); } else { radius = force->numeric(FLERR,arg[5]); if (axis == 'x') radius *= yscale; @@ -71,6 +128,11 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) : rstyle = CONSTANT; } + if (varshape) { + variable_check(); + shape_update(); + } + if (strcmp(arg[6],"INF") == 0 || strcmp(arg[6],"EDGE") == 0) { if (domain->box_exist == 0) error->all(FLERR,"Cannot use region INF or EDGE when box does not exist"); @@ -167,6 +229,8 @@ RegCylinder::RegCylinder(LAMMPS *lmp, int narg, char **arg) : RegCylinder::~RegCylinder() { + delete [] c1str; + delete [] c2str; delete [] rstr; delete [] contact; } @@ -176,7 +240,7 @@ RegCylinder::~RegCylinder() void RegCylinder::init() { Region::init(); - if (rstr) variable_check(); + if (varshape) variable_check(); } /* ---------------------------------------------------------------------- @@ -407,14 +471,14 @@ int RegCylinder::surface_exterior(double *x, double cutoff) if (x[0] < lo) xp = lo; else if (x[0] > hi) xp = hi; else xp = x[0]; - } + + } else { // closest point on curved surface - else { dr = r - radius; dr2 = dr*dr; - if (!open_faces[2]){ + if (!open_faces[2]) { yp = c1 + del1*radius/r; zp = c2 + del2*radius/r; if (x[0] < lo) { @@ -440,7 +504,7 @@ int RegCylinder::surface_exterior(double *x, double cutoff) else d2 = dr2 + dx*dx; if (d2 < d2prev) { xp = lo; - if (r < radius){ + if (r < radius) { yp = x[1]; zp = x[2]; } @@ -501,11 +565,11 @@ int RegCylinder::surface_exterior(double *x, double cutoff) if (x[1] < lo) yp = lo; else if (x[1] > hi) yp = hi; else yp = x[1]; - } + + } else { // closest point on curved surface - else { dr = r - radius; dr2 = dr*dr; if (!open_faces[2]){ @@ -595,25 +659,23 @@ int RegCylinder::surface_exterior(double *x, double cutoff) if (x[2] < lo) zp = lo; else if (x[2] > hi) zp = hi; else zp = x[2]; - } + + } else { // closest point on curved surface - else { dr = r - radius; dr2 = dr*dr; - if (!open_faces[2]){ + if (!open_faces[2]) { xp = c1 + del1*radius/r; yp = c2 + del2*radius/r; if (x[2] < lo) { dx = lo-x[2]; zp = lo; - } - else if (x[2] > hi) { + } else if (x[2] > hi) { dx = x[2]-hi; zp = hi; - } - else { + } else { dx = 0; zp = x[2]; } @@ -667,12 +729,27 @@ int RegCylinder::surface_exterior(double *x, double cutoff) void RegCylinder::shape_update() { - radius = input->variable->compute_equal(rvar); - if (radius < 0.0) - error->one(FLERR,"Variable evaluation in region gave bad value"); - if (axis == 'x') radius *= xscale; - else if (axis == 'y') radius*= yscale; - else radius *= zscale; + if (c1style == VARIABLE) c1 = input->variable->compute_equal(c1var); + if (c2style == VARIABLE) c2 = input->variable->compute_equal(c2var); + if (rstyle == VARIABLE) { + radius = input->variable->compute_equal(rvar); + if (radius < 0.0) + error->one(FLERR,"Variable evaluation in region gave bad value"); + } + + if (axis == 'x') { + if (c1style == VARIABLE) c1 *= yscale; + if (c2style == VARIABLE) c2 *= zscale; + if (rstyle == VARIABLE) radius *= yscale; + } else if (axis == 'y') { + if (c1style == VARIABLE) c1 *= xscale; + if (c2style == VARIABLE) c2 *= zscale; + if (rstyle == VARIABLE) radius *= xscale; + } else { // axis == 'z' + if (c1style == VARIABLE) c1 *= xscale; + if (c2style == VARIABLE) c2 *= yscale; + if (rstyle == VARIABLE) radius *= xscale; + } } /* ---------------------------------------------------------------------- @@ -681,11 +758,29 @@ void RegCylinder::shape_update() void RegCylinder::variable_check() { - rvar = input->variable->find(rstr); - if (rvar < 0) - error->all(FLERR,"Variable name for region cylinder does not exist"); - if (!input->variable->equalstyle(rvar)) - error->all(FLERR,"Variable for region cylinder is invalid style"); + if (c1style == VARIABLE) { + c1var = input->variable->find(c1str); + if (c1var < 0) + error->all(FLERR,"Variable name for region cylinder does not exist"); + if (!input->variable->equalstyle(c1var)) + error->all(FLERR,"Variable for region cylinder is invalid style"); + } + + if (c2style == VARIABLE) { + c2var = input->variable->find(c2str); + if (c2var < 0) + error->all(FLERR,"Variable name for region cylinder does not exist"); + if (!input->variable->equalstyle(c2var)) + error->all(FLERR,"Variable for region cylinder is invalid style"); + } + + if (rstyle == VARIABLE) { + rvar = input->variable->find(rstr); + if (rvar < 0) + error->all(FLERR,"Variable name for region cylinder does not exist"); + if (!input->variable->equalstyle(rvar)) + error->all(FLERR,"Variable for region cylinder is invalid style"); + } } @@ -698,17 +793,15 @@ void RegCylinder::variable_check() void RegCylinder::set_velocity_shape() { - if (axis == 'x'){ + if (axis == 'x') { xcenter[0] = 0; xcenter[1] = c1; xcenter[2] = c2; - } - else if (axis == 'y'){ + } else if (axis == 'y') { xcenter[0] = c1; xcenter[1] = 0; xcenter[2] = c2; - } - else{ + } else { xcenter[0] = c1; xcenter[1] = c2; xcenter[2] = 0; @@ -728,17 +821,15 @@ void RegCylinder::set_velocity_shape() void RegCylinder::velocity_contact_shape(double *vwall, double *xc) { double delx, dely, delz; // Displacement of contact point in x,y,z - if (axis == 'x'){ + if (axis == 'x') { delx = 0; dely = (xc[1] - xcenter[1])*(1 - rprev/radius); delz = (xc[2] - xcenter[2])*(1 - rprev/radius); - } - else if (axis == 'y'){ + } else if (axis == 'y') { delx = (xc[0] - xcenter[0])*(1 - rprev/radius); dely = 0; delz = (xc[2] - xcenter[2])*(1 - rprev/radius); - } - else{ + } else { delx = (xc[0] - xcenter[0])*(1 - rprev/radius); dely = (xc[1] - xcenter[1])*(1 - rprev/radius); delz = 0; @@ -746,6 +837,5 @@ void RegCylinder::velocity_contact_shape(double *vwall, double *xc) vwall[0] += delx/update->dt; vwall[1] += dely/update->dt; vwall[2] += delz/update->dt; - //printf ("R is %g, prev %g, velocity of wall at %g %g %g is %g %g %g\n",radius,rprev,xc[0],xc[1],xc[2],vwall[0],vwall[1],vwall[2]); } diff --git a/src/region_cylinder.h b/src/region_cylinder.h index a6b513b2d7..55b4bf3142 100644 --- a/src/region_cylinder.h +++ b/src/region_cylinder.h @@ -43,8 +43,10 @@ class RegCylinder : public Region { double c1,c2; double radius; double lo,hi; + int c1style,c1var; + int c2style,c2var; int rstyle,rvar; - char *rstr; + char *c1str,*c2str,*rstr; void variable_check(); diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 5645b3369d..8080ef5882 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -28,15 +28,46 @@ enum{CONSTANT,VARIABLE}; /* ---------------------------------------------------------------------- */ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) : - Region(lmp, narg, arg) + Region(lmp, narg, arg), xstr(NULL), ystr(NULL), zstr(NULL), rstr(NULL) { options(narg-6,&arg[6]); - xc = xscale*force->numeric(FLERR,arg[2]); - yc = yscale*force->numeric(FLERR,arg[3]); - zc = zscale*force->numeric(FLERR,arg[4]); + if (strstr(arg[2],"v_") == arg[2]) { + int n = strlen(arg[2]+2) + 1; + xstr = new char[n]; + strcpy(xstr,arg[2]+2); + xc = 0.0; + xstyle = VARIABLE; + varshape = 1; + } else { + xc = xscale*force->numeric(FLERR,arg[2]); + xstyle = CONSTANT; + } + + if (strstr(arg[3],"v_") == arg[3]) { + int n = strlen(arg[3]+2) + 1; + ystr = new char[n]; + strcpy(ystr,arg[3]+2); + yc = 0.0; + ystyle = VARIABLE; + varshape = 1; + } else { + yc = yscale*force->numeric(FLERR,arg[3]); + ystyle = CONSTANT; + } + + if (strstr(arg[4],"v_") == arg[4]) { + int n = strlen(arg[4]+2) + 1; + zstr = new char[n]; + strcpy(zstr,arg[4]+2); + zc = 0.0; + zstyle = VARIABLE; + varshape = 1; + } else { + zc = zscale*force->numeric(FLERR,arg[4]); + zstyle = CONSTANT; + } - rstr = NULL; if (strstr(arg[5],"v_") == arg[5]) { int n = strlen(&arg[5][2]) + 1; rstr = new char[n]; @@ -44,19 +75,22 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) : radius = 0.0; rstyle = VARIABLE; varshape = 1; - variable_check(); - shape_update(); } else { radius = xscale*force->numeric(FLERR,arg[5]); rstyle = CONSTANT; } + if (varshape) { + variable_check(); + shape_update(); + } + // error check if (radius < 0.0) error->all(FLERR,"Illegal region sphere command"); // extent of sphere - // for variable radius, uses initial radius + // for variable radius, uses initial radius and origin for variable center if (interior) { bboxflag = 1; @@ -77,6 +111,9 @@ RegSphere::RegSphere(LAMMPS *lmp, int narg, char **arg) : RegSphere::~RegSphere() { + delete [] xstr; + delete [] ystr; + delete [] zstr; delete [] rstr; delete [] contact; } @@ -86,7 +123,7 @@ RegSphere::~RegSphere() void RegSphere::init() { Region::init(); - if (rstr) variable_check(); + if (varshape) variable_check(); } /* ---------------------------------------------------------------------- @@ -168,9 +205,20 @@ int RegSphere::surface_exterior(double *x, double cutoff) void RegSphere::shape_update() { - radius = xscale * input->variable->compute_equal(rvar); - if (radius < 0.0) - error->one(FLERR,"Variable evaluation in region gave bad value"); + if (xstyle == VARIABLE) + xc = xscale * input->variable->compute_equal(xvar); + + if (ystyle == VARIABLE) + yc = yscale * input->variable->compute_equal(yvar); + + if (zstyle == VARIABLE) + zc = zscale * input->variable->compute_equal(zvar); + + if (rstyle == VARIABLE) { + radius = xscale * input->variable->compute_equal(rvar); + if (radius < 0.0) + error->one(FLERR,"Variable evaluation in region gave bad value"); + } } /* ---------------------------------------------------------------------- @@ -179,13 +227,38 @@ void RegSphere::shape_update() void RegSphere::variable_check() { - rvar = input->variable->find(rstr); - if (rvar < 0) - error->all(FLERR,"Variable name for region sphere does not exist"); - if (!input->variable->equalstyle(rvar)) - error->all(FLERR,"Variable for region sphere is invalid style"); -} + if (xstyle == VARIABLE) { + xvar = input->variable->find(xstr); + if (xvar < 0) + error->all(FLERR,"Variable name for region sphere does not exist"); + if (!input->variable->equalstyle(xvar)) + error->all(FLERR,"Variable for region sphere is invalid style"); + } + if (ystyle == VARIABLE) { + yvar = input->variable->find(ystr); + if (yvar < 0) + error->all(FLERR,"Variable name for region sphere does not exist"); + if (!input->variable->equalstyle(yvar)) + error->all(FLERR,"Variable for region sphere is invalid style"); + } + + if (zstyle == VARIABLE) { + zvar = input->variable->find(zstr); + if (zvar < 0) + error->all(FLERR,"Variable name for region sphere does not exist"); + if (!input->variable->equalstyle(zvar)) + error->all(FLERR,"Variable for region sphere is invalid style"); + } + + if (rstyle == VARIABLE) { + rvar = input->variable->find(rstr); + if (rvar < 0) + error->all(FLERR,"Variable name for region sphere does not exist"); + if (!input->variable->equalstyle(rvar)) + error->all(FLERR,"Variable for region sphere is invalid style"); + } +} /* ---------------------------------------------------------------------- Set values needed to calculate velocity due to shape changes. diff --git a/src/region_sphere.h b/src/region_sphere.h index c003a91651..82bac6a619 100644 --- a/src/region_sphere.h +++ b/src/region_sphere.h @@ -40,8 +40,11 @@ class RegSphere : public Region { private: double xc,yc,zc; double radius; + int xstyle,xvar; + int ystyle,yvar; + int zstyle,zvar; int rstyle,rvar; - char *rstr; + char *xstr,*ystr,*zstr,*rstr; void variable_check(); }; diff --git a/src/rerun.cpp b/src/rerun.cpp index f8a37b5946..063ea882c2 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -57,7 +57,7 @@ void Rerun::command(int narg, char **arg) if (nfile == 0 || nfile == narg) error->all(FLERR,"Illegal rerun command"); // parse optional args up until "dump" - // user MAXBIGINT -1 so Output can add 1 to it and still be a big int + // use MAXBIGINT -1 so Output can add 1 to it and still be a big int bigint first = 0; bigint last = MAXBIGINT - 1; diff --git a/src/set.cpp b/src/set.cpp index 7eca4e9a9c..00b2d8a9b0 100644 --- a/src/set.cpp +++ b/src/set.cpp @@ -890,7 +890,7 @@ void Set::set(int keyword) // enforce quat rotation vector in z dir for 2d systems else if (keyword == QUAT) { - double *quat; + double *quat = NULL; if (avec_ellipsoid && atom->ellipsoid[i] >= 0) quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat; else if (avec_tri && atom->tri[i] >= 0) @@ -964,6 +964,21 @@ void Set::set(int keyword) count++; } + // update bonus data numbers + if (keyword == SHAPE) { + bigint nlocal_bonus = avec_ellipsoid->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->nellipsoids,1, + MPI_LMP_BIGINT,MPI_SUM,world); + } + if (keyword == LENGTH) { + bigint nlocal_bonus = avec_line->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->nlines,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + if (keyword == TRI) { + bigint nlocal_bonus = avec_tri->nlocal_bonus; + MPI_Allreduce(&nlocal_bonus,&atom->ntris,1,MPI_LMP_BIGINT,MPI_SUM,world); + } + // clear up per-atom memory if allocated memory->destroy(vec1); diff --git a/src/thermo.cpp b/src/thermo.cpp index ddbbd0f496..3e777edf82 100644 --- a/src/thermo.cpp +++ b/src/thermo.cpp @@ -380,9 +380,8 @@ void Thermo::compute(int flag) loc += sprintf(&line[loc],format[ifield],dvalue); else if (vtype[ifield] == INT) loc += sprintf(&line[loc],format[ifield],ivalue); - else if (vtype[ifield] == BIGINT) { + else if (vtype[ifield] == BIGINT) loc += sprintf(&line[loc],format[ifield],bivalue); - } } // print line to screen and logfile diff --git a/src/universe.cpp b/src/universe.cpp index 410d12dcb3..f078590103 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -174,9 +174,9 @@ void Universe::add_world(char *str) // str may not be empty and may only consist of digits or 'x' - int len = strlen(str); + size_t len = strlen(str); if (len < 1) valid = false; - for (int i=0; i < len; ++i) + for (size_t i=0; i < len; ++i) if (isdigit(str[i]) || str[i] == 'x') continue; else valid = false; diff --git a/src/utils.cpp b/src/utils.cpp new file mode 100644 index 0000000000..c3c173a73f --- /dev/null +++ b/src/utils.cpp @@ -0,0 +1,440 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include +#include "utils.h" +#include "error.h" + +/*! \file utils.cpp */ + +/* + * Mini regex-module adapted from https://github.com/kokke/tiny-regex-c + * which is in the public domain. + * + * Supports: + * --------- + * '.' Dot, matches any character + * '^' Start anchor, matches beginning of string + * '$' End anchor, matches end of string + * '*' Asterisk, match zero or more (greedy) + * '+' Plus, match one or more (greedy) + * '?' Question, match zero or one (non-greedy) + * '[abc]' Character class, match if one of {'a', 'b', 'c'} + * '[a-zA-Z]' Character ranges, the character set of the ranges { a-z | A-Z } + * '\s' Whitespace, \t \f \r \n \v and spaces + * '\S' Non-whitespace + * '\w' Alphanumeric, [a-zA-Z0-9_] + * '\W' Non-alphanumeric + * '\d' Digits, [0-9] + * '\D' Non-digits + * + * *NOT* supported: + * '[^abc]' Inverted class + * 'a|b' Branches + * '(abc)+' Groups + */ + +extern "C" +{ + /** Match text against a (simplified) regular expression + * (regexp will be compiled automatically). */ + static int re_match(const char *text, const char *pattern); +} + +using namespace LAMMPS_NS; + +/** More flexible and specific matching of a string against a pattern. + * This function is supposed to be a more safe, more specific and + * simple to use API to find pattern matches. The purpose is to replace + * uses of either strncmp() or strstr() in the code base to find + * substrings safely. With strncmp() finding prefixes, the number of + * characters to match must be counted, which can lead to errors, + * while using "^pattern" will do the same with less problems. + * Matching for suffixes using strstr() is not as specific as 'pattern$', + * and complex matches, e.g. "^rigid.*\/small.*", to match all small + * body optimized rigid fixes require only one test. + * + * The use of std::string arguments allows for simple concatenation + * even with char * type variables. + * Example: utils::strmatch(text, std::string("^") + charptr) + */ +bool utils::strmatch(std::string text, std::string pattern) +{ + const int pos = re_match(text.c_str(),pattern.c_str()); + return (pos >= 0); +} + +/* utility function to avoid code repetition when parsing args */ +int utils::cfvarg(std::string mode, const char *arg, char *&cfv_id) +{ + int rv = utils::NONE; + cfv_id = NULL; + + if (!arg) return rv; + + if (utils::strmatch(arg,std::string("^[") + mode + "]_")) { + if (*arg == 'c') rv = utils::COMPUTE; + else if (*arg == 'f') rv = utils::FIX; + else if (*arg == 'v') rv = utils::VARIABLE; + else return rv; // should not happen + + arg += 2; + int n = strlen(arg)+1; + cfv_id = new char[n]; + strcpy(cfv_id,arg); + } + + return rv; +} + +/* like fgets() but aborts with an error or EOF is encountered */ +void utils::sfgets(const char *srcname, int srcline, char *s, int size, + FILE *fp, const char *filename, Error *error) +{ + char *rv = fgets(s,size,fp); + if (rv == NULL) { // something went wrong + std::string errmsg; + + if (feof(fp)) { + errmsg = "Unexpected end of file while reading file '"; + } else if (ferror(fp)) { + errmsg = "Unexpected error while reading file '"; + } else { + errmsg = "Unexpected short read while reading file '"; + } + errmsg += filename; + errmsg += "'"; + + if (error) error->one(srcname,srcline,errmsg.c_str()); + if (s) *s = '\0'; // truncate string to empty in case error is NULL + } + return; +} + +/* ------------------------------------------------------------------ */ + +extern "C" { + /* Typedef'd pointer to get abstract datatype. */ + typedef struct regex_t *re_t; + + /* Compile regex string pattern to a regex_t-array. */ + static re_t re_compile(const char *pattern); + + + /* Find matches of the compiled pattern inside text. */ + static int re_matchp(const char *text, re_t pattern); + + +/* Definitions: */ + +#define MAX_REGEXP_OBJECTS 30 /* Max number of regex symbols in expression. */ +#define MAX_CHAR_CLASS_LEN 40 /* Max length of character-class buffer in. */ + + + enum { UNUSED, DOT, BEGIN, END, QUESTIONMARK, STAR, PLUS, + CHAR, CHAR_CLASS, INV_CHAR_CLASS, DIGIT, NOT_DIGIT, + ALPHA, NOT_ALPHA, WHITESPACE, NOT_WHITESPACE /*, BRANCH */ }; + + typedef struct regex_t { + unsigned char type; /* CHAR, STAR, etc. */ + union { + unsigned char ch; /* the character itself */ + unsigned char *ccl; /* OR a pointer to characters in class */ + }; + } regex_t; + +/* Private function declarations: */ + static int matchpattern(regex_t *pattern, const char *text); + static int matchcharclass(char c, const char *str); + static int matchstar(regex_t p, regex_t *pattern, const char *text); + static int matchplus(regex_t p, regex_t *pattern, const char *text); + static int matchone(regex_t p, char c); + static int matchdigit(char c); + static int matchalpha(char c); + static int matchwhitespace(char c); + static int matchmetachar(char c, const char *str); + static int matchrange(char c, const char *str); + static int ismetachar(char c); + +/* Semi-public functions: */ + int re_match(const char *text, const char *pattern) + { + return re_matchp(text, re_compile(pattern)); + } + + int re_matchp(const char *text, re_t pattern) + { + if (pattern != 0) { + if (pattern[0].type == BEGIN) { + return ((matchpattern(&pattern[1], text)) ? 0 : -1); + } else { + int idx = -1; + + do { + idx += 1; + + if (matchpattern(pattern, text)) { + if (text[0] == '\0') + return -1; + + return idx; + } + } + while (*text++ != '\0'); + } + } + return -1; + } + + re_t re_compile(const char *pattern) + { + /* The sizes of the two static arrays below substantiates the static RAM usage of this module. + MAX_REGEXP_OBJECTS is the max number of symbols in the expression. + MAX_CHAR_CLASS_LEN determines the size of buffer for chars in all char-classes in the expression. */ + static regex_t re_compiled[MAX_REGEXP_OBJECTS]; + static unsigned char ccl_buf[MAX_CHAR_CLASS_LEN]; + int ccl_bufidx = 1; + + char c; /* current char in pattern */ + int i = 0; /* index into pattern */ + int j = 0; /* index into re_compiled */ + + while (pattern[i] != '\0' && (j+1 < MAX_REGEXP_OBJECTS)) { + c = pattern[i]; + + switch (c) { + /* Meta-characters: */ + case '^': { re_compiled[j].type = BEGIN; } break; + case '$': { re_compiled[j].type = END; } break; + case '.': { re_compiled[j].type = DOT; } break; + case '*': { re_compiled[j].type = STAR; } break; + case '+': { re_compiled[j].type = PLUS; } break; + case '?': { re_compiled[j].type = QUESTIONMARK; } break; + + /* Escaped character-classes (\s \w ...): */ + case '\\': { + if (pattern[i+1] != '\0') { + /* Skip the escape-char '\\' */ + i += 1; + /* ... and check the next */ + switch (pattern[i]) { + /* Meta-character: */ + case 'd': { re_compiled[j].type = DIGIT; } break; + case 'D': { re_compiled[j].type = NOT_DIGIT; } break; + case 'w': { re_compiled[j].type = ALPHA; } break; + case 'W': { re_compiled[j].type = NOT_ALPHA; } break; + case 's': { re_compiled[j].type = WHITESPACE; } break; + case 'S': { re_compiled[j].type = NOT_WHITESPACE; } break; + + /* Escaped character, e.g. '.' or '$' */ + default: { + re_compiled[j].type = CHAR; + re_compiled[j].ch = pattern[i]; + } break; + } + } + /* '\\' as last char in pattern -> invalid regular expression. */ + } break; + + /* Character class: */ + case '[': { + /* Remember where the char-buffer starts. */ + int buf_begin = ccl_bufidx; + + /* Look-ahead to determine if negated */ + if (pattern[i+1] == '^') { + re_compiled[j].type = INV_CHAR_CLASS; + i += 1; /* Increment i to avoid including '^' in the char-buffer */ + } else { + re_compiled[j].type = CHAR_CLASS; + } + + /* Copy characters inside [..] to buffer */ + while ((pattern[++i] != ']') && (pattern[i] != '\0')) { + /* Missing ] */ + if (pattern[i] == '\\') { + if (ccl_bufidx >= MAX_CHAR_CLASS_LEN - 1) { + return 0; + } + ccl_buf[ccl_bufidx++] = pattern[i++]; + } else if (ccl_bufidx >= MAX_CHAR_CLASS_LEN) { + return 0; + } + ccl_buf[ccl_bufidx++] = pattern[i]; + } + if (ccl_bufidx >= MAX_CHAR_CLASS_LEN) { + /* Catches cases such as [00000000000000000000000000000000000000][ */ + return 0; + } + /* Null-terminate string end */ + ccl_buf[ccl_bufidx++] = 0; + re_compiled[j].ccl = &ccl_buf[buf_begin]; + } break; + + /* Other characters: */ + default: { + re_compiled[j].type = CHAR; + re_compiled[j].ch = c; + } break; + } + i += 1; + j += 1; + } + /* 'UNUSED' is a sentinel used to indicate end-of-pattern */ + re_compiled[j].type = UNUSED; + + return (re_t) re_compiled; + } + + +/* Private functions: */ + static int matchdigit(char c) + { + return ((c >= '0') && (c <= '9')); + } + + static int matchalpha(char c) + { + return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z')); + } + + static int matchwhitespace(char c) + { + return ((c == ' ') || (c == '\t') || (c == '\n') || (c == '\r') || (c == '\f') || (c == '\v')); + } + + static int matchalphanum(char c) + { + return ((c == '_') || matchalpha(c) || matchdigit(c)); + } + + static int matchrange(char c, const char *str) + { + return ((c != '-') && (str[0] != '\0') + && (str[0] != '-') && (str[1] == '-') + && (str[1] != '\0') && (str[2] != '\0') + && ((c >= str[0]) && (c <= str[2]))); + } + + static int ismetachar(char c) + { + return ((c == 's') || (c == 'S') + || (c == 'w') || (c == 'W') + || (c == 'd') || (c == 'D')); + } + + static int matchmetachar(char c, const char *str) + { + switch (str[0]) { + case 'd': return matchdigit(c); + case 'D': return !matchdigit(c); + case 'w': return matchalphanum(c); + case 'W': return !matchalphanum(c); + case 's': return matchwhitespace(c); + case 'S': return !matchwhitespace(c); + default: return (c == str[0]); + } + } + + static int matchcharclass(char c, const char *str) + { + do { + if (matchrange(c, str)) { + return 1; + } else if (str[0] == '\\') { + /* Escape-char: increment str-ptr and match on next char */ + str += 1; + if (matchmetachar(c, str)) { + return 1; + } else if ((c == str[0]) && !ismetachar(c)) { + return 1; + } + } else if (c == str[0]) { + if (c == '-') { + return ((str[-1] == '\0') || (str[1] == '\0')); + } else { + return 1; + } + } + } + while (*str++ != '\0'); + + return 0; + } + + static int matchone(regex_t p, char c) + { + switch (p.type) { + case DOT: return 1; + case CHAR_CLASS: return matchcharclass(c, (const char *)p.ccl); + case INV_CHAR_CLASS: return !matchcharclass(c, (const char *)p.ccl); + case DIGIT: return matchdigit(c); + case NOT_DIGIT: return !matchdigit(c); + case ALPHA: return matchalphanum(c); + case NOT_ALPHA: return !matchalphanum(c); + case WHITESPACE: return matchwhitespace(c); + case NOT_WHITESPACE: return !matchwhitespace(c); + default: return (p.ch == c); + } + } + + static int matchstar(regex_t p, regex_t *pattern, const char *text) + { + do { + if (matchpattern(pattern, text)) + return 1; + } + while ((text[0] != '\0') && matchone(p, *text++)); + + return 0; + } + + static int matchplus(regex_t p, regex_t *pattern, const char *text) + { + while ((text[0] != '\0') && matchone(p, *text++)) { + if (matchpattern(pattern, text)) + return 1; + } + return 0; + } + + static int matchquestion(regex_t p, regex_t *pattern, const char *text) + { + if (p.type == UNUSED) + return 1; + if (matchpattern(pattern, text)) + return 1; + if (*text && matchone(p, *text++)) + return matchpattern(pattern, text); + return 0; + } + +/* Iterative matching */ + static int matchpattern(regex_t *pattern, const char *text) + { + do { + if ((pattern[0].type == UNUSED) || (pattern[1].type == QUESTIONMARK)) { + return matchquestion(pattern[0], &pattern[2], text); + } else if (pattern[1].type == STAR) { + return matchstar(pattern[0], &pattern[2], text); + } else if (pattern[1].type == PLUS) { + return matchplus(pattern[0], &pattern[2], text); + } else if ((pattern[0].type == END) && pattern[1].type == UNUSED) { + return (text[0] == '\0'); + } + } + while ((text[0] != '\0') && matchone(*pattern++, *text++)); + + return 0; + } +} diff --git a/src/utils.h b/src/utils.h new file mode 100644 index 0000000000..2596fcd774 --- /dev/null +++ b/src/utils.h @@ -0,0 +1,76 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_UTILS_H +#define LMP_UTILS_H + +/*! \file utils.h */ + +#include +#include + +namespace LAMMPS_NS { + + // forward declarations + class Error; + + namespace utils { + + /** \brief Match text against a simplified regex pattern + * + * \param text the text to be matched against the pattern + * \param pattern the search pattern, which may contain regexp markers + * \return true if the pattern matches, false if not + */ + bool strmatch(std::string text, std::string pattern); + + /** Categories of special arguments for cfvarg() function + * + * Enum starts from 100 to avoid conflicts with other local define flags + */ + enum {NONE=100, /// does not match any category + COMPUTE, /// processed a compute + FIX, /// processed a fix + VARIABLE /// processed a variable + }; + + /** \brief Convenience function to process 'c_', 'f_', and 'v_' arguments + * + * \param mode types to search for. 1-3 char string from 'c', 'f', or 'v' + * \param arg argument string to test against the prefixes + * \param cfv_id name or ID of the compute, fix, or variable + * \return utils::COMPUTE, utils::FIX, utils::VARIABLE or utils::NONE + */ + int cfvarg(std::string mode, const char *arg, char *&cfv_id); + + /** \brief safe wrapper around fgets() which aborts on errors + * or EOF and prints a suitable error message to help debugging + * + * \param srcname name of the calling source file (from FLERR macro) + * \param srcline line in the calling source file (from FLERR macro) + * \param s buffer for storing the result of fgets() + * \param size size of buffer s (max number of bytes read by fgets()) + * \param fp file pointer used by fgets() + * \param filename file name associated with fp (for error message) + * \param error pointer to Error class instance (for abort) + */ + void sfgets(const char *srcname, int srcline, char *s, int size, + FILE *fp, const char *filename, Error *error); + } +} + +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/variable.cpp b/src/variable.cpp index 1595456f33..c0e4dae7d0 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -34,7 +34,7 @@ #include "random_mars.h" #include "math_const.h" #include "atom_masks.h" -#include "python.h" +#include "lmppython.h" #include "memory.h" #include "info.h" #include "error.h" @@ -182,7 +182,7 @@ void Variable::set(int narg, char **arg) if (find(arg[0]) >= 0) return; if (nvar == maxvar) grow(); style[nvar] = LOOP; - int nfirst,nlast; + int nfirst = 0,nlast = 0; if (narg == 3 || (narg == 4 && strcmp(arg[3],"pad") == 0)) { nfirst = 1; nlast = force->inumeric(FLERR,arg[2]); @@ -956,7 +956,7 @@ double Variable::compute_equal(char *str) void Variable::compute_atom(int ivar, int igroup, double *result, int stride, int sumflag) { - Tree *tree; + Tree *tree = NULL; double *vstore; if (eval_in_progress[ivar]) @@ -971,6 +971,7 @@ void Variable::compute_atom(int ivar, int igroup, } else vstore = reader[ivar]->fixstore->vstore; if (result == NULL) { + if (style[ivar] == ATOM) free_tree(tree); eval_in_progress[ivar] = 0; return; } @@ -1028,7 +1029,7 @@ void Variable::compute_atom(int ivar, int igroup, int Variable::compute_vector(int ivar, double **result) { - Tree *tree; + Tree *tree = NULL; if (vecs[ivar].currentstep == update->ntimestep) { *result = vecs[ivar].values; return vecs[ivar].n; @@ -1100,6 +1101,7 @@ void Variable::remove(int n) pad[i-1] = pad[i]; reader[i-1] = reader[i]; data[i-1] = data[i]; + dvalue[i-1] = dvalue[i]; } nvar--; } @@ -1215,7 +1217,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) // evaluate contents and push on stack if (tree) { - Tree *newtree; + Tree *newtree = NULL; evaluate(contents,&newtree,ivar); treestack[ntreestack++] = newtree; } else argstack[nargstack++] = evaluate(contents,NULL,ivar); @@ -1351,7 +1353,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > compute->size_vector && compute->size_vector_variable == 0) print_var_error(FLERR,"Variable formula compute vector " - "is accessed out-of-range",ivar); + "is accessed out-of-range",ivar,0); if (update->whichflag == 0) { if (compute->invoked_vector != update->ntimestep) print_var_error(FLERR,"Compute used in variable between runs " @@ -1380,10 +1382,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > compute->size_array_rows && compute->size_array_rows_variable == 0) print_var_error(FLERR,"Variable formula compute array " - "is accessed out-of-range",ivar); + "is accessed out-of-range",ivar,0); if (index2 > compute->size_array_cols) print_var_error(FLERR,"Variable formula compute array " - "is accessed out-of-range",ivar); + "is accessed out-of-range",ivar,0); if (update->whichflag == 0) { if (compute->invoked_array != update->ntimestep) print_var_error(FLERR,"Compute used in variable between runs " @@ -1493,7 +1495,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index2 > compute->size_peratom_cols) print_var_error(FLERR,"Variable formula compute " - "array is accessed out-of-range",ivar); + "array is accessed out-of-range",ivar,0); if (update->whichflag == 0) { if (compute->invoked_peratom != update->ntimestep) print_var_error(FLERR,"Compute used in variable " @@ -1554,7 +1556,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) "vector-style variable formula",ivar); if (index1 > compute->size_peratom_cols) print_var_error(FLERR,"Variable formula compute array " - "is accessed out-of-range",ivar); + "is accessed out-of-range",ivar,0); if (update->whichflag == 0) { if (compute->invoked_peratom != update->ntimestep) print_var_error(FLERR,"Compute used in variable " @@ -1648,7 +1650,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > fix->size_vector && fix->size_vector_variable == 0) print_var_error(FLERR,"Variable formula fix vector is " - "accessed out-of-range",ivar); + "accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed " "at a compatible time",ivar); @@ -1670,10 +1672,10 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index1 > fix->size_array_rows && fix->size_array_rows_variable == 0) print_var_error(FLERR,"Variable formula fix array is " - "accessed out-of-range",ivar); + "accessed out-of-range",ivar,0); if (index2 > fix->size_array_cols) print_var_error(FLERR,"Variable formula fix array is " - "accessed out-of-range",ivar); + "accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->global_freq) print_var_error(FLERR,"Fix in variable not computed at a " "compatible time",ivar); @@ -1774,7 +1776,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) if (index2 > fix->size_peratom_cols) print_var_error(FLERR,"Variable formula fix array is " - "accessed out-of-range",ivar); + "accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) print_var_error(FLERR,"Fix in variable not computed " @@ -1821,7 +1823,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) "equal-style variable formula",ivar); if (index1 > fix->size_peratom_cols) print_var_error(FLERR,"Variable formula fix array " - "is accessed out-of-range",ivar); + "is accessed out-of-range",ivar,0); if (update->whichflag > 0 && update->ntimestep % fix->peratom_freq) print_var_error(FLERR,"Fix in variable not computed at " @@ -1915,7 +1917,7 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) print_var_error(FLERR,"Atom-style variable in " "vector-style variable formula",ivar); - Tree *newtree; + Tree *newtree = NULL; evaluate(data[ivar][0],&newtree,ivar); treestack[ntreestack++] = newtree; @@ -2201,18 +2203,18 @@ double Variable::evaluate(char *str, Tree **tree, int ivar) argstack[nargstack++] = value1 * value2; else if (opprevious == DIVIDE) { if (value2 == 0.0) - print_var_error(FLERR,"Divide by 0 in variable formula",ivar); + print_var_error(FLERR,"Divide by 0 in variable formula",ivar,0); argstack[nargstack++] = value1 / value2; } else if (opprevious == MODULO) { if (value2 == 0.0) - print_var_error(FLERR,"Modulo 0 in variable formula",ivar); + print_var_error(FLERR,"Modulo 0 in variable formula",ivar,0); argstack[nargstack++] = fmod(value1,value2); } else if (opprevious == CARAT) { if (value2 == 0.0) argstack[nargstack++] = 1.0; else if ((value1 == 0.0) && (value2 < 0.0)) print_var_error(FLERR,"Invalid power expression in " - "variable formula",ivar); + "variable formula",ivar,0); else argstack[nargstack++] = pow(value1,value2); } else if (opprevious == UNARY) { argstack[nargstack++] = -value2; @@ -3325,7 +3327,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, char *args[MAXFUNCARG]; int narg = parse_args(contents,args); - Tree *newtree; + Tree *newtree = NULL; double value1,value2; double values[MAXFUNCARG-2]; @@ -3333,7 +3335,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, newtree = new Tree(); newtree->first = newtree->second = NULL; newtree->nextra = 0; - Tree *argtree; + Tree *argtree = NULL; evaluate(args[0],&argtree,ivar); newtree->first = argtree; if (narg > 1) { @@ -3371,7 +3373,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, else { if (value1 < 0.0) print_var_error(FLERR,"Sqrt of negative value in " - "variable formula",ivar); + "variable formula",ivar,0); argstack[nargstack++] = sqrt(value1); } @@ -3387,7 +3389,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, else { if (value1 <= 0.0) print_var_error(FLERR,"Log of zero/negative value in " - "variable formula",ivar); + "variable formula",ivar,0); argstack[nargstack++] = log(value1); } } else if (strcmp(word,"log") == 0) { @@ -3397,7 +3399,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, else { if (value1 <= 0.0) print_var_error(FLERR,"Log of zero/negative value in " - "variable formula",ivar); + "variable formula",ivar,0); argstack[nargstack++] = log10(value1); } } else if (strcmp(word,"abs") == 0) { @@ -3428,7 +3430,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (tree) newtree->type = ASIN; else { if (value1 < -1.0 || value1 > 1.0) - print_var_error(FLERR,"Arcsin of invalid value in variable formula",ivar); + print_var_error(FLERR,"Arcsin of invalid value in variable formula",ivar,0); argstack[nargstack++] = asin(value1); } } else if (strcmp(word,"acos") == 0) { @@ -3437,7 +3439,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, if (tree) newtree->type = ACOS; else { if (value1 < -1.0 || value1 > 1.0) - print_var_error(FLERR,"Arccos of invalid value in variable formula",ivar); + print_var_error(FLERR,"Arccos of invalid value in variable formula",ivar,0); argstack[nargstack++] = acos(value1); } } else if (strcmp(word,"atan") == 0) { @@ -3983,7 +3985,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, strcmp(word,"max") == 0 || strcmp(word,"ave") == 0 || strcmp(word,"trap") == 0 || strcmp(word,"slope") == 0) { - int method; + int method = 0; if (strcmp(word,"sum") == 0) method = SUM; else if (strcmp(word,"min") == 0) method = XMIN; else if (strcmp(word,"max") == 0) method = XMAX; @@ -4031,7 +4033,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree, } else if (index && compute->array_flag) { if (index > compute->size_array_cols) print_var_error(FLERR,"Variable formula compute array " - "is accessed out-of-range",ivar); + "is accessed out-of-range",ivar,0); if (update->whichflag == 0) { if (compute->invoked_array != update->ntimestep) print_var_error(FLERR,"Compute used in variable between runs " @@ -4651,14 +4653,22 @@ char *Variable::find_next_comma(char *str) ------------------------------------------------------------------------- */ void Variable::print_var_error(const char *srcfile, int lineno, - const char *errmsg, int ivar) + const char *errmsg, int ivar, int global) { if ((ivar >= 0) && (ivar < nvar)) { char msg[128]; snprintf(msg,128,"Variable %s: %s",names[ivar],errmsg); - error->all(srcfile,lineno,msg); - } else error->all(srcfile,lineno,errmsg); + if (global) + error->all(srcfile,lineno,msg); + else + error->one(srcfile,lineno,msg); + } else { + if (global) + error->all(srcfile,lineno,errmsg); + else + error->one(srcfile,lineno,errmsg); + } } /* ---------------------------------------------------------------------- diff --git a/src/variable.h b/src/variable.h index b20eb7e6b9..a37ee4cff7 100644 --- a/src/variable.h +++ b/src/variable.h @@ -88,10 +88,15 @@ class Variable : protected Pointers { int nvector; // length of array for vector-style variable int nstride; // stride between atoms if array is a 2d array int selfalloc; // 1 if array is allocated here, else 0 - int ivalue1,ivalue2; // extra values for needed for gmask,rmask,grmask + int ivalue1,ivalue2; // extra values needed for gmask,rmask,grmask int nextra; // # of additional args beyond first 2 Tree *first,*second; // ptrs further down tree for first 2 args Tree **extra; // ptrs further down tree for nextra args + + Tree() : + array(NULL), iarray(NULL), barray(NULL), + selfalloc(0), ivalue1(0), ivalue2(0), nextra(0), + first(NULL), second(NULL), extra(NULL) {} }; int compute_python(int); @@ -120,7 +125,7 @@ class Variable : protected Pointers { double constant(char *); int parse_args(char *, char **); char *find_next_comma(char *); - void print_var_error(const char *, int, const char *, int); + void print_var_error(const char *, int, const char *, int, int global=1); void print_tree(Tree *, int); }; diff --git a/src/velocity.cpp b/src/velocity.cpp index 3a0b95fb4d..6d6027cc3c 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -641,7 +641,7 @@ void Velocity::ramp(int /*narg*/, char **arg) // parse args - int v_dim; + int v_dim = 0; if (strcmp(arg[0],"vx") == 0) v_dim = 0; else if (strcmp(arg[0],"vy") == 0) v_dim = 1; else if (strcmp(arg[0],"vz") == 0) v_dim = 2; @@ -662,7 +662,7 @@ void Velocity::ramp(int /*narg*/, char **arg) v_hi = zscale*force->numeric(FLERR,arg[2]); } - int coord_dim; + int coord_dim = 0; if (strcmp(arg[3],"x") == 0) coord_dim = 0; else if (strcmp(arg[3],"y") == 0) coord_dim = 1; else if (strcmp(arg[3],"z") == 0) coord_dim = 2; diff --git a/src/version.h b/src/version.h index 62ba229b7e..0539f757c9 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "24 Oct 2018" +#define LAMMPS_VERSION "28 Feb 2019" diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 99172c09f0..9bf54b3c08 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include +#include #include #include "write_coeff.h" #include "pair.h" @@ -24,9 +25,12 @@ #include "universe.h" #include "error.h" #include "domain.h" +#include "utils.h" using namespace LAMMPS_NS; +enum {REGULAR_MODE, CLASS2_MODE}; + /* ---------------------------------------------------------------------- called as write_coeff command in input script ------------------------------------------------------------------------- */ @@ -50,6 +54,7 @@ void WriteCoeff::command(int narg, char **arg) if (comm->me == 0) { char str[256], coeff[256]; FILE *one = fopen(file,"wb+"); + if (one == NULL) { snprintf(str,256,"Cannot open coeff file %s",file); error->one(FLERR,str); @@ -91,17 +96,79 @@ void WriteCoeff::command(int narg, char **arg) } fprintf(two,"# LAMMPS coeff file via write_coeff, version %s\n", universe->version); + while(1) { + int coeff_mode = REGULAR_MODE; if (fgets(str,256,one) == NULL) break; + + // some coeffs need special treatment + if (strstr(str,"class2") != NULL) { + if (strstr(str,"angle_style") != NULL) + coeff_mode = CLASS2_MODE; + else if (strstr(str,"dihedral_style") != NULL) + coeff_mode = CLASS2_MODE; + else if (strstr(str,"improper_style") != NULL) + coeff_mode = CLASS2_MODE; + } + + const char *section = (const char *)""; fputs(str,two); // style - fgets(str,256,one); // coeff + utils::sfgets(FLERR,str,256,one,file,error); // coeff n = strlen(str); strcpy(coeff,str); coeff[n-1] = '\0'; - fgets(str,256,one); + utils::sfgets(FLERR,str,256,one,file,error); + while (strcmp(str,"end\n") != 0) { - fprintf(two,"%s %s",coeff,str); - fgets(str,256,one); + + if (coeff_mode == REGULAR_MODE) { + + fprintf(two,"%s %s",coeff,str); + utils::sfgets(FLERR,str,256,one,file,error); + + } else if (coeff_mode == CLASS2_MODE) { + + // class2 angles, dihedrals, and impropers can have + // multiple sections and thus need special treatment + + if (strcmp(str,"\n") == 0) { + + // all but the the last section end with an empty line. + // skip it and read and parse the next section title + + utils::sfgets(FLERR,str,256,one,file,error); + + if (strcmp(str,"BondBond Coeffs\n") == 0) + section = (const char *)"bb"; + else if (strcmp(str,"BondAngle Coeffs\n") ==0) + section = (const char *)"ba"; + else if (strcmp(str,"MiddleBondTorsion Coeffs\n") == 0) + section = (const char *)"mbt"; + else if (strcmp(str,"EndBondTorsion Coeffs\n") == 0) + section = (const char *)"ebt"; + else if (strcmp(str,"AngleTorsion Coeffs\n") == 0) + section = (const char *)"at"; + else if (strcmp(str,"AngleAngleTorsion Coeffs\n") == 0) + section = (const char *)"aat"; + else if (strcmp(str,"BondBond13 Coeffs\n") == 0) + section = (const char *)"bb13"; + else if (strcmp(str,"AngleAngle Coeffs\n") == 0) + section = (const char *)"aa"; + + // gobble up one more empty line + utils::sfgets(FLERR,str,256,one,file,error); + utils::sfgets(FLERR,str,256,one,file,error); + } + + // parse type number and skip over it + int type = atoi(str); + char *p = str; + while ((*p != '\0') && (*p == ' ')) ++p; + while ((*p != '\0') && isdigit(*p)) ++p; + + fprintf(two,"%s %d %s %s",coeff,type,section,p); + utils::sfgets(FLERR,str,256,one,file,error); + } } fputc('\n',two); } diff --git a/src/write_data.cpp b/src/write_data.cpp index f18e30de52..decc92ea8c 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -177,6 +177,17 @@ void WriteData::write(char *file) MPI_Allreduce(&nimpropers_local,&nimpropers,1,MPI_LMP_BIGINT,MPI_SUM,world); } + // check for bonus data. + if (me == 0) { + if ((atom->nellipsoids > 0) + || (atom->nlines > 0) + || (atom->ntris > 0) + || (atom->nbodies > 0)) + error->warning(FLERR,"System has ellipsoids, lines, triangles, or bodies. " + "Those are not yet supported by write_data. The data file " + "will thus be incomplete."); + } + // open data file if (me == 0) { @@ -255,7 +266,7 @@ void WriteData::header() } } - if (fixflag) + if (fixflag) for (int i = 0; i < modify->nfix; i++) if (modify->fix[i]->wd_header) for (int m = 0; m < modify->fix[i]->wd_header; m++) diff --git a/src/write_dump.cpp b/src/write_dump.cpp index bb79c654b4..6c7375012e 100644 --- a/src/write_dump.cpp +++ b/src/write_dump.cpp @@ -45,7 +45,7 @@ void WriteDump::command(int narg, char **arg) // create the Dump instance // create dump command line with extra required args - Dump *dump; + Dump *dump = NULL; char **dumpargs = new char*[modindex+2]; dumpargs[0] = (char *) "WRITE_DUMP"; // dump id diff --git a/tools/README b/tools/README index e766e935b3..6bf7d6b878 100644 --- a/tools/README +++ b/tools/README @@ -31,7 +31,7 @@ lmp2arc convert LAMMPS output to Accelrys Insight format lmp2cfg convert LAMMPS output to CFG files for AtomEye viz matlab MatLab scripts for post-processing LAMMPS output micelle2d create a data file of small lipid chains in solvent -moltemplate Moltemplate builder program +moltemplate Instructions for installing the Moltemplate builder program msi2lmp use Accelrys Insight code to setup LAMMPS input phonon post-process output of the fix phonon command polybond Python tool for programmable polymer bonding diff --git a/tools/ch2lmp/charmm2lammps.pl b/tools/ch2lmp/charmm2lammps.pl index 0693c0a0ff..bda9ace2bc 100755 --- a/tools/ch2lmp/charmm2lammps.pl +++ b/tools/ch2lmp/charmm2lammps.pl @@ -794,9 +794,10 @@ $ids{$tmp[1]} = $tmp[2]; $masses{$tmp[1]} = $tmp[3]; $max_id = $tmp[1] if ($max_id<$tmp[1]); + } elsif ($read&&($tmp[0] eq "ATOM")) { + # quit reading when hitting the "ATOM" section + last; } - # $names{$tmp[1]} = $tmp[4] if ($read&&($tmp[0] eq "MASS")); - last if ($read&&!scalar(@tmp)); # quit reading } AddMass(HT, 1.00800); AddMass(OT, 15.99940); diff --git a/tools/moltemplate/.gitignore b/tools/moltemplate/.gitignore deleted file mode 100644 index d2053ce4dc..0000000000 --- a/tools/moltemplate/.gitignore +++ /dev/null @@ -1,180 +0,0 @@ -# from https://github.com/github/gitignore/blob/master/Python.gitignore - -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -env/ -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -*.egg-info/ -.installed.cfg -*.egg - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*,cover -.hypothesis/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# pyenv -.python-version - -# celery beat schedule file -celerybeat-schedule - -# dotenv -.env - -# virtualenv -.venv/ -venv/ -ENV/ - -# Spyder project settings -.spyderproject - -# Rope project settings -.ropeproject - -# text-editor temporary files: -*~ - -# misc rubbish -deleteme* -DELETEME* - -######## files specific to moltemplate and lammps ######## - -# latex/bibtex temporary files for the moltemplate manual: -moltemplate_manual*.aux -moltemplate_manual*.bbl -moltemplate_manual*.blg -moltemplate_manual*.log -moltemplate_manual*.out -moltemplate_manual*.toc - -######## files created by running LAMMPS: ######## - -log.lammps -log.cite -traj*.lammpstrj - -######## files generated by running moltemplate: ######## - -system.data -system.in -system.in.init -system.in.settings -system.in.charges -system.psf -ttree_assignments.txt -output_ttree/ - -# Sections from the LAMMPS data file generated by moltemplate.sh -"Data Header"* -"Data Atoms"* -"Data Masses"* -"Data Velocities"* -"Data Bonds"* -"Data Bond List"* -"Data Bonds AtomId AtomId"* -"Data Angles"* -"Data Dihedrals"* -"Data Impropers"* -"Data Bond Coeffs"* -"Data Angle Coeffs"* -"Data Dihedral Coeffs"* -"Data Improper Coeffs"* -"Data Pair Coeffs"* -"Data PairIJ Coeffs"* - -# interactions-by-type (not id. This is not part of the LAMMPS standard.) -"Data Charge By Bond"* -"Data Bonds By Type"* -"Data Angles By Type"* -"Data Dihedrals By Type"* -"Data Impropers By Type"* - -# class2 data sections -"Data BondBond Coeffs"* -"Data BondAngle Coeffs"* -"Data MiddleBondTorsion Coeffs"* -"Data EndBondTorsion Coeffs"* -"Data AngleTorsion Coeffs"* -"Data AngleAngleTorsion Coeffs"* -"Data BondBond13 Coeffs"* -"Data AngleAngle Coeffs"* - -# sections for non-point-like particles: -"Data Ellipsoids"* -"Data Lines"* -"Data Triangles"* - -# periodic boundary conditions -"Data Boundary"* - -# Sections from the LAMMPS input script(s) generated by moltemplate.sh - -"In Init"* -"In Settings"* -"In Coords"* -"In Charges"* -#temporary file created by moltemplate.sh for storing coordinates -tmp_atom_coords.dat - diff --git a/tools/moltemplate/LICENSE.md b/tools/moltemplate/LICENSE.md deleted file mode 100644 index d04220dc5f..0000000000 --- a/tools/moltemplate/LICENSE.md +++ /dev/null @@ -1,29 +0,0 @@ -Modified BSD License (BSD-3-Clause) -==================== - -_Copyright © `2012`, `University of California, Santa Barbara`_ -_All rights reserved._ - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - -1. Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. -2. Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. -3. Neither the name of the copyright holders nor the names of its - contributors may be used to endorse or promote products derived from - this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS†-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE -LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR -CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF -SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS -INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN -CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF -THE POSSIBILITY OF SUCH DAMAGE. diff --git a/tools/moltemplate/README.md b/tools/moltemplate/README.md deleted file mode 100644 index c0bcb28296..0000000000 --- a/tools/moltemplate/README.md +++ /dev/null @@ -1,104 +0,0 @@ -[![Build Status](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master)](https://travis-ci.org/jewettaij/moltemplate.svg?branch=master) - -Moltemplate -=========== - -## Description - -Moltemplate is a *general* cross-platform text-based molecule builder for **LAMMPS** and **ESPResSo**. Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well. It currently supports the **OPLS**, **COMPASS**, **AMBER**(GAFF,GAFF2), **MARTINI**, **SDK**, **LOPLS**(2015), and **TraPPE**(1998) force fields, and includes approximately 40 examples. (New force fields and examples are added continually by users.) - -## Typical usage - - moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd] system.lt - -## Web page - -Documentation, examples, and supporting code can be downloaded at: - -http://www.moltemplate.org - -## Requirements - -Moltemplate requires the Bourne-shell, and a recent version of python -(2.7, 3.0 or higher), and can run on OS X, linux, or windows. (...if a -suitable shell environment has been installed. See below.) - - -## INSTALLATION INSTRUCTIONS - -This directory should contain 3 folders: - - moltemplate/ <-- source code and force fields - doc/ <-- the moltemplate reference manual - examples/ <-- examples built with moltemplate - -There are two ways to install moltemplate: - -## Installation using pip -If you are familiar with pip, then run the following command from within the directory where this README file is located: - - pip install . - -If you receive an error regarding permissions, then run pip with the "--user" argument: - - pip install . --user - -Make sure that your default pip install bin directory is in your PATH. (This is usually something like ~/.local/bin/ or ~/anaconda3/bin/. If you have installed anaconda, this will be done for you automatically.) Later, you can uninstall moltemplate using: - - pip uninstall moltemplate - -If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "*virtualenv*", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands: - - cd ~/moltemplate - virtualenv venv - source venv/bin/activate - pip install . - #(now do something useful with moltemplate...) - -(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate. -The *virtualenv* tool is -[explained in detail here](http://docs.python-guide.org/en/latest/dev/virtualenvs/)) If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. - -## Manual installation: - -Alternatively, you can edit your $PATH environment variable manually to -include the subdirectory where the "moltemplate.sh" script is located, -as well as the subdirectory where most of the python scripts are located. -Suppose the directory with this README file is named "moltemplate" -and is located in your home directory: - -If you use the bash shell, typically you would edit your -`~/.profile`, `~/.bash_profile` or `~/.bashrc` files -to contain the following lines: - - export PATH="$PATH:$HOME/moltemplate/moltemplate" - export PATH="$PATH:$HOME/moltemplate/moltemplate/scripts" - -If you use the tcsh shell, typically you would edit your -`~/.login`, `~/.cshrc`, or `~/.tcshrc` files to contain the following lines: - - setenv PATH "$PATH:$HOME/moltemplate/moltemplate" - setenv PATH "$PATH:$HOME/moltemplate/moltemplate/scripts" - -After making these changes, you may need to start a new terminal (shell) for the changes to take effect. If you do not know what a `PATH` environment variable is and are curious, read: - http://www.linfo.org/path_env_var.html -(I receive this question often.) - - -### WINDOWS installation suggestions - -You can install both moltemplate and LAMMPS in windows, but you will first need to install the BASH shell environment on your computer. If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)" - -https://solarianprogrammer.com/2017/04/15/install-wsl-windows-subsystem-for-linux/ -https://msdn.microsoft.com/en-us/commandline/wsl/faq - -If you are using an older version of windows, try following the tutorial written by Yanqing Fu instead: - -https://sourceforge.net/p/lammps/mailman/message/32599824/ - -To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor. (Word, Wordpad, and Notepad will not work.) Popular free text editors which you can safely install and run from within the WSL terminal include: **nano**, **ne**, **emacs**, **vim**, and **jove**. (Unfortunately, as of 2017-5-17, [graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption. Avoid these editors for now.](https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/)) - -## License - -Moltemplate is available under the terms of the open-source 3-clause BSD -license. (See `LICENSE.md`.) diff --git a/tools/moltemplate/README.txt b/tools/moltemplate/README.txt new file mode 100644 index 0000000000..ca6a013244 --- /dev/null +++ b/tools/moltemplate/README.txt @@ -0,0 +1,142 @@ + +Moltemplate +=========== + +## Description + +This folder used to contain a distribution of Moltemplate, a general purpose, +cross-platform, text-based molecule and topology builder for LAMMPS. +Moltemplate was originally conceived for building custom coarse-grained +molecular models, but it has since been generalized for all-atom simulations +as well. It currently supports the OPLS, COMPASS, AMBER(GAFF,GAFF2), +MARTINI, SDK, LOPLS(2015), and TraPPE(1998) force fields, and includes +(New force fields and examples are added continually through user +contributions). + +Moltemplate is now distributed via the pip python package manager, +or can be downloaded from http://www.moltemplate.org/download.html +or https://github.com/jewettaij/moltemplate/releases +The most up-to-date version is usually available through GitHub + +## Typical usage + + moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd] system.lt + +## Web page + +Documentation, examples, and supporting code can be downloaded at: + +http://www.moltemplate.org + +## Requirements + +Moltemplate requires the Bourne-shell, and a recent version of python +(2.7, 3.0 or higher), and can run on OS X, linux, or windows. (...if a +suitable shell environment has been installed. See below.) + + +## INSTALLATION INSTRUCTIONS + +## Download / install via pip +If you have a working installation of "pip" and access to the internet, +you can download and install it into your home directory ($HOME/.local/bin +and the corresponding python package folders) simply by: + + pip install moltemplate --user + +If instead, you want a system-wide installation, you need superuser access, +e.g. via: + + sudo pip install moltemplate + +Updates to this distribution method are less frequent, than others, so if +you need a more recent version, you can download it as a .tar.gz or .zip +archive from the moltemplate home page or GitHub (see linke above). After +downloading an archive and unpacking it, you should have 3 folders. + + moltemplate/ <-- source code and force fields + doc/ <-- the moltemplate reference manual + examples/ <-- examples built with moltemplate + +From here on, you can use pip to install this downloaded version as well +by issuing the following command from within the top-level directory of +the unpacked source archive: + + pip install . --user + +If you want to install into a system folder, then you need to run pip with +superuser priviledges. e.g. with: + + sudo pip install . + +Make sure that your default pip install bin directory is in your PATH. +This is usually something like ~/.local/bin/ or ~/anaconda3/bin/. +If you have installed anaconda, this will be done for you automatically. +As you can see, this is mostly identical to the direct install with pip. + +Later, you can uninstall moltemplate using: + + pip uninstall moltemplate + +If you continue to run into difficulty, try installing moltemplate into +a temporary virtual environment by installing virtualenv, downloading +moltemplate (to "~/moltemplate" in the example below), and running +these commands: + + cd ~/moltemplate + virtualenv venv + source venv/bin/activate + pip install . + #(now do something useful with moltemplate...) + +(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand +every time you want to run moltemplate. +The *virtualenv* tool is explained in detail here: + +http://docs.python-guide.org/en/latest/dev/virtualenvs/ + +If all this fails, then try installing moltemplate by manually updating +your \$PATH environment variable. Instructions for doing that are included below. + +## Manual installation: + +Alternatively, after downloading and unpacking the moltemplate source archive, +you can edit your $PATH environment variable manually to include the subdirectory +where the "moltemplate.sh" script is located, as well as the subdirectory where +most of the python scripts are located. +Suppose the top-level directory of the unpacked archive "moltemplate" +and is located in your home directory: + +If you use the bash shell, typically you would edit your +`~/.profile`, `~/.bash_profile` or `~/.bashrc` files +to contain the following lines: + + export PATH="$PATH:$HOME/moltemplate/moltemplate" + export PATH="$PATH:$HOME/moltemplate/moltemplate/scripts" + +If you use the tcsh shell, typically you would edit your +`~/.login`, `~/.cshrc`, or `~/.tcshrc` files to contain the following lines: + + setenv PATH "$PATH:$HOME/moltemplate/moltemplate" + setenv PATH "$PATH:$HOME/moltemplate/moltemplate/scripts" + +After making these changes, you may need to start a new terminal (shell) for the changes to take effect. If you do not know what a `PATH` environment variable is and are curious, read: + http://www.linfo.org/path_env_var.html +(I receive this question often.) + + +### WINDOWS installation suggestions + +You can install both moltemplate and LAMMPS in windows, but you will +first need to install the BASH shell environment on your computer. +If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)" + +https://solarianprogrammer.com/2017/04/15/install-wsl-windows-subsystem-for-linux/ +https://msdn.microsoft.com/en-us/commandline/wsl/faq + +If you are using an older version of windows, try following the tutorial written by Yanqing Fu instead: + +https://sourceforge.net/p/lammps/mailman/message/32599824/ + +To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor. (Word, Wordpad, and Notepad will not work.) Popular free text editors which you can safely install and run from within the WSL terminal include: **nano**, **ne**, **emacs**, **vim**, and **jove**. (Unfortunately, as of 2017-5-17, [graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption. Avoid these editors for now.](https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/)) + diff --git a/tools/moltemplate/doc/moltemplate_manual.pdf b/tools/moltemplate/doc/moltemplate_manual.pdf deleted file mode 100644 index 54d8b132bf..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual.pdf and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg deleted file mode 100644 index 7666e22bf7..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/2bead_monomer.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg deleted file mode 100644 index e73c51d0ae..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymer.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg deleted file mode 100644 index a5fb40ae7c..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_nopbc_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg deleted file mode 100644 index b978b76d40..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/2bead_polymers_t=100ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/README.txt b/tools/moltemplate/doc/moltemplate_manual_src/README.txt deleted file mode 100644 index a54c345630..0000000000 --- a/tools/moltemplate/doc/moltemplate_manual_src/README.txt +++ /dev/null @@ -1,10 +0,0 @@ -To create the file "moltemplate_manual.pdf", install pdflatex and run -these commands: - -pdflatex moltemplate_manual -pdflatex moltemplate_manual -bibtex moltemplate_manual -bibtex moltemplate_manual -pdflatex moltemplate_manual -pdflatex moltemplate_manual - diff --git a/tools/moltemplate/doc/moltemplate_manual_src/author_email.png b/tools/moltemplate/doc/moltemplate_manual_src/author_email.png deleted file mode 100644 index a09b3df6dc..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/author_email.png and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/delete_holes1.jpg b/tools/moltemplate/doc/moltemplate_manual_src/delete_holes1.jpg deleted file mode 100644 index 304693e2ac..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/delete_holes1.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/lipid_bilayer_mixture.jpg b/tools/moltemplate/doc/moltemplate_manual_src/lipid_bilayer_mixture.jpg deleted file mode 100644 index e6f7e96e9a..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/lipid_bilayer_mixture.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/lipid_bilayer_vacancies.jpg b/tools/moltemplate/doc/moltemplate_manual_src/lipid_bilayer_vacancies.jpg deleted file mode 100644 index f7bfbebe9e..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/lipid_bilayer_vacancies.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg deleted file mode 100644 index 2369e2de13..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/mol_complex+mol_complex0_transparent_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg deleted file mode 100644 index c4aa70ce16..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/mol_complex_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex b/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex deleted file mode 100644 index f8ce810fd5..0000000000 --- a/tools/moltemplate/doc/moltemplate_manual_src/moltemplate_manual.tex +++ /dev/null @@ -1,5605 +0,0 @@ -\documentclass[11pt]{article} -%\documentclass[11pt,twocolumn,letterpaper]{article} -\setlength{\columnwidth}{8.6cm} -\setlength{\textheight}{23cm} -\setlength{\topmargin}{-0.8cm} -%\documentclass[11pt]{article} -\usepackage{textcomp} -\newcommand{\textapprox}{\raisebox{0.5ex}{\texttildelow}} -\usepackage{graphicx} -\usepackage{verbatim} -\usepackage{color} -\usepackage{url} -\usepackage{longtable} -\usepackage{hyperref} -%\usepackage{booktabs} -%\usepackage{amssymb,amsmath} -%\usepackage[dvips]{color, graphics, epsfig, graphicx} -\bibliographystyle{unsrt} -%\bibliographystyle{apsrev.bst} -%\topmargin 0mm -%\textheight 220mm -%\textwidth 160mm -%\oddsidemargin 5mm -%\mathsurround 2pt - -%\renewcommand{\textfraction}{0.10} -%\renewcommand{\topfraction}{0.85} -%\renewcommand{\bottomfraction}{0.65} -%\renewcommand{\floatpagefraction}{0.60} -%\renewcommand{\thetable}{\Roman{table}} - -%\setcounter{figure}{7} -%\setcounter{table}{8} - -\begin{document} - -\author{ - Andrew Jewett, \\ - MGL Lab (Scripps), Jensen Lab (Caltech), Shea Lab (UCSB) \\ -\includegraphics[height=0.3cm]{author_email.png} -} -\date \today - - -\title{Moltemplate Manual} - - - -\maketitle - - %This manual (like moltemplate) is under development. - -\tableofcontents - - %Additionally, several working examples of molecules created - %with moltemplate can be found in the ``examples/'' subdirectory - %(which is distributed with moltemplate). - %These were created to supplement the moltemplate documentation. - -\subsubsection*{Warning: This manual does not explain how to run ``active-matter'' simulations or use all-atom force fields.} -However numerous examples and README files are available to -demonstrate how to run these kinds of simulations. -Downloading these examples is \textit{highly recommended}. -(See section \ref{sec:installation}.) - -\section{Introduction} - - - -Moltemplate is a general molecule builder and force-field database system for LAMMPS. A simple file format has been created to store molecule definitions and force-fields (the LAMMPS-template format, “LTâ€). -LT files are templates containing \textit{all} of the text relevant to a particular molecule (including coordinates, bond-topology, angles, force-field parameters, constraints, groups and fixes). Moltemplate can then duplicate the molecule, customize it, and use it as a building-block for constructing larger, more complex molecules. (These molecules can be used to build even larger molecules.) Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be inserted, moved, deleted and/or replaced). - -Popular force-fields such as AMBER GAFF and OPLS-AA have been converted into LT format, allowing users to quickly create molecules using moltemplate. (With help, more popular force-fields can be converted.) This way moltemplate users can build a molecule by specifying only a list of atoms in the molecule and the bonds connecting them. End-users are not required to manually specify all of the force-field parameters. However they still have the freedom to easily customize individual interactions when needed. - %or generate all of its angle, dihedral, improper interactions manually. - -Moltemplate is extremely flexible. It supports all LAMMPS force-field styles and nearly all atom-styles (now and in the future). - - % OLD VERSION - %Moltemplate is a cross-platform text-based molecule builder for LAMMPS. It is typically used for building coarse-grained toy molecular models. Moltemplate users have access to (nearly) all of the standard and non-standard (custom, user-created) force-field and features available in LAMMPS. - % - %\textit{(Although optimized for LAMMPS, moltemplate is a general text manipulation tool which, in principle, could be used to generate topology and force-field files for other simulation programs. Please email \includegraphics[height=0.3cm]{author_email.png} if you want to attempt this.)} - % - %A file format has been created to store molecule definitions (the LAMMPS-template format, ``LT''). Typical ``.LT'' files contain atom coordinates, topology data (bonds), LAMMPS force-field data, and other LAMMPS settings (such as group definitions, fixes, and user-defined input files) for a type of molecule (or a molecular subunit). Molecules can be copied, combined, and linked together to define new molecules. (These can be used to define larger molecules.) - %%Unlimited levels of object composition, nesting, and inheritance are supported.) - %Once built, individual molecules and subunits can be customized (atoms and bonds, and subunits can be moved, deleted and replaced). - - -Moltemplate requires the Bourne-shell, and a recent version of python (2.7 or 3.0 or higher), and can run on OS X, linux, or windows (if a suitable shell environment has been installed). -\textbf{A substantial amount of memory is needed} to run moltemplate. -For example, building a system of 1000000 atoms typically requires -between 3 and 12 GB of \textit{available} memory. -(This depends on the number of bonds, molecules, and angular interactions. - See section \ref{sec:limitations} for details.) -%Memory requirements are discussed in section \ref{sec:limitations}. - - %Moltemplate is a text-manipulation tool for generating - %input files for molecular dynamics simulation programs. - %Moltemplate has been optimized for constructing input files for LAMMPS. - %from constituent parts. - %Molecules are stored in a hierarchical, - %object-oriented, - %template-based file format (``.LT''). - % %using an object-oriented style - % %which can mimic many popular molecular file formats. - % %such as PDB, amber TOP, Gromacs TOP, - % %PSF files, and some limited xplor parameter files. - % %existing LAMMPS file formats. - %Typical ``.LT'' files contains LAMMPS force-field data, - %topology data, and other settings (such as fixes and groups) - %for any molecule or repeating subunit. - %These subunits can be combined together - %to build larger, more complicated systems. - %With unlimited levels of nesting, object composition, and inheritance, - %these objects can be combined to build - %elaborate heterogeneous molecular assemblies. - - -% %%Moltemplate can also be used to automatically detect -% %%topological relationships between bonded atoms and determine -% %%(the parameters of) the forces between them accordingly. -% %Moltemplate also extends basic LAMMPS functionality. -% %It can also be used to automatically detect -% %bonded many-body interactions (such as dihedrals), -% %and programmed to determine (the parameters of) -% %the forces between them according to atom and bond type. -% %This makes the LT-file format useful in general -% %for storing force-field parameters. -% -%LT files can also be used for storing force-fields -%for molecules whose topology has not yet been determined. -%Moltemplate automatically detects -% % topological relationships between bonded atoms and -%bonded many-body interactions (such as dihedrals), -%and can determine (the parameters of) -%the forces between them according to atom and bond type. -%Once a system's geometry and bonds have been specified, -%a user can apply completely different force fields to the existing system -%by loading a different LT file containing force-field parameters. -% - -\subsection{Converting \textit{LT files} to LAMMPS input/data files} -The moltemplate.sh program converts LT-files (which contain -molecule definitions) into complete LAMMPS input-scripts and data-files: -\begin{verbatim} -moltemplate.sh -atomstyle "full" system.lt -\end{verbatim} - or -\begin{verbatim} -moltemplate.sh -xyz coords.xyz -atomstyle "full" -vmd system.lt -\end{verbatim} -In the first example, the coordinates of the atoms in the -system are built from commands inside the "system.lt" file. -In the second example coordinates for the atoms are read from an XYZ-file, -and then invokes VMD to visualize the system just created. -(PDB-files and other coordinate formats are also supported. -Note: The "full" atom style was used in this example, but other -LAMMPS atom styles are supported, including hybrid styles.) - -Either of these commands will construct a LAMMPS data file and a -LAMMPS input script (and possibly one or more auxiliary input files), -which can be directly run in LAMMPS with minimal editing. - - -\subsection{Converting LAMMPS input/data files to \textit{LT files}} -Existing LAMMPS input/data files can be converted into - %lammps-template -``.LT'' files using the ``ltemplify.py'' utility. -(\textit{Some additional manual editing may be required. - See appendix \ref{sec:ltemplify}.}) - % Some manual editing of the resulting LT files may be required, - % especially when exotic or many-body pair\_styles are used.) - - -%\subsection*{Strengths} -%Moltemplate is especially useful for defining new, exotic -%coarse-grained molecular models natively from scratch. -%Molecules defined this way have access to (nearly) -%\textit{all} of the -% %extraordinary -% bewildering -%menu of features and force-fields -%available in LAMMPS. This includes custom LAMMPS features -%created by end-users (now and probably in the future). -% -% %The ``.LT'' file format is \textit{not} specific to LAMMPS and -% %can also be useful for generating other files which store molecular data. -% %LT files are text templates. -%LT files are very flexible and can mimic almost any text file format -%which uses simple numerical counters. -%End users can accommodate gradual changes in the LAMMPS input and data file -%formats by altering their own molecule templates -%as LAMMPS independently grows and evolves. - -%\subsection*{Limitations} -% %Little effort has yet been made to allow moltemplate.sh to read and write -% %simulation files from other programs. -%Moltemplate.sh was \textit{not} designed to work seamlessly with -%files from other simulation or visualization programs -%(although such functionality could be added). -%Moltemplate.sh does not provide a quick or convenient way to perform an -%all-atom simulation of proteins or nucleic-acids in an box of water -%(for example). -%Moltemplate has only limited support for generating molecular geometry -%and it does not have a graphical interface. -%For these tasks, external utilities are very helpful. - -\subsection*{Additional tools} -The VMD topotools plugin \cite{topotools} is useful for -converting PDB files into LAMMPS format. These files can then -be converted to ``LT'' format using the ``ltemplify.py'' utility. -VMD \cite{VMD} and topotools are also useful for visualizing -the data files created by moltemplate.sh -(See section \ref{sec:vmd_topotools}.) - %Documentation for doing this is included - %in the \textit{online examples} discussed below. - - %Pizza.py \cite{pizzapy}, has a utility for building 1-bead polymer melts. - -The PACKMOL \cite{packmol} program is useful for generating -coordinates of dense heterogeneous mixtures of molecules, -which can be read by moltemplate. -(The VMD ``solvate'' plugin may also be helpful.) - %There are many other utilities, - %graphical modeling programs, - %and numerous scripts (which are in various stages of maintenance) - %which may be useful for file format conversion, and - %pre-and-post processing and analysis. - %Many other tools exist (not covered here) which can convert file formats - %used by other molecular dynamics software programs into LAMMPS format. - -\subsection*{Examples} - - %When using ``moltemplate.sh'' it does not hurt to have - %a modest familiarity LAMMPS and it's file formats, - %because this mirrors the ``.LT'' file format described here. - -%This manual assumes users have some basic familiarity with LAMMPS. -%This manual explains in detail how to use moltemplate.sh to build LAMMPS -%files from scratch, -%but it does not discuss how to run LAMMPS -%or how to visualize the results. -%provides only a very brief overview -%of how to run simple simulations in LAMMPS -%(see sections \ref{sec:spce_example} and \ref{sec:run}), -%and it does not discuss how to visualize or analyze LAMMPS -%simulation trajectories. - - -This manual explains in detail how to use moltemplate.sh to build LAMMPS -files from scratch. -You will also need to learn how to \textit{run} -LAMMPS and visualize your results. -%(see sections \ref{sec:spce_example} and \ref{sec:run}), -%It is not a comprehensive reference for using LAMMPS. -%For users who are not familiar with LAMMPS, -Section \ref{sec:tutorial} contains a brief tutorial -which explains how to build a box of water using moltemplate and -visualize initial conformation, run LAMMPS, and then visualize the trajectory. -Several complete working examples (with images and readme files) -which can be downloaded and modified are available online at: -\url{http://moltemplate.org/visual_examples.html} -A more comprehensive list of examples is included in -the ``examples/'' subdirectory distributed with moltemplate. -%The official LAMMPS examples and user manual -%are also a valuable reference. -These examples are a good starting point for learning LAMMPS and moltemplate. - - -\subsection*{License} -Moltemplate.sh is publicly available at \url{http://moltemplate.org} -under the terms of the open-source 3-clause BSD license. -\url{http://www.opensource.org/licenses/BSD-3-Clause} - - - - - - - -% \subsubsection*{Using ``lttree.py'' instead of ``moltemplate.sh''} -% The format of an ``.LT'' file closely mimics the syntax in -% current LAMMPS data and input script files (as of early 2013). -% However LAMMPS file formats are constantly changing -% as users add their own custom features to LAMMPS. -% (In addition, there are some currently known limitations of -% moltemplate.sh, which are discussed in section \ref{sec:limitations}.) -% %However this file format must be flexible enough -% %to handle potentially radical syntax changes in the future. -% %End users who add new features to LAMMPS may also modify the syntax -% %of these input files, and will likely introduce new file formats. -% Consequently, we also provide several simple python scripts: -% %(which should remain useful when/if moltemplate.sh breaks) -% ``ttree.py'', ``lttree.py'', and ``nbody\_by\_type.py''. -% %\begin{list} -% %\item -% %``ttree.py'', is a general text manipulation -% %tool which prints out the text contained in the -% %``write()'' and ``write\_once()'', commands in an LT file, -% %and substitutes numerical values into the \$ and \@ variables -% %contained inside. -% %\item -% %``lttree.py'' is a variant of ``ttree.py'' -% % %understand LAMMPS atom\_style syntax and -% %which also generates atomic coordinates. -% %(It process the ``.move()'' and ``.rot()'' commands.) -% %\item -% %``nbody\_by\_type.py'' is a utility which generates -% %many-body bonded interactions between atoms automatically, -% %according to the atom and bond type. -% %(It processes the ``Data Angles By Type'', -% %``Data Dihedrals By Type'', and ``Data Impropers By Type'' sections.) -% %\end{list} -% The ``ttree.py'' program is a general text manipulation tool which -% should continue to work in the distant future, -% even if the LAMMPS syntax changes radically, and ``moltemplate.sh'' breaks. -% (``ttree.py'' is nearly identical to and supports all the -% command line options used by ``moltemplate.sh'', -% with the exception of ``-pdb'', ``-xyz'', and ``-raw''.) -% %However this tool is intentionally simple and ignorant about LAMMPS. -% %This allows programmers to add features to LAMMPS without ever -% %breaking the ``.LT'' file format. -% %(although you may have to sacrifice some convenience -% %that using moltemplate.sh provides). -% A tutorial for using these programs -% is provided in appendix \ref{sec:ttree}. - - - - -\section{Installation} -\label{sec:installation} - -There are two ways to install moltemplate: - -\subsubsection*{Installation Method 1 (pip)} - -\textit{If you are familiar with pip}, you can install -moltemplate by typing following command in the terminal/shell: - %from within outermost directory: -\begin{verbatim} -pip install moltemplate -\end{verbatim} -%\textit{In order for this to work, this directory should contain a file named ``\textbf{setup.py}''.} (If no such file exists, then either proceed to ``Installation Method 2'' below, or download a newer version of moltemplate.) -If you receive an error regarding permissions, then run pip this way instead: -\begin{verbatim} -pip install moltemplate --user -\end{verbatim} -Make sure that your default pip install bin directory is in your PATH. (This is usually something like \textapprox/.local/bin/ or \textapprox/anaconda3/bin/. If you have installed anaconda, your PATH should have been updated for you automatically.) Later, you can uninstall moltemplate using: -\begin{verbatim} -pip uninstall moltemplate -\end{verbatim} - -\textit{Note: There are is a large variety of detailed moltemplate examples -which will be omitted if you install moltemplate this way. -\textbf{Downloading the examples is strongly recommended.}} -You can do this either by using git: -\begin{verbatim} -git clone https://github.com/jewettaij/moltemplate ~/moltemplate -\end{verbatim} -or by visiting the \url{http://www.moltemplate.org} web site. -They will be in the ``examples'' subdirectory.) - -\textit{If you run into difficulty with pip}, then try installing -moltemplate into a temporary virtual environment -by installing ``virtualenv'', -%downloading moltemplate (to ``\textapprox/moltemplate'' in the example below), -and running these commands: -\begin{verbatim} -mkdir ~/moltemplate_v -cd ~/moltemplate_v -virtualenv venv -source venv/bin/activate -pip install moltemplate - #(now do something useful with moltemplate...) -\end{verbatim} -You will have to ``run source \textapprox/moltemplate\_v/venv/bin/activate'' beforehand whenver you want to run moltemplate again. If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable. Instructions for doing that are included below. - - -\subsubsection*{Installation Method 2} - -Alternatively, you can download the moltemplate files and edit your -PATH variable manually to include -the subdirectory where the moltemplate.sh script is located -(typically ``\textapprox/moltemplate/moltemplate/scripts/''), as well as -the directory containing the most of the python scripts -(``\textapprox/moltemplate/moltemplate/''). - -\subsection*{Obtaining Moltemplate} -The most up-to-date version of moltemplate can be downloaded using git. -\begin{verbatim} -git clone https://github.com/jewettaij/moltemplate ~/moltemplate -\end{verbatim} -Later, you can update to the latest version of moltemplate using: -\begin{verbatim} -git pull -\end{verbatim} -Alternatively, you can also download moltemplate as a .tar.gz archive from -\url{http://www.moltemplate.org} -and can unpack it using: -\begin{verbatim} -tar -xzvf moltemplate_2017-8-22.tar.gz -\end{verbatim} -(The date will vary from version to version.) -Somewhat older versions of moltemplate are also bundled with the LAMMPS -source code and are located in the \textit{``tools''} subdirectory. - - -If you use the \textbf{bash} shell, typically you would edit your -\mbox{$\sim$/.bash\_profile}, -\mbox{$\sim$/.bashrc}, or -\mbox{$\sim$/.profile} files -and append the following lines: -\begin{verbatim} -export PATH="$PATH:$HOME/moltemplate/moltemplate" -export PATH="$PATH:$HOME/moltemplate/moltemplate/scripts" -\end{verbatim} -If instead you use the \textbf{tcsh} shell, typically you would edit your -\mbox{$\sim$/.login}, -\mbox{$\sim$/.cshrc}, or -\mbox{$\sim$/.tcshrc} files -and append the following lines: -\begin{verbatim} -setenv PATH "$PATH:$HOME/moltemplate/moltemplate" -setenv PATH "$PATH:$HOME/moltemplate/moltemplate/scripts" -\end{verbatim} - - - -\textit{Note: You may need to log out and then -log back in again for the changes to take effect.} - - -\subsubsection*{WINDOWS installation suggestions} - -You can install both moltemplate and LAMMPS in windows, but you will first need to install the BASH shell environment on your computer. If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)" -\url{https://solarianprogrammer.com/2017/04/15/install-wsl-windows-subsystem-for-linux/} -For more details, see the WSL FAQ: -\url{https://msdn.microsoft.com/en-us/commandline/wsl/faq} -If you are using an older version of windows, try following the tutorial written by Yanqing Fu instead: -\url{https://sourceforge.net/p/lammps/mailman/message/32599824/} - -To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor. (Word, Wordpad, and Notepad will not work.) Popular free text editors which you can safely install and run from within the WSL terminal include: nano, ne, emacs, vim, and jove. (Unfortunately, as of 2017-5-17, graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption. Avoid these editors for now. (\url{https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/}) - - -\pagebreak -\section{Quick reference \textit{(skip on first reading)}} - -\section*{ -\textit{Note: New users should skip to section \ref{sec:tutorial}} -} - - -\subsection{Moltemplate commands} - -%\begin{table} -\begin{longtable}[h]{l|p{9cm}} -\textbf{command} & \textbf{meaning} -\\ -\hline -\hline -\begin{tabular}[t]{l} -\\ -\textit{MolType} \textbf{\{} \\ -\\ -\hspace{0.35cm} \textit{content} ... \\ -\\ -\textbf{\}} \\ -\end{tabular} -& -Define a new type of molecule (or namespace) named \textit{MolType}. -The text enclosed in curly brackets (\textit{content}) -typically contains multiple write(), write\_once() -commands to define Atoms, Bonds, Angles, Coeffs, etc... -\textit{(If that molecule type exists already, -then this will append additional \textbf{content} to its definition.)} -\textbf{new} and \textbf{delete} commands can be used -to create or delete molecular subunits \textit{within} this molecule. -(See the \textit{SPCE}, \textit{Monomer}, and \textit{Butane} - molecules, and the \textit{TraPPE} namespace - defined in sections \ref{sec:spce_example}, \ref{sec:2bead}, - \ref{sec:inheritance}, \& \ref{sec:trappe}. -\\ -\hline -\textit{mol\_name} = \textbf{new} \textit{MolType} & -Create (instantiate) a copy of a molecule of type \textit{MolType} -and name it \textit{mol\_name}. -(See section \ref{sec:spce_example}.) -\\ -\hline -\textit{mol\_name} = \textbf{new} \textit{MolType}.\textit{xform()} & -Create a copy of a molecule and -apply coordinate transformation \textit{xform()} to its coordinates. -(See sections \ref{sec:coords_intro} and \ref{sec:xforms_table}.) -\\ -\hline -\textit{molecules} = - \textbf{new} \textit{MolType} [\textit{N}].\textit{xform()}& -Create \textit{N} copies of a molecule of type \textit{MolType} -and name them -\textit{molecules[0]}, \textit{molecules[1]}, \textit{molecules[2]}... -Coordinates in each successive copy are cumulatively transformed -according to \textit{xform()}. -(See sections \ref{sec:coords_intro}, \ref{sec:arrays+xform} -and \ref{sec:xforms_table}.) -Multidimensional arrays are also allowed. -(See section \ref{sec:multidimensional_arrays}.) -\\ -\hline -\begin{tabular}[t]{l} -\textit{molecules} = \textbf{new} \textit{MolType.xform1()} -\\ -\hspace{3.7cm} \textbf{[\textit{N}]}.\textit{xform2()} -\\ -\end{tabular} -& -Apply coordinate transformations (\mbox{\textit{xform1()}} -to \mbox{\textit{MolType}}, before making \textit{N} copies -of it while cumulatively applying \mbox{\textit{xform2()}}. -(See section \ref{sec:xform+arrays+xform} and \ref{sec:xform_order}.) -\\ -\hline -\begin{tabular}[t]{l} -\textit{molecules} = \textbf{new} -\\ - \hspace{0.6cm} \textbf{random}([\textit{M1.xf1()}, -\\ - \hspace{2.3cm} \textit{M2.xf2()}, -\\ - \hspace{2.3cm} \textit{M3.xf2()},...], -\\ - \hspace{2.25cm} [$p_1$, $p_2$, $p_3$,...], -\\ - \hspace{2.25cm} \textit{seed}) -\\ - \hspace{0.6cm} \textbf{[\textit{N}]}.\textit{xform()} -\end{tabular} -& -Generate an array of \textit{N} molecules randomly selected from -\mbox{\textit{M1,M2,M3,...}} -with probabilities \mbox{$p_1, p_2, p_3$...}, -using (optional) initial coordinate transformations -\textit{xf1(), xf2(), xf3, ...}, and applying transformation \textit{xform()} -cumulatively thereafter. -This also works with multidimensional arrays. -\textbf{You can directly specify the number of each type of molecule} -by replacing the list of probabilities \mbox{$[p_1, p_2, p_3\ldots]$}, -with a list of integers \mbox{$[n_1, n_2, n_3\ldots]$}. -(See sections \ref{sec:random_arrays} and \ref{sec:random_advanced}.) -\\ -\hline -\textit{NewMol} = \textit{OldMol} & -Create a new molecule \textbf{type} based on an existing molecule type. -Additional atoms (or bonds, etc...) can be added later to the new molecule -using \mbox{NewMol \{\textit{more\ content}...\}}. -(See section \ref{sec:molecule_customization}.) -\\ -\hline -\textit{NewMol} = \textit{OldMol}.\textit{xform()} -& -Create a new molecule \textbf{type} based on an existing molecule type, -and apply coordinate transformation \textit{xform()} to it. -(See section \ref{sec:molecule_customization}.) - % \textit{This feature is experimental as of 2012-9-28}.) -\\ -\hline - %\textit{NewMol} \textbf{inherits} \textit{Mol1} \textit{Mol2} \mbox{\{...\}} & -\begin{tabular}[t]{l} -\textit{NewMol} \textbf{inherits} \textit{Mol1} \textit{Mol2} ... \{ \\ -\\ -\hspace{0.35cm} \textit{additional content} ... \\ -\\ -\} \\ -\end{tabular} -& -Create a new molecule \textbf{type} based on multiple existing molecule types. -Atom types, bond types, angle types (etc) which are defined in -\textit{Mol1}, or \textit{Mol2}, ... are available inside the -new molecule. -\textit{Additional content} -(including more \textit{write()} or \textit{write\_once()} -or \textit{new} commands) -follows within the curly brackets. -(See sections \ref{sec:inheritance_intro}, -\ref{sec:inheritance}, and \ref{sec:multiple_inheritance}) -\\ -\hline -\textit{MolType}.\textit{xform()} -& -Apply the coordinate transform \textit{xform()} to the coordinates -of the atoms in all molecules of type \textit{MolType}. -(See section \ref{sec:molecule_customization}.) - % \textit{This feature is experimental as of 2012-9-28}.) -\\ -\hline -\textit{molecule}.\textit{xform()} -& -Apply the coordinate transform \textit{xform()} -to the coordinates in \textit{molecule}. -(Here \textit{molecule} refers to a specific instance or copy of - a particular molecule type. -See sections \ref{sec:custom_xform} and \ref{sec:coords_intro}.) -\\ -\hline -\textit{molecules}[\textit{range}].\textit{xform()} -& -Apply the coordinate transform \textit{xform()} -to the coordinates of molecules specified by -\mbox{\textit{molecule}[\textit{range}]}. -(This also works for multidimensional arrays. -See sections \ref{sec:array_wildcards_intro} and \ref{sec:custom_xform}.) -\\ -\hline -\textbf{delete} \textit{molecule} -& -Delete the \textit{molecule} instance. -(This command can appear inside a molecule's definition - to delete a specific molecular subunit within a molecule. In that case, - it will be carried out in every copy of that molecule type. - \textbf{delete} can also be used to delete specific - atoms, bonds, angles, dihedrals, and improper interactions.) -See section \ref{sec:delete}. -\\ -\hline -\textbf{delete} \textit{molecules}[\textit{range}] -& -Delete a range of molecules specified by -\mbox{\textit{molecule}[\textit{range}]}. -(This also works for multidimensional arrays. - See sections \ref{sec:delete} and \ref{sec:delete_holes}.) -\\ -\hline - %\mbox{write\_once}('\textit{file}') \mbox{$\{$\textit{text}\ldots$\}$} & -\begin{tabular}[t]{l} -\textbf{write\_once}('\textit{file}') \{ \\ -\hspace{0.35cm} \textit{text} ... \\ -\} \\ -\end{tabular} & -Write the text enclosed in curly brackets \mbox{$\{\ldots\}$} -to file \mbox{$file$}. -The \textit{text} can contain @variables which are replaced by integers. -(See sections \ref{sec:write} and \ref{sec:variables}.) -\\ -\hline - %\textit{write}('file') \mbox{$\{text\ldots{}\}$} & -\begin{tabular}[t]{l} -\textbf{write}('\textit{file}') $\{$ \\ -\hspace{0.35cm} \textit{text} ... \\ -$\}$ \\ -\end{tabular} & -Write the text enclosed in curly brackets \mbox{$\{\ldots\}$} -to file \textit{file}. -\textit{This is done every time a new copy of this molecule is -created using the ``new'' command.} -The \textit{text} can contain either @variables or \$variables -which will be replaced by integers. -(See sections \ref{sec:write} and \ref{sec:variables}.) -\\ -\hline -\multicolumn{2}{p{16.5cm}} { -Note: \textit{file} names beginning with ``Data '' or ``In '' -(such as ``Data Atoms'' or ``In Settings'') are inserted -into the relevant section of the LAMMPS data file or input script. -(See section \ref{sec:DataIn}.) -} -\\ -\hline -\textbf{include} \textit{file} -& -Insert the contents of file \textit{file} here. (Quotes optional.) -\\ -\hline -\textbf{import} \textit{file} -& -Insert the contents of file \textit{file} here, -preventing circular inclusions. -\textit{(recommended)} -\\ -\hline -\textbf{using namespace} \textit{X} -& -This enables you to refer to any of the molecule types, -defined within a \textbf{namespace} object (\textit{X} in this example), -\textit{without} needing to refer to these objects by their full path. - %(Unfortunately, atom types, or bond, angle, dihedral, or improper types - %must still be referred to explicitly, by their full path.) - %%(``Namespace objects'' are moltemplate objects containing - %% only molecule definitions.) -(This does not work for atom types. -See section \ref{sec:using_namespaces}.) -\\ -\hline -\begin{tabular}[t]{l} -\textbf{category} \textit{\$catname}($i_0$, $\Delta$) -\\ -or \\ -\textbf{category} \textit{@catname}($i_0$, $\Delta$) -\\ -\end{tabular} -& -Create a new variable category. -See section \ref{sec:custom_categories} for details. - %(Note: The round parenthesis containing the starting value, $i_0$, - % and the counter increment, $\Delta$, can be omitted.) -\\ -\hline -create\_var \{ \textit{variable} \} & -Create a variable specific to this molecule object. -(Typically this is used to create molecule-ID numbers, -for a molecule built from smaller components. -See section \ref{sec:2beadPolymer}.) -\\ -\hline -replace \{ \textit{oldvariable} \textit{newvariable} \} & -Allow alternate names for the same variable. This replaces all instances of \textit{oldvariable} with \textit{newvariable}. Both variable names must have a ``@'' prefix. This is typically used to reduce the length of long variables, for example to allow the shorthand ``@atom:C2'' to refer to ``@atom:C2\_bC2\_aC\_dC\_iC'' -\\ -\hline - \textbf{\#}\textit{commented text} & -All text following a ``\#'' character is treated as a comment and ignored. -\end{longtable} - -%\caption{List of moltemplate commands} -%\label{tab:commands} -%\end{table} - - - -%\pagebreak -\subsection{Common \$ and @ variables} - -(See section \ref{sec:variables} for details.) \\ -\begin{tabular}[h]{l|p{11cm}} -\textbf{variable type} & \textbf{meaning} -\\ -\hline -\hline -\$atom:\textit{name} & -A unique ID number assigned to atom \textit{name} in this molecule. -(Note: The \textit{:name} suffix can be omitted if the molecule -in which this variable appears only contains a single atom.) -%(This number is unique even if there are multiple copies of this molecule.) -\\ -\hline -@atom:\textit{type} & -A number which indicates an atom's \textit{type} - (typically used to lookup pair interactions.) -\\ -\hline -\$bond:\textit{name} & -A unique ID number assigned to bond \textit{name} -(Note: The \textit{:name} suffix can be omitted if the molecule -in which this variable appears only contains a single bond.) -\\ -\hline -@bond:\textit{type} & -A number which indicates a bond's \textit{type} -\\ -\hline -\$angle:\textit{name} & -A unique ID number assigned to angle \textit{name} -(Note: The \textit{:name} suffix can be omitted if the molecule -in which this variable appears only contains a single angle interaction.) -\\ -\hline -@angle:\textit{type} & -A number which indicates an angle's \textit{type} -\\ -\hline -\$dihedral:\textit{name} & -A unique ID number assigned to dihedral \textit{name} -(Note: The \textit{:name} suffix can be omitted if the molecule in which -this variable appears only contains a single dihedral-angle interaction.) -\\ -\hline -@dihedral:\textit{type} & -A number which indicates a dihedral's \textit{type} -\\ -\hline -\$improper:\textit{name} & -A unique ID number assigned to improper \textit{name} -(Note: The \textit{:name} suffix can be omitted if the molecule in which -this variable appears only contains a single improper interaction.) -\\ -\hline -@improper:\textit{type} & -A number which indicates an improper's \textit{type} -\\ -\hline -\$\textit{mol} \hspace{0.2cm} or \hspace{0.2cm} \$\textit{mol:.} & -This variable refers to the ID number of \textit{this} molecule object. -(See section \ref{sec:spce_example}. -Note: \mbox{\textit{``\$mol''}} is shorthand for \mbox{\textit{``\$mol:.''}}) -\\ -\hline -\$\textit{mol:}... & -The ID number assigned to the molecule to which this object belongs -(if applicable). -See sections \ref{sec:2beadPolymer}, -\ref{sec:ellipsis_mol}, -%\ref{sec:paths}, -and appendix \ref{sec:adv_variable_syntax}. -\\ -\hline -\hline -\multicolumn{2}{p{16.5cm}} { -%Variable operations -\textit{The numbers assigned to each variable are saved in the \textbf{output\_ttree/ttree\_assignments.txt} file} -%See section \ref{sec:output_ttree}. -} -\\ -\hline -\hline -\multicolumn{2}{l} { -%Variable operations -\quad \textit{\textbf{Advanced variable usage}} -} -\\ -\hline -\textit{\$category}:\textbf{query}() -& -Query the current value of the counter in this \textit{\$category} -without incrementing it. -(The ``\textit{\$category}'' is usually either \textit{\$atom}, \textit{\$bond}, \textit{\$angle}, \textit{\$dihedral}, \textit{\$improper}, or \textit{\$mol}.) -This is useful for counting the number of -atoms, bonds, angles, molecules, etc... created so far. -\\ -\hline -\textit{@category}:\textbf{query}() -& -Query the current value of the counter in this \textit{@category} -without incrementing it. -(The ``\textit{@category}'' is usually either \textit{@atom}, \textit{@bond}, \textit{@angle}, \textit{@dihedral}, or \textit{@improper}.) -This is useful for counting the number of -atom types, bond types, angle types, etc... declared so far.) -\\ -\hline -\begin{tabular}[t]{l} -\textit{@\textbf{\{}category:variable\textbf{\}}} \ or \\ -\textit{\$\textbf{\{}category:variable\textbf{\}}} \\ -\end{tabular} -& -%Counter variables in a template need not be separated by whitespace, -%%and variable names may also contain spaces and other non-standard characters. -%In these cases, variables can be enclosed -%in curly-brackets \textit{\textbf{\{\}}}. -Curly-brackets, \textit{\textbf{\{\}}}, are used to refer to variables -with non-standard delimiters or whitespace characters. -(See section \ref{sec:vardetails}.) -\\ -\hline -\begin{tabular}[t]{l} -@\{category:\textit{type}.rjust(n)\} \ or \\ -@\{category:\textit{type}.ljust(n)\} \ or \\ -\$\{category:\textit{name}.rjust(n)\} \ or \\ -\$\{category:\textit{name}.ljust(n)\} -\end{tabular} -& -Print the counter variable in a right-justified or a left-justified text-field -of fixed width $n$ characters. -(This is useful for generating text files which require fixed-width columns.) -\\ -\hline -\end{tabular} - -%\vspace{0.5cm} - - - - - -\subsection{Coordinate transformations} -\label{sec:xforms_table} - -(See sections \ref{sec:coords_intro}) and \ref{sec:arrays+xform}) for details.) -\\ -\\ -%\begin{table} -\begin{tabular}[h]{l|p{10cm}} -\textbf{suffix} & \textbf{meaning} -\\ -\hline -\hline -\textit{.move(x,y,z)} & - Add numbers \mbox{\textit{(x,y,z)}} to the coordinates of every atom -\\ -\hline - \textit{.rot($\theta,x,y,z$)} & - Rotate atom coordinates - by angle $\theta$ around axis \mbox{\textit{(x,y,z)}} - passing through the origin. - (Dipole directions are also rotated.) -\\ -\hline -\textit{.rot($\theta,x,y,z,x_0,y_0,z_0$)} & - Rotate atom coordinates - by angle $\theta$ around axis pointing in the direction - \mbox{\textit{(x,y,z)}}, - passing through the point \mbox{$(x_0,y_0,z_0)$}. - (This point will be a \textit{fixed point}.) -\\ -\hline - \textit{.rotvv($v_{1x},v_{1y},v_{1z},v_{2x},v_{2y},v_{2z}$)} & - Rotate atom coordinates - with an angle which rotates the vector $\mathbf{v}_1$ to $\mathbf{v}_2$ - (around an axis perpendicular to both $\mathbf{v}_1$ and $\mathbf{v}_2$). - %$(v_{1x},v_{1y},v_{1z})$ to $(v_{2x},v_{2y},v_{2z})$ - If you supply 3 additional numbers $x_0,y_0,z_0$, the axis of rotation - will pass through this location. -\\ -\hline -\textit{.scale(ratio)} & -Multiply all atomic coordinates by \textit{ratio}. -\textit{(\textbf{Important:} The scale() command does not update force-field -parameters such as atomic radii or bond-lengths. Dipole magnitudes are affected.)} -\\ -\hline -\textit{.scale($x_r,y_r,z_r$)} & -Multiply \mbox{\textit{x, y, z}} coordinates by -\mbox{$x_r, y_r, z_r$}, respectively -\\ -\hline -\begin{tabular}[t]{l} -\textit{.scale(ratio,$x_0,y_0,z_0$)} \ or \\ -\textit{.scale($x_r,y_r,z_r,x_0,y_0,z_0$)} \\ -\end{tabular} -& -You can supply 3 optional additional arguments -\mbox{$x_0,y_0,z_0$} which specify the point around which -you want the scaling to occur. -(This point will be a \textit{fixed point}. - Of omitted, the origin is used.) -\\ -\hline -\begin{tabular}[t]{l} - \textit{.quat($a,b,c,d$)} \\ - \textit{.quat($a,b,c,d,x_0,y_0,z_0$)} \\ - \textit{.quatT($a,b,c,d$)} \\ - \textit{.quatT($a,b,c,d,x_0,y_0,z_0$)} \\ -\end{tabular} - & - Rotate atom coordinates by the rotation corresponding - to quaternion $a+b\mathbf{i}+c\mathbf{j}+b\mathbf{k}$ - (around \mbox{$(x_0,y_0,z_0)$}, if specified) - The \textit{.quatT(a,b,c,d)} variant performs the inverse rotation. - (Equivalent to \textit{.quat(a,-b,-c,-d)}.) - % Otherwise around $(0,0,0)$) -\\ -\hline -\multicolumn{2}{c} { -\textbf{ -\textit{Note:} -Multiple transformations can be chained together into a compound operation.} -} -\\ -\multicolumn{2}{c} { -(For example: \mbox{``$.scale(2.0).rotate(45.2,1,0,0).move(25.0,0,0)$''}) -} -\\ -\multicolumn{2}{c} { -These are evaluated from left-to-right. -(See section \ref{sec:arrays+xform}.) -} -\\ -\hline -\begin{tabular}[t]{l} - \\ -\textit{push}(rot(152.3,0.79,0.43,-0.52)) \\ -% \textit{push}(move(0.0,34.1,-8.7)) \\ -monomer1 = new Monomer \\ -% pop() -% \textit{push}(rotvv(-0.01,0.96,-0.3,0,0.2,-0.98)) \\ -\textit{push}(move(0.01,35.3,-10.1)) \\ -monomer2 = new Monomer \\ -% \textit{pop } \\ -\textit{pop}() \\ -\textit{pop}() \\ -\end{tabular} -& -Coordinate transformations introduced using the \textit{push()} command are applied to molecules instantiated later (using the \textit{new}) command, and remain in effect until they are removed using the \textit{pop()} command. (And transformations appearing in arrays accumulate as well, but do not need to be removed with \textit{pop()}.) -%The \textit{push()} and \textit{pop()} commands allow the user to control exactly how coordinate transformations accumulate. The \textit{pop()} command undoes the transformations introduced in the most recent \textit{push()} command. -In this example, the first transformation, ``rot()'', is applied to both ``monomer1'' and ``monomer2''. The last transformation, ``move()'', is applied after ``rot()'' and only acts on ``monomer2''. -\\ -\hline -\end{tabular} -%\caption{Coordinate Transformation Commands} -%\label{tab:transformation_commands} -%\end{table} - - - - -\subsection{moltemplate.sh command line arguments:} -\label{sec:args_table} -%\begin{table} -\begin{tabular}[h]{l|p{10cm}} -\textbf{argument} & \textbf{meaning} -\\ -\hline -\hline --atomstyle \textit{style} -& -Inform moltemplate which atom\_style you are using. -(\textit{style} is "full" by default). -Other styles like "molecular" or "hybrid full dipole" are supported. -For custom atom styles, you can also specify the list of column -names manually. For example: -\textbf{-atomstyle "molid x y z atomid atomtype mux muy muz"} -Atom styles should be enclosed in quotes ("). -\\ -\hline --raw coords.raw -& -Read all of the atomic coordinates from an external RAW file. -(RAW files are simple 3-column ASCII files contain X Y Z coordinates - for every atom, separated by spaces.) -\\ -\hline --xyz coords.xyz -& -Read all of the atomic coordinates from an external XYZ file -(XYZ files are 4-column ascii files in ATOMTYPE X Y Z format. - The first column, ATOMTYPE, is skipped. - The first line should contain the number of atoms. - The second line is skipped. See section \ref{sec:coords_intro}.) -\\ -\hline --pdb coords.pdb -& -Read all of the atomic coordinates from an external PDB file -(Periodic boundary conditions are also read, if present. - Atoms are sorted by the chainID, resID, insertCode, and atomID - fields on every line beginning with ``ATOM'' or ``HETATM''. - This order must match the order that the atoms appear in the data file. - See section \ref{sec:coords_intro}.) -\\ -\hline --a '\textit{variable} \textit{value}' -& -Assign \textit{variable} to \textit{value}. -(The \textit{variable} should begin with either a @ character - or a \$ character. - Single-quotes and a space separator are required. - See appendix \ref{sec:manual_assignment}.) -\\ -\hline --a bindings\_file' -& -The variables in column 1 of -\textit{bindings\_file} -(which is a text file) -will be assigned to -the values in column 2 of that file. -(This is useful when there are many variable assignments to make. -See appendix \ref{sec:manual_assignment}.) -% \$-variables should \textit{not} be preceded by \textbackslash\ in this case.) -\\ -\hline -\begin{tabular}[t]{l} --b '\textit{variable} \textit{value}' -\\ -\hspace{0.35cm} \textit{or} \\ --b \textit{bindings\_file} -\\ -\end{tabular} -& -Assign variables to values. -Unlike assignments made with ``-a'', -assignments made using ``-b'' -are non-exclusive. -(They may overlap with other variables in the same category. - See appendix \ref{sec:manual_assignment}.) -\\ -\hline - -\begin{tabular}[t]{l} --overlay-bonds -\\ --overlay-angles -\\ --overlay-dihedrals -\\ --overlay-impropers -\\ -\end{tabular} -& -By default moltemplate overwrites -duplicate bonded interactions which -involve the same set of atoms. -These flags disable that behavior. -This can be useful when you want to superimpose -multiple angular or dihedral forces on the same set of atoms -(eg. to enable more complex force fields). -\\ -\hline --nocheck & -Do \textit{not} check for common LAMMPS/moltemplate syntax errors. -(This might be useful when using moltemplate - with simulation software other than LAMMPS, - \textit{or} to build systems which need new non-standard LAMMPS features.) -\\ -\hline --checkff & -This forces moltemplate.sh to check that there -are valid angle and dihedral interactions defined for every -3 or 4 consecutively bonded atoms in the system -(defined in ``Data Angles By Type'' and ``Data Dihedrals By Type'' sections). -\\ -\hline --vmd & -Invoke VMD after running moltemplate to view the system you have just created. -(VMD must be installed. - %This feature uses Axel Kohlmeyer's topotools plugin. - See sections \ref{sec:vmd_topotools}, \ref{sec:vmd_advanced} for details.) -\\ -\hline -%-import-path LOCATION -%& -%When a user imports an .LT file, moltemplate first looks in the directory -%where it was run, and then in the ``force\_fields'' subdirectory in the -%moltemplate installation. Additional directories can be appended using -%this command. (Multiple directories must be separated by ':' characters) -%This allows moltemplate to look for .LT files -%in other directories when using ``import''. -%(Multiple directories must be separated by ':' characters.) -%\\ -%\hline -\end{tabular} - -\begin{tabular}[h]{l|p{10cm}} -\hline -\begin{tabular}[t]{l} --dihedral-sym file.py -\\ --improper-sym file.py -\\ --bond-symmetry file.py -\\ --angle-symmetry file.py -\\ -\end{tabular} -& -Normally moltemplate.sh reorders the atoms in each bond, angle, dihedral, and improper interaction before writing them to the DATA file in order to help avoid duplicate interactions between the same atoms if listed in different but equivalent orders. Sometimes this is undesirable. \textit{\textbf{To disable this behavior, set ``file.py'' to ``None''.}} You can also manually choose alternate symmetry rules for unusual force fields. (Such as class2 force fields, dihedral\_style spherical, etc... For an example of the file format for ``file.py'', see the ``nbody\_Impropers.py'' file.) -\\ -\hline --allow-wildcards & -Allow the use of ``*'' and ``?'' characters within -``pair\_coeff'', ``bond\_coeff'', ``angle\_coeff'', ``dihedral\_coeff'', -and ``improper\_coeff'' commands. (Default) -\\ -\hline -\end{tabular} - - -\pagebreak - - - - -\section{Introductory tutorial} -\label{sec:tutorial} -\subsection*{\textit{Summary}} -\textit{Moltemplate is based on a very simple text generator (wrapper) which -repetitively copies short text fragments into one (or more) files -and keeps track of various kinds of counters.} - -LAMMPS is a powerful but complex program with many contributors. -Moltemplate is a front-end for LAMMPS. -Moltemplate users will have to tackle the same steep learning-curve -(and occasional bugs) that other LAMMPS users must face. - %Moltemplate is (intentionally) ignorant about LAMMPS - %and molecular dynamics in general. - %Gradually other features have been added to moltemplate.sh which make - %it somewhat more convenient for generating LAMMPS simulation files. -Moltemplate files (LT files) share the same file format and -syntax structure as LAMMPS DATA files and INPUT scripts. -%Moltemplate can understand some simple LAMMPS commands, -%and it will attempt to correct user mistakes. -Moltemplate will attempt to correct user mistakes, -however users must still learn -LAMMPS syntax and write LT files which obey it. -For users who are new to LAMMPS, the easiest way -to do this is to modify an existing example -(such as the water box example in this section). -(The official LAMMPS documentation -\url{http://lammps.sandia.gov/doc/Manual.html} -is an excellent reference to look up LAMMPS commands -you see in these examples that you are not familiar with.) - -%In addition to the examples here, there are more complex examples -%distributed with the moltemplate source code.} - - -\subsection{Simulating a box of water using moltemplate and LAMMPS} -\label{sec:spce_example} - -\begin{figure}[htbp] -\centering -\includegraphics[width=2.4cm]{single_water_LR.jpg} -\caption{ -\label{fig:single_water} -Coordinates of a single water molecule in our example. -(Atomic radii not to scale.) -} -\end{figure} - - Here we show an example of a lammps-template file for water. - %``.lt'' files can store topology and force-field settings in raw LAMMPS format. -(The settings shown here are borrowed from the simple-point-charge - \cite{Berendsen++StraatsmaJPhysChem1987} SPC/E model.) - %and can be overridden or modified by - %combining this LT file with other LT files.) -In addition to coordinates, topology and force-field settings, -``LT'' files can optionally include any other kind of LAMMPS settings -including SHAKE constraints, k-space settings, and even group definitions. - %\pagebreak -\begin{verbatim} -# (NOTE: Text following '#' characters are comments) -# -# file "spce_simple.lt" -# -# H1 H2 -# \ / -# O -# - -SPCE { - - ## Atom properties and molecular topology go in the various "Data ..." sections - - # We selected "atom_style full". That means we use this column format: - # atomID molID atomType charge coordX coordY coordZ - - write("Data Atoms") { - $atom:o $mol:. @atom:O -0.8476 0.0000000 0.000000 0.00000 - $atom:h1 $mol:. @atom:H 0.4238 0.8164904 0.5773590 0.00000 - $atom:h2 $mol:. @atom:H 0.4238 -0.8164904 0.5773590 0.00000 - } - - # Variables beginning with $ or @ will be replaced by numbers LAMMPS will - # eventually read. Each of the three atoms" will be assigned unique - # atomIDs (denoted here by "$atom:o", "$atom:h1", "$atom:h2"), even if - # they belong to different molecules. However, the atom types - # (denoted "@atom:O", "@atom:H") are shared for atoms in all molecules. - # All 3 atoms share same molID number (represeted here by "$mol:.") - # however that number is different for different water molecules. - - write_once("Data Masses") { - # atomType mass - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - # bondID bondType atomID1 atomID2 - $bond:oh1 @bond:OH $atom:o $atom:h1 - $bond:oh2 @bond:OH $atom:o $atom:h2 - } - - write("Data Angles") { - # angleID angleType atomID1 atomID2 atomID3 - $angle:hoh @angle:HOH $atom:h1 $atom:o $atom:h2 - } - - # --- Force-field parameters go in the "In Settings" section: --- - - write_once("In Settings") { - # -- Non-bonded (Pair) interactions -- - # atomType1 atomType2 parameter-list (epsilon, sigma) - pair_coeff @atom:O @atom:O 0.1553 3.166 - pair_coeff @atom:H @atom:H 0.0 2.058 - # (mixing rules determine interactions between types @atom:O and @atom:H) - - # -- Bonded interactions -- - # bondType parameter list (k_bond, r0) - bond_coeff @bond:OH 1000.00 1.0 - # angleType parameter-list (k_theta, theta0) - angle_coeff @angle:HOH 1000.0 109.47 - - # Group definitions and constraints can also go in the "In Settings" section - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (lammps quirk: Remember to "unfix fSHAKE" during minimization.) - } - - # LAMMPS supports a large number of force-field styles. We must select - # which ones we need. This information belongs in the "In Init" section. - - write_once("In Init") { - units real # angstroms, kCal/mole, Daltons, Kelvin - atom_style full # select column format for Atoms section - pair_style lj/charmm/coul/long 9.0 10.0 10 # params needed: epsilon sigma - bond_style harmonic # parameters needed: k_bond, r0 - angle_style harmonic # parameters needed: k_theta, theta0 - kspace_style pppm 0.0001 # long-range electrostatics sum method - pair_modify mix arithmetic # using Lorenz-Berthelot mixing rules - } - -} # SPCE -\end{verbatim} -Words which are preceded by ``\$'' or ``@'' characters -are counter variables and will be replaced by integers. -(See section \ref{sec:variables} for details.) -Users can include SPCE water in their simulations using commands like these: -\begin{verbatim} -# -- file "system.lt" -- -import "spce_simple.lt" -wat = new SPCE [1000] -\end{verbatim} -You can now use ``moltemplate.sh'' to create simulation input files for LAMMPS -\begin{verbatim} -moltemplate.sh -pdb coords.pdb -atomstyle "full" system.lt -\end{verbatim} -This command will create lammps input files -for the molecular system described in ``system.lt'', -using the desired atom style (``full'' by default). -In this example, moltemplate is relying on an external file (``coords.pdb'') -to supply the atomic coordinates of the water molecules, as well as -the periodic boundary conditions. -Coordinates in XYZ format are also supported using ``-xyz coords.xyz''. - -\subsubsection*{\textit{Details}} -\textit{Note that since XYZ files lack boundary information, you must also - include a ``Boundary'' section in your ``.lt'' file, as demonstrated - in section \ref{sec:pbc}. - In both cases, the order of the atom types in a PDB or XYZ file - (after sorting) should match the order they are created by moltemplate - (which is determined by the order of the ``new'' commands - in the LT file). - Unfortunately this may require careful manual editing of the PDB or XYZ file.} - %(See appendix \ref{sec:order_customization} for instructions - % how to customize the order of moltemplate counting). - -\subsection{Coordinate generation} -\label{sec:coords_intro} -It is not necessary to provide a separate file with atomic coordinates. -It is more common to manually specify the location -(and orientation) of the molecules in your system using the - ``.move()'' and ``.rot()'' commands %for rigid-body movement -in the LT file itself -(discussed in section \ref{sec:coordinates}). -For example you can replace the line: -\begin{verbatim} -wat = new SPCE [1000] -\end{verbatim} -from the example above with 1000 lines: -\begin{verbatim} -wat1 = new SPCE -wat2 = new SPCE.move(3.450, 0.0, 0.0) -wat3 = new SPCE.move(6.900, 0.0, 0.0) -wat4 = new SPCE.move(10.35, 0.0, 0.0) - : : -wat1000 = new SPCE.move(34.50, 34.50, 34.50) -\end{verbatim} -Specifying geometry this way is tedious. -Alternatively, moltemplate has simple commands for arranging multiple -copies of a molecule in periodic, crystalline, toroidal, and helical -1-D, 2-D, and 3-D lattices. -For example, you can generate a simple cubic lattice of -10$\times$10$\times$10 water molecules -(with a 3.45 Angstrom spacing) -using a single command -(which in this example we split into multiple lines) -\begin{verbatim} -wat = new SPCE [10].move(0,0,3.45) - [10].move(0,3.45,0) - [10].move(3.45,0,0) -\end{verbatim} -(See section \ref{sec:coordinates} for more details and examples.) -This will create 1000 molecules with names like -``wat[0][0][0]'', ``wat[0][0][1]'',$\ldots$, ``wat[9][9][9]''. -You can always access individual atomIDs, molIDs, bondIDs, angleIDs, -and dihedralIDs (if present), for any molecule -elsewhere in your LT files using this notation: -``\$atom:wat[2][3][4]/h1'', -``\$bond:wat[0][5][1]/oh1'', -``\$angle:wat[2][8][3]/hoh'', -``\$mol:wat[0][1][2]''. -This allows you to define interactions which link -different molecules together (see section \ref{sec:coordinates}). - -A list of available coordinate transformations -is provided in section \ref{sec:xforms_table}. - -%\subsubsection*{Defining the simulation boundary} -\subsubsection*{Boundary Conditions:} -\label{sec:pbc} -LAMMPS simulations have finite volume and are usually periodic. -We must specify the dimensions of the simulation boundary -using the ``write\_once(``Data Boundary'')'' command. -\begin{verbatim} -write_once("Data Boundary") { - 0.0 34.5 xlo xhi - 0.0 34.5 ylo yhi - 0.0 34.5 zlo zhi -} -\end{verbatim} -This is usually specified in the outermost LT file -(``system.lt'' in this example). -\textit{(Note: Boundary conditions do not have to be rectangular -or even periodic. For triclinic cells, additional -``xy'', ``xz'', and ``yz'' tilt parameters can be added. - %The ``write\_once("In Init") { boundary p p f }'' command - %can be used to turn off periodicity in the Z-direction, for example. -For details, lookup the ``read\_data'' and ``boundary'' -commands in the official LAMMPS documentation.)} - -This system is shown in figure \ref{fig:spce_x_1000}a). -After you have specified the geometry, -then you can run moltemplate.sh this way: -\begin{verbatim} -moltemplate.sh -atomstyle "full" system.lt -\end{verbatim} - -\begin{figure}[htbp] -\centering -\textbf{a)} -\includegraphics[width=5cm]{waterSPCEx1000_LR.jpg} -\textbf{b)} -\includegraphics[width=5cm]{waterSPCEx1000_t=25_LR.jpg} -\caption{ -\label{fig:spce_x_1000} -A box of 1000 water molecules (before and after pressure equilibration), -generated by moltemplate and visualized by VMD with the topotools plugin. -(The VMD console commands used for visualization were: -``topo readlammpsdata system.data full'', -``animate write psf system.psf'', -``pbc wrap -compound res -all'', and -``pbc box''. -See sections \ref{sec:vmd_topotools}, and \ref{sec:vmd_advanced} -for details. -} -\end{figure} - - %\subsubsection*{\textit{Non-periodic simulations}} - %The use of periodic boundary conditions in LAMMPS is optional. - %For example the ``boundary p p f'' command turns off - %periodic boundary conditions in the Z-direction. - % %When using LAMMPS, commands like this belong - % %near the beginning of a LAMMPS input script. - %In moltemplate.sh, these kinds of commands go in the ``In Init'' section: - %\begin{verbatim} - %write_once("In Init") { - % boundary p p f - %} - %\end{verbatim} - %Note that the simulation volume is still finite. - %(Currently, as of 2012-5-28, - % atoms which escape the simulation boundary are lost/destroyed.) - % %(Of course, you can always manually edit the LAMMPS input script - % % file that was generated by moltemplate.sh before running LAMMPS. - % % These files are explained below.) - -\subsection{Visualization using VMD \& topotools} -\label{sec:vmd_topotools} - -When you run moltemplate, it generates a LAMMPS \textit{data} file. -This file is usually called ``system.data''. -Geometric information, and bonded topology are stored in this file. -After you have run moltemplate, you should look at your system -to check it for mistakes. -Problems can easily occur with overlapping atoms (missing molecules), -periodic boundaries, incorrectly bonded atoms, incorrect rotation and movement. -Sometimes many iterations of running moltemplate and -visualization are necessary. - -\textit{Optional:} -If you have VMD installed, you can automatically visualize the system -you have just created automatically by invoking moltemplate with -the \textit{\textbf{-vmd}} command line argument. -(In other words invoke moltemplate.sh using \textit{moltemplate.sh -vmd} - instead of \textit{moltemplate.sh}. VMD must be installed.) -If you don't use the -vmd command line argument, you can always view the -system in VMD later manually. For instructions how to do that, -keep reading... - -Some very basic instructions how to use VMD are provided below: -\textit{(Note: These instructions were written for VMD 1.9 and topotools 1.2)} - %See appendix \ref{sec:vmd_advanced} for more details.) - -To view a \textit{data} file: -\begin{list}{} -\item a) start VMD -\item b) from the menu, select - \textbf{Extensions}$\rightarrow$\mbox{\textbf{Tk Console}} -\item c) enter: -\end{list} -\begin{verbatim} - topo readlammpsdata system.data full - animate write psf system.psf -\end{verbatim} -\begin{list}{} -\item The first command will display all of the atoms and bonds in your system -in VMD's 3-D window. (We use ``\textbf{full}'' because we are using the -``full'' atom\_style in this particular example. If you are using a different -atom\_style, then change the command above accordingly.) -\item The second command -%\begin{verbatim} -% \textit{``animate write psf system.psf''}, -%\end{verbatim} -will create a PSF file (``system.psf'') which will -be useful later for viewing a trajectory file created -during a LAMMPS simulation. -(See section \ref{sec:vmd_trajectory}.) -\end{list} - -Most likely, atoms and bonds will be represented by -ugly dots and lines by default. -To change the way molecules are displayed, control their color, -display periodic boundaries, and wrap atomic coordinates, -read the short VMD tutorial in appendix \ref{sec:vmd_advanced}. - -\textit{(Note: -As of 2012-12-18, -VMD does not have built-in support for exotic atom\_styles -such as ellipsoids and dipoles, but their are 3rd-party scripts, plugins -and settings you can use. Search the VMD and LAMMPS mailing lists -for help.}) - - - -\subsection{Running a LAMMPS simulation (after using moltemplate)} -\label{sec:run} -To run a simulation of one or more molecules, -LAMMPS requires an \textit{input script} and a \textit{data file}. -Input scripts typically contain -force field styles, parameters and run settings. -(They sometimes also contain atom coordinates.) -Data files typically contain atom coordinates and bonded topology data. -(They sometimes also contain force-field parameters.) - %LAMMPS does strictly not require users to supply a data file, but they - %are required for systems with nontrivial bonded molecular topology. - -Moltemplate will create the following files: -``system.data'', -``system.in'', -``system.in.init'', -``system.in.settings'', -(and possibly other files including ``system.in.coords''). -These are LAMMPS input/data files, and they can be run in LAMMPS -with minimal modification (see below). -The main input script file is named ``system.in'', and it usually contains -just three lines: -\begin{verbatim} -include "system.in.init" -read_data "system.data" -include "system.in.settings" -\end{verbatim} - -To \textit{run} a simulation, you will have to -edit this file in order to add a couple of run commands. -These commands tell LAMMPS about the simulation conditions -you want to use (temperature, pressure), -how long to run the simulation, -how to integrate the equations of motion, -and how to write the results to a file (file format, frequency, etc). -Moltemplate.sh can not do this for you. -Some simple examples (which you can paste into your input script) -are provided in the -\textit{online examples} -which can be downloaded from \url{http://moltemplate.org}. - %directories which are bundled with moltemplate. -(These example input scripts - typically have names like ``run.in.nvt'' and ``run.in.npt''.) -%below: - - In addition to the examples, an introduction to LAMMP -input scripts is provided at these links: -\url{http://lammps.sandia.gov/doc/Section_commands.html#cmd_1}. -\url{http://lammps.sandia.gov/doc/Section_howto.html} and -\url{http://lammps.sandia.gov/doc/Section_howto.html#howto_15} - - -Here is a list of basic input script commands -used in the moltemplate examples -(and links to their documentation): -\begin{list}{} -\item \textbf{run} \ -\url{http://lammps.sandia.gov/doc/run.html} -\item \textbf{timestep} \ -\url{http://lammps.sandia.gov/doc/timestep.html} -\item \textbf{thermo} \ \url{http://lammps.sandia.gov/doc/thermo.html} -\item \textbf{dump} \ \url{http://lammps.sandia.gov/doc/dump.html} -\item \textbf{read\_data} \ \url{http://lammps.sandia.gov/doc/read_data.html} -\item \textbf{restart} \ \url{http://lammps.sandia.gov/doc/restart.html} -\item \textbf{include} \ \url{http://lammps.sandia.gov/doc/include.html} -\item \textbf{fix nve} \ \url{http://lammps.sandia.gov/doc/fix_nve.html} -\item \textbf{fix nvt} \ \url{http://lammps.sandia.gov/doc/fix_nh.html} -\item \textbf{fix npt} \ \url{http://lammps.sandia.gov/doc/fix_nh.html} -\item \textbf{fix langevin} \ \url{http://lammps.sandia.gov/doc/fix_langevin.html} -\item \textbf{fix} \ \url{http://lammps.sandia.gov/doc/fix.html} -\item \textbf{group} \ \url{http://lammps.sandia.gov/doc/group.html} -\item \textbf{compute} \ \url{http://lammps.sandia.gov/doc/compute.html} -\item \textbf{print} \ \url{http://lammps.sandia.gov/doc/print.html} -\item \textbf{variable} \ \url{http://lammps.sandia.gov/doc/variable.html} -\item \textbf{rerun} \ \url{http://lammps.sandia.gov/doc/rerun.html} -\item \textbf{fix shake} \ \url{http://lammps.sandia.gov/doc/fix_shake.html} -\item \textbf{fix rigid} \ \url{http://lammps.sandia.gov/doc/fix_rigid.html} -\end{list} -In addition, all users should be familiar with the following commands: -(These appear in the ``In Init'' section of most LT files.) -\begin{list}{} -\item \textbf{atom\_style} \ \url{http://lammps.sandia.gov/doc/atom_style.html} -\item \textbf{pair\_style} \ \url{http://lammps.sandia.gov/doc/pair_style.html} -\item \textbf{bond\_style} \ \url{http://lammps.sandia.gov/doc/bond_style.html} -\item \textbf{angle\_style} \ \url{http://lammps.sandia.gov/doc/angle_style.html} -\end{list} - - -%\subsubsection{An overview of popular LAMMPS run settings} -% %Alternately you can -% %import or include this LT file -% %inside another LT file which has these run commands already. -% % containing the needed run settings. -% % to the end of this input script file, -% %OR include this file in a different input script file which has them. -%\begin{verbatim} -%# -- declare time step for numerical integration -- -%timestep 1.0 -%\end{verbatim} -%The Nose-Hoover thermostat \& barostat are popular for dense systems -%(typically liquids, solids, or liquid/solute mixtures). Choose between: -%\begin{verbatim} -%# -- run at constant temperature and pressure (Nose Hoover) -- -%fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 -%\end{verbatim} -%and -%\begin{verbatim} -%# -- ALTERNATELY run at constant temperature and volume (Nose Hoover) -- -%fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -%\end{verbatim} -%The user must also specify what kind of data they want to save, and how -%frequently they want to save it. Here are some simple examples: -%\begin{verbatim} -%thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -%thermo 500 # time interval for printing out "thermo" data -%dump 1 all custom 2000 traj.lammpstrj id mol type x y z ix iy iz -%\end{verbatim} -%Finally, you must specify the simulation duration. -%\begin{verbatim} -%run 200000 -%\end{verbatim} -% %A detailed description of these steps are not covered in this manual. -%If the starting geometry of your system is unfavorable (high energy) -%then numerical explosions may result (causing the infamous -%``Bond/Angle/Dihedral atoms missing on proc'' errors). -%To avoid this, you may want to insert a ``minimize'' command -%into your input script before the run command. -%\begin{verbatim} -%# -- minimize -- -%minimize 1.0e-5 1.0e-7 1000 10000 -%# (Note: Some fixes, for example "shake", interfere with the minimize command. -%# You can use the "unfix" command to disable them before minimization.) -%\end{verbatim} -%After these modifications, LAMMPS can then be run using: -%\begin{verbatim} -%lmp_linux -i system.in -%\end{verbatim} -%(Here we are assuming ``lmp\_linux'' is the name of your LAMMPS executable.) -%A detailed explanation of these commands -%can be found in the LAMMPS Users Manual. -% %\textit{(Simple examples of LAMMPS script commands may be found in -% %comments that appear at the end of ``system.in'' -% %files created by moltemplate.sh.)} -% %(More detailed explanation of these commands -% %can be found in the LAMMPS Users Manual.) -% -%Several examples of complete input scripts exist in the -%``examples'' section of the moltemplate web site at moltemplate.org. -% -%\subsubsection{Recommendations for dilute coarse-grained systems} -%\label{sec:runcg} -%The Nose-Hoover thermostats are a poor choice for -%dilute systems with a relatively small number of atoms -%(such as coarse-grained molecules in implicit solvent). -% %Note: Special care is required for \textit{coarse-grained} systems. -%(The Berendsen thermostat is also not recommended.) -%The Langevin thermostat is available in LAMMPS, -%however it (currently as of 2012-5) requires -%two ``fix'' commands, as shown below: -%\begin{verbatim} -%# -- run at constant volume using Langevin dynamics. -- -%fix fxlan all langevin 300.0 300.0 5000 48279 -%fix fxnve all nve # (needed by langevin) -%\end{verbatim} -%You may need to adjust the damping parameter (the 3rd numerical argument) -%to achieve efficient and physically reasonable dynamics -%\cite{Klimov+ThirumalaiPRL1997}. - - - - %More detailed instructions for running ``moltemplate.sh'' are provided - %in appendix \ref{sec:ttree_man_page}. - - %%%%%%% This comment is interesting (?), but no longer relevant: %%%%%% - %SPCE { - %# Note: This extra bracketed text augments (not overwrites) - %# the contents of "SPCE {}" defined in "spce_simple.lt". - %# Note: Here "@atom:O" and "@atom:H" refer to variables which were - %# originally defined in "spce_simple.lt". These variables will be - %# numbered consistently as if they belong to the same file - %} - %%%%%%%%%%%%%%%%%%%%% --Please Ignore -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -%Later on when we build the final LAMMPS input and data files, -%data from the different files (``Data Atoms'', ``Data Bonds'', -%``In Init'', ``In Settings'', etc...) -%must be pasted together in the correct order according to LAMMPS conventions. -%This is a simple task that can be performed by the ``moltemplate'' script -%(included with ttree), -%or manually by the user, depending on their familiarity with LAMMPS. -%LAMMPS has a complex and diverse syntax because -%it supports a wide variety of force-field types. -%The commands above are \textit{raw} LAMMPS commands, -%augmented by ttree variables -%(like ``@atom:O'' and ``\$atom:o''), which are explained below. - - - %and/or CHARMM27 parameter files. - %We hope ttree is flexible enough that it should remain useful in the future, - %even if the LAMMPS input syntax changes radically. - - %\subsection{Before ttree} - %The ability to load and combine data from multiple different types of - %molecules together is missing from LAMMPS. - %\textit{Normally} LAMMPS users are required to manually assign unique - %id numbers to \textit{every} atom, bonded, 3-body, and 4-body interaction - %in the entire simulation. - %Each molecule is assigned a unique id number as well. - %For a system with 6000 water molecules, a user would be required to - %specify 18000 atom ids, 12000 bond ids, 6000 3-body angle ids - %and 6000 molecule ids. - %(This should not be done by hand.) - - -\subsection{Visualizing Trajectories} -\label{sec:vmd_trajectory} -After you have run a simulation in LAMMPS, there are several programs which -can visualize the system. -If you have saved your trajectory in LAMMPS ``dump'' format, -later you can view it in VMD \cite{VMD}. -For the purpose of viewing trajectories in LAMMPS, -I recommend using the following style of ``dump'' commands in the LAMMPS -input-script that you use when you run LAMMPS: -\begin{verbatim} -dump 1 all custom 1000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz -\end{verbatim} -(The ``all'' and ``1000'', refer to the atom selection and save interval, which may differ depending on the kind of simulation you are running. See \url{http://lammps.sandia.gov/doc/dump.html} for details.) - - -Once you have a dump file, you can view it in VMD using: -\begin{list}{} -\item a) Start VMD - From the menu in the upper-left, select - \textbf{File}$\rightarrow$\mbox{\textbf{New Molecule}} -\item b) Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) -\item c) Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory". - Click on \textbf{OK}. -\item d) Click on the \textbf{Load} button. -\end{list} - - -Again, to customize molecule appearance, -display periodic boundary conditions and wrap molecule coordinates, -see the commands discussed in appendix \ref{sec:vmd_advanced}. - -\textit{(Note: VMD may not be able to correctly visualize simulations which do -not preserve the number of atoms and bonds over time, such as those run using -\textbf{fix bond/create}, -\textbf{fix bond/break}, or -\textbf{fix gcmc}.)} - -%\textit{(A note on trajectory format: -%It's a good idea to use an atom\_style which supports molecule-ID numbers -%(to make it easy to wrap atom coordinates without breaking molecules in half). -%I've been using this command in my LAMMPS scripts to create the trajectories: -%``dump 1 all custom 5000 DUMP\_FILE.lammpstrj id mol type x y z ix iy iz'')} - - - %Of course, you don't have to save your trajectories in DUMP format, - %(other formats like DCD work fine) I just mention dump files - %because these are the files I'm familiar with. - -\section{Overview} - %This paragraph below is an excellent - %summary/explanation of what moltemplate.sh does. - -\subsection{Basics: The \textit{write()} and \textit{write\_once()} commands} -\label{sec:write} -Each LT file typically contains one or more -``write'' or ``write\_once'' commands. -These commands have the following syntax -\begin{verbatim} -write_once(filename) {text_block} -\end{verbatim} -This creates a new file with the desired file name -and fills it with the text enclosed in curly brackets \{\}. - %(after any necessary variable substitutions have been made). -Text blocks usually span multiple lines and contain counter variables -(beginning with ``@'' or ``\$''). -which are replaced with numbers. -However the ``write()'' command will repeatedly append the -same block of text to the file every time the molecule -(in which the write command appears) is generated or copied -(using the ``new'' command, -after incrementing the appropriate counters, -as explained in \ref{sec:instance_variables}). - %incrementing any counter - %variables beginning with \$). - %When this happens, any counter variables beginning - %with \$ will be incremented.) -%On the other hand, ``write\_once()'' commands print their text only once. -%This is useful in certain cases. For example, there is no need to redundantly -%specify the mass of the ``O'' and ``H'' atoms every time you create another copy -%of the same molecule. This kind of data should be written only once using the -%``write\_once(``Data Masses'')'' command. - %However, new atoms are generated every time a new copy of a previously - %defined molecule is created. This kind of data should be written using the - %``write(``Data Atoms'')'' command. - - -\subsection{Basics: counter variables} -\label{sec:variables} - -Words following a ``@'' or a ``\$'' character -are \textit{counter variables}. -(These are not to be confused with \textit{LAMMPS variables} - \url{http://lammps.sandia.gov/doc/variable.html}). -By default, -\textit{all counter variables are substituted with a numeric counter} -before they are written to a file. - %(or to a section of a LAMMPS DATA file as - %explained in section \ref{sec:write}). -These counters begin at 1 (by default), and -are incremented as the system size and complexity grows (see below). - -These words typically contain a colon (:) followed by more text. -The text preceding this colon is the \textit{category name}. -(For example: ``\$atom:'', ``\$bond:'', ``\$angle:'', - ``@atom:'', ``@bond:'', ``@angle:'') -Variables belonging to different categories -are counted independently. - -Users can override these assignment rules and create custom categories. -(See appendices \ref{sec:manual_assignment} and \ref{sec:custom_categories} -for details.) - -\subsubsection{Static counters begin with ``@''} -\label{sec:static_variables} - -``@'' variables generally correspond to \textit{types}: -such as atom types, bond types, angle types, dihedral types, improper types. -These are simple variables and they assigned to unique integers in the -order they are read from your LT files. -Each uniquely named variable in each category is assigned to a different -integer. For example, ``@bond:'' type variables are numbered from ``1'' -to the number of \textit{bond types}. -(Pairs of bonded atoms are assigned a \textit{bond type}. -Later, LAMMPS will use this integer to lookup the bond-length and Hooke's-law -elastic constant describing the force between these two atoms.) - -%These numbers do not change if the number of molecule copies -%increases. - -\subsubsection{Instance counters begin with ``\$''} -\label{sec:instance_variables} - -On the other hand, ``\$'' variables correspond -to unique ID numbers: atom-IDs, bond-IDs, -angle-IDs, dihedral-IDs, improper-IDs, and molecule-IDs. These -variables are created whenever a copy of a molecule is created (using -the ``new'' command). -If you create 1000 copies of a water molecule using a command like -\begin{verbatim} -wat = new SPCE[10][10][10] -\end{verbatim} -then moltemplate creates 3000 ``\$atom'' variables with names like -\begin{verbatim} -$atom:wat[0][0][0]/o -$atom:wat[0][0][0]/h1 -$atom:wat[0][0][0]/h2 -$atom:wat[0][0][1]/o -$atom:wat[0][0][1]/h1 -$atom:wat[0][0][1]/h2 -\end{verbatim} -$\quad \vdots $ -\begin{verbatim} -$atom:wat[9][9][9]/o -$atom:wat[9][9][9]/h1 -$atom:wat[9][9][9]/h2 -\end{verbatim} - -\subsubsection{Variable names: short-names \textit{vs.} full-names} -\label{sec:full_names} - -In the example above, the \$ variables have full-names like -``\$atom:wat[8][3][7]/h1'', not ``\$atom:h1''. However inside the -definition of the water molecule, you don't specify the full name. -You can refer to this atom as ``\$atom:h1''. -Likewise, the full-name for the @atom variables is actually -``@atom:SPCE/H'', not ``@atom:H''. However inside the definition of the water -molecule, you typically use the shorthand notation ``@atom:H''. - -\subsubsection{Numeric substitution} -Before being written to a file, every variable (either \$ or @) -with a unique \textit{full-name} will be assigned to a unique integer, -starting at 1 by default. - %(You can override this choice if you want to using the "-a" flag.) - -The various \$atom variables in the water example will be substituted -with integers from 1 to 3000 (assuming no other molecules are present). -But the ``@atom:O'' and ``@atom:H'' variables -(which are shorthand for ``@atom:SPCE/O'' and ``@atom:SPCE/H'') -will be assigned to to ``1'' and ``2'' -(again, assuming no other molecule types are present). - -So, in summary, @ variables increase with the \textit{complexity} -of your system -(IE the number of molecule types or force-field parameters), -but \$ variables increase with the \textit{size} of your system. - -\subsubsection{Variable scope} -\label{sec:variable_scope} -This effectively means that all variables are specific to -local molecules they were defined in. -In other words, an atom type named ``@atom:H'' inside -the ``SPCE'' molecule, will be assigned to a different number -than an atom named ``@atom:H'' in an ``Arginine'' molecule. -This is because the two variables will have different \textit{full} names -(``@atom:SPCE/H'', and ``@atom:Arginine/H''). - - - - - - - -\subsubsection*{Sharing atom types or other variables between molecules} -There are several ways to share atom types between two molecules. -The \textit{recommended way} is to define them in a separate -file and refer to them when needed. -This approach is demonstrated in section \ref{sec:2bead}. - -\textit{(Alternately, you can define them outside the current molecule definition, -and use file-system-path-like syntax -(``../'', or ``../../'' or ``/'') -to access atoms (or molecules) outside of the current molecule. - %(or nested within the definition of another molecule). -For example, two different molecule types can share the same type of -hydrogen atom by referring to it using this syntax: ``@atom:../H''. - %(Two molecules could share the same atom-id in a similar way, - % using ``\$atom:../h1''. This is not recommended) -For details, see -section \ref{sec:paths}. -and appendix \ref{sec:adv_variable_syntax}.) - %To be on the safe side, if you want to define a single - %hydrogen atom type named ``H'' globally, for example, - %then you would refer to this atom everywhere using ``@atom:/H''. - %(A more portable alternative would be to use the ``@atom:.../H'' - % syntax explained in appendix \ref{sec:adv_variable_syntax}. - % This is similar to ``@atom:/H'', - % however using the ellipsis syntax ``@atom:.../H'' allows you to - % share your molecule definitions (ET files) with others - % who may have a different notion of what the ``H'' atom is.) -} - - - - - -\subsection{Troubleshooting using the \textit{output\_ttree} directory} -\label{sec:output_ttree} -Users can see what numbers were assigned to each variable -by inspecting the contents of the ``output\_ttree'' subdirectory -created by moltemplate. -Unfortunately, it not unusual for LAMMPS to crash the first time you -attempt to run it on a DATA file created by moltemplate. This often occurs -if you failed to spell atom types and other variables consistently. -The LAMMPS error message (located at the end of the ``log.lammps'' -file created by LAMMPS) will help you determine what type of mistake you made. -(For example, what type of variable was misspelled or placed in the wrong place?) - - -To help you, the ``output\_ttree'' directory contains a file named -``ttree\_assignments.txt''. -This is a simple 2-column text file containing a list of \textit{all} -of the variables you have created in one column, and the numbers they -were assigned to in the second column. -(There is also a comment on each line beginning with a ``\#'' character which -indicates the file and line number where this variable is first used.) - -The ``output\_ttree'' directory also contains all of the files that you created. -The versions with a ``.template'' extension contain text -interspersed with \textit{full} variable names (before numeric substitution). -(A spelling mistake, like using ``\$atom:h'' when you meant to say ``\$atom:h1'' -or ``@atom:H'' will show up in these files if you inspect them carefully.) -This can help you identify where the mistake occurred -in your LT files. - -Once a molecular system is debugged and working, users -can ignore or discard the contents of this directory. - - -\subsection{``Data'' and ``In''} -\label{sec:DataIn} -Again, LAMMPS requires an \textit{input script} and a \textit{data file} -to run. -\textit{Moltemplate's job is to generate these files.} -\textit{Input scripts} typically contain -force-field styles, parameters and run settings - %Moltemplate users control what goes in the input script - %by writing to files with names beginning with \mbox{``In ''}. -\textit{Data files} typically contain atom -coordinates and bonded topology data. - %Moltemplate users control what goes in the data file - %by writing to files with names beginning with \mbox{``Data ''}. - -If you are familiar with LAMMPS, -you may have noticed the file names above -(in the example from section \ref{sec:spce_example}) -sound suspiciously like sections from LAMMPS data files or input scripts, -such as ``Data Boundary'', ``Data Atoms'', ``Data Bonds'', ``Data Masses'', ``Data Angles'', ``Data Dihedrals'', ``Data Impropers'', ``In Init'', ``In Settings''). -All files whose names begin with ``In '' or ``Data '' are special. -For the user's convenience, -the moltemplate.sh script copies the contents -of these files into the corresponding section -(``Atoms'', ``Bonds'', ``Angles'', etc.) -of the -DATA file or INPUT scripts generated by moltemplate -(``system.data'', ``system.in.settings'', etc). -(Then the original files are moved to the ``output\_ttree/'' directory, - in an effort to clean things up and hide them from view.) -Users can create their own custom sections to a LAMMPS data file. -(See section \ref{sec:custom_data}. - %(Note: It is unwise to explicitly add blank lines to a data file section. - %because LAMMPS may interpret them as section breaks. - %Moltemplate will add the section headers - %and blank lines needed to keep LAMMPS happy.) - -More generally, the ``write()'' and ``write\_once()'' commands can be used to -create any other files you may need to run your simulations, -which refer to the same \textit{@atom} and \textit{@bond} types. - %Files whose names do not begin with ``In '' or ``Data '' can have any format - %(and are not moved or cleaned up). - %(These files are not removed or hidden later.) -(See section \ref{sec:aux_files} - % and \ref{sec:output_ttree} for examples -for an example.) - - -\subsection{\textit{(Advanced)} - Using moltemplate to generate auxiliary files} -\label{sec:aux_files} -The following excerpt from an LT file -creates a file named ``system.in.sw''. -(It contains parameters for the ``sw'' pair style. - This exotic many-body pair style requires a large number - of parameters, which are read from a separate file.) -This ``system.in.sw'' file file will be read later when you run the simulation. -(The pair\_coeff command below tells LAMPS to read that file.) -\begin{verbatim} -write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.33333 7.04956 0.602224 4 0 0 -} -write_once("In Settings") { - pair_coeff * * sw system.in.sw mW NULL NULL NULL -} -\end{verbatim} -As new force-field styles and/or fixes are added to LAMMPS, -the files they depend on can be embedded in an LT file in this way. - - -\subsection{\textit{(Advanced)} Making custom DATA sections} -\label{sec:custom_data} -Suppose that in the future, the format of the LAMMPS DATA file changes -so that it now becomes necessary to supply a new section named ``Foo Fee Fum'', -for example. You could do that using this command: -\begin{verbatim} -write_once("Data Foo Fee Fum") { - File contents goes here. (These files can contain - atom counters and/or other counter variables). -} -\end{verbatim} -This way moltemplate copy this text into the ``Foo Fee Fum'' section at -the end of the DATA file it is constructing. -This allows users to adapt to future changes in the LAMMPS data file format. - - - -\subsubsection*{Does ``@atom:H'' conflict with ``\$atom:H''?} -\label{sec:vardetails} -No. It is okay for static(@) and instance(\$) variables to share the same names. -(Moltemplate considers them distinct variables and they will be assigned independently.) - - -\subsubsection*{Addional Details} -Variable and molecule names can include unicode characters. -They can also include some whitespace characters and other special characters -by using backslashes and curly-brackets, for example: -``@\{atom: CA \}'' and ``@atom:\textbackslash\ CA\textbackslash\ ''. -Curly-brackets are useful to clarify when a variable name begins and ends, -such as in this example: ``@\{atom:C\}*@\{atom:H\}''. -This prevents the ``*'' character from being appended to the end of the -``C'' variable name. -(Note that using the ``*'' character in any of the \textit{coeff} commands -within moltemplate is discouraged. See section \ref{sec:wildcard_bug}.) - -\textit{(Unicode is supported.)} - - -\pagebreak -\section{ Object composition and coordinate generation } -\label{sec:coordinates} - -Objects can be connected together to form larger molecule objects. -These objects can be used to form still larger objects. -As an example, we define a small 2-atom molecule named ``Monomer'', -and use it to construct a short polymer (``Polymer''). - -\begin{figure}[htbp] -\centering -\textbf{a)} -\includegraphics[height=3cm]{2bead_monomer.jpg} -\quad \quad \quad \quad \quad -\textbf{b)} -\includegraphics[height=3cm]{2bead_polymer.jpg} -\newline -\vspace{10 mm} -\newline -\textbf{c)} -\includegraphics[width=4cm]{2bead_polymers_nopbc_t=0_LR.jpg} -\textbf{d)} -\includegraphics[width=4cm]{2bead_polymers_t=100ps_LR.jpg} -\caption{ -\label{fig:2bead_polymer} -\textbf{a)-b)} -\textit{Building a complex system from small pieces:} -Construction of a polymer (\textbf{b}) -out of smaller (2-atom) subunits (\textbf{a}) -using composition and rigid-body transformations. -Bonds connecting different monomer together (blue) -must be declared explicitly, -but angle and dihedral interactions will be generated automatically. -See section \ref{sec:2bead} for details. -\textbf{c)} -An irregular lattice of short polymers. -(See section \ref{sec:multidimensional_arrays}.) -\textbf{d)} -The same system after 100000 time steps using Langevin dynamics. - %the Langevin dynamics settings from section \ref{sec:runcg}. -(The VMD console commands used for visualization were: -``topo readlammpsdata system.data full'', -``animate write psf system.psf'', -``pbc wrap -compound res -all'', and -``pbc box''. -See sections \ref{sec:vmd_topotools}, and \ref{sec:vmd_advanced} -for details.} -\end{figure} - - - -\pagebreak - -\subsection{Building a large molecule from smaller pieces} -\label{sec:2bead} -Consider the following simple 2-atom dumbell-shaped molelule (``Monomer'') -\begin{verbatim} -# -- file "monomer.lt" -- - -import "forcefield.lt" # contains force-field parameters - -Monomer inherits ForceField { - - write("Data Atoms") { - # atomId molId atomType charge x y z - $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000 - $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 - } - write("Data Bonds") { - # bond-id bond-type atom-id1 atom-id2 - $bond:cr @bond:Sidechain $atom:ca $atom:r - } -} -\end{verbatim} - - -Soon will use it to construct a polymer (``Polymer'') -\textit{Note: The ellipsis notation used here ``\$mol:...''. -warns moltemplate that the ``Monomer'' molecule may be part of a larger -molecule. -(This is explained in more detail in section \ref{sec:ellipsis_mol}.) -(Note: The meaning of ``inherits ForceField'' - will be explained below in section \ref{sec:nbody_by_type_intro}) -} - -In this example we will define two kinds of molecule objects: -``Monomer'', and ``Polymer'' (\textit{defined later}). - -\subsubsection*{Building a simple polymer} -We construct a short polymer by making 7 copies of ``Monomer'', -rotating and moving each copy: -\label{sec:2beadPolymer} -\begin{verbatim} -# -- file "polymer.lt" -- - -import "monomer.lt" #(defines "Monomer" and "ForceField") - -Polymer inherits ForceField { - - # The next line is optional: - create_var {$mol} #(force all monomers to share the same molecule-ID) - - # Now create some monomers - - mon1 = new Monomer #(no need to move the first monomer) - mon2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) - mon3 = new Monomer.rot(360.0, 1,0,0).move(6.4,0,0) - mon4 = new Monomer.rot(540.0, 1,0,0).move(9.6,0,0) - mon5 = new Monomer.rot(720.0, 1,0,0).move(12.8,0,0) - mon6 = new Monomer.rot(900.0, 1,0,0).move(16.0,0,0) - mon7 = new Monomer.rot(1080.0, 1,0,0).move(19.2,0,0) - - # Now, link the monomers together this way: - write("Data Bonds") { - $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca - $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca - $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom:mon4/ca - $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom:mon5/ca - $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom:mon6/ca - $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom:mon7/ca - } -} -\end{verbatim} -The position and orientation of each copy of ``Monomer'' -is specified after the ``new'' statement. -Each ``new'' statement is typically followed by a chain of -move/rotate/scale functions separated by dots, evaluated left-to-right -(optionally followed by square brackets and then more dots). -For example, ``mon2'' is a copy of ``Monomer'' which is first rotated -180 degrees around the X axis (denoted by ``1,0,0''), -and \textbf{then} moved in the (3.2,0,0) direction. -(The last three arguments to the ``rot()'' command - denote the axis of rotation, which does not have to be normalized.) -(A list of available coordinate transformations -is provided in section \ref{sec:xforms_table}.) - -\textit{(Note: Although we did not do this here, -it is sometimes convenient to represent polymers as 1-dimensional arrays. -See sections \ref{sec:arrays} and \ref{sec:random_arrays} for examples.)} - -To bond atoms in different molecules or molecular subunits together, we used -the write(``Data Bonds'') command to append additional bonds to the system. - -%\subsubsection{Sharing atom, bond and angle types} -%Normally you must separately define the parameters for all of the atoms types, -%and bond types, angle types etc... in every type of molecule. -%However different kinds of monomers in a heteropolymer typically will -%share some common backbone atom types and other properties. -%You must be careful to indicate which atom and bond types are shared between -%different monomers by referring them using a ``../'' prefix. -%(See sections \ref{sec:variable_scope}, -%\ref{sec:paths}, and -%\ref{sec:butane} for details and examples.) -%\textit{Note: There is a heteropolymer example in the the -%``2bead\_heteropolymer/'' directory in the online examples. -%This example demonstrates how to share backbone atoms, bonds, and angles. -%You can also define specific angle or dihedral interactions which are -%specific to the atom types in different monomers.} - - -\subsection{Bonded interactions \textit{by type}} -\label{sec:nbody_by_type_intro} - -In this example we did \textit{not} provide a list of all 3-body -and 4-body angle forces between bonded atoms in the polymer. -Moltemplate allows you to manually list all of these interactions -(using the ``write\_once("Data Angles")'' command -from section \ref{sec:spce_example}, -\textit{or} -the ``write\_once("Data Dihedrals")'', -or ``write\_once("Data Impropers")'' commands). -However there are usually many of them. -For this reason, it is often more convenient to provide -moltemplate with instructions to help it automatically figure out -which atoms participate in 3-body and 4-body angle interactions, -and what force field parameters to assign to them. -We will do that below using the following commands: -``write\_once("Data Angles By Type")'', -``write\_once("Data Dihedrals By Type")'', and -``write\_once("Data Impropers By Type")'' - - %Moltemplate can detect consecutively bonded atoms and - %determine the forces between them based on atom type (and bond type). - -Furthermoree, since many different kinds molecules often share -the same rules for creating 3-body and 4-body angle interactions, -it is convenient to organize all of this information -together into one place (eg an object named ``ForceField''). -A ``ForceField'' object will typically include many -``write\_once("Data Angles By Type")'' -commands, as well as force field parameters and related atom type properties. -We also typically store that information in a separate file -(eg ``forcefield.lt'', ``oplsaa.lt'', ``gaff2.lt'', ``compass.lt'', etc...). - -\begin{verbatim} -# -- file "forcefield.lt" -- - -ForceField { - - # There are 2 atom types: "CA" and "R" - write_once("Data Masses") { - @atom:CA 13.0 - @atom:R 50.0 - } - - # Force-field parameters ("coeffs") go in the "In Settings" section: - - write_once("In Settings") { - # Pairwise (non-bonded) interactions: - # atomType1 atomType2 epsilon sigma - pair_coeff @atom:CA @atom:CA 0.10 2.0 - pair_coeff @atom:R @atom:R 0.50 3.6 - # (Interactions between different atoms are determined by mixing rules.) - } - - # 2-body (bonded) interactions: - # - # Ubond(r) = k*(r-r0)^2 - # - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:Sidechain 15.0 3.4 - bond_coeff @bond:Backbone 15.0 3.7 - } - - # Although the simple "Monomer" object we defined above has only - # two atoms, later on, we will create molecules with many bonds. - # By convention, in this file we keep track of all of the possible - # interactions which could exist between these atoms: - - # Rules for determining 3-body (angle) interactions by atom & bond type: - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:Backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:Sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - } - - # Force-field parameters for 3-body (angle) interactions: - # - # Uangle(theta) = k*(theta-theta0)^2 - # - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:Backbone 30.00 114 - angle_coeff @angle:Sidechain 30.00 132 - } - - # 4-body interactions in this example are listed by atomType - # Rules for determining 4-body (dihedral) interactions by atom & bond type: - write_once("Data Dihedrals By Type") { - # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 - @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* - } - - # The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is - # dihedral_coeff dihedralType K n d w(ignored) - - write_once("In Settings") { - dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 - dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 - } - - write_once("In Init") { - # -- Styles used in "ForceField" -- - # -- (Changing these styles will change the formulas above) -- - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style charmm - pair_style lj/cut 11.0 - } -} -\end{verbatim} -Any molecule that wants to access this information can use the -``inherits ForceField'' keyword. -\textit{(...as we did in the ``monomer.lt'' and ``polymer.lt'' files in theexample above. - Note: the ``import forcefield'' statement was also necessary because the - information is located in a separate file: ``forcefield.lt''.} -%\textit{(Note: You can also generate \textbf{improper} interactions -% %between any 4-atoms bonded together in a T-shaped topology -% the same way, using the ``write\_once("Impropers By Type")'' command. -% See appendix \ref{sec:nbody_by_type} for more details. -\textit{You can customize these ``By Type'' rules further - by altering the bond topology search rules and atom type symmetry. - See appendix \ref{sec:nbody_by_type_custom} for details.)} - - %\subsubsection*{\textit{(Advanced)} Order matters when sets overlap} - %Bonded-interactions are generated in the order they appear in the LT file. - %Interactions which are declared later may override the settings of - %interactions which appear earlier, such as in this example: - %\begin{verbatim} - % write_once("Data Angles By Type") { - % @angle:Backbone @atom:C* @atom:C* @atom:* @bond:* @bond:* - % @angle:Sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - % } - %\end{verbatim} - % %Here the first line of this file creates a 3-body angle interaction - % %of type ``@angle:Backbone'' between \textit{every} triplet of bonded atoms - % %in the molecule whose first two atom types begin with the letter ``C''. - %The second line creates 3body interactions (of type ``@angle:Sidechain'') - %specifically between atoms of type ``@atom:CA'', ``@atom:CA'', and - %``@atom:R'', overriding any triplets of this type which appeared earlier. - - - -%\subsection*{\textit{(Advanced)} Mixing regular and ``By Type'' interactions} - -%If an LT file contains both ``Data Angles'' and ``Data Angles By Type'', -%then the interactions explicitly defined in the ``Angles'' section will -%always override the assignments made in ``Data Angles By Type''. -%The also applies to Dihedrals and Impropers. - - %\begin{verbatim} - %write("Data Angles") { - % $angle:1 @angle:CCCgeneral $atom:c1 $atom:c2 $atom:c3 - % $angle:2 @angle:CCCgeneral $atom:c1 $atom:c3 $atom:c4 - %} - %\end{verbatim} - - -\section{Arrays, slices, and coordinate transformations} -\label{sec:arrays} -Moltemplate supports 1-dimensional, and multi-dimensional arrays. -These can be used to create straight (or helical) polymers -sheets, tubes, tori. -They are also to fill solid 3-dimensional volumes -with molecules or atoms. -(See sections \ref{sec:coords_intro} and \ref{sec:multidimensional_arrays}.) - -Here we show an easier way to create the short polymer -shown in section \ref{sec:2beadPolymer}. -You can make 7 copies of the \textit{Monomer} molecule this way: -\begin{verbatim} - monomers = new Monomer[7] -\end{verbatim} -This creates 7 new \textit{Monomer} molecules (named -\mbox{\textit{monomers[0]}}, -\mbox{\textit{monomers[1]}}, -\mbox{\textit{monomers[2]}}, -\mbox{\textit{monomers[3]}}, ... -\mbox{\textit{monomers[6]}}). -Unfortunately, by default, the coordinates of each molecule are identical. -To prevent the atom coordinates from overlapping, you have several choices: - -\subsection{Transformations following brackets [] in a new statement} -\label{sec:arrays+xform} - After every square-bracket [] in a new command, -you can specify a list of transformations to apply. -For example, we could have generated atomic coordinates for the -the short polymer in section \ref{sec:2beadPolymer} -using this command: -\begin{verbatim} - monomers = new Monomer [7].rot(180, 1,0,0).move(3.2,0,0) -\end{verbatim} -This will create 7 molecules. -The coordinates of the first molecule \textit{monomers[0]} are will be unmodified. -However each successive molecule will have its coordinates cumulatively -modified by the commands ``rot(180, 1,0,0)'' followed by ``move(3.2,0,0)''. -\subsubsection*{optional: initial customizations (preceding [] brackets)} -\label{sec:xform+arrays+xform} -You can also make adjustments to the initial coordinates of the molecule -before it is copied, and before any of the array transformations are applied. -For example: -\begin{verbatim} - monomers = new Monomer.scale(1.5) [7].rot(180, 1,0,0).move(3.2,0,0) -\end{verbatim} -In this example, the ``scale(1.5)'' transformation is applied once to -enlarge every \textit{Monomer} object initially. -This will happen before any of the rotation and move commands -are applied to build the polymer -(so the 3.2 Angstrom spacings between each monomer will not be effected). - -\subsection{Transformations following instantiation} -\label{sec:xform_after_instance} -Alternately you apply transformations to a molecule -after they have been created (even if they are part of an array). -\begin{verbatim} - monomers = new Monomer [7] - - # Again, the first line creates the molecules named - # "monomers[0]", "monomers[1]", "monomers[2]", ... "monomers[6]". - # The following lines move them into position. - monomers[1].rot(180.0, 1,0,0).move(3.2,0,0) - monomers[2].rot(360.0, 1,0,0).move(6.4,0,0) - monomers[3].rot(540.0, 1,0,0).move(9.6,0,0) - monomers[4].rot(720.0, 1,0,0).move(12.8,0,0) - monomers[5].rot(900.0, 1,0,0).move(16.0,0,0) - monomers[6].rot(1080.0, 1,0,0).move(19.2,0,0) -\end{verbatim} - -\subsection{Transformation order (general case)} -\label{sec:xform_order} -A typical array of molecules might be instantiated this way: -\begin{verbatim} -mols = new Molecule.XFORMS1() [N].XFORMS2() -mols[*].XFORMS3() -\end{verbatim} -The list of transformations denoted by ``XFORMS1'' in this example -are applied to the molecule first. -Then the transformations in ``XFORMS2'' are then applied to each -copy of the molecule multiple times. -(For the molecule with index ``$i$'', named ``Molecule[$i$]'', -XFORMS2 will be applied $i$ times.) -Finally after all the molecules have been created, the list -of transformations in XFORMS3 will be applied. -For example, to create a ring of 10 polymers of radius 30.0, -centered at position (0,25,0), use this notation: -\begin{verbatim} -polymer_ring = new Polymer.move(0,30,0) [10].rot(36,1,0,0) - # After creating it, we can move the entire ring - # (These commands are applied last.) -polymer_ring[*].move(0,25,0) -\end{verbatim} - - -\subsection{Random arrays} -\label{sec:random_arrays} - -\begin{figure}[htbp] -\centering -\textbf{a)} -\includegraphics[height=1.2cm]{random_2bead.jpg} -\hspace{0.2cm} -\textbf{b)} -\includegraphics[height=0.75cm]{random_3bead.jpg} -\hspace{0.2cm} -\textbf{c)} -\includegraphics[width=8cm]{random_heteropolymer.jpg} -%\newline -%\vspace{10 mm} -%\newline -\caption{ -\label{fig:random_heteropolymer} -A random heteropolymer (\textbf{c}), -composed of of \textit{Monomer} and \textit{Monomer3} monomer subunits -(\textbf{a} and \textbf{b}) with (target) probabilities 0.6 and 0.4. -(However, due to random fluctuations, the actual ratio - in this case was 68\% and 32\%. - To avoid this problem, see section \ref{sec:random_exact}.) -} -\end{figure} -Arrays of random molecules can be generated using the -\mbox{\textit{new random() []}} syntax. For example, -below we define a random polymer composed of 50 -\textit{Monomer} and \textit{Monomer3} monomer subunits. -(See figure \ref{fig:random_heteropolymer}.) -\begin{verbatim} -RandPoly50 inherits ForceField { - # Make a chain of randomly chosen monomers: - - monomers = new random([Monomer, Monomer3], [0.6, 0.4], 123456) - [50].rot(180,1,0,0).move(2.95, 0, 0) - - # Now, link the monomers together this way: - write("Data Bonds") { - $bond:bb1 @bond:Backbone $atom:monomers[0]/ca $atom:monomers[1]/ca - $bond:bb2 @bond:Backbone $atom:monomers[1]/ca $atom:monomers[2]/ca - $bond:bb3 @bond:Backbone $atom:monomers[2]/ca $atom:monomers[3]/ca - $bond:bb4 @bond:Backbone $atom:monomers[3]/ca $atom:monomers[4]/ca -\end{verbatim} -$\quad \quad \quad \vdots $ -% : : : : -\begin{verbatim} - $bond:bb50 @bond:Backbone $atom:monomers[48]/ca $atom:monomers[49]/ca - } - #(Note: Both the "Monomer" and "Monomer3" subunits contain atoms - # named "$atom:ca". -} #RandPoly50 -\end{verbatim} -It is also possible to fill a 2 or 3-dimensional volume with -molecules randomly. This is discussed in section -\ref{sec:random_advanced}. - -%\textit{Note: To specify the exactly number of molecules of each type, -%you can also use this notation (discussed below).} -%\begin{verbatim} -% monomers = new random([Monomer, Monomer3], [30, 20], 123456) -% [50].rot(180,1,0,0).move(2.95, 0, 0) -%\end{verbatim} - - -The \mbox{\textit{new random()}} function takes 2 or 3 arguments: -a list of molecule types -(\mbox{\textit{Monomer}} and \mbox{\textit{Monomer3}} in this example), -and a list of probabilities (\textit{0.6} and \textit{0.4}) -both enclosed in square-brackets []. - -\subsubsection{Random arrays with exact molecule type counts} -\label{sec:random_exact} -Recall that we requested that 60\% of the molecules be of type -``Monomer'' and 40\% type ``Monomer3'' (corresponding to 30 and 20, respectively). -However, the resulting polymer (shown in figure \ref{fig:random_heteropolymer}) -contains 34 ``Monomer'' and 16 ``Monomer3'' monomers (68\% and 34\%, respectively). -This is because each time a monomer is created, a random number is generated -to decide which type of monomer will be created. -There is no guarantee that the total final fraction of monomers will -match the target probabilities exactly (60\% and 40\%, respectively). -To specify the number of molecule types precisely, you can replace -the list of probabilities ``[0.6,0.4]'' -with a list of integers ``[30,20]''. -\begin{verbatim} - monomers = new random([Monomer, Monomer3], [30, 20], 123456) - [50].rot(180,1,0,0).move(2.95, 0, 0) -\end{verbatim} -This will create exactly 30 ``Monomer'' and 20 ``Monomer3'' monomers. -(You can do this with multidimensional arrays as well. -See section \ref{sec:random_multidim_exact}.) -%(In both case, the sum of the molecule type counts (30,20) must match the -%number of molecules in the array being created.) - - -\subsubsection*{Details regarding the \textit{new random} command:} - -\textit{Note:} You can tell moltemplate to customize the bond-types and - angles, depending on the (types of) monomers are connected - by each bond. The ``random\_heteropolymer'' example - downloadable at \url{www.moltemplate.org} demonstrates - how to do this. - -\textit{Note:} -Although this example, there are only two monomer types -(``Monomer'' and ``Monomer3''), there is no limit to the number -of molecule types which appear in these lists (eg ``[Monomer, Monomer3, 4bead],[0.2,0.3,0.2]'') - -\textit{Note:} -An optional random-seed argument can also be included. -(For example the \mbox{\textit{``123456''}} shown above. - If you omit this number, then you will get different - results each time you run moltemplate.) - -\textit{Note:} -These lists can also contain vacancies/blanks. -See section \ref{sec:random_vacancies}.) - -\textit{Note:} -Once a molecule containing random monomers is defined, -(\mbox{\textit{``RandPoly50''}} in this example), each copy of that molecule -(created using the \textit{new} command) is identical. - -\subsubsection*{Optional: Customizing molecule positions - in a \textit{random()} array} -You can customize the position of each type of molecule in the array, -before the array is constructed. -To do this, you can add additional movement commands after -each molecule's type name in the list (eg ``Monomer'' and ``Monomer3''): -\begin{verbatim} - monomers = new random([Monomer.move(0,0.01,0), - Monomer3.move(0,-0.01,0)], - [30,20], - 123456) - [50].rot(180,1,0,0).move(2.95, 0, 0) -\end{verbatim} -The \mbox{\textit{.move(0,0.01,0)}} and \mbox{\textit{.move(0,-0.01,0)}} -suffixes moves these monomers closer or further away from the -polymer axis (the x axis in this example). -This is not restricted to \mbox{\textit{.move()}} commands. -(You can also use \mbox{\textit{.rot()}}, and \mbox{\textit{.scale()}} -commands as well.) -These moves will be applied (in order from left to right), \textit{before} -any of the \mbox{\textit{.move()}} and \mbox{\textit{.rot()}} -commands appearing later (following ``[50]'') are carried out. - - - - -\subsection{[*] and [i-j] slice notation} -\label{sec:array_wildcards_intro} -You can move the entire array of molecules using ``[*]'' notation: -\begin{verbatim} - monomers[*].move(0,0,40) -\end{verbatim} -(Note that ``monomers.move(0,0,40)'' does not work. - You must include the ``[*]''.) -You can also use range limits to move only some of the monomers: -\begin{verbatim} - monomers[2-4].move(0,0,40) -\end{verbatim} -This will move only the third, fourth, and fifth monomers. -If you are more familiar with python's slice notation, you can -accomplish the same thing using: -\begin{verbatim} - monomers[2:5].move(0,0,40) -\end{verbatim} -(In this case, the second integer (eg ``5'') is interpreted as a - strict upper bound.) - -(If these customizations - are not enough for your needs, you can also always load atom -coordinates from an external PDB or XYZ file. -Such files can be generated by PACKMOL, -or a variety of advanced graphical molecular modeling programs. -For complex systems, this may be the best choice.) - - - - -\subsubsection{Building arrays one interval at a time (using slice notation)} - -For a more complicated example, you can build polymers using slice notation. -The example below demonstrates how to build a polymer, -specifying which part is random, and and which part is not: - -\begin{verbatim} - monomers[0] = new Monomer3 - monomers[1-48] = new random([Monomer, Monomer3], [30, 18], 123456) - [48].rot(180,1,0,0).move(2.95, 0, 0) - monomers[49] = new Monomer3 - # It's a good idea to move these monomers to keep them from overlapping - monomers[0].rotate(180,1,0,0) - monomers[1-48].move(2.95,0,0) - monomers[49].move(144.55,0,0) #(note: 144.55=49*2.95) -\end{verbatim} -In this example, we insure that monomers[0] and monomers[49] are both -of type ``Monomer3'' -(while keeping the total number of ``Monomer'' and ``Monomer3'' monomers at - 30 and 20, respectively). - -\textit{(Note: You can replace ``monomers[1-48]'' with -``monomers[1:49]'', or ``monomers[1*48]'', if you prefer that syntax style. -You can build multidimensional arrays using slice notation as well, for example -``molecules[3][10-19][4-6] = new Molecule[10][3]'')} - - - -\subsection{Multidimensional arrays} -\label{sec:multidimensional_arrays} -The same techniques work with multidimensional arrays. -Coordinate transformations can be applied to each layer -in a multi-dimensional array. -For example, to create a cubic lattice of 3x3x3 polymers: -you would use this syntax: -\begin{verbatim} -molecules = new Polymer [3].move(30.0, 0, 0) - [3].move(0, 30.0, 0) - [3].move(0, 0, 30.0) -\end{verbatim} -(Similar commands can be used with rotations to generate objects -with cylindrical, helical, conical, or toroidal symmetry.) - -\subsection{Customizing individual rows, columns, or layers} -Similarly, you can customize the position of individual polymers, -or layers or columns using the methods above: -\begin{verbatim} -molecules[1][*][*].move(0,20,0) -molecules[*][1][*].move(0,0,20) -molecules[*][*][1].move(20,0,0) -\end{verbatim} -See figure \ref{fig:2bead_polymer}c) -\textit{(You can also use slice notation, - eg ``molecules[1][0-2][0-1].move(20,0,0)'')} - -You can delete part of an array and replace it with something else -(eg \textit{``Lipid''}) -using slice notation: -\begin{verbatim} -delete molecules[0-1][1][1-2] # (shorthand for delete molecules[0][1][1] - # delete molecules[0][1][2] - # delete molecules[1][1][1] - # delete molecules[1][1][2]) - -# Now replace the array elements we deleted: -molecules[0-1][1][1-2] = new Lipid [2].move(30, 0.0, 0.0) - [2].move(0.0, 0.0, 30.0) - -# ...and move them back to the location of the vacancies we created -molecules[0-1][1][1-2].move(0, 30.0, 30.0) -\end{verbatim} -\textit{The word ``Lipid'' in this example is not important. - It is the name of some other molecule type.} - - -\subsection{Creating random mixtures using multidimensional arrays} -\label{sec:random_advanced} -You can use \mbox{\textit{``new random()''}} to fill space with -a random mixture of molecules. The following 2-dimensional example -creates a lipid bilayer (shown in figure \ref{fig:random_bilayer}) -composed of an equal mixture of -DPPC and DLPC lipids. (...Whose definition we omit here. -See the online examples for details.) -\begin{verbatim} -import "lipids" # define DPPC & DLPC -lipids = new random([DPPC,DLPC], [0.5,0.5], 123) # "123"=random_seed - [19].move(7.5, 0, 0) # lattice spacing 7.5 - [22].move(3.75, 6.49519, 0) # hexagonal lattice - [2].rot(180, 1, 0, 0) # 2 monolayers -\end{verbatim} -\begin{figure}[htbp] -\centering -\textbf{a)} -\includegraphics[width=5cm]{lipid_bilayer_mixture.jpg} -\hspace{0.5cm} -\textbf{b)} -\includegraphics[width=5cm]{lipid_bilayer_vacancies.jpg} -%\newline -%\vspace{10 mm} -%\newline -\caption{ -\label{fig:random_bilayer} -A lipid bilayer membrane composed of a random equal mixture of -two different lipid types in a 1:1 ratio. -(See section \ref{sec:random_advanced}.) -In \textbf{b)} one of the molecule types was left blank -leaving vacancies behind. -(See section \ref{sec:random_vacancies}.) -} -\end{figure} -\subsection{Inserting random vacancies} -\label{sec:random_vacancies} -The list of molecule types passed to the \mbox{\textit{random()}} function -may contain blanks. In the next example, 30\% of the lipids are missing: -\begin{verbatim} -lipids = new random([DPPC, ,DLPC], [0.35,0.3,0.35], 123) # 2nd element is blank - [19].move(7.5, 0, 0) - [22].move(3.75, 6.49519, 0) - [2].rot(180, 1, 0, 0) -\end{verbatim} -The results are shown in figure \ref{fig:random_bilayer}b). -\textit{(Note: When this happens, the array will contain missing elements. - Any attempt to access the atoms inside these missing molecules will - generate an error message, - however moving or deleting array entries - using [*] or [i-j] notation should be safe.)} - -\subsubsection{Random multidimensional arrays with exact type counts} -\label{sec:random_multidim_exact} -Due to random fluctuations the number of DPPC and DLPC lipids created -may not equal exactly 0.35 $\times$ of the number of entries in the array, - -Alternately, you can specify the exact number of DPPC and DLPC molecules -you desire (as opposed to a list of probabilities). -To do this, replace the list of probabilities with integers: -\begin{verbatim} -lipids = new random([DPPC, ,DLPC], [293,250,293], 123) - [19].move(7.5, 0, 0) - [22].move(3.75, 6.49519, 0) - [2].rot(180, 1, 0, 0) -\end{verbatim} -This will generate exactly 293 DPPC and DLPC molecules -(and 250 \textit{blank} entries, -since the second molecule type was unspecified). -The sum (ie 293+250+293) must equal the number of entries in the -array you are creating (ie 19x22x2). - -\subsection{Cutting rectangular holes using \textbf{delete}} -\label{sec:delete_holes} -The delete command can be used to cut large holes in -1, 2, and 3-dimensional objects. -For example, consider a simple 3-dimensional 12x12x12 cube of molecules. -(For simplicity, each ``molecule'' in this example contains only one atom. - These atoms appear as blue spheres in figure \ref{fig:delete_holes}.) -\begin{verbatim} -molecules = new OneAtomMolecule [12].move(3.0,0,0) - [12].move(0,3.0,0) - [12].move(0,0,3.0) -\end{verbatim} -Then, we cut out some rectangular vacancies: - %The first two commands below delete two layers of molecules - %near the top and bottom of the cube. - %The last command deletes a rectangular box of molecules near the center. -\begin{verbatim} -delete molecules[*][*][2] -delete molecules[*][*][8] -delete molecules[6-7][0-8][5-6] -\end{verbatim} -The result of these operations is shown in figure -\ref{fig:delete_holes}. -\textit{(Note: You may move or delete previously deleted array elements - more than once, and/or deleting overlapping rectangular regions - without error.)} - -\begin{figure}[htbp] -\centering -\includegraphics[width=4.0cm]{delete_holes1.jpg} -\caption{ -\label{fig:delete_holes} -Rectangular holes can be carved out of an array of molecules -(represented here by blue spheres) -using the ``delete'' command. Three delete commands were used to -remove the two planar regions and the rectangular hole in the center. -} -\end{figure} - - - - - - -\section{Customizing molecule position and topology} -\label{sec:custom_xform} -By default, each copy of a molecule created using the \textit{new} -command is identical. This need not be the case. - -As discussed in section \ref{sec:xform_after_instance}, -individual molecules which were recently created -can be moved, rotated, and scaled. -You can also overwrite or delete individual atoms, -bonds, and other interactions within a molecule, or their subunits. -(See sections -\ref{sec:delete_atoms_bonds}, -\ref{sec:custom_atom}, and \ref{sec:adding_atoms_bonds}.) -You make any of these modifications to \textit{some} copies -of the molecule without effecting other copies. -Furthermore, if those molecules are compound objects -(if they contain individual molecular subunits within them), -then you can rearrange the positions of their subunits as well. -And all of this can be done from anywhere else in the LT file. - %\textit{(The notation in section \ref{sec:paths} explains - % how to navigate the object hierarchy.)} - -For example, suppose we used the ``Polymer'' molecule we defined above -to create a larger, more complicated ``MolecularComplex'' molecule. -\begin{verbatim} -MolecularComplex { - polymers[0] = new Polymer - polymers[1] = new Polymer.rot(180,1,0,0).move(0, 12.4, 0) -} -mol_complex = new MolecularComplex -\end{verbatim} -The \textit{MolecularComplex} molecule is shown in figure \ref{fig:mol_complex}a). -\textit{Optional: If you want all the atoms in a ``MolecularComplex'' to share the same molecule-ID, -then define ``MolecularComplex'' this way:} -\begin{verbatim} -MolecularComplex inherits ForceField { - create_var { $mol } - polymers[0] = new Polymer - polymers[1] = new Polymer.rot(180,1,0,0).move(0, 12.4, 0) -} -\end{verbatim} -\textit{For this to work, you must also delete the - \mbox{\textit{``create\_var \{\$mol:.\}''}} line from - the definition of the Polymer molecule. See section \ref{sec:2bead}.} - - -We can subsquently customize the position of the 3rd monomer (``monomers[2]'') -of the second polymer (``polymers[1]''), this way: -\begin{verbatim} -mol_complex/polymers[1]/monomers[2].move(0,0.2,0.6) -\end{verbatim} - -This does not effect the position of -\textit{monomers[2]} in \textit{polymers[0]}. -(or in any other \textit{``Polymer''} or -\textit{``MolecularComplex''} molecule.) -If you want to do the same thing for both polymers, -you could use a wildcard character ``*'' -\begin{verbatim} -mol_complex/polymers[*]/res[2].move(0,0.2,0.6) -\end{verbatim} -If you want to move both polymers, you can use: -\begin{verbatim} -mol_complex/polymers[*].move(0,0.2,0.6) -\end{verbatim} -you could use a wildcard character ``*'' -(You can also use ranged (slice) notation, such as ``polymers[0-1]'', - as an alternative to ``polymers[*]''. -See section \ref{sec:array_wildcards_intro}. - -To make changes that apply to every subsequently created \textit{``Polymer''} -or \textit{``MolecularComplex''} molecule, -see section \ref{sec:molecule_customization}.) - - -\subsection{Customizing individual atom locations} -\label{sec:custom_atom} -The ``move'' or ``rot'' commands can not be used to control the positions -of \textit{individual atoms}. -Instead simply overwrite their coordinates this way: -%$atom:mol_complex/polymers[0]/res[2]/CA $mol:mol_complex/polymers[1] @atom:R 0 6.4 8.0 0 -\begin{verbatim} -write("Data Atoms") { - $atom:mol_complex/polymers[0]/res[2]/ca $mol:... @atom:R 0 6.4 8.2 0.6 -} -\end{verbatim} - -\subsection{Adding bonds and angles to individual molecules} -\label{sec:adding_atoms_bonds} -Adding additional bonds within a molecule can be accomplished -by writing additional lines of text to the ``Data Bonds'' section. -(This is what we did when we added bonds between monomers to create a polymer - in section \ref{sec:2beadPolymer}.) -Again, bonds and atom names must be referred to by their \textit{full} names. -Bonds and bonded interactions can be deleted using the ``delete'' command. -(See section \ref{sec:delete}.) - - -\subsection{The \textbf{delete} command} -\label{sec:delete} - -\subsubsection{Deleting molecules or molecular subunits} -Molecules can be further customized by deleting -individual atoms, bonds, bonded-interactions, and entire subunits. -We can \textbf{delete} the 3rd monomer of the second polymer, -use the ``delete'' command: -\begin{verbatim} -delete mol_complex/polymers[1]/res[2] -\end{verbatim} - -\subsubsection{Deleting atoms, bonds, angles, dihedrals, and impropers} -\label{sec:delete_atoms_bonds} -Individual atoms or bonds can be deleted in a similar way: -\begin{verbatim} -delete mol_complex/polymers[1]/res[3]/ca #<-- deletes the "ca" atom -delete mol_complex/polymers[1]/res[4]/cr #<-- deletes the "cr" bond -\end{verbatim} -Whenever an atom or a molecule is deleted, the bonds, angles, dihedrals, -and improper interactions involving those atoms are deleted as well. -\textit{Note: You must omit the ``\$'' character when deleting atoms, -bonds, or angles, as we did in the two lines above).} - - - %\textit{(In fact, any lines of text in any ``write()'' statement - %containing references to deleted atoms are omitted. - -When a bond is deleted, any angular, dihedral, or improper -interactions which were \textit{automatically} -generated by moltemplate are removed as well. -(However other bonded interactions explicitly listed by the user in their -``Data Angles'', ``Data Dihedrals'', or ``Data Impropers'' sections -are not removed. These need to be deleted manually.) - -Multiple molecules can moved or deleted in a single command. For example, -the following command deletes the third, fourth, and fifth monomers from -both polymers[0] and polymers[1]: -\begin{verbatim} -delete mol_complex/polymers[*]/res[2-4] -\end{verbatim} -See section \ref{sec:array_wildcards_intro} for an -explanation of ranged (``[2-4]'') array notation, -and wildcard characters (``*''). - -\textit{Minor bug notice: -Deleting atoms or molecules may cause -inaccuracies in the \$atoms, \$bonds, \$angles, \$dihedrals, and \$impropers -sections of the ``ttree\_assignments.txt'' file. -(If this is a problem, please email me. -Andrew 2014-12-09.) -Fortunately, this should not harm the resulting LAMMPS data files or input -scripts generated by moltemplate. They should still work with LAMMPS.} - -\textit{WARNING: The \textbf{delete} feature is experimental. -There have been a few bugs in the \textbf{delete} command, but by 2014-12-09 -these should be fixed. Please report any problems you find. -As always, be sure to visualize your structures -to make sure they look reasonable. -(...by running moltemplate.sh using the - ``-vmd'' command line option, for example. - See sections \ref{sec:vmd_topotools}, \ref{sec:vmd_advanced} for details.)} -%\textit{\textbf{BUG Warning:} -%As of 2014-4-02, delete does not always work -%when the deleted molecule is both bonded to other molecules, -%and when it contains sub-molecules of it's own. -%The temporary work-around is simply to avoid connecting bonds to any molecule -%which you plan to delete later. I plan to fix this bug eventually. -%} - - - - %\subsubsection*{The context() modifier.} - %\textit{THIS FEATURE DOES NOT WORK YET AS OF 2012-5} - %By default, this transformations is applied relative - %to the coordinate system in which the command was given. - %In other words, this command will move the third - %monomer of polymers[1] in the +Y direction - %regardless of the direction that the molecule ``res[2]'' is facing. - %Alternately, if we want to apply this transformation - %in polymers[1]'s local coordinate system, - %we would use the context(polymers[1]) command: - %\begin{verbatim} - %mol_complex/polymers[1]/res[2].context(polymers[1]).move(0,1,0) - %\end{verbatim} - - -%\subsubsection*{Examples using center-of-mass coordinate transformations} -%\textit{WARNING: experimental feature 2012-3-31} -% -%You can also center a molecule around it's center-of-mass using ``movecm()'', -%rotate it, and then move it this way: -%\begin{verbatim} -%re6s = new Monomer.movecm(0,0,0).rot(180.0, 1,0,0).move(14.2, 0, 0) -%\end{verbatim} -%By default all rotations are about the origin, not the center-of-mass. -%You can also rotate a molecule around it's center-of-mass using ``rotcm()'' -%(without centering it first), and them move the molecule this way: -%\begin{verbatim} -%res6 = new Monomer.rotcm(180.0, 1,0,0).move(14.2, 0, 0) -%\end{verbatim} - - -\subsection{Customizing molecule \textit{types}} -\label{sec:molecule_customization} -You can create modified versions of existing molecule \textit{types}, -without having to redefine the entire molecule. For example: -\begin{verbatim} -MolecularComplex0 = MolecularComplex.move(-9.6,-6.2, 0).scale(0.3125) -\end{verbatim} -or equivalently: -\begin{verbatim} -MolecularComplex0 = MolecularComplex -MolecularComplex0.move(-9.6,-6.2, 0).scale(0.3125) -\end{verbatim} -This creates a new type of molecule named ``MolecularComplex0'' whose -coordinates have been centered and rescaled. -(Note that the ``scale()'' command only effects the atomic coordinates. -(You will have to override earlier force field settings, -such as atomic radii and bond-lengths in order for this to work properly.) -If we want to make additional customizations -(such as adding atoms, bonds, or molecular subunits), we could use this syntax: -\begin{verbatim} -MolecularComplex0 = MolecularComplex - -# Add some new atoms connecting the two polymers in the mol_complex - -MolecularComplex0 inherits ForceField { - write("Data Atoms") { - $atom:t1 $mol:. @atom:CA 0.0 23.0 0.0 0.0 - $atom:t2 $mol:. @atom:CA 0.0 24.7 4.0 0.0 - $atom:t3 $mol:. @atom:CA 0.0 24.7 8.4 0.0 - $atom:t4 $mol:. @atom:CA 0.0 23.0 12.4 0.0 - } - write("Data Bonds") { - $bond:b1 @bond:Backbone $atom:polymers[0]/res7/CA $atom:t1 - $bond:b2 @bond:Backbone $atom:t1 $atom:t2 - $bond:b3 @bond:Backbone $atom:t2 $atom:t3 - $bond:b4 @bond:Backbone $atom:t3 $atom:t4 - $bond:b5 @bond:Backbone $atom:t4 $atom:polymers[1]/res7/ca - } -} - -# Center and rescale the atoms in all "MolecularComplex0" -MolecularComplex0.move(-9.6,-6.2, 0).scale(0.3125) -\end{verbatim} -The result of these modifications is shown in figure \ref{fig:mol_complex}b). -\begin{figure}[htbp] -\centering -\textbf{a)} -\includegraphics[height=3cm]{mol_complex_LR.jpg} -\hspace{1cm} -\textbf{b)} -\includegraphics[height=3cm]{mol_complex+mol_complex0_transparent_LR.jpg} -%\newline -%\vspace{10 mm} -%\newline -\caption{ -\label{fig:mol_complex} -\textbf{a)} -The ``MolecularComplex'' molecule. This is a contrived example consisting of -two ``Polymers''. See section \ref{sec:2beadPolymer} -\textbf{b)} -A customized version of the ``MolecularComplex'' molecule. -(The original ``MolecularComplex'' is shown faded in the background for comparison.) -} -\end{figure} - - %\textit{Note1: Coordinate transformations applied to entire - %molecule types are an experimental feature as of 2013-4-07.) - %SINCE THEN THIS FEATURE HAS BEEN TESTED. IT SEEMS TO WORK. - - -\textit{Note: These coordinate transformations will be -applied \textbf{after} the molecule is constructed. -(If you add atoms to the molecule, these will be added before -the coordinate transformations are applied, -even if you issue the command later.) -Consequently, to make things clear, -I recommend placing the coordinate transforms applied to -an entire molecule type \textbf{after} all of its internal details -(bonds, atoms, subunits) have been declared, as we did here.} - -\subsubsection*{\textit{(Advanced)} Inheritance} -\label{sec:inheritance_intro} -The \textit{MolecularComplex0} molecule is a type of \textit{MolecularComplex} molecule. -For those who are familiar with programming, -relationships like this are analogous to the relationship -between parent and child objects in an object-oriented programming language. - %What we have done is equivalent to saying that - %\textit{MolecularComplex0} inherits from \textit{MolecularComplex}. -More general kinds of inheritance are supported by moltemplate -and are discussed in section \ref{sec:inheritance}. - -\subsubsection*{\textit{(Advanced)} Multiple Inheritance} -If we wanted, we could have created a new molecule type -(like \textit{``MolecularComplex0''}) -which includes atom types and features from -\textit{multiple} different types of molecules. -Section \ref{sec:inheritance} mentions one way to do this -and section \ref{sec:inheritance_vs_object_composition} -discusses alternate approaches. - - - - - - - - -\section*{Advanced moltemplate usage} - - - -\section{Portability: Using \textit{LT files} for force-field storage} -\label{sec:spce_example_robust} -The ``.LT'' format is a flexible file format -for storing force field parameters in LAMMPS. -If you want to share your ``.LT'' file with others, it's -not safe to assume that all interactions use the same standard formula. - -\subsection{Mixing molecule types} -LAMMPS has the ability to combine molecules using multiple different -force-field styles together using. - %Atoms of one type may interact with - %each other using inexpensive Lennard-Jones potentials. - %Other atoms in the same simulation - %may interact using tabulated potentials, - %orientation-dependent ellipsoidal potentials, - %or even more complex 3-body forces (for example). - %Each of these different force-fields is calculated - %using code from different source files. - %LAMMPS is popular among users who add - %their own custom source files. -In section \ref{sec:spce_example}, -we provided an example of an SPCE water molecule model. -This example was simple to understand. -However, as written, it would be impossible to combine this definition of water -with other molecules which don't share the same simple bond or angle styles. -For example, we used harmonic restoring forces to preserve the water angle -at $109.47^\circ$, but other users may want to mix this SPCE water with a small -number of molecules which use a more complicated angular potential formula, -or tabular angle potentials. -Using the ``hybrid'' keyword, you can avoid this limitation. - %being limited to one particular - %formula to describe all of the bonds, angles, dihedrals - %(and pair and improper) interactions. -A more robust example is included below. - -\begin{verbatim} -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - # AtomID MolID("."=this) AtomType charge coordX coordY coordZ - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - # atom-type Mass - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - # -- Forces between atoms (non-bonded) -- - - # atomTypeI atomTypeJ pair-style-name parameter-list - write("In Settings") { - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - } - - # -- Forces between atoms (bonded) -- - - # bond-id bond-type atom-id1 atom-id2 - write("Data Bonds") { - $bond:oh1 @bond:OH $atom:O $atom:H1 - $bond:oh2 @bond:OH $atom:O $atom:H2 - } - - # bond-type bond-style-name parameter-list - write("In Settings") { - bond_coeff @bond:OH harmonic 200.0 1.0 - } - - # angle-id angle-type atom-id1 atom-id2 atom-id3 - write("Data Angles") { - $angle:hoh @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - # angle-type angle-style-name parameter-list - write("In Settings) { - angle_coeff @angle:HOH harmonic 200.0 109.47 - } - - # miscellaneous - write_once("In Settings") { - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - } - -} # SPCE -\end{verbatim} -There are two differences between this molecule definition -and the ``spce\_simple.lt'' example from section -\ref{sec:spce_example}: - -\subsubsection*{Hybrid force field styles} - %Each one of these ``\_style'' commands above contains the - %``hybrid'' keyword, and followed by a single force-field style - %(such as ``harmonic'', or ``lj/charmm/coul/long''). -To experienced LAMMPS users, it may seem strange -that in this example that we have chosen ``hybrid'' -styles followed by only one force-field style (``harmonic''). - %This is due to a quirk in the way LAMMPS reads input script files: - %We do this so that we later have the option to customize - %the force field style for every - %pair\_coeff, - %bond\_coeff, - %angle\_coeff, - %dihedral\_coeff, - %and improper\_coeff command. - %This syntax is only allowed when using ``hybrid'' styles. - %It's nice to have the option to be able to - %customize force-field style after every interaction. - %Again, we don't need to do that if we are only simulating water, - %it might be necessary if we are combining SPCE water with other - %molecule types which use different styles. -However this will make your molecule easier to share with others. -When other people use your LT file, they can override these -styles as explained in section \ref{sec:overriding_styles}. - -%\subsection{Include a default style:} -%LAMMPS requires users to include -%``atom\_style'',``bond\_style'', ``angle\_style'' -%commands in the ``Init'' section -%(which is part of the LAMMPS input script). -%We did this at the beginning of the definition of the ``SPCE'' molecule. -%The bond and angle styles may clash with the force-field styles -%used by other molecules we might want to interact with. -%Presumably the final list of styles will be specified later on by the users -%who include our ``spce.lt'' molecular file into their simulations, -%overriding our settings. -%However it's always a good idea to provide a list of \textit{default styles} -%just in case they don't. - -%\subsubsection*{Splitting molecule definitions into multiple files.} -%Alternately, we could eliminate the ``In Init'' section from our -%``spce.lt'' file and create another LT file containing the following -%additional text: -% %# -- All settings below are optional and can be overridden later.-- -%\begin{verbatim} -%# file "spce_defaultstyles.lt" -%SPCE { # <-- Append additional content to the "SPCE" molecule -% write_once("In Init") { -% # -- Default styles (for solo "SPCE" water) -- -% units real -% atom_style full -% pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 -% bond_style hybrid harmonic -% angle_style hybrid harmonic -% kspace_style pppm 0.0001 -% pair_modify mix arithmetic -% } -%} -%\end{verbatim} -%\textit{ -%(Note that additional ``SPCE \{...\}'' wrapper -%merely appends additional content -%to the ``SPCE'' molecule defined in ``spce.lt''. -%This does not overwrite SPCE.) -%} -%Splitting up a molecule into multiple files is usually -%not necessary, especially for small molecules. - - - %(We note that it is necessary to include the ``hybrid'' keyword in the - %``pair\_style'' and ``bond\_style'' commands because this changes the syntax - %of the ``pair\_coeffs'', ``bond\_coeffs'', and other ``coeffs'' commands.) - - - -\subsection{Combining molecules with different force field styles} -\label{sec:overriding_styles} -\textit{Later on}, if a user wants to combine the SPCE water molecule -with another molecule which uses a tabular pair\_style (for example), -they would have to specify the complete hybrid pair\_style in the -``Init'' section of their LT file. For example: -\begin{verbatim} -import "spce.lt" -import "other_molecule.lt" - -write_once("In Init") { - pair_style hybrid lj/charmm/coul/long 9 10 10 table spline 1000 -} -\end{verbatim} -Note: By placing the ``write\_once("In Init")\{ \}'' statement -\textit{after} ``import "spce.lt"'', this insures that -the pair\_style commands issued here will override the -pair\_style commands issued earlier ``spce.lt''. -% bond_style hybrid harmonic nonlinear -% angle_style hybrid harmonic cosine/periodic -This allows moltemplate users users to combine their molecules -``spce.lt'' file shown here -with other template files without modification -(assuming the atom styles match). - - -\subsubsection*{Warning: Force-field parameters belong in ``In Settings'', not ``Data''} - -LAMMPS allows users to store force-field parameters (``Coeffs'') in two places: -a DATA file, \textit{or} an INPUT script. -Similarly, moltemplate technicaly allows you to store these parameters in -in the ``Data'' sections of your .LT file: -\begin{list}{} -\item write\_once("Data Pair Coeffs") -\item write\_once("Data Bond Coeffs") -\item write\_once("Data Angle Coeffs") -\item write\_once("Data Dihedral Coeffs") -\item write\_once("Data Improper Coeffs") -\item -\end{list} - -\textit{However, for portability reasons, this is discouraged.} -Instead, declare your force field parameters -as we do in this manual, -using the corresponding input script commands. -(For example, ``pair\_coeff'', ``bond\_coeff'', ``angle\_coeff'', - ``dihedral\_coeff'', and ``improper\_coeff''. -As in the examples, all of these commands belong in the -``write\_once("In Settings")'' sections of your .LT files.) - - -\subsection{Nesting} -\label{sec:nesting} -Molecule names such as ``Solvent'' (or even ``Water'') -are short and easy to type, but are vague and are not portable. -If you use common, generic molecule names, you will not be able -to combine your molecule templates with templates written -by others (without carefully checking for naming conflicts). -LT files were meant to be used for storing -and exchanging libraries of different molecule types. - -Suppose, for example, that you want to run a simulation consisting of -different molecule types, each of which belong to different LT files. -Suppose two of the LT files both happen to contain definitions for -``Water''. -Moltemplate does not detect these name clashes automatically -and instead attempts to merge the two versions of ``Water'' together, -(most likely creating a molecule with 6 atoms instead of 3). -This is presumably not what you want. - -As the number of molecule types grows, -the possibility of naming clashes increases. -As the behavior of the same molecule can be approximated -using many different force fields, -one has to be careful to avoid clashing molecule names. - -To alleviate the problem, you can ``nest'' your -molecules inside the definition of other molecules or -namespace objects. -This reduces the scope in which your molecule is defined. -See section \ref{sec:butane} for an example. - - -\subsection{A simple force-field example} -Force-field parameters can be shared by groups of related molecules. -In the example below, we create an object named ``TraPPE''. -Later we use it to define a new molecule named ``Cyclopentane''. - -The following example defines a coarse-grained (united-atom) -version of a ``cyclopentane'' molecule. (Hydrogen atoms have been omitted.) -In this example, only the atom types (and positions) and the bonds -connecting them need to be specified. -The interactions between them are determined automatically -by the settings in the force-field file ``trappe1998.lt''. -\begin{verbatim} -import "trappe1998.lt" - -cyclopentane { - - # AtomID MolID('.'=this) AtomType charge coordX coordY coordZ - write("Data Atoms") { - $atom:c1 $mol:. @atom:TraPPE/CH2 0.0 0.0000 0.000000000 1.0000000 - $atom:c2 $mol:. @atom:TraPPE/CH2 0.0 0.0000 0.951056516 0.3090170 - $atom:c3 $mol:. @atom:TraPPE/CH2 0.0 0.0000 0.587785252 -0.809017 - $atom:c4 $mol:. @atom:TraPPE/CH2 0.0 0.0000 -0.587785252 -0.809017 - $atom:c5 $mol:. @atom:TraPPE/CH2 0.0 0.0000 -0.951056516 0.3090170 - } - - write("Data Bonds") { - $bond:bond1 @bond:TraPPE/CC $atom:c1 $atom:c2 - $bond:bond2 @bond:TraPPE/CC $atom:c2 $atom:c3 - $bond:bond3 @bond:TraPPE/CC $atom:c3 $atom:c4 - $bond:bond4 @bond:TraPPE/CC $atom:c4 $atom:c5 - $bond:bond5 @bond:TraPPE/CC $atom:c5 $atom:c1 - } -} -\end{verbatim} -(The ``TraPPE/'' is explained below.) -We can create copies of this molecule in the same way we did with SPCE: -\begin{verbatim} -# A cubic lattice of 125 cyclopentane molecules (12-angstrom spacing) -mols = new Cyclopentane [5].move(0,0,12) [5].move(0,12,0) [5].move(12,0,0) -\end{verbatim} -Unlike the SPCE example, we don't have to specify all of the interactions -between these atoms because the atom and bond types (CH2, CC). -match the type-names defined in the ``trappe1998.lt'' file. -This file contains a collection of atom types and -force-field parameters for coarse-grained hydrocarbon chains. -(See \cite{TraPPE} for details.) -This way, the ``CH2'' atoms in cyclopentane will interact with, -and behave identically to any ``CH2'' atom from any other molecule -which uses the TraPPE force field. -(The same is true for other atom types, and interaction-types - which are specific to ``TraPPE'', such as -``@atom:TraPPE/CH3'', ``@bond:TraPPE/CC'', etc... - %\textit{Note:} By default, all variables are \textit{local} variables. -Another molecule which uses the TraPPE force field is discussed -later in section \ref{sec:butane}.) -The important parts of the ``trappe1998.lt'' file are shown below: -\subsubsection{Namespace example} -\label{sec:trappe} -\begin{verbatim} -# -- file "trappe1998.lt" -- - -TraPPE { - write_once("Data Masses") { - @atom:CH2 14.1707 - @atom:CH3 15.2507 - } - write_once("In Settings") { - bond_coeff @bond:CC harmonic 120.0 1.54 - angle_coeff @angle:CCC harmonic 62.0022 114 - dihedral_coeff @dihedral:CCCC opls 1.411036 -0.271016 3.145034 0.0 - pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 - pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 - # (Interactions between different atom types use mixing rules.) - # (Hybrid styles were used for portability.) - } - write_once("Data Angles By Type") { - @angle:CCC @atom:C* @atom:C* @atom:C* @bond:CC @bond:CC - } - write_once("Data Dihedrals By Type") { - @dihedral:CCCC @atom:C* @atom:C* @atom:C* @atom:C* @bond:CC @bond:CC @bond:CC - } -} -\end{verbatim} -In addition to the atom-type names and masses, -this file stores the force-field parameters (coeffs) for the -interactions between them. - -\subsubsection*{Bonded interactions \textit{by type}} -Again, the ``Data Angles By Type'' and ``Data Dihedrals By Type'' sections -tell moltemplate.sh that bonded 3-body and 4-body interactions exist between -any 3 or 4 consecutively bonded carbon atoms (of type CH2, CH3, or CH4) -assuming they are bonded using ``CC'' (saturated) bonds. -The ``*'' character is a wild-card. -``C*'' matches ``CH2'', ``CH3'', and ``CH4''. -(Bond-types can be omitted or replaced with wild-cards ``@bond:*''.) - -%(moltemplate.sh can automatically generate bonded angle, dihedral, and improper -%interactions between bonded atoms according to their \textit{type} -%as well as bond type connecting them. -%Note: The syntax used in the ``Data Angles By Type'' and ``Data Dihedrals By Type'' -%sections is explained in more detail in appendix \ref{sec:nbody_by_type}. -% -%The ability to specify interactions by atom type instead of atom ID hardly -%matters for the simple water molecule example above but it is useful for -%large molecules. However it makes the LT file format useful for storing -%force-field parameters. It allows local interactions to be specified between -%atoms in complicated molecules which have not been defined yet, (based on -%their local connectivity and atom type). - - - -\subsubsection*{Namespaces and nesting:} -Names like ``CH2'' and ``CC'' are extremely common. -To avoid confusing them with similarly named atoms and bonds -in other molecules, we enclose them (``nest'' them) within a -\textit{namespace} (``TraPPE'', in this example). -Unlike ``SPCE'' and ``Cyclopentane'', ``TraPPE'' is not a molecule. -It is just a container of atom types, bond-types and -force-field parameters shared by other molecules. -We do this to distinguish them from other atoms and bonds -which have the same name, but mean something else. -Elsewhere we can refer to these atom/bond types as -``@atom:TraPPE/CH2'' and ``@bond:TraPPE/CC''. -(You can also avoid repeating the cumbersome ``TraPPE/'' prefix - for molecules defined within the TraPPE namespace. - For example, see section \ref{sec:butane}.) - - - - - -\subsection{Nested molecules} -\label{sec:butane} -Earlier in section \ref{sec:trappe}, we created an object named ``TraPPE'' -and used it to create a molecule named ``Cyclopentane''. -Here we use it to demonstrate nesting. -Suppose we define a new molecule ``Butane'' consisting of 4 coarse-grained -(united-atom) carbon-like beads, whose types are named ``CH2'' and ``CH3''. -\begin{verbatim} -# -- file "trappe_butane.lt" -- - -import "trappe1998.lt" - -Butane { - write("Data Atoms"){ - $atom:c1 $mol:. @atom:TraPPE/CH3 0.0 0.419372 0.000 -1.937329 - $atom:c2 $mol:. @atom:TraPPE/CH2 0.0 -0.419372 0.000 -0.645776 - $atom:c3 $mol:. @atom:TraPPE/CH2 0.0 0.419372 0.000 0.645776 - $atom:c4 $mol:. @atom:TraPPE/CH3 0.0 -0.419372 0.0000 1.937329 - } - write("Data Bonds"){ - $bond:b1 @bond:TraPPE/CC $atom:c1 $atom:c2 - $bond:b2 @bond:TraPPE/CC $atom:c2 $atom:c3 - $bond:b3 @bond:TraPPE/CC $atom:c3 $atom:c4 - } -} -\end{verbatim} - %Note that we inserted ``../TraPPE/'' prefix before ``CH2'', for example, - %to inform moltemplate/ttree that we want to use the ``CH2'' - %atom that defined inside ``../TraPPE''. - %(This is the same thing we did in section \ref{sec:trappe}.) - %The ``../'' before ``TraPPE'' is optional. - - %It informs moltemplate.sh that ``TraPPE'' was defined - %in the parent's environment (IE, one level up). - %(Note: If you omit the ``../'', moltemplate will automatically - %look for it there in any case, so this is optional.) - -Alternately, as mentioned above, it may be simpler to nest our ``Butane'' -within ``TraPPE'', so that so that it does not get confused with other -(perhaps all-atom) representations of butane. In that case, we would use: -\begin{verbatim} -# -- file "trappe_butane.lt" -- - -import "trappe1998.lt" - -TraPPE { - Butane { - write("Data Atoms"){ - $atom:c1 $mol:. @atom:../CH3 0.0 0.419372 0.000 -1.937329 - $atom:c2 $mol:. @atom:../CH2 0.0 -0.419372 0.000 -0.645776 - $atom:c3 $mol:. @atom:../CH2 0.0 0.419372 0.000 0.645776 - $atom:c4 $mol:. @atom:../CH3 0.0 -0.419372 0.0000 1.937329 - } - write("Data Bonds"){ - $bond:b1 @bond:../CC $atom:c1 $atom:c2 - $bond:b2 @bond:../CC $atom:c2 $atom:c3 - $bond:b3 @bond:../CC $atom:c3 $atom:c4 - } - } -} -\end{verbatim} -Note: Wrapping Butane within ``TraPPE\{ \}'' clause merely appends -additional content to be added to the ``TraPPE'' object defined -in the ``trappe1998.lt'' file (which was included earlier). -It does not overwrite it. -Again ``../'' tells moltemplate use the ``CH2'' atom -defined in the context of the TraPPE environment (IE. one level up). -This insures that moltemplate does not create a new ``CH2'' atom type -which is local to the Butane molecule. -(Again, by default all atom types and other variables are local. -See section \ref{sec:variable_scope}.) - % However moltemplate.sh does check the parent/ancestor environments - % before creating a new variable, so ``../'' is not strictly necessary - % in this example.) - -To use this butane molecule in a simulation, -you would import the file containing the butane definition, -and use a ``new'' command to create one or more butane molecules. -\begin{verbatim} -import "trappe_butane.lt" -new butane = TraPPE/Butane -\end{verbatim} -(You don't need to import ``trappe1998.lt'' in this example because -it was imported within ``trappe\_butane.lt''.) -The ``TraPPE/'' prefix before ``Butane'' lets moltemplate/ttree -know that butane was defined \textit{locally} within TraPPE. - - %Of course, additional molecules can be added to - %the existing TraPPE namespace by enclosing them within ``TraPPE\{ \}'', - %brackets, in addition to ``Butane''. - - -\textit{Note: An alternative procedure using \textbf{inheritance} -exists which may be a cleaner way to handle these kinds of relationships. -See sections \ref{sec:inheritance} and \ref{sec:multiple_inheritance}.} - -\subsection{Path syntax: ``../'', ``.../'', and ``\$mol:.''} -\label{sec:paths} -Generally, multiple slashes (``/'') as well as (``../'') can be -used build a path that indicates the (relative) location -of any other molecule in the object hierarchy. -(The ``.'', ``/'' and ``..'' symbols are used here in the same way -they are used to specify a path in a unix-like file-system. -For example, the ``.'' in ``\$mol:.'' refers to the -current molecule (instance), in the same way that -``./'' refers to the current directory. -(Note: \mbox{\textit{``\$mol''}} is shorthand for \mbox{\textit{``\$mol:.''}}) - -A slash by itself, ``/'', refers to the \textit{global environment}. -This is the outermost environment in which all molecules are defined/created. - %\textit{ - %(Details: These symbols can be used to navigate - %both the hierarchy of defined molecule \textbf{types}, - %(when preceded by @), - %or the hierarchy of \textbf{instantiated} molecules, - %(when preceded by \$).) - %} - - -\subsubsection{\textit{(Advanced)} Ellipsis notation ``.../''} -\label{sec:ellipsis_type} -If you are using multiple levels of nesting, -and if you don't know (or if you don't want to specify) where -a particular molecule type or atom type (such as ``CH2'') was defined, -you can refer to it using ``.../CH2'' -instead of ``../CH2''. -The ``...'' ellipsis syntax searches up the tree of nested -molecules to find the target (the text following the ``/'' slash). - -\subsubsection{\textit{(Advanced)} \$mol:... notation} -\label{sec:ellipsis_mol} -Recall that LAMMPS allows users the option to assign -\textit{molecule-IDs} to each atom. -(In the water example (section \ref{sec:spce_example}), atoms in -each water molecule is assigned to a molecule-ID, denoted ``\$mol:.''. -In that example, the ``.'' was the name of that molecule's ID.) - -If you want to build large molecules using smaller pieces as building-blocks -moltemplate has a way to allow all the the atoms to share the same molecule-ID. -To refer to the ID of the molecule to which you belong, -use ``\$mol:...''. (If none of the molecule-objects which -instantiate the current molecule-object define a variable in the \$mol category, -then a new local \$mol variable will be created automatically.) -This means that the second column of each line of the ``Data Atoms'' section -should contain ``\$mol:...'' -(assuming ``atom\_style full'' or ``molecular'' is used). - -The ``...'' syntax is explained more formally -in appendix \ref{sec:adv_variable_syntax}.) - - - - -\subsection{\textit{using namespace} syntax} -\label{sec:using_namespaces} - -Because the \textit{Butane} molecule was defined within the \textit{TraPPE} -environment, you normally have to indicate this when you refer to it later. -For example, to create a copy of a \textit{Butane} molecule, -you would normally use: -\begin{verbatim} -import "trappe_butane.lt" - -butane = new TraPPE/Butane -\end{verbatim} - -However for convenience, you can use the -\mbox{``\textbf{using namespace}''} declaration -so that, in the future, you can quickly refer to any -of the molecule types defined within \textit{TraPPE} directly, -without having to specify their path. -\begin{verbatim} -import "trappe_butane.lt" - -using namespace TraPPE - -butane = new Butane -\end{verbatim} -\subsubsection*{This only works for molecule types, not atom types} -Unfortunately, you still \textit{must} always -\textbf{refer to} atom types, bond types, and any other -\textbf{primitive types explicitly} (by their full path). -For example, the second line in the \textit{``Data Atoms''} in the example -below does not refer to the \textit{CH2} atom type defined in \textit{TraPPE}. -(Instead it creates a \textit{new} atom type, -which is probably not what you want.) -\begin{verbatim} -import "trappe_butane.lt" -using namespace TraPPE -butane = new Butane -write("Data Atoms") { - $atom:c1 $mol @atom:TraPPE/CH2 0.0 0.41937 0.00 1.9373 # <-- yes - $atom:c2 $mol @atom:CH2 0.0 -0.41937 0.00 -0.6457 # new atom type? -} -\end{verbatim} -If, for example, you want to leave out the ``TraPPE/'' prefix -when accessing the atom, bond, and angle types defined in TraPPE, -then instead you can define a new molecule which -\textit{inherits} from TraPPE. (See section \ref{sec:inheritance}.) - -\subsection{Inheritance} -\label{sec:inheritance} -We could have defined \textit{Butane} this way: -\begin{verbatim} -import "trappe1998.lt" - -Butane inherits TraPPE { - write("Data Atoms"){ - $atom:c1 $mol:. @atom:CH3 0.0 0.419372 0.000 -1.937329 - $atom:c2 $mol:. @atom:CH2 0.0 -0.419372 0.000 -0.645776 - $atom:c3 $mol:. @atom:CH2 0.0 0.419372 0.000 0.645776 - $atom:c4 $mol:. @atom:CH3 0.0 -0.419372 0.0000 1.937329 - } - write("Data Bonds"){ - $bond:b1 @bond:CC $atom:c1 $atom:c2 - $bond:b2 @bond:CC $atom:c2 $atom:c3 - $bond:b3 @bond:CC $atom:c3 $atom:c4 - } -} -\end{verbatim} -A molecule which \textit{inherits} from another molecule (or namespace) -\textit{is} a particular type of that molecule (or namespace). -Defining \textit{Butane} this way allows it to -access all of molecule types, atom types, and bond types, etc... -defined within \textit{TraPPE} as if they were defined locally. -(I did not have to refer to the CH3 atom types as ``@atom:TraPPE/CH3'', - for example.) - -\subsubsection{Multiple inheritance:} -\label{sec:multiple_inheritance} -A molecule can inherit from multiple parents. -This is one way you can allow the \textit{Butane} molecule -to borrow atom, bond, angle, dihedral, and improper types from -\textit{multiple} different force-field parents: -\begin{verbatim} -import "trappe1998.lt" -import "oplsaa.lt" - -Butane inherits TraPPE OPLSAA { - ... -} -\end{verbatim} -\textit{Details:Moltemplate attempts to resolve duplicate atom types or -molecule types if they are found in both parents, giving priority to the -first parent in the list of parents following the ``inherits'' keyword. -(``TraPPE'' in this example.) - %Note: This feature has not been rigorously tested as of 2013-4-07.) -} - -\subsubsection{Inheritance \textit{vs.} Nesting} -\label{sec:inheritance_vs_nesting} -If two molecules are related to each other this way: -\mbox{\textit{``A \textbf{is a} particular type of B''}}, -then consider using inheritance instead of nesting -(or object composition). -In this example (with \textit{Butane} and \textit{TraPPE}) -either nesting or inheritance would work. - - Again, one very minor advantage to nesting -\textit{Butane} inside \textit{TraPPE}, is that it prevents the name -\textit{Butane} from being confused with or conflicting with any other -versions of the \textit{Butane} molecule defined elsewhere. -(Usually this is not a consideration.) - -\subsubsection{Inheritance \textit{vs.} Object Composition} -\label{sec:inheritance_vs_object_composition} -On the other hand, if two molecules are related to each other this way: -\mbox{\textit{``A is \textbf{comprised of} B and C''}}, -then you might consider using object composition instead of inheritance. -For example: -\begin{verbatim} -import "B.lt" # <-- defines the molecule type "B" - -import "C.lt" # <-- defines the molecule type "C" - -A { - b = new B - c = new C -} -\end{verbatim} - - - - - - %\section{Inheritance} - %\label{sec:inheritance} - %\textit{New (experimental) feature as of 2012-3-31:} - % - %In this section we show a simple example of inheritance and nesting. - % - %\textit{INCOMPLETE DOCUMENTATION} - %\textit{I will finish this example later...} - % - %% \ref{fig:LPN} - %There's no need to define the tail twice. - %Instead use inheritance - %\begin{verbatim} - %CGLipid { - % # Both DOTAP and DOPC lipids share the same tail. - % # In the CGLipid model, the tail is represented by - % # a single linear chain. - % write("Data Atoms"){ - % $atom:c1 $mol:. @atom:C 0.0 0.419372 0.00000 -1.481799 - % $atom:c2 $mol:. @atom:C 0.0 -0.419372 0.00000 -2.773352 - % $atom:c3 $mol:. @atom:C 0.0 0.419372 0.00000 -4.064904 - % $atom:c4 $mol:. @atom:C 0.0 -0.419372 0.00000 -5.356457 - % $atom:c5 $mol:. @atom:C 0.0 0.419372 0.00000 -6.648010 - % } - % write("Data Bonds"){ - % $bond:c12 @bond:Tail $atom:c1 $atom:c2 - % $bond:c23 @bond:Tail $atom:c2 $atom:c3 - % $bond:c34 @bond:Tail $atom:c3 $atom:c4 - % $bond:c45 @bond:Tail $atom:c4 $atom:c5 - % } - % write("Data Angles"){ - % : - %} - %\end{verbatim} - %DOPC and DOTP differ only in the head group (which - %has only 1 atom in this coarse-grained version). - %\begin{verbatim} - %DOPC inherits CGLipid { - % write("Data Atoms"){ - % $atom:head $mol:. @atom:head 0.0 0.000 0.000 0.000 - % } - % write_once("Data Masses"){ - % @atom:. 245.0 - % } - % # Now connect the head to the tail - % write("Data Bonds"){ - % $bond:head-tail @bond:Head-Tail $atom:head $atom:c1 - % } - % : - %} - - %DOTAP inherits CGLipid { - % write("Data Atoms"){ - % $atom:head $mol:. @atom:head 0.0 0.000 0.000 0.000 - % } - % write_once("Data Masses") { - % @atom:. 122.0 - % } - % write("Data Bonds"){ - % $bond:head-tail @bond:Head-Tail $atom:head $atom:c1 - % } - % : - %} - %\end{verbatim} - % - %\textit{INCOMPLETE DOCUMENTATION} - %\textit{I will finish this example later...} - % - % - %\begin{verbatim} - %TubulinA { - % ... - %} - %TubulinB { - % ... - %} - %TubulinDimer { - % a = new A - % b = new B - %} - %\end{verbatim} - %\begin{verbatim} - %Tubulin { - % A { - % ... - % } - % B { - % ... - % } - % Dimer { - % a = new A - % b = new B - % } - %} - %\end{verbatim} - % - %\textit{INCOMPLETE DOCUMENTATION} - %\textit{I will finish this example later...} - - - -\section{Known bugs and limitations} -\label{sec:limitations} - -Please report any bugs you find by email to -\includegraphics[height=0.3cm]{author_email.png}, -or to the lammps-users mailing list. - -\textbf{1)} LAMMPS-style molecule-templates are \textit{not} supported. -The DATA files created by moltemplate are not -in the correct format to be read by the LAMMPS \textit{molecule} command. -(This is because this command was added after moltemplate was written.) -However the formats are similar, and the relevant information can be extracted -using a text-editor and converted to the other format. -(Using a text-editor and awk, or a spreadsheet program. -For more information on these file formats, -\url{http://lammps.sandia.gov/doc/read_data.html} -\url{http://lammps.sandia.gov/doc/molecule.html}.) -Again, feel free to contact \includegraphics[height=0.3cm]{author_email.png} -to request support for LAMMPS-style molecule templates. - - -\textbf{2)} \textbf{Moltemplate consumes a large amount of memory (RAM)} - -Memory use grows proportional to system size. -As of 2014-12-09, setting up a system of 1000000 atoms using moltemplate -currently requires between 2.7 and 12 GB of \textit{available} memory. -(Systems with many bonds and angles consume more memory, - as well as systems with a high molecule count.) - %(This is due to python's excessive memory usage.) -Unfortunately this code was not carefully written to minimize memory usage. -(In addition, python programs can require more than 10 -times as much memory as similar programs written in C/C++.) - %\textit{(I wish I had known this earlier.)} - -This problem might be alleviated by using other -python interpreters with a lower memory footprint. -Alternately, it may be necessary to split a large system into pieces, -run moltemplate on each piece, and combine the resulting data files -into one large data file later. - %(Each time, you can use the ``category()'' command to force the - % \$atom, \$bond, \$angle, \$dihedral, \$improper, and \$mol counters - % to begin at a number larger than 1, so that the values do not overlap.) - %A strategy for combining data files together is discussed - %in appendix \ref{sec:combining_data_files}. - -Also, computers with a moderate amount of RAM can be rented very cheaply. -(For example, see \url{https://cloud.google.com/compute/}.) - -\textit{When setting up large simulations with moltemplate, -consider using the \mbox{``ulimit''} command} -to prevent system crashes. -(If you are on a shared computer, ask an administrator to do this.) -If these options are not available, -you can always run a resource monitor (like ``top'') before -starting moltemplate and kill the process if it's memory usage exceeds 80\%. - - -\textbf{3)} Limited support for non-point-like atoms: - -As of 2017-8-31, only the ``full'', ``angle'', ``atomic'', ``charge'', -``sphere'', ``dipole'', and ``molecular'' styles have been tested. -Non-point-like atoms like ``ellipsoid'', ``tri'', ``line'' -\textit{should} also work with moltemplate. -However these objects -are \textit{not rotated correctly} -by the ``.rot()'' command -(or scaled correctly by the ``.scale()'' command). -More exotic exotic atom styles, such as -``wavepacket'', ``electron'', ``sphere'' and ``peri'' -have not been tested. -In addition, atom\_style \textbf{body} and -atom\_style \textbf{template} are \textit{not} -supported. -Feel free to contact \includegraphics[height=0.3cm]{author_email.png} -to request support for exotic atom styles. - - -\textbf{4)} -When placed at the end of a line, LAMMPS interprets -\textbf{the ``\&'' character} as a -request to merge two lines together. -\textit{It is usually safe to use this character inside -moltemplate write() or write\_once() commands.} -However in some rare cases, joining two lines together using -the ``\&'' character can confuse moltemplate. -For example, in a lammps input script command, -(like ``pair\_coeff'' or ``dihedral\_coeff''), -\textbf{the ``\&'' character should not appear before -the last ``@'' or ``\$'' variable is referenced.} -Also avoid using the ``\&'' character anywhere in the -``Data Atoms'', ``Data Bonds'', ``Data Angles'', ``Data Dihedrals'', ``Data Impropers'', ``Data Angles By Type'', ``Data Dihedrals By Type'', and ``Data Impropers By Type'' -sections. - -\textbf{5)} Triclinic boundary conditions have not been tested: - -As of 2014-12-09, support for PDB files with triclinic cells is experimental. -Please let me know if it is not working. - -\textbf{6)} Inconsistent support for wildcard characters (``*'' and ``?'') -\label{sec:wildcard_bug} - The wildcard character ``*'' - is interpreted differently in different parts of an LT file. - Wildcard characters work reliably and are used for \textit{string} - pattern matching when inside - ``bond\_coeff'', ``angle\_coeff'', ``dihedral\_coeff'', ``improper\_coeff'', - and most ``pair\_coeff'' commands, - as well as any of the \textit{``By Type''} sections - in an LT file (such as - \textit{``Data Angles By Type''}, - \textit{``Data Dihedrals By Type''}, and - \textit{``Data Impropers By Type''}). - However these wildcard characters \textit{do not} - within pair\_coeff commands that require \textit{more} - than 2 atom types as arguments. - (such as ``pair\_style hbond/dreiding/lj''. - However manybody pair\_styles which use ``pair\_coeff * *'' - notation work fine.) - As of 2017-8-31, wildcard characters (``*'', ``?'') also fail to work inside - \textit{``bond\_modify''} commands, and other commands used for running - active matter simulations. (Such commands are typically located within the - \textit{``write\_once("In Transitions")''} section of an .LT file.) - LAMMPS interprets ``*'' characters appearing here as - \textit{numeric ranges}, and their behavior depends on the - integers which moltemplate assigns to these variables, - \textit{not} the \textit{names} of the variables. - (See the official documentation for bond\_modify, and bond\_coeff - commands to see how ``*'' characters are interpreted. - This can lead to unintended side-effects and is discouraged. - The ``*'' character can be safely used in array brackets, \textit{[*]}, or in - the varios \textit{``\_coeff''} commands and \textit{``By Type''} sections. - (See section \ref{sec:array_wildcards_intro} - and appendix \ref{sec:nbody_by_type}.) - -\pagebreak - - - -\appendix -\section*{Appendices} - -\section{Bonded interactions ``By Type''} -\label{sec:nbody_by_type} - -Interactions between atoms in LAMMPS which are not bonded together -(ie ``non-bonded'' or ``pair'' interactions) -are specified \textit{by atom type}. -\textit{Bonded interactions} in LAMMPS, -(including 3-body angle, and 4-body dihedral and improper interactions), -are specified by unique \textit{atom ID number}. -(There are typically a large number of angles and bonds in -a typical molecule, and this information occupies the -majority of in a typical LAMMPS data file.) - -This has changed in moltemplate.sh. moltemplate.sh contains a -utility which can generate angles, dihedrals, and impropers -automatically by atom and bond \textit{type}. -(This utility is described in section \ref{sec:nbody_by_type_utility}.) -moltemplate.sh will inspect the network of bonds present in your system, -detect all 3-body, and 4-body interactions, and determine their type. -(Higher n-body interactions can also be defined by the user.) -Specifying interactions this way can eliminate significant redundancy -since many atoms share the same type. - -To make use of this feature, you would create a new section named -\mbox{``Data Angles By Type''}, \mbox{``Data Dihedrals By Type''}, -or \mbox{``Data Impropers By Type''} -whose syntax mimics the -\mbox{``Angles''}, \mbox{``Dihedrals''}, and \mbox{``Impropers''} -sections of a LAMMPS data file. -The syntax is best explained by example: - -\begin{verbatim} -write("Data Angles By Type") { - @angle:XCXgeneral * *C* * - @angle:CCCgeneral @atom:C @atom:C @atom:C * * - @angle:CCCsaturated @atom:C @atom:C @atom:C @bond:SAT @bond:SAT -} -\end{verbatim} - -%\begin{list}{} -%\item -The first line will generate a 3-body angle interaction -(of type \mbox{``@angle:XCXgeneral''}) -between any 3 consecutively bonded atoms -as long as the second atom's type-name contains the letter ``C''. -(Atom and bond type-names can contain wildcard characters *) - -%\item -The second line will generate a 3-body interaction -of type \mbox{``@angle:CCCgeneral''} -between any 3 atoms of type \mbox{``@atom:C''}, -regardless of the type of bonds connecting them. -(The last two columns, which are both wildcard characters, *, - tell moltemplate.sh to ignore the two bond types. - Since this is the default behavior - these two columns are optional and can be omitted.) - -%\item -The third line will generate a 3-body interaction of -type \mbox{``@angle:CCCsaturated''} -between any 3 atoms of type \mbox{``@atom:C''}, -if they are connected by bonds of type \mbox{``@bond:SAT''}. -%\end{list} - -Note: The 2nd and 3rd lines in this example will generate new interactions -which may override any angle interactions assigned earlier. - -\subsection*{Regular expressions} -Regular-expressions can also be used to match potential atom and bond types. -(To use regular expressions, surround the atom and -bond types on either side by slashes. -For example: \mbox{@atom:C[1-5]/}, should match -\mbox{@atom:C1} through \mbox{@atom:C6}.) -\textit{Note: This feature has not been tested as of 2014-12-09.} - -In a similar way, one can define ``Dihedrals By Type'' and -``Impropers By Type''. - - - % I THINK I FIXED THIS LIMITATION - % SO I COMMENTED OUT THIS NEXT SECTION: - % IGNORE ALL COMMENTED OUT TEXT IN THE PARAGRAPHS BELOW - %In all of these examples, the slash ``/'' following the - %@ character is explained below. - % - %\subsection*{Nesting: ``By Type'' interactions \textit{require full-path} variable syntax} - % - %Consider again the atom type named ``CH2'' defined within the ``trappe1998.lt'' - %example from section \ref{sec:nesting}. - %Every atom and bond type defined in that file was defined - %inside the ``TraPPE'' namespace. - %(That file contains a ``TraPPE {...}'' clause.) - %Consequently any atom types like ``CH2'' are \textit{nested variables}. - %It's \textit{full name} is ``@/atom:TraPPE/CH2'', not ``@atom:CH2''. - %However usually you don't have to refer to it this way. - %When you are inside the ``TraPPE{...}'' clause, it is sufficient - %to refer to this atom using ``@atom:CH2''. - % - %However moltemplate.sh uses an external program to automatically generate - %interactions by type. - %This program is not smart enough to understand nested variable syntax. - %So whenever ``write("Data Angles by Type") {...}'' is nested within - %a molecule definition, you must refer to the atom types using the - %\textit{full-path} syntax - %(for example: ``@/atom:TraPPE/CH2'', not ``@atom:CH2''). - - - - - - -\section{Using ltemplify.py to create an \textit{LT file}} -\label{sec:ltemplify} - -The ``ltemplify.py'' script can be used to convert existing simple LAMMPS -input script and data files into a single ``\textbf{.LT}'' file. -Users can pass one or more LAMMPS input scripts followed by a LAMMPS data file -to the ``ltemplify.py'' script as arguments. -(The data file must appear last in this list. See examples below.) -All atoms, bonds, angles, dihedrals, and impropers and their associated types -will be converted to moltemplate ``\$'' or ``@'' counter variables, -(and the relevant portion of each file will be moved to sections with the -correct header names). Coefficients, atom styles, and -most force-field styles and settings \textit{should} also -be included in the resulting .LT file. -ltemplify.py also understands simple group commands -(using ``id'', ``molecule'', or ``type'' styles) -and ``fix shake'' and ``fix rigid'' (untested 2015-1-04). -However most other fixes, and complex group commands are not understood. -Those commands must be added to the resulting .LT file manually. -(See section \ref{sec:ltemplify_limitations}.) - -\subsubsection*{Disclaimer} - -\textit{ltemplify.py is experimental software.} -The lemplify.py script has limited understanding of all of the features -available in LAMMPS. -Please look over the resulting ``.LT'' file and check for errors. -(If necessary, convert any remaining -atom, bond, angle, dihedral, or improper id or type numbers to the -corresponding \$ or @ variables.) -Some exotic pair styles which have their own special syntax -are not understood. -%(See section \ref{sec:ltemplify_limitations_pair}.) -These coeffs must be converted manually. -Support for ``group'' and ``fix'' commands is also limited. -(See section \ref{sec:ltemplify_fix_group}.) -Please report errors in the behavior of ltemplify.py. - -\subsubsection*{Reassigning variable names} - -Unfortunately, ltemplify.py does not attempt to pick \textit{good} -names for your atoms, bonds, or angles. -Currently, ltemplify.py generates type names and id names automatically, - %the numbers used in the original LAMMPS data file and input script(s), -resulting in atoms with names like ``\$atom:id1753'', -and types like ``@atom:type7''. -(Furthermore, if the user - %used the ``-atomtype'' or ``-mol'' or ``-atomid'' flags to extract -extracted only \textit{part} of the data file, then these -numbers probably do not begin at ``1''.) - %For example the first atom may be - %named and have atom-type ``@atom:type7''. - -Moltemplate will assign all of these variables to new numbers -when you run it on your LT file later (so the names and numbers do not matter). -Still, you may wish to use a text-editor (or \textit{sed}) to replace all -instances of ``@atom:type7'' with something more meaningful, like ``@atom:CG1'', -and ``@bond:Type3'' with ``@bond:C=C''. - - -\subsection{Examples} -\subsubsection*{Example 1} - -\begin{verbatim} -ltemplify.py -name Mol file.in file.data > mol.lt -\end{verbatim} - -This creates a template for a new type of molecule (named ``Mol''), -consisting of all the atoms in the lammps files you included, -and saves this data in a single LT file (``mol.lt''). -This file can be used with moltemplate.sh (and/or ttree.py) to -define large systems containing this molecule. - -Note: The input script (``file.in'' in this example) should appear - before the data file (``file.data'') in the argument list. - -In many cases, a LAMMPS data file may contain many copies of the same -molecule. In order to select one of these molecules you must manually -indicate the atoms which belong to that molecule. -To do that, use the following syntax: - -\subsubsection*{Example 2} - -\begin{verbatim} -ltemplify.py -name Mol -molid "1" file.in file.data > mol.lt -\end{verbatim} - - In this example, only atoms belonging to molecule 1 are extracted. - -This only works if you are using one of the ``molecular'' atom\_styles. -If you are using a different atom\_style, you can select the atoms you want -either by type or by id number. To do that use the following syntax: -\subsubsection*{Example 3} - -\begin{verbatim} -ltemplify.py -name Mol -atomtype "1 2 3" lammpsfile.in lammpsfile.data > mol.lt -\end{verbatim} - - In this example, only atoms whose type is 1, 2, or 3 are included. - -\subsubsection*{Example 4} - -\begin{verbatim} -ltemplify.py -name Mol -atomid "13 14 15 61*69" \ - lammpsfile.in lammpsfile.data > mol.lt -\end{verbatim} - - In this example, only atoms whose ids are - 13, 14, 15, and 61 through 69 are included. - - - -\subsubsection{ Fixes and Groups } -\label{sec:ltemplify_fix_group} - -ltemplify.py has \textit{limited} support for ``fix'' and ``group'' commands, -including ``fix shake'', ``fix rigid'', and ``fix poems''. -Other fixes must be added manually to the file generated by ltemplify.py. -(Such as fix ``restrain'', ``bond/create'', ``bond/break'', ``ttm'', etc...) - -ltemplify.py can understand simple (static) ``group'' commands, and will include them in the output file, if it can determine that they contain any relevant atoms. (Fixes depending on irrelevant groups are also deleted.) - - -\textit{Note: This feature has not been tested carefully. So please review all of the group and fix commands generated by ltemplify.py to make sure they refer to the correct atoms. And please report any bugs you find. (-Andrew 2014-10-29)} - - - - - -\subsection{Known bugs and limitations (ltemplify.py):} -\label{sec:ltemplify_limitations} -%\subsubsection*{Wildcard characters ``*''} -%Support for wildcards is not consistent throughout an LT file. -% -%Wildcard characters like ``*'' currently mean different things -%in different places. -%In the \textit{write\_once(``Data Angles By Type'') \{...\}} section, -%for example, the ``*'' and ``?'' wildcard characters are interpreted -%as \textit{string wildcards}. -%This means that ``@atom:C?'' will match ``@atom:C1'', ``@atom:C2'', and -%``@atom:CA'', but \textit{not} ``@atom:CA2''. -%However ``@atom:CH*'' will match all of these examples. -%(See appendix \ref{sec:nbody_by_type}.) -%Moltemplate ignores ``*'' characters elsewhere in an LT file, -%and leaves it up to LAMMPS. -% -% -%This means that a ``*'' character appearing in a -%\textit{pair\_coeff}, -%\textit{bond\_coeff}, -%\textit{angle\_coeff}, -%\textit{dihedral\_coeff}, -%\textit{improper\_coeff}, -%or -%\textit{group} -%command, for example, -%is interpreted (by LAMMPS) as a \textit{numeric wildcard}. -%A command like: -% %\mbox{``\textit{pair\_coeff @\{atom:B\}*@\{atom:D\} * lj/cut 0.15 3.6}''} -%\begin{verbatim} -%pair_coeff @{atom:B}*@{atom:D} * lj/cut 0.15 3.6 -%\end{verbatim} -%appearing in an LT file will be substituted with to a numeric equivalent: -% %\mbox{``\textit{pair\_coeff 2*4 * lj/cut 0.15 3.6}''}. -%\begin{verbatim} -%pair_coeff 2*4 * lj/cut 0.15 3.6 -%\end{verbatim} -%LAMMPS will then interpret the result according to its own rules. -%In this example, we have specified the pairwise interaction parameters -%between atom types 2,3,4 and all other atoms. (Subject to the constraint -%that the second atom type must be greater than the first atom type. -%This is a quirk in the way that LAMMPS interprets pair\_coeff commands.) -%For this reason, use of ``*'' characters in LT files is -%currently discouraged (unless part of a ``By Type'' section). - - -\subsubsection*{Exotic styles are not supported} -\label{sec:ltemplify_limitations_pair} -ltemplify.py does \textbf{not} understand the syntax of -exotic many-body pair\_styles such as tersoff, sw, meam, reax, dpd, edip, -dipole, lubricate, hbond/dreiding -(even though these styles are supported by moltemplate). -After running ltemplify.py, the user must manually edit the resulting ``.lt'' -files. For example: ltemplify.py will not understand wildcard characters -(``*'' characters) -which appear in the ``pair\_coeff'' commands or ``Pair Coeffs'' section. -You will have to remove the extra lines generated by ltemplify.py and -put the wildcard characters back (eg ``pair\_coeff * * ...'') manually. -(Later the user may need to run moltemplate using the appropriate ``-a'' - command line args to make sure the various atom types are assigned - to the correct numbers. This is usually needed in order to keep them - consistent with the order of parameters in the corresponding pair style's - input files. See section \ref{sec:manual_assignment}.) -In addition, auxiliary atom types (such as the ``hydrogen'' atom type -required by hbond/dreiding) -If you are using the ``hbond/dreiding'' pair style, you will -have to manually specify the atom type for the hydrogen-atom mediator -in every ``pair\_coeff'' command. - - -\subsubsection*{Wildcard characters (``*'') expansion} -As explained in section \ref{sec:limitations}, -moltemplate is often confused whenever wildcard characters (``*'' characters) -appear inside any of the the ``coeff'' commands -(or ``Coeff'' sections of the data file). -So ltemplify.py attempts to remove these characters and expand these commands, -generating multiple lines of output, and listing each atom type explicitly. -(This is also done for bond types, angle types, dihedral types, - and improper types.) -This may not be what you want. -(For example, this can be a problem if you are using a pair style -which requires you to specify ``* *'' for the atom types, such as -\textit{tersoff}, \textit{eam}, or \textit{sw}.) - - -\section{Visualization in VMD} -\label{sec:vmd_advanced} - -This appendix is only intended to give you a quick, -minimal list of features you need to know to -display your molecules using VMD. -These instructions were written for VMD 1.9 -and topotools 1.2. - %(See \cite{VMD} and \cite{topotools}). -For advanced VMD features, analysis, and rendering options, -consult the official VMD documentation at -\url{http://www.ks.uiuc.edu/Research/vmd/current/docs.html} - -\subsection{Customizing the appearance in VMD} -\label{sec:vmd_representation} -By default, VMD is likely to display your molecules with -points and lines, which can be ugly and difficult to see. -To alter the appearance of your molecules, select the -\textbf{Graphics}$\rightarrow$\textbf{Representations...} menu, -and then select an option from the -\mbox{\textbf{Drawing Method}} pull-down menu. -Atoms are colored by atom-type by default. -You can customize the color of each atom type by -\mbox{\textbf{Graphics}}$\rightarrow$\mbox{\textbf{Colors...}} -As of 2012-11-18, VMD arbitrarily allows you to -assign colors to \textit{only} the first 9 atom types. -However you can get around this limitation -using multiple \textit{representations} -customize the appearance of the -remaining atom types (as explained below). - -You may wish to use different representations for different molecules -or atom types. To do this, select the -\textbf{Graphics}$\rightarrow$\textbf{Representations...} menu -and click on then \mbox{\textbf{Selections}} tab. -Then click on the \mbox{\textbf{Create Rep}} -button to create multiple ``\textit{representations}'' of your system. -For each \textit{representation}, you can select different sets atoms, -and use different draw-styles, for those atoms. -For example, you can customize the color of these atoms manually -by choosing \textbf{ColorID} from the - %For each \textit{representation}, - %you can use different drawing and coloring - %methods, and change the atom and bond radii. - %To control the color manually, - %choose \textbf{ColorID} from the -\mbox{\textbf{Coloring Method}} pull-down menu. -Then, to the right of this menu, you can select the color -(which is represented by a number). -This will effect all of atoms in the current \textit{representation}. -You can also select a different \mbox{\textbf{Draw Style}} and -alter the atom and bond radii. - -You can select from the the list of \textit{representations} you have -already created -by clicking on the list under the \mbox{\textbf{Create Rep}} button. -(Double-clicking temporarily hides a \textit{representation} from view.) - %(You can also temporarily hide \textit{representations} by double-clicking - % on them in the list of selections below the \mbox{\textbf{Create Rep}} - % button.) - -Again, each \textit{representation} is usually assigned to -a different subset of atoms from the system. -To specify the atoms in each \textit{representation}, -click on the \mbox{\textbf{Selections}} tab. -By default ``all'' -atoms are selected, however you can select atoms according to atom -\textbf{type}, \textbf{index}, \textbf{molid}, -\textbf{charge}, \textbf{mass}, \textbf{x}, \textbf{y}, \textbf{z}. -This will limit the current display settings to a -subset of the atoms/bonds present in your system. -When selecting atoms, you can use complex boolean expressions -(containing one or more \textit{and} and \textit{or} operators -and parenthesis). -For more information and some examples, -see \url{http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node19.html} -and -\url{http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/ug/node87.html#ug:topic:selections}. - - %You can select from the list of \textit{representations} you have created - %You can selecting different atoms in each \textit{representation} - %as explained below. - -\textit{\textbf{Note:}} -In VMD/topotools, -the \textbf{type}, \textbf{index}, and \textbf{molid} -properties of each atom correspond -to the \textit{@atom}, \textit{\$atom}, and \textit{\$mol} -variables for each atom in moltemplate. - %associated with each atom in the ``Data Atoms'' section of your LT files. -Unfortunately, VMD does not understand moltemplate variable naming syntax -(discussed in section \ref{sec:variables}). -Instead, in VMD, variables must be -specified by their numeric equivalents. -You can determine these numbers by reading the -\textit{output\_ttree/ttree\_assignments.txt} file. -(See section \ref{sec:ttree_assignments} for details.) -That file contains a table containing a list of the -numbers assigned to each \textit{@atom} (type), \textit{\$atom} (id), -and \textit{\$mol} (molecule-id) variable. - - - - - -\subsection{Visualizing periodic boundaries} -\label{sec:vmd_pbc} -To view the periodic box boundaries, -select the \textbf{Extensions}$\rightarrow$\mbox{\textbf{Tk Console}} menu, -and in the \textit{Tk Console} window, enter: -\begin{verbatim} -pbc box -\end{verbatim} -Note that the molecules in your system might not lie inside this box. -You can \textit{wrap} them inside the box using this command: -\begin{verbatim} -pbc wrap -compound res -all -\end{verbatim} -You may wish to center the box around a molecule. There are several ways to -do this. You can move the box manually this way: -\begin{verbatim} -pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} -pbc box -shiftcenterrel {0.0 0.15 0.0} -\end{verbatim} -This will shift the position of the box by 15\% in the Y direction. -(Distances are measured in units of box-length fractions, not Angstroms.) - -\textit{(Advanced usage: if you have a solute whose atoms are all -of type ``1'', surrounded by a solvent of atoms of type ``2'' -then you can also try this to center the box around it using: -``pbc wrap -sel type=1 -all -centersel type=2 -center com''. -The ``1'' and ``2'' are the @atom type numbers assigned by moltemplate. -This can be found in the output\_ttree/ttree\_assignments.txt file. -If you are viewing a trajectory, then this will modify the appearance -of every step in the trajectory, centering the box around the solute atoms.)} - -For more details visualizing periodic-boundaries, visit: -\url{http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools} - -To prevent atom overlap, you should also check if your periodic boundary -conditions are too small. -To do that: -\begin{list}{} -\item a) select \mbox{\textit{Graphics}$\rightarrow$\textit{Representations}} -menu option -\item b) click on the "Periodic" tab, and -\item c) click on the - \textbf{+x}, \textbf{-x}, - \textbf{+y}, \textbf{-y}, - \textbf{+z}, \textbf{-z}, - and \textbf{self} checkboxes. -\end{list} - -When doing so, inspect the system to make sure the atoms which appear -occupy non-overlapping volumes in space. - - - -\section{Advanced moltemplate.sh Usage} -\label{sec:ttree_man_page} - - -moltemplate.sh has several optional command line arguments. -These are explained in below: - -\begin{verbatim} -Usage: - -moltemplate.sh [-atomstyle style] \ - [-pdb/-xyz/-raw coord_file] \ - [-a assignments.txt] file.lt - -Optional arguments: - --atomstyle style By default, moltemplate.sh assumes you are using the "full" - atom style in LAMMPS. You can change the atom style to "dipole" - using -atomstyle dipole. If you are using a hybrid style, - you must enclose the list of styles in quotes. For example: - -atomstyle "hybrid full dipole" - For custom atom styles, you can also specify the - list of column names manually (enclosed in quotes): - -atomstyle "molid x y z atomid atomtype mux muy muz" - Be careful to enclose the entire list in quotes("). - --raw raw_file The raw_file file should contain the atomic coordinates in RAW format. - RAW files are simple 3-column ASCII files containin the coordinates - for the atoms in the system. (One line per atom, 3 numbers per line. - The atoms must appear in the same order in the data file.) --xyz xyz_file An xyz_file argument should be supplied as an argument - following "-xyz". - This file should contain the atomic coordinates in xyz format. - (The atoms must appear in the same order in the data file.) - --pdb pdb_file The pdb_file file should contain the atomic coordinates in PDB format. - - This file should contain one ATOM or HETATM record per atom. Atoms - - are sorted by chainID, resID, insertCode, atomID (in that order). - This order must match the order the atoms appear in the data file. - - If the PDB file contains periodic boundary box information - (IE., a "CRYST1" record), this information is also copied - to the LAMMPS data file. - (Support for triclinic cells is experimental as of 2014-12-09. - Other molecular structure formats may be supported later. --a "@atom:x 1" --a assignments.txt - The user can customize the numbers assigned to atom, bond, - angle, dihedral, and improper types or id numbers by using - -a "VARIABLE_NAME VALUE" - for each variable you want to modify. If there are many - variables you want to modify, you can save them in a file - (one variable per line). For an example of the file format - run moltemplate.sh once and search for a file named - "ttree_assignments.txt". (This file is often located in - the "output_ttree/" directory.) Once assigned, the remaining - variables in the same category will be automatically assigned - to values which do not overlap with your chosen values. --b assignments.txt - "-b" is similar to "-a". However, in this case, no attempt - is made to assign exclusive (unique) values to each variable. --nocheck - Normally moltemplate.sh checks for common errors and typos and - halts if it thinks it has found one. This forces the variables - and categories as well as write(file) and write_once(file) - commands to obey standard naming conventions. The "-nocheck" - argument bypasses these checks and eliminates these restrictions. --checkff - This cause moltemplate.sh to check to make sure that there - are valid angle and dihedral interactions defined for every - 3 or 4 consecutively bonded atoms in the system - (defined in "Angles/Dihedrals By Type"). -\end{verbatim} - -\subsection{Manual variables assignment (``-a'' or ``-b'')} -\label{sec:manual_assignment} - -It is possible to manually customize the values assigned -to the atom types (or to any other ttree-style variables). - %Create a new file ("new\_assignments.txt" in the example below) - %containing the list of atom types you want to modify, - %and the numbers you want to assign them. - %(This is a two-column file which mimics the contents - %of the ``ttree\_assignments.txt'' file explained below.) -For example, consider the the ``spce.lt'' file shown earlier. -This file defines a single water molecule with two atom types -(hydrogen and oxygen). -Typically the ``O'' atom type is normally assigned to the integer ``1'', -and ``H'' would be assigned to ``2''. -This is because ``O'' appears before ``H'' in that file. -If you wanted to swap the order, you could swap the order -in which they first appear. - -Alternately you can specify the atom assignments directly -using one or more ``-a'' flags followed by a quoted assignment string: -\begin{verbatim} -moltemplate.sh -a '@atom:SPCE/O 2' system.lt -\end{verbatim} -This assigns the oxygen atom type to ``2''. -Note that quotes are necessary around the '@atom:SPCE/O 2' string, -which is a single argument. -(Also note that it is necessary to include SPCE/ before - %the ``H'' and - the O, - because in that example, - %these atoms - this atom - appeared (and - %were - was - thus defined) inside the SPCE molecule's environment. - Alternately, if - %they - it - had been defined outside, globally, - then you could refer to - %them - it - using - %``@atom:H'', or - ``@atom:O'') - -Variables need not be assigned to numbers. -If for some reason, you want to substitute ``a string'' everywhere -this atom type appears, you would do it this way: -\begin{verbatim} -moltemplate.sh -a '@atom:SPCE/O "a string"' system.lt -\end{verbatim} - -Multiple assignments can be made by using multiple ``-a'' flags: -\begin{verbatim} -moltemplate.sh -a '@atom:SPCE/O 2' -a '@atom:SPCE/H 1' system.lt -\end{verbatim} -However if you have a large number of assignments to make, -it may be more convenient to store them in a file. -You can create a two-column text file (for example ``new\_assignments.txt'') -and run moltemplate this way: -\begin{verbatim} -moltemplate.sh -a new_assignments.txt system.lt -\end{verbatim} -The contents of the ``new\_assignments.txt'' file in this example would be: -\begin{verbatim} -@atom:SPCE/O 2 -@atom:SPCE/H 1 -\end{verbatim} -The order of lines in this file does not matter. - - - %\subsubsection*{Using ``-pdb'' and ``-a'' together} - %If you are using the ``-pdb'', ``-xyz'', or ``-raw'' flags, - %these must appear first. - %The the ``-a'' (and ``-b'') flags must appear - %\textit{at the end} of the argument list - %(but before the ``.lt'' file). - %For example: - %\begin{verbatim} - %moltemplate.sh -pdb file.pdb -a '@atom:SPCE/O 2' system.lt - %\end{verbatim} - -\subsubsection*{Assigning \$angle, \$dihedral, \$improper variables} -In general any kind of variable can be assigned this way (not only atom types), -including \$mol, \$bond, @bond, @angle, \$angle, ... -as well as user-defined variable type. -\textit{Caveat: The only occasional exceptions are the -\$angle, \$dihedral, \$improper variables.} -(When ``Angles By Type'' interactions are selected by the user, -and mixed with regular ``Angles'', -all of the \$angle variables are automatically generated. - %The user does not have the freedom to assign any \$angle variables. -The same is true for ``Dihedrals By Type'' and ``Impropers By Type''. -See section \ref{sec:nbody_by_type_utility} for an explanation of -``By Type'' interactions.) - - -Angles, dihedrals, and impropers interactions are automatically generated, and -in this case the user does not have the freedom to assign these variables. - %``write('Data Angles By Types')'', - %``write('Data Dihedrals By Types')'', or - %``write('Data Angles By Types')'' - -\subsubsection*{The ``-b'' flag} -Note that when using the ``-a'' flag above, care will be taken to -insure that the assignment(s) are exclusive. -None of the atom types (other than @atom:SPCE/O) will be assigned ``2''. -(For this reason, using the ``-a'' flag to change the atom type - assignments can, in principle, alter the numbers assigned - other atom types, or variables.) - %in the same category.) -This usually the desired behavior. -However suppose, for some reason, that you wanted to -force a variable assignment, so that other -variables in the same category are not effected. -In that case, you can use the ``-b'' flag: -\begin{verbatim} -moltemplate.sh -b '@atom:SPCE/O 2' system.lt -\end{verbatim} -Keep in mind, that in this example, this could cause other atom-types -(for example ``@atom:SPCE/H'') to be assigned to overlapping numbers. - %For this reason, the ``-b'' flag is usually used only for - %custom user-defined variable categories - %(such as the ``\$monomerid'' counter example described - %in section \ref{sec:custom_categories}). - - -\subsubsection*{The ``ttree\_assignments.txt'' file} -\label{sec:ttree_assignments} -Generally, after running moltemplate.sh, a ``ttree\_assignments.txt'' -file will be created (or updated if it is already present) -to reflect any changes you made. -(This file is usually located in the ``output\_ttree/'' directory. - It can also be located the current directory ``./''.) -You can always check this to make sure that the atom types -(or any other ttree variables) were assigned correctly. - -The ``ttree\_assignments.txt'' file has the same format -as the ``new\_assignments.txt'' file example above. - -\textit{Note:} In both files, an optional slash, ``/'', - may follow the ``@'' or ``\$'' characters, - as in ``@/atom:SPCE/O''. -(This slash is optional and indicates -the environment in which the counter is defined. -The ``@atom'' counter is defined globally. -The ``\$resid'' counter example described -in section \ref{sec:custom_categories} is not.) - -\textit{Bug-warning: Using the ``delete'' command -may cause some of the instance variables -(specifically the \$atom, \$mol, \$bond, \$angle, \$dihedral, -and \$improper variables) -to be numbered incorrectly. -However static variables (beginning with @) should always be accurate. --Andrew 2013-4-07.} - - -\subsubsection*{lttree.py and ttree.py also accept ``-a'' and ``-b'' flags} -If for some reason, you are using ``lttree.py'' or ``ttree.py'' -instead of ``moltemplate.sh'', then the ``-a'' and ``-b'' flags explained -here also work with these scripts. They are not specific to moltemplate.sh. - - - - -\subsection{Customizing the counting method using \textit{category}} -\label{sec:custom_categories} -Variables in ``.lt'' files are assigned to integers by default, -starting with 1, and incrementing by 1. -This can be overridden using the ``category'' command. -For example, to create a new variable category named ``distance'' -which starts at $0$ and increments by $0.5$, -you would include this command in your LT file: -\begin{verbatim} -category $distance(0.0, 0.5) -\end{verbatim} -(This command should \textit{not} be used with traditional counter categories - like -\textit{\$atom, \$bond, \$angle, \$dihedral, \$improper, \$mol, -@atom, @bond, @angle, @dihedral,} and \textit{@improper}.) - - %\subsection{Combining files together} - %\label{sec:combining_data_files} - %This is useful if you are combining data files from two systems together. - %For example if a previous system contains - %317982 atoms, 292106 bonds, 275790 angles, - %259474 dihedrals, and 7520 impropers, - %then the next time you run moltemplate, you would insert the following text - %at the beginning of your LT file (system.lt) - %\begin{verbatim} - %category $atom(317983, 1) - %category $bond(292107, 1) - %category $angle(275791, 1) - %category $dihedral(259475, 1) - %category $improper(7521, 1) - %\end{verbatim} - %This will avoid overwriting the settings for these - %atoms, bonds, angles, dihedrals, and impropers in the previous system. - %The corresponding ``Atoms'', ``Bonds'', ``Angles'', ``Dihedrals'', - %and ``Impropers'' from the new DATA file can be directly appended to - %same sections from the old DATA file. - %(Note that the temporary files in the ``output\_ttree/'' - %with names like ``Data Atoms'', ``Data Bonds'', ``Data Angles'', ..., - %contain only the text from these sections and should make this task easier. - %See section \ref{sec:output_ttree}. - %If you need help to combine a large number of systems together, - %contact \includegraphics[height=0.3cm]{author_email.png} - %and we can work on an automated solution. - %I would like to eventually see moltemplate be used for large systems.) - -\subsection{Creating local independent counters} -\label{sec:cpath_simple} -By default variables in a given category are always assigned -to unique integers. -This can be overridden using the ``category'' command. -For example, you might have a variable that keeps track of -the monomer in every polymer. -The first monomer in a polymer is assigned ``1'', -the second monomer, ``2'', etc, -\textit{regardless} of the number of polymer in your system. - -To do this, we can create a new variable category named ``monomerid'' which -is defined within the scope of each instance of the ``Polymer'' molecule: -\begin{verbatim} -Monomer { - write("Data Atoms") { - $atom:ca @atom:CA $monomerid:. 0.0 0.0 0.0 0.0 - $atom:cb @atom:CB $monomerid:. 0.0 1.53 0.0 0.0 - } -} - -Polymer { - category $monomerid(1,1) - monomers = Monomer[100] -} - -polymers = Polymer[10] -\end{verbatim} -In this example, there are 10 polymers containing 100 monomers each. -The ``\$monomerid'' counters will be replaced with integers in the range -$1\ldots 100$, -(not $1\ldots 1000$, as you might expect). -Because the ``\$monomerid'' counter is local to the -protein it is defined within, -``\$monomerid'' variables in other proteins do not share the same counter, -and can overlap. - -\subsection{Counting order} -\label{sec:order} -Most variables are assigned automatically. -By default static variables (@) are assigned in the order -they appear in the file (or files, if multiple LT files are included). -Subsequently, instance variables (\$) -are assigned in the order they are created during instantiation. -However you can customize the order in which they are assigned. - -\subsubsection*{Ordering} - -LT files are parsed by moltemplate.sh/lttree.py -in multiple stages. -The ``write\_once()'' and ``write()'' commands are carried out -in the static and instance phases respectively, as explained below. - -\subsubsection*{The \textit{static} phase} - -In the ``static'' phase, -``write\_once()'' statements are carried out in the order they are read -from the user's input file(s) -(regardless of whether or not they appear in nested classes). -Any ``include'' commands will effect this order. -After processing the class definitions, and carrying out -the ``write\_once()'' commands, -lttree.py begins the instantiation phase. - -\subsubsection*{The \textit{instantiation} phase} - -During this phase, lttree.py makes copies of (instantiates) classes -which were requested by the user using the ``new'' command. -During this stage, lttree.py also appends data -to files using the ``write'' command. -(In this manual, the ``write()'' and ``new'' are called instance commands.) -The sequence of alternating ``write()'' and ``new'' commands in the -order that they appear in the user's input file(s). -``new'' commands recursively invoke any instance commands for each -copy of the class they create. - %Instantiation proceeds recursively, creating new copies of classes - %which appear in ``new'' statements defined within a class. - - %\subsubsection{Instance variables ordering (\$)} - %\label{sec:order_customization} - %By default, variables with a \$ prefix - %are assigned in exactly the same order - %that the ``write()'' commands are carried out - %(as described above). - % - %\subsubsection*{The ``-order-dfs'' command} - %\textit{(This is an experimental feature as of 2012-2-13.)} - %However, if the ``-order-dfs'' command line option is selected, - %then instance variables (\$) are counted in the order they appear - %in the tree of instantiated classes (IE. the ``instance tree''), with only - %secondary regard to the order of the ``write'' commands that created them. - %Specifically, this means that the lowest numbers are assigned - %to ordinary variables defined outside any class definitions - %(a.k.a. ``global instance frame''). - %Attention is then turned to the variables belonging to - %the first class which is instantiated, - % %(IE. using the ``new'' command). - %and numbers are then assigned to these variables. - %Whenever a class contains any sub-instances, - %the variables in that sub-instance are assigned to numbers, recursively. - %(In other words, when deciding variable order, - % the tree of instantiated classes is traversed - % with a depth-first-search order.) - %Static variables (@) are effected in a similar way (see below). - % %This method of ordering pays no attention to the the order that - % %``write()'' commands would be executed, and the counting order is different. - %(For reference, this is also the order that variables are - % listed in the ``ttree\_assignments.txt'' file.) - - %\subsubsection*{The ``-order-file'' command} - %\textit{(This is an experimental feature as of 2012-2-13.)} - %If ``-order-file'' command line option is selected, - %then instance variables (\$) are primarily sorted - %according to the position that the variable first - %appears in the user input files. - %Position in the instance tree (as described above) - %is used as a secondary sorting criteria. - %After sorting, variables are then assigned - %to numbers in the order they have been sorted. - %This will not match the order that the - %``write()'' commands are carried out by lttree.py. - - -%\subsubsection*{Static variable ordering (@)} -% -%By default, static @ variables are assigned in the order that -%they appear in the user's input file -%(after any ``include'' commands have been carried out). -%This is true regardless of whether they appear in -%``write()'' or ``write\_once()'' commands, -%and whether they appear in nested classes. -%If ``-order-dfs'' is selected, then static @ variables are defined -%in the order they appear in the tree, -%with variables defined in the outermost nested class, -%(the global class named ``/'') define first. -%If this option is selected then static variables defined in -%``write\_once()'' commands are assigned to numbers first -%before any variables in ``write()'' command are processed. -%(Position in the input file is used as a secondary sort criteria.) -%On the other hand, the ``-order-file'' command line option -%(described above) does not modify the numeric ordering of static variables -%(because they are ordered according to file position by default). - -Again, the counting of instance variables (prefixed by ``\$'') -does not interfere with static variable assignment. -For example ``@atom:x'' and ``\$atom:x'' -correspond to different variables and -belong to different variable categories -(``@atom'' and ``\$atom'') -and they are assigned to numerical values independently. - - - -\section{Using \textit{lttree.py} or \textit{ttree.py} directly} -\subsection*{(bypassing moltemplate.sh)} -\label{sec:ttree} - -``moltemplate.sh'' is only a simple script which invokes ``lttree.py'', -and then combines the various output files generated by lttree.py into a -single LAMMPS input script and a data file, along with coordinate data. -``lttree.py'' then invokes ``ttree.py''. -``ttree.py'' lacks the ability to read or generate coordinates, but -is otherwise nearly identical to ``lttree.py'' and ``moltemplate.sh''. - -If in the future moltemplate.sh no longer works with some new, recently added -LAMMPS feature, you can bypass moltemplate.sh and run lttree.py -or ttree.py directly. -Everything moltemplate.sh does can essentially be done by hand with -a unix shell and a text editor. This procedure is outlined below. - - -\subsection{First run ttree.py} - -The syntax for running ``ttree.py'' is identical to the syntax for running -moltemplate.sh. The moltemplate.sh syntax is explained above. - -Unfortunately, ttree.py does not understand the -pdb, -xyz, or -raw arguments -for processing coordinate data. If you run ``ttree.py'' directly, then you -must extract the coordinate data from these files yourself and insert it into -your lammps input files manually. This is explained below. - -Example: -Go to the examples/waterSPCE/ directory and run: - -ttree.py system.lt - -This will prepare LAMMPS input files for a system of 32 water molecules. -(In this example, we are using the ``SPCE'' water model.) - -Running the command above will probably create the following files: -``Data Atoms'' (The ``Atoms'' section of a LAMMPS data file, w/o coordinates) -``Data Bonds'' (The ``Bonds'' section of a LAMMPS data file) -``Data Angles'' (The ``Angles'' section of a LAMMPS data file) -``Data Masses'' (The ``Masses'' section of a LAMMPS data file) -``In Init'' (The ``Initialization'' section of a LAMMPS input script.) -``In Settings'' (The ``Settings'' section of a LAMMPS input script, which typically - contains force-field parameters, group defs, and constraints) -``Data Boundary'' (The ``Periodic Boundary Conditions'' section of a LAMMPS data file.) -``ttree\_assignments.txt'' (Variable assignments. See ``customization'' section.) - - -This data can be easily combined into a single LAMMPS data file and a -single lammps input script later on, using a text editor, or the unix -``cat'' and ``paste'' commands. - -It may also create these files: -``Data Angles By Type'', -``Data Dihedrals By Type'', -``Data Impropers By Type''. -These files tell moltemplate how to automatically generate bonded-interactions -by atom and bond type. They must be converted to lists of -angles, dihedrals, and impropers, using the ``nbody\_by\_type.py'' utility - %(and stored in files named - % ``Data Angles'' ``Data Dihedrals'' and ``Data Impropers''), -(as explained in appendix \ref{sec:nbody_by_type}). - - -\subsection{Then create a LAMMPS data file} - -Create a new file (``system.data'' in this example), -and paste the following text into it: - -\subsubsection*{Create the ``header'' section} -Example: -\begin{verbatim} -LAMMPS Description - - 96 atoms - 64 bonds - 32 angles - 0 dihedrals - - 2 atom types - 1 bond types - 1 angle types - 0 dihedral types - - 0.000000 9.043 xlo xhi - 0.000000 15.663 ylo yhi - 0.000000 7.361 zlo zhi -\end{verbatim} -If you use ttree.py, will have to count the number of -atoms, bonds, and atom types, bond types etc. yourself. - -Note: the numbers in the ``xlo xhi'' ``ylo yhi'' ``zlo zhi'' lines determine the -simulation box size, and will vary from system to system. -If ttree created a file named ``Data Boundary'', you can copy this information from there. -(Triclinic cells have a fourth line containing the ``xy xz yz'' parameters.) -(If you have a .PDB file, these boundary box numbers are in the ``CRYST1'' -line near the beginning of the file.) - - -Once you've created the ``header'' section of the data file, -paste the other sections to the end of your LAMMPS data file -(with the appropriate section headings and blank lines). -\begin{verbatim} -echo "" >> system.data -echo "Atoms" >> system.data -echo "" >> system.data -cat "Data Atoms" >> system.data -echo "" >> system.data -echo "Bonds" >> system.data -echo "" >> system.data -cat "Data Bonds" >> system.data -echo "" >> system.data -echo "Angles" >> system.data -echo "" >> system.data -cat "Data Angles" >> system.data -echo "" >> system.data -echo "Masses" >> system.data -echo "" >> system.data -cat "Data Masses" >> system.data -echo "" >> system.data -\end{verbatim} - -Depending on your system, you may also have these files as well: -``Data Dihedrals'' -``Data Impropers'' -``Data Bond Coeffs'' -``Data Angle Coeffs'' -``Data Dihedral Coeffs'' -``Data Improper Coeffs''. -If so, then then append them to the end of your data file as well. -(There are numerous other optional sections for ``class2'' force-fields. - Exotic atom styles also require their own sections - such as ``lines'' ``ellipsoids'' and ``triangles''. - Consult the LAMMPS documentation for details on these as well.) - - -\subsection{Now create the LAMMPS input script} - -\begin{verbatim} -echo "include \"In Init\"" > system.in -echo "read_data system.data" >> system.in -echo "include \"In Settings\"" >> system.in -\end{verbatim} -Lastly, you have to worry about supplying the atomic coordinates. -(Unlike moltemplate, ttree.py does not handle atom coordinates.) - -The following commands are useful for extracting coordinates from PDB or XYZ -files and converting them to LAMMPS input script commands: - -\subsection{Extract coordinates} -To extract coordinates from a .PDB file (``file.pdb''), use: - -\begin{verbatim} -awk '/^ATOM |^HETATM/{print substr($0,31,8) \ - " "substr($0,39,8) \ - " "substr($0,47,8)}' \ - < file.pdb \ - > tmp_atom_coords.dat -\end{verbatim} -\textit{(Note: There should be two spaces following the word ``ATOM'' above.)} -%between ``ATOM'' and ``$|$\textasciicircum{}HETATOM'' above.)} - - -To extract coordinates from an XYZ file (``file.xyz''), use: -\begin{verbatim} -awk 'function isnum(x){return(x==x+0)} \ - BEGIN{targetframe=1;framecount=0} \ - {if (isnum($0)) {framecount++} else \ - {if (framecount==targetframe) { \ - if (NF>0) { \ - if ((NF==3) && isnum($1)) { \ - print $1" "$2" "$3} \ - else if ((NF==4) && isnum($2)) { \ - print $2" "$3" "$4} }}}}' \ - < file.xyz \ - > tmp_atom_coords.dat -\end{verbatim} - -\subsection{Convert the coordinate file to LAMMPS input script format} - -\begin{verbatim} -awk '{if (NF>=3) { \ - natom++; print "set atom "natom" x "$1" y "$2" z "$3" "}}' \ - < tmp_atom_coords.dat \ - >> system.in.coords -\end{verbatim} -Finally import ``system.in.coords'' in your lammps input script using: -\begin{verbatim} -echo "include \"system.in.coords\"" >> system.in -\end{verbatim} - - -\section{Using the \textit{nbody\_by\_type.py} utility} -\subsection*{(bypassing moltemplate.sh)} -\label{sec:nbody_by_type_utility} - -moltemplate.sh uses the ``nbody\_by\_type.py'' utility -to generate many-body interactions between bonded atoms -by atom type. -In the event that moltemplate.sh crashes or is not up-to-date with LAMMPS, -you can assign interactions by type by manually invoking nbody\_by\_type.py -yourself. - - -As an example, the following command will generate a file ``Angles'' -containing lines of text which should eventually be pasted into the ``Angles'' -section of a LAMMPS data file: -\begin{verbatim} -nbody_by_type Angles \ - -atoms "Data Atoms" \ - -bonds "Data Bonds" \ - -subgraph "nbody_Angles.py" \ - -nbodybytype "Data Angles By Type" \ - > "Data Angles" -\end{verbatim} - -For dihedral or improper interactions, repeat the command above, and -replace ``Angles'' with ``Dihedrals'', or ``Impropers'' everywhere. - -\textit{Note: -The above instructions work assuming that you do not use any -wildcard characters (``*'' or ``?'') -or regular expressions -in your ``Angles By Type'' section. -If you use wildcards or regular expressions, -then you must run the program this way: -} -\begin{verbatim} -nbody_by_type Angles \ - -atoms "Data Atoms.template" \ - -bonds "Data Bonds.template" \ - -subgraph "nbody_Angles.py" \ - -nbodybytype "Data Angles By Type.template" \ - > "Data Angles.template" -\end{verbatim} -\textit{ -Afterwards, you must then replace each variable in the -``Angles.template'' file with the appropriate integer -before you copy the contents into the LAMMPS data file. -(The ttree\_render.py program may be useful for this. - Open the moltemplate.sh file with a text editor to - see how this was done.) -} - -Note that ``Data Atoms'', and ``Data Bonds'' refer to files which are normally -created by ``ttree.py'' or ``lttree.py'' which -contain atom and bond data in LAMMPS data file format, respectively. -Similarly ``Data Angles By Type'' refers to a file -containing instructions for how to automatically generate angles by atom type. -(Again, this would typically be generated by running ``ttree.py'' or - ``lttree.py'' on an LT file containing a block of text wrapped - inside a ``write\_once('Data Angles By Type')'' command.) - -Note: if you already have existing ``Data Angles'', you can add them to -the list of angle interactions created by nbody\_by\_type.py. - -\begin{verbatim} -nbody_by_type Angles \ - -atoms "Data Atoms" \ - -bonds "Data Bonds" \ - -subgraph "nbody_Angles.py" \ - -nbodyfile "Data Angles" \ - -nbodybytype "Data Angles By Type" \ - > extra_Angles.tmp -cat extra_Angles.tmp "Data Angles" > new_Angles -mv -f new_Angles "Data Angles" -rm -f extra_Angles.tmp -\end{verbatim} - - -\subsection{Usage} -For reference, the complete man page for the ``nbody\_by\_type.py'' -command is included below. -\begin{verbatim} - nbody_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS) - data file containing bonded many-body interactions by atom type - (and bond type), and generates a list of additional interactions - in LAMMPS format consistent with those type (to the standard out). - - Typical Usage: - - nbody_by_type.py X < old.data > new.data - - --or-- - - nbody_by_type.py X \ - -atoms atoms.data \ - -bonds bonds.data \ - -subgraph "nbody_X.py" \ - -nbody X.data \ - -nbodybytype X_by_type.data - > new_X.data - - In both cases "X" denotes the interaction type, which - is either "Angles", "Dihedrals", or "Impropers". - Support for other interaction types can be added by the user. See below. - - Note: The optional "-subgraph" argument allows you to customize the - rules used to match and generate interactions of that type. - It is optional, and is only useful for forcefields which - use non-standard dihedral or improper atom-order convetions.) - - -------- Example 1 ------- - - nbody_by_type.py X < old.data > new.data - - In this example, nbody_by_type.py reads a LAMMPS data file - "orig.data", and extracts the relevant section ("Angles", - "Dihedrals", or "Impropers"). It also looks a section named "X By Type", - (eg. "Angles By type", "Impropers By type", "Impropers By type") - which contains a list of criteria for automatically defining additional - interactions of that type. For example, this file might contain: - - Angle By Type - - 7 1 2 1 * * - 8 2 2 * * * - 9 3 4 3 * * - - The first column is an interaction type ID. - The next 3 columns are atom type identifiers. - The final 2 columns are bond type identifiers. - The * is a wildcard symbol indicating there is no preference for bond types - in this example. (Optionally, regular expressions can also be used to - define a type match, by enclosing the atom or bond type in / slashes.) - - The first line tells us to that there should be a 3-body "Angle" - interaction of type "7" whenever an atom of type 1 is bonded to an atom - of type "2", which is bonded to another atom of type "1" again. - The second line tells us that an angle is defined whenever three atoms - are bonded together and the first two are of type "2". - (Redundant angle interactions are filtered.) - - New interactions are created for every group of bonded - atoms which match these criteria if they are bonded together - in the relevant way for that interaction type (as determined by - nbody_X.py), and printed to the standard output. For example, - suppose you are automatically generating 3-body "Angle" interactions using: - - nbody_by_type Angles < old.data > new.data - - The file "new.data" will be identical to "old.data", however the - "Angles By Type" section will be deleted, and the following lines of - text will be added to the "Angles" section: - - 394 7 5983 5894 5895 - 395 7 5984 5895 5896 - 396 7 5985 5896 5897 - : : : : : - 847 9 14827 14848 14849 - - The numbers in the first column are counters which assign a ID to - every interaction of that type, and start where the original "Angles" - data left off (New angle ID numbers do not overlap with old ID numbers). - The text in the second column ("7", "9", ...) matches the text from the - first column of the "Angle By Type" section of the input file. - - -------- Example 2 ------- - - nbody_by_type.py X \ - -atoms atoms.data \ - -bonds bonds.data \ - -subgraph "nbody_X.py" \ - -nbody X.data \ - -nbodybytype X_by_type.data \ - > new_X.data - - In particular, for Angle interactions: - - nbody_by_type.py Angles \ - -atoms atoms.data \ - -bonds bonds.data \ - -subgraph "nbody_Angles.py" \ - -nbody angles.data \ - -nbodybytype angles_by_type.data \ - > new_Angles.data - - When run this way, nbody_by_type.py behaves exactly the same way - as in Example 1, however only the lines of text corresponding to - the new generated interactions are printed, (not the entire data file). - Also note, that when run this way, nbody_by_type.py does not read the - LAMMPS data from the standard input. Instead, it reads each section of - the data file from a different file indicated by the arguments following - the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags. - - "Angles" is a 3-body interaction style. So when run this way, - nbody_by_type.py will create a 5 (=3+2) column file (new_Angles.data). - -Note: the atom, bond and other IDs/types in need not be integers. - -Note: This program must be distributed with several python modules, including: - nbody_Angles.py, nbody_Dihedrals.py, and nbody_Impropers.py. These - contain bond definitions for angular, dihedral, and improper interactions. -\end{verbatim} - -\subsection{Custom bond topologies} -\label{sec:nbody_by_type_custom} - Currently nbody\_by\_type.py can detect and generate ``Angle'' -and ``Dihedral'' interactions between 3 and 4 consecutively bonded atoms. -It can also generate ``Improper'' interactions between 4 atoms bonded -with a T-shaped topology (one central atom with 3 branches). -The nbody\_by\_type.py script imports external modules named -``nbody\_Angles.py'', ``nbody\_Dihedrals.py'', and ``nbody\_Impropers.py'' -to help it detect angles, dihedrals, and improper interactions automatically. -In case any new interaction types are ever added to LAMMPS, -it is easy to define new bonded interaction types by supplying -a new ``nbody\_X.py'' python modules. -These python files are usually only a few lines long. -Copy one of the existing modules -``nbody\_Angles.py'', ``nbody\_Dihedrals.py'', or ``nbody\_Impropers.py'') -and modify it to the subgraph inside to match the bonded network -that you want to search for. - - - - - -\section{Variable syntax details} -\label{sec:adv_variable_syntax} - -Counter variables have names like: - -\$\textit{\textbf{cpath}}/\textit{\textbf{catname}}:\textit{\textbf{lpath}} - -or - -@\textit{\textbf{cpath}}/\textit{\textbf{catname}}:\textit{\textbf{lpath}} - -(Note: All of the variable examples in this appendix can refer to either -static @ variables or instance \$ variables. Both variable types obey the -same syntax rules. For brevity, only the instance \$ variables are shown.) - -All counter variables have 3 parts: - -\begin{list}{} -\item -\textit{\textbf{cpath}}, the category scope object (which is usually omitted) -\item -\textit{\textbf{catname}}, the category name -\item -\textit{\textbf{lpath}}, the ``leaf path''. - This includes the variable's name and (optionally) - the location of that variable in the object tree relative - to the object in which the variable is referenced - (the current-context object) -\item -\end{list} - -Typically the \textit{\textbf{cpath}} is omitted, -in which case it means that the category has global scope. -\textit{(This is true for all of the standard counter variable types: -``@atom'', ``\$atom'', ``\$mol'', -``@bond'', ``\$bond'', -``@angle'', ``\$angle'', -``@dihedral'', ``\$dihedral'', -``@improper'', and ``\$improper''.)} -However the \textit{\textbf{cpath}} can be specified -explicitly, as in this example: ``\$/atom:'' -(``/'' denotes explicitly that the counter has global scope). -Another example with an explicit \textit{\textbf{cpath}} is -the custom local counter variable named ``\$/proteins[5]/monomerid:.'' -(See section \ref{sec:cpath_simple}.) -In this example, the \textit{\textbf{cpath}} is ``\$/proteins[5]'', the -\textit{\textbf{catname}} is ``monomerid'', -and the \textit{\textbf{lpath}} is ``.''. -(In section -\ref{sec:cpath_simple}, -we never explicitly specified the \textit{\textbf{cpath}}. -This is a source of confusion. -When \textit{\textbf{cpath}} is omitted, -then the program searches up the tree for an ancestor node -containing a category with a matching \textit{\textbf{catname}}. Consequently -the \textit{\textbf{cpath}} rarely ever needs to be stated explicitly. -See section \ref{sec:variables_shorthand} for more details.) - - -\subsection{General variable syntax} -The ellipsis (``...'') commonly appears in counter variables -(or it is implied). The most complex and general variable syntax is: - -\$\textit{\textbf{cpath}}/.../\textit{\textbf{catname}}:\textit{\textbf{lpath}} - -This means: find the closest ancestor of the \textit{\textbf{cpath}} object containing a category named ``\textit{\textbf{catname}}''. This ancestor determines the category's scope. Counter variables in this category are local to ancestors of that object. In this usage example, \textit{\textbf{lpath}} identifies the location of the variable's corresponding ``leaf'' object -relative to the category scope object (\textit{\textbf{cpath}}). -On the other hand, if the the category's scope (\textit{\textbf{cpath}}) -was not explicitly stated by the user (which is typical), -then the \textit{\textbf{lpath}} identifies the location of the leaf object relative to -the object in which the variable was referenced -(the current-context ``.''). - -\subsection{Variable shorthand equivalents} -\label{sec:variables_shorthand} - -\subsubsection*{\$\textit{\textbf{catname}}:\textit{\textbf{lpath}} is equivalent to ``\$.../\textit{\textbf{catname}}:\textit{\textbf{lpath}}''} - %\label{sec:variables_shorthand_catname:lpath} -This means: find the closest direct ancestor of the current object containing a category whose name matches \textit{\textbf{catname}}. If not found, create a new category (at the global level). \textit{This is the syntax used most frequently in LT files.} - -If the colon is omitted, as in \$\textit{\textbf{lpath}}/\textit{\textbf{catname}}, -then it is equivalent to: \$\textit{\textbf{catname}}:\textit{\textbf{lpath}}. -Again, in these cases, \textit{\textbf{lpath}} is a path which is relative to the object -in which the variable was referenced. - -If \$\textit{\textbf{lpath}} is omitted, then this is equivalent to \$\textit{\textbf{catname}}:. In other words, the the leaf node is the current node, ``.''. (This syntax is often used to count keep track of molecule ID numbers. You can use the counter variable ``\$mol'' to keep track of the current molecule id number, because it counts the molecular objects in which this variable was defined. In this case the name of the category is ``mol''. As in most examples, the category object, \textit{\textbf{cpath}}, is not specified. This means the category object is automatically global. A global category object means that every molecule object is given a unique ID number which is unique for the entire system, not just unique within some local molecule. As a counter-example, consider amino acid residue counters. Each amino acid in a protein can be assigned a residue ID number which identifies it within a single protein chain. However because their category was defined locally at the protein level, these residue ID numbers are not global, and are not uniquely defined if there are multiple protein chains present.) (See section \ref{sec:cpath_simple} for details.) - - - -\subsubsection*{\$\textit{\textbf{cpath}}/\textit{\textbf{catname}}:\textit{\textbf{lpath}}/...} -\textit{(SHORTHAND equivalent)} - %\label{sec:variables_shorthand_catname:lpath_ellipsis} - -Find the category name and object corresponding to ``\$\textit{\textbf{cpath}}/\textit{\textbf{catname}}:'' -(see above) -If \$\textit{\textbf{cpath}}/ is blank, then search for an ancestor with a category whose name matches \textit{\textbf{catname}}, as described above. -To find the variable's corresponding ``leaf object'', start from the CURRENT object (not the category object). If \textit{\textbf{lpath}} is not empty, follow \textit{\textbf{lpath}} to a new position in the tree. Otherwise, start at the current object. (An empty \textit{\textbf{lpath}} corresponds to the current object.) From this position in the object tree search for a direct ancestor which happens to also be ``leaf object'' for some other variable which belongs to the desired category. If no such variable is found, then ttree creates a new variable whose leaf object is the object at the \textit{\textbf{lpath}} position, and put it in the desired category. - -\subsubsection*{\$\textit{\textbf{lpath}}/.../\textit{\textbf{catname}} is equivalent to \$\textit{\textbf{catname}}:\textit{\textbf{lpath}}/...} -\textit{(SHORTHAND equivalent)} - %\label{sec:variables_shorthand_lpathSellipsisScatname} - -If \textit{\textbf{lpath}} is omitted, then start from the current node. -(In the molecular examples, ``\$.../mol'' is a variable whose category name is ``mol''. The ``leaf object'' for the variable is either the current object in which this variable was defined, OR a direct ancestor of this object which has been assigned to a variable belonging to the category named ``mol''. In this way large objects (large molecules) can be comprised of smaller objects, without corrupting the ``mol'' counter which keeps track of which molecule we belong to. In other words, ``\$.../mol'' unambiguously refers to the ID\# of the large molecule to which this sub-molecule belongs (regardless of however many layers up that may be).) - -\subsubsection*{\$\textit{\textbf{cpath}}/\textit{\textbf{catname}}:\textit{\textbf{lpath}}} - %\label{sec:variables_shorthand_cpathScatname:lpath} -\textit{Variables in the output\_ttree/ttree\_assignments.txt file - use the this syntax.} - -If the user explicitly specifies the path leading up to the cat node, and avoids using ``...'', then \textit{\textbf{lpath}} is interpreted relative to the category object, not the current object (however \textit{\textbf{cpath}} is interpreted relative to the current object). This happens to be the format used in the ``ttree\_assignments.txt'' file (although you can use it anywhere else in an ``.LT'' file). In ``ttree\_assignments.txt'' file, \textit{\textbf{cpath}} is defined relative to the global object. The variables in that file always begin with ``\$/'' or ``@/''. The slash at the beginning takes us to the global environment object (to which all the other objects belong). (Since the variables in the ``ttree\_assignments.txt'' always begin with ``\$/'' or ``@/'', this distinction is usually not important because the category object for most variables usually is the ``global'' root object.) - - - -\bibliography{refs.bib} - -\end{document} - diff --git a/tools/moltemplate/doc/moltemplate_manual_src/random_2bead.jpg b/tools/moltemplate/doc/moltemplate_manual_src/random_2bead.jpg deleted file mode 100644 index f67da797f1..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/random_2bead.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/random_3bead.jpg b/tools/moltemplate/doc/moltemplate_manual_src/random_3bead.jpg deleted file mode 100644 index 15d7b29676..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/random_3bead.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/random_heteropolymer.jpg b/tools/moltemplate/doc/moltemplate_manual_src/random_heteropolymer.jpg deleted file mode 100644 index cc6822e7b3..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/random_heteropolymer.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/refs.bib b/tools/moltemplate/doc/moltemplate_manual_src/refs.bib deleted file mode 100644 index fd5276aaff..0000000000 --- a/tools/moltemplate/doc/moltemplate_manual_src/refs.bib +++ /dev/null @@ -1,161 +0,0 @@ -@STRING{CELL="Cell"} -@STRING{JMB="J. Mol. Biol."} -@STRING{BIOCHEMISTRY="Biochemistry"} -@STRING{BIOPHYSICALCHEMISTRY="Biophys. Chem."} -@STRING{JCP="J. Chem. Phys."} -@STRING{PNAS="Proc. Natl. Acad. Sci. USA"} -@STRING{BIOPOLYMERS="Biopolymers"} -@STRING{SCIENCE="Science"} -@STRING{MMBR="Microbiol. Mol. Biol. R."} -@STRING{NATURE="Nature"} -@STRING{NATSTRUCTBIOL="Nat. Struct. Biol."} -@STRING{NATBIOTECHNOL="Nat. Biotechnol."} -@STRING{JBIOLCHEM="J. Biol. Chem."} -@STRING{JSTRUCTBIOL="J. Struct. Biol."} -@STRING{FOLDINGANDDESIGN="Folding and Design"} -%@STRING{PROTSTRFUNCGEN="Prot. Str. Func. Gen."} -@STRING{PROTSTRFUNCGEN="Proteins"} -@STRING{PRL="Phys. Rev. Lett."} -@STRING{TIBS="Trends in Biochem. Sci."} -@STRING{EMBOJ="EMBO J."} -@STRING{FEBS="FEBS Letters"} -@STRING{FASEB="FASEB"} -@STRING{JBIOCHEMTOXICOL="J. Biochem. Toxicol."} -@STRING{CRBMB="Crit. Rev. Biochem. Mol. Biol."} -@STRING{CHEMREV="Chem. Rev."} -@STRING{ANNUREVBIOCHEM="Annu. Rev. Biochem."} -% ------------------ books ---------------------- - - -@INBOOK{vanKampenBook, - AUTHOR="van Kampen, N. G.", - TITLE="Stochastic Processes in Physics and Chemistry, 2nd Edition", - PUBLISHER="North Holland", - PAGES={96--127}, - MONTH="July", - DAY="1", - YEAR=2001 -} - - -@ARTICLE{LAMMPS, - AUTHOR="S. Plimpton", - TITLE="Fast Parallel Algorithms for Short-Range Molecular Dynamics", - JOURNAL="J. Comp. Phys.", - VOLUME=117, - PAGES={1--19}, - YEAR="1995", - NOTE={\url{http://lammps.sandia.gov/}} -} - - -@ARTICLE{packmol, - AUTHOR="Martínez, L. and Andrade, R. and Brigin, E. G. and Martínez, J. M.", - TITLE="Packmol: A package for building initial configurations for molecular dynamics simulations.", - JOURNAL="J. Comp. Chem.", - VOLUME=30, - NUMBER=13, - PAGES={2157--2164}, - YEAR=2009, - NOTE={\url{http://www.ime.unicamp.br/~martinez/packmol/}} -} - - -%% The primary VMD citation, should be used by all publications using VMD -@article{VMD, - author={William Humphrey and Andrew Dalke and Klaus Schulten}, - title={{VMD} -- {V}isual {M}olecular {D}ynamics}, - journal={Journal of Molecular Graphics}, - year=1996, - volume=14, - pages={33-38}, - tbstatus={Published.}, - techrep={}, - tbreference={222}, - NOTE={\url{http://www.ks.uiuc.edu/Research/vmd}} -} - -%% Interactive Molecular Dynamics, cited by papers doing IMD simulations -@inproceedings{VMDIMD, - author={John Stone and Justin Gullingsrud and Paul Grayson and Klaus Schulten}, - title={A System for Interactive Molecular Dynamics Simulation}, - booktitle={2001 ACM Symposium on Interactive 3D Graphics}, - publisher={ACM SIGGRAPH}, - address={New York}, - editor={John F. Hughes and Carlo H. S\'equin}, - pages={191-194}, - year={2001}, - note={}, - tbreference={304}, - tbstatus={Published.}, - annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.} -} - -@MISC{topotools, - AUTHOR="Axel Kohlmeyer", - TITLE="{The TopoTools VMD plugin}", - HOWPUBLISHED={\url{http://sites.google.com/site/akohlmey/software/topotools/}} -} - - -@MISC{pizzapy, - AUTHOR="Steve Plimpton", - TITLE="{The Pizza.py toolkit}", - HOWPUBLISHED={\url{http://www.cs.sandia.gov/~sjplimp/pizza.html}} -} - - -@ARTICLE{TraPPE, - AUTHOR="Marcus G. Martin and J. Ilja Siepmann", - TITLE="Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes", - JOURNAL="J. Phys. Chem. B", - VOLUME=102, - NUMBER=14, - PAGES={2569--2577}, - YEAR=1998 -} - - -@ARTICLE{Raviv++SafinyaBiophysJ2007, - AUTHOR="Uri Raviv and Toan Nguyen and Rouzbeh Ghafouri and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Robijn F. Bruinsma and Cyrus R. Safinya", - TITLE="Microtubule Protofilament Number Is Modulated in a Stepwise Fashion by the Charge Density of an Enveloping Layer", - JOURNAL="Biophys. J.", - VOLUME=92, - NUMBER=1, - PAGES={278--287}, - YEAR="2007", - MONTH={January}, - DAY={1} -} - - -@ARTICLE{Raviv++SafinyaPNAS2005, - AUTHOR="Uri Raviv and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Cyrus R. Safinya", - TITLE="Cationic liposome-microtubule complexes: Pathways to the formation of two-state lipid-protein nanotubes with open or closed ends", - JOURNAL="Proc. Natl. Acad. Sci. USA", - VOLUME=102, - NUMBER=32, - PAGES={11167--11172}, - YEAR="2005", - MONTH={August}, - DAY={9} -} - -@ARTICLE{Berendsen++StraatsmaJPhysChem1987, - AUTHOR="H. J. C. Berendsen and J. R. Grigera and T. P. Straatsma", - TITLE="The Missing Term in Effective Pair Potentials", - JOURNAL="J. Phys. Chem.", - VOLUME=91, - NUMBER=24, - PAGES={6269--6271}, - YEAR="1987", -} - - -@ARTICLE{Klimov+ThirumalaiPRL1997, - AUTHOR="Klimov, D. K. and Thirumalai, D.", - JOURNAL="Phys. Rev. Lett.", - VOLUME=79, - PAGES={317--320}, - YEAR="1997" -} diff --git a/tools/moltemplate/doc/moltemplate_manual_src/single_water_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/single_water_LR.jpg deleted file mode 100644 index 7961fa3b53..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/single_water_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/tether.jpg b/tools/moltemplate/doc/moltemplate_manual_src/tether.jpg deleted file mode 100644 index c7673b2cc8..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/tether.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/waterSPCEx1000_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/waterSPCEx1000_LR.jpg deleted file mode 100644 index b3d6f05d51..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/waterSPCEx1000_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/moltemplate_manual_src/waterSPCEx1000_t=25_LR.jpg b/tools/moltemplate/doc/moltemplate_manual_src/waterSPCEx1000_t=25_LR.jpg deleted file mode 100644 index 56344f9573..0000000000 Binary files a/tools/moltemplate/doc/moltemplate_manual_src/waterSPCEx1000_t=25_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/doc/utils/docs_dump2data.txt b/tools/moltemplate/doc/utils/docs_dump2data.txt deleted file mode 100644 index 2a29ba38d1..0000000000 --- a/tools/moltemplate/doc/utils/docs_dump2data.txt +++ /dev/null @@ -1,121 +0,0 @@ - (Rough-draft documentation for dump2data.py and raw2data.py) - - ---- Description ---- - -"dump2data.py" was originally designed to convert dump files into LAMMPS DATA format (for restarting a simulation from where it left off). However it also reads and writes .XYZ and .RAW (simple 3-column text format) files also. - - Comparison with pizza.py: -This script duplicates some of the tools in pizza.py, but you don't have to learn python to use it. If you are willing to learn a little python, pizza.py, can handle more general dump files which might cause dump2data.py to crash (eg "atom_style tri"). Unlike "dump2data.py", pizza.py is maintained by the lammps team: -http://pizza.sandia.gov/doc/Manual.html - - ----- General Usage ----- - -General usage: - -dump2data.py [old_data_file -xyz -raw -last -t time -tstart ta -tstop tb -interval n -multi -center -scale x -atomstyle style] < DUMP_FILE > OUTPUT_FILE - - ----- examples ----- - - If your LAMMPS dump file is named "traj.lammpstrj", you can -extract the coordinates this way: - -dump2data.py -xyz < traj.lammpstrj > traj.xyz - -This generates a 3-column text file containing the xyz coordinates on each line of each atom (sorted by atomid). If there are multiple frames in the trajectory file, it will concatenate them together this way: - -8192 -LAMMPS data from timestep 50000 -1 -122.28 -19.2293 -7.93705 -2 -121.89 -19.2417 -8.85591 -3 -121.6 -19.2954 -7.20586 -: : : : -8192 -LAMMPS data from timestep 100000 -1 -121.59 -20.3273 -2.0079 -2 -122.2 -19.8527 -2.64669 -3 -120.83 -19.7342 -2.2393 - -(When using the "-raw" argument to create simple 3-column .RAW files, blank lines are used to delimit different frames in the trajectory.) - ----- optional command line arguments --- - -If you want to select a particular frame from the trajectory, use: - -dump2data.py -xyz -t 10000 < traj.lammpstrj > coords.xyz - -To select the most recent (complete) frame, use: - -dump2data.py -xyz -last < traj.lammpstrj > coords.xyz - -(If the last frame is incomplete, this script will attempt to use the previous frame.) - -If you want to select multiple frames, but there are too many frames in your trajectory, you can run dump2data.py this way... - -dump2data.py -xyz -interval 10000 < traj.lammpstrj > traj.xyz - -...to indicate the desired interval between frames (it must be a multiple of -the save interval). You can also use "-tstart 500000 and "-tstop 1000000" arguments to limit the output to a particular range of time. (500000-1000000 in this example). - ---- creating DATA files --- - -"dump2data.py" can also create lammps DATA files. You must supply it with an existing DATA file containing the correct number of atoms and topology information. - -If your coordinates are stored in a DUMP file (eg "traj.lammpstrj"), you can create a new data file this way: - -dump2data.py -t 10000 data_file < traj.lammpstrj > new_file - -Again, in this example, "10000" is the timestep for the frame you have selected. You can use "-last" to select the last frame. If you do not specify the frame you want, multiple data files may be created... - -Creating multiple data files: -The "-multi" command line argument tells "dump2data.py" to generate a new data file for each frame in the trajectory/dump-file. Those files will have names ending in ".1", ".2", ".3", ... (If you use the "-interval" argument, frames in the trajectory whose timestep is not a multiple of the interval will be discarded.) I can't remember if this behavior is switched on by default. - -Reading simple 3-column coordinate files: -If you have a file containing only the coordinates of the atoms (in sorted order), you can use "raw2data.py" to create a data file with those atoms coordinates. - -raw2data.py -atomstyle ATOMSTYLE data_file < coords.raw > new_data_file - -(where ATOMSTYLE is a quoted string, such as "full" or "hybrid sphere dipole" discussed earlier. Warning: "raw2data.py" is not a stand-alone script. Make sure raw2data.py is located in the same directory with dump2data.py.) - ---- scaling and centering coordinates --- - --center - This will center the coordinates around the geometric center, so that the average position of the atoms in each frame is located at the origin. (This script attempts to pay attention to the periodic image flags. As such, I think this script works with triclinic cells, but I have not tested that feature carefully.) - --scale 1.6 - This will multiply the coordinates by a constant (eg "1.6") (Please email me if this fails with periodic image flags.) - ----- limitations ---- - -Speed. -The program is somewhat slow, although it should be able to handle big trajectories. If speed is important to you, you probably should write your own custom script or use pizza.py which might be faster. - -triclinic cells - Support for triclinic cells has been added, but not tested. - -exotic atom_styles - - This script was designed to work with point-like atoms, and it extracts the x,y,z (and if present vx,vy,vz velocity) degrees of freedom and (by default) copies it to the new data being created by this script. - -By default, this script assumes you are using "atom_style full". -If you are using some other atom style (eg "hybrid bond dipole"), then you can try to run it this way: - -dump2data.py -t 10000 \ - -atomstyle "hybrid bond dipole" \ - old_data_file < traj.lammpstrj > new_data_file - -In general, the -atomstyle argument can be any of the atom styles listed in the -table at: -http://lammps.sandia.gov/doc/atom_style.html -...such as "angle", "bond", "charge", "full", "molecular", "dipole", "ellipsoid", or any hybrid combination of these styles. (When using hybrid atom styles, you must enclose the argument in quotes, for example: "hybrid sphere dipole") -Warning: I have not tested using dump2data.py with exotic (non-point-like) atom -styles. (I suspect that the script will not crash, but the dipole orientations -will not be updated.) - -You can also customize the order columns you want to appear in that file using -atomstyle â€molid x y z atomid atomtype mux muy muzâ€, but again, I don't think the mux, muy, muz information in the new data file will be accurate. - -I also strongly suspect that "dump2data.py" does not currently work with the "tri", "ellipsoid", and new "body" styles. - -Again, try using pizza.py if you are simulating systems with exotic data types. -http://pizza.sandia.gov/doc/Manual.html - -I hope this is useful to someone. diff --git a/tools/moltemplate/doc/utils/docs_extract_lammps_data.txt b/tools/moltemplate/doc/utils/docs_extract_lammps_data.txt deleted file mode 100644 index 0e1bf1ae26..0000000000 --- a/tools/moltemplate/doc/utils/docs_extract_lammps_data.txt +++ /dev/null @@ -1,59 +0,0 @@ -extract_lammps_data.py is a simple script which extracts sections of text from -a LAMMPS data file. (Of coarse, you can accomplish the same thing with a text -editor, but this script turns it into a one-line command.) - -Typical usage: - -extract_lammps_data.py SECTION_NAME < FILE.DATA > EXCERPT.TXT - -This extracts a section from a LAMMPS data file and saves it in EXCERPT.TXT. - -More general usage: - -extract_lammps_data.py [-n] SECTION_LIST < FILE.DATA > EXCERPT.TXT - -The SECTION_LIST is a list of sections you want in your output file -(eg "EXCERPT.TXT"). Each section must be a quoted-string, and spaces -(not commas) should separate each section name. - -The optional "-n" flag negates the selection. (Selecting instead, everything -except the sections you listed.) - -Examples: - -extract_lammps_data.py "Atoms" < FILE.DATA > Atoms.txt -extract_lammps_data.py "Header" < FILE.DATA > Header.txt -extract_lammps_data.py -n "Header" < FILE.DATA > everything_except_Header.txt - -extract_lammps_data.py "Bonds" "Angles" "Dihedrals" "Impropers" \ - < FILE.DATA > topology.txt - -extract_lammps_data.py "Pair Coeffs" "Bond Coeffs" "Angle Coeffs" \ - "Dihedral Coeffs" "Improper Coeffs" \ - < FILE.DATA > force_field.txt - - -The following section names are allowed: - -"Header" # The header section at the beginning of the file. -"Atoms" -"Masses" -"Bonds" -"Bond Coeffs" -"Angles" -"Angle Coeffs" -"Dihedrals" -"Dihedral Coeffs" -"Impropers" -"Improper Coeffs" -"BondBond Coeffs" # class2 angles -"BondAngle Coeffs" # class2 angles -"MiddleBondTorsion Coeffs" # class2 dihedrals -"EndBondTorsion Coeffs" # class2 dihedrals -"AngleTorsion Coeffs" # class2 dihedrals -"AngleAngleTorsion Coeffs" # class2 dihedrals -"BondBond13 Coeffs" # class2 dihedrals -"AngleAngle Coeffs" # class2 impropers -"Angles By Type" # moltemplate-specific. (not standard LAMMPS) -"Dihedrals By Type" # moltemplate-specific. (not standard LAMMPS) -"Angles By Type' # moltemplate-specific. (not standard LAMMPS) diff --git a/tools/moltemplate/doc/utils/docs_genpoly_lt.txt b/tools/moltemplate/doc/utils/docs_genpoly_lt.txt deleted file mode 100644 index 31a0359b6d..0000000000 --- a/tools/moltemplate/doc/utils/docs_genpoly_lt.txt +++ /dev/null @@ -1,206 +0,0 @@ -Explanation: - - Generate a moltemplate file containing a definition of a Polymer - molecule containing monomers located at the positions specified in - "coords.raw" (a 3-column text file). Monomers will be rotated so - that they point along the polymer axis direction (see "-dir-indices") - with an optional helical twist added (see "-helix"). Users can - specify one or more bonds connecting each monomer to the next monomer - (see "-bond"). Similarly, 3-body and 4-body angular interactions between - atoms in different monomers can either be generated automatically - (using the standard moltemplate "Angle By Type" rules) - OR generated manually (using "-angle", "-dihedral", "-improper" arguments). - -Usage: - - genpoly_lt.py \ - [-bond btype a1 a2] \ - [-helix deltaphi] \ - [-axis x,y,z] \ - [-circular yes/no/connected] \ - [-dir-indices ia ib] \ - [-angle atype a1 a2 a3 i1 i2 i3] \ - [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \ - [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \ - [-monomer-name mname] \ - [-sequence sequence.txt] \ - [-polymer-name pname] \ - [-inherits ForceFieldObject] \ - [-header "import monomer.lt"] \ - [-cuts cuts.txt] \ - [-box paddingX,paddingY,paddingZ] \ - < coords.raw > polymer.lt - -Arguments (optional): - - -axis x,y,z direction of the polymer axis in the original monomer object. - These three numbers (separated by commas with no spaces) - define the direction that the monomer subunit is pointing in. - By default, the three numbers are 1 0 0 (ie, the X axis) - - -helix deltaphi = Optionally, rotate each monomer around it's axis by - angle deltaphi (in degrees) beforehand - - -circular keyword - keyword must be one of these: - "no" The polymer is a linear chain with the two ends - not connected. - "yes" The polymer is a circular loop with the two ends - connected pointing in similar directions. - "connected" Connect the two ends together with bonds (and angles, - and dihedrals, if applicable) to make a closed loop. - But do not adjust the orientation of the first and - last monomers so that they point towards eachother. - (Use this if you plan to simulate an "infinitely" - long polymer using periodic boundary conditions, - with the two ends are connected on opposite sides.) - - -dir-indices ia ib - The program attempts to orient each monomer in a direction that - the polymer is pointing. By default, the program will - orient monomer i in the direction connecting the monomers before - and after it (monomers i-1 and i+1). The user can override this - using the -dir-indices command line argument. The ia and ib - arguments are integer offsets. To point monomer i in the direction - connecting it to the following monomer (i+1), use -dir-indices 0 1 - (For circular polymers, the indices will be wrapped appropriately.) - - -bond btype a1 a2 - Add a bond between successive monomers of type btype. - between atoms named a1 and a2 (all three arguments are strings and - omit the @bond: and $atom: prefixes in moltemplate variables) - Multiple bonds between successive monomers can be added by having - "-bond bt a1 a2" appear several times in the argument list. - For example, double-stranded DNA can be implemented as a polymer - with 2 bonds connecting separate monomers (if each "monomer - corresponds to a base pair). - - -angle atype a1 a2 a3 i1 i2 i3 - Add a 3-body angle interaction between atoms a1 a2 a3 in monomers - i1 i2 and i3. (The aname atype a1, a2, a3 arguments are strings - containing moltemplate variable names. The standard moltemplate - prefixes "$angle:", "@angle:", and "$atom:" should be omitted. - The i1, i2, i3 arguments are integer indices indicating the monomer - that each atom belongs to. - 0 corresponds to the current monomer - 1 corresponds to the next monomer - 2 corresponds to the following monomer, etc... - (For circular polymers, the indices will be wrapped appropriately.) - Multiple angles per monomer can be added by having: - "-angle aname atype a1 a2 a3 i1 i2 i3" - appear several times in the argument list. - - - -dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4 - Add a 4-body dihedral interaction between atoms a1 a2 a3 a4 in - monomers i1 i2 and i3. (The dname dtype a1, a2, a3, a4, arguments - are strings containing moltemplate variable names. The moltemplate - prefixes "$dihedral:", "@dihedral:", and "$atom:" should be omitted - The i1, i2, i3, i4 arguments are integer indices indicating the - monomer that each atom belongs to. (See explanation above.) - Multiple dihedrals per monomer can be added by having: - "-dihedral dname dtype a1 a2 a3 a4 i1 i2 i3 i4" - appear several times in the argument list. - - -improper itype a1 a2 a3 a4 i1 i2 i3 i4 - Add a 4-body improper interaction between atoms a1 a2 a3 a4 in - monomers i1 i2 and i3. (The iname itype a1, a2, a3, a4, arguments - are strings containing moltemplate variable names. The moltemplate - prefixes "$improper:", "@improper:", and "$atom:" should be omitted - The i1, i2, i3, i4 arguments are integer indices indicating the - that each atom belongs to. (See explanation above.) - Multiple impropers per monomer can be added by having: - "-improper iname itype a1 a2 a3 a4 i1 i2 i3 i4" - appear several times in the argument list. - - -monomer-name name - Name of the moltemplate object that will be created. - (By default "Monomer") Note: You can include 1 or more - coordinate transformations added to the monomer subunit - before it is moved into position. For example, it is - often useful to to use a modified version of the monomer - whose initial coordinates are compressed to avoid collisions - with other monomers. To do this, use something like - "Monomer.scale(0.5,0.7,0.7)" instead of "Monomer". - This typically would compress each monomer lengthwise by 0.5 - and 0.7 laterally. (After minimization, each monomer should - expand back to its ordinary size and shape.) - - -header 'some text' - This is a way to add text at the beginning of the file. - It was intended to be used to define the force fields and - the monomer subunits you are using. For example: - -header 'import "FILE_WHICH_DEFINES_Monomer.lt"' - - -sequence sequence.txt - If you are building a heteropolymer this argument allows - you to specify the sequence of monomers in the polymer. - Here "sequence.txt" file contains the sequence of monomers - you want in your polymer. Each line of this file should - be the name of a moltemplate object for the monomer subunit - you want at that location. The number of lines in this file - should match the number of lines in the coordinate file. - As before, you can include coordinate transforms in each - monomer's name. - - -polymer-name name - Name of the moltemplate object that will be created. - (By default "Polymer") - - -inherits ForceFieldObject - "ForceFieldObject" is the name of a moltemplate object which - defines any rules for creating angles, dihedrals, impropers - which you want to be generated automatically. Hopefully - this is object was defined somewhere in the file that - you imported using the "-header" argument. - - -cuts cut_locations.txt - Cut the polymer in several places along its length. - This can be useful if your goal is to create many - polymers of different lenthgs. Rather than being forced - to define a new Polymer object for each polymer, simply - cut the polymer N times along its length. The file - "cut_locations.txt" is a text file containing a list of - positive integers (one per line) indicating where you would - like the polymer to be cut. For each integer, i, which - appears in this file, a cut is made between monomers - i-1 and i (Indexing begins at 0, so a value of 1 - corresonds to a cut between the first and second monomers.) - A separate polymer object will be created for each polymer, - and an integer suffix will be added to the name, to - distinguish them from eachother. (Each of these - polymers will be part of a larger object defined by this - program. Instantiating that object will create all of the - individual polymers.) - - -box paddingX,paddingY,paddingZ - This will cause the program to attempt to estimate the size - of the smallest rectangular box which encloses all of the - coordinates in the coordinate file. The user must supply - 3 comma-separated numbers (no spaces) which indicate how much - extra room is needed in the x,y,z directions, at both ends. - - -Examples: - - 1) Make a simple polymer, adding "@bond:Backbone" type bonds between - "$atom:c2" from each monomer with "$atom:c1" from the next monomer. - - genpoly_lt.py -bond Backbone c2 c1 < crds.raw > poly.lt - - 2) Make a circular twisted double-stranded DNA model, treating each base-pair - as a monomer, and connecting each base-pair monomer with 2 bonds - with the next base-pair. This is done using 2 "-bond" - commands connecting the "O3p_a" atom with the "P_a" atom (in strand A), - and the "P_b" atom with the "O3p_b" atom (from the opposite strand, B). - - genpoly_lt.py -circular yes -helix 34.2857 \ - -header 'import "basepair.lt" #<--defines "BasePair"' \ - -monomer-name "BasePair" \ - -polymer-name "Plasmid" \ - -bond Backbone O3p_a P_a \ - -bond Backbone P_b O3p_b \ - < dna_basepair_CM_coords.raw \ - > chromosome.lt - If you want to control the sequence of the polymer, replace the - "-monomer-name" argument with "-sequence sequence.txt". diff --git a/tools/moltemplate/doc/utils/docs_raw2data.txt b/tools/moltemplate/doc/utils/docs_raw2data.txt deleted file mode 100644 index 0bcb951c8d..0000000000 --- a/tools/moltemplate/doc/utils/docs_raw2data.txt +++ /dev/null @@ -1,56 +0,0 @@ -raw2data.py replaces the coordinates of a LAMMPS data file with new coordinates. - - -Typical usage: - -raw2data.py -atomstyle ATOMSTYLE FILE_OLD.data < COORDS.raw > FILE_NEW.data - - -This will create a new LAMMPS DATA file named "FILE_NEW.data" whose atom -coordinates are copied from the COORDS.raw file, but is otherwise identical -to the original DATA file (eg, "FILE_OLD.data"). The optional --atomstyle ATOMSTYLE argument tells raw2data.py about the format of the DATA -file. If not specified, the atom style is "full" by default. - - -Arguments: - -ATOMSTYLE is a quoted string, such as "full" or "hybrid sphere dipole" indicating the format of the data file. It can be any of the atom styles listed in the table at: -http://lammps.sandia.gov/doc/atom_style.html -...such as "angle", "bond", "charge", "full", "molecular", "dipole", "ellipsoid" -or any hybrid combination of these styles. - -FILE_OLD.data -The second argument to raw2data.py is the name of a DATA file you want to read. -raw2data.py will replace the coordinates in the "Atoms" section of this file, -while preserving the rest of the data file. - -COORDS.raw is a simple 3-column ASCII file containing the coordinates of the -atoms in your system. It has a very simple format: --122.28 -19.2293 -7.93705 --121.89 -19.2417 -8.85591 --121.6 -19.2954 -7.20586 --121.59 -20.3273 -2.0079 --122.2 -19.8527 -2.64669 --120.83 -19.7342 -2.2393 - : : : - -The order of the atoms in this file should match the ATOM-ID number in the -first column of the "Atoms" section of the FILE_OLD.data file. -(...I THINK... - To be on the safe side, use a DATA file with the atoms in sorted order.) - -Exotic atom styles: - When using hybrid atom styles, you must enclose the argument in quotes, -for example: "hybrid sphere dipole" - - Warning 1: I have not tested using raw2data.py with exotic (non-point-like) -atom styles. (I suspect that the script will not crash, but dipole orientations -and other internal degrees of freedom will not be updated.) - - Warning 2: "raw2data.py" is not a stand-alone script. Make sure dump2data.py is located in the same directory with raw2data.py. - - Note: I have not tested it, but I suspect many of the other arguments that work with "dump2data.py", such as "-scale", and "-xyz" also work with raw2data.py. - -Try using pizza.py if you are simulating systems with exotic data types. -http://pizza.sandia.gov/doc/Manual.html diff --git a/tools/moltemplate/examples/README.txt b/tools/moltemplate/examples/README.txt deleted file mode 100644 index e024bffcdc..0000000000 --- a/tools/moltemplate/examples/README.txt +++ /dev/null @@ -1,24 +0,0 @@ -These are examples for the "moltemplate" molecule builder for LAMMPS. -http://www.moltemplate.org - -Each directory contains one or more examples. - -Each example directory contains: - - images/ This folder has pictures of the molecules in the system - moltemplate_files/ This folder contains LT files and other auxiliary files - README_setup.sh Instructions for how to use moltemplate (executable) - README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD - - ...and one or more LAMMPS input scripts with names like - - run.in.min - run.in.npt - run.in.nvt - -You can run these scripts using - lmp_linux -i run.in.npt -(The name of your lammps binary, "lmp_linux" in this example, may vary. - Sometimes, these scripts must be run in a certain order. For example - it may be necessary to run run.in.min to minimize the system before you can use run.in.npt, and later run.in.nvt. The README_run.sh file in each subdirectory - specifies indicates the order. These files have not been optimized.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/WARNING.txt deleted file mode 100644 index f7e65cf482..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/WARNING.txt +++ /dev/null @@ -1,54 +0,0 @@ -# -------- WARNING: -------- - -This directory contains some examples of all-atom simulations using the GAFF -force field, prepared using moltemplate. - -This software is experimental, and the force-fields and equilbration protocols -have not been tested carefully by me. There is no gaurantee that simulations -prepared using moltemplate will reproduce the behavior of AmberTools/AMBER. - -# -------- REQUEST FOR HELP: -------- - -If you notice a problem with these examples, please report it. -Peer-review is the only way to improve this software (or any software). -Other suggestions are also welcome! - -(Contact jewett.aij@gmail.com, 2013-12-01) - - ---- Charge --- - -Some force-fields (such as OPLSAA) can assign charge based on atom type. -But AMBER simulations, charge is usually assigned using AmberTools which -typically estimates partial charges using quantum chemistry. - -You must assign partial charges to each atom or LAMMPS will crash -when it discovers your system has no charged particles. -(To disable this, change the pair_style to lj/cut or something similar.) - -You have to assign charge manually, just as you would for an ordinary molecule. - -(For example, charges are explicitly assigned to each atom in these files: - waterTIP3P+isobutane/moltemplate_files/isobutane.lt - hexadecane/moltemplate_files/ch2group.lt - hexadecane/moltemplate_files/ch3group.lt) - -(How you do this is up to you. In these examples, I obtained -partial charges from the OPLSAA parameter file located here: -http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm) - ---- Improper angles --- - -I am also uncertain whether the improper angle interactions generated by -moltemplate are equivalent to those generated by AmberTools. (I think they are, -but I am worried that I might have listed the atom types in the wrong order.) - ---- Bloated lammps input scripts --- - -LAMMPS input scripts prepared using moltemplate contain the entire contents -of the GAFF force-field, even when simulating small systems with just a few -atom types. - -This is harmless, but if you want to get rid of this extra information, -follow the README instructions in the "optional_cleanup" directories. - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README.txt deleted file mode 100644 index ba0f5e6f45..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README.txt +++ /dev/null @@ -1,10 +0,0 @@ -This example shows how to build a box of benzene molecules using the -AMBER/GAFF force-field. - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_remove_irrelevant_info.sh deleted file mode 100755 index 67528d426e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in AMGER/GAFF ("gaff.lt") which you -# are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_run.sh deleted file mode 100755 index ac39fa950c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_run.sh +++ /dev/null @@ -1,39 +0,0 @@ -# --- Running LAMMPS --- -# -------- REQUIREMENTS: --------- -# 1) This example requires building LAMMPS with the "USER-MISC" package. -# (because it makes use of "gaff.lt" which uses dihedral_style fourier) -# To do this, type "make yes-user-misc" before compiling LAMMPS. -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# -------- PREREQUISITES: -------- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_setup.sh deleted file mode 100755 index e8d8be3f50..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_setup.sh +++ /dev/null @@ -1,35 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - #rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt deleted file mode 100644 index 8d736e72b3..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/benzene.lt +++ /dev/null @@ -1,52 +0,0 @@ - -import "gaff.lt" - -# The "gaff.lt" file is usually located in the "force_fields" -# subdirectory distributed with moltemplate. -# Excerpt: -# -# @atom:ca # Sp2 C in pure aromatic systems -# @atom:ha # H bonded to aromatic carbon -# -# I looked up the charge of each atom using the OPLSAA parameters -# from the "oplsaa.prm" file distributed with TINKER -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# --------------------------------------------------------------- -# This is NOT how AmberTools assigns charge, and it will NOT -# reproduce the behavior of AMBER force-fields. - - -Benzene inherits GAFF { - - # atomID molID atomType charge X Y Z - write('Data Atoms') { - $atom:C1 $mol @atom:ca -0.115 -0.739 1.189 -0.00733 - $atom:C2 $mol @atom:ca -0.115 0.614 1.208 0.35167 - $atom:C3 $mol @atom:ca -0.115 1.353 0.019 0.35867 - $atom:C4 $mol @atom:ca -0.115 0.739 -1.189 0.00667 - $atom:C5 $mol @atom:ca -0.115 -0.614 -1.208 -0.35133 - $atom:C6 $mol @atom:ca -0.115 -1.353 -0.019 -0.35833 - $atom:H11 $mol @atom:ha 0.115 -1.309 2.106 -0.01233 - $atom:H21 $mol @atom:ha 0.115 1.088 2.14 0.62267 - $atom:H31 $mol @atom:ha 0.115 2.397 0.034 0.63467 - $atom:H41 $mol @atom:ha 0.115 1.309 -2.106 0.01267 - $atom:H51 $mol @atom:ha 0.115 -1.088 -2.14 -0.62233 - $atom:H61 $mol @atom:ha 0.115 -2.397 -0.034 -0.63533 - } - - write('Data Bond List') { - $bond:C12 $atom:C1 $atom:C2 - $bond:C23 $atom:C2 $atom:C3 - $bond:C34 $atom:C3 $atom:C4 - $bond:C45 $atom:C4 $atom:C5 - $bond:C56 $atom:C5 $atom:C6 - $bond:C61 $atom:C6 $atom:C1 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C2H2 $atom:C2 $atom:H21 - $bond:C3H3 $atom:C3 $atom:H31 - $bond:C4H4 $atom:C4 $atom:H41 - $bond:C5H5 $atom:C5 $atom:H51 - $bond:C6H6 $atom:C6 $atom:H61 - } - -} # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/system.lt deleted file mode 100644 index 002c538dad..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/moltemplate_files/system.lt +++ /dev/null @@ -1,14 +0,0 @@ -import "benzene.lt" # <- defines the "Benzene" molecule type. - - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 64.00 xlo xhi - 0.0 64.00 ylo yhi - 0.0 64.00 zlo zhi -} - -benzenes = new Benzene [8].move(8,0,0) - [8].move(0,8,0) - [8].move(0,0,8) - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/run.in.npt deleted file mode 100644 index b2ee94440a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/run.in.npt +++ /dev/null @@ -1,72 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -minimize 1.0e-4 1.0e-6 100000 400000 - -# -- simulation protocol -- - -timestep 1.0 - -thermo 100 -dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz - -print "---------------------------------------------------------------------------" -print "First, use Langevin dynamics to randomize the initial shape of the molecules" -print "---------------------------------------------------------------------------" - - -fix 1 all momentum 100 linear 0 0 0 -fix fxlan all langevin 1000.0 1000.0 5000.0 123456 # temp: 1000 K -fix fxnve all nve - -run 20000 -unfix fxlan -unfix fxnve - - - -print "---------------------------------------------------------------------------" -print "Optional: use short high pressure run to get rid of small bubbles." -print " (In case there are any. I'm not certain there are." -print " Later we will restore ordinary pressure.)" -print "---------------------------------------------------------------------------" -fix fxlan all langevin 298.0 298.0 5000 123456 # temp: 298 K -fix fxnph all nph iso 500.0 500.0 1000.0 # pressure: 500 barr - -run 80000 -unfix fxlan -unfix fxnph - - - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" -# temperature: 298 K, pressure: 1 barr -fix fxnpt all npt temp 298.0 298.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -#thermo_modify flush yes - -run 5000000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/run.in.nvt deleted file mode 100644 index 3901723ddd..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/benzene/run.in.nvt +++ /dev/null @@ -1,51 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# OPLSAA atom charges are stored in a separate file. -# Load that file now: - -include "system.in.charges" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 200000 - -write_restart system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README.txt deleted file mode 100644 index b02f184dde..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README.txt +++ /dev/null @@ -1,13 +0,0 @@ -This example shows how to simulate a mixture of ethylene and benzene -using the AMBER/GAFF force field. - -As of 2016-11-21, this code has not been tested for accuracy. -(See the WARNING.TXT file.) - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_remove_irrelevant_info.sh deleted file mode 100755 index 67528d426e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in AMGER/GAFF ("gaff.lt") which you -# are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_run.sh deleted file mode 100755 index ac39fa950c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_run.sh +++ /dev/null @@ -1,39 +0,0 @@ -# --- Running LAMMPS --- -# -------- REQUIREMENTS: --------- -# 1) This example requires building LAMMPS with the "USER-MISC" package. -# (because it makes use of "gaff.lt" which uses dihedral_style fourier) -# To do this, type "make yes-user-misc" before compiling LAMMPS. -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# -------- PREREQUISITES: -------- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_setup.sh deleted file mode 100755 index dda26cd444..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - #rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt deleted file mode 100644 index b39d8901ad..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} - pbc box -shiftcenterrel {-0.05 -0.05 -0.05} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/benzene.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/benzene.jpg deleted file mode 100644 index 356c784256..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/benzene.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg deleted file mode 100644 index b9ff053fcb..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg deleted file mode 100644 index 65949a4684..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene.jpg deleted file mode 100644 index ab5bbbf49b..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/images/ethylene.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt deleted file mode 100644 index 25f58dfde8..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/benzene.lt +++ /dev/null @@ -1,49 +0,0 @@ - -import "gaff.lt" - -# The "gaff.lt" file is usually located in "force_fields" subdirectory -# of the moltemplate distribution. -# It contains definitions of the atoms "ca", "ha", as well as the bonded -# and non-bonded interactions between them (and many other atoms). -# -# Moltemplate is only a simple text manipulation tool. It cannot -# calculate atomic charge using quantom chemistry methods. -# Atom charges for this example were taken from the OPLSAA force field file: -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# However, normally simulations in AMBER are assigned charges using the -# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. - -Benzene inherits GAFF { - - # atomID molID atomType charge X Y Z - write('Data Atoms') { - $atom:C1 $mol @atom:ca -0.115 -0.739 1.189 -0.00733 - $atom:C2 $mol @atom:ca -0.115 0.614 1.208 0.35167 - $atom:C3 $mol @atom:ca -0.115 1.353 0.019 0.35867 - $atom:C4 $mol @atom:ca -0.115 0.739 -1.189 0.00667 - $atom:C5 $mol @atom:ca -0.115 -0.614 -1.208 -0.35133 - $atom:C6 $mol @atom:ca -0.115 -1.353 -0.019 -0.35833 - $atom:H11 $mol @atom:ha 0.115 -1.309 2.106 -0.01233 - $atom:H21 $mol @atom:ha 0.115 1.088 2.14 0.62267 - $atom:H31 $mol @atom:ha 0.115 2.397 0.034 0.63467 - $atom:H41 $mol @atom:ha 0.115 1.309 -2.106 0.01267 - $atom:H51 $mol @atom:ha 0.115 -1.088 -2.14 -0.62233 - $atom:H61 $mol @atom:ha 0.115 -2.397 -0.034 -0.63533 - } - - write('Data Bond List') { - $bond:C12 $atom:C1 $atom:C2 - $bond:C23 $atom:C2 $atom:C3 - $bond:C34 $atom:C3 $atom:C4 - $bond:C45 $atom:C4 $atom:C5 - $bond:C56 $atom:C5 $atom:C6 - $bond:C61 $atom:C6 $atom:C1 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C2H2 $atom:C2 $atom:H21 - $bond:C3H3 $atom:C3 $atom:H31 - $bond:C4H4 $atom:C4 $atom:H41 - $bond:C5H5 $atom:C5 $atom:H51 - $bond:C6H6 $atom:C6 $atom:H61 - } - -} # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm deleted file mode 100644 index 8493a39f6c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/charges_come_from_OPLSAA/oplsaa_subset.prm +++ /dev/null @@ -1,94 +0,0 @@ -# This is a modified version of the file "oplsaa.prm" distributed with TINKER -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# In this version, all of the lines beginning with "atom" have been deleted -# except for the atom types we will be using in this simulation -# -# If you use this file, please also cite the software this file comes from: -# -# Ponder, J. W., and Richards, F. M. J. Comput. Chem. (1987) 8(7), 1016-1024 -# "An efficient newtonâ€like method for molecular mechanics energy -# minimization of large molecules." -# -# Ponder, J. W, (2004) -# "TINKER: Software tools for molecular design" -# http://dasher.wustl.edu/tinker/ - - ############################## - ## ## - ## Force Field Definition ## - ## ## - ############################## - - -forcefield OPLS-AA - -vdwindex TYPE -vdwtype LENNARD-JONES -radiusrule GEOMETRIC -radiustype SIGMA -radiussize DIAMETER -epsilonrule GEOMETRIC -vdw-14-scale 2.0 -chg-14-scale 2.0 -electric 332.06 -dielectric 1.0 - - - ############################# - ## ## - ## Literature References ## - ## ## - ############################# - - -The parameters supplied with TINKER are from "OPLS All-Atom Parameters -for Organic Molecules, Ions, Peptides & Nucleic Acids, July 2008" as -provided by W. L. Jorgensen, Yale University during June 2009. These -parameters are taken from those distributed with BOSS Version 4.8. - -Note that "atom type" numbers and not "atom class" numbers are used -to index van der Waals parameters, see the "vdwindex" keyword above - -The atom types with (UA) in the description are "united atom" values, -ie, OPLS-UA, where any nonpolar hydrogen atoms are combined onto their -attached atoms. All other parameters are "all-atom", OPLS-AA, including -explicit hydrogen atoms. - - - ############################# - ## ## - ## Atom Type Definitions ## - ## ## - ############################# - - -atom 88 47 CM "Alkene H2-C=" 6 12.011 3 -atom 89 46 HC "Alkene H-C=" 1 1.008 1 -atom 90 48 CA "Aromatic C" 6 12.011 3 -atom 91 49 HA "Aromatic H-C" 1 1.008 1 - - - ################################ - ## ## - ## Van der Waals Parameters ## - ## ## - ################################ - - -vdw 88 3.5500 0.0760 -vdw 89 2.4200 0.0300 -vdw 90 3.5500 0.0700 -vdw 91 2.4200 0.0300 - - - ######################################## - ## ## - ## Atomic Partial Charge Parameters ## - ## ## - ######################################## - - -charge 88 -0.2300 -charge 89 0.1150 -charge 90 -0.1150 -charge 91 0.1150 diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt deleted file mode 100644 index e4b72922fb..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/ethylene.lt +++ /dev/null @@ -1,39 +0,0 @@ - -import "gaff.lt" - -# The "gaff.lt" file is usually located in "force_fields" subdirectory -# of the moltemplate distribution. -# It contains definitions of the atoms "c2", "hc", as well as the bonded -# and non-bonded interactions between them (and many other atoms). -# -# Moltemplate is only a simple text manipulation tool. It cannot -# calculate atomic charge using quantom chemistry methods. -# Atom charges for this example were taken from the OPLSAA force field file: -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# However, normally simulations in AMBER are assigned charges using the -# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. - - -Ethylene inherits GAFF { - - # atom-id mol-id atom-type charge X Y Z - - write('Data Atoms') { - $atom:C1 $mol @atom:c2 -0.23 -0.6695 0.000000 0.000000 - $atom:C2 $mol @atom:c2 -0.23 0.6695 0.000000 0.000000 - $atom:H11 $mol @atom:hc 0.115 -1.234217 -0.854458 0.000000 - $atom:H12 $mol @atom:hc 0.115 -1.234217 0.854458 0.000000 - $atom:H21 $mol @atom:hc 0.115 1.234217 -0.854458 0.000000 - $atom:H22 $mol @atom:hc 0.115 1.234217 0.854458 0.000000 - } - - write('Data Bond List') { - $bond:C12 $atom:C1 $atom:C2 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C1H2 $atom:C1 $atom:H12 - $bond:C2H1 $atom:C2 $atom:H21 - $bond:C2H2 $atom:C2 $atom:H22 - } - -} # Ethylene - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt deleted file mode 100644 index 994b66b2cd..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/moltemplate_files/system.lt +++ /dev/null @@ -1,28 +0,0 @@ -import "ethylene.lt" # <- defines the "Ethylene" molecule type. -import "benzene.lt" # <- defines the "Benzene" molecule type. - - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 48.00 xlo xhi - 0.0 48.00 ylo yhi - 0.0 48.00 zlo zhi -} - -# Create 216 ethylenes and 108 benzenes - -ethylenes = new Ethylene[6].move(8.0, 0, 0) - [6].move(0, 8.0, 0) - [6].move(0, 0, 8.0) - -benzenes = new Benzene[6].move(8.0, 0, 0) - [6].move(0, 8.0, 0) - [3].move(0, 0, 16.0) - -# Now shift the positions of all of the benzene molecules, -# to reduce the chance that they overlap with the ethylene molecules. - -benzenes[*][*][*].move(4.0, 4.0, 4.0) - -# Note: There is also an example which shows how to generate the coordinates -# using PACKMOL. (That allows us to omit the coordinates and .move() commands.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt deleted file mode 100644 index 9e529624d5..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.npt +++ /dev/null @@ -1,53 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -minimize 1.0e-4 1.0e-6 100000 400000 - -# -- simulation protocol -- - -timestep 1.0 - -print "---------------------------------------------------------------------------" -print "First, use Langevin dynamics to randomize the initial shape of the molecules" -print "(This is not really necessary, but it seems to speed up equilibration.)" -print "---------------------------------------------------------------------------" - -fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K -fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr -run 2000 -unfix fxlan -unfix fxnph - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" -dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 50 barr -fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 -thermo 100 -#thermo_modify flush yes - -run 100000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt deleted file mode 100644 index e06cd825b3..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/ethylene+benzene/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 2.0 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 200000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README.txt deleted file mode 100644 index 8289270f04..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README.txt +++ /dev/null @@ -1,44 +0,0 @@ -This example is a simple simulation of 288 hexadecane molecules in a box at -room temperature and atmospheric pressure. Please read the WARNING.TXT file. - --------- REQUIREMENTS: --------- -This example requires building LAMMPS with the "USER-MISC" package. -(because it uses dihedral_style fourier) -To do this, type "make yes-user-misc" before compiling LAMMPS. -http://lammps.sandia.gov/doc/Section_start.html#start_3 - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files: - -step 1) to setup the LAMMPS input files, run this file: -README_setup.sh - - (Currently there is a bug which makes this step slow. - I'll fix it later -Andrew 2013-10-15.) - -step 2) to run LAMMPS, follow the instructions in this file: -README_run.sh - ------------- NOTE: There are two versions of this example. ---------------- - -Both examples use the same force-field parameters. - -1) -In this version, the force-field parameters are loaded from the "gaff.lt" file -(located in the "force_fields" subdirectory of the moltemplate distribution). -This frees the user from the drudgery of manually specifying all of these -force-field details for every molecule. (However, the user must be careful -to choose @atom-type names which match AMBER GAFF conventions, -such as the "c3" and "h1" atoms, in this example.) - -2) -Alternately, there is another "hexadecane" example in the "all_atom_examples" -directory. In that example, force-field parameters are loaded from a file -named "alkanes.lt" (instead of "gaff.lt"). The "alkanes.lt" file contains -only the excerpts from "gaff.lt" which are relevant to the hydrocarbon -molcules used in that example. ("gaff.lt" contains parameters for most -small organic molecules, not just hydrocarbons.) -In this way, by editing "alkanes.lt", the user can manually control all of the -force-field details in the simulation. (Without feeling as though they are -relying on some kind of mysterious "black box" to do it for them.) - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_remove_irrelevant_info.sh deleted file mode 100755 index 67528d426e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in AMGER/GAFF ("gaff.lt") which you -# are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_run.sh deleted file mode 100755 index ac39fa950c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_run.sh +++ /dev/null @@ -1,39 +0,0 @@ -# --- Running LAMMPS --- -# -------- REQUIREMENTS: --------- -# 1) This example requires building LAMMPS with the "USER-MISC" package. -# (because it makes use of "gaff.lt" which uses dihedral_style fourier) -# To do this, type "make yes-user-misc" before compiling LAMMPS. -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# -------- PREREQUISITES: -------- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_setup.sh deleted file mode 100755 index e8d8be3f50..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_setup.sh +++ /dev/null @@ -1,35 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - #rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/WARNING.txt deleted file mode 100644 index 81183f9270..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/WARNING.txt +++ /dev/null @@ -1,16 +0,0 @@ -# -------- WARNING: -------- - -This software is experimental, and the force-fields and equilbration protocols -have not been tested carefully by me. There is no gaurantee that the simulation -will reproduce the behavior of real hexadecane molecules, -(or even of hexadecane molecules simulated using AMBER, which should - be using the same force-field). - -# -------- REQUEST FOR HELP: -------- - -However, if you notice a problem with this example, please report it. -I confess I do not have a lot of experience running all-atom simulations. -Peer-review is the only way to improve this software (or any software). -Other suggestions are also welcome! - -(Contact jewett.aij@gmail.com, 2013-10-16) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg deleted file mode 100644 index b0d31f8845..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg deleted file mode 100644 index f7c13d0989..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg deleted file mode 100644 index 3ad353dbb4..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/images/hexadecane_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt deleted file mode 100644 index 69978eecae..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,59 +0,0 @@ - -import "gaff.lt" # <-- defines the "GAFF" force field - - -# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is -# distributed with moltemplate. See the "Installation" section in the manual.) -# It contains definitions of the atoms "c3", "hc", as well as the force-field -# parameters for bonded and non-bonded interactions between them -# (and many other atoms). - -# Atom charges were taken from the OPLSAA force field file: -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm - - -CH2 inherits GAFF { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c3 -0.120 0.000 0.000 0.000 - $atom:H1 $mol:... @atom:hc 0.060 0.000 0.63104384422426 0.892430762954 - $atom:H2 $mol:... @atom:hc 0.060 0.000 0.63104384422426 -0.892430762954 - } - - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # parent object's molecule id number as it's own. - # The CH2 group is part of the Hexadecane molecule. - - # Now specify which pairs of atoms are bonded: - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - -} # CH2 - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt deleted file mode 100644 index ef431f8d75..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,65 +0,0 @@ -import "gaff.lt" # <-- defines the "GAFF" force field - - -# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is -# distributed with moltemplate. See the "Installation" section in the manual.) -# It contains definitions of the atoms "c3", "hc", as well as the force-field -# parameters for bonded and non-bonded interactions between them -# (and many other atoms). -# -# Moltemplate is only a simple text manipulation tool. It cannot -# calculate atomic charge using quantom chemistry methods. -# Atom charges for this example were taken from the OPLSAA force field file: -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# However, normally simulations in AMBER are assigned charges using the -# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. - - -CH3 inherits GAFF { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c3 -0.180 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:hc 0.060 0.000000 0.6310438442242609 0.8924307629540046 - $atom:H2 $mol:... @atom:hc 0.060 0.000000 0.6310438442242609 -0.8924307629540046 - $atom:H3 $mol:... @atom:hc 0.060 -0.8924307629540046 -0.6310438442242609 0.000000 - } - - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # parent object's molecule id number as it's own. - # The CH3 group is part of the Hexadecane molecule. - - # Now specify which pairs of atoms are bonded: - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - -} # CH3 - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt deleted file mode 100644 index d28502f486..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/hexadecane.lt +++ /dev/null @@ -1,89 +0,0 @@ -# This example looks complicated because I split the -# hexadecane molecule into individual CH2 and CH3 monomers. -# -# I defined it this way so that you can easily modify -# it to change the length of the alkane chain. - - -import "gaff.lt" # load the "GAFF" force-field information -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - - -Hexadecane inherits GAFF { - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - - # Now create an array of 16 "CH2" objects distributed along the X axis - - monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0) - - # Each monomer is rotated 180 degrees with respect to the previous - # monomer, and then moved 1.2533223 Angstroms down the X axis. - - # ---- Now, modify the ends: --- - # Delete the CH2 groups at the beginning and end, and replace them with CH3. - # (Note: Alternately, instead of deleting the CH2 groups at each end, you - # could modify them by adding an extra hydrogen atom to those carbons.) - - delete monomers[0] - delete monomers[15] - monomers[0] = new CH3 - monomers[15] = new CH3 - - # Move the CH3 groups to the correct location at either end of the chain: - - monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0) - - # Note: 18.7998345 = (16-1) * 1.2533223 - - - # Now add a list of bonds connecting the carbon atoms together: - - write('Data Bond List') { - $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C - $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C - $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C - $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C - $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C - $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C - $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C - $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C - $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C - $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C - $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C - $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C - $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C - $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C - $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C - } - -} # Hexadecane - - - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# -# 1.2533223 = DeltaXc = how far each CH2 group is shifted along -# the X axis (in Angstoms). -# 0.4431163 = DeltaYc/2 = lateral displacement of carbons away -# from the central axis. (See below.) -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/system.lt deleted file mode 100644 index 4e0cfaec69..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/moltemplate_files/system.lt +++ /dev/null @@ -1,18 +0,0 @@ -import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 62.4 xlo xhi - 0.0 62.4 ylo yhi - 0.0 62.4 zlo zhi -} - -molecules = new Hexadecane [12].move(0, 0, 5.2) - [12].move(0, 5.2, 0) - [2].move(31.2, 0, 0) - - -# NOTE: The spacing between molecules is large. There should be extra room to -# move during the initial stages of equilibration. However, you will have to -# run the simulation at NPT conditions later to compress the system to a -# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt deleted file mode 100644 index a1b9345229..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/run.in.npt +++ /dev/null @@ -1,86 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize, -# reorient, compress). The system (as defined in the "system.data" file) -# is already expanded. That means there are 3 steps left: - -dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz -thermo 50 - -# -- Equilibration: part 1: initial minimization -- - -# Note: In general, it's always a good idea to minimize the system at first. - -minimize 1.0e-5 1.0e-7 100000 400000 -undump dumpeq1 - -write_data system_after_eq1_min.data - -# -- Equilibration part 2: reorienting the molecules (NVT) -- - -timestep 1.0 -dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz - -# Run the system at high temperature (at constant volume) to reorient the -# the molecules (which would otherwise be pointing in the same direction). - -# To speed it up, I randomize the atomic positions for a few thousand steps -# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). -# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) - - -fix fxlan all langevin 900.0 900.0 120 48279 -fix fxnve all nve - -run 4000 - -unfix fxlan -unfix fxnve -# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). -fix fxnvt all nvt temp 900.0 900.0 100.0 - -run 50000 -undump dumpeq2 - - -write_data system_after_eq2_reorient.data - -unfix fxnvt - -# -- equilibration part 3: Equilibrating the density (NPT) -- - -# Originally, the simulation box (in "system.data" and "system.lt") was -# unrealistically large. The spacing between the molecules was large also. -# I did this to enable the molecules to move freely and reorient themselves. -# After doing that, we should run the simulation under NPT conditions to -# allow the simulation box to contract to it's natural size. We do that here: -# We begin the simulation at 100 barr (a relatively low pressure), and -# slowly decrease it to 1 barr, maintianing the temperature at 300K. - -dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0 - -timestep 1.0 -run 100000 - -write_data system_after_eq3_npt.data - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/run.in.nvt deleted file mode 100644 index 0bb7699896..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/hexadecane/run.in.nvt +++ /dev/null @@ -1,43 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_eq3_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1 -thermo 100 -#thermo_modify flush yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README.txt deleted file mode 100644 index 605ea7d6a1..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README.txt +++ /dev/null @@ -1,37 +0,0 @@ -The simulation consists of a mixture of isobutane and water. -Over time (less than 1 ns), the two molecules phase-separate. - -The GAFF parameters are applied only to the isobutane molecule. -(The water molecule paramters are defined explicitly in the - "force_fields/tip3p_2004.lt" file distributed with moltemplate.) - -WARNING: THIS EXAMPLE HAS NOT BEEN CAREFULLY TESTED. - PLEASE REPORT BUGS AND/OR SEND CORRECTIONS. -A 2016-12-16 - ------------------ CHARGE ---------------------- - -NOTE: The GAFF force-field DOES NOT ASSIGN ATOM CHARGE. - In this example, atom charges were taken from the OPLSAA force field file: - http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm - This is not the charge in AMBER simunlations is typically assigned. - (As of 2014, it is assigned using the "HF/6-31G* RESP2" or "AM1-BCC3" - methods using AmberTools (which are not available in moltemplate). - http://ambermd.org/doc6/html/AMBER-sh-19.4.html - http://ambermd.org/tutorials/basic/tutorial4b/) - - --------- REQUIREMENTS: --------- - - This example requires building LAMMPS with the "USER-MISC" package. - (because it makes use of "gaff.lt" which uses dihedral_style fourier) - To do this, type "make yes-user-misc" before compiling LAMMPS. - http://lammps.sandia.gov/doc/Section_start.html#start_3 - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_remove_irrelevant_info.sh deleted file mode 100755 index 67528d426e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in AMGER/GAFF ("gaff.lt") which you -# are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_run.sh deleted file mode 100755 index ac39fa950c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_run.sh +++ /dev/null @@ -1,39 +0,0 @@ -# --- Running LAMMPS --- -# -------- REQUIREMENTS: --------- -# 1) This example requires building LAMMPS with the "USER-MISC" package. -# (because it makes use of "gaff.lt" which uses dihedral_style fourier) -# To do this, type "make yes-user-misc" before compiling LAMMPS. -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# -------- PREREQUISITES: -------- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh deleted file mode 100755 index eb9df9e448..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_setup.sh +++ /dev/null @@ -1,29 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - #rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg deleted file mode 100644 index 8c548fba84..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/isobutane.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg deleted file mode 100644 index fab496aa20..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg deleted file mode 100644 index aaa4abaf5e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water+isobutane_t=840ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg deleted file mode 100644 index 9d578b4ef8..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/images/water.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt deleted file mode 100644 index 9acd858b95..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/isobutane.lt +++ /dev/null @@ -1,57 +0,0 @@ - -import "gaff.lt" - -# The "gaff.lt" file is usually located in "force_fields" subdirectory -# of the moltemplate distribution. -# It contains definitions of the atoms "c3", "h1", as well as the bonded -# and non-bonded interactions between them (and many other atoms). -# -# Moltemplate is only a simple text manipulation tool. It cannot -# calculate atomic charge using quantom chemistry methods. -# Atom charges for this example were taken from the OPLSAA force field file: -# http://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# However, normally simulations in AMBER are assigned charges using the -# "HF/6-31G* RESP2" or "AM1-BCC3" methods using AmberTools. - - -Isobutane inherits GAFF { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:C0 $mol:. @atom:c3 -0.0600 -0.001 -0.001 -0.439 - $atom:C1 $mol:. @atom:c3 -0.1800 -1.257 -0.726 0.078 - $atom:C2 $mol:. @atom:c3 -0.1800 1.258 -0.726 0.072 - $atom:C3 $mol:. @atom:c3 -0.1800 -0.001 1.453 0.069 - $atom:H0 $mol:. @atom:hc 0.0600 -0.003 -0.004 -1.439 - $atom:H11 $mol:. @atom:hc 0.0600 -2.075 -0.255 -0.254 - $atom:H12 $mol:. @atom:hc 0.0600 -1.256 -0.724 1.078 - $atom:H13 $mol:. @atom:hc 0.0600 -1.259 -1.669 -0.253 - $atom:H21 $mol:. @atom:hc 0.0600 2.074 -0.255 -0.264 - $atom:H22 $mol:. @atom:hc 0.0600 1.258 -1.669 -0.259 - $atom:H23 $mol:. @atom:hc 0.0600 1.261 -0.724 1.072 - $atom:H31 $mol:. @atom:hc 0.0600 -0.817 1.923 -0.263 - $atom:H32 $mol:. @atom:hc 0.0600 0.816 1.923 -0.268 - $atom:H33 $mol:. @atom:hc 0.0600 0.003 1.456 1.070 - } - - # The "." in "$mol:." refers to this molecule object's molecule ID - # (It means we do not expect this molecule to be a group or a subunit - # of a larger molecule. Otherwise we would use "$mol:..." instead.) - - write('Data Bond List') { - $bond:C01 $atom:C0 $atom:C1 - $bond:C02 $atom:C0 $atom:C2 - $bond:C03 $atom:C0 $atom:C3 - $bond:C0H $atom:C0 $atom:H0 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C1H2 $atom:C1 $atom:H12 - $bond:C1H3 $atom:C1 $atom:H13 - $bond:C2H1 $atom:C2 $atom:H21 - $bond:C2H2 $atom:C2 $atom:H22 - $bond:C2H3 $atom:C2 $atom:H23 - $bond:C3H1 $atom:C3 $atom:H31 - $bond:C3H2 $atom:C3 $atom:H32 - $bond:C3H3 $atom:C3 $atom:H33 - } - -} # Isobutane diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt deleted file mode 100644 index ac9965e588..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/moltemplate_files/system.lt +++ /dev/null @@ -1,30 +0,0 @@ - -import "tip3p_2004.lt" # <-- This defines the TIP3P water molecule. This file - # is located in the "force_fields" subdirectory - # of the moltemplate distribution. - -import "isobutane.lt" # <- defines the "Isobutane" molecule type. - - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 41.50 xlo xhi - 0.0 41.50 ylo yhi - 0.0 41.50 zlo zhi -} - - -# The next command generates a (rather dense) cubic lattice with -# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) - -wat = new TIP3P_2004 [12].move(0.00, 0.00, 3.45) - [12].move(0.00, 3.45, 0.00) - [12].move(3.45, 0.00, 0.00) - -isobutane = new Isobutane [4].move(0, 0, 10.35) - [4].move(0, 10.35, 0) - [4].move(10.35, 0, 0) - -# move the isobutane molecules slightly to reduce overlap with the water -isobutane[*][*][*].move(1.725, 1.725, 1.725) - diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/run.in.npt deleted file mode 100644 index b4e4078891..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/run.in.npt +++ /dev/null @@ -1,44 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fShakeTIP3P was defined in system.in.settings. It is incompatible with "minimize". -unfix fShakeTIP3P -minimize 1.0e-4 1.0e-6 100000 400000 -# Now read "system.in.settings" in order to redefine fShakeTIP3P again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -thermo 100 -#thermo_modify flush yes - -run 40000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt deleted file mode 100644 index 602b8c3295..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt +++ /dev/null @@ -1,52 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# COMMENTING OUT MINIMIZATION STEPS: -# If you are reading the coordinates generated by the NPT run -# then you should not need to minimize the system beforehand. -# -- minimization protocol -- -## ("fix shake" is incompatible with "minimize".) -#unfix fShakeTIP3P -#minimize 1.0e-4 1.0e-6 100000 400000 -## Now read "system.in.settings" in order to redefine fShakeTIP3P again: -#include system.in.settings - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt deleted file mode 100644 index 5b2fcfb4b2..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/WARNING.txt +++ /dev/null @@ -1,38 +0,0 @@ -# -------- WARNING: -------- - -This directory contains some examples of all-atom simulations using the COMPASS -force field. - -This software is experimental, and the force-fields and equilbration protocols -have not been tested carefully by me. There is no gaurantee that simulations -prepared using moltemplate will reproduce the behavior of other MD codes. - -The moltemplate implementation of COMPASS currently relies on the same -incomplete force-field file that "msi2lmp" uses ("compass_published.frc"). -Unfortunately this means that many force field parameters and some atom types -(such as sp2-carbons) have not (yet) been publicly released and are not -available. - -Currently I recommend that users should run the "cleanup_moltemplate.sh" -script after running "moltemplate.sh system.lt". Then manually check that -the "system.in.settings" and "system.in.charges" files which remain -make sense. Specifically, you must check that the angle_coeff, -dihedral_coeff, bond_coeff commands are not full of zeros (in places -where they should not be zero. This is another consequence of the -fact that the .FRC files I mentioned above are incomplete.) It's a -good idea to also check that the charges in the "system.in.charges" -file seem reasonable (ie. not all zeros). (There is a list of -warnings at the end of the "compass_published.lt" file. You can check -to see if any of the bonds in your system are covered by these -warnings.) Later on hopefully I'll add some automated way to warn -users when these problems arise, but now you should check for them -manually. - -# -------- REQUEST FOR HELP: -------- - -If you notice a problem with these examples, please report it. -Peer-review is the only way to improve this software (or any software). -Other suggestions are also welcome! - -(Contact jewett.aij@gmail.com, 2017-10-03) - diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt deleted file mode 100644 index 7bf9a484d7..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README.txt +++ /dev/null @@ -1,37 +0,0 @@ -This example is a simple simulation of a long alkane chain, -in a vacuum at room temperature using the COMPASS force field. - -1) Create the "system.data", "system.in.init", and "system.in.settings" -files which LAMMPS will read by running: - -moltemplate.sh system.lt - - -2) Run LAMMPS in this order: - -lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before... -lmp_mpi -i run.in.nvt # running the simulation at constant temperature - -(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) - ----- Details ---- - -The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains -use the COMPASS force-field. This means that when we define these molecules, -we only specify the atom names, bond list, and coordinates. -We do not have to list the atom charges, angles, dihedrals, or impropers. -The rules for creating atomic charge and angle topology are contained in -the "compass_published.lt" file created by step 3) above. The "ch2group.lt", -"ch3group.lt", and "alkane50.lt" files all refer to "compass_published.lt", -(as well as the "COMPASS" force-field object which it defines). Excerpt: - -import "compass_published.lt" -CH2 inherits COMPASS { ... -CH3 inherits COMPASS { ... -Alkane50 inherits COMPASS { ... - -Alternatively, you can manually define a list of angles, dihedrals, and -improper interactions in these files, instead of asking the force-field -to generate them for you. You can also specify some of the angles and -dihedrals explicitly, and let the force-field handle the rest. -(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh deleted file mode 100755 index 94d6de972c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh deleted file mode 100755 index 5cd2142a41..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg deleted file mode 100644 index 39a8879557..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch2_ry90.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg deleted file mode 100644 index ab140a8f9e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/ch3_ry60.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg deleted file mode 100644 index 39633edd5e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg deleted file mode 100644 index da2fe1185e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/images/t=1ns.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt deleted file mode 100644 index da75694c45..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/alkane50.lt +++ /dev/null @@ -1,137 +0,0 @@ -# This is a simple example showing how to build a long polymer -# (in this case, an alkane chain). I split the -# hexadecane molecule into individual CH2 and CH3 monomers. -# I defined it this way so that you can easily modify -# it to change the length of the alkane chain. - - -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - - -Alkane50 inherits COMPASS { - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - # This is a long polymer consisting of 48 CH2 groups and 2 CH3 end-caps. - # Rather than create them one-by-one, I decided to create them all - # using a single "new" command. Later, I can modify this array. - - # Create an array of 50 "CH2" objects distributed along the X axis - - monomers = new CH2 [50].rot(180,1,0,0).move(1.2533223,0,0) - - # NOTE: the ".rot(180,1,0,0).move(1.2533223,0,0)" means that each - # successive monomer is rotated 180 degrees (with respect to the previous - # monomer), and then moved 1.2533223 Angstroms down the X axis. - # Alternately, if you are reading the coordinates from a file, you don't have - # to indicate the position & orientation of each monomer. In that case, use: - # monomers = new CH2 [50] - - - # ---- Now, modify the ends: --- - # Delete the CH2 groups at the beginning and end, and replace them with CH3. - - delete monomers[0] - delete monomers[49] - - monomers[0] = new CH3 - monomers[49] = new CH3 - - # Move the CH3 groups to the correct location at either end of the chain: - - #monomers[0].move(0,0,0) # <--(this monomer is already in the correct place) - monomers[49].rot(180.0,0,0,1).move(61.4127927,0,0) #61.4127927=49*1.2533223 - - - ## NOTE: Alternately, you can define the polymer without deleting the ends: - # monomers[0] = new CH3 - # monomers[1-48] = new CH2[48].rot(180,1,0,0).move(1.2533223,0,0) - ## Note: monomers[0] and monomers[1] overlap, so we move 1-48 to make room: - # monomers[1-48].rot(180,1,0,0).move(1.2533223,0,0) # move many monomers - ## Now add the final monomer at the end: - # monomers[49] = new CH3.rot(180.0,0,0,1).move(61.4127927,0,0) - # - ## NOTE: Alternately, you can read the coordinates from a file. - ## In that case, you can use simpler commands: - # monomers[0] = new CH3 - # monomers[1-48] = new CH2[48] - # monomers[49] = new CH3 - - - - # Now add a list of bonds connecting the carbon atoms together: - # (Angles, dihedrals, impropers will be automatically added later.) - - write('Data Bond List') { - $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C - $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C - $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C - $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C - $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C - $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C - $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C - $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C - $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C - $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C - $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C - $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C - $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C - $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C - $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C - $bond:b16 $atom:monomers[15]/C $atom:monomers[16]/C - $bond:b17 $atom:monomers[16]/C $atom:monomers[17]/C - $bond:b18 $atom:monomers[17]/C $atom:monomers[18]/C - $bond:b19 $atom:monomers[18]/C $atom:monomers[19]/C - $bond:b20 $atom:monomers[19]/C $atom:monomers[20]/C - $bond:b21 $atom:monomers[20]/C $atom:monomers[21]/C - $bond:b22 $atom:monomers[21]/C $atom:monomers[22]/C - $bond:b23 $atom:monomers[22]/C $atom:monomers[23]/C - $bond:b24 $atom:monomers[23]/C $atom:monomers[24]/C - $bond:b25 $atom:monomers[24]/C $atom:monomers[25]/C - $bond:b26 $atom:monomers[25]/C $atom:monomers[26]/C - $bond:b27 $atom:monomers[26]/C $atom:monomers[27]/C - $bond:b28 $atom:monomers[27]/C $atom:monomers[28]/C - $bond:b29 $atom:monomers[28]/C $atom:monomers[29]/C - $bond:b30 $atom:monomers[29]/C $atom:monomers[30]/C - $bond:b31 $atom:monomers[30]/C $atom:monomers[31]/C - $bond:b32 $atom:monomers[31]/C $atom:monomers[32]/C - $bond:b33 $atom:monomers[32]/C $atom:monomers[33]/C - $bond:b34 $atom:monomers[33]/C $atom:monomers[34]/C - $bond:b35 $atom:monomers[34]/C $atom:monomers[35]/C - $bond:b36 $atom:monomers[35]/C $atom:monomers[36]/C - $bond:b37 $atom:monomers[36]/C $atom:monomers[37]/C - $bond:b38 $atom:monomers[37]/C $atom:monomers[38]/C - $bond:b39 $atom:monomers[38]/C $atom:monomers[39]/C - $bond:b40 $atom:monomers[39]/C $atom:monomers[40]/C - $bond:b41 $atom:monomers[40]/C $atom:monomers[41]/C - $bond:b42 $atom:monomers[41]/C $atom:monomers[42]/C - $bond:b43 $atom:monomers[42]/C $atom:monomers[43]/C - $bond:b44 $atom:monomers[43]/C $atom:monomers[44]/C - $bond:b45 $atom:monomers[44]/C $atom:monomers[45]/C - $bond:b46 $atom:monomers[45]/C $atom:monomers[46]/C - $bond:b47 $atom:monomers[46]/C $atom:monomers[47]/C - $bond:b48 $atom:monomers[47]/C $atom:monomers[48]/C - $bond:b49 $atom:monomers[48]/C $atom:monomers[49]/C - } - -} # Alkane50 - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt deleted file mode 100644 index 9bf2c82d7d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,76 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. - -# First, load the COMPASS force field parameters we will need: - -import "compass_published.lt" # <-- defines the "COMPASS" force field - -# (The "compass_published.lt" file is located in the "force_fields" -# subdirectory distributed with moltemplate.) - - -# Then define "CH2": - - -CH2 inherits COMPASS { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - - # COMMENTS: - # 1) Atom type names are defined in "compass_published.lt". - # 2) In this example, the atomic charge of an atom is calculated by summing - # partial charge contributions from neighboring atoms bonded to this atom. - # (according to the rules in "compass_published.lt"). For this reason, - # we can ignore the "charge" column in the "Data Atoms" section. Just - # leave theses charges as "0.0" for now. Moltemplate will recalculate them. - # 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH2 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt deleted file mode 100644 index e66579bf0b..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,78 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. - -# First, load the COMPASS force field parameters we will need: - -import "compass_published.lt" # <-- defines the "COMPASS" force field - -# (The "compass_published.lt" file is located in the "force_fields" -# subdirectory distributed with moltemplate.) - - -# Then define "CH3": - - -CH3 inherits COMPASS { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - - # COMMENTS: - # 1) Atom type names are defined in "compass_published.lt". - # 2) In this example, the atomic charge of an atom is calculated by summing - # partial charge contributions from neighboring atoms bonded to this atom. - # (according to the rules in "compass_published.lt"). For this reason, - # we can ignore the "charge" column in the "Data Atoms" section. Just - # leave theses charges as "0.0" for now. Moltemplate will recalculate them. - # 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH3 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt deleted file mode 100644 index 39c8e4f78d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/moltemplate_files/system.lt +++ /dev/null @@ -1,30 +0,0 @@ -import "alkane50.lt" # Defines the "Alkane50" molecule - - -polymer = new Alkane50 - - -# Specify the size of the world the polymer lives in: -write_once("Data Boundary") { - 0.0 72.0 xlo xhi - 0.0 72.0 ylo yhi - 0.0 72.0 zlo zhi -} - - - - - -############################################################################### -# Note: If you want to create multiple polymers, and/or mix them with other -# molecules, just add more "new" commands, for example: -# polymer1 = new Alkane50.move(0,0,10) -# polymer2 = new Alkane50.move(0,0,20) -# : -# ...or use array notation, for example: -# polymers = new Alkane50[20].move(0,0,10) -# -# Note: Multidimensional arrays can be used to fill a planar region or a volume -# polymers = new Alkane50 [4].move(0, 0, 30.0) -# [4].move(0, 30.0, 0) -# [2].move(70.0, 0, 0) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min deleted file mode 100644 index 5d0bcffd8e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.min +++ /dev/null @@ -1,37 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. - -thermo 50 -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz -minimize 1.0e-4 1.0e-6 100000 400000 - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -write_data system_after_min.data - - diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt deleted file mode 100644 index d5b77423a2..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/alkane_chain_single/run.in.nvt +++ /dev/null @@ -1,38 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must minimize the system beforehand by using "run.in.min". -# This will create the file "system_after_min.data" which this file reads. - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier simulation - -read_data "system_after_min.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 1000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt deleted file mode 100644 index 7a16faaed7..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README.txt +++ /dev/null @@ -1,37 +0,0 @@ -This example is a simple simulation of many short alkane chains (butane) in -a box near the boiling point at atmospheric pressure.(Please read "WARNING.TXT") - -1) Create the "system.data", "system.in.init", and "system.in.settings" -files which LAMMPS will read by running: - -moltemplate.sh system.lt - - -2) Run LAMMPS in this order: - -lmp_mpi -i run.in.npt # running the simulation at constant pressure -lmp_mpi -i run.in.nvt # running the simulation at constant temperature - -(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) - ----- Details ---- - -The "Butane" molecule, as well as the "CH2", and "CH3" monomers it contains -use the COMPASS force-field. This means that when we define these molecules, -we only specify the atom names, bond list, and coordinates. -We do not have to list the atom charges, angles, dihedrals, or impropers. -The rules for creating atomic charge and angle topology are contained in -the "compass_published.lt" file created by step 3) above. The "ch2group.lt", -"ch3group.lt", and "butane.lt" files all refer to "compass_published.lt", -(as well as the "COMPASS" force-field object which it defines). Excerpt: - -import "compass_published.lt" -CH2 inherits COMPASS { ... -CH3 inherits COMPASS { ... -Butane inherits COMPASS { ... - -Alternatively, you can manually define a list of angles, dihedrals, and -improper interactions in these files, instead of asking the force-field -to generate them for you. You can also specify some of the angles and -dihedrals explicitly, and let the force-field handle the rest. -(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh deleted file mode 100755 index 94d6de972c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh deleted file mode 100755 index 5cd2142a41..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt deleted file mode 100644 index 3ddb8e6065..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} - pbc box -shiftcenterrel {-0.05 -0.05 -0.05} -width 0.9 -style tubes - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg deleted file mode 100644 index 093f557dd9..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/after_pressure_equilibration_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg deleted file mode 100644 index d1a6e5060b..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/butane.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg deleted file mode 100644 index 39a8879557..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch2_ry90.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg deleted file mode 100644 index 3fa79ce360..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/ch3_ry60.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg deleted file mode 100644 index 9fa7d195f3..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/images/initial_configuration_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt deleted file mode 100644 index ed2c65640e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/butane.lt +++ /dev/null @@ -1,39 +0,0 @@ -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - -Butane inherits COMPASS { - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - # Create an array of 4 objects distributed along the X axis - - monomer1 = new CH3 - monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) - monomer3 = new CH2.move(2.5066446,0,0) - monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) - - # Now add a list of bonds connecting the carbon atoms together: - # (Angles, dihedrals, impropers will be automatically added later.) - - write('Data Bond List') { - $bond:b1 $atom:monomer1/C $atom:monomer2/C - $bond:b2 $atom:monomer2/C $atom:monomer3/C - $bond:b3 $atom:monomer3/C $atom:monomer4/C - } - -} # Butane - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt deleted file mode 100644 index c281e4d6ff..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,71 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. -# First, load the COMPASS force field parameters we will need: - -import "compass_published.lt" # <-- defines the "COMPASS" force field - -# (The "compass_published.lt" file is located in the "force_fields" -# subdirectory distributed with moltemplate.) -# Then define "CH2": - - - - -CH2 inherits COMPASS { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - -} # CH2 - - - - -# COMMENTS: -# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". -# 2) In this example, the atomic charge of an atom is calculated by summing -# partial charge contributions from neighboring atoms bonded to this atom. -# (according to the rules in "compass_published.lt"). For this reason, -# we can ignore the "charge" column in the "Data Atoms" section. Just -# leave theses charges as "0.0" for now. Moltemplate will recalculate them. -# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part -# of a larger molecule, and (if so) to use the larger parent object's -# molecule id number as it's own. - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt deleted file mode 100644 index 394080230a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,70 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. -# First, load the COMPASS force field parameters we will need: - -import "compass_published.lt" # <-- defines the "COMPASS" force field - -# (The "compass_published.lt" file is located in the "force_fields" -# subdirectory distributed with moltemplate.) -# Then define "CH3": - - - - -CH3 inherits COMPASS { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - -} # CH3 - - - - -# COMMENTS: -# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". -# 2) In this example, the atomic charge of an atom is calculated by summing -# partial charge contributions from neighboring atoms bonded to this atom. -# (according to the rules in "compass_published.lt"). For this reason, -# we can ignore the "charge" column in the "Data Atoms" section. Just -# leave theses charges as "0.0" for now. Moltemplate will recalculate them. -# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part -# of a larger molecule, and (if so) to use the larger parent object's -# molecule id number as it's own. - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt deleted file mode 100644 index 1f25ac8e96..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/moltemplate_files/system.lt +++ /dev/null @@ -1,24 +0,0 @@ -import "butane.lt" # <- defines the "Butane" molecule type. - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 62.4 xlo xhi - 0.0 62.4 ylo yhi - 0.0 62.4 zlo zhi -} - - - -# Generate an array of 864 = 12 x 12 x 6 Butane molecules -# which (more or less) uniformly fills the simulation box: - -molecules = new Butane [12].move(0, 0, 5.2) - [12].move(0, 5.2, 0) - [6].move(10.4, 0, 0) - - - -# NOTE: The spacing between molecules is large. There should be extra room to -# move during the initial stages of equilibration. However, you will have to -# run the simulation at NPT conditions later to compress the system to a -# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt deleted file mode 100644 index ec9af62c40..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.npt +++ /dev/null @@ -1,103 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, -# reorient, compress). The system (as defined in the "system.data" file) -# is already expanded. That means there are 3 steps left: - -dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz -thermo_style custom step temp pe etotal epair ebond eangle edihed press vol -thermo 50 -thermo_modify norm yes - -# -- Equilibration: part 1: initial minimization -- - -# Note: In general, it's always a good idea to minimize the system at first. - -minimize 1.0e-5 1.0e-7 100000 400000 -undump dumpeq1 - -write_data system_after_eq1_min.data - -# -- Equilibration part 2: reorienting the molecules (NVT) -- - -timestep 1.0 -dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz - -# Run the system at high temperature (at constant volume) to reorient the -# the molecules (which would otherwise be pointing in the same direction). - -# To speed it up, I randomize the atomic positions for a few thousand steps -# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). -# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) - - -fix fxlan all langevin 900.0 900.0 120 48279 -fix fxnve all nve - -run 4000 - -unfix fxlan -unfix fxnve -# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). -fix fxnvt all nvt temp 900.0 900.0 100.0 - -run 10000 -undump dumpeq2 - - -write_data system_after_eq2_reorient.data - -unfix fxnvt - - -# -- equilibration part 3: Equilibrating the density (NPT) -- - -# Originally, the simulation box (in "system.data" and "system.lt") was -# unrealistically large. The spacing between the molecules was large also. -# I did this to enable the molecules to move freely and reorient themselves. -# After doing that, we should run the simulation under NPT conditions to -# allow the simulation box to contract to it's natural size. -# To help it collapse, we begin the simulation at a relatively high pressure -# Later on, we will slowly decrease it to 1 bar. - -# First cool the system. (Do this at high pressure to avoid bubble formation.) - -dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 - -timestep 1.0 -run 20000 - -# At the very end of the previous simulation, the temperature dropped below -# the boiling point. Run the simulation for longer at these conditions to -# give it a chance for the vapor -> liquid transition to complete. -# We will also slowly decrease the pressure to 1 bar. - -unfix fxnpt -fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 - -timestep 1.0 -run 100000 - -write_data system_after_eq3_npt.data - diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt deleted file mode 100644 index ea3ac42167..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/butane/run.in.nvt +++ /dev/null @@ -1,45 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_eq3_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 260.0 260.0 500.0 tchain 1 -thermo_style custom step temp pe etotal epair ebond eangle edihed -thermo 100 -thermo_modify norm yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt deleted file mode 100644 index 5ffefbc7f3..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README.txt +++ /dev/null @@ -1,42 +0,0 @@ -This example is a simple simulation of many long alkane chains (hexadecane) in a -box near the boiling point at atmospheric pressure. Please read "WARNING.TXT". - -NOTE: This particular example uses the COMPASS force-field - However, moltemplate is not limited to COMPASS. - -1) Create the "system.data", "system.in.init", and "system.in.settings" -files which LAMMPS will read by running: - -moltemplate.sh system.lt - - -2) Run LAMMPS in this order: - -lmp_mpi -i run.in.npt # running the simulation at constant pressure -lmp_mpi -i run.in.nvt # running the simulation at constant temperature - -(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) - ----- Details ---- - -The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains -use the COMPASS force-field. This means that when we define these molecules, -we only specify the atom names, bond list, and coordinates. -We do not have to list the atom charges, angles, dihedrals, or impropers. -The rules for creating atomic charge and angle topology are contained in -the "compass_published.lt" file created by step 3) above. The "ch2group.lt", -"ch3group.lt", and "hexadecane.lt" files all refer to "compass_published.lt", -(as well as the "COMPASS" force-field object which it defines). Excerpt: - -import "compass_published.lt" -CH2 inherits COMPASS { ... -CH3 inherits COMPASS { ... -Hexadecane inherits COMPASS { ... - -Alternatively, you can manually define a list of angles, dihedrals, and -improper interactions in these files, instead of asking the force-field -to generate them for you. You can also specify some of the angles and -dihedrals explicitly, and let the force-field handle the rest. -(Many of the examples which come with moltemplate do this.) - - diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh deleted file mode 100755 index 4871a06495..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # simulation at constant volume - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh deleted file mode 100755 index 15a3a963c8..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt deleted file mode 100644 index ab508fc894..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/WARNING.txt +++ /dev/null @@ -1,13 +0,0 @@ -# -------- WARNING: -------- - -This software is experimental, and the force-fields and equilbration protocols -have not been tested carefully by me. There is no gaurantee that the simulation -will reproduce the behavior of real hexadecane molecules, - -# -------- REQUEST FOR HELP: -------- - -However, if you notice a problem with this example, please report it. -Peer-review is the only way to improve this software (or any software). -Other suggestions are also welcome! - -(Contact jewett.aij@gmail.com, 2017-10-03) diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg deleted file mode 100644 index b0d31f8845..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg deleted file mode 100644 index f7c13d0989..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg deleted file mode 100644 index a4151a5fd3..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/images/hexadecane_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt deleted file mode 100644 index db7ccabdc9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,70 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. -# First, load the COMPASS force field parameters we will need: - -import "compass_published.lt" # <-- defines the "COMPASS" force field - -# (The "compass_published.lt" file is located in the "force_fields" -# subdirectory distributed with moltemplate.) -# Then define "CH2": - - - - -CH2 inherits COMPASS { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - -} # CH2 - - - - -# COMMENTS: -# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". -# 2) In this example, the atomic charge of an atom is calculated by summing -# partial charge contributions from neighboring atoms bonded to this atom. -# (according to the rules in "compass_published.lt"). For this reason, -# we can ignore the "charge" column in the "Data Atoms" section. Just -# leave theses charges as "0.0" for now. Moltemplate will recalculate them. -# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part -# of a larger molecule, and (if so) to use the larger parent object's -# molecule id number as it's own. - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt deleted file mode 100644 index 394080230a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,70 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. -# First, load the COMPASS force field parameters we will need: - -import "compass_published.lt" # <-- defines the "COMPASS" force field - -# (The "compass_published.lt" file is located in the "force_fields" -# subdirectory distributed with moltemplate.) -# Then define "CH3": - - - - -CH3 inherits COMPASS { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:c4 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:h1 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:h1 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:h1 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - -} # CH3 - - - - -# COMMENTS: -# 1) Atom type names (eg. "c4", "h1") are defined in "compass_published.lt". -# 2) In this example, the atomic charge of an atom is calculated by summing -# partial charge contributions from neighboring atoms bonded to this atom. -# (according to the rules in "compass_published.lt"). For this reason, -# we can ignore the "charge" column in the "Data Atoms" section. Just -# leave theses charges as "0.0" for now. Moltemplate will recalculate them. -# 3) The "..." in "$mol:..." tells moltemplate that this molecule may be part -# of a larger molecule, and (if so) to use the larger parent object's -# molecule id number as it's own. - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt deleted file mode 100644 index 23d1c229a1..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/hexadecane.lt +++ /dev/null @@ -1,79 +0,0 @@ -# This example looks complicated because I split the -# hexadecane molecule into individual CH2 and CH3 monomers. -# -# I defined it this way so that you can easily modify -# it to change the length of the alkane chain. - - -import "compass_published.lt" # load the "COMPASS" force-field information -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - - -Hexadecane inherits COMPASS { - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - - # Now create an array of 16 "CH2" objects distributed along the X axis - - monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0) - - # Each monomer is rotated 180 degrees with respect to the previous - # monomer, and then moved 1.2533223 Angstroms down the X axis. - - # ---- Now, modify the ends: --- - # Delete the CH2 groups at the beginning and end, and replace them with CH3. - - delete monomers[0] - delete monomers[15] - - monomers[0] = new CH3 - monomers[15] = new CH3 - - # Move the CH3 groups to the correct location at either end of the chain: - - monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0) - # Note: 18.7998345 = (16-1) * 1.2533223 - - - # Now add a list of bonds connecting the carbon atoms together: - - write('Data Bond List') { - $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C - $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C - $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C - $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C - $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C - $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C - $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C - $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C - $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C - $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C - $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C - $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C - $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C - $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C - $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C - } - -} # Hexadecane - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt deleted file mode 100644 index 9d90d39c20..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/moltemplate_files/system.lt +++ /dev/null @@ -1,20 +0,0 @@ -import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 62.4 xlo xhi - 0.0 62.4 ylo yhi - 0.0 62.4 zlo zhi -} - -molecules = new Hexadecane [12].move(0, 0, 5.2) - [12].move(0, 5.2, 0) - [2].move(31.2, 0, 0) - - - - -# NOTE: The spacing between molecules is large. There should be extra room to -# move during the initial stages of equilibration. However, you will have to -# run the simulation at NPT conditions later to compress the system to a -# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt deleted file mode 100644 index 2e9c496817..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.npt +++ /dev/null @@ -1,102 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, -# reorient, compress). The system (as defined in the "system.data" file) -# is already expanded. That means there are 3 steps left: - -dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz -thermo_style custom step temp pe etotal epair ebond eangle edihed press vol -thermo 50 -thermo_modify norm yes - -# -- Equilibration: part 1: initial minimization -- - -# Note: In general, it's always a good idea to minimize the system at first. - -minimize 1.0e-5 1.0e-7 100000 400000 -undump dumpeq1 - -write_data system_after_eq1_min.data - -# -- Equilibration part 2: reorienting the molecules (NVT) -- - -timestep 1.0 -dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz - -# Run the system at high temperature (at constant volume) to reorient the -# the molecules (which would otherwise be pointing in the same direction). - -# To speed it up, I randomize the atomic positions for a few thousand steps -# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). -# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) - - -fix fxlan all langevin 900.0 900.0 120 48279 -fix fxnve all nve - -run 4000 - -unfix fxlan -unfix fxnve -# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). -fix fxnvt all nvt temp 900.0 900.0 100.0 - -run 50000 -undump dumpeq2 - - -write_data system_after_eq2_reorient.data - -unfix fxnvt - -# -- equilibration part 3: Equilibrating the density (NPT) -- - -# Originally, the simulation box (in "system.data" and "system.lt") was -# unrealistically large. The spacing between the molecules was large also. -# I did this to enable the molecules to move freely and reorient themselves. -# After doing that, we should run the simulation under NPT conditions to -# allow the simulation box to contract to it's natural size. We do that here: -# To help it collapse, we begin the simulation at a relatively high pressure -# Later on, we will slowly decrease it to 1 bar. - -# First cool the system. (Do this at high pressure to avoid bubble formation.) - -dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 - -timestep 1.0 -run 20000 - -# At the very end of the previous simulation, the temperature dropped below -# the boiling point. Run the simulation for longer at these conditions to -# give it a chance for the vapor -> liquid transition to complete. -# We will also slowly decrease the pressure to 1 bar. - -unfix fxnpt -fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 - -timestep 1.0 -run 100000 - -write_data system_after_eq3_npt.data - diff --git a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt deleted file mode 100644 index 7393961924..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_COMPASS/hexadecane/run.in.nvt +++ /dev/null @@ -1,45 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_eq3_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo_style custom step temp pe etotal epair ebond eangle edihed -thermo 100 -thermo_modify norm yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/WARNING.txt deleted file mode 100644 index 99b50a744e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/WARNING.txt +++ /dev/null @@ -1,28 +0,0 @@ -# -------- WARNING: -------- - -This directory contains some examples of all-atom simulations using the OPLSAA -force field. - -This software is experimental, and the force-fields and equilbration protocols -have not been tested carefully by me. There is no gaurantee that simulations -prepared using moltemplate will reproduce the behavior of other MD codes. - -# -------- REQUEST FOR HELP: -------- - -If you notice a problem with these examples, please report it. -Peer-review is the only way to improve this software (or any software). -Other suggestions are also welcome! - -(Contact jewett.aij@gmail.com, 2014-4-19) - ---- Improper angles --- - -I am also uncertain whether the improper angle interactions generated by -moltemplate are equivalent to those generated by BOSS or other molecule -builders. (I think they are, but I am worried that we might have listed -the atom types in the wrong order. Let us know if you see discrepancies -between what moltemplate and other molecule builders generates.) - ------------ -For more details how to use the OPLSAA force-field, read the "README.TXT" -file located in "ethylene/moltemplate_files/oplsaa_lt_generator/README.TXT" diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README.txt deleted file mode 100644 index 5ddb4ae8f6..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README.txt +++ /dev/null @@ -1,37 +0,0 @@ -This example is a simple simulation of a long alkane chain, -in a vacuum at room temperature using the OPLSAA force field. - -1) Create the "system.data", "system.in.init", and "system.in.settings" -files which LAMMPS will read by running: - -moltemplate.sh system.lt - - -2) Run LAMMPS in this order: - -lmp_mpi -i run.in.min # minimize the energy (to avoid atom overlap) before... -lmp_mpi -i run.in.nvt # running the simulation at constant temperature - -(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) - ----- Details ---- - -The "Alkane50" molecule, as well as the "CH2", and "CH3" monomers it contains -use the OPLSAA force-field. This means that when we define these molecules, -we only specify the atom names, bond list, and coordinates. -We do not have to list the atom charges, angles, dihedrals, or impropers. -The rules for creating atomic charge and angle topology are contained in -the "loplsaa.lt" file created by step 3) above. The "ch2group.lt", -"ch3group.lt", and "alkane50.lt" files all refer to "loplsaa.lt", -(as well as the "OPLSAA" force-field object which it defines). Excerpt: - -import "loplsaa.lt" -CH2 inherits OPLSAA { ... -CH3 inherits OPLSAA { ... -Alkane50 inherits OPLSAA { ... - -Alternatively, you can manually define a list of angles, dihedrals, and -improper interactions in these files, instead of asking the force-field -to generate them for you. You can also specify some of the angles and -dihedrals explicitly, and let the force-field handle the rest. -(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_run.sh deleted file mode 100755 index 94d6de972c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_setup.sh deleted file mode 100755 index 5cd2142a41..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg deleted file mode 100644 index 39a8879557..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/ch2_ry90.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg deleted file mode 100644 index ab140a8f9e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/ch3_ry60.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg deleted file mode 100644 index 39633edd5e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg deleted file mode 100644 index da2fe1185e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/images/t=1ns.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt deleted file mode 100644 index b15ef139fd..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/alkane50.lt +++ /dev/null @@ -1,137 +0,0 @@ -# This is a simple example showing how to build a long polymer -# (in this case, an alkane chain). I split the -# hexadecane molecule into individual CH2 and CH3 monomers. -# I defined it this way so that you can easily modify -# it to change the length of the alkane chain. - - -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - - -Alkane50 inherits OPLSAA { - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - # This is a long polymer consisting of 48 CH2 groups and 2 CH3 end-caps. - # Rather than create them one-by-one, I decided to create them all - # using a single "new" command. Later, I can modify this array. - - # Create an array of 50 "CH2" objects distributed along the X axis - - monomers = new CH2 [50].rot(180,1,0,0).move(1.2533223,0,0) - - # NOTE: the ".rot(180,1,0,0).move(1.2533223,0,0)" means that each - # successive monomer is rotated 180 degrees (with respect to the previous - # monomer), and then moved 1.2533223 Angstroms down the X axis. - # Alternately, if you are reading the coordinates from a file, you don't have - # to indicate the position & orientation of each monomer. In that case, use: - # monomers = new CH2 [50] - - - # ---- Now, modify the ends: --- - # Delete the CH2 groups at the beginning and end, and replace them with CH3. - - delete monomers[0] - delete monomers[49] - - monomers[0] = new CH3 - monomers[49] = new CH3 - - # Move the CH3 groups to the correct location at either end of the chain: - - #monomers[0].move(0,0,0) # <--(this monomer is already in the correct place) - monomers[49].rot(180.0,0,0,1).move(61.4127927,0,0) #61.4127927=49*1.2533223 - - - ## NOTE: Alternately, you can define the polymer without deleting the ends: - # monomers[0] = new CH3 - # monomers[1-48] = new CH2[48].rot(180,1,0,0).move(1.2533223,0,0) - ## Note: monomers[0] and monomers[1] overlap, so we move 1-48 to make room: - # monomers[1-48].rot(180,1,0,0).move(1.2533223,0,0) # move many monomers - ## Now add the final monomer at the end: - # monomers[49] = new CH3.rot(180.0,0,0,1).move(61.4127927,0,0) - # - ## NOTE: Alternately, you can read the coordinates from a file. - ## In that case, you can use simpler commands: - # monomers[0] = new CH3 - # monomers[1-48] = new CH2[48] - # monomers[49] = new CH3 - - - - # Now add a list of bonds connecting the carbon atoms together: - # (Angles, dihedrals, impropers will be automatically added later.) - - write('Data Bond List') { - $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C - $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C - $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C - $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C - $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C - $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C - $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C - $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C - $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C - $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C - $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C - $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C - $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C - $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C - $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C - $bond:b16 $atom:monomers[15]/C $atom:monomers[16]/C - $bond:b17 $atom:monomers[16]/C $atom:monomers[17]/C - $bond:b18 $atom:monomers[17]/C $atom:monomers[18]/C - $bond:b19 $atom:monomers[18]/C $atom:monomers[19]/C - $bond:b20 $atom:monomers[19]/C $atom:monomers[20]/C - $bond:b21 $atom:monomers[20]/C $atom:monomers[21]/C - $bond:b22 $atom:monomers[21]/C $atom:monomers[22]/C - $bond:b23 $atom:monomers[22]/C $atom:monomers[23]/C - $bond:b24 $atom:monomers[23]/C $atom:monomers[24]/C - $bond:b25 $atom:monomers[24]/C $atom:monomers[25]/C - $bond:b26 $atom:monomers[25]/C $atom:monomers[26]/C - $bond:b27 $atom:monomers[26]/C $atom:monomers[27]/C - $bond:b28 $atom:monomers[27]/C $atom:monomers[28]/C - $bond:b29 $atom:monomers[28]/C $atom:monomers[29]/C - $bond:b30 $atom:monomers[29]/C $atom:monomers[30]/C - $bond:b31 $atom:monomers[30]/C $atom:monomers[31]/C - $bond:b32 $atom:monomers[31]/C $atom:monomers[32]/C - $bond:b33 $atom:monomers[32]/C $atom:monomers[33]/C - $bond:b34 $atom:monomers[33]/C $atom:monomers[34]/C - $bond:b35 $atom:monomers[34]/C $atom:monomers[35]/C - $bond:b36 $atom:monomers[35]/C $atom:monomers[36]/C - $bond:b37 $atom:monomers[36]/C $atom:monomers[37]/C - $bond:b38 $atom:monomers[37]/C $atom:monomers[38]/C - $bond:b39 $atom:monomers[38]/C $atom:monomers[39]/C - $bond:b40 $atom:monomers[39]/C $atom:monomers[40]/C - $bond:b41 $atom:monomers[40]/C $atom:monomers[41]/C - $bond:b42 $atom:monomers[41]/C $atom:monomers[42]/C - $bond:b43 $atom:monomers[42]/C $atom:monomers[43]/C - $bond:b44 $atom:monomers[43]/C $atom:monomers[44]/C - $bond:b45 $atom:monomers[44]/C $atom:monomers[45]/C - $bond:b46 $atom:monomers[45]/C $atom:monomers[46]/C - $bond:b47 $atom:monomers[46]/C $atom:monomers[47]/C - $bond:b48 $atom:monomers[47]/C $atom:monomers[48]/C - $bond:b49 $atom:monomers[48]/C $atom:monomers[49]/C - } - -} # Alkane50 - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt deleted file mode 100644 index c800d56679..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,82 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. - -# First, load the OPLS force field parameters we will need. -# These 2 files are located in the "force_fields" subdirectory -# distributed with moltemplate. - -import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field -import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from - # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459 - # To use the ordinary OPLSAA force field parameters, - # (instead of the Sui et al. parameters), change the - # atom types below from "@atom:81L","@atom:85LCH2" to - # "@atom:81" and "@atom:85" (defined in "oplsaa.lt") - - - -# Then define "CH2": - - -CH2 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:81L 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - - # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt": - # @atom:80L "Alkane CH3- (LOPLS CT_CH3)" - # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)" - # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)" - # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)" - # In this example, atomic charges are generated by atom type (according to the - # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now. - # The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH2 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt deleted file mode 100644 index 95d48d8530..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,84 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. - -# First, load the OPLS force field parameters we will need. -# These 2 files are located in the "force_fields" subdirectory -# of the moltemplate distribution. - -import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field -import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from - # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459 - # To use the ordinary OPLSAA force field parameters, - # (instead of the Sui et al. parameters), change the - # atom types below from "@atom:80L","@atom:85LCH3" to - # "@atom:80" and "@atom:85" (defined in "oplsaa.lt") - - - -# Then define "CH3": - - -CH3 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:80L 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:85LCH3 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - - # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt", - # @atom:80L "Alkane CH3- (LOPLS CT_CH3)" - # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)" - # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)" - # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)" - # In this example, atomic charges are generated by atom type (according to the - # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now. - # The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH3 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt deleted file mode 100644 index f62ecc09b6..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/moltemplate_files/system.lt +++ /dev/null @@ -1,31 +0,0 @@ -import "alkane50.lt" # Defines the "Alkane50" molecule - - -polymer = new Alkane50 - - - -# Specify the size of the world the polymer lives in: -write_once("Data Boundary") { - 0.0 72.0 xlo xhi - 0.0 72.0 ylo yhi - 0.0 72.0 zlo zhi -} - - - - - -############################################################################### -# Note: If you want to create multiple polymers, and/or mix them with other -# molecules, just add more "new" commands, for example: -# polymer1 = new Alkane50.move(0,0,10) -# polymer2 = new Alkane50.move(0,0,20) -# : -# ...or use array notation, for example: -# polymers = new Alkane50[20].move(0,0,10) -# -# Note: Multidimensional arrays can be used to fill a planar region or a volume -# polymers = new Alkane50 [4].move(0, 0, 30.0) -# [4].move(0, 30.0, 0) -# [2].move(70.0, 0, 0) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/run.in.min b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/run.in.min deleted file mode 100644 index 5d0bcffd8e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/run.in.min +++ /dev/null @@ -1,37 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. - -thermo 50 -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz -minimize 1.0e-4 1.0e-6 100000 400000 - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -write_data system_after_min.data - - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/run.in.nvt deleted file mode 100644 index d5b77423a2..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/alkane_chain_single/run.in.nvt +++ /dev/null @@ -1,38 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must minimize the system beforehand by using "run.in.min". -# This will create the file "system_after_min.data" which this file reads. - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier simulation - -read_data "system_after_min.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 1000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt deleted file mode 100644 index 4a6377569d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README.txt +++ /dev/null @@ -1,37 +0,0 @@ -This example is a simple simulation of many short alkane chains (butane) in a -box near the boiling point at atmospheric pressure. Please read "WARNING.TXT". - -1) Create the "system.data", "system.in.init", and "system.in.settings" -files which LAMMPS will read by running: - -moltemplate.sh system.lt - - -2) Run LAMMPS in this order: - -lmp_mpi -i run.in.npt # running the simulation at constant pressure -lmp_mpi -i run.in.nvt # running the simulation at constant temperature - -(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) - ----- Details ---- - -The "Butane50" molecule, as well as the "CH2", and "CH3" monomers it contains -use the OPLSAA force-field. This means that when we define these molecules, -we only specify the atom names, bond list, and coordinates. -We do not have to list the atom charges, angles, dihedrals, or impropers. -The rules for creating atomic charge and angle topology are contained in -the "oplsaa.lt" file created by step 3) above. The "ch2group.lt", -"ch3group.lt", and "butane.lt" files all refer to "oplsaa.lt", -(as well as the "OPLSAA" force-field object which it defines). Excerpt: - -import "oplsaa.lt" -CH2 inherits OPLSAA { ... -CH3 inherits OPLSAA { ... -Butane inherits OPLSAA { ... - -Alternatively, you can manually define a list of angles, dihedrals, and -improper interactions in these files, instead of asking the force-field -to generate them for you. You can also specify some of the angles and -dihedrals explicitly, and let the force-field handle the rest. -(Many of the examples which come with moltemplate do this.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh deleted file mode 100755 index 94d6de972c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh deleted file mode 100755 index 5cd2142a41..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt deleted file mode 100644 index b39d8901ad..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} - pbc box -shiftcenterrel {-0.05 -0.05 -0.05} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg deleted file mode 100644 index 093f557dd9..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/after_pressure_equilibration_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg deleted file mode 100644 index a1bcb4aee6..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/butane.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg deleted file mode 100644 index 39a8879557..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch2_ry90.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg deleted file mode 100644 index ab140a8f9e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/ch3_ry60.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg deleted file mode 100644 index 9fa7d195f3..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/images/initial_configuration_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt deleted file mode 100644 index 8c21db265c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/butane.lt +++ /dev/null @@ -1,42 +0,0 @@ -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - -Butane inherits OPLSAA { - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - # Create an array of 4 objects distributed along the X axis - - monomer1 = new CH3 - monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0) - monomer3 = new CH2.move(2.5066446,0,0) - monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0) - - # Now add a list of bonds connecting the carbon atoms together: - # (Angles, dihedrals, impropers will be automatically added later.) - - write('Data Bond List') { - $bond:b1 $atom:monomer1/C $atom:monomer2/C - $bond:b2 $atom:monomer2/C $atom:monomer3/C - $bond:b3 $atom:monomer3/C $atom:monomer4/C - } - -} # Butane - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt deleted file mode 100644 index 665e8e6607..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,67 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. - -# First, load the OPLS force field parameters we will need. -# This file is located in the "force_fields" subdirectory -# of the moltemplate distribution. - -import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field - - -# Then define "CH2": - - -CH2 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:81 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:85 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:85 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - -} # CH2 - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - -# ---- NOTES: ---- -# -# Atom type numbers (@atom:80,81,85) are defined in "oplsaa.lt", -# @atom:80 "Alkane CH3-" -# @atom:81 "Alkane -CH2-" -# @atom:85 "Alkane H-C CH3" -# @atom:85 "Alkane H-C CH2" -# In this example, atomic charges are generated by atom type (according to the -# rules in oplsaa.lt), and can be omitted. Just leave them as "0.00" for now. -# The "..." in "$mol:..." tells moltemplate that this molecule may be part -# of a larger molecule, and (if so) to use the larger parent object's -# molecule id number as it's own. -# -######### (scratchwork calculations for the atomic coordinates) ######### -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt deleted file mode 100644 index bf802b3162..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,69 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. - -# First, load the OPLS force field parameters we will need. -# This file is located in the "force_fields" subdirectory -# of the moltemplate distribution. - -import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field - - -# Then define "CH3": - - -CH3 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:80 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:85 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:85 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:85 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - -} # CH3 - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -# ---- NOTES: ---- -# -# Atom type numbers (@atom:80,81,85) are defined in "oplsaa.lt", -# @atom:80 "Alkane CH3-" -# @atom:81 "Alkane -CH2-" -# @atom:85 "Alkane H-C CH3" -# @atom:85 "Alkane H-C CH2" -# In this example, atomic charges are generated by atom type (according to the -# rules in oplsaa.lt), and can be omitted. Just leave them as "0.00" for now. -# The "..." in "$mol:..." tells moltemplate that this molecule may be part -# of a larger molecule, and (if so) to use the larger parent object's -# molecule id number as it's own. -# -######### (scratchwork calculations for the atomic coordinates) ######### -# -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt deleted file mode 100644 index 52b5126494..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/moltemplate_files/system.lt +++ /dev/null @@ -1,25 +0,0 @@ -import "butane.lt" # <- defines the "Butane" molecule type. - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 62.4 xlo xhi - 0.0 62.4 ylo yhi - 0.0 62.4 zlo zhi -} - - - -# Generate an array of 864 = 12 x 12 x 6 Butane molecules -# which (more or less) uniformly fills the simulation box: - -molecules = new Butane [12].move(0, 0, 5.2) - [12].move(0, 5.2, 0) - [6].move(10.4, 0, 0) - - - - -# NOTE: The spacing between molecules is large. There should be extra room to -# move during the initial stages of equilibration. However, you will have to -# run the simulation at NPT conditions later to compress the system to a -# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt deleted file mode 100644 index ec9af62c40..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.npt +++ /dev/null @@ -1,103 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, -# reorient, compress). The system (as defined in the "system.data" file) -# is already expanded. That means there are 3 steps left: - -dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz -thermo_style custom step temp pe etotal epair ebond eangle edihed press vol -thermo 50 -thermo_modify norm yes - -# -- Equilibration: part 1: initial minimization -- - -# Note: In general, it's always a good idea to minimize the system at first. - -minimize 1.0e-5 1.0e-7 100000 400000 -undump dumpeq1 - -write_data system_after_eq1_min.data - -# -- Equilibration part 2: reorienting the molecules (NVT) -- - -timestep 1.0 -dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz - -# Run the system at high temperature (at constant volume) to reorient the -# the molecules (which would otherwise be pointing in the same direction). - -# To speed it up, I randomize the atomic positions for a few thousand steps -# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). -# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) - - -fix fxlan all langevin 900.0 900.0 120 48279 -fix fxnve all nve - -run 4000 - -unfix fxlan -unfix fxnve -# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). -fix fxnvt all nvt temp 900.0 900.0 100.0 - -run 10000 -undump dumpeq2 - - -write_data system_after_eq2_reorient.data - -unfix fxnvt - - -# -- equilibration part 3: Equilibrating the density (NPT) -- - -# Originally, the simulation box (in "system.data" and "system.lt") was -# unrealistically large. The spacing between the molecules was large also. -# I did this to enable the molecules to move freely and reorient themselves. -# After doing that, we should run the simulation under NPT conditions to -# allow the simulation box to contract to it's natural size. -# To help it collapse, we begin the simulation at a relatively high pressure -# Later on, we will slowly decrease it to 1 bar. - -# First cool the system. (Do this at high pressure to avoid bubble formation.) - -dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 - -timestep 1.0 -run 20000 - -# At the very end of the previous simulation, the temperature dropped below -# the boiling point. Run the simulation for longer at these conditions to -# give it a chance for the vapor -> liquid transition to complete. -# We will also slowly decrease the pressure to 1 bar. - -unfix fxnpt -fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 - -timestep 1.0 -run 100000 - -write_data system_after_eq3_npt.data - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt deleted file mode 100644 index ea3ac42167..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/butane/run.in.nvt +++ /dev/null @@ -1,45 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_eq3_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 260.0 260.0 500.0 tchain 1 -thermo_style custom step temp pe etotal epair ebond eangle edihed -thermo 100 -thermo_modify norm yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt deleted file mode 100644 index 470df87550..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README.txt +++ /dev/null @@ -1,9 +0,0 @@ -This is an example of how to use the OPLSAA force-field in LAMMPS - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_run.sh deleted file mode 100755 index c27520076e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_setup.sh deleted file mode 100755 index 0869d7b783..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_setup.sh +++ /dev/null @@ -1,35 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt deleted file mode 100644 index 642c85c24c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.05 -0.05} - pbc box -shiftcenterrel {-0.05 -0.05 -0.05} -width 0.5 - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg deleted file mode 100644 index 356c784256..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/benzene.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg deleted file mode 100644 index b9ff053fcb..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_50bar_t=100000_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg deleted file mode 100644 index 65949a4684..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene+benzene_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg deleted file mode 100644 index ab5bbbf49b..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/images/ethylene.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt deleted file mode 100644 index 5f5e8d904a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/benzene.lt +++ /dev/null @@ -1,55 +0,0 @@ -import "oplsaa.lt" - -# The "oplsaa.lt" file contains force-field definitions, -# partial charges and masses for the atoms in your system. - -# Note: -# Atom type @atom:90 corresponds to "Aromatic C" -# Atom type @atom:91 corresponds to "Aromatic H-C" - -Benzene inherits OPLSAA { - - # atom-id mol-id atom-type charge X Y Z # comment - - write("Data Atoms") { - $atom:C1 $mol @atom:90 0.00 -0.739 1.189 -0.00733 # 90 = "Aromatic C" - $atom:C2 $mol @atom:90 0.00 0.614 1.208 0.35167 # 90 = "Aromatic C" - $atom:C3 $mol @atom:90 0.00 1.353 0.019 0.35867 # 90 = "Aromatic C" - $atom:C4 $mol @atom:90 0.00 0.739 -1.189 0.00667 # 90 = "Aromatic C" - $atom:C5 $mol @atom:90 0.00 -0.614 -1.208 -0.35133 # 90 = "Aromatic C" - $atom:C6 $mol @atom:90 0.00 -1.353 -0.019 -0.35833 # 90 = "Aromatic C" - $atom:H11 $mol @atom:91 0.00 -1.309 2.106 -0.01233 # 91 = "Aromatic H-C" - $atom:H21 $mol @atom:91 0.00 1.088 2.14 0.62267 # 91 = "Aromatic H-C" - $atom:H31 $mol @atom:91 0.00 2.397 0.034 0.63467 # 91 = "Aromatic H-C" - $atom:H41 $mol @atom:91 0.00 1.309 -2.106 0.01267 # 91 = "Aromatic H-C" - $atom:H51 $mol @atom:91 0.00 -1.088 -2.14 -0.62233 # 91 = "Aromatic H-C" - $atom:H61 $mol @atom:91 0.00 -2.397 -0.034 -0.63533 # 91 = "Aromatic H-C" - } - # Note: You don't have to specify the charge in this example because - # we are using the OPLSAA force-field assigns this by atom-type. - # Just leave these numbers as 0.00 for now. - # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). - # If we put "$mol" there, moltemplate will generate this integer for you - - # A list of the bonds in the molecule - # BondID AtomID1 AtomID2 - - write("Data Bond List") { - $bond:C12 $atom:C1 $atom:C2 - $bond:C23 $atom:C2 $atom:C3 - $bond:C34 $atom:C3 $atom:C4 - $bond:C45 $atom:C4 $atom:C5 - $bond:C56 $atom:C5 $atom:C6 - $bond:C61 $atom:C6 $atom:C1 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C2H2 $atom:C2 $atom:H21 - $bond:C3H3 $atom:C3 $atom:H31 - $bond:C4H4 $atom:C4 $atom:H41 - $bond:C5H5 $atom:C5 $atom:H51 - $bond:C6H6 $atom:C6 $atom:H61 - } - - # In the "Data Bond List" section we don't have to specify the bond type. - # The bond-type will be determined by the atom type (according to "oplsaa.lt") - -} # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt deleted file mode 100644 index 3515702d1d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/ethylene.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "oplsaa.lt" - -# The "oplsaa.lt" file contains force-field definitions, -# partial charges and masses for the atoms in your system. - -# Note: -# Atom type 88 corresponds to "Alkene H2-C=" -# Atom type 89 corresponds to "Alkene H-C=" - - - -Ethylene inherits OPLSAA { - - # atom-id mol-id atom-type charge X Y Z # comment - - write('Data Atoms') { - $atom:C1 $mol @atom:88 0.00 -0.6695 0.00000 0.000 #88 = "Alkene H2-C=" - $atom:C2 $mol @atom:88 0.00 0.6695 0.00000 0.000 #88 = "Alkene H2-C=" - $atom:H11 $mol @atom:89 0.00 -1.23422 -0.85446 0.000 #89 = "Alkene H-C=" - $atom:H12 $mol @atom:89 0.00 -1.23422 0.85446 0.000 #89 = "Alkene H-C=" - $atom:H21 $mol @atom:89 0.00 1.23422 -0.85446 0.000 #89 = "Alkene H-C=" - $atom:H22 $mol @atom:89 0.00 1.23422 0.85446 0.000 #89 = "Alkene H-C=" - } - # Note: You don't have to specify the charge in this example because - # we are using the OPLSAA force-field assigns this by atom-type. - # Just leave these numbers as 0.00 for now. - # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). - # If we put "$mol" there, moltemplate will generate this integer for you - - # A list of the bonds in the molecule - # BondID AtomID1 AtomID2 - - write('Data Bond List') { - $bond:C12 $atom:C1 $atom:C2 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C1H2 $atom:C1 $atom:H12 - $bond:C2H1 $atom:C2 $atom:H21 - $bond:C2H2 $atom:C2 $atom:H22 - } - - # In the "Data Bond List" section we don't have to specify the bond type. - # The bond-type will be determined by the atom type (according to "oplsaa.lt") - -} # Ethylene - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt deleted file mode 100644 index a28fd9f4af..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/moltemplate_files/system.lt +++ /dev/null @@ -1,28 +0,0 @@ -import "ethylene.lt" # <- defines the "Ethylene" molecule type. -import "benzene.lt" # <- defines the "Benzene" molecule type. - - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 48.00 xlo xhi - 0.0 48.00 ylo yhi - 0.0 48.00 zlo zhi -} - -# Create 216 ethylenes and 108 benzenes - -ethylenes = new Ethylene[6].move(8.0, 0, 0) - [6].move(0, 8.0, 0) - [6].move(0, 0, 8.0) - -benzenes = new Benzene[6].move(8.0, 0, 0) - [6].move(0, 8.0, 0) - [3].move(0, 0, 16.0) - -# Now shift the positions of all of the benzene molecules, -# to reduce the chance that they overlap with the ethylene molecules. - -benzenes[*][*][*].move(4.0, 4.0, 4.0) - -# Note: There is also an example which shows how to generate the coordinates -# using PACKMOL. (That allows us to omit the coordinates and .move() commands.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt deleted file mode 100644 index 527599ba88..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.npt +++ /dev/null @@ -1,58 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# OPLSAA atom charges are stored in a separate file. -# Load that file now: - -include "system.in.charges" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -minimize 1.0e-4 1.0e-6 100000 400000 - -# -- simulation protocol -- - -timestep 1.0 - -print "---------------------------------------------------------------------------" -print "First, use Langevin dynamics to randomize the initial shape of the molecules" -print "(This is not really necessary, but it seems to speed up equilibration.)" -print "---------------------------------------------------------------------------" - -fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K -fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr -run 2000 -unfix fxlan -unfix fxnph - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" -dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 50 barr -fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 -thermo 100 -#thermo_modify flush yes - -run 100000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt deleted file mode 100644 index 09b6a6b146..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene/run.in.nvt +++ /dev/null @@ -1,51 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# OPLSAA atom charges are stored in a separate file. -# Load that file now: - -include "system.in.charges" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 2.0 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 200000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.txt deleted file mode 100644 index 1ba9acc219..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README.txt +++ /dev/null @@ -1,23 +0,0 @@ - -This is an example of how to use the OPLSAA force-field in LAMMPS - -This example also shows how to use moltemplate in combination with PACKMOL. -(PACKMOL is a useful program for generating atomic coordinates. In this example, - moltemplate.sh is only used to create the topology, force-field and charges, - and PACKMOL generates the coordinates, which moltemplate reads (in "step 1"). - Moltemplate can also be used for generating atomic coordinates, especially - for mixing many small molecules together, as we do in this example. However - I wanted to demonstrate how to combine PACKMOL with moltemplate.sh. - In some other scenarios, such as protein solvation, PACKMOL does a much - better job than moltemplate.) - -As of 2016-11-21, this code has not been tested for accuracy. -(See the WARNING.TXT file.) - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh deleted file mode 100755 index c27520076e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh deleted file mode 100755 index c4550c60d2..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_setup.sh +++ /dev/null @@ -1,43 +0,0 @@ - -# Create the coordinates of the atoms using PACKMOL -cd packmol_files - - packmol < mix_ethylene+benzene.inp - mv -f system.xyz ../moltemplate_files/ - -cd .. - - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -xyz system.xyz system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -xyz system.xyz -checkff system.lt - - # This will generate various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg deleted file mode 100644 index 356c784256..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/benzene.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg deleted file mode 100644 index 00c82d3d9f..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene+benzene_box80x80x80_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg deleted file mode 100644 index ab5bbbf49b..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/images/ethylene.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt deleted file mode 100644 index 5f5e8d904a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/benzene.lt +++ /dev/null @@ -1,55 +0,0 @@ -import "oplsaa.lt" - -# The "oplsaa.lt" file contains force-field definitions, -# partial charges and masses for the atoms in your system. - -# Note: -# Atom type @atom:90 corresponds to "Aromatic C" -# Atom type @atom:91 corresponds to "Aromatic H-C" - -Benzene inherits OPLSAA { - - # atom-id mol-id atom-type charge X Y Z # comment - - write("Data Atoms") { - $atom:C1 $mol @atom:90 0.00 -0.739 1.189 -0.00733 # 90 = "Aromatic C" - $atom:C2 $mol @atom:90 0.00 0.614 1.208 0.35167 # 90 = "Aromatic C" - $atom:C3 $mol @atom:90 0.00 1.353 0.019 0.35867 # 90 = "Aromatic C" - $atom:C4 $mol @atom:90 0.00 0.739 -1.189 0.00667 # 90 = "Aromatic C" - $atom:C5 $mol @atom:90 0.00 -0.614 -1.208 -0.35133 # 90 = "Aromatic C" - $atom:C6 $mol @atom:90 0.00 -1.353 -0.019 -0.35833 # 90 = "Aromatic C" - $atom:H11 $mol @atom:91 0.00 -1.309 2.106 -0.01233 # 91 = "Aromatic H-C" - $atom:H21 $mol @atom:91 0.00 1.088 2.14 0.62267 # 91 = "Aromatic H-C" - $atom:H31 $mol @atom:91 0.00 2.397 0.034 0.63467 # 91 = "Aromatic H-C" - $atom:H41 $mol @atom:91 0.00 1.309 -2.106 0.01267 # 91 = "Aromatic H-C" - $atom:H51 $mol @atom:91 0.00 -1.088 -2.14 -0.62233 # 91 = "Aromatic H-C" - $atom:H61 $mol @atom:91 0.00 -2.397 -0.034 -0.63533 # 91 = "Aromatic H-C" - } - # Note: You don't have to specify the charge in this example because - # we are using the OPLSAA force-field assigns this by atom-type. - # Just leave these numbers as 0.00 for now. - # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). - # If we put "$mol" there, moltemplate will generate this integer for you - - # A list of the bonds in the molecule - # BondID AtomID1 AtomID2 - - write("Data Bond List") { - $bond:C12 $atom:C1 $atom:C2 - $bond:C23 $atom:C2 $atom:C3 - $bond:C34 $atom:C3 $atom:C4 - $bond:C45 $atom:C4 $atom:C5 - $bond:C56 $atom:C5 $atom:C6 - $bond:C61 $atom:C6 $atom:C1 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C2H2 $atom:C2 $atom:H21 - $bond:C3H3 $atom:C3 $atom:H31 - $bond:C4H4 $atom:C4 $atom:H41 - $bond:C5H5 $atom:C5 $atom:H51 - $bond:C6H6 $atom:C6 $atom:H61 - } - - # In the "Data Bond List" section we don't have to specify the bond type. - # The bond-type will be determined by the atom type (according to "oplsaa.lt") - -} # Benzene diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt deleted file mode 100644 index 3515702d1d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/ethylene.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "oplsaa.lt" - -# The "oplsaa.lt" file contains force-field definitions, -# partial charges and masses for the atoms in your system. - -# Note: -# Atom type 88 corresponds to "Alkene H2-C=" -# Atom type 89 corresponds to "Alkene H-C=" - - - -Ethylene inherits OPLSAA { - - # atom-id mol-id atom-type charge X Y Z # comment - - write('Data Atoms') { - $atom:C1 $mol @atom:88 0.00 -0.6695 0.00000 0.000 #88 = "Alkene H2-C=" - $atom:C2 $mol @atom:88 0.00 0.6695 0.00000 0.000 #88 = "Alkene H2-C=" - $atom:H11 $mol @atom:89 0.00 -1.23422 -0.85446 0.000 #89 = "Alkene H-C=" - $atom:H12 $mol @atom:89 0.00 -1.23422 0.85446 0.000 #89 = "Alkene H-C=" - $atom:H21 $mol @atom:89 0.00 1.23422 -0.85446 0.000 #89 = "Alkene H-C=" - $atom:H22 $mol @atom:89 0.00 1.23422 0.85446 0.000 #89 = "Alkene H-C=" - } - # Note: You don't have to specify the charge in this example because - # we are using the OPLSAA force-field assigns this by atom-type. - # Just leave these numbers as 0.00 for now. - # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). - # If we put "$mol" there, moltemplate will generate this integer for you - - # A list of the bonds in the molecule - # BondID AtomID1 AtomID2 - - write('Data Bond List') { - $bond:C12 $atom:C1 $atom:C2 - $bond:C1H1 $atom:C1 $atom:H11 - $bond:C1H2 $atom:C1 $atom:H12 - $bond:C2H1 $atom:C2 $atom:H21 - $bond:C2H2 $atom:C2 $atom:H22 - } - - # In the "Data Bond List" section we don't have to specify the bond type. - # The bond-type will be determined by the atom type (according to "oplsaa.lt") - -} # Ethylene - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt deleted file mode 100644 index fae58d65c9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/moltemplate_files/system.lt +++ /dev/null @@ -1,21 +0,0 @@ -import "ethylene.lt" # <- defines the "Ethylene" molecule type. -import "benzene.lt" # <- defines the "Benzene" molecule type. - - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 80.00 xlo xhi - 0.0 80.00 ylo yhi - 0.0 80.00 zlo zhi -} - - -# Create 1000 ethylenes and 500 benzenes -# List them in the same order they appear in the PACKMOL .inp file(s). - -ethylenes = new Ethylene[1000] -benzenes = new Benzene[500] - -# Note: We can omit the .move() and .rot() commands which normally appear -# after the "new" command because we will be using a separate program -# (PACKMOL) to generate the coordinates of these molecules. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.txt deleted file mode 100644 index f0e39ec90a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/README.txt +++ /dev/null @@ -1,5 +0,0 @@ -You can use packmol to create a file containing the atomic coordinates -for a system of ethylene mixed with benzene using this command: - -packmol < mix_ethylene+benzene.inp - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz deleted file mode 100644 index 76af485144..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/benzene.xyz +++ /dev/null @@ -1,14 +0,0 @@ -12 - Benzene -C1 -0.739 1.189 -0.00733 -C2 0.614 1.208 0.35167 -C3 1.353 0.019 0.35867 -C4 0.739 -1.189 0.00667 -C5 -0.614 -1.208 -0.35133 -C6 -1.353 -0.019 -0.35833 -H11 -1.309 2.106 -0.01233 -H21 1.088 2.14 0.62267 -H31 2.397 0.034 0.63467 -H41 1.309 -2.106 0.01267 -H51 -1.088 -2.14 -0.62233 -H61 -2.397 -0.034 -0.63533 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz deleted file mode 100644 index 35326fe81f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/ethylene.xyz +++ /dev/null @@ -1,8 +0,0 @@ -6 - Ethylene -C1 -0.6695 0.000000 0.000000 -C2 0.6695 0.000000 0.000000 -H11 -1.234217 -0.854458 0.000000 -H12 -1.234217 0.854458 0.000000 -H21 1.234217 -0.854458 0.000000 -H22 1.234217 0.854458 0.000000 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp deleted file mode 100644 index 76202ebf30..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/packmol_files/mix_ethylene+benzene.inp +++ /dev/null @@ -1,31 +0,0 @@ -# -# A mixture of ethylene and benzene -# - -# All the atoms from diferent molecules will be separated at least 2.0 -# Anstroms at the solution. - -tolerance 2.0 - -# The file type of input and output files is XYZ - -filetype xyz - -# The name of the output file - -output system.xyz - -# 1000 water molecules and 500 urea molecules will be put in a box -# defined by the minimum coordinates x, y and z = 0. 0. 0. and maximum -# coordinates 80. 80. 80. That is, they will be put in a cube of side -# 80. (the keyword "inside cube 0. 0. 0. 80.") could be used as well. - -structure ethylene.xyz - number 1000 - inside box 0. 0. 0. 80. 80. 80. -end structure - -structure benzene.xyz - number 500 - inside box 0. 0. 0. 80. 80. 80. -end structure diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt deleted file mode 100644 index 1066f810d7..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.npt +++ /dev/null @@ -1,58 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# OPLSAA atom charges are stored in a separate file. -# Load that file now: - -include "system.in.charges" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -minimize 1.0e-4 1.0e-6 100000 400000 - -# -- simulation protocol -- - -timestep 1.0 - -print "---------------------------------------------------------------------------" -print "First, use Langevin dynamics to randomize the initial shape of the molecules" -print "(This is not really necessary, but it seems to speed up equilibration.)" -print "---------------------------------------------------------------------------" - -fix fxlan all langevin 300.0 300.0 120 123456 # temp: 300 K -fix fxnph all nph iso 50.0 50.0 1000.0 # pressure: 50 barr -run 2000 -unfix fxlan -unfix fxnph - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" -dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz -# temperature: 300 K, pressure: 50 barr -fix fxnpt all npt temp 300.0 300.0 100.0 iso 50.0 50.0 1000.0 drag 1.0 -thermo 100 -#thermo_modify flush yes - -run 200000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt deleted file mode 100644 index 2f3b81c186..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/ethylene+benzene_PACKMOL/run.in.nvt +++ /dev/null @@ -1,51 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# OPLSAA atom charges are stored in a separate file. -# Load that file now: - -include "system.in.charges" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 200000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt deleted file mode 100644 index bfd39e8f47..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README.txt +++ /dev/null @@ -1,42 +0,0 @@ -This example is a simple simulation of many long alkane chains (hexadecane) in a -box near the boiling point atmospheric pressure. Please read "WARNING.TXT". - -NOTE: This particular example uses the OPLSAA force-field - However, moltemplate is not limited to OPLSAA. - -1) Create the "system.data", "system.in.init", and "system.in.settings" -files which LAMMPS will read by running: - -moltemplate.sh system.lt - - -2) Run LAMMPS in this order: - -lmp_mpi -i run.in.npt # running the simulation at constant pressure -lmp_mpi -i run.in.nvt # running the simulation at constant temperature - -(The name of the LAMMPS executable, eg "lmp_mpi", may vary.) - ----- Details ---- - -The "Hexadecane" molecule, as well as the "CH2", and "CH3" monomers it contains -use the OPLSAA force-field. This means that when we define these molecules, -we only specify the atom names, bond list, and coordinates. -We do not have to list the atom charges, angles, dihedrals, or impropers. -The rules for creating atomic charge and angle topology are contained in -the "loplsaa.lt" file created by step 3) above. The "ch2group.lt", -"ch3group.lt", and "hexadecane.lt" files all refer to "loplsaa.lt", -(as well as the "OPLSAA" force-field object which it defines). Excerpt: - -import "loplsaa.lt" -CH2 inherits OPLSAA { ... -CH3 inherits OPLSAA { ... -Hexadecane inherits OPLSAA { ... - -Alternatively, you can manually define a list of angles, dihedrals, and -improper interactions in these files, instead of asking the force-field -to generate them for you. You can also specify some of the angles and -dihedrals explicitly, and let the force-field handle the rest. -(Many of the examples which come with moltemplate do this.) - - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_run.sh deleted file mode 100755 index 4871a06495..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # simulation at constant volume - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_setup.sh deleted file mode 100755 index 15a3a963c8..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt deleted file mode 100644 index 215e7fcf91..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/WARNING.txt +++ /dev/null @@ -1,13 +0,0 @@ -# -------- WARNING: -------- - -This software is experimental, and the force-fields and equilbration protocols -have not been tested carefully by me. There is no gaurantee that the simulation -will reproduce the behavior of real hexadecane molecules - -# -------- REQUEST FOR HELP: -------- - -However, if you notice a problem with this example, please report it. -Peer-review is the only way to improve this software (or any software). -Other suggestions are also welcome! - -(Contact jewett.aij@gmail.com, 2014-12-16) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg deleted file mode 100644 index 5a5a188aed..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch2_ry60_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg deleted file mode 100644 index 65e20353ca..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/ch3_ry60_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg deleted file mode 100644 index b0d31f8845..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg deleted file mode 100644 index f7c13d0989..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_12x12x2_t=10ps_npt_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg deleted file mode 100644 index a4151a5fd3..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/images/hexadecane_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt deleted file mode 100644 index c800d56679..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch2group.lt +++ /dev/null @@ -1,82 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. - -# First, load the OPLS force field parameters we will need. -# These 2 files are located in the "force_fields" subdirectory -# distributed with moltemplate. - -import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field -import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from - # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459 - # To use the ordinary OPLSAA force field parameters, - # (instead of the Sui et al. parameters), change the - # atom types below from "@atom:81L","@atom:85LCH2" to - # "@atom:81" and "@atom:85" (defined in "oplsaa.lt") - - - -# Then define "CH2": - - -CH2 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:81L 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:85LCH2 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - - # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt": - # @atom:80L "Alkane CH3- (LOPLS CT_CH3)" - # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)" - # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)" - # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)" - # In this example, atomic charges are generated by atom type (according to the - # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now. - # The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH2 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt deleted file mode 100644 index 95d48d8530..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/ch3group.lt +++ /dev/null @@ -1,84 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. - -# First, load the OPLS force field parameters we will need. -# These 2 files are located in the "force_fields" subdirectory -# of the moltemplate distribution. - -import "oplsaa.lt" # <-- defines the standard "OPLSAA" force field -import "loplsaa.lt" # <-- custom parameters for long alkane chains taken from - # Sui et al. J.Chem.Theory.Comp (2012), 8, 1459 - # To use the ordinary OPLSAA force field parameters, - # (instead of the Sui et al. parameters), change the - # atom types below from "@atom:80L","@atom:85LCH3" to - # "@atom:80" and "@atom:85" (defined in "oplsaa.lt") - - - -# Then define "CH3": - - -CH3 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:80L 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:85LCH3 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:85LCH3 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - - # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt", - # @atom:80L "Alkane CH3- (LOPLS CT_CH3)" - # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)" - # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)" - # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)" - # In this example, atomic charges are generated by atom type (according to the - # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now. - # The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH3 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt deleted file mode 100644 index 96e9e6b4bf..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/hexadecane.lt +++ /dev/null @@ -1,79 +0,0 @@ -# This example looks complicated because I split the -# hexadecane molecule into individual CH2 and CH3 monomers. -# -# I defined it this way so that you can easily modify -# it to change the length of the alkane chain. - - -import "oplsaa.lt" # load the "OPLSAA" force-field information -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - - -Hexadecane inherits OPLSAA { - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - - # Now create an array of 16 "CH2" objects distributed along the X axis - - monomers = new CH2 [16].rot(180,1,0,0).move(1.2533223,0,0) - - # Each monomer is rotated 180 degrees with respect to the previous - # monomer, and then moved 1.2533223 Angstroms down the X axis. - - # ---- Now, modify the ends: --- - # Delete the CH2 groups at the beginning and end, and replace them with CH3. - - delete monomers[0] - delete monomers[15] - - monomers[0] = new CH3 - monomers[15] = new CH3 - - # Move the CH3 groups to the correct location at either end of the chain: - - monomers[15].rot(180.0,0,0,1).move(18.7998345,0,0) - # Note: 18.7998345 = (16-1) * 1.2533223 - - - # Now add a list of bonds connecting the carbon atoms together: - - write('Data Bond List') { - $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C - $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C - $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C - $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C - $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C - $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C - $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C - $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C - $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C - $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C - $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C - $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C - $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C - $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C - $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C - } - -} # Hexadecane - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt deleted file mode 100644 index 4e0cfaec69..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/moltemplate_files/system.lt +++ /dev/null @@ -1,18 +0,0 @@ -import "hexadecane.lt" # <- defines the "Hexadecane" molecule type. - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 62.4 xlo xhi - 0.0 62.4 ylo yhi - 0.0 62.4 zlo zhi -} - -molecules = new Hexadecane [12].move(0, 0, 5.2) - [12].move(0, 5.2, 0) - [2].move(31.2, 0, 0) - - -# NOTE: The spacing between molecules is large. There should be extra room to -# move during the initial stages of equilibration. However, you will have to -# run the simulation at NPT conditions later to compress the system to a -# more realistic density. diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt deleted file mode 100644 index f30c796b47..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.npt +++ /dev/null @@ -1,100 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# To avoid explosions, I have a 4-step equilibraion process (expand, minimize, -# reorient, compress). The system (as defined in the "system.data" file) -# is already expanded. That means there are 3 steps left: - -dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz -thermo 50 - -# -- Equilibration: part 1: initial minimization -- - -# Note: In general, it's always a good idea to minimize the system at first. - -minimize 1.0e-5 1.0e-7 100000 400000 -undump dumpeq1 - -write_data system_after_eq1_min.data - -# -- Equilibration part 2: reorienting the molecules (NVT) -- - -timestep 1.0 -dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz - -# Run the system at high temperature (at constant volume) to reorient the -# the molecules (which would otherwise be pointing in the same direction). - -# To speed it up, I randomize the atomic positions for a few thousand steps -# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover). -# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.) - - -fix fxlan all langevin 900.0 900.0 120 48279 -fix fxnve all nve - -run 4000 - -unfix fxlan -unfix fxnve -# Now continue the simulation at high temperature using fix nvt (Nose-Hoover). -fix fxnvt all nvt temp 900.0 900.0 100.0 - -run 50000 -undump dumpeq2 - - -write_data system_after_eq2_reorient.data - -unfix fxnvt - -# -- equilibration part 3: Equilibrating the density (NPT) -- - -# Originally, the simulation box (in "system.data" and "system.lt") was -# unrealistically large. The spacing between the molecules was large also. -# I did this to enable the molecules to move freely and reorient themselves. -# After doing that, we should run the simulation under NPT conditions to -# allow the simulation box to contract to it's natural size. We do that here: -# To help it collapse, we begin the simulation at a relatively high pressure -# Later on, we will slowly decrease it to 1 bar. - -# First cool the system. (Do this at high pressure to avoid bubble formation.) - -dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 900.0 260.0 100.0 iso 500.0 500.0 1000.0 drag 2.0 - -timestep 1.0 -run 20000 - -# At the very end of the previous simulation, the temperature dropped below -# the boiling point. Run the simulation for longer at these conditions to -# give it a chance for the vapor -> liquid transition to complete. -# We will also slowly decrease the pressure to 1 bar. - -unfix fxnpt -fix fxnpt all npt temp 260.0 260.0 100.0 iso 500.0 1.0 1000.0 drag 2.0 - -timestep 1.0 -run 100000 - -write_data system_after_eq3_npt.data - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt deleted file mode 100644 index 6f74ef0870..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/hexadecane/run.in.nvt +++ /dev/null @@ -1,45 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_eq3_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings -include system.in.charges - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 270.0 270.0 500.0 tchain 1 -thermo_style custom step temp pe etotal epair ebond eangle edihed -thermo 100 -thermo_modify norm yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README.txt deleted file mode 100644 index 9114c637a8..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README.txt +++ /dev/null @@ -1,24 +0,0 @@ -This example demonstrates how to build a simulation containing a box of methane. -(Not a very interesting example.) - ----- Details ---- - -The methane molecules in this example use the OPLSAA force-field. -This means that the database of force-field parameters in "oplsaa.lt" -will be used to generate angles, dihedrals, and impropers. -The "moltemplate_files/methane.lt" file -contains these lines which refer to OPLSAA: - -import "oplsaa.lt" -Methane inherits OPLSAA { ... - --------- Instructions: --------- - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_run.sh deleted file mode 100755 index c27520076e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_setup.sh deleted file mode 100755 index 5cd2142a41..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/moltemplate_files/methane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/moltemplate_files/methane.lt deleted file mode 100644 index bb8f0469cf..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/moltemplate_files/methane.lt +++ /dev/null @@ -1,32 +0,0 @@ -import "oplsaa.lt" - -# Atom type numbers are from the "oplsaa_subset.prm" -# file used to generate "oplsaa.lt". - -# atom 83 13 CT "Methane CH4" -# atom 85 46 HC "Alkane H-C" - -Methane inherits OPLSAA { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:C $mol:. @atom:83 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:. @atom:85 0.0 0.000000 0.000000 1.089000 - $atom:H2 $mol:. @atom:85 0.0 1.026719 0.000000 -0.363000 - $atom:H3 $mol:. @atom:85 0.0 -0.513360 -0.889165 -0.363000 - $atom:H4 $mol:. @atom:85 0.0 -0.513360 0.889165 -0.363000 - } - - # Charges will be assigned by OPLSAA, so we leave them 0.0 here. - # - # (The "." in "$mol:." refers to this molecule-object's molecule-ID number. - # The "." simply means this molecule is not a part of a larger molecule.) - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - $bond:CH4 $atom:C $atom:H4 - } - -} # Methane diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/moltemplate_files/system.lt deleted file mode 100644 index 7c846cd937..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/moltemplate_files/system.lt +++ /dev/null @@ -1,15 +0,0 @@ -import "methane.lt" # <- defines the "Methane" molecule type (uses OPLSAA) - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 103.5 xlo xhi - 0.0 103.5 ylo yhi - 0.0 103.5 zlo zhi -} - -# Now add methane molecules: - -methanes = new Methane [10].move(0, 0, 10.35) - [10].move(0, 10.35, 0) - [10].move(10.35, 0, 0) - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/run.in.npt deleted file mode 100644 index 208d4b681f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/run.in.npt +++ /dev/null @@ -1,51 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# (The "fShakeSPCE" fix was defined in system.in.settings. -# It is incompatible with "minimize", so we disable it first.) -#unfix fShakeSPCE -thermo 500 -minimize 1.0e-4 1.0e-6 100000 400000 - -# Now read "system.in.settings" in order to enable fShakeSPCE again: -#include system.in.settings - -# Optional: write the coordinates after minimization -write_data system_after_min.data - - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 2500 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 - -run 500000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/run.in.nvt deleted file mode 100644 index a4f382118f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/methane/run.in.nvt +++ /dev/null @@ -1,42 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# (The "write_restart" and "reagd_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 50000 - -write_restart system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README.txt deleted file mode 100644 index 9c318e6654..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README.txt +++ /dev/null @@ -1,30 +0,0 @@ -This example contains a mixture of water(SPCE) and methane. -The methane molecules use OPLSAA force-field, but the water molecules do not. - ----- Details ---- - -The methane molecules in this example use the OPLSAA force-field. -This means that the database of force-field parameters in "oplsaa.lt" -will be used to generate angles, dihedrals, and impropers. -The "moltemplate_files/methane.lt" file -contains these lines which refer to OPLSAA: - -import "oplsaa.lt" -Methane inherits OPLSAA { ... - -However the "SPCE" (water) molecules does NOT use a database to look up the -force-field parameters for this tiny molecule. -Instead, the "moltemplate_files/spce.lt" file declares all of the angle -interactions, atom properties and force-field parameters for water explicitly. -(Consequently, it makes no mention of "oplsaa.lt" or "OPLSAA".) - --------- Instructions: --------- - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_run.sh deleted file mode 100755 index c27520076e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_setup.sh deleted file mode 100755 index 4fc8dda6d5..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_setup.sh +++ /dev/null @@ -1,29 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt deleted file mode 100644 index bb8f0469cf..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/methane.lt +++ /dev/null @@ -1,32 +0,0 @@ -import "oplsaa.lt" - -# Atom type numbers are from the "oplsaa_subset.prm" -# file used to generate "oplsaa.lt". - -# atom 83 13 CT "Methane CH4" -# atom 85 46 HC "Alkane H-C" - -Methane inherits OPLSAA { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:C $mol:. @atom:83 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:. @atom:85 0.0 0.000000 0.000000 1.089000 - $atom:H2 $mol:. @atom:85 0.0 1.026719 0.000000 -0.363000 - $atom:H3 $mol:. @atom:85 0.0 -0.513360 -0.889165 -0.363000 - $atom:H4 $mol:. @atom:85 0.0 -0.513360 0.889165 -0.363000 - } - - # Charges will be assigned by OPLSAA, so we leave them 0.0 here. - # - # (The "." in "$mol:." refers to this molecule-object's molecule-ID number. - # The "." simply means this molecule is not a part of a larger molecule.) - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - $bond:CH4 $atom:C $atom:H4 - } - -} # Methane diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt deleted file mode 100644 index fdf6172a4b..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 600.0 1.0 - angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 0.0 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) - } - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/cut/coul/long 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt deleted file mode 100644 index 3957d08eb7..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/moltemplate_files/system.lt +++ /dev/null @@ -1,26 +0,0 @@ -import "spce.lt" # <- defines the "SPCE" (water) molecule type. -import "methane.lt" # <- defines the "Methane" molecule type (uses OPLSAA) - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 41.50 xlo xhi - 0.0 41.50 ylo yhi - 0.0 41.50 zlo zhi -} - -# The next command generates a (rather dense) cubic lattice with -# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) - -waters = new SPCE [12].move(0.00, 0.00, 3.45) - [12].move(0.00, 3.45, 0.00) - [12].move(3.45, 0.00, 0.00) - -# Now add methane molecules: - -methanes = new Methane [4].move(0, 0, 10.35) - [4].move(0, 10.35, 0) - [4].move(10.35, 0, 0) - -# Move the methane molecules slightly to reduce overlap with the water -methanes[*][*][*].move(1.725, 1.725, 1.725) - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.npt deleted file mode 100644 index df9c1f95f2..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.npt +++ /dev/null @@ -1,52 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# (The "fShakeSPCE" fix was defined in system.in.settings. -# It is incompatible with "minimize", so we disable it first.) -unfix fShakeSPCE -thermo 50 -minimize 1.0e-4 1.0e-6 100000 400000 - -# Now read "system.in.settings" in order to enable fShakeSPCE again: -include system.in.settings - -# Optional: write the coordinates after minimization -write_data system_after_min.data - - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -thermo 100 - -run 2000000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.nvt deleted file mode 100644 index 9652779bb0..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPCE+methane/run.in.nvt +++ /dev/null @@ -1,42 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README.txt deleted file mode 100644 index 8c00fe07fb..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README.txt +++ /dev/null @@ -1,18 +0,0 @@ -The purpose of this example is to test the density of water -constructed using the OPLSAA force-field. (I think this is SPC water, not SPCE) - -I just wanted some kind of sanity check to make sure we are converting -the OPLSAA parameters into moltemplate/LAMMPS format correctly. - -The "TEST_density_estimate.txt" contains the results of that test. - --------- Instructions: --------- - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_remove_irrelevant_info.sh deleted file mode 100755 index 049a1eac48..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,9 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh deleted file mode 100755 index 1c46d9d416..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_run.sh +++ /dev/null @@ -1,20 +0,0 @@ -# --- Running LAMMPS --- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # simulation at constant volume - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh deleted file mode 100755 index ed4ac6f041..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_setup.sh +++ /dev/null @@ -1,34 +0,0 @@ - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # Optional: - # To check for missing angle,dihedral params run moltemplate this way instead: - # moltemplate.sh -checkff system.lt - - - # This will generate various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt deleted file mode 100644 index 9dc50b389e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/TEST_density_estimate.txt +++ /dev/null @@ -1,20 +0,0 @@ -This system contains 1728 water molecules -(This is SPC water I think.) - -Then I ran a short simulation for 170000 timesteps at 300Kelvin and 1 atm. -(that's when it crashed. I'll worry about why later...) - -Anyway, the average volume was 52149.8 (in Angstroms^3) -(for the last 80000 timesteps, after it had equilibrated) - -Given that the mass of water is 18.0154 grams per mole, I'm getting -this value for the density: - -density = (1728*18.0154/6.02214129e23) / (52149.8*1e-30*1e6) - = 0.991 (in grams per mL) - -I'm only looking for gross errors in the OPLSAA force-field. -So I'm satisfied with a 1% error. -But I realize this is not a particularly rigorous test. - -Andrew 2014-5-21 diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt deleted file mode 100644 index e7f3d6d843..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/spc.lt +++ /dev/null @@ -1,86 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - - -import "oplsaa.lt" - -SPC inherits OPLSAA { - - # Atom types from "oplsaa_lt_generator/oplsaa_subset.prm" - # @atom:76 <--> OW "SPC Water O" - # @atom:77 <--> HW "SPC Water H" - - write("Data Atoms") { - $atom:O $mol:. @atom:76 -0.8200 0.0000000 0.0000 0.000000 - $atom:H1 $mol:. @atom:77 0.4100 0.8164904 0.0000 0.577359 - $atom:H2 $mol:. @atom:77 0.4100 -0.8164904 0.0000 0.577359 - } - - write("Data Bond List") { - $bond:OH1 $atom:O $atom:H1 - $bond:OH2 $atom:O $atom:H2 - } - -} # end of definition of "SPC" water molecule type - - - - - - - - - - - -###################### old version (SPCE) ###################### -# -#SPCE { -# -# write("Data Atoms") { -# $atom:O $mol:. @atom:O -0.8476 0.0000000 0.0000 0.000000 -# $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.0000 0.577359 -# $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.0000 0.577359 -# } -# -# write_once("Data Masses") { -# @atom:O 15.9994 -# @atom:H 1.008 -# } -# -# write("Data Bonds") { -# $bond:OH1 @bond:OH $atom:O $atom:H1 -# $bond:OH2 @bond:OH $atom:O $atom:H2 -# } -# -# write("Data Angles") { -# $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 -# } -# -# write_once("In Settings") { -# bond_coeff @bond:OH harmonic 1000.0 1.0 -# angle_coeff @angle:HOH harmonic 1000.0 109.47 -# pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 -# pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 2.058 -# group spce type @atom:O @atom:H -# fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH -# # (Remember to "unfix" fShakeSPCE during minimization.) -# } -# -# write_once("In Init") { -# # -- Default styles (for solo "SPCE" water) -- -# units real -# atom_style full -# # (Hybrid force fields were not necessary but are used for portability.) -# pair_style hybrid lj/cut/coul/long 10.0 -# bond_style hybrid harmonic -# angle_style hybrid harmonic -# kspace_style pppm 0.0001 -# pair_modify shift yes -# } -# -#} SPCE -################################################################### diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt deleted file mode 100644 index 5dd56c116f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/moltemplate_files/system.lt +++ /dev/null @@ -1,16 +0,0 @@ -import "spc.lt" # <- defines the "SPC" (water) molecule type (uses OPLSAA) - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 41.40 xlo xhi - 0.0 41.40 ylo yhi - 0.0 41.40 zlo zhi -} - -# The next command generates a (rather dense) cubic lattice with -# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) - -waters = new SPC [12].move(0.00, 0.00, 3.45) - [12].move(0.00, 3.45, 0.00) - [12].move(3.45, 0.00, 0.00) - diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt deleted file mode 100644 index 642880af2d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.npt +++ /dev/null @@ -1,52 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# (The "fShakeSPCE" fix was defined in system.in.settings. -# It is incompatible with "minimize", so we disable it first.) -#unfix fShakeSPCE -thermo 50 -minimize 1.0e-4 1.0e-6 100000 400000 - -# Now read "system.in.settings" in order to enable fShakeSPCE again: -#include system.in.settings - -# Optional: write the coordinates after minimization -write_data system_after_min.data - - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 2500 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -thermo 100 - -run 2000000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt deleted file mode 100644 index 9652779bb0..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSAA/waterSPC_using_OPLSAA/run.in.nvt +++ /dev/null @@ -1,42 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data "system_after_npt.data" - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README.txt deleted file mode 100644 index f3ccf3b084..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README.txt +++ /dev/null @@ -1,21 +0,0 @@ -This example was contributed by Yue Chun Chiu (Chinese University of Hong Kong) -(Thanks!) - -This is a simulation of propane using the OPLSUA force-field. -(It uses the OPLSUA force field even though the file names begin with "oplsaa") - -IMPORTANT: This is NOT an all-atom simulation. - OPLSUA is a united-atom force-field. - Hydrogen atoms are not represented explicitly. - The force-field has been adjusted accordingly. - --------- Instructions: --------- - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_run.sh deleted file mode 100755 index c27520076e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_run.sh +++ /dev/null @@ -1,34 +0,0 @@ -# --- Running LAMMPS --- -# -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation might be ignored when beginning the simulation at constant -# volume. (This is because restart files in LAMMPS don't always work, -# and I was spending a lot of time trying to convince people it was a -# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.) -# Read the "run.in.nvt" file to find out how to use the "read_restart" -# command to load the results of the pressure-equilibration simulation, -# before beginning a constant-volume run. - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_setup.sh deleted file mode 100755 index 38a79dbf19..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_setup.sh +++ /dev/null @@ -1,47 +0,0 @@ -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - ######################### WEIRD LAMMPS QUIRK:############################### - # The default pair_style used with the OPLSAA forcefield requires that SOME - # atoms have non-zero charge. Unfortunately, in this example none of them do. - # (This does not happen very often.) - # Since you don't need long-range coulombics in this example, LAMMPS will - # print out an error message and tell you to use a more efficient pair_style. - # To get around this AFTER RUNNING MOLTEMPLATE, run these commands in the - # shell: - - echo "pair_style hybrid lj/cut 10.0" >> system.in.init - sed 's/lj\/cut\/coul\/long/lj\/cut/g' system.in.settings > system.in.settings_ - sed 's/kspace_style/#kspace_style/g' system.in.init > system.in.init_ - mv system.in.settings_ system.in.settings - mv system.in.init_ system.in.init - - # This will override the pair_style and pair_coeff commands in the - # system.in.init and system.in.settings files (created by moltemplate): - - # Moltemplate generates various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - - - - -# Optional: -# Note: The system.data and system.in.settings files contain extra information -# for atoms defined in OPLSAA which you are not using in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: -# -# cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt deleted file mode 100644 index d147a6d4c4..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/moltemplate_files/propane.lt +++ /dev/null @@ -1,31 +0,0 @@ -import "oplsaa.lt" - - -Propane inherits OPLSAA { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:CH3a $mol:. @atom:10 0.0 -0.748 -0.015 0.024 - $atom:CH2 $mol:. @atom:13 0.0 0.558 0.420 -0.278 - $atom:CH3b $mol:. @atom:10 0.0 0.716 1.404 0.137 - } - - write('Data Bond List') { - $bond:CC1 $atom:CH3a $atom:CH2 - $bond:CC2 $atom:CH2 $atom:CH3b - } - - # These atom types are defined in the "oplsaa.lt" file (usually located - # in the "force_fields" subdirectory of the moltemplate distribution). - # @atom:10 "N-Alkane CH3- (UA)" - # @atom:13 "Alkanes -CH2- (UA)" - # - # NOTE: UA means united atom (no explicit hydrogens). - # The first 56 atoms in the "oplsaa.lt" file are united atoms - # - # NOTE: Charges will be assigned by OPLSAA, so we leave them 0.0 here. - # - # (The "." in "$mol:." refers to this molecule-object's molecule-ID number. - # The "." simply means this molecule is not a part of a larger molecule.) - -} diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt deleted file mode 100644 index 6f266aac3d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/moltemplate_files/system.lt +++ /dev/null @@ -1,37 +0,0 @@ -import "propane.lt" - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 36.0 xlo xhi - 0.0 36.0 ylo yhi - 0.0 36.0 zlo zhi -} - -# Now add methane molecules: - -propanes = new Propane [6].move(0, 0, 6) - [6].move(0, 6, 0) - [6].move(6, 0, 0) - -propanes[*][*][*].move(2.0, 2.0, 2.0) - - - - - - - -######################### WEIRD LAMMPS QUIRK:############################### -# The default pair_style used with the OPLSAA forcefield requires that SOME -# atoms have non-zero charge. Unfortunately, in this example none of them do. -# (This does not happen very often.) -# Since you don't need long-range coulombics in this example, LAMMPS will -# terminate with an error message and ask you to use a more efficient pair_style -# To get around this AFTER RUNNING MOLTEMPLATE, run these commands in the shell -# -# echo "pair_style hybrid lj/cut 10.0" >> system.in.init -# sed -i 's/lj\/cut\/coul\/long/lj\/cut/g' system.in.settings -# sed -i 's/kspace_style/#kspace_style/g' system.in.init -# -# This will override the pair_style and pair_coeff commands in the -# system.in.init and system.in.settings files (created by moltemplate): diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/run.in.npt deleted file mode 100644 index c1115f67bb..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/run.in.npt +++ /dev/null @@ -1,43 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -thermo 500 -thermo_style custom step temp etotal press vol -minimize 6.0e-5 1.0e-6 500 400000 - -write_data system_after_min.data - -# -- simulation protocol -- - -reset_timestep 0 -timestep 1.0 -dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz element -velocity all create 200.0 4928459 rot yes mom yes dist gaussian -fix fxnpt all npt temp 200.0 200.0 100.0 iso 1.0 1.0 1000.0 -neigh_modify delay 5 every 1 check yes - -run 100000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/run.in.nvt deleted file mode 100644 index 115bfe527f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_OPLSUA_united_atom/propane/run.in.nvt +++ /dev/null @@ -1,39 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, -# or run the file as a script using ./README_setup.sh) -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -#read_data "system.data" -read_data "system_after_npt.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - - -# -- simulation protocol -- - -reset_timestep 0 -timestep 2.0 -thermo 500 -thermo_style custom step temp etotal press -dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz element type -dump_modify 1 element "C" "C" -velocity all create 200.0 4928459 rot yes mom yes dist gaussian -fix fxnvt all nvt temp 200.0 200.0 100.0 -neigh_modify delay 5 every 1 check yes - -run 1000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README.txt deleted file mode 100644 index 1303acbcac..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README.txt +++ /dev/null @@ -1,54 +0,0 @@ -NOTE: This example requires the "Al99.eam.alloy" file. - (It was not included in this directory because if its large size.) - As of 2012-11, I was able to obtain it here: - http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - Copy it to the directory containing this README file. ------------------------------------------------------------------------- -This example shows an alternative way to setup the -aluminum crystal loading simulation described here: -http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression -by Mark Tschopp and Nathan R. Rhodes -For additional backgroumd information, please consult that web page. - -In this example, I use moltemplate to build a "DATA" file for this system. -(I can't think of a compelling reason to do this for simple simulations like -this. But this approach might be useful if you want to artificially create -unusual structures out of aluminum crystals, or mix them with other molecules. -I created this example in response to a user request.) - - - --- To build the system --- - -Carry out the instructions in README_setup.sh, -to generate the LAMMPS DATA file and input scripts you need: -system.data, system.in.init, system.in.settings. -(The run.in script contains references to these files.) - - - --- To run LAMMPS, try a command like: --- - -lmp_mpi -i run.in - - or (if you have mpi installed) - -mpirun -np 4 lmp_mpi -i run.in - -This will create an ordinary LAMMPS dump file you can visualize with VMD -traj.lammpstrj (See README_visualize.txt) - -It will also create a number of other files, such as: -dump.comp_0.cfg -dump.comp_500.cfg -dump.comp_20000.cfg -Al_comp_100.def1.txt - -The dump.comp_*.cfg files can be visualized using -AtomEye if you have AtomEye and ImageJ installed. -The procedure for doing this is explained in the original tutorial at: -http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression - -The "Al_comp_100.def1.txt" file is a four-column text file containing: -column 1: v_strain = (lx - v_L0)/v_L0 -column 2: -pxx/10000 (diagonal components of the stress tensor) -column 3: -pyy/10000 -column 4: -pzz/10000 diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README_setup.sh deleted file mode 100755 index 74e00f2510..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README_setup.sh +++ /dev/null @@ -1,29 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # We will also need the "Al99.eam.alloy" file: - #cp -f Al99.eam.alloy ../ - # This file was (can be) downloaded from: - # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCell_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCell_LR.jpg deleted file mode 100644 index bf07914dac..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCell_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg deleted file mode 100644 index 8650cf5cb0..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg deleted file mode 100644 index 582cf5fe6d..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/README.sh deleted file mode 100755 index 393ceb8d86..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/README.sh +++ /dev/null @@ -1,22 +0,0 @@ -# This example shows an alternative way to setup the -# aluminum crystal loading simulation described here: -# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression -# by Mark Tschopp and Nathan R. Rhodes -# For additional backgroumd information, please consult that web page. -# -# In this example, I use moltemplate to build a "DATA" file for this system. -# (I can't think of a compelling reason to do this for simple simulations like -# this. But this approach might be useful if you want to artificially create -# unusual structures out of aluminum crystals, or mix them with other molecules. -# I created this example in response to a user request.) -# -# Use these commands to generate the LAMMPS input script and data file: - -moltemplate.sh system.lt - -# This will generate system.data, system.in.init, system.in.settings. -# In addition to will need to download "Al99.eam.alloy" file. -# (It was not included in this directory because if its large size.) -# As of 2012-11, I was able to obtain it here: -# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/al_cell.lt deleted file mode 100644 index 3054a45e01..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/al_cell.lt +++ /dev/null @@ -1,64 +0,0 @@ -# "AlCell" defines the 4-atom FCC unit cell -# of Aluminum (with a 4.05 angstrom spacing) - -AlCell { - - # AtomID MolID(IGNORE!) AtomType Charge X Y Z - - write("Data Atoms") { - $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 - $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 - $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 - $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 - } - - write_once("In Init") { - units metal - atom_style full # <- Requires each atom has a MolID and Charge. - # This is not necessary. (Why use "full"? - # The "full" atom style is useful if you want to - # mix the aluminum with other molecules later. - # Otherwise, just use "atom_style atomic", and - # and remove the 2nd and 4th columns above.) - pair_style eam/alloy - } - - write_once("In Settings") { - pair_coeff * * Al99.eam.alloy Al - } - - write_once("Data Masses") { - @atom:Al 27.0 - } - -} # AlCell - - - - - -# Here is an alternate way to define AlCell -# using "scale(4.05)" to select the lattice spacing: -# -#FccCell { -# write("Data Atoms") { -# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 -# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 -# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 -# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 -# } -# write_once("Data Masses") { -# @atom:Al 27.0 -# } -# write_once("In Init") { -# units metal -# atom_style full -# pair_style eam/alloy -# } -# write_once("In Settings") { -# pair_coeff * * Al99.eam.alloy Al -# } -#} -# -#AlCell = FccCell.scale(4.05) -# diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/system.lt deleted file mode 100644 index f813c6f662..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/moltemplate_files/system.lt +++ /dev/null @@ -1,35 +0,0 @@ - -import "al_cell.lt" # <- this defines the unit cell for aluminum - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 40.50 xlo xhi - 0.0 40.50 ylo yhi - 0.0 40.50 zlo zhi -} - -# The next command generates an array of 10x10x10 AlCell unit cells with -# spacing 4.05 Angstroms. - -unitcells = new AlCell [10].move(0.00, 0.00, 4.05) - [10].move(0.00, 4.05, 0.00) - [10].move(4.05, 0.00, 0.00) - - - - - - - - - - - - -################################################################ -# The next command is not necessary: -# - create_var { $mol } # <-This forces all of the Al atoms in the crystal -# # to share the same molecule ID number. -# # Molecule ID numbers are not necessary. Ignore this. -# diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/run.in b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/run.in deleted file mode 100644 index 677cc60cab..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/aluminum_crystal_strain/run.in +++ /dev/null @@ -1,76 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- -# -# The run-settings below were stolen from: -# -# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression - - -compute csym all centro/atom fcc -compute peratom all pe/atom - -# EQUILIBRATION -reset_timestep 0 -timestep 0.001 -velocity all create 300 12345 mom yes rot no -fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 - -# Set thermo output -thermo 1000 -thermo_style custom step lx ly lz press pxx pyy pzz pe temp - -# Run for at least 10 picosecond (assuming 1 fs timestep) -run 20000 -unfix 1 - -# Store final cell length for strain calculations -variable tmp equal "lx" -variable L0 equal ${tmp} -print "Initial Length, L0: ${L0}" - -###################################### -# DEFORMATION -reset_timestep 0 - -fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1 -variable srate equal 1.0e10 -variable srate1 equal "-v_srate / 1.0e12" -fix 2 all deform 1 x erate ${srate1} units box remap x - -# Output strain and stress info to file -# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] -# p2, p3, p4 are in GPa -variable strain equal "(lx - v_L0)/v_L0" -variable p1 equal "v_strain" -variable p2 equal "-pxx/10000" -variable p3 equal "-pyy/10000" -variable p4 equal "-pzz/10000" -fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Al_comp_100.def1.txt screen no - -# Use cfg for AtomEye -dump dAtomEye all cfg 250 dump.comp_*.cfg id type xs ys zs c_csym c_peratom fx fy fz -dump_modify dAtomEye element Al - -# For users without AtomEye (like me), I decided to create a regular dump file: -dump dCoords all custom 250 traj.lammpstrj id type x y z ix iy iz - -# Display thermo -thermo 1000 -thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press - -run 20000 - -###################################### -# SIMULATION DONE -print "All done" diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_run.sh deleted file mode 100755 index c041ccb9f9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure - -# to be followed by - -lmp_mpi -i run.in.nvt # simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -# or -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_setup.sh deleted file mode 100755 index 68cad16a79..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_visualize.txt deleted file mode 100644 index 88d0e22c41..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 500 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg deleted file mode 100644 index 2cdc08b312..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/images/ice_rect8_unitcell.png b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/images/ice_rect8_unitcell.png deleted file mode 100644 index 5bd6057e1e..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/images/ice_rect8_unitcell.png and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt deleted file mode 100644 index 1f0f0f61b5..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 600.0 1.0 - angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) - } - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect16.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect16.lt deleted file mode 100644 index e67b228e9e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect16.lt +++ /dev/null @@ -1,81 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 16 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 9.043 7.832 7.361 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect16 { - - # Create a 3-dimensional array of 16 water molecules - - wat = new SPCE[4][2][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 3.545 1.970 - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.371 1.711 - $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300 - $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970 - $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 2.611 3.291 - $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381 - $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711 - $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 1.305 0.390 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 5.221 0.390 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291 - $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381 - $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711 - $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 4.287 1.711 - $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300 - $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970 - $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 2.611 4.070 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.972 - $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061 - $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391 - $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 3.545 5.391 - $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981 - $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651 - $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 0.371 5.651 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 4.287 5.651 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391 - $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981 - $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651 - $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 5.221 6.972 - $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061 - $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391 - $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070 - } -} # SpceIceRect16 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect32.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect32.lt deleted file mode 100644 index 0a52d82981..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect32.lt +++ /dev/null @@ -1,129 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 32 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 9.043 15.663 7.361 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect32 { - - # Create a 3-dimensional array of 32 water molecules - - wat = new SPCE[4][4][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.291 - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 1.305 0.390 - $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300 - $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970 - $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 3.545 1.970 - $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381 - $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711 - $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 0.371 1.711 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.287 1.711 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291 - $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381 - $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711 - $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 5.221 0.390 - $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300 - $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970 - $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970 - $atom:wat[0][2][0]/O $mol:wat[0][2][0] @atom:SPCE/O -0.8476 1.131 10.443 2.300 - $atom:wat[0][2][0]/H1 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 0.322 9.976 1.970 - $atom:wat[0][2][0]/H2 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 1.131 11.377 1.970 - $atom:wat[1][2][0]/O $mol:wat[1][2][0] @atom:SPCE/O -0.8476 3.391 9.137 1.381 - $atom:wat[1][2][0]/H1 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 2.582 9.604 1.711 - $atom:wat[1][2][0]/H2 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 3.391 8.203 1.711 - $atom:wat[2][2][0]/O $mol:wat[2][2][0] @atom:SPCE/O -0.8476 5.652 10.443 2.300 - $atom:wat[2][2][0]/H1 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 4.843 9.976 1.970 - $atom:wat[2][2][0]/H2 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 5.652 10.443 3.291 - $atom:wat[3][2][0]/O $mol:wat[3][2][0] @atom:SPCE/O -0.8476 7.912 9.137 1.381 - $atom:wat[3][2][0]/H1 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.103 9.604 1.711 - $atom:wat[3][2][0]/H2 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.912 9.137 0.390 - $atom:wat[0][3][0]/O $mol:wat[0][3][0] @atom:SPCE/O -0.8476 1.131 13.053 1.381 - $atom:wat[0][3][0]/H1 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.940 13.520 1.711 - $atom:wat[0][3][0]/H2 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.131 13.053 0.390 - $atom:wat[1][3][0]/O $mol:wat[1][3][0] @atom:SPCE/O -0.8476 3.391 14.358 2.300 - $atom:wat[1][3][0]/H1 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 4.200 13.891 1.970 - $atom:wat[1][3][0]/H2 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 3.391 15.292 1.970 - $atom:wat[2][3][0]/O $mol:wat[2][3][0] @atom:SPCE/O -0.8476 5.652 13.053 1.381 - $atom:wat[2][3][0]/H1 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 6.461 13.520 1.711 - $atom:wat[2][3][0]/H2 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 5.652 12.119 1.711 - $atom:wat[3][3][0]/O $mol:wat[3][3][0] @atom:SPCE/O -0.8476 7.912 14.358 2.300 - $atom:wat[3][3][0]/H1 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 8.721 13.891 1.970 - $atom:wat[3][3][0]/H2 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 7.912 14.358 3.291 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.545 5.391 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 0.371 5.651 - $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061 - $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391 - $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 2.611 4.070 - $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981 - $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651 - $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 1.305 6.972 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.972 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391 - $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981 - $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651 - $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 4.287 5.651 - $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061 - $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391 - $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070 - $atom:wat[0][2][1]/O $mol:wat[0][2][1] @atom:SPCE/O -0.8476 1.131 10.443 5.061 - $atom:wat[0][2][1]/H1 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.940 9.976 5.391 - $atom:wat[0][2][1]/H2 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.131 10.443 4.070 - $atom:wat[1][2][1]/O $mol:wat[1][2][1] @atom:SPCE/O -0.8476 3.391 9.137 5.981 - $atom:wat[1][2][1]/H1 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 4.200 9.604 5.651 - $atom:wat[1][2][1]/H2 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 3.391 9.137 6.972 - $atom:wat[2][2][1]/O $mol:wat[2][2][1] @atom:SPCE/O -0.8476 5.652 10.443 5.061 - $atom:wat[2][2][1]/H1 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 6.461 9.976 5.391 - $atom:wat[2][2][1]/H2 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 5.652 11.377 5.391 - $atom:wat[3][2][1]/O $mol:wat[3][2][1] @atom:SPCE/O -0.8476 7.912 9.137 5.981 - $atom:wat[3][2][1]/H1 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 8.721 9.604 5.651 - $atom:wat[3][2][1]/H2 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 7.912 8.203 5.651 - $atom:wat[0][3][1]/O $mol:wat[0][3][1] @atom:SPCE/O -0.8476 1.131 13.053 5.981 - $atom:wat[0][3][1]/H1 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 0.322 13.520 5.651 - $atom:wat[0][3][1]/H2 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 1.131 12.119 5.651 - $atom:wat[1][3][1]/O $mol:wat[1][3][1] @atom:SPCE/O -0.8476 3.391 14.358 5.061 - $atom:wat[1][3][1]/H1 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 2.582 13.891 5.391 - $atom:wat[1][3][1]/H2 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 3.391 14.358 4.070 - $atom:wat[2][3][1]/O $mol:wat[2][3][1] @atom:SPCE/O -0.8476 5.652 13.053 5.981 - $atom:wat[2][3][1]/H1 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 4.843 13.520 5.651 - $atom:wat[2][3][1]/H2 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 5.652 13.053 6.972 - $atom:wat[3][3][1]/O $mol:wat[3][3][1] @atom:SPCE/O -0.8476 7.912 14.358 5.061 - $atom:wat[3][3][1]/H1 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.103 13.891 5.391 - $atom:wat[3][3][1]/H2 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.912 15.292 5.391 - } -} # SpceIceRect32 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect8.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect8.lt deleted file mode 100644 index f887c6efd1..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/spce_ice_rect8.lt +++ /dev/null @@ -1,57 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 8 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect8 { - - # Create a 3-dimensional array of 8 water molecules - - wat = new SPCE[2][2][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 - } -} # SpceIceRect8 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/system.lt deleted file mode 100644 index b4f22f9dcf..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/moltemplate_files/system.lt +++ /dev/null @@ -1,11 +0,0 @@ -import "spce_ice_rect8.lt" - -cells = new SpceIceRect8 [3].move(4.521, 0.0, 0.0) - [2].move( 0.0, 7.832, 0.0) - [2].move( 0.0, 0.0, 7.362) - -write_once("Data Boundary") { - 0 13.563 xlo xhi - 0 15.664 ylo yhi - 0 14.724 zlo zhi -} diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt deleted file mode 100644 index efa4fca484..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.npt +++ /dev/null @@ -1,48 +0,0 @@ -# You can run LAMMPS this way -# lmp_linux -i run.in.npt -# (Assuming your LAMMPS binary is named "lmp_linux") -# -# PREREQUISITES: -# You will need these files (created by moltemplate.sh): -# system.data, system.in.init, system.in.settings -# (See README_setup.sh for details) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fShakeSPCE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 2.0 -dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 400.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 - -thermo 100 - -#restart 10000 restart_npt - -run 20000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.nvt deleted file mode 100644 index 1815e1da70..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/ice_crystal/run.in.nvt +++ /dev/null @@ -1,45 +0,0 @@ -# You can run LAMMPS this way -# lmp_linux -i run.in.nvt -# (Assuming your LAMMPS binary is named "lmp_linux") -# -# PREREQUISITES: -# You will need these files (created by moltemplate.sh): -# system.in.init, system.in.settings (See README_setup.sh) -# You will also need this file: system_after_npt.data -# This file is created by running LAMMPS on the run.in.npt file. -# -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates after pressure equilibration -read_data system_after_npt.data - -# (Or, if you prefer, you can read the original coordinates using -# read_data system.data) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -timestep 2.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - - -thermo 500 - - -#restart 10000 restart_nvt - - -run 50000 - -write_data system_after_nvt.data - - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README.txt deleted file mode 100644 index 3c58fd009e..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README.txt +++ /dev/null @@ -1,51 +0,0 @@ -This is a small version of a carbon-nanotube, water capillary system. -It was inspired by this paper: - - Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) - --------- Requirements: ------- -To run this system at constant pressure, it might help to compile LAMMPS -with the optional RIGID package, and use "fix rigid" on the carbon. -(The use of fix rigid is controversial.) Running at NVT does not require this. ------------------------------- - -Note: To investigate the behavior from that paper, it might be a good - idea to increase the size of the water reservoir, the spacing between - the walls, and the size of the system in the X and Y directions. - -Note: Explicit carbon-carbon bonds: - In the graphene and nanotube structures, I did not try to connect the - carbon atoms together with bonds. Instead we will hold these structures - rigid by not integrating their equations of motion. - (If you want to simulate movement of the carbon atoms at high - temperatures or tension, LAMMPS has 3-body/many-body LAMMPS force-fields - available for simulating the behaviour of carbon in graphite. I know - that you don't need to specify bonds to use these force fields. I do - not know know if these force fields work for nanotubes or graphene.) - -Note: Other modeling tools: - If you need explicit bonds between carbon atoms, then you must add them - yourself or use a different tool. Currently (2012-10-20), moltemplate does - not generate bonds automatically. The "Nanotube Builder" and "topotools" - plugins for for VMD can generate a nanotube with bonds in LAMMPS data - format. You can then convert this data file to .LT format using the - ltemplify.py utility and then import it into another .LT file and play - with it later. (In the "cnad-cnt" example, the carbon nanotube was built - using "Nanotube Builder" and topotools, and processed with ltemplify.py) - - -# WARNING: THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. -# A real junction would be curved and deformed near the boundary, -# (not 90 degrees) and it would not be built entirely from hexagons. -# (This is not a problem in this example because the carbon atoms -# are immobilized.) If you want to simulate the behavior of -# real graphene or nanotube junctions, you must be more careful. -# To solve this problem: -# Moltemplate allows you to move, customize or delete individual -# atoms near the boundary. You can move atoms by overwriting their -# coordinates using additional write("Data Atoms") statements (after -# the walls and tube are created). You can also change their charge. -# Alternately, you could start with the structure provided here, and -# relax/minimize the coordinates of the carbon atoms using LAMMPS -# before using it in other simulations. -# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_run.sh deleted file mode 100755 index 98054c5551..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_run.sh +++ /dev/null @@ -1,24 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure - # (WARNING: The "run.in.npt" example has not been - # rigorously tested and may fail.) - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_visualize.txt deleted file mode 100644 index 04ff1f2e75..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/README_visualize.txt +++ /dev/null @@ -1,77 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - To shift the box by a fraction in the x direction (for example) - do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } - pbc box -shiftcenterrel {-0.50 -0.52 0.0 } - - # Alternately if you have a solute whose atoms are all of type 1, - # then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/graphene_unit_cell.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/graphene_unit_cell.jpg deleted file mode 100644 index 12dbf8fca2..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/graphene_unit_cell.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg deleted file mode 100644 index 15d3f189d3..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg deleted file mode 100644 index 298957864f..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=108ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg deleted file mode 100644 index 4aa301ce8b..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_side_pbc_t=305ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg deleted file mode 100644 index 920354c544..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls+water_top_nopbc_t=0_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg deleted file mode 100644 index aa26f13948..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube+walls_side_nopbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube_capillary_bbk_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube_capillary_bbk_LR.jpg deleted file mode 100644 index 9cba533530..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/nanotube_capillary_bbk_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/water_side_nopbc_LR.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/water_side_nopbc_LR.jpg deleted file mode 100644 index cdc143510b..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/images/water_side_nopbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh deleted file mode 100755 index 15fe07133f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/README.sh +++ /dev/null @@ -1,32 +0,0 @@ -# This is a small version of a carbon-nanotube, water capillary system. -# It was inspired by this paper: -# -# Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) -# -# Note: To investigate the behavior from that paper, you would have to increase -# the spacing between the two graphene sheets to prevent the water from -# making contact with the lower graphene wall. -# -# Requirements: 1) Set your $MOLTEMPLATE_PATH variable -# 2) The "RIGID" LAMMPS package may be needed later -# To run this system at constant pressure, it might help to compile LAMMPS with -# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) -# -# Also, if you have not yet done this set your MOLTEMPLATE_PATH environment -# variable to access it. (See installation instructions.) -# Most likely some of the files in this example (like graphene.lt, tip3p2004.lt) -# are not in this directory, but are in the "force_fields" subdirectory -# distributed with moltemplate. -# -# ----------------------------------------------------------- -# -# To run moltemplate, use: - -moltemplate.sh system.lt - -# If you have VMD installed, you can run it this way to visualize the system: -# -# moltemplate.sh -vmd system.lt -# -# Either way, this will generate the following files (which LAMMPS reads): -# system.data, system.in, system.in.init, system.in.settings diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt deleted file mode 100644 index 3bc476c3ab..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene.lt +++ /dev/null @@ -1,61 +0,0 @@ -# The minimal unit cell for graphine contains only 2 atoms: -# (which I arbitrarily named "C1" and "C2") - -Graphene { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0000 - $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0000 - } - - # Now define the "C" atom type - write_once("Data Masses") { - @atom:C 12.0 - } - write_once("In Settings") { - # i j epsilon sigma - pair_coeff @atom:C @atom:C lj/cut/coul/long 0.068443 3.407 - - # The Lennard-Jones parameters above were chosen to realistically model - # the interaction between graphene and water - # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, - # Chem Phys Lett, 348:187 (2001) - # NOTE: If you want to simulate movement of the carbon atoms, then you must - # choose a more appropriate force field for the carbon atoms, such as - # AIREBO or Tersoff. You can do this by editing the "pair_coeff" above. - # (The paper by C.F. Cornwell, C.R. Welch, J. Chem. Phys. (2011), Vol 134, - # demonstrates how to use the AIREBO potential in LAMMPS.) - - # Define a group consisting of only carbon atoms in graphene molecules - group Cgraphene type @atom:C - } - write_once("In Init") { - # -- Default styles (used in this file for graphene carbon) -- - units real - atom_style full #(full enables you to to add other molecules later) - pair_style hybrid lj/cut/coul/long 10.0 - } -} # Graphene - - - - -# This is a 2-dimensional hexagonal unit cell. The unit vectors are: -# -# (2.4595121467478, 0, 0) -# (1.2297560733739, 2.13, 0) -# -# You can create a sheet of single-layer graphene this way: -# -# small_crystal = new Graphene [3].move(2.45951214, 0, 0) -# [3].move(1.229756, 2.13, 0) -# -# For thicker sheets, follow the instructions in the "graphite.lt" file. -# -# Note: The length of each carbon-carbon bond is currently 1.42 Angstroms. -# To increase it to 1.422 Angstroms, uncomment the following line: -# -# Graphene.scale(1.0014084507042254) # 1.0014084507042254 = 1.422 / 1.42 -# -# You will have to change the unit cell lattice vectors (see above) accordingly diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt deleted file mode 100644 index 888b9cce8c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphene_walls.lt +++ /dev/null @@ -1,57 +0,0 @@ - -import "graphene.lt" - -# -------------- graphene sheet ----------------- - -# Notes: -# Hexagonal lattice with: -# d = length of each hexagonal side = 1.42 Angstroms -# L = length of each hexagon = 2*d = 2.84 Angstroms -# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478 Angstroms -# w = width of hexagon rows = 1.5*d = 2.13 Angstroms - -Wall { - unitcells = new Graphene [14].move(1.2297560733739, 2.13, 0) - [13].move(2.4595121467478, 0, 0) - - unitcells[*][*].move(-24.595121467478, -14.91, 0.000) - - # Now cut a hole in the graphene sheet roughly where the nanotube is located - delete unitcells[5][7-8] # delete 2 unit cells (2 atoms each, 4 atoms total) - delete unitcells[6][6-8] # delete 3 unit cells (2 atoms each, 6 atoms total) - delete unitcells[7][5-8] # delete 4 unit cells (2 atoms each, 8 atoms total) - delete unitcells[8][5-7] # delete 3 unit cells (2 atoms each, 6 atoms total) - delete unitcells[9][5-6] # delete 2 unit cells (2 atoms each, 4 atoms total) - # Optional fine tuning: delete a few additional atoms around the edges - delete unitcells[5][6]/C2 # delete a single atom - delete unitcells[6][5]/C2 # delete a single atom - delete unitcells[6][9]/C1 # delete a single atom - delete unitcells[8][4]/C2 # delete a single atom - delete unitcells[8][8]/C1 # delete a single atom - delete unitcells[9][7]/C1 # delete a single atom -} - -# Make two copies of the wall, and place them on either end of the nanotube - -wall1 = new Wall.move(0, 0, 32.0) -wall2 = new Wall.move(0, 0, 58.26) - -# WARNING: A reader has pointed out : -# THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. -# A real junction would likely be curved near the boundary, -# not a 90 degree junction. (Although both graphene and nanotubes -# consist of hexagons of carbon atoms, you would need 6 heptagons -# near the junction between the nanotube and the graphene -# to account for the negative Gaussian curvature there). -# To solve this problem: -# Moltemplate allows you to move, add, customize or delete individual -# atoms near the boundary. You can move atoms by overwriting their -# coordinates using additional write("Data Atoms") statements (after -# the walls and tube are created). You can also adjust their partial charge. -# Alternately, you could start with the structure provided here, add or delete -# atoms if necessary, and relax/minimize the coordinates of the carbon -# atoms using LAMMPS. You could also run a high temperature annealing -# simulation to relax their positions. If it helps, the AIREBO -# force-field has used in LAMMPS to simulate carbon nanotubes breaking: -# http://scitation.aip.org/content/aip/journal/jcp/134/20/10.1063/1.3594197 -# http://lammps.sandia.gov/pictures.html#cnt diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt deleted file mode 100644 index 49fb49fb08..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/graphite.lt +++ /dev/null @@ -1,61 +0,0 @@ -import "graphene.lt" # defines "Graphene" - - -# ------------ Graphite ----------- -# -# Note: For graphite: sheets stacked in the Z direction are separated by a -# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction -# by a distance of d (1.42 Angstroms). To add additional graphene layers -# you could use: -# sheet2 = new Graphene [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet2[*][*].move(0, 1.42, 3.35) -# sheet3 = new Graphene [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet3[*][*].move(0, -1.42, 6.70) -# etc... -# -# This should work fine. -# However, to build a thick sheet of graphite, it may be less trouble -# to use a 4-atom unit cell which includes two graphene layers. -# Here is one way to do that: - -Graphite inherits Graphene { - - # This allows us to access access the "@atom:C" carbon atom type - # whose properties are defined in the "Graphene" object (see "graphene.lt"). - # That atom is NOT globally defined. It belongs to the "Graphene" object. - # This is one way to access it. Alternately, you could redefine it here - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0 - $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0 - $atom:C3 $mol:... @atom:C 0.0 -0.61487803668695 1.065 3.35 - $atom:C4 $mol:... @atom:C 0.0 0.61487803668695 1.775 3.35 - } - - # Note: The first two lines in the "Data Atoms" section override the positions - # of the $atom:C1 and $atom:C2 atoms previously defined in "Graphene" - # (which this object inherits). This is okay. - -} # Graphite - - - - - - -# This is a 3-dimensional hexagonal unit cell. The unit vectors are: -# -# (2.4595121467478, 0, 0 ) -# (1.2297560733739, 2.13, 0 ) -# ( 0, 0, 6.70) - -# Then you could create a thick sheet of graphite this way: -# -# graphite = new Graphite [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# [5].move(0,0,6.70) -# -# (Your graphite slab will contain an even number of graphene sheets.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt deleted file mode 100644 index 06a5e94338..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/nanotube.lt +++ /dev/null @@ -1,101 +0,0 @@ -import "graphene.lt" - -# The "Graphene" unit cell defined in "graphene.lt" lies in the XY plane. -# In the next line, we will create a new version of the graphene unit cell -# which lies in the XZ plane, by rotating Graphene 90 degrees around the X axis: - -GrapheneXZ = Graphene.rot(90,1,0,0) - -# ------------------ nanotube --------------- - -# Now use this to build a simple ("zigzag") nanotube where the long-axis of each -# hexagon is aligned with the tube axis (along the Z direction). If the -# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of -# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon -# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms -# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms. - - - -nanotube = new GrapheneXZ.move(0, 5.457193512764, 0) # 5.45 = R - [14].rot(25.7142857,0,0,1) #25.7=360/14 - [12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14 - #2.13= d*1.5 - - - # Note: The length is 12 hexegons, the circumference is - # 14 hexegons (~=25.56 and 34.43 Angstroms, respectively). - - -# Move all of the unit-cells in the nanotube between the two graphene sheets. - -nanotube[*][*].move(0, 0, 33.42) - - - - - -# ---------- BUILDING CHIRAL NANOTUBES USING EXTERNAL SOFTWARE ------------- -# -# The approach shown here works well for "zig-zag" nanotubes. -# Nanotubes with other chiralities are more difficult to make this way -# (because the tube axis is no longer perpendicular to graphene basis vectors). -# For those nanotubes, I recommend using an external program to generate -# a LAMMPS data file for the nanotube. If you want to combine the tube -# with other molecules created by moltemplate, you can then import it into -# moltemplate as a molecule object using the "ltemplify.py" utility. Details: -# -# --- VMD plugins (by Axel Kohlmeyer and Robert R. Johnson) --- -# -# The nanotube-builder for VMD can generate nanotubes (with smooth tips) -# for any chirality. These tubes also have explicit bonds between carbons: -# http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/ -# -# The resulting nanotube can be converted to a data file using topotools: -# https://sites.google.com/site/akohlmey/software/topotools -# To do that, select the "Extensions"->"Tk Console" menu and enter -# -# topo writelammpsdata nanotube.data full -# -# --- ltemplify.py --- -# -# That data file can be converted to moltemplate format (an .LT file) -# using the "ltemplify.py" utility. -# -# The first step is to create a short input script containing the atom_style -# command (ltemplify.py will read this script. Presumably atom_style is "full"). -# -# echo "atom_style full" > nanotube.in -# -# Then run ltemplify to convert nanotube.data into a moltemplate file: -# ltemplify.py -name Nanotube nanotube.in nanotube.data > nanotube.lt -# -# You will need to edit the "nanotube.lt" file to replace all of the -# "@atom:type1" atoms types file to match the carbon atom types in the other lt -# files (ie "@atom:../C"). If you don't plan on defining bonded interactions -# between carbon atoms, then be sure to remove the write("Data Bonds") section -# of the "nanotube.lt" file (if it is present). -# -# Finally make sure the "system.lt" contains these lines: -# -# import "nanotube.lt" -# nanotube = new Nanotube.move(?,?,?) -# -# (Replace ?,?,? with the location where you want the nanotube to go. -# You can also rotate it using .rot(angle,axisx,axisy,axiz).) -# -# ... and then run moltemplate the normal way -# -# Let me know if you run into trouble with this approach, -# and I will make note of that in this file. -# -# --- links --- -# Note: there are numerous programs for specifying the coordinates -# of the atoms in a nanotube, some of which are below. -# http://www.nanotube.msu.edu/tubeASP/ -# http://turin.nss.udel.edu/research/tubegenonline.html -# http://www.ugr.es/~gmdm/java/contub/contub.html -# (You can load coordinates into moltemplate using the "-xyz" or "-pdb" -# arguments. However currently (2013-12-01), the file must contain coordinates -# for all of the atoms in your sytem, not just the nanotube.) -# ------------------------------------------------------------------------- diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt deleted file mode 100644 index d40da62b99..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 600.0 1.0 - angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/cut/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/cut/coul/long 0.0 0.0 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) - } - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/cut/coul/long 9.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt deleted file mode 100644 index d7c610fc0c..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/system.lt +++ /dev/null @@ -1,29 +0,0 @@ -# This is a small version of a carbon-nanotube, water capillary system. It was -# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) - -import "graphene_walls.lt" - -import "nanotube.lt" - -import "water_box.lt" - - -# ------------ boundary conditions ------------ - -write_once("Data Boundary") { - -15.98682895386 15.98682895386 xlo xhi - -14.91 14.91 ylo yhi - -31.0 31.00 zlo zhi -} - -# --------------------------------------------- - -write_once("In Settings") { - # --- We must eventually specify the interactions between the atoms --- - # --- in different molecule types (graphene-water interactions). --- - # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details - - pair_coeff @atom:Graphene/C @atom:SPCE/O lj/cut/coul/long 0.114 3.28 - pair_coeff @atom:Graphene/C @atom:SPCE/H lj/cut/coul/long 0.0 3.28 -} - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt deleted file mode 100644 index c825276f5a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/moltemplate_files/water_box.lt +++ /dev/null @@ -1,20 +0,0 @@ -import "spce.lt" - -# --------------- water ------------------ - -# Create a rhombohedral box of water. (A rectangular box works also.) - -wat = new SPCE [9].move(3.5526287, 0, 0 ) - [9].move(1.77631435, 3.3133, 0 ) - [6].move( 0, 0, 3.45) - -# Optional: Center the water box at the origin. (Not really necessary.) - -wat[*][*][*].move(-23.9802437, -14.90985, 11.47) - -# --------------- Note: ----------------- -# The spacing between water molecules does not matter much as long as it is -# reasonable. (I adjusted the spacing try to insure that the waters are spread -# uniformly throughout the box. We do not want bubles to form if there are -# gaps near the XY periodic boundaries.) We will have to equilibrate it later. - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/run.in.npt deleted file mode 100644 index 2728a1f5ac..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/run.in.npt +++ /dev/null @@ -1,147 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (You do not need to run LAMMPS to equilibrate the system before -# using this file.) -# -# Requirements: -# To run this system at constant pressure, it might help to compile LAMMPS with -# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) -# The use of fix rigid is controversial. This method is demonstrated below. -# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. This simulation may fail. -# (However the "run.in.nvt" example in this directory should work.) -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# Use "neigh_modify" to turn off calculation of interactions between immobilized -# atoms. (Note: group "cGraphene" was defined in the file "system.insettings") -neigh_modify exclude group Cgraphene Cgraphene - -# ------------------------------- Run Section ------------------------------- - - -# Only the Cgraphene atoms are immobile. -group mobile subtract all Cgraphene - -# (Note: The "Cgraphene" group was defined in system.in.settings.) - - -# Unfortunately you can not use the LAMMPS "minimize" command on this system -# because there is no way to immobilize the carbon graphene & nanotube atoms -# during minimization. Instead, we can use langevin dynamics with a fast -# damping parameter and a small timestep. - -print "--------- beginning minimization (using fix langevin) ---------" - -timestep 0.1 -fix fxlan mobile langevin 1.0 1.0 100.0 48279 -fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) -thermo 100 -run 2500 - -unfix fxlan -unfix fxnve - -# -- simulation protocol -- - -print "--------- beginning simulation (using fix nvt) ---------" - -dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 200 # time interval for printing out "thermo" data - - - - - -# ------------------------- NPT --------------------------- - - -# ------ QUESTIONABLE (see below): ------ - -fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off - -# Comment: -# The use of "fix rigid" to immobilize an object is somewhat controversial. -# Feel free to omit it. -# (Neither Trung or Steve Plimpton use fix rigid for immobilizing -# molecules, but I noticed that at NPT, it does a better job of maintaining -# the correct volume. However "fix rigid" has changed since then (2011), -# so this may no longer be true. Please use this example with caution.) - - - -# Thermostat+Barostat -# Set temp=300K, pressure=200bar, and equilibrate volume only in the z direction - -fix fxMoveStuff mobile npt temp 300 300 100 z 200 200 1000.0 dilate mobile drag 2.0 - -# ---------------------------------------- - -# The next two lines recalculate the temperature using -# only the mobile degrees of freedom (ie. water atom velocities): - -compute tempMobile mobile temp -compute pressMobile all pressure tempMobile - -thermo_style custom step c_tempMobile c_pressMobile temp press vol - -fix_modify fxMoveStuff temp tempMobile - -reset_timestep 0 - -timestep 0.25 - -run 100000 - -timestep 0.5 - -run 200000 - -# Hopefully the barostat is no longer oscillating. Increase the timestep and -# also get get rid of "drag 2.0". (A non-zero drag parameter will result in -# unrealistic fluctuations of volume under NPT conditions.) -# drag 2.0 <-- commenting out -# -# Set temp=300K, pressure=0bar, and equilibrate volume only in the z direction -unfix fxMoveStuff -fix fxMoveStuff mobile npt temp 300 300 100 z 0 0 1000.0 dilate mobile -fix_modify fxMoveStuff temp tempMobile - -timestep 0.5 - -run 1000000 - -write_data system_after_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also.) - - - - - - - -# ----- Comment: Avoid using fix rigid/npt on large single rigid objects ----- -# -# Use of the following is not recommended: -# -# fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 200 200 1000.0 force * off off off torque * off off off dilate mobile -# (temp=300K, pressure=200bar, and equilibrate volume only in the z direction) -# -# In my experience, the system becomes unstable when applying "fix rigid/npt" -# to the immobile atoms, while also applying "fix npt" on the solvent atoms. -# (It is probably a bad idea to use two barostats simultaneously.) -# ---------------------------------------------------------------------------- diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/run.in.nvt deleted file mode 100644 index 86253c45b9..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/nanotube+water/run.in.nvt +++ /dev/null @@ -1,78 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (You do not need to run LAMMPS to equilibrate the system before -# using this file.) - -# ----------------------------- Initialization Section -------------------- - -include system.in.init - - -# ----------------------------- Atom Definition Section ------------------- - -read_data system.data - - -# ----------------------------- Settings Section -------------------------- - -include system.in.settings - -# Use "neigh_modify" to turn off calculation of interactions between immobilized -# atoms. (Note: group "cGraphene" was defined in the file "system.insettings") -neigh_modify exclude group Cgraphene Cgraphene - -# ----------------------------- Run Section ------------------------------- - - - -# Only the Cgraphene atoms are immobile. -group mobile subtract all Cgraphene - -# (Note: The "Cgraphene" group was defined in system.in.settings.) - - - -# -- minimization protocol -- - -# Unfortunately you can not use the LAMMPS "minimize" command on this system -# because there is no way to immobilize the carbon graphene & nanotube atoms -# during minimization. Instead, we can use langevin dynamics with a fast -# damping parameter and a small timestep. - -print "--------- beginning minimization (using fix langevin) ---------" - -timestep 0.1 -fix fxlan mobile langevin 1.0 1.0 100.0 48279 -fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) -thermo 100 -run 2500 - -unfix fxlan -unfix fxnve - -# -- simulation protocol -- - -print "--------- beginning simulation (using fix nvt) ---------" - -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - -# Integrate the equations of motion: -fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0 - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp -fix_modify fxMoveStuff temp tempMobile - - -timestep 2.0 -run 5000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh deleted file mode 100755 index 6f66c68f1a..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure - -# or - -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -# or -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh deleted file mode 100755 index 68cad16a79..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt deleted file mode 100644 index e345be951d..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.05 0.14 -0.05} - pbc box -shiftcenterrel {-0.05 0.14 -0.05} -width 0.5 -style tubes - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Cl.jpg deleted file mode 100644 index 5261bedc2c..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Cl.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Na.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Na.jpg deleted file mode 100644 index 78c4056f8c..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/Na.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/wat.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/wat.jpg deleted file mode 100644 index 60aaf90b95..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/wat.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg deleted file mode 100644 index bf00edc9c4..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg deleted file mode 100644 index af70c23997..0000000000 Binary files a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=100ps.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt deleted file mode 100644 index ff52a7db97..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/ions.lt +++ /dev/null @@ -1,68 +0,0 @@ -# We define two molecule classes to represent Na+ and Cl- ions, respectively. -# They both contain only one atom. - -# In moltemplate each molecule type is stored in a file whose format mimics the -# format of a LAMMPS "data" file, with "Atoms", "Bonds", and "Angles" sections. -# Once defined, these molecules may be copied and moved to build larger systems. - - -NaIon { - - # ---- Definition of "NaIon" ---- - - # AtomID MolID AtomType charge X Y Z - write("Data Atoms") { - $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 - } - - write_once("Data Masses") { - @atom:Na 22.9898 - } - - write_once("In Settings") { - pair_coeff @atom:Na @atom:Na 0.3526418 1.079769246386 - } - # (explanation: http://lammps.sandia.gov/doc/pair_charmm.html) - -} # NaIon - - - - -ClIon { - - # ---- Definition of "ClIon" ---- - - # AtomID MolID AtomType charge X Y Z - write("Data Atoms") { - $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 - } - - write_once("Data Masses") { - @atom:Cl 35.453 - } - - write_once("In Settings") { - pair_coeff @atom:Cl @atom:Cl 0.0127850 2.711 - } - # (explanation: http://lammps.sandia.gov/doc/pair_charmm.html) - -} # ClIon - - - - - - -# Note: Monovalent ion parameters for Ewald and SPC/E water -# are from: Joung & Cheatham JPCB (2008) -# These Lennard Jones parameters match the parameters for ions -# in SPC/E water in the "frcmod.ionsjc_spce" file distributed -# with Amber (the 2010 version). -# -# The epsilong & sigma parameters from that paper were 0.3526418 & 1.212. -# However sigma must be divided by 2^(1/6), because they use the alternate -# Lennard-Jones convention: U(r)=epsilon*((s/r)^12 - 2*(s/r)^6), and -# pair_style lj/charmm/coul/long uses U(r)=4*epsilon*((s/r)^12 - (s/r)^6) -# (Note: This change does not effect the epsilon parameter.) - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt deleted file mode 100644 index db5e7df3b3..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/spce.lt +++ /dev/null @@ -1,114 +0,0 @@ -# In moltemplate each molecule type is stored in a file whose format mimics the -# format of a LAMMPS "data" file, with "Atoms", "Bonds", and "Angles" sections. -# Once defined, these molecules can be copied and moved to build larger systems. -# -# "SPCE" ("extended simple point charge") is one of several popular water models -# (See Berendsen H.J.C et al., J.Phys.Chem. Vol91 pp.6269-6271,1987 for details) -# -# file "spce.lt" -# -# H1 H2 -# \ / -# O - - -SPCE { - - # ---- Definition of the "SPCE" (water molecule type) ---- - - # The "Data Atoms" section is a list of atom attributes (type, charge, x,y,z) - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:o $mol @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:h1 $mol @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:h2 $mol @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - # Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number). - # If we put "$mol" there, moltemplate will generate this integer for you - - # A list of the bonds in the molecule: - # BondID BondType AtomID1 AtomID2 - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:o $atom:h1 - $bond:OH2 @bond:OH $atom:o $atom:h2 - } - - # A list of the angles in the molecule: - # AngleID AngleType AtomID1 AtomID2 AtomID3 - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:h1 $atom:o $atom:h2 - } - - # The mass of each atom type: - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - - # ---- Where to put force field parameters? ---- - # Moltemplate allows you to specify force-field parameters anywhere you want. - # Sometimes it is convenient to nest them within a molecule's definition. - # For more complicated simulations, it's convenient to define a "ForceField" - # object containing force field parameters shared by many different types of - # molecules. (Since this is a simple example, there is no need to do that.) - - # The "In Settings" section contains LAMMPS commands which typically define - # force-field parameters (eg "pair_coeff") and constraints (eg "fix shake") - - write_once("In Settings") { - bond_coeff @bond:OH 1000.0 1.0 - # explanation: http://lammps.sandia.gov/doc/bond_harmonic.html - - angle_coeff @angle:HOH 1000.0 109.47 - # explanation: http://lammps.sandia.gov/doc/angle_harmonic.html - - pair_coeff @atom:O @atom:O 0.1553 3.166 - pair_coeff @atom:H @atom:H 0.0 2.058 - # explanation: http://lammps.sandia.gov/doc/pair_charmm.html - - # OPTIONAL: We want the water molecules to behave like rigid objects, so - # we apply the "SHAKE" constraint to the group of atoms in water molecules. - # (SHAKE is used to make bonds and angles rigid.) - - group gSPCE type @atom:O @atom:H - # explanation: http://lammps.sandia.gov/doc/group.html - - fix fShakeSPCE gSPCE shake 0.0001 10 100 b @bond:OH a @angle:HOH - # explanation: http://lammps.sandia.gov/doc/fix_shake.html - # (Remember to "unfix" fSHAKE during minimization.) - - } - - # LAMMPS requires that some commands must be issued in a certain order. - # (IE. You must inform LAMMPS the kind of simulation you wish to run - # before supplying LAMMPS with numeric parameters for that simulation.) - # The "In Init" section is where you put commands which must be run before - # all other commands in the simulation (such as the commands in "In Settings") - - write_once("In Init") { - - units real - # explanation: http://lammps.sandia.gov/doc/units.html - - # Specify the attributes of the particles in our system (eg. "full") - atom_style full - # explanation: http://lammps.sandia.gov/doc/atom_style.html - - # Specify the kinds of formulas we want to use to calculate - # the forces in our system (ie. force-field "styles") - bond_style harmonic - angle_style harmonic - pair_style lj/charmm/coul/long 9.0 10.0 10.0 - pair_modify mix arithmetic - # explanation: http://lammps.sandia.gov/doc/pair_modify.html - kspace_style pppm 0.0001 - # explanation: http://lammps.sandia.gov/doc/kspace_style.html - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt deleted file mode 100644 index 284d042d73..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/moltemplate_files/system.lt +++ /dev/null @@ -1,50 +0,0 @@ -import "spce.lt" # <- This defines the SPCE water molecule. - -import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 34.50 xlo xhi - 0.0 34.50 ylo yhi - 0.0 34.50 zlo zhi -} - - -# The next command generates a (rather dense) cubic lattice with -# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) - -wat = new SPCE [10].move(0.00, 0.00, 3.45) - [10].move(0.00, 3.45, 0.01) - [10].move(3.45, 0.01, 0.01) - -# We now create a 2x2x2 lattice of Na+ and Cl- ions: - -na = new NaIon [2].move(0,0,17.25) - [2].move(0,17.25,0) - [2].move(17.25,0,0) - - -cl = new ClIon [2].move(0,0,17.25) - [2].move(0,17.25,0) - [2].move(17.25,0,0) - -na[*][*][*].move(5,5,5) -cl[*][*][*].move(12,12,12) - -# (The (5,5,5) and (12,12,12) translational shifts -# prevent the Na and Cl ions from overlapping -# with the water molecules or each other.) - - - - -# Comment: Fortunately the ions and the water in this example share the -# same force-field styles (so their was no need to use "hybrid" styles). -# If this were not the case, you might need to add something like this. -# -# write_once("In Init") { -# # -- Styles for the combined system (overrides earlier settings) -- -# pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 NEWPAIRSTYLE -# bond_style hybrid harmonic NEWBONDSTYLE -# angle_style hybrid harmonic NEWANGLESTYLE -# } diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt deleted file mode 100644 index 9bd2f15f46..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.npt +++ /dev/null @@ -1,48 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize". -unfix fShakeSPCE -minimize 1.0e-3 1.0e-5 100000 400000 -# Now read "system.in.settings" in order to redefine fShakeSPCE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -thermo 100 - -run 10000 - -# Now that the system's temperature has become more equilibrated, -# we can increase the timestep: - -timestep 2.0 -run 50000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt deleted file mode 100644 index fb0642332f..0000000000 --- a/tools/moltemplate/examples/all_atom/force_field_explicit_parameters/waterSPCE+Na+Cl/run.in.nvt +++ /dev/null @@ -1,58 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_npt.data - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- -# Note: If you are reading the restart file instead of the data file, -# then you should not need to minimize the system beforehand.. -# fShakeSPCE was defined in system.in.settings. -# (It is incompatible with "minimize".) -unfix fShakeSPCE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fShakeSPCE again: -include system.in.settings - -# -- simulation protocol -- - - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 - -run 10000 - -# Now that the system's temperature has become more equilibrated, -# we can increase the timestep: - -timestep 2.0 -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README.txt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README.txt deleted file mode 100644 index 6b8cc5a172..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README.txt +++ /dev/null @@ -1,30 +0,0 @@ -This example was intended to demonstrate the flexibility of LAMMPS and -moltemplate. - -This is a relatively complex example containing two different types of -coarse-grained (united-atom) molecules. This simulation uses the 3-body -(non-pairwise-additive) coarse-grained "mW" water model: -Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016 -Simulations using the "mW" water model can be several orders of magnitude -faster than simulations using simple all-atom models such as SPCE or TIP3P. - -The united-atom TraPPE force field was used for the cyclododecane molecules. - -Any force-field available in LAMMPS can be used with moltemplate. New force-fields are added by end users regularly. For a current list, see: -http://lammps.sandia.gov/doc/Section_commands.html#pair-style-potentials - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh - - --------- REQUIREMENTS: --------- - This example requires the "MANYBODY" package. - If lammps complains of a missing pair style enter "make yes-MANYBODY" - into the shell before compiling lammps. For details see: - http://lammps.sandia.gov/doc/Section_start.html#start_3 diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh deleted file mode 100755 index c2e6bae3ba..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, system.in.sw -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh deleted file mode 100755 index 55d633894e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_setup.sh +++ /dev/null @@ -1,30 +0,0 @@ - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - - # Each atom type (eg "mW") must be assigned to an integer (because LAMMPS - # does not understand descriptive names). Normally LAMMPS does not care what - # these numbers are, however many-body force-fields (used in this example) - # are an exception. Here we just want to make sure that the "mW" atom - # type is assigned to number "1" so we use -a "@atom:WatMW/mW 1" - # (The full-name of the atom is "WatMW/mW", not "mW", because it is part - # of the "WatMW" molecule-object. See "watmw.lt" for details.) - - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=0ps_LR.jpg deleted file mode 100644 index 5123dc7f60..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=400ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=400ps_LR.jpg deleted file mode 100644 index 4003ac5f06..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=400ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=50ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=50ps_LR.jpg deleted file mode 100644 index f1dd1467cb..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclododecane+watMW_t=50ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane.jpg b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane.jpg deleted file mode 100644 index 6591b236a3..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane_unrelaxed.jpg b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane_unrelaxed.jpg deleted file mode 100644 index 9b4ca06fb8..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/cyclopentane_unrelaxed.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/watMW.jpg b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/watMW.jpg deleted file mode 100644 index 0ac8c2c011..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/images/watMW.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/README.sh deleted file mode 100755 index 1e16d360e0..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/README.sh +++ /dev/null @@ -1,11 +0,0 @@ -# Use this command to generate the LAMMPS input files: - -moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt - -# The -a argument insures that the "mW" atom type is assigned to "1". -# (This is necessary for the pair_coeff command to work. -# See system.lt for details.) - -# Note: To get rid of the annoying "atom_style unspecified warnings, -# use the "-atomstyle" command line argument, as in: -# moltemplate.sh -atomstyle full -a "@atom:/WatMW/mW 1" system.lt diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/cyclododecane.lt deleted file mode 100644 index 5c06c60c6c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/cyclododecane.lt +++ /dev/null @@ -1,55 +0,0 @@ -import "trappe1998.lt" - -# The "trappe1998.lt" file is usually located in $MOLTEMPLATE_PATH (and is -# distributed with moltemplate. See the "Installation" section in the manual.) -# It contains definitions of the atoms "CH2", "CH3", and "CH4", as well -# as "saturated" bonds, and the parameters for (bonded/nonbonded) -# interactions between these atoms (all enclosed within the "TraPPE" namespace). - - -Cyclododecane inherits TraPPE { - - write('Data Atoms') { - $atom:C1 $mol:. @atom:CH2 0.0 0.00000 2.94118 0.0 - $atom:C2 $mol:. @atom:CH2 0.0 0.00000 2.54714 1.47059 - $atom:C3 $mol:. @atom:CH2 0.0 0.00000 1.47059 2.54714 - $atom:C4 $mol:. @atom:CH2 0.0 0.00000 0.0 2.94118 - $atom:C5 $mol:. @atom:CH2 0.0 0.00000 -1.47059 2.54714 - $atom:C6 $mol:. @atom:CH2 0.0 0.00000 -2.54714 1.47059 - $atom:C7 $mol:. @atom:CH2 0.0 0.00000 -2.94118 0.0 - $atom:C8 $mol:. @atom:CH2 0.0 0.00000 -2.54714 -1.47059 - $atom:C9 $mol:. @atom:CH2 0.0 0.00000 -1.47059 -2.54714 - $atom:C10 $mol:. @atom:CH2 0.0 0.00000 -0.0 -2.94118 - $atom:C11 $mol:. @atom:CH2 0.0 0.00000 1.47059 -2.54714 - $atom:C12 $mol:. @atom:CH2 0.0 0.00000 2.54714 -1.47059 - } - - # The "." in "$mol:." refers to the current object's molecule ID, - # and "@atom:CH2" refers to the "CH2" atom-type defined in "trappe1998.lt" - - write('Data Bonds') { - $bond:bond1 @bond:saturated $atom:C1 $atom:C2 - $bond:bond2 @bond:saturated $atom:C2 $atom:C3 - $bond:bond3 @bond:saturated $atom:C3 $atom:C4 - $bond:bond4 @bond:saturated $atom:C4 $atom:C5 - $bond:bond5 @bond:saturated $atom:C5 $atom:C6 - $bond:bond6 @bond:saturated $atom:C6 $atom:C7 - $bond:bond7 @bond:saturated $atom:C7 $atom:C8 - $bond:bond8 @bond:saturated $atom:C8 $atom:C9 - $bond:bond9 @bond:saturated $atom:C9 $atom:C10 - $bond:bond10 @bond:saturated $atom:C10 $atom:C11 - $bond:bond11 @bond:saturated $atom:C11 $atom:C12 - $bond:bond12 @bond:saturated $atom:C12 $atom:C1 - } - -} # Cyclododecane - - -# coordinates in the "Data Atoms" section generated by this python code: -# from math import * -# bond_length=1.54 -# N=12 -# R=(N*bond_length)/(2*pi) -# for i in range(0,N): -# print('$atom:C'+str(i+1)+' $mol:... @atom:CH2 0.0 0.00000 '+ -# str(round(R*cos(i*2*pi/N),5))+' '+str(round(R*sin(i*2*pi/N),5))) diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt deleted file mode 100644 index 4a7063491b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/system.lt +++ /dev/null @@ -1,62 +0,0 @@ -# This is a relatively complex example containing two different types of -# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. - -import "watmw.lt" -import "cyclododecane.lt" - -write_once("Data Boundary") { - 0.000000 48.000 xlo xhi - 0.000000 48.000 ylo yhi - 0.000000 48.000 zlo zhi -} - -wat = new WatMW [12].move(0, 0, 4.0) - [12].move(0, 4.0, 0) - [12].move(4.0, 0, 0) - -cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) - [4].move(0, 12.0, 0) - [4].move(12.0, 0, 0) - -# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) -cyclododecane[*][*][*].move(6.0,6.0,6.0) - -write_once("In Init") { - # -- Tell LAMMPS we want to use two different pair styles - # -- (This overrides earlier settings.) - pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 -} - - -write_once("In Settings") { - # -- Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) -} - - - -# -- Somewhere we must eventually define interactions -# -- between atoms from different molecule types - -write_once("In Settings") { - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 -} - - - diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/trappe1998.lt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/trappe1998.lt deleted file mode 100644 index 9bcc80cb1c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/trappe1998.lt +++ /dev/null @@ -1,50 +0,0 @@ -# This file stores complete LAMMPS data for the TraPPE model of saturated -# hydrocarbon chains. In this "united-atom" model, each methyl group is -# represented by a single atom. Forces between "atoms" are taken from the -# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) - -TraPPE { - - write_once("In Init") { - # -- Default styles for "TraPPE" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style none - pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:CH2 14.1707 - @atom:CH3 15.2507 - @atom:CH4 16.3307 - } - - write_once("Data Angles By Type") { - @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated - } - - write_once("Data Dihedrals By Type") { - @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated - } - - write_once("In Settings") { - pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 - pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 - pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 - bond_coeff @bond:saturated harmonic 120.0 1.54 - angle_coeff @angle:backbone harmonic 62.0022 114 - dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 - } - - write_once("In Settings") { - group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 - } - -} # class TraPPE - diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments/system.lt deleted file mode 100644 index 34bdfead77..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/version_more_comments/system.lt +++ /dev/null @@ -1,80 +0,0 @@ -# This is a relatively complex example containing two different types of -# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. - -import "watmw.lt" -import "cyclododecane.lt" - -write_once("Data Boundary") { - 0.000000 48.000 xlo xhi - 0.000000 48.000 ylo yhi - 0.000000 48.000 zlo zhi -} - -wat = new WatMW [12].move(0, 0, 4.0) - [12].move(0, 4.0, 0) - [12].move(4.0, 0, 0) - -cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) - [4].move(0, 12.0, 0) - [4].move(12.0, 0, 0) - -# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) -cyclododecane[*][*][*].move(6.0,6.0,6.0) - -write_once("In Init") { - # -- Tell LAMMPS we want to use two different pair styles - # -- (This overrides earlier settings.) - pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 -} - - - -write_once("In Settings") { - # -- Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # - # For this to work, the first atom type (assigned to "1") - # must refer to the "mW" atom type (defined in watmw.lt). - # (This is why we included "watmw.lt" first, to insure that the - # atom counters in WatMW are assinged first, starting with 1.) - # Alternately we can further insure that this happens, it's - # a good idea to run moltemplate.sh using the "-a" argument: - # moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt - # This assigns the atom type named @atom:/WatMW/mW to 1 -} - - - - -# -- Somewhere we must eventually define interactions -# -- between atoms from different molecule types -# -- Now define interactions between DIFFERENT molecules -# Note: In the SPC/E model, the epsilon,sigma parameters for water is 0.1553 -# 3.166. As a crude guess, I chose the LJ parameters for the interaction -# between water & the CH2,CH3,CH4 atoms using Lorentz-Berthelot mixing rules - -write_once("In Settings") { - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 -} - - - - - - - - - diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/watmw.lt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/watmw.lt deleted file mode 100644 index c7aaecebbc..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/moltemplate_files/watmw.lt +++ /dev/null @@ -1,54 +0,0 @@ -# This file stores LAMMPS data for the "mW" water model. -# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) -# -# In this model, each water molecule is represented by a single "mW" particle. -# These particles interact with their neighbors via 3-body Stillinger-Weber -# forces whose parameters are tuned to mimic directional hydrogen-bonding -# in liquid water (as well as hexagonal ice, type II ice, and -# low-density super-cooled liquid/amorphous water phases). - -WatMW { - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 - } - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # --Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) - } - - # -- optional -- - - write_once("In Settings") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/run.in.npt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/run.in.npt deleted file mode 100644 index 544daee70d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/run.in.npt +++ /dev/null @@ -1,61 +0,0 @@ -# run.in.npt -# -# -- Usage -- -# -# lmp_linux -i run.in.npt -# (assuming lmp_linux is the name of your lammps binary) -# -# -- Prerequisite Input Files: -- -# systen.data, system.in.init, system.in.settings, system.in.sw -# -# You can generate these files with this command: -# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt -# --------------------------------- - -# ----- Init Section ----- - - -include system.in.init - - -# ----- Atom Definition Section ----- - - -read_data system.data - - -# ----- Settings Section ----- - - -include system.in.settings - - -# ----- Run Section ----- - - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. - -minimize 1.0e-5 1.0e-7 100000 400000 - - -# -- simulation protocol -- - - -timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water -dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - -run 200000 - -write_data system_after_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also.) diff --git a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt b/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt deleted file mode 100644 index 4a74ecd318..0000000000 --- a/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt +++ /dev/null @@ -1,81 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# run.in.nvt -# -# -- Usage -- -# -# lmp_g++ -i run.in.nvt -# (assuming lmp_g++ is the name of your lammps binary) -# -# -- Prerequisite Input Files: -- -# systen.data, system.in.init, system.in.settings, system.in.sw -# system_after_npt.data -# -# You can generate these files using this procedure -# -# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt -# -# lmp_linux -i run.in.npt - -# --------------------------------- - - -# -- init section -- - - -include system.in.init - - - -# -- atom definition section -- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# -- settings section -- - - -include system.in.settings - - -# -- run section -- - - -timestep 2.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - -# The following commands are useful if you want to calculate the distribution -# of alkane-chain radius-of-gyration at a given temperature & pressure. -#compute cRg TraPPE gyration -#variable vRg equal c_cRg -#compute cPE all pe -#variable vPE equal c_cPE -#fix FprintPE all print 1000 "${vPE}" file U.dat -#fix FprintRg all print 1000 "${vRg}" file Rg.dat - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data -#thermo_modify flush yes - -restart 100000 restart_nvt - -run 1000000 - -write_data system_after_nvt.data - - diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt deleted file mode 100644 index b2996dab29..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README.txt +++ /dev/null @@ -1,11 +0,0 @@ -This is an example of all-atom methanol immersed in coarse grained ELBA water. -It was provided by Oscar Matus Rivas at McGill University. - - -References: -1. Orsi, Mario, Wei Ding, and Michail Palaiokostas. "Direct mixing of atomistic solutes and coarse-grained water." Journal of chemical theory and computation 10.10 (2014): 4684-4693. - -2. Orsi, Mario. "Comparative assessment of the ELBA coarse-grained model for water." Molecular Physics 112.11 (2014): 1566-1576. - -3. ELBA coarse-grained water model tutorial: -https://github.com/orsim/elba-lammps/tree/master/examples/water-bulk diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh deleted file mode 100644 index 91e79124e1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_run.sh +++ /dev/null @@ -1,20 +0,0 @@ -# --- Running LAMMPS --- -# -# The file "run.in.npt" is a LAMMPS -# input script which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - -lmp_mpi -i run.in.npt # simulation at constant pressure - -# (Note: The "lmp_mpi" program is also frequently called "lmp_ubuntu", -# and has many other names depending upon how it was compiled.) - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh deleted file mode 100755 index 20d5eac231..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ - -# Create the coordinates of the atoms using PACKMOL -cd packmol_files - - packmol < input.packmol - mv -f system.xyz ../moltemplate_files/ - -cd .. - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - moltemplate.sh -atomstyle "hybrid sphere dipole molecular" \ - -xyz system.xyz system.lt - - - # This will generate various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ system.xyz - -cd ../ - diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg deleted file mode 100644 index 88773055a1..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/images/ELBAwater+methanol_rendered_with_ovito.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt deleted file mode 100644 index e5a35fbfd9..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/elba.lt +++ /dev/null @@ -1,39 +0,0 @@ - -ElbaFF { - - write_once("Data Masses") { - @atom:W 18.0153 # Water - } - - write_once("In Settings") { - pair_coeff @atom:W @atom:W lj/sf/dipole/sf 0.55 3.05 - } - - # select the LAMMPS force field styles and other settings we will need - write_once("In Init") { - units real - atom_style hybrid sphere dipole molecular - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid harmonic - pair_style hybrid lj/sf/dipole/sf 12.0 lj/charmm/coul/long 11.0 12.0 - kspace_style pppm/cg 1.0e-5 - pair_modify mix arithmetic - special_bonds amber - } - -} # end of definition of "ElbaFF" - - -ElbaWater inherits ElbaFF { - - # atom-ID atom-Type x y z diameter density q mux muy muz molecule-ID - write("Data Atoms") { - $atom:id1 @atom:W 0.0 0.0 0.0 4.080749 0.5063179 0.0 0.541 0.0 0.0 $mol:. - } - - write_once("In Settings") { - group gElbaWater type @atom:W - } - -} # end of definition of "ElbaWater" diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt deleted file mode 100644 index 1d556ab13b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/methanol.lt +++ /dev/null @@ -1,84 +0,0 @@ -# This version of the methanol molecule uses the GAFF force -# field. (BCC) Charges were assigned using AmberTools - -Methanol { - - write_once("In Settings") { - pair_coeff @atom:type1 @atom:type1 lj/charmm/coul/long 0.2104000002486992 3.066473387458142 0.2104000002486992 3.066473387458142 - pair_coeff @atom:type2 @atom:type2 lj/charmm/coul/long 0.10939999991572773 3.399669508450741 0.10939999991572773 3.399669508450741 - pair_coeff @atom:type3 @atom:type3 lj/charmm/coul/long 0.01570000009846142 2.4713530426421655 0.01570000009846142 2.4713530426421655 - pair_coeff @atom:type4 @atom:type4 lj/charmm/coul/long 0.0 0.0 0.0 0.0 - } - - write_once("In Settings") { - bond_coeff @bond:type1 harmonic 316.7 1.4233 - bond_coeff @bond:type2 harmonic 371.4 0.973 - bond_coeff @bond:type3 harmonic 330.6 1.0969 - } - - write_once("In Settings") { - angle_coeff @angle:type1 harmonic 50.93 110.260047369346 - angle_coeff @angle:type2 harmonic 47.38 107.26004608361897 - angle_coeff @angle:type3 harmonic 39.24 108.46004659790978 - } - - write_once("In Settings") { - dihedral_coeff @dihedral:type1 harmonic 0.166666667 1 3 - } - - - ### DATA sections - - - write_once("Data Masses") { - @atom:type1 16.0 - @atom:type2 12.01 - @atom:type3 1.008 - @atom:type4 1.008 - } - - - # NOTE: This molecule uses atom_style hybrid sphere dipole molecular - # (This is the same atom_style used by ELBA.) Hence the extra - # columns for "diam", "mux", "muy", "muz" are not relevant - # for this molecule and can be ignored. - - write("Data Atoms") { - # atom-ID atom-Type x y z diam dens q mux muy muz molecule-ID - $atom:id1 @atom:type1 0.708 0.0 0.0 0.0 16.0 -0.598800 0.0 0.0 0.0 $mol:id0 - $atom:id2 @atom:type2 -0.708 0.0 0.0 0.0 12.01 0.116700 0.0 0.0 0.0 $mol:id0 - $atom:id3 @atom:type3 -1.073 -0.769 0.685 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 - $atom:id4 @atom:type3 -1.073 -0.195 -1.011 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 - $atom:id5 @atom:type3 -1.063 0.979 0.331 0.0 1.008 0.028700 0.0 0.0 0.0 $mol:id0 - $atom:id6 @atom:type4 0.994 -0.88 -0.298 0.0 1.008 0.396000 0.0 0.0 0.0 $mol:id0 - } - - write("Data Bonds") { - $bond:id1 @bond:type2 $atom:id1 $atom:id6 - $bond:id2 @bond:type3 $atom:id2 $atom:id3 - $bond:id3 @bond:type3 $atom:id2 $atom:id4 - $bond:id4 @bond:type3 $atom:id2 $atom:id5 - $bond:id5 @bond:type1 $atom:id1 $atom:id2 - } - - write("Data Angles") { - $angle:id1 @angle:type1 $atom:id1 $atom:id2 $atom:id3 - $angle:id2 @angle:type1 $atom:id1 $atom:id2 $atom:id4 - $angle:id3 @angle:type1 $atom:id1 $atom:id2 $atom:id5 - $angle:id4 @angle:type2 $atom:id2 $atom:id1 $atom:id6 - $angle:id5 @angle:type3 $atom:id3 $atom:id2 $atom:id4 - $angle:id6 @angle:type3 $atom:id3 $atom:id2 $atom:id5 - $angle:id7 @angle:type3 $atom:id4 $atom:id2 $atom:id5 - } - - write("Data Dihedrals") { - $dihedral:id1 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id3 - $dihedral:id2 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id4 - $dihedral:id3 @dihedral:type1 $atom:id6 $atom:id1 $atom:id2 $atom:id5 - } - - write_once("In Settings") { - group gMethanol type @atom:type1 @atom:type2 @atom:type3 @atom:type4 - } - -} # end of "Methanol" type definition diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt deleted file mode 100644 index 1a077a92f1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/moltemplate_files/system.lt +++ /dev/null @@ -1,29 +0,0 @@ -import "methanol.lt" - -import "elba.lt" - -write_once("Data Boundary") { - -15.5 15.5 xlo xhi - -15.5 15.5 ylo yhi - -15.5 15.5 zlo zhi -} - -solute = new Methanol [1] - -solvent = new ElbaWater [1000] - -# Lorentz-Berthelot mixing -write_once("In Settings") { - pair_coeff @atom:Methanol/type1 @atom:Methanol/type2 lj/charmm/coul/long 0.151716 3.233071 0.151716 3.233071 - pair_coeff @atom:Methanol/type1 @atom:Methanol/type3 lj/charmm/coul/long 0.057474 2.768913 0.057474 2.768913 - pair_coeff @atom:Methanol/type1 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.533237 0.000000 1.533237 - pair_coeff @atom:Methanol/type1 @atom:ElbaFF/W lj/sf/dipole/sf 0.340176 3.058237 - pair_coeff @atom:Methanol/type2 @atom:Methanol/type3 lj/charmm/coul/long 0.041444 2.935511 0.041444 2.935511 - pair_coeff @atom:Methanol/type2 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.699835 0.000000 1.699835 - pair_coeff @atom:Methanol/type2 @atom:ElbaFF/W lj/sf/dipole/sf 0.245296 3.224835 - pair_coeff @atom:Methanol/type3 @atom:Methanol/type4 lj/charmm/coul/long 0.000000 1.235677 0.000000 1.235677 - pair_coeff @atom:Methanol/type3 @atom:ElbaFF/W lj/sf/dipole/sf 0.092925 2.760677 - pair_coeff @atom:Methanol/type4 @atom:ElbaFF/W lj/sf/dipole/sf 0.000000 1.525000 -} - -} diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt deleted file mode 100644 index 3d310d44d3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/README.txt +++ /dev/null @@ -1,12 +0,0 @@ -Packmol is a program that generates non-overlapping atomic coordinates for -mixtures of molecules. - -Usage: - - packmol < input.packmol - -Ouput: - - system.xyz - -(a file containing the coordinates of all of the molecules packed together.) diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz deleted file mode 100644 index fc495c0564..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/coord.xyz +++ /dev/null @@ -1,1008 +0,0 @@ - 1006 - Built with Packmol - O 1.077217 0.144250 0.048817 - C -0.338583 0.144250 0.048817 - H -0.703883 -0.624750 0.734017 - H -0.703783 -0.050450 -0.962483 - H -0.693883 1.122850 0.380017 - H 1.362917 -0.736150 -0.249183 - OW -1.412297 -7.446504 10.904602 - OW 4.452292 7.235571 -6.250955 - OW -6.020558 -4.280954 1.868432 - OW -5.179618 11.632347 -13.999700 - OW 3.301355 8.558586 5.180801 - OW -12.174570 -4.025488 11.826522 - OW -12.212121 7.659684 7.004107 - OW 12.507397 4.123302 -9.139812 - OW -4.390714 -13.339157 -13.935723 - OW -2.347127 -13.464377 -11.186378 - OW -0.390430 -4.494023 -0.873365 - OW 12.653213 11.245608 -10.879975 - OW 10.928733 -0.256067 -13.979839 - OW 3.113899 10.464514 7.381244 - OW 6.444145 7.878126 9.347764 - OW 13.995822 10.713223 -2.070525 - OW -5.824617 -5.506497 5.519803 - OW 13.421557 7.738992 -11.788954 - OW 6.168350 10.067253 -13.538591 - OW -0.045394 -7.883676 -11.050038 - OW -3.936470 2.908840 -9.461076 - OW -4.549773 13.172554 -11.300363 - OW -5.580400 2.956314 4.820040 - OW 11.434233 -11.982027 13.827720 - OW 7.091228 7.641158 6.689051 - OW -1.871254 8.389547 -14.001775 - OW 2.119354 4.690267 5.686549 - OW -3.541398 -12.042127 -0.197612 - OW 6.900566 8.166603 -0.762935 - OW -2.817436 -12.543902 -4.403389 - OW 11.377874 11.322904 6.601112 - OW -12.836109 -1.875201 8.127625 - OW 5.672028 12.401154 -8.459143 - OW 7.430035 3.240706 -1.450096 - OW -10.038995 -2.292621 -7.235657 - OW -0.218358 -14.000125 -13.132499 - OW 6.332077 8.585353 -11.008466 - OW 10.567812 12.324117 12.601731 - OW 2.132468 -10.209125 -5.560252 - OW 6.914302 3.158258 -5.462909 - OW 2.241182 -10.532752 2.836470 - OW 9.635500 9.933016 13.781636 - OW -4.708872 2.474080 13.999972 - OW 7.469570 -2.650997 -3.855276 - OW -1.785179 -2.947809 -11.955006 - OW -3.182880 7.924869 5.582130 - OW -10.963632 -6.890214 1.596607 - OW -7.601594 -13.998048 11.439208 - OW 13.867823 1.437609 9.958940 - OW 7.010889 -1.261509 6.040167 - OW 3.088922 0.408610 -4.511697 - OW 7.180459 4.012658 13.073386 - OW 13.998578 -8.166874 -10.383155 - OW -6.177568 -7.960618 6.710820 - OW -0.448222 10.484860 9.868052 - OW 5.978025 11.555205 8.681871 - OW 0.540473 9.289780 -8.581696 - OW -1.754998 -13.998344 4.024525 - OW -3.574741 2.151926 11.515749 - OW -13.988996 3.004087 5.767812 - OW -13.223941 9.959500 10.674000 - OW -7.944482 -12.350002 8.700562 - OW -3.825796 6.104725 -10.176144 - OW -8.249098 -11.727255 -3.894413 - OW -3.839773 10.822793 -2.561436 - OW -0.022941 -1.585678 -6.872414 - OW 10.753131 1.256594 1.994780 - OW -0.641529 -4.772826 11.794099 - OW 10.903997 -13.999524 1.480173 - OW -6.220238 -7.278258 3.458533 - OW 9.223878 -13.995048 6.688774 - OW -13.999693 5.714904 6.228812 - OW -7.732501 1.681527 3.562151 - OW -10.154518 -3.876261 -2.168790 - OW 10.113875 6.637798 -3.816278 - OW 2.109401 2.517593 13.340956 - OW 0.853589 2.721590 7.292615 - OW -10.758243 1.342025 9.200936 - OW 13.998782 1.450435 -0.982643 - OW 0.749056 5.408736 3.259202 - OW -13.945043 -4.717521 -13.218608 - OW -9.974815 4.688036 -8.922533 - OW 2.648123 1.662568 -7.792379 - OW -4.060440 -2.171149 2.430150 - OW 6.659202 -11.565822 2.502042 - OW 10.613702 12.363202 4.185430 - OW 9.743672 10.512624 -0.600977 - OW 1.752790 -4.833507 4.027928 - OW -4.885400 8.260226 -2.754463 - OW 8.769009 1.053307 5.248508 - OW 7.771876 11.964858 12.793976 - OW -0.354292 11.533225 -6.820807 - OW 12.431203 -11.294337 6.476258 - OW 11.787631 2.944158 11.056967 - OW 4.725230 -11.753600 7.739280 - OW 13.984207 -4.047093 -11.497797 - OW -4.189502 -5.938038 -7.171294 - OW 9.154839 4.748747 -5.568048 - OW 13.999368 -6.874417 12.857476 - OW 5.764184 -14.000737 8.943560 - OW -11.679127 7.841006 9.853676 - OW 5.855922 -7.323640 8.144783 - OW -0.856467 -13.999217 -8.938668 - OW -1.510832 -6.867279 -8.407693 - OW 13.057644 13.993825 4.399118 - OW 12.245484 13.999382 7.058515 - OW 12.491779 -1.199806 -8.167213 - OW 12.227457 8.116886 -4.773668 - OW -7.295620 -6.141930 10.603053 - OW -8.339049 9.466253 -7.439146 - OW -13.994744 6.725998 8.878174 - OW 10.731737 -11.109604 4.322355 - OW 9.315062 -13.996962 10.025622 - OW -5.203478 -11.084016 -9.996006 - OW -11.234152 7.158703 -10.562518 - OW 7.281894 -2.368904 -11.196682 - OW 8.243298 -11.965867 5.113684 - OW 3.631637 -11.535788 -7.444179 - OW -6.915922 6.611712 -7.091841 - OW -4.424692 -3.527799 6.816775 - OW -11.447203 -9.097963 3.158769 - OW -13.999027 -9.212939 12.350423 - OW -4.514890 13.342819 -0.340089 - OW 2.190372 8.072372 2.375695 - OW 9.737678 -9.483691 13.998301 - OW -4.918463 -9.944898 9.666069 - OW -8.534034 0.453217 7.268876 - OW 9.386532 -9.668250 10.400223 - OW -2.933913 -12.888900 12.505280 - OW 13.259195 11.339162 10.784140 - OW 2.788170 -0.644772 10.227169 - OW -7.977370 6.527205 -13.581637 - OW 11.391197 9.039117 1.030315 - OW -4.128507 -0.438343 12.247371 - OW -13.998899 3.852881 8.382207 - OW 14.001469 3.211643 -3.879073 - OW 0.097779 -9.682666 -0.976412 - OW -13.673484 10.846509 7.347071 - OW -2.578592 10.316648 4.364568 - OW 2.940164 -11.184188 -10.912565 - OW 7.544534 4.210972 -13.516515 - OW 3.331310 4.845755 -7.023535 - OW -2.626270 13.091969 9.430091 - 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OW -7.195577 -6.976201 -5.299771 - OW 5.870064 -11.282885 -9.971276 - OW -5.633981 8.452908 4.455279 - OW 8.991048 -2.573175 -7.911399 - OW -10.978209 -1.133653 -11.320642 - OW -13.028980 -4.572247 6.526645 - OW -11.916202 6.703233 4.334316 - OW 3.573667 6.353047 8.225506 - OW -12.050997 4.450930 -7.134920 - OW 0.957895 -3.518908 -10.803105 - OW -13.920213 -10.600014 -7.734417 - OW 13.995643 0.606674 6.762347 - OW -11.075273 0.590448 6.225712 - OW 5.275710 -9.971316 -3.892260 - OW -11.527104 0.245516 11.861492 - OW -1.747353 -4.627752 1.775315 - OW 13.440927 -7.239370 -7.859647 - OW 5.734642 0.582466 -1.372705 - OW 0.665369 9.291919 -13.444192 - OW -5.758073 -8.210381 -7.593076 - OW -1.997570 11.697927 -0.661254 - OW -3.135579 10.046901 -5.121617 - OW 11.791809 -5.933214 7.596812 - OW 7.815492 1.001428 -9.412914 - OW -13.535245 -11.141362 0.465505 diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/elba_water.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/elba_water.xyz deleted file mode 100644 index 3ed22d1fad..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/elba_water.xyz +++ /dev/null @@ -1,4 +0,0 @@ -1 - - OW 0.000000 0.000000 0.000000 - diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol deleted file mode 100644 index 9c640263d9..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/input.packmol +++ /dev/null @@ -1,17 +0,0 @@ -tolerance 2.5 -filetype xyz -output system.xyz - -# Methanol -structure methanol.xyz - number 1 - center - fixed 0. 0. 0. 0. 0. 0. -end structure - -# ELBA Solvent -structure elba_water.xyz - number 1000 - inside box -14.0 -14.0 -14.0 14.0 14.0 14.0 -end structure - diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz deleted file mode 100644 index b06d93fa5f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/packmol_files/methanol.xyz +++ /dev/null @@ -1,8 +0,0 @@ -6 - -O 0.70790 0.00000 0.00000 -C -0.70790 0.00000 0.00000 -H -1.07320 -0.76900 0.68520 -H -1.07310 -0.19470 -1.01130 -H -1.06320 0.97860 0.33120 -H 0.99360 -0.88040 -0.29800 diff --git a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt b/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt deleted file mode 100644 index ad8076d7fd..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ELBAwater+methanol/run.in.npt +++ /dev/null @@ -1,54 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh (& packmol?) to create 3 files: -# system.data system.in.init system.in.settings -# -# See "README_setup.sh" for instructions how to use moltemplate.sh -# Note: This input script file only covers equilibration of the system. -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -# (Groups "gElbaWater" and "gMethanol" are defined in "system.in.settings" -# Rename them to "gSolvent" and "gSolute") -group gSolvent union gElbaWater gElbaWater -group gSolute union gMethanol gMethanol - -# Randomize the direction of the solvent dipoles -set group gSolvent dipole/random 9876 0.541 - -velocity all create 298.0 9876 - -neighbor 1.0 bin -neigh_modify every 1 delay 0 check yes - -timestep 2.0 - -fix 1 gSolute nve # integrate gSolute -fix 2 gSolvent nve/sphere update dipole # integrate gSolvent -fix 3 gSolute langevin 298.0 298.0 1000 9876 # thermostat gSolute -fix 4 gSolvent langevin 298.0 298.0 1000 9876 omega yes zero yes # thermostat gSolvent -fix 5 all press/berendsen iso 1.0 1.0 1000 modulus 21740 # barostat -fix 6 all momentum 500 linear 1 1 1 -fix 7 gSolute shake 1.0e-6 100 0 m 1.0 - -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z mux muy muz ix iy iz - -thermo_style custom step temp etotal pe epair press -thermo_modify norm yes flush yes -thermo 100 - -run 10000 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README.txt deleted file mode 100644 index fe92ffeaf3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README.txt +++ /dev/null @@ -1,18 +0,0 @@ - -This example of the formation of a coarse-grained DOPC lipid-bilayer uses the -Martini force-field v2.0 (2013-10), was provided by Saeed Momeni Bashusqeh. -It's probably a good idea to run the simulation for a few ns to allow the -lipids to reorient themselves. - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh - -------- CITE ----------------------------- -NOTE: We extracted the parameters in the MARTINI force field from the files -distributed with the "EMC" tool. If you use these .lt files, please also cite: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358. diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_remove_irrelevant_info.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_remove_irrelevant_info.sh deleted file mode 100755 index 5957289da9..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_remove_irrelevant_info.sh +++ /dev/null @@ -1,8 +0,0 @@ - -# Note: By default, the system.data and system.in.settings files contain -# extra information for atoms defined in OPLSAA which you are not using -# in this simulation. -# This is harmless, but if you to delete this information from your -# system.in.settings and system.in.data files, run this script: - -cleanup_moltemplate.sh diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_run.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_run.sh deleted file mode 100755 index 65213b0963..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# --- Running LAMMPS --- -# -------- PREREQUISITES: -------- -# The 2 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.npt # simulation at constant pressure -lmp_mpi -i run.in.nvt # simulation at constant volume - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_setup.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_visualize.txt deleted file mode 100644 index e8ad744015..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 -0.5} - pbc box -shiftcenterrel {0.0 0.0 -0.5} -style tubes -width 0.75 - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/DOPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/DOPC.lt deleted file mode 100644 index 00a4ed7e7c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/DOPC.lt +++ /dev/null @@ -1,39 +0,0 @@ -import "martini.lt" #(This file is located in moltemplate/force_fields/) - -DOPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.596 0.518 2.453 - $atom:PO4 $mol:. @atom:Qa -1.0 0.413 0.591 2.167 - $atom:GL1 $mol:. @atom:Na 0.0 0.525 0.626 1.829 - $atom:GL2 $mol:. @atom:Na 0.0 0.749 0.434 1.795 - $atom:C1A $mol:. @atom:C1 0.0 0.428 0.686 1.448 - $atom:D2A $mol:. @atom:C3 0.0 0.395 0.491 1.197 - $atom:C3A $mol:. @atom:C1 0.0 0.389 0.575 0.899 - $atom:C4A $mol:. @atom:C1 0.0 0.423 0.497 0.555 - $atom:C1B $mol:. @atom:C1 0.0 0.944 0.505 1.503 - $atom:D2B $mol:. @atom:C3 0.0 0.906 0.476 1.192 - $atom:C3B $mol:. @atom:C1 0.0 0.899 0.567 0.905 - $atom:C4B $mol:. @atom:C1 0.0 0.921 0.637 0.557 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:D2B - $bond:b12 $atom:D2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } -} -DOPC.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DOPC.move(-6.32333,-5.5025,-3.2) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/system.lt deleted file mode 100644 index 4e16407821..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/system.lt +++ /dev/null @@ -1,21 +0,0 @@ -import "martini.lt" #(This file is located in moltemplate/force_fields/) -import "water.lt" -import "DOPC.lt" - -lipids = new DOPC [12].move(8.333, 0, 0) - [12].move(0, 8.333, 0) - [2].rot(180, 1, 0, 0) - -waters = new MW [24].move(4.1667, 0, 0) - [24].move(0, 4.1667, 0) - [10].move(0, 0, 4.54) - -# Move the waters upwards so that they don't overlap with the lipids. - -waters[*][*][*].move(0, 0, 28.5) - -write_once("Data Boundary") { - 0.0 100 xlo xhi - 0.0 100 ylo yhi - -50 50 zlo zhi -} diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/water.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/water.lt deleted file mode 100644 index 6513d83413..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/moltemplate_files/water.lt +++ /dev/null @@ -1,10 +0,0 @@ -import "martini.lt" - -#water molecules in MARTINI contain only one particle - -MW inherits MARTINI { - #AtomID MolID AtomType Charge x y z - write("Data Atoms") { - $atom $mol @atom:P4 0 0 0 0 - } -} diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt deleted file mode 100644 index c61369a225..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/README.txt +++ /dev/null @@ -1,8 +0,0 @@ -You can use packmol to create a file containing the atomic coordinates -for a system of coarse-grained lipids mixed with water using this command: - -If it takes too long for packmol to run, try lowering the tolerance. -(tolerance 2.0 should work) - -packmol < mix_lipids+water.inp - diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz deleted file mode 100644 index 7caffdc159..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/dopc.xyz +++ /dev/null @@ -1,14 +0,0 @@ -12 - DOPC -Q0 0.596 0.518 2.453 -Qa 0.413 0.591 2.167 -Na 0.525 0.626 1.829 -Na 0.749 0.434 1.795 -C1 0.428 0.686 1.448 -C3 0.395 0.491 1.197 -C1 0.389 0.575 0.899 -C1 0.423 0.497 0.555 -C1 0.944 0.505 1.503 -C3 0.906 0.476 1.192 -C1 0.899 0.567 0.905 -C1 0.921 0.637 0.557 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp deleted file mode 100644 index 9e1388a137..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/mix_lipids+water.inp +++ /dev/null @@ -1,35 +0,0 @@ -# -# A mixture of coarse-grained (martini) DPPC (lipid) and water. -# - -# All the atoms from diferent molecules will be separated at least 3.0 -# Anstroms at the solution. - -tolerance 3.0 # minimal distance between atoms in different molecules - # (you should also consider changing the "discale" - # parameter. I think discale=1.0 by default.) - -seed 12345 # seed for random number generator - -# The file type of input and output files is XYZ - -filetype xyz - -# The name of the output file - -output system.xyz - -# DPPC (lipid) molecules and water molecules will be put in a box -# defined by the minimum coordinates x, y and z = 0 0 0. and maximum -# coordinates 100 100 100. (Box size: 100x100x100) - -structure dopc.xyz - number 300 - inside box 0.0 0.0 0.0 100.0 100.0 100.0 -end structure - -structure water.xyz - number 6000 - inside box 0.0 0.0 0.0 100.0 100.0 100.0 -end structure - diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz deleted file mode 100644 index 84fe1f74c2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/packmol_files/water.xyz +++ /dev/null @@ -1,3 +0,0 @@ -1 - water -W 0 0 0 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.min b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.min deleted file mode 100644 index 360ded2373..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.min +++ /dev/null @@ -1,30 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -thermo 5 -thermo_style custom step temp pe etotal epair ebond eangle -dump 1 all custom 1000 traj_min.lammpstrj id mol type x y z ix iy iz -min_style sd -min_modify dmax 0.1 -minimize 1.0e-4 1.0e-6 100000 400000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.npt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.npt deleted file mode 100644 index 0967272ffe..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.npt +++ /dev/null @@ -1,80 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) -# 2) You must minimize the coordinates using by running lammps witn -# run.in.min -# - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -#read_data "system.data" -read_data "system_after_min.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -print "---------------------------------------------------------------------------" -print "I often use Langevin dynamics initially at high temperatures and small" -print "timesteps to relax the system. It seems more stable than Nose-Hoover." -print "(This is probably not necessary.)" -print "---------------------------------------------------------------------------" - -#(first, a short run at NVT conditions, to randomize the waters) - -fix fxlan all langevin 450.0 450.0 100 12345 # temp: 450 K -fix fxnve all nve -thermo 100 -thermo_style custom step temp pe press vol etotal epair ebond eangle -dump dmNPTall all custom 5000 traj_npt_step1.lammpstrj id mol type x y z ix iy iz - -timestep 1.0 # (safer to use a small timestep initially) -run 1000 -timestep 3.0 -run 1000 -timestep 10.0 -run 1000 -timestep 30.0 # (40.0 should be possible for lipid systems) -run 20000 - -unfix fxnve -fix fxnph all nph aniso 200.0 200.0 1000.0 couple xy drag 1.0 #pressure:200barr -timestep 1.0 # (safer to use a small timestep initially) -run 1000 -timestep 3.0 -run 1000 -timestep 10.0 -run 1000 -timestep 30.0 # (40.0 should be possible for lipid systems) -run 100000 - -unfix fxlan -unfix fxnph -undump dmNPTall - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" - -velocity all zero linear # <- eliminate drift due to non-zero total momentum - #fix 1 all momentum 1000 linear 1 1 1 # also works - -# temperature: 300 K, pressure: 1 barr -fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0 couple xy -thermo 100 -#thermo_modify flush yes -dump dmNPTall all custom 10000 traj_npt_step2.lammpstrj id mol type x y z ix iy iz - -run 100000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.nvt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.nvt deleted file mode 100644 index 4653fefe67..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/DOPC_bilayer_example/run.in.nvt +++ /dev/null @@ -1,48 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) -# 2) You must minimize the coordinates using by running lammps witn -# run.in.min -# 3) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier simulation - -#read_data "system.data" -#read_data "system_after_min.data" -read_data "system_after_npt.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -velocity all zero linear # <- eliminate drift due to non-zero total momentum - #fix 1 all momentum 1000 linear 1 1 1 # also works - -timestep 30.0 # (40.0 should be possible for lipid systems) -dump 1 all custom 20000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 100 -thermo_style custom step temp pe etotal epair ebond eangle -#thermo_modify flush yes - -run 10000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/BOLA.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/BOLA.lt deleted file mode 100644 index 46e8bd572e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/BOLA.lt +++ /dev/null @@ -1,67 +0,0 @@ -import "martini.lt" - -BOLA inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - # (guessing the coordinates, and scaling them manually) - write('Data Atoms') { - $atom:NC1 $mol:. @atom:Q0 1.0 0.000000 0.000000 6.000000 - $atom:PO1 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C3A $mol:. @atom:C1 0.0 0.000000 -1.000000 2.000000 - $atom:C4A $mol:. @atom:C1 0.0 0.000000 -1.000000 1.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - $atom:C3B $mol:. @atom:C1 0.0 0.000000 1.000000 1.000000 - $atom:C4B $mol:. @atom:C1 0.0 0.000000 1.000000 0.000000 - $atom:NC2 $mol:. @atom:Q0 1.0 1.000000 0.000000 6.000000 - $atom:PO2 $mol:. @atom:Qa -1.0 1.000000 0.000000 5.000000 - $atom:GL3 $mol:. @atom:Na 0.0 1.000000 0.000000 4.000000 - $atom:GL4 $mol:. @atom:Na 0.0 1.000000 1.000000 4.000000 - $atom:C1C $mol:. @atom:C1 0.0 1.000000 -1.000000 4.000000 - $atom:C2C $mol:. @atom:C1 0.0 1.000000 -1.000000 3.000000 - $atom:C3C $mol:. @atom:C1 0.0 1.000000 -1.000000 2.000000 - $atom:C4C $mol:. @atom:C1 0.0 1.000000 -1.000000 1.000000 - $atom:C1D $mol:. @atom:C1 0.0 1.000000 1.000000 3.000000 - $atom:C2D $mol:. @atom:C1 0.0 1.000000 1.000000 2.000000 - $atom:C3D $mol:. @atom:C1 0.0 1.000000 1.000000 1.000000 - $atom:C4D $mol:. @atom:C1 0.0 1.000000 1.000000 0.000000 - - } - - write('Data Bond List') { - $bond:b1 $atom:NC1 $atom:PO1 - $bond:b2 $atom:PO1 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b7 $atom:C3A $atom:C4A - $bond:b8 $atom:GL2 $atom:C1B - $bond:b9 $atom:C1B $atom:C2B - $bond:b10 $atom:C2B $atom:C3B - $bond:b11 $atom:C3B $atom:C4B - $bond:b12 $atom:NC2 $atom:PO2 - $bond:b13 $atom:PO2 $atom:GL3 - $bond:b14 $atom:GL3 $atom:GL4 - $bond:b15 $atom:GL3 $atom:C1C - $bond:b16 $atom:C1C $atom:C2C - $bond:b17 $atom:C2C $atom:C3C - $bond:b18 $atom:C3C $atom:C4C - $bond:b19 $atom:GL4 $atom:C1D - $bond:b20 $atom:C1D $atom:C2D - $bond:b21 $atom:C2D $atom:C3D - $bond:b22 $atom:C3D $atom:C4D - $bond:b23 $atom:C4A $atom:C4C - $bond:b24 $atom:C4B $atom:C4D - } - -} -BOLA.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -BOLA.move(-5,-0.833333,2.35).rot(-45.0,0,0,1) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/BOLB.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/BOLB.lt deleted file mode 100644 index 8d4fbc3ac7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/BOLB.lt +++ /dev/null @@ -1,66 +0,0 @@ -import "martini.lt" - -BOLB inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - # (guessing the coordinates, and scaling them manually) - write('Data Atoms') { - $atom:NC1 $mol:. @atom:Q0 1.0 0.000000 0.000000 6.000000 - $atom:PO1 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C3A $mol:. @atom:C1 0.0 0.000000 -1.000000 2.000000 - $atom:C4A $mol:. @atom:C1 0.0 0.000000 -1.000000 1.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - $atom:C3B $mol:. @atom:C1 0.0 0.000000 1.000000 1.000000 - $atom:C4B $mol:. @atom:C1 0.0 0.000000 1.000000 0.000000 - $atom:NC2 $mol:. @atom:Q0 1.0 1.000000 0.000000 6.000000 - $atom:PO2 $mol:. @atom:Qa -1.0 1.000000 0.000000 5.000000 - $atom:GL3 $mol:. @atom:Na 0.0 1.000000 0.000000 4.000000 - $atom:GL4 $mol:. @atom:Na 0.0 1.000000 1.000000 4.000000 - $atom:C1C $mol:. @atom:C1 0.0 1.000000 -1.000000 4.000000 - $atom:C2C $mol:. @atom:C1 0.0 1.000000 -1.000000 3.000000 - $atom:C3C $mol:. @atom:C1 0.0 1.000000 -1.000000 2.000000 - $atom:C4C $mol:. @atom:C1 0.0 1.000000 -1.000000 1.000000 - $atom:C1D $mol:. @atom:C1 0.0 1.000000 1.000000 3.000000 - $atom:C2D $mol:. @atom:C1 0.0 1.000000 1.000000 2.000000 - $atom:C3D $mol:. @atom:C1 0.0 1.000000 1.000000 1.000000 - $atom:C4D $mol:. @atom:C1 0.0 1.000000 1.000000 0.000000 - - } - - write('Data Bond List') { - $bond:b1 $atom:NC1 $atom:PO1 - $bond:b2 $atom:PO1 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b7 $atom:C3A $atom:C4A - $bond:b8 $atom:GL2 $atom:C1B - $bond:b9 $atom:C1B $atom:C2B - $bond:b10 $atom:C2B $atom:C3B - $bond:b11 $atom:C3B $atom:C4B - $bond:b12 $atom:NC2 $atom:PO2 - $bond:b13 $atom:PO2 $atom:GL3 - $bond:b14 $atom:GL3 $atom:GL4 - $bond:b15 $atom:GL3 $atom:C1C - $bond:b16 $atom:C1C $atom:C2C - $bond:b17 $atom:C2C $atom:C3C - $bond:b18 $atom:C3C $atom:C4C - $bond:b19 $atom:GL4 $atom:C1D - $bond:b20 $atom:C1D $atom:C2D - $bond:b21 $atom:C2D $atom:C3D - $bond:b22 $atom:C3D $atom:C4D - $bond:b23 $atom:C4A $atom:C4C - } - -} -BOLB.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -BOLB.move(-2.35,-0.391667,2.35).rot(-45.0,0,0,1) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DAPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DAPC.lt deleted file mode 100644 index d5f7370756..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DAPC.lt +++ /dev/null @@ -1,44 +0,0 @@ -import "martini.lt" - -DAPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.566 0.559 2.614 - $atom:PO4 $mol:. @atom:Qa -1.0 0.464 0.444 2.297 - $atom:GL1 $mol:. @atom:Na 0.0 0.486 0.539 1.967 - $atom:GL2 $mol:. @atom:Na 0.0 0.766 0.678 1.938 - $atom:D1A $mol:. @atom:C4 0.0 0.360 0.508 1.627 - $atom:D2A $mol:. @atom:C4 0.0 0.446 0.509 1.339 - $atom:D3A $mol:. @atom:C4 0.0 0.422 0.485 1.047 - $atom:D4A $mol:. @atom:C4 0.0 0.474 0.570 0.752 - $atom:C5A $mol:. @atom:C1 0.0 0.390 0.478 0.404 - $atom:D1B $mol:. @atom:C4 0.0 0.917 0.470 1.666 - $atom:D2B $mol:. @atom:C4 0.0 0.937 0.498 1.346 - $atom:D3B $mol:. @atom:C4 0.0 0.920 0.584 1.055 - $atom:D4B $mol:. @atom:C4 0.0 0.975 0.647 0.749 - $atom:C5B $mol:. @atom:C1 0.0 0.898 0.557 0.399 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:D1A - $bond:b5 $atom:D1A $atom:D2A - $bond:b6 $atom:D2A $atom:D3A - $bond:b7 $atom:D3A $atom:D4A - $bond:b8 $atom:D4A $atom:C5A - $bond:b9 $atom:GL2 $atom:D1B - $bond:b10 $atom:D1B $atom:D2B - $bond:b11 $atom:D2B $atom:D3B - $bond:b12 $atom:D3B $atom:D4B - $bond:b13 $atom:D4B $atom:C5B - } - -} -DAPC.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DAPC.move(-6.44357,-5.37571,-1.64) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DHPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DHPC.lt deleted file mode 100644 index 75b77b17e8..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DHPC.lt +++ /dev/null @@ -1,32 +0,0 @@ -import "martini.lt" - -DHPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.000000 0.000000 6.000000 - $atom:PO4 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:GL2 $atom:C1B - $bond:b7 $atom:C1B $atom:C2B - } - -} -DHPC.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DHPC.move(-0,-0.5875,-7.65).rot(-30.0,0,0,1) \ No newline at end of file diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DHPE.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DHPE.lt deleted file mode 100644 index a27af13a44..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DHPE.lt +++ /dev/null @@ -1,33 +0,0 @@ -import "martini.lt" - -DHPE inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - # (guessing the coordinates, and scaling them manually) - write('Data Atoms') { - $atom:NH3 $mol:. @atom:Qd 1.0 0.000000 0.000000 6.000000 - $atom:PO4 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - } - - write('Data Bond List') { - $bond:b1 $atom:NH3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:GL2 $atom:C1B - $bond:b7 $atom:C1B $atom:C2B - } - -} -DHPE.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DHPE.move(-0,-0.5875,-7.15).rot(-30.0,0,0,1) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DLPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DLPC.lt deleted file mode 100644 index be3f261416..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DLPC.lt +++ /dev/null @@ -1,36 +0,0 @@ -import "martini.lt" - -DLPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.556 0.486 2.340 - $atom:PO4 $mol:. @atom:Qa -1.0 0.522 0.626 2.022 - $atom:GL1 $mol:. @atom:Na 0.0 0.484 0.520 1.678 - $atom:GL2 $mol:. @atom:Na 0.0 0.793 0.572 1.640 - $atom:C1A $mol:. @atom:C1 0.0 0.415 0.488 1.322 - $atom:C2A $mol:. @atom:C1 0.0 0.388 0.510 1.025 - $atom:C3A $mol:. @atom:C1 0.0 0.395 0.529 0.684 - $atom:C1B $mol:. @atom:C1 0.0 0.959 0.570 1.354 - $atom:C2B $mol:. @atom:C1 0.0 0.885 0.638 1.043 - $atom:C3B $mol:. @atom:C1 0.0 0.911 0.531 0.691 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:GL2 $atom:C1B - $bond:b10 $atom:C1B $atom:C2B - $bond:b11 $atom:C2B $atom:C3B - } - -} -DLPC.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DLPC.move(-6.308,-5.47,-4.49) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DLPE.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DLPE.lt deleted file mode 100644 index 08ce4b1d64..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DLPE.lt +++ /dev/null @@ -1,36 +0,0 @@ -import "martini.lt" - -DLPE inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NH3 $mol:. @atom:Qd 1.0 0.523 0.508 2.312 - $atom:PO4 $mol:. @atom:Qa -1.0 0.457 0.463 2.011 - $atom:GL1 $mol:. @atom:Na 0.0 0.535 0.471 1.678 - $atom:GL2 $mol:. @atom:Na 0.0 0.755 0.669 1.650 - $atom:C1A $mol:. @atom:C1 0.0 0.393 0.605 1.310 - $atom:C2A $mol:. @atom:C1 0.0 0.413 0.565 1.032 - $atom:C3A $mol:. @atom:C1 0.0 0.436 0.548 0.704 - $atom:C1B $mol:. @atom:C1 0.0 0.933 0.534 1.346 - $atom:C2B $mol:. @atom:C1 0.0 0.917 0.629 1.043 - $atom:C3B $mol:. @atom:C1 0.0 0.945 0.494 0.714 - } - - write('Data Bond List') { - $bond:b1 $atom:NH3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:GL2 $atom:C1B - $bond:b10 $atom:C1B $atom:C2B - $bond:b11 $atom:C2B $atom:C3B - } - -} -DLPE.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DLPE.move(-6.307,-5.486,-4.69) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPC.lt deleted file mode 100644 index fdc5af63c1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPC.lt +++ /dev/null @@ -1,39 +0,0 @@ -import "martini.lt" - -DOPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.596 0.518 2.453 - $atom:PO4 $mol:. @atom:Qa -1.0 0.413 0.591 2.167 - $atom:GL1 $mol:. @atom:Na 0.0 0.525 0.626 1.829 - $atom:GL2 $mol:. @atom:Na 0.0 0.749 0.434 1.795 - $atom:C1A $mol:. @atom:C1 0.0 0.428 0.686 1.448 - $atom:D2A $mol:. @atom:C3 0.0 0.395 0.491 1.197 - $atom:C3A $mol:. @atom:C1 0.0 0.389 0.575 0.899 - $atom:C4A $mol:. @atom:C1 0.0 0.423 0.497 0.555 - $atom:C1B $mol:. @atom:C1 0.0 0.944 0.505 1.503 - $atom:D2B $mol:. @atom:C3 0.0 0.906 0.476 1.192 - $atom:C3B $mol:. @atom:C1 0.0 0.899 0.567 0.905 - $atom:C4B $mol:. @atom:C1 0.0 0.921 0.637 0.557 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:D2B - $bond:b12 $atom:D2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } -} -DOPC.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DOPC.move(-6.32333,-5.5025,-3.2) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPE.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPE.lt deleted file mode 100644 index 1c30e3271c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPE.lt +++ /dev/null @@ -1,36 +0,0 @@ -import "martini.lt" - -DOPE inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NH3 $mol:. @atom:Qd 1.0 0.551 0.470 2.458 - $atom:PO4 $mol:. @atom:Qa -1.0 0.546 0.626 2.182 - $atom:GL1 $mol:. @atom:Na 0.0 0.528 0.592 1.831 - $atom:GL2 $mol:. @atom:Na 0.0 0.808 0.524 1.774 - $atom:C1A $mol:. @atom:C1 0.0 0.397 0.568 1.465 - $atom:D2A $mol:. @atom:C3 0.0 0.436 0.417 1.187 - $atom:C3A $mol:. @atom:C1 0.0 0.438 0.544 0.903 - $atom:C4A $mol:. @atom:C1 0.0 0.452 0.543 0.554 - $atom:C1B $mol:. @atom:C1 0.0 0.955 0.563 1.486 - $atom:D2B $mol:. @atom:C3 0.0 0.889 0.663 1.193 - $atom:C3B $mol:. @atom:C1 0.0 0.951 0.528 0.911 - $atom:C4B $mol:. @atom:C1 0.0 0.963 0.530 0.556 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:D2B - $bond:b12 $atom:D2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -DOPE.scale(10) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPG.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPG.lt deleted file mode 100644 index bee0ae972b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPG.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -DOPG inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:GL0 $mol:. @atom:P4 0.0 0.510 0.547 2.484 - $atom:PO4 $mol:. @atom:Qa -1.0 0.557 0.450 2.156 - $atom:GL1 $mol:. @atom:Na 0.0 0.475 0.603 1.834 - $atom:GL2 $mol:. @atom:Na 0.0 0.774 0.662 1.768 - $atom:C1A $mol:. @atom:C1 0.0 0.337 0.509 1.478 - $atom:D2A $mol:. @atom:C3 0.0 0.482 0.634 1.190 - $atom:C3A $mol:. @atom:C1 0.0 0.401 0.486 0.902 - $atom:C4A $mol:. @atom:C1 0.0 0.468 0.569 0.543 - $atom:C1B $mol:. @atom:C1 0.0 0.893 0.507 1.499 - $atom:D2B $mol:. @atom:C3 0.0 0.985 0.539 1.202 - $atom:C3B $mol:. @atom:C1 0.0 0.905 0.527 0.896 - $atom:C4B $mol:. @atom:C1 0.0 0.980 0.627 0.549 - } - - write('Data Bond List') { - $bond:b1 $atom:GL0 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:D2B - $bond:b12 $atom:D2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -DOPG.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DOPG.move(-6.4725,-5.55,-3.08) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPS.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPS.lt deleted file mode 100644 index 9230037369..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DOPS.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -DOPS inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:CNO $mol:. @atom:P5 0.0 0.529 0.555 2.503 - $atom:PO4 $mol:. @atom:Qa -1.0 0.488 0.431 2.145 - $atom:GL1 $mol:. @atom:Na 0.0 0.540 0.568 1.828 - $atom:GL2 $mol:. @atom:Na 0.0 0.855 0.628 1.813 - $atom:C1A $mol:. @atom:C1 0.0 0.411 0.565 1.495 - $atom:D2A $mol:. @atom:C3 0.0 0.370 0.690 1.155 - $atom:C3A $mol:. @atom:C1 0.0 0.451 0.410 0.923 - $atom:C4A $mol:. @atom:C1 0.0 0.477 0.460 0.523 - $atom:C1B $mol:. @atom:C1 0.0 0.951 0.445 1.499 - $atom:D2B $mol:. @atom:C3 0.0 0.858 0.501 1.182 - $atom:C3B $mol:. @atom:C1 0.0 0.905 0.701 0.911 - $atom:C4B $mol:. @atom:C1 0.0 0.960 0.639 0.524 - } - - write('Data Bond List') { - $bond:b1 $atom:CNO $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:D2B - $bond:b12 $atom:D2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -DOPS.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DOPS.move(-6.49583,-5.49417,-2.88) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DPPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DPPC.lt deleted file mode 100644 index 0f7641dd5e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DPPC.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -DPPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.485 0.515 2.472 - $atom:PO4 $mol:. @atom:Qa -1.0 0.589 0.568 2.201 - $atom:GL1 $mol:. @atom:Na 0.0 0.509 0.536 1.838 - $atom:GL2 $mol:. @atom:Na 0.0 0.772 0.531 1.760 - $atom:C1A $mol:. @atom:C1 0.0 0.396 0.476 1.453 - $atom:C2A $mol:. @atom:C1 0.0 0.446 0.522 1.174 - $atom:C3A $mol:. @atom:C1 0.0 0.421 0.596 0.897 - $atom:C4A $mol:. @atom:C1 0.0 0.434 0.607 0.553 - $atom:C1B $mol:. @atom:C1 0.0 0.922 0.644 1.490 - $atom:C2B $mol:. @atom:C1 0.0 0.943 0.481 1.201 - $atom:C3B $mol:. @atom:C1 0.0 0.926 0.607 0.904 - $atom:C4B $mol:. @atom:C1 0.0 0.936 0.514 0.557 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b12 $atom:C3B $atom:C4B - } - -} -DPPC.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DPPC.move(-6.4825,-5.4975,-3.18) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DPPE.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DPPE.lt deleted file mode 100644 index ee31133566..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DPPE.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -DPPE inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NH3 $mol:. @atom:Qd 1.0 0.661 0.516 2.470 - $atom:PO4 $mol:. @atom:Qa -1.0 0.366 0.541 2.169 - $atom:GL1 $mol:. @atom:Na 0.0 0.474 0.578 1.822 - $atom:GL2 $mol:. @atom:Na 0.0 0.782 0.642 1.834 - $atom:C1A $mol:. @atom:C1 0.0 0.359 0.556 1.498 - $atom:C2A $mol:. @atom:C1 0.0 0.419 0.532 1.179 - $atom:C3A $mol:. @atom:C1 0.0 0.471 0.476 0.877 - $atom:C4A $mol:. @atom:C1 0.0 0.461 0.629 0.523 - $atom:C1B $mol:. @atom:C1 0.0 0.916 0.482 1.520 - $atom:C2B $mol:. @atom:C1 0.0 0.911 0.555 1.202 - $atom:C3B $mol:. @atom:C1 0.0 0.977 0.547 0.890 - $atom:C4B $mol:. @atom:C1 0.0 0.953 0.463 0.517 - } - - write('Data Bond List') { - $bond:b1 $atom:NH3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -DPPE.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DPPE.move(-6.45833,-5.43083,-2.82) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DSPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DSPC.lt deleted file mode 100644 index d68a266506..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DSPC.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "martini.lt" - -DSPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - # (guessing the coordinates, and scaling them manually) - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.000000 0.000000 6.000000 - $atom:PO4 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C3A $mol:. @atom:C1 0.0 0.000000 -1.000000 2.000000 - $atom:C4A $mol:. @atom:C1 0.0 0.000000 -1.000000 1.000000 - $atom:C5A $mol:. @atom:C1 0.0 0.000000 -1.000000 0.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - $atom:C3B $mol:. @atom:C1 0.0 0.000000 1.000000 1.000000 - $atom:C4B $mol:. @atom:C1 0.0 0.000000 1.000000 0.000000 - $atom:C5B $mol:. @atom:C1 0.0 0.000000 1.000000 -1.000000 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:C4A $atom:C5A - $bond:b11 $atom:GL2 $atom:C1B - $bond:b12 $atom:C1B $atom:C2B - $bond:b13 $atom:C2B $atom:C3B - $bond:b14 $atom:C3B $atom:C4B - $bond:b15 $atom:C4B $atom:C5B - } - -} -DSPC.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DSPC.move(-0,-0.335714,7.05).rot(-30.0,0,0,1) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DSPE.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DSPE.lt deleted file mode 100644 index 2e10ed6629..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DSPE.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -DSPE inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NH3 $mol:. @atom:Qd 1.0 0.000000 0.000000 6.000000 - $atom:PO4 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C3A $mol:. @atom:C1 0.0 0.000000 -1.000000 2.000000 - $atom:C4A $mol:. @atom:C1 0.0 0.000000 -1.000000 1.000000 - $atom:C5A $mol:. @atom:C1 0.0 0.000000 -1.000000 0.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - $atom:C3B $mol:. @atom:C1 0.0 0.000000 1.000000 1.000000 - $atom:C4B $mol:. @atom:C1 0.0 0.000000 1.000000 0.000000 - $atom:C5B $mol:. @atom:C1 0.0 0.000000 1.000000 -1.000000 - } - - write('Data Bond List') { - $bond:b1 $atom:NH3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:C4A $atom:C5A - $bond:b11 $atom:GL2 $atom:C1B - $bond:b12 $atom:C1B $atom:C2B - $bond:b13 $atom:C2B $atom:C3B - $bond:b14 $atom:C3B $atom:C4B - $bond:b15 $atom:C4B $atom:C5B - } - -} -DSPE.scale(4.7) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DUPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DUPC.lt deleted file mode 100644 index 89144c3d23..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/DUPC.lt +++ /dev/null @@ -1,41 +0,0 @@ -import "martini.lt" - -DUPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - # (guessing the coordinates, and scaling them manually) - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.000000 0.000000 6.000000 - $atom:PO4 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:GL1 $mol:. @atom:Na 0.0 0.000000 0.000000 4.000000 - $atom:GL2 $mol:. @atom:Na 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:E2A $mol:. @atom:C41 0.0 0.000000 -1.000000 3.000000 - $atom:D3A $mol:. @atom:C4 0.0 0.000000 -1.000000 2.000000 - $atom:C4A $mol:. @atom:C1 0.0 0.000000 -1.000000 1.000000 - $atom:C1B $mol:. @atom:C1 0.0 0.000000 1.000000 3.000000 - $atom:F2B $mol:. @atom:C42 0.0 0.000000 1.000000 2.000000 - $atom:D3B $mol:. @atom:C4 0.0 0.000000 1.000000 1.000000 - $atom:C4B $mol:. @atom:C1 0.0 0.000000 1.000000 0.000000 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:E2A - $bond:b6 $atom:E2A $atom:D3A - $bond:b9 $atom:D3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:F2B - $bond:b12 $atom:F2B $atom:D3B - $bond:b13 $atom:D3B $atom:C4B - } - -} -DUPC.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -DUPC.move(-0,-0.391667,2.35) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPC.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPC.lt deleted file mode 100644 index 2fef27f876..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPC.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -POPC inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.561 0.534 2.457 - $atom:PO4 $mol:. @atom:Qa -1.0 0.435 0.553 2.166 - $atom:GL1 $mol:. @atom:Na 0.0 0.478 0.512 1.813 - $atom:GL2 $mol:. @atom:Na 0.0 0.778 0.470 1.805 - $atom:C1A $mol:. @atom:C1 0.0 0.415 0.469 1.422 - $atom:D2A $mol:. @atom:C3 0.0 0.451 0.703 1.201 - $atom:C3A $mol:. @atom:C1 0.0 0.412 0.577 0.903 - $atom:C4A $mol:. @atom:C1 0.0 0.415 0.606 0.559 - $atom:C1B $mol:. @atom:C1 0.0 0.938 0.611 1.512 - $atom:C2B $mol:. @atom:C1 0.0 0.919 0.457 1.196 - $atom:C3B $mol:. @atom:C1 0.0 0.924 0.591 0.907 - $atom:C4B $mol:. @atom:C1 0.0 0.927 0.557 0.559 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -POPC.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -POPC.move(-6.3775,-5.53333,-3.24) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPE.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPE.lt deleted file mode 100644 index 4781cbf04a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPE.lt +++ /dev/null @@ -1,36 +0,0 @@ -import "martini.lt" - -POPE inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:NH3 $mol:. @atom:Qd 1.0 0.641 0.577 2.464 - $atom:PO4 $mol:. @atom:Qa -1.0 0.418 0.543 2.154 - $atom:GL1 $mol:. @atom:Na 0.0 0.500 0.593 1.818 - $atom:GL2 $mol:. @atom:Na 0.0 0.804 0.535 1.822 - $atom:C1A $mol:. @atom:C1 0.0 0.377 0.595 1.479 - $atom:D2A $mol:. @atom:C3 0.0 0.495 0.498 1.182 - $atom:C3A $mol:. @atom:C1 0.0 0.418 0.660 0.899 - $atom:C4A $mol:. @atom:C1 0.0 0.448 0.518 0.542 - $atom:C1B $mol:. @atom:C1 0.0 0.925 0.442 1.498 - $atom:C2B $mol:. @atom:C1 0.0 0.985 0.564 1.204 - $atom:C3B $mol:. @atom:C1 0.0 0.907 0.473 0.900 - $atom:C4B $mol:. @atom:C1 0.0 0.968 0.530 0.537 - } - - write('Data Bond List') { - $bond:b1 $atom:NH3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -POPE.scale(10) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPG.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPG.lt deleted file mode 100644 index a6f47af165..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPG.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -POPG inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:GL0 $mol:. @atom:P4 0.0 0.601 0.560 2.480 - $atom:PO4 $mol:. @atom:Qa -1.0 0.501 0.608 2.161 - $atom:GL1 $mol:. @atom:Na 0.0 0.534 0.516 1.827 - $atom:GL2 $mol:. @atom:Na 0.0 0.813 0.629 1.783 - $atom:C1A $mol:. @atom:C1 0.0 0.381 0.522 1.477 - $atom:D2A $mol:. @atom:C3 0.0 0.502 0.645 1.187 - $atom:C3A $mol:. @atom:C1 0.0 0.442 0.489 0.901 - $atom:C4A $mol:. @atom:C1 0.0 0.397 0.635 0.555 - $atom:C1B $mol:. @atom:C1 0.0 0.948 0.614 1.482 - $atom:C2B $mol:. @atom:C1 0.0 0.968 0.454 1.207 - $atom:C3B $mol:. @atom:C1 0.0 0.958 0.520 0.898 - $atom:C4B $mol:. @atom:C1 0.0 0.896 0.515 0.542 - } - - write('Data Bond List') { - $bond:b1 $atom:GL0 $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -POPG.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -POPG.move(-6.6175,-5.58917,-3.07) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPS.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPS.lt deleted file mode 100644 index 158f19db80..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/POPS.lt +++ /dev/null @@ -1,40 +0,0 @@ -import "martini.lt" - -POPS inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - write('Data Atoms') { - $atom:CNO $mol:. @atom:P5 0.0 0.612 0.590 2.506 - $atom:PO4 $mol:. @atom:Qa -1.0 0.497 0.582 2.177 - $atom:GL1 $mol:. @atom:Na 0.0 0.517 0.589 1.823 - $atom:GL2 $mol:. @atom:Na 0.0 0.843 0.573 1.782 - $atom:C1A $mol:. @atom:C1 0.0 0.383 0.633 1.484 - $atom:D2A $mol:. @atom:C3 0.0 0.419 0.429 1.206 - $atom:C3A $mol:. @atom:C1 0.0 0.440 0.530 0.892 - $atom:C4A $mol:. @atom:C1 0.0 0.441 0.611 0.527 - $atom:C1B $mol:. @atom:C1 0.0 0.937 0.511 1.490 - $atom:C2B $mol:. @atom:C1 0.0 0.917 0.474 1.186 - $atom:C3B $mol:. @atom:C1 0.0 0.938 0.627 0.897 - $atom:C4B $mol:. @atom:C1 0.0 0.947 0.502 0.530 - } - - write('Data Bond List') { - $bond:b1 $atom:CNO $atom:PO4 - $bond:b2 $atom:PO4 $atom:GL1 - $bond:b3 $atom:GL1 $atom:GL2 - $bond:b4 $atom:GL1 $atom:C1A - $bond:b5 $atom:C1A $atom:D2A - $bond:b6 $atom:D2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:GL2 $atom:C1B - $bond:b11 $atom:C1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -POPS.scale(10) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -POPS.move(-6.57583,-5.5425,-2.92) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/PPCS.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/PPCS.lt deleted file mode 100644 index 09a5ff8781..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/PPCS.lt +++ /dev/null @@ -1,41 +0,0 @@ -import "martini.lt" - -PPCS inherits MARTINI { - - # atomID molID atomTyle charge X Y Z - # (guessing the coordinates, and scaling them manually) - write('Data Atoms') { - $atom:NC3 $mol:. @atom:Q0 1.0 0.000000 0.000000 6.000000 - $atom:PO4 $mol:. @atom:Qa -1.0 0.000000 0.000000 5.000000 - $atom:CNO $mol:. @atom:P5 0.0 0.000000 0.000000 4.000000 - $atom:CN1 $mol:. @atom:P1 0.0 0.000000 1.000000 4.000000 - $atom:C1A $mol:. @atom:C1 0.0 0.000000 -1.000000 4.000000 - $atom:C2A $mol:. @atom:C1 0.0 0.000000 -1.000000 3.000000 - $atom:C3A $mol:. @atom:C1 0.0 0.000000 -1.000000 2.000000 - $atom:C4A $mol:. @atom:C1 0.0 0.000000 -1.000000 1.000000 - $atom:D1B $mol:. @atom:C3 0.0 0.000000 1.000000 3.000000 - $atom:C2B $mol:. @atom:C1 0.0 0.000000 1.000000 2.000000 - $atom:C3B $mol:. @atom:C1 0.0 0.000000 1.000000 1.000000 - $atom:C4B $mol:. @atom:C1 0.0 0.000000 1.000000 0.000000 - } - - write('Data Bond List') { - $bond:b1 $atom:NC3 $atom:PO4 - $bond:b2 $atom:PO4 $atom:CNO - $bond:b3 $atom:CNO $atom:CN1 - $bond:b4 $atom:CNO $atom:C1A - $bond:b5 $atom:C1A $atom:C2A - $bond:b6 $atom:C2A $atom:C3A - $bond:b9 $atom:C3A $atom:C4A - $bond:b10 $atom:CN1 $atom:D1B - $bond:b11 $atom:D1B $atom:C2B - $bond:b12 $atom:C2B $atom:C3B - $bond:b13 $atom:C3B $atom:C4B - } - -} -PPCS.scale(4.7) - -# Optional: Move the molecule to a convenient location for buildling a bilayer: -# Center the molecule in the X,Y directions and set the min Z value. -PPCS.move(-0,-0.391667,2.35).rot(-30.0,0,0,1) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/README.txt deleted file mode 100644 index c498fbe4d5..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/README.txt +++ /dev/null @@ -1,74 +0,0 @@ -This directory contains many .LT files molecules -which have been parameterized with the MARTINI force field -and converted into moltemplate format. - -------- CITE ----------------------------- -NOTE: We extracted the parameters in the MARTINI force field from the files -distributed with the "EMC" tool. If you use these .lt files, please also cite: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358. ---------------------------------------------- -THESE FILES HAVE NOT BEEN CAREFULLY TESTED. PLEASE REPORT BROKEN EXAMPLES TO: -jewett.aij -at- gmail.com, or report issues at github.com/jewettaij/moltemplate ---------------------------------------------- -PLEASE SHARE ANY NEW EXAMPLES YOU CREATE WITH THE COMMUNITY, either by emailing: -jewett.aij -at- gmail.com, or a pull request at github.com/jewettaij/moltemplate ---------------------------------------------- - -How to use these files: - -Look at the "DOPC_bilayer_preformed" example. -In particular, look at the "moltemplate_files/system.lt" file. - -This example contains only one kind of lipid, but you can create a mixture -by replacing the "lipids = new DPPC" command with a command like: -lipids = new random([DPPC, DSPC], [195,195], 1234) - ------ comments ----- - -Several of the examples in the "MARTINI_examples" directory are limited to -only one kind of lipid. In these examples, the force field parameters were -hard coded inside the definition of the lipid molecule -(specifically, the DPPC.lt file). -This makes the examples slightly easier to read and understand because -everything is contained in the same file, but not useful for general use. - -This directory, on the other hand, contains more general .LT files useful -for building multi-component membranes with multiple types of lipids and -sterols. Because most of these molecules share many of the the same atom -types and force field parameters, all of this information has been saved -in a separate file, "martini.lt", which is located in the -"moltemplate/force_fields" subdirectory (distributed with moltemplate). - -The conversion to MOLTEMPLATE (.LT) format was done by -David Stelter and Saeed Momeni Bashusqeh, converting the -EMC files distributed by Pieter J. in 't Veld. - ---- Generalizing to other Lipids --- - -More Lipids and Sterols can be downloaded at: -http://cgmartini.nl/index.php/force-field-parameters/lipids -(http://cgmartini.nl) -in gromacs .itp and .GRO formats and converted into moltemplate format. - -For inspiration how this should be done, download the DPPC molecule files from -http://cgmartini.nl/index.php/force-field-parameters/lipids2/351-lipid.html?dir=PC&lipid=DOPC -and compare these files with the DOPC.lt file in this directory. - -We copied the coordinates from the DOPC.gro file into the DOPC.lt file, -and (attempted to) make sure that the atom types matched the atom types -in the "martini.lt" file (which should also match the names in the .ITP files). - ---- Generalizing to other kinds of molecules (eg. amino acids --- - -The "martini.lt" file currently only contains the definitions of atoms -used to simulate lipids and sterols. -To simulate other molecules such as proteins using the MARTINI force field, -you will need to create a more comprehensive "martini.lt" file which includes -these new particle types. One way to do that is to download the .PRM files -(EMC format) for the molecule types you are interested in, and include them -in the list of .PRM files when you run the "emcprm2lt.py" conversion script. - -For more details how this can be done, go to the "force_field" subdirectory -and look for the "martini.lt" file. Additional .PRM files are located in -the "martini" subdirectory in that folder. - diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/water.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/water.lt deleted file mode 100644 index 6513d83413..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/MARTINI_lipid_files/water.lt +++ /dev/null @@ -1,10 +0,0 @@ -import "martini.lt" - -#water molecules in MARTINI contain only one particle - -MW inherits MARTINI { - #AtomID MolID AtomType Charge x y z - write("Data Atoms") { - $atom $mol @atom:P4 0 0 0 0 - } -} diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README.txt deleted file mode 100644 index f9a4fe3f68..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README.txt +++ /dev/null @@ -1,15 +0,0 @@ - -This example of the formation of a coarse-grained DPPC lipid-bilayer uses the -Martini force-field v2.0 (2013-10), was provided by Saeed Momeni Bashusqeh. -In this example, the initial coordinates are generated by PACKMOL. -If you prefer, there is also an example of a Martini DPPC bilayer -which has been preassembled using moltemplate commands. -(That example does not require PACKMOL.) - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_run.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_run.sh deleted file mode 100755 index 905a9f7b0e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# --- Running LAMMPS --- -# -------- PREREQUISITES: -------- -# The 2 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.npt # simulation at constant pressure -lmp_mpi -i run.in.nvt # simulation at constant volume - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_setup.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_setup.sh deleted file mode 100755 index 964f151f4e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ - -# Create the coordinates of the atoms using PACKMOL -cd packmol_files - - packmol < mix_lipids+water.inp - mv -f system.xyz ../moltemplate_files/ - -cd .. - - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -xyz system.xyz system.lt - - # This will generate various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_visualize.txt deleted file mode 100644 index e8ad744015..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 -0.5} - pbc box -shiftcenterrel {0.0 0.0 -0.5} -style tubes -width 0.75 - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/DPPC_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/DPPC_martini_LR.jpg deleted file mode 100644 index cc85e79ff1..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/DPPC_martini_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=0_after_minimization_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=0_after_minimization_LR.jpg deleted file mode 100644 index 3fa786295c..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=0_after_minimization_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=13ns_450K_NVT_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=13ns_450K_NVT_LR.jpg deleted file mode 100644 index b0df1a0aaa..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=13ns_450K_NVT_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=26ns_300K_NPT_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=26ns_300K_NPT_LR.jpg deleted file mode 100644 index e38e81006a..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=26ns_300K_NPT_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=6ns_300K_NPT_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=6ns_300K_NPT_LR.jpg deleted file mode 100644 index e1ef3f6fba..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/t=6ns_300K_NPT_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/water_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/water_martini_LR.jpg deleted file mode 100644 index a43675a5aa..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/images/water_martini_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt deleted file mode 100644 index 2ffc3887aa..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/lipid.lt +++ /dev/null @@ -1,78 +0,0 @@ -DPPC { - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid cosine/squared - dihedral_style none - improper_style none - pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 - special_bonds lj/coul 0 1 1 - dielectric 15 - neigh_modify every 10 - } - - write("Data Atoms") { - $atom:1 $mol:. @atom:Q0 1.0 9.09 9.83 0.75 - $atom:2 $mol:. @atom:Qa -1.0 5.68 7.31 0.00 - $atom:3 $mol:. @atom:Na 0.0 5.50 5.61 3.28 - $atom:4 $mol:. @atom:Na 0.0 6.65 2.22 3.04 - $atom:5 $mol:. @atom:C1 0.0 5.15 7.65 7.06 - $atom:6 $mol:. @atom:C1 0.0 7.91 7.17 10.54 - $atom:7 $mol:. @atom:C1 0.0 9.24 8.25 14.96 - $atom:8 $mol:. @atom:C1 0.0 12.19 11.75 16.38 - $atom:9 $mol:. @atom:C1 0.0 5.52 1.61 7.40 - $atom:10 $mol:. @atom:C1 0.0 6.53 2.26 12.25 - $atom:11 $mol:. @atom:C1 0.0 3.51 1.81 16.01 - $atom:12 $mol:. @atom:C1 0.0 0.00 0.00 18.19 - } - write("Data Bonds") { - $bond:b1 @bond:Bo $atom:1 $atom:2 - $bond:b2 @bond:Bo $atom:2 $atom:3 - $bond:b3 @bond:Short $atom:3 $atom:4 - $bond:b4 @bond:Bo $atom:3 $atom:5 - $bond:b5 @bond:Bo $atom:5 $atom:6 - $bond:b6 @bond:Bo $atom:6 $atom:7 - $bond:b7 @bond:Bo $atom:7 $atom:8 - $bond:b8 @bond:Bo $atom:4 $atom:9 - $bond:b9 @bond:Bo $atom:9 $atom:10 - $bond:b10 @bond:Bo $atom:10 $atom:11 - $bond:b11 @bond:Bo $atom:11 $atom:12 - } - write("Data Angles") { - $angle:a1 @angle:An1 $atom:1 $atom:2 $atom:3 - $angle:a2 @angle:An2 $atom:2 $atom:3 $atom:5 - $angle:a3 @angle:An2 $atom:2 $atom:3 $atom:4 - $angle:a4 @angle:An2 $atom:4 $atom:3 $atom:5 - $angle:a5 @angle:An1 $atom:3 $atom:4 $atom:9 - $angle:a6 @angle:An1 $atom:3 $atom:5 $atom:6 - $angle:a7 @angle:An1 $atom:5 $atom:6 $atom:7 - $angle:a8 @angle:An1 $atom:6 $atom:7 $atom:8 - $angle:a9 @angle:An1 $atom:4 $atom:9 $atom:10 - $angle:a10 @angle:An1 $atom:9 $atom:10 $atom:11 - $angle:a11 @angle:An1 $atom:10 $atom:11 $atom:12 - } - write_once("Data Masses") { - @atom:Q0 72.0 - @atom:Qa 72.0 - @atom:Na 72.0 - @atom:C1 72.0 - } - write_once("In Settings") { - pair_coeff @atom:Q0 @atom:Q0 lj/gromacs/coul/gromacs 0.8365200764818 4.7 - pair_coeff @atom:Q0 @atom:Qa lj/gromacs/coul/gromacs 1.0755258126195 4.7 - pair_coeff @atom:Q0 @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 - pair_coeff @atom:Q0 @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2 - pair_coeff @atom:Qa @atom:Qa lj/gromacs/coul/gromacs 1.1950286806883 4.7 - pair_coeff @atom:Qa @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 - pair_coeff @atom:Qa @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2 - pair_coeff @atom:Na @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 - pair_coeff @atom:Na @atom:C1 lj/gromacs/coul/gromacs 0.6453154875717 4.7 - pair_coeff @atom:C1 @atom:C1 lj/gromacs/coul/gromacs 0.8365200764818 4.7 - bond_coeff @bond:Bo harmonic 1.4937858508604 4.7 - bond_coeff @bond:Short harmonic 1.4937858508604 3.7 - angle_coeff @angle:An1 cosine/squared 2.9875717017208 180 - angle_coeff @angle:An2 cosine/squared 2.9875717017208 120 - } -} #DPPC diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/system.lt deleted file mode 100644 index 1879e6845f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/system.lt +++ /dev/null @@ -1,24 +0,0 @@ -import "water.lt" -import "lipid.lt" - -# The lipids and water must be listed instantiated in the same order -# they appear in the packmol_files/mix_lipids+water.inp file: - -lipids = new DPPC[300] - -waters = new MW[6000] - - -write_once("Data Boundary") { - 0 100.0 xlo xhi - 0 100.0 ylo yhi - 0 100.0 zlo zhi -} - - -write_once("In Settings") { -pair_coeff @atom:MW/P4 @atom:DPPC/Q0 lj/gromacs/coul/gromacs 1.3384321223709 4.7 -pair_coeff @atom:MW/P4 @atom:DPPC/Qa lj/gromacs/coul/gromacs 1.3384321223709 4.7 -pair_coeff @atom:MW/P4 @atom:DPPC/Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 -pair_coeff @atom:MW/P4 @atom:DPPC/C1 lj/gromacs/coul/gromacs 0.4780114722753 4.7 -} diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/water.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/water.lt deleted file mode 100644 index c58c897082..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/moltemplate_files/water.lt +++ /dev/null @@ -1,17 +0,0 @@ -MW { - write_once("In Init") { - units real - atom_style full - pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 - } - - write("Data Atoms") { - $atom:1 $mol:. @atom:P4 0 0 0 0 - } - write_once("Data Masses") { - @atom:P4 72.0 - } - write_once("In Settings") { - pair_coeff @atom:P4 @atom:P4 lj/gromacs/coul/gromacs 1.1950286806883 4.7 - } -} #MW diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/README.txt deleted file mode 100644 index c61369a225..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/README.txt +++ /dev/null @@ -1,8 +0,0 @@ -You can use packmol to create a file containing the atomic coordinates -for a system of coarse-grained lipids mixed with water using this command: - -If it takes too long for packmol to run, try lowering the tolerance. -(tolerance 2.0 should work) - -packmol < mix_lipids+water.inp - diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/lipid.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/lipid.xyz deleted file mode 100644 index 673f5e8afe..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/lipid.xyz +++ /dev/null @@ -1,14 +0,0 @@ -12 - DPPC -Q0 9.09 9.83 0.75 -Qa 5.68 7.31 0.00 -Na 5.50 5.61 3.28 -Na 6.65 2.22 3.04 -C1 5.15 7.65 7.06 -C1 7.91 7.17 10.54 -C1 9.24 8.25 14.96 -C1 12.19 11.75 16.38 -C1 5.52 1.61 7.40 -C1 6.53 2.26 12.25 -C1 3.51 1.81 16.01 -C1 0.00 0.00 18.19 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/mix_lipids+water.inp b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/mix_lipids+water.inp deleted file mode 100644 index 6273cea506..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/mix_lipids+water.inp +++ /dev/null @@ -1,35 +0,0 @@ -# -# A mixture of coarse-grained (martini) DPPC (lipid) and water. -# - -# All the atoms from diferent molecules will be separated at least 3.0 -# Anstroms at the solution. - -tolerance 3.0 # minimal distance between atoms in different molecules - # (you should also consider changing the "discale" - # parameter. I think discale=1.0 by default.) - -seed 12345 # seed for random number generator - -# The file type of input and output files is XYZ - -filetype xyz - -# The name of the output file - -output system.xyz - -# DPPC (lipid) molecules and water molecules will be put in a box -# defined by the minimum coordinates x, y and z = 0 0 0. and maximum -# coordinates 100 100 100. (Box size: 100x100x100) - -structure lipid.xyz - number 300 - inside box 0.0 0.0 0.0 100.0 100.0 100.0 -end structure - -structure water.xyz - number 6000 - inside box 0.0 0.0 0.0 100.0 100.0 100.0 -end structure - diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/water.xyz b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/water.xyz deleted file mode 100644 index 84fe1f74c2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/packmol_files/water.xyz +++ /dev/null @@ -1,3 +0,0 @@ -1 - water -W 0 0 0 diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.min b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.min deleted file mode 100644 index b08497f633..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.min +++ /dev/null @@ -1,32 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -thermo 5 -dump 1 all custom 100 traj_equib0_min.lammpstrj id mol type x y z ix iy iz -min_style sd -min_modify dmax 0.01 -minimize 1.0e-4 1.0e-6 100000 400000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.npt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.npt deleted file mode 100644 index a6a6143b3a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.npt +++ /dev/null @@ -1,116 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# 2) You must minimize the coordinates using by running lammps using: -# lmp_mpi -i run.in.min (the name of your binary "lmp_mpi" may vary) -# - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -#read_data "system.data" -read_data "system_after_min.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -print "---------------------------------------------------------------------------" -print "I often use Langevin dynamics initially at high temperatures and small" -print "timesteps to relax the system. It seems more stable than Nose-Hoover." -print "(This is probably not necessary.)" -print "---------------------------------------------------------------------------" -print " Note: Turning off 1-3 interactions during equilibration. (Turn them on later)" -print "---------------------------------------------------------------------------" -special_bonds lj/coul 0 0 1 - -fix fxlan all langevin 450.0 450.0 100 123456 # temp: 450 K -fix fxnph all nph iso 170.0 170.0 10000.0 # pressure: 170 barr -thermo 100 -dump dmAll all custom 2000 traj_equib1_npt.lammpstrj id mol type x y z ix iy iz - -timestep 1.0 # (safer to use a small timestep initially) -run 1000 -timestep 2.0 -run 1000 -timestep 5.0 -run 1000 -timestep 10.0 -run 2000 -timestep 20.0 -run 5000 -timestep 30.0 # (40.0 should be possible for lipid systems) - -run 50000 - -unfix fxlan -unfix fxnph -undump dmAll - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" - -velocity all zero linear # <- eliminate drift due to non-zero total momentum - #fix 1 all momentum 1000 linear 1 1 1 # also works -thermo 100 -#thermo_modify flush yes - -# temperature: 300 K, pressure: 1 barr -fix fxnpt all npt temp 300.0 300.0 3000.0 iso 1.0 1.0 30000.0 drag 1.0 -dump dmAll all custom 5000 traj_equib2_npt.lammpstrj id mol type x y z ix iy iz - -run 50000 -unfix fxnpt -undump dmAll - - -# Pressure was equilibrated at 300K, but I initially run the simulation at -# higher temperatures temporarily to speed up the proces of bilayer formation. -# (Note: The boiling point of Martini-water is -# I have to keep the volume constant (NVT) to prevent the water from boiling. -dump dmAll all custom 10000 traj_equib3_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 450.0 450.0 1000.0 tchain 1 - -run 1000000 -unfix fxnvt -undump dmAll - - -print "---------------------------------------------------------------------------" -print " Note: Turning ON 1-3 interactions again." -print "---------------------------------------------------------------------------" -special_bonds lj/coul 0 1 1 - -dump dmAll all custom 100 traj_equib4_min.lammpstrj id mol type x y z ix iy iz -minimize 1.0e-4 1.0e-6 100000 400000 -undump dmAll - - -# Hopefully a bilayer has formed at this point. -# (If not, run the equilibration simulation for longer.) -# Now I lower the temperature back to 300K. -# I should probably re-equilibrate the solvent pressure and surface tension -# (Simulation under NPT conditions using "anisotropic" boundaries.) -# (so that the surface tension in the plane is allowed to relax independently -# of the water volume, perpendicular to the plane.) I do that now: -# temperature: 300 K, pressure: 1 barr -fix fxnpt all npt temp 300.0 300.0 30000.0 couple xy aniso 1.0 1.0 1000.0 drag 1.0 -dump dmAll all custom 10000 traj_equib5_npt.lammpstrj id mol type x y z ix iy iz - -timestep 30.0 -run 100000 -unfix fxnpt -undump dmAll - - -write_data system_after_npt.data - diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.nvt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.nvt deleted file mode 100644 index cd33289198..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_formation_PACKMOL/run.in.nvt +++ /dev/null @@ -1,50 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# 2) You must minimize the coordinates using by running lammps: -# lmp_mpi -i run.in.min (the name of your binary "lmp_mpi" may vary) -# 3) You must equilibrate the system beforehand using "run.in.npt". -# lmp_mpi -i run.in.npt -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier simulation - -#read_data "system.data" -#read_data "system_after_min.data" -read_data "system_after_npt.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -velocity all zero linear # <- eliminate drift due to non-zero total momentum - #fix 1 all momentum 1000 linear 1 1 1 # also works -timestep 30.0 # (40.0 should be possible for lipid systems) -thermo 100 -#thermo_modify flush yes - - - -# Continue the simulation at constant volume (NVT) at 300K. -dump dmAll all custom 10000 traj_nvt_300K.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 3000.0 tchain 1 - -run 10000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README.txt deleted file mode 100644 index 8f875b400d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README.txt +++ /dev/null @@ -1,13 +0,0 @@ - -This example of the formation of a coarse-grained DPPC lipid-bilayer uses the -Martini force-field v2.0 (2013-10), was provided by Saeed Momeni Bashusqeh. -It's probably a good idea to run the simulation for a few ns to allow the -lipids to reorient themselves. - -step 1) -To build the files which LAMMPS needs, follow the instructions in: -README_setup.sh - -step 2) -To run LAMMPS with these files, follow these instructions: -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_run.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_run.sh deleted file mode 100755 index 65213b0963..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# --- Running LAMMPS --- -# -------- PREREQUISITES: -------- -# The 2 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.min # minimization -lmp_mpi -i run.in.npt # simulation at constant pressure -lmp_mpi -i run.in.nvt # simulation at constant volume - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_setup.sh b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_visualize.txt deleted file mode 100644 index e8ad744015..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 -0.5} - pbc box -shiftcenterrel {0.0 0.0 -0.5} -style tubes -width 0.75 - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/DPPC_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/DPPC_martini_LR.jpg deleted file mode 100644 index cc85e79ff1..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/DPPC_martini_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/t=0_bilayer_preformed_GL_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/t=0_bilayer_preformed_GL_LR.jpg deleted file mode 100644 index 8f092c926c..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/t=0_bilayer_preformed_GL_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/t=4ns_bilayer_preformed_GL_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/t=4ns_bilayer_preformed_GL_LR.jpg deleted file mode 100644 index 9d5b6b5942..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/t=4ns_bilayer_preformed_GL_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/water_martini_LR.jpg b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/water_martini_LR.jpg deleted file mode 100644 index a43675a5aa..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/images/water_martini_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/lipid.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/lipid.lt deleted file mode 100644 index 402dbae49c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/lipid.lt +++ /dev/null @@ -1,78 +0,0 @@ -DPPC { - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid cosine/squared - dihedral_style none - improper_style none - pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 - special_bonds lj/coul 0 1 1 - dielectric 15 - neigh_modify every 10 - } - - write("Data Atoms") { - $atom:1 $mol:. @atom:Q0 1.0 2.67583 4.37417 19.25 - $atom:2 $mol:. @atom:Qa -1.0 -0.73417 1.85417 20.00 - $atom:3 $mol:. @atom:Na 0.0 -0.91417 0.15417 16.72 - $atom:4 $mol:. @atom:Na 0.0 0.23583 -3.23583 16.96 - $atom:5 $mol:. @atom:C1 0.0 -1.26417 2.19417 12.94 - $atom:6 $mol:. @atom:C1 0.0 1.49583 1.71417 9.46 - $atom:7 $mol:. @atom:C1 0.0 2.82583 2.79417 5.04 - $atom:8 $mol:. @atom:C1 0.0 5.77583 6.29417 3.62 - $atom:9 $mol:. @atom:C1 0.0 -0.89417 -3.84583 12.6 - $atom:10 $mol:. @atom:C1 0.0 0.11583 -3.19583 7.75 - $atom:11 $mol:. @atom:C1 0.0 -2.90417 -3.64583 3.99 - $atom:12 $mol:. @atom:C1 0.0 -6.41417 -5.45583 1.81 - } - write("Data Bonds") { - $bond:b1 @bond:Bo $atom:1 $atom:2 - $bond:b2 @bond:Bo $atom:2 $atom:3 - $bond:b3 @bond:Short $atom:3 $atom:4 - $bond:b4 @bond:Bo $atom:3 $atom:5 - $bond:b5 @bond:Bo $atom:5 $atom:6 - $bond:b6 @bond:Bo $atom:6 $atom:7 - $bond:b7 @bond:Bo $atom:7 $atom:8 - $bond:b8 @bond:Bo $atom:4 $atom:9 - $bond:b9 @bond:Bo $atom:9 $atom:10 - $bond:b10 @bond:Bo $atom:10 $atom:11 - $bond:b11 @bond:Bo $atom:11 $atom:12 - } - write("Data Angles") { - $angle:a1 @angle:An1 $atom:1 $atom:2 $atom:3 - $angle:a2 @angle:An2 $atom:2 $atom:3 $atom:5 - $angle:a3 @angle:An2 $atom:2 $atom:3 $atom:4 - $angle:a4 @angle:An2 $atom:4 $atom:3 $atom:5 - $angle:a5 @angle:An1 $atom:3 $atom:4 $atom:9 - $angle:a6 @angle:An1 $atom:3 $atom:5 $atom:6 - $angle:a7 @angle:An1 $atom:5 $atom:6 $atom:7 - $angle:a8 @angle:An1 $atom:6 $atom:7 $atom:8 - $angle:a9 @angle:An1 $atom:4 $atom:9 $atom:10 - $angle:a10 @angle:An1 $atom:9 $atom:10 $atom:11 - $angle:a11 @angle:An1 $atom:10 $atom:11 $atom:12 - } - write_once("Data Masses") { - @atom:Q0 72.0 - @atom:Qa 72.0 - @atom:Na 72.0 - @atom:C1 72.0 - } - write_once("In Settings") { - pair_coeff @atom:Q0 @atom:Q0 lj/gromacs/coul/gromacs 0.8365200764818 4.7 - pair_coeff @atom:Q0 @atom:Qa lj/gromacs/coul/gromacs 1.0755258126195 4.7 - pair_coeff @atom:Q0 @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 - pair_coeff @atom:Q0 @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2 - pair_coeff @atom:Qa @atom:Qa lj/gromacs/coul/gromacs 1.1950286806883 4.7 - pair_coeff @atom:Qa @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 - pair_coeff @atom:Qa @atom:C1 lj/gromacs/coul/gromacs 0.4780114722753 6.2 - pair_coeff @atom:Na @atom:Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 - pair_coeff @atom:Na @atom:C1 lj/gromacs/coul/gromacs 0.6453154875717 4.7 - pair_coeff @atom:C1 @atom:C1 lj/gromacs/coul/gromacs 0.8365200764818 4.7 - bond_coeff @bond:Bo harmonic 1.4937858508604 4.7 - bond_coeff @bond:Short harmonic 1.4937858508604 3.7 - angle_coeff @angle:An1 cosine/squared 2.9875717017208 180 - angle_coeff @angle:An2 cosine/squared 2.9875717017208 120 - } -} #DPPC diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/system.lt deleted file mode 100644 index d42749daf9..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/system.lt +++ /dev/null @@ -1,27 +0,0 @@ -import "water.lt" -import "lipid.lt" - -write_once("Data Boundary") { - 0.0 100.0 xlo xhi - 0.0 100.0 ylo yhi - -50.0 50.0 zlo zhi -} - -lipids = new DPPC [13].move(7.6923, 0, 0) - [13].move(0, 7.6923, 0) - [2].rot(180, 1, 0, 0) - -waters = new MW [25].move(4.0, 0, 0) - [25].move(0, 4.0, 0) - [13].move(0, 0, 4.23) - -# Move the waters upwards so that they don't overlap with the lipids. - -waters[*][*][*].move(0, 0, 22.4) - -write_once("In Settings") { -pair_coeff @atom:MW/P4 @atom:DPPC/Q0 lj/gromacs/coul/gromacs 1.3384321223709 4.7 -pair_coeff @atom:MW/P4 @atom:DPPC/Qa lj/gromacs/coul/gromacs 1.3384321223709 4.7 -pair_coeff @atom:MW/P4 @atom:DPPC/Na lj/gromacs/coul/gromacs 0.9560229445507 4.7 -pair_coeff @atom:MW/P4 @atom:DPPC/C1 lj/gromacs/coul/gromacs 0.4780114722753 4.7 -} diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/water.lt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/water.lt deleted file mode 100644 index 49ce589b95..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/moltemplate_files/water.lt +++ /dev/null @@ -1,17 +0,0 @@ -MW { - write_once("In Init") { - units real - atom_style full - pair_style hybrid lj/gromacs/coul/gromacs 9 12 0.000001 12 - } - - write("Data Atoms") { - $atom:1 $mol:. @atom:P4 0 0 0 0 - } - write_once("Data Masses") { - @atom:P4 72.0 - } - write_once("In Settings") { - pair_coeff @atom:P4 @atom:P4 lj/gromacs/coul/gromacs 1.1950286806883 4.7 - } -} #MW diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.min b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.min deleted file mode 100644 index 6a17d20734..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.min +++ /dev/null @@ -1,33 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -thermo 5 -dump 1 all custom 100 traj_min.lammpstrj id mol type x y z ix iy iz -min_style fire -min_modify dmax 0.01 -minimize 1.0e-4 1.0e-6 100000 400000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.npt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.npt deleted file mode 100644 index 1a995edcc6..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.npt +++ /dev/null @@ -1,66 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) -# 2) You must minimize the coordinates using by running lammps witn -# run.in.min -# - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -#read_data "system.data" -read_data "system_after_min.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -print "---------------------------------------------------------------------------" -print "I often use Langevin dynamics initially at high temperatures and small" -print "timesteps to relax the system. It seems more stable than Nose-Hoover." -print "(This is probably not necessary.)" -print "---------------------------------------------------------------------------" - -fix fxlan all langevin 450.0 450.0 100 12345 # temp: 450 K -fix fxnph all nph aniso 100.0 100.0 1000.0 couple xy drag 1.0 #pressure:100barr -thermo 100 -dump dmNPTall all custom 5000 traj_npt_step1.lammpstrj id mol type x y z ix iy iz - -timestep 1.0 # (safer to use a small timestep initially) -run 1000 -timestep 3.0 -run 1000 -timestep 10.0 -run 1000 -timestep 30.0 # (40.0 should be possible for lipid systems) -run 100000 - -unfix fxlan -unfix fxnph -undump dmNPTall - -print "---------------------------------------------------------------------------" -print "--- Now continue the simulation using a Nose-Hoover Thermostat/Barostat ---" -print "---------------------------------------------------------------------------" - -velocity all zero linear # <- eliminate drift due to non-zero total momentum - #fix 1 all momentum 1000 linear 1 1 1 # also works - -# temperature: 300 K, pressure: 1 barr -fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0 couple xy -thermo 100 -#thermo_modify flush yes -dump dmNPTall all custom 10000 traj_npt_step2.lammpstrj id mol type x y z ix iy iz - -run 100000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.nvt b/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.nvt deleted file mode 100644 index 14b0cb5fa2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/MARTINI_examples/force_field_explicit/DPPC_bilayer_preformed/run.in.nvt +++ /dev/null @@ -1,47 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details.) -# 2) You must minimize the coordinates using by running lammps witn -# run.in.min -# 3) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier simulation - -#read_data "system.data" -#read_data "system_after_min.data" -read_data "system_after_npt.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - -velocity all zero linear # <- eliminate drift due to non-zero total momentum - #fix 1 all momentum 1000 linear 1 1 1 # also works - -timestep 30.0 # (40.0 should be possible for lipid systems) -dump 1 all custom 20000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 100 -#thermo_modify flush yes - -run 10000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README.txt deleted file mode 100644 index eca0a1b7f4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README.txt +++ /dev/null @@ -1,17 +0,0 @@ - -This directory contains an example of a couarse-grained (vaguely protein-like) -heteropolymer consisting of 14 residues, each of which has 2 atoms -(one backbone atom, one residue atom.) - -There are two types of residues, H and P. -The R-atom for the H residue are attracted to eachother. -All other atoms are repulsive. - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_run.sh deleted file mode 100755 index 8bf8e27648..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_run.sh +++ /dev/null @@ -1,20 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.nvt - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_visualize.txt deleted file mode 100644 index 90b102a080..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/README_visualize.txt +++ /dev/null @@ -1,86 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/monomer_H.png b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/monomer_H.png deleted file mode 100644 index efd7022e7f..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/monomer_H.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/monomer_P.png b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/monomer_P.png deleted file mode 100644 index 70dd7ce601..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/monomer_P.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/polymer_LR.png b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/polymer_LR.png deleted file mode 100644 index b239cef972..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/polymer_LR.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/trajectory.png b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/trajectory.png deleted file mode 100644 index dc4d6ccdfd..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/images/trajectory.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/README.sh deleted file mode 100755 index bcc5947b1f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/README.sh +++ /dev/null @@ -1,6 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): -moltemplate.sh system.lt - -# This will generate various files with names ending in *.in* and *.data. - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/README.txt deleted file mode 100644 index d06b4356c2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/README.txt +++ /dev/null @@ -1,26 +0,0 @@ -# In this example, we define two types of molecules: "H" and "P", -# both containing two atoms, whose ids (names) are "ca" and "r", -# and whose atom-types vary. -# -# "H" molecules: "P" molecules: -# ("hydrophobic") ("polar"/"hydrophilic") -# -# @HR @PR -# | | -# @CA @CA -# -# Eventually, we will connect multiple "H" and "P" molecules -# together to form a polymer, as shown below: -# -# @HR @HR -# | | -# _@CA_ _@CA_ -# ... -.@CA-' `-@CA-' ` ... -# | | -# @PR @PR -# -# The "H" and "P" molecules both share the same type of -# backbone atom ("CA"), but have their own custom "r" -# sidechain atoms with different properties: -# The "HR" atoms belonging to "H" molecules are attracted to each other. -# The "PR" atoms in "P" molecules are not. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt deleted file mode 100644 index e177c136e3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/forcefield.lt +++ /dev/null @@ -1,146 +0,0 @@ -# Define a "ForceField" object. -# A force field in moltemplate is any object containing mostly pair_coeff, -# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", -# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") -# information. Later, when we define molecules (such as "H" and "P"), we can -# borrow these atom types, bond-rules and force field parameters. This way, -# bonds and angular interactions are generated automatically according to -# atom (and bond) type. -# (You can also assign charge by atom type. However in this example I assigned -# charge to each atom manually (not by type). The OPLSAA examples in the -# "all_atoms" directory demonstrate how to assign charge by atom type.) - - - -HPForceField { - - # LAMMPS supports a large number of "styles" (ie. equations for calculating - # forces between particles). At some point, we must eventually select the - # formulas we want to use. This can be done anywhere, but we might as - # well specify that now. Later on we will specify the parameters - # which go into these equations. - - write_once("In Init") { - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style charmm - pair_style lj/cut 11.0 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style lj/cut/coul/debye 0.1 11.0 - # or (for short distances, below a couple nm) - #pair_style lj/charmm/coul/charmm/implicit 9.0 11.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - - # There are 3 atom types: - - write_once("Data Masses") { - @atom:CA 13.0 - @atom:HR 50.0 - @atom:PR 50.0 - } - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) - # (for details see http://lammps.sandia.gov/doc/pair_lj.html) - # - # Hydrophobic side-chain (R) atoms are attractive (large epsilon parameter). - # Polar side-chains and backbone atoms are not attractive (small epsilon). - # - # i j eps sig - # - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.10 2.0 - pair_coeff @atom:HR @atom:HR 2.50 3.6 - pair_coeff @atom:PR @atom:PR 0.10 3.6 - } - - # (By default, interactions between different AtomTypes use "arithmetic"rules: - # eps_ij=sqrt(eps_ii*eps_ij) and sig_ij=0.5*(sig_ii+sig_jj) - # Look for the line containing "pair_modify mix arithmetic" below...) - - # Optional: Assign bond types @bond:Backbone or @bond:Sidechain - # according to atom type. (This can be overridden.) - - write_once("Data Bonds By Type") { - @bond:Backbone @atom:CA @atom:CA - @bond:Sidechain @atom:CA @atom:HR - @bond:Sidechain @atom:CA @atom:PR - } - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) - # - # The corresponding command is: - # - # bond_coeff bondType k r0 - # - - write_once("In Settings") { - bond_coeff @bond:Sidechain 30.0 3.4 - bond_coeff @bond:Backbone 30.0 3.7 - } - - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 - - write_once("Data Angles By Type") { - @angle:Backbone @atom:CA @atom:CA @atom:CA - @angle:Sidechain @atom:CA @atom:CA @atom:*R # Note: "*R" <--> "HR" or "PR" - } - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 - - write_once("Data Dihedrals By Type") { - @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA - @dihedral:RCCR @atom:*R @atom:CA @atom:CA @atom:*R #"*R" <--> "HR" or "PR" - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) - # - # The corresponding command is: - # - # angle_coeff angleType k theta0 - - write_once("In Settings") { - angle_coeff @angle:Backbone 30.00 114 - angle_coeff @angle:Sidechain 30.00 123 - } - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # (for details, see http://lammps.sandia.gov/doc/dihedral_charmm.html) - # - # The corresponding command is - # dihedral_coeff dihedralType K n d w (ignore "w") - - write_once("In Settings") { - dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 - dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 - } # write_once("In Settings") - - -} # HPForceField - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/monomer_H.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/monomer_H.lt deleted file mode 100644 index 8a2bf4de8a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/monomer_H.lt +++ /dev/null @@ -1,22 +0,0 @@ -# Define the "H" monomer type ("H" <--> "hydrophobic") - -import "forcefield.lt" # defines "HPForceField" - -H inherits HPForceField { - - # atom-id(name) mol-id atom-type charge x y z - write("Data Atoms") { - $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000 - $atom:r $mol:... @atom:HR 0.0 0.000 4.4000 0.0000000 - } - - write("Data Bond List") { - $bond:cr $atom:ca $atom:r - } - -} - - -# Note: The "..." in "$mol:..." tells moltemplate that this molecule may -# be a part of a larger molecule, and (if so) to use the larger -# molecule's id number as it's own. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/monomer_P.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/monomer_P.lt deleted file mode 100644 index 2e89e31f83..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/monomer_P.lt +++ /dev/null @@ -1,22 +0,0 @@ -# Define the "P" monomer type ("P" <--> "polar") - -import "forcefield.lt" # defines "HPForceField" - -P inherits HPForceField { - - # atom-id(name) mol-id atom-type charge x y z - write("Data Atoms") { - $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000 - $atom:r $mol:... @atom:PR 0.0 0.000 4.4000 0.0000000 - } - - write("Data Bond List") { - $bond:cr $atom:ca $atom:r - } - -} - - -# Note: The "..." in "$mol:..." tells moltemplate that this molecule may -# be a part of a larger molecule, and (if so) to use the larger -# molecule's id number as it's own. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/polymer.lt deleted file mode 100644 index 0b07e14719..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/polymer.lt +++ /dev/null @@ -1,64 +0,0 @@ -import "monomer_H.lt" # defines the "H" molecular subunit -import "monomer_P.lt" # defines the "P" molecular subunit - - - -Polymer { - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - # (The "Data Atoms" in H and P must use "$mol:..." notation.) - - # This causes mon1,mon2,mon3,...,mon14 to share the same molecule counter - # because in the forcefield.lt file, the "..." in "$mol:..." preferentially - # looks for a counter of that type in a parent molecule or earlier ancestor. - - - # A polymer of alternating "H" and "P" monomers: - - mon1 = new P - mon2 = new P.rot(180.0, 1,0,0).move(3.2,0,0) - mon3 = new H.rot( 0.0, 1,0,0).move(6.4,0,0) - mon4 = new H.rot(180.0, 1,0,0).move(9.6,0,0) - mon5 = new H.rot( 0.0, 1,0,0).move(12.8,0,0) - mon6 = new H.rot(180.0, 1,0,0).move(16.0,0,0) - mon7 = new P.rot( 0.0, 1,0,0).move(19.2,0,0) - mon8 = new P.rot(180.0, 1,0,0).move(22.4,0,0) - mon9 = new P.rot( 0.0, 1,0,0).move(25.6,0,0) - mon10 = new H.rot(180.0, 1,0,0).move(28.8,0,0) - mon11 = new H.rot( 0.0, 1,0,0).move(32.0,0,0) - mon12 = new H.rot(180.0, 1,0,0).move(35.2,0,0) - mon13 = new P.rot( 0.0, 1,0,0).move(38.4,0,0) - mon14 = new P.rot(180.0, 1,0,0).move(41.6,0,0) - - - # Now, link the monomers together this way: - write("Data Bond List") { - $bond:backbone1 $atom:mon1/ca $atom:mon2/ca - $bond:backbone2 $atom:mon2/ca $atom:mon3/ca - $bond:backbone3 $atom:mon3/ca $atom:mon4/ca - $bond:backbone4 $atom:mon4/ca $atom:mon5/ca - $bond:backbone5 $atom:mon5/ca $atom:mon6/ca - $bond:backbone6 $atom:mon6/ca $atom:mon7/ca - $bond:backbone7 $atom:mon7/ca $atom:mon8/ca - $bond:backbone8 $atom:mon8/ca $atom:mon9/ca - $bond:backbone9 $atom:mon9/ca $atom:mon10/ca - $bond:backbone10 $atom:mon10/ca $atom:mon11/ca - $bond:backbone11 $atom:mon11/ca $atom:mon12/ca - $bond:backbone12 $atom:mon12/ca $atom:mon13/ca - $bond:backbone13 $atom:mon13/ca $atom:mon14/ca - } - - - # Use "Data Bonds" instead if you prefer to assign the bond types manually: - # write("Data Bonds") { - # $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca - # $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca - # : : : : - # } - -} # Polymer - - - -# Angle, dihedral and improper interactions between monomers will be generated -# automatically according to the instructions in the "forcefield.lt" file. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/system.lt deleted file mode 100644 index e3d8317aa0..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/moltemplate_files/system.lt +++ /dev/null @@ -1,36 +0,0 @@ -import "polymer.lt" - - -# Specify the periodic boundary conditions: -write_once("Data Boundary") { - 0 180.0 xlo xhi - 0 180.0 ylo yhi - 0 180.0 zlo zhi -} - - -# Create 27 polymers (=3x3x3) in a rectangular grid - -polymers = new Polymer [3].move(60.0, 0, 0) - [3].move(0, 60.0, 0) - [3].move(0, 0, 60.0) - - - - - - - - -# ----- everything below is optional: ----- -# Shift some of the polymers in the Z direction by a distance of 20.0 - -polymers[1][*][*].move(0,0,20) - -# We applied this move command to all the -# polymers in the middle slab (with constant X). -# More examples of applying the "move" command: - -polymers[*][1][*].move(20,0,0) -polymers[*][*][1].move(0,20,0) - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/run.in.nvt deleted file mode 100644 index e9fdbf41fd..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_heteropolymer/run.in.nvt +++ /dev/null @@ -1,32 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 2.0 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 300.0 300.0 5000.0 48279 -fix fxnve all nve - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data - -run 40000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt deleted file mode 100644 index eca0a1b7f4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README.txt +++ /dev/null @@ -1,17 +0,0 @@ - -This directory contains an example of a couarse-grained (vaguely protein-like) -heteropolymer consisting of 14 residues, each of which has 2 atoms -(one backbone atom, one residue atom.) - -There are two types of residues, H and P. -The R-atom for the H residue are attracted to eachother. -All other atoms are repulsive. - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh deleted file mode 100755 index 8bf8e27648..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_run.sh +++ /dev/null @@ -1,20 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.nvt - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt deleted file mode 100644 index 518df2c20a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/README_visualize.txt +++ /dev/null @@ -1,86 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.05 -0.15 -0.05} - pbc box -shiftcenterrel {-0.05 -0.15 -0.05} -width 1.6 -style tubes - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg deleted file mode 100644 index 35af99387e..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_monomer.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_LR.jpg deleted file mode 100644 index 76ded4f486..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_array3x3x3_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_array3x3x3_LR.jpg deleted file mode 100644 index fbc31e6525..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_polymer_array3x3x3_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg deleted file mode 100644 index 18ca16001c..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/images/2bead_t=4850000_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh deleted file mode 100755 index bcc5947b1f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.sh +++ /dev/null @@ -1,6 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): -moltemplate.sh system.lt - -# This will generate various files with names ending in *.in* and *.data. - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt deleted file mode 100644 index 3d9fdab320..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/README.txt +++ /dev/null @@ -1,19 +0,0 @@ -# In this example, we construct a large molecule ("Polymer") -# from multiple smaller molecular subunits ("Monomer"). -# The "Monomer" molecule contains two atoms (type "CA", and "R") -# -# "Monomer" -# -# @R -# | -# @CA -# -# Eventually, we will connect multiple "Monomer" molecular subunits -# together to form a polymer, as shown below: -# -# @R @R -# | | -# _@CA_ _@CA_ -# ... -.@CA-' `-@CA-' ` ... -# | | -# @R @R diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt deleted file mode 100644 index 8dfdf98a41..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/forcefield.lt +++ /dev/null @@ -1,110 +0,0 @@ - -# Define a "ForceField" object. -# A force field in moltemplate is any object containing mostly pair_coeff, -# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", -# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") -# information. Later on when we define molecule objects, we can access all -# of the atom types and force field parameters here using "inherits ForceField". -# (See "monomer.lt" for example.) - - -ForceField { - - - # LAMMPS supports a large number of "styles" (ie. equations for calculating - # forces between particles). At some point, we must eventually select the - # formulas we want to use. This can be done anywhere, but we might as - # well specify that now. Later on we will specify the parameters - # which go into these equations. - - write_once("In Init") { - # -- Styles used in "ForceField" -- - # -- (Changing these styles will change the formulas above) -- - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style charmm - pair_style lj/cut 11.0 - } - - - # There are 2 atom types: "CA" and "R" - write_once("Data Masses") { - @atom:CA 13.0 - @atom:R 50.0 - } - - # ---- 2-body (non-bonded) interactions: ---- - # U(r) = 4*epsilon((sigma/r)^12 - (sigma/r)^6) - # (for details see http://lammps.sandia.gov/doc/pair_lj.html) - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - # Pairwise (non-bonded) interactions: - # atomType1 atomType2 epsilon sigma - pair_coeff @atom:CA @atom:CA 0.10 2.0 - pair_coeff @atom:R @atom:R 0.50 3.6 - # (Interactions between different atoms are determined by mixing rules.) - } - - # ---- 2-body (bonded) interactions: ---- - # - # Ubond(r) = k*(r-r0)^2 - # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) - # - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:Sidechain 15.0 3.4 - bond_coeff @bond:Backbone 15.0 3.7 - } - - # ---- 3-body angle (hinge) interactions: ---- - - # Rules for determining 3-body (angle) interactions by atom & bond type: - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:Backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:Sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - } - - # Force-field parameters for 3-body (angle) interactions: - # - # Uangle(theta) = k*(theta-theta0)^2 - # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) - # - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:Backbone 30.00 114 - angle_coeff @angle:Sidechain 30.00 132 - } - - # ---- 4-body dihedral interactions ---- - - # 4-body interactions in this example are listed by atomType - # Rules for determining 4-body (dihedral) interactions by atom & bond type: - write_once("Data Dihedrals By Type") { - # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 - @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* - } - - # The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # (for details, see http://lammps.sandia.gov/doc/dihedral_charmm.html) - # - # The corresponding command is - # dihedral_coeff dihedralType K n d w(ignored) - - write_once("In Settings") { - dihedral_coeff @dihedral:CCCC -0.5 1 -180 0.0 - dihedral_coeff @dihedral:RCCR -1.5 1 -180 0.0 - } - -} # "ForceField" - - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt deleted file mode 100644 index 286eb12ff4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/monomer.lt +++ /dev/null @@ -1,20 +0,0 @@ -import "forcefield.lt" # contains force-field parameters - -Monomer inherits ForceField { - - write("Data Atoms") { - # atomId molId atomType charge x y z - $atom:ca $mol:... @atom:CA 0.0 0.000 1.0000 0.0000000 - $atom:r $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 - } - write("Data Bonds") { - # bond-id bond-type atom-id1 atom-id2 - $bond:cr @bond:Sidechain $atom:ca $atom:r - } -} - - - -# NOTE: The "..." in "$mol:..." tells moltemplate that this molecule is part -# of a larger molecule, and to use the larger parent object's -# molecule id number as it's own. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt deleted file mode 100644 index 5ca8eb03e9..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/polymer.lt +++ /dev/null @@ -1,27 +0,0 @@ -import "monomer.lt" # <-- defines "Monomer" and "ForceField" - -Polymer inherits ForceField { - - # The next line is optional - create_var {$mol} # force all monomers to share the same molecule-ID - - # Now create some monomers - - mon1 = new Monomer - mon2 = new Monomer.rot(180.0, 1,0,0).move(3.2,0,0) - mon3 = new Monomer.move(6.4,0,0) - mon4 = new Monomer.rot(180.0, 1,0,0).move(9.6,0,0) - mon5 = new Monomer.move(12.8,0,0) - mon6 = new Monomer.rot(180.0, 1,0,0).move(16.0,0,0) - mon7 = new Monomer.move(19.2,0,0) - - # Now, link the monomers together this way: - write("Data Bonds") { - $bond:backbone1 @bond:Backbone $atom:mon1/ca $atom:mon2/ca - $bond:backbone2 @bond:Backbone $atom:mon2/ca $atom:mon3/ca - $bond:backbone3 @bond:Backbone $atom:mon3/ca $atom:mon4/ca - $bond:backbone4 @bond:Backbone $atom:mon4/ca $atom:mon5/ca - $bond:backbone5 @bond:Backbone $atom:mon5/ca $atom:mon6/ca - $bond:backbone6 @bond:Backbone $atom:mon6/ca $atom:mon7/ca - } -} diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt deleted file mode 100644 index 480f8c0216..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/moltemplate_files/system.lt +++ /dev/null @@ -1,29 +0,0 @@ -import "polymer.lt" - - -# Specify the periodic boundary conditions: -write_once("Data Boundary") { - 0 90.0 xlo xhi - 0 90.0 ylo yhi - 0 90.0 zlo zhi -} - -# Create 27 polymers in a rectangular grid - -polymers = new Polymer [3].move(0, 0, 30.0) - [3].move(0, 30.0, 0) - [3].move(30.0, 0, 0) - - - -# ------------ Optional: ------------ -# Now (for fun) shift some of the polymers -# in the x direction by a distance of 20.0 -# Suppose we want to move the middle slice -# (which has constant Z). We do that this way: -# polymers[1][*][*].move(20,0,0) -# more examples: -# polymers[*][1][*].move(0,0,20) -# polymers[*][*][1].move(0,20,0) - - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt deleted file mode 100644 index e9fdbf41fd..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_2bead_polymer/run.in.nvt +++ /dev/null @@ -1,32 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 2.0 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 300.0 300.0 5000.0 48279 -fix fxnve all nve - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data - -run 40000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README.txt deleted file mode 100644 index 01f2353d2f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README.txt +++ /dev/null @@ -1,14 +0,0 @@ - -This example demonstrates how to build a simple system -containing mobile and immobile atoms using moltemplate. -An immobile tube is constructed of Lennard Jones particles (see "system.lt") -interacting with a fluid composed of (similar sized) Lennard Jones particles. - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_run.sh deleted file mode 100755 index cb2307f525..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_run.sh +++ /dev/null @@ -1,23 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.nvt # Run a simulation at constant volume - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -# (But for a system of this small size, it should not be necessary.) -#mpirun -np 4 lmp_mpi -i run.in.nvt -#or -#mpirun -np 4 lmp_mpi -i run.in.npt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_visualize.txt deleted file mode 100644 index 3bb7f5ff47..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 -0.5 -0.5} - pbc box -shiftcenterrel {0.0 -0.5 -0.5} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/images/tubewall+solvent_t=0steps.jpg b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/images/tubewall+solvent_t=0steps.jpg deleted file mode 100644 index 8c5df6540c..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/images/tubewall+solvent_t=0steps.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/images/tubewall+solvent_t=3000steps.png b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/images/tubewall+solvent_t=3000steps.png deleted file mode 100644 index f2f29ec4e8..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/images/tubewall+solvent_t=3000steps.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/solvent_particle.lt b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/solvent_particle.lt deleted file mode 100644 index ebf5eeaf0d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/solvent_particle.lt +++ /dev/null @@ -1,21 +0,0 @@ -# The two files "wall_particle.lt" and "solvent_particle.lt" -# define two very simple molecules containing one atom each. -# Both atoms have the same size (the have the same LJ sigma parameter). - -SolventParticle { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:s $mol:. @atom:s 0.0 0.0 0.0 0.0 - } - write_once("Data Masses") { - @atom:s 10.0 - } - write_once("In Settings") { - # i j epsilon sigma cutoff - pair_coeff @atom:s @atom:s 0.60 3.0 7.5 #<--attractive - group groupS type @atom:s #(Atoms of this type belong to the "S" group) - } - -} - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/system.lt deleted file mode 100644 index c68d8a650e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/system.lt +++ /dev/null @@ -1,53 +0,0 @@ -import "wall_particle.lt" - -# Create an immobile "wall" out of "WallParticle"s -# arranged in the shape of a tube with radius 9.6 - -tube = new WallParticle.move(0,9.6,0) [20].rot(18,3.0,0,0) - [20].move(3.0,0,0) - - -# Add some "SolventParticle"s to the center of the tube: - -import "solvent_particle.lt" -solvent = new SolventParticle [20].move(3.0,0,0) - [3].move(0,3.0,0) - [3].move(0,0,3.0) - -# These "solvent" particles currently occupy a rectangular region from -# 0 to 6.0 in the y and z directions. Center them all using .move(): - -solvent[*][*][*].move(0,-3.0,-3.0) - - -# Define the periodic boundary conditions for our system - -write_once("Data Boundary") { - 0.0 60.0 xlo xhi - -20.0 20.0 ylo yhi - -20.0 20.0 zlo zhi -} - - - - -# LAMMPS supports a large number of force-field styles. We must select -# which ones we need. This information belongs in the "In Init" section (and -# (you can specify it anywhere in your LT files, multiple times if you like). -# If different molecules use different force-field styles, you can use hybrid -# styles. (In this example the molecules share the same pair_style.) - -write_once("In Init") { - units real - atom_style full - pair_style lj/cut 9.0 - # If you have charged molecules immersed in a salty implicit - # solvent, you might try something like this this instead: - # pair_style lj/cut/coul/debye 0.1 9.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 -} - - - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/wall_particle.lt b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/wall_particle.lt deleted file mode 100644 index 434a318655..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/moltemplate_files/wall_particle.lt +++ /dev/null @@ -1,21 +0,0 @@ -# The two files "wall_particle.lt" and "solvent_particle.lt" -# define two very simple molecules containing one atom each. -# Both atoms have the same size (the have the same LJ sigma parameter). - -WallParticle { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:w $mol:. @atom:w 0.0 0.0 0.0 0.0 - } - write_once("Data Masses") { - @atom:w 10.0 - } - write_once("In Settings") { - # i j epsilon sigma cutoff - pair_coeff @atom:w @atom:w 0.05 3.0 7.5 #<--repulsive (approximately) - group groupW type @atom:w #(Atoms of this type belong to the "W" group) - } - -} - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/run.in.nvt deleted file mode 100644 index 16fdffb05a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_lennard_jones_tube/run.in.nvt +++ /dev/null @@ -1,53 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details) - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Use "neigh_modify" to turn off calculation of interactions between immobilized -# atoms. (Note: The "groupW" group was defined in the file "system.in.settings") -neigh_modify exclude group groupW groupW - -# -- Run Section -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - - -# Optional: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms. (Note: This is not optional under NPT conditions.) -neigh_modify exclude group groupW groupW - -# Only the groupW atoms are immobile. -group mobile subtract all groupW - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp - -# Integrate the equations of motion: -fix fMoveStuff mobile nvt temp 300.0 300.0 100.0 -fix_modify fMoveStuff temp tempMobile - - -run 100000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README.txt deleted file mode 100644 index 8c6ca7947f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README.txt +++ /dev/null @@ -1,19 +0,0 @@ -This is an example of how to build a polymer out of randomly-chosen monomers. -In this case, monomers will be chosen at random from two types -(denoted "2bead" and "3bead", although you can have as many types as you like). -You can also constrain the end-caps to be a particular type (eg "3bead"). - -The properties of the bonds connecting monomers (ie length, rigidity) will -be automatically determined, depending on the type of monomers at that location -in the polymer. The same is true for the 3-body angle, and 4-body dihedral -interactions. - - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_run.sh deleted file mode 100755 index 9343d763f7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_run.sh +++ /dev/null @@ -1,14 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.nvt diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/2bead.jpg deleted file mode 100644 index f67da797f1..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/2bead.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/3bead.jpg b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/3bead.jpg deleted file mode 100644 index 15d7b29676..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/3bead.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=0.jpg b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=0.jpg deleted file mode 100644 index 75d67b42fb..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=700ps.jpg b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=700ps.jpg deleted file mode 100644 index 8f1c6f99bf..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/images/random_heteropolymer_30_20_t=700ps.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/forcefield.lt deleted file mode 100644 index 6bdb4697b7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/forcefield.lt +++ /dev/null @@ -1,107 +0,0 @@ -# The "ForceField" object contains a list of atom types, masses, force-field -# parameters, and rules for generating 3-body & 4-body bonded interactions. -# Molecules which use "inherit ForceField" share these rules, and consequently -# can usually be written in a much more concise way. - - -ForceField { - - # LAMMPS supports a large number of force-field styles. We must select - # which ones we need. This information belongs in the "In Init" section (and - # (you can specify it anywhere in your LT files, multiple times if you like). - # If different molecules use different force-field styles, you can use hybrid - # styles. (In this example the molecules share the same pair_style.) - - write_once("In Init") { - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style opls - pair_style lj/cut 9.0 - # If you have charged molecules immersed in a salty implicit - # solvent, you might try something like this this instead: - # pair_style lj/cut/coul/debye 0.1 9.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 - } - - # atom-type mass - - write_once("Data Masses") { - @atom:CA2 12.0 - @atom:R2 17.0 - @atom:CA3 12.0 - @atom:R3 17.0 - } - - - # Connect different monomers together with bonds whose type - # (length, rigidity, etc) depend on the type of atom at either end. - - write_once("Data Bonds By Type") { - @bond:sidechain @atom:CA* @atom:R* - @bond:two_two @atom:CA2 @atom:CA2 - @bond:two_three @atom:CA2 @atom:CA3 - @bond:three_three @atom:CA3 @atom:CA3 - } - # Note: The next line is redundant and unnecessary: - # @bond:two_three @atom:CA3 @atom:CA2 - - - - # You can also generate angles and dihedrals and impropers in a similar way: - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA* @atom:CA* @atom:CA* @bond:* @bond:* - @angle:sidechain @atom:CA* @atom:CA* @atom:R* @bond:* @bond:* - @angle:RCR @atom:R* @atom:CA* @atom:R* @bond:* @bond:* - } - # Note: The next line is redundant and unnecessary: - # @angle:sidechain @atom:R* @atom:CA* @atom:CA* @bond:* @bond:* - - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbone @atom:CA* @atom:CA* @atom:CA* @atom:CA* * * * - @dihedral:two_two @atom:R2 @atom:CA* @atom:CA* @atom:R2 * * * - @dihedral:two_three @atom:R2 @atom:CA* @atom:CA* @atom:R3 * * * - @dihedral:three_three @atom:R3 @atom:CA* @atom:CA* @atom:R3 * * * - } - # Note: The next line is redundant and unnecessary: - # @dihedral:two_three @atom:R3 @atom:CA* @atom:CA* @atom:R2 * * * - - # Force field parameters: - write_once("In Settings") { - # atom-type atom-type epsilon sigma - pair_coeff @atom:CA2 @atom:CA2 0.05 3.0 - pair_coeff @atom:R2 @atom:R2 0.60 4.0 - pair_coeff @atom:CA3 @atom:CA3 0.10 2.0 - pair_coeff @atom:R3 @atom:R3 0.50 3.0 - - # bond-type k r0 - bond_coeff @bond:sidechain 20.0 3.4 - bond_coeff @bond:two_two 20.0 3.7 - bond_coeff @bond:two_three 20.0 3.5 - bond_coeff @bond:three_three 20.0 3.3 - - # angle-type k theta0 - angle_coeff @angle:backbone 40.00 120 - angle_coeff @angle:sidechain 40.00 120 - angle_coeff @angle:RCR 40.00 120 - - # dihedral-type K1 K2 K3 K4 - dihedral_coeff @dihedral:backbone 0.3 0.0 0.0 0.0 - dihedral_coeff @dihedral:two_two 0.08 0.0 0.0 0.0 - dihedral_coeff @dihedral:two_three 0.08 0.0 -0.05 0.0 - dihedral_coeff @dihedral:three_three 0.08 0.0 0.0 0.05 - } - -} # ForceField - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/monomers.lt deleted file mode 100644 index a6b685cc96..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/monomers.lt +++ /dev/null @@ -1,62 +0,0 @@ -import "forcefield.lt" #<-- "forcefield.lt" contains atom type definitions, - # force-field parameters, and rules for generating - # 3-body and 4-body angle, dihedral, and improper - # interactions for molecules (polymers) made using - # "2bead" and "3bead" objects as building blocks. - - - - # ---------------------------------------------------------------------- - # -- General comment: -- - # -- The write() and write_once() commands create and append text to -- - # -- files (replacing variables beginning with @ or $ with counters.) -- - # -- File names beginning with "In " or "Data " are special. -- - # -- They will be pasted into the LAMMPS input script and -- - # -- data files which are generated by moltemplate. The syntax -- - # -- of these files is exactly the same as the syntax from the -- - # -- corresponding sections of a LAMMPS input script or data file. -- - # ---------------------------------------------------------------------- - - - - - - -3bead inherits ForceField { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA3 0.0 0.000 1.000 0.000 - $atom:R1 $mol:... @atom:R3 0.0 0.000 2.700 2.950 - $atom:R2 $mol:... @atom:R3 0.0 0.000 2.700 -2.950 - } - - # bond-id atom-id1 atom-id2 - write("Data Bond List") { - $bond:CR1 $atom:CA $atom:R1 - $bond:CR2 $atom:CA $atom:R2 - } - -} # 3bead - - - - -2bead inherits ForceField { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA2 0.0 0.000 1.000 0.0000 - $atom:R $mol:... @atom:R2 0.0 0.000 4.400 0.0000 - } - - # bond-id atom-id1 atom-id2 - write("Data Bond List") { - $bond:CR $atom:CA $atom:R - } - -} # 2bead - - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/polymer.lt deleted file mode 100644 index 4502934eb2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/polymer.lt +++ /dev/null @@ -1,163 +0,0 @@ -import "forcefield.lt" # <-- Defines force-field parameters, and rules. -import "monomers.lt" # <-- Defines the "2bead", "3bead" objects we will use - # as building-blocks to build the polymer. - - - - -RandomHeteropolymer inherits ForceField { - - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - # If you want to share molecule-IDs, do this first - # (This matches with "$mol:..." in "monomers.lt") - - - - monomers[0] = new 3bead # Let the first monomer be of type "3bead" - - # Now, fill the middle of the chain with random monomers (2bead, 3bead): - - monomers[1-48] = new random([2bead,3bead], - [30, # <-- 30 "2bead" molecules and - 18], # <-- 18 "3bead" molecules - 12345) # <-- optional random seed - - # and place them on the X-axis (separated by 2.95 Angstroms) - [48].rot(180,1,0,0).move(2.95, 0, 0) - - # Note: The two numbers (30 and 18) must sum up to the number of - # monomers we created ("[48]"). - - monomers[49] = new 3bead # Let the last monomer be of type "3bead" - - - # Afterwards, there should be 20 "3bead" monomers and 30 "2bead" monomers - - - - - # Now, physically move the monomers to make sure the monomers on the end of - # the chain (monomers[0] & monomers[49]) don't overlap with monomers[1-48] - - monomers[0].rot(180,1,0,0) #leave monomer[0] where it is, but rotate it - monomers[1-48].move(2.95,0,0) #move the remaining monomers to make room for it - monomers[49].move(144.55,0,0) #move the last monomer (note:144.55=2.95*50)) - - - - - # Now, link the monomers together using "Data Bond List" - # (Using "Data Bond List" instead of "Data Bonds", allows you to omit the - # bond type. This tells moltemplate to look up the appropriate - # bond type according to the type of atom at either end of the bond, which - # depends on what type of monomer is on either side: "2bead" or "3bead". - # This all happens automatically. The user can control how this is done - # by editing the file "forcefield.lt".) - - - write("Data Bond List") { - $bond:bb1 $atom:monomers[0]/CA $atom:monomers[1]/CA - $bond:bb2 $atom:monomers[1]/CA $atom:monomers[2]/CA - $bond:bb3 $atom:monomers[2]/CA $atom:monomers[3]/CA - $bond:bb4 $atom:monomers[3]/CA $atom:monomers[4]/CA - $bond:bb5 $atom:monomers[4]/CA $atom:monomers[5]/CA - $bond:bb6 $atom:monomers[5]/CA $atom:monomers[6]/CA - $bond:bb7 $atom:monomers[6]/CA $atom:monomers[7]/CA - $bond:bb8 $atom:monomers[7]/CA $atom:monomers[8]/CA - $bond:bb9 $atom:monomers[8]/CA $atom:monomers[9]/CA - $bond:bb10 $atom:monomers[9]/CA $atom:monomers[10]/CA - $bond:bb11 $atom:monomers[10]/CA $atom:monomers[11]/CA - $bond:bb12 $atom:monomers[11]/CA $atom:monomers[12]/CA - $bond:bb13 $atom:monomers[12]/CA $atom:monomers[13]/CA - $bond:bb14 $atom:monomers[13]/CA $atom:monomers[14]/CA - $bond:bb15 $atom:monomers[14]/CA $atom:monomers[15]/CA - $bond:bb16 $atom:monomers[15]/CA $atom:monomers[16]/CA - $bond:bb17 $atom:monomers[16]/CA $atom:monomers[17]/CA - $bond:bb18 $atom:monomers[17]/CA $atom:monomers[18]/CA - $bond:bb19 $atom:monomers[18]/CA $atom:monomers[19]/CA - $bond:bb20 $atom:monomers[19]/CA $atom:monomers[20]/CA - $bond:bb21 $atom:monomers[20]/CA $atom:monomers[21]/CA - $bond:bb22 $atom:monomers[21]/CA $atom:monomers[22]/CA - $bond:bb23 $atom:monomers[22]/CA $atom:monomers[23]/CA - $bond:bb24 $atom:monomers[23]/CA $atom:monomers[24]/CA - $bond:bb25 $atom:monomers[24]/CA $atom:monomers[25]/CA - $bond:bb26 $atom:monomers[25]/CA $atom:monomers[26]/CA - $bond:bb27 $atom:monomers[26]/CA $atom:monomers[27]/CA - $bond:bb28 $atom:monomers[27]/CA $atom:monomers[28]/CA - $bond:bb29 $atom:monomers[28]/CA $atom:monomers[29]/CA - $bond:bb30 $atom:monomers[29]/CA $atom:monomers[30]/CA - $bond:bb31 $atom:monomers[30]/CA $atom:monomers[31]/CA - $bond:bb32 $atom:monomers[31]/CA $atom:monomers[32]/CA - $bond:bb33 $atom:monomers[32]/CA $atom:monomers[33]/CA - $bond:bb34 $atom:monomers[33]/CA $atom:monomers[34]/CA - $bond:bb35 $atom:monomers[34]/CA $atom:monomers[35]/CA - $bond:bb36 $atom:monomers[35]/CA $atom:monomers[36]/CA - $bond:bb37 $atom:monomers[36]/CA $atom:monomers[37]/CA - $bond:bb38 $atom:monomers[37]/CA $atom:monomers[38]/CA - $bond:bb39 $atom:monomers[38]/CA $atom:monomers[39]/CA - $bond:bb40 $atom:monomers[39]/CA $atom:monomers[40]/CA - $bond:bb41 $atom:monomers[40]/CA $atom:monomers[41]/CA - $bond:bb42 $atom:monomers[41]/CA $atom:monomers[42]/CA - $bond:bb43 $atom:monomers[42]/CA $atom:monomers[43]/CA - $bond:bb44 $atom:monomers[43]/CA $atom:monomers[44]/CA - $bond:bb45 $atom:monomers[44]/CA $atom:monomers[45]/CA - $bond:bb46 $atom:monomers[45]/CA $atom:monomers[46]/CA - $bond:bb47 $atom:monomers[46]/CA $atom:monomers[47]/CA - $bond:bb48 $atom:monomers[47]/CA $atom:monomers[48]/CA - $bond:bb49 $atom:monomers[48]/CA $atom:monomers[49]/CA - } - -} # RandomHeteropolymer - - - - -# COMMENTS: -# -# -# 1) -# Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "monomers.lt" -# -# -# -# -# 2) -# These lines in the "Data Bond List" section can be quickly generated in python -# N = 50 -# for i in range(0,N-1): -# print(' $bond:bb'+str(i+1)+' $atom:monomers[' -# +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA') -# -# -# -# 3) -# The "[1-50]" in "monomers[1-50] = new random([2bead,3bead], ..." -# causes moltemplate to create a list of molecules with names beginning with -# "monomers[1]", for example: -# "monomers[1], "monomers[2]", "monomers[3], ..., "monomers[50]" -# (This causes the indexing to begin at [1] instead of [0].) -# -# -# -# 4) -# ALTERNATE METHOD: You can also generate a random array this way: -# -# monomers[1-48] = new random([2bead,3bead], -# [0.625, 0.375], # <-- probabilities -# 12345) # <-- optional random seed -# [48].rot(180,1,0,0).move(2.95, 0, 0) -# -# The command above also works, but it chooses each molecule (monomer) randomly -# (independently of the others). Consequently, this does not gaurantee that -# exactly 62.5% and 37.5% of the monomers will be of type 2bead and 3bead. -# -# -# -# 5) RandomHeteropolymer uses "2bead" and "3bead" objects as building-blocks, -# and these objects inherit the properties from the "ForceField" object -# (atom types, bond types, etc, defined in "forcefield.lt" in this example). -# So I declared that "RandomHeteropolymer inherits ForceField {" so that -# you can easily access those atom types, bond types, etc as well. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/system.lt deleted file mode 100644 index 565edc3f00..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/moltemplate_files/system.lt +++ /dev/null @@ -1,11 +0,0 @@ - -write_once("Data Boundary") { - 0.0 150.0 xlo xhi - 0.0 150.0 ylo yhi - 0.0 150.0 zlo zhi -} - - -import "polymer.lt" - -polymer = new RandomHeteropolymer diff --git a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/run.in.nvt deleted file mode 100644 index 645dac3446..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_random_heteropolymer/run.in.nvt +++ /dev/null @@ -1,29 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - -timestep 2.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Temperature = 500 degrees - -run 500000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README.txt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/README.txt deleted file mode 100644 index ed9de408f2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README.txt +++ /dev/null @@ -1,23 +0,0 @@ - -This example contains a (crude and somewhat simple) example of -the translocation of a (rather short) polymer through a hole in a wall, -surrounded by an explicit LJ solvent. - -(I used a short polymer because a longer polymer would require a larger box. - But this example looked more impressive visually when I used a smaller box.) ----- -Note: You must compile LAMMPS with the optional "RIGID" package installed. To - do this, go to the "src" directory of your lammps installation and type: - make yes-RIGID - make clean-all - make NAME_OF_TARGET #<--("make ubuntu", "make g++", "make linux".) ----- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_run.sh b/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_run.sh deleted file mode 100755 index f402d7b7c4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_run.sh +++ /dev/null @@ -1,28 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.nvt # Run a simulation at constant volume - -#or - -lmp_mpi -i run.in.npt # Run a simulation at constant pressure - # (Note: Constant pressure conditions have not been - # well tested. The "run.in.npt" script may fail.) - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.nvt -#or -#mpirun -np 4 lmp_mpi -i run.in.npt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_setup.sh b/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/polymer_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/polymer_LR.jpg deleted file mode 100644 index 5529fc74b9..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/polymer_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/solvent_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/solvent_LR.jpg deleted file mode 100644 index 304693e2ac..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/solvent_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/walls+solvent+polymer_t=0.jpg b/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/walls+solvent+polymer_t=0.jpg deleted file mode 100644 index c1dcc4c186..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/walls+solvent+polymer_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/walls_LR.jpg b/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/walls_LR.jpg deleted file mode 100644 index 319427ae61..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/abstract_translocation/images/walls_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt deleted file mode 100644 index 88c1f6e322..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/monomer.lt +++ /dev/null @@ -1,40 +0,0 @@ - # ---------------------------------------------------------------------- - # -- General comment: -- - # -- The write() and write_once() commands create and append text to -- - # -- files (replacing variables beginning with @ or $ with counters.) -- - # -- File names beginning with "In " or "Data " are special. -- - # -- They will be pasted into the LAMMPS input script and -- - # -- data files which are generated by moltemplate. The syntax -- - # -- of these files is exactly the same as the syntax from the -- - # -- corresponding sections of a LAMMPS input script or data file. -- - # ---------------------------------------------------------------------- - - -import "polymer_forcefield.lt" # contains force-field parameters - - -Monomer inherits ForceField { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA 0.0 0.000 0.4000 0.00000 - $atom:R1 $mol:... @atom:R 0.0 0.000 1.000 1.000 - $atom:R2 $mol:... @atom:R 0.0 0.000 1.000 -1.000 - } - - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # parent object's molecule id number as it's own - - # bond-id bond-type atom-id1 atom-id2 - - write("Data Bonds") { - $bond:CR1 @bond:sidechain $atom:CA $atom:R1 - $bond:CR2 @bond:sidechain $atom:CA $atom:R2 - } - # atom-type mass - -} # Monomer - - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt deleted file mode 100644 index 5eae2abe29..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer.lt +++ /dev/null @@ -1,32 +0,0 @@ -import "monomer.lt" # <-- defines "Monomer" and "ForceField" - -Polymer inherits ForceField { - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - #(The "Data Atoms" in Monomer must use "$mol:..." notation.) - - # Make a chain of monomers - monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) - - - # Now, link the monomers together this way: - write("Data Bonds") { - $bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA - $bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA - $bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA - $bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA - $bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA - $bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA - $bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA - $bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA - $bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA - $bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA - $bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA - } - -} # Polymer - - - -# Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "forcefield.lt" diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt deleted file mode 100644 index ef7efe24e4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/polymer_forcefield.lt +++ /dev/null @@ -1,120 +0,0 @@ -# Define a "ForceField" object. -# A force field in moltemplate is any object containing mostly pair_coeff, -# bond_coeff, angle_coeff, dihedral_coeff, "Bonds By Type", "Angles By Type", -# "Dihedrals By Type", "Impropers By Type", "Data Masses" (and "In Charges") -# information. Later on when we define molecule objects, we can access all -# of the atom types and force field parameters here using "inherits ForceField". -# (See "monomer.lt" for example.) - - -ForceField { - - # LAMMPS supports a large number of "styles" (ie. equations for calculating - # forces between particles). At some point, we must eventually select the - # formulas we want to use. This can be done anywhere, but we might as - # well specify that now. Later on we will specify the parameters - # which go into these equations. - - write_once("In Init") { - # -- Styles used in "ForceField" -- - # -- (Changing these styles will change the formulas above) -- - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style opls - pair_style lj/cut 11.0 - } - - - # There are 2 atom types: "CA" and "R" - - write_once("Data Masses") { - @atom:CA 13.0 - @atom:R 50.0 - } - - # ---- 2-body (non-bonded) interactions: ---- - # U(r) = 4*epsilon((sigma/r)^12 - (sigma/r)^6) - # (for details see http://lammps.sandia.gov/doc/pair_lj.html) - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.05 2.0 - pair_coeff @atom:R @atom:R 0.50 2.0 - # (Interactions between different atoms are determined by mixing rules.) - } - - # ---- 2-body (bonded) interactions: ---- - # - # Ubond(r) = k*(r-r0)^2 - # (for details see http://lammps.sandia.gov/doc/bond_harmonic.html) - # - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:sidechain 30.0 1.2 - bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" - } - - # For a compound molecule consisting of smaller building blocks (such as a - # polymer built from monomers), it is tedious to explicitly list all of the - # angles, dihedrals in the entire molecule. Instead, you can define rules - # for automatically generating all the angular interactions between bonded - # atoms according to their connectivity and the atom/bond type. - # Later, when you connect multiple monomers together to form a polymer, - # appropriate bond-angle forces will be applied to these atoms automatically - # (as well as dihedral and improper forces, if defined). - - # ---- 3-body angle (hinge) interactions ---- - # Rules for determining 3-body interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* - } - - # ("@angle:RCR" defines the angle between the R-C-R atoms within a monomer. - # The other angular interactions are between atoms in neighboring monomers.) - - # Force-field parameters for 3-body (angle) interactions: - # - # Uangle(theta) = k*(theta-theta0)^2 - # (for details see http://lammps.sandia.gov/doc/angle_harmonic.html) - # - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:backbone 50.00 160 - angle_coeff @angle:sidechain 50.00 120 - angle_coeff @angle:RCR 50.00 120 - } - - # ---- 4-body dihedral interactions ---- - - # Rules for determining 4-body (dihedral) interactions by atom & bond type: - # dihedralType atmType1 atmType2 atmType3 atmType4 bondType1 bType2 bType3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - } - # (A more realistic force field would have more dihedral and angle types) - - - # The forumula used for dihedral interactions is: - # - # Udihedral(phi) = (K1/2)*(1+cos(phi)) + (K2/2)*(1+cos(2*phi)) + - # ... (K3/2)*(1+cos(3*phi)) + (K4/2)*(1+cos(4*phi)) - # (for details, see http://lammps.sandia.gov/doc/dihedral_opls.html) - # - # The corresponding command is - - write_once("In Settings") { - # dihedral-type K1 K2 K3 K4 - dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 - } - -} # "ForceField" - - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/solvent.lt deleted file mode 100644 index 1073a58a14..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/solvent.lt +++ /dev/null @@ -1,23 +0,0 @@ -###################### SOLVENT ######################### - -import "solvent_single.lt" - -# Fill the simulation box with a solvent. -# In this example, the solvent is made of many -# copies of "MoleculeA" (which has only one atom). - -solvent = new MoleculeA [12].move(3.0,0,0) - [12].move(0,3.0,0) - [12].move(0,0,3.0) - -# To start with a reasonable conformation, it's a good idea to delete the -# solvent where the walls or the polymer is going to be. Here we do it manually: - -delete solvent[*][*][2] # <-- 1st wall will go here -delete solvent[*][*][8] # <-- 2nd wall will go here -delete solvent[6-7][0-8][5-6] # <-- polymer will go here - -# Alternate notation: -# [a:b] notation also works, however the "b" is a strict upper bound... -# ...hence the last line is equivalent to "delete solvent[6:8][0:9][5:7]" -# [a*b] notation also works, and is equivalent to [a-b] diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/solvent_single.lt deleted file mode 100644 index 8057e3c6fc..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/solvent_single.lt +++ /dev/null @@ -1,22 +0,0 @@ -# The two files "solvent_single.lt" and "wall_single.lt" -# define two very simple molecules containing one atom each. -# Both atoms have a similar size (the have the same sigma parameter). - - -MoleculeA { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:a $mol:. @atom:a 0.0 0.0 0.0 0.0 - } - write_once("Data Masses") { - @atom:a 10.0 - } - write_once("In Settings") { - # i j epsilon sigma cutoff - pair_coeff @atom:a @atom:a 0.60 3.0 7.5 #<--attractive - group groupA type @atom:a #(Atoms of this type belong to the "A" group) - } - -} - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/system.lt deleted file mode 100644 index 0ed2727108..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/system.lt +++ /dev/null @@ -1,57 +0,0 @@ - -# LAMMPS supports a large number of force-field styles. We must select -# which ones we need. This information belongs in the "In Init" section (and -# (you can specify it anywhere in your LT files, multiple times if you like). -# If different molecules use different force-field styles, you can use hybrid -# styles. (In this example the molecules share the same pair_style.) - -write_once("In Init") { - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style opls - pair_style lj/cut 9.0 - # If you have charged molecules immersed in a salty implicit - # solvent, you might try something like this this instead: - # pair_style lj/cut/coul/debye 0.1 9.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 -} - - -write_once("Data Boundary") { - 0.0 36.0 xlo xhi - 0.0 36.0 ylo yhi - -18.0 18.0 zlo zhi -} - - -import "solvent.lt" - -import "walls.lt" - -import "polymer.lt" - -polymer = new Polymer -polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis -polymer.move(19.5,22.5,16.5) # move it near the openning of the hole - - - -####################### Notes: ######################### -# -# In this example we deleted solvent and wall molecule objects. -# You can also delete a monomer inside the polymer. To do that use: -# delete polymer/monomers[6] -# You can also delete individual atoms, bonds, angles, dihedrals, & impropers -# from existing molecules. For example to delete an atom in the middle -# of the polymer try this. (Bonds and other interactions will also be removed.) -# delete polymer/monomers[6]/CA -# To delete a bond, try this -# delete polymer/bb6 -# Note: This will not delete the angular interactions if they were explicitly -# defined (ie, using "Data Angles" instead of "Data Angles By Type"). -# Delete explicit angle, dihedral, and improper interactions manually. -# Note: In both cases the two molecule fragments will keep the same mol counter. diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/wall_single.lt deleted file mode 100644 index 79275a06b4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/wall_single.lt +++ /dev/null @@ -1,21 +0,0 @@ -# The two files "solvent_single.lt" and "wall_single.lt" -# define two very simple molecules containing one atom each. -# Both atoms have a similar size (the have the same sigma parameter). - -MoleculeB { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:b $mol:. @atom:b 0.0 0.0 0.0 0.0 - } - write_once("Data Masses") { - @atom:b 10.0 - } - write_once("In Settings") { - # i j epsilon sigma cutoff - pair_coeff @atom:b @atom:b 0.05 3.0 7.5 #<--repulsive (approximately) - group groupB type @atom:b #(Atoms of this type belong to the "B" group) - } - -} - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/walls.lt deleted file mode 100644 index dcccac941e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/moltemplate_files/walls.lt +++ /dev/null @@ -1,23 +0,0 @@ -####################### WALLS ########################## - -import "wall_single.lt" - -# Create a wall at position z=6.0 (6.0 = 2*3.0) - -wall1 = new MoleculeB [12].move(3.0, 0, 0) - [12].move(0, 3.0, 0) - -wall1[*][*].move(0,0,6.0) - -# Create a second wall at position z=24.0 (24.0 = 8*3.0) - -wall2 = new MoleculeB [12].move(3.0, 0, 0) - [12].move(0, 3.0, 0) - -wall2[*][*].move(0,0,24.0) - -# Now delete some of the molecules in "wall2" to create a hole. - -delete wall2[6-7][6-9] -delete wall2[5-8][7-8] - diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/run.in.npt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/run.in.npt deleted file mode 100644 index 0b58a8e1b0..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/run.in.npt +++ /dev/null @@ -1,120 +0,0 @@ -# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. -# (This simulation may fail. -# However the "run.in.nvt" example in this directory should work.) -# -# Requirements: -# To run this system at constant pressure, it might help to compile LAMMPS with -# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) -# The use of fix rigid is controversial. This method is demonstrated below. - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# Only the groupB atoms are immobile. -group mobile subtract all groupB - -# Unfortunately you can not use the LAMMPS "minimize" command on this system -# because there is no way to immobilize the wall atoms during minimization. -# Instead, we can use langevin dynamics with a fast -# damping parameter and a small timestep. - -print "--------- beginning minimization (using fix langevin) ---------" - -timestep 0.1 -fix fxlan mobile langevin 1.0 1.0 100.0 48279 -fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) -thermo 100 -run 2500 - -unfix fxlan -unfix fxnve - -# -- simulation protocol -- - -print "--------- beginning simulation (using fix nvt) ---------" - -dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 200 # time interval for printing out "thermo" data - - -# ------------------------- NPT --------------------------- - - -# ------ QUESTIONABLE (see below): ------ - -fix Ffreezestuff groupB rigid single force * off off off torque * off off off - -# Comment: -# The use of "fix rigid" to immobilize an object is somewhat controversial. -# Feel free to omit it. -# (Neither Trung or Steve Plimpton use fix rigid for immobilizing -# molecules, but I noticed that at NPT, it does a better job of maintaining -# the correct volume. However "fix rigid" has changed since then (2011), -# so this may no longer be true. Please use this example with caution.) - - - -# Thermostat+Barostat -# Set temp=300K, pressure=200bar, and equilibrate volume only in the z direction - -fix fxMoveStuff mobile npt temp 300 300 100 z 200 200 1000.0 dilate mobile drag 2.0 - -# ---------------------------------------- - -# The next two lines recalculate the temperature using -# only the mobile degrees of freedom (ie. water atom velocities): - -compute tempMobile mobile temp -compute pressMobile all pressure tempMobile - -thermo_style custom step c_tempMobile c_pressMobile temp press vol - -fix_modify fxMoveStuff temp tempMobile - -reset_timestep 0 - -timestep 0.5 - -run 100000 - -timestep 1.0 - -run 100000 - - -write_data system_after_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also.) - - - - - - - -# ----- Comment: Avoid using fix rigid/npt on large single rigid objects ----- -# -# Use of the following is not recommended: -# -# fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 200 200 1000.0 force * off off off torque * off off off dilate mobile -# (temp=300K, pressure=200bar, and equilibrate volume only in the z direction) -# -# In my experience, the system becomes unstable when applying "fix rigid/npt" -# to the immobile atoms, while also applying "fix npt" on the solvent atoms. -# (It is probably a bad idea to use two barostats simultaneously.) -# ---------------------------------------------------------------------------- diff --git a/tools/moltemplate/examples/coarse_grained/abstract_translocation/run.in.nvt b/tools/moltemplate/examples/coarse_grained/abstract_translocation/run.in.nvt deleted file mode 100644 index c483d0b9ab..0000000000 --- a/tools/moltemplate/examples/coarse_grained/abstract_translocation/run.in.nvt +++ /dev/null @@ -1,53 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (See README_setup.sh for details) - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Use "neigh_modify" to turn off calculation of interactions between immobilized -# atoms. (Note: The "groupB" group was defined in the file "system.insettings") -neigh_modify exclude group groupB groupB - -# -- Run Section -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - - -# Optional: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms. (Note: This is not optional under NPT conditions.) -neigh_modify exclude group groupB groupB - -# Only the groupB atoms are immobile. -group mobile subtract all groupB - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp - -# Integrate the equations of motion: -fix fMoveStuff mobile nvt temp 300.0 300.0 100.0 -fix_modify fMoveStuff temp tempMobile - - -run 100000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_FIRST.txt b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_FIRST.txt deleted file mode 100644 index 5420d95da3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_FIRST.txt +++ /dev/null @@ -1,48 +0,0 @@ -This is an implementation of the "two-stage" model used by Maxim Imakaev -in the Naumova et Al 2013 Science paper on metaphase chromatin. -(Download the supplemental materials section and scroll down to the section: - "Two-stage process: linear compaction - axial compression") - ----- SMALL MODIFICATION ---- - -Unlike that study, I did not use "softened" Lennard-Jones potentials -(which allow the chains to pass through each other). - ---- Why use moltemplate? --- - -Honestly, you don't need to use moltemplate to build this polymer. -It is almost counter-productive to use moltemplate to build this kind of -polymer because it is so simple. (The polymer has only 1 bead per atom. -It just makes it more complicated to introduce all these extra -files including monomer.lt, condensin.lt and system.lt, especially considering -that system.lt is a complex file which is generated by a separate script.) - -However building the sytem using moltemplate may pay off if you -replace each point-like monomer with a multi-atom molecule later on. -(Right now, using moltemplate to build this system is sort of overkill. - I'll post an example of building more complex models of chromatin eventually.) - -Anyway, the two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section. - ----- 10-nm fiber model: ---- - -For the 10nm model, - n=128000, - L=200, - U(alpha)=5*(1 - cos(alpha)) - bond_length=1.0 (=10nm) - sigma=1.0 (particle radius = 10nm) - ----- 30-nm fiber model: ---- - -"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level." - -I interpret this to mean that, for the 30nm model, - n=128000/4.25~=30117 (however I rounded up to 32768=2^15) - L=200/4.25~=47 (however I rounded up to 51) - U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647) - -To increase the volume by a factor o 4.25, I increase both the diameter of each -bead (the "sigma" parameter), and the bond-lengths connecting them from -1.0 (corresponding to 10nm) to 4.25^(1/3)~=1.6198 (corresponding to 16.198nm). - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt deleted file mode 100644 index 38ad9c1c06..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt +++ /dev/null @@ -1,29 +0,0 @@ ---------------- -The average diameter of a mammalian cell nucleus is is 6 micrometers (μm), -which occupies about 10% of the total cell volume. - -(See "Molecular Biology of the Cell, Chapter 4, pages 191–234 (4th ed.)", by - Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 2002) - -... of that, 25% of it is occupied by the nucleolus -http://en.wikipedia.org/wiki/Nucleolus -("citation needed") ---------------- - -From the supplemental material for the original HiC paper -(Lieberman-Aiden et al., Science 2009) - -Appendix 1. - Estimate of the Volume Fraction of Chromatin in Human Cells -In the simulations we sought to obtain an ensemble of structures that, in their statistical properties, resemble some of the features of chromatin arrangement in the cell. Below we demonstrate that chromatin occupies a significant fraction of cell volume, a property that we reproduced in simulations. Taking the nuclear diameter of a tissue culture cell to be 5-10um, and assuming close to a spherical shape we obtain the volume in the range 50-500 um^3, with a (geometric) mean of ~160 um^3. If we assume that the chromatin is built of DNA wrapped around nucleosomes, then we have 6x10^9bp/200bp=3x10^7 nucleosomes. Each may be approximated as a cylinder ~10nm in diameter and ~5nm in height, suggesting a volume of about 500nm3 each. The linker DNA after each nucleosome is about 50bps long, suggesting a volume of about 50*0.34nm*3.14*1nm^2=50nm^3. Thus the total volume of chromatin = 550x3x10^7 =16 um^3, or ~10% (3-23%) of the nuclear volume. This strikingly large volume fraction is itself a significant underestimate, since we ignored, among other things, all other DNA-bound proteins. Note that any further packing or localization of chromatin inside the nucleus will increase local density. ----- This next section mostly only justifies why they ---- ----- they did not stop the simulation when the globules ---- ----- were fully crumpled (ie with uniform density) ---- - In our simulations, the radius of the final crumpled globule was R≈12.5 and the volume V≈8000 cubic units. The total volume of the 4000 monomers, 1 unit in diameters each, is V≈2000. This implies a volume fraction of about 25%, which is consistent with the volume fraction estimated above. - ---- ---- - -Appendix 2. - Monomer length in base pairs -Each monomer of the chain corresponds to a fragment of chromatin that equals the Kuhn length of the chromatin fiber, i.e. approximately twice the persistence length of the fiber. Although the persistence length of the chromatin fiber is unknown it can be estimated using the following arguments. DNA is packed into nucleosomes, where 150 bps are wrapped around the histone core and do not contribute to flexibility of the fiber. The linker DNA of about 50 bps that connects consecutive nucleosomes is bendable, and is the source of flexibility in the fiber. Since the persistence length of double-stranded DNA is 150 bps, an equally flexible region of the nucleosomal DNA should contain 3 linkers, i.e. 3 consecutive nucleosomes packing about 600 bps of DNA. The excluded volume of the nucleosomes, nucleosome interactions, and other DNA-bound proteins can make the fiber less flexible or prohibit certain conformation and may tend to increase the persistence length of the fiber. Using this estimated lower bound estimate for the persistence length, we obtain the Kuhn length of the equivalent freely-jointed chain to be 6 nucleosomes, or ~ 1200bp. A simulated chain of 4000 monomers corresponds to 4.8Mb of packed DNA. The size of each monomer was chosen such that its volume is equal to (or slightly above) that of 6 nucleosomes (V=6 x 600 nm^3); thus the radius of the spherical monomer is R=10nm. The diameter of each globule shown in Figure 4 is about 200 nm. - - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_run.sh b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_run.sh deleted file mode 100755 index 19674c88bd..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_run.sh +++ /dev/null @@ -1,7 +0,0 @@ -# Run lammps using the following 3 commands: -# (assuming "lmp_mpi" is the name of your LAMMPS binary) - -lmp_mpi -i run.in.min -lmp_mpi -i run.in.stage1 -lmp_mpi -i run.in.stage2 - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_setup.sh b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_setup.sh deleted file mode 100755 index 3f261528b4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_setup.sh +++ /dev/null @@ -1,58 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # First, rescale and interpolate the positions - # where the monomers will be located. (This step is - # not needed if the coords_orig.raw file already has correct coordinates.) - - ./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw - - # Then, build the "system.lt" file - - ./generate_system_lt.py 32768 51 < coords.raw > system.lt - - # 32768 is the number of monomers in the polymer - # (which may be different from the number of coordinates - # in the "coords_orig.raw" file) This number will vary - # depending on how long you want the polymer to be. - # The second argument "51" is the average interval between - # condensin anchors (IE the "loop size" in monomers.) - - - # Run moltemplate - - moltemplate.sh system.lt -a "@bond:stage1 1" \ - -a "@bond:stage2 2" \ - -a "@atom:Monomer/A 1" - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - # - # We used the "-a" command to set the variable @bond:condensin to "2" - # because we will refer to it later in the "run.in" LAMMPS input script. - # (Of coarse, LAMMPS knows nothing about moltemplate variables, - # so in that file we refer to it as dihedral type "1") - - mv -f system.in* system.data ../ - - # We also need the table of bond forces used during "stage 2". - # (Like the system.data and the various input scripts, this file is needed by - # LAMMPS, so we need to copy it to the directory where we will run the sim.) - cp -f table_bonds_stage2.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - - # Optional: - # Remove the "system.lt" file created by "generate_system_lt.py" - #rm -f system.lt - -cd ../ - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_visualize.txt deleted file mode 100644 index 31abe1e1ec..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_visualize.txt +++ /dev/null @@ -1,131 +0,0 @@ -NOTE: VMD DOES NOT ALLOW YOU TO VISUALIZE SYSTEMS WITH MANY BONDS ATTACHED - TO EACH ATOM. (IF IT DID, THE RESULTS WOULD BE UGLY ANWAY.) - -HOWEVER THIS MODEL ATTACHES APPROXIMATELY 60 BONDS TO EACH CONDENSIN ATOM. -IN ORDER TO PULL THE CONDENSIN MONOMERS TOGETHER. YOU MUST DELETE THOSE -BONDS (of type "1" or "2") FROM THE "system.data" FILE BEFORE YOU CARRY -OUT THE COMMANDS BELOW. (...And backup your "system.data" file. You'll need -all the bonds when you run the simulations.) - --------------- COLORS --------------- -In order to show how the polymer is distributed along the length of the -cylinder, I recommend to select the -Graphics->Graphical Representations -menu option, and select "Index" from the "Coloring Method" pull-down menu. - -After doing this, you can switch from a red-white-blue scheme, to a -rainbow ("jet") scheme, by selecting the Extensions->Tk Console menu option -and loading the "vmd_colorscale_jet.tcl" file located in the "images" directory. -------------------------------------------- - -First, if you have not done so, download and install VMD: - -http://www.ks.uiuc.edu/Research/vmd/ -http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD - - - ------- To view a lammps trajectory in VMD -------- - -The system coordinates are initialy stored in a LAMMPS' ".data" file. -(If that file was built with moltemplate, it will be named "system.data".) - -The first step is to view that file. -Then you should create a ".psf" file -(The .psf file is necessary after you run the simulation - for viewing trajectories.) - -1) Build a PSF file for use in viewing with VMD - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -You will see a snapshot of the system on the screen. -(presumably the initial conformation at t=0) - -2) - -Later once you have run a simulation, -to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file - (It usually has names like "traj.lammpstrj". It depends on how you saved it.) - If necessary, for "file type" select: "LAMMPS Trajectory". - (However VMD should recognize the file type by the file extension.) - Load it. - - - - - -##################### PERIODIC BOUNDARY CONDITIONS ##################### - If you are only simulating a single molecule and you are not - using periodic boundary conditions, then ignore everything below. -######################################################################## - - ---- A note on trajectory format: ----- -If the trajectory is the standard LAMMPS format, (aka a "DUMP" file with -a ".lammpstrj" extension), then it's a good idea when you run the simulation -to tell LAMMPS you want to store the information needed for showing periodic -boundary conditions. (Even if you are not using periodic boundaries. -It never hurts to include a tiny bit of extra information.) To do that, -I've been using this command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 traj.lammpstrj id mol type x y z ix iy iz - -(Also: it's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. I think this is needed -to wrap atom coordinates visually without breaking molecules in half. Again -you don't need to worry about this if you are not using periodic boundaries.) - - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.5 -0.5 -0.5} - pbc box -shiftcenterrel {-0.5 -0.5 -0.5} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/stage2_interior.jpg b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/stage2_interior.jpg deleted file mode 100644 index 8765cec85e..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/stage2_interior.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/stage2_interior_rotated.jpg b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/stage2_interior_rotated.jpg deleted file mode 100644 index 2d46cc6a43..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/stage2_interior_rotated.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/t=0_before_minimizaion.jpg b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/t=0_before_minimizaion.jpg deleted file mode 100644 index 06600ecc99..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/t=0_before_minimizaion.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/vmd_colorscale_jet.tcl b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/vmd_colorscale_jet.tcl deleted file mode 100644 index 7434eca99e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/images/vmd_colorscale_jet.tcl +++ /dev/null @@ -1,87 +0,0 @@ - -proc lerpcolor { col1 col2 alpha } { - set dc [vecsub $col2 $col1] - set nc [vecadd $col1 [vecscale $dc $alpha]] - return $nc -} - -proc coltogs { col } { - foreach {r g b} $col {} - set gray [expr ($r + $g + $b) / 3.0] - return [list $gray $gray $gray] -} - -proc jet_tricolor_scale {} { - display update off - set mincolorid [expr [colorinfo num] - 1] - set maxcolorid [expr [colorinfo max] - 1] - set colrange [expr $maxcolorid - $mincolorid] - set colhalf [expr $colrange / 2] - for {set i $mincolorid} {$i < $maxcolorid} {incr i} { - set colpcnt [expr ($i - $mincolorid) / double($colrange)] - - # The following color definitions for "jet" sort-of came from: - #http://stackoverflow.com/questions/7706339/grayscale-to-red-green-blue-matlab-jet-color-scale - # but it was missing "green", so I inserted a green somewhere in the middle. - - # darkblue/violet 0.0 - set color0 { 0.08 0.0 0.77 } - - # blue 0.19 - set color1 { 0.0 0.0 1.0 } - - # cyan 0.34 - set color2 { 0.0 1.0 1.0 } - - # turquoise 0.4001 - set color3 { 0.0 1.0 0.78 } - - # green 0.445 - set color4 { 0.0 1.0 0.0 } - - # chartreuse 0.535 - set color5 { 0.875 1.0 0.0 } - - # yellow 0.69 - set color6 { 1.0 1.0 0.0 } - - # orange 0.73 - set color7 { 1.0 0.25 0.0 } - - # red 0.755 - set color8 { 1.0 0.0 0.0 } - - # darkred 1.0 - set color9 { 0.93 0.0 0.0 } - - if { $colpcnt < 0.19 } { - set nc [lerpcolor $color0 $color1 [expr $colpcnt/(0.19-0.0)]] - } elseif { $colpcnt < 0.34 } { - set nc [lerpcolor $color1 $color2 [expr ($colpcnt-0.19)/(0.34-0.19)]] - } elseif { $colpcnt < 0.4001 } { - set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.34)/(0.4001-0.34)]] - } elseif { $colpcnt < 0.445 } { - set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.4001)/(0.445-0.4001)]] - } elseif { $colpcnt < 0.535 } { - set nc [lerpcolor $color3 $color4 [expr ($colpcnt-0.445)/(0.535-0.445)]] - } elseif { $colpcnt < 0.69 } { - set nc [lerpcolor $color4 $color5 [expr ($colpcnt-0.535)/(0.69-0.535)]] - } elseif { $colpcnt < 0.73} { - set nc [lerpcolor $color5 $color6 [expr ($colpcnt-0.69)/(0.73-0.69)]] - } elseif { $colpcnt < 0.755} { - set nc [lerpcolor $color6 $color7 [expr ($colpcnt-0.73)/(0.755-0.73)]] - } else { - set nc [lerpcolor $color7 $color8 [expr ($colpcnt-0.755)/(1.0-0.755)]] - } - - # set nc [coltogs $nc] - foreach {r g b} $nc {} - puts "index: $i $r $g $b -- $colpcnt" - display update ui - color change rgb $i $r $g $b - } - display update on -} - -jet_tricolor_scale - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/README_how_to_generate_system_lt.sh b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/README_how_to_generate_system_lt.sh deleted file mode 100755 index 829b4c6be0..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/README_how_to_generate_system_lt.sh +++ /dev/null @@ -1,19 +0,0 @@ - # First, rescale and interpolate the positions - # where the monomers will be located. (This step is not needed - # if the coords_orig.raw file already has correct coordinates.) - # The first argument, 32768 is the number of atoms in the desired file. - # The second argument, 1.6198059 = 4.25^(1/3), tells interpolate_coords.py - # to multiply all the coordinates (scale them up) by 1.6198059. - - ./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw - - # Then, build the "system.lt" file - - ./generate_system_lt.py 32768 51 < coords.raw > system.lt - - # 32768 is the number of monomers in the polymer - # (which may be different from the number of coordinates - # in the "coords_orig.raw" file) This number will vary - # depending on how long you want the polymer to be. - # The second argument "51" is the average interval between - # condensin anchors (IE the "loop size" in monomers.) diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/README_length_flexibility_details.txt b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/README_length_flexibility_details.txt deleted file mode 100644 index f2cd91c0b4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/README_length_flexibility_details.txt +++ /dev/null @@ -1,57 +0,0 @@ ----- Andrew's comments ---- - -The two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section. - -For the 10nm model, - n=128000, - L=200, - U(alpha)=5*(1 - cos(alpha)) - bond_length=1.0 (=10nm) - sigma=1.0 (particle radius = 10nm) - -30nm-fiber model details: -"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level." - -I interpret this to mean that, for the 30nm model, - n=128000/4.25~=30117 - L=200/4.25~=47 - U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647) -To increase the volume by a factor o 4.25, originally I thought I should increase the "sigma" parameter from 1.0 to 4.25^(1/3)~=1.6198. But I suspect that the bond-lengths between monomers should be fixed at 1.0. If that is the case, then, perhaps I should increase "sigma" from 1.0 to 4.25^(1/2)~=2.061552, and keep the bond-length fixed at 1.0 (which in the units used by thsi paper, corresponds to 10nm). (That would increase the volume of a cylinder of radius "sigma" and length="bond-length" by a factor of 4.25) - bond_length=1.0 (10nm again) - sigma=2.061552 (Yes, this is less than 3.0<-->30nm. See below.) - - - - ---- Excerpts from the Supplemental section of Naumova et al Science 2013 --- - -From p. 18 of the supplemental materials section of Naumova et al Science 2013. - - (This section was probably written by Maxim Imakaev.) - - In vivo, the structure of the chromatin fiber can be complicated and many details remain unknown, particularly in metaphase. Given this uncertainty, we simulated chromatin as a homogeneous “beads-on-a-string†polymer fiber. We consider a 10nm fiber, as the pervasiveness of the 30nm fiber in vivo has become increasingly contested. In our simulations, 77Mb is represented by a densely-packed 10nm fiber of 128,000 monomers. Each monomer represents a 10nm-sized DNA-histone complex containing 3 nucleosomes (around 600bp). The fiber has a persistence length of 4 monomers (~2.4Kb), which is based on earlier estimates of 5-10 nucleosomes for interphase (14). Those estimates arise from the assumption that 5-10 linker DNA fragments, each of 20-40bp, can collectively provide flexibility equal to that of the 150bp persistence length of DNA. Binding of proteins to the linker DNA (e.g. histone H1) and interactions between neighboring nucleosomes can further constrain dynamics, requiring more linkers to provide the persistence length. Due to the tight packing of nucleosomes in metaphase, we use the upper limit of this range, i.e. 12 nucleosomes. - For the consecutive loops on a scaffold model (the final folded state model with the best agreement with Hi-C data), we also performed simulations with a more flexible 10nm fiber, or with a 30nm fiber, and found similar results. The more flexible 10nm fiber was modeled by decreasing persistence length to 1.8 monomers. The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level. We note that a classic model of a 30nm fiber is much less dense than a compact metaphase chromosome. A textbook model of a 30nm fiber assumes packing of about 6 nucleosomes per 10nm of fiber length. This model predicts that only 28% of the volume of the fiber (a 30nm-diameter cylinder) is occupied by nucleosomes, assuming a nucleosome shell volume of 328 nm^3. This is much less than the estimated 30-50% density of nucleosomes in a metaphase chromosome, assuming a diameter of 600nm, a packing density of 50-70 Mb/um, and the same nucleosome volume. (See also (15), which gives an estimate of 0.14-0.18 pg/μm for DNA only, and would give about twice the density if DNA is counted with nucleosomes). As follows, these fibers would have to interdigitate, and fill in gaps within each other. We account for this overlap by assuming the effective diameter of the fiber to be less than 30nm. The effective diameter was chosen to make the volume of the fiber equal the total volume of all the nucleosomes. - - We accounted for topoisomerase II activity by allowing chromatin fibers to pass through each other, while still having excluded volume interactions. This was achieved by using a soft-core Lennard-Jones potential with 1kT energy cost for monomer overlap (see below). This allows for changes in the topological state of a chromosome that are known to occur during compaction in vivo. - -Our simulations of a two-step folding process show that Hi-C data for mitotic chromosomes is consistent with a linearly compressed array of consecutive chromatin loops. Whereas mechanisms for formation of consecutive chromatin loops have been proposed, the process of axial compression is less understood. Chromatid compression cannot be accomplished by increased chromatin-chromatin affinity alone, as this would lead to condensation into a globular geometry (14, 16, 17). However, mechanisms which locally compress the fiber of loop bases naturally allow for anisotropic compression into a shorter and thicker fiber, with the same width regardless of chromosome length (18). Differences in the duration or efficiency of the first and second stages of chromosomal condensation provide a natural mechanism for condensation-related proteins to separately affect mitotic chromosome length and width (19). We also note that the axis of loop-bases in our two-stage model does not necessarily form a continuous and rigid scaffold (Figure S26). As follows, we remain agnostic about the molecular details of the chromosomal scaffold, which might for example be formed by a network consisting of protein-protein and/or protein-DNA interactions (20). - - 1. Polymer simulations - - To perform Langevin dynamics polymer simulations we used OpenMM, a high-performance GPU-assisted molecular dynamics API (21, 22). To represent chromatin fibers as polymers, we used a sequence of spherical monomers of 1 unit of length in diameter. Here and below all distances are measured in monomer sizes, set to be 10nm unless specified otherwise. Neighboring monomers are connected by harmonic bonds, with a potential U = 100*(r - 1)^2 (here and below in units of kT). Polymer stiffness is modeled with a three point interaction term, with the potential U = 5*(1 - cos(alpha)), where alpha is the angle between neighboring bonds. All monomers interact via either a shifted Lennard-Jones (LJ) repulsive potential, or an attractive Lennard-Jones potential. At high densities in a confined volume, the details of the inter-monomer interactions become negligible due to screening (23), and we therefore used the computationally efficient shifted LJ potential. The shifted LJ potential allows for a short-range repulsion by truncating the LJ potential at its minimum and shifting the minimum to zero: U = 4 * (1/r^12 - 1/r^6) + 1, for r<2^(1/6); U=0 for r > 2^(1/6). The shifted LJ potential is one of the most computationally efficient repulsive potentials due to a very short cutoff radius. - - To allow chain passing, which represents activity of topoisomerase II, we softened the shifted LJ potential by truncating the interaction energy at Ecutoff = 1 kT. At energies more than 0.5 Ecutoff, the LJ potential was softened via: Usoftened = 0.5 * Ecutoff * (1 + tanh(2*U/Ecutoff - 1)). To avoid numerical 19instabilities in the calculation of U at r ~ 0, the interaction radius r was truncated at r=0.3 via: rtruncated = (r^10 + (0.3)^10)^0.1, which introduced negligible shift in a final softened potential. For an attractive LJ potential, we used: U = 4 * e * (1/r^12 - 1/r^6), with e = 0.46 kT, slightly below the theta-temperature. The attractive potential was similarly softened at 2 kT and cut off at r=2.5. Unless noted, we used a softened shifted LJ repulsive potential. - - Polymer models were visualized using Pymol and Rasmol. For images with loop bases highlighted, a base of each loop and 3 monomers surrounding it in each direction were labeled in red. - - SECTIONS 2-5 SKIPPED - -6. Two-stage process: linear compaction - axial compression - -To simulate the two-stage process of metaphase chromosome folding, we used the 30nm fiber representation described above for its computational efficiency. Simulations were initialized from 30000 monomer fractal globule conformations; fractal globule is a model for interphase chromatin organization. First, random consecutive loops with L=100 monomers (see above) were introduced, and anchors of neighboring loops were brought together using harmonic springs with a potential U = k * (r – r0)2; r0=0.5. To avoid abrupt motion of the loop anchors, the force was gradually turned on over the first -300000 timesteps, with k linearly increasing in time from 0 to 10 kT. We used softened shifted repulsive LJ potential for inter-monomer interaction. - -Upon completion of linear compaction, axial compression was initiated. This involves following changes: the repulsive LJ force is replaced with an attractive LJ force for all monomers, and the chromosomal core of loop anchors is homogeneously compressed. To achieve the latter, all anchor pairs separated by less than 30 anchors were attracted via a potential U = step(d-3) * abs(d-3) * 10 kT, which implements a constant attractive force between two anchors if they are separated by a distance larger than 3. The interactions between neighboring loop anchors were kept throughout this process. - -To obtain the contact map from this simulation, 50 independent runs of 1.5e7 timesteps were performed, and 250 conformations were collected from the second half of each run. The contact map was calculated from all conformations of all runs at a 30-monomer resolution, and was further averaged over three 10000-monomer blocks along the diagonal of the heatmap. The latter was done to show contact map at a relevant length scale (0 to 25 Mb), and to achieve a better averaging of the contact map. - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/calc_table.sh b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/calc_table.sh deleted file mode 100755 index aed66719f0..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/calc_table.sh +++ /dev/null @@ -1,8 +0,0 @@ - - -for ((i=0; i<60; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` 0 0; done - -echo 61 3.0 0 -5 - -for ((i=61; i<=4000; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` `echo "($i-60)*0.5"|bc` -10; done - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/condensin.lt b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/condensin.lt deleted file mode 100644 index f8dfea089b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/condensin.lt +++ /dev/null @@ -1,47 +0,0 @@ -# This file contains the definition of a molecule named "CondensinMonomer". -# (This particular molecule contain only one atom, but that is up to you.) -# Later, multiple CondensinMonomers can be connected together to build a molecule. - - - -CondensinMonomer { - - # atom-id mol-id(ignore) atom-type q x y z - - write("Data Atoms") { - $atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000 - } - - # (The x y z positions will be changed later with move commands - # You can spedify charge and other properties by changing the atom_style.) - - - - # atom-type mass - - write_once("Data Masses") { - @atom:A 1.0 - } - - # pairwise interactions (between non-bonded atoms): - # - # U(r) = 4*eps*((r/sig)^12 - (r/sig)^6) - # - # Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0 - # - # atom-type atom-type pair_style epsilon sigma - - write_once("In Settings") { - # I usually use sigma = 2^(-(1/6)), with a cutoff of 1 - #pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0 - # In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0 - # with a cutoff of 2^(1/6). Here we are trying to reproduce his results. - # 10nm fiber - #pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373 - # 30nm fiber (4.25^(1/2)=2.0615528128088303) - #pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349 - # 30nm fiber (4.25^(1/3)=1.6198059006387417) - pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708 - } - -} # CondensinMonomer diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/coords_orig.raw b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/coords_orig.raw deleted file mode 100644 index 9137c70616..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/coords_orig.raw +++ /dev/null @@ -1,32768 +0,0 @@ --25.8563 0.5868639 -10.5686 --26.7104 0.5123159 -10.988 --26.6472 -0.3489721 -10.3989 --27.477 0.09032793 -9.96323 --27.5656 0.5432849 -9.07679 --26.9532 1.30193 -9.02479 --27.7767 1.68179 -8.50491 --28.3972 2.40457 -8.91213 --28.6132 3.17136 -9.43966 --29.5915 2.93084 -9.73989 --29.9486 2.90331 -8.78678 --29.5668 3.82558 -8.58056 --29.4603 4.69627 -9.07626 --29.3895 5.66981 -9.03451 --30.1683 5.95262 -9.57885 --29.7252 6.82771 -9.62399 --29.3815 6.72967 -10.6049 --29.3359 7.11535 -11.5251 --28.6608 7.01853 -12.2411 --29.4269 7.23933 -12.8807 --28.8974 7.95352 -13.1355 --28.0615 8.41522 -13.369 --28.0899 7.83209 -14.2049 --28.9177 7.60378 -14.7609 --28.5783 7.72824 -15.6631 --28.8091 8.6176 -15.7699 --27.8292 8.72143 -15.4435 --27.0719 9.11061 -15.8328 --27.6533 9.78633 -16.3367 --27.7805 10.078 -15.4008 --27.4267 11.0102 -15.2806 --26.759 11.2425 -15.9727 --25.8124 10.7779 -16.0688 --25.9429 9.74176 -16.1052 --25.4567 8.84701 -16.0595 --25.0517 8.38721 -16.808 --24.4227 9.04521 -17.207 --23.8866 9.76185 -17.5133 --24.3909 10.0475 -16.6904 --25.0046 9.89792 -16.0027 --24.2884 10.043 -15.2759 --23.7492 10.8581 -14.9341 --23.4663 10.2023 -14.2305 --22.567 9.78524 -14.4336 --22.3801 10.3667 -13.6503 --22.207 11.2232 -14.0766 --22.1804 11.7239 -14.9411 --21.7644 12.6471 -14.7781 --20.9193 12.8327 -14.2212 --20.6343 13.0464 -15.1856 --20.0922 13.5451 -14.5286 --19.2983 13.914 -15.0082 --19.4023 13.0675 -15.5298 --18.5232 13.3107 -15.1504 --18.7586 12.7611 -14.334 --18.131 13.2514 -13.8647 --17.6729 12.5626 -13.1865 --16.7235 12.2766 -12.9417 --16.4151 12.9808 -12.2597 --16.515 12.6115 -11.3464 --17.2797 13.2961 -11.2699 --18.0935 13.8348 -11.2771 --19.1087 14.0856 -11.266 --20.0859 13.9469 -11.2803 --20.6702 13.1886 -11.171 --21.1132 13.6779 -10.4824 --20.7554 14.0923 -9.66475 --20.0092 13.3717 -9.46904 --20.2154 12.4286 -9.67692 --20.3212 12.0637 -10.6268 --20.6477 11.3656 -11.2997 --19.6829 11.205 -11.3344 --19.8476 11.8356 -12.123 --20.6059 11.9227 -12.7203 --19.6468 11.9213 -13.2611 --19.1986 11.5456 -14.0954 --19.4092 11.422 -15.1036 --18.97 10.6398 -15.5632 --19.2307 10.3891 -16.4246 --19.7998 9.63451 -16.5879 --19.0267 9.23752 -17.0947 --18.9718 8.51511 -16.4976 --18.5581 8.14381 -15.6756 --17.8601 8.72615 -16.1132 --16.8864 8.95457 -16.1283 --17.2573 8.65394 -17.0059 --16.8834 8.877 -17.9317 --16.9804 7.93611 -17.8517 --16.3517 7.18904 -18.1058 --15.44 7.46366 -18.4049 --14.6079 8.00931 -18.3901 --13.993 7.99908 -19.2032 --14.6716 7.33714 -19.1401 --15.2908 6.5047 -19.3095 --15.7928 5.64885 -19.0565 --14.9593 5.79763 -18.5547 --14.8818 5.10065 -19.2857 --14.9343 4.63209 -20.1751 --14.819 3.75787 -19.7859 --14.9014 2.77884 -19.7258 --15.8254 2.34137 -19.8546 --16.7518 2.11938 -19.9102 --17.2858 1.38873 -19.6316 --17.6051 2.23194 -19.3101 --17.4759 2.2122 -18.2935 --16.555 1.90863 -17.996 --16.3599 1.18543 -17.2873 --16.6597 0.2817609 -17.0068 --17.4192 -0.1762871 -16.5829 --17.5676 0.3030899 -15.6993 --18.4786 0.2816979 -16.1894 --19.3873 -0.03042487 -15.8965 --19.1305 -0.9198991 -16.3767 --18.8053 -1.89678 -16.5631 --17.8952 -2.29912 -16.367 --17.881 -1.7091 -15.4693 --18.034 -2.7152 -15.2978 --17.6676 -3.55164 -14.8756 --16.7023 -3.52134 -15.1619 --15.9315 -4.17398 -15.1337 --15.0123 -4.0393 -14.7833 --14.3289 -4.18259 -14.1178 --14.8199 -3.5703 -13.5025 --14.0673 -3.45279 -12.9118 --13.8652 -2.4677 -12.6746 --14.7013 -2.51433 -12.1349 --14.7591 -1.57501 -12.6047 --14.3849 -0.7913011 -12.8965 --15.0335 -0.6417921 -12.0814 --15.9264 -1.16147 -11.9717 --15.4966 -1.75734 -11.2786 --16.3186 -1.89513 -10.7004 --17.3447 -1.99074 -10.7706 --16.8078 -2.28381 -11.5947 --17.5234 -2.81286 -12.0644 --18.1535 -2.10741 -11.7565 --19.0461 -2.18436 -11.3109 --18.9286 -1.33458 -11.7392 --18.6673 -1.3773 -12.7462 --18.9847 -2.20517 -13.2055 --19.0146 -1.52805 -13.9914 --19.5602 -1.22894 -14.7766 --19.9174 -0.6614531 -13.9545 --19.3542 0.1054139 -14.1998 --20.0903 0.7562789 -14.2155 --20.2834 1.58939 -14.6348 --19.7527 2.45077 -14.9298 --20.7223 2.72193 -15.1458 --20.74 2.42061 -15.9961 --19.8152 2.19964 -16.3204 --18.971 2.3405 -15.7096 --18.6579 3.23116 -16.186 --17.7978 3.59352 -16.3547 --16.97 4.12994 -16.4791 --16.5011 3.5915 -15.7777 --16.0202 3.89081 -14.8962 --15.6429 3.25724 -14.3553 --14.7397 3.4752 -14.0485 --14.7642 3.81665 -13.1634 --14.4103 3.11518 -12.5644 --14.1883 3.73765 -11.7934 --14.3687 4.55216 -11.3856 --14.3268 4.88789 -12.3038 --15.1957 5.38065 -12.2756 --15.6408 5.01672 -13.0703 --15.754 4.13848 -12.5652 --16.3934 3.81218 -11.8968 --17.3731 3.98553 -11.5679 --17.384 4.61053 -12.3523 --17.0088 4.58629 -13.3268 --16.9114 5.16535 -14.0992 --16.9721 4.49621 -14.7963 --17.4023 3.56368 -14.6457 --18.2437 3.01085 -14.8456 --18.9477 3.16093 -14.2124 --19.6747 3.18298 -13.6077 --19.7802 2.66669 -12.7379 --20.4554 2.80231 -11.9906 --20.4431 2.28754 -11.1622 --21.1143 2.59765 -10.4807 --20.9793 1.72854 -10.0128 --21.0842 1.50483 -11.0246 --20.9463 1.76967 -12.0029 --21.5215 1.65595 -12.8724 --20.7484 1.53806 -13.5953 --21.5147 1.8493 -14.0826 --22.1459 1.33063 -14.7072 --22.9431 1.84812 -14.4744 --22.7432 1.55197 -13.5012 --22.5353 0.9422309 -12.7665 --23.4761 0.6851639 -12.5404 --23.8994 1.26011 -11.8804 --24.8117 1.00207 -12.25 --24.7453 0.6228869 -11.2856 --24.4099 1.46353 -10.7859 --24.2156 1.08345 -9.92118 --23.9937 2.01383 -9.72414 --23.8821 1.55967 -8.80694 --23.1616 1.83299 -8.1557 --22.9368 0.9799999 -7.79402 --22.7938 1.01153 -6.77103 --22.282 1.33482 -6.03303 --21.7229 1.39943 -6.76258 --21.5632 2.28103 -7.17858 --22.1153 2.04263 -7.95071 --21.1521 1.81223 -7.9383 --20.2267 1.89201 -7.51006 --20.4022 2.54211 -8.20325 --20.1076 3.39324 -7.89601 --19.5829 3.63982 -7.07314 --20.4682 4.13108 -7.05735 --21.4609 4.07088 -7.26429 --22.4326 4.22327 -6.95141 --22.893 4.43111 -6.15759 --23.7141 4.5535 -5.56708 --23.7779 5.31258 -6.18703 --23.8107 5.5558 -5.2089 --24.1892 5.16575 -4.31158 --24.2642 4.19842 -4.181 --24.2279 3.45123 -4.79567 --23.4687 2.77491 -4.99256 --23.0143 2.26585 -4.25556 --22.2432 2.16176 -4.87894 --21.7419 1.2533 -4.75704 --22.0968 1.21416 -3.8024 --22.7806 0.5350559 -4.01422 --23.6328 0.2559729 -4.35221 --24.0303 -0.3617141 -3.7317 --24.9241 -0.5948691 -3.83129 --25.6046 -1.01985 -4.47234 --26.5494 -0.6524121 -4.43946 --26.4332 -0.2285731 -3.51306 --26.922 0.4146309 -3.98824 --26.4263 0.8423219 -3.24398 --25.4875 0.9672159 -3.0102 --24.7855 0.3162459 -3.03382 --24.9032 -0.1652891 -2.20006 --24.1983 0.3436869 -1.65527 --24.2367 -0.1167971 -0.8324459 --23.3077 -0.04702097 -0.4668039 --23.1737 -0.7292341 0.2001991 --22.5559 -1.46595 0.4460061 --21.577 -1.35345 0.2161661 --20.8363 -1.9097 -0.1096419 --20.7858 -1.61539 -1.07873 --21.4913 -2.36956 -0.8332489 --22.0615 -1.61814 -1.21159 --22.6785 -1.58587 -2.02932 --22.7663 -2.63773 -2.08106 --23.7854 -2.85467 -2.09393 --24.4557 -2.43234 -2.47204 --25.0568 -1.88463 -3.05873 --25.9844 -1.50836 -2.92654 --26.2935 -2.2406 -3.56529 --25.8251 -2.26259 -4.43451 --26.2848 -2.88835 -5.07604 --25.5881 -2.8131 -5.77061 --25.9173 -1.98419 -5.91531 --25.277 -2.31206 -6.55531 --24.5189 -1.64248 -6.34188 --24.4214 -0.9918181 -7.13427 --24.1118 -0.7030901 -8.02954 --23.5344 -0.8902171 -8.84978 --22.9726 -1.68293 -8.90733 --22.2013 -1.96503 -9.50532 --21.3167 -2.39383 -9.55061 --20.3198 -2.15525 -9.52206 --19.4324 -2.51221 -9.13619 --19.1059 -2.8896 -10.0447 --19.506 -3.69665 -10.5051 --20.3179 -4.18677 -10.3733 --21.1743 -4.01533 -10.9126 --21.298 -4.49088 -11.774 --20.2387 -4.52844 -11.5665 --20.025 -5.19714 -12.1984 --20.0741 -5.31846 -13.2354 --20.1441 -4.34337 -13.4481 --20.4303 -4.25003 -14.3514 --21.0711 -3.57061 -14.0453 --21.8848 -3.75512 -13.5328 --22.8333 -3.96238 -13.6698 --23.0963 -4.29805 -12.7972 --23.897 -4.26723 -12.2585 --23.7472 -3.32062 -12.0912 --24.039 -2.43183 -11.8307 --24.1953 -1.43199 -11.9438 --23.5045 -1.71444 -12.517 --22.8381 -1.75465 -11.8201 --21.9794 -1.50973 -11.4719 --21.3081 -2.27073 -11.6703 --21.4259 -1.65348 -12.4337 --21.4072 -0.6430501 -12.7374 --21.2197 -1.15077 -13.5402 --21.4653 -1.61533 -14.3711 --21.678 -2.3134 -15.1053 --21.761 -1.80632 -15.8858 --22.3001 -2.39992 -16.4375 --21.8204 -3.30329 -16.4608 --22.7742 -3.17108 -16.1462 --23.0109 -4.12131 -16.396 --22.8974 -4.42068 -17.3218 --22.1833 -3.684 -17.5638 --22.0104 -2.63463 -17.5245 --22.3573 -1.72001 -17.4698 --22.6746 -1.38056 -18.3316 --21.701 -1.1273 -18.1019 --21.3841 -0.2681041 -17.7462 --20.8202 0.5212819 -17.5229 --20.7075 0.6440079 -16.5444 --20.3167 -0.3074361 -16.4489 --20.5917 -0.8066811 -15.6528 --20.3695 -1.45208 -16.4174 --20.322 -1.19686 -17.4115 --19.4338 -0.8807341 -17.9648 --18.7188 -1.56991 -17.9256 --18.0042 -2.10615 -18.4145 --17.217 -1.69111 -18.8235 --16.2306 -1.41386 -18.5311 --16.7092 -0.9373331 -17.9111 --16.4979 -1.22498 -16.9822 --15.8415 -0.7155781 -16.33 --16.0524 -1.64982 -16.0909 --16.0128 -1.34105 -15.1715 --15.6615 -2.09726 -14.6692 --15.7354 -1.26878 -14.055 --16.0778 -2.01875 -13.5013 --15.9748 -3.09989 -13.4163 --16.1937 -4.0262 -13.2199 --15.4769 -4.06166 -12.555 --15.7424 -4.9739 -12.405 --14.9714 -4.94772 -13.0002 --15.3565 -4.93115 -13.9477 --16.1099 -5.42589 -14.4363 --15.6769 -6.23915 -14.6239 --15.246 -5.98584 -13.7634 --14.6791 -5.83302 -14.4935 --14.4311 -5.99171 -15.4273 --13.591 -6.59059 -15.5913 --12.9453 -7.1745 -16.1371 --12.568 -6.26884 -16.5108 --11.6704 -6.64677 -16.5889 --11.2363 -6.5454 -15.7211 --10.6347 -5.81869 -15.9475 --10.0673 -5.08615 -15.5708 --9.45484 -4.91716 -14.7951 --8.75531 -4.93882 -14.1485 --8.40791 -4.1225 -14.7833 --9.14234 -3.81697 -14.2233 --9.77868 -4.5475 -13.8726 --10.0638 -4.62782 -12.9383 --10.4512 -3.63414 -12.8536 --11.0145 -3.87285 -11.9944 --10.0697 -3.81642 -11.6787 --9.31059 -4.30305 -11.26 --9.60032 -5.16846 -10.8412 --9.34082 -6.08307 -11.3031 --10.0144 -6.29671 -11.9917 --10.9442 -6.62142 -11.6513 --10.6611 -6.17844 -10.747 --11.6936 -6.10385 -10.6628 --11.5512 -6.26953 -9.73332 --12.0704 -7.02388 -9.51283 --11.4924 -7.47781 -10.1873 --11.1993 -7.43765 -11.1675 --12.1786 -7.27366 -10.9058 --13.1519 -7.2406 -10.5898 --13.6418 -7.28857 -11.4881 --13.5321 -8.25764 -11.6171 --14.2794 -8.84029 -11.7908 --13.6941 -8.99123 -12.5348 --14.1924 -9.78237 -12.7769 --14.6249 -10.3013 -13.5206 --14.3375 -11.2162 -13.6007 --13.5142 -11.1185 -14.1652 --12.5665 -11.3487 -14.1106 --11.8236 -11.9771 -14.3079 --11.394 -11.8163 -15.2164 --12.2585 -11.5803 -15.5423 --12.0044 -12.1814 -16.2783 --12.116 -11.7947 -17.174 --11.8405 -10.7974 -16.9867 --11.4812 -10.1428 -17.6056 --12.0887 -10.7471 -18.0865 --12.3105 -10.9978 -19.0697 --11.4504 -11.527 -18.9875 --10.5527 -11.2132 -19.4602 --10.5049 -10.2766 -19.2505 --10.4926 -10.2592 -18.2383 --9.96593 -9.93874 -17.4711 --8.98651 -10.233 -17.2828 --8.23076 -10.7276 -16.8663 --7.69255 -11.5365 -16.4764 --7.04511 -10.9534 -16.9666 --7.57158 -10.5399 -17.6979 --7.3741 -10.7509 -18.6718 --7.95722 -10.6033 -19.4512 --8.4977 -10.7575 -20.3146 --8.9983 -11.6007 -20.4842 --8.85562 -11.3792 -21.4364 --8.02492 -10.9297 -21.2218 --7.10975 -11.2055 -21.0615 --6.36105 -10.565 -20.9116 --7.07769 -9.84954 -20.876 --7.5931 -9.45155 -21.6635 --8.37761 -9.79051 -22.2354 --8.40777 -10.5986 -22.9075 --7.50114 -10.7609 -23.3428 --8.27201 -10.6911 -23.9728 --8.51983 -11.2028 -24.8071 --9.50126 -11.468 -25.0398 --9.8036 -10.5247 -25.2166 --9.80368 -11.1068 -26.0207 --9.06524 -11.337 -26.6722 --8.25793 -10.6206 -26.4318 --8.30776 -9.93345 -25.697 --8.54232 -9.00526 -25.8649 --8.68932 -8.4119 -25.0727 --9.11495 -7.70466 -25.6204 --8.89314 -6.76075 -25.8332 --9.63848 -6.21479 -25.4451 --9.90435 -5.35585 -25.9436 --10.286 -4.89325 -26.7268 --10.0949 -4.03774 -27.2203 --10.5785 -3.15085 -27.5332 --10.3264 -2.18899 -27.3749 --11.3071 -1.83547 -27.477 --11.0284 -2.1312 -28.4142 --10.5218 -2.40206 -29.2192 --11.4386 -2.85941 -29.2217 --11.7134 -2.42087 -30.0074 --12.5133 -2.94645 -30.3289 --13.3245 -3.45081 -30.1944 --12.6231 -3.87517 -29.6183 --13.2653 -4.14952 -28.9035 --13.5664 -3.70777 -28.0554 --14.3033 -3.36063 -27.4786 --14.5378 -3.87703 -26.5963 --15.5347 -3.94854 -27.021 --15.43 -2.90776 -26.9528 --15.0983 -2.34711 -27.7501 --15.8232 -2.5726 -28.3329 --16.691 -3.08293 -28.5635 --17.0077 -2.91261 -27.6673 --17.9846 -3.26305 -27.8179 --18.8816 -2.96541 -27.3956 --19.8258 -3.00054 -27.4892 --20.2731 -3.6932 -26.974 --21.0432 -3.71531 -26.4228 --22.0423 -3.58205 -26.3708 --22.2475 -4.41891 -26.9783 --22.7614 -3.68557 -27.1679 --23.3486 -2.99866 -26.6913 --23.3934 -3.3804 -25.8036 --24.3682 -3.6321 -25.579 --24.1188 -4.22707 -26.379 --25.0067 -3.70569 -26.4685 --24.3258 -3.06929 -26.4077 --24.7793 -2.28548 -26.1638 --23.8414 -1.85395 -26.3087 --24.1964 -1.43747 -25.4912 --24.2769 -1.18498 -24.5353 --24.4843 -0.2016161 -24.593 --23.5664 0.3086119 -24.5668 --23.2719 -0.3460051 -23.9883 --22.4987 -0.8680051 -23.4815 --22.1155 -1.4125 -22.7351 --22.784 -1.16018 -22.0382 --23.6298 -1.76748 -22.0793 --23.8022 -1.47638 -23.0535 --24.5079 -2.10188 -22.6156 --25.2085 -2.8521 -22.6358 --25.6327 -3.43621 -21.8898 --24.6709 -3.66382 -21.8703 --24.1058 -4.3945 -22.2365 --24.6879 -4.2968 -23.0118 --23.8328 -3.80287 -23.1386 --23.0237 -3.57034 -22.5497 --22.3468 -3.92298 -23.2242 --21.5371 -4.25193 -22.6711 --20.7385 -3.72843 -22.3017 --19.7313 -3.73469 -22.1907 --19.7719 -3.03947 -22.8797 --20.609 -2.94401 -23.3899 --21.5685 -2.7852 -23.3197 --21.9797 -2.04976 -23.7793 --21.1369 -1.83748 -24.2499 --20.3198 -1.39421 -23.8686 --19.9618 -0.4840651 -23.5973 --20.3029 -0.4283571 -22.7109 --19.3745 0.003753084 -22.7948 --18.5246 -0.06300757 -22.2009 --18.403 0.7198969 -22.7784 --19.0691 0.9318659 -23.5268 --19.9428 1.32639 -23.8487 --19.7276 1.94972 -24.6686 --19.4553 0.9763519 -24.8638 --19.6463 0.1258659 -25.2377 --19.7933 -0.1393001 -26.2108 --18.9664 -0.8306961 -26.3255 --19.0494 -0.9137051 -25.4034 --18.3153 -1.50045 -25.7667 --18.6257 -1.68272 -24.7786 --17.7605 -1.82306 -24.4216 --17.5338 -1.06268 -23.7354 --16.9073 -1.14972 -22.9642 --16.1363 -1.66513 -22.7661 --15.9561 -0.7064121 -22.7082 --15.1493 -0.1638731 -22.8609 --14.1708 0.1030579 -22.998 --13.5673 0.4471589 -23.6569 --13.1588 0.6514069 -24.5773 --13.8787 1.32222 -24.9563 --13.6371 1.7181 -25.8494 --13.4406 1.16625 -26.6492 --13.9156 1.4352 -27.4876 --14.3891 0.5685549 -27.7966 --14.412 0.1471539 -26.8736 --13.4903 -0.1858781 -26.9779 --13.7806 -0.3997161 -27.9497 --12.7852 -0.6466661 -28.164 --12.7712 0.2598879 -27.6997 --11.971 0.9045509 -27.9052 --11.4918 1.75427 -28.0334 --10.9562 1.77833 -28.9214 --11.2952 2.46877 -29.5439 --11.7232 3.33069 -29.3916 --12.5304 3.06653 -28.8165 --12.0592 3.28713 -28.0584 --12.7883 3.08135 -27.4393 --13.6429 2.6475 -27.1292 --14.2345 2.51575 -26.3703 --15.1804 2.17383 -26.4581 --15.9157 1.91143 -27.1101 --16.1481 0.9636179 -26.8481 --16.9105 0.7018659 -26.2791 --16.4335 0.2572729 -25.5955 --15.5872 0.3805739 -26.1178 --14.8654 1.01253 -25.9001 --14.5621 0.2318229 -25.3964 --14.0702 -0.4297191 -24.746 --13.0937 -0.8027531 -24.8256 --13.4949 -0.7447681 -25.7676 --14.4473 -0.9047931 -25.8069 --15.0988 -1.27633 -25.1426 --16.1185 -1.44734 -25.2172 --16.7215 -1.13494 -26.024 --17.0873 -0.6425631 -26.7745 --16.1534 -0.5712581 -27.136 --15.9354 -0.9912921 -28.0354 --16.2302 -1.0986 -28.9917 --15.3606 -0.7399631 -29.0913 --15.4607 0.1021469 -29.5757 --15.4081 1.0926 -29.7703 --15.683 1.97354 -29.3951 --16.7075 1.89867 -29.3432 --17.376 1.78135 -28.6269 --17.31 2.02941 -27.6077 --16.8212 2.83513 -27.1585 --16.8788 2.02027 -26.6443 --17.0923 2.50362 -25.7796 --17.6422 1.7203 -25.5951 --18.4417 1.81351 -25.0321 --17.8929 2.43164 -24.5866 --17.8667 3.29302 -24.8957 --17.069 3.68208 -24.5792 --16.1049 3.79114 -24.7344 --15.9806 4.48272 -25.4426 --15.5136 4.97326 -26.185 --15.2777 5.95951 -26.1206 --15.7975 6.47755 -25.3934 --14.9728 7.0361 -25.6069 --15.0511 7.9821 -25.3925 --14.7347 8.11099 -24.4858 --15.0234 8.28564 -23.62 --14.5984 7.62586 -23.0384 --13.8575 7.17583 -23.5805 --13.6437 6.5699 -24.3299 --14.3268 5.99542 -23.9076 --13.786 5.83896 -23.1077 --13.85 5.42903 -22.2 --13.5308 4.75701 -21.5152 --13.3157 5.44949 -20.8592 --12.7238 5.94298 -21.494 --12.3516 6.48505 -22.2703 --11.5198 6.70707 -22.6846 --11.8851 7.16386 -23.4582 --12.2304 7.38446 -24.3907 --11.65 8.13018 -24.1328 --11.4788 8.50117 -23.2482 --12.1581 9.21967 -23.3188 --13.0971 9.11135 -23.2279 --13.8029 8.97546 -22.5626 --14.1024 9.58313 -23.2839 --15.0245 9.44259 -23.7292 --15.1087 9.41592 -22.7526 --15.3262 8.96901 -21.8587 --15.0665 8.90728 -20.9134 --15.542 8.90633 -20.0151 --15.8199 8.48343 -19.0673 --15.5289 9.36219 -18.6891 --15.0782 10.1105 -18.2245 --14.4669 9.80677 -17.5089 --14.9014 9.06404 -17.0326 --15.1635 8.15976 -17.495 --14.9351 7.30085 -16.9297 --15.1475 6.98199 -16.0979 --14.7508 7.91614 -15.9661 --15.0764 7.46294 -15.1466 --14.3953 7.41372 -14.4446 --13.8092 6.65822 -14.8363 --13.292 6.4189 -13.9991 --13.2894 5.75966 -13.1682 --12.5019 5.29636 -12.9255 --11.5011 5.2434 -12.7439 --10.7536 4.70814 -13.0932 --10.4187 3.83934 -13.5491 --10.3923 2.95502 -13.2064 --10.7381 2.88137 -14.0818 --11.2661 3.43146 -14.7193 --11.6551 2.9874 -15.4448 --11.5854 3.91449 -15.7018 --11.5552 4.35131 -16.6595 --11.137 4.74654 -17.4655 --10.4221 5.02237 -16.9458 --9.71197 5.12683 -17.6277 --8.83725 4.83988 -17.2381 --8.88538 4.65888 -16.3297 --9.57604 5.35886 -16.1615 --9.13474 5.73116 -15.3628 --9.13042 6.21202 -14.5436 --9.94948 6.79624 -14.6417 --10.8865 6.48214 -14.7772 --11.9544 6.61477 -14.7121 --11.6597 7.00546 -15.5667 --12.4381 6.8123 -16.1907 --12.4057 6.03222 -15.5426 --11.5273 5.64895 -15.8117 --11.532 5.38656 -16.728 --11.591 5.66589 -17.6646 --12.5932 5.53358 -17.379 --12.6347 5.36413 -18.3777 --12.2989 5.81521 -19.1927 --11.6157 5.14812 -19.0257 --11.5948 5.45521 -20.0043 --11.3668 4.52142 -20.1566 --10.4705 4.69271 -19.83 --9.77194 5.40387 -19.7421 --9.77878 6.36477 -19.61 --9.40138 6.20925 -18.6334 --8.58776 6.4536 -18.0963 --7.74504 7.03884 -18.1918 --7.20188 7.76355 -18.6132 --7.7134 8.33719 -17.9293 --7.35443 7.69153 -17.2412 --6.48074 7.20294 -17.0333 --5.91669 6.64721 -17.5466 --5.20684 6.43124 -18.1012 --5.47036 7.30161 -18.5243 --5.54396 8.14056 -19.0888 --4.79284 8.67187 -18.9327 --4.38714 8.86877 -18.1019 --3.76949 9.70272 -18.1709 --4.48128 10.379 -18.5119 --4.79145 10.7156 -19.4329 --5.18038 9.99577 -20.2104 --5.61257 9.8526 -21.0794 --4.93884 9.52865 -21.7385 --5.20249 8.87644 -22.4878 --5.37311 8.60411 -21.4697 --5.7918 7.87792 -20.8753 --6.6202 7.36896 -20.6852 --7.15142 8.29436 -20.9982 --7.05435 9.33876 -21.2149 --7.96668 9.54404 -20.7737 --8.73077 9.70239 -20.0854 --8.47981 10.5871 -19.681 --8.19693 11.5536 -19.5107 --7.80598 11.9031 -20.3831 --7.56485 11.1827 -21.0652 --7.80432 11.8229 -21.7507 --8.03175 12.296 -22.5631 --7.34928 13.2119 -22.5716 --7.98101 13.34 -23.3127 --8.61221 13.7687 -23.9656 --9.54158 13.5263 -24.185 --9.77004 14.527 -24.1728 --9.43491 14.2821 -23.3086 --9.13346 14.3512 -22.3618 --9.36129 15.3342 -22.4936 --8.3367 15.2938 -22.7589 --7.41589 14.9901 -22.3982 --6.66353 14.3231 -22.4849 --6.49007 14.1959 -23.4769 --6.41634 14.2999 -24.4873 --5.6011 13.7938 -24.1463 --5.91981 12.8627 -23.8923 --6.16215 12.0831 -23.2633 --5.81201 12.4721 -22.3599 --5.5599 12.1475 -21.5351 --5.96835 12.2793 -20.6994 --5.00364 11.8383 -20.6168 --4.64198 12.6928 -20.3398 --4.05812 13.1228 -19.741 --3.60403 12.9907 -18.8149 --3.15329 12.2647 -18.2303 --2.30949 12.6965 -18.5033 --2.55074 12.8643 -19.4554 --1.63642 13.1478 -19.8705 --1.3597 13.6129 -19.06 --1.34937 14.3394 -18.3281 --1.35559 13.4486 -17.9689 --1.3002 12.706 -17.2235 --1.05004 13.1238 -16.3434 --1.49723 13.8118 -15.7247 --2.38258 14.3252 -15.9611 --2.99734 13.607 -16.3238 --2.84211 12.7632 -15.7478 --3.36914 12.0644 -16.1572 --3.9657 11.5672 -15.6938 --3.2478 11.832 -14.9438 --2.99585 10.8357 -15.1468 --2.56491 10.1104 -14.5974 --2.40933 9.13073 -14.3786 --3.36063 9.05637 -13.8779 --4.33247 9.27712 -13.7847 --4.99479 9.30484 -14.5985 --4.84807 8.35826 -15.0281 --5.77462 8.03437 -15.4531 --5.99319 8.74293 -14.8063 --6.31852 9.16294 -15.6597 --6.08742 10.0391 -15.8945 --5.91921 10.9666 -15.5192 --5.76961 11.4011 -16.4502 --5.41827 10.9374 -17.211 --4.81489 10.0796 -17.1079 --4.63718 10.9134 -16.5284 --3.82243 10.3758 -16.8657 --2.85741 10.4849 -16.7408 --2.30615 11.3129 -16.5077 --1.81277 11.2645 -17.3607 --0.840396 11.3652 -17.7354 --0.198197 11.9893 -17.2515 --0.01884423 11.3805 -16.4976 --0.752929 11.207 -15.8391 --1.0341 11.3315 -14.905 --0.714034 11.9221 -14.1348 --1.34841 11.8609 -13.3913 --1.63952 12.7005 -12.9051 --2.18417 12.5998 -13.7095 --2.24902 11.5828 -13.3987 --3.23614 11.4275 -13.7107 --3.74989 10.7502 -13.1799 --4.68411 10.8137 -12.7606 --4.92419 9.8593 -12.4386 --5.75549 9.2036 -12.3514 --6.16583 9.80532 -12.9615 --6.20426 10.475 -13.7062 --6.43772 11.0795 -14.4379 --7.20501 10.6198 -14.8933 --8.0165 10.1688 -14.8465 --8.63629 10.1431 -14.0581 --9.25197 10.5659 -14.7338 --8.81672 10.9947 -15.5471 --9.49481 10.3521 -15.8232 --10.2319 9.74245 -16.2206 --9.89958 10.4054 -16.8952 --10.4335 10.4479 -17.7681 --10.67 9.4728 -17.6017 --10.8786 8.53515 -17.8965 --11.7891 8.45758 -18.2489 --11.8777 7.53139 -18.3992 --12.1713 7.42677 -19.3116 --12.6844 7.29423 -20.1393 --11.7842 7.05778 -20.4534 --11.6284 7.96778 -20.7592 --12.5245 8.31246 -21.1789 --12.0089 9.1548 -21.3868 --11.1327 8.89798 -21.0663 --11.0813 9.88473 -20.9762 --11.6194 9.68921 -20.1269 --12.6093 9.71676 -20.2664 --13.6163 9.79655 -20.0931 --13.6504 10.1861 -21.0249 --13.0311 10.9462 -21.3592 --12.5307 10.5681 -22.1415 --11.991 11.4287 -22.2519 --11.2951 10.6241 -22.3841 --10.678 11.4285 -22.3333 --10.2719 11.149 -23.2077 --9.67635 10.4485 -23.6213 --10.4328 10.2984 -22.9904 --10.6665 9.88724 -23.8537 --11.0712 9.38184 -24.644 --10.9614 9.97458 -25.4246 --11.6713 10.5648 -25.7854 --11.4407 11.5036 -25.6859 --12.2005 12.1474 -25.6939 --11.6101 12.8345 -26.2027 --11.8256 13.7849 -26.1083 --10.8849 13.648 -25.8221 --10.3544 12.905 -25.4385 --9.83372 12.1079 -25.3286 --9.10863 11.9729 -24.5663 --8.24733 12.4259 -24.2467 --7.84933 12.8564 -25.0217 --7.59603 12.4778 -25.882 --6.83581 12.5847 -26.531 --7.30478 12.8352 -27.3951 --7.66747 12.0858 -27.8366 --7.89393 11.1603 -27.4827 --8.84208 10.797 -27.5523 --8.81668 11.7878 -27.7691 --9.54085 11.4194 -28.3533 --9.38809 11.4541 -29.336 --8.95109 11.7855 -30.1588 --8.86157 12.248 -31.1243 --8.84027 11.2373 -31.3378 --8.09185 10.9227 -31.9329 --7.68461 10.8415 -30.9864 --7.34468 9.94694 -30.8145 --7.59725 9.42885 -30.0005 --6.71674 9.43393 -29.4685 --5.81975 9.54084 -29.0788 --5.15482 8.81418 -29.1457 --5.13595 8.75231 -28.1364 --5.53545 9.13414 -27.2412 --5.88517 8.66464 -26.4563 --6.56028 8.22266 -25.8375 --6.46397 7.99074 -24.8309 --6.8106 7.06288 -25.0631 --5.88605 6.65292 -25.0386 --4.94506 6.42313 -25.0747 --4.03398 6.72634 -25.3896 --4.58623 6.2821 -26.0836 --5.2129 5.8494 -26.6915 --5.48835 5.1726 -27.3021 --6.00016 5.57662 -28.074 --5.56169 6.51913 -28.1246 --4.56557 6.6857 -28.1041 --4.89687 6.25895 -29.0359 --4.43688 5.56367 -29.568 --4.52641 4.59313 -29.8936 --5.39333 4.17028 -29.6387 --5.39954 4.90034 -28.9512 --6.33679 4.58825 -29.2605 --6.3002 3.77915 -29.8247 --6.71517 3.07819 -29.1702 --7.60913 3.56664 -29.0199 --8.44848 4.07393 -28.7565 --8.83271 5.01744 -28.4563 --9.11738 5.42913 -29.3571 --10.0974 5.24037 -29.3991 --11.0795 4.97349 -29.4387 --10.5449 5.16459 -28.5236 --11.2049 5.93098 -28.2954 --11.3447 6.43796 -29.1855 --11.067 6.50677 -30.1584 --11.9495 6.53043 -30.6313 --11.7867 5.83286 -29.9358 --12.6141 5.62445 -30.3733 --13.0057 6.50663 -30.5894 --13.6109 6.69925 -29.8516 --13.5891 7.64104 -29.6056 --14.1249 7.4484 -30.3611 --13.5283 7.96846 -30.9664 --12.7007 8.47657 -30.9103 --11.981 8.81888 -30.4023 --11.0093 8.69983 -30.4913 --11.1124 8.59187 -29.5845 --10.3085 8.94883 -29.0734 --10.7784 9.80614 -28.7684 --10.0983 9.64579 -28.0666 --9.70578 10.1412 -27.3079 --9.7016 9.15713 -27.1018 --8.90857 8.46981 -27.0382 --9.29676 8.66718 -26.143 --9.37678 8.1671 -25.2922 --8.93205 8.70872 -24.6296 --9.48431 9.36024 -24.0977 --8.74272 9.45467 -23.4648 --7.91199 9.42553 -22.857 --8.40639 8.93988 -22.0876 --8.53644 8.3689 -21.27 --8.82862 9.29892 -21.0899 --8.63285 9.92067 -21.8582 --9.28205 10.7495 -21.9625 --8.88327 11.1102 -21.0753 --9.65291 11.7436 -20.8835 --9.55643 12.5677 -21.4828 --9.52448 13.2032 -20.7014 --9.03444 13.9323 -20.2626 --8.96044 14.9127 -19.917 --8.22267 15.0851 -19.3193 --7.33625 14.912 -19.4895 --7.88342 14.1668 -19.8706 --7.01692 13.7403 -19.4629 --6.21268 13.3191 -19.9231 --5.5082 13.3579 -19.1838 --6.16723 13.6787 -18.4414 --5.47532 14.4207 -18.3353 --5.3065 13.5481 -17.8596 --5.69651 13.1246 -17.0973 --5.08776 13.1197 -16.3101 --4.38563 13.7633 -16.5989 --4.4488 14.4334 -15.8491 --5.37335 14.6601 -16.0628 --5.87564 13.8002 -15.8378 --6.65798 13.5142 -15.1775 --7.39787 13.3369 -15.8583 --8.11089 13.1368 -15.1876 --8.93282 13.0613 -14.6012 --8.75013 12.0903 -14.6497 --7.79478 12.2616 -14.9781 --7.5959 12.4452 -14.0723 --6.93719 12.1 -13.4016 --7.10599 12.2072 -12.388 --7.68004 11.6434 -11.8283 --7.87251 11.4613 -12.7593 --7.19433 10.7912 -12.5637 --6.33868 11.0757 -12.1074 --6.55863 10.8774 -11.1718 --6.62067 11.2632 -10.22 --6.68299 11.4522 -9.26033 --7.68457 11.3516 -9.34793 --7.55667 11.8853 -10.1947 --7.23066 12.4485 -9.44352 --6.40759 12.7699 -9.82458 --6.21356 12.9267 -8.86006 --5.46219 13.4195 -9.37219 --5.23186 13.7009 -10.294 --5.0249 14.6666 -10.6695 --5.5473 14.6341 -9.81682 --5.70543 15.4688 -10.3522 --5.42229 16.2507 -9.76258 --5.05268 16.6456 -8.89764 --6.01752 16.5732 -8.74238 --6.62911 16.1008 -8.07648 --6.31691 15.9218 -7.16945 --6.75727 16.2534 -6.38673 --7.44906 16.3476 -7.10622 --7.70191 16.6848 -8.02413 --7.36285 17.6295 -7.75691 --7.10702 18.2831 -8.46273 --8.10953 18.3411 -8.26804 --8.69371 19.1442 -8.04799 --8.73203 19.7411 -7.24909 --9.441 19.7927 -6.62153 --8.87665 19.5024 -5.82869 --8.12414 18.9269 -5.73722 --7.39845 18.3899 -6.22259 --7.32706 17.8955 -5.39713 --7.59885 16.9699 -5.83055 --8.32335 16.999 -6.40057 --8.60232 16.1344 -5.9744 --9.25312 15.7062 -6.55112 --9.93262 16.0946 -5.8609 --10.8348 16.2408 -5.32242 --10.7397 15.9873 -4.41068 --10.8483 15.0473 -4.61938 --11.2239 14.4467 -3.81256 --11.2737 14.276 -2.86954 --12.2358 14.1116 -2.89413 --12.252 14.5285 -3.79552 --13.1726 14.591 -3.35383 --12.4961 15.3694 -3.43879 --12.2439 15.7341 -2.58923 --11.3841 15.4578 -2.26473 --11.1036 16.3508 -2.53392 --11.1473 16.9843 -3.34181 --11.0943 17.3355 -4.25812 --10.5575 18.0285 -3.84859 --9.81164 18.5607 -3.76729 --9.02434 19.1694 -3.52172 --9.03875 20.2052 -3.35068 --9.03034 20.2821 -4.30302 --9.90998 20.72 -4.49403 --10.552 21.3906 -4.74543 --10.0491 22.0122 -5.44036 --9.43635 21.3099 -5.83062 --8.70144 20.7891 -6.22122 --8.50298 21.0931 -7.21871 --7.87161 21.7378 -6.8709 --7.66742 22.6654 -7.17604 --7.48931 23.2181 -8.02182 --7.46265 24.2408 -8.19642 --7.14917 23.992 -9.09705 --7.64431 23.5154 -9.85873 --8.35374 24.188 -9.6397 --9.26145 23.7371 -9.60265 --9.69329 24.021 -10.5353 --8.95878 24.6742 -10.6669 --8.92723 24.5451 -11.6794 --9.07898 24.8834 -12.5727 --8.74298 25.7791 -13.0569 --8.07377 25.8316 -13.8465 --7.71686 25.6117 -12.909 --7.40328 25.0727 -13.7173 --6.62004 24.6951 -14.2192 --7.16876 24.1326 -13.6555 --7.98595 23.7591 -13.4645 --7.38097 23.4834 -12.7017 --7.86497 22.7313 -12.2631 --8.06629 21.7182 -12.2309 --8.35686 22.2414 -11.396 --7.83597 22.9864 -11.0938 --6.80798 22.9684 -11.099 --5.84453 23.3532 -11.2588 --5.7992 22.6729 -11.9171 --6.37186 22.4792 -12.6627 --5.62042 22.4701 -13.3353 --5.16033 21.7262 -13.8134 --4.92312 20.9147 -14.3171 --4.34958 21.3089 -14.9457 --3.45974 21.0543 -14.5971 --3.08799 20.1124 -14.7643 --3.52132 19.8524 -15.6208 --4.10587 20.0696 -16.4248 --4.63929 19.2318 -16.3324 --5.56699 19.1843 -16.0752 --5.97637 18.3971 -16.6007 --6.4876 17.9563 -17.2823 --7.40066 18.1673 -16.9129 --7.92915 17.3285 -17.2336 --7.81041 16.321 -17.0412 --8.01089 15.4336 -16.615 --8.40725 16.2607 -16.3026 --8.30766 16.2342 -15.3339 --9.06053 16.0441 -14.5637 --9.94426 15.7435 -14.6289 --9.81075 15.4061 -15.6041 --10.6846 15.8754 -15.7046 --11.4879 15.7415 -16.3153 --11.938 15.6974 -17.211 --12.6911 15.4863 -17.7974 --12.9398 14.4902 -17.6318 --13.0998 14.2006 -16.6606 --13.7845 14.9 -16.4361 --14.5738 14.8816 -15.748 --15.1198 15.6918 -15.6931 --14.6609 16.2475 -14.9097 --14.5919 15.5283 -14.1889 --14.7879 16.277 -13.5707 --15.842 16.2262 -13.4623 --15.7049 15.3865 -13.8956 --15.9816 15.0608 -12.9823 --15.6369 15.5146 -12.1715 --15.7606 14.794 -11.4569 --16.6453 15.1755 -11.3082 --17.2218 15.6922 -12.0367 --17.5977 16.2447 -11.2573 --18.0732 16.8713 -12.0066 --18.2866 16.8079 -13.0375 --19.0086 17.0397 -12.3424 --18.903 17.944 -12.0537 --18.9825 18.2895 -12.9553 --19.6997 17.7232 -13.3911 --20.0717 18.4491 -14.0011 --20.8306 18.6387 -14.5282 --21.6854 18.0822 -14.7946 --22.1024 18.8436 -15.3247 --22.6787 18.0656 -15.3652 --23.034 17.2768 -14.8665 --23.6267 16.5183 -14.9407 --23.0007 15.81 -15.3062 --22.3673 15.8483 -14.5818 --21.5114 15.9443 -14.165 --21.4138 15.2544 -14.7364 --20.5514 15.1988 -15.2355 --20.683 14.5479 -14.4978 --21.3071 14.1725 -15.2447 --22.2635 14.3645 -15.1455 --22.9047 14.0905 -14.3697 --23.8364 14.1286 -14.5894 --23.9613 13.1312 -14.6961 --24.7271 12.5144 -14.9604 --24.8189 12.5871 -13.9736 --25.6619 12.3705 -14.4284 --26.483 12.494 -13.764 --27.3443 11.9703 -13.4754 --27.6551 11.4477 -12.7068 --27.7581 10.4714 -12.4545 --27.7287 10.0806 -13.4089 --28.3284 10.1659 -14.1943 --29.2365 10.1411 -13.9867 --30.0324 10.4924 -14.5021 --30.573 10.729 -13.6865 --31.0133 9.77099 -13.4948 --30.7233 8.86599 -13.8294 --31.1793 8.81603 -12.9566 --31.8783 8.1708 -12.6912 --32.5963 8.09343 -12.0373 --33.4971 8.23352 -12.4577 --33.9419 7.84661 -11.6561 --34.0181 6.87722 -11.7534 --34.6612 6.18256 -11.5629 --35.0742 6.66139 -12.3504 --34.2041 6.08759 -12.5931 --33.4019 6.07228 -13.1654 --32.7463 6.5219 -13.6608 --32.8809 6.31311 -14.6489 --33.618 5.62674 -14.7963 --34.5162 5.7196 -14.7244 --35.282 6.0968 -15.3304 --35.0515 5.45537 -16.1148 --34.2724 6.02933 -16.3637 --33.9339 5.23007 -16.974 --33.1552 5.16241 -17.5752 --33.7516 4.9817 -18.3 --33.6843 5.8228 -18.832 --33.6578 6.75957 -18.5393 --32.7787 6.31146 -18.3152 --31.9556 6.71907 -17.9816 --31.0576 6.42412 -18.096 --30.7205 7.15985 -18.7699 --29.7438 7.33477 -19.027 --29.2126 6.6401 -19.4965 --29.2256 6.42344 -18.4874 --28.3242 6.50571 -18.0186 --28.0767 5.55244 -18.3024 --28.5948 4.86554 -18.8725 --28.3001 5.62413 -19.4981 --27.5485 5.02038 -19.6554 --27.4502 5.72467 -20.4039 --26.8666 6.27561 -19.8473 --26.0651 6.57334 -19.3783 --26.3357 7.47622 -19.3197 --25.9304 8.1933 -18.6886 --26.2324 9.20527 -18.68 --26.2092 8.73711 -19.5578 --25.2089 8.8877 -19.344 --24.844 9.52151 -18.7197 --24.8006 10.5485 -19.0004 --23.9539 10.7528 -19.5711 --23.001 11.2007 -19.4998 --22.6704 12.0216 -18.9145 --23.2087 12.8536 -18.9075 --23.1836 13.0499 -19.8592 --22.3841 13.5373 -19.4646 --21.8722 14.1032 -20.1754 --22.2211 14.8263 -19.5295 --22.2988 15.0292 -20.4628 --21.4158 15.3003 -20.4314 --20.8401 15.8031 -19.8128 --20.2297 15.9837 -19.0716 --20.9956 15.613 -18.5868 --21.2568 14.6864 -18.3197 --21.5641 13.9022 -18.7076 --21.2678 13.3029 -19.441 --20.4719 12.7184 -19.5171 --20.0559 13.5055 -19.123 --20.0186 14.1618 -19.8662 --19.114 13.8345 -20.2094 --18.3413 13.4294 -20.7518 --17.9386 12.5128 -20.5193 --16.9701 12.6392 -20.36 --16.7362 11.7357 -20.6216 --17.3205 11.4166 -19.8312 --16.939 12.1733 -19.2894 --16.2936 11.6888 -18.7263 --15.3265 11.7955 -18.778 --14.8316 11.1882 -18.065 --15.7392 11.3087 -17.6247 --16.012 11.7 -16.7402 --16.3903 10.8736 -16.1296 --15.4026 11.0541 -15.9139 --14.7383 11.5492 -15.2862 --14.2846 12.2994 -15.7144 --14.8362 12.9226 -15.3 --15.4459 12.2681 -14.8004 --14.8314 12.176 -13.9867 --14.0515 11.6611 -14.2213 --13.4492 10.976 -13.718 --13.2327 10.221 -14.4192 --14.0626 10.2318 -15.0111 --13.3039 9.76234 -15.4871 --13.4072 9.14027 -16.2241 --12.7828 8.74219 -16.8863 --12.9779 8.28706 -17.761 --13.2658 7.31958 -17.6865 --13.5936 7.09838 -16.7683 --13.7201 6.34969 -16.1261 --14.6298 5.89118 -16.1166 --15.2543 5.43877 -16.715 --16.0091 4.96097 -17.3208 --16.6034 4.24669 -17.6394 --15.6374 4.0503 -18.0545 --16.0006 3.57473 -17.2105 --15.6712 2.72174 -16.8691 --14.7838 3.21309 -16.6815 --14.1712 3.53582 -17.42 --13.3023 3.16923 -17.0605 --13.3787 2.21152 -17.2254 --13.4559 1.36747 -17.7489 --14.3763 1.78208 -17.9943 --14.6492 2.13757 -17.1416 --14.5477 1.08883 -17.2835 --14.0675 0.6063239 -18.1056 --13.5537 -0.1024331 -17.6276 --12.5668 0.02020193 -17.4539 --11.8988 -0.2837721 -16.743 --10.888 -0.1374441 -16.9168 --10.6578 -0.1781361 -15.971 --10.8687 -0.7140171 -15.2035 --11.2238 -1.22669 -14.4592 --11.4322 -2.06389 -14.988 --12.008 -2.26883 -14.2612 --11.8021 -2.98359 -13.6022 --11.7427 -2.42911 -12.7723 --12.4759 -1.83269 -12.5987 --12.3301 -1.2894 -11.7748 --11.4409 -1.54055 -11.4622 --10.6389 -1.3974 -12.1779 --10.4376 -0.6918561 -12.8097 --9.55442 -0.2919981 -13.1729 --9.05818 -0.8190191 -12.448 --9.32121 -1.74202 -12.3299 --8.78283 -2.51179 -11.9168 --8.66779 -2.72829 -12.9149 --7.82722 -3.14845 -12.4986 --7.10964 -2.49019 -12.4076 --6.8233 -1.53771 -12.2442 --7.37608 -0.8277261 -12.6125 --7.39569 -0.3250271 -11.7675 --6.96381 -0.7737071 -10.9432 --7.75423 -1.45378 -11.1053 --7.92566 -2.36644 -10.8302 --7.25855 -3.06364 -11.2714 --7.00364 -3.87577 -10.7336 --6.15385 -3.99123 -10.2302 --6.46917 -4.33442 -9.35048 --6.85588 -4.28688 -8.45322 --6.92485 -4.22438 -7.43521 --7.84734 -3.73364 -7.31931 --8.4827 -4.499 -7.42994 --8.14458 -4.92797 -6.61065 --7.32791 -4.85503 -5.95261 --6.4179 -5.07963 -6.21829 --6.13383 -4.3385 -5.66193 --6.49289 -3.59732 -6.19215 --6.53558 -3.18173 -7.10875 --5.79542 -2.83778 -7.72254 --4.96306 -2.57088 -7.23495 --5.37551 -3.15559 -6.56679 --5.89014 -2.37465 -6.14468 --5.2015 -2.52328 -5.34671 --4.78255 -1.58928 -5.40413 --4.6808 -0.5926911 -5.26923 --4.17532 0.06954653 -5.79454 --5.13747 0.3046149 -6.00534 --4.77446 0.9149219 -6.78899 --4.93364 -0.05221067 -7.07768 --5.06036 -0.7942051 -6.56268 --5.99724 -0.6720131 -6.74385 --6.46051 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-15.6615 --8.05345 3.38484 -15.3465 --7.35256 3.5749 -14.7127 --6.5733 3.55457 -15.3277 --6.44216 4.51285 -15.5744 --5.84389 4.14217 -16.2522 --6.552 4.00952 -16.883 --6.97634 3.32496 -17.4312 --7.39032 3.92426 -18.123 --6.94919 3.90841 -18.9773 --5.99748 3.74981 -18.8278 --6.40755 2.81061 -19.0601 --6.33415 3.43249 -19.9122 --5.37771 3.67652 -20.0107 --5.88406 3.01556 -20.605 --5.17999 2.3568 -20.9473 --5.06615 2.74155 -21.856 --5.26278 3.72677 -21.7879 --4.30002 3.77711 -21.3256 --3.77028 3.35203 -22.073 --3.8274 4.0454 -22.8465 --4.32612 4.81192 -23.2454 --3.9924 5.34391 -23.9519 --3.29951 5.86792 -24.4538 --3.55941 6.78079 -24.0667 --3.66199 7.82679 -23.9944 --3.09838 8.35195 -23.2393 --2.39708 8.93836 -23.7103 --2.81642 8.93499 -24.6212 --3.69678 9.27277 -24.9233 --3.15622 9.38475 -25.7644 --2.52736 10.1475 -25.4687 --2.02056 9.99594 -24.5703 --1.61619 10.6391 -25.1887 --0.575806 10.8752 -25.2638 --0.576208 10.4627 -26.1316 --1.29127 11.0811 -26.4169 --1.2238 11.1625 -27.4079 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--21.0993 -10.2084 -0.4303749 --20.1693 -10.102 -0.4862069 --19.442 -10.1163 -1.1543 --19.5984 -9.30872 -1.72092 --19.78 -8.94724 -0.7901939 --19.219 -8.30481 -1.30817 --18.8594 -8.42836 -2.167 --19.8349 -8.32685 -2.29785 --20.0504 -9.20156 -2.72843 --20.5851 -10.0627 -2.44479 --20.5687 -10.9643 -2.03752 --21.5718 -10.9278 -1.89905 --21.518 -11.2736 -0.9153659 --21.4069 -11.7994 -1.71363 --21.969 -12.5137 -1.27429 --22.8333 -12.1605 -1.45836 --23.7243 -12.6779 -1.65155 --23.6564 -13.7049 -1.7039 --23.604 -13.7172 -0.7090639 --23.4119 -14.3982 0.02548502 --24.3577 -14.3871 0.03944372 --24.4985 -14.5549 -0.9035829 --24.8444 -15.431 -0.4577419 --25.6475 -14.8906 -0.7021109 --25.9562 -14.0475 -1.26335 --26.7976 -13.5948 -1.59723 --27.2995 -14.1695 -2.30216 --27.7743 -14.7383 -3.03548 --28.0544 -15.5547 -2.54447 --27.8334 -16.1241 -1.81521 --27.5888 -16.135 -0.8802419 --26.9404 -15.3167 -0.7427449 --26.8653 -15.9364 0.08066272 --26.0706 -15.4556 0.4948221 --25.6067 -14.7679 0.9731351 --25.4462 -13.9545 1.58306 --25.0399 -13.1577 1.15769 --25.2672 -12.3348 0.6995141 --25.7869 -12.5659 1.52162 --26.0478 -11.7249 2.06 --25.1009 -11.8928 2.09528 --25.3837 -11.3155 2.88302 --25.3943 -11.1769 3.89573 --24.4795 -10.9497 4.38772 --24.5039 -9.99064 4.14349 --25.3949 -10.0779 4.61474 --26.1865 -10.3106 5.23337 --26.0977 -9.61525 5.97599 --25.178 -9.67518 6.11553 --24.461 -9.7104 5.39108 --23.7357 -10.2595 5.78088 --23.9504 -11.1859 5.45311 --24.1436 -12.2091 5.45513 --24.1344 -13.1178 5.83205 --24.216 -13.3321 6.78767 --24.5114 -14.3347 6.60887 --23.565 -14.3017 6.33314 --23.4666 -14.9382 5.59089 --22.5205 -15.1254 5.69376 --21.9518 -15.2936 4.86378 --21.0152 -15.6423 4.63879 --20.8048 -14.8924 4.11101 --20.8347 -14.0539 4.67221 --20.7715 -14.5242 5.52782 --20.0098 -15.1266 5.34222 --19.4278 -16.0094 5.46612 --19.2671 -16.9669 5.72791 --18.8841 -16.6071 6.53155 --18.7367 -17.2537 7.29884 --18.4041 -17.4589 8.27543 --18.7058 -17.7103 9.19448 --19.2236 -18.1289 9.89915 --18.6684 -18.0592 10.7555 --18.3369 -17.5656 11.5327 --19.0581 -17.4156 12.2669 --18.7819 -18.0584 13.0634 --17.929 -18.373 13.5768 --17.3029 -17.7252 13.0988 --17.9428 -17.306 13.7603 --17.9521 -16.4526 14.2408 --17.2988 -16.143 13.6366 --16.3052 -15.8037 13.5681 --15.5476 -15.1807 13.5569 --15.9253 -14.9494 12.5818 --16.2534 -14.3944 11.8909 --16.8939 -13.6725 11.7425 --17.7469 -14.2887 11.7164 --18.7794 -14.1501 11.7972 --18.6372 -13.4653 12.5188 --19.3636 -13.1087 12.0196 --20.3571 -13.0839 11.9352 --21.1263 -13.6909 12.1855 --21.8292 -13.0317 12.0364 --21.8385 -13.6053 11.1961 --21.5903 -14.4481 10.715 --20.8676 -14.9772 10.9795 --21.1673 -15.4593 10.1499 --20.9148 -16.2147 9.59287 --20.8382 -16.6032 10.5589 --20.6283 -16.3808 11.4997 --21.3657 -16.1675 12.1776 --20.8605 -16.8955 12.6522 --21.0447 -17.8908 12.9839 --21.3973 -18.5855 12.2955 --20.6589 -18.279 11.6545 --19.8586 -18.8825 11.7498 --18.9661 -18.6813 11.4107 --18.7595 -19.2177 12.1729 --18.5484 -19.8531 12.905 --19.5634 -19.9964 13.0224 --20.3051 -20.6907 12.939 --19.7244 -21.5264 12.9207 --18.9719 -21.3214 13.5234 --18.4637 -21.9871 14.0377 --17.8017 -22.3104 13.5105 --17.3343 -21.4535 13.5202 --16.3115 -21.4311 13.3609 --16.6297 -21.852 12.5159 --15.9962 -21.0336 12.4124 --15.0484 -20.7638 12.5325 --14.0627 -20.6744 12.6968 --13.8441 -20.0664 13.4683 --13.104 -20.5765 13.0934 --12.1883 -20.3204 13.4098 --11.5591 -20.3789 14.1527 --11.2895 -21.3743 14.0379 --11.9626 -21.2837 14.7753 --11.4696 -22.1592 14.6469 --10.9447 -22.0515 15.4943 --10.5079 -22.9447 15.2828 --10.7278 -23.796 14.8563 --10.7421 -24.6517 14.3642 --11.1529 -24.0305 13.6006 --11.5962 -23.4798 14.2489 --12.299 -23.211 14.8693 --13.1839 -22.7269 15.0591 --13.2492 -22.8073 16.0282 --12.8923 -22.2384 16.7674 --13.012 -21.2766 16.393 --13.9915 -21.6347 16.2412 --13.6089 -21.1342 15.5023 --13.1324 -21.0067 14.5818 --12.7497 -20.4532 15.3168 --12.2761 -19.6925 14.8657 --12.0728 -19.1457 15.6102 --12.9825 -19.4205 15.4093 --13.9045 -19.4558 15.8422 --14.7193 -19.7738 16.4446 --14.2653 -19.4316 17.254 --15.1146 -18.9917 17.728 --15.5661 -19.5924 17.1626 --16.3288 -20.1362 17.5054 --16.994 -20.8572 17.4288 --17.4274 -20.8904 16.5199 --17.6577 -19.9385 16.5808 --18.6032 -19.6533 16.3646 --19.5205 -19.5256 15.9222 --18.8349 -19.2105 15.1948 --19.2482 -19.1882 14.3209 --20.1591 -18.7486 14.4798 --20.3373 -19.7321 14.5778 --20.6573 -19.7873 15.5689 --20.8237 -20.7689 15.5374 --21.5217 -21.3051 15.2584 --21.9278 -22.1577 14.8761 --22.6444 -21.4355 15.2531 --23.1584 -21.0337 16.0264 --23.0232 -20.8485 16.95 --23.6428 -20.0754 16.7791 --24.4553 -20.3345 16.2629 --24.9368 -19.5604 16.5357 --24.4211 -18.7356 16.6847 --25.2904 -18.2277 16.8456 --25.4538 -17.26 16.5058 --26.171 -16.9013 15.876 --25.7376 -15.9631 15.9395 --26.1431 -15.6236 15.1244 --26.0883 -15.0571 14.3439 --26.3336 -14.0926 14.1812 --26.2734 -14.1292 13.2455 --25.4074 -13.7129 13.3116 --26.1322 -13.1317 13.5918 --27.0469 -13.4303 13.2943 --27.9957 -13.191 13.6699 --28.0827 -12.9088 14.5878 --27.2764 -12.4171 15.0245 --27.3657 -11.5363 15.5231 --26.6972 -11.2559 16.2733 --26.6698 -12.2093 16.1537 --26.1697 -12.219 15.3311 --26.4021 -12.0994 14.3754 --26.1615 -11.679 13.436 --25.5072 -11.8015 12.7364 --24.6673 -12.06 12.2173 --23.7025 -11.6135 12.1575 --23.285 -10.9902 11.5062 --23.1126 -11.5867 10.7076 --23.5537 -12.5054 10.9306 --23.8663 -13.5064 10.8958 --24.5095 -14.303 10.9756 --23.9126 -14.7005 11.7059 --23.3533 -15.5691 11.7906 --22.7966 -15.6796 12.5884 --22 -15.4936 13.1441 --22.8068 -15.4745 13.7714 --22.5884 -15.9992 14.6084 --22.1379 -16.8288 14.7241 --21.5285 -16.7903 15.4752 --20.6366 -16.747 16.0173 --20.0355 -16.2817 16.634 --19.0982 -16.565 16.6498 --18.5463 -17.0372 17.2952 --18.2818 -18.0402 17.5299 --17.737 -17.8907 16.7918 --16.7876 -18.1121 16.7343 --16.4419 -18.964 17.2723 --16.2805 -18.551 18.1721 --16.8584 -19.2654 18.2119 --17.3122 -20.1372 18.3085 --18.2512 -19.9257 18.5022 --18.7986 -19.3183 19.1464 --19.5851 -19.0391 19.6614 --20.3504 -19.4437 20.1835 --20.5525 -18.6696 20.6966 --21.2067 -18.5027 20.0739 --20.797 -17.8698 19.3874 --21.5811 -18.0503 18.7517 --22.4921 -17.707 18.7149 --22.4027 -18.1117 19.5833 --22.6112 -17.3828 20.2676 --21.7865 -16.9157 20.3254 --21.5787 -17.4157 21.1869 --21.5131 -17.4152 22.1062 --22.3403 -16.8677 22.1879 --21.7466 -16.014 22.1118 --22.0557 -15.4338 22.8854 --21.994 -14.4361 23.1085 --21.4903 -13.9457 22.4406 --20.4903 -14.012 22.0919 --20.0846 -13.4732 21.3579 --19.4658 -13.2444 20.5956 --18.9733 -12.4195 20.5214 --18.6361 -11.7144 21.15 --18.6892 -10.8799 20.6117 --17.7894 -10.4831 20.4078 --17.6217 -10.3245 19.4129 --18.5027 -10.2979 18.8875 --17.9305 -11.0514 18.465 --17.6904 -11.5552 19.2858 --18.4133 -12.2878 19.4562 --17.8725 -12.7589 20.0785 --17.4596 -13.2801 20.9618 --18.1337 -13.6603 21.5942 --18.3444 -14.6398 21.6665 --18.2308 -15.501 21.2293 --17.3258 -15.1668 20.9423 --16.9849 -14.3486 20.596 --17.3797 -13.8064 19.8859 --16.6583 -13.2558 19.8958 --16.0322 -13.4125 19.1404 --15.3341 -12.6801 19.0193 --15.4397 -13.3465 18.1972 --14.5927 -13.7878 18.2811 --13.781 -14.3821 18.1964 --13.3763 -15.1586 17.7349 --14.0932 -15.6389 17.2564 --13.9407 -16.185 18.1581 --14.2897 -17.0431 17.9353 --14.8107 -17.1079 17.0567 --14.9836 -16.4462 16.384 --15.1414 -17.1592 15.7517 --15.8036 -17.2972 14.9962 --16.0969 -16.4274 14.6547 --15.514 -16.9957 14.0159 --14.8127 -17.4236 14.5469 --14.55 -18.3656 14.3801 --14.4733 -19.2259 14.7652 --15.4649 -19.064 14.6034 --15.6662 -18.8711 13.6296 --15.9454 -19.7936 14.0393 --15.6533 -20.5896 14.4661 --15.4067 -21.2956 15.1713 --15.6371 -22.186 15.6411 --15.2899 -23.0906 15.668 --15.0702 -22.9481 14.7001 --15.8364 -23.0486 14.0812 --16.8405 -22.729 14.0058 --17.3164 -23.213 13.2862 --18.142 -23.5531 12.9598 --19.063 -24.0638 12.819 --18.926 -24.9774 12.3338 --17.9582 -24.7229 12.0608 --16.9392 -24.7838 11.8896 --16.8896 -24.1334 12.6942 --16.9457 -23.6763 11.7814 --16.7802 -24.1677 10.9519 --16.553 -24.1677 9.96368 --16.867 -24.2428 9.03106 --15.9881 -23.8607 8.73761 --16.152 -24.4616 8.03724 --16.3945 -23.8817 7.24581 --16.7537 -24.1899 6.33066 --17.4032 -23.4182 6.5211 --17.406 -22.5961 7.12925 --16.5341 -22.4752 6.7605 --16.8892 -22.6667 5.87923 --17.3553 -22.4494 4.98818 --18.0102 -22.6108 4.21594 --17.2798 -23.1635 3.77436 --16.6265 -23.8049 4.17177 --16.505 -24.2144 5.04199 --15.9567 -24.8943 5.4971 --15.347 -25.3652 6.20004 --15.0025 -24.5023 6.52599 --14.2681 -24.1568 6.01331 --13.3886 -24.5329 6.25802 --13.2841 -25.3968 5.79701 --12.5842 -25.9677 5.29897 --11.9655 -26.1404 6.01336 --11.7533 -26.9817 6.44744 --11.5911 -27.9659 6.59363 --12.2713 -28.4011 7.19685 --13.0167 -28.2581 6.48996 --13.4544 -27.3787 6.65791 --14.3005 -26.8613 6.58845 --14.3922 -26.0477 7.06044 --14.0706 -25.6242 7.78914 --13.465 -26.3361 7.42795 --13.2916 -26.7711 8.32618 --13.2629 -27.4941 9.00212 --12.8385 -28.2732 9.32759 --12.0129 -28.0631 9.8657 --12.4833 -28.4626 10.6264 --12.4033 -29.2338 11.2593 --11.7663 -29.0647 12.0628 --11.0853 -28.3129 12.1202 --11.4432 -28.4734 13.0569 --11.8124 -27.7118 12.4426 --11.3759 -26.9726 13.0097 --10.7024 -26.2411 12.7046 --10.1676 -27.0021 12.3404 --9.33749 -26.8593 12.8543 --8.68249 -27.4808 12.3361 --7.72813 -27.4037 12.543 --7.70318 -26.5052 13.1014 --7.47899 -26.3807 12.0972 --7.94657 -25.5057 12.306 --7.99804 -24.7211 12.9444 --7.06884 -24.3353 13.0986 --7.52057 -23.5684 13.4719 --6.4991 -23.3537 13.4791 --5.67189 -23.5212 12.927 --5.41447 -24.1764 12.2397 --6.12909 -24.6829 11.9207 --6.73531 -25.0746 11.2408 --7.28631 -25.5997 10.5006 --7.61487 -26.1817 9.72923 --7.78173 -25.2934 9.26495 --6.99246 -24.8107 9.08603 --6.62649 -24.1273 9.64255 --5.68124 -24.193 9.48956 --4.83651 -24.0197 9.11793 --4.61761 -24.5427 8.33205 --4.11979 -24.9814 7.58152 --4.15021 -25.6946 6.91754 --5.03723 -26.1731 6.9267 --5.47597 -27.0965 6.88921 --4.99915 -27.4012 7.68266 --5.53606 -26.7236 8.19024 --6.54216 -26.9328 8.37616 --6.99211 -27.4364 7.71676 --7.38671 -28.3599 7.35999 --7.8555 -27.5988 6.95629 --8.35456 -26.8653 6.42789 --8.28665 -26.0962 5.80234 --9.23205 -26.4384 5.87059 --9.51788 -26.1555 6.81829 --9.07878 -26.6719 7.53198 --9.28952 -26.0168 8.26427 --9.65753 -25.2936 8.82026 --9.50596 -24.2894 8.49566 --8.83624 -24.4706 7.83024 --7.95976 -24.055 7.97713 --7.88607 -23.2767 7.33717 --7.42865 -22.7217 6.70699 --8.09596 -23.0572 6.00346 --8.95418 -23.473 6.39012 --9.3165 -24.2745 6.94998 --10.2881 -24.3344 6.97775 --10.7448 -25.1476 7.23885 --11.5631 -25.0172 6.8082 --12.2475 -24.3676 7.16706 --13.0819 -24.6389 7.5666 --14.0012 -24.3454 7.47721 --14.3827 -23.8045 8.26867 --14.0679 -24.0224 9.24947 --13.8202 -23.0809 9.06259 --13.4141 -22.1905 8.95065 --12.7452 -22.7677 8.52214 --11.8881 -22.2578 8.43814 --12.5483 -21.4479 8.46872 --12.851 -21.4677 7.49163 --12.9582 -20.536 7.69096 --13.825 -20.7836 7.25713 --14.2753 -20.2822 6.55418 --13.5163 -19.7728 6.68312 --12.7233 -19.3739 6.36414 --12.2661 -20.2379 6.45753 --11.5988 -19.9514 7.11634 --10.7939 -19.5645 7.50264 --10.1618 -20.1686 7.08363 --9.9247 -20.4212 6.18356 --10.2284 -19.5664 5.64438 --10.5442 -18.6805 5.09204 --10.1762 -18.2118 5.97434 --10.8134 -17.6876 6.54978 --11.2323 -16.7288 6.48077 --11.3677 -16.3823 7.35604 --11.1453 -16.7198 8.30394 --12.0877 -16.6145 7.9436 --12.9975 -16.6557 7.45222 --12.9982 -17.2788 8.20977 --13.5021 -17.6291 7.44686 --13.4891 -18.5064 7.05224 --14.1053 -17.9478 6.47906 --14.6324 -18.1926 5.67485 --15.5372 -18.696 5.69861 --15.6554 -17.7038 5.57472 --15.8988 -17.0734 6.30473 --15.2031 -16.5114 5.78592 --15.328 -16.5237 4.87456 --14.4384 -16.1358 4.979 --13.738 -16.281 5.7085 --13.1559 -15.553 5.9372 --14.107 -15.3993 6.05629 --14.5699 -15.0644 6.81135 --14.1732 -14.1299 6.98683 --13.9006 -14.8216 7.69782 --14.8362 -15.0377 7.73358 --15.2494 -15.8888 8.02317 --15.441 -16.023 7.08581 --16.2723 -16.1634 6.61066 --16.2955 -15.4056 5.97924 --16.152 -15.8768 5.0707 --17.1057 -15.7198 4.79409 --17.7617 -15.9428 5.45625 --18.0114 -16.286 4.60124 --17.1727 -16.8631 4.68151 --17.6949 -17.623 5.17391 --17.2023 -18.4895 5.26712 --17.047 -18.0075 6.11938 --17.9232 -18.2383 6.53618 --17.1476 -18.8953 6.88663 --17.9367 -18.8557 7.52722 --18.8318 -18.9422 7.14218 --19.7401 -19.3098 7.28826 --19.1996 -19.8847 7.9638 --18.5398 -20.3548 8.51733 --18.1975 -20.754 7.7049 --17.662 -21.0949 8.45369 --16.7077 -20.7471 8.66188 --16.2248 -21.3278 8.01383 --15.2823 -20.8271 8.07027 --14.8112 -19.9347 7.80203 --15.212 -18.994 8.21173 --15.3186 -18.6193 9.13512 --14.9647 -17.7391 9.35845 --15.2644 -18.0987 10.2124 --14.375 -18.3946 10.7023 --13.3405 -18.1941 10.8595 --12.6917 -18.8627 11.2491 --13.0693 -19.5194 10.5889 --13.2702 -20.422 10.9583 --12.5535 -20.6783 10.3192 --12.1998 -21.6036 10.7328 --12.5562 -22.3532 11.3133 --13.354 -22.4882 12.0326 --13.9429 -22.8689 12.7318 --13.0382 -23.2082 13.0815 --12.4436 -23.428 12.3464 --11.7385 -23.0571 11.6751 --11.4078 -22.9099 10.7626 --10.5413 -23.2801 11.1334 --10.2565 -24.2312 11.2577 --9.68239 -24.1788 12.0454 --10.3905 -23.4431 12.2075 --9.90236 -23.1593 13.028 --9.16788 -22.5631 13.2756 --9.15498 -21.6045 13.3775 --10.104 -21.3457 13.3369 --9.89748 -21.2044 14.3275 --9.23217 -20.4627 14.3614 --8.51968 -20.2167 15.0205 --7.68666 -20.3247 14.444 --7.92769 -20.3738 13.4745 --8.39157 -20.2988 12.5319 --8.83479 -19.4594 12.1655 --9.6842 -18.8926 11.9347 --10.2479 -19.4202 12.5913 --10.5801 -20.2817 12.907 --9.79529 -20.475 12.3211 --9.67152 -20.814 11.401 --9.00982 -20.3376 10.8706 --8.4768 -21.1685 10.6208 --7.67661 -21.0306 11.2776 --6.99726 -21.0987 11.9833 --6.53079 -21.9344 12.2905 --7.06129 -22.6589 11.8483 --7.50473 -23.1309 11.0706 --7.56649 -23.5013 10.1628 --8.16134 -22.7726 10.3414 --8.41355 -22.1358 9.63778 --7.63565 -22.068 9.02319 --7.02765 -21.8009 8.27645 --6.54382 -21.4861 7.44843 --6.56549 -20.6385 6.94967 --6.94432 -19.8355 7.3074 --7.21638 -19.9444 8.27236 --7.58838 -20.2023 9.16827 --8.4904 -20.4526 8.84445 --8.15222 -21.077 8.21029 --8.96232 -21.7121 8.00589 --9.52266 -22.4849 7.61783 --9.62458 -22.5674 6.63579 --10.018 -21.6277 6.55751 --10.616 -22.1384 7.2223 --11.2484 -22.0098 6.36159 --11.2696 -21.0791 5.91874 --12.1994 -21.4702 5.76509 --12.8321 -21.6355 4.97413 --13.1821 -21.5384 4.06886 --14.0043 -21.1221 3.71267 --13.7598 -20.6485 2.95362 --14.6706 -21.0981 2.80594 --15.3308 -21.0423 3.52278 --16.0334 -20.3948 3.16527 --15.6037 -20.7701 2.34816 --15.4398 -21.0736 1.37482 --14.5664 -20.7507 0.9463291 --14.2682 -20.8852 0.01858372 --13.5598 -21.3331 -0.5194279 --13.3889 -21.3806 -1.53008 --13.221 -20.4881 -1.12524 --13.3949 -19.7353 -1.7655 --12.4829 -20.0615 -2.02771 --12.6649 -19.8074 -2.93458 --12.7942 -20.3404 -3.8572 --12.9722 -19.3794 -3.84331 --13.776 -19.6413 -4.40887 --13.1151 -20.2232 -4.85247 --12.2432 -20.6669 -4.95343 --12.8731 -20.819 -5.68872 --12.8724 -20.5833 -6.65003 --12.1177 -20.7313 -7.23155 --11.9441 -19.7531 -7.05954 --11.224 -19.495 -7.71541 --10.856 -19.1028 -8.52595 --11.3479 -19.8051 -8.9675 --10.7873 -20.3108 -9.7458 --11.0878 -20.6928 -10.5823 --11.6754 -21.5731 -10.7885 --12.4922 -21.2441 -11.1545 --12.6379 -20.2787 -10.9958 --13.2944 -19.9427 -10.3066 --13.278 -19.0142 -10.4932 --12.8489 -18.325 -9.94689 --13.1326 -17.6801 -9.21585 --12.6 -16.8763 -9.5432 --12.5673 -16.5999 -10.4984 --12.3289 -16.7772 -11.4412 --11.6131 -16.0952 -11.3532 --11.9656 -15.3665 -10.8125 --12.2511 -14.9777 -9.96247 --13.0461 -15.0876 -9.38049 --13.8361 -15.1606 -8.79472 --14.1214 -14.8897 -7.90009 --14.5047 -15.2207 -7.13997 --14.8039 -16.0133 -6.65692 --13.8165 -16.0261 -6.58335 --13.7425 -16.9206 -6.17175 --13.8782 -17.721 -6.69159 --14.4253 -18.263 -7.3693 --14.7873 -19.2154 -7.64236 --14.4434 -19.1845 -6.64762 --15.3359 -18.5956 -6.70453 --16.1349 -19.0441 -7.17505 --16.7457 -18.9961 -7.89677 --16.503 -19.9239 -8.22841 --15.9415 -19.8744 -9.02668 --15.995 -20.8236 -9.17704 --15.5528 -21.0666 -10.0479 --14.7764 -21.6959 -10.0796 --14.0092 -22.3424 -10.0379 --14.7596 -22.7696 -9.46997 --14.4478 -23.6251 -9.09634 --13.909 -22.8932 -8.68726 --14.2586 -21.8985 -8.78402 --14.3306 -21.7199 -7.79238 --13.7608 -22.4404 -7.64928 --14.4073 -23.0971 -7.35915 --14.2086 -24.1782 -7.57188 --13.9273 -24.9503 -8.03676 --13.347 -24.4604 -8.61005 --13.0951 -23.6118 -9.09704 --12.5978 -22.8234 -9.49982 --12.1433 -22.1701 -8.9156 --12.5837 -21.4307 -9.39614 --13.4584 -21.1117 -9.06271 --12.8076 -20.6945 -8.41343 --12.5209 -21.6032 -8.07223 --12.0999 -22.0736 -7.26527 --12.0653 -23.0643 -7.17083 --11.101 -22.6429 -7.35272 --10.6343 -23.5125 -7.61482 --10.4575 -22.7285 -8.21005 --9.96988 -23.5058 -8.53786 --10.5366 -23.2984 -9.29094 --9.88833 -22.4993 -9.1612 --9.26189 -22.4335 -9.88935 --9.55457 -23.4853 -9.7156 --8.90766 -24.1433 -9.38025 --9.01619 -25.1001 -8.99852 --9.67157 -24.878 -9.71847 --9.82782 -24.8393 -10.6609 --9.44734 -24.0063 -11.1339 --10.3723 -23.7731 -11.5216 --11.2876 -23.3968 -11.4059 --11.531 -22.9328 -12.1825 --11.4163 -22.02 -12.5226 --10.4566 -22.3641 -12.6166 --10.6108 -21.3649 -12.8519 --11.1795 -20.8355 -13.5105 --10.9386 -20.3124 -12.7109 --11.1902 -19.4211 -13.0419 --10.9048 -18.526 -12.7767 --11.2434 -17.9221 -12.0505 --10.2955 -17.6203 -12.1797 --9.92415 -16.8283 -12.6878 --9.12948 -16.7316 -12.1084 --9.27972 -16.6311 -11.1319 --9.42417 -16.4717 -10.1605 --10.1302 -16.0325 -10.7755 --9.65797 -15.2152 -10.3101 --9.02813 -15.4776 -11.0147 --8.61998 -14.943 -11.8026 --8.14703 -14.9286 -10.914 --7.77494 -15.1843 -10.0007 --7.96588 -15.1283 -9.08874 --7.11457 -14.8896 -8.63949 --7.19579 -14.7987 -7.66504 --7.017 -14.6114 -6.74066 --6.35252 -15.3321 -6.56384 --5.61036 -15.9225 -6.27199 --5.99849 -16.353 -5.45015 --6.54826 -17.0565 -5.80272 --6.25956 -18.0303 -6.06956 --7.13261 -17.7163 -6.47061 --6.62804 -17.4804 -7.24971 --7.15244 -17.5008 -8.10202 --7.63518 -17.2121 -8.94411 --8.28479 -17.6428 -9.52161 --7.30211 -17.8117 -9.60037 --7.37105 -18.7661 -9.06496 --7.07755 -18.9179 -10.0825 --6.28563 -18.8405 -10.7027 --5.58628 -19.568 -11.0817 --5.79526 -20.4977 -10.8608 --6.27432 -20.409 -11.744 --7.24757 -20.6862 -12.018 --8.15805 -20.5775 -12.2194 --8.31647 -20.3899 -11.2231 --8.29053 -20.3758 -10.3001 --8.67418 -21.2769 -10.0863 --8.48523 -21.8136 -9.27615 --7.64932 -21.5046 -9.67972 --7.11744 -22.2369 -9.48083 --7.828 -22.848 -9.8071 --7.89367 -22.5407 -8.87451 --8.26425 -22.9456 -8.03499 --8.37579 -23.7695 -8.56829 --8.50131 -24.3071 -7.75776 --8.49888 -23.7913 -6.8924 --9.17588 -24.5362 -6.52647 --9.50766 -25.3503 -6.04282 --8.96764 -26.0578 -6.2432 --8.11769 -26.233 -6.75096 --7.10561 -26.2423 -6.81527 --6.76705 -25.4356 -7.14745 --7.40931 -24.844 -7.53426 --6.69106 -24.4561 -8.01994 --6.02256 -23.8157 -7.67025 --6.20572 -23.0797 -7.12119 --6.08308 -22.7013 -6.21072 --5.68986 -23.5723 -6.06144 --4.70475 -23.5465 -5.7099 --3.73891 -23.7694 -5.58015 --3.82096 -24.697 -5.15173 --3.18043 -25.1851 -5.79163 --3.22962 -26.014 -6.3186 --3.98791 -26.1603 -7.02967 --4.04843 -27.138 -7.27386 --3.73774 -27.3562 -8.26264 --2.93542 -27.4988 -7.53847 --2.15808 -27.4925 -6.85493 --1.43666 -27.2389 -7.52501 --1.13951 -26.643 -8.25546 --0.725724 -26.3944 -9.10349 --0.472588 -27.2314 -8.7066 -0.499898 -27.6188 -8.75347 -0.143184 -28.1725 -9.44328 -0.136604 -28.2008 -10.3848 --0.11103 -29.1345 -10.6821 --0.934206 -28.8613 -11.0161 --0.13751 -28.461 -11.4908 --0.981858 -28.3806 -12.0691 --1.13454 -27.3521 -12.084 --1.12787 -27.7758 -13.0637 --0.819436 -26.8047 -13.0455 --1.80558 -26.7112 -12.7577 --2.45577 -26.1518 -13.1337 --3.34388 -25.5549 -13.2242 --2.76254 -24.84 -13.6323 --3.24447 -24.0743 -14.0482 --3.79388 -23.4323 -13.5969 --4.59307 -22.9295 -13.2195 --3.94612 -22.1821 -13.0333 --3.36086 -21.5246 -12.4689 --3.86109 -21.0096 -13.2093 --4.74792 -20.6364 -13.1366 --5.74703 -20.6531 -13.24 --5.88603 -21.2075 -14.0374 --6.86543 -21.1261 -14.3301 --7.12213 -21.9691 -14.6901 --7.85535 -22.457 -15.211 --8.31898 -23.165 -14.7588 --8.9423 -23.5721 -14.0914 --9.42133 -22.7836 -13.924 --9.69196 -22.3709 -14.8085 --10.202 -21.5466 -14.5286 --10.0143 -20.8813 -15.2666 --10.3761 -20.4542 -16.1064 --10.9596 -20.2244 -15.3272 --10.3723 -19.401 -15.3935 --11.279 -19.1054 -15.2567 --11.936 -19.0337 -16.0444 --12.3857 -19.6689 -15.4527 --13.4088 -19.5879 -15.6301 --13.5709 -19.561 -14.6339 --12.8504 -20.2059 -14.2538 --12.3849 -21.0689 -14.5911 --12.9318 -21.8604 -14.2797 --13.533 -22.6388 -14.0402 --13.7299 -23.3735 -14.7526 --13.2148 -24.215 -14.7948 --14.1174 -24.6117 -14.9603 --14.6346 -24.4306 -14.1159 --14.7008 -23.5476 -13.7352 --15.36 -22.9131 -14.0506 --15.3866 -22.1889 -14.646 --15.3568 -21.2775 -14.9564 --16.0829 -20.8157 -14.4074 --16.9192 -20.6079 -13.8993 --16.7569 -20.3645 -12.9324 --16.8299 -19.282 -12.9742 --16.6276 -18.8496 -13.851 --15.9906 -19.6322 -13.869 --15.5251 -19.0013 -13.2945 --14.7471 -19.6809 -13.5244 --14.2373 -20.5787 -13.7725 --14.967 -21.0627 -13.3746 --15.5325 -20.5066 -12.7205 --15.2301 -20.545 -11.7359 --15.8551 -19.952 -11.1761 --16.0745 -19.6756 -10.2686 --16.5242 -18.7647 -10.1876 --16.5984 -17.723 -10.2773 --16.5008 -17.1923 -11.1768 --16.3464 -16.9284 -12.1925 --15.34 -17.0308 -12.0289 --15.1819 -16.0599 -12.12 --14.4238 -16.0075 -11.3475 --13.4576 -16.3736 -11.4686 --14.1803 -16.5862 -12.1421 --14.5338 -17.0523 -12.8609 --14.107 -17.0137 -13.7309 --13.2044 -16.7527 -14.1259 --13.3583 -15.8632 -14.5897 --12.5531 -15.6829 -15.0489 --12.4227 -14.6678 -15.1679 --11.5565 -14.9995 -14.803 --11.6983 -15.9886 -14.5967 --11.362 -16.1785 -13.6542 --11.0492 -15.9417 -12.7086 --10.6 -15.1744 -13.0968 --10.1666 -14.7475 -12.2688 --9.44794 -15.0493 -12.8736 --8.49653 -14.8824 -13.247 --8.81841 -14.1996 -12.5821 --7.96716 -14.0308 -13.0033 --8.43431 -13.7718 -13.7615 --7.65446 -13.1659 -13.5363 --8.34226 -12.5435 -13.2238 --8.52802 -11.5937 -13.1017 --9.30574 -11.2003 -13.6291 --9.80624 -10.3499 -13.4331 --10.0444 -9.69738 -14.1297 --10.0754 -9.81018 -15.1363 --9.8795 -9.16093 -15.8663 --10.5429 -9.83804 -16.2578 --11.5259 -9.68728 -15.8694 --11.6962 -9.94201 -14.951 --11.4894 -9.24164 -14.2768 --11.8353 -9.35848 -13.3738 --12.2148 -8.90278 -12.4119 --11.9745 -8.97873 -11.439 --11.8663 -8.98779 -10.4354 --12.3039 -9.67367 -9.9081 --12.9551 -10.3449 -9.65211 --13.8853 -9.87676 -9.56722 --14.3192 -10.3577 -10.2371 --14.7295 -11.0798 -10.6773 --15.579 -11.2043 -10.1358 --16.2706 -10.8584 -10.8387 --17.1044 -10.4235 -10.5238 --17.8584 -10.2669 -9.9036 --17.6818 -10.1205 -8.9502 --16.7673 -9.78922 -8.76368 --16.5064 -8.94285 -8.11516 --16.1621 -8.73573 -8.99555 --15.6864 -7.86448 -8.75967 --16.6297 -7.47522 -8.89807 --17.5751 -7.63204 -8.72659 --17.4796 -8.54748 -8.50572 --17.4467 -8.82631 -7.52997 --18.1386 -8.13692 -7.19666 --19.1017 -8.02345 -7.49203 --19.9528 -7.95476 -7.03812 --20.1486 -8.64701 -6.33458 --20.2513 -7.94858 -5.68077 --19.729 -7.45329 -4.92872 --20.2646 -7.01327 -4.22355 --19.3784 -6.46367 -4.30845 --19.6552 -6.43267 -3.30225 --20.3752 -6.4752 -2.61933 --20.776 -6.42029 -1.72763 --21.1992 -6.40713 -0.7997119 --20.391 -6.3823 -0.1923939 --19.8198 -5.55654 0.01164772 --19.1724 -4.82056 -0.1785469 --19.3771 -3.90495 -0.3838039 --19.3791 -3.87271 0.5837311 --18.6646 -4.46205 0.9876451 --17.9089 -3.84488 1.21453 --17.0382 -3.58044 0.7685451 --16.2756 -2.96242 1.00736 --15.7662 -3.22111 0.1551691 --14.8394 -2.91861 0.2195821 --14.1003 -2.99436 -0.4231549 --14.3107 -3.87486 -0.6035919 --14.812 -3.99221 0.1947461 --15.6618 -4.32746 0.5983531 --16.0432 -4.55389 1.54497 --15.3625 -5.18534 1.5587 --15.6738 -5.06168 2.49132 --15.9402 -4.59686 3.35144 --16.6698 -4.91667 3.90083 --17.3155 -4.72286 4.67708 --17.2938 -5.25495 5.53783 --17.0234 -4.6354 6.26558 --16.1578 -4.90776 5.81193 --15.2355 -4.47531 5.85946 --15.8973 -3.788 5.75904 --15.7798 -2.95246 6.2692 --15.7483 -2.50349 5.35126 --15.4331 -2.94906 4.50676 --16.0557 -2.58374 3.81593 --15.8787 -3.04676 2.96388 --15.9972 -2.29615 2.30121 --16.1267 -1.97578 1.42077 --16.8369 -1.3167 1.28679 --16.058 -0.7835421 1.49372 --15.6832 -0.7113371 2.41064 --15.0327 -1.15419 3.06755 --14.3452 -1.90395 3.34137 --13.4261 -1.52129 3.35235 --12.9898 -2.33326 3.07922 --12.4202 -2.98834 3.49489 --13.2636 -2.87704 4.07157 --13.6832 -2.86589 4.91188 --12.8038 -2.44596 5.31538 --12.7799 -3.32537 5.71349 --12.6386 -4.29337 5.58884 --11.9486 -4.84216 5.12124 --11.2765 -5.29368 4.52103 --11.1398 -4.35515 4.81135 --10.6339 -4.96699 5.42908 --9.79203 -4.62082 5.97331 --9.17254 -5.16942 5.43182 --8.78006 -4.42862 5.97138 --9.26452 -3.6096 5.56715 --9.93569 -3.25498 5.03078 --9.96967 -2.55754 5.70166 --10.5474 -3.33241 5.91895 --11.086 -4.09027 6.03541 --11.7119 -4.69089 6.46124 --10.8575 -4.95048 6.9115 --10.4807 -5.78502 7.28742 --9.58549 -5.34867 7.25215 --9.39893 -5.05111 8.2133 --10.0505 -4.36912 8.68728 --10.8147 -4.89375 8.33165 --11.0356 -5.73451 8.73633 --11.0966 -5.94194 9.75565 --10.5275 -6.41378 10.374 --9.87853 -6.01013 11.026 --10.4758 -5.15619 11.0545 --10.0132 -4.27231 11.3602 --9.08272 -4.01094 10.9746 --8.90522 -4.93951 11.3952 --8.33723 -5.72516 11.1234 --9.023 -5.77277 10.3776 --8.56447 -5.80485 9.44343 --8.3043 -6.42847 8.65353 --7.51808 -6.83428 9.20507 --6.70502 -6.78155 8.43065 --6.71977 -5.86244 8.04901 --6.62272 -4.8802 7.89203 --5.64226 -5.0111 7.99195 --5.08753 -4.07972 7.95821 --4.39494 -4.76425 7.64201 --3.83094 -3.90342 7.68716 --4.53908 -3.76438 7.02605 --4.38354 -3.58936 6.08466 --5.37858 -3.64986 6.20524 --6.01797 -2.99528 5.86675 --6.59123 -2.26971 6.31672 --5.81362 -2.16206 6.91571 --5.63513 -2.98077 7.51847 --4.82395 -2.43203 7.32438 --5.15097 -2.53927 6.38838 --4.26555 -2.00484 6.29065 --4.94455 -1.7315 5.56578 --4.75652 -0.7486931 5.22918 --4.46964 -0.7553121 6.15169 --5.18528 -0.7845931 6.84445 --6.01954 -0.4532861 7.17508 --6.62281 -0.5498241 6.35162 --6.00195 -0.9854971 5.74488 --5.71222 -1.11899 4.88937 --5.94191 -0.3045241 4.3211 --6.8678 -0.5669891 4.40275 --7.85919 -0.3573041 4.3583 --8.60722 -0.5088911 5.01202 --7.97803 -0.7016081 5.73115 --8.83773 -1.24123 5.70997 --8.24352 -1.51878 4.93922 --8.11763 -1.39559 3.9485 --8.11107 -0.9225461 3.04287 --9.01039 -1.25281 3.19073 --9.59776 -1.07874 3.9924 --9.81386 -0.3727041 3.23401 --10.7395 -0.3352581 2.79539 --11.0687 0.2903989 3.39023 --11.7957 -0.1601571 3.0549 --12.0852 -0.5209101 3.9749 --13.0459 -0.1670491 3.93156 --12.9527 0.4941859 4.63192 --13.531 1.25565 4.3018 --14.372 1.47667 3.78559 --14.9153 2.20225 3.46413 --14.7057 3.08711 3.85997 --14.8622 3.02498 2.84426 --14.2424 2.36166 2.28653 --13.9323 1.40603 2.23147 --14.5297 0.6203589 2.48261 --13.7906 -0.03764047 2.33515 --13.0222 -0.4058851 1.77962 --12.5057 0.4099019 2.12422 --12.6552 1.39709 2.25869 --11.8956 1.01694 2.86521 --11.1882 1.57688 3.28315 --10.7285 2.45735 3.19473 --11.3791 3.1841 3.16284 --11.1185 4.07796 3.58982 --11.2164 3.84546 4.57493 --11.5161 3.85476 5.60774 --11.1118 4.03025 6.52711 --10.4405 4.00961 7.24299 --10.7112 4.57037 8.05698 --10.4746 4.96883 7.13558 --10.5036 5.5026 6.26675 --11.1165 5.26008 5.48093 --11.9149 5.46017 6.08186 --12.8005 5.40061 6.4296 --13.0807 4.89487 5.63728 --13.621 4.50336 6.23903 --13.6097 3.6563 5.63557 --14.1386 2.78433 5.72102 --14.7738 3.25107 6.34383 --14.9097 2.79043 7.17578 --15.796 3.09873 7.54928 --15.9473 4.11107 7.73067 --15.0869 3.79916 8.22323 --14.3965 3.38305 8.80668 --13.8068 2.63716 8.42092 --13.7394 2.79194 7.41173 --12.7473 2.7407 7.54516 --13.0681 1.86228 7.7641 --13.4419 1.17769 7.02783 --13.7117 1.34211 6.10247 --13.6134 0.3240039 5.78509 --14.3406 -0.05361427 6.34564 --14.8288 -0.1119711 7.13977 --15.2968 0.1123499 8.04979 --14.5568 0.4393679 8.58934 --14.1493 1.12858 9.14711 --13.4485 0.5788939 8.78103 --12.4863 0.5617279 8.46262 --12.1899 1.36656 8.90693 --11.2493 1.21452 8.60203 --11.4785 1.46627 7.6622 --10.9225 2.22764 7.38696 --10.4154 1.34779 7.29626 --9.89205 2.16592 7.63292 --9.44254 2.85217 7.06337 --9.43421 1.95681 6.54825 --9.0842 2.46779 5.78483 --8.88354 3.48261 5.64114 --9.21494 4.25375 5.22915 --9.01866 4.60854 4.29529 --8.63661 3.87097 3.68728 --9.1384 3.64763 2.78767 --9.30456 2.7955 2.22956 --9.45433 1.80527 1.92864 --8.63877 2.0875 2.45126 --8.61315 2.19098 1.45455 --8.35515 1.38131 0.8427641 --8.25447 0.9756569 1.79137 --7.68088 0.2944719 1.42081 --6.84013 0.3388589 0.8719101 --6.01135 -0.06096017 1.28423 --5.93933 0.09975353 2.30953 --6.68531 -0.4572251 1.94505 --7.18932 -1.20412 2.41098 --7.5843 -1.8185 1.62495 --7.23387 -1.84713 0.6847041 --6.302 -2.28609 0.6344571 --5.52941 -2.13219 1.3005 --5.4779 -1.28709 1.87646 --6.20941 -1.93287 2.2536 --6.62967 -2.553 2.88679 --7.02854 -3.16343 3.54892 --7.99486 -3.3656 3.82128 --8.15122 -3.90975 2.99702 --7.29322 -4.33651 2.83366 --6.79101 -5.20174 3.05847 --6.09105 -4.98455 2.43387 --5.73687 -5.2648 3.34214 --5.34191 -4.65067 3.98402 --5.15339 -3.85842 4.57996 --4.23012 -3.72544 4.22188 --3.95078 -2.83416 3.80795 --3.07631 -3.20513 4.12576 --3.44236 -3.81631 3.46795 --3.9209 -4.05829 2.59333 --4.64418 -3.69999 2.02868 --5.49073 -3.30092 1.56871 --5.97373 -3.91878 0.9930761 --5.54785 -3.36368 0.3296711 --4.81969 -2.82203 0.2987471 --4.39013 -3.46394 0.9279961 --3.67425 -4.01 1.32668 --3.11742 -4.00121 0.4906761 --2.77258 -3.03472 0.7616961 --3.07109 -2.13407 1.08126 --2.95524 -2.16469 2.0659 --2.51045 -2.7833 2.65426 --1.85273 -2.76276 1.92425 --1.1358 -2.20054 2.33061 --0.366167 -2.86178 2.22672 -0.633552 -3.05299 1.95327 -1.1288 -3.83965 2.21643 -0.662937 -3.7429 3.10808 -0.473197 -4.13049 4.06621 -0.654465 -3.75697 5.01782 -1.1221 -4.65893 5.13865 -0.896134 -5.53483 5.57291 -0.483727 -5.76333 6.50213 -1.12115 -5.09921 6.83344 -0.593266 -4.80691 7.60844 -0.277929 -3.99256 8.08445 -1.13135 -4.35739 8.42962 -1.89057 -3.68144 8.29871 -2.59607 -3.03767 8.41704 -3.21142 -2.29975 8.81261 -3.47267 -1.57445 8.15014 -2.50681 -1.42939 8.52403 -2.84609 -0.4857551 8.32088 -1.93829 -0.5989861 7.85749 -1.41974 -1.31854 8.36879 -1.72793 -2.08971 7.79963 -2.63801 -2.02612 7.31876 -2.46893 -1.58131 6.4461 -2.74607 -1.24101 5.434 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15.6149 -11.3459 --11.0416 16.6221 -11.5991 --11.9965 16.93 -11.9481 --11.7907 16.2391 -12.643 --11.019 16.1459 -13.2435 --11.3424 16.9234 -13.8054 --12.2293 16.6471 -13.4913 --12.8466 16.9463 -14.3352 --13.5462 17.582 -13.897 --12.9279 18.0186 -14.5581 --13.2302 18.6221 -13.857 --13.6477 19.3211 -13.3342 --13.076 19.8372 -12.6638 --12.2211 19.8471 -12.1552 --12.3387 20.7215 -12.5581 --13.1613 20.9466 -12.9803 --14.0885 20.6239 -12.8002 --14.8475 21.2154 -12.9402 --15.1789 21.2769 -13.8733 --14.5499 20.7825 -14.4527 --14.5058 20.3139 -15.3127 --13.7783 20.2632 -15.961 --13.0518 19.6639 -16.2813 --13.2409 20.496 -16.8483 --13.1642 21.4637 -16.8193 --12.5436 22.2172 -17.1356 --12.6471 23.2191 -16.9373 --12.4117 23.911 -17.6622 --12.0578 23.2736 -18.4592 --11.5811 23.9834 -19.141 --11.4354 24.1089 -20.0668 --10.7445 23.4248 -19.8052 --10.0787 24.0327 -20.1635 --9.6097 23.4547 -19.5119 --9.90029 22.5059 -19.2356 --10.0523 22.298 -20.113 --9.3344 21.7811 -20.5119 --9.07794 22.4998 -21.1212 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22.6509 -23.2302 --5.393 22.5389 -24.1259 --5.68906 23.5321 -24.088 --6.19553 24.3429 -24.5565 --7.0294 24.0385 -25.0881 --6.82001 23.5032 -24.2645 --7.56611 22.9496 -24.6594 --8.4883 22.877 -24.2504 --8.59055 22.0901 -24.7802 --8.3167 21.6662 -25.6681 --7.68023 21.1118 -26.1844 --7.8354 20.1774 -25.8419 --8.42681 20.0461 -26.664 --8.18065 19.0552 -26.6916 --7.51311 18.5187 -26.1717 --7.07185 19.4411 -26.1841 --6.50884 20.2265 -25.959 --5.84644 20.9367 -26.0056 --5.39991 20.0602 -25.7313 --4.89503 19.3826 -25.1075 --4.02356 19.6633 -24.7456 --4.51957 19.6615 -23.9052 --4.38959 20.619 -23.8046 --4.36685 21.2171 -24.5208 --4.49771 20.6147 -25.367 --4.05613 20.2195 -26.1561 --4.26248 20.6057 -27.0956 --3.31589 20.7395 -27.4278 --2.41163 20.7148 -27.7637 --1.92951 21.2675 -28.2867 --0.922388 21.2329 -28.2031 --0.08968983 20.8633 -27.8661 -0.579416 21.4294 -28.3143 -1.42354 21.8358 -27.9173 -2.23043 21.2793 -27.8389 -1.98013 20.284 -27.6042 -1.8996 19.3417 -27.2977 -2.36922 18.7285 -26.708 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-18.7758 --6.06184 24.7097 -19.3217 --5.63641 24.0331 -18.6887 --4.87343 23.3651 -18.2794 --4.12726 22.7446 -18.3242 --3.87981 21.9268 -17.6624 --3.31338 21.3461 -17.136 --2.59596 21.7727 -16.6364 --1.74225 21.4149 -16.3054 --1.48782 22.223 -15.7457 --1.9112 22.6999 -14.9424 --1.69264 22.3421 -14.0948 --1.52592 21.284 -14.0444 --0.679564 20.6696 -14.1256 --0.743139 20.4553 -15.1513 -0.228292 20.1203 -14.8937 -0.384682 21.1527 -14.9868 -1.32462 20.7329 -14.7043 -2.02934 20.1062 -14.8325 -1.22964 19.9941 -15.4352 -1.74351 19.9673 -16.2447 -1.76725 20.7604 -16.8306 -1.83915 20.4504 -17.772 -1.09727 19.9095 -17.3408 -0.178765 20.3928 -17.525 --0.765846 20.2346 -17.8901 --1.40564 19.5188 -17.7863 --1.81134 18.8542 -18.4161 --2.76669 18.9306 -18.5772 --2.75645 18.3511 -19.3725 --3.24746 17.841 -20.1006 --2.86227 17.3824 -20.8545 --2.7866 17.2876 -21.9126 --3.70177 17.1064 -22.0908 --4.62685 17.3987 -21.909 --5.56296 17.7387 -22.2044 --6.13527 17.4277 -21.4118 --6.48379 16.6517 -20.9178 --6.21196 15.7736 -20.5809 --6.39129 16.5155 -19.9413 --5.69978 17.2098 -19.6148 --4.74718 17.4475 -19.9659 --5.08473 17.4052 -20.8509 --4.13209 17.7419 -21.0555 --4.38059 18.616 -21.4297 --4.84587 18.7286 -22.3187 --5.81624 18.7224 -22.5462 --6.30509 19.5408 -22.7177 --7.09012 19.6783 -23.2878 --7.65822 18.9128 -23.7005 --8.19639 18.8836 -24.5589 --8.94636 18.822 -23.9591 --9.1262 18.1071 -24.6472 --8.62223 17.6387 -25.2888 --8.879 16.6541 -25.4349 --9.84046 16.2638 -25.3929 --10.5389 16.6681 -24.7457 --11.3337 16.9714 -25.1467 --11.6457 17.6255 -24.4843 --11.2794 17.559 -23.5804 --10.475 16.9619 -23.1827 --10.255 17.0667 -22.2102 --10.4036 18.0419 -22.1949 --10.9966 17.8599 -21.4517 --11.2797 18.8102 -21.4447 --11.9142 19.0787 -20.7627 --12.5144 19.5275 -21.409 --12.2066 19.965 -22.2321 --12.5156 20.552 -23.001 --12.5045 21.187 -22.2053 --12.7417 21.7502 -21.4423 --12.8964 22.7084 -21.3866 --13.9131 22.681 -21.8258 --14.3758 22.2431 -21.0263 --14.8647 23.0525 -21.0359 --14.5584 22.8218 -20.1286 --14.7985 22.0132 -19.6184 --14.4688 22.6363 -18.8827 --14.0488 23.0163 -18.0261 --14.886 22.7135 -17.6643 --15.4933 22.7031 -16.8333 --16.4472 22.6861 -16.6845 --16.9297 23.4613 -17.0486 --17.4553 23.1975 -16.1974 --17.4384 22.1895 -16.1858 --17.7671 21.8853 -17.0631 --18.1505 22.7583 -17.3282 --19.1199 22.9503 -17.492 --18.9713 23.4582 -18.3745 --18.7788 24.0348 -17.5689 --18.8353 24.8945 -17.0022 --17.931 24.8506 -16.5234 --18.3413 25.4879 -15.8873 --18.9195 26.2724 -15.6417 --19.5567 26.0758 -14.9093 --20.2492 25.3409 -14.9651 --20.1547 24.3467 -14.8352 --20.3806 23.4084 -14.4959 --21.2508 23.0048 -14.1167 --20.608 23.3982 -13.4364 --21.135 24.224 -12.9775 --21.082 24.165 -11.9555 --21.078 25.0963 -12.2913 --20.4379 25.7596 -12.3275 --20.8087 25.6697 -11.4048 --21.2058 26.5472 -11.1733 --21.3568 27.4252 -11.5125 --21.6976 28.2583 -11.0988 --21.2907 29.0528 -11.3912 --21.3143 29.9547 -10.904 --21.1055 29.2174 -10.2362 --21.5275 29.0688 -9.38615 --21.4881 28.3554 -8.66938 --20.8954 27.9523 -7.94807 --20.7617 27.8161 -7.00101 --20.0983 28.0024 -6.21194 --19.8757 28.2517 -7.16327 --19.2405 28.8017 -6.59631 --18.9174 28.1814 -5.8509 --19.0103 27.216 -5.65812 --18.1281 26.8665 -5.3782 --17.8572 26.7595 -6.27854 --17.1569 26.0102 -6.12834 --17.4746 25.3195 -5.53645 --17.9898 24.5048 -5.77223 --18.6454 25.1992 -6.01774 --19.0855 25.2177 -6.90051 --18.682 24.3913 -7.28745 --18.0553 24.8679 -7.95185 --17.6638 24.8329 -8.8879 --18.3294 25.5536 -8.91988 --18.4088 24.8576 -9.68244 --18.586 24.026 -10.1039 --17.9249 23.6456 -10.7845 --17.0516 24.0411 -11.0483 --16.5017 23.3233 -10.6564 --16.3561 22.41 -11.0781 --17.0744 22.0984 -11.7084 --18.0378 22.3456 -11.6975 --18.6827 21.5415 -11.3946 --18.3013 21.6857 -10.4365 --18.5177 20.7327 -10.6681 --18.4506 20.191 -9.87382 --18.3471 21.0885 -9.4306 --18.9093 21.8011 -9.16562 --19.7787 21.7505 -9.6283 --20.6002 21.7779 -9.23764 --21.2625 21.3139 -9.87976 --22.0529 21.9663 -9.95112 --22.1166 22.6007 -9.17604 --22.5304 23.2615 -8.56953 --23.3 22.5608 -8.70092 --23.8527 21.702 -8.40181 --23.1102 21.3415 -8.91992 --22.3285 20.7602 -8.78978 --22.2323 19.857 -8.353 --21.9189 18.8744 -8.26196 --21.2515 18.1592 -8.406 --20.9144 18.3185 -9.26767 --20.2254 18.4852 -9.946 --19.5078 18.9801 -10.4429 --19.5167 18.8383 -11.4589 --18.8223 19.5437 -11.6419 --18.7482 19.5817 -12.6358 --18.0227 19.8982 -13.2685 --17.9326 19.7366 -14.218 --18.8692 20.0523 -14.2485 --18.6917 20.6717 -14.9964 --19.1649 21.4311 -15.4676 --19.2534 20.6509 -16.0826 --19.8237 19.9375 -16.4357 --19.1954 20.2994 -17.1942 --20.1831 20.3139 -17.5205 --20.9911 19.7129 -17.9003 --20.4916 18.7791 -17.922 --19.7263 18.3784 -18.3821 --19.7377 19.1666 -18.9322 --19.0996 18.4747 -19.3618 --18.1837 18.9355 -19.2861 --18.391 19.6242 -18.5737 --17.5957 19.9307 -17.9814 --16.8431 19.6886 -17.4423 --16.8194 20.3625 -16.7043 --16.3663 19.4509 -16.5989 --15.4786 18.9334 -16.7035 --15.3092 18.0174 -16.3338 --15.7429 17.1098 -16.1361 --16.5245 17.6533 -16.3658 --16.8815 17.0972 -17.1226 --17.583 16.4027 -16.8388 --17.2917 15.4887 -16.6956 --16.5927 16.1753 -16.368 --16.8966 15.5209 -15.6342 --17.6566 16.0222 -15.2716 --17.4462 16.9166 -15.5493 --16.473 17.0864 -15.3048 --16.2915 17.8754 -14.7387 --17.1547 17.5974 -14.3945 --17.3836 18.3211 -13.8207 --18.3659 18.255 -14.044 --18.9548 17.5688 -14.4273 --18.5931 16.6554 -14.6458 --18.763 16.2806 -15.5964 --18.2192 15.6625 -16.093 --18.6562 16.1156 -16.7741 --19.3915 15.6097 -17.1961 --19.1605 14.5608 -17.1772 --18.3917 13.8977 -17.1245 --17.7561 13.6735 -17.8765 --17.0842 13.5022 -17.198 --16.5036 12.7112 -17.4272 --15.9118 13.4112 -17.6533 --15.1072 13.3128 -17.0732 --14.511 12.5122 -17.1067 --14.1634 13.0431 -17.8051 --14.537 12.7238 -18.6061 --13.7921 13.4773 -18.6616 --13.327 14.2591 -19.0998 --13.1053 13.8357 -19.9241 --13.2167 12.9288 -20.3814 --13.5809 12.5038 -21.0877 --12.6369 12.4815 -21.2536 --13.2132 11.8524 -21.6836 --13.5629 12.3368 -22.5119 --13.3936 12.4595 -23.5634 --12.8153 13.3182 -23.622 --12.6197 14.1346 -22.9946 --12.5796 13.5425 -22.2309 --12.6147 13.7285 -21.2203 --11.8391 13.7961 -20.6729 --11.098 14.4858 -20.6641 --10.4501 15.1228 -20.2752 --10.8671 15.6371 -19.5243 --10.1616 16.2579 -19.1302 --10.4056 17.1487 -18.8327 --9.5936 17.2362 -18.1701 --9.15413 17.6697 -18.9167 --9.91365 18.2464 -19.0658 --9.91894 18.2469 -20.0817 --8.9767 17.9107 -20.2262 --8.62208 18.6668 -19.8859 --8.10516 19.0714 -19.1382 --8.4135 19.9056 -18.6176 --7.51944 20.1954 -18.2364 --7.73067 21.129 -18.5238 --7.89111 20.8226 -19.513 --7.09605 21.0392 -20.053 --6.32802 21.3295 -20.622 --6.17189 20.4461 -21.1387 --5.44292 20.5008 -21.7746 --5.72821 21.3836 -21.4194 --5.91619 22.3155 -21.1032 --5.32545 22.0619 -20.2886 --5.57911 21.7088 -19.4318 --6.64238 21.7151 -19.3333 --6.42805 22.1402 -18.5104 --6.39052 22.6156 -17.6179 --6.45965 22.9552 -16.6638 --6.85692 22.6823 -15.8675 --7.82127 22.5429 -16.0288 --7.72525 21.934 -16.831 --7.34732 21.2336 -16.157 --7.34853 20.6421 -15.3204 --8.34664 20.4928 -15.1199 --9.18492 20.4306 -15.5828 --9.78814 19.8163 -16.095 --9.57579 19.9918 -17.0262 --8.95784 20.6611 -17.5431 --8.95119 21.5849 -17.3349 --9.00486 21.3433 -16.4091 --9.92302 21.5234 -16.1066 --10.1711 22.2567 -16.7326 --10.5909 23.0654 -16.4196 --11.1981 22.9869 -15.7007 --11.4304 22.3251 -14.9874 --12.4792 22.5263 -14.9055 --12.1108 22.0145 -14.1324 --13.0069 21.4681 -14.0622 --13.3425 22.036 -13.2905 --14.1079 22.5278 -13.6366 --15.0095 22.7575 -13.2273 --15.3384 23.681 -13.1197 --15.959 23.6504 -12.3366 --15.8609 24.3801 -11.7011 --14.8786 24.4823 -11.5535 --14.2846 25.2791 -11.208 --13.4996 25.9202 -11.4407 --12.9262 26.7071 -11.5314 --12.3071 26.8692 -10.7963 --11.5622 27.5212 -11.0253 --10.9882 28.2486 -11.2888 --10.3941 27.5025 -11.6372 --10.5639 26.7779 -12.2363 --10.898 26.7859 -13.166 --9.95706 26.7578 -13.5291 --9.81758 26.0716 -14.3025 --9.71486 25.6984 -15.2364 --10.3761 25.055 -14.9765 --11.3496 25.129 -14.5475 --11.5316 24.289 -14.1536 --12.391 24.4356 -13.6826 --12.337 24.2292 -12.672 --13.1242 24.8186 -12.7432 --13.0318 25.5835 -13.2752 --13.904 25.1778 -13.4806 --14.897 25.2101 -13.4445 --14.809 25.0855 -12.4429 --15.2903 25.9466 -12.4582 --15.053 26.8761 -12.4189 --15.2812 27.2016 -11.4913 --15.3351 26.2812 -11.1775 --16.0617 25.616 -10.8492 --16.0032 25.1854 -9.99845 --16.1285 25.5489 -9.04365 --15.8078 26.3847 -9.44892 --16.1391 26.5524 -8.49049 --16.1832 27.0683 -7.69951 --15.4427 27.5391 -8.11986 --14.6918 28.2627 -7.97198 --14.2284 28.3085 -8.8646 --13.6451 29.0907 -9.13281 --12.9748 28.4782 -8.75857 --12.2486 28.0951 -9.4765 --11.5454 28.2528 -8.78302 --10.633 28.2504 -8.45806 --10.186 28.4538 -9.32573 --10.2765 27.6491 -9.92267 --9.40239 27.8343 -9.68725 --9.40993 26.8368 -9.65988 --8.42934 26.7872 -9.35304 --7.58915 26.7174 -9.8157 --8.3341 26.7774 -10.5435 --8.01295 27.6919 -10.735 --7.32195 28.3 -10.9202 --6.89106 28.3345 -11.8235 --7.00012 28.0228 -12.7399 --6.50072 28.9055 -12.7716 --6.38786 28.8971 -13.7371 --5.91539 29.0708 -14.5948 --5.34064 28.3723 -14.3382 --4.59722 28.6356 -13.6717 --5.11382 27.8475 -13.2373 --4.80814 26.9477 -13.1581 --4.04938 26.2223 -13.3405 --3.36292 25.4816 -13.1822 --3.58533 24.546 -12.9209 --3.49651 23.6117 -12.8316 --3.68158 23.511 -13.7937 --3.736 24.4278 -14.1601 --2.89986 24.087 -13.8382 --1.90157 24.12 -13.6564 --1.02048 24.6681 -13.6493 --0.618797 25.5464 -13.5999 -0.227835 25.6452 -14.1878 -0.993462 26.2216 -14.0015 -0.982784 27.1191 -14.4854 -1.26824 28.006 -14.9575 -0.931845 28.6786 -14.334 -1.79264 29.1347 -14.3002 -2.80076 29.3221 -14.5685 -2.83231 30.206 -15.0177 -2.86297 30.7271 -14.1903 -2.42485 31.0256 -13.3156 -2.36078 31.0829 -12.3558 -1.37177 30.6735 -12.2671 -0.514087 30.0633 -12.1655 -0.546746 29.165 -12.568 --0.08639763 28.6649 -11.9709 --1.02798 28.3833 -11.8806 --0.607485 27.6295 -12.3139 -0.05152617 27.5321 -13.0036 -0.771882 28.1804 -13.2704 -1.56261 28.6007 -12.8092 -1.817 27.818 -12.1854 -1.55247 27.2198 -11.4174 -0.652395 26.9853 -11.0497 -0.518275 25.9693 -10.8833 --0.02905953 25.1009 -10.7926 --0.449576 24.7718 -11.641 --1.29751 24.8414 -11.2169 --1.54881 24.0928 -11.8488 --2.46114 24.0608 -11.6715 --2.79427 23.1107 -11.6258 --2.93695 22.8085 -10.6563 --3.14385 23.638 -10.1544 --3.76922 23.8345 -9.47365 --3.47175 23.137 -8.86847 --2.84627 23.8544 -8.56338 --2.73572 23.7725 -7.61683 --2.39551 24.7604 -7.64407 --2.22387 25.52 -7.00309 --2.32173 26.3907 -6.5404 --1.61036 26.6172 -5.96735 --2.26756 26.3504 -5.18927 --2.78497 25.9674 -4.44158 --3.72655 26.1852 -4.60136 --4.07239 25.3857 -4.19268 --4.46312 26.322 -3.964 --4.59394 25.7484 -3.16226 --4.38522 24.7752 -3.04061 --5.08541 24.3265 -3.7155 --5.0262 24.1421 -4.68081 --5.95318 24.282 -5.01652 --5.76498 25.26 -4.99598 --6.72967 25.1512 -4.52696 --7.14742 24.8176 -5.36489 --7.59333 25.6694 -5.05452 --8.24176 25.1675 -5.58518 --8.35875 25.556 -6.50822 --8.55512 24.6626 -6.81904 --8.88901 24.4082 -5.86374 --9.79949 24.7059 -5.72231 --10.157 24.5206 -6.65131 --10.7042 25.3713 -6.64679 --9.94041 25.8535 -7.04461 --9.33635 25.8341 -6.22062 --9.26124 26.3752 -5.40983 --9.43016 27.1609 -4.79076 --8.40748 27.0483 -4.61062 --8.44901 27.3246 -3.66324 --7.40141 27.4138 -3.65667 --6.86415 27.9894 -4.21675 --6.57933 28.0353 -3.22844 --6.86289 27.6708 -2.32014 --6.63123 26.6647 -2.35695 --7.50026 26.2705 -2.22904 --6.80416 25.5621 -2.28186 --6.8485 25.5709 -1.33995 --7.40782 24.7808 -1.06255 --8.42413 24.7414 -0.7557619 --9.00158 25.5502 -0.6837289 --9.05794 26.4305 -0.2883169 --9.9976 26.2224 -0.1894149 --9.9276 27.0359 0.4121051 --10.7148 26.4639 0.6651241 --11.4159 26.2644 1.21016 --11.5337 25.2677 1.51979 --12.3684 24.9942 1.01142 --12.9266 24.1716 0.7160131 --13.1949 23.3046 0.2486961 --12.7128 22.3727 0.2580371 --12.9944 21.594 -0.1386649 --12.5942 20.7376 0.04480232 --12.1467 21.1022 -0.7755619 --11.6112 21.0742 -1.59928 --12.0619 21.8298 -2.00038 --11.3036 21.7713 -2.63458 --10.9871 22.6595 -2.40475 --10.0629 22.6028 -2.64965 --9.4831 22.5397 -3.50657 --8.60425 22.5618 -3.17175 --7.75394 22.9604 -3.28385 --7.67708 22.0517 -3.76677 --6.9395 21.361 -3.81976 --7.24653 20.5995 -3.28062 --6.53168 20.5713 -2.56719 --5.60198 20.8814 -2.48193 --5.97888 20.0964 -1.99376 --5.74671 19.9216 -1.01853 --6.33028 19.1381 -1.41105 --7.05727 19.8352 -1.25061 --7.45247 20.5159 -1.87352 --8.31444 20.0625 -1.83087 --9.31825 20.0491 -1.91194 --10.3203 20.0759 -1.74 --9.867 19.429 -2.4166 --10.4809 20.0657 -2.78223 --11.3258 19.9226 -2.23257 --11.6383 19.4476 -1.39513 --12.3968 18.8033 -1.05563 --12.2435 17.7914 -0.9772189 --12.4967 17.35 -0.1290289 --13.0849 16.8398 -0.7972539 --13.9668 17.3002 -0.9750299 --14.829 16.8964 -0.5425189 --15.5051 16.3379 -0.9757509 --16.0163 17.1366 -1.05127 --16.0248 18.0935 -0.6910139 --15.169 18.3382 -1.16318 --14.7944 18.9713 -1.79521 --14.701 19.9892 -2.18799 --13.7672 20.297 -2.0093 --13.5998 19.8725 -2.90031 --12.8092 20.4746 -2.78521 --13.4468 21.0603 -3.27559 --13.2875 22.0099 -3.13464 --13.2867 22.4821 -4.07998 --13.1075 21.6904 -4.76617 --12.632 21.6981 -5.67303 --11.7608 21.9768 -6.11895 --11.6352 22.8496 -6.45865 --11.2403 23.7859 -6.45098 --12.0597 23.996 -6.06343 --11.6674 23.3905 -5.36961 --10.734 23.1127 -5.22569 --10.1546 23.9623 -5.03411 --9.70812 23.2441 -4.55054 --8.86842 23.5807 -4.07795 --8.35516 24.4287 -4.01282 --8.46593 24.6916 -3.05857 --8.88929 25.2915 -2.34038 --9.68188 24.6697 -2.26132 --10.5765 25.1186 -2.2224 --10.9996 26.0825 -2.28861 --10.7139 27.0046 -2.02301 --10.7619 27.9468 -1.67302 --11.7349 28.0126 -1.47576 --11.4493 28.8837 -2.08002 --11.9556 29.2223 -2.9112 --11.9022 28.5577 -3.6642 --12.8697 28.5462 -3.6301 --13.7971 28.6232 -3.92375 --14.13 28.4966 -2.98685 --13.3368 28.0875 -2.57327 --13.9647 28.0662 -1.80142 --14.2893 28.8454 -1.23268 --14.3923 28.5564 -0.3124949 --14.3484 27.6115 -0.2961499 --14.4705 27.0422 0.5481081 --14.3481 26.376 1.30187 --14.5002 25.4276 1.11822 --14.0699 24.7213 0.6465191 --14.3993 24.7542 -0.2956739 --15.0262 24.0047 -0.4039019 --14.8595 23.4295 0.4349161 --14.2523 23.8298 1.18446 --15.1098 24.2484 1.11124 --15.4309 23.9022 2.00157 --15.9966 23.4999 1.25703 --16.7886 22.9665 1.25572 --17.1677 22.1289 0.8845051 --16.4092 21.5685 1.17879 --16.2491 20.5752 1.31363 --15.8362 20.2401 2.11894 --15.9536 21.0893 2.58863 --16.8857 20.7321 2.38378 --17.6349 20.2364 2.84403 --17.7201 19.7541 3.84054 --17.9795 18.8167 3.54854 --17.4485 18.0926 3.9157 --16.6928 18.5542 4.44577 --16.3243 17.6367 4.78648 --15.5163 17.3144 4.68146 --14.7939 16.7051 4.41267 --15.1713 16.5617 3.5159 --14.3761 16.9463 3.04978 --13.3997 17.0154 2.84784 --13.1107 17.9976 2.9204 --12.2514 17.6833 2.53412 --12.124 16.765 2.34532 --12.4115 16.0783 1.60561 --12.6731 16.8234 0.9824071 --12.3746 16.0283 0.4567341 --11.4884 16.4839 0.4543361 --11.1686 17.4527 0.4818031 --10.9695 17.9587 -0.4017159 --10.0807 18.3351 -0.5785599 --9.59265 17.9943 0.2143811 --8.95347 18.6159 0.6346391 --8.7249 17.9349 1.20472 --9.04812 17.6102 2.1561 --9.96379 17.2137 2.01083 --10.1869 16.2446 2.3471 --9.1699 16.2802 2.6654 --8.31943 15.8844 2.37684 --7.78271 15.0215 2.57593 --8.50082 14.8202 1.90673 --8.78066 14.4989 0.9468371 --8.86754 15.5442 0.9048101 --8.30696 16.2558 0.3159841 --8.04601 16.9612 0.9563871 --7.69183 17.4963 1.70479 --7.13855 18.1835 1.2749 --7.4281 18.3633 0.3808761 --7.00259 17.4979 0.06798982 --6.7232 17.803 -0.8083129 --6.19165 17.5697 -1.62483 --6.28592 16.8958 -2.25856 --6.67185 17.6004 -2.87322 --7.4868 17.2876 -3.28144 --7.51301 17.9413 -4.08848 --8.0112 17.4127 -4.7376 --8.74263 17.1766 -4.0921 --9.36036 16.3988 -3.78561 --9.70093 15.4757 -3.51676 --9.49753 15.5486 -4.53466 --9.19841 14.714 -4.11965 --8.36881 15.1722 -3.77303 --7.38705 15.258 -3.69663 --6.94743 15.8081 -2.98187 --5.9228 15.7434 -2.95574 --6.12196 14.8308 -3.31287 --6.7352 14.6883 -2.53791 --6.15258 15.0674 -1.74672 --5.56504 14.2638 -1.58806 --4.90893 14.8907 -1.19285 --4.01576 14.5625 -1.40581 --4.13094 13.6902 -1.7212 --4.00395 13.5656 -2.67316 --3.63922 12.6484 -2.97125 --3.90605 13.1123 -3.84034 --4.33045 13.8595 -4.31179 --3.53014 14.133 -4.79562 --2.96688 14.1699 -3.95276 --2.34956 13.4127 -4.21847 --1.9445 13.2196 -5.13027 --1.73125 13.0277 -6.09755 --2.31753 12.1487 -6.18908 --3.04616 11.7121 -6.70155 --3.38088 12.4201 -7.25242 --3.63451 12.653 -8.19642 --4.06455 13.4223 -7.67528 --3.67569 13.8755 -6.90435 --4.63842 13.6236 -6.62689 --4.16669 14.1612 -5.89694 --4.97391 14.0091 -5.26327 --5.75549 13.4699 -5.1642 --5.76082 13.2638 -6.08387 --5.25742 12.38 -6.48447 --4.49101 11.9739 -6.03591 --3.65751 11.8585 -5.63941 --4.27313 12.0383 -4.87845 --4.82404 11.1501 -5.12182 --5.33104 11.8989 -4.71756 --6.01499 11.1007 -4.67094 --6.56198 11.4859 -3.97679 --6.19297 11.0599 -3.11253 --6.19286 11.6618 -2.31901 --7.08648 11.8787 -1.91788 --7.27496 10.9286 -2.14475 --7.57549 10.6198 -1.18939 --8.40308 10.5346 -1.69016 --7.67286 9.90782 -2.13826 --6.83968 9.48635 -2.63757 --5.96889 9.64263 -2.20968 --5.2546 9.72186 -1.46231 --5.54801 9.44483 -0.5157079 --4.9479 8.64131 -0.7690009 --5.08498 7.94854 -1.40208 --4.66366 8.66612 -1.92837 --4.59865 9.38835 -2.55612 --3.6967 9.10581 -2.99902 --4.06092 9.61925 -3.7225 --3.27418 10.3177 -3.52223 --3.59235 11.2144 -3.83125 --4.57677 11.1786 -3.94186 --5.33152 10.5437 -3.80092 --5.13124 10.2729 -2.80878 --4.61791 10.7122 -2.10895 --3.76775 11.2416 -2.13944 --2.74771 11.0717 -2.06481 --2.50457 11.7525 -2.82554 --2.01723 11.2731 -3.55926 --1.91899 10.4028 -3.3217 --1.76519 9.64807 -3.96587 --1.3535 10.3545 -4.45657 --0.390397 10.6946 -4.17235 --0.355152 11.1812 -4.97259 --0.287418 12.2081 -5.27012 -0.531012 11.8584 -4.85601 -1.33026 12.2606 -5.3401 -1.29225 13.1862 -5.80974 -2.00121 13.1626 -6.49269 -2.69158 13.8873 -6.3547 -1.7968 14.4144 -6.21558 -0.863647 14.7099 -6.27182 -0.259662 15.1109 -7.03757 -0.289103 15.9579 -6.51088 --0.415133 16.1376 -7.18242 --0.419349 17.1618 -7.14214 --1.10525 16.9006 -7.8289 --1.66516 16.1055 -7.74411 --2.0667 15.7719 -8.66119 --2.94657 15.8772 -8.28159 --3.21487 15.9315 -7.32682 --3.99887 16.2272 -6.86744 --4.52851 15.633 -6.25469 --4.44251 15.328 -7.19392 --4.22855 15.3672 -8.18677 --4.62213 15.1531 -9.07548 --3.88642 15.7396 -9.29181 --3.25961 16.4842 -9.47357 --3.5545 17.4455 -9.61166 --4.01084 17.8092 -8.80678 --4.46403 18.5802 -8.38168 --4.85587 17.6472 -8.38634 --5.28183 17.7818 -7.46286 --5.60067 17.4537 -6.49386 --4.8209 18.0863 -6.63749 --4.98311 18.4147 -5.69404 --5.28415 19.2468 -6.08955 --4.5794 19.1643 -6.78392 --4.42917 19.9329 -7.42815 --5.06808 20.2583 -8.18302 --4.69449 20.1681 -9.07598 --3.96771 20.4893 -8.56137 --3.65166 21.5439 -8.53391 --4.30005 21.4194 -9.29377 --3.44383 21.4643 -9.72771 --3.02155 20.5957 -9.51807 --2.84679 19.9663 -10.2751 --3.26211 19.0727 -10.2317 --3.05739 18.8914 -11.1916 --3.88404 18.4152 -11.2376 --4.90936 18.6182 -11.0904 --5.53993 19.0963 -10.4939 --6.5366 19.059 -10.6481 --6.80076 20.0625 -10.4798 --7.60172 19.8863 -9.79531 --8.43092 19.9642 -9.18499 --8.25176 20.8935 -8.87036 --7.76198 21.2613 -8.08439 --7.39067 22.0731 -8.51964 --7.26226 21.7124 -9.45001 --6.40944 21.6815 -8.96149 --6.52191 22.5251 -9.53758 --5.98349 23.3807 -9.50507 --6.2184 23.7251 -8.64267 --5.35877 23.5766 -8.09541 --5.35856 22.9059 -7.35165 --5.10302 22.3702 -6.56531 --5.92263 21.8157 -6.19349 --5.72603 22.2477 -5.33475 --5.26709 22.302 -4.4414 --4.2781 22.4073 -4.24303 --4.40142 21.4096 -4.10673 --3.87639 21.3731 -4.92357 --3.09583 20.8076 -5.05922 --2.32437 21.3868 -5.10054 --1.81244 21.4566 -6.0185 --0.852445 21.3461 -5.84917 -0.01403387 20.8616 -5.93731 -0.497137 21.2607 -6.70716 --0.277966 21.0185 -7.26883 -0.611793 21.1124 -7.91477 -0.948975 20.3431 -8.46567 -1.22346 20.6265 -9.37459 -1.29313 21.6333 -9.23882 -1.11346 22.6149 -9.30655 -1.95525 22.5548 -9.87906 -2.01301 22.2365 -10.8663 -2.20081 22.03 -11.8715 -2.90779 21.9597 -12.6723 -2.23999 21.3174 -12.9892 -2.42604 20.3577 -12.7357 -2.01968 19.6332 -12.3708 -1.65707 19.114 -11.5947 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13.4923 -11.7207 --4.19157 12.7017 -12.2927 --4.08828 11.7107 -12.6622 --3.3268 11.2279 -12.2299 --3.86211 10.3457 -12.0529 --3.27857 10.2264 -11.2526 --3.14626 9.99729 -10.277 --3.46659 9.14845 -10.8192 --4.4038 9.53905 -10.6231 --4.33956 9.50306 -9.58421 --5.28329 9.73236 -9.19061 --5.84372 10.3504 -8.61994 --5.34746 11.2356 -8.8756 --4.7227 11.5892 -9.62785 --3.76336 11.3415 -9.75719 --4.06817 12.1895 -10.1867 --3.20752 12.2387 -10.6294 --2.41706 12.3025 -11.2187 --2.34656 11.3253 -10.9052 --1.84434 10.8353 -10.0826 --1.11819 11.4849 -10.1743 --0.76599 12.422 -10.5402 --0.551324 13.4151 -10.4299 --1.25956 13.2745 -9.75641 --1.933 12.5318 -9.83292 --2.02667 12.0519 -8.94831 --2.43133 11.5517 -8.12499 --1.94149 11.6148 -7.23882 --1.21497 11.1301 -7.79861 --0.615793 11.7121 -8.34671 --0.08581463 10.8716 -8.45062 -0.567703 10.1438 -8.40204 -0.762083 9.7094 -9.26543 -0.46003 9.5404 -10.2618 --0.377936 9.27577 -10.6489 --0.496771 8.87046 -9.80765 --0.906243 8.16166 -9.26814 --1.78581 7.91451 -9.62325 --1.67609 8.07027 -10.544 --2.06931 7.17125 -10.8292 --2.99579 7.17955 -11.1908 --3.88988 7.46934 -11.5089 --4.61256 6.95759 -11.1734 --4.67273 6.04005 -11.345 --3.69902 6.11349 -11.0277 --3.32484 5.93219 -10.1475 --3.24871 5.50527 -9.18841 --3.3437 4.65139 -8.57026 --3.57046 5.00437 -7.63426 --4.17362 5.7842 -7.83702 --4.61494 4.83575 -7.92231 --4.71294 4.9682 -6.95481 --4.80155 5.2848 -5.96035 --5.59108 5.86767 -5.61954 --5.68297 6.74112 -5.28063 --4.70028 6.7435 -5.64149 --4.58893 7.35633 -6.46836 --4.5073 7.94525 -7.23491 --5.18837 8.6192 -6.96901 --5.48383 7.70912 -7.50708 --5.43538 6.69158 -7.41726 --6.06478 6.64859 -6.69581 --6.58671 7.44297 -6.61669 --7.02309 8.25184 -7.06953 --7.56143 9.06633 -6.80492 --7.44444 9.02759 -7.82064 --7.12863 8.7977 -8.73415 --6.27837 8.30008 -8.95541 --6.56364 7.69307 -8.21319 --6.88015 7.39894 -9.1607 --6.01058 7.0083 -9.44681 --5.12674 6.74993 -9.16801 --4.93409 7.05933 -10.0641 --4.33663 7.83822 -10.2151 --4.54725 7.53602 -9.29842 --4.12896 7.08277 -8.52776 --3.56849 6.6009 -7.74393 --2.63792 6.11892 -7.8781 --2.95627 5.90923 -6.93389 --3.37386 5.00946 -6.60434 --2.83803 4.27737 -6.10877 --2.32326 3.5119 -6.39674 --1.54856 3.52375 -6.96717 --1.43064 3.96997 -7.86722 --1.12725 3.09882 -8.26499 --0.252824 2.656 -8.31311 --0.663174 1.87559 -8.87059 --1.60028 1.55443 -9.01272 --2.396 1.35454 -9.64133 --3.36983 1.57123 -9.70477 --3.43018 1.13041 -8.76877 --3.68363 1.10105 -7.81803 --2.63607 0.9607329 -7.76946 --1.75374 1.16921 -7.32227 --1.49169 1.99444 -6.81276 --1.39008 2.22432 -5.86815 --2.01341 2.3387 -5.12064 --2.24158 3.32375 -5.15132 --1.49862 3.66353 -4.4822 --0.864174 4.20874 -4.88409 -0.170589 4.14368 -4.97997 -0.953858 3.70259 -5.37518 -1.10106 4.51766 -5.87344 -1.1186 4.43987 -6.86728 -0.138193 4.70997 -6.86253 --0.26306 3.8155 -7.21113 -0.07826977 3.96414 -8.1794 --0.310053 4.88113 -8.54882 -0.575658 5.12903 -8.10954 --0.05582573 5.65266 -7.59286 --0.807636 6.06042 -7.24303 --0.769283 6.36135 -8.18495 --1.70359 6.30886 -8.65551 --1.4149 7.19253 -8.25863 --1.83125 8.05613 -7.88887 --2.627 7.55898 -7.86139 --3.18049 8.13962 -7.19263 --3.82262 8.57185 -7.7934 --3.24336 9.30747 -8.07919 --2.32235 9.31646 -7.67268 --2.40194 10.1918 -7.21213 --2.22063 9.66392 -6.37196 --1.45458 9.82944 -5.79745 --0.519792 9.55642 -5.97219 --0.05265373 8.85499 -6.43673 -0.08805297 7.91542 -6.03734 --0.279133 7.13915 -6.54593 -0.522977 6.89158 -7.04247 --0.009465155 7.45581 -7.70637 -0.140243 8.42911 -7.80688 -0.421607 8.83755 -8.69437 -1.13504 8.32393 -9.23863 -1.62792 9.13673 -9.66148 -2.26688 9.01052 -10.3716 -2.22123 9.97457 -10.2987 -1.52217 10.0099 -11.0302 -1.72557 10.9619 -11.3765 -1.82378 11.9245 -11.6844 -2.43868 12.6925 -11.2117 -3.34129 12.9784 -11.5234 -4.23704 13.2159 -10.9528 -4.80981 13.9278 -11.3958 -3.99378 14.3923 -11.0661 -3.29938 15.0486 -11.0586 -2.99814 15.2719 -10.1287 -3.37493 14.3676 -10.2233 -2.41158 14.2161 -9.91831 -2.36832 13.1892 -9.97264 -3.08774 13.4266 -9.31097 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-6.08628 17.6762 -3.95245 -6.16534 16.9648 -3.31089 -5.36519 16.7929 -3.9663 -5.64957 15.947 -4.30342 -4.98074 15.5782 -4.96766 -3.96556 15.7417 -5.04029 -3.0203 15.7345 -5.34455 -2.24568 16.328 -5.33307 -1.33373 16.3362 -4.99447 -0.89807 15.9694 -4.20497 -0.871094 16.4777 -3.32951 -1.68744 17.0772 -3.43147 -0.891682 17.4931 -2.94578 -1.41952 18.1041 -2.24829 -1.85624 19.001 -2.35287 -2.19853 19.7552 -2.86864 -2.96189 20.4068 -2.53603 -3.89199 20.2634 -2.19075 -4.75771 20.1875 -2.47302 -4.27176 19.5536 -2.99405 -4.25385 20.4898 -3.38377 -4.15021 21.3938 -3.12109 -4.01892 22.3334 -3.35751 -3.24947 22.765 -2.89011 -2.52136 23.3772 -2.74757 -1.91848 23.8057 -2.15674 -1.65984 24.7739 -1.9307 -1.5365 25.0221 -0.9925239 -0.928666 25.5763 -1.55277 -0.451051 25.4977 -2.37548 -0.311332 26.11 -3.13363 -0.817934 25.5204 -3.75542 -0.09596857 24.8243 -3.76455 --0.80987 24.6976 -3.49872 --1.53429 25.4104 -3.13797 --1.66816 25.3927 -4.12101 --1.71159 24.8407 -4.93091 --2.60132 24.3786 -4.9334 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-1.00006 --3.73429 32.042 -0.6553929 --3.55747 31.6976 0.2217321 --3.07338 31.3927 1.01787 --2.65202 31.1353 1.92554 --3.29957 30.8531 2.61722 --4.11254 30.3284 2.30378 --4.11964 29.5557 2.9238 --4.94517 28.9952 3.19731 --5.24214 28.707 2.25672 --6.14416 28.6769 2.40584 --6.53914 29.3688 3.00292 --7.43784 29.3054 2.56336 --8.24169 28.6526 2.59794 --8.88821 29.1778 1.97046 --8.42479 30.0898 1.91363 --9.19729 30.3555 1.42448 --10.0964 30.4538 1.03751 --10.702 29.838 1.51218 --11.5917 29.5718 2.00446 --12.3678 28.976 2.08915 --13.128 29.5293 1.92096 --13.4164 29.415 0.9413711 --14.3768 29.7233 0.9179961 --15.0251 30.4365 0.7104011 --15.4782 31.2714 0.3161891 --15.0088 32.0131 0.6320801 --14.7495 31.9926 -0.3134299 --13.7501 31.9685 -0.5969969 --13.1513 31.3128 -0.9320179 --12.4397 30.6947 -0.4256129 --12.0249 30.6958 -1.40449 --11.8647 31.4803 -1.94959 --10.9002 31.478 -1.72169 --10.373 31.5295 -0.9139339 --9.7965 32.0939 -1.54774 --8.75692 31.9585 -1.19774 --7.77427 32.3404 -1.22765 --7.87702 33.1625 -1.84391 --7.16611 33.7385 -1.77668 --7.55527 34.6425 -1.7363 --6.76853 35.1712 -1.28314 --5.94382 35.3885 -0.8633469 --6.33886 35.5142 0.08145962 --7.02974 34.8142 -0.1394109 --7.60879 35.4437 0.3690931 --7.90159 36.3626 0.5828591 --8.00082 36.2182 1.60105 --8.9555 36.3684 1.83033 --8.65038 35.4533 2.12037 --8.65281 35.2336 1.09613 --9.05811 34.3651 1.27529 --9.38013 34.7124 0.4015691 --10.1681 34.6614 -0.03629528 --11.1581 34.6728 0.2770401 --10.5232 35.3808 0.4492561 --10.5128 35.8002 -0.4176029 --11.5195 36.0247 -0.3566409 --11.7164 35.6577 -1.28217 --12.2895 35.2112 -1.93386 --12.1598 34.969 -2.84266 --12.7899 35.2519 -3.57748 --13.6664 35.7889 -3.52062 --14.5986 35.6237 -3.62834 --14.549 36.4889 -4.08186 --13.5811 36.7464 -4.15018 --13.3111 36.4101 -5.08034 --13.8498 36.1271 -5.89633 --13.2452 36.8637 -6.23324 --12.3628 37.1122 -6.13566 --11.5113 36.5219 -6.33313 --10.7025 36.0134 -6.02406 --9.79561 36.0085 -6.27028 --9.26793 35.1676 -6.62764 --10.075 34.7026 -6.50401 --9.94211 33.8696 -5.93646 --9.39054 33.0792 -5.85284 --8.72588 32.4357 -5.61659 --9.24534 32.1388 -4.75888 --9.6295 31.4265 -5.3126 --10.483 31.2822 -5.8151 --9.93805 30.6359 -6.44165 --10.1612 29.9241 -5.80772 --9.59946 29.3771 -5.29024 --8.76407 29.6499 -5.66905 --9.07322 28.9045 -6.23688 --8.2435 28.3569 -6.68556 --7.34344 28.1158 -6.45939 --7.6192 27.7867 -5.5644 --6.72882 27.8812 -5.43861 --6.6068 26.9726 -5.2444 --5.77749 27.3196 -4.87182 --5.62143 26.6083 -5.51526 --4.91028 26.2641 -6.11898 --5.27422 26.5982 -7.00966 --5.12325 26.6151 -8.00203 --4.19758 26.7887 -7.66085 --3.34978 26.4552 -8.14885 --2.92657 27.1567 -7.55578 --2.93921 27.3615 -8.53039 --2.18222 26.8012 -8.79302 --1.36673 27.0627 -8.29153 --1.99763 27.6738 -7.87468 --1.30842 27.9974 -8.58431 --1.23887 28.9795 -8.25522 --0.403265 29.3763 -7.84262 --0.28253 29.0488 -6.91868 --0.642839 30.0442 -6.94809 --1.14596 30.5863 -6.40865 --0.586428 31.2946 -5.88146 --1.04519 31.9821 -5.40463 --0.221327 32.2531 -4.96117 -0.115777 32.9057 -5.64915 --0.779199 33.335 -5.6079 --0.718813 34.2161 -5.28741 --1.08568 35.1238 -5.38603 --0.944038 35.7175 -6.23396 --1.25636 34.7639 -6.41798 --2.01362 34.3918 -6.96988 --2.72462 33.8541 -7.40201 --3.2829 33.063 -7.47193 --4.01673 32.6415 -6.89943 --4.16528 32.92 -5.92928 --5.20726 33.0174 -5.85081 --5.57561 33.9062 -5.90624 --6.58718 33.7711 -5.81647 --6.1676 32.929 -5.9218 --6.1158 32.8305 -4.89903 --5.89646 32.0335 -5.51982 --5.15893 32.2793 -4.78035 --4.28304 31.887 -4.41032 --4.8279 32.0147 -3.58512 --5.12399 31.1103 -3.55506 --6.07002 30.8315 -3.73675 --5.61405 29.9114 -3.6375 --5.29811 29.027 -3.36657 --4.46187 28.5703 -3.56907 --3.53347 28.8199 -3.38953 --3.1563 28.0579 -2.8795 --3.03774 27.6528 -1.96877 --3.56876 26.8851 -1.62935 --3.84142 26.1854 -0.9115909 --3.23823 26.9089 -0.6148229 --2.29375 27.1068 -0.2153419 --2.28849 26.6519 0.7219641 --1.58742 27.4168 0.7723061 --2.07682 28.2219 0.7629331 --2.58421 28.6502 1.55457 --3.42861 28.965 2.01409 --3.88025 28.9584 1.13364 --4.25316 28.1812 0.6223221 --4.39479 27.1252 0.6810341 --3.46576 26.7763 0.4864701 --3.62229 26.5869 1.41911 --3.84727 25.8376 0.7606571 --3.33141 24.9088 0.6629501 --2.3871 24.7265 0.5470561 --1.8722 24.5808 -0.2684759 --2.33996 24.9482 -1.09996 --1.94896 25.2123 -1.94291 --1.34704 24.4567 -2.16147 --0.881582 24.1452 -1.32727 -0.05731957 24.5258 -1.37871 -0.01081447 24.5799 -0.3821189 -0.06028677 24.9415 0.5447481 -0.720344 24.3663 1.1336 -0.389512 24.1846 2.05443 --0.12885 23.7598 2.76759 --0.373567 24.5903 3.20918 --0.399037 24.3651 4.15771 --1.20352 24.9251 3.88259 --1.32044 25.9029 3.72326 --1.39141 25.942 4.75342 --2.38591 26.1606 4.58754 --3.11655 26.7577 4.75753 --3.68771 25.9718 4.57151 --4.28328 26.5728 4.05436 --4.95466 26.8151 3.45734 --5.41849 26.4222 2.69783 --6.40864 26.1944 2.77823 --6.98668 25.5684 3.33821 --6.57949 24.9885 4.06287 --5.6542 25.3081 3.84591 --6.05908 25.6954 4.69874 --5.98463 24.9077 5.4115 --6.0568 24.1348 6.04231 --6.95235 24.6339 6.1841 --6.73519 25.5102 6.513 --7.01314 26.2261 5.83519 --7.44436 26.3449 4.99031 --8.20531 26.1139 4.42455 --8.72787 25.6559 5.02419 --8.1653 24.843 5.0002 --8.41207 23.9066 4.97985 --8.67069 24.0019 3.99131 --7.70083 24.2352 3.81193 --7.94957 24.2787 2.83801 --7.72664 23.3035 2.89557 --6.84576 23.7231 2.64432 --5.94032 23.9818 2.31573 --5.78547 24.5767 3.05555 --5.98115 25.2986 2.38576 --6.92079 24.9546 2.38556 --7.57061 25.1444 1.64447 --6.95319 25.3672 0.8867401 --6.09321 25.6381 0.3708411 --5.3592 26.2191 0.5892371 --4.9325 25.4517 0.00815367 --5.42193 24.6363 0.1828431 --5.10492 23.6875 0.2053401 --5.32426 23.131 0.9929951 --4.83646 22.4216 1.5426 --4.02062 22.8576 1.84647 --3.74661 22.293 2.60514 --4.21102 21.7749 3.3157 --3.58229 21.0404 3.5106 --4.17664 20.2092 3.34811 --4.54572 20.4387 4.24323 --4.08404 21.2659 4.56684 --4.98129 21.7001 4.63108 --5.5415 21.7172 5.3966 --5.54169 22.6447 5.06409 --5.84643 23.5924 4.83574 --5.30939 23.4956 5.65634 --5.35936 23.4691 6.6542 --6.07607 23.7546 7.25969 --6.01784 24.5863 7.84923 --5.58553 25.344 8.39298 --5.98508 25.5364 9.21597 --6.84137 25.2178 8.83013 --6.69244 24.2341 8.80802 --5.88883 24.0697 9.41446 --5.84233 23.0663 9.49857 --5.50628 22.3773 8.96647 --4.88463 22.9386 8.37951 --4.68049 23.8953 8.0961 --4.44779 24.8714 8.01635 --4.60973 25.5314 7.29506 --5.10913 25.1421 6.47988 --4.46363 25.0403 5.71182 --3.85496 24.3095 5.4336 --3.5544 24.8744 6.29658 --2.98237 25.285 5.67092 --1.98425 25.1829 5.86711 --1.94154 25.4879 6.87341 --2.20494 25.7029 7.74889 --1.43238 25.1368 7.87075 --1.72595 24.5375 8.60984 --1.04091 23.951 8.15911 --0.374104 23.1673 8.44135 -0.200434 23.3861 9.22563 -0.625364 24.0235 8.62792 -1.565 23.7492 8.91318 -1.56927 24.1007 7.97938 -1.9009 24.066 7.07811 -2.47254 24.7348 7.59463 -2.8728 25.4289 6.93957 -3.72549 25.7873 7.23667 -3.49076 25.6963 8.19929 -3.11532 26.2848 8.95176 -3.48422 26.334 9.91602 -4.34196 26.3147 10.4414 -4.16966 25.3585 10.5833 -3.98052 24.4027 10.8783 -4.34375 23.4995 11.0523 -3.6548 23.3615 11.7932 -4.64356 23.2432 12.0813 -4.95101 23.3855 12.9588 -5.76779 23.6052 13.6099 -6.32103 24.303 13.1245 -7.19917 24.1669 13.5383 -8.07128 24.5421 13.0713 -8.6735 25.2829 13.1728 -8.41718 26.2274 13.037 -7.74779 26.9557 13.2952 -7.41915 27.5339 14.0005 -7.03155 27.5085 14.9136 -7.64374 26.8023 15.29 -7.02049 26.1281 15.6659 -7.7618 25.4399 15.6979 -7.09938 24.7524 16.0272 -6.88241 24.2998 15.246 -6.01043 24.2046 15.7749 -5.92909 23.9256 16.739 -4.98639 23.5744 16.5254 -4.32475 24.2407 16.1846 -4.32958 25.1432 16.6547 -5.18068 25.424 16.21 -5.30387 25.976 15.306 -5.74838 26.48 16.0816 -5.33377 27.4117 16.1127 -4.71565 27.5516 16.9351 -3.87749 27.568 16.3776 -3.46667 27.2388 15.4699 -2.62861 27.0347 15.9497 -2.12911 26.9227 15.0447 -2.19746 26.9446 14.0543 -1.76275 27.6755 13.4142 -0.858209 27.2628 13.3545 -0.798871 28.0823 12.8046 -0.165199 28.7795 12.4367 --0.601192 28.3972 12.8524 --1.36019 28.1195 12.3627 --2.1282 28.0332 11.7677 --2.39566 27.2658 11.045 --3.25478 27.3655 10.541 --4.09646 26.8483 11.0105 --3.84542 26.4754 10.1214 --3.17747 25.6991 9.88881 --2.79756 24.9397 10.4629 --2.80823 23.9541 10.4612 --2.41126 23.4329 11.2486 --2.72616 23.3711 12.2099 --3.57313 23.0941 12.6526 --4.57359 23.3179 12.7047 --4.4732 24.2715 12.9772 --5.35121 24.5551 13.4249 --5.36753 25.2542 14.2046 --4.64914 24.877 14.7575 --4.60197 23.8989 15.0149 --4.45984 23.3608 15.8749 --4.24253 22.3549 15.8295 --4.23686 21.7892 14.9984 --4.61953 21.1999 14.2812 --4.83951 20.4333 13.7433 --4.41586 21.2761 13.3969 --3.79156 20.4977 13.5373 --2.9538 20.8898 13.7505 --2.26467 21.4726 14.0725 --2.31232 22.5126 14.2164 --2.28534 23.3248 14.7459 --2.74748 23.4274 15.5834 --2.61819 24.3016 15.1136 --2.81689 24.9856 15.8709 --3.5793 25.5041 15.4177 --4.12039 25.6056 16.2359 --4.11598 25.4946 17.2301 --4.40204 25.6311 18.165 --5.17168 25.4593 17.6076 --5.49244 25.9859 16.7389 --5.01978 26.7189 17.1655 --4.94943 27.3594 16.4315 --4.46305 28.1638 16.8332 --4.56374 29.1023 16.9777 --3.80231 29.2941 17.6132 --3.1089 29.1271 16.8993 --2.54083 29.9196 16.9993 --1.59066 30.3134 17.0923 --1.1229 29.4637 17.2553 --1.14312 28.9605 18.2044 --1.30184 28.0762 17.768 --1.05529 28.1404 16.8585 --1.68432 28.2153 16.1193 --2.42842 28.3236 15.4337 --1.92905 29.1171 15.1302 --2.54604 28.7882 14.4 --2.0673 28.2568 13.6843 --2.60336 28.0729 12.8254 --3.12155 27.1834 12.7914 --2.35718 26.8774 12.2586 --2.43114 25.8504 12.3694 --1.63722 25.254 12.2677 --1.5684 24.5114 12.9763 --1.48359 23.6657 12.4284 --1.96742 23.1762 13.1371 --1.18358 22.794 13.6898 --0.507825 22.8599 14.4092 --0.05433643 23.5241 14.8403 -0.668893 22.958 15.1637 -1.50856 22.6407 15.5632 -1.028 21.8296 15.4829 -0.07321817 21.9168 15.2226 --0.65852 21.4606 14.9177 --1.61644 21.6846 15.0972 --1.8735 20.7882 15.4069 --1.46234 21.1457 16.3133 --2.32776 20.6292 16.3941 --2.75861 20.0501 15.7049 --3.16543 19.569 16.5029 --2.43822 19.6946 17.1356 --1.61724 19.1937 16.8644 --1.15335 18.9746 17.7189 --1.68777 18.6003 18.4684 --2.25573 17.9106 18.0308 --2.87305 17.1668 17.8954 --3.77453 17.5305 17.9836 --3.52465 18.4716 17.7732 --2.82061 18.5605 18.4642 --3.00986 19.4183 19.0047 --3.23499 20.3556 19.2438 --3.79123 20.7477 20.019 --3.80244 21.4727 20.7766 --2.94677 21.5422 21.2447 --2.64418 21.0888 22.0964 --3.57737 20.8015 22.0233 --4.01319 21.5928 22.3278 --3.43601 22.4478 22.217 --2.88411 22.9589 21.5848 --2.12563 23.2235 21.0188 --2.61697 24.0469 21.2506 --2.03738 24.8801 21.1534 --2.0287 25.2974 20.2898 --2.23007 24.7035 19.4541 --1.46051 24.8875 18.8351 --2.10912 24.0858 18.4674 --1.19084 23.8358 18.1737 --0.740076 23.3516 17.3989 --0.265618 22.9754 16.603 -0.605279 23.2541 16.6948 -1.11872 22.7831 17.3811 -1.91475 22.4608 16.8281 -2.86022 22.713 16.6807 -2.88863 23.6636 17.0036 -2.86322 24.1841 16.1518 -2.10197 24.0707 15.5295 -2.84132 24.1226 14.82 -3.52462 24.817 15.1271 -3.8884 24.8706 14.1975 -4.0354 25.799 14.7331 -4.08933 26.7577 14.6183 -4.68638 27.4735 14.1669 -4.95238 27.7266 13.2267 -5.77237 28.3535 13.2546 -5.95079 27.8683 12.4157 -5.70663 27.3071 11.6404 -6.31632 26.5029 11.3883 -5.93388 26.0987 10.5981 -6.52741 26.109 9.80137 -7.30859 25.9932 9.24034 -8.10113 25.4722 9.39725 -7.95904 24.9823 10.2077 -8.1429 24.0128 10.4877 -7.42868 24.4346 10.9488 -6.44971 24.3737 10.674 -6.89257 23.6778 10.1628 -6.27228 23.0026 9.79615 -6.02409 22.128 9.48066 -5.12978 22.4611 9.0305 -4.53577 21.6145 8.9449 -3.71109 21.0241 8.90119 -2.85057 21.2636 9.35446 -1.9413 20.7537 9.44108 -2.65522 20.3665 8.74518 -3.15351 19.5544 8.35806 -3.15054 20.2241 7.60034 -3.98942 19.7089 7.8961 -3.70201 18.891 7.40375 -3.6261 18.9236 6.43456 -4.16954 19.3119 5.66922 -4.1138 19.2312 4.64166 -4.97744 18.8078 4.50366 -5.23305 17.8891 4.36048 -4.52341 17.182 4.11835 -3.68574 17.7747 3.91331 -2.96962 17.1117 3.90105 -2.14822 16.9828 4.40229 -2.68032 16.1602 4.36198 -3.17917 15.2834 4.52826 -3.66863 15.1609 3.63661 -2.86535 15.2134 2.99398 -3.0322 14.5755 2.27037 -3.60448 15.0631 1.62054 -3.94464 15.7259 2.23522 -3.46124 16.5334 2.49204 -4.38066 16.9094 2.74684 -5.24202 17.4352 2.54948 -6.06459 18.0134 2.57911 -5.80759 18.3402 1.64035 -5.34395 18.3589 0.6857281 -4.70443 19.0692 1.06119 -3.84141 19.4112 0.5961561 -3.62905 20.3411 0.1899651 -2.79543 20.1032 0.7393601 -3.33326 20.7304 1.29807 -3.00398 20.3368 2.1975 -2.96129 19.9202 3.16747 -2.84788 18.972 2.88304 -3.87748 19.0423 2.68859 -4.39104 19.8519 2.29307 -4.3144 20.0069 3.32605 -5.0928 20.6129 3.44193 -5.72143 21.441 3.63143 -5.32545 22.1055 3.05773 -4.49515 21.694 2.74134 -3.86052 21.0872 3.11457 -3.98154 21.411 4.06191 -3.3495 22.0227 3.59418 -3.46253 23.0207 3.52452 -4.37022 23.3338 3.17152 -5.31206 23.4749 2.76176 -5.65437 24.3527 2.35673 -5.61541 25.211 1.8534 -4.88303 25.88 1.96793 -4.36757 26.3118 1.23545 -3.72583 25.9778 0.6072841 -3.69551 26.3701 -0.3369459 -3.66503 25.465 -0.7755199 -2.97724 25.9493 -1.39636 -2.8005 26.6879 -2.16618 -2.06061 27.0988 -1.66501 -1.39155 27.487 -1.03251 -1.15039 28.4291 -0.6387749 -0.8435 27.7264 -0.00639932 -0.124248 27.394 -0.6469309 -0.269962 27.5182 -1.58935 --0.499252 27.2253 -2.03533 --0.952158 28.0261 -1.94637 --1.44845 28.4741 -2.72132 --0.485889 28.8051 -2.57439 -0.497312 28.8501 -2.58795 -0.523447 28.7435 -1.54201 --0.250615 29.3583 -1.54753 --0.362953 30.3365 -1.44712 --1.09124 30.7275 -0.8671219 --1.17616 31.383 -0.1576239 --0.428744 32.0069 -0.4520039 -0.175879 32.7988 -0.2103159 -0.411969 32.9642 0.7638831 -1.24031 32.2633 0.8783661 -1.0915 32.3433 1.8541 -0.114211 32.594 2.12278 --0.557941 33.228 2.48707 --1.34849 33.807 2.51853 --2.30215 33.5235 2.20824 --3.17343 33.0944 2.12705 --3.20241 34.0361 2.39952 --2.82042 34.5035 3.27026 --3.52549 33.8527 3.51665 --4.19088 33.8782 2.85603 --4.21389 34.8432 2.50092 --4.19283 34.1982 1.74094 --4.9787 34.3679 1.2182 --5.81559 33.7637 1.03629 --6.2667 33.286 1.68496 --6.52858 32.4562 1.09322 --7.03132 32.3765 1.9672 --6.51764 31.8131 2.56158 --6.15298 32.2851 3.42521 --6.04543 33.2621 3.05697 --5.13561 32.9053 3.15449 --5.04502 31.9013 3.00551 --5.17065 31.1069 3.69411 --5.03831 31.595 4.62143 --4.60065 31.4296 5.47344 --5.07482 31.0482 6.33279 --5.27723 30.08 6.35773 --4.36464 29.857 6.07885 --3.6201 29.3621 5.54776 --4.18881 28.954 4.83172 --4.09797 28.0199 4.47954 --3.32376 28.3566 3.93839 --2.42124 28.0405 3.88556 --1.63586 27.5052 3.61714 --1.71052 27.8762 2.68082 --0.807552 28.2881 2.56586 -0.146168 27.7659 2.62488 -0.315976 27.7058 3.57063 -0.546676 28.6977 3.46387 -0.942399 29.4421 2.99156 -1.44555 29.3176 3.88401 -2.02803 28.7137 4.46746 -2.81691 28.1783 4.1128 -1.939 27.6026 3.9745 -2.0084 26.9151 4.7554 -2.85507 27.114 5.24292 -3.53069 26.7457 5.85298 -4.43976 26.4595 5.50072 -5.03002 26.9691 4.87841 -5.83226 27.5268 4.98194 -6.06497 26.6018 5.30864 -6.07821 25.5863 5.47849 -7.03218 25.8635 5.35358 -7.85524 25.478 4.96221 -7.93833 26.1519 4.31092 -8.05976 26.8523 3.55811 -7.16932 27.335 3.49088 -6.68866 26.548 3.79262 -6.03497 25.79 4.00531 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-3.8894 16.3063 9.49597 -3.18246 16.2392 8.85902 -2.78192 16.6922 9.61597 -2.59334 17.3952 10.2974 -3.59087 17.6622 10.2543 -4.61264 17.6259 10.3181 -5.20812 17.6742 9.59419 -5.43794 16.9196 8.94688 -4.72046 17.4591 8.60737 -4.00994 17.4685 7.84092 -3.2647 17.5378 8.49736 -2.74716 18.3854 8.5677 -1.99862 18.79 7.97817 -1.5164 19.1932 7.23904 -0.624325 19.6568 7.51545 --0.06048783 19.5806 8.35444 --0.52539 20.4709 8.33128 --1.36677 21.0827 8.49806 --1.2512 22.0951 8.42742 --1.41451 22.4664 7.50865 --2.05723 21.9586 6.9184 --1.8983 20.9876 6.90132 --0.996995 21.2622 6.87722 --0.733533 21.9082 6.17622 --1.61291 21.8025 5.88257 --1.89453 20.9557 5.45389 --1.13375 20.3186 5.64063 --0.946787 19.3182 5.84295 --1.7866 19.3859 5.2993 --2.54299 20.0131 5.3037 --2.9938 20.498 6.07214 --3.71919 20.2434 5.49413 --3.9281 19.3279 5.9686 --4.19202 18.3431 6.09192 --5.02676 18.4131 5.56337 --5.16027 18.877 6.41773 --5.2888 18.1382 7.08718 --4.73672 18.7081 7.62508 --3.74544 18.6487 7.63749 --3.5871 19.6834 7.55872 --2.55659 19.6981 7.57298 --2.23199 19.2637 6.74297 --2.02805 18.3281 6.53404 --2.26304 17.4023 6.32353 --1.7874 16.6838 5.75903 --1.42245 15.8191 6.07022 --1.15527 15.2126 6.76944 --1.67334 14.3673 6.44217 --2.59624 14.6765 6.48107 --2.25319 14.9696 5.53179 --1.24346 15.0899 5.50036 --1.24152 14.3561 4.77137 --1.01712 13.6194 5.43449 --0.165073 13.4877 5.90748 --0.344089 12.9885 6.72692 -0.170122 12.6919 7.5525 -0.856537 12.6687 8.30853 -1.19168 13.4238 7.78978 -0.843016 13.8562 6.9856 -0.497063 14.6782 6.43598 -0.987224 14.2537 5.66626 -0.97415 15.1545 5.15463 -0.754054 14.9442 4.20441 -1.25312 14.4422 3.42775 -1.98992 13.9128 3.35292 -2.64772 13.9833 4.19103 -3.15463 13.5335 4.93587 -3.23733 12.7239 5.4081 -2.40366 12.1578 5.62925 -1.72917 12.8371 5.36006 -1.34361 12.0461 5.84586 -0.439896 11.8431 5.51642 -0.653859 11.4607 4.63538 --0.365478 11.5811 4.60041 --0.582618 12.5703 4.82899 --1.50038 12.6282 5.22958 --1.77765 12.8064 6.23654 --2.46151 12.3094 5.73303 --3.26406 12.9173 5.54064 --4.19563 13.2809 5.92031 --3.7498 14.1176 5.70755 --3.38601 15.0786 5.81031 --3.46643 16.0532 5.55687 --3.55266 15.9249 4.60491 --3.42449 15.4783 3.76771 --4.35322 15.1399 4.13377 --3.72416 14.5024 3.68028 --3.94446 14.05 2.78798 --4.46877 13.2378 2.43268 --5.07211 13.9186 2.00011 --4.70697 14.4417 1.24035 --3.75031 14.2793 1.3437 --3.75385 14.6448 0.3652931 --3.68044 14.0747 -0.3757729 --2.7763 14.2921 -0.08460558 --2.08005 14.9841 0.2148171 --1.16099 15.1793 -0.02616548 --0.914376 15.1192 0.9394001 --0.842282 16.0243 0.4220811 -0.06495947 15.7628 0.1862331 -0.441015 16.4712 -0.4377529 -0.380865 17.0878 -1.21726 -1.23863 17.4652 -1.51679 -1.67899 16.6344 -1.28902 -2.66465 16.4733 -1.32675 -2.78594 17.4195 -1.29102 -2.77903 17.8583 -0.3950459 -3.23536 17.2737 0.2824581 -2.89888 17.7271 1.0711 -2.1202 17.7307 1.65862 -1.50747 17.5527 0.9664801 -1.14867 16.6395 1.13757 -1.34209 16.1387 1.93622 -0.384462 15.9773 1.56542 --0.641332 16.0509 1.586 --0.675315 15.6496 2.5297 --1.25586 16.4816 2.71904 --0.25321 16.5734 2.86834 -0.12381 17.4354 2.56546 -0.02889827 18.2421 3.13185 --0.08362913 18.6968 2.36022 -0.460568 19.4027 1.94047 --0.176184 20.1338 1.8605 --0.005404535 21.0883 1.68407 --0.923716 20.9229 1.25333 --1.18397 20.28 0.5181501 --0.50181 19.5299 0.6296351 --1.13942 19.0193 0.03415492 --1.99437 18.7508 0.5891121 --1.67405 17.973 1.12654 --2.02125 17.742 2.02912 --2.78851 18.271 2.4401 --3.04128 17.3312 2.51895 --3.47363 16.5652 2.03891 --3.32641 15.6433 1.59156 --2.31402 15.8681 1.63882 --1.98204 16.0918 0.7037461 --2.32094 16.9963 0.7324481 --2.56964 17.6899 0.05118072 --3.46455 17.2733 0.1348021 --3.92358 16.9164 0.9495841 --3.68374 17.7302 1.41665 --4.15213 18.5586 1.29552 --3.94066 18.6875 2.23518 --3.70992 18.3973 3.16562 --4.42848 17.7327 3.04279 --4.42269 16.8093 2.5853 --4.6135 17.5477 1.95493 --5.48583 17.3385 1.48943 --5.56177 17.8833 2.32269 --6.25062 17.2807 2.75285 --6.04636 16.3377 3.06366 --5.99379 15.3661 2.67272 --5.25129 14.9935 2.20611 --5.11506 14.7025 3.13457 --5.94825 14.742 3.70721 --6.76718 14.5218 4.17508 --7.64833 14.286 3.91217 --8.48066 13.6841 4.13956 --8.71028 12.7621 3.98458 --8.63706 11.8824 4.10091 --9.30519 11.9795 4.791 --9.60779 12.0998 5.71001 --9.9182 12.9455 5.97602 --10.4378 12.0748 6.27581 --11.3385 12.3258 6.58796 --11.9591 12.1253 7.34451 --11.1922 11.5639 7.31083 --10.7892 12.0831 8.01671 --10.8355 12.4553 9.00503 --10.7723 13.4059 9.3979 --9.99219 12.7641 9.51741 --9.7969 13.5445 9.03142 --9.21419 14.055 9.70512 --8.52356 14.1249 9.11537 --8.77146 14.3335 8.03152 --8.30906 13.442 8.13381 --7.65795 12.9101 7.5233 --7.77102 12.0284 7.06002 --8.54402 12.2986 6.58778 --8.00956 13.0284 6.1516 --8.32556 13.9354 5.98031 --9.26822 14.2408 5.7195 --10.2079 13.7981 5.6056 --11.1499 13.5043 5.94127 --11.4798 14.4963 6.07898 --11.2424 15.3901 5.61624 --12.1883 15.2412 5.31857 --12.9426 15.3517 5.96643 --13.257 14.9004 6.79878 --13.7201 15.7343 6.96362 --14.4846 16.1115 6.4297 --14.1576 17.0949 6.35454 --14.4024 18.0921 6.46292 --15.066 18.1074 7.21868 --14.7815 18.9005 7.73993 --14.3657 19.5818 7.08913 --14.3808 19.8247 6.07255 --13.4988 19.9126 6.4124 --12.8453 20.5526 6.94732 --12.8238 19.9155 7.66816 --12.7426 19.5732 8.57616 --12.3106 20.4421 8.54757 --11.7231 21.1386 8.19128 --11.1314 21.8719 8.50927 --11.0786 21.5382 9.40812 --11.1045 22.226 10.171 --11.224 23.1621 10.6017 --11.4934 23.8042 9.84163 --10.4935 23.8568 9.82033 --10.7217 23.1408 9.1468 --11.2725 23.8095 8.65374 --11.672 24.6458 8.92554 --12.0286 24.3617 8.05158 --11.3882 25.0955 7.76713 --11.5551 25.1529 6.75539 --11.2307 24.7723 5.85754 --10.998 25.4796 5.07811 --11.0224 24.9294 4.28228 --10.8878 24.7804 3.27606 --11.73 25.1761 3.60869 --11.8049 26.0698 3.97484 --12.4826 26.6494 3.57317 --12.6851 25.9648 2.8803 --12.2619 26.7898 2.38118 --11.2916 27.1111 2.37654 --10.3008 27.161 2.05817 --9.42947 27.0509 2.56853 --9.22768 26.2152 2.1585 --9.96686 25.8072 2.71565 --9.81155 26.4315 3.56138 --10.8184 26.6037 3.69458 --10.1974 27.3207 3.8354 --10.8469 27.9044 4.44608 --11.2456 28.4248 5.15947 --11.8924 28.6839 4.44442 --11.161 29.2096 3.88545 --10.5821 29.2773 4.70696 --10.0537 28.6776 5.33458 --10.1136 27.7222 5.62623 --9.16808 27.7237 5.37345 --8.32391 27.3597 4.94792 --8.50325 26.9036 5.84446 --8.39876 27.2097 6.82726 --9.08623 26.692 7.22173 --8.93361 25.7721 7.62513 --9.80909 25.5841 8.00477 --9.50356 25.4566 8.96193 --10.2822 24.7968 8.72291 --9.41941 24.5431 9.22336 --8.65687 25.1673 9.10779 --8.64887 26.0797 8.69144 --8.40991 26.9931 8.92713 --8.4163 27.9153 8.70296 --9.22486 27.5475 8.17626 --9.62621 27.2897 9.06818 --10.2576 28.03 9.10986 --9.41572 28.4272 8.71245 --10.0344 29.2053 8.72285 --10.3824 29.761 8.01683 --9.98536 30.5008 7.31604 --10.3977 30.4182 6.39354 --9.63828 30.9024 5.99087 --9.14583 31.6435 6.53671 --8.88123 30.6531 6.53538 --8.6163 30.6703 7.5364 --8.32974 30.1851 8.31819 --7.72426 29.9617 9.05667 --7.78054 29.5889 9.92911 --8.72622 29.5672 10.2577 --9.40472 28.8636 9.97381 --8.8878 28.0066 10.1673 --8.63503 27.0435 10.3864 --8.23552 26.8562 11.2144 --8.30371 25.9597 10.8453 --7.49626 25.4387 10.9248 --7.64323 25.9456 11.7435 --6.67118 25.8329 11.7934 --6.22392 25.4922 12.6391 --6.68724 25.2604 13.5174 --6.53063 24.2547 13.5146 --6.50803 24.1951 14.5109 --6.35159 23.1884 14.5512 --6.64698 22.3832 14.9289 --5.87524 22.0155 14.386 --6.46311 21.3609 13.8934 --5.8008 20.653 13.7103 --5.95663 20.8194 14.7108 --5.78892 20.0562 15.2081 --6.79034 20.1367 15.4707 --6.56838 19.4126 16.158 --6.33411 19.7905 17.1093 --5.69806 20.4256 17.5693 --6.38729 20.025 18.1749 --6.82747 20.8672 17.7611 --7.75607 20.5323 18.0544 --7.77128 21.4468 17.7469 --7.98902 21.4098 16.7648 --7.94715 21.6949 15.8156 --8.84359 21.9206 15.5293 --8.25721 22.4538 14.8739 --8.66028 21.5561 14.633 --7.73426 21.1808 14.4599 --7.7267 21.2213 13.4928 --7.91768 20.387 13.0664 --7.15212 19.9307 13.4764 --6.9748 20.0812 12.5389 --6.85838 19.0735 12.4001 --6.373 19.4113 11.5983 --5.53408 19.4063 11.096 --5.58046 18.3944 11.0819 --6.57878 18.2776 11.0732 --6.7716 19.1791 10.6589 --6.9496 18.8242 9.71626 --7.85146 18.7582 9.30556 --8.06712 17.9619 9.82626 --9.09339 18.0908 9.58696 --9.05845 18.5796 8.72757 --9.6113 19.286 9.18257 --9.10444 20.1718 9.28276 --8.43095 20.6762 9.80312 --8.15731 21.4969 9.38439 --7.38779 21.7312 8.8319 --7.06982 20.9082 8.39547 --7.07745 20.6091 7.42619 --6.75878 20.2437 6.46491 --7.16854 19.5161 7.03336 --7.28399 19.2871 6.06526 --8.16095 19.6872 6.26839 --8.55798 18.9445 5.70717 --7.79387 18.6912 5.21884 --8.15762 17.9344 5.56196 --8.32685 17.8129 6.57243 --8.09152 17.7756 7.59261 --7.13533 17.4485 7.56962 --7.19984 16.5419 7.06124 --6.37244 16.7261 7.59603 --5.53516 16.7906 7.10694 --6.0836 16.8038 6.33158 --5.36871 16.253 5.86744 --4.64863 15.7612 5.40358 --4.40184 16.0482 6.3464 --3.38989 15.9972 6.59618 --2.45828 15.6984 6.87665 --2.70979 15.0941 7.63502 --2.65614 14.4068 8.30152 --3.29823 13.8992 7.73664 --4.13357 13.314 7.63234 --3.93549 13.254 8.62703 --4.27471 13.7032 9.47636 --4.36827 14.2682 8.62852 --4.286 15.2722 8.68175 --5.16707 15.0771 8.20588 --5.71445 14.243 7.98784 --6.54056 14.6811 8.31724 --7.09888 14.4876 7.51583 --7.15116 14.4101 6.51772 --6.19464 14.1804 6.25818 --6.6048 14.7068 5.57449 --6.61881 15.7001 5.72489 --6.85365 16.0628 4.80607 --7.35745 16.4124 5.56792 --8.29022 16.015 5.61004 --8.95671 15.8277 6.27251 --9.85121 16.2713 5.94911 --9.28472 17.1194 5.97091 --9.91582 17.2196 5.2101 --10.7076 17.4083 5.87625 --11.3668 18.1029 5.93351 --11.3316 17.7913 6.86248 --11.9532 17.0945 6.55653 --12.0157 16.1564 6.19636 --11.1582 16.0164 6.71534 --10.636 16.5423 7.39594 --10.0846 16.3599 8.21242 --10.1966 15.6697 8.85723 --10.6821 16.5589 9.09104 --10.2897 17.4765 8.91214 --10.3983 18.4758 8.82049 --11.0062 18.1958 9.56373 --11.3912 18.9653 10.012 --11.9633 19.3029 10.6606 --12.6825 19.9727 10.2453 --13.001 19.2707 10.8808 --13.2225 18.4832 11.4649 --13.7364 17.9652 10.7489 --13.491 18.1487 9.8152 --13.6688 18.3196 8.90111 --14.0924 19.2215 9.15673 --14.8303 18.6162 9.01769 --15.546 18.5869 9.68826 --15.189 19.5417 9.94389 --15.3261 20.3852 9.54826 --16.0816 20.8648 10.0648 --16.0719 20.7038 11.0051 --15.392 21.2836 11.4137 --15.0814 21.6424 12.2386 --14.2255 22.0773 12.0597 --14.3175 21.5717 11.2119 --14.35 22.5412 10.9471 --15.1716 22.8083 10.4862 --14.6032 23.4951 10.9884 --15.0184 23.7336 11.8908 --15.6177 24.4219 11.4799 --14.9831 25.1431 11.806 --14.6591 25.9902 12.29 --14.0069 26.0659 11.5154 --13.7821 25.7609 10.5684 --14.0382 26.1255 9.65701 --14.6192 25.7191 9.07794 --14.1662 26.5375 8.57947 --13.4996 26.5519 7.78394 --13.0565 27.2796 7.28131 --12.3376 27.8084 7.70364 --12.5647 27.8163 8.73361 --12.3268 28.7715 8.73811 --11.6648 28.0278 8.98065 --12.1483 28.281 9.87824 --12.5058 29.0296 10.4544 --12.2797 29.8363 9.84363 --11.3144 29.8429 9.83197 --11.1412 30.8539 9.70813 --10.7327 31.2912 10.501 --9.95005 30.9185 10.9683 --9.51922 31.812 11.215 --8.61395 31.7393 11.5796 --7.62069 32.0891 11.4878 --6.98543 32.8509 11.6546 --6.65956 33.0836 10.7357 --5.76803 32.9386 11.1103 --5.03468 32.5617 10.5058 --4.18745 33.1165 10.898 --3.44285 33.7988 10.6909 --3.24273 33.6595 9.70195 --2.30534 33.5947 9.52734 --2.41434 32.8554 8.77001 --2.52222 33.5038 8.00066 --2.94476 33.217 7.12054 --3.27383 33.2976 6.1558 --3.81845 33.8591 6.73014 --3.46499 34.464 5.985 --4.19114 33.8307 5.53504 --4.40603 34.6095 6.07078 --5.27736 35.0532 6.11532 --5.26815 36.0484 6.0582 --4.70028 35.713 6.85318 --4.9557 35.9791 7.79962 --4.55111 35.1734 8.14245 --4.47178 34.4408 8.73101 --4.82932 33.5637 8.8421 --5.57064 33.2414 8.33791 --5.35456 32.2679 8.23034 --5.09874 31.3946 8.68109 --4.39697 30.7347 9.09035 --4.03461 29.8492 9.21395 --4.62377 30.043 9.99314 --5.02053 29.2529 10.446 --5.28538 28.4704 9.85525 --4.76731 29.2107 9.33744 --4.55711 29.5407 8.32919 --4.92283 28.6502 8.25345 --4.38789 27.7592 8.24648 --3.92974 28.2239 8.98901 --3.074 27.7321 8.62432 --2.1566 28.3162 8.49676 --2.64666 29.1577 8.89111 --2.84533 30.0454 8.53329 --2.20925 30.7923 8.63508 --2.21372 31.0146 9.62304 --2.55124 30.0652 9.43756 --2.70216 29.3833 10.1943 --3.12436 28.6663 10.7847 --4.067 28.8361 10.7292 --4.73832 28.6901 11.388 --4.14375 29.3822 11.8856 --4.43699 29.6376 12.8162 --5.17753 29.1313 12.3363 --5.88799 28.8099 12.81 --6.58178 28.043 12.5943 --6.31946 27.6086 13.401 --7.02774 26.9316 13.6603 --6.77608 27.0635 14.6372 --7.75785 27.2986 14.5927 --8.57901 27.8709 14.4942 --8.75431 27.1342 13.8436 --8.90921 27.4392 12.8929 --8.45285 28.2449 13.2187 --8.97362 29.0072 12.9034 --9.44538 29.1884 11.971 --10.1764 28.5595 11.8837 --10.7553 29.4404 11.9314 --10.9765 29.6709 12.84 --11.9793 29.4459 13.1197 --11.708 28.6105 13.4334 --12.4655 27.9558 13.4221 --12.6194 27.0188 13.5918 --12.5193 26.5194 14.4168 --12.7919 25.659 13.9317 --12.0326 25.7529 13.1727 --11.8423 24.8606 12.8716 --11.6441 23.9478 12.5819 --10.7338 24.3655 12.5403 --10.8929 24.3589 13.4936 --10.8971 24.919 14.3146 --10.0419 24.6402 14.7477 --10.4208 23.869 15.1769 --10.1459 23.2333 15.9657 --10.1997 22.281 15.869 --10.9178 21.7459 15.419 --10.4627 20.9052 15.2484 --9.45757 20.6309 15.045 --10.2096 20.7305 14.4045 --9.67737 19.9426 14.0449 --9.44708 20.0456 13.0371 --10.1636 20.3439 12.3764 --9.93726 21.2046 11.9582 --10.878 21.294 12.2193 --11.0462 20.4784 11.6643 --11.4437 20.3958 10.7256 --10.6169 19.9642 10.3173 --10.1121 20.7638 10.7503 --9.43844 20.1096 11.04 --8.42068 19.9867 11.2016 --8.13712 21.0161 11.011 --8.64852 21.8369 11.3814 --7.80182 22.2698 11.1089 --7.31843 22.9664 11.5622 --7.02471 23.8627 11.2141 --6.93736 23.6424 10.2278 --7.16013 23.413 9.31045 --6.88097 22.9832 8.49811 --7.31563 22.9877 7.5938 --7.49454 23.9111 7.78464 --8.24513 24.4824 7.5042 --8.64645 23.6841 8.02038 --9.45013 23.46 7.49977 --10.1766 22.7506 7.52309 --10.0913 21.7704 7.92333 --9.44326 21.0654 8.15634 --9.00747 20.5215 7.4962 --9.9194 20.3362 6.96614 --9.46075 20.8893 6.29151 --8.59556 20.6725 5.76904 --7.62193 20.9777 6.01872 --7.54378 21.6425 6.71835 --7.8336 22.3778 5.99442 --8.7014 22.0745 5.51478 --9.10231 22.8232 6.14775 --9.59108 23.7135 6.13938 --10.2764 22.9355 6.10374 --9.81053 22.7523 5.29022 --10.2986 22.1687 4.5773 --9.61676 22.6684 4.04598 --8.79499 22.8737 3.48155 --8.47979 21.9083 3.5764 --7.53564 21.9349 3.84552 --7.92729 21.6249 4.65492 --8.8892 21.3891 4.48529 --9.15564 20.4375 4.74056 --9.25875 19.9003 3.86467 --8.89102 20.0785 2.95756 --8.54433 20.2421 2.02005 --8.91626 19.354 1.83075 --9.83942 19.2573 2.38232 --10.6488 18.8306 1.94635 --11.324 18.8496 1.17435 --11.8358 19.2555 1.87561 --12.6039 19.1611 1.34553 --13.5834 18.8576 1.55826 --14.2076 18.4108 2.28143 --13.9109 19.2972 2.75964 --14.7489 19.3971 3.11732 --14.9109 19.8329 4.03503 --14.7385 20.196 5.06777 --15.4177 20.8694 5.08697 --14.8295 21.5392 4.62584 --14.5365 22.1167 3.89493 --14.7519 22.6375 4.82695 --15.0782 23.5123 4.38845 --14.4927 23.6345 3.49799 --14.4519 22.7284 3.10642 --13.5399 23.0164 3.06224 --12.7164 23.5819 2.77078 --12.4721 22.9288 3.51393 --13.2704 22.6873 4.05963 --13.2012 22.4541 5.0679 --12.5861 21.7299 5.41543 --12.3906 21.3418 4.56663 --12.1357 20.356 4.59511 --11.2186 20.7629 4.20567 --10.5819 21.3839 3.69541 --9.91111 21.3597 2.97195 --9.89914 20.3967 2.96763 --10.5884 20.3676 2.19941 --11.2271 20.5709 1.40792 --11.1249 21.4148 0.9303571 --10.9337 21.6488 0.0077598 --10.4352 21.933 -0.7746409 --10.2809 22.7056 -0.1415739 --10.1535 23.7122 -0.04546008 --9.6787 24.3731 -0.6079469 --10.2933 24.2237 -1.37613 --10.1628 23.2727 -1.43883 --9.588 22.4226 -1.41399 --8.82102 22.019 -1.84663 --7.87165 22.244 -1.65591 --8.20335 21.5092 -1.02498 --8.71766 22.0299 -0.2738599 --7.91513 22.2563 0.3206021 --8.01555 23.2288 0.2909331 --7.06753 22.9125 0.3337921 --6.75596 22.4776 1.15229 --6.09146 21.6744 1.39407 --6.35746 21.1275 2.1671 --6.23289 20.491 1.45777 --6.72771 19.7569 1.06988 --6.40541 20.4255 0.4028791 --5.87898 19.5314 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--0.711168 0.8334549 8.38534 --1.57076 0.5482409 8.72195 --1.16663 1.23719 9.34863 --1.99713 1.57378 8.8652 --2.5053 1.35477 8.01614 --2.93512 1.74288 7.19111 --3.37891 2.3733 6.57435 --3.67903 1.4562 6.20588 --3.66256 0.8233679 7.04884 --3.72016 1.17107 7.98768 --3.7146 1.85782 8.77204 --3.7232 2.35397 9.64058 --4.0995 3.2967 9.51425 --4.70535 3.60286 8.85224 --5.1693 2.99983 9.49489 --6.08956 3.05233 8.99466 --6.36721 3.97462 8.99291 --7.07708 4.19029 8.38901 --7.58076 4.4913 9.20248 --8.26433 4.16024 9.89639 --7.67349 4.55512 10.647 --8.05597 3.62925 10.7198 --7.9435 2.66495 11.1024 --7.58396 2.10884 10.3881 --7.79608 2.5195 9.52343 --7.82724 1.80054 8.87151 --8.66111 1.63352 8.38357 --9.07222 0.6767219 8.13744 --9.04338 -0.07914377 8.74978 --8.35766 -0.8584791 8.69146 --8.94506 -1.06356 7.89374 --8.25392 -0.4423921 7.50055 --8.06382 0.4155509 7.96232 --7.10606 0.2042439 7.84407 --6.31425 0.7975399 7.76879 --6.05446 1.74309 7.63503 --5.88319 1.3502 6.77837 --6.73816 1.09281 6.31818 --6.94238 0.6198309 5.42342 --7.76214 0.6800769 6.04483 --8.47298 0.8085199 5.22459 --9.01502 0.5352019 4.47289 --9.54604 0.2382199 5.29358 --8.80023 0.2170779 5.92721 --9.58948 0.4590359 6.37502 --10.5543 0.6497139 6.48332 --11.07 0.04291493 7.1491 --11.3052 -0.8343971 6.71035 --11.3939 -1.77962 6.97069 --11.9776 -2.4537 6.57936 --12.6991 -2.16566 7.24874 --13.1025 -2.59641 8.06675 --13.416 -1.74848 8.59796 --14.3265 -2.33733 8.5582 --14.9986 -1.57715 8.33084 --14.6866 -1.9283 7.43078 --15.6436 -2.31022 7.38312 --15.7321 -3.23239 7.6272 --14.9336 -3.24806 7.04557 --14.7495 -3.49552 7.99958 --15.1343 -3.90888 8.87761 --15.0341 -4.52608 9.69246 --14.1579 -4.5706 9.19657 --13.4306 -3.86419 8.91343 --12.6615 -3.45573 9.32579 --12.7748 -2.48016 8.95163 --11.8583 -2.23176 9.22924 --11.2258 -2.41529 9.93093 --12.1409 -2.283 10.2977 --12.7554 -1.4789 10.0736 --12.5042 -1.79145 11.0162 --13.1771 -2.50625 11.3292 --13.2945 -1.49843 11.5007 --13.8119 -1.28833 10.6254 --14.3558 -0.8961241 11.3476 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21.7154 -2.81372 -2.31656 21.1796 -3.46503 -1.73192 21.683 -2.66096 -1.15928 21.4143 -2.6485 -0.7028631 20.5356 -2.12429 -0.2663201 19.777 -3.06664 0.05919313 19.9468 -3.85488 0.3177169 19.4501 -4.33606 1.20229 19.4487 -5.0291 1.74488 18.9759 -5.48394 1.62962 18.0449 -5.9931 2.11609 17.3565 -6.37403 1.77953 16.4263 -5.51985 1.17202 16.6704 -5.00785 0.3111489 16.5561 -4.16592 -0.2699511 16.7416 -3.92832 -1.23754 16.4783 -3.06472 -0.8148631 16.3995 -2.66105 -0.9033481 17.3546 -1.76597 -0.6670981 16.9414 -1.17155 0.04145303 16.5867 -1.27731 -0.04189287 15.5874 -1.38275 -0.01368457 14.5944 -1.80543 0.8325329 14.603 -2.27593 0.5375979 13.8068 -3.17183 0.3607529 13.2837 -2.69916 0.1099769 12.4164 -3.4684 -0.4760131 12.4491 -3.30701 -0.8636271 11.5095 -2.59701 -1.54083 11.8007 -1.55811 -1.55701 11.823 -1.08775 -1.89783 11.0172 -0.201415 -2.42139 11.0824 --0.31046 -3.20176 10.8383 --1.08673 -3.6115 11.2771 --1.96286 -3.175 11.3155 --2.36532 -2.56449 10.7426 --1.78186 -2.15825 11.3982 --2.55721 -1.55925 11.6222 --3.48048 -1.80568 11.6969 --4.26734 -1.502 11.1485 --4.38318 -1.88096 12.0259 --5.31622 -1.6945 12.3863 --5.81347 -1.31165 11.6474 --6.57582 -1.62228 12.241 --6.67339 -2.54324 11.8885 --7.14547 -3.19361 12.4623 --6.2835 -3.0541 12.9902 --7.01693 -3.74057 13.2794 --6.51933 -4.46214 13.6805 --5.59484 -4.42649 14.1102 --4.98107 -5.11707 14.3852 --4.99679 -5.80987 15.0447 --4.75859 -5.8398 16.0042 --4.41752 -5.08356 15.4812 --5.34609 -4.59699 15.4305 --6.25967 -4.48022 15.0236 --6.86339 -5.17119 15.5447 --7.61267 -4.6245 15.2369 --7.76317 -4.97882 14.3007 --8.17076 -4.11313 14.5715 --9.06604 -3.9654 15.1836 --9.9874 -4.31267 15.1241 --10.7519 -4.74422 14.6497 --10.2125 -5.58494 14.5989 --11.0049 -6.24681 14.6806 --11.9153 -6.1098 14.5788 --11.6426 -5.56417 13.7195 --11.9427 -5.01632 14.5179 --12.3533 -4.34539 13.8568 --11.4068 -3.99973 13.6988 --11.1456 -4.79498 13.2304 --10.4258 -4.48666 12.7825 --9.75879 -5.30265 12.9364 --9.26915 -6.15436 12.9441 --8.25579 -6.37472 12.8387 --7.93373 -5.52437 13.2511 --7.6288 -4.78464 12.5702 --7.95103 -3.83464 12.553 --8.6281 -3.30244 11.9897 --9.11928 -2.63023 12.503 --9.55589 -1.91505 11.8893 --9.88033 -2.28109 10.9434 --10.2263 -1.29291 11.0682 --10.3243 -0.3518891 10.6634 --9.46919 -0.7696521 10.7087 --8.77558 -1.07513 10.0204 --7.98919 -0.9010871 10.5287 --7.56678 -0.4289851 11.3262 --7.98073 -0.6038271 12.1817 --7.10857 -0.3790811 12.7083 --6.22826 -0.2657351 13.2311 --5.45704 -0.8869851 13.4521 --4.47777 -1.00322 13.1363 --3.68001 -0.9675711 12.5266 --3.75388 0.05887803 12.7101 --3.49299 -0.3281581 11.8339 --4.07029 -0.08476177 11.0325 --4.2986 0.8120999 10.6537 --3.46415 1.1876 11.1414 --3.08395 1.87231 11.7315 --2.13524 2.09825 11.8641 --2.38496 2.39053 10.9266 --1.49337 2.1048 10.5673 --0.521907 1.77636 10.6294 --0.435242 2.76544 10.984 --0.687999 3.58377 10.5102 --1.16898 3.73031 9.59166 --2.02277 3.14273 9.80519 --2.45887 4.10897 9.98994 --2.7961 3.77995 10.9186 --3.67594 3.44272 10.8472 --4.48219 3.4942 11.4632 --4.89968 3.08074 12.3513 --4.49068 3.37885 13.2037 --4.05352 4.25809 13.1394 --3.94307 4.81927 12.2588 --3.38518 3.99847 12.2677 --2.5382 4.46164 12.7445 --2.46159 4.16418 13.6911 --2.5648 4.80279 14.4812 --3.52272 5.00023 14.5712 --2.81483 5.35908 15.2352 --3.31535 4.79501 15.9251 --2.6123 5.24337 16.4454 --3.19615 5.70898 17.0755 --3.86599 6.38646 17.3141 --3.79796 6.18136 16.3679 --4.39236 6.84587 15.8972 --5.17015 7.29948 16.2787 --5.84197 7.54013 15.608 --6.01217 6.57423 15.5502 --5.51044 6.06141 14.8673 --4.58584 6.25247 14.6593 --4.66033 6.03996 13.6564 --3.89407 6.41103 13.034 --3.71748 6.22819 12.0787 --4.16699 6.91125 11.4762 --3.94628 7.89989 11.693 --3.28022 7.29523 12.0774 --2.72851 7.85606 11.43 --2.13459 8.50736 11.1061 --1.23353 8.36916 10.8326 --0.527177 7.71125 10.5514 --0.349383 7.03771 11.314 --0.314746 8.01542 11.5593 -0.591904 8.4892 11.5448 -1.4389 8.57948 12.0841 -1.33297 9.46995 12.5998 -0.851472 9.78219 13.4219 --0.177644 9.87428 13.7594 --0.427083 9.74756 12.7678 --1.3353 9.35121 12.9537 --1.70024 10.2721 12.9008 --2.0931 10.032 11.9578 --1.92929 10.1051 11.0302 --1.0527 10.528 11.2508 --0.334725 10.4059 10.5211 --1.09095 10.0234 10.0642 --1.60538 9.21796 9.96238 --2.62858 9.21152 9.82606 --3.43167 9.23115 10.4479 --3.22991 10.2541 9.99223 --3.55133 9.85172 9.11907 --3.54485 10.8632 8.95226 --3.89975 11.2833 8.09805 --4.76235 11.4185 7.70406 --4.62139 12.2467 7.08888 --4.67567 11.5898 6.34321 --5.3691 10.8657 6.38637 --4.44004 10.4611 6.55982 --3.45934 10.2287 6.61719 --4.04349 9.42249 6.44824 --4.55902 8.63555 6.92527 --4.01416 8.36923 7.70348 --3.05104 7.99184 7.63369 --2.13766 8.30584 7.60096 --1.81268 9.14375 7.17488 --1.66329 10.1056 6.95987 --1.76072 9.74184 6.03042 --1.44697 10.6545 5.80372 --1.02043 11.6261 5.86735 --0.347541 11.2177 6.4096 -0.258269 12.0513 6.59011 --0.10767 11.7881 7.49317 -0.893676 11.7674 7.55022 -1.09597 10.841 7.58973 -0.34784 10.6952 8.26225 --0.474442 10.0596 8.18613 --0.446257 10.8234 8.85446 -0.154289 10.0281 9.08933 -0.257695 9.22195 8.57897 -1.25171 8.9118 8.4777 -0.736533 8.53479 7.74322 --0.149708 7.99524 7.80566 -0.522899 7.33793 8.12932 --0.326996 6.97648 8.4417 -0.08116177 6.28844 9.07703 --0.747868 6.66108 9.4683 --0.839754 7.63454 9.22486 --1.432 7.43562 8.43939 --1.6246 6.57431 7.98528 --0.953214 6.94702 7.25577 --1.72726 6.72931 6.63524 --1.3209 7.16476 5.89604 --1.99405 6.87298 5.12553 --2.44381 7.57684 4.63766 --2.82326 8.04941 5.44157 --3.30461 7.44274 6.03957 --3.69629 7.23254 6.90383 --3.6088 6.39884 6.41614 --3.94607 6.23195 5.51548 --4.90221 6.48635 5.6415 --5.45531 5.95674 5.03023 --6.4002 6.10951 5.19897 --6.04406 6.91052 4.68128 --5.32295 6.76913 3.88619 --6.28906 7.06921 3.68998 --6.82914 6.31462 3.39299 --6.61596 5.37988 3.03909 --7.3079 5.00114 3.6307 --6.91151 4.66733 4.39263 --6.87273 4.92055 5.40103 --6.56384 4.03523 5.58065 --6.14801 3.77822 6.391 --5.98561 4.34983 7.15874 --5.6288 4.59255 8.10602 --4.8601 5.21066 7.89073 --4.40017 6.03088 7.67945 --4.23645 6.55095 8.54546 --3.32219 6.20531 8.3474 --2.68214 6.07936 9.12878 --1.97887 5.50561 8.65302 --1.87406 4.75613 9.31545 --1.14324 5.00448 9.9003 --0.869637 5.42802 10.693 --0.54364 4.58634 10.9918 --1.53977 4.4375 11.1283 --2.28043 4.73818 11.8244 --1.89965 5.63832 12.1339 --2.26837 6.41493 11.6423 --1.70387 6.92853 12.2248 --1.7907 6.53942 13.1453 --0.994715 6.15224 13.6917 --1.38114 5.87656 14.5962 --2.32418 6.08959 14.4726 --2.69008 6.98905 14.5035 --2.90216 7.89765 14.274 --2.82982 8.22728 13.3217 --3.81647 8.3475 13.2422 --4.20021 8.94536 14.0087 --4.38557 7.98575 14.2251 --4.55239 8.29604 15.1019 --5.39764 8.56019 14.6008 --6.27325 8.94769 14.9773 --6.80551 8.7503 15.8325 --7.79511 8.5195 15.943 --7.68748 8.87793 14.9678 --8.52514 9.41219 14.9546 --9.17728 10.1236 15.1858 --9.20804 11.125 15.0151 --9.84193 10.5516 14.4456 --10.2261 10.5041 13.596 --10.3534 9.55721 13.8659 --9.9089 8.75648 14.3288 --9.59659 8.13428 13.6277 --9.43179 7.7906 12.6733 --10.3678 7.58929 12.6974 --9.67188 6.79784 12.9465 --8.92323 6.65916 13.6417 --8.94491 5.74159 13.799 --9.81286 5.87387 14.1247 --10.7117 5.91548 14.5639 --11.0074 5.5899 15.412 --11.2619 4.91773 16.118 --11.2675 5.74598 16.7119 --12.2139 6.14628 16.5112 --13.081 5.63259 16.3911 --13.3993 5.0809 17.0905 --12.541 4.60097 16.955 --12.0568 3.94054 16.4125 --11.4901 3.49721 15.6613 --10.6168 3.13161 15.7515 --10.0492 3.79341 15.1847 --9.21478 4.00485 15.7191 --9.06616 3.04213 15.8331 --9.55061 2.22841 15.5237 --9.96275 1.34043 15.206 --9.81048 0.6915399 14.5041 --9.13119 0.06653543 14.8625 --8.66643 0.07178103 15.7017 --9.07906 0.8022029 16.2011 --8.47326 0.9682909 15.3753 --7.74446 1.61575 14.9932 --7.14814 0.7939719 15.1816 --7.13582 0.1740409 15.9863 --7.22022 0.5054089 16.8598 --6.64208 0.8622849 17.6311 --7.05831 1.46514 18.344 --6.30095 0.9823999 18.7832 --6.45359 0.1881929 19.3683 --6.27281 0.9946179 20.0133 --6.5212 1.80965 19.3878 --7.55521 1.56817 19.4224 --7.89385 2.07691 18.5435 --8.85226 2.27199 18.2555 --9.08515 1.44169 18.8415 --8.91947 0.4828319 19.1229 --8.08843 0.3127129 19.5711 --7.69407 -0.3244541 18.9996 --7.27086 -1.0763 19.3933 --7.05641 -1.41415 20.3437 --7.82329 -1.38555 20.9946 --7.29391 -0.9320491 21.7121 --6.67076 -0.7502901 22.4474 --7.23388 -0.5022371 23.3413 --7.50842 -0.5256911 24.3238 --7.63703 -1.50683 24.6253 --8.21939 -2.18865 24.2094 --8.22691 -1.62573 23.3819 --7.91253 -2.22182 22.6522 --7.09197 -2.15326 23.1464 --6.95474 -3.09519 22.8865 --6.93542 -4.02553 23.3071 --6.88006 -3.33281 24.0833 --6.67724 -4.02408 24.7692 --6.49662 -4.5802 25.5943 --5.73096 -3.98693 26.013 --6.50824 -3.2626 25.9869 --7.29116 -3.75803 25.8734 --8.03204 -3.52123 26.5657 --8.53601 -4.32659 26.5969 --9.4934 -4.52432 26.7511 --9.19591 -5.15098 27.5242 --10.2157 -5.26457 27.356 --10.4582 -5.29809 28.2956 --10.8022 -4.5565 28.9102 --10.8178 -3.76798 29.5732 --11.5312 -3.88711 28.966 --10.8459 -3.13255 28.7077 --10.1623 -2.41776 28.651 --10.9445 -2.42123 27.9418 --11.4935 -1.7409 28.4434 --10.972 -1.04424 28.9034 --10.1436 -1.47161 29.2654 --9.34568 -1.82636 29.7777 --9.81818 -1.92695 30.7014 --10.6304 -2.21054 31.225 --11.3369 -1.56574 31.297 --11.6165 -2.04865 32.0672 --12.0948 -2.94435 31.6494 --11.8791 -2.46847 30.7249 --12.1532 -3.45362 30.4995 --12.1272 -4.45112 30.8605 --11.7169 -5.24954 31.0187 --11.1793 -4.46529 30.7829 --10.5961 -4.06153 31.4418 --9.94057 -3.56386 30.9229 --9.26757 -3.70083 30.2425 --8.25234 -3.4932 29.9969 --7.68623 -3.01594 30.7236 --6.88053 -2.62972 30.397 --5.88347 -2.56345 30.715 --5.01156 -2.11087 30.8838 --4.48271 -2.97004 30.9932 --3.77305 -2.62339 31.5378 --3.71318 -1.65077 31.1442 --2.92682 -1.10004 30.9526 --2.33131 -0.3124831 31.2791 --1.64065 -1.12122 31.3048 --1.10939 -0.8661781 30.5027 --1.08712 -1.3632 29.586 --0.24091 -1.96752 29.4656 --0.429319 -1.75874 28.4853 --0.783835 -2.15648 27.5835 --1.6561 -1.98449 27.7426 --1.69679 -2.98727 27.9991 --2.37261 -3.03852 27.296 --3.2781 -2.8864 26.8666 --3.21352 -2.12205 26.2981 --2.59796 -2.40522 25.5345 --1.73365 -1.95194 25.5726 --1.64609 -1.32461 24.7223 --2.4568 -1.02371 25.3029 --2.96442 -0.2594071 24.6979 --3.57426 -1.04627 24.8369 --4.5425 -0.6538601 24.6278 --5.44121 -0.9810181 24.8567 --4.90843 -1.41591 25.6075 --5.12613 -2.3005 25.2039 --4.64385 -2.64852 24.3723 --3.78141 -2.57055 24.804 --2.86772 -2.90469 24.6501 --2.15604 -3.45435 24.1998 --2.47706 -4.2908 23.7343 --3.44741 -4.09293 23.946 --3.19349 -3.76077 23.0241 --3.52078 -3.38444 22.2145 --3.86066 -2.62264 21.8457 --2.85942 -2.8387 21.7735 --1.93879 -2.41375 21.9507 --1.77573 -2.28829 20.9488 --1.31199 -1.36995 21.123 --0.802421 -1.95324 20.4106 --1.1651 -2.52156 19.8437 --2.14068 -2.19427 19.8958 --2.75939 -2.60443 19.3321 --1.84206 -2.40191 18.8747 --1.06792 -2.75147 18.3181 --1.35313 -3.70872 18.6384 --1.15728 -4.24904 17.7849 --1.98613 -4.88198 17.531 --1.64816 -4.79613 18.4637 --2.18902 -5.08388 19.2484 --3.1157 -5.47209 19.1725 --4.00392 -4.94444 19.2225 --3.92378 -5.2015 18.2462 --3.69565 -4.67564 17.4142 --2.9967 -4.46789 16.7217 --2.6737 -5.38769 16.9716 --2.03776 -6.15211 16.7494 --2.70852 -6.51883 17.3921 --3.70212 -6.4088 17.2801 --3.4814 -7.10076 16.6073 --4.32392 -7.50704 16.9362 --4.31912 -8.30834 17.4777 --5.27928 -8.10106 17.7386 --6.30521 -8.41238 17.7195 --5.95601 -8.27572 16.8171 --5.59574 -8.43346 15.9225 --5.80591 -7.58254 15.4705 --6.24395 -7.00943 14.8071 --6.58093 -6.1752 14.4879 --7.33803 -6.63504 15.0727 --7.35287 -7.26471 15.9336 --6.83367 -6.39506 15.9244 --7.2978 -6.76241 16.7244 --6.5587 -7.35353 16.4628 --6.94321 -8.24447 16.1485 --6.72081 -9.07574 16.8284 --5.80016 -9.48924 16.6334 --5.35016 -10.2833 16.8487 --5.78981 -11.1168 17.0087 --6.62125 -11.2196 17.5397 --7.10156 -10.5272 17.1386 --7.37522 -9.71971 17.5889 --7.07531 -9.85534 18.529 --8.01196 -10.3285 18.4998 --7.98373 -9.61958 19.1575 --8.61213 -8.96609 18.6798 --8.84074 -9.12058 17.7213 --8.77405 -9.80681 16.8979 --9.13785 -10.3994 16.1503 --10.124 -10.6844 16.0407 --11.1375 -10.6023 15.86 --11.0375 -10.5126 16.8605 --10.6826 -10.8534 17.6821 --9.6329 -10.8626 17.7922 --9.67044 -11.1272 18.7127 --8.95365 -11.461 19.3005 --9.34314 -11.461 20.1984 --9.42022 -11.955 21.076 --8.77519 -12.586 20.6106 --7.95002 -12.7926 20.0492 --6.98403 -13.1237 19.986 --7.02688 -13.8101 20.6748 --6.83362 -13.3739 21.5413 --6.32111 -12.6212 21.8621 --6.54723 -12.4777 20.8939 --6.95839 -11.7282 21.4445 --7.1198 -10.8358 21.7547 --6.12733 -10.9464 21.9014 --5.76075 -10.9846 20.931 --5.48358 -10.2446 20.2315 --5.02342 -9.53439 20.7755 --4.94829 -8.84202 20.024 --4.22582 -9.02331 19.407 --3.91009 -8.51404 18.607 --3.06391 -8.56756 19.0534 --2.23907 -8.75966 18.5815 --2.32046 -8.74538 17.5747 --2.90261 -8.90824 16.7905 --3.11086 -8.56597 15.8316 --3.62599 -8.74579 14.9704 --4.2833 -9.40074 15.2515 --4.43787 -9.67338 14.2448 --3.83644 -9.95462 13.4035 --4.24018 -10.6613 12.8104 --3.59824 -10.0719 12.2166 --3.86213 -10.0443 11.2367 --3.60415 -9.27304 10.7547 --2.93779 -9.66163 10.1537 --2.56607 -8.95812 10.7162 --1.75285 -8.77549 11.3065 --1.25895 -9.53537 11.8097 --0.392311 -9.94437 11.5503 --1.02561 -9.9082 10.8417 --0.274919 -9.42106 10.3838 -0.149082 -8.57021 10.3815 --0.12514 -8.72708 11.2997 -0.605462 -8.06588 11.406 -0.486002 -7.64826 12.3685 -1.38987 -7.09402 12.6473 -1.54931 -6.83413 11.6812 -2.17167 -6.29376 12.2161 -1.8855 -5.35329 12.0156 -1.99903 -5.81926 11.1326 -1.04462 -5.6966 10.7749 -0.256095 -6.12228 10.2572 --0.310421 -5.59981 10.8494 -0.468424 -5.35838 11.451 -0.681269 -4.46656 11.0998 -1.65952 -4.35086 11.18 -2.24714 -3.75328 11.5912 -1.75759 -4.20899 12.1983 -1.06196 -3.58475 12.5059 -0.336286 -4.19673 12.4228 --0.03167633 -4.96928 12.9654 --0.452136 -4.30665 13.4969 --0.599502 -5.07432 14.0854 --0.08005263 -5.84849 14.1312 -0.790041 -5.27308 14.1979 -1.17571 -4.71181 14.9512 -2.02791 -4.73739 15.4269 -1.24608 -4.625 16.0875 -1.08559 -3.93566 16.8071 -1.64291 -3.45855 17.6014 -1.23463 -4.33852 18.0695 -1.13245 -5.03726 17.3642 -1.43692 -5.71395 18.0108 -0.862523 -6.35186 17.5004 --0.06090333 -6.71719 17.5568 --0.311585 -6.28907 16.6344 --0.563513 -7.0607 16.1976 --0.872112 -6.29358 15.6758 --0.46517 -5.48299 15.1916 --1.10867 -4.75024 15.0563 --2.01375 -4.35534 15.0505 --2.72631 -4.5263 14.348 --2.67638 -3.70669 13.6913 --3.00621 -2.82511 14.1227 --2.21063 -2.62621 14.6233 --2.45501 -1.96208 13.793 --2.84394 -2.46605 12.9868 --2.06715 -3.03915 12.738 --1.14589 -3.4519 13.0479 --1.19278 -3.18115 14.0265 --0.548949 -2.35636 14.2431 --0.358188 -1.93434 15.1926 --1.29288 -1.74581 15.5282 --1.79159 -1.70995 16.4533 --2.08949 -2.60781 16.2329 --1.36415 -3.0747 16.7165 --1.34129 -3.59945 15.9775 --0.493915 -3.33835 15.6348 -0.381722 -2.89778 15.4777 -1.34917 -2.73743 15.3064 -1.05328 -1.92416 15.6699 -0.53346 -1.45169 16.3717 -0.710963 -1.54428 17.2761 -0.485846 -1.12302 18.0722 --0.175816 -0.4101681 18.1205 -0.522107 0.01083293 17.5461 --0.183227 0.7050479 17.5736 --0.09816243 1.09841 16.5934 --0.882653 1.41526 16.1129 --1.76628 0.8978589 15.8006 --1.09268 0.1896959 15.6147 --1.79488 -0.3547611 15.0799 --2.33796 -0.1611101 15.8618 --2.5377 0.4531059 15.1295 --2.64039 0.4649719 14.1403 --3.35878 0.5101699 13.4452 --4.23745 0.9225439 13.3935 --4.76698 0.2835549 12.9055 --4.85113 0.3164519 11.8754 --5.6994 0.6042979 12.2902 --6.00093 0.8590669 11.3323 --6.06907 1.81673 11.0426 --6.67463 1.26325 10.5502 --7.31623 0.6363999 10.1247 --8.2455 0.5818589 10.0451 --8.88437 1.2162 9.51508 --9.31783 2.06746 9.70156 --10.1044 2.73036 9.48264 --10.5632 1.82053 9.39042 --10.2028 1.97337 10.2713 --10.4588 1.69637 11.171 --11.4505 1.95156 11.1066 --11.8244 1.40418 10.3259 --12.589 1.45814 10.9687 --12.5297 2.08772 11.7639 --11.951 2.76806 11.4434 --12.8439 2.75987 10.9884 --12.3644 3.57143 10.6289 --12.9402 3.75365 11.4237 --13.5825 4.27895 10.8917 --13.4086 5.13209 11.3238 --12.5889 5.65374 11.3923 --13.1343 6.1937 11.9381 --12.3227 6.84616 11.9491 --13.0663 7.43543 11.5406 --13.2373 7.57946 10.5686 --14.2485 7.47404 10.5257 --14.8986 7.86916 9.85107 --15.856 7.42691 9.71315 --15.8452 7.54053 8.6943 --15.307 7.45361 7.85508 --16.0107 6.72168 7.82421 --15.8389 6.17202 7.04386 --15.9353 5.25408 6.67924 --15.9432 4.48542 6.0295 --16.9013 4.3364 6.29861 --17.5701 3.64247 6.55703 --17.1462 2.85743 7.04756 --18.133 2.68737 6.87938 --18.899 2.95836 7.52941 --18.8691 2.11515 8.08872 --18.7004 1.16265 7.81354 --18.19 0.3010649 7.66665 --18.8371 -0.3056651 8.07971 --19.0493 0.2309129 8.91455 --18.576 1.13695 9.05767 --18.573 1.88912 9.68494 --19.3754 2.1555 9.16054 --19.979 2.71011 9.78031 --20.6344 3.49517 9.78648 --20.3889 3.43901 10.782 --19.6876 4.15156 10.9233 --19.9252 5.00812 11.3467 --19.6186 5.83298 10.7654 --20.1573 6.58012 10.42 --19.6918 7.44918 10.0712 --18.9742 7.49434 10.7154 --17.931 7.47347 10.6981 --17.8508 7.72414 9.71155 --18.5615 7.95478 9.04417 --17.7006 8.14471 8.60276 --16.6642 8.24952 8.57516 --15.9058 8.59178 7.9672 --15.3552 8.34372 8.81139 --14.6084 8.75239 9.40578 --14.2244 9.04614 8.52393 --14.4015 8.68682 7.60671 --14.1742 9.19992 6.79667 --13.8524 8.25601 6.62931 --14.5706 8.05865 5.96413 --14.5233 8.99312 5.55202 --14.4294 9.96627 5.46254 --13.4951 9.81921 5.64735 --12.8862 9.50485 6.41514 --11.9925 9.8182 6.76104 --11.5511 9.56146 7.63152 --10.8186 9.9835 8.23854 --10.2462 9.22586 8.64381 --9.88788 9.77025 9.37055 --9.62609 9.68278 10.3025 --8.90211 10.4222 10.4391 --8.32482 10.6296 9.70637 --7.59984 10.8031 10.3587 --6.84556 10.1265 10.431 --6.10837 10.5092 11.0591 --6.02022 11.3494 10.4642 --5.21203 11.5956 9.88522 --4.85507 10.8236 10.5581 --4.85994 9.84128 10.697 --4.39634 9.47594 9.91131 --4.33216 8.51271 9.80911 --5.20243 8.54133 9.31447 --6.03103 8.12546 8.9545 --5.85982 8.10103 7.91277 --5.51729 7.19683 8.01301 --6.10864 6.98984 7.24208 --6.86437 6.50129 7.44652 --7.56231 6.86398 6.87495 --6.99548 7.58646 6.56137 --7.11816 8.46963 6.94121 --6.50016 9.06276 7.42661 --6.51745 10.0346 7.34926 --7.27642 10.1134 8.01784 --7.70651 10.7867 7.33845 --8.00549 9.95435 6.96353 --8.21929 9.04247 7.24914 --8.68047 8.82474 8.15967 --7.85611 8.25914 8.08098 --8.23501 8.1751 9.05778 --7.53581 8.91789 8.90755 --7.33967 8.48725 9.74887 --7.14959 8.85293 10.7401 --8.0018 8.47298 10.7505 --8.61432 8.70168 9.96665 --9.26014 7.86009 9.78408 --9.90223 7.33489 10.3644 --9.65105 7.97972 11.0722 --8.8714 8.63809 11.07 --9.203 9.00601 11.8991 --9.80544 9.55419 12.3783 --9.28456 10.3352 12.8621 --9.69225 11.1767 12.5662 --9.03911 11.6404 12.0258 --8.69329 11.924 11.12 --8.96591 12.9182 11.1665 --8.10278 12.8059 10.5753 --7.99085 13.2565 9.77194 --7.08784 13.3365 9.38313 --7.22932 12.7954 8.49965 --8.07834 12.2391 8.59635 --9.00125 12.2408 9.02422 --9.87248 11.7442 9.12226 --10.2701 10.8446 9.13956 --10.6811 10.7863 10.0386 --10.4239 11.2996 10.8185 --11.3231 10.7404 10.8041 --12.1982 10.9808 11.2628 --11.992 11.624 10.6102 --12.9867 11.8279 10.4976 --13.1912 12.4494 9.83758 --12.8578 12.1833 8.91052 --11.9216 12.0799 9.1765 --11.9463 11.097 9.14009 --12.5984 10.4129 9.49229 --12.8375 10.0412 10.4131 --11.8179 9.98614 10.1741 --11.1639 9.65139 9.41039 --10.837 8.71439 9.36759 --11.1589 7.74809 9.0863 --12.1579 7.96713 9.22428 --11.8695 7.88005 8.28571 --11.1597 7.28984 7.79508 --10.5411 7.89865 7.35078 --10.1158 7.64266 8.29519 --9.97184 6.99227 9.01332 --9.06727 6.68901 9.32356 --8.5644 6.96219 10.1706 --8.5637 5.92967 10.1221 --8.46588 5.65961 11.0521 --8.98366 4.95696 10.5783 --9.79828 4.52449 10.297 --10.6292 4.92354 10.6273 --10.2768 5.75586 10.0816 --10.5825 5.43513 9.17456 --11.4547 4.97996 9.29558 --11.3104 4.03905 9.01654 --11.6262 4.48819 8.17471 --12.6485 4.31601 8.31302 --13.045 4.84579 7.59517 --13.3186 5.76796 7.78117 --13.9159 5.23765 8.4153 --14.5389 4.58841 8.88079 --15.0265 5.43951 8.83734 --14.5364 6.17146 8.338 --14.3918 6.21084 7.31039 --14.1634 6.36404 6.39368 --14.6739 5.73099 5.80543 --15.2847 5.14738 5.22985 --15.6926 4.34405 4.90062 --15.7585 5.0093 4.18366 --15.5031 4.01591 3.89373 --16.1272 3.77777 3.1988 --16.4634 2.82813 3.1113 --17.3157 3.01116 2.64126 --17.6723 3.86891 2.33719 --18.0409 3.3833 1.53222 --18.2165 2.88017 0.7361461 --17.7357 2.0963 0.2453051 --16.7372 1.83455 0.2045991 --16.913 2.81088 -0.1856809 --16.7582 3.12696 -1.1201 --15.9276 3.37958 -0.6253209 --15.6897 3.02213 0.2853951 --15.3035 2.07581 0.4431411 --14.3681 2.28554 0.1505561 --14.2132 1.65168 -0.6012719 --14.1456 0.6139589 -0.7033069 --14.9476 0.3851959 -0.2966519 --14.9304 0.9993829 0.4873221 --15.8009 1.01347 0.9975961 --14.9195 0.9405769 1.40845 --15.5823 0.9411189 2.21365 --15.9164 1.19222 3.20517 --15.5115 0.8742359 3.95977 --15.8877 1.40779 4.74973 --16.4428 1.36976 5.63769 --16.4298 0.5734729 6.16709 --16.184 -0.3402871 6.18573 --16.1932 0.1013339 5.26551 --16.7967 0.2425449 4.45964 --17.1429 -0.7417671 4.54086 --17.4037 -1.02883 3.61758 --17.492 -1.94334 3.24891 --17.9636 -2.31334 2.41669 --18.8062 -1.96075 2.70663 --19.677 -1.41924 2.57433 --18.8454 -0.8433801 2.72582 --19.542 -0.1429751 2.9508 --18.6644 0.1049059 3.41709 --17.8275 0.6973629 3.72347 --18.0774 1.67127 3.58641 --18.8037 1.66641 4.32622 --18.1919 1.99438 5.03676 --18.8035 1.28023 5.42442 --19.795 1.5297 5.50707 --20.4929 1.43578 6.11578 --21.1094 2.12254 5.77178 --21.7258 2.03652 6.58769 --21.1802 1.4012 7.0708 --20.7785 1.63918 7.92788 --20.3834 0.7471979 8.00737 --21.3151 0.3441479 7.92243 --20.9722 0.1772349 8.83804 --20.8551 0.8378309 9.57737 --21.7451 0.6685049 9.91822 --22.2344 1.00464 9.14864 --22.0374 1.98432 9.12114 --22.7204 2.14435 8.45576 --23.1886 2.2542 7.46494 --23.9576 1.70007 7.8585 --24.1455 2.59411 8.28077 --24.7304 2.15813 8.86213 --25.1769 2.2918 9.80419 --24.4549 1.85282 10.3922 --24.3285 2.69548 10.7831 --23.3499 2.51133 11.0813 --22.5664 3.10964 10.78 --22.3368 3.38533 9.87491 --23.2836 3.88289 9.82612 --24.1449 4.07483 9.38539 --24.9055 4.61902 8.98251 --25.5013 5.42584 8.98782 --25.631 5.19946 8.01619 --24.6605 4.86676 7.70353 --23.8525 4.31714 7.4083 --22.9661 4.24454 7.07742 --22.7094 4.43687 8.05281 --22.9206 4.94653 8.89688 --23.8284 4.93664 8.59372 --24.3819 5.7347 8.9128 --23.6262 6.18228 9.39338 --24.1193 6.98848 9.33498 --24.2053 7.94083 9.05715 --23.5087 7.46045 8.43986 --23.2834 8.42186 8.63737 --22.4341 8.89123 8.41329 --22.2178 9.82719 8.46512 --21.8106 9.43343 7.69509 --20.894 9.55573 7.30492 --20.0654 8.93305 7.34534 --19.265 9.2212 7.67301 --18.3816 9.44673 8.08812 --17.731 9.01057 7.45689 --17.0426 9.6192 7.17253 --17.8298 9.79194 6.55086 --17.7975 10.4472 7.3119 --17.5255 10.7146 8.25237 --17.5148 10.6378 9.17237 --18.0964 10.7002 9.99016 --18.3907 10.025 9.30533 --17.8138 9.57765 9.97503 --18.1396 8.75761 10.448 --19.0531 8.78066 10.2435 --20.0016 9.12187 10.0988 --20.9569 8.94695 10.1869 --21.2294 8.0352 9.98872 --21.2522 7.04759 10.3436 --21.9704 6.9235 9.67152 --21.424 6.12567 9.42417 --20.6913 5.48032 9.16043 --20.1316 6.24326 9.07872 --19.1846 5.76322 9.07801 --18.3793 6.30126 8.81004 --18.3877 6.48004 7.85202 --17.624 7.14808 7.66342 --17.3135 7.04684 8.60807 --16.791 6.77513 9.38353 --16.7177 5.82704 9.14941 --15.8721 5.61947 9.71921 --16.3782 5.68636 10.6139 --17.092 6.38617 10.4225 --17.5443 6.01977 11.3014 --17.4926 7.01393 11.5026 --16.7948 7.54734 11.9959 --16.1046 8.08924 11.4435 --15.7626 8.46777 12.2784 --15.451 9.34608 12.7352 --14.5988 8.9751 12.4451 --13.7541 9.33552 12.8393 --12.8093 9.43466 12.7085 --11.8455 9.60099 12.9044 --12.151 10.3416 13.5544 --12.6952 11.1258 13.6531 --13.3494 10.9226 12.9499 --14.1793 10.2769 12.8838 --14.9149 10.6537 13.535 --15.7255 11.0605 13.8447 --16.011 10.7479 14.704 --16.5302 10.193 15.3665 --16.7084 9.57036 14.6131 --16.3208 9.14181 13.7861 --16.183 9.93505 13.1251 --16.1441 9.83574 12.0746 --16.4508 10.7008 12.4501 --15.6069 11.0145 12.0189 --14.8987 11.5184 11.6545 --15.7185 12.006 11.3271 --15.938 11.8136 10.3686 --16.8683 12.104 10.5214 --16.8324 11.951 11.529 --17.5017 12.5844 11.9231 --17.2066 13.284 12.6174 --17.7894 13.3066 13.4123 --18.4096 13.2529 12.5747 --18.7857 12.799 11.7594 --19.4022 12.9778 11.0081 --19.256 13.0572 9.98591 --18.9843 13.9964 10.1475 --19.424 14.5778 10.7953 --18.6411 13.9838 11.1966 --17.8826 13.4844 10.7573 --17.4838 14.1388 10.0833 --17.8797 14.9957 9.87011 --18.4656 14.8126 9.0389 --17.708 14.89 8.34478 --17.0876 14.5853 7.58974 --16.9398 13.7786 6.90326 --17.7986 13.4707 6.46897 --17.984 14.0686 5.6947 --18.8587 13.7561 6.15374 --19.7151 13.525 6.58214 --20.549 13.998 6.78496 --20.128 14.6763 6.09772 --20.6034 14.3541 5.36744 --20.6517 14.9447 4.59836 --20.8325 13.989 4.30592 --20.6443 13.286 3.54381 --20.6099 12.2927 3.83175 --20.3392 11.3376 3.95222 --20.8127 11.4973 3.06679 --21.1908 10.5753 2.98861 --20.6391 10.3568 2.25131 --19.9263 10.1488 1.51188 --19.9415 9.25403 1.85054 --20.1778 8.32909 2.31379 --19.1781 8.5781 2.44287 --18.2118 8.89288 2.19981 --18.189 8.18421 1.54535 --17.2635 7.73017 1.58547 --16.2463 7.6142 1.91922 --15.5176 7.76538 2.56686 --15.3397 8.59926 3.15022 --15.8387 8.99711 2.40566 --16.4118 9.66885 2.10903 --17.1142 10.3377 2.45246 --17.3022 10.7597 3.34678 --16.5022 10.774 3.88684 --17.1771 10.3029 4.53561 --18.0962 9.89471 4.39263 --18.486 9.33381 5.04918 --18.5809 8.28918 5.03958 --19.5188 8.6987 4.76335 --19.4279 9.28357 5.59085 --20.2121 8.82827 6.06637 --20.379 9.78455 6.03393 --21.3931 10.0218 5.82224 --21.5361 9.80027 4.87176 --22.1762 8.96009 4.77926 --22.8106 8.64893 5.44921 --23.0546 7.9394 4.70827 --23.9556 8.14012 5.03945 --24.019 7.36455 4.30359 --23.5155 6.69216 4.80071 --22.5853 6.72563 5.16006 --22.0262 6.14553 5.73502 --22.3174 5.1675 5.73996 --22.7515 4.86146 4.85073 --23.1434 5.34025 4.09166 --22.1286 5.32383 4.17827 --22.1876 4.40554 3.74044 --22.8822 3.74534 3.47025 --23.4825 3.07868 3.14208 --22.6275 2.6008 3.21842 --21.7224 2.17732 3.08397 --21.5842 2.70189 2.29208 --22.165 1.92888 2.03428 --22.4924 1.50822 2.84415 --21.8621 1.0041 3.45336 --21.1759 0.2799409 3.28811 --21.0304 0.2124569 2.27987 --21.3837 1.16093 1.96968 --22.2112 0.5795699 1.80891 --23.0982 0.1978249 2.00713 --24.1497 0.3661199 1.93656 --23.6551 1.1789 2.34114 --24.555 1.43592 2.12021 --23.9178 2.04451 2.5067 --24.8894 2.4385 2.52078 --25.8899 2.73038 2.58456 --26.6693 2.16676 2.80186 --27.073 2.81954 2.13128 --26.9129 3.3228 2.99943 --27.3178 3.50801 3.92297 --27.2207 2.63251 4.37337 --26.229 2.35594 4.22659 --26.3975 2.64501 5.29685 --26.8708 3.21998 5.94523 --25.9895 3.55013 5.96744 --25.5536 3.71375 6.84865 --24.6839 4.2482 6.75215 --23.8419 3.83795 6.39327 --23.7753 2.98498 6.97288 --24.6835 2.61338 6.88265 --25.4888 2.26979 7.40431 --25.2094 1.36746 7.67867 --25.6337 0.4587559 7.83589 --26.1738 -0.2643041 7.44691 --26.661 -0.002927916 6.62758 --27.0067 -0.4739781 5.929 --26.4206 -1.19371 6.24662 --26.8951 -1.65527 5.47457 --27.2878 -2.57816 5.19238 --26.9049 -2.91502 4.4399 --27.5745 -3.65088 4.63716 --27.7888 -4.4724 5.2032 --27.622 -5.39409 5.63329 --27.3587 -6.17373 6.09738 --26.5949 -6.13382 6.70862 --25.913 -6.51277 7.31244 --25.8241 -5.54823 7.14249 --25.3221 -5.19484 7.95659 --24.8095 -4.78294 7.19599 --24.7227 -3.80322 7.55181 --25.1905 -2.95663 7.43491 --25.0433 -1.91334 7.35149 --25.1718 -1.71685 8.40801 --25.7352 -1.68866 9.12552 --26.7156 -1.52124 9.39455 --26.6334 -1.50479 8.44095 --27.3795 -1.96952 8.09198 --28.3869 -2.14528 8.23809 --28.9592 -2.93868 8.14789 --28.6778 -3.58252 7.4632 --28.6849 -4.54608 7.63074 --28.2698 -4.49694 8.54397 --28.7294 -5.39869 8.29093 --27.815 -5.46194 8.71017 --28.4464 -5.74467 9.44507 --28.5756 -6.39893 10.2765 --27.695 -6.56968 10.7968 --26.9222 -6.74896 10.2126 --26.0672 -6.18078 10.3836 --25.5458 -5.71525 11.1128 --26.3116 -5.00214 11.0959 --26.9211 -4.47307 10.5559 --27.8409 -4.66015 10.9436 --28.7333 -4.47199 10.3964 --29.6235 -4.09016 10.6213 --29.6489 -3.60498 11.4264 --29.2607 -4.07263 12.1852 --29.6919 -4.89626 12.5819 --29.5036 -5.93351 12.346 --29.5514 -5.89086 13.4324 --30.5406 -5.89542 13.4369 --30.6046 -6.88492 13.2592 --30.5874 -7.81331 12.8694 --29.8998 -7.59022 13.552 --29.5483 -7.04016 14.3898 --29.0501 -6.68898 15.1997 --28.6048 -6.07493 15.852 --27.9426 -5.2967 16.0139 --27.6255 -6.03937 16.5874 --26.932 -5.99301 15.8604 --26.2152 -6.50559 16.2546 --25.8946 -5.56365 16.1367 --26.1557 -4.94182 16.8582 --26.6813 -5.17347 17.6412 --26.3552 -4.87469 18.5749 --26.4466 -4.87485 19.5439 --26.426 -3.99058 20.1414 --25.3924 -3.78557 20.095 --25.737 -3.56701 19.1945 --26.4127 -2.88894 19.1771 --25.8383 -2.3688 19.9157 --25.6628 -1.96139 19.0106 --26.1634 -1.26354 19.3518 --25.7259 -0.9780581 18.467 --25.4726 -1.36614 17.549 --25.5181 -1.03141 16.6284 --26.0615 -1.18691 15.8425 --26.7691 -0.6453001 15.3685 --27.1294 0.3092749 15.3441 --26.175 0.1346859 15.0941 --25.9244 0.8306779 14.4312 --26.2439 1.76041 14.5625 --25.2909 1.88427 14.7343 --25.7226 2.79308 14.4321 --26.7024 3.07729 14.3015 --27.1107 2.78929 15.1246 --26.8287 3.42657 15.8962 --26.7458 3.89007 16.7561 --27.5244 3.34692 17.0329 --27.3048 2.7958 17.7646 --27.8155 2.04417 17.4256 --28.0311 1.24354 16.9189 --27.8608 0.3248159 17.381 --26.9659 0.6720039 17.1127 --26.0145 0.3812559 17.295 --25.4984 1.0873 17.8029 --25.9629 0.7850579 18.6848 --25.5012 1.66542 18.6498 --25.5098 1.96987 19.5741 --26.3406 2.40596 20.0832 --26.4778 3.08405 20.715 --27.3261 3.33753 21.1002 --27.6467 3.30042 20.1082 --28.6334 3.23709 20.3253 --28.9656 2.75438 19.5715 --28.6018 1.94368 19.0667 --28.5901 1.37771 19.8464 --29.3769 1.28387 20.4473 --29.9444 0.6443659 20.087 --30.5315 0.6079549 19.2905 --30.7536 1.37473 18.6587 --30.7115 0.5954319 18.0366 --31.032 0.2717729 17.1549 --30.585 1.18309 16.9244 --29.7137 1.3711 17.1544 --30.0091 1.18551 16.2038 --29.5971 1.66975 15.4238 --29.8192 1.83544 14.4535 --29.6197 1.14179 13.7434 --29.9036 0.3976679 13.2225 --30.6415 1.03978 13.1375 --30.4247 0.6434279 12.3539 --29.8227 0.9300449 11.5827 --29.6146 1.18524 10.6353 --29.2406 0.4148709 10.0241 --29.1917 -0.5860941 9.85622 --29.5733 -0.9123691 8.98424 --30.2338 -0.1837881 9.1785 --31.2422 -0.1645041 9.33978 --32.0625 0.2955899 9.09603 --32.3144 0.02087193 10.0355 --32.6589 0.05482133 11.0179 --33.5811 -0.2577951 10.9777 --33.5369 -1.20973 11.0289 --34.3822 -0.8621801 10.6339 --34.4271 -0.1483141 9.92666 --34.5935 -1.11388 9.75276 --35.5686 -0.7767251 9.61908 --35.9287 -0.7006961 10.5651 --36.0204 -1.07848 11.4621 --35.6144 -0.5265201 12.2236 --35.1228 0.2258789 12.5105 --34.6471 0.8125789 13.1486 --33.6877 1.10518 13.3468 --33.4504 0.3123529 12.8487 --32.9189 -0.1629371 12.1558 --32.3695 -0.8340281 12.6936 --31.9384 -1.2792 13.5926 --32.2016 -2.1487 13.0573 --31.8808 -3.05301 13.3475 --32.088 -3.34308 14.1983 --32.2819 -4.19825 14.6467 --32.2157 -4.9378 15.3663 --32.1769 -4.2263 16.0915 --31.4863 -4.78034 16.5957 --31.0919 -5.67472 16.9641 --31.7465 -6.39528 17.3529 --30.8769 -6.64758 17.8482 --30.3276 -7.45781 17.6335 --29.3745 -7.41106 17.2507 --28.7972 -7.77078 17.9453 --29.4418 -7.11485 18.2928 --29.2917 -6.61958 19.1649 --28.5758 -7.27643 19.1616 --28.0044 -8.10029 19.3007 --27.2758 -8.75037 19.2871 --26.6174 -8.04401 19.1936 --26.1801 -8.95255 19.39 --25.7653 -9.37365 18.6135 --25.1379 -9.1714 17.907 --25.1235 -8.42584 17.3577 --24.7928 -9.06175 16.7351 --24.9504 -10.0159 16.54 --24.8699 -9.77813 15.6412 --25.0956 -9.07198 14.9029 --24.8203 -9.88053 14.3753 --25.3639 -9.45066 13.6468 --25.7938 -10.3574 13.7914 --26.181 -9.60109 14.344 --26.6214 -9.08793 15.0733 --27.2731 -9.1365 15.8825 --26.8726 -8.31058 15.6607 --25.9779 -7.94232 15.4374 --25.2731 -7.62731 14.7613 --24.4756 -7.18516 14.487 --24.4357 -6.45831 13.8776 --25.2016 -6.7355 13.2178 --25.4334 -5.90063 12.588 --25.6407 -5.70514 13.643 --25.5877 -5.43469 14.5828 --25.3086 -4.56376 14.3085 --24.9828 -4.45121 13.3622 --25.5608 -3.85998 12.7932 --26.4282 -4.13316 12.5627 --26.5913 -3.22701 12.2309 --26.594 -2.57208 12.9443 --26.7012 -1.65764 13.3035 --26.5448 -0.9621601 12.4862 --26.318 -1.31883 11.5684 --25.9956 -1.33097 10.5858 --25.1867 -1.47943 11.1941 --24.4411 -1.30972 11.9535 --24.1108 -1.91808 11.2221 --24.7178 -2.5368 10.7569 --25.1267 -2.81965 11.5721 --24.5432 -3.39903 12.2095 --24.1356 -4.10669 11.6764 --23.3814 -4.69434 11.4393 --23.2924 -5.46786 10.8707 --23.0496 -5.89221 9.97981 --23.0862 -5.15294 9.27277 --22.5623 -5.65117 8.5702 --23.3728 -5.21873 8.18617 --23.0198 -4.37009 7.6553 --22.8381 -4.76251 6.71531 --22.4025 -5.6544 6.88766 --21.8221 -6.45513 7.243 --21.4399 -6.59555 8.18776 --22.1237 -7.14151 8.58826 --21.8435 -6.77451 9.50511 --21.2562 -7.56791 9.7564 --20.5894 -6.89216 9.59344 --20.3391 -6.22386 10.2844 --21.0593 -6.43292 10.9253 --20.9335 -5.79832 11.6809 --20.8546 -4.91165 11.3315 --21.1234 -4.60186 12.2539 --21.0476 -3.60482 11.9846 --22.0568 -3.72156 12.0656 --22.4229 -2.82583 11.736 --23.0751 -2.32674 12.3562 --23.0196 -1.62668 11.6531 --22.5608 -1.46798 10.7824 --21.6715 -1.09373 10.4522 --21.9586 -1.86487 9.92097 --22.1036 -1.50299 8.96405 --23.008 -1.81229 8.835 --23.7661 -2.40563 8.67985 --24.1793 -3.41455 8.76174 --23.5123 -3.5909 9.4388 --23.0986 -3.65306 10.3602 --22.4397 -3.07975 9.9437 --21.5916 -2.8296 9.34811 --20.6621 -3.15761 9.29913 --19.9371 -2.50022 9.01235 --20.0823 -2.05663 9.89497 --19.9478 -1.2457 9.36902 --20.3781 -0.3988081 9.59321 --20.669 -0.5058181 10.6278 --20.7362 -1.21023 11.3537 --20.9524 -1.95235 12.0299 --20.917 -2.31427 11.0806 --20.2164 -3.12942 11.0688 --19.333 -2.81914 10.6488 --18.3306 -2.4761 10.8219 --18.5234 -3.33856 11.3669 --18.0789 -4.18241 11.7876 --18.2974 -5.13544 11.6135 --18.9086 -5.65157 12.2542 --19.7744 -5.88956 12.7234 --20.214 -5.43267 13.4804 --21.1858 -5.07583 13.5286 --21.9615 -4.97327 14.2053 --21.2514 -4.36003 14.6096 --20.8825 -3.51733 14.24 --21.5032 -2.73668 14.1229 --21.3228 -1.75946 14.0414 --22.2305 -1.71753 14.0759 --22.1674 -0.7294791 14.37 --22.0211 -1.13287 15.2912 --22.3259 -0.1691421 15.1527 --22.0435 0.7877679 15.4526 --22.3099 1.59379 14.923 --22.9086 2.14088 15.5381 --23.4327 2.19119 14.7137 --22.7349 1.81394 14.0991 --22.6901 1.57563 13.0961 --23.4556 1.34372 12.395 --23.3723 1.18505 11.4991 --24.0724 0.5088469 11.8057 --25.0408 0.4713649 11.4617 --25.1557 -0.09699677 10.6388 --25.02 -0.1401261 9.68332 --25.6469 0.6376149 9.80482 --26.5643 0.4899109 9.95259 --26.7515 1.48182 10.0958 --26.9032 1.8316 9.17495 --26.5597 2.40939 8.51712 --26.8924 3.35555 8.42586 --27.7733 3.52738 8.79957 --28.3822 4.28917 9.00815 --28.6496 5.2499 8.82537 --29.6425 4.95198 8.8216 --30.4606 5.61892 8.98038 --30.1607 6.49139 9.39425 --30.4715 7.38861 9.15895 --29.4783 7.2489 9.21563 --29.839 7.62772 8.36497 --29.5285 8.60337 8.43811 --29.1279 8.85688 7.47968 --28.8618 8.38022 6.66563 --29.4202 7.62422 6.4091 --29.9015 7.98832 7.17886 --30.5979 8.20259 6.56177 --30.0707 8.87246 5.94509 --30.2015 9.1251 4.99271 --30.7867 8.36685 5.0261 --31.2618 7.47672 4.78821 --30.5924 6.9089 5.31942 --29.9046 7.19666 4.60303 --29.449 7.11285 3.73079 --28.5334 6.73935 3.78008 --27.6569 6.55922 3.17472 --27.3774 7.52569 2.93154 --27.5228 8.2953 3.62326 --27.6777 8.93256 4.31182 --27.1814 9.84019 4.38613 --27.0152 9.60859 3.44533 --26.3463 8.95344 3.11016 --25.6799 8.27405 2.90184 --25.7444 7.55789 3.56676 --26.3772 6.86647 3.51086 --26.3306 6.46957 2.56274 --26.0678 7.10853 1.85843 --25.3259 6.60063 1.42614 --24.674 6.87871 2.18589 --24.354 6.083 1.6884 --23.5238 5.64476 1.49169 --23.1774 6.50247 1.9926 --23.2332 5.91862 2.80852 --22.3693 5.68014 3.01948 --22.5636 6.50465 3.49103 --22.291 7.30925 2.90422 --21.6475 7.14927 3.67409 --21.0724 7.29506 2.86575 --20.8297 6.32276 2.94965 --20.4663 6.84285 3.74954 --20.0391 7.61978 3.45209 --19.2188 7.04228 3.30296 --18.7128 7.40049 2.52101 --19.2925 7.05546 1.86764 --20.017 7.28315 1.12108 --19.5185 6.9241 0.3487671 --19.3133 6.15189 0.9070231 --19.12 5.12737 0.8892201 --18.3041 5.34847 0.5083491 --17.6825 6.1404 0.2806821 --17.0173 6.88321 0.3004321 --16.0731 6.93146 0.3805461 --15.2503 6.97544 -0.09340078 --14.2809 7.28241 -0.1451879 --14.387 8.00765 -0.8039309 --13.7467 8.73298 -0.8390829 --13.9077 9.42991 -1.53027 --12.9481 9.31915 -1.16294 --12.7976 8.69424 -2.00782 --12.6919 7.82858 -1.48348 --11.8145 7.60694 -1.95208 --12.1959 7.58755 -2.93171 --12.2179 6.78221 -3.49398 --12.1477 5.75598 -3.39928 --11.5753 5.39412 -4.13109 --11.026 5.04966 -3.31778 --10.3764 4.99756 -2.62078 --9.99884 4.72605 -1.81986 --10.1489 4.85244 -0.8291499 --10.8322 5.5111 -0.5173629 --10.4136 6.04495 -1.2101 --10.8189 5.96071 -2.10283 --9.99905 6.37485 -2.52359 --10.2281 7.32643 -2.3023 --10.8462 8.05843 -2.0083 --10.4431 8.86394 -2.46212 --10.5238 9.85859 -2.67218 --10.573 10.2239 -3.58413 --11.1936 9.44463 -3.68638 --11.8969 8.8309 -4.03931 --11.5148 8.57704 -4.95341 --10.7034 8.39303 -4.4113 --11.1362 7.59297 -4.70944 --11.4201 6.65187 -5.10396 --11.5737 7.43668 -5.68176 --11.7163 7.71046 -6.58638 --11.9643 6.9971 -7.19448 --11.6017 6.08987 -7.32509 --12.0146 6.09939 -8.23126 --12.1436 5.76275 -9.24258 --11.2345 6.24773 -9.19245 --10.7806 6.60431 -9.98494 --10.7353 7.31581 -9.29093 --10.682 8.01087 -8.6196 --9.91061 8.16822 -9.17815 --9.4224 7.82109 -8.36584 --8.97017 8.65965 -8.0773 --9.17949 9.32574 -7.448 --9.41558 9.5921 -6.50229 --8.45853 9.65419 -6.22249 --8.21816 9.30679 -5.33379 --9.12762 9.82034 -5.30476 --8.9603 9.46731 -4.39415 --9.30718 9.92934 -3.55473 --9.07754 9.45559 -2.70166 --8.33858 8.83144 -2.84237 --8.99419 8.19712 -3.29516 --9.5087 7.95641 -4.12814 --10.0324 7.43393 -4.83318 --10.1041 6.72933 -5.50667 --9.72162 5.75797 -5.44711 --10.3026 5.33063 -6.06774 --10.9271 5.05992 -5.25096 --10.572 4.6707 -4.45718 --11.232 4.05549 -3.81071 --11.523 3.15866 -3.57359 --11.7099 3.48213 -2.64392 --12.6717 3.65958 -2.88172 --12.8725 4.47958 -2.30565 --12.4899 5.38334 -1.95287 --13.0053 5.73168 -1.09357 --13.9061 5.21626 -1.34658 --14.8517 5.19284 -0.9763229 --15.4197 5.8456 -0.5109169 --14.6106 6.31987 -0.8499519 --15.0447 6.24913 -1.72514 --15.4784 6.89131 -2.3545 --15.3086 7.83123 -2.7843 --15.6989 7.37366 -3.53719 --15.5233 6.48981 -3.96339 --14.9225 6.60173 -4.74889 --13.9844 6.616 -4.59388 --13.1216 6.86571 -5.13909 --13.4635 7.81867 -5.1507 --13.3419 7.40184 -4.31827 --13.4263 6.67262 -3.61472 --13.4004 5.62871 -3.86149 --14.1281 5.40602 -4.4228 --14.1154 4.8013 -5.19037 --15.0817 4.84439 -5.41049 --15.2717 5.73521 -5.79179 --16.1499 6.05564 -6.16595 --16.4682 7.04597 -6.32428 --16.9302 7.60502 -5.6828 --16.7302 8.48559 -5.46507 --16.6885 9.4595 -5.64372 --17.6839 9.73689 -5.42704 --18.5986 9.95378 -5.85043 --19.0719 9.57111 -5.00026 --18.8877 9.83801 -4.0256 --19.513 10.6138 -3.80188 --20.5051 10.6743 -4.01591 --21.1561 9.86307 -4.00896 --21.1519 8.81741 -3.94878 --20.2235 9.21195 -3.89795 --19.3659 8.88726 -3.47903 --18.8006 8.23273 -4.00827 --19.3687 7.9456 -4.731 --19.2728 6.95202 -4.7615 --19.5983 6.10917 -4.32602 --20.2171 5.8745 -5.006 --19.6539 5.08108 -4.9063 --18.9857 4.38213 -5.23773 --18.1075 4.75558 -4.92255 --18.4641 4.84977 -3.98064 --18.6762 3.87172 -3.79692 --18.6936 3.19802 -3.04861 --19.5227 3.79903 -2.98037 --19.5678 4.41394 -3.80523 --20.3094 4.35352 -4.41732 --20.0781 3.53678 -4.98257 --19.6286 2.67122 -5.3583 --19.1439 2.1681 -4.5849 --18.2724 1.59576 -4.7822 --18.6027 1.32736 -3.92941 --19.1592 1.24493 -3.06267 --19.3896 0.3918949 -3.52466 --20.197 -0.1223351 -3.90723 --20.7291 0.3309289 -4.60034 --19.8374 0.4542819 -5.07212 --19.8426 -0.5311451 -4.83943 --20.8073 -0.7432431 -5.10712 --20.8311 -0.1517291 -5.91389 --21.7451 -0.5019971 -6.32989 --21.5395 -1.47848 -6.30417 --22.46 -1.31902 -5.96875 --23.3597 -1.07899 -6.26087 --23.5589 -1.99185 -6.35131 --23.8154 -2.08836 -5.43432 --23.0947 -2.77464 -5.67373 --22.1498 -2.45761 -5.83004 --21.2261 -2.9042 -5.63276 --20.3115 -2.98593 -5.85292 --20.3545 -3.7125 -6.56958 --19.452 -3.26868 -6.45938 --18.6563 -2.81125 -6.20628 --18.7165 -1.89256 -6.66738 --17.9805 -1.21646 -6.75457 --17.4952 -0.3717351 -6.9934 --18.1942 0.2106499 -7.45817 --18.8957 0.8307839 -7.09259 --18.2028 1.30242 -7.58214 --18.3339 2.14608 -7.11048 --17.9077 1.32662 -6.60519 --17.3929 2.21233 -6.65665 --17.2748 2.77727 -7.44567 --16.9876 3.53021 -8.02394 --16.1106 3.72551 -7.73011 --15.5881 4.04524 -8.519 --15.7128 4.76379 -9.20817 --15.4165 5.51476 -8.63714 --15.5077 5.88234 -7.73269 --16.407 5.60722 -8.10002 --17.2045 5.95662 -7.62466 --17.9496 6.11831 -8.29189 --18.6815 5.41541 -8.49745 --19.2042 5.66753 -7.74727 --19.7477 4.95403 -7.50318 --19.8178 4.41262 -8.25808 --20.0241 3.80419 -9.03675 --20.4819 4.63743 -9.00464 --19.9207 5.45914 -9.25423 --19.7921 6.37978 -8.85907 --20.3507 7.14918 -8.73126 --20.3127 8.10657 -8.52184 --21.1233 8.20438 -7.89168 --20.8153 8.87648 -7.21366 --20.4778 7.99613 -6.94637 --20.4482 7.49316 -6.10296 --21.058 7.89083 -5.44367 --21.5354 8.44194 -6.14296 --22.4881 8.47635 -5.92487 --22.7136 9.20825 -6.58032 --23.0945 9.95473 -7.12956 --23.7045 9.14438 -7.23641 --23.6321 9.31128 -8.29303 --24.4334 9.87863 -8.43637 --24.3875 10.4852 -7.62894 --24.805 11.1656 -8.1772 --25.7983 11.3854 -8.00778 --25.4015 12.2749 -8.1789 --24.8728 12.1863 -9.04184 --25.174 12.6379 -9.863 --25.929 12.1036 -10.3058 --26.6911 11.4667 -10.2268 --26.2995 10.5914 -10.5764 --25.9527 10.5517 -9.60666 --25.0238 10.7722 -9.78144 --24.5026 10.6294 -10.6642 --24.907 11.2179 -11.3722 --24.8136 12.1902 -11.2656 --24.318 12.8448 -10.7686 --23.2926 12.9205 -10.7046 --23.5386 12.5011 -9.85447 --23.3961 11.6934 -10.4083 --22.5949 11.7602 -9.75761 --23.3465 11.1792 -9.39475 --22.6368 10.4139 -9.17901 --23.0775 9.5903 -9.40562 --22.3863 9.23677 -8.76261 --22.084 8.27614 -8.83622 --21.3969 8.96469 -9.25081 --20.4875 9.30637 -9.28358 --19.8938 9.44747 -10.0615 --18.9414 9.34533 -9.6246 --18.4628 10.2351 -9.55128 --17.7164 10.9549 -9.60271 --16.9629 11.347 -9.09945 --17.5345 12.2014 -9.2866 --17.4949 12.4905 -8.33908 --16.6387 12.4656 -7.77493 --15.9646 12.0387 -7.23904 --15.9506 11.1949 -6.65031 --16.3122 10.4972 -7.25315 --16.8471 9.73084 -6.93524 --17.5557 10.25 -6.61611 --17.9021 10.9991 -7.16127 --18.7917 11.1719 -6.67434 --18.6056 11.7968 -5.88554 --17.8028 12.2446 -5.49451 --17.0098 12.7118 -5.0387 --16.107 12.2979 -4.95444 --15.6959 11.9438 -4.10595 --16.4418 12.3408 -3.53487 --15.6307 12.9079 -3.50283 --15.8986 13.6975 -4.02855 --15.067 14.1614 -4.48553 --15.2637 13.6706 -5.38181 --14.829 13.2131 -6.20256 --15.3153 12.4525 -5.88979 --14.7749 11.6948 -5.40584 --15.2776 10.9008 -5.06106 --15.0973 10.0995 -5.56591 --14.9843 10.5632 -6.41795 --14.179 10.3675 -7.02502 --13.3261 10.5878 -6.63335 --12.6441 11.1266 -6.32804 --12.8244 11.679 -5.50818 --13.4707 12.3861 -5.07084 --12.7579 12.3411 -4.42671 --12.7696 11.5541 -3.80566 --13.2534 10.9773 -4.45564 --13.9531 10.7666 -5.06869 --13.6843 9.96968 -5.61857 --13.6596 9.00316 -5.91481 --14.6007 8.80708 -5.83626 --15.5779 8.71023 -6.06432 --15.2 9.33495 -6.80079 --15.462 8.3841 -7.10268 --14.8532 7.9097 -7.79004 --14.3834 7.69091 -6.86761 --15.0428 6.93855 -6.85699 --14.3667 6.37514 -7.23178 --14.2355 5.42794 -7.12098 --13.3347 4.95422 -7.26355 --13.3137 4.34339 -8.14099 --13.1848 4.01897 -9.10932 --13.2269 3.04417 -8.93466 --13.176 2.08737 -8.58898 --12.7201 2.7952 -8.01062 --12.9957 1.94764 -7.60114 --12.6957 1.34224 -6.80831 --13.0986 1.86618 -6.14069 --12.7098 2.82953 -6.48367 --11.8794 2.94885 -6.04148 --11.1762 3.3857 -6.62258 --10.4282 4.03399 -6.41549 --9.49174 4.21107 -6.71154 --9.0332 4.23622 -7.55147 --8.86703 4.85123 -8.30278 --7.90794 5.25144 -8.33654 --7.24138 4.82035 -8.94138 --7.81053 4.02614 -8.89511 --8.18457 3.08894 -9.15466 --7.42925 3.3879 -9.77915 --6.89185 3.38358 -8.93517 --5.94623 3.5893 -8.74905 --5.78587 4.23851 -7.97279 --6.26167 3.5626 -7.44097 --6.19006 3.27009 -6.42184 --6.76573 2.4857 -6.04426 --7.06767 3.08365 -5.36044 --6.46502 2.81042 -4.59868 --6.72946 2.46806 -3.73044 --6.81441 1.50719 -4.11158 --7.41403 1.55898 -4.95001 --7.60858 1.1741 -5.81483 --8.15298 2.01416 -5.65738 --8.32222 2.35061 -4.81961 --7.78286 3.19303 -4.63598 --7.41137 4.07246 -4.86739 --7.96127 4.73726 -4.54939 --8.72482 4.73233 -5.17417 --9.55905 4.28055 -4.92535 --9.41737 5.00148 -4.28272 --8.66152 5.61794 -4.03895 --8.65811 6.61591 -3.82767 --8.16763 7.27356 -3.21333 --8.49703 7.29976 -2.33935 --7.56766 7.28921 -2.07419 --7.24899 8.10509 -1.49993 --7.29901 8.82218 -0.8172299 --7.22757 9.58276 -0.2351349 --7.75972 10.2704 0.3407071 --8.39822 9.8774 1.02347 --7.77825 9.43214 1.67385 --7.63851 8.55739 1.2645 --8.55409 8.40194 1.49906 --9.54712 8.29805 1.27062 --9.48876 8.30276 0.2935551 --9.54763 7.32849 0.1585261 --9.15259 6.72385 -0.5299689 --9.12374 5.68915 -0.5333089 --8.09509 5.87984 -0.6329369 --7.16409 6.14663 -0.8649879 --7.14394 5.9342 0.1448351 --7.30989 5.50204 0.9595921 --7.30882 5.40363 1.96032 --7.83346 4.75494 1.41691 --8.31249 4.63033 2.26168 --8.70018 5.45677 1.88069 --9.39198 4.82683 1.5159 --10.2497 4.40521 1.48668 --10.2421 3.60649 0.9856751 --10.1543 3.35928 1.8981 --10.9459 2.79278 1.76277 --11.7209 2.84382 1.17626 --11.3249 3.23014 0.2801721 --11.3316 3.8874 -0.4748329 --10.6441 4.18692 0.1500721 --11.43 4.27712 0.8062941 --12.0001 4.59456 -0.03282558 --12.4536 4.36807 -0.8914329 --12.9656 3.52097 -1.2395 --13.6665 3.77073 -1.95519 --14.4875 4.00539 -2.39507 --14.4788 3.12328 -2.81467 --14.3877 3.63809 -3.71945 --15.1304 4.19263 -4.03044 --15.682 5.05209 -4.08885 --16.3302 4.40658 -4.46787 --16.4883 5.17977 -5.12836 --17.3295 5.18545 -5.77468 --17.8902 4.72852 -6.43217 --17.4978 3.78816 -6.54906 --17.5214 4.3233 -7.38828 --18.3023 3.76164 -7.73416 --18.8648 3.01798 -8.16287 --19.1935 2.13466 -8.25581 --19.0216 2.45282 -9.17873 --18.3109 1.78565 -9.29458 --17.5879 1.07993 -9.50118 --17.1957 0.4337719 -10.1499 --17.4094 -0.2813301 -9.49481 --17.12 0.1725629 -8.69921 --17.8142 -0.5341421 -8.44098 --16.948 -0.7491441 -8.08392 --16.726 -1.59539 -8.54765 --16.3894 -2.43117 -8.11806 --16.4664 -2.68833 -9.07415 --17.161 -3.37969 -9.37019 --17.2573 -3.63693 -10.2407 --17.5699 -4.48494 -10.7465 --18.0462 -5.24585 -10.2972 --17.046 -5.36345 -10.1238 --16.7919 -6.11464 -10.7784 --15.768 -5.89248 -10.8483 --14.8823 -5.45584 -10.6175 --14.002 -5.85806 -10.778 --14.6287 -6.6302 -10.9128 --15.5864 -7.01671 -10.9074 --15.6101 -6.77318 -11.8627 --15.1765 -7.60365 -12.2757 --16.0408 -8.00621 -12.2907 --17.1017 -7.90177 -12.1747 --17.237 -7.3157 -12.9705 --17.3192 -6.8145 -12.1483 --18.2605 -6.82124 -12.0673 --18.1814 -7.70392 -12.5244 --18.0131 -7.93409 -13.4833 --18.1246 -7.9925 -14.3695 --17.7641 -7.63038 -15.2641 --18.416 -6.81336 -15.1016 --18.793 -5.96586 -14.6921 --18.8685 -5.31119 -15.4316 --19.5514 -5.76792 -15.9477 --19.617 -4.86232 -16.1876 --20.2038 -4.38558 -16.9137 --19.7246 -3.58536 -16.662 --19.1114 -3.23296 -17.4619 --18.3767 -3.85677 -17.7577 --19.0424 -4.08823 -18.4836 --19.0869 -4.32678 -19.4445 --19.0292 -4.38935 -20.4728 --19.6078 -4.51076 -21.3364 --18.992 -4.9738 -21.9051 --18.6579 -4.11071 -21.9686 --17.9432 -4.45063 -22.6153 --17.599 -4.74409 -23.5639 --17.2532 -3.97686 -23.0387 --16.7655 -3.12116 -23.0206 --16.9809 -2.59668 -22.2243 --16.2563 -2.51724 -21.5019 --15.6278 -3.04796 -21.0019 --15.9348 -3.03495 -20.0513 --15.8446 -4.10863 -19.9915 --14.9598 -3.84776 -19.7083 --14.6766 -2.95459 -19.2593 --14.7783 -2.15762 -19.7842 --15.5933 -1.64263 -19.9579 --15.651 -0.7080521 -20.0752 --16.2167 -1.18483 -20.7433 --16.5569 -0.3364211 -21.0875 --17.1472 0.4057409 -21.2424 --17.9906 0.1318169 -20.8425 --18.6775 -0.4637851 -21.0886 --18.7367 -1.44185 -20.9611 --18.4745 -0.8322611 -20.2082 --18.624 -0.1363201 -19.4956 --19.248 0.7037379 -19.5028 --18.7388 1.50873 -19.328 --19.4803 1.68564 -18.7561 --20.5044 1.59286 -18.7326 --21.0812 0.8775759 -18.4469 --20.5804 0.1627119 -18.9419 --20.6042 -0.5437181 -19.6138 --20.4984 -1.60833 -19.5088 --19.8959 -1.34725 -20.3103 --19.2489 -1.86451 -19.8101 --19.8442 -2.68179 -19.9903 --20.2627 -3.24886 -20.657 --20.8206 -4.02545 -20.3054 --21.5284 -4.34913 -20.9234 --21.744 -5.30256 -21.2814 --21.2637 -5.49298 -22.1912 --20.9915 -6.22891 -21.6213 --21.2326 -6.62476 -20.7031 --20.4457 -6.48843 -20.1067 --21.3012 -6.19876 -19.5073 --20.7945 -6.82727 -18.9251 --20.1509 -6.07596 -18.816 --19.1103 -5.81893 -18.852 --18.9732 -6.8106 -18.9741 --19.3705 -6.80477 -19.8954 --19.0736 -7.5246 -20.585 --18.2613 -6.99293 -20.5625 --17.6523 -6.42853 -20.0983 --16.6682 -6.14715 -19.8434 --16.2363 -5.27509 -20.1385 --15.4526 -5.95183 -20.1411 --15.6922 -6.92491 -20.3256 --16.2187 -7.5523 -19.7738 --16.3353 -8.45429 -20.1194 --15.8048 -8.60722 -19.3075 --16.0203 -8.95795 -18.4104 --16.8407 -8.51878 -17.9814 --17.5036 -7.9811 -18.462 --17.496 -8.0029 -17.4706 --17.4311 -7.07083 -17.9247 --18.4112 -7.3029 -17.8965 --19.3189 -7.63071 -18.0912 --19.6758 -8.14119 -18.8633 --20.1928 -8.83599 -19.2276 --20.5362 -9.20437 -18.4003 --20.1805 -9.13986 -17.4574 --19.6885 -8.58674 -16.7814 --18.8646 -9.23245 -16.8201 --19.4287 -9.88693 -17.2959 --19.9701 -10.1985 -18.1452 --19.2643 -10.2044 -18.8829 --18.2471 -10.3698 -18.7306 --18.2607 -10.8714 -19.5212 --17.349 -10.9621 -19.0757 --17.1728 -10.5634 -18.2374 --16.6719 -11.1398 -17.6331 --15.8123 -11.2429 -17.1 --15.7415 -10.9853 -16.1459 --15.484 -11.6851 -15.438 --14.8397 -11.2007 -14.8804 --14.5464 -12.1573 -14.7748 --14.0417 -12.7586 -14.1692 --14.8255 -13.3139 -13.8861 --15.0649 -13.0726 -12.9215 --14.855 -12.0544 -13.0681 --15.4749 -11.8212 -13.777 --16.0516 -11.4088 -14.4742 --15.7481 -10.627 -13.913 --15.5705 -9.68453 -14.126 --16.1726 -8.89964 -14.4031 --16.2877 -9.02743 -13.4751 --17.1869 -9.52963 -13.2164 --17.9365 -10.1629 -12.9775 --18.4047 -9.6677 -13.7014 --18.9411 -9.50943 -12.9037 --19.519 -9.88829 -12.166 --19.7399 -10.7148 -12.7402 --18.7289 -11.0874 -12.7754 --18.6871 -11.3638 -13.72 --19.3376 -12.1078 -13.5416 --19.273 -12.7159 -12.8039 --19.3146 -13.4692 -12.1574 --19.6442 -14.2849 -12.7201 --19.1709 -13.6961 -13.4347 --19.4704 -13.5126 -14.3045 --18.7866 -12.7799 -14.2901 --18.9128 -12.538 -15.2347 --19.7194 -11.9218 -15.5499 --19.9831 -11.4333 -14.6918 --20.613 -10.7654 -14.3199 --21.154 -11.5483 -14.4957 --21.6933 -11.096 -15.1568 --22.5262 -10.5591 -15.0268 --23.4114 -10.887 -15.4288 --23.2281 -9.91541 -15.4572 --22.6999 -9.16141 -15.8944 --21.8371 -8.81149 -16.3126 --21.5408 -8.08511 -15.6972 --20.7441 -7.47828 -15.9343 --19.8581 -7.46703 -15.4813 --20.6733 -7.19067 -14.9009 --20.7967 -6.22852 -14.7009 --20.7077 -5.90648 -15.6517 --21.4205 -6.09353 -16.361 --21.8981 -6.54667 -15.7191 --22.8655 -6.34797 -15.5698 --22.6583 -6.70301 -14.6793 --21.9507 -6.98463 -13.9696 --21.9822 -7.96415 -14.3465 --21.329 -8.16353 -13.6978 --21.5021 -8.49353 -12.7555 --21.3996 -8.9939 -11.9011 --22.2397 -9.63093 -11.9988 --21.4169 -10.1236 -11.7952 --21.9706 -10.4008 -12.5368 --22.704 -10.7317 -11.9997 --22.6154 -10.889 -10.9681 --22.7963 -11.4315 -10.0462 --21.8905 -11.1696 -10.1984 --21.4624 -10.6179 -9.50345 --21.8774 -9.85874 -9.03791 --21.5885 -10.1511 -8.1827 --20.6214 -9.94133 -8.52348 --19.7331 -9.66824 -8.24706 --19.6182 -9.73862 -7.21172 --20.6276 -9.68963 -6.88797 --21.5595 -9.44883 -6.98547 --22.321 -9.46369 -6.37868 --22.0547 -9.14463 -5.43934 --21.3056 -8.4327 -5.28123 --21.2383 -7.67902 -4.65624 --22.2536 -7.81655 -4.78297 --22.6313 -7.02882 -5.30861 --23.5355 -6.67441 -5.47654 --23.0509 -6.39894 -6.3581 --22.3575 -6.95432 -6.78931 --23.1048 -6.82569 -7.40569 --23.2714 -6.84595 -8.35925 --22.4942 -7.42973 -8.40523 --22.3994 -8.44993 -8.43815 --21.4312 -8.85421 -8.50906 --20.614 -8.47026 -8.87779 --20.5102 -8.30614 -7.90502 --20.737 -7.40812 -8.28047 --20.6615 -7.2783 -9.26135 --21.1854 -7.4988 -10.0818 --22.1749 -7.44367 -10.1385 --23.1307 -7.16925 -10.4427 --23.3337 -8.15553 -10.3792 --23.3214 -9.06716 -10.0132 --22.9874 -9.00068 -9.09937 --23.6518 -8.46115 -8.56621 --24.6083 -8.33062 -8.71314 --24.5775 -7.91479 -9.68922 --25.5722 -7.97489 -9.72691 --25.2321 -8.79316 -10.1483 --25.3648 -8.14991 -10.93 --25.5658 -7.31133 -11.4628 --25.5347 -6.48646 -10.8568 --26.3106 -7.05684 -10.5244 --27.1367 -6.95092 -10.9095 --28.1496 -6.81726 -10.6646 --28.0746 -6.81552 -11.6432 --28.9204 -6.85949 -12.2347 --29.5158 -7.2523 -12.8443 --28.9312 -7.97094 -13.0851 --28.1701 -8.52727 -13.4394 --28.5058 -8.79837 -14.3177 --27.8614 -9.45037 -14.5719 --27.3165 -8.70347 -14.7457 --26.4687 -9.19666 -14.9029 --25.7113 -9.8013 -14.9567 --25.0643 -10.0408 -15.6758 --25.9843 -10.3556 -16.0932 --26.5471 -11.0352 -15.6051 --27.021 -11.9086 -15.5411 --26.4241 -11.7843 -14.7318 --26.3814 -12.5812 -15.1366 --26.3795 -12.964 -15.9997 --27.2844 -13.4095 -15.7998 --26.9271 -14.3325 -15.7698 --26.8113 -15.2286 -15.3016 --27.2849 -16.0883 -15.543 --28.2021 -16.4883 -15.6375 --28.9118 -15.8527 -15.9496 --29.4905 -15.2836 -15.3033 --30.1107 -15.2602 -14.5336 --29.4673 -15.4286 -13.7832 --30.1651 -16.0709 -13.5739 --30.3851 -16.3978 -12.6314 --31.1881 -15.853 -12.8245 --30.7387 -15.434 -12.0495 --30.337 -15.4006 -11.1233 --29.3268 -15.5851 -11.1554 --28.7961 -15.1826 -11.9621 --29.2135 -14.4098 -12.5822 --28.7026 -14.049 -11.7903 --29.4718 -13.48 -12.1127 --30.3263 -14.0433 -12.2379 --31.0087 -13.3105 -12.562 --31.6191 -13.3637 -11.8237 --31.2445 -12.8141 -11.0915 --31.5801 -11.8785 -11.3345 --30.854 -11.3279 -11.0837 --29.9775 -10.9221 -11.2704 --29.6001 -10.0102 -11.1846 --30.2067 -9.21227 -11.0269 --29.6461 -8.63992 -11.5282 --29.6166 -7.73654 -11.0927 --29.7743 -6.80952 -10.7688 --30.6488 -6.25998 -10.778 --30.0154 -5.45339 -10.6363 --29.3968 -5.19754 -9.86278 --29.0682 -5.79428 -10.6034 --28.5322 -4.99089 -11.0523 --28.0498 -5.41028 -11.9037 --28.1254 -4.4165 -11.9805 --27.5696 -4.33426 -11.134 --26.6569 -4.53009 -10.6749 --26.7596 -3.51603 -10.5138 --26.5177 -2.56203 -10.3385 --26.2748 -2.24011 -9.46086 --26.7587 -2.48875 -8.58775 --26.8949 -1.6167 -8.91524 --27.1001 -0.8727731 -8.26105 --28.1074 -0.9495181 -8.52323 --28.2406 -1.86336 -8.14695 --29.1279 -1.81261 -7.73355 --30.0412 -1.87763 -7.39229 --30.0373 -1.7388 -6.4421 --30.3653 -1.61133 -5.57153 --30.0071 -1.9172 -4.68311 --29.0639 -1.58439 -4.84869 --29.1542 -0.6287571 -5.20699 --29.2945 -1.31735 -5.92125 --28.6951 -0.5709951 -6.29527 --27.7625 -0.6045741 -5.95797 --27.413 -1.32677 -5.32575 --27.3992 -2.23503 -5.52083 --28.2173 -2.67215 -4.96722 --28.1936 -2.80461 -3.98196 --28.1394 -2.86364 -2.98111 --28.998 -2.21684 -3.113 --28.9801 -1.242 -3.07789 --29.2173 -0.3706141 -3.23703 --29.8633 0.3819099 -3.15063 --29.9937 1.08532 -3.89204 --30.9831 0.8294419 -4.2029 --31.265 1.46323 -3.45368 --30.7796 1.99087 -2.73087 --31.2593 2.55891 -3.41221 --31.4322 2.98219 -4.3087 --30.7454 2.85519 -4.96846 --30.6785 1.85998 -5.16275 --30.9227 1.4169 -6.02006 --31.6726 1.76526 -6.55666 --31.2014 1.66531 -7.40743 --30.4989 2.27539 -7.55355 --30.0193 2.82024 -6.87711 --30.4914 2.96861 -6.00159 --30.0943 3.84834 -5.80823 --30.6935 4.0374 -6.61104 --30.7213 4.58755 -7.46554 --31.5334 5.04326 -7.2008 --31.1986 5.99822 -6.85385 --30.3724 6.58032 -7.15795 --29.3241 6.71562 -7.03353 --29.408 5.85247 -6.44407 --30.3863 5.90785 -6.15416 --30.6005 5.27053 -5.28232 --29.6812 5.30733 -4.97177 --29.0914 4.54776 -5.4126 --29.0042 4.16937 -6.32179 --28.1731 3.87765 -5.90747 --27.7317 4.31836 -6.68478 --27.1357 3.83249 -6.05319 --27.1404 4.576 -5.42171 --26.9549 5.35894 -4.83619 --27.1806 5.66493 -3.87852 --27.6136 6.5081 -4.13241 --28.0098 7.12844 -3.52965 --28.9461 6.82156 -3.27433 --29.8856 6.99889 -3.12897 --30.1669 6.13522 -3.59491 --29.5307 5.33017 -3.27734 --29.6611 5.03957 -2.37958 --29.6776 4.34286 -1.72301 --30.4161 4.74929 -1.17822 --30.2437 4.5608 -0.2020719 --30.4996 3.67256 0.2289931 --31.4015 3.32453 -0.1085739 --30.9705 2.40719 -0.2701209 --31.0933 1.89655 0.5632351 --30.9248 2.7794 0.9543811 --30.2854 3.33134 1.45602 --31.2458 3.30808 1.80708 --31.7923 4.19225 1.65734 --31.6637 3.99849 2.6438 --32.4203 4.55891 2.36126 --33.0296 5.21834 2.84718 --33.7203 5.31557 2.09953 --34.082 6.23692 2.01545 --34.0994 6.96242 2.64027 --34.4457 7.61008 1.90678 --34.7105 8.57714 1.82871 --34.0877 8.57656 2.65179 --33.1361 8.84915 2.76592 --32.6935 9.81024 2.84905 --32.0533 9.89021 2.10025 --31.2653 10.2474 1.46962 --30.4456 10.7164 1.50993 --30.2051 11.1495 0.6525131 --29.3704 11.5622 0.3392291 --29.0961 10.8239 1.00084 --28.3957 11.1394 1.64397 --28.0562 10.3644 1.16143 --28.3535 9.57279 0.7101611 --28.0068 9.21822 -0.07460388 --27.4338 10.0198 -0.1065269 --26.5419 9.91777 -0.5325629 --25.691 9.62774 -0.9747849 --26.2127 8.83648 -0.7282919 --25.4684 8.13927 -0.9196469 --26.0544 7.41042 -0.5711419 --26.827 7.32799 -1.18345 --27.3038 8.16727 -0.9387929 --27.8678 7.84512 -1.68295 --27.1304 7.59791 -2.31056 --27.2293 6.70011 -1.90829 --26.8836 6.26997 -1.16938 --27.3018 6.18946 -0.2832759 --28.037 5.51473 -0.5245249 --28.6713 5.05802 0.01936942 --28.0733 4.30539 -0.1666699 --27.1442 4.61702 -0.3198909 --26.636 3.80858 -0.6461129 --25.8913 4.17893 -1.24135 --25.0973 3.59859 -1.56521 --24.1104 3.5199 -1.7993 --23.2448 3.36908 -1.21603 --22.8379 4.22902 -0.9817719 --22.6878 3.69788 -0.1510819 --22.8014 2.73863 -0.4565029 --22.1681 2.19973 -1.03789 --21.6676 1.98279 -1.87826 --20.9072 2.27907 -2.36655 --20.1649 1.88298 -1.77811 --19.8448 2.704 -1.19085 --19.7198 2.22191 -0.2348379 --19.796 1.22464 -0.2212119 --20.2013 0.6173169 -0.8109259 --20.6323 -0.1289691 -1.30149 --21.0184 -0.4701381 -2.13347 --21.9924 -0.8434491 -2.1511 --22.1048 -0.2135791 -2.91264 --22.1701 -1.21145 -3.15308 --21.7026 -2.02938 -2.82892 --21.3088 -1.56701 -3.57607 --21.0296 -2.52795 -3.42786 --20.2286 -2.21479 -2.95583 --19.556 -2.37035 -2.22653 --19.0579 -3.23614 -2.21581 --19.0841 -4.16074 -1.71935 --19.9574 -4.28446 -2.17821 --20.3215 -4.22641 -1.26593 --21.1023 -3.69402 -0.8745999 --21.8834 -3.45944 -0.3635359 --22.5017 -3.22909 0.3661381 --22.4834 -4.09257 0.8167011 --21.5981 -4.01555 0.4854791 --20.9798 -3.4286 1.06973 --20.9027 -3.77549 1.94949 --20.3769 -3.58769 2.72147 --20.1407 -3.17675 3.57266 --21.1653 -3.16098 3.57952 --20.9782 -2.27462 3.1002 --20.3876 -2.62354 2.36148 --19.9176 -2.36989 1.4723 --20.1849 -1.55414 0.9620751 --19.302 -1.78172 0.5458511 --18.925 -1.26163 -0.1415559 --18.9466 -1.24642 -1.08482 --19.0094 -0.2684201 -0.8252439 --19.1629 0.6642769 -1.21335 --18.2093 0.5788819 -1.6319 --17.3051 0.2144849 -1.50494 --17.2411 -0.7821791 -1.29343 --16.7012 -1.1842 -2.05998 --17.5821 -1.80669 -1.90968 --18.4715 -1.3398 -2.19486 --17.7284 -0.9058841 -2.68097 --17.6384 -0.2451301 -3.46826 --16.7318 -0.6941181 -3.14707 --16.4766 0.2915919 -3.27827 --15.7853 0.6780629 -3.82778 --15.8603 1.50818 -3.23086 --15.7459 2.07613 -4.00552 --15.2129 2.88055 -4.0293 --16.0441 3.42008 -3.83803 --16.772 3.26847 -3.2713 --17.0481 3.3034 -2.42299 --17.0217 4.29937 -2.69255 --17.16 5.08265 -3.21892 --16.9064 6.04569 -3.04884 --17.1141 6.52947 -2.23896 --17.9371 6.11381 -2.4441 --18.5396 6.10409 -1.67245 --18.7904 5.13153 -1.43602 --19.742 4.70114 -1.26851 --20.8105 4.81562 -1.37206 --20.279 5.0724 -0.5808339 --20.5637 6.05837 -0.7662359 --21.3611 5.42848 -0.5774549 --21.8805 6.24901 -0.2935159 --21.5627 6.91469 -0.8801249 --21.5593 7.85506 -1.19665 --20.6389 7.51594 -1.36899 --20.6276 8.18319 -2.11801 --19.6517 7.99789 -2.04951 --19.0489 8.05402 -1.33813 --19.2651 8.92334 -0.8753659 --18.5154 8.54232 -0.3257789 --17.6089 8.69884 0.03967842 --17.1403 9.08983 -0.7550079 --16.9603 10.056 -0.5056299 --17.9172 9.68384 -0.5207209 --18.6496 9.94074 -1.12208 --18.4394 10.9176 -0.8580399 --19.0533 10.9664 -1.68637 --19.8101 11.004 -2.38598 --20.7845 10.8062 -2.26362 --21.1219 11.3299 -1.47701 --20.9482 11.3215 -0.4693609 --20.71 10.4062 -0.1801799 --21.0843 10.8111 0.6727461 --21.2236 11.8224 0.7412651 --21.1444 12.7528 1.06079 --20.4231 12.792 1.73867 --20.1444 11.7771 1.78825 --19.2816 11.2987 1.84473 --18.534 11.8831 1.86232 --18.3155 12.4794 1.07325 --18.0288 11.9086 0.2957631 --17.2602 12.0692 -0.3634309 --16.6704 11.4872 -0.9307299 --15.8787 11.5024 -0.3678059 --15.716 11.9939 -1.22029 --16.5647 12.2562 -1.61285 --17.4659 12.5964 -1.28113 --17.1926 13.4919 -1.53298 --18.1052 13.6124 -1.11044 --18.1941 14.6358 -1.13917 --18.2533 15.5634 -1.53841 --18.0922 16.0379 -2.43636 --17.2652 15.9983 -1.85595 --17.0449 16.2069 -0.9480219 --16.7956 15.3813 -0.3285369 --16.9527 15.5094 0.6097181 --17.8223 15.4493 0.1317881 --17.4999 16.3532 0.04342042 --17.6824 17.3436 0.2827471 --16.7608 17.234 0.01388132 --16.0495 16.9437 0.6636041 --15.682 16.9122 1.58698 --16.3201 16.2658 1.97051 --15.4319 16.0201 2.37906 --14.4113 15.856 2.2497 --14.8501 14.9799 1.88701 --14.82 14.3542 1.10958 --15.8331 14.2965 1.22881 --16.2445 14.6604 0.3874261 --15.7014 14.0032 -0.1797499 --15.9365 14.4009 -1.06157 --15.3602 15.0854 -1.49592 --15.1333 14.4738 -2.23859 --15.5205 13.5288 -2.42807 --14.6305 13.1686 -2.75663 --13.9132 13.7144 -2.3277 --13.6816 13.8455 -1.37311 --14.4415 14.2573 -0.8110849 --14.3554 13.5372 -0.1144269 --13.7907 14.1178 0.4429241 --12.7852 14.5064 0.5747421 --12.1441 13.7682 0.3527431 --11.688 14.3426 0.9270441 --10.7748 13.8259 1.12115 --10.5129 13.1552 0.4652031 --9.58483 13.3521 0.6175021 --9.22793 12.95 -0.1874239 --9.7248 12.5731 -0.8963849 --10.2519 13.4463 -1.19285 --10.0482 14.4197 -1.05956 --9.67124 15.204 -1.48424 --8.81303 15.3445 -0.9836239 --8.47364 14.3015 -1.05084 --7.9609 13.7315 -0.4515009 --8.26246 13.3183 -1.25289 --8.69615 12.4512 -1.26109 --9.17819 11.8925 -1.87343 --8.83367 12.6726 -2.30815 --8.9503 11.911 -2.96 --8.6432 11.1689 -2.48141 --8.12989 10.6492 -3.11618 --7.94359 11.6142 -2.99665 --7.97105 12.3899 -3.58071 --6.9739 12.3943 -3.4197 --7.26801 13.2369 -3.23288 --6.97999 13.8113 -4.02231 --6.92008 14.6376 -4.63393 --7.53537 14.9196 -5.27154 --7.96711 14.778 -6.17542 --7.5502 14.2287 -6.80799 --7.33518 13.4245 -7.32246 --7.72637 12.4931 -7.47226 --7.55834 11.5023 -7.51813 --6.70259 11.6085 -7.13863 --6.43262 11.2629 -7.99468 --5.54268 11.481 -7.84943 --4.63687 11.0848 -7.74788 --5.08443 11.2419 -6.86425 --5.66808 10.9941 -6.13455 --6.08059 10.1061 -5.85343 --6.97294 10.5134 -6.19523 --7.94161 10.6136 -6.33629 --8.15188 10.3585 -5.36927 --8.0922 11.3303 -5.52918 --8.99209 11.5979 -5.87808 --9.92692 11.4512 -5.55554 --10.0826 10.6945 -4.95855 --10.7765 11.4011 -4.90368 --11.0336 11.9935 -4.16836 --10.5407 12.0206 -3.33543 --10.6531 12.8807 -2.8566 --11.5429 13.1202 -2.39561 --10.9235 12.5665 -1.85422 --10.5163 11.7391 -1.40956 --9.90543 11.6102 -0.6683979 --10.4072 11.2504 0.1456631 --9.52574 11.5282 0.5662861 --8.64568 11.8081 1.00293 --7.88446 11.1769 1.1497 --8.08232 11.3108 0.1626221 --7.18421 11.8266 0.2426351 --7.24949 11.9894 -0.7513159 --6.23237 11.9241 -0.8250039 --6.07268 12.3117 0.1014301 --6.04794 12.3869 1.09335 --5.96504 12.096 2.09355 --5.07852 11.6742 2.45208 --4.28603 11.9515 1.80456 --3.70267 12.4549 2.32543 --2.9301 12.3577 2.87326 --3.44473 13.1004 3.40741 --3.3138 12.1803 3.79436 --2.49269 12.6558 4.13073 --2.41089 13.5245 3.73553 --2.11934 13.8182 2.85582 --2.52019 13.2114 2.11124 --3.41986 13.4062 1.87485 --3.06329 13.1585 0.8697611 --3.9995 13.127 0.9693941 --4.01159 12.9922 -0.01687538 --4.22385 12.125 -0.4425529 --4.97685 11.5549 -0.1999029 --5.58967 10.8626 0.07890422 --6.32567 10.1799 0.3687851 --5.62422 9.84683 0.9763101 --4.81629 9.39697 0.9220071 --4.34857 8.75712 1.45231 --4.49018 8.25065 2.30054 --5.17739 7.53342 2.19485 --5.09667 6.56227 2.37434 --4.43315 5.95 2.87397 --3.66142 5.39437 2.5951 --3.35113 6.23413 3.18002 --3.78233 6.9097 2.63368 --3.16112 7.67651 2.33602 --3.17266 7.12838 1.49074 --2.25199 6.82092 1.68701 --1.63599 7.4975 2.0485 --1.14057 8.06816 2.66717 --0.943707 8.9445 3.19157 --0.523393 9.35895 3.95422 -0.138476 9.32388 3.25424 --0.05106053 10.2376 3.15861 --0.467388 10.297 2.28472 --1.42604 9.9836 2.64822 --1.39225 9.2125 2.03716 --1.23256 9.89802 1.34827 --0.630075 9.0384 1.38951 --0.197621 9.19934 0.5481991 -0.500995 9.9097 0.3311831 --0.397804 10.3138 0.5555881 --0.675505 9.67825 -0.1702709 --0.16712 9.78222 -1.01045 --0.998259 10.3881 -1.11482 --0.920501 9.51418 -1.60061 --1.94264 9.80166 -1.74254 --1.53469 10.3641 -2.44212 --0.638988 10.7543 -2.23828 -0.201844 10.516 -1.68564 -0.920025 10.2319 -2.38864 -0.455667 10.9991 -2.72112 -0.713161 11.6499 -2.10046 -0.20238 11.9739 -1.28766 -0.104399 12.4805 -2.11503 --0.966686 12.3141 -2.17912 --1.30656 12.0716 -1.26156 --2.21253 11.7856 -1.00077 --2.9335 11.6857 -0.3863279 --3.42189 10.8942 0.01735252 --3.58319 10.5459 0.9069221 --3.7044 9.81174 1.57709 --3.77973 9.82443 2.53497 --2.851 10.0689 2.76759 --3.45555 10.2612 3.58823 --3.80881 10.677 4.36824 --4.72178 10.941 4.78482 --5.47869 11.5377 4.47239 --6.27348 10.9534 4.1462 --6.48655 11.9178 3.99542 --6.68245 11.3893 4.86824 --6.87899 10.4046 5.04178 --5.95811 10.1154 5.02666 --5.40197 9.78294 4.21071 --6.23872 9.27706 4.1427 --6.47454 8.90191 5.08216 --7.33146 9.46059 4.90457 --8.01468 9.64651 4.15873 --8.71902 9.77885 3.50136 --8.55013 10.6763 2.98853 --9.22218 10.0502 2.72389 --9.76576 10.0101 3.54905 --9.97286 9.81187 4.45313 --10.0048 8.82189 4.53382 --9.57051 8.84071 5.37917 --10.1784 8.84496 6.16289 --10.9031 8.34496 5.79803 --10.6291 7.73698 4.9934 --11.1001 8.62124 4.84391 --11.3462 9.59761 4.85225 --12.3006 9.4094 4.76371 --12.368 10.3994 4.47912 --12.9045 11.0341 5.04143 --13.8185 10.9916 4.74271 --14.3137 11.8216 4.57588 --13.684 12.3941 5.18215 --12.8348 12.7914 5.1748 --12.9865 13.0324 4.18706 --12.0703 13.0901 3.76773 --11.2235 13.4361 3.3739 --11.4317 12.8314 2.6787 --10.725 12.2958 3.06964 --9.73611 12.1754 2.92224 --9.01346 12.4598 2.34894 --8.02159 12.4875 2.18395 --8.3084 13.3929 1.79439 --9.24621 13.4545 2.06868 --9.6104 13.817 2.84323 --10.0444 14.681 2.5691 --10.9408 14.9928 2.54087 --11.5731 14.4263 3.05553 --11.9768 13.7978 2.45794 --12.4719 13.2176 1.90662 --13.3796 12.8951 1.70326 --12.6242 12.3082 1.4323 --12.1726 12.4424 0.5583481 --12.3234 11.748 -0.1147959 --12.1942 11.1321 0.6867151 --11.9975 10.255 0.3832561 --12.1673 9.48752 -0.1296799 --13.0863 9.48525 0.3646551 --13.9329 9.72229 0.8873411 --14.1335 10.2679 1.66849 --14.2663 9.93174 2.56269 --13.6847 10.5604 3.00298 --12.7353 10.6814 2.72734 --12.0841 9.79055 2.91298 --11.3355 9.1549 3.10306 --10.7172 8.46235 3.25931 --9.90185 8.15034 2.906 --8.90559 7.98822 2.96448 --7.96794 7.53812 2.77102 --7.30097 7.35341 2.03517 --7.57113 7.58127 1.05269 --6.74494 8.11031 1.31677 --6.57104 8.04585 0.3078651 --6.37077 7.04694 0.5089971 --5.86905 6.21928 0.1842841 --5.30755 6.53274 0.9329481 --4.61563 5.98095 0.4786811 --4.55691 5.57784 1.30031 --5.31523 5.45697 1.92796 --5.09862 4.56844 1.45552 --6.0706 4.85085 1.45983 --6.24581 4.26475 2.12015 --7.14755 4.03691 2.60903 --7.1344 3.34806 3.36118 --6.56381 2.53526 3.52535 --6.21593 2.84172 4.4143 --7.18956 3.08622 4.39527 --6.88186 2.7388 5.30143 --7.73512 2.74521 5.7571 --7.81345 2.09734 6.42784 --7.86885 2.61475 7.29455 --7.21275 3.03907 6.75808 --8.02079 3.65558 6.48527 --8.32819 4.38637 7.05048 --7.75026 5.17371 7.37131 --8.53449 5.56414 6.86893 --9.0705 6.18399 6.29359 --9.18547 6.43868 5.37004 --10.1309 6.48984 4.95711 --10.075 5.90596 4.10914 --10.6033 5.77477 3.25684 --11.4915 5.55095 2.86298 --11.4826 6.45165 2.88619 --12.2541 6.34856 2.26058 --12.2754 7.03374 1.60909 --13.2132 7.28498 1.75081 --13.3072 6.29687 1.88416 --14.0779 6.51246 1.24737 --14.5756 5.70484 1.49237 --15.3501 6.2173 1.3197 --14.995 5.94206 0.4915031 --14.9704 4.97506 0.2475571 --14.8867 4.56571 1.12685 --14.2057 3.94815 1.39534 --13.5976 4.61955 1.78343 --13.2819 5.16665 2.51034 --14.2472 5.23537 2.79707 --14.5276 5.70771 3.56346 --13.9732 6.28778 2.90681 --13.0992 6.37031 3.40807 --13.0369 7.09092 4.03209 --13.9625 7.06634 4.32548 --14.5867 7.38594 3.6435 --14.5972 8.02436 4.4101 --15.0789 7.18608 4.62539 --15.5561 6.9159 5.49025 --15.8378 7.82428 5.45924 --16.6706 8.33384 5.64102 --17.2497 8.3269 6.36882 --17.1027 7.29181 6.47553 --17.7013 6.74951 5.9415 --18.2728 5.92549 6.08992 --19.2061 5.69527 5.75225 --19.6374 6.25774 5.06496 --20.5171 5.82204 5.06144 --20.8216 4.94617 5.40425 --20.5654 3.93048 5.26953 --20.0435 3.55313 4.5116 --19.3611 3.88696 3.78356 --20.2026 3.96436 3.1476 --20.2079 4.27207 2.14607 --19.1955 4.02096 2.10907 --19.7393 3.77259 1.3072 --20.7043 3.54772 1.53513 --21.217 4.03306 2.22869 --22.1289 4.3414 2.40394 --21.9778 4.90727 1.56706 --22.188 5.94708 1.6234 --21.5108 5.90785 0.9634941 --21.4206 6.92175 0.7647941 --21.8534 7.82194 0.6919021 --21.4815 8.44541 1.34703 --22.1249 9.13216 1.70433 --22.7184 8.39449 1.3292 --23.5615 8.67741 1.67106 --23.3613 8.92225 0.7785541 --23.4343 9.47534 0.00611501 --24.1533 10.0249 -0.4309919 --24.6745 9.84649 -1.23417 --24.0765 10.5448 -1.45637 --24.4249 11.1656 -2.01152 --25.2414 10.9792 -1.40261 --25.264 10.9464 -2.40865 --25.9243 11.0546 -3.19418 --25.9954 12.0134 -3.6847 --25.7067 11.7566 -4.58168 --25.1907 12.5228 -4.92813 --25.7522 12.8548 -5.57639 --26.0894 13.7857 -5.23268 --26.5051 14.687 -5.24813 --27.1509 14.7527 -4.50099 --27.7902 14.0271 -4.71781 --28.4303 13.3382 -4.33287 --28.0604 12.425 -4.41673 --28.4449 11.5527 -4.20893 --29.0154 10.7519 -4.1762 --29.7423 10.3848 -3.62626 --29.0771 9.75529 -3.25114 --28.4636 9.27589 -3.7982 --28.4591 9.67989 -4.72995 --27.4414 9.93293 -4.63921 --26.7807 9.54115 -3.95225 --27.0007 10.2308 -3.35417 --26.376 9.9653 -2.60018 --25.4792 9.49245 -2.891 --25.7081 8.57828 -2.63242 --25.4127 7.63445 -2.56097 --24.9193 6.77252 -2.79835 --25.4321 6.87424 -3.62368 --24.9536 6.91598 -4.53667 --25.0949 7.85999 -4.18235 --24.2061 8.35185 -4.33653 --24.0745 8.13365 -3.37724 --23.7429 9.05495 -3.05611 --23.1248 9.58027 -2.4885 --23.0958 9.76121 -3.53426 --23.8494 10.2686 -3.91943 --24.7529 10.0975 -4.39213 --24.8167 9.38584 -5.07081 --24.698 9.24554 -6.08325 --23.6644 9.51425 -5.94048 --23.0072 10.2645 -6.1597 --23.2065 10.8913 -5.3995 --22.9179 11.8494 -5.22899 --22.3579 12.1402 -4.40142 --21.4823 11.9736 -4.64223 --21.6031 11.268 -3.95098 --22.1912 11.307 -3.09905 --21.5912 11.8038 -2.47285 --20.8983 12.4775 -2.24333 --20.7455 13.487 -2.37434 --20.4978 13.1116 -1.3607 --19.4836 13.0475 -1.3608 --20.0161 12.7365 -0.5693919 --20.6945 13.2766 0.1004561 --19.9245 13.9454 0.2604961 --19.7888 14.8249 0.6497151 --20.4989 15.3962 1.09294 --20.0252 15.9409 0.4255741 --20.2931 16.2695 -0.4628899 --20.5303 17.1873 -0.3129499 --21.2132 17.3517 -0.9993989 --21.635 17.9579 -1.60284 --22.345 17.2457 -1.3793 --22.4363 17.5096 -2.34842 --22.9029 18.0194 -3.03752 --22.9782 18.6477 -2.34791 --23.9264 18.5152 -2.34204 --24.8799 18.1686 -2.28032 --25.1159 18.438 -1.36889 --25.6816 17.6265 -1.35756 --26.686 17.5441 -1.22327 --27.6022 17.3711 -1.52778 --28.2623 16.8536 -1.01294 --28.8707 17.6311 -1.08455 --29.0186 17.534 -2.06428 --28.7005 17.1163 -2.93395 --28.341 18.0369 -2.89251 --27.5369 18.6453 -3.01391 --26.7437 19.1256 -3.33699 --27.0187 20.0332 -3.47797 --26.7939 20.9147 -3.97372 --26.0383 20.5862 -4.57897 --26.8681 19.9342 -4.52514 --27.51 20.4963 -5.08118 --27.4115 21.4944 -4.88639 --27.7067 21.5405 -5.86996 --26.8684 21.4281 -6.42509 --26.7811 22.3653 -6.87811 --26.2189 22.7569 -6.2405 --25.3222 22.2456 -6.40021 --25.515 21.9115 -5.45219 --25.9744 21.1455 -5.87659 --26.3903 20.289 -5.39732 --27.0644 19.5572 -5.69625 --27.2876 20.3711 -6.25585 --27.7232 19.5245 -6.62455 --27.7964 18.5628 -6.37271 --28.3471 17.6687 -6.37751 --29.303 17.357 -6.44679 --30.1309 16.9536 -6.76217 --30.1254 17.9 -6.42401 --30.7841 17.9221 -7.20002 --29.9551 17.6989 -7.75358 --29.7982 17.8458 -8.741 --29.5214 18.8017 -9.10434 --29.4123 19.7589 -8.8559 --28.8884 20.1688 -8.06704 --28.736 19.3068 -7.59176 --27.9653 19.0667 -8.15494 --27.3462 18.3032 -8.3921 --27.8302 17.4797 -8.01376 --26.9467 17.3914 -7.60317 --26.2098 16.9931 -8.22539 --26.6651 16.121 -8.0663 --26.7417 15.4237 -7.38068 --26.722 14.55 -6.91892 --27.7368 14.6145 -7.08392 --27.6104 14.1286 -7.8877 --28.1844 14.396 -8.62136 --27.3314 13.9342 -8.99711 --27.5018 14.8597 -9.38141 --28.3075 15.4985 -9.42071 --28.0202 16.4543 -9.64596 --28.023 17.3171 -10.0645 --27.3961 17.3127 -10.8207 --26.8957 16.5055 -10.3832 --26.5178 15.6131 -10.1191 --25.6128 15.376 -10.296 --25.821 15.4928 -11.2368 --25.8867 15.3031 -12.2493 --26.4143 14.5556 -12.7675 --27.1197 13.8768 -12.4997 --26.8881 13.941 -11.5509 --27.6134 14.571 -11.3278 --27.5728 15.5615 -11.3652 --28.1417 15.4807 -12.1459 --27.2196 15.3352 -12.4232 --27.166 16.1074 -13.0977 --27.0001 15.6534 -13.9297 --26.0174 15.5751 -13.7829 --25.4125 16.0702 -13.1154 --24.4883 16.3813 -12.8174 --24.979 16.9082 -13.4551 --25.1786 17.3334 -12.5648 --24.5872 18.1127 -12.3256 --24.7345 17.5935 -11.4842 --25.1916 18.3315 -10.9061 --24.2546 18.1091 -10.6206 --23.9746 17.166 -10.1873 --23.5969 16.2928 -10.4534 --23.2238 15.6065 -9.86313 --23.9213 15.1287 -9.38353 --23.5008 15.4741 -8.52616 --24.0574 16.047 -7.88749 --24.5925 15.2674 -7.78446 --24.467 14.2615 -7.53027 --23.6026 13.9358 -7.11613 --23.9574 13.0749 -7.59301 --23.0137 13.2333 -7.47244 --22.5732 12.6268 -8.17045 --21.908 12.4193 -7.50595 --21.9517 13.3393 -7.13227 --21.0207 13.0488 -7.33482 --21.0543 13.6763 -6.55256 --21.3229 14.1302 -5.70845 --21.2057 15.0624 -5.64534 --20.5999 14.8946 -4.87888 --19.8768 14.3607 -5.32014 --19.4179 14.9342 -6.00833 --18.9145 14.9028 -6.83603 --17.8739 14.9603 -6.99184 --17.0261 14.6461 -7.38891 --16.3469 14.168 -6.74876 --16.8644 13.9676 -5.93651 --17.7358 14.5059 -6.02316 --17.241 15.2846 -5.66113 --17.8274 15.4273 -4.91201 --17.2299 16.1751 -4.79841 --16.5514 16.8753 -5.12565 --15.6381 16.7989 -5.55577 --15.2454 17.646 -5.95612 --15.7655 18.472 -5.62926 --16.0848 17.8171 -4.96095 --16.6722 18.2557 -4.21249 --15.8172 18.8644 -4.02979 --15.7053 19.2636 -3.11082 --16.4607 19.6336 -2.54308 --16.6843 19.2845 -1.61709 --17.5188 19.2527 -1.11674 --17.1611 19.6001 -0.2062059 --16.4673 20.2052 0.01248912 --16.0251 20.6163 -0.8306439 --16.7016 21.3305 -0.5482349 --16.0445 21.7821 0.01715102 --15.9532 22.8407 -0.1033119 --15.3756 23.1929 -0.8594319 --15.7502 23.4709 -1.73059 --14.9266 23.5486 -2.25361 --15.1675 23.8165 -3.14253 --15.3971 24.3701 -3.8841 --16.3762 24.4987 -3.86461 --16.9741 24.3455 -3.03916 --17.0251 23.4715 -2.47501 --17.3392 22.5895 -2.69669 --16.5629 22.1377 -3.12897 --16.5372 21.213 -3.1029 --16.3689 20.98 -4.02925 --16.7142 20.6673 -4.92059 --16.2397 19.7774 -5.27578 --16.9679 20.0878 -5.97046 --17.5778 20.8576 -5.74077 --17.8773 19.9557 -5.3316 --18.2429 20.572 -4.61467 --19.0427 20.3617 -5.08644 --19.1487 19.5967 -5.78266 --19.8825 19.5655 -5.11237 --20.4516 18.9214 -4.46369 --21.0092 18.6274 -3.707 --20.7478 19.6016 -3.81768 --21.3001 20.43 -3.74292 --21.5369 21.2207 -4.33797 --21.2397 22.0744 -3.89597 --21.3034 22.1076 -2.89636 --20.6904 21.391 -2.55568 --20.9453 21.1632 -1.68586 --21.403 20.4856 -1.13059 --20.7789 20.9561 -0.5809199 --20.0703 21.0208 0.1376621 --20.1104 21.8118 0.6710611 --20.7752 22.5307 0.7884611 --20.6672 22.9081 -0.1135699 --19.668 22.9947 -0.2081149 --19.7263 23.8208 -0.7670739 --18.8289 23.6473 -1.25644 --18.5119 22.7366 -1.20805 --18.9605 21.9497 -1.55782 --19.6015 22.6866 -1.28634 --18.9762 22.7279 -2.07258 --19.2685 23.5262 -2.60457 --18.298 23.4183 -2.70705 --17.9895 24.3855 -2.41585 --17.8728 24.577 -1.42913 --18.6013 24.9962 -1.8703 --18.0303 25.6088 -2.42637 --18.2884 26.1646 -1.66489 --18.4338 26.4762 -0.7297489 --18.7918 27.1729 -0.1346639 --19.6605 26.7341 -0.1613239 --19.3557 27.0029 0.7704401 --20.21 26.6679 1.18685 --21.15 26.7924 1.48169 --21.7172 27.1796 0.6030421 --22.1836 26.9732 -0.3066439 --22.8798 26.3874 -0.5714109 --22.7718 26.815 -1.49837 --23.026 26.4193 -2.43276 --22.6467 25.5935 -2.85048 --23.1096 25.418 -3.68799 --22.2579 25.5119 -4.32435 --21.8873 24.6409 -4.08363 --21.0859 25.0882 -4.4901 --20.6818 24.5285 -5.23986 --20.9811 23.8705 -4.53334 --21.4337 23.0242 -4.46447 --22.2123 22.4424 -4.48595 --22.8078 22.4809 -5.31991 --23.7937 22.3538 -5.47556 --23.722 23.1272 -4.85262 --23.6754 22.8204 -3.92155 --24.6307 22.6493 -4.1455 --24.4383 21.6185 -4.31251 --23.7152 21.6416 -3.68451 --23.2661 20.8856 -4.11076 --22.7141 20.4717 -4.86332 --22.4343 19.9218 -5.62493 --22.9901 19.1984 -5.9858 --23.9717 19.2426 -5.53193 --24.9155 19.2299 -5.23056 --25.0507 18.7312 -6.11858 --24.579 18.4944 -6.97285 --24.5991 18.0484 -7.83112 --23.8067 17.5434 -8.10522 --23.5594 17.1253 -8.98751 --22.5861 17.1319 -8.91695 --21.8963 17.0707 -9.6787 --21.7816 16.3642 -8.97446 --20.9871 16.1606 -8.38401 --21.1544 16.0508 -7.41429 --21.6133 16.7622 -6.8895 --22.0408 16.3322 -6.05358 --22.048 16.0566 -5.13699 --21.746 16.6427 -4.39104 --21.6479 17.3945 -4.97827 --20.7598 17.4419 -5.3567 --19.7022 17.6338 -5.4915 --19.358 16.7486 -5.20092 --19.0001 17.3722 -4.4464 --18.5239 16.9971 -3.64144 --18.3371 17.6953 -2.96645 --18.1286 18.6031 -2.54258 --17.6263 18.2391 -3.30854 --16.7564 17.992 -2.97297 --16.6435 17.1642 -3.34224 --15.7174 17.1278 -3.65505 --15.0994 17.0504 -2.98033 --14.7041 16.1081 -2.85636 --14.3438 16.1251 -3.78035 --14.1199 15.2154 -3.69995 --13.7826 15.7556 -4.51511 --13.9673 15.1114 -5.24786 --14.6043 14.9931 -5.94873 --14.2982 14.5801 -6.84063 --13.2676 14.6621 -6.79775 --12.9044 15.3863 -6.10743 --12.8412 15.7652 -7.03848 --13.8179 15.8575 -7.30687 --14.6254 15.3766 -7.49181 --14.0515 15.7506 -8.26604 --13.1913 15.2587 -7.93743 --13.0704 14.2871 -7.83145 --13.4616 13.5505 -7.36322 --14.4263 13.5978 -7.71193 --15.2117 12.9592 -7.53646 --15.2397 13.0261 -8.54244 --16.0182 13.1075 -9.2427 --16.1446 14.0665 -9.00893 --16.9791 14.482 -9.39612 --16.8226 15.5094 -9.50108 --15.8756 15.0612 -9.68899 --15.0489 15.0452 -9.02557 --15.5042 15.9341 -8.90758 --16.3871 16.5033 -8.84363 --16.003 17.2138 -8.26638 --15.6224 16.3936 -7.92268 --16.1133 16.8876 -7.26187 --15.2117 16.7569 -6.78134 --15.1319 17.7027 -7.0536 --14.6081 18.31 -7.79186 --14.4354 18.6365 -8.72435 --14.8117 19.4652 -9.13069 --14.2434 19.6458 -9.92601 --14.3219 20.6575 -9.82757 --14.0835 20.7993 -8.88724 --13.9327 21.5816 -8.16964 --14.5541 22.3568 -8.0369 --14.658 21.8784 -7.19371 --13.8476 22.4947 -7.28846 --13.1293 22.6959 -7.94246 --13.057 22.746 -8.9288 --12.5474 22.2119 -9.64743 --11.9517 21.4312 -9.92479 --11.8358 20.5409 -10.4811 --11.1943 20.6219 -9.7497 --11.0011 19.6637 -9.68605 --10.8798 19.5162 -8.71657 --9.95039 19.7176 -9.1393 --10.2293 18.7665 -8.912 --10.8756 18.312 -8.23975 --10.1583 18.5922 -7.59052 --10.8745 19.199 -7.70335 --11.6061 19.0235 -7.09627 --12.6042 18.9966 -7.07194 --13.2068 19.7329 -6.76609 --13.8319 19.9756 -6.00731 --13.0161 20.5032 -5.88355 --12.162 20.6556 -5.40298 --11.762 20.438 -4.4417 --12.5221 19.7955 -4.65782 --11.8664 18.9985 -4.80993 --12.6669 18.587 -4.27297 --12.8672 17.6193 -4.18833 --12.5956 17.1176 -5.08277 --12.203 16.6142 -5.82685 --11.8658 16.0125 -6.47415 --11.5753 15.1731 -6.92645 --11.7731 14.2235 -6.50198 --10.8166 14.0033 -6.66395 --11.0973 13.0481 -6.76632 --11.5704 12.8444 -7.62293 --12.4405 12.5718 -8.08819 --13.0043 11.7803 -8.32459 --12.2821 11.4216 -7.85587 --11.7687 10.8394 -7.25353 --12.0237 9.86803 -7.11939 --11.4147 9.07688 -7.09721 --10.7838 8.42444 -7.56457 --10.4151 9.33783 -7.81213 --10.2323 9.55048 -8.70194 --10.2827 9.72087 -9.69325 --10.1096 9.08885 -10.4169 --10.4883 8.16055 -10.8184 --11.1526 8.5869 -11.4837 --11.4697 9.437 -11.9319 --10.5088 9.46296 -12.2137 --10.3767 10.3581 -12.4279 --10.717 10.4237 -11.4621 --9.92347 9.8409 -11.3087 --9.55691 10.5271 -10.6603 --9.10839 10.4323 -11.559 --9.51822 11.2099 -12.0698 --9.14634 12.0132 -12.5399 --9.54934 12.9027 -12.539 --9.66126 13.6804 -11.8361 --10.0432 13.9192 -10.9677 --9.175 14.2558 -10.7876 --8.59333 13.7615 -11.4713 --8.20658 14.0092 -12.3009 --8.06564 14.7557 -12.9799 --7.11117 14.9362 -13.1302 --7.11484 15.1668 -14.1267 --6.97525 16.1983 -14.0874 --7.0651 16.5686 -13.1717 --6.69712 17.3523 -13.6148 --7.50508 17.6674 -14.117 --7.74932 18.1271 -14.976 --8.35414 18.2974 -14.1387 --8.25858 19.2334 -14.2412 --9.07242 19.338 -14.8047 --8.58525 19.2552 -15.6633 --8.26629 18.9956 -16.4798 --8.567 18.3031 -15.8747 --8.80339 17.4338 -15.4985 --9.75833 17.4694 -15.3841 --9.36128 18.038 -14.7831 --9.38421 17.9274 -13.7571 --10.2788 18.3979 -13.5484 --10.4713 19.1978 -14.0332 --10.7922 19.6961 -13.2183 --10.4323 20.5686 -12.7662 --9.98238 21.4728 -12.8408 --10.8427 21.9415 -12.5412 --10.7064 22.2364 -11.5734 --11.1324 22.7032 -10.7209 --11.2107 22.602 -9.79223 --10.8261 22.5659 -8.82583 --10.7865 23.448 -9.26818 --10.9828 24.2413 -8.69829 --10.7695 24.751 -9.53057 --11.1639 25.5935 -9.87693 --12.0084 25.2794 -9.45695 --12.4676 26.1394 -9.47454 --11.9253 26.9795 -9.62965 --11.524 26.9126 -8.74322 --11.8592 27.2985 -7.83905 --11.9028 26.5259 -7.26944 --12.252 27.0343 -6.54635 --11.925 26.5711 -5.6401 --12.2735 25.8123 -5.0876 --13.333 25.7755 -5.06785 --13.7338 26.607 -5.48742 --14.7046 26.7939 -5.22075 --14.3441 27.562 -5.71306 --13.6199 28.1988 -6.09958 --13.3856 28.7841 -6.96125 --14.2819 29.133 -6.5449 --14.7881 29.652 -5.83118 --15.6172 30.0653 -6.4153 --16.2761 29.4167 -6.45287 --16.6825 28.7275 -7.11752 --16.2966 29.3663 -7.89281 --16.2354 30.347 -8.08221 --16.162 31.3416 -7.96722 --16.496 32.2945 -7.83379 --17.3264 32.7154 -7.49502 --17.376 33.5557 -6.93961 --16.8113 33.4386 -6.131 --16.6423 34.0835 -5.41732 --17.1078 33.7308 -4.60787 --17.2842 33.2345 -3.73526 --17.389 32.3048 -3.30006 --17.2397 31.3122 -3.03504 --17.2413 30.3907 -2.64011 --16.5926 30.5672 -1.84714 --17.1896 29.7607 -1.8157 --18.014 29.7614 -1.14562 --18.681 29.249 -0.6840529 --18.3695 28.7979 0.06311092 --17.6367 28.4164 0.6559691 --16.908 27.8562 0.5002321 --16.2512 27.201 0.1392141 --16.6372 26.3252 -0.06420178 --16.652 25.368 0.02058682 --17.3823 24.8261 0.5051641 --17.3577 25.0698 1.51502 --16.5441 25.6434 1.39153 --17.3571 26.1716 1.52671 --17.7062 26.103 2.48346 --18.6487 25.8187 2.64534 --18.5521 26.5653 3.28568 --18.7105 27.0455 4.20171 --19.0466 27.1345 5.1465 --18.4477 26.9204 5.96335 --19.0226 26.1491 6.07822 --18.1793 25.661 5.89391 --17.7542 24.9286 5.33894 --18.1528 24.0702 4.99122 --18.3483 23.5145 5.7748 --18.8345 23.3947 4.87795 --19.5237 23.134 4.29889 --20.4269 23.453 4.74846 --20.1462 22.6607 5.24028 --19.4624 21.9384 5.24599 --19.0344 21.2359 4.61044 --20.0438 21.0211 4.55822 --20.1742 20.0749 4.17666 --20.4124 19.7532 3.18938 --20.3512 19.3684 2.24161 --21.3262 18.9831 2.05396 --21.6577 18.307 2.78903 --21.5432 17.4068 2.42242 --21.2031 16.6442 1.86931 --20.5953 16.1426 2.47472 --20.1128 15.504 3.10221 --20.3034 15.197 2.206 --21.0868 14.629 1.82692 --21.0724 13.6413 2.02561 --21.9421 13.0763 1.78881 --22.791 12.7266 1.42813 --22.5489 13.4204 0.6979761 --22.5506 14.2707 0.1187931 --22.1294 13.7172 -0.6949629 --22.9919 13.9234 -1.19015 --22.9355 13.2158 -1.9869 --22.2086 13.4632 -2.70325 --21.7641 12.721 -3.21914 --20.7798 12.7595 -3.30013 --20.0417 12.1756 -3.70404 --19.1801 12.2047 -4.16001 --19.3397 12.8714 -4.84206 --19.2116 13.3472 -3.97008 --19.5105 13.0772 -3.08555 --19.0718 13.7675 -2.67992 --18.5089 14.467 -2.08895 --17.8783 13.8531 -2.57886 --18.3345 14.5452 -3.08744 --18.7348 15.4627 -3.22581 --18.7648 15.7871 -4.15544 --19.5971 15.9225 -3.62038 --20.2367 15.5349 -2.94867 --21.0424 15.6029 -3.49934 --21.6068 14.8602 -3.78628 --22.3289 15.1333 -4.47335 --23.1823 15.2826 -4.89144 --23.6153 14.5158 -4.47327 --23.8314 14.3534 -3.56048 --23.9375 15.2556 -3.09432 --24.3321 15.1762 -2.18371 --24.3672 14.3527 -1.58666 --25.3829 14.2879 -1.74964 --25.4659 14.88 -0.8951009 --26.4019 15.0424 -1.02345 --26.9868 14.4858 -0.4004199 --26.8645 15.1911 0.2493721 --26.3235 16.1093 0.05859842 --25.8803 16.7781 0.6393861 --24.9563 16.7921 0.1940701 --25.0996 16.336 -0.6739559 --24.3119 15.9334 -1.15031 --23.8007 15.2316 -0.6280479 --23.9731 15.457 0.4097101 --24.8664 15.4716 0.8796181 --24.4259 15.0229 1.67603 --23.4921 15.1887 1.42569 --23.7305 14.4782 0.7219131 --23.3165 13.9112 1.47808 --23.0257 13.2915 2.2304 --23.7803 12.689 2.12232 --24.4119 12.0659 2.53427 --24.4182 12.6209 3.34293 --24.929 13.3691 3.80775 --25.4502 12.7318 4.36143 --25.8512 12.1795 3.5829 --25.4181 11.5205 4.12192 --25.9251 10.6986 4.04321 --25.5372 9.77124 4.11009 --26.2067 9.07982 4.1542 --25.8902 8.35485 4.69446 --25.8821 8.37883 5.70717 --25.8623 7.53283 6.09484 --25.4361 6.86883 6.53671 --24.6974 6.41979 7.02067 --23.87 6.99475 6.91026 --24.5923 7.64689 6.62208 --24.1649 8.35164 6.10246 --24.6057 9.09881 6.64412 --24.9698 8.72895 7.5009 --25.7037 8.18324 7.88089 --26.3136 7.59813 7.27027 --26.3394 7.03508 8.04692 --26.3881 6.98992 9.08835 --25.9138 6.30267 9.57715 --25.8675 6.16545 10.5967 --26.8063 6.26047 11.0099 --26.5931 6.72695 11.8751 --26.2179 6.90624 12.7936 --25.2465 7.30104 13.047 --25.3453 8.31153 13.0389 --24.4232 7.91459 13.0303 --23.5092 7.90253 13.441 --22.9538 7.01711 13.4548 --22.5872 7.50755 12.74 --22.2369 6.61735 12.8477 --22.0503 6.73493 11.8281 --21.1634 6.85252 12.1497 --20.7454 7.38964 12.8935 --21.2391 7.74877 13.665 --20.7657 8.39357 14.2468 --20.1741 9.05597 13.7239 --19.2922 8.84092 13.4098 --18.2613 8.61245 13.4545 --17.3313 8.55324 13.5982 --16.6771 8.09225 14.1734 --16.8749 7.73011 15.0722 --16.5035 8.40804 15.7052 --17.056 7.85696 16.3241 --17.6971 7.29309 15.6975 --17.7149 6.31407 16.0366 --16.7403 6.38689 15.7 --15.9321 6.98927 15.6124 --16.0061 7.2112 16.6014 --15.8823 8.17923 16.8116 --15.4259 8.92929 17.3787 --14.8292 8.17444 17.7032 --14.2908 8.94322 17.4345 --14.6731 9.68795 18.0248 --15.5522 10.0785 17.6068 --15.6188 10.6859 18.4356 --16.6778 10.5182 18.1317 --17.4791 10.0612 17.7321 --17.8909 10.0258 16.8248 --17.921 8.96961 16.7033 --18.555 8.81343 17.3734 --19.2952 8.17621 17.3342 --19.7527 8.20408 16.4947 --20.3705 7.45076 16.1219 --21.2392 7.09885 15.9159 --21.7878 6.86279 15.1013 --21.2726 6.03072 14.8494 --20.919 5.1416 14.4963 --20.5809 4.2791 14.1208 --19.6913 4.65939 13.9702 --19.9715 5.59716 13.9264 --19.9639 6.43817 13.368 --19.2771 6.75974 13.9822 --18.9022 7.18996 13.1897 --19.5178 6.95863 12.452 --19.8683 7.78218 11.9343 --19.8172 8.63613 11.4069 --20.1734 9.56271 11.4286 --19.5866 10.4284 11.5639 --18.8471 10.3077 10.854 --19.6518 10.3152 10.3084 --20.2489 11.0885 9.95757 --19.8349 11.1896 9.1057 --19.648 11.9471 8.55018 --18.784 11.6062 8.86745 --18.3999 12.4673 8.40962 --18.4576 13.2196 8.9674 --17.482 13.2973 9.19661 --17.3843 12.3167 9.09221 --17.0247 12.2152 8.23006 --16.5096 12.9649 8.39694 --16.0057 13.0896 9.24742 --15.47 13.386 8.45323 --14.5254 13.2475 8.13213 --14.5648 12.2852 7.97273 --14.248 11.3098 8.32196 --14.136 10.5755 9.05648 --13.5737 10.3379 8.28268 --13.4713 10.507 7.31698 --12.5268 11.0092 7.42202 --12.8953 11.1881 6.46385 --13.8749 11.0223 6.13864 --14.156 11.5154 6.87835 --15.087 11.7657 6.87356 --16.0105 11.4358 6.56211 --16.887 11.166 6.2063 --17.7985 11.4229 5.8213 --18.6831 11.1254 5.36312 --18.7592 12.0543 5.62443 --19.2681 12.7588 5.11956 --19.8938 11.9562 5.15318 --19.9173 12.4085 6.09814 --20.735 11.8197 6.16165 --20.9851 11.0521 5.59494 --21.605 11.6003 6.01024 --22.1693 11.3284 6.80579 --21.9585 12.1164 7.27986 --21.8408 12.9514 7.87306 --21.4309 13.6178 8.55351 --22.2791 14.1324 8.41686 --22.9403 14.095 7.61227 --23.0426 13.4 6.9402 --23.8973 13.3357 7.43953 --23.6753 13.1139 8.36916 --24.5475 13.5451 8.42096 --24.2539 14.3101 8.93708 --23.5541 14.6482 8.27878 --23.4007 15.3319 7.53493 --23.3954 15.6122 8.4527 --22.739 15.3695 9.11169 --21.8491 15.5739 8.60609 --22.0091 15.272 7.63976 --21.585 16.0737 7.29546 --20.7148 16.5114 7.05836 --19.9115 16.9825 7.38713 --19.2248 17.1676 8.00019 --18.6335 16.3387 8.01078 --19.5078 16.3171 8.63004 --19.0149 16.9145 9.22063 --18.1045 17.3256 9.20764 --17.7458 17.2574 8.23598 --17.3275 16.4184 7.80737 --17.9038 16.6816 7.02377 --16.8832 16.6372 6.79607 --16.2193 16.0582 7.018 --15.6133 15.7253 7.79258 --15.6229 15.1301 8.6298 --15.0039 14.7373 9.31337 --14.0242 14.3474 9.4133 --13.6635 13.4528 9.65456 --12.9142 14.0499 9.30707 --12.6699 14.0819 10.3109 --13.1564 14.062 11.1319 --13.45 14.0443 12.1246 --12.9146 14.81 12.5125 --12.7008 13.8253 12.7662 --12.1545 14.2783 13.5278 --11.2733 14.1245 13.2201 --10.5426 14.812 13.0884 --11.1482 15.245 13.7764 --11.0641 15.9947 14.4443 --10.4815 16.8227 14.3761 --9.98879 17.0668 13.5391 --9.05994 17.3959 13.6144 --8.19289 17.4039 13.181 --7.65756 17.2894 12.3649 --7.16487 16.5748 12.9074 --6.98068 15.603 13.1991 --7.67139 15.5444 13.8697 --8.28259 16.1781 13.3888 --8.33855 15.4953 12.7495 --8.89007 14.7235 13.0004 --9.60722 14.8262 13.6606 --8.77268 14.8758 14.1918 --8.03127 14.1437 14.0803 --7.20942 13.5155 13.8929 --6.2819 13.9041 13.8605 --6.83052 14.1727 14.6781 --5.92842 14.657 14.598 --5.77372 13.6693 14.7089 --5.75952 12.8729 14.0547 --5.58857 12.9468 13.0404 --5.10265 12.0979 12.9197 --5.88789 11.8027 12.3595 --5.92109 12.7766 12.1148 --6.57022 13.4384 12.2217 --6.97838 14.2192 11.7786 --7.95746 14.2366 11.6211 --8.626 14.7911 11.1321 --8.96517 15.0432 10.2731 --8.57396 15.5019 9.44626 --7.96744 16.0681 8.78005 --8.20721 17.0102 9.00009 --7.42603 17.6826 8.87803 --6.74053 16.9046 8.90941 --6.14497 16.2155 9.00159 --6.85879 16.1485 9.75054 --7.55159 16.822 10.003 --8.31841 16.9826 10.6294 --9.12416 16.3801 10.2891 --10.0102 16.0504 10.0585 --9.93582 15.6495 10.968 --10.8388 15.4002 11.4115 --11.4594 16.1693 11.5813 --11.2778 15.574 12.3644 --12.1019 16.1606 12.5878 --12.6767 16.6684 11.9149 --13.5802 16.9518 11.4864 --14.0161 16.8458 10.6048 --13.6635 16.4451 9.75534 --14.077 16.6095 8.9101 --14.7558 16.9514 9.4831 --15.0319 17.4544 10.28 --15.9202 17.087 10.5756 --15.4991 16.2211 10.3806 --15.2889 16.548 11.2732 --15.194 16.4643 12.3621 --15.6553 15.9154 13.0805 --15.2944 16.243 13.8931 --14.4844 16.2308 13.39 --14.0201 16.9981 14.0054 --13.6357 17.8312 13.7303 --12.9477 18.5798 13.6604 --13.8287 18.8912 14.1531 --14.3676 18.6614 14.9535 --13.7809 18.5327 15.7608 --13.5159 19.4704 15.5759 --13.4606 20.2137 16.1982 --13.4157 21.049 16.6962 --12.4002 20.8872 16.5409 --12.0948 20.7366 15.4981 --12.7483 20.8652 14.7679 --12.2798 20.1365 14.344 --12.2062 19.2142 14.7405 --11.3736 19.4835 15.1831 --10.4242 19.4571 15.5601 --11.0002 18.6398 15.4126 --10.4488 18.0537 15.8184 --10.1777 17.0319 15.7714 --10.6429 16.1411 15.8823 --10.5366 15.1479 15.9519 --10.8437 14.6083 16.7023 --9.90431 14.7944 17.078 --9.85153 13.9508 17.5722 --9.56544 12.9779 17.7015 --10.3984 12.7535 17.2475 --10.4571 13.4697 16.5361 --9.52556 13.4076 16.6856 --9.26236 14.2916 16.1494 --9.37813 15.2612 16.3747 --8.38562 15.4282 16.711 --8.48184 15.6856 17.6591 --9.04587 16.5333 17.8117 --8.72542 17.4947 17.5006 --9.13356 17.9715 16.7171 --8.40605 18.5871 16.3313 --7.66544 18.4304 15.6566 --7.12335 18.4769 16.4799 --6.29528 18.4865 15.9011 --5.39158 18.6192 16.3981 --4.58314 18.2498 15.9979 --3.71007 17.7153 15.9009 --3.46745 17.7477 14.898 --4.28655 17.0509 14.6446 --3.99694 16.1035 14.5151 --4.31983 15.8808 15.4774 --3.49901 15.3249 15.5872 --2.95548 14.7453 16.1881 --2.85346 13.981 15.5902 --2.98141 13.2149 15.0277 --2.8911 12.3545 14.5577 --3.44351 13.0338 13.9651 --2.9431 13.0783 13.076 --2.55568 13.7207 12.4316 --3.45137 14.125 12.6074 --4.22841 14.3716 13.1864 --5.1837 14.7054 13.0432 --5.2242 15.7048 12.9008 --5.84823 15.3585 12.2435 --6.24252 15.3934 11.2625 --5.23606 15.3105 11.2369 --4.94791 16.1198 11.7909 --4.06508 15.9562 11.3657 --3.29488 16.0104 10.73 --2.79668 16.7057 11.3276 --1.90597 16.2979 11.074 --1.17183 16.9147 11.2801 --0.528299 16.6144 10.6304 -0.386695 16.8347 10.5259 -1.24483 16.7373 11.1079 -0.807577 15.824 11.2417 -1.00112 15.0994 10.5336 -0.827965 14.2257 10.9292 -1.04077 14.2725 11.8933 -0.82922 14.3329 12.8334 -0.265262 13.7264 13.4105 --0.145116 14.4998 13.8882 -0.234522 15.2684 13.3393 -0.838451 15.9264 12.999 -1.61164 16.198 13.5262 -2.58748 16.3696 13.8902 -2.53291 16.9452 14.7124 -1.91124 16.1443 14.8088 -2.48864 15.6801 15.4017 -2.85488 15.0965 16.1046 -3.19848 15.4336 16.9883 -3.37567 15.7194 17.9336 -3.68576 15.6472 18.9038 -3.73133 16.4755 19.5336 -2.97927 16.6775 18.8444 -2.3151 16.0307 19.2025 -1.42982 15.4404 18.99 -0.686562 14.7958 19.1064 -0.185258 14.1025 18.4768 --0.02865873 13.7737 17.5867 -0.549877 13.2132 17.0376 -0.35408 12.9203 16.0825 -1.23961 12.8438 16.4375 -2.22795 12.5609 16.3193 -2.8305 12.452 15.6038 -3.05241 12.2764 14.6807 -2.75195 12.9566 14.021 -3.66967 13.1078 13.6776 -4.23362 12.4455 13.3202 -5.19663 12.2563 13.0821 -4.69977 11.3401 13.1315 -5.5189 10.774 13.3025 -6.45332 10.6969 12.8958 -7.04664 10.6529 13.6536 -6.65558 11.5059 14.0257 -6.69998 12.1839 13.3709 -6.71824 13.0966 13.7324 -7.05121 14.088 13.582 -7.86337 13.6618 13.9823 -7.6852 14.3234 14.7008 -8.23142 14.8411 14.1352 -7.68516 15.5874 14.4377 -6.99505 15.7995 15.1716 -6.60596 16.4343 15.7577 -7.01105 17.0814 16.3325 -6.27136 17.6878 16.7447 -6.20135 17.8799 15.7463 -5.31077 17.447 15.6763 -4.94453 17.4954 14.7145 -4.97427 18.378 15.2491 -4.73987 18.0723 16.1844 -3.77326 17.6909 16.0876 -2.7631 17.3667 15.8566 -3.26067 17.0428 16.7168 -2.41126 16.4844 16.4742 -1.43 16.5098 16.6895 -0.726538 16.1897 17.3227 -0.338607 16.2627 16.3811 --0.340568 16.7954 15.871 --0.07459183 17.5418 16.475 --0.59678 17.3296 17.299 --0.50361 17.9657 18.0093 --1.11964 17.7331 18.7979 --1.84589 17.0462 18.8015 --2.50168 17.2567 19.4967 --3.23881 16.8432 19.0173 --3.77709 16.0569 18.7703 --3.64453 16.1423 17.7281 --3.90108 16.2293 16.7888 --4.85859 16.2068 16.6398 --4.32727 15.3166 16.5973 --4.54688 15.2931 17.6156 --4.30761 14.4432 17.0892 --4.89151 13.9237 16.3779 --4.85531 13.0398 16.8944 --4.59658 12.1778 17.3483 --4.57442 11.3451 17.9624 --4.35027 11.9708 18.7095 --4.86944 12.6624 19.2308 --5.70099 13.0731 19.5085 --5.59782 12.6426 20.3648 --4.60837 12.6136 20.685 --3.85789 12.7689 21.3312 --2.93737 12.6661 21.1216 --2.81741 13.2868 20.3856 --3.10154 14.1308 20.8294 --3.87658 14.3672 20.1952 --3.18628 15.0192 20.0057 --3.05176 15.8248 19.4832 --2.35921 15.6286 18.9129 --2.13738 15.2307 18.0519 --1.20429 14.9701 18.3182 --1.55634 14.7108 19.1984 --0.805312 14.3251 19.6892 --1.14344 15.2517 20.0725 --0.119287 15.5422 19.9042 --0.36607 16.3919 19.4238 -0.218311 17.2113 19.5215 -0.346517 17.6086 18.5822 -0.762423 18.5307 18.3856 -1.00527 18.7467 19.3784 -1.69244 18.815 20.0727 -1.61412 18.082 20.702 -1.07048 17.2656 20.4804 -0.824042 16.9264 21.4494 -0.08582117 16.3527 21.3355 --0.688262 16.5827 20.7341 --0.780652 17.3891 20.1664 --1.4795 17.9024 20.6411 --2.27095 18.1667 20.0808 --2.72659 17.764 20.9109 --3.66608 17.4102 21.1872 --3.80204 16.4528 20.8775 --4.66378 16.0681 20.5835 --4.8135 17.0747 20.4427 --5.13339 16.9208 21.3677 --6.11843 16.622 21.2725 --6.94947 16.0064 21.2379 --7.51166 16.0827 22.0957 --8.35459 16.5282 21.7075 --8.50244 15.5476 21.901 --8.46655 14.6384 21.4204 --7.86248 15.1912 20.8568 --7.90182 15.0691 19.8211 --8.37037 14.2333 19.4651 --8.29704 13.4427 20.0026 --7.43897 13.4211 20.6086 --8.23265 13.6654 21.1192 --7.31675 13.7893 21.5215 --7.25485 14.7595 21.762 --6.79238 14.1726 22.5461 --7.23238 14.0376 23.4248 --7.24069 14.8912 23.9504 --6.54127 14.5151 24.5538 --5.88258 15.2255 24.7757 --4.94877 15.2131 24.4247 --5.37139 15.5978 23.5777 --5.37452 16.1942 24.3427 --5.51242 16.6954 25.2287 --5.04655 17.2975 24.5667 --5.14016 18.1517 24.2719 --5.81691 18.6789 23.7819 --6.73069 19.2107 24.0555 --7.41599 19.26 24.7329 --7.87022 19.1669 25.5419 --8.27463 19.823 26.1166 --8.30631 20.8405 26.111 --9.31349 20.6029 25.8025 --10.2905 20.4134 25.7888 --10.2037 19.8813 24.9397 --9.87627 18.8644 24.9883 --9.67419 18.7185 24.0558 --10.2779 17.914 23.837 --9.86146 17.5132 23.019 --10.0957 16.5405 23.0317 --10.7712 15.8827 23.2531 --10.1436 15.5172 23.9845 --10.2324 14.558 24.1485 --9.58726 14.5299 24.9397 --9.37194 14.6121 25.9783 --9.62032 14.2507 26.8247 --10.3952 13.6669 27.1437 --10.6463 12.8703 27.763 --11.2845 12.2594 27.375 --10.5351 11.6409 27.4895 --10.017 10.9889 26.9377 --10.5975 10.529 27.5968 --11.2831 9.7591 27.4231 --10.7157 9.15571 26.942 --10.0847 8.38955 27.0552 --9.73312 8.43277 26.0879 --10.2059 8.28163 25.2074 --10.6597 7.67908 25.7945 --9.9097 7.13266 26.0911 --10.0345 6.9663 27.0687 --9.03112 6.88526 27.2665 --8.82971 7.3601 26.4405 --8.12374 7.46326 25.7888 --8.89146 7.64394 25.1789 --9.12288 8.2631 24.4524 --8.59247 9.01232 24.0349 --7.65658 8.77161 24.1142 --7.4076 7.89838 23.7247 --8.27022 7.81844 23.2961 --8.48534 7.44544 24.1641 --9.35665 7.68762 23.5703 --10.1939 7.11957 23.7268 --9.50617 6.48509 23.8388 --10.1321 5.93411 24.422 --10.9152 5.5422 23.812 --11.3791 5.83057 24.6021 --11.5888 4.86936 24.4333 --11.3926 4.98143 25.4291 --11.1943 4.63544 26.3195 --11.5296 4.94264 27.2556 --10.6465 4.71999 27.7355 --9.64945 4.72284 27.8732 --9.58739 5.74216 27.6969 --9.15043 6.22818 28.4825 --9.91748 6.74908 28.3092 --9.25988 7.33337 28.6391 --8.45 7.50959 29.2634 --8.26468 7.00572 30.022 --8.58737 6.11286 29.7657 --7.90935 5.37691 29.6679 --7.92276 4.45147 29.3318 --8.41873 5.1656 28.7733 --8.27556 5.52567 27.8693 --7.35548 5.90001 28.1699 --6.56946 6.50166 28.1443 --6.30949 6.86527 27.2232 --5.73822 7.62067 26.8621 --6.10448 8.53336 26.8803 --6.49722 9.3667 27.1806 --7.40786 9.72059 26.9601 --7.45054 8.81854 27.3262 --7.94959 9.5869 27.7374 --8.47139 10.365 27.7188 --8.90216 10.6466 26.8866 --9.2844 10.3427 26.0088 --8.78512 10.6915 25.252 --9.11905 11.4863 25.8133 --8.46718 12.1411 26.1402 --7.88891 12.2382 26.9795 --7.89813 12.7563 27.8246 --7.68476 12.3442 28.7757 --8.14219 12.9307 29.4364 --7.44078 13.4392 28.9339 --6.47496 13.2427 28.7759 --6.36921 14.1393 28.2426 --6.95787 14.8775 28.5838 --6.82252 15.0671 27.5782 --7.21055 14.3391 27.1057 --7.07835 14.8096 26.2124 --7.38949 14.3575 25.4073 --7.78507 13.502 24.9861 --7.21225 12.7466 25.0678 --7.85074 12.5767 24.2857 --7.67553 12.6739 23.3704 --8.69544 12.8511 23.3331 --9.29841 13.1462 22.5553 --9.32475 14.0062 22.0615 --10.1832 13.6839 22.5201 --10.775 12.853 22.5391 --11.7399 13.0367 22.7952 --11.0081 13.4303 23.4196 --11.752 13.7055 24.0221 --11.877 14.3786 23.3001 --11.8261 14.7629 22.3423 --11.0113 14.3669 21.907 --11.1206 13.5911 21.3335 --10.9593 14.0013 20.4239 --11.749 14.5106 20.1334 --11.5972 15.5032 19.9772 --10.8026 16.04 20.3984 --10.4304 16.7902 21.0268 --9.62272 17.3794 21.2207 --9.08679 18.1847 21.4167 --8.71931 19.037 21.6905 --9.15964 19.9298 21.7145 --9.22379 19.8998 20.69 --9.58439 20.5615 19.9389 --10.4929 20.1667 19.8993 --11.3644 20.656 19.6432 --10.7333 20.9026 18.8673 --10.8593 20.4903 17.9141 --11.3916 19.7509 17.4479 --10.5613 19.2566 17.6988 --10.7844 19.106 18.7282 --10.4148 18.2184 18.3312 --10.8064 17.273 18.4647 --11.4186 16.5512 18.6024 --12.0162 15.9261 18.0243 --12.5256 15.2488 18.5891 --13.4478 15.472 19.0047 --14.1135 15.2872 18.1791 --15.0066 15.1557 17.7208 --14.7781 14.1801 17.6872 --15.2625 13.3551 17.5449 --14.8851 12.8353 16.8242 --13.9499 12.362 16.9257 --13.5383 13.0428 16.3611 --13.6088 12.7353 15.4402 --12.8933 12.8591 14.727 --12.4887 12.3143 15.5195 --11.6162 12.3067 15.1164 --11.1751 12.6006 15.9511 --11.4776 12.4802 16.8523 --12.4121 12.3243 16.7223 --12.7809 12.7162 17.4788 --12.7912 13.5059 16.8618 --12.1356 13.7076 17.5817 --12.7888 14.4745 17.3984 --13.6732 14.6349 16.873 --13.179 14.8563 16.06 --12.6793 15.6412 15.6744 --12.2449 14.8953 15.0648 --12.3185 13.9296 15.1516 --13.2074 14.1845 14.7177 --14.2425 14.1984 14.9103 --14.5828 14.8819 15.5581 --14.316 15.8535 15.2641 --15.1631 16.4316 15.0817 --16.0766 16.3278 15.3044 --16.6604 15.5164 15.4091 --17.3376 14.8604 14.9808 --18.1667 14.475 14.5652 --19.0187 14.7234 14.9343 --19.583 14.1536 15.5205 --19.8463 13.4387 16.0107 --18.9629 12.8297 16.1806 --19.1386 11.8046 16.1918 --18.2131 11.5093 15.9648 --17.7369 12.2524 15.5134 --16.7936 11.9571 15.5616 --16.3299 12.7826 15.2521 --15.7132 13.5462 15.5829 --16.5108 13.3054 16.1483 --15.6732 13.6171 16.6448 --16.3137 14.3486 16.6398 --15.8638 15.2298 16.6701 --15.6635 16.2157 16.6935 --15.3727 17.0416 16.2747 --15.0865 17.5259 15.4751 --15.7871 18.2198 15.3505 --15.3271 19.1155 15.3146 --16.2434 19.2611 14.9797 --16.7097 18.9534 15.7695 --17.5659 18.5002 15.8649 --17.5395 19.487 15.7356 --17.6871 20.1054 16.5296 --17.6724 19.2189 16.9308 --17.5602 18.4719 17.5933 --17.7957 18.4445 18.5929 --18.305 17.6112 18.6374 --18.1872 16.673 18.8222 --18.2193 16.4391 17.8813 --18.9028 17.16 17.8339 --19.2283 16.7168 16.9826 --18.9506 15.9568 16.4447 --18.5746 15.1322 16.2332 --18.8276 14.8532 17.1804 --18.7575 15.0307 18.1254 --17.8326 15.14 18.3704 --16.9473 14.6204 18.1047 --16.2059 14.884 18.6507 --16.2432 14.5058 19.5919 --15.6099 13.9464 18.9756 --14.6 13.8912 18.9512 --13.9923 13.0595 18.8172 --13.5292 13.425 19.5613 --13.993 13.1978 20.3636 --14.6867 12.6162 20.7416 --15.6073 12.3189 20.9675 --15.0435 11.5698 21.0191 --15.9571 11.3637 21.1133 --15.4662 10.5029 21.4542 --15.9484 10.3951 20.5226 --16.3642 10.0661 21.358 --16.1419 10.185 22.3113 --16.0294 11.1358 22.6692 --16.9598 10.8475 22.5855 --16.6693 11.3827 23.3619 --16.4477 10.7754 24.1139 --17.1124 10.8549 24.7868 --17.7863 11.1782 24.0938 --18.7602 10.816 23.9367 --18.5658 10.0266 23.3521 --19.1886 9.47953 23.9322 --19.8598 10.1438 23.6414 --19.5933 10.6886 22.8562 --19.6146 10.1273 22.0806 --18.706 10.3396 21.7782 --18.6018 10.0445 20.8997 --18.9033 9.17041 20.6803 --18.1376 8.5393 20.4996 --18.9054 8.00844 20.1879 --18.1587 7.74695 19.532 --17.1859 7.75635 19.8588 --17.1805 7.76995 18.8747 --17.1921 7.58457 17.9073 --16.9178 8.50808 18.1169 --17.1231 9.06721 18.8469 --18.0986 9.21289 18.5359 --18.7347 9.6992 18.0076 --19.1564 10.2727 18.8313 --18.7465 10.9604 18.2588 --18.8217 11.7192 18.9407 --18.8928 11.5145 19.9152 --18.4903 12.2012 20.4674 --17.6254 12.7732 20.6308 --17.4326 13.5587 20.1046 --16.4533 13.6925 20.2607 --16.4676 13.3188 21.1241 --16.5107 13.8741 21.9462 --15.6627 14.4111 21.752 --14.8775 13.7723 21.4931 --14.2863 14.3221 20.7981 --13.3127 14.178 20.7393 --13.3767 15.1493 20.3617 --12.5997 15.7726 20.2586 --12.155 16.693 20.3165 --11.8306 17.6467 20.4318 --11.8732 18.5882 20.6413 --12.7358 18.2127 20.7232 --13.1773 17.3858 20.2496 --13.9549 17.0154 19.7743 --13.8654 17.8525 19.2735 --14.0577 17.6219 18.3307 --13.7845 17.4361 17.3413 --14.3983 18.2368 17.258 --15.1951 18.3822 16.6477 --16.0136 17.9061 16.7761 --16.6729 17.2911 16.4149 --17.5746 17.208 15.93 --18.4328 17.4644 15.4581 --18.3357 16.7684 14.7144 --18.045 17.6165 14.1574 --18.1341 18.3125 13.4303 --18.3734 17.6653 12.6935 --17.6663 17.8491 11.9878 --16.8991 17.2766 11.6611 --17.4872 16.7457 11.0615 --17.1805 17.0327 10.1114 --17.7324 17.8299 10.3488 --18.6746 18.0004 10.3405 --19.0055 18.5259 9.58436 --18.5974 19.4175 9.55676 --18.7359 20.4072 9.37613 --19.0353 21.2985 9.78009 --18.3791 21.2753 10.5014 --18.5936 22.0402 11.1632 --18.917 22.9438 11.4671 --18.1151 22.4043 11.9458 --17.6567 22.4105 12.7858 --17.1338 23.2648 12.6985 --16.8677 23.311 13.6922 --16.3439 22.8639 14.5396 --16.171 21.8763 14.4748 --16.2591 22.3087 13.5273 --15.632 22.5935 12.8258 --15.4894 23.4592 13.1395 --15.3173 22.6868 13.778 --14.7481 22.7939 14.5766 --14.9006 22.827 15.5538 --14.8145 23.835 15.3272 --14.0736 24.1743 15.953 --13.9518 25.1392 15.7091 --13.2104 25.7307 16.1456 --12.4487 26.1901 16.4891 --11.9071 25.5218 16.0092 --11.4205 25.4112 16.9006 --11.9475 25.8285 17.6469 --11.277 26.5033 17.9087 --10.7053 27.3219 17.8562 --9.76829 27.2794 18.1556 --10.3519 26.9594 18.9083 --9.94576 26.261 18.4027 --9.38996 25.6628 19.0171 --9.28986 24.8435 19.6535 --8.55894 24.1343 19.5846 --8.27845 23.5274 20.2925 --9.25769 23.3377 20.5657 --10.202 23.2442 21.0384 --11.1574 23.3491 20.7525 --12.1588 23.3874 20.9074 --12.4513 22.6004 21.3801 --12.9049 22.4265 20.5409 --13.6599 22.6359 19.959 --13.9145 23.0959 20.8372 --14.7721 22.6526 20.8068 --14.9544 22.2173 19.9097 --14.7328 22.6622 19.0809 --14.9607 23.3032 18.2774 --14.5427 22.6814 17.6736 --15.4136 22.7159 17.2668 --16.4153 22.7397 17.1208 --16.5893 22.4149 18.1155 --15.9289 22.7518 18.7312 --15.9244 21.7882 18.958 --15.5509 21.1278 18.217 --14.7189 20.9664 17.5766 --14.6613 21.0822 18.5472 --15.0285 20.2393 19.0311 --15.3518 19.3254 18.6501 --15.9325 18.7599 19.2964 --15.7713 18.2651 18.4171 --15.6912 17.6564 19.1452 --15.2923 16.7898 19.2253 --15.4367 16.6545 20.151 --15.9839 15.9609 20.6077 --16.6227 16.7121 20.7775 --17.4859 17.1689 20.5891 --18.4602 16.743 20.7645 --18.3479 16.8156 21.7094 --19.0509 17.5038 21.5016 --19.7257 16.977 22.1125 --19.7439 16.8085 23.1147 --20.6924 16.5805 23.3813 --21.4412 16.4257 22.8399 --20.7082 15.7547 22.641 --20.6844 14.829 22.283 --19.9474 14.961 22.9103 --19.7388 14.0187 22.9859 --19.8466 13.1608 22.4646 --19.4046 13.1681 23.4718 --19.1536 13.9338 23.962 --18.5485 13.2238 24.0471 --18.0648 13.8546 23.4377 --17.5799 14.5686 22.9081 --17.6619 14.8168 23.8613 --18.2578 15.4619 24.2781 --17.9582 16.4469 24.109 --17.6755 16.9236 24.8957 --18.5215 16.9373 25.4714 --19.4183 17.338 25.1469 --18.8808 17.9821 25.637 --18.6362 18.6545 24.9821 --19.5073 18.3459 24.7167 --20.1164 18.8315 23.9816 --19.4923 18.3585 23.3881 --18.8849 17.6557 22.9788 --18.2202 17.8708 22.2271 --17.5589 17.1464 22.1975 --17.2932 17.5585 23.0651 --16.5432 17.7389 22.3837 --15.7144 17.9381 22.9173 --16.3513 17.6815 23.6964 --16.0213 16.7027 23.7297 --15.2124 16.1975 23.5581 --15.2011 15.7188 22.7401 --14.8047 14.8412 22.9806 --14.1778 14.1342 23.2934 --13.1686 14.0071 23.3134 --12.6884 13.2599 23.8103 --13.2402 13.1828 24.7196 --12.9157 12.7744 25.5448 --12.1142 12.5019 26.0817 --12.4625 11.8811 26.7922 --13.317 12.4758 26.6899 --13.7725 11.7677 27.2093 --13.4431 11.0788 26.6688 --13.0654 10.2098 26.3977 --12.7548 10.4749 25.5205 --12.8074 11.4701 25.6319 --13.1337 11.6686 24.729 --12.5095 11.0255 24.1895 --11.5039 10.9275 24.3846 --10.7034 11.2197 24.9484 --10.4626 10.3553 25.4186 --9.9755 10.3003 24.5521 --9.91432 9.29653 24.4089 --10.857 8.89677 24.5524 --11.3036 9.26059 23.7477 --11.8072 9.51852 22.9215 --11.7967 8.56454 23.2307 --11.3209 7.79167 22.9254 --10.7523 7.40492 22.248 --11.5007 6.99869 21.7899 --12.0769 7.31457 20.9871 --11.5715 7.9607 20.44 --11.4073 8.98442 20.5984 --11.3918 9.94881 20.897 --12.2319 10.4451 21.1892 --13.0199 11.055 20.982 --13.3564 11.2534 19.9807 --13.7865 10.5222 19.5117 --13.4502 10.5107 18.5976 --13.043 10.4438 17.749 --12.2273 10.0108 17.4723 --12.5577 9.08826 17.5507 --11.6459 8.66923 17.4206 --11.6707 9.36542 18.1345 --11.117 10.0741 18.4398 --10.8395 9.95574 19.3871 --9.90197 9.49041 19.2377 --9.11125 9.28621 19.9098 --8.4818 9.57175 19.2234 --8.42459 10.3954 18.6877 --8.57474 11.3183 19.1904 --8.74988 12.2759 19.056 --9.40394 12.3205 19.7482 --10.4485 12.3756 19.5622 --10.7964 12.7804 20.4525 --10.5762 12.0403 21.0676 --10.3543 11.1889 20.529 --9.38529 11.3239 20.5157 --8.46428 10.9455 20.5807 --7.50961 11.1828 20.2997 --6.83598 11.6451 20.7898 --6.79848 12.1087 19.9114 --7.01947 12.3553 18.8988 --6.57618 12.6541 18.0601 --6.68889 11.9181 17.3753 --6.43095 12.5005 16.6678 --6.09319 11.6329 16.3833 --5.70758 11.1032 15.6192 --5.4642 10.1379 15.5568 --5.73957 10.029 14.6754 --5.83837 10.6101 13.8236 --6.0324 9.76151 13.3437 --6.5066 8.92616 13.7816 --6.12758 8.49811 12.9124 --5.58692 7.70963 12.5082 --5.65621 7.29758 13.4577 --6.23639 6.82122 12.8195 --6.52923 6.18239 13.4826 --7.12281 6.47546 14.2025 --7.51973 6.02518 13.4423 --7.62218 5.09288 13.2347 --7.0392 4.28759 13.3086 --6.41266 3.61001 12.9435 --6.82261 4.09686 12.1687 --7.80549 4.20824 11.9885 --8.30621 3.41747 12.1095 --9.2627 3.54989 12.316 --10.023 4.08509 12.4124 --9.72938 3.90804 13.3742 --10.0912 2.96597 13.2832 --9.15341 2.98966 13.5886 --8.59627 2.24224 13.5587 --7.60002 2.23444 13.4752 --6.63667 2.17544 13.41 --6.98481 1.4074 13.9763 --6.9083 0.5065679 13.4237 --6.9112 0.9622379 12.596 --7.53448 0.7725789 11.9144 --7.60953 1.6602 11.4576 --8.36788 1.93418 12.1355 --9.34165 1.94978 12.4718 --10.1182 1.22617 12.4151 --9.66928 0.3470699 12.4145 --10.0608 -0.3770331 13.0348 --10.8053 0.04534363 13.5136 --10.9185 -0.2201981 14.4826 --10.0884 -0.8247281 14.357 --9.89581 -1.72135 13.9119 --10.3052 -2.20956 14.6204 --9.43827 -1.7697 14.6702 --9.29361 -2.75503 14.7466 --8.7679 -2.93523 13.9322 --8.77967 -1.97943 13.6263 --8.00721 -1.71124 14.2108 --7.20527 -2.39233 14.3776 --6.28708 -2.46018 14.7517 --5.50978 -2.99763 15.0035 --4.87456 -3.32088 15.7476 --5.09218 -2.82564 16.6017 --5.67044 -3.31431 17.1573 --4.84077 -3.5213 17.587 --4.12491 -2.92833 17.0893 --3.70147 -2.38648 17.8064 --4.15076 -2.14764 18.6848 --5.00106 -2.15323 19.223 --5.76624 -1.47259 19.4341 --6.11242 -1.90146 18.5689 --6.56273 -2.51765 19.1764 --7.39541 -3.01351 19.5393 --8.09007 -2.91378 20.1831 --8.2729 -3.61092 20.8907 --8.15377 -4.62146 20.8853 --7.568 -4.93991 21.6478 --6.63677 -4.55956 21.5797 --5.85004 -3.95808 21.6858 --6.18667 -3.33517 20.9813 --6.18737 -3.78658 20.091 --5.53664 -3.81778 19.2804 --4.74382 -3.39137 19.5492 --4.48988 -4.11556 20.1403 --3.96259 -3.8037 20.977 --4.41188 -4.54418 21.4637 --4.04224 -5.35216 21.9567 --4.40963 -5.44066 22.9089 --5.38588 -5.64926 23.2517 --6.13691 -6.27672 23.4865 --5.57736 -7.13338 23.6287 --5.26086 -7.74733 24.3534 --4.76193 -8.5053 23.9714 --5.01191 -9.00159 23.1045 --5.48674 -9.15889 23.9406 --5.71304 -10.015 24.4442 --5.4502 -11.0022 24.3822 --6.33849 -11.3386 23.9728 --7.02374 -10.8667 23.4476 --7.53232 -11.2014 24.1847 --7.49145 -10.6107 25.0168 --6.9053 -11.4621 25.2611 --6.38879 -12.1357 25.8535 --6.36445 -11.198 26.0922 --5.92291 -10.3555 25.8464 --5.17424 -10.0078 26.3332 --4.17552 -10.1896 26.3951 --4.27346 -11.1812 26.4777 --4.42498 -11.7999 27.2648 --4.90142 -10.9772 27.4722 --5.30733 -11.2148 28.3398 --6.20028 -10.7248 28.3176 --6.33272 -10.5286 29.3213 --6.43742 -9.55612 29.1571 --7.29997 -9.20025 29.2828 --7.58897 -9.9788 29.8861 --6.93379 -10.0995 30.58 --6.14338 -9.92119 31.1486 --6.1572 -10.7217 31.7428 --5.82427 -11.5901 31.4013 --5.30131 -11.6555 30.5361 --4.93664 -10.7189 30.6573 --4.19201 -11.3324 30.9709 --3.68283 -10.5157 31.2255 --3.73708 -9.71466 30.5821 --4.44 -9.83453 31.3634 --3.94838 -9.294 32.0201 --3.18098 -9.11628 31.345 --2.39008 -8.55957 31.2029 --2.05082 -8.53588 32.1061 --2.26029 -8.27083 33.0851 --2.07005 -7.81418 33.9578 --2.96949 -8.29667 34.1874 --2.87032 -9.29739 34.5377 --3.18066 -8.5738 35.1983 --3.65129 -7.86996 35.7071 --4.32729 -7.48876 35.096 --5.23578 -7.74284 34.741 --5.35578 -6.726 34.8471 --6.05153 -6.76102 35.5926 --6.54671 -5.89182 35.2567 --6.68215 -5.98972 34.2487 --6.52886 -5.29829 33.5225 --6.88663 -4.53885 33.0493 --7.16786 -5.23523 32.4089 --8.06323 -5.48035 31.9662 --8.29513 -6.48819 31.8019 --8.82276 -6.89359 31.0891 --9.27165 -6.00209 30.9584 --9.80357 -5.40461 31.6331 --10.405 -5.39372 32.4776 --11.415 -5.11379 32.3357 --11.1509 -5.96425 32.7861 --11.5918 -6.63834 33.4712 --12.4635 -6.42018 33.8848 --13.1562 -6.45987 33.2074 --14.0476 -6.77484 32.8405 --14.3378 -7.0149 31.9364 --14.5929 -6.07239 31.7581 --15.4385 -6.07943 31.1631 --14.6744 -5.57146 30.7134 --15.2822 -4.82025 30.9771 --14.7682 -4.04592 31.1709 --15.084 -3.21782 30.6917 --14.112 -3.10347 30.7817 --13.9216 -3.18426 29.8556 --13.1466 -2.87235 29.3618 --12.5682 -2.92074 28.6379 --12.5167 -2.33895 27.8458 --11.7169 -2.29985 27.2916 --12.0668 -1.42706 27.0851 --11.1609 -1.30288 26.6055 --10.5427 -1.99737 26.7869 --9.74331 -2.47059 27.1014 --9.41825 -3.032 26.2967 --9.80622 -2.55707 25.5282 --9.44122 -1.90508 24.8764 --8.83089 -1.39274 25.4942 --8.6453 -0.8265411 26.2531 --9.56127 -1.1234 26.155 --9.71968 -0.2689041 26.6388 --8.83494 -0.1100241 27.0623 --8.1758 -0.8948181 27.1743 --7.27594 -0.7465051 27.6738 --6.7384 -1.54388 27.2822 --5.96771 -0.9817801 27.0766 --5.40222 -0.5206561 26.3983 --4.97203 -0.09070167 27.2626 --4.24461 0.4979579 26.7936 --3.38887 0.04514773 26.6222 --2.9279 0.9747779 26.6634 --3.2322 1.92719 26.5999 --3.84125 2.3788 27.2713 --3.39326 3.28384 27.4414 --4.11535 3.67397 27.983 --4.75974 4.08214 28.5839 --5.08527 4.21383 27.6826 --5.8542 4.41118 26.9439 --6.01378 3.82445 27.7835 --5.67777 2.99541 27.7152 --5.52844 2.80348 28.68 --5.03618 3.08359 29.472 --4.3058 2.43601 29.6745 --4.42237 1.52481 29.2594 --5.11775 1.03787 28.7661 --5.88508 1.18043 29.402 --6.06451 1.42617 30.3362 --6.70212 1.76528 29.6544 --6.24947 2.67021 29.7726 --6.03974 3.49465 30.1951 --6.7946 4.07921 29.7849 --6.05298 4.8147 29.7259 --5.20269 5.12236 29.349 --5.21677 5.85871 29.9603 --5.41315 6.78781 29.8875 --4.79568 6.81262 29.0268 --3.99514 6.66947 28.3858 --3.03944 6.46079 28.3659 --2.73542 7.34365 27.9838 --1.75812 7.2557 28.2258 --2.25347 7.04342 29.0599 --1.61236 6.25496 28.986 --1.02287 6.91168 29.4939 --0.451451 7.1928 28.7106 -0.365517 7.16305 29.3096 -0.730573 6.38164 29.7813 -0.227381 5.60288 30.2386 -1.17522 5.2819 30.0144 -0.527798 4.85559 29.3264 -1.30285 4.54081 28.7769 -1.77442 5.03089 28.0603 -2.00437 4.99447 27.117 -2.53116 4.7549 26.2939 -3.29996 4.29444 26.6396 -3.29535 3.46968 26.056 -3.30932 3.2663 25.0624 -3.16526 2.49723 24.4967 -3.78679 2.08986 25.2208 -3.4458 1.47527 24.4779 -2.48671 1.31702 24.7223 -1.95008 2.09493 24.3169 -1.35608 2.75267 23.8601 -2.0616 2.64606 23.1265 -2.00713 1.63868 23.3914 -2.00937 1.14744 22.5003 -2.59985 0.6195839 21.9239 -1.80939 0.8462109 21.3958 -1.85162 -0.1277821 21.6161 -1.02254 -0.7200291 21.9197 -0.690945 -0.7312221 22.9215 -0.403874 -0.8673551 23.8584 -0.434681 -1.50882 24.6346 --0.274303 -1.89818 25.2585 --0.639269 -2.74045 25.6398 --0.04237533 -3.49552 25.4272 -0.514925 -4.27574 24.9553 -1.15316 -3.50431 24.9077 -1.60065 -2.75995 25.3418 -1.99883 -2.9098 24.4127 -2.05443 -3.16592 23.4693 -1.33345 -3.77129 23.6844 -1.29112 -4.43999 22.9496 -0.322235 -4.35958 22.7196 -0.105746 -3.45459 23.1529 --0.362931 -2.87389 23.7947 -0.146905 -2.02739 23.5413 -0.44663 -2.24749 22.6242 --0.526826 -2.14007 22.4105 --0.622878 -3.00554 21.9627 --1.08994 -3.85938 21.9486 --1.12968 -4.37923 21.1123 --1.01048 -5.38815 21.1541 --1.76751 -5.03038 20.6074 --1.94746 -5.96863 20.2533 --2.26909 -6.36072 19.3439 --2.0392 -7.05389 18.658 --2.28634 -7.32747 19.5801 --1.62751 -7.22985 20.2615 --1.09849 -7.78448 20.9566 --0.218492 -7.36891 20.9073 --0.419421 -6.39214 20.514 -0.304016 -6.48977 21.2594 --0.28069 -6.40402 22.0212 --0.210638 -5.9323 22.9262 --0.716771 -5.1326 22.6556 --1.68668 -5.40062 22.5905 --2.61417 -5.76572 22.6832 --2.14844 -6.67534 22.4849 --1.75015 -6.63236 23.3474 --2.49746 -6.51173 24.0638 --3.3793 -6.60586 24.5469 --4.36157 -6.31374 24.9615 --4.47375 -5.64805 25.6552 --3.69084 -5.24956 26.2145 --3.89047 -4.7364 27.1186 --4.37352 -4.23448 27.8074 --4.29441 -5.18286 28.1244 --5.17571 -4.87955 28.1981 --4.7282 -4.52529 29.0677 --5.72619 -4.5132 29.0892 --5.54859 -5.22415 29.7358 --4.82587 -4.74857 30.2636 --5.42183 -5.28575 30.8639 --5.76328 -6.18681 31.2043 --5.75381 -7.1412 31.5102 --5.66724 -8.12792 31.6831 --4.91815 -7.36239 31.8159 --4.1578 -6.84564 32.1882 --3.47264 -6.3744 31.6824 --2.87729 -5.71147 31.2161 --2.12123 -6.21802 30.8012 --1.49863 -6.99656 30.7192 --0.845301 -7.36273 29.9408 --0.497765 -8.08031 30.5426 --0.524816 -8.764 31.3038 -0.208163 -9.21771 31.8504 -1.01749 -8.8485 31.4359 -1.17272 -7.85719 31.4748 -1.93303 -7.613 32.1547 -2.86436 -7.56703 32.507 -2.51494 -6.87016 33.0712 -2.85106 -6.25975 33.8482 -2.30752 -6.41459 34.6217 -1.51016 -5.96997 34.3861 -1.43944 -5.28215 35.0192 -2.33784 -5.01546 34.5743 -2.33009 -4.74999 33.6209 -2.73395 -5.14368 32.8468 -2.63126 -5.17544 31.8521 -2.88054 -4.79449 31.0063 -1.8996 -5.00915 30.982 -1.25565 -4.33824 30.5591 -0.58151 -3.69609 30.2306 --0.362328 -3.85429 30.4364 --0.35023 -4.60746 31.1467 -0.330081 -5.18736 30.6682 --0.18175 -5.73773 30.0651 -0.185889 -6.67063 29.8782 -0.811363 -7.14157 29.2376 -1.12166 -6.41543 29.9564 -1.40391 -5.9569 29.1649 -1.46552 -5.33913 28.3903 -2.32138 -5.27667 27.8152 -3.01919 -5.02694 28.4559 -3.4678 -5.92059 28.1798 -3.90833 -5.59594 28.975 -4.82014 -5.35005 29.3698 -4.93707 -4.75136 30.215 -4.41362 -4.10462 30.7744 -4.27884 -4.19642 31.7609 -3.56153 -3.59741 31.8484 -3.7201 -2.60856 32.1932 -4.04701 -1.94419 31.4713 -3.37178 -1.30375 31.511 -3.57398 -0.2698791 31.5979 -3.56605 -0.4208131 30.5606 -4.31313 0.01836233 31.008 -4.83208 0.7215209 30.5145 -5.34699 1.5726 30.4245 -4.85389 2.24517 29.9415 -4.52996 3.18367 29.7697 -4.32128 2.72043 30.6236 -3.51084 2.38909 31.0544 -2.75497 2.84588 31.5962 -1.90812 3.47994 31.7825 -0.929293 3.38519 31.7505 -0.196676 3.09466 32.3419 --0.316065 2.3669 31.8835 -0.200461 1.5933 31.7226 --0.608195 1.03412 31.6335 --0.395155 0.8490619 30.6816 --0.949291 1.29104 29.9099 --1.30035 2.05812 29.3079 --1.95375 1.93891 28.5546 --1.24183 2.22192 27.9019 --1.07515 3.01533 27.2496 --1.07866 3.57916 28.0733 --0.964031 3.73296 29.0427 --0.337105 3.35158 29.6822 -0.271269 3.51284 29.018 -0.736709 2.74606 28.4829 -0.446781 1.99857 27.8718 -0.108797 1.89724 26.9177 -0.777923 1.21703 26.7383 -0.924952 1.71474 25.8795 -0.618567 1.14264 25.0979 -0.378764 0.7466329 24.1631 -0.93713 1.23846 23.4462 -0.855474 1.63827 22.4858 -0.009510075 1.86773 21.9857 --0.710412 1.28226 22.3759 --0.276635 0.9320909 21.4944 --1.20145 0.7377259 21.1138 --1.83873 0.5309719 21.8034 --2.32477 1.28549 22.1568 --2.27728 0.9553069 23.1345 --3.26512 1.22654 23.3708 --3.03484 2.09794 23.8566 --3.60286 2.89649 23.6691 --3.33235 2.93765 24.6656 --3.41956 3.95703 24.7783 --4.40116 3.79314 24.9308 --5.37141 3.73399 24.9075 --5.89451 3.82524 24.0423 --6.48751 3.02895 24.2291 --7.38622 2.73971 24.2945 --8.15523 2.51628 23.7183 --8.74059 2.72597 24.4821 --8.28493 1.90851 24.9018 --8.08307 1.97452 25.9377 --8.18537 1.78968 26.8694 --7.93235 2.06713 27.8024 --6.94646 2.11559 27.3285 --6.75307 2.72775 26.6202 --5.91853 2.25696 26.6893 --6.51786 1.55874 26.2707 --5.97372 1.83486 25.4904 --6.14115 1.52343 24.5476 --6.2118 0.8391489 23.8398 --5.47006 1.14165 23.3156 --5.95577 1.1052 22.4598 --5.17949 1.36423 21.9619 --4.46204 0.9758969 22.5612 --3.79432 1.67466 22.464 --3.72159 2.50009 21.9158 --4.49495 3.10369 21.9539 --5.3014 3.28906 22.5334 --5.0138 4.19 22.7672 --5.45061 4.916 22.2848 --5.48488 5.16796 21.2641 --5.94861 5.2914 20.3308 --5.62445 5.36652 19.3903 --5.22768 6.29182 19.1841 --6.14341 6.26712 18.8145 --5.61719 6.39452 17.9652 --6.10534 5.55273 17.8517 --6.98833 5.62487 17.5105 --7.34195 4.86915 16.8934 --6.48641 4.60352 17.3568 --5.51965 4.48477 17.8496 --4.6781 4.1692 17.2818 --4.99704 4.98921 16.8027 --4.66352 4.23928 16.2949 --4.7597 3.24288 16.4605 --5.02135 3.37023 15.5684 --5.9268 3.40904 15.8462 --5.93066 2.69033 15.1967 --6.46015 1.89183 15.4298 --5.97087 1.25547 16.0639 --5.48825 0.9569169 15.2301 --5.01502 0.6202689 16.016 --5.40873 -0.2522141 16.1655 --5.84557 -0.001250536 17.073 --5.66956 -0.7742791 17.6143 --4.73681 -0.6064961 17.6853 --3.94726 -0.1405641 17.3354 --3.42055 0.3823579 17.9432 --2.43536 0.6982449 18.1111 --1.67294 1.06096 17.5337 --1.92632 1.94263 17.3153 --1.66695 2.4393 16.5278 --2.33579 2.66821 15.8142 --2.26839 3.23438 15.0128 --1.72216 2.55147 14.455 --0.792499 2.39492 13.963 --1.01595 1.47049 13.6366 --0.435737 1.55502 14.4676 -0.281482 2.09536 14.0451 -0.452657 3.02221 13.9832 --0.03647023 3.9488 13.9494 -0.295026 4.51042 14.6784 -0.39807 5.24785 15.291 -1.1862 5.4817 15.9281 -1.30632 6.31889 15.4169 -0.956525 7.22962 15.7198 -0.717265 8.17721 15.9127 -1.48833 8.58118 15.4004 -1.35629 9.61416 15.1757 -0.756229 9.41195 14.4451 -0.233297 8.55392 14.4531 --0.657418 8.36828 14.8184 --1.27213 7.79572 15.3577 --1.56239 6.88016 15.6475 --1.69537 7.17001 16.7054 --1.16217 7.32904 17.5741 --0.519996 6.93806 18.21 -0.001502085 6.94523 19.0375 -0.319531 7.63463 18.4952 -1.08252 7.9272 17.9665 -1.92018 8.48213 17.906 -2.37683 9.36327 17.5847 -3.01797 9.26593 16.8635 -3.05938 9.92907 16.1827 -2.71254 10.8397 15.9111 -1.95224 11.2068 15.419 -1.39757 11.897 15.9257 -0.440535 11.5693 16.0728 --0.431982 11.1584 16.2884 --0.823348 11.7711 16.9477 --1.79572 12.0241 17.0228 --2.44767 11.2706 17.0925 --3.27913 11.5439 17.435 --3.98258 11.1465 16.9052 --4.52637 11.0621 16.0153 --3.96333 11.8639 16.1102 --3.31606 11.4527 15.4064 --3.3598 10.5127 15.1708 --3.07717 9.90199 15.9513 --2.84445 9.41486 15.0957 --1.90804 9.55034 15.0367 --1.95755 9.40783 15.9949 --2.3107 9.64181 16.9336 --1.91241 8.88985 17.5614 --2.3557 7.99968 17.3585 --3.29489 7.82852 17.2924 --4.35085 7.64661 17.2769 --4.52483 8.59425 17.5392 --5.52312 8.61525 17.4682 --6.43929 8.67011 17.9125 --6.62915 8.44699 16.9832 --7.48997 8.93207 17.1254 --8.35121 8.67164 17.4766 --8.73507 7.79997 17.9218 --9.17031 6.96659 18.1828 --9.46145 6.55346 19.0879 --9.99601 6.35177 18.1984 --10.8072 6.10779 17.6038 --10.1708 5.88915 16.8632 --9.32302 5.5957 17.2592 --9.79567 4.85061 17.7652 --9.84323 3.97941 18.1793 --10.3379 3.77281 17.3482 --11.0041 3.11954 17.6233 --11.1846 2.34166 18.2699 --11.3077 2.15845 17.3224 --11.2598 1.68814 16.4474 --10.3608 1.68617 16.956 --10.4009 0.8290709 16.3585 --9.97106 0.4625279 17.1954 --9.72376 0.7649709 18.1487 --9.42196 -0.1227481 17.9359 --9.93362 -1.03028 17.7878 --10.7726 -1.39647 17.2498 --10.1325 -2.14979 16.8517 --10.2503 -3.10051 17.2427 --9.77458 -3.39673 16.3668 --9.07681 -3.00125 15.836 --8.68544 -2.13801 15.6461 --8.46047 -1.29713 15.1198 --7.52676 -0.9147031 15.25 --7.78187 -0.5061731 16.174 --7.61409 -1.22045 16.7775 --8.47026 -1.64882 17.1196 --8.23695 -1.10643 18.0179 --8.87871 -1.79948 18.3726 --9.47966 -2.27646 19.0046 --10.3828 -1.99695 19.4502 --11.3457 -2.32622 19.2508 --11.4249 -1.91662 18.3106 --11.4643 -1.27815 19.057 --12.145 -1.05747 18.3592 --12.3441 -1.8133 18.9196 --12.3564 -2.67689 18.5365 --11.7751 -2.94705 17.7541 --12.7356 -2.60118 17.5336 --12.8955 -2.83162 16.6069 --13.8152 -3.11445 16.8873 --13.2377 -3.9447 16.8912 --13.2704 -4.63087 16.1736 --12.5908 -4.6114 15.4655 --12.364 -4.00137 16.2124 --11.5665 -3.33246 16.1004 --11.1276 -2.91386 15.3262 --12.1046 -2.70158 15.325 --12.3588 -2.89598 14.3428 --12.7441 -3.7051 14.7497 --13.3798 -3.46943 15.4666 --14.2902 -3.85219 15.8335 --15.2945 -3.54731 15.9353 --14.6511 -3.02693 15.3534 --15.2812 -2.305 15.1662 --14.9897 -1.71937 15.9627 --15.9162 -1.74234 15.9776 --16.1593 -0.9150431 15.5164 --16.7863 -1.09016 14.795 --16.9673 -1.87161 14.142 --16.8965 -2.2246 14.9936 --17.6086 -2.91009 14.8043 --17.4582 -3.91199 14.4678 --17.5109 -4.5784 15.2454 --17.3387 -3.67502 15.6705 --17.5511 -3.53909 16.6148 --17.0708 -3.19278 17.4277 --16.7491 -2.56466 18.1019 --16.2673 -1.65735 17.9786 --15.7559 -0.7729371 18.3099 --15.5531 -1.02127 17.3238 --14.9254 -1.44104 17.8584 --14.8566 -2.31879 17.3559 --15.2033 -2.51268 18.296 --14.5085 -2.28098 18.9709 --14.2126 -1.6524 19.6825 --13.8885 -0.8455291 20.2602 --14.0771 0.1001789 20.3876 --14.132 1.08998 20.3361 --14.0657 1.67083 19.5364 --13.561 0.9319009 19.2784 --12.6583 1.18574 18.7263 --12.376 1.57846 19.6251 --12.3124 1.4091 20.6053 --12.2302 0.4217849 20.6174 --12.1371 -0.6572291 20.5515 --11.1698 -0.3581631 20.7003 --10.8272 0.5140509 21.0789 --10.979 1.45377 20.7236 --11.172 2.23599 21.2647 --10.7487 1.78645 22.0483 --10.0083 1.80938 22.7537 --9.81458 1.3421 23.6951 --10.1977 2.0792 24.1954 --11.0591 1.94857 23.6274 --11.946 2.1409 23.8964 --12.8461 1.86973 24.2515 --13.5169 1.02771 24.2243 --13.6795 0.6323989 25.19 --14.5057 1.03741 24.7954 --14.464 1.45838 25.7284 --14.3281 0.8274849 26.5187 --15.2384 1.29468 26.4223 --15.9738 1.91644 26.6419 --16.6474 2.43745 26.1147 --16.4351 3.35893 26.251 --17.1533 3.69354 26.7755 --17.0724 4.67839 26.6334 --16.6069 5.46636 26.807 --15.6239 5.66349 26.9223 --14.7689 5.31954 27.0369 --15.3619 4.64461 27.3967 --14.8233 3.97708 27.823 --14.4789 3.07267 27.7415 --14.0386 3.29948 28.5975 --13.0364 3.38173 28.3586 --12.2707 3.88933 27.8666 --11.9399 4.05107 28.812 --12.5444 4.89123 28.7826 --12.1118 5.57835 29.3341 --11.3539 6.31362 29.3602 --11.2644 6.38652 30.3147 --10.4343 6.39975 29.8653 --10.8 7.30987 30.1272 --10.3176 8.0031 29.5132 --9.83753 8.90007 29.3571 --9.66591 9.70606 28.7058 --8.80694 9.96169 29.1745 --8.72459 10.9123 29.6128 --7.95256 11.4525 29.3908 --7.46787 10.582 29.3119 --7.1167 9.59736 29.1131 --6.38114 10.1605 29.3588 --6.11763 10.2431 28.4125 --5.10435 10.0179 28.2777 --4.6689 10.9536 28.3371 --4.04731 10.2733 27.929 --3.56455 9.77776 27.3134 --4.25147 9.49787 26.5559 --3.41422 9.30634 25.9967 --3.11605 8.40876 25.9881 --2.75844 8.61951 25.0464 --2.77269 7.57708 25.3082 --3.33558 6.76937 25.2797 --3.27294 6.35714 26.1728 --3.49942 5.45805 25.7926 --3.70976 5.52042 24.7639 --3.95999 5.19512 23.8186 --3.76067 4.89075 22.86 --3.18962 5.60944 22.51 --3.36531 6.29943 21.8091 --4.20933 6.31208 21.3261 --3.76648 7.15583 21.6139 --4.23427 6.9834 22.5762 --5.15967 7.42483 22.5685 --5.45973 7.69452 23.4668 --6.18652 7.08279 23.7398 --6.14138 7.36286 24.6649 --6.86478 6.75831 25.0105 --6.43099 5.86369 24.9167 --6.15543 5.16122 24.2012 --6.78254 5.01731 23.3778 --7.29719 4.44378 22.7711 --7.47646 5.22517 22.1777 --7.97357 5.7412 22.9103 --8.48787 5.06287 22.4028 --8.49454 4.26179 21.7851 --8.14959 4.7407 20.9451 --8.62406 4.04348 20.312 --9.33584 4.74227 20.2345 --9.85887 4.74565 21.0707 --10.6094 4.20086 21.2982 --10.4969 3.42628 20.6048 --10.1057 2.49366 20.4265 --9.37048 2.22283 21.0553 --8.83847 1.72776 20.4262 --8.6225 1.48771 21.3957 --8.06066 1.04873 20.6955 --7.13799 1.46432 20.8415 --6.47869 1.54816 21.5671 --5.73978 1.87458 21.2111 --5.06796 1.63251 20.4382 --4.22272 1.0339 20.2933 --3.5307 1.40266 20.8684 --2.71778 1.23901 20.4073 --2.96053 0.3081989 20.4421 --3.78127 -0.01714367 20.8348 --3.72428 -0.7656301 20.1231 --2.76204 -0.7804141 20.0242 --1.86907 -0.4687881 19.6155 --1.16157 0.07829463 19.0897 --0.436628 0.5155719 19.4964 -0.03167987 1.17807 18.9355 --0.129245 2.1454 19.0315 --1.15818 1.96742 19.1921 --1.1119 1.58037 20.0905 --0.263751 2.10266 20.1601 --0.443674 2.60316 21.0204 --1.10246 3.39687 20.7365 --1.56616 3.95572 21.3721 --2.43138 3.45957 21.4434 --2.63951 2.84926 22.1802 --1.67232 2.94211 22.2395 --1.23175 2.31914 22.9423 --0.898716 1.59364 23.641 --0.849194 2.43031 24.2867 --0.739508 3.29586 24.9016 --0.2869 3.80642 25.6161 -0.382319 4.43077 26.0251 --0.333737 4.99124 25.749 --1.12413 4.36119 25.9818 --0.990136 4.78225 25.0796 --1.88272 5.17638 24.8547 --2.55426 5.35055 24.1026 --2.3602 6.14073 23.5913 --2.2866 6.74255 24.3889 --1.79421 7.37781 23.8535 --2.79383 7.52572 23.85 --2.42566 7.3134 22.9673 --1.82791 8.11642 23.0738 --1.61817 8.15036 22.0384 --2.28356 7.40483 21.9268 --2.74413 8.00422 21.212 --1.82105 7.73237 20.9685 --0.857884 7.85424 21.0725 --0.452438 8.3524 20.277 --1.2691 8.80815 20.3247 --1.65149 8.17832 19.6802 --2.02312 7.85721 18.8287 --2.17635 6.85522 18.7187 --1.48834 6.97156 19.3413 --1.61762 5.96273 19.5437 --1.03759 5.47769 18.8034 --0.241701 5.62291 19.4102 --0.75936 4.82325 19.7137 --1.54036 5.05784 20.4184 --2.15771 5.81791 20.7536 --1.43818 6.51241 20.9279 --1.1543 5.63139 21.2759 --0.368647 6.11537 21.6567 -0.374717 6.69013 21.2831 -0.696121 7.41715 20.701 -1.07549 6.46229 20.4345 -1.31146 5.53953 20.0625 -0.556378 5.14609 20.4766 -0.328547 4.22771 20.7173 -0.539241 3.26422 20.7252 -0.776523 3.36445 19.7335 -1.48603 3.03193 20.432 -2.40116 2.7974 20.1711 -3.17091 2.5932 19.6627 -3.06762 2.72151 18.6879 -2.70799 3.43746 18.0576 -2.23343 4.24034 17.7069 -1.35904 4.24038 18.3211 -0.97544 4.48125 17.5101 -1.42054 3.67879 17.1654 -1.34919 2.81517 16.8282 -0.474079 2.82814 16.4032 --0.490896 3.08253 16.1635 --0.555686 2.6366 15.2565 -0.350867 2.97499 15.2968 -1.34414 3.10165 15.0029 -1.04434 2.11463 15.009 -1.75337 1.72056 15.5334 -2.18154 2.34409 16.1841 -2.70576 3.13702 16.0116 -2.91837 3.49003 16.9114 -3.68883 4.09484 16.8241 -4.61692 3.90823 16.6394 -4.33343 3.09237 17.2112 -4.53191 2.12044 17.3156 -4.39102 1.19616 17.041 -3.35443 1.36223 17.262 -2.50747 1.10441 16.8571 -1.73581 0.7118349 16.3518 -0.965049 1.31485 16.5103 -1.3411 0.9003579 17.3351 -1.27293 1.75257 17.9252 -0.739971 2.54536 17.7007 --0.258172 2.64237 17.5495 --0.350157 3.5073 18.1163 --1.32713 3.07561 18.0399 --2.24884 2.67137 18.1282 --3.06663 3.1052 18.6492 --2.92911 2.76705 19.5906 --3.12354 3.3917 20.3402 --2.70003 4.27346 20.2754 --3.33379 4.86894 20.7886 --2.56856 4.89235 21.4081 --2.15486 5.35642 22.2041 --1.41339 5.8773 22.6134 --0.43116 5.73971 22.9834 --0.129524 5.00308 22.368 --0.241375 4.29839 21.693 --0.003512875 3.43022 21.9456 -0.717606 3.14719 22.6411 -0.227399 3.72732 23.3243 -0.340758 3.64375 24.3295 -0.763954 4.28826 24.964 -1.58353 3.77099 25.2489 -2.32893 4.38341 24.9709 -1.85703 5.27578 24.9063 -1.20565 5.9386 24.5953 -1.96457 6.59727 24.4432 -2.87749 6.97947 24.6976 -2.187 7.20575 25.3032 -2.01651 7.87504 26.086 -1.23468 8.419 25.9756 -0.833214 9.03684 26.6049 -0.226623 8.24739 26.9123 -0.128653 8.50486 27.9073 -1.00834 8.63921 28.1557 -1.42311 8.83476 28.9471 -1.26653 9.85496 29.0708 -1.87353 10.5133 28.502 -1.40795 11.0028 29.1941 -0.756412 11.5488 28.7964 -0.142976 12.307 29.0997 -0.925243 12.891 28.7958 -1.25841 12.3249 27.9889 -1.42472 13.1732 27.5042 -0.617704 13.7005 27.2997 --0.270467 13.3004 27.2187 --0.757277 14.1908 27.1943 --0.56207 14.9415 27.7447 --0.240886 15.3555 26.9476 -0.229181 16.0181 26.3045 --0.532917 15.7778 25.7283 --0.959145 15.5875 24.8121 --0.615544 15.8656 23.945 -0.141355 16.0089 23.2849 -0.611625 15.2467 22.8725 -1.05582 15.4761 23.6938 -0.83154 16.1086 24.387 -1.33632 15.9539 25.2726 -1.80584 15.3969 25.9736 -2.3371 14.5656 25.7281 -2.10599 14.366 26.6934 -2.11803 13.3646 26.6438 -1.15599 13.0709 26.5428 -1.67481 12.8631 25.743 -2.5154 12.444 25.2497 -2.61927 11.493 25.4907 -2.16088 10.6256 25.1818 -1.82656 10.6273 24.3044 -2.08344 11.591 24.482 -1.23242 12.1235 24.2612 -1.40502 12.706 23.4598 -1.48481 12.7294 22.4484 -1.79703 11.9219 21.9126 -2.17305 11.4043 22.6274 -1.70389 10.5727 22.8207 -1.56933 9.66225 23.2736 -1.42951 8.77509 22.8014 -1.70107 8.78999 23.6827 -0.742673 8.63485 23.6347 --0.257419 8.61138 23.5598 --0.774801 9.50415 23.5392 --1.56579 9.98542 23.2583 --1.62114 10.9991 23.2331 --1.82707 11.331 22.2793 --1.73312 11.3004 21.2518 --0.776017 10.9841 21.0314 -0.09542387 10.8025 20.5483 -0.273923 9.79455 20.6568 --0.005826175 9.20497 19.9338 --0.835264 9.61603 19.4875 --0.703451 9.83437 18.5096 --0.387791 10.7553 18.5097 --1.05126 11.132 19.231 --0.396326 11.9487 19.1533 --0.06319823 12.9725 19.307 -0.360388 12.877 20.2414 -1.33045 12.5664 20.4017 -1.24448 13.5474 20.5848 -0.906824 13.4818 21.5328 -0.710028 14.4649 21.3322 -0.452694 14.8508 20.4626 -1.43237 15.1947 20.7094 -2.19565 15.4112 21.3972 -1.78387 16.3378 21.6194 -2.73019 16.3739 21.3692 -3.61439 15.917 21.222 -3.71144 15.3155 21.9306 -4.39425 14.9263 22.5009 -4.58766 15.6884 21.8812 -4.3378 16.7289 21.6719 -4.53804 16.6389 20.7162 -4.74376 15.6451 20.7504 -5.58622 15.2612 20.2791 -6.38089 15.4745 20.8395 -6.76335 15.2998 19.9139 -7.68337 15.7348 20.0025 -7.84459 15.6741 19.015 -8.05188 16.5339 18.5067 -7.87005 17.5245 18.6452 -7.96272 17.3367 19.6141 -8.7142 17.5652 19.0509 -8.87512 17.7599 18.0945 -9.13599 17.3845 17.1687 -8.60628 17.115 16.2897 -8.45493 18.1287 16.2216 -9.38024 18.5574 15.999 -9.8873 17.8435 16.53 -10.5558 18.4526 16.891 -10.9788 18.1191 15.9944 -10.4884 18.656 15.2742 -10.4957 18.8953 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30.8296 --5.27053 10.9557 29.9762 --4.30525 11.01 30.0811 --3.59771 11.6917 30.1106 --4.06496 12.4745 30.6189 --4.30454 13.3517 30.1327 --4.7354 13.146 29.2417 --4.43759 13.8247 28.5367 --4.44589 13.2246 27.6776 --3.54471 12.8259 27.4431 --2.97426 11.9721 27.7024 --2.63082 11.8427 26.7701 --1.79132 11.478 26.4223 --2.04564 11.1707 25.5062 --1.69896 10.2715 25.6491 --2.54514 10.2078 26.0737 --2.92259 10.3012 25.1281 --3.89321 10.1545 25.0886 --4.69932 10.5023 25.4382 --5.44236 10.7704 26.0223 --5.92612 10.8491 25.1167 --5.94666 11.3521 24.2954 --5.98103 10.6516 23.7341 --5.79544 10.9259 22.7268 --6.03681 10.4138 21.8686 --5.02499 10.3981 21.6933 --5.3175 9.76208 20.978 --4.95117 9.22439 20.3478 --4.50195 8.48961 20.7825 --5.14891 7.64304 20.9614 --5.50693 6.71433 21.0533 --6.39082 7.16387 21.3137 --6.15971 7.96535 20.6806 --5.97209 8.60679 21.3932 --6.88254 8.96117 21.3908 --7.5414 8.35542 21.777 --7.96573 9.11367 22.3164 --8.20687 9.93344 21.8859 --9.11952 9.75923 21.4376 --9.37911 8.78747 21.275 --8.92006 8.18755 21.8607 --9.74585 7.6449 21.675 --9.4214 6.74282 21.319 --9.78391 6.42066 20.425 --10.3614 7.0081 19.8029 --10.9148 7.34918 19.0422 --11.4588 7.86553 18.3409 --12.2094 8.21997 18.9922 --12.6787 7.97777 19.7537 --12.5555 7.10324 20.1042 --12.9064 6.45121 19.4266 --13.1518 6.44791 18.4829 --13.7867 5.87947 17.9239 --14.4616 5.30524 17.4434 --15.1579 5.24338 16.7547 --15.8657 5.72659 17.3279 --16.3316 5.04445 17.8508 --17.0806 4.83549 18.3979 --17.6606 5.33174 17.7499 --18.5623 4.85001 17.7364 --19.2185 4.69888 16.9889 --19.6732 3.8089 17.2818 --20.3651 4.52437 17.2226 --20.3227 5.51888 17.5012 --21.1094 6.06236 17.4214 --21.5878 5.23942 17.5871 --21.8801 5.38857 18.5018 --21.2377 6.0622 18.8767 --20.475 5.72109 19.2422 --19.6627 5.69619 18.7191 --18.987 6.17167 19.2432 --19.1327 6.56931 20.1538 --18.5137 5.91762 20.6247 --17.6884 6.37321 20.9763 --17.7948 6.11681 21.9682 --18.2732 5.5893 22.6585 --17.5667 4.89982 22.8932 --16.9097 4.39922 22.5233 --17.2295 3.98463 23.4291 --16.3819 3.36921 23.2535 --16.5822 3.15409 24.2063 --16.9198 3.47553 25.0464 --15.9589 3.19106 24.9607 --15.1913 2.67156 24.5982 --14.6271 3.44168 24.4893 --13.702 3.2744 24.9376 --13.3353 3.43365 24.0285 --13.2848 4.0862 23.2894 --13.1972 3.81034 22.3193 --13.7756 2.99899 22.2779 --14.3248 3.75364 22.6128 --14.5164 3.98136 21.6338 --15.3875 4.31297 21.9605 --15.4825 3.98837 22.8994 --14.8565 4.62548 23.3565 --15.5014 5.18696 22.7354 --16.3159 5.52307 22.2651 --16.3509 6.23878 21.6301 --15.8843 6.24583 22.5212 --16.2967 7.11448 22.3753 --15.4056 7.47757 22.1632 --14.7867 7.79749 22.877 --14.9281 8.57886 23.5063 --14.2384 8.78297 22.75 --14.1538 9.67032 22.3508 --13.4932 9.61191 23.1463 --14.3558 10.0762 23.2016 --14.6818 10.6731 22.4813 --14.1785 10.694 21.6536 --14.067 9.93799 20.9663 --14.6433 9.93238 20.1828 --13.7416 9.56059 20.0677 --13.7089 8.79542 19.3993 --14.7065 8.71758 19.3935 --14.52 8.04798 20.1101 --13.8356 7.39021 20.4236 --14.0701 7.14491 19.4882 --14.5609 6.74878 18.7875 --15.0772 5.91119 19.0819 --14.5916 5.26851 19.6679 --14.383 4.45901 20.1809 --14.6783 3.62418 19.6494 --15.0126 3.5617 20.5823 --15.5845 2.83548 21.047 --14.6093 2.73084 21.4115 --14.7656 1.83973 21.6722 --14.8885 0.9385479 22.1 --15.0353 0.1008669 22.7377 --15.5127 0.3108749 23.6096 --16.2659 0.1665499 23.003 --17.2289 -0.1924341 22.9495 --18.187 -0.4523701 23.2256 --17.827 -0.5251921 24.1657 --18.5091 0.1946159 24.0059 --18.3242 0.6734629 24.8986 --17.5131 0.9857489 24.3253 --16.887 1.66044 24.8039 --17.2923 1.50815 25.6913 --16.9746 0.9162689 26.3324 --16.7503 0.2726529 27.0097 --17.6748 0.5326559 26.7803 --18.2759 -0.3542361 26.7608 --17.9529 -1.32186 26.7978 --18.5836 -1.4212 27.6086 --18.6726 -1.23734 28.6199 --18.8478 -1.38532 29.5823 --18.4953 -0.4692981 29.3457 --18.3006 0.3741809 28.9452 --17.9279 1.13785 28.4125 --17.9008 2.07153 27.968 --18.6189 1.41648 27.6179 --19.1111 0.6868579 28.1118 --19.2358 -0.3026581 28.3022 --19.7716 -0.9590701 27.6981 --20.6998 -1.07101 27.4757 --21.3647 -1.03349 28.1435 --21.0213 -0.1422501 28.4678 --21.1997 -0.09121377 29.5062 --20.8746 0.6891999 28.9494 --21.6105 1.10457 29.4108 --22.0436 0.7902849 28.5038 --23.0433 0.7767919 28.2355 --22.5049 -0.09148827 28.2411 --23.3058 -0.3401701 27.6968 --23.6874 -0.3061921 26.7915 --23.4645 -0.8401271 25.9568 --22.9186 -1.11428 25.0957 --22.5432 -2.06446 25.0774 --23.0421 -2.91505 24.6293 --23.1389 -3.66669 23.9348 --23.1328 -2.78367 23.5223 --23.9242 -2.17944 23.4265 --24.6522 -2.87911 23.3929 --24.9237 -2.18173 22.7169 --25.7609 -2.60663 22.722 --25.8535 -1.64407 22.6945 --24.9753 -1.07581 22.8646 --25.6662 -0.5610121 22.3817 --24.9302 -0.1339661 21.9277 --24.4414 -0.06187377 21.0273 --25.1635 -0.6854571 20.8387 --25.0061 -0.04801927 20.1002 --24.4987 0.6623519 19.7567 --23.6091 0.9984749 20.1518 --23.1415 1.00536 20.9724 --22.3655 0.4108719 21.2204 --22.1078 -0.04754077 20.4028 --21.135 -0.3402271 20.3023 --21.375 -0.8269201 21.1243 --20.4018 -0.6765591 21.2813 --19.8768 -1.42046 20.8733 --20.1698 -1.28786 19.9457 --19.5924 -0.4982951 19.721 --18.876 -0.4377271 18.9896 --18.4751 0.04940623 19.7843 --17.485 0.09339073 19.5815 --17.2054 -0.8796381 19.5343 --17.0477 -1.51909 20.2887 --16.4202 -2.16723 20.7375 --16.8472 -3.02566 20.2944 --17.4558 -3.72183 19.9951 --17.3843 -2.83138 19.4716 --18.217 -2.63031 19.0868 --18.2203 -3.47036 18.5185 --18.2298 -2.99064 17.6879 --19.0302 -2.42943 17.6569 --19.5831 -1.67385 18.1481 --19.1171 -0.8631901 17.8222 --18.6735 -0.002140926 17.8457 --18.3604 -0.7143201 17.2014 --17.6891 -0.7642781 16.444 --17.2961 0.1484479 16.4754 --17.3642 1.06322 16.0277 --17.819 0.9107539 15.2332 --18.7358 1.12058 15.4803 --19.492 0.4399269 15.275 --19.7423 0.9311009 14.4676 --19.1859 0.5498339 13.6909 --18.7957 -0.1102041 14.3288 --17.9028 0.1782979 14.1812 --17.0647 0.4568279 13.8636 --16.9756 1.02058 13.0128 --17.1094 1.68858 13.7578 --17.6488 2.17114 14.4762 --17.7305 2.97121 15.1112 --18.3347 2.89887 15.8646 --18.417 2.94332 16.8662 --17.7097 3.42381 17.3961 --17.3964 3.79071 18.1895 --17.4759 2.98301 18.7294 --18.4235 3.15251 19.1381 --18.7122 3.8279 19.9054 --17.9672 4.27111 20.4602 --17.6016 4.1241 21.2569 --18.586 4.29568 21.2717 --18.5869 3.27437 21.2148 --18.9814 3.11216 22.1666 --18.8782 2.32694 22.7118 --19.6415 2.3604 23.3047 --20.171 1.5208 23.2643 --20.4765 0.6036149 23.3414 --20.772 -0.2996321 22.9523 --21.7501 -0.6225901 23.0502 --22.1293 -0.4463941 23.98 --22.9202 0.1508989 23.8526 --23.784 0.6846109 23.7916 --23.7461 0.7440459 24.7518 --22.7576 0.9736189 25.0705 --22.0851 1.69822 24.889 --22.677 2.25563 24.2488 --22.5912 3.22156 24.5038 --22.5096 4.14021 24.7509 --23.3451 4.72148 24.8352 --23.5204 5.61384 24.8606 --23.1995 5.4771 23.8936 --24.1696 5.25899 24.0561 --25.1103 5.35062 23.7679 --24.5585 6.06632 23.3036 --25.3713 5.97427 22.6805 --25.6226 6.84513 22.1932 --26.4593 6.44698 22.3166 --27.1419 6.05425 21.6622 --26.2487 5.61692 21.8215 --25.292 5.4875 21.5434 --24.6662 5.33119 20.7531 --24.8024 6.28559 20.6408 --24.1696 6.0273 19.8554 --23.3697 5.35595 19.8139 --23.169 4.40361 20.0098 --24.1013 4.20402 19.9151 --24.2843 3.66161 19.0574 --25.0243 3.75273 18.3058 --25.9239 3.7334 18.0207 --25.5343 4.56337 18.4349 --25.8316 5.19426 17.8066 --25.6949 6.17609 18.1529 --24.9472 6.4964 17.4398 --24.1164 7.05103 17.6821 --23.8077 7.66947 18.4121 --23.3644 7.72344 19.3241 --22.4556 7.26196 19.0668 --22.062 8.1736 19.1313 --22.7414 8.69509 18.7794 --22.5631 9.54953 18.2858 --23.1351 10.4148 18.3445 --22.6109 10.7452 19.0418 --22.7223 11.706 18.7633 --23.2833 12.3945 19.3447 --22.6369 11.8544 19.9075 --23.3586 11.3006 20.3522 --23.095 10.6678 21.0036 --23.4794 9.87139 20.5985 --22.5339 9.69464 20.3483 --21.6549 10.0544 20.6277 --20.8194 10.4701 20.1893 --21.0914 11.4228 20.0725 --20.5795 11.5807 19.1729 --20.8305 12.4212 19.6876 --20.8346 12.706 18.7376 --21.7635 12.2962 18.5502 --22.4295 13.0798 18.4389 --21.8848 13.8665 18.1076 --22.7587 14.1077 18.3949 --22.6501 14.9562 18.9063 --23.6685 15.0673 19.0213 --23.7942 14.1084 18.7776 --24.642 13.6849 18.363 --24.8586 13.7307 17.4818 --24.179 13.0176 17.3696 --24.3911 12.0283 17.3361 --24.7808 11.1869 17.1098 --25.7773 10.8549 17.1482 --26.3579 10.7844 16.3098 --26.0516 11.6282 16.05 --25.4175 12.2595 15.4909 --24.9002 11.4044 15.7678 --24.0854 11.5598 15.2399 --24.8667 11.3335 14.6596 --24.3341 12.207 14.4296 --25.2852 12.5713 14.2966 --25.6353 12.8046 13.3467 --24.6491 12.6971 13.2806 --23.7816 12.2378 12.9397 --24.1335 11.6613 12.1639 --23.5195 11.0872 12.6337 --23.1104 10.8908 13.5469 --22.5324 10.0805 13.5635 --22.0808 9.27491 13.1962 --21.8137 9.13135 12.2911 --21.2631 9.10459 11.4543 --21.2817 9.98759 11.0646 --22.1565 10.162 10.6345 --22.5652 10.9669 11.0457 --23.2005 11.5551 11.5629 --23.6474 11.4888 10.6656 --23.9356 10.5341 10.5563 --24.8606 10.1712 10.3967 --25.8043 10.3689 10.0093 --26.3324 11.1998 9.68461 --25.6072 11.5576 9.0225 --25.8804 10.7354 8.56323 --26.6143 10.6941 7.88041 --26.1792 11.0693 7.07356 --26.5145 11.5714 6.23982 --27.2654 11.7498 5.56775 --27.7374 12.1084 6.37974 --28.4716 12.806 6.67095 --29.3842 12.4335 7.00184 --29.7947 11.6028 6.70223 --30.31 10.781 6.71252 --31.0686 11.2663 6.25234 --32.0348 11.5843 6.28058 --31.6137 12.0296 7.01392 --32.3661 12.2151 7.75306 --31.7357 12.9675 8.10269 --31.0297 13.6469 8.12657 --31.5147 13.7893 7.25154 --32.0401 13.1777 6.66333 --31.3428 13.2869 5.98396 --30.8962 13.0869 5.08818 --30.5843 12.1392 5.1499 --29.6671 12.5074 4.92466 --29.1215 13.2127 4.44513 --28.6476 13.6821 5.18371 --27.6386 13.7717 4.97338 --27.022 14.4491 5.29122 --27.2057 14.6123 6.25409 --26.805 15.5738 6.39628 --25.8825 15.4069 6.11553 --24.9938 15.3025 6.59875 --24.279 15.6334 6.00895 --23.9109 16.1239 5.23267 --23.7267 17.0443 4.91467 --22.7246 17.3931 5.04679 --22.4811 17.104 4.09164 --21.6916 16.631 3.70478 --21.0977 16.1224 4.23216 --21.0794 15.683 5.12673 --20.0854 15.518 5.16461 --19.739 16.4343 5.25751 --19.2131 16.6617 6.12038 --18.8459 15.7934 5.83032 --18.1789 15.0831 5.81031 --17.1661 15.1198 5.98822 --17.4644 16.1376 5.85744 --17.6513 16.1619 4.84522 --18.4936 16.7053 4.85462 --18.5345 17.5423 5.41013 --18.2709 18.2763 6.06027 --17.894 19.1554 6.36879 --17.4666 19.4769 7.30791 --17.4344 20.4177 7.12227 --17.9044 21.02 7.83779 --17.6188 21.6705 8.48269 --18.2492 22.3563 8.68685 --19.0491 21.7112 8.33057 --19.883 21.7093 7.91159 --19.4908 22.0909 7.01876 --19.2065 22.9475 6.53505 --19.5051 23.1516 7.43552 --19.8127 23.9034 8.01308 --20.4853 24.4388 8.51202 --20.724 25.3547 8.95203 --21.2292 26.0688 9.45084 --21.1646 26.014 10.4375 --22.1422 25.831 10.1633 --22.5471 26.2039 10.9396 --23.0646 26.3172 11.7763 --22.1152 26.1027 12.0249 --21.7604 26.9981 12.4579 --21.1577 27.7658 12.6511 --21.648 27.6858 11.8031 --20.679 27.9025 11.5702 --20.0775 27.378 12.2064 --19.1424 27.0219 12.4217 --19.0808 26.6068 11.5361 --18.9778 25.6653 11.918 --18.9056 24.7452 12.2398 --18.6698 24.4249 13.1544 --19.5193 24.5188 13.6219 --20.5115 24.6694 13.3884 --20.4561 23.6492 13.3375 --20.7069 23.1358 12.5338 --20.0188 22.7979 11.8716 --20.1708 23.7303 11.4051 --20.7842 23.3466 10.7554 --21.6192 22.8548 10.8845 --21.6499 22.9888 9.86657 --22.0685 22.0659 9.79239 --22.1637 21.7139 10.7249 --21.3694 21.643 11.4308 --21.4744 20.7723 12.0477 --22.1068 20.4377 12.7222 --21.6536 21.1993 13.3045 --21.3793 20.7101 14.1314 --20.6809 21.2881 14.5455 --20.6798 21.4975 15.475 --21.3182 21.4736 16.1669 --22.2474 21.8894 16.0612 --22.5953 21.5518 16.9836 --21.9156 21.9263 17.5473 --22.4599 21.4552 18.255 --23.1808 20.8412 18.05 --22.4578 20.3071 18.258 --22.202 19.4807 17.6634 --21.3894 20.1193 17.7696 --20.6776 20.7987 17.873 --20.3446 21.1227 17.0654 --19.6232 20.3901 16.8719 --19.0894 20.4375 16.0204 --19.1272 19.4581 15.8261 --19.0966 19.217 14.7902 --19.6694 18.7072 14.1803 --20.4552 18.6888 14.8226 --20.6674 18.4306 15.7422 --20.3408 17.5103 15.5035 --20.0707 16.6032 15.1799 --20.8879 16.3217 15.6853 --21.4775 15.8705 16.2557 --22.3568 15.4909 16.382 --22.1894 15.8427 15.5012 --22.3371 16.6869 15.1445 --22.0333 16.0297 14.4469 --22.4082 16.0744 13.5085 --23.3656 16.2672 13.5158 --23.2192 17.1578 12.9702 --23.916 16.9904 12.2647 --24.5851 17.213 11.6874 --24.146 17.2091 10.772 --23.8156 17.4951 9.82253 --23.691 16.5761 9.65023 --24.235 15.861 10.1599 --25.0708 15.571 10.635 --24.3581 15.2828 11.3218 --23.907 14.4246 10.9911 --23.1818 14.3431 10.2233 --22.1994 14.4153 10.3133 --21.3913 13.8928 10.2759 --21.4987 13.5508 11.2282 --20.7441 13.7107 11.7399 --20.2721 14.3938 12.3467 --20.925 14.0418 12.9704 --20.3734 13.3743 13.6485 --20.1928 13.1362 14.5835 --21.0726 12.619 14.8008 --21.907 12.6852 15.3948 --22.6271 12.3618 15.9153 --22.6921 11.4694 16.2772 --23.5591 11.8821 16.8167 --23.5735 10.8329 16.8661 --23.6823 9.95208 16.3182 --23.1899 9.25396 16.9063 --23.6422 8.68967 16.2652 --23.2204 7.80625 16.0122 --23.1589 8.21481 15.0417 --23.6382 7.33632 14.6345 --23.8257 6.44376 15.1577 --23.3361 5.7585 14.6132 --22.541 5.15062 14.3652 --22.4227 4.30402 14.8777 --23.4149 4.40223 14.7731 --24.1127 3.93343 15.271 --24.4207 3.13992 14.8008 --24.4093 2.67677 13.8488 --24.3873 3.18045 13.0363 --24.6592 3.93111 13.6143 --23.979 4.54525 13.1312 --23.3618 3.84353 12.7459 --22.364 3.62566 12.8998 --21.6034 4.25903 12.669 --21.3495 4.03056 11.7903 --21.6773 3.0411 11.8116 --21.0703 2.72507 12.535 --20.2631 3.20918 12.1574 --20.2497 2.23959 11.987 --19.3155 2.55164 11.9415 --18.6353 3.24762 11.9546 --18.0776 3.05433 12.767 --17.7847 3.93117 12.3158 --16.8872 3.99144 11.9943 --17.1921 3.01748 12.3963 --17.2927 2.07128 12.7641 --16.4518 2.48771 13.1928 --16.157 2.64031 12.2582 --16.0055 2.44711 11.2432 --15.144 2.83982 11.4457 --14.5094 2.21121 12.024 --14.3463 1.40988 12.6389 --13.4321 0.9371269 12.7704 --13.4447 -0.04806037 12.5063 --12.5911 -0.1811881 12.9986 --12.0812 0.6491789 12.9888 --11.3775 1.40001 12.7907 --11.7397 1.64666 13.6832 --11.4468 2.254 14.3736 --11.7889 2.98437 13.7965 --11.2182 3.69827 13.9589 --11.7046 4.57666 14.3271 --12.0426 3.98731 13.5007 --12.5908 4.80649 13.5827 --12.6416 4.66244 12.5739 --11.8579 4.12006 12.0974 --11.1874 4.80016 11.8683 --11.3776 5.23437 12.759 --11.4915 6.2562 12.9629 --11.5046 6.70273 13.8868 --12.3315 7.25776 13.9563 --12.7117 6.72575 14.6714 --12.5316 6.85418 15.6202 --11.8064 7.36243 15.1744 --11.8451 8.36513 14.9547 --12.7174 7.92712 14.8537 --13.5642 7.70128 15.2866 --13.8657 8.29963 14.6168 --13.9564 7.79027 13.8161 --14.4094 7.15712 14.3501 --14.3468 6.58089 15.1467 --14.4884 5.90523 14.4795 --14.7155 5.06278 14.9991 --14.0505 4.66439 14.3347 --14.5294 3.93128 13.8956 --14.2364 2.97003 13.9428 --14.6069 2.13064 14.2792 --14.688 1.18424 14.5292 --14.5071 0.1902699 14.7433 --14.2823 -0.5606821 15.3974 --13.524 -1.20811 15.1652 --13.5942 -1.13658 14.2053 --14.0867 -1.97968 14.258 --14.5769 -2.56252 13.5928 --15.4902 -3.04816 13.7549 --15.7385 -2.59165 12.9073 --15.8357 -2.01715 12.0372 --16.445 -2.81988 12.097 --17.0792 -2.68862 12.8949 --17.9881 -2.75599 13.2879 --18.8346 -2.99186 12.9635 --19.4988 -3.02283 12.1673 --20.1976 -3.4139 12.8359 --19.7532 -4.32533 12.5259 --18.839 -4.56991 12.7099 --18.3951 -4.17272 13.4829 --17.4917 -4.52357 13.5213 --17.0641 -4.60136 12.6009 --16.2549 -4.68362 13.1621 --15.4939 -4.12084 13.4292 --14.6691 -4.4765 12.9728 --14.6656 -3.65752 12.4391 --14.6476 -4.32313 11.753 --13.6776 -4.66283 11.7215 --13.7301 -5.69202 11.6376 --13.1448 -6.35061 11.2179 --12.7574 -5.52365 11.584 --12.1736 -4.94371 12.1848 --12.842 -5.2083 12.9384 --13.5783 -5.27939 13.644 --13.4902 -6.17651 13.1994 --14.4057 -6.52402 13.2866 --14.3562 -6.97354 12.3591 --14.615 -7.62887 11.6458 --14.8069 -8.36125 10.8896 --14.5856 -9.17328 11.5389 --13.8087 -9.39008 10.9573 --13.8174 -8.65073 10.2559 --14.0519 -9.47135 9.66708 --14.7789 -9.66902 8.96843 --15.0803 -10.4636 8.54218 --15.0374 -11.4846 8.78984 --14.4105 -11.9962 9.33588 --13.7812 -12.0743 10.1845 --13.1962 -12.9 10.0741 --13.0538 -13.5696 9.34185 --12.2246 -13.1869 9.76267 --12.4798 -12.2357 9.69031 --12.0714 -11.6186 10.3804 --12.1794 -10.6208 10.0733 --12.5165 -10.1044 10.8808 --12.4184 -9.44783 10.1353 --12.1539 -8.6806 10.76 --12.1976 -8.27962 11.7027 --11.4265 -7.86601 11.1753 --10.9556 -7.92769 11.9986 --11.1915 -8.30279 12.8651 --11.8023 -9.12923 13.0127 --11.828 -9.07229 14.0063 --11.2001 -9.0135 14.7836 --11.5952 -9.84168 15.1764 --10.6904 -10.0223 14.9038 --10.1302 -10.8396 14.7605 --10.5029 -11.4179 14.1174 --11.1416 -11.5842 14.9066 --11.2242 -12.5605 15.1777 --11.5317 -13.4836 15.0639 --11.725 -14.4905 15.3132 --12.3741 -13.7678 15.5667 --12.435 -13.9258 14.5695 --11.9904 -14.289 13.7641 --12.6238 -15.1122 14.1629 --13.04 -15.782 14.771 --13.9029 -15.5369 15.2656 --13.7377 -14.5597 15.1611 --14.1663 -13.6683 15.224 --14.217 -12.7216 15.1278 --13.6967 -11.942 14.8575 --14.499 -11.2963 14.8886 --13.7169 -10.6717 15.0105 --14.1385 -9.8111 15.3582 --14.056 -8.81631 15.2429 --14.4813 -8.57581 14.3953 --15.1847 -8.71191 15.0675 --15.0514 -7.71003 14.9407 --15.3321 -7.51251 15.8825 --14.908 -6.58921 15.9068 --14.6714 -5.67807 15.6459 --15.5342 -5.24074 15.5652 --16.2389 -5.21051 14.8716 --17.1144 -5.6317 14.9657 --18.0109 -5.24926 14.7811 --18.3465 -4.32793 14.7115 --19.0306 -5.16055 14.7123 --19.3714 -4.30282 15.1305 --18.8486 -4.78579 15.7512 --19.2384 -5.2351 16.5672 --19.8194 -4.53081 16.9817 --19.7381 -3.62079 16.601 --20.5704 -3.84518 16.0759 --21.5085 -4.2948 15.9969 --21.9579 -3.45094 15.764 --21.2816 -3.02928 15.1384 --21.2253 -2.10826 15.3897 --21.7034 -2.24058 16.2761 --21.0459 -2.78734 16.7232 --20.626 -3.60996 17.2528 --19.8026 -3.20319 17.6697 --20.1867 -2.53149 18.2412 --21.1643 -2.39693 18.3186 --22.1375 -2.51574 18.6108 --22.4368 -3.37668 18.9218 --22.8845 -3.80557 18.125 --22.565 -4.75155 18.0827 --22.6369 -5.53053 17.3699 --22.2214 -6.45394 17.5042 --21.2175 -6.59485 17.2436 --20.6093 -6.59152 16.4205 --21.2274 -6.13979 15.765 --21.007 -6.29038 14.8 --20.1658 -5.87802 14.393 --20.4347 -6.50318 13.659 --20.1294 -7.3614 13.3379 --20.2815 -8.31904 13.6495 --21.1411 -7.81407 13.6691 --21.2453 -8.77627 13.4552 --20.4355 -9.31786 13.6686 --20.464 -10.0844 13.0139 --21.3752 -10.5898 13.1139 --21.8539 -11.4582 12.8058 --22.3566 -10.6054 12.7918 --23.2847 -10.4304 13.1392 --22.8335 -9.86882 13.7944 --22.9326 -9.0004 13.265 --22.8225 -8.2001 12.7304 --22.2137 -7.76809 12.1041 --22.5538 -8.06583 11.2631 --23.4181 -8.13162 10.7142 --23.5371 -9.01777 10.1883 --22.8542 -9.48906 9.59995 --21.9935 -9.85428 10.0257 --21.2578 -10.1448 9.40457 --20.3342 -9.78064 9.55296 --19.8757 -10.0564 10.4057 --20.2877 -10.8476 10.8672 --21.2219 -10.9051 10.7232 --21.232 -11.285 9.76872 --20.976 -11.7902 8.91172 --20.1906 -12.2223 9.4151 --20.1321 -12.2628 10.3815 --19.4145 -11.5355 10.6352 --18.8021 -11.0408 11.2093 --18.0605 -10.9506 11.8919 --18.0788 -10.845 12.8903 --17.2406 -10.3265 12.3753 --17.5709 -9.4526 12.6933 --17.0711 -8.58167 12.3955 --16.1007 -8.82916 12.0808 --15.7548 -8.87283 13.0025 --15.2406 -9.65447 12.7039 --14.4041 -9.93805 13.1609 --13.8399 -9.72105 13.9656 --12.9552 -9.29287 14.2124 --12.3149 -10.0254 14.0559 --11.6958 -10.6328 13.5311 --11.2286 -10.4575 12.616 --11.1151 -11.3363 12.1987 --12.1197 -11.344 11.8726 --12.3337 -11.6469 12.7798 --13.07 -12.2801 13.0694 --13.7741 -12.9705 12.9666 --12.913 -13.4556 13.2667 --12.7811 -13.1876 12.2675 --13.4142 -13.7861 11.7717 --14.1294 -13.6347 11.0755 --13.7435 -14.5436 11.2214 --13.2462 -15.2746 11.6231 --13.619 -15.7563 10.8342 --13.4032 -16.6958 10.5545 --14.1442 -17.177 11.0633 --14.3038 -17.0154 12.0063 --14.2937 -18.0898 12.1521 --13.3573 -18.0653 11.9491 --13.008 -17.1619 12.0144 --12.569 -16.5856 11.3765 --12.0342 -16.2705 12.175 --11.29 -15.682 11.7911 --11.3462 -14.9688 12.5186 --11.3175 -14.3164 11.7542 --11.6705 -13.8169 12.5716 --11.6079 -13.0055 11.9091 --11.0558 -12.5212 11.3573 --11.1217 -12.8611 10.3926 --11.1717 -12.9499 9.44344 --11.4883 -13.4336 8.65279 --11.3911 -14.0536 9.45605 --11.0154 -14.8942 9.90665 --10.9107 -15.7418 9.31658 --10.1674 -15.1091 9.31277 --9.25543 -14.7441 9.48574 --9.35603 -14.8184 8.48217 --9.01679 -15.7862 8.38727 --8.42185 -16.5203 8.69078 --7.71336 -15.9321 8.1799 --7.5319 -15.7941 9.18166 --8.15522 -15.7054 9.99015 --7.27699 -15.5965 10.3733 --6.39986 -15.2661 10.8049 --6.99323 -14.98 11.575 --7.21043 -15.3354 12.513 --7.61294 -16.2207 12.2547 --8.52252 -15.7352 12.159 --8.89485 -16.5281 12.712 --9.44335 -16.5552 13.5329 --9.97968 -15.8482 12.9906 --10.1016 -15.1833 13.7344 --9.76662 -14.3857 13.2031 --10.4265 -13.5756 13.275 --10.1803 -13.1596 14.098 --9.38299 -12.8067 13.616 --9.35298 -12.1008 12.8896 --8.71844 -11.3585 13.0916 --8.48646 -11.9451 13.8439 --8.17243 -12.7794 14.3115 --7.47383 -12.8095 14.9691 --6.70691 -12.5244 14.3243 --6.29636 -12.0625 13.5451 --5.77251 -12.1324 12.7276 --4.96963 -11.957 13.3266 --4.37885 -12.6061 12.8797 --3.4751 -12.7535 13.1224 --2.46644 -12.5955 13.2734 --2.29336 -13.5335 13.3964 --2.28724 -14.2212 14.0714 --3.01944 -13.9878 14.7322 --3.64286 -13.378 15.0489 --4.07825 -14.2475 14.6776 --4.00845 -15.222 14.9321 --3.50938 -15.5669 14.0639 --2.64177 -15.9914 14.1924 --1.78684 -15.6144 14.575 --1.03774 -14.8316 14.5595 --0.257539 -15.0141 13.9101 --0.814122 -14.5346 13.3128 --0.279798 -14.2109 12.5227 --1.13092 -14.0016 11.9281 --1.68929 -14.8867 12.1271 --2.2502 -15.1814 11.3779 --3.22441 -15.4114 11.3595 --3.95495 -15.7002 10.8825 --4.93527 -15.3058 10.6727 --4.52089 -14.4495 10.5088 --5.03661 -13.7371 11.1481 --5.2316 -13.384 10.2465 --4.91356 -13.611 9.38488 --5.13142 -14.5975 9.17386 --4.28 -15.02 8.91954 --3.42342 -15.3088 8.55623 --4.00123 -16.0499 8.4121 --4.26571 -16.1461 9.37968 --5.11562 -15.9241 8.96915 --4.97638 -15.9521 7.98776 --4.82796 -15.4948 7.0453 --4.98525 -16.0406 6.16289 --5.93043 -16.3144 6.1374 --5.8433 -16.0465 5.14941 --6.80047 -16.0544 5.55214 --6.71995 -16.9712 5.07558 --7.29431 -17.7093 5.45684 --8.08481 -17.7934 4.88759 --8.83237 -17.7277 4.31484 --9.29485 -17.406 5.10454 --9.50908 -16.8318 4.2715 --10.0262 -16.4766 3.50252 --9.76806 -15.741 2.95711 --10.4393 -14.9967 2.73803 --10.6939 -13.9773 2.837 --9.86313 -13.4496 3.10292 --9.4669 -12.5588 3.2127 --9.32951 -11.5627 3.1926 --9.49092 -11.8666 2.24387 --8.51063 -12.0104 2.2545 --7.647 -11.7223 2.52399 --7.16154 -11.4849 3.32388 --7.58521 -11.7138 4.1843 --8.08859 -11.2034 3.49062 --8.43055 -10.3051 3.80534 --8.36071 -10.9378 4.66446 --8.52729 -11.7573 5.22929 --8.12353 -12.0899 6.05005 --7.6002 -11.1451 6.04934 --8.22611 -11.223 6.86227 --8.17027 -10.2027 6.81395 --7.66758 -9.85711 6.08457 --6.70709 -9.80032 5.72645 --5.73627 -10.0756 5.73279 --5.90122 -10.6519 4.95043 --6.19392 -11.3805 5.67116 --5.19158 -11.3663 5.79466 --4.21011 -11.3152 5.3763 --3.42291 -11.6358 5.91709 --2.47573 -11.9692 6.03712 --2.82688 -11.7363 6.84839 --3.46379 -11.3149 7.4446 --3.82628 -11.0748 6.58181 --4.14163 -11.9973 6.82995 --5.02245 -11.5529 6.97695 --4.96484 -11.8054 7.93043 --4.97512 -11.9889 8.90666 --5.80108 -12.3064 9.25755 --6.18154 -12.2917 8.31973 --6.86248 -12.9804 8.76474 --7.60562 -13.5297 8.95671 --8.47612 -13.359 9.19352 --8.97273 -12.599 8.88789 --8.88602 -11.7999 8.27398 --8.83056 -10.8708 8.56809 --8.01839 -10.3895 8.4692 --7.56872 -10.0371 9.38398 --8.48196 -9.64187 9.26905 --9.25637 -9.73074 8.65801 --8.94671 -8.73462 8.73173 --8.68501 -7.84965 8.63449 --9.67852 -7.89738 8.57039 --10.5474 -8.17671 9.05984 --10.9916 -8.7796 9.61118 --10.5077 -9.49113 10.1048 --10.9201 -9.65617 10.9771 --11.0191 -9.16513 11.8401 --10.056 -8.98558 11.8441 --9.48656 -9.83375 11.8815 --8.52771 -9.40361 11.9027 --7.65701 -9.19628 11.5324 --7.28913 -8.98857 10.6557 --6.85527 -9.25242 9.75601 --5.8838 -9.45995 9.73748 --6.17547 -10.3458 10.1679 --6.38789 -11.3313 10.4024 --5.60911 -10.9228 10.7947 --5.26977 -11.7576 11.1855 --4.31387 -11.9952 10.8125 --3.81708 -11.2754 10.4831 --3.63662 -10.5949 9.80697 --3.83197 -9.66397 9.35883 --3.23304 -9.97363 8.67636 --4.05337 -9.99381 8.05107 --4.00879 -9.60027 7.20057 --3.24219 -10.2628 7.46003 --2.21937 -10.0085 7.54237 --1.5086 -9.3663 7.61932 --2.03755 -8.64762 7.22902 --2.60656 -7.91609 7.52817 --3.07442 -7.78088 6.71161 --3.90213 -7.30732 6.52288 --4.46595 -6.69211 7.1664 --5.32853 -6.27249 7.12371 --4.85495 -6.14359 8.00402 --4.60717 -6.93374 8.54844 --3.68486 -7.14225 8.26117 --2.76403 -6.97013 8.74928 --2.83071 -5.96947 8.8676 --2.32492 -5.91072 9.68941 --1.43914 -5.59526 9.46368 --0.718796 -5.09829 8.94702 --1.68619 -5.01923 8.72194 --1.86715 -5.94074 8.46423 --1.24196 -5.34578 7.92916 --1.15171 -5.94459 7.08821 --0.978512 -5.92971 6.07717 --1.35606 -6.8707 6.0425 --0.767922 -7.64702 6.42272 --0.865564 -7.45187 7.38743 --0.896027 -6.76326 7.98738 --0.812824 -7.50732 8.60398 --0.9275 -7.38563 9.56079 -0.03925537 -7.66421 9.74743 -0.979635 -8.01612 9.50727 -1.37164 -7.13546 9.24982 -2.22756 -7.59726 8.86003 -2.13468 -8.45454 9.2289 -3.02987 -8.1633 9.69418 -2.89406 -9.09685 9.3726 -3.91906 -9.48224 9.38328 -3.54115 -9.60345 10.25 -2.81453 -10.3028 10.5753 -1.82304 -10.141 10.4085 -1.87521 -10.5727 9.56157 -1.10952 -11.242 9.50076 -0.480168 -11.276 10.2902 --0.181517 -11.7603 10.8565 --0.654144 -12.4303 11.4198 -0.169415 -12.3388 12.0215 -1.11456 -11.87 12.2915 -1.4029 -11.0693 11.6927 -1.96894 -10.3992 12.2367 -2.59011 -11.1355 12.3341 -2.85567 -11.8283 13.0112 -2.89577 -11.3065 13.8757 -3.29015 -10.6659 13.2455 -3.76112 -9.99368 13.9789 -3.70739 -9.27913 13.3061 -3.61942 -8.64505 12.4664 -4.31742 -8.05681 13.0009 -4.67152 -7.25635 12.4987 -4.02476 -7.19478 11.7987 -4.65541 -7.95778 11.5507 -4.26264 -8.4686 10.7116 -5.12178 -8.893 10.6796 -5.9996 -8.6933 11.1762 -6.6614 -8.06781 10.7916 -6.84345 -7.13375 10.7941 -7.11938 -6.21555 11.1719 -6.94666 -5.38361 10.7529 -7.0666 -4.91156 11.6361 -6.12999 -5.16393 11.9884 -5.70367 -5.96256 12.4204 -6.32633 -6.35782 13.1015 -6.16522 -6.99838 13.842 -5.23511 -7.24871 13.7518 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19.1768 -5.2283 -8.99934 19.471 -4.74273 -9.82793 19.8541 -3.97734 -10.2775 20.4163 -4.38304 -9.43663 20.9001 -5.20799 -8.81106 20.8057 -5.29995 -8.25845 21.666 -5.55068 -9.08412 22.2561 -5.62191 -8.38517 22.9529 -5.45372 -8.9074 23.8446 -4.97544 -9.68615 23.4533 -4.04899 -9.7301 23.2144 -3.02538 -9.72771 23.4248 -2.27777 -9.25773 23.9092 -2.60637 -9.83146 24.642 -2.06834 -10.4691 25.1648 -2.98501 -10.1383 25.4648 -3.77338 -10.2511 24.8341 -3.21226 -11.0752 24.7921 -3.81998 -11.5338 24.1775 -4.53746 -11.2246 24.7592 -5.36673 -11.1681 24.2911 -6.15237 -11.1392 24.9052 -6.94253 -11.2748 25.5101 -7.97556 -11.3918 25.3732 -8.75444 -11.9416 25.4657 -9.3552 -11.9684 26.202 -9.11418 -12.9378 26.0338 -8.35194 -12.4012 26.3399 -7.50797 -12.8752 25.9981 -7.214 -13.4463 26.7573 -7.14874 -12.4359 27.0891 -7.18785 -12.0551 27.9787 -7.87135 -12.7175 27.8276 -8.54403 -13.3965 28.3346 -8.35464 -13.6686 29.2886 -7.86525 -12.8595 29.6467 -7.2894 -12.1995 30.0984 -6.79961 -13.0791 30.1172 -7.02606 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-20.8726 13.575 -0.09470097 -21.3602 13.5353 -0.777126 -21.9583 13.7832 -0.44622 -22.7062 13.2566 --0.03000863 -23.3829 12.7188 --0.610865 -23.7343 12.0372 --1.55232 -24.1415 12.1249 --2.30107 -24.3469 11.5733 --2.523 -24.5548 12.5104 --2.58265 -24.3953 13.4867 --2.83629 -23.497 13.3208 --2.25993 -23.4314 14.1756 --2.13969 -22.7912 14.9809 --2.15603 -23.3361 15.8462 --2.79124 -23.2592 16.6183 --3.59935 -23.6207 17.0977 --3.89708 -23.5245 18.059 --3.3101 -22.747 17.9856 --2.44118 -22.3407 18.0574 --2.15803 -21.4529 18.0049 --1.90881 -21.0118 18.8369 --1.13707 -21.5799 18.9824 --0.484177 -21.4616 19.7388 -0.01251117 -21.727 20.5728 -0.161859 -22.6651 20.8715 --0.03410003 -23.6637 20.9497 -0.52687 -24.5226 21.0192 -0.532925 -25.442 21.5028 --0.472655 -25.446 21.4809 --1.37446 -25.7227 21.1811 --1.46507 -25.8269 22.1564 --1.2881 -24.8042 22.0565 --1.62893 -24.4157 21.1819 --1.85474 -25.0453 20.3475 --2.36318 -25.8979 20.1873 --3.16894 -25.2585 20.4277 --3.57156 -24.4207 20.4528 --4.54503 -24.4209 20.2405 --5.52895 -24.3369 20.3074 --6.37144 -24.9365 19.9056 --6.9838 -24.5353 19.2033 --7.24008 -23.5232 19.2774 --7.07351 -22.6728 18.7672 --8.02285 -22.4234 18.8033 --8.23905 -23.3358 19.0896 --9.14556 -23.6939 19.0285 --8.73742 -24.5376 18.6243 --9.51019 -25.2223 18.718 --9.70246 -26.1939 18.6072 --10.708 -26.3182 18.7596 --11.6716 -26.4342 18.3661 --12.4937 -27.081 18.4881 --11.9714 -27.8286 18.9425 --11.5439 -28.6414 19.2627 --11.4074 -29.1572 20.089 --10.4892 -29.3092 20.3638 --10.5159 -29.0347 19.4368 --10.5257 -30.02 19.3037 --10.6489 -29.6384 18.3807 --11.0138 -28.9419 17.7084 --10.1331 -28.7683 18.3149 --9.3416 -28.5523 17.6763 --9.6858 -28.0625 16.9398 --9.24671 -27.7551 16.14 --9.54019 -27.8586 15.2271 --10.1879 -27.2647 15.7918 --10.0849 -26.8799 16.7249 --9.31915 -26.5037 16.2415 --8.97102 -26.6635 15.2804 --9.14834 -26.2854 14.3889 --8.23188 -26.3753 14.4552 --7.84262 -27.2627 14.7027 --8.06001 -27.8947 14.0239 --7.45887 -28.5814 14.3882 --7.00771 -28.6853 13.5042 --6.53022 -28.1486 12.8046 --5.62054 -28.2274 13.3704 --5.06215 -27.7064 12.6767 --5.81477 -26.9588 12.6801 --5.14186 -26.7293 11.8991 --5.03935 -26.3616 12.8136 --4.9154 -26.3598 13.7381 --4.08197 -26.0099 14.2226 --3.46725 -25.4384 14.8404 --4.27884 -24.9136 14.7485 --5.10321 -24.8342 15.27 --4.42001 -24.4131 15.8104 --4.79508 -24.4356 16.7017 --5.53575 -23.7539 17.033 --5.7501 -23.6396 18.0262 --5.94048 -22.6733 17.98 --6.52284 -22.9874 17.2244 --6.44533 -22.2642 16.5577 --7.15121 -21.8054 16.0598 --6.72604 -20.9542 16.5032 --7.46794 -20.5757 15.9841 --7.19369 -19.8468 16.5603 --7.88099 -20.1815 17.2086 --7.60257 -19.6976 17.9871 --6.74804 -19.4884 18.4008 --6.03555 -19.7087 18.9722 --5.38873 -19.1204 19.3274 --5.78765 -18.318 18.8767 --5.06561 -17.8807 19.4545 --4.25904 -17.2328 19.2205 --3.92603 -16.5096 19.8651 --3.1054 -15.8943 19.6587 --2.64585 -16.6987 20.12 --3.28847 -16.8075 20.826 --3.7815 -17.6139 21.1534 --4.44437 -17.1303 20.6506 --5.13194 -16.4811 21.0998 --5.70077 -16.4709 20.3017 --6.51383 -15.8338 20.1565 --7.46278 -15.5791 20.0643 --7.27834 -15.6984 19.0724 --6.78736 -16.4565 18.6168 --6.44325 -15.6733 18.1997 --5.93119 -14.8477 18.4148 --5.39244 -13.9372 18.3976 --5.71618 -13.5547 19.2177 --5.50961 -12.5173 19.1616 --5.25301 -12.0544 18.3319 --4.53676 -11.6754 17.8329 --4.85151 -11.9309 16.9261 --5.03605 -12.6697 16.2686 --5.87721 -13.2378 16.0872 --6.41311 -13.2366 16.8715 --7.23485 -12.6469 17.2036 --7.42276 -13.2718 17.858 --7.8791 -14.2312 17.8216 --8.79398 -13.8059 17.6695 --9.30439 -14.4913 17.084 --9.09481 -13.635 16.5333 --9.72135 -13.9192 15.7891 --10.4781 -13.3417 15.5439 --10.6267 -13.9545 16.2763 --11.5079 -14.2793 16.7263 --11.1142 -14.6404 17.5589 --10.528 -14.7966 18.3273 --9.70582 -15.2743 18.5442 --10.1866 -16.2123 18.4838 --10.165 -17.0995 19.0494 --11.0962 -17.4082 19.3316 --10.4385 -18.0636 19.2244 --11.298 -18.6121 19.2929 --11.2919 -18.3803 20.3298 --10.6828 -18.4118 21.1192 --10.7422 -17.4101 21.0978 --11.2026 -17.4099 21.9795 --12.1396 -17.1143 21.7081 --12.4634 -16.5833 22.473 --12.5368 -15.5895 22.6296 --11.5426 -15.7873 22.5737 --11.8052 -15.9041 21.6364 --11.2329 -16.1212 20.8557 --10.7455 -16.132 20.041 --11.6815 -16.2169 19.7123 --12.0337 -16.1453 18.7399 --12.6742 -16.5683 18.1314 --12.0149 -16.8951 17.393 --12.438 -16.3624 16.7644 --11.5579 -16.6103 16.3077 --10.6908 -16.2303 16.5427 --10.0058 -15.6926 16.8669 --9.19448 -15.968 16.2911 --9.44073 -15.7699 15.3374 --9.67662 -16.6259 14.8305 --10.3851 -16.3487 14.2622 --10.8591 -16.4952 13.3854 --11.5681 -17.2469 13.6592 --11.9074 -18.1433 13.8545 --11.8994 -18.381 12.9376 --11.4135 -18.4116 12.1058 --10.8809 -17.9966 12.81 --10.2183 -18.6004 13.3459 --9.86835 -19.1208 14.1503 --8.87507 -19.144 13.9304 --8.05983 -18.578 13.9249 --8.09784 -17.7121 14.4711 --8.60621 -16.807 14.6001 --8.4019 -17.1634 15.4354 --7.62568 -16.4589 15.5323 --7.66705 -15.8741 16.3795 --7.60255 -16.1253 17.365 --7.76913 -17.1362 17.3297 --7.54774 -17.6674 18.131 --7.98511 -17.1014 18.8467 --7.28034 -17.1813 19.5231 --7.96595 -17.9258 19.5959 --8.26694 -17.7012 20.5269 --8.05197 -18.1396 21.4358 --7.30349 -17.5781 21.1136 --7.28509 -17.449 22.091 --7.58323 -16.9566 22.892 --7.5624 -16.3028 22.0871 --7.07354 -15.7103 22.6975 --7.76889 -15.4759 23.4416 --8.2801 -15.6595 24.3045 --8.19737 -16.0739 25.2486 --8.04954 -17.0596 25.3942 --8.51606 -17.8368 25.7287 --8.62742 -18.4899 26.5581 --9.38812 -18.2545 27.1518 --8.75255 -18.8434 27.599 --8.66947 -19.7066 27.1025 --8.35385 -20.7039 27.2569 --8.5254 -20.6776 26.3212 --9.16916 -21.3531 26.0486 --9.68347 -20.5781 25.6684 --9.93035 -20.9536 24.7293 --9.31292 -21.4752 24.0775 --9.11485 -20.781 23.3248 --8.65679 -20.2238 24.0518 --7.66083 -20.016 23.9571 --7.91193 -19.0385 23.8127 --7.6372 -18.5029 24.5857 --8.27473 -19.0409 25.1389 --7.68575 -19.7244 25.6739 --6.68931 -19.6899 25.4424 --6.8236 -20.6117 25.9194 --5.86874 -20.1621 26.0383 --5.47412 -20.5625 26.8344 --4.71573 -20.7621 26.1404 --4.56754 -19.7668 26.3823 --3.98006 -20.2297 27.0652 --3.92964 -19.2061 26.9898 --4.89529 -18.9113 27.0637 --5.10632 -17.9097 27.1824 --5.5715 -17.2045 26.6137 --4.84944 -16.7634 26.1001 --3.94242 -16.6438 25.7508 --3.14103 -16.4021 25.2192 --3.35132 -15.7486 25.9304 --2.76775 -15.3024 25.2748 --2.17604 -14.5139 25.1945 --1.70435 -13.895 24.5228 --1.26579 -14.5957 23.966 --0.48509 -14.7577 23.431 --0.272772 -15.4431 24.1348 -0.103813 -15.5876 25.0554 --0.369081 -14.7419 25.2415 --1.07511 -14.5062 25.8214 --1.08398 -15.5327 26.0883 --2.05371 -15.324 26.3184 --2.45094 -15.1741 27.2699 --2.61954 -15.0977 28.2162 --2.97413 -15.4522 29.1344 --3.06894 -15.9939 29.931 --2.61721 -16.776 29.5453 --3.23666 -16.4799 28.8108 --2.73721 -16.3844 27.944 --3.59764 -15.9838 27.7563 --3.83091 -15.3349 26.9642 --3.68725 -14.3879 26.6733 --3.57378 -13.4284 26.3879 --3.74693 -12.4219 26.273 --3.99801 -12.4045 25.2997 --4.73538 -13.138 25.0926 --5.04249 -13.6616 25.9451 --5.08535 -14.4448 26.5524 --5.75517 -14.0775 27.0102 --5.59186 -13.617 27.8681 --5.20866 -14.6125 27.9267 --6.11328 -14.9814 28.073 --6.39469 -14.2661 28.7306 --7.0818 -13.5561 28.4887 --6.44385 -13.2595 27.8282 --7.42289 -13.2061 27.5456 --7.94154 -14.0528 27.4468 --7.64038 -13.9516 26.5447 --8.18159 -14.0816 25.6834 --8.63178 -14.5505 24.9002 --9.43736 -14.7685 24.396 --9.76875 -15.5633 23.9243 --10.1182 -16.3703 23.4132 --10.6146 -17.2777 23.4551 --11.2882 -17.9909 23.3277 --11.995 -18.2389 22.6706 --11.4503 -19.0615 22.5932 --11.232 -19.647 23.3482 --11.7662 -20.1125 22.6946 --10.9726 -20.7058 22.2877 --10.5666 -20.7442 21.365 --11.4259 -20.5239 21.4039 --11.9979 -19.6795 21.652 --12.7592 -18.9781 21.6011 --13.2415 -19.7656 21.3758 --13.1434 -19.2594 20.4534 --12.1236 -19.2168 20.44 --11.8405 -19.8443 19.7302 --12.5574 -20.0584 19.0178 --13.2557 -20.7334 19.3396 --14.2063 -20.8814 19.2499 --14.6876 -20.0991 19.6854 --14.2323 -20.0109 20.5348 --14.689 -19.8672 21.4413 --14.309 -19.1562 22.0289 --14.4431 -18.5881 22.9321 --14.3278 -19.5094 23.3333 --14.1228 -19.3539 24.3298 --14.5235 -20.0491 25.0076 --14.3519 -19.1686 25.3429 --14.2934 -19.5688 26.2989 --15.2791 -19.6515 26.4714 --15.2584 -19.3511 27.4474 --15.5372 -18.4223 27.1582 --15.513 -17.4517 27.2419 --14.9016 -16.7657 27.5097 --14.176 -16.3833 28.0416 --13.8883 -16.2869 28.8918 --14.6883 -16.8679 28.8448 --15.1372 -17.7551 29.122 --15.8524 -17.2092 28.5187 --16.3952 -16.5583 27.9363 --16.5391 -16.6507 26.9058 --16.7358 -15.7097 26.6077 --16.1617 -15.961 25.8889 --15.6037 -15.2783 26.2909 --15.3217 -14.9598 27.2333 --14.8587 -14.9614 28.1458 --15.0774 -14.1763 28.7593 --15.2979 -13.2778 29.0163 --16.0244 -12.7038 29.3932 --16.9587 -12.9738 28.9447 --16.7835 -12.0703 28.6068 --17.4411 -11.9027 29.4084 --17.8886 -11.5403 28.6411 --17.3513 -10.8472 28.2815 --16.8358 -10.4771 27.5794 --16.7526 -9.47209 27.6357 --16.6165 -8.46407 27.6533 --17.1518 -7.5669 27.811 --17.1646 -6.70497 27.3267 --16.4303 -6.02934 27.308 --16.4266 -6.54797 26.4411 --16.0054 -6.89585 25.6954 --15.0374 -6.84129 25.4815 --15.0911 -6.06164 26.0504 --14.4521 -5.40231 25.703 --13.9652 -4.55283 25.2846 --14.9797 -4.31418 25.4686 --14.9092 -4.07382 24.5592 --14.7151 -3.21017 24.9593 --14.5621 -2.4174 25.5106 --14.973 -1.89718 26.3119 --15.9683 -1.71531 26.3502 --16.9596 -1.47679 26.1897 --16.7071 -0.5897181 25.8218 --16.0002 -0.4847961 25.1537 --16.6024 -1.28446 24.9286 --17.0393 -1.74433 24.1344 --17.0457 -2.69663 23.863 --17.1312 -3.58911 24.3428 --16.6889 -4.00914 23.5284 --15.8246 -3.46588 23.6833 --15.67 -3.50121 22.7003 --16.427 -2.95036 22.3833 --17.0308 -3.49368 21.8502 --17.7311 -2.89337 21.4696 --18.737 -2.61047 21.2764 --18.275 -2.79591 20.3799 --18.8206 -3.64982 20.5265 --19.6051 -3.75862 19.8246 --20.3738 -3.61352 19.2042 --20.6824 -2.66151 19.3487 --21.4669 -3.03126 19.8227 --22.0037 -3.58308 20.534 --21.3179 -4.28817 20.583 --20.4879 -4.59355 21.0812 --20.6328 -4.30987 22.0609 --20.6024 -3.90417 22.9094 --21.2951 -4.02918 23.5881 --21.584 -4.67228 24.3601 --21.3234 -4.40695 25.2496 --20.375 -4.69147 25.1209 --19.7256 -5.4119 25.037 --19.1675 -5.1292 24.2648 --19.7328 -4.3966 23.9174 --19.7064 -4.95229 23.097 --19.7359 -5.09788 22.1259 --19.391 -4.75572 21.2171 --18.8103 -5.5442 21.2532 --18.4147 -6.30364 20.7949 --18.8577 -7.01715 20.2805 --18.5467 -7.50618 19.5048 --17.9568 -7.65583 20.2486 --17.487 -8.54174 20.4205 --16.7588 -8.98013 19.8326 --16.5758 -8.00815 19.5956 --16.2571 -7.0243 19.6966 --16.0143 -6.31483 18.9925 --15.2344 -6.00696 18.3795 --14.4323 -6.05816 17.8213 --15.2716 -6.30961 17.2729 --15.9724 -6.95308 17.2688 --16.8955 -6.59841 17.1697 --17.7682 -7.30675 17.2205 --18.5367 -7.49246 17.8403 --18.2989 -8.34145 17.3868 --17.337 -8.57548 17.1086 --16.5474 -8.93688 16.7022 --16.6185 -9.15321 17.662 --16.5483 -10.0871 17.2301 --17.1672 -10.7683 17.6011 --16.3082 -11.1802 17.7183 --15.9479 -11.6197 16.8738 --15.1189 -11.0084 17.0329 --14.7565 -11.9251 16.7229 --13.7592 -12.1883 16.905 --14.2061 -13.0513 16.5453 --14.9642 -13.0271 17.0654 --15.2854 -13.5587 16.3513 --15.8904 -14.0551 16.9848 --16.0984 -14.8679 16.4998 --16.8958 -15.3377 16.8462 --17.4431 -14.6573 17.3816 --17.8947 -13.835 17.1725 --18.8192 -13.9604 16.7034 --19.613 -13.5918 16.3105 --20.3084 -13.6606 16.9341 --20.2769 -14.6266 16.6566 --21.2026 -14.9576 16.8346 --21.3421 -15.259 15.9106 --21.8675 -14.5042 15.4322 --21.2252 -14.3667 14.6204 --20.2483 -14.3586 14.2852 --20.1064 -13.3779 14.3925 --20.1835 -13.0456 15.2669 --20.515 -12.3431 15.9907 --20.2812 -11.5879 15.462 --21.2773 -11.3453 15.0964 --21.7985 -10.6008 15.445 --21.4939 -10.7128 16.3995 --20.692 -10.2363 16.9441 --20.654 -9.77944 17.8815 --21.5376 -10.1128 18.1064 --22.0979 -10.9348 18.1857 --22.6792 -11.6444 18.6224 --22.5154 -12.2933 19.4096 --22.5723 -11.7236 20.2381 --23.2694 -12.1977 20.8684 --22.4455 -12.7398 20.9281 --23.1573 -13.1984 20.4309 --23.3559 -13.9609 19.7631 --23.2379 -13.2547 19.1031 --23.4759 -13.8726 18.3867 --24.4327 -13.8269 18.656 --25.4578 -13.6325 18.8294 --25.5707 -13.6451 19.8314 --24.9504 -12.9648 20.2063 --25.1186 -12.0285 20.4371 --25.9551 -11.5178 20.3335 --25.876 -10.9292 21.0863 --25.2456 -10.4434 21.6051 --24.9783 -11.4033 21.5771 --24.4422 -12.192 21.7103 --23.6387 -11.5575 21.7145 --23.4415 -10.8955 20.9646 --23.0785 -10.461 21.8559 --23.1605 -9.87577 22.6797 --23.0962 -10.4397 23.4798 --22.6508 -11.1436 22.9126 --21.876 -11.4645 23.4086 --21.7159 -11.6546 24.3664 --21.2289 -12.3501 24.8992 --20.9433 -11.468 25.3777 --21.4905 -10.7767 25.8702 --21.303 -10.5342 26.7716 --20.433 -10.9788 26.8105 --20.1955 -10.2023 26.1829 --19.4408 -10.3201 26.8463 --19.0637 -9.44911 27.1705 --19.5797 -8.90732 26.4761 --20.497 -8.6222 26.6891 --20.7885 -7.82599 26.2452 --21.4229 -7.92819 25.425 --21.7291 -7.05132 25.0931 --22.4997 -7.40124 25.683 --22.6616 -7.59947 24.7542 --22.5917 -7.12027 23.9675 --22.4931 -7.4293 22.9852 --23.2204 -7.22561 22.3092 --22.7929 -6.70239 21.5699 --22.7681 -6.3387 20.6226 --23.4158 -6.76184 19.9514 --23.3657 -5.80011 19.8908 --23.8214 -5.03201 19.5487 --24.2249 -5.57196 18.8657 --24.8174 -5.87683 19.675 --25.5617 -5.95881 20.2926 --24.9291 -5.93948 21.0136 --24.0678 -5.71726 21.4522 --23.7052 -5.66963 22.3666 --23.071 -5.13882 21.9123 --22.9869 -5.02625 22.9209 --22.3019 -5.75401 22.8445 --21.5147 -6.27022 23.0202 --20.8394 -6.72651 23.6688 --20.303 -7.46143 24.0319 --19.3662 -7.30051 24.4012 --19.4187 -7.23002 25.3772 --18.6602 -7.79517 25.0335 --18.1273 -8.58633 25.0186 --17.3517 -8.9683 24.5408 --17.0837 -9.64125 23.7853 --16.1265 -9.96092 24.0671 --15.3586 -9.4639 23.7846 --15.624 -9.09088 24.6663 --15.8706 -8.26117 24.1895 --16.2806 -7.55833 24.6397 --16.2503 -7.04426 23.8273 --16.1328 -6.62698 22.8536 --16.8318 -6.23575 22.2791 --16.8299 -5.34595 21.8877 --15.9808 -4.87865 21.863 --15.4175 -5.65394 22.0081 --15.0505 -6.44001 22.4856 --14.84 -5.72865 23.0758 --13.8677 -6.15882 23.0146 --13.1397 -5.98502 22.282 --13.0941 -5.12391 21.793 --13.5292 -5.67529 21.044 --13.7913 -6.60061 21.0412 --13.6184 -7.23404 20.2868 --13.1319 -7.88142 20.9542 --12.3106 -7.98622 21.4035 --12.1476 -7.80767 22.3451 --12.3106 -8.33743 23.1602 --11.3976 -8.19743 23.4937 --10.6271 -7.77336 23.0571 --11.2756 -6.9686 22.9895 --12.3022 -6.74315 22.9404 --12.8889 -7.44288 23.2993 --12.1911 -6.94348 23.9019 --11.522 -7.4256 24.4598 --10.8649 -7.58938 25.1334 --10.8823 -8.45499 24.7193 --9.92946 -8.64666 24.8669 --10.0608 -9.18774 25.7178 --9.26556 -9.6382 25.3365 --8.475 -9.34272 25.8805 --8.87636 -8.43431 25.9445 --8.54313 -8.44303 25.0122 --8.68253 -7.54128 25.3381 --8.5132 -7.146 24.3579 --9.35516 -6.59228 24.4788 --8.84671 -6.39116 23.6097 --7.99895 -6.35855 23.0846 --7.88448 -6.88183 22.19 --6.89793 -6.75182 21.8784 --6.26864 -6.99816 22.6544 --6.68149 -7.77815 22.9729 --7.3633 -8.06454 23.6666 --7.97337 -7.39204 23.2191 --8.63881 -7.92766 23.661 --8.99322 -8.76848 24.095 --9.76219 -9.4128 24.0899 --9.72335 -10.2925 23.6721 --10.5807 -10.7911 23.7854 --10.9255 -10.7031 24.7423 --10.5605 -10.4276 25.6299 --10.6524 -10.427 26.6021 --10.7348 -11.4241 26.3535 --11.1754 -12.3096 26.5236 --11.3409 -12.2899 25.4973 --11.0069 -13.0497 24.8685 --9.99027 -13.0507 25.0812 --9.43625 -12.2813 24.7316 --8.64563 -12.4617 25.2939 --8.55912 -13.1647 24.568 --8.56346 -13.3295 23.5321 --8.07098 -13.5159 22.661 --7.75684 -12.5524 22.8464 --7.78074 -11.5666 22.7628 --8.6118 -11.2963 22.3509 --7.96638 -10.4891 22.3557 --8.72854 -10.157 22.8887 --9.58592 -9.99251 22.368 --9.54366 -9.85945 21.3744 --8.62648 -9.41592 21.0322 --8.72938 -10.3802 21.3882 --7.84309 -10.6841 21.1092 --7.89715 -10.112 20.3013 --7.01173 -9.67758 20.638 --6.25085 -9.31552 21.1516 --6.77076 -8.44659 21.2927 --6.58973 -8.54534 20.3003 --6.52735 -7.98891 19.4617 --6.77199 -7.62752 18.5687 --6.95144 -7.00528 19.3177 --6.69129 -6.03699 19.4183 --5.9621 -5.98704 20.2022 --5.25744 -5.3858 19.6458 --5.87893 -5.20311 18.8712 --6.47162 -4.47113 18.5365 --6.88199 -3.91654 17.8393 --7.23761 -4.80785 17.5495 --8.12624 -4.51024 17.9324 --9.07345 -4.75816 18.1272 --9.66788 -5.51897 17.7675 --10.5639 -5.08309 17.5697 --10.0731 -4.76253 18.4181 --10.1913 -4.7029 19.4439 --10.6915 -5.51886 19.416 --10.0917 -6.15035 19.8272 --9.50178 -6.88919 20.1233 --8.52426 -7.14324 19.7996 --8.45161 -6.97396 18.7867 --8.81078 -7.07562 17.8277 --8.38704 -7.76464 17.2272 --8.80422 -7.62946 16.3327 --8.39979 -7.93653 15.4825 --8.05114 -8.82905 15.4812 --8.28114 -9.75574 15.1497 --8.97959 -9.36762 14.5247 --9.89542 -9.34574 14.871 --9.73039 -8.91341 15.7845 --10.3752 -8.87255 16.5613 --10.3599 -7.86416 16.3597 --11.3265 -7.84972 15.8942 --12.3186 -7.72608 16.2106 --12.9499 -6.92321 16.2028 --12.7351 -7.15484 17.186 --12.8097 -7.89174 17.9096 --12.7746 -7.91037 18.9275 --13.5501 -8.56062 18.8628 --14.3495 -8.80163 19.2871 --14.9009 -9.14188 20.0401 --14.5734 -9.85185 20.7145 --13.8939 -10.048 20.0459 --13.3633 -10.4018 19.1655 --12.4734 -10.7407 18.7963 --12.0398 -11.6115 18.8743 --12.4961 -11.6901 19.7345 --13.1879 -12.2574 20.2301 --13.9948 -12.1687 19.8259 --14.539 -12.1786 20.6512 --15.2155 -12.105 21.3049 --14.4407 -11.4568 21.5728 --14.9724 -10.6056 21.3467 --15.055 -10.6173 22.3641 --14.9821 -11.4167 22.8041 --15.94 -11.372 23.1827 --15.974 -12.2738 22.7926 --16.2737 -13.1435 23.1906 --17.1505 -13.0583 22.8491 --17.023 -14.018 22.7491 --16.9612 -14.9577 22.3334 --16.6308 -15.6678 22.8782 --16.543 -15.4906 23.8701 --15.6579 -15.2354 23.6288 --15.3509 -14.233 23.7797 --14.5266 -13.8087 24.1113 --13.619 -13.6441 23.6613 --13.4555 -12.7003 23.7173 --14.0966 -11.9588 23.7972 --14.4793 -12.2022 24.6443 --15.4839 -12.3055 24.9095 --15.8294 -11.3123 24.9249 --15.4906 -10.4806 25.4167 --14.7888 -9.90048 25.1738 --14.8462 -10.4824 24.3447 --13.8945 -10.2966 24.6139 --13.3354 -10.6145 25.4171 --13.5112 -9.60895 25.2843 --12.6915 -9.31112 24.8737 --12.0937 -9.68026 25.633 --12.1601 -10.2951 26.3733 --11.8913 -10.5554 27.3399 --12.6401 -11.2411 27.111 --12.7128 -11.8584 26.3429 --13.0572 -12.6683 25.8101 --12.7667 -13.07 26.7037 --13.7584 -13.1668 26.9926 --13.3018 -13.2807 27.85 --13.7195 -12.7147 28.4569 --14.1759 -12.2872 29.2316 --13.6923 -11.4739 28.8769 --14.4353 -11.3904 28.1861 --14.6913 -10.4763 27.9851 --13.9752 -9.90171 28.2723 --12.9442 -9.9411 28.1352 --12.776 -9.98031 29.0935 --12.7506 -10.1391 30.0842 --12.592 -10.8268 30.7909 --12.4352 -10.5791 31.729 --12.706 -9.72422 31.2908 --12.4446 -8.84752 31.7444 --12.4602 -7.89314 31.4568 --11.8107 -7.82755 30.6483 --11.4676 -6.85624 30.7978 --11.2739 -6.17709 30.1011 --10.3384 -6.47646 29.9639 --10.8872 -7.25832 29.5934 --10.7392 -7.92567 30.3007 --10.9245 -8.52177 29.5084 --10.4337 -8.11911 28.7592 --10.5782 -8.1771 27.7933 --11.3223 -8.11876 27.1622 --11.1668 -7.47903 26.4067 --11.8484 -6.97418 25.9909 --12.7121 -6.95536 26.4379 --12.2262 -6.11749 26.6943 --12.7724 -5.32829 27.0418 --13.0548 -4.65336 26.3032 --13.1012 -4.18886 25.3584 --12.4986 -4.75048 24.8162 --11.7017 -4.53946 24.2716 --12.0264 -3.64389 24.055 --12.0688 -3.92831 23.0334 --12.0435 -3.14987 22.4682 --11.3999 -2.6444 23.0745 --11.4227 -2.59358 24.0787 --11.3753 -2.4753 25.0866 --12.2667 -2.06435 24.8185 --12.5848 -1.81631 23.8717 --12.0096 -1.68228 23.1234 --11.9091 -1.86169 22.1114 --11.0285 -2.25799 22.1598 --10.559 -1.57914 21.5817 --10.8128 -2.06642 20.7531 --10.4803 -3.02095 20.5875 --10.401 -3.59043 19.7656 --11.1343 -4.26348 20.0563 --12.0449 -4.4754 20.3364 --11.8838 -3.45458 20.6074 --12.4225 -2.91007 21.2617 --13.019 -2.74261 22.0016 --13.1923 -3.26322 22.7933 --14.2001 -3.46362 22.7229 --14.4232 -2.94191 21.9151 --14.9467 -3.18348 21.0548 --14.8441 -4.09531 20.7972 --15.5072 -3.69947 20.1486 --15.7368 -4.23401 19.3423 --16.1448 -4.05363 18.4323 --15.8052 -4.80459 17.8201 --16.3903 -5.46796 17.4357 --17.2901 -5.38252 17.1133 --18.0764 -5.23962 17.7126 --18.6074 -6.03023 17.9997 --19.2671 -6.6645 18.0932 --19.9199 -7.38276 17.883 --20.2001 -7.98733 18.6157 --19.8692 -8.67504 18.0391 --19.5243 -8.7733 19.0198 --20.3166 -9.23116 19.4277 --20.0842 -10.2228 19.5742 --19.4385 -10.2009 18.8354 --19.3343 -10.2716 17.8946 --19.1319 -11.0613 17.2941 --18.4564 -11.164 16.5692 --17.4024 -11.1156 16.6734 --17.3879 -11.131 15.6775 --17.9397 -10.4549 15.2394 --17.8559 -10.5041 14.2974 --17.9709 -11.3806 13.9071 --17.3818 -11.961 13.2727 --16.5816 -12.5189 13.7007 --15.7899 -12.0165 14.0791 --14.8625 -12.0951 13.8824 --14.8263 -11.153 13.702 --15.4132 -10.6632 12.9975 --15.9967 -11.3467 12.5275 --16.2252 -11.0667 11.5492 --15.4034 -10.4851 11.2336 --15.7317 -9.8602 10.4954 --16.3598 -9.79076 9.69623 --16.6558 -9.47758 8.86158 --16.9034 -8.51422 9.16669 --17.1514 -8.18166 10.0722 --17.9136 -7.65713 9.7389 --18.4221 -7.54334 8.89693 --18.9739 -7.35429 8.04365 --19.5353 -7.78264 7.34318 --18.5828 -7.98184 7.05121 --17.5422 -8.01225 6.88422 --17.4067 -7.04716 6.9567 --17.7364 -6.22406 6.40823 --17.6647 -7.15582 5.95328 --18.0995 -7.3024 5.15454 --19.123 -7.40957 5.258 --19.3571 -8.4383 5.1358 --18.4206 -8.69245 5.04938 --18.8868 -9.18479 4.36119 --19.5662 -9.84982 4.68354 --18.928 -9.86664 5.36154 --18.1402 -10.3628 5.82505 --17.8677 -10.9856 6.57123 --17.2168 -11.2934 7.26523 --17.5769 -10.6648 7.99151 --18.2202 -10.5203 8.62465 --18.8863 -10.9446 7.97711 --18.6643 -11.6209 8.69037 --17.6858 -11.5833 9.06897 --18.169 -12.3931 9.43196 --17.2372 -12.8759 9.35416 --16.3767 -12.327 9.34308 --15.8093 -12.878 9.89257 --15.7391 -13.695 9.41949 --16.2584 -14.5249 9.02677 --16.4353 -13.7727 8.36688 --16.708 -13.2385 7.56292 --15.9808 -12.6088 7.33496 --14.93 -12.4963 7.4124 --14.0421 -12.7034 7.09583 --13.4657 -12.8725 7.81163 --13.2073 -13.4659 7.03725 --13.6635 -13.6677 6.10394 --14.5061 -14.1862 5.85012 --14.0589 -13.7359 5.13811 --14.3586 -13.5461 4.20289 --13.7307 -14.0883 3.65636 --14.2577 -13.3186 3.12609 --15.0485 -12.8493 2.95356 --14.815 -11.8899 3.16312 --15.5913 -11.3731 3.30834 --16.284 -10.6567 3.01516 --16.4799 -10.0128 3.72987 --17.4047 -10.3474 3.60083 --17.7145 -11.3193 3.40233 --17.8889 -11.2387 2.38898 --18.8365 -10.9893 2.35673 --19.2202 -10.0996 2.55681 --19.4736 -9.87045 3.48042 --19.5157 -8.9874 2.92432 --19.3594 -8.35047 3.72188 --18.479 -7.74866 3.74324 --18.0082 -7.04627 3.14702 --18.1096 -6.77018 4.10902 --18.4375 -5.89883 4.39956 --17.6916 -5.85959 3.76617 --16.8817 -6.07979 3.30263 --15.8755 -6.31547 3.34363 --15.3912 -5.6536 3.87336 --15.7007 -5.58853 4.81143 --16.0415 -6.30549 5.55861 --15.9028 -7.01093 6.18353 --15.2602 -7.67732 5.79662 --15.0215 -7.64629 4.79729 --14.8575 -7.63943 3.80743 --14.595 -8.07339 2.9713 --15.0289 -7.20545 2.80891 --15.5401 -7.64142 2.01924 --15.8021 -8.05141 1.16597 --14.953 -8.50671 1.52955 --15.6337 -8.84338 2.26251 --15.5121 -9.72314 2.86245 --14.924 -10.1041 2.13461 --15.6794 -10.7311 2.02913 --15.23 -11.6146 2.0006 --16.1379 -11.8946 2.00282 --16.7927 -12.3432 2.66807 --17.0449 -13.0291 2.02622 --17.262 -13.3969 1.08434 --17.7444 -13.7664 1.84922 --18.5771 -14.2984 1.54221 --19.2692 -13.788 2.00877 --18.8916 -14.1964 2.80971 --19.2573 -13.3565 3.25119 --18.8947 -12.5911 2.87434 --19.0372 -12.7262 1.92061 --19.078 -12.4863 0.9606911 --19.1666 -12.8393 0.01094332 --19.9425 -13.4201 0.02750622 --20.2017 -12.9685 -0.7489729 --20.5391 -12.0617 -1.12257 --19.5228 -12.2508 -1.02169 --18.878 -11.5984 -0.7495329 --18.4902 -11.0235 -0.1191279 --17.5753 -10.5778 -0.4269879 --16.6481 -10.484 -0.08099628 --15.9208 -11.115 -0.1107389 --14.9639 -11.0593 0.2473411 --15.2254 -10.352 0.9017971 --15.0128 -9.4141 0.5678031 --15.2243 -8.91337 -0.2213079 --14.4357 -8.41789 0.05288872 --14.9062 -7.61987 0.3556751 --15.3704 -6.75526 0.5436391 --16.1359 -6.4294 1.02381 --16.2401 -5.67312 1.58794 --16.8932 -6.14203 2.09978 --16.8832 -7.14329 2.07646 --17.0415 -8.13897 1.9131 --16.727 -8.93318 1.37605 --16.2795 -9.00624 0.4360171 --17.261 -8.83958 0.2443261 --17.9771 -8.35304 -0.2831419 --17.6254 -7.4618 -0.5650039 --17.058 -6.62278 -0.8506389 --17.2646 -5.65965 -0.6844559 --17.9705 -6.1158 -1.24358 --18.5333 -6.44615 -1.97525 --17.8681 -6.49678 -2.74695 --17.802 -6.795 -3.70499 --18.6053 -6.25349 -3.42826 --18.6125 -5.24346 -3.27733 --18.066 -4.79734 -4.01595 --18.8342 -4.17637 -3.85408 --18.9706 -4.51385 -4.79125 --19.3243 -5.21392 -5.4699 --19.8725 -5.99635 -5.39059 --19.1327 -6.65718 -5.3248 --18.3803 -7.34925 -5.48122 --18.3687 -8.37562 -5.30182 --17.5574 -8.11834 -5.78981 --17.2588 -7.27937 -6.20958 --18.0258 -6.83771 -6.68384 --18.0607 -5.93849 -6.21315 --17.1578 -6.29659 -6.45402 --17.7706 -5.60213 -6.99269 --17.6282 -5.12089 -7.88915 --16.6785 -5.10921 -7.94746 --16.2191 -5.84324 -7.60147 --15.6737 -5.69921 -8.49004 --14.9898 -5.07629 -8.69215 --14.2561 -5.69313 -8.94822 --13.3916 -5.14971 -9.01518 --12.55 -4.62941 -8.67044 --11.9107 -4.65164 -9.45559 --11.9755 -3.70739 -9.53065 --12.1684 -2.79261 -9.06541 --13.072 -2.85207 -9.46023 --13.0864 -3.44881 -8.60713 --13.9591 -3.26053 -9.14504 --14.1503 -3.92701 -8.36496 --14.9291 -3.70891 -8.95277 --15.2839 -3.53075 -8.05999 --16.2271 -3.41963 -7.76014 --17.1745 -3.52467 -7.36912 --17.462 -3.36917 -6.4266 --16.4947 -3.26251 -6.20248 --16.0781 -4.25785 -6.38463 --15.1869 -4.56692 -6.75814 --14.4118 -4.20819 -7.22915 --14.4164 -5.16593 -7.47513 --14.1406 -6.05357 -7.50263 --14.3648 -6.22788 -6.52053 --15.1773 -5.83078 -6.15556 --15.4744 -5.06855 -5.5926 --16.3414 -4.69841 -5.18431 --16.4251 -5.5353 -4.62981 --16.518 -6.33316 -3.97281 --16.7132 -6.95145 -3.20446 --16.3473 -7.44269 -3.98513 --17.0442 -8.10241 -3.82256 --17.4463 -9.03437 -3.97039 --17.182 -9.74464 -3.40873 --16.2472 -9.46887 -3.11862 --15.9342 -10.1372 -3.77919 --16.1449 -11.1775 -3.91878 --15.9684 -11.1982 -4.96147 --16.4456 -11.7821 -5.57034 --17.412 -11.5047 -5.65659 --17.877 -11.1857 -6.47036 --18.5086 -10.8761 -7.18474 --19.518 -10.9205 -7.05448 --20.2377 -11.3981 -7.41556 --20.8019 -12.0096 -8.03957 --20.5975 -12.9392 -7.72241 --20.3029 -13.1653 -6.74794 --20.7535 -12.897 -5.88058 --20.7381 -13.8678 -5.49862 --20.0035 -13.255 -5.40206 --19.6195 -12.3737 -5.44454 --19.3345 -12.1513 -4.53613 --18.5603 -12.6606 -4.17183 --18.751 -12.0942 -3.32654 --17.8015 -11.8378 -3.62336 --17.7644 -11.1347 -2.92758 --17.5999 -11.3204 -1.97151 --16.9838 -11.5329 -1.25655 --16.4929 -12.3701 -1.22113 --16.3407 -13.0503 -1.94762 --16.9218 -13.6103 -1.26664 --17.2174 -14.2967 -1.87939 --16.7642 -14.6161 -1.02679 --17.5262 -14.6179 -0.2676219 --18.524 -14.5808 -0.01440028 --18.3591 -13.6411 -0.1706759 --18.8882 -13.517 -1.00386 --19.4842 -13.8192 -1.77767 --19.2044 -12.9459 -2.19962 --18.4029 -12.2898 -2.16865 --18.0908 -13.2077 -2.36105 --18.2333 -14.1323 -2.08134 --18.8586 -13.9902 -2.80542 --19.0883 -14.7135 -3.50955 --18.2839 -15.256 -3.32026 --18.3209 -15.8923 -2.47859 --17.6021 -15.8769 -1.82759 --16.7083 -15.6773 -2.32738 --16.7014 -16.0352 -1.44363 --16.4211 -16.2315 -0.4430339 --17.1477 -16.8488 -0.1877479 --17.167 -17.6278 0.4337811 --16.861 -18.0754 1.2904 --17.6047 -17.788 1.80629 --17.6229 -17.0618 2.45654 --18.6084 -17.3201 2.47297 --19.2016 -16.9174 1.70555 --18.8674 -16.8098 0.8007271 --18.8294 -15.8853 0.4150321 --19.5529 -15.266 0.5794591 --19.7042 -14.9409 1.55854 --20.536 -14.6914 1.06234 --21.1002 -15.3471 1.62685 --22.0746 -15.765 1.80648 --22.4927 -14.9835 2.27899 --22.6096 -14.006 1.95844 --22.5236 -13.0623 1.98658 --22.6799 -12.8275 1.02312 --22.1896 -12.2068 1.60314 --21.6665 -11.3148 1.79851 --21.2978 -10.7213 1.16423 --20.7986 -10.272 1.9968 --20.9159 -10.5977 2.97381 --20.1285 -10.982 3.54118 --20.8203 -11.3228 4.13951 --20.2017 -10.6704 4.49365 --20.6835 -11.0611 5.34768 --20.8511 -11.9998 5.57333 --21.8526 -11.8397 5.41481 --21.9526 -12.5821 6.08797 --22.8295 -12.2875 6.52534 --23.1368 -11.3705 6.34837 --22.2961 -11.3946 6.87562 --21.844 -10.9842 7.56685 --21.9915 -11.4163 8.46386 --22.827 -12.0585 8.3727 --22.2571 -12.5046 9.05202 --21.9944 -13.3021 9.51221 --22.9378 -13.517 9.14622 --23.9079 -13.8427 9.2615 --24.3702 -13.0761 8.6829 --24.9555 -13.5982 8.10246 --25.4204 -14.3529 7.54206 --25.8092 -15.1807 7.13748 --26.5197 -15.901 7.27795 --27.0284 -16.0673 8.10792 --26.6683 -15.1575 8.33945 --26.0209 -14.4598 8.66714 --25.7611 -13.7258 9.31001 --25.4286 -13.9632 10.2178 --25.6033 -14.7569 9.7819 --24.7775 -15.0775 9.2928 --24.7076 -15.8936 8.8172 --24.1289 -16.5151 9.42323 --24.3925 -17.1213 10.1547 --23.5673 -17.6156 10.0587 --22.6976 -18.1315 10.0034 --22.2642 -17.9675 9.12324 --22.8581 -18.5158 8.59345 --22.1849 -19.2428 8.42504 --23.0899 -19.243 7.95142 --24.0782 -19.3861 7.72719 --24.0992 -20.1718 7.02174 --24.4663 -20.899 7.61354 --24.1845 -21.9016 7.82978 --23.1899 -21.7722 7.61118 --22.8199 -21.9008 6.75469 --22.4817 -20.9476 6.61434 --23.2397 -20.8565 5.96029 --24.1189 -21.3763 5.81774 --24.1471 -22.2542 5.33011 --23.2495 -22.5661 5.07807 --22.2767 -22.3499 5.1588 --22.236 -21.603 4.43457 --22.1575 -21.1807 5.42874 --21.2758 -20.7228 5.74039 --21.7909 -19.892 5.69952 --21.662 -19.6551 4.71008 --21.8475 -19.0744 3.97977 --21.9095 -18.4841 4.80406 --20.8704 -18.7249 4.85504 --20.6593 -17.7463 4.69751 --20.7583 -17.6991 5.72459 --20.2781 -17.7523 6.64265 --19.6909 -17.8401 7.45255 --19.6183 -16.8502 7.55147 --20.0272 -16.1811 6.85039 --20.7177 -15.4989 6.70258 --20.0271 -14.868 7.0509 --20.0891 -13.8671 6.75451 --20.3426 -13.8064 7.7883 --20.2222 -14.5718 8.44451 --19.5391 -14.3686 9.11965 --18.6989 -14.6208 8.60513 --18.1485 -14.1603 7.96201 --18.7457 -13.3924 7.93491 --18.604 -13.0846 6.97472 --18.926 -13.6583 6.23641 --18.2356 -14.1621 5.62244 --17.8578 -13.2786 5.51122 --17.2634 -12.5949 5.02639 --16.4796 -12.1079 4.67754 --15.5677 -11.7076 4.50541 --14.6414 -11.2841 4.58037 --15.0051 -10.6528 5.18583 --14.2951 -11.0756 5.70686 --14.0702 -11.9169 5.21958 --13.6892 -12.3722 4.42763 --13.1195 -11.6957 3.81921 --12.5624 -12.1939 3.15205 --12.322 -13.1602 3.23067 --11.6648 -13.2714 4.00083 --11.7563 -12.4 4.53912 --11.7976 -11.482 4.15239 --11.1524 -11.1616 3.47078 --11.7528 -10.6017 2.8644 --12.7139 -10.913 2.9438 --12.5803 -10.3437 2.10094 --11.6701 -10.6091 1.70348 --11.3316 -11.5911 1.73756 --10.749 -11.898 0.9526371 --10.5551 -12.7077 1.548 --10.9885 -13.2144 0.8109861 --11.3604 -12.5737 0.1236011 --10.7736 -11.8306 -0.1829209 --10.1609 -12.4889 0.02782242 --9.44033 -12.9272 0.5497491 --9.08814 -12.1416 0.1162441 --8.3989 -12.1433 -0.6025449 --8.3176 -12.9172 -0.06511018 --8.50949 -12.8249 0.9439171 --8.47264 -13.7168 1.42527 --8.3198 -13.9101 2.36208 --8.7295 -14.6818 2.65583 --8.37203 -15.619 2.55081 --8.68207 -16.1834 1.72766 --8.18224 -16.7351 1.00774 --8.57297 -16.7215 0.1399021 --7.97885 -16.744 -0.6450729 --7.43054 -17.217 -1.34063 --6.71517 -17.7187 -1.63362 --6.62189 -17.8027 -0.6146229 --6.50536 -17.2932 0.2981031 --6.02331 -16.8521 1.09006 --5.35079 -16.3477 0.4553941 --6.11783 -16.2396 -0.2509479 --6.54796 -15.6138 0.4008321 --6.48742 -15.6361 1.42974 --7.13988 -15.2444 2.17204 --7.3448 -15.2186 3.1547 --6.9691 -15.2354 4.06684 --6.69408 -16.1796 3.88808 --6.26311 -16.7761 3.28375 --5.7262 -17.6232 3.67206 --5.53528 -18.5636 3.38286 --6.14371 -18.2428 2.69458 --5.18081 -18.4872 2.38342 --4.42132 -18.1866 1.86216 --3.96041 -17.5998 1.17445 --3.63592 -16.6552 1.07837 --3.80473 -16.7126 0.09609402 --3.1401 -16.3779 -0.5458699 --2.51979 -16.9387 -0.06550528 --2.44478 -17.912 0.1262581 --1.58416 -17.8928 0.6103961 --1.02168 -17.1028 0.8116451 --0.698401 -17.2784 1.66179 --1.29405 -16.4718 1.7535 --1.20491 -16.6565 2.70536 --1.83627 -17.3383 2.51024 --2.41765 -16.9109 1.83713 --2.93634 -16.0722 1.92531 --3.30215 -15.1277 1.85612 --2.68966 -14.6529 1.19532 --2.09517 -13.8614 0.8158601 --1.59787 -14.6848 0.9300581 --0.979176 -14.633 0.2424121 --1.43266 -15.3157 -0.3772699 --1.38441 -15.8767 -1.15919 --1.63294 -16.6299 -1.84423 --0.979846 -17.3623 -1.62137 --0.26691 -16.8839 -1.05171 --0.01836083 -17.7326 -0.5577269 -0.311614 -18.6345 -0.2386659 --0.300772 -19.1707 0.3533641 --0.45909 -18.9769 1.33908 --0.765792 -18.7706 2.27261 --0.267866 -17.9749 2.66323 --0.476554 -17.9033 3.65093 --0.04862893 -18.6448 4.1154 -0.160754 -19.1816 3.32306 -0.432145 -20.0162 2.86337 -1.35828 -19.9421 3.20509 -0.918236 -20.851 3.25794 -1.00792 -21.6939 3.71865 -0.01846787 -21.9635 3.63551 --0.03478893 -22.8796 3.965 --0.44018 -23.3375 4.74781 --1.29316 -23.6069 5.09817 --1.4422 -23.8758 4.1608 --2.18571 -24.2742 3.69094 --2.84799 -23.7683 4.21335 --2.42618 -22.9348 3.90019 --2.46041 -23.2094 2.95356 --2.39758 -23.2739 1.94176 --2.98297 -22.9221 1.19968 --2.92175 -22.2346 0.5027861 --2.61479 -21.406 0.08836602 --1.72104 -21.5423 0.5203291 --1.36492 -20.7139 0.2088941 --0.681441 -21.3719 0.3890411 -0.221378 -21.737 -0.08934318 --0.01296833 -21.8795 0.8959241 -0.596142 -22.5959 0.6715991 -1.40294 -23.0858 0.4111251 -1.38058 -23.6248 -0.4516429 -1.35347 -24.6271 -0.3329969 -0.476824 -24.7115 0.2140341 --0.118841 -23.9082 0.1092351 -0.162551 -23.5464 0.9382481 --0.528495 -22.8752 0.7937701 --1.22243 -22.4509 0.1072601 --1.94009 -22.2481 -0.5394919 --2.14375 -23.1794 -0.9199809 --2.68979 -23.5751 -1.67526 --3.13772 -24.1382 -2.39865 --3.03463 -25.1308 -2.13476 --3.52823 -25.2435 -2.97538 --4.11751 -24.541 -2.92176 --4.98222 -25.145 -2.96032 --5.28442 -25.6283 -3.73908 --6.24526 -25.5695 -3.52539 --5.69793 -26.1943 -2.89561 --6.10714 -26.8499 -2.29479 --5.51818 -27.2647 -2.97214 --5.18347 -27.0796 -3.90706 --4.28836 -27.3998 -4.09418 --3.36446 -27.6429 -4.18591 --2.82066 -26.8267 -4.15093 --2.53327 -26.1742 -3.36111 --2.53883 -25.7304 -4.16075 --1.83245 -25.1139 -4.50631 --0.970865 -25.526 -4.44269 --1.28663 -26.2739 -3.85732 --1.59705 -27.0396 -4.42883 --1.52632 -27.7935 -5.0979 --0.800441 -28.4785 -5.12727 --0.744699 -28.3136 -6.13472 --0.720131 -29.1246 -6.65237 --0.629731 -28.78 -7.55645 --0.377451 -29.4107 -8.29517 --0.996488 -29.4598 -8.99045 --0.599697 -30.4016 -9.05727 --1.05784 -30.574 -9.88977 --0.277431 -31.1161 -10.1052 -0.408644 -30.4338 -10.2678 -0.978395 -29.7866 -9.76467 -1.29804 -30.5431 -9.27597 -1.76449 -30.7711 -10.1503 -2.72658 -30.573 -10.0078 -3.25293 -30.1211 -9.28215 -3.51152 -30.303 -8.42115 -3.31075 -29.2896 -8.29259 -2.46667 -29.6373 -8.74994 -2.01793 -29.7625 -9.58242 -1.81954 -28.8668 -9.90537 -2.65316 -28.6716 -9.44185 -2.33536 -27.7881 -9.76625 -3.34896 -27.4633 -10.0527 -3.97128 -27.7919 -10.8043 -4.30927 -26.8921 -11.1651 -4.7887 -26.0184 -11.3504 -5.70995 -26.1383 -11.3205 -6.10342 -26.3904 -12.1577 -5.41486 -27.146 -12.2684 -5.54559 -27.9474 -11.7159 -5.04998 -28.5559 -12.2761 -4.11678 -29.0272 -12.3376 -3.28746 -28.39 -12.1586 -2.77907 -28.9011 -12.8448 -2.71111 -28.2776 -13.6278 -2.54822 -28.9496 -14.3251 -3.32498 -28.3929 -14.7103 -4.30863 -28.4893 -14.4465 -5.15146 -27.9711 -14.1983 -5.91513 -27.4989 -13.7535 -6.60183 -27.5979 -14.4791 -7.30611 -28.0657 -15.0896 -7.61482 -28.5404 -15.9428 -6.72906 -29.0013 -16.1311 -6.57845 -29.3164 -17.1116 -5.7474 -29.6489 -17.5644 -5.21519 -30.3931 -17.9417 -4.76158 -29.5123 -17.877 -5.11433 -28.5404 -18.0793 -4.61588 -27.7529 -17.694 -4.30396 -27.9973 -16.7823 -4.87471 -28.7588 -17.0524 -4.37257 -29.4196 -16.515 -4.34907 -30.36 -16.7674 -3.71661 -31.1385 -16.8334 -3.18788 -31.4624 -17.6259 -3.09708 -30.8725 -18.4167 -2.63163 -30.0338 -18.7512 -1.81601 -29.8788 -19.3065 -1.39484 -28.9596 -19.4089 -1.64554 -27.9775 -19.4681 -2.59088 -27.7061 -19.6773 -3.53325 -27.469 -19.8316 -3.70637 -27.0416 -20.7882 -3.97953 -26.526 -21.6369 -4.00849 -25.6369 -22.0054 -4.67819 -24.9864 -22.411 -5.00228 -24.615 -23.2314 -5.30182 -25.4954 -23.6215 -5.18228 -25.8779 -24.57 -4.65137 -26.3726 -25.2504 -5.00133 -27.2703 -24.9781 -5.68137 -27.0381 -25.6138 -5.54698 -26.2542 -26.1818 -4.80806 -26.1418 -26.771 -4.78139 -25.1744 -27.0733 -5.18275 -25.2179 -28.0197 -5.64785 -26.1033 -28.3246 -5.11108 -26.9582 -28.3317 diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py deleted file mode 100755 index 21f263d382..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/generate_system_lt.py +++ /dev/null @@ -1,301 +0,0 @@ -#!/usr/bin/env python - -err_msg = """ -Usage: - - generate_system_lt.py n < monomer_coords.raw > system.lt - -Example: - - generate_system_lt.py 30118 47 < coords.raw > system.lt - -Explanation: - ARGUMENTS: - n = total length of the polymer (in monomers) - L = the (average) length of each condensin interval (Poisson- - distributed) This is also 1/probability that each monomer - is a "condensin monomer". - - (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner, - and 47 = 200/4.25. Note that 128000 and 200 are for the 10nm model. - See the supplemental section of Naumova et al Science 2013, p 18.) - -""" - - -import sys -import random -from math import * - -# Parse the argument list: -if len(sys.argv) <= 2: - sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n") - exit(1) -N=int(sys.argv[1]) -L=float(sys.argv[2]) -if len(sys.argv) > 3: - delta_x = float(sys.argv[3]) -else: - delta_x = 2.0 -if len(sys.argv) > 4: - x_offset = float(sys.argv[4]) -else: - x_offset = -((N-1.0)/2) * delta_x - - -coords = [[0.0, 0.0, 0.0] for i in range(0,N)] -lines = sys.stdin.readlines() -if len(lines) != N: - sys.stderr.write("Error: Number of lines in input file ("+str(len(lines))+")\n" - " does not match first argument ("+str(N)+")\n") - exit(1) -for i in range(0, N): - coords[i] = list(map(float, lines[i].split())) - -# Now calculate the box_boundaries: -box_bounds_min = [0.0, 0.0, 0.0] -box_bounds_max = [0.0, 0.0, 0.0] -for i in range(0, N): - for d in range(0, 3): - if i == 0: - box_bounds_min[d] = coords[i][d] - box_bounds_max[d] = coords[i][d] - else: - if coords[i][d] > box_bounds_max[d]: - box_bounds_max[d] = coords[i][d] - if coords[i][d] < box_bounds_min[d]: - box_bounds_min[d] = coords[i][d] - -# Now scale the box boundaries outward by 50% -box_scale = 1.5 -for d in range(0,3): - box_bounds_cen = 0.5*(box_bounds_max[d] + box_bounds_min[d]) - box_bounds_width = box_bounds_max[d] - box_bounds_min[d] - box_bounds_min[d] = box_bounds_cen - 0.5*box_scale*box_bounds_width - box_bounds_max[d] = box_bounds_cen + 0.5*box_scale*box_bounds_width - -# Now calculate the direction each molecule should be pointing at: -direction_vects = [[0.0, 0.0, 0.0] for i in range(0,N)] -for d in range(0, 3): - direction_vects[0][d] = coords[1][d] - coords[0][d] - direction_vects[N-1][d] = coords[N-1][d] - coords[N-2][d] -for i in range(1, N-1): - for d in range(0, 3): - direction_vects[i][d] = coords[i+1][d] - coords[i-1][d] - -# Optional: normalize the direction vectors -for i in range(1, N-1): - direction_len = 0.0 - for d in range(0, 3): - direction_len += (direction_vects[i][d])**2 - direction_len = sqrt(direction_len) - for d in range(0, 3): - direction_vects[i][d] /= direction_len - -# Now, begin writing the text for the system.lt file: - -sys.stdout.write( -""" -import "monomer.lt" # <-- defines "Monomer" -import "condensin.lt" # <-- defines "CondensinMonomer" - - -""" -) - - - -# Figure out which monomers are "Monomers" and which monomers are -# "CondensinMonomers" - -ic = 0 # count the number of condensins added so far -condensin_is_here = [False for i in range(0, N)] -for i in range(0, N): - #add_condensin_here = random.random() < (1.0 / L) - add_condensin_here = random.random() < (1.0 / (L-2.0)) - - # We do not allow condensin at successive sites separated by less than 2 - # subunits (the "L-2.0" above is to compensate for this) - if (((i > 0) and condensin_is_here[i-1]) or - ((i > 1) and condensin_is_here[i-2])): - add_condensin_here = False - - if add_condensin_here: - condensin_is_here[i] = True - ic += 1 -Nc = ic - - -ic = 0 -for i in range(0, N): - if condensin_is_here[i]: - sys.stdout.write("condensins["+str(ic)+"] = new CondensinMonomer.scale(0.5,0.8,0.8).rotvv(1,0,0,") - ic+=1 - else: - sys.stdout.write("monomers["+str(i)+"] = new Monomer.scale(0.5,0.8,0.8).rotvv(1,0,0,") - sys.stdout.write(str(direction_vects[i][0])+"," - +str(direction_vects[i][1])+"," - +str(direction_vects[i][2])+ - ").move(" - +str(coords[i][0])+"," - +str(coords[i][1])+"," - +str(coords[i][2])+")\n") - - #if condensin_is_here[i]: - # if i < N-1: - # sys.stdout.write("\n" - # "#(override the dihedral angle for this monomer)\n" - # "write(\"Data Dihedrals\") {\n" - # " $dihedral:twistor"+str(i+1)+" @dihedral:CondensinMonomer/TWISTOR $atom:monomers["+str(i)+"]/t $atom:monomers["+str(i)+"]/c $atom:monomers["+str(i+1)+"]/c $atom:monomers["+str(i+1)+"]/t\n" - # "}\n" - # "\n") - - - -sys.stdout.write( -""" - -# ---------------- simulation box ----------------- - -# Now define a box big enough to hold a polymer with this (initial) shape - -""" -) - - -sys.stdout.write("write_once(\"Data Boundary\") {\n" - +str(box_bounds_min[0])+" "+str(box_bounds_max[0])+" xlo xhi\n" - +str(box_bounds_min[1])+" "+str(box_bounds_max[1])+" ylo yhi\n" - +str(box_bounds_min[2])+" "+str(box_bounds_max[2])+" zlo zhi\n" - "}\n\n\n") - - -sys.stdout.write( -""" -# What kind of boundary conditions are we using? - -write_once("In Init") { - boundary s s s # <-- boundary conditions in x y z directions - #boundary p p p # <-- boundary conditions in x y z directions -} -# "p" stands for "periodic" -# "s" stands for "shrink-wrapped" (non-periodic) - - -# ---- Bonds ---- - - -write_once("In Settings") { - # 10nm model: - #bond_coeff @bond:backbone harmonic 100.0 1.0 - # 30nm fiber (4.25^(1/3)=1.6198059006387417) - bond_coeff @bond:backbone harmonic 100.0 1.6198059006387417 -} - - -""" -) - - -sys.stdout.write("write(\"Data Bonds\") {\n") - -# Old bond-loop was simple: -#for i in range(0, N-1): -# sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a $atom:monomers["+str(i+1)+"]/a\n") - -ic = 0 -for i in range(0, N-1): - #sys.stderr.write("i="+str(i)+", ic="+str(ic)+", Nc="+str(Nc)+"\n") - - # Figure out if the first atom in the bond pair - # belongs to a regular Monomer or a CondensinMonomer - if condensin_is_here[i]: - sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:condensins["+str(ic)+"]/a") - ic+=1 - else: - sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a") - - # Do the same thing for the second atom in the bond pair - if condensin_is_here[i+1]: - assert(ic coords.raw - -Example: - - interpolate_coords.py 30118 3.0 < coords_orig.raw > coords.raw - - # (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner. - # See the supplemental section of Naumova et al Science 2013, p 18.) - -""" - - -import sys -from math import floor - -# Parse the argument list: -if len(sys.argv) <= 1: - sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n") - exit(1) - -n_new = int(sys.argv[1]) - -if len(sys.argv) > 2: - scale = float(sys.argv[2]) -else: - scale = 1.0 - -coords_orig = [] - -lines = sys.stdin.readlines() - -for line in lines: - tokens = line.split() - if (len(tokens) > 0): - coords_orig.append(list(map(float, tokens))) - g_dim = len(tokens) - -n_orig = len(coords_orig) - -if n_orig < 2: - sys.stderr.write("Error:\n\nInput file contains less than two lines of coordinates\n") - exit(1) - -if n_new < 2: - sys.stderr.write("Error:\n\nOutput file will contain less than two lines of coordinates\n") - exit(1) - -coords_new = [[0.0 for d in range(0, g_dim)] for i in range(0, n_new)] - -for i_new in range(0, n_new): - I_orig = (i_new) * (float(n_orig-1) / float(n_new-1)) - i_orig = int(floor(I_orig)) - i_remainder = I_orig - i_orig - - if (i_new < n_new-1): - for d in range(0, g_dim): - coords_new[i_new][d] = scale*(coords_orig[i_orig][d] - + - i_remainder*(coords_orig[i_orig+1][d]- - coords_orig[i_orig][d])) - else: - for d in range(0, g_dim): - coords_new[i_new][d] = scale*coords_orig[n_orig-1][d] - - # print the coordates - for d in range(0, g_dim-1): - sys.stdout.write(str(coords_new[i_new][d]) + ' ') - sys.stdout.write(str(coords_new[i_new][g_dim-1]) + "\n") diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/monomer.lt b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/monomer.lt deleted file mode 100644 index 9ef2b03984..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/monomer.lt +++ /dev/null @@ -1,84 +0,0 @@ -# This file contains the definition of a molecule named "Monomer". -# (This particular molecule contain only one atom, but that is up to you.) -# Later, multiple monomers can be connected together to build a molecule. - - - -Monomer { - - # atom-id mol-id(ignore) atom-type q x y z - - write("Data Atoms") { - $atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000 - } - - # (The x y z positions will be changed later with move commands - # You can spedify charge and other properties by changing the atom_style.) - - - - # atom-type mass - - write_once("Data Masses") { - @atom:A 1.0 - } - - # pairwise interactions (between non-bonded atoms): - # - # U(r) = 4*eps*((r/sig)^12 - (r/sig)^6) - # - # Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0 - # - # atom-type atom-type pair_style epsilon sigma rcutoff - - write_once("In Settings") { - # I usually use sigma = 2^(-(1/6)), with a cutoff of 1 - #pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0 - # In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0 - # with a cutoff of 2^(1/6). Here we are trying to reproduce his results. - # 10nm fiber - #pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373 - # 30nm fiber (4.25^(1/2)=2.0615528128088303) - #pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349 - # 30nm fiber (4.25^(1/3)=1.6198059006387417) - pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708 - } - -} # Monomer - - - - -# -------------------------------------------------------------------- -# -# At some point we need to specify which force-field styles we want. -# LAMMPS also allows you to customize the kinds of properties you want -# each atom to have (the "atom_style"), such as charge, molecule-id, dipole etc. -# I typically specify this here. Doing it this way means that all systems built -# from "Monomers" (ie which import "monomer.lt") share these atom-styles -# and force-field styles by default. You can override these settings later. - - -write_once("In Init") { - # Default styles for molecules built out of "Monomers" - units lj - atom_style full - - bond_style hybrid harmonic table linear 4001 - angle_style hybrid cosine - dihedral_style none - - # If you need angles, dihedrals and impropers, uncomment or replace: - # angle_style hybrid harmonic - # dihedral_style hybrid fourier - - pair_style hybrid lj/cut 2.5 - - # If you are using gpu acceleration uncomment these lines: - # package gpu force/neigh 0 0 1.0 - # pair_style hybrid lj/cut/gpu 4.0 - - pair_modify mix arithmetic - special_bonds lj/coul 1 1 1 -} - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/table_bonds_stage2.dat b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/table_bonds_stage2.dat deleted file mode 100644 index 1bfb911c09..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/moltemplate_files/table_bonds_stage2.dat +++ /dev/null @@ -1,4011 +0,0 @@ -# This table contains the bond potential between condensin-anchors -# used by Imakaev in the Science 2013 (metaphase chromatin HiC) paper, -# two-stage model, during stage 2. -# -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = step(d-3) * abs(d-3) * 10 - -STAGE2 -N 4001 FP 0 0 EQ 0 - -1 0 0 0 -2 .05 0 0 -3 .10 0 0 -4 .15 0 0 -5 .20 0 0 -6 .25 0 0 -7 .30 0 0 -8 .35 0 0 -9 .40 0 0 -10 .45 0 0 -11 .50 0 0 -12 .55 0 0 -13 .60 0 0 -14 .65 0 0 -15 .70 0 0 -16 .75 0 0 -17 .80 0 0 -18 .85 0 0 -19 .90 0 0 -20 .95 0 0 -21 1.00 0 0 -22 1.05 0 0 -23 1.10 0 0 -24 1.15 0 0 -25 1.20 0 0 -26 1.25 0 0 -27 1.30 0 0 -28 1.35 0 0 -29 1.40 0 0 -30 1.45 0 0 -31 1.50 0 0 -32 1.55 0 0 -33 1.60 0 0 -34 1.65 0 0 -35 1.70 0 0 -36 1.75 0 0 -37 1.80 0 0 -38 1.85 0 0 -39 1.90 0 0 -40 1.95 0 0 -41 2.00 0 0 -42 2.05 0 0 -43 2.10 0 0 -44 2.15 0 0 -45 2.20 0 0 -46 2.25 0 0 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-10 -3936 196.75 1937.5 -10 -3937 196.80 1938.0 -10 -3938 196.85 1938.5 -10 -3939 196.90 1939.0 -10 -3940 196.95 1939.5 -10 -3941 197.00 1940.0 -10 -3942 197.05 1940.5 -10 -3943 197.10 1941.0 -10 -3944 197.15 1941.5 -10 -3945 197.20 1942.0 -10 -3946 197.25 1942.5 -10 -3947 197.30 1943.0 -10 -3948 197.35 1943.5 -10 -3949 197.40 1944.0 -10 -3950 197.45 1944.5 -10 -3951 197.50 1945.0 -10 -3952 197.55 1945.5 -10 -3953 197.60 1946.0 -10 -3954 197.65 1946.5 -10 -3955 197.70 1947.0 -10 -3956 197.75 1947.5 -10 -3957 197.80 1948.0 -10 -3958 197.85 1948.5 -10 -3959 197.90 1949.0 -10 -3960 197.95 1949.5 -10 -3961 198.00 1950.0 -10 -3962 198.05 1950.5 -10 -3963 198.10 1951.0 -10 -3964 198.15 1951.5 -10 -3965 198.20 1952.0 -10 -3966 198.25 1952.5 -10 -3967 198.30 1953.0 -10 -3968 198.35 1953.5 -10 -3969 198.40 1954.0 -10 -3970 198.45 1954.5 -10 -3971 198.50 1955.0 -10 -3972 198.55 1955.5 -10 -3973 198.60 1956.0 -10 -3974 198.65 1956.5 -10 -3975 198.70 1957.0 -10 -3976 198.75 1957.5 -10 -3977 198.80 1958.0 -10 -3978 198.85 1958.5 -10 -3979 198.90 1959.0 -10 -3980 198.95 1959.5 -10 -3981 199.00 1960.0 -10 -3982 199.05 1960.5 -10 -3983 199.10 1961.0 -10 -3984 199.15 1961.5 -10 -3985 199.20 1962.0 -10 -3986 199.25 1962.5 -10 -3987 199.30 1963.0 -10 -3988 199.35 1963.5 -10 -3989 199.40 1964.0 -10 -3990 199.45 1964.5 -10 -3991 199.50 1965.0 -10 -3992 199.55 1965.5 -10 -3993 199.60 1966.0 -10 -3994 199.65 1966.5 -10 -3995 199.70 1967.0 -10 -3996 199.75 1967.5 -10 -3997 199.80 1968.0 -10 -3998 199.85 1968.5 -10 -3999 199.90 1969.0 -10 -4000 199.95 1969.5 -10 -4001 200.00 1970.0 -10 diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.min b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.min deleted file mode 100644 index c8c28cd7a1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.min +++ /dev/null @@ -1,41 +0,0 @@ -######################################################### -# Example how to run this file: -# -# 1) Choose a ransom seed (in this case 141203) -# (or use `bash -c 'echo $RANDOM'`) -# -# 2) Then, from the shell, invoke LAMMPS to collapse the polymer: -# -# lmp_ubuntu_parallel -i run.in -var seed 141203 -# -######################################################### -# eg: -# time mpirun -np 2 lmp_ubuntu_parallel -i run.in.min -######################################################### - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - -dump 1 all custom 10000 traj_min.lammpstrj id mol type x y z ix iy iz -thermo_style custom step pe etotal vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 100 #(time interval for printing out "thermo" data) - -# Now minimize the system: - -min_style quickmin -min_modify dmax 0.05 -minimize 1.0e-7 1.0e-8 30000 100000000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.stage1 b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.stage1 deleted file mode 100644 index bf129df04f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.stage1 +++ /dev/null @@ -1,110 +0,0 @@ -# PREREQUISITES: You must run LAMMPS using "run.in.min" beforehand. -# (This will create the "system_after_min0.data" file needed below.) -######################################################### -# Run using: -# -# lmp_ubuntu_parallel -i run.in.stage1 -# -######################################################### -# GPUs: -# To enable gpu acceleration, make sure settings.in.init includes this line: -# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.) -# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings" -# files with "lj/cut/gpu" - - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -#read_data system.data -read_data system_after_min.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - -# DON'T MINIMIZE FIRST UNLESS YOU CHOOSE THE CORRECT INITIAL KbondC FORMULA -#thermo_style custom step pe etotal vol epair ebond eangle edihed -#thermo_modify norm no #(report total energy not energy / num_atoms) -#thermo 20 #(time interval for printing out "thermo" data) -#min_style sd -#min_modify dmax 0.05 -#minimize 1.0e-7 1.0e-8 20000 1000000 -#write_data system_after_min_t=0.data - - -mass * 1.0 -timestep 0.005 # "dt" -dump 1 all custom 25000 traj_stage1.lammpstrj id mol type x y z ix iy iz -reset_timestep 0 - - -# --- run the simulation --- - - -# set the velocity to zero -velocity all create 0.0 123456 - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Tstart Tstop tdamp randomseed - -fix fxlan all langevin 1.0 1.0 10.0 123456 - -# pstart pstop pdamp(time-units, 2000 iters usually) -#fix fxnph all nph x -0.000 -0.000 1.0 -fix fxnve all nve -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - -fix fxcenter all recenter 0.0 0.0 0.0 - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 1000 #(time interval for printing out "thermo" data) - -#balance dynamic x 20 1.0 -out tmp.balance -#balance x uniform - - -variable nloop1 loop 300 - - label loop1 - - print "############### LOOP ${nloop1} ###############" - - # Now, change the bond-strength between condensin monomers. - # From the Naumova et al Science 2013 paper (supp materials) - # "Two-stage model: linear compaction + axial compression" - # "First, random consecutive loops with L=100 monomers (see above) were - # introduced, and anchors of neighboring loops were brought together - # using harmonic springs with a potential U = k * (r – r0)2; r0=0.5. - # To avoid abrupt motion of the loop anchors, the force was gradually - # turned on over the first 300000 timesteps, with k linearly increasing - # in time from 0 to 10 kT." - # Do this by changing the parameters in the force-field for these - # bonds. - # - # Formula used for "bond_style harmonic": - # Ubond(r) = k*(r-r0)^2 - # bondType style - #bond_coeff 1 harmonic 0.1 0.5 - - variable time equal step - variable KbondC equal $((v_time+1)*(10.0/300000.0)) - print "timestep = ${time}, KbondC = ${KbondC}" file KbondC_vs_time.dat - - #bond_coeff 1 harmonic ${KbondC} 0.5 - bond_coeff 1 harmonic ${KbondC} 0.5 - run 1000 - - next nloop1 - jump SELF loop1 - -write_data system_after_stage1.data - diff --git a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.stage2 b/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.stage2 deleted file mode 100644 index e429fc8825..0000000000 --- a/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/run.in.stage2 +++ /dev/null @@ -1,90 +0,0 @@ -# PREREQUISITES: You must run LAMMPS using "run.in.stage1" beforehand. -# (This will create the "system_after_stage1.data" file.) -######################################################### -# Run using: -# -# lmp_ubuntu_parallel -i run.in.stage2 -# -######################################################### -# eg: -# time mpirun -np 2 lmp_ubuntu_parallel -i run.in -var seed 1 -######################################################### -# GPUs: -# To enable gpu acceleration, make sure settings.in.init includes this line: -# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.) -# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings" -# files with "lj/cut/gpu" - - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -#read_data system.data -read_data system_after_stage1.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -mass * 1.0 -timestep 0.005 # "dt" -dump 1 all custom 50000 traj_stage2.lammpstrj id mol type x y z ix iy iz -reset_timestep 300000 - - -# --- run the simulation --- - -# set the velocity to zero -velocity all create 0.0 123456 - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Tstart Tstop tdamp randomseed - -fix fxlan all langevin 1.0 1.0 10.0 123456 - -# pstart pstop pdamp(time-units, 2000 iters usually) -fix fxnve all nve -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - -fix fxcenter all recenter 0.0 0.0 0.0 - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 1000 #(time interval for printing out "thermo" data) - -#balance dynamic x 20 1.0 -out tmp.balance -#balance x uniform - -# atomTypes pairStyle epsilon sigma rcutoff -# 10nm-fiber -#pair_coeff 1 1 lj/cut 1.0 1.0 2.5 -#pair_coeff 2 2 lj/cut 1.0 1.0 2.5 -# 30nm fiber (4.25^(1/3)=1.6198059006387417) -pair_coeff 1 1 lj/cut 1.0 1.6198059006387417 4.049514751596854 -pair_coeff 2 2 lj/cut 1.0 1.6198059006387417 4.049514751596854 - - -# During stage 2, add attractive forces between all pairs of non-consecutive -# condensin anchors. These forces are stored in the table file below: -# bondType bondStyle filename label -bond_coeff 2 table table_bonds_stage2.dat STAGE2 - -# During stage 2, I assume the stage-1 bonds remain in place -# (They have length 0.5. -# After 300000 timesteps during stage 1, the "k" value should be 10.0.) - -# bondType bondStyle k r0 -bond_coeff 1 harmonic 10.0 0.5 - -timestep 0.005 -run 1700000 - -write_data system_after_stage2.data diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt deleted file mode 100644 index c3c4faecb1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README.txt +++ /dev/null @@ -1,20 +0,0 @@ -# CG model of benzene where each molecule is represented as an ellipsoid -# and the intermolecular interactions are described with the Gay-Berne potential -# -# Do not expect realistic behaviour from this example. -# The long-range electrostatic interactions are missing. -# -# To build the files which LAMMPS needs, follow the instructions in -# README_setup.sh -# -# To run the simulation in LAMMPS, follow the instructions in: -# README_run.sh -# -# Finally, to view the simulation results in OVITO, follow the instructions in: -# README_visualization_OVITO.txt -# README_visualization_OVITO_ellipsoids.png -# -# -# This example was provided by Otello M. Roscion (U.Southampton) -# and Matteo Ricci(U.Bologna) Many thanks for editing and debugging -# moltemplate code to get this working! diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh deleted file mode 100755 index 91e79124e1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_run.sh +++ /dev/null @@ -1,20 +0,0 @@ -# --- Running LAMMPS --- -# -# The file "run.in.npt" is a LAMMPS -# input script which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - -lmp_mpi -i run.in.npt # simulation at constant pressure - -# (Note: The "lmp_mpi" program is also frequently called "lmp_ubuntu", -# and has many other names depending upon how it was compiled.) - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh deleted file mode 100755 index 3a5a6d2e67..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_setup.sh +++ /dev/null @@ -1,19 +0,0 @@ -# Create LAMMPS input files this way: -cd moltemplate_files - - # Run moltemplate with the "-allow-wildcards" and "-nocheck" arguments - # as well as a custom -atomstyle - - moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt \ - -allow-wildcards -nocheck - - # This will generate various files with names ending in *.in* and *.data. - # Move them to the directory where you plan to run LAMMPS (in this case "../") - mv -f system.data system.in* ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt deleted file mode 100644 index cd2498b1a1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO.txt +++ /dev/null @@ -1,12 +0,0 @@ -You can visualize the trajectory (dump file) with the program OVITO (www.ovito.org). You will have to define few parameters, thought. Invoke ovito using: - -ovito traj.lammpstrj - -On the right panel of ovito, under the section "LAMMPS dump" click on the button "Edit column mapping" and enter the fields as specified in the attached png file. On the same panel, tick "File contains a time series" to display the entire trajectory. - -A screenshot of these settings is available: -README_visualization_OVITO_ellipsoids.png - - -Otello M. Roscioni -roscioni@gmail.com diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png deleted file mode 100644 index 15e5e77c4b..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/README_visualization_OVITO_ellipsoids.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png deleted file mode 100644 index 89629bde48..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/benzene_cg_ellipsoid.png and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg deleted file mode 100644 index b3514f4c8a..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg deleted file mode 100644 index 7c35039c01..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/images/t=14900.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt deleted file mode 100644 index 036847ea4a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/benzene_cg.lt +++ /dev/null @@ -1,62 +0,0 @@ -# CG model of benzene where each molecule is represented as an ellipsoid -# and the intermolecular interactions are described with the Gay-Berne potential -# -# Do not expect a physical behaviour from this sample: long-range electrostatic -# interactions are missing. -# -# Otello M. Roscioni -# roscioni@gmail.com - -# Run with the command: -# moltemplate.sh -atomstyle "atomid atomtype flag density x y z" system.lt -allow-wildcards -nocheck - - -BENZ { - - # atom-ID atom-type ellipsoidflag density x y z - write("Data Atoms"){ - $atom:ben @atom:b1 1 1.14337 0.0 0.0 0.0 - } - - # atom-ID width1 width2 width3 qw qx qy qz - write("Data Ellipsoids"){ - $atom:ben 6.3888 6.3888 3.1967 1.0 0.0 0.0 0.0 - } - - write_once("In Init") { - units real - atom_style ellipsoid - pair_style gayberne 1.0 1.0 -3.0 25.0 - pair_modify mix arithmetic - - # Neighbour list. (Can be overridden) - neighbor 1.0 bin - neigh_modify check yes one 5000 - } - - - write_once("In Settings") { - # Gay-Berne parameters. - pair_coeff @atom:b1 @atom:b1 1.0 3.7275 0.7797 0.7797 3.6200 0.7797 0.7797 3.6200 25.0 - } - - - write_once("In Settings") { # <-- append to "In Settings" - - # It's probably useful to put the following computes and settings here since - # I imagine that most people who use this model would find them useful: - - compute q all property/atom quatw quati quatj quatk - compute shape all property/atom shapex shapey shapez - compute temp_trasl all temp - compute temp_rototrasl all temp/asphere dof all - compute press_trasl all pressure temp_trasl - compute myMSD all msd com yes - - # Modify temperature to include ellipsoidal degrees of freedom. - thermo_modify temp temp_rototrasl - thermo_modify press press_trasl - } - -} #BENZ - diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt deleted file mode 100644 index 00d669063b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/moltemplate_files/system.lt +++ /dev/null @@ -1,24 +0,0 @@ -# Run with the command: -# moltemplate.sh -atomstyle "atomid atomtype flag density x y z" benzene_sample01.lt -allow-wildcards -nocheck - -import "benzene_cg.lt" - -# Specify the periodic boundary conditions: -write_once("Data Boundary") { - 0 35.0 xlo xhi - 0 35.0 ylo yhi - 0 35.0 zlo zhi -} - -bulk = new BENZ [5].move(7, 0, 0) - [5].move(0, 7, 0).rot(10,0,1,0) - [5].move(0, 0, 7) - -# NOTE: -# I included a .rot() rotation command above in order to demonstrate -# that moltemplate can control ellipsoid orientation as well as position. -# Unfortunately, this example may be difficult to understand. Explanation: -# When ".rot(10,0,1,0)" appears in the middle of a 3-D array declaration, -# it applies a rotation of 10 degrees around the y axis ("0,1,0", into the -# screen) each time the middle index ("j" in "BENZ[i][j][k]") increases by one. -# This will cause the k-columns to be twisted around the y axis as y increases. diff --git a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in b/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in deleted file mode 100644 index 94ad81659b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/ellipsoids_CG_benzene/run.in +++ /dev/null @@ -1,37 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh (& packmol?) to create 3 files: -# system.data system.in.init system.in.settings -# -# See "README_setup.sh" for instructions how to use moltemplate.sh -# Note: This input script file only covers equilibration of the system. -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" -boundary p p p - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" - -# ------------------------------- Run Section ------------------------------- - -# Output: -thermo 100 -thermo_style custom step etotal evdwl ke pe temp press vol density & - c_myMSD[1] c_myMSD[2] c_myMSD[3] c_myMSD[4] cpu -dump 1 all custom 100 traj.lammpstrj & -id type x y z c_q[1] c_q[2] c_q[3] c_q[4] & -c_shape[1] c_shape[2] c_shape[3] & -angmomx angmomy angmomz - -# Dynamics: -timestep 10.0 -fix 2 all npt/asphere temp 300. 300. 1000. iso 1. 1. 10000. -fix_modify 2 press press_trasl -run 20000 diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/README.txt b/tools/moltemplate/examples/coarse_grained/membrane+protein/README.txt deleted file mode 100644 index a2b9dc91eb..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/README.txt +++ /dev/null @@ -1,70 +0,0 @@ - This example shows how to put a protein (inclusion) in a - lipid bilayer mixture composed of two different lipids (DPPC and DLPC). - The DPPC lipid model is described here: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) - (The DLPC model is a truncated version of DPPC. Modifications discussed below.) - The protein model is described here: - G. Bellesia, AI Jewett, and J-E Shea, - Protein Science, Vol19 141-154 (2010) - ---- PREREQUISITES: --- - -1) This example requires the "dihedral_style fourier", which is currently -in the USER-MISC package. Build LAMMPS with this package enabled using - make yes-user-misc -before compiling LAMMPS. -(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) - -2) This example may require additional features to be added to LAMMPS. -If LAMMPS complains about an "Invalid pair_style", then - a) download the "additional_lammps_code" from - http://moltemplate.org (upper-left corner menu) - b) unpack it - c) copy the .cpp and .h files to the src folding of your lammps installation. - d) (re)compile LAMMPS. - - ------ Details -------- - -This example contains a coarse-grained model of a 4-helix bundle protein -inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). - - -- Protein Model: -- - -The coarse-grained protein is described in: - G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -Here we use the "AUF2" model described in that paper. -(The hydrophobic beads face outwards.) - - -- Memebrane Model: -- - -The DPPC lipid bilayer described in: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) -and: - M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown - J. Chem. Phys. 135, 244701 (2011) - -As in Watson(JCP 2011), rigid bond-length constraints -have been replaced by harmonic bonds. - -A truncated version of this lipid (named "DLPC") has also been added. -The bending stiffness of each lipid has been increased to compensate -for the additional disorder resulting from mixing two different types -of lipids together. (Otherwise pores appear.) -Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models -have not been carefully parameterized to reproduce the correct behavior in -a lipid bilayer mixture. - - -------------- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_WARNING.txt b/tools/moltemplate/examples/coarse_grained/membrane+protein/README_WARNING.txt deleted file mode 100644 index f4b6763524..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_WARNING.txt +++ /dev/null @@ -1,10 +0,0 @@ -WARNING: - - This is not a realistic simulation of proteins in a lipid membrane. This -example was only intented to be a technical demonstration to show how to -combine totally different kinds of coarse-grained molecules (with different -kinds of force-fields) together in the same simulation in LAMMPS. Tuning the -force-field parameters to get realistic results was not the goal. I did -not take the extra time to do this. If you have suggestions for changes, -please email me (jewett.aij at gmail dot com). - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_run.sh b/tools/moltemplate/examples/coarse_grained/membrane+protein/README_run.sh deleted file mode 100755 index 29958f73a3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension) - -#or - -lmp_mpi -i run.in.nvt # Run a simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#or -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_setup.sh b/tools/moltemplate/examples/coarse_grained/membrane+protein/README_setup.sh deleted file mode 100755 index ee7d9efdd7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f table_int.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/membrane+protein/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg deleted file mode 100644 index 246ee54625..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_LR.jpg deleted file mode 100644 index fdbb446eed..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg deleted file mode 100644 index 142f3f706f..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg deleted file mode 100644 index 5d4b15b291..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg deleted file mode 100644 index 285389039d..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index 2e510ebd9e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,233 +0,0 @@ -# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle (or a 4-strand beta-barrel). -# This approach is optional. If your protein has helices which are not -# identical, you should probably just include all 4 helices in a single -# "Data Atoms" section and don't try to subdivide the protein into pieces.) - - - -1beadProtSci2010 { # <-- enclose definitions in a namespace for portability - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 - $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 - $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 - $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 - $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 - $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 - $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 - $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 - $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 - $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 - $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 - $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 - $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 - $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 - $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 - $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 - $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 - $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - - # ----- Now build a larger molecule using A16 and T3 ------- - - # Create a 4-Helix bundle. - # In this version, the hydrophobic beads are poing outward. - # I oriented them this way because I want to place this protein in a membrane. - # (There is another file in this directory containing alternate version - # of this same molecule with the hydrophobic beads pointing inward.) - - 4HelixInsideOut { - helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) - - turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) - turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) - turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOut - - - # -------- Minor coordinates adjustment: ----------- - - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6 = 0.8) - - 4HelixInsideOut.scale(0.8) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - - - # -------------- Force-Field Parameters ------------ - - # Units and force-field styles for this protein model - # (These can be overridden later.) - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - # --- Distance Units --- - # In this version of the model, sigma (the bond-length - # and particle diameter) is rounded to 4.8 Angstroms. - # - # --- Energy & Temperature Units --- - # In this protein model, "epsilon" represents the free energy - # bonus for bringing two hydrophobic amino acids together. - # Here I choose to set epsilon to 1.806551818181818 kCal/mole. - # This value was chosen so that a temperature of 300 Kelvin lies at - # 0.33 epsilon, which is the unfolding temperature of the marginally stable - # "ASF1" protein model from the Bellesia et al 2010 paper. - # This choice insures that both the "ASF1" model from that paper, - # as well as the much more stable "AUF2" protein we use here (which - # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, - # in the bulk at least. (However it's not clear that these energy - # parameters will work well for a protein in membrane. Perhaps I'll - # run some tests and fine tune these parameters for this scenario.) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 4.8 1 -1 - pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0 - pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0 - } - - # The exact value of the bond_coeff does not matter too much as long as - # it is "stiff enough". Here I use a softer bond spring than the one - # used in the paper so that I can increase the time step. - # I also use a relatively soft spring to constrain the bond angles. - - # bond_coeff bondType bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 4.8 - } - - - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # angle_coeff angleType anglestylename k theta0 - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 100.0 105.0 - } - - - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - write_once("Data Dihedrals By Type") { - # For a chain of sH and sL atoms, use the @dihedral:delta65_0 - # parameters. (This corresponds to the "AUF2" model from the - # Bellesia et. al 2010 paper.) - - @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * - - # If "tN" (turn) atoms are present, use the @dihedral:turn parameters - - @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * - } - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 - dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - } - - - # --- Mass Units --- - # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): - write_once("Data Masses") { - @atom:1beadProtSci2010/sH 100.0 - @atom:1beadProtSci2010/sL 100.0 - @atom:1beadProtSci2010/tN 100.0 - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt deleted file mode 100644 index 38b1b48f88..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt +++ /dev/null @@ -1,225 +0,0 @@ -### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## -### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## -# -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) - -import "1beadProtSci2010.lt" - -# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. - - -1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier - # This way we don't have to start from scratch. We can - # use all the atom types and angle settings defined earlier - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 - $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 - $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 - $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 - $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 - $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 - $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 - $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 - $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 - $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 - $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 - $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 - $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 - $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 - $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 - $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - # ----- Now build larger molecules using B16 and T3 ------- - - - 4SheetBarrel { - sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) - sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) - sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) - sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # Below I define several alternate conformations of the"4HelixBundleInsideOut" - # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. - - 4HelixBundle { - helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - - turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) - turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) - turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) - - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixBundle - - - - - # --- alternate conformations (same molecule) ---- - - # In the following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixBundleLoose { - - helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # In following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixInsideOutLoose { - helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) - turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) - turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOutLoose - - - - - # In the following version, the 4 helices are arranged next to each other, - # side-by-side, in a planar conformation (instead of a compact bundle). - - 4HelixPlanar { - helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) - helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) - helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) - helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) - turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) - turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixPlanar - - - # -------- Minor coordinates adjustment: ----------- - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6.0 = 0.8) - - 4SheetBarrel.scale(0.8) - 4HelixBundle.scale(0.8) - 4HelixBundleLoose.scale(0.8) - 4HelixInsideOutLoose.scale(0.8) - 4HelixPlanar.scale(0.8) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/CGLipidBr2005.lt deleted file mode 100644 index 24be50aced..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/CGLipidBr2005.lt +++ /dev/null @@ -1,196 +0,0 @@ -# Note: -# -# This example may require additional features to be added to LAMMPS. If -# LAMMPS complains about an "Invalid pair_style", then download copy the -# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS -# "src" directory and recompile LAMMPS. -# -# -------- Description -------- -# -# This example contains an implementation of the DPPC lipid bilayer described in -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# and: -# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown -# J. Chem. Phys. 135, 244701 (2011) -# -# As in Watson(JCP 2011), rigid bond-length constraints have been replaced -# by harmonic bonds. -# -# A truncated version of this lipid (named "DLPC") has also been added. -# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -# parameterized to reproduce the correct behavior in a lipid bilayer mixture. -# -# Units: -# -# The "epsilon" parameter in their model is approximately 2.75 kJ/mole -# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) -# The "sigma" parameter corresponds to 7.5 angstroms. - - -CGLipidBr2005 { - - - write_once("In Init") { - # -- Default styles for "CGLipidBr2005" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - - #angle_style hybrid cosine/delta # <- used in the original article - angle_style hybrid harmonic # <- prevents unphysical acute angle turns - # Explanation: - # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - # angle_style harmonic: U(theta) = k*(theta-theta0)^2 - - dihedral_style none - improper_style none - - pair_style hybrid table linear 1130 & - lj/charmm/coul/charmm/inter es4k4l 14.5 15 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - } - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 - $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - $bond:b4 @bond:../backbone $atom:t2 $atom:t3 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 - } - - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - - } #DPPC - - - DLPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - } - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - } #DLPC - - - # Particles and properties shared by all lipid types: - - write_once("Data Masses") { - @atom:int 200.0 - @atom:tail 200.0 - } - - write_once("In Settings") { - # -- Default settings/parameters for "CGLipidBr2005" -- - # (Hybrid bond & angle styles were used for portability.) - - # As in Watson(JCP 2011), rigid bond-length constraints - # have been replaced by harmonic bonds. - # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. - bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 - } - - write_once("In Settings") { - # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps - # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 - angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps - } - # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper - # to attempt to compensate for the fact that here we are using a lipid - # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal - # of disorder into the bilayer which would not be present in a DPPC bilayer. - # This causes pores to form. Increasing the angle stiffness prevents this.) - - write_once("In Settings") { - - # The interaction of "atom:int" with other "atom:int" atoms is given by - # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at - # r=3*sigma. This was implemented using pair_style table. - # Unfortunately, mixing lj/charmm and "table" pair styles in the same - # simulation is very inneficient. - - pair_coeff @atom:int @atom:int table table_int.dat INT - - # The interaction of tail beads with eachother is given by the formula below - # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: - # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction between head beads from different types of lipids - # is (currently) repulsive: - pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - } # write_once("In Settings") - - - # Note: I divided epsilon by 4 to get "0.1643" because we are using the - # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) - # (The "es4k4l" coeffstyle is the default.) Using this convention makes it - # easier to mix this coarse-grained lipid model with other molecular models. - - - -} # CGLipidBr2005 - - - - - - - - -# Note: This example has not been optimized for speed. -# -# Unfortunately, using both lj/charmm and "table" pair styles in the same -# simulation seems to be very inneficient. (The simulation is twice as slow -# as using only the "lj/charmm" pair styles for every pairwise interaction, -# ...and about 25% slower than using "table" for every pairwise interaction. -# However the lennard-jones pair styles support mixing, so we use them to -# make it easier to run these molecules with other molecules which don't use -# pair_table. I felt that portability was worth the extra 25% slow down.) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py deleted file mode 100755 index 1158a9cf75..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -rcut = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) - F_r = F(r, epsilon, sigma) - if r > rcut: - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index e7f0fe462e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# I realized later this is not what we want because although energy is conserved -# all enrgies are shifted with respect to energies used in the Brannigan paper -# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). -# (So don't use this.) - -# Calculate and print a - -def S(r, rc1, rc2, derivative=False): - """ - Calculate the switching function S(r) which decays continuously - between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): - S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 - I'm using the same smoothing/switching cutoff function used by the CHARMM - force-fields. (I'm even using the same code to implement it, taken - from lammps charmm/coul/charmm pair style, rewritten in python.) - - """ - assert(rc2>rc1) - rsq = r*r - rc1sq = rc1*rc1 - rc2sq = rc2*rc2 - denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* - (rc2sq-rc1sq)* - (rc2sq-rc1sq))) - if rsq > rc2sq: - return 0.0 - elif rsq < rc1sq: - if derivative: - return 0.0 - else: - return 1.0 - else: - rc2sq_minus_rsq = (rc2sq - rsq) - rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq - if derivative: - return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) - else: - return (rc2sq_minus_rsq_sq * - (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) - - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) - -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - F_r = F(r, epsilon, sigma) - # Multiply U(r) & F(r) by the smoothing/switch function - U_r = U_r * S(r, Rc1, Rc2) - F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/system.lt deleted file mode 100644 index 3e521b0f90..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/system.lt +++ /dev/null @@ -1,178 +0,0 @@ -# Description: - -# This example shows how to put a protein (inclusion) in a -# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). -# The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# The protein model is described here: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) -# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to -# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 - -# Note: -# This example may require additional features to be added to LAMMPS. -# If LAMMPS complains about an "Invalid pair_style", then copy the code -# in the "additional_lammps_code" directory into your LAMMPS "src" directory -# and recompile LAMMPS. - - - -import "CGLipidBr2005.lt" - -using namespace CGLipidBr2005 - -# The "= new random" syntax chooses one of several molecules at random - -lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed - [13].move(7.5, 0, 0) - [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice - [2].rot(180, 1, 0, 0) # <-- 2 monolayers - -# Move all the lipds up to the center of the box - -lipids[*][*][*].move(0,0,75.0) - - - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. (Check by visualising in VMD.) - - -write_once("Data Boundary") { - 0 97.5 xlo xhi - 0 97.42785792 ylo yhi - 0 150.0 zlo zhi -} - - -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 15 rows (each row is aligned with the x-axis) -# 13 columns (aligned at a 60 degree angle from the x axis) -# The lattice spacing is 7.5 Angstroms. -# When wrapped onto a rectangular box, the dimensions of the system are: -# 13 * 7.5 Angstroms in the X direction -# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction - - - - - - - -# ------------------- protein inclusion --------------------- - -import "1beadProtSci2010.lt" - -using namespace 1beadProtSci2010 - -protein = new 4HelixInsideOut - -protein.move(45.0, 25.98076211, 75.0) - - -# Delete a hole in the membrane to create space for the protein. -# (In the future moltemplate will be able to avoid occlusion automatically.) - - -delete lipids[4][2][*] -delete lipids[6][2][*] -delete lipids[3-6][3][*] -delete lipids[3-5][4][*] -delete lipids[2-5][5][*] -delete lipids[2][6][*] -delete lipids[4][6][*] - - -# -------- interactions between protein and lipids ---------- - -# Note: All atom types must include the full path (the name of -# the namespace which defined them as well as the atom type name). -# (This is because we are no longer inside that namespace.) - - -write_once("In Settings") { - - # Interactions between the protein and lipid atoms are usually - # determined by mixing rules. However this is not possible some - # for atoms (such as the "int" atoms in the lipid model which - # interact using -1/r^2 attraction). Lorentz-Berthelot mixing - # rules do not make sense for these atoms so we must explicitly - # define their interaction with all other atoms. - - # i j pairstylename eps sig K L - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - - # We want the interactions between hydrophobic residues and atoms in - # the interior of the lipid to be energetically similar to the attractive - # interactions between hydrophobic residues. (See 1beadProtSci2010.) - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1 - - # All other interactions between proteins and lipids are steric. - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - - - # We also add an artificial attractive interaction between the - # turn residues of the protein and the lipid head groups in - # order to keep the protein upright. This might not be necessary - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - - # Add a weak attractive interaction between hydrophilic "sL" beads - # (Whose strength mimics the strength of interaction between tail beads - # in the lipid. This was absent from the original protein model. - # However without some kind of weak attraction between residues, - # the negative pressure in the interior of the bilayer membrane - # allways pulls the protein apart. Recall that in the membrane, - # the hydrophobic beads in the protein will face outwards towards the lipid - # tails leaving the hydrophilic amino acids of the protein in the interior. - # In reality, these polar groups form hydrogen bonds with each other.) - - pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 6.0 0.4 -1 - - # However these hydrophilic amino acids are not attrected to - # the bilayer interior. - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - -} - - - - -# Finally, we must combine the two force-field styles which were used for -# the coarse-grained lipid and protein. To do that, we write one last time -# to the "In Init" section. When reading the "Init" section LAMMPS will -# read these commands last and this will override any earlier settings. - -write_once("In Init") { - # -- These styles override earlier settings -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid cosine/delta harmonic - dihedral_style hybrid fourier - improper_style none - pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" -} - diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/table_int.dat deleted file mode 100644 index b0d651d67f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1139 +0,0 @@ -# Table for the INT-INT interaction from -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# This table contains -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) - -INT -N 1130 - -1 0.02 2.0331818401e+30 1.21990910406e+33 -2 0.04 4.9638228518e+26 1.48914685554e+29 -3 0.06 3.82579033251e+24 7.65158066501e+26 -4 0.08 1.21187081343e+23 1.81780622014e+25 -5 0.1 8.32791281704e+21 9.99349538045e+23 -6 0.12 9.34030842897e+20 9.34030842897e+22 -7 0.14 1.46892540453e+20 1.25907891817e+22 -8 0.16 2.95866897809e+19 2.21900173357e+21 -9 0.18 7.19889946863e+18 4.79926631242e+20 -10 0.2 2.0331818401e+18 1.21990910406e+20 -11 0.22 6.47834392264e+17 3.53364213962e+19 -12 0.24 2.28034873754e+17 1.14017436877e+19 -13 0.26 8.72681951932e+16 4.02776285507e+18 -14 0.28 3.58624366341e+16 1.53696157003e+18 -15 0.3 1.56704372019e+16 6.26817488078e+17 -16 0.32 7.2233129348e+15 2.70874235055e+17 -17 0.34 3.48970861422e+15 1.23166186384e+17 -18 0.36 1.75754381558e+15 5.85847938527e+16 -19 0.38 9.18613895646e+14 2.90088598625e+16 -20 0.4 4.96382285179e+14 1.48914685554e+16 -21 0.42 2.76404230108e+14 7.89726371739e+15 -22 0.44 1.58162693423e+14 4.31352800247e+15 -23 0.46 9.27773983256e+13 2.42027995633e+15 -24 0.48 5.56725765996e+13 1.391814415e+15 -25 0.5 3.41111308981e+13 8.18667141564e+14 -26 0.52 2.13057117167e+13 4.91670270393e+14 -27 0.54 1.35459994024e+13 3.0102220895e+14 -28 0.56 8.75547769351e+12 1.87617379153e+14 -29 0.58 5.74645813711e+12 1.18892237325e+14 -30 0.6 3.8257903322e+12 7.65158066491e+13 -31 0.62 2.58128463312e+12 4.99603477424e+13 -32 0.64 1.7635041342e+12 3.30657025205e+13 -33 0.66 1.21901470178e+12 2.21639036726e+13 -34 0.68 8.51979641904e+11 1.50349348607e+13 -35 0.7 6.0167184547e+11 1.0314374497e+13 -36 0.72 4.29087845387e+11 7.15146409276e+12 -37 0.74 3.08855637556e+11 5.00846980094e+12 -38 0.76 2.24270970425e+11 3.54112058818e+12 -39 0.78 1.64210505205e+11 2.52631546702e+12 -40 0.8 1.2118708117e+11 1.81780621971e+12 -41 0.82 90109367359.1 1.31867367068e+12 -42 0.84 67481501334.4 9.64021449503e+11 -43 0.86 50880896383.4 7.09965997788e+11 -44 0.88 38613938681.2 5.26553710913e+11 -45 0.9 29486692086.8 3.93155896009e+11 -46 0.92 22650731882.4 2.95444330322e+11 -47 0.94 17498544395.3 2.23385674464e+11 -48 0.96 13591937526.4 1.69899220331e+11 -49 0.98 10612635712.6 1.29950642555e+11 -50 1.0 8327912706.34 99934953582.6 -51 1.02 6566502316.69 77252969474.2 -52 1.04 5201589672.36 60018343356.8 -53 1.06 4138717434.11 46853405843.3 -54 1.08 3307128665.58 36745874940.0 -55 1.1 2653529579.27 28947596241.1 -56 1.12 2137567708.15 22902511945.9 -57 1.14 1728534024.3 18195095739.0 -58 1.16 1402943799.0 14513212422.1 -59 1.18 1142752163.37 11621209113.9 -60 1.2 934030766.093 9340308300.6 -61 1.22 765981286.774 7534242773.65 -62 1.24 630196371.787 6098675145.29 -63 1.26 520103253.414 4953364870.6 -64 1.28 430542934.103 4036340534.04 -65 1.3 357450462.101 3299543229.91 -66 1.32 297610947.802 2705554551.18 -67 1.34 248472587.186 2225128105.44 -68 1.36 208002782.573 1835319108.76 -69 1.38 174576985.011 1518061159.35 -70 1.4 146892484.084 1259078837.33 -71 1.42 123901294.937 1047053582.16 -72 1.44 104757721.536 872981382.419 -73 1.46 88777241.639 729676313.267 -74 1.48 75404158.02 611385405.387 -75 1.5 64186061.7033 513488820.507 -76 1.52 54753607.1486 432265633.695 -77 1.54 46804443.7318 364710253.134 -78 1.56 40090410.0598 308388060.159 -79 1.58 34407297.9713 261321529.95 -80 1.6 29586646.6744 221900119.2 -81 1.62 25489145.661 188808745.634 -82 1.64 21999316.2868 160970856.824 -83 1.66 19021212.5921 137502982.517 -84 1.68 16474936.8715 117678352.86 -85 1.7 14293808.3245 100897694.735 -86 1.72 12422056.6082 86665727.6626 -87 1.74 10812938.3788 74572197.8496 -88 1.76 9427195.57103 64276535.39 -89 1.78 8231790.46096 55495411.7777 -90 1.8 7198865.45512 47992625.088 -91 1.82 6304885.77339 41570857.9644 -92 1.84 5529931.32911 36064946.1544 -93 1.86 4857110.59557 31336368.341 -94 1.88 4272074.43377 27268725.7382 -95 1.9 3762612.01167 23764025.6584 -96 1.92 3318314.28383 20739619.609 -97 1.94 2930293.18879 18125675.4316 -98 1.96 2590946.89128 15863086.114 -99 1.98 2293763.15199 13901736.4186 -100 2.0 2033154.33079 12199063.3122 -101 2.02 1804318.68586 10718858.1296 -102 2.04 1603123.57305 9430268.02169 -103 2.06 1426006.91783 8306962.01537 -104 2.08 1269893.96121 7326433.30293 -105 2.1 1132126.79514 6469414.48445 -106 2.12 1010404.62602 5719386.63441 -107 2.14 902733.052344 5062166.44376 -108 2.16 807380.928986 4485558.44681 -109 2.18 722843.627253 3979061.59742 -110 2.2 647811.695319 3533621.30686 -111 2.22 581144.085827 3141419.57242 -112 2.24 521845.251959 2795697.07302 -113 2.26 469045.525153 2490602.13576 -114 2.28 421984.280794 2221062.32522 -115 2.3 379995.475978 1982675.10836 -116 2.32 342495.208369 1771614.62868 -117 2.34 308970.999537 1584552.10475 -118 2.36 278972.551763 1418587.76828 -119 2.38 252103.765513 1271192.59046 -120 2.4 228015.837009 1140158.32224 -121 2.42 206401.282366 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-0.00354788564052 -0.0199492167196 -1117 22.34 -0.0031494369093 -0.0198956883597 -1118 22.36 -0.00275205683071 -0.0198423513132 -1119 22.38 -0.00235574158704 -0.0197892047262 -1120 22.4 -0.00196048737759 -0.0197362477497 -1121 22.42 -0.00156629041861 -0.0196834795391 -1122 22.44 -0.00117314694319 -0.0196308992543 -1123 22.46 -0.000781053201174 -0.0195785060596 -1124 22.48 -0.000390005459079 -0.019526299124 -1125 22.5 0.0 -0.0194742776206 -1126 22.52 0.0 0.0 -1127 22.54 0.0 0.0 -1128 22.56 0.0 0.0 -1129 22.58 0.0 0.0 -1130 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min deleted file mode 100644 index 9e1ccb360a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.min +++ /dev/null @@ -1,35 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. - - - -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.npt b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.npt deleted file mode 100644 index cbf76ac2db..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.npt +++ /dev/null @@ -1,66 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. -# - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -#read_data system.data -read_data system_after_min.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - -#minimize 1.0e-5 1.0e-7 500 2000 - -timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy - - -# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon -# (for the "epsilon" used by the coarse-grained lipid), and -# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein) -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. -# Note: We maintain the system system at constant (zero) tention -# using a barostat damping parameter Pdamp=1000 ("0 0 1000") - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -run 100000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.nvt b/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.nvt deleted file mode 100644 index 05f533339f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane+protein/run.in.nvt +++ /dev/null @@ -1,71 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) -# -# -------- LAMMPS REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. -# -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_npt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. -# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. - -#restart 500000 - -run 50000000 - - -write_data system_after_nvt.data - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also.) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README.txt b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README.txt deleted file mode 100644 index f8f542e77e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README.txt +++ /dev/null @@ -1,33 +0,0 @@ -Note: - This example may require additional features to be added to LAMMPS. -If LAMMPS complains about an "Invalid pair_style", then copy the code -in the "additional_lammps_code" directory into your LAMMPS "src" directory -and recompile LAMMPS. - ------ Description -------- - -This example contains an implementation of the DPPC lipid bilayer described in: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) -and: - M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown - J. Chem. Phys. 135, 244701 (2011) - -As in Watson(JCP 2011), rigid bond-length constraints -have been replaced by harmonic bonds. - -A truncated version of this lipid (named "DLPC") has also been added. -Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -parameterized to reproduce the correct behavior in a lipid bilayer. - - -------------- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_run.sh deleted file mode 100755 index 29958f73a3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension) - -#or - -lmp_mpi -i run.in.nvt # Run a simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#or -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_setup.sh deleted file mode 100755 index ee7d9efdd7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f table_int.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DLPC.jpg deleted file mode 100644 index 637f2f1c7a..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DLPC.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg deleted file mode 100644 index 14f1a1ed2c..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg deleted file mode 100644 index 757abe2684..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg deleted file mode 100644 index 2322449c1d..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC.jpg deleted file mode 100644 index 57e093023d..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/images/DPPC.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt deleted file mode 100644 index aabf2bcc8f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt +++ /dev/null @@ -1,208 +0,0 @@ -# Note: -# -# This example may require additional features to be added to LAMMPS. If -# LAMMPS complains about an "Invalid pair_style", then download copy the -# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS -# "src" directory and recompile LAMMPS. -# -# -------- Description -------- -# -# This example contains an implementation of the DPPC lipid bilayer described in -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# and: -# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown -# J. Chem. Phys. 135, 244701 (2011) -# -# As in Watson(JCP 2011), rigid bond-length constraints have been replaced -# by harmonic bonds. -# -# --- DLPC lipids --- -# A truncated version of the DPPC lipid (named "DLPC") has also been added. -# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -# parameterized to reproduce the correct behavior in a lipid bilayer/mixture. -# (You may need to stiffen the bond-angle forces to make it behave correctly, -# but I did not do this here.) -# -# Units: -# -# The "epsilon" parameter in their model is approximately 2.75 kJ/mole -# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) -# The "sigma" parameter corresponds to 7.5 angstroms. -# -# -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) - - - -CGLipidBr2005 { - - - write_once("In Init") { - # -- Default styles for "CGLipidBr2005" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - - angle_style hybrid cosine/delta # <- used in the original article - #angle_style hybrid harmonic # <- prevents unphysical acute angle turns - # Explanation: - # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - # angle_style harmonic: U(theta) = k*(theta-theta0)^2 - - dihedral_style none - improper_style none - - pair_style hybrid table linear 1130 & - lj/charmm/coul/charmm/inter es4k4l 14.5 15 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - } - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 - $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - $bond:b4 @bond:../backbone $atom:t2 $atom:t3 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 - } - - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - - } #DPPC - - - DLPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - } - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - } #DLPC - - - # Particles and properties shared by all lipid types: - - write_once("Data Masses") { - @atom:int 200.0 - @atom:tail 200.0 - } - - write_once("In Settings") { - # -- Default settings/parameters for "CGLipidBr2005" -- - # (Hybrid bond & angle styles were used for portability.) - - # As in Watson(JCP 2011), rigid bond-length constraints - # have been replaced by harmonic bonds. - # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. - bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 - } - - write_once("In Settings") { - - # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps - - ## Alternately, to stiffen the bond-angles, try this: - ##angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps - ## harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 - ##angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps - } - # Note: You may want to use a stiffer bond-angle than the original - # Brannigan&Brown 2005 paper if you want to mix two different lipids together. - # (The mixture of lipids introduces a great deal of disorder into the bilayer - # which would not be present in a DPPC bilayer. This caused pores to form - # in my simulations. But increasing the angle stiffness prevents this.) - - write_once("In Settings") { - - # The interaction of "atom:int" with other "atom:int" atoms is given by - # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at - # r=3*sigma. This was implemented using pair_style table. - # Unfortunately, mixing lj/charmm and "table" pair styles in the same - # simulation is very inneficient. - - pair_coeff @atom:int @atom:int table table_int.dat INT - - # The interaction of tail beads with eachother is given by the formula below - # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: - # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction between head beads from different types of lipids - # is (currently) repulsive: - pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - } # write_once("In Settings") - - - # Note: I divided epsilon by 4 to get "0.1643" because we are using the - # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) - # (The "es4k4l" coeffstyle is the default.) Using this convention makes it - # easier to mix this coarse-grained lipid model with other molecular models. - - - -} # CGLipidBr2005 - - - - - - - - -# Note: This example has not been optimized for speed. -# -# Unfortunately, using both lj/charmm and "table" pair styles in the same -# simulation seems to be very inneficient. (The simulation is twice as slow -# as using only the "lj/charmm" pair styles for every pairwise interaction, -# ...and about 25% slower than using "table" for every pairwise interaction. -# However the lennard-jones pair styles support mixing, so we use them to -# make it easier to run these molecules with other molecules which don't use -# pair_table. I felt that portability was worth the extra 25% slow down.) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py deleted file mode 100755 index 1158a9cf75..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -rcut = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) - F_r = F(r, epsilon, sigma) - if r > rcut: - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index e7f0fe462e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# I realized later this is not what we want because although energy is conserved -# all enrgies are shifted with respect to energies used in the Brannigan paper -# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). -# (So don't use this.) - -# Calculate and print a - -def S(r, rc1, rc2, derivative=False): - """ - Calculate the switching function S(r) which decays continuously - between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): - S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 - I'm using the same smoothing/switching cutoff function used by the CHARMM - force-fields. (I'm even using the same code to implement it, taken - from lammps charmm/coul/charmm pair style, rewritten in python.) - - """ - assert(rc2>rc1) - rsq = r*r - rc1sq = rc1*rc1 - rc2sq = rc2*rc2 - denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* - (rc2sq-rc1sq)* - (rc2sq-rc1sq))) - if rsq > rc2sq: - return 0.0 - elif rsq < rc1sq: - if derivative: - return 0.0 - else: - return 1.0 - else: - rc2sq_minus_rsq = (rc2sq - rsq) - rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq - if derivative: - return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) - else: - return (rc2sq_minus_rsq_sq * - (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) - - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) - -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - F_r = F(r, epsilon, sigma) - # Multiply U(r) & F(r) by the smoothing/switch function - U_r = U_r * S(r, Rc1, Rc2) - F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/system.lt deleted file mode 100644 index c556233c0d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/system.lt +++ /dev/null @@ -1,94 +0,0 @@ -# Description: - -# This constructs a bilayer constructed from coarse-grained DPPC lipids -# (implicit solvent). The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# -# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture -# in the "membrane+protein" and "vesicle" examples. - - - - - - -import "CGLipidBr2005Orig.lt" - -using namespace CGLipidBr2005 - -lipids = new DPPC [32].move(7.5, 0, 0) - [37].move(3.75, 6.49519, 0) - [2].rot(180, 1, 0, 0) - - -# Move the lipds up to the center of the box -lipids[*][*][*].move(0,0,75.0) - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. We apply them below: -# width: 240 = 32*7.5 -# height: 240.322 = 37*6.49519 - -write_once("Data Boundary") { - 0 240 xlo xhi - 0 240.322 ylo yhi - 0 150.0 zlo zhi -} - - - - - - - - -# -------------- File ends here. Only comments below.------------------- - -# ------------------------------------ -# ------------- COMMENTS: ------------ -# ------------------------------------ -# -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 32 rows (each row is aligned with the x-axis) -# 37 columns (aligned at a 60 degree angle from the x axis) -# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5) -# When wrapped onto a rectangular box, the dimensions of the system are: -# 32 * 7.5 Angstroms in the X direction -# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction -# ------------------------------------ -# -# Below I show simple ways to create a lipid bilayer: -# -# 1) If you just want to make lipid bilayer out of DPPC, -# without specifying the location of each lipid, you could use this syntax: -# lipids = new DPPC [32][37][2] # 3-D array -# Later you can load in the coordinates of the lipds from a PDB file. -# Alternately you could also use a 1-dimensional array: -# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2 -# It does not matter as long as the number of lipids is correct. -# Multidimensional arrays are only useful if you plan to apply independent -# coordinate transformations to each row and column and monolayer. See below: -# -# 2) Instead of loading a PDB file later, we can directly specify the location -# of each DPPC lipid in the LT file itself. For lipid bilayers, this is -# easy, because the bilayer structure resembles 2 planar lattices. -# We can use "move" commands to place each lipid, and the "rot" command -# to turn the lipids in one of the monolayers upside down. -# -# lipids = new DPPC [32].move(7.5, 0, 0) -# [37].move(3.75, 6.49519, 0) -# [2].rot(180, 1, 0, 0) -# -# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must -# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345) -# Here "0.5,0.5" are the probabilities for each molecule type, and "12345" -# is an optional random seed. -# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345) -# [32].move(7.5, 0, 0) -# [37].move(3.75, 6.49519, 0) -# [2].rot(180, 1, 0, 0) -# diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/table_int.dat deleted file mode 100644 index b0d651d67f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1139 +0,0 @@ -# Table for the INT-INT interaction from -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# This table contains -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) - -INT -N 1130 - -1 0.02 2.0331818401e+30 1.21990910406e+33 -2 0.04 4.9638228518e+26 1.48914685554e+29 -3 0.06 3.82579033251e+24 7.65158066501e+26 -4 0.08 1.21187081343e+23 1.81780622014e+25 -5 0.1 8.32791281704e+21 9.99349538045e+23 -6 0.12 9.34030842897e+20 9.34030842897e+22 -7 0.14 1.46892540453e+20 1.25907891817e+22 -8 0.16 2.95866897809e+19 2.21900173357e+21 -9 0.18 7.19889946863e+18 4.79926631242e+20 -10 0.2 2.0331818401e+18 1.21990910406e+20 -11 0.22 6.47834392264e+17 3.53364213962e+19 -12 0.24 2.28034873754e+17 1.14017436877e+19 -13 0.26 8.72681951932e+16 4.02776285507e+18 -14 0.28 3.58624366341e+16 1.53696157003e+18 -15 0.3 1.56704372019e+16 6.26817488078e+17 -16 0.32 7.2233129348e+15 2.70874235055e+17 -17 0.34 3.48970861422e+15 1.23166186384e+17 -18 0.36 1.75754381558e+15 5.85847938527e+16 -19 0.38 9.18613895646e+14 2.90088598625e+16 -20 0.4 4.96382285179e+14 1.48914685554e+16 -21 0.42 2.76404230108e+14 7.89726371739e+15 -22 0.44 1.58162693423e+14 4.31352800247e+15 -23 0.46 9.27773983256e+13 2.42027995633e+15 -24 0.48 5.56725765996e+13 1.391814415e+15 -25 0.5 3.41111308981e+13 8.18667141564e+14 -26 0.52 2.13057117167e+13 4.91670270393e+14 -27 0.54 1.35459994024e+13 3.0102220895e+14 -28 0.56 8.75547769351e+12 1.87617379153e+14 -29 0.58 5.74645813711e+12 1.18892237325e+14 -30 0.6 3.8257903322e+12 7.65158066491e+13 -31 0.62 2.58128463312e+12 4.99603477424e+13 -32 0.64 1.7635041342e+12 3.30657025205e+13 -33 0.66 1.21901470178e+12 2.21639036726e+13 -34 0.68 8.51979641904e+11 1.50349348607e+13 -35 0.7 6.0167184547e+11 1.0314374497e+13 -36 0.72 4.29087845387e+11 7.15146409276e+12 -37 0.74 3.08855637556e+11 5.00846980094e+12 -38 0.76 2.24270970425e+11 3.54112058818e+12 -39 0.78 1.64210505205e+11 2.52631546702e+12 -40 0.8 1.2118708117e+11 1.81780621971e+12 -41 0.82 90109367359.1 1.31867367068e+12 -42 0.84 67481501334.4 9.64021449503e+11 -43 0.86 50880896383.4 7.09965997788e+11 -44 0.88 38613938681.2 5.26553710913e+11 -45 0.9 29486692086.8 3.93155896009e+11 -46 0.92 22650731882.4 2.95444330322e+11 -47 0.94 17498544395.3 2.23385674464e+11 -48 0.96 13591937526.4 1.69899220331e+11 -49 0.98 10612635712.6 1.29950642555e+11 -50 1.0 8327912706.34 99934953582.6 -51 1.02 6566502316.69 77252969474.2 -52 1.04 5201589672.36 60018343356.8 -53 1.06 4138717434.11 46853405843.3 -54 1.08 3307128665.58 36745874940.0 -55 1.1 2653529579.27 28947596241.1 -56 1.12 2137567708.15 22902511945.9 -57 1.14 1728534024.3 18195095739.0 -58 1.16 1402943799.0 14513212422.1 -59 1.18 1142752163.37 11621209113.9 -60 1.2 934030766.093 9340308300.6 -61 1.22 765981286.774 7534242773.65 -62 1.24 630196371.787 6098675145.29 -63 1.26 520103253.414 4953364870.6 -64 1.28 430542934.103 4036340534.04 -65 1.3 357450462.101 3299543229.91 -66 1.32 297610947.802 2705554551.18 -67 1.34 248472587.186 2225128105.44 -68 1.36 208002782.573 1835319108.76 -69 1.38 174576985.011 1518061159.35 -70 1.4 146892484.084 1259078837.33 -71 1.42 123901294.937 1047053582.16 -72 1.44 104757721.536 872981382.419 -73 1.46 88777241.639 729676313.267 -74 1.48 75404158.02 611385405.387 -75 1.5 64186061.7033 513488820.507 -76 1.52 54753607.1486 432265633.695 -77 1.54 46804443.7318 364710253.134 -78 1.56 40090410.0598 308388060.159 -79 1.58 34407297.9713 261321529.95 -80 1.6 29586646.6744 221900119.2 -81 1.62 25489145.661 188808745.634 -82 1.64 21999316.2868 160970856.824 -83 1.66 19021212.5921 137502982.517 -84 1.68 16474936.8715 117678352.86 -85 1.7 14293808.3245 100897694.735 -86 1.72 12422056.6082 86665727.6626 -87 1.74 10812938.3788 74572197.8496 -88 1.76 9427195.57103 64276535.39 -89 1.78 8231790.46096 55495411.7777 -90 1.8 7198865.45512 47992625.088 -91 1.82 6304885.77339 41570857.9644 -92 1.84 5529931.32911 36064946.1544 -93 1.86 4857110.59557 31336368.341 -94 1.88 4272074.43377 27268725.7382 -95 1.9 3762612.01167 23764025.6584 -96 1.92 3318314.28383 20739619.609 -97 1.94 2930293.18879 18125675.4316 -98 1.96 2590946.89128 15863086.114 -99 1.98 2293763.15199 13901736.4186 -100 2.0 2033154.33079 12199063.3122 -101 2.02 1804318.68586 10718858.1296 -102 2.04 1603123.57305 9430268.02169 -103 2.06 1426006.91783 8306962.01537 -104 2.08 1269893.96121 7326433.30293 -105 2.1 1132126.79514 6469414.48445 -106 2.12 1010404.62602 5719386.63441 -107 2.14 902733.052344 5062166.44376 -108 2.16 807380.928986 4485558.44681 -109 2.18 722843.627253 3979061.59742 -110 2.2 647811.695319 3533621.30686 -111 2.22 581144.085827 3141419.57242 -112 2.24 521845.251959 2795697.07302 -113 2.26 469045.525153 2490602.13576 -114 2.28 421984.280794 2221062.32522 -115 2.3 379995.475978 1982675.10836 -116 2.32 342495.208369 1771614.62868 -117 2.34 308970.999537 1584552.10475 -118 2.36 278972.551763 1418587.76828 -119 2.38 252103.765513 1271192.59046 -120 2.4 228015.837009 1140158.32224 -121 2.42 206401.282366 1023554.60663 -122 2.44 186988.75765 919692.114521 -123 2.46 169538.563484 827090.818108 -124 2.48 153838.739168 744452.651831 -125 2.5 139701.665073 670637.92543 -126 2.52 126961.103835 604644.949624 -127 2.54 115469.620781 545592.416037 -128 2.56 105096.332511 492704.141327 -129 2.58 95724.9397832 445295.843157 -130 2.6 87252.0069441 402763.664479 -131 2.62 79585.4554502 364574.203947 -132 2.64 72643.2434671 330255.845328 -133 2.66 66352.2073932 299391.208536 -134 2.68 60647.0444312 271610.570248 -135 2.7 55469.4181565 246586.123584 -136 2.72 50767.1714483 224026.964698 -137 2.74 46493.633237 203674.709811 -138 2.76 42607.0073083 185299.659567 -139 2.78 39069.8329526 168697.439095 -140 2.8 35848.5085794 153686.051901 -141 2.82 32912.8705664 140103.294183 -142 2.84 30235.8206098 127804.483324 -143 2.86 27792.9956998 116660.460548 -144 2.88 25562.4755962 106555.833042 -145 2.9 23524.5233195 97387.4254387 -146 2.92 21661.3547409 89062.9145204 -147 2.94 19956.9338374 81499.6244039 -148 2.96 18396.7906059 74623.4624292 -149 2.98 16967.8589974 68367.9785194 -150 3.0 15658.3325568 62673.5329856 -151 3.02 14457.5357325 57486.5596649 -152 3.04 13355.809067 52758.912937 -153 3.06 12344.4066925 48447.2886046 -154 3.08 11415.4047444 44512.7098736 -155 3.1 10561.6194689 40920.0707567 -156 3.12 9776.5339459 37637.7301715 -157 3.14 9054.23247117 34637.1508274 -158 3.16 8389.34175838 31892.5777179 -159 3.18 7776.97821258 29380.7516608 -160 3.2 7212.7006167 27080.6538766 -161 3.22 6692.4676457 24973.2780793 -162 3.24 6212.59969004 23041.4269669 -163 3.26 5769.74452856 21269.5303734 -164 3.28 5360.84644195 19643.4826615 -165 3.3 4983.1184041 18150.4972204 -166 3.32 4634.01702836 16778.97618 -167 3.34 4311.21998136 15518.393672 -168 3.36 4012.60560869 14359.191159 -169 3.38 3736.23454428 13292.6835236 -170 3.4 3480.33310029 12310.9747549 -171 3.42 3243.27825585 11406.8822043 -172 3.44 3023.58408279 10573.8684961 -173 3.46 2819.88946345 9805.98028003 -174 3.48 2630.94697101 9097.79310596 -175 3.5 2455.61279669 8444.36177626 -176 3.52 2292.83761972 7841.17560602 -177 3.54 2141.65832756 7284.11808108 -178 3.56 2001.19050257 6769.43046025 -179 3.58 1870.62160083 6293.67891689 -180 3.6 1749.20475558 5853.72485855 -181 3.62 1636.25314534 5446.69810179 -182 3.64 1531.13487237 5069.97261409 -183 3.66 1433.26830277 4721.1445646 -184 3.68 1342.11782445 4398.01245332 -185 3.7 1257.18998347 4098.55911171 -186 3.72 1178.02996319 3820.93539003 -187 3.74 1104.21837425 3563.44536511 -188 3.76 1035.36832639 3324.53291993 -189 3.78 971.122756088 3102.76956138 -190 3.8 911.151986554 2896.84335615 -191 3.82 855.151498616 2705.54887715 -192 3.84 802.83989347 2527.77806329 -193 3.86 753.957029799 2362.51190574 -194 3.88 708.262319576 2208.81288195 -195 3.9 665.533168297 2065.81806693 -196 3.92 625.563546756 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/dev/null @@ -1,28 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Optional: Make sure the pairwise energies look reasonable: -#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0 -#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0 -#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0 -#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0 -#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0 -#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0 - - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/run.in.npt deleted file mode 100644 index ab37d34b39..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/run.in.npt +++ /dev/null @@ -1,57 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example may require additional features and bug fixes for LAMMPS. -# Be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 2) Unpack it -# 3) copy the .cpp and .h files to the src folding of your lammps installation. -# 4) Compile LAMMPS. -# -# (If LAMMPS complains about an "Invalid pair_style" -# then you made a mistake in the instructions above.) -# - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy - - -# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon -# for the "epsilon" used by the coarse-grained lipid. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. -# Note: We maintain the system system at constant (zero) tention -# using a barostat damping parameter Pdamp=1000 ("0 0 1000") - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -#restart 1000000 - -run 2000000 - -write_data system_after_npt.data - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/run.in.nvt deleted file mode 100644 index 63d4cde4a1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/run.in.nvt +++ /dev/null @@ -1,45 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a data file "system_after_npt.data" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_data system_after_npt.data - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. -# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. - -#restart 1000000 - -run 1000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README.txt b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README.txt deleted file mode 100644 index c0fc605b6f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README.txt +++ /dev/null @@ -1,16 +0,0 @@ ------ Description -------- - -This example contains an implementation of the DPPC lipid bilayer described in: -"Tunable generic model for fluid bilayer membranes" -Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 - -------------- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_run.sh b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_run.sh deleted file mode 100755 index 940205ff47..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_run.sh +++ /dev/null @@ -1,27 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension) - -# and, after that: - -lmp_mpi -i run.in.nvt # Run a simulation at constant volume - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpiexec -np 4 lmp_mpi -i run.in.npt -#or -#mpiexec -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_setup.sh b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_setup.sh deleted file mode 100755 index 0d1c3fd00e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f tabulated_potential.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_visualize.txt deleted file mode 100644 index f70bc3b753..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 0.0} - pbc box -shiftcenterrel {0.0 0.0 0.0} -width 0.5 - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid.jpg b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid.jpg deleted file mode 100644 index f3445b18e6..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=0_nopbc_occ.jpg b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=0_nopbc_occ.jpg deleted file mode 100644 index e4f7ae0c9f..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=0_nopbc_occ.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=0_occ.jpg b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=0_occ.jpg deleted file mode 100644 index 8e125da5c1..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=0_occ.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=600000steps_npt_occ.jpg b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=600000steps_npt_occ.jpg deleted file mode 100644 index 0e0d095318..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_t=600000steps_npt_occ.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/calc_table/gen_potential-cooke.py b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/calc_table/gen_potential-cooke.py deleted file mode 100755 index 7240296584..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/calc_table/gen_potential-cooke.py +++ /dev/null @@ -1,144 +0,0 @@ -#!/usr/bin/python2.7 - -import os,sys -from fractions import Fraction -from numpy import * - -### PARAMETERS ### -sigma = 1.00 -epsilon = 1.00 - -b_hh = 0.95 * sigma -b_ht = 0.95 * sigma -b_tt = 1.00 * sigma - -r_init = 0.000001 -r_max = sigma * 3. -r_space = 0.01 -################## - -### INPUTS ### -if len(sys.argv) == 2: - w_cut = float(sys.argv[1]) -else: - w_cut = 1.6 -# 1.6 seems to be 'good' for vesicles, bilayers 1.4 -############## - -def WCA_energy(b, r): -# Calculate WCA energy - E_pot = 0 - val1 = math.pow((b / r), 12) - val2 = -math.pow((b / r), 6) - E_pot = 4 * epsilon * (val1 + val2 + 0.25) - return E_pot - -def WCA_forces(b, r): -# Calculate WCA forces - Force = 0 - val1 = 24 * math.pow(b, 6) / math.pow(r, 7) - val2 = -48 * math.pow(b, 12) / math.pow(r, 13) - Force = -(val1 + val2) - return Force - -def Tail_energy(b, r, r_cut): -# Calculate extra Tail energy - E_pot = 0 - if (r < r_cut): - E_pot = -1 * epsilon - else: - val1 = math.cos((math.pi * (r - r_cut)) / (2 * w_cut)) - E_pot = -1 * epsilon * math.pow(val1, 2) - return E_pot - -def Tail_forces(b, r, r_cut): - Force = 0 - if (r < r_cut): - Force = 0; - else: - val1 = math.sin((math.pi * (r - r_cut)) / w_cut) - Force = -math.pi * val1 / (2 * w_cut) - return Force - - -############## -ofile = open('tabulated_potential.dat', 'w') -tot_potential_hh = zeros((int(r_max / r_space) + 1, 4)) -tot_potential_ht = zeros((int(r_max / r_space) + 1, 4)) -tot_potential_tt = zeros((int(r_max / r_space) + 1, 4)) - -# Setup up formatting & distances in all arrays -for i in range(int(r_max / r_space)+1): - tot_potential_hh[:,0][i] = i+1 - tot_potential_ht[:,0][i] = i+1 - tot_potential_tt[:,0][i] = i+1 -for i in range(1, int(r_max / r_space)+1): - tot_potential_hh[:,1][i] = tot_potential_hh[:,1][i-1] + r_space - tot_potential_ht[:,1][i] = tot_potential_ht[:,1][i-1] + r_space - tot_potential_tt[:,1][i] = tot_potential_tt[:,1][i-1] + r_space -tot_potential_hh[:,1][0] = r_init -tot_potential_ht[:,1][0] = r_init -tot_potential_tt[:,1][0] = r_init - - - -ofile.write("# Tabulated potential for Cooke 3-bead lipid model, Wc = %f\n\n" % w_cut) -num = len(tot_potential_hh[:,0]) - -### Calcaulte first potential, H-H -ofile.write("HEAD_HEAD\n") -r_cut = 2**Fraction('1/6') * b_hh -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_hh[:,1][0], tot_potential_hh[:,2][0], tot_potential_hh[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_hh[:,2][i] = WCA_energy(b_hh, tot_potential_hh[:,1][i]) - tot_potential_hh[:,3][i] = WCA_forces(b_hh, tot_potential_hh[:,1][i]) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_hh[:,1][i], tot_potential_hh[:,2][i], tot_potential_hh[:,3][i])) -ofile.write("\n") - - - -### Calcaulte second potential, H-T -ofile.write("HEAD_TAIL\n") -r_cut = 2**Fraction('1/6') * b_ht -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_ht[:,1][0], tot_potential_ht[:,2][0], tot_potential_ht[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_ht[:,2][i] = WCA_energy(b_ht, tot_potential_ht[:,1][i]) - tot_potential_ht[:,3][i] = WCA_forces(b_ht, tot_potential_ht[:,1][i]) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_ht[:,1][i], tot_potential_ht[:,2][i], tot_potential_ht[:,3][i])) -ofile.write("\n") - - - -### Calcaulte third potential, T-T -# Also include extra tail-tail attraction term -ofile.write("TAIL_TAIL\n") -r_cut = 2**Fraction('1/6') * b_tt -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_tt[:,1][0], tot_potential_tt[:,2][0], tot_potential_tt[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_tt[:,2][i] = WCA_energy(b_tt, tot_potential_tt[:,1][i]) - tot_potential_tt[:,3][i] = WCA_forces(b_tt, tot_potential_tt[:,1][i]) - -max2 = int( (r_cut + w_cut) / r_space) -for i in range(1, max2+1): - tot_potential_tt[:,2][i] = tot_potential_tt[:,2][i] + Tail_energy(b_tt, tot_potential_tt[:,1][i], r_cut) - tot_potential_tt[:,3][i] = tot_potential_tt[:,3][i] + Tail_forces(b_tt, tot_potential_tt[:,1][i], r_cut) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_tt[:,1][i], tot_potential_tt[:,2][i], tot_potential_tt[:,3][i])) -ofile.write("\n") - - -sys.exit() diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/cooke_deserno_lipid.lt b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/cooke_deserno_lipid.lt deleted file mode 100644 index 64ea1785f3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/cooke_deserno_lipid.lt +++ /dev/null @@ -1,46 +0,0 @@ -# CDlipid is a lipid model from: -# "Tunable generic model for fluid bilayer membranes" -# Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 -# (Author: David Stelter, BU) - -CDlipid { - # 3-bead model of COOKE, KREMER, DESERNO - write_once("In Init") { - units lj - atom_style full - - bond_style hybrid fene - angle_style hybrid harmonic - pair_style hybrid table linear 600 - pair_modify shift yes - special_bonds lj 0.0 1.0 1.0 - - neigh_modify every 1 delay 1 - neighbor 0.3 bin - } - write_once("In Settings") { - pair_coeff @atom:H @atom:H table tabulated_potential.dat HEAD_HEAD - pair_coeff @atom:H @atom:T table tabulated_potential.dat HEAD_TAIL - # (Note: The "HEAD_TAIL" table is the same as the "HEAD_HEAD" table.) - pair_coeff @atom:T @atom:T table tabulated_potential.dat TAIL_TAIL_Wc_1.5 - bond_coeff @bond:B fene 30.0 1.5 1.0 1.0 - angle_coeff @angle:An harmonic 10.0 180 - } - write("Data Atoms") { - $atom:1 $mol:. @atom:H 0.0 0.00 0.00 2.46 - $atom:2 $mol:. @atom:T 0.0 0.00 0.00 1.51 - $atom:3 $mol:. @atom:T 0.0 0.00 0.00 0.56 - } - write("Data Bonds") { - $bond:b1 @bond:B $atom:1 $atom:2 - $bond:b2 @bond:B $atom:2 $atom:3 - } - write("Data Angles") { - $angle:a1 @angle:An $atom:1 $atom:2 $atom:3 - } - write_once("Data Masses") { - @atom:H 1.0 ## Head Bead - @atom:T 1.0 ## Tail Bead - } -} # CDlipid - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/system.lt deleted file mode 100644 index 59e08aeb2b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/system.lt +++ /dev/null @@ -1,74 +0,0 @@ -# Description: - -# This constructs a bilayer constructed from coarse-grained lipids -# (implicit solvent). "Tunable generic model for fluid bilayer membranes" -# Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 - - - -import "cooke_deserno_lipid.lt" - -lipids = new CDlipid [32].move(1.178585, 0, 0) - [37].move(0.589293, 1.02068, 0) - [2].rot(180, 1, 0, 0) - - -# Move the lipds up to the center of the box -lipids[*][*][*].move(0,0,10.0) - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. We apply them below: -# width: 37.71472 = 32 * 1.05 * 2^(1/6) -# height: 37.76516 = 37 * 1.05 * 2^(1/6) * sqrt(3)/2 - -write_once("Data Boundary") { - 0 37.71472 xlo xhi - 0 37.76516 ylo yhi - 0 20.0 zlo zhi -} - - - - - - - - -# -------------- File ends here. Only comments below.------------------- - -# ------------------------------------ -# ------------- COMMENTS: ------------ -# ------------------------------------ -# -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 32 rows (each row is aligned with the x-axis) -# 37 columns (aligned at a 60 degree angle from the x axis) -# When wrapped onto a rectangular box, the dimensions of the system are: -# 32 * 2^(1/6) σ units in the X direction -# 37 * 2^(1/6) * sqrt(3)/2 σ units in the Y direction -# ------------------------------------ -# -# Below I show simple ways to create a lipid bilayer: -# -# 1) If you just want to make lipid bilayer out of lipids, -# without specifying the location of each lipid, you could use this syntax: -# lipids = new CDlipid [32][37][2] # 3-D array -# Later you can load in the coordinates of the lipds from a PDB file. -# Alternately you could also use a 1-dimensional array: -# lipids = new CDlipid [2368] # 1-D array. Note: 2368 = 32x37x2 -# It does not matter as long as the number of lipids is correct. -# Multidimensional arrays are only useful if you plan to apply independent -# coordinate transformations to each row and column and monolayer as above. -# -# 2) If you want to create a bilayer from a mixture of two lipids (named -# "lipidA", "lipidB"), you must replace "CDlipid" in the command above with -# random([lipidA,lipidB],[710,1658],12345) -# Here "710,1658" are the number of each molecule type (must sum to 32*37*2), -# and "12345" is an optional random seed: -# lipids = new random([lipidA,lipidB], [710,1658], 12345) -# [32].move(1.178585, 0, 0) -# [37].move(0.589293, 1.02068, 0) -# [2].rot(180, 1, 0, 0) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/tabulated_potential.dat b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/tabulated_potential.dat deleted file mode 100644 index cd8dd4db7d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/moltemplate_files/tabulated_potential.dat +++ /dev/null @@ -1,4589 +0,0 @@ -# Tabulated potential for Cooke 3-bead lipid model, with various values of Wc - -HEAD_HEAD -N 301 R 0.000001 3.000000 - -1 0.000001 0.000000 0.000000 -2 0.010000 2161440350647607518822400.000000 2593728420778890895481110528.000000 -3 0.020000 527695398062100709376.000000 316617238851043104653312.000000 -4 0.030000 4067131343850062336.000000 1626852538346708926464.000000 -5 0.040000 128831883585858496.000000 38649565183436988416.000000 -6 0.050000 8853259488081101.000000 2124782299721489152.000000 -7 0.060000 992951926207085.500000 198590391543644928.000000 -8 0.070000 156158887055179.062500 26770097065977256.000000 -9 0.080000 31453085537227.195312 4717963671829832.000000 -10 0.090000 7653019634383.599609 1020402986772367.875000 -11 0.100000 2161437410283.985352 259372665656012.125000 -12 0.110000 688699846600.110840 75130982888675.812500 -13 0.120000 242418934523.303925 24241942688387.753906 -14 0.130000 92772695554.949768 8563661551482.013672 -15 0.140000 38124343876.568542 3267817639811.164551 -16 0.150000 16658711862.666004 1332707274503.870850 -17 0.160000 7678803441.103481 575916830241.413208 -18 0.170000 3709726886.129636 261867373669.903687 -19 0.180000 1868327898.144181 124558074820.194244 -20 0.190000 976500000.999998 61675657894.736687 -21 0.200000 527649455.864879 31660345589.187614 -22 0.210000 293806260.511241 16789908645.082933 -23 0.220000 168114083.438129 9170566326.526011 -24 0.230000 98610181.495127 5145397135.359623 -25 0.240000 59169165.297856 2958842872.372237 -26 0.250000 36250908.888444 1740332628.538169 -27 0.260000 22640215.252607 1045152619.667436 -28 0.270000 14392928.420337 639854320.962319 -29 0.280000 9301695.744822 398774811.984595 -30 0.290000 6104017.717125 252682276.475626 -31 0.300000 4063098.921872 162604585.395105 -32 0.310000 2740806.847436 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2.970000 0.000000 0.000000 -299 2.980000 0.000000 0.000000 -300 2.990000 0.000000 0.000000 -301 3.000000 0.000000 0.000000 - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.min b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.min deleted file mode 100644 index 712eca1a76..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.min +++ /dev/null @@ -1,25 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz -thermo_style custom step pe etotal vol epair ebond eangle -thermo 20 # time interval for printing out "thermo" data - -#min_style quickmin -#min_modify dmax 0.03 -#min_style hftn -#min_modify dmax 0.05 -minimize 1.0e-7 1.0e-9 100000 300000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.npt b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.npt deleted file mode 100644 index e9294a96d8..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.npt +++ /dev/null @@ -1,58 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example may require additional features and bug fixes for LAMMPS. -# Be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 2) Unpack it -# 3) copy the .cpp and .h files to the src folding of your lammps installation. -# 4) Compile LAMMPS. -# -# (If LAMMPS complains about an "Invalid pair_style" -# then you made a mistake in the instructions above.) -# - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.01 -dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 200 # time interval for printing out "thermo" data - -velocity all create 1.1 12345 - -fix fxlan all langevin 1.1 1.1 50.0 48279 -fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy - -# Note: The temperature is 1.1*ε -# (ε = "epsilon" used by the coarse-grained lipid) -# Note: The langevin damping parameter is now "50.0" in units of time -# (which are (m/(ε*σ^2))^(1/2) because we are using "units lj" -# This is grossly underdamped compared to the real system, -# but it leads to more efficient sampling.) -# Note: We maintain the system system at constant (zero) tention -# using a barostat damping parameter Pdamp=1000 ("0 0 1000") - - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -run 1000000 - -write_data system_after_npt.data - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.nvt b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.nvt deleted file mode 100644 index 85c16a0b73..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/run.in.nvt +++ /dev/null @@ -1,49 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# To run this simulation, you should first equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a data file "system_after_npt.data" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: - -read_data system_after_npt.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -timestep 0.01 -dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - -velocity all create 1.1 12345 - -fix fxlan all langevin 1.1 1.1 500.0 48279 -fix fxnve all nve - -# Note: The temperature is 1.1*ε -# (ε = "epsilon" used by the coarse-grained lipid) -# Note: The langevin damping parameter is "500.0" in units of time -# (which are (m/(ε*σ^2))^(1/2) because we are using "units lj" -# This is grossly underdamped compared to the real system, -# but it leads to more efficient sampling.) - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -run 20000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/tabulated_potential.dat b/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/tabulated_potential.dat deleted file mode 100644 index cd8dd4db7d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_Cooke_Kremer_DesernoPRE2005/tabulated_potential.dat +++ /dev/null @@ -1,4589 +0,0 @@ -# Tabulated potential for Cooke 3-bead lipid model, with various values of Wc - -HEAD_HEAD -N 301 R 0.000001 3.000000 - -1 0.000001 0.000000 0.000000 -2 0.010000 2161440350647607518822400.000000 2593728420778890895481110528.000000 -3 0.020000 527695398062100709376.000000 316617238851043104653312.000000 -4 0.030000 4067131343850062336.000000 1626852538346708926464.000000 -5 0.040000 128831883585858496.000000 38649565183436988416.000000 -6 0.050000 8853259488081101.000000 2124782299721489152.000000 -7 0.060000 992951926207085.500000 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2.890000 -0.000802 -0.049416 -291 2.900000 -0.000384 -0.034203 -292 2.910000 -0.000118 -0.018979 -293 2.920000 -0.000005 -0.003750 -294 2.930000 0.000000 0.000000 -295 2.940000 0.000000 0.000000 -296 2.950000 0.000000 0.000000 -297 2.960000 0.000000 0.000000 -298 2.970000 0.000000 0.000000 -299 2.980000 0.000000 0.000000 -300 2.990000 0.000000 0.000000 -301 3.000000 0.000000 0.000000 - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README.txt b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README.txt deleted file mode 100644 index c0fc605b6f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README.txt +++ /dev/null @@ -1,16 +0,0 @@ ------ Description -------- - -This example contains an implementation of the DPPC lipid bilayer described in: -"Tunable generic model for fluid bilayer membranes" -Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 - -------------- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_run.sh b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_run.sh deleted file mode 100755 index eb3fe7089a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # Run a simulation at constant pressure (tension) - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpiexec -np 4 lmp_mpi -i run.in.npt -#or -#mpiexec -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_setup.sh b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_setup.sh deleted file mode 100755 index 0d1c3fd00e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f tabulated_potential.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_visualize.txt deleted file mode 100644 index f70bc3b753..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.0 0.0} - pbc box -shiftcenterrel {0.0 0.0 0.0} -width 0.5 - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_A.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_A.jpg deleted file mode 100644 index fb45910d88..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_A.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_B.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_B.jpg deleted file mode 100644 index 2fc365bd44..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_B.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=0_nopbc_occ_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=0_nopbc_occ_LR.jpg deleted file mode 100644 index 1f85ace52a..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=0_nopbc_occ_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=0_occ_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=0_occ_LR.jpg deleted file mode 100644 index 810b8d79a2..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=0_occ_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=1000000steps_npt_occ_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=1000000steps_npt_occ_LR.jpg deleted file mode 100644 index 983c4ec248..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=1000000steps_npt_occ_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=120000steps_npt_occ_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=120000steps_npt_occ_LR.jpg deleted file mode 100644 index 6b7b6bc63f..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=120000steps_npt_occ_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=40000steps_npt_occ_LR.jpg b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=40000steps_npt_occ_LR.jpg deleted file mode 100644 index 9e7a593fc9..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/images/CDlipid_bilayer_mixture_t=40000steps_npt_occ_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/calc_table/gen_potential-cooke.py b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/calc_table/gen_potential-cooke.py deleted file mode 100755 index 7240296584..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/calc_table/gen_potential-cooke.py +++ /dev/null @@ -1,144 +0,0 @@ -#!/usr/bin/python2.7 - -import os,sys -from fractions import Fraction -from numpy import * - -### PARAMETERS ### -sigma = 1.00 -epsilon = 1.00 - -b_hh = 0.95 * sigma -b_ht = 0.95 * sigma -b_tt = 1.00 * sigma - -r_init = 0.000001 -r_max = sigma * 3. -r_space = 0.01 -################## - -### INPUTS ### -if len(sys.argv) == 2: - w_cut = float(sys.argv[1]) -else: - w_cut = 1.6 -# 1.6 seems to be 'good' for vesicles, bilayers 1.4 -############## - -def WCA_energy(b, r): -# Calculate WCA energy - E_pot = 0 - val1 = math.pow((b / r), 12) - val2 = -math.pow((b / r), 6) - E_pot = 4 * epsilon * (val1 + val2 + 0.25) - return E_pot - -def WCA_forces(b, r): -# Calculate WCA forces - Force = 0 - val1 = 24 * math.pow(b, 6) / math.pow(r, 7) - val2 = -48 * math.pow(b, 12) / math.pow(r, 13) - Force = -(val1 + val2) - return Force - -def Tail_energy(b, r, r_cut): -# Calculate extra Tail energy - E_pot = 0 - if (r < r_cut): - E_pot = -1 * epsilon - else: - val1 = math.cos((math.pi * (r - r_cut)) / (2 * w_cut)) - E_pot = -1 * epsilon * math.pow(val1, 2) - return E_pot - -def Tail_forces(b, r, r_cut): - Force = 0 - if (r < r_cut): - Force = 0; - else: - val1 = math.sin((math.pi * (r - r_cut)) / w_cut) - Force = -math.pi * val1 / (2 * w_cut) - return Force - - -############## -ofile = open('tabulated_potential.dat', 'w') -tot_potential_hh = zeros((int(r_max / r_space) + 1, 4)) -tot_potential_ht = zeros((int(r_max / r_space) + 1, 4)) -tot_potential_tt = zeros((int(r_max / r_space) + 1, 4)) - -# Setup up formatting & distances in all arrays -for i in range(int(r_max / r_space)+1): - tot_potential_hh[:,0][i] = i+1 - tot_potential_ht[:,0][i] = i+1 - tot_potential_tt[:,0][i] = i+1 -for i in range(1, int(r_max / r_space)+1): - tot_potential_hh[:,1][i] = tot_potential_hh[:,1][i-1] + r_space - tot_potential_ht[:,1][i] = tot_potential_ht[:,1][i-1] + r_space - tot_potential_tt[:,1][i] = tot_potential_tt[:,1][i-1] + r_space -tot_potential_hh[:,1][0] = r_init -tot_potential_ht[:,1][0] = r_init -tot_potential_tt[:,1][0] = r_init - - - -ofile.write("# Tabulated potential for Cooke 3-bead lipid model, Wc = %f\n\n" % w_cut) -num = len(tot_potential_hh[:,0]) - -### Calcaulte first potential, H-H -ofile.write("HEAD_HEAD\n") -r_cut = 2**Fraction('1/6') * b_hh -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_hh[:,1][0], tot_potential_hh[:,2][0], tot_potential_hh[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_hh[:,2][i] = WCA_energy(b_hh, tot_potential_hh[:,1][i]) - tot_potential_hh[:,3][i] = WCA_forces(b_hh, tot_potential_hh[:,1][i]) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_hh[:,1][i], tot_potential_hh[:,2][i], tot_potential_hh[:,3][i])) -ofile.write("\n") - - - -### Calcaulte second potential, H-T -ofile.write("HEAD_TAIL\n") -r_cut = 2**Fraction('1/6') * b_ht -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_ht[:,1][0], tot_potential_ht[:,2][0], tot_potential_ht[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_ht[:,2][i] = WCA_energy(b_ht, tot_potential_ht[:,1][i]) - tot_potential_ht[:,3][i] = WCA_forces(b_ht, tot_potential_ht[:,1][i]) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_ht[:,1][i], tot_potential_ht[:,2][i], tot_potential_ht[:,3][i])) -ofile.write("\n") - - - -### Calcaulte third potential, T-T -# Also include extra tail-tail attraction term -ofile.write("TAIL_TAIL\n") -r_cut = 2**Fraction('1/6') * b_tt -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_tt[:,1][0], tot_potential_tt[:,2][0], tot_potential_tt[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_tt[:,2][i] = WCA_energy(b_tt, tot_potential_tt[:,1][i]) - tot_potential_tt[:,3][i] = WCA_forces(b_tt, tot_potential_tt[:,1][i]) - -max2 = int( (r_cut + w_cut) / r_space) -for i in range(1, max2+1): - tot_potential_tt[:,2][i] = tot_potential_tt[:,2][i] + Tail_energy(b_tt, tot_potential_tt[:,1][i], r_cut) - tot_potential_tt[:,3][i] = tot_potential_tt[:,3][i] + Tail_forces(b_tt, tot_potential_tt[:,1][i], r_cut) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_tt[:,1][i], tot_potential_tt[:,2][i], tot_potential_tt[:,3][i])) -ofile.write("\n") - - -sys.exit() diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/cooke_deserno_lipids.lt b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/cooke_deserno_lipids.lt deleted file mode 100644 index 04953c97b7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/cooke_deserno_lipids.lt +++ /dev/null @@ -1,96 +0,0 @@ -# CDlipid is a lipid model from: -# "Tunable generic model for fluid bilayer membranes" -# Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 -# (Author: David Stelter, BU) -# 3-bead model of COOKE, KREMER, DESERNO -# -# In this example, there are two types of identical lipids "A" and "B". -# The attractive interaction between the tail beads of different lipids (AB) -# is weaker than it is for lipids of the same type (as it was in the paper). -# (Wc = 1.3σ, instead of Wc = 1.5σ) - - -CDlipids { - # Settings common to both lipids ("LipidA" and "LipidB") - write_once("In Init") { - units lj - atom_style full - - bond_style hybrid fene - angle_style hybrid harmonic - pair_style hybrid table linear 600 - pair_modify shift yes - special_bonds lj 0.0 1.0 1.0 - - neigh_modify every 1 delay 1 - neighbor 0.3 bin - } - write_once("In Settings") { - pair_coeff @atom:H @atom:H table tabulated_potential.dat HEAD_HEAD - bond_coeff @bond:Bond fene 30.0 1.5 1.0 1.0 - angle_coeff @angle:An harmonic 10.0 180 - } - write_once("Data Masses") { - @atom:H 1.0 ## Head Bead - } - - - A { - write_once("In Settings") { - pair_coeff @atom:../H @atom:T table tabulated_potential.dat HEAD_TAIL - # (Note: The "HEAD_TAIL" table is the same as the "HEAD_HEAD" table.) - pair_coeff @atom:T @atom:T table tabulated_potential.dat TAIL_TAIL_Wc_1.5 - } - write("Data Atoms") { - $atom:1 $mol:. @atom:../H 0.0 0.00 0.00 2.46 - $atom:2 $mol:. @atom:T 0.0 0.00 0.00 1.51 - $atom:3 $mol:. @atom:T 0.0 0.00 0.00 0.56 - } - write("Data Bonds") { - $bond:b1 @bond:../Bond $atom:1 $atom:2 - $bond:b2 @bond:../Bond $atom:2 $atom:3 - } - write("Data Angles") { - $angle:a1 @angle:../An $atom:1 $atom:2 $atom:3 - } - write_once("Data Masses") { - @atom:T 1.0 ## Tail Bead - } - } # lipid "A" - - - B { - write_once("In Settings") { - pair_coeff @atom:../H @atom:T table tabulated_potential.dat HEAD_TAIL - # (Note: The "HEAD_TAIL" table is the same as the "HEAD_HEAD" table.) - pair_coeff @atom:T @atom:T table tabulated_potential.dat TAIL_TAIL_Wc_1.5 - } - write("Data Atoms") { - $atom:1 $mol:. @atom:../H 0.0 0.00 0.00 2.46 - $atom:2 $mol:. @atom:T 0.0 0.00 0.00 1.51 - $atom:3 $mol:. @atom:T 0.0 0.00 0.00 0.56 - } - write("Data Bonds") { - $bond:b1 @bond:../Bond $atom:1 $atom:2 - $bond:b2 @bond:../Bond $atom:2 $atom:3 - } - write("Data Angles") { - $angle:a1 @angle:../An $atom:1 $atom:2 $atom:3 - } - write_once("Data Masses") { - @atom:T 1.0 ## Tail Bead - } - } # lipid "B" - - - - # Finally, weaken the interaction between the tail beads - # belonging to different types of lipids (ie "A" and "B"). - - write_once("In Settings") { - pair_coeff @atom:A/T @atom:B/T table tabulated_potential.dat TAIL_TAIL_Wc_1.3 - } - - -} # CDlipids - diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/system.lt deleted file mode 100644 index 4a35cd10de..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/system.lt +++ /dev/null @@ -1,73 +0,0 @@ -# Description: - -# This constructs a bilayer constructed from coarse-grained lipids -# (implicit solvent). "Tunable generic model for fluid bilayer membranes" -# Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 - - - -import "cooke_deserno_lipids.lt" - - -# Create a random mixture of lipids of type "CDlipids/A" and "CDlipids/B" - -lipids = new random([CDlipids/A, CDlipids/B], [710,1658], 12345) - [32].move(1.178585, 0, 0) - [37].move(0.589293, 1.02068, 0) - [2].rot(180, 1, 0, 0) - -# Here "710,1658" are the number of each molecule type (must sum to 32*37*2), -# and "12345" is an optional random seed: - - - -# Move the lipds up to the center of the box -lipids[*][*][*].move(0,0,10.0) - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. We apply them below: -# width: 37.71472 = 32 * 1.05 * 2^(1/6) -# height: 37.76516 = 37 * 1.05 * 2^(1/6) * sqrt(3)/2 - -write_once("Data Boundary") { - 0 37.71472 xlo xhi - 0 37.76516 ylo yhi - 0 20.0 zlo zhi -} - - - - - - - - -# -------------- File ends here. Only comments below.------------------- - -# ------------------------------------ -# ------------- COMMENTS: ------------ -# ------------------------------------ -# -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 32 rows (each row is aligned with the x-axis) -# 37 columns (aligned at a 60 degree angle from the x axis) -# When wrapped onto a rectangular box, the dimensions of the system are: -# 32 * 2^(1/6) σ units in the X direction -# 37 * 2^(1/6) * sqrt(3)/2 σ units in the Y direction -# ------------------------------------ -# -# Below I show simple ways to create a lipid bilayer: -# -# 1) If you just want to make lipid bilayer out of lipids, -# without specifying the location of each lipid, you could use this syntax: -# lipids = new CDlipid/A [32][37][2] # 3-D array -# Later you can load in the coordinates of the lipds from a PDB file. -# Alternately you could also use a 1-dimensional array: -# lipids = new CDlipid/A [2368] # 1-D array. Note: 2368 = 32x37x2 -# It does not matter as long as the number of lipids is correct. -# Multidimensional arrays are only useful if you plan to apply independent -# coordinate transformations to each row and column and monolayer as above. -# diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/tabulated_potential.dat b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/tabulated_potential.dat deleted file mode 100644 index cd8dd4db7d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/moltemplate_files/tabulated_potential.dat +++ /dev/null @@ -1,4589 +0,0 @@ -# Tabulated potential for Cooke 3-bead lipid model, with various values of Wc - -HEAD_HEAD -N 301 R 0.000001 3.000000 - -1 0.000001 0.000000 0.000000 -2 0.010000 2161440350647607518822400.000000 2593728420778890895481110528.000000 -3 0.020000 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a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/run.in.min +++ /dev/null @@ -1,21 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz -thermo_style custom step pe etotal vol epair ebond eangle -thermo 40 # time interval for printing out "thermo" data - -minimize 1.0e-7 1.0e-9 100000 300000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/run.in.npt b/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/run.in.npt deleted file mode 100644 index b305e1d590..0000000000 --- a/tools/moltemplate/examples/coarse_grained/membrane_mixture_Cooke_Kremer_DesernoPRE2005/run.in.npt +++ /dev/null @@ -1,58 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example may require additional features and bug fixes for LAMMPS. -# Be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 2) Unpack it -# 3) copy the .cpp and .h files to the src folding of your lammps installation. -# 4) Compile LAMMPS. -# -# (If LAMMPS complains about an "Invalid pair_style" -# then you made a mistake in the instructions above.) -# - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.01 -dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 200 # time interval for printing out "thermo" data - -velocity all create 1.1 12345 - -fix fxlan all langevin 1.1 1.1 50.0 48279 -fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy - -# Note: The temperature is 1.1*ε -# (ε = "epsilon" used by the coarse-grained lipid) -# Note: The langevin damping parameter is now "50.0" in units of time -# (which are (m/(ε*σ^2))^(1/2) because we are using "units lj" -# This is grossly underdamped compared to the real system, -# but it leads to more efficient sampling.) -# Note: We maintain the system system at constant (zero) tention -# using a barostat damping parameter Pdamp=1000 ("0 0 1000") - - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -run 5000000 - -write_data system_after_npt.data - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/README.txt deleted file mode 100644 index e5f1544eab..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/README.txt +++ /dev/null @@ -1,33 +0,0 @@ -# This directory contains examples of how to run a short simulation of a -# coarse-grained protein-like polymer, folding in the presence and absence of -# a chaperone (modeled as an attractive or repulsie spherical shell). -# -# The protein models and the chaperone models are described and used here: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# ...and also here: -# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) -# -# (In the "frustrated+minichaperone" directory, the protein is -# placed outside the chaperone sphere, as opposed to inside.) -# -# -------- REQUIREMENTS: --------- -# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) They also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files in each directory. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.txt deleted file mode 100644 index 63517aa125..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.txt +++ /dev/null @@ -1,32 +0,0 @@ -# This directory demonstrates how to run a long simulation of -# the "frustrated" coarse-grained protein confined in a frustrated -# coarse-grained chaperonin (R=6, h=0.475) as described in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 -# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" -# (at the end of "system.lt") with "CHAP_INTERIOR_H0" -# -# Because this process takes a long time (even with the help of the chaperone) -# I save the data relatively infrequently. -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh deleted file mode 100755 index d5ae1fe5a3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_mpi" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh deleted file mode 100755 index 042f73a287..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg deleted file mode 100644 index 31853cd5ad..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg deleted file mode 100644 index fdc5c890b1..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index e43026ba9f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt +++ /dev/null @@ -1,216 +0,0 @@ -# This file defines the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadFrustrated { - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 - $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 - $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 - $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 - $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 - $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 - $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 - $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 - $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 - $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 - $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 - $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 - $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 - $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 - $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 - $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 - $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 - $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 - $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 - $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 - $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 - $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 - $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 - $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 - $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 - $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 - $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 - } - - # bond-ID bond-Type atom-ID atom-ID - - write('Data Bonds') { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write('Data Dihedrals') { - - $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 - # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 - # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 - - $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 - # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 - - $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once('Data Angles By Type') { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadFrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - - # We use tabular dihedral potentials to implement the dihedral forces. - # (Actually there is a way to use Fourier series, using multiple charmm - # style dihedral interactions, but it's slower and messier.) - - write_once("In Settings") { - # style file keyword - dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadFrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadFrustrated - - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt +++ /dev/null @@ -1,85 +0,0 @@ -import "1beadFrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadMisfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated". - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 - $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 - $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 - $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 - $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 - $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 - $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 - $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 - $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 - $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 - $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 - $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 - $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 - $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 - $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 - $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 - $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 - $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 - $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 - $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 - $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 - $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 - $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 - $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 - $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 - $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 - $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 - } - -} # 1beadMisfolded - - -1beadUnfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt deleted file mode 100644 index 8266d2a898..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt +++ /dev/null @@ -1,41 +0,0 @@ -# Here we define a trivial molecule containing only one particle. - -Chaperonin { - - # atomID molID atomType charge x y z - - write("Data Atoms") { - $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:C 100.0 - } - - write_once("In Settings") { - # If for some reason there are multiple chaperones present, - # I assume that they interact repulsively (hence, L=0) - # i j epsilon sigma K L - - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 - - # Optional: define the atoms in the "chaperonins" group: - # (Defining a group for the chaperone makes it easy to immobilize it later.) - - group chaperonins type @atom:C - } - - - # Specify which pair_styles, and atom styles work well with - # this model. (Again this can be overridden later.) - - write_once("In Init") { - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 - } - -} # Chaperonin - -# We have not specified how this particle interacts with other particles -# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py deleted file mode 100755 index 4c787de565..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between atoms in the -# protein and a chaperone provided in the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# This is stored in a tabulated force field with a singularity at a distance R. -# -# To calculate the table for interaction between -# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 -# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 -# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True -# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True - -from math import * -import sys - -def U(r, eps, sigma, R, h): - #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) - - h*pow((sigma/R), 6.0)) - xp = sigma/(r+R) - xm = sigma/(r-R) - term10 = pow(xm, 10.0) - pow(xp, 10.0) - term4 = pow(xm, 4.0) - pow(xp, 4.0) - return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) - -def F(r, eps, sigma, R, h): - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 0.0 - product_term_a = U(r, eps, sigma, R, h) / r - ixp = (r+R)/sigma - ixm = (r-R)/sigma - dix_dr = 1.0/sigma - term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) - term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) - product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) - return product_term_a + product_term_b - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - - """ - def __init__(self, err_msg): - self.err_msg = err_msg - def __str__(self): - return self.err_msg - def __repr__(self): - return str(self) - -if len(sys.argv) < 8: - sys.stderr.write("Error: expected 7 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") - sys.exit(-1) - -epsilon = float(sys.argv[1]) -sigma = float(sys.argv[2]) -R = float(sys.argv[3]) -h = float(sys.argv[4]) -rmin = float(sys.argv[5]) -rmax = float(sys.argv[6]) -N = int(sys.argv[7]) - -subtract_Urcut = False -if len(sys.argv) == 9: - subtract_Urcut = True -rcut = rmax - -for i in range(0,N): - r = rmin + i*(rmax-rmin)/(N-1) - U_r = U(r, epsilon, sigma, R, h) - F_r = F(r, epsilon, sigma, R, h) - if subtract_Urcut: - U_r -= U(rcut, epsilon, sigma, R, h) - if (r >= rcut) or (i==N-1): - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py deleted file mode 100755 index 907732fa19..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of dihedral angle interactions used in the alpha-helix -# and beta-sheet regions of the frustrated protein model described in -# provided in figure 8 of the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# Note that the "A" and "B" parameters were incorrectly reported to be -# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. -# The phiA and phiB values were 57.29577951308232 degrees (1 rad) -# and 180 degrees, respectively. Both expA and expB were 6.0. -# -# To generate the table used for the alpha-helix (1 degree resolution) use this: -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 -# To generate the table used for the beta-sheets (1 degree resolution) use this: -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 -# -# (If you're curious as to why I set the location of the minima at phi_alpha -# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. -# I think the correct value turns out to be something closer to 50 degrees.) - - -from math import * -import sys - - -# The previous version included the repulsive core term -def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) - termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) - return -A*termA - B*termB - -# The previous version included the repulsive core term -def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * - expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) - termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * - expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) - return -conv_units*(A*termA + B*termB) - -if len(sys.argv) != 10: - sys.stderr.write("Error: expected 9 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") - sys.exit(-1) - -A = float(sys.argv[1]) -phiA = float(sys.argv[2]) -expA = float(sys.argv[3]) -B = float(sys.argv[4]) -phiB = float(sys.argv[5]) -expB = float(sys.argv[6]) -phi_min = float(sys.argv[7]) -phi_max = float(sys.argv[8]) -N = int(sys.argv[9]) - -for i in range(0,N): - phi = phi_min + i*(phi_max - phi_min)/(N-1) - U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt deleted file mode 100644 index d70ea9b1f2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt +++ /dev/null @@ -1,45 +0,0 @@ -write_once("Data Boundary") { - 0.0 20.0 xlo xhi - 0.0 20.0 ylo yhi - 0.0 20.0 zlo zhi -} - - -import "1beadFrustrated_variants.lt" -import "chaperonin.lt" - - -protein = new 1beadMisfolded # (frustrated protein, misfolded conformation) -chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile) - - - -# ---- Now define interactions between the atoms in the protein ---- -# ---- (named "B", "L", "N") and the atom which represents the ---- -# ---- chaperone ("C"). These interactions are tabulated. ---- - -write_once("In Settings") { - pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 - pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0 - pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0 -} - -# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475) -# then replace "table_chaperonin_h=0_475.dat CH_H0.475" -# with "table_chaperonin_h=0.dat CH_H0" - -# LAMMPS has many available force field styles (and atom styles). Here we -# select the ones which work well for the full combine system. (This should -# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt") - - -write_once("In Init") { - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) -} diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat deleted file mode 100644 index 675d228a90..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat +++ /dev/null @@ -1,1188 +0,0 @@ -# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). -# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) - -CH_H0.475 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 -0.018422088583 0.0 -2 0.005 -0.0184221525389 2.55824082873e-05 -3 0.01 -0.0184223444081 5.11654127471e-05 -4 0.015 -0.018422664195 7.67496107175e-05 -5 0.02 -0.0184231119071 0.000102335598797 -6 0.025 -0.018423687555 0.000127923973785 -7 0.03 -0.0184243911519 0.000153515332637 -8 0.035 -0.0184252227143 0.000179110272379 -9 0.04 -0.0184261822615 0.000204709390236 -10 0.045 -0.0184272698161 0.000230313283607 -11 0.05 -0.0184284854033 0.000255922550119 -12 0.055 -0.0184298290516 0.000281537787625 -13 0.06 -0.0184313007922 0.000307159594253 -14 0.065 -0.0184329006595 0.000332788568419 -15 0.07 -0.0184346286908 0.000358425308862 -16 0.075 -0.0184364849265 0.000384070414671 -17 0.08 -0.0184384694099 0.000409724485298 -18 0.085 -0.0184405821873 0.000435388120601 -19 0.09 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5.855 626872755.056 -43125823862.6 -1173 5.86 889629660.718 -63393502739.0 -1174 5.865 1278740106.83 -94503868935.1 -1175 5.87 1863446791.23 -1.43025101229e+11 -1176 5.875 2756012237.96 -2.20012469835e+11 -1177 5.88 4141901662.1 -3.44454801129e+11 -1178 5.885 6333810219.82 -5.49690750348e+11 -1179 5.89 9870702215.02 -8.95661856872e+11 -1180 5.895 15704120493.1 -1.49296797827e+12 -1181 5.9 25558689542.6 -2.55153879404e+12 - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat deleted file mode 100644 index 2ad6d7b691..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat +++ /dev/null @@ -1,1187 +0,0 @@ -# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) - -CH_H0 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 8.31299178857e-07 0.0 -2 0.005 8.31311879342e-07 -5.08022586688e-09 -3 0.01 8.31349981758e-07 -1.01608369733e-08 -4 0.015 8.31413488996e-07 -1.52422186449e-08 -5 0.02 8.31502405871e-07 -2.03247562721e-08 -6 0.025 8.31616739127e-07 -2.54088353865e-08 -7 0.03 8.31756497437e-07 -3.04948417048e-08 -8 0.035 8.319216914e-07 -3.55831611709e-08 -9 0.04 8.32112333547e-07 -4.06741800058e-08 -10 0.045 8.32328438343e-07 -4.57682847516e-08 -11 0.05 8.32570022183e-07 -5.08658623183e-08 -12 0.055 8.328371034e-07 -5.59673000292e-08 -13 0.06 8.33129702263e-07 -6.10729856679e-08 -14 0.065 8.33447840983e-07 -6.61833075238e-08 -15 0.07 8.33791543713e-07 -7.12986544391e-08 -16 0.075 8.34160836552e-07 -7.64194158551e-08 -17 0.08 8.34555747546e-07 -8.15459818584e-08 -18 0.085 8.34976306696e-07 -8.66787432278e-08 -19 0.09 8.35422545957e-07 -9.18180914814e-08 -20 0.095 8.35894499243e-07 -9.69644189231e-08 -21 0.1 8.36392202433e-07 -1.0211811869e-07 -22 0.105 8.36915693374e-07 -1.07279584798e-07 -23 0.11 8.37465011883e-07 -1.12449212192e-07 -24 0.115 8.38040199757e-07 -1.17627396792e-07 -25 0.12 8.38641300774e-07 -1.22814535539e-07 -26 0.125 8.392683607e-07 -1.28011026445e-07 -27 0.13 8.39921427291e-07 -1.33217268641e-07 -28 0.135 8.40600550305e-07 -1.38433662423e-07 -29 0.14 8.41305781504e-07 -1.43660609303e-07 -30 0.145 8.42037174658e-07 -1.48898512057e-07 -31 0.15 8.42794785557e-07 -1.54147774771e-07 -32 0.155 8.43578672015e-07 -1.59408802894e-07 -33 0.16 8.44388893873e-07 -1.64682003285e-07 -34 0.165 8.45225513015e-07 -1.69967784262e-07 -35 0.17 8.46088593367e-07 -1.75266555654e-07 -36 0.175 8.46978200908e-07 -1.80578728847e-07 -37 0.18 8.4789440368e-07 -1.85904716839e-07 -38 0.185 8.48837271792e-07 -1.91244934288e-07 -39 0.19 8.49806877432e-07 -1.96599797561e-07 -40 0.195 8.50803294874e-07 -2.01969724788e-07 -41 0.2 8.51826600486e-07 -2.07355135913e-07 -42 0.205 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d660fee308..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat +++ /dev/null @@ -1,735 +0,0 @@ -# Table of the potential and its negative derivative for frustrated alpha helix -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 - -FRUSTRATED_ALPHA -N 360 DEGREES - -1 0.0 -2.74081145103 0.0783990792662 -2 1.0 -2.81950869101 0.0789852583442 -3 2.0 -2.89876136749 0.0795096391909 -4 3.0 -2.97850675562 0.0799703813963 -5 4.0 -3.05868032959 0.0803657243943 -6 5.0 -3.13921584545 0.0806939935737 -7 6.0 -3.22004543014 0.0809536062381 -8 7.0 -3.30109967628 0.0811430773977 -9 8.0 -3.38230774267 0.0812610253741 -10 9.0 -3.46359746038 0.0813061772009 -11 10.0 -3.54489544401 0.0812773738039 -12 11.0 -3.62612720812 0.0811735749433 -13 12.0 -3.70721728841 0.0809938639029 -14 13.0 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-1.53878331313 0.061018148454 -345 344.0 -1.60045794659 0.0623272072653 -346 345.0 -1.66342954101 0.0636117049668 -347 346.0 -1.72767243359 0.0648694329207 -348 347.0 -1.79315873807 0.0660981537565 -349 348.0 -1.85985831882 0.0672956071568 -350 349.0 -1.92773877092 0.0684595158069 -351 350.0 -1.99676540616 0.0695875914917 -352 351.0 -2.06690124527 0.0706775413231 -353 352.0 -2.13810701636 0.0717270740805 -354 353.0 -2.21034115987 0.0727339066469 -355 354.0 -2.28355983986 0.0736957705223 -356 355.0 -2.35771696194 0.0746104183955 -357 356.0 -2.43276419776 0.0754756307561 -358 357.0 -2.50865101613 0.0762892225281 -359 358.0 -2.58532472075 0.0770490497051 -360 359.0 -2.66273049463 0.0777530159679 - -# Table of the potential and its negative derivative for frustrated beta sheet -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 - -FRUSTRATED_BETA -N 360 DEGREES - -1 0.0 -2.55809068762 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-334 333.0 -0.93112967973 0.0438687355968 -335 334.0 -0.975674613021 0.0452203404434 -336 335.0 -1.02156854218 0.0465664874361 -337 336.0 -1.06880527714 0.0479056997168 -338 337.0 -1.11737711415 0.0492364272675 -339 338.0 -1.16727476416 0.0505570500574 -340 339.0 -1.2184872845 0.051865881477 -341 340.0 -1.27100201415 0.0531611720525 -342 341.0 -1.32480451282 0.0544411134304 -343 342.0 -1.37987850417 0.055703842622 -344 343.0 -1.43620582346 0.0569474464963 -345 344.0 -1.49376636966 0.0581699665097 -346 345.0 -1.55253806258 0.05936940366 -347 346.0 -1.61249680493 0.0605437236497 -348 347.0 -1.67361644969 0.0616908622471 -349 348.0 -1.73586877296 0.0628087308273 -350 349.0 -1.79922345238 0.0638952220804 -351 350.0 -1.86364805137 0.0649482158688 -352 351.0 -1.92910800931 0.0659655852184 -353 352.0 -1.9955666377 0.066945202426 -354 353.0 -2.06298512258 0.0678849452658 -355 354.0 -2.13132253309 0.0687827032771 -356 355.0 -2.20053583647 0.0696363841147 -357 356.0 -2.27057991931 0.0704439199439 -358 357.0 -2.3414076153 0.0712032738621 -359 358.0 -2.41296973939 0.0719124463259 -360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min deleted file mode 100644 index 88ff31635b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min +++ /dev/null @@ -1,25 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Optional: Make sure the pairwise energies look reasonable: -pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0 -pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0 -pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0 - - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt deleted file mode 100644 index 01b156a2a8..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt +++ /dev/null @@ -1,48 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. -# (Try using "run.in.min" and uncomment the line below.) -# read_data system_after_min.data - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Keep the chaperonin fixed. Only let the protein move. - -fix fxlan proteins langevin 0.25 0.25 1.0 48279 -fix fxnve proteins nve - -# Notes: -# The temperature is in reduced units and is set to 0.25 -# which is the folding temperature for the frustrated protein -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50000 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 1000000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.txt deleted file mode 100644 index d934e3ab6c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.txt +++ /dev/null @@ -1,38 +0,0 @@ -# This directory demonstrates how to run a long simulation of -# the "frustrated" coarse-grained protein in the presence of one -# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in: -# -# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) -# and earlier in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# -# Because this process takes a long time (even with the help of the chaperone) -# I save the data relatively infrequently. -# -# Note: In the 2006 paper, only one protein and one chaperone was simulated. -# In this example, 8 proteins and 8 chaperones were simulated. -# -# Note: In this case, the chaperones appear to catalyze aggregation. -# This is due to an artifact in the protein model. That model -# was not designed to study aggregation. However the simulation -# is suitable for making pretty pictures (to show off moltemplate). -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh deleted file mode 100755 index d5ae1fe5a3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_mpi" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh deleted file mode 100755 index 042f73a287..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg deleted file mode 100644 index c62a881b2a..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg deleted file mode 100644 index 38ef54396e..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index e43026ba9f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt +++ /dev/null @@ -1,216 +0,0 @@ -# This file defines the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadFrustrated { - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 - $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 - $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 - $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 - $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 - $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 - $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 - $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 - $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 - $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 - $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 - $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 - $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 - $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 - $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 - $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 - $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 - $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 - $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 - $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 - $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 - $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 - $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 - $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 - $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 - $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 - $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 - } - - # bond-ID bond-Type atom-ID atom-ID - - write('Data Bonds') { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write('Data Dihedrals') { - - $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 - # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 - # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 - - $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 - # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 - - $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once('Data Angles By Type') { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadFrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - - # We use tabular dihedral potentials to implement the dihedral forces. - # (Actually there is a way to use Fourier series, using multiple charmm - # style dihedral interactions, but it's slower and messier.) - - write_once("In Settings") { - # style file keyword - dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadFrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadFrustrated - - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt +++ /dev/null @@ -1,85 +0,0 @@ -import "1beadFrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadMisfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated". - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 - $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 - $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 - $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 - $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 - $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 - $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 - $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 - $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 - $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 - $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 - $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 - $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 - $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 - $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 - $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 - $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 - $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 - $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 - $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 - $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 - $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 - $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 - $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 - $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 - $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 - $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 - } - -} # 1beadMisfolded - - -1beadUnfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py deleted file mode 100755 index 4c787de565..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between atoms in the -# protein and a chaperone provided in the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# This is stored in a tabulated force field with a singularity at a distance R. -# -# To calculate the table for interaction between -# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 -# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 -# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True -# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True - -from math import * -import sys - -def U(r, eps, sigma, R, h): - #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) - - h*pow((sigma/R), 6.0)) - xp = sigma/(r+R) - xm = sigma/(r-R) - term10 = pow(xm, 10.0) - pow(xp, 10.0) - term4 = pow(xm, 4.0) - pow(xp, 4.0) - return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) - -def F(r, eps, sigma, R, h): - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 0.0 - product_term_a = U(r, eps, sigma, R, h) / r - ixp = (r+R)/sigma - ixm = (r-R)/sigma - dix_dr = 1.0/sigma - term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) - term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) - product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) - return product_term_a + product_term_b - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - - """ - def __init__(self, err_msg): - self.err_msg = err_msg - def __str__(self): - return self.err_msg - def __repr__(self): - return str(self) - -if len(sys.argv) < 8: - sys.stderr.write("Error: expected 7 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") - sys.exit(-1) - -epsilon = float(sys.argv[1]) -sigma = float(sys.argv[2]) -R = float(sys.argv[3]) -h = float(sys.argv[4]) -rmin = float(sys.argv[5]) -rmax = float(sys.argv[6]) -N = int(sys.argv[7]) - -subtract_Urcut = False -if len(sys.argv) == 9: - subtract_Urcut = True -rcut = rmax - -for i in range(0,N): - r = rmin + i*(rmax-rmin)/(N-1) - U_r = U(r, epsilon, sigma, R, h) - F_r = F(r, epsilon, sigma, R, h) - if subtract_Urcut: - U_r -= U(rcut, epsilon, sigma, R, h) - if (r >= rcut) or (i==N-1): - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py deleted file mode 100755 index 907732fa19..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of dihedral angle interactions used in the alpha-helix -# and beta-sheet regions of the frustrated protein model described in -# provided in figure 8 of the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# Note that the "A" and "B" parameters were incorrectly reported to be -# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. -# The phiA and phiB values were 57.29577951308232 degrees (1 rad) -# and 180 degrees, respectively. Both expA and expB were 6.0. -# -# To generate the table used for the alpha-helix (1 degree resolution) use this: -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 -# To generate the table used for the beta-sheets (1 degree resolution) use this: -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 -# -# (If you're curious as to why I set the location of the minima at phi_alpha -# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. -# I think the correct value turns out to be something closer to 50 degrees.) - - -from math import * -import sys - - -# The previous version included the repulsive core term -def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) - termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) - return -A*termA - B*termB - -# The previous version included the repulsive core term -def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * - expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) - termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * - expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) - return -conv_units*(A*termA + B*termB) - -if len(sys.argv) != 10: - sys.stderr.write("Error: expected 9 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") - sys.exit(-1) - -A = float(sys.argv[1]) -phiA = float(sys.argv[2]) -expA = float(sys.argv[3]) -B = float(sys.argv[4]) -phiB = float(sys.argv[5]) -expB = float(sys.argv[6]) -phi_min = float(sys.argv[7]) -phi_max = float(sys.argv[8]) -N = int(sys.argv[9]) - -for i in range(0,N): - phi = phi_min + i*(phi_max - phi_min)/(N-1) - U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt deleted file mode 100644 index 1d37823b7a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt +++ /dev/null @@ -1,41 +0,0 @@ -# Here we define a trivial molecule containing only one particle. - -Minichaperone { - - # atomID molID atomType charge x y z - - write("Data Atoms") { - $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:C 100.0 - } - - write_once("In Settings") { - # If for some reason there are multiple chaperones present, - # I assume that they interact repulsively (hence, L=0) - - # i j pairStyle eps sig K L - - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0 - - # Optional: define the atoms in the "chaperonins" group: - # (Defining a group for the chaperone makes it easy to immobilize it later.) - - group chaperones type @atom:C - } - - # Specify which pair_styles, and atom styles work well with - # this model. (Again this can be overridden later.) - - write_once("In Init") { - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 - } - -} # Minichaperone - -# We have not specified how this particle interacts with other particles -# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt deleted file mode 100644 index 8f8c37d08b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt +++ /dev/null @@ -1,72 +0,0 @@ -write_once("Data Boundary") { - 0.0 80.0 xlo xhi - 0.0 80.0 ylo yhi - 0.0 80.0 zlo zhi -} - - -import "1beadFrustrated_variants.lt" -import "minichaperone.lt" - - -# Create 8 proteins and 8 chaperones (2x2x2 array): -# NOTE: Below I create multiple proteins and multiple chaperones -# to see what would happen. (I suspect nothing good. In the -# 2006 paper, only 1 protein and 1 chaperone were present.) - - -proteins = new 1beadUnfolded [2].move(40,0,0) - [2].move(0,40,0) - [2].move(0,0,40) - -chaperones = new Minichaperone [2].move(40,0,0) - [2].move(0,40,0) - [2].move(0,0,40) - -proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones - - - -# If you only want 1 protein and 1 chaperone -# then replace the lines above with: -# -# protein = new 1beadMisfolded -# chaperone = new Minichaperone - - - - - -# ---- Now define interactions between the atoms in the protein ---- -# ---- (named "B", "L", "N") and the atom which represents the ---- -# ---- chaperone ("c"). These interactions are tabulated. ---- - -write_once("In Settings") { - pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6 - pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0 - pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0 -} - -# Note: If you want purely repulsive spheres (crowding, h=0.0) -# instead of an attractive "hydrophobic" chaperone (h=0.6) -# then replace "table_minichaperone_h=0_6.dat CH_H0_6" -# with "table_minichaperone_h=0.dat CH_H0" -# (... or just use an ordinary Lennard-Jones interaction -# with sigma = 6.0 and epsilon near 0.0) - - -# LAMMPS has many available force field styles (and atom styles). Here we -# select the ones which work well for the full combine system. (This should -# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt") - - -write_once("In Init") { - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) -} diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat deleted file mode 100644 index d660fee308..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat +++ /dev/null @@ -1,735 +0,0 @@ -# Table of the potential and its negative derivative for frustrated alpha helix -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 - -FRUSTRATED_ALPHA -N 360 DEGREES - -1 0.0 -2.74081145103 0.0783990792662 -2 1.0 -2.81950869101 0.0789852583442 -3 2.0 -2.89876136749 0.0795096391909 -4 3.0 -2.97850675562 0.0799703813963 -5 4.0 -3.05868032959 0.0803657243943 -6 5.0 -3.13921584545 0.0806939935737 -7 6.0 -3.22004543014 0.0809536062381 -8 7.0 -3.30109967628 0.0811430773977 -9 8.0 -3.38230774267 0.0812610253741 -10 9.0 -3.46359746038 0.0813061772009 -11 10.0 -3.54489544401 0.0812773738039 -12 11.0 -3.62612720812 0.0811735749433 -13 12.0 -3.70721728841 0.0809938639029 -14 13.0 -3.78808936748 0.080737451911 -15 14.0 -3.86866640485 0.0804036822781 -16 15.0 -3.94887077101 0.0799920342374 -17 16.0 -4.02862438516 0.0795021264757 -18 17.0 -4.10784885622 0.0789337203415 -19 18.0 -4.18646562704 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-1.85985831882 0.0672956071568 -350 349.0 -1.92773877092 0.0684595158069 -351 350.0 -1.99676540616 0.0695875914917 -352 351.0 -2.06690124527 0.0706775413231 -353 352.0 -2.13810701636 0.0717270740805 -354 353.0 -2.21034115987 0.0727339066469 -355 354.0 -2.28355983986 0.0736957705223 -356 355.0 -2.35771696194 0.0746104183955 -357 356.0 -2.43276419776 0.0754756307561 -358 357.0 -2.50865101613 0.0762892225281 -359 358.0 -2.58532472075 0.0770490497051 -360 359.0 -2.66273049463 0.0777530159679 - -# Table of the potential and its negative derivative for frustrated beta sheet -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 - -FRUSTRATED_BETA -N 360 DEGREES - -1 0.0 -2.55809068762 0.0731724739818 -2 1.0 -2.63154144494 0.0737195744566 -3 2.0 -2.70551060968 0.0742089966437 -4 3.0 -2.77993963883 0.074639023134 -5 4.0 -2.85476830901 0.0750080115297 -6 5.0 -2.92993479441 0.0753144003899 -7 6.0 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a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat deleted file mode 100644 index d2b1ed3aaf..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat +++ /dev/null @@ -1,988 +0,0 @@ -# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6) -# Generated using: -# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True - -CH_H0.6 -N 981 R 3.1 8.0 - -1 3.1 24321971157.7 2.4400451019e+12 -2 3.105 14907528428.0 1.42456746092e+12 -3 3.11 9347010266.92 8.52735030437e+11 -4 3.115 5983057175.03 5.22187648991e+11 -5 3.12 3902942155.05 3.26496996649e+11 -6 3.125 2590648415.38 2.0808159227e+11 -7 3.13 1747350825.1 1.34970444886e+11 -8 3.135 1196139798.89 88984974583.5 -9 3.14 830130182.341 59559787515.6 -10 3.145 583518174.975 40428507749.3 -11 3.15 415078797.287 27803974550.9 -12 3.155 298562827.719 19356989964.4 -13 3.16 217001769.743 13631486848.5 -14 3.165 159270305.159 9703243449.66 -15 3.17 117976881.962 6977184032.49 -16 3.175 88149161.6455 5064988683.98 -17 3.18 66402860.1298 3710042118.5 -18 3.185 50409022.6215 2740737360.59 -19 3.19 38548170.6708 2041021063.98 -20 3.195 29683036.1074 1531572773.33 -21 3.2 23007502.8905 1157631256.92 -22 3.205 17945109.6836 881028781.898 -23 3.21 14080149.2893 674921399.554 -24 3.215 11110438.2418 520266326.167 -25 3.22 8814639.75879 403443800.764 -26 3.225 7029455.47123 314636408.027 -27 3.23 5633571.16439 246714657.082 -28 3.235 4536265.59262 194464091.949 -29 3.24 3669265.83647 154044868.616 -30 3.245 2980881.1453 122610915.077 -31 3.25 2431748.15466 98039536.8272 -32 3.255 1991724.07297 78738058.3506 -33 3.26 1637603.46485 63504600.2322 -34 3.265 1351429.90872 51427172.534 -35 3.27 1119240.11293 41810074.9071 -36 3.275 930124.378436 34119886.2947 -37 3.28 775519.857832 27945597.578 -38 3.285 648676.115123 22969017.4933 -39 3.29 544248.919174 18942684.9889 -40 3.295 457989.984944 15673297.5619 -41 3.3 386508.875651 13009215.1485 -42 3.305 327089.446276 10830991.226 -43 3.31 277547.709074 9044163.93118 -44 3.315 236121.303553 7573742.76366 -45 3.32 201383.18845 6359973.47163 -46 3.325 172173.978278 5355070.91875 -47 3.33 147548.691578 4520688.28477 -48 3.335 126734.684289 3825948.80978 -49 3.34 109098.298235 3245909.11014 -50 3.345 94118.3261235 2760354.93052 -51 3.35 81364.827777 2352853.97713 -52 3.355 70482.1624146 2010008.31682 -53 3.36 61175.3541703 1720862.26897 -54 3.365 53199.1018261 1476431.88582 -55 3.37 46348.8930587 1269329.84244 -56 3.375 40453.7990113 1093465.44786 -57 3.38 35370.6146686 943803.998782 -58 3.385 30979.0803706 816173.162054 -59 3.39 27177.9744013 707106.743488 -60 3.395 23881.9094124 613718.268337 -61 3.4 21018.6991377 533598.403624 -62 3.405 18527.1884441 464731.50307 -63 3.41 16355.4608211 405427.532611 -64 3.415 14459.3541284 354266.400629 -65 3.42 12801.228731 310052.319542 -66 3.425 11348.9427887 271776.300627 -67 3.43 10074.9979765 238585.259865 -68 3.435 8955.82575185 209756.510836 -69 3.44 7971.18978782 184676.657916 -70 3.445 7103.68463562 162824.092297 -71 3.45 6338.31427303 143754.444665 -72 3.455 5662.13711315 127088.469763 -73 3.46 5063.9664184 112501.9356 -74 3.465 4534.11699728 99717.1686967 -75 3.47 4064.19064042 88495.970274 -76 3.475 3646.89404446 78633.6696895 -77 3.48 3275.88403311 69954.1231906 -78 3.485 2945.63575657 62305.4999784 -79 3.49 2651.33026883 55556.7252625 -80 3.495 2388.75847582 49594.4725913 -81 3.5 2154.23893796 44320.6162531 -82 3.505 1944.54741747 39650.0697323 -83 3.51 1756.8563988 35508.9486835 -84 3.515 1588.68309151 31833.0071751 -85 3.52 1437.84465949 28566.3044359 -86 3.525 1302.41961585 25660.0663588 -87 3.53 1180.71448694 23071.7118275 -88 3.535 1071.23498579 20764.0187577 -89 3.54 972.661050857 18704.4087568 -90 3.545 883.825202407 16864.3326446 -91 3.55 803.693750954 15218.7418698 -92 3.555 731.350460573 13745.6331832 -93 3.56 665.982328363 12425.6558809 -94 3.565 606.867190408 11241.7725673 -95 3.57 553.362906393 10178.9657593 -96 3.575 504.897910387 9223.98381086 -97 3.58 460.962945446 8365.12060921 -98 3.585 421.103825306 7592.02431669 -99 3.59 384.915088285 6895.53112553 -100 3.595 352.034427161 6267.5205811 -101 3.6 322.137794751 5700.78952663 -102 3.605 294.935098544 5188.94214534 -103 3.61 270.166409464 4726.29393494 -104 3.615 247.598619855 4307.78775517 -105 3.62 227.022494431 3928.92034957 -106 3.625 208.250065337 3585.67796495 -107 3.63 191.112328875 3274.47988201 -108 3.635 175.457206974 2992.12883298 -109 3.64 161.147741205 2735.76742147 -110 3.645 148.060491326 2502.83977901 -111 3.65 136.084113848 2291.05779528 -112 3.655 125.118099223 2098.37134728 -113 3.66 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-3.09346599767e-05 -0.00207982254527 -979 7.99 -2.05648617073e-05 -0.00206810960966 -980 7.995 -1.0253435891e-05 -0.00205647346771 -981 8.0 0.0 0.0 diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat deleted file mode 100644 index 82eaa7e158..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat +++ /dev/null @@ -1,989 +0,0 @@ -# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0) -# Generated using: -# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True - -CH_H0 -N 981 R 3.1 8.0 - -1 3.1 24322007640.7 2.44004657299e+12 -2 3.105 14907558394.3 1.42456861215e+12 -3 3.11 9347035105.18 8.52735941633e+11 -4 3.115 5983077933.86 5.22188377701e+11 -5 3.12 3902959636.31 3.26497584961e+11 -6 3.125 2590663239.27 2.08082071378e+11 -7 3.13 1747363476.38 1.34970838198e+11 -8 3.135 1196150660.14 88985299862.7 -9 3.14 830139558.184 59560058382.9 -10 3.145 583526310.01 40428734750.9 -11 3.15 415085889.414 27804165925.8 -12 3.155 298569038.21 19357152203.7 -13 3.16 217007230.904 13631625105.8 -14 3.165 159275126.218 9703361847.17 -15 3.17 117981153.625 6977285889.84 -16 3.175 88152959.6539 5065076691.93 -17 3.18 66406248.0614 3710118471.36 -18 3.185 50412054.1061 2740803858.1 -19 3.19 38550891.1571 2041079190.29 -20 3.195 29685484.2812 1531623758.63 -21 3.2 23009711.8183 1157676125.86 -22 3.205 17947107.7408 881068391.885 -23 3.21 14081960.9175 674956471.214 -24 3.215 11112084.5698 520297467.685 -25 3.22 8816139.11379 403471527.483 -26 3.225 7030823.80219 314661158.279 -27 3.23 5634822.39381 246736805.049 -28 3.235 4537411.91017 194483958.161 -29 3.24 3670317.94503 154062728.557 -30 3.245 2981848.4679 122627006.268 -31 3.25 2432639.00923 98054064.6797 -32 3.255 1992545.82032 78751201.0309 -33 3.26 1638362.63452 63516512.707 -34 3.265 1352132.30623 51437989.9558 -35 3.27 1119890.91156 41819915.4536 -36 3.275 930728.197936 34128853.5593 -37 3.28 776080.832192 27953782.5881 -38 3.285 649197.950984 22976500.4202 -39 3.29 544734.946388 18949536.6006 -40 3.295 458443.200409 15679580.461 -41 3.3 386931.981432 13014984.83 -42 3.305 327484.882814 10836296.983 -43 3.31 277917.684205 9049049.63384 -44 3.315 236467.817902 7578247.52911 -45 3.32 201708.057716 6364132.2427 -46 3.325 172478.852825 5358914.96458 -47 3.33 147835.073691 4524245.63494 -48 3.335 127003.943407 3829244.63171 -49 3.34 109351.684422 3248966.03768 -50 3.345 94356.982001 2763193.35086 -51 3.35 81589.7991199 2355492.28163 -52 3.355 70694.4075656 2012463.12085 -53 3.36 61375.7524283 1723148.60489 -54 3.365 53388.4609277 1478563.37272 -55 3.37 46527.9558627 1271318.83571 -56 3.375 40623.2494805 1095323.17118 -57 3.38 35531.0832305 945540.660872 -58 3.385 31131.1487289 817798.059995 -59 3.39 27322.1798598 708628.354433 -60 3.395 24018.7487675 615144.330958 -61 3.4 21148.6321858 534935.990585 -62 3.405 18650.6411473 465987.08561 -63 3.41 16472.8281676 406607.038172 -64 3.415 14571.00272 355375.264352 -65 3.42 12907.4991276 311095.530355 -66 3.425 11450.1516342 272758.442538 -67 3.43 10171.439929 239510.549012 -68 3.435 9047.7752383 210628.82877 -69 3.44 8058.90260095 185499.581541 -70 3.445 7187.39938846 163600.920836 -71 3.45 6418.25372556 144488.223969 -72 3.455 5738.50938334 127782.014261 -73 3.46 5136.9660889 113157.848128 -74 3.465 4603.92612777 100337.85845 -75 3.47 4130.97969454 89083.6690543 -76 3.475 3710.8227393 79190.4466465 -77 3.48 3337.10211855 70481.8981958 -78 3.485 3004.28373073 62806.0557792 -79 3.49 2707.54003568 56031.718535 -80 3.495 2442.65394998 50045.4440029 -81 3.5 2205.93660145 44748.9996316 -82 3.505 1994.15683268 40057.2004294 -83 3.51 1804.48068152 35896.0712099 -84 3.515 1634.41934741 32201.2821773 -85 3.52 1481.78438725 28916.8150767 -86 3.525 1344.64907977 25993.8241582 -87 3.53 1221.31506159 23389.6620133 -88 3.535 1110.28347503 21067.0451721 -89 3.54 1010.22998333 18993.3383579 -90 3.545 919.9831055 17139.9396418 -91 3.55 838.505404885 15481.7515237 -92 3.555 764.877134293 13996.7253013 -93 3.56 698.281998657 12665.4680354 -94 3.565 637.994745566 11470.9030593 -95 3.57 583.370335637 10397.9763514 -96 3.575 533.834480178 9433.40224818 -97 3.58 488.875363677 8565.44294671 -98 3.585 448.036394307 7783.71706925 -99 3.59 410.909847488 7079.03325566 -100 3.595 377.131286207 6443.24533767 -101 3.6 346.374657747 5869.126147 -102 3.605 318.34798013 5350.25743201 -103 3.61 292.789543287 4880.93371692 -104 3.615 269.464560006 4456.07824337 -105 3.62 248.162210353 4071.16939457 -106 3.625 228.693030668 3722.17622503 -107 3.63 210.886604667 3405.5019084 -108 3.635 194.589519671 3117.93407879 -109 3.64 179.663555764 2856.60118023 -110 3.645 165.984079802 2618.93405823 -111 3.65 153.438619766 2402.63212994 -112 3.655 141.925598023 2205.6335579 -113 3.66 131.353204775 2026.08892777 -114 3.665 121.638395266 1862.33799643 -115 3.67 112.705996374 1712.88913275 -116 3.675 104.487909965 1576.40112248 -117 3.68 96.9224019089 1451.66705065 -118 3.685 89.9534670245 1337.6000114 -119 3.69 83.5302613658 1233.22042683 -120 3.695 77.6065942935 1137.6447839 -121 3.7 72.1404736708 1050.07562216 -122 3.705 67.0936983024 969.792625804 -123 3.71 62.431492423 896.144691745 -124 3.715 58.1221776441 828.54286083 -125 3.72 54.1368782948 766.454013201 -126 3.725 50.4492565603 709.395240693 -127 3.73 47.0352742263 656.928819585 -128 3.735 43.8729782026 608.65771617 -129 3.74 40.9423073113 564.221565572 -130 3.745 38.2249181088 523.293071279 -131 3.75 35.7040277571 485.57477893 -132 3.755 33.3642721761 450.796183363 -133 3.76 31.1915779041 418.711132572 -134 3.765 29.1730462649 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67.0913657925 -161 3.9 5.54461511838 63.0285320059 -162 3.905 5.23907089671 59.2319187891 -163 3.91 4.95188356739 55.6827704829 -164 3.915 4.68185972707 52.3637443466 -165 3.92 4.42788939186 49.2587972858 -166 3.925 4.18893976204 46.353082203 -167 3.93 3.96404948281 43.6328531095 -168 3.935 3.75232335915 41.0853782151 -169 3.94 3.55292748687 38.6988602882 -170 3.945 3.36508476491 36.4623636443 -171 3.95 3.18807075749 34.3657471793 -172 3.955 3.021209877 32.3996029206 -173 3.96 2.86387186138 30.5551996145 -174 3.965 2.71546852189 28.8244309147 -175 3.97 2.57545073925 27.1997677761 -176 3.975 2.44330568809 25.6742146917 -177 3.98 2.31855427126 24.2412694474 -178 3.985 2.20074874724 22.8948860937 -179 3.99 2.08947053515 21.6294408646 -180 3.995 1.98432818342 20.4397007945 -181 4.0 1.88495548901 19.3207948084 -182 4.005 1.79100975549 18.2681870794 -183 4.01 1.70217017901 17.2776524655 -184 4.015 1.61813635232 16.3452538542 -185 4.02 1.53862687753 15.467321259 -186 4.025 1.4633780794 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1.48397270459e-07 5.6702701955e-07 -898 7.585 1.45579978125e-07 5.59906179576e-07 -899 7.59 1.42798047202e-07 5.52882216872e-07 -900 7.595 1.40050996861e-07 5.4595371212e-07 -901 7.6 1.37338353314e-07 5.39119268281e-07 -902 7.605 1.34659649703e-07 5.32377510221e-07 -903 7.61 1.32014425993e-07 5.25727084341e-07 -904 7.615 1.29402228861e-07 5.19166658223e-07 -905 7.62 1.26822611598e-07 5.12694920274e-07 -906 7.625 1.24275133998e-07 5.06310579376e-07 -907 7.63 1.21759362262e-07 5.0001236455e-07 -908 7.635 1.19274868896e-07 4.93799024619e-07 -909 7.64 1.16821232612e-07 4.87669327877e-07 -910 7.645 1.14398038233e-07 4.8162206177e-07 -911 7.65 1.120048766e-07 4.75656032572e-07 -912 7.655 1.09641344473e-07 4.69770065082e-07 -913 7.66 1.07307044442e-07 4.63963002309e-07 -914 7.665 1.05001584841e-07 4.58233705177e-07 -915 7.67 1.02724579651e-07 4.52581052224e-07 -916 7.675 1.0047564842e-07 4.47003939317e-07 -917 7.68 9.82544161708e-08 4.41501279361e-07 -918 7.685 9.60605133226e-08 4.36072002025e-07 -919 7.69 9.38935756035e-08 4.30715053459e-07 -920 7.695 9.17532439703e-08 4.25429396028e-07 -921 7.7 8.96391645283e-08 4.20214008047e-07 -922 7.705 8.75509884516e-08 4.15067883513e-07 -923 7.71 8.54883719059e-08 4.09990031857e-07 -924 7.715 8.34509759714e-08 4.04979477684e-07 -925 7.72 8.14384665682e-08 4.00035260529e-07 -926 7.725 7.94505143815e-08 3.95156434615e-07 -927 7.73 7.74867947896e-08 3.90342068606e-07 -928 7.735 7.55469877916e-08 3.85591245382e-07 -929 7.74 7.36307779372e-08 3.80903061797e-07 -930 7.745 7.17378542573e-08 3.76276628463e-07 -931 7.75 6.9867910196e-08 3.71711069515e-07 -932 7.755 6.80206435432e-08 3.67205522401e-07 -933 7.76 6.61957563687e-08 3.62759137662e-07 -934 7.765 6.43929549576e-08 3.5837107872e-07 -935 7.77 6.26119497457e-08 3.54040521671e-07 -936 7.775 6.08524552575e-08 3.49766655078e-07 -937 7.78 5.91141900435e-08 3.45548679773e-07 -938 7.785 5.73968766201e-08 3.41385808656e-07 -939 7.79 5.57002414093e-08 3.37277266505e-07 -940 7.795 5.402401468e-08 3.33222289779e-07 -941 7.8 5.23679304898e-08 3.29220126433e-07 -942 7.805 5.07317266285e-08 3.25270035737e-07 -943 7.81 4.91151445613e-08 3.21371288087e-07 -944 7.815 4.75179293742e-08 3.17523164833e-07 -945 7.82 4.59398297194e-08 3.13724958102e-07 -946 7.825 4.43805977617e-08 3.09975970624e-07 -947 7.83 4.28399891263e-08 3.06275515564e-07 -948 7.835 4.13177628469e-08 3.02622916355e-07 -949 7.84 3.98136813144e-08 2.99017506534e-07 -950 7.845 3.83275102273e-08 2.95458629582e-07 -951 7.85 3.68590185422e-08 2.91945638765e-07 -952 7.855 3.54079784251e-08 2.8847789698e-07 -953 7.86 3.39741652039e-08 2.85054776599e-07 -954 7.865 3.25573573211e-08 2.81675659322e-07 -955 7.87 3.11573362879e-08 2.78339936025e-07 -956 7.875 2.97738866382e-08 2.7504700662e-07 -957 7.88 2.84067958844e-08 2.71796279909e-07 -958 7.885 2.70558544725e-08 2.68587173443e-07 -959 7.89 2.57208557397e-08 2.65419113385e-07 -960 7.895 2.44015958707e-08 2.62291534374e-07 -961 7.9 2.30978738564e-08 2.59203879393e-07 -962 7.905 2.18094914519e-08 2.56155599635e-07 -963 7.91 2.05362531363e-08 2.53146154374e-07 -964 7.915 1.92779660724e-08 2.50175010842e-07 -965 7.92 1.8034440067e-08 2.47241644098e-07 -966 7.925 1.68054875325e-08 2.44345536912e-07 -967 7.93 1.55909234484e-08 2.41486179638e-07 -968 7.935 1.43905653237e-08 2.38663070101e-07 -969 7.94 1.32042331597e-08 2.35875713474e-07 -970 7.945 1.20317494138e-08 2.33123622171e-07 -971 7.95 1.08729389636e-08 2.30406315726e-07 -972 7.955 9.72762907123e-09 2.27723320689e-07 -973 7.96 8.59564934896e-09 2.2507417051e-07 -974 7.965 7.47683172465e-09 2.2245840544e-07 -975 7.97 6.37101040818e-09 2.19875572416e-07 -976 7.975 5.27802185823e-09 2.17325224966e-07 -977 7.98 4.19770474957e-09 2.148069231e-07 -978 7.985 3.12989994095e-09 2.12320233213e-07 -979 7.99 2.07445044336e-09 2.09864727985e-07 -980 7.995 1.03120138888e-09 2.07439986287e-07 -981 8.0 0.0 0.0 - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min deleted file mode 100644 index 0cde82b1f5..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min +++ /dev/null @@ -1,24 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Optional: Make sure the pairwise energies look reasonable: -pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0 -pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0 -pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0 - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt deleted file mode 100644 index d28f48dd88..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. -# (Try using "run.in.min" and uncomment the line below.) -# read_data system_after_min.data - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 0.25 0.25 1.0 48279 -fix fxnve all nve - -# Notes: -# The temperature is in reduced units and is set to 0.25 -# which is the folding temperature for the frustrated protein -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 5000 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 1000000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README.txt deleted file mode 100644 index 7b02e02a32..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README.txt +++ /dev/null @@ -1,29 +0,0 @@ -# This directory demonstrates how to run a short simulation of -# the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# During this short simulation (run_short_sim.nvt.in) the protein evolves -# from an unfolded initial conformation to a misfolded conformation. -# (Visualize using VMD. Note: It can take hundreds of millions of -# timesteps to escape from this conformation and reach the folded state.) -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh deleted file mode 100755 index 6c5417239b..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - -# ----------------------------------- - -LAMMPS_COMMAND="lmp_mpi" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh deleted file mode 100755 index 042f73a287..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg deleted file mode 100644 index 0869126bd0..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg deleted file mode 100644 index 357bc780a2..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index 074b55c735..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt +++ /dev/null @@ -1,216 +0,0 @@ -# This file defines the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadFrustrated { - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 - $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 - $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 - $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 - $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 - $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 - $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 - $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 - $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 - $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 - $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 - $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 - $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 - $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 - $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 - $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 - $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 - $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 - $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 - $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 - $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 - $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 - $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 - $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 - $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 - $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 - $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 - } - - # bond-ID bond-Type atom-ID atom-ID - - write("Data Bonds") { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write("Data Dihedrals") { - - $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 - # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 - # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 - - $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 - # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 - - $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadFrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - - # We use tabular dihedral potentials to implement the dihedral forces. - # (Actually there is a way to use Fourier series, using multiple charmm - # style dihedral interactions, but it's slower and messier.) - - write_once("In Settings") { - # style file keyword - dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadFrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadFrustrated - - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt +++ /dev/null @@ -1,85 +0,0 @@ -import "1beadFrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadMisfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated". - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 - $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 - $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 - $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 - $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 - $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 - $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 - $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 - $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 - $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 - $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 - $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 - $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 - $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 - $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 - $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 - $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 - $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 - $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 - $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 - $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 - $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 - $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 - $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 - $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 - $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 - $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 - } - -} # 1beadMisfolded - - -1beadUnfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py deleted file mode 100755 index 907732fa19..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of dihedral angle interactions used in the alpha-helix -# and beta-sheet regions of the frustrated protein model described in -# provided in figure 8 of the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# Note that the "A" and "B" parameters were incorrectly reported to be -# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. -# The phiA and phiB values were 57.29577951308232 degrees (1 rad) -# and 180 degrees, respectively. Both expA and expB were 6.0. -# -# To generate the table used for the alpha-helix (1 degree resolution) use this: -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 -# To generate the table used for the beta-sheets (1 degree resolution) use this: -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 -# -# (If you're curious as to why I set the location of the minima at phi_alpha -# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. -# I think the correct value turns out to be something closer to 50 degrees.) - - -from math import * -import sys - - -# The previous version included the repulsive core term -def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) - termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) - return -A*termA - B*termB - -# The previous version included the repulsive core term -def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * - expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) - termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * - expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) - return -conv_units*(A*termA + B*termB) - -if len(sys.argv) != 10: - sys.stderr.write("Error: expected 9 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") - sys.exit(-1) - -A = float(sys.argv[1]) -phiA = float(sys.argv[2]) -expA = float(sys.argv[3]) -B = float(sys.argv[4]) -phiB = float(sys.argv[5]) -expB = float(sys.argv[6]) -phi_min = float(sys.argv[7]) -phi_max = float(sys.argv[8]) -N = int(sys.argv[9]) - -for i in range(0,N): - phi = phi_min + i*(phi_max - phi_min)/(N-1) - U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt deleted file mode 100644 index a27595559e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt +++ /dev/null @@ -1,20 +0,0 @@ -import "1beadFrustrated_variants.lt" - - -protein = new 1beadUnfolded - - - -# Note: The protein begins in an "Unfolded" conformation. If instead -# you want it to begin in the folded or misfolded conformations use: -# protein = new 1beadFrustrated # or -# protein = new 1beadMisfolded - - - -# ("27.0" is the length of the protein when maximally extended) -write_once("Data Boundary") { - 0.0 27.0 xlo xhi - 0.0 27.0 ylo yhi - 0.0 27.0 zlo zhi -} diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat deleted file mode 100644 index d660fee308..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat +++ /dev/null @@ -1,735 +0,0 @@ -# Table of the potential and its negative derivative for frustrated alpha helix -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 - -FRUSTRATED_ALPHA -N 360 DEGREES - -1 0.0 -2.74081145103 0.0783990792662 -2 1.0 -2.81950869101 0.0789852583442 -3 2.0 -2.89876136749 0.0795096391909 -4 3.0 -2.97850675562 0.0799703813963 -5 4.0 -3.05868032959 0.0803657243943 -6 5.0 -3.13921584545 0.0806939935737 -7 6.0 -3.22004543014 0.0809536062381 -8 7.0 -3.30109967628 0.0811430773977 -9 8.0 -3.38230774267 0.0812610253741 -10 9.0 -3.46359746038 0.0813061772009 -11 10.0 -3.54489544401 0.0812773738039 -12 11.0 -3.62612720812 0.0811735749433 -13 12.0 -3.70721728841 0.0809938639029 -14 13.0 -3.78808936748 0.080737451911 -15 14.0 -3.86866640485 0.0804036822781 -16 15.0 -3.94887077101 0.0799920342374 -17 16.0 -4.02862438516 0.0795021264757 -18 17.0 -4.10784885622 0.0789337203415 -19 18.0 -4.18646562704 0.0782867227197 -20 19.0 -4.26439612115 0.0775611885609 -21 20.0 -4.34156189202 0.0767573230567 -22 21.0 -4.41788477419 0.0758754834523 -23 22.0 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0.0706775413231 -353 352.0 -2.13810701636 0.0717270740805 -354 353.0 -2.21034115987 0.0727339066469 -355 354.0 -2.28355983986 0.0736957705223 -356 355.0 -2.35771696194 0.0746104183955 -357 356.0 -2.43276419776 0.0754756307561 -358 357.0 -2.50865101613 0.0762892225281 -359 358.0 -2.58532472075 0.0770490497051 -360 359.0 -2.66273049463 0.0777530159679 - -# Table of the potential and its negative derivative for frustrated beta sheet -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 - -FRUSTRATED_BETA -N 360 DEGREES - -1 0.0 -2.55809068762 0.0731724739818 -2 1.0 -2.63154144494 0.0737195744566 -3 2.0 -2.70551060968 0.0742089966437 -4 3.0 -2.77993963883 0.074639023134 -5 4.0 -2.85476830901 0.0750080115297 -6 5.0 -2.92993479441 0.0753144003899 -7 6.0 -3.00537575069 0.0755567150326 -8 7.0 -3.08102640456 0.0757335731758 -9 8.0 -3.15682064892 0.0758436903983 -10 9.0 -3.23269114341 0.075885885404 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0.0531611720525 -342 341.0 -1.32480451282 0.0544411134304 -343 342.0 -1.37987850417 0.055703842622 -344 343.0 -1.43620582346 0.0569474464963 -345 344.0 -1.49376636966 0.0581699665097 -346 345.0 -1.55253806258 0.05936940366 -347 346.0 -1.61249680493 0.0605437236497 -348 347.0 -1.67361644969 0.0616908622471 -349 348.0 -1.73586877296 0.0628087308273 -350 349.0 -1.79922345238 0.0638952220804 -351 350.0 -1.86364805137 0.0649482158688 -352 351.0 -1.92910800931 0.0659655852184 -353 352.0 -1.9955666377 0.066945202426 -354 353.0 -2.06298512258 0.0678849452658 -355 354.0 -2.13132253309 0.0687827032771 -356 355.0 -2.20053583647 0.0696363841147 -357 356.0 -2.27057991931 0.0704439199439 -358 357.0 -2.3414076153 0.0712032738621 -359 358.0 -2.41296973939 0.0719124463259 -360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/run.in.min b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/run.in.min deleted file mode 100644 index 8eb3a03cbb..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt deleted file mode 100644 index 185d03cf15..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt +++ /dev/null @@ -1,50 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. -# (Try using "run.in.min" and uncomment line below.) -# read_data system_after_min.data - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Keep the chaperonin fixed. Only let the protein move. - -fix fxlan proteins langevin 0.25 0.25 1.0 48279 -fix fxnve proteins nve - -# Notes: -# The temperature is in reduced units and is set to 0.25 -# which is the folding temperature for the frustrated protein -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -# Just run it long enough for it to collapse (not fold) -# (If you need to run it longer, then dump trajectory data less frequently.) -run 50000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.txt deleted file mode 100644 index fd7c2ba7d1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.txt +++ /dev/null @@ -1,32 +0,0 @@ -# This directory demonstrates how to run a short simulation of -# the "unfrustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# In this example, the protein is placed inside a repulsive sphere -# of radius 6.0 sigma which confines its motion. -# (This sphere is sometimes called the "chaperonin", because -# we were using it to model the crude behavior of a chaperonin cavity.) -# -# During this short simulation (run.in.nvt) the protein evolves -# from an unfolded initial conformation to the folded state. -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh deleted file mode 100755 index 042f73a287..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg deleted file mode 100644 index a0da344db5..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg deleted file mode 100644 index a1aa5bd855..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt deleted file mode 100644 index 0dc1f5dd05..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt +++ /dev/null @@ -1,255 +0,0 @@ -# This file defines a pair of coarse-grained protein models used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadUnfrustrated { - - # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 - $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 - $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 - $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 - $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 - $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 - $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 - $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 - $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 - $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 - $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 - $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 - $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 - $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 - $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 - $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 - $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 - $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 - $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 - $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 - $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 - $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 - $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 - $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 - $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 - $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 - $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 - } - - # bond-ID bond-Type atom-ID atom-ID - - write("Data Bonds") { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - # - # Note that some quartets of atoms are listed because their - # potentials contain multiple terms in the Fourier expansion. - # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) - # - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write("Data Dihedrals") { - $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 - $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 - $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 - $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 - $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 - $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadUnfrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - # dihedral_coeff dihedralType dihedralstylename K n d w - # ("w" is the weight for 1-4 pair interactions, which we set to 0) - - # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d - # parameters. I'm hoping this will be fixed eventually. - - write_once("In Settings") { - # Correct version: - #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 - # Correct version: - #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 - dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 - dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 - dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 - # Correct version: - # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 - # Replacing with - dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 - dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 - dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 - dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadUnfrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadUnfrustrated - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt deleted file mode 100644 index cbc8fe217c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "1beadUnfrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadUnfolded inherits 1beadUnfrustrated { - - # This molecule "inherits" all of its features from "1beadUnfrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt deleted file mode 100644 index 8266d2a898..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt +++ /dev/null @@ -1,41 +0,0 @@ -# Here we define a trivial molecule containing only one particle. - -Chaperonin { - - # atomID molID atomType charge x y z - - write("Data Atoms") { - $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:C 100.0 - } - - write_once("In Settings") { - # If for some reason there are multiple chaperones present, - # I assume that they interact repulsively (hence, L=0) - # i j epsilon sigma K L - - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 - - # Optional: define the atoms in the "chaperonins" group: - # (Defining a group for the chaperone makes it easy to immobilize it later.) - - group chaperonins type @atom:C - } - - - # Specify which pair_styles, and atom styles work well with - # this model. (Again this can be overridden later.) - - write_once("In Init") { - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 - } - -} # Chaperonin - -# We have not specified how this particle interacts with other particles -# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py deleted file mode 100755 index 4c787de565..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between atoms in the -# protein and a chaperone provided in the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# This is stored in a tabulated force field with a singularity at a distance R. -# -# To calculate the table for interaction between -# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 -# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 -# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True -# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True - -from math import * -import sys - -def U(r, eps, sigma, R, h): - #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) - - h*pow((sigma/R), 6.0)) - xp = sigma/(r+R) - xm = sigma/(r-R) - term10 = pow(xm, 10.0) - pow(xp, 10.0) - term4 = pow(xm, 4.0) - pow(xp, 4.0) - return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) - -def F(r, eps, sigma, R, h): - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 0.0 - product_term_a = U(r, eps, sigma, R, h) / r - ixp = (r+R)/sigma - ixm = (r-R)/sigma - dix_dr = 1.0/sigma - term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) - term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) - product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) - return product_term_a + product_term_b - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - - """ - def __init__(self, err_msg): - self.err_msg = err_msg - def __str__(self): - return self.err_msg - def __repr__(self): - return str(self) - -if len(sys.argv) < 8: - sys.stderr.write("Error: expected 7 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") - sys.exit(-1) - -epsilon = float(sys.argv[1]) -sigma = float(sys.argv[2]) -R = float(sys.argv[3]) -h = float(sys.argv[4]) -rmin = float(sys.argv[5]) -rmax = float(sys.argv[6]) -N = int(sys.argv[7]) - -subtract_Urcut = False -if len(sys.argv) == 9: - subtract_Urcut = True -rcut = rmax - -for i in range(0,N): - r = rmin + i*(rmax-rmin)/(N-1) - U_r = U(r, epsilon, sigma, R, h) - F_r = F(r, epsilon, sigma, R, h) - if subtract_Urcut: - U_r -= U(rcut, epsilon, sigma, R, h) - if (r >= rcut) or (i==N-1): - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt deleted file mode 100644 index d8781c26f5..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt +++ /dev/null @@ -1,45 +0,0 @@ -write_once("Data Boundary") { - 0.0 20.0 xlo xhi - 0.0 20.0 ylo yhi - 0.0 20.0 zlo zhi -} - - -import "chaperonin.lt" -import "1beadUnfrustrated_variants.lt" - - -chaperinin = new Chaperonin # (hollow chaperonin, encloses protein) -protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) - - - -# Now define interactions between the "c" atom in the -# chaperone and the "B", "L", "N" atoms in the protein: - -write_once("In Settings") { - pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.dat CH_H0 - pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/L table table_chaperonin_h=0.dat CH_H0 - pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/N table table_chaperonin_h=0.dat CH_H0 - # Note: In this example, the chaperone is playing the role of a repulsive wall - # (confinement). To use a sticky chaperonin, replace the first line with this: - # pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 -} - - - -# LAMMPS has many available force field styles (and atom styles). -# Here, we pick the ones which work well for this molecular model: - -write_once("In Init") { - # --- Default options for the "1BeadUnfrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) -} diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat deleted file mode 100644 index 675d228a90..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat +++ /dev/null @@ -1,1188 +0,0 @@ -# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). -# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) - -CH_H0.475 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 -0.018422088583 0.0 -2 0.005 -0.0184221525389 2.55824082873e-05 -3 0.01 -0.0184223444081 5.11654127471e-05 -4 0.015 -0.018422664195 7.67496107175e-05 -5 0.02 -0.0184231119071 0.000102335598797 -6 0.025 -0.018423687555 0.000127923973785 -7 0.03 -0.0184243911519 0.000153515332637 -8 0.035 -0.0184252227143 0.000179110272379 -9 0.04 -0.0184261822615 0.000204709390236 -10 0.045 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b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat deleted file mode 100644 index 2ad6d7b691..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat +++ /dev/null @@ -1,1187 +0,0 @@ -# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) - -CH_H0 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 8.31299178857e-07 0.0 -2 0.005 8.31311879342e-07 -5.08022586688e-09 -3 0.01 8.31349981758e-07 -1.01608369733e-08 -4 0.015 8.31413488996e-07 -1.52422186449e-08 -5 0.02 8.31502405871e-07 -2.03247562721e-08 -6 0.025 8.31616739127e-07 -2.54088353865e-08 -7 0.03 8.31756497437e-07 -3.04948417048e-08 -8 0.035 8.319216914e-07 -3.55831611709e-08 -9 0.04 8.32112333547e-07 -4.06741800058e-08 -10 0.045 8.32328438343e-07 -4.57682847516e-08 -11 0.05 8.32570022183e-07 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-2.55154000294e+12 - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min deleted file mode 100644 index 8eb3a03cbb..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt deleted file mode 100644 index 3e14f82b19..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt +++ /dev/null @@ -1,48 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. -# (Try using "run.in.min" and uncomment the line below.) -# read_data system_after_min.data - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Keep the chaperonin fixed. Only let the protein move. - -fix fxlan proteins langevin 0.39 0.39 1.0 48279 -fix fxnve proteins nve - -# Notes: -# The temperature is in reduced units and is set to 0.39 -# which is the folding temperature for the unfrustrated protein. -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 5000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README.txt deleted file mode 100644 index 7756b566db..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README.txt +++ /dev/null @@ -1,27 +0,0 @@ -# This directory demonstrates how to run a short simulation of -# the "unfrustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# During this short simulation (run.in.nvt) the protein evolves -# from an unfolded initial conformation to the folded state. -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh deleted file mode 100755 index d5ae1fe5a3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_mpi" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...). Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh deleted file mode 100755 index 886551ffb3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg deleted file mode 100644 index 152fa88ff9..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg deleted file mode 100644 index bb269f47f2..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt deleted file mode 100644 index 0dc1f5dd05..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt +++ /dev/null @@ -1,255 +0,0 @@ -# This file defines a pair of coarse-grained protein models used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadUnfrustrated { - - # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 - $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 - $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 - $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 - $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 - $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 - $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 - $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 - $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 - $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 - $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 - $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 - $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 - $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 - $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 - $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 - $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 - $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 - $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 - $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 - $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 - $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 - $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 - $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 - $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 - $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 - $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 - } - - # bond-ID bond-Type atom-ID atom-ID - - write("Data Bonds") { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - # - # Note that some quartets of atoms are listed because their - # potentials contain multiple terms in the Fourier expansion. - # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) - # - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write("Data Dihedrals") { - $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 - $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 - $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 - $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 - $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 - $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadUnfrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - # dihedral_coeff dihedralType dihedralstylename K n d w - # ("w" is the weight for 1-4 pair interactions, which we set to 0) - - # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d - # parameters. I'm hoping this will be fixed eventually. - - write_once("In Settings") { - # Correct version: - #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 - # Correct version: - #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 - dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 - dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 - dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 - # Correct version: - # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 - # Replacing with - dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 - dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 - dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 - dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadUnfrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadUnfrustrated - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt deleted file mode 100644 index cbc8fe217c..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "1beadUnfrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadUnfolded inherits 1beadUnfrustrated { - - # This molecule "inherits" all of its features from "1beadUnfrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt deleted file mode 100644 index 5ebe6efb88..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt +++ /dev/null @@ -1,11 +0,0 @@ -import "1beadUnfrustrated_variants.lt" - - -protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) - - -write_once("Data Boundary") { - 0.0 27.0 xlo xhi - 0.0 27.0 ylo yhi - 0.0 27.0 zlo zhi -} diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min deleted file mode 100644 index 8eb3a03cbb..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt deleted file mode 100644 index e49206ee3a..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. -# (Try using "run.in.min" and uncomment the line below.) -# read_data system_after_min.data - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 0.39 0.39 1.0 48279 -fix fxnve all nve - -# Notes: -# The temperature is in reduced units and is set to 0.39 -# which is the folding temperature for the unfrustrated protein. -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 8000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README.txt deleted file mode 100644 index 03361928e1..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README.txt +++ /dev/null @@ -1,44 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -This is an example of a very simple coarse-grained protein. - -This example contains a 1-bead (C-alpha model) representation of the -"unfrustrated" 4-helix bundle model used in this paper: -G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) - -In this model, there are three atom-types (bead-types), H, L, and N -representing one amino-acid each. The "H" beads represent the hydrophobic -amino acids, and are attracted to eachother with a strength of "1.0" -(in dimensionless units of "epsilon"). The "L" and "N" atoms are -hydrophilic and purely repulsive, and only differ in their secondary-structure -propensity (ie their dihedral parameters). - -The dihedral-interaction is bi-stable with two deep local minima (corresponding -to helix-like and sheet-like secondary structure). You can adjust the bias -in favor of one minima or another by modifying the angle-shift parameter in -the appropriate "dihedral_coeff" command in the other .lt file. - -A definition for the 4-sheet beta-barell protein model is also included. -If you want to simulate that molecule instead, then edit the "system.lt" -file (in the "moltemplate_files" subdirectory), and replace this line: -prot = new 4HelixBundle - with -prot = new 4SheetBundle - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_run.sh deleted file mode 100755 index 4b0229453e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_mpi" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_ubuntu, lmp_mac_mpi, lmp_cygwin etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_setup.sh deleted file mode 100755 index 886551ffb3..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg deleted file mode 100644 index b4d919f9e6..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg deleted file mode 100644 index cd65146ffa..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index 9b4ff25354..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,274 +0,0 @@ -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. -# This approach is optional. If your protein has helices which are not -# identical, you should probably just include all 4 helices in a single -# "Data Atoms" section and don't try to subdivide the protein into pieces.) - - -1beadProtSci2010 { # <-- enclose definitions in a namespace for portability - - write_once("In Init") { - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 - $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 - $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 - $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 - $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 - $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 - $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 - $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 - $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 - $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 - $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 - $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 - $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 - $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 - $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 - $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 - $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 - $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 - $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 - $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 - $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 - $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 - $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 - $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 - $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 - $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 - $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 - $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 - $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 - $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 - $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 - $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 - $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - # ----- Now build larger molecules using A16, B16 and T3 ------- - - 4SheetBarrel { - - sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, -6) - sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, -6) - sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, -6) - sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, -6) - - turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,6.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-6.9) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,6.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - 4HelixBundle { - - helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, -4.5) - helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, -4.5) - helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, -4.5) - helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, -4.5) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,5.4) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-4.8) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,5.4) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - } - # Interactions between different atoms use "repulsive wins" mixing rules - - - # bond_coeff bondType bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 66.6 1.0 - } - - - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 66.6 105.0 - } - - # We use the same bond-angle forces whenever - # there are 3 consecutively-bonded atoms: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - - - # From the Bellesia et al 2010 paper: - # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) - # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) - # - # General formula used for "dihedral_style fourier": - # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] - # - # Syntax: - # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 - dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 - dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - } - - - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - write_once("Data Dihedrals By Type") { - @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * - @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * - @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * - } - # Note: This next rule is not needed: - # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * - # (By reflection symmetry, it's equivalent to the rule above.) - # - # Note: The example in ../../membrane+protein/moltemplate_files/ - # demonstrates how to define dihedral angles for this model - # in an alternate way which might be easier to understand. - - - # --- Mass Units --- - # There are 3 atom types (referred to above as ../H, ../L, and ../N) - # Define their masses (in reduced units): - - write_once("Data Masses") { - @atom:H 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh deleted file mode 100755 index 852b9b76f2..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh +++ /dev/null @@ -1,13 +0,0 @@ -# run moltemplate this way - -moltemplate.sh system.lt - -# This will generate various files with names ending in *.in* and *.data -# which are needed by LAMMPS. - -# ------ Other versions: -------- -# -# If you are using the "other_versions/charmm/1beadProtSci2010.lt" file, -# then you must run moltemplate this way: -# -# moltemplate.sh -overlay-dihdedrals system.lt diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.txt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.txt deleted file mode 100644 index 82bc8c5c43..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.txt +++ /dev/null @@ -1,13 +0,0 @@ -This directory contains other versions of the same molecule -(with the same force-field), implemented in different ways. - -charmm/1beadProtSci2010.lt <-- This applies multiple "charmm" dihedral angle - forces to the same quartet of atoms to create - a Fourier series. (No packages needed.) - - NOTE: You must run moltemplate this way: - - moltemplate.sh -overlay-dihdedrals system.lt - -class2/1beadProtSci2010.lt <-- This uses the "class2" dihedral angles forces - (You must build LAMMPS with the CLASS2 package) diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt deleted file mode 100644 index d57186bee7..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt +++ /dev/null @@ -1,411 +0,0 @@ -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -# -# -# For portability, all definitions in this file are enclosed within -# the "1beadProtSci2010" namespace. To access them, put -# "using namespace 1beadProtSci2010" in your LT file. - -# Strategy: -# -#1) First I'll define some building blocks -# (short helices, sheets and turns of a predetermined length) -# -#2) Then I'll cut and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. -# -# Doing it this way is optional. It's simpler (but longer) to simply write -# out the entire sequence of all 73 atoms in a single "Data Atoms" section. -# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the -# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions -# manually (instead of inferring them from the atom type). If your protein -# has helices which are not identical, this would probably be easier. -# Use whichever style you prefer. -# -# -# Note that atom types, bond types, angle types, and dihedral types -# are shared between all molecules defined in the "1beadProtSci2010" family. -# (That's why there is a "../" in their path-names. Otherwise atom, bond, -# angle types, etc... are not shared between different molecules.) -# -# Confusing detail: -# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). -# These are represented by the "$mol" variable written next to each atom. -# Our protein has multiple subunits (in this case: helices, sheets, turns). -# Because we want the subunits to share the same molecule-ID counter we use -# "$mol:..." instead of "$mol" which tells moltemplate to search for the -# parent molecule's ID. This is optional. If it bothers you, just use "$mol" - - - -1beadProtSci2010 { - - write_once("In Init") { - # -- Default styles for "1beadProtSci2010" -- - units lj - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 4.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - - # ---- Building blocks: A16, B16, Turn3 ---- - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 - $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 - $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 - $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 - $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 - $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 - $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 - $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 - $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 - $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 - $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 - $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 - $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 - $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 - $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 - $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 - $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 - $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 - $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 - $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 - $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 - $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 - $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 - $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 - $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 - $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 - $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 - $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 - $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 - $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 - $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 - $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 - $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) - # can be shared. The ".." in "@atom:../CA" tells moltemplate that - # atom type CA is defined in the parent's environment. (We are - # sharing the CA atom type between both the H and P residues. - # The same is true of the ".." in "@bond:../sidechain". - # - # - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # molecule's id number as it's own. - - - - # ----- Now build larger molecules using A16, B16 and T3 ------- - - 4HelixBundle { - - helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) - helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) - helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) - helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) - # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) - - # Note: In the paper, this is described as the "UA2" conformation - # (I played around with the angles until it looked "okay". This is not - # the minimum energy conformation. Further minimization is necessary.) - - # Now bond the pieces together. - # (Note: angle & dihedral interactions will be generated automatically.) - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # <-- create a variable for the parent's Molecule-ID - } - - 4SheetBundle { - - sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) - sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) - sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) - sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) - # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) - - turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # There are 3 atom types (referred to above as ../H, ../L, and ../N) - # Define their masses: - - write_once("Data Masses") { - @atom:H 1.0 - @atom:L 1.0 - @atom:N 1.0 - - } - - - - # -------------------------------------------------------------------- - # -- In this example, all force field parameters are stored in the -- - # -- file named "In Settings". They can also go in sections like -- - # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- - # -------------------------------------------------------------------- - - - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - } - # (Interactions between different atom types use "arithmetic" - # and "maxmax" ("repulsion-wins") mixing rules.) - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond_coeff bondType bondstylename k r0 - # - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 66.6 1.0 - } - - - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # The corresponding command is: - # - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 66.6 105.0 - } - - # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded - # together. We do this by to asking moltemplate to generate this - # 3-body interaction whenever 3 consecutively bonded atoms satisfy - # the following type requirement: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone * * * * * - } - - - - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - # dihedral_coeff dihedralType dihedralstylename K n d w - # ("w" is the weight for 1-4 pair interactions, which we set to 0) - - write_once("In Settings") { - dihedral_coeff @dihedral:turn charmm 0.2 3 0 0 - dihedral_coeff @dihedral:term3 charmm 1.2 3 0 0 - - dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65 0 - dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62 0 - dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60 0 - dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57 0 - dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55 0 - } - - #write_once("In Settings") { - # dihedral_coeff @dihedral:turn charmm 0.2 3 0.0 0 - # dihedral_coeff @dihedral:term3 charmm 1.2 3 0.0 0 - # dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65.0 0 - # dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62.5 0 - # dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60.0 0 - # dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57.5 0 - # dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55.5 0 - #} - - # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy - # the following type requirements: - - write_once("Data Dihedrals By Type") { - # The dihedral interaction between backbone atoms in the helix or sheet-like - # regions is proportional to the sum of two terms: cos(phi+delta)+cos(3*phi) - # where delta is a constant used to control the bias between helices/sheets. - # As of 2013-4-07, the "fourier", "table", "class2", and "charmm", - " dihedral_styles can implement this potential. - # However dihedral_style "charmm" can only handle one cosine term at a time. - # So we use two commands to create two dihedral interactions for the same - # set of of four atoms ("cos3" and "delta60_0"). (To allow the - # superposition of multiple dihedral interactions on the same atoms, - # be sure to run moltemplate with the "-overlay-dihdedrals" argument.) - # - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - @dihedral:term3 @atom:H @atom:L @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * - - @dihedral:term3 @atom:H @atom:L @atom:L @atom:H * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * - - @dihedral:term3 @atom:L @atom:H @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * - - @dihedral:term3 @atom:H @atom:H @atom:L @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * - - # Comment out the next 4 lines: (They are redundant with the lines above) - #@dihedral:term3 @atom:L @atom:L @atom:H @atom:H * * * - #@dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * - #@dihedral:term3 @atom:L @atom:H @atom:L @atom:H * * * - #@dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * - # (Redundant: The LLHH pattern is identical to HHLL after order reversal) - # (Redundant: The LHLH pattern is identical to HLHL after order reversal) - - # Right now the dihedral-angle settings are "unfrustrated", meaning that the - # peptide backbone is equally happy to adopt helical or sheet-like secondary - # structure (See Table IV of Bellesia et. al, Prot Sci, 19, 141 (2010)). - # You can change that by changing "delta60_0" to one of the other choices. - - # Any dihedral interactions containing "N" atoms use the @dihedral:turn - # interaction (which is much weaker). - @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - # Comment out the next 4 lines: (They are redundant with the lines above) - # @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - # @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * - # @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * - # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt deleted file mode 100644 index a0e305f844..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt +++ /dev/null @@ -1,385 +0,0 @@ -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -# -# -# For portability, all definitions in this file are enclosed within -# the "1beadProtSci2010" namespace. To access them, put -# "using namespace 1beadProtSci2010" in your LT file. - -# Strategy: -# -#1) First I'll define some building blocks -# (short helices, sheets and turns of a predetermined length) -# -#2) Then I'll cut and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. -# -# Doing it this way is optional. It's simpler (but longer) to simply write -# out the entire sequence of all 73 atoms in a single "Data Atoms" section. -# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the -# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions -# manually (instead of inferring them from the atom type). If your protein -# has helices which are not identical, this would probably be easier. -# Use whichever style you prefer. -# -# -# Note that atom types, bond types, angle types, and dihedral types -# are shared between all molecules defined in the "1beadProtSci2010" family. -# (That's why there is a "../" in their path-names. Otherwise atom, bond, -# angle types, etc... are not shared between different molecules.) -# -# Confusing detail: -# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). -# These are represented by the "$mol" variable written next to each atom. -# Our protein has multiple subunits (in this case: helices, sheets, turns). -# Because we want the subunits to share the same molecule-ID counter we use -# "$mol:..." instead of "$mol" which tells moltemplate to search for the -# parent molecule's ID. This is optional. If it bothers you, just use "$mol" - - - -1beadProtSci2010 { - - write_once("In Init") { - # -- Default styles for "1beadProtSci2010" -- - units lj - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid class2 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 rsoftcore 1 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 4.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - - # ---- Building blocks: A16, B16, Turn3 ---- - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 - $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 - $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 - $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 - $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 - $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 - $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 - $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 - $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 - $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 - $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 - $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 - $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 - $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 - $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 - $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 - $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 - $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 - $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 - $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 - $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 - $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 - $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 - $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 - $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 - $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 - $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 - $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 - $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 - $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 - $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 - $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 - $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) - # can be shared. The ".." in "@atom:../CA" tells moltemplate that - # atom type CA is defined in the parent's environment. (We are - # sharing the CA atom type between both the H and P residues. - # The same is true of the ".." in "@bond:../sidechain". - # - # - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # molecule's id number as it's own. - - - - # ----- Now build larger molecules using A16, B16 and T3 ------- - - 4HelixBundle { - - helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) - helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) - helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) - helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) - # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) - - # Note: In the paper, this is described as the "UA2" conformation - # (I played around with the angles until it looked "okay". This is not - # the minimum energy conformation. Further minimization is necessary.) - - # Now bond the pieces together. - # (Note: angle & dihedral interactions will be generated automatically.) - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # <-- create a variable for the parent's Molecule-ID - } - - 4SheetBundle { - - sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) - sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) - sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) - sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) - # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) - - turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # There are 3 atom types (referred to above as ../H, ../L, and ../N) - # Define their masses: - - write_once("Data Masses") { - @atom:H 1.0 - @atom:L 1.0 - @atom:N 1.0 - - } - - - - # -------------------------------------------------------------------- - # -- In this example, all force field parameters are stored in the -- - # -- file named "In Settings". They can also go in sections like -- - # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- - # -------------------------------------------------------------------- - - - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 0 0 0 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 - } - # (Interactions between different atom types use "arithmetic" - # and "maxmax" ("repulsion-wins") mixing rules.) - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond_coeff bondType bondstylename k r0 - # - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 66.6 1.0 - } - - - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # The corresponding command is: - # - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 66.6 105.0 - } - - # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded - # together. We do this by to asking moltemplate to generate this - # 3-body interaction whenever 3 consecutively bonded atoms satisfy - # the following type requirement: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone * * * * * - } - - - - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - - # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60) - # (scratchwork: 1.2*cos(x+60) = -1.2*cos(x+60-180) = -1.2*cos(x-120)) - # and 1.2*cos(3x) = -1.2*cos(3x-180) - # and 0.2*cos(x) = -0.2*cos(x - 180) - # This way, the energies match exactly with the implementation using charmm dihedrals.) - # - # dihedralType dihedralstylename K1 phi1 K2 phi2 K3 phi3 - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 class2 1.2 120.0 0 0 1.2 180.0 - dihedral_coeff @dihedral:turn class2 0 0 0 0 0.2 180.0 - - # All of the cross-terms (for the class2 force-field) are zero (see docs): - dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0 - dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0 - dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:turn class2 aat 0 0 0 - dihedral_coeff @dihedral:turn class2 bb13 0 0 0 - } - - # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy - # the following type requirements: - - write_once("Data Dihedrals By Type") { - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * - @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * - - @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - - #### Comment out the next 6 lines: (They are redundant with the lines above) - ## @dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * - ## @dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * - ## @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - ## @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * - ## @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * - ## @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * - ################################################################### - } - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt deleted file mode 100644 index 6300c4ce3f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt +++ /dev/null @@ -1,12 +0,0 @@ -import "1beadProtSci2010.lt" - -using namespace 1beadProtSci2010 - -prot = new 4HelixBundle - -write_once("Data Boundary") { - 0 100 xlo xhi - 0 100 ylo yhi - 0 100 zlo zhi -} - diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/run.in.min deleted file mode 100644 index 8eb3a03cbb..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/run.in.nvt deleted file mode 100644 index a0f02dc738..0000000000 --- a/tools/moltemplate/examples/coarse_grained/protein_folding_examples/1beadProtSci2010/run.in.nvt +++ /dev/null @@ -1,44 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. -# (Try using "run.in.min" and uncomment the line below) -# read_data system_after_min.data - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.008 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 0.4 0.4 1.0 48279 -fix fxnve all nve - -# Notes: -# The temperature is in reduced units and is set to 0.4. -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0. -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 500 #(time interval for printing out "thermo" data) - -restart 10000000 restart_nvt - -run 1000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README.txt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README.txt deleted file mode 100644 index 990c6f2f56..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README.txt +++ /dev/null @@ -1,114 +0,0 @@ - This example shows how to build a multicomponent spherical vesicle. - The lipid bilayer is composed of two different lipids (DPPC and DLPC). - The vesicle also contains trans-membrane protein inclusions. - - The coordinates for the vesicle are constructed by PACKMOL (see below). - - The DPPC lipid model is described here: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) - (The DLPC model is a truncated version of DPPC. Modifications discussed below.) - The protein model is described here: - G. Bellesia, AI Jewett, and J-E Shea, - Protein Science, Vol19 141-154 (2010) - ---- PREREQUISITES: --- - -1) This example requires PACKMOL. You can download PACKMOL here: - - http://www.ime.unicamp.br/~martinez/packmol/ - - (Moltemplate does not come with an easy way to generate spherically-symmetric - structures, so I used the PACKMOL program to move the molecules into position.) - -2) This example requires the "dihedral_style fourier", which is currently -in the USER-MISC package. Build LAMMPS with this package enabled using - make yes-user-misc -before compiling LAMMPS. -(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) - -3) This example may require additional features to be added to LAMMPS. -If LAMMPS complains about an "Invalid pair_style", then - a) download the "additional_lammps_code" from - http://moltemplate.org (upper-left corner menu) - b) unpack it - c) copy the .cpp and .h files to the src folding of your lammps installation. - d) (re)compile LAMMPS. - ------- Details ------- - -This example contains a coarse-grained model of a 4-helix bundle protein -inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). - - -- Protein Model: -- - -The coarse-grained protein is described in: - G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -Here we use the "AUF2" model described in that paper. -(The hydrophobic beads face outwards.) - - -- Memebrane Model: -- - -The DPPC lipid bilayer described in: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) -and: - M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown - J. Chem. Phys. 135, 244701 (2011) - -As in Watson(JCP 2011), rigid bond-length constraints -have been replaced by harmonic bonds. - -A truncated version of this lipid (named "DLPC") has also been added. -The bending stiffness of each lipid has been increased to compensate -for the additional disorder resulting from mixing two different types -of lipids together. (Otherwise pores appear.) -Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models -have not been carefully parameterized to reproduce the correct behavior in -a lipid bilayer mixture. - - -- Interactions between the proteins and lipids -- - -This is discussed in the "system.lt" file. - ---- Building the files necessary to run a simulation in LAMMPS --- - -step 1) Run PACKMOL - - Type these commands into the shell. - (Each command could take several hours.) - -cd packmol_files - packmol < step1_proteins.inp # This step determines the protein's location - packmol < step2_innerlayer.inp # this step builds the inner monolayer - packmol < step3_outerlayer.inp # this step builds the outer monolayer -cd .. - -step 2) Run MOLTEMPLATE - Type these commands into the shell. - (This could take up to 10 minutes.) - -cd moltemplate_files - moltemplate.sh system.lt -xyz ../system.xyz - mv -f system.in* system.data ../ - cp -f table_int.dat ../ -cd .. - ---- Running LAMMPS --- - -step3) Run LAMMPS: - Type these commands into the shell. - (This could take days.) - -lmp_linux -i run.in.min # Minimize the system (important, and very slow) - -lmp_linux -i run.in.nvt # Run a simulation at constant volume - -If you have compiled the MPI version of lammps, you can run lammps in parallel: - -mpirun -np 4 lmp_linux -i run.in.min - or -mpirun -np 4 lmp_linux -i run.in.nvt - -(Assuming you have 4 cores, for example.) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_WARNING.txt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_WARNING.txt deleted file mode 100644 index f1b1904a8d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_WARNING.txt +++ /dev/null @@ -1,20 +0,0 @@ -WARNING: - - This is not a realistic simulation of proteins in a lipid membrane. This -example was only intented to be a technical demonstration to show how to -combine totally different kinds of coarse-grained molecules (with different -kinds of force-fields) together in the same simulation in LAMMPS. Tuning the -force-field parameters to get realistic results was not the goal. I did -not take the extra time to do this. If you have suggestions for changes, -please email me (jewett.aij at gmail dot com). - - In addition, I have noticed that newer versions of PACKMOL do not -always succeed at generating a spherical vesicle in a reasonable amount of time. -(You may have to play with the .inp files in the packmol_files directory - to get PACKMOL to produce any files at all. - -(NOTE: This example also demonstrantes how to use an external program - ("packmol") to generate the coordinates for the atoms in the system. - PLEASE USE "packmol", NOT "ppackmol". -the parallel version of "packmol". - This is because "ppackmol" is more likely to get caught in infinite loops.) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_run.sh b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_run.sh deleted file mode 100755 index fcc87a6bf4..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_run.sh +++ /dev/null @@ -1,24 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with MOLTEMPLATE and PACKMOL: -# system.in.init, system.in.settings, system.in.coords, system.data, -# and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - -lmp_mpi -i run.in.min # Minimize the system (important, and very slow) - -lmp_mpi -i run.in.nvt # Run a simulation at constant volume - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.min -#or -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_setup.sh b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_setup.sh deleted file mode 100755 index fa3986e737..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_setup.sh +++ /dev/null @@ -1,69 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - -# First, generate the coordinates (the "system.xyz" file). -# (This can be a very slow process.) - -# check if packmol exists before running -if ! hash packmol 2>/dev/null; then - echo "packmol not found. This example cannot be run." - exit 1 -fi - -cd packmol_files - - # You must run each packmol commend one after the other. - # NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding - # "inp" file. This should not happen. You can also usually interrupt - # packmol after 30 minutes, and the solution at that point (an .xyz file) - # should be good enough for use. - packmol < step1_proteins.inp # This step determines the protein's location - # It takes ~20 minutes (on an intel i7) - packmol < step2_innerlayer.inp # this step builds the inner monolayer - # It takes ~90 minutes - packmol < step3_outerlayer.inp # this step builds the outer monolayer - # It takes ~4 hours - - - # NOTE: PLEASE USE "packmol", NOT "ppackmol". ("ppackmol" is the parallel - # version of packmol using OpemMP. This example has NOT been tested - # with "ppackmol". Our impression was that the "ppackmol" version - # is more likely to get stuck in an infinite loop. -Andrew 2015-8) - - - # Step3 creates a file named "step3_outerlayer.xyz" containing the coordinates - # in all the atoms of all the molecules. Later we will run moltemplate.sh - # using the "-xyz ../system.xyz" command line argument. That will instruct - # moltemplate to look for a file named "system.xyz" in the parent directory. - # So I rename the "step3_outerlayer.xyz" file to "system.xyz", and move it - # to this directory so that later moltemplate.sh can find it. - - mv -f step3_outerlayer.xyz ../system.xyz -cd .. - - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -xyz ../system.xyz system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f table_int.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt deleted file mode 100644 index a3e3ed620e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg deleted file mode 100644 index c3ff599560..0000000000 Binary files a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/images/vesicle_membrane+protein_L.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index 2e510ebd9e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,233 +0,0 @@ -# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle (or a 4-strand beta-barrel). -# This approach is optional. If your protein has helices which are not -# identical, you should probably just include all 4 helices in a single -# "Data Atoms" section and don't try to subdivide the protein into pieces.) - - - -1beadProtSci2010 { # <-- enclose definitions in a namespace for portability - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 - $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 - $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 - $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 - $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 - $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 - $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 - $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 - $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 - $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 - $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 - $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 - $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 - $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 - $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 - $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 - $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 - $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - - # ----- Now build a larger molecule using A16 and T3 ------- - - # Create a 4-Helix bundle. - # In this version, the hydrophobic beads are poing outward. - # I oriented them this way because I want to place this protein in a membrane. - # (There is another file in this directory containing alternate version - # of this same molecule with the hydrophobic beads pointing inward.) - - 4HelixInsideOut { - helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) - - turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) - turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) - turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOut - - - # -------- Minor coordinates adjustment: ----------- - - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6 = 0.8) - - 4HelixInsideOut.scale(0.8) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - - - # -------------- Force-Field Parameters ------------ - - # Units and force-field styles for this protein model - # (These can be overridden later.) - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - # --- Distance Units --- - # In this version of the model, sigma (the bond-length - # and particle diameter) is rounded to 4.8 Angstroms. - # - # --- Energy & Temperature Units --- - # In this protein model, "epsilon" represents the free energy - # bonus for bringing two hydrophobic amino acids together. - # Here I choose to set epsilon to 1.806551818181818 kCal/mole. - # This value was chosen so that a temperature of 300 Kelvin lies at - # 0.33 epsilon, which is the unfolding temperature of the marginally stable - # "ASF1" protein model from the Bellesia et al 2010 paper. - # This choice insures that both the "ASF1" model from that paper, - # as well as the much more stable "AUF2" protein we use here (which - # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, - # in the bulk at least. (However it's not clear that these energy - # parameters will work well for a protein in membrane. Perhaps I'll - # run some tests and fine tune these parameters for this scenario.) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 4.8 1 -1 - pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0 - pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 4.8 1 0 - } - - # The exact value of the bond_coeff does not matter too much as long as - # it is "stiff enough". Here I use a softer bond spring than the one - # used in the paper so that I can increase the time step. - # I also use a relatively soft spring to constrain the bond angles. - - # bond_coeff bondType bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 4.8 - } - - - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # angle_coeff angleType anglestylename k theta0 - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 100.0 105.0 - } - - - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - write_once("Data Dihedrals By Type") { - # For a chain of sH and sL atoms, use the @dihedral:delta65_0 - # parameters. (This corresponds to the "AUF2" model from the - # Bellesia et. al 2010 paper.) - - @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * - - # If "tN" (turn) atoms are present, use the @dihedral:turn parameters - - @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * - } - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 - dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - } - - - # --- Mass Units --- - # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): - write_once("Data Masses") { - @atom:1beadProtSci2010/sH 100.0 - @atom:1beadProtSci2010/sL 100.0 - @atom:1beadProtSci2010/tN 100.0 - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt deleted file mode 100644 index 38b1b48f88..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/1beadProtSci2010_variations.lt +++ /dev/null @@ -1,225 +0,0 @@ -### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## -### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## -# -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) - -import "1beadProtSci2010.lt" - -# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. - - -1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier - # This way we don't have to start from scratch. We can - # use all the atom types and angle settings defined earlier - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 - $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 - $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 - $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 - $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 - $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 - $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 - $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 - $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 - $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 - $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 - $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 - $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 - $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 - $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 - $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - # ----- Now build larger molecules using B16 and T3 ------- - - - 4SheetBarrel { - sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) - sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) - sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) - sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # Below I define several alternate conformations of the"4HelixBundleInsideOut" - # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. - - 4HelixBundle { - helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - - turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) - turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) - turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) - - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixBundle - - - - - # --- alternate conformations (same molecule) ---- - - # In the following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixBundleLoose { - - helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # In following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixInsideOutLoose { - helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) - turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) - turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOutLoose - - - - - # In the following version, the 4 helices are arranged next to each other, - # side-by-side, in a planar conformation (instead of a compact bundle). - - 4HelixPlanar { - helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) - helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) - helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) - helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) - turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) - turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixPlanar - - - # -------- Minor coordinates adjustment: ----------- - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=4.8 Angstroms. 4.8/6.0 = 0.8) - - 4SheetBarrel.scale(0.8) - 4HelixBundle.scale(0.8) - 4HelixBundleLoose.scale(0.8) - 4HelixInsideOutLoose.scale(0.8) - 4HelixPlanar.scale(0.8) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt deleted file mode 100644 index 24be50aced..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/CGLipidBr2005.lt +++ /dev/null @@ -1,196 +0,0 @@ -# Note: -# -# This example may require additional features to be added to LAMMPS. If -# LAMMPS complains about an "Invalid pair_style", then download copy the -# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS -# "src" directory and recompile LAMMPS. -# -# -------- Description -------- -# -# This example contains an implementation of the DPPC lipid bilayer described in -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# and: -# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown -# J. Chem. Phys. 135, 244701 (2011) -# -# As in Watson(JCP 2011), rigid bond-length constraints have been replaced -# by harmonic bonds. -# -# A truncated version of this lipid (named "DLPC") has also been added. -# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -# parameterized to reproduce the correct behavior in a lipid bilayer mixture. -# -# Units: -# -# The "epsilon" parameter in their model is approximately 2.75 kJ/mole -# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) -# The "sigma" parameter corresponds to 7.5 angstroms. - - -CGLipidBr2005 { - - - write_once("In Init") { - # -- Default styles for "CGLipidBr2005" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - - #angle_style hybrid cosine/delta # <- used in the original article - angle_style hybrid harmonic # <- prevents unphysical acute angle turns - # Explanation: - # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - # angle_style harmonic: U(theta) = k*(theta-theta0)^2 - - dihedral_style none - improper_style none - - pair_style hybrid table linear 1130 & - lj/charmm/coul/charmm/inter es4k4l 14.5 15 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - } - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 - $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - $bond:b4 @bond:../backbone $atom:t2 $atom:t3 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 - } - - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - - } #DPPC - - - DLPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - } - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../tail @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - } #DLPC - - - # Particles and properties shared by all lipid types: - - write_once("Data Masses") { - @atom:int 200.0 - @atom:tail 200.0 - } - - write_once("In Settings") { - # -- Default settings/parameters for "CGLipidBr2005" -- - # (Hybrid bond & angle styles were used for portability.) - - # As in Watson(JCP 2011), rigid bond-length constraints - # have been replaced by harmonic bonds. - # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. - bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 - } - - write_once("In Settings") { - # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps - # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 - angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps - } - # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper - # to attempt to compensate for the fact that here we are using a lipid - # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal - # of disorder into the bilayer which would not be present in a DPPC bilayer. - # This causes pores to form. Increasing the angle stiffness prevents this.) - - write_once("In Settings") { - - # The interaction of "atom:int" with other "atom:int" atoms is given by - # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at - # r=3*sigma. This was implemented using pair_style table. - # Unfortunately, mixing lj/charmm and "table" pair styles in the same - # simulation is very inneficient. - - pair_coeff @atom:int @atom:int table table_int.dat INT - - # The interaction of tail beads with eachother is given by the formula below - # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: - # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction between head beads from different types of lipids - # is (currently) repulsive: - pair_coeff @atom:DPPC/head @atom:DLPC/head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - } # write_once("In Settings") - - - # Note: I divided epsilon by 4 to get "0.1643" because we are using the - # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) - # (The "es4k4l" coeffstyle is the default.) Using this convention makes it - # easier to mix this coarse-grained lipid model with other molecular models. - - - -} # CGLipidBr2005 - - - - - - - - -# Note: This example has not been optimized for speed. -# -# Unfortunately, using both lj/charmm and "table" pair styles in the same -# simulation seems to be very inneficient. (The simulation is twice as slow -# as using only the "lj/charmm" pair styles for every pairwise interaction, -# ...and about 25% slower than using "table" for every pairwise interaction. -# However the lennard-jones pair styles support mixing, so we use them to -# make it easier to run these molecules with other molecules which don't use -# pair_table. I felt that portability was worth the extra 25% slow down.) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh deleted file mode 100755 index a5590ffa00..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/README.sh +++ /dev/null @@ -1,22 +0,0 @@ -# This example shows how to build a multicomponent spherical vesicle. -# The lipid bilayer is composed of two different lipids (DPPC and DLPC), -# The vesicle contains 120 trans-membrane protein inclusions. -# -# ---------------- Prerequisites: ------------------ -# You must run packmol to generate the coordinates beforehand. -# Afterwards, move and rename the final coordinate file to "../system.xyz" -# To do this, check the README.sh file in the ../packmol_files directory. -# (or follow these instructions below) -# -# cd ../packmol_files -# packmol < step1_proteins.inp -# packmol < step2_innerlayer.inp -# packmol < step3_outerlayer.inp -# cp step3_outerlayer.xyz ../system.xyz -# -# These steps could take a few hours. -# -# --- After you have done that, you can run moltemplate using this command: --- - -moltemplate.sh system.lt -xyz ../system.xyz - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py deleted file mode 100755 index 1158a9cf75..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -rcut = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) - F_r = F(r, epsilon, sigma) - if r > rcut: - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index e7f0fe462e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# I realized later this is not what we want because although energy is conserved -# all enrgies are shifted with respect to energies used in the Brannigan paper -# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). -# (So don't use this.) - -# Calculate and print a - -def S(r, rc1, rc2, derivative=False): - """ - Calculate the switching function S(r) which decays continuously - between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): - S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 - I'm using the same smoothing/switching cutoff function used by the CHARMM - force-fields. (I'm even using the same code to implement it, taken - from lammps charmm/coul/charmm pair style, rewritten in python.) - - """ - assert(rc2>rc1) - rsq = r*r - rc1sq = rc1*rc1 - rc2sq = rc2*rc2 - denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* - (rc2sq-rc1sq)* - (rc2sq-rc1sq))) - if rsq > rc2sq: - return 0.0 - elif rsq < rc1sq: - if derivative: - return 0.0 - else: - return 1.0 - else: - rc2sq_minus_rsq = (rc2sq - rsq) - rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq - if derivative: - return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) - else: - return (rc2sq_minus_rsq_sq * - (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) - - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) - -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - F_r = F(r, epsilon, sigma) - # Multiply U(r) & F(r) by the smoothing/switch function - U_r = U_r * S(r, Rc1, Rc2) - F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt deleted file mode 100644 index f73c0d5f1d..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt +++ /dev/null @@ -1,166 +0,0 @@ -# Description: -# -# This example shows how to build a multicomponent spherical vesicle. -# The lipid bilayer is composed of two different lipids (DPPC and DLPC), -# The vesicle contains 120 trans-membrane protein inclusions. -# -# The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# The protein model is described here: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) -# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to -# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 -# -# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below) -# -# NOTE: -# This example may require additional features to be added to LAMMPS. -# If LAMMPS complains about an "Invalid pair_style", then copy the code -# in the "additional_lammps_code" directory into your LAMMPS "src" directory -# and recompile LAMMPS. - -# First, load the definitions of the molecules we will need: - -import "CGLipidBr2005.lt" -using namespace CGLipidBr2005 - -import "1beadProtSci2010.lt" -using namespace 1beadProtSci2010 - -# PREREQUISITES: -# Coordinates for the molecules in this example are loaded from an .XYZ file -# created by PACKMOL. This must be done in advance. (See ../packmol_files/) -# -# The XYZ file was created by PACKMOL in 3 steps: -# (Add the proteins, then pack lipids in the inner & outer layers around them.) -# -# step1) Creae 120 proteins. Distribute them on the surface of the sphere. -# -# step2) Keeping the coordinates from step1 fixed, -# a) first we add 9500 DPPC lipids to the inner monolayer -# b) then we add 9500 DLPC lipids to the inner monolayer -# -# step3) Keeping the coordinates from steps 1 and 2 fixed, -# a) first we add 12500 DPPC lipids to the outer monolayer -# b) then we add 12500 DLPC lipids to the outer monolayer -# -# The order that molecules are created in moltemplate should match the order -# they appear in the final XYZ file created by PACKMOL. (See above.) -# Consequently I instantiate the molecules in the same order here: - - -# Step 1) ---- protein inclusions ---- - -proteins = new 4HelixInsideOut [120] - -# Step 2a) ---- inner monolayer ---- -dppc_in = new DPPC [9500] -# Step 2b) -dlpc_in = new DLPC [9500] - -# Step 3a) ---- outer monolayer ---- -dppc_out = new DPPC [12500] -# Step 3b) -dlpc_out = new DLPC [12500] - - - -# ------------------ boundary conditions -------------------- - -write_once("Data Boundary") { - -500.0 500.0 xlo xhi - -500.0 500.0 ylo yhi - -500.0 500.0 zlo zhi -} - - -# -------- interactions between protein and lipids ---------- - -# Note: All atom types must include the full path (the name of -# the namespace which defined them as well as the atom type name). -# (This is because we are no longer inside that namespace.) - - -write_once("In Settings") { - - # Interactions between the protein and lipid atoms are usually - # determined by mixing rules. However this is not possible some - # for atoms (such as the "int" atoms in the lipid model which - # interact using -1/r^2 attraction). Lorentz-Berthelot mixing - # rules do not make sense for these atoms so we must explicitly - # define their interaction with all other atoms. - - # i j pairstylename eps sig K L - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - - # We want the interactions between hydrophobic residues and atoms in - # the interior of the lipid to be energetically similar to the attractive - # interactions between hydrophobic residues. (See 1beadProtSci2010.) - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1 - - # All other interactions between proteins and lipids are steric. - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0 - - - # We also add an artificial attractive interaction between the - # turn residues of the protein and the lipid head groups in - # order to keep the protein upright. This might not be necessary - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - - # Add a weak attractive interaction between hydrophilic "sL" beads - # (Whose strength mimics the strength of interaction between tail beads - # in the lipid. This was absent from the original protein model. - # However without some kind of weak attraction between residues, - # the negative pressure in the interior of the bilayer membrane - # allways pulls the protein apart. Recall that in the membrane, - # the hydrophobic beads in the protein will face outwards towards the lipid - # tails leaving the hydrophilic amino acids of the protein in the interior. - # In reality, these polar groups form hydrogen bonds with each other.) - - pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 6.0 0.4 -1 - - # However these hydrophilic amino acids are not attracted to - # the bilayer interior. - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - -} - - - - -# Finally, we must combine the two force-field styles which were used for -# the coarse-grained lipid and protein. To do that, we write one last time -# to the "In Init" section. When reading the "Init" section LAMMPS will -# read these commands last and this will override any earlier settings. - -write_once("In Init") { - # -- These styles override earlier settings -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid cosine/delta harmonic - dihedral_style hybrid fourier - improper_style none - pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" -} - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat deleted file mode 100644 index b0d651d67f..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1139 +0,0 @@ -# Table for the INT-INT interaction from -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# This table contains -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) - -INT -N 1130 - -1 0.02 2.0331818401e+30 1.21990910406e+33 -2 0.04 4.9638228518e+26 1.48914685554e+29 -3 0.06 3.82579033251e+24 7.65158066501e+26 -4 0.08 1.21187081343e+23 1.81780622014e+25 -5 0.1 8.32791281704e+21 9.99349538045e+23 -6 0.12 9.34030842897e+20 9.34030842897e+22 -7 0.14 1.46892540453e+20 1.25907891817e+22 -8 0.16 2.95866897809e+19 2.21900173357e+21 -9 0.18 7.19889946863e+18 4.79926631242e+20 -10 0.2 2.0331818401e+18 1.21990910406e+20 -11 0.22 6.47834392264e+17 3.53364213962e+19 -12 0.24 2.28034873754e+17 1.14017436877e+19 -13 0.26 8.72681951932e+16 4.02776285507e+18 -14 0.28 3.58624366341e+16 1.53696157003e+18 -15 0.3 1.56704372019e+16 6.26817488078e+17 -16 0.32 7.2233129348e+15 2.70874235055e+17 -17 0.34 3.48970861422e+15 1.23166186384e+17 -18 0.36 1.75754381558e+15 5.85847938527e+16 -19 0.38 9.18613895646e+14 2.90088598625e+16 -20 0.4 4.96382285179e+14 1.48914685554e+16 -21 0.42 2.76404230108e+14 7.89726371739e+15 -22 0.44 1.58162693423e+14 4.31352800247e+15 -23 0.46 9.27773983256e+13 2.42027995633e+15 -24 0.48 5.56725765996e+13 1.391814415e+15 -25 0.5 3.41111308981e+13 8.18667141564e+14 -26 0.52 2.13057117167e+13 4.91670270393e+14 -27 0.54 1.35459994024e+13 3.0102220895e+14 -28 0.56 8.75547769351e+12 1.87617379153e+14 -29 0.58 5.74645813711e+12 1.18892237325e+14 -30 0.6 3.8257903322e+12 7.65158066491e+13 -31 0.62 2.58128463312e+12 4.99603477424e+13 -32 0.64 1.7635041342e+12 3.30657025205e+13 -33 0.66 1.21901470178e+12 2.21639036726e+13 -34 0.68 8.51979641904e+11 1.50349348607e+13 -35 0.7 6.0167184547e+11 1.0314374497e+13 -36 0.72 4.29087845387e+11 7.15146409276e+12 -37 0.74 3.08855637556e+11 5.00846980094e+12 -38 0.76 2.24270970425e+11 3.54112058818e+12 -39 0.78 1.64210505205e+11 2.52631546702e+12 -40 0.8 1.2118708117e+11 1.81780621971e+12 -41 0.82 90109367359.1 1.31867367068e+12 -42 0.84 67481501334.4 9.64021449503e+11 -43 0.86 50880896383.4 7.09965997788e+11 -44 0.88 38613938681.2 5.26553710913e+11 -45 0.9 29486692086.8 3.93155896009e+11 -46 0.92 22650731882.4 2.95444330322e+11 -47 0.94 17498544395.3 2.23385674464e+11 -48 0.96 13591937526.4 1.69899220331e+11 -49 0.98 10612635712.6 1.29950642555e+11 -50 1.0 8327912706.34 99934953582.6 -51 1.02 6566502316.69 77252969474.2 -52 1.04 5201589672.36 60018343356.8 -53 1.06 4138717434.11 46853405843.3 -54 1.08 3307128665.58 36745874940.0 -55 1.1 2653529579.27 28947596241.1 -56 1.12 2137567708.15 22902511945.9 -57 1.14 1728534024.3 18195095739.0 -58 1.16 1402943799.0 14513212422.1 -59 1.18 1142752163.37 11621209113.9 -60 1.2 934030766.093 9340308300.6 -61 1.22 765981286.774 7534242773.65 -62 1.24 630196371.787 6098675145.29 -63 1.26 520103253.414 4953364870.6 -64 1.28 430542934.103 4036340534.04 -65 1.3 357450462.101 3299543229.91 -66 1.32 297610947.802 2705554551.18 -67 1.34 248472587.186 2225128105.44 -68 1.36 208002782.573 1835319108.76 -69 1.38 174576985.011 1518061159.35 -70 1.4 146892484.084 1259078837.33 -71 1.42 123901294.937 1047053582.16 -72 1.44 104757721.536 872981382.419 -73 1.46 88777241.639 729676313.267 -74 1.48 75404158.02 611385405.387 -75 1.5 64186061.7033 513488820.507 -76 1.52 54753607.1486 432265633.695 -77 1.54 46804443.7318 364710253.134 -78 1.56 40090410.0598 308388060.159 -79 1.58 34407297.9713 261321529.95 -80 1.6 29586646.6744 221900119.2 -81 1.62 25489145.661 188808745.634 -82 1.64 21999316.2868 160970856.824 -83 1.66 19021212.5921 137502982.517 -84 1.68 16474936.8715 117678352.86 -85 1.7 14293808.3245 100897694.735 -86 1.72 12422056.6082 86665727.6626 -87 1.74 10812938.3788 74572197.8496 -88 1.76 9427195.57103 64276535.39 -89 1.78 8231790.46096 55495411.7777 -90 1.8 7198865.45512 47992625.088 -91 1.82 6304885.77339 41570857.9644 -92 1.84 5529931.32911 36064946.1544 -93 1.86 4857110.59557 31336368.341 -94 1.88 4272074.43377 27268725.7382 -95 1.9 3762612.01167 23764025.6584 -96 1.92 3318314.28383 20739619.609 -97 1.94 2930293.18879 18125675.4316 -98 1.96 2590946.89128 15863086.114 -99 1.98 2293763.15199 13901736.4186 -100 2.0 2033154.33079 12199063.3122 -101 2.02 1804318.68586 10718858.1296 -102 2.04 1603123.57305 9430268.02169 -103 2.06 1426006.91783 8306962.01537 -104 2.08 1269893.96121 7326433.30293 -105 2.1 1132126.79514 6469414.48445 -106 2.12 1010404.62602 5719386.63441 -107 2.14 902733.052344 5062166.44376 -108 2.16 807380.928986 4485558.44681 -109 2.18 722843.627253 3979061.59742 -110 2.2 647811.695319 3533621.30686 -111 2.22 581144.085827 3141419.57242 -112 2.24 521845.251959 2795697.07302 -113 2.26 469045.525153 2490602.13576 -114 2.28 421984.280794 2221062.32522 -115 2.3 379995.475978 1982675.10836 -116 2.32 342495.208369 1771614.62868 -117 2.34 308970.999537 1584552.10475 -118 2.36 278972.551763 1418587.76828 -119 2.38 252103.765513 1271192.59046 -120 2.4 228015.837009 1140158.32224 -121 2.42 206401.282366 1023554.60663 -122 2.44 186988.75765 919692.114521 -123 2.46 169538.563484 827090.818108 -124 2.48 153838.739168 744452.651831 -125 2.5 139701.665073 670637.92543 -126 2.52 126961.103835 604644.949624 -127 2.54 115469.620781 545592.416037 -128 2.56 105096.332511 492704.141327 -129 2.58 95724.9397832 445295.843157 -130 2.6 87252.0069441 402763.664479 -131 2.62 79585.4554502 364574.203947 -132 2.64 72643.2434671 330255.845328 -133 2.66 66352.2073932 299391.208536 -134 2.68 60647.0444312 271610.570248 -135 2.7 55469.4181565 246586.123584 -136 2.72 50767.1714483 224026.964698 -137 2.74 46493.633237 203674.709811 -138 2.76 42607.0073083 185299.659567 -139 2.78 39069.8329526 168697.439095 -140 2.8 35848.5085794 153686.051901 -141 2.82 32912.8705664 140103.294183 -142 2.84 30235.8206098 127804.483324 -143 2.86 27792.9956998 116660.460548 -144 2.88 25562.4755962 106555.833042 -145 2.9 23524.5233195 97387.4254387 -146 2.92 21661.3547409 89062.9145204 -147 2.94 19956.9338374 81499.6244039 -148 2.96 18396.7906059 74623.4624292 -149 2.98 16967.8589974 68367.9785194 -150 3.0 15658.3325568 62673.5329856 -151 3.02 14457.5357325 57486.5596649 -152 3.04 13355.809067 52758.912937 -153 3.06 12344.4066925 48447.2886046 -154 3.08 11415.4047444 44512.7098736 -155 3.1 10561.6194689 40920.0707567 -156 3.12 9776.5339459 37637.7301715 -157 3.14 9054.23247117 34637.1508274 -158 3.16 8389.34175838 31892.5777179 -159 3.18 7776.97821258 29380.7516608 -160 3.2 7212.7006167 27080.6538766 -161 3.22 6692.4676457 24973.2780793 -162 3.24 6212.59969004 23041.4269669 -163 3.26 5769.74452856 21269.5303734 -164 3.28 5360.84644195 19643.4826615 -165 3.3 4983.1184041 18150.4972204 -166 3.32 4634.01702836 16778.97618 -167 3.34 4311.21998136 15518.393672 -168 3.36 4012.60560869 14359.191159 -169 3.38 3736.23454428 13292.6835236 -170 3.4 3480.33310029 12310.9747549 -171 3.42 3243.27825585 11406.8822043 -172 3.44 3023.58408279 10573.8684961 -173 3.46 2819.88946345 9805.98028003 -174 3.48 2630.94697101 9097.79310596 -175 3.5 2455.61279669 8444.36177626 -176 3.52 2292.83761972 7841.17560602 -177 3.54 2141.65832756 7284.11808108 -178 3.56 2001.19050257 6769.43046025 -179 3.58 1870.62160083 6293.67891689 -180 3.6 1749.20475558 5853.72485855 -181 3.62 1636.25314534 5446.69810179 -182 3.64 1531.13487237 5069.97261409 -183 3.66 1433.26830277 4721.1445646 -184 3.68 1342.11782445 4398.01245332 -185 3.7 1257.18998347 4098.55911171 -186 3.72 1178.02996319 3820.93539003 -187 3.74 1104.21837425 3563.44536511 -188 3.76 1035.36832639 3324.53291993 -189 3.78 971.122756088 3102.76956138 -190 3.8 911.151986554 2896.84335615 -191 3.82 855.151498616 2705.54887715 -192 3.84 802.83989347 2527.77806329 -193 3.86 753.957029799 2362.51190574 -194 3.88 708.262319576 2208.81288195 -195 3.9 665.533168297 2065.81806693 -196 3.92 625.563546756 1932.73285812 -197 3.94 588.162682667 1808.82525631 -198 3.96 553.153861545 1693.42065104 -199 3.98 520.373327227 1585.89706361 -200 4.0 489.669273313 1485.68080556 -201 4.02 460.900917596 1392.24251449 -202 4.04 433.937652306 1305.09353282 -203 4.06 408.6582636 1223.78259822 -204 4.08 384.950214367 1147.89281764 -205 4.1 362.708984933 1077.03889938 -206 4.12 341.837466738 1010.86461999 -207 4.14 322.245404503 949.040505266 -208 4.16 303.848882793 891.261706073 -209 4.18 286.569853265 837.246052066 -210 4.2 270.33569919 786.732267446 -211 4.22 255.078834164 739.47833469 -212 4.24 240.736332164 695.259993326 -213 4.26 227.249586386 653.869362042 -214 4.28 214.563994495 615.113673492 -215 4.3 202.628668126 578.814112106 -216 4.32 191.396164684 544.804746089 -217 4.34 180.822239621 512.931545605 -218 4.36 170.865617553 483.051479815 -219 4.38 161.487780703 455.031686127 -220 4.4 152.652773286 428.748705595 -221 4.42 144.327020575 404.087778912 -222 4.44 136.479161479 380.942197972 -223 4.46 129.07989358 359.212708377 -224 4.48 122.101829632 338.806958688 -225 4.5 115.519364658 319.638992577 -226 4.52 109.308552789 301.628780369 -227 4.54 103.446993117 284.701786758 -228 4.56 97.9137238447 268.788571763 -229 4.58 92.6891241175 253.824422244 -230 4.6 87.7548229339 239.749011508 -231 4.62 83.0936146036 226.506084761 -232 4.64 78.6893802546 214.043168343 -233 4.66 74.5270149351 202.31130085 -234 4.68 70.5923598871 191.264784422 -235 4.7 66.8721396072 180.860954593 -236 4.72 63.353903336 171.05996726 -237 4.74 60.0259706488 161.824601429 -238 4.76 56.8773808439 153.120076496 -239 4.78 53.8978458491 144.913882966 -240 4.8 51.0777063884 137.175625538 -241 4.82 48.4078911713 129.876877635 -242 4.84 45.8798788842 122.991046476 -243 4.86 43.485662782 116.493247913 -244 4.88 41.2177176913 110.360190267 -245 4.9 39.0689692529 104.570066494 -246 4.92 37.0327652428 99.1024540566 -247 4.94 35.102848823 93.9382219092 -248 4.96 33.2733335874 89.05944408 -249 4.98 31.5386802724 84.4493193479 -250 5.0 29.8936750183 80.0920965658 -251 5.02 28.3334090704 75.9730052143 -252 5.04 26.8532598202 72.0781907976 -253 5.06 25.4488730938 68.3946547294 -254 5.08 24.116146599 64.9101983786 -255 5.1 22.8512144543 61.6133709734 -256 5.12 21.650432722 58.4934210835 -257 5.14 20.5103658787 55.5402514226 -258 5.16 19.4277741591 52.7443767307 -259 5.18 18.3996017121 50.0968845179 -260 5.2 17.4229655155 47.5893984632 -261 5.22 16.4951449988 45.2140442802 -262 5.24 15.6135723236 42.9634178757 -263 5.26 14.775823281 40.8305556374 -264 5.28 13.979608762 38.808906703 -265 5.3 13.2227667648 36.8923070701 -266 5.32 12.5032549016 35.0749554196 -267 5.34 11.8191433738 33.3513905323 -268 5.36 11.1686083831 31.7164701895 -269 5.38 10.5499259512 30.1653514539 -270 5.4 9.96146612005 28.693472236 -271 5.42 9.40168750976 27.2965340593 -272 5.44 8.86913220892 25.9704859397 -273 5.46 8.36242097742 24.7115093061 -274 5.48 7.88024874079 23.5160038893 -275 5.5 7.4213803577 22.3805745153 -276 5.52 6.98464664308 21.3020187412 -277 5.54 6.56894063048 20.2773152771 -278 5.56 6.1732140587 19.3036131423 -279 5.58 5.79647406826 18.3782215059 -280 5.6 5.43778009463 17.4986001669 -281 5.62 5.09624094585 16.6623506308 -282 5.64 4.77101205293 15.867207745 -283 5.66 4.46129288233 15.1110318537 -284 5.68 4.16632450031 14.3918014404 -285 5.7 3.88538727999 13.7076062261 -286 5.72 3.61779874199 13.0566406912 -287 5.74 3.36291152072 12.4371979973 -288 5.76 3.12011144838 11.8476642796 -289 5.78 2.8888157497 11.2865132882 -290 5.8 2.66847134042 10.7523013555 -291 5.82 2.45855322349 10.2436626676 -292 5.84 2.25856297681 9.7593048226 -293 5.86 2.06802732724 9.2980046552 -294 5.88 1.88649680546 8.85860431242 -295 5.9 1.71354447704 8.44000756375 -296 5.92 1.548764745 8.04117633127 -297 5.94 1.39177221978 7.66112742597 -298 5.96 1.24220065245 7.29892947717 -299 5.98 1.09970192753 6.9537000433 -300 6.0 0.963945111861 6.62460289254 -301 6.02 0.83461555631 6.31084544295 -302 6.04 0.711414047074 6.01167635216 -303 6.06 0.594056003831 5.72638324756 -304 6.08 0.482270721937 5.45429058822 -305 6.1 0.375800656137 5.19475765055 -306 6.12 0.274400743381 4.94717663025 -307 6.14 0.177837762511 4.71097085338 -308 6.16 0.0858897286772 4.48559308998 -309 6.18 -0.00165467948361 4.27052396409 -310 6.2 -0.0849966617872 4.06527045435 -311 6.22 -0.164327809314 3.8693644797 -312 6.24 -0.239830589745 3.68236156522 -313 6.26 -0.311678806773 3.50383958321 -314 6.28 -0.380038035049 3.33339756513 -315 6.3 -0.445066032049 3.17065458013 -316 6.32 -0.506913128135 3.0152486763 -317 6.34 -0.56572259604 2.866835881 -318 6.36 -0.621631000928 2.72508925658 -319 6.38 -0.674768532081 2.58969800863 -320 6.4 -0.725259317268 2.46036664323 -321 6.42 -0.773221720709 2.33681417085 -322 6.44 -0.818768625574 2.21877335375 -323 6.46 -0.862007701832 2.10598999469 -324 6.48 -0.90304166028 1.99822226439 -325 6.5 -0.941968493479 1.8952400656 -326 6.52 -0.978881704324 1.79682443166 -327 6.54 -1.01387052292 1.70276695755 -328 6.56 -1.04702011237 1.61286926168 -329 6.58 -1.07841176412 1.52694247655 -330 6.6 -1.10812308336 1.44480676668 -331 6.62 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-0.00394740685922 -0.0200029372512 -1116 22.32 -0.00354788564052 -0.0199492167196 -1117 22.34 -0.0031494369093 -0.0198956883597 -1118 22.36 -0.00275205683071 -0.0198423513132 -1119 22.38 -0.00235574158704 -0.0197892047262 -1120 22.4 -0.00196048737759 -0.0197362477497 -1121 22.42 -0.00156629041861 -0.0196834795391 -1122 22.44 -0.00117314694319 -0.0196308992543 -1123 22.46 -0.000781053201174 -0.0195785060596 -1124 22.48 -0.000390005459079 -0.019526299124 -1125 22.5 0.0 -0.0194742776206 -1126 22.52 0.0 0.0 -1127 22.54 0.0 0.0 -1128 22.56 0.0 0.0 -1129 22.58 0.0 0.0 -1130 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh deleted file mode 100755 index ade4281035..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh +++ /dev/null @@ -1,33 +0,0 @@ -# Here we generate the starting coordinates of the simulation -# using PACKMOL. - - - -# You must run each packmol commend one after the other. -# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding -# "inp" file. This should not happen. You can also usually interrupt -# packmol after 30 minutes, and the solution at that point (an .xyz file) -# should be good enough for use. -packmol < step1_proteins.inp # This step determines the protein's location - # It takes ~20 minutes (on an intel i7) -packmol < step2_innerlayer.inp # this step builds the inner monolayer - # It takes ~90 minutes -packmol < step3_outerlayer.inp # this step builds the outer monolayer - # It takes ~4 hours - - -# NOTE: PLEASE USE "packmol", NOT "ppackmol". ("ppackmol" is the -# parallel-version of packmol using OpemMP. This example has NOT been -# tested with "ppackmol". Our impression was that the "ppackmol" -# version is more likely to get stuck in an infinite loop. -Andrew 2015-8) - - -# Step3 creates a file named "step3_outerlayer.xyz" containing the coordinates -# in all the atoms of all the molecules. Later we will run moltemplate.sh -# using the "-xyz ../system.xyz" command line argument. That will instruct -# moltemplate to look for a file named "system.xyz" in the parent directory. -# So I rename the "step3_outerlayer.xyz" file to "system.xyz", and move it -# to this directory so that later moltemplate.sh can find it. - -mv -f step3_outerlayer.xyz ../system.xyz - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp deleted file mode 100644 index abb48db7d6..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step1_proteins.inp +++ /dev/null @@ -1,49 +0,0 @@ -# Step 1: Create a sphere of proteins lying -# (In step 2 we will pack lipids around these proteins -# -# ----- Run using: ----- -# packmol < step1_proteins.inp -# (This takes about 30 minutes on an Intel i7 processor) - - -# ----- Settings: ----- - -# All the atoms from diferent proteins will be at least 50.0 Angstrons apart. -tolerance 50.0 -# (Setting "discale" to 2.0 increases the typical separation -# distance to approximately 2.0*50.0 = 100.0 Angstroms.) -discale 2.0 -# The other parameters below are optional: -nloop 10000 -maxit 20 -seed 12345 -sidemax 3000.0 -# What fraction of the molecules are moved during "large moves"? (default 0.05) -movefrac 0.05 - - -# The output file name - -output step1_proteins.xyz - - -# File types are in xyz format - -filetype xyz - - - -# First, specify the protein inclusions -# We will pack the lipids around these later - -structure protein.xyz - number 120 - atoms 68 69 70 - inside sphere 0. 0. 0. 273.75 - end atoms - atoms 65 66 67 71 72 73 - outside sphere 0. 0. 0. 325.0 - end atoms -end structure - - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp deleted file mode 100644 index 9f61960f2e..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step2_innerlayer.inp +++ /dev/null @@ -1,70 +0,0 @@ -# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE - -# Step 2: Pack the lipids in the inner monolayer around the proteins from step1. -# -# ----- Run using: ----- -# packmol < step2_innerlayer.inp -# (This takes about 90 minutes on an Intel i7 processor) - - -# ----- Settings: ----- - -# All the atoms from diferent molecules will be at least 5.5 Angstrons apart -tolerance 5.5 -# (Setting "discale" to 1.4 increases the typical separation -# distance to approximately 1.4*5.5 = 7.7 Angstroms.) -discale 1.4 -# The other parameters below are optional: -nloop 10000 -maxit 20 -seed 12345 -sidemax 3000.0 -# What fraction of the molecules are moved during "large moves"? (default 0.05) -movefrac 0.05 - - -# The output file name - -output step2_innerlayer.xyz - -# File types are in xyz format - -filetype xyz - - -# The proteins whose position we determined earlier in step 1 -# will be frozen in place during this step. - -structure step1_proteins.xyz - number 1 - fixed 0. 0. 0. 0. 0. 0. -end structure - - -# 9500 DPPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards. - - -structure DPPC.xyz - number 9500 - atoms 1 - inside sphere 0. 0. 0. 270.0 - end atoms - atoms 5 - outside sphere 0. 0. 0. 295.0 - end atoms -end structure - -# 9500 DLPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards. - -structure DLPC.xyz - number 9500 - atoms 1 - inside sphere 0. 0. 0. 273.0 - end atoms - atoms 4 - outside sphere 0. 0. 0. 295.0 - end atoms -end structure - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp deleted file mode 100644 index bed1c04246..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/packmol_files/step3_outerlayer.inp +++ /dev/null @@ -1,70 +0,0 @@ -# NOTE: YOU MUST COMPLETE STEPS 1 AND 2 BEFORE RUNNING PACKMOL ON THIS FILE - -# Step 3: Pack the lipids in the outer monolayer around the proteins from step1. -# -# ----- Run using: ----- -# packmol < step3_outerlayer.inp -# (This takes about 4 hours on an Intel i7 processor) - - -# ----- Settings: ----- - -# All the atoms from diferent molecules will be at least 5.5 Angstrons apart -tolerance 5.5 -# (Setting "discale" to 1.4 increases the typical separation -# distance to approximately 1.4*5.5 = 7.7 Angstroms.) -discale 1.4 -# The other parameters below are optional: -nloop 10000 -maxit 20 -seed 12345 -sidemax 3000.0 -# What fraction of the molecules are moved during "large moves"? (default 0.05) -movefrac 0.05 - - -# The output file name - -output step3_outerlayer.xyz - -# File types are in xyz format - -filetype xyz - - -# The proteins and lipids whose position we determined earlier in steps 1-2 -# will be frozen in place during this step. - -structure step2_innerlayer.xyz - number 1 - fixed 0. 0. 0. 0. 0. 0. -end structure - - -# 12500 DPPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing outwards, and their tails (atom 5) pointing inwards. - - -structure DPPC.xyz - number 12500 - atoms 5 - inside sphere 0. 0. 0. 310.0 - end atoms - atoms 1 - outside sphere 0. 0. 0. 336.0 - end atoms -end structure - -# 12500 DLPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing outwards, and their tails (atom 4) pointing inwards. - -structure DLPC.xyz - number 12500 - atoms 4 - inside sphere 0. 0. 0. 313.0 - end atoms - atoms 1 - outside sphere 0. 0. 0. 332.0 - end atoms -end structure - diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.min deleted file mode 100644 index 25ed25ad77..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.min +++ /dev/null @@ -1,50 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. - - - -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 250 traj_min.lammpstrj id mol type x y z ix iy iz - -# minimize - -#balance 1.3 rcb - -min_style quickmin -min_modify dmax 0.1 -minimize 1.0e-5 1.0e-7 5000 20000 - -# If minimization crashes, then instead try Langevin dynamics -# with a small timestep and a fast damping parameter. For example: -# -# timestep 0.05 -# fix fxlan all langevin 300.0 300.0 100.0 48279 -# fix fxnve all nve -# -# run 10000 - -write_data system_after_min.data diff --git a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.nvt b/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.nvt deleted file mode 100644 index dee8526a01..0000000000 --- a/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/run.in.nvt +++ /dev/null @@ -1,66 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# 6) Minimize the system using: -# lmp_mpi -i run.in.npt -# (assuming "lmp_mpi" is the name of the lammps binary you created in step 5) -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. -# -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -# Commenting out: -# -# read_data system.data -# -# Instead read the data file created by "run.in.min". - -read_data system_after_min.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# Just in case the previous minimization failed, try again. -# (I don't know why this helps, but sometimes it does. Magic.) - -minimize 1.0e-5 1.0e-7 5000 20000 - -# Run main simulation - -timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 100 # time interval for printing out "thermo" data - - - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. -# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. - -run 1000000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.txt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.txt deleted file mode 100644 index 83a733e1f9..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.txt +++ /dev/null @@ -1,83 +0,0 @@ -########################################################### -# Interaction of a carbon nanotube with a pair of "mystery -# molecules" (extracted from the cnat-cnt.data/in files). -########################################################### -# Author: Aysun Itai and Andrew Jewett - -This example uses "ltemplify.py" to create molecule templates out -of two different molecules in a pre-existing LAMMPS IN/DATA file. -Then I show how to use "moltemplate.sh" to make copies of these -molecules and to move and rotate them (creating new LAMMPS IN/DATA files). - - Disclaimer: -The molecules in this example are not physically realistic. -The purpose of this example is to demonstrate ltemplify usage. - - REQUIRED INPUT FILES - -cnad-cnt.data cnad-cnt.in system.lt - - cnad-cnt.data - This is a LAMMPS data file containing the coordinates and the topology - for a system combining the two molecules together. ltemplify will extract - molecules from this file, one at a time. - - cnad-cnt.in - This file contains force-field parameters and old run settings for the system. - (We ignore the run settings in this file.) The force-field parameters in - the "cnad-cnt.in" file are only necessary because we are going to build - a completely new set of simulation input files. (We are not only going to - rotate them and duplicate the molecules.) ltemplify.py will extract the - force field parameters from this file. This approach allows us to combine - these molecules with other types of molecules later on.) - - system.lt - The "system.lt" contains the instructions what we will do with these molecules - after ltemplify.py has converted them into .LT format. In this example - it contains instructions for rotating and copying the two molecules, - (It also defines the periodic boundary conditions.) - - OUTPUT FILES - -cnad.lt -cnt.lt - -These files are referenced in system.lt. -Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt") -creates new LAMMPS data and input files: -system.data, system.in, system.in.init, system.in.settings -(These files are referenced in run.in.nvt.) - -You can run a simulation from the files created by moltemplate using - -lmp_linux -i run.in.nvt - -NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY - ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED. - (This was done to protect the original source of the files.) - The goal of this example is only to demonstrate how to use - "ltemplify.py" to convert lammps input and data files into - LT format and back again.) - - ----------- - -Instructions: -Run the commands (follow the instructions) in these files: - -step 1) -README_step1_run_ltemplify.sh - -and then - -step 2) -README_step2_run_moltemplate.sh - -step 3) OPTIONAL - -To run a short LAMMPS simulation, you can use the "in.nvt" file, for example: - -$LAMMPS_BINARY -i run.in.nvt - -where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...). - ----------- diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh deleted file mode 100755 index 4bb42d7ea6..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step1_run_ltemplify.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/sh - -# Aysun Itai's LAMMPS files contain two molecules: - -# The CNAD molecule has molecule-id 1 - -ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt - -# The CNT (carbon nanotube) corresponds to molecule-id 2 -ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt - -# This will extract both molecules and save them as separate .LT files. -# (We can include these files later when preparing new simulations.) diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh deleted file mode 100755 index c236489936..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step2_run_moltemplate.sh +++ /dev/null @@ -1,22 +0,0 @@ -# --- Running Moltemplate --- -# -- Prerequisites: -- -# The "system.lt" moltemplate file links to other ".lt" files -# files you hopefully have created earlier when you ran "ltemplify.py: -# cnad.lt and cnt.lt -# If not, carry out the instructions in "README_run_ltemplify.sh". - -moltemplate.sh system.lt - -# (Note: If you have VMD installed, try this instead:) -# moltemplate.sh system.lt -vmd - - -# Moltemplate will generate various files with names ending in *.in* and *.data. -# These files are the input files directly read by LAMMPS. - -# Optional: -# The "./output_ttree/" directory is full of temporary files generated by -# moltemplate. They can be useful for debugging, but are usually thrown away. - -rm -rf output_ttree/ - diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh deleted file mode 100755 index 6a3f57fac5..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_step3_run_lammps.sh +++ /dev/null @@ -1,16 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" LAMMPS input script links to the input -# scripts and data files you hopefully have created earlier -# with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_run_moltemplate.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps this way: - -lmp_mpi -i run.in.nvt - -# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY -# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY. diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt deleted file mode 100644 index 82315d2bde..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt +++ /dev/null @@ -1,50 +0,0 @@ - - ------- To view the trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - - -Later, to Load a trajectory in VMD: - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it - ------ Wrap the coordinates to the unit cell - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Enter: - - DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. - LOOKUP "pbctools" FOR DETAILS. - - pbc wrap -compound res -all - pbc box - -3) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data deleted file mode 100644 index 1f18ff4aef..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data +++ /dev/null @@ -1,1157 +0,0 @@ -Created by Aysun Itai and modified by Andrew Jewett -NOTE: This file has been extensively modified. -Only the bond connectivity and atomic positions are accurate. - - 101 atoms - 134 bonds - 252 angles - 457 dihedrals - 0 impropers - - 16 atom types - 24 bond types - 50 angle types - 78 dihedral types - 0 improper types - - 0 50 xlo xhi - 0 50 ylo yhi - 0 50 zlo zhi - -Masses - - 1 10.0 - 2 10.0 # atom type names often appear - 3 10.0 # in the comments follwing - 4 10.0 # each line in the Masses section - 5 10.0 - 6 10.0 - 7 10.0 - 8 10.0 - 9 10.0 - 10 10.0 - 11 10.0 - 12 10.0 - 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12.031 11.173 10.709 -28 2 1 0.000000 11.173 12.031 11.418 -29 2 1 0.000000 11.173 12.031 8.582 -30 2 1 0.000000 10.000 12.345 9.291 -31 2 1 0.000000 10.000 12.345 10.709 -32 2 1 0.000000 8.827 12.031 11.418 -33 2 1 0.000000 8.827 12.031 8.582 -34 2 1 0.000000 7.969 11.173 9.291 -35 2 1 0.000000 7.969 11.173 10.709 -36 2 1 0.000000 7.655 10.000 11.418 -37 2 1 0.000000 7.655 10.000 8.582 -38 2 1 0.000000 7.969 8.827 9.291 -39 2 1 0.000000 7.969 8.827 10.709 -40 2 1 0.000000 8.827 7.969 11.418 -41 2 1 0.000000 8.827 7.969 8.582 -42 2 1 0.000000 10.000 7.655 9.291 -43 2 1 0.000000 10.000 7.655 10.709 -44 2 1 0.000000 11.173 7.969 11.418 -45 2 1 0.000000 11.173 7.969 8.582 -46 2 1 0.000000 12.031 8.827 9.291 -47 2 1 0.000000 12.031 8.827 10.709 -48 2 1 0.000000 12.345 10.000 11.418 -49 2 1 0.000000 12.345 10.000 12.836 -50 2 1 0.000000 12.031 11.173 13.545 -51 2 1 0.000000 12.031 11.173 14.963 -52 2 1 0.000000 11.173 12.031 15.672 -53 2 1 0.000000 11.173 12.031 12.836 -54 2 1 0.000000 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86 -420 69 82 81 83 84 -421 69 82 81 83 85 -422 65 83 86 76 92 -423 59 83 81 86 87 -424 54 84 83 81 86 -425 73 84 83 86 87 -426 54 85 83 81 86 -427 73 85 83 86 87 -428 23 86 76 92 97 -429 9 86 76 92 90 -430 72 87 86 76 92 -431 17 88 98 99 100 -432 17 88 98 99 101 -433 12 88 98 93 94 -434 7 88 97 92 90 -435 14 88 97 96 94 -436 29 88 89 90 92 -437 28 88 89 90 91 -438 22 89 90 92 97 -439 75 89 88 98 99 -440 77 89 88 98 93 -441 76 89 88 97 92 -442 78 89 88 97 96 -443 8 90 92 97 96 -444 4 90 89 88 98 -445 16 90 89 88 97 -446 21 91 90 92 97 -447 15 92 97 96 94 -448 2 92 97 88 98 -449 66 93 98 99 100 -450 66 93 98 99 101 -451 19 93 98 88 97 -452 27 93 94 96 97 -453 13 94 93 98 99 -454 5 95 94 93 98 -455 26 95 94 96 97 -456 3 96 97 88 98 -457 6 96 94 93 98 diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in deleted file mode 100644 index 1f403e2bd0..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in +++ /dev/null @@ -1,49 +0,0 @@ -#Created by Aysun Itai and modified by Andrew Jewett -# NOTE: This file has been extensively modified. -# Only the bond connectivity and atomic positions are accurate. - -units real - -neigh_modify delay 2 every 1 - -atom_style full -bond_style harmonic -angle_style charmm -dihedral_style charmm -pair_style lj/charmm/coul/charmm 8.0 10.0 -pair_modify mix arithmetic - -read_data cnad-cnt.data - -pair_coeff 1 1 0.02 4.0 -pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically -pair_coeff 3 3 0.02 2.0 # in this version of the file. -pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed) -pair_coeff 5 5 0.02 2.0 -pair_coeff 6 6 0.02 3.0 -pair_coeff 7 7 0.02 3.0 -pair_coeff 8 8 0.02 3.0 -pair_coeff 9 9 0.02 4.0 -pair_coeff 10 10 0.02 4.0 -pair_coeff 11 11 0.02 4.0 -pair_coeff 12 12 0.02 4.0 -pair_coeff 13 13 0.02 3.0 -pair_coeff 14 14 0.02 3.0 -pair_coeff 15 15 0.02 3.0 -pair_coeff 16 16 0.02 3.0 - -group cnt type 1 -group cnad type 2:16 - -displace_atoms cnad move 0 -7 0 units box -special_bonds charmm - -velocity all create 0.0 54321 dist uniform - -thermo 1 -thermo_style multi -timestep 0.005 - -dump 1 all atom 10 cnad-cnt.dump - -run 20000 diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg deleted file mode 100644 index 3b79b405ef..0000000000 Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg deleted file mode 100644 index 1f46c1b7b2..0000000000 Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg deleted file mode 100644 index 628371b0d7..0000000000 Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg deleted file mode 100644 index 3489773adb..0000000000 Binary files a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt deleted file mode 100644 index abaa3a2254..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -########################################################### -# Interaction of a carbon nanotube with a pair of mystery -# molecules (extracted from the cnat-cnt.data/in files). -########################################################### -# -# define the system being simulated: - -# -- init section -- -include system.in.init - -# -- atom definition section -- - -read_data system.data - -# -- settings section -- - -include system.in.settings - -# -- run section -- - - -timestep 0.05 -dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking -# dynamics in dilute systems with few atoms (such as this one). -# Commenting this next line out: - -# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - -# Alternately, I receive fewer questions if I use langevin/nve instead: -fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5 -fix fxnve all nve - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data -#thermo_modify flush yes - -#restart 1000000 restart_nvt - -run 500000 - -write_data system_after_nvt.data - - diff --git a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt deleted file mode 100644 index 70fdb7548b..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt +++ /dev/null @@ -1,29 +0,0 @@ -#Define the CNT and CNAD molecules, by including the files which define them -import cnt.lt -import cnad.lt - -# The cnt's center was originally at position 10,10,10, -# so I moved it back to the origin -cnt = new CNT.move(-10,-10,-10) - -# Rotation around the center of mass does not work (yet), -# so instead you have to move the molecule to the origin, -# rotate it, and move it back to where you want it. -# That's why the next line contains move().rot().move() -# I'll add center-of-mass rotation as a later feature. - -cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0) -cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0) - - -# You can leave the periodic boundary conditions unspecified -# and change them later, OR you can declare them -# using the "write_once("Data Boundary") {}" command: - -write_once("Data Boundary") -{ - 0 50.0 xlo xhi - 0 50.0 ylo yhi - 0 50.0 zlo zhi -} - diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.txt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.txt deleted file mode 100644 index d27267f365..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.txt +++ /dev/null @@ -1,10 +0,0 @@ -This is a simple system of 260 water molecules. - -In this example, the coordinates of the atoms are read from a PDB file -instead of being specified manually (as well as the boundary information). - -The PDB file was generated by the useful "solvate" utility which comes with VMD. -(To generate this file yourself, run VMD, click on the "Extensions" menu, -and select Modeling-->Add Solvation Box. -In this example, I made a box whose x,y,z dimensions were 16,24,24.) - diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh deleted file mode 100755 index 6072277b54..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_mpi" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_mpi -i run.in.npt # minimization and simulation at constant pressure -lmp_mpi -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_mpi -i run.in.npt -#mpirun -np 4 lmp_mpi -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh deleted file mode 100755 index bdd22c1487..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh +++ /dev/null @@ -1,32 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - -cd moltemplate_files/ # (The .lt input files are in this directory) - - moltemplate.sh -pdb solvate.pdb system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - -# -#This will prepare LAMMPS input files for a box of water -#(In this example, we are using the "SPC/E" water model.) -#The number of water molecules in the "wat = new SPCE [260]" command -#must equal the number of water molecules in the PDB file. -# -#Coordinates and boundary-box information is read from the .pdb file. -# -#You can also specify this information directly in the ttree file. -#See the comments section in "system.lt" for details. -# diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt deleted file mode 100644 index 5f9b27e5bf..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt +++ /dev/null @@ -1,64 +0,0 @@ - ------- Instructions to view a trajectory in VMD -------- - - ------- Disclaimer ------- - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - - (Note, at this point the image shown in the VMD graphics window may - not appear correct or incomplete. The coordinates of the atoms may - overlap if you asked moltemplate.sh to load your coordinates from - a PDB or XYZ file. - However, later after you have run a simulation, the trajectories - should appear reasonably correct when you load them in VMD using - the PSF file you just generated.) - - -Later, to Load a trajectory in VMD: - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it - ------ Wrap the coordinates to the unit cell - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Enter: - - DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. - LOOKUP "pbctools" FOR DETAILS. - - pbc wrap -compound res -all - pbc box - - # If you have a solute of type 1, then use this: - #pbc wrap -sel type=1 -all -centersel type=2 -center com - -"1" corresponds to the "O" atom type -"2" corresponds to the "H" atom type - -3) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types: - -sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf - -(If you do this, I guess that you might have to use - "type=O" and "type=H" in step 2 above.) diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/.0 deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh deleted file mode 100755 index 36505562fe..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh +++ /dev/null @@ -1,11 +0,0 @@ - -# Run moltemplate this way: - -moltemplate.sh -pdb solvate.pdb system.lt - - -# The PDB file was generated by the "solvate" utility which comes with VMD. -# (To generate this file yourself, run VMD, click on the "Extensions" menu, -# and select Modeling-->Add Solvation Box. -# In this example, I made a box whose x,y,z dimensions were 16,24,24.) - diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb deleted file mode 100644 index 0ed5103cbb..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb +++ /dev/null @@ -1,782 +0,0 @@ -CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1 -ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O -ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H -ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H -ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O -ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H -ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H -ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O -ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H -ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H -ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O -ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H -ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H -ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O -ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H -ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H -ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O -ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H -ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H -ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O -ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H -ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H -ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O -ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H -ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H -ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O -ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H -ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H -ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O -ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H -ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H -ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O -ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H -ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H -ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O -ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H -ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H -ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O -ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H -ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H -ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O -ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H -ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H -ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O -ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H -ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H -ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O -ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H -ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H -ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O -ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H -ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H -ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O -ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H -ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H -ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O -ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H -ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H -ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O -ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H -ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H -ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O -ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H -ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H -ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O -ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H -ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H -ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O -ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H -ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H -ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O -ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H -ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H -ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O -ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H -ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H -ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O -ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H -ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H -ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O -ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H -ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H -ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O -ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H -ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H -ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O -ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H -ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H -ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O -ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H -ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H -ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O -ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H -ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H -ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O -ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H -ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H -ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O -ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H -ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H -ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O -ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H -ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H -ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O -ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H -ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H -ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O -ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H -ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H -ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O -ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H -ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H -ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O -ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H -ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H -ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O -ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H -ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H -ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O -ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H -ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H -ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O -ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H -ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H -ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O -ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H -ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H -ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O -ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H -ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H -ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O -ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H -ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H -ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O -ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H -ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H -ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O -ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H -ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H -ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O -ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H -ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H -ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O -ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H -ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H -ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O -ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H -ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H -ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O -ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H -ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H -ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O -ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H -ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H -ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O -ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H -ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H -ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O -ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H -ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H -ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O -ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H -ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H -ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O -ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H -ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H -ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O -ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H -ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H -ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O -ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H -ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H -ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O -ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H -ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H -ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O -ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H -ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H -ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O -ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H -ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H -ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O -ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H -ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H -ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O -ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H -ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H -ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O -ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H -ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H -ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O -ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H -ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H -ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O -ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H -ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H -ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O -ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H -ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H -ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O -ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H -ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H -ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O -ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H -ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H -ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O -ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H -ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H -ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O -ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H -ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H -ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O -ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H -ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H -ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O -ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H -ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H -ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O -ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H -ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H -ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O -ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H -ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H -ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O -ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H -ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H -ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O -ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H -ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H -ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O -ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H -ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H -ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O -ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H -ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H -ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O -ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H -ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H -ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O -ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H -ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H -ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O -ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H -ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H -ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O -ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H -ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H -ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O -ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H -ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H -ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O -ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H -ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H -ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O -ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H -ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H -ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O -ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H -ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H -ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O -ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H -ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H -ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O -ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H -ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H -ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O -ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H -ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H -ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O -ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H -ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H -ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O -ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H -ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H -ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O -ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H -ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H -ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O -ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H -ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H -ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O -ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H -ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H -ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O -ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H -ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H -ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O -ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H -ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H -ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O -ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H -ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H -ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O -ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H -ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H -ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O -ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H -ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H -ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O -ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H -ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H -ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O -ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H -ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H -ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O -ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H -ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H -ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O -ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H -ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H -ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O -ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H -ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H -ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O -ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H -ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H -ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O -ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H -ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H -ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O -ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H -ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H -ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O -ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H -ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H -ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O -ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H -ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H -ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O -ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H -ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H -ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O -ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H -ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H -ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O -ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H -ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H -ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O -ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H -ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H -ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O -ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H -ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H -ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O -ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H -ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H -ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O -ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H -ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H -ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O -ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H -ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H -ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O -ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H -ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H -ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O -ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H -ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H -ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O -ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H -ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H -ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O -ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H -ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H -ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O -ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H -ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H -ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O -ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H -ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H -ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O -ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H -ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H -ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O -ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H -ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H -ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O -ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H -ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H -ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O -ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H -ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H -ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O -ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H -ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H -ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O -ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H -ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H -ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O -ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H -ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H -ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O -ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H -ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H -ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O -ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H -ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H -ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O -ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H -ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H -ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O -ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H -ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H -ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O -ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H -ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H -ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O -ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H -ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H -ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O -ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H -ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H -ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O -ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H -ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H -ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O -ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H -ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H -ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O -ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H -ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H -ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O -ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H -ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H -ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O -ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H -ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H -ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O -ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H -ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H -ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O -ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H -ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H -ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O -ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H -ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H -ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O -ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H -ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H -ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O -ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H -ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H -ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O -ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H -ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H -ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O -ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H -ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H -ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O -ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H -ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H -ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O -ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H -ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H -ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O -ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H -ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H -ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O -ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H -ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H -ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O -ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H -ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H -ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O -ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H -ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H -ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O -ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H -ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H -ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O -ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H -ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H -ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O -ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H -ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H -ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O -ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H -ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H -ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O -ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H -ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H -ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O -ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H -ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H -ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O -ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H -ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H -ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O -ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H -ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H -ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O -ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H -ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H -ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O -ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H -ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H -ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O -ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H -ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H -ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O -ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H -ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H -ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O -ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H -ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H -ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O -ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H -ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H -ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O -ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H -ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H -ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O -ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H -ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H -ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O -ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H -ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H -ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O -ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H -ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H -ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O -ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H -ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H -ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O -ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H -ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H -ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O -ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H -ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H -ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O -ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H -ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H -ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O -ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H -ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H -ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O -ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H -ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H -ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O -ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H -ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H -ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O -ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H -ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H -ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O -ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H -ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H -ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O -ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H -ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H -ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O -ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H -ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H -ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O -ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H -ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H -ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O -ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H -ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H -ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O -ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H -ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H -ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O -ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H -ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H -ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O -ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H -ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H -ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O -ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H -ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H -ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O -ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H -ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H -ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O -ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H -ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H -ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O -ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H -ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H -ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O -ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H -ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H -ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O -ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H -ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H -ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O -ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H -ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H -ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O -ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H -ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H -ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O -ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H -ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H -ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O -ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H -ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H -ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O -ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H -ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H -ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O -ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H -ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H -ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O -ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H -ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H -ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O -ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H -ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H -ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O -ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H -ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H -ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O -ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H -ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H -ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O -ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H -ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H -ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O -ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H -ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H -ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O -ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H -ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H -ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O -ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H -ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H -ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O -ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H -ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H -ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O -ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H -ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H -ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O -ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H -ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H -ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O -ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H -ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H -ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O -ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H -ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H -ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O -ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H -ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H -ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O -ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H -ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H -ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O -ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H -ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H -ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O -ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H -ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H -ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O -ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H -ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H -ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O -ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H -ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H -ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O -ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H -ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H -ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O -ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H -ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H -ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O -ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H -ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H -ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O -ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H -ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H -ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O -ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H -ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H -ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O -ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H -ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H -ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O -ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H -ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H -ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O -ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H -ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H -ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O -ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H -ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H -ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O -ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H -ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H -ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O -ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H -ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H -ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O -ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H -ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H -ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O -ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H -ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H -ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O -ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H -ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H -ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O -ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H -ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H -ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O -ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H -ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H -ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O -ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H -ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H -ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O -ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H -ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H -ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O -ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H -ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H -ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O -ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H -ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H -ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O -ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H -ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H -ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O -ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H -ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H -ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O -ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H -ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H -ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O -ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H -ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H -ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O -ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H -ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H -ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O -ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H -ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H -ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O -ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H -ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H -ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O -ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H -ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H -ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O -ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H -ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H -ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O -ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H -ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H -ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O -ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H -ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H -ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O -ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H -ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H -ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O -ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H -ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H -ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O -ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H -ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H -ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O -ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H -ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H -ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O -ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H -ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H -ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O -ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H -ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H -ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O -ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H -ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H -ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O -ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H -ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H -ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O -ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H -ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H -END diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt deleted file mode 100644 index 1f0f0f61b5..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 600.0 1.0 - angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) - } - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt deleted file mode 100644 index 274d8aeb11..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt +++ /dev/null @@ -1,16 +0,0 @@ -import "spce.lt" - -wat = new SPCE [260] - - - - - - - -# Open up the PDB file to count the number of water molecules inside. (Or just -# divide the number of atoms by 3). Put that in between the brackets ("[260]") -# -# The command above does not set the positions of the atoms. -# So they will have to be loaded later from a PDB or an XYZ file. -# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt") diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt deleted file mode 100644 index 4d8af42b5d..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt +++ /dev/null @@ -1,48 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize". -unfix fShakeSPCE -minimize 1.0e-3 1.0e-5 100000 400000 -# Now read "system.in.settings" in order to redefine fShakeSPCE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -thermo 100 - -run 10000 - -# Now that the system's temperature has become more equilibrated, -# we can increase the timestep: - -timestep 2.0 -run 50000 - -write_data system_after_npt.data diff --git a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt deleted file mode 100644 index d039a5370f..0000000000 --- a/tools/moltemplate/examples/file_conversion_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt +++ /dev/null @@ -1,61 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# (Follow the instructions in README_setup.sh, or run it using ./README_sh.) -# 2) You must equilibrate the system beforehand using "run.in.npt". -# This will create the file "system_after_npt.data" which this file reads. -# (Note: I have not verified that this equilibration protocol works well.) - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier NPT simulation - -read_data system_after_npt.data - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- -# Note: If you are reading the data file created by run.in.npt, -# then you should not need to minimize the system beforehand. -# fShakeSPCE was defined in system.in.settings. -# (It is incompatible with "minimize".) - -unfix fShakeSPCE -minimize 1.0e-5 1.0e-7 100000 400000 - -# Now read "system.in.settings" in order to redefine fShakeSPCE again: - -include system.in.settings - - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 - -run 10000 - -# Now that the system's temperature has become more equilibrated, -# we can increase the timestep: - -timestep 2.0 -run 50000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt deleted file mode 100644 index 5f5fd61bd3..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README.txt +++ /dev/null @@ -1,25 +0,0 @@ -This example using the electron Force Field (eFF) was created by -Andres Jaramillo-Botero and distributed with LAMMPS in the -"examples/USERS/eff/CH4" subdirectory. -The files from that example were converted into moltemplate format using -"ltemplify.py" and then edited by hand (to rename the atom types, -and replace all of the "pair_coeff ..." commands with "pair_coeff * *") - - ---- Original README: --- -Methane, valence electron ionization and full molecule tests (spe, dynamics). -Note: electron mass set to 1 - - ------ -WARNING: Regarding the "run.in.ch4_ionized" file - As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command - located in "orig_files/in.ch4_ionized.dynamics" (as well as the - files "moltemplate_files/ch4_ionized.lt" and "system.in.settings", - which are both derived from it) causes LAMMPS to hang. - Running LAMMPS on Andres' original eFF example has the same behavior. - This appears to be an eFF/LAMMPS issue (not a moltemplate issue). - The "pair_style eff/cut 100" command works, so - try reducing the cutoff (or ask Andres Jaramillo-Botero for help). - Please let me know if you solve this issue (jewett.aij -at- g mail) - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh deleted file mode 100644 index 527ff19442..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_run.sh +++ /dev/null @@ -1,3 +0,0 @@ - -lmp_mpi -i run.in.ch4 - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh deleted file mode 100644 index 8433d10fa2..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/README_setup.sh +++ /dev/null @@ -1,14 +0,0 @@ -cd moltemplate_files/ - - moltemplate.sh -atomstyle electron system_ch4.lt - - # This will generate 3 files: - # "system_ch4.data", "system_ch4.in.init", "system_ch4.in.settings" - - mv -f system_ch4.data system_ch4.in.init system_ch4.in.settings ../ - - # optional: delete temporary files - - rm -rf output_ttree - -cd ../ diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt deleted file mode 100644 index b5989e5a1b..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4.lt +++ /dev/null @@ -1,45 +0,0 @@ - -CH4 { - - write_once("Data Masses") { - @atom:C 12.01070 - @atom:H 1.000794 - @atom:e 1.000000 - } - - # id type q spin eradius x y z - - write("Data Atoms") { - $atom:c @atom:C 6.0 0 0.0 0.0 0.0 0.0 - $atom:h1 @atom:H 1.0 0 0.0 1.0 1.0 1.0 - $atom:h2 @atom:H 1.0 0 0.0 -1.0 -1.0 1.0 - $atom:h3 @atom:H 1.0 0 0.0 1.0 -1.0 -1.0 - $atom:h4 @atom:H 1.0 0 0.0 -1.0 1.0 -1.0 - $atom:esr @atom:e 0.0 -1 0.5 0.0 0.0 0.0 - $atom:esR1 @atom:e 0.0 -1 1.0 1.0 1.0 1.0 - $atom:esR2 @atom:e 0.0 -1 1.0 -1.0 -1.0 1.0 - $atom:esR3 @atom:e 0.0 -1 1.0 1.0 -1.0 -1.0 - $atom:esR4 @atom:e 0.0 -1 1.0 -1.0 1.0 -1.0 - $atom:eSr @atom:e 0.0 1 0.5 0.0 0.0 0.0 - $atom:eSR1 @atom:e 0.0 1 1.0 1.0 1.0 1.0 - $atom:eSR2 @atom:e 0.0 1 1.0 -1.0 -1.0 1.0 - $atom:eSR2 @atom:e 0.0 1 1.0 1.0 -1.0 -1.0 - $atom:eSR3 @atom:e 0.0 1 1.0 -1.0 1.0 -1.0 - } - - # -- styles and force-field parameters -- - # (these can be overridden later) - - write_once("In Init") { - atom_style electron - units electron - pair_style eff/cut 100.0 - newton on - comm_modify vel yes - } - write_once("In Settings") { - pair_coeff * * - } - -} # end of "CH4" object definition - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt deleted file mode 100644 index 62865418e8..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/ch4_ionized.lt +++ /dev/null @@ -1,55 +0,0 @@ -# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command -# located in "orig_files/in.ch4_ionized.dynamics" (as well as the -# files "moltemplate_files/ch4_ionized.lt" (this file) -# ...causes LAMMPS to hang. -# Running LAMMPS on Andres' original eFF example has the same behavior. -# This appears to be an eFF/LAMMPS issue, not a moltemplate issue. -# The "pair_style eff/cut 100" command works, so -# try reducing the cutoff (or ask Andres Jaramillo-Botero for help). -# Please let me know if you solve this issue (jewett.aij -at- g mail ) - - -CH4_ionized { - - write_once("Data Masses") { - @atom:C 12.01070 - @atom:H 1.000794 - @atom:e 1.000000 - } - - # id type q spin eradius x y z - - write("Data Atoms") { - $atom:c @atom:C 6.000000 0 0.0 0.000000 -0.000000 0.000000 - $atom:h1 @atom:H 1.000000 0 0.0 1.247211 1.247211 1.247211 - $atom:h2 @atom:H 1.000000 0 0.0 -1.247211 -1.247211 1.247211 - $atom:h3 @atom:H 1.000000 0 0.0 1.247211 -1.247211 -1.247211 - $atom:h4 @atom:H 1.000000 0 0.0 -1.247211 1.247211 -1.247211 - $atom:esr @atom:e 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000 - $atom:esR1 @atom:e 0.000000 -1 1.486181 0.979221 0.979221 0.979221 - $atom:esR2 @atom:e 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221 - $atom:esR3 @atom:e 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221 - $atom:esR4 @atom:e 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221 - $atom:eSr @atom:e 0.000000 1 0.329128 -0.000000 0.000000 0.000000 - $atom:eSR1 @atom:e 0.000000 1 1.486181 -0.979221 -0.979221 0.979221 - $atom:eSR2 @atom:e 0.000000 1 1.486181 0.979221 -0.979221 -0.979221 - $atom:eSR3 @atom:e 0.000000 1 1.486181 -0.979221 0.979221 -0.979221 - } - - # -- styles and force-field parameters -- - # (these can be overridden later) - - write_once("In Init") { - atom_style electron - units electron - pair_style eff/cut 5000.0 0 0 - newton on - comm_modify vel yes - } - - write_once("In Settings") { - pair_coeff * * - } - -} # end of "CH4_ionized" object definition - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in deleted file mode 100644 index 8ba9365a9b..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.in +++ /dev/null @@ -1,42 +0,0 @@ - - -# ----------------- Init Section ----------------- - -include "system_ch4.in.init" - - -# ----------------- Atom Definition Section ----------------- - -read_data "system_ch4.data" - -# ----------------- Settings Section ----------------- - -include "system_ch4.in.settings" - - -# ----------------- Run Section ----------------- - -# The lines above define the system you want to simulate. -# What you do next is up to you. -# Typically a user would minimize and equilibrate -# the system using commands similar to the following: -# ---- examples ---- -# -# -- minimize -- -# minimize 1.0e-5 1.0e-7 1000 10000 -# (Note: Some fixes, for example "shake", interfere with the minimize command, -# You can use the "unfix" command to disable them before minimization.) -# -- declare time step for normal MD -- -# timestep 1.0 -# -- run at constant pressure (Nose-Hoover)-- -# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -# -- ALTERNATELY, run at constant volume (Nose-Hoover) -- -# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -# -- ALTERNATELY, run at constant volume using Langevin dynamics. -- -# -- (This is good for sparse CG polymers in implicit solvent.) -- -# fix fxLAN all langevin 300.0 300.0 5000 48279 -# fix fxNVE all nve #(<--needed by fix langevin) -# -- Now, finally run the simulation -- -# run 50000 -# ---- (end of examples) ---- - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt deleted file mode 100644 index 3b0e6d7894..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4.lt +++ /dev/null @@ -1,28 +0,0 @@ - -import "ch4.lt" # <-- defines "CH4" - - -# instantiate one or more copies of the "CH4" object: - -# Instantiate two copies of CH4: - -molecule1 = new CH4.move(-5.0,0,0) -molecule2 = new CH4.move(5.0,0,0) -# : : : - - -# alternate example: -# instantiate 2*2*2 = 8 copies, separated by 10.0 in each direction: -# molecules = new CH4 [2].move(0,0,10) [2].move(0,10,0) [2].move(10,0,0) -# molecules[*][*][*].move(-5,-5,-5) - - -# optional "Boundary" (goes in header of generated DATA file) -# (-200 200 by default) - -write_once("Data Boundary") { - -500.0 500.0 xlo xhi - -500.0 500.0 ylo yhi - -500.0 500.0 zlo zhi -} - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt deleted file mode 100644 index cd44be380e..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/moltemplate_files/system_ch4_ionized.lt +++ /dev/null @@ -1,29 +0,0 @@ - -import "ch4.lt" # <-- defines "CH4" -import "ch4_ionized.lt" # <-- defines "CH4_ionized" - - -# instantiate one or more copies of the "CH4" object: - -# Instantiate two copies of CH4: - -molecule1 = new CH4_ionized.move(-5.0,0,0) -molecule2 = new CH4_ionized.move(5.0,0,0) -# : : : - - -# alternate example: -# instantiate 2*2*2 = 8 copies, separated by 10.0 in each direction: -# molecules = new CH4 [2].move(0,0,10) [2].move(0,10,0) [2].move(10,0,0) -# molecules[*][*][*].move(-5,-5,-5) - - -# optional "Boundary" (goes in header of generated DATA file) -# (-200 200 by default) - -write_once("Data Boundary") { - -500.0 500.0 xlo xhi - -500.0 500.0 ylo yhi - -500.0 500.0 zlo zhi -} - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README deleted file mode 100644 index 20714b24c0..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/README +++ /dev/null @@ -1,2 +0,0 @@ -Methane, valence electron ionization and full molecule tests (spe, min, dynamics). -Note: electron mass set to 1 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 deleted file mode 100644 index ebe29be4ed..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4 +++ /dev/null @@ -1,32 +0,0 @@ -Created by AJB - -15 atoms -3 atom types - --500.0 500.0 xlo xhi --500.0 500.0 ylo yhi --500.0 500.0 zlo zhi - -Masses - -1 12.01070 # C nuclei mass -2 1.000794 # H nuclei mass -3 1.000000 # electron mass - -Atoms -#id|type|q|spin|eradius|x|y|z| -1 1 6.0 0 0.0 0.0 0.0 0.0 -2 2 1.0 0 0.0 1.0 1.0 1.0 -3 2 1.0 0 0.0 -1.0 -1.0 1.0 -4 2 1.0 0 0.0 1.0 -1.0 -1.0 -5 2 1.0 0 0.0 -1.0 1.0 -1.0 -6 3 0.0 -1 0.5 0.0 0.0 0.0 -7 3 0.0 -1 1.0 1.0 1.0 1.0 -8 3 0.0 -1 1.0 -1.0 -1.0 1.0 -9 3 0.0 -1 1.0 1.0 -1.0 -1.0 -10 3 0.0 -1 1.0 -1.0 1.0 -1.0 -11 3 0.0 1 0.5 0.0 0.0 0.0 -12 3 0.0 1 1.0 1.0 1.0 1.0 -13 3 0.0 1 1.0 -1.0 -1.0 1.0 -14 3 0.0 1 1.0 1.0 -1.0 -1.0 -15 3 0.0 1 1.0 -1.0 1.0 -1.0 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized deleted file mode 100644 index 8c21a281a1..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/data.ch4_ionized +++ /dev/null @@ -1,31 +0,0 @@ -Created by AJB - -14 atoms -3 atom types - --5000.0 5000.0 xlo xhi --5000.0 5000.0 ylo yhi --5000.0 5000.0 zlo zhi - -Masses - -1 12.01070 # C nuclei mass -2 1.000794 # H nuclei mass -3 1.000000 # electron mass - -Atoms - -1 1 6.000000 0 0.0 0.000000 -0.000000 0.000000 -2 2 1.000000 0 0.0 1.247211 1.247211 1.247211 -3 2 1.000000 0 0.0 -1.247211 -1.247211 1.247211 -4 2 1.000000 0 0.0 1.247211 -1.247211 -1.247211 -5 2 1.000000 0 0.0 -1.247211 1.247211 -1.247211 -6 3 0.000000 -1 0.329128 -0.000000 0.000000 -0.000000 -7 3 0.000000 -1 1.486181 0.979221 0.979221 0.979221 -8 3 0.000000 -1 1.486181 -0.979221 -0.979221 0.979221 -9 3 0.000000 -1 1.486181 0.979221 -0.979221 -0.979221 -10 3 0.000000 -1 1.486181 -0.979221 0.979221 -0.979221 -11 3 0.000000 1 0.329128 -0.000000 0.000000 0.000000 -12 3 0.000000 1 1.486181 -0.979221 -0.979221 0.979221 -13 3 0.000000 1 1.486181 0.979221 -0.979221 -0.979221 -14 3 0.000000 1 1.486181 -0.979221 0.979221 -0.979221 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics deleted file mode 100644 index 2536fa8f48..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.dynamics +++ /dev/null @@ -1,41 +0,0 @@ -variable sname index ch4 -log ${sname}.nve.log - -units electron -newton on -boundary f f f - -atom_style electron - -read_data data.${sname} - -pair_style eff/cut 100.0 -pair_coeff * * - -comm_modify vel yes - -# Minimize -min_style cg -compute 1 all property/atom spin eradius -dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z -min_modify line quadratic dmax 0.1 -minimize 0 1.0e-6 1000 10000 - -# Dynamics - -compute effTemp all temp/eff - -thermo 1000 -thermo_style custom step pe temp press -thermo_modify temp effTemp - -velocity all create 300.0 4928459 dist gaussian rot yes mom yes - -timestep 0.005 -fix 1 all nve/eff - -# the custom dump includes the radii -dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z -dump 3 all xyz 1000 ${sname}.nve.xyz - -run 100000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min deleted file mode 100644 index 69b7c15bd4..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4.min +++ /dev/null @@ -1,32 +0,0 @@ -variable sname index ch4 -log ${sname}.nve.log - -units electron -newton on -boundary f f f - -atom_style electron - -read_data data.${sname} - -pair_style eff/cut 100.0 -pair_coeff * * - -comm_modify vel yes - -compute effTemp all temp/eff - -compute energies all pair eff/cut -variable eke equal c_energies[1] -variable epauli equal c_energies[2] -variable ecoul equal c_energies[3] -variable erres equal c_energies[4] - -thermo 1 -thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres - -min_style cg -compute 1 all property/atom spin eradius erforce -dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3] -minimize 0 1e-6 2000 4000 - diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics deleted file mode 100644 index 14f214296f..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/orig_files/in.ch4_ionized.dynamics +++ /dev/null @@ -1,42 +0,0 @@ -variable sname index ch4_ionized -log ${sname}.nvt.log - -units electron -newton on -boundary f f f - -atom_style electron - -read_data data.${sname} - -pair_style eff/cut 5000.0 0 0 -pair_coeff * * - -comm_modify vel yes - -# minimize -min_style cg -min_modify line quadratic -minimize 0 1.0e-6 10000 100000 - -# dynamics -compute effTemp all temp/eff - -thermo 100 -thermo_style custom step etotal pe ke temp press -thermo_modify temp effTemp - -# equilibrate -timestep 0.001 -fix 1 all nvt/eff temp 300.0 300.0 0.1 - -# the custom dump includes the radii -compute 1 all property/atom spin eradius -dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] -dump 2 all xyz 100 ${sname}.nvt.xyz - -run 1000000 - -fix 2 all nve/eff - -run 1000000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 deleted file mode 100644 index a822608768..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4 +++ /dev/null @@ -1,49 +0,0 @@ -# PREREQUISITES: -# system_ch4.data, system_ch4.in.init, system.in.settings -# Generate these files using: -# cd moltemplate_files/ -# moltemplate.sh -atomstyle electron system_ch4.lt - - -variable sname index ch4 -log ${sname}.nve.log - - -boundary f f f -include system_${sname}.in.init - - -read_data system_${sname}.data - - -include system_${sname}.in.settings - - - -# Minimize - -min_style cg -compute 1 all property/atom spin eradius -dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z -min_modify line quadratic dmax 0.1 -minimize 0 1.0e-6 1000 10000 - - -# Dynamics - -compute effTemp all temp/eff - -thermo 1000 -thermo_style custom step pe temp press -thermo_modify temp effTemp - -velocity all create 300.0 4928459 dist gaussian rot yes mom yes - -timestep 0.005 -fix 1 all nve/eff - -# the custom dump includes the radii -dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z -dump 3 all xyz 1000 ${sname}.nve.xyz - -run 100000 diff --git a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized b/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized deleted file mode 100644 index 73e93b1cd2..0000000000 --- a/tools/moltemplate/examples/misc_examples/explicit_electrons/eff_CH4/run.in.ch4_ionized +++ /dev/null @@ -1,62 +0,0 @@ -# PREREQUISITES: -# system_ch4_ionized.data, system_ch4_ionized.in.init, system.in.settings -# Generate these files using: -# cd moltemplate_files/ -# moltemplate.sh -atomstyle electron system_ch4_ionized.lt - -# WARNING: As of 2014-3-12, the "pair_style eff/cut 5000.0 0 0" command -# located in "orig_files/in.ch4_ionized.dynamics" (as well as the -# files "moltemplate_files/ch4_ionized.lt" and "system.in.settings", -# which are both derived from it) causes LAMMPS to hang. -# Running LAMMPS on Andres' original eFF example has the same behavior. -# This appears to be an eFF/LAMMPS issue, not a moltemplate issue. -# The "pair_style eff/cut 100" command works, so -# try reducing the cutoff (or ask Andres Jaramillo-Botero for help). -# Please let me know if you solve this issue (jewett.aij -at- g mail ) - - -variable sname index ch4 -log ${sname}.nve.log - - -boundary f f f -include system_${sname}.in.init - - -read_data system_${sname}.data - - -include system_${sname}.in.settings - - - -# Minimize - -min_style cg -min_modify line quadratic -minimize 0 1.0e-6 10000 100000 - - - -# Dynamics - -compute effTemp all temp/eff - -thermo 100 -thermo_style custom step etotal pe ke temp press -thermo_modify temp effTemp - -# Equilibrate -timestep 0.001 -fix 1 all nvt/eff temp 300.0 300.0 0.1 - -# the custom dump includes the radii -compute 1 all property/atom spin eradius -dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2] -dump 2 all xyz 100 ${sname}.nvt.xyz - -run 1000000 - -fix 2 all nve/eff - -run 1000000 diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README.txt b/tools/moltemplate/examples/misc_examples/menger_sponge/README.txt deleted file mode 100644 index 5046c978da..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/README.txt +++ /dev/null @@ -1,59 +0,0 @@ -NOTE: This example requires the "Al99.eam.alloy" file. - (It was not included in this directory because if its large size.) - As of 2012-11, I was able to obtain it here: - http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - Copy it to the directory containing this README file. ------------------------------------------------------------------------- -3D fractal test - -Moltemplate is useful for building larger molecular structures from smaller -pieces. The purpose of this example is to show how to build large (many-level) -heirarchical objects (a Menger sponge) using moltemplate. - -A Menger sponge is a fractal composed of subunits that resemble a Rubik's-cubes -with a hollow interior: - - ___ - ###| - # #| - ###' - - | - \|/ - V - - _________ - / /| - ######### | - # ## ## # | - ######### | - ### ### | - # # # # | - ### ### | - ######### | - # ## ## #/ - ######### - -In this example, we will build a periodic lattice of Menger sponges. - -The smallest cube subunits consist of 4 atoms of Aluminum -(arranged in a cubic FCC unit-cell for bulk Aluminum). -This was an arbitrary choice. The resulting construct is not stable. - - --- To build the system --- - -Carry out the instructions in README_setup.sh, -to generate the LAMMPS DATA file and input scripts you need: -system.data, system.in.init, system.in.settings. -(The run.in script contains references to these files.) - - --- To run LAMMPS, try a command like: --- - -lmp_mpi -i run.in - - or (if you have mpi installed) - -mpirun -np 4 lmp_mpi -i run.in - -This will create an ordinary LAMMPS dump file you can visualize with VMD -traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh b/tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh deleted file mode 100755 index ac42516942..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/README_setup.sh +++ /dev/null @@ -1,29 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # We will also need the "Al99.eam.alloy" file: - #cp -f Al99.eam.alloy ../ - # This file was downloaded from: - # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/README_visualize.txt b/tools/moltemplate/examples/misc_examples/menger_sponge/README_visualize.txt deleted file mode 100644 index 9cf2aa7157..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/README_visualize.txt +++ /dev/null @@ -1,85 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes it is useful to shift the location of the periodic boundary box - and its contents: - - pbc wrap -compound res -all -shiftcenterrel {0.5 0.5 0.5} - pbc box -shiftcenterrel {0.5 0.5 0.5} - - Distances are measured in units of box-length fractions, not Angstroms. - - (If you want to focus the box on a system of atoms which are all of type 1, - then you can also try this to center the box around it: - pbc wrap -sel type=1 -all -centersel type=2 -center com) - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/AlCell_LR.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/AlCell_LR.jpg deleted file mode 100644 index bf07914dac..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/menger_sponge/images/AlCell_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/README.txt b/tools/moltemplate/examples/misc_examples/menger_sponge/images/README.txt deleted file mode 100644 index ce504acd7c..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/images/README.txt +++ /dev/null @@ -1,9 +0,0 @@ -This is not a simulation of a single menger sponge. -Instead it is a simulation of a periodic lattice of Menger sponges. -(See "../moltemplate_files/system.lt" for details.) -To demonstrate this, several of the images in this directory show the system -after it has been replicated (twice) in the x,y,z directions. Please note that -the system is actually 8 times smaller than it appears in these images. - -(Note: In VMD you can visualize the system this way by selecting the -"Graphics"->"Representations" menu option and clicking on the "Periodic" tab.) diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl1_LR.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl1_LR.jpg deleted file mode 100644 index 11174969a3..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl1_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl2_LR.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl2_LR.jpg deleted file mode 100644 index 744c9af633..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl2_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl3_LR.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl3_LR.jpg deleted file mode 100644 index a72a1ea8d0..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/menger_sponge/images/lvl3_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/menger_sponge_lattice_8cells_t=0_zoom1_LR2.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/menger_sponge_lattice_8cells_t=0_zoom1_LR2.jpg deleted file mode 100644 index 9020a3be0e..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/menger_sponge/images/menger_sponge_lattice_8cells_t=0_zoom1_LR2.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/images/menger_sponge_lattice_8cells_t=7400_LR.jpg b/tools/moltemplate/examples/misc_examples/menger_sponge/images/menger_sponge_lattice_8cells_t=7400_LR.jpg deleted file mode 100644 index 0036c903a2..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/menger_sponge/images/menger_sponge_lattice_8cells_t=7400_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/README.txt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/README.txt deleted file mode 100644 index ce94a83d45..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/README.txt +++ /dev/null @@ -1,28 +0,0 @@ -A Menger cube is a fractal composed of subunits that resemble -a Rubik's-cubes with a hollow interior: - _________ - / /| - ######### | - # ## ## # | - ######### | - ### ### | - # # # # | - ### ### | - ######### | - # ## ## #/ - ######### - -There are several ways to build them in moltemplate: -1) You can define each cube as a 3x3x3 array of smaller cubes, and then delete - the 7 interior cubes using the "delete" command. (Each smaller cube is a - similar structure containing an array of 3x3x3 even smaller cubes...) -2) You can define each cube as a list of 20 smaller cubes corresponding to the - cubes that would have remained after deleting the 7 interior cubes. - -Method 1 is a little bit simpler, but method 2 is much more efficient because -it never has to create sub-cubes which will be deleted later. - -This example uses method 1. - -If you are running out of memory, or if moltemplate is taking too long use -method2. It is located in the "memory_efficient_but_ugly_version/" subdirectory. diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/al_cell.lt deleted file mode 100644 index 3054a45e01..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/al_cell.lt +++ /dev/null @@ -1,64 +0,0 @@ -# "AlCell" defines the 4-atom FCC unit cell -# of Aluminum (with a 4.05 angstrom spacing) - -AlCell { - - # AtomID MolID(IGNORE!) AtomType Charge X Y Z - - write("Data Atoms") { - $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 - $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 - $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 - $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 - } - - write_once("In Init") { - units metal - atom_style full # <- Requires each atom has a MolID and Charge. - # This is not necessary. (Why use "full"? - # The "full" atom style is useful if you want to - # mix the aluminum with other molecules later. - # Otherwise, just use "atom_style atomic", and - # and remove the 2nd and 4th columns above.) - pair_style eam/alloy - } - - write_once("In Settings") { - pair_coeff * * Al99.eam.alloy Al - } - - write_once("Data Masses") { - @atom:Al 27.0 - } - -} # AlCell - - - - - -# Here is an alternate way to define AlCell -# using "scale(4.05)" to select the lattice spacing: -# -#FccCell { -# write("Data Atoms") { -# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 -# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 -# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 -# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 -# } -# write_once("Data Masses") { -# @atom:Al 27.0 -# } -# write_once("In Init") { -# units metal -# atom_style full -# pair_style eam/alloy -# } -# write_once("In Settings") { -# pair_coeff * * Al99.eam.alloy Al -# } -#} -# -#AlCell = FccCell.scale(4.05) -# diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/README.txt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/README.txt deleted file mode 100644 index 0d4f00eddb..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/README.txt +++ /dev/null @@ -1,29 +0,0 @@ -A Menger cube is a fractal composed of subunits that resemble -a Rubik's-cubes with a hollow interior: - _________ - / /| - ######### | - # ## ## # | - ######### | - ### ### | - # # # # | - ### ### | - ######### | - # ## ## #/ - ######### - -There are several ways to build them in moltemplate: -1) You can define each cube as a 3x3x3 array of smaller cubes, and then delete - the 7 interior cubes using the "delete" command. (Each smaller cube is a - similar structure containing an array of 3x3x3 even smaller cubes...) -2) You can define each cube as a list of 20 smaller cubes corresponding to the - cubes that would have remained after deleting the 7 interior cubes. - -Method 1 is a little bit simpler, but method 2 is much more efficient because -it never has to create sub-cubes which will be deleted later. - -This example uses method 2. - - - - diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/al_cell.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/al_cell.lt deleted file mode 100644 index 3054a45e01..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/al_cell.lt +++ /dev/null @@ -1,64 +0,0 @@ -# "AlCell" defines the 4-atom FCC unit cell -# of Aluminum (with a 4.05 angstrom spacing) - -AlCell { - - # AtomID MolID(IGNORE!) AtomType Charge X Y Z - - write("Data Atoms") { - $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 - $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 - $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 - $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 - } - - write_once("In Init") { - units metal - atom_style full # <- Requires each atom has a MolID and Charge. - # This is not necessary. (Why use "full"? - # The "full" atom style is useful if you want to - # mix the aluminum with other molecules later. - # Otherwise, just use "atom_style atomic", and - # and remove the 2nd and 4th columns above.) - pair_style eam/alloy - } - - write_once("In Settings") { - pair_coeff * * Al99.eam.alloy Al - } - - write_once("Data Masses") { - @atom:Al 27.0 - } - -} # AlCell - - - - - -# Here is an alternate way to define AlCell -# using "scale(4.05)" to select the lattice spacing: -# -#FccCell { -# write("Data Atoms") { -# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 -# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 -# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 -# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 -# } -# write_once("Data Masses") { -# @atom:Al 27.0 -# } -# write_once("In Init") { -# units metal -# atom_style full -# pair_style eam/alloy -# } -# write_once("In Settings") { -# pair_coeff * * Al99.eam.alloy Al -# } -#} -# -#AlCell = FccCell.scale(4.05) -# diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/menger_cubes.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/menger_cubes.lt deleted file mode 100644 index 797d899a63..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/menger_cubes.lt +++ /dev/null @@ -1,60 +0,0 @@ -import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell - - - - -MengerCubeLvl1 { - # Again, a Menger-cube is constructed of 20 smaller cube-shaped objects. - # Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt"). - # I could list out the positions of all 20 AlCells, (and this would be clearer - # for the reader). However instead I built it from a combination of - # two-dimensional and three-dimensional arrays of AlCells (explained below). - - # The next command creates 12 AlCells (2x2x3) at: - # (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1) - # (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1) - # (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1) - - cells_z = new AlCell [2].move(8.10, 0.00, 0.00) - [2].move(0.00, 8.10, 0.00) - [3].move(0.00, 0.00, 4.05) - - # The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0), - # (0, 4.05, 8.1), (8.1, 4.05, 8.1) - - cells_xz= new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 ) - [2].move(0.0, 0.0, 8.10) - - # The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0), - # (4.05, 0, 8.1), (4.05, 8.1, 8.1) - - cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 ) - [2].move(0.0, 0.0, 8.10) -} - - - -MengerCubeLvl2 { - # Identical arrangement to MengerCube1 (with 3x larger length scales) - cells_z = new MengerCubeLvl1 [2].move(24.3, 0.00, 0.00) - [2].move(0.00, 24.3, 0.00) - [3].move(0.00, 0.00, 12.15) - cells_xz = new MengerCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 ) - [2].move(0.0, 0.0, 24.3) - cells_yz = new MengerCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 ) - [2].move(0.0, 0.0, 24.3) -} - - - -MengerCubeLvl3 { - # Identical arrangement to MengerCube2 (with 3x larger length scales) - cells_z = new MengerCubeLvl2 [2].move(72.9, 0.00, 0.00) - [2].move(0.00, 72.9, 0.00) - [3].move(0.00, 0.00, 36.45) - cells_xz = new MengerCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 ) - [2].move(0.0, 0.0, 72.9) - cells_yz = new MengerCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 ) - [2].move(0.0, 0.0, 72.9) -} - diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/system.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/system.lt deleted file mode 100644 index 51313b9d7c..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/memory_efficient_but_ugly_version/system.lt +++ /dev/null @@ -1,33 +0,0 @@ -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 218.7 xlo xhi - 0.0 218.7 ylo yhi - 0.0 218.7 zlo zhi -} - -import "menger_cubes.lt" - -cube_at_000 = new MengerCubeLvl3.move(0.0000, 0.0000, 0.0000) -cube_at_100 = new MengerCubeLvl3.move(109.35, 0.0000, 0.0000) -cube_at_010 = new MengerCubeLvl3.move(0.0000, 109.35, 0.0000) -cube_at_001 = new MengerCubeLvl3.move(0.0000, 0.0000, 109.35) - - - - - - - - - - - - - - -################################################################ -# The next command is not necessary. Commenting out: -# -# create_var { $mol } # <-This forces all of the Al atoms in the crystal -# # to share the same molecule ID number. -# # (Molecule ID numbers are not necessary.) diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/menger_cubes.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/menger_cubes.lt deleted file mode 100644 index afafd46e9f..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/menger_cubes.lt +++ /dev/null @@ -1,34 +0,0 @@ -import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell - -# This approach uses the "delete" command. -# It works and it is elegant, but because the majority of atoms will be -# deleted, (and because memory is allocated for all atoms, including -# deleted atoms) this approach is not very memory efficient. - -MengerCubeLvl1 { - cells = new AlCell [3].move(0.00, 0.00, 4.05) - [3].move(0.00, 4.05, 0.00) - [3].move(4.05, 0.00, 0.00) - delete cells[*][1][1] - delete cells[1][*][1] - delete cells[1][1][*] -} - -MengerCubeLvl2 { - cells = new MengerCubeLvl1 [3].move(0.00, 0.00, 12.15) - [3].move(0.00, 12.15, 0.00) - [3].move(12.15, 0.00, 0.00) - delete cells[*][1][1] - delete cells[1][*][1] - delete cells[1][1][*] -} - -MengerCubeLvl3 { - cells = new MengerCubeLvl2 [3].move(0.00, 0.00, 36.45) - [3].move(0.00, 36.45, 0.00) - [3].move(36.45, 0.00, 0.00) - delete cells[*][1][1] - delete cells[1][*][1] - delete cells[1][1][*] -} - diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/system.lt b/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/system.lt deleted file mode 100644 index 75ae976b34..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/moltemplate_files/system.lt +++ /dev/null @@ -1,34 +0,0 @@ -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 218.7 xlo xhi - 0.0 218.7 ylo yhi - 0.0 218.7 zlo zhi -} - -import "menger_cubes.lt" - -cube_at_000 = new MengerCubeLvl3.move(0.0000, 0.0000, 0.0000) -cube_at_100 = new MengerCubeLvl3.move(109.35, 0.0000, 0.0000) -cube_at_010 = new MengerCubeLvl3.move(0.0000, 109.35, 0.0000) -cube_at_001 = new MengerCubeLvl3.move(0.0000, 0.0000, 109.35) - - - - - - - - - - - - - - -################################################################ -# The next command is not necessary. Commenting out: -# -# create_var { $mol } # <-This forces all of the Al atoms in the crystal -# # to share the same molecule ID number. -# # (Molecule ID numbers are not necessary.) -# diff --git a/tools/moltemplate/examples/misc_examples/menger_sponge/run.in b/tools/moltemplate/examples/misc_examples/menger_sponge/run.in deleted file mode 100644 index 6b9ad17e6e..0000000000 --- a/tools/moltemplate/examples/misc_examples/menger_sponge/run.in +++ /dev/null @@ -1,38 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- -# -# Some of the run-settings below were stolen from: -# -# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression - -# EQUILIBRATION -reset_timestep 0 -timestep 0.001 -velocity all create 300 12345 mom yes rot no -fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 - -# Output files -thermo 100 -thermo_style custom step ke pe press -dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz - -run 20000 - -# Run for at least 10 picosecond (assuming 1 fs timestep) -run 10000 - - -###################################### -# SIMULATION DONE -print "All done" diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README.txt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README.txt deleted file mode 100644 index 3e126b04aa..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README.txt +++ /dev/null @@ -1,23 +0,0 @@ - Description: - -This is a simulation of pyramid-shaped objects resting on an immobile surface -(resembling graphene). Each pyramid is built from spherical particles stacked -like cannon-balls (or fruit). Ordinarily, the stack does not move -because the particles at the ground layer are immobilized. However, -given an initial (small) perturbation the pyramids collapse in an avalanche. - -(In this example, the perturbation is due to shock because we (intentionally) - did not minimize the system before starting the simulation. This shock - causes an avalanche to begin approximately 5000 timesteps later.) - -The particles roll down the pyramid and bounce off the "ground". The bouncing -is due to a repulsive external force which is added artificially. -(See the "run.in" file.) The simulation looks weird without something -to bounce off of. So I added a graphene surface at the bottom as scenery. -(It does not exert any force on the atoms.) - -(Random comment: This could be a fun example to illustrate the Boltzmann - distribution. Because there is no damping, in a small region, I'm guessing - the particle heights should eventually approach the Boltzmann distribution - for some temperature consistent with the initial potential energy of the - system.) diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_VMD_graphene.txt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_VMD_graphene.txt deleted file mode 100644 index 8bb1bc89f6..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_VMD_graphene.txt +++ /dev/null @@ -1,28 +0,0 @@ - ------- A note on building the graphene sheet in VMD: ------ - -Probably you can ignore these instructions. -These instructions are not necessary for this example to run. - -This example contains several pyramid shaped objects resting on a surface -made of graphene. The instructions in this file explain how to build the -graphene (representing the "ground") using VMD instead of with moltemplate. - Why do this? -VMD can create graphene sheets with bonds connecting neighboring carbon atoms, -(which looks more pretty). However, as of 2013-4-29, moltemplate currently -can not generate these bonds. It does not matter physically in this case, -because the graphene sheet used here does not move. It is only used as -scenery, to graphically represent the ground surface. - -Select "Extensions"->"Modeling"->"Carbon Nanotube Builder" - Build a graphene sheet of size 39.8 x 39.8 (units: nm) - 400.3358398 399.876008 - (try to use a size compatible with the periodic boundaries) -Select "Extensions"->"Tk Console", and type - display backgroundgradient on - -Note: If you want to do this, before you run moltemplate, you may want to delete - the sections of the "system.lt" file (located in "moltemplate_files") - which define the graphene wall. Instead create the graphene data file - in VMD. You will have to manually merge the data file for graphene - with the data file for the pyramids created by moltemplate, - (taking care to avoid overlapping atom-id numbers). diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_setup.sh b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_setup.sh deleted file mode 100755 index cf22ee0fa1..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_visualize.txt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_visualize.txt deleted file mode 100644 index e2c77bafb5..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/README_visualize.txt +++ /dev/null @@ -1,76 +0,0 @@ - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - To shift the box by a fraction in the x direction (for example) - do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } - pbc box -shiftcenterrel {-0.50 -0.52 0.0 } - - # Alternately if you have a solute whose atoms are all of type 1, - # then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=04800steps_LR.jpg b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=04800steps_LR.jpg deleted file mode 100644 index dc010258f0..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=04800steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=12200steps_LR.jpg b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=12200steps_LR.jpg deleted file mode 100644 index 53dc98f3e8..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=12200steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=33000steps_LR.jpg b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=33000steps_LR.jpg deleted file mode 100644 index ba07b25372..0000000000 Binary files a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/images/pyramids_vs_gravity_t=33000steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/README.sh b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/README.sh deleted file mode 100755 index 1f083af18e..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/README.sh +++ /dev/null @@ -1,15 +0,0 @@ -# This directory contains moltemplate files for the "Pyramids of Giza" example. -# (Note: the ground lattice work that appears in some images was not generated -# by moltemplate. Moltemplate can not currently create bonded periodic -# structures as of 2013-4-04. Those were generated by topotools.) -# -# To run moltemplate, use: - -moltemplate.sh system.lt - -# This will generate:system.data, system.in, system.in.init, system.in.settings -# -# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds" -# which contain the corresponding structures of the system.data file. -# (This might make it slightly easier to combine them with atom data and -# bond data generated by other programs, such as topotools, for example.) diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/graphene.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/graphene.lt deleted file mode 100644 index 3b3e21333f..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/graphene.lt +++ /dev/null @@ -1,61 +0,0 @@ -# This file contains a unit cell for building graphene and nanotubes -# -# -# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell -# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg") -# Surfaces constructed with this unit cell can be flat or curved into tubes. -# The distance between nearest-neighbor carbon atoms (ie the length of a -# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. -# -# d = length of each hexagon's side = 1.42 Angstroms -# L = length of each hexagon = 2*d = 2.84 Angstroms -# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms -# 2w = width of hexagon rows = 3*l = 4.26 Angstroms -# -# Consequently, the Lattice-cell vectors for singe-layer graphene are: -# (2.4595121467478, 0, 0) (aligned with X axis) -# (0, 4.26, 0) (aligned with Y axis) -# So, to build a sheet of graphite, you could use: -# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0) -# [10].move(0, 4.26, 0) - - - - -Graphene { - - 4AtomRectCellXY - { - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0 - $atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0 - $atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0 - $atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0 - } - } - - # Now define properties of the Carbon graphene atom - - write_once("In Init") { - pair_style hybrid lj/cut 9.0 - } - - write_once("Data Masses") { - @atom:C 12.0 - } - - write_once("In Settings") { - # i j epsilon sigma - pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 - - # These Lennard-Jones parameters come from - # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, - # Chem Phys Lett, 348:187 (2001) - - # Define a group consisting of only carbon atoms in graphene molecules - group gGraphene type @atom:C - } - -} # Graphene - diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/graphene_wall.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/graphene_wall.lt deleted file mode 100644 index 759f0f5d06..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/graphene_wall.lt +++ /dev/null @@ -1,21 +0,0 @@ -import "graphene.lt" - -# -------------- graphene sheet ----------------- - -# Notes: -# Hexagonal lattice with: -# l = length of each hexagonal side = 1.42 Angstroms -# L = length of each hexagon = 2*l = 2.84 Angstroms -# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms -# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms - - -GrapheneWall { - - unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0) - [94].move(0, 4.254, 0) - - # (Note: I fudged the spacing slightly to make it line up better with the - # lattice spacing for graphene generated by VMD's graphene builder.) -} - diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/pyramids.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/pyramids.lt deleted file mode 100644 index 84c2b6f6d1..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/pyramids.lt +++ /dev/null @@ -1,283 +0,0 @@ -# Brick is a very simple molecule containing one "atom". -# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are -# given different atom types. (This makes it easier to put them in -# different groups and apply different LAMMPS "fixes" to them.) - -Brick { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom $mol @atom 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom 1.0 - } - - write_once("In Settings") { - # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) - # - # i j eps sig - pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 - } - - write_once("In Settings") { - group gMobile type @atom - # (Atoms of this type belong to the "gMobile" group) - } - - write_once("In Init") { - atom_style full - units lj - pair_style lj/cut 1.0 - } -} - - - -#We want to stack "Brick"s the same way a green-grocer sometimes stack apples: -#Place the apples at the base an square lattice of apples at the base. -#The apples in the next layer up are placed in between the 4 apples beneath them. -#Each new layer is smaller and placed above the previous layer at a height -#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick". -#We will artificially hold the apples at the base in place -#(to keep the entire stack from collapsing). -# -# The lines below were generated from the following python loop: -# -#from math import * -#N=50 -#s=1.0 -#for i in range(0,N): -# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+ -# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+ -# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)") - - -PyramidKhufu { - layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0) - layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0) - layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0) - layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0) - layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0) - layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0) - layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0) - layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0) - layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0) - layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0) - layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0) - layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0) - layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0) - layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0) - layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0) - layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0) - layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0) - layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0) - layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0) - layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0) - layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0) - layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0) - layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0) - layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0) - layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0) - layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0) - layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0) - layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0) - layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0) - layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0) - layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0) - layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0) - layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0) - layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0) - layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0) - layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0) - layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0) - layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0) - layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0) - layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0) - layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0) - layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0) - layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - - -PyramidKhafre { - layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0) - layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0) - layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0) - layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0) - layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0) - layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0) - layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0) - layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0) - layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0) - layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0) - layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0) - layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0) - layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0) - layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0) - layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0) - layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0) - layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0) - layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0) - layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0) - layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0) - layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0) - layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0) - layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0) - layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0) - layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0) - layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0) - layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0) - layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0) - layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0) - layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0) - layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0) - layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0) - layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0) - layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0) - layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0) - layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0) - layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0) - layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0) - layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0) - layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0) - layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - - -PyramidMenkaure { - layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0) - layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0) - layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0) - layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0) - layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0) - layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0) - layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0) - layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0) - layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0) - layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0) - layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0) - layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - -PyramidQueens1 { - layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - -PyramidQueens2 { - layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - -PyramidQueens3 { - layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - - - - -# "ImmobileBrick"s are identical to "Brick"s, -# except that they have a different atom type. -# We can define groups based on atom type -# and apply fixes to them. - -ImmobileBrick { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom $mol @atom 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom 1.0 - } - - write_once("In Settings") { - # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) - # - # i j eps sig - pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 - } - - write_once("In Settings") { - group gImmobile type @atom - # (Atoms of this type belong to the "gImmobile" group) - } - - write_once("In Init") { - atom_style full - units lj - pair_style hybrid lj/cut 1.0 - } -} - - - -GoldBrick { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom $mol @atom 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom 1.0 - } - - write_once("In Settings") { - # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) - # - # i j eps sig - pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 - } - - write_once("In Settings") { - group gMobile type @atom - # (Atoms of this type belong to the "gMobile" group) - } - - write_once("In Init") { - atom_style full - units lj - pair_style lj/cut 1.0 - } -} - diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/system.lt b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/system.lt deleted file mode 100644 index 0c9c50ae9b..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/moltemplate_files/system.lt +++ /dev/null @@ -1,80 +0,0 @@ -# Description. -# This is a simulation of pyramid-like objects made of particles stacked -# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack -# does not collapse because the particles at the ground layer are immobilized. -# However given an initial perterbation the pyramids collapse in an avalanche. -# (This can happen, for example when you do not minimize the system beforehand.) -# The particles roll down the pyramid and bounce off the "ground". The bouncing -# is due to a repulsive external force which is added artificially. -# (See the "run.in" file.) The simulation looks weird without something -# to bounce off of. So I added a graphene surface at the bottom as scenery. -# The ground does not serve any purpose except to look pretty. -# -# (Because there is no damping, I suspect that the distribution of heights of -# the particles in a small area should approach the Boltzmann distribution, -# if you run the simulation long enough.) - - -# ----------------- Pyramids: ----------------- - -import "pyramids.lt" - -# Move the pyramids into their locations in Giza (approximate) - -pyramidKhufu = new PyramidKhufu.move(210, 215, 1) -pyramidKhafre = new PyramidKhafre.move(150, 150, 1) -pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1) -PyramidQueens1 = new PyramidQueens1.move(089, 059, 1) -PyramidQueens2 = new PyramidQueens2.move(100, 059, 1) -PyramidQueens3 = new PyramidQueens3.move(111, 059, 1) - - -# --------------- Scenery: -------------------- - -import "graphene_wall.lt" - -graphene_wall = new GrapheneWall - -write_once("In Settings") { - # Turn off all interactions with the graphene atoms by setting epsilon to 0. - # (We will use a different repulsive barrier to represent the ground instead.) - # These atoms are just "for show". epsilon sigma - pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407 - - # Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them - group gImmobile type @atom:Graphene/C -} - -# Unfortunately, the ground still looks kind of ugly because moltemplate does -# not yet know how to automatically connect nearby carbon atoms with C-C bonds -# (based on distance). (As of 2013-4-29, moltemplate is not good at -# generating crystalline objects containing explicit bonds.) -# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin" -# (which creates data files with bonds) and then merge the two data files -# manually later. (This is not done here.) - - -# -------- override earlier settings ---------- - -write_once("In Init") { - # Override any earlier style settings - atom_style full - units lj - pair_style hybrid lj/cut 1.0 - bond_style none - angle_style none - dihedral_style none - improper_style none - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 -} - -# ------------ boundary conditions ------------ - -write_once("Data Boundary") { - -1.842033 398.493813 xlo xhi - -0.708994 399.167013 ylo yhi - 0.0 400.0 zlo zhi -} -# --------------------------------------------- - diff --git a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/run.in b/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/run.in deleted file mode 100644 index a99dfda28f..0000000000 --- a/tools/moltemplate/examples/misc_examples/pyramids_vs_LAMMPS/run.in +++ /dev/null @@ -1,68 +0,0 @@ -# -- Init Section -- - -include system.in.init -boundary p p f - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.0025 -dump 1 all custom 200 traj.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal -thermo 100 # time interval for printing out "thermo" data - -# ---- Set up the physical environment ---- - -# Add gravity: -fix fxGrav gMobile gravity 0.05 vector 0 0 -1 - -# Create a "ground" surface. -# This is a repulsive "wall" which particles can bounce off of: - -fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0 - - -# ---- Evolve the system: ---- - -# Evolve the (mobile) atoms using ordinary Newton's laws (NVE) - -fix fxNVE gMobile nve - - -# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE: -#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279 -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) -# This was not tested. - -# OPTIONAL: -# For efficient simulation in parallel, try using "fix balance": -# (This will adjust the spatial decomposition as the distribution of -# particles changes over time.) -# http://lammps.sandia.gov/doc/fix_balance.html -# fix fxBalance gMobile balance 1000 1.1 shift 1000 xy 20 1.1 -# Alternatiely, try this: -#fix fxBalance gMobile balance 1000 1.2 rcb - - -# OPTIONAL: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms: - -neigh_modify exclude group gImmobile gImmobile - - -restart 50000 restart_nvt - -run 200000 - -write_data system_after_nvt.data - diff --git a/tools/moltemplate/examples/misc_examples/twelve_days/README.sh b/tools/moltemplate/examples/misc_examples/twelve_days/README.sh deleted file mode 100644 index c6c839dc58..0000000000 --- a/tools/moltemplate/examples/misc_examples/twelve_days/README.sh +++ /dev/null @@ -1,9 +0,0 @@ -# Try this: - -moltemplate.sh twelve_days.lt - -# Moltemplate is a hierarchical template renderer. It can be used -# to create other kinds of text files which are not related to LAMMPS. -# -# Happy holidays -# -andrew 2016-12-20 diff --git a/tools/moltemplate/examples/misc_examples/twelve_days/twelve_days.lt b/tools/moltemplate/examples/misc_examples/twelve_days/twelve_days.lt deleted file mode 100644 index 6610649cb2..0000000000 --- a/tools/moltemplate/examples/misc_examples/twelve_days/twelve_days.lt +++ /dev/null @@ -1,19 +0,0 @@ -Msg {write() { On the ${day}th day of Christmas, my true love gave to me: -} -} -Gifts1 {write(){@day partridge in a pear tree. - -}} Gifts2 {write(){@day turtle doves, and -} gifts = new Gifts1 } Gifts3 {write(){@day french hens, -} gifts = new Gifts2 } Gifts4 {write(){@day calling birds, -} gifts = new Gifts3 } Gifts5 {write(){@day golden rings, -} gifts = new Gifts4 } Gifts6 {write(){@day geese a-laying, -} gifts = new Gifts5 } Gifts7 {write(){@day swans a-swimming, -} gifts = new Gifts6 } Gifts8 {write(){@day maids a-milking, -} gifts = new Gifts7 } Gifts9 {write(){@day ladies dancing, -} gifts = new Gifts8 } Gifts10 {write(){@day lords a-leaping, -} gifts = new Gifts9 } Gifts11 {write(){@day pipers piping, -} gifts = new Gifts10 } Gifts12 {write(){@day drummers drumming, -} gifts = new Gifts11 } -Msg1 inherits Msg{g = new Gifts1} Msg2 inherits Msg{g = new Gifts2} Msg3 inherits Msg{g = new Gifts3} Msg4 inherits Msg{g = new Gifts4} Msg5 inherits Msg{g = new Gifts5} Msg6 inherits Msg{g = new Gifts6} Msg7 inherits Msg{g = new Gifts7} Msg8 inherits Msg{g = new Gifts8} Msg9 inherits Msg{g = new Gifts9} Msg10 inherits Msg{g = new Gifts10} Msg11 inherits Msg{g = new Gifts11} Msg12 inherits Msg{g = new Gifts12} -msg1 = new Msg1 msg2 = new Msg2 msg3 = new Msg3 msg4 = new Msg4 msg5 = new Msg5 msg6 = new Msg6 msg7 = new Msg7 msg8 = new Msg8 msg9 = new Msg9 msg10 = new Msg10 msg11 = new Msg11 msg12 = new Msg12 diff --git a/tools/moltemplate/moltemplate/__init__.py b/tools/moltemplate/moltemplate/__init__.py deleted file mode 100644 index ccd228a8c1..0000000000 --- a/tools/moltemplate/moltemplate/__init__.py +++ /dev/null @@ -1,18 +0,0 @@ -from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ - StackableCommand, PopCommand, PopRightCommand, PopLeftCommand, \ - PushCommand, PushLeftCommand, PushRightCommand, ScopeCommand, \ - WriteVarBindingsFile, StaticObj, InstanceObj, ExtractFormattingCommands, \ - BasicUI, ScopeBegin, ScopeEnd, WriteFileCommand, Render -from .ttree_lex import TtreeShlex, split, LineLex, SplitQuotedString, \ - EscCharStrToChar, SafelyEncodeString, RemoveOuterQuotes, MaxLenStr, \ - HasWildcard, InputError, ErrorLeader, SrcLoc, OSrcLoc, TextBlock, VarRef, \ - VarNPtr, VarBinding, SplitTemplate, SplitTemplateMulti, TableFromTemplate, \ - ExtractCatName, DeleteLinesWithBadVars, TemplateLexer -from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid, \ - ColNames2Coords, ColNames2Vects, ColNames2Vects, data_atoms, data_masses -from .ettree_styles import \ - LinesWSlashes, SplitMultiDelims, SplitAtomLine, \ - iEsptAtomCoords, iEsptAtomVects, iEsptAtomType, iEsptAtomID -from .ttree_matrix_stack import MultMat, MatToStr, LinTransform, \ - AffineTransform, AffineCompose, CopyMat, ScaleMat, RotMatAXYZ, \ - CrossProd, DotProd, Length, Normalize, RotMatXYZXYZ, MultiAffineStack diff --git a/tools/moltemplate/moltemplate/bonds_by_type.py b/tools/moltemplate/moltemplate/bonds_by_type.py deleted file mode 100755 index 3df4a26582..0000000000 --- a/tools/moltemplate/moltemplate/bonds_by_type.py +++ /dev/null @@ -1,376 +0,0 @@ -#!/usr/bin/env python - -# Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2011, Regents of the University of California -# All rights reserved. - -""" - bonds_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS) - data file containing bonded many-body interactions by atom type - (and bond type), and generates a list of additional interactions - in LAMMPS format consistent with those type (to the standard out). - - Typical Usage: - - bonds_by_type.py -atoms atoms.data \\ - -bonds bonds.data \\ - -bondsbytype bonds_by_type.data \\ - > new_bonds.data - -""" - - -g_program_name = __file__.split('/')[-1] # = 'bonds_by_type.py' -g_date_str = '2016-12-21' -g_version_str = '0.12.0' - - -import sys - -try: - from . import ttree_lex - from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (ImportError, SystemError, ValueError): - # not installed as a package - import ttree_lex - from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid - - -def LookupBondTypes(bond_types, - bond_ids, - bond_pairs, - lines_atoms, - lines_bonds, - lines_bondsbytype, - atom_style, - section_name, - prefix='', - suffix='', - bond_ids_offset=0): - # report_progress = False): - """ - LookupBondTypes() looks up bond types. - - Output: - ...It looks up the corresponding type of each bond and store it in the - "bond_types" list. (If the bond_ids were not specified by the user, - generate them and store them in the bond_ids list.) - - - Input (continued): - This function requires: - ...a list of bonded pairs of atoms - stored in the lines_bonds variable (from the "Data Bond List" - or "Data Bonds AtomId AtomId" sections) - ...and a list of atom types - stored in the lines_atoms variable (from the "Data Atoms" section) - ...and a list of bond-types-as-a-function-of-atom-types - stored in the lines_bondsbytype (from the "Data Bonds By Type" section) - - Generated bond_ids (if applicable) are of the form - prefix + str(number) + suffix - (where "number" begins at bond_ids_offset+1) - - """ - - column_names = AtomStyle2ColNames(atom_style) - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) - - atomids = [] - atomtypes = [] - atomids2types = {} - - for iv in range(0, len(lines_atoms)): - line = lines_atoms[iv].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - if len(line) > 0: - tokens = ttree_lex.SplitQuotedString(line) - if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)): - sys.stderr.write("\"" + line + "\"\n") - raise(ttree_lex.InputError( - 'Error not enough columns on line ' + str(iv + 1) + ' of \"Atoms\" section.')) - tokens = ttree_lex.SplitQuotedString(line) - atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid]) - atomids.append(atomid) - atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype]) - atomtypes.append(atomtype) - atomids2types[atomid] = atomtype - - assert(isinstance(bond_ids, list)) - assert(isinstance(bond_types, list)) - assert(isinstance(bond_pairs, list)) - del bond_ids[:] - del bond_types[:] - del bond_pairs[:] - - for ie in range(0, len(lines_bonds)): - - line = lines_bonds[ie].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - - if len(line) == 0: - continue - - tokens = ttree_lex.SplitQuotedString(line) - - if section_name == "Data Bonds AtomId AtomId": - if len(tokens) == 2: - bondid_n = bond_ids_offset + len(bond_ids) + 1 - bond_ids.append(prefix + str(bondid_n) + suffix) - bond_pairs.append((ttree_lex.EscCharStrToChar(tokens[0]), - ttree_lex.EscCharStrToChar(tokens[1]))) - else: - raise(ttree_lex.InputError('Incorrect number of columns on line ' + - str(ie + 1) + ' of \"' + section_name + '\" section.')) - - elif section_name == "Data Bond List": - if len(tokens) == 3: - bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0])) - bond_pairs.append((ttree_lex.EscCharStrToChar(tokens[1]), - ttree_lex.EscCharStrToChar(tokens[2]))) - else: - raise(ttree_lex.InputError('Incorrect number of columns on line ' + - str(ie + 1) + ' of \"' + section_name + '\" section.')) - - else: - raise(ttree_lex.InputError('Internal Error (' + g_program_name + - '): Unknown section name: \"' + section_name + '\"')) - - assert(len(bond_types) == 0) - typepattern_to_coefftypes = [] - - for i in range(0, len(lines_bondsbytype)): - line = lines_bondsbytype[i].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - if len(line) > 0: - tokens = ttree_lex.SplitQuotedString(line) - - if (len(tokens) != 3): - raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Bonds By Type\" section of data file.\n' - 'Offending line:\n' + - '\"' + line + '\"\n' - 'Expected 3 columns\n')) - - coefftype = ttree_lex.EscCharStrToChar(tokens[0]) - typepattern = [] - - for typestr in tokens[1:]: - if ((len(typestr) >= 2) and - (typestr[0] == '/') and (typestr[-1] == '/')): - regex_str = typestr[1:-1] - typepattern.append(re.compile(regex_str)) - else: - typepattern.append(ttree_lex.EscCharStrToChar(typestr)) - - typepattern_to_coefftypes.append([typepattern, coefftype]) - - assert(len(bond_ids) == len(bond_pairs)) - - for ie in range(0, len(bond_ids)): - bond_types.append(None) - - for ie in range(0, len(bond_ids)): - bondid = bond_ids[ie] - (atomid1, atomid2) = bond_pairs[ie] - - if atomid1 not in atomids2types: - raise ttree_lex.InputError('Error: atom \"' + atomid1 + '\" not defined in \"Data Atoms\".\n' - ' This usually happens when the user mistypes one of the names of the\n' - ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' - ' To find out where the mistake occured, search the \n' - ' \"ttree_assignments.txt\" file for:\n' - ' \"' + atomid1 + '\"\n') - - if atomid2 not in atomids2types: - raise ttree_lex.InputError('Error: atom \"' + atomid2 + '\" not defined in \"Data Atoms\".\n' - ' This usually happens when the user mistypes one of the names of the\n' - ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' - ' To find out where the mistake occured, search the \n' - ' \"ttree_assignments.txt\" file for:\n' - ' \"' + atomid2 + '\"\n') - - atomtype1 = atomids2types[atomid1] - atomtype2 = atomids2types[atomid2] - - for typepattern, coefftype in typepattern_to_coefftypes: - - # use string comparisons to check if atom types match the pattern - if (ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern) or - ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern)): - # ("MatchesAll()" defined in "ttree_lex.py") - - bond_types[ie] = coefftype - - for ie in range(0, len(bond_ids)): - if not bond_types[ie]: - (atomid1, atomid2) = bond_pairs[ie] - atomtype1 = atomids2types[atomid1] - atomtype2 = atomids2types[atomid2] - raise ttree_lex.InputError('Error: No bond types defined for the bond between\n' - ' atoms ' + atomid1 + - ' (type ' + atomtype1 + ')\n' - ' and ' + atomid2 + ' (type ' + atomtype2 + ')\n') - - -def main(): - sys.stderr.write(g_program_name + ' v' + - g_version_str + ' ' + g_date_str + ' ') - if sys.version < '3': - sys.stderr.write(' (python version < 3)\n') - else: - sys.stderr.write('\n') - - try: - fname_atoms = None - fname_bond_list = None - fname_bondsbytype = None - section_name = 'Data Bond List' # (This will be replaced later.) - atom_style = 'full' - prefix = '' - suffix = '' - bond_lack_types = False - - argv = [arg for arg in sys.argv] - - # Loop over the remaining arguments not processed yet. - # These arguments are specific to the lttree.py program - # and are not understood by ttree.py: - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if ((argv[i].lower() == '-?') or - (argv[i].lower() == '--?') or - (argv[i].lower() == '-help') or - (argv[i].lower() == '-help')): - if i + 1 >= len(argv): - sys.stdout.write(man_page_text + '\n') - sys.exit(0) - - elif argv[i].lower() == '-atoms': - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a file name containing lines of\n' - ' text which might appear in the "Atoms" section of a LAMMPS data file.\n') - fname_atoms = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i].lower() == '-bonds': - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a file name containing lines of\n' - ' text which might appear in the "Bonds" section of a LAMMPS data file.\n') - fname_bond_list = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i].lower() == '-bond-list': - if i + 1 >= len(argv): - raise ttree_lex.InputError( - 'Error: ' + argv[i] + ' flag should be followed by a file name\n') - # raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' - # ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n') - fname_bond_list = argv[i + 1] - section_name = "Data Bond List" - del(argv[i:i + 2]) - - elif argv[i].lower() == '-bondsbytype': - if i + 1 >= len(argv): - raise ttree_lex.InputError( - 'Error: ' + argv[i] + ' flag should be followed by a file name\n') - - # raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n' - # ' text which might appear in the "'+section_name+' By Type" section\n' - # ' of a LAMMPS data file.\n') - fname_bondsbytype = argv[i + 1] - del(argv[i:i + 2]) - - elif ((argv[i].lower() == '-atom-style') or - (argv[i].lower() == '-atom_style')): - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a an atom_style name.\n' - ' (Or single quoted string which includes a space-separated\n' - ' list of column names.)\n') - atom_style = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i].lower() == '-prefix': - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a prefix string\n' - ' (a string you want to appear to the left of the integer\n' - ' which counts the bonded interactions you have generated.)\n') - prefix = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i].lower() == '-suffix': - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a suffix string\n' - ' (a string you want to appear to the right of the integer\n' - ' which counts the bonded interactions you have generated.)\n') - prefix = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i][0] == '-': - raise ttree_lex.InputError('Error(' + g_program_name + '):\n' - 'Unrecogized command line argument \"' + argv[i] + '\"\n') - else: - i += 1 - - if len(argv) != 1: - # if there are more than 2 remaining arguments, - problem_args = ['\"' + arg + '\"' for arg in argv[1:]] - raise ttree_lex.InputError('Syntax Error(' + g_program_name + '):\n\n' - ' Problem with argument list.\n' - ' The remaining arguments are:\n\n' - ' ' + - (' '.join(problem_args)) + '\n\n' - ' (The actual problem may be earlier in the argument list.)\n') - - bond_types = [] - bond_ids = [] - bond_pairs = [] - - fatoms = open(fname_atoms, 'r') - fbonds = open(fname_bond_list, 'r') - fbondsbytype = open(fname_bondsbytype, 'r') - lines_atoms = fatoms.readlines() - lines_bonds = fbonds.readlines() - lines_bondsbytype = fbondsbytype.readlines() - fatoms.close() - fbonds.close() - fbondsbytype.close() - - LookupBondTypes(bond_types, - bond_ids, - bond_pairs, - lines_atoms, - lines_bonds, - lines_bondsbytype, - atom_style, - section_name, - prefix='', - suffix='') - - assert(len(bond_types) == len(bond_ids) == len(bond_pairs)) - - ie = 0 - N = len(bond_types) - for ie in range(0, N): - sys.stdout.write(bond_ids[ie] + ' ' + - bond_types[ie] + ' ' + - bond_pairs[ie][0] + ' ' + - bond_pairs[ie][1] + '\n') - - except (ValueError, ttree_lex.InputError) as err: - sys.stderr.write('\n' + str(err) + '\n') - sys.exit(-1) - - return - - -if __name__ == "__main__": - main() diff --git a/tools/moltemplate/moltemplate/charge_by_bond.py b/tools/moltemplate/moltemplate/charge_by_bond.py deleted file mode 100755 index 83acb83935..0000000000 --- a/tools/moltemplate/moltemplate/charge_by_bond.py +++ /dev/null @@ -1,398 +0,0 @@ -#!/usr/bin/env python -# Author: Andrew Jewett (jewett.aij at g mail) -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2017, California Institute of Technology -# All rights reserved. - -g_program_name = __file__.split('/')[-1] # = 'charge_by_bond.py' -g_date_str = '2017-10-03' -g_version_str = '0.14.0' - - -import sys -import re -from collections import defaultdict - -try: - from . import ttree_lex - from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid -except (ImportError, SystemError, ValueError): - # not installed as a package - import ttree_lex - from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid - - - -def LookupChargePairs(chargebyatomid, - # bond_ids, - # bond_types, - # bond_pairs, - lines_atoms, - lines_bonds, - lines_bond_list, - lines_chargebybond, - atom_style, - section_name, - prefix='', - suffix=''): - # bond_ids_offset=0): - # report_progress = False): - """ - LookupChargePairs() looks up partial-charge pair contributions from the - types of atoms participating in a bond. - - Output: - ...It looks up the corresponding change in the partial charges for - each pair of atoms and stores this in the "chargebyatomid" dictionary. - - Input (continued): - This function requires: - ...a list of bonded pairs of atoms - stored in the lines_bonds variable (from the "Data Bond List" - or "Data Bonds AtomId AtomId" sections) - ...and a list of atom types - stored in the lines_atoms variable (from the "Data Atoms" section) - - ...and a list of charge-pairs-as-a-function-of-atom-types - stored in the lines_chargebybond (from the "Data Bonds By Type" section) - - """ - - column_names = AtomStyle2ColNames(atom_style) - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) - - atomids = [] - atomtypes = [] - atomids2types = {} - - for iv in range(0, len(lines_atoms)): - line = lines_atoms[iv].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - if len(line) > 0: - tokens = ttree_lex.SplitQuotedString(line) - if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)): - sys.stderr.write("\"" + line + "\"\n") - raise(ttree_lex.InputError( - 'Error not enough columns on line ' + str(iv + 1) + ' of \"Atoms\" section.')) - tokens = ttree_lex.SplitQuotedString(line) - atomid = ttree_lex.EscCharStrToChar(tokens[i_atomid]) - atomids.append(atomid) - atomtype = ttree_lex.EscCharStrToChar(tokens[i_atomtype]) - atomtypes.append(atomtype) - atomids2types[atomid] = atomtype - - #assert(isinstance(bond_ids, list)) - #assert(isinstance(bond_types, list)) - #assert(isinstance(bond_pairs, list)) - #del bond_ids[:] - #del bond_types[:] - #del bond_pairs[:] - bond_pairs = [] - - for ie in range(0, len(lines_bond_list)): - line = lines_bond_list[ie].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - if len(line) == 0: - continue - tokens = ttree_lex.SplitQuotedString(line) - if len(tokens) == 3: - # bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0])) - bond_pairs.append((ttree_lex.EscCharStrToChar(tokens[1]), - ttree_lex.EscCharStrToChar(tokens[2]))) - else: - raise(ttree_lex.InputError('Incorrect number of columns on line ' + - str(ie + 1) + ' of \"' + section_name + '\" section.')) - - for ie in range(0, len(lines_bonds)): - line = lines_bonds[ie].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - if len(line) == 0: - continue - tokens = ttree_lex.SplitQuotedString(line) - if len(tokens) == 4: - # bond_ids.append(ttree_lex.EscCharStrToChar(tokens[0])) - # bond_types.append(ttree_lex.EscCharStrToChar(tokens[1])) - bond_pairs.append((ttree_lex.EscCharStrToChar(tokens[2]), - ttree_lex.EscCharStrToChar(tokens[3]))) - else: - raise(ttree_lex.InputError('Incorrect number of columns on line ' + - str(ie + 1) + ' of \"' + section_name + '\" section.')) - - # for ie in range(0, len(lines_bonds_atomid_atomid)): - # line = lines_bonds_atomid_atomid[ie].strip() - # if '#' in line: - # icomment = line.find('#') - # line = (line[:icomment]).strip() - # if len(line) == 0: - # continue - # tokens = ttree_lex.SplitQuotedString(line) - # if len(tokens) == 2: - # #bondid_n = bond_ids_offset + len(bond_ids) + 1 - # #bond_ids.append(prefix+str(bondid_n)+suffix) - # bond_pairs.append( (ttree_lex.EscCharStrToChar(tokens[0]), - # ttree_lex.EscCharStrToChar(tokens[1])) ) - # else: - # raise(ttree_lex.InputError('Incorrect number of columns on line '+str(ie+1)+' of \"'+section_name+'\" section.')) - - #assert(len(bond_types) == 0) - typepattern_to_chargepairs = [] - warning_unassigned_chargepairs = None - - for i in range(0, len(lines_chargebybond)): - line = lines_chargebybond[i].strip() - if '#' in line: - icomment = line.find('#') - line = (line[:icomment]).strip() - if len(line) > 0: - tokens = ttree_lex.SplitQuotedString(line) - - if (len(tokens) != 4): - raise(ttree_lex.InputError('Error: Wrong number of columns in the \"Charge Pairs By Type\" section of data file.\n' - 'Offending line:\n' + - '\"' + line + '\"\n' - 'Expected 4 columns\n')) - - chargepair = (float(tokens[2]), - float(tokens[3])) - - typepattern = [] - - for typestr in tokens[:2]: - if ((len(typestr) >= 2) and - (typestr[0] == '/') and (typestr[-1] == '/')): - regex_str = typestr[1:-1] - typepattern.append(re.compile(regex_str)) - else: - typepattern.append(ttree_lex.EscCharStrToChar(typestr)) - - typepattern_to_chargepairs.append([typepattern, chargepair]) - - for atomid1, atomid2 in bond_pairs: - - if atomid1 not in atomids2types: - raise ttree_lex.InputError('Error: atom \"' + atomid1 + '\" not defined in \"Data Atoms\".\n' - ' This usually happens when the user mistypes one of the names of the\n' - ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' - ' To find out where the mistake occured, search the \n' - ' \"ttree_assignments.txt\" file for:\n' - ' \"' + atomid1 + '\"\n') - - if atomid2 not in atomids2types: - raise ttree_lex.InputError('Error: atom \"' + atomid2 + '\" not defined in \"Data Atoms\".\n' - ' This usually happens when the user mistypes one of the names of the\n' - ' $atoms in either a \"Data Atoms\" or \"Data Bond List\" section.\n' - ' To find out where the mistake occured, search the \n' - ' \"ttree_assignments.txt\" file for:\n' - ' \"' + atomid2 + '\"\n') - - atomtype1 = atomids2types[atomid1] - atomtype2 = atomids2types[atomid2] - - found = False - for typepattern, chargepair in typepattern_to_chargepairs: - # use string comparisons to check if atom types match the pattern - if ttree_lex.MatchesAll((atomtype1, atomtype2), typepattern): - # ("MatchesAll()" defined in "ttree_lex.py") - chargebyatomid[atomid1] += chargepair[0] - chargebyatomid[atomid2] += chargepair[1] - found = True - elif ttree_lex.MatchesAll((atomtype2, atomtype1), typepattern): - chargebyatomid[atomid1] += chargepair[1] - chargebyatomid[atomid2] += chargepair[0] - found = True - if (not found) and (not warning_unassigned_chargepairs): - warning_unassigned_chargepairs = (atomid1, atomid2) - - if warning_unassigned_chargepairs: - sys.stderr.write('---------------------------------------------------------------------------\n' - 'Warning: bonds found between atoms with no partial-charge rules.\n' - ' This means that somewhere you are using a force-field\n' - ' which assigns atomic charge according to the bonds these atoms\n' - ' participate in, AND at least one pair of bonded atoms does NOT have\n' - ' a rule defined to assign charges to that pair of atoms.\n' - ' This can happen if there is a problem with the force-field file\n' - ' OR if you are defining the charges for these atoms manually\n' - ' In the later case, it is not a problem.\n' - ' The first bond with this problem is between this pair of atoms:\n' - ' ' + - str(warning_unassigned_chargepairs[0]) + '\n' - ' ' + - str(warning_unassigned_chargepairs[1]) + '\n' - '---------------------------------------------------------------------------\n') - -def main(): - """ - This is is a "main module" wrapper for invoking chargepairs_by_type.py - as a stand alone program. This program: - This program reads a LAMMPS data file (or an excerpt of a LAMMPS) - data file containing bonded many-body interactions by atom type - (and bond type), and generates a list of atom charges in LAMMPS input - script format consistent with those types (to the standard out). - - Typical Usage: - - chargepairs_by_type.py -atoms atoms.data \\ - -bonds bonds.data \\ - -chargebybond chargepairs_by_type.data \\ - > list_of_atom_charges.in - - """ - - ####### Main Code Below: ####### - sys.stderr.write(g_program_name + ' v' + - g_version_str + ' ' + g_date_str + ' ') - if sys.version < '3': - sys.stderr.write(' (python version < 3)\n') - else: - sys.stderr.write('\n') - - try: - fname_atoms = None - fname_bonds = None - fname_bond_list = None - fname_chargebybond = None - section_name = 'Data Bond List' # (This will be replaced later.) - atom_style = 'full' - prefix = '' - suffix = '' - bond_lack_types = False - - argv = [arg for arg in sys.argv] - - # Loop over the remaining arguments not processed yet. - # These arguments are specific to the lttree.py program - # and are not understood by ttree.py: - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if ((argv[i].lower() == '-?') or - (argv[i].lower() == '--?') or - (argv[i].lower() == '-help') or - (argv[i].lower() == '-help')): - if i + 1 >= len(argv): - sys.stdout.write(man_page_text + '\n') - sys.exit(0) - - elif argv[i].lower() == '-atoms': - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a file name containing lines of\n' - ' text which might appear in the "Atoms" section of a LAMMPS data file.\n') - fname_atoms = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i].lower() == '-bonds': - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a file name containing lines of\n' - ' text which might appear in the "Bonds" section of a LAMMPS data file.\n') - fname_bonds = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i].lower() == '-bond-list': - if i + 1 >= len(argv): - raise ttree_lex.InputError( - 'Error: ' + argv[i] + ' flag should be followed by a file name\n') - # raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n' - # ' text which might appear in the "Bonds No Types" section of a LAMMPS data file.\n') - fname_bond_list = argv[i + 1] - section_name = "Data Bond List" - del(argv[i:i + 2]) - - elif ((argv[i].lower() == '-chargebybond') or - (argv[i].lower() == '-chargesbybond') or - (argv[i].lower() == '-charge-by-bond') or - (argv[i].lower() == '-charges-by-bond') or - (argv[i].lower() == '-chargepairsbytype') or - (argv[i].lower() == '-chargepairs-by-type') or - (argv[i].lower() == '-charge-pairs-by-type')): - if i + 1 >= len(argv): - raise ttree_lex.InputError( - 'Error: ' + argv[i] + ' flag should be followed by a file name\n') - - # raise ttree_lex.InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n' - # ' text which might appear in the "'+section_name+' By Type" section\n' - # ' of a LAMMPS data file.\n') - fname_chargebybond = argv[i + 1] - del(argv[i:i + 2]) - - elif ((argv[i].lower() == '-atom-style') or - (argv[i].lower() == '-atom_style')): - if i + 1 >= len(argv): - raise ttree_lex.InputError('Error: ' + argv[i] + ' flag should be followed by a an atom_style name.\n' - ' (Or single quoted string which includes a space-separated\n' - ' list of column names.)\n') - atom_style = argv[i + 1] - del(argv[i:i + 2]) - - elif argv[i][0] == '-': - raise ttree_lex.InputError('Error(' + g_program_name + '):\n' - 'Unrecogized command line argument \"' + argv[i] + '\"\n') - else: - i += 1 - - if len(argv) != 1: - # if there are more than 2 remaining arguments, - problem_args = ['\"' + arg + '\"' for arg in argv[1:]] - raise ttree_lex.InputError('Syntax Error(' + g_program_name + '):\n\n' - ' Problem with argument list.\n' - ' The remaining arguments are:\n\n' - ' ' + - (' '.join(problem_args)) + '\n\n' - ' (The actual problem may be earlier in the argument list.)\n') - - #bond_types = [] - fatoms = open(fname_atoms, 'r') - lines_bonds = [] - lines_bond_list = [] - fbonds = fbond_list = None - try: - if fname_bonds != None: - fbonds = open(fname_bonds, 'r') - lines_bonds = fbonds.readlines() - fbonds.close() - except IOError: - pass - try: - if fname_bond_list != None: - fbond_list = open(fname_bond_list, 'r') - lines_bond_list = fbond_list.readlines() - fbond_list.close() - except IOError: - pass - if ((len(lines_bonds) == 0) and (len(lines_bond_list) == 0)): - sys.stderr.write('Error(' + g_program_name + '): No bonds defined for this system\n' - ' (This error may be a bug in moltemplate.)\n') - fchargebybond = open(fname_chargebybond, 'r') - lines_atoms = fatoms.readlines() - - lines_chargebybond = fchargebybond.readlines() - fatoms.close() - fchargebybond.close() - chargebyatomid = defaultdict(float) - - LookupChargePairs(chargebyatomid, - lines_atoms, - lines_bonds, - lines_bond_list, - lines_chargebybond, - atom_style, - section_name) - - for atomid, charge in chargebyatomid.items(): - sys.stdout.write(' set atom ' + str(atomid) + - ' charge ' + str(charge) + '\n') - - except (ValueError, ttree_lex.InputError) as err: - sys.stderr.write('\n' + str(err) + '\n') - sys.exit(-1) - - - -if __name__ == "__main__": - main() - diff --git a/tools/moltemplate/moltemplate/depreciated/oplsaa_moltemplate.py b/tools/moltemplate/moltemplate/depreciated/oplsaa_moltemplate.py deleted file mode 100644 index 984dc6415d..0000000000 --- a/tools/moltemplate/moltemplate/depreciated/oplsaa_moltemplate.py +++ /dev/null @@ -1,488 +0,0 @@ -#! /usr/bin/env python -# -# The purpose of this script is to create a moltemplate lt file for the oplsaa. -# forcefield. This will assist researchers in building complex simulations using -# this OPLS-UA and the OPLS-AA forcefields. - -__author__="Jason Lambert" -# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu, and Andrew Jewett) -__version__="0.21" - - - -import sys -import os -from operator import itemgetter - -g_program_name = __file__.split('/')[-1] - -# First make a copy of the \"oplsaa.prm\" file -# (which can be downloaded from the TINKER web site). -# The lines in this file beginning with the word \"atoms\" should -# define the atoms which you plan to put in your simulation. All other -# lines beginning with the word \"atoms\" should be deleted. -# (Leave the other sections of this file alone.) -#""") - - -if sys.version > '3': - import io -else: - import cStringIO - -try: - if sys.version < '2.7': - raise Exception('Error: Using python '+sys.version+'\n'+ - ' Alas, your version of python is too old.\n' - ' You must upgrade to a newer version of python (2.7 or later).') -except Exception as err: - sys.stderr.write('\n\n'+str(err)+'\n') - sys.exit(-1) - - - -#input data from file containing oplsaa force field parameters. -try: - f=open(sys.argv[1],"r") -except: - sys.stderr.write("Error: \n" - " You need to specify a file name as an input argument:\n" - " python oplsaa_moltemplate.py \n" - " (or the file name is specified incorrectly)\n") - sys.exit() - - -sys.stderr.write(g_program_name+", version "+__version__+"\n" - "Reading parameter file...\n") - - -#output lt file -g=open("oplsaa.lt","w") - - - -lines = f.readlines() - - - -# Ignore/Comment out lines before the "## Atom Type Definitions ##" section. - -for i in range(0, len(lines)): - if (lines[i].find("## Atom Type Definitions ##") != -1): - break - else: - lines[i] = '# ' + lines[i] - - -# As of late 2014, there appear to be 906 atom types, but we don't assume this. -# First try to infer out how many atom types there were in the original -# oplsaa.prm file, or at least find an upper bound on the atom-type numbers. -# (Keep track of the maximum value of the first column in the "atom" section.) -max_atomType = 0 -num_atomTypes = 0 -for line in lines: - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - # now look for lines beginning with the word "atom" - tokens = line.split() - if ((len(tokens)>2) and (tokens[0] == "atom")): - num_atomTypes += 1 - if (int(tokens[1]) > max_atomType): - max_atomType = int(tokens[1]) - -if num_atomTypes > 25: - sys.stderr.write("\n" - "(Note: If your computer freezes while running "+g_program_name+",\n" - " it could be because you forgot to edit the .prm file.\n" - " The original \"oplsaa.prm\" file distributed with TINKER has over 900 atom\n" - " types. If you run "+g_program_name+" on this file, it may freeze or\n" - " crash. Instead, run "+g_program_name+" on a SUBSET of the OPLS atoms\n" - " relevant to your problem. To do that, delete the lines from the .prm\n" - " file beginning with \"atom\" which you do not need.)\n\n") - -#temporary storage file -atom_lookup={} #this dictionary contains all the atom ffid's as a key and the number of atoms with that key -#atom=[[10000,10000] for i in range(906)] <- don't assume there are 906 atoms -atom=[[-10000,-10000] for i in range(0,max_atomType+1)] -#charge_by_type={} # lookup charge by atom type -#vdw_by_type={} # lookup epsilon & sigma paramters by atom type -charge_by_type=[0.0 for i in range(0,max_atomType+1)] # lookup charge by atom -vdw_by_type=[(0.0,0.0) for i in range(0,max_atomType+1)] # lookup epsilon & sigma - - - -#atom is declared this way so for sorting purposes. -#atom contains the following data upon allocation -#atom[][0]=atom_id( Important for partial charges and non_bonded interactions) -#atom[][1]=atom_ffid( Important for stretches, bending, torsions and impropers) -#atom[][2]=atom_mass -#atom[][3]=partial charge -#atom[][4]=non_bonding sigma -#atom[][5]=non_bonding epsilon -#atom[][6]=atom comment -bond=[] -#bond contains the following data -#bond[0]=atom 1 ffid -#bond[1]=atom 2 ffid -#bond[2]=bond spring constant(OPLS-aa compatible) -#bond[3]=equilibrium bond distance(Angstrom) -angle=[] -#angle contains the following data -#angle[0]=atom 1 ffid -#angle[1]=atom 2 ffid -#angle[2]=atom 3 ffid -#angle[3]=spring constant -#angle[4]=equilibrium angle (degrees) -dihedral=[] -#dihedral contains the following data -#dihedral[0]=atom 1 ffid -#dihedral[1]=atom 2 ffid -#dihedral[2]=atom 3 ffid -#dihedral[3]=atom 4 ffid -#dihedral[4]=v1 -#dihedral[5]=v2 -#dihedral[6]=v3 -#dihedral[7]=v4 -improper=[] -#improper[0]=atom 1 ffid -#improper[1]=atom 2 ffid(central atom) -#improper[2]=atom 3 ffid -#improper[3]=atom 4 ffid -#improper[4]=spring coefficient -#improper[5]=equilibrium angle - - -#This section gets all the parameters from the force field file -for line in lines: - - # skip over text after a # comment character - ic = line.find('#') - if ic != -1: - line = (line[:ic]).strip() - else: - line = line.strip() - - if line.find("atom") == 0: - line=line.split() - atom[int(line[1])-1]=[int(line[1]),int(line[2]),float(line[-2]), - 0.0,0.0,0.0," ".join(line[3:-2])] - elif line.find("vdw") == 0: - line=line.split() - #vdw_temp.append([float(line[1]),float(line[2]),float(line[3])]) - if (int(line[1]) <= max_atomType): - vdw_by_type[int(line[1])] = (float(line[2]),float(line[3])) - elif line.find("bond") == 0: - line=line.split() - bond.append([int(line[1]),int(line[2]),float(line[3]),float(line[4])]) - elif line.find("angle") == 0: - line=line.split() - angle.append([int(line[1]),int(line[2]),int(line[3]), - float(line[4]),float(line[5])]) - elif line.find("torsion") == 0: - line=line.split() - dihedral.append([int(line[1]),int(line[2]),int(line[3]),int(line[4]), - float(line[5]),float(line[8]), float(line[11]), 0.0]) - elif line.find("charge") == 0: - line=line.split() - #charge_temp.append([int(line[1]),float(line[2])]) - if (int(line[1]) <= max_atomType): - charge_by_type[int(line[1])] = float(line[2]) - elif line.find("imptors") == 0: - line=line.split() - improper.append([int(line[1]), int(line[2]), - int(line[3]), int(line[4]), float(line[5]), float(line[6])]) - - -#if len(atom) > 600: -# sys.stderr.write("WARNING: The number of atom types in your file exceeds 600\n" -# " (You were supposed to edit out the atoms you don't need.\n" -# " Not doing this may crash your computer.)\n" -# "\n" -# " Proceed? (Y/N): ") -# reply = sys.stdin.readline() -# if find(reply.strip().lower(), 'y') != 0: -# exit(0) - - - -#adding the charge and Lennard Jones parameters to -#to each atom type. -#----------------------------------------------# - -system_is_charged = False - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #q = charge_by_type.get(atomTypeNum) - #if q: - # atom[i][3] = q - if atom_type_num != -10000: - q = charge_by_type[atom_type_num] - atom[i][3] = q - if q != 0.0: - # the system has some charged atoms - system_is_charged = True - -for i in range(0,len(atom)): - atom_type_num = atom[i][0] - #vdw_params = vdw_by_type.get(atomTypeNum) - #if vdw_params: - # atom[i][4] = vdw_params[0] - # atom[i][5] = vdw_params[1] - if atom_type_num != -10000: - vdw_params = vdw_by_type[atom_type_num] - atom[i][4] = vdw_params[0] - atom[i][5] = vdw_params[1] - -del(charge_by_type) -del(vdw_by_type) - - - -if system_is_charged: - pair_style = "lj/cut/coul/long" - pair_style_params = "10.0 10.0" - kspace_style = " kspace_style pppm 0.0001\n" -else: - pair_style = "lj/cut" - pair_style_params = "10.0" - kspace_style = "" - -pair_style_command = " pair_style hybrid "+pair_style+" "+pair_style_params+"\n" - - - -#----------------------------------------------------------# -#begin writing content to lt file -g.write("# NOTE: This file was created automatically using:\n" - "# "+g_program_name+" \""+sys.argv[1]+"\"\n\n\n") - -g.write("OPLSAA {\n\n" ) - -#write out the atom masses -#----------------------------------------------------------# -g.write(" write_once(\"Data Masses\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" @atom:{} {} #{} partial charge={}\n".format( - x[0],x[2],x[6],x[3])) -g.write(" } #(end of atom masses)\n\n") -#----------------------------------------------------------# - - -#write out the pair coefficients -#----------------------------------------------------------# -g.write(" write_once(\"In Settings\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - fmt = " pair_coeff @atom:{0} @atom:{0} "+pair_style+" {1} {2}\n" - g.write(fmt.format(x[0],x[5],x[4])) -g.write(" } #(end of pair coeffs)\n\n") - -g.write(" write_once(\"In Charges\"){\n")#checked with gaff -for i,x in enumerate(atom): - if x[0] != -10000: - g.write(" set type @atom:{0} charge {1}\n".format(x[0],x[3])) -g.write(" } #(end of atom charges)\n\n") - -#-----------------------------------------------------------# - -# This part of the code creates a lookup dictionary -# that allows you to find every type of atom by its -# force field id. force field id is the id number -# relevant to bonds, angles, dihedrals, and impropers. -# This greatly increases the speed of angle, bond, dihedral -# and improper assignment. -#------------------------------------------------------------# -atom=sorted(atom,key=itemgetter(1)) -atom_ffid=0 -for x in atom: - if x[1]==atom_ffid: - atom_lookup[x[1]].append(x[0]) - elif x[1]>atom_ffid: - atom_lookup[x[1]]=[x[0]] - atom_ffid=x[1] -atom_lookup[0]=["*"] - -#-------------------------------------------------------------# -#writing out the bond coefficients and bond parameters# -#-------------------------------------------------------------# - -# First check if the atoms in system can potentially form bonds -might_have_bonds = False -for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - might_have_bonds = True - -if might_have_bonds: - h=open("temp.txt","w+") - g.write(" write_once(\"In Settings\") {\n") - index1=0 - for x in bond: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - #g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2]/2,x[3])) - # Miguel Gonzales corrected this line to: - g.write(" bond_coeff @bond:{}-{} harmonic {} {}\n".format(y,z,x[2],x[3])) - h.write(" @bond:{0}-{1} @atom:{0} @atom:{1}\n".format(y,z)) - g.write(" } #(end of bond_coeffs)\n\n") - h.seek(0,0) - g.write(" write_once(\"Data Bonds By Type\") {\n") - for line in h.readlines(): - g.write(line) - g.write(" } #(end of bonds by type)\n\n") - del(bond) - h.close() - - -#-----------------------------------------------------------# -#writing out angle coefficients and angles by type.---------# -#-----------------------------------------------------------# - -# First check if the atoms in system can potentially form angle interactions -might_have_angles = False -for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - might_have_angles = True - -if might_have_angles: - h=open("temp.txt","w+") - g.write(" write_once(\"Data Angles By Type\"){\n") - for x in angle: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - #print(y,z,u,x) - #h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3]/2.0,x[4])) - # Miguel Gonzales corrected this line: - h.write(" angle_coeff @angle:{}-{}-{} harmonic {} {}\n".format(y,z,u,x[3],x[4])) - g.write(" @angle:{0}-{1}-{2} @atom:{0} @atom:{1} @atom:{2}\n".format(y,z,u)) - - g.write(" } #(end of angles by type)\n\n") - h.seek(0,0) - g.write(" write_once(\"In Settings\" ){\n") - for line in h.readlines(): - g.write(line) - g.write(" } #(end of angle_coeffs)\n\n") - del(angle) - h.close() - -#----------------------------------------------------------# -#writing dihedrals by type and dihedral coefficients-------# -#----------------------------------------------------------# - -# First check if the atoms in system can potentially form dihedral interactions -might_have_dihedrals = False -for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - might_have_dihedrals = True - -if might_have_dihedrals: - h=open("temp.txt","w+") - g.write(" write_once(\"Data Dihedrals By Type\") {\n") - #print(atom_lookup) - for x in dihedral: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - if x[0]!=0 and x[3]!=0: - g.write(" @dihedral:{0}-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" dihedral_coeff @dihedral:{}-{}-{}-{} opls {} {} {} {}\n".format(y,z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]!=0: - g.write(" @dihedral:0-{1}-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format( - y,z,u,v)) - h.write(" dihedral_coeff @dihedral:0-{}-{}-{} opls {} {} {} {}\n".format(z,u,v,x[4],x[5],x[6],x[7])) - elif x[0]==0 and x[3]==0: - g.write(" @dihedral:0-{1}-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - #h.write(" dihedral_coeff @dihedral:0-{}-{}-0 harmonic {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7])) - h.write(" dihedral_coeff @dihedral:0-{}-{}-0 opls {} {} {} {}\n".format(z,u,x[4],x[5],x[6],x[7])) - - del(dihedral) - g.write(" } #(end of Dihedrals by type)\n\n") - h.seek(0,0) - g.write(" write_once(\"In Settings\") {\n") - for line in h.readlines(): - g.write(line) - g.write(" } #(end of dihedral_coeffs)\n\n") - h.close() - -#-----------------------------------------------------------------------# -#----writing out improper coefficients and impropers by type------------# -#-----------------------------------------------------------------------# - -# First check if the atoms in system can potentially form improper interactions -might_have_impropers = False -for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - might_have_impropers = True - -if might_have_impropers: - h=open("temp.txt","w+") - g.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") - for x in improper: - for y in atom_lookup.get(x[0],[]): - for z in atom_lookup.get(x[1],[]): - for u in atom_lookup.get(x[2],[]): - for v in atom_lookup.get(x[3],[]): - # Notation: let I,J,K,L denote the atom types ("biotypes") - # listed in the order they appear in the "oplsaa.prm" file. - # (I think J and L are represented by "u" and "v" in the code here.) - # It looks like the "oplsaa.prm" file distributed with tinker - # treats the third atom ("K") as the central atom. - # After checking the code, it appears that the improper angle is - # calculated as the angle between the I,J,K and the J,K,L planes - if x[0]==0 and x[1]==0 and x[3]==0: - g.write(" @improper:0-0-{2}-0 @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-0 harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - else: - g.write(" @improper:0-0-{2}-{3} @atom:{0} @atom:{1} @atom:{2} @atom:{3}\n".format(y,z,u,v)) - h.write(" improper_coeff @improper:0-0-{2}-{3} harmonic {4} {5} \n".format(y,z,u,v,x[4]/2,180)) - - - g.write(" } #(end of impropers by type)\n\n") - h.seek(0,0) - g.write(" write_once(\"In Settings\") {\n") - for line in h.readlines(): - g.write(line) - g.write(" } #(end of improp_coeffs)\n\n") - h.close() - -#-----------------------------------------------------------------------# - -#This section writes out the input parameters required for an opls-aa simulation -# lammps. - - -g.write(" write_once(\"In Init\") {\n") -g.write(" units real\n") -g.write(" atom_style full\n") -g.write(" bond_style hybrid harmonic\n") -g.write(" angle_style hybrid harmonic\n") -g.write(" dihedral_style hybrid opls\n") -g.write(" improper_style hybrid harmonic\n") -g.write(pair_style_command) -g.write(" pair_modify mix geometric\n") -g.write(" special_bonds lj/coul 0.0 0.0 0.5\n") -g.write(kspace_style) -g.write(" } #end of init parameters\n\n") -g.write("} # OPLSAA\n") -f.close() -g.close() -os.remove("temp.txt") - - -sys.stderr.write("...finished.\n") diff --git a/tools/moltemplate/moltemplate/dump2data.py b/tools/moltemplate/moltemplate/dump2data.py deleted file mode 100755 index 249e6c9b2e..0000000000 --- a/tools/moltemplate/moltemplate/dump2data.py +++ /dev/null @@ -1,1311 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- -""" -dump2data.py - -Extract dynamical degrees of freedom from a lammps DUMP file (from the stdin) -and construct a new DATA file (to the stdout). -A reference DATA file is needed (argument). - - basic usage -./dump2data.py orig_file.data < dump.lammpstrj > new_file.data - (This extract last frame, uses "full" atom_style.) - - options: -./dump2data.py [-t t -atomstyle style] orig.data < dump.lammpstrj > new.data - -""" - -# Authors: Andrew Jewett -# License: New BSD License -# Copyright (c) 2014 -# All rights reserved. - -g_program_name = 'dump2data.py' -g_date_str = '2017-9-12' -g_version_str = '0.54.1' - -import sys -from collections import defaultdict -from operator import itemgetter, attrgetter - - -class InputError(Exception): - - def __init__(self, err_msg): - self.err_msg = err_msg - - def __str__(self): - return self.err_msg - - -def ErrorLeader(infile, lineno): - return '\"' + infile + '\", line ' + str(lineno) + ': ' - - -class MiscSettings(object): - - def __init__(self): - self.tstart = None - self.tstop = None - self.timestep_str = '' - self.last_frame = False - self.center_frame = False - self.output_format = 'data' - self.input_format = 'dump' - self.multi = True - self.skip_interval = 1 - self.scale = None - - -class AtomStyleSettings(object): - - def __init__(self): - # The following new member data indicate which columns store - # LAMMPS-specific information. - # The next 6 members store keep track of the different columns - # of the "Atoms" section of a LAMMPS data file: - self.column_names = [] # <--A list of column names (optional) - # <--A triplet of integers indicating which columns store coordinate data - self.i_coords = [] - # self.ii_coords= [] #<--A list of triplets of column indexes storing - # coordinate data - self.ii_vects = [] # <--A list of triplets of column indexes storing directional data - # (such as dipole or ellipsoid orientations) - self.i_atomid = None # <--An integer indicating which column has the atomid - self.i_atomtype = None # <--An integer indicating which column has the atomtype - self.i_molid = None # <--An integer indicating which column has the molid, if applicable - - -class DataSettings(AtomStyleSettings): - - def __init__(self): - AtomStyleSettings.__init__(self) - self.contents = '' - self.file_name = '' - - -# Atom Styles in LAMMPS as of 2011-7-29 -g_style_map = {'angle': ['atom-ID', 'molecule-ID', 'atom-type', 'x', 'y', 'z'], - 'atomic': ['atom-ID', 'atom-type', 'x', 'y', 'z'], - 'body': ['atom-ID', 'atom-type', 'bodyflag', 'mass', 'x', 'y', 'z'], - 'bond': ['atom-ID', 'molecule-ID', 'atom-type', 'x', 'y', 'z'], - 'charge': ['atom-ID', 'atom-type', 'q', 'x', 'y', 'z'], - 'dipole': ['atom-ID', 'atom-type', 'q', 'x', 'y', 'z', 'mux', 'muy', 'muz'], - 'dpd': ['atom-ID', 'atom-type', 'theta', 'x', 'y', 'z'], - 'electron': ['atom-ID', 'atom-type', 'q', 'spin', 'eradius', 'x', 'y', 'z'], - 'ellipsoid': ['atom-ID', 'atom-type', 'x', 'y', 'z', 'quatw', 'quati', 'quatj', 'quatk'], - 'full': ['atom-ID', 'molecule-ID', 'atom-type', 'q', 'x', 'y', 'z'], - 'line': ['atom-ID', 'molecule-ID', 'atom-type', 'lineflag', 'density', 'x', 'y', 'z'], - 'meso': ['atom-ID', 'atom-type', 'rho', 'e', 'cv', 'x', 'y', 'z'], - 'molecular': ['atom-ID', 'molecule-ID', 'atom-type', 'x', 'y', 'z'], - 'peri': ['atom-ID', 'atom-type', 'volume', 'density', 'x', 'y', 'z'], - 'smd': ['atom-ID', 'atom-type', 'molecule-ID' 'volume', 'mass', 'kernel-radius', 'contact-radius', 'x', 'y', 'z'], - 'sphere': ['atom-ID', 'atom-type', 'diameter', 'density', 'x', 'y', 'z'], - 'template': ['atom-ID', 'molecule-ID', 'template-index', 'template-atom', 'atom-type', 'x', 'y', 'z'], - 'tri': ['atom-ID', 'molecule-ID', 'atom-type', 'triangleflag', 'density', 'x', 'y', 'z'], - 'wavepacket': ['atom-ID', 'atom-type', 'charge', 'spin', 'eradius', 'etag', 'cs_re', 'cs_im', 'x', 'y', 'z'], - 'hybrid': ['atom-ID', 'atom-type', 'x', 'y', 'z'], - # The following styles were removed from LAMMPS as of 2012-3 - 'colloid': ['atom-ID', 'atom-type', 'x', 'y', 'z'], - 'granular': ['atom-ID', 'atom-type', 'diameter', 'density', 'x', 'y', 'z']} - - -def AtomStyle2ColNames(atom_style_string): - - atom_style_string = atom_style_string.strip() - if len(atom_style_string) == 0: - raise InputError('Error(dump2data): Invalid atom_style\n' - ' (The atom_style command was followed by an empty string.)\n') - atom_style_args = atom_style_string.split() - atom_style = atom_style_args[0] - - hybrid_args = atom_style_args[1:] - - if (atom_style not in g_style_map): - if (len(atom_style_args) >= 2): - # If the atom_style_string includes at least 2 words, then we - # interpret this as a list of the individual column names - return atom_style_args - else: - raise InputError( - 'Error(dump2data): Unrecognized atom_style: \"' + atom_style + '\"\n') - - if (atom_style != 'hybrid'): - return g_style_map[atom_style] - else: - column_names = ['atom-ID', 'atom-type', 'x', 'y', 'z'] - if (len(hybrid_args) == 0): - raise InputError( - 'Error(dump2data): atom_style hybrid must be followed by a sub_style.\n') - for sub_style in hybrid_args: - if (sub_style not in g_style_map): - raise InputError( - 'Error(dump2data): Unrecognized atom_style: \"' + sub_style + '\"\n') - for cname in g_style_map[sub_style]: - if cname not in column_names: - column_names.append(cname) - - return column_names - - -def ColNames2AidAtypeMolid(column_names): - # Because of the diversity of ways that these - # numbers are referred to in the LAMMPS documentation, - # we have to be flexible and allow the user to refer - # to these quantities in a variety of ways. - # Hopefully this covers everything: - - i_atomid = None - if 'atom-ID' in column_names: - i_atomid = column_names.index('atom-ID') - elif 'atom−ID' in column_names: # (− is the character used in the manual) - i_atomid = column_names.index('atom−ID') - elif 'atomID' in column_names: - i_atomid = column_names.index('atomID') - elif 'atomid' in column_names: - i_atomid = column_names.index('atomid') - elif 'id' in column_names: - i_atomid = column_names.index('id') - elif 'atom' in column_names: - i_atomid = column_names.index('atom') - elif '$atom' in column_names: - i_atomid = column_names.index('$atom') - else: - raise InputError( - 'Error(dump2data): List of column names lacks an \"atom-ID\"\n') - - i_atomtype = None - if 'atom-type' in column_names: - i_atomtype = column_names.index('atom-type') - elif 'atom−type' in column_names: # (− hyphen character used in manual) - i_atomtype = column_names.index('atom−type') - elif 'atomtype' in column_names: - i_atomtype = column_names.index('atomtype') - elif 'type' in column_names: - i_atomtype = column_names.index('type') - elif '@atom' in column_names: - i_atomtype = column_names.index('@atom') - else: - raise InputError( - 'Error(dump2data): List of column names lacks an \"atom-type\"\n') - - i_molid = None - if 'molecule-ID' in column_names: - i_molid = column_names.index('molecule-ID') - elif 'molecule−ID' in column_names: # (− hyphen character used in manual) - i_molid = column_names.index('molecule−ID') - elif 'moleculeID' in column_names: - i_molid = column_names.index('moleculeID') - elif 'moleculeid' in column_names: - i_molid = column_names.index('moleculeid') - elif 'molecule' in column_names: - i_molid = column_names.index('molecule') - elif 'molID' in column_names: - i_molid = column_names.index('molID') - elif 'molid' in column_names: - i_molid = column_names.index('molid') - elif 'mol' in column_names: - i_molid = column_names.index('mol') - elif '$mol' in column_names: - i_molid = column_names.index('$mol') - else: - pass # some atom_types do not have a valid molecule-ID - - return i_atomid, i_atomtype, i_molid - - -def ColNames2Coords(column_names): - """ Which of the columns correspond to coordinates - which must be transformed using rigid-body - (affine: rotation + translation) transformations? - This function outputs a list of lists of triplets of integers. - - """ - i_x = None - i_y = None - i_z = None - if 'x' in column_names: - i_x = column_names.index('x') - if 'y' in column_names: - i_y = column_names.index('y') - if 'z' in column_names: - i_z = column_names.index('z') - if (((i_x != None) != (i_y != None)) or - ((i_y != None) != (i_z != None)) or - ((i_z != None) != (i_x != None))): - raise InputError( - 'Error(dump2data): columns must include \"x\", \"y\", and \"z\".\n') - return [[i_x, i_y, i_z]] - - -def ColNames2Vects(column_names): - """ Which of the columns correspond to coordinates - which must be transformed using rotations? - Some coordinates like dipole moments and - ellipsoid orientations should only be rotated - (not translated). - This function outputs a list of lists of triplets of integers. - - """ - vects = [] - i_mux = None - i_muy = None - i_muz = None - if 'mux' in column_names: - i_mux = column_names.index('mux') - if 'muy' in column_names: - i_muy = column_names.index('muy') - if 'muz' in column_names: - i_muz = column_names.index('muz') - if (((i_mux != None) != (i_muy != None)) or - ((i_muy != None) != (i_muz != None)) or - ((i_muz != None) != (i_mux != None))): - raise InputError( - 'Error(dump2data): custom atom_style list must define mux, muy, and muz or none.\n') - if i_mux != None: - vects.append([i_mux, i_muy, i_muz]) - i_quati = None - i_quatj = None - i_quatk = None - if 'quati' in column_names: - i_quati = column_names.index('quati') - if 'quatj' in column_names: - i_quatj = column_names.index('quatj') - if 'quatk' in column_names: - i_quatk = column_names.index('quatk') - if (((i_quati != None) != (i_quatj != None)) or - ((i_quatj != None) != (i_quatk != None)) or - ((i_quatk != None) != (i_quati != None))): - raise InputError( - 'Error(dump2data): custom atom_style list must define quati, quatj, and quatk or none.\n') - if i_quati != None: - vects.append([i_quati, i_quatj, i_quatk]) - return vects - - -def ParseArgs(argv, - misc_settings, - data_settings, - warning_strings=None): - - # Loop over the remaining arguments not processed yet. - # These arguments are specific to the lttree.py program - # and are not understood by this program. - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if ((argv[i].lower() == '-atomstyle') or - (argv[i].lower() == '-atom_style') or - (argv[i].lower() == '-atom-style')): - in_init = [] - if i + 1 >= len(argv): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by a an atom_style name.\n' - ' (Or single quoted string which includes a space-separated\n' - ' list of column names.)\n') - data_settings.column_names = AtomStyle2ColNames(argv[i + 1]) - sys.stderr.write(' \"Atoms\" column format:\n') - sys.stderr.write( - ' ' + (' '.join(data_settings.column_names)) + '\n') - - # ColNames2Coords() and ColNames2Vects() generate lists of - # triplets of integers, storing the column numbers containing - # x, y, and z coordinate values, and vx,vy,vz direction vectors. - data_settings.ii_vects = ColNames2Vects(data_settings.column_names) - ii_coords = ColNames2Coords(data_settings.column_names) - # This program assumes that there is only one coordinate triplet - # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1 - assert(len(ii_coords) == 1) - data_settings.i_coords = ii_coords[0] - - # Now figure out which columns correspond to atomid, atomtype, - # molid - data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid( - data_settings.column_names) - del(argv[i:i + 2]) - - elif (argv[i].lower() == '-icoord'): - if i + 1 >= len(argv): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by list of integers\n' - ' corresponding to column numbers for coordinates in\n' - ' the \"Atoms\" section of a LAMMPS data file.\n') - ilist = argv[i + 1].split() - if (len(ilist) % 3) != 0: - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by list of integers.\n' - ' This is usually a list of 3 intebers, but it can contain more.\n' - ' The number of cooridnate columns must be divisible by 3,\n' - ' (even if the simulation is in 2 dimensions)\n') - - #ii_coords = [] - # for i in range(0, len(ilist)/3): - # cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1] - # ii_coords.append(cols) - # if ((len(ii_coords) != 0) or (len(ii_coords[0]) != 3)): - # raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n') - - data_settings.i_coords = ilist - if (len(i_coords) != 3): - raise InputError('Error(dump2data): Argument \"' + - argv[i] + '\" must be followed by exactly 3 integers.\n') - - data_settings.i_coords = ii_coords[0] - - del(argv[i:i + 2]) - - elif (argv[i].lower() == '-ivect'): - if i + 1 >= len(argv): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by list of integers\n' - ' corresponding to column numbers for direction vectors in\n' - ' the \"Atoms\" section of a LAMMPS data file.\n') - ilist = argv[i + 1].split() - if (len(ilist) % 3) != 0: - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by list of integers.\n' - ' This is usually a list of 3 intebers, but it can contain more.\n' - ' The number of cooridnate columns must be divisible by 3,\n' - ' (even if the simulation is in 2 dimensions)\n') - - data_settings.ii_vects = [] - for i in range(0, len(ilist) / 3): - cols = [ilist[3 * i] + 1, ilist[3 * i + 1] + - 1, ilist[3 * i + 2] + 1] - setting.ii_vects.append(cols) - # This should override any earlier settings as a result of the - # -atomstyle argument. So you can specify a custom list of column - # names using -atomstyle "list of column names", and then afterwards - # specify which of these columns correspond to direction vectors - # using the "-ivect" command line argument later on. - # This way, in theory you should be able to read columns from - # new custom atom-styles that have not been invented yet. - # (Although I haven't tested this.) - - del(argv[i:i + 2]) - # i_atomid is not really needed for this program, but I load it anyway - elif ((argv[i].lower() == '-iatomid') or - (argv[i].lower() == '-iid') or - (argv[i].lower() == '-iatom-id')): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"Atoms\" section of a\n' - ' LAMMPS data file contains the atom id number (typically 1).\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_atomid = int(argv[i + 1]) - 1 - del(argv[i:i + 2]) - # i_atomtype is not really needed for this program, but I load it - # anyway - elif ((argv[i].lower() == '-iatomtype') or - (argv[i].lower() == '-itype') or - (argv[i].lower() == '-iatom-type')): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"Atoms\" section of a\n' - ' LAMMPS data file contains the atom type.\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_atomtype = int(argv[i + 1]) - 1 - del(argv[i:i + 2]) - # i_molid is not really needed for this program, but I load it anyway - elif ((argv[i].lower() == '-imolid') or - (argv[i].lower() == '-imol') or - (argv[i].lower() == '-imol-id') or - (argv[i].lower() == '-imoleculeid') or - (argv[i].lower() == '-imolecule-id')): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"Atoms\" section of a\n' - ' LAMMPS data file contains the molecule id number.\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - del(argv[i:i + 2]) - # Which frame do we want? - elif (argv[i].lower() == '-t'): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by an integer indicating\n' - ' the frame you want to extract from the dump file (trajectory).\n' - ' This integer should match the timestep corresponding to the frame\n' - ' whose coordinates you wish to extract.\n') - misc_settings.timestep_str = argv[i + 1] - del(argv[i:i + 2]) - misc_settings.multi = False - misc_settings.last_frame = False - - elif (argv[i].lower() == '-tstart'): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by an integer indicating\n' - ' the first frame you want to extract from the dump file (trajectory).\n' - ' This integer should match the timestep corresponding to the frame\n' - ' (after which) you wish to extract coordinates.\n') - misc_settings.tstart = float(argv[i + 1]) - del(argv[i:i + 2]) - misc_settings.multi = True - - elif (argv[i].lower() == '-tstop'): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error(dump2data): ' + argv[i] + ' flag should be followed by an number indicating\n' - ' the first frame you want to extract from the dump file (trajectory).\n' - ' Frames after this timestep will be ignored.\n') - misc_settings.tstop = float(argv[i + 1]) - del(argv[i:i + 2]) - misc_settings.multi = True - - elif (argv[i].lower() == '-center'): - misc_settings.center_frame = True - del(argv[i:i + 1]) - - elif ((argv[i].lower() == '-raw') or (argv[i].lower() == '-rawout')): - misc_settings.output_format = 'raw' - del(argv[i:i + 1]) - - elif (argv[i].lower() == '-rawin'): - misc_settings.input_format = 'raw' - misc_settings.multi = False - del(argv[i:i + 1]) - - elif ((argv[i].lower() == '-xyz') or (argv[i].lower() == '-xyzout')): - misc_settings.output_format = 'xyz' - del(argv[i:i + 1]) - - elif (argv[i].lower() == '-xyzin'): - misc_settings.input_format = 'xyz' - misc_settings.multi = False - del(argv[i:i + 1]) - - elif (argv[i].lower() == '-multi'): - misc_settings.multi = True - del(argv[i:i + 1]) - - elif (argv[i].lower() == '-last'): - misc_settings.last_frame = True - misc_settings.multi = False - del(argv[i:i + 1]) - - elif (argv[i].lower() == '-interval'): - misc_settings.skip_interval = int(argv[i + 1]) - del(argv[i:i + 2]) - - elif (argv[i].lower() == '-scale'): - misc_settings.scale = float(argv[i + 1]) - del(argv[i:i + 2]) - - elif ((argv[i][0] == '-') and (__name__ == "__main__")): - raise InputError( - 'Error(dump2data): Unrecogized command line argument \"' + argv[i] + '\"\n') - else: - i += 1 - - usage_examples = \ - """ Typical usage: -dump2data.py orig_file.data < dump.lammpstrj > new_file.data - (This extracts last frame, uses "full" atom_style.) - Additional options: -dump2data.py -t t -atomstyle style orig.data < dump.lammpstrj > new.data -""" - - # if __name__ == "__main__": - - if (len(argv) > 2): - # if there are more than 2 remaining arguments, - # AND - # no other function will process the remaining argument list - # (ie. if __name__ == "__main__") - # THEN - raise InputError(' ----\n' - 'ERROR(dump2data): You have too many arguments (or unrecognized arguments):\n' - ' \"' + (' '.join(argv)) + '\"\n' - ' ----\n' - + usage_examples) - elif (len(argv) < 2): - if misc_settings.output_format == 'data': - raise InputError(' ----\n' - 'ERROR(dump2data): Problem with argument list:\n' - ' Expected a LAMMPS .data file as an argument.\n' - ' ----\n' - + usage_examples) - else: - in_data_file = open(argv[1], 'r') - data_settings.file_name = argv[1] - data_settings.contents = in_data_file.readlines() - in_data_file.close() - - # end of if-then statement for "if __name__ == "__main__"" - - if len(data_settings.i_coords) == 0: - if warning_strings != None: - warning_strings.append( - 'WARNING(dump2data): atom_style unknown. (Use -atomstyle style. Assuming \"full\")') - warn_atom_style_unspecified = True - # The default atom_style is "full" - data_settings.column_names = AtomStyle2ColNames('full') - ii_coords = ColNames2Coords(data_settings.column_names) - # This program assumes that there is only one coordinate triplet - # (x,y,z) for each atom. Hence we assume that len(ii_coords)==1 - assert(len(ii_coords) == 1) - data_settings.i_coords = ii_coords[0] - data_settings.ii_vects = ColNames2Vects(data_settings.column_names) - data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid( - data_settings.column_names) - - # sys.stderr.write('########################################################\n' - # '## WARNING: atom_style unspecified ##\n' - # '## --> \"Atoms\" column data has an unknown format. ##\n' - # '## Assuming atom_style = \"full\" ##\n' - # '########################################################\n' - # '## To specify the \"Atoms\" column format you can: ##\n' - # '## 1) Use the -atom_style \"STYLE\" argument ##\n' - # '## where \"STYLE\" is a string indicating a LAMMPS ##\n' - # '## atom_style, including hybrid styles.(Standard ##\n' - # '## atom styles defined in 2011 are supported.) ##\n' - # '## 2) Use the -atom_style \"COL_LIST\" argument ##\n' - # '## where \"COL_LIST" is a quoted list of strings ##\n' - # '## indicating the name of each column. ##\n' - # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' - # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' - # '## and \"quati\",\"quatj\",\"quatk\" are ##\n' - # '## interpreted as direction vectors. ##\n' - # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' - # '## where \"cx cy cz\" is a list of integers ##\n' - # '## indicating the column numbers for the x,y,z ##\n' - # '## coordinates of each atom. ##\n' - # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' - # '## where \"cmux cmuy cmuz...\" is a list of ##\n' - # '## integers indicating the column numbers for ##\n' - # '## the vector that determines the direction of a ##\n' - # '## dipole or ellipsoid (ie. a rotateable vector).##\n' - # '## (More than one triplet can be specified. The ##\n' - # '## number of entries must be divisible by 3.) ##\n' - # '## 5) Include a ##\n' - # '## write(\"in_init.txt\"){atom_style ...} ##\n' - # '## statement in your .ttree file. ##\n' - # '########################################################\n') - - -def GetIntAtomID(pair): - return int(pair[0]) - - -def WriteFrameToData(out_file, - descr_str, - misc_settings, - data_settings, - dump_column_names, - natoms, - coords, - coords_ixiyiz, - vects, - velocities, - atomtypes, - molids, - xlo_str, xhi_str, - ylo_str, yhi_str, - zlo_str, zhi_str, - xy_str, xz_str, yz_str): - """ - Open a data file. Read the LAMMPS DATA file line by line. - When the line contains information which is also in the dump file, - replace that information with information from the dump file. - (Information from a dump file is stored in the arguments to this function.) - The resulting file also has LAMMPS DATA format. - - """ - - section = '' - firstline = True - for line in data_settings.contents: - ic = line.find('#') - if ic != -1: - line = line[:ic] - line = line.strip() - - if firstline: # Construct a new descriptive header line: - if descr_str != None: - line = descr_str - firstline = False - - if (len(line) > 0): - # The initial section (section='') is assumed to be - # the "LAMMPS Description" section. This is where the - # box boundaries are specified. - if section == '': - tokens = line.split() - if ((len(tokens) >= 2) and - ((tokens[-2] == 'xlo') and (tokens[-1] == 'xhi')) and - ((xlo_str != None) and (xhi_str != None))): - tokens[0] = xlo_str - tokens[1] = xhi_str - line = ' '.join(tokens) - elif ((len(tokens) >= 2) and - ((tokens[-2] == 'ylo') and (tokens[-1] == 'yhi')) and - ((ylo_str != None) and (yhi_str != None))): - tokens[0] = ylo_str - tokens[1] = yhi_str - line = ' '.join(tokens) - elif ((len(tokens) >= 2) and - ((tokens[-2] == 'zlo') and (tokens[-1] == 'zhi')) and - ((zlo_str != None) and (zhi_str != None))): - tokens[0] = zlo_str - tokens[1] = zhi_str - line = ' '.join(tokens) - elif ((len(tokens) >= 3) and - ((tokens[-3] == 'xy') and - (tokens[-2] == 'xz') and - (tokens[-1] == 'yz')) and - ((xy_str != None) and - (xz_str != None) and - (yz_str != None))): - tokens[0] = xy_str - tokens[1] = xz_str - tokens[2] = yz_str - line = ' '.join(tokens) - if (line in set(['Masses', 'Velocities', 'Atoms', - 'Bond Coeffs', 'Angle Coeffs', - 'Dihedral Coeffs', 'Improper Coeffs', - 'Bonds', 'Angles', 'Dihedrals', 'Impropers'])): - section = line - else: - if (section == 'Atoms'): - tokens = line.split() - atomid = tokens[0] - - # update the atomtype and molID - # (which may change during the simulation) - if atomtypes: - tokens[data_settings.i_atomtype] = atomtypes[atomid] - if molids and data_settings.i_molid: - tokens[data_settings.i_molid] = molids[atomid] - - if atomid in coords: - # Loop over all of the vector degrees of - # freedom of the particle, excluding coords - # (for example: mu_x, mu_y, mu_z, - # or quat_i, quat_j, quat_k) - # In principle, depending on the atom_style, - # there could be multiple vectors per atom. - for I in range(0, len(data_settings.ii_vects)): - i_vx = data_settings.ii_vects[I][0] - i_vy = data_settings.ii_vects[I][1] - i_vz = data_settings.ii_vects[I][2] - if atomid in vects: - vxvyvz = vects[atomid][I] - assert((type(vxvyvz) is tuple) and - (len(vxvyvz) == 3)) - if ((i_vx >= len(tokens)) or - (i_vy >= len(tokens)) or - (i_vz >= len(tokens))): - raise InputError('Error(dump2data): Atom style incompatible with data file.\n' - ' Specify the atom_style using -atomstyle style.\n') - - # Replace the vector components with numbers - # from the dump file - tokens[i_vx] = vxvyvz[0] - tokens[i_vy] = vxvyvz[1] - tokens[i_vz] = vxvyvz[2] - - else: - if (dump_column_names and - (data_settings.column_names[ - i_vx] not in dump_column_names)): - raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"' + data_settings.column_names[i_vx] + '\"\n' - ' However there are no columns with this name in your DUMP file\n' - ' (or the column was not in the expected place).\n' - ' Hence, the atom styles in the dump and data files do not match.') - - # Now loop over the coordinates of each atom. - # for I in range(0,len(data_settings.ii_coords)): - # xyz = coords[atomid][I] - # THIS LOOP IS SILLY. - # EACH ATOM ONLY HAS ONE SET OF X,Y,Z - # COORDINATES. COMMENTING OUT THIS LOOP: - # i_x = data_settings.ii_coords[I][0] - # i_y = data_settings.ii_coords[I][1] - # i_z = data_settings.ii_coords[I][2] - # USING THIS INSTEAD: - - xyz = coords[atomid] - i_x = data_settings.i_coords[0] - i_y = data_settings.i_coords[1] - i_z = data_settings.i_coords[2] - if ((i_x >= len(tokens)) or - (i_y >= len(tokens)) or - (i_z >= len(tokens))): - raise InputError('Error(dump2data): Atom style incompatible with data file.\n' - ' Specify the atom_style using -atomstyle style.\n') - # Replace the coordinates with coordinates from - # the dump file into tokens[i_x]... - tokens[i_x] = str(xyz[0]) - tokens[i_y] = str(xyz[1]) - tokens[i_z] = str(xyz[2]) - - # Are there there any integer coords - # (ix, iy, iz) in the dump file? - if coords_ixiyiz[atomid]: - assert(len(coords_ixiyiz[atomid]) == 3) - # Integer coords stored in the DATA file too? - if len(tokens) == (len(data_settings.column_names) + 3): - # Then replace the last 3 columns of the - # line in the data file with: ix iy iz - tokens[-3] = coords_ixiyiz[atomid][0] - tokens[-2] = coords_ixiyiz[atomid][1] - tokens[-1] = coords_ixiyiz[atomid][2] - else: - if (not misc_settings.center_frame): - # Append them to the end of the line: - tokens.append(coords_ixiyiz[atomid][0]) - tokens.append(coords_ixiyiz[atomid][1]) - tokens.append(coords_ixiyiz[atomid][2]) - - # Now finally paste all the tokens together: - line = ' '.join(tokens) - - elif (section == 'Velocities'): - tokens = line.split() - atomid = tokens[0] - if atomid in velocities: - - vxvyvz = velocities[atomid] - if len(tokens) < 4: - raise InputError( - 'Error(dump2data): Not enough columns in the \"Velocities\" file.\n') - # Replace the coordinates with coordinates from - # the dump file into tokens[i_x]... - tokens[1] = str(vxvyvz[0]) - tokens[2] = str(vxvyvz[1]) - tokens[3] = str(vxvyvz[2]) - - # Now finally paste all the tokens together: - line = ' '.join(tokens) - - out_file.write(line + '\n') - - return - - -def main(): - sys.stderr.write(g_program_name + ' v' + - g_version_str + ' ' + g_date_str + ' ') - # if sys.version < '3': - # sys.stderr.write(' (python version < 3)\n') - # else: - sys.stderr.write('\n') - - try: - data_settings = DataSettings() - misc_settings = MiscSettings() - warning_strings = [] - ParseArgs(sys.argv, - misc_settings, - data_settings, - warning_strings) - - # Open the lammps dump file (trajectory file) - # Skip to the line containing the correct frame/timestep. - # (this is the last frame by default). - # Read the "BOX BOUNDS" and the "ATOMS" sections. - # Store the x,y,z coordinates in the "coords" associative array - # (indexed by atom id, which could be non-numeric in general). - - section = '' - - #coords = defaultdict(list) - #coords_ixiyiz = defaultdict(list) - #vects = defaultdict(list) - #xlo_str = xhi_str = ylo_str = yhi_str = zlo_str = zhi_str = None - #xy_str = xz_str = yz_str = None - #natoms = -1 - #timestep_str = '' - - frame_coords = defaultdict(list) - frame_coords_ixiyiz = defaultdict(list) - frame_vects = defaultdict(list) - frame_velocities = defaultdict(list) - frame_atomtypes = defaultdict(list) - frame_molid = defaultdict(list) - frame_xlo_str = frame_xhi_str = None - frame_ylo_str = frame_yhi_str = None - frame_zlo_str = frame_zhi_str = None - frame_xy_str = frame_xz_str = frame_yz_str = None - frame_natoms = -1 - frame_timestep_str = '' - i_atomid = i_atomtype = i_molid = -1 - i_x = i_y = i_z = i_xu = i_yu = i_zu = -1 - i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1 - - dump_column_names = [] - - #num_frames_in = -1 - num_frames_out = 0 - finished_reading_frame = False - read_last_frame = False - - #in_coord_file = open('tmp_atom_coords.dat','r') - in_coord_file = sys.stdin - - while True: - - line = in_coord_file.readline() - if line == '': # if EOF - if len(frame_coords) > 0: - finished_reading_frame = True - read_last_frame = True - - line = line.strip() - if (line.find('ITEM:') == 0): - section = line - if (section.find('ITEM: ATOMS ') == 0): - dump_column_names = line[12:].split() - i_atomid, i_atomtype, i_molid = \ - ColNames2AidAtypeMolid(dump_column_names) - #ii_coords = ColNames2Coords(dump_column_names) - - x_already_unwrapped = False - y_already_unwrapped = False - z_already_unwrapped = False - - if 'x' in dump_column_names: - i_x = dump_column_names.index('x') - elif 'xu' in dump_column_names: - i_xu = dump_column_names.index('xu') - x_already_unwrapped = True - elif 'xs' in dump_column_names: - i_xs = dump_column_names.index('xs') - elif 'xsu' in dump_column_names: - i_xsu = dump_column_names.index('xsu') - x_already_unwrapped = True - else: - raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"x\" column.\n' + - ' (excerpt below)\n' + line) - - if 'y' in dump_column_names: - i_y = dump_column_names.index('y') - elif 'yu' in dump_column_names: - i_yu = dump_column_names.index('yu') - y_already_unwrapped = True - elif 'ys' in dump_column_names: - i_ys = dump_column_names.index('ys') - elif 'ysu' in dump_column_names: - i_ysu = dump_column_names.index('ysu') - y_already_unwrapped = True - else: - raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"y\" column.\n' + - ' (excerpt below)\n' + line) - - if 'z' in dump_column_names: - i_z = dump_column_names.index('z') - elif 'zu' in dump_column_names: - i_zu = dump_column_names.index('zu') - z_already_unwrapped = True - elif 'zs' in dump_column_names: - i_zs = dump_column_names.index('zs') - elif 'zsu' in dump_column_names: - i_zsu = dump_column_names.index('zsu') - z_already_unwrapped = True - else: - raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"z\" column.\n' + - ' (excerpt below)\n' + line) - - ii_vects = ColNames2Vects(dump_column_names) - if (len(ii_vects) != len(data_settings.ii_vects)): - raise InputError('Error(dump2data): atom styles in data and dump files differ.\n' - ' Some needed columns from the atom_styles are missing in the dump file.') - - i_ix = i_iy = i_iz = -1 - if 'ix' in dump_column_names: - i_ix = dump_column_names.index('ix') - if 'iy' in dump_column_names: - i_iy = dump_column_names.index('iy') - if 'iz' in dump_column_names: - i_iz = dump_column_names.index('iz') - - i_vx = i_vy = i_vz = -1 - if 'vx' in dump_column_names: - i_vx = dump_column_names.index('vx') - if 'vy' in dump_column_names: - i_vy = dump_column_names.index('vy') - if 'vz' in dump_column_names: - i_vz = dump_column_names.index('vz') - - elif (section.find('ITEM: BOX BOUNDS') == 0): - avec = [1.0, 0.0, 0.0] - bvec = [0.0, 1.0, 0.0] - cvec = [0.0, 0.0, 1.0] - - elif (section.find('ITEM: TIMESTEP') == 0): - if len(frame_coords) > 0: - finished_reading_frame = True - - elif ((len(line) > 0) and (line[0] != '#')): - if (section.find('ITEM: TIMESTEP') == 0): - finished_reading_frame = False - frame_timestep_str = line - frame_coords = defaultdict(list) - frame_coords_ixiyiz = defaultdict(list) - frame_vects = defaultdict(list) - frame_velocities = defaultdict(list) - frame_atomtypes = defaultdict(list) - frame_molids = defaultdict(list) - frame_xlo_str = frame_xhi_str = None - frame_ylo_str = frame_yhi_str = None - frame_zlo_str = frame_zhi_str = None - frame_xy_str = frame_xz_str = frame_yz_str = None - - elif (section == 'ITEM: NUMBER OF ATOMS'): - frame_natoms = int(line) - - elif (section.find('ITEM: BOX BOUNDS') == 0): - is_triclinic = (section.find('xy xz yz') == 0) - - tokens = line.split() - if not frame_xlo_str: - assert(not frame_xhi_str) - frame_xlo_str = tokens[0] - frame_xhi_str = tokens[1] - avec[0] = float(frame_xhi_str) - float(frame_xlo_str) - if (is_triclinic and (len(tokens) > 2)): - frame_xy_str = tokens[2] - bvec[0] = float(frame_xy_str) - # See http://lammps.sandia.gov/doc/Section-howto.html#howto_12 - # sys.stderr.write('avec='+str(avec)+'\n') - - elif not frame_ylo_str: - assert(not frame_yhi_str) - frame_ylo_str = tokens[0] - frame_yhi_str = tokens[1] - bvec[1] = float(frame_yhi_str) - float(frame_ylo_str) - if (is_triclinic and (len(tokens) > 2)): - frame_xz_str = tokens[2] - cvec[0] = float(frame_xz_str) - # See http://lammps.sandia.gov/doc/Section-howto.html#howto_12 - # sys.stderr.write('bvec='+str(bvec)+'\n') - - elif not frame_zlo_str: - assert(not frame_zhi_str) - frame_zlo_str = tokens[0] - frame_zhi_str = tokens[1] - cvec = [0.0, 0.0, float( - frame_zhi_str) - float(frame_zlo_str)] - if (is_triclinic and (len(tokens) > 2)): - frame_yz_str = tokens[2] - cvec[1] = float(frame_yz_str) - # See http://lammps.sandia.gov/doc/Section-howto.html#howto_12 - # sys.stderr.write('cvec='+str(cvec)+'\n') - - elif (section.find('ITEM: ATOMS') == 0): - tokens = line.split() - atomid = tokens[i_atomid] - atomtype = tokens[i_atomtype] - frame_atomtypes[atomid] = atomtype - if i_molid: - molid = tokens[i_molid] - frame_molids[atomid] = molid - - if ((i_x != -1) and (i_y != -1) and (i_z != -1)): - x = float(tokens[i_x]) # i_x determined above - y = float(tokens[i_y]) - z = float(tokens[i_z]) - - elif ((i_xu != -1) and (i_yu != -1) and (i_zu != -1)): - x = float(tokens[i_xu]) # i_x determined above - y = float(tokens[i_yu]) - z = float(tokens[i_zu]) - - elif ((i_xs != -1) and (i_ys != -1) and (i_zs != -1)): - xs = float(tokens[i_xs]) # i_xs determined above - ys = float(tokens[i_ys]) - zs = float(tokens[i_zs]) - - x = float(xlo_str) + xs * \ - avec[0] + ys * bvec[0] + zs * cvec[0] - y = float(ylo_str) + xs * \ - avec[1] + ys * bvec[1] + zs * cvec[1] - z = float(zlo_str) + xs * \ - avec[2] + ys * bvec[2] + zs * cvec[2] - - # avec, bvec, cvec described here: - # http://lammps.sandia.gov/doc/Section-howto.html#howto_12 - - elif ((i_xsu != -1) and (i_ysu != -1) and (i_zsu != -1)): - xsu = float(tokens[i_xsu]) # i_xs determined above - ysu = float(tokens[i_ysu]) - zsu = float(tokens[i_zsu]) - - x = float(xlo_str) + xsu * \ - avec[0] + ysu * bvec[0] + zsu * cvec[0] - y = float(ylo_str) + xsu * \ - avec[1] + ysu * bvec[1] + zsu * cvec[1] - z = float(zlo_str) + xsu * \ - avec[2] + ysu * bvec[2] + zsu * cvec[2] - - # Now deal with ix, iy, iz - if (i_ix != -1) and (not x_already_unwrapped): - ix = int(tokens[i_ix]) - if (misc_settings.center_frame or - (misc_settings.output_format != 'data')): - #sys.stderr.write('atomid='+str(atomid)+', ix = '+str(ix)+', avec='+str(avec)+'\n') - x += ix * avec[0] - y += ix * avec[1] - z += ix * avec[2] - else: - if atomid not in frame_coords_ixiyiz: - frame_coords_ixiyiz[atomid] = ["0", "0", "0"] - frame_coords_ixiyiz[atomid][0] = str(ix) - - if (i_iy != -1) and (not y_already_unwrapped): - iy = int(tokens[i_iy]) - if (misc_settings.center_frame or - (misc_settings.output_format != 'data')): - #sys.stderr.write('atomid='+str(atomid)+', iy = '+str(iy)+', bvec='+str(bvec)+'\n') - x += iy * bvec[0] - y += iy * bvec[1] - z += iy * bvec[2] - else: - if atomid not in frame_coords_ixiyiz: - frame_coords_ixiyiz[atomid] = ["0", "0", "0"] - frame_coords_ixiyiz[atomid][1] = str(iy) - - if (i_iz != -1) and (not z_already_unwrapped): - iz = int(tokens[i_iz]) - if (misc_settings.center_frame or - (misc_settings.output_format != 'data')): - #sys.stderr.write('atomid='+str(atomid)+', iz = '+str(iz)+', cvec='+str(cvec)+'\n') - x += iz * cvec[0] - y += iz * cvec[1] - z += iz * cvec[2] - else: - if atomid not in frame_coords_ixiyiz: - frame_coords_ixiyiz[atomid] = ["0", "0", "0"] - frame_coords_ixiyiz[atomid][2] = str(iz) - - #frame_coords[atomid] = [str(x), str(y), str(z)] - frame_coords[atomid] = [x, y, z] - - vx = 0.0 - vy = 0.0 - vz = 0.0 - if i_vx != -1: - vx = float(tokens[i_vx]) - if i_vy != -1: - vy = float(tokens[i_vy]) - if i_vz != -1: - vz = float(tokens[i_vz]) - - frame_velocities[atomid] = [vx, vy, vz] - - # NOTE: - # There can be multiple "vects" associated with each atom - # (for example, dipole moments, ellipsoid directions, etc..) - - if atomid not in frame_vects: - frame_vects[atomid] = [ - None for I in range(0, len(ii_vects))] - - for I in range(0, len(ii_vects)): - i_vx = ii_vects[I][0] - i_vy = ii_vects[I][1] - i_vz = ii_vects[I][2] - vx_str = tokens[i_vx] - vy_str = tokens[i_vy] - vz_str = tokens[i_vz] - - # Now the annoying part: - # Which vect is it (mux,muy,muz) or (quati,quatj,quatk)? - # The columns could be listed in a different order - # in the data file and in the dump file. - # Figure out which vector it is in the data file (stored - # in the integer "I_data") so that column names match. - name_vx = dump_column_names[i_vx] - name_vy = dump_column_names[i_vy] - name_vz = dump_column_names[i_vz] - i_vx_data = 0 - I_data = -1 - # This code is ugly and inneficient. - # I never want to touch this code again. (Hope it - # works) - while i_vx_data < len(data_settings.column_names): - if name_vx == data_settings.column_names[i_vx_data]: - I_data = 0 - while I_data < len(data_settings.ii_vects): - if ii_vects[I] == data_settings.ii_vects[I_data]: - break - I_data += 1 - - if (0 < I_data) and (I_data < len(data_settings.ii_vects)): - break - - i_vx_data += 1 - - if (0 <= I_data) and (I_data < len(data_settings.ii_vects)): - frame_vects[atomid][I_data] = ( - vx_str, vy_str, vz_str) - else: - raise InputError('Error(dump2data): You have a vector coordinate in your dump file named \"' + name_vx + '\"\n' - ' However there are no columns with this name in your data file\n' - ' (or the column was not in the expected place).\n' - ' Hence, the atom styles in the dump and data files do not match.') - - if finished_reading_frame: - - if misc_settings.scale != None: - for atomid in frame_coords: - for d in range(0, 3): - crd = float(frame_coords[atomid][d]) - frame_coords[atomid][d] = str( - crd * misc_settings.scale) - - if len(frame_coords) != frame_natoms: - err_msg = 'Number of lines in \"ITEM: ATOMS\" section disagrees with\n' \ - + ' \"ITEM: NUMBER OF ATOMS\" declared earlier in this file.\n' - raise InputError(err_msg) - - if misc_settings.center_frame: - cm = [0.0, 0.0, 0.0] - for atomid in frame_coords: - for d in range(0, 3): - cm[d] += float(frame_coords[atomid][d]) - for d in range(0, 3): - cm[d] /= float(len(frame_coords)) - for atomid in frame_coords: - for d in range(0, 3): - frame_coords[atomid][d] = "%.7g" % ( - float(frame_coords[atomid][d]) - cm[d]) - frame_coords_ixiyiz[atomid] = ["0", "0", "0"] - - if misc_settings.output_format != 'data': - frame_coords_ixiyiz[atomid] = ["0", "0", "0"] - - # if (num_frames_in == -1): - # if (misc_settings.timestep_str != ''): - # if (float(frame_timestep_str) >= - # float(misc_settings.timestep_str)): - # num_frames_in = 1 - # if not misc_settings.multi: - # read_last_frame = True - # else: - # num_frames_in = 1 - - # Should we write out the coordinates in this frame? - write_this_frame = False - - if misc_settings.multi: - - write_this_frame = True - if (misc_settings.tstart and - (int(frame_timestep_str) < misc_settings.tstart)): - write_this_frame = False - if (misc_settings.tstop and - (int(frame_timestep_str) > misc_settings.tstop)): - write_this_frame = False - read_last_frame = True - - if misc_settings.tstart: - tstart = misc_settings.tstart - else: - tstart = 0 - - if ((int(frame_timestep_str) - tstart) - % - misc_settings.skip_interval) != 0: - write_this_frame = False - - else: - if misc_settings.last_frame: - if read_last_frame: - write_this_frame = True - else: - assert(misc_settings.timestep_str) - if (int(frame_timestep_str) >= - int(misc_settings.timestep_str)): - write_this_frame = True - read_last_frame = True - - if write_this_frame: - - num_frames_out += 1 - - sys.stderr.write(' (writing frame ' + str(num_frames_out) + - ' at timestep ' + frame_timestep_str + ')\n') - - # Print the frame - # First check which format to output the data: - if misc_settings.output_format == 'raw': - # Print out the coordinates in simple 3-column text - # format - for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)): - if misc_settings.scale == None: - sys.stdout.write( - str(xyz[0]) + ' ' + str(xyz[1]) + ' ' + str(xyz[2]) + '\n') - else: - # Only convert to float and back if - # misc_settings.scale != None - sys.stdout.write(str(misc_settings.scale * float(xyz[0])) + ' ' + - str(misc_settings.scale * float(xyz[1])) + ' ' + - str(misc_settings.scale * float(xyz[2])) + '\n') - sys.stdout.write('\n') - - elif misc_settings.output_format == 'xyz': - # Print out the coordinates in simple 3-column text - # format - sys.stdout.write(str(len(frame_coords)) + '\n') - descr_str = 'LAMMPS data from timestep ' + frame_timestep_str - sys.stdout.write(descr_str + '\n') - for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)): - if misc_settings.scale == None: - sys.stdout.write(str(atomid) + ' ' + - str(xyz[0]) + ' ' + - str(xyz[1]) + ' ' + - str(xyz[2]) + '\n') - else: - # Only convert to float and back if - # misc_settings.scale != None - sys.stdout.write(str(atomid) + ' ' + - str(misc_settings.scale * float(xyz[0])) + ' ' + - str(misc_settings.scale * float(xyz[1])) + ' ' + - str(misc_settings.scale * float(xyz[2])) + '\n') - - else: - # Parse the DATA file specified by the user - # and replace appropriate lines or fields with - # the corresponding text from the DUMP file. - descr_str = 'LAMMPS data from timestep ' + frame_timestep_str - if misc_settings.multi and (misc_settings.output_format == 'data'): - out_file_name = data_settings.file_name + '.'\ - + str(num_frames_out) - sys.stderr.write( - ' (creating file \"' + out_file_name + '\")\n') - out_file = open(out_file_name, 'w') - else: - out_file = sys.stdout - - WriteFrameToData(out_file, - descr_str, - misc_settings, - data_settings, - dump_column_names, - frame_natoms, - frame_coords, - frame_coords_ixiyiz, - frame_vects, - frame_velocities, - frame_atomtypes, - frame_molids, - frame_xlo_str, frame_xhi_str, - frame_ylo_str, frame_yhi_str, - frame_zlo_str, frame_zhi_str, - frame_xy_str, frame_xz_str, frame_yz_str) - - # if misc_settings.multi: - # out_file.close() - - # if num_frames_in >= 0: - # num_frames_in += 1 - - if read_last_frame: - exit(0) - - for warning_str in warning_strings: - sys.stderr.write(warning_str + '\n') - - except (ValueError, InputError) as err: - sys.stderr.write('\n' + str(err) + '\n') - sys.exit(-1) - - return - - -if __name__ == '__main__': - main() diff --git a/tools/moltemplate/moltemplate/ettree.py b/tools/moltemplate/moltemplate/ettree.py deleted file mode 100755 index 20353a86ef..0000000000 --- a/tools/moltemplate/moltemplate/ettree.py +++ /dev/null @@ -1,580 +0,0 @@ -#!/usr/bin/env python - -# Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2011, Regents of the University of California -# All rights reserved. - -""" -ettree.py - -ettree.py is an extension of the generic ttree.py program. -This version can understand and manipulate ttree-style templates which -are specialized for storing molecule-specific data for use in ESPresSo/TCL. - -The main difference between ettree.py and ttree.py is: -Unlike ttree.py, ettree.py understands rigid-body movement commands like -"rot()" and "move()" which allows it to reorient and move each copy -of a molecule to a new location. (ttree.py just ignores these commands. -Consequently ESPresSo/TCL input file (fragments) created with ttree.py have -invalid (overlapping) atomic coordinates and must be modified or aguemted -later (by loading atomic coordinates from a PDB file or an XYZ file). -ettree.py understands and can manipulate atomic coordinates. - -Additional ESPresSo/TCL-specific features may be added in the future. - -""" - -import sys - -# Problem: -# One of the python files I need is in a different git repository -# which is linked to the parent directory using "git subtree". -# The result of this is that he python code I need to access is in -# a directory which is outside the current one (in "../moltemplate/src") -# For now, I'm willing to resort to using a hack to import this file. - -import os, inspect -# use this if you want to include modules from a subfolder -# http://stackoverflow.com/questions/279237/import-a-module-from-a-relative-path -cmd_subfolder = os.path.realpath(os.path.abspath(os.path.join(os.path.split(inspect.getfile( inspect.currentframe() ))[0],"..","moltemplate","src"))) -if cmd_subfolder not in sys.path: - sys.path.insert(0, cmd_subfolder) - - -try: - from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ - StackableCommand, PopCommand, PopRightCommand, PopLeftCommand, \ - PushCommand, PushLeftCommand, PushRightCommand, ScopeCommand, \ - WriteVarBindingsFile, StaticObj, InstanceObj, \ - BasicUI, ScopeBegin, ScopeEnd, WriteFileCommand, Render - from .ttree_lex import InputError, TextBlock, DeleteLinesWithBadVars, \ - TemplateLexer - from .ettree_styles import espt_delim_atom_fields, \ - LinesWSlashes, SplitMultiDelims, SplitAtomLine, \ - iEsptAtomCoords, iEsptAtomVects, iEsptAtomType, iEsptAtomID - from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ - LinTransform -except (ImportError, SystemError, ValueError): - # not installed as a package - from ttree import * - from ttree_lex import * - from ettree_styles import * - from ttree_matrix_stack import * - -try: - unicode -except NameError: - # Python 3 - basestring = unicode = str - - -data_atoms = 'Data Atoms' # <-- The name of the file/section storing Atom data. - - - -class EttreeSettings(BasicUISettings): - """ Currently EttreeSettings is identical to BasicUISettings. - Later on, if I find I need to add custom settings specific to ESPresSoTCL, - I will add them here. - (See "class LttreeSettings" in "lttree.py" for comparison.) - - """ - - def __init__(self, - user_bindings_x=None, - user_bindings=None, - order_method='by_command'): - - BasicUISettings.__init__(self, - user_bindings_x, - user_bindings, - order_method) - - - -def EttreeParseArgs(argv, settings): - """ - This function currently does nothing except invoke BasicUIParseArgs() - (and throw an error message if the user forgot to specify an file name). - Later on, if I think of some command-line arguments specific - to ESPresSo(tcl), then I will deal with them here. - (See the "LttreeParseArgs()" function in "lttree.py" for comparison.) - - """ - - BasicUIParseArgs(argv, settings) - - # Loop over the remaining arguments not processed yet. - # These arguments are specific to the ettree.py program - # and are not understood by ttree.py: - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if ((argv[i][0] == '-') and (__name__ == "__main__")): - #elif (__name__ == "__main__"): - raise InputError('Error('+__file__+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') - else: - i += 1 - - - if __name__ == "__main__": - - # Instantiate the lexer we will be using. - # (The lexer's __init__() function requires an openned file. - # Assuming __name__ == "__main__", then the name of that file should - # be the last remaining (unprocessed) argument in the argument list. - # Otherwise, then name of that file will be determined later by the - # python script which imports this module, so we let them handle it.) - - if len(argv) == 1: - raise InputError('Error: This program requires at least one argument\n' - ' the name of a file containing ttree template commands\n') - elif len(argv) == 2: - try: - # Parse text from the file named argv[1] - settings.lex.infile = argv[1] - settings.lex.instream = open(argv[1], 'r') - except IOError: - sys.stderr.write('Error: unable to open file\n' - ' \"'+argv[1]+'\"\n' - ' for reading.\n') - sys.exit(1) - del(argv[1:2]) - - else: - # if there are more than 2 remaining arguments, - problem_args = ['\"'+arg+'\"' for arg in argv[1:]] - raise InputError('Syntax Error('+__file__+'):\n\n' - ' Problem with argument list.\n' - ' The remaining arguments are:\n\n' - ' '+(' '.join(problem_args))+'\n\n' - ' (The actual problem may be earlier in the argument list.\n' - ' If these arguments are source files, then keep in mind\n' - ' that this program can not parse multiple source files.)\n' - ' Check the syntax of the entire argument list.\n') - - - - - -def TransformAtomText(text, matrix): - """ Apply transformations to the coordinates and other vector degrees - of freedom stored in the atom declaration section. - This is the \"text\" argument. - The \"matrix\" stores the aggregate sum of combined transformations - to be applied. - - """ - - #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') - - # lines = text.split('\n') <-- this does not work because a backslash at - # the end of a line can merge multiple lines - - lines = [line for line in LinesWSlashes(text)] # <-- handles backslashes - for i in range(0, len(lines)): - line = lines[i] - tokens = SplitAtomLine(line) - if len(tokens) > 0: - x0 = [0.0, 0.0, 0.0] - x = [0.0, 0.0, 0.0] - for icrd in iEsptAtomCoords(tokens): - coords_str = tokens[icrd].split() - for d in range(0,3): - x0[d] = float(coords_str[d]) - AffineTransform(x, matrix, x0) # x = matrix * x0 + b - for d in range(0,3): # ("b" is part of "matrix") - coords_str[d] = str(x[d]) - tokens[icrd] = ' '.join(coords_str) - - for ivect in iEsptAtomVects(tokens): - coords_str = tokens[ivect].split() - for d in range(0,3): - x0[d] = float(coords_str[d]) - LinearTransform(x, matrix, x0) # x = matrix * x0 - for d in range(0,3): - coords_str[d] = str(x[d]) - tokens[ivect] = ' '.join(coords_str) - line = ' '.join(tokens) - lines[i] = line - return '\n'.join(lines)+'\n' - - -# NOT IMPLEMENTED YET: -def CalcCM(text_Atoms, - text_Masses=None, - settings=None): - # FILL IN THE CONTENTS OF THIS FUNCTION LATER - xcm = [0.0, 0.0, 0.0] - return xcm - - - -def _ExecCommands(command_list, - index, - global_files_content, - settings, - matrix_stack, - current_scope_id=None, - substitute_vars=True): - """ - _ExecCommands(): - The argument "commands" is a nested list of lists of - "Command" data structures (defined in ttree.py). - - Carry out the write() and write_once() commands (which - write out the contents of the templates contain inside them). - Instead of writing the files, save their contents in a string. - - The argument "global_files_content" should be of type defaultdict(list) - It is an associative array whose key is a string (a filename) - and whose value is a lists of strings (of rendered templates). - - """ - files_content = defaultdict(list) - postprocessing_commands = [] - - while index < len(command_list): - command = command_list[index] - index += 1 - - # For debugging only - # sys.stderr.write(str(command)+'\n') - - if isinstance(command, PopCommand): - assert(current_scope_id != None) - if command.context_node == None: - command.context_node = current_scope_id - if isinstance(command, PopRightCommand): - matrix_stack.PopRight(which_stack = command.context_node) - elif isinstance(command, PopLeftCommand): - matrix_stack.PopLeft(which_stack = command.context_node) - else: - assert(False) - - elif isinstance(command, PushCommand): - assert(current_scope_id != None) - if command.context_node == None: - command.context_node = current_scope_id - # Some commands are post-processing commands, and must be - # carried out AFTER all the text has been rendered. For example - # the "movecm(0,0,0)" waits until all of the coordinates have - # been rendered, calculates the center-of-mass, and then applies - # a translation moving the center of mass to the origin (0,0,0). - # We need to figure out which of these commands need to be - # postponed, and which commands can be carried out now. - # ("now"=pushing transformation matrices onto the matrix stack). - # UNFORTUNATELY POSTPONING SOME COMMANDS MAKES THE CODE UGLY - transform_list = command.contents.split('.') - transform_blocks = [] - i_post_process = -1 - # Example: Suppose: - #command.contents = '.rot(30,0,0,1).movecm(0,0,0).rot(45,1,0,0).scalecm(2.0).move(-2,1,0)' - # then - #transform_list = ['rot(30,0,0,1)', 'movecm(0,0,0)', 'rot(45,1,0,0)', 'scalecm(2.0)', 'move(-2,1,0)'] - # Note: the first command 'rot(30,0,0,1)' is carried out now. - # The remaining commands are carried out during post-processing, - # (when processing the "ScopeEnd" command. - # - # We break up the commands into "blocks" separated by center- - # of-mass transformations ('movecm', 'rotcm', or 'scalecm') - # - # transform_blocks = ['.rot(30,0,0,1)', - # '.movecm(0,0,0).rot(45,1,0,0)', - # '.scalecm(2.0).move(-2,1,0)'] - - i = 0 - while i < len(transform_list): - transform_block = '' - while i < len(transform_list): - transform = transform_list[i] - i += 1 - if transform != '': - transform_block += '.' + transform - transform = transform.split('(')[0] - if ((transform == 'movecm') or - (transform == 'rotcm') or - (transform == 'scalecm')): - - #break - - raise InputError("Error: center-of-mass transformations are not yet implemented\n" - " Avoid using \""+transform+"()\" transformations.\n") - - transform_blocks.append(transform_block) - - if len(postprocessing_commands) == 0: - # The first block (before movecm, rotcm, or scalecm) - # can be executed now by modifying the matrix stack. - if isinstance(command, PushRightCommand): - matrix_stack.PushCommandsRight(transform_blocks[0].strip('.'), - command.srcloc, - which_stack=command.context_node) - elif isinstance(command, PushLeftCommand): - matrix_stack.PushCommandsLeft(transform_blocks[0].strip('.'), - command.srcloc, - which_stack=command.context_node) - # Everything else must be saved for later. - postprocessing_blocks = transform_blocks[1:] - else: - # If we already encountered a "movecm" "rotcm" or "scalecm" - # then all of the command blocks must be handled during - # postprocessing. - postprocessing_blocks = transform_blocks - - for transform_block in postprocessing_blocks: - assert(isinstance(block, basestring)) - if isinstance(command, PushRightCommand): - postprocessing_commands.append(PushRightCommand(transform_block, - command.srcloc, - command.context_node)) - elif isinstance(command, PushLeftCommand): - postprocessing_commands.append(PushLeftCommand(transform_block, - command.srcloc, - command.context_node)) - - - elif isinstance(command, WriteFileCommand): - - # --- Throw away lines containin references to deleted variables:--- - - # First: To edit the content of a template, - # you need to make a deep local copy of it - tmpl_list = [] - for entry in command.tmpl_list: - if isinstance(entry, TextBlock): - tmpl_list.append(TextBlock(entry.text, - entry.srcloc)) #, entry.srcloc_end)) - else: - tmpl_list.append(entry) - - - # --- Now throw away lines with deleted variables --- - - DeleteLinesWithBadVars(tmpl_list) - - # --- Now render the text --- - text = Render(tmpl_list, - substitute_vars) - - # ---- Coordinates of the atoms, must be rotated - # and translated after rendering. - # In addition, other vectors (dipoles, ellipsoid orientations) - # must be processed. - # This requires us to re-parse the contents of this text - # (after it has been rendered), and apply these transformations - # before passing them on to the caller. - if command.filename == data_atoms: - text = TransformAtomText(text, matrix_stack.M) - - files_content[command.filename].append(text) - - - elif isinstance(command, ScopeBegin): - - if isinstance(command.node, InstanceObj): - if ((command.node.children != None) and - (len(command.node.children) > 0)): - matrix_stack.PushStack(command.node) - - # "command_list" is a long list of commands. - # ScopeBegin and ScopeEnd are (usually) used to demarcate/enclose - # the commands which are issued for a single class or - # class instance. _ExecCommands() carries out the commands for - # a single class/instance. If we reach a ScopeBegin(), - # then recursively process the commands belonging to the child. - index = _ExecCommands(command_list, - index, - files_content, - settings, - matrix_stack, - command.node, - substitute_vars) - - elif isinstance(command, ScopeEnd): - if 'Data Atoms' in files_content: - for ppcommand in postprocessing_commands: - if 'Data Masses' in files_content: - pass - #xcm = CalcCM(files_content['Data Atoms'], - # files_content['Data Masses'], - # settings) - else: - pass - #xcm = CalcCM(files_content['Data Atoms']) - - if isinstance(ppcommand, PushRightCommand): - matrix_stack.PushCommandsRight(ppcommand.contents, - ppcommand.srcloc, - xcm, - which_stack=command.context_node) - elif isinstance(ppcommand, PushLeftCommand): - matrix_stack.PushCommandsLeft(ppcommand.contents, - ppcommand.srcloc, - xcm, - which_stack=command.context_node) - files_content['Data Atoms'] = \ - TransformAtomText(Files_content['Data Atoms'], - matrix_stack.M) - - for ppcommand in postprocessing_commands: - matrix_stack.Pop(which_stack = command.context_node) - #(same as PopRight()) - - if isinstance(command.node, InstanceObj): - if ((command.node.children != None) and - (len(command.node.children) > 0)): - matrix_stack.PopStack() - - # "ScopeEnd" means we're done with this class/instance. - break - - else: - assert(False) - # no other command types allowed at this point - - - # After processing the commands in this list, - # merge the templates with the callers template list - for file_name, tmpl_list in files_content.items(): - global_files_content[file_name] += \ - files_content[file_name] - - return index - - - -def ExecCommands(commands, - files_content, - settings, - substitute_vars=True): - - matrix_stack = MultiAffineStack() - - index = _ExecCommands(commands, - 0, - files_content, - settings, - matrix_stack, - None, - substitute_vars) - assert(index == len(commands)) - - - - -def WriteFiles(files_content, suffix='', write_to_stdout=True): - for file_name, str_list in files_content.items(): - if file_name != None: - out_file = None - if file_name == '': - if write_to_stdout: - out_file = sys.stdout - else: - out_file = open(file_name+suffix, 'a') - if out_file != None: - out_file.write(''.join(str_list)) - if file_name != '': - out_file.close() - - - -def main(): - """ - This is is a "main module" wrapper for invoking ettree.py - as a stand alone program. This program: - - 1)reads a ttree file, - 2)constructs a tree of class definitions (g_objectdefs) - 3)constructs a tree of instantiated class objects (g_objects), - 4)automatically assigns values to the variables, - 5)and carries out the "write" commands to write the templates a file(s). - - """ - g_program_name = 'ettree.py' - g_date_str = '2018-6-26' - g_version_str = '0.37.0' - - SimpleCounter.default_n0 = 0 # counters in Espresso begin at 0, not 1 - - ####### Main Code Below: ####### - sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ') - sys.stderr.write('\n(python version '+str(sys.version)+')\n') - if sys.version < '2.6': - raise InputError('Error: Alas, you must upgrade to a newever version of python.') - - try: - - #settings = BasicUISettings() - #BasicUIParseArgs(sys.argv, settings) - settings = EttreeSettings() - EttreeParseArgs(sys.argv, settings) - - # Data structures to store the class definitionss and instances - g_objectdefs = StaticObj('', None) # The root of the static tree - # has name '' (equivalent to '/') - g_objects = InstanceObj('', None) # The root of the instance tree - # has name '' (equivalent to '/') - - # A list of commands to carry out - g_static_commands = [] - g_instance_commands = [] - - - BasicUI(settings, - g_objectdefs, - g_objects, - g_static_commands, - g_instance_commands) - - # Now, carry out the commands - # This involves rendering the templates and post-processing them. - - sys.stderr.write(' done\nbuilding templates...') - - files_content = defaultdict(list) - - ExecCommands(g_static_commands, - files_content, - settings, - False) - ExecCommands(g_instance_commands, - files_content, - settings, - False) - - # Erase the files that will be written to: - sys.stderr.write(' done\nwriting templates...') - EraseTemplateFiles(g_static_commands) - EraseTemplateFiles(g_instance_commands) - - # Write the files as templates - # (with the original variable names present) - WriteFiles(files_content, suffix=".template", write_to_stdout=False) - - # Write the files with the variables substituted by values - sys.stderr.write(' done\nbuilding and rendering templates...') - files_content = defaultdict(list) - ExecCommands(g_static_commands, files_content, settings, True) - ExecCommands(g_instance_commands, files_content, settings, True) - sys.stderr.write(' done\nwriting rendered templates...\n') - WriteFiles(files_content) - - # Now write the variable bindings/assignments table. - sys.stderr.write('writing \"ttree_assignments.txt\" file...') - open('ttree_assignments.txt', 'w').close() # <-- erase previous version. - WriteVarBindingsFile(g_objectdefs) - WriteVarBindingsFile(g_objects) - sys.stderr.write(' done\n') - - except (ValueError, InputError) as err: - sys.stderr.write('\n\n'+str(err)+'\n') - sys.exit(-1) - - - -if __name__ == "__main__": - main() diff --git a/tools/moltemplate/moltemplate/ettree_styles.py b/tools/moltemplate/moltemplate/ettree_styles.py deleted file mode 100644 index e5a842b5e1..0000000000 --- a/tools/moltemplate/moltemplate/ettree_styles.py +++ /dev/null @@ -1,115 +0,0 @@ - - -espt_delim_atom_fields = set(["pos", "type", "v", "f", - "bond", - "temp", "gamma", - "q", - "quat", "omega", "torque", - "rinertia", "fix", "unfix", "ext_force", - "exclude", "delete", - "mass", - "dipm", "dip", "virtual", - "vs_relative", "distance", "vs_auto_relate_to"]) - - - -def LinesWSlashes(text): - """ - Iterate over the lines contained in a string of text. - Merge lines ending in backslashes. - - """ - - current_line = '' - for line in text.split('\n'): - current_line += line - if (len(line) > 0) and (line[-1] != '\\'): - yield current_line - current_line = '' - if len(current_line) > 0: - yield current_line - - - - -def SplitMultiDelims(line, delimiters): - """ - Split a string into tokens using one or more (multi-character) delimiters. - (Bug: The current version of this function does not preserve white space, - but this should not matter.) - - """ - - token = '' - for sub_token in line.strip().split(): - if sub_token in delimiters: - yield token - yield sub_token - token = '' - elif len(token) > 0: - token += ' ' + sub_token - else: - token += sub_token - if len(token) > 0: - yield token - - - -def SplitAtomLine(line): - l = [] - for token in SplitMultiDelims(line, espt_delim_atom_fields): - l.append(token) - return l - - # In this type of TCL command, all of the delimiters - # (like 'pos', 'type', 'q', ...) - # are supposed to be followed by an argument. If the last - # token on this line IS a delimiter, then this is a syntax error. - - if token in espt_delim_atom_fields: - raise InputError("Error: Incomplete line:\n" - "\""+line+"\"\n") - - - -def iEsptAtomCoords(tokens): - #tokens = SplitMultiDelims(line) - i = 0 - while i < len(tokens): - if tokens[i] in set(['pos', 'fix', 'unfix']): - assert(i+1 < len(tokens)) - yield i+1 - i += 1 - i += 1 - - - - -def iEsptAtomVects(tokens): - #tokens = SplitMultiDelims(line) - i = 0 - while i < len(tokens): - if tokens[i] in set(['dip', 'rinertia', 'v', 'f', 'omega', 'torque']): - assert(i+1 < len(tokens)) - yield i+1 - i += 1 - i += 1 - - -def iEsptAtomType(tokens): - #tokens = SplitMultiDelims(line) - i = 0 - while i < len(tokens): - if tokens[i] == 'type': - assert(i+1 < len(tokens)) - yield i+1 - i += 1 - i += 1 - -def iEsptAtomID(tokens): - if len(tokens) > 1: - return 1 - else: - raise InputError("Error: Incomplete line:\n" - "\""+line+"\"\n") - diff --git a/tools/moltemplate/moltemplate/extract_espresso_atom_types.py b/tools/moltemplate/moltemplate/extract_espresso_atom_types.py deleted file mode 100755 index 8d95928cec..0000000000 --- a/tools/moltemplate/moltemplate/extract_espresso_atom_types.py +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env python - -import sys - -def main(): - for line_orig in sys.stdin: - line = line_orig.rstrip('\n') - comment = '' - if '#' in line_orig: - ic = line.find('#') - line = line_orig[:ic] - comment = ' '+line_orig[ic:].rstrip('\n') - - tokens = line.strip().split() - if len(tokens) > 2: - atomid = -1 - atomtype = -1 - pos_found = False - for i in range(0,len(tokens)): - if (tokens[i] == 'part') and (i+1 < len(tokens)): - atomid = tokens[i+1] - elif (tokens[i] == 'type') and (i+1 < len(tokens)): - atomtype = tokens[i+1] - elif (tokens[i] == 'pos') and (i+2 < len(tokens)): - pos_found = True - if (atomid != -1) and (atomtype != -1) and pos_found: - sys.stdout.write(atomid+' '+atomtype+'\n') - -if __name__ == "__main__": - main() diff --git a/tools/moltemplate/moltemplate/extract_lammps_data.py b/tools/moltemplate/moltemplate/extract_lammps_data.py deleted file mode 100755 index 23f5f172cf..0000000000 --- a/tools/moltemplate/moltemplate/extract_lammps_data.py +++ /dev/null @@ -1,138 +0,0 @@ -#!/usr/bin/env python -""" -extract_lammps_data.py is a simple script which extracts sections of text from -a LAMMPS data file. - -Typical usage: - -extract_lammps_data.py SECTION_NAME < FILE.DATA > EXCERPT.TXT - -This extracts a section from a LAMMPS data file and saves it in EXCERPT.TXT. - -More general usage: - -extract_lammps_data.py [-n] SECTION_LIST < FILE.DATA > EXCERPT.TXT - -For more details, see "doc/utils/docs_extract_lammps_data.txt" -""" - -import sys - -lammps_data_sections = set(['Atoms', - 'Masses', - 'Bonds', - 'Bond Coeffs', - 'Angles', - 'Angle Coeffs', - 'Dihedrals', - 'Dihedral Coeffs', - 'Impropers', - 'Improper Coeffs', - 'BondBond Coeffs', # class2 angles - 'BondAngle Coeffs', # class2 angles - 'MiddleBondTorsion Coeffs', # class2 dihedrals - 'EndBondTorsion Coeffs', # class2 dihedrals - 'AngleTorsion Coeffs', # class2 dihedrals - 'AngleAngleTorsion Coeffs', # class2 dihedrals - 'BondBond13 Coeffs', # class2 dihedrals - 'AngleAngle Coeffs', # class2 impropers - 'Angles By Type', # new. not standard LAMMPS - 'Dihedrals By Type', # new. not standard LAMMPS - 'Angles By Type']) # new. not standard LAMMPS - - -def DeleteComments(string, - escape='\\', - comment_char='#'): - escaped_state = False - for i in range(0, len(string)): - if string[i] in escape: - if escaped_state: - escaped_state = False - else: - escaped_state = True - elif string[i] == comment_char: - if not escaped_state: - return string[0:i] - return string - - -def ExtractDataSection(f, - section_name, - comment_char='#', - include_section_name=False, - return_line_nums=False): - - inside_section = False - if section_name in ('header', 'Header'): # "Header" section includes beginning - inside_section = True - - nonblank_encountered = False - nonheader_encountered = False - - i = 0 - for line_orig in f: - return_this_line = False - line = DeleteComments(line_orig).strip() - if line in lammps_data_sections: - nonheader_encountered = True - if section_name in ('header', 'Header'): - # The "header" section includes all lines at the beginning of the - # before any other section is encountered. - if nonheader_encountered: - return_this_line = False - else: - return_this_line = True - elif line == section_name: - inside_section = True - nonblank_encountered = False - if include_section_name: - return_this_line = True - # A block of blank lines (which dont immediately follow - # the section_name) signal the end of a section: - elif len(line) == 0: - if inside_section and include_section_name: - return_this_line = True - if nonblank_encountered: - inside_section = False - elif line[0] != comment_char: - if inside_section: - nonblank_encountered = True - return_this_line = True - - if return_this_line: - if return_line_nums: - yield i - else: - yield line_orig - - i += 1 - - -def main(): - lines = sys.stdin.readlines() - exclude_sections = False - if sys.argv[1] == '-n': - exclude_sections = True - del sys.argv[1] - - if not exclude_sections: - for section_name in sys.argv[1:]: - for line in ExtractDataSection(lines, section_name): - sys.stdout.write(line) - else: - line_nums_exclude = set([]) - for section_name in sys.argv[1:]: - for line_num in ExtractDataSection(lines, - section_name, - include_section_name=True, - return_line_nums=True): - line_nums_exclude.add(line_num) - for i in range(0, len(lines)): - if i not in line_nums_exclude: - sys.stdout.write(lines[i]) - - return - -if __name__ == "__main__": - main() diff --git a/tools/moltemplate/moltemplate/force_fields/README.txt b/tools/moltemplate/moltemplate/force_fields/README.txt deleted file mode 100644 index d0650a0f72..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/README.txt +++ /dev/null @@ -1,13 +0,0 @@ - -If moltemplate is unable to locate an .LT file that the user has requested -(ie. using the "import" command) in the current local directory, -moltemplate will search for that file here. - -This directory contains moltemplate files (.LT files) containing common -force fields (including parameters and rules for creating bonded interactions), -as well as definitions of molecules which are frequently used (for example -SPCE water). - -The scripts used to convert these force fields are located here as well, along -with the original files containing the force field parameters (when available). - diff --git a/tools/moltemplate/moltemplate/force_fields/__init__.py b/tools/moltemplate/moltemplate/force_fields/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/oplsaa_simple.lt b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/oplsaa_simple.lt deleted file mode 100644 index 5469790965..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/oplsaa_simple.lt +++ /dev/null @@ -1,284 +0,0 @@ -# Force-field example: -# -# This is an example of a general force-field file in moltemplate -# format. I hope that end-users can read this file and modify -# it to build their own custom force-field files. -# This is an abbreviated version of the full "oplsaa.lt" file -# (...which I hope is easier to read. It contains only the atom -# types and relevant parameters needed for simple alkanes and alkenes) -# -# USAGE: You can create molecules using this force-field this way: -# -# MyMolecule inherits OPLSAA { -# # atom-id mol-id atom-type charge X Y Z -# write('Data Atoms') { -# $atom:C1 $mol @atom:CTH2 0.00 -0.6695 0.000000 0.000000 -# $atom:H11 $mol @atom:HCen 0.00 -1.234217 -0.854458 0.000000 -# : : : : : : -# } -# } -# -# (Do not use this file. Use the full "oplsaa.lt" instead.) - - - -OPLSAA { - - - # Below we will use lammps "set" command to assign atom charges - # by atom type. http://lammps.sandia.gov/doc/set.html - - write_once("In Charges") { - set type @atom:CT3 charge -0.18 # "Alkane CH3-" - set type @atom:CT2 charge -0.12 # "Alkane -CH2-" - set type @atom:CTH charge -0.06 # "Alkane >CH-" - set type @atom:CT charge 0.0 # "Alkane >C<" - set type @atom:HCal charge 0.06 # "Alkane H-C" - set type @atom:CH2en charge -0.23 # "Alkene H2-C=" - set type @atom:HCen charge 0.115 # "Alkene H-C=" - } #(end of atom partial charges) - - # NOTE: In addition to setting atom charge by atom type, you can add - # write_once("Data Charge By Bond") { - # @atom:A @atom:B 0.05 -0.05 - # } - # sections to your force-field file. This defines rules to assign - # incremental charges to pairs of atoms depending on who they are bonded to. - # (These are also called "bond_increments".) - - - write_once("Data Masses") { - @atom:CT3 12.011 - @atom:CT2 12.011 - @atom:CTH 12.011 - @atom:CT 12.011 - @atom:HCal 1.008 - @atom:CH2en 12.011 - @atom:HCen 1.008 - } #(end of atom masses) - - - - # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- - # Each type of atom has a separate ID used for looking up bond parameters - # and a separate ID for looking up 3-body angle interaction parameters - # and a separate ID for looking up 4-body dihedral interaction parameters - # and a separate ID for looking up 4-body improper interaction parameters - # The complete @atom type name includes ALL of these ID numbers. There's - # no need to force the end-user to type the complete name of each atom. - # The "replace" command used below informs moltemplate that the short - # @atom names we have been using above are equivalent to the complete - # @atom names used below: - - replace{ @atom:CT3 @atom:CT3_b13_a13_d13_i13 } - replace{ @atom:CT2 @atom:CT2_b13_a13_d13_i13 } - replace{ @atom:CTH @atom:CTH_b13_a13_d13_i13 } - replace{ @atom:CT @atom:CT_b13_a13_d13_i13 } - replace{ @atom:HCal @atom:HCal_b46_a46_d46_i46 } - replace{ @atom:CH2en @atom:CH2en_b47_a47_d47_i47 } - replace{ @atom:HCen @atom:HCen_b46_a46_d46_i46 } - - - # ------------------ Non-Bonded Interactions: ------------------------- - # http://lammps.sandia.gov/doc/pair_lj.html - # Syntax: - # pair_coeff AtomType1 AtomType2 pair_style_name parameters... - - write_once("In Settings") { - pair_coeff @atom:CT3_b13_a13_d13_i13 @atom:CT3_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:CT2_b13_a13_d13_i13 @atom:CT2_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:CTH_b13_a13_d13_i13 @atom:CTH_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:CT_b13_a13_d13_i13 @atom:CT_b13_a13_d13_i13 lj/cut/coul/long 0.066 3.5 - pair_coeff @atom:HCal_b46_a46_d46_i46 @atom:HCal_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.5 - pair_coeff @atom:CH2en_b47_a47_d47_i47 @atom:CH2en_b47_a47_d47_i47 lj/cut/coul/long 0.076 3.55 - pair_coeff @atom:HCen_b46_a46_d46_i46 @atom:HCen_b46_a46_d46_i46 lj/cut/coul/long 0.03 2.42 - } #(end of pair_coeffs) - - - - # ------- Bonded Interactions: ------- - # http://lammps.sandia.gov/doc/bond_harmonic.html - # Syntax: - # bond_coeff BondTypeName BondStyle parameters... - - write_once("In Settings") { - bond_coeff @bond:13-13 harmonic 268.0 1.529 - bond_coeff @bond:13-46 harmonic 340.0 1.09 - bond_coeff @bond:13-47 harmonic 317.0 1.51 - bond_coeff @bond:46-47 harmonic 340.0 1.08 - bond_coeff @bond:47-47 harmonic 549.0 1.34 - } #(end of bond_coeffs) - - # Rules for assigning bond types by atom type: - # BondTypeName AtomType1 AtomType2 - # (* = wildcard) - - write_once("Data Bonds By Type") { - @bond:13-13 @atom:*_b13_a*_d*_i* @atom:*_b13_a*_d*_i* - @bond:13-46 @atom:*_b13_a*_d*_i* @atom:*_b46_a*_d*_i* - @bond:13-47 @atom:*_b13_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:46-47 @atom:*_b46_a*_d*_i* @atom:*_b47_a*_d*_i* - @bond:47-47 @atom:*_b47_a*_d*_i* @atom:*_b47_a*_d*_i* - } #(end of bonds by type) - - - - # ------- Angle Interactions ------- - # http://lammps.sandia.gov/doc/angle_harmonic.html - # Syntax: - # angle_coeff AngleTypeName AngleStyle parameters... - - write_once("In Settings") { - angle_coeff @angle:13-13-13 harmonic 58.35 112.7 - angle_coeff @angle:13-13-46 harmonic 37.5 110.7 - angle_coeff @angle:13-13-47 harmonic 63.0 111.1 - angle_coeff @angle:13-47-13 harmonic 70.0 130.0 - angle_coeff @angle:13-47-46 harmonic 35.0 117.0 - angle_coeff @angle:13-47-47 harmonic 70.0 124.0 - angle_coeff @angle:46-13-46 harmonic 33.0 107.8 - angle_coeff @angle:46-13-47 harmonic 35.0 109.5 - angle_coeff @angle:46-47-46 harmonic 35.0 117.0 - angle_coeff @angle:46-47-47 harmonic 35.0 120.0 - angle_coeff @angle:47-13-47 harmonic 63.0 112.4 - } #(end of angle_coeffs) - - # Rules for creating angle interactions according to atom type: - # AngleTypeName AtomType1 AtomType2 AtomType3 - # (* = wildcard) - - write_once("Data Angles By Type") { - @angle:13-13-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a13_d*_i* @atom:*_b*_a13_d*_i* - @angle:13-13-46 @atom:*_b*_a13_d*_i* @atom:*_b*_a13_d*_i* @atom:*_b*_a46_d*_i* - @angle:13-13-47 @atom:*_b*_a13_d*_i* @atom:*_b*_a13_d*_i* @atom:*_b*_a47_d*_i* - @angle:13-47-13 @atom:*_b*_a13_d*_i* @atom:*_b*_a47_d*_i* @atom:*_b*_a13_d*_i* - @angle:13-47-46 @atom:*_b*_a13_d*_i* @atom:*_b*_a47_d*_i* @atom:*_b*_a46_d*_i* - @angle:13-47-47 @atom:*_b*_a13_d*_i* @atom:*_b*_a47_d*_i* @atom:*_b*_a47_d*_i* - @angle:46-13-46 @atom:*_b*_a46_d*_i* @atom:*_b*_a13_d*_i* @atom:*_b*_a46_d*_i* - @angle:46-13-47 @atom:*_b*_a46_d*_i* @atom:*_b*_a13_d*_i* @atom:*_b*_a47_d*_i* - @angle:46-47-46 @atom:*_b*_a46_d*_i* @atom:*_b*_a47_d*_i* @atom:*_b*_a46_d*_i* - @angle:46-47-47 @atom:*_b*_a46_d*_i* @atom:*_b*_a47_d*_i* @atom:*_b*_a47_d*_i* - @angle:47-13-47 @atom:*_b*_a47_d*_i* @atom:*_b*_a13_d*_i* @atom:*_b*_a47_d*_i* - } #(end of angles by type) - - - - # ----------- Dihedral Interactions ------------ - # http://lammps.sandia.gov/doc/dihedral_opls.html - # Syntax: - # dihedral_coeff DihedralTypeName DihedralStyle parameters... - - write_once("In Settings") { - # General rules: - dihedral_coeff @dihedral:X-47-47-X opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:X-13-13-13 opls 1.711 -0.5 0.663 0.0 - dihedral_coeff @dihedral:X-13-47-13 opls 1.711 -0.5 0.663 0.0 - dihedral_coeff @dihedral:X-13-47-46 opls 0.0 0.0 0.468 0.0 - dihedral_coeff @dihedral:X-13-47-47 opls 0.5 0.0 0.0 0.0 - - # Specific rules (which override the general rules): - dihedral_coeff @dihedral:13-13-13-13 opls 1.3 -0.05 0.2 0.0 - dihedral_coeff @dihedral:13-13-13-47 opls 1.3 -0.05 0.2 0.0 - dihedral_coeff @dihedral:13-13-47-13 opls 2.817 -0.169 0.543 0.0 - dihedral_coeff @dihedral:13-13-47-47 opls 0.346 0.405 -0.904 0.0 - dihedral_coeff @dihedral:13-47-47-13 opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:13-47-47-46 opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:46-13-13-46 opls 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:46-13-13-47 opls 0.0 0.0 0.366 0.0 - dihedral_coeff @dihedral:46-13-47-13 opls 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:46-13-47-46 opls 0.0 0.0 0.318 0.0 - dihedral_coeff @dihedral:46-13-47-47 opls 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:46-47-47-46 opls 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:47-13-47-13 opls 0.0 -8.0 0.0 0.0 - dihedral_coeff @dihedral:47-13-47-46 opls 0.0 -8.0 0.0 0.0 - dihedral_coeff @dihedral:47-46-47-13 opls 0.0 -8.0 0.0 0.0 - dihedral_coeff @dihedral:47-46-47-46 opls 0.0 -8.0 0.0 0.0 - } #(end of dihedral_coeffs) - - # Rules for creating dihedral interactions according to atom type: - # DihedralTypeName AtomType1 AtomType2 AtomType3 AtomType4 - # (* = wildcard) - - write_once("Data Dihedrals By Type") { - @dihedral:X-47-47-X @atom:* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:* - @dihedral:X-13-13-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-47-13 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:X-13-47-46 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:X-13-47-47 @atom:* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-13-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-13-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* - @dihedral:13-13-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:13-13-47-47 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:13-47-47-13 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:13-47-47-46 @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-13-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-13-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* - @dihedral:46-13-47-13 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:46-13-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:46-13-47-47 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* - @dihedral:46-47-47-46 @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:47-13-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:47-13-47-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - @dihedral:47-46-47-13 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d13_i* - @dihedral:47-46-47-46 @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* @atom:*_b*_a*_d47_i* @atom:*_b*_a*_d46_i* - } #(end of dihedrals by type) - - - - - # ---------- Improper Interactions ---------- - # http://lammps.sandia.gov/doc/improper_harmonic.html - - write_once("In Settings") { - improper_coeff @improper:X-X-47-X harmonic 15.0 180.0 - } - - # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4 - # (* = wildcard) - - write_once("Data Impropers By Type (opls_imp.py)") { - @improper:X-X-47-X @atom:* @atom:* @atom:*_b*_a*_d*_i47 @atom:* - } - - # NOTE: Sometimes the default improper-creation rules do not work for a - # particular force-field. The "(opls_imp.py)" text above tells - # moltemplate to look for a file named "opls_imp.py" (normally found in - # "src/nbody_alternate_symmetry/") which tells moltemplate to change - # the order in the list of atoms in an improper interaction, or the - # criteria used to decide whether a new improper interaction should - # be created. The default rules are located in "src/nbody_Impropers.py" - - - # ------- Choosing LAMMPS Interaction Styles ------- - # LAMMPS supports many different kinds of bonded and non-bonded interactions - # which can be selected at run time. Although we specified these above in the - # pair_coeff, bond_coeff, angle_coeff, dihedral_coeff, and improper_coeff - # commands, we must also specify this in the "In Init" section: - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style hybrid harmonic - pair_style hybrid lj/cut/coul/long 10.0 10.0 - pair_modify mix geometric - special_bonds lj/coul 0.0 0.0 0.5 - kspace_style pppm 0.0001 - } #end of init parameters - - # Optional: - # I use "hybrid" styles in case the user later wishes to - # combine the molecules built using this force-field with other - # molecules that use other styles. (This is not necessarily - # a good idea, but LAMMPS and moltemplate both allow it.) - # For more information: - # http://lammps.sandia.gov/doc/pair_hybrid.html - # http://lammps.sandia.gov/doc/bond_hybrid.html - # http://lammps.sandia.gov/doc/angle_hybrid.html - # http://lammps.sandia.gov/doc/dihedral_hybrid.html - # http://lammps.sandia.gov/doc/improper_hybrid.html - - -} # OPLSAA - diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/alkane50.lt b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/alkane50.lt deleted file mode 100644 index b15ef139fd..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/alkane50.lt +++ /dev/null @@ -1,137 +0,0 @@ -# This is a simple example showing how to build a long polymer -# (in this case, an alkane chain). I split the -# hexadecane molecule into individual CH2 and CH3 monomers. -# I defined it this way so that you can easily modify -# it to change the length of the alkane chain. - - -import "ch2group.lt" # load the definition of the "CH2" object -import "ch3group.lt" # load the definition of the "CH3" object - - - -Alkane50 inherits OPLSAA { - - - create_var {$mol} # optional:force all monomers to share the same molecule-ID - - # This is a long polymer consisting of 48 CH2 groups and 2 CH3 end-caps. - # Rather than create them one-by-one, I decided to create them all - # using a single "new" command. Later, I can modify this array. - - # Create an array of 50 "CH2" objects distributed along the X axis - - monomers = new CH2 [50].rot(180,1,0,0).move(1.2533223,0,0) - - # NOTE: the ".rot(180,1,0,0).move(1.2533223,0,0)" means that each - # successive monomer is rotated 180 degrees (with respect to the previous - # monomer), and then moved 1.2533223 Angstroms down the X axis. - # Alternately, if you are reading the coordinates from a file, you don't have - # to indicate the position & orientation of each monomer. In that case, use: - # monomers = new CH2 [50] - - - # ---- Now, modify the ends: --- - # Delete the CH2 groups at the beginning and end, and replace them with CH3. - - delete monomers[0] - delete monomers[49] - - monomers[0] = new CH3 - monomers[49] = new CH3 - - # Move the CH3 groups to the correct location at either end of the chain: - - #monomers[0].move(0,0,0) # <--(this monomer is already in the correct place) - monomers[49].rot(180.0,0,0,1).move(61.4127927,0,0) #61.4127927=49*1.2533223 - - - ## NOTE: Alternately, you can define the polymer without deleting the ends: - # monomers[0] = new CH3 - # monomers[1-48] = new CH2[48].rot(180,1,0,0).move(1.2533223,0,0) - ## Note: monomers[0] and monomers[1] overlap, so we move 1-48 to make room: - # monomers[1-48].rot(180,1,0,0).move(1.2533223,0,0) # move many monomers - ## Now add the final monomer at the end: - # monomers[49] = new CH3.rot(180.0,0,0,1).move(61.4127927,0,0) - # - ## NOTE: Alternately, you can read the coordinates from a file. - ## In that case, you can use simpler commands: - # monomers[0] = new CH3 - # monomers[1-48] = new CH2[48] - # monomers[49] = new CH3 - - - - # Now add a list of bonds connecting the carbon atoms together: - # (Angles, dihedrals, impropers will be automatically added later.) - - write('Data Bond List') { - $bond:b1 $atom:monomers[0]/C $atom:monomers[1]/C - $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C - $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C - $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C - $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C - $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C - $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C - $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C - $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C - $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C - $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C - $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C - $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C - $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C - $bond:b15 $atom:monomers[14]/C $atom:monomers[15]/C - $bond:b16 $atom:monomers[15]/C $atom:monomers[16]/C - $bond:b17 $atom:monomers[16]/C $atom:monomers[17]/C - $bond:b18 $atom:monomers[17]/C $atom:monomers[18]/C - $bond:b19 $atom:monomers[18]/C $atom:monomers[19]/C - $bond:b20 $atom:monomers[19]/C $atom:monomers[20]/C - $bond:b21 $atom:monomers[20]/C $atom:monomers[21]/C - $bond:b22 $atom:monomers[21]/C $atom:monomers[22]/C - $bond:b23 $atom:monomers[22]/C $atom:monomers[23]/C - $bond:b24 $atom:monomers[23]/C $atom:monomers[24]/C - $bond:b25 $atom:monomers[24]/C $atom:monomers[25]/C - $bond:b26 $atom:monomers[25]/C $atom:monomers[26]/C - $bond:b27 $atom:monomers[26]/C $atom:monomers[27]/C - $bond:b28 $atom:monomers[27]/C $atom:monomers[28]/C - $bond:b29 $atom:monomers[28]/C $atom:monomers[29]/C - $bond:b30 $atom:monomers[29]/C $atom:monomers[30]/C - $bond:b31 $atom:monomers[30]/C $atom:monomers[31]/C - $bond:b32 $atom:monomers[31]/C $atom:monomers[32]/C - $bond:b33 $atom:monomers[32]/C $atom:monomers[33]/C - $bond:b34 $atom:monomers[33]/C $atom:monomers[34]/C - $bond:b35 $atom:monomers[34]/C $atom:monomers[35]/C - $bond:b36 $atom:monomers[35]/C $atom:monomers[36]/C - $bond:b37 $atom:monomers[36]/C $atom:monomers[37]/C - $bond:b38 $atom:monomers[37]/C $atom:monomers[38]/C - $bond:b39 $atom:monomers[38]/C $atom:monomers[39]/C - $bond:b40 $atom:monomers[39]/C $atom:monomers[40]/C - $bond:b41 $atom:monomers[40]/C $atom:monomers[41]/C - $bond:b42 $atom:monomers[41]/C $atom:monomers[42]/C - $bond:b43 $atom:monomers[42]/C $atom:monomers[43]/C - $bond:b44 $atom:monomers[43]/C $atom:monomers[44]/C - $bond:b45 $atom:monomers[44]/C $atom:monomers[45]/C - $bond:b46 $atom:monomers[45]/C $atom:monomers[46]/C - $bond:b47 $atom:monomers[46]/C $atom:monomers[47]/C - $bond:b48 $atom:monomers[47]/C $atom:monomers[48]/C - $bond:b49 $atom:monomers[48]/C $atom:monomers[49]/C - } - -} # Alkane50 - - - - - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163316030377 -# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046 -# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609 diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/ch2group.lt b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/ch2group.lt deleted file mode 100644 index 3431892f4e..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/ch2group.lt +++ /dev/null @@ -1,74 +0,0 @@ -# This file contains a definition for the "CH2" molecular subunit. - - - -import "oplsaa_simple.lt" # Load the force field settings we will need - - - -# Then define "CH2": - - -CH2 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:CT2 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:HCal 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:HCal 0.0 0.000000 0.631044 -0.892431 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - } - - # Atom type numbers (@atom:80L,@atom:85LCH3) are defined in "loplsaa.lt": - # @atom:80L "Alkane CH3- (LOPLS CT_CH3)" - # @atom:81L "Alkane -CH2- (LOPLS CT_CH2)" - # @atom:85LCH3 "Alkane H-C CH3 (LOPLS HC_CH3)" - # @atom:85LCH2 "Alkane H-C CH2 (LOPLS HC_CH2)" - # In this example, atomic charges are generated by atom type (according to the - # rules in loplsaa.lt), and can be omitted. Just leave them as "0.00" for now. - # The "..." in "$mol:..." tells moltemplate that this molecule may be part - # of a larger molecule, and (if so) to use the larger parent object's - # molecule id number as it's own. - -} # CH2 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH2.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/ch3group.lt b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/ch3group.lt deleted file mode 100644 index 686715e895..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/ch3group.lt +++ /dev/null @@ -1,65 +0,0 @@ -# This file contains a definition for the "CH3" molecular subunit. - - - -import "oplsaa_simple.lt" # Load the force field settings we will need - - - -# Then define "CH3": - - -CH3 inherits OPLSAA { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C $mol:... @atom:CT3 0.0 0.000000 0.000000 0.000000 - $atom:H1 $mol:... @atom:HCal 0.0 0.000000 0.631044 0.892431 - $atom:H2 $mol:... @atom:HCal 0.0 0.000000 0.631044 -0.892431 - $atom:H3 $mol:... @atom:HCal 0.0 -0.892431 -0.631044 0.000000 - } - - write('Data Bond List') { - $bond:CH1 $atom:C $atom:H1 - $bond:CH2 $atom:C $atom:H2 - $bond:CH3 $atom:C $atom:H3 - } - -} # CH3 - - - - - - - - - - - - - - - -# Optional: Shift all the coordinates in the +Y direction by 0.4431163. -# This way, the carbon atom is no longer located at 0,0,0, but the -# axis of an alkane chain containing this monomer is at 0,0,0. -# (This makes it more convenient to construct a polymer later. -# If this is confusing, then simply add 0.4431163 to the Y -# coordinates in the "Data Atoms" section above.) - -CH3.move(0,0.4431163,0) - - - - -######### (scratchwork calculations for the atomic coordinates) ######### -# Lcc = 1.5350 # length of the C-C bond (Sp3) -# Lch = 1.0930 # length of the C-H bond -# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle) -# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594 -# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754 -# # 0.5*DeltaYc = 0.4431163 -# DeltaZh = Lch*sin(theta/2) # = 0.892431 -# DeltaYh = Lch*cos(theta/2) # = 0.631044 diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/run.in.min b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/run.in.min deleted file mode 100644 index 5d0bcffd8e..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/run.in.min +++ /dev/null @@ -1,37 +0,0 @@ -# PREREQUISITES: -# -# You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -read_data "system.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. - -thermo 50 -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz -minimize 1.0e-4 1.0e-6 100000 400000 - - -# (The "write_restart" and "read_restart" commands were buggy in 2012, -# but they should work also. I prefer "write_data" and "read_data".) - -write_data system_after_min.data - - diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/run.in.nvt b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/run.in.nvt deleted file mode 100644 index 676cd8ec90..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/run.in.nvt +++ /dev/null @@ -1,36 +0,0 @@ -# PREREQUISITES: -# -# 1) You must use moltemplate.sh to create 3 files: -# system.data system.in.init system.in.settings -# 2) You must minimize the system beforehand by using "run.in.min". -# This will create the file "system_after_min.data" which this file reads. - -# ------------------------------- Initialization Section -------------------- - -include "system.in.init" - -# ------------------------------- Atom Definition Section ------------------- - -# Read the coordinates generated by an earlier simulation - -read_data "system_after_min.data" - -# ------------------------------- Settings Section -------------------------- - -include "system.in.settings" -include "system.in.charges" - -# ------------------------------- Run Section ------------------------------- - -# -- simulation protocol -- - - -timestep 1.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -thermo 500 -#thermo_modify flush yes - -run 1000000 - -write_data system_after_nvt.data diff --git a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/system.lt b/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/system.lt deleted file mode 100644 index f62ecc09b6..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/build_your_own_force_field/usage_example/system.lt +++ /dev/null @@ -1,31 +0,0 @@ -import "alkane50.lt" # Defines the "Alkane50" molecule - - -polymer = new Alkane50 - - - -# Specify the size of the world the polymer lives in: -write_once("Data Boundary") { - 0.0 72.0 xlo xhi - 0.0 72.0 ylo yhi - 0.0 72.0 zlo zhi -} - - - - - -############################################################################### -# Note: If you want to create multiple polymers, and/or mix them with other -# molecules, just add more "new" commands, for example: -# polymer1 = new Alkane50.move(0,0,10) -# polymer2 = new Alkane50.move(0,0,20) -# : -# ...or use array notation, for example: -# polymers = new Alkane50[20].move(0,0,10) -# -# Note: Multidimensional arrays can be used to fill a planar region or a volume -# polymers = new Alkane50 [4].move(0, 0, 30.0) -# [4].move(0, 30.0, 0) -# [2].move(70.0, 0, 0) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt deleted file mode 100644 index d228c3c18f..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/compass_original_format/README.txt +++ /dev/null @@ -1,30 +0,0 @@ -This directoroy contains the COMPASS force field parameters in the original -MSI file format ("compass_published.frc" which is distributed with "msi2lmp"). -It can be converted into moltemplate format using the following command: - -msifrc2lt.py -name COMPASS < compass_published.frc > compass_published.lt - ---- Credits: ---- - This is an incomplete version of the COMPASS force field based on available -public sources. Parameters for some common chemical groups are missing -(for example, the NH2 amine group). The commercial version of COMPASS is -much larger and presumably includes more up to date parameters and parameters -for a wider range of atom types and molecule types. (However files -containing those force field parameters are not publicly available.) - - This file has been graciously made available by Materials Design Inc. - - Here is a comment from "compass_published.frc": - - "This file created by Materials Design, Inc. (www.materialsdesign.com) -Please realize that we neither support this version, nor make any warranty -as to the correctness of the parameters. We have checked the numbers against -the literature, but of course there may still be errors, including errors of -interpretation. Also, the current version of COMPASS may well be different -that that originally published. - If you have comments or suggestions, feel free to email Paul Saxe -at psaxe (at) materialsdesign.com" - -(Note: This file predates moltemplate and was intended for use with other - software. Paul Saxe cannot be expected to answer questions related to - moltemplate.) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc b/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc deleted file mode 100644 index 6c2e681b5c..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/compass_original_format/compass_published.frc +++ /dev/null @@ -1,1381 +0,0 @@ -!BIOSYM forcefield 1 - -#version compass_published.frc 1.1 30-Jun-09 -#version compass_published.frc 1.0 01-Jun-09 - -#define compass - -!Ver Ref Function Label -!---- --- --------------------------------- ------ - 1.0 1 atom_types compass - 1.0 1 equivalence compass - 1.0 1 quartic_bond compass - 1.0 1 quartic_angle compass - 1.0 1 bond-bond compass - 1.0 1 bond-bond_1_3 compass - 1.0 1 bond-angle compass - 1.0 1 torsion_3 compass - 1.0 1 end_bond-torsion_3 compass - 1.0 1 middle_bond-torsion_3 compass - 1.0 1 angle-torsion_3 compass - 1.0 1 wilson_out_of_plane compass - 1.0 1 angle-angle compass - 1.0 1 angle-angle-torsion_1 compass - 1.0 1 nonbond(9-6) compass - 1.0 1 bond_increments compass - 1.0 1 templates compass - -#atom_types compass - -> Atom type definitions for any variant of compass -> Masses from CRC 1973/74 pages B-250. - -!Ver Ref Type Mass Element Comment -!---- --- ---- ---------- ------- ----------------------------------------- - 1.0 5 ar 39.94400 Ar argon - 1.0 1 c3a 12.01115 C aromatic carbon - 1.0 5 c1o 12.01115 C carbon in CO - 1.0 5 c2= 12.01115 C carbon in CO2 and CS2 - 1.0 7 c3' 12.01115 C carbonyl carbon [one polar substituent] - 1.0 1 c4 12.01115 C generic sp3 carbon - 1.0 8 c41o 12.01115 C carbon, sp3, in methanol - 1.0 8 c43o 12.01115 C carbon, sp3 in secondary alcohols - 1.0 1 c43 12.01115 C sp3 carbon with three heavy atoms attached - 1.0 1 c44 12.01115 C sp3 carbon with four heavy atoms attached - 1.0 3 c4o 12.01115 C alpha carbon - 1.0 9 c4z 12.01115 C carbon, sp3, bonded to -N3 - 1.0 1 h1 1.00797 H nonpolar hydrogen - 1.0 5 h1h 1.00797 H hydrogen in H2 - 1.0 3 h1o 1.00797 H strongly polar hydrogen, bonded to O,F - 1.0 5 he 4.00300 He helium - 1.0 5 kr 83.80000 Kr krypton - 1.0 5 n1n 14.00670 N nitrogen in N2 - 1.0 5 n1o 14.00670 N nitrogen in NO - 1.0 5 n1z 14.00670 N nitrogen, terminal atom in -N3 - 1.0 4 n2= 14.00670 N nitrogen - 1.0 5 n2o 14.00670 N nitrogen in NO2 - 1.0 9 n2t 14.00670 N nitrogen, central atom in -N3 - 1.0 9 n2z 14.00670 N nitrogen, first atom in -N3 - 1.0 7 n3m 14.00670 N sp3 nitrogen in amides without hydrogen - 1.0 6 n3o 14.00670 N nitrogen in nitro group - 1.0 5 ne 20.18300 Ne neon - 1.0 5 o1= 15.99940 O oxygen in NO2 and SO2 [and carbonyl] - 1.0 5 o1=* 15.99940 O oxygen in CO2 - 1.0 6 o12 15.99940 O oxygen in nitro group (-NO2) - 1.0 5 o1c 15.99940 O oxygen in CO - 1.0 5 o1n 15.99940 O oxygen in NO - 1.0 5 o1o 15.99940 O oxygen in O2 - 1.0 2 o2 15.99940 O generic oxygen with two bonds attached - 1.0 3 o2e 15.99940 O ether oxygen - 1.0 3 o2h 15.99940 O hydroxyl oxygen - 1.0 6 o2n 15.99940 O oxygen in nitrates - 1.0 7 o2s 15.99940 O ester oxygen - 1.0 2 o2z 15.99940 O oxygen, in siloxanes and zeolites - 1.0 4 p4= 30.97380 P phosphorous - 1.0 5 s1= 32.06400 S sulfur in CS2 - 1.0 5 s2= 32.06400 S sulfur in SO2 - 1.0 2 si4 28.08600 Si generic silicon with four bonds attached - 1.0 2 si4c 28.08600 Si a subset of si4, non-hydrogen atom attached [siloxanes] - 1.0 5 xe 131.30000 Xe xenon - - -#equivalence compass - -! Equivalences -! ----------------------------------------- -!Ver Ref Type NonB Bond Angle Torsion OOP -!---- --- ---- ---- ---- ----- ------- ---- - 1.0 5 ar ar ar ar ar ar - 1.0 5 c1o c1o c1o c1o c1o c1o - 1.0 5 c2= c2= c2= c2= c2= c2= - 1.0 1 c3a c3a c3a c3a c3a c3a - 1.0 7 c3' c3' c3' c3' c3' c3' - 1.0 1 c4 c4 c4 c4 c4 c4 - 1.0 8 c41o c41o c4 c4 c4 c4 - 1.0 8 c43o c43o c4 c4 c4 c4 - 1.0 1 c43 c43 c4 c4 c4 c4 - 1.0 1 c44 c44 c4 c4 c4 c4 - 1.0 3 c4o c4o c4 c4 c4 c4 - 1.0 9 c4z c4z c4 c4 c4 c4 - 1.0 1 h1 h1 h1 h1 h1 h1 - 1.0 5 h1h h1h h1h h1 h1 h1 - 1.0 3 h1o h1o h1 h1 h1 h1 - 1.0 5 he he he he he he - 1.0 5 kr kr kr kr kr kr - 1.0 5 n1n n1n n1n n1n n1n n1n - 1.0 5 n1o n1o n1o n1o n1o n1o - 1.0 9 n1z n1z n1t n1t n1t n1t - 1.0 4 n2= n2= n2= n2= n2= n2= - 1.0 5 n2o n2o n2o n2o n2o n2o - 1.0 9 n2t n2t n2t n2t n2t n2t - 1.0 9 n2z n2z n2z n2z n2z n2z - 1.0 7 n3m n3m n3m n3m n3m n3m - 1.0 6 n3o n3o n3o n3o n3o n3o - 1.0 5 ne ne ne ne ne ne - 1.0 5 o1= o1= o1= o1= o1= o1= - 1.0 5 o1=* o1=* o1= o1= o1= o1= - 1.0 6 o12 o12 o1= o1= o1= o1= - 1.0 5 o1c o1c o1c o1c o1c o1c - 1.0 5 o1n o1n o1n o1n o1n o1n - 1.0 5 o1o o1o o1o o1o o1o o1o - 1.0 2 o2 o2 o2 o2 o2 o2 - 1.0 3 o2h o2h o2h o2 o2 o2 - 1.0 3 o2e o2e o2e o2 o2 o2 - 1.0 6 o2n o2n o2n o2n o2 o2 - 1.0 7 o2s o2s o2e o2 o2 o2 - 1.0 2 o2z o2z o2z o2z o2z o2z - 1.0 4 p4= p4= p4= p4= p4= p4= - 1.0 5 s1= s1= s1= s1= s1= s1= - 1.0 5 s2= s2= s2= s2= s2= s2= - 1.0 2 si4 si4 si4 si4 si4 si4 - 1.0 2 si4c si4c si4 si4 si4 si4 - 1.0 5 xe xe xe xe xe xe - - -#quartic_bond compass - -> E = K2 * (R - R0)^2 + K3 * (R - R0)^3 + K4 * (R - R0)^4 - -!Ver Ref I J R0 K2 K3 K4 -!---- --- ---- ---- ------- -------- --------- -------- - 1.0 1 c3a c3a 1.4170 470.8361 -627.6179 1327.6345 - 1.0 1 c3a c4 1.5010 321.9021 -521.8208 572.1628 - 1.0 1 c3a h1 1.0982 372.8251 -803.4526 894.3173 - 1.0 1 c4 c4 1.5300 299.6700 -501.7700 679.8100 - 1.0 1 c4 h1 1.1010 345.0000 -691.8900 844.6000 - 1.0 2 o2z si4 1.6400 350.1232 -517.3424 673.7067 - 1.0 3 c3a o2 1.3768 428.8798 -738.2350 1114.9655 - 1.0 3 c3a o2e 1.3768 428.8798 -738.2351 1114.9655 - 1.0 3 c3a o2h 1.3768 428.8798 -738.2351 1114.9655 - 1.0 3 c4 o2e 1.4200 400.3954 -835.1951 1313.0142 - 1.0 3 c4 o2h 1.4200 400.3954 -835.1951 1313.0142 - 1.0 3 h1 o2h 0.9494 540.3633 -1311.8663 2132.4446 - 1.0 4 c3a n2= 1.4000 350.0000 0.0000 0.0000 - 1.0 4 c3a p4= 1.7890 197.7020 -332.2510 325.7160 - 1.0 4 c4 n2= 1.4740 337.0600 -147.3700 213.6330 - 1.0 4 c4 p4= 1.8000 218.1400 -329.5110 290.3490 - 1.0 4 cl1p p4= 2.0000 158.7770 -239.1290 210.0840 - 1.0 4 f1p p4= 1.5650 340.0000 -882.3840 1197.9190 - 1.0 4 h1 n2= 1.0310 540.1120 -1500.2952 2431.0080 - 1.0 4 h1 p4= 1.4300 285.2040 -575.6850 677.8460 - 1.0 4 n2= p4= 1.5980 393.0060 -751.4050 767.4310 - 1.0 4 n3 p4= 1.6780 329.0000 -713.7950 902.9190 - 1.0 4 o2 p4= 1.6000 333.0980 -726.6230 924.6200 - 1.0 5 h1h h1h 0.7412 414.2185 -805.6549 914.1296 - 1.0 5 n1n n1n 1.0977 1651.3730 -4069.3178 5984.9629 - 1.0 5 o1o o1o 1.2074 846.7150 -2247.1760 3478.9900 - 1.0 5 c1o o1c 1.1283 1368.7676 -3157.0007 4247.5298 - 1.0 5 n1o o1n 1.1506 1147.8362 -3167.7349 5099.5811 - 1.0 5 o1= s2= 1.4308 730.8387 -1531.7910 1859.7753 - 1.0 5 c2= o1= 1.1600 1161.3421 -2564.5706 3932.8735 - 1.0 5 n2o o1= 1.1930 620.0000 -1808.6018 3077.5918 - 1.0 5 c2= s1= 1.5540 559.0065 -1348.6633 1248.8604 - 1.0 6 c3a n3o 1.4300 313.8329 -568.6087 600.9597 - 1.0 6 c4 n3o 1.4740 301.6051 -535.7028 555.0420 - 1.0 6 c4 o2n 1.4350 400.3954 -835.1951 1313.0142 - 1.0 6 h1 n3o 1.0400 439.9346 -943.7307 1180.9318 - 1.0 6 n3o o1= 1.2100 765.0664 -2070.2830 2793.3218 - 1.0 6 n3o o2n 1.4020 300.0000 -1000.0000 2000.0000 - 1.0 7 c3' o2e 1.3750 368.7309 -832.4784 1274.0231 - 1.0 7 c3' c4 1.5140 312.3719 -465.8290 473.8300 - 1.0 7 c3' o1= 1.2160 823.7948 -1878.7939 2303.5310 - 1.0 7 c3' c3a 1.4890 339.3574 -655.7236 670.2362 - 1.0 7 c3' n3m 1.3850 359.1591 -558.4730 1146.3810 - 1.0 7 c3a n3m 1.3950 344.0452 -652.1208 1022.2242 - 1.0 9 n1t n1t 1.1354 1337.7450 -2675.4900 3121.4049 - 1.0 9 n2z n2t 1.2343 720.3345 -1542.6689 1799.7804 - 1.0 9 n2t n1t 1.1354 1198.7450 -2675.4900 3121.4049 - 1.0 9 n2z c4 1.4814 324.4578 -648.9156 757.0681 - 1.0 9 n2z h1 1.0221 440.1623 -960.3246 1120.3787 - 1.0 10 c3a si4 1.8634 233.2433 -276.8692 161.6659 - 1.0 10 c4 si4 1.8995 189.6536 -279.4210 307.5135 - 1.0 10 h1 si4 1.4783 202.7798 -305.3603 280.2685 - 1.0 10 si4 si4 2.3384 114.2164 -140.4212 80.7084 - 1.0 10 c4 n3m 1.4000 350.0000 0.0000 0.0000 - - -#quartic_angle compass - -> Delta = Theta - Theta0 -> E = K2 * Delta^2 + K3 * Delta^3 + K4 * Delta^4 - -!Ver Ref I J K Theta0 K2 K3 K4 -!---- --- ---- ---- ---- -------- ------- -------- -------- - 1.0 1 c3a c3a c3a 118.9000 61.0226 -34.9931 0.0000 - 1.0 1 c3a c3a c4 120.0500 44.7148 -22.7352 0.0000 - 1.0 1 c3a c3a h1 117.9400 35.1558 -12.4682 0.0000 - 1.0 1 c3a c4 c3a 111.0000 44.3234 -9.4454 0.0000 - 1.0 1 c3a c4 c4 108.4000 43.9594 -8.3924 -9.3379 - 1.0 1 c3a c4 h1 111.0000 44.3234 -9.4454 0.0000 - 1.0 1 c4 c4 c4 112.6700 39.5160 -7.4430 -9.5583 - 1.0 1 c4 c4 h1 110.7700 41.4530 -10.6040 5.1290 - 1.0 1 h1 c4 h1 107.6600 39.6410 -12.9210 -2.4318 - 1.0 2 h1 o2z si4 122.8000 23.7764 -19.8152 9.6331 - 1.0 2 si4 o2z si4 159.0000 8.5000 -13.4188 -4.1785 - 1.0 2 c3a si4 o2z 114.9060 23.0218 -31.3993 24.9814 - 1.0 2 c4 si4 o2z 114.9060 23.0218 -31.3993 24.9814 - 1.0 2 h1 si4 o2z 107.4000 57.6643 -10.6506 4.6274 - 1.0 2 o2z si4 o2z 110.7000 70.3069 -6.9375 0.0000 - 1.0 3 c3a c3a o2 123.4200 73.6781 -21.6787 0.0000 - 1.0 3 c4 c4 o2 111.2700 54.5381 -8.3642 -13.0838 - 1.0 3 h1 c4 o2 108.7280 58.5446 -10.8088 -12.4006 - 1.0 3 c3a o2 c4 102.9695 38.9739 -6.2595 -8.1710 - 1.0 3 c3a o2 h1 108.1900 53.1250 -8.5016 0.0000 - 1.0 3 c4 o2 c4 104.5000 35.7454 -10.0067 -6.2729 - 1.0 3 c4 o2 h1 105.8000 52.7061 -12.1090 -9.8681 - 1.0 4 c3a c3a n2= 120.0000 60.0000 0.0000 0.0000 - 1.0 4 c3a c3a p4= 120.0010 47.8410 -15.2290 -10.9070 - 1.0 4 c4 c4 n2= 117.3170 55.2420 0.0000 0.0000 - 1.0 4 h1 c4 n2= 107.4990 62.7310 0.0000 0.0000 - 1.0 4 h1 c4 p4= 110.8860 33.8300 -7.0430 -7.2460 - 1.0 4 c4 n2= h1 117.2000 37.2620 0.0000 0.0000 - 1.0 4 h1 n2= h1 110.9100 31.0910 0.0000 0.0000 - 1.0 4 h1 n2= p4= 120.0000 26.0680 -8.2980 -5.9430 - 1.0 4 p4= n2= p4= 135.0000 23.8680 -8.7360 0.0000 - 1.0 4 c4 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 - 1.0 4 h1 n3 p4= 120.0830 25.0010 -6.1170 -5.4570 - 1.0 4 c4 o2 p4= 118.2830 35.0010 -10.3600 -7.8700 - 1.0 4 h1 o2 p4= 117.0000 26.0310 -5.8280 -5.6200 - 1.0 4 c3a p4= c3a 110.2310 56.1850 -17.3160 -12.7280 - 1.0 4 c3a p4= h1 108.2310 36.1850 -6.4880 -7.6460 - 1.0 4 c3a p4= n2= 109.6000 63.0620 -19.7400 -14.3290 - 1.0 4 c3a p4= n3 108.1650 70.9770 -11.5480 -15.1090 - 1.0 4 c3a p4= o2 107.3650 71.9770 -10.9430 -15.2900 - 1.0 4 c4 p4= c4 102.5000 48.2320 -5.7980 -9.9660 - 1.0 4 c4 p4= h1 102.9000 52.0710 -6.4680 -10.7730 - 1.0 4 c4 p4= n2= 119.3000 47.3660 -14.6410 -10.7360 - 1.0 4 h1 p4= h1 101.4080 39.6950 -5.1340 -8.2270 - 1.0 4 h1 p4= n2= 110.0330 45.9780 -14.0520 -10.3990 - 1.0 4 h1 p4= n3 103.9780 68.2570 -9.2210 -14.1740 - 1.0 4 h1 p4= o2 103.9780 73.2570 -9.8970 -15.2120 - 1.0 4 n2= p4= n2= 125.0000 90.5230 -20.8010 -19.6020 - 1.0 4 n2= p4= n3 123.2150 89.9230 -32.6120 -21.0960 - 1.0 4 n2= p4= o2 112.2150 99.9230 -32.0930 -22.8210 - 1.0 4 n3 p4= n3 107.1000 85.7690 -5.7790 -17.4890 - 1.0 4 n3 p4= o2 108.3000 86.7690 -5.1750 -17.6710 - 1.0 4 o2 p4= o2 107.5000 86.7690 -4.5700 -17.8520 - 1.0 5 o1= c2= o1= 180.0000 57.1000 0.0000 0.0000 - 1.0 5 s1= c2= s1= 180.0000 48.0000 0.0000 0.0000 - 1.0 5 o1= n2o o1= 134.1000 150.0000 -82.1013 -40.0005 - 1.0 5 o1= s2= o1= 119.3000 115.2627 -35.6278 -26.1261 - 1.0 6 c3a c3a n3o 118.8000 29.2436 -8.8495 -6.6020 - 1.0 6 h1 c4 n3o 107.0000 54.9318 -9.1333 -11.5434 - 1.0 6 h1 c4 o2n 108.7280 58.5446 -10.8088 -12.4006 - 1.0 6 c3a n3o o1= 117.7000 63.9404 -18.4524 -14.3129 - 1.0 6 c4 n3o o1= 117.5000 64.5228 -18.4582 -14.4215 - 1.0 6 h1 n3o o1= 115.7000 53.8034 -14.1991 -11.8708 - 1.0 6 o1= n3o o1= 128.0000 95.1035 -47.4240 -27.9164 - 1.0 6 c4 o2n n3o 108.5000 55.7454 -10.0067 -6.2729 - 1.0 6 c4 c4 o2n 105.0000 54.5381 -8.3642 -13.0838 - 1.0 6 o2n n3o o1= 112.8000 85.5228 -18.4582 -14.4215 - 1.0 7 c3' o2 c4 109.0000 38.9739 -6.2595 -8.1710 - 1.0 7 c3' c4 h1 107.8594 38.0833 -17.5074 0.0000 - 1.0 7 c3' n3m c3' 121.9556 76.3105 -26.3166 -17.6944 - 1.0 7 c3a c3a c3' 116.0640 71.2598 -15.8273 2.0506 - 1.0 7 c3a c3' n3m 108.4400 84.8377 -19.9640 2.7405 - 1.0 7 c3a c3' o1= 125.5320 72.3167 -16.0650 2.0818 - 1.0 7 c3a c3a n3m 120.7640 73.2738 -27.4033 13.3920 - 1.0 7 c3a n3m c3' 120.0700 47.1131 -32.5592 13.1257 - 1.0 7 o1= c3' o2 118.9855 98.6813 -22.2485 10.3673 - 1.0 7 o1= c3' c4 119.3000 65.1016 -17.9766 0.0000 - 1.0 7 o2 c3' c4 100.3182 88.8631 -3.8323 -7.9802 - 1.0 7 n3m c3' o1= 121.5420 92.5720 -34.4800 -11.1871 - 1.0 9 n2z n2t n1t 171.6211 47.7899 0.0000 0.0000 - 1.0 9 n2t n2z h1 110.0345 55.7635 0.6618 0.0022 - 1.0 9 n2t n2z c4 113.5017 82.6294 0.9845 0.0033 - 1.0 9 n2z c4 h1 107.9744 52.7803 0.6615 0.0023 - 1.0 9 n2z c4 c4 110.9900 77.9387 0.9499 0.0033 - 1.0 10 c3a c3a si4 120.0000 30.4689 -23.5439 0.0000 - 1.0 10 c4 c4 si4 112.6700 39.5160 -7.4430 0.0000 - 1.0 10 h1 c4 si4 112.0355 28.7721 -13.9523 0.0000 - 1.0 10 c3a si4 h1 109.5932 41.9497 -42.3639 48.1442 - 1.0 10 c4 si4 c4 113.1855 36.2069 -20.3939 20.0172 - 1.0 10 c4 si4 h1 112.0977 36.4832 -12.8094 0.0000 - 1.0 10 h1 si4 h1 108.6051 32.5415 -8.3164 0.0000 - 1.0 10 c4 si4 si4 113.0000 19.4692 -34.3471 0.0000 - 1.0 10 h1 si4 si4 112.0893 22.5062 -11.5926 0.0000 - 1.0 10 si4 si4 si4 114.2676 24.9501 -19.5949 0.0000 - -#bond-bond compass - -> E = K(b,b') * (R - R0) * (R' - R0') - -!Ver Ref I J K K(b,b') -!---- --- ---- ---- ---- ------- - 1.0 1 c3a c3a c3a 68.2856 - 1.0 1 c3a c3a c4 12.0676 - 1.0 1 c3a c3a h1 1.0795 - 1.0 1 c3a c4 h1 2.9168 - 1.0 1 c4 c4 h1 3.3872 - 1.0 1 h1 c4 h1 5.3316 - 1.1 2 h1 c4 si4 6.3820 - 1.0 2 h1 o2z si4 6.3820 - 1.0 2 si4 o2z si4 41.1143 - 1.0 2 c4 si4 o2z 5.4896 - 1.0 2 h1 si4 o2z 11.6183 - 1.0 2 o2z si4 o2z 41.1143 - 1.0 3 c3a c3a o2 48.4754 - 1.0 3 h1 c3a o2 4.5800 - 1.0 3 c4 c4 o2 11.4318 - 1.0 3 h1 c4 o2 23.1979 - 1.0 3 o2 c4 o2 8.2983 - 1.0 3 c3a o2 h1 20.6577 - 1.0 3 c4 o2 c4 -7.1131 - 1.0 3 c4 o2 h1 -9.6879 - 1.0 4 c4 c4 n2= 22.7100 - 1.0 4 h1 c4 n2= 5.6640 - 1.0 4 h1 c4 p4= 1.0500 - 1.0 4 c4 n2= h1 12.5630 - 1.0 4 h1 n2= h1 1.4570 - 1.0 4 h1 n2= p4= -18.2870 - 1.0 4 p4= n2= p4= 20.0000 - 1.0 4 c4 p4= c4 6.2460 - 1.0 4 c4 p4= h1 3.8820 - 1.0 4 c4 p4= n2= 1.0720 - 1.0 4 h1 p4= h1 20.0000 - 1.0 4 h1 p4= n2= 12.5700 - 1.0 4 n2= p4= n2= 20.0000 - 1.0 5 o1= c2= o1= 275.4350 - 1.0 5 s1= c2= s1= 100.7369 - 1.0 5 o1= n2o o1= 20.0000 - 1.0 5 o1= s2= o1= 20.0000 - 1.0 6 c3a c3a n3o 21.0495 - 1.0 6 c4 c4 o2n 11.4318 - 1.0 6 h1 c4 n3o 3.3770 - 1.0 6 h1 c4 o2n 23.1979 - 1.0 6 c3a n3o o1= 93.7948 - 1.0 6 o2n n3o o1= 80.0000 - 1.0 6 c4 n3o o1= 48.1403 - 1.0 6 h1 n3o o1= 14.8226 - 1.0 6 o1= n3o o1= 265.7106 - 1.0 7 c3' o2 c3a 69.5999 - 1.0 7 c3' c4 h1 2.2522 - 1.0 7 c3' n3m c3' 25.9530 - 1.0 7 c3a c4 o2 0.0000 - 1.0 7 c3a o2 c3a 0.0000 - 1.0 7 c3' c3a c3a 37.8749 - 1.0 7 c3a c3' n3m 0.0000 - 1.0 7 c3a c3' o1= 116.9445 - 1.0 7 c3a c3a n3m 37.8749 - 1.0 7 c3a n3m c3' 0.0000 - 1.0 7 o1= c3' o2 210.1813 - 1.0 7 c4 c3' o1= 77.5201 - 1.0 7 c4 c3' o2 19.1069 - 1.0 7 n3m c3' o1= 138.4954 - 1.0 9 h1 n2z n2t 14.9026 - 1.0 9 n2z n2t n1t 204.9909 - 1.0 9 n2t n2z c4 84.2075 - 1.0 9 n2z c4 h1 18.4621 - 1.0 9 n2z c4 c4 36.9309 - 1.0 10 h1 c4 si4 1.6561 - 1.0 10 c3a c3a si4 21.3938 - 1.0 10 c3a si4 h1 3.9264 - 1.0 10 c4 si4 c4 3.7419 - 1.0 10 c4 si4 h1 3.9340 - 1.0 10 c4 si4 si4 2.3030 - 1.0 10 h1 si4 h1 4.6408 - 1.0 10 h1 si4 si4 3.5172 - 1.0 10 si4 si4 si4 6.0704 - - -#bond-bond_1_3 compass - -> E = K(b,b') * (R - R0) * (R' - R0') - -!Ver Ref I J K L K(b,b') -!--- --- ----- ----- ----- ----- -------- - 1.0 1 c3a c3a c3a c3a 53.0000 - 1.0 1 c3a c3a c3a c4 2.5085 - 1.0 1 c3a c3a c3a h1 -6.2741 - 1.0 1 c4 c3a c3a h1 0.8743 - 1.0 1 h1 c3a c3a h1 -1.7077 - 1.0 1 c3a c3a c4 h1 -3.4826 - 1.0 3 c3a c3a c3a o2 -2.2436 - 1.0 3 h1 c3a c3a o2 -2.0517 - 1.0 3 c3a c3a o2 h1 1.1590 - - -#bond-angle compass - -> E = K * (R - R0) * (Theta - Theta0) - -!Ver Ref I J K K(b,theta) K(b',theta) -!---- --- ---- ---- ---- ---------- ----------- - 1.0 1 c3a c3a c3a 28.8708 - 1.0 1 c3a c3a c4 31.0771 47.0579 - 1.0 1 c3a c3a h1 20.0033 24.2183 - 1.0 1 c3a c4 h1 26.4608 11.7717 - 1.0 1 c4 c4 c4 8.0160 - 1.0 1 c4 c4 h1 20.7540 11.4210 - 1.0 1 h1 c4 h1 18.1030 - 1.0 2 h1 o2z si4 18.0902 31.0726 - 1.0 2 si4 o2z si4 28.6686 - 1.0 2 c4 si4 o2z 6.4278 20.5669 - 1.0 2 h1 si4 o2z 6.4278 20.5669 - 1.0 2 o2z si4 o2z 23.4380 - 1.0 3 c3a c3a o2 58.4790 107.6806 - 1.0 3 c4 c4 o2 2.6868 20.4033 - 1.0 3 h1 c4 o2 4.6189 55.3270 - 1.0 3 c3a o2 h1 53.8614 23.9224 - 1.0 3 c4 o2 c4 -2.8112 - 1.0 3 c4 o2 h1 28.5800 18.9277 - 1.0 4 c4 c4 n2= 19.2440 59.4220 - 1.0 4 h1 c4 n2= 6.4070 46.3730 - 1.0 4 h1 c4 p4= 19.8120 16.9400 - 1.0 4 c4 n2= h1 18.4860 7.8370 - 1.0 4 h1 n2= h1 8.4900 - 1.0 4 h1 n2= p4= 40.0630 90.7910 - 1.0 4 c4 p4= c4 12.8050 - 1.0 4 c4 p4= h1 11.1260 -19.4700 - 1.0 4 c4 p4= n2= -7.1280 26.3530 - 1.0 4 h1 p4= n2= -24.3830 72.9250 - 1.0 5 o1= n2o o1= -50.0000 - 1.0 5 o1= s2= o1= 45.0585 - 1.0 6 c3a c3a n3o 30.5211 59.8025 - 1.0 6 c4 c4 o2n 2.6868 20.4033 - 1.0 6 h1 c4 n3o 12.2491 30.5314 - 1.0 6 h1 c4 o2n 4.6189 55.3270 - 1.0 6 c3a n3o o1= 40.3757 92.1955 - 1.0 6 c4 n3o o1= 27.2141 93.9927 - 1.0 6 h1 n3o o1= -8.6275 58.6036 - 1.0 6 o1= n3o o1= 95.6936 - 1.0 7 c3' o2 c4 21.5366 -16.6748 - 1.0 7 c3' c4 h1 15.5988 14.6287 - 1.0 7 c3' n3m c3' 20.0533 - 1.0 7 c3' c3a c3a 23.6977 45.8865 - 1.0 7 c3a c3a n3m 35.8865 53.6977 - 1.0 7 c3a c3' o1= 72.8758 76.1093 - 1.0 7 o1= c3' o2 79.4497 57.0987 - 1.0 7 c4 c3' o1= 31.8455 46.6613 - 1.0 7 c4 c3' o2 1.3435 4.6978 - 1.0 7 n3m c3' o1= 62.7124 52.4045 - 1.0 9 h1 n2z n2t 37.4419 141.1218 - 1.0 9 n2z n2t n1t 25.5611 1.2222 - 1.0 9 n2t n2z c4 195.9722 88.2679 - 1.0 9 n2z c4 h1 61.9652 3.3182 - 1.0 9 n2z c4 c4 67.8888 34.8803 - 1.0 10 c3a c3a si4 14.5831 23.7679 - 1.0 10 h1 c4 si4 16.6908 18.2764 - 1.0 10 c3a si4 h1 22.5947 8.7811 - 1.0 10 c4 si4 c4 18.5805 - 1.0 10 c4 si4 h1 13.3961 7.4104 - 1.0 10 c4 si4 si4 16.9455 11.4377 - 1.0 10 h1 si4 h1 9.3467 - 1.0 10 h1 si4 si4 5.6630 2.0706 - 1.0 10 si4 si4 si4 8.9899 - - -#torsion_3 compass - -> E = SUM(n=1,3) { V(n) * [ 1 - cos(n*Phi - Phi0(n)) ] } - -!Ver Ref I J K L V1 Phi0 V2 Phi0 V3 Phi0 -!---- --- ---- ---- ---- ---- ------- ------ ------- ------ ------- ------ - 1.0 1 c3a c3a c3a c3a 8.3667 0.0 1.2000 0.0 0.0000 0.0 - 1.0 1 c3a c3a c3a c4 0.0000 0.0 4.4072 0.0 0.0000 0.0 - 1.0 1 c3a c3a c3a h1 0.0000 0.0 3.9661 0.0 0.0000 0.0 - 1.0 1 c4 c3a c3a h1 0.0000 0.0 1.5590 0.0 0.0000 0.0 - 1.0 1 h1 c3a c3a h1 0.0000 0.0 2.3500 0.0 0.0000 0.0 - 1.0 1 c3a c3a c4 c3a -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 - 1.0 1 c3a c3a c4 c4 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 - 1.0 1 c3a c3a c4 h1 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 - 1.0 1 c3a c4 c4 h1 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 - 1.0 1 c4 c4 c4 c4 0.0000 0.0 0.0514 0.0 -0.1430 0.0 - 1.0 1 c4 c4 c4 h1 0.0000 0.0 0.0316 0.0 -0.1681 0.0 - 1.0 1 h1 c4 c4 h1 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 - 1.0 1 * c3a c3a * 0.0000 0.0 4.5000 0.0 0.0000 0.0 - 1.0 1 * c4 c4 * 0.0000 0.0 0.0000 0.0 -0.1530 0.0 - 1.0 2 h1 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0500 0.0 - 1.0 2 h1 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0500 0.0 - 1.0 2 h1 o2z si4 o2z 0.0000 0.0 0.0000 0.0 -0.0500 0.0 - 1.0 2 si4 o2z si4 c4 0.0000 0.0 0.0000 0.0 -0.0100 0.0 - 1.0 2 si4 o2z si4 h1 0.0000 0.0 0.0000 0.0 -0.0100 0.0 - 1.0 2 si4 o2z si4 o2z -0.2250 0.0 0.0000 0.0 -0.0100 0.0 - 1.0 2 * o2z si4 * 0.0000 0.0 0.0000 0.0 -0.0100 0.0 - 1.0 3 c3a c3a c3a o2 0.0000 0.0 4.8498 0.0 0.0000 0.0 - 1.0 3 h1 c3a c3a o2 0.0000 0.0 1.7234 0.0 0.0000 0.0 - 1.0 3 c3a c3a o2 c4 0.0000 0.0 1.5000 0.0 0.0000 0.0 - 1.0 3 c3a c3a o2 h1 -0.6900 0.0 0.5097 0.0 0.0095 0.0 - 1.0 3 c4 c4 c4 o2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 - 1.0 3 h1 c4 c4 o2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 - 1.0 3 o2 c4 c4 o2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 - 1.0 3 c4 c4 o2 c4 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 - 1.0 3 c4 c4 o2 h1 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 - 1.0 3 h1 c4 o2 c3a 0.9513 0.0 0.1155 0.0 0.0720 0.0 - 1.0 3 h1 c4 o2 c4 0.5302 0.0 0.0000 0.0 -0.3966 0.0 - 1.0 3 h1 c4 o2 h1 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 - 1.0 4 c3a c3a c3a p4= 0.0000 0.0 5.4770 0.0 0.0000 0.0 - 1.0 4 h1 c3a c3a p4= 0.0000 0.0 2.2700 0.0 0.0000 0.0 - 1.0 4 c3a c3a p4= h1 -0.2720 0.0 1.1900 0.0 0.0000 0.0 - 1.0 4 c3a c3a p4= n2= -0.2720 0.0 1.1900 0.0 0.0000 0.0 - 1.0 4 c4 c4 c4 n2= 0.0970 0.0 0.0720 0.0 -0.2580 0.0 - 1.0 4 h1 c4 c4 n2= -0.1510 0.0 0.0100 0.0 -0.1860 0.0 - 1.0 4 c4 c4 n2= h1 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 - 1.0 4 h1 c4 n2= h1 1.2660 0.0 -0.7740 0.0 0.0380 0.0 - 1.0 4 h1 c4 p4= c4 0.0000 0.0 0.0000 0.0 -0.0680 0.0 - 1.0 4 h1 c4 p4= h1 0.0000 0.0 0.0000 0.0 -0.0680 0.0 - 1.0 4 h1 c4 p4= n2= 0.0000 0.0 0.0000 0.0 -0.0680 0.0 - 1.0 4 h1 n2= p4= c3a 0.0000 0.0 0.0000 0.0 -0.3500 0.0 - 1.0 4 h1 n2= p4= c4 0.0000 0.0 0.0000 0.0 -0.3690 0.0 - 1.0 4 h1 n2= p4= h1 0.0000 0.0 0.0000 0.0 -0.3500 0.0 - 1.0 4 h1 n2= p4= o2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 - 1.0 4 p4= n2= p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 4 p4= n2= p4= n2= 1.8000 0.0 0.5000 0.0 2.0000 0.0 - 1.0 4 h1 n3 p4= h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 4 h1 n3 p4= n2= 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 4 h1 n3 p4= o2 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 4 h1 o2 p4= h1 5.7080 0.0 2.1180 0.0 0.0000 0.0 - 1.0 4 h1 o2 p4= n2= 5.7080 0.0 2.1180 0.0 0.0000 0.0 - 1.0 4 h1 o2 p4= o2 5.7080 0.0 2.1180 0.0 0.0000 0.0 - 1.0 4 * o2 p4= * 5.7080 0.0 2.1180 0.0 0.0000 0.0 - 1.0 4 * c3a n2= * 0.0000 0.0 1.0000 0.0 0.0000 0.0 - 1.0 4 * c3a p4= * -0.2720 0.0 1.1900 0.0 0.0000 0.0 - 1.0 4 * c4 n2= * 0.0000 0.0 0.0000 0.0 -0.0200 0.0 - 1.0 4 * c4 p4= * 0.0000 0.0 0.0000 0.0 -0.0680 0.0 - 1.0 4 * n2= p4= * 0.0000 0.0 0.0000 0.0 -0.3500 0.0 - 1.0 4 * n3 p4= * 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 6 c3a c3a c3a n3o 0.0000 0.0 7.2124 0.0 0.0000 0.0 - 1.0 6 h1 c3a c3a n3o 0.0000 0.0 2.9126 0.0 0.0000 0.0 - 1.0 6 c3a c3a n3o o1= 0.0000 0.0 1.1600 0.0 0.0000 0.0 - 1.0 6 c4 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 - 1.0 6 h1 c4 n3o o1= 0.0000 0.0 0.0000 0.0 -0.3500 0.0 - 1.0 6 c4 c4 o2 n3o 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 - 1.0 6 o1= n3o o2 c4 0.0000 0.0 2.0000 0.0 0.0000 0.0 - 1.0 7 c3' c3a c3a c3a 0.0000 0.0 4.6282 0.0 0.0000 0.0 - 1.0 7 c3' c3a c3a h1 0.0000 0.0 2.1670 0.0 0.0000 0.0 - 1.0 7 c3' n3m c3a c3a 0.0000 0.0 0.6500 0.0 0.0000 0.0 - 1.0 7 c3' n3m c3' o1 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 - 1.0 7 c3' o2 c4 c4 0.1302 0.0 -0.3250 0.0 0.1134 0.0 - 1.0 7 c3' o2 c4 h1 0.9513 0.0 0.1155 0.0 0.0000 0.0 - 1.0 7 c3a c3a c3' o1= 0.0000 0.0 0.7800 0.0 0.0000 0.0 - 1.0 7 c3a c3a c3a n3m 0.0000 0.0 3.4040 0.0 0.0000 0.0 - 1.0 7 c3a n3m c3' o1= 0.0000 0.0 2.0521 0.0 0.0000 0.0 - 1.0 7 c4 o2 c3' c4 -2.5594 0.0 2.2013 0.0 0.0325 0.0 - 1.0 7 c4 o2 c3' o1= 0.8905 0.0 3.2644 0.0 0.2646 0.0 - 1.0 7 o1= c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 7 o2 c3' c4 h1 0.0000 0.0 0.0000 0.0 0.0000 0.0 - 1.0 7 n3m c3a c3a h1 0.0000 0.0 3.4040 0.0 0.0000 0.0 - 1.0 9 h1 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.2637 0.0 - 1.0 9 c4 n2z n2t n1t 0.0000 0.0 0.0000 0.0 -0.1823 0.0 - 1.0 9 n2t n2z c4 h1 0.0000 0.0 0.0000 0.0 -0.2181 0.0 - 1.0 9 n2t n2z c4 c4 0.0000 0.0 0.0000 0.0 -0.2021 0.0 - 1.0 9 n2z c4 c4 h1 0.0000 0.0 0.0000 0.0 -0.2259 0.0 - 1.0 10 c3a c3a c3a si4 0.0000 0.0 4.3270 0.0 0.0000 0.0 - 1.0 10 h1 c3a c3a si4 0.0000 0.0 1.5093 0.0 0.0000 0.0 - 1.0 10 c3a c3a si4 * 0.0000 0.0 0.0000 0.0 -0.0231 0.0 - 1.0 10 c4 c4 si4 si4 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 - 1.0 10 * c4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 - 1.0 10 * si4 si4 * 0.0000 0.0 0.0000 0.0 -0.0657 0.0 - - -#end_bond-torsion_3 compass - -> E = (R - R0) * -> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } - -! LEFT RIGHT -! ------------------------------- ------------------------------- -!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) -!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- - 1.0 1 c3a c3a c3a c3a -0.1185 6.3204 0.0000 - 1.0 1 c3a c3a c3a c4 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 - 1.0 1 c3a c3a c3a h1 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 - 1.0 1 c4 c3a c3a h1 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 - 1.0 1 h1 c3a c3a h1 0.0000 -0.6890 0.0000 - 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 - 1.0 1 c3a c3a c4 h1 -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 - 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 - 1.0 1 c4 c4 c4 c4 -0.0732 0.0000 0.0000 - 1.0 1 c4 c4 c4 h1 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 - 1.0 1 h1 c4 c4 h1 0.2130 0.3120 0.0777 - 1.0 3 c3a c3a c3a o2 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 - 1.0 3 h1 c3a c3a o2 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 - 1.0 3 c3a c3a o2 h1 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 - 1.0 3 c4 c4 c4 o2 -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 - 1.0 3 h1 c4 c4 o2 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 - 1.0 3 o2 c4 c4 o2 1.0165 0.7553 -0.4609 - 1.0 3 c4 c4 o2 c4 -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 - 1.0 3 c4 c4 o2 h1 -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 - 1.0 3 h1 c4 o2 c4 -0.6054 1.3339 0.9648 -0.1620 0.1564 -1.1408 - 1.0 3 h1 c4 o2 h1 -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 - 1.0 7 o1= c3' n3m c3' -0.7019 0.8305 -0.6874 0.1726 -0.4823 0.2666 - 1.0 7 c4 c4 o2 c3' -1.2164 -0.1715 -0.0964 0.2560 0.8133 -0.0728 - 1.0 7 h1 c4 o2 c3' 0.9589 0.9190 -0.6015 0.2282 2.2998 -0.4473 - 1.0 7 c4 c3' o2 c4 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 - 1.0 7 o1= c3' o2 c4 -4.2421 10.1102 1.6824 0.0882 -2.4309 -0.7426 - 1.0 7 o1= c3' c4 h1 0.0536 0.0354 0.3853 2.9036 0.5307 0.1439 - 1.0 7 o2 c3' c4 h1 0.4160 -0.1140 0.7099 0.7800 1.3339 0.3268 - - -#middle_bond-torsion_3 compass - -> E = (R - R0) * -> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } - -!Ver Ref I J K L F(1) F(2) F(3) -!---- --- ---- ---- ---- ---- -------- ------- ------- - 1.0 1 c3a c3a c3a c3a 27.5989 -2.3120 0.0000 - 1.0 1 c3a c3a c3a c4 0.0000 9.1792 0.0000 - 1.0 1 c3a c3a c3a h1 0.0000 -1.1521 0.0000 - 1.0 1 c4 c3a c3a h1 0.0000 3.9421 0.0000 - 1.0 1 h1 c3a c3a h1 0.0000 4.8228 0.0000 - 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 - 1.0 1 c3a c3a c4 h1 -5.5679 1.4083 0.3010 - 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 - 1.0 1 c4 c4 c4 c4 -17.7870 -7.1877 0.0000 - 1.0 1 c4 c4 c4 h1 -14.8790 -3.6581 -0.3138 - 1.0 1 h1 c4 c4 h1 -14.2610 -0.5322 -0.4864 - 1.0 3 c3a c3a c3a o2 0.0000 4.8255 0.0000 - 1.0 3 h1 c3a c3a o2 0.0000 5.5432 0.0000 - 1.0 3 c3a c3a o2 h1 1.1580 3.2697 3.5132 - 1.0 3 c4 c4 c4 o2 -21.8842 -7.6764 -0.6868 - 1.0 3 h1 c4 c4 o2 -16.7975 -1.2296 -0.2750 - 1.0 3 o2 c4 c4 o2 -17.2585 -3.6157 -0.8364 - 1.0 3 c4 c4 o2 c4 -5.9288 -2.7007 -0.3175 - 1.0 3 c4 c4 o2 h1 1.2472 0.0000 0.7485 - 1.0 3 h1 c4 o2 c4 -6.8007 -4.6546 -1.4101 - 1.0 3 h1 c4 o2 h1 0.0000 0.9241 -0.5889 - 1.0 4 c4 c4 c4 n2= 0.0000 0.0000 0.0000 - 1.0 4 h1 c4 c4 n2= -3.5150 -2.2980 -1.2770 - 1.0 4 c4 c4 n2= h1 -2.3800 2.5290 -0.7300 - 1.0 4 h1 c4 n2= h1 -0.4140 -2.8620 0.0070 - 1.0 4 p4= n2= p4= n2= 0.0000 0.0000 0.0000 - 1.0 7 c3' c3a c3a c3a 0.0000 3.8762 0.0000 - 1.0 7 o1= c3' n3m c3' -0.1118 -1.1990 0.6784 - 1.0 7 c4 c4 o2 c3' 9.9416 2.6421 2.2333 - 1.0 7 h1 c4 o2 c3' 7.7147 4.2557 -1.0118 - 1.0 7 o1= c3' c3a c3a 0.0000 2.4002 0.0000 - 1.0 7 c3a c3a c3a n3m 0.0000 5.2012 0.0000 - 1.0 7 c4 c3' o2 c4 1.3445 3.5515 -4.9202 - 1.0 7 o1= c3' o2 c4 0.4552 7.3091 0.2842 - 1.0 7 o1= c3' c4 h1 0.0000 0.0000 -1.0000 - 1.0 7 o2 c3' c4 h1 -13.7686 -2.5959 1.1934 - 1.0 7 h1 c3a c3a n3m 0.0000 5.2012 0.0000 - 1.0 10 c3a c3a c3a si4 0.0000 11.1576 0.0000 - 1.0 10 h1 c3a c3a si4 0.0000 6.2168 0.0000 - 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.3146 - 1.0 10 h1 c4 si4 h1 0.0000 0.0000 -0.5906 - 1.0 10 h1 c4 si4 si4 0.0000 0.0000 -0.1909 - 1.0 10 c4 si4 si4 h1 0.0000 0.0000 -0.6941 - 1.0 10 h1 si4 si4 h1 0.0000 0.0000 -0.6302 - - -#angle-torsion_3 compass - -> E = (Theta - Theta0) * -> { F(1) * cos(phi) + F(2) * cos(2 * phi) + F(3) * cos(3 * phi) } - -! LEFT RIGHT -! ------------------------------- ------------------------------- -!Ver Ref I J K L F(1) F(2) F(3) F(1) F(2) F(3) -!---- --- ---- ---- ---- ---- ------- ------- ------- ------- ------- ------- - 1.0 1 c3a c3a c3a c3a 1.9767 1.0239 0.0000 - 1.0 1 c3a c3a c3a c4 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 - 1.0 1 c3a c3a c3a h1 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 - 1.0 1 c4 c3a c3a h1 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 - 1.0 1 h1 c3a c3a h1 0.0000 2.4501 0.0000 - 1.0 1 c3a c3a c4 c4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 - 1.0 1 c3a c3a c4 h1 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 - 1.0 1 c3a c4 c4 h1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 - 1.0 1 c4 c4 c4 c4 0.3886 -0.3139 0.1389 - 1.0 1 c4 c4 c4 h1 -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 - 1.0 1 h1 c4 c4 h1 -0.8085 0.5569 -0.2466 - 1.0 3 c3a c3a c3a o2 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 - 1.0 3 h1 c3a c3a o2 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 - 1.0 3 c3a c3a o2 h1 -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 - 1.0 3 c4 c4 c4 o2 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 - 1.0 3 h1 c4 c4 o2 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 - 1.0 3 o2 c4 c4 o2 0.5511 0.9737 -0.6673 - 1.0 3 c4 c4 o2 c4 -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 - 1.0 3 c4 c4 o2 h1 -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 - 1.0 3 h1 c4 o2 c4 -1.8234 1.6393 0.5144 -0.7777 0.4340 -0.6653 - 1.0 3 h1 c4 o2 h1 -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 - 1.0 4 c4 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 - 1.0 4 h1 c4 c4 n2= -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 - 1.0 4 c4 c4 n2= h1 -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 - 1.0 4 h1 c4 n2= h1 -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 - 1.0 6 c3a c3a c3a n3o 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 - 1.0 6 h1 c3a c3a n3o 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 - 1.0 6 c3a c3a n3o o1= 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 - 1.0 6 h1 c4 n3o o1= 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 - 1.0 6 o1= n3o o2 c4 -3.0000 0.0000 0.0000 0.0000 0.0000 0.0000 - 1.0 7 o1= c3' n3m c3' -1.5747 2.3997 -0.2851 -0.3038 -0.0548 -0.3188 - 1.0 7 c4 c4 o2 c3' -0.4620 1.4492 -0.6765 -0.0890 -0.9159 0.7229 - 1.0 7 h1 c4 o2 c3' -0.4990 2.8061 -0.0401 -0.3142 -0.8699 0.0971 - 1.0 7 c4 c3' o2 c4 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 - 1.0 7 o1= c3' o2 c4 5.9732 2.7261 1.9052 2.3573 1.0059 -0.0327 - 1.0 7 o1= c3' c4 h1 -2.0667 0.7308 -0.2083 14.4728 0.3339 0.0800 - 1.0 7 o2 c3' c4 h1 -0.0241 1.4427 0.1212 13.2959 0.8005 -0.0071 - 1.0 10 c3a c3a c3a si4 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 - 1.0 10 h1 c3a c3a si4 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 - 1.0 10 c3a c3a si4 h1 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 - 1.0 10 h1 c4 si4 c4 0.0000 0.0000 0.3382 0.0000 0.0000 0.4272 - - -#wilson_out_of_plane compass - -> E = K * (Chi - Chi0)^2 - -!Ver Ref I J K L K Chi0 -!---- --- ---- ---- ---- ---- ------- ---- - 1.0 1 c3a c3a c3a c3a 7.1794 0.0 - 1.0 1 c3a c3a c3a c4 7.8153 0.0 - 1.0 1 c3a c3a c3a h1 4.8912 0.0 - 1.0 3 c3a c3a c3a o2 13.0421 0.0 - 1.0 4 c3a c3a c3a n2= 8.0000 0.0 - 1.0 4 c3a c3a c3a p4= 6.7090 0.0 - 1.0 6 c3a c3a c3a n3o 0.9194 0.0 - 1.0 6 c3a n3o o1= o1= 36.2612 0.0 - 1.0 6 c4 n3o o1= o1= 44.3062 0.0 - 1.0 6 h1 n3o o1= o1= 38.5581 0.0 - 1.0 6 o1= n3o o1= o2 45.0000 0.0 - 1.0 7 c3' c3' n3m c3a 0.0000 0.0 - 1.0 7 c3' c3a c3a c3a 17.0526 0.0 - 1.0 7 c3' n3m c3' c3a 0.0000 0.0 - 1.0 7 c3a c3a n3m c3a 17.0526 0.0 -!1.0 7 c3a c3a c3a n3m 17.0526 0.0 - 1.0 7 c3a c3' n3m o1= 30.0000 0.0 -!1.0 7 c3a c3a c3' c3a 17.0526 0.0 -!1.0 7 c3a c3' o1= n3m 30.0000 0.0 - 1.0 7 c3a o1= c3' n3m 30.0000 0.0 - 1.0 7 c4 c3' o2 o1= 46.9264 0.0 - 1.0 10 c3a c3a si4 c3a 5.3654 0.0 - - -#angle-angle compass - -> E = K * (Theta - Theta0) * (Theta' - Theta0') - -! J' I' K' -!Ver Ref I J K K -!---- --- ---- ---- ---- ---- ------- - 1.0 1 c3a c3a c3a c3a 0.0000 - 1.0 1 c3a c3a c3a h1 0.0000 - 1.0 1 c3a c3a h1 c3a 0.0000 - 1.0 1 c4 c4 c3a h1 2.0403 - 1.0 1 h1 c4 c3a h1 3.0118 - 1.0 1 c3a c4 c4 h1 -1.8202 - 1.0 1 c4 c4 c4 c4 -0.1729 - 1.0 1 c4 c4 c4 h1 -1.3199 - 1.0 1 h1 c4 c4 h1 -0.4825 - 1.0 1 c3a c4 h1 c4 1.0827 - 1.0 1 c3a c4 h1 h1 2.3794 - 1.0 1 c4 c4 h1 c4 0.1184 - 1.0 1 c4 c4 h1 h1 0.2738 - 1.0 1 h1 c4 h1 h1 -0.3157 - 1.0 3 c3a c3a c3a o2 0.0000 - 1.0 3 c3a c3a o2 c3a 0.0000 - 1.0 3 c4 c4 c4 o2 -0.8330 - 1.0 3 h1 c4 c4 o2 2.5926 - 1.0 3 c4 c4 h1 o2 3.9177 - 1.0 3 h1 c4 h1 o2 2.4259 - 1.0 3 c4 c4 o2 c4 -3.5744 - 1.0 3 c4 c4 o2 h1 0.1689 - 1.0 3 h1 c4 o2 h1 2.1283 - 1.0 4 h1 c4 c4 n2= 1.0910 - 1.0 4 c4 c4 h1 n2= 2.7530 - 1.0 4 h1 c4 h1 n2= 1.7680 - 1.0 4 c4 c4 n2= h1 -1.3060 - 1.0 4 h1 c4 n2= h1 -2.9470 - 1.0 7 h1 c4 c3' o2 4.7955 - 1.0 7 c3' c4 h1 h1 -1.7653 - 1.0 11 h1 c4 c3' h1 0.0 - 1.0 10 h1 c4 h1 si4 0.0000 - 1.0 10 h1 c4 si4 h1 2.2050 - 1.0 10 c4 si4 c4 h1 3.3827 - 1.0 10 c4 si4 c4 si4 1.3465 - 1.0 10 h1 si4 c4 h1 4.6809 - 1.0 10 si4 si4 c4 si4 -5.6849 - 1.0 10 c4 si4 h1 c4 2.7963 - 1.0 10 c4 si4 h1 h1 4.4559 - 1.0 10 c4 si4 h1 si4 3.4758 - 1.0 10 h1 si4 h1 h1 2.0665 - 1.0 10 si4 si4 h1 si4 3.4924 - 1.0 10 c4 si4 si4 c4 2.0805 - 1.0 10 c4 si4 si4 h1 -2.9623 - 1.0 10 c4 si4 si4 si4 4.5272 - 1.0 10 h1 si4 si4 h1 1.6082 - 1.0 10 si4 si4 si4 h1 4.1996 - - -#angle-angle-torsion_1 compass - -> E = K * (Theta - Theta0) * (Theta' - Theta0') * cos(Phi) - -!Ver Ref I J K L K(Ang,Ang,Tor) -!---- --- ---- ---- ---- ---- -------------- - 1.0 1 c3a c3a c3a c3a 0.0000 - 1.0 1 c3a c3a c3a c4 -14.4097 - 1.0 1 c3a c3a c3a h1 -4.8141 - 1.0 1 c4 c3a c3a h1 4.4444 - 1.0 1 h1 c3a c3a h1 0.3598 - 1.0 1 c3a c3a c4 h1 -5.8888 - 1.0 1 c4 c4 c4 c4 -22.0450 - 1.0 1 c4 c4 c4 h1 -16.1640 - 1.0 1 h1 c4 c4 h1 -12.5640 - 1.0 3 c3a c3a c3a o2 -21.0247 - 1.0 3 h1 c3a c3a o2 4.2296 - 1.0 3 c3a c3a o2 h1 -4.6072 - 1.0 3 c4 c4 c4 o2 -29.0420 - 1.0 3 h1 c4 c4 o2 -20.2006 - 1.0 3 o2 c4 c4 o2 -14.0484 - 1.0 3 c4 c4 o2 c4 -19.0059 - 1.0 3 c4 c4 o2 h1 -12.1038 - 1.0 3 h1 c4 o2 c4 -16.4438 - 1.0 3 h1 c4 o2 h1 -10.5093 - 1.0 4 c4 c4 c4 n2= 0.0000 - 1.0 4 h1 c4 c4 n2= -27.5060 - 1.0 4 c4 c4 n2= h1 -8.8980 - 1.0 4 h1 c4 n2= h1 -9.6280 - 1.0 4 h1 c4 p4= c4 -25.5460 - 1.0 4 h1 c4 p4= h1 -16.0180 - 1.0 4 h1 c4 p4= n2= -19.9340 - 1.0 4 h1 n2= p4= c4 -11.1020 - 1.0 4 h1 n2= p4= h1 -3.7880 - 1.0 6 c3a c3a c3a n3o -34.9681 - 1.0 6 h1 c3a c3a n3o 2.1508 - 1.0 6 c3a c3a n3o o1= -18.0436 - 1.0 6 h1 c4 n3o o1= -16.2615 - 1.0 7 o1= c3' n3m c3' -3.3556 - 1.0 7 c4 c4 o2 c3' -15.7082 - 1.0 7 h1 c4 o2 c3' -13.1500 - 1.0 7 c4 c3' o2 c4 -12.2070 - 1.0 7 o1= c3' o2 c4 -32.9368 - 1.0 7 o1= c3' c4 h1 -23.1923 - 1.0 7 o2 c3' c4 h1 -13.9734 - 1.0 10 c4 si4 c4 h1 -17.5802 - 1.0 10 h1 si4 c4 h1 -12.9341 - 1.0 10 h1 c4 si4 si4 -13.3679 - 1.0 10 c4 si4 si4 h1 -16.9141 - 1.0 10 h1 si4 si4 h1 -10.8232 - 1.0 10 h1 si4 si4 si4 -12.2900 - - -#nonbond(9-6) compass - -> E = eps(ij) [2(r(ij)*/r(ij))**9 - 3(r(ij)*/r(ij))**6] -> where r(ij) = [(r(i)**6 + r(j)**6))/2]**(1/6) -> -> eps(ij) = 2 sqrt(eps(i) * eps(j)) * -> r(i)^3 * r(j)^3/[r(i)^6 + r(j)^6] - -@combination sixth-power -@type r-eps - -!Ver Ref I r eps -!---- --- ---- --------- --------- - 1.0 1 c3a 3.9150 0.0680 - 1.0 1 c4 3.8540 0.0620 - 1.0 1 c43 3.8540 0.0400 - 1.0 1 c44 3.8540 0.0200 - 1.0 1 h1 2.8780 0.0230 - 1.0 2 o2z 3.3000 0.0800 - 1.0 2 si4 4.4050 0.1980 - 1.0 2 si4c 4.2900 0.1310 - 1.0 3 c4o 3.8150 0.0680 - 1.0 3 h1o 1.0870 0.0080 - 1.0 3 o2 3.3000 0.0800 - 1.0 3 o2e 3.3000 0.1200 - 1.0 3 o2h 3.5800 0.0960 - 1.0 4 n2= 3.8300 0.0960 - 1.0 4 p4= 4.2950 0.0650 - 1.0 5 he 2.9000 0.0050 - 1.0 5 ne 3.2000 0.0550 - 1.0 5 ar 3.8800 0.2000 - 1.0 5 kr 4.3000 0.2800 - 1.0 5 xe 4.2600 0.3900 - 1.0 5 h1h 1.4210 0.0216 - 1.0 5 n1n 3.8008 0.0598 - 1.0 5 c1o 4.0120 0.0530 - 1.0 5 o1o 3.4758 0.0780 - 1.0 5 o1c 3.6020 0.0850 - 1.0 5 n1o 3.4600 0.1280 - 1.0 5 o1n 3.3000 0.1560 - 1.0 5 c2= 3.9150 0.0680 - 1.0 5 s2= 4.0470 0.1250 - 1.0 5 n2o 3.5290 0.3330 - 1.0 5 o1= 3.4300 0.1920 - 1.0 5 o1=* 3.3600 0.0670 - 1.0 5 s1= 4.0070 0.3130 - 1.0 6 n3o 3.7600 0.0480 - 1.0 6 o12 3.4000 0.0480 - 1.0 6 o2n 3.6500 0.2000 - 1.0 7 c3' 3.9000 0.0640 - 1.0 7 n3m 3.7200 0.1500 - 1.0 7 o2s 3.3000 0.0960 - 1.1 8 c4o 3.8700 0.0748 - 1.1 8 c41o 3.8700 0.1080 - 1.1 8 c43o 3.6700 0.0498 - 1.0 9 c4z 3.6500 0.0800 - 1.0 9 n1z 3.5200 0.0850 - 1.0 9 n2t 3.3000 0.0500 - 1.0 9 n2z 3.4000 0.1200 - - -#bond_increments compass - -!Ver Ref I J DeltaIJ DeltaJI -!---- --- ---- ---- ------- ------- - 1.0 1 c3a c3a 0.0000 0.0000 - 1.0 1 c3a c4 0.0000 0.0000 - 1.0 1 c3a h1 -0.1268 0.1268 - 1.0 1 c4 c4 0.0000 0.0000 - 1.0 1 c4 h1 -0.0530 0.0530 - 1.0 2 o2z si4 -0.2225 0.2225 - 1.0 3 c3a o2e 0.0420 -0.0420 - 1.0 3 c3a o2h 0.0420 -0.0420 - 1.0 3 c4 o2e 0.1600 -0.1600 - 1.0 3 c4 o2h 0.1600 -0.1600 - 1.0 3 h1 o2 0.4200 -0.4200 - 1.0 3 h1 o2h 0.4200 -0.4200 - 1.0 4 c3a n2= 0.1990 -0.1990 - 1.0 4 c3a p4= -0.0600 0.0600 - 1.0 4 c4 n2= 0.3450 -0.3450 - 1.0 4 c4 p4= -0.0500 0.0500 - 1.0 4 cl1p p4= -0.1200 0.1200 - 1.0 4 f1p p4= -0.1800 0.1800 - 1.0 4 h1 n2= 0.3280 -0.3280 - 1.0 4 h1 p4= -0.0500 0.0500 - 1.0 4 n2= n2= 0.0000 0.0000 - 1.0 4 n2= n3 0.0250 -0.0250 - 1.0 4 n2= o2 -0.0430 0.0430 - 1.0 4 n2= p4= -0.3500 0.3500 - 1.0 4 n3 p4= -0.1200 0.1200 - 1.0 4 o2 p4= -0.1400 0.1400 - 1.0 5 c1o o1c -0.0203 0.0203 - 1.0 5 c2= o1= 0.4000 -0.4000 - 1.0 5 c2= s1= 0.0258 -0.0258 - 1.0 5 n2o o1= 0.0730 -0.0730 - 1.0 5 h1h h1h 0.0000 0.0000 - 1.0 5 n1n n1n 0.0000 0.0000 - 1.0 5 n1o o1n 0.0288 -0.0288 - 1.0 5 o1= s2= -0.2351 0.2351 - 1.0 5 o1o o1o 0.0000 0.0000 - 1.0 6 c3a n3o 0.2390 -0.2390 - 1.0 6 c4 n3o 0.2100 -0.2100 - 1.0 6 c4 o2n 0.3170 -0.3170 - 1.0 6 h1 n3o 0.1880 -0.1880 - 1.0 6 n3o o1= 0.4280 -0.4280 - 1.0 6 n3o o2n 0.0010 -0.0010 - 1.0 7 c3' o2e 0.1120 -0.1120 - 1.0 7 c3' c4 0.0000 0.0000 - 1.0 7 c3' o1= 0.4500 -0.4500 - 1.0 7 c3' c3a 0.0350 -0.0350 - 1.0 7 c3' n3m 0.0000 0.0000 - 1.0 7 c3a n3m 0.0950 -0.0950 - 1.1 8 h1 o2h 0.4100 -0.4100 - 1.0 9 n2z c4 -0.3110 0.3110 - 1.0 9 n2z h1 -0.3350 0.3350 - 1.0 9 n2t n1t 0.3860 -0.3860 - 1.0 9 n2t n2z 0.2470 -0.2470 - 1.0 10 c3a si4 -0.1170 0.1170 - 1.0 10 c4 si4 -0.1350 0.1350 - 1.0 10 h1 si4 -0.1260 0.1260 - -#templates compass - -type: ? - ! anything - template: (>*) -end_type - -type: ar - ! Argon atom - template: (>Ar) -end_type - -type:c1o - ! Carbon in CO - template: [>C[~O]] -end_type - -type:c2= - ! Carbon in =C= (e.g. CO2, CS2) - template: [>C[~*][~*]] -end_type - -type:c3' - ! Carbonyl carbon [one polar substituent such as O,N] - ! e.g. amide, acid and ester - template: (>C (~O) (~*) (~*)) - atom_test:1 - hybridization:sp2 - end_test - atom_test:3 - allowed_elements: C, H - end_test - atom_test:4 - allowed_elements: O, N - end_test -end_type - -type:c3a - ! SP2 aromatic carbon - template:(>C(~*)(~*)(~*)) - atom_test:1 - hybridization: SP2 - aromaticity:AROMATIC - end_test -end_type - -type:c3a - ! Transferred from pcff - may not be required. - ! This is used for aromatic carbons that fail the aromaticity test because - ! the current ring checker is too lame to figure on a ring with more than - ! seven or eight sides. The NON_AROMATIC test is to eliminate the conflict - ! with the above 'c3a' definition. This can be removed when the ring checker - ! is made more robust. - template: [>C(-*)(:*)(:*)] - atom_test:1 - hybridization:SP2 - aromaticity:NON_AROMATIC - end_test -end_type - -type:c4 - ! generic SP3 carbon - template: (>C(-*)(-*)(-*)(-*)) - atom_test:1 - hybridization:SP3 - end_test -end_type - -type:c41o - ! Carbon, sp3, in methanol (and dimethyl ether?) - template: [>C(-O(-*))(-H)(-H)(-H)] - atom_test:1 - hybridization:SP3 - end_test - atom_test:3 - allowed_elements:C,H -end_type - -type: c43 - ! sp3 carbon with 1 h and 3 heavy atoms - template: (>C(-H)(-*)(-*)(-*)) - atom_test:1 - hybridization:SP3 - atom_test:3 - disallowed_elements:H - atom_test:4 - disallowed_elements:H - atom_test:5 - disallowed_elements:H - end_test -end_type - -type:c43o - ! Carbon, sp3, in secondary alcohols - template: [>C(-O(-H))(-H)(-C)(-C)] - atom_test:1 - hybridization:SP3 - end_test -end_type - -type: c44 - ! sp3 carbon with four heavy atoms attached - template: (>C(-*)(-*)(-*)(-*)) - atom_test:1 - hybridization:SP3 - atom_test:2 - disallowed_elements:H - atom_test:3 - disallowed_elements:H - atom_test:4 - disallowed_elements:H - atom_test:5 - disallowed_elements:H - end_test -end_type - -type: c4o - ! alpha carbon (e.g. alpha to oxygen in ethers and alcohols) - template: (>C(-O)(-*)(-*)(-*)) - atom_test:1 - hybridization:SP3 - end_test -end_type - -type: c4z - ! Carbon, sp3, bonded to -N3 (azides) - template: (>C(-N(~N(~N)))(-*)(-*)(-*)) - atom_test:1 - hybridization:SP3 - end_test -end_type - -type:h1 - ! nonpolar hydrogen - template: (>H (-*) ) - atom_test:2 - allowed_elements:C,Si - end_test -end_type - -type:h1h - ! Hydrogen in H2 - template: [>H[-H]] -end_type - -type:h1o - ! strongly polar hydrogen (bonded to fluorine, nitrogen, Oxygen - h* in pcff) - template: (>H(-*)) - atom_test:2 - allowed_elements:O,N,F - end_test -end_type - -type: he - ! Helium atom - template: (>He) -end_type - -type: kr - ! Krypton atom - template: (>Kr) -end_type - -type:n1n - ! Nitrogen in N2 - template: [>N[~N]] -end_type - -type:n1o - ! Nitrogen in NO - template: [>N[~O]] -end_type - -type:n1z - ! Nitrogen, terminal atom in -N3 - template: [>N[~N[~N(~*)]]] -end_type - -type:n2= - ! Nitrogen (in phosphazenes, or generic???) - template: [>N(~*)(~*)] -end_type - -type:n2o - ! Nitrogen in NO2 - template: [>N[~O][~O]] -end_type - -type:n2t - ! Nitrogen, central atom in -N3 - template: [>N[~N][~N(~*)]] -end_type - -type:n2z - ! Nitrogen, first atom in -N3 - template: (>N[~N[~N]](~*)) -end_type - -type: n3m - ! sp3 nitrogen in amides without hydrogen - template: (>N(-C[=O])(-C)(-C)) - atom_test:1 - hybridization:SP3 - end_test -end_type - -type: n3o - ! Nitrogen in nitro group - template: (>N[~O][~O](~O(~C))) -end_type - -type: ne - ! Neon atom - template: (>Ne) -end_type - -type:o1= - ! Oxygen in NO2 and SO2 [and carbonyl] - template: (>O(~*)) - atom_test:2 - allowed_elements:N,S,C - end_test -end_type - -type:o1=* - ! Oxygen in CO2 - template: [>O[~C[~O]]] -end_type - -type:o12 - ! Oxygen in nitro group -NO2 - template: [>O[~N[~O](~*)]] -end_type - -type:o1c - ! Oxygen in CO - template: [>O[~C]] -end_type - -type:o1n - ! Oxygen in NO - template: [>O[~N]] -end_type - -type:o1o - ! Oxygen in O2 - template: [>O[~O]] -end_type - -type:o2 - ! Generic oxygen with two bonds attached - template: [>O(~*)(~*)] -end_type - -type:o2e - ! Ether oxygen - template: [>O(-C)(-C)] - atom_test: 1 - aromaticity:NON_AROMATIC - end_test -end_type - -type:o2h - ! Hydroxyl oxygen - template: (>O[-H](~*)) -end_type - -type:o2n - ! Oxygen in nitrates - template: (>O[~N[~O][~O]](~C)) -end_type - -type:o2s - ! Ester oxygen - template: (>O[~C[~O](~*)](~C)) -end_type - -type: o2z - ! Oxygen in siloxanes and zeolites - template: (>O(-Si)(-*) ) - atom_test: 3 - allowed_elements: Si, H - end_test -end_type - -type: p4= - ! Phosphorous [in phosphazenes] - template: (>P(~*)(~*)(~*)(~*)) -end_type - -type:s1= - ! Sulfur in CS2 - template: [>S[~C[~S]]] -end_type - -type:s2= - ! Sulfur in SO2 - template: [>S[~O][~O]] -end_type - -type: si4 - ! Generic silicon with four bonds attached - template: (>Si(-*)(-*)(-*)(-*)) -end_type - -type: si4c - ! A subset of si4, non-hydrogen atom attached [siloxanes??] - template: (>Si(-O)(-*)(-*)(-*)) - atom_test: 3 - allowed_elements: O, C - end_test - atom_test: 4 - allowed_elements: O, C - end_test - atom_test: 5 - allowed_elements: O, C - end_test -end_type - -type: xe - ! Xenon atom - template: (>Xe) -end_type - -precedence: -(? - (ar) - (c1o) - (c2=) - (c3a) (c3') - (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) - (h1) (h1h) (h1o) - (he) - (kr) - (n1n) (n1o) (n1z) - (n2= (n2o) (n2t) (n2z) ) - (n3m) (n3o) - (ne) - (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) - (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) - (p4=) - (s1=) - (s2=) - (si4 (si4c) ) - (xe) -) -end_precedence - - - -#reference 1 -@Author tester -@Date 01-Jun-09 -Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) - -This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that -we neither support this version, nor make any warranty as to the correctness of the parameters. -We have checked the numbers against the literature, but of course there may still be errors, -including errors of interpretation. Also, the current version of COMPASS may well be different -that that originally published. - -If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com - -#reference 2 -@Author tester -@Date 27-Jun-09 -Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) - -#reference 3 -@Author tester -@Date 27-Jun-09 -Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) - -#reference 4 -@Author tester -@Date 30-Jun-09 -Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) - -#reference 5 -@Author tester -@Date 28-Jun-09 -Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) - -#reference 6 -@Author tester -@Date 29-Jun-09 -Parameters for nitrate esters from JPC B104, 2477-89 (2000) - -#reference 7 -@Author tester -@Date 30-Jun-09 -Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) - -#reference 8 -@Author tester -@Date 30-Jun-09 -Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) - -#reference 9 -@Author tester -@Date 30-Jun-09 -Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) - -#reference 10 -@Author tester -@Date 02-Jul-09 -Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff) diff --git a/tools/moltemplate/moltemplate/force_fields/compass_published.lt b/tools/moltemplate/moltemplate/force_fields/compass_published.lt deleted file mode 100644 index 3ec7595f28..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/compass_published.lt +++ /dev/null @@ -1,4148 +0,0 @@ -# This file was generated automatically using: -# msifrc2lt.py -name COMPASS < compass_published.frc > compass_published.lt - -# This is an incomplete version of the COMPASS force field based on available -# public sources. Parameters for common atoms and many groups are missing -# (for example, sp2 carbons and the NH2 amine group). The commercial version -# of COMPASS is much larger and presumably includes more up to date -# parameters and parameters for a wider range of atom types and molecule types. -# (However files containing those force field parameters have not been publicly -# disclosed.) We would like to thank Materials Design Inc. for collecting -# these force field parameters and making them publicly available. - -# USAGE: You can create molecules using this force-field this way: -# -# MyMolecule inherits COMPASS { -# # atom-id mol-id atom-type charge X Y Z -# write('Data Atoms') { -# $atom:C1 $mol @atom:c4 0.00 -0.6695 0.000000 0.000000 -# $atom:H11 $mol @atom:h1 0.00 -1.234217 -0.854458 0.000000 -# : : : : : : -# } -# } -# -# You can omit the atom charge in your molecule definition. -# (Partial charges will be assigned later according to the force field rules.) -# Responsibility for choosing the atom types (eg "@atom:c4", "@atom:h1") falls -# on the user. You must select the type of each atom in the molecule carefully -# by looking at the description in the "Data Masses" section of this file -# (see below), and looking for a reasonable match. If your simulation is -# non-neutral, or moltemplate complains that you have missing bond, angle, or -# dihedral types, this means at least one of your atom types is incorrect. - - - -COMPASS { - - - # AtomType Mass # "Description" (version, reference) - - write_once("Data Masses") { - @atom:ar 39.944 # Ar, "argon" (ver=1.0, ref=5) - @atom:c3a 12.01115 # C, "aromatic carbon" (ver=1.0, ref=1) - @atom:c1o 12.01115 # C, "carbon in CO" (ver=1.0, ref=5) - @atom:c2= 12.01115 # C, "carbon in CO2 and CS2" (ver=1.0, ref=5) - @atom:c3prime 12.01115 # C, "carbonyl carbon [one polar substituent]" (ver=1.0, ref=7) - @atom:c4 12.01115 # C, "generic sp3 carbon" (ver=1.0, ref=1) - @atom:c41o 12.01115 # C, "carbon, sp3, in methanol" (ver=1.0, ref=8) - @atom:c43o 12.01115 # C, "carbon, sp3 in secondary alcohols" (ver=1.0, ref=8) - @atom:c43 12.01115 # C, "sp3 carbon with three heavy atoms attached" (ver=1.0, ref=1) - @atom:c44 12.01115 # C, "sp3 carbon with four heavy atoms attached" (ver=1.0, ref=1) - @atom:c4o 12.01115 # C, "alpha carbon" (ver=1.0, ref=3) - @atom:c4z 12.01115 # C, "carbon, sp3, bonded to -N3" (ver=1.0, ref=9) - @atom:h1 1.00797 # H, "nonpolar hydrogen" (ver=1.0, ref=1) - @atom:h1h 1.00797 # H, "hydrogen in H2" (ver=1.0, ref=5) - @atom:h1o 1.00797 # H, "strongly polar hydrogen, bonded to O,F" (ver=1.0, ref=3) - @atom:he 4.003 # He, "helium" (ver=1.0, ref=5) - @atom:kr 83.8 # Kr, "krypton" (ver=1.0, ref=5) - @atom:n1n 14.0067 # N, "nitrogen in N2" (ver=1.0, ref=5) - @atom:n1o 14.0067 # N, "nitrogen in NO" (ver=1.0, ref=5) - @atom:n1z 14.0067 # N, "nitrogen, terminal atom in -N3" (ver=1.0, ref=5) - @atom:n2= 14.0067 # N, "nitrogen" (ver=1.0, ref=4) - @atom:n2o 14.0067 # N, "nitrogen in NO2" (ver=1.0, ref=5) - @atom:n2t 14.0067 # N, "nitrogen, central atom in -N3" (ver=1.0, ref=9) - @atom:n2z 14.0067 # N, "nitrogen, first atom in -N3" (ver=1.0, ref=9) - @atom:n3m 14.0067 # N, "sp3 nitrogen in amides without hydrogen" (ver=1.0, ref=7) - @atom:n3o 14.0067 # N, "nitrogen in nitro group" (ver=1.0, ref=6) - @atom:ne 20.183 # Ne, "neon" (ver=1.0, ref=5) - @atom:o1= 15.9994 # O, "oxygen in NO2 and SO2 [and carbonyl]" (ver=1.0, ref=5) - @atom:o1=star 15.9994 # O, "oxygen in CO2" (ver=1.0, ref=5) - @atom:o12 15.9994 # O, "oxygen in nitro group (-NO2)" (ver=1.0, ref=6) - @atom:o1c 15.9994 # O, "oxygen in CO" (ver=1.0, ref=5) - @atom:o1n 15.9994 # O, "oxygen in NO" (ver=1.0, ref=5) - @atom:o1o 15.9994 # O, "oxygen in O2" (ver=1.0, ref=5) - @atom:o2 15.9994 # O, "generic oxygen with two bonds attached" (ver=1.0, ref=2) - @atom:o2e 15.9994 # O, "ether oxygen" (ver=1.0, ref=3) - @atom:o2h 15.9994 # O, "hydroxyl oxygen" (ver=1.0, ref=3) - @atom:o2n 15.9994 # O, "oxygen in nitrates" (ver=1.0, ref=6) - @atom:o2s 15.9994 # O, "ester oxygen" (ver=1.0, ref=7) - @atom:o2z 15.9994 # O, "oxygen, in siloxanes and zeolites" (ver=1.0, ref=2) - @atom:p4= 30.9738 # P, "phosphorous" (ver=1.0, ref=4) - @atom:s1= 32.064 # S, "sulfur in CS2" (ver=1.0, ref=5) - @atom:s2= 32.064 # S, "sulfur in SO2" (ver=1.0, ref=5) - @atom:si4 28.086 # Si, "generic silicon with four bonds attached" (ver=1.0, ref=2) - @atom:si4c 28.086 # Si, "a subset of si4, non-hydrogen atom attached [siloxanes]" (ver=1.0, ref=2) - @atom:xe 131.3 # Xe, "xenon" (ver=1.0, ref=5) - } #(end of atom masses) - - - # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- - # Each type of atom has a separate ID used for looking up bond parameters - # and a separate ID for looking up 3-body angle interaction parameters - # and a separate ID for looking up 4-body dihedral interaction parameters - # and a separate ID for looking up 4-body improper interaction parameters - # The complete @atom type name includes ALL of these ID numbers. There's - # no need to force the end-user to type the complete name of each atom. - # The "replace" command used below informs moltemplate that the short - # @atom names we have been using abovee are equivalent to the complete - # @atom names used below: - - replace{ @atom:ar @atom:ar,par,bar,aar,dar,iar } - replace{ @atom:c3a @atom:c3a,pc3a,bc3a,ac3a,dc3a,ic3a } - replace{ @atom:c1o @atom:c1o,pc1o,bc1o,ac1o,dc1o,ic1o } - replace{ @atom:c2= @atom:c2=,pc2=,bc2=,ac2=,dc2=,ic2= } - replace{ @atom:c3prime @atom:c3prime,pc3prime,bc3prime,ac3prime,dc3prime,ic3prime } - replace{ @atom:c4 @atom:c4,pc4,bc4,ac4,dc4,ic4 } - replace{ @atom:c41o @atom:c41o,pc41o,bc4,ac4,dc4,ic4 } - replace{ @atom:c43o @atom:c43o,pc43o,bc4,ac4,dc4,ic4 } - replace{ @atom:c43 @atom:c43,pc43,bc4,ac4,dc4,ic4 } - replace{ @atom:c44 @atom:c44,pc44,bc4,ac4,dc4,ic4 } - replace{ @atom:c4o @atom:c4o,pc4o,bc4,ac4,dc4,ic4 } - replace{ @atom:c4z @atom:c4z,pc4z,bc4,ac4,dc4,ic4 } - replace{ @atom:h1 @atom:h1,ph1,bh1,ah1,dh1,ih1 } - replace{ @atom:h1h @atom:h1h,ph1h,bh1h,ah1,dh1,ih1 } - replace{ @atom:h1o @atom:h1o,ph1o,bh1,ah1,dh1,ih1 } - replace{ @atom:he @atom:he,phe,bhe,ahe,dhe,ihe } - replace{ @atom:kr @atom:kr,pkr,bkr,akr,dkr,ikr } - replace{ @atom:n1n @atom:n1n,pn1n,bn1n,an1n,dn1n,in1n } - replace{ @atom:n1o @atom:n1o,pn1o,bn1o,an1o,dn1o,in1o } - replace{ @atom:n1z @atom:n1z,pn1z,bn1t,an1t,dn1t,in1t } - replace{ @atom:n2= @atom:n2=,pn2=,bn2=,an2=,dn2=,in2= } - replace{ @atom:n2o @atom:n2o,pn2o,bn2o,an2o,dn2o,in2o } - replace{ @atom:n2t @atom:n2t,pn2t,bn2t,an2t,dn2t,in2t } - replace{ @atom:n2z @atom:n2z,pn2z,bn2z,an2z,dn2z,in2z } - replace{ @atom:n3m @atom:n3m,pn3m,bn3m,an3m,dn3m,in3m } - replace{ @atom:n3o @atom:n3o,pn3o,bn3o,an3o,dn3o,in3o } - replace{ @atom:ne @atom:ne,pne,bne,ane,dne,ine } - replace{ @atom:o1= @atom:o1=,po1=,bo1=,ao1=,do1=,io1= } - replace{ @atom:o1=star @atom:o1=star,po1=star,bo1=,ao1=,do1=,io1= } - replace{ @atom:o12 @atom:o12,po12,bo1=,ao1=,do1=,io1= } - replace{ @atom:o1c @atom:o1c,po1c,bo1c,ao1c,do1c,io1c } - replace{ @atom:o1n @atom:o1n,po1n,bo1n,ao1n,do1n,io1n } - replace{ @atom:o1o @atom:o1o,po1o,bo1o,ao1o,do1o,io1o } - replace{ @atom:o2 @atom:o2,po2,bo2,ao2,do2,io2 } - replace{ @atom:o2e @atom:o2e,po2e,bo2e,ao2,do2,io2 } - replace{ @atom:o2h @atom:o2h,po2h,bo2h,ao2,do2,io2 } - replace{ @atom:o2n @atom:o2n,po2n,bo2n,ao2n,do2,io2 } - replace{ @atom:o2s @atom:o2s,po2s,bo2e,ao2,do2,io2 } - replace{ @atom:o2z @atom:o2z,po2z,bo2z,ao2z,do2z,io2z } - replace{ @atom:p4= @atom:p4=,pp4=,bp4=,ap4=,dp4=,ip4= } - replace{ @atom:s1= @atom:s1=,ps1=,bs1=,as1=,ds1=,is1= } - replace{ @atom:s2= @atom:s2=,ps2=,bs2=,as2=,ds2=,is2= } - replace{ @atom:si4 @atom:si4,psi4,bsi4,asi4,dsi4,isi4 } - replace{ @atom:si4c @atom:si4c,psi4c,bsi4,asi4,dsi4,isi4 } - replace{ @atom:xe @atom:xe,pxe,bxe,axe,dxe,ixe } - - - - - # --------------- Non-Bonded Interactions: --------------------- - # Syntax: - # pair_coeff AtomType1 AtomType2 pair_style_name parameters... - - write_once("In Settings") { - pair_coeff @atom:*,pc3a,b*,a*,d*,i* @atom:*,pc3a,b*,a*,d*,i* lj/class2/coul/long 0.0680 3.9150 # (ver=1.0, ref=1) - pair_coeff @atom:*,pc4,b*,a*,d*,i* @atom:*,pc4,b*,a*,d*,i* lj/class2/coul/long 0.0620 3.8540 # (ver=1.0, ref=1) - pair_coeff @atom:*,pc43,b*,a*,d*,i* @atom:*,pc43,b*,a*,d*,i* lj/class2/coul/long 0.0400 3.8540 # (ver=1.0, ref=1) - pair_coeff @atom:*,pc44,b*,a*,d*,i* @atom:*,pc44,b*,a*,d*,i* lj/class2/coul/long 0.0200 3.8540 # (ver=1.0, ref=1) - pair_coeff @atom:*,ph1,b*,a*,d*,i* @atom:*,ph1,b*,a*,d*,i* lj/class2/coul/long 0.0230 2.8780 # (ver=1.0, ref=1) - pair_coeff @atom:*,po2z,b*,a*,d*,i* @atom:*,po2z,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.3000 # (ver=1.0, ref=2) - pair_coeff @atom:*,psi4,b*,a*,d*,i* @atom:*,psi4,b*,a*,d*,i* lj/class2/coul/long 0.1980 4.4050 # (ver=1.0, ref=2) - pair_coeff @atom:*,psi4c,b*,a*,d*,i* @atom:*,psi4c,b*,a*,d*,i* lj/class2/coul/long 0.1310 4.2900 # (ver=1.0, ref=2) - pair_coeff @atom:*,pc4o,b*,a*,d*,i* @atom:*,pc4o,b*,a*,d*,i* lj/class2/coul/long 0.0748 3.8700 # (ver=1.1, ref=8) - pair_coeff @atom:*,ph1o,b*,a*,d*,i* @atom:*,ph1o,b*,a*,d*,i* lj/class2/coul/long 0.0080 1.0870 # (ver=1.0, ref=3) - pair_coeff @atom:*,po2,b*,a*,d*,i* @atom:*,po2,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.3000 # (ver=1.0, ref=3) - pair_coeff @atom:*,po2e,b*,a*,d*,i* @atom:*,po2e,b*,a*,d*,i* lj/class2/coul/long 0.1200 3.3000 # (ver=1.0, ref=3) - pair_coeff @atom:*,po2h,b*,a*,d*,i* @atom:*,po2h,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.5800 # (ver=1.0, ref=3) - pair_coeff @atom:*,pn2=,b*,a*,d*,i* @atom:*,pn2=,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.8300 # (ver=1.0, ref=4) - pair_coeff @atom:*,pp4=,b*,a*,d*,i* @atom:*,pp4=,b*,a*,d*,i* lj/class2/coul/long 0.0650 4.2950 # (ver=1.0, ref=4) - pair_coeff @atom:*,phe,b*,a*,d*,i* @atom:*,phe,b*,a*,d*,i* lj/class2/coul/long 0.0050 2.9000 # (ver=1.0, ref=5) - pair_coeff @atom:*,pne,b*,a*,d*,i* @atom:*,pne,b*,a*,d*,i* lj/class2/coul/long 0.0550 3.2000 # (ver=1.0, ref=5) - pair_coeff @atom:*,par,b*,a*,d*,i* @atom:*,par,b*,a*,d*,i* lj/class2/coul/long 0.2000 3.8800 # (ver=1.0, ref=5) - pair_coeff @atom:*,pkr,b*,a*,d*,i* @atom:*,pkr,b*,a*,d*,i* lj/class2/coul/long 0.2800 4.3000 # (ver=1.0, ref=5) - pair_coeff @atom:*,pxe,b*,a*,d*,i* @atom:*,pxe,b*,a*,d*,i* lj/class2/coul/long 0.3900 4.2600 # (ver=1.0, ref=5) - pair_coeff @atom:*,ph1h,b*,a*,d*,i* @atom:*,ph1h,b*,a*,d*,i* lj/class2/coul/long 0.0216 1.4210 # (ver=1.0, ref=5) - pair_coeff @atom:*,pn1n,b*,a*,d*,i* @atom:*,pn1n,b*,a*,d*,i* lj/class2/coul/long 0.0598 3.8008 # (ver=1.0, ref=5) - pair_coeff @atom:*,pc1o,b*,a*,d*,i* @atom:*,pc1o,b*,a*,d*,i* lj/class2/coul/long 0.0530 4.0120 # (ver=1.0, ref=5) - pair_coeff @atom:*,po1o,b*,a*,d*,i* @atom:*,po1o,b*,a*,d*,i* lj/class2/coul/long 0.0780 3.4758 # (ver=1.0, ref=5) - pair_coeff @atom:*,po1c,b*,a*,d*,i* @atom:*,po1c,b*,a*,d*,i* lj/class2/coul/long 0.0850 3.6020 # (ver=1.0, ref=5) - pair_coeff @atom:*,pn1o,b*,a*,d*,i* @atom:*,pn1o,b*,a*,d*,i* lj/class2/coul/long 0.1280 3.4600 # (ver=1.0, ref=5) - pair_coeff @atom:*,po1n,b*,a*,d*,i* @atom:*,po1n,b*,a*,d*,i* lj/class2/coul/long 0.1560 3.3000 # (ver=1.0, ref=5) - pair_coeff @atom:*,pc2=,b*,a*,d*,i* @atom:*,pc2=,b*,a*,d*,i* lj/class2/coul/long 0.0680 3.9150 # (ver=1.0, ref=5) - pair_coeff @atom:*,ps2=,b*,a*,d*,i* @atom:*,ps2=,b*,a*,d*,i* lj/class2/coul/long 0.1250 4.0470 # (ver=1.0, ref=5) - pair_coeff @atom:*,pn2o,b*,a*,d*,i* @atom:*,pn2o,b*,a*,d*,i* lj/class2/coul/long 0.3330 3.5290 # (ver=1.0, ref=5) - pair_coeff @atom:*,po1=,b*,a*,d*,i* @atom:*,po1=,b*,a*,d*,i* lj/class2/coul/long 0.1920 3.4300 # (ver=1.0, ref=5) - pair_coeff @atom:*,po1=star,b*,a*,d*,i* @atom:*,po1=star,b*,a*,d*,i* lj/class2/coul/long 0.0670 3.3600 # (ver=1.0, ref=5) - pair_coeff @atom:*,ps1=,b*,a*,d*,i* @atom:*,ps1=,b*,a*,d*,i* lj/class2/coul/long 0.3130 4.0070 # (ver=1.0, ref=5) - pair_coeff @atom:*,pn3o,b*,a*,d*,i* @atom:*,pn3o,b*,a*,d*,i* lj/class2/coul/long 0.0480 3.7600 # (ver=1.0, ref=6) - pair_coeff @atom:*,po12,b*,a*,d*,i* @atom:*,po12,b*,a*,d*,i* lj/class2/coul/long 0.0480 3.4000 # (ver=1.0, ref=6) - pair_coeff @atom:*,po2n,b*,a*,d*,i* @atom:*,po2n,b*,a*,d*,i* lj/class2/coul/long 0.2000 3.6500 # (ver=1.0, ref=6) - pair_coeff @atom:*,pc3prime,b*,a*,d*,i* @atom:*,pc3prime,b*,a*,d*,i* lj/class2/coul/long 0.0640 3.9000 # (ver=1.0, ref=7) - pair_coeff @atom:*,pn3m,b*,a*,d*,i* @atom:*,pn3m,b*,a*,d*,i* lj/class2/coul/long 0.1500 3.7200 # (ver=1.0, ref=7) - pair_coeff @atom:*,po2s,b*,a*,d*,i* @atom:*,po2s,b*,a*,d*,i* lj/class2/coul/long 0.0960 3.3000 # (ver=1.0, ref=7) - pair_coeff @atom:*,pc41o,b*,a*,d*,i* @atom:*,pc41o,b*,a*,d*,i* lj/class2/coul/long 0.1080 3.8700 # (ver=1.1, ref=8) - pair_coeff @atom:*,pc43o,b*,a*,d*,i* @atom:*,pc43o,b*,a*,d*,i* lj/class2/coul/long 0.0498 3.6700 # (ver=1.1, ref=8) - pair_coeff @atom:*,pc4z,b*,a*,d*,i* @atom:*,pc4z,b*,a*,d*,i* lj/class2/coul/long 0.0800 3.6500 # (ver=1.0, ref=9) - pair_coeff @atom:*,pn1z,b*,a*,d*,i* @atom:*,pn1z,b*,a*,d*,i* lj/class2/coul/long 0.0850 3.5200 # (ver=1.0, ref=9) - pair_coeff @atom:*,pn2t,b*,a*,d*,i* @atom:*,pn2t,b*,a*,d*,i* lj/class2/coul/long 0.0500 3.3000 # (ver=1.0, ref=9) - pair_coeff @atom:*,pn2z,b*,a*,d*,i* @atom:*,pn2z,b*,a*,d*,i* lj/class2/coul/long 0.1200 3.4000 # (ver=1.0, ref=9) - } #(end of pair_coeffs) - - - - # ---------- Charge By Bond (a.k.a. "bond equivalences") ---------- - - - - write_once("Data Charge By Bond") { - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1260 0.1260 # (ver=1.0, ref=10) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1350 0.1350 # (ver=1.0, ref=10) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.1170 0.1170 # (ver=1.0, ref=10) - @atom:*,p*,bn2t,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.2470 -0.2470 # (ver=1.0, ref=9) - @atom:*,p*,bn1t,a*,d*,i* @atom:*,p*,bn2t,a*,d*,i* -0.3860 0.3860 # (ver=1.0, ref=9) - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.3350 -0.3350 # (ver=1.0, ref=9) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn2z,a*,d*,i* 0.3110 -0.3110 # (ver=1.0, ref=9) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn3m,a*,d*,i* 0.0950 -0.0950 # (ver=1.0, ref=7) - @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bn3m,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=7) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc3prime,a*,d*,i* -0.0350 0.0350 # (ver=1.0, ref=7) - @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4500 -0.4500 # (ver=1.0, ref=7) - @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=7) - @atom:*,p*,bc3prime,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.1120 -0.1120 # (ver=1.0, ref=7) - @atom:*,p*,bn3o,a*,d*,i* @atom:*,p*,bo2n,a*,d*,i* 0.0010 -0.0010 # (ver=1.0, ref=6) - @atom:*,p*,bn3o,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4280 -0.4280 # (ver=1.0, ref=6) - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.1880 -0.1880 # (ver=1.0, ref=6) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2n,a*,d*,i* 0.3170 -0.3170 # (ver=1.0, ref=6) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.2100 -0.2100 # (ver=1.0, ref=6) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn3o,a*,d*,i* 0.2390 -0.2390 # (ver=1.0, ref=6) - @atom:*,p*,bo1o,a*,d*,i* @atom:*,p*,bo1o,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) - @atom:*,p*,bo1=,a*,d*,i* @atom:*,p*,bs2=,a*,d*,i* -0.2351 0.2351 # (ver=1.0, ref=5) - @atom:*,p*,bn1o,a*,d*,i* @atom:*,p*,bo1n,a*,d*,i* 0.0288 -0.0288 # (ver=1.0, ref=5) - @atom:*,p*,bn1n,a*,d*,i* @atom:*,p*,bn1n,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) - @atom:*,p*,bh1h,a*,d*,i* @atom:*,p*,bh1h,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=5) - @atom:*,p*,bn2o,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.0730 -0.0730 # (ver=1.0, ref=5) - @atom:*,p*,bc2=,a*,d*,i* @atom:*,p*,bs1=,a*,d*,i* 0.0258 -0.0258 # (ver=1.0, ref=5) - @atom:*,p*,bc2=,a*,d*,i* @atom:*,p*,bo1=,a*,d*,i* 0.4000 -0.4000 # (ver=1.0, ref=5) - @atom:*,p*,bc1o,a*,d*,i* @atom:*,p*,bo1c,a*,d*,i* -0.0203 0.0203 # (ver=1.0, ref=5) - @atom:*,p*,bo2,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1400 0.1400 # (ver=1.0, ref=4) - @atom:*,p*,bn3,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1200 0.1200 # (ver=1.0, ref=4) - @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.3500 0.3500 # (ver=1.0, ref=4) - @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bo2,a*,d*,i* -0.0430 0.0430 # (ver=1.0, ref=4) - @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bn3,a*,d*,i* 0.0250 -0.0250 # (ver=1.0, ref=4) - @atom:*,p*,bn2=,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=4) - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0500 0.0500 # (ver=1.0, ref=4) - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.3280 -0.3280 # (ver=1.0, ref=4) - @atom:*,p*,bf1p,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1800 0.1800 # (ver=1.0, ref=4) - @atom:*,p*,bcl1p,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.1200 0.1200 # (ver=1.0, ref=4) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0500 0.0500 # (ver=1.0, ref=4) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.3450 -0.3450 # (ver=1.0, ref=4) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bp4=,a*,d*,i* -0.0600 0.0600 # (ver=1.0, ref=4) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bn2=,a*,d*,i* 0.1990 -0.1990 # (ver=1.0, ref=4) - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bo2,a*,d*,i* 0.4200 -0.4200 # (ver=1.0, ref=3) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.1600 -0.1600 # (ver=1.0, ref=3) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.1600 -0.1600 # (ver=1.0, ref=3) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.0420 -0.0420 # (ver=1.0, ref=3) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bo2e,a*,d*,i* 0.0420 -0.0420 # (ver=1.0, ref=3) - @atom:*,p*,bo2z,a*,d*,i* @atom:*,p*,bsi4,a*,d*,i* -0.2225 0.2225 # (ver=1.0, ref=2) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bh1,a*,d*,i* -0.0530 0.0530 # (ver=1.0, ref=1) - @atom:*,p*,bc4,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bh1,a*,d*,i* -0.1268 0.1268 # (ver=1.0, ref=1) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc4,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) - @atom:*,p*,bc3a,a*,d*,i* @atom:*,p*,bc3a,a*,d*,i* 0.0000 0.0000 # (ver=1.0, ref=1) - @atom:*,p*,bh1,a*,d*,i* @atom:*,p*,bo2h,a*,d*,i* 0.4100 -0.4100 # (ver=1.1, ref=8) - } #(end of Charge by Bond (bond equivalences)) - - - - - - # --------------- Bond Interactions: --------------------- - - - # -- Rules for generating (2-body) "bond" interactions: -- - # BondType AtomType1 AtomType2 - - write_once("Data Bonds By Type") { - @bond:c4,n3m @atom:*,bc4,a*,d*,i* @atom:*,bn3m,a*,d*,i* - @bond:si4,si4 @atom:*,bsi4,a*,d*,i* @atom:*,bsi4,a*,d*,i* - @bond:h1,si4 @atom:*,bh1,a*,d*,i* @atom:*,bsi4,a*,d*,i* - @bond:c4,si4 @atom:*,bc4,a*,d*,i* @atom:*,bsi4,a*,d*,i* - @bond:c3a,si4 @atom:*,bc3a,a*,d*,i* @atom:*,bsi4,a*,d*,i* - @bond:h1,n2z @atom:*,bh1,a*,d*,i* @atom:*,bn2z,a*,d*,i* - @bond:c4,n2z @atom:*,bc4,a*,d*,i* @atom:*,bn2z,a*,d*,i* - @bond:n1t,n2t @atom:*,bn1t,a*,d*,i* @atom:*,bn2t,a*,d*,i* - @bond:n2t,n2z @atom:*,bn2t,a*,d*,i* @atom:*,bn2z,a*,d*,i* - @bond:n1t,n1t @atom:*,bn1t,a*,d*,i* @atom:*,bn1t,a*,d*,i* - @bond:c3a,n3m @atom:*,bc3a,a*,d*,i* @atom:*,bn3m,a*,d*,i* - @bond:c3prime,n3m @atom:*,bc3prime,a*,d*,i* @atom:*,bn3m,a*,d*,i* - @bond:c3a,c3prime @atom:*,bc3a,a*,d*,i* @atom:*,bc3prime,a*,d*,i* - @bond:c3prime,o1= @atom:*,bc3prime,a*,d*,i* @atom:*,bo1=,a*,d*,i* - @bond:c3prime,c4 @atom:*,bc3prime,a*,d*,i* @atom:*,bc4,a*,d*,i* - @bond:c3prime,o2e @atom:*,bc3prime,a*,d*,i* @atom:*,bo2e,a*,d*,i* - @bond:n3o,o2n @atom:*,bn3o,a*,d*,i* @atom:*,bo2n,a*,d*,i* - @bond:n3o,o1= @atom:*,bn3o,a*,d*,i* @atom:*,bo1=,a*,d*,i* - @bond:h1,n3o @atom:*,bh1,a*,d*,i* @atom:*,bn3o,a*,d*,i* - @bond:c4,o2n @atom:*,bc4,a*,d*,i* @atom:*,bo2n,a*,d*,i* - @bond:c4,n3o @atom:*,bc4,a*,d*,i* @atom:*,bn3o,a*,d*,i* - @bond:c3a,n3o @atom:*,bc3a,a*,d*,i* @atom:*,bn3o,a*,d*,i* - @bond:c2=,s1= @atom:*,bc2=,a*,d*,i* @atom:*,bs1=,a*,d*,i* - @bond:n2o,o1= @atom:*,bn2o,a*,d*,i* @atom:*,bo1=,a*,d*,i* - @bond:c2=,o1= @atom:*,bc2=,a*,d*,i* @atom:*,bo1=,a*,d*,i* - @bond:o1=,s2= @atom:*,bo1=,a*,d*,i* @atom:*,bs2=,a*,d*,i* - @bond:n1o,o1n @atom:*,bn1o,a*,d*,i* @atom:*,bo1n,a*,d*,i* - @bond:c1o,o1c @atom:*,bc1o,a*,d*,i* @atom:*,bo1c,a*,d*,i* - @bond:o1o,o1o @atom:*,bo1o,a*,d*,i* @atom:*,bo1o,a*,d*,i* - @bond:n1n,n1n @atom:*,bn1n,a*,d*,i* @atom:*,bn1n,a*,d*,i* - @bond:h1h,h1h @atom:*,bh1h,a*,d*,i* @atom:*,bh1h,a*,d*,i* - @bond:o2,p4= @atom:*,bo2,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:n3,p4= @atom:*,bn3,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:n2=,p4= @atom:*,bn2=,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:h1,p4= @atom:*,bh1,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:h1,n2= @atom:*,bh1,a*,d*,i* @atom:*,bn2=,a*,d*,i* - @bond:f1p,p4= @atom:*,bf1p,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:cl1p,p4= @atom:*,bcl1p,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:c4,p4= @atom:*,bc4,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:c4,n2= @atom:*,bc4,a*,d*,i* @atom:*,bn2=,a*,d*,i* - @bond:c3a,p4= @atom:*,bc3a,a*,d*,i* @atom:*,bp4=,a*,d*,i* - @bond:c3a,n2= @atom:*,bc3a,a*,d*,i* @atom:*,bn2=,a*,d*,i* - @bond:h1,o2h @atom:*,bh1,a*,d*,i* @atom:*,bo2h,a*,d*,i* - @bond:c4,o2h @atom:*,bc4,a*,d*,i* @atom:*,bo2h,a*,d*,i* - @bond:c4,o2e @atom:*,bc4,a*,d*,i* @atom:*,bo2e,a*,d*,i* - @bond:c3a,o2h @atom:*,bc3a,a*,d*,i* @atom:*,bo2h,a*,d*,i* - @bond:c3a,o2e @atom:*,bc3a,a*,d*,i* @atom:*,bo2e,a*,d*,i* - @bond:c3a,o2 @atom:*,bc3a,a*,d*,i* @atom:*,bo2,a*,d*,i* - @bond:o2z,si4 @atom:*,bo2z,a*,d*,i* @atom:*,bsi4,a*,d*,i* - @bond:c4,h1 @atom:*,bc4,a*,d*,i* @atom:*,bh1,a*,d*,i* - @bond:c4,c4 @atom:*,bc4,a*,d*,i* @atom:*,bc4,a*,d*,i* - @bond:c3a,h1 @atom:*,bc3a,a*,d*,i* @atom:*,bh1,a*,d*,i* - @bond:c3a,c4 @atom:*,bc3a,a*,d*,i* @atom:*,bc4,a*,d*,i* - @bond:c3a,c3a @atom:*,bc3a,a*,d*,i* @atom:*,bc3a,a*,d*,i* - } # end of "Data Bonds By Type" section - - - - # ------------ Bond Parameters: ---------- - # For an explanation of these parameters, visit: - # http://lammps.sandia.gov/doc/bond_class2.html - - # Syntax: - # bond_coeff BondTypeName BondStyle parameters... - - - write_once("In Settings") { - bond_coeff @bond:c4,n3m class2 1.4000 350.0000 0.0000 0.0000 # (ver=1.0, ref=10) - bond_coeff @bond:si4,si4 class2 2.3384 114.2164 -140.4212 80.7084 # (ver=1.0, ref=10) - bond_coeff @bond:h1,si4 class2 1.4783 202.7798 -305.3603 280.2685 # (ver=1.0, ref=10) - bond_coeff @bond:c4,si4 class2 1.8995 189.6536 -279.4210 307.5135 # (ver=1.0, ref=10) - bond_coeff @bond:c3a,si4 class2 1.8634 233.2433 -276.8692 161.6659 # (ver=1.0, ref=10) - bond_coeff @bond:h1,n2z class2 1.0221 440.1623 -960.3246 1120.3787 # (ver=1.0, ref=9) - bond_coeff @bond:c4,n2z class2 1.4814 324.4578 -648.9156 757.0681 # (ver=1.0, ref=9) - bond_coeff @bond:n1t,n2t class2 1.1354 1198.7450 -2675.4900 3121.4049 # (ver=1.0, ref=9) - bond_coeff @bond:n2t,n2z class2 1.2343 720.3345 -1542.6689 1799.7804 # (ver=1.0, ref=9) - bond_coeff @bond:n1t,n1t class2 1.1354 1337.7450 -2675.4900 3121.4049 # (ver=1.0, ref=9) - bond_coeff @bond:c3a,n3m class2 1.3950 344.0452 -652.1208 1022.2242 # (ver=1.0, ref=7) - bond_coeff @bond:c3prime,n3m class2 1.3850 359.1591 -558.4730 1146.3810 # (ver=1.0, ref=7) - bond_coeff @bond:c3a,c3prime class2 1.4890 339.3574 -655.7236 670.2362 # (ver=1.0, ref=7) - bond_coeff @bond:c3prime,o1= class2 1.2160 823.7948 -1878.7939 2303.5310 # (ver=1.0, ref=7) - bond_coeff @bond:c3prime,c4 class2 1.5140 312.3719 -465.8290 473.8300 # (ver=1.0, ref=7) - bond_coeff @bond:c3prime,o2e class2 1.3750 368.7309 -832.4784 1274.0231 # (ver=1.0, ref=7) - bond_coeff @bond:n3o,o2n class2 1.4020 300.0000 -1000.0000 2000.0000 # (ver=1.0, ref=6) - bond_coeff @bond:n3o,o1= class2 1.2100 765.0664 -2070.2830 2793.3218 # (ver=1.0, ref=6) - bond_coeff @bond:h1,n3o class2 1.0400 439.9346 -943.7307 1180.9318 # (ver=1.0, ref=6) - bond_coeff @bond:c4,o2n class2 1.4350 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=6) - bond_coeff @bond:c4,n3o class2 1.4740 301.6051 -535.7028 555.0420 # (ver=1.0, ref=6) - bond_coeff @bond:c3a,n3o class2 1.4300 313.8329 -568.6087 600.9597 # (ver=1.0, ref=6) - bond_coeff @bond:c2=,s1= class2 1.5540 559.0065 -1348.6633 1248.8604 # (ver=1.0, ref=5) - bond_coeff @bond:n2o,o1= class2 1.1930 620.0000 -1808.6018 3077.5918 # (ver=1.0, ref=5) - bond_coeff @bond:c2=,o1= class2 1.1600 1161.3421 -2564.5706 3932.8735 # (ver=1.0, ref=5) - bond_coeff @bond:o1=,s2= class2 1.4308 730.8387 -1531.7910 1859.7753 # (ver=1.0, ref=5) - bond_coeff @bond:n1o,o1n class2 1.1506 1147.8362 -3167.7349 5099.5811 # (ver=1.0, ref=5) - bond_coeff @bond:c1o,o1c class2 1.1283 1368.7676 -3157.0007 4247.5298 # (ver=1.0, ref=5) - bond_coeff @bond:o1o,o1o class2 1.2074 846.7150 -2247.1760 3478.9900 # (ver=1.0, ref=5) - bond_coeff @bond:n1n,n1n class2 1.0977 1651.3730 -4069.3178 5984.9629 # (ver=1.0, ref=5) - bond_coeff @bond:h1h,h1h class2 0.7412 414.2185 -805.6549 914.1296 # (ver=1.0, ref=5) - bond_coeff @bond:o2,p4= class2 1.6000 333.0980 -726.6230 924.6200 # (ver=1.0, ref=4) - bond_coeff @bond:n3,p4= class2 1.6780 329.0000 -713.7950 902.9190 # (ver=1.0, ref=4) - bond_coeff @bond:n2=,p4= class2 1.5980 393.0060 -751.4050 767.4310 # (ver=1.0, ref=4) - bond_coeff @bond:h1,p4= class2 1.4300 285.2040 -575.6850 677.8460 # (ver=1.0, ref=4) - bond_coeff @bond:h1,n2= class2 1.0310 540.1120 -1500.2952 2431.0080 # (ver=1.0, ref=4) - bond_coeff @bond:f1p,p4= class2 1.5650 340.0000 -882.3840 1197.9190 # (ver=1.0, ref=4) - bond_coeff @bond:cl1p,p4= class2 2.0000 158.7770 -239.1290 210.0840 # (ver=1.0, ref=4) - bond_coeff @bond:c4,p4= class2 1.8000 218.1400 -329.5110 290.3490 # (ver=1.0, ref=4) - bond_coeff @bond:c4,n2= class2 1.4740 337.0600 -147.3700 213.6330 # (ver=1.0, ref=4) - bond_coeff @bond:c3a,p4= class2 1.7890 197.7020 -332.2510 325.7160 # (ver=1.0, ref=4) - bond_coeff @bond:c3a,n2= class2 1.4000 350.0000 0.0000 0.0000 # (ver=1.0, ref=4) - bond_coeff @bond:h1,o2h class2 0.9494 540.3633 -1311.8663 2132.4446 # (ver=1.0, ref=3) - bond_coeff @bond:c4,o2h class2 1.4200 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=3) - bond_coeff @bond:c4,o2e class2 1.4200 400.3954 -835.1951 1313.0142 # (ver=1.0, ref=3) - bond_coeff @bond:c3a,o2h class2 1.3768 428.8798 -738.2351 1114.9655 # (ver=1.0, ref=3) - bond_coeff @bond:c3a,o2e class2 1.3768 428.8798 -738.2351 1114.9655 # (ver=1.0, ref=3) - bond_coeff @bond:c3a,o2 class2 1.3768 428.8798 -738.2350 1114.9655 # (ver=1.0, ref=3) - bond_coeff @bond:o2z,si4 class2 1.6400 350.1232 -517.3424 673.7067 # (ver=1.0, ref=2) - bond_coeff @bond:c4,h1 class2 1.1010 345.0000 -691.8900 844.6000 # (ver=1.0, ref=1) - bond_coeff @bond:c4,c4 class2 1.5300 299.6700 -501.7700 679.8100 # (ver=1.0, ref=1) - bond_coeff @bond:c3a,h1 class2 1.0982 372.8251 -803.4526 894.3173 # (ver=1.0, ref=1) - bond_coeff @bond:c3a,c4 class2 1.5010 321.9021 -521.8208 572.1628 # (ver=1.0, ref=1) - bond_coeff @bond:c3a,c3a class2 1.4170 470.8361 -627.6179 1327.6345 # (ver=1.0, ref=1) - } # end of bond_coeff commands - - - # --------------- Angle Interactions: --------------------- - - - # -- Rules for generating (3-body) "angle" interactions: -- - # AngleType AtomType1 AtomType2 AtomType3 [BondType1 BondType2] - - write_once("Data Angles By Type") { - @angle:c3a,o2,c3a,c3a,o2h,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* - @angle:c3a,o2,c3a,c3a,o2e,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* - @angle:c3a,o2,c3a,c3a,o2,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* - @angle:c3a,c4,o2,c3a,c4,o2h @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:c3a,c4,o2,c3a,c4,o2e @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:c3a,o2,c3prime,c3a,o2e,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @angle:o2,c4,o2,o2h,c4,o2h @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:o2,c4,o2,o2h,c4,o2e @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:o2,c4,o2,o2e,c4,o2h @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:o2,c4,o2,o2e,c4,o2e @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:h1,c3a,o2,h1,c3a,o2h @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:h1,c3a,o2,h1,c3a,o2e @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:h1,c3a,o2,h1,c3a,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* - @angle:si4,si4,si4,si4,si4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:h1,si4,si4,h1,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:c4,si4,si4,c4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:h1,si4,h1,h1,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,si4,h1,c4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,si4,c4,c4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,si4,h1,c3a,si4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:h1,c4,si4,h1,c4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:c4,c4,si4,c4,c4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:c3a,c3a,si4,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:c4,c4,n2z,c4,c4,n2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* - @angle:h1,c4,n2z,h1,c4,n2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* - @angle:c4,n2z,n2t,c4,n2z,n2t @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bn2t,an2t,d*,i* - @angle:h1,n2z,n2t,h1,n2z,n2t @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bn2t,an2t,d*,i* - @angle:n1t,n2t,n2z,n1t,n2t,n2z @atom:*,p*,bn1t,an1t,d*,i* @atom:*,p*,bn2t,an2t,d*,i* @atom:*,p*,bn2z,an2z,d*,i* - @angle:n3m,c3prime,o1=,n3m,c3prime,o1= @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:c4,c3prime,o2,c4,c3prime,o2e @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:c4,c3prime,o1=,c4,c3prime,o1= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:o1=,c3prime,o2,o1=,c3prime,o2e @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:c3a,n3m,c3prime,c3a,n3m,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @angle:c3a,c3a,n3m,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3m,an3m,d*,i* - @angle:c3a,c3prime,o1=,c3a,c3prime,o1= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:c3a,c3prime,n3m,c3a,c3prime,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bn3m,an3m,d*,i* - @angle:c3a,c3a,c3prime,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @angle:c3prime,c4,h1,c3prime,c4,h1 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c3prime,o2,c4,c3prime,o2e,c4 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:o1=,n3o,o2n,o1=,n3o,o2n @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* - @angle:c4,c4,o2n,c4,c4,o2n @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* - @angle:c4,o2n,n3o,c4,o2n,n3o @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bn3o,an3o,d*,i* - @angle:o1=,n3o,o1=,o1=,n3o,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:h1,n3o,o1=,h1,n3o,o1= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:c4,n3o,o1=,c4,n3o,o1= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:c3a,n3o,o1=,c3a,n3o,o1= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:h1,c4,o2n,h1,c4,o2n @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2n,ao2n,d*,i* - @angle:h1,c4,n3o,h1,c4,n3o @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn3o,an3o,d*,i* - @angle:c3a,c3a,n3o,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn3o,an3o,d*,i* - @angle:o1=,s2=,o1=,o1=,s2=,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bs2=,as2=,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:o1=,n2o,o1=,o1=,n2o,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bn2o,an2o,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:s1=,c2=,s1=,s1=,c2=,s1= @atom:*,p*,bs1=,as1=,d*,i* @atom:*,p*,bc2=,ac2=,d*,i* @atom:*,p*,bs1=,as1=,d*,i* - @angle:o1=,c2=,o1=,o1=,c2=,o1= @atom:*,p*,bo1=,ao1=,d*,i* @atom:*,p*,bc2=,ac2=,d*,i* @atom:*,p*,bo1=,ao1=,d*,i* - @angle:o2,p4=,o2,o2,p4=,o2 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* - @angle:n2=,p4=,o2,n2=,p4=,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* - @angle:n2=,p4=,n2=,n2=,p4=,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:h1,p4=,o2,h1,p4=,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* - @angle:h1,p4=,n2=,h1,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:h1,p4=,h1,h1,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,p4=,n2=,c4,p4=,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:c4,p4=,h1,c4,p4=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,p4=,c4,c4,p4=,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,p4=,o2,c3a,p4=,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bo2,ao2,d*,i* - @angle:c3a,p4=,n2=,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:c3a,p4=,h1,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c3a,p4=,c3a,c3a,p4=,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* - @angle:p4=,n2=,p4=,p4=,n2=,p4= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* - @angle:h1,n2=,p4=,h1,n2=,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* - @angle:h1,n2=,h1,h1,n2=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,n2=,h1,c4,n2=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:h1,c4,p4=,h1,c4,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* - @angle:h1,c4,n2=,h1,c4,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:c4,c4,n2=,c4,c4,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:c3a,c3a,p4=,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bp4=,ap4=,d*,i* - @angle:c3a,c3a,n2=,c3a,c3a,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bn2=,an2=,d*,i* - @angle:c4,o2,h1,c4,o2h,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,o2,c4,c4,o2h,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c4,o2,c4,c4,o2e,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,o2,h1,c3a,o2h,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c3a,o2,c4,c3a,o2h,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,o2,c4,c3a,o2e,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:h1,c4,o2,h1,c4,o2h @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:h1,c4,o2,h1,c4,o2e @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:c4,c4,o2,c4,c4,o2h @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:c4,c4,o2,c4,c4,o2e @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:c3a,c3a,o2,c3a,c3a,o2h @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2h,ao2,d*,i* - @angle:c3a,c3a,o2,c3a,c3a,o2e @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2e,ao2,d*,i* - @angle:c3a,c3a,o2,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bo2,ao2,d*,i* - @angle:o2z,si4,o2z,o2z,si4,o2z @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* - @angle:h1,si4,o2z,h1,si4,o2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* - @angle:c4,si4,o2z,c4,si4,o2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* - @angle:c3a,si4,o2z,c3a,si4,o2z @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* - @angle:si4,o2z,si4,si4,o2z,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,d*,i* - @angle:h1,c4,h1,h1,c4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,c4,h1,c4,c4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,c4,h1,c3a,c4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c3a,c4,c4,c3a,c4,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,c4,c3a,c3a,c4,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* - @angle:c3a,c3a,h1,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bh1,ah1,d*,i* - @angle:c3a,c3a,c4,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,d*,i* - @angle:c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,d*,i* - @angle:n3,p4=,o2,X,X,X @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,ao2,d*,i* - @angle:n3,p4=,n3,X,X,X @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* - @angle:n2=,p4=,n3,X,X,X @atom:*,p*,b*,an2=,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* - @angle:h1,p4=,n3,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* - @angle:c3a,p4=,n3,X,X,X @atom:*,p*,b*,ac3a,d*,i* @atom:*,p*,b*,ap4=,d*,i* @atom:*,p*,b*,an3,d*,i* - @angle:h1,o2,p4=,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ao2,d*,i* @atom:*,p*,b*,ap4=,d*,i* - @angle:c4,o2,p4=,X,X,X @atom:*,p*,b*,ac4,d*,i* @atom:*,p*,b*,ao2,d*,i* @atom:*,p*,b*,ap4=,d*,i* - @angle:h1,n3,p4=,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* - @angle:c4,n3,p4=,X,X,X @atom:*,p*,b*,ac4,d*,i* @atom:*,p*,b*,an3,d*,i* @atom:*,p*,b*,ap4=,d*,i* - @angle:h1,o2z,si4,X,X,X @atom:*,p*,b*,ah1,d*,i* @atom:*,p*,b*,ao2z,d*,i* @atom:*,p*,b*,asi4,d*,i* - } # end of "Data Angles By Type" section - - - - # ------- Angle Force Field Parameters: ------- # For an explanation of these parameters, visit: - # http://lammps.sandia.gov/doc/angle_class2.html - - # Syntax: - # angle_coeff AngleTypeName AngleStyle parameters... - - - write_once("In Settings") { - angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2h,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2e,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 bb 0.0000 1.3768 1.3768 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3a,c3a,o2,c3a class2 ba 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 bb 0.0000 1.5010 1.4200 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c4,o2,c3a,c4,o2h class2 ba 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 bb 0.0000 1.5010 1.4200 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c4,o2,c3a,c4,o2e class2 ba 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 bb 69.5999 1.3768 1.3750 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,o2,c3prime,c3a,o2e,c3prime class2 ba 0.0 0.0 1.3768 1.3750 # (ver=1.0, ref=7) - angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2h,c4,o2h class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2h,c4,o2e class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2e,c4,o2h class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 bb 8.2983 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:o2,c4,o2,o2e,c4,o2e class2 ba 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2h class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2e class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 0.0 0.0 0.0 0.0 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 bb 4.5800 1.0982 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c3a,o2,h1,c3a,o2 class2 ba 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 114.2676 24.9501 -19.5949 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 bb 6.0704 2.3384 2.3384 # (ver=1.0, ref=10) - angle_coeff @angle:si4,si4,si4,si4,si4,si4 class2 ba 8.9899 8.9899 2.3384 2.3384 # (ver=1.0, ref=10) - angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 112.0893 22.5062 -11.5926 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 bb 3.5172 1.4783 2.3384 # (ver=1.0, ref=10) - angle_coeff @angle:h1,si4,si4,h1,si4,si4 class2 ba 5.6630 2.0706 1.4783 2.3384 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 113.0000 19.4692 -34.3471 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 bb 2.3030 1.8995 2.3384 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,si4,c4,si4,si4 class2 ba 16.9455 11.4377 1.8995 2.3384 # (ver=1.0, ref=10) - angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 108.6051 32.5415 -8.3164 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 bb 4.6408 1.4783 1.4783 # (ver=1.0, ref=10) - angle_coeff @angle:h1,si4,h1,h1,si4,h1 class2 ba 9.3467 9.3467 1.4783 1.4783 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 112.0977 36.4832 -12.8094 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 bb 3.9340 1.8995 1.4783 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,h1,c4,si4,h1 class2 ba 13.3961 7.4104 1.8995 1.4783 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 113.1855 36.2069 -20.3939 20.0172 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 bb 3.7419 1.8995 1.8995 # (ver=1.0, ref=10) - angle_coeff @angle:c4,si4,c4,c4,si4,c4 class2 ba 18.5805 18.5805 1.8995 1.8995 # (ver=1.0, ref=10) - angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 109.5932 41.9497 -42.3639 48.1442 # (ver=1.0, ref=10) - angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 bb 3.9264 1.8634 1.4783 # (ver=1.0, ref=10) - angle_coeff @angle:c3a,si4,h1,c3a,si4,h1 class2 ba 22.5947 8.7811 1.8634 1.4783 # (ver=1.0, ref=10) - angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 112.0355 28.7721 -13.9523 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 bb 1.6561 1.1010 1.8995 # (ver=1.0, ref=10) - angle_coeff @angle:h1,c4,si4,h1,c4,si4 class2 ba 16.6908 18.2764 1.1010 1.8995 # (ver=1.0, ref=10) - angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 112.6700 39.5160 -7.4430 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 bb 0.0 1.5300 1.8995 # (ver=1.0, ref=10) - angle_coeff @angle:c4,c4,si4,c4,c4,si4 class2 ba 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=10) - angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 120.0000 30.4689 -23.5439 0.0000 # (ver=1.0, ref=10) - angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 bb 21.3938 1.4170 1.8634 # (ver=1.0, ref=10) - angle_coeff @angle:c3a,c3a,si4,c3a,c3a,si4 class2 ba 14.5831 23.7679 1.4170 1.8634 # (ver=1.0, ref=10) - angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 110.9900 77.9387 0.9499 0.0033 # (ver=1.0, ref=9) - angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 bb 36.9309 1.5300 1.4814 # (ver=1.0, ref=9) - angle_coeff @angle:c4,c4,n2z,c4,c4,n2z class2 ba 34.8803 67.8888 1.5300 1.4814 # (ver=1.0, ref=9) - angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 107.9744 52.7803 0.6615 0.0023 # (ver=1.0, ref=9) - angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 bb 18.4621 1.1010 1.4814 # (ver=1.0, ref=9) - angle_coeff @angle:h1,c4,n2z,h1,c4,n2z class2 ba 3.3182 61.9652 1.1010 1.4814 # (ver=1.0, ref=9) - angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 113.5017 82.6294 0.9845 0.0033 # (ver=1.0, ref=9) - angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 bb 84.2075 1.4814 1.2343 # (ver=1.0, ref=9) - angle_coeff @angle:c4,n2z,n2t,c4,n2z,n2t class2 ba 88.2679 195.9722 1.4814 1.2343 # (ver=1.0, ref=9) - angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 110.0345 55.7635 0.6618 0.0022 # (ver=1.0, ref=9) - angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 bb 14.9026 1.0221 1.2343 # (ver=1.0, ref=9) - angle_coeff @angle:h1,n2z,n2t,h1,n2z,n2t class2 ba 37.4419 141.1218 1.0221 1.2343 # (ver=1.0, ref=9) - angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 171.6211 47.7899 0.0000 0.0000 # (ver=1.0, ref=9) - angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 bb 204.9909 1.1354 1.2343 # (ver=1.0, ref=9) - angle_coeff @angle:n1t,n2t,n2z,n1t,n2t,n2z class2 ba 1.2222 25.5611 1.1354 1.2343 # (ver=1.0, ref=9) - angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 121.5420 92.5720 -34.4800 -11.1871 # (ver=1.0, ref=7) - angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 bb 138.4954 1.3850 1.2160 # (ver=1.0, ref=7) - angle_coeff @angle:n3m,c3prime,o1=,n3m,c3prime,o1= class2 ba 62.7124 52.4045 1.3850 1.2160 # (ver=1.0, ref=7) - angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 100.3182 88.8631 -3.8323 -7.9802 # (ver=1.0, ref=7) - angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 bb 19.1069 1.5140 1.3750 # (ver=1.0, ref=7) - angle_coeff @angle:c4,c3prime,o2,c4,c3prime,o2e class2 ba 1.3435 4.6978 1.5140 1.3750 # (ver=1.0, ref=7) - angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 119.3000 65.1016 -17.9766 0.0000 # (ver=1.0, ref=7) - angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 bb 77.5201 1.5140 1.2160 # (ver=1.0, ref=7) - angle_coeff @angle:c4,c3prime,o1=,c4,c3prime,o1= class2 ba 31.8455 46.6613 1.5140 1.2160 # (ver=1.0, ref=7) - angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 118.9855 98.6813 -22.2485 10.3673 # (ver=1.0, ref=7) - angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 bb 210.1813 1.2160 1.3750 # (ver=1.0, ref=7) - angle_coeff @angle:o1=,c3prime,o2,o1=,c3prime,o2e class2 ba 79.4497 57.0987 1.2160 1.3750 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 120.0700 47.1131 -32.5592 13.1257 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 bb 0.0000 1.3950 1.3850 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,n3m,c3prime,c3a,n3m,c3prime class2 ba 0.0 0.0 1.3950 1.3850 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 120.7640 73.2738 -27.4033 13.3920 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 bb 37.8749 1.4170 1.3950 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3a,n3m,c3a,c3a,n3m class2 ba 35.8865 53.6977 1.4170 1.3950 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 125.5320 72.3167 -16.0650 2.0818 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 bb 116.9445 1.4890 1.2160 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3prime,o1=,c3a,c3prime,o1= class2 ba 72.8758 76.1093 1.4890 1.2160 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 108.4400 84.8377 -19.9640 2.7405 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 bb 0.0000 1.4890 1.3850 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3prime,n3m,c3a,c3prime,n3m class2 ba 0.0 0.0 1.4890 1.3850 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 116.0640 71.2598 -15.8273 2.0506 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 bb 37.8749 1.4170 1.4890 # (ver=1.0, ref=7) - angle_coeff @angle:c3a,c3a,c3prime,c3a,c3a,c3prime class2 ba 45.8865 23.6977 1.4170 1.4890 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 121.9556 76.3105 -26.3166 -17.6944 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 bb 25.9530 1.3850 1.3850 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,n3m,c3prime,c3prime,n3m,c3prime class2 ba 20.0533 20.0533 1.3850 1.3850 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 107.8594 38.0833 -17.5074 0.0000 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 bb 2.2522 1.5140 1.1010 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,c4,h1,c3prime,c4,h1 class2 ba 15.5988 14.6287 1.5140 1.1010 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 109.0000 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 bb 0.0 1.3750 1.4200 # (ver=1.0, ref=7) - angle_coeff @angle:c3prime,o2,c4,c3prime,o2e,c4 class2 ba 21.5366 -16.6748 1.3750 1.4200 # (ver=1.0, ref=7) - angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 112.8000 85.5228 -18.4582 -14.4215 # (ver=1.0, ref=6) - angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 bb 80.0000 1.2100 1.4020 # (ver=1.0, ref=6) - angle_coeff @angle:o1=,n3o,o2n,o1=,n3o,o2n class2 ba 0.0 0.0 1.2100 1.4020 # (ver=1.0, ref=6) - angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 105.0000 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=6) - angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 bb 11.4318 1.5300 1.4350 # (ver=1.0, ref=6) - angle_coeff @angle:c4,c4,o2n,c4,c4,o2n class2 ba 2.6868 20.4033 1.5300 1.4350 # (ver=1.0, ref=6) - angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 108.5000 55.7454 -10.0067 -6.2729 # (ver=1.0, ref=6) - angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 bb 0.0 1.4350 1.4020 # (ver=1.0, ref=6) - angle_coeff @angle:c4,o2n,n3o,c4,o2n,n3o class2 ba 0.0 0.0 1.4350 1.4020 # (ver=1.0, ref=6) - angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 128.0000 95.1035 -47.4240 -27.9164 # (ver=1.0, ref=6) - angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 bb 265.7106 1.2100 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:o1=,n3o,o1=,o1=,n3o,o1= class2 ba 95.6936 95.6936 1.2100 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 115.7000 53.8034 -14.1991 -11.8708 # (ver=1.0, ref=6) - angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 bb 14.8226 1.0400 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:h1,n3o,o1=,h1,n3o,o1= class2 ba -8.6275 58.6036 1.0400 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 117.5000 64.5228 -18.4582 -14.4215 # (ver=1.0, ref=6) - angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 bb 48.1403 1.4740 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:c4,n3o,o1=,c4,n3o,o1= class2 ba 27.2141 93.9927 1.4740 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 117.7000 63.9404 -18.4524 -14.3129 # (ver=1.0, ref=6) - angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 bb 93.7948 1.4300 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:c3a,n3o,o1=,c3a,n3o,o1= class2 ba 40.3757 92.1955 1.4300 1.2100 # (ver=1.0, ref=6) - angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=6) - angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 bb 23.1979 1.1010 1.4350 # (ver=1.0, ref=6) - angle_coeff @angle:h1,c4,o2n,h1,c4,o2n class2 ba 4.6189 55.3270 1.1010 1.4350 # (ver=1.0, ref=6) - angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 107.0000 54.9318 -9.1333 -11.5434 # (ver=1.0, ref=6) - angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 bb 3.3770 1.1010 1.4740 # (ver=1.0, ref=6) - angle_coeff @angle:h1,c4,n3o,h1,c4,n3o class2 ba 12.2491 30.5314 1.1010 1.4740 # (ver=1.0, ref=6) - angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 118.8000 29.2436 -8.8495 -6.6020 # (ver=1.0, ref=6) - angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 bb 21.0495 1.4170 1.4300 # (ver=1.0, ref=6) - angle_coeff @angle:c3a,c3a,n3o,c3a,c3a,n3o class2 ba 30.5211 59.8025 1.4170 1.4300 # (ver=1.0, ref=6) - angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 119.3000 115.2627 -35.6278 -26.1261 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 bb 20.0000 1.4308 1.4308 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,s2=,o1=,o1=,s2=,o1= class2 ba 45.0585 45.0585 1.4308 1.4308 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 134.1000 150.0000 -82.1013 -40.0005 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 bb 20.0000 1.1930 1.1930 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,n2o,o1=,o1=,n2o,o1= class2 ba -50.0000 -50.0000 1.1930 1.1930 # (ver=1.0, ref=5) - angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 180.0000 48.0000 0.0000 0.0000 # (ver=1.0, ref=5) - angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 bb 100.7369 1.5540 1.5540 # (ver=1.0, ref=5) - angle_coeff @angle:s1=,c2=,s1=,s1=,c2=,s1= class2 ba 0.0 0.0 1.5540 1.5540 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 180.0000 57.1000 0.0000 0.0000 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 bb 275.4350 1.1600 1.1600 # (ver=1.0, ref=5) - angle_coeff @angle:o1=,c2=,o1=,o1=,c2=,o1= class2 ba 0.0 0.0 1.1600 1.1600 # (ver=1.0, ref=5) - angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 107.5000 86.7690 -4.5700 -17.8520 # (ver=1.0, ref=4) - angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 bb 0.0 1.6000 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:o2,p4=,o2,o2,p4=,o2 class2 ba 0.0 0.0 1.6000 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 112.2150 99.9230 -32.0930 -22.8210 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 bb 0.0 1.5980 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,o2,n2=,p4=,o2 class2 ba 0.0 0.0 1.5980 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 125.0000 90.5230 -20.8010 -19.6020 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 bb 20.0000 1.5980 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,n2=,n2=,p4=,n2= class2 ba 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 103.9780 73.2570 -9.8970 -15.2120 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 bb 0.0 1.4300 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,o2,h1,p4=,o2 class2 ba 0.0 0.0 1.4300 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 110.0330 45.9780 -14.0520 -10.3990 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 bb 12.5700 1.4300 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,n2=,h1,p4=,n2= class2 ba -24.3830 72.9250 1.4300 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 101.4080 39.6950 -5.1340 -8.2270 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 bb 20.0000 1.4300 1.4300 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,h1,h1,p4=,h1 class2 ba 0.0 0.0 1.4300 1.4300 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 119.3000 47.3660 -14.6410 -10.7360 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 bb 1.0720 1.8000 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,n2=,c4,p4=,n2= class2 ba -7.1280 26.3530 1.8000 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 102.9000 52.0710 -6.4680 -10.7730 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 bb 3.8820 1.8000 1.4300 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,h1,c4,p4=,h1 class2 ba 11.1260 -19.4700 1.8000 1.4300 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 102.5000 48.2320 -5.7980 -9.9660 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 bb 6.2460 1.8000 1.8000 # (ver=1.0, ref=4) - angle_coeff @angle:c4,p4=,c4,c4,p4=,c4 class2 ba 12.8050 12.8050 1.8000 1.8000 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 107.3650 71.9770 -10.9430 -15.2900 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 bb 0.0 1.7890 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,o2,c3a,p4=,o2 class2 ba 0.0 0.0 1.7890 1.6000 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 109.6000 63.0620 -19.7400 -14.3290 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 bb 0.0 1.7890 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,n2=,c3a,p4=,n2= class2 ba 0.0 0.0 1.7890 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 108.2310 36.1850 -6.4880 -7.6460 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 bb 0.0 1.7890 1.4300 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,h1,c3a,p4=,h1 class2 ba 0.0 0.0 1.7890 1.4300 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 110.2310 56.1850 -17.3160 -12.7280 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 bb 0.0 1.7890 1.7890 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,c3a,c3a,p4=,c3a class2 ba 0.0 0.0 1.7890 1.7890 # (ver=1.0, ref=4) - angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 135.0000 23.8680 -8.7360 0.0000 # (ver=1.0, ref=4) - angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 bb 20.0000 1.5980 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:p4=,n2=,p4=,p4=,n2=,p4= class2 ba 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 120.0000 26.0680 -8.2980 -5.9430 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 bb -18.2870 1.0310 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n2=,p4=,h1,n2=,p4= class2 ba 40.0630 90.7910 1.0310 1.5980 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 110.9100 31.0910 0.0000 0.0000 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 bb 1.4570 1.0310 1.0310 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n2=,h1,h1,n2=,h1 class2 ba 8.4900 8.4900 1.0310 1.0310 # (ver=1.0, ref=4) - angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 117.2000 37.2620 0.0000 0.0000 # (ver=1.0, ref=4) - angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 bb 12.5630 1.4740 1.0310 # (ver=1.0, ref=4) - angle_coeff @angle:c4,n2=,h1,c4,n2=,h1 class2 ba 18.4860 7.8370 1.4740 1.0310 # (ver=1.0, ref=4) - angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 110.8860 33.8300 -7.0430 -7.2460 # (ver=1.0, ref=4) - angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 bb 1.0500 1.1010 1.8000 # (ver=1.0, ref=4) - angle_coeff @angle:h1,c4,p4=,h1,c4,p4= class2 ba 19.8120 16.9400 1.1010 1.8000 # (ver=1.0, ref=4) - angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 107.4990 62.7310 0.0000 0.0000 # (ver=1.0, ref=4) - angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 bb 5.6640 1.1010 1.4740 # (ver=1.0, ref=4) - angle_coeff @angle:h1,c4,n2=,h1,c4,n2= class2 ba 6.4070 46.3730 1.1010 1.4740 # (ver=1.0, ref=4) - angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 117.3170 55.2420 0.0000 0.0000 # (ver=1.0, ref=4) - angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 bb 22.7100 1.5300 1.4740 # (ver=1.0, ref=4) - angle_coeff @angle:c4,c4,n2=,c4,c4,n2= class2 ba 19.2440 59.4220 1.5300 1.4740 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 120.0010 47.8410 -15.2290 -10.9070 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 bb 0.0 1.4170 1.7890 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,c3a,p4=,c3a,c3a,p4= class2 ba 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 120.0000 60.0000 0.0000 0.0000 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 bb 0.0 1.4170 1.4000 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,c3a,n2=,c3a,c3a,n2= class2 ba 0.0 0.0 1.4170 1.4000 # (ver=1.0, ref=4) - angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 105.8000 52.7061 -12.1090 -9.8681 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 bb -9.6879 1.4200 0.9494 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,h1,c4,o2h,h1 class2 ba 28.5800 18.9277 1.4200 0.9494 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 104.5000 35.7454 -10.0067 -6.2729 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 bb -7.1131 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,c4,c4,o2h,c4 class2 ba -2.8112 -2.8112 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 104.5000 35.7454 -10.0067 -6.2729 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 bb -7.1131 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,o2,c4,c4,o2e,c4 class2 ba -2.8112 -2.8112 1.4200 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 108.1900 53.1250 -8.5016 0.0000 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 bb 20.6577 1.3768 0.9494 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,h1,c3a,o2h,h1 class2 ba 53.8614 23.9224 1.3768 0.9494 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 102.9695 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 bb 0.0 1.3768 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,c4,c3a,o2h,c4 class2 ba 0.0 0.0 1.3768 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 102.9695 38.9739 -6.2595 -8.1710 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 bb 0.0 1.3768 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,o2,c4,c3a,o2e,c4 class2 ba 0.0 0.0 1.3768 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 bb 23.1979 1.1010 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c4,o2,h1,c4,o2h class2 ba 4.6189 55.3270 1.1010 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 108.7280 58.5446 -10.8088 -12.4006 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 bb 23.1979 1.1010 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:h1,c4,o2,h1,c4,o2e class2 ba 4.6189 55.3270 1.1010 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 111.2700 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=3) - angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 bb 11.4318 1.5300 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,c4,o2,c4,c4,o2h class2 ba 2.6868 20.4033 1.5300 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 111.2700 54.5381 -8.3642 -13.0838 # (ver=1.0, ref=3) - angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 bb 11.4318 1.5300 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c4,c4,o2,c4,c4,o2e class2 ba 2.6868 20.4033 1.5300 1.4200 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2h class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2e class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 123.4200 73.6781 -21.6787 0.0000 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 bb 48.4754 1.4170 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:c3a,c3a,o2,c3a,c3a,o2 class2 ba 58.4790 107.6806 1.4170 1.3768 # (ver=1.0, ref=3) - angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 110.7000 70.3069 -6.9375 0.0000 # (ver=1.0, ref=2) - angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 bb 41.1143 1.6400 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:o2z,si4,o2z,o2z,si4,o2z class2 ba 23.4380 23.4380 1.6400 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 107.4000 57.6643 -10.6506 4.6274 # (ver=1.0, ref=2) - angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 bb 11.6183 1.4783 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:h1,si4,o2z,h1,si4,o2z class2 ba 6.4278 20.5669 1.4783 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 114.9060 23.0218 -31.3993 24.9814 # (ver=1.0, ref=2) - angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 bb 5.4896 1.8995 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:c4,si4,o2z,c4,si4,o2z class2 ba 6.4278 20.5669 1.8995 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 114.9060 23.0218 -31.3993 24.9814 # (ver=1.0, ref=2) - angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 bb 0.0 1.8634 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:c3a,si4,o2z,c3a,si4,o2z class2 ba 0.0 0.0 1.8634 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 159.0000 8.5000 -13.4188 -4.1785 # (ver=1.0, ref=2) - angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 bb 41.1143 1.6400 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:si4,o2z,si4,si4,o2z,si4 class2 ba 28.6686 28.6686 1.6400 1.6400 # (ver=1.0, ref=2) - angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 107.6600 39.6410 -12.9210 -2.4318 # (ver=1.0, ref=1) - angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 bb 5.3316 1.1010 1.1010 # (ver=1.0, ref=1) - angle_coeff @angle:h1,c4,h1,h1,c4,h1 class2 ba 18.1030 18.1030 1.1010 1.1010 # (ver=1.0, ref=1) - angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 110.7700 41.4530 -10.6040 5.1290 # (ver=1.0, ref=1) - angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 bb 3.3872 1.5300 1.1010 # (ver=1.0, ref=1) - angle_coeff @angle:c4,c4,h1,c4,c4,h1 class2 ba 20.7540 11.4210 1.5300 1.1010 # (ver=1.0, ref=1) - angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 112.6700 39.5160 -7.4430 -9.5583 # (ver=1.0, ref=1) - angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 bb 0.0 1.5300 1.5300 # (ver=1.0, ref=1) - angle_coeff @angle:c4,c4,c4,c4,c4,c4 class2 ba 8.0160 8.0160 1.5300 1.5300 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 111.0000 44.3234 -9.4454 0.0000 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 bb 2.9168 1.5010 1.1010 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,h1,c3a,c4,h1 class2 ba 26.4608 11.7717 1.5010 1.1010 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 108.4000 43.9594 -8.3924 -9.3379 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 bb 0.0 1.5010 1.5300 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,c4,c3a,c4,c4 class2 ba 0.0 0.0 1.5010 1.5300 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 111.0000 44.3234 -9.4454 0.0000 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 bb 0.0 1.5010 1.5010 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c4,c3a,c3a,c4,c3a class2 ba 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 117.9400 35.1558 -12.4682 0.0000 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 bb 1.0795 1.4170 1.0982 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,h1,c3a,c3a,h1 class2 ba 20.0033 24.2183 1.4170 1.0982 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 120.0500 44.7148 -22.7352 0.0000 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 bb 12.0676 1.4170 1.5010 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,c4,c3a,c3a,c4 class2 ba 31.0771 47.0579 1.4170 1.5010 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 118.9000 61.0226 -34.9931 0.0000 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 bb 68.2856 1.4170 1.4170 # (ver=1.0, ref=1) - angle_coeff @angle:c3a,c3a,c3a,c3a,c3a,c3a class2 ba 28.8708 28.8708 1.4170 1.4170 # (ver=1.0, ref=1) - angle_coeff @angle:n3,p4=,o2,X,X,X class2 108.3000 86.7690 -5.1750 -17.6710 # (ver=1.0, ref=4) - angle_coeff @angle:n3,p4=,o2,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:n3,p4=,o2,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:n3,p4=,n3,X,X,X class2 107.1000 85.7690 -5.7790 -17.4890 # (ver=1.0, ref=4) - angle_coeff @angle:n3,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:n3,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,n3,X,X,X class2 123.2150 89.9230 -32.6120 -21.0960 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:n2=,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,n3,X,X,X class2 103.9780 68.2570 -9.2210 -14.1740 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,n3,X,X,X class2 108.1650 70.9770 -11.5480 -15.1090 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,n3,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:c3a,p4=,n3,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,o2,p4=,X,X,X class2 117.0000 26.0310 -5.8280 -5.6200 # (ver=1.0, ref=4) - angle_coeff @angle:h1,o2,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,o2,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:c4,o2,p4=,X,X,X class2 118.2830 35.0010 -10.3600 -7.8700 # (ver=1.0, ref=4) - angle_coeff @angle:c4,o2,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:c4,o2,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n3,p4=,X,X,X class2 120.0830 25.0010 -6.1170 -5.4570 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n3,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,n3,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:c4,n3,p4=,X,X,X class2 120.0830 25.0010 -6.1170 -5.4570 # (ver=1.0, ref=4) - angle_coeff @angle:c4,n3,p4=,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:c4,n3,p4=,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - angle_coeff @angle:h1,o2z,si4,X,X,X class2 122.8000 23.7764 -19.8152 9.6331 # (ver=1.0, ref=2) - angle_coeff @angle:h1,o2z,si4,X,X,X class2 bb 0.0 1.0 1.0 # (ver=1.0, ref=2) - angle_coeff @angle:h1,o2z,si4,X,X,X class2 ba 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) - } # end of angle_coeff commands - - - # --------------- Dihedral Interactions: --------------------- - - - # -- Rules for generating (4-body) "dihedral" interactions: -- - # DihedralType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3] - - - write_once("Data Dihedrals By Type") { - @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* - @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* - @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a @atom:*,p*,bo2z,ao2z,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* - @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* - @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* - @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* - @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* - @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* @atom:*,p*,bn1t,an1t,dn1t,i* - @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2z,an2z,dn2z,i* @atom:*,p*,bn2t,an2t,dn2t,i* @atom:*,p*,bn1t,an1t,dn1t,i* - @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* - @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* - @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,dn3m,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* - @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 @atom:*,p*,bc3prime,ac3prime,dc3prime,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,dc3prime,i* - @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bn3o,an3o,dn3o,i* - @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* @atom:*,p*,bo1=,ao1=,do1=,i* - @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* - @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,dn3o,i* - @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* - @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* - @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bo2,ao2,do2,i* - @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* - @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* - @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,dn2=,i* - @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bn2=,an2=,dn2=,i* - @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* - @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,dp4=,i* - @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* - @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* - @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* - @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* - @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,do2,i* - @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,d*,i* - @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,dsi4,i* @atom:*,p*,bo2z,ao2z,do2z,i* @atom:*,p*,bsi4,asi4,dsi4,i* - @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a @atom:*,p*,bo2n,ao2n,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a @atom:*,p*,bn2z,an2z,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2n,ao2n,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2z,an2z,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a @atom:*,p*,bsi4,asi4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a @atom:*,p*,bp4=,ap4=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a @atom:*,p*,bo2h,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a @atom:*,p*,bo2e,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a @atom:*,p*,bo2,ao2,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a @atom:*,p*,bn3o,an3o,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a @atom:*,p*,bn3m,an3m,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a @atom:*,p*,bn2=,an2=,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a @atom:*,p*,bh1,ah1,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a @atom:*,p*,bc4,ac4,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a @atom:*,p*,bc3prime,ac3prime,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bsi4,asi4,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bp4=,ap4=,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3o,an3o,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn3m,an3m,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bn2=,an2=,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3prime,ac3prime,d*,i* - @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,d*,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,d*,i* - @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* - @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,do2,i* - @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2h,ao2,do2,i* - @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2e,ao2,do2,i* - @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bo2,ao2,do2,i* - @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 @atom:*,p*,bh1,ah1,dh1,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 @atom:*,p*,bc4,ac4,dc4,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bh1,ah1,dh1,i* - @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc4,ac4,dc4,i* - @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* @atom:*,p*,bc3a,ac3a,dc3a,i* - @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc3prime,i* @atom:*,p*,b*,a*,dn3m,i* @atom:*,p*,b*,a*,dc3prime,i* @atom:*,p*,b*,a*,do1,i* - @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dn3o,i* @atom:*,p*,b*,a*,do1=,i* - @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,d*,i* - @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,dc3a,i* @atom:*,p*,b*,a*,dn2=,i* @atom:*,p*,b*,a*,d*,i* - @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,d*,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,d*,i* - @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,do2,i* - @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dn2=,i* - @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dh1,i* - @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,do2,i* - @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dn2=,i* - @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,dn3,i* @atom:*,p*,b*,a*,dp4=,i* @atom:*,p*,b*,a*,dh1,i* - @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,do2z,i* - @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dh1,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,dh1,i* - @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X @atom:*,p*,b*,a*,dc4,i* @atom:*,p*,b*,a*,dsi4,i* @atom:*,p*,b*,a*,do2z,i* @atom:*,p*,b*,a*,dh1,i* - } # end of "Data Dihedrals By Type" section - - - - # ------- Dihedral Force Field Parameters: ------- - # For an explanation of these parameters, visit: - # http://lammps.sandia.gov/doc/dihedral_class2.html - - # Syntax: - # dihedral_coeff DihedralTypeName DihedralStyle parameters... - - - write_once("In Settings") { - dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 aat -12.2900 112.0893 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,si4,h1,si4,si4,si4,h1,si4,si4,si4 class2 bb13 0.0 1.4783 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.1010 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0977 112.0355 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 aat -12.9341 112.0977 112.0355 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,c4,h1,h1,si4,c4,h1,h1,si4,c4,h1 class2 bb13 0.0 1.4783 1.1010 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.1010 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 at 0.4272 0.0000 0.0000 0.3382 0.0000 0.0000 113.1855 112.0355 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 aat -17.5802 113.1855 112.0355 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,c4,h1,c4,si4,c4,h1,c4,si4,c4,h1 class2 bb13 0.0 1.8995 1.1010 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 mbt 0.0000 0.0000 -0.6302 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 aat -10.8232 112.0893 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,si4,si4,h1,h1,si4,si4,h1,h1,si4,si4,h1 class2 bb13 0.0 1.4783 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 mbt 0.0000 0.0000 -0.6941 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 aat -16.9141 113.0000 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4,h1 class2 bb13 0.0 1.8995 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 mbt 0.0000 0.0000 -0.1909 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 aat -13.3679 112.0355 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,si4,h1,c4,si4,si4,h1,c4,si4,si4 class2 bb13 0.0 1.1010 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 mbt 0.0000 0.0000 -0.5906 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 112.0977 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 aat 0.0 112.0355 112.0977 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,si4,h1,h1,c4,si4,h1,h1,c4,si4,h1 class2 bb13 0.0 1.1010 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 mbt 0.0000 0.0000 -0.3146 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 at 0.0000 0.0000 -0.2779 0.0000 0.0000 -0.1932 120.0000 109.5932 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 aat 0.0 120.0000 109.5932 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1 class2 bb13 0.0 1.4170 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 mbt 1.3445 3.5515 -4.9202 1.3750 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 ebt 0.1928 1.3187 0.8599 0.0004 -1.0975 0.4831 1.5140 1.4200 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 at 0.9701 -2.5169 1.7195 0.8831 -0.8203 0.2405 100.3182 109.0000 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 aat -12.2070 100.3182 109.0000 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4 class2 bb13 0.0 1.5140 1.4200 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 0.0 0.0 0.0 0.0 0.0 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 mbt -0.1118 -1.1990 0.6784 1.3850 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 ebt 0.1726 -0.4823 0.2666 -0.7019 0.8305 -0.6874 1.3850 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 at -0.3188 -0.0548 -0.3038 -0.2851 2.3997 -1.5747 121.9556 121.5420 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 aat -3.3556 121.9556 121.5420 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1=,c3prime,n3m,c3prime,o1= class2 bb13 0.0 1.3850 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 aat 0.0 114.2676 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,si4,si4,si4,si4,si4 class2 bb13 0.0 2.3384 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 aat 0.0 114.2676 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,h1,si4,si4,si4,h1 class2 bb13 0.0 2.3384 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 2.3384 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.2676 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 aat 0.0 114.2676 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,si4,si4,si4,c4,si4,si4,si4,c4 class2 bb13 0.0 2.3384 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 aat 0.0 112.0893 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,si4,h1,si4,si4,si4 class2 bb13 0.0 1.4783 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 aat 0.0 112.0893 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,h1,h1,si4,si4,h1 class2 bb13 0.0 1.4783 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0893 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 aat 0.0 112.0893 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,h1,si4,si4,c4,h1,si4,si4,c4 class2 bb13 0.0 1.4783 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 aat 0.0 113.0000 114.2676 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,si4,c4,si4,si4,si4 class2 bb13 0.0 1.8995 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 aat 0.0 113.0000 112.0893 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,h1,c4,si4,si4,h1 class2 bb13 0.0 1.8995 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 mbt 0.0 0.0 0.0 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.0000 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 aat 0.0 113.0000 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,si4,X,c4,si4,si4,c4,c4,si4,si4,c4 class2 bb13 0.0 1.8995 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 aat 0.0 112.0355 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,si4,h1,c4,si4,si4 class2 bb13 0.0 1.1010 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.6400 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 114.9060 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 aat 0.0 112.0355 114.9060 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,o2z,h1,c4,si4,o2z class2 bb13 0.0 1.1010 1.6400 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 112.0977 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 aat 0.0 112.0355 112.0977 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,h1,h1,c4,si4,h1 class2 bb13 0.0 1.1010 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.0355 113.1855 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 aat 0.0 112.0355 113.1855 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,h1,c4,si4,c4,h1,c4,si4,c4 class2 bb13 0.0 1.1010 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 aat 0.0 112.6700 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,si4,c4,c4,si4,si4 class2 bb13 0.0 1.5300 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.6400 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 114.9060 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 aat 0.0 112.6700 114.9060 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,o2z,c4,c4,si4,o2z class2 bb13 0.0 1.5300 1.6400 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.0977 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 aat 0.0 112.6700 112.0977 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,h1,c4,c4,si4,h1 class2 bb13 0.0 1.5300 1.4783 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.1855 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 aat 0.0 112.6700 113.1855 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,c4,si4,X,c4,c4,si4,c4,c4,c4,si4,c4 class2 bb13 0.0 1.5300 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 -0.3500 0.0 0.0000 0.0 -0.0657 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 mbt 0.0 0.0 0.0 1.8995 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 aat 0.0 112.6700 113.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c4,c4,si4,si4,c4,c4,si4,si4,c4,c4,si4,si4 class2 bb13 0.0 1.5300 2.3384 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 0.0000 0.0 0.0000 0.0 -0.0231 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 mbt 0.0 0.0 0.0 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.4170 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.9060 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 aat 0.0 114.9060 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,o2z,si4,c3a,c3a,o2z,si4,c3a,c3a class2 bb13 0.0 1.6400 1.4170 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 0.0000 0.0 0.0000 0.0 -0.0231 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 mbt 0.0 0.0 0.0 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.4170 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.5932 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 aat 0.0 109.5932 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:X,si4,c3a,c3a,h1,si4,c3a,c3a,h1,si4,c3a,c3a class2 bb13 0.0 1.4783 1.4170 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 0.0000 0.0 1.5093 0.0 0.0000 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 mbt 0.0000 6.2168 0.0000 1.4170 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 at 0.0000 4.5914 0.0000 0.0000 1.1079 0.0000 117.9400 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c3a,c3a,si4,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 bb13 0.0 1.0982 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 0.0000 0.0 4.3270 0.0 0.0000 0.0 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 mbt 0.0000 11.1576 0.0000 1.4170 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 at 0.0000 -5.5448 0.0000 0.0000 4.3281 0.0000 118.9000 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 bb13 0.0 1.4170 1.8634 # (ver=1.0, ref=10) - dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.2259 0.0 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4814 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.9900 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 aat 0.0 110.7700 110.9900 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,c4,n2z,h1,c4,c4,n2z,h1,c4,c4,n2z class2 bb13 0.0 1.1010 1.4814 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 0.0000 0.0 0.0000 0.0 -0.2021 0.0 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 mbt 0.0 0.0 0.0 1.4814 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.2343 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 113.5017 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 aat 0.0 110.9900 113.5017 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,c4,n2z,n2t,c4,c4,n2z,n2t,c4,c4,n2z,n2t class2 bb13 0.0 1.5300 1.2343 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 0.0000 0.0 0.0000 0.0 -0.2181 0.0 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 mbt 0.0 0.0 0.0 1.4814 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.2343 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.9744 113.5017 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 aat 0.0 107.9744 113.5017 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c4,n2z,n2t,h1,c4,n2z,n2t,h1,c4,n2z,n2t class2 bb13 0.0 1.1010 1.2343 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 0.0000 0.0 0.0000 0.0 -0.1823 0.0 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 mbt 0.0 0.0 0.0 1.2343 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.1354 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 113.5017 171.6211 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 aat 0.0 113.5017 171.6211 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:c4,n2z,n2t,n1t,c4,n2z,n2t,n1t,c4,n2z,n2t,n1t class2 bb13 0.0 1.4814 1.1354 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 0.0000 0.0 0.0000 0.0 -0.2637 0.0 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 mbt 0.0 0.0 0.0 1.2343 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0221 1.1354 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.0345 171.6211 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 aat 0.0 110.0345 171.6211 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,n2z,n2t,n1t,h1,n2z,n2t,n1t,h1,n2z,n2t,n1t class2 bb13 0.0 1.0221 1.1354 # (ver=1.0, ref=9) - dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 0.0000 0.0 3.4040 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 mbt 0.0000 5.2012 0.0000 1.4170 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3950 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.7640 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 aat 0.0 117.9400 120.7640 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c3a,c3a,n3m,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 bb13 0.0 1.0982 1.3950 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 mbt -13.7686 -2.5959 1.1934 1.5140 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 ebt 0.7800 1.3339 0.3268 0.4160 -0.1140 0.7099 1.1010 1.3750 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 at -0.0071 0.8005 13.2959 0.1212 1.4427 -0.0241 107.8594 100.3182 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 aat -13.9734 107.8594 100.3182 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o2,h1,c4,c3prime,o2e,h1,c4,c3prime,o2 class2 bb13 0.0 1.1010 1.3750 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 mbt 0.0000 0.0000 -1.0000 1.5140 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 ebt 2.9036 0.5307 0.1439 0.0536 0.0354 0.3853 1.1010 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 at 0.0800 0.3339 14.4728 -0.2083 0.7308 -2.0667 107.8594 119.3000 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 aat -23.1923 107.8594 119.3000 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:h1,c4,c3prime,o1=,h1,c4,c3prime,o1=,h1,c4,c3prime,o1= class2 bb13 0.0 1.1010 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 0.8905 0.0 3.2644 0.0 0.2646 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 mbt 0.4552 7.3091 0.2842 1.3750 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 ebt 0.0882 -2.4309 -0.7426 -4.2421 10.1102 1.6824 1.4200 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 at -0.0327 1.0059 2.3573 1.9052 2.7261 5.9732 109.0000 118.9855 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 aat -32.9368 109.0000 118.9855 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,o1=,c4,o2e,c3prime,o1=,c4,o2,c3prime,o1= class2 bb13 0.0 1.4200 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 -2.5594 0.0 2.2013 0.0 0.0325 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 mbt 0.0 0.0 0.0 1.3750 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5140 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.0000 100.3182 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 aat 0.0 109.0000 100.3182 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,c3prime,c4,c4,o2e,c3prime,c4,c4,o2,c3prime,c4 class2 bb13 0.0 1.4200 1.5140 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 0.0000 0.0 2.0521 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 mbt 0.0 0.0 0.0 1.3850 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0700 121.5420 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 aat 0.0 120.0700 121.5420 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1=,c3a,n3m,c3prime,o1= class2 bb13 0.0 1.3950 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 0.0000 0.0 3.4040 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 mbt 0.0000 5.2012 0.0000 1.4170 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3950 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.7640 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aat 0.0 118.9000 120.7640 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 bb13 0.0 1.4170 1.3950 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 0.0000 0.0 0.7800 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 mbt 0.0000 2.4002 0.0000 1.4890 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 125.5320 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 aat 0.0 116.0640 125.5320 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1=,c3a,c3a,c3prime,o1= class2 bb13 0.0 1.4170 1.2160 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 mbt 7.7147 4.2557 -1.0118 1.4200 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 ebt 0.2282 2.2998 -0.4473 0.9589 0.9190 -0.6015 1.3750 1.1010 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 at 0.0971 -0.8699 -0.3142 -0.0401 2.8061 -0.4990 109.0000 108.7280 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 aat -13.1500 109.0000 108.7280 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,h1,c3prime,o2e,c4,h1,c3prime,o2,c4,h1 class2 bb13 0.0 1.3750 1.1010 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 0.1302 0.0 -0.3250 0.0 0.1134 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 mbt 9.9416 2.6421 2.2333 1.4200 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 ebt 0.2560 0.8133 -0.0728 -1.2164 -0.1715 -0.0964 1.3750 1.5300 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 at 0.7229 -0.9159 -0.0890 -0.6765 1.4492 -0.4620 109.0000 111.2700 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 aat -15.7082 109.0000 111.2700 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,o2,c4,c4,c3prime,o2e,c4,c4,c3prime,o2,c4,c4 class2 bb13 0.0 1.3750 1.5300 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 0.0000 0.0 0.6500 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 mbt 0.0 0.0 0.0 1.3950 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3850 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0700 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 aat 0.0 120.7640 120.0700 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m,c3prime class2 bb13 0.0 1.4170 1.3850 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 0.0000 0.0 2.1670 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.0982 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 117.9400 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 aat 0.0 116.0640 117.9400 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 bb13 0.0 1.4890 1.0982 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 0.0000 0.0 4.6282 0.0 0.0000 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 mbt 0.0000 3.8762 0.0000 1.4170 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4890 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 116.0640 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aat 0.0 118.9000 116.0640 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 bb13 0.0 1.4170 1.4890 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 0.0000 0.0 2.0000 0.0 0.0000 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4020 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.2100 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 -3.0000 108.5000 112.8000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 aat 0.0 108.5000 112.8000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,o2,n3o,o1=,c4,o2n,n3o,o1=,c4,o2n,n3o,o1= class2 bb13 0.0 1.4350 1.2100 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 0.0000 0.0 -0.4000 0.0 -0.2000 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 mbt 0.0 0.0 0.0 1.4350 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4020 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 108.5000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 aat 0.0 105.0000 108.5000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,o2,n3o,c4,c4,o2n,n3o,c4,c4,o2n,n3o class2 bb13 0.0 1.5300 1.4020 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.2100 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 at 0.0000 -0.3086 0.0000 0.0000 1.0352 0.0000 107.0000 117.5000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 aat -16.2615 107.0000 117.5000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c4,n3o,o1=,h1,c4,n3o,o1=,h1,c4,n3o,o1= class2 bb13 0.0 1.1010 1.2100 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 0.0000 0.0 1.1600 0.0 0.0000 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 mbt 0.0 0.0 0.0 1.4300 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.2100 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 at 0.0000 0.0000 0.0000 0.0000 -3.4207 0.0000 118.8000 117.7000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 aat -18.0436 118.8000 117.7000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1=,c3a,c3a,n3o,o1= class2 bb13 0.0 1.4170 1.2100 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 0.0000 0.0 2.9126 0.0 0.0000 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4300 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 at 0.0000 -8.0369 0.0000 0.0000 0.0000 0.0000 117.9400 118.8000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 aat 2.1508 117.9400 118.8000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:h1,c3a,c3a,n3o,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 bb13 0.0 1.0982 1.4300 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.0000 0.0 7.2124 0.0 0.0000 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 at 0.0000 7.7594 0.0000 0.0000 0.0000 0.0000 118.9000 118.8000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aat -34.9681 118.9000 118.8000 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 112.2150 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 aat 0.0 135.0000 112.2150 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,o2,p4=,n2=,p4=,o2 class2 bb13 0.0 1.5980 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 125.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 aat 0.0 135.0000 125.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2= class2 bb13 0.0 1.5980 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 110.0330 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 aat 0.0 135.0000 110.0330 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1 class2 bb13 0.0 1.5980 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 aat 0.0 135.0000 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c4,p4=,n2=,p4=,c4 class2 bb13 0.0 1.5980 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 135.0000 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 aat 0.0 135.0000 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,p4=,n2=,p4=,c3a,p4=,n2=,p4=,c3a class2 bb13 0.0 1.5980 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 112.2150 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 aat 0.0 120.0000 112.2150 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 bb13 0.0 1.0310 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 125.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 aat 0.0 120.0000 125.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,n2=,h1,n2=,p4=,n2= class2 bb13 0.0 1.0310 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 110.0330 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 aat 0.0 120.0000 110.0330 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 bb13 0.0 1.0310 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 aat 0.0 120.0000 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c4,h1,n2=,p4=,c4 class2 bb13 0.0 1.0310 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 aat 0.0 120.0000 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n2=,p4=,X,h1,n2=,p4=,c3a,h1,n2=,p4=,c3a class2 bb13 0.0 1.0310 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 aat 0.0 110.8860 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 bb13 0.0 1.1010 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.9000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 aat 0.0 110.8860 102.9000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 bb13 0.0 1.1010 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.5000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 aat 0.0 110.8860 102.5000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,p4=,X,h1,c4,p4=,c4,h1,c4,p4=,c4 class2 bb13 0.0 1.1010 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0200 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.4990 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 aat 0.0 107.4990 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 bb13 0.0 1.1010 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0200 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 mbt 0.0 0.0 0.0 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 aat 0.0 117.3170 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c4,n2=,X,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 bb13 0.0 1.5300 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 107.3650 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 aat 0.0 120.0010 107.3650 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,o2,c3a,c3a,p4=,o2 class2 bb13 0.0 1.4170 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 aat 0.0 120.0010 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 bb13 0.0 1.4170 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 108.2310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 aat 0.0 120.0010 108.2310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 110.2310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 aat 0.0 120.0010 110.2310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,p4=,X,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 1.8000 0.0 0.5000 0.0 2.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 mbt 0.0000 0.0000 0.0000 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5980 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 125.0000 135.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 aat 0.0 125.0000 135.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4=,n2=,p4= class2 bb13 0.0 1.5980 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.0330 135.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 aat 0.0 110.0330 135.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,p4=,n2=,p4=,h1,p4=,n2=,p4=,h1,p4=,n2=,p4= class2 bb13 0.0 1.4300 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 112.2150 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 aat 0.0 120.0000 112.2150 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,o2,h1,n2=,p4=,o2,h1,n2=,p4=,o2 class2 bb13 0.0 1.0310 1.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0310 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 110.0330 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 aat -3.7880 120.0000 110.0330 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n2=,p4=,h1,h1,n2=,p4=,h1,h1,n2=,p4=,h1 class2 bb13 0.0 1.0310 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3690 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8000 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 119.3000 120.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 aat -11.1020 119.3000 120.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1 class2 bb13 0.0 1.8000 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 mbt 0.0 0.0 0.0 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 109.6000 120.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 aat 0.0 109.6000 120.0000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,p4=,n2=,h1,c3a,p4=,n2=,h1,c3a,p4=,n2=,h1 class2 bb13 0.0 1.7890 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 aat -19.9340 110.8860 119.3000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,n2=,h1,c4,p4=,n2=,h1,c4,p4=,n2= class2 bb13 0.0 1.1010 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.8860 102.9000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 aat -16.0180 110.8860 102.9000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,p4=,h1,h1,c4,p4=,h1,h1,c4,p4=,h1 class2 bb13 0.0 1.1010 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0680 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 mbt 0.0 0.0 0.0 1.8000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8000 1.1010 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.5000 110.8860 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 aat -25.5460 102.5000 110.8860 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,p4=,c4,h1,c4,p4=,c4,h1,c4,p4=,c4,h1 class2 bb13 0.0 1.8000 1.1010 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 1.2660 0.0 -0.7740 0.0 0.0380 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 mbt -0.4140 -2.8620 0.0070 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 at -1.8950 1.2210 -0.7460 0.1100 0.0650 0.1090 107.4990 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 aat -9.6280 107.4990 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,n2=,h1,h1,c4,n2=,h1,h1,c4,n2=,h1 class2 bb13 0.0 1.1010 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 -5.0720 0.0 -0.4980 0.0 -0.4380 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 mbt -2.3800 2.5290 -0.7300 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 at -2.5230 2.8480 2.0590 -3.6920 4.0610 -1.5440 117.3170 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 aat -8.8980 117.3170 117.2000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2=,h1 class2 bb13 0.0 1.5300 1.0310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 -0.1510 0.0 0.0100 0.0 -0.1860 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 mbt -3.5150 -2.2980 -1.2770 1.5300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 at -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 110.7700 117.3170 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 aat -27.5060 110.7700 117.3170 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,c4,n2=,h1,c4,c4,n2=,h1,c4,c4,n2= class2 bb13 0.0 1.1010 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 0.0970 0.0 0.0720 0.0 -0.2580 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 mbt 0.0000 0.0000 0.0000 1.5300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 at -2.0980 1.8610 -1.6890 -0.1220 1.8930 -0.5670 112.6700 117.3170 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 aat 0.0000 112.6700 117.3170 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c4,c4,c4,n2=,c4,c4,c4,n2=,c4,c4,c4,n2= class2 bb13 0.0 1.5300 1.4740 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 aat 0.0 120.0010 109.6000 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4=,n2= class2 bb13 0.0 1.4170 1.5980 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 -0.2720 0.0 1.1900 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 mbt 0.0 0.0 0.0 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 108.2310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 aat 0.0 120.0010 108.2310 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1 class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 0.0000 0.0 2.2700 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0010 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 aat 0.0 117.9400 120.0010 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c3a,c3a,p4=,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 bb13 0.0 1.0982 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 0.0000 0.0 5.4770 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0010 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aat 0.0 118.9000 120.0010 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 0.1863 0.0 -0.4338 0.0 -0.2121 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 mbt 0.0000 0.9241 -0.5889 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 ebt -1.7554 1.3145 0.2263 0.2493 0.6803 0.0000 1.1010 0.9494 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 at -3.4060 1.6396 0.0737 0.0000 -0.2810 -0.5944 108.7280 105.8000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 aat -10.5093 108.7280 105.8000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,o2,h1,h1,c4,o2h,h1,h1,c4,o2,h1 class2 bb13 0.0 1.1010 0.9494 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 0.5302 0.0 0.0000 0.0 -0.3966 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 mbt -6.8007 -4.6546 -1.4101 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 ebt -0.1620 0.1564 -1.1408 -0.6054 1.3339 0.9648 1.4200 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 at -0.6653 0.4340 -0.7777 0.5144 1.6393 -1.8234 104.5000 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 aat -16.4438 104.5000 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2h,c4,h1,c4,o2,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 0.5302 0.0 0.0000 0.0 -0.3966 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 mbt -6.8007 -4.6546 -1.4101 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 ebt -0.1620 0.1564 -1.1408 -0.6054 1.3339 0.9648 1.4200 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 at -0.6653 0.4340 -0.7777 0.5144 1.6393 -1.8234 104.5000 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 aat -16.4438 104.5000 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,o2,c4,h1,c4,o2e,c4,h1,c4,o2,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0720 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 mbt 0.0 0.0 0.0 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.9695 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 aat 0.0 102.9695 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2h,c4,h1,c3a,o2,c4,h1 class2 bb13 0.0 1.3768 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 0.9513 0.0 0.1155 0.0 0.0720 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 mbt 0.0 0.0 0.0 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 102.9695 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 aat 0.0 102.9695 108.7280 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,o2,c4,h1,c3a,o2e,c4,h1,c3a,o2,c4,h1 class2 bb13 0.0 1.3768 1.1010 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 -0.6732 0.0 -0.4778 0.0 -0.1670 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 mbt 1.2472 0.0000 0.7485 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 ebt -0.5800 0.9004 0.0000 0.0000 0.5343 0.9025 1.5300 0.9494 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 at -3.5903 2.5225 0.4888 0.8726 -0.3577 0.3888 111.2700 105.8000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 aat -12.1038 111.2700 105.8000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2,h1 class2 bb13 0.0 1.5300 0.9494 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 mbt -5.9288 -2.7007 -0.3175 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 ebt -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 at -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 aat -19.0059 111.2700 104.5000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2,c4 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 -0.4000 0.0 -0.4028 0.0 -0.2450 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 mbt -5.9288 -2.7007 -0.3175 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 ebt -0.2456 1.0517 -0.7795 0.4741 1.2635 0.5576 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 at -2.7466 1.4877 -0.8955 0.5676 0.9450 0.0703 111.2700 104.5000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 aat -19.0059 111.2700 104.5000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2,c4 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 aat -14.0484 105.0000 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 bb13 0.0 1.4350 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 aat -14.0484 105.0000 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4350 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 105.0000 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 aat -14.0484 105.0000 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 aat -14.0484 111.2700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 aat -14.0484 111.2700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 1.1000 0.0 -0.0500 0.0 -0.1441 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 mbt -17.2585 -3.6157 -0.8364 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 1.0165 0.7553 -0.4609 1.0165 0.7553 -0.4609 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.5511 0.9737 -0.6673 0.5511 0.9737 -0.6673 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 aat -14.0484 111.2700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:o2,c4,c4,o2,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 aat -20.2006 110.7700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2n,h1,c4,c4,o2n class2 bb13 0.0 1.1010 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 aat -20.2006 110.7700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2h,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 -0.1435 0.0 0.2530 0.0 -0.0905 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 mbt -16.7975 -1.2296 -0.2750 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 ebt 0.9681 0.9551 0.0436 0.5903 0.6669 0.8584 1.1010 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 at 2.3668 2.4920 -1.0122 -0.1892 0.4918 0.7273 110.7700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 aat -20.2006 110.7700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c4,c4,o2,h1,c4,c4,o2e,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 aat -29.0420 112.6700 105.0000 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2n,c4,c4,c4,o2n class2 bb13 0.0 1.5300 1.4350 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 aat -29.0420 112.6700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2h,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 0.7137 0.0 0.2660 0.0 -0.2545 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 mbt -21.8842 -7.6764 -0.6868 1.5300 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 ebt -0.3190 0.4411 -0.7174 1.1538 0.8409 -0.9138 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 at 0.5623 -0.3041 -0.4015 0.9672 -0.7566 -1.2331 112.6700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 aat -29.0420 112.6700 111.2700 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c4,c4,c4,o2,c4,c4,c4,o2e,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 0.0000 0.0 1.5000 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 mbt 0.0 0.0 0.0 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 102.9695 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 aat 0.0 123.4200 102.9695 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2h,c4,c3a,c3a,o2,c4 class2 bb13 0.0 1.4170 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 0.0000 0.0 1.5000 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 mbt 0.0 0.0 0.0 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 102.9695 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 aat 0.0 123.4200 102.9695 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,c4,c3a,c3a,o2e,c4,c3a,c3a,o2,c4 class2 bb13 0.0 1.4170 1.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 110.7000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 aat 0.0 159.0000 110.7000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,o2z,si4,o2z,si4,o2z class2 bb13 0.0 1.6400 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.4783 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 107.4000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 aat 0.0 159.0000 107.4000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,h1,si4,o2z,si4,h1 class2 bb13 0.0 1.6400 1.4783 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.8995 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 114.9060 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 aat 0.0 159.0000 114.9060 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c4,si4,o2z,si4,c4 class2 bb13 0.0 1.6400 1.8995 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.8634 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 159.0000 114.9060 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 aat 0.0 159.0000 114.9060 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,o2z,si4,X,si4,o2z,si4,c3a,si4,o2z,si4,c3a class2 bb13 0.0 1.6400 1.8634 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 -0.2250 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.6400 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7000 159.0000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 aat 0.0 110.7000 159.0000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4,o2z,si4 class2 bb13 0.0 1.6400 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4783 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 107.4000 159.0000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 aat 0.0 107.4000 159.0000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,si4,o2z,si4,h1,si4,o2z,si4,h1,si4,o2z,si4 class2 bb13 0.0 1.4783 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 0.0000 0.0 0.0000 0.0 -0.0100 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 mbt 0.0 0.0 0.0 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 114.9060 159.0000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 aat 0.0 114.9060 159.0000 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,si4,c4,si4,o2z,si4,c4,si4,o2z,si4 class2 bb13 0.0 1.8995 1.6400 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,si4,si4,c4,c4,si4 class2 bb13 0.0 1.8995 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 aat 0.0 112.6700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2n,si4,c4,c4,o2n class2 bb13 0.0 1.8995 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2h,si4,c4,c4,o2 class2 bb13 0.0 1.8995 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,o2e,si4,c4,c4,o2 class2 bb13 0.0 1.8995 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 aat 0.0 112.6700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2z,si4,c4,c4,n2z class2 bb13 0.0 1.8995 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 aat 0.0 112.6700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,n2=,si4,c4,c4,n2= class2 bb13 0.0 1.8995 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 aat 0.0 112.6700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,h1,si4,c4,c4,h1 class2 bb13 0.0 1.8995 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c4,si4,c4,c4,c4 class2 bb13 0.0 1.8995 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8995 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 aat 0.0 112.6700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,si4,c4,c4,c3a,si4,c4,c4,c3a class2 bb13 0.0 1.8995 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 aat 0.0 105.0000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,si4,o2n,c4,c4,si4 class2 bb13 0.0 1.4350 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 aat 0.0 105.0000 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2n,o2n,c4,c4,o2n class2 bb13 0.0 1.4350 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 aat 0.0 105.0000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2h,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 aat 0.0 105.0000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,o2e,o2n,c4,c4,o2 class2 bb13 0.0 1.4350 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 aat 0.0 105.0000 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2z,o2n,c4,c4,n2z class2 bb13 0.0 1.4350 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 aat 0.0 105.0000 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,n2=,o2n,c4,c4,n2= class2 bb13 0.0 1.4350 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 aat 0.0 105.0000 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,h1,o2n,c4,c4,h1 class2 bb13 0.0 1.4350 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 aat 0.0 105.0000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c4,o2n,c4,c4,c4 class2 bb13 0.0 1.4350 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4350 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 105.0000 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 aat 0.0 105.0000 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2n,c4,c4,c3a,o2n,c4,c4,c3a class2 bb13 0.0 1.4350 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,si4,o2,c4,c4,si4 class2 bb13 0.0 1.4200 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 aat 0.0 111.2700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 aat 0.0 111.2700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2z,o2,c4,c4,n2z class2 bb13 0.0 1.4200 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 aat 0.0 111.2700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,n2=,o2,c4,c4,n2= class2 bb13 0.0 1.4200 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 aat 0.0 111.2700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,h1,o2,c4,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c4,o2,c4,c4,c4 class2 bb13 0.0 1.4200 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 aat 0.0 111.2700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2h,c4,c4,c3a,o2,c4,c4,c3a class2 bb13 0.0 1.4200 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,si4,o2,c4,c4,si4 class2 bb13 0.0 1.4200 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 aat 0.0 111.2700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2n,o2,c4,c4,o2n class2 bb13 0.0 1.4200 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2h,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 aat 0.0 111.2700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,o2e,o2,c4,c4,o2 class2 bb13 0.0 1.4200 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 aat 0.0 111.2700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2z,o2,c4,c4,n2z class2 bb13 0.0 1.4200 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 aat 0.0 111.2700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,n2=,o2,c4,c4,n2= class2 bb13 0.0 1.4200 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 aat 0.0 111.2700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,h1,o2,c4,c4,h1 class2 bb13 0.0 1.4200 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 aat 0.0 111.2700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c4,o2,c4,c4,c4 class2 bb13 0.0 1.4200 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4200 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 111.2700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 aat 0.0 111.2700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,o2e,c4,c4,c3a,o2,c4,c4,c3a class2 bb13 0.0 1.4200 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 aat 0.0 110.9900 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,si4,n2z,c4,c4,si4 class2 bb13 0.0 1.4814 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 aat 0.0 110.9900 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2n,n2z,c4,c4,o2n class2 bb13 0.0 1.4814 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 aat 0.0 110.9900 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2h,n2z,c4,c4,o2 class2 bb13 0.0 1.4814 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 aat 0.0 110.9900 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,o2e,n2z,c4,c4,o2 class2 bb13 0.0 1.4814 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 aat 0.0 110.9900 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2z,n2z,c4,c4,n2z class2 bb13 0.0 1.4814 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 aat 0.0 110.9900 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,n2=,n2z,c4,c4,n2= class2 bb13 0.0 1.4814 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 aat 0.0 110.9900 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,h1,n2z,c4,c4,h1 class2 bb13 0.0 1.4814 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 aat 0.0 110.9900 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c4,n2z,c4,c4,c4 class2 bb13 0.0 1.4814 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4814 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.9900 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 aat 0.0 110.9900 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2z,c4,c4,c3a,n2z,c4,c4,c3a class2 bb13 0.0 1.4814 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 aat 0.0 117.3170 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,si4,n2=,c4,c4,si4 class2 bb13 0.0 1.4740 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 aat 0.0 117.3170 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2n,n2=,c4,c4,o2n class2 bb13 0.0 1.4740 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 aat 0.0 117.3170 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2h,n2=,c4,c4,o2 class2 bb13 0.0 1.4740 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 aat 0.0 117.3170 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,o2e,n2=,c4,c4,o2 class2 bb13 0.0 1.4740 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 aat 0.0 117.3170 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2z,n2=,c4,c4,n2z class2 bb13 0.0 1.4740 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 aat 0.0 117.3170 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,n2=,n2=,c4,c4,n2= class2 bb13 0.0 1.4740 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 aat 0.0 117.3170 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,h1,n2=,c4,c4,h1 class2 bb13 0.0 1.4740 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 aat 0.0 117.3170 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c4,n2=,c4,c4,c4 class2 bb13 0.0 1.4740 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4740 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.3170 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 aat 0.0 117.3170 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,n2=,c4,c4,c3a,n2=,c4,c4,c3a class2 bb13 0.0 1.4740 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 aat 0.0 110.7700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,si4,h1,c4,c4,si4 class2 bb13 0.0 1.1010 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 aat 0.0 110.7700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2n,h1,c4,c4,o2n class2 bb13 0.0 1.1010 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 aat 0.0 110.7700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2h,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 aat 0.0 110.7700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,o2e,h1,c4,c4,o2 class2 bb13 0.0 1.1010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 aat 0.0 110.7700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2z,h1,c4,c4,n2z class2 bb13 0.0 1.1010 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 aat 0.0 110.7700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,n2=,h1,c4,c4,n2= class2 bb13 0.0 1.1010 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 aat 0.0 110.7700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,h1,h1,c4,c4,h1 class2 bb13 0.0 1.1010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 aat 0.0 110.7700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c4,h1,c4,c4,c4 class2 bb13 0.0 1.1010 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.1010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 110.7700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 aat 0.0 110.7700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,h1,c4,c4,c3a,h1,c4,c4,c3a class2 bb13 0.0 1.1010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,si4,c4,c4,c4,si4 class2 bb13 0.0 1.5300 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 aat 0.0 112.6700 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2n,c4,c4,c4,o2n class2 bb13 0.0 1.5300 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2h,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 aat 0.0 112.6700 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,o2e,c4,c4,c4,o2 class2 bb13 0.0 1.5300 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 aat 0.0 112.6700 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2z,c4,c4,c4,n2z class2 bb13 0.0 1.5300 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 aat 0.0 112.6700 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,n2=,c4,c4,c4,n2= class2 bb13 0.0 1.5300 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 aat 0.0 112.6700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,h1,c4,c4,c4,h1 class2 bb13 0.0 1.5300 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 aat 0.0 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c4,c4,c4,c4,c4 class2 bb13 0.0 1.5300 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5300 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 112.6700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 aat 0.0 112.6700 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c4,c4,c4,c3a,c4,c4,c4,c3a class2 bb13 0.0 1.5300 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 aat 0.0 108.4000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,si4,c3a,c4,c4,si4 class2 bb13 0.0 1.5010 1.8995 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 aat 0.0 108.4000 105.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2n,c3a,c4,c4,o2n class2 bb13 0.0 1.5010 1.4350 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 aat 0.0 108.4000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2h,c3a,c4,c4,o2 class2 bb13 0.0 1.5010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 aat 0.0 108.4000 111.2700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,o2e,c3a,c4,c4,o2 class2 bb13 0.0 1.5010 1.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 aat 0.0 108.4000 110.9900 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2z,c3a,c4,c4,n2z class2 bb13 0.0 1.5010 1.4814 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 aat 0.0 108.4000 117.3170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,n2=,c3a,c4,c4,n2= class2 bb13 0.0 1.5010 1.4740 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aat 0.0 108.4000 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 bb13 0.0 1.5010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 aat 0.0 108.4000 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c4,c3a,c4,c4,c4 class2 bb13 0.0 1.5010 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 0.0000 0.0 0.0000 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 mbt 0.0 0.0 0.0 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 108.4000 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 aat 0.0 108.4000 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c4,c4,X,c3a,c4,c4,c3a,c3a,c4,c4,c3a class2 bb13 0.0 1.5010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,si4,si4,c3a,c3a,si4 class2 bb13 0.0 1.8634 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 aat 0.0 120.0000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,p4=,si4,c3a,c3a,p4= class2 bb13 0.0 1.8634 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2h,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2e,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,o2,si4,c3a,c3a,o2 class2 bb13 0.0 1.8634 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 aat 0.0 120.0000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3o,si4,c3a,c3a,n3o class2 bb13 0.0 1.8634 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 aat 0.0 120.0000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n3m,si4,c3a,c3a,n3m class2 bb13 0.0 1.8634 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,n2=,si4,c3a,c3a,n2= class2 bb13 0.0 1.8634 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 aat 0.0 120.0000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,h1,si4,c3a,c3a,h1 class2 bb13 0.0 1.8634 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 aat 0.0 120.0000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c4,si4,c3a,c3a,c4 class2 bb13 0.0 1.8634 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 aat 0.0 120.0000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3prime,si4,c3a,c3a,c3prime class2 bb13 0.0 1.8634 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.8634 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 aat 0.0 120.0000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,si4,c3a,c3a,c3a,si4,c3a,c3a,c3a class2 bb13 0.0 1.8634 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 aat 0.0 120.0010 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,si4,p4=,c3a,c3a,si4 class2 bb13 0.0 1.7890 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 aat 0.0 120.0010 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,p4=,p4=,c3a,c3a,p4= class2 bb13 0.0 1.7890 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2h,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2e,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 aat 0.0 120.0010 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,o2,p4=,c3a,c3a,o2 class2 bb13 0.0 1.7890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 aat 0.0 120.0010 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3o,p4=,c3a,c3a,n3o class2 bb13 0.0 1.7890 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 aat 0.0 120.0010 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n3m,p4=,c3a,c3a,n3m class2 bb13 0.0 1.7890 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 aat 0.0 120.0010 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,n2=,p4=,c3a,c3a,n2= class2 bb13 0.0 1.7890 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 aat 0.0 120.0010 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,h1,p4=,c3a,c3a,h1 class2 bb13 0.0 1.7890 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 aat 0.0 120.0010 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c4,p4=,c3a,c3a,c4 class2 bb13 0.0 1.7890 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 aat 0.0 120.0010 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3prime,p4=,c3a,c3a,c3prime class2 bb13 0.0 1.7890 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.7890 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0010 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 aat 0.0 120.0010 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,p4=,c3a,c3a,c3a,p4=,c3a,c3a,c3a class2 bb13 0.0 1.7890 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2h,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2e,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,si4,o2,c3a,c3a,si4 class2 bb13 0.0 1.3768 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 aat 0.0 123.4200 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,p4=,o2,c3a,c3a,p4= class2 bb13 0.0 1.3768 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2h,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2e,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 aat 0.0 123.4200 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,o2,o2,c3a,c3a,o2 class2 bb13 0.0 1.3768 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 aat 0.0 123.4200 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3o,o2,c3a,c3a,n3o class2 bb13 0.0 1.3768 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 aat 0.0 123.4200 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n3m,o2,c3a,c3a,n3m class2 bb13 0.0 1.3768 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 aat 0.0 123.4200 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,n2=,o2,c3a,c3a,n2= class2 bb13 0.0 1.3768 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 aat 0.0 123.4200 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,h1,o2,c3a,c3a,h1 class2 bb13 0.0 1.3768 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 aat 0.0 123.4200 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c4,o2,c3a,c3a,c4 class2 bb13 0.0 1.3768 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 aat 0.0 123.4200 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3prime,o2,c3a,c3a,c3prime class2 bb13 0.0 1.3768 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3768 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 123.4200 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 aat 0.0 123.4200 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a class2 bb13 0.0 1.3768 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 aat 0.0 118.8000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,si4,n3o,c3a,c3a,si4 class2 bb13 0.0 1.4300 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 aat 0.0 118.8000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,p4=,n3o,c3a,c3a,p4= class2 bb13 0.0 1.4300 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2h,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2e,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 aat 0.0 118.8000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,o2,n3o,c3a,c3a,o2 class2 bb13 0.0 1.4300 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 aat 0.0 118.8000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3o,n3o,c3a,c3a,n3o class2 bb13 0.0 1.4300 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 aat 0.0 118.8000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n3m,n3o,c3a,c3a,n3m class2 bb13 0.0 1.4300 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 aat 0.0 118.8000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,n2=,n3o,c3a,c3a,n2= class2 bb13 0.0 1.4300 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 aat 0.0 118.8000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,h1,n3o,c3a,c3a,h1 class2 bb13 0.0 1.4300 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 aat 0.0 118.8000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c4,n3o,c3a,c3a,c4 class2 bb13 0.0 1.4300 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 aat 0.0 118.8000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3prime,n3o,c3a,c3a,c3prime class2 bb13 0.0 1.4300 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4300 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.8000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 aat 0.0 118.8000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3o,c3a,c3a,c3a,n3o,c3a,c3a,c3a class2 bb13 0.0 1.4300 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 aat 0.0 120.7640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,si4,n3m,c3a,c3a,si4 class2 bb13 0.0 1.3950 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 aat 0.0 120.7640 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,p4=,n3m,c3a,c3a,p4= class2 bb13 0.0 1.3950 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2h,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2e,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 aat 0.0 120.7640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,o2,n3m,c3a,c3a,o2 class2 bb13 0.0 1.3950 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 aat 0.0 120.7640 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3o,n3m,c3a,c3a,n3o class2 bb13 0.0 1.3950 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 aat 0.0 120.7640 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n3m,n3m,c3a,c3a,n3m class2 bb13 0.0 1.3950 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 aat 0.0 120.7640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,n2=,n3m,c3a,c3a,n2= class2 bb13 0.0 1.3950 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 aat 0.0 120.7640 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,h1,n3m,c3a,c3a,h1 class2 bb13 0.0 1.3950 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 aat 0.0 120.7640 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c4,n3m,c3a,c3a,c4 class2 bb13 0.0 1.3950 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 aat 0.0 120.7640 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3prime,n3m,c3a,c3a,c3prime class2 bb13 0.0 1.3950 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.3950 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.7640 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 aat 0.0 120.7640 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n3m,c3a,c3a,c3a,n3m,c3a,c3a,c3a class2 bb13 0.0 1.3950 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,si4,n2=,c3a,c3a,si4 class2 bb13 0.0 1.4000 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 aat 0.0 120.0000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,p4=,n2=,c3a,c3a,p4= class2 bb13 0.0 1.4000 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2h,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2e,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 aat 0.0 120.0000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,o2,n2=,c3a,c3a,o2 class2 bb13 0.0 1.4000 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 aat 0.0 120.0000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3o,n2=,c3a,c3a,n3o class2 bb13 0.0 1.4000 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 aat 0.0 120.0000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n3m,n2=,c3a,c3a,n3m class2 bb13 0.0 1.4000 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 aat 0.0 120.0000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,n2=,n2=,c3a,c3a,n2= class2 bb13 0.0 1.4000 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 aat 0.0 120.0000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,h1,n2=,c3a,c3a,h1 class2 bb13 0.0 1.4000 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 aat 0.0 120.0000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c4,n2=,c3a,c3a,c4 class2 bb13 0.0 1.4000 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 aat 0.0 120.0000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3prime,n2=,c3a,c3a,c3prime class2 bb13 0.0 1.4000 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 aat 0.0 120.0000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,n2=,c3a,c3a,c3a,n2=,c3a,c3a,c3a class2 bb13 0.0 1.4000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,si4,h1,c3a,c3a,si4 class2 bb13 0.0 1.0982 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 aat 0.0 117.9400 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,p4=,h1,c3a,c3a,p4= class2 bb13 0.0 1.0982 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 aat 0.0 117.9400 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 bb13 0.0 1.0982 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 aat 0.0 117.9400 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3o,h1,c3a,c3a,n3o class2 bb13 0.0 1.0982 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 aat 0.0 117.9400 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n3m,h1,c3a,c3a,n3m class2 bb13 0.0 1.0982 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 aat 0.0 117.9400 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,n2=,h1,c3a,c3a,n2= class2 bb13 0.0 1.0982 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 aat 0.0 117.9400 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 bb13 0.0 1.0982 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 aat 0.0 117.9400 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c4,h1,c3a,c3a,c4 class2 bb13 0.0 1.0982 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 aat 0.0 117.9400 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3prime,h1,c3a,c3a,c3prime class2 bb13 0.0 1.0982 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0982 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 117.9400 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 aat 0.0 117.9400 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a class2 bb13 0.0 1.0982 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 aat 0.0 120.0500 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,si4,c4,c3a,c3a,si4 class2 bb13 0.0 1.5010 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 aat 0.0 120.0500 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,p4=,c4,c3a,c3a,p4= class2 bb13 0.0 1.5010 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2h,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2e,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 aat 0.0 120.0500 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,o2,c4,c3a,c3a,o2 class2 bb13 0.0 1.5010 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 aat 0.0 120.0500 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3o,c4,c3a,c3a,n3o class2 bb13 0.0 1.5010 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 aat 0.0 120.0500 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n3m,c4,c3a,c3a,n3m class2 bb13 0.0 1.5010 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 aat 0.0 120.0500 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,n2=,c4,c3a,c3a,n2= class2 bb13 0.0 1.5010 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 aat 0.0 120.0500 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 bb13 0.0 1.5010 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 aat 0.0 120.0500 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c4,c4,c3a,c3a,c4 class2 bb13 0.0 1.5010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 aat 0.0 120.0500 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3prime,c4,c3a,c3a,c3prime class2 bb13 0.0 1.5010 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.5010 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 aat 0.0 120.0500 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a class2 bb13 0.0 1.5010 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 aat 0.0 116.0640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,si4,c3prime,c3a,c3a,si4 class2 bb13 0.0 1.4890 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 aat 0.0 116.0640 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,p4=,c3prime,c3a,c3a,p4= class2 bb13 0.0 1.4890 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2h,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2e,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 aat 0.0 116.0640 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,o2,c3prime,c3a,c3a,o2 class2 bb13 0.0 1.4890 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 aat 0.0 116.0640 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3o,c3prime,c3a,c3a,n3o class2 bb13 0.0 1.4890 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 aat 0.0 116.0640 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n3m,c3prime,c3a,c3a,n3m class2 bb13 0.0 1.4890 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 aat 0.0 116.0640 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,n2=,c3prime,c3a,c3a,n2= class2 bb13 0.0 1.4890 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 aat 0.0 116.0640 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,h1,c3prime,c3a,c3a,h1 class2 bb13 0.0 1.4890 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 aat 0.0 116.0640 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c4,c3prime,c3a,c3a,c4 class2 bb13 0.0 1.4890 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 aat 0.0 116.0640 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3prime,c3prime,c3a,c3a,c3prime class2 bb13 0.0 1.4890 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4890 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 116.0640 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 aat 0.0 116.0640 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3prime,c3a,c3a,c3a,c3prime,c3a,c3a,c3a class2 bb13 0.0 1.4890 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 bb13 0.0 1.4170 1.8634 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aat 0.0 118.9000 120.0010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 bb13 0.0 1.4170 1.7890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aat 0.0 118.9000 123.4200 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 bb13 0.0 1.4170 1.3768 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aat 0.0 118.9000 118.8000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 bb13 0.0 1.4170 1.4300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aat 0.0 118.9000 120.7640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 bb13 0.0 1.4170 1.3950 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 aat 0.0 118.9000 120.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 bb13 0.0 1.4170 1.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aat 0.0 118.9000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 bb13 0.0 1.4170 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aat 0.0 118.9000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 bb13 0.0 1.4170 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aat 0.0 118.9000 116.0640 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 bb13 0.0 1.4170 1.4890 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 0.0000 0.0 4.5000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 mbt 0.0 0.0 0.0 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 118.9000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aat 0.0 118.9000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:X,c3a,c3a,X,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 bb13 0.0 1.4170 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 -0.1432 0.0 0.0617 0.0 -0.1530 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 mbt -14.2610 -0.5322 -0.4864 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 ebt 0.2130 0.3120 0.0777 0.2130 0.3120 0.0777 1.1010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 at -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.7700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 aat -12.5640 110.7700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c4,c4,h1,h1,c4,c4,h1,h1,c4,c4,h1 class2 bb13 0.0 1.1010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0000 0.0 0.0316 0.0 -0.1681 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 mbt -14.8790 -3.6581 -0.3138 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 ebt 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.5300 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 at -0.2454 0.0000 -0.1136 0.3113 0.4516 -0.1988 112.6700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 aat -16.1640 112.6700 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,h1,c4,c4,c4,h1,c4,c4,c4,h1 class2 bb13 0.0 1.5300 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0000 0.0 0.0514 0.0 -0.1430 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 mbt -17.7870 -7.1877 0.0000 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 ebt -0.0732 0.0000 0.0000 -0.0732 0.0000 0.0000 1.5300 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 at 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 aat -22.0450 112.6700 112.6700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4,c4 class2 bb13 0.0 1.5300 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 -0.0228 0.0 0.0280 0.0 -0.1863 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 mbt 0.0000 0.0000 0.0000 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.5010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 108.4000 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aat 0.0 108.4000 110.7700 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c4,c4,h1,c3a,c4,c4,h1,c3a,c4,c4,h1 class2 bb13 0.0 1.5010 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 mbt 0.0000 0.0000 0.0000 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 ebt 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 1.4170 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 at 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 120.0500 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 aat 0.0 120.0500 108.4000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c4,c3a,c3a,c4,c4,c3a,c3a,c4,c4 class2 bb13 0.0 1.4170 1.5300 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 mbt 0.0 0.0 0.0 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.4170 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0500 111.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 aat 0.0 120.0500 111.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a class2 bb13 0.0 1.4170 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 -0.6900 0.0 0.5097 0.0 0.0095 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 mbt 1.1580 3.2697 3.5132 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 ebt 0.9000 -1.3456 1.1900 3.4132 0.5873 -0.1323 1.4170 0.9494 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 at -5.1360 -1.0122 0.0000 4.6852 0.0230 -0.5980 123.4200 108.1900 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 aat -4.6072 123.4200 108.1900 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2,h1 class2 bb13 1.1590 1.4170 0.9494 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2h,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2e,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 0.0000 0.0 1.7234 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 mbt 0.0000 5.5432 0.0000 1.4170 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 ebt 0.0000 -1.5867 0.0000 0.0000 4.2641 0.0000 1.0982 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 at 0.0000 1.8729 0.0000 0.0000 2.5706 0.0000 117.9400 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 aat 4.2296 117.9400 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:h1,c3a,c3a,o2,h1,c3a,c3a,o2,h1,c3a,c3a,o2 class2 bb13 -2.0517 1.0982 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2h,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2e,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 0.0000 0.0 4.8498 0.0 0.0000 0.0 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 mbt 0.0000 4.8255 0.0000 1.4170 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 ebt 0.0000 0.2655 0.0000 0.0000 4.8905 0.0000 1.4170 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 at 0.0000 10.0155 0.0000 0.0000 1.7404 0.0000 118.9000 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aat -21.0247 118.9000 123.4200 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 bb13 -2.2436 1.4170 1.3768 # (ver=1.0, ref=3) - dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 -0.2802 0.0 -0.0678 0.0 -0.0122 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 mbt -5.5679 1.4083 0.3010 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 ebt -0.5835 1.1220 0.3978 1.3997 0.7756 0.0000 1.4170 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 at 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.0500 111.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 aat -5.8888 120.0500 111.0000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c4,h1,c3a,c3a,c4,h1,c3a,c3a,c4,h1 class2 bb13 -3.4826 1.4170 1.1010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 0.0000 0.0 2.3500 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 mbt 0.0000 4.8228 0.0000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 ebt 0.0000 -0.6890 0.0000 0.0000 -0.6890 0.0000 1.0982 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 at 0.0000 2.4501 0.0000 0.0000 2.4501 0.0000 117.9400 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 aat 0.3598 117.9400 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:h1,c3a,c3a,h1,h1,c3a,c3a,h1,h1,c3a,c3a,h1 class2 bb13 -1.7077 1.0982 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 0.0000 0.0 1.5590 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 mbt 0.0000 3.9421 0.0000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 ebt 0.0000 -1.7970 0.0000 0.0000 -0.4879 0.0000 1.5010 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 at 0.0000 -0.1242 0.0000 0.0000 3.4601 0.0000 120.0500 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 aat 4.4444 120.0500 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c4,c3a,c3a,h1,c4,c3a,c3a,h1,c4,c3a,c3a,h1 class2 bb13 0.8743 1.5010 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 0.0000 0.0 3.9661 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 mbt 0.0000 -1.1521 0.0000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 ebt 0.0000 -6.8958 0.0000 0.0000 -0.4669 0.0000 1.4170 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 at 0.0000 2.5014 0.0000 0.0000 2.7147 0.0000 118.9000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aat -4.8141 118.9000 117.9400 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 bb13 -6.2741 1.4170 1.0982 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 0.0000 0.0 4.4072 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 mbt 0.0000 9.1792 0.0000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 ebt 0.0000 -0.6918 0.0000 0.0000 0.2421 0.0000 1.4170 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 at 0.0000 3.8987 0.0000 0.0000 -4.4683 0.0000 118.9000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aat -14.4097 118.9000 120.0500 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 bb13 2.5085 1.4170 1.5010 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 8.3667 0.0 1.2000 0.0 0.0000 0.0 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 mbt 27.5989 -2.3120 0.0000 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 ebt -0.1185 6.3204 0.0000 -0.1185 6.3204 0.0000 1.4170 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 at 1.9767 1.0239 0.0000 1.9767 1.0239 0.0000 118.9000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aat 0.0000 118.9000 118.9000 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 bb13 53.0000 1.4170 1.4170 # (ver=1.0, ref=1) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 -0.4066 0.0 1.2513 0.0 -0.7507 0.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c3prime,n3m,c3prime,o1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=7) - dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.3500 0.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:c4,c4,n3o,o1=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=6) - dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,n3,p4=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 0.0000 0.0 1.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,c3a,n2=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:X,o2,p4=,X,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,o2,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,n2=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 5.7080 0.0 2.1180 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2,p4=,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,o2,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,n2=,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 0.0000 0.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,n3,p4=,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=4) - dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,o2z,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:h1,o2z,si4,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 0.0000 0.0 0.0000 0.0 -0.0500 0.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 mbt 0.0 0.0 0.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 ebt 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 at 0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 aat 0.0 120.0 120.0 # (ver=1.0, ref=2) - dihedral_coeff @dihedral:c4,si4,o2z,h1,X,X,X,X,X,X,X,X class2 bb13 0.0 1.0 1.0 # (ver=1.0, ref=2) - } # end of dihedral_coeff commands - - - # --------------- Improper Interactions: --------------------- - - - # -- Rules for generating (4-body) "improper" interactions: -- - # ImproperType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3] - - write_once("Data Impropers By Type (cenJsortIKL)") { - @improper:c4,c4,c4,c4,c4,c4,c4,c4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 - @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 - @improper:c4,c4,h1,o2,c4,c4,h1,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ao2,d*,io2 - @improper:h1,c4,h1,n2=,h1,c4,h1,n2= @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an2=,d*,in2= - @improper:h1,c4,h1,si4,h1,c4,h1,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 - @improper:c4,si4,c4,h1,c4,si4,c4,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 - @improper:h1,c4,h1,h1,h1,c4,h1,h1 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 - @improper:c4,c4,c4,h1,c4,c4,c4,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 - @improper:c4,si4,c4,si4,c4,si4,c4,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 - @improper:c4,c4,h1,h1,c4,c4,h1,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 - @improper:h1,si4,h1,h1,h1,si4,h1,h1 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 - @improper:h1,si4,si4,si4,h1,si4,si4,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 - @improper:c4,si4,si4,si4,c4,si4,si4,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,asi4,d*,isi4 - @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 - @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 - @improper:c4,si4,h1,si4,c4,si4,h1,si4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 - @improper:c4,c4,c4,o2,c4,c4,c4,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ao2,d*,io2 - @improper:h1,c4,h1,o2,h1,c4,h1,o2 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ao2,d*,io2 - @improper:c4,c4,h1,n2=,c4,c4,h1,n2= @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an2=,d*,in2= - @improper:c4,si4,h1,h1,c4,si4,h1,h1 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,ah1,d*,ih1 - @improper:h1,si4,h1,si4,h1,si4,h1,si4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,asi4,d*,isi4 - @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,an3m,d*,in3m @atom:*,p*,b*,ao1=,d*,io1= - @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an2=,d*,in2= - @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3m,d*,in3m @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ac3prime,d*,ic3prime - @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,asi4,d*,isi4 - @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ap4=,d*,ip4= - @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3prime,d*,ic3prime - @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3m,d*,in3m - @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3o,d*,in3o - @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao2n,d*,io2 - @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ao2,d*,io2 - @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= @atom:*,p*,b*,ah1,d*,ih1 @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= - @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ah1,d*,ih1 - @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,ac3prime,d*,ic3prime @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao2,d*,io2 - @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= @atom:*,p*,b*,ac4,d*,ic4 @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= - @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,an3o,d*,in3o @atom:*,p*,b*,ao1=,d*,io1= @atom:*,p*,b*,ao1=,d*,io1= - @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac4,d*,ic4 - @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a @atom:*,p*,b*,ac3a,d*,ic3a - @improper:c3a,c3prime,c3prime,n3m,X,X,X,X @atom:*,p*,b*,a*,d*,ic3a @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,in3m - @improper:c3a,o1=,c3prime,n3m,X,X,X,X @atom:*,p*,b*,a*,d*,ic3a @atom:*,p*,b*,a*,d*,io1= @atom:*,p*,b*,a*,d*,ic3prime @atom:*,p*,b*,a*,d*,in3m - } # end of "Data Impropers By Type" section - - - - # ------- Improper Force Field Parameters: ------- - # For an explanation of these parameters, visit: - # http://lammps.sandia.gov/doc/improper_class2.html - -# Syntax: - # improper_coeff ImproperTypeName ImproperStyle parameters... - - - write_once("In Settings") { - improper_coeff @improper:c4,c4,c4,c4,c4,c4,c4,c4 class2 0.0 0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c4,c4,c4,c4,c4,c4,c4,c4 class2 aa -0.1729 -0.1729 -0.1729 112.6700 112.6700 112.6700 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c4,h1,h1,c3a,c4,h1,h1 class2 aa 2.3794 3.0118 2.3794 111.0000 111.0000 107.6600 # (ver=1.0, ref=1) - improper_coeff @improper:c4,c4,h1,o2,c4,c4,h1,o2 class2 0.0 0.0 # (ver=1.0, ref=3) - improper_coeff @improper:c4,c4,h1,o2,c4,c4,h1,o2 class2 aa 3.9177 2.5926 0.1689 110.7700 111.2700 108.7280 # (ver=1.0, ref=3) - improper_coeff @improper:h1,c4,h1,n2=,h1,c4,h1,n2= class2 0.0 0.0 # (ver=1.0, ref=4) - improper_coeff @improper:h1,c4,h1,n2=,h1,c4,h1,n2= class2 aa 1.7680 1.7680 -2.9470 107.6600 107.4990 107.4990 # (ver=1.0, ref=4) - improper_coeff @improper:h1,c4,h1,si4,h1,c4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:h1,c4,h1,si4,h1,c4,h1,si4 class2 aa 0.0000 0.0000 2.2050 107.6600 112.0355 112.0355 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,c4,h1,c4,si4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,c4,h1,c4,si4,c4,h1 class2 aa 3.3827 3.3827 2.7963 113.1855 112.0977 112.0977 # (ver=1.0, ref=10) - improper_coeff @improper:h1,c4,h1,h1,h1,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=1) - improper_coeff @improper:h1,c4,h1,h1,h1,c4,h1,h1 class2 aa -0.3157 -0.3157 -0.3157 107.6600 107.6600 107.6600 # (ver=1.0, ref=1) - improper_coeff @improper:c4,c4,c4,h1,c4,c4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c4,c4,c4,h1,c4,c4,c4,h1 class2 aa -1.3199 -1.3199 0.1184 112.6700 110.7700 110.7700 # (ver=1.0, ref=1) - improper_coeff @improper:c4,si4,c4,si4,c4,si4,c4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,c4,si4,c4,si4,c4,si4 class2 aa 1.3465 1.3465 2.0805 113.1855 113.0000 113.0000 # (ver=1.0, ref=10) - improper_coeff @improper:c4,c4,h1,h1,c4,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c4,c4,h1,h1,c4,c4,h1,h1 class2 aa 0.2738 -0.4825 0.2738 110.7700 110.7700 107.6600 # (ver=1.0, ref=7) - improper_coeff @improper:h1,si4,h1,h1,h1,si4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:h1,si4,h1,h1,h1,si4,h1,h1 class2 aa 2.0665 2.0665 2.0665 108.6051 108.6051 108.6051 # (ver=1.0, ref=10) - improper_coeff @improper:h1,si4,si4,si4,h1,si4,si4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:h1,si4,si4,si4,h1,si4,si4,si4 class2 aa 4.1996 3.4924 4.1996 112.0893 112.0893 114.2676 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,si4,si4,c4,si4,si4,si4 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,si4,si4,c4,si4,si4,si4 class2 aa 4.5272 -5.6849 4.5272 113.0000 113.0000 114.2676 # (ver=1.0, ref=10) - improper_coeff @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 class2 0.0 0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c4,c4,h1,c3a,c4,c4,h1 class2 aa -1.8202 2.0403 1.0827 108.4000 111.0000 110.7700 # (ver=1.0, ref=1) - improper_coeff @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3prime,c4,h1,h1,c3prime,c4,h1,h1 class2 aa -1.7653 0.0 -1.7653 107.8594 107.8594 107.6600 # (ver=1.0, ref=7) - improper_coeff @improper:c4,si4,h1,si4,c4,si4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,h1,si4,c4,si4,h1,si4 class2 aa 3.4758 0.0 -2.9623 112.0977 113.0000 112.0893 # (ver=1.0, ref=10) - improper_coeff @improper:c4,c4,c4,o2,c4,c4,c4,o2 class2 0.0 0.0 # (ver=1.0, ref=3) - improper_coeff @improper:c4,c4,c4,o2,c4,c4,c4,o2 class2 aa -0.8330 -0.8330 -3.5744 112.6700 111.2700 111.2700 # (ver=1.0, ref=3) - improper_coeff @improper:h1,c4,h1,o2,h1,c4,h1,o2 class2 0.0 0.0 # (ver=1.0, ref=3) - improper_coeff @improper:h1,c4,h1,o2,h1,c4,h1,o2 class2 aa 2.4259 2.4259 2.1283 107.6600 108.7280 108.7280 # (ver=1.0, ref=3) - improper_coeff @improper:c4,c4,h1,n2=,c4,c4,h1,n2= class2 0.0 0.0 # (ver=1.0, ref=4) - improper_coeff @improper:c4,c4,h1,n2=,c4,c4,h1,n2= class2 aa 2.7530 1.0910 -1.3060 110.7700 117.3170 107.4990 # (ver=1.0, ref=4) - improper_coeff @improper:c4,si4,h1,h1,c4,si4,h1,h1 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:c4,si4,h1,h1,c4,si4,h1,h1 class2 aa 4.4559 4.6809 4.4559 112.0977 112.0977 108.6051 # (ver=1.0, ref=10) - improper_coeff @improper:h1,si4,h1,si4,h1,si4,h1,si4 class2 0.0 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:h1,si4,h1,si4,h1,si4,h1,si4 class2 aa 0.0 0.0 1.6082 108.6051 112.0893 112.0893 # (ver=1.0, ref=10) - improper_coeff @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= class2 30.0000 -0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3prime,n3m,o1=,c3a,c3prime,n3m,o1= class2 aa 0.0 0.0 0.0 108.4400 125.5320 121.5420 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 8.0000 -0.0 # (ver=1.0, ref=4) - improper_coeff @improper:c3a,c3a,c3a,n2=,c3a,c3a,c3a,n2= class2 aa 0.0 0.0 0.0 118.9000 120.0000 120.0000 # (ver=1.0, ref=4) - improper_coeff @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime class2 0.0000 -0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,n3m,c3prime,c3prime,c3a,n3m,c3prime,c3prime class2 aa 0.0 0.0 0.0 120.0700 120.0700 121.9556 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 5.3654 0.0 # (ver=1.0, ref=10) - improper_coeff @improper:c3a,c3a,c3a,si4,c3a,c3a,c3a,si4 class2 aa 0.0 0.0 0.0 118.9000 120.0000 120.0000 # (ver=1.0, ref=10) - improper_coeff @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 6.7090 -0.0 # (ver=1.0, ref=4) - improper_coeff @improper:c3a,c3a,c3a,p4=,c3a,c3a,c3a,p4= class2 aa 0.0 0.0 0.0 118.9000 120.0010 120.0010 # (ver=1.0, ref=4) - improper_coeff @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 17.0526 -0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3a,c3a,c3prime,c3a,c3a,c3a,c3prime class2 aa 0.0 0.0 0.0 118.9000 116.0640 116.0640 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 17.0526 0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3a,c3a,n3m,c3a,c3a,c3a,n3m class2 aa 0.0 0.0 0.0 118.9000 120.7640 120.7640 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 0.9194 -0.0 # (ver=1.0, ref=6) - improper_coeff @improper:c3a,c3a,c3a,n3o,c3a,c3a,c3a,n3o class2 aa 0.0 0.0 0.0 118.9000 118.8000 118.8000 # (ver=1.0, ref=6) - improper_coeff @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n class2 45.0000 -0.0 # (ver=1.0, ref=6) - improper_coeff @improper:o1=,n3o,o1=,o2,o1=,n3o,o1=,o2n class2 aa 0.0 0.0 0.0 128.0000 112.8000 112.8000 # (ver=1.0, ref=6) - improper_coeff @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 13.0421 -0.0 # (ver=1.0, ref=3) - improper_coeff @improper:c3a,c3a,c3a,o2,c3a,c3a,c3a,o2 class2 aa 0.0000 0.0000 0.0000 118.9000 123.4200 123.4200 # (ver=1.0, ref=3) - improper_coeff @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= class2 38.5581 -0.0 # (ver=1.0, ref=6) - improper_coeff @improper:h1,n3o,o1=,o1=,h1,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 115.7000 115.7000 128.0000 # (ver=1.0, ref=6) - improper_coeff @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 4.8912 -0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c3a,c3a,h1,c3a,c3a,c3a,h1 class2 aa 0.0000 0.0000 0.0000 118.9000 117.9400 117.9400 # (ver=1.0, ref=1) - improper_coeff @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 class2 46.9264 0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c4,c3prime,o1=,o2,c4,c3prime,o1=,o2 class2 aa 0.0 0.0 0.0 119.3000 100.3182 118.9855 # (ver=1.0, ref=7) - improper_coeff @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= class2 44.3062 -0.0 # (ver=1.0, ref=6) - improper_coeff @improper:c4,n3o,o1=,o1=,c4,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 117.5000 117.5000 128.0000 # (ver=1.0, ref=6) - improper_coeff @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= class2 36.2612 -0.0 # (ver=1.0, ref=6) - improper_coeff @improper:c3a,n3o,o1=,o1=,c3a,n3o,o1=,o1= class2 aa 0.0 0.0 0.0 117.7000 117.7000 128.0000 # (ver=1.0, ref=6) - improper_coeff @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 7.8153 -0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c3a,c3a,c4,c3a,c3a,c3a,c4 class2 aa 0.0 0.0 0.0 118.9000 120.0500 120.0500 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 7.1794 -0.0 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c3a,c3a,c3a,c3a,c3a,c3a,c3a class2 aa 0.0000 0.0000 0.0000 118.9000 118.9000 118.9000 # (ver=1.0, ref=1) - improper_coeff @improper:c3a,c3prime,c3prime,n3m,X,X,X,X class2 0.0000 -0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,c3prime,c3prime,n3m,X,X,X,X class2 aa 0.0 0.0 0.0 120.0 120.0 120.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,o1=,c3prime,n3m,X,X,X,X class2 30.0000 -0.0 # (ver=1.0, ref=7) - improper_coeff @improper:c3a,o1=,c3prime,n3m,X,X,X,X class2 aa 0.0 0.0 0.0 120.0 120.0 120.0 # (ver=1.0, ref=7) - } # end of improper_coeff commands - - - - - - - # -------------------- Select LAMMPS style(s) ------------------ - - - # LAMMPS supports many different kinds of bonded and non-bonded - # interactions which can be selected at run time. Eventually - # we must inform LAMMPS which of them we will need. We specify - # this in the "In Init" section: - - write_once("In Init") { - units real - atom_style full - bond_style hybrid class2 - # http://lammps.sandia.gov/doc/bond_class2.html - - angle_style hybrid class2 - # http://lammps.sandia.gov/doc/angle_class2.html - - dihedral_style hybrid class2 - # http://lammps.sandia.gov/doc/dihedral_class2.html - - improper_style hybrid class2 - # http://lammps.sandia.gov/doc/improper_class2.html - - pair_style hybrid lj/class2/coul/long 10.0 - # http://lammps.sandia.gov/doc/pair_class2.html - - pair_modify mix sixthpower tail yes - special_bonds lj/coul 0.0 0.0 1.0 dihedral yes - kspace_style pppm 0.0001 - } #end of init parameters - -} # COMPASS - -# -# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED: -# special_bonds lj/coul 0.0 0.0 1.0 dihedral yes -# (See http://lammps.sandia.gov/doc/special_bonds.html for details) - - - - -# ---- templates from the original .frc file used for atom type selection: --- -# -# type: ? -# template: (>*) -# end_type -# -# type: ar -# template: (>Ar) -# end_type -# -# type:c1o -# template: [>C[~O]] -# end_type -# -# type:c2= -# template: [>C[~*][~*]] -# end_type -# -# type:c3' -# template: (>C (~O) (~*) (~*)) -# atom_test:1 -# hybridization:sp2 -# end_test -# atom_test:3 -# allowed_elements: C, H -# end_test -# atom_test:4 -# allowed_elements: O, N -# end_test -# end_type -# -# type:c3a -# template:(>C(~*)(~*)(~*)) -# atom_test:1 -# hybridization: SP2 -# aromaticity:AROMATIC -# end_test -# end_type -# -# type:c3a -# template: [>C(-*)(:*)(:*)] -# atom_test:1 -# hybridization:SP2 -# aromaticity:NON_AROMATIC -# end_test -# end_type -# -# type:c4 -# template: (>C(-*)(-*)(-*)(-*)) -# atom_test:1 -# hybridization:SP3 -# end_test -# end_type -# -# type:c41o -# template: [>C(-O(-*))(-H)(-H)(-H)] -# atom_test:1 -# hybridization:SP3 -# end_test -# atom_test:3 -# allowed_elements:C,H -# end_type -# -# type: c43 -# template: (>C(-H)(-*)(-*)(-*)) -# atom_test:1 -# hybridization:SP3 -# atom_test:3 -# disallowed_elements:H -# atom_test:4 -# disallowed_elements:H -# atom_test:5 -# disallowed_elements:H -# end_test -# end_type -# -# type:c43o -# template: [>C(-O(-H))(-H)(-C)(-C)] -# atom_test:1 -# hybridization:SP3 -# end_test -# end_type -# -# type: c44 -# template: (>C(-*)(-*)(-*)(-*)) -# atom_test:1 -# hybridization:SP3 -# atom_test:2 -# disallowed_elements:H -# atom_test:3 -# disallowed_elements:H -# atom_test:4 -# disallowed_elements:H -# atom_test:5 -# disallowed_elements:H -# end_test -# end_type -# -# type: c4o -# template: (>C(-O)(-*)(-*)(-*)) -# atom_test:1 -# hybridization:SP3 -# end_test -# end_type -# -# type: c4z -# template: (>C(-N(~N(~N)))(-*)(-*)(-*)) -# atom_test:1 -# hybridization:SP3 -# end_test -# end_type -# -# type:h1 -# template: (>H (-*) ) -# atom_test:2 -# allowed_elements:C,Si -# end_test -# end_type -# -# type:h1h -# template: [>H[-H]] -# end_type -# -# type:h1o -# template: (>H(-*)) -# atom_test:2 -# allowed_elements:O,N,F -# end_test -# end_type -# -# type: he -# template: (>He) -# end_type -# -# type: kr -# template: (>Kr) -# end_type -# -# type:n1n -# template: [>N[~N]] -# end_type -# -# type:n1o -# template: [>N[~O]] -# end_type -# -# type:n1z -# template: [>N[~N[~N(~*)]]] -# end_type -# -# type:n2= -# template: [>N(~*)(~*)] -# end_type -# -# type:n2o -# template: [>N[~O][~O]] -# end_type -# -# type:n2t -# template: [>N[~N][~N(~*)]] -# end_type -# -# type:n2z -# template: (>N[~N[~N]](~*)) -# end_type -# -# type: n3m -# template: (>N(-C[=O])(-C)(-C)) -# atom_test:1 -# hybridization:SP3 -# end_test -# end_type -# -# type: n3o -# template: (>N[~O][~O](~O(~C))) -# end_type -# -# type: ne -# template: (>Ne) -# end_type -# -# type:o1= -# template: (>O(~*)) -# atom_test:2 -# allowed_elements:N,S,C -# end_test -# end_type -# -# type:o1=* -# template: [>O[~C[~O]]] -# end_type -# -# type:o12 -# template: [>O[~N[~O](~*)]] -# end_type -# -# type:o1c -# template: [>O[~C]] -# end_type -# -# type:o1n -# template: [>O[~N]] -# end_type -# -# type:o1o -# template: [>O[~O]] -# end_type -# -# type:o2 -# template: [>O(~*)(~*)] -# end_type -# -# type:o2e -# template: [>O(-C)(-C)] -# atom_test: 1 -# aromaticity:NON_AROMATIC -# end_test -# end_type -# -# type:o2h -# template: (>O[-H](~*)) -# end_type -# -# type:o2n -# template: (>O[~N[~O][~O]](~C)) -# end_type -# -# type:o2s -# template: (>O[~C[~O](~*)](~C)) -# end_type -# -# type: o2z -# template: (>O(-Si)(-*) ) -# atom_test: 3 -# allowed_elements: Si, H -# end_test -# end_type -# -# type: p4= -# template: (>P(~*)(~*)(~*)(~*)) -# end_type -# -# type:s1= -# template: [>S[~C[~S]]] -# end_type -# -# type:s2= -# template: [>S[~O][~O]] -# end_type -# -# type: si4 -# template: (>Si(-*)(-*)(-*)(-*)) -# end_type -# -# type: si4c -# template: (>Si(-O)(-*)(-*)(-*)) -# atom_test: 3 -# allowed_elements: O, C -# end_test -# atom_test: 4 -# allowed_elements: O, C -# end_test -# atom_test: 5 -# allowed_elements: O, C -# end_test -# end_type -# -# type: xe -# template: (>Xe) -# end_type -# -# precedence: -# (? -# (ar) -# (c1o) -# (c2=) -# (c3a) (c3') -# (c4 (c43 (c43o)) (c44) (c4o(c41o)) (c4z) ) -# (h1) (h1h) (h1o) -# (he) -# (kr) -# (n1n) (n1o) (n1z) -# (n2= (n2o) (n2t) (n2z) ) -# (n3m) (n3o) -# (ne) -# (o1= (o1=*) (o12) (o1c) (o1n) ) (o1o) -# (o2 (o2e(o2s)) (o2h) (o2n) (o2z) ) -# (p4=) -# (s1=) -# (s2=) -# (si4 (si4c) ) -# (xe) -# ) -# end_precedence -# -# -# - - - - -# ---- references from the original .frc file: ---- - -# reference 1 -# @Author tester -# @Date 01-Jun-09 -# Barebones compass for aromatic & aliphatic hydrocarbons from H. Sun JCP B102, 7361-2 (1998) -# This file created by Materials Design, Inc. (www.materialsdesign.com) Please realize that -# we neither support this version, nor make any warranty as to the correctness of the parameters. -# We have checked the numbers against the literature, but of course there may still be errors, -# including errors of interpretation. Also, the current version of COMPASS may well be different -# that that originally published. -# If you have comments or suggestions, feel free to email Paul Saxe at psaxe (at) materialsdesign.com - -# reference 2 -# @Author tester -# @Date 27-Jun-09 -# Parameters for siloxanes from Sun/Rigby Spectrochim. Acta A53, 1301-23 (1997) (o2 later renamed to o2z) - -# reference 3 -# @Author tester -# @Date 27-Jun-09 -# Parameters for ethers and alcohols from Rigby/Sun/Eichinger Polym. Int. 44, 311-330 (1997) - -# reference 4 -# @Author tester -# @Date 30-Jun-09 -# Parameters for phosphazenes from Comput. Theor. Polym. Sci. 8, 229-246 (1998) - -# reference 5 -# @Author tester -# @Date 28-Jun-09 -# Parameters for He,Ne,Ar,Kr,Xe,H2,O2,N2,NO,CO,CO2,NO2,CS2,SO2 from JPC B104, 4951-7 (2000) - -# reference 6 -# @Author tester -# @Date 29-Jun-09 -# Parameters for nitrate esters from JPC B104, 2477-89 (2000) - -# reference 7 -# @Author tester -# @Date 30-Jun-09 -# Parameters for Ultem (imides) from Polymer 43, 599-607 (2002) - -# reference 8 -# @Author tester -# @Date 30-Jun-09 -# Parameters for 2y and 3y alcohols from Fluid Phase Equilibria 217, 77-87 (2004) - -# reference 9 -# @Author tester -# @Date 30-Jun-09 -# Parameters for aliphatic azides from J. Comput. Chem. 25, 61-71 (2004) - -# reference 10 -# @Author tester -# @Date 02-Jul-09 -# Ref 2 missing -C-Si- params; assume values from Macromols 28, 701-712 (1995) (see pcff) - - - - - -# ---- additional warnings: ---- -# WARNING: Undefined bond length (r0) in angle: h1 o2z si4 -# WARNING: Undefined bond length (r0) in angle: c4 n3 p4= -# WARNING: Undefined bond length (r0) in angle: h1 n3 p4= -# WARNING: Undefined bond length (r0) in angle: c4 o2 p4= -# WARNING: Undefined bond length (r0) in angle: h1 o2 p4= -# WARNING: Undefined bond length (r0) in angle: c3a p4= n3 -# WARNING: Undefined bond length (r0) in angle: h1 p4= n3 -# WARNING: Undefined bond length (r0) in angle: n2= p4= n3 -# WARNING: Undefined bond length (r0) in angle: n3 p4= n3 -# WARNING: Undefined bond length (r0) in angle: n3 p4= o2 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c4 si4 o2z h1 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2z si4 h1 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2z si4 o2z -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= h1 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= n2= -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 n3 p4= o2 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= h1 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= n2= -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: h1 o2 p4= o2 -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X o2 p4= X -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X c3a n2= X -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: X n3 p4= X -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c4 c4 n3o o1= -# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: c3prime n3m c3prime o1 -# WARNING: Undefined rest angle (theta0) in improper: c3a o1= c3prime n3m -# WARNING: Undefined rest angle (theta0) in improper: c3a c3prime c3prime n3m diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt deleted file mode 100644 index 226e0eb297..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/README.txt +++ /dev/null @@ -1,73 +0,0 @@ -This directory contains scripts used for converting AMBER parameter files -into moltemplate (.LT) format. When a newer version of the AMBER parameters -is eventually published, you can use these scripts to convert the new files -again. (Some tinkering may be necessary.) - -The main bash script is a wrapper which simply splits up the parameter (".dat") -file into fragments which (it thinks) correspond to the mass, pair, bond, -angle, dihedral, and improper section of the original .dat file. -(However sometimes it gets this wrong and you have to split it up manually!) - -Then this bash script invokes the relevant python script to convert -each section into .LT format: -amberparm_to_mass.py -amberparm_to_pair.py -amberparm_to_bond.py -amberparm_to_angle.py -amberparm_to_dihedral.py -amberparm_to_improper.py -In case this goes wrong, you may have to run these scripts manaully. - - -Find out how to run this bash script by invoking it without any arguments: - -./amberparm2lt.sh - ------------- IMPORTANT ------------ - -BEFORE YOU RUN THIS SCRIPT, BE SURE TO CHANGE THE ORDER OF THE IMPROPER DIHEDRAL -PARAMETERS SO THAT THE "SPECIFIC" IMPROPER DIHEDRALS APPEAR LAST, AND THE -"GENERIC" IMPROPER DIHEDRALS APPEAR FIRST. - -For example replace these two lines: - -X -o -c -o 1.1 180. 2. JCC,7,(1986),230 -X -X -c -o 10.5 180. 2. JCC,7,(1986),230 - -with these two lines: - -X -X -c -o 10.5 180. 2. JCC,7,(1986),230 -X -o -c -o 1.1 180. 2. JCC,7,(1986),230 - -Why: -This is the order that moltemplate expects: generic first. specific last. -So far only the improper dihedral parameters in the gaff.dat file seem -to violate this order. The bonds, angles and dihedrals seem to obey this, -but check to make sure. - - -There is a discussion of these parameters here: -http://structbio.vanderbilt.edu/archives/amber-archive/2005/3444.php - -excerpt: - -> > In the parm99 file (for example), sometimes the wild-card is used, as it -> > is done in the following example: -> > -> > X -X -C -O 10.5 180. 2. JCC,7,(1986),230 -> > -> > The first example is the specific case while the second one is the generic -> > case. In page # 257 of the AMBER Manual, it is talking about Dihedral -> > Angle, and how these dihedral parameters are used to calculate the -> > energies. I am wondering what the difference between generic and specific -> > case is for improper torsions. -> -> "specific" torsions are search for first, and used if a match is found. If -> no match is found, then a search is made to see if a "generic" (aka wild-card) -> torsion with match. -> ...good luck...dac - -Good luck - --Andrew -2014-4-19 diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh deleted file mode 100755 index 98a77f3b05..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm2lt.sh +++ /dev/null @@ -1,204 +0,0 @@ -#!/bin/sh - -SYNTAX_MSG=$(cat < gaff.lt - - You can also try: -amberparm2lt.sh parm94.dat "AMBERFF94 inherits GAFF" > amberff94.lt - (However, this later usage may not work. - You may need to manually split the .dat file and run these scripts instead: - amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...) - Be sure that all of these .py files are in your PATH as well.) - -EOF -) - -if [ "$#" != "2" ]; then - echo "${SYNTAX_MSG}" >&2 - echo "" >&2 - echo "Error: This script requires two arguments," >&2 - echo " 1) the name of the amber parm file to be converted (eg \"gaff.dat\")" >&2 - echo " 2) the name of the moltemplate object to be created (eg \"GAFF\")" >&2 - echo " (This may include the \"inherits\" keyword and parent classes.)" >&2 - exit 1 -fi - -MOLTEMPLATE_USAGE_MSG=$(cat < /dev/null; then - echo "\nError: \"amberparm_mass_to_lt.py\" not found.\n" >&2 - echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 - exit 2 -fi -if ! which ./amberparm_pair_to_lt.py > /dev/null; then - echo "\nError: \"amberparm_pair_to_lt.py\" not found.\n" >&2 - echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 - exit 2 -fi -if ! which ./amberparm_bond_to_lt.py > /dev/null; then - echo "\nError: \"amberparm_bond_to_lt.py\" not found.\n" >&2 - echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 - exit 2 -fi -if ! which ./amberparm_angle_to_lt.py > /dev/null; then - echo "\nError: \"amberparm_angle_to_lt.py\" not found.\n" >&2 - echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 - exit 2 -fi -if ! which ./amberparm_dihedral_to_lt.py > /dev/null; then - echo "\nError: \"amberparm_dihedral_to_lt.py\" not found.\n" >&2 - echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 - exit 2 -fi -if ! which ./amberparm_improper_to_lt.py > /dev/null; then - echo "\nError: \"amberparm_improper_to_lt.py\" not found. (Update your PATH?)\n" >&2 - echo " (Try running this script from the directory containing amberparm2lt.sh)" >&2 - exit 2 -fi - - -#PARM_FILE='gaff.dat' -PARM_FILE=$1 - -# sections are separated by blank lines -# some sections have comment lines at the beginning - -# The 1st section is the mass (note: skip the first line) -tail -n +2 < "$PARM_FILE" | \ - awk -v n=1 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - > "${PARM_FILE}.mass" - -# The 2nd section has the list of 2-body bond force-field params -awk -v n=2 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - < "$PARM_FILE" \ - | tail -n +2 \ - > "${PARM_FILE}.bond" - -# The 3rd section has the list of 3-body angle force-field params -awk -v n=3 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - < "$PARM_FILE" \ - > "${PARM_FILE}.angle" - -# The 4th section has the list of 4-body dihedral force-field params -awk -v n=4 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - < "$PARM_FILE" \ - > "${PARM_FILE}.dihedral" - -# The 5th section has the list of 4-body improper force-field params -awk -v n=5 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - < "$PARM_FILE" \ - > "${PARM_FILE}.improper" - -# The 6th section has the hbond-parameters (no-longer used. ignore) -awk -v n=6 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - < "$PARM_FILE" \ - > "${PARM_FILE}.hbond" - -# The 7th "section" is just a blank line. (skip that) - -# The 8th section has the list of non-bonded ("pair") force-field parameters -awk -v n=8 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \ - < "$PARM_FILE" \ - | tail -n +2 \ - > "${PARM_FILE}.pair" - - -./amberparm_mass_to_lt.py < "${PARM_FILE}.mass" > "${PARM_FILE}.mass.lt" -./amberparm_pair_to_lt.py < "${PARM_FILE}.pair" > "${PARM_FILE}.pair.lt" -./amberparm_bond_to_lt.py < "${PARM_FILE}.bond" > "${PARM_FILE}.bond.lt" -./amberparm_angle_to_lt.py < "${PARM_FILE}.angle" > "${PARM_FILE}.angle.lt" -./amberparm_dihedral_to_lt.py \ - < "${PARM_FILE}.dihedral" > "${PARM_FILE}.dihedral.lt" -./amberparm_improper_to_lt.py \ - < "${PARM_FILE}.improper" > "${PARM_FILE}.improper.lt" - -echo "$2 {" -echo "" -echo " # ----------------------------------------------------------------------" -#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\"" -echo " # The basic atom nomenclature and conventions are explained here:" -echo " # http://ambermd.org/antechamber/gaff.pdf" -echo " # For reference, the original gaff.dat file and format documentation are here:" -echo " # http://ambermd.org/AmberTools-get.html" -echo " # http://ambermd.org/formats.html#parm.dat" -echo " # ----------------------------------------------------------------------" -echo "" - -cat "$PARM_FILE.mass.lt" \ - "$PARM_FILE.pair.lt" \ - "$PARM_FILE.bond.lt" \ - "$PARM_FILE.angle.lt" \ - "$PARM_FILE.dihedral.lt" \ - "$PARM_FILE.improper.lt" - -AMBER_STYLES_INIT=$(cat < 0: - sys.stdout.write(' # '+comments) - sys.stdout.write('\n') - - -sys.stdout.write(' } # (end of angle_coeffs)\n') -sys.stdout.write('\n') -sys.stdout.write(' write_once("Data Angles By Type") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - atypes = line[:8].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - atype3 = atypes[2].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - at3 = atype3.replace('X','*') - angletype = '@angle:'+atype1+'-'+atype2+'-'+atype3 - - #tokens= line[8:].split() - #keq = tokens[0] - #req = tokens[1] - #comments=' '.join(tokens[2:]) - sys.stdout.write(' '+angletype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+'\n') - -sys.stdout.write(' } # (end of Angles By Type)\n') -sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py deleted file mode 100755 index abfde23dab..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_bond_to_lt.py +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env python - -import sys - -lines_gaff = sys.stdin.readlines() -bond_style_name = 'harmonic' - -sys.stdout.write(' write_once("In Settings") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - tokens= line.split() - atypes = line[:6].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - bondtype = '@bond:'+atype1+'-'+atype2 - - tokens= line[5:].split() - keq = tokens[0] - req = tokens[1] - comments=' '.join(tokens[2:]) - sys.stdout.write(' bond_coeff '+bondtype+' '+bond_style_name+' '+keq+' '+req) - if len(comments.strip()) > 0: - sys.stdout.write(' # '+comments) - sys.stdout.write('\n') - - -sys.stdout.write(' } # (end of bond_coeffs)\n') -sys.stdout.write('\n') -sys.stdout.write(' write_once("Data Bonds By Type") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - atypes = line[:6].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - bondtype = '@bond:'+atype1+'-'+atype2 - - #tokens= line[5:].split() - #keq = tokens[0] - #req = tokens[1] - #comments=' '.join(tokens[2:]) - sys.stdout.write(' '+bondtype+' @atom:'+at1+' @atom:'+at2+'\n') - -sys.stdout.write(' } # (end of Bonds By Type)\n') -sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py deleted file mode 100755 index f4f8e3a645..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_dihedral_to_lt.py +++ /dev/null @@ -1,159 +0,0 @@ -#!/usr/bin/env python - -# SOME UGLY CODE HERE - -import sys - -lines_gaff = sys.stdin.readlines() -dihedral_style_name = 'fourier' -in_dihedral_coeffs = [] - - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - atypes = line[:11].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - atype3 = atypes[2].strip() - atype4 = atypes[3].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - at3 = atype3.replace('X','*') - at4 = atype4.replace('X','*') - dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 - - tokens= line[11:].split() - npth = float(tokens[0]) - Kn = float(tokens[1]) - Kn /= npth # The coeff for each fourier term is Kn/npth - # ...I THINK (?). (Very confusing. See documentation below...) - dn = float(tokens[2]) - n = int(float(tokens[3])) - comments=' '.join(tokens[4:]) - if len(comments.strip()) > 0: - comments = ' # ' + comments - in_dihedral_coeffs.append([dihedraltype, Kn, n, dn, comments]) - #print(Kn, n, dn) - -#for entry in in_dihedral_coeffs: -# print(entry) -#exit() - - -# ---- processing dihedral fourier series ---- -# ---- (negative "n" values means the -# ---- Fourier series is not yet complete. - -i = 0 -while i < len(in_dihedral_coeffs): - type_str = in_dihedral_coeffs[i][0] - Kn = in_dihedral_coeffs[i][1] - n = in_dihedral_coeffs[i][2] - dn = in_dihedral_coeffs[i][3] - - #if (i>0): - # sys.stderr.write('prev_n='+str(in_dihedral_coeffs[i-1][-3])+'\n') - #sys.stderr.write('n='+str(n)+'\n') - - if ((i>0) and (in_dihedral_coeffs[i-1][-3] < 0)): - - #sys.stdout.write('interaction_before_append: '+str(in_dihedral_coeffs[i-1])+'\n') - assert(in_dihedral_coeffs[i-1][0] == in_dihedral_coeffs[i][0]) - in_dihedral_coeffs[i-1][-3] = -in_dihedral_coeffs[i-1][-3] - comments = in_dihedral_coeffs[i-1][-1] - in_dihedral_coeffs[i-1][-1] = Kn - in_dihedral_coeffs[i-1].append(n) - in_dihedral_coeffs[i-1].append(dn) - in_dihedral_coeffs[i-1].append(comments) - #sys.stdout.write('interaction_after_append: '+str(in_dihedral_coeffs[i-1])+'\n') - del in_dihedral_coeffs[i] - - #elif len(in_dihedral_coeffs) < 3: - # del in_dihedral_coeffs[i] - else: - i += 1 - - - -for i in range(0, len(in_dihedral_coeffs)): - type_str = in_dihedral_coeffs[i][0] - params = in_dihedral_coeffs[i][1:] - params = map(str, params) - num_fourier_terms = (len(params)-1)/3 - dihedral_coeff_str = 'dihedral_coeff '+type_str+' '+\ - dihedral_style_name+' '+ \ - str(num_fourier_terms)+' '+ \ - ' '.join(params) - in_dihedral_coeffs[i] = dihedral_coeff_str - -# ---- finished processing dihedral fourier series ---- - - -sys.stdout.write(' write_once(\"In Settings\") {\n ') -sys.stdout.write('\n '.join(in_dihedral_coeffs)+'\n') -sys.stdout.write(' } # (end of dihedral_coeffs)\n') - - - - - -sys.stdout.write('\n') - -sys.stdout.write(' write_once("Data Dihedrals By Type") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - atypes = line[:11].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - atype3 = atypes[2].strip() - atype4 = atypes[3].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - at3 = atype3.replace('X','*') - at4 = atype4.replace('X','*') - dihedraltype = '@dihedral:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 - - sys.stdout.write(' '+dihedraltype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') - -sys.stdout.write(' } # (end of Dihedrals By Type)\n') -sys.stdout.write('\n') - - -""" - - 6 - ***** INPUT FOR DIHEDRAL PARAMETERS ***** - - IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN - - FORMAT(A2,1X,A2,1X,A2,1X,A2,I4,3F15.2) - - IPT, ... The atom symbols for the atoms forming a dihedral - angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then - any dihedrals in the system involving the atoms "JPT" and - and "KPT" are assigned the same parameters. This is - called the general dihedral type and is of the form - "X "-"JPT"-"KPT"-"X ". - - IDIVF The factor by which the torsional barrier is divided. - Consult Weiner, et al., JACS 106:765 (1984) p. 769 for - details. Basically, the actual torsional potential is - - (PK/IDIVF) * (1 + cos(PN*phi - PHASE)) - - PK The barrier height divided by a factor of 2. - - PHASE The phase shift angle in the torsional function. - - The unit is degrees. - - PN The periodicity of the torsional barrier. - NOTE: If PN .lt. 0.0 then the torsional potential - is assumed to have more than one term, and the - values of the rest of the terms are read from the - next cards until a positive PN is encountered. The - negative value of pn is used only for identifying - the existence of the next term and only the - absolute value of PN is kept. - - The input is terminated by a blank card. -""" diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py deleted file mode 100755 index ebf48d4f18..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_improper_to_lt.py +++ /dev/null @@ -1,92 +0,0 @@ -#!/usr/bin/env python - -import sys - -lines_gaff = sys.stdin.readlines() -improper_style_name = 'cvff' - -sys.stdout.write(' write_once("In Settings") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - atypes = line[:11].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - atype3 = atypes[2].strip() - atype4 = atypes[3].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - at3 = atype3.replace('X','*') - at4 = atype4.replace('X','*') - impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 - #sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') - # Oops. This is incorrect. - # In moltemplate, the central atom is the first atom, - # In "gaff.dat", the central atom is the third atom - # http://archive.ambermd.org/201307/0519.html - #impropertype = '@improper:'+atype3+'-'+atype1+'-'+atype2+'-'+atype4 - - tokens= line[11:].split() - Kn = float(tokens[0]) - dn = float(tokens[1]) - n = int(float(tokens[2])) - comments=' '.join(tokens[3:]) - if len(comments.strip()) > 0: - comments = ' # ' + comments - - if (dn < 0.001): - sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' 1 '+str(n)+comments+'\n') - elif (179.999 < abs(dn) < 180.001): - sys.stdout.write(' improper_coeff '+impropertype+' '+improper_style_name+' '+str(Kn)+' -1 '+str(n)+comments+'\n') - else: - sys.stderr.write('Error: Illegal bondImproper parameters:\n' - ' As of 2013-8-03, LAMMPS doens hot have an improper style\n' - ' which can handle impropers with gamma != 0 or 180\n') - exit(-1) - - - -sys.stdout.write(' } # (end of improper_coeffs)\n') -sys.stdout.write('\n') -sys.stdout.write(' write_once("Data Impropers By Type (gaff_imp.py)") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - atypes = line[:11].split('-') - atype1 = atypes[0].strip() - atype2 = atypes[1].strip() - atype3 = atypes[2].strip() - atype4 = atypes[3].strip() - at1 = atype1.replace('X','*') - at2 = atype2.replace('X','*') - at3 = atype3.replace('X','*') - at4 = atype4.replace('X','*') - - impropertype = '@improper:'+atype1+'-'+atype2+'-'+atype3+'-'+atype4 - sys.stdout.write(' '+impropertype+' @atom:'+at1+' @atom:'+at2+' @atom:'+at3+' @atom:'+at4+'\n') - # The improper-angle is the angle between the planes - # defined by at1,at2,at3, and at2,at3,at3 - # and we list the atoms in this order. - # NOTE: In "gaff.dat", the central atom is the third atom (at3) - # so we have to take this into account when matching atom order. - # http://archive.ambermd.org/201307/0519.html - - -sys.stdout.write(' } # (end of Impropers By Type)\n') -sys.stdout.write('\n') - -# NOTE: AMBER documentation is not clear how the improper angle is defined. -# It's not clear if we should be using the dihedral angle between -# planes I-J-K and J-K-L. As of 2014-4, improper_style cvff does this. -# Even if we create improper interactions with the angle defined between -# the wrong planes, at least the minima should be the same -# (0 degrees or 180 degrees). -# So I'm not too worried we are getting this detail wrong long as -# we generate new impropers realizing that the 3rd atom (K) is the -# central atom (according to AMBER conventions). -# -# http://structbio.vanderbilt.edu/archives/amber-archive/2007/0408.php -# -# Currently, we only apply improper torsional angles for atoms -# in a planar conformations. Is it clear? -# Junmei diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py deleted file mode 100755 index 818b1fa303..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_mass_to_lt.py +++ /dev/null @@ -1,19 +0,0 @@ -#!/usr/bin/env python - -import sys - -lines_gaff = sys.stdin.readlines() - -sys.stdout.write(' write_once(\"Data Masses\") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - tokens= line.split() - atype = tokens[0] - mass=tokens[1] - # what is the next number? (the one in tokens[2]?) - comments=' '.join(tokens[3:]) - sys.stdout.write(' @atom:'+atype+' '+mass+' # '+comments+'\n') - -sys.stdout.write(' } # (end of masses)\n') -sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py b/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py deleted file mode 100755 index f24a92b78f..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_AMBER_files_to_LT_files/amberparm_pair_to_lt.py +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env python - -import sys - -lines_gaff = sys.stdin.readlines() - -#pair_style = 'lj/charmm/coul/long' - - # NOTE: Long-range coulombic forces were disabled intentionally. (See below) - # If you want to use long-range electrostatics, uncomment these lines: - # Instead I use hybrid lj/charmm/coul/charmm by default, because - # LAMMPS complains if you attempt to use lj/charmm/coul/long on a - # system if it does not contain any charged particles. - # Currently, moltemplate does not assign atomic charge, - # so this problem occurs frequently. - -#pair_style = 'lj/charmm/coul/charmm' -pair_style = 'lj/charmm/coul/long' - -sys.stdout.write(' write_once(\"In Settings\") {\n') - -for i in range(0, len(lines_gaff)): - line = lines_gaff[i] - tokens= line.split() - atype = tokens[0] - - # UGGHHH - - # OLD CODE: - #sig=tokens[1] - - # CORRECTION #1 - # It looks the number in this part of the file is an atom radii, not a - # diameter. In other words, this number is 0.5*sigma instead of sigma. - # So we multiply it by 2.0. - #sig=str(2.0*float(tokens[1])) - # - # CORRECTION #2 - # It also appears as though they are using this convention for LennardJones - # U(r)=epsilon*((s/r)^12-2*(s/r)^6) instead of 4*eps*((s/r)^12-(s/r)^6) - # ...where "s" is shorthand for "sigma".. - # This means we must ALSO multiply sigma in gaff.dat by 2**(-1.0/6) - # (This change makes the two U(r) formulas equivalent.) - - # I had to figure this out by iterations of trial and error. - # The official AMBER documentation is quite vague about the LJ parameters. - # My apologies to everyone effected by this bug! -Andrew 2014-5-19 - # http://ambermd.org/formats.html#parm.dat - # http://structbio.vanderbilt.edu/archives/amber-archive/2009/5072.php) - - sig=str(float(tokens[1])*2.0*pow(2.0, (-1.0/6.0))) - eps=tokens[2] - comments=' '.join(tokens[3:]) - sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig) - if len(comments.strip()) > 0: - sys.stdout.write(' # '+comments) - sys.stdout.write('\n') - - -sys.stdout.write(' } # (end of pair_coeffs)\n') -sys.stdout.write('\n') diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt deleted file mode 100644 index f110af62ca..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/README.txt +++ /dev/null @@ -1,18 +0,0 @@ -This directory contains a tool "emcprm2lt.py" which -converts ".PRM" files containing lists of force-field parameters -in EMC format into MOLTEMPLATE files in ".LT" format. -(Several force fields including MARTINI and SDK have been - converted into moltemplate format using this tool.) - ----- Credit: ---- - -The "emcprm2lt.py" converter was writtin by David Stelter. -The .PRM files we use were written by Pieter J. in 't Veld. - ----- Citation request: ---- - -Since we borrowed force field parameters from files distributed with EMC, -if you use files generated by "emcprm2lt.py", please also cite the EMC paper: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 - - diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/__init__.py b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py deleted file mode 100755 index 7e97770899..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_EMC_files_to_LT_files/emcprm2lt.py +++ /dev/null @@ -1,613 +0,0 @@ -#!/usr/bin/python - -import os, sys, getopt -import datetime - -__version__ = 0.2 - -#################### UNITS #################### -# Only used with --units flag -econv = 1.0 # Additional Factor for unit conversion if needed (energies) -lconv = 1.0 # Additional Factor for unit conversion if neededa (lengths) -dconv = 1.0 # Additional Factor for unit conversion if neededa (densities) -############################################### - -print('\nEMC 2 LT conversion tool: v%s\n' % __version__) - -def helpme(): - print 'Help for the EMC 2 LT conversion tool\n' - print 'Input takes a list of files in EMC .prm format to be read.' - print 'Additional styles (bond, angle, etc) can be modified via the',\ - 'command line. Any valid LAMMPS style can be used.\n' - print 'Styles include:' - print '--pair-style=' - print '--bond-style=' - print '--angle-style=' - print '--dihedral-style=' - print '--improper-style=\n' - print 'Default styles are lj/cut/coul/long, harmonic, harmonic, harmonic,',\ - 'harmonic \n' - print 'Other commands:' - print '--name= provides basename for output file if desired\n' - print '--units flag for manual units (no parameter needed)\n' - print 'Usage example:' - print 'emcprm2lt.py file1 file2 --bond-style=harmonic --angle-style=harmonic' - print '' - -def Abort(): - print 'Aborting...' - sys.exit() - -def WriteInit(): -# Write generic LAMMPS settings, likely need additional on a per-ff basis - foutput.write(' write_once("In Init") {\n') - foutput.write(' # Warning: This is a very generic "In Init" section, further\n') - foutput.write(' # modification prior to any simulation is extremely likely\n') - foutput.write(' units real\n') - foutput.write(' atom_style full\n') - foutput.write(' bond_style hybrid %s\n' % bstyle) - if angle_flag: - foutput.write(' angle_style hybrid %s\n' % astyle) - if torsion_flag: - foutput.write(' dihedral_style hybrid %s\n' % dstyle) - if improp_flag: - foutput.write(' improper_style hybrid %s\n' % istyle) - foutput.write(' pair_style hybrid %s %f %f\n' % (pstyle, - float(inner[0])*lconv, float(cutoff[0])*lconv)) - if pair14[0] == 'OFF': - foutput.write(' special_bonds lj/coul 0.0 0.0 0.0\n') - else: - print 'Warning: special_bonds needed, add to "In Init" section\n' - foutput.write(' } # end init\n') - -def Units(length_flag, energy_flag, density_flag): -# Check flags for all units, determine what conversions are needed, hard-coded for LAMMPS 'real' - print 'Attempting to auto-convert units... This should always be double-checked',\ - ' especially for unique potential styles' - global lconv; global econv; global dconv - if length_flag: - print 'Warning: length scale does not match LAMMPS real units, attempting conversion to angstroms' - if length[0] == 'NANOMETER': - lconv = 10.0 - print ' nanometer -> angstrom' - elif length[0] == 'MICROMETER': - lconv = 10000.0 - print ' micrometer -> angstrom' - elif length[0] == 'METER': - lconv = 10000000000.0 - print ' meter -> angstrom' - else: - print 'Length units NOT converted' - if energy_flag: - print 'Warning: energy units do not match LAMMPS real units, attempting conversion to kcal/mol' - if energy[0] == 'KJ/MOL': - econv = 0.239006 - print ' kj/mol -> kcal/mol' - elif energy[0] == 'J/MOL': - econv = 0.000239006 - print ' j/mol -> kcal/mol' - elif energy[0] == 'CAL/MOL': - econv = 0.001 - print ' cal/mol -> kcal/mol' - else: - print 'Energy units NOT converted' - if density_flag: - print 'Warning: density units do not match LAMMPS real units, attempting conversion to gram/cm^3' - if density[0] == 'KG/M^3': - dconv = 0.001 - print ' kg/m^3 -> g/cm^3' - else: - print 'Density units NOT converted' - return lconv, econv, dconv - -def ChkPotential(manual_flag, angle_flag, torsion_flag, improp_flag): -# Check type of potential, determine type of unit conversion is necessary - global beconv - if angle_flag: - global aeconv - if torsion_flag: - global deconv - if improp_flag: - global ieconv - if manual_flag == False: - # Chk bond potential - if bstyle == '' or bstyle == 'harmonic': - beconv = econv / (2*pow(lconv,2)) - else: - print 'Cannot find bond potential type, use manual units' - Abort() - if angle_flag: - if astyle == '' or astyle == 'harmonic': - aeconv = econv - elif astyle == 'cosine/squared': - aeconv = econv / 2 - elif astyle == 'sdk': - aeconv = econv - else: - print 'Cannot find angle potential type, use manual units' - Abort() - # torsion and improper not implemented fully - elif torsion_flag: - if dstyle == '' or dstyle == 'harmonic': - deconv = econv - else: - print 'Cannot find torsion potential type, use manual units' - Abort() - elif improp_flag: - if istyle == '' or istyle == 'harmonic': - ieconv = econv - else: - print 'Cannot find improper potential type, use manual units' - Abort() - else: - # Modify as needed - print 'Warning: Manual units used, set potential conversion units in script' - beconv = 1 - if angle_flag: - aeconv = 1 - if torsion_flag: - deconv = 1 - if improp_flag: - ieconv = 1 - - -### Parse input ### -if len(sys.argv) == 1: - helpme() - sys.exit() -manual_units = False # Turned on via command line -args = list(sys.argv[1:]) -myopts, args = getopt.gnu_getopt(args, 'fh', ['pair-style=', 'bond-style=', 'angle-style=', - 'dihedral-style=', 'improper-style=', 'name=', 'units']) -filenames = list(args) -pstyle = ''; bstyle = ''; astyle = ''; dstyle = ''; istyle = '' -name = '' -for opt, arg in myopts: - if opt in ('-f'): - filenames = arg - elif opt in ('--pair-style'): - pstyle = arg - elif opt in ('--bond-style'): - bstyle = arg - elif opt in ('--angle-style'): - astyle = arg - elif opt in ('--dihedral-style'): - dstyle = arg - elif opt in ('--improper-style'): - istyle = arg - elif opt in ('--name'): - name = arg - elif opt in ('--units'): - manual_units = True - print 'Manual units enabled, modify python script accordingly' - elif opt in ('-h', '--help'): - helpme() - sys.exit() - -### Check input filenames, make sure they exist ### -print 'Converting: ' -for i in range(len(filenames)): - if os.path.isfile(filenames[i]): - print '', filenames[i] - else: - print 'invalid filename:', filenames[i] - Abort() -print 'from EMC .prm to moltemplate .lt format\n' - -### Open all files ### -f = [open(fname, 'r') for fname in filenames] - -### All these settings from DEFINE should be list of fixed size ### -ffname = [[] for i in range(len(f))] -fftype = [[] for i in range(len(f))] -version = [[] for i in range(len(f))] -created1 = [[] for i in range(len(f))] -created2 = [[] for i in range(len(f))] -length = [[] for i in range(len(f))] -energy = [[] for i in range(len(f))] -density = [[] for i in range(len(f))] -mix = [[] for i in range(len(f))] -nbonded = [[] for i in range(len(f))] -inner = [[] for i in range(len(f))] -cutoff = [[] for i in range(len(f))] -pair14 = [[] for i in range(len(f))] -angle_def = [[] for i in range(len(f))] -torsion_def = [[] for i in range(len(f))] -improp_def = [[] for i in range(len(f))] # not all prm have this - -### Parse DEFINE section, save info for each file ### -for i in range(len(f)): - grab = False - for line in f[i]: - if line.strip() == 'ITEM DEFINE': - grab = True - elif line.strip() == 'ITEM END': - grab = False - elif grab: - if line.startswith('FFNAME'): - ffname[i] = line.split()[1].strip() - if line.startswith('FFTYPE'): - fftype[i] = line.split()[1].strip() - if line.startswith('VERSION'): - version[i] = line.split()[1].strip() - if line.startswith('CREATED'): - created1[i] = line.split()[1].strip() - created2[i] = line.split()[2].strip() - if line.startswith('LENGTH'): - length[i] = line.split()[1].strip() - if line.startswith('ENERGY'): - energy[i] = line.split()[1].strip() - if line.startswith('DENSITY'): - density[i] = line.split()[1].strip() - if line.startswith('MIX'): - mix[i] = line.split()[1].strip() - if line.startswith('NBONDED'): - nbonded[i] = line.split()[1].strip() - if line.startswith('INNER'): - inner[i] = line.split()[1].strip() - if line.startswith('CUTOFF'): - cutoff[i] = line.split()[1].strip() - if line.startswith('PAIR14'): - pair14[i] = line.split()[1].strip() - if line.startswith('ANGLE'): - angle_def[i] = line.split()[1].strip() - if line.startswith('TORSION'): - torsion_def[i] = line.split()[1].strip() - if line.startswith('IMPROP'): - improp_def[i] = line.split()[1].strip() - -### Sanity Checks ### -for i in range(len(f)): - for j in range(len(f)): - if ffname[j] != ffname[i]: - print 'force field files do not match' - Abort() - if length[j] != length[i]: - print 'units not identical between files' - Abort() - if energy[j] != energy[i]: - print 'units not identical between files' - Abort() - if density[j] != density[i]: - print 'units not identical between files' - Abort() - if inner[j] != inner[i]: - print 'inner cutoff not identical between files' - Abort() - if cutoff[j] != cutoff[i]: - print 'cutoff not identical between files' - Abort() - if pair14[j] != pair14[i]: - print '1-4 pair interaction not consistent between files' - Abort() - -### Check if sections exist in PRM file ### -angle_flag = False; torsion_flag = False; improp_flag = False -for i in range(len(f)): - if angle_def[i] == 'WARN': - angle_flag = True - if torsion_def[i] == 'WARN': - torsion_flag = True - if improp_def[i] == 'WARN': - improp_flag = True - -### Check which units to use, trip convert flags ### -length_flag = False; energy_flag = False; density_flag = False -if length[0] != 'ANGSTROM': - length_flag = True -if energy[0] != 'KCAL/MOL': - energy_flag = True -if density[0] != 'G/CC': - density_flag = True -if manual_units == True: - length_flag = False - energy_flag = False - density_flag = False -Units(length_flag, energy_flag, density_flag) - -### Read Whole File, save to lists ### -# Non-crucial sections include -# BONDS, ANGLE, TORSION, IMPROP, NONBOND -# Read all sections every time, only output sections when flags tripped -f = [open(fname, 'r') for fname in filenames] -masses = []; nonbond = []; bond = []; angle = []; torsion = []; improp = [] -equiv = [] -for i in range(len(f)): - MASS = False - NONBOND = False - BOND = False - ANGLE = False - TORSION = False - IMPROP = False - EQUIV = False - for line in f[i]: - if line.strip() == 'ITEM MASS': - MASS = True - elif line.strip() == 'ITEM END': - MASS = False - elif MASS: - if not line.startswith('#'): - if not line.startswith('\n'): - masses.append(line.strip().split()) - if line.strip() == 'ITEM NONBOND': - NONBOND = True - elif line.strip() == 'ITEM END': - NONBOND = False - elif NONBOND: - if not line.startswith('#'): - if not line.startswith('\n'): - nonbond.append(line.strip().split()) - if line.strip() == 'ITEM BOND': - BOND = True - elif line.strip() == 'ITEM END': - BOND = False - elif BOND: - if not line.startswith('#'): - if not line.startswith('\n'): - bond.append(line.strip().split()) - if line.strip() == 'ITEM ANGLE': - ANGLE = True - elif line.strip() == 'ITEM END': - ANGLE = False - elif ANGLE: - if not line.startswith('#'): - if not line.startswith('\n'): - angle.append(line.strip().split()) - if line.strip() == 'ITEM TORSION': - TORSION = True - elif line.strip() == 'ITEM END': - TORSION = False - elif TORSION: - if not line.startswith('#'): - if not line.startswith('\n'): - torsion.append(line.strip().split()) - if line.strip() == 'ITEM IMPROP': - IMPROP = True - elif line.strip() == 'ITEM END': - IMPROP = False - elif IMPROP: - if not line.startswith('#'): - if not line.startswith('\n'): - improp.append(line.strip().split()) - if line.strip() == 'ITEM EQUIVALENCE': - EQUIV = True - elif line.strip() == 'ITEM END': - EQUIV = False - elif EQUIV: - if not line.startswith('#'): - if not line.startswith('\n'): - equiv.append(line.strip().split()) -### Close prm files ### -for fname in f: - fname.close() - -### Sanity checks before writing LT files ### -# Check Equiv -for i in range(len(equiv)): - for j in range(len(equiv)): - if (equiv[i][0] == equiv[j][0]) and (equiv[i] != equiv[j]): - print 'Error: Identical atom types with different equivalences' - Abort() -# Check Masses -for i in range(len(masses)): - for j in range(len(masses)): - if (masses[i][0] == masses[j][0]) and (masses[i][1] != masses[j][1]): - print 'Error: Identical types with different mass' - Abort() -# Check Nonbond -for i in range(len(nonbond)): - for j in range(len(nonbond)): - if (nonbond[i][0] == nonbond[j][0]) and (nonbond[i][1] == nonbond[j][1]) and ((nonbond[i][2] != nonbond[j][2]) or (nonbond[i][3] != nonbond[j][3])): - print nonbond[i], nonbond[j] - print 'Error: Identical types with different pair-interactions' - Abort() - -### Remove double equivalences ### -for i in range(len(equiv)): - once = True - for j in range(len(equiv)): - if (equiv[i][0] == equiv[j][0]) and once: - once = False - elif (equiv[i][0] == equiv[j][0]): - equiv[j][1] = None - equiv[j][2] = 'duplicate' - if len(equiv[i]) != 6: - print 'Warning: Incorrect equivalence formatting for type %s' % equiv[i][0],\ - 'skipping type, topology may not be complete' - equiv[i][1] = None - equiv[i][2] = 'invalid_format' - -### Check Potential Styles and Set Units ### -ChkPotential(manual_units, angle_flag, torsion_flag, improp_flag) - -### Set output LT file ### -fname = 'ff_output.lt' -if name == '': - fname = ffname[0] + '.lt' -else: - fname = name + '.lt' -foutput = open(fname, 'w') - -### Output to LT format ### -foutput.write('# Autogenerated by EMC 2 LT tool v%s on %s\n' % (__version__, str(datetime.date.today()))) -foutput.write('#\n# ') -for i in range(len(sys.argv)): - foutput.write('%s ' % sys.argv[i]) -foutput.write('\n') -foutput.write('#\n') -foutput.write('# Adapted from EMC by Pieter J. in \'t Veld\n') -foutput.write('# Originally written as, FFNAME:%s STYLE:%s VERSION:%s on %s %s\n' % - (ffname[0], fftype[0], version[0], created1[0], created2[0])) -foutput.write('\n') -foutput.write('%s {\n' % ffname[0]) - -# Charges not necessary? emc file assign charges in smiles, which would -# be in the per-molecule files created by moltemplate user... not here - -### Mass Info ### -foutput.write(' write_once("Data Masses") {\n') -for i in range(len(masses)): - if equiv[i][1] != None: - foutput.write(' @atom:%s %f # %s\n' % - (masses[i][0], float(masses[i][1]), masses[i][0])) -foutput.write(' } # end of atom masses\n\n') - -### Equiv Info ### -# Write Equivalence -foutput.write(' # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup -----\n') -for i in range(len(equiv)): - if equiv[i][1] != None: - foutput.write(' replace{ @atom:%s @atom:%s_b%s_a%s_d%s_i%s}\n' % - (equiv[i][0], equiv[i][0], equiv[i][2], equiv[i][3], equiv[i][4], equiv[i][5])) -foutput.write(' # END EQUIVALENCE\n\n') -# Sanity check equivalences vs masses -for i in range(len(equiv)): - check = None - for j in range(len(masses)): - if equiv[i][0] == masses[j][0]: - check = 'success' - if check == None: - print equiv[i], masses[j] - print 'Atom defined in Equivlances, but not found in Masses' - Abort() -# Sanity check masses vs equivalences -for i in range(len(masses)): - check = None - for j in range(len(masses)): - if masses[i][0] == equiv[j][0]: - check = 'success' - if check == None: - print masses[i], equiv[j] - print 'Atom defined in Masses, but not found in Equivlances' - Abort() - -### Nonbonded Info ### -if pstyle == '': - print 'Warning: no non-bonded potential provided, assuming lj/cut/coul/long' - pstyle = 'lj/cut/coul/long' -foutput.write(' write_once("In Settings") {\n') -foutput.write(' # ----- Non-Bonded interactions -----\n') -# Add new types from equivalence -for i in range(len(equiv)): - once = True - for j in range(len(nonbond)): - # Get terms for new types - if (equiv[i][0] != equiv[i][1]) and (equiv[i][1] == nonbond[j][0]): - if not equiv[i][1] == nonbond[j][1]: - line = '%s %s %s %s' % (equiv[i][0], nonbond[j][1], nonbond[j][2], nonbond[j][3]) - nonbond.append(line.split()) - if once: - once = False - line = '%s %s %s %s' % (equiv[i][0], equiv[i][0], nonbond[j][2], nonbond[j][3]) - nonbond.append(line.split()) - if (equiv[i][0] != equiv[i][1]) and (equiv[i][1] == nonbond[j][1]): - line = '%s %s %s %s' % (equiv[i][0], nonbond[j][0], nonbond[j][2], nonbond[j][3]) - if line.split() != nonbond[-1]: - nonbond.append(line.split()) -for i in range(len(nonbond)): - atom1name = None - atom2name = None - stylename = pstyle - if pstyle == 'lj/sdk' or pstyle == 'lj/sdk/coul/long': - stylename = 'lj%s_%s' % (nonbond[i][4], nonbond[i][5]) - # Cross Terms + Diagonal, normal - for j in range(len(equiv)): - if nonbond[i][0] == equiv[j][0]: - atom1name = '%s_b%s_a%s_d%s_i%s' % (nonbond[i][0], equiv[j][2], equiv[j][3], equiv[j][4], equiv[j][5]) - if nonbond[i][1] == equiv[j][0]: - atom2name = '%s_b%s_a%s_d%s_i%s' % (nonbond[i][1], equiv[j][2], equiv[j][3], equiv[j][4], equiv[j][5]) - if atom1name == None or atom2name == None: - print atom1name, atom2name, nonbond[i] - print 'Error: Atom in Nonbonded Pairs not found in Equivalences' - Abort() - foutput.write(' pair_coeff @atom:%s @atom:%s %s %f %f' % - (atom1name, atom2name, stylename, float(nonbond[i][3])*econv, float(nonbond[i][2])*lconv)) - foutput.write(' # %s-%s\n' % (nonbond[i][0], nonbond[i][1])) -foutput.write(' } # end of nonbonded parameters\n\n') - -### Bond Info ### -if bstyle == '': - print 'Warning: no bond potential provided, assuming harmonic' - bstyle == 'harmonic' -foutput.write(' write_once("In Settings") {\n') -foutput.write(' # ----- Bonds -----\n') -for i in range(len(bond)): - foutput.write(' bond_coeff @bond:%s-%s %s %f %f' % - (bond[i][0], bond[i][1], bstyle, float(bond[i][2])*beconv, float(bond[i][3])*lconv)) - foutput.write(' # %s-%s\n' % (bond[i][0], bond[i][1])) -foutput.write(' }\n\n') -foutput.write(' write_once("Data Bonds By Type") {\n') -for i in range(len(bond)): - foutput.write(' @bond:%s-%s @atom:*_b%s_a*_d*_i* @atom:*_b%s_a*_d*_i*\n' % - (bond[i][0], bond[i][1], bond[i][0], bond[i][1])) -foutput.write(' } # end of bonds\n\n') - -### Angle Info ### -if angle_flag: - if astyle == '': - print 'Warning: no angle potential provided, assuming harmonic' - astyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Angles -----\n') - for i in range(len(angle)): - if (len(angle[i]) > 5): # Check if extra data in angle array - foutput.write(' angle_coeff @angle:%s-%s-%s %s %f %f' % - (angle[i][0], angle[i][1], angle[i][2], str(angle[i][5]), float(angle[i][3])*aeconv, float(angle[i][4]))) - foutput.write(' # %s-%s-%s\n' % (angle[i][0], angle[i][1], angle[i][2])) - else: - foutput.write(' angle_coeff @angle:%s-%s-%s %s %f %f' % - (angle[i][0], angle[i][1], angle[i][2], astyle, float(angle[i][3])*aeconv, float(angle[i][4]))) - foutput.write(' # %s-%s-%s\n' % (angle[i][0], angle[i][1], angle[i][2])) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Angles By Type") {\n') - for i in range(len(angle)): - foutput.write(' @angle:%s-%s-%s @atom:*_b*_a%s_d*_i* @atom:*_b*_a%s_d*_i* @atom:*_b*_a%s_d*_i*\n' % - (angle[i][0], angle[i][1], angle[i][2], angle[i][0], angle[i][1], angle[i][2])) - foutput.write(' } # end of angles\n\n') - -### Torsion/Dihedral Info ###a -# Incomplete -if torsion_flag: - if dstyle == '': - print 'Warning: no dihedral/torsion potential provided, assuming harmonic' - dstyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Dihedrals -----\n') - for i in range(len(torsion)): - foutput.write(' dihedral_coeff @dihedral:%s-%s-%s-%s %s %f %f %f %f\n' % - (torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3], dstyle, float(torsion[i][4])*deconv, float(torsion[i][5]), float(torsion[i][6]))) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Dihedrals By Type") {\n') - for i in range(len(torsion)): - foutput.write(' @dihedral:%s-%s-%s-%s @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i* @atom:*_b*_a*_d%s_i*' % - (torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3], torsion[i][0], torsion[i][1], torsion[i][2], torsion[i][3])) - foutput.write(' } # end of dihedrals\n\n') - -### Improper Info ### -# Incomplete -ieconv = econv # improper coeff conversion -if improp_flag: - if istyle == '': - print 'Warning: no improper potential provided, assuming harmonic' - istyle == 'harmonic' - foutput.write(' write_once("In Settings") {\n') - foutput.write(' # ----- Impropers -----\n') - # As discussed, a check for convention of impropers is probably needed here - for i in range(len(improp)): - foutput.write(' improper_coeff @improper:%s-%s-%s-%s %s %f %f\n' % - (improp[i][0], improp[i][1], improp[i][2], improp[i][3], istyle, - float(improp[i][4]), float(improp[i][5]))) - foutput.write(' }\n\n') - foutput.write(' write_once("Data Impropers By Type") {\n') - for i in range(len(improp)): - foutput.write(' @improper:%s-%s-%s-%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s @atom:*_b*_a*_d*_i%s' % - (improp[i][0], improp[i][1], improp[i][2], improp[i][3], improp[i][0], improp[i][1], improp[i][2], improp[i][3])) - foutput.write(' } # end of impropers\n\n') - -### Initialization Info ### -print 'Warning: Attempting to write generic "In Init" section,',\ - 'further modification after this script is extremely likely' -WriteInit() - -foutput.write('} # %s\n' % ffname[0]) -sys.exit() diff --git a/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py deleted file mode 100755 index 7c4c6abc73..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_MSI_files_to_LT_files/msifrc2lt.py +++ /dev/null @@ -1,4536 +0,0 @@ -#! /usr/bin/env python -# Author: Andrew Jewett (jewett.aij at g mail) -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2017, California Institute of Technology -# All rights reserved. - -""" -This standalone python script can be used to convert force-field data -in FRC files (a.k.a. "MSI", "Accelrys", "BIOSYM", "DISCOVERY" files) -...into MOLTEMPLATE/LAMMPS compatible format (.LT files). - -Once converted into moltemplate (.LT) format, users can use these files with -MOLTEMPLATE to prepare LAMMPS simulations of molecules using these force fields -(without needing any additional software such as msi2lmp). - -There are several examples of MSI files in the "tools/msi2lmp/frc_files/" -directory which is distributed with LAMMPS. - -Limitations: - -Currently (2017-10) this script ignores the "template" information in .FRC files. -When defining a new type of molecule, the user must carefully choose the -complete atom type for each type of atom in the molecule. In other words, -MOLTEMPLATE will not attempt to determine (from local context) whether -a carbon atom somewhere in your molecule happens to be an SP3 carbon -(ie. "c4" in the COMPASS force-field), or an aromatic carbon ("c3a"), -or something else (for example). This information is typically contained -in the "templates" section of these files, and this script currently ignores -that information. Instead, the user must determine which type of carbon atom -it is manually, for all of the carbon atoms in that kind of molecule. -(This only needs to be done once per molecule definition. - Once a type of molecule is defined, it can be copied indefinitely.) - -""" - - -__author__ = 'Andrew Jewett' -__version__ = '0.2.1' -__date__ = '2017-10-15' - - -import sys -import os - -from collections import defaultdict, OrderedDict -from operator import itemgetter - - -g_program_name = __file__.split('/')[-1] - - -doc_msg = \ - "Typical Usage:\n\n" + \ - " " + g_program_name + " -name COMPASS < compass_published.frc > compass.lt\n\n" + \ - " where \"compass_published.frc\" is a force-field file in MSI format.\n" + \ - " \"comass.lt\" is the corresponding file converted to moltemplate format\n" + \ - " and \"COMPASS\" is the name that future moltemplate users will use to refer\n" + \ - " to this force-field (optional).\n" + \ - "Optional Arguments\n" + \ - " -name FORCEFIELDNAME # Give the force-field a name\n" + \ - " -file FILE_NAME # Read force field parameters from a file\n" + \ - " -url URL # Read force field parameters from a file on the web\n" + \ - " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + \ - " Sometimes an FRC file contains multiple versions. In that case,\n"+\ - " you can select between them using these optional arguments:\n"+\ - " -pair-style \"PAIRSTYLE ARGS\" # LAMMPS pair style and cutoff arg(s)\n" + \ - " -bond-style BONDSTYLE # desired LAMMPS bond style (default: \"class2\")\n" + \ - " -angle-style ANGLESTYLE # desired LAMMPS angle style\n" + \ - " -dihedral-style DIHEDRALSTYLE # desired LAMMPS dihedral style\n" + \ - " -improper-style IMPROPERSTYLE # desired LAMMPS improper style\n" + \ - " -hbond-style \"HBONDTYLE ARGS\" # LAMMPS hydrogen-bond style and args\n" - - -# " -auto # Consider auto_equivalences in the .frc file \n"+\ - - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - (Raising this exception implies that the caller has provided - a faulty input file or argument.) - - """ - - def __init__(self, err_msg): - self.err_msg = err_msg - - def __str__(self): - return self.err_msg - - def __repr__(self): - return str(self) - -# It seems like there are no ordered sets in python, (a set that remembers the -# order that you added elements), so I built one by wrapping OrderedDict() - -class MyOrderedSet(object): - def __init__(self, l): - self.d = OrderedDict() - for x in l: - self.d[x] = True - def __add__(self, x): - self.d[x] = True - def __delitem__(self, x): - del self.d[x] - def __contains__(self, x): - return x in self.d - def __iter__(self): - self.p = iter(self.d) - return self - def __next__(self): - return next(self.p) - # the following wrappers might be necessary for python2/3 compatibility: - def add(self, x): - self.__add__(x) - def del_item(self, x): - self.__del_item__(x) - def iter(self): - return self.__iter__() - def next(self): - return self.__next__() - # no need to bother with set unions and intersections - - -def NSplitQuotedString(string, - nmax, - quotes, - delimiters=' \t\r\f\n', - escape='\\', - comment_char='#'): - """ - Split a quoted & commented string into at most "nmax" tokens (if nmax>0), - where each token is separated by one or more delimeter characters - in the origingal string, and quoted substrings are not split, - This function returns a list of strings. Once the string is split Nmax - times, any remaining text will be appended to the last entry of the list. - Comments are stripped from the string before splitting begins. - """ - tokens = [] - token = '' - reading_token = True - escaped_state = False - quote_state = None - for c in string: - - if (c in comment_char) and (not escaped_state) and (quote_state == None): - if len(token) > 0: - tokens.append(token) - return tokens - - elif (c in delimiters) and (not escaped_state) and (quote_state == None): - if reading_token: - if (nmax == 0) or (len(tokens) < nmax-1): - if len(token) > 0: - tokens.append(token) - token = '' - reading_token = False - else: - token += c - elif c in escape: - if escaped_state: - token += c - reading_token = True - escaped_state = False - else: - escaped_state = True - # and leave c (the '\' character) out of token - elif (c in quotes) and (not escaped_state): - if (quote_state != None): - if (c == quote_state): - quote_state = None - else: - quote_state = c - token += c - reading_token = True - else: - if (c == 'n') and (escaped_state == True): - c = '\n' - elif (c == 't') and (escaped_state == True): - c = '\t' - elif (c == 'r') and (escaped_state == True): - c = '\r' - elif (c == 'f') and (escaped_state == True): - c = '\f' - token += c - reading_token = True - escaped_state = False - - if len(token) > 0: - tokens.append(token) - return tokens - - - - -def SplitQuotedString(string, - quotes='\'\"', - delimiters=' \t\r\f\n', - escape='\\', - comment_char='#'): - - return NSplitQuotedString(string, - 0, - quotes, - delimiters, - escape, - comment_char) - - - - -def RemoveOuterQuotes(text, quotes='\"\''): - if ((len(text) >= 2) and (text[0] in quotes) and (text[-1] == text[0])): - return text[1:-1] - else: - return text - - -def SortByEnds(l_orig): - """ - Convenient to have a one-line macro for swapping list order if first>last - """ - l = [x for x in l_orig] - if l[0] > l[-1]: - l.reverse() - return l - - - -#def Repl(tokens, a, b): -# return [(b if x==a else x) for x in tokens] - -def DecodeAName(s): - if s.find('auto') == 0: - s = s[4:] - if s == 'X': # special case: deal with strings like 'X' - return '*' - return s - - -def EncodeAName(s): - """ - Handle * characters in MSI atom names - """ - - if s.find('auto') == 0: - s = s[4:] - # If the atom name begins with *, then it is a wildcard - if s[:1] == '*': # special case: deal with strings like *7 - return 'X' # These have special meaning. Throw away the integer. - # (and replace the * with an X) - - # If the * character occurs later on in the atom name, then it is actually - # part of the atom's name. (MSI force fields use many strange characters in - # atom names.) Here we change the * to \* to prevent the atom name from - # being interpreted as a wild card in the rules for generating bonds, - # angles, dihedrals, and impropers. - - return s.replace('*','star').replace('\'','prime').replace('"','dblpr') - # '*' is reserved for wildcards in moltemplate - # 'star' is a string that is unused in any - # of the force fields I have seen so far. - # Similarly quote characters (' and ") confuse - # moltemplate, so we replace them with something else. - - # The following approach doesn't work (mistakenly thinks '\*' = wildcard) - #return s.replace('*','\\*') # this prevents ttree_lex.MatchesAll() - # # from interpreting the '*' as a wildcard - - -def DetermineAutoPriority(anames): - """ - Given a list of atom names (including wildcards), generate a number - indicating the priority the interaction between these atoms should have: - Scan through list of strings anames, looking for patterns of the form - *n - where n is an integer. - Make sure this pattern only appears once and return n to the caller. - (These patterns are used by MSI software when using "auto_equivalences" - to look up force field parameters for bonded interactions. - The higher the integer, the lower the priority. - For details, see "Forcefield based simulations" PDF, Cerius2, p 87) - Ordinary wildcards ('*' characters not followed by integers) have the - lowest possible priority. (Each time a '*' string appears in the - list of arguments, the priority value increases by HUGE_VAL.) - """ - - # This is terrible code. - - n = -1.0 - num_blank_wildcards = 0 - for a in anames: - # Sometimes the first atom name contains the prefix 'auto'. Remove this - if a.find('auto') == 0: - a = a[4:] - if a[:1] == '*': - #if a[:1] == 'X': - if len(a) > 1: - if n == -1.0: - n = float(a[1:]) - elif n != float(a[1:]): - # Make sure if present, the number appears only once in the list of atom names - raise InputError('Error: Inconsistent priority integers in the following interaction:\n' - ' ' + ' '.join(anames) + '\n') - else: - num_blank_wildcards += 1 - - # A "blank" wildcard (not followed by a number eg '*') has a very low priority - # Give it a high number, because this corresponds to low priority. Very confusing - # For details, see "Forcefield based simulations" PDF, Cerius2, p 87) - HUGE_VAL = 1.0e5 - return n + num_blank_wildcards*HUGE_VAL - - - - -#def DeterminePriority(is_auto, -# anames, -# version): -# """ -# Determine the priority of an interaction from -# 1) whether or not it is an "auto" interaction -# 2) what is the force-field "version" (a number) -# 3) what are the names of the atoms (for auto_equivalences only, -# some atom "names" are wildcards followed by integers. use the integer) -# """ -# -# if is_auto: -# n = DetermineAutoPriority(anames) -# return (is_auto, n) -# else: -# return (is_auto, -version) - - -def DetermineNumericPriority(is_auto, - anames, - version): - """ - Determine the priority of an interaction from - 2) what is the force-field "version" (a number) - 3) what are the names of the atoms (for auto_equivalences only, - some atom "names" are wildcards followed by integers. use the integer) - """ - - if is_auto: - n = DetermineAutoPriority(anames) - return n # low priority integers <--> high priority () - else: - return -float(version) # later version numbers <--> higher priority - # (multiplying by -1 compensates for this) - # Note: this means auto interactions always have - # lower priority because their numeric priority - # will be a positive number. Otherwise the - # numeric priority will be a negative number - # (...corresponding to a higher priority - # I don't like this complicated priority system - # but I didn't invent it. It's not my fault.) - - -def IsAutoAtom(atom_name): - return atom_name[-1:] == '_' - - -#def PossibleAutoAtom(atom_name): -# """ Auto-equivalences are alternate atom names used in "auto" -# interactions. (These are low priority interactions used as a -# last resort when the interaction parameters could not be located -# by any other means). Each atom is given an alternate name which -# is used in this kind of interaction. These names typically end -# '_' followed by an optional integer. Example "auto" atom names -# are 'c3m_' and 'c=_3'. Unfortunately some ordinary atom names -# also end in an integer preceeded by a _ character. But they -# never end in a '_' character. Here we check for both.""" -# -# i = atom_name.rfind('_') -# if (i == -1) or str.isdigit(atom_name[i:]): -# return True -# return False - - - -def IsAutoInteraction(interaction_name): - return interaction_name.find('auto') == 0 - - -#def IsAutoInteraction(interaction_name): -# anames = ExtractAtomNames(interaction_name) -# for a in anames: -# if IsAutoAtom(a): -# return True -# if not PossibleAutoAtom(a): -# return False -# return True - - - - -def EncodeInteractionName(anames, - is_auto = False): - if is_auto == False: - is_auto = False - # Is the line containing anames from an "_auto" section of - # the FRC file? (I am trying to infer this from whether or - # not any of the atom names are followed by the '_' character.) - for s in anames: - if IsAutoAtom(s): - is_auto = True - if is_auto: - priority = DetermineAutoPriority(anames) - # (If an atom name is a wildcard '*' followed by - # an integer, DetermineAutoPriority() will return - # that integer. Otherwise it will return '') - #return str(priority)+'auto'+','.join(anames) - return 'auto'+','.join(anames) - - return ','.join(anames) - - - -def ExtractANames(interaction_name): - if IsAutoInteraction(interaction_name): - return interaction_name[4:].split(',') - return interaction_name.split(',') - - - -def OOPImproperNameSort(aorig): - assert(len(aorig) == 4) - atom_names = map(EncodeAName, aorig) - if atom_names[0] < atom_names[3]: - return (atom_names, [0,1,2,3]) - else: - return ([atom_names[3], - atom_names[1], - atom_names[2], - atom_names[0]], - [3,1,2,0]) - - -def Class2ImproperNameSort(aorig): - """ - This function takes a list of 4 strings as an argument representing 4 atom - names for atoms participating in an "improper" ("wilson-out-of-plane") - interaction. This function assumes the second atom is the central ("hub") - atom in the interaction, and it sorts the remaining atoms names. - This function also replaces any occurence of \"*\" with \"X\". - The new list is returned to the caller, along with the permutation. - """ - assert(len(aorig) == 4) - atom_names = [a for a in map(EncodeAName, aorig)] - z = [x for x in zip([atom_names[0], atom_names[2], atom_names[3]], - [0,2,3])] - z.sort() - l = [z[0][0], atom_names[1], z[1][0], z[2][0]] - p = [z[0][1], 1, z[1][1], z[2][1]] - return (l, p) - - - -def Parity(p): - """ compute the parity of a permutation - (credit: "Weeble") - """ - permutation = list(p) - length = len(permutation) - elements_seen = [False] * length - cycles = 0 - for index, already_seen in enumerate(elements_seen): - if already_seen: - continue - cycles += 1 - current = index - while not elements_seen[current]: - elements_seen[current] = True - current = permutation[current] - return (length-cycles) % 2 == 0 - - - -def ImCrossTermID(atom_names): - """ - # From a list of 4 atom names, corresponding two a pair - # of angles between atoms# 3,2,1 and 3,2,4, - # and replaces the list of atoms with a canonical tuple - # which eliminates order ambiguity. - # If you swap the first and last atom (#1 and #4), then - # the -pair- of angles is the same. Hence if atom #1 - # has a name which is lexicographically less than atom #4, - # swap atoms 1 and 4. - """ - if atom_names[0] <= atom_names[3]: - return (atom_names[0]+','+atom_names[1]+','+ - atom_names[2]+','+atom_names[3]) - else: - return (atom_names[3]+','+atom_names[1]+','+ - atom_names[2]+','+atom_names[0]) - - - - -def AtomsMatchPattern(anames, pattern): - """ - Check whether the list of atom names "anames" matches "pattern" - (Both arguments are lists of strings, but some of the strings - in pattern may contain wildcard characters followed by - "priority" numbers. Matches with lower priority numbers are - given preference whenever multiple distinct matches are found. - (Note: This function does not check patterns in reverse order.) - """ - #sys.stderr.write('DEBUG: checking whether '+str(anames)+' matches '+str(pattern)+'\n') - assert(len(anames) == len(pattern)) - matched = True - for d in range(0, len(pattern)): - if (pattern[d] == anames[d]) or (pattern[d][0] == '*'): - if pattern[d][0] == '*': - priority = int(pattern[d][1:]) - else: - priority = 0 - else: - matched = False - if matched: - #sys.stderr.write('DEBUG: '+str(anames)+' matches '+str(pattern)+'\n') - return priority - else: - return None - - -def LookupBondLength(a1, a2, - atom2equiv_bond, - bond2r0, - atom2auto_bond, - bond2r0_auto): - """ - Try to find bond parameters between atoms whose original - atom names (without equivalences) are a1 and a2. - Then return both the equilibrium bond length for that bond, - as well as the equivalent atom names used to lookup that bond. - (These could be stored in either atom2equiv_bond or atom2auto_bond.) - If a match was not found, return None. - """ - return_val = None - anames = (atom2equiv_bond[a1], atom2equiv_bond[a2]) - bond_name = EncodeInteractionName(SortByEnds(anames)) - if bond_name in bond2r0: - return_val = (bond2r0[bond_name], - [anames[0], anames[1]], - False) - # If no bond between these atoms is defined, - # check the bonds in the _auto section(s) - # This is a lot messier. - elif ((a1 in atom2auto_bond) and (a2 in atom2auto_bond)): - anames = [atom2auto_bond[a1], atom2auto_bond[a2]] - # Because _auto interactions can contain wildcards, - # there can be multiple entries in bond2r0_auto[] - # for the same list of atom names, and we have to - # consider all of them, and pick the one with the - # most priority (ie. whose priority number is lowest). - # (Note: The MSI file format uses low priority numbers - # to indicate high priority. Somewhat confusing. - # For details, see "Forcefield based simulations" PDF, Cerius2, p 87) - HUGE_VAL = 2000000000 - best_priority = HUGE_VAL - pattern = ['',''] - for (pattern[0],pattern[1]), r0 in bond2r0_auto.items(): - priority = AtomsMatchPattern(anames, pattern) - if (priority != None) and (priority < best_priority): - best_priority = priority - return_val = (r0, anames, True) - # try again with the atom type names in reverse order - priority = AtomsMatchPattern([anames[1],anames[0]], pattern) - if ((priority != None) and - (priority < best_priority)): #(note: low priority numbers = high priority) - best_priority = priority - return_val = (r0, anames, True) - #if return_val != None: - # sys.stderr.write('DEBUG: For atoms '+str((a1,a2))+' ... bond_length, batom_names = '+str(return_val)+'\n') - return return_val - - - - - - - - -def LookupBondAngle(a1, a2, a3, - atom2equiv_angle, - angle2theta0_or, - atom2auto_angle, - angle2theta0_auto_or): - """ - Try to find angle parameters between atoms whose original atom - names (without equivalences) are a1, a2, and a3. Then return - both the equilibrium rest angle for that 3body interaction - as well as the equivalent atom names used to look it up. (These - could be stored in either atom2equiv_angle or atom2auto_angle.) - If a match was not found, return None. - """ - return_val = None - anames = (atom2equiv_angle[a1], atom2equiv_angle[a2], atom2equiv_angle[a3]) - angle_name = EncodeInteractionName(SortByEnds(anames)) - if angle_name in angle2theta0_or: - return_val = (angle2theta0_or[angle_name], - [anames[0], anames[1], anames[2]], - False) - - # If no angle between these atoms is defined, - # check the angles in the _auto section(s) - # This is a lot messier. - elif ((a1 in atom2auto_angle[0]) and - (a2 in atom2auto_angle[1]) and - (a3 in atom2auto_angle[2])): - - anames = [atom2auto_angle[0][a1], - atom2auto_angle[1][a2], - atom2auto_angle[2][a3]] - #sys.stderr.write('DEBUG: LookupBondAngle(): a1,a2,a3=('+ - # a1+','+a2+','+a3+'), anames='+str(anames)+'\n') - - # Because _auto interactions can contain wildcards, - # there can be multiple entries in angle2theta0_auto_or[] - # for the same list of atom names, and we have to - # consider all of them, and pick the one with the - # most priority (ie. whose priority number is lowest). - # (Note: The MSI file format uses low priority numbers - # to indicate high priority. Somewhat confusing.) - HUGE_VAL = 2000000000 - best_priority = HUGE_VAL # (ie. low priority) - pattern = ['','',''] - for (pattern[0],pattern[1],pattern[2]), theta0 in angle2theta0_auto_or.items(): - priority = AtomsMatchPattern(anames, pattern) - if ((priority != None) and - (priority < best_priority)): #(note: low priority numbers = high priority) - best_priority = priority - return_val = (theta0, anames, True) - # try again with the atom type names in reverse order - priority = AtomsMatchPattern([anames[2],anames[1],anames[0]], pattern) - if (priority != None) and (priority < best_priority): - best_priority = priority - return_val = (theta0, anames, True) - #if return_val != None: - # sys.stderr.write('DEBUG: For atoms '+str((a1,a2,a3))+' ... rest_angle, anames = '+str(return_val)+'\n') - return return_val - - - - - - - - -def Equivalences2ffids(lines_equivalences, - atom_types, - atom2equiv_pair, - atom2equiv_bond, - atom2equiv_angle, - atom2equiv_dihedral, - atom2equiv_improper): - """ - This function reads a list of lines containing "equivalences" and - "auto_equivalences" from an MSI-formatted .FRC file. - Then, for each atom type, it generates a long string which includes the - original atom type name as well as all of the equivalences it belongs to. - Later on, when it is time to generate angles, dihedrals, or impropers, - moltemplate will search for patterns contained in these strings to decide - which type of interaction to generate. - This function returns a dictionary that converts the original atom type name - into these strings. - """ - for line in lines_equivalences: - #tokens = SplitQuotedString(line.strip(), - # comment_char='!>') - - # skip past both '!' and '>' characters - ic1 = line.find('!') - ic = ic1 - ic2 = line.find('>') - if ic2 != -1 and ic2 < ic1: - ic = ic2 - if ic != -1: - line = line[:ic] - else: - line = line.rstrip('\n') - tokens = line.strip().split() - #sys.stderr.write('DEBUG Equivalences2ffids():\n' - # ' tokens = '+str(tokens)+'\n') - atype = EncodeAName(tokens[2]) - atom2equiv_pair[atype] = EncodeAName(tokens[3]) - atom2equiv_bond[atype] = EncodeAName(tokens[4]) - atom2equiv_angle[atype] = EncodeAName(tokens[5]) - atom2equiv_dihedral[atype] = EncodeAName(tokens[6]) - atom2equiv_improper[atype] = EncodeAName(tokens[7]) - - atom2ffid = OrderedDict() - for atom in atom_types: - atom2ffid[atom] = (atom + - ',p'+atom2equiv_pair.get(atom,'') + - ',b'+atom2equiv_bond.get(atom,'') + - ',a'+atom2equiv_angle.get(atom,'') + - ',d'+atom2equiv_dihedral.get(atom,'') + - ',i'+atom2equiv_improper.get(atom,'')) - return atom2ffid - - - - - - -def AutoEquivalences2ffids(lines_equivalences, - lines_auto_equivalences, - atom_types, - atom2equiv_pair, - atom2equiv_bond, - atom2equiv_angle, - atom2equiv_dihedral, - atom2equiv_improper, - atom2auto_pair, - atom2auto_bondincr, - atom2auto_bond, - atom2auto_angleend, - atom2auto_anglecenter, - atom2auto_dihedralend, - atom2auto_dihedralcenter, - atom2auto_improperend, - atom2auto_impropercenter): - """ - This function is a variant of Equivalences2ffids() which also considers - "auto_equivalences". - This function returns a dictionary that converts the original atom type name - into a string that includes that atom's "equivalences", - as well as its "auto_equivalences". - moltemplate will search for patterns contained in these strings to decide - which type of interaction to generate. - """ - Equivalences2ffids(lines_equivalences, - atom_types, - atom2equiv_pair, - atom2equiv_bond, - atom2equiv_angle, - atom2equiv_dihedral, - atom2equiv_improper) - - # ------ The following lines are for processing "auto_equivalences" ----- - # - # What is the difference between "equivalences" and "auto_equivalences"? - # - # equivalences: - # Here is an excerpt from the Discover manual describing "equivalences": - # "Chemically distinct atoms often differ in some, but not all, - # of their forcefield parameters. For example, the bond parameters - # for the C-C bonds in ethene and in benzene are quite different, - # but the nonbond parameters for the carbon atoms are essentially - # the same. Rather than duplicating the nonbond parameters in the - # forcefield parameter file, the Discover program uses atom type - # equivalences to simplify the problem. In the example, the phenyl - # carbon atom type is equivalent to the pure sp2 carbons of ethene - # insofar as the nonbond parameters are concerned. The Discover - # program recognizes five types of equivalences for each atom - # type: nonbond, bond, angle, torsion, and out-of-plane. - # Cross terms such as bond-bond terms have the same equivalences - # (insofar as atom types are concerned) as the diagonal term of - # the topology of all the atoms defining the internal coordinates. - # For the bond-bond term, this means that the atom type - # equivalences for angles would be used - # - # auto_equivalences: - # Are similar to equivalences, but apparently with lower priority. - # In addition, it seems that, when looking up some of the class2 terms - # in the interaction according to atom type using "auto_equivalences" - # a distinction is made between end atoms and central atoms. - # The parameters for these interactions are also stored in different - # tables in the .frc file, with different comments/tags. - # (for example, "cff91_auto" as opposed to "cff91") - # An excerpt from the Discover manual is somewhat vague: - # "A forcefield may include automatic parameters for use when - # better-quality explicit parameters are not defined for a - # particular bond, angle, torsion, or out-of-plane interaction. - # These parameters are intended as temporary patches, to allow - # you to begin calculations immediately." - - for line in lines_auto_equivalences: - #tokens = SplitQuotedString(line.strip(), - # comment_char='!>') - - # skip past both '!' and '>' characters - ic1 = line.find('!') - ic = ic1 - ic2 = line.find('>') - if ic2 != -1 and ic2 < ic1: - ic = ic2 - if ic != -1: - line = line[:ic] - else: - line = line.rstrip('\n') - tokens = line.strip().split() - #sys.stderr.write('DEBUG Equivalences2ffids():\n' - # ' tokens = '+str(tokens)+'\n') - atype = EncodeAName(tokens[2]) - atom2auto_pair[atype] = EncodeAName(tokens[3]) - atom2auto_bondincr[atype] = EncodeAName(tokens[4]) - atom2auto_bond[atype] = EncodeAName(tokens[5]) - atom2auto_angleend[atype] = EncodeAName(tokens[6]) - atom2auto_anglecenter[atype] = EncodeAName(tokens[7]) - atom2auto_dihedralend[atype] = EncodeAName(tokens[8]) - atom2auto_dihedralcenter[atype] = EncodeAName(tokens[9]) - atom2auto_improperend[atype] = EncodeAName(tokens[10]) - atom2auto_impropercenter[atype] = EncodeAName(tokens[11]) - - atom2ffid = OrderedDict() - for atom in atom_types: - atom2ffid[atom] = (atom + - ',p'+atom2equiv_pair.get(atom,'') + - ',b'+atom2equiv_bond.get(atom,'') + - ',a'+atom2equiv_angle.get(atom,'') + - ',d'+atom2equiv_dihedral.get(atom,'') + - ',i'+atom2equiv_improper.get(atom,'') + - ',ap'+atom2auto_pair.get(atom,'') + - ',aq'+atom2auto_bondincr.get(atom,'') + - ',ab'+atom2auto_bond.get(atom,'') + - ',aae'+atom2auto_angleend.get(atom,'') + - ',aac'+atom2auto_anglecenter.get(atom,'') + - ',ade'+atom2auto_dihedralend.get(atom,'') + - ',adc'+atom2auto_dihedralcenter.get(atom,'') + - ',aie'+atom2auto_improperend.get(atom,'') + - ',aic'+atom2auto_impropercenter.get(atom,'') + - '' - ) - return atom2ffid - - - - - - -def main(): - try: - sys.stderr.write(g_program_name + ", version " + - __version__ + ", " + __date__ + "\n") - if sys.version < '2.6': - raise InputError('Error: Using python ' + sys.version + '\n' + - ' Alas, your version of python is too old.\n' - ' You must upgrade to a newer version of python (2.6 or later).') - - if sys.version < '2.7': - from ordereddict import OrderedDict - else: - from collections import OrderedDict - - if sys.version > '3': - import io - else: - import cStringIO - - # defaults: - ffname = 'BIOSYM_MSI_FORCE_FIELD' - type_subset = set([]) - filename_in = '' - file_in = sys.stdin - #file_in = open('pcff_repaired.frc','r') #CONTINUEHERE - include_auto_equivalences = False - #pair_style_name = 'lj/class2/coul/long' - #pair_style_params = "10.0 10.0" - pair_style2docs = {} - pair_style2args = defaultdict(str) - pair_style2docs['lj/cut/coul/long'] = 'http://lammps.sandia.gov/doc/pair_lj.html' - pair_style2args['lj/cut/coul/long'] = '10.0' - pair_style2docs['lj/class2/coul/long'] = 'http://lammps.sandia.gov/doc/pair_class2.html' - pair_style2args['lj/class2/coul/long'] = '10.0' - pair_style2docs['lj/class2/coul/cut'] = 'http://lammps.sandia.gov/doc/pair_class2.html' - pair_style2args['lj/class2/coul/cut'] = '10.0' - - bond_style2docs = {} - #bond_style2args = defaultdict(str) - bond_style2docs['harmonic'] = 'http://lammps.sandia.gov/doc/bond_harmonic.html' - bond_style2docs['class2'] = 'http://lammps.sandia.gov/doc/bond_class2.html' - bond_style2docs['morse'] = 'http://lammps.sandia.gov/doc/bond_morse.html' - bond_symmetry_subgraph = '' # default - - angle_style2docs = {} - #angle_style2args = defaultdict(str) - angle_style2docs['harmonic'] = 'http://lammps.sandia.gov/doc/angle_harmonic.html' - angle_style2docs['class2'] = 'http://lammps.sandia.gov/doc/angle_class2.html' - angle_symmetry_subgraph = '' # default - - dihedral_style2docs = {} - #dihedral_style2args = defaultdict(str) - dihedral_style2docs['charmm'] = 'http://lammps.sandia.gov/doc/dihedral_charmm.html' - dihedral_style2docs['class2'] = 'http://lammps.sandia.gov/doc/dihedral_class2.html' - dihedral_symmetry_subgraph = '' # default - - improper_style2docs = {} - #improper_style2args = defaultdict(str) - improper_style2docs['cvff'] = 'http://lammps.sandia.gov/doc/improper_cvff.html' - improper_style2docs['class2'] = 'http://lammps.sandia.gov/doc/improper_class2.html' - improper_symmetry_subgraph = {} #'cenJsortIKL' - - pair_mixing_style = 'sixthpower tail yes' - - special_bonds_command = 'special_bonds lj/coul 0.0 0.0 1.0 dihedral yes' - # Thanks to Paul Saxe for is suggestions - # http://lammps.sandia.gov/threads/msg11270.html - - - kspace_style = 'kspace_style pppm 0.0001' - pair_styles_selected = set([]) - #pair_style_link = 'http://lammps.sandia.gov/doc/pair_class2.html' - pair_style_args = {} - pair_cutoff = '10.0' - #pair_style_command = " pair_style hybrid " + \ - # pair_style_name + " " + pair_style_args + "\n" - bond_styles_selected = set([]) - #bond_style_link = bond_style2docs[bond_style_name] - #bond_style_args = '' - angle_styles_selected = set([]) - #angle_style_link = angle_style2docs[angle_style_name] - #angle_style_args = '' - dihedral_styles_selected = set([]) - #dihedral_style_link = dihedral_style2docs[dihedral_style_name] - #dihedral_style_args = '' - improper_styles_selected = set([]) - #improper_style_link = improper_style2docs[improper_style_name] - #improper_style_args = '' - hbond_style_name = '' - hbond_style_link = '' - hbond_style_args = '' - - lines_templates = [] - lines_references = defaultdict(list) - lines_warnings = [] - - - argv = [arg for arg in sys.argv] - - i = 1 - - while i < len(argv): - - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - - if argv[i] == '-atoms': - if i + 1 >= len(argv): - raise InputError('Error: the \"' + argv[i] + '\" argument should be followed by a quoted string\n' - ' which contains a space-delimited list of of a subset of atom types\n' - ' you want to use from the original force-field.\n' - ' Make sure you enclose the entire list in quotes.\n') - type_subset = set(argv[i + 1].strip('\"\'').strip().split()) - del argv[i:i + 2] - - elif argv[i] == '-name': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by the name of the force-field\n') - ffname = argv[i + 1] - del argv[i:i + 2] - - elif argv[i] in ('-file', '-in-file'): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by the name of a force-field file\n') - filename_in = argv[i + 1] - try: - file_in = open(filename_in, 'r') - except IOError: - sys.stderr.write('Error: Unable to open file\n' - ' \"' + filename_in + '\"\n' - ' for reading.\n') - sys.exit(1) - del argv[i:i + 2] - - elif argv[i] == '-pair-cutoff': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by a number' - ' (the distance cutoff for non-bonded (pair) interactions)\n') - pair_style_cutoff = argv[i+1] - del argv[i:i + 2] - - elif argv[i] == '-pair-style': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by either \"lj/class2/coul/cut\" or \"lj/class2/coul/long\"\n') - pair_style_list = argv[i + 1].split(',') - for pair_style in pair_style_list: - if pair_style == '9-6': - pair_style = 'lj/class2/coul/long' - elif pair_style in ('12-6', 'lj', 'LJ'): - pair_style = 'lj/cut/coul/long' - - if pair_style.find('lj/class2/coul/long') == 0: - kspace_style = 'kspace_style pppm 0.0001' - elif pair_style.find('lj/cut/coul/long') == 0: - kspace_style = 'kspace_style pppm 0.0001' - elif pair_style.find('lj/class2/coul/cut') == 0: - pass - #kspace_style = '' - elif pair_style.find('lj/cut') == 0: - pass - #kspace_style = '' - else: - raise InputError('Error: ' + argv[i] + ' ' + pair_style + ' not supported.\n' - ' The following pair_styles are supported:\n' - ' lj/class2/coul/cut\n' - ' lj/class2/coul/long\n' - ' lj/cut\n' - ' lj/cut/coul/long\n') - pair_styles_selected.add(pair_style) - - del argv[i:i + 2] - - elif argv[i] == '-bond-style': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' - ' a compatible bond_style.\n') - bond_styles = argv[i + 1].split(',') - for bond_style in bond_styles: - bond_styles_selected.add(bond_style) - #bond_style2args[bond_style] = argv[i + 1].split()[1:] - #if bond_style_name.find('harmonic') == 0: - # pass - # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_harmonic.html' - #elif bond_style_name.find('morse') == 0: - # pass - # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_morse.html' - #elif bond_style_name.find('class2') == 0: - # pass - # #bond_style_link = 'http://lammps.sandia.gov/doc/bond_class2.html' - #else: - # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' - # ' \"harmonic\", \"class2\", or \"morse\".\n') - del argv[i:i + 2] - - elif argv[i] == '-angle-style': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' - ' a compatible angle_style.\n') - angle_styles = argv[i + 1].split(',') - for angle_style in angle_styles: - angle_styles_selected.add(angle_style) - #if angle_style_name.find('harmonic') == 0: - # pass - # #angle_style_link = 'http://lammps.sandia.gov/doc/angle_harmonic.html' - #elif angle_style_name.find('class2') == 0: - # pass - # #angle_style_link = 'http://lammps.sandia.gov/doc/angle_class2.html' - #else: - # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' - # ' \"harmonic\" or \"class2\"\n') - del argv[i:i + 2] - - elif argv[i] == '-dihedral-style': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' - ' a compatible dihedral_style.\n') - dihedral_styles = argv[i + 1].split(',') - for dihedral_style in dihedral_styles: - dihedral_styles_selected.add(dihedral_style) - #if dihedral_style_name.find('charmm') == 0: - # pass - # #dihedral_style_link = 'http://lammps.sandia.gov/doc/dihedral_charmm.html' - #elif dihedral_style_name.find('class2') == 0: - # pass - # #dihedral_style_link = 'http://lammps.sandia.gov/doc/dihedral_class2.html' - #else: - # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' - # ' \"harmonic\" or \"class2\"\n') - del argv[i:i + 2] - - elif argv[i] == '-improper-style': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by\n' - ' a compatible impropoer_style.\n') - improper_styles = argv[i + 1].split(',') - for improper_style in improper_styles: - improper_styles_selected.add(improper_style) - #if impropoer_style_name.find('harmonic') == 0: - # pass - # #impropoer_style_link = 'http://lammps.sandia.gov/doc/impropoer_harmonic.html' - #elif impropoer_style_name.find('class2') == 0: - # pass - # #impropoer_style_link = 'http://lammps.sandia.gov/doc/impropoer_class2.html' - #else: - # raise InputError('Error: ' + argv[i] + ' must be followed by either:\n' - # ' \"harmonic\" or \"class2\"\n') - del argv[i:i + 2] - - elif argv[i] == '-hbond-style': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' ' + hbond_style_name + '\n' - ' should be followed by a compatible pair_style.\n') - hbond_style_name = argv[i + 1] - hbond_style_link = 'http://lammps.sandia.gov/doc/pair_hbond_dreiding.html' - if hbond_style_name.find('none') == 0: - hbond_style_name = '' - hbond_style_args = '' - elif hbond_style_name.find('hbond/dreiding/lj') == 0: - n = len('hbond/dreiding/lj') - hbond_style_args = hbond_style_name[n+1:] - hbond_style_name = hbond_style_name[:n] - elif hbond_style_name.find('hbond/dreiding/morse') == 0: - n = len('hbond/dreiding/morse') - hbond_style_args = hbond_style_name[n+1:] - hbond_style_name = hbond_style_name[:n] - else: - raise InputError('Error: ' + argv[i] + ' flag should be followed by either\n' - ' \"hbond/dreiding/lj\" or \"hbond/dreiding/morse"\n') - del argv[i:i + 2] - - elif argv[i] in ('-url', '-in-url'): - import urllib2 - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by a URL pointing to\n' - ' a file containing force-field information in msi/frc format.\n') - url = argv[i + 1] - try: - request = urllib2.Request(url) - file_in = urllib2.urlopen(request) - except urllib2.URLError: - sys.stdout.write("Error: Unable to open link:\n" + url + "\n") - sys.exit(1) - del argv[i:i + 2] - - elif argv[i] == '-auto': - include_auto_equivalences = True - del argv[i:i + 1] - - elif argv[i] in ('-help', '--help', '-?', '--?'): - sys.stderr.write(doc_msg) - sys.exit(0) - del argv[i:i + 1] - - else: - i += 1 - - if len(argv) != 1: - raise InputError('Error: Unrecongized arguments: ' + ' '.join(argv[1:]) + - '\n\n' + doc_msg) - - # Default styles: - if len(bond_styles_selected) == 0: - bond_styles_selected.add('class2') - if len(angle_styles_selected) == 0: - angle_styles_selected.add('class2') - if len(dihedral_styles_selected) == 0: - dihedral_styles_selected.add('class2') - if len(improper_styles_selected) == 0: - improper_styles_selected.add('class2') - if len(pair_styles_selected) == 0: - pair_styles_selected.add('lj/class2/coul/long') - - #sys.stderr.write("Reading parameter file...\n") - - lines = file_in.readlines() - atom2charge = OrderedDict() # lookup charge from atom type - atom2mass = OrderedDict() # lookup mass from atom type - # equivalences lookup - atom2ffid = OrderedDict() # lookup "force-field-ID" a string containing - # equivalences to lookup bonded interactions - atom2equiv_pair = OrderedDict() # lookup the equivalent symbol used for - # looking up pair interactions - atom2equiv_bond = OrderedDict() - atom2equiv_angle = OrderedDict() - atom2equiv_dihedral = OrderedDict() - atom2equiv_improper = OrderedDict() - # inverse equivalences lookup - equiv_pair2atom = defaultdict(set) - equiv_bond2atom = defaultdict(set) - equiv_angle2atom = defaultdict(set) - equiv_dihedral2atom = defaultdict(set) - equiv_improper2atom = defaultdict(set) - - # auto equivalences lookup - atom2auto_pair = OrderedDict() - atom2auto_bondincr = OrderedDict() - atom2auto_bond = OrderedDict() - atom2auto_angleend = OrderedDict() - atom2auto_anglecenter = OrderedDict() - atom2auto_dihedralend = OrderedDict() - atom2auto_dihedralcenter = OrderedDict() - atom2auto_improperend = OrderedDict() - atom2auto_impropercenter = OrderedDict() - # inverse auto equivalences lookup - auto_pair2atom = defaultdict(set) - auto_bondincr2atom = defaultdict(set) - auto_bond2atom = defaultdict(set) - auto_angleend2atom = defaultdict(set) - auto_anglecenter2atom = defaultdict(set) - auto_dihedralend2atom = defaultdict(set) - auto_dihedralcenter2atom = defaultdict(set) - auto_improperend2atom = defaultdict(set) - auto_impropercenter2atom = defaultdict(set) - - - atom2element = OrderedDict() # Optional: - # which element (eg 'C', 'O') ? (Note this - # is different from atom type: 'C1', 'Oh') - atom2numbonds = OrderedDict() # Optional: how many bonds emanate from - atom2descr = OrderedDict() # Optional: a brief description - atom2ver = OrderedDict() # atoms introduced in different versions of ff - atom2ref = OrderedDict() # reference to paper where atom introduced - lines_equivalences = [] # equivalences for force-field lookup - lines_auto_equivalences = [] # auto_equivalences have lower priority - - pair2params = OrderedDict() - pair2style = OrderedDict() - pair_styles = set([]) - pair2ver = OrderedDict() - pair2ref = OrderedDict() - - bond2chargepair = OrderedDict() # a.k.a "bond increments" - charge_pair_priority = OrderedDict() # priority in case multiple entries - # exist for the same pair of atoms - charge_pair_ver = OrderedDict() # which version of the force field? - charge_pair_ref = OrderedDict() # paper introducing this chargepair - - bond2params = OrderedDict() # store a tuple with the 2-body bond - # interaction type, and its parameters - # for every type of bond - bond2priority = OrderedDict() # What is the priority of this interaction? - bond2style = OrderedDict() # What LAMMPS bond style (formula) - # is used for a given interaction? - bond_styles = set([]) # Contains all bond styles used. - bond2ver = OrderedDict() - bond2ref = OrderedDict() - bond2r0 = OrderedDict() - bond2r0_auto = OrderedDict() - - angle2params = OrderedDict() # store a tuple with the 3-body angle - # interaction type, and its parameters - # for every type of angle - - angle2params_or = OrderedDict() - # http://lammps.sandia.gov/doc/angle_class2.html - #angle2class2_a = OrderedDict() # params for the "a" class2 terms - angle2class2_bb = OrderedDict() # params for the "bb" class2 terms - angle2class2_bb_or = OrderedDict() - angle2class2_ba = OrderedDict() # params for the "ba" class2 terms - angle2class2_ba_or = OrderedDict() - angle2priority = OrderedDict() # What is the priority of this interaction? - angle2priority_or = OrderedDict() - angle_is_secondary_or = OrderedDict() - angle2style = OrderedDict() # What LAMMPS angle style (formula) - # is used for a given interaction? - angle2style_or = OrderedDict() - angle_styles = set([]) # Contains all angle styles used. - angle2ref = OrderedDict() - angle2ver = OrderedDict() - angle2ref_or = OrderedDict() - angle2ver_or = OrderedDict() - angle2ver_bb = OrderedDict() - angle2ver_bb_or = OrderedDict() - angle2ref_bb = OrderedDict() - angle2ref_bb_or = OrderedDict() - angle2ver_ba = OrderedDict() - angle2ver_ba_or = OrderedDict() - angle2ref_ba = OrderedDict() - angle2ref_ba_or = OrderedDict() - angle2theta0_or = OrderedDict() - angle2theta0_auto_or = OrderedDict() - - # http://lammps.sandia.gov/doc/dihedral_class2.html - dihedral2params = OrderedDict() # store a tuple with the 4-body dihedral - # interaction type, and its parameters - # for every type of dihedral - dihedral2params_or = OrderedDict() - #dihedral2class2_d = OrderedDict() # params for the "d" class2 term - dihedral2class2_mbt = OrderedDict() # params for the "mbt" class2 term - dihedral2class2_mbt_or = OrderedDict() - dihedral2class2_ebt = OrderedDict() # params for the "ebt" class2 term - dihedral2class2_ebt_or = OrderedDict() - #dihedral2sym_ebt = OrderedDict() - dihedral2class2_at = OrderedDict() # params for the "at" class2 term - dihedral2class2_at_or = OrderedDict() - #dihedral2sym_at = OrderedDict() - dihedral2class2_aat = OrderedDict() # params for the "aat" class2 term - dihedral2class2_aat_or = OrderedDict() - #dihedral2sym_aat = OrderedDict() - dihedral2class2_bb13 = OrderedDict() # params for the "bb13" class2 term - dihedral2class2_bb13_or = OrderedDict() - #dihedral2sym_bb13 = OrderedDict() - dihedral2priority = OrderedDict() # What is the priority of this interaction? - dihedral2priority_or = OrderedDict() - dihedral_is_secondary_or = OrderedDict() - dihedral2style = OrderedDict() # What LAMMPS dihedral style (formula) - # is used for a given interaction? - dihedral2style_or = OrderedDict() - dihedral_styles = set([]) # Contains all dihedral styles used. - dihedral2ref = OrderedDict() - dihedral2ver = OrderedDict() - dihedral2ver_or = OrderedDict() - dihedral2ref_or = OrderedDict() - dihedral2ver_mbt = OrderedDict() - dihedral2ver_mbt_or = OrderedDict() - dihedral2ref_mbt = OrderedDict() - dihedral2ref_mbt_or = OrderedDict() - dihedral2ver_ebt = OrderedDict() - dihedral2ver_ebt_or = OrderedDict() - dihedral2ref_ebt = OrderedDict() - dihedral2ref_ebt_or = OrderedDict() - dihedral2ver_at = OrderedDict() - dihedral2ver_at_or = OrderedDict() - dihedral2ref_at = OrderedDict() - dihedral2ref_at_or = OrderedDict() - dihedral2ver_aat = OrderedDict() - dihedral2ver_aat_or = OrderedDict() - dihedral2ref_aat = OrderedDict() - dihedral2ref_aat_or = OrderedDict() - dihedral2ver_bb13 = OrderedDict() - dihedral2ver_bb13_or = OrderedDict() - dihedral2ref_bb13 = OrderedDict() - dihedral2ref_bb13_or = OrderedDict() - - - # http://lammps.sandia.gov/doc/improper_class2.html - improper2params = OrderedDict() # store a tuple with the 4-body improper - # interaction type, and its parameters - # for every type of imporpoer - improper2params_or = OrderedDict() - improper2class2_aa = OrderedDict() # params for the "aa" class2 term - improper2class2_aa_or = OrderedDict() - - improper2cross = defaultdict(dict) - # improper2cross[imp_name][atoms] stores the - # coefficient (K) for the angle-angle ("aa") - # improper interactions between a pair of - # neighboring 3-body angles (in the .FRC file). - # "imp_name" is the name of the improper interaction - # (which is a concatination of the central atom and - # the 3 surrounding leaf atoms (which are sorted)) - # "atoms" indicates, for that K value, the list of - # leaf atoms for that K value as they appear in the - # corresponding line of the .frc file (however the - # and last atom names are swapped if the first - # atom name is lexicographically > the last, to - # eliminate redundancy and ambiguity.) - - improper2sym = defaultdict(set) - # improper2sym[imp_name] indicates which subset of - # leaf atoms (from 0 to 2) are equivalent and can - # tolerate having their order rearranged without - # effecting the energy. Later on this will be used - # to reduce the number of improper interactions that - # will be generated by moltemplate. - - improper2priority = OrderedDict() # What is the priority of this interaction? - improper2priority_or = OrderedDict() - improper_is_secondary_or = OrderedDict() - improper2style = OrderedDict() # What LAMMPS improper style (formula) - # is used for a given interaction? - improper2style_or = OrderedDict() - improper_styles = set([]) # Contains all improper styles used. - improper2ver = OrderedDict() - improper2ver_or = OrderedDict() - improper2ref = OrderedDict() - improper2ref_or = OrderedDict() - improper2ver_aa = OrderedDict() - improper2ver_aa_or = OrderedDict() - improper2ref_aa = OrderedDict() - improper2ref_aa_or = OrderedDict() - - - # Warn users if force field contains terms which cannot yet - # be simulated with LAMMPS (as of 2017-10-13) - display_OOP_OOP_warning = False - display_torsion_torsion_1_warning = False - - - """ - --- these next few lines of code appear to be unnecessary. - --- I'll probably delete this code in a later version - hbond2params = OrderedDict() # lookup hbond parameters and atom types - hbond2donors = OrderedDict() # according to the identifier in the 2nd - hbond2acceptors = OrderedDict() # column of the "#hbond_definition" - hbond2hydrogens = OrderedDict() # section of an .frc file. - """ - - allowed_section_names = set(['#define', - # sections used in all MSI force-fields - '#atom_types', - '#equivalence', - '#auto_equivalence', - '#nonbond(9-6)', - '#nonbond(12-6)', - '#quadratic_bond', - '#quartic_bond', - '#morse_bond', - '#quadratic_angle', - '#quartic_angle', - '#bond-bond', - '#bond-angle', - '#torsion_1', - '#torsion_3', - '#middle_bond-torsion_3', - '#end_bond-torsion_3', - '#angle-torsion_3', - '#angle-angle-torsion_1',#(class2 dihedral) - '#bond-bond_1_3', #(a class2 dihedral term) - '#out_of_plane', - '#wilson_out_of_plane', - '#angle-angle', #(a class2 improper term) - '#out_of_plane-out_of_plane', # UNSUPPORTED - '#torsion-torsion_1', # UNSUPPORTED - '#bond_increments', - '#hbond_definition', # irrelevant? - '#templates', - '#reference', - '#end' - ]) - - icol_type = icol_mass = icol_elem = icol_nbonds = icol_comment = icol_ver = icol_ref = -1 - - section_name = '' - section_is_auto = False - - sys.stderr.write("parsing file pass1: look for atom types and equivalences...") - - for iline in range(0, len(lines)): - line = lines[iline] - sys.stderr.write('line=\"' + line.strip() + '\"\n') - tokens = SplitQuotedString(line.strip(), - quotes='', - comment_char='>') - #sys.stderr.write('tokens = ' + str(tokens) + '\n') - if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': - continue - if line.lstrip(' ').find('#') == 0: - #sys.stderr.write('allowed_section_names = ' + - # str(allowed_section_names) + '\n') - if tokens[0] in allowed_section_names: - section_name = tokens[0] - section_is_auto = tokens[-1].endswith('_auto') - tokens_after_section_name = tokens[1:] - sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') - continue - elif not tokens[0] in ('#version', - '#define'): - raise InputError('Error: Line# '+str(iline) +'\n' - ' Unrecognized section name:\n' - ' \"' + tokens[0] + '\"\n') - elif (len(tokens) == 8) and (section_name == '#equivalence'): - if line.lstrip().find('!') == 0: - continue - lines_equivalences.append(line) - elif (len(tokens) == 12) and (section_name == '#auto_equivalence'): - if line.lstrip().find('!') == 0: - continue - lines_auto_equivalences.append(line) - elif (len(tokens) > 0) and (section_name == '#atom_types'): - # Different FRC files put this information in different - # columns. Column order is stored in the !Ver comment line: - if line.lstrip().find('!Ver') == 0: - tokens = line.strip().split() - for i in range(0, len(tokens)): - if tokens[i].lower() == 'type': - icol_type = i - elif tokens[i].lower() == 'mass': - icol_mass = i - elif tokens[i].lower() == 'element': - icol_elem = i - elif tokens[i].lower() == 'connections': - icol_nbonds = i - elif tokens[i].lower() == 'comment': - icol_comment = i - elif tokens[i].lower() == '!ver': #(version of ff) - icol_ver = i - elif tokens[i].lower() == 'ref': - icol_ref = i - assert(icol_ver == 0) - - if -1 in (icol_type, icol_mass): - raise InputError('Error: Invalid #atom_types section.\n' - ' The meaning of each column cannot be determined.\n' - ' This file needs a valid "!Ver..." comment.\n') - if icol_comment == -1: - icol_comment = max(icol_type, icol_mass, - icol_elem, icol_nbonds) + 1 - - sys.stderr.write('icol_ver = '+str(icol_ver)+'\n') - sys.stderr.write('icol_ref = '+str(icol_ref)+'\n') - sys.stderr.write('icol_mass = '+str(icol_mass)+'\n') - sys.stderr.write('icol_nelem = '+str(icol_elem)+'\n') - sys.stderr.write('icol_nbonds = '+str(icol_nbonds)+'\n') - sys.stderr.write('icol_comment = '+str(icol_comment)+'\n') - continue - - tokens = map(RemoveOuterQuotes, - NSplitQuotedString(line.strip(), - icol_comment+1, - quotes='', - comment_char='>')) - tokens = list(tokens) - - if (len(tokens) > 4): - if ((len(type_subset) == 0) or (tokens[1] in type_subset)): - aname = EncodeAName(tokens[icol_type]) - atom2mass[aname] = str(max(float(tokens[icol_mass]), 1.0e-06)) - # Some atoms in cvff.prm have zero mass. Unfortunately this - # causes LAMMPS to crash, even if these atoms are never used, - # so I give the mass a non-zero value instead. - - if icol_elem != -1: - atom2element[aname] = tokens[icol_elem] - if icol_nbonds != -1: - atom2numbonds[aname] = int(tokens[icol_nbonds]) - atom2descr[aname] = tokens[icol_comment] - atom2ver[aname] = tokens[icol_ver] - atom2ref[aname] = tokens[icol_ref] - - elif len(tokens) > 0: - raise InputError('Error: Invalid atom line: (line#'+str(iline)+')\n' + - '\"'+line.strip()+'\"') - - atom_types = [x for x in atom2mass] - - # Now construct the lookup tables and inverse tables - # we will need to understand the remainder of the file: - if not include_auto_equivalences: - atom2ffid = Equivalences2ffids(lines_equivalences, - atom_types, - atom2equiv_pair, - atom2equiv_bond, - atom2equiv_angle, - atom2equiv_dihedral, - atom2equiv_improper) - else: - atom2ffid = AutoEquivalences2ffids(lines_equivalences, - lines_auto_equivalences, - atom_types, - atom2equiv_pair, - atom2equiv_bond, - atom2equiv_angle, - atom2equiv_dihedral, - atom2equiv_improper, - atom2auto_pair, - atom2auto_bondincr, - atom2auto_bond, - atom2auto_angleend, - atom2auto_anglecenter, - atom2auto_dihedralend, - atom2auto_dihedralcenter, - atom2auto_improperend, - atom2auto_impropercenter) - - for a,e in atom2equiv_pair.items(): - equiv_pair2atom[e].add(a) - for a,e in atom2equiv_bond.items(): - equiv_bond2atom[e].add(a) - for a,e in atom2equiv_angle.items(): - equiv_angle2atom[e].add(a) - for a,e in atom2equiv_dihedral.items(): - equiv_dihedral2atom[e].add(a) - for a,e in atom2equiv_improper.items(): - equiv_improper2atom[e].add(a) - - # the inverse lookup for '*' matches all atom types - for a in atom_types: - #equiv_pair2atom['*'].add(EncodeAName(a)) - equiv_pair2atom['X'].add(EncodeAName(a)) - #equiv_bond2atom['*'].add(EncodeAName(a)) - equiv_bond2atom['X'].add(EncodeAName(a)) - #equiv_angle2atom['*'].add(EncodeAName(a)) - equiv_angle2atom['X'].add(EncodeAName(a)) - #equiv_dihedral2atom['*'].add(EncodeAName(a)) - equiv_dihedral2atom['X'].add(EncodeAName(a)) - #equiv_improper2atom['*'].add(EncodeAName(a)) - equiv_improper2atom['X'].add(EncodeAName(a)) - - for a,e in atom2auto_pair.items(): - auto_pair2atom[e].add(a) - for a,e in atom2auto_bondincr.items(): - auto_bondincr2atom[e].add(a) - for a,e in atom2auto_bond.items(): - auto_bond2atom[e].add(a) - for a,e in atom2auto_angleend.items(): - auto_angleend2atom[e].add(a) - #auto_angle[0][e].add(a) - #auto_angle[2][e].add(a) - for a,e in atom2auto_anglecenter.items(): - auto_anglecenter2atom[e].add(a) - #auto_angle[1][e].add(a) - for a,e in atom2auto_dihedralend.items(): - auto_dihedralend2atom[e].add(a) - #auto_dihedral2atom[0][e].add(a) - #auto_dihedral2atom[3][e].add(a) - for a,e in atom2auto_dihedralcenter.items(): - auto_dihedralcenter2atom[e].add(a) - #auto_dihedral2atom[1][e].add(a) - #auto_dihedral2atom[2][e].add(a) - for a,e in atom2auto_improperend.items(): - auto_improperend2atom[e].add(a) - for a,e in atom2auto_impropercenter.items(): - auto_impropercenter2atom[e].add(a) - - # the inverse lookup for '*' matches all atom types - for a in atom_types: - #auto_pair2atom['*'].add(EncodeAName(a)) - auto_pair2atom['X'].add(EncodeAName(a)) - #auto_bondincr2atom['*'].add(EncodeAName(a)) - auto_bondincr2atom['X'].add(EncodeAName(a)) - #auto_bond2atom['*'].add(EncodeAName(a)) - auto_bond2atom['X'].add(EncodeAName(a)) - #auto_angleend2atom['*'].add(EncodeAName(a)) - auto_angleend2atom['X'].add(EncodeAName(a)) - #auto_anglecenter2atom['*'].add(EncodeAName(a)) - auto_anglecenter2atom['X'].add(EncodeAName(a)) - #auto_dihedralend2atom['*'].add(EncodeAName(a)) - auto_dihedralend2atom['X'].add(EncodeAName(a)) - #auto_dihedralcenter2atom['*'].add(EncodeAName(a)) - auto_dihedralcenter2atom['X'].add(EncodeAName(a)) - #auto_improperend2atom['*'].add(EncodeAName(a)) - auto_improperend2atom['X'].add(EncodeAName(a)) - #auto_impropercenter2atom['*'].add(EncodeAName(a)) - auto_impropercenter2atom['X'].add(EncodeAName(a)) - - - - - - - - - sys.stderr.write("parsing file pass2: look for bonds, bond_increments and nonbonded (pair) interactions...") - - for iline in range(0, len(lines)): - line = lines[iline] - sys.stderr.write('line=\"' + line.strip() + '\"\n') - tokens = SplitQuotedString(line.strip(), - quotes='', - comment_char='>') - #sys.stderr.write('tokens = ' + str(tokens) + '\n') - if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': - continue - if line.lstrip(' ').find('#') == 0: - #sys.stderr.write('allowed_section_names = ' + - # str(allowed_section_names) + '\n') - if (tokens[0] in allowed_section_names): - section_name = tokens[0] - section_is_auto = tokens[-1].endswith('_auto') - tokens_after_section_name = tokens[1:] - sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') - continue - elif (not tokens[0] in ('#version','#define')): - raise InputError('Error: Line# '+str(iline) +'\n' - ' Unrecognized section name:\n' - ' \"' + tokens[0] + '\"\n') - - - elif ((len(tokens) > 4) and (section_name == '#nonbond(12-6)') - and (pair_styles_selected & set(['lj','lj/cut','lj/cut/coul/long', - 'lj/cut/coul/cut','lj/cut/coul/debye', - 'lj/cut/coul/dsf','lj/cut/coul/msm', - '12-6','nonbond(12-6)']))): - - if line.lstrip().find('!') == 0: - continue - atom_name = EncodeAName(tokens[2]) - pair2ver[atom_name] = tokens[0] - pair2ref[atom_name] = tokens[1] - A = float(tokens[3]) - B = float(tokens[4]) - epsilon = B*B/(4*A) - sigma = pow(B/A, 1.0/6) - if sigma == 0.0: - sigma = 1.0 #(non-zero to avoid nan error later) - pair_styles.add('lj/cut/coul/long') - pair_style_args['lj/cut/coul/long'] = pair_cutoff - pair2style[atom_name] = 'lj/cut/coul/long' - pair2params[atom_name] = (str(epsilon)+' '+str(sigma)) - pair_mixing_style = 'geometric tail yes' - #if pair_style_name.find('lj/cut') == 0: - # pair2params[atom_name] = (str(epsilon)+' '+str(sigma)) - # pair_mixing_style = 'geometric tail yes' - - - elif ((len(tokens) > 4) and (section_name == '#nonbond(9-6)') - and (pair_styles_selected & - set(['class2', '9-6', 'nonbond(9-6)', - 'lj/class2/coul/long']))): - if line.lstrip().find('!') == 0: - continue - atom_name = EncodeAName(tokens[2]) - pair2ver[atom_name] = tokens[0] - pair2ref[atom_name] = tokens[1] - sigma = tokens[3] - epsilon = tokens[4] - pair_styles.add('lj/class2/coul/long') - pair_style_args['lj/class2/coul/long'] = pair_cutoff - pair2style[atom_name] = 'lj/class2/coul/long' - pair2params[atom_name] = (epsilon+' '+sigma) - pair_mixing_style = 'sixthpower tail yes' - #if pair_style_name.find('lj/class2') == 0: - # pair2params[atom_name] = (epsilon+' '+sigma) - # pair_mixing_style = 'sixthpower tail yes' - - - elif (len(tokens) == 6) and (section_name == '#bond_increments'): - if line.lstrip().find('!') == 0: - continue - aorig = [a for a in map(EncodeAName, tokens[2:4])] - delta_q = tokens[4:6] - atom_names = [a for a in aorig] - # swap the order of the atoms? - order_reversed = aorig[0] > aorig[-1] - if order_reversed: - delta_q.reverse() - atom_names.reverse() - bond_name = EncodeInteractionName(atom_names, section_is_auto) - charge_pair_ver[bond_name] = tokens[0] - charge_pair_ref[bond_name] = tokens[1] - charge_pair_priority[bond_name] = \ - (section_is_auto, - DetermineNumericPriority(section_is_auto, - tokens[2:4], - float(charge_pair_ver[bond_name]))) - bond2chargepair[bond_name] = (delta_q[0] + ' ' + delta_q[1]) - - - elif ((len(tokens) > 5) and (section_name == '#quadratic_bond') - and (bond_styles_selected & set(['harmonic','quadratic','quadratic_bond']))): - if line.lstrip().find('!') == 0: - continue - bond_styles.add('harmonic') - atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) - bond_name = EncodeInteractionName(atom_names, section_is_auto) - bond2ver[bond_name] = tokens[0] - bond2ref[bond_name] = tokens[1] - bond2priority[bond_name] = \ - (section_is_auto, - DetermineNumericPriority(section_is_auto, - tokens[2:4], - float(bond2ver[bond_name]))) - r0 = tokens[4] - k = tokens[5] - if not section_is_auto: - bond2r0[bond_name] = r0 - sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') - else: - bond2r0_auto[(atom_names[0], atom_names[1])] = r0 - sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') - bond2style[bond_name] = 'harmonic' - bond2params[bond_name] = (k+' '+r0) - - - elif ((len(tokens) > 6) and (section_name == '#morse_bond') - and (bond_styles_selected & set(['morse','morse_bond']))): - if line.lstrip().find('!') == 0: - continue - bond_styles.add('morse') - atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) - bond_name = EncodeInteractionName(atom_names, section_is_auto) - bond2ver[bond_name] = tokens[0] - bond2ref[bond_name] = tokens[1] - bond2priority[bond_name] = \ - (section_is_auto, - DetermineNumericPriority(section_is_auto, - tokens[2:4], - float(bond2ver[bond_name]))) - r0 = tokens[4] - D = tokens[5] - alpha = tokens[6] - sys.stderr.write('DEBUG: morse: atom_names = '+str(atom_names)+'\n') - if not section_is_auto: - bond2r0[bond_name] = r0 - sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') - else: - bond2r0_auto[(atom_names[0], atom_names[1])] = r0 - sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') - bond2style[bond_name] = 'morse' - bond2params[bond_name] = (D+' '+alpha+' '+r0) - - - - elif ((len(tokens) > 7) and (section_name == '#quartic_bond') - and (bond_styles_selected & set(['class2','quartic','quartic_bond']))): - if line.lstrip().find('!') == 0: - continue - bond_styles.add('class2') - atom_names = SortByEnds(map(EncodeAName, tokens[2:4])) - bond_name = EncodeInteractionName(atom_names, section_is_auto) - bond2ver[bond_name] = tokens[0] - bond2ref[bond_name] = tokens[1] - bond2priority[bond_name] = \ - (section_is_auto, - DetermineNumericPriority(section_is_auto, - tokens[2:4], - float(bond2ver[bond_name]))) - r0 = tokens[4] - if not section_is_auto: - bond2r0[bond_name] = r0 - sys.stderr.write('bond2r0['+bond_name+'] = ' + str(r0) + '\n') - else: - bond2r0_auto[(atom_names[0], atom_names[1])] = r0 - sys.stderr.write('bond2r0_auto['+str(atom_names)+'] = ' + str(r0) + '\n') - K2 = tokens[5] - K3 = tokens[6] - K4 = tokens[7] - bond2style[bond_name] = 'class2' - bond2params[bond_name] = (r0+' '+K2+' '+K3+' '+K4) - - - - - - sys.stderr.write("parsing file pass3: look for (3-body) angle interactions...") - - for iline in range(0, len(lines)): - line = lines[iline] - sys.stderr.write('line=\"' + line.strip() + '\"\n') - tokens = SplitQuotedString(line.strip(), - quotes='', - comment_char='>') - #sys.stderr.write('tokens = ' + str(tokens) + '\n') - if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': - continue - if line.lstrip(' ').find('#') == 0: - #sys.stderr.write('allowed_section_names = ' + - # str(allowed_section_names) + '\n') - if (tokens[0] in allowed_section_names): - section_name = tokens[0] - section_is_auto = tokens[-1].endswith('_auto') - tokens_after_section_name = tokens[1:] - sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') - continue - elif (not tokens[0] in ('#version','#define')): - raise InputError('Error: Line# '+str(iline) +'\n' - ' Unrecognized section name:\n' - ' \"' + tokens[0] + '\"\n') - - - - - - - - elif (len(tokens) > 6) and (section_name == '#quadratic_angle'): - if line.lstrip().find('!') == 0: - continue - atom_names = SortByEnds(map(EncodeAName, tokens[2:5])) - angle_name = EncodeInteractionName(atom_names, section_is_auto) - - angle2ver[angle_name] = tokens[0] - angle2ref[angle_name] = tokens[1] - angle2priority_or[angle_name] = \ - DetermineNumericPriority(section_is_auto, - tokens[2:5], - float(angle2ver[angle_name])) - angle_is_secondary_or[angle_name] = False - angle2priority[angle_name] = \ - (section_is_auto, - angle_is_secondary_or[angle_name], - angle2priority_or[angle_name]) - theta0 = tokens[5] - k = tokens[6] - if not section_is_auto: - angle2theta0_or[angle_name] = theta0 - sys.stderr.write('angle2theta0_or['+angle_name+'] = ' + str(theta0) + '\n') - else: - angle2theta0_auto_or[(atom_names[0], atom_names[1], atom_names[2])] = theta0 - sys.stderr.write('angle2theta0_auto_or['+str(atom_names)+'] = ' + str(theta0) + '\n') - if (angle_styles_selected & set(['harmonic', - 'quadratic', - 'quadratic_angle'])): - angle_styles.add('harmonic') - angle2style[angle_name] = 'harmonic' - angle2params[angle_name] = (k+' '+theta0) - elif (angle_styles_selected & set(['class2', - 'quartic', - 'quartic_angle'])): - # Then this is a special case of the class2 angle where - # the (theta-theta0)^3 and (theta-theta0)^4 terms = 0 - angle_styles.add('class2') - angle2style_or[angle_name] = 'class2' - angle2params_or[angle_name] = (theta0+' '+k+' 0 0') - - - - elif ((len(tokens) > 8) and (section_name == '#quartic_angle') - and (angle_styles_selected & set(['class2','quartic','quartic_angle']))): - if line.lstrip().find('!') == 0: - continue - angle_styles.add('class2') - atom_names = SortByEnds(map(EncodeAName, tokens[2:5])) - ang_name_orig = EncodeInteractionName(atom_names, section_is_auto) - version = tokens[0] - reference = tokens[1] - angle2ver_or[ang_name_orig] = version - angle2ref_or[ang_name_orig] = reference - angle2priority_or[ang_name_orig] = \ - DetermineNumericPriority(section_is_auto, - tokens[2:5], - float(angle2ver_or[ang_name_orig])) - angle_is_secondary_or[ang_name_orig] = False - #angle2priority[ang_name_orig] = \ - # (section_is_auto, - # angle_is_secondary_or[ang_name_orig], - # angle2priority_or[ang_name_orig]) - theta0 = tokens[5] - if not section_is_auto: - angle2theta0_or[ang_name_orig] = theta0 - sys.stderr.write('angle2theta0_or['+ang_name_orig+'] = ' + str(theta0) + '\n') - else: - angle2theta0_auto_or[(atom_names[0], atom_names[1], atom_names[2])] = theta0 - sys.stderr.write('angle2theta0_auto_or['+str(atom_names)+'] = ' + str(theta0) + '\n') - K2 = tokens[6] - K3 = tokens[7] - K4 = tokens[8] - angle2style_or[ang_name_orig] = 'class2' - angle2params_or[ang_name_orig] = [theta0, K2, K3, K4] - if not ang_name_orig in angle2class2_bb_or: - angle2class2_bb_or[ang_name_orig] = '0.0' # default value - angle2ver_bb_or[ang_name_orig] = version # default value - angle2ref_bb_or[ang_name_orig] = reference # default value - if not ang_name_orig in angle2class2_ba_or: - angle2class2_ba_or[ang_name_orig] = ['0.0', '0.0'] # default value - angle2ver_ba_or[ang_name_orig] = version # default value - angle2ref_ba_or[ang_name_orig] = reference # default value - - elif ((len(tokens) > 5) and - (section_name in ('#bond-bond', '#bond-angle')) and - (angle_styles_selected & - set(['class2', 'quartic', 'quartic_angle']))): - if line.lstrip().find('!') == 0: - continue - version = tokens[0] - reference = tokens[1] - if line.lstrip().find('!') == 0: - continue - aorig = [a for a in map(EncodeAName, tokens[2:5])] - atom_names = SortByEnds(aorig) - ang_name_orig = EncodeInteractionName(atom_names, section_is_auto) - K = ['', ''] - K[0] = tokens[5] - K[1] = K[0] - if len(tokens) > 6: - K[1] = tokens[6] - order_reversed = aorig[0] > aorig[-1] - if order_reversed: - K.reverse() - if (section_name == '#bond-bond'): - angle2class2_bb_or[ang_name_orig] = K[0] - angle2ver_bb_or[ang_name_orig] = version - angle2ref_bb_or[ang_name_orig] = reference - elif (section_name == '#bond-angle'): - angle2class2_ba_or[ang_name_orig] = [k for k in K] - angle2ver_ba_or[ang_name_orig] = version - angle2ref_ba_or[ang_name_orig] = reference - if not ang_name_orig in angle2params_or: - angle_is_secondary_or[ang_name_orig] = True #only cross terms have been defined so far - angle2params_or[ang_name_orig] = ['0.0', '0.0', '0.0', '0.0'] # default value - angle2ver_or[ang_name_orig] = version - angle2ref_or[ang_name_orig] = reference - angle2priority_or[ang_name_orig] = 0.0 - - - - - - - - - - sys.stderr.write("parsing file pass4: look for dihedrals(torsions) and impropers(out_of_plane)...") - - for iline in range(0, len(lines)): - line = lines[iline] - sys.stderr.write('line=\"' + line.strip() + '\"\n') - tokens = SplitQuotedString(line.strip(), - quotes='', - comment_char='>') - #sys.stderr.write('tokens = ' + str(tokens) + '\n') - if line.lstrip().find('!') == 0 and tokens[0] != '!Ver': - continue - - - if line.lstrip(' ').find('#') == 0: - #sys.stderr.write('allowed_section_names = ' + - # str(allowed_section_names) + '\n') - if (tokens[0] in allowed_section_names): - section_name = tokens[0] - section_is_auto = tokens[-1].endswith('_auto') - tokens_after_section_name = tokens[1:] - sys.stderr.write(' encountered section \"'+tokens[0]+'\"\n') - continue - elif (not tokens[0] in ('#version','#define')): - raise InputError('Error: Line# '+str(iline) +'\n' - ' Unrecognized section name:\n' - ' \"' + tokens[0] + '\"\n') - - - - - elif (len(tokens) > 8) and (section_name == '#torsion_1'): - if line.lstrip().find('!') == 0: - continue - atom_names = SortByEnds(map(EncodeAName, tokens[2:6])) - dihedral_name = EncodeInteractionName(atom_names, section_is_auto) - dihedral2ver[dihedral_name] = tokens[0] - dihedral2ref[dihedral_name] = tokens[1] - dihedral2priority_or[dihedral_name] = \ - DetermineNumericPriority(section_is_auto, - tokens[2:6], - float(dihedral2ver[dihedral_name])) - dihedral_is_secondary_or[dihedral_name] = False - dihedral2priority[dihedral_name] = \ - (section_is_auto, - dihedral_is_secondary_or[dihedral_name], - dihedral2priority_or[dihedral_name]) - K = tokens[6] - n = tokens[7] - d = tokens[8] - - w = '0.0' #ignore: this is only used by the CHARMM force field - - if (dihedral_styles_selected & set(['charmm','torsion_1'])): - dihedral_styles.add('charmm') - dihedral2style[dihedral_name] = 'charmm' - #dihedral2params_or[dihedral_name] = [K,n,d,w] - dihedral2params[dihedral_name] = (K+' '+n+' '+d+' '+w) - elif (dihedral_styles_selected & set(['class2','torsion_3'])): - # Then this is a special case of the class2 angle - # lacking the higher terms in the Fourier series - dihedral_styles.add('class2') - dihedral2style[dihedral_name] = 'class2' - dihedral2params_or[dihedral_name] = [K,d,0,0,0,0] - - - - - elif ((len(tokens) > 7) and (section_name == '#torsion_3') - and (dihedral_styles_selected & set(['class2','torsion_3']))): - if line.lstrip().find('!') == 0: - continue - dihedral_styles.add('class2') - atom_names = SortByEnds(map(EncodeAName, tokens[2:6])) - dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) - version = tokens[0] - reference = tokens[1] - dihedral2priority_or[dih_name_orig] = \ - DetermineNumericPriority(section_is_auto, - tokens[2:6], - float(version)) - dihedral_is_secondary_or[dih_name_orig] = False - #dihedral2priority[dih_name_orig] = \ - # (section_is_auto, - # dihedral_is_secondary_or[dih_name_orig], - # dihedral2priority_or[dih_name_orig]) - V1 = tokens[6] - phi0_1 = tokens[7] - V2 = phi0_2 = V3 = phi0_3 = '0.0' - if len(tokens) > 9: - V2 = tokens[8] - phi0_2 = tokens[9] - if len(tokens) > 11: - V3 = tokens[10] - phi0_3 = tokens[11] - dihedral2style_or[dih_name_orig] = 'class2' - dihedral2ver_or[dih_name_orig] = version - dihedral2ref_or[dih_name_orig] = reference - dihedral2params_or[dih_name_orig] = [V1, phi0_1, V2, phi0_2, V3, phi0_3] - # default values for cross terms: - if not dih_name_orig in dihedral2class2_mbt_or: - dihedral2class2_mbt_or[dih_name_orig] = ['0.0','0.0','0.0'] # default value - dihedral2ver_mbt_or[dih_name_orig] = version - dihedral2ref_mbt_or[dih_name_orig] = reference - if not dih_name_orig in dihedral2class2_ebt_or: - dihedral2class2_ebt_or[dih_name_orig] = [['0.0','0.0','0.0'],['0.0','0.0','0.0']] # default value - dihedral2ver_ebt_or[dih_name_orig] = version - dihedral2ref_ebt_or[dih_name_orig] = reference - if not dih_name_orig in dihedral2class2_bb13_or: - dihedral2class2_bb13_or[dih_name_orig] = '0.0' # default value - dihedral2ver_bb13_or[dih_name_orig] = version - dihedral2ref_bb13_or[dih_name_orig] = reference - if not dih_name_orig in dihedral2class2_at_or: - dihedral2class2_at_or[dih_name_orig] = [['0.0','0.0','0.0'],['0.0','0.0','0.0']] # default value - dihedral2ver_at_or[dih_name_orig] = version - dihedral2ref_at_or[dih_name_orig] = reference - if not dih_name_orig in dihedral2class2_aat_or: - dihedral2class2_aat_or[dih_name_orig] = '0.0' # default value - dihedral2ver_aat_or[dih_name_orig] = version - dihedral2ref_aat_or[dih_name_orig] = reference - - - - - - elif ((len(tokens) > 6) and (section_name == '#middle_bond-torsion_3') - and (dihedral_styles_selected & set(['class2','torsion_3']))): - if line.lstrip().find('!') == 0: - continue - dihedral_styles.add('class2') - version = tokens[0] - reference = tokens[1] - if line.lstrip().find('!') == 0: - continue - aorig = [a for a in map(EncodeAName, tokens[2:6])] - atom_names = SortByEnds(aorig) - - Fmbt = [tokens[6], '0.0', '0.0'] - if len(tokens) > 7: - Fmbt[1] = tokens[7] - if len(tokens) > 8: - Fmbt[2] = tokens[8] - - dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) - - #sys.stderr.write('DEBUG: (a2,a3) = '+str((a2,a3))+', ' - # ' (b1,b2) = '+str(batoms)+'\n') - dihedral2style[dih_name_orig] = 'class2' - dihedral2class2_mbt_or[dih_name_orig] = [F for F in Fmbt] - dihedral2ver_mbt_or[dih_name_orig] = version - dihedral2ref_mbt_or[dih_name_orig] = reference - if not dih_name_orig in dihedral2params_or: - dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far - dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] - dihedral2ver_or[dih_name_orig] = version - dihedral2ref_or[dih_name_orig] = reference - dihedral2priority_or[dih_name_orig] = 0.0 - - - - - elif ((len(tokens) > 6) and - (section_name in ('#end_bond-torsion_3', - '#bond-bond_1_3')) and - (dihedral_styles_selected & - set(['class2', 'torsion_3']))): - if line.lstrip().find('!') == 0: - continue - dihedral_styles.add('class2') - version = tokens[0] - reference = tokens[1] - if line.lstrip().find('!') == 0: - continue - aorig = [a for a in map(EncodeAName, tokens[2:6])] - atom_names = SortByEnds(aorig) - - dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) - - dihedral2style[dih_name_orig] = 'class2' - if section_name == '#end_bond-torsion_3': - Febt = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] - Febt[0][0] = tokens[6] - if len(tokens) > 7: - Febt[0][1] = tokens[7] - if len(tokens) > 8: - Febt[0][2] = tokens[8] - Febt[1][0] = Febt[0][0] - Febt[1][1] = Febt[0][1] - Febt[1][2] = Febt[0][2] - if len(tokens) > 9: - Febt[1][0] = tokens[9] - if len(tokens) > 10: - Febt[1][1] = tokens[10] - if len(tokens) > 11: - Febt[1][2] = tokens[11] - order_reversed = aorig[0] > aorig[-1] - if order_reversed: - Febt.reverse() - dihedral2class2_ebt_or[dih_name_orig] = [ [F_ij for F_ij in F_i] for F_i in Febt] #deep copy of Febt[][] - dihedral2ver_ebt_or[dih_name_orig] = version - dihedral2ref_ebt_or[dih_name_orig] = reference - - elif section_name == '#bond-bond_1_3': - Kbb13 = tokens[6] - #dihedral2ver_bb13[dih_name_orig] = version - dihedral2class2_bb13_or[dih_name_orig] = Kbb13 - dihedral2ver_bb13_or[dih_name_orig] = version - dihedral2ref_bb13_or[dih_name_orig] = reference - else: - assert(False) - if not dih_name_orig in dihedral2params_or: - dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far - dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] - dihedral2ver_or[dih_name_orig] = version - dihedral2ref_or[dih_name_orig] = reference - dihedral2priority_or[dih_name_orig] = 0.0 - - - - - - - - - - - elif ((len(tokens) > 6) and - (section_name in ('#angle-torsion_3', - '#angle-angle-torsion_1')) and - (dihedral_styles_selected & - set(['class2', 'torsion_3']))): - if line.lstrip().find('!') == 0: - continue - dihedral_styles.add('class2') - version = tokens[0] - reference = tokens[1] - if line.lstrip().find('!') == 0: - continue - aorig = [a for a in map(EncodeAName, tokens[2:6])] - atom_names = SortByEnds(aorig) - - dih_name_orig = EncodeInteractionName(atom_names, section_is_auto) - - dihedral2style[dih_name_orig] = 'class2' - - if section_name == '#angle-torsion_3': - Fat = [[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]] - Fat[0][0] = tokens[6] - if len(tokens) > 7: - Fat[0][1] = tokens[7] - if len(tokens) > 8: - Fat[0][2] = tokens[8] - Fat[1][0] = Fat[0][0] - Fat[1][1] = Fat[0][1] - Fat[1][2] = Fat[0][2] - if len(tokens) > 9: - Fat[1][0] = tokens[9] - if len(tokens) > 10: - Fat[1][1] = tokens[10] - if len(tokens) > 11: - Fat[1][2] = tokens[11] - order_reversed = aorig[0] > aorig[-1] - if order_reversed: - Fat.reverse() - Fat[0].reverse() - Fat[1].reverse() - dihedral2class2_at_or[dih_name_orig] = [ [F_ij for F_ij in F_i] for F_i in Fat] #deep copy of Fat - dihedral2ver_at_or[dih_name_orig] = version - dihedral2ref_at_or[dih_name_orig] = reference - elif section_name == '#angle-angle-torsion_1': - Kaat = tokens[6] - dihedral2class2_aat_or[dih_name_orig] = Kaat - dihedral2ver_aat_or[dih_name_orig] = version - dihedral2ref_aat_or[dih_name_orig] = reference - else: - assert(False) - - if not dih_name_orig in dihedral2params_or: - dihedral_is_secondary_or[dih_name_orig] = True #only cross terms have been defined so far - dihedral2params_or[dih_name_orig] = ['0.0', '0.0', '0.0', '0.0', '0.0', '0.0'] # default value - dihedral2ver_or[dih_name_orig] = version - dihedral2ref_or[dih_name_orig] = reference - dihedral2priority_or[dih_name_orig] = 0.0 - - - - - - - - - - - elif ((len(tokens) > 8) and (section_name == '#out_of_plane') - and (improper_styles_selected & set(['cvff','out_of_plane']))): - if line.lstrip().find('!') == 0: - continue - improper_styles.add('cvff') - aorig = [a for a in map(EncodeAName, tokens[2:6])] - atom_names,_ignore = OOPImproperNameSort(tokens[2:6]) - improper_name = EncodeInteractionName(atom_names, section_is_auto) - imsym = improper_symmetry_subgraph[improper_name] = 'cenJflipIL' - subgraph2impname['cenJflipIL'].add(improper_name) CONTINUEHERE - improper2ver[imsym][improper_name] = tokens[0] - improper2ref[imsym][improper_name] = tokens[1] - improper2priority_or[imsym][improper_name] = \ - DetermineNumericPriority(section_is_auto, - tokens[2:6], - float(improper2ver[imsym][improper_name])) - improper_is_secondary_or[imsym][imp_name_orig] = False - improper2priority[imsym][improper_name] = \ - (section_is_auto, - improper_is_secondary_or[imsym][imp_name_orig], - improper2priority_or[imsym][improper_name]) - K = tokens[6] - n = tokens[7] - chi0 = tokens[8] - improper2style[imsym][improper_name] = 'cvff' - improper2params[imsym][improper_name] = (Kchi+' '+n+' '+chi0) - #if improper_style_name == 'cvff': - # improper2params[improper_name] = (Kchi+' '+n+' '+chi0) - # improper_symmetry_subgraph[improper_name] = 'cenJswapIL' - - - elif ((len(tokens) > 7) and (section_name == '#wilson_out_of_plane') - and (improper_styles_selected and set(['class2','wilson_out_of_plane']))): - if line.lstrip().find('!') == 0: - continue - improper_styles.add('class2') - sys.stderr.write('tokens = ' + str(tokens) + '\n') - - version = tokens[0] - reference = tokens[1] - aorig = [a for a in map(EncodeAName, tokens[2:6])] - - # To avoid redundancy, it is necessary to order the atoms - # in the interaction so that two equivalent ways of ordering - # the atoms in an improper interaction do not get misinterpreted - # as two different types of improper interactions. So we sort - # the 3 "leaf" atoms surrounding the central "hub" by name. - - atom_names, permutation = Class2ImproperNameSort(tokens[2:6]) - - # This will effect the formula for the energy. - # (specifically the "chi0" parameter) - # When we lookup the various cross-term interactions for that - # same improper interaction, we will be sure to sort them - # in the same way to make sure those interactions are - # associated with the same improper interaction. - - imp_name_orig = EncodeInteractionName(atom_names, section_is_auto) - #improper_symmetry_subgraph_or[improper_name] = 'dihedrals_nosym' (<--no) - imsym = improper_symmetry_subgraph_or[imp_name_orig] = 'cenJsortIKL' - improper2ver_or[imsym][imp_name_orig] = version - improper2ref_or[imsym][imp_name_orig] = reference - improper2priority_or[imsym][imp_name_orig] = \ - DetermineNumericPriority(section_is_auto, - tokens[2:6], - float(improper2ver_or[imp_name_orig])) - improper_is_secondary_or[imsym][imp_name_orig] = False - #improper2priority[imp_name_orig] = \ - # (section_is_auto, - # improper_is_secondary_or[imp_name_orig], - # improper2priority_or[imp_name_orig]) - K = tokens[6] - chi0 = tokens[7] - - if Parity(permutation) != 0: - # Each time the order of a pair of atoms is swapped in - # the interaction, all 3 of the "X" (chi) angles change sign - # The formula for the ordinary term in the improper - # interaction is Ei = K*((Xijkl + Xkjli + Xljik)/3 - chi0)^2 - # This formula is invariant if we change the sign of all - # Xijkl, Xkjli, Xljik, chi0 - # Hence, we can account for a change in atom order by - # changing the sign of the "chi0" parameter. - # We calculate the "Parity" of the permutation (ie whether - # the permutation has an even or odd number of swaps) - # and multiply chi0 by -1 for each swap. - # It's not clear if this is necessary since in practice - # the "chi0" parameter is usually zero. - - chi0 = str(-1.0*float(chi0)) # same as ('-' + chi0) - - improper2style_or[imsym][imp_name_orig] = 'class2' - improper2params_or[imsym][imp_name_orig] = [K, chi0] - #improper2params[imp_name_orig] = K + ' ' + chi0 - # default values for cross terms: - if not imp_name_orig in improper2class2_aa_or: - improper2class2_aa_or[imsym][imp_name_orig] = '0.0' #(default) - improper2ver_aa_or[imsym][imp_name_orig] = version - improper2ref_aa_or[imsym][imp_name_orig] = reference - # Initially, set all of the angle-angle cross terms to zero - # Start with the first cross term between aorig[0],aorig[1],aorig[2] & aorig[2],aorig[1],aorig[3] - improper2cross[imp_name_orig][ImCrossTermID([aorig[0],aorig[1],aorig[2],aorig[3]])] = '0.0' - # ...then cyclically permute the 3 "leaf" atoms (aorig[0], aorig[2], aorig[3]) around the "hub" atom (aorig[1]) - improper2cross[imp_name_orig][ImCrossTermID([aorig[2],aorig[1],aorig[3],aorig[0]])] = '0.0' - improper2cross[imp_name_orig][ImCrossTermID([aorig[3],aorig[1],aorig[0],aorig[2]])] = '0.0' - - elif ((len(tokens) > 6) and (section_name == '#angle-angle') - and (improper_styles_selected and set(['class2','wilson_out_of_plane']))): - if line.lstrip().find('!') == 0: - continue - improper_styles.add('class2') - version = tokens[0] - reference = tokens[1] - aorig = [a for a in map(EncodeAName, tokens[2:6])] - atom_names, permutation = Class2ImproperNameSort(tokens[2:6]) - imp_name_orig = EncodeInteractionName(atom_names, section_is_auto) - imsym = improper_symmetry_subgraph_or[imp_name_orig] = 'cenJsortIKL' - improper2ver_aa_or[imsym][imp_name_orig] = version - improper2ref_aa_or[imsym][imp_name_orig] = reference - K = tokens[6] - improper2style_or[imsym][imp_name_orig] = 'class2' - if not imp_name_orig in improper2params_or: - improper_is_secondary_or[imsym][imp_name_orig] = True #only cross terms have been defined so far - improper2params_or[imsym][imp_name_orig] = ['0.0', '0.0'] - improper2ver_or[imsym][imp_name_orig] = version - improper2ref_or[imsym][imp_name_orig] = reference - improper2priority_or[imsym][imp_name_orig] = 0.0 - if not imp_name_orig in improper2cross: - # then initialize all of the cross terms to zero - improper2cross[imp_name_orig][ImCrossTermID([aorig[0],aorig[1],aorig[2],aorig[3]])] = '0.0' - # ...then cyclically permute the 3 "leaf" atoms (aorig[0], aorig[2], aorig[3]) around the "hub" atom (aorig[1]) - improper2cross[imp_name_orig][ImCrossTermID([aorig[2],aorig[1],aorig[3],aorig[0]])] = '0.0' - improper2cross[imp_name_orig][ImCrossTermID([aorig[3],aorig[1],aorig[0],aorig[2]])] = '0.0' - #improper2class2_aa_or[imp_name_orig] = K (not needed) - improper2cross[imp_name_orig][ImCrossTermID(aorig)] = K - - elif (len(tokens) > 0) and (section_name == '#out_of_plane-out_of_plane'): - if line.lstrip().find('!') == 0: - continue - display_OOP_OOP_warning = True - - elif (len(tokens) > 0) and (section_name == '#torsion-torsion_1'): - if line.lstrip().find('!') == 0: - continue - display_torsion_torsion_1_warning = True - - elif section_name == '#templates': - #if line.lstrip().find('!') == 0: - # continue - lines_templates.append(line) - - elif section_name == '#reference': - if line.lstrip().find('!') == 0: - continue - if len(tokens_after_section_name) > 0: - ref_number = int(tokens_after_section_name[0]) - if len(line.strip()) > 0: - lines_references[ref_number].append(line) - - - - """ - --- these next few lines of code appear to be unnecessary. - --- I'll probably delete this code in a later version - elif (len(tokens) > 3) and (section_name == '#hbond_definition'): - hbondID = tokens[1] - if tokens[2] == 'distance': - hbond2distance[hbondID] = tokens[3] - if tokens[2] == 'angle': - hbond2angle[hbondID] = tokens[3] - if tokens[2] == 'donors': - hbond2donors[hbondID] = map(EncodeAName, tokens[2:]) - if tokens[2] == 'acceptors': - hbond2acceptors[hbondID] = map(EncodeAname(),tokens[2:]) - """ - - - if display_OOP_OOP_warning: - lines_warnings.append('###########################################################\n' - '# WARNING\n' - '# ALL \"out-of-plane_out-of_plane\" INTERACTIONS ARE IGNORED.\n' - '# CHECK THAT THESE TERMS ARE NEGLEGIBLY SMALL.\n' - '# \"out-of-plane_out-of_plane\" interactions are not yet supported in LAMMPS\n' - '# (...as of 2017-10-13) There is no way that moltemplate can produce\n' - '# LAMMPS compatible parameter files for these interactions.\n' - '###########################################################\n') - - if display_torsion_torsion_1_warning: - lines_warnings.append('###########################################################\n' - '# WARNING\n' - '# ALL \"torsion_torsion_1\" INTERACTIONS ARE IGNORED.\n' - '# CHECK THAT THESE TERMS ARE NEGLEGIBLY SMALL.\n' - '# \"torsion_torsion_1\" interactions are not yet supported in LAMMPS\n' - '# (...as of 2017-10-13) There is no way that moltemplate can produce\n' - '# LAMMPS compatible parameter files for these interactions.\n' - '###########################################################\n') - - - sys.stderr.write(' done.\n' - 'building lookup tables...') - - - - - - - - """ - --- these next few lines of code appear to be unnecessary. - --- I'll probably delete them eventually - if len(hbond2params) > 0: - sys.stdout.write('\n\n write_once("In Settings") {\n') - if hbond_style == 'hbond/dreiding/lj': - for hbondID, angle in hbond2angle: - hbond2params[hbondID] = hbond2distance[hbondID]+' '+hbond2angle[hbondID] ##<--this is not correct - for hbondID, params in hbond2params: - for donor in hbond2donors[hbondID]: - for acceptor in hbond2acceptors[hbondID]: - for hydrogen in hbond2hydrogens[hbondID]: - sys.stdout.write('pair_coeff @atom:'+donor+' @atom:'+acceptor+' '+hbond_style+' @atom:'+hydrogen+' i '+params+'\n') - sys.stdout.write(' } # (DREIDING style H-bond parameters)\n\n\n') - """ - - - - - - - sys.stderr.write(" done.\n") - sys.stderr.write("Trying all combinations of atom types...") - - - - - - - - ##################### POST-PROCESSING ######################## - - - - - - for ang_name_orig in angle2params_or: - - is_auto = (ang_name_orig.find('auto_') == 0) - - atom_names = ExtractANames(ang_name_orig) - - num_angles = 0 - - atom_combos = [set([]), set([]), set([])] - - # We must consider every possible combination of atom types - # which satisfy BOTH angle_equivalences and bond_equivalences. - # ...AND we must consider BOTH regular AND auto equivalences. - # For each combination generate a separate @angle interaction. - # (I fear this will make the resulting .LT file large.) - - # Use different auto equivalence lookup tables for different - # atoms in the interaction. (ie the "center" and "end" atoms) - auto_angle2atom = [auto_angleend2atom, - auto_anglecenter2atom, - auto_angleend2atom] - - for i in range(0, 3): - angle_atom_name = atom_names[i] - sys.stderr.write('DEBUG: angle_atom_name = '+angle_atom_name+'\n') - if not is_auto: - assert(angle_atom_name[-1] != '_') - # assume regular equivalences when looking up atom types - sys.stderr.write('DEBUG: equiv_angle2atom['+angle_atom_name+'] = '+ - str(equiv_angle2atom[angle_atom_name])+'\n') - for a in equiv_angle2atom[angle_atom_name]: - atom_combos[i].add(a) - else: - #assert((angle_atom_name[-1] == '_') or (angle_atom_name[0] == '*')) (<--some exceptions. don't assert this) - - # assume "auto" equivalences when looking up atom types - sys.stderr.write('DEBUG: auto_angle2atom['+str(i)+']['+angle_atom_name+'] = \n' - ' '+str(equiv_angle2atom[i][angle_atom_name])+'\n') - for a in auto_angle2atom[i][angle_atom_name]: - atom_combos[i].add(a) - - found_at_least_one = False - #for a1 in atom_combos[0]: - for a1 in sorted(list(atom_combos[0])): - #for a2 in atom_combos[1]: - for a2 in sorted(list(atom_combos[1])): - #sys.stderr.write('atom2auto_bond = '+str(atom2auto_bond)+'\n') - bond_data1 = LookupBondLength(a1, a2, - atom2equiv_bond, - bond2r0, - atom2auto_bond, - bond2r0_auto) - if bond_data1 == None: # Save time by continuing only if a - continue # bond was defined between a1 and a2 - - #for a3 in atom_combos[2]: - for a3 in sorted(list(atom_combos[2])): - bond_data2 = LookupBondLength(a2, a3, - atom2equiv_bond, - bond2r0, - atom2auto_bond, - bond2r0_auto) - if bond_data2 == None: - continue - - #bond lengths: - r0s = [0.0, 0.0] - #equivalent atom names used to lookup the bonds: - batoms = [['', ''], ['', '']] - #were "auto" equivalences needed to lookup the bond length? - b_is_auto = [False, False] - r0s[0], batoms[0], b_is_auto[0] = bond_data1 - r0s[1], batoms[1], b_is_auto[1] = bond_data2 - order_reversed = aorig[0] > aorig[-1] - if order_reversed: - batoms.reverse() - batoms[0].reverse() - batoms[1].reverse() - b_is_auto.reverse() - ang_name_full = (ang_name_orig + ',' + - EncodeInteractionName(batoms[0], b_is_auto[0]) + ',' + - EncodeInteractionName(batoms[1], b_is_auto[1])) - - - #sys.stderr.write('DEBUG: (a1,a2,a3) = '+str((a1,a2,a3))+', ' - # ' (b11,b12,b21,b22) = '+str(batoms)+'\n') - angle2ref_or[ang_name_full] = reference - angle2style_or[ang_name_full] = 'class2' - theta0_K_params = angle2params_or[ang_name_orig] - angle2params[ang_name_full] = ' '.join(theta0_K_params) - if ang_name_orig in angle2class2_bb_or: - Kbb = angle2class2_bb_or[ang_name_orig] - assert(ang_name_orig in angle2ver_bb_or) - assert(ang_name_orig in angle2ref_bb_or) - else: #(use default values) - Kbb = '0.0' - angle2class2_bb_or[ang_name_orig] = Kbb - angle2ver_bb_or[ang_name_orig] = angle2ver_or[ang_name_orig] - angle2ref_bb_or[ang_name_orig] = angle2ref_or[ang_name_orig] - angle2class2_bb[ang_name_full] = (Kbb+' '+r0s[0]+' '+r0s[1]) - angle2priority_bb = \ - DetermineNumericPriority(is_auto, - batoms[0] + batoms[1], - float(angle2ver_bb_or[ang_name_orig])) - angle2ver_bb[ang_name_full] = angle2ver_bb_or[ang_name_orig] - angle2ref_bb[ang_name_full] = angle2ref_bb_or[ang_name_orig] - - if ang_name_orig in angle2class2_ba_or: - Kba = angle2class2_ba_or[ang_name_orig] - assert(ang_name_orig in angle2ver_ba_or) - assert(ang_name_orig in angle2ref_ba_or) - else: #(use default values) - Kba = ['0.0', '0.0'] - angle2class2_ba_or[ang_name_orig] = Kba - angle2ver_ba_or[ang_name_orig] = angle2ver_or[ang_name_orig] - angle2ref_ba_or[ang_name_orig] = angle2ref_or[ang_name_orig] - angle2class2_ba[ang_name_full] = (Kba[0]+' '+Kba[1]+' '+r0s[0]+' '+r0s[1]) - angle2sym_ba = (Kba[0] == Kba[1]) - angle2priority_ba = \ - DetermineNumericPriority(is_auto, - batoms[0] + batoms[1], - angle2ver_ba_or[ang_name_orig]) - angle2ver_ba[ang_name_full] = angle2ver_ba_or[ang_name_orig] - angle2ref_ba[ang_name_full] = angle2ref_ba_or[ang_name_orig] - - version = max((angle2ver_or[ang_name_orig], - angle2ver_bb_or[ang_name_orig], - angle2ver_ba_or[ang_name_orig])) - angle2ver[ang_name_full] = version - angle2ref[ang_name_full] = angle2ref_or[ang_name_orig] - angle2style[ang_name_full] = 'class2' - angle2priority[ang_name_full] = \ - (is_auto, - angle_is_secondary_or[ang_name_orig], - angle2priority_or[ang_name_orig], - angle2priority_bb, - angle2priority_ba) - - if num_angles < len(angle2params): - sys.stderr.write('DEBUG: '+section_name[1:]+' r0 ('+ang_name_full+') = ('+r0s[0]+', '+r0s[1]+')\n') - sys.stderr.write('DEBUG: len(angle2class2_bb) = '+str(len(angle2class2_bb))+'\n') - sys.stderr.write('DEBUG: '+section_name[1:]+' r0 ('+ang_name_full+') = ('+r0s[0]+', '+r0s[1]+')\n') - #sys.stderr.write('DEBUG: len(angle2class2_ba) = '+str(len(angle2class2_ba))+'\n') - num_angles = len(angle2params) - - if ((not angle2sym_ba) - and - (atom_names[0] == atom_names[2])): - raise InputError('Error: Unsupported angle interaction: \"@angle:'+str(ang_name_orig)+'\"\n' - ' This interaction has symmetric atom names:\n' - ', '.join(atom_names)+'\n' - ' and yet it lacks symmetry in the corresponding force field parameters.\n' - ' (If this is not a mistake in the .frc file, then explain\n' - ' why to andrew so he can fix this.)\n') - - - found_at_least_one = True - - - if not found_at_least_one: - lines_warnings.append('# WARNING: Undefined bond length (r0) in angle: ' + - ' '.join(atom_names)+'\n') - # Then we were unable to define cross terms for this interaction - # because at least one of the bond lengths could not be determined. - # This usually occurs because most of the .FRC files which are - # in circulation are incomplete. We have to handle this gracefully. - ang_name_full = (ang_name_orig + ',X,X,X,X,X,X') - version = angle2ver_or[ang_name_orig] - reference = angle2ref_or[ang_name_orig] - angle2ref[ang_name_full] = reference - angle2ver[ang_name_full] = version - angle2style[ang_name_full] = 'class2' - angle2params[ang_name_full] = ' '.join(angle2params_or[ang_name_orig]) - # substitute zeros for all the cross term interactions - angle2priority[ang_name_full] = angle2priority_or[ang_name_orig] - angle2class2_bb[ang_name_full] = '0.0 1.0 1.0' - angle2ref_bb[ang_name_full] = reference - angle2ver_bb[ang_name_full] = version - angle2class2_ba[ang_name_full] = '0.0 0.0 1.0 1.0' - angle2ref_ba[ang_name_full] = reference - angle2ver_ba[ang_name_full] = version - #sys.stderr.write('bond_names = ' + str(bond_names) + '\n') - - - - - - ############ POST-PROCESSING DIHEDRALS ########### - - - - for dih_name_orig in dihedral2params_or: - #assert(dih_name_orig in dihedral2class2_mbt_or) - #assert(dih_name_orig in dihedral2class2_ebt_or) - #assert(dih_name_orig in dihedral2class2_bb13_or) - #assert(dih_name_orig in dihedral2class2_at_or) - #assert(dih_name_orig in dihedral2class2_aat_or) - - is_auto = (dih_name_orig.find('auto_') == 0) - - atom_names = ExtractANames(dih_name_orig) - - num_dihedrals = 0 - - atom_combos = [set([]), set([]), set([]), set([])] - - # We must consider every possible combination of atom types - # which satisfy all three: - # dihedral_equivalences - # bond_equivalences - # angle_equivalences - # ...AND we must consider BOTH regular AND auto equivalences. - # For each combination generate a separate @dihedral interaction. - # (I fear this will make the resulting .LT file large.) - - # Use different auto equivalence lookup tables for different - # atoms in the interaction. (ie the "center" and "end" atoms) - auto_dihedral2atom = [auto_dihedralend2atom, - auto_dihedralcenter2atom, - auto_dihedralcenter2atom, - auto_dihedralend2atom] - - for i in range(0, 4): - dihedral_atom_name = atom_names[i] - sys.stderr.write('DEBUG: dihedral_atom_name = '+dihedral_atom_name+'\n') - if not is_auto: - assert(dihedral_atom_name[-1] != '_') - # assume regular equivalences when looking up atom types - sys.stderr.write('DEBUG: equiv_dihedral2atom['+dihedral_atom_name+'] = '+ - str(equiv_dihedral2atom[dihedral_atom_name])+'\n') - for a in equiv_dihedral2atom[dihedral_atom_name]: - atom_combos[i].add(a) - else: - assert((dihedral_atom_name[-1] == '_') or (ange_atom_name[0] == '*')) - # assume "auto" equivalences when looking up atom types - sys.stderr.write('DEBUG: auto_dihedral2atom['+str(i)+']['+dihedral_atom_name+'] = \n' - ' '+str(equiv_dihedral2atom[i][dihedral_atom_name])+'\n') - for a in auto_dihedral2atom[i][dihedral_atom_name]: - atom_combos[i].add(a) - - found_at_least_one = False - - #for a1 in atom_combos[0]: - for a1 in sorted(list(atom_combos[0])): - - #for a2 in atom_combos[1]: - for a2 in sorted(list(atom_combos[1])): - - #sys.stderr.write('atom2auto_bond = '+str(atom2auto_bond)+'\n') - bond_data12 = LookupBondLength(a1, a2, - atom2equiv_bond, - bond2r0, - atom2auto_bond, - bond2r0_auto) - if bond_data12 == None: - # Save time by only continuing if a bond was - # found between a1 and a2 - continue - #for a3 in atom_combos[2]: - for a3 in sorted(list(atom_combos[2])): - bond_data23 = LookupBondLength(a2, a3, - atom2equiv_bond, - bond2r0, - atom2auto_bond, - bond2r0_auto) - if bond_data23 == None: - # Save time by only continuing if a bond was - # found between a2 and a3 - continue - - angle_data123 = LookupBondAngle(a1, a2, a3, - atom2equiv_angle, - angle2theta0_or, - [atom2auto_angleend, - atom2auto_anglecenter, - atom2auto_anglecenter], - angle2theta0_auto_or) - if angle_data123 == None: - # Save time by only continuing if an angle was - # found between a1, a2, a3 - continue - - - #for a4 in atom_combos[3]: - for a4 in sorted(list(atom_combos[3])): - bond_data34 = LookupBondLength(a3, a4, - atom2equiv_bond, - bond2r0, - atom2auto_bond, - bond2r0_auto) - if bond_data34 == None: - # Save time by only continuing if a bond was - # found between a3 and a4 - continue - - #rest bond lengths: - r0s = [0.0, 0.0, 0,0] - #equivalent atom names used to lookup the bonds: - batoms = [['', ''], ['', ''], ['','']] - #are these bond interactions "auto" interactions? - #were "auto" equivalences needed to lookup the bond length? - b_is_auto = [False, False, False] - r0s[0], batoms[0], b_is_auto[0] = bond_data12 - r0s[1], batoms[1], b_is_auto[1] = bond_data23 - r0s[2], batoms[2], b_is_auto[2] = bond_data34 - - angle_data234 = LookupBondAngle(a2, a3, a4, - atom2equiv_angle, - angle2theta0_or, - [atom2auto_angleend, - atom2auto_anglecenter, - atom2auto_anglecenter], - angle2theta0_auto_or) - if angle_data234 == None: - # Save time by only continuing if an angle was - # found between a2, a3, a4 - continue - - #rest angles: - theta0s = [0.0, 0.0] - #equivalent atom names used to lookup angles: - aatoms = [['', '',''], ['', '','']] - #were "auto" equivalences needed to lookup the bond-angle? - a_is_auto = [False, False] - theta0s[0], aatoms[0], a_is_auto[0] = angle_data123 - theta0s[1], aatoms[1], a_is_auto[1] = angle_data234 - order_reversed = aorig[0] > aorig[-1] - if order_reversed: - batoms.reverse() - batoms[0].reverse() - batoms[1].reverse() - batoms[2].reverse() - b_is_auto.reverse() - theta0s.reverse() - aatoms.reverse() - aatoms[0].reverse() - aatoms[1].reverse() - a_is_auto.reverse() - - #if is_auto: - dih_name_full = (dih_name_orig + ',' + - EncodeInteractionName(batoms[0], b_is_auto[0]) + ',' + - EncodeInteractionName(batoms[1], b_is_auto[1]) + ',' + - EncodeInteractionName(batoms[2], b_is_auto[2]) + ',' + - EncodeInteractionName(aatoms[0], a_is_auto[0]) + ',' + - EncodeInteractionName(aatoms[1], a_is_auto[1])) - #else: - # assert(batoms[0][1] == batoms[1][0]) - # assert(batoms[1][1] == batoms[2][0]) - # assert(aatoms[0][1] == aatoms[1][0]) - # assert(aatoms[0][2] == aatoms[1][1]) - # dih_name_full = dih_name_orig + ',' + \ - # EncodeInteractionName([batoms[0][0], batoms[0][1] - # batoms[2][0], batoms[2][1], - # aatoms[0][0], aatoms[0][1], - # aatoms[0][2], aatoms[1][0]], - # False) - - ########### Fourier terms ########### - #if dih_name_orig in dihedral2param_or: - V_phi0_params = dihedral2params_or[dih_name_orig] - dihedral2params[dih_name_full] = ' '.join(V_phi0_params) - #else: - # dihedral2params[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0' - - ########### "mbt", "ebt", and "aat" terms ########### - # "mbt" terms: - if dih_name_orig in dihedral2class2_mbt_or: - Fmbt = dihedral2class2_mbt_or[dih_name_orig] - else: - Fmbt = ['0.0', '0.0', '0.0'] - dihedral2class2_mbt_or[dih_name_orig] = Fmbt - dihedral2ver_mbt_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] - dihedral2ref_mbt_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] - dihedral2class2_mbt[dih_name_full] = \ - (Fmbt[0]+' '+Fmbt[1]+' '+Fmbt[2]+' '+r0s[1]) - dihedral2priority_mbt = \ - DetermineNumericPriority(is_auto, - batoms[1], - float(dihedral2ver_mbt_or[dih_name_orig])) - dihedral2ver_mbt[dih_name_full] = dihedral2ver_mbt_or[dih_name_orig] - dihedral2ref_mbt[dih_name_full] = dihedral2ref_mbt_or[dih_name_orig] - - # "ebt" terms: - if dih_name_orig in dihedral2class2_ebt_or: - Febt = dihedral2class2_ebt_or[dih_name_orig] - dihedral2sym_ebt = ((Febt[0][0] == Febt[1][0]) and - (Febt[0][1] == Febt[1][1]) and - (Febt[0][2] == Febt[1][2])) - #and (r0s[0] == r0s[2])) - else: - Febt = [['0.0','0.0','0.0'], ['0.0','0.0','0.0']] - dihedral2class2_ebt_or[dih_name_orig] = Febt - dihedral2ver_ebt_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] - dihedral2ref_ebt_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] - dihedral2sym_ebt = True - dihedral2class2_ebt[dih_name_full]= (Febt[0][0] + ' ' + - Febt[0][1] + ' ' + - Febt[0][2] + ' ' + - Febt[1][0] + ' ' + - Febt[1][1] + ' ' + - Febt[1][2] + ' ' + - r0s[0]+' '+r0s[2]) - - dihedral2priority_ebt = \ - DetermineNumericPriority(is_auto, - batoms[0] + batoms[2], - float(dihedral2ver_ebt_or[dih_name_orig])) - dihedral2ver_ebt[dih_name_full] = dihedral2ver_ebt_or[dih_name_orig] - dihedral2ref_ebt[dih_name_full] = dihedral2ref_ebt_or[dih_name_orig] - - #(Note: large atom_priority number <==> low priority - # Only one of the atom priority numbers should be > 0) - - # "bb13" terms: - if dih_name_orig in dihedral2class2_bb13_or: - Kbb13 = dihedral2class2_bb13_or[dih_name_orig] - #dihedral2sym_bb13 = (r0s[0] == r0s[2]) - dihedral2sym_bb13 = True - else: - Kbb13 = '0.0' - dihedral2class2_bb13_or[dih_name_orig] = Kbb13 - dihedral2ver_bb13_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] - dihedral2ref_bb13_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] - dihedral2sym_bb13 = True - - dihedral2class2_bb13[dih_name_full] = (Kbb13+' '+r0s[0]+' '+r0s[2]) - dihedral2priority_bb13 = \ - DetermineNumericPriority(is_auto, - batoms[0] + batoms[2], - float(dihedral2ver_bb13_or[dih_name_orig])) - dihedral2ver_bb13[dih_name_full] = dihedral2ver_bb13_or[dih_name_orig] - dihedral2ref_bb13[dih_name_full] = dihedral2ref_bb13_or[dih_name_orig] - - - ########### "at" and "aat" terms ########### - # "at" terms: - if dih_name_orig in dihedral2class2_at_or: - Fat = dihedral2class2_at_or[dih_name_orig] - dihedral2sym_at = ((Fat[0][0] == Fat[1][0]) and - (Fat[0][1] == Fat[1][1]) and - (Fat[0][2] == Fat[1][2])) - #and (theta0[0] == theta0[1])) - else: - Fat = [['0.0','0.0','0.0'], ['0.0','0.0','0.0']] - dihedral2class2_at_or[dih_name_orig] = Fat - dihedral2ver_at_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] - dihedral2ref_at_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] - dihedral2sym_at = True - dihedral2class2_at[dih_name_full] = \ - (Fat[0][0] + ' ' + - Fat[0][1] + ' ' + - Fat[0][2] + ' ' + - Fat[1][0] + ' ' + - Fat[1][1] + ' ' + - Fat[1][2] + ' ' + - theta0s[0] + ' ' + - theta0s[1]) - dihedral2priority_at = \ - DetermineNumericPriority(is_auto, - aatoms[0] + aatoms[1], - float(dihedral2ver_at_or[dih_name_orig])) - dihedral2ver_at[dih_name_full] = dihedral2ver_at_or[dih_name_orig] - dihedral2ref_at[dih_name_full] = dihedral2ref_at_or[dih_name_orig] - - - # "aat" terms: - if dih_name_orig in dihedral2class2_aat_or: - Kaat = dihedral2class2_aat_or[dih_name_orig] - #dihedral2sym_aat = (theta0[0] == theta0[1]) - dihedral2sym_aat = True - else: - Kaat = '0.0' - dihedral2class2_aat_or[dih_name_orig] = Kaat - dihedral2ver_aat_or[dih_name_orig] = dihedral2ver_or[dih_name_orig] - dihedral2ref_aat_or[dih_name_orig] = dihedral2ref_or[dih_name_orig] - dihedral2sym_aat = True - dihedral2class2_aat[dih_name_full] = \ - (Kaat+' '+theta0s[0]+' '+theta0s[1]) - dihedral2priority_aat = \ - DetermineNumericPriority(is_auto, - aatoms[0] + aatoms[1], - float(dihedral2ver_aat_or[dih_name_orig])) - dihedral2ver_aat[dih_name_full] = dihedral2ver_aat_or[dih_name_orig] - dihedral2ref_aat[dih_name_full] = dihedral2ref_aat_or[dih_name_orig] - - if len(dihedral2params) > num_dihedrals: - sys.stderr.write('DEBUG: dihedral['+dih_name_full+']:\n' - '(r12,r23,r34) = (' - +r0s[0]+','+r0s[1]+','+r0s[2]+') \n' - '(theta123,theta234) = (' - +theta0s[0]+','+theta0s[1]+') \n') - sys.stderr.write('DEBUG: num_dihedrals = len(dihedral2params) = ' - +str(len(dihedral2params))+'\n') - version = max((dihedral2ver_or[dih_name_orig], - dihedral2ver_mbt_or[dih_name_orig], - dihedral2ver_ebt_or[dih_name_orig], - dihedral2ver_bb13_or[dih_name_orig], - dihedral2ver_at_or[dih_name_orig], - dihedral2ver_aat_or[dih_name_orig])) - - dihedral2style[dih_name_full] = 'class2' - dihedral2ver[dih_name_full] = version - dihedral2ref[dih_name_full] = dihedral2ref_or[dih_name_orig] - dihedral2priority[dih_name_full] = \ - (is_auto, - dihedral_is_secondary_or[dih_name_orig], - dihedral2priority_or[dih_name_orig], - dihedral2priority_mbt, - dihedral2priority_ebt, - dihedral2priority_bb13, - dihedral2priority_at, - dihedral2priority_aat) - - num_dihedrals = len(dihedral2params) - - if ((not (dihedral2sym_ebt and - #dihedral2sym_mbt and - # (note: symmetry doesn't make sense for mbt) - dihedral2sym_at and - dihedral2sym_aat and - dihedral2sym_bb13)) - and - ((atom_names[0] == atom_names[3]) and - (atom_names[1] == atom_names[2]))): - raise InputError('Error: Unsupported dihedral interaction: \"@dihedral:'+str(dih_name_orig)+'\"\n' - ' This interaction has symmetric atom names:\n'+ - ', '.join(atom_names)+'\n'+ - ' and yet it lacks symmetry in the corresponding force field parameters.\n'+ - ' (If this is not a mistake in the .frc file, then explain\n'+ - ' why to andrew so he can fix this.)\n') - - found_at_least_one = True - - - #sys.stderr.write('DEBUG: number of interactions = '+str(len(dihedral2class2_bb))+'\n') - if not found_at_least_one: - lines_warnings.append('# WARNING: Undefined bond length (r0) or rest angle (theta0) in dihedral: ' + - #'# the dihedral interaction between: ' + - ' '.join(atom_names)+'\n') - # Then we were unable to define cross terms for this interaction because - # at least one of the bond lengths or bond angles could not be determined. - # This usually occurs because most of the .FRC files which are - # in circulation are incomplete. We have to handle this gracefully. - dih_name_full = (dih_name_orig + ',X,X,X,X,X,X,X,X,X,X,X,X') - reference = dihedral2ref_or[dih_name_orig] - version = dihedral2ver_or[dih_name_orig] - dihedral2ref[dih_name_full] = reference - dihedral2ver[dih_name_full] = version - dihedral2style[dih_name_full] = 'class2' - dihedral2priority[dih_name_full] = dihedral2priority_or[dih_name_orig] - dihedral2params[dih_name_full] = ' '.join(dihedral2params_or[dih_name_orig]) - # substitute zeros for all the cross term interactions - - dihedral2class2_mbt[dih_name_full] = '0.0 0.0 0.0 1.0' - dihedral2ref_mbt[dih_name_full] = reference - dihedral2ver_mbt[dih_name_full] = version - - dihedral2class2_ebt[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0' - dihedral2ref_ebt[dih_name_full] = reference - dihedral2ver_ebt[dih_name_full] = version - - dihedral2class2_bb13[dih_name_full] = '0.0 1.0 1.0' - dihedral2ref_bb13[dih_name_full] = reference - dihedral2ver_bb13[dih_name_full] = version - - dihedral2class2_at[dih_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0 120.0 120.0' - dihedral2ref_at[dih_name_full] = reference - dihedral2ver_at[dih_name_full] = version - - dihedral2class2_aat[dih_name_full] = '0.0 120.0 120.0' - dihedral2ref_aat[dih_name_full] = reference - dihedral2ver_aat[dih_name_full] = version - - - - - - - - - ############ POST-PROCESSING IMPROPERS ########### - - - - - imsym = 'cenJsortIKL' - for imp_name_orig in improper2cross[imsym]: - - if improper2style_or[imsym][imp_name_orig] != 'class2': - continue - - assert(imp_name_orig in improper2params_or[imsym]) - assert(imp_name_orig in improper2class2_aa_or[imsym]) - - is_auto = (imp_name_orig.find('auto') == 0) - - atom_names = ExtractANames(imp_name_orig) - - num_impropers = 0 - - atom_combos = [set([]), set([]), set([]), set([])] - - # We must consider every possible combination of atom types - # which satisfy both: - # improper_equivalences - # angle_equivalences - # ...AND we must consider BOTH regular AND auto equivalences. - # For each combination generate a separate @improper interaction. - # (I fear this will make the resulting .LT file large.) - - # Use different auto equivalence lookup tables for different - # atoms in the interaction. (ie the "center" and "end" atoms) - - auto_improper2atom = [auto_improperend2atom, - auto_impropercenter2atom, - auto_improperend2atom, - auto_improperend2atom] - - for i in range(0, 4): - improper_atom_name = atom_names[i] - sys.stderr.write('DEBUG: improper_atom_name = '+improper_atom_name+'\n') - if not is_auto: - assert(improper_atom_name[-1] != '_') - # assume regular equivalences when looking up atom types - sys.stderr.write('DEBUG: equiv_improper2atom['+improper_atom_name+'] = '+ - str(equiv_improper2atom[improper_atom_name])+'\n') - for a in equiv_improper2atom[improper_atom_name]: - atom_combos[i].add(a) - else: - assert((improper_atom_name[-1] == '_') or (improper_atom_name[0] == 'X')) - # assume "auto" equivalences when looking up atom types - sys.stderr.write('DEBUG: auto_improper2atom['+str(i)+']['+improper_atom_name+'] = \n' - ' '+str(auto_improper2atom[i][improper_atom_name])+'\n') - for a in auto_improper2atom[i][improper_atom_name]: - atom_combos[i].add(a) - - is_auto = IsAutoInteraction(imp_name_orig) # is this an "auto" interaction? - - atom_names = ExtractANames(imp_name_orig) # names of all 4 atoms - lnames = [atom_names[0], atom_names[2], atom_names[3]] # names of "leaf" atoms - - #M1 = improper2cross[imp_name_orig][ 2 ] - #M2 = improper2cross[imp_name_orig][ 0 ] - #M3 = improper2cross[imp_name_orig][ 3 ] - - #try: - M1 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[0], - atom_names[1], - atom_names[2], - atom_names[3]])] - #except KeyError: - # M1 = '0.0' - - #try: - M2 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[2], - atom_names[1], - atom_names[0], - atom_names[3]])] - #except KeyError: - # M2 = '0.0' - - #try: - M3 = improper2cross[imp_name_orig][ImCrossTermID([atom_names[0], - atom_names[1], - atom_names[3], - atom_names[2]])] - #except KeyError: - # M3 = '0.0' - - - - - - - # ###### Symmetry: ###### - # Unfortunately, it's time to wade into the messy issue of symmetry. - # We desire a way to detect whether an improper interaction - # between 4 atoms is invariant with respect to atom reordering - # of the 3 peripheral "leaf" atoms which surround the central atom. - # In principle, any rearrangement of atoms would require a separate - # class2 improper interaction. However, in some cases, when the - # parameters for these rearrangements are symmetric, we can detect - # that and warn moltemplate that it is not necessary to generate new - # improper interactions for every conceivable permutation of these - # atoms. Figuring out when it is safe to do that is a headache. - # (...but it's necessary. Otherwise each junction in the molecule - # will generate 3*2*1=6 improper interactions which are usually - # redundant. This will slow down the simulation significantly - # and may make it difficult to compare the resulting LAMMPS - # input files with those generated by other tools like msi2lmp.) - # - # To make this easier, I store the parameters in arrays which - # are arranged in a more symmetric way - M = [0.0, 0.0, 0.0] - theta0 = [0.0, 0.0, 0.0] - # noti3[i] = the sorted tuple of integers from the - # set {0,1,2} which remain after deleting i - noti3 = ((1,2), (0,2), (0,1)) - i_neigh = [ ([0,2,3][ noti3[i][0] ], # neighbor leaves of ith leaf - [0,2,3][ noti3[i][1] ]) for i in range(0,3)] - for i in range(0, 3): - # You will notice the pattern "[0,2,3][i]" appears often in the - # code below because for class 2 force-fields, the second atom - # (with index 1) is the central atom ("hub" atom), and the three - # that surround it ("leaf" atoms) have indices 0,2,3. I want - # to skip over the central atoms and loop over the leaf atoms - imTermID = ImCrossTermID([atom_names[ i_neigh[i][0] ], - atom_names[ 1 ], - atom_names[ [0,2,3][i] ], - atom_names[ i_neigh[i][1] ]]) - M[i] = float(improper2cross[imp_name_orig][imTermID]) - ##i_leaf = [0,2,3][i] - ##M[i] = float(improper2cross[imp_name_orig][ i_leaf ]) - #angle_name_l = SortByEnds([atom_names[i_neigh[i][0]], - # atom_names[ 1 ], - # atom_names[i_neigh[i][1]]]) - #angle_name = EncodeInteractionName(angle_name_l, is_auto) - #theta0[i] = float(angle2theta0_or[angle_name]) - - for i in range(0, 3): - if (M[ noti3[i][0] ] == M[ noti3[i][1] ]): - #and (theta0[ noti3[i][0] ] == theta0[ noti3[i][1] ])): - # Then it is safe to swap the order of these two atoms in - # the list of atoms when looking up force-field parameters - improper2sym[imp_name_orig].add(i_neigh[i][0]) - improper2sym[imp_name_orig].add(i_neigh[i][1]) - # Later, I can use these to decide whether or not I need to - # change the default script with symmetry rules. (I'm hoping - # that "cenJsortIKL.py" should work in most cases.) - # CONTINUEHERE: FIGURE OUT WHETHER TO WORRY ABOUT improper2sym - else: - if atom_names[i_neigh[i][0]] == atom_names[i_neigh[i][1]]: - raise InputError('Error: Unsupported improper interaction: \"@improper:'+str(imp_name_orig)+'\"\n' - ' This interaction has matching atom aliases:\n' - ' (@atom:'+str(atom_names[i_neigh[i][0]])+ - ', @atom:'+str(atom_names[i_neigh[i][1]])+')\n' - ' and yet it lacks symmetry in the corresponding force field parameters.\n' - ' (If this is not a mistake in the .frc file, then ask andrew to\n' - ' fix this limitation.)\n') - - - found_at_least_one = False - for a1 in sorted(list(atom_combos[0])): - for a2 in sorted(list(atom_combos[1])): - sys.stderr.write('DEBUG: improper '+imp_name_orig+' substitutions: '+a1+','+a2+',...\n') - for a3 in sorted(list(atom_combos[2])): - #(Note: sorting "atom_combos" makes it faster and easier - # to follow the loop's progress. This nested loop can be very slow.) - theta0s = ['0.0', '0.0', '0.0'] - aatoms = [['', '',''], ['', '',''], ['', '', '']] - #were "auto" equivalences needed to lookup the bond-angle? - a_is_auto = [False, False, False] - # Collect information from the different terms in a class2 improper: - # http://lammps.sandia.gov/doc/improper_class2.html - - # Loop over the neighbors of the central atom in each improper - # interaction and collect all the Mi and Ti parameters. Collect - # them in the order they appear in the formula for the Eaa - # term as it appears in the documentation for improper_style class2: - # - # http://lammps.sandia.gov/doc/improper_class2.html - # - # Eaa = M1 (Tijk - T0)(Tkjl - T2) + #common leaf node: k (index 2) - # M2 (Tijk - T0)(Tijl - T1) + #common leaf node: i (index 0) - # M3 (Tijl - T1)(Tkjl - T2) #common leaf node: l (index 3) - # (I'm trying to match the variable names used in this web page - # I wish the author had chosen the M1,M2,M3, T1,T2,T3 order in more - # symmetric way, or at least in a way that makes more sense to me.) - - #angle_name_l = SortByEnds([atom_names[0], atom_names[1], atom_names[2]]) - #angle_name = EncodeInteractionName(angle_name_l, is_auto) - #theta01 = angle2theta0_or[angle_name] - angle_data = LookupBondAngle(a1, a2, a3, - atom2equiv_angle, - angle2theta0_or, - [atom2auto_improperend, - atom2auto_impropercenter, - atom2auto_improperend], - angle2theta0_auto_or) - if angle_data == None: - # Save time by only continuing if an angle was - # found between a1, a2, a3 - continue - theta0s[0], aatoms[0], a_is_auto[0] = angle_data - - - for a4 in sorted(list(atom_combos[3])): - theta0s[1] = theta0s[2] = '0.0' - aatoms[1] = aatoms[2] = ['', '',''] - - #angle_name_l = SortByEnds(aatoms[0]) - #angle_name = EncodeInteractionName(angle_name_l[0], is_auto) - - #theta02 = angle2theta0_or[angle_name] - angle_data = LookupBondAngle(a1, a2, a4, - atom2equiv_angle, - angle2theta0_or, - [atom2auto_improperend, - atom2auto_impropercenter, - atom2auto_improperend], - angle2theta0_auto_or) - if angle_data == None: - # Save time by only continuing if an angle was - # found between a1, a2, a4 - continue - theta0s[1], aatoms[1], a_is_auto[1] = angle_data - - #angle_name_l = SortByEnds(aatoms[1]) - #angle_name = EncodeInteractionName(angle_name_l, is_auto) - - - #theta03 = angle2theta0_or[angle_name] - angle_data = LookupBondAngle(a3, a2, a4, - atom2equiv_angle, - angle2theta0_or, - [atom2auto_improperend, - atom2auto_impropercenter, - atom2auto_improperend], - angle2theta0_auto_or) - if angle_data == None: - # Save time by only continuing if an angle was - # found between a3, a2, a4 - continue - theta0s[2], aatoms[2], a_is_auto[2] = angle_data - - - # The following asserts checks that the two theta0s - # are defined whenever the corresponding M is defined. - # (Note: The order is LAMMPS-implementation specific. - # See http://lammps.sandia.gov/doc/improper_class2.html) - assert((float(theta0s[0]) != 0) or (float(M1) == 0)) - assert((float(theta0s[2]) != 0) or (float(M1) == 0)) - assert((float(theta0s[0]) != 0) or (float(M2) == 0)) - assert((float(theta0s[1]) != 0) or (float(M2) == 0)) - assert((float(theta0s[1]) != 0) or (float(M3) == 0)) - assert((float(theta0s[2]) != 0) or (float(M3) == 0)) - - #angle_name_l = SortByEnds(aatoms[2]) - #angle_name = EncodeInteractionName(angle_name_l, is_auto) - - - imp_name_full = (imp_name_orig + ',' + - EncodeInteractionName(aatoms[0], a_is_auto[0]) + ',' + - EncodeInteractionName(aatoms[1], a_is_auto[1]) + ',' + - EncodeInteractionName(aatoms[2], a_is_auto[2])) - - #if imp_name_orig in improper2params_or[imsym][imp_name_orig]: - improper2params[imsym][imp_name_full] = ' '.join(improper2params_or[imsym][imp_name_orig]) - #else: - # improper2params[imsym][imp_name_full] = '0.0 0.0' - - #if imp_name_orig in improper2cross: - improper2class2_aa[imsym][imp_name_full] = \ - (str(M1)+' '+str(M2)+' '+str(M3)+' '+ - str(theta0s[0])+' '+str(theta0s[1])+' '+str(theta0s[2])) - #else: - # improper2class2_aa[imsym][imp_name_full] = '0.0 0.0 0.0 0.0 0.0 0.0' - # improper2ver_aa_or[imsym][imp_name_orig] = improper2ver_or[imsym][imp_name_orig] - # improper2ref_aa_or[imsym][imp_name_orig] = improper2ref_or[imsym][imp_name_orig] - - improper2priority_aa = \ - DetermineNumericPriority(is_auto, - aatoms[0] + aatoms[1] + aatoms[2], - float(improper2ver_aa_or[imsym][imp_name_orig])) - improper2ver_aa[imsym][imp_name_full] = improper2ver_aa_or[imsym][imp_name_orig] - improper2ref_aa[imsym][imp_name_full] = improper2ref_aa_or[imsym][imp_name_orig] - - - version = max((improper2ver_or[imsym][imp_name_orig], - improper2ver_aa_or[imsym][imp_name_orig])) - improper2style[imsym][imp_name_full] = 'class2' - improper2ref[imsym][imp_name_full] = improper2ref_or[imsym][imp_name_orig] - improper2ver[imsym][imp_name_full] = version - improper2priority[imsym][imp_name_full] = \ - (is_auto, - improper_is_secondary_or[imsym][imp_name_orig], - improper2priority_or[imsym][imp_name_orig], - improper2priority_aa) - - if len(improper2params) > num_impropers: - sys.stderr.write('DEBUG: improper['+imp_name_full+']:\n' - 'theta0 = (' - +theta0s[0]+','+theta0s[1]+','+theta0s[2]+')\n') - sys.stderr.write('DEBUG: num_impropers = len(improper2params) = ' - +str(len(improper2params))+'\n') - num_impropers = len(improper2params) - - - found_at_least_one = True - - - if not found_at_least_one: - lines_warnings.append('# WARNING: Undefined rest angle (theta0) in improper: ' + - #'# the improper interaction between: ' + - ' '.join(atom_names)+'\n') - # Then we were unable to define cross terms for this interaction because - # at least one of the equilibrium rest angles could not be determined. - # This usually occurs because most of the .FRC files which are - # in circulation are incomplete. We have to handle this gracefully. - imp_name_full = (imp_name_orig + ',X,X,X,X,X,X,X,X,X') - reference = improper2ref_or[imsym][imp_name_orig] - version = improper2ver_or[imsym][imp_name_orig] - improper2ref[imsym][imp_name_full] = reference - improper2ver[imsym][imp_name_full] = version - improper2params[imsym][imp_name_full] = ' '.join(improper2params_or[imp_name_orig]) - CONTINUEHERE - improper2style[imp_name_full] = 'class2' - improper2priority[imp_name_full] = improper2priority_or[imp_name_orig] - # substitute zeros for the cross term interactions - improper2class2_aa[imp_name_full] = '0.0 0.0 0.0 120.0 120.0 120.0' - improper2ref_aa[imp_name_full] = reference - improper2ver_aa[imp_name_full] = version - - - - - - sys.stderr.write("done\n") - sys.stderr.write("Converting to moltemplate format...\n") - - - - - - ##################### BEGIN WRITING FILE ##################### - - - - - - sys.stdout.write("# This file was generated automatically using:\n") - sys.stdout.write("# " + g_program_name + " " + " ".join(sys.argv[1:]) + "\n") - sys.stdout.write("\n\n") - sys.stdout.write(ffname + " {\n\n") - - sys.stdout.write("\n" - " # AtomType Mass # \"Description\" (version, reference)\n\n") - sys.stdout.write(" write_once(\"Data Masses\") {\n") - for atype in atom2mass: - sys.stdout.write(" @atom:" + atype + " " + str(atom2mass[atype])) - sys.stdout.write(" # ") - if atype in atom2element: - sys.stdout.write(atom2element[atype] + ", ") - #sys.stdout.write(atom2descr[atype]) - sys.stdout.write("\"" + atom2descr[atype] + "\"") - sys.stdout.write(" (") - if atype in atom2numbonds: - sys.stdout.write("nbonds="+str(atom2numbonds[atype])+", ") - sys.stdout.write("ver=" + atom2ver[atype] + - ", ref=" + atom2ref[atype]) - sys.stdout.write(")\n") - sys.stdout.write(" } #(end of atom masses)\n\n\n") - - - - - - - - - - - - - sys.stdout.write(" # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ----------\n" - " # Each type of atom has a separate ID used for looking up bond parameters\n" - " # and a separate ID for looking up 3-body angle interaction parameters\n" - " # and a separate ID for looking up 4-body dihedral interaction parameters\n" - " # and a separate ID for looking up 4-body improper interaction parameters\n" - #" # (This is because there are several different types of sp3 carbon atoms\n" - #" # which have the same torsional properties when within an alkane molecule,\n" - #" # for example. If they share the same dihedral-ID, then this frees us\n" - #" # from being forced define separate dihedral interaction parameters\n" - #" # for all of them.)\n" - " # The complete @atom type name includes ALL of these ID numbers. There's\n" - " # no need to force the end-user to type the complete name of each atom.\n" - " # The \"replace\" command used below informs moltemplate that the short\n" - " # @atom names we have been using abovee are equivalent to the complete\n" - " # @atom names used below:\n\n") - - for atype in atom2ffid: - #ffid = atype + "_ffid" + atom2ffid[atype] - sys.stdout.write(" replace{ @atom:" + atype + - " @atom:" + atom2ffid[atype] + " }\n") - - sys.stdout.write("\n\n\n\n") - - - sys.stdout.write(" # --------------- Non-Bonded Interactions: ---------------------\n" - " # Syntax:\n" - " # pair_coeff AtomType1 AtomType2 pair_style_name parameters...\n\n") - - sys.stdout.write(" write_once(\"In Settings\") {\n") - - for atype in pair2params: - assert(atype in pair2style) - if IsAutoInteraction(bond_name): - assert(atype in atom2auto_pair) - if include_auto_equivalences: - sys.stdout.write(' pair_coeff @atom:*,ap' + atom2auto_pair[atype] + - ',aq*,ab*,aae*,aac*,ade*,adc*,aie*,aic*' + - ' @atom:*,ap' + atom2auto_pair[atype] + - ',aq*,ab*,aae*,aac*,ade*,adc*,aie*,aic* ' + - pair2style[atype] + ' ' + - pair2params[atype] + - ' # (ver=' + pair2ver[atype] + - ', ref=' +pair2ref[atype] + ')\n') - else: - continue - else: - assert(atype in atom2equiv_pair) - sys.stdout.write(' pair_coeff ' + - '@atom:*,p' + atom2equiv_pair[atype] + ',b*,a*,d*,i* ' + - '@atom:*,p' + atom2equiv_pair[atype] + ',b*,a*,d*,i* ' + - pair2style[atype] + ' ' + - pair2params[atype] + - ' # (ver=' + pair2ver[atype] + - ', ref=' +pair2ref[atype] + ')\n') - sys.stdout.write(" } #(end of pair_coeffs)\n\n\n\n") - - - - - - - - ################# Print Charge By Bond Interactions ################## - charge_pair_priority_high_to_low = [x[0] for x in - sorted([x for x in reversed(charge_pair_priority.items())], - key=itemgetter(1), - reverse=True)] - - if len(charge_pair_priority) > 0: - sys.stdout.write(" # ---------- Charge By Bond (a.k.a. \"bond equivalences\") ----------\n") - # Print rules for generating (2-body) "bond" interactions: - sys.stdout.write('\n\n\n' - ' write_once("Data Charge By Bond") {\n') - for bond_name in charge_pair_priority_high_to_low: - anames = ['*' if x=='X' else x - for x in ExtractANames(bond_name)] - # Did the user ask us to include "auto" interactions? - if IsAutoInteraction(bond_name): - if include_auto_equivalences: - sys.stdout.write(' @atom:*,ap*,aq' + anames[0] + - ',ab*,aae*,aac*,ade*,adc*,aie*,aic*' + - ' @atom:*,ap*,aq' + anames[1] + - ',ab*,aae*,aac*,ade*,adc*,aie*,aic*' + - ' ' + bond2chargepair[bond_name] + - " # (ver=" + charge_pair_ver[bond_name] + - ", ref=" + charge_pair_ref[bond_name] + ")\n") - else: - continue - else: - sys.stdout.write(' @atom:*,p*,b' + anames[0] + ',a*,d*,i* ' + - ' @atom:*,p*,b' + anames[1] + ',a*,d*,i* ' + - ' ' + bond2chargepair[bond_name] + - " # (ver=" + charge_pair_ver[bond_name] + - ", ref=" + charge_pair_ref[bond_name] + ")\n") - sys.stdout.write(' } #(end of Charge by Bond (bond equivalences))\n\n' - '\n\n\n\n') - - - - - - - - ################# Print 2-body Bond Interactions ################## - - bond_names_priority_high_to_low = [x[0] for x in - sorted([x for x in reversed(bond2priority.items())], - key=itemgetter(1), - reverse=True)] - - if len(bond2priority) > 0: - sys.stdout.write(" # --------------- Bond Interactions: ---------------------\n") - sys.stdout.write('\n' - '\n' - ' # -- Rules for generating (2-body) "bond" interactions: --\n' - ' # BondType AtomType1 AtomType2\n') - sys.stdout.write('\n' - ' write_once("Data Bonds By Type') - if bond_symmetry_subgraph != '': - sys.stdout.write(' ('+bond_symmetry_subgraph+')') - sys.stdout.write('") {\n') - for bond_name in bond_names_priority_high_to_low: - if not (bond2style[bond_name] in - bond_styles_selected): - continue - anames = ['*' if x=='X' else x - for x in ExtractANames(bond_name)] - # Did the user ask us to include "auto" interactions? - if IsAutoInteraction(bond_name): - if include_auto_equivalences: - sys.stdout.write(' @bond:' + bond_name + ' ' + - ' @atom:*,ap*,aq*,ab' + anames[0] + - ',aae*,aac*,ade*,adc*,aie*,aic*' + - ' @atom:*,ap*,aq*,ab' + anames[1] + - ',aae*,aac*,ade*,adc*,aie*,aic*' + - '\n') - else: - continue - else: - sys.stdout.write(' @bond:' + bond_name + ' ' + - ' @atom:*,b' + anames[0] + ',a*,d*,i* ' + - ' @atom:*,b' + anames[1] + ',a*,d*,i* ' + - '\n') - - sys.stdout.write(' } # end of "Data Bonds By Type" section\n' - '\n') - - # Print the force-field parameters for these bond interactions: - sys.stdout.write('\n\n' - ' # ------------ Bond Parameters: ----------\n') - sys.stdout.write(' # For an explanation of these parameters, visit:\n') - for bond_style in bond_styles: - if not (bond_style in bond_styles_selected): - continue - sys.stdout.write(' # '+bond_style2docs[bond_style]+'\n') - sys.stdout.write('\n' - ' # Syntax: \n' - ' # bond_coeff BondTypeName BondStyle parameters...\n\n') - sys.stdout.write('\n' - ' write_once("In Settings") {\n') - for bond_name in bond_names_priority_high_to_low: - if not (bond2style[bond_name] in - bond_styles_selected): - continue - # Did the user ask us to include "auto" interactions? - if (IsAutoInteraction(bond_name) and - (not include_auto_equivalences)): - continue - sys.stdout.write(' bond_coeff @bond:'+bond_name+' '+ - bond2style[bond_name] + ' ' + - bond2params[bond_name] + - " # (ver=" + bond2ver[bond_name] + - ", ref=" +bond2ref[bond_name] + ")\n") - - sys.stdout.write(' } # end of bond_coeff commands\n' - '\n\n') - - - - - - - ################# Print 3-body Angle Interactions ################## - - ang_names_priority_high_to_low = [x[0] for x in - sorted([x for x in reversed(angle2priority.items())], - key=itemgetter(1), - reverse=True)] - - ang_name_abbr = {} #optional abbreviated name for each interaction - ang_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names - - if len(angle2priority) > 0: - sys.stdout.write(" # --------------- Angle Interactions: ---------------------\n") - sys.stdout.write('\n' - '\n' - ' # -- Rules for generating (3-body) "angle" interactions: --\n' - ' # AngleType AtomType1 AtomType2 AtomType3 [BondType1 BondType2]\n') - sys.stdout.write('\n' - ' write_once("Data Angles By Type') - if angle_symmetry_subgraph != '': - sys.stdout.write(' ('+angle_symmetry_subgraph+')') - sys.stdout.write('") {\n') - for angle_name in ang_names_priority_high_to_low: - if not (angle2style[angle_name] in - angle_styles_selected): - continue - anames = ['*' if x=='X' else x - for x in ExtractANames(angle_name)] - - angle_is_auto = IsAutoInteraction(angle_name) - if angle2style[angle_name] == 'class2': - anm = [a for a in map(DecodeAName, anames)] - bnames = [[a for a in map(DecodeAName, anames[3:5])], - [a for a in map(DecodeAName, anames[5:7])]] - bond_is_auto1 = IsAutoInteraction(anames[3]) - bond_is_auto2 = IsAutoInteraction(anames[5]) - - if ((angle_is_auto or bond_is_auto1 or bond_is_auto2) and - (not include_auto_equivalences)): - continue - - # Can we ignore "auto" interactions? - # (If so, life is much easier) - if not (angle_is_auto or bond_is_auto1 or bond_is_auto2): - if angle2style[angle_name] == 'class2': - assert(bnames[0][1] == bnames[1][0]) - # Optional: Shorten the angle name since some of the atom's bond names are redundant: - ang_name_abbr[angle_name] = EncodeInteractionName(map(EncodeAName, - anm[0:3] + - #[anm[3],anm[4],anm[6]], - [bnames[0][0],bnames[0][1],bnames[1][1]]), - angle_is_auto) - sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + - ' @atom:*,p*,b'+bnames[0][0]+',a'+anames[0]+',d*,i* ' + - ' @atom:*,p*,b'+bnames[0][1]+',a'+anames[1]+',d*,i* ' + - ' @atom:*,p*,b'+bnames[1][1]+',a'+anames[2]+',d*,i*' - '\n') - else: - ang_name_abbr[angle_name] = angle_name - sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + - ' @atom:*,p*,b*,a'+anames[0]+',d*,i* ' + - ' @atom:*,p*,b*,a'+anames[1]+',d*,i* ' + - ' @atom:*,p*,b*,a'+anames[2]+',d*,i*' - '\n') - else: - # Consider "auto" interactions and "auto" atom equivalences - ang_name_abbr[angle_name] = angle_name #(full name) - sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ') - - if angle2style[angle_name] == 'class2': - - bshared = 'b*' #(default. overidden below) - abshared = 'ab*' #(default. overidden below) - - if angle_is_auto: - a1 = a2 = a3 = 'a*' #Then, dont use regular equivalences for these atoms. - aa1 = 'aae' + anames[0] + ',aac*' #Instead use the corresponding "auto" equivalence names - aa2 = 'aae*,aac*' + anames[1] #for these atoms. (There are different auto equivalence names depending - aa3 = 'aae' + anames[2] + ',aac*' #on if the atom appears in the center (c) or end(e) of the 3-body angle) - else: - a1 = 'a' + anames[0] #In this case, use use (regular) equivalence names - a2 = 'a' + anames[1] #for these atoms - a3 = 'a' + anames[2] - aa1 = aa2 = aa3 = 'aae*,aac*' - - if not bond_is_auto1: - b11 = 'b' + bnames[0][0] #(bond atom equivalent name) - b12 = 'b' + bnames[0][1] #(bond atom equivalent name) - bshared = 'b' + bnames[0][1] #(bond atom equivalent name) - ab11 = ab12 = 'ab*' - else: - b11 = b12 = 'b*' - ab11 = 'ab' + bnames[0][0] #(auto bond atom name) - ab12 = 'ab' + bnames[0][1] #(auto bond atom name) - abshared = 'ab' + bnames[0][1] #(auto bond atom name) - # print atom 1 information: - sys.stdout.write(' @atom:*,p*,'+b11+','+a1+',d*,i*,' + - 'ap*,aq*,'+ab11+','+aa1+ - ',ade*,adc*,aie*,aic*') - if not bond_is_auto2: - b21 = 'b' + bnames[1][0] #(bond atom equivalent name) - b22 = 'b' + bnames[1][1] #(bond atom equivalent name) - assert((bshared == 'b*') or (bshared == 'b' + bnames[1][0])) - bshared = 'b' + bnames[1][0] - ab21 = ab22 = 'ab*' - else: - b21 = b22 = 'b*' - ab21 = 'ab' + bnames[1][0] #(auto bond atom name) - ab22 = 'ab' + bnames[1][1] #(auto bond atom name) - assert((abshared == 'ab*') or (abshared == 'ab' + bnames[1][0])) - abshared = 'ab' + bnames[1][0] - # print atom 2 information: - sys.stdout.write(' @atom:*,p*,'+bshared+','+a2+',d*,i*,' + - 'ap*,aq*,'+abshared+','+aa2+ - ',ade*,adc*,aie*,aic*') - # print atom 3 information: - sys.stdout.write(' @atom:*,p*,'+b22+','+a3+',d*,i*,' + - 'ap*,aq*,'+ab22+','+aa3+ - ',ade*,adc*,aie*,aic*') - sys.stdout.write('\n') - else: - sys.stdout.write(' @angle:' + ang_name_abbr[angle_name] + ' ' + - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae'+anames[0]+'aac*,ade*,adc*,aie*,aic* ' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac'+anames[1]+',ade*,adc*,aie*,aic* ' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae'+anames[2]+'aac*,ade*,adc*,aie*,aic* ' - '\n') - - assert(ang_name_abbr[angle_name] not in ang_name_abbr_used) - ang_name_abbr_used.add(ang_name_abbr[angle_name]) - - sys.stdout.write(' } # end of "Data Angles By Type" section\n' - '\n') - - # Print the force-field parameters for these angle interactions: - sys.stdout.write('\n\n' - ' # ------- Angle Force Field Parameters: -------') - sys.stdout.write(' # For an explanation of these parameters, visit:\n') - for angle_style in angle_styles: - if not (angle_style in angle_styles_selected): - continue - sys.stdout.write(' # '+angle_style2docs[angle_style]+'\n') - sys.stdout.write('\n' - ' # Syntax: \n' - ' # angle_coeff AngleTypeName AngleStyle parameters...\n\n') - sys.stdout.write('\n' - ' write_once("In Settings") {\n') - for angle_name in ang_names_priority_high_to_low: - anames = ['*' if x=='X' else x - for x in ExtractANames(angle_name)] - if not (angle2style[angle_name] in - angle_styles_selected): - continue - - - # Did the user ask us to include "auto" interactions? - #if (IsAutoInteraction(angle_name) and - # (not include_auto_equivalences)): - # continue - # the if statement above is covered by the following: - if angle_name not in ang_name_abbr: - continue - - sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ - angle2style[angle_name] + ' ' + - angle2params[angle_name] + - " # (ver=" + angle2ver[angle_name] + - ", ref=" + angle2ref[angle_name] + ")\n") - if angle_name in angle2class2_bb: - sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ - angle2style[angle_name] + ' bb ' + - angle2class2_bb[angle_name] + - " # (ver=" + angle2ver_bb[angle_name] + - ", ref=" + angle2ref_bb[angle_name] + ")\n") - - assert(angle_name in angle2class2_ba) - sys.stdout.write(' angle_coeff @angle:'+ang_name_abbr[angle_name]+' '+ - angle2style[angle_name] + ' ba ' + - angle2class2_ba[angle_name] + - " # (ver=" + angle2ver_ba[angle_name] + - ", ref=" + angle2ref_ba[angle_name] + ")\n") - sys.stdout.write(' } # end of angle_coeff commands\n' - '\n\n') - - - - - - - - ################# Print 4-body Dihedral Interactions ################## - - dih_names_priority_high_to_low = [x[0] for x in - sorted([x for x in reversed(dihedral2priority.items())], - key=itemgetter(1), - reverse=True)] - - dih_name_abbr = {} #optional abbreviated name for each interaction - dih_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names - - if len(dih_names_priority_high_to_low) > 0: - sys.stdout.write(' # --------------- Dihedral Interactions: ---------------------\n') - sys.stdout.write('\n' - '\n' - ' # -- Rules for generating (4-body) "dihedral" interactions: --\n' - ' # DihedralType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3]\n') - sys.stdout.write('\n\n' - ' write_once("Data Dihedrals By Type') - if dihedral_symmetry_subgraph != '': - sys.stdout.write(' ('+dihedral_symmetry_subgraph+')') - sys.stdout.write('") {\n') - - - - for dihedral_name in dih_names_priority_high_to_low: - if not (dihedral2style[dihedral_name] in - dihedral_styles_selected): - continue - anames = ['*' if x=='X' else x - for x in ExtractANames(dihedral_name)] - - dihedral_is_auto = IsAutoInteraction(dihedral_name) - if dihedral2style[dihedral_name] == 'class2': - anm = [a for a in map(DecodeAName, anames)] - bnames = [[a for a in map(DecodeAName, anames[4:6])], - [a for a in map(DecodeAName, anames[6:8])], - [a for a in map(DecodeAName, anames[8:10])]] - bond_is_auto1 = IsAutoInteraction(anames[4]) - bond_is_auto2 = IsAutoInteraction(anames[6]) - bond_is_auto3 = IsAutoInteraction(anames[8]) - ang_names = [[a for a in map(DecodeAName, anames[10:13])], - [a for a in map(DecodeAName, anames[13:16])]] - angle_is_auto1 = IsAutoInteraction(anames[10]) - angle_is_auto2 = IsAutoInteraction(anames[13]) - - if ((dihedral_is_auto or - angle_is_auto1 or angle_is_auto2 or - bond_is_auto1 or bond_is_auto2 or bond_is_auto3) and - (not include_auto_equivalences)): - continue - - # Can we ignore "auto" interactions? - # (If so, life is much easier) - if not (dihedral_is_auto or - angle_is_auto1 or angle_is_auto2 or - bond_is_auto1 or bond_is_auto2 or bond_is_auto3): - - if dihedral2style[dihedral_name] == 'class2': - assert(bnames[0][1] == bnames[1][0]) - assert(bnames[1][1] == bnames[2][0]) - assert(ang_names[0][1] == ang_names[1][0]) - assert(ang_names[0][2] == ang_names[1][1]) - - # Optional: Shorten the dihedral name since some of the atom's bond names are redundant: - dih_name_abbr[dihedral_name] = EncodeInteractionName(map(EncodeAName, - anm[0:4] + - #[bnames[0][0], bnames[0][1], - # bnames[1][1], bnames[2][1]] - [anm[4],anm[5],anm[7],anm[9]]+ - #[ang_names[0][0], - # ang_names[0][1], - # ang_names[0][2], - # ang_names[1][2]] - [anm[10],anm[11],anm[12],anm[15]]), - is_auto) - - sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + - ' @atom:*,p*,b'+bnames[0][0]+',a'+ang_names[0][0]+',d'+anames[0]+',i* ' + - ' @atom:*,p*,b'+bnames[0][1]+',a'+ang_names[0][1]+',d'+anames[1]+',i* ' + - ' @atom:*,p*,b'+bnames[1][1]+',a'+ang_names[0][2]+',d'+anames[2]+',i* ' - ' @atom:*,p*,b'+bnames[2][1]+',a'+ang_names[1][2]+',d'+anames[3]+',i*' - '\n') - else: - dih_name_abbr[dihedral_name] = dihedral_name - sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + - ' @atom:*,p*,b*,a*,d'+anames[0]+',i* ' + - ' @atom:*,p*,b*,a*,d'+anames[1]+',i* ' + - ' @atom:*,p*,b*,a*,d'+anames[2]+',i* ' - ' @atom:*,p*,b*,a*,d'+anames[3]+',i*' + - '\n') - else: - # Consider "auto" interactions and "auto" atom equivalences - dih_name_abbr[dihedral_name] = dihedral_name #(full name) - sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ') - - if dihedral2style[dihedral_name] == 'class2': - - # equivalent names of atoms shared by more than one bond: - # (names ending in * mean they were unspecified for this - # dihedral interaction. By default, this is the case.) - bshared1 = 'b*' #(default. overidden below) - bshared2 = 'b*' #(default. overidden below) - abshared1 = 'ab*' #(default. overidden below) - abshared2 = 'ab*' #(default. overidden below) - - # equivalent names of atoms shared by more than one angle interaction: - # (names ending in * mean they were unspecified for this - # dihedral interaction. By default, this is the case.) - ashared1 = 'a*' #(default. overidden below) - ashared2 = 'a*' #(default. overidden below) - aac_shared1 = 'aac*' #(default. overidden below) - aae_shared1 = 'aae*' #(default. overidden below) - aac_shared2 = 'aac*' #(default. overidden below) - aae_shared2 = 'aae*' #(default. overidden below) - - if dihedral_is_auto: - d1 = d2 = d3 = d4 = 'd*' #Then, dont use regular equivalences for these atoms. - ad1 = 'ade' + anames[0] + ',adc*' #Instead use the corresponding "auto" - ad2 = 'ade*,adc*' + anames[1] #equivalence names for these atoms. - ad3 = 'ade*,adc*' + anames[1] #(There are different auto equivalence names depending upon - ad4 = 'ade' + anames[2] + ',adc*' # if the atom appears in the center (c) or end(e) of the dihedral) - else: - d1 = 'd' + anames[0] # In this case, use use (regular) equivalence names - d2 = 'd' + anames[1] # for these atoms - d3 = 'd' + anames[2] - d4 = 'd' + anames[3] - ad1 = ad2 = ad3 = ad4 = 'ade*,adc*' - - if not bond_is_auto1: - b11 = 'b' + bnames[0][0] #(bond atom equivalent name) - b12 = 'b' + bnames[0][1] #(bond atom equivalent name) - bshared1 = 'b' + bnames[0][1] #(bond atom equivalent name) - ab11 = ab12 = 'ab*' - else: - b11 = b12 = 'b*' - ab11 = 'ab' + bnames[0][0] #(auto bond atom name) - ab12 = 'ab' + bnames[0][1] #(auto bond atom name) - abshared1 = 'ab' + bnames[0][1] #(auto bond atom name) - - if not bond_is_auto2: - b21 = 'b' + bnames[1][0] #(bond atom equivalent name) - b22 = 'b' + bnames[1][1] #(bond atom equivalent name) - assert((bshared1 == 'b*') or (bshared1 == 'b' + bnames[1][0])) - bshared1 = 'b' + bnames[1][0] #(bond atom equivalent name) - assert((bshared2 == 'b*') or (bshared2 == 'b' + bnames[1][1])) - bshared2 = 'b' + bnames[1][1] #(bond atom equivalent name) - ab21 = ab22 = 'ab*' - else: - b21 = b22 = 'b*' - ab21 = 'ab' + bnames[1][0] #(auto bond atom name) - ab22 = 'ab' + bnames[1][1] #(auto bond atom name) - assert((abshared1 == 'ab*') or (abshared1 == 'ab' + bnames[1][0])) - abshared1 = 'ab' + bnames[1][0] #(auto bond atom name) - assert((abshared2 == 'ab*') or (abshared2 == 'ab' + bnames[1][1])) - abshared2 = 'ab' + bnames[1][1] #(auto bond atom name) - - if not bond_is_auto3: - b31 = 'b' + bnames[2][0] #(bond atom equivalent name) - b32 = 'b' + bnames[2][1] #(bond atom equivalent name) - assert((bshared2 == 'b*') or (bshared2 == 'b' + bnames[2][0])) - bshared2 = 'b' + bnames[2][0] #(bond atom equivalent name) - ab31 = ab32 = 'ab*' - else: - b31 = b32 = 'b*' - ab31 = 'ab' + bnames[2][0] #(auto bond atom name) - ab32 = 'ab' + bnames[2][1] #(auto bond atom name) - assert((abshared2 == 'ab*') or (abshared2 == 'ab' + bnames[2][0])) - abshared2 = 'ab' + bnames[2][0] #(auto bond atom name) - - if not angle_is_auto1: - a11 = 'a' + ang_names[0][0] #(angle atom equivalent name) - a12 = 'a' + ang_names[0][1] #(angle atom equivalent name) - a13 = 'a' + ang_names[0][2] #(angle atom equivalent name) - ashared1 = 'a' + ang_names[0][1] #(angle atom equivalent name) - ashared2 = 'a' + ang_names[0][2] #(angle atom equivalent name) - aa11 = 'aae*,aac*' - aa12 = 'aae*,aac*' - aa13 = 'aae*,aac*' - else: - a11 = a12 = a13 = 'a*' - aa11 = 'aae'+ang_names[0][0]+'aac*' #(auto angle atom name) - aa12 = 'aae*,aac'+ang_names[0][1] #(auto angle atom name) - aa13 = 'aae'+ang_names[0][2]+'aac*' #(auto angle atom name) - aac_shared1 = 'aac'+ang_names[0][1] #(auto angle atom name) - aae_shared2 = 'aae'+ang_names[0][2] #(auto angle atom name) - - if not angle_is_auto2: - a21 = 'a' + ang_names[1][0] #(angle atom equivalent name) - a22 = 'a' + ang_names[1][1] #(angle atom equivalent name) - a23 = 'a' + ang_names[1][2] #(angle atom equivalent name) - assert((ashared1 == 'a*') or (ashared1 == 'a' + ang_names[1][0])) - ashared1 = 'a' + ang_names[1][0] #(angle atom equivalent name) - assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[1][1])) - ashared2 = 'a' + ang_names[1][1] #(angle atom equivalent name) - aa21 = 'aae*,aac*' - aa22 = 'aae*,aac*' - aa23 = 'aae*,aac*' - else: - a21 = a22 = a23 = 'a*' - aa21 = 'aae'+ang_names[1][0]+',aac*' #(auto angle atom name) - aa22 = 'aae*,aac'+ang_names[1][1] #(auto angle atom name) - aa23 = 'aae'+ang_names[1][2]+',aac*' #(auto angle atom name) - aae_shared1 = 'aae'+ang_names[1][0] #(auto angle atom name) - aac_shared2 = 'aac'+ang_names[1][1] #(auto angle atom name) - - - # print atom 1 information: - sys.stdout.write(' @atom:*,p*,'+b11+','+a11+','+d1+',i*,' + - 'ap*,aq*,'+ab11+','+aa11+',' + - ad1+',aie*,aic*') - # print atom 2 information: - sys.stdout.write(' @atom:*,p*,'+bshared1+','+ashared1+','+d2+',i*,' + - 'ap*,aq*,'+abshared1+','+aae_shared1+','+aac_shared1+',' + - ad2+',aie*,aic*') - # print atom 3 information: - sys.stdout.write(' @atom:*,p*,'+bshared2+','+ashared2+','+d3+',i*,' + - 'ap*,aq*,'+abshared2+','+aae_shared2+','+aac_shared2+',' + - ad3+',aie*,aic*') - # print atom 4 information: - sys.stdout.write(' @atom:*,p*,'+b32+','+a23+','+d4+',i*,' + - 'ap*,aq*,'+ab32+','+aa23+',' + - ad4+',aie*,aic*') - sys.stdout.write('\n') - else: - assert(dihedral_is_auto) #(so we should use "auto" equivalence names for these atoms) - sys.stdout.write(' @dihedral:' + dih_name_abbr[dihedral_name] + ' ' + - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade'+anames[0]+',adc*,aie*,aic* ' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade*,adc'+anames[1]+',aie*,aic* ' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade*,adc'+anames[2]+',aie*,aic* ' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade'+anames[3]+',adc*,aie*,aic* ' - '\n') - - - - - assert(dih_name_abbr[dihedral_name] not in dih_name_abbr_used) - dih_name_abbr_used.add(dih_name_abbr[dihedral_name]) - - sys.stdout.write(' } # end of "Data Dihedrals By Type" section\n' - '\n') - - # Print the force-field parameters for these dihedral interactions: - sys.stdout.write('\n\n' - ' # ------- Dihedral Force Field Parameters: -------\n') - sys.stdout.write(' # For an explanation of these parameters, visit:\n') - for dihedral_style in dihedral_styles: - if not (dihedral_style in dihedral_styles_selected): - continue - sys.stdout.write(' # '+dihedral_style2docs[dihedral_style]+'\n') - sys.stdout.write('\n' - ' # Syntax: \n' - ' # dihedral_coeff DihedralTypeName DihedralStyle parameters...\n\n') - sys.stdout.write('\n' - ' write_once("In Settings") {\n') - for dihedral_name in dih_names_priority_high_to_low: - anames = ['*' if x=='X' else x - for x in ExtractANames(dihedral_name)] - #if (len(anames) == 4) and dihedral2style[dihedral_name] == 'class2': - # continue - if not (dihedral2style[dihedral_name] in - dihedral_styles_selected): - continue - - # Did the user ask us to include "auto" interactions? - #if (IsAutoInteraction(dihedral_name) and - # (not include_auto_equivalences)): - # continue - # the if statement above is covered by the following: - if dihedral_name not in dih_name_abbr: - continue - - sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ - dihedral2style[dihedral_name] + ' ' + - dihedral2params[dihedral_name] + - " # (ver=" + dihedral2ver[dihedral_name] + - ", ref=" + dihedral2ref[dihedral_name] + ")\n") - if dihedral_name in dihedral2class2_mbt: - sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ - dihedral2style[dihedral_name] + ' mbt ' + - dihedral2class2_mbt[dihedral_name] + - " # (ver=" + dihedral2ver_mbt[dihedral_name] + - ", ref=" + dihedral2ref_mbt[dihedral_name] + ")\n") - - assert(dihedral_name in dihedral2class2_ebt) - sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ - dihedral2style[dihedral_name] + ' ebt ' + - dihedral2class2_ebt[dihedral_name] + - " # (ver=" + dihedral2ver_ebt[dihedral_name] + - ", ref=" + dihedral2ref_ebt[dihedral_name] + ")\n") - - assert(dihedral_name in dihedral2class2_at) - sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ - dihedral2style[dihedral_name] + ' at ' + - dihedral2class2_at[dihedral_name] + - " # (ver=" + dihedral2ver_at[dihedral_name] + - ", ref=" + dihedral2ref_at[dihedral_name] + ")\n") - - assert(dihedral_name in dihedral2class2_aat) - sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ - dihedral2style[dihedral_name] + ' aat ' + - dihedral2class2_aat[dihedral_name] + - " # (ver=" + dihedral2ver_aat[dihedral_name] + - ", ref=" + dihedral2ref_aat[dihedral_name] + ")\n") - assert(dihedral_name in dihedral2class2_bb13) - sys.stdout.write(' dihedral_coeff @dihedral:'+dih_name_abbr[dihedral_name]+' '+ - dihedral2style[dihedral_name] + ' bb13 ' + - dihedral2class2_bb13[dihedral_name] + - " # (ver=" + dihedral2ver_bb13[dihedral_name] + - ", ref=" + dihedral2ref_bb13[dihedral_name] + ")\n") - sys.stdout.write(' } # end of dihedral_coeff commands\n' - '\n\n') - - - - - - ################# Print 4-body Improper Interactions ################## - - imp_names_priority_high_to_low = [x[0] for x in - sorted([x for x in reversed(improper2priority.items())], - key=itemgetter(1), - reverse=True)] - - imp_name_abbr = {} #optional abbreviated name for each interaction - imp_name_abbr_used = set([]) #make sure we don't reuse these abbreviated names - - if len(imp_names_priority_high_to_low) > 0: - sys.stdout.write(" # --------------- Improper Interactions: ---------------------\n") - sys.stdout.write('\n' - '\n' - ' # -- Rules for generating (4-body) "improper" interactions: --\n' - ' # ImproperType AtmType1 AtmType2 AtmType3 AtmType3 [BondType1 Bnd2 Bnd3]\n') - sys.stdout.write('\n' - ' write_once("Data Impropers By Type') - if improper_symmetry_subgraph != '': - sys.stdout.write(' ('+improper_symmetry_subgraph+')') - sys.stdout.write('") {\n') - for improper_name in imp_names_priority_high_to_low: - if not (improper2style[improper_name] in - improper_styles_selected): - continue - anames = ['*' if x=='X' else x - for x in ExtractANames(improper_name)] - #if (len(anames) == 4) and improper2style[improper_name] == 'class2': - # continue - ang_names = [[a for a in map(DecodeAName, anames[4:7])], - [a for a in map(DecodeAName, anames[7:10])], - [a for a in map(DecodeAName, anames[10:13])]] - anm = [a for a in map(DecodeAName, anames)] - - improper_is_auto = IsAutoInteraction(improper_name) - if improper2style[improper_name] == 'class2': - angle_is_auto1 = IsAutoInteraction(anames[4]) - angle_is_auto2 = IsAutoInteraction(anames[7]) - angle_is_auto3 = IsAutoInteraction(anames[10]) - - if ((improper_is_auto or - angle_is_auto1 or - angle_is_auto2 or - angle_is_auto3) and - (not include_auto_equivalences)): - continue - - # Can we ignore "auto" interactions? - # (If so, life is much easier) - if not (improper_is_auto or - angle_is_auto1 or - angle_is_auto2 or - angle_is_auto3): - if improper2style[improper_name] == 'class2': - # NOTE: atom orderings here are LAMMPS implementation specific. - # http://lammps.sandia.gov/doc/improper_class2.html - #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) - #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) - #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) - assert(ang_names[0][1] == ang_names[1][1] == ang_names[2][1]) - assert(ang_names[0][0] == ang_names[1][0]) - assert(ang_names[1][2] == ang_names[2][2]) - assert(ang_names[2][0] == ang_names[0][2]) - - # Optional: Shorten the improper name since some of the atom's bond names are redundant: - imp_name_abbr[improper_name] = EncodeInteractionName(map(EncodeAName, anm[0:4] + - [ang_names[0][0], - ang_names[0][1], - ang_names[0][2], - ang_names[1][2]]), - #[anm[4],anm[5],anm[6], - #anm[9]], - improper_is_auto) - sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + - ' @atom:*,p*,b*,a'+ang_names[0][0]+',d*,i' + anames[0] + - ' @atom:*,p*,b*,a'+ang_names[0][1]+',d*,i' + anames[1] + - ' @atom:*,p*,b*,a'+ang_names[0][2]+',d*,i' + anames[2] + - ' @atom:*,p*,b*,a'+ang_names[1][2]+',d*,i' + anames[3] + - '\n') - else: - imp_name_abbr[improper_name] = improper_name - sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + - ' @atom:*,p*,b*,a*,d*,i' + anames[0] + - ' @atom:*,p*,b*,a*,d*,i' + anames[1] + - ' @atom:*,p*,b*,a*,d*,i' + anames[2] + - ' @atom:*,p*,b*,a*,d*,i' + anames[3] + - '\n') - else: - # Consider "auto" interactions and "auto" atom equivalences - imp_name_abbr[improper_name] = improper_name #(full name) - sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ') - - if improper2style[improper_name] == 'class2': - - #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) - #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) - #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) - - # default angle atom equivalence names: - ashared1 = 'a*' #(default for a1 <-> ang_names[0][0], ang_names[1][0]) - ashared2 = 'a*' #(default for a2 <-> ang_names[0][1], ang_names[1][1], ang_names[2][1]) - ashared3 = 'a*' #(default for a3 <-> ang_names[2][0], ang_names[0][2]) - ashared4 = 'a*' #(default for a4 <-> ang_names[1][2], ang_names[2][2]) - - # default auto angle atom equivalence names: - aashared1 = 'aae*,aac*' #(default for a1 <-> ang_names[0][0], ang_names[1][0]) - aashared2 = 'aae*,aac*' #(default for a2 <-> ang_names[0][1], ang_names[1][1], ang_names[2][1]) - aashared3 = 'aae*,aac*' #(default for a3 <-> ang_names[2][0], ang_names[0][2]) - aashared4 = 'aae*,aac*' #(default for a4 <-> ang_names[1][2], ang_names[2][2]) - - if improper_is_auto: - i1 = i2 = i3 = i4 = 'i*' #Then, dont use regular equivalences for these atoms. - ai1 = 'aie' + anames[0] + ',aic*' #Instead use the corresponding "auto" equivalence names - ai2 = 'aie*,aic*' + anames[1] #for these atoms. (There are different auto equivalence names depending - ai3 = 'aie' + anames[2] + ',aic*' #on if the atom appears in the center (c) or end(e) - ai4 = 'aie' + anames[3] + ',aic*' - else: - i1 = 'i' + anames[0] #In this case, use use (regular) equivalence names - i2 = 'i' + anames[1] #for these atoms - i3 = 'i' + anames[2] - i4 = 'i' + anames[3] - ai1 = ai2 = ai3 = 'aie*,aic*' - - #For reference, LAMMPS-specific atom ordering: - #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) - #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) - #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) - if not angle_is_auto1: - ashared1 = 'a' + ang_names[0][0] - ashared2 = 'a' + ang_names[0][1] - ashared3 = 'a' + ang_names[0][2] - else: - aashared1 = 'aae' + ang_names[0][0] + ',aac*' - aashared2 = 'aae*,aac' + ang_names[0][1] - aashared3 = 'aae' + ang_names[0][2] + ',aac*' - - #For reference, LAMMPS-specific atom ordering: - #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) - #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) - #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) - if not angle_is_auto2: - assert((ashared1 == 'a*') or (ashared1 == 'a' + ang_names[1][0])) - ashared1 = 'a' + ang_names[1][0] - assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[1][1])) - ashared2 = 'a' + ang_names[1][1] - ashared4 = 'a' + ang_names[1][2] - else: - assert((aashared1 == 'aae*,aac*') or (aashared1 == 'aae' + ang_names[1][0] + ',aac*')) - aashared1 = 'aae' + ang_names[1][0] + ',aac*' - assert((aashared2 == 'aae*,aac*') or (aashared2 == 'aae*,aac' + ang_names[1][1])) - aashared2 = 'aae*,aac' + ang_names[1][1] - aashared4 = 'aae' + ang_names[1][2] + ',aac*' - - #For reference, LAMMPS-specific atom ordering: - #ang_names[0] <==> (a1, a2, a3) <==> (i, j, k) - #ang_names[1] <==> (a1, a2, a4) <==> (i, j, l) - #ang_names[2] <==> (a3, a2, a4) <==> (k, j, l) - if not angle_is_auto3: - assert((ashared3 == 'a*') or (ashared3 == 'a' + ang_names[2][0])) - ashared3 = 'a' + ang_names[2][0] - assert((ashared2 == 'a*') or (ashared2 == 'a' + ang_names[2][1])) - ashared2 = 'a' + ang_names[2][1] - assert((ashared4 == 'a*') or (ashared4 == 'a' + ang_names[2][2])) - ashared4 = 'a' + ang_names[2][2] - else: - assert((aashared3 == 'aae*,aac*') or (aashared3 == 'aae' + ang_names[2][0] + ',aac*')) - aashared3 = 'aae' + ang_names[2][0] + ',aac*' - assert((aashared2 == 'aae*,aac*') or (aashared2 == 'aae*,aac' + ang_names[2][1])) - aashared2 = 'aae*,aac' + ang_names[2][1] - assert((aashared4 == 'aae*,aac*') or (aashared4 == 'aae' + ang_names[2][2] + ',aac*')) - aashared4 = 'aae' + ang_names[2][2] + ',aac*' - - # print atom 1 information: - sys.stdout.write(' @atom:*,p*,b*,'+ashared1+',d*,'+i1+','+ - 'ap*,aq*,ab*,'+aashared1+',ad*,'+ai1) - # print atom 2 information: - sys.stdout.write(' @atom:*,p*,b*,'+ashared2+',d*,'+i2+','+ - 'ap*,aq*,ab*,'+aashared2+',ad*,'+ai2) - # print atom 3 information: - sys.stdout.write(' @atom:*,p*,b*,'+ashared3+',d*,'+i3+','+ - 'ap*,aq*,ab*,'+aashared3+',ad*,'+ai3) - # print atom 4 information: - sys.stdout.write(' @atom:*,p*,b*,'+ashared4+',d*,'+i4+','+ - 'ap*,aq*,ab*,'+aashared4+',ad*,'+ai4) - sys.stdout.write('\n') - else: - sys.stdout.write(' @improper:' + imp_name_abbr[improper_name] + ' ' + - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[0]+',aic*' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie*,aic'+anames[1]+ - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[2]+',aic*' - ' @atom:*,p*,b*,d*,i*,' + - 'ap*,aq*,ab*,aae*,aac*,ade*,adc*,aie*,aie'+anames[3]+',aic*' - '\n') - - assert(imp_name_abbr[improper_name] not in imp_name_abbr_used) - imp_name_abbr_used.add(imp_name_abbr[improper_name]) - - - - - sys.stdout.write(' } # end of "Data Impropers By Type" section\n' - '\n') - - # Print the force-field parameters for these improper interactions: - sys.stdout.write('\n\n' - ' # ------- Improper Force Field Parameters: -------\n') - sys.stdout.write(' # For an explanation of these parameters, visit:\n') - for improper_style in improper_styles: - if not (improper_style in improper_styles_selected): - continue - sys.stdout.write(' # '+improper_style2docs[improper_style]+'\n') - sys.stdout.write('\n' - '# Syntax: \n' - ' # improper_coeff ImproperTypeName ImproperStyle parameters...\n\n') - sys.stdout.write('\n' - ' write_once("In Settings") {\n') - for improper_name in imp_names_priority_high_to_low: - anames = ['*' if x=='X' else x - for x in ExtractANames(improper_name)] - #if (len(anames) == 4) and improper2style[improper_name] == 'class2': - # continue - # Optional: Shorten the angle name since some of the bnames are redundant: - - is_auto = IsAutoInteraction(improper_name) - - if not (improper2style[improper_name] in - improper_styles_selected): - continue - - # Did the user ask us to include "auto" interactions? - #if (IsAutoInteraction(improper_name) and - # (not include_auto_equivalences)): - # continue - # the if statement above is covered by the following: - if improper_name not in imp_name_abbr: - continue - - sys.stdout.write(' improper_coeff @improper:'+imp_name_abbr[improper_name]+' '+ - improper2style[improper_name] + ' ' + - improper2params[improper_name] + - " # (ver=" + improper2ver[improper_name] + - ", ref=" + improper2ref[improper_name] + ")\n") - if improper_name in improper2class2_aa: - sys.stdout.write(' improper_coeff @improper:'+imp_name_abbr[improper_name]+' '+ - improper2style[improper_name] + ' aa ' + - improper2class2_aa[improper_name] + - " # (ver=" + improper2ver_aa[improper_name] + - ", ref=" + improper2ref[improper_name] + ")\n") - sys.stdout.write(' } # end of improper_coeff commands\n' - '\n\n') - - - - sys.stdout.write('\n\n\n\n' - ' # -------------------- Select LAMMPS style(s) ------------------\n' - '\n') - - - sys.stdout.write('\n' - ' # LAMMPS supports many different kinds of bonded and non-bonded\n' - ' # interactions which can be selected at run time. Eventually\n' - ' # we must inform LAMMPS which of them we will need. We specify\n' - ' # this in the "In Init" section: \n\n') - - sys.stdout.write(' write_once("In Init") {\n') - sys.stdout.write(' units real\n') - sys.stdout.write(' atom_style full\n') - - if len(bond_styles) > 0: - sys.stdout.write(' bond_style hybrid') - for bond_style in bond_styles: - if not (bond_style in bond_styles_selected): - continue - sys.stdout.write(' ' + bond_style) - sys.stdout.write('\n') - for bond_style in bond_styles: - if not (bond_style in bond_styles_selected): - continue - sys.stdout.write(' # '+bond_style2docs[bond_style]+'\n') - sys.stdout.write('\n') - - if len(angle_styles) > 0: - sys.stdout.write(' angle_style hybrid') - for angle_style in angle_styles: - if not (angle_style in angle_styles_selected): - continue - sys.stdout.write(' ' + angle_style) - sys.stdout.write('\n') - for angle_style in angle_styles: - if not (angle_style in angle_styles_selected): - continue - sys.stdout.write(' # '+angle_style2docs[angle_style]+'\n') - sys.stdout.write('\n') - - if len(dihedral_styles) > 0: - sys.stdout.write(' dihedral_style hybrid') - for dihedral_style in dihedral_styles: - if not (dihedral_style in dihedral_styles_selected): - continue - sys.stdout.write(' ' + dihedral_style) - sys.stdout.write('\n') - for dihedral_style in dihedral_styles: - if not (dihedral_style in dihedral_styles_selected): - continue - sys.stdout.write(' # '+dihedral_style2docs[dihedral_style]+'\n') - sys.stdout.write('\n') - - if len(improper_styles) > 0: - sys.stdout.write(' improper_style hybrid') - for improper_style in improper_styles: - if not (improper_style in improper_styles_selected): - continue - sys.stdout.write(' ' + improper_style) - sys.stdout.write('\n') - for improper_style in improper_styles: - if not (improper_style in improper_styles_selected): - continue - sys.stdout.write(' # '+improper_style2docs[improper_style]+'\n') - sys.stdout.write('\n') - - if len(pair_styles) > 0: - sys.stdout.write(' pair_style hybrid') - for pair_style in pair_styles: - if not (pair_style in pair_styles_selected): - continue - sys.stdout.write(' ' + pair_style + - ' ' + pair_style_args[pair_style]) - sys.stdout.write('\n') - for pair_style in pair_styles: - sys.stdout.write(' # '+pair_style2docs[pair_style]+'\n') - sys.stdout.write('\n') - - sys.stdout.write(' pair_modify mix ' + pair_mixing_style + '\n') - sys.stdout.write(' ' + special_bonds_command + '\n') - sys.stdout.write(' ' + kspace_style + '\n') - sys.stdout.write(' } #end of init parameters\n\n') - sys.stdout.write('} # ' + ffname + '\n\n') - - - sys.stdout.write("#\n" - "# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:\n") - sys.stdout.write("# " + special_bonds_command + "\n") - sys.stdout.write("# (See http://lammps.sandia.gov/doc/special_bonds.html for details)\n") - - #sys.stderr.write(' done.\n') - - - if len(lines_templates) > 0: - sys.stdout.write('\n\n\n\n' - '# ---- templates from the original .frc file used for atom type selection: ---\n') - for line in lines_templates: - sys.stdout.write('# '+line) - - if len(lines_references) > 0: - sys.stdout.write('\n\n\n\n' - '# ---- references from the original .frc file: ----\n\n') - for ref_number,lines in sorted(lines_references.items()): - sys.stdout.write('# reference '+str(ref_number)+'\n') - for line in lines: - sys.stdout.write('# '+line) - sys.stdout.write('\n') - - - if len(lines_warnings) > 0: - sys.stdout.write('\n\n\n\n' - '# ---- additional warnings: ----\n') - for line in lines_warnings: - sys.stdout.write(line) - - - if filename_in != '': - file_in.close() - - - - - except InputError as err: - sys.stderr.write('\n\n' + str(err) + '\n') - sys.exit(1) - - - -if __name__ == '__main__': - main() diff --git a/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/__init__.py b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/__init__.py deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py b/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py deleted file mode 100755 index c5bf317e52..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/convert_TINKER_files_to_LT_files/tinkerparm2lt.py +++ /dev/null @@ -1,746 +0,0 @@ -#! /usr/bin/env python - -""" -This standalone python script can be used to convert the force-fields -distributed with TINKER (".prm" files) into moltemplate (".lt") format. - -This script has only been tested with the OPLSAA force field (oplsaa.prm). -The full list of force-field files distributed with TINKER is available at: -http://dasher.wustl.edu/tinker/distribution/params - -Other TINKER compatible force fields may not work. (One reason for this is that -some force fields require features, such as point-dipole polarizability, which, -to my knowledge, have not yet been implemented in LAMMPS as of 2017-2-01.) - -""" - - -__author__ = 'Jason Lambert and Andrew Jewett' -# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others) -__version__ = '0.3.2' -__date__ = '2018-6-15' - - -import sys -import os -from sets import Set -from operator import itemgetter - - -g_program_name = __file__.split('/')[-1] - - -doc_msg = \ - "Typical Usage:\n\n" + \ - " " + g_program_name + " -name OPLS < oplsaa.prm > oplsaa.lt\n\n" + \ - " where \"oplsaa.prm\" is a force-field file downloaded from the TINKER website,\n" + \ - " \"oplsaa.lt\" is the corresponding file converted into moltemplate (.lt) format.\n" + \ - " and \"OPLS\" is the name that future moltemplate users will use to refer to\n" + \ - " this force-field (optional).\n" + \ - "Optional Arguments\n" + \ - " -name FORCEFIELDNAME # Give the force-field a name (recommended)\n" + \ - " -file FILE_NAME # Read force field parameters from a file\n" + \ - " -url URL # Read force field parameters from a file online\n" + \ - " -atoms \"QUOTED LIST\" # Restrict output to a subset of atom types\n" + \ - " -hybrid # Optional LAMMPS \"hybrid\" style compatibility\n" + \ - " -zeropad N # Optional zero-padding for bonded interactions\n" - - -def SplitQuotedString(string, - quotes='\'\"', - delimiters=' \t\r\f\n', - escape='\\', - comment_char='#'): - tokens = [] - token = '' - reading_token = True - escaped_state = False - quote_state = None - for c in string: - - if (c in comment_char) and (not escaped_state) and (quote_state == None): - tokens.append(token) - return tokens - - elif (c in delimiters) and (not escaped_state) and (quote_state == None): - if reading_token: - tokens.append(token) - token = '' - reading_token = False - - elif c in escape: - if escaped_state: - token += c - reading_token = True - escaped_state = False - else: - escaped_state = True - # and leave c (the '\' character) out of token - elif (c in quotes) and (not escaped_state): - if (quote_state != None): - if (c == quote_state): - quote_state = None - else: - quote_state = c - token += c - reading_token = True - else: - if (c == 'n') and (escaped_state == True): - c = '\n' - elif (c == 't') and (escaped_state == True): - c = '\t' - elif (c == 'r') and (escaped_state == True): - c = '\r' - elif (c == 'f') and (escaped_state == True): - c = '\f' - token += c - reading_token = True - escaped_state = False - - if len(string) > 0: - tokens.append(token) - return tokens - - -def RemoveOuterQuotes(text, quotes='\"\''): - if ((len(text) >= 2) and (text[0] in quotes) and (text[-1] == text[0])): - return text[1:-1] - else: - return text - - - -def main(): - try: - sys.stderr.write(g_program_name + ", version " + - __version__ + ", " + __date__ + "\n") - if sys.version < '2.6': - raise Exception('Error: Using python ' + sys.version + '\n' + - ' Alas, your version of python is too old.\n' - ' You must upgrade to a newer version of python (2.6 or later).') - - if sys.version < '2.7': - from ordereddict import OrderedDict - else: - from collections import OrderedDict - - if sys.version > '3': - import io - else: - import cStringIO - - # defaults: - ffname = "TINKER_FORCE_FIELD" - type_subset = Set([]) - filename_in = "" - file_in = sys.stdin - pair_style_name = "lj/cut/coul/long" - pair_style_link = "http://lammps.sandia.gov/doc/pair_lj.html" - bond_style_name = "harmonic" - bond_style_link = "http://lammps.sandia.gov/doc/bond_harmonic.html" - angle_style_name = "harmonic" - angle_style_link = "http://lammps.sandia.gov/doc/angle_harmonic.html" - dihedral_style_name = "fourier" - dihedral_style_link = "http://lammps.sandia.gov/doc/dihedral_fourier.html" - improper_style_name = "harmonic" - improper_style_link = "http://lammps.sandia.gov/doc/improper_harmonic.html" - #improper_style_name = "cvff" - #improper_style_link = "http://lammps.sandia.gov/doc/improper_cvff.html" - special_bonds_command = "special_bonds lj/coul 0.0 0.0 0.5" - mixing_style = "geometric" - use_hybrid = False - contains_united_atoms = False - zeropad_ffid = 1 - - argv = [arg for arg in sys.argv] - - i = 1 - - while i < len(argv): - - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - - if argv[i] == '-atoms': - if i + 1 >= len(argv): - raise Exception('Error: the \"' + argv[i] + '\" argument should be followed by a quoted string\n' - ' which contains a space-delimited list of of a subset of atom types\n' - ' you want to use from the original force-field.\n' - ' Make sure you enclose the entire list in quotes.\n') - type_subset = Set(argv[i + 1].strip('\"\'').strip().split()) - del argv[i:i + 2] - - elif argv[i] == '-name': - if i + 1 >= len(argv): - raise Exception( - 'Error: ' + argv[i] + ' flag should be followed by the name of the force-field\n') - ffname = argv[i + 1] - del argv[i:i + 2] - - elif argv[i] in ('-file', '-in-file'): - if i + 1 >= len(argv): - raise Exception( - 'Error: ' + argv[i] + ' flag should be followed by the name of a force-field file\n') - filename_in = argv[i + 1] - try: - file_in = open(filename_in, 'r') - except IOError: - sys.stderr.write('Error: Unable to open file\n' - ' \"' + filename_in + '\"\n' - ' for reading.\n') - sys.exit(1) - del argv[i:i + 2] - - elif argv[i] == '-dihedral-style': - if i + 1 >= len(argv): - raise Exception( - 'Error: ' + argv[i] + ' flag should be followed by either \"opls\" or \"fourier\"\n') - dihedral_style_name = argv[i + 1] - if dihedral_style_name == "fourier": - dihedral_style_link = "http://lammps.sandia.gov/doc/dihedral_fourier.html" - if dihedral_style_name == "opls": - dihedral_style_link = "http://lammps.sandia.gov/doc/dihedral_opls.html" - else: - raise Exception( - 'Error: ' + argv[i] + ' ' + dihedral_style_name + ' not supported.\n') - del argv[i:i + 2] - - elif argv[i] in ('-url', '-in-url'): - import urllib2 - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by a URL pointing to\n' - - ' a TINKER file containing force-field information.\n') - url = argv[i + 1] - try: - request = urllib2.Request(url) - file_in = urllib2.urlopen(request) - except urllib2.URLError: - sys.stdout.write("Error: Unable to open link:\n" + url + "\n") - sys.exit(1) - del argv[i:i + 2] - - elif argv[i] == '-hybrid': - use_hybrid = True - del argv[i:i + 1] - - elif (argv[i] == '-zeropad' or argv[i] == '-zero-pad'): - if (i + 1 >= len(argv)) or (argv[i+1][1:] == '-'): - raise Exception( - 'Error: ' + argv[i] + ' flag should be followed by a positive integer\n') - zeropad_ffid = int(argv[i+1]) - del argv[i:i + 2] - - elif argv[i] in ('-help', '--help', '-?', '--?'): - sys.stderr.write(doc_msg) - sys.exit(0) - del argv[i:i + 1] - - else: - i += 1 - - if len(argv) != 1: - raise Exception('Error: Unrecongized arguments: ' + ' '.join(argv[1:]) + - '\n\n' + doc_msg) - - #sys.stderr.write("Reading parameter file...\n") - - lines = file_in.readlines() - - atom2charge = OrderedDict() # lookup charge from atom type - atom2mass = OrderedDict() # lookup mass from atom type - atom2vdw_e = OrderedDict() # lookup Lennard-Jones "epsilon" parameter - atom2vdw_s = OrderedDict() # lookup Lennard-Jones "sigma" parameter - atom2descr = OrderedDict() - atom2ffid = OrderedDict() # lookup force-field-ID from atom type - # force-field-ID is an id number/string used to assign - # bonds, angles, dihedrals, and impropers. - - bonds_by_type = OrderedDict() # lookup bond parameters by force-field-ID - angles_by_type = OrderedDict() # lookup angle parameters by force-field-ID - dihedrals_by_type = OrderedDict() # lookup dihedral parameters by force-field-ID - impropers_by_type = OrderedDict() # lookup improper parameters by force-field-ID - lines_ureybrad = [] - lines_biotype = [] - - for iline in range(0, len(lines)): - line = lines[iline] - tokens = SplitQuotedString(line.strip(), - comment_char='#') - - if (len(tokens) > 1) and (tokens[0] == 'atom'): - tokens = map(RemoveOuterQuotes, - SplitQuotedString(line.strip(), - comment_char='')) - if (len(tokens) > 6): - if ((len(type_subset) == 0) or (tokens[1] in type_subset)): - atom2ffid[tokens[1]] = tokens[2] - #atom2mass[tokens[1]] = float(tokens[6]) - # Some atoms in oplsaa.prm have zero mass. Unfortunately this - # causes LAMMPS to crash, even if these atoms are never used, - # so I give the mass a non-zero value instead. - atom2mass[tokens[1]] = max(float(tokens[6]), 1e-30) - atom2descr[tokens[1]] = tokens[4] - if tokens[4].find('(UA)') != -1: - contains_united_atoms = True - else: - raise Exception('Error: Invalid atom line:\n' + line) - elif (len(tokens) > 2) and (tokens[0] == 'charge'): - if ((len(type_subset) == 0) or (tokens[1] in type_subset)): - atom2charge[tokens[1]] = float(tokens[2]) - elif (len(tokens) > 3) and (tokens[0] == 'vdw'): - if ((len(type_subset) == 0) or (tokens[1] in type_subset)): - atom2vdw_e[tokens[1]] = float(tokens[3]) # "epsilon" - atom2vdw_s[tokens[1]] = float(tokens[2]) # "sigma" - elif (len(tokens) > 4) and (tokens[0] == 'bond'): - k = float(tokens[3]) - r0 = float(tokens[4]) - bonds_by_type[tokens[1].rjust(zeropad_ffid,'0'), - tokens[2].rjust(zeropad_ffid,'0')] = (k, r0) - elif (len(tokens) > 5) and (tokens[0] == 'angle'): - k = float(tokens[4]) - angle0 = float(tokens[5]) - angles_by_type[tokens[1].rjust(zeropad_ffid,'0'), - tokens[2].rjust(zeropad_ffid,'0'), - tokens[3].rjust(zeropad_ffid,'0')] = (k, angle0) - elif (len(tokens) > 11) and (tokens[0] == 'torsion'): - if dihedral_style_name == 'fourier': - # http://lammps.sandia.gov/doc/dihedral_fourier.html - m = (len(tokens) - 5) / 3 - K = [0.0 for i in range(0, m)] - n = [0.0 for i in range(0, m)] - d = [0.0 for i in range(0, m)] - for i in range(0, m): - K[i] = float(tokens[5 + 3 * i]) - d[i] = float(tokens[5 + 3 * i + 1]) - n[i] = float(tokens[5 + 3 * i + 2]) - dihedrals_by_type[tokens[1].rjust(zeropad_ffid,'0'), - tokens[2].rjust(zeropad_ffid,'0'), - tokens[3].rjust(zeropad_ffid,'0'), - tokens[4].rjust(zeropad_ffid,'0')] = (K, n, d) - elif dihedral_style_name == 'opls': - # http://lammps.sandia.gov/doc/dihedral_opls.html - K1 = float(tokens[5]) - K2 = float(tokens[8]) - K3 = float(tokens[11]) - K4 = 0.0 - if len(tokens) > 14: - K4 = float(tokens[14]) - if ((float(tokens[6]) != 0.0) or (float(tokens[7]) != 1.0) or - (float(tokens[9]) not in (180.0, -180.0)) or (float(tokens[10]) != 2.0) or - (float(tokens[12]) != 0.0) or (float(tokens[13]) != 3.0) or - ((K4 != 0.0) and - ((len(tokens) <= 16) or - (float(tokens[15]) not in (180.0, -180.0)) or - (float(tokens[16]) != 4.0)))): - raise Exception("Error: This parameter file is incompatible with -dihedral-style \"" + dihedral_style_name + "\"\n" + - " (See line number " + str(iline + 1) + " of parameter file.)\n") - dihedrals_by_type[tokens[1].rjust(zeropad_ffid,'0'), - tokens[2].rjust(zeropad_ffid,'0'), - tokens[3].rjust(zeropad_ffid,'0'), - tokens[4].rjust(zeropad_ffid,'0')] = (K1, K2, K3, K4) - else: - assert(False) - - elif (len(tokens) > 7) and (tokens[0] == 'imptors'): - k = float(tokens[5]) - angle0 = float(tokens[6]) - multiplicity = float(tokens[7]) - impropers_by_type[tokens[1].rjust(zeropad_ffid,'0'), - tokens[2].rjust(zeropad_ffid,'0'), - tokens[3].rjust(zeropad_ffid,'0'), - tokens[4].rjust(zeropad_ffid,'0')] = (k / multiplicity, angle0) - elif ((len(tokens) > 0) and (tokens[0] == 'biotype')): - # I'm not sure what to do with these, so I'll store them for now and - # append them as comments to the .lt file generated by the program. - lines_biotype.append(line.rstrip()) - elif ((len(tokens) > 0) and (tokens[0] == 'ureybrad')): - # I'm not sure what to do with these, so I'll store them for now and - # append them as comments to the .lt file generated by the program. - lines_ureybrad.append(line.rstrip()) - elif ((len(tokens) > 1) and (tokens[0] == 'radiusrule')): - if tokens[1] == 'GEOMETRIC': - mixing_style = 'geometric' - elif tokens[1] == 'ARITHMETIC': - mixing_style = 'arithmetic' - else: - raise Exception("Error: Unrecognized mixing style: " + tokens[1] + ", found here:\n" + - line) - elif ((len(tokens) > 1) and (tokens[0] == 'epsilonrule')): - if tokens[1] != 'GEOMETRIC': - raise Exception("Error: As of 2016-9-21, LAMMPS only supports GEOMETRIC mixing of energies\n" + - " This force field simply cannot be used with LAMMPS in a general way.\n" + - " One way around this is to manually change the \"epsilonrule\" back to\n" + - " GEOMETRIC, and limit the number of atom types considered by this\n" + - " program by using the -atoms \"LIST OF ATOMS\" argument,\n" + - " to only include the atoms you care about, and then explicitly\n" + - " define pair_coeffs for all possible pairs of these atom types.\n" + - " If this is a popular force-field, then lobby the LAMMPS developers\n" + - " to consider alternate mixing rules.\n\n" + - "The offending line from the file is line number " + str(iline) + ":\n" + - line + "\n") - - # Zero-pad the atom2ffid values so that they have the same number - # of digits. This is usually not necessary, but it can be helpful - # to remove uncertainty about the meaning of '4*' which could - # pattern match with '4', '4L', '47', '47L'... If you replace '4' - # with '04', '04*' becomes distinguishable from '47*'. - # This can be useful if you want to augment the force field later, - # (for example, adding additional atoms to the LOPLSAA variant of OPLSAA) - - for k in atom2ffid.keys(): - atom2ffid[k] = atom2ffid[k].rjust(zeropad_ffid, '0') - - # Horrible hack: for LOPLSAA, uncomment the next 3 lines: - #ki = atom2ffid[k].find('L') - #if ki!=-1: - # atom2ffid[k] = atom2ffid[k].rjust(zeropad_ffid + len(atom2ffid[k]) - ki, '0') - - - #sys.stderr.write(" done.\n") - #sys.stderr.write("Converting to moltemplate format...\n") - - - system_is_charged = False - for atom_type in atom2charge: - if atom2charge[atom_type] != 0.0: - system_is_charged = True - - if system_is_charged: - pair_style_name = "lj/cut/coul/long" - pair_style_params = "10.0 10.0" - kspace_style = " kspace_style pppm 0.0001\n" - pair_style_link = "http://lammps.sandia.gov/doc/pair_lj.html" - else: - pair_style_name = "lj/cut" - pair_style_params = "10.0" - kspace_style = "" - pair_style_link = "http://lammps.sandia.gov/doc/pair_lj.html" - - pair_style_command = " pair_style " + ("hybrid " if use_hybrid else "") + \ - pair_style_name + " " + pair_style_params + "\n" - - sys.stdout.write("# This file was generated automatically using:\n") - sys.stdout.write("# " + g_program_name + " " + " ".join(sys.argv[1:]) + "\n") - if contains_united_atoms: - sys.stdout.write("#\n" - "# WARNING: Many of these atoms are probably UNITED-ATOM (UA) atoms.\n" - "# The hydrogen atoms have been absorbed into the heavy atoms, and the\n" - "# force-field modified accordingly. Do not mix with ordinary atoms.\n") - sys.stdout.write("#\n" - "# WARNING: The following 1-2, 1-3, and 1-4 weighting parameters were ASSUMED:\n") - sys.stdout.write("# " + special_bonds_command + "\n") - sys.stdout.write( - "# (See http://lammps.sandia.gov/doc/special_bonds.html for details)\n") - if len(lines_ureybrad) > 0: - sys.stdout.write("#\n" - "# WARNING: All Urey-Bradley interactions have been IGNORED including:\n") - sys.stdout.write("# ffid1 ffid2 ffid3 K r0\n# ") - sys.stdout.write("\n# ".join(lines_ureybrad)) - sys.stdout.write("\n\n") - sys.stdout.write("\n\n") - sys.stdout.write(ffname + " {\n\n") - - sys.stdout.write(" # Below we will use lammps \"set\" command to assign atom charges\n" - " # by atom type. http://lammps.sandia.gov/doc/set.html\n\n") - - sys.stdout.write(" write_once(\"In Charges\") {\n") - for atype in atom2mass: - assert(atype in atom2descr) - sys.stdout.write(" set type @atom:" + atype + " charge " + str(atom2charge[atype]) + - " # \"" + atom2descr[atype] + "\"\n") - sys.stdout.write(" } #(end of atom partial charges)\n\n\n") - - - sys.stdout.write(" write_once(\"Data Masses\") {\n") - for atype in atom2mass: - sys.stdout.write(" @atom:" + atype + " " + str(atom2mass[atype]) + "\n") - sys.stdout.write(" } #(end of atom masses)\n\n\n") - - - sys.stdout.write(" # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ----------\n" - " # Each type of atom has a separate ID used for looking up bond parameters\n" - " # and a separate ID for looking up 3-body angle interaction parameters\n" - " # and a separate ID for looking up 4-body dihedral interaction parameters\n" - " # and a separate ID for looking up 4-body improper interaction parameters\n" - #" # (This is because there are several different types of sp3 carbon atoms\n" - #" # which have the same torsional properties when within an alkane molecule,\n" - #" # for example. If they share the same dihedral-ID, then this frees us\n" - #" # from being forced define separate dihedral interaction parameters\n" - #" # for all of them.)\n" - " # The complete @atom type name includes ALL of these ID numbers. There's\n" - " # no need to force the end-user to type the complete name of each atom.\n" - " # The \"replace\" command used below informs moltemplate that the short\n" - " # @atom names we have been using abovee are equivalent to the complete\n" - " # @atom names used below:\n\n") - - for atype in atom2ffid: - ffid = atype + "_ffid" + atom2ffid[atype] - sys.stdout.write(" replace{ @atom:" + atype + - " @atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " }\n") - sys.stdout.write("\n\n\n\n") - - - sys.stdout.write(" # --------------- Non-Bonded interactions: ---------------------\n" - " # " + pair_style_link + "\n" - " # Syntax:\n" - " # pair_coeff AtomType1 AtomType2 " + - ("PairStyleName " if use_hybrid else "") + - "parameters...\n\n") - - sys.stdout.write(" write_once(\"In Settings\") {\n") - for atype in atom2vdw_e: - assert(atype in atom2vdw_s) - if not (atype in atom2ffid): - continue - - sys.stdout.write(" pair_coeff " + - "@atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[ - atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " " - "@atom:" + atype + "_b" + atom2ffid[atype] + "_a" + atom2ffid[atype] + "_d" + atom2ffid[atype] + "_i" + atom2ffid[atype] + " " + - (pair_style_name if use_hybrid else "") + - " " + str(atom2vdw_e[atype]) + - " " + str(atom2vdw_s[atype]) + "\n") - sys.stdout.write(" } #(end of pair_coeffs)\n\n\n\n") - - - sys.stdout.write(" # ------- Bonded Interactions: -------\n" - " # " + bond_style_link + "\n" - " # Syntax: \n" - " # bond_coeff BondTypeName " + - ("BondStyleName " if use_hybrid else "") + - "parameters...\n\n") - - sys.stdout.write(" write_once(\"In Settings\") {\n") - for btype in bonds_by_type: - ffid1 = btype[0] if btype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = btype[1] if btype[1] != ("0"*zeropad_ffid) else "X" - (k, r0) = bonds_by_type[btype] - sys.stdout.write(" bond_coeff @bond:" + ffid1 + "_" + ffid2 + " " + - (bond_style_name if use_hybrid else "") + - " " + str(k) + " " + str(r0) + "\n") - sys.stdout.write(" } #(end of bond_coeffs)\n\n") - - sys.stdout.write(" # Rules for assigning bond types by atom type:\n" - " # BondTypeName AtomType1 AtomType2\n" - " # (* = wildcard)\n\n") - - sys.stdout.write(" write_once(\"Data Bonds By Type\") {\n") - for btype in bonds_by_type: - ffid1 = btype[0] if btype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = btype[1] if btype[1] != ("0"*zeropad_ffid) else "X" - sys.stdout.write(" @bond:" + ffid1 + "_" + ffid2) - ffid1 = "@atom:*_b" + btype[0] + \ - "*_a*_d*_i*" if btype[0] != ("0"*zeropad_ffid) else "@atom:*" - ffid2 = "@atom:*_b" + btype[1] + \ - "*_a*_d*_i*" if btype[1] != ("0"*zeropad_ffid) else "@atom:*" - sys.stdout.write(" " + ffid1 + " " + ffid2 + "\n") - sys.stdout.write(" } #(end of bonds by type)\n\n\n\n\n") - - - sys.stdout.write(" # ------- Angle Interactions: -------\n" - " # " + angle_style_link + "\n" - " # Syntax: \n" - " # angle_coeff AngleTypeName "+ - ("AngleStyleName " if use_hybrid else "") + - "parameters...\n\n") - - sys.stdout.write(" write_once(\"In Settings\") {\n") - for atype in angles_by_type: - ffid1 = atype[0] if atype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = atype[1] if atype[1] != ("0"*zeropad_ffid) else "X" - ffid3 = atype[2] if atype[2] != ("0"*zeropad_ffid) else "X" - (k, angle0) = angles_by_type[atype] - sys.stdout.write(" angle_coeff @angle:" + ffid1 + "_" + ffid2 + "_" + ffid3 + " " + - (angle_style_name if use_hybrid else "") + - " " + str(k) + " " + str(angle0) + "\n") - sys.stdout.write(" } #(end of angle_coeffs)\n\n") - - - sys.stdout.write(" # Rules for creating angle interactions according to atom type:\n" - " # AngleTypeName AtomType1 AtomType2 AtomType3\n" - " # (* = wildcard)\n\n") - - sys.stdout.write(" write_once(\"Data Angles By Type\") {\n") - for atype in angles_by_type: - ffid1 = atype[0] if atype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = atype[1] if atype[1] != ("0"*zeropad_ffid) else "X" - ffid3 = atype[2] if atype[2] != ("0"*zeropad_ffid) else "X" - sys.stdout.write(" @angle:" + ffid1 + "_" + ffid2 + "_" + ffid3) - ffid1 = "@atom:*_b*_a" + atype[0] + \ - "*_d*_i*" if atype[0] != ("0"*zeropad_ffid) else "@atom:*" - ffid2 = "@atom:*_b*_a" + atype[1] + \ - "*_d*_i*" if atype[1] != ("0"*zeropad_ffid) else "@atom:*" - ffid3 = "@atom:*_b*_a" + atype[2] + \ - "*_d*_i*" if atype[2] != ("0"*zeropad_ffid) else "@atom:*" - sys.stdout.write(" " + ffid1 + " " + ffid2 + " " + ffid3 + "\n") - sys.stdout.write(" } #(end of angles by type)\n\n\n\n\n") - - - sys.stdout.write(" # ----------- Dihedral Interactions: ------------\n" - " # " + dihedral_style_link + "\n" - " # Syntax:\n" - " # dihedral_coeff DihedralTypeName " + - ("DihedralStyleName " if use_hybrid else "") + - "parameters...\n\n") - - sys.stdout.write(" write_once(\"In Settings\") {\n") - for dtype in dihedrals_by_type: - ffid1 = dtype[0] if dtype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = dtype[1] if dtype[1] != ("0"*zeropad_ffid) else "X" - ffid3 = dtype[2] if dtype[2] != ("0"*zeropad_ffid) else "X" - ffid4 = dtype[3] if dtype[3] != ("0"*zeropad_ffid) else "X" - sys.stdout.write(" dihedral_coeff @dihedral:" + - ffid1 + "_" + ffid2 + "_" + ffid3 + "_" + ffid4 + " " + - (dihedral_style_name if use_hybrid else "") + - " ") - if dihedral_style_name == 'fourier': - # http://lammps.sandia.gov/doc/dihedral_fourier.html - (K, n, d) = dihedrals_by_type[dtype] - m = len(K) - assert((m == len(n)) and (m == len(d))) - sys.stdout.write(str(m)) - for i in range(0, m): - sys.stdout.write(" " + str(K[i]) + - " " + str(n[i]) + " " + str(d[i])) - sys.stdout.write("\n") - elif dihedral_style_name == 'opls': - # http://lammps.sandia.gov/doc/dihedral_opls.html - (K1, K2, K3, K4) = dihedrals_by_type[dtype] - sys.stdout.write(str(K1) + " " + str(K2) + " " + - str(K3) + " " + str(K4) + "\n") - else: - assert(False) - sys.stdout.write(" } #(end of dihedral_coeffs)\n\n") - - - sys.stdout.write(" # Rules for creating dihedral interactions according to atom type:\n" - " # DihedralTypeName AtomType1 AtomType2 AtomType3 AtomType4\n" - " # (* = wildcard)\n\n") - - sys.stdout.write(" write_once(\"Data Dihedrals By Type\") {\n") - for dtype in dihedrals_by_type: - ffid1 = dtype[0] if dtype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = dtype[1] if dtype[1] != ("0"*zeropad_ffid) else "X" - ffid3 = dtype[2] if dtype[2] != ("0"*zeropad_ffid) else "X" - ffid4 = dtype[3] if dtype[3] != ("0"*zeropad_ffid) else "X" - sys.stdout.write(" @dihedral:" + - ffid1 + "_" + ffid2 + "_" + - ffid3 + "_" + ffid4) - ffid1 = "@atom:*_b*_a*_d" + dtype[0] + \ - "*_i*" if dtype[0] != ("0"*zeropad_ffid) else "@atom:*" - ffid2 = "@atom:*_b*_a*_d" + dtype[1] + \ - "*_i*" if dtype[1] != ("0"*zeropad_ffid) else "@atom:*" - ffid3 = "@atom:*_b*_a*_d" + dtype[2] + \ - "*_i*" if dtype[2] != ("0"*zeropad_ffid) else "@atom:*" - ffid4 = "@atom:*_b*_a*_d" + dtype[3] + \ - "*_i*" if dtype[3] != ("0"*zeropad_ffid) else "@atom:*" - - sys.stdout.write(" " + ffid1 + " " + ffid2 + - " " + ffid3 + " " + ffid4 + "\n") - sys.stdout.write(" } #(end of dihedrals by type)\n\n\n\n\n") - - - sys.stdout.write(" # ---------- Improper Interactions: ----------\n" - " # " + improper_style_link + "\n" - " # Syntax:\n" - " # improper_coeff ImproperTypeName " + - ("ImproperStyleName " if use_hybrid else "") + - "parameters\n\n") - - sys.stdout.write(" write_once(\"In Settings\") {\n") - for itype in impropers_by_type: - ffid1 = itype[0] if itype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = itype[1] if itype[1] != ("0"*zeropad_ffid) else "X" - ffid3 = itype[2] if itype[2] != ("0"*zeropad_ffid) else "X" - ffid4 = itype[3] if itype[3] != ("0"*zeropad_ffid) else "X" - (k, angle0) = impropers_by_type[itype] - sys.stdout.write(" improper_coeff @improper:" + - ffid1 + "_" + ffid2 + "_" + ffid3 + "_" + ffid4 + " " + - (improper_style_name if use_hybrid else "") + - " " + str(k) + " " + str(angle0) + "\n") - sys.stdout.write(" } #(end of improper_coeffs)\n\n") - - - sys.stdout.write(" # Rules for creating improper interactions according to atom type:\n" - " # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4\n" - " # (* = wildcard)\n") - - sys.stdout.write(" write_once(\"Data Impropers By Type (opls_imp.py)\") {\n") - for itype in impropers_by_type: - ffid1 = itype[0] if itype[0] != ("0"*zeropad_ffid) else "X" - ffid2 = itype[1] if itype[1] != ("0"*zeropad_ffid) else "X" - ffid3 = itype[2] if itype[2] != ("0"*zeropad_ffid) else "X" - ffid4 = itype[3] if itype[3] != ("0"*zeropad_ffid) else "X" - sys.stdout.write(" @improper:" + - ffid1 + "_" + ffid2 + "_" + - ffid3 + "_" + ffid4) - ffid1 = "@atom:*_b*_a*_d*_i" + itype[0]+"*" if itype[0] != ("0"*zeropad_ffid) else "@atom:*" - ffid2 = "@atom:*_b*_a*_d*_i" + itype[1]+"*" if itype[1] != ("0"*zeropad_ffid) else "@atom:*" - ffid3 = "@atom:*_b*_a*_d*_i" + itype[2]+"*" if itype[2] != ("0"*zeropad_ffid) else "@atom:*" - ffid4 = "@atom:*_b*_a*_d*_i" + itype[3]+"*" if itype[3] != ("0"*zeropad_ffid) else "@atom:*" - sys.stdout.write(" " + ffid1 + " " + ffid2 + - " " + ffid3 + " " + ffid4 + "\n") - sys.stdout.write(" } #(end of impropers by type)\n\n\n\n\n") - - sys.stdout.write(" # -------- (descriptive comment) --------\n") - sys.stdout.write(" # ---- biologically relevant atom types: ----\n # ") - sys.stdout.write("\n # ".join(lines_biotype)) - sys.stdout.write("\n # ---------- (end of comment) ----------\n") - sys.stdout.write("\n\n\n\n") - - - sys.stdout.write(" # LAMMPS supports many different kinds of bonded and non-bonded\n" - " # interactions which can be selected at run time. Eventually\n" - " # we must inform LAMMPS which of them we will need. We specify\n" - " # this in the \"In Init\" section: \n\n") - - sys.stdout.write(" write_once(\"In Init\") {\n") - sys.stdout.write(" units real\n") - sys.stdout.write(" atom_style full\n") - sys.stdout.write(" bond_style " + - ("hybrid " if use_hybrid else "") + - bond_style_name + "\n") - sys.stdout.write(" angle_style " + - ("hybrid " if use_hybrid else "") + - angle_style_name + "\n") - sys.stdout.write(" dihedral_style " + - ("hybrid " if use_hybrid else "") + - dihedral_style_name + "\n") - sys.stdout.write(" improper_style " + - ("hybrid " if use_hybrid else "") + - improper_style_name + "\n") - sys.stdout.write(pair_style_command) - sys.stdout.write(" pair_modify mix " + mixing_style + "\n") - sys.stdout.write(" " + special_bonds_command + "\n") - sys.stdout.write(kspace_style) - sys.stdout.write(" } #end of init parameters\n\n") - - sys.stdout.write(" # Note: We use \"hybrid\" styles in case the user later wishes to\n" - " # combine the molecules built using this force-field with other\n" - " # molecules that use other styles. (This is not necessarily\n" - " # a good idea, but LAMMPS and moltemplate both allow it.)\n" - " # For more information:\n" - " # http://lammps.sandia.gov/doc/pair_hybrid.html\n" - " # http://lammps.sandia.gov/doc/bond_hybrid.html\n" - " # http://lammps.sandia.gov/doc/angle_hybrid.html\n" - " # http://lammps.sandia.gov/doc/dihedral_hybrid.html\n" - " # http://lammps.sandia.gov/doc/improper_hybrid.html\n\n\n") - - sys.stdout.write("} # " + ffname + "\n\n") - - - #sys.stderr.write(" done.\n") - - if filename_in != "": - file_in.close() - - - - - except Exception as err: - sys.stderr.write('\n\n' + str(err) + '\n') - sys.exit(1) - - -if __name__ == '__main__': - main() diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_lipid.lt b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_lipid.lt deleted file mode 100644 index 949a81b1e7..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_lipid.lt +++ /dev/null @@ -1,43 +0,0 @@ -# CDlipid is a lipid model from: -# "Tunable generic model for fluid bilayer membranes" -# Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 -# (Author: David Stelter, BU) - -CDlipid { - # 3-bead model of COOKE, KREMER, DESERNO - write_once("In Init") { - units lj - atom_style full - - bond_style hybrid harmonic fene - pair_style hybrid table linear 600 - pair_modify shift yes - special_bonds lj 0.0 1.0 1.0 - - neigh_modify every 1 delay 1 - neighbor 0.3 bin - } - write_once("In Settings") { - pair_coeff @atom:H @atom:H table tabulated_potential.dat HEAD_HEAD - pair_coeff @atom:H @atom:T table tabulated_potential.dat HEAD_TAIL - # (Note: The "HEAD_TAIL" table is the same as the "HEAD_HEAD" table.) - pair_coeff @atom:T @atom:T table tabulated_potential.dat TAIL_TAIL_Wc_1.5 - bond_coeff @bond:har harmonic 10.0 4.0 - bond_coeff @bond:fene fene 30.0 1.5 0.0 0.0 - } - write("Data Atoms") { - $atom:1 $mol:. @atom:H 0.0 0.00 0.00 2.20 - $atom:2 $mol:. @atom:T 0.0 0.00 0.00 1.10 - $atom:3 $mol:. @atom:T 0.0 0.00 0.00 0.00 - } - write("Data Bonds") { - $bond:b1 @bond:fene $atom:1 $atom:2 - $bond:b2 @bond:fene $atom:2 $atom:3 - $bond:b3 @bond:har $atom:1 $atom:3 - } - write_once("Data Masses") { - @atom:H 1.0 ## Head Bead - @atom:T 1.0 ## Tail Bead - } -} # CDlipid - diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README deleted file mode 100644 index 6713725d0b..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/README +++ /dev/null @@ -1,16 +0,0 @@ ----Cooke Deserno coarse-grained bilayer model--- - -This folder contains an lt file for a Cooke-type 3-bead lipid, as described in: - -"Tunable generic model for fluid bilayer membranes" - Cooke IR, Kremer K, Deserno M, Physical Review E, 2005 - -Due to the form of the forcefield, this requires a 'tabulated potential' style in lammps. This is easily generated using the included python script. Usage as follows: - - gen_potential-cooke.py w_c - -where w_c is an optional parameter as described in the original paper (10.1103/PhysRevE.72.011506) with default value of 1.6 - -This creates the 'tabulated_potential' file which is needed by lammps during the simulation. - ---- diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py deleted file mode 100755 index 7240296584..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/gen_potential-cooke.py +++ /dev/null @@ -1,144 +0,0 @@ -#!/usr/bin/python2.7 - -import os,sys -from fractions import Fraction -from numpy import * - -### PARAMETERS ### -sigma = 1.00 -epsilon = 1.00 - -b_hh = 0.95 * sigma -b_ht = 0.95 * sigma -b_tt = 1.00 * sigma - -r_init = 0.000001 -r_max = sigma * 3. -r_space = 0.01 -################## - -### INPUTS ### -if len(sys.argv) == 2: - w_cut = float(sys.argv[1]) -else: - w_cut = 1.6 -# 1.6 seems to be 'good' for vesicles, bilayers 1.4 -############## - -def WCA_energy(b, r): -# Calculate WCA energy - E_pot = 0 - val1 = math.pow((b / r), 12) - val2 = -math.pow((b / r), 6) - E_pot = 4 * epsilon * (val1 + val2 + 0.25) - return E_pot - -def WCA_forces(b, r): -# Calculate WCA forces - Force = 0 - val1 = 24 * math.pow(b, 6) / math.pow(r, 7) - val2 = -48 * math.pow(b, 12) / math.pow(r, 13) - Force = -(val1 + val2) - return Force - -def Tail_energy(b, r, r_cut): -# Calculate extra Tail energy - E_pot = 0 - if (r < r_cut): - E_pot = -1 * epsilon - else: - val1 = math.cos((math.pi * (r - r_cut)) / (2 * w_cut)) - E_pot = -1 * epsilon * math.pow(val1, 2) - return E_pot - -def Tail_forces(b, r, r_cut): - Force = 0 - if (r < r_cut): - Force = 0; - else: - val1 = math.sin((math.pi * (r - r_cut)) / w_cut) - Force = -math.pi * val1 / (2 * w_cut) - return Force - - -############## -ofile = open('tabulated_potential.dat', 'w') -tot_potential_hh = zeros((int(r_max / r_space) + 1, 4)) -tot_potential_ht = zeros((int(r_max / r_space) + 1, 4)) -tot_potential_tt = zeros((int(r_max / r_space) + 1, 4)) - -# Setup up formatting & distances in all arrays -for i in range(int(r_max / r_space)+1): - tot_potential_hh[:,0][i] = i+1 - tot_potential_ht[:,0][i] = i+1 - tot_potential_tt[:,0][i] = i+1 -for i in range(1, int(r_max / r_space)+1): - tot_potential_hh[:,1][i] = tot_potential_hh[:,1][i-1] + r_space - tot_potential_ht[:,1][i] = tot_potential_ht[:,1][i-1] + r_space - tot_potential_tt[:,1][i] = tot_potential_tt[:,1][i-1] + r_space -tot_potential_hh[:,1][0] = r_init -tot_potential_ht[:,1][0] = r_init -tot_potential_tt[:,1][0] = r_init - - - -ofile.write("# Tabulated potential for Cooke 3-bead lipid model, Wc = %f\n\n" % w_cut) -num = len(tot_potential_hh[:,0]) - -### Calcaulte first potential, H-H -ofile.write("HEAD_HEAD\n") -r_cut = 2**Fraction('1/6') * b_hh -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_hh[:,1][0], tot_potential_hh[:,2][0], tot_potential_hh[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_hh[:,2][i] = WCA_energy(b_hh, tot_potential_hh[:,1][i]) - tot_potential_hh[:,3][i] = WCA_forces(b_hh, tot_potential_hh[:,1][i]) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_hh[:,1][i], tot_potential_hh[:,2][i], tot_potential_hh[:,3][i])) -ofile.write("\n") - - - -### Calcaulte second potential, H-T -ofile.write("HEAD_TAIL\n") -r_cut = 2**Fraction('1/6') * b_ht -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_ht[:,1][0], tot_potential_ht[:,2][0], tot_potential_ht[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_ht[:,2][i] = WCA_energy(b_ht, tot_potential_ht[:,1][i]) - tot_potential_ht[:,3][i] = WCA_forces(b_ht, tot_potential_ht[:,1][i]) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_ht[:,1][i], tot_potential_ht[:,2][i], tot_potential_ht[:,3][i])) -ofile.write("\n") - - - -### Calcaulte third potential, T-T -# Also include extra tail-tail attraction term -ofile.write("TAIL_TAIL\n") -r_cut = 2**Fraction('1/6') * b_tt -rmax = int(r_cut / r_space) -ofile.write("N %d R %f %f\n\n" % (num, r_init, r_max)) -ofile.write("1 %f %f %f\n" % (tot_potential_tt[:,1][0], tot_potential_tt[:,2][0], tot_potential_tt[:,3][0])) - -for i in range(1, rmax+1): - tot_potential_tt[:,2][i] = WCA_energy(b_tt, tot_potential_tt[:,1][i]) - tot_potential_tt[:,3][i] = WCA_forces(b_tt, tot_potential_tt[:,1][i]) - -max2 = int( (r_cut + w_cut) / r_space) -for i in range(1, max2+1): - tot_potential_tt[:,2][i] = tot_potential_tt[:,2][i] + Tail_energy(b_tt, tot_potential_tt[:,1][i], r_cut) - tot_potential_tt[:,3][i] = tot_potential_tt[:,3][i] + Tail_forces(b_tt, tot_potential_tt[:,1][i], r_cut) - -for i in range(1, int(r_max / r_space)+1): - ofile.write("%d %f %f %f\n" % (i+1, tot_potential_tt[:,1][i], tot_potential_tt[:,2][i], tot_potential_tt[:,3][i])) -ofile.write("\n") - - -sys.exit() diff --git a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat b/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat deleted file mode 100644 index cd8dd4db7d..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/cooke_deserno_supporting_files/tabulated_potential.dat +++ /dev/null @@ -1,4589 +0,0 @@ -# Tabulated potential for Cooke 3-bead lipid model, with various values of Wc - -HEAD_HEAD -N 301 R 0.000001 3.000000 - -1 0.000001 0.000000 0.000000 -2 0.010000 2161440350647607518822400.000000 2593728420778890895481110528.000000 -3 0.020000 527695398062100709376.000000 316617238851043104653312.000000 -4 0.030000 4067131343850062336.000000 1626852538346708926464.000000 -5 0.040000 128831883585858496.000000 38649565183436988416.000000 -6 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1.680000 -0.781375 -0.721368 -170 1.690000 -0.774119 -0.729829 -171 1.700000 -0.766779 -0.738068 -172 1.710000 -0.759358 -0.746081 -173 1.720000 -0.751858 -0.753868 -174 1.730000 -0.744282 -0.761425 -175 1.740000 -0.736631 -0.768750 -176 1.750000 -0.728908 -0.775840 -177 1.760000 -0.721115 -0.782695 -178 1.770000 -0.713254 -0.789311 -179 1.780000 -0.705329 -0.795686 -180 1.790000 -0.697341 -0.801819 -181 1.800000 -0.689294 -0.807708 -182 1.810000 -0.681188 -0.813351 -183 1.820000 -0.673027 -0.818746 -184 1.830000 -0.664814 -0.823892 -185 1.840000 -0.656550 -0.828787 -186 1.850000 -0.648239 -0.833429 -187 1.860000 -0.639883 -0.837818 -188 1.870000 -0.631484 -0.841951 -189 1.880000 -0.623045 -0.845828 -190 1.890000 -0.614568 -0.849447 -191 1.900000 -0.606056 -0.852807 -192 1.910000 -0.597513 -0.855908 -193 1.920000 -0.588939 -0.858748 -194 1.930000 -0.580339 -0.861326 -195 1.940000 -0.571714 -0.863642 -196 1.950000 -0.563067 -0.865695 -197 1.960000 -0.554401 -0.867484 -198 1.970000 -0.545718 -0.869009 -199 1.980000 -0.537021 -0.870269 -200 1.990000 -0.528313 -0.871264 -201 2.000000 -0.519597 -0.871994 -202 2.010000 -0.510874 -0.872458 -203 2.020000 -0.502149 -0.872657 -204 2.030000 -0.493422 -0.872589 -205 2.040000 -0.484698 -0.872256 -206 2.050000 -0.475978 -0.871657 -207 2.060000 -0.467265 -0.870792 -208 2.070000 -0.458563 -0.869663 -209 2.080000 -0.449873 -0.868268 -210 2.090000 -0.441198 -0.866609 -211 2.100000 -0.432542 -0.864686 -212 2.110000 -0.423906 -0.862499 -213 2.120000 -0.415293 -0.860050 -214 2.130000 -0.406705 -0.857339 -215 2.140000 -0.398147 -0.854367 -216 2.150000 -0.389619 -0.851134 -217 2.160000 -0.381125 -0.847642 -218 2.170000 -0.372667 -0.843892 -219 2.180000 -0.364248 -0.839885 -220 2.190000 -0.355870 -0.835622 -221 2.200000 -0.347536 -0.831105 -222 2.210000 -0.339249 -0.826334 -223 2.220000 -0.331010 -0.821311 -224 2.230000 -0.322824 -0.816039 -225 2.240000 -0.314691 -0.810518 -226 2.250000 -0.306614 -0.804750 -227 2.260000 -0.298596 -0.798737 -228 2.270000 -0.290640 -0.792480 -229 2.280000 -0.282748 -0.785982 -230 2.290000 -0.274921 -0.779245 -231 2.300000 -0.267163 -0.772270 -232 2.310000 -0.259477 -0.765061 -233 2.320000 -0.251863 -0.757618 -234 2.330000 -0.244325 -0.749944 -235 2.340000 -0.236865 -0.742042 -236 2.350000 -0.229485 -0.733914 -237 2.360000 -0.222187 -0.725562 -238 2.370000 -0.214974 -0.716989 -239 2.380000 -0.207848 -0.708198 -240 2.390000 -0.200811 -0.699191 -241 2.400000 -0.193865 -0.689971 -242 2.410000 -0.187012 -0.680541 -243 2.420000 -0.180255 -0.670904 -244 2.430000 -0.173595 -0.661062 -245 2.440000 -0.167034 -0.651019 -246 2.450000 -0.160575 -0.640778 -247 2.460000 -0.154220 -0.630342 -248 2.470000 -0.147969 -0.619713 -249 2.480000 -0.141826 -0.608896 -250 2.490000 -0.135792 -0.597893 -251 2.500000 -0.129869 -0.586708 -252 2.510000 -0.124058 -0.575344 -253 2.520000 -0.118362 -0.563805 -254 2.530000 -0.112783 -0.552095 -255 2.540000 -0.107321 -0.540216 -256 2.550000 -0.101979 -0.528173 -257 2.560000 -0.096758 -0.515968 -258 2.570000 -0.091660 -0.503607 -259 2.580000 -0.086686 -0.491092 -260 2.590000 -0.081839 -0.478428 -261 2.600000 -0.077118 -0.465618 -262 2.610000 -0.072527 -0.452666 -263 2.620000 -0.068066 -0.439576 -264 2.630000 -0.063736 -0.426352 -265 2.640000 -0.059539 -0.412998 -266 2.650000 -0.055476 -0.399519 -267 2.660000 -0.051549 -0.385918 -268 2.670000 -0.047758 -0.372199 -269 2.680000 -0.044105 -0.358367 -270 2.690000 -0.040591 -0.344426 -271 2.700000 -0.037217 -0.330380 -272 2.710000 -0.033984 -0.316233 -273 2.720000 -0.030893 -0.301990 -274 2.730000 -0.027945 -0.287655 -275 2.740000 -0.025140 -0.273232 -276 2.750000 -0.022480 -0.258726 -277 2.760000 -0.019966 -0.244141 -278 2.770000 -0.017598 -0.229482 -279 2.780000 -0.015376 -0.214753 -280 2.790000 -0.013303 -0.199959 -281 2.800000 -0.011377 -0.185103 -282 2.810000 -0.009601 -0.170192 -283 2.820000 -0.007974 -0.155228 -284 2.830000 -0.006496 -0.140217 -285 2.840000 -0.005170 -0.125164 -286 2.850000 -0.003993 -0.110072 -287 2.860000 -0.002968 -0.094947 -288 2.870000 -0.002095 -0.079793 -289 2.880000 -0.001372 -0.064614 -290 2.890000 -0.000802 -0.049416 -291 2.900000 -0.000384 -0.034203 -292 2.910000 -0.000118 -0.018979 -293 2.920000 -0.000005 -0.003750 -294 2.930000 0.000000 0.000000 -295 2.940000 0.000000 0.000000 -296 2.950000 0.000000 0.000000 -297 2.960000 0.000000 0.000000 -298 2.970000 0.000000 0.000000 -299 2.980000 0.000000 0.000000 -300 2.990000 0.000000 0.000000 -301 3.000000 0.000000 0.000000 - diff --git a/tools/moltemplate/moltemplate/force_fields/gaff.lt b/tools/moltemplate/moltemplate/force_fields/gaff.lt deleted file mode 100644 index d9e367e8ce..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/gaff.lt +++ /dev/null @@ -1,11788 +0,0 @@ -# This is the 1.7 version of GAFF (from AmberTools15), downloaded 2015-8-17. -# NOTE: Corrections were made to the amberparm2lt.sh converter on 2014-5-19, so -# this version of gaff.lt differs from earlier versions using the same source -#################################################################### -# To use this, LAMMPS currently must be compiled with the USER-MISC package. -# (Type "make yes-user-misc" into the shell before compiling LAMMPS.) -#################################################################### -# This moltemplate (LT) file was generated automatically using -# amber/amberparm2lt.sh gaff.dat GAFF > gaff.lt -#################################################################### -# Background information and usage explanation: -# This file contanis a list of atom types and rules for generating bonded -# interactions between these atoms (hopefully) according to AMBER conventions. -# By using the atom types shown below in your own molecules, bonds and angular -# interactions will be automatically generated. -# AMBER (GAFF) force-field parameters will also be assigned to each angle -# interaction (according to these atom types). -# One way to apply the GAFF force field to a particular type of molecule, is -# to use the "inherits" keyword when you define that molecule. For example: -# -# import("gaff.lt") -# MoleculeType inherits GAFF { -# write_once("Data Atoms") { -# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285 -# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382 -# : : : -# } -# } -# -#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) -#################################################################### -# Moltemplate can not assign atom charge. You must assign atomic -# charges yourself. (Moltemplate is only a simple text manipulation tool. -# You can do this afterwards using commands like "set atom 70 charge -0.212" -# For details, see http://lammps.sandia.gov/doc/set.html) -#################################################################### - - - - -GAFF { - - # ---------------------------------------------------------------------- - # The basic atom nomenclature and conventions are explained here: - # http://ambermd.org/antechamber/gaff.pdf - # For reference, the original gaff.dat file and format documentation are here: - # http://ambermd.org/AmberTools-get.html - # http://ambermd.org/formats.html#parm.dat - # ---------------------------------------------------------------------- - - write_once("Data Masses") { - @atom:c 12.01 # Sp2 C carbonyl group - @atom:c1 12.01 # Sp C - @atom:c2 12.01 # Sp2 C - @atom:c3 12.01 # Sp3 C - @atom:ca 12.01 # Sp2 C in pure aromatic systems - @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys. - @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp - @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems - @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc - @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems - @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce - @atom:cg 12.01 # Inner Sp carbons in conjugated systems - @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg - @atom:cx 12.01 # Sp3 carbons in triangle systems - @atom:cy 12.01 # Sp3 carbons in square systems - @atom:cu 12.01 # Sp2 carbons in triangle systems - @atom:cv 12.01 # Sp2 carbons in square systems - @atom:cz 12.01 # Sp2 carbon in guanidine group - @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group - @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group - @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group - @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group - @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group - @atom:ha 1.008 # H bonded to aromatic carbon - @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group - @atom:hn 1.008 # H bonded to nitrogen atoms - @atom:ho 1.008 # Hydroxyl group - @atom:hp 1.008 # H bonded to phosphate - @atom:hs 1.008 # Hydrogen bonded to sulphur - @atom:hw 1.008 # Hydrogen in water - @atom:hx 1.008 # H bonded to C next to positively charged group - @atom:f 19.00 # Fluorine - @atom:cl 35.45 # Chlorine - @atom:br 79.90 # Bromine - @atom:i 126.9 # Iodine - @atom:n 14.01 # Sp2 nitrogen in amide groups - @atom:n1 14.01 # Sp N - @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms - @atom:n3 14.01 # Sp3 N with three connected atoms - @atom:n4 14.01 # Sp3 N with four connected atoms - @atom:na 14.01 # Sp2 N with three connected atoms - @atom:nb 14.01 # Sp2 N in pure aromatic systems - @atom:nc 14.01 # Sp2 N in non-pure aromatic systems - @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc - @atom:ne 14.01 # Inner Sp2 N in conjugated systems - @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne - @atom:nh 14.01 # Amine N connected one or more aromatic rings - @atom:no 14.01 # Nitro N - @atom:o 16.00 # Oxygen with one connected atom - @atom:oh 16.00 # Oxygen in hydroxyl group - @atom:os 16.00 # Ether and ester oxygen - @atom:ow 16.00 # Oxygen in water - @atom:p2 30.97 # Phosphate with two connected atoms - @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3 - @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2 - @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3 - @atom:pb 30.97 # Sp2 P in pure aromatic systems - @atom:pc 30.97 # Sp2 P in non-pure aromatic systems - @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc - @atom:pe 30.97 # Inner Sp2 P in conjugated systems - @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe - @atom:px 30.97 # Special p4 in conjugated systems - @atom:py 30.97 # Special p5 in conjugated systems - @atom:s 32.06 # S with one connected atom - @atom:s2 32.06 # S with two connected atom, involved at least one double bond - @atom:s4 32.06 # S with three connected atoms - @atom:s6 32.06 # S with four connected atoms - @atom:sh 32.06 # Sp3 S connected with hydrogen - @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether - @atom:sx 32.06 # Special s4 in conjugated systems - @atom:sy 32.06 # Special s6 in conjugated systems - } # (end of masses) - - write_once("In Settings") { - pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0157 2.47135304412 # Veenstra et al JCC,8,(1992),963 - pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0157 2.29317330049 # Veenstra et al JCC,8,(1992),963 - pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0157 2.11499355687 # Veenstra et al JCC,8,(1992),963 - pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0150 2.51055258772 # Spellmeyer, one electrowithdr. neighbor - pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0150 2.42146271591 # Spellmeyer, two electrowithdr. neighbor - pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0150 2.59964245953 # Spellmeyer - pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0157 2.64953278775 # OPLS - pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0157 1.06907846177 # !Ferguson base pair geom. - pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0000 0.0 # OPLS Jorgensen, JACS,110,(1988),1657 - pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0157 1.06907846177 # same to hs (be careful !) - pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0157 1.06907846177 # W. Cornell CH3SH --> CH3OH FEP - pair_coeff @atom:hw @atom:hw lj/charmm/coul/long 0.0000 0.0 # OPLS Jorgensen, JACS,110,(1988),1657 - pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0157 1.95997717991 # Veenstra et al JCC,8,(1992),963 - pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.2100 2.95992190115 # OPLS - pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.2104 3.06647338784 # OPLS - pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.1700 3.00001234347 # OPLS ether - pair_coeff @atom:ow @atom:ow lj/charmm/coul/long 0.1520 3.15075240658 # TIP3P water model - pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.2100 3.39966950842 # cp C DLM 11/2007 well depth from OPLS replacing 0.0860 - pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0860 3.39966950842 # sp2 atom in the middle of C=CD-CD=C - pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1094 3.39966950842 # OPLS - pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.2100 3.39966950842 # DLM 12/2007 as c1 - pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.2100 3.39966950842 # DLM 12/2007 as c1 - pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0860 3.39966950842 # OPLS - pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.1700 3.24999852378 # OPLS - pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2500 3.56359487256 # W. Cornell CH3SH and CH3SCH3 FEP's - pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2000 3.74177461619 # JCC,7,(1986),230; - pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.061 3.11814551349 # Gough et al. JCC 13,(1992),963. - pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.265 3.47094140587 # Fox, JPCB,102,8070,(98),flex.mdl CHCl3 - pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.420 3.59923082129 # Junmei, 2010 - pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.50 3.830864488 # Junmei, 2010 - } # (end of pair_coeffs) - - write_once("In Settings") { - bond_coeff @bond:ow-hw harmonic 553.0 0.9572 # TIP3P_Water 1 - bond_coeff @bond:hw-hw harmonic 553.0 1.5136 # TIP3P_Water 1 - bond_coeff @bond:br-br harmonic 123.2 2.5420 # SOURCE1 4 0.0000 - bond_coeff @bond:br-c1 harmonic 352.7 1.7870 # SOURCE2 4 0.0024 - bond_coeff @bond:br-c2 harmonic 278.7 1.8830 # SOURCE1 31 0.0000 - bond_coeff @bond:br-c harmonic 240.3 1.9460 # SOURCE2 2 0.0285 - bond_coeff @bond:br-c3 harmonic 229.5 1.9660 # SOURCE1 100 0.0000 - bond_coeff @bond:br-ca harmonic 269.6 1.8970 # SOURCE1 127 0.0058 - bond_coeff @bond:br-cc harmonic 277.6 1.8847 # SOURCE4 39 0.0068 - bond_coeff @bond:br-cx harmonic 261.4 1.9100 # SOURCE1 8 0.0000 - bond_coeff @bond:br-i harmonic 142.4 2.6710 # SOURCE1 2 0.0245 - bond_coeff @bond:br-n1 harmonic 330.4 1.8600 # SOUECE3 1 - bond_coeff @bond:br-n2 harmonic 219.0 2.0380 # SOURCE3 5 0.1082 - bond_coeff @bond:br-n harmonic 320.2 1.8730 # SOURCE3 4 0.0046 - bond_coeff @bond:br-n3 harmonic 265.9 1.9520 # SOURCE3 2 0.0000 - bond_coeff @bond:br-n4 harmonic 282.4 1.9260 # SOURCE3 3 0.0013 - bond_coeff @bond:br-na harmonic 237.3 2.0020 # SOURCE3 7 0.2156 - bond_coeff @bond:br-nh harmonic 270.9 1.9440 # SOURCE3 1 0.0000 - bond_coeff @bond:br-no harmonic 191.0 2.1010 # SOURCE3 1 0.0000 - bond_coeff @bond:br-o harmonic 278.9 1.8000 # SOUECE3 1 - bond_coeff @bond:br-oh harmonic 237.2 1.8660 # SOURCE3 1 0.0000 - bond_coeff @bond:br-os harmonic 225.6 1.8870 # SOURCE3 2 0.0000 - bond_coeff @bond:br-p2 harmonic 174.3 2.2100 # SOURCE3 9 0.0510 - bond_coeff @bond:br-p3 harmonic 167.0 2.2310 # SOURCE3 3 0.0101 - bond_coeff @bond:br-p4 harmonic 188.8 2.1710 # SOUECE3 1 - bond_coeff @bond:br-p5 harmonic 179.3 2.1960 # SOURCE3 3 0.0099 - bond_coeff @bond:br-s harmonic 170.6 2.2200 # SOUECE3 1 - bond_coeff @bond:br-s4 harmonic 134.3 2.3410 # SOURCE3 1 0.0000 - bond_coeff @bond:br-s6 harmonic 172.7 2.2140 # SOURCE3 3 0.0443 - bond_coeff @bond:br-sh harmonic 174.4 2.2090 # SOURCE3 1 0.0000 - bond_coeff @bond:br-ss harmonic 176.6 2.2030 # SOURCE3 3 0.0035 - bond_coeff @bond:c1-c1 harmonic 986.2 1.1810 # SOURCE1 265 0.0031 - bond_coeff @bond:c1-c2 harmonic 625.0 1.3070 # SOURCE1 18 0.0000 - bond_coeff @bond:c1-c3 harmonic 368.3 1.4700 # SOURCE1 215 0.0017 - bond_coeff @bond:c1-ca harmonic 404.1 1.4400 # SOUECE3 1 - bond_coeff @bond:c1-ce harmonic 607.4 1.3153 # SOURCE4 6 0.0086 - bond_coeff @bond:c1-cg harmonic 845.8 1.2220 # SOURCE3 22 0.0101 - bond_coeff @bond:c1-ch harmonic 845.8 1.2220 # SOURCE3 22 same_as_c1-cg - bond_coeff @bond:c1-cl harmonic 419.7 1.6310 # SOURCE2 6 0.0050 - bond_coeff @bond:c1-cx harmonic 399.1 1.4440 # SOURCE1 38 0.0000 - bond_coeff @bond:c1-f harmonic 469.4 1.2700 # SOURCE2 2 0.0085 - bond_coeff @bond:c1-ha harmonic 375.9 1.0660 # SOURCE3 63 0.0035 - bond_coeff @bond:c1-hc harmonic 385.6 1.0600 # SOUECE3 1 - bond_coeff @bond:c1-i harmonic 318.8 1.9890 # SOURCE2 4 0.0032 - bond_coeff @bond:c1-n1 harmonic 1014.5 1.1380 # SOURCE1 170 0.0055 - bond_coeff @bond:c1-n2 harmonic 769.8 1.2100 # SOURCE3 5 0.0115 - bond_coeff @bond:c1-n3 harmonic 409.8 1.3920 # SOURCE2 1 0.0000 - bond_coeff @bond:c1-n4 harmonic 378.2 1.4170 # SOURCE3 3 0.0032 - bond_coeff @bond:c1-n harmonic 503.0 1.3300 # SOUECE3 1 - bond_coeff @bond:c1-na harmonic 452.0 1.3620 # SOURCE3 8 0.0034 - bond_coeff @bond:c1-ne harmonic 803.3 1.1986 # SOURCE4 10 0.0088 - bond_coeff @bond:c1-nf harmonic 803.3 1.1986 # SOURCE4 10 same_as_c1-ne - bond_coeff @bond:c1-nh harmonic 485.0 1.3408 # SOURCE4 11 0.0037 - bond_coeff @bond:c1-no harmonic 393.0 1.4050 # SOURCE3 3 0.0005 - bond_coeff @bond:c1-o harmonic 777.0 1.1660 # SOURCE2 9 0.0052 - bond_coeff @bond:c1-oh harmonic 435.6 1.3260 # SOURCE3 1 0.0000 - bond_coeff @bond:c1-os harmonic 437.1 1.3250 # SOURCE3 3 0.0148 - bond_coeff @bond:c1-p2 harmonic 289.3 1.7700 # SOUECE3 1 - bond_coeff @bond:c1-p3 harmonic 275.1 1.7900 # SOUECE3 1 - bond_coeff @bond:c1-p4 harmonic 275.1 1.7900 # SOUECE3 1 - bond_coeff @bond:c1-p5 harmonic 302.2 1.7530 # SOURCE3 2 0.0000 - bond_coeff @bond:c1-s2 harmonic 410.0 1.5950 # SOURCE3 1 0.0000 - bond_coeff @bond:c1-s harmonic 371.8 1.6300 # SOURCE1 14 0.0000 - bond_coeff @bond:c1-s4 harmonic 272.9 1.7460 # SOURCE3 2 0.0000 - bond_coeff @bond:c1-s6 harmonic 290.4 1.7220 # SOURCE3 2 0.0000 - bond_coeff @bond:c1-sh harmonic 324.5 1.6800 # SOUECE3 1 - bond_coeff @bond:c1-ss harmonic 325.4 1.6790 # SOURCE1 10 0.0000 - bond_coeff @bond:c2-c2 harmonic 589.7 1.3240 # SOURCE1 974 0.0096 - bond_coeff @bond:c2-c3 harmonic 328.3 1.5080 # SOURCE1 2536 0.0021 - bond_coeff @bond:c2-ca harmonic 357.2 1.4800 # SOUECE3 1 - bond_coeff @bond:c2-cc harmonic 522.6 1.3600 # SOURCE1 771 0.0185 - bond_coeff @bond:c2-cd harmonic 522.6 1.3600 # SOURCE1 771 0.0185 - bond_coeff @bond:c2-ce harmonic 560.5 1.3390 # SOURCE3 62 0.0128 - bond_coeff @bond:c2-cf harmonic 560.5 1.3390 # SOURCE3 62 same_as_c2-ce - bond_coeff @bond:c2-cl harmonic 328.8 1.7220 # SOURCE1 163 0.0098 - bond_coeff @bond:c2-cu harmonic 573.9 1.3320 # SOURCE2 1 0.0000 - bond_coeff @bond:c2-cx harmonic 353.3 1.4836 # SOURCE4 26 0.0064 - bond_coeff @bond:c2-cy harmonic 331.7 1.5046 # SOURCE4 9 0.0053 - bond_coeff @bond:c2-f harmonic 368.7 1.3400 # SOURCE1 34 0.0000 - bond_coeff @bond:c2-h4 harmonic 348.6 1.0840 # SOURCE3 40 0.0058 - bond_coeff @bond:c2-h5 harmonic 338.0 1.0915 # SOURCE4 42 0.0017 - bond_coeff @bond:c2-ha harmonic 344.3 1.0870 # SOURCE3 797 0.0046 - bond_coeff @bond:c2-hc harmonic 344.3 1.0870 # SOURCE3 789 0.0046 - bond_coeff @bond:c2-hx harmonic 350.1 1.0830 # SOURCE3 3 0.0008 - bond_coeff @bond:c2-i harmonic 223.2 2.1530 # SOURCE3 2 0.0000 - bond_coeff @bond:c2-n1 harmonic 546.0 1.3060 # SOURCE3 4 0.0161 - bond_coeff @bond:c2-n2 harmonic 581.1 1.2880 # SOURCE1 103 0.0100 - bond_coeff @bond:c2-n3 harmonic 486.3 1.3400 # SOUECE3 1 - bond_coeff @bond:c2-n harmonic 390.5 1.4070 # SOURCE3 9 0.0124 - bond_coeff @bond:c2-n4 harmonic 309.1 1.4820 # SOURCE3 5 0.0064 - bond_coeff @bond:c2-na harmonic 411.1 1.3910 # SOURCE3 31 0.0289 - bond_coeff @bond:c2-nc harmonic 533.0 1.3130 # SOURCE1 99 0.0095 - bond_coeff @bond:c2-nd harmonic 533.0 1.3130 # SOURCE1 99 same_as_c2-nc - bond_coeff @bond:c2-ne harmonic 597.7 1.2800 # SOURCE3 37 0.0110 - bond_coeff @bond:c2-nf harmonic 597.7 1.2800 # SOURCE3 37 same_as_c2-ne - bond_coeff @bond:c2-nh harmonic 462.6 1.3550 # SOURCE3 38 0.0413 - bond_coeff @bond:c2-no harmonic 345.6 1.4457 # SOURCE4 7 0.0087 - bond_coeff @bond:c2-o harmonic 623.6 1.2244 # SOURCE4 15 0.0036 - bond_coeff @bond:c2-oh harmonic 425.4 1.3330 # SOURCE1 53 0.0000 - bond_coeff @bond:c2-os harmonic 392.6 1.3570 # SOURCE1 315 0.0097 - bond_coeff @bond:c2-p2 harmonic 375.9 1.6700 # SOURCE3 62 0.0147 - bond_coeff @bond:c2-p3 harmonic 246.6 1.8340 # SOURCE3 5 0.0042 - bond_coeff @bond:c2-p4 harmonic 254.0 1.8220 # SOUECE3 1 - bond_coeff @bond:c2-p5 harmonic 228.2 1.8658 # SOURCE4 5 0.0025 - bond_coeff @bond:c2-pe harmonic 355.3 1.6910 # SOURCE3 52 0.0542 - bond_coeff @bond:c2-pf harmonic 355.3 1.6910 # SOURCE3 52 same_as_c2-pe - bond_coeff @bond:c2-s2 harmonic 393.1 1.6100 # SOURCE2 1 0.0000 - bond_coeff @bond:c2-s harmonic 281.5 1.7340 # SOURCE3 4 0.0034 - bond_coeff @bond:c2-s4 harmonic 263.2 1.7600 # SOUECE3 1 - bond_coeff @bond:c2-s6 harmonic 263.2 1.7600 # SOUECE3 1 - bond_coeff @bond:c2-sh harmonic 252.0 1.7771 # SOURCE4 5 0.0037 - bond_coeff @bond:c2-ss harmonic 280.0 1.7360 # SOURCE1 209 0.0155 - bond_coeff @bond:c3-c3 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048 - bond_coeff @bond:c3-ca harmonic 323.5 1.5130 # SOURCE1 1813 0.0000 - bond_coeff @bond:c3-cc harmonic 337.3 1.4990 # SOURCE3 50 0.0096 - bond_coeff @bond:c3-cd harmonic 337.3 1.4990 # SOURCE3 50 0.0096 - bond_coeff @bond:c3-ce harmonic 331.3 1.5050 # SOURCE3 9 0.0024 - bond_coeff @bond:c3-cf harmonic 331.3 1.5050 # SOURCE3 9 same_as_c3-ce - bond_coeff @bond:c3-cl harmonic 279.0 1.7860 # SOURCE1 267 0.0194 - bond_coeff @bond:c3-cu harmonic 359.4 1.4780 # SOURCE1 7 0.0000 - bond_coeff @bond:c3-cv harmonic 347.6 1.4890 # SOURCE1 11 0.0000 - bond_coeff @bond:c3-cx harmonic 322.5 1.5140 # SOURCE1 712 0.0045 - bond_coeff @bond:c3-cy harmonic 308.5 1.5290 # SOURCE1 376 0.0000 - bond_coeff @bond:c3-f harmonic 363.8 1.3440 # SOURCE1 617 0.0281 - bond_coeff @bond:c3-h1 harmonic 335.9 1.0930 # SOURCE3 2175 0.0082 - bond_coeff @bond:c3-h2 harmonic 326.4 1.1000 # SOURCE3 66 0.0280 - bond_coeff @bond:c3-h3 harmonic 333.4 1.0948 # SOURCE4 25 0.0026 - bond_coeff @bond:c3-hc harmonic 337.3 1.0920 # SOURCE3 2815 0.0059 - bond_coeff @bond:c3-hx harmonic 338.7 1.0910 # SOURCE3 146 0.0066 - bond_coeff @bond:c3-i harmonic 219.1 2.1620 # SOURCE1 15 0.0000 - bond_coeff @bond:c3-n1 harmonic 325.1 1.4700 # SOURCE3 0 - bond_coeff @bond:c3-n2 harmonic 313.8 1.4770 # SOURCE1 129 0.0138 - bond_coeff @bond:c3-n harmonic 330.6 1.4600 # SOURCE1 187 0.0079 - bond_coeff @bond:c3-n3 harmonic 320.6 1.4700 # SOURCE1 1678 0.0017 - bond_coeff @bond:c3-n4 harmonic 293.6 1.4990 # SOURCE1 1370 0.0000 - bond_coeff @bond:c3-na harmonic 334.7 1.4560 # SOURCE3 23 0.0119 - bond_coeff @bond:c3-nc harmonic 334.7 1.4560 # SOURCE3 9 0.0109 - bond_coeff @bond:c3-nd harmonic 334.7 1.4560 # SOURCE3 9 same_as_c3-nc - bond_coeff @bond:c3-nh harmonic 332.7 1.4580 # SOURCE3 27 0.0085 - bond_coeff @bond:c3-no harmonic 265.4 1.5330 # SOURCE1 83 0.0212 - bond_coeff @bond:c3-o harmonic 449.9 1.3165 # SOURCE4 8 0.0193 - bond_coeff @bond:c3-oh harmonic 314.1 1.4260 # SOURCE1 914 0.0129 - bond_coeff @bond:c3-os harmonic 301.5 1.4390 # SOURCE1 3123 0.0126 - bond_coeff @bond:c3-p2 harmonic 234.3 1.8550 # SOURCE3 9 0.0125 - bond_coeff @bond:c3-p3 harmonic 240.6 1.8440 # SOURCE3 109 0.0107 - bond_coeff @bond:c3-p4 harmonic 247.2 1.8330 # SOURCE3 29 0.0138 - bond_coeff @bond:c3-p5 harmonic 259.7 1.8130 # SOURCE1 84 0.0000 - bond_coeff @bond:c3-px harmonic 252.7 1.8240 # SOURCE3 28 0.0098 - bond_coeff @bond:c3-py harmonic 259.7 1.8130 # SOURCE3 13 0.0163 - bond_coeff @bond:c3-s harmonic 212.9 1.8450 # SOURCE3 4 0.0185 - bond_coeff @bond:c3-s4 harmonic 233.8 1.8070 # SOURCE1 139 0.0023 - bond_coeff @bond:c3-s6 harmonic 254.0 1.7740 # SOURCE1 118 0.0103 - bond_coeff @bond:c3-sh harmonic 225.3 1.8220 # SOURCE3 12 0.0051 - bond_coeff @bond:c3-ss harmonic 225.8 1.8210 # SOURCE1 358 0.0075 - bond_coeff @bond:c3-sx harmonic 232.6 1.8090 # SOURCE3 30 0.0067 - bond_coeff @bond:c3-sy harmonic 248.9 1.7820 # SOURCE3 31 0.0039 - bond_coeff @bond:ca-ca harmonic 478.4 1.3870 # SOURCE1 6228 0.0147 - bond_coeff @bond:ca-cc harmonic 411.7 1.4340 # SOURCE1 80 0.0000 - bond_coeff @bond:ca-cd harmonic 411.7 1.4340 # SOURCE1 80 0.0000 - bond_coeff @bond:ca-ce harmonic 366.0 1.4720 # SOURCE1 71 0.0030 - bond_coeff @bond:ca-cf harmonic 366.0 1.4720 # SOURCE1 71 0.0030 - bond_coeff @bond:ca-cg harmonic 406.6 1.4380 # SOURCE1 71 0.0045 - bond_coeff @bond:ca-ch harmonic 406.6 1.4380 # SOURCE1 71 0.0045 - bond_coeff @bond:ca-cl harmonic 322.8 1.7290 # SOURCE1 704 0.0095 - bond_coeff @bond:ca-cp harmonic 461.8 1.3980 # CORR 28 - bond_coeff @bond:ca-cq harmonic 461.8 1.3980 # CORR 28 - bond_coeff @bond:ca-cx harmonic 350.8 1.4860 # SOURCE1 98 0.0118 - bond_coeff @bond:ca-cy harmonic 323.0 1.5135 # SOURCE4 8 0.0043 - bond_coeff @bond:ca-f harmonic 363.8 1.3440 # SOURCE1 205 0.0089 - bond_coeff @bond:ca-h4 harmonic 342.9 1.0880 # SOURCE3 57 0.0026 - bond_coeff @bond:ca-h5 harmonic 347.2 1.0850 # SOURCE3 15 0.0048 - bond_coeff @bond:ca-ha harmonic 344.3 1.0870 # SOURCE3 1496 0.0045 - bond_coeff @bond:ca-i harmonic 252.4 2.0950 # SOURCE1 51 0.0000 - bond_coeff @bond:ca-n1 harmonic 398.1 1.4000 # SOURCE3 0 - bond_coeff @bond:ca-n2 harmonic 551.6 1.3030 # SOURCE4 7 0.0058 - bond_coeff @bond:ca-n harmonic 372.3 1.4220 # SOURCE3 9 0.0098 - bond_coeff @bond:ca-n4 harmonic 325.6 1.4650 # SOURCE1 23 0.0000 - bond_coeff @bond:ca-na harmonic 470.3 1.3500 # SOURCE1 150 0.0103 - bond_coeff @bond:ca-nb harmonic 483.1 1.3420 # SOURCE3 104 0.0076 - bond_coeff @bond:ca-nc harmonic 492.9 1.3360 # SOURCE1 1826 0.0020 - bond_coeff @bond:ca-nd harmonic 492.9 1.3360 # SOURCE1 1826 0.0020 - bond_coeff @bond:ca-ne harmonic 361.8 1.4310 # SOURCE1 52 0.0000 - bond_coeff @bond:ca-nf harmonic 361.8 1.4310 # SOURCE1 52 0.0000 - bond_coeff @bond:ca-nh harmonic 449.0 1.3640 # SOURCE1 137 0.0085 - bond_coeff @bond:ca-no harmonic 322.6 1.4680 # SOURCE1 556 0.0000 - bond_coeff @bond:ca-o harmonic 610.0 1.2304 # SOURCE4 5 0.0026 - bond_coeff @bond:ca-oh harmonic 386.1 1.3620 # SOURCE1 551 0.0000 - bond_coeff @bond:ca-os harmonic 372.4 1.3730 # SOURCE1 1092 0.0071 - bond_coeff @bond:ca-p2 harmonic 243.0 1.8400 # SOUECE3 1 - bond_coeff @bond:ca-p3 harmonic 252.7 1.8240 # SOURCE1 145 0.0187 - bond_coeff @bond:ca-p4 harmonic 264.3 1.8060 # SOUECE3 1 - bond_coeff @bond:ca-p5 harmonic 271.6 1.7950 # SOURCE1 571 0.0028 - bond_coeff @bond:ca-pe harmonic 249.6 1.8290 # SOURCE3 10 0.0042 - bond_coeff @bond:ca-pf harmonic 249.6 1.8290 # SOURCE3 10 0.0042 - bond_coeff @bond:ca-px harmonic 252.1 1.8250 # SOURCE3 5 0.0168 - bond_coeff @bond:ca-py harmonic 268.3 1.7999 # SOURCE4 5 0.0072 - bond_coeff @bond:ca-s harmonic 277.9 1.7390 # SOURCE3 2 0.0000 - bond_coeff @bond:ca-s4 harmonic 245.2 1.7880 # SOURCE1 51 0.0048 - bond_coeff @bond:ca-s6 harmonic 263.9 1.7590 # SOURCE1 229 0.0036 - bond_coeff @bond:ca-sh harmonic 251.3 1.7783 # SOURCE4 12 0.0041 - bond_coeff @bond:ca-ss harmonic 256.6 1.7700 # SOURCE1 297 0.0041 - bond_coeff @bond:ca-sx harmonic 223.5 1.8252 # SOURCE4 24 0.0032 - bond_coeff @bond:ca-sy harmonic 247.7 1.7840 # SOURCE3 13 0.0094 - bond_coeff @bond:c-c1 harmonic 379.8 1.4600 # SOUECE3 1 - bond_coeff @bond:c-c2 harmonic 449.9 1.4060 # SOURCE3 2 0.0370 - bond_coeff @bond:c-c harmonic 290.1 1.5500 # SOURCE1 31 0.0100 - bond_coeff @bond:c-c3 harmonic 328.3 1.5080 # SOURCE1 2949 0.0060 - bond_coeff @bond:c-ca harmonic 349.7 1.4870 # SOURCE1 480 0.0055 - bond_coeff @bond:c-cc harmonic 377.4 1.4620 # SOURCE3 132 0.0210 - bond_coeff @bond:cc-cc harmonic 418.3 1.4290 # SOURCE1 740 0.0069 - bond_coeff @bond:cc-cd harmonic 504.0 1.3710 # SOURCE3 523 0.0217 - bond_coeff @bond:cc-ce harmonic 387.9 1.4532 # CORR 249 - bond_coeff @bond:cc-cf harmonic 511.3 1.3666 # CORR 70 - bond_coeff @bond:cc-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000 - bond_coeff @bond:cc-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000 - bond_coeff @bond:cc-cl harmonic 317.1 1.7359 # CORR 66 - bond_coeff @bond:cc-cx harmonic 366.6 1.4715 # CORR 24 - bond_coeff @bond:c-cd harmonic 377.4 1.4620 # SOURCE3 132 0.0210 - bond_coeff @bond:c-ce harmonic 363.8 1.4740 # SOURCE1 601 0.0105 - bond_coeff @bond:c-cf harmonic 363.8 1.4740 # SOURCE1 601 0.0105 - bond_coeff @bond:cc-f harmonic 368.6 1.3401 # SOURCE4 24 0.0034 - bond_coeff @bond:c-cg harmonic 389.3 1.4520 # SOURCE3 2 0.0000 - bond_coeff @bond:c-ch harmonic 389.3 1.4520 # SOURCE3 2 same_as_c-cg - bond_coeff @bond:cc-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037 - bond_coeff @bond:cc-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051 - bond_coeff @bond:cc-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039 - bond_coeff @bond:c-cl harmonic 293.5 1.7660 # SOURCE3 6 0.0250 - bond_coeff @bond:cc-n2 harmonic 573.8 1.2917 # CORR 81 - bond_coeff @bond:cc-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109 - bond_coeff @bond:cc-n4 harmonic 299.0 1.4930 # SOURCE4 7 0.0148 - bond_coeff @bond:cc-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144 - bond_coeff @bond:cc-nc harmonic 431.6 1.3760 # SOURCE1 88 0.0000 - bond_coeff @bond:cc-nd harmonic 494.6 1.3350 # SOURCE3 203 0.0239 - bond_coeff @bond:cc-ne harmonic 427.4 1.3790 # SOURCE4 30 0.0126 - bond_coeff @bond:cc-nf harmonic 565.4 1.2960 # CORR 23 - bond_coeff @bond:cc-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040 - bond_coeff @bond:cc-no harmonic 367.4 1.4262 # SOURCE4 133 0.0061 - bond_coeff @bond:cc-oh harmonic 408.5 1.3451 # CORR 121 - bond_coeff @bond:cc-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192 - bond_coeff @bond:cc-pd harmonic 318.2 1.7330 # SOURCE3 84 0.0161 - bond_coeff @bond:cc-sh harmonic 257.9 1.7681 # SOURCE4 8 0.0027 - bond_coeff @bond:cc-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194 - bond_coeff @bond:cc-sx harmonic 231.3 1.8113 # SOURCE4 16 0.0050 - bond_coeff @bond:cc-sy harmonic 248.1 1.7834 # CORR 55 - bond_coeff @bond:c-cu harmonic 441.4 1.4120 # SOURCE2 1 0.0000 - bond_coeff @bond:c-cx harmonic 350.8 1.4860 # SOURCE1 105 0.0000 - bond_coeff @bond:c-cy harmonic 308.5 1.5290 # SOURCE1 18 0.0000 - bond_coeff @bond:cd-cd harmonic 418.3 1.4290 # SOURCE1 740 0.0069 - bond_coeff @bond:cd-ce harmonic 511.3 1.3666 # CORR 70 - bond_coeff @bond:cd-cf harmonic 387.9 1.4532 # CORR 249 - bond_coeff @bond:cd-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000 - bond_coeff @bond:cd-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000 - bond_coeff @bond:cd-cl harmonic 317.1 1.7359 # CORR 66 - bond_coeff @bond:cd-cx harmonic 366.6 1.4715 # CORR 24 - bond_coeff @bond:cd-cy harmonic 330.9 1.5054 # SOURCE4 10 0.0008 - bond_coeff @bond:cd-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037 - bond_coeff @bond:cd-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051 - bond_coeff @bond:cd-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039 - bond_coeff @bond:cd-n2 harmonic 573.8 1.2917 # CORR 81 - bond_coeff @bond:cd-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109 - bond_coeff @bond:cd-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144 - bond_coeff @bond:cd-nc harmonic 494.6 1.3350 # SOURCE3 203 0.0239 - bond_coeff @bond:cd-nd harmonic 431.6 1.3760 # SOURCE1 88 0.0000 - bond_coeff @bond:cd-ne harmonic 565.4 1.2960 # CORR 23 - bond_coeff @bond:cd-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040 - bond_coeff @bond:cd-oh harmonic 408.5 1.3451 # CORR 121 - bond_coeff @bond:cd-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192 - bond_coeff @bond:cd-pc harmonic 318.2 1.7330 # SOURCE3 84 same_as_cc-pd - bond_coeff @bond:cd-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194 - bond_coeff @bond:cd-sy harmonic 248.1 1.7834 # CORR 55 - bond_coeff @bond:ce-ce harmonic 390.5 1.4510 # SOURCE1 66 0.0060 - bond_coeff @bond:ce-cf harmonic 562.4 1.3380 # SOURCE1 543 0.0045 - bond_coeff @bond:ce-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000 - bond_coeff @bond:ce-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000 - bond_coeff @bond:ce-cl harmonic 292.6 1.7671 # SOURCE4 24 0.0062 - bond_coeff @bond:ce-cx harmonic 337.0 1.4993 # SOURCE4 5 0.0066 - bond_coeff @bond:ce-cy harmonic 323.0 1.5135 # SOURCE4 17 0.0024 - bond_coeff @bond:ce-h4 harmonic 337.4 1.0919 # CORR 144 - bond_coeff @bond:ce-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056 - bond_coeff @bond:ce-n1 harmonic 536.1 1.3113 # CORR 13 - bond_coeff @bond:ce-n2 harmonic 599.8 1.2790 # SOURCE1 75 0.0000 - bond_coeff @bond:ce-n harmonic 368.9 1.4249 # CORR 136 - bond_coeff @bond:ce-na harmonic 373.8 1.4207 # SOURCE4 5 0.0051 - bond_coeff @bond:ce-ne harmonic 381.8 1.4140 # SOURCE3 7 0.0103 - bond_coeff @bond:ce-nf harmonic 574.0 1.2916 # CORR 42 - bond_coeff @bond:ce-nh harmonic 412.3 1.3901 # CORR 168 - bond_coeff @bond:ce-oh harmonic 402.9 1.3493 # CORR 37 - bond_coeff @bond:ce-os harmonic 372.8 1.3727 # CORR 45 - bond_coeff @bond:ce-p2 harmonic 259.1 1.8140 # SOUECE3 1 - bond_coeff @bond:ce-pe harmonic 256.5 1.8180 # SOURCE3 8 0.0108 - bond_coeff @bond:ce-px harmonic 254.6 1.8210 # SOURCE3 6 0.0046 - bond_coeff @bond:ce-py harmonic 272.3 1.7940 # SOURCE3 5 0.0045 - bond_coeff @bond:ce-s harmonic 324.5 1.6800 # SOUECE3 1 - bond_coeff @bond:ce-ss harmonic 243.6 1.7906 # SOURCE4 10 0.0064 - bond_coeff @bond:ce-sx harmonic 239.7 1.7970 # SOURCE3 5 0.0082 - bond_coeff @bond:ce-sy harmonic 248.9 1.7820 # SOURCE3 5 0.0114 - bond_coeff @bond:c-f harmonic 387.9 1.3250 # SOURCE2 6 0.0147 - bond_coeff @bond:cf-cf harmonic 390.5 1.4510 # SOURCE1 66 0.0060 - bond_coeff @bond:cf-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000 - bond_coeff @bond:cf-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000 - bond_coeff @bond:cf-h4 harmonic 337.4 1.0919 # CORR 144 - bond_coeff @bond:cf-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056 - bond_coeff @bond:cf-n1 harmonic 536.1 1.3113 # CORR 13 - bond_coeff @bond:cf-n2 harmonic 599.8 1.2790 # SOURCE1 75 same_as_ce-n2 - bond_coeff @bond:cf-n harmonic 368.9 1.4249 # CORR 136 - bond_coeff @bond:cf-ne harmonic 574.0 1.2916 # CORR 42 - bond_coeff @bond:cf-nf harmonic 381.8 1.4140 # SOURCE3 7 same_as_ce-ne - bond_coeff @bond:cf-nh harmonic 412.3 1.3901 # CORR 168 - bond_coeff @bond:cf-oh harmonic 402.9 1.3493 # CORR 37 - bond_coeff @bond:cf-os harmonic 372.8 1.3727 # CORR 45 - bond_coeff @bond:cf-p2 harmonic 259.1 1.8140 # SOUECE3 1 same_as_ce-p2 - bond_coeff @bond:cf-pf harmonic 256.5 1.8180 # SOURCE3 8 same_as_ce-pe - bond_coeff @bond:cf-px harmonic 254.6 1.8210 # SOURCE3 6 same_as_ce-px - bond_coeff @bond:cf-py harmonic 272.3 1.7940 # SOURCE3 5 same_as_ce-py - bond_coeff @bond:cf-s harmonic 324.5 1.6800 # SOUECE3 1 same_as_ce-s - bond_coeff @bond:cf-sx harmonic 239.7 1.7970 # SOURCE3 5 same_as_ce-sx - bond_coeff @bond:cf-sy harmonic 248.9 1.7820 # SOURCE3 5 same_as_ce-sy - bond_coeff @bond:cg-cg harmonic 494.2 1.3770 # SOURCE1 42 0.0000 - bond_coeff @bond:cg-ch harmonic 949.5 1.1910 # SOURCE1 80 0.0015 - bond_coeff @bond:cg-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018 - bond_coeff @bond:cg-ne harmonic 509.5 1.3262 # SOURCE4 17 0.0009 - bond_coeff @bond:cg-pe harmonic 429.8 1.6210 # SOURCE3 11 0.2008 - bond_coeff @bond:c-h4 harmonic 310.5 1.1123 # SOURCE4 125 0.0023 - bond_coeff @bond:c-h5 harmonic 319.4 1.1053 # SOURCE4 42 0.0028 - bond_coeff @bond:c-ha harmonic 325.1 1.1010 # SOURCE3 53 0.0102 - bond_coeff @bond:ch-ch harmonic 494.2 1.3770 # SOURCE1 42 0.0000 - bond_coeff @bond:ch-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018 - bond_coeff @bond:ch-nf harmonic 509.5 1.3262 # SOURCE4 17 same_as_cg-ne - bond_coeff @bond:ch-pf harmonic 429.8 1.6210 # SOURCE3 11 same_as_cg-pe - bond_coeff @bond:c-i harmonic 198.9 2.2090 # SOURCE3 4 0.0365 - bond_coeff @bond:cl-cl harmonic 143.3 2.2670 # SOURCE1 2 0.0395 - bond_coeff @bond:cl-cx harmonic 301.8 1.7550 # SOURCE1 64 0.0000 - bond_coeff @bond:cl-cy harmonic 292.0 1.7680 # SOURCE2 2 0.0070 - bond_coeff @bond:cl-f harmonic 298.6 1.6480 # SOURCE2 2 0.0500 - bond_coeff @bond:cl-i harmonic 163.5 2.5500 # SOURCE1 6 0.0893 - bond_coeff @bond:cl-n1 harmonic 431.6 1.6300 # SOUECE3 1 - bond_coeff @bond:cl-n2 harmonic 263.4 1.8190 # SOURCE3 6 0.1020 - bond_coeff @bond:cl-n3 harmonic 290.4 1.7800 # SOURCE4 5 0.0021 - bond_coeff @bond:cl-n harmonic 344.2 1.7140 # SOURCE4 5 0.0005 - bond_coeff @bond:cl-n4 harmonic 311.1 1.7530 # SOURCE3 4 0.0098 - bond_coeff @bond:cl-na harmonic 253.2 1.8350 # SOURCE3 7 0.2083 - bond_coeff @bond:cl-nh harmonic 303.2 1.7630 # SOURCE3 1 0.0000 - bond_coeff @bond:cl-no harmonic 250.1 1.8400 # SOURCE2 1 0.0000 - bond_coeff @bond:cl-o harmonic 557.6 1.4830 # SOURCE3 4 0.0000 - bond_coeff @bond:cl-oh harmonic 309.7 1.6900 # SOURCE2 1 0.0000 - bond_coeff @bond:cl-os harmonic 278.8 1.7300 # SOURCE3 4 0.0000 - bond_coeff @bond:cl-p2 harmonic 217.5 2.0700 # SOURCE3 6 0.0108 - bond_coeff @bond:cl-p3 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 - bond_coeff @bond:cl-p4 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 - bond_coeff @bond:cl-p5 harmonic 249.4 2.0080 # SOURCE1 111 0.0000 - bond_coeff @bond:cl-pb harmonic 255.6 1.9970 # SOURCE1 46 0.0000 - bond_coeff @bond:cl-s harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:cl-s2 harmonic 172.7 2.1610 # SOURCE2 1 0.0000 - bond_coeff @bond:cl-s4 harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:cl-s6 harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:cl-sh harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:cl-ss harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:cl-sx harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:cl-sy harmonic 208.7 2.0720 # SOURCE1 6 0.0000 - bond_coeff @bond:c-n2 harmonic 374.6 1.4200 # SOUECE3 1 - bond_coeff @bond:c-n4 harmonic 255.5 1.5460 # SOURCE3 4 0.0388 - bond_coeff @bond:c-n harmonic 478.2 1.3450 # SOURCE1 1235 0.0215 - bond_coeff @bond:c-nc harmonic 412.1 1.3906 # CORR 124 - bond_coeff @bond:c-nd harmonic 412.1 1.3906 # CORR 124 - bond_coeff @bond:c-ne harmonic 408.2 1.3932 # CORR 52 - bond_coeff @bond:c-nf harmonic 408.2 1.3932 # CORR 52 - bond_coeff @bond:c-no harmonic 260.1 1.5400 # SOUECE3 1 - bond_coeff @bond:c-o harmonic 648.0 1.2140 # SOURCE1 3682 0.0165 - bond_coeff @bond:c-oh harmonic 466.4 1.3060 # SOURCE1 271 0.0041 - bond_coeff @bond:c-os harmonic 411.3 1.3430 # SOURCE1 1044 0.0171 - bond_coeff @bond:c-p2 harmonic 210.3 1.9000 # SOUECE3 1 - bond_coeff @bond:c-p3 harmonic 219.0 1.8830 # SOURCE3 6 0.0129 - bond_coeff @bond:c-p4 harmonic 220.6 1.8800 # SOUECE3 1 - bond_coeff @bond:c-p5 harmonic 219.8 1.8815 # SOURCE4 11 0.0078 - bond_coeff @bond:cp-cp harmonic 346.5 1.4900 # SOURCE1 242 0.0010 - bond_coeff @bond:cp-cq harmonic 419.3 1.4282 # SOURCE4 7 0.0034 - bond_coeff @bond:c-pe harmonic 204.9 1.9110 # SOURCE3 3 0.0025 - bond_coeff @bond:c-pf harmonic 204.9 1.9110 # SOURCE3 3 same_as_c-pe - bond_coeff @bond:cp-na harmonic 420.5 1.3840 # SOURCE4 7 0.0181 - bond_coeff @bond:cp-nb harmonic 486.7 1.3398 # SOURCE4 70 0.0062 - bond_coeff @bond:c-px harmonic 208.3 1.9040 # SOURCE3 1 0.0000 - bond_coeff @bond:c-py harmonic 227.6 1.8670 # SOURCE3 6 0.0199 - bond_coeff @bond:cq-cq harmonic 346.5 1.4900 # SOURCE1 242 0.0010 - bond_coeff @bond:c-s harmonic 328.9 1.6750 # SOURCE1 401 0.0128 - bond_coeff @bond:c-s4 harmonic 200.4 1.8700 # SOUECE3 1 - bond_coeff @bond:c-s6 harmonic 200.4 1.8700 # SOUECE3 1 - bond_coeff @bond:c-sh harmonic 249.6 1.7810 # SOURCE3 6 0.0171 - bond_coeff @bond:c-ss harmonic 261.9 1.7620 # SOURCE1 20 0.0000 - bond_coeff @bond:c-sx harmonic 193.3 1.8850 # SOURCE3 5 0.0088 - bond_coeff @bond:c-sy harmonic 202.8 1.8650 # SOURCE3 5 0.0085 - bond_coeff @bond:cu-cu harmonic 653.7 1.2940 # SOURCE1 10 0.0000 - bond_coeff @bond:cu-cx harmonic 327.3 1.5090 # SOURCE1 20 0.0000 - bond_coeff @bond:cu-ha harmonic 353.0 1.0810 # SOURCE2 3 0.0111 - bond_coeff @bond:cv-cv harmonic 568.1 1.3350 # SOURCE1 25 0.0000 - bond_coeff @bond:cv-cy harmonic 323.5 1.5130 # SOURCE1 50 0.0000 - bond_coeff @bond:cv-ha harmonic 344.3 1.0870 # SOURCE3 2 0.0000 - bond_coeff @bond:cx-cv harmonic 328.3 1.5080 # SOURCE1 2536 as - bond_coeff @bond:cx-cx harmonic 337.3 1.4990 # SOURCE1 1204 0.0183 - bond_coeff @bond:cx-cy harmonic 321.5 1.5150 # SOURCE3 2 0.0000 - bond_coeff @bond:cx-f harmonic 347.2 1.3580 # SOURCE2 3 0.0050 - bond_coeff @bond:cx-h1 harmonic 344.3 1.0870 # SOURCE3 10 0.0017 - bond_coeff @bond:cx-h2 harmonic 350.1 1.0830 # SOURCE3 2 0.0000 - bond_coeff @bond:cx-hc harmonic 345.8 1.0860 # SOURCE3 44 0.0011 - bond_coeff @bond:cx-hx harmonic 347.2 1.0850 # SOURCE4 5 0.0002 - bond_coeff @bond:cx-n2 harmonic 309.1 1.4820 # SOURCE3 2 0.0000 - bond_coeff @bond:cx-n3 harmonic 318.7 1.4720 # SOURCE1 134 0.0000 - bond_coeff @bond:cx-n harmonic 350.6 1.4411 # SOURCE4 11 0.0092 - bond_coeff @bond:cx-na harmonic 329.0 1.4616 # SOURCE4 11 0.0016 - bond_coeff @bond:cx-nh harmonic 336.7 1.4541 # SOURCE4 83 0.0076 - bond_coeff @bond:cx-oh harmonic 387.4 1.3610 # SOURCE3 3 0.0018 - bond_coeff @bond:cx-os harmonic 320.1 1.4200 # SOURCE3 7 0.0222 - bond_coeff @bond:cx-p3 harmonic 227.6 1.8670 # SOURCE2 1 0.0000 - bond_coeff @bond:cx-s4 harmonic 225.3 1.8220 # SOURCE2 1 0.0000 - bond_coeff @bond:cx-s6 harmonic 283.7 1.7310 # SOURCE2 1 0.0000 - bond_coeff @bond:cx-ss harmonic 229.2 1.8150 # SOURCE2 1 0.0000 - bond_coeff @bond:cy-cy harmonic 286.8 1.5540 # SOURCE1 742 0.0041 - bond_coeff @bond:cy-f harmonic 355.5 1.3509 # SOURCE4 8 0.0047 - bond_coeff @bond:cy-h1 harmonic 330.4 1.0970 # SOURCE3 17 0.0058 - bond_coeff @bond:cy-h2 harmonic 335.8 1.0931 # SOURCE4 80 0.0019 - bond_coeff @bond:cy-hc harmonic 334.5 1.0940 # SOURCE3 63 0.0014 - bond_coeff @bond:cy-n harmonic 321.3 1.4693 # SOURCE4 250 0.0102 - bond_coeff @bond:cy-n3 harmonic 307.2 1.4840 # SOURCE1 21 0.0000 - bond_coeff @bond:cy-oh harmonic 325.2 1.4150 # SOURCE3 2 0.0000 - bond_coeff @bond:cy-os harmonic 308.6 1.4316 # SOURCE4 23 0.0136 - bond_coeff @bond:cy-s6 harmonic 209.6 1.8514 # SOURCE4 9 0.0166 - bond_coeff @bond:cy-ss harmonic 211.3 1.8481 # SOURCE4 78 0.0080 - bond_coeff @bond:cz-nh harmonic 487.8 1.3391 # SOURCE4 32 0.0045 - bond_coeff @bond:f-n1 harmonic 375.7 1.4100 # SOUECE3 1 - bond_coeff @bond:f-n2 harmonic 337.5 1.4440 # SOURCE3 5 0.0377 - bond_coeff @bond:f-n3 harmonic 380.6 1.4060 # SOURCE1 9 0.0000 - bond_coeff @bond:f-n harmonic 391.7 1.3970 # SOURCE3 3 0.0112 - bond_coeff @bond:f-n4 harmonic 526.8 1.3080 # SOURCE3 2 0.0000 - bond_coeff @bond:f-na harmonic 374.5 1.4110 # SOURCE3 7 0.0611 - bond_coeff @bond:f-nh harmonic 357.1 1.4260 # SOURCE3 3 0.0085 - bond_coeff @bond:f-no harmonic 314.4 1.4670 # SOURCE2 1 0.0000 - bond_coeff @bond:f-o harmonic 442.2 1.3300 # SOUECE3 1 - bond_coeff @bond:f-oh harmonic 305.4 1.4440 # SOURCE3 1 0.0000 - bond_coeff @bond:f-os harmonic 326.2 1.4230 # SOURCE3 2 0.0000 - bond_coeff @bond:f-p2 harmonic 287.3 1.5360 # SOURCE3 7 0.2054 - bond_coeff @bond:f-p3 harmonic 254.5 1.5780 # SOURCE2 8 0.0103 - bond_coeff @bond:f-p4 harmonic 246.0 1.5900 # SOUECE3 1 - bond_coeff @bond:f-p5 harmonic 253.8 1.5790 # SOURCE1 72 0.0000 - bond_coeff @bond:f-s2 harmonic 244.4 1.6430 # SOURCE2 1 0.0000 - bond_coeff @bond:f-s harmonic 233.3 1.6600 # SOUECE3 1 - bond_coeff @bond:f-s4 harmonic 282.4 1.5910 # SOURCE2 4 0.0065 - bond_coeff @bond:f-s6 harmonic 312.1 1.5560 # SOURCE2 5 0.0220 - bond_coeff @bond:f-sh harmonic 240.4 1.6490 # SOURCE3 1 0.0000 - bond_coeff @bond:f-ss harmonic 250.5 1.6340 # SOURCE3 3 0.0156 - bond_coeff @bond:hn-n1 harmonic 455.1 0.9860 # SOURCE2 1 0.0000 - bond_coeff @bond:hn-n2 harmonic 375.5 1.0290 # SOURCE3 108 0.0096 - bond_coeff @bond:hn-n3 harmonic 394.1 1.0180 # SOURCE3 157 0.0086 - bond_coeff @bond:hn-n harmonic 410.2 1.0090 # SOURCE3 149 0.0098 - bond_coeff @bond:hn-n4 harmonic 369.0 1.0330 # SOURCE3 264 0.0082 - bond_coeff @bond:hn-na harmonic 406.6 1.0110 # SOURCE3 46 0.0107 - bond_coeff @bond:hn-nh harmonic 401.2 1.0140 # SOURCE3 209 0.0091 - bond_coeff @bond:hn-no harmonic 385.6 1.0230 # SOURCE3 1 0.0000 - bond_coeff @bond:ho-o harmonic 357.9 0.9810 # SOURCE3 1 0.0000 - bond_coeff @bond:ho-oh harmonic 369.6 0.9740 # SOURCE3 367 0.0105 - bond_coeff @bond:hp-p2 harmonic 385.1 1.3360 # SOURCE3 87 0.1706 - bond_coeff @bond:hp-p3 harmonic 303.1 1.4090 # SOURCE3 101 0.0617 - bond_coeff @bond:hp-p4 harmonic 368.7 1.3490 # SOURCE3 17 0.1577 - bond_coeff @bond:hp-p5 harmonic 305.0 1.4070 # SOURCE3 7 0.0062 - bond_coeff @bond:hs-s harmonic 286.4 1.3530 # SOURCE3 1 0.0000 - bond_coeff @bond:hs-s4 harmonic 266.4 1.3750 # SOURCE3 5 0.0004 - bond_coeff @bond:hs-s6 harmonic 280.8 1.3590 # SOURCE3 5 0.0015 - bond_coeff @bond:hs-sh harmonic 302.2 1.3370 # SOURCE3 98 0.0486 - bond_coeff @bond:i-i harmonic 109.2 2.9170 # SOURCE1 1 0.0000 - bond_coeff @bond:i-n1 harmonic 302.1 2.0600 # SOUECE3 1 - bond_coeff @bond:i-n2 harmonic 182.6 2.3040 # SOURCE3 6 0.1186 - bond_coeff @bond:i-n harmonic 278.3 2.0980 # SOURCE3 5 0.0156 - bond_coeff @bond:i-n3 harmonic 231.8 2.1850 # SOURCE3 3 0.0437 - bond_coeff @bond:i-n4 harmonic 246.6 2.1550 # SOURCE3 3 0.0168 - bond_coeff @bond:i-na harmonic 260.5 2.1290 # SOURCE3 8 0.1276 - bond_coeff @bond:i-nh harmonic 249.2 2.1500 # SOURCE3 1 0.0000 - bond_coeff @bond:i-no harmonic 211.0 2.2310 # SOURCE3 1 0.0000 - bond_coeff @bond:i-o harmonic 323.8 1.9800 # SOUECE3 1 - bond_coeff @bond:i-oh harmonic 247.9 2.1010 # SOURCE3 2 0.0000 - bond_coeff @bond:i-os harmonic 233.6 2.1290 # SOURCE3 3 0.0146 - bond_coeff @bond:i-p2 harmonic 108.2 2.6430 # SOURCE3 6 0.0297 - bond_coeff @bond:i-p3 harmonic 123.6 2.5660 # SOURCE3 3 0.0016 - bond_coeff @bond:i-p4 harmonic 183.0 2.3520 # SOURCE3 4 0.2600 - bond_coeff @bond:i-p5 harmonic 117.3 2.5960 # SOURCE3 3 0.0143 - bond_coeff @bond:i-s harmonic 175.1 2.4300 # SOUECE3 1 - bond_coeff @bond:i-s4 harmonic 82.8 2.8700 # SOUECE3 1 - bond_coeff @bond:i-s6 harmonic 82.8 2.8700 # SOURCE3 1 0.0000 - bond_coeff @bond:i-sh harmonic 138.5 2.5600 # SOUECE3 1 - bond_coeff @bond:i-ss harmonic 135.9 2.5710 # SOURCE3 3 0.0065 - bond_coeff @bond:n1-n1 harmonic 1221.7 1.1240 # SOURCE1 19 0.0000 - bond_coeff @bond:n1-n2 harmonic 857.4 1.2160 # SOURCE1 19 0.0000 - bond_coeff @bond:n1-n3 harmonic 535.7 1.3500 # SOUECE3 1 - bond_coeff @bond:n1-n4 harmonic 518.2 1.3600 # SOUECE3 1 - bond_coeff @bond:n1-na harmonic 535.7 1.3500 # SOUECE3 1 - bond_coeff @bond:n1-nc harmonic 857.4 1.2160 # SOURCE1 38 0.0000 - bond_coeff @bond:n1-nd harmonic 857.4 1.2160 # SOURCE1 38 0.0000 - bond_coeff @bond:n1-ne harmonic 751.9 1.2520 # SOURCE2 1 0.0000 - bond_coeff @bond:n1-nf harmonic 751.9 1.2520 # SOURCE2 1 same_as_n1-ne - bond_coeff @bond:n1-nh harmonic 553.9 1.3400 # SOUECE3 1 - bond_coeff @bond:n1-no harmonic 454.8 1.4000 # SOUECE3 1 - bond_coeff @bond:n1-o harmonic 617.5 1.2770 # SOURCE3 5 0.0438 - bond_coeff @bond:n1-oh harmonic 569.8 1.3000 # SOUECE3 1 - bond_coeff @bond:n1-os harmonic 550.5 1.3100 # SOUECE3 1 - bond_coeff @bond:n1-p2 harmonic 358.8 1.6780 # SOURCE3 2 0.0282 - bond_coeff @bond:n1-p3 harmonic 376.7 1.6600 # SOUECE3 1 - bond_coeff @bond:n1-p4 harmonic 353.0 1.6800 # SOURCE3 0 - bond_coeff @bond:n1-p5 harmonic 482.7 1.5710 # SOURCE1 132 0.0000 - bond_coeff @bond:n1-s2 harmonic 604.3 1.4490 # SOURCE2 2 0.0010 - bond_coeff @bond:n1-s harmonic 328.7 1.6590 # SOURCE3 6 0.0789 - bond_coeff @bond:n1-s4 harmonic 336.8 1.6500 # SOUECE3 1 - bond_coeff @bond:n1-s6 harmonic 670.3 1.4160 # SOURCE2 2 0.0000 - bond_coeff @bond:n1-sh harmonic 376.1 1.6100 # SOUECE3 1 - bond_coeff @bond:n1-ss harmonic 376.1 1.6100 # SOUECE3 1 - bond_coeff @bond:n2-n2 harmonic 702.7 1.2710 # SOURCE3 27 0.0347 - bond_coeff @bond:n2-n3 harmonic 574.8 1.3290 # SOURCE2 1 0.0000 - bond_coeff @bond:n2-n4 harmonic 200.8 1.6790 # SOURCE3 7 0.3138 - bond_coeff @bond:n2-na harmonic 503.9 1.3685 # SOURCE4 18 0.0066 - bond_coeff @bond:n2-nc harmonic 743.9 1.2550 # SOURCE1 13 0.0000 - bond_coeff @bond:n2-nd harmonic 743.9 1.2550 # SOURCE1 13 same_as_n2_nc - bond_coeff @bond:n2-ne harmonic 685.5 1.2780 # SOURCE3 30 0.0302 - bond_coeff @bond:n2-nf harmonic 685.5 1.2780 # SOURCE3 30 same_as_n2-ne - bond_coeff @bond:n2-nh harmonic 525.1 1.3560 # SOURCE3 22 0.0300 - bond_coeff @bond:n2-no harmonic 231.9 1.6260 # SOURCE3 4 0.1933 - bond_coeff @bond:n2-o harmonic 789.9 1.2090 # SOURCE3 20 0.0344 - bond_coeff @bond:n2-oh harmonic 416.2 1.3940 # SOURCE1 67 0.0000 - bond_coeff @bond:n2-os harmonic 400.5 1.4060 # SOURCE3 10 0.0147 - bond_coeff @bond:n2-p2 harmonic 438.3 1.6050 # SOURCE3 35 0.0737 - bond_coeff @bond:n2-p3 harmonic 286.5 1.7640 # SOURCE3 7 0.0374 - bond_coeff @bond:n2-p4 harmonic 317.7 1.7240 # SOUECE3 1 - bond_coeff @bond:n2-p5 harmonic 445.8 1.5990 # SOURCE1 7 0.0000 - bond_coeff @bond:n2-pe harmonic 527.9 1.5400 # SOURCE3 20 0.1392 - bond_coeff @bond:n2-pf harmonic 527.9 1.5400 # SOURCE3 20 same_as_n2-pe - bond_coeff @bond:n2-s2 harmonic 499.0 1.5120 # SOURCE2 1 0.0000 - bond_coeff @bond:n2-s4 harmonic 376.1 1.6100 # SOUECE3 1 - bond_coeff @bond:n2-s harmonic 458.1 1.5410 # SOURCE1 37 0.0000 - bond_coeff @bond:n2-s6 harmonic 444.6 1.5513 # SOURCE4 5 0.0011 - bond_coeff @bond:n2-sh harmonic 266.6 1.7380 # SOURCE3 5 0.0511 - bond_coeff @bond:n2-ss harmonic 331.4 1.6560 # SOURCE1 36 0.0000 - bond_coeff @bond:n3-n3 harmonic 383.6 1.4540 # SOURCE1 44 0.0000 - bond_coeff @bond:n3-n4 harmonic 434.9 1.4140 # SOURCE1 13 0.0000 - bond_coeff @bond:n3-na harmonic 426.7 1.4200 # SOURCE1 68 0.0000 - bond_coeff @bond:n3-nh harmonic 426.7 1.4200 # SOURCE1 68 0.0000 - bond_coeff @bond:n3-no harmonic 394.5 1.4450 # SOURCE3 3 0.0208 - bond_coeff @bond:n3-o harmonic 564.0 1.3030 # SOURCE3 4 0.1217 - bond_coeff @bond:n3-oh harmonic 413.5 1.3960 # SOURCE1 28 0.0000 - bond_coeff @bond:n3-os harmonic 359.6 1.4400 # SOURCE1 34 0.0315 - bond_coeff @bond:n3-p2 harmonic 366.6 1.6700 # SOUECE3 1 - bond_coeff @bond:n3-p3 harmonic 312.8 1.7300 # SOURCE1 40 0.0000 - bond_coeff @bond:n3-p4 harmonic 341.1 1.6970 # SOURCE1 88 0.0000 - bond_coeff @bond:n3-p5 harmonic 373.6 1.6630 # SOURCE1 501 0.0086 - bond_coeff @bond:n3-py harmonic 338.1 1.7003 # SOURCE4 6 0.0044 - bond_coeff @bond:n3-s harmonic 232.3 1.7920 # SOURCE3 3 0.0178 - bond_coeff @bond:n3-s4 harmonic 251.3 1.7610 # SOURCE3 6 0.0766 - bond_coeff @bond:n3-s6 harmonic 353.8 1.6320 # SOURCE1 99 0.0136 - bond_coeff @bond:n3-sh harmonic 265.9 1.7390 # SOURCE3 3 0.0154 - bond_coeff @bond:n3-ss harmonic 277.9 1.7220 # SOURCE3 5 0.0207 - bond_coeff @bond:n3-sy harmonic 297.3 1.6964 # SOURCE4 226 0.0081 - bond_coeff @bond:n4-n4 harmonic 349.9 1.4840 # SOURCE3 4 0.0089 - bond_coeff @bond:n4-na harmonic 407.0 1.4350 # SOURCE3 9 0.0390 - bond_coeff @bond:n4-nh harmonic 369.7 1.4660 # SOURCE3 5 0.0108 - bond_coeff @bond:n4-no harmonic 354.2 1.4800 # SOUECE3 1 - bond_coeff @bond:n4-o harmonic 463.6 1.3610 # SOURCE3 3 0.0041 - bond_coeff @bond:n4-oh harmonic 408.2 1.4000 # SOURCE3 3 0.0115 - bond_coeff @bond:n4-os harmonic 381.8 1.4210 # SOURCE3 5 0.0249 - bond_coeff @bond:n4-p2 harmonic 185.9 1.9420 # SOURCE3 10 0.0643 - bond_coeff @bond:n4-p3 harmonic 215.1 1.8800 # SOURCE3 5 0.0146 - bond_coeff @bond:n4-p4 harmonic 187.6 1.9380 # SOURCE3 1 0.0000 - bond_coeff @bond:n4-p5 harmonic 242.9 1.8300 # SOURCE3 5 0.0087 - bond_coeff @bond:n4-py harmonic 204.2 1.9020 # SOURCE3 4 0.0000 - bond_coeff @bond:n4-s harmonic 210.3 1.8320 # SOURCE3 3 0.0004 - bond_coeff @bond:n4-s4 harmonic 151.0 1.9720 # SOURCE3 3 0.0198 - bond_coeff @bond:n4-s6 harmonic 172.7 1.9140 # SOURCE3 5 0.0432 - bond_coeff @bond:n4-sh harmonic 221.5 1.8110 # SOURCE3 3 0.0027 - bond_coeff @bond:n4-ss harmonic 221.0 1.8120 # SOURCE3 5 0.0064 - bond_coeff @bond:na-na harmonic 453.3 1.4010 # SOURCE1 40 0.0000 - bond_coeff @bond:na-nb harmonic 546.5 1.3440 # SOURCE4 5 0.0070 - bond_coeff @bond:na-nc harmonic 535.7 1.3500 # SOURCE3 152 0.0180 - bond_coeff @bond:na-nd harmonic 535.7 1.3500 # SOURCE3 152 0.0180 - bond_coeff @bond:na-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000 - bond_coeff @bond:na-no harmonic 401.9 1.4390 # SOURCE3 9 0.0289 - bond_coeff @bond:na-o harmonic 644.3 1.2650 # SOURCE1 25 0.0347 - bond_coeff @bond:na-oh harmonic 412.2 1.3970 # SOURCE3 9 0.0217 - bond_coeff @bond:na-os harmonic 355.2 1.4440 # SOURCE3 45 0.0423 - bond_coeff @bond:na-p2 harmonic 297.8 1.7490 # SOURCE3 11 0.0192 - bond_coeff @bond:na-p3 harmonic 288.0 1.7620 # SOURCE3 8 0.0113 - bond_coeff @bond:na-p4 harmonic 492.4 1.5640 # SOURCE3 5 0.2161 - bond_coeff @bond:na-p5 harmonic 325.3 1.7150 # SOURCE3 11 0.0238 - bond_coeff @bond:na-pc harmonic 311.1 1.7320 # SOURCE3 81 0.0207 - bond_coeff @bond:na-pd harmonic 311.1 1.7320 # SOURCE3 81 same_as_na-pc - bond_coeff @bond:na-py harmonic 327.8 1.7120 # SOURCE3 2 0.0000 - bond_coeff @bond:na-s harmonic 248.7 1.7650 # SOURCE3 8 0.0095 - bond_coeff @bond:na-s4 harmonic 231.7 1.7930 # SOURCE3 10 0.0421 - bond_coeff @bond:na-s6 harmonic 274.3 1.7270 # SOURCE3 10 0.0201 - bond_coeff @bond:na-sh harmonic 278.6 1.7210 # SOURCE3 9 0.0113 - bond_coeff @bond:na-ss harmonic 270.1 1.7330 # SOURCE3 38 0.0412 - bond_coeff @bond:na-sy harmonic 274.3 1.7270 # SOURCE3 1 - bond_coeff @bond:nb-nb harmonic 550.2 1.3420 # SOURCE1 15 0.0314 - bond_coeff @bond:nb-pb harmonic 461.1 1.5870 # SOURCE1 162 0.0091 - bond_coeff @bond:nc-nc harmonic 486.8 1.3790 # SOURCE3 9 0.0164 - bond_coeff @bond:nc-nd harmonic 602.9 1.3150 # SOURCE3 9 0.0221 - bond_coeff @bond:nc-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188 - bond_coeff @bond:nc-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000 - bond_coeff @bond:nc-sy harmonic 439.8 1.5550 # SOURCE3 2 - bond_coeff @bond:nd-nd harmonic 486.8 1.3790 # SOURCE3 9 0.0164 - bond_coeff @bond:nd-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188 - bond_coeff @bond:nd-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000 - bond_coeff @bond:nd-sy harmonic 439.8 1.5550 # SOURCE3 2 - bond_coeff @bond:ne-ne harmonic 355.3 1.4790 # SOURCE3 19 0.1705 - bond_coeff @bond:ne-nf harmonic 721.6 1.2635 # SOURCE4 25 0.0034 - bond_coeff @bond:ne-o harmonic 736.4 1.2280 # SOURCE3 40 0.0255 - bond_coeff @bond:ne-p2 harmonic 493.9 1.5630 # SOURCE3 14 0.1325 - bond_coeff @bond:ne-pe harmonic 327.8 1.7120 # SOURCE3 28 0.1076 - bond_coeff @bond:ne-px harmonic 336.6 1.7020 # SOURCE3 11 0.0883 - bond_coeff @bond:ne-py harmonic 425.4 1.6157 # SOURCE4 10 0.0094 - bond_coeff @bond:ne-s harmonic 463.5 1.5370 # SOURCE3 22 0.1708 - bond_coeff @bond:ne-sx harmonic 207.3 1.8380 # SOURCE3 7 0.1060 - bond_coeff @bond:ne-sy harmonic 257.1 1.7520 # SOURCE3 7 0.0814 - bond_coeff @bond:nf-nf harmonic 355.3 1.4790 # SOURCE3 19 same_as_ne-ne - bond_coeff @bond:nf-o harmonic 736.4 1.2280 # SOURCE3 40 same_as_ne-o - bond_coeff @bond:nf-p2 harmonic 493.9 1.5630 # SOURCE3 14 same_as_ne-p2 - bond_coeff @bond:nf-pf harmonic 327.8 1.7120 # SOURCE3 28 same_as_ne-pe - bond_coeff @bond:nf-px harmonic 336.6 1.7020 # SOURCE3 11 same_as_ne-px - bond_coeff @bond:nf-py harmonic 425.4 1.6157 # SOURCE4 10 same_as_ne-py - bond_coeff @bond:nf-s harmonic 463.5 1.5370 # SOURCE3 22 same_as_ne-s - bond_coeff @bond:nf-sx harmonic 207.3 1.8380 # SOURCE3 7 same_as_ne-sx - bond_coeff @bond:nf-sy harmonic 257.1 1.7520 # SOURCE3 7 same_as_ne-sy - bond_coeff @bond:nh-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000 - bond_coeff @bond:nh-no harmonic 477.4 1.3850 # SOURCE4 7 0.0036 - bond_coeff @bond:nh-o harmonic 596.2 1.2870 # SOURCE3 3 0.0450 - bond_coeff @bond:nh-oh harmonic 389.9 1.4144 # SOURCE4 19 0.0064 - bond_coeff @bond:nh-os harmonic 387.8 1.4161 # SOURCE4 6 0.0039 - bond_coeff @bond:nh-p2 harmonic 357.8 1.6790 # SOURCE3 17 0.0872 - bond_coeff @bond:nh-p3 harmonic 312.8 1.7300 # SOURCE3 3 0.0016 - bond_coeff @bond:nh-p4 harmonic 333.1 1.7060 # SOURCE3 3 0.0008 - bond_coeff @bond:nh-p5 harmonic 365.6 1.6710 # SOURCE3 3 0.0007 - bond_coeff @bond:nh-s harmonic 237.0 1.7840 # SOURCE3 3 0.0076 - bond_coeff @bond:nh-s4 harmonic 259.1 1.7490 # SOURCE3 3 0.0203 - bond_coeff @bond:nh-s6 harmonic 297.2 1.6965 # SOURCE4 33 0.0062 - bond_coeff @bond:nh-sh harmonic 288.3 1.7080 # SOURCE3 1 0.0000 - bond_coeff @bond:nh-ss harmonic 288.3 1.7080 # SOURCE1 52 0.0015 - bond_coeff @bond:nh-sy harmonic 283.5 1.7144 # SOURCE4 80 0.0066 - bond_coeff @bond:n-n1 harmonic 553.9 1.3400 # SOUECE3 1 - bond_coeff @bond:n-n2 harmonic 499.7 1.3710 # SOURCE3 9 0.0200 - bond_coeff @bond:n-n3 harmonic 443.3 1.4080 # SOURCE3 5 0.0087 - bond_coeff @bond:n-n4 harmonic 410.8 1.4320 # SOURCE3 5 0.0098 - bond_coeff @bond:n-n harmonic 469.7 1.3900 # SOURCE3 5 0.0038 - bond_coeff @bond:n-na harmonic 486.8 1.3790 # SOURCE3 11 0.0071 - bond_coeff @bond:n-nc harmonic 523.7 1.3568 # CORR 76 - bond_coeff @bond:n-nd harmonic 523.7 1.3568 # CORR 76 - bond_coeff @bond:n-nh harmonic 451.2 1.4025 # SOURCE4 20 0.0074 - bond_coeff @bond:n-no harmonic 381.2 1.4560 # SOURCE3 4 0.0327 - bond_coeff @bond:n-o harmonic 646.6 1.2640 # SOURCE3 9 0.0381 - bond_coeff @bond:n-oh harmonic 395.4 1.4100 # SOURCE3 6 0.0106 - bond_coeff @bond:no-no harmonic 138.3 1.8240 # SOURCE3 1 0.0000 - bond_coeff @bond:no-o harmonic 761.2 1.2190 # SOURCE1 1838 0.0049 - bond_coeff @bond:no-oh harmonic 400.5 1.4060 # SOURCE2 1 0.0000 - bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076 - bond_coeff @bond:no-p2 harmonic 306.3 1.7380 # SOURCE3 10 0.2231 - bond_coeff @bond:no-p3 harmonic 234.7 1.8440 # SOURCE3 3 0.0005 - bond_coeff @bond:no-p4 harmonic 220.4 1.8700 # SOURCE3 3 0.0006 - bond_coeff @bond:no-p5 harmonic 240.5 1.8340 # SOURCE3 4 0.0020 - bond_coeff @bond:no-s harmonic 263.8 1.7420 # SOURCE3 2 0.0000 - bond_coeff @bond:n-os harmonic 395.0 1.4103 # SOURCE4 30 0.0112 - bond_coeff @bond:no-s4 harmonic 143.0 1.9960 # SOURCE3 3 0.0313 - bond_coeff @bond:no-s6 harmonic 149.6 1.9760 # SOURCE3 3 0.0520 - bond_coeff @bond:no-sh harmonic 225.4 1.8040 # SOURCE3 1 0.0000 - bond_coeff @bond:no-ss harmonic 212.4 1.8280 # SOURCE3 3 0.0244 - bond_coeff @bond:n-p2 harmonic 310.3 1.7330 # SOURCE3 8 0.0217 - bond_coeff @bond:n-p3 harmonic 282.2 1.7700 # SOURCE3 9 0.0118 - bond_coeff @bond:n-p4 harmonic 309.5 1.7340 # SOURCE3 1 0.0000 - bond_coeff @bond:n-p5 harmonic 331.3 1.7080 # SOURCE4 6 0.0022 - bond_coeff @bond:n-pc harmonic 304.8 1.7400 # SOURCE3 3 0.0010 - bond_coeff @bond:n-pd harmonic 304.8 1.7400 # SOURCE3 3 same_as_n-pc - bond_coeff @bond:n-s harmonic 247.5 1.7670 # SOURCE3 3 0.0011 - bond_coeff @bond:n-s4 harmonic 238.2 1.7820 # SOURCE3 4 0.0214 - bond_coeff @bond:n-s6 harmonic 283.0 1.7151 # SOURCE4 13 0.0138 - bond_coeff @bond:n-sh harmonic 273.6 1.7280 # SOURCE3 4 0.0128 - bond_coeff @bond:n-ss harmonic 281.6 1.7170 # SOURCE3 7 0.0133 - bond_coeff @bond:n-sy harmonic 282.9 1.7152 # SOURCE4 51 0.0079 - bond_coeff @bond:oh-oh harmonic 340.5 1.4690 # SOURCE3 1 0.0000 - bond_coeff @bond:oh-os harmonic 355.8 1.4547 # SOURCE4 19 0.0050 - bond_coeff @bond:oh-p2 harmonic 316.8 1.6300 # SOURCE3 8 0.0916 - bond_coeff @bond:oh-p3 harmonic 278.8 1.6770 # SOURCE3 3 0.0148 - bond_coeff @bond:oh-p4 harmonic 307.4 1.6410 # SOURCE3 4 0.0092 - bond_coeff @bond:oh-p5 harmonic 321.2 1.6250 # SOURCE3 92 0.0451 - bond_coeff @bond:oh-py harmonic 332.1 1.6130 # SOURCE3 79 0.0138 - bond_coeff @bond:oh-s harmonic 190.0 1.8120 # SOURCE3 2 0.0000 - bond_coeff @bond:oh-s4 harmonic 256.3 1.6954 # SOURCE4 10 0.0091 - bond_coeff @bond:oh-s6 harmonic 344.1 1.5880 # SOURCE3 13 0.0091 - bond_coeff @bond:oh-sh harmonic 258.6 1.6920 # SOURCE3 2 0.0003 - bond_coeff @bond:oh-ss harmonic 265.6 1.6820 # SOURCE3 4 0.0131 - bond_coeff @bond:oh-sy harmonic 290.4 1.6490 # SOURCE4 33 0.0044 - bond_coeff @bond:o-o harmonic 384.3 1.4300 # SOURCE3 2 0.0500 - bond_coeff @bond:o-oh harmonic 294.6 1.5170 # SOURCE3 2 0.0000 - bond_coeff @bond:o-os harmonic 306.3 1.5040 # SOURCE3 3 0.0117 - bond_coeff @bond:o-p2 harmonic 449.7 1.5080 # SOURCE3 17 0.0306 - bond_coeff @bond:o-p3 harmonic 440.4 1.5150 # SOURCE3 35 0.0297 - bond_coeff @bond:o-p4 harmonic 456.4 1.5030 # SOURCE3 42 0.0749 - bond_coeff @bond:o-p5 harmonic 487.7 1.4810 # SOURCE1 263 0.0205 - bond_coeff @bond:o-pe harmonic 432.6 1.5210 # SOURCE3 20 0.0171 - bond_coeff @bond:o-pf harmonic 432.6 1.5210 # SOURCE3 20 same_as_o-pe - bond_coeff @bond:o-px harmonic 459.2 1.5010 # SOURCE3 37 0.0160 - bond_coeff @bond:o-py harmonic 477.5 1.4880 # SOURCE3 63 0.0091 - bond_coeff @bond:o-s harmonic 194.8 1.8020 # SOURCE3 2 0.0000 - bond_coeff @bond:o-s2 harmonic 333.6 1.5990 # SOURCE3 3 0.0707 - bond_coeff @bond:o-s4 harmonic 448.7 1.4970 # SOURCE1 90 0.0000 - bond_coeff @bond:o-s6 harmonic 541.1 1.4360 # SOURCE1 1038 0.0128 - bond_coeff @bond:o-sh harmonic 328.0 1.6050 # SOURCE3 2 0.0000 - bond_coeff @bond:os-os harmonic 343.6 1.4660 # SOURCE1 20 0.0067 - bond_coeff @bond:os-p2 harmonic 371.9 1.5730 # SOURCE1 16 0.0000 - bond_coeff @bond:os-p3 harmonic 272.2 1.6860 # SOURCE3 6 0.0201 - bond_coeff @bond:os-p4 harmonic 311.6 1.6360 # SOURCE3 4 0.0057 - bond_coeff @bond:os-p5 harmonic 342.5 1.6020 # SOURCE1 248 0.0400 - bond_coeff @bond:os-py harmonic 328.5 1.6170 # SOURCE3 17 0.0139 - bond_coeff @bond:os-s harmonic 195.8 1.8000 # SOURCE3 3 0.0052 - bond_coeff @bond:o-ss harmonic 398.5 1.5370 # SOURCE3 3 0.0501 - bond_coeff @bond:os-s4 harmonic 253.9 1.6990 # SOURCE3 8 0.0223 - bond_coeff @bond:os-s6 harmonic 355.0 1.5770 # SOURCE1 75 0.0030 - bond_coeff @bond:os-sh harmonic 273.6 1.6710 # SOURCE3 3 0.0106 - bond_coeff @bond:os-ss harmonic 250.5 1.7040 # SOURCE3 9 0.0277 - bond_coeff @bond:os-sy harmonic 253.9 1.6990 # SOURCE3 1 0.0000 - bond_coeff @bond:o-sx harmonic 434.2 1.5080 # SOURCE3 40 0.0130 - bond_coeff @bond:o-sy harmonic 493.0 1.4660 # SOURCE3 92 0.0114 - bond_coeff @bond:p2-p2 harmonic 490.3 1.7860 # SOURCE3 25 0.3488 - bond_coeff @bond:p2-p3 harmonic 211.9 2.1520 # SOURCE3 9 0.1777 - bond_coeff @bond:p2-p4 harmonic 200.4 2.1790 # SOUECE3 1 - bond_coeff @bond:p2-p5 harmonic 199.9 2.1800 # SOUECE3 1 - bond_coeff @bond:p2-pe harmonic 401.6 1.8670 # SOURCE3 16 0.3571 - bond_coeff @bond:p2-pf harmonic 401.6 1.8670 # SOURCE3 16 same_as_p2-pe - bond_coeff @bond:p2-s harmonic 361.6 1.7720 # SOURCE3 26 0.3014 - bond_coeff @bond:p2-s4 harmonic 139.4 2.1900 # SOUECE3 1 - bond_coeff @bond:p2-s6 harmonic 142.3 2.1800 # SOUECE3 1 - bond_coeff @bond:p2-sh harmonic 224.0 1.9710 # SOURCE3 10 0.2829 - bond_coeff @bond:p2-ss harmonic 226.6 1.9660 # SOURCE3 10 0.2739 - bond_coeff @bond:p3-p3 harmonic 186.5 2.2140 # SOURCE1 41 0.0000 - bond_coeff @bond:p3-p4 harmonic 185.7 2.2160 # SOURCE3 3 0.0011 - bond_coeff @bond:p3-p5 harmonic 186.9 2.2130 # SOURCE3 9 0.0265 - bond_coeff @bond:p3-s harmonic 179.7 2.0700 # SOUECE3 1 - bond_coeff @bond:p3-s4 harmonic 173.2 2.0870 # SOURCE3 8 0.2235 - bond_coeff @bond:p3-s6 harmonic 176.9 2.0770 # SOURCE3 11 0.1420 - bond_coeff @bond:p3-sh harmonic 157.3 2.1320 # SOURCE3 3 0.0078 - bond_coeff @bond:p3-ss harmonic 161.0 2.1210 # SOURCE3 3 0.0059 - bond_coeff @bond:p4-p4 harmonic 273.1 2.0340 # SOURCE1 1 0.0000 - bond_coeff @bond:p4-p5 harmonic 178.0 2.2370 # SOUECE3 1 - bond_coeff @bond:p4-s harmonic 152.7 2.1460 # SOURCE3 5 0.0601 - bond_coeff @bond:p4-s4 harmonic 123.2 2.2510 # SOUECE3 1 - bond_coeff @bond:p4-s6 harmonic 118.9 2.2690 # SOUECE3 1 - bond_coeff @bond:p4-sh harmonic 163.1 2.1150 # SOURCE3 4 0.0008 - bond_coeff @bond:p4-ss harmonic 167.0 2.1040 # SOURCE3 4 0.0044 - bond_coeff @bond:p5-p5 harmonic 261.4 2.0540 # SOURCE1 1 0.0000 - bond_coeff @bond:p5-s harmonic 250.8 1.9220 # SOURCE1 89 0.0140 - bond_coeff @bond:p5-s4 harmonic 191.9 2.0400 # SOUECE3 1 - bond_coeff @bond:p5-s6 harmonic 191.9 2.0400 # SOUECE3 1 - bond_coeff @bond:p5-sh harmonic 175.0 2.0820 # SOURCE3 3 0.0035 - bond_coeff @bond:p5-ss harmonic 163.1 2.1149 # SOURCE4 24 0.0106 - bond_coeff @bond:pe-pe harmonic 240.7 2.0920 # SOURCE3 7 0.1369 - bond_coeff @bond:pe-pf harmonic 260.8 2.0550 # SOURCE3 1 0.0000 - bond_coeff @bond:pe-px harmonic 291.4 2.0050 # SOURCE3 12 0.2609 - bond_coeff @bond:pe-py harmonic 278.6 2.0250 # SOURCE3 12 0.2617 - bond_coeff @bond:pe-s harmonic 374.7 1.7580 # SOURCE3 31 0.3197 - bond_coeff @bond:pe-sx harmonic 145.9 2.1680 # SOURCE3 9 0.1743 - bond_coeff @bond:pe-sy harmonic 133.0 2.2130 # SOURCE3 6 0.0127 - bond_coeff @bond:pf-pf harmonic 240.7 2.0920 # SOURCE3 7 same_as_pe-pe - bond_coeff @bond:pf-px harmonic 291.4 2.0050 # SOURCE3 12 same_as_pe-px - bond_coeff @bond:pf-py harmonic 278.6 2.0250 # SOURCE3 12 same_as_pe-py - bond_coeff @bond:pf-s harmonic 374.7 1.7580 # SOURCE3 31 same_as_pe-s - bond_coeff @bond:pf-sx harmonic 145.9 2.1680 # SOURCE3 9 same_as_pe-sx - bond_coeff @bond:pf-sy harmonic 133.0 2.2130 # SOURCE3 6 same_as_pe-sy - bond_coeff @bond:px-py harmonic 192.3 2.1990 # SOURCE3 5 0.0238 - bond_coeff @bond:px-sx harmonic 125.4 2.2420 # SOURCE3 3 0.0119 - bond_coeff @bond:px-sy harmonic 123.7 2.2490 # SOURCE3 3 0.0272 - bond_coeff @bond:py-py harmonic 197.5 2.1860 # SOURCE3 8 0.0132 - bond_coeff @bond:py-sx harmonic 121.2 2.2590 # SOURCE3 7 0.0603 - bond_coeff @bond:py-sy harmonic 141.7 2.1820 # SOURCE3 5 0.0047 - bond_coeff @bond:s4-s4 harmonic 151.5 2.0800 # SOUECE3 1 - bond_coeff @bond:s4-s6 harmonic 151.5 2.0800 # SOUECE3 1 - bond_coeff @bond:s4-sh harmonic 125.7 2.1680 # SOURCE3 3 0.0227 - bond_coeff @bond:s4-ss harmonic 126.2 2.1660 # SOURCE3 5 0.0247 - bond_coeff @bond:s6-s6 harmonic 151.5 2.0800 # SOUECE3 1 - bond_coeff @bond:s6-sh harmonic 142.6 2.1080 # SOURCE3 3 0.0144 - bond_coeff @bond:s6-ss harmonic 139.6 2.1180 # SOURCE3 5 0.0209 - bond_coeff @bond:sh-sh harmonic 158.9 2.0580 # SOURCE2 1 0.0000 - bond_coeff @bond:sh-ss harmonic 155.8 2.0670 # SOURCE3 3 0.0029 - bond_coeff @bond:s-s harmonic 169.0 2.0300 # SOURCE3 1 0.0000 - bond_coeff @bond:s-s2 harmonic 229.2 1.8970 # SOURCE1 5 0.0000 - bond_coeff @bond:s-s4 harmonic 152.8 2.0760 # SOURCE3 4 0.0345 - bond_coeff @bond:s-s6 harmonic 166.0 2.0380 # SOURCE3 3 0.0311 - bond_coeff @bond:s-sh harmonic 142.0 2.1100 # SOURCE3 2 0.0000 - bond_coeff @bond:s-ss harmonic 148.5 2.0890 # SOURCE3 1 0.0000 - bond_coeff @bond:ss-ss harmonic 161.7 2.0500 # SOURCE1 225 0.0015 - bond_coeff @bond:sx-sx harmonic 80.9 2.3910 # SOURCE3 3 0.0185 - bond_coeff @bond:sx-sy harmonic 105.3 2.2550 # SOURCE3 5 0.0737 - bond_coeff @bond:sy-sy harmonic 106.4 2.2500 # SOURCE3 3 0.0289 - bond_coeff @bond:br-cd harmonic 277.6 1.8847 # NEW 39 - bond_coeff @bond:c1-cf harmonic 607.4 1.3153 # NEW 6 - bond_coeff @bond:cd-f harmonic 368.6 1.3401 # NEW 24 - bond_coeff @bond:cd-n4 harmonic 299.0 1.4930 # NEW 7 - bond_coeff @bond:cd-nf harmonic 427.4 1.3790 # NEW 30 - bond_coeff @bond:cd-no harmonic 367.4 1.4262 # NEW 133 - bond_coeff @bond:cd-sh harmonic 257.9 1.7681 # NEW 8 - bond_coeff @bond:cd-sx harmonic 231.3 1.8113 # NEW 16 - bond_coeff @bond:cc-cy harmonic 330.9 1.5054 # NEW 10 - bond_coeff @bond:cf-cl harmonic 292.6 1.7671 # NEW 24 - bond_coeff @bond:cf-cx harmonic 337.0 1.4993 # NEW 5 - bond_coeff @bond:cf-cy harmonic 323.0 1.5135 # NEW 17 - bond_coeff @bond:cf-na harmonic 373.8 1.4207 # NEW 5 - bond_coeff @bond:cf-ss harmonic 243.6 1.7906 # NEW 10 - bond_coeff @bond:cq-na harmonic 420.5 1.3840 # NEW 7 - bond_coeff @bond:cq-nb harmonic 486.7 1.3398 # NEW 70 - } # (end of bond_coeffs) - - write_once("Data Bonds By Type") { - @bond:ow-hw @atom:ow @atom:hw - @bond:hw-hw @atom:hw @atom:hw - @bond:br-br @atom:br @atom:br - @bond:br-c1 @atom:br @atom:c1 - @bond:br-c2 @atom:br @atom:c2 - @bond:br-c @atom:br @atom:c - @bond:br-c3 @atom:br @atom:c3 - @bond:br-ca @atom:br @atom:ca - @bond:br-cc @atom:br @atom:cc - @bond:br-cx @atom:br @atom:cx - @bond:br-i @atom:br @atom:i - @bond:br-n1 @atom:br @atom:n1 - @bond:br-n2 @atom:br @atom:n2 - @bond:br-n @atom:br @atom:n - @bond:br-n3 @atom:br @atom:n3 - @bond:br-n4 @atom:br @atom:n4 - @bond:br-na @atom:br @atom:na - @bond:br-nh @atom:br @atom:nh - @bond:br-no @atom:br @atom:no - @bond:br-o @atom:br @atom:o - @bond:br-oh @atom:br @atom:oh - @bond:br-os @atom:br @atom:os - @bond:br-p2 @atom:br @atom:p2 - @bond:br-p3 @atom:br @atom:p3 - @bond:br-p4 @atom:br @atom:p4 - @bond:br-p5 @atom:br @atom:p5 - @bond:br-s @atom:br @atom:s - @bond:br-s4 @atom:br @atom:s4 - @bond:br-s6 @atom:br @atom:s6 - @bond:br-sh @atom:br @atom:sh - @bond:br-ss @atom:br @atom:ss - @bond:c1-c1 @atom:c1 @atom:c1 - @bond:c1-c2 @atom:c1 @atom:c2 - @bond:c1-c3 @atom:c1 @atom:c3 - @bond:c1-ca @atom:c1 @atom:ca - @bond:c1-ce @atom:c1 @atom:ce - @bond:c1-cg @atom:c1 @atom:cg - @bond:c1-ch @atom:c1 @atom:ch - @bond:c1-cl @atom:c1 @atom:cl - @bond:c1-cx @atom:c1 @atom:cx - @bond:c1-f @atom:c1 @atom:f - @bond:c1-ha @atom:c1 @atom:ha - @bond:c1-hc @atom:c1 @atom:hc - @bond:c1-i @atom:c1 @atom:i - @bond:c1-n1 @atom:c1 @atom:n1 - @bond:c1-n2 @atom:c1 @atom:n2 - @bond:c1-n3 @atom:c1 @atom:n3 - @bond:c1-n4 @atom:c1 @atom:n4 - @bond:c1-n @atom:c1 @atom:n - @bond:c1-na @atom:c1 @atom:na - @bond:c1-ne @atom:c1 @atom:ne - @bond:c1-nf @atom:c1 @atom:nf - @bond:c1-nh @atom:c1 @atom:nh - @bond:c1-no @atom:c1 @atom:no - @bond:c1-o @atom:c1 @atom:o - @bond:c1-oh @atom:c1 @atom:oh - @bond:c1-os @atom:c1 @atom:os - @bond:c1-p2 @atom:c1 @atom:p2 - @bond:c1-p3 @atom:c1 @atom:p3 - @bond:c1-p4 @atom:c1 @atom:p4 - @bond:c1-p5 @atom:c1 @atom:p5 - @bond:c1-s2 @atom:c1 @atom:s2 - @bond:c1-s @atom:c1 @atom:s - @bond:c1-s4 @atom:c1 @atom:s4 - @bond:c1-s6 @atom:c1 @atom:s6 - @bond:c1-sh @atom:c1 @atom:sh - @bond:c1-ss @atom:c1 @atom:ss - @bond:c2-c2 @atom:c2 @atom:c2 - @bond:c2-c3 @atom:c2 @atom:c3 - @bond:c2-ca @atom:c2 @atom:ca - @bond:c2-cc @atom:c2 @atom:cc - @bond:c2-cd @atom:c2 @atom:cd - @bond:c2-ce @atom:c2 @atom:ce - @bond:c2-cf @atom:c2 @atom:cf - @bond:c2-cl @atom:c2 @atom:cl - @bond:c2-cu @atom:c2 @atom:cu - @bond:c2-cx @atom:c2 @atom:cx - @bond:c2-cy @atom:c2 @atom:cy - @bond:c2-f @atom:c2 @atom:f - @bond:c2-h4 @atom:c2 @atom:h4 - @bond:c2-h5 @atom:c2 @atom:h5 - @bond:c2-ha @atom:c2 @atom:ha - @bond:c2-hc @atom:c2 @atom:hc - @bond:c2-hx @atom:c2 @atom:hx - @bond:c2-i @atom:c2 @atom:i - @bond:c2-n1 @atom:c2 @atom:n1 - @bond:c2-n2 @atom:c2 @atom:n2 - @bond:c2-n3 @atom:c2 @atom:n3 - @bond:c2-n @atom:c2 @atom:n - @bond:c2-n4 @atom:c2 @atom:n4 - @bond:c2-na @atom:c2 @atom:na - @bond:c2-nc @atom:c2 @atom:nc - @bond:c2-nd @atom:c2 @atom:nd - @bond:c2-ne @atom:c2 @atom:ne - @bond:c2-nf @atom:c2 @atom:nf - @bond:c2-nh @atom:c2 @atom:nh - @bond:c2-no @atom:c2 @atom:no - @bond:c2-o @atom:c2 @atom:o - @bond:c2-oh @atom:c2 @atom:oh - @bond:c2-os @atom:c2 @atom:os - @bond:c2-p2 @atom:c2 @atom:p2 - @bond:c2-p3 @atom:c2 @atom:p3 - @bond:c2-p4 @atom:c2 @atom:p4 - @bond:c2-p5 @atom:c2 @atom:p5 - @bond:c2-pe @atom:c2 @atom:pe - @bond:c2-pf @atom:c2 @atom:pf - @bond:c2-s2 @atom:c2 @atom:s2 - @bond:c2-s @atom:c2 @atom:s - @bond:c2-s4 @atom:c2 @atom:s4 - @bond:c2-s6 @atom:c2 @atom:s6 - @bond:c2-sh @atom:c2 @atom:sh - @bond:c2-ss @atom:c2 @atom:ss - @bond:c3-c3 @atom:c3 @atom:c3 - @bond:c3-ca @atom:c3 @atom:ca - @bond:c3-cc @atom:c3 @atom:cc - @bond:c3-cd @atom:c3 @atom:cd - @bond:c3-ce @atom:c3 @atom:ce - @bond:c3-cf @atom:c3 @atom:cf - @bond:c3-cl @atom:c3 @atom:cl - @bond:c3-cu @atom:c3 @atom:cu - @bond:c3-cv @atom:c3 @atom:cv - @bond:c3-cx @atom:c3 @atom:cx - @bond:c3-cy @atom:c3 @atom:cy - @bond:c3-f @atom:c3 @atom:f - @bond:c3-h1 @atom:c3 @atom:h1 - @bond:c3-h2 @atom:c3 @atom:h2 - @bond:c3-h3 @atom:c3 @atom:h3 - @bond:c3-hc @atom:c3 @atom:hc - @bond:c3-hx @atom:c3 @atom:hx - @bond:c3-i @atom:c3 @atom:i - @bond:c3-n1 @atom:c3 @atom:n1 - @bond:c3-n2 @atom:c3 @atom:n2 - @bond:c3-n @atom:c3 @atom:n - @bond:c3-n3 @atom:c3 @atom:n3 - @bond:c3-n4 @atom:c3 @atom:n4 - @bond:c3-na @atom:c3 @atom:na - @bond:c3-nc @atom:c3 @atom:nc - @bond:c3-nd @atom:c3 @atom:nd - @bond:c3-nh @atom:c3 @atom:nh - @bond:c3-no @atom:c3 @atom:no - @bond:c3-o @atom:c3 @atom:o - @bond:c3-oh @atom:c3 @atom:oh - @bond:c3-os @atom:c3 @atom:os - @bond:c3-p2 @atom:c3 @atom:p2 - @bond:c3-p3 @atom:c3 @atom:p3 - @bond:c3-p4 @atom:c3 @atom:p4 - @bond:c3-p5 @atom:c3 @atom:p5 - @bond:c3-px @atom:c3 @atom:px - @bond:c3-py @atom:c3 @atom:py - @bond:c3-s @atom:c3 @atom:s - @bond:c3-s4 @atom:c3 @atom:s4 - @bond:c3-s6 @atom:c3 @atom:s6 - @bond:c3-sh @atom:c3 @atom:sh - @bond:c3-ss @atom:c3 @atom:ss - @bond:c3-sx @atom:c3 @atom:sx - @bond:c3-sy @atom:c3 @atom:sy - @bond:ca-ca @atom:ca @atom:ca - @bond:ca-cc @atom:ca @atom:cc - @bond:ca-cd @atom:ca @atom:cd - @bond:ca-ce @atom:ca @atom:ce - @bond:ca-cf @atom:ca @atom:cf - @bond:ca-cg @atom:ca @atom:cg - @bond:ca-ch @atom:ca @atom:ch - @bond:ca-cl @atom:ca @atom:cl - @bond:ca-cp @atom:ca @atom:cp - @bond:ca-cq @atom:ca @atom:cq - @bond:ca-cx @atom:ca @atom:cx - @bond:ca-cy @atom:ca @atom:cy - @bond:ca-f @atom:ca @atom:f - @bond:ca-h4 @atom:ca @atom:h4 - @bond:ca-h5 @atom:ca @atom:h5 - @bond:ca-ha @atom:ca @atom:ha - @bond:ca-i @atom:ca @atom:i - @bond:ca-n1 @atom:ca @atom:n1 - @bond:ca-n2 @atom:ca @atom:n2 - @bond:ca-n @atom:ca @atom:n - @bond:ca-n4 @atom:ca @atom:n4 - @bond:ca-na @atom:ca @atom:na - @bond:ca-nb @atom:ca @atom:nb - @bond:ca-nc @atom:ca @atom:nc - @bond:ca-nd @atom:ca @atom:nd - @bond:ca-ne @atom:ca @atom:ne - @bond:ca-nf @atom:ca @atom:nf - @bond:ca-nh @atom:ca @atom:nh - @bond:ca-no @atom:ca @atom:no - @bond:ca-o @atom:ca @atom:o - @bond:ca-oh @atom:ca @atom:oh - @bond:ca-os @atom:ca @atom:os - @bond:ca-p2 @atom:ca @atom:p2 - @bond:ca-p3 @atom:ca @atom:p3 - @bond:ca-p4 @atom:ca @atom:p4 - @bond:ca-p5 @atom:ca @atom:p5 - @bond:ca-pe @atom:ca @atom:pe - @bond:ca-pf @atom:ca @atom:pf - @bond:ca-px @atom:ca @atom:px - @bond:ca-py @atom:ca @atom:py - @bond:ca-s @atom:ca @atom:s - @bond:ca-s4 @atom:ca @atom:s4 - @bond:ca-s6 @atom:ca @atom:s6 - @bond:ca-sh @atom:ca @atom:sh - @bond:ca-ss @atom:ca @atom:ss - @bond:ca-sx @atom:ca @atom:sx - @bond:ca-sy @atom:ca @atom:sy - @bond:c-c1 @atom:c @atom:c1 - @bond:c-c2 @atom:c @atom:c2 - @bond:c-c @atom:c @atom:c - @bond:c-c3 @atom:c @atom:c3 - @bond:c-ca @atom:c @atom:ca - @bond:c-cc @atom:c @atom:cc - @bond:cc-cc @atom:cc @atom:cc - @bond:cc-cd @atom:cc @atom:cd - @bond:cc-ce @atom:cc @atom:ce - @bond:cc-cf @atom:cc @atom:cf - @bond:cc-cg @atom:cc @atom:cg - @bond:cc-ch @atom:cc @atom:ch - @bond:cc-cl @atom:cc @atom:cl - @bond:cc-cx @atom:cc @atom:cx - @bond:c-cd @atom:c @atom:cd - @bond:c-ce @atom:c @atom:ce - @bond:c-cf @atom:c @atom:cf - @bond:cc-f @atom:cc @atom:f - @bond:c-cg @atom:c @atom:cg - @bond:c-ch @atom:c @atom:ch - @bond:cc-h4 @atom:cc @atom:h4 - @bond:cc-h5 @atom:cc @atom:h5 - @bond:cc-ha @atom:cc @atom:ha - @bond:c-cl @atom:c @atom:cl - @bond:cc-n2 @atom:cc @atom:n2 - @bond:cc-n @atom:cc @atom:n - @bond:cc-n4 @atom:cc @atom:n4 - @bond:cc-na @atom:cc @atom:na - @bond:cc-nc @atom:cc @atom:nc - @bond:cc-nd @atom:cc @atom:nd - @bond:cc-ne @atom:cc @atom:ne - @bond:cc-nf @atom:cc @atom:nf - @bond:cc-nh @atom:cc @atom:nh - @bond:cc-no @atom:cc @atom:no - @bond:cc-oh @atom:cc @atom:oh - @bond:cc-os @atom:cc @atom:os - @bond:cc-pd @atom:cc @atom:pd - @bond:cc-sh @atom:cc @atom:sh - @bond:cc-ss @atom:cc @atom:ss - @bond:cc-sx @atom:cc @atom:sx - @bond:cc-sy @atom:cc @atom:sy - @bond:c-cu @atom:c @atom:cu - @bond:c-cx @atom:c @atom:cx - @bond:c-cy @atom:c @atom:cy - @bond:cd-cd @atom:cd @atom:cd - @bond:cd-ce @atom:cd @atom:ce - @bond:cd-cf @atom:cd @atom:cf - @bond:cd-cg @atom:cd @atom:cg - @bond:cd-ch @atom:cd @atom:ch - @bond:cd-cl @atom:cd @atom:cl - @bond:cd-cx @atom:cd @atom:cx - @bond:cd-cy @atom:cd @atom:cy - @bond:cd-h4 @atom:cd @atom:h4 - @bond:cd-h5 @atom:cd @atom:h5 - @bond:cd-ha @atom:cd @atom:ha - @bond:cd-n2 @atom:cd @atom:n2 - @bond:cd-n @atom:cd @atom:n - @bond:cd-na @atom:cd @atom:na - @bond:cd-nc @atom:cd @atom:nc - @bond:cd-nd @atom:cd @atom:nd - @bond:cd-ne @atom:cd @atom:ne - @bond:cd-nh @atom:cd @atom:nh - @bond:cd-oh @atom:cd @atom:oh - @bond:cd-os @atom:cd @atom:os - @bond:cd-pc @atom:cd @atom:pc - @bond:cd-ss @atom:cd @atom:ss - @bond:cd-sy @atom:cd @atom:sy - @bond:ce-ce @atom:ce @atom:ce - @bond:ce-cf @atom:ce @atom:cf - @bond:ce-cg @atom:ce @atom:cg - @bond:ce-ch @atom:ce @atom:ch - @bond:ce-cl @atom:ce @atom:cl - @bond:ce-cx @atom:ce @atom:cx - @bond:ce-cy @atom:ce @atom:cy - @bond:ce-h4 @atom:ce @atom:h4 - @bond:ce-ha @atom:ce @atom:ha - @bond:ce-n1 @atom:ce @atom:n1 - @bond:ce-n2 @atom:ce @atom:n2 - @bond:ce-n @atom:ce @atom:n - @bond:ce-na @atom:ce @atom:na - @bond:ce-ne @atom:ce @atom:ne - @bond:ce-nf @atom:ce @atom:nf - @bond:ce-nh @atom:ce @atom:nh - @bond:ce-oh @atom:ce @atom:oh - @bond:ce-os @atom:ce @atom:os - @bond:ce-p2 @atom:ce @atom:p2 - @bond:ce-pe @atom:ce @atom:pe - @bond:ce-px @atom:ce @atom:px - @bond:ce-py @atom:ce @atom:py - @bond:ce-s @atom:ce @atom:s - @bond:ce-ss @atom:ce @atom:ss - @bond:ce-sx @atom:ce @atom:sx - @bond:ce-sy @atom:ce @atom:sy - @bond:c-f @atom:c @atom:f - @bond:cf-cf @atom:cf @atom:cf - @bond:cf-cg @atom:cf @atom:cg - @bond:cf-ch @atom:cf @atom:ch - @bond:cf-h4 @atom:cf @atom:h4 - @bond:cf-ha @atom:cf @atom:ha - @bond:cf-n1 @atom:cf @atom:n1 - @bond:cf-n2 @atom:cf @atom:n2 - @bond:cf-n @atom:cf @atom:n - @bond:cf-ne @atom:cf @atom:ne - @bond:cf-nf @atom:cf @atom:nf - @bond:cf-nh @atom:cf @atom:nh - @bond:cf-oh @atom:cf @atom:oh - @bond:cf-os @atom:cf @atom:os - @bond:cf-p2 @atom:cf @atom:p2 - @bond:cf-pf @atom:cf @atom:pf - @bond:cf-px @atom:cf @atom:px - @bond:cf-py @atom:cf @atom:py - @bond:cf-s @atom:cf @atom:s - @bond:cf-sx @atom:cf @atom:sx - @bond:cf-sy @atom:cf @atom:sy - @bond:cg-cg @atom:cg @atom:cg - @bond:cg-ch @atom:cg @atom:ch - @bond:cg-n1 @atom:cg @atom:n1 - @bond:cg-ne @atom:cg @atom:ne - @bond:cg-pe @atom:cg @atom:pe - @bond:c-h4 @atom:c @atom:h4 - @bond:c-h5 @atom:c @atom:h5 - @bond:c-ha @atom:c @atom:ha - @bond:ch-ch @atom:ch @atom:ch - @bond:ch-n1 @atom:ch @atom:n1 - @bond:ch-nf @atom:ch @atom:nf - @bond:ch-pf @atom:ch @atom:pf - @bond:c-i @atom:c @atom:i - @bond:cl-cl @atom:cl @atom:cl - @bond:cl-cx @atom:cl @atom:cx - @bond:cl-cy @atom:cl @atom:cy - @bond:cl-f @atom:cl @atom:f - @bond:cl-i @atom:cl @atom:i - @bond:cl-n1 @atom:cl @atom:n1 - @bond:cl-n2 @atom:cl @atom:n2 - @bond:cl-n3 @atom:cl @atom:n3 - @bond:cl-n @atom:cl @atom:n - @bond:cl-n4 @atom:cl @atom:n4 - @bond:cl-na @atom:cl @atom:na - @bond:cl-nh @atom:cl @atom:nh - @bond:cl-no @atom:cl @atom:no - @bond:cl-o @atom:cl @atom:o - @bond:cl-oh @atom:cl @atom:oh - @bond:cl-os @atom:cl @atom:os - @bond:cl-p2 @atom:cl @atom:p2 - @bond:cl-p3 @atom:cl @atom:p3 - @bond:cl-p4 @atom:cl @atom:p4 - @bond:cl-p5 @atom:cl @atom:p5 - @bond:cl-pb @atom:cl @atom:pb - @bond:cl-s @atom:cl @atom:s - @bond:cl-s2 @atom:cl @atom:s2 - @bond:cl-s4 @atom:cl @atom:s4 - @bond:cl-s6 @atom:cl @atom:s6 - @bond:cl-sh @atom:cl @atom:sh - @bond:cl-ss @atom:cl @atom:ss - @bond:cl-sx @atom:cl @atom:sx - @bond:cl-sy @atom:cl @atom:sy - @bond:c-n2 @atom:c @atom:n2 - @bond:c-n4 @atom:c @atom:n4 - @bond:c-n @atom:c @atom:n - @bond:c-nc @atom:c @atom:nc - @bond:c-nd @atom:c @atom:nd - @bond:c-ne @atom:c @atom:ne - @bond:c-nf @atom:c @atom:nf - @bond:c-no @atom:c @atom:no - @bond:c-o @atom:c @atom:o - @bond:c-oh @atom:c @atom:oh - @bond:c-os @atom:c @atom:os - @bond:c-p2 @atom:c @atom:p2 - @bond:c-p3 @atom:c @atom:p3 - @bond:c-p4 @atom:c @atom:p4 - @bond:c-p5 @atom:c @atom:p5 - @bond:cp-cp @atom:cp @atom:cp - @bond:cp-cq @atom:cp @atom:cq - @bond:c-pe @atom:c @atom:pe - @bond:c-pf @atom:c @atom:pf - @bond:cp-na @atom:cp @atom:na - @bond:cp-nb @atom:cp @atom:nb - @bond:c-px @atom:c @atom:px - @bond:c-py @atom:c @atom:py - @bond:cq-cq @atom:cq @atom:cq - @bond:c-s @atom:c @atom:s - @bond:c-s4 @atom:c @atom:s4 - @bond:c-s6 @atom:c @atom:s6 - @bond:c-sh @atom:c @atom:sh - @bond:c-ss @atom:c @atom:ss - @bond:c-sx @atom:c @atom:sx - @bond:c-sy @atom:c @atom:sy - @bond:cu-cu @atom:cu @atom:cu - @bond:cu-cx @atom:cu @atom:cx - @bond:cu-ha @atom:cu @atom:ha - @bond:cv-cv @atom:cv @atom:cv - @bond:cv-cy @atom:cv @atom:cy - @bond:cv-ha @atom:cv @atom:ha - @bond:cx-cv @atom:cx @atom:cv - @bond:cx-cx @atom:cx @atom:cx - @bond:cx-cy @atom:cx @atom:cy - @bond:cx-f @atom:cx @atom:f - @bond:cx-h1 @atom:cx @atom:h1 - @bond:cx-h2 @atom:cx @atom:h2 - @bond:cx-hc @atom:cx @atom:hc - @bond:cx-hx @atom:cx @atom:hx - @bond:cx-n2 @atom:cx @atom:n2 - @bond:cx-n3 @atom:cx @atom:n3 - @bond:cx-n @atom:cx @atom:n - @bond:cx-na @atom:cx @atom:na - @bond:cx-nh @atom:cx @atom:nh - @bond:cx-oh @atom:cx @atom:oh - @bond:cx-os @atom:cx @atom:os - @bond:cx-p3 @atom:cx @atom:p3 - @bond:cx-s4 @atom:cx @atom:s4 - @bond:cx-s6 @atom:cx @atom:s6 - @bond:cx-ss @atom:cx @atom:ss - @bond:cy-cy @atom:cy @atom:cy - @bond:cy-f @atom:cy @atom:f - @bond:cy-h1 @atom:cy @atom:h1 - @bond:cy-h2 @atom:cy @atom:h2 - @bond:cy-hc @atom:cy @atom:hc - @bond:cy-n @atom:cy @atom:n - @bond:cy-n3 @atom:cy @atom:n3 - @bond:cy-oh @atom:cy @atom:oh - @bond:cy-os @atom:cy @atom:os - @bond:cy-s6 @atom:cy @atom:s6 - @bond:cy-ss @atom:cy @atom:ss - @bond:cz-nh @atom:cz @atom:nh - @bond:f-n1 @atom:f @atom:n1 - @bond:f-n2 @atom:f @atom:n2 - @bond:f-n3 @atom:f @atom:n3 - @bond:f-n @atom:f @atom:n - @bond:f-n4 @atom:f @atom:n4 - @bond:f-na @atom:f @atom:na - @bond:f-nh @atom:f @atom:nh - @bond:f-no @atom:f @atom:no - @bond:f-o @atom:f @atom:o - @bond:f-oh @atom:f @atom:oh - @bond:f-os @atom:f @atom:os - @bond:f-p2 @atom:f @atom:p2 - @bond:f-p3 @atom:f @atom:p3 - @bond:f-p4 @atom:f @atom:p4 - @bond:f-p5 @atom:f @atom:p5 - @bond:f-s2 @atom:f @atom:s2 - @bond:f-s @atom:f @atom:s - @bond:f-s4 @atom:f @atom:s4 - @bond:f-s6 @atom:f @atom:s6 - @bond:f-sh @atom:f @atom:sh - @bond:f-ss @atom:f @atom:ss - @bond:hn-n1 @atom:hn @atom:n1 - @bond:hn-n2 @atom:hn @atom:n2 - @bond:hn-n3 @atom:hn @atom:n3 - @bond:hn-n @atom:hn @atom:n - @bond:hn-n4 @atom:hn @atom:n4 - @bond:hn-na @atom:hn @atom:na - @bond:hn-nh @atom:hn @atom:nh - @bond:hn-no @atom:hn @atom:no - @bond:ho-o @atom:ho @atom:o - @bond:ho-oh @atom:ho @atom:oh - @bond:hp-p2 @atom:hp @atom:p2 - @bond:hp-p3 @atom:hp @atom:p3 - @bond:hp-p4 @atom:hp @atom:p4 - @bond:hp-p5 @atom:hp @atom:p5 - @bond:hs-s @atom:hs @atom:s - @bond:hs-s4 @atom:hs @atom:s4 - @bond:hs-s6 @atom:hs @atom:s6 - @bond:hs-sh @atom:hs @atom:sh - @bond:i-i @atom:i @atom:i - @bond:i-n1 @atom:i @atom:n1 - @bond:i-n2 @atom:i @atom:n2 - @bond:i-n @atom:i @atom:n - @bond:i-n3 @atom:i @atom:n3 - @bond:i-n4 @atom:i @atom:n4 - @bond:i-na @atom:i @atom:na - @bond:i-nh @atom:i @atom:nh - @bond:i-no @atom:i @atom:no - @bond:i-o @atom:i @atom:o - @bond:i-oh @atom:i @atom:oh - @bond:i-os @atom:i @atom:os - @bond:i-p2 @atom:i @atom:p2 - @bond:i-p3 @atom:i @atom:p3 - @bond:i-p4 @atom:i @atom:p4 - @bond:i-p5 @atom:i @atom:p5 - @bond:i-s @atom:i @atom:s - @bond:i-s4 @atom:i @atom:s4 - @bond:i-s6 @atom:i @atom:s6 - @bond:i-sh @atom:i @atom:sh - @bond:i-ss @atom:i @atom:ss - @bond:n1-n1 @atom:n1 @atom:n1 - @bond:n1-n2 @atom:n1 @atom:n2 - @bond:n1-n3 @atom:n1 @atom:n3 - @bond:n1-n4 @atom:n1 @atom:n4 - @bond:n1-na @atom:n1 @atom:na - @bond:n1-nc @atom:n1 @atom:nc - @bond:n1-nd @atom:n1 @atom:nd - @bond:n1-ne @atom:n1 @atom:ne - @bond:n1-nf @atom:n1 @atom:nf - @bond:n1-nh @atom:n1 @atom:nh - @bond:n1-no @atom:n1 @atom:no - @bond:n1-o @atom:n1 @atom:o - @bond:n1-oh @atom:n1 @atom:oh - @bond:n1-os @atom:n1 @atom:os - @bond:n1-p2 @atom:n1 @atom:p2 - @bond:n1-p3 @atom:n1 @atom:p3 - @bond:n1-p4 @atom:n1 @atom:p4 - @bond:n1-p5 @atom:n1 @atom:p5 - @bond:n1-s2 @atom:n1 @atom:s2 - @bond:n1-s @atom:n1 @atom:s - @bond:n1-s4 @atom:n1 @atom:s4 - @bond:n1-s6 @atom:n1 @atom:s6 - @bond:n1-sh @atom:n1 @atom:sh - @bond:n1-ss @atom:n1 @atom:ss - @bond:n2-n2 @atom:n2 @atom:n2 - @bond:n2-n3 @atom:n2 @atom:n3 - @bond:n2-n4 @atom:n2 @atom:n4 - @bond:n2-na @atom:n2 @atom:na - @bond:n2-nc @atom:n2 @atom:nc - @bond:n2-nd @atom:n2 @atom:nd - @bond:n2-ne @atom:n2 @atom:ne - @bond:n2-nf @atom:n2 @atom:nf - @bond:n2-nh @atom:n2 @atom:nh - @bond:n2-no @atom:n2 @atom:no - @bond:n2-o @atom:n2 @atom:o - @bond:n2-oh @atom:n2 @atom:oh - @bond:n2-os @atom:n2 @atom:os - @bond:n2-p2 @atom:n2 @atom:p2 - @bond:n2-p3 @atom:n2 @atom:p3 - @bond:n2-p4 @atom:n2 @atom:p4 - @bond:n2-p5 @atom:n2 @atom:p5 - @bond:n2-pe @atom:n2 @atom:pe - @bond:n2-pf @atom:n2 @atom:pf - @bond:n2-s2 @atom:n2 @atom:s2 - @bond:n2-s4 @atom:n2 @atom:s4 - @bond:n2-s @atom:n2 @atom:s - @bond:n2-s6 @atom:n2 @atom:s6 - @bond:n2-sh @atom:n2 @atom:sh - @bond:n2-ss @atom:n2 @atom:ss - @bond:n3-n3 @atom:n3 @atom:n3 - @bond:n3-n4 @atom:n3 @atom:n4 - @bond:n3-na @atom:n3 @atom:na - @bond:n3-nh @atom:n3 @atom:nh - @bond:n3-no @atom:n3 @atom:no - @bond:n3-o @atom:n3 @atom:o - @bond:n3-oh @atom:n3 @atom:oh - @bond:n3-os @atom:n3 @atom:os - @bond:n3-p2 @atom:n3 @atom:p2 - @bond:n3-p3 @atom:n3 @atom:p3 - @bond:n3-p4 @atom:n3 @atom:p4 - @bond:n3-p5 @atom:n3 @atom:p5 - @bond:n3-py @atom:n3 @atom:py - @bond:n3-s @atom:n3 @atom:s - @bond:n3-s4 @atom:n3 @atom:s4 - @bond:n3-s6 @atom:n3 @atom:s6 - @bond:n3-sh @atom:n3 @atom:sh - @bond:n3-ss @atom:n3 @atom:ss - @bond:n3-sy @atom:n3 @atom:sy - @bond:n4-n4 @atom:n4 @atom:n4 - @bond:n4-na @atom:n4 @atom:na - @bond:n4-nh @atom:n4 @atom:nh - @bond:n4-no @atom:n4 @atom:no - @bond:n4-o @atom:n4 @atom:o - @bond:n4-oh @atom:n4 @atom:oh - @bond:n4-os @atom:n4 @atom:os - @bond:n4-p2 @atom:n4 @atom:p2 - @bond:n4-p3 @atom:n4 @atom:p3 - @bond:n4-p4 @atom:n4 @atom:p4 - @bond:n4-p5 @atom:n4 @atom:p5 - @bond:n4-py @atom:n4 @atom:py - @bond:n4-s @atom:n4 @atom:s - @bond:n4-s4 @atom:n4 @atom:s4 - @bond:n4-s6 @atom:n4 @atom:s6 - @bond:n4-sh @atom:n4 @atom:sh - @bond:n4-ss @atom:n4 @atom:ss - @bond:na-na @atom:na @atom:na - @bond:na-nb @atom:na @atom:nb - @bond:na-nc @atom:na @atom:nc - @bond:na-nd @atom:na @atom:nd - @bond:na-nh @atom:na @atom:nh - @bond:na-no @atom:na @atom:no - @bond:na-o @atom:na @atom:o - @bond:na-oh @atom:na @atom:oh - @bond:na-os @atom:na @atom:os - @bond:na-p2 @atom:na @atom:p2 - @bond:na-p3 @atom:na @atom:p3 - @bond:na-p4 @atom:na @atom:p4 - @bond:na-p5 @atom:na @atom:p5 - @bond:na-pc @atom:na @atom:pc - @bond:na-pd @atom:na @atom:pd - @bond:na-py @atom:na @atom:py - @bond:na-s @atom:na @atom:s - @bond:na-s4 @atom:na @atom:s4 - @bond:na-s6 @atom:na @atom:s6 - @bond:na-sh @atom:na @atom:sh - @bond:na-ss @atom:na @atom:ss - @bond:na-sy @atom:na @atom:sy - @bond:nb-nb @atom:nb @atom:nb - @bond:nb-pb @atom:nb @atom:pb - @bond:nc-nc @atom:nc @atom:nc - @bond:nc-nd @atom:nc @atom:nd - @bond:nc-os @atom:nc @atom:os - @bond:nc-ss @atom:nc @atom:ss - @bond:nc-sy @atom:nc @atom:sy - @bond:nd-nd @atom:nd @atom:nd - @bond:nd-os @atom:nd @atom:os - @bond:nd-ss @atom:nd @atom:ss - @bond:nd-sy @atom:nd @atom:sy - @bond:ne-ne @atom:ne @atom:ne - @bond:ne-nf @atom:ne @atom:nf - @bond:ne-o @atom:ne @atom:o - @bond:ne-p2 @atom:ne @atom:p2 - @bond:ne-pe @atom:ne @atom:pe - @bond:ne-px @atom:ne @atom:px - @bond:ne-py @atom:ne @atom:py - @bond:ne-s @atom:ne @atom:s - @bond:ne-sx @atom:ne @atom:sx - @bond:ne-sy @atom:ne @atom:sy - @bond:nf-nf @atom:nf @atom:nf - @bond:nf-o @atom:nf @atom:o - @bond:nf-p2 @atom:nf @atom:p2 - @bond:nf-pf @atom:nf @atom:pf - @bond:nf-px @atom:nf @atom:px - @bond:nf-py @atom:nf @atom:py - @bond:nf-s @atom:nf @atom:s - @bond:nf-sx @atom:nf @atom:sx - @bond:nf-sy @atom:nf @atom:sy - @bond:nh-nh @atom:nh @atom:nh - @bond:nh-no @atom:nh @atom:no - @bond:nh-o @atom:nh @atom:o - @bond:nh-oh @atom:nh @atom:oh - @bond:nh-os @atom:nh @atom:os - @bond:nh-p2 @atom:nh @atom:p2 - @bond:nh-p3 @atom:nh @atom:p3 - @bond:nh-p4 @atom:nh @atom:p4 - @bond:nh-p5 @atom:nh @atom:p5 - @bond:nh-s @atom:nh @atom:s - @bond:nh-s4 @atom:nh @atom:s4 - @bond:nh-s6 @atom:nh @atom:s6 - @bond:nh-sh @atom:nh @atom:sh - @bond:nh-ss @atom:nh @atom:ss - @bond:nh-sy @atom:nh @atom:sy - @bond:n-n1 @atom:n @atom:n1 - @bond:n-n2 @atom:n @atom:n2 - @bond:n-n3 @atom:n @atom:n3 - @bond:n-n4 @atom:n @atom:n4 - @bond:n-n @atom:n @atom:n - @bond:n-na @atom:n @atom:na - @bond:n-nc @atom:n @atom:nc - @bond:n-nd @atom:n @atom:nd - @bond:n-nh @atom:n @atom:nh - @bond:n-no @atom:n @atom:no - @bond:n-o @atom:n @atom:o - @bond:n-oh @atom:n @atom:oh - @bond:no-no @atom:no @atom:no - @bond:no-o @atom:no @atom:o - @bond:no-oh @atom:no @atom:oh - @bond:no-os @atom:no @atom:os - @bond:no-p2 @atom:no @atom:p2 - @bond:no-p3 @atom:no @atom:p3 - @bond:no-p4 @atom:no @atom:p4 - @bond:no-p5 @atom:no @atom:p5 - @bond:no-s @atom:no @atom:s - @bond:n-os @atom:n @atom:os - @bond:no-s4 @atom:no @atom:s4 - @bond:no-s6 @atom:no @atom:s6 - @bond:no-sh @atom:no @atom:sh - @bond:no-ss @atom:no @atom:ss - @bond:n-p2 @atom:n @atom:p2 - @bond:n-p3 @atom:n @atom:p3 - @bond:n-p4 @atom:n @atom:p4 - @bond:n-p5 @atom:n @atom:p5 - @bond:n-pc @atom:n @atom:pc - @bond:n-pd @atom:n @atom:pd - @bond:n-s @atom:n @atom:s - @bond:n-s4 @atom:n @atom:s4 - @bond:n-s6 @atom:n @atom:s6 - @bond:n-sh @atom:n @atom:sh - @bond:n-ss @atom:n @atom:ss - @bond:n-sy @atom:n @atom:sy - @bond:oh-oh @atom:oh @atom:oh - @bond:oh-os @atom:oh @atom:os - @bond:oh-p2 @atom:oh @atom:p2 - @bond:oh-p3 @atom:oh @atom:p3 - @bond:oh-p4 @atom:oh @atom:p4 - @bond:oh-p5 @atom:oh @atom:p5 - @bond:oh-py @atom:oh @atom:py - @bond:oh-s @atom:oh @atom:s - @bond:oh-s4 @atom:oh @atom:s4 - @bond:oh-s6 @atom:oh @atom:s6 - @bond:oh-sh @atom:oh @atom:sh - @bond:oh-ss @atom:oh @atom:ss - @bond:oh-sy @atom:oh @atom:sy - @bond:o-o @atom:o @atom:o - @bond:o-oh @atom:o @atom:oh - @bond:o-os @atom:o @atom:os - @bond:o-p2 @atom:o @atom:p2 - @bond:o-p3 @atom:o @atom:p3 - @bond:o-p4 @atom:o @atom:p4 - @bond:o-p5 @atom:o @atom:p5 - @bond:o-pe @atom:o @atom:pe - @bond:o-pf @atom:o @atom:pf - @bond:o-px @atom:o @atom:px - @bond:o-py @atom:o @atom:py - @bond:o-s @atom:o @atom:s - @bond:o-s2 @atom:o @atom:s2 - @bond:o-s4 @atom:o @atom:s4 - @bond:o-s6 @atom:o @atom:s6 - @bond:o-sh @atom:o @atom:sh - @bond:os-os @atom:os @atom:os - @bond:os-p2 @atom:os @atom:p2 - @bond:os-p3 @atom:os @atom:p3 - @bond:os-p4 @atom:os @atom:p4 - @bond:os-p5 @atom:os @atom:p5 - @bond:os-py @atom:os @atom:py - @bond:os-s @atom:os @atom:s - @bond:o-ss @atom:o @atom:ss - @bond:os-s4 @atom:os @atom:s4 - @bond:os-s6 @atom:os @atom:s6 - @bond:os-sh @atom:os @atom:sh - @bond:os-ss @atom:os @atom:ss - @bond:os-sy @atom:os @atom:sy - @bond:o-sx @atom:o @atom:sx - @bond:o-sy @atom:o @atom:sy - @bond:p2-p2 @atom:p2 @atom:p2 - @bond:p2-p3 @atom:p2 @atom:p3 - @bond:p2-p4 @atom:p2 @atom:p4 - @bond:p2-p5 @atom:p2 @atom:p5 - @bond:p2-pe @atom:p2 @atom:pe - @bond:p2-pf @atom:p2 @atom:pf - @bond:p2-s @atom:p2 @atom:s - @bond:p2-s4 @atom:p2 @atom:s4 - @bond:p2-s6 @atom:p2 @atom:s6 - @bond:p2-sh @atom:p2 @atom:sh - @bond:p2-ss @atom:p2 @atom:ss - @bond:p3-p3 @atom:p3 @atom:p3 - @bond:p3-p4 @atom:p3 @atom:p4 - @bond:p3-p5 @atom:p3 @atom:p5 - @bond:p3-s @atom:p3 @atom:s - @bond:p3-s4 @atom:p3 @atom:s4 - @bond:p3-s6 @atom:p3 @atom:s6 - @bond:p3-sh @atom:p3 @atom:sh - @bond:p3-ss @atom:p3 @atom:ss - @bond:p4-p4 @atom:p4 @atom:p4 - @bond:p4-p5 @atom:p4 @atom:p5 - @bond:p4-s @atom:p4 @atom:s - @bond:p4-s4 @atom:p4 @atom:s4 - @bond:p4-s6 @atom:p4 @atom:s6 - @bond:p4-sh @atom:p4 @atom:sh - @bond:p4-ss @atom:p4 @atom:ss - @bond:p5-p5 @atom:p5 @atom:p5 - @bond:p5-s @atom:p5 @atom:s - @bond:p5-s4 @atom:p5 @atom:s4 - @bond:p5-s6 @atom:p5 @atom:s6 - @bond:p5-sh @atom:p5 @atom:sh - @bond:p5-ss @atom:p5 @atom:ss - @bond:pe-pe @atom:pe @atom:pe - @bond:pe-pf @atom:pe @atom:pf - @bond:pe-px @atom:pe @atom:px - @bond:pe-py @atom:pe @atom:py - @bond:pe-s @atom:pe @atom:s - @bond:pe-sx @atom:pe @atom:sx - @bond:pe-sy @atom:pe @atom:sy - @bond:pf-pf @atom:pf @atom:pf - @bond:pf-px @atom:pf @atom:px - @bond:pf-py @atom:pf @atom:py - @bond:pf-s @atom:pf @atom:s - @bond:pf-sx @atom:pf @atom:sx - @bond:pf-sy @atom:pf @atom:sy - @bond:px-py @atom:px @atom:py - @bond:px-sx @atom:px @atom:sx - @bond:px-sy @atom:px @atom:sy - @bond:py-py @atom:py @atom:py - @bond:py-sx @atom:py @atom:sx - @bond:py-sy @atom:py @atom:sy - @bond:s4-s4 @atom:s4 @atom:s4 - @bond:s4-s6 @atom:s4 @atom:s6 - @bond:s4-sh @atom:s4 @atom:sh - @bond:s4-ss @atom:s4 @atom:ss - @bond:s6-s6 @atom:s6 @atom:s6 - @bond:s6-sh @atom:s6 @atom:sh - @bond:s6-ss @atom:s6 @atom:ss - @bond:sh-sh @atom:sh @atom:sh - @bond:sh-ss @atom:sh @atom:ss - @bond:s-s @atom:s @atom:s - @bond:s-s2 @atom:s @atom:s2 - @bond:s-s4 @atom:s @atom:s4 - @bond:s-s6 @atom:s @atom:s6 - @bond:s-sh @atom:s @atom:sh - @bond:s-ss @atom:s @atom:ss - @bond:ss-ss @atom:ss @atom:ss - @bond:sx-sx @atom:sx @atom:sx - @bond:sx-sy @atom:sx @atom:sy - @bond:sy-sy @atom:sy @atom:sy - @bond:br-cd @atom:br @atom:cd - @bond:c1-cf @atom:c1 @atom:cf - @bond:cd-f @atom:cd @atom:f - @bond:cd-n4 @atom:cd @atom:n4 - @bond:cd-nf @atom:cd @atom:nf - @bond:cd-no @atom:cd @atom:no - @bond:cd-sh @atom:cd @atom:sh - @bond:cd-sx @atom:cd @atom:sx - @bond:cc-cy @atom:cc @atom:cy - @bond:cf-cl @atom:cf @atom:cl - @bond:cf-cx @atom:cf @atom:cx - @bond:cf-cy @atom:cf @atom:cy - @bond:cf-na @atom:cf @atom:na - @bond:cf-ss @atom:cf @atom:ss - @bond:cq-na @atom:cq @atom:na - @bond:cq-nb @atom:cq @atom:nb - } # (end of Bonds By Type) - - write_once("In Settings") { - angle_coeff @angle:hw-ow-hw harmonic 100.00 104.52 # AMBER 1 TIP3P_water - angle_coeff @angle:hw-hw-ow harmonic 0.00 127.74 # AMBER 1 (found_in_crystallographic_water_with_3_bonds) - angle_coeff @angle:br-c1-br harmonic 57.76 180.00 # Guess 0 - angle_coeff @angle:br-c1-c1 harmonic 54.93 180.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-c1 harmonic 64.41 180.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-c2 harmonic 60.84 180.00 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-c1-c3 harmonic 56.28 178.46 # SOURCE4 188 0.6631 - angle_coeff @angle:c1-c1-ca harmonic 56.92 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-cl harmonic 51.40 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-f harmonic 61.02 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-ha harmonic 44.84 178.38 # SOURCE3 41 2.0683 - angle_coeff @angle:c1-c1-hc harmonic 44.73 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-i harmonic 49.80 180.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-n1 harmonic 67.17 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-n2 harmonic 65.17 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-n3 harmonic 59.77 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-n4 harmonic 59.09 179.56 # SOURCE3 3 0.3096 - angle_coeff @angle:c1-c1-n harmonic 62.13 177.18 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-na harmonic 61.23 176.75 # SOURCE3 8 2.9328 - angle_coeff @angle:c1-c1-nh harmonic 61.44 179.27 # SOURCE3 3 0.2357 - angle_coeff @angle:c1-c1-no harmonic 59.38 180.00 # SOURCE3 3 0.0000 - angle_coeff @angle:c1-c1-o harmonic 66.79 180.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-oh harmonic 62.70 176.65 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-os harmonic 62.77 176.42 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-c1-p2 harmonic 65.19 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-p3 harmonic 66.41 169.63 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-c1-p4 harmonic 64.47 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-p5 harmonic 66.52 176.17 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-c1-s4 harmonic 54.12 167.47 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-c1-s6 harmonic 53.74 174.38 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-c1-s harmonic 55.65 179.97 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c1-sh harmonic 54.14 180.00 # SOURCE3 1 - angle_coeff @angle:c1-c1-ss harmonic 55.22 173.22 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-c1-c2 harmonic 58.20 180.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-c1-ce harmonic 58.18 179.01 # SOURCE4 6 0.4656 - angle_coeff @angle:c2-c1-n1 harmonic 63.14 180.00 # HF/6-31G* 1 - angle_coeff @angle:c2-c1-o harmonic 63.07 179.50 # SOURCE2 1 0.0000 - angle_coeff @angle:c2-c1-s2 harmonic 56.73 172.98 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-c1-c3 harmonic 51.75 180.00 # Guess 0 - angle_coeff @angle:c3-c1-cg harmonic 55.79 178.52 # SOURCE4 39 0.5063 - angle_coeff @angle:c3-c1-n1 harmonic 58.10 178.50 # SOURCE4 77 0.5443 - angle_coeff @angle:ca-c1-ca harmonic 52.83 180.00 # Guess 0 - angle_coeff @angle:c-c1-c1 harmonic 56.33 180.00 # SOURCE3 1 - angle_coeff @angle:cg-c1-ha harmonic 43.98 177.41 # SOURCE3 22 2.4947 - angle_coeff @angle:ch-c1-ha harmonic 43.98 177.41 # SOURCE3 22 same_as_cg-c1-ha - angle_coeff @angle:cl-c1-cl harmonic 46.64 180.00 # Guess 0 - angle_coeff @angle:f-c1-f harmonic 58.19 180.00 # Guess 0 - angle_coeff @angle:i-c1-i harmonic 53.41 180.00 # Guess 0 - angle_coeff @angle:n1-c1-n1 harmonic 93.20 102.01 # SOURCE3 1 - angle_coeff @angle:n1-c1-n3 harmonic 63.71 169.70 # SOURCE2 1 0.0000 - angle_coeff @angle:n1-c1-nh harmonic 64.02 177.43 # SOURCE4 7 0.7877 - angle_coeff @angle:n1-c1-os harmonic 64.72 178.59 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-c1-p3 harmonic 67.69 171.20 # SOURCE2 1 0.0000 - angle_coeff @angle:n1-c1-ss harmonic 55.82 178.68 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-c1-n2 harmonic 65.99 180.00 # Guess 0 - angle_coeff @angle:n2-c1-o harmonic 69.15 171.79 # SOURCE3 2 0.3594 - angle_coeff @angle:n2-c1-s harmonic 57.48 176.01 # SOURCE4 9 0.1123 - angle_coeff @angle:n3-c1-n3 harmonic 57.36 180.00 # Guess 0 - angle_coeff @angle:n4-c1-n4 harmonic 56.35 180.00 # Guess 0 - angle_coeff @angle:na-c1-na harmonic 58.62 180.00 # Guess 0 - angle_coeff @angle:ne-c1-o harmonic 69.39 172.33 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-c1-s harmonic 57.59 175.81 # SOURCE4 8 0.2356 - angle_coeff @angle:nf-c1-o harmonic 69.39 172.33 # SOURCE3 1 same_as_ne-c1-o - angle_coeff @angle:nh-c1-nh harmonic 59.55 180.00 # Guess 0 - angle_coeff @angle:n-c1-n harmonic 60.03 180.00 # Guess 0 - angle_coeff @angle:no-c1-no harmonic 56.83 180.00 # Guess 0 - angle_coeff @angle:oh-c1-oh harmonic 60.91 180.00 # Guess 0 - angle_coeff @angle:o-c1-o harmonic 69.27 180.00 # Guess 0 - angle_coeff @angle:os-c1-os harmonic 60.96 180.00 # Guess 0 - angle_coeff @angle:p2-c1-p2 harmonic 80.59 180.00 # Guess 0 - angle_coeff @angle:p3-c1-p3 harmonic 79.69 180.00 # Guess 0 - angle_coeff @angle:p4-c1-p4 harmonic 79.69 180.00 # Guess 0 - angle_coeff @angle:p5-c1-p5 harmonic 81.37 180.00 # Guess 0 - angle_coeff @angle:s2-c1-s2 harmonic 55.83 180.00 # Guess 0 - angle_coeff @angle:s4-c1-s4 harmonic 51.00 180.00 # Guess 0 - angle_coeff @angle:s6-c1-s6 harmonic 51.72 180.00 # Guess 0 - angle_coeff @angle:sh-c1-sh harmonic 53.01 180.00 # Guess 0 - angle_coeff @angle:s-c1-s harmonic 54.63 180.00 # Guess 0 - angle_coeff @angle:ss-c1-ss harmonic 53.04 180.00 # Guess 0 - angle_coeff @angle:br-c2-br harmonic 68.56 115.06 # SOURCE3 1 0.0000 - angle_coeff @angle:br-c2-c2 harmonic 63.97 118.96 # SOURCE4 6 0.4902 - angle_coeff @angle:br-c2-c3 harmonic 63.71 115.33 # SOURCE4 6 0.5872 - angle_coeff @angle:br-c2-ce harmonic 63.21 121.59 # SOURCE4 7 0.7078 - angle_coeff @angle:br-c2-h4 harmonic 43.04 113.94 # SOURCE4 6 0.4017 - angle_coeff @angle:br-c2-ha harmonic 43.18 113.28 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-c2-c1 harmonic 72.26 116.77 # SOURCE3 1 - angle_coeff @angle:c1-c2-c2 harmonic 70.34 121.62 # SOURCE3 1 - angle_coeff @angle:c1-c2-c3 harmonic 64.22 124.92 # SOURCE4 17 0.7576 - angle_coeff @angle:c1-c2-f harmonic 67.99 124.90 # SOURCE2 1 0.0000 - angle_coeff @angle:c1-c2-ha harmonic 50.43 121.37 # SOURCE3 8 0.0055 - angle_coeff @angle:c2-c2-c2 harmonic 69.84 121.81 # SOURCE3 10 0.3843 - angle_coeff @angle:c2-c2-c3 harmonic 64.33 123.42 # SOURCE3 41 2.6057 - angle_coeff @angle:c2-c2-ca harmonic 66.88 117.00 # SOURCE3 1 - angle_coeff @angle:c2-c2-cc harmonic 70.22 117.21 # SOURCE3 2 0.3418 - angle_coeff @angle:c2-c2-cd harmonic 70.22 117.21 # SOURCE3 2 same_as_c2-c2-cc - angle_coeff @angle:c2-c2-cl harmonic 58.43 122.85 # SOURCE4 23 0.6711 - angle_coeff @angle:c2-c2-cx harmonic 64.50 125.40 # SOURCE4 12 1.8494 - angle_coeff @angle:c2-c2-cy harmonic 70.42 103.30 # SOURCE2 1 0.0000 - angle_coeff @angle:c2-c2-f harmonic 68.11 122.92 # SOURCE4 12 0.5301 - angle_coeff @angle:c2-c2-h4 harmonic 49.75 122.54 # SOURCE4 69 1.1900 - angle_coeff @angle:c2-c2-ha harmonic 50.04 120.94 # SOURCE3 254 1.3150 - angle_coeff @angle:c2-c2-hc harmonic 50.30 119.70 # SOURCE3 1 - angle_coeff @angle:c2-c2-hx harmonic 48.98 126.45 # SOURCE3 3 0.0219 - angle_coeff @angle:c2-c2-i harmonic 56.28 121.03 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-c2-n1 harmonic 71.69 122.98 # HF/6-31G* 1 - angle_coeff @angle:c2-c2-n2 harmonic 71.29 126.01 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-c2-n3 harmonic 70.33 124.55 # SOURCE3 1 - angle_coeff @angle:c2-c2-n4 harmonic 67.18 121.52 # SOURCE3 5 1.2656 - angle_coeff @angle:c2-c2-n harmonic 68.86 123.20 # SOURCE4 15 1.8657 - angle_coeff @angle:c2-c2-na harmonic 69.83 121.38 # SOURCE3 26 6.9463 - angle_coeff @angle:c2-c2-nh harmonic 69.80 124.99 # SOURCE3 7 0.9929 - angle_coeff @angle:c2-c2-no harmonic 67.52 124.09 # SOURCE4 6 1.2772 - angle_coeff @angle:c2-c2-o harmonic 71.92 130.89 # SOURCE3 2 0.0201 - angle_coeff @angle:c2-c2-oh harmonic 71.64 122.07 # SOURCE4 6 1.0883 - angle_coeff @angle:c2-c2-os harmonic 71.04 121.89 # SOURCE4 33 1.3457 - angle_coeff @angle:c2-c2-p2 harmonic 84.73 115.10 # SOURCE3 1 - angle_coeff @angle:c2-c2-p3 harmonic 75.19 124.83 # SOURCE3 5 2.1222 - angle_coeff @angle:c2-c2-p4 harmonic 77.22 119.76 # SOURCE3 1 - angle_coeff @angle:c2-c2-p5 harmonic 73.70 125.97 # SOURCE3 1 - angle_coeff @angle:c2-c2-s4 harmonic 62.85 119.84 # SOURCE3 1 - angle_coeff @angle:c2-c2-s6 harmonic 62.81 120.01 # SOURCE3 1 - angle_coeff @angle:c2-c2-s harmonic 61.25 129.37 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-c2-sh harmonic 60.87 125.70 # SOURCE3 3 1.3390 - angle_coeff @angle:c2-c2-ss harmonic 62.79 122.86 # SOURCE4 13 1.7467 - angle_coeff @angle:c3-c2-c3 harmonic 62.70 116.52 # SOURCE3 15 3.1001 - angle_coeff @angle:c3-c2-cc harmonic 63.22 125.39 # CORR 27 - angle_coeff @angle:c3-c2-cd harmonic 63.22 125.39 # CORR 27 - angle_coeff @angle:c3-c2-ce harmonic 64.17 123.08 # CORR 1288 - angle_coeff @angle:c3-c2-cf harmonic 64.17 123.08 # CORR 1288 - angle_coeff @angle:c3-c2-h4 harmonic 45.30 119.25 # SOURCE4 22 2.1707 - angle_coeff @angle:c3-c2-ha harmonic 45.66 117.30 # SOURCE3 33 1.7453 - angle_coeff @angle:c3-c2-hc harmonic 45.15 120.00 # SOURCE3 1 - angle_coeff @angle:c3-c2-n2 harmonic 66.47 123.52 # SOURCE4 141 2.2935 - angle_coeff @angle:c3-c2-n harmonic 66.79 114.80 # SOURCE4 12 1.8112 - angle_coeff @angle:c3-c2-na harmonic 64.95 122.54 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-c2-ne harmonic 66.96 122.15 # SOURCE3 4 0.2197 - angle_coeff @angle:c3-c2-nf harmonic 66.96 122.15 # SOURCE3 4 same_as_c3-c2-ne - angle_coeff @angle:c3-c2-nh harmonic 66.69 118.59 # SOURCE3 6 2.2622 - angle_coeff @angle:c3-c2-o harmonic 67.88 123.18 # SOURCE4 5 0.9226 - angle_coeff @angle:c3-c2-oh harmonic 68.50 115.04 # SOURCE4 36 2.0110 - angle_coeff @angle:c3-c2-os harmonic 68.77 112.69 # SOURCE4 50 2.4254 - angle_coeff @angle:c3-c2-p2 harmonic 78.98 122.74 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-c2-s harmonic 62.79 115.44 # SOURCE3 2 0.0115 - angle_coeff @angle:c3-c2-ss harmonic 61.62 119.66 # SOURCE4 45 1.9732 - angle_coeff @angle:ca-c2-ca harmonic 63.51 117.88 # SOURCE3 1 - angle_coeff @angle:ca-c2-hc harmonic 45.28 123.30 # SOURCE3 1 - angle_coeff @angle:c-c2-c2 harmonic 67.93 120.70 # SOURCE3 1 - angle_coeff @angle:c-c2-c3 harmonic 63.87 119.70 # SOURCE3 1 - angle_coeff @angle:c-c2-c harmonic 66.57 118.88 # SOURCE3 1 - angle_coeff @angle:cc-c2-h4 harmonic 49.19 120.33 # SOURCE4 7 0.0865 - angle_coeff @angle:cc-c2-ha harmonic 49.07 120.76 # SOURCE3 11 1.4155 - angle_coeff @angle:cc-c2-nh harmonic 69.46 122.96 # SOURCE4 10 0.7347 - angle_coeff @angle:cc-c2-o harmonic 72.80 123.59 # SOURCE4 6 0.0560 - angle_coeff @angle:cd-c2-ha harmonic 49.07 120.76 # SOURCE3 11 1.4155 - angle_coeff @angle:ce-c2-cl harmonic 58.06 123.90 # SOURCE4 11 0.3570 - angle_coeff @angle:ce-c2-h4 harmonic 49.38 122.29 # SOURCE4 75 1.4008 - angle_coeff @angle:ce-c2-ha harmonic 49.57 121.19 # SOURCE3 122 0.5318 - angle_coeff @angle:ce-c2-na harmonic 68.82 123.71 # SOURCE4 6 2.0109 - angle_coeff @angle:ce-c2-nh harmonic 70.64 120.72 # SOURCE4 93 2.2537 - angle_coeff @angle:ce-c2-no harmonic 68.45 119.65 # SOURCE4 5 0.9817 - angle_coeff @angle:ce-c2-o harmonic 73.66 123.08 # SOURCE4 5 0.2391 - angle_coeff @angle:ce-c2-oh harmonic 70.90 123.27 # SOURCE4 42 1.8111 - angle_coeff @angle:ce-c2-os harmonic 70.47 122.52 # SOURCE4 51 2.4680 - angle_coeff @angle:cf-c2-ha harmonic 49.57 121.19 # SOURCE3 122 same_as_ce-c2-ha - angle_coeff @angle:c-c2-ha harmonic 47.67 121.33 # SOURCE3 4 0.2462 - angle_coeff @angle:c-c2-hc harmonic 48.00 119.70 # SOURCE3 1 - angle_coeff @angle:cl-c2-cl harmonic 55.44 114.27 # SOURCE4 10 0.5850 - angle_coeff @angle:cl-c2-h4 harmonic 40.76 113.77 # SOURCE4 9 0.6228 - angle_coeff @angle:cl-c2-ha harmonic 40.86 113.20 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-c2-ha harmonic 46.61 115.89 # SOURCE4 15 0.3682 - angle_coeff @angle:f-c2-f harmonic 70.67 109.60 # SOURCE2 2 0.6000 - angle_coeff @angle:f-c2-ha harmonic 51.25 110.00 # SOURCE2 1 0.0000 - angle_coeff @angle:h4-c2-n2 harmonic 52.40 120.69 # SOURCE4 13 1.3105 - angle_coeff @angle:h4-c2-n harmonic 50.48 113.57 # SOURCE4 26 1.0283 - angle_coeff @angle:h4-c2-na harmonic 51.03 113.22 # SOURCE4 9 0.6345 - angle_coeff @angle:h4-c2-ne harmonic 52.87 119.63 # SOURCE4 10 1.6786 - angle_coeff @angle:h4-c2-nh harmonic 51.55 115.64 # SOURCE4 31 1.0081 - angle_coeff @angle:h4-c2-no harmonic 49.39 113.38 # SOURCE4 6 0.1240 - angle_coeff @angle:h4-c2-os harmonic 52.23 113.70 # SOURCE3 13 2.0464 - angle_coeff @angle:h4-c2-ss harmonic 42.85 118.47 # SOURCE3 9 2.5335 - angle_coeff @angle:h5-c2-n2 harmonic 52.41 120.16 # SOURCE4 27 1.8999 - angle_coeff @angle:h5-c2-na harmonic 48.23 126.39 # SOURCE3 4 0.3299 - angle_coeff @angle:h5-c2-ne harmonic 52.76 119.62 # SOURCE4 17 1.3235 - angle_coeff @angle:h5-c2-nh harmonic 51.85 113.93 # SOURCE4 50 0.8394 - angle_coeff @angle:ha-c2-ha harmonic 38.02 117.65 # SOURCE3 349 1.3426 - angle_coeff @angle:ha-c2-n1 harmonic 51.83 120.76 # SOURCE3 8 0.6632 - angle_coeff @angle:ha-c2-n2 harmonic 52.39 120.54 # SOURCE3 92 1.4571 - angle_coeff @angle:ha-c2-n3 harmonic 52.44 113.54 # SOURCE3 1 - angle_coeff @angle:ha-c2-n harmonic 50.49 113.40 # SOURCE3 4 1.2182 - angle_coeff @angle:ha-c2-na harmonic 51.18 112.42 # SOURCE3 8 0.6507 - angle_coeff @angle:ha-c2-ne harmonic 52.48 121.18 # SOURCE3 68 0.6824 - angle_coeff @angle:ha-c2-nf harmonic 52.48 121.18 # SOURCE3 68 same_as_ha-c2-ne - angle_coeff @angle:ha-c2-nh harmonic 51.29 116.68 # SOURCE3 13 2.5734 - angle_coeff @angle:ha-c2-no harmonic 49.64 112.14 # SOURCE3 2 0.0264 - angle_coeff @angle:ha-c2-o harmonic 55.30 117.23 # SOURCE3 2 0.0201 - angle_coeff @angle:ha-c2-oh harmonic 52.34 116.18 # SOURCE3 2 0.0000 - angle_coeff @angle:ha-c2-os harmonic 52.43 112.69 # SOURCE3 13 2.5851 - angle_coeff @angle:ha-c2-p2 harmonic 55.74 121.48 # SOURCE3 122 0.4329 - angle_coeff @angle:ha-c2-p3 harmonic 52.04 114.31 # SOURCE3 3 0.0000 - angle_coeff @angle:ha-c2-p4 harmonic 51.62 117.86 # SOURCE3 1 - angle_coeff @angle:ha-c2-p5 harmonic 49.81 120.10 # SOURCE3 2 0.0000 - angle_coeff @angle:ha-c2-pe harmonic 55.05 121.46 # SOURCE3 104 0.7821 - angle_coeff @angle:ha-c2-pf harmonic 55.05 121.46 # SOURCE3 104 same_as_ha-c2-pe - angle_coeff @angle:ha-c2-s2 harmonic 46.19 118.74 # SOURCE3 2 0.0000 - angle_coeff @angle:ha-c2-s4 harmonic 42.81 115.30 # SOURCE3 2 0.0000 - angle_coeff @angle:ha-c2-s harmonic 43.42 115.70 # SOURCE3 2 0.0000 - angle_coeff @angle:ha-c2-s6 harmonic 42.58 116.60 # SOURCE3 2 0.0000 - angle_coeff @angle:ha-c2-sh harmonic 43.04 111.74 # SOURCE3 1 0.0000 - angle_coeff @angle:ha-c2-ss harmonic 43.18 116.72 # SOURCE3 7 2.7543 - angle_coeff @angle:hc-c2-hc harmonic 37.81 118.92 # SOURCE3 1 - angle_coeff @angle:hc-c2-n2 harmonic 52.42 120.40 # SOURCE3 1 - angle_coeff @angle:hc-c2-n harmonic 50.35 114.04 # SOURCE3 1 - angle_coeff @angle:hc-c2-na harmonic 49.73 119.10 # SOURCE3 1 - angle_coeff @angle:hc-c2-nh harmonic 52.03 113.36 # SOURCE3 1 - angle_coeff @angle:hc-c2-no harmonic 49.64 112.12 # SOURCE3 1 - angle_coeff @angle:hc-c2-oh harmonic 52.33 116.22 # SOURCE3 1 - angle_coeff @angle:hc-c2-os harmonic 51.65 116.11 # SOURCE3 1 - angle_coeff @angle:hc-c2-p3 harmonic 51.40 117.19 # SOURCE3 1 - angle_coeff @angle:hc-c2-p5 harmonic 49.92 119.58 # SOURCE3 1 - angle_coeff @angle:hc-c2-s4 harmonic 42.66 116.12 # SOURCE3 1 - angle_coeff @angle:hc-c2-s6 harmonic 42.79 115.45 # SOURCE3 1 - angle_coeff @angle:hc-c2-sh harmonic 42.31 115.63 # SOURCE3 1 - angle_coeff @angle:hc-c2-ss harmonic 43.38 115.62 # SOURCE3 1 - angle_coeff @angle:hx-c2-n4 harmonic 48.42 113.03 # SOURCE3 3 0.3873 - angle_coeff @angle:i-c2-i harmonic 60.96 117.94 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-c2-n1 harmonic 73.61 124.15 # HF/6-31G* 1 - angle_coeff @angle:n2-c2-n2 harmonic 77.96 113.82 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-c2-n4 harmonic 72.03 113.05 # SOURCE4 6 0.3318 - angle_coeff @angle:n2-c2-na harmonic 71.71 123.62 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-c2-nh harmonic 72.62 124.27 # SOURCE3 12 2.4114 - angle_coeff @angle:n2-c2-oh harmonic 74.36 122.08 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-c2-os harmonic 74.32 119.82 # SOURCE4 20 1.2664 - angle_coeff @angle:n2-c2-ss harmonic 62.86 129.77 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-c2-n3 harmonic 73.45 118.47 # SOURCE3 1 - angle_coeff @angle:n4-c2-n4 harmonic 67.72 113.93 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-c2-ss harmonic 64.40 116.26 # SOURCE4 7 2.4226 - angle_coeff @angle:na-c2-na harmonic 73.65 109.33 # SOURCE3 3 3.0187 - angle_coeff @angle:ne-c2-nh harmonic 73.03 123.56 # CORR 128 - angle_coeff @angle:ne-c2-os harmonic 74.86 118.76 # SOURCE4 5 0.3382 - angle_coeff @angle:ne-c2-ss harmonic 65.41 120.06 # SOURCE4 9 1.3423 - angle_coeff @angle:nf-c2-nh harmonic 73.03 123.56 # CORR 128 - angle_coeff @angle:nh-c2-nh harmonic 74.46 112.72 # SOURCE4 257 1.8176 - angle_coeff @angle:nh-c2-oh harmonic 74.05 117.16 # SOURCE4 7 0.8698 - angle_coeff @angle:nh-c2-os harmonic 74.32 114.29 # SOURCE4 18 1.0900 - angle_coeff @angle:nh-c2-ss harmonic 67.23 111.55 # SOURCE4 37 1.1778 - angle_coeff @angle:n-c2-n2 harmonic 70.56 125.95 # SOURCE3 2 5.0202 - angle_coeff @angle:n-c2-n harmonic 71.55 113.23 # SOURCE3 1 0.0000 - angle_coeff @angle:n-c2-na harmonic 74.57 105.42 # SOURCE3 1 0.0000 - angle_coeff @angle:n-c2-ne harmonic 70.89 125.38 # SOURCE4 10 1.6819 - angle_coeff @angle:n-c2-nh harmonic 74.20 109.14 # SOURCE4 22 1.5634 - angle_coeff @angle:no-c2-no harmonic 69.43 113.90 # SOURCE3 1 0.0000 - angle_coeff @angle:n-c2-ss harmonic 66.83 111.06 # SOURCE4 9 0.5522 - angle_coeff @angle:oh-c2-oh harmonic 76.03 114.33 # SOURCE3 1 0.0000 - angle_coeff @angle:o-c2-o harmonic 80.23 121.69 # SOURCE3 1 - angle_coeff @angle:o-c2-oh harmonic 76.69 121.23 # SOURCE4 6 0.0958 - angle_coeff @angle:o-c2-s harmonic 64.15 127.68 # SOURCE3 2 0.0547 - angle_coeff @angle:os-c2-os harmonic 74.21 115.80 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-c2-p2 harmonic 100.59 129.80 # SOURCE3 1 - angle_coeff @angle:p3-c2-p3 harmonic 97.08 115.54 # SOURCE3 1 0.0000 - angle_coeff @angle:p5-c2-p5 harmonic 92.92 121.85 # SOURCE3 1 - angle_coeff @angle:s4-c2-s4 harmonic 61.89 120.32 # SOURCE3 1 - angle_coeff @angle:s4-c2-s6 harmonic 61.98 119.95 # SOURCE3 1 - angle_coeff @angle:s6-c2-s6 harmonic 61.98 119.97 # SOURCE3 1 - angle_coeff @angle:sh-c2-sh harmonic 63.96 110.48 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-c2-ss harmonic 62.65 117.82 # SOURCE3 1 - angle_coeff @angle:s-c2-s harmonic 62.47 121.67 # SOURCE3 1 - angle_coeff @angle:ss-c2-ss harmonic 62.77 120.24 # SOURCE3 1 0.0000 - angle_coeff @angle:br-c3-br harmonic 67.46 109.03 # SOURCE4 6 0.5435 - angle_coeff @angle:br-c3-c1 harmonic 62.77 111.80 # SOURCE2 3 0.2160 - angle_coeff @angle:br-c3-c3 harmonic 63.03 109.25 # SOURCE3 10 0.5685 - angle_coeff @angle:br-c3-c harmonic 62.92 110.37 # SOURCE4 13 2.4747 - angle_coeff @angle:br-c3-h1 harmonic 43.12 103.04 # SOURCE3 5 0.3092 - angle_coeff @angle:br-c3-h2 harmonic 42.34 107.10 # SOURCE4 7 0.2378 - angle_coeff @angle:br-c3-hc harmonic 42.40 106.50 # SOURCE3 1 - angle_coeff @angle:c1-c3-c1 harmonic 66.50 109.00 # SOURCE2 1 0.0000 - angle_coeff @angle:c1-c3-c2 harmonic 65.00 111.11 # SOURCE4 12 0.7366 - angle_coeff @angle:c1-c3-c3 harmonic 64.29 111.42 # SOURCE4 197 1.2106 - angle_coeff @angle:c1-c3-ca harmonic 64.93 110.95 # SOURCE4 28 1.1203 - angle_coeff @angle:c1-c3-cc harmonic 64.32 114.20 # CORR 13 - angle_coeff @angle:c1-c3-cd harmonic 64.32 114.20 # CORR 13 - angle_coeff @angle:c1-c3-cl harmonic 58.49 110.63 # SOURCE2 3 1.2257 - angle_coeff @angle:c1-c3-h1 harmonic 48.35 109.29 # SOURCE4 133 0.5701 - angle_coeff @angle:c1-c3-hc harmonic 48.25 109.75 # SOURCE3 12 0.8436 - angle_coeff @angle:c1-c3-hx harmonic 47.76 112.05 # SOURCE4 17 0.2587 - angle_coeff @angle:c1-c3-n3 harmonic 67.03 112.59 # SOURCE4 28 0.9555 - angle_coeff @angle:c1-c3-n4 harmonic 66.53 112.04 # SOURCE4 11 0.5701 - angle_coeff @angle:c1-c3-n harmonic 67.41 112.08 # SOURCE4 18 0.9568 - angle_coeff @angle:c1-c3-nh harmonic 67.25 112.79 # SOURCE4 8 0.9453 - angle_coeff @angle:c1-c3-oh harmonic 69.49 109.14 # SOURCE4 39 0.6500 - angle_coeff @angle:c1-c3-os harmonic 69.27 108.88 # SOURCE4 31 0.9597 - angle_coeff @angle:c2-c3-c2 harmonic 63.93 112.08 # SOURCE4 153 0.7742 - angle_coeff @angle:c2-c3-c3 harmonic 63.53 111.44 # SOURCE4 2891 1.7167 - angle_coeff @angle:c2-c3-ca harmonic 63.71 112.45 # SOURCE4 141 1.6755 - angle_coeff @angle:c2-c3-cc harmonic 64.24 111.64 # CORR 32 - angle_coeff @angle:c2-c3-cd harmonic 64.24 111.64 # CORR 32 - angle_coeff @angle:c2-c3-ce harmonic 64.05 111.87 # CORR 38 - angle_coeff @angle:c2-c3-cf harmonic 64.05 111.87 # CORR 38 - angle_coeff @angle:c2-c3-cl harmonic 57.71 112.07 # SOURCE4 6 0.9936 - angle_coeff @angle:c2-c3-cx harmonic 63.65 112.62 # SOURCE4 17 1.3287 - angle_coeff @angle:c2-c3-cy harmonic 66.76 101.33 # SOURCE4 58 0.9262 - angle_coeff @angle:c2-c3-f harmonic 66.52 110.96 # SOURCE4 25 0.2829 - angle_coeff @angle:c2-c3-h1 harmonic 47.03 110.46 # SOURCE3 17 1.1525 - angle_coeff @angle:c2-c3-h2 harmonic 46.84 111.19 # SOURCE4 17 0.8311 - angle_coeff @angle:c2-c3-hc harmonic 47.03 110.49 # SOURCE3 159 0.7479 - angle_coeff @angle:c2-c3-hx harmonic 46.83 111.45 # SOURCE4 20 0.9004 - angle_coeff @angle:c2-c3-n2 harmonic 67.09 108.99 # SOURCE4 10 1.2025 - angle_coeff @angle:c2-c3-n3 harmonic 66.47 111.52 # SOURCE4 158 1.4012 - angle_coeff @angle:c2-c3-n harmonic 66.73 111.38 # SOURCE4 67 1.7559 - angle_coeff @angle:c2-c3-na harmonic 66.24 113.30 # SOURCE4 27 1.2945 - angle_coeff @angle:c2-c3-nh harmonic 67.10 110.27 # SOURCE4 56 1.8018 - angle_coeff @angle:c2-c3-oh harmonic 68.18 110.21 # SOURCE4 220 1.4197 - angle_coeff @angle:c2-c3-os harmonic 68.45 108.48 # SOURCE4 204 1.6082 - angle_coeff @angle:c2-c3-s4 harmonic 62.57 109.73 # SOURCE4 6 0.1722 - angle_coeff @angle:c2-c3-ss harmonic 63.62 104.97 # SOURCE3 2 2.2248 - angle_coeff @angle:c3-c3-c3 harmonic 63.21 110.63 # SOURCE3 507 2.7845 - angle_coeff @angle:c3-c3-ca harmonic 63.25 112.09 # SOURCE4 3859 1.5523 - angle_coeff @angle:c3-c3-cc harmonic 63.58 111.89 # CORR 700 - angle_coeff @angle:c3-c3-cd harmonic 63.58 111.89 # CORR 700 - angle_coeff @angle:c3-c3-ce harmonic 63.70 111.06 # CORR 490 - angle_coeff @angle:c3-c3-cf harmonic 63.70 111.06 # CORR 490 - angle_coeff @angle:c3-c3-cl harmonic 57.85 110.33 # SOURCE3 20 1.1495 - angle_coeff @angle:c3-c3-cx harmonic 63.30 111.82 # SOURCE4 179 2.4814 - angle_coeff @angle:c3-c3-cy harmonic 63.63 109.62 # SOURCE3 5 2.0747 - angle_coeff @angle:c3-c3-f harmonic 66.22 109.41 # SOURCE3 18 1.1878 - angle_coeff @angle:c3-c3-h1 harmonic 46.36 110.07 # SOURCE3 457 1.1542 - angle_coeff @angle:c3-c3-h2 harmonic 46.02 111.59 # SOURCE3 8 1.1217 - angle_coeff @angle:c3-c3-hc harmonic 46.37 110.05 # SOURCE3 2092 0.6991 - angle_coeff @angle:c3-c3-hx harmonic 46.02 111.74 # SOURCE3 15 1.2365 - angle_coeff @angle:c3-c3-i harmonic 58.48 110.96 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-c3-n1 harmonic 66.64 108.86 # SOURCE4 9 0.8093 - angle_coeff @angle:c3-c3-n2 harmonic 66.40 109.16 # SOURCE3 8 1.4079 - angle_coeff @angle:c3-c3-n3 harmonic 66.18 110.38 # SOURCE3 69 2.9054 - angle_coeff @angle:c3-c3-n4 harmonic 64.45 114.32 # SOURCE4 567 2.4412 - angle_coeff @angle:c3-c3-n harmonic 65.85 112.13 # SOURCE3 31 2.0700 - angle_coeff @angle:c3-c3-na harmonic 65.73 112.81 # SOURCE4 595 1.5050 - angle_coeff @angle:c3-c3-nh harmonic 66.39 110.45 # SOURCE4 1514 1.3881 - angle_coeff @angle:c3-c3-no harmonic 65.21 109.27 # SOURCE4 25 1.1817 - angle_coeff @angle:c3-c3-o harmonic 68.59 112.97 # SOURCE4 14 1.0277 - angle_coeff @angle:c3-c3-oh harmonic 67.72 109.43 # SOURCE3 48 1.5023 - angle_coeff @angle:c3-c3-os harmonic 67.78 108.42 # SOURCE3 122 1.6759 - angle_coeff @angle:c3-c3-p3 harmonic 76.46 113.19 # SOURCE4 15 0.2974 - angle_coeff @angle:c3-c3-p5 harmonic 77.70 112.32 # SOURCE4 106 1.1753 - angle_coeff @angle:c3-c3-s4 harmonic 62.16 110.07 # SOURCE4 38 0.8510 - angle_coeff @angle:c3-c3-s6 harmonic 62.98 110.00 # SOURCE4 152 1.4278 - angle_coeff @angle:c3-c3-sh harmonic 60.98 113.02 # SOURCE4 80 1.3442 - angle_coeff @angle:c3-c3-ss harmonic 61.10 112.69 # SOURCE3 24 2.1842 - angle_coeff @angle:c3-c3-sy harmonic 62.81 109.91 # SOURCE4 22 0.9248 - angle_coeff @angle:ca-c3-ca harmonic 63.66 112.26 # SOURCE4 385 1.7047 - angle_coeff @angle:ca-c3-cc harmonic 63.92 112.38 # CORR 69 - angle_coeff @angle:ca-c3-cd harmonic 63.92 112.38 # CORR 69 - angle_coeff @angle:ca-c3-ce harmonic 63.81 112.33 # SOURCE4 51 1.1929 - angle_coeff @angle:ca-c3-cl harmonic 57.85 111.31 # SOURCE4 16 0.8077 - angle_coeff @angle:ca-c3-cx harmonic 63.69 112.10 # SOURCE4 5 2.1117 - angle_coeff @angle:ca-c3-f harmonic 66.14 111.76 # SOURCE4 449 0.3492 - angle_coeff @angle:ca-c3-h1 harmonic 46.78 110.95 # SOURCE3 12 1.1170 - angle_coeff @angle:ca-c3-h2 harmonic 47.03 109.66 # SOURCE4 29 1.2184 - angle_coeff @angle:ca-c3-hc harmonic 46.96 110.15 # SOURCE3 47 1.2602 - angle_coeff @angle:ca-c3-hx harmonic 46.69 111.44 # SOURCE4 33 0.4691 - angle_coeff @angle:ca-c3-n2 harmonic 65.92 112.49 # SOURCE4 22 1.1043 - angle_coeff @angle:ca-c3-n3 harmonic 66.18 112.13 # SOURCE4 387 1.2309 - angle_coeff @angle:ca-c3-n4 harmonic 64.87 114.54 # SOURCE4 22 2.3986 - angle_coeff @angle:ca-c3-n harmonic 66.29 112.43 # SOURCE4 201 1.5133 - angle_coeff @angle:ca-c3-na harmonic 66.27 112.81 # SOURCE4 104 1.5807 - angle_coeff @angle:ca-c3-nc harmonic 68.20 106.51 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-c3-nd harmonic 68.20 106.51 # SOURCE3 1 same_as_ca-c3-nc - angle_coeff @angle:ca-c3-nh harmonic 66.64 111.41 # SOURCE4 147 1.0074 - angle_coeff @angle:ca-c3-oh harmonic 67.94 110.55 # SOURCE4 348 1.2310 - angle_coeff @angle:ca-c3-os harmonic 68.19 108.89 # SOURCE4 411 1.0102 - angle_coeff @angle:ca-c3-p5 harmonic 77.64 113.41 # SOURCE4 19 1.4444 - angle_coeff @angle:ca-c3-s6 harmonic 62.87 111.36 # SOURCE4 15 1.4775 - angle_coeff @angle:ca-c3-ss harmonic 61.90 110.66 # SOURCE4 78 1.4797 - angle_coeff @angle:ca-c3-sx harmonic 62.16 110.80 # SOURCE4 16 0.5396 - angle_coeff @angle:c-c3-c1 harmonic 64.56 112.64 # SOURCE4 11 1.0678 - angle_coeff @angle:c-c3-c2 harmonic 64.14 111.32 # SOURCE4 92 1.8522 - angle_coeff @angle:c-c3-c3 harmonic 63.79 110.53 # SOURCE3 62 1.9636 - angle_coeff @angle:c-c3-c harmonic 64.06 111.61 # SOURCE4 151 2.1872 - angle_coeff @angle:c-c3-ca harmonic 64.13 110.99 # SOURCE4 481 1.7257 - angle_coeff @angle:c-c3-cc harmonic 63.89 112.89 # CORR 104 - angle_coeff @angle:cc-c3-cc harmonic 64.61 111.05 # CORR 19 - angle_coeff @angle:cc-c3-cd harmonic 67.30 102.35 # SOURCE3 1 0.0000 - angle_coeff @angle:cc-c3-cx harmonic 63.85 112.55 # SOURCE4 5 1.4317 - angle_coeff @angle:c-c3-cd harmonic 63.89 112.89 # CORR 104 - angle_coeff @angle:c-c3-ce harmonic 64.02 111.98 # SOURCE4 16 2.1388 - angle_coeff @angle:cc-c3-f harmonic 66.70 111.22 # CORR 69 - angle_coeff @angle:cc-c3-h1 harmonic 47.03 111.62 # SOURCE3 20 1.0215 - angle_coeff @angle:cc-c3-hc harmonic 47.20 110.86 # SOURCE3 85 1.0276 - angle_coeff @angle:cc-c3-hx harmonic 47.17 111.02 # SOURCE4 9 0.7503 - angle_coeff @angle:c-c3-cl harmonic 57.94 111.16 # SOURCE4 41 1.2257 - angle_coeff @angle:cc-c3-n2 harmonic 66.85 110.47 # SOURCE4 11 0.5153 - angle_coeff @angle:cc-c3-n3 harmonic 66.79 111.17 # CORR 111 - angle_coeff @angle:cc-c3-n4 harmonic 64.88 115.58 # SOURCE4 6 1.1723 - angle_coeff @angle:cc-c3-n harmonic 66.84 111.71 # CORR 32 - angle_coeff @angle:cc-c3-na harmonic 66.43 113.39 # SOURCE4 8 0.8010 - angle_coeff @angle:cc-c3-nc harmonic 68.37 107.04 # SOURCE3 2 0.0000 - angle_coeff @angle:cc-c3-nh harmonic 66.68 112.38 # CORR 21 - angle_coeff @angle:cc-c3-oh harmonic 68.13 111.10 # CORR 116 - angle_coeff @angle:cc-c3-os harmonic 68.51 109.01 # CORR 91 - angle_coeff @angle:cc-c3-p5 harmonic 76.89 116.23 # SOURCE4 6 0.7766 - angle_coeff @angle:cc-c3-sh harmonic 61.11 114.02 # SOURCE3 1 same_as_cd-c3-sh - angle_coeff @angle:cc-c3-ss harmonic 61.95 111.06 # CORR 43 - angle_coeff @angle:c-c3-cx harmonic 64.08 111.09 # SOURCE4 9 1.2357 - angle_coeff @angle:cd-c3-cd harmonic 64.61 111.05 # CORR 19 - angle_coeff @angle:cd-c3-f harmonic 66.70 111.22 # CORR 69 - angle_coeff @angle:cd-c3-h1 harmonic 47.03 111.62 # SOURCE3 20 1.0215 - angle_coeff @angle:cd-c3-hc harmonic 47.20 110.86 # SOURCE3 85 1.0276 - angle_coeff @angle:cd-c3-n3 harmonic 66.79 111.17 # CORR 111 - angle_coeff @angle:cd-c3-n harmonic 66.84 111.71 # CORR 32 - angle_coeff @angle:cd-c3-nd harmonic 68.37 107.04 # SOURCE3 2 same_as_cc-c3-nc - angle_coeff @angle:cd-c3-nh harmonic 66.68 112.38 # CORR 21 - angle_coeff @angle:cd-c3-oh harmonic 68.13 111.10 # CORR 116 - angle_coeff @angle:cd-c3-os harmonic 68.51 109.01 # CORR 91 - angle_coeff @angle:cd-c3-sh harmonic 61.11 114.02 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-c3-ss harmonic 61.95 111.06 # CORR 43 - angle_coeff @angle:ce-c3-ce harmonic 64.24 111.44 # SOURCE4 18 0.3695 - angle_coeff @angle:ce-c3-cy harmonic 66.33 102.85 # CORR 55 - angle_coeff @angle:ce-c3-h1 harmonic 47.30 109.59 # CORR 119 - angle_coeff @angle:ce-c3-hc harmonic 47.00 110.98 # SOURCE3 27 0.1559 - angle_coeff @angle:ce-c3-n3 harmonic 66.45 111.83 # CORR 28 - angle_coeff @angle:ce-c3-n harmonic 67.09 110.41 # SOURCE4 6 1.1405 - angle_coeff @angle:ce-c3-oh harmonic 68.00 111.05 # SOURCE4 17 1.5159 - angle_coeff @angle:ce-c3-os harmonic 68.64 108.10 # SOURCE4 16 1.9583 - angle_coeff @angle:ce-c3-ss harmonic 61.87 111.10 # SOURCE4 7 2.0156 - angle_coeff @angle:c-c3-f harmonic 66.82 109.98 # SOURCE4 38 0.9895 - angle_coeff @angle:cf-c3-cy harmonic 66.33 102.85 # CORR 55 - angle_coeff @angle:cf-c3-h1 harmonic 47.30 109.59 # CORR 119 - angle_coeff @angle:cf-c3-hc harmonic 47.00 110.98 # SOURCE3 27 same_as_ce-c3-hc - angle_coeff @angle:cf-c3-n3 harmonic 66.45 111.83 # CORR 28 - angle_coeff @angle:c-c3-h1 harmonic 47.63 107.66 # SOURCE3 66 1.4015 - angle_coeff @angle:c-c3-h2 harmonic 47.16 109.69 # SOURCE4 38 1.0614 - angle_coeff @angle:c-c3-hc harmonic 47.20 109.68 # SOURCE3 614 0.6426 - angle_coeff @angle:c-c3-hx harmonic 47.23 109.54 # SOURCE4 47 0.6627 - angle_coeff @angle:cl-c3-cl harmonic 54.23 111.03 # SOURCE2 6 1.1324 - angle_coeff @angle:cl-c3-f harmonic 59.15 109.02 # SOURCE4 15 0.3609 - angle_coeff @angle:cl-c3-h1 harmonic 40.66 105.93 # SOURCE3 19 1.1883 - angle_coeff @angle:cl-c3-h2 harmonic 40.44 107.14 # SOURCE4 50 0.5973 - angle_coeff @angle:cl-c3-hc harmonic 40.33 107.65 # SOURCE2 2 2.2500 - angle_coeff @angle:cl-c3-os harmonic 60.38 111.40 # SOURCE4 8 0.8275 - angle_coeff @angle:cl-c3-ss harmonic 57.60 112.94 # SOURCE4 10 1.4625 - angle_coeff @angle:c-c3-n2 harmonic 66.92 109.55 # SOURCE4 55 1.4579 - angle_coeff @angle:c-c3-n3 harmonic 66.59 111.14 # SOURCE4 629 1.6673 - angle_coeff @angle:c-c3-n4 harmonic 65.07 114.21 # SOURCE4 27 1.5388 - angle_coeff @angle:c-c3-n harmonic 66.67 111.56 # SOURCE3 28 1.7981 - angle_coeff @angle:c-c3-na harmonic 66.81 111.37 # SOURCE4 31 1.6229 - angle_coeff @angle:c-c3-nh harmonic 67.36 109.43 # SOURCE4 42 1.7022 - angle_coeff @angle:c-c3-oh harmonic 68.65 108.70 # SOURCE4 299 1.3415 - angle_coeff @angle:c-c3-os harmonic 68.03 109.82 # SOURCE3 10 2.0612 - angle_coeff @angle:c-c3-p5 harmonic 78.76 110.41 # SOURCE4 15 2.2683 - angle_coeff @angle:c-c3-s6 harmonic 63.26 110.22 # SOURCE4 5 2.0076 - angle_coeff @angle:c-c3-sh harmonic 62.46 108.82 # SOURCE4 12 0.8354 - angle_coeff @angle:c-c3-ss harmonic 61.70 111.58 # SOURCE3 5 1.9506 - angle_coeff @angle:cx-c3-cx harmonic 63.53 112.58 # SOURCE4 7 1.2211 - angle_coeff @angle:cx-c3-h1 harmonic 47.04 109.64 # SOURCE4 175 0.8822 - angle_coeff @angle:cx-c3-hc harmonic 46.92 110.20 # SOURCE4 356 0.8798 - angle_coeff @angle:cx-c3-hx harmonic 46.38 112.81 # SOURCE4 12 0.0977 - angle_coeff @angle:cx-c3-n3 harmonic 65.83 113.22 # SOURCE4 33 1.3978 - angle_coeff @angle:cx-c3-n4 harmonic 68.88 101.51 # SOURCE4 12 0.0760 - angle_coeff @angle:cx-c3-n harmonic 66.22 112.59 # SOURCE4 22 0.8034 - angle_coeff @angle:cx-c3-oh harmonic 68.10 109.97 # SOURCE4 25 1.3176 - angle_coeff @angle:cx-c3-os harmonic 68.40 108.16 # SOURCE4 26 1.0162 - angle_coeff @angle:cy-c3-h1 harmonic 47.00 107.88 # SOURCE4 162 0.9624 - angle_coeff @angle:cy-c3-hc harmonic 46.51 110.17 # SOURCE3 16 0.5693 - angle_coeff @angle:cy-c3-n3 harmonic 65.63 112.72 # SOURCE4 7 1.0639 - angle_coeff @angle:cy-c3-oh harmonic 67.22 111.56 # SOURCE4 138 0.5051 - angle_coeff @angle:cy-c3-os harmonic 68.45 106.79 # SOURCE4 5 1.0955 - angle_coeff @angle:f-c3-f harmonic 71.26 107.16 # SOURCE2 10 1.1324 - angle_coeff @angle:f-c3-h1 harmonic 51.57 107.85 # SOURCE3 14 0.9537 - angle_coeff @angle:f-c3-h2 harmonic 51.36 108.41 # SOURCE3 6 0.5081 - angle_coeff @angle:f-c3-h3 harmonic 51.05 110.01 # SOURCE4 19 0.6811 - angle_coeff @angle:f-c3-hc harmonic 51.33 108.92 # SOURCE2 5 3.0534 - angle_coeff @angle:f-c3-n2 harmonic 69.23 110.40 # SOURCE2 3 2.6470 - angle_coeff @angle:f-c3-os harmonic 70.66 110.61 # SOURCE4 45 1.1755 - angle_coeff @angle:f-c3-p5 harmonic 80.63 107.25 # SOURCE4 11 1.1735 - angle_coeff @angle:f-c3-s6 harmonic 64.18 109.67 # SOURCE4 24 0.4116 - angle_coeff @angle:f-c3-ss harmonic 62.13 111.89 # SOURCE4 11 0.9479 - angle_coeff @angle:h1-c3-h1 harmonic 39.18 109.55 # SOURCE3 1888 1.1205 - angle_coeff @angle:h1-c3-n1 harmonic 49.99 107.31 # HF/6-31G* 1 - angle_coeff @angle:h1-c3-n2 harmonic 49.26 109.61 # SOURCE3 63 1.0452 - angle_coeff @angle:h1-c3-n3 harmonic 49.39 109.92 # SOURCE3 313 1.1810 - angle_coeff @angle:h1-c3-n harmonic 49.82 109.32 # SOURCE3 91 1.0325 - angle_coeff @angle:h1-c3-na harmonic 49.90 109.45 # SOURCE3 53 0.9555 - angle_coeff @angle:h1-c3-nc harmonic 50.11 108.57 # SOURCE3 6 0.0764 - angle_coeff @angle:h1-c3-nd harmonic 50.11 108.57 # SOURCE3 6 same_as_h1-c3-nc - angle_coeff @angle:h1-c3-nh harmonic 49.73 109.96 # SOURCE3 70 0.7000 - angle_coeff @angle:h1-c3-no harmonic 48.66 105.15 # SOURCE4 16 0.4950 - angle_coeff @angle:h1-c3-o harmonic 52.53 117.19 # SOURCE3 6 0.0003 - angle_coeff @angle:h1-c3-oh harmonic 50.97 109.88 # SOURCE3 63 1.3172 - angle_coeff @angle:h1-c3-os harmonic 50.84 108.82 # SOURCE3 541 0.8042 - angle_coeff @angle:h1-c3-p5 harmonic 54.25 107.99 # SOURCE4 72 1.1862 - angle_coeff @angle:h1-c3-s4 harmonic 42.89 108.66 # SOURCE3 201 0.3834 - angle_coeff @angle:h1-c3-s harmonic 41.18 112.60 # SOURCE3 6 0.0026 - angle_coeff @angle:h1-c3-s6 harmonic 43.86 108.11 # SOURCE3 160 0.5518 - angle_coeff @angle:h1-c3-sh harmonic 42.40 109.21 # SOURCE3 22 1.2028 - angle_coeff @angle:h1-c3-ss harmonic 42.40 109.34 # SOURCE3 356 0.6573 - angle_coeff @angle:h1-c3-sx harmonic 42.83 108.69 # SOURCE3 90 0.2749 - angle_coeff @angle:h1-c3-sy harmonic 43.65 108.09 # SOURCE3 93 0.2556 - angle_coeff @angle:h2-c3-h2 harmonic 39.00 109.19 # SOURCE3 29 3.1352 - angle_coeff @angle:h2-c3-i harmonic 38.69 104.99 # SOURCE3 2 0.0000 - angle_coeff @angle:h2-c3-n2 harmonic 49.08 110.22 # SOURCE3 6 0.2133 - angle_coeff @angle:h2-c3-n3 harmonic 49.37 109.80 # SOURCE4 189 1.2893 - angle_coeff @angle:h2-c3-n harmonic 50.22 107.38 # SOURCE4 258 1.3140 - angle_coeff @angle:h2-c3-na harmonic 50.27 107.66 # SOURCE3 6 1.4096 - angle_coeff @angle:h2-c3-nc harmonic 49.85 109.47 # SOURCE3 10 0.3133 - angle_coeff @angle:h2-c3-nd harmonic 49.85 109.47 # SOURCE3 10 same_as_h2-c3-nc - angle_coeff @angle:h2-c3-nh harmonic 49.60 110.33 # SOURCE4 102 1.0596 - angle_coeff @angle:h2-c3-no harmonic 47.83 108.69 # SOURCE3 4 0.0000 - angle_coeff @angle:h2-c3-o harmonic 54.38 108.97 # SOURCE3 4 0.0000 - angle_coeff @angle:h2-c3-oh harmonic 51.29 108.30 # SOURCE3 6 0.5715 - angle_coeff @angle:h2-c3-os harmonic 50.84 108.58 # SOURCE3 44 1.2773 - angle_coeff @angle:h2-c3-s4 harmonic 42.93 108.58 # SOURCE3 8 0.2408 - angle_coeff @angle:h2-c3-s harmonic 42.32 106.75 # SOURCE3 4 0.0000 - angle_coeff @angle:h2-c3-s6 harmonic 44.20 106.54 # SOURCE4 27 0.9934 - angle_coeff @angle:h2-c3-sh harmonic 42.68 107.87 # SOURCE3 6 0.4376 - angle_coeff @angle:h2-c3-ss harmonic 42.34 109.75 # SOURCE3 10 0.3442 - angle_coeff @angle:h3-c3-n3 harmonic 49.73 108.39 # SOURCE4 12 1.7932 - angle_coeff @angle:h3-c3-nc harmonic 49.91 109.37 # SOURCE3 1 0.0000 - angle_coeff @angle:h3-c3-nd harmonic 49.91 109.37 # SOURCE3 1 same_as_h3-c3-nc - angle_coeff @angle:h3-c3-nh harmonic 49.53 110.78 # SOURCE4 5 1.5993 - angle_coeff @angle:h3-c3-os harmonic 50.09 112.03 # SOURCE4 17 1.0957 - angle_coeff @angle:h3-c3-ss harmonic 42.42 109.27 # SOURCE4 8 0.8367 - angle_coeff @angle:hc-c3-hc harmonic 39.43 108.35 # SOURCE3 2380 0.9006 - angle_coeff @angle:hc-c3-i harmonic 38.62 104.99 # SOURCE3 1 - angle_coeff @angle:hc-c3-n2 harmonic 49.29 109.50 # SOURCE3 1 - angle_coeff @angle:hc-c3-n3 harmonic 49.42 109.80 # SOURCE2 5 2.0070 - angle_coeff @angle:hc-c3-n4 harmonic 49.01 107.90 # SOURCE3 1 - angle_coeff @angle:hc-c3-n harmonic 49.78 109.50 # SOURCE3 1 - angle_coeff @angle:hc-c3-na harmonic 49.90 109.50 # SOURCE3 1 - angle_coeff @angle:hc-c3-nh harmonic 49.38 111.54 # SOURCE3 1 - angle_coeff @angle:hc-c3-no harmonic 48.19 107.20 # SOURCE2 1 0.0000 - angle_coeff @angle:hc-c3-oh harmonic 51.07 109.50 # SOURCE3 1 - angle_coeff @angle:hc-c3-os harmonic 50.87 108.70 # SOURCE2 13 2.3739 - angle_coeff @angle:hc-c3-p2 harmonic 52.37 110.18 # SOURCE3 25 0.4057 - angle_coeff @angle:hc-c3-p3 harmonic 52.73 110.14 # SOURCE3 325 0.5126 - angle_coeff @angle:hc-c3-p4 harmonic 53.21 109.59 # SOURCE3 87 0.3196 - angle_coeff @angle:hc-c3-p5 harmonic 53.84 109.64 # SOURCE3 69 0.8112 - angle_coeff @angle:hc-c3-px harmonic 53.46 109.74 # SOURCE3 84 0.3474 - angle_coeff @angle:hc-c3-py harmonic 53.86 109.54 # SOURCE3 39 0.1999 - angle_coeff @angle:hc-c3-s4 harmonic 43.12 107.50 # SOURCE2 1 0.0000 - angle_coeff @angle:hc-c3-s6 harmonic 43.84 108.20 # SOURCE3 1 - angle_coeff @angle:hc-c3-sh harmonic 42.66 107.87 # SOURCE2 3 2.0981 - angle_coeff @angle:hc-c3-ss harmonic 42.51 108.76 # SOURCE2 3 1.6891 - angle_coeff @angle:hx-c3-hx harmonic 39.04 110.74 # SOURCE3 137 0.5531 - angle_coeff @angle:hx-c3-n4 harmonic 49.02 107.91 # SOURCE3 148 0.5899 - angle_coeff @angle:i-c3-i harmonic 61.98 113.12 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-c3-n1 harmonic 71.09 105.07 # HF/6-31G* 1 - angle_coeff @angle:n2-c3-n2 harmonic 69.89 107.70 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-c3-nh harmonic 69.26 111.06 # SOURCE4 5 0.7868 - angle_coeff @angle:n2-c3-oh harmonic 70.15 111.82 # SOURCE4 10 0.3451 - angle_coeff @angle:n2-c3-os harmonic 70.04 111.23 # SOURCE4 6 1.0463 - angle_coeff @angle:n3-c3-n3 harmonic 69.61 109.59 # SOURCE4 27 1.8125 - angle_coeff @angle:n3-c3-nc harmonic 68.79 113.29 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-c3-nd harmonic 68.79 113.29 # SOURCE3 1 same_as_n3-c3-nc - angle_coeff @angle:n3-c3-nh harmonic 69.74 110.08 # SOURCE4 21 1.0686 - angle_coeff @angle:n3-c3-oh harmonic 70.71 110.63 # SOURCE4 20 1.0177 - angle_coeff @angle:n3-c3-os harmonic 71.15 108.33 # SOURCE4 17 1.9545 - angle_coeff @angle:n3-c3-p5 harmonic 81.55 109.51 # SOURCE4 10 1.5002 - angle_coeff @angle:n3-c3-ss harmonic 64.75 107.73 # SOURCE4 18 1.7621 - angle_coeff @angle:n4-c3-n4 harmonic 67.13 113.32 # SOURCE3 1 0.0000 - angle_coeff @angle:na-c3-na harmonic 69.06 113.49 # SOURCE3 1 0.0000 - angle_coeff @angle:na-c3-os harmonic 71.27 109.06 # SOURCE4 170 0.5450 - angle_coeff @angle:nc-c3-nc harmonic 69.96 110.61 # SOURCE3 1 0.0000 - angle_coeff @angle:nc-c3-nh harmonic 69.34 112.43 # SOURCE3 1 0.0000 - angle_coeff @angle:nc-c3-os harmonic 69.28 115.41 # SOURCE3 3 1.0288 - angle_coeff @angle:nd-c3-nd harmonic 69.96 110.61 # SOURCE3 1 same_as_nc-c3-nc - angle_coeff @angle:nd-c3-nh harmonic 69.34 112.43 # SOURCE3 1 same_as_nc-c3-nh - angle_coeff @angle:nd-c3-os harmonic 69.28 115.41 # SOURCE3 3 same_as_nc-c3-os - angle_coeff @angle:nh-c3-nh harmonic 71.41 105.87 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-c3-oh harmonic 70.47 112.36 # SOURCE4 12 0.7775 - angle_coeff @angle:nh-c3-os harmonic 71.26 108.93 # SOURCE4 17 1.3775 - angle_coeff @angle:nh-c3-p5 harmonic 80.62 112.50 # SOURCE4 5 1.7371 - angle_coeff @angle:nh-c3-ss harmonic 64.53 108.88 # SOURCE4 8 2.1521 - angle_coeff @angle:n-c3-n2 harmonic 68.82 112.34 # SOURCE4 5 1.1443 - angle_coeff @angle:n-c3-n3 harmonic 69.39 111.03 # SOURCE4 15 1.8216 - angle_coeff @angle:n-c3-n harmonic 68.78 113.81 # SOURCE3 1 0.0000 - angle_coeff @angle:n-c3-nh harmonic 70.54 108.34 # SOURCE4 11 2.1727 - angle_coeff @angle:n-c3-oh harmonic 70.36 112.54 # SOURCE4 31 1.1295 - angle_coeff @angle:no-c3-no harmonic 68.37 104.47 # SOURCE4 5 0.9726 - angle_coeff @angle:n-c3-os harmonic 71.14 109.16 # SOURCE4 153 0.8778 - angle_coeff @angle:n-c3-p5 harmonic 81.48 110.05 # SOURCE4 5 1.2965 - angle_coeff @angle:oh-c3-oh harmonic 72.71 109.23 # SOURCE4 8 1.4978 - angle_coeff @angle:oh-c3-os harmonic 72.38 109.21 # SOURCE4 85 1.1964 - angle_coeff @angle:oh-c3-p5 harmonic 82.83 108.86 # SOURCE4 33 1.2025 - angle_coeff @angle:oh-c3-sh harmonic 63.30 115.46 # SOURCE3 1 0.0000 - angle_coeff @angle:o-c3-o harmonic 74.43 122.30 # SOURCE3 1 0.0000 - angle_coeff @angle:os-c3-os harmonic 71.72 110.24 # SOURCE3 17 2.1340 - angle_coeff @angle:os-c3-p5 harmonic 82.86 108.36 # SOURCE4 22 2.1937 - angle_coeff @angle:os-c3-ss harmonic 65.36 107.98 # SOURCE4 20 1.7464 - angle_coeff @angle:p2-c3-p2 harmonic 98.16 110.48 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-c3-p3 harmonic 98.88 110.16 # SOURCE3 1 0.0000 - angle_coeff @angle:p5-c3-p5 harmonic 100.59 110.13 # SOURCE4 33 2.4116 - angle_coeff @angle:p5-c3-ss harmonic 78.88 111.30 # SOURCE4 5 2.0560 - angle_coeff @angle:s4-c3-s4 harmonic 62.40 112.29 # SOURCE3 2 1.2724 - angle_coeff @angle:s4-c3-s6 harmonic 62.62 113.52 # SOURCE3 1 - angle_coeff @angle:s6-c3-s6 harmonic 63.71 111.75 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-c3-sh harmonic 60.82 116.26 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-c3-ss harmonic 62.33 110.73 # SOURCE3 1 - angle_coeff @angle:s-c3-s harmonic 58.31 123.35 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-c3-ss harmonic 62.40 110.57 # SOURCE4 15 1.4311 - angle_coeff @angle:br-ca-br harmonic 67.31 117.60 # SOURCE3 1 - angle_coeff @angle:br-ca-ca harmonic 63.48 118.13 # SOURCE3 8 0.6041 - angle_coeff @angle:c1-ca-c1 harmonic 64.70 120.00 # SOURCE3 1 - angle_coeff @angle:c1-ca-ca harmonic 65.86 120.00 # SOURCE3 1 - angle_coeff @angle:c2-ca-c2 harmonic 62.95 120.00 # SOURCE3 1 - angle_coeff @angle:c2-ca-ca harmonic 64.69 120.60 # SOURCE3 1 - angle_coeff @angle:c3-ca-c2 harmonic 62.24 120.00 # SOURCE3 1 - angle_coeff @angle:c3-ca-c3 harmonic 62.41 116.80 # SOURCE3 1 - angle_coeff @angle:c3-ca-ca harmonic 63.84 120.63 # SOURCE3 60 0.7175 - angle_coeff @angle:c3-ca-cp harmonic 63.64 120.63 # CORR 120 - angle_coeff @angle:c3-ca-cq harmonic 63.64 120.63 # CORR 120 - angle_coeff @angle:c3-ca-na harmonic 66.59 118.78 # SOURCE4 59 1.1184 - angle_coeff @angle:c3-ca-nb harmonic 67.33 116.66 # SOURCE4 408 0.9380 - angle_coeff @angle:ca-ca-ca harmonic 67.18 119.97 # SOURCE3 1969 0.3480 - angle_coeff @angle:ca-ca-cc harmonic 65.99 120.10 # SOURCE3 103 0.3451 - angle_coeff @angle:ca-ca-cd harmonic 65.99 120.10 # SOURCE3 103 0.3451 - angle_coeff @angle:ca-ca-ce harmonic 64.88 120.66 # SOURCE3 14 0.1564 - angle_coeff @angle:ca-ca-cf harmonic 64.88 120.66 # SOURCE3 14 same_as_ca-ca-ce - angle_coeff @angle:ca-ca-cg harmonic 65.90 120.05 # SOURCE3 6 0.2397 - angle_coeff @angle:ca-ca-ch harmonic 65.90 120.05 # SOURCE3 6 same_as_ca-ca-cg - angle_coeff @angle:ca-ca-cl harmonic 58.52 119.40 # SOURCE4 2459 0.5283 - angle_coeff @angle:ca-ca-cp harmonic 67.16 119.07 # CORR 28 - angle_coeff @angle:ca-ca-cq harmonic 67.16 119.07 # CORR 28 - angle_coeff @angle:ca-ca-cx harmonic 64.48 120.83 # SOURCE4 71 1.3062 - angle_coeff @angle:ca-ca-cy harmonic 63.77 120.86 # SOURCE4 17 2.0287 - angle_coeff @angle:ca-ca-f harmonic 67.51 118.95 # SOURCE4 967 0.3369 - angle_coeff @angle:ca-ca-h4 harmonic 48.24 121.09 # SOURCE3 57 1.4696 - angle_coeff @angle:ca-ca-ha harmonic 48.46 120.01 # SOURCE3 2980 0.2511 - angle_coeff @angle:ca-ca-i harmonic 58.59 118.47 # SOURCE3 10 0.6181 - angle_coeff @angle:ca-ca-n1 harmonic 68.92 118.50 # HF/6-31G* 1 - angle_coeff @angle:ca-ca-n2 harmonic 70.95 119.57 # SOURCE3 1 - angle_coeff @angle:ca-ca-n4 harmonic 67.28 118.41 # SOURCE3 6 0.1691 - angle_coeff @angle:ca-ca-n harmonic 67.97 119.89 # SOURCE3 18 0.2095 - angle_coeff @angle:ca-ca-na harmonic 70.21 118.34 # SOURCE3 54 3.6168 - angle_coeff @angle:ca-ca-nb harmonic 69.16 122.63 # SOURCE3 83 1.1249 - angle_coeff @angle:ca-ca-nc harmonic 70.14 119.72 # SOURCE3 22 3.3994 - angle_coeff @angle:ca-ca-nd harmonic 70.14 119.72 # SOURCE3 22 3.3994 - angle_coeff @angle:ca-ca-ne harmonic 67.74 119.88 # SOURCE3 24 0.3637 - angle_coeff @angle:ca-ca-nf harmonic 67.74 119.88 # SOURCE3 24 0.3637 - angle_coeff @angle:ca-ca-nh harmonic 69.34 120.13 # SOURCE3 193 0.6341 - angle_coeff @angle:ca-ca-no harmonic 66.88 119.54 # SOURCE3 10 1.3187 - angle_coeff @angle:ca-ca-o harmonic 71.85 123.29 # SOURCE4 11 1.2526 - angle_coeff @angle:ca-ca-oh harmonic 69.85 119.94 # SOURCE3 14 0.1627 - angle_coeff @angle:ca-ca-os harmonic 69.79 119.20 # SOURCE3 52 0.5240 - angle_coeff @angle:ca-ca-p2 harmonic 77.87 114.36 # SOURCE3 1 - angle_coeff @angle:ca-ca-p3 harmonic 76.34 120.73 # SOURCE3 6 0.1273 - angle_coeff @angle:ca-ca-p4 harmonic 77.11 120.30 # SOURCE3 1 - angle_coeff @angle:ca-ca-p5 harmonic 77.50 120.28 # SOURCE4 5 0.0177 - angle_coeff @angle:ca-ca-pe harmonic 76.26 120.45 # SOURCE3 20 0.2719 - angle_coeff @angle:ca-ca-pf harmonic 76.26 120.45 # SOURCE3 20 0.2719 - angle_coeff @angle:ca-ca-px harmonic 76.37 120.53 # SOURCE3 10 0.4509 - angle_coeff @angle:ca-ca-py harmonic 77.43 119.98 # SOURCE3 6 0.0670 - angle_coeff @angle:ca-ca-s4 harmonic 61.72 119.15 # SOURCE3 1 - angle_coeff @angle:ca-ca-s6 harmonic 62.18 120.54 # SOURCE4 36 1.2154 - angle_coeff @angle:ca-ca-s harmonic 62.22 122.55 # SOURCE3 4 0.0000 - angle_coeff @angle:ca-ca-sh harmonic 61.32 121.78 # SOURCE4 17 1.2849 - angle_coeff @angle:ca-ca-ss harmonic 62.03 119.93 # SOURCE3 16 0.3901 - angle_coeff @angle:ca-ca-sx harmonic 60.68 119.18 # SOURCE3 6 0.0434 - angle_coeff @angle:ca-ca-sy harmonic 61.64 119.89 # SOURCE3 24 1.8813 - angle_coeff @angle:c-ca-c3 harmonic 62.61 118.06 # SOURCE3 1 - angle_coeff @angle:c-ca-c harmonic 62.65 120.00 # SOURCE3 1 - angle_coeff @angle:c-ca-ca harmonic 64.64 120.14 # SOURCE3 40 0.4788 - angle_coeff @angle:cc-ca-cp harmonic 64.63 124.30 # SOURCE4 10 0.6423 - angle_coeff @angle:cc-ca-nb harmonic 69.19 118.02 # CORR 64 - angle_coeff @angle:cd-ca-nb harmonic 69.19 118.02 # CORR 64 - angle_coeff @angle:ce-ca-na harmonic 67.44 119.85 # SOURCE4 9 0.7001 - angle_coeff @angle:ce-ca-nb harmonic 68.24 117.59 # CORR 44 - angle_coeff @angle:cf-ca-nb harmonic 68.24 117.59 # CORR 44 - angle_coeff @angle:cg-ca-cp harmonic 65.26 121.53 # SOURCE4 12 0.1831 - angle_coeff @angle:c-ca-ha harmonic 46.51 115.90 # SOURCE3 1 - angle_coeff @angle:cl-ca-cl harmonic 54.17 118.72 # SOURCE3 1 - angle_coeff @angle:cl-ca-cp harmonic 58.19 120.31 # SOURCE4 18 0.5607 - angle_coeff @angle:cl-ca-nb harmonic 61.21 116.15 # SOURCE4 50 0.6047 - angle_coeff @angle:c-ca-nb harmonic 67.71 117.94 # SOURCE4 91 1.0536 - angle_coeff @angle:c-ca-nc harmonic 64.40 130.80 # SOURCE3 1 - angle_coeff @angle:c-ca-nd harmonic 64.40 130.80 # SOURCE3 1 same_as_c-ca-nc - angle_coeff @angle:cp-ca-f harmonic 67.10 119.39 # SOURCE4 16 0.1724 - angle_coeff @angle:cp-ca-h4 harmonic 48.15 120.03 # SOURCE4 27 0.4431 - angle_coeff @angle:cp-ca-ha harmonic 47.94 121.08 # CORR 24 - angle_coeff @angle:cp-ca-na harmonic 72.91 108.79 # SOURCE4 165 0.5166 - angle_coeff @angle:cp-ca-nb harmonic 68.56 123.72 # SOURCE4 50 0.8176 - angle_coeff @angle:cp-ca-nh harmonic 68.66 121.52 # SOURCE4 11 0.5438 - angle_coeff @angle:cp-ca-oh harmonic 69.26 120.96 # SOURCE4 12 1.1400 - angle_coeff @angle:cp-ca-ss harmonic 63.87 112.75 # SOURCE4 8 0.6216 - angle_coeff @angle:cp-ca-sy harmonic 63.91 111.18 # CORR 4 - angle_coeff @angle:cq-ca-ha harmonic 47.94 121.08 # CORR 24 - angle_coeff @angle:cq-ca-sy harmonic 63.91 111.18 # CORR 4 - angle_coeff @angle:f-ca-f harmonic 68.05 117.50 # SOURCE3 1 - angle_coeff @angle:f-ca-nb harmonic 71.69 114.58 # SOURCE4 19 0.2987 - angle_coeff @angle:h4-ca-n harmonic 49.48 116.02 # SOURCE3 1 - angle_coeff @angle:h4-ca-na harmonic 51.88 114.65 # SOURCE3 5 1.5484 - angle_coeff @angle:h4-ca-nb harmonic 51.82 115.94 # SOURCE3 52 0.7370 - angle_coeff @angle:h4-ca-nc harmonic 51.46 118.36 # SOURCE3 1 - angle_coeff @angle:h4-ca-nd harmonic 51.46 118.36 # SOURCE3 1 same_as_h4-ca-nc - angle_coeff @angle:h4-ca-os harmonic 52.30 111.15 # SOURCE3 1 - angle_coeff @angle:h4-ca-ss harmonic 42.40 116.19 # SOURCE3 1 - angle_coeff @angle:h5-ca-nb harmonic 51.76 116.35 # SOURCE3 30 0.5545 - angle_coeff @angle:h5-ca-nc harmonic 50.70 122.11 # SOURCE3 1 - angle_coeff @angle:h5-ca-nd harmonic 50.70 122.11 # SOURCE3 1 same_as_h5-ca-nc - angle_coeff @angle:ha-ca-n2 harmonic 52.97 116.00 # SOURCE2 1 0.0000 - angle_coeff @angle:ha-ca-p2 harmonic 50.08 122.56 # SOURCE3 1 - angle_coeff @angle:i-ca-i harmonic 62.29 119.28 # SOURCE3 1 - angle_coeff @angle:n1-ca-n1 harmonic 70.73 117.03 # HF/6-31G* 1 - angle_coeff @angle:n2-ca-n2 harmonic 75.05 120.00 # SOURCE3 1 - angle_coeff @angle:n2-ca-na harmonic 73.80 119.60 # SOURCE3 1 - angle_coeff @angle:n4-ca-n4 harmonic 67.65 116.82 # SOURCE3 1 - angle_coeff @angle:na-ca-na harmonic 76.48 107.65 # SOURCE4 5 0.8751 - angle_coeff @angle:na-ca-nb harmonic 70.60 127.07 # SOURCE4 237 1.9392 - angle_coeff @angle:na-ca-nh harmonic 72.48 118.62 # SOURCE4 29 0.9759 - angle_coeff @angle:nb-ca-nb harmonic 70.78 127.19 # SOURCE4 585 1.1793 - angle_coeff @angle:nb-ca-nc harmonic 71.12 126.53 # CORR 22 - angle_coeff @angle:nb-ca-nd harmonic 71.12 126.53 # CORR 22 - angle_coeff @angle:nb-ca-nh harmonic 73.20 116.95 # SOURCE4 765 0.8040 - angle_coeff @angle:nb-ca-oh harmonic 73.57 117.30 # SOURCE4 64 0.9290 - angle_coeff @angle:nb-ca-os harmonic 72.54 119.66 # SOURCE4 76 0.6493 - angle_coeff @angle:nb-ca-sh harmonic 64.31 117.59 # SOURCE4 15 1.4616 - angle_coeff @angle:nb-ca-ss harmonic 64.10 119.30 # SOURCE4 41 1.3420 - angle_coeff @angle:nc-ca-nc harmonic 70.67 128.74 # SOURCE3 1 - angle_coeff @angle:nc-ca-nh harmonic 72.77 118.86 # SOURCE3 1 - angle_coeff @angle:nd-ca-nd harmonic 70.67 128.74 # SOURCE3 1 same_as_nc-ca-nc - angle_coeff @angle:nd-ca-nh harmonic 72.77 118.86 # SOURCE3 1 same_as_nc-ca-nh - angle_coeff @angle:nh-ca-nh harmonic 71.40 120.98 # SOURCE3 1 - angle_coeff @angle:n-ca-nc harmonic 69.66 123.86 # SOURCE3 1 - angle_coeff @angle:n-ca-nd harmonic 69.66 123.86 # SOURCE3 1 same_as_n-ca-nc - angle_coeff @angle:n-ca-nh harmonic 71.29 116.16 # SOURCE3 1 - angle_coeff @angle:no-ca-no harmonic 67.42 117.14 # SOURCE3 1 - angle_coeff @angle:oh-ca-oh harmonic 72.63 120.00 # SOURCE3 1 - angle_coeff @angle:o-ca-o harmonic 78.21 126.82 # SOURCE3 1 - angle_coeff @angle:os-ca-os harmonic 74.01 113.73 # SOURCE3 1 - angle_coeff @angle:p2-ca-p2 harmonic 94.48 121.20 # SOURCE3 1 - angle_coeff @angle:p3-ca-p3 harmonic 95.21 121.46 # SOURCE3 1 - angle_coeff @angle:p5-ca-p5 harmonic 97.33 120.00 # SOURCE3 1 - angle_coeff @angle:s4-ca-s4 harmonic 64.96 105.81 # SOURCE3 1 - angle_coeff @angle:s6-ca-s6 harmonic 66.03 105.81 # SOURCE3 1 - angle_coeff @angle:sh-ca-sh harmonic 61.27 120.24 # SOURCE3 1 - angle_coeff @angle:s-ca-s harmonic 61.42 125.14 # SOURCE3 1 - angle_coeff @angle:ss-ca-ss harmonic 62.91 115.15 # SOURCE3 1 - angle_coeff @angle:br-c-br harmonic 66.91 113.10 # SOURCE3 1 - angle_coeff @angle:br-c-c3 harmonic 63.34 110.74 # SOURCE3 1 0.0000 - angle_coeff @angle:br-c-o harmonic 63.19 121.46 # SOURCE3 5 1.6264 - angle_coeff @angle:c1-c-c1 harmonic 65.09 115.32 # SOURCE3 1 - angle_coeff @angle:c1-c-o harmonic 69.92 122.34 # SOURCE3 1 - angle_coeff @angle:c2-c-c2 harmonic 67.17 116.78 # SOURCE3 1 - angle_coeff @angle:c2-c-ha harmonic 48.65 115.95 # SOURCE3 1 - angle_coeff @angle:c2-c-o harmonic 72.77 119.12 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-c-s harmonic 64.67 119.16 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-c-c3 harmonic 62.82 116.05 # SOURCE3 11 1.0986 - angle_coeff @angle:c3-c-ca harmonic 62.59 118.54 # SOURCE4 240 1.3614 - angle_coeff @angle:c3-c-cc harmonic 63.38 117.47 # CORR 46 - angle_coeff @angle:c3-c-cd harmonic 63.38 117.47 # CORR 46 - angle_coeff @angle:c3-c-ce harmonic 63.44 116.37 # CORR 233 - angle_coeff @angle:c3-c-cf harmonic 63.44 116.37 # CORR 233 - angle_coeff @angle:c3-c-cg harmonic 64.26 115.00 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-c-ch harmonic 64.26 115.00 # SOURCE2 1 same_as_c3-c-cg - angle_coeff @angle:c3-c-cl harmonic 58.18 111.99 # SOURCE3 2 0.0125 - angle_coeff @angle:c3-c-f harmonic 66.93 110.70 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-c-h4 harmonic 46.11 114.40 # SOURCE4 57 0.4032 - angle_coeff @angle:c3-c-ha harmonic 46.01 115.22 # SOURCE3 15 0.3181 - angle_coeff @angle:c3-c-i harmonic 56.87 112.94 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-c-n2 harmonic 66.62 114.53 # SOURCE3 1 - angle_coeff @angle:c3-c-n4 harmonic 64.61 112.26 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-c-n harmonic 67.86 115.15 # SOURCE3 153 2.7443 - angle_coeff @angle:c3-c-ne harmonic 68.03 111.56 # CORR 12 - angle_coeff @angle:c3-c-nf harmonic 68.03 111.56 # CORR 12 - angle_coeff @angle:c3-c-o harmonic 68.03 123.11 # SOURCE3 267 3.0977 - angle_coeff @angle:c3-c-oh harmonic 69.84 112.20 # SOURCE3 14 1.8324 - angle_coeff @angle:c3-c-os harmonic 69.26 111.96 # SOURCE3 15 2.3072 - angle_coeff @angle:c3-c-p3 harmonic 74.55 116.42 # SOURCE3 3 0.1291 - angle_coeff @angle:c3-c-p5 harmonic 73.81 118.90 # SOURCE3 1 - angle_coeff @angle:c3-c-pe harmonic 74.19 114.85 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-c-pf harmonic 74.19 114.85 # SOURCE3 1 same_as_c3-c-pe - angle_coeff @angle:c3-c-px harmonic 74.17 115.60 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-c-py harmonic 74.48 118.16 # SOURCE3 3 1.0735 - angle_coeff @angle:c3-c-s4 harmonic 59.64 114.79 # SOURCE3 1 - angle_coeff @angle:c3-c-s6 harmonic 59.65 114.72 # SOURCE3 1 - angle_coeff @angle:c3-c-s harmonic 62.03 123.73 # SOURCE3 9 1.4528 - angle_coeff @angle:c3-c-sh harmonic 61.97 114.21 # SOURCE3 3 2.3916 - angle_coeff @angle:c3-c-ss harmonic 62.41 114.32 # SOURCE3 5 2.7478 - angle_coeff @angle:c3-c-sx harmonic 59.48 113.97 # SOURCE3 3 0.0610 - angle_coeff @angle:c3-c-sy harmonic 59.89 114.28 # SOURCE3 3 0.7341 - angle_coeff @angle:ca-c-ca harmonic 63.03 118.58 # SOURCE4 144 2.1146 - angle_coeff @angle:ca-c-cc harmonic 64.24 116.07 # CORR 257 - angle_coeff @angle:ca-c-cd harmonic 64.24 116.07 # CORR 257 - angle_coeff @angle:ca-c-ce harmonic 63.21 118.92 # CORR 36 - angle_coeff @angle:ca-c-cf harmonic 63.21 118.92 # CORR 36 - angle_coeff @angle:ca-c-h4 harmonic 46.52 115.14 # SOURCE4 30 0.7320 - angle_coeff @angle:ca-c-ha harmonic 46.80 114.12 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-c-n harmonic 68.47 115.14 # SOURCE4 571 1.4648 - angle_coeff @angle:ca-c-ne harmonic 67.74 114.39 # SOURCE4 5 0.2958 - angle_coeff @angle:ca-c-o harmonic 68.67 123.44 # SOURCE3 18 2.5574 - angle_coeff @angle:ca-c-oh harmonic 70.11 113.44 # SOURCE4 222 0.8421 - angle_coeff @angle:ca-c-os harmonic 68.78 115.54 # SOURCE3 5 2.6708 - angle_coeff @angle:ca-c-s harmonic 62.52 123.04 # SOURCE4 12 0.7935 - angle_coeff @angle:ca-c-sh harmonic 61.05 118.63 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-c-ss harmonic 62.45 115.13 # SOURCE4 12 1.0069 - angle_coeff @angle:br-cc-c harmonic 63.98 115.68 # SOURCE4 8 0.4970 - angle_coeff @angle:br-cc-cc harmonic 61.82 124.89 # SOURCE4 8 1.9479 - angle_coeff @angle:br-cc-cd harmonic 62.26 124.56 # SOURCE4 32 2.4696 - angle_coeff @angle:br-cc-na harmonic 64.60 121.42 # SOURCE4 6 0.5507 - angle_coeff @angle:c2-cc-c3 harmonic 63.27 126.11 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-cc-ca harmonic 65.34 124.66 # CORR 16 - angle_coeff @angle:c2-cc-cc harmonic 66.24 121.77 # CORR 32 - angle_coeff @angle:c2-cc-cd harmonic 69.09 117.02 # SOURCE3 2 0.0703 - angle_coeff @angle:c2-cc-ha harmonic 48.69 122.72 # SOURCE3 2 0.0092 - angle_coeff @angle:c2-cc-n harmonic 67.74 126.90 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-cc-os harmonic 70.10 120.79 # CORR 13 - angle_coeff @angle:c-c-c3 harmonic 61.72 116.86 # SOURCE3 5 0.1653 - angle_coeff @angle:c3-cc-ca harmonic 61.96 125.89 # CORR 127 - angle_coeff @angle:c3-cc-cc harmonic 64.66 115.97 # SOURCE3 4 3.0507 - angle_coeff @angle:c3-cc-cd harmonic 64.81 119.45 # SOURCE3 35 8.2040 - angle_coeff @angle:c3-cc-cf harmonic 65.34 117.84 # CORR 2 - angle_coeff @angle:c3-cc-ha harmonic 45.11 121.52 # SOURCE3 32 3.2091 - angle_coeff @angle:c3-cc-n2 harmonic 65.80 126.87 # CORR 9 - angle_coeff @angle:c3-cc-n harmonic 66.33 119.11 # CORR 68 - angle_coeff @angle:c3-cc-na harmonic 65.50 122.78 # CORR 632 - angle_coeff @angle:c3-cc-nc harmonic 65.90 120.94 # CORR 309 - angle_coeff @angle:c3-cc-nd harmonic 66.32 122.13 # CORR 475 - angle_coeff @angle:c3-cc-os harmonic 67.54 116.88 # CORR 203 - angle_coeff @angle:c3-cc-ss harmonic 61.21 121.66 # CORR 171 - angle_coeff @angle:c-c-c harmonic 62.30 111.68 # SOURCE3 2 6.1226 - angle_coeff @angle:c-c-ca harmonic 61.73 118.34 # SOURCE4 26 1.0692 - angle_coeff @angle:ca-cc-cc harmonic 67.66 111.04 # SOURCE3 9 7.9455 - angle_coeff @angle:ca-cc-cd harmonic 68.23 113.51 # SOURCE3 26 7.4229 - angle_coeff @angle:ca-cc-ce harmonic 62.51 127.87 # SOURCE4 11 1.7579 - angle_coeff @angle:ca-cc-h4 harmonic 45.57 128.66 # SOURCE3 10 3.1167 - angle_coeff @angle:ca-cc-ha harmonic 46.40 124.04 # SOURCE3 34 3.6691 - angle_coeff @angle:ca-cc-n harmonic 68.46 117.67 # CORR 18 - angle_coeff @angle:ca-cc-nc harmonic 67.69 120.67 # CORR 162 - angle_coeff @angle:ca-cc-nd harmonic 67.92 123.02 # CORR 188 - angle_coeff @angle:ca-cc-nh harmonic 67.46 122.45 # SOURCE4 9 1.4092 - angle_coeff @angle:ca-cc-oh harmonic 69.61 117.71 # CORR 21 - angle_coeff @angle:ca-cc-os harmonic 69.82 115.16 # CORR 134 - angle_coeff @angle:ca-cc-ss harmonic 62.30 120.51 # CORR 43 - angle_coeff @angle:c-cc-c2 harmonic 65.60 120.92 # CORR 22 - angle_coeff @angle:c-cc-c3 harmonic 63.60 117.42 # CORR 126 - angle_coeff @angle:c-cc-c harmonic 63.42 121.17 # CORR 64 - angle_coeff @angle:c-c-cc harmonic 64.02 111.67 # SOURCE3 4 5.5146 - angle_coeff @angle:c-cc-ca harmonic 63.55 122.95 # SOURCE3 1 0.0000 - angle_coeff @angle:c-cc-cc harmonic 63.72 122.69 # SOURCE3 2 0.0000 - angle_coeff @angle:cc-c-cc harmonic 64.80 116.04 # CORR 56 - angle_coeff @angle:cc-cc-cc harmonic 67.88 110.70 # SOURCE3 54 3.4091 - angle_coeff @angle:cc-cc-cd harmonic 68.16 114.19 # SOURCE3 517 6.5960 - angle_coeff @angle:cc-cc-ce harmonic 62.78 127.20 # CORR 42 - angle_coeff @angle:cc-cc-cf harmonic 65.88 122.59 # CORR 39 - angle_coeff @angle:cc-cc-cg harmonic 63.63 126.15 # CORR 27 - angle_coeff @angle:c-cc-cd harmonic 65.25 121.42 # CORR 1708 - angle_coeff @angle:cc-c-cd harmonic 65.73 112.79 # SOURCE3 1 0.0000 - angle_coeff @angle:c-cc-ce harmonic 63.20 122.73 # CORR 10 - angle_coeff @angle:cc-c-ce harmonic 64.64 115.68 # SOURCE4 6 1.2033 - angle_coeff @angle:cc-cc-f harmonic 66.35 119.41 # SOURCE4 7 0.4917 - angle_coeff @angle:c-cc-cg harmonic 64.98 118.14 # SOURCE4 7 0.7745 - angle_coeff @angle:cc-cc-h4 harmonic 45.56 129.47 # SOURCE3 171 2.2734 - angle_coeff @angle:cc-cc-ha harmonic 47.14 120.86 # CORR 1751 - angle_coeff @angle:c-cc-cl harmonic 58.39 116.05 # CORR 24 - angle_coeff @angle:cc-cc-n2 harmonic 69.48 121.15 # CORR 12 - angle_coeff @angle:cc-cc-n harmonic 67.95 119.89 # SOURCE3 36 0.2095 - angle_coeff @angle:cc-cc-na harmonic 72.21 106.80 # SOURCE3 33 0.6297 - angle_coeff @angle:cc-cc-nc harmonic 67.53 121.69 # CORR 105 - angle_coeff @angle:cc-cc-nd harmonic 71.15 112.56 # SOURCE3 141 4.2871 - angle_coeff @angle:cc-cc-nh harmonic 68.41 119.51 # CORR 228 - angle_coeff @angle:cc-cc-oh harmonic 68.53 121.96 # CORR 27 - angle_coeff @angle:cc-cc-os harmonic 69.34 117.23 # CORR 211 - angle_coeff @angle:cc-cc-pd harmonic 80.79 115.36 # SOURCE3 84 same_as_cd-cd-pc - angle_coeff @angle:cc-cc-ss harmonic 62.45 120.12 # CORR 31 - angle_coeff @angle:cc-cc-sy harmonic 59.22 128.36 # SOURCE4 8 0.9813 - angle_coeff @angle:c-c-cd harmonic 64.02 111.67 # SOURCE3 4 5.5146 - angle_coeff @angle:cd-cc-cd harmonic 67.89 120.23 # CORR 133 - angle_coeff @angle:cd-cc-ce harmonic 63.67 128.41 # CORR 210 - angle_coeff @angle:cd-cc-cl harmonic 57.46 123.70 # CORR 62 - angle_coeff @angle:cd-cc-f harmonic 67.42 121.08 # SOURCE4 28 0.8788 - angle_coeff @angle:cd-cc-h4 harmonic 47.19 129.11 # SOURCE3 418 3.1355 - angle_coeff @angle:cd-cc-ha harmonic 48.35 122.89 # SOURCE3 584 2.9334 - angle_coeff @angle:cd-cc-n harmonic 70.72 115.52 # SOURCE3 52 1.3322 - angle_coeff @angle:cd-cc-na harmonic 72.91 109.42 # SOURCE3 265 2.6051 - angle_coeff @angle:cd-cc-nc harmonic 72.01 111.75 # CORR 1101 - angle_coeff @angle:cd-cc-nh harmonic 68.69 123.89 # CORR 106 - angle_coeff @angle:cd-cc-no harmonic 65.78 128.95 # SOURCE4 117 1.4740 - angle_coeff @angle:cd-cc-oh harmonic 69.56 123.89 # CORR 106 - angle_coeff @angle:cd-cc-os harmonic 69.96 120.30 # SOURCE3 64 5.4354 - angle_coeff @angle:cd-cc-ss harmonic 65.44 111.55 # CORR 884 - angle_coeff @angle:cd-cc-sy harmonic 60.54 124.91 # CORR 41 - angle_coeff @angle:ce-cc-na harmonic 66.32 124.22 # CORR 48 - angle_coeff @angle:ce-cc-nc harmonic 67.01 121.29 # CORR 37 - angle_coeff @angle:ce-cc-nd harmonic 67.80 121.51 # CORR 37 - angle_coeff @angle:ce-cc-os harmonic 68.17 119.03 # CORR 66 - angle_coeff @angle:ce-cc-ss harmonic 61.83 121.44 # CORR 38 - angle_coeff @angle:c-cc-f harmonic 66.16 116.87 # SOURCE4 16 0.5322 - angle_coeff @angle:cg-cc-na harmonic 67.51 122.35 # SOURCE4 5 0.8112 - angle_coeff @angle:cg-cc-ss harmonic 62.33 120.70 # SOURCE4 12 0.9090 - angle_coeff @angle:cc-c-h4 harmonic 47.13 115.45 # SOURCE4 5 0.8021 - angle_coeff @angle:c-cc-ha harmonic 46.99 117.02 # SOURCE3 56 1.9713 - angle_coeff @angle:cl-cc-na harmonic 59.37 121.61 # SOURCE4 12 0.3436 - angle_coeff @angle:cl-cc-nd harmonic 59.35 122.97 # CORR 6 - angle_coeff @angle:cl-cc-ss harmonic 58.09 119.85 # SOURCE4 11 1.0626 - angle_coeff @angle:c-cc-n2 harmonic 68.54 120.89 # CORR 2 - angle_coeff @angle:c-cc-n harmonic 68.11 116.32 # CORR 21 - angle_coeff @angle:cc-c-n harmonic 70.19 111.86 # SOURCE3 36 2.3407 - angle_coeff @angle:c-cc-nc harmonic 66.19 123.47 # CORR 24 - angle_coeff @angle:cc-c-nd harmonic 67.92 116.21 # CORR 33 - angle_coeff @angle:c-cc-nd harmonic 67.50 121.67 # CORR 47 - angle_coeff @angle:c-cc-ne harmonic 67.11 119.88 # SOURCE4 6 0.3139 - angle_coeff @angle:cc-c-o harmonic 68.91 125.71 # SOURCE3 66 2.4784 - angle_coeff @angle:c-cc-oh harmonic 70.04 113.64 # CORR 53 - angle_coeff @angle:cc-c-oh harmonic 71.00 113.10 # CORR 85 - angle_coeff @angle:c-cc-os harmonic 67.83 119.39 # CORR 78 - angle_coeff @angle:cc-c-os harmonic 70.50 112.30 # SOURCE3 6 2.7842 - angle_coeff @angle:cc-c-s harmonic 61.67 127.94 # SOURCE4 12 0.9342 - angle_coeff @angle:cc-c-ss harmonic 63.47 112.52 # SOURCE4 10 0.6933 - angle_coeff @angle:cx-cc-nd harmonic 65.61 127.75 # SOURCE4 12 1.7156 - angle_coeff @angle:cx-cc-os harmonic 67.94 118.08 # SOURCE4 10 0.0955 - angle_coeff @angle:cd-c-cd harmonic 64.80 116.04 # CORR 56 - angle_coeff @angle:cd-c-cx harmonic 63.88 117.46 # SOURCE4 13 0.1625 - angle_coeff @angle:cd-c-n harmonic 70.19 111.86 # SOURCE3 36 2.3407 - angle_coeff @angle:cd-c-nc harmonic 67.92 116.21 # CORR 33 - angle_coeff @angle:cd-c-nd harmonic 68.65 113.75 # SOURCE4 14 0.0860 - angle_coeff @angle:cd-c-o harmonic 68.91 125.71 # SOURCE3 66 2.4784 - angle_coeff @angle:cd-c-oh harmonic 71.00 113.10 # CORR 85 - angle_coeff @angle:cd-c-os harmonic 70.50 112.30 # SOURCE3 6 2.7842 - angle_coeff @angle:ce-c-ce harmonic 64.34 115.80 # CORR 74 - angle_coeff @angle:ce-c-cf harmonic 64.04 116.89 # SOURCE4 11 1.6021 - angle_coeff @angle:ce-c-cx harmonic 63.95 116.25 # SOURCE4 6 0.6351 - angle_coeff @angle:ce-c-h4 harmonic 46.93 114.88 # SOURCE4 19 0.3355 - angle_coeff @angle:ce-c-ha harmonic 46.93 115.22 # SOURCE3 7 2.4188 - angle_coeff @angle:ce-c-n harmonic 68.80 115.27 # CORR 32 - angle_coeff @angle:ce-c-o harmonic 69.27 122.92 # SOURCE3 17 3.5085 - angle_coeff @angle:ce-c-oh harmonic 70.32 114.09 # CORR 128 - angle_coeff @angle:ce-c-os harmonic 70.16 112.28 # CORR 149 - angle_coeff @angle:ce-c-s harmonic 64.09 117.80 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-c-ss harmonic 63.94 110.39 # SOURCE4 5 0.6050 - angle_coeff @angle:cf-c-cf harmonic 64.34 115.80 # CORR 74 - angle_coeff @angle:cf-c-ha harmonic 46.93 115.22 # SOURCE3 7 same_as_ce-c-ha - angle_coeff @angle:cf-c-n harmonic 68.80 115.27 # CORR 32 - angle_coeff @angle:cf-c-o harmonic 69.27 122.92 # SOURCE3 17 3.5085 - angle_coeff @angle:cf-c-oh harmonic 70.32 114.09 # CORR 128 - angle_coeff @angle:cf-c-os harmonic 70.16 112.28 # CORR 149 - angle_coeff @angle:cf-c-s harmonic 64.09 117.80 # SOURCE3 1 same_as_ce-c-s - angle_coeff @angle:cg-c-cg harmonic 65.44 115.38 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-c-ha harmonic 47.80 113.90 # SOURCE2 1 0.0000 - angle_coeff @angle:cg-c-o harmonic 70.21 122.31 # SOURCE3 2 0.0000 - angle_coeff @angle:c-c-h4 harmonic 44.62 116.36 # SOURCE4 5 0.5586 - angle_coeff @angle:h4-cc-n harmonic 50.39 117.62 # SOURCE3 53 0.9721 - angle_coeff @angle:h4-cc-na harmonic 50.22 119.66 # SOURCE3 294 2.4702 - angle_coeff @angle:h4-cc-nc harmonic 50.00 120.03 # SOURCE3 16 2.3863 - angle_coeff @angle:h4-cc-nd harmonic 51.39 119.11 # SOURCE3 135 1.6946 - angle_coeff @angle:h4-cc-os harmonic 52.27 111.89 # SOURCE3 61 2.3500 - angle_coeff @angle:h4-cc-ss harmonic 42.95 117.75 # SOURCE3 40 3.1156 - angle_coeff @angle:h5-cc-n harmonic 50.84 115.72 # CORR 20 - angle_coeff @angle:h5-cc-na harmonic 49.76 122.10 # SOURCE3 16 1.4626 - angle_coeff @angle:h5-cc-nc harmonic 49.29 123.70 # SOURCE3 6 0.3547 - angle_coeff @angle:h5-cc-nd harmonic 50.13 125.38 # SOURCE3 40 2.2157 - angle_coeff @angle:h5-cc-os harmonic 51.30 116.33 # SOURCE3 12 3.2919 - angle_coeff @angle:h5-cc-ss harmonic 42.19 122.00 # SOURCE3 6 0.7237 - angle_coeff @angle:c-c-ha harmonic 44.85 115.43 # SOURCE2 3 0.6549 - angle_coeff @angle:ha-cc-na harmonic 49.82 121.50 # SOURCE2 1 0.0000 - angle_coeff @angle:ha-cc-nc harmonic 50.73 116.54 # SOURCE3 5 1.4482 - angle_coeff @angle:ha-cc-nd harmonic 51.41 118.88 # SOURCE3 20 2.8923 - angle_coeff @angle:ha-cc-os harmonic 52.49 110.86 # SOURCE3 7 1.3846 - angle_coeff @angle:ha-cc-pd harmonic 53.59 121.76 # SOURCE3 84 same_as_ha-cd-pc - angle_coeff @angle:ha-cc-ss harmonic 42.26 121.64 # SOURCE2 5 1.3276 - angle_coeff @angle:ch-c-ch harmonic 65.44 115.38 # SOURCE3 1 same_as_cg-c-cg - angle_coeff @angle:ch-c-ha harmonic 47.80 113.90 # SOURCE2 1 same_as_cg-c-ha - angle_coeff @angle:ch-c-o harmonic 70.21 122.31 # SOURCE3 2 same_as_cg-c-o - angle_coeff @angle:cl-c-cl harmonic 54.78 111.30 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-c-f harmonic 59.05 112.00 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-c-ha harmonic 40.42 109.90 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-c-o harmonic 59.78 121.51 # SOURCE3 6 1.6987 - angle_coeff @angle:cl-c-s harmonic 56.74 127.60 # SOURCE2 1 0.0000 - angle_coeff @angle:c-c-n harmonic 67.53 112.14 # SOURCE4 53 2.1247 - angle_coeff @angle:na-cc-nc harmonic 70.72 121.62 # CORR 231 - angle_coeff @angle:na-cc-nd harmonic 74.78 112.02 # SOURCE3 17 2.2434 - angle_coeff @angle:na-cc-no harmonic 68.48 124.90 # SOURCE4 48 0.7933 - angle_coeff @angle:na-cc-oh harmonic 73.25 117.26 # SOURCE4 16 0.9090 - angle_coeff @angle:na-cc-sx harmonic 63.25 117.04 # SOURCE4 13 0.4187 - angle_coeff @angle:na-cc-sy harmonic 63.13 120.55 # SOURCE4 7 1.7547 - angle_coeff @angle:nc-cc-nd harmonic 73.35 115.96 # CORR 222 - angle_coeff @angle:nc-cc-nh harmonic 72.33 116.85 # CORR 35 - angle_coeff @angle:nc-cc-no harmonic 69.31 121.54 # SOURCE4 7 0.9221 - angle_coeff @angle:nc-cc-ss harmonic 64.63 119.86 # SOURCE3 2 0.0000 - angle_coeff @angle:nd-cc-nd harmonic 70.88 128.17 # SOURCE4 7 0.0269 - angle_coeff @angle:nd-cc-ne harmonic 69.29 129.66 # SOURCE4 7 0.4306 - angle_coeff @angle:nd-cc-nh harmonic 72.41 120.11 # SOURCE3 5 0.9313 - angle_coeff @angle:nd-cc-no harmonic 69.90 122.68 # SOURCE4 16 0.3393 - angle_coeff @angle:nd-cc-oh harmonic 72.93 121.54 # CORR 22 - angle_coeff @angle:nd-cc-os harmonic 73.85 116.29 # CORR 209 - angle_coeff @angle:nd-cc-sh harmonic 62.75 124.92 # SOURCE4 5 0.9563 - angle_coeff @angle:nd-cc-ss harmonic 66.51 114.51 # SOURCE3 8 0.3449 - angle_coeff @angle:nd-cc-sx harmonic 60.81 127.60 # SOURCE4 14 1.1650 - angle_coeff @angle:nd-cc-sy harmonic 62.75 123.08 # SOURCE4 13 1.0531 - angle_coeff @angle:ne-cc-ss harmonic 65.39 116.99 # SOURCE4 7 0.1657 - angle_coeff @angle:nh-cc-nh harmonic 72.93 115.96 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-cc-os harmonic 72.96 116.69 # CORR 25 - angle_coeff @angle:nh-cc-ss harmonic 64.19 121.94 # CORR 91 - angle_coeff @angle:n-cc-n2 harmonic 74.78 114.48 # SOURCE4 15 2.3208 - angle_coeff @angle:n-cc-na harmonic 70.47 122.14 # CORR 59 - angle_coeff @angle:n-cc-nc harmonic 69.35 125.66 # CORR 64 - angle_coeff @angle:n-cc-nd harmonic 71.12 122.98 # CORR 229 - angle_coeff @angle:n-cc-nh harmonic 72.22 116.87 # CORR 79 - angle_coeff @angle:no-cc-os harmonic 71.01 117.59 # SOURCE4 62 0.2199 - angle_coeff @angle:no-cc-ss harmonic 63.76 121.10 # SOURCE4 10 0.0957 - angle_coeff @angle:n-cc-ss harmonic 63.75 123.03 # CORR 45 - angle_coeff @angle:c-c-o harmonic 67.16 120.99 # SOURCE4 233 2.0333 - angle_coeff @angle:c-c-oh harmonic 68.20 113.23 # SOURCE3 5 0.5615 - angle_coeff @angle:c-c-os harmonic 68.18 111.39 # SOURCE4 14 0.4038 - angle_coeff @angle:os-cc-ss harmonic 61.99 132.01 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-cc-ss harmonic 62.44 121.37 # CORR 22 - angle_coeff @angle:ss-cc-sy harmonic 61.51 121.70 # CORR 39 - angle_coeff @angle:cx-c-cx harmonic 85.45 64.60 # SOURCE2 1 0.0000 - angle_coeff @angle:cx-c-n harmonic 68.69 114.49 # SOURCE4 23 1.4914 - angle_coeff @angle:cx-c-o harmonic 68.88 122.82 # SOURCE4 97 2.2075 - angle_coeff @angle:cx-c-oh harmonic 70.49 112.32 # SOURCE4 10 0.6413 - angle_coeff @angle:cx-c-os harmonic 70.06 111.48 # SOURCE4 16 1.3998 - angle_coeff @angle:cy-c-cy harmonic 70.14 90.55 # SOURCE2 2 2.4500 - angle_coeff @angle:cy-c-n harmonic 75.43 91.54 # SOURCE4 249 0.5104 - angle_coeff @angle:cy-c-o harmonic 64.27 135.04 # SOURCE4 253 1.3450 - angle_coeff @angle:cy-c-oh harmonic 69.09 112.48 # SOURCE4 5 1.0793 - angle_coeff @angle:cy-c-os harmonic 74.55 94.89 # SOURCE4 8 0.6016 - angle_coeff @angle:c2-cd-c3 harmonic 63.27 126.11 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-cd-ca harmonic 65.34 124.66 # CORR 16 - angle_coeff @angle:c2-cd-cc harmonic 69.09 117.02 # SOURCE3 2 same_as_c2-cc-cd - angle_coeff @angle:c2-cd-cd harmonic 66.24 121.77 # CORR 32 - angle_coeff @angle:c2-cd-ha harmonic 48.69 122.72 # SOURCE3 2 same_as_c2-cc-ha - angle_coeff @angle:c2-cd-n harmonic 67.74 126.90 # SOURCE3 1 same_as_c2-cc-n - angle_coeff @angle:c2-cd-os harmonic 70.10 120.79 # CORR 13 - angle_coeff @angle:c3-cd-ca harmonic 61.96 125.89 # CORR 127 - angle_coeff @angle:c3-cd-cc harmonic 64.81 119.45 # SOURCE3 35 8.2040 - angle_coeff @angle:c3-cd-cd harmonic 64.66 115.97 # SOURCE3 4 3.0507 - angle_coeff @angle:c3-cd-ce harmonic 65.34 117.84 # CORR 2 - angle_coeff @angle:c3-cd-ha harmonic 45.11 121.52 # SOURCE3 32 3.2091 - angle_coeff @angle:c3-cd-n2 harmonic 65.80 126.87 # CORR 9 - angle_coeff @angle:c3-cd-n harmonic 66.33 119.11 # CORR 68 - angle_coeff @angle:c3-cd-na harmonic 65.50 122.78 # CORR 632 - angle_coeff @angle:c3-cd-nc harmonic 66.32 122.13 # CORR 475 - angle_coeff @angle:c3-cd-nd harmonic 65.90 120.94 # CORR 309 - angle_coeff @angle:c3-cd-os harmonic 67.54 116.88 # CORR 203 - angle_coeff @angle:c3-cd-ss harmonic 61.21 121.66 # CORR 171 - angle_coeff @angle:ca-cd-cc harmonic 68.23 113.51 # SOURCE3 26 7.4229 - angle_coeff @angle:ca-cd-cd harmonic 67.66 111.04 # SOURCE3 9 7.9455 - angle_coeff @angle:ca-cd-ce harmonic 65.09 125.10 # SOURCE4 9 1.9265 - angle_coeff @angle:ca-cd-h4 harmonic 45.57 128.66 # SOURCE3 10 3.1167 - angle_coeff @angle:ca-cd-ha harmonic 46.40 124.04 # SOURCE3 34 3.6691 - angle_coeff @angle:ca-cd-n harmonic 68.46 117.67 # CORR 18 - angle_coeff @angle:ca-cd-na harmonic 67.03 123.45 # SOURCE4 39 1.9138 - angle_coeff @angle:ca-cd-nc harmonic 67.92 123.02 # CORR 188 - angle_coeff @angle:ca-cd-nd harmonic 67.69 120.67 # CORR 162 - angle_coeff @angle:ca-cd-oh harmonic 69.61 117.71 # CORR 21 - angle_coeff @angle:ca-cd-os harmonic 69.82 115.16 # CORR 134 - angle_coeff @angle:ca-cd-ss harmonic 62.30 120.51 # CORR 43 - angle_coeff @angle:c-cd-c2 harmonic 65.60 120.92 # CORR 22 - angle_coeff @angle:c-cd-c3 harmonic 63.60 117.42 # CORR 126 - angle_coeff @angle:c-cd-c harmonic 63.42 121.17 # CORR 64 - angle_coeff @angle:c-cd-ca harmonic 63.55 122.95 # SOURCE3 1 same_as_c-cc-ca - angle_coeff @angle:c-cd-cc harmonic 65.25 121.42 # CORR 1708 - angle_coeff @angle:cc-cd-cc harmonic 67.89 120.23 # CORR 133 - angle_coeff @angle:cc-cd-cd harmonic 68.16 114.19 # SOURCE3 517 6.5960 - angle_coeff @angle:cc-cd-cf harmonic 63.67 128.41 # CORR 210 - angle_coeff @angle:cc-cd-ch harmonic 64.92 126.05 # SOURCE4 30 1.4695 - angle_coeff @angle:cc-cd-cl harmonic 57.46 123.70 # CORR 62 - angle_coeff @angle:cc-cd-cy harmonic 63.93 122.13 # SOURCE4 10 0.8509 - angle_coeff @angle:c-cd-cd harmonic 63.72 122.69 # SOURCE3 2 0.0000 - angle_coeff @angle:c-cd-cf harmonic 63.20 122.73 # CORR 10 - angle_coeff @angle:cc-cd-h4 harmonic 47.19 129.11 # SOURCE3 418 3.1355 - angle_coeff @angle:cc-cd-ha harmonic 48.35 122.89 # SOURCE3 584 2.9334 - angle_coeff @angle:c-cd-cl harmonic 58.39 116.05 # CORR 24 - angle_coeff @angle:cc-cd-n harmonic 70.72 115.52 # SOURCE3 52 1.3322 - angle_coeff @angle:cc-cd-na harmonic 72.91 109.42 # SOURCE3 265 2.6051 - angle_coeff @angle:cc-cd-nc harmonic 69.42 123.82 # SOURCE4 14 0.3678 - angle_coeff @angle:cc-cd-nd harmonic 72.01 111.75 # CORR 1101 - angle_coeff @angle:cc-cd-nh harmonic 68.69 123.89 # CORR 106 - angle_coeff @angle:cc-cd-oh harmonic 69.56 123.89 # CORR 106 - angle_coeff @angle:cc-cd-os harmonic 69.96 120.30 # SOURCE3 64 5.4354 - angle_coeff @angle:cc-cd-ss harmonic 65.44 111.55 # CORR 884 - angle_coeff @angle:cc-cd-sy harmonic 60.54 124.91 # CORR 41 - angle_coeff @angle:cd-cd-cd harmonic 67.88 110.70 # SOURCE3 54 3.4091 - angle_coeff @angle:cd-cd-ce harmonic 65.88 122.59 # CORR 39 - angle_coeff @angle:cd-cd-cf harmonic 62.78 127.20 # CORR 42 - angle_coeff @angle:cd-cd-ch harmonic 63.63 126.15 # CORR 27 - angle_coeff @angle:cd-cd-cy harmonic 63.17 120.93 # SOURCE4 6 1.2205 - angle_coeff @angle:cd-cd-h4 harmonic 45.56 129.47 # SOURCE3 171 2.2734 - angle_coeff @angle:cd-cd-ha harmonic 47.14 120.86 # CORR 1751 - angle_coeff @angle:cd-cd-n2 harmonic 69.48 121.15 # CORR 12 - angle_coeff @angle:cd-cd-n harmonic 67.95 119.89 # SOURCE3 36 0.2095 - angle_coeff @angle:cd-cd-na harmonic 72.21 106.80 # SOURCE3 33 same_as_cc-cc-na - angle_coeff @angle:cd-cd-nc harmonic 71.15 112.56 # SOURCE3 141 4.2871 - angle_coeff @angle:cd-cd-nd harmonic 67.53 121.69 # CORR 105 - angle_coeff @angle:cd-cd-nh harmonic 68.41 119.51 # CORR 228 - angle_coeff @angle:cd-cd-oh harmonic 68.53 121.96 # CORR 27 - angle_coeff @angle:cd-cd-os harmonic 69.34 117.23 # CORR 211 - angle_coeff @angle:cd-cd-pc harmonic 80.79 115.36 # SOURCE3 84 3.2889 - angle_coeff @angle:cd-cd-ss harmonic 62.45 120.12 # CORR 31 - angle_coeff @angle:ce-cd-nd harmonic 68.22 124.90 # SOURCE4 5 2.3975 - angle_coeff @angle:cf-cd-na harmonic 66.32 124.22 # CORR 48 - angle_coeff @angle:cf-cd-nc harmonic 67.80 121.51 # CORR 37 - angle_coeff @angle:cf-cd-nd harmonic 67.01 121.29 # CORR 37 - angle_coeff @angle:cf-cd-os harmonic 68.17 119.03 # CORR 66 - angle_coeff @angle:cf-cd-ss harmonic 61.83 121.44 # CORR 38 - angle_coeff @angle:c-cd-h4 harmonic 46.77 118.19 # SOURCE4 8 0.2226 - angle_coeff @angle:c-cd-ha harmonic 46.99 117.02 # SOURCE3 56 1.9713 - angle_coeff @angle:cl-cd-nc harmonic 59.35 122.97 # CORR 6 - angle_coeff @angle:c-cd-n2 harmonic 68.54 120.89 # CORR 2 - angle_coeff @angle:c-cd-n harmonic 68.11 116.32 # CORR 21 - angle_coeff @angle:c-cd-nc harmonic 67.50 121.67 # CORR 47 - angle_coeff @angle:c-cd-nd harmonic 66.19 123.47 # CORR 24 - angle_coeff @angle:c-cd-oh harmonic 70.04 113.64 # CORR 53 - angle_coeff @angle:c-cd-os harmonic 67.83 119.39 # CORR 78 - angle_coeff @angle:h4-cd-n harmonic 50.39 117.62 # SOURCE3 53 0.9721 - angle_coeff @angle:h4-cd-na harmonic 50.22 119.66 # SOURCE3 294 2.4702 - angle_coeff @angle:h4-cd-nc harmonic 51.39 119.11 # SOURCE3 135 1.6946 - angle_coeff @angle:h4-cd-nd harmonic 50.00 120.03 # SOURCE3 16 2.3863 - angle_coeff @angle:h4-cd-os harmonic 52.27 111.89 # SOURCE3 61 2.3500 - angle_coeff @angle:h4-cd-ss harmonic 42.95 117.75 # SOURCE3 40 3.1156 - angle_coeff @angle:h5-cd-n harmonic 50.84 115.72 # CORR 20 - angle_coeff @angle:h5-cd-na harmonic 49.76 122.10 # SOURCE3 16 1.4626 - angle_coeff @angle:h5-cd-nc harmonic 50.13 125.38 # SOURCE3 40 2.2157 - angle_coeff @angle:h5-cd-nd harmonic 49.29 123.70 # SOURCE3 6 0.3547 - angle_coeff @angle:h5-cd-os harmonic 51.30 116.33 # SOURCE3 12 3.2919 - angle_coeff @angle:h5-cd-ss harmonic 42.19 122.00 # SOURCE3 6 0.7237 - angle_coeff @angle:ha-cd-na harmonic 49.82 121.50 # SOURCE2 1 same_as_ha-cc-na - angle_coeff @angle:ha-cd-nc harmonic 51.41 118.88 # SOURCE3 20 2.8923 - angle_coeff @angle:ha-cd-nd harmonic 50.73 116.54 # SOURCE3 5 1.4482 - angle_coeff @angle:ha-cd-os harmonic 52.49 110.86 # SOURCE3 7 1.3846 - angle_coeff @angle:ha-cd-pc harmonic 53.59 121.76 # SOURCE3 84 2.2216 - angle_coeff @angle:ha-cd-ss harmonic 42.26 121.64 # SOURCE2 5 same_as_ha-cc-ss - angle_coeff @angle:na-cd-nc harmonic 74.78 112.02 # SOURCE3 17 2.2434 - angle_coeff @angle:na-cd-nd harmonic 70.72 121.62 # CORR 231 - angle_coeff @angle:na-cd-nh harmonic 72.43 116.98 # SOURCE4 46 1.4937 - angle_coeff @angle:na-cd-ss harmonic 67.07 111.46 # SOURCE4 20 0.8600 - angle_coeff @angle:nc-cd-nd harmonic 73.35 115.96 # CORR 222 - angle_coeff @angle:nc-cd-nh harmonic 72.41 120.11 # SOURCE3 5 0.9313 - angle_coeff @angle:nc-cd-oh harmonic 72.93 121.54 # CORR 22 - angle_coeff @angle:nc-cd-os harmonic 73.85 116.29 # CORR 209 - angle_coeff @angle:nc-cd-ss harmonic 66.51 114.51 # SOURCE3 8 0.3449 - angle_coeff @angle:nd-cd-nd harmonic 69.47 125.58 # SOURCE4 13 0.4672 - angle_coeff @angle:nd-cd-nh harmonic 72.33 116.85 # CORR 35 - angle_coeff @angle:nd-cd-ss harmonic 64.63 119.86 # SOURCE3 2 same_as_nc-cc-ss - angle_coeff @angle:nh-cd-nh harmonic 72.93 115.96 # SOURCE3 1 same_as_nh-cc-nh - angle_coeff @angle:nh-cd-os harmonic 72.96 116.69 # CORR 25 - angle_coeff @angle:nh-cd-ss harmonic 64.19 121.94 # CORR 91 - angle_coeff @angle:n-cd-na harmonic 70.47 122.14 # CORR 59 - angle_coeff @angle:n-cd-nc harmonic 71.12 122.98 # CORR 229 - angle_coeff @angle:n-cd-nd harmonic 69.35 125.66 # CORR 64 - angle_coeff @angle:n-cd-nh harmonic 72.22 116.87 # CORR 79 - angle_coeff @angle:n-cd-ss harmonic 63.75 123.03 # CORR 45 - angle_coeff @angle:oh-cd-os harmonic 75.54 111.61 # SOURCE4 6 1.1909 - angle_coeff @angle:os-cd-ss harmonic 61.99 132.01 # SOURCE3 1 same_as_os-cc-ss - angle_coeff @angle:ss-cd-ss harmonic 62.44 121.37 # CORR 22 - angle_coeff @angle:ss-cd-sy harmonic 61.51 121.70 # CORR 39 - angle_coeff @angle:c2-ce-c3 harmonic 64.30 122.89 # SOURCE3 7 1.0449 - angle_coeff @angle:c2-ce-ca harmonic 65.16 123.08 # SOURCE3 6 2.1589 - angle_coeff @angle:c2-ce-cc harmonic 65.62 123.27 # CORR 72 - angle_coeff @angle:c2-ce-ce harmonic 65.73 123.08 # SOURCE3 12 0.6518 - angle_coeff @angle:c2-ce-cg harmonic 66.66 121.67 # CORR 21 - angle_coeff @angle:c2-ce-cl harmonic 57.87 119.51 # SOURCE4 24 1.4963 - angle_coeff @angle:c2-ce-h4 harmonic 48.64 125.58 # SOURCE4 11 0.9381 - angle_coeff @angle:c2-ce-ha harmonic 49.56 121.10 # SOURCE3 46 2.4054 - angle_coeff @angle:c2-ce-n1 harmonic 72.67 117.85 # SOURCE4 7 0.3180 - angle_coeff @angle:c2-ce-n2 harmonic 70.34 128.70 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-ce-na harmonic 69.29 119.19 # SOURCE4 5 0.8452 - angle_coeff @angle:c2-ce-ne harmonic 69.73 118.32 # SOURCE3 7 1.0468 - angle_coeff @angle:c2-ce-oh harmonic 70.32 123.78 # SOURCE4 10 1.8182 - angle_coeff @angle:c2-ce-p2 harmonic 77.91 118.24 # SOURCE3 1 - angle_coeff @angle:c2-ce-pe harmonic 77.59 118.76 # SOURCE3 8 2.3984 - angle_coeff @angle:c2-ce-px harmonic 77.17 119.72 # SOURCE3 6 0.5213 - angle_coeff @angle:c2-ce-py harmonic 77.39 122.13 # SOURCE3 5 3.1367 - angle_coeff @angle:c2-ce-sx harmonic 61.64 119.87 # SOURCE3 5 0.8557 - angle_coeff @angle:c2-ce-sy harmonic 61.96 120.35 # SOURCE3 5 0.5401 - angle_coeff @angle:c3-ce-ca harmonic 62.76 119.28 # CORR 178 - angle_coeff @angle:c3-ce-cc harmonic 63.42 118.22 # CORR 39 - angle_coeff @angle:c3-ce-ce harmonic 63.80 116.99 # CORR 244 - angle_coeff @angle:c3-ce-cf harmonic 64.52 122.11 # CORR 221 - angle_coeff @angle:c3-ce-cg harmonic 63.79 118.48 # SOURCE4 8 1.4756 - angle_coeff @angle:c3-ce-n2 harmonic 66.92 122.70 # CORR 81 - angle_coeff @angle:c3-ce-nf harmonic 67.26 120.75 # SOURCE4 6 2.1938 - angle_coeff @angle:c3-ce-nh harmonic 65.76 119.90 # SOURCE4 5 0.9634 - angle_coeff @angle:ca-ce-ca harmonic 63.94 117.58 # CORR 112 - angle_coeff @angle:ca-ce-cc harmonic 64.21 118.06 # CORR 17 - angle_coeff @angle:ca-ce-ce harmonic 63.84 119.62 # SOURCE4 14 1.9171 - angle_coeff @angle:ca-ce-cf harmonic 64.07 127.39 # CORR 318 - angle_coeff @angle:ca-ce-cl harmonic 57.99 114.22 # SOURCE4 6 1.3164 - angle_coeff @angle:ca-ce-h4 harmonic 46.71 116.86 # SOURCE4 74 0.9179 - angle_coeff @angle:ca-ce-ha harmonic 47.07 115.16 # CORR 345 - angle_coeff @angle:ca-ce-n2 harmonic 68.51 120.72 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-ce-nf harmonic 67.74 122.66 # CORR 22 - angle_coeff @angle:ca-ce-nh harmonic 67.87 115.51 # SOURCE4 93 0.9284 - angle_coeff @angle:ca-ce-oh harmonic 68.85 116.37 # CORR 11 - angle_coeff @angle:ca-ce-os harmonic 68.60 115.58 # SOURCE4 8 1.0735 - angle_coeff @angle:ca-ce-ss harmonic 61.21 117.73 # SOURCE4 5 1.1596 - angle_coeff @angle:c-ce-c2 harmonic 65.82 120.42 # SOURCE3 13 1.8877 - angle_coeff @angle:c-ce-c3 harmonic 63.35 116.92 # CORR 188 - angle_coeff @angle:c-ce-c harmonic 62.59 122.38 # CORR 23 - angle_coeff @angle:c-ce-ca harmonic 63.79 117.98 # SOURCE4 8 1.5129 - angle_coeff @angle:cc-ce-cd harmonic 63.28 130.36 # SOURCE4 5 2.3402 - angle_coeff @angle:cc-ce-cf harmonic 64.87 126.20 # CORR 88 - angle_coeff @angle:c-ce-cd harmonic 63.81 126.07 # CORR 2 - angle_coeff @angle:c-ce-ce harmonic 63.46 120.89 # SOURCE4 16 1.8719 - angle_coeff @angle:c-ce-cf harmonic 64.26 126.41 # SOURCE3 2 5.7847 - angle_coeff @angle:c-ce-cg harmonic 64.57 118.32 # SOURCE4 15 1.0595 - angle_coeff @angle:cc-ce-h4 harmonic 47.52 115.40 # SOURCE4 29 0.8744 - angle_coeff @angle:cc-ce-ha harmonic 47.53 115.45 # CORR 113 - angle_coeff @angle:c-ce-cl harmonic 57.67 115.40 # SOURCE4 6 1.0958 - angle_coeff @angle:cc-ce-n2 harmonic 68.94 121.28 # CORR 69 - angle_coeff @angle:cc-ce-nh harmonic 67.31 119.17 # SOURCE4 8 2.1378 - angle_coeff @angle:c-ce-cy harmonic 72.72 88.22 # SOURCE4 19 0.3234 - angle_coeff @angle:cd-ce-ce harmonic 64.81 124.49 # CORR 12 - angle_coeff @angle:cd-ce-ha harmonic 49.97 115.48 # CORR 39 - angle_coeff @angle:ce-ce-ce harmonic 64.55 118.74 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-ce-cf harmonic 65.46 124.19 # CORR 341 - angle_coeff @angle:ce-ce-cl harmonic 57.29 117.93 # SOURCE4 12 0.2639 - angle_coeff @angle:ce-ce-h4 harmonic 47.06 117.97 # CORR 19 - angle_coeff @angle:ce-ce-ha harmonic 47.50 115.90 # SOURCE3 12 0.4670 - angle_coeff @angle:ce-ce-n1 harmonic 66.79 127.15 # CORR 4 - angle_coeff @angle:ce-ce-n2 harmonic 69.57 119.33 # CORR 13 - angle_coeff @angle:ce-ce-oh harmonic 69.29 116.89 # SOURCE4 11 2.0380 - angle_coeff @angle:cf-ce-cg harmonic 66.10 123.79 # CORR 41 - angle_coeff @angle:cf-ce-cy harmonic 60.53 137.74 # SOURCE4 13 0.3952 - angle_coeff @angle:cf-ce-h4 harmonic 49.02 123.76 # SOURCE4 5 1.0909 - angle_coeff @angle:cf-ce-ha harmonic 50.21 118.12 # CORR 655 - angle_coeff @angle:cf-ce-n1 harmonic 72.03 120.03 # SOURCE4 6 1.9451 - angle_coeff @angle:cf-ce-n harmonic 72.60 108.25 # CORR 64 - angle_coeff @angle:cf-ce-nh harmonic 69.48 121.52 # SOURCE4 12 2.0106 - angle_coeff @angle:cf-ce-oh harmonic 70.92 121.78 # CORR 24 - angle_coeff @angle:cg-ce-cg harmonic 65.58 118.26 # CORR 7 - angle_coeff @angle:cg-ce-ha harmonic 47.93 116.54 # CORR 18 - angle_coeff @angle:cg-ce-n1 harmonic 69.49 119.50 # CORR 2 - angle_coeff @angle:cg-ce-n2 harmonic 69.59 121.43 # SOURCE4 6 0.8382 - angle_coeff @angle:c-ce-ha harmonic 46.59 117.26 # SOURCE3 11 2.7158 - angle_coeff @angle:c-ce-n harmonic 66.20 118.62 # CORR 137 - angle_coeff @angle:c-ce-nh harmonic 67.79 115.62 # CORR 19 - angle_coeff @angle:c-ce-oh harmonic 68.34 117.92 # SOURCE4 5 1.4580 - angle_coeff @angle:c-ce-os harmonic 69.09 113.78 # SOURCE4 21 1.8258 - angle_coeff @angle:h4-ce-n1 harmonic 52.58 116.36 # SOURCE4 7 0.2182 - angle_coeff @angle:h4-ce-n2 harmonic 52.36 121.58 # CORR 116 - angle_coeff @angle:h4-ce-ne harmonic 49.72 115.81 # SOURCE4 7 1.9836 - angle_coeff @angle:ha-ce-n1 harmonic 52.70 115.96 # CORR 4 - angle_coeff @angle:ha-ce-n2 harmonic 52.85 119.51 # SOURCE3 2 0.4623 - angle_coeff @angle:ha-ce-ne harmonic 49.16 118.59 # SOURCE3 5 1.1113 - angle_coeff @angle:ha-ce-nh harmonic 50.62 114.99 # CORR 2 - angle_coeff @angle:ha-ce-p2 harmonic 51.40 120.11 # SOURCE3 1 - angle_coeff @angle:ha-ce-pe harmonic 51.44 119.33 # SOURCE3 6 0.8966 - angle_coeff @angle:ha-ce-px harmonic 51.66 117.90 # SOURCE3 6 0.1809 - angle_coeff @angle:ha-ce-py harmonic 52.32 118.72 # SOURCE3 3 0.3064 - angle_coeff @angle:ha-ce-sx harmonic 41.85 115.45 # SOURCE3 3 0.6640 - angle_coeff @angle:ha-ce-sy harmonic 42.34 114.86 # SOURCE3 3 0.4717 - angle_coeff @angle:n2-ce-nh harmonic 71.56 124.96 # CORR 92 - angle_coeff @angle:n2-ce-os harmonic 74.58 118.13 # SOURCE4 6 0.1367 - angle_coeff @angle:n2-ce-ss harmonic 64.40 117.23 # SOURCE4 6 2.0518 - angle_coeff @angle:ne-ce-ne harmonic 68.07 123.87 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-ce-nh harmonic 71.89 112.91 # SOURCE4 12 1.1263 - angle_coeff @angle:nf-ce-nh harmonic 73.31 118.13 # SOURCE4 6 0.5842 - angle_coeff @angle:pe-ce-pe harmonic 92.40 129.79 # SOURCE3 1 0.0000 - angle_coeff @angle:py-ce-py harmonic 102.62 108.06 # SOURCE3 1 0.0000 - angle_coeff @angle:sx-ce-sx harmonic 60.61 120.32 # SOURCE3 1 0.0000 - angle_coeff @angle:sy-ce-sy harmonic 61.21 119.97 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-cf-c3 harmonic 64.30 122.89 # SOURCE3 7 same_as_c2-ce-c3 - angle_coeff @angle:c2-cf-ca harmonic 65.16 123.08 # SOURCE3 6 same_as_c2-ce-ca - angle_coeff @angle:c2-cf-cd harmonic 65.62 123.27 # CORR 72 - angle_coeff @angle:c2-cf-cf harmonic 65.73 123.08 # SOURCE3 12 same_as_c2-ce-ce - angle_coeff @angle:c2-cf-ch harmonic 66.66 121.67 # CORR 21 - angle_coeff @angle:c2-cf-ha harmonic 49.56 121.10 # SOURCE3 46 same_as_c2-ce-ha - angle_coeff @angle:c2-cf-n2 harmonic 70.34 128.70 # SOURCE3 1 same_as_c2-ce-n2 - angle_coeff @angle:c2-cf-nf harmonic 69.73 118.32 # SOURCE3 7 same_as_c2-ce-ne - angle_coeff @angle:c2-cf-p2 harmonic 77.91 118.24 # SOURCE3 1 same_as_c2-ce-p2 - angle_coeff @angle:c2-cf-pf harmonic 77.59 118.76 # SOURCE3 8 same_as_c2-ce-pe - angle_coeff @angle:c2-cf-px harmonic 77.17 119.72 # SOURCE3 6 same_as_c2-ce-px - angle_coeff @angle:c2-cf-py harmonic 77.39 122.13 # SOURCE3 5 same_as_c2-ce-py - angle_coeff @angle:c2-cf-sx harmonic 61.64 119.87 # SOURCE3 5 same_as_c2-ce-sx - angle_coeff @angle:c2-cf-sy harmonic 61.96 120.35 # SOURCE3 5 same_as_c2-ce-sy - angle_coeff @angle:c3-cf-ca harmonic 62.76 119.28 # CORR 178 - angle_coeff @angle:c3-cf-cd harmonic 63.42 118.22 # CORR 39 - angle_coeff @angle:c3-cf-ce harmonic 64.52 122.11 # CORR 221 - angle_coeff @angle:c3-cf-cf harmonic 63.80 116.99 # CORR 244 - angle_coeff @angle:c3-cf-n2 harmonic 66.92 122.70 # CORR 81 - angle_coeff @angle:ca-cf-ca harmonic 63.94 117.58 # CORR 112 - angle_coeff @angle:ca-cf-cc harmonic 62.70 130.80 # SOURCE4 12 1.2696 - angle_coeff @angle:ca-cf-cd harmonic 64.21 118.06 # CORR 17 - angle_coeff @angle:ca-cf-ce harmonic 64.07 127.39 # CORR 318 - angle_coeff @angle:ca-cf-ha harmonic 47.07 115.16 # CORR 345 - angle_coeff @angle:ca-cf-n2 harmonic 68.51 120.72 # SOURCE3 1 same_as_ca-ce-n2 - angle_coeff @angle:ca-cf-ne harmonic 67.74 122.66 # CORR 22 - angle_coeff @angle:ca-cf-oh harmonic 68.85 116.37 # CORR 11 - angle_coeff @angle:c-cf-c2 harmonic 65.82 120.42 # SOURCE3 13 same_as_c-ce-c2 - angle_coeff @angle:c-cf-c3 harmonic 63.35 116.92 # CORR 188 - angle_coeff @angle:c-cf-c harmonic 62.59 122.38 # CORR 23 - angle_coeff @angle:c-cf-cc harmonic 63.81 126.07 # CORR 2 - angle_coeff @angle:cc-cf-cf harmonic 64.81 124.49 # CORR 12 - angle_coeff @angle:c-cf-cd harmonic 64.25 117.76 # SOURCE4 10 1.2451 - angle_coeff @angle:c-cf-ce harmonic 64.26 126.41 # SOURCE3 2 same_as_c-ce-cf - angle_coeff @angle:cc-cf-ha harmonic 49.97 115.48 # CORR 39 - angle_coeff @angle:cd-cf-ce harmonic 64.87 126.20 # CORR 88 - angle_coeff @angle:cd-cf-ha harmonic 47.53 115.45 # CORR 113 - angle_coeff @angle:cd-cf-n2 harmonic 68.94 121.28 # CORR 69 - angle_coeff @angle:ce-cf-cf harmonic 65.46 124.19 # CORR 341 - angle_coeff @angle:ce-cf-ch harmonic 66.10 123.79 # CORR 41 - angle_coeff @angle:ce-cf-ha harmonic 50.21 118.12 # CORR 655 - angle_coeff @angle:ce-cf-n harmonic 72.60 108.25 # CORR 64 - angle_coeff @angle:ce-cf-oh harmonic 70.92 121.78 # CORR 24 - angle_coeff @angle:cf-cf-cf harmonic 64.55 118.74 # SOURCE3 1 same_as_ce-ce-ce - angle_coeff @angle:cf-cf-h4 harmonic 47.06 117.97 # CORR 19 - angle_coeff @angle:cf-cf-ha harmonic 47.50 115.90 # SOURCE3 12 0.4670 - angle_coeff @angle:cf-cf-n1 harmonic 66.79 127.15 # CORR 4 - angle_coeff @angle:cf-cf-n2 harmonic 69.57 119.33 # CORR 13 - angle_coeff @angle:c-cf-ha harmonic 46.59 117.26 # SOURCE3 11 2.7158 - angle_coeff @angle:ch-cf-ch harmonic 65.58 118.26 # CORR 7 - angle_coeff @angle:ch-cf-ha harmonic 47.93 116.54 # CORR 18 - angle_coeff @angle:ch-cf-n1 harmonic 69.49 119.50 # CORR 2 - angle_coeff @angle:c-cf-n2 harmonic 70.16 114.88 # SOURCE4 5 1.3647 - angle_coeff @angle:c-cf-n harmonic 66.20 118.62 # CORR 137 - angle_coeff @angle:c-cf-nh harmonic 67.79 115.62 # CORR 19 - angle_coeff @angle:f-c-f harmonic 72.22 107.35 # SOURCE2 2 0.2500 - angle_coeff @angle:h4-cf-n2 harmonic 52.36 121.58 # CORR 116 - angle_coeff @angle:h4-cf-ne harmonic 52.29 120.21 # SOURCE4 6 0.8104 - angle_coeff @angle:ha-cf-n1 harmonic 52.70 115.96 # CORR 4 - angle_coeff @angle:ha-cf-n2 harmonic 52.85 119.51 # SOURCE3 2 same_as_ha-ce-n2 - angle_coeff @angle:ha-cf-nf harmonic 49.16 118.59 # SOURCE3 5 same_as_ha-ce-ne - angle_coeff @angle:ha-cf-nh harmonic 50.62 114.99 # CORR 2 - angle_coeff @angle:ha-cf-p2 harmonic 51.40 120.11 # SOURCE3 1 same_as_ha-ce-p2 - angle_coeff @angle:ha-cf-pf harmonic 51.44 119.33 # SOURCE3 6 same_as_ha-ce-pe - angle_coeff @angle:ha-cf-px harmonic 51.66 117.90 # SOURCE3 6 same_as_ha-ce-px - angle_coeff @angle:ha-cf-py harmonic 52.32 118.72 # SOURCE3 3 same_as_ha-ce-py - angle_coeff @angle:ha-cf-sx harmonic 41.85 115.45 # SOURCE3 3 same_as_ha-ce-sx - angle_coeff @angle:ha-cf-sy harmonic 42.34 114.86 # SOURCE3 3 same_as_ha-ce-sy - angle_coeff @angle:n2-cf-nh harmonic 71.56 124.96 # CORR 92 - angle_coeff @angle:nf-cf-nf harmonic 68.07 123.87 # SOURCE3 1 same_as_ne-ce-ne - angle_coeff @angle:f-c-o harmonic 73.21 123.44 # SOURCE3 1 - angle_coeff @angle:pf-cf-pf harmonic 92.40 129.79 # SOURCE3 1 same_as_pe-ce-pe - angle_coeff @angle:py-cf-py harmonic 102.62 108.06 # SOURCE3 1 same_as_py-ce-py - angle_coeff @angle:f-c-s harmonic 63.41 124.00 # SOURCE2 1 0.0000 - angle_coeff @angle:sx-cf-sx harmonic 60.61 120.32 # SOURCE3 1 same_as_sx-ce-sx - angle_coeff @angle:sy-cf-sy harmonic 61.21 119.97 # SOURCE3 1 same_as_sy-ce-sy - angle_coeff @angle:c1-cg-ca harmonic 56.52 179.52 # CORR 19 - angle_coeff @angle:c1-cg-cc harmonic 56.97 178.60 # SOURCE4 6 0.3822 - angle_coeff @angle:c1-cg-ce harmonic 56.95 178.05 # CORR 7 - angle_coeff @angle:c1-cg-cg harmonic 58.17 179.70 # CORR 18 - angle_coeff @angle:c1-cg-ne harmonic 62.73 170.02 # SOURCE3 4 1.1724 - angle_coeff @angle:c1-cg-pe harmonic 71.80 173.29 # SOURCE3 11 4.9305 - angle_coeff @angle:ca-cg-ch harmonic 56.91 179.64 # CORR 13 - angle_coeff @angle:ca-cg-n1 harmonic 58.93 179.43 # CORR 103 - angle_coeff @angle:c-cg-c1 harmonic 56.19 179.14 # SOURCE3 2 0.0000 - angle_coeff @angle:cc-cg-n1 harmonic 59.43 178.54 # CORR 50 - angle_coeff @angle:ce-cg-ch harmonic 57.39 177.94 # CORR 17 - angle_coeff @angle:ce-cg-n1 harmonic 59.39 177.97 # CORR 67 - angle_coeff @angle:n1-cg-ne harmonic 64.98 174.44 # CORR 17 - angle_coeff @angle:h4-c-o harmonic 54.28 120.93 # SOURCE4 129 0.5769 - angle_coeff @angle:h5-c-n harmonic 52.39 112.19 # SOURCE4 33 0.4220 - angle_coeff @angle:h5-c-o harmonic 53.89 123.26 # SOURCE4 38 0.4806 - angle_coeff @angle:ha-c-ha harmonic 37.86 115.61 # SOURCE3 4 0.0458 - angle_coeff @angle:ha-c-i harmonic 36.71 110.58 # SOURCE3 1 0.0000 - angle_coeff @angle:ha-c-n harmonic 52.40 112.37 # SOURCE3 4 0.6424 - angle_coeff @angle:ha-c-o harmonic 54.27 121.94 # SOURCE3 51 2.3235 - angle_coeff @angle:ha-c-oh harmonic 53.97 111.82 # SOURCE3 4 1.9375 - angle_coeff @angle:ha-c-os harmonic 53.24 110.34 # SOURCE3 8 1.9344 - angle_coeff @angle:ha-c-s harmonic 44.27 119.56 # SOURCE3 3 0.7586 - angle_coeff @angle:c1-ch-ca harmonic 56.52 179.52 # CORR 19 - angle_coeff @angle:c1-ch-cf harmonic 56.95 178.05 # CORR 7 - angle_coeff @angle:c1-ch-ch harmonic 58.17 179.70 # CORR 18 - angle_coeff @angle:c1-ch-nf harmonic 62.73 170.02 # SOURCE3 4 same_as_c1-cg-ne - angle_coeff @angle:c1-ch-pf harmonic 71.80 173.29 # SOURCE3 11 same_as_c1-cg-pe - angle_coeff @angle:ca-ch-cg harmonic 56.91 179.64 # CORR 13 - angle_coeff @angle:ca-ch-n1 harmonic 58.93 179.43 # CORR 103 - angle_coeff @angle:c-ch-c1 harmonic 56.19 179.14 # SOURCE3 2 same_as_c-cg-c1 - angle_coeff @angle:cd-ch-n1 harmonic 59.43 178.54 # CORR 50 - angle_coeff @angle:cf-ch-cg harmonic 57.39 177.94 # CORR 17 - angle_coeff @angle:cf-ch-n1 harmonic 59.39 177.97 # CORR 67 - angle_coeff @angle:cg-ch-ch harmonic 58.68 179.67 # SOURCE4 7 0.1439 - angle_coeff @angle:n1-ch-nf harmonic 64.98 174.44 # CORR 17 - angle_coeff @angle:i-c-i harmonic 59.79 116.45 # SOURCE3 1 0.0000 - angle_coeff @angle:i-c-o harmonic 55.51 122.02 # SOURCE3 4 1.2961 - angle_coeff @angle:f-cl-f harmonic 0.00 87.50 # SOURCE2 1 estimated_force_constant - angle_coeff @angle:n2-c-n2 harmonic 71.83 110.31 # SOURCE3 1 - angle_coeff @angle:n2-c-o harmonic 73.02 122.50 # SOURCE3 1 - angle_coeff @angle:n4-c-n4 harmonic 64.71 114.64 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-c-o harmonic 69.58 118.83 # SOURCE3 4 3.8516 - angle_coeff @angle:nc-c-o harmonic 73.92 122.97 # CORR 121 - angle_coeff @angle:nd-c-o harmonic 73.92 122.97 # CORR 121 - angle_coeff @angle:ne-c-ne harmonic 73.21 110.31 # CORR 2 - angle_coeff @angle:ne-c-o harmonic 72.96 125.91 # CORR 42 - angle_coeff @angle:nf-c-nf harmonic 73.21 110.31 # CORR 2 - angle_coeff @angle:nf-c-o harmonic 72.96 125.91 # CORR 42 - angle_coeff @angle:n-c-n harmonic 74.80 113.38 # SOURCE4 635 1.4358 - angle_coeff @angle:n-c-nc harmonic 72.35 117.05 # CORR 77 - angle_coeff @angle:n-c-nd harmonic 72.35 117.05 # CORR 77 - angle_coeff @angle:n-c-ne harmonic 74.43 110.37 # SOURCE4 10 1.7492 - angle_coeff @angle:n-c-o harmonic 75.83 122.03 # SOURCE3 221 2.3565 - angle_coeff @angle:n-c-oh harmonic 76.22 113.63 # SOURCE4 5 1.1209 - angle_coeff @angle:no-c-no harmonic 66.54 109.28 # SOURCE3 1 - angle_coeff @angle:no-c-o harmonic 67.95 125.36 # SOURCE3 1 - angle_coeff @angle:n-c-os harmonic 76.68 109.28 # SOURCE4 318 0.8749 - angle_coeff @angle:n-c-s harmonic 65.73 123.88 # SOURCE3 5 1.2935 - angle_coeff @angle:n-c-sh harmonic 65.61 112.61 # SOURCE4 8 1.2601 - angle_coeff @angle:n-c-ss harmonic 66.85 110.42 # SOURCE4 59 1.5507 - angle_coeff @angle:oh-c-oh harmonic 78.91 110.56 # SOURCE3 2 0.5498 - angle_coeff @angle:oh-c-s harmonic 66.64 123.44 # SOURCE3 1 0.0000 - angle_coeff @angle:o-c-o harmonic 78.17 130.38 # SOURCE4 429 1.0315 - angle_coeff @angle:o-c-oh harmonic 77.38 122.88 # SOURCE3 33 2.1896 - angle_coeff @angle:o-c-os harmonic 75.93 123.33 # SOURCE4 1708 1.0632 - angle_coeff @angle:o-c-p2 harmonic 75.65 123.10 # SOURCE3 1 - angle_coeff @angle:o-c-p3 harmonic 77.08 120.79 # SOURCE3 1 - angle_coeff @angle:o-c-p5 harmonic 77.01 121.20 # SOURCE4 8 1.2117 - angle_coeff @angle:o-c-pe harmonic 75.23 123.02 # SOURCE3 3 0.1404 - angle_coeff @angle:o-c-pf harmonic 75.23 123.02 # SOURCE3 3 same_as_o-c-pe - angle_coeff @angle:o-c-px harmonic 76.75 119.10 # SOURCE3 1 0.0000 - angle_coeff @angle:o-c-py harmonic 77.45 121.71 # SOURCE4 5 0.3133 - angle_coeff @angle:o-c-s4 harmonic 61.24 121.15 # SOURCE3 1 - angle_coeff @angle:o-c-s6 harmonic 61.67 119.45 # SOURCE3 1 - angle_coeff @angle:o-c-s harmonic 68.21 120.44 # SOURCE3 2 0.0000 - angle_coeff @angle:o-c-sh harmonic 64.19 121.41 # SOURCE3 4 1.4052 - angle_coeff @angle:os-c-os harmonic 76.45 111.38 # SOURCE4 12 0.8309 - angle_coeff @angle:o-c-ss harmonic 64.62 122.29 # SOURCE3 7 1.9240 - angle_coeff @angle:os-c-s harmonic 65.82 125.03 # SOURCE4 18 0.9978 - angle_coeff @angle:os-c-ss harmonic 66.30 113.63 # SOURCE4 5 0.7367 - angle_coeff @angle:o-c-sx harmonic 60.75 121.15 # SOURCE3 5 3.6452 - angle_coeff @angle:o-c-sy harmonic 61.88 119.32 # SOURCE3 5 2.4495 - angle_coeff @angle:p2-c-p2 harmonic 94.44 113.75 # SOURCE3 1 - angle_coeff @angle:p3-c-p3 harmonic 93.55 118.04 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-c-py harmonic 107.54 90.08 # SOURCE3 1 0.0000 - angle_coeff @angle:p5-c-p5 harmonic 91.43 123.76 # SOURCE3 1 - angle_coeff @angle:ca-cp-ca harmonic 67.11 118.33 # CORR 526 - angle_coeff @angle:ca-cp-cp harmonic 64.09 121.13 # CORR 991 - angle_coeff @angle:ca-cp-na harmonic 68.78 119.43 # SOURCE4 21 0.6591 - angle_coeff @angle:ca-cp-nb harmonic 69.19 121.65 # SOURCE4 63 0.6564 - angle_coeff @angle:cp-cp-cp harmonic 72.20 90.00 # SOURCE3 4 0.0000 - angle_coeff @angle:cp-cp-cq harmonic 62.64 124.47 # CORR 10 - angle_coeff @angle:cp-cp-nb harmonic 68.05 116.60 # SOURCE4 88 1.1887 - angle_coeff @angle:pe-c-pe harmonic 93.89 113.77 # SOURCE3 1 0.0000 - angle_coeff @angle:pf-c-pf harmonic 93.89 113.77 # SOURCE3 1 same_as_pe-c-pe - angle_coeff @angle:nb-cp-nb harmonic 71.31 125.72 # SOURCE4 5 0.6674 - angle_coeff @angle:py-c-py harmonic 92.13 123.80 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-cq-ca harmonic 67.11 118.33 # CORR 526 - angle_coeff @angle:ca-cq-cq harmonic 64.09 121.13 # CORR 991 - angle_coeff @angle:ca-cq-nb harmonic 69.19 121.65 # SOURCE4 63 same as ca-cp-nb - angle_coeff @angle:cp-cq-cq harmonic 62.64 124.47 # CORR 10 - angle_coeff @angle:cq-cq-cq harmonic 72.20 90.00 # SOURCE3 4 0.0000 - angle_coeff @angle:cq-cq-nb harmonic 68.05 116.60 # SOURCE4 88 same as cp-cp-nb - angle_coeff @angle:s4-c-s4 harmonic 61.25 108.81 # SOURCE3 1 - angle_coeff @angle:s6-c-s6 harmonic 59.39 115.75 # SOURCE3 1 - angle_coeff @angle:sh-c-sh harmonic 62.47 115.33 # SOURCE3 1 0.0000 - angle_coeff @angle:s-c-s harmonic 65.01 120.40 # SOURCE3 2 1.2766 - angle_coeff @angle:s-c-sh harmonic 62.29 122.76 # SOURCE4 11 1.5734 - angle_coeff @angle:s-c-ss harmonic 61.88 125.90 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-c-ss harmonic 63.79 113.00 # SOURCE3 1 0.0000 - angle_coeff @angle:sx-c-sx harmonic 60.77 108.80 # SOURCE3 1 0.0000 - angle_coeff @angle:sy-c-sy harmonic 59.54 115.78 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-cu-cx harmonic 58.56 148.21 # SOURCE4 6 1.8305 - angle_coeff @angle:c-cu-cu harmonic 94.97 62.60 # SOURCE2 1 0.0000 - angle_coeff @angle:cu-cu-cx harmonic 100.97 50.80 # SOURCE2 1 0.0000 - angle_coeff @angle:cu-cu-ha harmonic 46.11 147.73 # SOURCE2 3 2.0950 - angle_coeff @angle:cv-cv-cy harmonic 73.28 94.17 # SOURCE3 2 0.0000 - angle_coeff @angle:cv-cv-ha harmonic 47.30 133.70 # SOURCE3 2 0.0000 - angle_coeff @angle:cx-cv-cx harmonic 84.66 63.90 # SOURCE2 1 0.0000 - angle_coeff @angle:cy-cv-ha harmonic 42.89 132.14 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-cx-cx harmonic 63.10 120.66 # SOURCE4 9 0.9067 - angle_coeff @angle:c2-cx-cx harmonic 62.33 120.54 # SOURCE4 51 2.2377 - angle_coeff @angle:c2-cx-h1 harmonic 46.63 115.78 # SOURCE4 8 0.2332 - angle_coeff @angle:c2-cx-hc harmonic 46.77 115.10 # SOURCE4 12 0.7463 - angle_coeff @angle:c2-cx-os harmonic 67.14 116.17 # SOURCE4 14 1.2782 - angle_coeff @angle:c3-cx-c3 harmonic 63.00 114.48 # SOURCE4 46 1.9627 - angle_coeff @angle:c3-cx-cx harmonic 61.82 120.06 # SOURCE4 448 2.1467 - angle_coeff @angle:c3-cx-h1 harmonic 45.87 115.42 # SOURCE4 89 1.1096 - angle_coeff @angle:c3-cx-hc harmonic 46.12 114.16 # SOURCE4 85 1.1118 - angle_coeff @angle:c3-cx-n3 harmonic 64.31 118.50 # SOURCE4 17 2.4897 - angle_coeff @angle:c3-cx-os harmonic 66.57 115.50 # SOURCE4 161 1.3016 - angle_coeff @angle:ca-cx-cx harmonic 61.86 122.18 # SOURCE4 65 1.6898 - angle_coeff @angle:ca-cx-h1 harmonic 46.81 114.57 # SOURCE4 7 0.6498 - angle_coeff @angle:ca-cx-hc harmonic 47.05 113.41 # SOURCE4 18 0.7843 - angle_coeff @angle:ca-cx-oh harmonic 69.25 112.93 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-cx-os harmonic 66.42 118.50 # SOURCE4 6 0.7514 - angle_coeff @angle:c-cx-c3 harmonic 62.91 116.93 # SOURCE4 18 1.8253 - angle_coeff @angle:cc-cx-cx harmonic 62.90 119.31 # CORR 39 - angle_coeff @angle:cc-cx-hc harmonic 47.37 113.84 # SOURCE4 15 0.6682 - angle_coeff @angle:c-cx-cx harmonic 62.96 117.96 # SOURCE4 147 1.8483 - angle_coeff @angle:cd-cx-cx harmonic 62.90 119.31 # CORR 39 - angle_coeff @angle:c-cx-h1 harmonic 46.27 117.25 # SOURCE4 24 0.7935 - angle_coeff @angle:c-cx-hc harmonic 46.42 116.53 # SOURCE4 36 1.2830 - angle_coeff @angle:cl-cx-cl harmonic 54.42 114.20 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-cx-cx harmonic 56.53 120.10 # SOURCE4 15 0.5917 - angle_coeff @angle:cl-cx-h1 harmonic 40.37 111.43 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-cx-hc harmonic 39.60 115.80 # SOURCE2 1 0.0000 - angle_coeff @angle:c-cx-os harmonic 67.25 115.59 # SOURCE4 36 0.8227 - angle_coeff @angle:cu-cx-cu harmonic 91.53 54.60 # SOURCE2 1 0.0000 - angle_coeff @angle:cu-cx-cx harmonic 88.72 58.50 # SOURCE4 7 0.1333 - angle_coeff @angle:cu-cx-hc harmonic 45.49 118.09 # SOURCE4 7 1.0126 - angle_coeff @angle:cx-cx-cx harmonic 87.90 60.00 # SOURCE4 681 0.6259 - angle_coeff @angle:cx-cx-cy harmonic 67.54 100.53 # SOURCE3 4 0.0000 - angle_coeff @angle:cx-cx-f harmonic 64.53 117.93 # SOURCE4 7 1.1613 - angle_coeff @angle:cx-cx-h1 harmonic 45.45 119.66 # SOURCE3 12 0.4529 - angle_coeff @angle:cx-cx-hc harmonic 45.79 117.92 # SOURCE3 92 1.1927 - angle_coeff @angle:cx-cx-hx harmonic 45.47 119.62 # SOURCE4 9 0.1118 - angle_coeff @angle:cx-cx-n3 harmonic 91.17 59.59 # SOURCE4 154 0.3104 - angle_coeff @angle:cx-cx-na harmonic 62.94 125.85 # SOURCE4 16 2.0385 - angle_coeff @angle:cx-cx-nh harmonic 92.03 59.15 # SOURCE4 116 0.6758 - angle_coeff @angle:cx-cx-os harmonic 93.61 59.07 # SOURCE4 306 0.5253 - angle_coeff @angle:cy-cx-hc harmonic 43.98 125.43 # SOURCE3 2 0.0000 - angle_coeff @angle:f-cx-f harmonic 70.61 106.90 # SOURCE2 2 1.4000 - angle_coeff @angle:f-cx-h1 harmonic 50.35 111.68 # SOURCE3 1 0.0000 - angle_coeff @angle:f-cx-hc harmonic 50.22 112.30 # SOURCE2 1 0.0000 - angle_coeff @angle:h1-cx-h1 harmonic 38.38 115.45 # SOURCE4 230 0.3302 - angle_coeff @angle:h1-cx-n3 harmonic 47.97 116.43 # SOURCE4 173 1.4531 - angle_coeff @angle:h1-cx-n harmonic 49.06 115.42 # SOURCE4 12 1.0443 - angle_coeff @angle:h1-cx-na harmonic 49.96 108.67 # SOURCE4 8 1.6134 - angle_coeff @angle:h1-cx-nh harmonic 48.50 116.32 # SOURCE4 151 1.0310 - angle_coeff @angle:h1-cx-os harmonic 50.01 115.17 # SOURCE3 8 0.0226 - angle_coeff @angle:h2-cx-h2 harmonic 37.87 119.43 # SOURCE3 1 0.0000 - angle_coeff @angle:h2-cx-n2 harmonic 47.55 117.18 # SOURCE3 4 0.0000 - angle_coeff @angle:hc-cx-hc harmonic 38.58 114.47 # SOURCE3 19 0.3295 - angle_coeff @angle:hc-cx-os harmonic 50.25 114.10 # SOURCE2 1 0.0000 - angle_coeff @angle:hx-cx-n4 harmonic 49.89 114.47 # SOURCE4 8 0.1059 - angle_coeff @angle:n2-cx-n2 harmonic 102.06 50.16 # SOURCE3 1 0.0000 - angle_coeff @angle:n-cx-oh harmonic 70.16 119.75 # SOURCE3 2 0.0000 - angle_coeff @angle:n-cx-os harmonic 92.71 65.98 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-cx-oh harmonic 76.67 107.85 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-cx-os harmonic 71.64 118.12 # SOURCE3 4 1.3581 - angle_coeff @angle:os-cx-os harmonic 70.90 115.84 # SOURCE4 7 2.0760 - angle_coeff @angle:c2-cy-cy harmonic 66.57 100.40 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-cy-c3 harmonic 63.19 111.58 # SOURCE4 15 1.0060 - angle_coeff @angle:c3-cy-cy harmonic 60.76 118.70 # SOURCE4 293 1.8510 - angle_coeff @angle:c3-cy-h1 harmonic 46.16 111.77 # SOURCE4 119 0.4412 - angle_coeff @angle:c3-cy-hc harmonic 46.21 111.55 # SOURCE3 5 0.6276 - angle_coeff @angle:c3-cy-n3 harmonic 65.28 112.92 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-cy-n harmonic 68.32 104.05 # SOURCE4 122 0.5745 - angle_coeff @angle:c3-cy-os harmonic 66.99 111.96 # SOURCE4 11 1.0668 - angle_coeff @angle:c-cy-c3 harmonic 61.78 116.72 # SOURCE4 129 0.5236 - angle_coeff @angle:cc-cy-cy harmonic 60.58 121.17 # CORR 19 - angle_coeff @angle:c-cy-cy harmonic 71.81 84.99 # SOURCE4 263 0.6952 - angle_coeff @angle:cd-cy-cy harmonic 60.58 121.17 # CORR 19 - angle_coeff @angle:ce-cy-h2 harmonic 45.50 117.25 # SOURCE4 17 0.5351 - angle_coeff @angle:ce-cy-n harmonic 74.69 88.02 # SOURCE4 14 0.1416 - angle_coeff @angle:ce-cy-ss harmonic 58.47 121.33 # SOURCE4 13 0.1599 - angle_coeff @angle:c-cy-h1 harmonic 45.89 113.10 # SOURCE4 71 0.7655 - angle_coeff @angle:c-cy-hc harmonic 45.75 113.85 # SOURCE3 8 0.2067 - angle_coeff @angle:cl-cy-cy harmonic 57.58 112.00 # SOURCE3 2 0.0000 - angle_coeff @angle:cl-cy-h1 harmonic 40.98 106.59 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-cy-hc harmonic 39.62 114.00 # SOURCE2 1 0.0000 - angle_coeff @angle:c-cy-n harmonic 64.32 117.39 # SOURCE4 70 1.0742 - angle_coeff @angle:c-cy-os harmonic 66.27 114.42 # SOURCE4 6 1.2052 - angle_coeff @angle:cv-cy-cy harmonic 71.46 86.67 # SOURCE4 6 1.1600 - angle_coeff @angle:cv-cy-hc harmonic 46.06 114.47 # SOURCE4 7 0.4307 - angle_coeff @angle:cx-cy-cy harmonic 66.08 101.23 # SOURCE3 4 0.0000 - angle_coeff @angle:cx-cy-hc harmonic 45.25 118.30 # SOURCE2 3 5.7799 - angle_coeff @angle:cy-cy-cy harmonic 70.16 87.61 # SOURCE3 32 1.5407 - angle_coeff @angle:cy-cy-f harmonic 64.55 112.87 # SOURCE4 13 1.6772 - angle_coeff @angle:cy-cy-h1 harmonic 44.87 114.84 # SOURCE3 20 2.5651 - angle_coeff @angle:cy-cy-h2 harmonic 44.51 116.77 # SOURCE4 83 0.8683 - angle_coeff @angle:cy-cy-hc harmonic 44.82 115.14 # SOURCE3 114 0.8364 - angle_coeff @angle:cy-cy-n3 harmonic 73.47 87.58 # SOURCE3 4 0.6135 - angle_coeff @angle:cy-cy-n harmonic 65.22 112.13 # SOURCE3 31 2.0700 - angle_coeff @angle:cy-cy-na harmonic 63.12 119.70 # SOURCE4 9 0.3333 - angle_coeff @angle:cy-cy-oh harmonic 66.00 114.19 # SOURCE3 4 0.0000 - angle_coeff @angle:cy-cy-os harmonic 66.41 111.77 # SOURCE4 18 2.1334 - angle_coeff @angle:cy-cy-s6 harmonic 58.93 117.46 # SOURCE4 7 1.2423 - angle_coeff @angle:cy-cy-ss harmonic 58.83 118.18 # SOURCE4 55 0.9860 - angle_coeff @angle:h1-cy-h1 harmonic 39.01 109.72 # SOURCE3 6 0.8087 - angle_coeff @angle:h1-cy-n3 harmonic 48.21 113.36 # SOURCE3 6 1.4509 - angle_coeff @angle:h1-cy-n harmonic 49.10 111.18 # SOURCE4 141 0.5848 - angle_coeff @angle:h1-cy-oh harmonic 50.89 111.49 # SOURCE3 2 0.0000 - angle_coeff @angle:h1-cy-os harmonic 50.53 110.94 # SOURCE3 8 0.6522 - angle_coeff @angle:h1-cy-s6 harmonic 41.05 112.57 # SOURCE4 5 1.2943 - angle_coeff @angle:h2-cy-n harmonic 48.42 114.44 # SOURCE4 88 0.7114 - angle_coeff @angle:h2-cy-os harmonic 50.97 109.19 # SOURCE4 6 0.4162 - angle_coeff @angle:h2-cy-s6 harmonic 42.11 106.85 # SOURCE4 6 0.3975 - angle_coeff @angle:h2-cy-ss harmonic 41.64 109.73 # SOURCE4 92 0.7424 - angle_coeff @angle:hc-cy-hc harmonic 39.24 109.04 # SOURCE3 28 0.5962 - angle_coeff @angle:n-cy-os harmonic 71.62 107.50 # SOURCE4 9 2.3773 - angle_coeff @angle:n-cy-s6 harmonic 65.24 103.45 # SOURCE4 6 0.7197 - angle_coeff @angle:n-cy-ss harmonic 64.81 105.12 # SOURCE4 69 0.3987 - angle_coeff @angle:nh-cz-nh harmonic 72.97 120.17 # SOURCE4 26 0.3964 - angle_coeff @angle:br-n1-c1 harmonic 51.10 180.00 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-c1 harmonic 64.91 179.92 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-c2 harmonic 60.25 177.73 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-c3 harmonic 54.83 180.00 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-ca harmonic 56.97 179.99 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-cl harmonic 50.10 179.95 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-f harmonic 55.86 179.96 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-hn harmonic 45.62 179.98 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-i harmonic 46.23 179.95 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n1 harmonic 66.89 180.00 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n2 harmonic 65.70 171.56 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n3 harmonic 60.69 175.59 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n4 harmonic 59.68 179.69 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-na harmonic 59.95 180.00 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-nh harmonic 60.88 176.35 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-o harmonic 62.62 179.95 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-oh harmonic 62.88 174.31 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-os harmonic 62.15 176.61 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p2 harmonic 68.11 172.83 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p3 harmonic 68.68 173.51 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p4 harmonic 67.87 173.64 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p5 harmonic 71.49 177.28 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s2 harmonic 60.33 178.11 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s4 harmonic 55.20 169.60 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s harmonic 53.31 179.99 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s6 harmonic 61.81 175.92 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-sh harmonic 55.72 174.25 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-ss harmonic 55.44 176.06 # HF/6-31G* 1 - angle_coeff @angle:c2-n1-n1 harmonic 61.58 180.00 # HF/6-31G* 1 - angle_coeff @angle:c2-n1-o harmonic 73.09 116.94 # SOURCE3 2 0.0060 - angle_coeff @angle:c2-n1-s harmonic 64.71 118.00 # SOURCE3 2 0.0121 - angle_coeff @angle:c3-n1-n1 harmonic 56.30 180.00 # HF/6-31G* 1 - angle_coeff @angle:ca-n1-n1 harmonic 58.54 180.00 # HF/6-31G* 1 - angle_coeff @angle:ce-n1-o harmonic 71.28 122.40 # CORR 2 - angle_coeff @angle:ce-n1-s harmonic 64.84 117.34 # CORR 2 - angle_coeff @angle:cf-n1-o harmonic 71.28 122.40 # CORR 2 - angle_coeff @angle:cf-n1-s harmonic 64.84 117.34 # CORR 2 - angle_coeff @angle:cl-n1-n1 harmonic 51.37 179.94 # HF/6-31G* 1 - angle_coeff @angle:f-n1-n1 harmonic 57.39 179.93 # HF/6-31G* 1 - angle_coeff @angle:hn-n1-n1 harmonic 47.14 179.91 # HF/6-31G* 1 - angle_coeff @angle:i-n1-n1 harmonic 47.26 179.94 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n1 harmonic 68.97 179.97 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n2 harmonic 67.65 171.57 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n3 harmonic 62.49 175.09 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n4 harmonic 61.31 179.91 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-na harmonic 61.63 179.97 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-nh harmonic 62.66 176.00 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-o harmonic 64.43 179.94 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-oh harmonic 64.78 173.77 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-os harmonic 64.01 176.12 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-p2 harmonic 69.42 174.71 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-p3 harmonic 70.24 174.27 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-s harmonic 54.64 180.00 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-n1-sh harmonic 57.01 175.07 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-ss harmonic 56.92 175.61 # HF/6-31G* 1 - angle_coeff @angle:o-n1-p2 harmonic 84.67 116.05 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n1-s harmonic 80.34 119.93 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n2-br harmonic 63.89 106.60 # SOURCE3 1 - angle_coeff @angle:br-n2-c2 harmonic 59.13 112.40 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n2-n2 harmonic 61.08 110.42 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n2-o harmonic 60.10 114.47 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n2-p2 harmonic 80.05 111.03 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n2-s harmonic 62.40 115.78 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-n2-c1 harmonic 74.41 121.10 # SOURCE3 1 - angle_coeff @angle:c1-n2-c3 harmonic 58.67 151.88 # SOURCE3 4 15.8282 - angle_coeff @angle:c1-n2-cl harmonic 55.36 118.80 # SOURCE2 1 0.0000 - angle_coeff @angle:c1-n2-hn harmonic 51.47 126.50 # SOURCE2 3 7.6267 - angle_coeff @angle:c1-n2-n2 harmonic 76.75 113.40 # SOURCE3 1 - angle_coeff @angle:c1-n2-o harmonic 79.20 113.59 # SOURCE3 1 - angle_coeff @angle:c1-n2-p2 harmonic 84.76 119.57 # SOURCE3 1 - angle_coeff @angle:c1-n2-s harmonic 69.80 117.67 # SOURCE3 1 - angle_coeff @angle:c2-n2-c2 harmonic 70.76 118.18 # SOURCE3 1 - angle_coeff @angle:c2-n2-c3 harmonic 66.13 115.30 # SOURCE3 8 4.2940 - angle_coeff @angle:c2-n2-ca harmonic 69.83 119.94 # SOURCE3 1 - angle_coeff @angle:c2-n2-cl harmonic 56.69 112.64 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n2-f harmonic 68.30 108.14 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n2-hn harmonic 52.63 110.33 # SOURCE3 9 0.6498 - angle_coeff @angle:c2-n2-i harmonic 51.86 114.74 # SOURCE3 2 0.0139 - angle_coeff @angle:c2-n2-n1 harmonic 75.45 115.09 # HF/6-31G* 1 - angle_coeff @angle:c2-n2-n2 harmonic 77.94 103.59 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-n2-n3 harmonic 71.34 118.14 # SOURCE3 1 - angle_coeff @angle:c2-n2-n4 harmonic 62.39 112.22 # SOURCE3 3 0.0406 - angle_coeff @angle:c2-n2-n harmonic 70.16 117.98 # SOURCE4 11 0.9019 - angle_coeff @angle:c2-n2-na harmonic 70.35 117.58 # SOURCE3 8 1.6671 - angle_coeff @angle:c2-n2-nh harmonic 70.71 117.61 # SOURCE3 6 3.2642 - angle_coeff @angle:c2-n2-no harmonic 64.22 111.54 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n2-o harmonic 75.47 116.94 # SOURCE3 1 - angle_coeff @angle:c2-n2-oh harmonic 72.08 110.89 # SOURCE4 22 1.2709 - angle_coeff @angle:c2-n2-os harmonic 71.83 110.51 # SOURCE4 13 0.7888 - angle_coeff @angle:c2-n2-p2 harmonic 85.03 116.00 # SOURCE3 1 - angle_coeff @angle:c2-n2-p3 harmonic 77.54 119.30 # SOURCE3 3 2.8489 - angle_coeff @angle:c2-n2-p4 harmonic 79.28 118.77 # SOURCE3 1 - angle_coeff @angle:c2-n2-s4 harmonic 68.12 112.29 # SOURCE3 1 - angle_coeff @angle:c2-n2-s6 harmonic 68.85 116.24 # SOURCE3 1 - angle_coeff @angle:c2-n2-s harmonic 68.67 118.00 # SOURCE3 1 - angle_coeff @angle:c2-n2-sh harmonic 63.09 115.48 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n2-ss harmonic 64.97 118.04 # SOURCE3 4 2.2804 - angle_coeff @angle:c3-n2-c3 harmonic 63.76 110.70 # SOURCE3 1 - angle_coeff @angle:c3-n2-ca harmonic 65.97 114.95 # SOURCE4 5 0.9744 - angle_coeff @angle:c3-n2-ce harmonic 65.37 118.53 # CORR 123 - angle_coeff @angle:c3-n2-cf harmonic 65.37 118.53 # CORR 123 - angle_coeff @angle:c3-n2-hn harmonic 45.18 118.40 # SOURCE3 1 - angle_coeff @angle:c3-n2-n1 harmonic 68.64 116.20 # SOURCE4 12 0.5407 - angle_coeff @angle:c3-n2-n2 harmonic 69.29 111.18 # SOURCE3 7 0.4349 - angle_coeff @angle:c3-n2-nh harmonic 68.08 109.99 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n2-o harmonic 70.29 112.40 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-n2-p2 harmonic 82.11 114.21 # SOURCE3 2 2.2772 - angle_coeff @angle:c3-n2-s6 harmonic 66.28 113.84 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n2-s harmonic 65.70 116.72 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-n2-ca harmonic 71.79 112.20 # SOURCE3 1 - angle_coeff @angle:ca-n2-hn harmonic 50.01 120.00 # SOURCE3 1 - angle_coeff @angle:ca-n2-n2 harmonic 74.00 113.53 # SOURCE3 1 - angle_coeff @angle:ca-n2-o harmonic 75.26 116.00 # SOURCE2 1 0.0000 - angle_coeff @angle:ca-n2-p2 harmonic 84.03 118.11 # SOURCE3 1 - angle_coeff @angle:ca-n2-s harmonic 67.84 120.11 # SOURCE3 1 - angle_coeff @angle:c-n2-c2 harmonic 66.22 120.97 # SOURCE3 1 - angle_coeff @angle:c-n2-c harmonic 62.71 123.80 # SOURCE3 1 - angle_coeff @angle:c-n2-ca harmonic 66.05 120.50 # SOURCE3 1 - angle_coeff @angle:cc-n2-cl harmonic 55.90 115.79 # CORR 2 - angle_coeff @angle:cc-n2-hn harmonic 52.42 110.72 # CORR 20 - angle_coeff @angle:cc-n2-na harmonic 73.01 108.92 # SOURCE4 9 1.6245 - angle_coeff @angle:cc-n2-nh harmonic 70.37 118.47 # SOURCE4 6 1.7995 - angle_coeff @angle:cd-n2-cl harmonic 55.90 115.79 # CORR 2 - angle_coeff @angle:cd-n2-hn harmonic 52.42 110.72 # CORR 20 - angle_coeff @angle:ce-n2-hn harmonic 52.74 111.05 # CORR 69 - angle_coeff @angle:ce-n2-n harmonic 70.35 118.04 # CORR 101 - angle_coeff @angle:ce-n2-nh harmonic 70.64 118.57 # CORR 54 - angle_coeff @angle:ce-n2-o harmonic 77.37 112.16 # SOURCE3 1 - angle_coeff @angle:ce-n2-oh harmonic 71.48 113.38 # CORR 37 - angle_coeff @angle:ce-n2-os harmonic 71.23 112.97 # CORR 40 - angle_coeff @angle:ce-n2-s harmonic 69.30 116.28 # SOURCE3 1 - angle_coeff @angle:cf-n2-hn harmonic 52.74 111.05 # CORR 69 - angle_coeff @angle:cf-n2-n harmonic 70.35 118.04 # CORR 101 - angle_coeff @angle:cf-n2-nh harmonic 70.64 118.57 # CORR 54 - angle_coeff @angle:cf-n2-o harmonic 77.37 112.16 # SOURCE3 1 same_as_ce-n2-o - angle_coeff @angle:cf-n2-oh harmonic 71.48 113.38 # CORR 37 - angle_coeff @angle:cf-n2-os harmonic 71.23 112.97 # CORR 40 - angle_coeff @angle:cf-n2-s harmonic 69.30 116.28 # SOURCE3 1 same_as_ce-n2-s - angle_coeff @angle:cl-n2-n1 harmonic 59.29 108.70 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-n2-n2 harmonic 58.70 110.47 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-n2-o harmonic 58.23 114.03 # SOURCE3 1 - angle_coeff @angle:cl-n2-p2 harmonic 73.98 112.98 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-n2-s harmonic 58.50 115.77 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-n2-n2 harmonic 90.46 64.92 # SOURCE3 2 0.0000 - angle_coeff @angle:f-n2-n2 harmonic 68.29 114.60 # SOURCE2 1 0.0000 - angle_coeff @angle:f-n2-o harmonic 71.17 110.10 # SOURCE2 1 0.0000 - angle_coeff @angle:f-n2-p2 harmonic 84.30 107.10 # SOURCE3 1 0.0000 - angle_coeff @angle:f-n2-s harmonic 67.14 110.73 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n2-hn harmonic 38.61 120.00 # SOURCE3 1 - angle_coeff @angle:hn-n2-n1 harmonic 55.33 114.10 # SOURCE2 1 0.0000 - angle_coeff @angle:hn-n2-n2 harmonic 55.84 105.01 # SOURCE3 19 1.5183 - angle_coeff @angle:hn-n2-ne harmonic 54.69 108.56 # SOURCE3 29 5.5708 - angle_coeff @angle:hn-n2-nf harmonic 54.69 108.56 # SOURCE3 29 same_as_hn-n2-ne - angle_coeff @angle:hn-n2-o harmonic 57.61 107.37 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n2-p2 harmonic 58.61 112.09 # SOURCE3 18 4.0663 - angle_coeff @angle:hn-n2-p4 harmonic 54.50 111.33 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n2-p5 harmonic 56.32 122.34 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n2-pe harmonic 61.28 111.41 # SOURCE3 20 4.9895 - angle_coeff @angle:hn-n2-pf harmonic 61.28 111.41 # SOURCE3 20 same_as_hn-n2-pe - angle_coeff @angle:hn-n2-s2 harmonic 48.34 115.80 # SOURCE2 1 0.0000 - angle_coeff @angle:hn-n2-s4 harmonic 46.34 111.21 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n2-s harmonic 49.11 108.17 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n2-s6 harmonic 47.82 112.59 # SOURCE3 2 0.0000 - angle_coeff @angle:i-n2-n2 harmonic 53.71 111.79 # SOURCE3 1 0.0000 - angle_coeff @angle:i-n2-o harmonic 52.33 116.82 # SOURCE3 1 0.0000 - angle_coeff @angle:i-n2-p2 harmonic 72.31 113.26 # SOURCE3 1 0.0000 - angle_coeff @angle:i-n2-s harmonic 56.35 116.85 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-n2-n1 harmonic 80.82 112.00 # HF/6-31G* 1 - angle_coeff @angle:n2-n2-n1 harmonic 62.28 180.00 # dac_for_azides 0 - angle_coeff @angle:n2-n2-n2 harmonic 78.20 109.49 # SOURCE3 2 0.0000 - angle_coeff @angle:n2-n2-n3 harmonic 76.59 108.88 # SOURCE3 1 - angle_coeff @angle:n2-n2-n4 harmonic 65.78 106.45 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n2-na harmonic 74.18 112.23 # SOURCE3 1 - angle_coeff @angle:n2-n2-nh harmonic 74.76 111.70 # SOURCE3 5 0.3475 - angle_coeff @angle:n2-n2-no harmonic 67.68 105.97 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n2-o harmonic 80.17 110.43 # SOURCE3 1 - angle_coeff @angle:n2-n2-oh harmonic 74.02 111.51 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n2-os harmonic 74.69 108.38 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n2-p2 harmonic 90.07 109.15 # SOURCE3 1 - angle_coeff @angle:n2-n2-p3 harmonic 81.73 113.05 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n2-p4 harmonic 81.37 118.77 # SOURCE3 1 - angle_coeff @angle:n2-n2-p5 harmonic 89.80 110.46 # SOURCE3 1 - angle_coeff @angle:n2-n2-s4 harmonic 71.60 107.30 # SOURCE3 1 - angle_coeff @angle:n2-n2-s6 harmonic 72.35 111.25 # SOURCE3 1 - angle_coeff @angle:n2-n2-s harmonic 71.24 115.91 # SOURCE3 1 - angle_coeff @angle:n2-n2-sh harmonic 66.00 111.10 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n2-ss harmonic 68.46 112.14 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-n2-n3 harmonic 72.95 115.07 # SOURCE3 1 - angle_coeff @angle:n3-n2-o harmonic 76.86 114.00 # SOURCE2 1 0.0000 - angle_coeff @angle:n3-n2-p2 harmonic 86.69 115.34 # SOURCE3 1 - angle_coeff @angle:n3-n2-s harmonic 69.96 117.13 # SOURCE3 1 - angle_coeff @angle:n4-n2-n4 harmonic 59.97 106.70 # SOURCE3 1 - angle_coeff @angle:n4-n2-o harmonic 64.86 112.20 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-n2-p2 harmonic 79.54 113.07 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-n2-s harmonic 62.44 118.50 # SOURCE3 1 0.0000 - angle_coeff @angle:na-n2-na harmonic 73.47 107.00 # SOURCE3 1 - angle_coeff @angle:na-n2-o harmonic 75.74 113.09 # SOURCE3 1 0.0000 - angle_coeff @angle:na-n2-p2 harmonic 84.58 119.16 # SOURCE3 1 0.0000 - angle_coeff @angle:na-n2-s harmonic 68.94 118.26 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-n2-nh harmonic 74.13 113.09 # CORR 12 - angle_coeff @angle:ne-n2-o harmonic 79.97 110.31 # SOURCE3 1 - angle_coeff @angle:ne-n2-s harmonic 71.04 116.22 # SOURCE3 1 - angle_coeff @angle:nf-n2-nh harmonic 74.13 113.09 # CORR 12 - angle_coeff @angle:nf-n2-o harmonic 79.97 110.31 # SOURCE3 1 same_as_ne-n2-o - angle_coeff @angle:nf-n2-s harmonic 71.04 116.22 # SOURCE3 1 same_as_ne-n2-s - angle_coeff @angle:nh-n2-nh harmonic 69.67 121.20 # SOURCE3 1 - angle_coeff @angle:nh-n2-o harmonic 76.02 113.60 # SOURCE4 13 1.0945 - angle_coeff @angle:nh-n2-p2 harmonic 84.93 118.83 # SOURCE3 2 0.1024 - angle_coeff @angle:nh-n2-s harmonic 69.56 116.90 # SOURCE3 2 0.2276 - angle_coeff @angle:n-n2-n2 harmonic 75.48 108.18 # SOURCE4 8 0.3496 - angle_coeff @angle:n-n2-o harmonic 74.99 115.10 # SOURCE4 31 0.2796 - angle_coeff @angle:no-n2-no harmonic 62.81 103.70 # SOURCE3 1 - angle_coeff @angle:no-n2-o harmonic 70.40 100.76 # SOURCE3 1 0.0000 - angle_coeff @angle:no-n2-p2 harmonic 81.32 111.95 # SOURCE3 1 0.0000 - angle_coeff @angle:n-n2-p2 harmonic 85.20 117.30 # SOURCE3 1 0.0000 - angle_coeff @angle:n-n2-s harmonic 69.64 115.74 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-n2-oh harmonic 74.84 101.70 # SOURCE3 1 - angle_coeff @angle:oh-n2-p2 harmonic 86.05 115.11 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-n2-s harmonic 69.52 116.08 # SOURCE3 1 0.0000 - angle_coeff @angle:o-n2-o harmonic 81.02 115.37 # SOURCE3 1 - angle_coeff @angle:o-n2-oh harmonic 75.56 112.15 # SOURCE2 2 1.4500 - angle_coeff @angle:o-n2-os harmonic 75.73 110.35 # SOURCE3 2 0.0042 - angle_coeff @angle:o-n2-p2 harmonic 88.65 116.08 # SOURCE3 1 - angle_coeff @angle:o-n2-p3 harmonic 82.37 113.43 # SOURCE3 1 0.0000 - angle_coeff @angle:o-n2-p4 harmonic 85.23 110.61 # SOURCE3 1 - angle_coeff @angle:o-n2-p5 harmonic 91.73 109.11 # SOURCE3 1 - angle_coeff @angle:o-n2-pe harmonic 85.18 134.56 # SOURCE3 1 - angle_coeff @angle:o-n2-pf harmonic 85.18 134.56 # SOURCE3 1 same_as_o-n2-pe - angle_coeff @angle:o-n2-s4 harmonic 72.12 108.91 # SOURCE3 1 - angle_coeff @angle:o-n2-s6 harmonic 73.56 111.34 # SOURCE3 1 - angle_coeff @angle:o-n2-s harmonic 72.09 117.18 # SOURCE3 1 - angle_coeff @angle:o-n2-sh harmonic 65.55 114.98 # SOURCE3 1 0.0000 - angle_coeff @angle:os-n2-os harmonic 71.25 110.29 # SOURCE3 1 - angle_coeff @angle:os-n2-p2 harmonic 87.70 110.20 # SOURCE3 1 0.0000 - angle_coeff @angle:o-n2-ss harmonic 68.39 115.34 # SOURCE3 1 0.0000 - angle_coeff @angle:os-n2-s harmonic 70.47 112.23 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n2-p2 harmonic 107.12 116.80 # SOURCE3 1 - angle_coeff @angle:p2-n2-p3 harmonic 98.43 124.48 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n2-p4 harmonic 98.27 128.37 # SOURCE3 1 - angle_coeff @angle:p2-n2-p5 harmonic 104.38 123.47 # SOURCE3 1 - angle_coeff @angle:p2-n2-s4 harmonic 86.26 112.10 # SOURCE3 1 - angle_coeff @angle:p2-n2-s6 harmonic 86.44 115.70 # SOURCE3 1 - angle_coeff @angle:p2-n2-s harmonic 85.91 117.84 # SOURCE3 1 - angle_coeff @angle:p2-n2-sh harmonic 80.45 118.45 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n2-ss harmonic 82.01 120.43 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-n2-p3 harmonic 96.00 120.40 # SOURCE3 1 - angle_coeff @angle:p3-n2-s harmonic 80.08 120.86 # SOURCE3 1 0.0000 - angle_coeff @angle:p4-n2-s harmonic 77.83 131.84 # SOURCE3 1 - angle_coeff @angle:p5-n2-p5 harmonic 105.81 120.60 # SOURCE3 1 - angle_coeff @angle:p5-n2-s harmonic 85.34 119.89 # SOURCE3 1 - angle_coeff @angle:pe-n2-s harmonic 88.59 115.73 # SOURCE3 1 - angle_coeff @angle:pf-n2-s harmonic 88.59 115.73 # SOURCE3 1 same_as_pe-n2-s - angle_coeff @angle:s4-n2-s4 harmonic 66.00 119.18 # SOURCE3 1 - angle_coeff @angle:s4-n2-s6 harmonic 67.18 119.18 # SOURCE3 1 - angle_coeff @angle:s6-n2-s6 harmonic 68.49 119.18 # SOURCE3 1 - angle_coeff @angle:sh-n2-sh harmonic 59.95 123.93 # SOURCE3 1 - angle_coeff @angle:sh-n2-ss harmonic 61.33 123.93 # SOURCE3 1 - angle_coeff @angle:s-n2-s harmonic 68.47 120.88 # SOURCE3 1 - angle_coeff @angle:s-n2-s4 harmonic 69.20 113.00 # SOURCE3 1 - angle_coeff @angle:s-n2-s6 harmonic 68.60 119.61 # SOURCE3 1 - angle_coeff @angle:s-n2-sh harmonic 63.58 122.05 # SOURCE3 1 0.0000 - angle_coeff @angle:s-n2-ss harmonic 66.58 118.19 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-n2-ss harmonic 62.92 123.93 # SOURCE3 1 - angle_coeff @angle:br-n3-br harmonic 66.54 107.15 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n3-c3 harmonic 62.70 106.93 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-n3-c1 harmonic 64.09 123.34 # SOURCE3 1 - angle_coeff @angle:c1-n3-f harmonic 68.22 104.70 # SOURCE2 1 0.0000 - angle_coeff @angle:c1-n3-hn harmonic 47.74 118.31 # SOURCE3 1 - angle_coeff @angle:c1-n3-o harmonic 70.01 116.63 # SOURCE3 1 - angle_coeff @angle:c2-n3-c2 harmonic 66.22 124.68 # SOURCE3 1 - angle_coeff @angle:c2-n3-hn harmonic 49.11 119.38 # SOURCE3 1 - angle_coeff @angle:c3-n3-c3 harmonic 64.01 110.90 # SOURCE3 40 2.3048 - angle_coeff @angle:c3-n3-cl harmonic 57.82 107.23 # SOURCE3 3 0.3673 - angle_coeff @angle:c3-n3-cx harmonic 62.45 116.32 # SOURCE4 24 0.5119 - angle_coeff @angle:c3-n3-cy harmonic 61.69 118.26 # SOURCE4 14 0.8788 - angle_coeff @angle:c3-n3-f harmonic 66.81 103.13 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-n3-hn harmonic 47.13 109.92 # SOURCE3 120 2.2590 - angle_coeff @angle:c3-n3-i harmonic 56.98 108.48 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-n3-n2 harmonic 66.23 118.75 # SOURCE2 2 2.6500 - angle_coeff @angle:c3-n3-n3 harmonic 66.76 108.15 # SOURCE3 15 1.3999 - angle_coeff @angle:c3-n3-n4 harmonic 67.18 109.65 # SOURCE3 3 0.1146 - angle_coeff @angle:c3-n3-n harmonic 66.67 111.75 # SOURCE4 50 1.6777 - angle_coeff @angle:c3-n3-nh harmonic 66.37 111.89 # SOURCE4 21 1.3006 - angle_coeff @angle:c3-n3-no harmonic 66.02 111.27 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n3-o harmonic 68.68 113.31 # SOURCE3 5 8.9081 - angle_coeff @angle:c3-n3-oh harmonic 69.07 106.14 # SOURCE4 14 1.1040 - angle_coeff @angle:c3-n3-os harmonic 68.48 104.95 # SOURCE4 9 0.9687 - angle_coeff @angle:c3-n3-p3 harmonic 75.79 121.93 # SOURCE3 3 5.6009 - angle_coeff @angle:c3-n3-p5 harmonic 78.53 119.81 # SOURCE4 58 1.8367 - angle_coeff @angle:c3-n3-s4 harmonic 61.45 112.91 # SOURCE3 3 0.8983 - angle_coeff @angle:c3-n3-s6 harmonic 63.67 116.57 # SOURCE4 73 1.8772 - angle_coeff @angle:c3-n3-s harmonic 61.46 110.02 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n3-sh harmonic 62.06 112.70 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n3-ss harmonic 61.59 116.01 # SOURCE3 3 1.1944 - angle_coeff @angle:c3-n3-sy harmonic 62.43 115.27 # SOURCE4 108 1.7647 - angle_coeff @angle:cl-n3-cl harmonic 53.49 108.28 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-n3-hn harmonic 39.61 104.39 # SOURCE3 2 0.0000 - angle_coeff @angle:cl-n3-n3 harmonic 59.29 107.65 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-n3-cx harmonic 86.39 60.71 # SOURCE4 57 0.2359 - angle_coeff @angle:cx-n3-hn harmonic 47.15 109.57 # SOURCE4 26 0.7439 - angle_coeff @angle:cx-n3-p5 harmonic 78.66 119.32 # SOURCE4 71 1.1948 - angle_coeff @angle:cx-n3-py harmonic 76.73 121.75 # SOURCE4 10 1.0295 - angle_coeff @angle:cy-n3-cy harmonic 70.04 90.87 # SOURCE4 10 0.5777 - angle_coeff @angle:cy-n3-hn harmonic 46.25 112.12 # SOURCE4 9 1.9058 - angle_coeff @angle:f-n3-f harmonic 67.71 102.22 # SOURCE2 4 0.7562 - angle_coeff @angle:f-n3-hn harmonic 50.78 99.80 # SOURCE2 1 0.0000 - angle_coeff @angle:hn-n3-hn harmonic 41.30 107.13 # SOURCE3 44 1.9687 - angle_coeff @angle:hn-n3-i harmonic 35.43 109.98 # SOURCE3 2 0.0000 - angle_coeff @angle:hn-n3-n1 harmonic 52.05 110.17 # HF/6-31G* 1 - angle_coeff @angle:hn-n3-n2 harmonic 51.40 115.94 # SOURCE3 1 - angle_coeff @angle:hn-n3-n3 harmonic 50.16 103.98 # SOURCE3 18 1.8593 - angle_coeff @angle:hn-n3-n4 harmonic 50.87 106.40 # SOURCE3 5 0.5863 - angle_coeff @angle:hn-n3-n harmonic 51.02 106.57 # SOURCE3 6 1.0767 - angle_coeff @angle:hn-n3-na harmonic 50.32 107.89 # SOURCE3 1 - angle_coeff @angle:hn-n3-nh harmonic 50.44 107.39 # SOURCE3 11 1.6294 - angle_coeff @angle:hn-n3-no harmonic 50.25 104.78 # SOURCE3 3 1.1126 - angle_coeff @angle:hn-n3-o harmonic 53.14 113.32 # SOURCE3 3 4.3945 - angle_coeff @angle:hn-n3-oh harmonic 53.08 101.11 # SOURCE3 4 0.9921 - angle_coeff @angle:hn-n3-os harmonic 51.67 100.92 # SOURCE3 6 0.7295 - angle_coeff @angle:hn-n3-p2 harmonic 54.24 120.26 # SOURCE3 1 - angle_coeff @angle:hn-n3-p3 harmonic 52.93 116.89 # SOURCE3 9 3.8816 - angle_coeff @angle:hn-n3-p4 harmonic 54.97 113.05 # SOURCE3 2 0.0000 - angle_coeff @angle:hn-n3-p5 harmonic 56.04 113.68 # SOURCE3 6 2.1781 - angle_coeff @angle:hn-n3-s4 harmonic 42.47 108.93 # SOURCE3 7 1.7819 - angle_coeff @angle:hn-n3-s harmonic 41.53 109.47 # SOURCE3 1 - angle_coeff @angle:hn-n3-s6 harmonic 46.06 109.33 # SOURCE4 86 0.9610 - angle_coeff @angle:hn-n3-sh harmonic 43.12 108.67 # SOURCE3 3 2.5025 - angle_coeff @angle:hn-n3-ss harmonic 43.36 109.85 # SOURCE3 5 2.3215 - angle_coeff @angle:hn-n3-sy harmonic 44.15 109.49 # SOURCE4 278 0.7897 - angle_coeff @angle:i-n3-i harmonic 60.04 111.27 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-n3-n1 harmonic 72.40 113.21 # HF/6-31G* 1 - angle_coeff @angle:n2-n3-n2 harmonic 71.82 118.73 # SOURCE3 1 - angle_coeff @angle:n2-n3-o harmonic 74.13 114.91 # SOURCE3 1 - angle_coeff @angle:n3-n3-n3 harmonic 69.57 105.71 # SOURCE3 3 0.3561 - angle_coeff @angle:n4-n3-n4 harmonic 69.04 113.48 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-n3-nh harmonic 70.91 107.14 # SOURCE3 1 - angle_coeff @angle:na-n3-na harmonic 69.21 112.00 # SOURCE3 1 - angle_coeff @angle:nh-n3-nh harmonic 70.75 107.15 # SOURCE3 1 0.0000 - angle_coeff @angle:n-n3-n harmonic 70.25 110.55 # SOURCE3 1 0.0000 - angle_coeff @angle:no-n3-no harmonic 67.04 115.26 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-n3-oh harmonic 72.79 107.18 # SOURCE3 1 0.0000 - angle_coeff @angle:o-n3-o harmonic 71.89 126.14 # SOURCE3 1 - angle_coeff @angle:o-n3-p2 harmonic 84.34 117.02 # SOURCE3 1 - angle_coeff @angle:o-n3-p4 harmonic 83.38 116.65 # SOURCE3 1 - angle_coeff @angle:o-n3-s4 harmonic 64.56 114.09 # SOURCE3 1 - angle_coeff @angle:o-n3-s6 harmonic 68.82 113.80 # SOURCE3 1 - angle_coeff @angle:o-n3-s harmonic 62.04 119.81 # SOURCE3 1 - angle_coeff @angle:os-n3-os harmonic 70.79 106.52 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n3-p2 harmonic 97.53 130.13 # SOURCE3 1 - angle_coeff @angle:p3-n3-p3 harmonic 98.56 118.74 # SOURCE3 3 3.3755 - angle_coeff @angle:p4-n3-p4 harmonic 101.51 116.35 # SOURCE3 1 - angle_coeff @angle:p5-n3-p5 harmonic 102.24 119.42 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-n3-s4 harmonic 60.13 120.02 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-n3-s6 harmonic 61.99 120.95 # SOURCE3 1 - angle_coeff @angle:s6-n3-s6 harmonic 63.29 126.13 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-n3-sh harmonic 61.24 118.63 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-n3-ss harmonic 61.27 119.67 # SOURCE3 1 - angle_coeff @angle:s-n3-s harmonic 56.48 131.36 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-n3-ss harmonic 61.60 119.57 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n4-br harmonic 65.14 114.82 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n4-hn harmonic 41.38 108.44 # SOURCE3 7 0.5630 - angle_coeff @angle:c1-n4-c1 harmonic 65.53 113.87 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-n4-hn harmonic 48.62 110.19 # SOURCE3 7 1.0847 - angle_coeff @angle:c2-n4-c2 harmonic 63.01 112.58 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n4-c3 harmonic 63.10 110.96 # SOURCE4 13 2.4632 - angle_coeff @angle:c2-n4-hn harmonic 46.43 111.36 # SOURCE3 13 1.2672 - angle_coeff @angle:c3-n4-c3 harmonic 62.84 110.64 # SOURCE3 13 1.3060 - angle_coeff @angle:c3-n4-ca harmonic 63.61 110.40 # SOURCE4 46 1.4643 - angle_coeff @angle:c3-n4-cc harmonic 62.84 111.09 # SOURCE4 7 0.7065 - angle_coeff @angle:c3-n4-cl harmonic 57.92 108.04 # SOURCE3 3 0.0000 - angle_coeff @angle:c3-n4-hn harmonic 46.19 110.11 # SOURCE3 100 1.3136 - angle_coeff @angle:c3-n4-n3 harmonic 66.73 108.72 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-n4-n4 harmonic 63.72 114.07 # SOURCE3 4 0.0000 - angle_coeff @angle:c3-n4-n harmonic 66.20 109.26 # SOURCE4 7 1.9859 - angle_coeff @angle:c3-n4-nh harmonic 64.76 111.73 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-no harmonic 65.25 109.08 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-o harmonic 67.25 111.66 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-oh harmonic 65.90 113.73 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-os harmonic 67.38 107.42 # SOURCE3 3 3.5920 - angle_coeff @angle:c3-n4-p2 harmonic 71.92 112.52 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-p3 harmonic 74.40 110.73 # SOURCE3 3 2.1084 - angle_coeff @angle:c3-n4-p5 harmonic 75.11 113.22 # SOURCE3 3 0.4021 - angle_coeff @angle:c3-n4-s4 harmonic 57.21 108.23 # SOURCE3 3 0.4195 - angle_coeff @angle:c3-n4-s6 harmonic 57.75 111.56 # SOURCE3 3 1.8851 - angle_coeff @angle:c3-n4-s harmonic 59.21 113.55 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-sh harmonic 59.13 115.81 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-n4-ss harmonic 59.66 113.68 # SOURCE3 3 1.1405 - angle_coeff @angle:ca-n4-ca harmonic 63.21 114.48 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-n4-hn harmonic 47.54 108.52 # SOURCE3 5 1.1693 - angle_coeff @angle:c-n4-c harmonic 61.50 108.61 # SOURCE3 1 0.0000 - angle_coeff @angle:c-n4-hn harmonic 44.68 110.86 # SOURCE3 10 1.0073 - angle_coeff @angle:cl-n4-cl harmonic 52.73 114.91 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-n4-hn harmonic 39.53 108.87 # SOURCE3 7 0.7719 - angle_coeff @angle:f-n4-f harmonic 70.47 109.05 # SOURCE3 1 0.0000 - angle_coeff @angle:f-n4-hn harmonic 51.67 108.39 # SOURCE3 4 0.0000 - angle_coeff @angle:hn-n4-hn harmonic 40.52 108.11 # SOURCE3 208 1.4126 - angle_coeff @angle:hn-n4-i harmonic 36.44 108.72 # SOURCE3 7 1.2717 - angle_coeff @angle:hn-n4-n1 harmonic 51.79 109.39 # HF/6-31G* 1 - angle_coeff @angle:hn-n4-n2 harmonic 42.29 109.68 # SOURCE3 19 0.6266 - angle_coeff @angle:hn-n4-n3 harmonic 49.85 110.40 # SOURCE3 11 0.7307 - angle_coeff @angle:hn-n4-n4 harmonic 48.09 108.66 # SOURCE3 18 1.2967 - angle_coeff @angle:hn-n4-n harmonic 49.59 109.08 # SOURCE3 13 1.6047 - angle_coeff @angle:hn-n4-na harmonic 49.43 109.38 # SOURCE3 25 1.0758 - angle_coeff @angle:hn-n4-nh harmonic 48.36 109.92 # SOURCE3 12 0.7304 - angle_coeff @angle:hn-n4-no harmonic 49.19 104.38 # SOURCE3 2 0.0000 - angle_coeff @angle:hn-n4-o harmonic 52.09 109.26 # SOURCE3 6 2.1203 - angle_coeff @angle:hn-n4-oh harmonic 51.12 108.09 # SOURCE3 6 1.6728 - angle_coeff @angle:hn-n4-os harmonic 50.15 109.39 # SOURCE3 10 1.4403 - angle_coeff @angle:hn-n4-p2 harmonic 47.71 110.50 # SOURCE3 25 1.0664 - angle_coeff @angle:hn-n4-p3 harmonic 49.73 109.89 # SOURCE3 10 2.3870 - angle_coeff @angle:hn-n4-p4 harmonic 47.65 111.33 # SOURCE3 3 0.0000 - angle_coeff @angle:hn-n4-p5 harmonic 51.29 110.00 # SOURCE3 10 1.0282 - angle_coeff @angle:hn-n4-py harmonic 47.36 117.89 # SOURCE3 8 0.0000 - angle_coeff @angle:hn-n4-s4 harmonic 37.07 110.10 # SOURCE3 6 0.8471 - angle_coeff @angle:hn-n4-s harmonic 41.06 106.89 # SOURCE3 6 1.0775 - angle_coeff @angle:hn-n4-s6 harmonic 38.64 108.94 # SOURCE3 10 0.5715 - angle_coeff @angle:hn-n4-sh harmonic 41.29 108.56 # SOURCE3 6 0.8535 - angle_coeff @angle:hn-n4-ss harmonic 41.15 109.17 # SOURCE3 10 0.8455 - angle_coeff @angle:i-n4-i harmonic 58.99 118.49 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-n4-n1 harmonic 72.69 110.67 # HF/6-31G* 1 - angle_coeff @angle:n2-n4-n2 harmonic 59.43 108.64 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-n4-n3 harmonic 69.79 111.07 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-n4-n4 harmonic 65.21 115.49 # SOURCE3 1 0.0000 - angle_coeff @angle:na-n4-na harmonic 66.27 119.60 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-n4-nh harmonic 67.83 109.38 # SOURCE3 1 0.0000 - angle_coeff @angle:n-n4-n harmonic 66.68 118.62 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-n4-oh harmonic 72.25 108.19 # SOURCE3 1 0.0000 - angle_coeff @angle:o-n4-o harmonic 70.28 120.97 # SOURCE3 1 0.0000 - angle_coeff @angle:os-n4-os harmonic 72.46 104.40 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n4-p2 harmonic 89.65 113.91 # SOURCE3 2 0.0000 - angle_coeff @angle:p3-n4-p3 harmonic 89.71 121.38 # SOURCE3 1 0.0000 - angle_coeff @angle:p5-n4-p5 harmonic 98.15 107.02 # SOURCE3 1 0.0000 - angle_coeff @angle:py-n4-py harmonic 116.94 69.79 # SOURCE3 2 0.0000 - angle_coeff @angle:s4-n4-s4 harmonic 54.75 115.43 # SOURCE3 1 - angle_coeff @angle:s6-n4-s6 harmonic 57.91 109.51 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-n4-sh harmonic 60.37 112.59 # SOURCE3 1 0.0000 - angle_coeff @angle:s-n4-s harmonic 56.74 124.55 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-n4-ss harmonic 61.26 109.20 # SOURCE3 1 0.0000 - angle_coeff @angle:br-na-br harmonic 60.55 123.00 # SOURCE3 1 - angle_coeff @angle:br-na-c2 harmonic 63.61 100.48 # SOURCE3 2 1.0536 - angle_coeff @angle:br-na-ca harmonic 57.15 124.81 # SOURCE3 1 - angle_coeff @angle:br-na-cc harmonic 57.16 124.62 # SOURCE3 3 0.5348 - angle_coeff @angle:br-na-cd harmonic 57.16 124.62 # SOURCE3 3 same_as_br-na-cc - angle_coeff @angle:br-na-nc harmonic 59.86 119.42 # SOURCE3 4 1.6703 - angle_coeff @angle:br-na-nd harmonic 59.86 119.42 # SOURCE3 4 same_as_br-na-nc - angle_coeff @angle:br-na-os harmonic 63.92 104.99 # SOURCE3 1 0.0000 - angle_coeff @angle:br-na-p2 harmonic 75.91 121.01 # SOURCE3 1 - angle_coeff @angle:br-na-pc harmonic 76.39 120.26 # SOURCE3 3 2.1456 - angle_coeff @angle:br-na-pd harmonic 76.39 120.26 # SOURCE3 3 same_as_br-na-pc - angle_coeff @angle:br-na-ss harmonic 62.46 112.28 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-na-c1 harmonic 67.20 117.20 # SOURCE3 1 - angle_coeff @angle:c1-na-c2 harmonic 64.32 125.20 # SOURCE3 1 - angle_coeff @angle:c1-na-ca harmonic 66.54 120.57 # SOURCE3 1 - angle_coeff @angle:c1-na-cc harmonic 65.82 121.35 # SOURCE3 6 0.6517 - angle_coeff @angle:c1-na-cd harmonic 65.82 121.35 # SOURCE3 6 0.6517 - angle_coeff @angle:c1-na-nc harmonic 68.27 120.24 # SOURCE3 4 1.6849 - angle_coeff @angle:c1-na-nd harmonic 68.27 120.24 # SOURCE3 4 same_as_c1-na-nc - angle_coeff @angle:c1-na-os harmonic 70.24 106.96 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-na-p2 harmonic 76.49 122.25 # SOURCE3 1 - angle_coeff @angle:c1-na-pc harmonic 77.33 121.48 # SOURCE3 3 2.1681 - angle_coeff @angle:c1-na-pd harmonic 77.33 121.48 # SOURCE3 3 same_as_c1-na-pc - angle_coeff @angle:c1-na-ss harmonic 61.89 118.30 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-na-c2 harmonic 67.80 110.37 # SOURCE3 6 0.5121 - angle_coeff @angle:c2-na-c3 harmonic 64.23 117.20 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-na-ca harmonic 64.55 125.33 # SOURCE4 7 0.5648 - angle_coeff @angle:c2-na-cc harmonic 63.98 125.75 # SOURCE3 10 1.5856 - angle_coeff @angle:c2-na-cd harmonic 63.98 125.75 # SOURCE3 10 1.5856 - angle_coeff @angle:c2-na-cl harmonic 58.85 101.01 # SOURCE3 2 1.5799 - angle_coeff @angle:c2-na-f harmonic 68.64 103.11 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-na-hn harmonic 47.62 119.28 # SOURCE3 14 6.6027 - angle_coeff @angle:c2-na-i harmonic 58.98 106.74 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-na-n1 harmonic 66.27 124.81 # HF/6-31G* 1 - angle_coeff @angle:c2-na-n2 harmonic 65.80 125.00 # SOURCE3 1 - angle_coeff @angle:c2-na-n3 harmonic 64.64 124.80 # SOURCE3 1 - angle_coeff @angle:c2-na-n4 harmonic 65.19 121.32 # SOURCE3 1 - angle_coeff @angle:c2-na-n harmonic 65.63 124.70 # SOURCE3 1 - angle_coeff @angle:c2-na-na harmonic 65.14 124.60 # SOURCE3 1 - angle_coeff @angle:c2-na-nc harmonic 67.42 120.61 # CORR 9 - angle_coeff @angle:c2-na-nd harmonic 67.42 120.61 # CORR 9 - angle_coeff @angle:c2-na-nh harmonic 65.04 124.98 # SOURCE3 1 - angle_coeff @angle:c2-na-no harmonic 64.34 124.20 # SOURCE3 1 - angle_coeff @angle:c2-na-o harmonic 68.21 125.90 # SOURCE3 1 - angle_coeff @angle:c2-na-oh harmonic 65.80 123.90 # SOURCE3 1 - angle_coeff @angle:c2-na-os harmonic 68.53 110.33 # SOURCE3 4 3.2172 - angle_coeff @angle:c2-na-p2 harmonic 76.19 122.14 # SOURCE3 1 - angle_coeff @angle:c2-na-p3 harmonic 74.55 126.10 # SOURCE3 1 - angle_coeff @angle:c2-na-p4 harmonic 81.58 125.00 # SOURCE3 1 - angle_coeff @angle:c2-na-p5 harmonic 76.43 125.10 # SOURCE3 1 - angle_coeff @angle:c2-na-pc harmonic 76.96 121.56 # SOURCE3 3 1.6252 - angle_coeff @angle:c2-na-pd harmonic 76.96 121.56 # SOURCE3 3 same_as_c2-na-pc - angle_coeff @angle:c2-na-s4 harmonic 58.37 124.90 # SOURCE3 1 - angle_coeff @angle:c2-na-s6 harmonic 60.24 124.40 # SOURCE3 1 - angle_coeff @angle:c2-na-s harmonic 58.90 125.80 # SOURCE3 1 - angle_coeff @angle:c2-na-sh harmonic 60.23 125.10 # SOURCE3 1 - angle_coeff @angle:c2-na-ss harmonic 62.34 115.53 # SOURCE3 5 1.4036 - angle_coeff @angle:c3-na-c3 harmonic 60.72 125.59 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-na-ca harmonic 63.15 124.36 # SOURCE3 5 4.2557 - angle_coeff @angle:c3-na-cc harmonic 62.56 125.09 # SOURCE3 18 1.2138 - angle_coeff @angle:c3-na-cd harmonic 62.56 125.09 # SOURCE3 18 1.2138 - angle_coeff @angle:c3-na-cp harmonic 63.76 119.46 # SOURCE4 7 0.4108 - angle_coeff @angle:c3-na-n2 harmonic 65.48 120.05 # SOURCE4 5 0.8795 - angle_coeff @angle:c3-na-n harmonic 67.37 112.68 # SOURCE4 12 0.5122 - angle_coeff @angle:c3-na-nc harmonic 65.74 120.46 # SOURCE3 8 2.1625 - angle_coeff @angle:c3-na-nd harmonic 65.74 120.46 # SOURCE3 8 2.1625 - angle_coeff @angle:c3-na-os harmonic 68.91 104.39 # SOURCE3 3 1.2017 - angle_coeff @angle:c3-na-p2 harmonic 75.04 123.12 # SOURCE3 1 - angle_coeff @angle:c3-na-pc harmonic 75.89 122.11 # SOURCE3 3 2.8504 - angle_coeff @angle:c3-na-pd harmonic 75.89 122.11 # SOURCE3 3 same_as_c3-na-pc - angle_coeff @angle:c3-na-sh harmonic 63.38 110.28 # SOURCE3 1 - angle_coeff @angle:c3-na-ss harmonic 62.90 110.87 # SOURCE3 3 0.8260 - angle_coeff @angle:ca-na-ca harmonic 66.98 120.09 # SOURCE4 321 1.7366 - angle_coeff @angle:ca-na-cc harmonic 68.46 113.15 # SOURCE3 18 9.8644 - angle_coeff @angle:ca-na-cd harmonic 68.46 113.15 # SOURCE3 18 9.8644 - angle_coeff @angle:ca-na-cl harmonic 53.17 124.79 # SOURCE3 1 - angle_coeff @angle:ca-na-cp harmonic 65.88 120.96 # SOURCE4 20 1.2820 - angle_coeff @angle:ca-na-cx harmonic 63.07 124.09 # SOURCE4 12 1.8167 - angle_coeff @angle:ca-na-f harmonic 65.51 116.40 # SOURCE3 1 - angle_coeff @angle:ca-na-hn harmonic 47.63 125.59 # SOURCE4 437 1.1893 - angle_coeff @angle:ca-na-i harmonic 55.21 121.62 # SOURCE3 1 - angle_coeff @angle:ca-na-n2 harmonic 68.21 119.85 # SOURCE4 6 1.2043 - angle_coeff @angle:ca-na-n4 harmonic 66.37 120.19 # SOURCE3 1 - angle_coeff @angle:ca-na-n harmonic 67.34 122.00 # SOURCE3 1 - angle_coeff @angle:ca-na-na harmonic 66.29 123.76 # SOURCE3 1 - angle_coeff @angle:ca-na-nb harmonic 68.18 122.16 # SOURCE4 7 0.8543 - angle_coeff @angle:ca-na-nc harmonic 69.27 117.85 # SOURCE3 6 3.6536 - angle_coeff @angle:ca-na-nd harmonic 69.27 117.85 # SOURCE3 6 same_as_ca-na-nc - angle_coeff @angle:ca-na-nh harmonic 66.14 124.33 # SOURCE4 7 1.3855 - angle_coeff @angle:ca-na-o harmonic 71.14 119.99 # SOURCE4 51 1.2671 - angle_coeff @angle:ca-na-oh harmonic 66.69 124.08 # SOURCE3 1 - angle_coeff @angle:ca-na-os harmonic 69.70 109.46 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-na-p2 harmonic 75.51 125.85 # SOURCE3 1 - angle_coeff @angle:ca-na-p3 harmonic 75.50 124.38 # SOURCE3 1 - angle_coeff @angle:ca-na-p4 harmonic 82.41 124.97 # SOURCE3 1 - angle_coeff @angle:ca-na-p5 harmonic 77.51 123.30 # SOURCE3 1 - angle_coeff @angle:ca-na-pc harmonic 77.26 122.13 # SOURCE3 3 2.2393 - angle_coeff @angle:ca-na-pd harmonic 77.26 122.13 # SOURCE3 3 same_as_ca-na-pc - angle_coeff @angle:ca-na-py harmonic 72.61 140.88 # SOURCE3 2 0.0000 - angle_coeff @angle:ca-na-s4 harmonic 60.55 117.23 # SOURCE3 1 - angle_coeff @angle:ca-na-s6 harmonic 61.55 120.69 # SOURCE3 1 - angle_coeff @angle:ca-na-s harmonic 59.27 125.64 # SOURCE3 1 - angle_coeff @angle:ca-na-sh harmonic 60.55 125.44 # SOURCE3 1 - angle_coeff @angle:ca-na-ss harmonic 59.16 129.91 # SOURCE4 8 0.1449 - angle_coeff @angle:cc-na-cc harmonic 68.94 109.90 # SOURCE3 109 1.5547 - angle_coeff @angle:cc-na-cd harmonic 63.88 128.01 # SOURCE3 1 0.0000 - angle_coeff @angle:cc-na-ce harmonic 63.05 126.61 # SOURCE4 8 0.5158 - angle_coeff @angle:cc-na-cl harmonic 53.10 124.61 # SOURCE3 3 0.5208 - angle_coeff @angle:cc-na-f harmonic 64.60 118.03 # SOURCE3 4 0.3081 - angle_coeff @angle:cc-na-hn harmonic 47.02 125.50 # CORR 861 - angle_coeff @angle:cc-na-i harmonic 54.34 125.70 # SOURCE3 6 0.7821 - angle_coeff @angle:cc-na-n2 harmonic 66.83 122.96 # SOURCE3 15 0.9350 - angle_coeff @angle:cc-na-n4 harmonic 65.90 120.31 # SOURCE3 10 3.4394 - angle_coeff @angle:cc-na-n harmonic 66.52 123.19 # SOURCE3 13 0.3010 - angle_coeff @angle:cc-na-na harmonic 65.91 123.43 # SOURCE3 23 0.2088 - angle_coeff @angle:cc-na-nc harmonic 70.18 113.02 # SOURCE3 38 2.2867 - angle_coeff @angle:cc-na-nd harmonic 66.41 126.22 # CORR 124 - angle_coeff @angle:cc-na-nh harmonic 66.23 122.25 # SOURCE3 19 0.2010 - angle_coeff @angle:cc-na-no harmonic 65.40 121.78 # SOURCE3 9 0.3521 - angle_coeff @angle:cc-na-o harmonic 69.01 125.21 # SOURCE3 10 0.0124 - angle_coeff @angle:cc-na-oh harmonic 66.67 122.38 # SOURCE3 10 0.1570 - angle_coeff @angle:cc-na-os harmonic 67.01 116.86 # CORR 48 - angle_coeff @angle:cc-na-p2 harmonic 75.29 125.86 # SOURCE3 14 2.2993 - angle_coeff @angle:cc-na-p3 harmonic 75.02 125.25 # SOURCE3 8 0.1998 - angle_coeff @angle:cc-na-p4 harmonic 81.11 127.73 # SOURCE3 7 3.6077 - angle_coeff @angle:cc-na-p5 harmonic 76.81 124.70 # SOURCE3 13 1.4225 - angle_coeff @angle:cc-na-s4 harmonic 59.45 121.03 # SOURCE3 10 0.5589 - angle_coeff @angle:cc-na-s6 harmonic 60.98 122.19 # SOURCE3 10 0.9634 - angle_coeff @angle:cc-na-s harmonic 59.10 125.66 # SOURCE3 8 0.1880 - angle_coeff @angle:cc-na-sh harmonic 60.71 123.96 # SOURCE3 10 0.3424 - angle_coeff @angle:cc-na-ss harmonic 61.34 120.10 # CORR 44 - angle_coeff @angle:cd-na-cd harmonic 68.94 109.90 # SOURCE3 109 1.5547 - angle_coeff @angle:cd-na-cl harmonic 53.10 124.61 # SOURCE3 3 same_as_cc-na-cl - angle_coeff @angle:cd-na-f harmonic 64.60 118.03 # SOURCE3 4 0.3081 - angle_coeff @angle:cd-na-hn harmonic 47.02 125.50 # CORR 861 - angle_coeff @angle:cd-na-i harmonic 54.34 125.70 # SOURCE3 6 0.7821 - angle_coeff @angle:cd-na-n2 harmonic 66.83 122.96 # SOURCE3 15 0.9350 - angle_coeff @angle:cd-na-n4 harmonic 65.90 120.31 # SOURCE3 10 3.4394 - angle_coeff @angle:cd-na-n harmonic 66.52 123.19 # SOURCE3 13 0.3010 - angle_coeff @angle:cd-na-na harmonic 65.91 123.43 # SOURCE3 23 0.2088 - angle_coeff @angle:cd-na-nc harmonic 66.41 126.22 # CORR 124 - angle_coeff @angle:cd-na-nd harmonic 70.18 113.02 # SOURCE3 38 2.2867 - angle_coeff @angle:cd-na-nh harmonic 66.23 122.25 # SOURCE3 19 0.2010 - angle_coeff @angle:cd-na-no harmonic 65.40 121.78 # SOURCE3 9 0.3521 - angle_coeff @angle:cd-na-o harmonic 69.01 125.21 # SOURCE3 10 0.0124 - angle_coeff @angle:cd-na-oh harmonic 66.67 122.38 # SOURCE3 10 0.1570 - angle_coeff @angle:cd-na-os harmonic 67.01 116.86 # CORR 48 - angle_coeff @angle:cd-na-p2 harmonic 75.29 125.86 # SOURCE3 14 2.2993 - angle_coeff @angle:cd-na-p3 harmonic 75.02 125.25 # SOURCE3 8 0.1998 - angle_coeff @angle:cd-na-p4 harmonic 81.11 127.73 # SOURCE3 7 same_as_cc-na-p4 - angle_coeff @angle:cd-na-p5 harmonic 76.81 124.70 # SOURCE3 13 1.4225 - angle_coeff @angle:cd-na-s4 harmonic 59.45 121.03 # SOURCE3 10 0.5589 - angle_coeff @angle:cd-na-s6 harmonic 60.98 122.19 # SOURCE3 10 0.9634 - angle_coeff @angle:cd-na-s harmonic 59.10 125.66 # SOURCE3 8 0.1880 - angle_coeff @angle:cd-na-sh harmonic 60.71 123.96 # SOURCE3 10 0.3424 - angle_coeff @angle:cd-na-ss harmonic 61.34 120.10 # CORR 44 - angle_coeff @angle:cl-na-cl harmonic 48.73 122.80 # SOURCE3 1 - angle_coeff @angle:cl-na-nc harmonic 55.70 119.36 # SOURCE3 4 1.7128 - angle_coeff @angle:cl-na-nd harmonic 55.70 119.36 # SOURCE3 4 same_as_cl-na-nc - angle_coeff @angle:cl-na-os harmonic 58.63 106.58 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-na-p2 harmonic 68.67 121.29 # SOURCE3 1 - angle_coeff @angle:cl-na-pc harmonic 69.19 120.51 # SOURCE3 3 2.1985 - angle_coeff @angle:cl-na-pd harmonic 69.19 120.51 # SOURCE3 3 same_as_cl-na-pc - angle_coeff @angle:cl-na-ss harmonic 56.71 111.91 # SOURCE3 1 0.0000 - angle_coeff @angle:f-na-f harmonic 62.22 120.20 # SOURCE3 1 - angle_coeff @angle:f-na-nc harmonic 66.64 118.05 # SOURCE3 4 1.7931 - angle_coeff @angle:f-na-nd harmonic 66.64 118.05 # SOURCE3 4 same_as_f-na-nc - angle_coeff @angle:f-na-os harmonic 69.15 103.86 # SOURCE3 1 0.0000 - angle_coeff @angle:f-na-p2 harmonic 75.54 119.95 # SOURCE3 1 - angle_coeff @angle:f-na-pc harmonic 76.37 119.10 # SOURCE3 3 2.3967 - angle_coeff @angle:f-na-pd harmonic 76.37 119.10 # SOURCE3 3 same_as_f-na-pc - angle_coeff @angle:f-na-ss harmonic 63.34 108.01 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-na-hn harmonic 39.83 116.80 # SOURCE3 1 - angle_coeff @angle:hn-na-n harmonic 50.90 111.26 # SOURCE4 5 1.1280 - angle_coeff @angle:hn-na-nc harmonic 50.00 119.61 # SOURCE3 16 1.8079 - angle_coeff @angle:hn-na-nd harmonic 50.00 119.61 # SOURCE3 16 1.8079 - angle_coeff @angle:hn-na-os harmonic 51.44 101.41 # SOURCE3 7 3.0814 - angle_coeff @angle:hn-na-p2 harmonic 51.02 122.52 # SOURCE3 1 - angle_coeff @angle:hn-na-pc harmonic 51.81 121.48 # SOURCE3 3 2.9355 - angle_coeff @angle:hn-na-pd harmonic 51.81 121.48 # SOURCE3 3 same_as_hn-na-pc - angle_coeff @angle:hn-na-ss harmonic 42.24 113.95 # SOURCE3 1 0.0000 - angle_coeff @angle:i-na-i harmonic 58.32 124.20 # SOURCE3 1 - angle_coeff @angle:i-na-nc harmonic 56.94 120.03 # SOURCE3 4 2.0032 - angle_coeff @angle:i-na-nd harmonic 56.94 120.03 # SOURCE3 4 same_as_i-na-nc - angle_coeff @angle:i-na-os harmonic 59.85 109.91 # SOURCE3 1 0.0000 - angle_coeff @angle:i-na-p2 harmonic 73.36 122.28 # SOURCE3 1 - angle_coeff @angle:i-na-pc harmonic 73.81 121.40 # SOURCE3 3 2.4763 - angle_coeff @angle:i-na-pd harmonic 73.81 121.40 # SOURCE3 3 same_as_i-na-pc - angle_coeff @angle:i-na-ss harmonic 59.04 118.40 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-na-n2 harmonic 70.35 116.71 # SOURCE3 1 - angle_coeff @angle:n2-na-nc harmonic 69.85 119.96 # SOURCE3 4 4.5041 - angle_coeff @angle:n2-na-nd harmonic 69.85 119.96 # SOURCE3 4 same_as_n2-na-nc - angle_coeff @angle:n2-na-os harmonic 70.33 111.53 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-na-p2 harmonic 77.46 124.88 # SOURCE3 1 - angle_coeff @angle:n2-na-pc harmonic 78.60 123.18 # SOURCE3 3 4.7947 - angle_coeff @angle:n2-na-pd harmonic 78.60 123.18 # SOURCE3 3 same_as_n2-na-pc - angle_coeff @angle:n2-na-ss harmonic 61.71 124.64 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-na-n3 harmonic 65.77 124.00 # SOURCE3 1 - angle_coeff @angle:n4-na-n4 harmonic 68.57 111.70 # SOURCE3 1 - angle_coeff @angle:n4-na-nc harmonic 69.09 116.44 # SOURCE3 4 3.6604 - angle_coeff @angle:n4-na-nd harmonic 69.09 116.44 # SOURCE3 4 same_as_n4-na-nc - angle_coeff @angle:n4-na-os harmonic 71.61 102.97 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-na-p2 harmonic 77.04 123.56 # SOURCE3 1 - angle_coeff @angle:n4-na-pc harmonic 78.10 121.98 # SOURCE3 3 4.4884 - angle_coeff @angle:n4-na-pd harmonic 78.10 121.98 # SOURCE3 3 same_as_n4-na-pc - angle_coeff @angle:na-na-na harmonic 66.77 123.60 # SOURCE3 1 - angle_coeff @angle:na-na-nc harmonic 69.08 119.64 # SOURCE3 4 1.6920 - angle_coeff @angle:na-na-nd harmonic 69.08 119.64 # SOURCE3 4 same_as_na-na-nc - angle_coeff @angle:na-na-os harmonic 70.25 109.47 # SOURCE3 1 0.0000 - angle_coeff @angle:na-na-p2 harmonic 78.07 121.72 # SOURCE3 1 - angle_coeff @angle:na-na-pc harmonic 78.92 120.91 # SOURCE3 3 2.3033 - angle_coeff @angle:na-na-pd harmonic 78.92 120.91 # SOURCE3 3 same_as_na-na-pc - angle_coeff @angle:na-na-ss harmonic 63.50 116.50 # SOURCE3 1 0.0000 - angle_coeff @angle:nc-na-nc harmonic 71.20 117.08 # SOURCE3 31 1.8121 - angle_coeff @angle:nc-na-nd harmonic 69.53 122.77 # SOURCE4 5 0.1352 - angle_coeff @angle:nc-na-nh harmonic 68.82 120.55 # SOURCE3 8 1.1436 - angle_coeff @angle:nc-na-no harmonic 68.19 119.15 # SOURCE3 4 1.6049 - angle_coeff @angle:nc-na-o harmonic 72.04 122.79 # SOURCE3 6 1.3154 - angle_coeff @angle:nc-na-oh harmonic 69.71 119.22 # SOURCE3 4 1.7201 - angle_coeff @angle:nc-na-os harmonic 68.30 119.65 # SOURCE3 4 1.5019 - angle_coeff @angle:nc-na-p2 harmonic 79.23 119.99 # SOURCE3 4 3.6009 - angle_coeff @angle:nc-na-p3 harmonic 78.72 120.07 # SOURCE3 4 3.7188 - angle_coeff @angle:nc-na-p4 harmonic 86.25 119.77 # SOURCE3 3 0.3747 - angle_coeff @angle:nc-na-p5 harmonic 80.84 118.95 # SOURCE3 4 3.1194 - angle_coeff @angle:nc-na-pc harmonic 80.31 118.66 # SOURCE3 27 1.5082 - angle_coeff @angle:nc-na-s4 harmonic 61.52 119.20 # SOURCE3 4 2.3841 - angle_coeff @angle:nc-na-s6 harmonic 63.45 119.24 # SOURCE3 4 2.2262 - angle_coeff @angle:nc-na-s harmonic 61.55 122.26 # SOURCE3 4 0.9173 - angle_coeff @angle:nc-na-sh harmonic 63.29 120.50 # SOURCE3 4 1.5016 - angle_coeff @angle:nc-na-ss harmonic 62.94 120.50 # SOURCE3 4 1.5615 - angle_coeff @angle:nd-na-nd harmonic 71.20 117.08 # SOURCE3 31 1.8121 - angle_coeff @angle:nd-na-nh harmonic 68.82 120.55 # SOURCE3 8 same_as_nc-na-nh - angle_coeff @angle:nd-na-no harmonic 68.19 119.15 # SOURCE3 4 same_as_nc-na-no - angle_coeff @angle:nd-na-o harmonic 72.04 122.79 # SOURCE3 6 same_as_nc-na-o - angle_coeff @angle:nd-na-oh harmonic 69.71 119.22 # SOURCE3 4 same_as_nc-na-oh - angle_coeff @angle:nd-na-os harmonic 68.30 119.65 # SOURCE3 4 same_as_nc-na-os - angle_coeff @angle:nd-na-p2 harmonic 79.23 119.99 # SOURCE3 4 same_as_nc-na-p2 - angle_coeff @angle:nd-na-p3 harmonic 78.72 120.07 # SOURCE3 4 same_as_nc-na-p3 - angle_coeff @angle:nd-na-p4 harmonic 86.25 119.77 # SOURCE3 3 same_as_nc-na-p4 - angle_coeff @angle:nd-na-p5 harmonic 80.84 118.95 # SOURCE3 4 same_as_nc-na-p5 - angle_coeff @angle:nd-na-pd harmonic 80.31 118.66 # SOURCE3 27 same_as_nc-na-pc - angle_coeff @angle:nd-na-s4 harmonic 61.52 119.20 # SOURCE3 4 same_as_nc-na-s4 - angle_coeff @angle:nd-na-s6 harmonic 63.45 119.24 # SOURCE3 4 same_as_nc-na-s6 - angle_coeff @angle:nd-na-s harmonic 61.55 122.26 # SOURCE3 4 same_as_nc-na-s - angle_coeff @angle:nd-na-sh harmonic 63.29 120.50 # SOURCE3 4 same_as_nc-na-sh - angle_coeff @angle:nd-na-ss harmonic 62.94 120.50 # SOURCE3 4 same_as_nc-na-ss - angle_coeff @angle:nh-na-nh harmonic 66.77 123.60 # SOURCE3 1 - angle_coeff @angle:nh-na-os harmonic 69.65 111.37 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-na-p2 harmonic 78.35 120.86 # SOURCE3 1 - angle_coeff @angle:nh-na-pc harmonic 79.10 120.38 # SOURCE3 6 1.3513 - angle_coeff @angle:nh-na-pd harmonic 79.10 120.38 # SOURCE3 6 same_as_nh-na-pc - angle_coeff @angle:nh-na-ss harmonic 64.66 112.35 # SOURCE3 2 5.2951 - angle_coeff @angle:n-na-n harmonic 67.78 123.80 # SOURCE3 1 - angle_coeff @angle:n-na-nc harmonic 69.61 119.85 # SOURCE3 4 1.6156 - angle_coeff @angle:n-na-nd harmonic 69.61 119.85 # SOURCE3 4 same_as_n-na-nc - angle_coeff @angle:no-na-no harmonic 65.22 122.80 # SOURCE3 1 - angle_coeff @angle:no-na-os harmonic 70.30 106.55 # SOURCE3 1 0.0000 - angle_coeff @angle:no-na-pc harmonic 78.65 120.11 # SOURCE3 3 2.0821 - angle_coeff @angle:no-na-pd harmonic 78.65 120.11 # SOURCE3 3 same_as_no-na-pc - angle_coeff @angle:n-na-os harmonic 72.34 104.71 # SOURCE3 1 0.0000 - angle_coeff @angle:no-na-ss harmonic 63.49 114.95 # SOURCE3 1 0.0000 - angle_coeff @angle:n-na-p2 harmonic 78.46 121.35 # SOURCE3 1 - angle_coeff @angle:n-na-pc harmonic 79.30 120.64 # SOURCE3 3 2.0168 - angle_coeff @angle:n-na-pd harmonic 79.30 120.64 # SOURCE3 3 same_as_n-na-pc - angle_coeff @angle:n-na-ss harmonic 63.84 116.10 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-na-oh harmonic 68.13 122.20 # SOURCE3 1 - angle_coeff @angle:oh-na-p2 harmonic 78.88 120.76 # SOURCE3 1 - angle_coeff @angle:oh-na-pc harmonic 79.74 119.99 # SOURCE3 3 2.1734 - angle_coeff @angle:oh-na-pd harmonic 79.74 119.99 # SOURCE3 3 same_as_oh-na-pc - angle_coeff @angle:oh-na-ss harmonic 64.88 113.04 # SOURCE3 1 0.0000 - angle_coeff @angle:o-na-o harmonic 74.03 126.20 # SOURCE3 1 - angle_coeff @angle:o-na-os harmonic 70.76 118.39 # SOURCE3 1 0.0000 - angle_coeff @angle:o-na-p2 harmonic 79.51 122.80 # SOURCE3 1 - angle_coeff @angle:o-na-pc harmonic 80.36 122.34 # SOURCE3 3 1.2908 - angle_coeff @angle:o-na-pd harmonic 80.36 122.34 # SOURCE3 3 same_as_o-na-pc - angle_coeff @angle:os-na-os harmonic 71.29 104.45 # SOURCE3 2 0.0983 - angle_coeff @angle:os-na-p2 harmonic 79.21 117.86 # SOURCE3 1 0.0000 - angle_coeff @angle:os-na-p3 harmonic 83.58 104.70 # SOURCE3 1 0.0000 - angle_coeff @angle:os-na-p5 harmonic 82.64 111.41 # SOURCE3 1 0.0000 - angle_coeff @angle:os-na-pc harmonic 79.09 119.91 # SOURCE3 3 1.9002 - angle_coeff @angle:os-na-pd harmonic 79.09 119.91 # SOURCE3 3 same_as_os-na-pc - angle_coeff @angle:os-na-s4 harmonic 64.81 105.88 # SOURCE3 2 0.0000 - angle_coeff @angle:os-na-s6 harmonic 64.80 112.00 # SOURCE3 2 0.0000 - angle_coeff @angle:os-na-ss harmonic 65.33 109.64 # SOURCE3 3 4.1395 - angle_coeff @angle:p2-na-p2 harmonic 96.62 120.91 # SOURCE3 1 - angle_coeff @angle:p2-na-p3 harmonic 94.74 124.80 # SOURCE3 1 - angle_coeff @angle:p2-na-p5 harmonic 96.33 123.99 # SOURCE3 1 - angle_coeff @angle:p2-na-pc harmonic 97.16 120.72 # SOURCE3 3 0.2407 - angle_coeff @angle:p2-na-pd harmonic 97.16 120.72 # SOURCE3 3 same_as_p2-na-pc - angle_coeff @angle:p2-na-s4 harmonic 74.88 122.47 # SOURCE3 1 - angle_coeff @angle:p2-na-s6 harmonic 76.31 122.50 # SOURCE3 1 - angle_coeff @angle:p2-na-s harmonic 75.69 121.85 # SOURCE3 1 - angle_coeff @angle:p2-na-sh harmonic 76.68 121.75 # SOURCE3 1 - angle_coeff @angle:p2-na-ss harmonic 76.38 121.88 # SOURCE3 1 - angle_coeff @angle:p3-na-p3 harmonic 93.72 126.60 # SOURCE3 1 - angle_coeff @angle:p3-na-pc harmonic 95.76 123.32 # SOURCE3 3 4.1781 - angle_coeff @angle:p3-na-pd harmonic 95.76 123.32 # SOURCE3 3 same_as_p3-na-pc - angle_coeff @angle:p5-na-p5 harmonic 97.06 124.60 # SOURCE3 1 - angle_coeff @angle:p5-na-pc harmonic 97.33 122.69 # SOURCE3 3 3.6738 - angle_coeff @angle:p5-na-pd harmonic 97.33 122.69 # SOURCE3 3 same_as_p5-na-pc - angle_coeff @angle:p5-na-ss harmonic 78.22 118.52 # SOURCE3 1 0.0000 - angle_coeff @angle:pc-na-pc harmonic 97.62 120.78 # SOURCE3 27 1.6457 - angle_coeff @angle:pc-na-s4 harmonic 75.52 121.51 # SOURCE3 3 2.7242 - angle_coeff @angle:pc-na-s6 harmonic 76.99 121.55 # SOURCE3 3 2.7065 - angle_coeff @angle:pc-na-s harmonic 76.17 121.47 # SOURCE3 3 1.0668 - angle_coeff @angle:pc-na-sh harmonic 77.28 121.08 # SOURCE3 3 1.8942 - angle_coeff @angle:pc-na-ss harmonic 76.97 121.20 # SOURCE3 3 1.9295 - angle_coeff @angle:pd-na-pd harmonic 97.62 120.78 # SOURCE3 27 same_as_pc-na-pc - angle_coeff @angle:pd-na-s4 harmonic 75.52 121.51 # SOURCE3 3 same_as_pc-na-s4 - angle_coeff @angle:pd-na-s6 harmonic 76.99 121.55 # SOURCE3 3 same_as_pc-na-s6 - angle_coeff @angle:pd-na-s harmonic 76.17 121.47 # SOURCE3 3 same_as_pc-na-s - angle_coeff @angle:pd-na-sh harmonic 77.28 121.08 # SOURCE3 3 same_as_pc-na-sh - angle_coeff @angle:pd-na-ss harmonic 76.97 121.20 # SOURCE3 3 same_as_pc-na-ss - angle_coeff @angle:py-na-py harmonic 122.69 78.25 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-na-s4 harmonic 58.05 124.20 # SOURCE3 1 - angle_coeff @angle:s4-na-s6 harmonic 62.00 112.86 # SOURCE3 1 - angle_coeff @angle:s4-na-ss harmonic 62.16 111.92 # SOURCE3 1 0.0000 - angle_coeff @angle:s6-na-s6 harmonic 60.51 123.20 # SOURCE3 1 - angle_coeff @angle:s6-na-ss harmonic 61.44 119.10 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-na-sh harmonic 60.38 124.60 # SOURCE3 1 - angle_coeff @angle:sh-na-ss harmonic 61.63 118.79 # SOURCE3 1 0.0000 - angle_coeff @angle:s-na-s harmonic 58.55 126.00 # SOURCE3 1 - angle_coeff @angle:s-na-ss harmonic 62.52 112.49 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-na-ss harmonic 62.90 113.24 # SOURCE3 2 6.6084 - angle_coeff @angle:sy-na-sy harmonic 60.51 123.20 # SOURCE3 1 - angle_coeff @angle:ca-nb-ca harmonic 68.59 115.86 # SOURCE3 46 1.1645 - angle_coeff @angle:ca-nb-cp harmonic 68.01 118.04 # SOURCE4 58 0.7819 - angle_coeff @angle:ca-nb-cq harmonic 68.01 118.04 # SOURCE4 58 same as ca-nb-cp - angle_coeff @angle:ca-nb-nb harmonic 69.37 118.89 # SOURCE3 10 0.6031 - angle_coeff @angle:cp-nb-nb harmonic 68.79 121.11 # SOURCE4 12 0.4315 - angle_coeff @angle:nb-nb-nb harmonic 70.44 121.04 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n-br harmonic 66.59 116.20 # SOURCE3 1 0.0000 - angle_coeff @angle:br-n-c harmonic 61.85 120.77 # SOURCE3 5 2.6390 - angle_coeff @angle:br-n-ca harmonic 62.07 118.19 # SOURCE3 1 - angle_coeff @angle:br-n-cc harmonic 62.34 118.19 # SOURCE3 1 same_as_br-n-cd - angle_coeff @angle:br-n-cd harmonic 62.34 118.19 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-n-c1 harmonic 73.52 102.69 # SOURCE3 1 - angle_coeff @angle:c1-n-ca harmonic 65.90 118.88 # SOURCE3 1 - angle_coeff @angle:c1-n-cc harmonic 67.02 118.88 # SOURCE3 1 same_as_c1-n-cd - angle_coeff @angle:c1-n-cd harmonic 67.02 118.88 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n-c2 harmonic 65.18 116.75 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n-c3 harmonic 63.06 119.98 # SOURCE4 23 2.3373 - angle_coeff @angle:c2-n-ca harmonic 64.88 116.54 # SOURCE3 1 - angle_coeff @angle:c2-n-cc harmonic 65.85 116.54 # SOURCE3 1 same_as_c2-n-cd - angle_coeff @angle:c2-n-cd harmonic 65.85 116.54 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-n-hn harmonic 47.33 118.36 # SOURCE4 40 1.8005 - angle_coeff @angle:c3-n-c3 harmonic 63.13 115.56 # SOURCE4 392 2.0191 - angle_coeff @angle:c3-n-ca harmonic 62.76 119.96 # SOURCE4 165 2.0808 - angle_coeff @angle:c3-n-cc harmonic 63.33 121.00 # CORR 267 - angle_coeff @angle:c3-n-cd harmonic 63.33 121.00 # CORR 267 - angle_coeff @angle:c3-n-cy harmonic 62.51 117.11 # SOURCE4 49 1.0344 - angle_coeff @angle:c3-n-hn harmonic 46.04 116.78 # SOURCE3 39 2.1985 - angle_coeff @angle:c3-n-n2 harmonic 64.89 121.68 # SOURCE4 52 1.3175 - angle_coeff @angle:c3-n-n harmonic 66.40 114.82 # SOURCE4 9 0.7008 - angle_coeff @angle:c3-n-nc harmonic 66.97 115.21 # CORR 48 - angle_coeff @angle:c3-n-nd harmonic 66.97 115.21 # CORR 48 - angle_coeff @angle:c3-n-oh harmonic 66.88 113.05 # SOURCE4 31 0.8144 - angle_coeff @angle:c3-n-os harmonic 66.99 112.65 # SOURCE4 16 1.5399 - angle_coeff @angle:c3-n-sy harmonic 60.53 121.27 # SOURCE4 5 1.1298 - angle_coeff @angle:ca-n-ca harmonic 64.31 117.39 # SOURCE4 39 1.6465 - angle_coeff @angle:ca-n-cc harmonic 66.19 114.06 # CORR 34 - angle_coeff @angle:ca-n-cd harmonic 66.19 114.06 # CORR 34 - angle_coeff @angle:ca-n-cl harmonic 57.24 117.72 # SOURCE3 1 - angle_coeff @angle:ca-n-f harmonic 64.62 114.92 # SOURCE3 1 - angle_coeff @angle:ca-n-hn harmonic 47.36 115.94 # SOURCE4 537 1.8890 - angle_coeff @angle:ca-n-i harmonic 56.58 119.30 # SOURCE3 1 - angle_coeff @angle:ca-n-n2 harmonic 65.72 122.17 # SOURCE4 5 0.2545 - angle_coeff @angle:ca-n-n4 harmonic 64.15 122.98 # SOURCE3 1 - angle_coeff @angle:ca-n-n harmonic 66.30 118.54 # SOURCE4 21 0.3399 - angle_coeff @angle:ca-n-na harmonic 66.33 119.31 # SOURCE4 16 0.3168 - angle_coeff @angle:ca-n-nc harmonic 68.25 114.36 # CORR 6 - angle_coeff @angle:ca-n-nd harmonic 68.25 114.36 # CORR 6 - angle_coeff @angle:ca-n-nh harmonic 66.60 116.45 # SOURCE3 1 - angle_coeff @angle:ca-n-p2 harmonic 79.60 112.32 # SOURCE3 1 - angle_coeff @angle:ca-n-p3 harmonic 74.22 125.11 # SOURCE3 1 - angle_coeff @angle:ca-n-s4 harmonic 59.97 118.40 # SOURCE3 1 - angle_coeff @angle:ca-n-s6 harmonic 62.01 117.32 # SOURCE3 1 - angle_coeff @angle:ca-n-ss harmonic 62.15 116.60 # SOURCE3 1 - angle_coeff @angle:c-n-c1 harmonic 68.47 117.04 # SOURCE3 1 0.0000 - angle_coeff @angle:c-n-c2 harmonic 65.09 122.15 # SOURCE3 9 5.1016 - angle_coeff @angle:c-n-c3 harmonic 63.92 121.35 # SOURCE3 54 2.3808 - angle_coeff @angle:c3-nc-cd harmonic 67.60 109.51 # SOURCE3 9 5.4142 - angle_coeff @angle:c-n-c harmonic 65.33 127.14 # SOURCE4 514 2.0111 - angle_coeff @angle:c-n-ca harmonic 64.29 123.71 # SOURCE3 10 3.8159 - angle_coeff @angle:ca-nc-ca harmonic 70.73 109.95 # SOURCE3 1 - angle_coeff @angle:ca-nc-cd harmonic 72.43 104.94 # CORR 437 - angle_coeff @angle:ca-nc-n harmonic 73.68 104.69 # CORR 2 - angle_coeff @angle:ca-nc-na harmonic 74.57 102.74 # CORR 14 - angle_coeff @angle:ca-nc-os harmonic 73.08 104.48 # CORR 10 - angle_coeff @angle:ca-nc-ss harmonic 67.84 116.29 # SOURCE3 1 - angle_coeff @angle:c-n-cc harmonic 65.24 124.19 # SOURCE3 57 2.2262 - angle_coeff @angle:c-nc-ca harmonic 66.11 120.66 # CORR 2 - angle_coeff @angle:cc-n-cc harmonic 68.80 108.92 # SOURCE3 11 0.3167 - angle_coeff @angle:cc-nc-cc harmonic 70.50 104.34 # CORR 6 - angle_coeff @angle:cc-nc-cd harmonic 71.08 105.67 # CORR 1240 - angle_coeff @angle:c-nc-cd harmonic 66.18 120.48 # CORR 138 - angle_coeff @angle:cc-n-cl harmonic 57.67 117.72 # SOURCE3 1 same_as_cd-n-cl - angle_coeff @angle:cc-nc-na harmonic 73.38 102.97 # SOURCE3 1 0.0000 - angle_coeff @angle:cc-nc-nd harmonic 72.54 107.94 # SOURCE3 6 1.4052 - angle_coeff @angle:c-n-cd harmonic 65.24 124.19 # SOURCE3 57 2.2262 - angle_coeff @angle:cd-nc-cd harmonic 68.53 117.28 # CORR 17 - angle_coeff @angle:cd-nc-n harmonic 69.66 117.19 # CORR 64 - angle_coeff @angle:cd-nc-na harmonic 74.24 103.73 # SOURCE3 122 2.3292 - angle_coeff @angle:cd-nc-nc harmonic 71.99 107.88 # CORR 355 - angle_coeff @angle:cd-nc-os harmonic 73.04 104.66 # CORR 116 - angle_coeff @angle:cd-nc-ss harmonic 70.36 108.15 # CORR 45 - angle_coeff @angle:c-n-ce harmonic 62.21 131.83 # SOURCE4 146 1.3048 - angle_coeff @angle:cc-n-f harmonic 65.61 114.92 # SOURCE3 1 same_as_cd-n-f - angle_coeff @angle:cc-n-hn harmonic 47.99 119.14 # CORR 276 - angle_coeff @angle:cc-n-i harmonic 56.61 119.30 # SOURCE3 1 same_as_cd-n-i - angle_coeff @angle:c-n-cl harmonic 58.34 116.35 # SOURCE4 11 0.6829 - angle_coeff @angle:cc-n-n2 harmonic 70.09 110.87 # SOURCE3 1 same_as_cd-n-n2 - angle_coeff @angle:cc-n-n harmonic 66.53 121.37 # SOURCE3 1 same_as_cd-n-n - angle_coeff @angle:cc-n-na harmonic 67.87 117.57 # SOURCE3 1 same_as_cd-n-na - angle_coeff @angle:cc-n-nc harmonic 70.08 112.03 # CORR 14 - angle_coeff @angle:cc-n-nh harmonic 67.30 117.52 # SOURCE3 1 same_as_cd-n-nh - angle_coeff @angle:cc-n-no harmonic 66.40 115.92 # SOURCE3 1 same_as_cd-n-no - angle_coeff @angle:cc-n-o harmonic 70.07 120.54 # SOURCE3 1 same_as_cd-n-o - angle_coeff @angle:cc-n-oh harmonic 67.32 118.15 # SOURCE3 1 same_as_cd-n-oh - angle_coeff @angle:cc-n-os harmonic 68.06 115.56 # SOURCE3 1 same_as_cd-n-os - angle_coeff @angle:cc-n-p2 harmonic 80.17 112.32 # SOURCE3 1 same_as_cd-n-p2 - angle_coeff @angle:cc-n-p3 harmonic 74.70 125.11 # SOURCE3 1 same_as_cd-n-p3 - angle_coeff @angle:cc-n-p5 harmonic 78.11 121.00 # SOURCE3 1 same_as_cd-n-p5 - angle_coeff @angle:cc-n-s4 harmonic 60.34 118.40 # SOURCE3 1 same_as_cd-n-s4 - angle_coeff @angle:cc-n-s6 harmonic 62.48 117.32 # SOURCE3 1 same_as_cd-n-s6 - angle_coeff @angle:cc-n-s harmonic 60.78 118.29 # SOURCE3 1 same_as_cd-n-s - angle_coeff @angle:cc-n-sh harmonic 61.64 119.13 # SOURCE3 1 same_as_cd-n-sh - angle_coeff @angle:cc-n-ss harmonic 62.62 116.60 # SOURCE3 2 same_as_cd-n-ss - angle_coeff @angle:c-n-cx harmonic 64.22 122.07 # SOURCE4 11 1.9478 - angle_coeff @angle:c-n-cy harmonic 72.26 94.23 # SOURCE4 270 1.3777 - angle_coeff @angle:cd-n-cd harmonic 68.80 108.92 # SOURCE3 11 same_as_cc-n-cc - angle_coeff @angle:cd-n-cl harmonic 57.67 117.72 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-f harmonic 65.61 114.92 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-hn harmonic 47.99 119.14 # CORR 276 - angle_coeff @angle:cd-n-i harmonic 56.61 119.30 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-n2 harmonic 70.09 110.87 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-n harmonic 66.53 121.37 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-na harmonic 67.87 117.57 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-nd harmonic 70.08 112.03 # CORR 14 - angle_coeff @angle:cd-n-nh harmonic 67.30 117.52 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-no harmonic 66.40 115.92 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-o harmonic 70.07 120.54 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-oh harmonic 67.32 118.15 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-os harmonic 68.06 115.56 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-p2 harmonic 80.17 112.32 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-p3 harmonic 74.70 125.11 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-p5 harmonic 78.11 121.00 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-s4 harmonic 60.34 118.40 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-s6 harmonic 62.48 117.32 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-s harmonic 60.78 118.29 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-sh harmonic 61.64 119.13 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-n-ss harmonic 62.62 116.60 # SOURCE3 2 1.8318 - angle_coeff @angle:ce-n-cy harmonic 64.70 111.89 # CORR 152 - angle_coeff @angle:c-n-f harmonic 68.30 108.63 # SOURCE3 3 4.6785 - angle_coeff @angle:cf-n-cy harmonic 64.70 111.89 # CORR 152 - angle_coeff @angle:c-n-hn harmonic 49.21 118.46 # SOURCE3 157 2.4094 - angle_coeff @angle:c-n-i harmonic 56.34 120.38 # SOURCE3 5 2.1600 - angle_coeff @angle:cl-n-cl harmonic 54.70 111.69 # SOURCE3 1 0.0000 - angle_coeff @angle:c-n-n2 harmonic 68.06 120.59 # SOURCE3 9 3.2410 - angle_coeff @angle:c-n-n3 harmonic 67.13 120.43 # SOURCE3 5 0.9481 - angle_coeff @angle:c-n-n4 harmonic 68.85 112.32 # SOURCE3 5 1.2622 - angle_coeff @angle:c-n-n harmonic 68.18 118.42 # SOURCE3 10 2.8922 - angle_coeff @angle:c-n-na harmonic 68.25 119.20 # SOURCE3 11 2.3032 - angle_coeff @angle:na-nc-nd harmonic 75.97 105.47 # SOURCE3 6 0.6349 - angle_coeff @angle:c-n-nc harmonic 67.16 125.19 # CORR 84 - angle_coeff @angle:nc-nc-nd harmonic 73.11 111.29 # CORR 61 - angle_coeff @angle:c-n-nd harmonic 67.16 125.19 # CORR 84 - angle_coeff @angle:nd-nc-os harmonic 74.42 107.22 # SOURCE3 3 0.4707 - angle_coeff @angle:c-n-nh harmonic 68.02 117.81 # SOURCE4 21 1.5935 - angle_coeff @angle:c-n-no harmonic 66.47 118.16 # SOURCE3 4 5.4870 - angle_coeff @angle:c-n-o harmonic 71.64 118.90 # SOURCE3 9 5.4085 - angle_coeff @angle:c-n-oh harmonic 69.53 113.39 # SOURCE3 6 1.3345 - angle_coeff @angle:c-n-os harmonic 69.60 113.14 # SOURCE3 7 3.0839 - angle_coeff @angle:c-n-p2 harmonic 76.53 124.56 # SOURCE3 8 3.6907 - angle_coeff @angle:c-n-p3 harmonic 75.82 122.54 # SOURCE3 9 4.4802 - angle_coeff @angle:c-n-p4 harmonic 76.84 123.44 # SOURCE3 1 0.0000 - angle_coeff @angle:c-n-p5 harmonic 76.23 128.50 # SOURCE4 6 0.5353 - angle_coeff @angle:c-n-pc harmonic 77.00 122.23 # SOURCE3 3 2.8787 - angle_coeff @angle:c-n-pd harmonic 77.00 122.23 # SOURCE3 3 same_as_c-n-pc - angle_coeff @angle:c-n-s4 harmonic 60.09 120.41 # SOURCE3 4 3.1760 - angle_coeff @angle:c-n-s6 harmonic 60.86 125.01 # SOURCE4 13 1.6314 - angle_coeff @angle:c-n-s harmonic 59.04 126.55 # SOURCE3 3 4.3365 - angle_coeff @angle:c-n-sh harmonic 61.87 119.54 # SOURCE3 4 1.7681 - angle_coeff @angle:c-n-ss harmonic 61.97 120.37 # SOURCE3 7 1.4450 - angle_coeff @angle:c-n-sy harmonic 60.91 124.81 # SOURCE4 51 1.0517 - angle_coeff @angle:cx-n-hn harmonic 46.26 118.58 # SOURCE4 5 0.3288 - angle_coeff @angle:cx-n-os harmonic 97.40 54.04 # SOURCE3 1 0.0000 - angle_coeff @angle:cy-n-hn harmonic 45.34 119.00 # SOURCE4 65 1.3840 - angle_coeff @angle:c3-nd-cc harmonic 67.60 109.51 # SOURCE3 9 same_as_c3-nc-cd - angle_coeff @angle:ca-nd-ca harmonic 70.73 109.95 # SOURCE3 1 same_as_ca-nc-ca - angle_coeff @angle:ca-nd-cc harmonic 72.43 104.94 # CORR 437 - angle_coeff @angle:ca-nd-n harmonic 73.68 104.69 # CORR 2 - angle_coeff @angle:ca-nd-na harmonic 74.57 102.74 # CORR 14 - angle_coeff @angle:ca-nd-nc harmonic 73.55 108.41 # SOURCE4 9 0.1575 - angle_coeff @angle:ca-nd-os harmonic 73.08 104.48 # CORR 10 - angle_coeff @angle:ca-nd-ss harmonic 67.84 116.29 # SOURCE3 1 same_as_ca-nc-ss - angle_coeff @angle:c-nd-ca harmonic 66.11 120.66 # CORR 2 - angle_coeff @angle:c-nd-cc harmonic 66.18 120.48 # CORR 138 - angle_coeff @angle:cc-nd-cc harmonic 68.53 117.28 # CORR 17 - angle_coeff @angle:cc-nd-cd harmonic 71.08 105.67 # CORR 1240 - angle_coeff @angle:cc-nd-n harmonic 69.66 117.19 # CORR 64 - angle_coeff @angle:cc-nd-na harmonic 74.24 103.73 # SOURCE3 122 2.3292 - angle_coeff @angle:cc-nd-nd harmonic 71.99 107.88 # CORR 355 - angle_coeff @angle:cc-nd-os harmonic 73.04 104.66 # CORR 116 - angle_coeff @angle:cc-nd-ss harmonic 70.36 108.15 # CORR 45 - angle_coeff @angle:cd-nd-cd harmonic 70.50 104.34 # CORR 6 - angle_coeff @angle:cd-nd-na harmonic 73.38 102.97 # SOURCE3 1 same_as_cc-nc-na - angle_coeff @angle:cd-nd-nc harmonic 72.54 107.94 # SOURCE3 6 1.4052 - angle_coeff @angle:na-nd-nc harmonic 75.97 105.47 # SOURCE3 6 0.6349 - angle_coeff @angle:nc-nd-nd harmonic 73.11 111.29 # CORR 61 - angle_coeff @angle:nc-nd-os harmonic 74.42 107.22 # SOURCE3 3 same_as_nd-nc-os - angle_coeff @angle:c1-ne-ca harmonic 60.41 150.84 # CORR 9 - angle_coeff @angle:c1-ne-cg harmonic 66.00 140.00 # SOURCE2 1 0.0000 - angle_coeff @angle:c2-ne-ca harmonic 66.09 120.84 # CORR 55 - angle_coeff @angle:c2-ne-ce harmonic 67.33 118.17 # SOURCE3 3 1.2374 - angle_coeff @angle:c2-ne-cg harmonic 68.36 123.58 # SOURCE4 12 0.8560 - angle_coeff @angle:c2-ne-n2 harmonic 74.56 113.31 # SOURCE3 1 - angle_coeff @angle:c2-ne-ne harmonic 69.17 110.86 # SOURCE3 7 4.5874 - angle_coeff @angle:c2-ne-p2 harmonic 80.83 134.03 # SOURCE3 1 - angle_coeff @angle:c2-ne-pe harmonic 79.24 120.52 # SOURCE3 8 8.1381 - angle_coeff @angle:c2-ne-px harmonic 80.57 117.75 # SOURCE3 5 0.8581 - angle_coeff @angle:c2-ne-py harmonic 84.33 117.04 # SOURCE3 3 1.4398 - angle_coeff @angle:c2-ne-sx harmonic 60.95 111.98 # SOURCE3 3 0.4090 - angle_coeff @angle:c2-ne-sy harmonic 61.78 118.92 # CORR 9 - angle_coeff @angle:ca-ne-cf harmonic 65.56 121.98 # CORR 15 - angle_coeff @angle:ca-ne-n2 harmonic 69.73 114.06 # CORR 11 - angle_coeff @angle:ca-ne-nf harmonic 69.69 115.12 # CORR 44 - angle_coeff @angle:ca-ne-o harmonic 71.10 113.96 # SOURCE3 3 1.1253 - angle_coeff @angle:ca-ne-p2 harmonic 83.08 118.09 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-ne-s harmonic 65.75 120.11 # SOURCE3 1 0.0000 - angle_coeff @angle:c-ne-c2 harmonic 67.85 118.53 # CORR 6 - angle_coeff @angle:ce-ne-n2 harmonic 71.16 111.19 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-ne-o harmonic 72.26 112.16 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-ne-p2 harmonic 83.85 117.02 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-ne-s harmonic 67.15 116.28 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-ne-n1 harmonic 71.71 120.20 # SOURCE2 1 0.0000 - angle_coeff @angle:cg-ne-n2 harmonic 73.16 113.39 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-ne-o harmonic 74.43 114.70 # SOURCE2 1 0.0000 - angle_coeff @angle:cg-ne-p2 harmonic 84.75 119.57 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-ne-s harmonic 68.28 117.70 # SOURCE3 1 0.0000 - angle_coeff @angle:c-ne-sy harmonic 61.66 116.05 # SOURCE4 6 1.2661 - angle_coeff @angle:n2-ne-n2 harmonic 78.59 107.22 # SOURCE3 1 - angle_coeff @angle:n2-ne-ne harmonic 70.94 110.72 # SOURCE3 9 6.1488 - angle_coeff @angle:n2-ne-o harmonic 78.09 114.10 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-ne-p2 harmonic 91.59 109.66 # SOURCE3 1 - angle_coeff @angle:n2-ne-pe harmonic 84.18 112.15 # SOURCE3 7 6.5273 - angle_coeff @angle:n2-ne-px harmonic 83.20 115.97 # SOURCE3 3 1.9854 - angle_coeff @angle:n2-ne-py harmonic 87.34 114.60 # SOURCE3 3 2.9261 - angle_coeff @angle:n2-ne-s harmonic 71.27 115.90 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-ne-sx harmonic 63.80 107.29 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-ne-sy harmonic 65.46 111.21 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-ne-o harmonic 72.28 110.45 # SOURCE3 10 1.8535 - angle_coeff @angle:ne-ne-p2 harmonic 85.32 114.39 # SOURCE3 6 4.0528 - angle_coeff @angle:ne-ne-s harmonic 67.59 115.95 # SOURCE3 6 3.4604 - angle_coeff @angle:o-ne-o harmonic 76.91 124.09 # SOURCE3 2 8.7534 - angle_coeff @angle:o-ne-pe harmonic 78.32 132.32 # SOURCE3 11 23.9559 - angle_coeff @angle:o-ne-px harmonic 86.11 110.62 # SOURCE3 1 0.0000 - angle_coeff @angle:o-ne-py harmonic 90.01 110.79 # SOURCE3 4 1.6818 - angle_coeff @angle:o-ne-s harmonic 71.99 117.19 # SOURCE3 2 0.0225 - angle_coeff @angle:o-ne-sx harmonic 63.79 108.92 # SOURCE3 1 0.0000 - angle_coeff @angle:o-ne-sy harmonic 66.05 111.34 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-ne-pe harmonic 104.56 116.81 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-ne-px harmonic 100.10 128.35 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-ne-py harmonic 105.15 123.47 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-ne-sx harmonic 80.48 112.12 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-ne-sy harmonic 81.80 115.73 # SOURCE3 1 0.0000 - angle_coeff @angle:pe-ne-s harmonic 83.52 115.73 # SOURCE3 1 0.0000 - angle_coeff @angle:px-ne-s harmonic 78.54 131.84 # SOURCE3 1 0.0000 - angle_coeff @angle:py-ne-s harmonic 86.30 116.18 # SOURCE3 4 3.7135 - angle_coeff @angle:s-ne-s harmonic 68.65 120.87 # SOURCE3 1 0.0000 - angle_coeff @angle:s-ne-sx harmonic 63.66 112.96 # SOURCE3 1 0.0000 - angle_coeff @angle:s-ne-sy harmonic 63.94 119.63 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-nf-ca harmonic 60.41 150.84 # CORR 9 - angle_coeff @angle:c1-nf-ch harmonic 66.00 140.00 # SOURCE2 1 same_as_c1-ne-cg - angle_coeff @angle:c2-nf-ca harmonic 66.09 120.84 # CORR 55 - angle_coeff @angle:c2-nf-cf harmonic 67.33 118.17 # SOURCE3 3 same_as_c2-ne-ce - angle_coeff @angle:c2-nf-n2 harmonic 74.56 113.31 # SOURCE3 1 same_as_c2-ne-n2 - angle_coeff @angle:c2-nf-nf harmonic 69.17 110.86 # SOURCE3 7 same_as_c2-ne-ne - angle_coeff @angle:c2-nf-p2 harmonic 80.83 134.03 # SOURCE3 1 same_as_c2-ne-p2 - angle_coeff @angle:c2-nf-pf harmonic 79.24 120.52 # SOURCE3 8 same_as_c2-ne-pe - angle_coeff @angle:c2-nf-px harmonic 80.57 117.75 # SOURCE3 5 same_as_c2-ne-px - angle_coeff @angle:c2-nf-py harmonic 84.33 117.04 # SOURCE3 3 same_as_c2-ne-py - angle_coeff @angle:c2-nf-sx harmonic 60.95 111.98 # SOURCE3 3 same_as_c2-ne-sx - angle_coeff @angle:c2-nf-sy harmonic 61.78 118.92 # CORR 9 - angle_coeff @angle:ca-nf-ce harmonic 65.56 121.98 # CORR 15 - angle_coeff @angle:ca-nf-n2 harmonic 69.73 114.06 # CORR 11 - angle_coeff @angle:ca-nf-ne harmonic 69.69 115.12 # CORR 44 - angle_coeff @angle:ca-nf-o harmonic 71.10 113.96 # SOURCE3 3 same_as_ca-ne-o - angle_coeff @angle:ca-nf-p2 harmonic 83.08 118.09 # SOURCE3 1 same_as_ca-ne-p2 - angle_coeff @angle:ca-nf-s harmonic 65.75 120.11 # SOURCE3 1 same_as_ca-ne-s - angle_coeff @angle:c-nf-c2 harmonic 67.85 118.53 # CORR 6 - angle_coeff @angle:cf-nf-n2 harmonic 71.16 111.19 # SOURCE3 1 same_as_ce-ne-n2 - angle_coeff @angle:cf-nf-o harmonic 72.26 112.16 # SOURCE3 1 same_as_ce-ne-o - angle_coeff @angle:cf-nf-p2 harmonic 83.85 117.02 # SOURCE3 1 same_as_ce-ne-p2 - angle_coeff @angle:cf-nf-s harmonic 67.15 116.28 # SOURCE3 1 same_as_ce-ne-s - angle_coeff @angle:ch-nf-n1 harmonic 71.71 120.20 # SOURCE2 1 same_as_cg-ne-n1 - angle_coeff @angle:ch-nf-n2 harmonic 73.16 113.39 # SOURCE3 1 same_as_cg-ne-n2 - angle_coeff @angle:ch-nf-o harmonic 74.43 114.70 # SOURCE2 1 same_as_cg-ne-o - angle_coeff @angle:ch-nf-p2 harmonic 84.75 119.57 # SOURCE3 1 same_as_cg-ne-p2 - angle_coeff @angle:ch-nf-s harmonic 68.28 117.70 # SOURCE3 1 same_as_cg-ne-s - angle_coeff @angle:f-n-f harmonic 67.90 102.98 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-nf-n2 harmonic 78.59 107.22 # SOURCE3 1 same_as_n2-ne-n2 - angle_coeff @angle:n2-nf-nf harmonic 70.94 110.72 # SOURCE3 9 same_as_n2-ne-ne - angle_coeff @angle:n2-nf-o harmonic 78.09 114.10 # SOURCE3 1 same_as_n2-ne-o - angle_coeff @angle:n2-nf-p2 harmonic 91.59 109.66 # SOURCE3 1 same_as_n2-ne-p2 - angle_coeff @angle:n2-nf-pf harmonic 84.18 112.15 # SOURCE3 7 same_as_n2-ne-pe - angle_coeff @angle:n2-nf-px harmonic 83.20 115.97 # SOURCE3 3 same_as_n2-ne-px - angle_coeff @angle:n2-nf-py harmonic 87.34 114.60 # SOURCE3 3 same_as_n2-ne-py - angle_coeff @angle:n2-nf-s harmonic 71.27 115.90 # SOURCE3 1 same_as_n2-ne-s - angle_coeff @angle:n2-nf-sx harmonic 63.80 107.29 # SOURCE3 1 same_as_n2-ne-sx - angle_coeff @angle:n2-nf-sy harmonic 65.46 111.21 # SOURCE3 1 same_as_n2-ne-sy - angle_coeff @angle:nf-nf-o harmonic 72.28 110.45 # SOURCE3 10 same_as_ne-ne-o - angle_coeff @angle:nf-nf-p2 harmonic 85.32 114.39 # SOURCE3 6 same_as_ne-ne-p2 - angle_coeff @angle:nf-nf-s harmonic 67.59 115.95 # SOURCE3 6 same_as_ne-ne-s - angle_coeff @angle:o-nf-o harmonic 76.91 124.09 # SOURCE3 2 same_as_o-ne-o - angle_coeff @angle:o-nf-pf harmonic 78.32 132.32 # SOURCE3 11 same_as_o-ne-pe - angle_coeff @angle:o-nf-px harmonic 86.11 110.62 # SOURCE3 1 same_as_o-ne-px - angle_coeff @angle:o-nf-py harmonic 90.01 110.79 # SOURCE3 4 same_as_o-ne-py - angle_coeff @angle:o-nf-s harmonic 71.99 117.19 # SOURCE3 2 same_as_o-ne-s - angle_coeff @angle:o-nf-sx harmonic 63.79 108.92 # SOURCE3 1 same_as_o-ne-sx - angle_coeff @angle:o-nf-sy harmonic 66.05 111.34 # SOURCE3 1 same_as_o-ne-sy - angle_coeff @angle:p2-nf-pf harmonic 104.56 116.81 # SOURCE3 1 same_as_p2-ne-pe - angle_coeff @angle:p2-nf-px harmonic 100.10 128.35 # SOURCE3 1 same_as_p2-ne-px - angle_coeff @angle:p2-nf-py harmonic 105.15 123.47 # SOURCE3 1 same_as_p2-ne-py - angle_coeff @angle:p2-nf-sx harmonic 80.48 112.12 # SOURCE3 1 same_as_p2-ne-sx - angle_coeff @angle:p2-nf-sy harmonic 81.80 115.73 # SOURCE3 1 same_as_p2-ne-sy - angle_coeff @angle:pf-nf-s harmonic 83.52 115.73 # SOURCE3 1 same_as_pe-ne-s - angle_coeff @angle:px-nf-s harmonic 78.54 131.84 # SOURCE3 1 same_as_px-ne-s - angle_coeff @angle:py-nf-s harmonic 86.30 116.18 # SOURCE3 4 same_as_py-ne-s - angle_coeff @angle:s-nf-s harmonic 68.65 120.87 # SOURCE3 1 same_as_s-ne-s - angle_coeff @angle:s-nf-sx harmonic 63.66 112.96 # SOURCE3 1 same_as_s-ne-sx - angle_coeff @angle:s-nf-sy harmonic 63.94 119.63 # SOURCE3 1 same_as_s-ne-sy - angle_coeff @angle:br-nh-br harmonic 67.09 106.27 # SOURCE3 1 - angle_coeff @angle:br-nh-ca harmonic 62.04 111.88 # SOURCE3 1 0.0000 - angle_coeff @angle:br-nh-hn harmonic 42.11 101.56 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-nh-c1 harmonic 68.33 116.98 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-nh-c2 harmonic 66.36 122.71 # SOURCE4 5 1.0077 - angle_coeff @angle:c1-nh-ca harmonic 66.22 122.36 # SOURCE3 3 1.2016 - angle_coeff @angle:c1-nh-hn harmonic 49.55 117.30 # SOURCE4 8 0.7120 - angle_coeff @angle:c2-nh-c2 harmonic 65.54 124.50 # SOURCE4 43 1.7515 - angle_coeff @angle:c2-nh-c3 harmonic 63.17 123.71 # SOURCE3 8 3.5348 - angle_coeff @angle:c2-nh-ca harmonic 64.59 127.34 # SOURCE4 97 2.4321 - angle_coeff @angle:c2-nh-cc harmonic 64.92 126.03 # CORR 11 - angle_coeff @angle:c2-nh-cd harmonic 64.92 126.03 # CORR 11 - angle_coeff @angle:c2-nh-cx harmonic 63.08 124.44 # SOURCE4 10 1.6817 - angle_coeff @angle:c2-nh-hn harmonic 49.62 114.89 # SOURCE4 1000 1.4571 - angle_coeff @angle:c2-nh-n2 harmonic 68.36 120.00 # SOURCE4 33 1.1823 - angle_coeff @angle:c2-nh-n3 harmonic 67.57 116.98 # SOURCE4 14 1.4183 - angle_coeff @angle:c2-nh-no harmonic 66.09 125.63 # SOURCE4 7 0.7554 - angle_coeff @angle:c2-nh-oh harmonic 69.45 112.51 # SOURCE4 12 1.1687 - angle_coeff @angle:c2-nh-os harmonic 69.27 112.93 # SOURCE4 6 0.3945 - angle_coeff @angle:c2-nh-sy harmonic 61.76 121.13 # SOURCE4 10 0.5133 - angle_coeff @angle:c3-nh-c3 harmonic 63.53 114.44 # SOURCE4 523 2.1428 - angle_coeff @angle:c3-nh-ca harmonic 64.56 117.77 # SOURCE3 8 1.7521 - angle_coeff @angle:c3-nh-cc harmonic 64.17 119.23 # CORR 163 - angle_coeff @angle:c3-nh-cd harmonic 64.17 119.23 # CORR 163 - angle_coeff @angle:c3-nh-cf harmonic 63.47 119.92 # SOURCE4 20 1.8571 - angle_coeff @angle:c3-nh-cz harmonic 63.01 125.51 # SOURCE4 12 0.5177 - angle_coeff @angle:c3-nh-hn harmonic 46.46 114.95 # SOURCE3 19 2.4787 - angle_coeff @angle:c3-nh-n2 harmonic 67.89 112.35 # SOURCE3 9 4.0058 - angle_coeff @angle:c3-nh-n harmonic 67.10 111.71 # SOURCE4 6 2.4251 - angle_coeff @angle:c3-nh-na harmonic 66.92 112.43 # SOURCE4 8 1.4219 - angle_coeff @angle:c3-nh-p2 harmonic 77.12 123.35 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-nh-sy harmonic 61.91 116.12 # SOURCE4 13 1.2830 - angle_coeff @angle:ca-nh-ca harmonic 64.34 127.46 # SOURCE3 2 0.0002 - angle_coeff @angle:ca-nh-cc harmonic 63.77 129.77 # CORR 38 - angle_coeff @angle:ca-nh-cd harmonic 63.77 129.77 # CORR 38 - angle_coeff @angle:ca-nh-cl harmonic 57.67 113.15 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-nh-cx harmonic 63.11 123.63 # SOURCE4 36 0.5899 - angle_coeff @angle:ca-nh-f harmonic 67.90 106.09 # SOURCE3 3 1.0660 - angle_coeff @angle:ca-nh-hn harmonic 49.08 116.13 # SOURCE4 1780 1.2853 - angle_coeff @angle:ca-nh-i harmonic 55.55 117.83 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-nh-n1 harmonic 69.37 117.13 # HF/6-31G* 1 - angle_coeff @angle:ca-nh-n2 harmonic 67.82 121.11 # SOURCE4 19 0.9700 - angle_coeff @angle:ca-nh-n3 harmonic 68.18 114.21 # SOURCE3 6 2.2412 - angle_coeff @angle:ca-nh-n4 harmonic 68.56 108.94 # SOURCE3 5 0.6562 - angle_coeff @angle:ca-nh-n harmonic 68.07 116.15 # SOURCE4 12 0.8135 - angle_coeff @angle:ca-nh-na harmonic 68.58 114.54 # SOURCE3 8 0.7807 - angle_coeff @angle:ca-nh-nh harmonic 68.49 114.87 # SOURCE3 6 2.1432 - angle_coeff @angle:ca-nh-no harmonic 69.19 113.92 # SOURCE3 4 2.9561 - angle_coeff @angle:ca-nh-o harmonic 69.64 121.92 # SOURCE3 2 3.9630 - angle_coeff @angle:ca-nh-oh harmonic 69.15 112.80 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-nh-os harmonic 69.93 110.17 # SOURCE3 3 0.6448 - angle_coeff @angle:ca-nh-p2 harmonic 77.99 125.27 # SOURCE3 8 5.1798 - angle_coeff @angle:ca-nh-p3 harmonic 76.07 125.70 # SOURCE3 3 5.7796 - angle_coeff @angle:ca-nh-p4 harmonic 77.43 124.01 # SOURCE3 3 2.5810 - angle_coeff @angle:ca-nh-p5 harmonic 78.16 125.61 # SOURCE3 3 0.5287 - angle_coeff @angle:ca-nh-s4 harmonic 62.13 115.62 # SOURCE3 3 0.3434 - angle_coeff @angle:ca-nh-s6 harmonic 61.56 123.53 # SOURCE4 33 2.0385 - angle_coeff @angle:ca-nh-s harmonic 59.38 122.54 # SOURCE3 3 2.7001 - angle_coeff @angle:ca-nh-sh harmonic 61.78 121.41 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-nh-ss harmonic 61.75 121.50 # SOURCE3 3 2.6255 - angle_coeff @angle:ca-nh-sy harmonic 60.64 125.26 # SOURCE4 41 1.7517 - angle_coeff @angle:cc-nh-cx harmonic 63.09 123.72 # CORR 58 - angle_coeff @angle:cc-nh-hn harmonic 48.86 117.16 # SOURCE3 11 2.6137 - angle_coeff @angle:cc-nh-n2 harmonic 68.23 119.66 # SOURCE4 5 1.3903 - angle_coeff @angle:cc-nh-sy harmonic 61.22 122.91 # SOURCE4 23 1.2029 - angle_coeff @angle:cd-nh-cx harmonic 63.09 123.72 # CORR 58 - angle_coeff @angle:cd-nh-hn harmonic 48.86 117.16 # SOURCE3 11 2.6137 - angle_coeff @angle:ce-nh-hn harmonic 48.38 115.62 # CORR 203 - angle_coeff @angle:ce-nh-o harmonic 66.85 129.43 # CORR 2 - angle_coeff @angle:ce-nh-sy harmonic 63.58 112.97 # SOURCE4 7 1.0636 - angle_coeff @angle:cf-nh-hn harmonic 48.38 115.62 # CORR 203 - angle_coeff @angle:cf-nh-o harmonic 66.85 129.43 # CORR 2 - angle_coeff @angle:cl-nh-cl harmonic 54.43 106.60 # SOURCE3 1 - angle_coeff @angle:cl-nh-hn harmonic 40.07 104.14 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-nh-cx harmonic 86.53 62.02 # SOURCE4 45 0.6189 - angle_coeff @angle:cx-nh-hn harmonic 45.79 118.89 # SOURCE4 8 0.1391 - angle_coeff @angle:cz-nh-hn harmonic 48.79 121.24 # SOURCE4 40 0.5682 - angle_coeff @angle:f-nh-f harmonic 66.93 101.70 # SOURCE3 1 0.0000 - angle_coeff @angle:f-nh-hn harmonic 49.80 101.23 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-nh-hn harmonic 40.05 114.85 # SOURCE4 1108 2.0811 - angle_coeff @angle:hn-nh-i harmonic 36.55 107.57 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-nh-n1 harmonic 52.31 110.57 # HF/6-31G* 1 - angle_coeff @angle:hn-nh-n2 harmonic 50.08 118.22 # SOURCE4 75 2.3319 - angle_coeff @angle:hn-nh-n3 harmonic 50.05 109.12 # SOURCE3 5 2.3680 - angle_coeff @angle:hn-nh-n4 harmonic 49.69 104.40 # SOURCE3 3 0.5056 - angle_coeff @angle:hn-nh-n harmonic 50.89 107.96 # SOURCE4 16 1.2025 - angle_coeff @angle:hn-nh-na harmonic 50.95 107.91 # SOURCE3 26 1.5528 - angle_coeff @angle:hn-nh-nh harmonic 50.32 110.64 # SOURCE4 8 1.3390 - angle_coeff @angle:hn-nh-no harmonic 50.99 109.93 # SOURCE4 7 0.2027 - angle_coeff @angle:hn-nh-o harmonic 52.99 116.45 # SOURCE3 2 0.6063 - angle_coeff @angle:hn-nh-oh harmonic 51.13 106.55 # SOURCE4 8 0.4590 - angle_coeff @angle:hn-nh-os harmonic 51.51 104.76 # SOURCE3 3 0.4883 - angle_coeff @angle:hn-nh-p2 harmonic 54.38 118.18 # SOURCE3 21 3.6927 - angle_coeff @angle:hn-nh-p3 harmonic 53.06 116.19 # SOURCE3 3 3.0539 - angle_coeff @angle:hn-nh-p4 harmonic 54.74 112.60 # SOURCE3 3 0.8237 - angle_coeff @angle:hn-nh-p5 harmonic 55.35 115.26 # SOURCE3 3 0.9168 - angle_coeff @angle:hn-nh-s4 harmonic 43.06 107.48 # SOURCE3 3 1.3960 - angle_coeff @angle:hn-nh-s harmonic 40.81 114.37 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-nh-s6 harmonic 44.04 109.98 # SOURCE4 29 0.7478 - angle_coeff @angle:hn-nh-sh harmonic 43.27 112.25 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-nh-ss harmonic 42.95 113.89 # SOURCE3 3 1.4030 - angle_coeff @angle:hn-nh-sy harmonic 43.28 111.23 # SOURCE4 62 1.1413 - angle_coeff @angle:i-nh-i harmonic 59.80 115.82 # SOURCE3 1 - angle_coeff @angle:n1-nh-n1 harmonic 75.13 106.71 # HF/6-31G* 1 - angle_coeff @angle:n2-nh-n2 harmonic 70.76 117.50 # SOURCE3 2 1.1907 - angle_coeff @angle:n2-nh-n3 harmonic 69.63 115.54 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-nh-o harmonic 70.40 126.06 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-nh-n3 harmonic 69.52 110.98 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-nh-n4 harmonic 68.15 108.36 # SOURCE3 1 0.0000 - angle_coeff @angle:na-nh-na harmonic 70.14 112.01 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-hn harmonic 39.73 117.85 # SOURCE3 15 2.3694 - angle_coeff @angle:nh-nh-nh harmonic 70.07 112.23 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-i harmonic 36.08 117.24 # SOURCE3 2 0.4435 - angle_coeff @angle:hn-n-n2 harmonic 49.62 118.33 # SOURCE3 5 2.2377 - angle_coeff @angle:hn-n-n3 harmonic 48.69 117.22 # SOURCE4 37 1.3737 - angle_coeff @angle:hn-n-n4 harmonic 48.90 112.68 # SOURCE3 3 1.9746 - angle_coeff @angle:hn-n-n harmonic 50.14 113.12 # SOURCE3 7 3.2954 - angle_coeff @angle:hn-n-na harmonic 50.40 113.55 # SOURCE3 8 1.9324 - angle_coeff @angle:hn-n-nc harmonic 50.74 115.24 # SOURCE4 10 0.4966 - angle_coeff @angle:hn-n-nh harmonic 49.74 113.13 # SOURCE4 12 1.2125 - angle_coeff @angle:hn-n-no harmonic 48.71 110.11 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-o harmonic 53.83 116.32 # SOURCE3 2 0.0175 - angle_coeff @angle:n-nh-o harmonic 72.07 115.63 # SOURCE3 1 - angle_coeff @angle:hn-n-oh harmonic 50.33 110.71 # SOURCE4 46 1.1278 - angle_coeff @angle:no-nh-no harmonic 72.07 108.55 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-os harmonic 50.52 109.82 # SOURCE4 12 0.6996 - angle_coeff @angle:hn-n-p2 harmonic 52.51 118.05 # SOURCE3 7 3.0564 - angle_coeff @angle:hn-n-p3 harmonic 50.93 119.63 # SOURCE3 2 0.0000 - angle_coeff @angle:hn-n-p4 harmonic 53.00 115.71 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-p5 harmonic 54.50 113.20 # SOURCE4 6 1.0341 - angle_coeff @angle:hn-n-s4 harmonic 41.18 112.46 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-s harmonic 41.14 114.92 # SOURCE3 2 0.0260 - angle_coeff @angle:hn-n-s6 harmonic 43.06 112.18 # SOURCE4 6 0.6101 - angle_coeff @angle:hn-n-sh harmonic 42.19 114.91 # SOURCE3 1 0.0000 - angle_coeff @angle:hn-n-ss harmonic 42.36 115.60 # SOURCE3 3 0.6414 - angle_coeff @angle:hn-n-sy harmonic 43.02 112.34 # SOURCE4 38 0.6039 - angle_coeff @angle:oh-nh-oh harmonic 72.15 106.27 # SOURCE3 1 - angle_coeff @angle:o-nh-o harmonic 72.24 128.06 # SOURCE3 1 - angle_coeff @angle:os-nh-os harmonic 72.41 105.27 # SOURCE3 1 - angle_coeff @angle:p2-nh-p2 harmonic 98.07 127.33 # SOURCE3 2 2.7857 - angle_coeff @angle:p3-nh-p3 harmonic 96.03 125.08 # SOURCE3 1 - angle_coeff @angle:p5-nh-p5 harmonic 104.72 112.76 # SOURCE3 1 - angle_coeff @angle:s4-nh-s4 harmonic 62.56 112.39 # SOURCE3 1 - angle_coeff @angle:s6-nh-s6 harmonic 62.35 120.27 # SOURCE3 1 - angle_coeff @angle:sh-nh-sh harmonic 62.26 119.00 # SOURCE3 1 - angle_coeff @angle:s-nh-s harmonic 59.67 118.73 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-nh-ss harmonic 62.19 119.25 # SOURCE3 1 - angle_coeff @angle:i-n-i harmonic 60.66 118.20 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-n-n2 harmonic 70.16 116.89 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-n-n3 harmonic 68.02 117.94 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-n-n4 harmonic 68.42 112.69 # SOURCE3 1 0.0000 - angle_coeff @angle:na-n-na harmonic 69.61 117.38 # SOURCE3 1 0.0000 - angle_coeff @angle:nc-n-nc harmonic 71.04 116.41 # CORR 2 - angle_coeff @angle:nc-n-p2 harmonic 80.69 117.21 # CORR 2 - angle_coeff @angle:nc-n-pc harmonic 80.42 117.21 # CORR 2 - angle_coeff @angle:nd-n-nd harmonic 71.04 116.41 # CORR 2 - angle_coeff @angle:nd-n-p2 harmonic 80.69 117.21 # CORR 2 - angle_coeff @angle:nd-n-pd harmonic 80.42 117.21 # CORR 2 - angle_coeff @angle:nh-n-nh harmonic 69.10 115.18 # SOURCE3 1 0.0000 - angle_coeff @angle:n-n-n harmonic 69.89 114.62 # SOURCE3 1 0.0000 - angle_coeff @angle:no-n-no harmonic 68.52 108.66 # SOURCE3 1 0.0000 - angle_coeff @angle:br-no-o harmonic 58.48 113.19 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-no-o harmonic 71.34 116.63 # SOURCE3 6 0.0000 - angle_coeff @angle:c2-no-o harmonic 69.87 116.87 # SOURCE3 8 0.4200 - angle_coeff @angle:c3-no-o harmonic 66.96 116.56 # SOURCE3 6 0.3959 - angle_coeff @angle:ca-no-o harmonic 68.74 118.10 # SOURCE3 10 1.1524 - angle_coeff @angle:cc-no-o harmonic 70.34 117.52 # SOURCE4 198 0.6255 - angle_coeff @angle:cl-no-o harmonic 57.30 115.08 # SOURCE3 2 0.0000 - angle_coeff @angle:c-no-o harmonic 67.10 115.26 # SOURCE3 1 - angle_coeff @angle:hn-no-o harmonic 55.31 115.49 # SOURCE3 2 0.0000 - angle_coeff @angle:oh-n-oh harmonic 72.05 107.26 # SOURCE3 1 0.0000 - angle_coeff @angle:i-no-o harmonic 54.60 116.31 # SOURCE3 2 0.0000 - angle_coeff @angle:n1-no-o harmonic 73.78 115.00 # HF/6-31G* 1 - angle_coeff @angle:n2-no-o harmonic 65.79 115.10 # SOURCE2 2 2.4000 - angle_coeff @angle:n3-no-o harmonic 72.01 115.56 # SOURCE3 6 0.6427 - angle_coeff @angle:n4-no-o harmonic 72.87 109.00 # SOURCE3 2 0.0000 - angle_coeff @angle:na-no-o harmonic 72.24 115.49 # SOURCE3 18 0.5640 - angle_coeff @angle:nh-no-o harmonic 74.08 115.71 # SOURCE3 8 0.4811 - angle_coeff @angle:n-no-o harmonic 71.67 115.41 # SOURCE3 8 0.3748 - angle_coeff @angle:no-no-o harmonic 59.92 112.38 # SOURCE3 4 0.0000 - angle_coeff @angle:o-n-o harmonic 73.39 128.61 # SOURCE3 3 1.0626 - angle_coeff @angle:o-no-o harmonic 77.15 125.13 # SOURCE4 461 0.7605 - angle_coeff @angle:o-no-oh harmonic 74.09 114.70 # SOURCE3 2 0.0000 - angle_coeff @angle:o-no-os harmonic 73.71 114.01 # SOURCE3 8 0.9778 - angle_coeff @angle:o-no-p2 harmonic 82.07 117.38 # SOURCE3 20 0.8083 - angle_coeff @angle:o-no-p3 harmonic 77.73 116.78 # SOURCE3 6 0.4929 - angle_coeff @angle:o-no-p4 harmonic 76.69 116.64 # SOURCE3 6 0.0089 - angle_coeff @angle:o-no-p5 harmonic 78.18 116.69 # SOURCE3 8 0.4507 - angle_coeff @angle:o-no-s4 harmonic 57.15 114.49 # SOURCE3 6 0.5674 - angle_coeff @angle:o-no-s6 harmonic 57.79 114.39 # SOURCE3 6 0.8311 - angle_coeff @angle:o-no-s harmonic 64.05 119.81 # SOURCE3 4 0.0042 - angle_coeff @angle:o-no-sh harmonic 62.94 116.10 # SOURCE3 2 0.0000 - angle_coeff @angle:o-no-ss harmonic 62.27 115.58 # SOURCE3 6 0.5860 - angle_coeff @angle:os-n-os harmonic 72.28 106.53 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-n-p2 harmonic 98.03 119.62 # SOURCE3 1 - angle_coeff @angle:p3-n-p3 harmonic 100.67 108.73 # SOURCE3 3 0.2591 - angle_coeff @angle:p4-n-p4 harmonic 102.85 108.55 # SOURCE3 1 - angle_coeff @angle:p5-n-p5 harmonic 108.79 99.99 # SOURCE3 1 - angle_coeff @angle:pc-n-pc harmonic 97.64 119.62 # SOURCE3 1 0.0000 - angle_coeff @angle:pd-n-pd harmonic 97.64 119.62 # SOURCE3 1 same_as_pc-n-pc - angle_coeff @angle:s4-n-s4 harmonic 61.03 113.75 # SOURCE3 1 0.0000 - angle_coeff @angle:s6-n-s6 harmonic 61.82 119.68 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-n-sh harmonic 61.53 119.03 # SOURCE3 1 0.0000 - angle_coeff @angle:s-n-s harmonic 58.48 126.00 # SOURCE3 1 - angle_coeff @angle:ss-n-ss harmonic 62.06 118.49 # SOURCE3 1 0.0000 - angle_coeff @angle:br-oh-ho harmonic 42.15 101.60 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-oh-ho harmonic 50.20 108.76 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-oh-ho harmonic 49.91 108.98 # SOURCE3 6 2.2379 - angle_coeff @angle:c3-oh-ho harmonic 47.09 108.16 # SOURCE3 42 1.3034 - angle_coeff @angle:ca-oh-ho harmonic 48.85 109.47 # SOURCE3 7 1.0405 - angle_coeff @angle:cc-oh-ho harmonic 49.96 107.06 # CORR 117 - angle_coeff @angle:cd-oh-ho harmonic 49.96 107.06 # CORR 117 - angle_coeff @angle:ce-oh-ho harmonic 49.85 106.95 # CORR 34 - angle_coeff @angle:cf-oh-ho harmonic 49.85 106.95 # CORR 34 - angle_coeff @angle:c-oh-ho harmonic 51.19 107.37 # SOURCE3 34 1.6830 - angle_coeff @angle:cl-oh-ho harmonic 40.51 102.40 # SOURCE2 1 0.0000 - angle_coeff @angle:cx-oh-ho harmonic 49.64 106.17 # SOURCE3 3 0.0644 - angle_coeff @angle:cy-oh-ho harmonic 47.62 107.32 # SOURCE4 5 0.4955 - angle_coeff @angle:f-oh-ho harmonic 48.47 96.80 # SOURCE2 1 0.0000 - angle_coeff @angle:ho-oh-ho harmonic 41.93 104.80 # SOURCE2 1 0.0000 - angle_coeff @angle:ho-oh-i harmonic 35.67 107.98 # SOURCE3 2 0.0000 - angle_coeff @angle:ho-oh-n1 harmonic 52.55 107.81 # HF/6-31G* 1 - angle_coeff @angle:ho-oh-n2 harmonic 50.57 102.74 # SOURCE3 9 2.1286 - angle_coeff @angle:ho-oh-n3 harmonic 50.61 102.33 # SOURCE3 5 1.2591 - angle_coeff @angle:ho-oh-n4 harmonic 49.44 106.63 # SOURCE3 3 0.2770 - angle_coeff @angle:ho-oh-n harmonic 50.46 101.03 # SOURCE3 6 1.4086 - angle_coeff @angle:ho-oh-na harmonic 50.24 103.71 # SOURCE3 9 1.2590 - angle_coeff @angle:ho-oh-nh harmonic 49.97 102.42 # SOURCE4 15 0.6819 - angle_coeff @angle:ho-oh-no harmonic 50.31 102.17 # SOURCE3 1 0.0000 - angle_coeff @angle:ho-oh-o harmonic 47.26 100.87 # SOURCE3 1 - angle_coeff @angle:ho-oh-oh harmonic 49.34 98.72 # SOURCE3 2 0.0000 - angle_coeff @angle:ho-oh-os harmonic 49.58 99.69 # SOURCE4 18 0.3384 - angle_coeff @angle:ho-oh-p2 harmonic 55.87 109.45 # SOURCE3 8 3.3491 - angle_coeff @angle:ho-oh-p3 harmonic 53.84 110.64 # SOURCE3 3 0.5191 - angle_coeff @angle:ho-oh-p4 harmonic 55.27 110.19 # SOURCE3 4 0.2372 - angle_coeff @angle:ho-oh-p5 harmonic 55.88 110.14 # SOURCE3 92 3.8033 - angle_coeff @angle:ho-oh-py harmonic 56.18 110.73 # SOURCE3 79 1.7835 - angle_coeff @angle:ho-oh-s4 harmonic 42.77 106.76 # SOURCE4 9 0.4035 - angle_coeff @angle:ho-oh-s harmonic 40.86 100.15 # SOURCE3 2 0.0000 - angle_coeff @angle:ho-oh-s6 harmonic 45.46 109.20 # SOURCE3 13 0.1856 - angle_coeff @angle:ho-oh-sh harmonic 42.97 106.24 # SOURCE3 2 0.0661 - angle_coeff @angle:ho-oh-ss harmonic 43.10 107.06 # SOURCE3 4 0.9967 - angle_coeff @angle:ho-oh-sy harmonic 44.20 106.41 # SOURCE4 33 0.3729 - angle_coeff @angle:br-os-br harmonic 65.08 110.63 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-os-c1 harmonic 66.99 115.02 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-os-c3 harmonic 64.47 113.39 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-os-c2 harmonic 65.95 113.14 # SOURCE3 6 2.1932 - angle_coeff @angle:c2-os-c3 harmonic 64.21 112.09 # SOURCE3 7 4.1809 - angle_coeff @angle:c2-os-ca harmonic 65.43 113.59 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-os-n2 harmonic 64.91 118.13 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-os-na harmonic 68.21 103.85 # SOURCE3 4 0.6297 - angle_coeff @angle:c2-os-os harmonic 68.35 102.77 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-os-p5 harmonic 77.31 126.37 # SOURCE4 7 1.7939 - angle_coeff @angle:c2-os-ss harmonic 63.08 108.13 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-os-c3 harmonic 62.39 112.45 # SOURCE4 1293 1.6468 - angle_coeff @angle:c3-os-ca harmonic 62.27 117.97 # SOURCE4 2495 1.4576 - angle_coeff @angle:c3-os-cc harmonic 62.50 117.33 # CORR 248 - angle_coeff @angle:c3-os-cd harmonic 62.50 117.33 # CORR 248 - angle_coeff @angle:c3-os-ce harmonic 62.79 116.05 # CORR 37 - angle_coeff @angle:c3-os-cf harmonic 62.79 116.05 # CORR 37 - angle_coeff @angle:c3-os-cl harmonic 56.20 110.50 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-os-cy harmonic 61.67 115.65 # SOURCE4 5 0.2390 - angle_coeff @angle:c3-os-i harmonic 54.88 113.70 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-os-n1 harmonic 66.31 113.50 # HF/6-31G* 1 - angle_coeff @angle:c3-os-n2 harmonic 65.92 108.12 # SOURCE3 7 0.3048 - angle_coeff @angle:c3-os-n3 harmonic 64.52 110.28 # SOURCE4 14 1.9026 - angle_coeff @angle:c3-os-n4 harmonic 64.88 110.50 # SOURCE3 3 0.5426 - angle_coeff @angle:c3-os-n harmonic 65.40 109.52 # SOURCE4 14 0.6827 - angle_coeff @angle:c3-os-na harmonic 64.54 109.91 # SOURCE3 9 1.8268 - angle_coeff @angle:c3-os-nc harmonic 64.80 112.73 # SOURCE3 2 1.0358 - angle_coeff @angle:c3-os-nd harmonic 64.80 112.73 # SOURCE3 2 same_as_c3-os-nc - angle_coeff @angle:c3-os-nh harmonic 65.22 109.69 # SOURCE4 8 0.1662 - angle_coeff @angle:c3-os-no harmonic 63.89 113.80 # SOURCE4 42 0.2726 - angle_coeff @angle:c3-os-o harmonic 65.62 103.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-os-oh harmonic 65.24 107.97 # SOURCE4 11 0.4333 - angle_coeff @angle:c3-os-os harmonic 65.89 105.01 # SOURCE3 7 0.6328 - angle_coeff @angle:c3-os-p2 harmonic 80.24 115.47 # SOURCE3 8 2.6374 - angle_coeff @angle:c3-os-p3 harmonic 76.51 115.97 # SOURCE3 3 0.3597 - angle_coeff @angle:c3-os-p4 harmonic 77.59 117.48 # SOURCE3 4 0.3850 - angle_coeff @angle:c3-os-p5 harmonic 78.48 118.00 # SOURCE3 31 1.2882 - angle_coeff @angle:c3-os-py harmonic 78.07 117.80 # SOURCE3 16 0.9654 - angle_coeff @angle:c3-os-s4 harmonic 61.32 111.50 # SOURCE3 6 1.4240 - angle_coeff @angle:c3-os-s6 harmonic 63.21 115.79 # SOURCE4 60 1.2588 - angle_coeff @angle:c3-os-s harmonic 59.28 109.55 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-os-sh harmonic 61.67 112.82 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-os-ss harmonic 60.74 113.19 # SOURCE3 3 0.2455 - angle_coeff @angle:ca-os-ca harmonic 63.31 119.95 # SOURCE4 107 1.6535 - angle_coeff @angle:ca-os-cc harmonic 67.21 106.65 # CORR 62 - angle_coeff @angle:ca-os-cd harmonic 67.21 106.65 # CORR 62 - angle_coeff @angle:ca-os-n3 harmonic 65.39 112.19 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-os-na harmonic 66.47 108.24 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-os-nc harmonic 66.09 113.68 # SOURCE3 2 - angle_coeff @angle:ca-os-nd harmonic 66.09 113.68 # SOURCE3 2 - angle_coeff @angle:ca-os-p5 harmonic 77.96 123.42 # SOURCE4 54 1.1358 - angle_coeff @angle:ca-os-s6 harmonic 63.95 116.97 # SOURCE4 15 0.9514 - angle_coeff @angle:c-os-c2 harmonic 64.91 118.02 # SOURCE4 7 0.3666 - angle_coeff @angle:c-os-c3 harmonic 63.63 115.14 # SOURCE3 17 1.8967 - angle_coeff @angle:c-os-c harmonic 64.54 120.64 # SOURCE4 7 1.5114 - angle_coeff @angle:c-os-ca harmonic 63.75 120.87 # SOURCE4 257 1.7209 - angle_coeff @angle:c-os-cc harmonic 64.15 119.62 # SOURCE3 5 6.0675 - angle_coeff @angle:cc-os-cc harmonic 67.27 106.69 # CORR 252 - angle_coeff @angle:cc-os-cd harmonic 63.80 118.62 # SOURCE4 14 1.9764 - angle_coeff @angle:c-os-cd harmonic 64.15 119.62 # SOURCE3 5 6.0675 - angle_coeff @angle:cc-os-na harmonic 65.51 111.66 # SOURCE3 28 4.1343 - angle_coeff @angle:cc-os-nc harmonic 68.12 107.23 # SOURCE3 6 2.7507 - angle_coeff @angle:cc-os-os harmonic 66.27 108.47 # SOURCE3 2 0.0000 - angle_coeff @angle:cc-os-ss harmonic 59.85 119.59 # SOURCE3 1 0.0000 - angle_coeff @angle:c-os-cy harmonic 71.75 91.10 # SOURCE3 2 0.0155 - angle_coeff @angle:cd-os-cd harmonic 67.27 106.69 # CORR 252 - angle_coeff @angle:cd-os-na harmonic 65.51 111.66 # SOURCE3 28 4.1343 - angle_coeff @angle:cd-os-nd harmonic 68.12 107.23 # SOURCE3 6 2.7507 - angle_coeff @angle:cd-os-os harmonic 66.27 108.47 # SOURCE3 2 same_as_cc-os-os - angle_coeff @angle:cd-os-ss harmonic 59.85 119.59 # SOURCE3 1 same_as_cc-os-ss - angle_coeff @angle:cl-os-cl harmonic 52.29 110.76 # SOURCE3 2 0.0000 - angle_coeff @angle:c-os-n2 harmonic 66.95 112.08 # SOURCE4 6 0.1154 - angle_coeff @angle:c-os-n harmonic 66.83 112.10 # SOURCE4 6 0.6163 - angle_coeff @angle:c-os-oh harmonic 66.50 110.50 # SOURCE3 1 0.0000 - angle_coeff @angle:c-os-os harmonic 66.25 110.28 # SOURCE4 10 1.3612 - angle_coeff @angle:c-os-p5 harmonic 78.89 122.10 # SOURCE4 5 0.5870 - angle_coeff @angle:c-os-sy harmonic 61.85 113.49 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-os-cx harmonic 85.27 61.82 # SOURCE4 107 0.1793 - angle_coeff @angle:cx-os-n harmonic 88.98 59.99 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-os-os harmonic 90.38 56.52 # SOURCE3 2 0.0000 - angle_coeff @angle:cy-os-cy harmonic 68.81 93.40 # SOURCE2 2 1.4000 - angle_coeff @angle:f-os-f harmonic 63.94 103.30 # SOURCE2 1 0.0000 - angle_coeff @angle:f-os-os harmonic 63.94 109.50 # SOURCE2 1 0.0000 - angle_coeff @angle:i-os-i harmonic 58.06 115.67 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-os-n1 harmonic 70.28 117.79 # HF/6-31G* 1 - angle_coeff @angle:n2-os-n2 harmonic 68.76 106.83 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-os-s6 harmonic 66.63 111.30 # SOURCE4 7 0.5651 - angle_coeff @angle:n3-os-n3 harmonic 67.76 104.88 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-os-n4 harmonic 65.66 114.68 # SOURCE3 1 0.0000 - angle_coeff @angle:na-os-na harmonic 66.10 109.59 # SOURCE3 1 0.0000 - angle_coeff @angle:na-os-ss harmonic 64.75 104.34 # SOURCE3 1 0.0000 - angle_coeff @angle:nc-os-nc harmonic 68.17 110.40 # SOURCE2 1 0.0000 - angle_coeff @angle:nc-os-ss harmonic 63.38 110.97 # SOURCE3 1 0.0000 - angle_coeff @angle:nd-os-nd harmonic 68.17 110.40 # SOURCE2 1 same_as_nc-os-nc - angle_coeff @angle:nd-os-ss harmonic 63.38 110.97 # SOURCE3 1 same_as_nc-os-ss - angle_coeff @angle:nh-os-nh harmonic 67.81 108.29 # SOURCE3 1 0.0000 - angle_coeff @angle:n-os-n harmonic 68.08 108.31 # SOURCE3 1 0.0000 - angle_coeff @angle:no-os-no harmonic 66.40 111.86 # SOURCE3 1 0.0000 - angle_coeff @angle:n-os-s6 harmonic 65.87 113.62 # SOURCE4 5 0.0928 - angle_coeff @angle:o-os-o harmonic 62.76 114.68 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-os-p2 harmonic 103.59 120.02 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-os-p5 harmonic 108.26 107.86 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-os-p3 harmonic 96.17 121.22 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-os-py harmonic 105.11 105.58 # SOURCE3 1 0.0000 - angle_coeff @angle:p5-os-p5 harmonic 99.18 126.25 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-os-s4 harmonic 62.09 111.63 # SOURCE3 1 0.0000 - angle_coeff @angle:s6-os-s6 harmonic 64.77 119.07 # SOURCE3 2 0.4318 - angle_coeff @angle:sh-os-sh harmonic 61.15 118.95 # SOURCE3 1 0.0000 - angle_coeff @angle:s-os-s harmonic 56.98 118.08 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-os-ss harmonic 60.82 115.64 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p2-br harmonic 40.68 108.60 # SOURCE3 1 - angle_coeff @angle:br-p2-c2 harmonic 39.43 102.32 # SOURCE3 2 0.0146 - angle_coeff @angle:br-p2-n2 harmonic 40.42 103.33 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p2-o harmonic 39.43 110.87 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p2-p2 harmonic 50.16 115.46 # SOURCE3 4 7.8622 - angle_coeff @angle:br-p2-s harmonic 40.59 110.52 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-p2-c1 harmonic 39.20 99.04 # SOURCE3 1 - angle_coeff @angle:c1-p2-c2 harmonic 39.82 101.29 # SOURCE3 1 - angle_coeff @angle:c1-p2-n2 harmonic 41.36 101.79 # SOURCE3 1 - angle_coeff @angle:c1-p2-o harmonic 41.32 107.62 # SOURCE3 1 - angle_coeff @angle:c1-p2-p2 harmonic 53.31 99.54 # SOURCE3 1 - angle_coeff @angle:c1-p2-s harmonic 41.00 105.90 # SOURCE3 1 - angle_coeff @angle:c2-p2-c2 harmonic 40.45 104.50 # SOURCE3 1 - angle_coeff @angle:c2-p2-c3 harmonic 38.60 101.90 # SOURCE3 4 0.1132 - angle_coeff @angle:c2-p2-ca harmonic 38.79 101.95 # SOURCE3 1 - angle_coeff @angle:c2-p2-cl harmonic 35.61 102.72 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-p2-f harmonic 41.60 103.47 # SOURCE3 2 0.0136 - angle_coeff @angle:c2-p2-hp harmonic 30.13 97.19 # SOURCE3 3 0.0216 - angle_coeff @angle:c2-p2-i harmonic 33.85 101.94 # SOURCE3 2 0.0368 - angle_coeff @angle:c2-p2-n2 harmonic 43.20 99.88 # SOURCE3 1 - angle_coeff @angle:c2-p2-n3 harmonic 41.99 101.80 # SOURCE3 1 - angle_coeff @angle:c2-p2-n4 harmonic 39.07 98.26 # SOURCE3 6 0.1522 - angle_coeff @angle:c2-p2-n harmonic 40.89 103.28 # SOURCE3 4 3.3113 - angle_coeff @angle:c2-p2-na harmonic 40.54 103.99 # SOURCE3 8 1.6834 - angle_coeff @angle:c2-p2-nh harmonic 41.20 105.17 # SOURCE3 8 0.8263 - angle_coeff @angle:c2-p2-no harmonic 41.91 97.97 # SOURCE3 3 0.4175 - angle_coeff @angle:c2-p2-o harmonic 41.51 115.16 # SOURCE3 1 - angle_coeff @angle:c2-p2-oh harmonic 42.50 102.89 # SOURCE3 3 0.8191 - angle_coeff @angle:c2-p2-os harmonic 43.35 102.12 # SOURCE3 4 0.8783 - angle_coeff @angle:c2-p2-p2 harmonic 54.72 99.56 # SOURCE3 1 - angle_coeff @angle:c2-p2-p3 harmonic 48.11 99.27 # SOURCE3 4 1.1590 - angle_coeff @angle:c2-p2-p4 harmonic 48.19 96.94 # SOURCE3 1 - angle_coeff @angle:c2-p2-p5 harmonic 48.01 97.61 # SOURCE3 1 - angle_coeff @angle:c2-p2-s4 harmonic 38.27 95.15 # SOURCE3 1 - angle_coeff @angle:c2-p2-s6 harmonic 38.35 95.51 # SOURCE3 1 - angle_coeff @angle:c2-p2-s harmonic 42.19 105.53 # SOURCE3 1 - angle_coeff @angle:c2-p2-sh harmonic 40.19 101.49 # SOURCE3 3 0.0057 - angle_coeff @angle:c2-p2-ss harmonic 40.19 101.81 # SOURCE3 4 0.5883 - angle_coeff @angle:c3-p2-c3 harmonic 37.36 99.30 # SOURCE3 1 - angle_coeff @angle:c3-p2-n2 harmonic 40.30 100.82 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p2-o harmonic 40.10 106.72 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p2-os harmonic 40.68 101.34 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p2-p2 harmonic 51.78 100.48 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p2-s harmonic 40.04 105.68 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-p2-ca harmonic 37.59 99.70 # SOURCE3 1 - angle_coeff @angle:ca-p2-n2 harmonic 40.53 100.82 # SOURCE3 1 - angle_coeff @angle:ca-p2-n harmonic 41.68 89.97 # SOURCE3 1 - angle_coeff @angle:ca-p2-na harmonic 41.69 89.21 # SOURCE3 1 - angle_coeff @angle:ca-p2-o harmonic 40.31 106.88 # SOURCE3 1 - angle_coeff @angle:ca-p2-s harmonic 39.79 107.93 # SOURCE3 1 - angle_coeff @angle:c-p2-c2 harmonic 38.89 97.30 # SOURCE3 1 - angle_coeff @angle:c-p2-c harmonic 38.29 90.10 # SOURCE3 1 - angle_coeff @angle:ce-p2-o harmonic 40.63 107.44 # SOURCE3 1 - angle_coeff @angle:ce-p2-s harmonic 40.55 105.54 # SOURCE3 1 - angle_coeff @angle:cf-p2-o harmonic 40.63 107.44 # SOURCE3 1 same_as_ce-p2-o - angle_coeff @angle:cf-p2-s harmonic 40.55 105.54 # SOURCE3 1 same_as_ce-p2-s - angle_coeff @angle:cl-p2-cl harmonic 32.00 108.70 # SOURCE3 1 - angle_coeff @angle:cl-p2-n2 harmonic 36.67 103.38 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-p2-o harmonic 36.00 110.57 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-p2-p2 harmonic 47.78 103.11 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-p2-s harmonic 36.62 110.11 # SOURCE3 1 0.0000 - angle_coeff @angle:f-p2-f harmonic 42.20 107.10 # SOURCE3 1 - angle_coeff @angle:f-p2-n2 harmonic 43.59 103.57 # SOURCE3 1 0.0000 - angle_coeff @angle:f-p2-o harmonic 43.81 110.61 # SOURCE3 1 0.0000 - angle_coeff @angle:f-p2-p2 harmonic 54.54 103.48 # SOURCE3 1 0.0000 - angle_coeff @angle:f-p2-s harmonic 41.15 114.71 # SOURCE3 2 5.2794 - angle_coeff @angle:hp-p2-hp harmonic 22.84 98.76 # SOURCE3 1 - angle_coeff @angle:hp-p2-n1 harmonic 31.08 95.18 # SOURCE3 2 1.5708 - angle_coeff @angle:hp-p2-n2 harmonic 32.08 95.54 # SOURCE3 19 4.7352 - angle_coeff @angle:hp-p2-ne harmonic 31.94 100.10 # SOURCE3 14 6.1290 - angle_coeff @angle:hp-p2-nf harmonic 31.94 100.10 # SOURCE3 14 same_as_hp-p2-ne - angle_coeff @angle:hp-p2-o harmonic 32.04 105.58 # SOURCE3 1 0.0000 - angle_coeff @angle:hp-p2-p2 harmonic 38.16 101.88 # SOURCE3 27 12.9535 - angle_coeff @angle:hp-p2-p4 harmonic 32.69 94.51 # SOURCE3 1 0.0000 - angle_coeff @angle:hp-p2-p5 harmonic 33.66 89.07 # SOURCE3 1 0.0000 - angle_coeff @angle:hp-p2-pe harmonic 37.56 97.25 # SOURCE3 16 8.8916 - angle_coeff @angle:hp-p2-pf harmonic 37.56 97.25 # SOURCE3 16 same_as_hp-p2-pe - angle_coeff @angle:hp-p2-s4 harmonic 26.33 89.99 # SOURCE3 1 0.0000 - angle_coeff @angle:hp-p2-s harmonic 30.26 102.52 # SOURCE3 1 0.0000 - angle_coeff @angle:hp-p2-s6 harmonic 26.74 88.13 # SOURCE3 1 0.0000 - angle_coeff @angle:i-p2-i harmonic 35.75 104.16 # SOURCE3 1 - angle_coeff @angle:i-p2-n2 harmonic 34.63 101.77 # SOURCE3 1 0.0000 - angle_coeff @angle:i-p2-o harmonic 33.34 109.51 # SOURCE3 1 0.0000 - angle_coeff @angle:i-p2-p2 harmonic 46.22 102.63 # SOURCE3 1 0.0000 - angle_coeff @angle:i-p2-s harmonic 35.18 110.60 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-p2-n1 harmonic 46.52 86.22 # HF/6-31G* 1 - angle_coeff @angle:n2-p2-n2 harmonic 45.62 98.00 # SOURCE3 1 - angle_coeff @angle:n2-p2-n3 harmonic 44.14 100.42 # SOURCE3 1 - angle_coeff @angle:n2-p2-n4 harmonic 41.53 93.42 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-na harmonic 42.63 102.03 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-nh harmonic 43.69 101.87 # SOURCE3 2 0.8491 - angle_coeff @angle:n2-p2-no harmonic 43.64 98.12 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-o harmonic 43.53 115.34 # SOURCE3 1 - angle_coeff @angle:n2-p2-oh harmonic 43.02 109.72 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-os harmonic 45.35 102.29 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-p3 harmonic 49.55 99.51 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-p4 harmonic 48.48 101.73 # SOURCE3 1 - angle_coeff @angle:n2-p2-p5 harmonic 50.50 93.68 # SOURCE3 1 - angle_coeff @angle:n2-p2-s4 harmonic 38.89 97.83 # SOURCE3 1 - angle_coeff @angle:n2-p2-s6 harmonic 38.99 98.14 # SOURCE3 1 - angle_coeff @angle:n2-p2-s harmonic 42.45 112.94 # SOURCE3 1 - angle_coeff @angle:n2-p2-sh harmonic 41.75 100.82 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-p2-ss harmonic 41.64 101.76 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-p2-n3 harmonic 42.10 106.30 # SOURCE3 1 - angle_coeff @angle:n3-p2-o harmonic 44.16 106.83 # SOURCE3 1 - angle_coeff @angle:n3-p2-p2 harmonic 55.78 100.58 # SOURCE3 1 - angle_coeff @angle:n3-p2-s harmonic 43.18 105.75 # SOURCE3 1 - angle_coeff @angle:n4-p2-n4 harmonic 39.61 88.80 # SOURCE3 1 - angle_coeff @angle:n4-p2-o harmonic 40.67 101.36 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-p2-p2 harmonic 52.72 96.53 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-p2-s harmonic 40.06 104.98 # SOURCE3 1 0.0000 - angle_coeff @angle:na-p2-na harmonic 40.23 106.10 # SOURCE3 1 - angle_coeff @angle:na-p2-o harmonic 42.71 107.46 # SOURCE3 1 0.0000 - angle_coeff @angle:na-p2-s harmonic 41.81 108.15 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-p2-o harmonic 45.72 107.71 # SOURCE3 1 - angle_coeff @angle:ne-p2-s harmonic 44.34 105.50 # SOURCE3 1 - angle_coeff @angle:nf-p2-o harmonic 45.72 107.71 # SOURCE3 1 same_as_ne-p2-o - angle_coeff @angle:nf-p2-s harmonic 44.34 105.50 # SOURCE3 1 same_as_ne-p2-s - angle_coeff @angle:nh-p2-nh harmonic 42.33 104.00 # SOURCE3 1 - angle_coeff @angle:nh-p2-o harmonic 43.75 108.11 # SOURCE3 2 0.6773 - angle_coeff @angle:nh-p2-p2 harmonic 53.77 107.73 # SOURCE3 3 3.1678 - angle_coeff @angle:nh-p2-s harmonic 42.31 109.62 # SOURCE3 2 1.7725 - angle_coeff @angle:n-p2-n2 harmonic 43.55 98.85 # SOURCE3 1 0.0000 - angle_coeff @angle:n-p2-o harmonic 43.46 105.08 # SOURCE3 1 0.0000 - angle_coeff @angle:no-p2-no harmonic 42.08 98.20 # SOURCE3 1 - angle_coeff @angle:no-p2-o harmonic 43.42 104.87 # SOURCE3 1 0.0000 - angle_coeff @angle:no-p2-p2 harmonic 52.75 108.57 # SOURCE3 3 8.2121 - angle_coeff @angle:no-p2-s harmonic 41.76 109.06 # SOURCE3 2 5.4074 - angle_coeff @angle:n-p2-p2 harmonic 54.46 102.12 # SOURCE3 1 0.0000 - angle_coeff @angle:n-p2-s harmonic 41.20 112.34 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-p2-oh harmonic 44.96 100.10 # SOURCE3 1 - angle_coeff @angle:oh-p2-p2 harmonic 54.71 107.82 # SOURCE3 2 2.6708 - angle_coeff @angle:oh-p2-s harmonic 43.05 109.75 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p2-o harmonic 44.39 119.96 # SOURCE3 1 - angle_coeff @angle:o-p2-oh harmonic 44.33 110.46 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p2-os harmonic 45.59 108.81 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p2-p2 harmonic 54.57 114.23 # SOURCE3 1 - angle_coeff @angle:o-p2-p3 harmonic 48.45 106.69 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p2-p4 harmonic 48.42 104.37 # SOURCE3 1 - angle_coeff @angle:o-p2-p5 harmonic 48.37 104.49 # SOURCE3 1 - angle_coeff @angle:o-p2-pe harmonic 46.73 145.96 # SOURCE3 1 - angle_coeff @angle:o-p2-pf harmonic 46.73 145.96 # SOURCE3 1 same_as_o-p2-pe - angle_coeff @angle:o-p2-s4 harmonic 37.68 106.59 # SOURCE3 1 - angle_coeff @angle:o-p2-s6 harmonic 38.12 105.04 # SOURCE3 1 - angle_coeff @angle:o-p2-s harmonic 42.77 117.42 # SOURCE3 1 - angle_coeff @angle:o-p2-sh harmonic 40.81 109.60 # SOURCE3 1 0.0000 - angle_coeff @angle:os-p2-os harmonic 47.01 98.30 # SOURCE3 1 - angle_coeff @angle:os-p2-p2 harmonic 57.14 101.46 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p2-ss harmonic 40.89 109.60 # SOURCE3 1 0.0000 - angle_coeff @angle:os-p2-s harmonic 43.89 108.47 # SOURCE3 3 1.7065 - angle_coeff @angle:p2-p2-n2 harmonic 57.57 97.40 # SOURCE3 1 - angle_coeff @angle:p2-p2-p3 harmonic 64.09 101.73 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-p2-p4 harmonic 63.42 101.98 # SOURCE3 1 - angle_coeff @angle:p2-p2-p5 harmonic 64.24 99.33 # SOURCE3 1 - angle_coeff @angle:p2-p2-s4 harmonic 51.53 95.73 # SOURCE3 1 - angle_coeff @angle:p2-p2-s6 harmonic 51.64 95.95 # SOURCE3 1 - angle_coeff @angle:p2-p2-s harmonic 54.52 111.28 # SOURCE3 1 - angle_coeff @angle:p2-p2-sh harmonic 50.78 113.94 # SOURCE3 3 8.5009 - angle_coeff @angle:p3-p2-p3 harmonic 59.88 101.00 # SOURCE3 1 - angle_coeff @angle:p3-p2-s harmonic 48.09 113.28 # SOURCE3 2 6.7035 - angle_coeff @angle:p4-p2-s harmonic 49.75 103.89 # SOURCE3 1 - angle_coeff @angle:p5-p2-p5 harmonic 62.82 89.40 # SOURCE3 1 - angle_coeff @angle:p5-p2-s harmonic 50.38 101.21 # SOURCE3 1 - angle_coeff @angle:pe-p2-s harmonic 54.45 106.35 # SOURCE3 1 - angle_coeff @angle:pf-p2-s harmonic 54.45 106.35 # SOURCE3 1 same_as_pe-p2-s - angle_coeff @angle:s4-p2-s4 harmonic 39.97 85.30 # SOURCE3 1 - angle_coeff @angle:s6-p2-s6 harmonic 37.42 98.20 # SOURCE3 1 - angle_coeff @angle:sh-p2-sh harmonic 41.33 98.50 # SOURCE3 1 - angle_coeff @angle:s-p2-s harmonic 44.19 106.60 # SOURCE3 1 - angle_coeff @angle:s-p2-s4 harmonic 38.90 105.29 # SOURCE3 1 - angle_coeff @angle:s-p2-s6 harmonic 38.73 106.93 # SOURCE3 1 - angle_coeff @angle:s-p2-sh harmonic 40.82 110.73 # SOURCE3 2 0.0232 - angle_coeff @angle:s-p2-ss harmonic 40.27 114.14 # SOURCE3 4 5.9223 - angle_coeff @angle:ss-p2-ss harmonic 41.56 97.90 # SOURCE3 1 - angle_coeff @angle:br-p3-br harmonic 41.27 103.54 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p3-hp harmonic 26.94 96.36 # SOURCE3 4 0.6701 - angle_coeff @angle:c1-p3-c1 harmonic 38.48 100.50 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-p3-f harmonic 40.73 96.90 # SOURCE2 1 0.0000 - angle_coeff @angle:c1-p3-hp harmonic 28.14 97.67 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-p3-c2 harmonic 37.32 101.77 # SOURCE3 3 0.0000 - angle_coeff @angle:c2-p3-hp harmonic 27.57 97.85 # SOURCE3 4 0.0000 - angle_coeff @angle:c3-p3-c3 harmonic 37.51 99.66 # SOURCE3 40 0.9854 - angle_coeff @angle:c3-p3-ca harmonic 37.29 101.94 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-p3-cl harmonic 35.74 99.89 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p3-f harmonic 39.74 97.80 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-p3-hp harmonic 27.47 97.66 # SOURCE3 9 0.4096 - angle_coeff @angle:c3-p3-n2 harmonic 39.87 96.55 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-p3-n3 harmonic 39.28 101.18 # SOURCE3 10 2.2338 - angle_coeff @angle:c3-p3-n4 harmonic 38.58 96.94 # SOURCE3 6 0.4815 - angle_coeff @angle:c3-p3-n harmonic 38.78 101.77 # SOURCE3 12 2.4449 - angle_coeff @angle:c3-p3-na harmonic 39.16 100.17 # SOURCE3 4 0.0554 - angle_coeff @angle:c3-p3-nh harmonic 38.65 104.50 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-p3-no harmonic 38.96 96.98 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-p3-o harmonic 39.33 111.67 # SOURCE3 28 5.3387 - angle_coeff @angle:c3-p3-oh harmonic 40.60 98.21 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-p3-os harmonic 40.25 99.53 # SOURCE3 3 1.7678 - angle_coeff @angle:c3-p3-p3 harmonic 45.77 100.31 # SOURCE3 18 2.1836 - angle_coeff @angle:c3-p3-p5 harmonic 45.65 100.90 # SOURCE3 10 2.7070 - angle_coeff @angle:c3-p3-s4 harmonic 37.94 98.88 # SOURCE3 8 6.2235 - angle_coeff @angle:c3-p3-s6 harmonic 37.62 101.18 # SOURCE3 12 6.4536 - angle_coeff @angle:c3-p3-sh harmonic 37.43 98.71 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-p3-ss harmonic 37.44 99.37 # SOURCE3 2 0.0000 - angle_coeff @angle:ca-p3-ca harmonic 37.89 99.86 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-p3-hp harmonic 27.74 97.50 # SOURCE3 2 0.0000 - angle_coeff @angle:c-p3-c3 harmonic 37.60 97.06 # SOURCE3 3 1.1490 - angle_coeff @angle:c-p3-c harmonic 36.51 100.90 # SOURCE3 1 0.0000 - angle_coeff @angle:c-p3-hp harmonic 27.15 96.55 # SOURCE3 6 0.5223 - angle_coeff @angle:cl-p3-cl harmonic 33.91 102.82 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-p3-f harmonic 37.03 99.20 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-p3-hp harmonic 25.67 96.30 # SOURCE3 3 0.6203 - angle_coeff @angle:c-p3-os harmonic 43.95 81.32 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-p3-hp harmonic 27.54 95.20 # SOURCE2 1 0.0000 - angle_coeff @angle:f-p3-f harmonic 43.08 97.40 # SOURCE2 8 1.6636 - angle_coeff @angle:f-p3-hp harmonic 30.56 96.41 # SOURCE3 2 0.0000 - angle_coeff @angle:f-p3-n3 harmonic 41.86 100.60 # SOURCE2 1 0.0000 - angle_coeff @angle:f-p3-os harmonic 42.42 102.20 # SOURCE2 1 0.0000 - angle_coeff @angle:f-p3-p3 harmonic 47.13 97.20 # SOURCE2 1 0.0000 - angle_coeff @angle:hp-p3-hp harmonic 22.02 95.52 # SOURCE3 44 2.4200 - angle_coeff @angle:hp-p3-i harmonic 23.42 96.19 # SOURCE3 4 0.6454 - angle_coeff @angle:hp-p3-n1 harmonic 31.27 92.98 # HF/6-31G* 1 - angle_coeff @angle:hp-p3-n2 harmonic 29.07 98.28 # SOURCE3 10 1.8860 - angle_coeff @angle:hp-p3-n3 harmonic 30.10 94.46 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-n4 harmonic 28.34 93.21 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-n harmonic 29.47 95.15 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-na harmonic 29.25 97.27 # SOURCE3 12 0.9318 - angle_coeff @angle:hp-p3-nh harmonic 30.16 94.10 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-no harmonic 28.83 93.06 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-o harmonic 32.01 101.02 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-oh harmonic 30.73 95.95 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-os harmonic 30.39 97.35 # SOURCE3 6 2.8326 - angle_coeff @angle:hp-p3-p2 harmonic 32.41 99.11 # SOURCE3 16 4.3022 - angle_coeff @angle:hp-p3-p3 harmonic 32.07 95.52 # SOURCE3 4 0.0844 - angle_coeff @angle:hp-p3-p4 harmonic 31.97 95.95 # SOURCE3 6 0.0489 - angle_coeff @angle:hp-p3-p5 harmonic 32.08 95.54 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-s4 harmonic 26.89 95.49 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-s6 harmonic 27.38 92.95 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-sh harmonic 26.51 94.21 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p3-ss harmonic 26.59 94.61 # SOURCE3 2 0.0000 - angle_coeff @angle:i-p3-i harmonic 36.63 105.25 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-p3-n1 harmonic 45.91 90.44 # HF/6-31G* 1 - angle_coeff @angle:n2-p3-n2 harmonic 40.40 103.46 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-p3-n3 harmonic 39.27 113.80 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-p3-o harmonic 43.04 107.10 # SOURCE3 4 0.0000 - angle_coeff @angle:n3-p3-oh harmonic 43.13 98.36 # SOURCE3 1 - angle_coeff @angle:n4-p3-n4 harmonic 38.45 100.53 # SOURCE3 1 0.0000 - angle_coeff @angle:na-p3-na harmonic 39.91 106.22 # SOURCE3 1 - angle_coeff @angle:nh-p3-nh harmonic 40.11 109.11 # SOURCE3 1 0.0000 - angle_coeff @angle:n-p3-n harmonic 40.04 104.58 # SOURCE3 1 - angle_coeff @angle:n-p3-o harmonic 42.80 104.99 # SOURCE3 4 0.0000 - angle_coeff @angle:no-p3-no harmonic 39.64 98.33 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-p3-oh harmonic 42.77 104.48 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p3-o harmonic 43.78 122.18 # SOURCE3 2 7.8556 - angle_coeff @angle:o-p3-p3 harmonic 45.09 116.74 # SOURCE3 14 0.7525 - angle_coeff @angle:o-p3-p5 harmonic 46.98 107.62 # SOURCE3 4 0.0000 - angle_coeff @angle:o-p3-s4 harmonic 38.63 110.70 # SOURCE3 4 0.7259 - angle_coeff @angle:o-p3-s6 harmonic 39.52 106.66 # SOURCE3 6 3.4017 - angle_coeff @angle:os-p3-os harmonic 42.11 106.65 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-p3-p2 harmonic 59.12 103.58 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-p3-p3 harmonic 57.00 105.31 # SOURCE3 4 3.5864 - angle_coeff @angle:p4-p3-p4 harmonic 58.70 99.09 # SOURCE3 1 - angle_coeff @angle:p5-p3-p5 harmonic 58.78 99.10 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-p3-s4 harmonic 39.08 98.26 # SOURCE3 1 0.0000 - angle_coeff @angle:s6-p3-s6 harmonic 39.36 97.78 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-p3-sh harmonic 36.56 107.58 # SOURCE3 1 0.0000 - angle_coeff @angle:s-p3-s harmonic 34.08 131.32 # SOURCE3 1 - angle_coeff @angle:ss-p3-ss harmonic 36.47 109.24 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p4-br harmonic 41.07 110.41 # SOURCE3 1 - angle_coeff @angle:br-p4-o harmonic 37.80 124.80 # SOURCE3 1 - angle_coeff @angle:c2-p4-c2 harmonic 37.13 104.21 # SOURCE3 1 - angle_coeff @angle:c2-p4-hp harmonic 27.68 99.50 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-p4-o harmonic 39.43 113.59 # SOURCE3 1 - angle_coeff @angle:c3-p4-c3 harmonic 37.20 102.55 # SOURCE3 4 0.0192 - angle_coeff @angle:c3-p4-n2 harmonic 39.09 103.17 # SOURCE3 1 - angle_coeff @angle:c3-p4-n3 harmonic 39.50 102.37 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p4-n4 harmonic 37.54 99.57 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p4-n harmonic 38.98 103.26 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p4-na harmonic 37.92 117.67 # SOURCE3 5 19.0404 - angle_coeff @angle:c3-p4-nh harmonic 39.33 102.79 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p4-no harmonic 38.24 99.80 # SOURCE3 3 0.2151 - angle_coeff @angle:c3-p4-o harmonic 38.77 116.44 # SOURCE3 25 2.6494 - angle_coeff @angle:c3-p4-oh harmonic 41.01 98.56 # SOURCE3 2 0.4558 - angle_coeff @angle:c3-p4-os harmonic 41.17 98.01 # SOURCE3 2 0.0931 - angle_coeff @angle:c3-p4-p2 harmonic 44.43 109.27 # SOURCE3 1 - angle_coeff @angle:c3-p4-p3 harmonic 45.09 103.53 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p4-p4 harmonic 48.14 102.12 # SOURCE3 1 - angle_coeff @angle:c3-p4-p5 harmonic 44.64 104.15 # SOURCE3 1 - angle_coeff @angle:c3-p4-sh harmonic 37.43 100.17 # SOURCE3 2 0.0815 - angle_coeff @angle:c3-p4-ss harmonic 37.38 101.19 # SOURCE3 1 - angle_coeff @angle:ca-p4-ca harmonic 36.83 107.77 # SOURCE3 1 - angle_coeff @angle:ca-p4-o harmonic 40.03 111.64 # SOURCE3 1 - angle_coeff @angle:cl-p4-cl harmonic 33.80 103.51 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-p4-o harmonic 36.03 116.53 # SOURCE3 2 0.0000 - angle_coeff @angle:hp-p4-hp harmonic 22.57 99.21 # SOURCE3 4 6.4572 - angle_coeff @angle:hp-p4-n1 harmonic 30.24 99.91 # HF/6-31G* 1 - angle_coeff @angle:hp-p4-o harmonic 31.44 109.35 # SOURCE3 6 10.8284 - angle_coeff @angle:hp-p4-p3 harmonic 31.40 98.96 # SOURCE3 4 0.0000 - angle_coeff @angle:hp-p4-s harmonic 24.32 110.24 # SOURCE3 4 4.1081 - angle_coeff @angle:i-p4-i harmonic 38.53 113.22 # SOURCE3 2 6.7916 - angle_coeff @angle:i-p4-o harmonic 37.71 110.22 # SOURCE3 4 9.7726 - angle_coeff @angle:n1-p4-n1 harmonic 43.01 100.61 # HF/6-31G* 1 - angle_coeff @angle:n1-p4-o harmonic 42.53 114.59 # HF/6-31G* 1 - angle_coeff @angle:n2-p4-n2 harmonic 41.52 102.54 # SOURCE3 1 - angle_coeff @angle:n2-p4-o harmonic 40.81 120.28 # SOURCE3 1 - angle_coeff @angle:n3-p4-o harmonic 42.50 113.27 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-p4-o harmonic 39.56 107.61 # SOURCE3 1 0.0000 - angle_coeff @angle:na-p4-o harmonic 45.17 110.60 # SOURCE3 5 1.3133 - angle_coeff @angle:nh-p4-nh harmonic 43.52 95.30 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-p4-o harmonic 41.87 115.86 # SOURCE3 3 3.2712 - angle_coeff @angle:n-p4-o harmonic 41.05 117.99 # SOURCE3 1 0.0000 - angle_coeff @angle:no-p4-o harmonic 39.42 114.69 # SOURCE3 3 0.1070 - angle_coeff @angle:oh-p4-oh harmonic 45.67 95.71 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p4-o harmonic 45.06 117.22 # SOURCE3 6 2.7792 - angle_coeff @angle:o-p4-oh harmonic 42.88 117.39 # SOURCE3 4 1.0083 - angle_coeff @angle:o-p4-os harmonic 43.10 116.67 # SOURCE3 4 0.6923 - angle_coeff @angle:o-p4-p2 harmonic 44.91 121.35 # SOURCE3 1 - angle_coeff @angle:o-p4-p3 harmonic 45.60 114.00 # SOURCE3 3 0.6663 - angle_coeff @angle:o-p4-p4 harmonic 48.81 116.43 # SOURCE3 1 - angle_coeff @angle:o-p4-p5 harmonic 46.05 109.76 # SOURCE3 1 - angle_coeff @angle:o-p4-s4 harmonic 35.77 112.19 # SOURCE3 1 - angle_coeff @angle:o-p4-s6 harmonic 35.22 113.89 # SOURCE3 1 - angle_coeff @angle:o-p4-s harmonic 37.34 112.78 # SOURCE3 2 0.0000 - angle_coeff @angle:o-p4-sh harmonic 36.99 118.09 # SOURCE3 1 - angle_coeff @angle:os-p4-os harmonic 44.74 100.34 # SOURCE3 1 0.0000 - angle_coeff @angle:o-p4-ss harmonic 37.47 116.14 # SOURCE3 4 1.0636 - angle_coeff @angle:p2-p4-p2 harmonic 56.48 110.71 # SOURCE3 1 - angle_coeff @angle:p3-p4-p3 harmonic 54.50 114.98 # SOURCE3 1 0.0000 - angle_coeff @angle:p4-p4-p4 harmonic 61.44 107.38 # SOURCE3 1 - angle_coeff @angle:p5-p4-p5 harmonic 55.76 107.78 # SOURCE3 1 - angle_coeff @angle:s4-p4-s4 harmonic 36.61 96.24 # SOURCE3 1 - angle_coeff @angle:s6-p4-s6 harmonic 35.22 102.36 # SOURCE3 1 - angle_coeff @angle:sh-p4-sh harmonic 38.45 98.81 # SOURCE3 1 0.0000 - angle_coeff @angle:s-p4-s harmonic 36.54 106.30 # SOURCE3 2 25.0119 - angle_coeff @angle:ss-p4-ss harmonic 37.60 104.41 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p5-br harmonic 41.96 103.38 # SOURCE3 1 0.0000 - angle_coeff @angle:br-p5-o harmonic 39.04 114.65 # SOURCE3 3 1.0910 - angle_coeff @angle:br-p5-oh harmonic 40.90 102.92 # SOURCE3 4 0.5468 - angle_coeff @angle:c1-p5-c1 harmonic 38.83 102.89 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-p5-o harmonic 40.32 115.77 # SOURCE3 2 0.0000 - angle_coeff @angle:c1-p5-oh harmonic 41.43 102.79 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-p5-c2 harmonic 35.85 106.56 # SOURCE3 1 - angle_coeff @angle:c2-p5-o harmonic 39.62 109.24 # SOURCE4 7 2.2628 - angle_coeff @angle:c2-p5-oh harmonic 40.04 101.69 # SOURCE3 1 - angle_coeff @angle:c2-p5-os harmonic 39.90 103.34 # SOURCE3 1 - angle_coeff @angle:c3-p5-c3 harmonic 36.95 106.23 # SOURCE3 14 2.6389 - angle_coeff @angle:c3-p5-hp harmonic 27.05 103.62 # SOURCE4 7 1.1616 - angle_coeff @angle:c3-p5-n3 harmonic 40.01 102.76 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-p5-o harmonic 39.91 112.50 # SOURCE3 23 4.4203 - angle_coeff @angle:c3-p5-oh harmonic 40.83 101.56 # SOURCE3 17 2.1803 - angle_coeff @angle:c3-p5-os harmonic 41.20 100.77 # SOURCE4 51 2.0928 - angle_coeff @angle:c3-p5-p4 harmonic 44.32 106.27 # SOURCE3 1 - angle_coeff @angle:c3-p5-s harmonic 37.51 113.40 # SOURCE3 4 2.0067 - angle_coeff @angle:c3-p5-ss harmonic 36.91 103.76 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-p5-ca harmonic 37.10 107.53 # SOURCE3 1 - angle_coeff @angle:ca-p5-o harmonic 39.95 113.98 # SOURCE3 1 - angle_coeff @angle:ca-p5-oh harmonic 41.04 101.77 # SOURCE3 1 - angle_coeff @angle:ca-p5-os harmonic 40.86 103.75 # SOURCE3 1 - angle_coeff @angle:c-p5-c harmonic 35.96 104.16 # SOURCE3 1 - angle_coeff @angle:cl-p5-cl harmonic 33.77 103.70 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-p5-o harmonic 36.29 115.32 # SOURCE3 2 0.0000 - angle_coeff @angle:cl-p5-oh harmonic 37.85 102.44 # SOURCE3 2 0.0000 - angle_coeff @angle:c-p5-o harmonic 39.74 107.19 # SOURCE4 16 0.5711 - angle_coeff @angle:c-p5-oh harmonic 39.73 102.12 # SOURCE3 1 - angle_coeff @angle:f-p5-f harmonic 42.49 99.96 # SOURCE2 4 0.9197 - angle_coeff @angle:f-p5-o harmonic 43.22 112.03 # SOURCE4 7 0.5178 - angle_coeff @angle:f-p5-oh harmonic 43.33 101.98 # SOURCE3 2 0.0000 - angle_coeff @angle:f-p5-os harmonic 43.51 102.70 # SOURCE4 5 0.1524 - angle_coeff @angle:f-p5-s harmonic 38.09 117.40 # SOURCE2 1 0.0000 - angle_coeff @angle:hp-p5-hp harmonic 21.44 101.09 # SOURCE3 4 1.3036 - angle_coeff @angle:hp-p5-n1 harmonic 31.09 101.32 # HF/6-31G* 1 - angle_coeff @angle:hp-p5-o harmonic 30.21 116.58 # SOURCE3 7 1.3282 - angle_coeff @angle:hp-p5-oh harmonic 30.57 101.45 # SOURCE3 5 0.9084 - angle_coeff @angle:hp-p5-s harmonic 25.97 119.20 # SOURCE2 1 0.0000 - angle_coeff @angle:i-p5-i harmonic 35.88 107.17 # SOURCE3 1 0.0000 - angle_coeff @angle:i-p5-o harmonic 32.99 115.93 # SOURCE3 3 0.0415 - angle_coeff @angle:i-p5-oh harmonic 35.44 102.26 # SOURCE3 4 1.9577 - angle_coeff @angle:n1-p5-n1 harmonic 45.78 101.55 # HF/6-31G* 1 - angle_coeff @angle:n1-p5-o harmonic 44.71 113.78 # HF/6-31G* 1 - angle_coeff @angle:n2-p5-n2 harmonic 43.96 106.34 # SOURCE3 1 - angle_coeff @angle:n2-p5-o harmonic 44.30 113.53 # SOURCE3 1 - angle_coeff @angle:n2-p5-oh harmonic 44.68 102.40 # SOURCE3 1 - angle_coeff @angle:n3-p5-n3 harmonic 42.87 103.37 # SOURCE4 47 2.1009 - angle_coeff @angle:n3-p5-nh harmonic 42.63 104.02 # SOURCE4 5 1.8740 - angle_coeff @angle:n3-p5-o harmonic 43.02 114.64 # SOURCE4 76 2.2728 - angle_coeff @angle:n3-p5-oh harmonic 43.43 104.18 # SOURCE3 6 0.4373 - angle_coeff @angle:n3-p5-os harmonic 44.20 101.94 # SOURCE4 34 2.3553 - angle_coeff @angle:n3-p5-s harmonic 39.05 117.12 # SOURCE4 7 0.7109 - angle_coeff @angle:n4-p5-n4 harmonic 39.18 102.20 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-p5-o harmonic 41.10 109.78 # SOURCE3 5 2.7519 - angle_coeff @angle:n4-p5-oh harmonic 42.23 98.48 # SOURCE3 6 0.4104 - angle_coeff @angle:n4-p5-os harmonic 43.31 94.55 # SOURCE3 2 0.0000 - angle_coeff @angle:na-p5-na harmonic 40.56 108.57 # SOURCE3 1 0.0000 - angle_coeff @angle:na-p5-o harmonic 42.38 113.43 # SOURCE3 11 0.8968 - angle_coeff @angle:na-p5-oh harmonic 43.14 102.07 # SOURCE3 16 1.4144 - angle_coeff @angle:na-p5-os harmonic 43.20 103.06 # SOURCE3 4 0.7463 - angle_coeff @angle:nh-p5-nh harmonic 43.48 99.51 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-p5-o harmonic 42.11 118.91 # SOURCE3 3 1.3237 - angle_coeff @angle:nh-p5-oh harmonic 43.40 103.81 # SOURCE3 2 0.0000 - angle_coeff @angle:nh-p5-os harmonic 44.39 100.51 # SOURCE3 2 0.0000 - angle_coeff @angle:n-p5-n3 harmonic 42.13 104.11 # SOURCE4 11 1.4088 - angle_coeff @angle:n-p5-n harmonic 41.80 103.09 # SOURCE3 1 0.0000 - angle_coeff @angle:n-p5-o harmonic 43.40 108.73 # SOURCE4 5 0.2571 - angle_coeff @angle:n-p5-oh harmonic 43.17 102.44 # SOURCE3 4 0.0999 - angle_coeff @angle:no-p5-no harmonic 40.40 95.68 # SOURCE3 1 0.0000 - angle_coeff @angle:no-p5-o harmonic 40.49 112.75 # SOURCE3 4 3.3684 - angle_coeff @angle:no-p5-oh harmonic 41.56 101.35 # SOURCE3 2 0.0000 - angle_coeff @angle:no-p5-os harmonic 41.69 101.70 # SOURCE3 4 0.0565 - angle_coeff @angle:n-p5-os harmonic 43.85 100.48 # SOURCE3 2 0.0000 - angle_coeff @angle:oh-p5-oh harmonic 44.58 102.45 # SOURCE3 39 2.4223 - angle_coeff @angle:oh-p5-os harmonic 44.91 102.37 # SOURCE3 8 1.5063 - angle_coeff @angle:oh-p5-p2 harmonic 48.24 103.53 # SOURCE3 1 - angle_coeff @angle:oh-p5-p3 harmonic 47.55 103.83 # SOURCE3 13 0.4303 - angle_coeff @angle:oh-p5-p4 harmonic 47.57 101.79 # SOURCE3 1 - angle_coeff @angle:oh-p5-p5 harmonic 51.43 100.45 # SOURCE3 1 - angle_coeff @angle:oh-p5-s4 harmonic 40.30 103.24 # SOURCE3 1 - angle_coeff @angle:oh-p5-s6 harmonic 40.65 101.48 # SOURCE3 1 - angle_coeff @angle:oh-p5-s harmonic 42.20 102.88 # SOURCE3 3 1.6044 - angle_coeff @angle:oh-p5-sh harmonic 40.01 101.41 # SOURCE3 2 0.0000 - angle_coeff @angle:oh-p5-ss harmonic 38.95 104.33 # SOURCE3 6 2.0112 - angle_coeff @angle:o-p5-o harmonic 46.01 115.80 # SOURCE3 17 5.7902 - angle_coeff @angle:o-p5-oh harmonic 43.79 115.26 # SOURCE4 740 1.3004 - angle_coeff @angle:o-p5-os harmonic 44.01 116.09 # SOURCE3 35 3.2062 - angle_coeff @angle:o-p5-p2 harmonic 46.23 114.60 # SOURCE3 1 - angle_coeff @angle:o-p5-p3 harmonic 45.38 115.48 # SOURCE3 9 2.1084 - angle_coeff @angle:o-p5-p4 harmonic 45.07 114.66 # SOURCE3 1 - angle_coeff @angle:o-p5-p5 harmonic 49.11 113.44 # SOURCE3 1 - angle_coeff @angle:o-p5-s4 harmonic 39.61 110.23 # SOURCE3 1 - angle_coeff @angle:o-p5-s6 harmonic 39.34 111.75 # SOURCE3 1 - angle_coeff @angle:o-p5-s harmonic 40.46 116.94 # SOURCE3 3 2.9506 - angle_coeff @angle:o-p5-sh harmonic 38.14 114.56 # SOURCE3 3 1.7645 - angle_coeff @angle:os-p5-os harmonic 45.37 101.77 # SOURCE4 243 2.0816 - angle_coeff @angle:os-p5-p3 harmonic 47.66 103.67 # SOURCE3 2 0.0000 - angle_coeff @angle:os-p5-p5 harmonic 50.58 104.48 # SOURCE3 1 - angle_coeff @angle:os-p5-s4 harmonic 40.57 102.52 # SOURCE3 1 - angle_coeff @angle:os-p5-s6 harmonic 40.69 101.89 # SOURCE3 1 - angle_coeff @angle:o-p5-ss harmonic 37.95 112.46 # SOURCE3 6 2.7392 - angle_coeff @angle:os-p5-s harmonic 39.69 117.28 # SOURCE4 74 0.7542 - angle_coeff @angle:os-p5-sh harmonic 39.51 104.59 # SOURCE3 2 0.0000 - angle_coeff @angle:os-p5-ss harmonic 39.36 102.65 # SOURCE4 25 1.8093 - angle_coeff @angle:p2-p5-p2 harmonic 57.39 107.14 # SOURCE3 1 - angle_coeff @angle:p3-p5-p3 harmonic 57.04 105.23 # SOURCE3 3 5.1024 - angle_coeff @angle:p4-p5-p4 harmonic 57.42 101.62 # SOURCE3 1 - angle_coeff @angle:p5-p5-p5 harmonic 59.38 112.72 # SOURCE3 1 - angle_coeff @angle:s6-p5-s6 harmonic 38.64 105.18 # SOURCE3 1 - angle_coeff @angle:sh-p5-sh harmonic 37.97 104.56 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-p5-ss harmonic 37.22 107.13 # SOURCE3 1 - angle_coeff @angle:s-p5-s harmonic 39.37 114.13 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-p5-ss harmonic 36.51 109.61 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-pc-n harmonic 42.75 90.80 # SOURCE3 3 2.3423 - angle_coeff @angle:cd-pc-na harmonic 43.00 90.18 # SOURCE3 81 2.7619 - angle_coeff @angle:cc-pd-n harmonic 42.75 90.80 # SOURCE3 3 same_as_cd-pc-n - angle_coeff @angle:cc-pd-na harmonic 43.00 90.18 # SOURCE3 81 same_as_cd-pc-na - angle_coeff @angle:c2-pe-ca harmonic 38.84 101.44 # SOURCE3 3 0.7177 - angle_coeff @angle:c2-pe-ce harmonic 38.68 103.01 # SOURCE3 4 1.4470 - angle_coeff @angle:c2-pe-cg harmonic 40.85 104.03 # SOURCE3 3 3.8740 - angle_coeff @angle:c2-pe-n2 harmonic 44.94 94.14 # SOURCE3 1 - angle_coeff @angle:c2-pe-ne harmonic 41.85 98.70 # SOURCE3 12 5.3383 - angle_coeff @angle:c2-pe-o harmonic 41.06 115.16 # SOURCE3 2 0.0149 - angle_coeff @angle:c2-pe-p2 harmonic 50.94 107.82 # SOURCE3 1 - angle_coeff @angle:c2-pe-pe harmonic 48.17 102.99 # SOURCE3 9 8.2860 - angle_coeff @angle:c2-pe-px harmonic 51.11 97.37 # SOURCE3 4 0.6655 - angle_coeff @angle:c2-pe-py harmonic 50.92 96.71 # SOURCE3 4 1.2755 - angle_coeff @angle:c2-pe-s harmonic 41.06 111.16 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-pe-sx harmonic 38.51 95.11 # SOURCE3 4 0.2676 - angle_coeff @angle:c2-pe-sy harmonic 37.78 95.56 # SOURCE3 2 0.0462 - angle_coeff @angle:ca-pe-n2 harmonic 40.97 102.03 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-pe-o harmonic 40.40 106.88 # SOURCE3 2 0.0018 - angle_coeff @angle:ca-pe-p2 harmonic 50.96 100.79 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-pe-pf harmonic 48.44 99.70 # SOURCE3 2 0.0000 - angle_coeff @angle:ca-pe-s harmonic 40.07 107.93 # SOURCE3 1 0.0000 - angle_coeff @angle:c-pe-c2 harmonic 38.58 97.30 # SOURCE3 3 0.0335 - angle_coeff @angle:ce-pe-n2 harmonic 41.45 100.55 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-pe-o harmonic 40.47 107.44 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-pe-p2 harmonic 51.42 99.56 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-pe-s harmonic 40.65 105.54 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-pe-n2 harmonic 44.31 101.79 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-pe-o harmonic 43.57 107.62 # SOURCE3 1 0.0000 - angle_coeff @angle:cg-pe-p2 harmonic 52.47 104.68 # SOURCE3 2 5.1435 - angle_coeff @angle:cg-pe-s harmonic 42.30 108.60 # SOURCE3 4 2.6981 - angle_coeff @angle:n2-pe-n2 harmonic 45.26 108.14 # SOURCE3 1 - angle_coeff @angle:n2-pe-ne harmonic 42.89 106.80 # SOURCE3 6 4.5981 - angle_coeff @angle:n2-pe-o harmonic 44.34 115.39 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-pe-p2 harmonic 52.85 111.60 # SOURCE3 1 - angle_coeff @angle:n2-pe-pe harmonic 48.70 109.40 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-pe-px harmonic 50.28 110.30 # SOURCE3 3 6.0548 - angle_coeff @angle:n2-pe-py harmonic 54.11 93.68 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-pe-s harmonic 42.94 114.84 # SOURCE3 3 3.6512 - angle_coeff @angle:n2-pe-sx harmonic 39.42 97.83 # SOURCE3 1 0.0000 - angle_coeff @angle:n2-pe-sy harmonic 38.61 98.14 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-pe-o harmonic 42.65 110.24 # SOURCE3 3 3.8478 - angle_coeff @angle:ne-pe-p2 harmonic 52.77 104.48 # SOURCE3 2 7.1207 - angle_coeff @angle:ne-pe-s harmonic 42.21 109.19 # SOURCE3 5 3.6708 - angle_coeff @angle:o-pe-o harmonic 44.01 119.96 # SOURCE3 1 0.0000 - angle_coeff @angle:o-pe-p2 harmonic 52.71 114.23 # SOURCE3 1 0.0000 - angle_coeff @angle:o-pe-pe harmonic 42.47 145.96 # SOURCE3 1 0.0000 - angle_coeff @angle:o-pe-px harmonic 52.10 104.37 # SOURCE3 1 0.0000 - angle_coeff @angle:o-pe-py harmonic 51.64 104.49 # SOURCE3 1 0.0000 - angle_coeff @angle:o-pe-s harmonic 42.89 117.42 # SOURCE3 2 0.0426 - angle_coeff @angle:o-pe-sx harmonic 38.02 106.59 # SOURCE3 1 0.0000 - angle_coeff @angle:o-pe-sy harmonic 37.56 105.04 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-pe-pe harmonic 65.58 98.24 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-pe-px harmonic 64.12 108.28 # SOURCE3 2 6.2959 - angle_coeff @angle:p2-pe-py harmonic 62.99 110.87 # SOURCE3 3 8.1645 - angle_coeff @angle:p2-pe-s harmonic 53.42 111.28 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-pe-sx harmonic 51.26 95.73 # SOURCE3 1 0.0000 - angle_coeff @angle:p2-pe-sy harmonic 50.47 95.95 # SOURCE3 1 0.0000 - angle_coeff @angle:pe-pe-s harmonic 50.40 107.91 # SOURCE3 2 1.5577 - angle_coeff @angle:px-pe-s harmonic 51.97 107.62 # SOURCE3 2 3.7266 - angle_coeff @angle:py-pe-s harmonic 51.36 108.73 # SOURCE3 3 5.3201 - angle_coeff @angle:s-pe-s harmonic 34.43 178.44 # SOURCE3 1 0.0000 - angle_coeff @angle:s-pe-sx harmonic 38.72 108.32 # SOURCE3 2 3.0318 - angle_coeff @angle:s-pe-sy harmonic 38.35 106.93 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-pf-ca harmonic 38.84 101.44 # SOURCE3 3 same_as_c2-pe-ca - angle_coeff @angle:c2-pf-cf harmonic 38.68 103.01 # SOURCE3 4 same_as_c2-pe-ce - angle_coeff @angle:c2-pf-ch harmonic 40.85 104.03 # SOURCE3 3 same_as_c2-pe-cg - angle_coeff @angle:c2-pf-n2 harmonic 44.94 94.14 # SOURCE3 1 same_as_c2-pe-n2 - angle_coeff @angle:c2-pf-nf harmonic 41.85 98.70 # SOURCE3 12 same_as_c2-pe-ne - angle_coeff @angle:c2-pf-o harmonic 41.06 115.16 # SOURCE3 2 same_as_c2-pe-o - angle_coeff @angle:c2-pf-p2 harmonic 50.94 107.82 # SOURCE3 1 same_as_c2-pe-p2 - angle_coeff @angle:c2-pf-pf harmonic 48.17 102.99 # SOURCE3 9 same_as_c2-pe-pe - angle_coeff @angle:c2-pf-px harmonic 51.11 97.37 # SOURCE3 4 same_as_c2-pe-px - angle_coeff @angle:c2-pf-py harmonic 50.92 96.71 # SOURCE3 4 same_as_c2-pe-py - angle_coeff @angle:c2-pf-s harmonic 41.06 111.16 # SOURCE3 2 same_as_c2-pe-s - angle_coeff @angle:c2-pf-sx harmonic 38.51 95.11 # SOURCE3 4 same_as_c2-pe-sx - angle_coeff @angle:c2-pf-sy harmonic 37.78 95.56 # SOURCE3 2 same_as_c2-pe-sy - angle_coeff @angle:ca-pf-n2 harmonic 40.97 102.03 # SOURCE3 1 same_as_ca-pe-n2 - angle_coeff @angle:ca-pf-o harmonic 40.40 106.88 # SOURCE3 2 same_as_ca-pe-o - angle_coeff @angle:ca-pf-p2 harmonic 50.96 100.79 # SOURCE3 1 same_as_ca-pe-p2 - angle_coeff @angle:ca-pf-pe harmonic 48.44 99.70 # SOURCE3 2 0.0000 - angle_coeff @angle:ca-pf-s harmonic 40.07 107.93 # SOURCE3 1 same_as_ca-pe-s - angle_coeff @angle:c-pf-c2 harmonic 38.58 97.30 # SOURCE3 3 same_as_c-pe-c2 - angle_coeff @angle:cf-pf-n2 harmonic 41.45 100.55 # SOURCE3 1 same_as_ce-pe-n2 - angle_coeff @angle:cf-pf-o harmonic 40.47 107.44 # SOURCE3 1 same_as_ce-pe-o - angle_coeff @angle:cf-pf-p2 harmonic 51.42 99.56 # SOURCE3 1 same_as_ce-pe-p2 - angle_coeff @angle:cf-pf-s harmonic 40.65 105.54 # SOURCE3 1 same_as_ce-pe-s - angle_coeff @angle:ch-pf-n2 harmonic 44.31 101.79 # SOURCE3 1 same_as_cg-pe-n2 - angle_coeff @angle:ch-pf-o harmonic 43.57 107.62 # SOURCE3 1 same_as_cg-pe-o - angle_coeff @angle:ch-pf-p2 harmonic 52.47 104.68 # SOURCE3 2 same_as_cg-pe-p2 - angle_coeff @angle:ch-pf-s harmonic 42.30 108.60 # SOURCE3 4 same_as_cg-pe-s - angle_coeff @angle:n2-pf-n2 harmonic 45.26 108.14 # SOURCE3 1 same_as_n2-pe-n2 - angle_coeff @angle:n2-pf-nf harmonic 42.89 106.80 # SOURCE3 6 same_as_n2-pe-ne - angle_coeff @angle:n2-pf-o harmonic 44.34 115.39 # SOURCE3 1 same_as_n2-pe-o - angle_coeff @angle:n2-pf-p2 harmonic 52.85 111.60 # SOURCE3 1 same_as_n2-pe-p2 - angle_coeff @angle:n2-pf-pf harmonic 48.70 109.40 # SOURCE3 1 same_as_n2-pe-pe - angle_coeff @angle:n2-pf-px harmonic 50.28 110.30 # SOURCE3 3 same_as_n2-pe-px - angle_coeff @angle:n2-pf-py harmonic 54.11 93.68 # SOURCE3 1 same_as_n2-pe-py - angle_coeff @angle:n2-pf-s harmonic 42.94 114.84 # SOURCE3 3 same_as_n2-pe-s - angle_coeff @angle:n2-pf-sx harmonic 39.42 97.83 # SOURCE3 1 same_as_n2-pe-sx - angle_coeff @angle:n2-pf-sy harmonic 38.61 98.14 # SOURCE3 1 same_as_n2-pe-sy - angle_coeff @angle:nf-pf-o harmonic 42.65 110.24 # SOURCE3 3 same_as_ne-pe-o - angle_coeff @angle:nf-pf-p2 harmonic 52.77 104.48 # SOURCE3 2 same_as_ne-pe-p2 - angle_coeff @angle:nf-pf-s harmonic 42.21 109.19 # SOURCE3 5 same_as_ne-pe-s - angle_coeff @angle:o-pf-o harmonic 44.01 119.96 # SOURCE3 1 same_as_o-pe-o - angle_coeff @angle:o-pf-p2 harmonic 52.71 114.23 # SOURCE3 1 same_as_o-pe-p2 - angle_coeff @angle:o-pf-pf harmonic 42.47 145.96 # SOURCE3 1 same_as_o-pe-pe - angle_coeff @angle:o-pf-px harmonic 52.10 104.37 # SOURCE3 1 same_as_o-pe-px - angle_coeff @angle:o-pf-py harmonic 51.64 104.49 # SOURCE3 1 same_as_o-pe-py - angle_coeff @angle:o-pf-s harmonic 42.89 117.42 # SOURCE3 2 same_as_o-pe-s - angle_coeff @angle:o-pf-sx harmonic 38.02 106.59 # SOURCE3 1 same_as_o-pe-sx - angle_coeff @angle:o-pf-sy harmonic 37.56 105.04 # SOURCE3 1 same_as_o-pe-sy - angle_coeff @angle:p2-pf-pf harmonic 65.58 98.24 # SOURCE3 1 same_as_p2-pe-pe - angle_coeff @angle:p2-pf-px harmonic 64.12 108.28 # SOURCE3 2 same_as_p2-pe-px - angle_coeff @angle:p2-pf-py harmonic 62.99 110.87 # SOURCE3 3 same_as_p2-pe-py - angle_coeff @angle:p2-pf-s harmonic 53.42 111.28 # SOURCE3 1 same_as_p2-pe-s - angle_coeff @angle:p2-pf-sx harmonic 51.26 95.73 # SOURCE3 1 same_as_p2-pe-sx - angle_coeff @angle:p2-pf-sy harmonic 50.47 95.95 # SOURCE3 1 same_as_p2-pe-sy - angle_coeff @angle:pf-pf-s harmonic 50.40 107.91 # SOURCE3 2 same_as_pe-pe-s - angle_coeff @angle:px-pf-s harmonic 51.97 107.62 # SOURCE3 2 same_as_px-pe-s - angle_coeff @angle:py-pf-s harmonic 51.36 108.73 # SOURCE3 3 same_as_py-pe-s - angle_coeff @angle:s-pf-s harmonic 34.43 178.44 # SOURCE3 1 same_as_s-pe-s - angle_coeff @angle:s-pf-sx harmonic 38.72 108.32 # SOURCE3 2 same_as_s-pe-sx - angle_coeff @angle:s-pf-sy harmonic 38.35 106.93 # SOURCE3 1 same_as_s-pe-sy - angle_coeff @angle:c3-px-ca harmonic 36.97 104.79 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-px-ce harmonic 37.00 104.86 # SOURCE3 4 0.6354 - angle_coeff @angle:c3-px-cf harmonic 37.00 104.86 # SOURCE3 4 same_as_c3-px-ce - angle_coeff @angle:c3-px-ne harmonic 39.55 102.46 # SOURCE3 7 1.8685 - angle_coeff @angle:c3-px-nf harmonic 39.55 102.46 # SOURCE3 7 same_as_c3-px-ne - angle_coeff @angle:c3-px-o harmonic 39.39 113.68 # SOURCE3 28 4.8990 - angle_coeff @angle:c3-px-pe harmonic 47.82 105.73 # SOURCE3 10 4.4059 - angle_coeff @angle:c3-px-pf harmonic 47.82 105.73 # SOURCE3 10 same_as_c3-px-pe - angle_coeff @angle:c3-px-py harmonic 45.50 103.11 # SOURCE3 3 0.8680 - angle_coeff @angle:c3-px-sx harmonic 36.06 99.55 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-px-sy harmonic 35.30 103.41 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-px-ca harmonic 37.08 104.15 # SOURCE3 2 3.6168 - angle_coeff @angle:ca-px-o harmonic 40.49 107.50 # SOURCE3 5 5.7355 - angle_coeff @angle:c-px-c3 harmonic 36.70 101.72 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-px-ce harmonic 37.15 104.21 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-px-o harmonic 39.42 113.79 # SOURCE3 6 0.3877 - angle_coeff @angle:cf-px-cf harmonic 37.15 104.21 # SOURCE3 1 same_as_ce-px-ce - angle_coeff @angle:cf-px-o harmonic 39.42 113.79 # SOURCE3 6 same_as_ce-px-o - angle_coeff @angle:c-px-o harmonic 37.98 114.47 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-px-ne harmonic 41.92 103.22 # SOURCE3 2 0.6807 - angle_coeff @angle:ne-px-o harmonic 42.27 114.13 # SOURCE3 11 8.9737 - angle_coeff @angle:nf-px-nf harmonic 41.92 103.22 # SOURCE3 2 same_as_ne-px-ne - angle_coeff @angle:nf-px-o harmonic 42.27 114.13 # SOURCE3 11 same_as_ne-px-o - angle_coeff @angle:o-px-pe harmonic 49.41 116.50 # SOURCE3 12 8.2925 - angle_coeff @angle:o-px-pf harmonic 49.41 116.50 # SOURCE3 12 same_as_o-px-pe - angle_coeff @angle:o-px-py harmonic 45.90 114.20 # SOURCE3 5 1.7165 - angle_coeff @angle:o-px-sx harmonic 35.81 112.81 # SOURCE3 3 0.8799 - angle_coeff @angle:o-px-sy harmonic 35.59 113.54 # SOURCE3 3 0.5010 - angle_coeff @angle:pe-px-pe harmonic 61.38 110.71 # SOURCE3 1 0.0000 - angle_coeff @angle:pf-px-pf harmonic 61.38 110.71 # SOURCE3 1 same_as_pe-px-pe - angle_coeff @angle:py-px-py harmonic 56.72 107.78 # SOURCE3 1 0.0000 - angle_coeff @angle:sx-px-sx harmonic 36.76 96.24 # SOURCE3 1 0.0000 - angle_coeff @angle:sy-px-sy harmonic 35.53 102.36 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-py-n4 harmonic 37.34 103.83 # SOURCE3 4 0.0000 - angle_coeff @angle:c3-py-na harmonic 38.76 106.89 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-py-o harmonic 38.95 117.87 # SOURCE3 13 2.3554 - angle_coeff @angle:c3-py-oh harmonic 41.22 100.16 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-py-os harmonic 40.15 105.39 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-py-px harmonic 44.89 106.27 # SOURCE3 2 0.0000 - angle_coeff @angle:c3-py-py harmonic 43.54 113.97 # SOURCE3 10 1.6346 - angle_coeff @angle:c3-py-sx harmonic 34.74 106.36 # SOURCE3 4 0.0000 - angle_coeff @angle:ca-py-ca harmonic 36.99 107.55 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-py-o harmonic 39.82 113.98 # SOURCE3 3 0.5309 - angle_coeff @angle:ca-py-oh harmonic 40.90 102.68 # SOURCE4 5 1.2945 - angle_coeff @angle:ca-py-os harmonic 40.66 103.75 # SOURCE3 2 0.0000 - angle_coeff @angle:c-py-c3 harmonic 35.71 110.36 # SOURCE3 1 0.0000 - angle_coeff @angle:c-py-c harmonic 36.23 104.20 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-py-ce harmonic 37.29 106.54 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-py-o harmonic 40.24 112.16 # SOURCE3 5 3.2594 - angle_coeff @angle:ce-py-oh harmonic 40.58 104.77 # SOURCE3 6 2.1852 - angle_coeff @angle:ce-py-os harmonic 40.82 103.34 # SOURCE3 2 0.0000 - angle_coeff @angle:cf-py-cf harmonic 37.29 106.54 # SOURCE3 1 same_as_ce-py-ce - angle_coeff @angle:cf-py-o harmonic 40.24 112.16 # SOURCE3 5 same_as_ce-py-o - angle_coeff @angle:cf-py-oh harmonic 40.58 104.77 # SOURCE3 6 same_as_ce-py-oh - angle_coeff @angle:cf-py-os harmonic 40.82 103.34 # SOURCE3 2 same_as_ce-py-os - angle_coeff @angle:c-py-o harmonic 38.52 115.25 # SOURCE3 6 2.6519 - angle_coeff @angle:c-py-oh harmonic 40.03 102.14 # SOURCE3 6 1.0654 - angle_coeff @angle:c-py-os harmonic 41.32 95.74 # SOURCE3 3 9.0999 - angle_coeff @angle:n3-py-ne harmonic 41.93 108.44 # SOURCE4 12 0.9498 - angle_coeff @angle:n4-py-o harmonic 38.83 115.58 # SOURCE3 4 0.0000 - angle_coeff @angle:n4-py-py harmonic 63.24 55.10 # SOURCE3 4 0.0000 - angle_coeff @angle:na-py-o harmonic 40.78 122.40 # SOURCE3 2 0.0000 - angle_coeff @angle:na-py-py harmonic 67.66 50.88 # SOURCE3 2 0.0000 - angle_coeff @angle:ne-py-ne harmonic 43.51 106.29 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-py-o harmonic 44.00 113.21 # SOURCE3 15 3.8894 - angle_coeff @angle:ne-py-oh harmonic 44.13 104.70 # SOURCE3 26 2.7513 - angle_coeff @angle:ne-py-os harmonic 44.80 101.33 # SOURCE3 2 0.0000 - angle_coeff @angle:nf-py-nf harmonic 43.51 106.29 # SOURCE3 1 same_as_ne-py-ne - angle_coeff @angle:nf-py-o harmonic 44.00 113.21 # SOURCE3 15 same_as_ne-py-o - angle_coeff @angle:nf-py-oh harmonic 44.13 104.70 # SOURCE3 26 same_as_ne-py-oh - angle_coeff @angle:nf-py-os harmonic 44.80 101.33 # SOURCE3 2 same_as_ne-py-os - angle_coeff @angle:oh-py-oh harmonic 45.06 101.78 # SOURCE3 35 2.2937 - angle_coeff @angle:oh-py-pe harmonic 50.99 104.84 # SOURCE3 22 2.0337 - angle_coeff @angle:oh-py-pf harmonic 50.99 104.84 # SOURCE3 22 same_as_oh-py-pe - angle_coeff @angle:oh-py-px harmonic 47.75 104.30 # SOURCE3 8 1.2772 - angle_coeff @angle:oh-py-py harmonic 48.91 100.45 # SOURCE3 6 0.0000 - angle_coeff @angle:oh-py-sx harmonic 37.44 100.94 # SOURCE3 4 0.0000 - angle_coeff @angle:oh-py-sy harmonic 38.51 101.47 # SOURCE3 6 0.2490 - angle_coeff @angle:o-py-oh harmonic 43.74 116.14 # SOURCE3 79 2.1455 - angle_coeff @angle:o-py-os harmonic 43.55 116.79 # SOURCE3 17 1.3534 - angle_coeff @angle:o-py-pe harmonic 49.46 114.56 # SOURCE3 12 3.6114 - angle_coeff @angle:o-py-pf harmonic 49.46 114.56 # SOURCE3 12 same_as_o-py-pe - angle_coeff @angle:o-py-px harmonic 46.50 111.37 # SOURCE3 5 0.3803 - angle_coeff @angle:o-py-py harmonic 44.97 120.43 # SOURCE3 16 6.0629 - angle_coeff @angle:os-py-os harmonic 45.06 101.25 # SOURCE3 8 2.0860 - angle_coeff @angle:os-py-py harmonic 47.94 104.48 # SOURCE3 4 0.0000 - angle_coeff @angle:os-py-sx harmonic 36.90 103.86 # SOURCE3 2 0.0000 - angle_coeff @angle:os-py-sy harmonic 38.37 102.12 # SOURCE3 2 0.0000 - angle_coeff @angle:o-py-sx harmonic 34.68 118.56 # SOURCE3 7 6.2976 - angle_coeff @angle:o-py-sy harmonic 36.96 111.71 # SOURCE3 5 1.1937 - angle_coeff @angle:pe-py-pe harmonic 61.78 107.14 # SOURCE3 1 0.0000 - angle_coeff @angle:pf-py-pf harmonic 61.78 107.14 # SOURCE3 1 same_as_pe-py-pe - angle_coeff @angle:py-py-py harmonic 55.80 112.70 # SOURCE3 1 0.0000 - angle_coeff @angle:py-py-sx harmonic 58.65 61.54 # SOURCE3 4 0.0000 - angle_coeff @angle:sy-py-sy harmonic 36.13 105.17 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-s2-o harmonic 65.76 117.25 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-s2-n2 harmonic 68.67 110.84 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-s2-o harmonic 66.18 114.70 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-s2-n1 harmonic 53.42 117.70 # SOURCE2 1 0.0000 - angle_coeff @angle:f-s2-n1 harmonic 66.15 116.90 # SOURCE2 1 0.0000 - angle_coeff @angle:n1-s2-o harmonic 73.05 108.46 # HF/6-31G* 1 - angle_coeff @angle:n2-s2-o harmonic 67.93 121.20 # SOURCE2 2 0.8000 - angle_coeff @angle:o-s2-o harmonic 67.99 116.17 # SOURCE3 1 0.0000 - angle_coeff @angle:o-s2-s harmonic 63.79 118.30 # SOURCE2 1 0.0000 - angle_coeff @angle:s-s2-s harmonic 63.50 115.04 # SOURCE3 1 0.0000 - angle_coeff @angle:br-s4-br harmonic 64.61 98.02 # SOURCE3 1 - angle_coeff @angle:br-s4-c3 harmonic 62.19 92.98 # SOURCE3 1 0.0000 - angle_coeff @angle:br-s4-o harmonic 59.20 112.07 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-s4-c1 harmonic 65.35 93.55 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-s4-o harmonic 65.98 110.36 # SOURCE3 2 0.0000 - angle_coeff @angle:c2-s4-c2 harmonic 62.00 102.29 # SOURCE3 1 - angle_coeff @angle:c2-s4-c3 harmonic 63.48 94.95 # SOURCE3 1 - angle_coeff @angle:c2-s4-o harmonic 66.61 107.09 # SOURCE3 1 - angle_coeff @angle:c3-s4-c3 harmonic 62.07 96.82 # SOURCE3 11 1.5580 - angle_coeff @angle:c3-s4-ca harmonic 62.99 95.00 # SOURCE3 1 - angle_coeff @angle:c3-s4-f harmonic 66.32 91.70 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-hs harmonic 46.55 90.60 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-i harmonic 52.86 90.53 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-n2 harmonic 69.07 90.59 # SOURCE3 1 - angle_coeff @angle:c3-s4-n3 harmonic 65.18 94.49 # SOURCE3 4 1.5570 - angle_coeff @angle:c3-s4-n harmonic 64.28 96.07 # SOURCE3 4 1.0354 - angle_coeff @angle:c3-s4-n4 harmonic 61.99 92.47 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-na harmonic 65.11 93.07 # SOURCE3 10 1.8813 - angle_coeff @angle:c3-s4-nh harmonic 64.51 97.08 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-no harmonic 62.53 89.53 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-o harmonic 65.63 106.21 # SOURCE3 60 2.0426 - angle_coeff @angle:c3-s4-oh harmonic 68.22 90.25 # SOURCE4 8 0.3023 - angle_coeff @angle:c3-s4-os harmonic 68.23 90.06 # SOURCE3 4 0.4484 - angle_coeff @angle:c3-s4-p2 harmonic 76.43 94.37 # SOURCE3 1 - angle_coeff @angle:c3-s4-p3 harmonic 78.19 96.54 # SOURCE3 4 1.3634 - angle_coeff @angle:c3-s4-p4 harmonic 73.69 97.40 # SOURCE3 1 - angle_coeff @angle:c3-s4-p5 harmonic 78.32 99.18 # SOURCE3 1 - angle_coeff @angle:c3-s4-s4 harmonic 64.31 89.50 # SOURCE3 1 - angle_coeff @angle:c3-s4-s harmonic 61.31 98.72 # SOURCE3 2 0.0185 - angle_coeff @angle:c3-s4-s6 harmonic 61.62 97.48 # SOURCE3 1 - angle_coeff @angle:c3-s4-sh harmonic 60.74 94.66 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s4-ss harmonic 60.58 95.31 # SOURCE3 3 1.4101 - angle_coeff @angle:ca-s4-ca harmonic 63.26 95.21 # SOURCE3 1 - angle_coeff @angle:ca-s4-o harmonic 66.01 106.63 # SOURCE3 1 - angle_coeff @angle:c-s4-c3 harmonic 61.53 95.07 # SOURCE3 1 - angle_coeff @angle:c-s4-c harmonic 63.34 86.83 # SOURCE3 1 - angle_coeff @angle:cl-s4-cl harmonic 53.89 97.68 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-s4-o harmonic 58.13 108.34 # SOURCE3 2 0.0000 - angle_coeff @angle:c-s4-o harmonic 63.97 106.17 # SOURCE3 1 - angle_coeff @angle:cx-s4-cx harmonic 86.71 48.80 # SOURCE2 1 0.0000 - angle_coeff @angle:cx-s4-o harmonic 64.10 110.00 # SOURCE2 1 0.0000 - angle_coeff @angle:f-s4-f harmonic 69.99 92.71 # SOURCE2 3 0.1490 - angle_coeff @angle:f-s4-o harmonic 70.11 106.81 # SOURCE2 2 0.0100 - angle_coeff @angle:f-s4-s harmonic 59.78 107.50 # SOURCE2 1 0.0000 - angle_coeff @angle:hs-s4-hs harmonic 37.79 87.00 # SOURCE3 2 0.0202 - angle_coeff @angle:hs-s4-n1 harmonic 51.22 90.51 # HF/6-31G* 1 - angle_coeff @angle:hs-s4-o harmonic 49.80 110.27 # SOURCE3 5 0.1908 - angle_coeff @angle:i-s4-i harmonic 54.45 97.29 # SOURCE3 1 - angle_coeff @angle:i-s4-o harmonic 47.32 113.91 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-s4-n1 harmonic 72.41 94.02 # HF/6-31G* 1 - angle_coeff @angle:n1-s4-o harmonic 70.24 110.09 # HF/6-31G* 1 - angle_coeff @angle:n2-s4-n2 harmonic 75.77 90.17 # SOURCE3 1 - angle_coeff @angle:n2-s4-o harmonic 72.12 107.57 # SOURCE3 1 - angle_coeff @angle:n3-s4-n3 harmonic 68.89 91.19 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-s4-o harmonic 67.59 109.07 # SOURCE3 6 2.3605 - angle_coeff @angle:n4-s4-n4 harmonic 60.39 94.61 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-s4-o harmonic 63.17 104.91 # SOURCE3 3 0.4370 - angle_coeff @angle:na-s4-na harmonic 63.63 103.10 # SOURCE3 1 - angle_coeff @angle:na-s4-o harmonic 66.52 109.75 # SOURCE3 10 2.6919 - angle_coeff @angle:nh-s4-nh harmonic 68.96 92.24 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-s4-o harmonic 68.40 107.54 # SOURCE3 3 0.0401 - angle_coeff @angle:n-s4-n harmonic 68.03 91.30 # SOURCE3 1 - angle_coeff @angle:n-s4-o harmonic 68.09 105.70 # SOURCE3 4 1.6857 - angle_coeff @angle:no-s4-no harmonic 63.55 83.40 # SOURCE3 1 0.0000 - angle_coeff @angle:no-s4-o harmonic 62.93 103.58 # SOURCE3 3 1.5109 - angle_coeff @angle:oh-s4-oh harmonic 69.00 100.34 # SOURCE3 1 - angle_coeff @angle:o-s4-o harmonic 74.43 110.61 # SOURCE3 5 3.6413 - angle_coeff @angle:o-s4-oh harmonic 69.42 110.13 # SOURCE4 10 0.5760 - angle_coeff @angle:o-s4-os harmonic 69.67 109.02 # SOURCE3 8 1.5005 - angle_coeff @angle:o-s4-p2 harmonic 76.18 106.77 # SOURCE3 1 - angle_coeff @angle:o-s4-p3 harmonic 79.76 106.51 # SOURCE3 8 4.0943 - angle_coeff @angle:o-s4-p4 harmonic 75.38 103.36 # SOURCE3 1 - angle_coeff @angle:o-s4-p5 harmonic 85.32 96.95 # SOURCE3 1 - angle_coeff @angle:o-s4-s4 harmonic 63.80 104.55 # SOURCE3 1 - angle_coeff @angle:o-s4-s harmonic 61.69 112.22 # SOURCE3 4 2.8682 - angle_coeff @angle:o-s4-s6 harmonic 64.33 102.84 # SOURCE3 1 - angle_coeff @angle:o-s4-sh harmonic 60.56 107.51 # SOURCE3 3 0.7511 - angle_coeff @angle:os-s4-os harmonic 71.26 93.68 # SOURCE3 2 2.4166 - angle_coeff @angle:o-s4-ss harmonic 60.06 109.49 # SOURCE3 5 1.8509 - angle_coeff @angle:p2-s4-p2 harmonic 98.20 92.62 # SOURCE3 1 - angle_coeff @angle:p3-s4-p3 harmonic 101.37 95.71 # SOURCE3 2 1.2239 - angle_coeff @angle:p5-s4-p5 harmonic 104.72 93.86 # SOURCE3 1 - angle_coeff @angle:s4-s4-s4 harmonic 65.42 90.17 # SOURCE3 1 - angle_coeff @angle:s4-s4-s6 harmonic 65.42 90.17 # SOURCE3 1 - angle_coeff @angle:s6-s4-s6 harmonic 64.23 93.52 # SOURCE3 1 - angle_coeff @angle:sh-s4-sh harmonic 58.79 102.76 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-s4-ss harmonic 58.85 102.64 # SOURCE3 1 - angle_coeff @angle:s-s4-s harmonic 59.87 108.08 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-s4-ss harmonic 61.05 95.47 # SOURCE3 1 0.0000 - angle_coeff @angle:br-s6-br harmonic 67.11 101.57 # SOURCE3 1 0.0000 - angle_coeff @angle:br-s6-c3 harmonic 63.24 98.99 # SOURCE3 1 0.0000 - angle_coeff @angle:br-s6-f harmonic 63.06 100.60 # SOURCE2 1 0.0000 - angle_coeff @angle:br-s6-o harmonic 63.90 107.58 # SOURCE3 6 0.3000 - angle_coeff @angle:c1-s6-c1 harmonic 64.09 99.99 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-s6-o harmonic 68.10 108.23 # SOURCE3 4 0.0000 - angle_coeff @angle:c2-s6-c2 harmonic 61.86 102.75 # SOURCE3 1 - angle_coeff @angle:c2-s6-c3 harmonic 61.23 104.05 # SOURCE3 1 - angle_coeff @angle:c2-s6-o harmonic 67.53 106.58 # SOURCE3 1 - angle_coeff @angle:c3-s6-c3 harmonic 61.35 102.83 # SOURCE3 7 1.2531 - angle_coeff @angle:c3-s6-ca harmonic 61.51 103.17 # SOURCE3 1 - angle_coeff @angle:c3-s6-cy harmonic 62.55 94.57 # SOURCE4 8 0.4183 - angle_coeff @angle:c3-s6-f harmonic 65.73 97.11 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s6-hs harmonic 44.94 100.62 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s6-i harmonic 50.82 97.74 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s6-n2 harmonic 63.42 112.95 # SOURCE4 11 0.7920 - angle_coeff @angle:c3-s6-n3 harmonic 65.71 101.38 # SOURCE4 60 0.9507 - angle_coeff @angle:c3-s6-n harmonic 63.84 102.97 # SOURCE3 4 0.8785 - angle_coeff @angle:c3-s6-n4 harmonic 61.33 99.40 # SOURCE3 3 0.4695 - angle_coeff @angle:c3-s6-na harmonic 63.68 102.81 # SOURCE3 10 3.1256 - angle_coeff @angle:c3-s6-nh harmonic 63.74 104.31 # SOURCE4 34 1.5848 - angle_coeff @angle:c3-s6-no harmonic 60.08 99.57 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s6-o harmonic 66.59 108.32 # SOURCE3 112 1.8014 - angle_coeff @angle:c3-s6-oh harmonic 67.71 98.60 # SOURCE4 42 0.8366 - angle_coeff @angle:c3-s6-os harmonic 68.68 96.32 # SOURCE4 30 0.4539 - angle_coeff @angle:c3-s6-p2 harmonic 72.54 106.47 # SOURCE3 1 - angle_coeff @angle:c3-s6-p3 harmonic 76.24 103.40 # SOURCE3 3 0.8516 - angle_coeff @angle:c3-s6-p4 harmonic 71.10 104.12 # SOURCE3 1 - angle_coeff @angle:c3-s6-p5 harmonic 77.16 103.46 # SOURCE3 1 - angle_coeff @angle:c3-s6-s4 harmonic 61.78 98.10 # SOURCE3 1 - angle_coeff @angle:c3-s6-s harmonic 60.70 104.50 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s6-s6 harmonic 60.60 101.95 # SOURCE3 1 - angle_coeff @angle:c3-s6-sh harmonic 60.07 101.84 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-s6-ss harmonic 59.68 102.47 # SOURCE3 3 1.7451 - angle_coeff @angle:ca-s6-ca harmonic 61.80 103.08 # SOURCE3 1 - angle_coeff @angle:ca-s6-o harmonic 68.37 104.07 # SOURCE4 59 0.5636 - angle_coeff @angle:c-s6-c3 harmonic 60.12 101.24 # SOURCE3 1 - angle_coeff @angle:c-s6-c harmonic 59.07 99.82 # SOURCE3 1 - angle_coeff @angle:cc-s6-o harmonic 65.29 103.63 # SOURCE4 9 0.5934 - angle_coeff @angle:cl-s6-cl harmonic 52.93 101.25 # SOURCE3 1 0.0000 - angle_coeff @angle:cl-s6-f harmonic 57.88 99.00 # SOURCE2 1 0.0000 - angle_coeff @angle:cl-s6-o harmonic 58.51 107.66 # SOURCE3 4 0.0000 - angle_coeff @angle:c-s6-o harmonic 63.97 107.97 # SOURCE3 1 - angle_coeff @angle:c-s6-os harmonic 64.36 102.12 # SOURCE3 1 - angle_coeff @angle:cx-s6-cx harmonic 86.21 54.70 # SOURCE2 1 0.0000 - angle_coeff @angle:cy-s6-o harmonic 63.83 110.22 # SOURCE4 20 1.1009 - angle_coeff @angle:f-s6-f harmonic 70.81 94.70 # SOURCE2 3 0.9899 - angle_coeff @angle:f-s6-o harmonic 72.38 106.48 # SOURCE3 2 0.0000 - angle_coeff @angle:hs-s6-hs harmonic 35.84 99.02 # SOURCE3 2 0.0595 - angle_coeff @angle:hs-s6-n1 harmonic 54.71 97.27 # HF/6-31G* 1 - angle_coeff @angle:hs-s6-o harmonic 51.91 107.60 # SOURCE3 10 0.0343 - angle_coeff @angle:i-s6-i harmonic 53.90 99.25 # SOURCE3 1 - angle_coeff @angle:i-s6-o harmonic 47.73 109.74 # SOURCE3 2 0.0000 - angle_coeff @angle:n1-s6-n1 harmonic 83.71 95.52 # HF/6-31G* 1 - angle_coeff @angle:n1-s6-o harmonic 78.79 107.52 # HF/6-31G* 1 - angle_coeff @angle:n2-s6-n2 harmonic 75.20 98.61 # SOURCE3 1 - angle_coeff @angle:n2-s6-o harmonic 72.08 116.41 # SOURCE3 3 5.0830 - angle_coeff @angle:n2-s6-oh harmonic 71.75 106.96 # SOURCE3 2 0.0000 - angle_coeff @angle:n2-s6-os harmonic 73.30 103.25 # SOURCE3 1 - angle_coeff @angle:n3-s6-n3 harmonic 71.49 98.57 # SOURCE4 7 0.2690 - angle_coeff @angle:n3-s6-o harmonic 72.90 106.80 # SOURCE3 14 1.7908 - angle_coeff @angle:n3-s6-os harmonic 72.84 99.26 # SOURCE4 8 0.5141 - angle_coeff @angle:n4-s6-n4 harmonic 59.97 101.85 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-s6-o harmonic 65.83 102.92 # SOURCE3 10 1.5434 - angle_coeff @angle:na-s6-na harmonic 67.74 98.04 # SOURCE3 1 - angle_coeff @angle:na-s6-o harmonic 70.46 105.67 # SOURCE3 20 0.8019 - angle_coeff @angle:nh-s6-nh harmonic 70.22 94.56 # SOURCE3 1 0.0000 - angle_coeff @angle:nh-s6-o harmonic 70.23 109.12 # SOURCE3 6 0.9556 - angle_coeff @angle:n-s6-n harmonic 66.18 104.16 # SOURCE3 1 - angle_coeff @angle:n-s6-o harmonic 70.74 105.91 # SOURCE3 8 0.2953 - angle_coeff @angle:no-s6-no harmonic 61.24 91.63 # SOURCE3 1 0.0000 - angle_coeff @angle:no-s6-o harmonic 62.67 107.43 # SOURCE3 6 1.5494 - angle_coeff @angle:n-s6-os harmonic 70.81 99.23 # SOURCE4 5 0.9794 - angle_coeff @angle:oh-s6-oh harmonic 73.67 100.34 # SOURCE3 6 0.0076 - angle_coeff @angle:oh-s6-os harmonic 75.33 96.62 # SOURCE4 26 0.6688 - angle_coeff @angle:oh-s6-p2 harmonic 75.13 109.67 # SOURCE3 2 0.0000 - angle_coeff @angle:o-s6-o harmonic 74.58 119.73 # SOURCE4 324 2.0530 - angle_coeff @angle:o-s6-oh harmonic 74.13 108.21 # SOURCE3 18 0.7437 - angle_coeff @angle:o-s6-os harmonic 74.58 107.84 # SOURCE3 12 0.7025 - angle_coeff @angle:o-s6-p2 harmonic 76.65 106.61 # SOURCE3 1 - angle_coeff @angle:o-s6-p3 harmonic 80.16 107.07 # SOURCE3 22 1.0550 - angle_coeff @angle:o-s6-p4 harmonic 73.92 105.67 # SOURCE3 1 - angle_coeff @angle:o-s6-p5 harmonic 81.69 106.64 # SOURCE3 1 - angle_coeff @angle:o-s6-s4 harmonic 63.02 107.85 # SOURCE3 1 - angle_coeff @angle:o-s6-s harmonic 63.52 110.29 # SOURCE3 6 2.2405 - angle_coeff @angle:o-s6-s6 harmonic 63.55 106.07 # SOURCE3 1 - angle_coeff @angle:o-s6-sh harmonic 62.53 106.81 # SOURCE3 6 0.6292 - angle_coeff @angle:os-s6-os harmonic 74.80 98.70 # SOURCE3 1 0.0000 - angle_coeff @angle:o-s6-ss harmonic 62.06 107.43 # SOURCE3 10 1.1423 - angle_coeff @angle:p3-s6-p3 harmonic 94.93 110.17 # SOURCE3 4 5.3678 - angle_coeff @angle:p5-s6-p5 harmonic 99.25 104.49 # SOURCE3 1 - angle_coeff @angle:s4-s6-s4 harmonic 61.51 101.99 # SOURCE3 1 - angle_coeff @angle:s4-s6-s6 harmonic 65.42 90.17 # SOURCE3 1 - angle_coeff @angle:s6-s6-s6 harmonic 61.12 103.29 # SOURCE3 1 - angle_coeff @angle:sh-s6-sh harmonic 59.41 106.43 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-s6-ss harmonic 60.36 102.64 # SOURCE3 1 - angle_coeff @angle:s-s6-s harmonic 60.63 109.34 # SOURCE3 1 0.0000 - angle_coeff @angle:ss-s6-ss harmonic 60.46 101.82 # SOURCE3 1 0.0000 - angle_coeff @angle:br-sh-hs harmonic 43.54 95.64 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-sh-hs harmonic 48.23 95.99 # calculated_based_on_C#C-SH 0 - angle_coeff @angle:c2-sh-hs harmonic 45.81 97.08 # SOURCE4 5 0.3132 - angle_coeff @angle:c3-sh-hs harmonic 44.94 96.60 # SOURCE3 12 0.8009 - angle_coeff @angle:ca-sh-hs harmonic 46.32 94.84 # SOURCE4 13 0.4130 - angle_coeff @angle:cc-sh-hs harmonic 46.41 95.38 # SOURCE4 8 1.1410 - angle_coeff @angle:c-sh-hs harmonic 45.96 96.07 # SOURCE3 6 1.1164 - angle_coeff @angle:f-sh-hs harmonic 48.09 96.50 # SOURCE3 1 0.0000 - angle_coeff @angle:hs-sh-hs harmonic 37.45 93.72 # SOURCE3 3 0.4777 - angle_coeff @angle:hs-sh-i harmonic 37.09 96.44 # SOURCE3 1 0.0000 - angle_coeff @angle:hs-sh-n1 harmonic 51.69 93.51 # HF/6-31G* 1 - angle_coeff @angle:hs-sh-n2 harmonic 48.12 95.82 # SOURCE3 5 3.1495 - angle_coeff @angle:hs-sh-n harmonic 48.41 95.59 # SOURCE3 4 3.9065 - angle_coeff @angle:hs-sh-n3 harmonic 48.06 95.98 # SOURCE3 3 1.1735 - angle_coeff @angle:hs-sh-n4 harmonic 47.15 93.13 # SOURCE3 3 0.1675 - angle_coeff @angle:hs-sh-na harmonic 48.12 97.38 # SOURCE3 9 1.0223 - angle_coeff @angle:hs-sh-nh harmonic 47.52 101.11 # SOURCE3 1 0.0000 - angle_coeff @angle:hs-sh-no harmonic 47.35 92.93 # SOURCE3 1 0.0000 - angle_coeff @angle:hs-sh-o harmonic 48.22 109.23 # SOURCE3 2 0.0068 - angle_coeff @angle:hs-sh-oh harmonic 48.75 98.64 # SOURCE3 2 0.0605 - angle_coeff @angle:hs-sh-os harmonic 49.35 98.15 # SOURCE3 3 0.1661 - angle_coeff @angle:hs-sh-p2 harmonic 56.52 99.12 # SOURCE3 10 5.4110 - angle_coeff @angle:hs-sh-p3 harmonic 53.11 95.81 # SOURCE3 3 0.4396 - angle_coeff @angle:hs-sh-p4 harmonic 54.01 94.22 # SOURCE3 4 0.7605 - angle_coeff @angle:hs-sh-p5 harmonic 54.80 94.52 # SOURCE3 3 0.5589 - angle_coeff @angle:hs-sh-s harmonic 40.94 102.87 # SOURCE3 2 0.0000 - angle_coeff @angle:hs-sh-s4 harmonic 42.04 92.16 # SOURCE3 3 1.6519 - angle_coeff @angle:hs-sh-s6 harmonic 42.91 93.83 # SOURCE3 3 1.2561 - angle_coeff @angle:hs-sh-sh harmonic 42.80 99.07 # SOURCE3 2 0.0000 - angle_coeff @angle:hs-sh-ss harmonic 42.59 99.17 # SOURCE3 3 0.2457 - angle_coeff @angle:br-ss-br harmonic 67.00 102.92 # SOURCE3 1 0.0000 - angle_coeff @angle:br-ss-c3 harmonic 63.06 99.03 # SOURCE3 1 0.0000 - angle_coeff @angle:c1-ss-c1 harmonic 66.30 98.30 # SOURCE2 1 0.0000 - angle_coeff @angle:c1-ss-c3 harmonic 62.89 99.90 # SOURCE2 1 0.0000 - angle_coeff @angle:c2-ss-c2 harmonic 63.71 99.56 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-ss-c3 harmonic 61.87 100.37 # SOURCE4 100 2.3280 - angle_coeff @angle:c2-ss-cy harmonic 65.30 88.61 # SOURCE4 27 0.4481 - angle_coeff @angle:c2-ss-n2 harmonic 64.45 106.76 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-ss-na harmonic 65.02 100.51 # SOURCE3 6 6.9702 - angle_coeff @angle:c2-ss-os harmonic 69.78 89.76 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-ss-ss harmonic 64.78 92.26 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-c3 harmonic 60.63 99.92 # SOURCE3 14 2.0723 - angle_coeff @angle:c3-ss-ca harmonic 60.80 102.12 # SOURCE4 161 1.3084 - angle_coeff @angle:c3-ss-cc harmonic 61.74 100.75 # CORR 87 - angle_coeff @angle:c3-ss-cd harmonic 61.74 100.75 # CORR 87 - angle_coeff @angle:c3-ss-cl harmonic 56.40 99.40 # SOURCE2 1 0.0000 - angle_coeff @angle:c3-ss-cy harmonic 61.94 94.32 # SOURCE4 62 0.3646 - angle_coeff @angle:c3-ss-f harmonic 63.40 97.49 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-i harmonic 56.03 100.00 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-n1 harmonic 65.93 98.44 # HF/6-31G* 1 - angle_coeff @angle:c3-ss-n2 harmonic 65.94 96.42 # SOURCE3 5 1.3604 - angle_coeff @angle:c3-ss-n3 harmonic 64.10 98.83 # SOURCE3 3 0.2909 - angle_coeff @angle:c3-ss-n harmonic 63.71 100.30 # SOURCE3 4 0.6579 - angle_coeff @angle:c3-ss-n4 harmonic 62.94 97.79 # SOURCE3 3 0.2002 - angle_coeff @angle:c3-ss-na harmonic 63.51 100.14 # SOURCE3 12 1.7415 - angle_coeff @angle:c3-ss-nh harmonic 63.75 100.63 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-no harmonic 62.40 98.62 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-o harmonic 64.67 106.60 # SOURCE3 2 1.6714 - angle_coeff @angle:c3-ss-oh harmonic 65.29 98.28 # SOURCE3 2 1.4326 - angle_coeff @angle:c3-ss-os harmonic 64.97 98.21 # SOURCE3 4 1.7097 - angle_coeff @angle:c3-ss-p2 harmonic 80.22 98.41 # SOURCE3 8 0.9454 - angle_coeff @angle:c3-ss-p3 harmonic 76.29 98.70 # SOURCE3 3 0.0356 - angle_coeff @angle:c3-ss-p4 harmonic 76.93 98.16 # SOURCE3 4 0.1361 - angle_coeff @angle:c3-ss-p5 harmonic 75.86 100.22 # SOURCE4 23 1.1410 - angle_coeff @angle:c3-ss-s4 harmonic 60.11 96.37 # SOURCE3 3 0.0202 - angle_coeff @angle:c3-ss-s harmonic 59.94 101.90 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-s6 harmonic 60.94 96.76 # SOURCE3 3 1.5680 - angle_coeff @angle:c3-ss-sh harmonic 60.36 101.93 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-ss-ss harmonic 60.34 103.10 # SOURCE4 70 1.3377 - angle_coeff @angle:ca-ss-ca harmonic 62.76 98.71 # SOURCE4 97 1.2321 - angle_coeff @angle:ca-ss-cc harmonic 66.53 89.47 # CORR 134 - angle_coeff @angle:ca-ss-cd harmonic 66.53 89.47 # CORR 134 - angle_coeff @angle:ca-ss-cl harmonic 56.45 101.05 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-ss-n harmonic 65.76 97.16 # SOURCE3 1 - angle_coeff @angle:ca-ss-na harmonic 64.76 99.32 # SOURCE3 1 - angle_coeff @angle:ca-ss-nc harmonic 69.21 94.76 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-ss-nd harmonic 69.21 94.76 # SOURCE3 1 same_as_ca-ss-nc - angle_coeff @angle:ca-ss-ss harmonic 60.39 104.90 # SOURCE4 19 0.8743 - angle_coeff @angle:c-ss-c2 harmonic 65.63 92.43 # SOURCE3 1 0.0000 - angle_coeff @angle:c-ss-c3 harmonic 61.48 100.29 # SOURCE3 5 2.2127 - angle_coeff @angle:c-ss-c harmonic 62.20 101.40 # SOURCE3 1 0.0000 - angle_coeff @angle:c-ss-cc harmonic 65.61 92.43 # SOURCE4 14 2.3600 - angle_coeff @angle:cc-ss-cc harmonic 67.01 89.91 # SOURCE3 11 2.2164 - angle_coeff @angle:cc-ss-cd harmonic 67.07 89.74 # SOURCE4 49 0.7509 - angle_coeff @angle:cc-ss-n harmonic 66.42 97.16 # SOURCE3 1 same_as_cd-ss-n - angle_coeff @angle:cc-ss-na harmonic 65.39 99.33 # SOURCE3 18 same_as_cd-ss-na - angle_coeff @angle:cc-ss-nc harmonic 70.31 94.08 # CORR 13 - angle_coeff @angle:cc-ss-os harmonic 66.48 98.81 # SOURCE3 2 2.1583 - angle_coeff @angle:cc-ss-ss harmonic 63.91 94.76 # CORR 13 - angle_coeff @angle:cd-ss-cd harmonic 67.01 89.91 # SOURCE3 11 2.2164 - angle_coeff @angle:cd-ss-n harmonic 66.42 97.16 # SOURCE3 1 0.0000 - angle_coeff @angle:cd-ss-na harmonic 65.39 99.33 # SOURCE3 18 2.5847 - angle_coeff @angle:cd-ss-nd harmonic 70.31 94.08 # CORR 13 - angle_coeff @angle:cd-ss-os harmonic 66.48 98.81 # SOURCE3 2 same_as_cc-ss-os - angle_coeff @angle:cd-ss-ss harmonic 63.91 94.76 # CORR 13 - angle_coeff @angle:cl-ss-cl harmonic 52.39 103.37 # SOURCE3 1 0.0000 - angle_coeff @angle:cx-ss-cx harmonic 87.49 48.30 # SOURCE2 1 0.0000 - angle_coeff @angle:f-ss-f harmonic 66.18 98.30 # SOURCE2 1 0.0000 - angle_coeff @angle:f-ss-ss harmonic 59.85 108.30 # SOURCE2 1 0.0000 - angle_coeff @angle:i-ss-i harmonic 58.15 106.29 # SOURCE3 1 0.0000 - angle_coeff @angle:n1-ss-n1 harmonic 73.07 96.96 # HF/6-31G* 1 - angle_coeff @angle:n2-ss-n2 harmonic 71.12 96.75 # SOURCE3 1 0.0000 - angle_coeff @angle:n3-ss-n3 harmonic 66.50 102.34 # SOURCE3 1 0.0000 - angle_coeff @angle:n4-ss-n4 harmonic 63.55 101.19 # SOURCE3 1 0.0000 - angle_coeff @angle:na-ss-na harmonic 65.92 102.81 # SOURCE3 1 0.0000 - angle_coeff @angle:nc-ss-nc harmonic 75.03 97.94 # CORR 9 - angle_coeff @angle:nd-ss-nd harmonic 75.03 97.94 # CORR 9 - angle_coeff @angle:nh-ss-nh harmonic 65.30 107.89 # SOURCE3 1 0.0000 - angle_coeff @angle:n-ss-n harmonic 66.45 103.10 # SOURCE3 1 0.0000 - angle_coeff @angle:no-ss-no harmonic 61.43 106.43 # SOURCE3 1 0.0000 - angle_coeff @angle:oh-ss-oh harmonic 68.23 104.25 # SOURCE3 1 0.0000 - angle_coeff @angle:o-ss-o harmonic 69.80 119.30 # SOURCE2 1 0.0000 - angle_coeff @angle:o-ss-p5 harmonic 78.64 106.41 # SOURCE3 1 0.0000 - angle_coeff @angle:o-ss-s6 harmonic 62.35 105.39 # SOURCE3 1 - angle_coeff @angle:os-ss-os harmonic 67.76 102.99 # SOURCE3 1 0.0000 - angle_coeff @angle:o-ss-ss harmonic 62.04 112.70 # SOURCE2 1 0.0000 - angle_coeff @angle:p2-ss-p2 harmonic 105.52 99.52 # SOURCE3 1 0.0000 - angle_coeff @angle:p3-ss-p3 harmonic 96.77 101.67 # SOURCE3 1 - angle_coeff @angle:p5-ss-p5 harmonic 103.25 89.83 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-ss-s4 harmonic 60.86 96.08 # SOURCE3 1 0.0000 - angle_coeff @angle:s4-ss-s6 harmonic 59.93 101.26 # SOURCE3 1 - angle_coeff @angle:s6-ss-s6 harmonic 60.46 101.81 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-ss-sh harmonic 60.28 107.54 # SOURCE3 1 0.0000 - angle_coeff @angle:sh-ss-ss harmonic 60.81 106.53 # SOURCE3 1 - angle_coeff @angle:s-ss-s harmonic 57.67 115.04 # SOURCE3 1 - angle_coeff @angle:ss-ss-ss harmonic 60.44 108.76 # SOURCE4 8 0.2385 - angle_coeff @angle:c3-sx-ca harmonic 61.85 96.41 # SOURCE4 13 0.3130 - angle_coeff @angle:c3-sx-cc harmonic 62.52 95.11 # SOURCE4 17 0.6557 - angle_coeff @angle:c3-sx-ce harmonic 62.82 94.95 # SOURCE3 3 0.0007 - angle_coeff @angle:c3-sx-cf harmonic 62.82 94.95 # SOURCE3 3 same_as_c3-sx-ce - angle_coeff @angle:c3-sx-ne harmonic 65.33 90.06 # SOURCE3 5 1.9627 - angle_coeff @angle:c3-sx-nf harmonic 65.33 90.06 # SOURCE3 5 same_as_c3-sx-ne - angle_coeff @angle:c3-sx-o harmonic 64.94 107.88 # SOURCE3 30 0.8721 - angle_coeff @angle:c3-sx-pe harmonic 76.99 94.32 # SOURCE3 7 0.5547 - angle_coeff @angle:c3-sx-pf harmonic 76.99 94.32 # SOURCE3 7 same_as_c3-sx-pe - angle_coeff @angle:c3-sx-px harmonic 74.26 96.46 # SOURCE3 3 1.3351 - angle_coeff @angle:c3-sx-py harmonic 74.13 95.67 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-sx-sx harmonic 57.22 91.47 # SOURCE3 4 1.9919 - angle_coeff @angle:c3-sx-sy harmonic 58.71 95.47 # SOURCE3 3 2.8422 - angle_coeff @angle:ca-sx-ca harmonic 61.97 95.21 # SOURCE3 1 0.0000 - angle_coeff @angle:ca-sx-o harmonic 64.82 106.89 # SOURCE4 25 0.5562 - angle_coeff @angle:c-sx-c3 harmonic 62.01 92.71 # SOURCE3 3 0.3095 - angle_coeff @angle:c-sx-c harmonic 62.83 86.85 # SOURCE3 1 0.0000 - angle_coeff @angle:cc-sx-o harmonic 65.92 104.49 # SOURCE4 17 1.7759 - angle_coeff @angle:ce-sx-ce harmonic 63.02 94.96 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-sx-o harmonic 65.38 107.47 # SOURCE3 5 0.3128 - angle_coeff @angle:cf-sx-cf harmonic 63.02 94.96 # SOURCE3 1 same_as_ce-sx-ce - angle_coeff @angle:cf-sx-o harmonic 65.38 107.47 # SOURCE3 5 same_as_ce-sx-o - angle_coeff @angle:c-sx-o harmonic 63.47 106.17 # SOURCE3 5 0.9477 - angle_coeff @angle:ne-sx-ne harmonic 66.37 90.17 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-sx-o harmonic 65.36 109.20 # SOURCE3 7 1.4542 - angle_coeff @angle:nf-sx-nf harmonic 66.37 90.17 # SOURCE3 1 same_as_ne-sx-ne - angle_coeff @angle:nf-sx-o harmonic 65.36 109.20 # SOURCE3 7 same_as_ne-sx-o - angle_coeff @angle:o-sx-pe harmonic 77.00 106.43 # SOURCE3 9 2.8345 - angle_coeff @angle:o-sx-pf harmonic 77.00 106.43 # SOURCE3 9 same_as_o-sx-pe - angle_coeff @angle:o-sx-px harmonic 75.16 104.77 # SOURCE3 3 1.9810 - angle_coeff @angle:o-sx-py harmonic 73.10 109.13 # SOURCE3 7 5.6840 - angle_coeff @angle:o-sx-sx harmonic 55.68 104.65 # SOURCE3 6 3.0524 - angle_coeff @angle:o-sx-sy harmonic 59.44 103.41 # SOURCE3 5 0.9618 - angle_coeff @angle:pe-sx-pe harmonic 99.19 92.62 # SOURCE3 1 0.0000 - angle_coeff @angle:pf-sx-pf harmonic 99.19 92.62 # SOURCE3 1 same_as_pe-sx-pe - angle_coeff @angle:py-sx-py harmonic 110.11 69.23 # SOURCE3 3 17.4143 - angle_coeff @angle:sx-sx-sx harmonic 58.65 84.90 # SOURCE3 1 0.0000 - angle_coeff @angle:sy-sx-sy harmonic 59.25 93.52 # SOURCE3 1 0.0000 - angle_coeff @angle:c3-sy-ca harmonic 60.74 103.86 # SOURCE4 54 0.3180 - angle_coeff @angle:c3-sy-cc harmonic 61.24 102.19 # SOURCE4 12 1.5324 - angle_coeff @angle:c3-sy-ce harmonic 60.79 103.81 # SOURCE3 3 0.3368 - angle_coeff @angle:c3-sy-cf harmonic 60.79 103.81 # SOURCE3 3 same_as_c3-sy-ce - angle_coeff @angle:c3-sy-ne harmonic 63.01 103.12 # SOURCE3 5 4.1882 - angle_coeff @angle:c3-sy-nf harmonic 63.01 103.12 # SOURCE3 5 same_as_c3-sy-ne - angle_coeff @angle:c3-sy-o harmonic 65.97 108.48 # SOURCE3 62 0.8576 - angle_coeff @angle:c3-sy-pe harmonic 71.79 106.03 # SOURCE3 6 2.6117 - angle_coeff @angle:c3-sy-pf harmonic 71.79 106.03 # SOURCE3 6 same_as_c3-sy-pe - angle_coeff @angle:c3-sy-px harmonic 71.71 103.62 # SOURCE3 3 0.7078 - angle_coeff @angle:c3-sy-py harmonic 73.48 103.39 # SOURCE3 3 0.4563 - angle_coeff @angle:c3-sy-sx harmonic 56.27 104.64 # SOURCE3 3 4.6276 - angle_coeff @angle:c3-sy-sy harmonic 57.43 100.78 # SOURCE3 4 1.1633 - angle_coeff @angle:ca-sy-ca harmonic 60.65 104.04 # SOURCE4 25 2.0762 - angle_coeff @angle:ca-sy-cc harmonic 60.36 105.09 # SOURCE4 5 0.3628 - angle_coeff @angle:ca-sy-n3 harmonic 64.10 102.48 # SOURCE4 180 1.0802 - angle_coeff @angle:ca-sy-n harmonic 62.89 105.45 # SOURCE4 51 1.1497 - angle_coeff @angle:ca-sy-ne harmonic 62.86 103.47 # SOURCE4 11 1.6071 - angle_coeff @angle:ca-sy-nh harmonic 62.86 105.59 # SOURCE4 78 1.5805 - angle_coeff @angle:ca-sy-o harmonic 65.84 108.73 # SOURCE3 26 1.2638 - angle_coeff @angle:ca-sy-oh harmonic 65.64 101.25 # SOURCE4 23 0.9100 - angle_coeff @angle:ca-sy-os harmonic 67.64 92.98 # SOURCE3 1 0.0000 - angle_coeff @angle:c-sy-c3 harmonic 60.09 101.25 # SOURCE3 3 1.1850 - angle_coeff @angle:c-sy-c harmonic 59.23 99.81 # SOURCE3 1 0.0000 - angle_coeff @angle:cc-sy-n3 harmonic 64.10 102.54 # CORR 30 - angle_coeff @angle:cc-sy-o harmonic 66.17 107.71 # CORR 100 - angle_coeff @angle:cd-sy-n3 harmonic 64.10 102.54 # CORR 30 - angle_coeff @angle:cd-sy-nh harmonic 65.53 97.20 # SOURCE4 6 0.2429 - angle_coeff @angle:cd-sy-o harmonic 66.17 107.71 # CORR 100 - angle_coeff @angle:ce-sy-ce harmonic 61.09 102.78 # SOURCE3 1 0.0000 - angle_coeff @angle:ce-sy-o harmonic 66.35 107.25 # SOURCE3 10 0.5477 - angle_coeff @angle:cf-sy-cf harmonic 61.09 102.78 # SOURCE3 1 same_as_ce-sy-ce - angle_coeff @angle:cf-sy-o harmonic 66.35 107.25 # SOURCE3 10 same_as_ce-sy-o - angle_coeff @angle:c-sy-o harmonic 64.07 107.23 # SOURCE3 10 0.8425 - angle_coeff @angle:f-sy-o harmonic 63.64 105.60 # SOURCE4 7 0.2000 - angle_coeff @angle:n2-sy-o harmonic 61.16 123.53 # SOURCE4 6 1.2388 - angle_coeff @angle:n3-sy-ne harmonic 66.36 102.40 # SOURCE4 5 1.3390 - angle_coeff @angle:n3-sy-o harmonic 70.45 107.11 # SOURCE4 375 1.1257 - angle_coeff @angle:na-sy-na harmonic 67.74 98.04 # SOURCE3 1 - angle_coeff @angle:nc-sy-nc harmonic 75.24 98.04 # SOURCE3 2 - angle_coeff @angle:nd-sy-nd harmonic 75.24 98.04 # SOURCE3 2 - angle_coeff @angle:ne-sy-ne harmonic 66.58 98.62 # SOURCE3 1 0.0000 - angle_coeff @angle:ne-sy-o harmonic 68.89 107.06 # SOURCE3 14 2.2705 - angle_coeff @angle:nf-sy-nf harmonic 66.58 98.62 # SOURCE3 1 same_as_ne-sy-ne - angle_coeff @angle:nf-sy-o harmonic 68.89 107.06 # SOURCE3 14 same_as_ne-sy-o - angle_coeff @angle:nh-sy-o harmonic 70.18 106.38 # SOURCE4 123 1.6517 - angle_coeff @angle:n-sy-o harmonic 69.79 107.50 # SOURCE4 61 1.8720 - angle_coeff @angle:o-sy-o harmonic 72.40 121.88 # SOURCE3 46 0.9495 - angle_coeff @angle:o-sy-oh harmonic 72.26 106.93 # SOURCE3 8 0.7424 - angle_coeff @angle:o-sy-os harmonic 70.39 108.31 # SOURCE4 7 0.1222 - angle_coeff @angle:o-sy-pe harmonic 75.40 106.90 # SOURCE3 12 1.4524 - angle_coeff @angle:o-sy-pf harmonic 75.40 106.90 # SOURCE3 12 same_as_o-sy-pe - angle_coeff @angle:o-sy-px harmonic 74.45 106.17 # SOURCE3 6 0.7059 - angle_coeff @angle:o-sy-py harmonic 76.54 106.67 # SOURCE3 10 0.6478 - angle_coeff @angle:o-sy-sx harmonic 58.62 106.33 # SOURCE3 10 2.0456 - angle_coeff @angle:o-sy-sy harmonic 58.79 106.19 # SOURCE3 12 0.1754 - angle_coeff @angle:py-sy-py harmonic 92.79 104.49 # SOURCE3 1 0.0000 - angle_coeff @angle:sx-sy-sx harmonic 56.74 101.99 # SOURCE3 1 0.0000 - angle_coeff @angle:sy-sy-sy harmonic 56.50 103.29 # SOURCE3 1 0.0000 - angle_coeff @angle:c2-c1-cf harmonic 58.18 179.01 # NEW 6 - angle_coeff @angle:c3-c1-ch harmonic 55.79 178.52 # NEW 39 - angle_coeff @angle:nf-c1-s harmonic 57.59 175.81 # NEW 8 - angle_coeff @angle:br-c2-cf harmonic 63.21 121.59 # NEW 7 - angle_coeff @angle:cd-c2-h4 harmonic 49.19 120.33 # NEW 7 - angle_coeff @angle:cd-c2-nh harmonic 69.46 122.96 # NEW 10 - angle_coeff @angle:cd-c2-o harmonic 72.80 123.59 # NEW 6 - angle_coeff @angle:cf-c2-cl harmonic 58.06 123.90 # NEW 11 - angle_coeff @angle:cf-c2-h4 harmonic 49.38 122.29 # NEW 75 - angle_coeff @angle:cf-c2-na harmonic 68.82 123.71 # NEW 6 - angle_coeff @angle:cf-c2-nh harmonic 70.64 120.72 # NEW 93 - angle_coeff @angle:cf-c2-no harmonic 68.45 119.65 # NEW 5 - angle_coeff @angle:cf-c2-o harmonic 73.66 123.08 # NEW 5 - angle_coeff @angle:cf-c2-oh harmonic 70.90 123.27 # NEW 42 - angle_coeff @angle:cf-c2-os harmonic 70.47 122.52 # NEW 51 - angle_coeff @angle:h4-c2-nf harmonic 52.87 119.63 # NEW 10 - angle_coeff @angle:h5-c2-nf harmonic 52.76 119.62 # NEW 17 - angle_coeff @angle:nf-c2-os harmonic 74.86 118.76 # NEW 5 - angle_coeff @angle:nf-c2-ss harmonic 65.41 120.06 # NEW 9 - angle_coeff @angle:n-c2-nf harmonic 70.89 125.38 # NEW 10 - angle_coeff @angle:ca-c3-cf harmonic 63.81 112.33 # NEW 51 - angle_coeff @angle:cd-c3-cx harmonic 63.85 112.55 # NEW 5 - angle_coeff @angle:c-c3-cf harmonic 64.02 111.98 # NEW 16 - angle_coeff @angle:cd-c3-hx harmonic 47.17 111.02 # NEW 9 - angle_coeff @angle:cd-c3-n2 harmonic 66.85 110.47 # NEW 11 - angle_coeff @angle:cd-c3-n4 harmonic 64.88 115.58 # NEW 6 - angle_coeff @angle:cd-c3-na harmonic 66.43 113.39 # NEW 8 - angle_coeff @angle:cd-c3-p5 harmonic 76.89 116.23 # NEW 6 - angle_coeff @angle:cf-c3-cf harmonic 64.24 111.44 # NEW 18 - angle_coeff @angle:cf-c3-n harmonic 67.09 110.41 # NEW 6 - angle_coeff @angle:cf-c3-oh harmonic 68.00 111.05 # NEW 17 - angle_coeff @angle:cf-c3-os harmonic 68.64 108.10 # NEW 16 - angle_coeff @angle:cf-c3-ss harmonic 61.87 111.10 # NEW 7 - angle_coeff @angle:cd-ca-cq harmonic 64.63 124.30 # NEW 10 - angle_coeff @angle:cf-ca-na harmonic 67.44 119.85 # NEW 9 - angle_coeff @angle:ch-ca-cq harmonic 65.26 121.53 # NEW 12 - angle_coeff @angle:cl-ca-cq harmonic 58.19 120.31 # NEW 18 - angle_coeff @angle:cq-ca-f harmonic 67.10 119.39 # NEW 16 - angle_coeff @angle:cq-ca-h4 harmonic 48.15 120.03 # NEW 27 - angle_coeff @angle:cq-ca-na harmonic 72.91 108.79 # NEW 165 - angle_coeff @angle:cq-ca-nb harmonic 68.56 123.72 # NEW 50 - angle_coeff @angle:cq-ca-nh harmonic 68.66 121.52 # NEW 11 - angle_coeff @angle:cq-ca-oh harmonic 69.26 120.96 # NEW 12 - angle_coeff @angle:cq-ca-ss harmonic 63.87 112.75 # NEW 8 - angle_coeff @angle:ca-c-nf harmonic 67.74 114.39 # NEW 5 - angle_coeff @angle:br-cd-c harmonic 63.98 115.68 # NEW 8 - angle_coeff @angle:br-cd-cd harmonic 61.82 124.89 # NEW 8 - angle_coeff @angle:br-cd-cc harmonic 62.26 124.56 # NEW 32 - angle_coeff @angle:br-cd-na harmonic 64.60 121.42 # NEW 6 - angle_coeff @angle:ca-cd-cf harmonic 62.51 127.87 # NEW 11 - angle_coeff @angle:ca-cd-nh harmonic 67.46 122.45 # NEW 9 - angle_coeff @angle:cd-c-cf harmonic 64.64 115.68 # NEW 6 - angle_coeff @angle:cd-cd-f harmonic 66.35 119.41 # NEW 7 - angle_coeff @angle:c-cd-ch harmonic 64.98 118.14 # NEW 7 - angle_coeff @angle:cd-cd-sy harmonic 59.22 128.36 # NEW 8 - angle_coeff @angle:cc-cd-f harmonic 67.42 121.08 # NEW 28 - angle_coeff @angle:cc-cd-no harmonic 65.78 128.95 # NEW 117 - angle_coeff @angle:c-cd-f harmonic 66.16 116.87 # NEW 16 - angle_coeff @angle:ch-cd-na harmonic 67.51 122.35 # NEW 5 - angle_coeff @angle:ch-cd-ss harmonic 62.33 120.70 # NEW 12 - angle_coeff @angle:cd-c-h4 harmonic 47.13 115.45 # NEW 5 - angle_coeff @angle:cl-cd-na harmonic 59.37 121.61 # NEW 12 - angle_coeff @angle:cl-cd-ss harmonic 58.09 119.85 # NEW 11 - angle_coeff @angle:c-cd-nf harmonic 67.11 119.88 # NEW 6 - angle_coeff @angle:cd-c-s harmonic 61.67 127.94 # NEW 12 - angle_coeff @angle:cd-c-ss harmonic 63.47 112.52 # NEW 10 - angle_coeff @angle:cx-cd-nc harmonic 65.61 127.75 # NEW 12 - angle_coeff @angle:cx-cd-os harmonic 67.94 118.08 # NEW 10 - angle_coeff @angle:cc-c-cx harmonic 63.88 117.46 # NEW 13 - angle_coeff @angle:cc-c-nc harmonic 68.65 113.75 # NEW 14 - angle_coeff @angle:cf-c-cx harmonic 63.95 116.25 # NEW 6 - angle_coeff @angle:cf-c-h4 harmonic 46.93 114.88 # NEW 19 - angle_coeff @angle:cf-c-ss harmonic 63.94 110.39 # NEW 5 - angle_coeff @angle:na-cd-no harmonic 68.48 124.90 # NEW 48 - angle_coeff @angle:na-cd-oh harmonic 73.25 117.26 # NEW 16 - angle_coeff @angle:na-cd-sx harmonic 63.25 117.04 # NEW 13 - angle_coeff @angle:na-cd-sy harmonic 63.13 120.55 # NEW 7 - angle_coeff @angle:nd-cd-no harmonic 69.31 121.54 # NEW 7 - angle_coeff @angle:nc-cd-nc harmonic 70.88 128.17 # NEW 7 - angle_coeff @angle:nc-cd-nf harmonic 69.29 129.66 # NEW 7 - angle_coeff @angle:nc-cd-no harmonic 69.90 122.68 # NEW 16 - angle_coeff @angle:nc-cd-sh harmonic 62.75 124.92 # NEW 5 - angle_coeff @angle:nc-cd-sx harmonic 60.81 127.60 # NEW 14 - angle_coeff @angle:nc-cd-sy harmonic 62.75 123.08 # NEW 13 - angle_coeff @angle:nf-cd-ss harmonic 65.39 116.99 # NEW 7 - angle_coeff @angle:n-cd-n2 harmonic 74.78 114.48 # NEW 15 - angle_coeff @angle:no-cd-os harmonic 71.01 117.59 # NEW 62 - angle_coeff @angle:no-cd-ss harmonic 63.76 121.10 # NEW 10 - angle_coeff @angle:ca-cc-cf harmonic 65.09 125.10 # NEW 9 - angle_coeff @angle:ca-cc-na harmonic 67.03 123.45 # NEW 39 - angle_coeff @angle:cd-cc-cg harmonic 64.92 126.05 # NEW 30 - angle_coeff @angle:cd-cc-cy harmonic 63.93 122.13 # NEW 10 - angle_coeff @angle:cd-cc-nd harmonic 69.42 123.82 # NEW 14 - angle_coeff @angle:cc-cc-cy harmonic 63.17 120.93 # NEW 6 - angle_coeff @angle:cf-cc-nc harmonic 68.22 124.90 # NEW 5 - angle_coeff @angle:c-cc-h4 harmonic 46.77 118.19 # NEW 8 - angle_coeff @angle:na-cc-nh harmonic 72.43 116.98 # NEW 46 - angle_coeff @angle:na-cc-ss harmonic 67.07 111.46 # NEW 20 - angle_coeff @angle:nc-cc-nc harmonic 69.47 125.58 # NEW 13 - angle_coeff @angle:oh-cc-os harmonic 75.54 111.61 # NEW 6 - angle_coeff @angle:c2-cf-cl harmonic 57.87 119.51 # NEW 24 - angle_coeff @angle:c2-cf-h4 harmonic 48.64 125.58 # NEW 11 - angle_coeff @angle:c2-cf-n1 harmonic 72.67 117.85 # NEW 7 - angle_coeff @angle:c2-cf-na harmonic 69.29 119.19 # NEW 5 - angle_coeff @angle:c2-cf-oh harmonic 70.32 123.78 # NEW 10 - angle_coeff @angle:c3-cf-ch harmonic 63.79 118.48 # NEW 8 - angle_coeff @angle:c3-cf-ne harmonic 67.26 120.75 # NEW 6 - angle_coeff @angle:c3-cf-nh harmonic 65.76 119.90 # NEW 5 - angle_coeff @angle:ca-cf-cf harmonic 63.84 119.62 # NEW 14 - angle_coeff @angle:ca-cf-cl harmonic 57.99 114.22 # NEW 6 - angle_coeff @angle:ca-cf-h4 harmonic 46.71 116.86 # NEW 74 - angle_coeff @angle:ca-cf-nh harmonic 67.87 115.51 # NEW 93 - angle_coeff @angle:ca-cf-os harmonic 68.60 115.58 # NEW 8 - angle_coeff @angle:ca-cf-ss harmonic 61.21 117.73 # NEW 5 - angle_coeff @angle:c-cf-ca harmonic 63.79 117.98 # NEW 8 - angle_coeff @angle:cd-cf-cc harmonic 63.28 130.36 # NEW 5 - angle_coeff @angle:c-cf-cf harmonic 63.46 120.89 # NEW 16 - angle_coeff @angle:c-cf-ch harmonic 64.57 118.32 # NEW 15 - angle_coeff @angle:cd-cf-h4 harmonic 47.52 115.40 # NEW 29 - angle_coeff @angle:c-cf-cl harmonic 57.67 115.40 # NEW 6 - angle_coeff @angle:cd-cf-nh harmonic 67.31 119.17 # NEW 8 - angle_coeff @angle:c-cf-cy harmonic 72.72 88.22 # NEW 19 - angle_coeff @angle:cf-cf-cl harmonic 57.29 117.93 # NEW 12 - angle_coeff @angle:cf-cf-oh harmonic 69.29 116.89 # NEW 11 - angle_coeff @angle:ce-cf-cy harmonic 60.53 137.74 # NEW 13 - angle_coeff @angle:ce-cf-h4 harmonic 49.02 123.76 # NEW 5 - angle_coeff @angle:ce-cf-n1 harmonic 72.03 120.03 # NEW 6 - angle_coeff @angle:ce-cf-nh harmonic 69.48 121.52 # NEW 12 - angle_coeff @angle:ch-cf-n2 harmonic 69.59 121.43 # NEW 6 - angle_coeff @angle:c-cf-oh harmonic 68.34 117.92 # NEW 5 - angle_coeff @angle:c-cf-os harmonic 69.09 113.78 # NEW 21 - angle_coeff @angle:h4-cf-n1 harmonic 52.58 116.36 # NEW 7 - angle_coeff @angle:h4-cf-nf harmonic 49.72 115.81 # NEW 7 - angle_coeff @angle:n2-cf-os harmonic 74.58 118.13 # NEW 6 - angle_coeff @angle:n2-cf-ss harmonic 64.40 117.23 # NEW 6 - angle_coeff @angle:nf-cf-nh harmonic 71.89 112.91 # NEW 12 - angle_coeff @angle:ne-cf-nh harmonic 73.31 118.13 # NEW 6 - angle_coeff @angle:ca-ce-cd harmonic 62.70 130.80 # NEW 12 - angle_coeff @angle:c-ce-cc harmonic 64.25 117.76 # NEW 10 - angle_coeff @angle:c-ce-n2 harmonic 70.16 114.88 # NEW 5 - angle_coeff @angle:h4-ce-nf harmonic 52.29 120.21 # NEW 6 - angle_coeff @angle:c1-ch-cd harmonic 56.97 178.60 # NEW 6 - angle_coeff @angle:ch-cg-cg harmonic 58.68 179.67 # NEW 7 - angle_coeff @angle:n-c-nf harmonic 74.43 110.37 # NEW 10 - angle_coeff @angle:ca-cq-na harmonic 68.78 119.43 # NEW 21 - angle_coeff @angle:nb-cq-nb harmonic 71.31 125.72 # NEW 5 - angle_coeff @angle:cd-cx-hc harmonic 47.37 113.84 # NEW 15 - angle_coeff @angle:cf-cy-h2 harmonic 45.50 117.25 # NEW 17 - angle_coeff @angle:cf-cy-n harmonic 74.69 88.02 # NEW 14 - angle_coeff @angle:cf-cy-ss harmonic 58.47 121.33 # NEW 13 - angle_coeff @angle:cd-n2-na harmonic 73.01 108.92 # NEW 9 - angle_coeff @angle:cd-n2-nh harmonic 70.37 118.47 # NEW 6 - angle_coeff @angle:c3-n4-cd harmonic 62.84 111.09 # NEW 7 - angle_coeff @angle:c3-na-cq harmonic 63.76 119.46 # NEW 7 - angle_coeff @angle:ca-na-cq harmonic 65.88 120.96 # NEW 20 - angle_coeff @angle:cd-na-cf harmonic 63.05 126.61 # NEW 8 - angle_coeff @angle:cq-nb-nb harmonic 68.79 121.11 # NEW 12 - angle_coeff @angle:c-n-cf harmonic 62.21 131.83 # NEW 146 - angle_coeff @angle:ca-nc-nd harmonic 73.55 108.41 # NEW 9 - angle_coeff @angle:c2-nf-ch harmonic 68.36 123.58 # NEW 12 - angle_coeff @angle:c-nf-sy harmonic 61.66 116.05 # NEW 6 - angle_coeff @angle:c3-nh-ce harmonic 63.47 119.92 # NEW 20 - angle_coeff @angle:cd-nh-n2 harmonic 68.23 119.66 # NEW 5 - angle_coeff @angle:cd-nh-sy harmonic 61.22 122.91 # NEW 23 - angle_coeff @angle:cf-nh-sy harmonic 63.58 112.97 # NEW 7 - angle_coeff @angle:hn-n-nd harmonic 50.74 115.24 # NEW 10 - angle_coeff @angle:cd-no-o harmonic 70.34 117.52 # NEW 198 - angle_coeff @angle:n3-py-nf harmonic 41.93 108.44 # NEW 12 - angle_coeff @angle:cd-s6-o harmonic 70.23 103.63 # NEW 9 - angle_coeff @angle:cd-sh-hs harmonic 46.41 95.38 # NEW 8 - angle_coeff @angle:c-ss-cd harmonic 65.61 92.43 # NEW 14 - angle_coeff @angle:c3-sx-cd harmonic 62.52 95.11 # NEW 17 - angle_coeff @angle:cd-sx-o harmonic 65.92 104.49 # NEW 17 - angle_coeff @angle:c3-sy-cd harmonic 61.24 102.19 # NEW 12 - angle_coeff @angle:ca-sy-cd harmonic 60.36 105.09 # NEW 5 - angle_coeff @angle:ca-sy-nf harmonic 62.86 103.47 # NEW 11 - angle_coeff @angle:cc-sy-nh harmonic 65.53 97.20 # NEW 6 - angle_coeff @angle:n3-sy-nf harmonic 66.36 102.40 # NEW 5 - } # (end of angle_coeffs) - - write_once("Data Angles By Type") { - @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw - @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow - @angle:br-c1-br @atom:br @atom:c1 @atom:br - @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1 - @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1 - @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2 - @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3 - @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca - @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl - @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f - @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha - @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc - @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i - @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1 - @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2 - @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3 - @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4 - @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n - @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na - @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh - @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no - @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o - @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh - @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os - @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2 - @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3 - @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4 - @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5 - @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4 - @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6 - @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s - @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh - @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss - @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2 - @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce - @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1 - @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o - @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2 - @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3 - @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg - 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@angle:c2-c2-na @atom:c2 @atom:c2 @atom:na - @angle:c2-c2-nh @atom:c2 @atom:c2 @atom:nh - @angle:c2-c2-no @atom:c2 @atom:c2 @atom:no - @angle:c2-c2-o @atom:c2 @atom:c2 @atom:o - @angle:c2-c2-oh @atom:c2 @atom:c2 @atom:oh - @angle:c2-c2-os @atom:c2 @atom:c2 @atom:os - @angle:c2-c2-p2 @atom:c2 @atom:c2 @atom:p2 - @angle:c2-c2-p3 @atom:c2 @atom:c2 @atom:p3 - @angle:c2-c2-p4 @atom:c2 @atom:c2 @atom:p4 - @angle:c2-c2-p5 @atom:c2 @atom:c2 @atom:p5 - @angle:c2-c2-s4 @atom:c2 @atom:c2 @atom:s4 - @angle:c2-c2-s6 @atom:c2 @atom:c2 @atom:s6 - @angle:c2-c2-s @atom:c2 @atom:c2 @atom:s - @angle:c2-c2-sh @atom:c2 @atom:c2 @atom:sh - @angle:c2-c2-ss @atom:c2 @atom:c2 @atom:ss - @angle:c3-c2-c3 @atom:c3 @atom:c2 @atom:c3 - @angle:c3-c2-cc @atom:c3 @atom:c2 @atom:cc - @angle:c3-c2-cd @atom:c3 @atom:c2 @atom:cd - @angle:c3-c2-ce @atom:c3 @atom:c2 @atom:ce - @angle:c3-c2-cf @atom:c3 @atom:c2 @atom:cf - @angle:c3-c2-h4 @atom:c3 @atom:c2 @atom:h4 - @angle:c3-c2-ha @atom:c3 @atom:c2 @atom:ha - @angle:c3-c2-hc @atom:c3 @atom:c2 @atom:hc - 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@angle:ce-c2-h4 @atom:ce @atom:c2 @atom:h4 - @angle:ce-c2-ha @atom:ce @atom:c2 @atom:ha - @angle:ce-c2-na @atom:ce @atom:c2 @atom:na - @angle:ce-c2-nh @atom:ce @atom:c2 @atom:nh - @angle:ce-c2-no @atom:ce @atom:c2 @atom:no - @angle:ce-c2-o @atom:ce @atom:c2 @atom:o - @angle:ce-c2-oh @atom:ce @atom:c2 @atom:oh - @angle:ce-c2-os @atom:ce @atom:c2 @atom:os - @angle:cf-c2-ha @atom:cf @atom:c2 @atom:ha - @angle:c-c2-ha @atom:c @atom:c2 @atom:ha - @angle:c-c2-hc @atom:c @atom:c2 @atom:hc - @angle:cl-c2-cl @atom:cl @atom:c2 @atom:cl - @angle:cl-c2-h4 @atom:cl @atom:c2 @atom:h4 - @angle:cl-c2-ha @atom:cl @atom:c2 @atom:ha - @angle:cx-c2-ha @atom:cx @atom:c2 @atom:ha - @angle:f-c2-f @atom:f @atom:c2 @atom:f - @angle:f-c2-ha @atom:f @atom:c2 @atom:ha - @angle:h4-c2-n2 @atom:h4 @atom:c2 @atom:n2 - @angle:h4-c2-n @atom:h4 @atom:c2 @atom:n - @angle:h4-c2-na @atom:h4 @atom:c2 @atom:na - @angle:h4-c2-ne @atom:h4 @atom:c2 @atom:ne - @angle:h4-c2-nh @atom:h4 @atom:c2 @atom:nh - @angle:h4-c2-no @atom:h4 @atom:c2 @atom:no - 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@angle:ha-c2-pe @atom:ha @atom:c2 @atom:pe - @angle:ha-c2-pf @atom:ha @atom:c2 @atom:pf - @angle:ha-c2-s2 @atom:ha @atom:c2 @atom:s2 - @angle:ha-c2-s4 @atom:ha @atom:c2 @atom:s4 - @angle:ha-c2-s @atom:ha @atom:c2 @atom:s - @angle:ha-c2-s6 @atom:ha @atom:c2 @atom:s6 - @angle:ha-c2-sh @atom:ha @atom:c2 @atom:sh - @angle:ha-c2-ss @atom:ha @atom:c2 @atom:ss - @angle:hc-c2-hc @atom:hc @atom:c2 @atom:hc - @angle:hc-c2-n2 @atom:hc @atom:c2 @atom:n2 - @angle:hc-c2-n @atom:hc @atom:c2 @atom:n - @angle:hc-c2-na @atom:hc @atom:c2 @atom:na - @angle:hc-c2-nh @atom:hc @atom:c2 @atom:nh - @angle:hc-c2-no @atom:hc @atom:c2 @atom:no - @angle:hc-c2-oh @atom:hc @atom:c2 @atom:oh - @angle:hc-c2-os @atom:hc @atom:c2 @atom:os - @angle:hc-c2-p3 @atom:hc @atom:c2 @atom:p3 - @angle:hc-c2-p5 @atom:hc @atom:c2 @atom:p5 - @angle:hc-c2-s4 @atom:hc @atom:c2 @atom:s4 - @angle:hc-c2-s6 @atom:hc @atom:c2 @atom:s6 - @angle:hc-c2-sh @atom:hc @atom:c2 @atom:sh - @angle:hc-c2-ss @atom:hc @atom:c2 @atom:ss - @angle:hx-c2-n4 @atom:hx @atom:c2 @atom:n4 - @angle:i-c2-i @atom:i @atom:c2 @atom:i - @angle:n1-c2-n1 @atom:n1 @atom:c2 @atom:n1 - @angle:n2-c2-n2 @atom:n2 @atom:c2 @atom:n2 - @angle:n2-c2-n4 @atom:n2 @atom:c2 @atom:n4 - @angle:n2-c2-na @atom:n2 @atom:c2 @atom:na - @angle:n2-c2-nh @atom:n2 @atom:c2 @atom:nh - @angle:n2-c2-oh @atom:n2 @atom:c2 @atom:oh - @angle:n2-c2-os @atom:n2 @atom:c2 @atom:os - @angle:n2-c2-ss @atom:n2 @atom:c2 @atom:ss - @angle:n3-c2-n3 @atom:n3 @atom:c2 @atom:n3 - @angle:n4-c2-n4 @atom:n4 @atom:c2 @atom:n4 - @angle:n4-c2-ss @atom:n4 @atom:c2 @atom:ss - @angle:na-c2-na @atom:na @atom:c2 @atom:na - @angle:ne-c2-nh @atom:ne @atom:c2 @atom:nh - @angle:ne-c2-os @atom:ne @atom:c2 @atom:os - @angle:ne-c2-ss @atom:ne @atom:c2 @atom:ss - @angle:nf-c2-nh @atom:nf @atom:c2 @atom:nh - @angle:nh-c2-nh @atom:nh @atom:c2 @atom:nh - @angle:nh-c2-oh @atom:nh @atom:c2 @atom:oh - @angle:nh-c2-os @atom:nh @atom:c2 @atom:os - @angle:nh-c2-ss @atom:nh @atom:c2 @atom:ss - @angle:n-c2-n2 @atom:n @atom:c2 @atom:n2 - @angle:n-c2-n @atom:n @atom:c2 @atom:n - @angle:n-c2-na @atom:n @atom:c2 @atom:na - @angle:n-c2-ne @atom:n @atom:c2 @atom:ne - @angle:n-c2-nh @atom:n @atom:c2 @atom:nh - @angle:no-c2-no @atom:no @atom:c2 @atom:no - @angle:n-c2-ss @atom:n @atom:c2 @atom:ss - @angle:oh-c2-oh @atom:oh @atom:c2 @atom:oh - @angle:o-c2-o @atom:o @atom:c2 @atom:o - @angle:o-c2-oh @atom:o @atom:c2 @atom:oh - @angle:o-c2-s @atom:o @atom:c2 @atom:s - @angle:os-c2-os @atom:os @atom:c2 @atom:os - @angle:p2-c2-p2 @atom:p2 @atom:c2 @atom:p2 - @angle:p3-c2-p3 @atom:p3 @atom:c2 @atom:p3 - @angle:p5-c2-p5 @atom:p5 @atom:c2 @atom:p5 - @angle:s4-c2-s4 @atom:s4 @atom:c2 @atom:s4 - @angle:s4-c2-s6 @atom:s4 @atom:c2 @atom:s6 - @angle:s6-c2-s6 @atom:s6 @atom:c2 @atom:s6 - @angle:sh-c2-sh @atom:sh @atom:c2 @atom:sh - @angle:sh-c2-ss @atom:sh @atom:c2 @atom:ss - @angle:s-c2-s @atom:s @atom:c2 @atom:s - @angle:ss-c2-ss @atom:ss @atom:c2 @atom:ss - @angle:br-c3-br @atom:br @atom:c3 @atom:br - @angle:br-c3-c1 @atom:br @atom:c3 @atom:c1 - @angle:br-c3-c3 @atom:br @atom:c3 @atom:c3 - 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@angle:cf-c-h4 @atom:cf @atom:c @atom:h4 - @angle:cf-c-ss @atom:cf @atom:c @atom:ss - @angle:na-cd-no @atom:na @atom:cd @atom:no - @angle:na-cd-oh @atom:na @atom:cd @atom:oh - @angle:na-cd-sx @atom:na @atom:cd @atom:sx - @angle:na-cd-sy @atom:na @atom:cd @atom:sy - @angle:nd-cd-no @atom:nd @atom:cd @atom:no - @angle:nc-cd-nc @atom:nc @atom:cd @atom:nc - @angle:nc-cd-nf @atom:nc @atom:cd @atom:nf - @angle:nc-cd-no @atom:nc @atom:cd @atom:no - @angle:nc-cd-sh @atom:nc @atom:cd @atom:sh - @angle:nc-cd-sx @atom:nc @atom:cd @atom:sx - @angle:nc-cd-sy @atom:nc @atom:cd @atom:sy - @angle:nf-cd-ss @atom:nf @atom:cd @atom:ss - @angle:n-cd-n2 @atom:n @atom:cd @atom:n2 - @angle:no-cd-os @atom:no @atom:cd @atom:os - @angle:no-cd-ss @atom:no @atom:cd @atom:ss - @angle:ca-cc-cf @atom:ca @atom:cc @atom:cf - @angle:ca-cc-na @atom:ca @atom:cc @atom:na - @angle:cd-cc-cg @atom:cd @atom:cc @atom:cg - @angle:cd-cc-cy @atom:cd @atom:cc @atom:cy - @angle:cd-cc-nd @atom:cd @atom:cc @atom:nd - @angle:cc-cc-cy @atom:cc @atom:cc @atom:cy - @angle:cf-cc-nc @atom:cf @atom:cc @atom:nc - @angle:c-cc-h4 @atom:c @atom:cc @atom:h4 - @angle:na-cc-nh @atom:na @atom:cc @atom:nh - @angle:na-cc-ss @atom:na @atom:cc @atom:ss - @angle:nc-cc-nc @atom:nc @atom:cc @atom:nc - @angle:oh-cc-os @atom:oh @atom:cc @atom:os - @angle:c2-cf-cl @atom:c2 @atom:cf @atom:cl - @angle:c2-cf-h4 @atom:c2 @atom:cf @atom:h4 - @angle:c2-cf-n1 @atom:c2 @atom:cf @atom:n1 - @angle:c2-cf-na @atom:c2 @atom:cf @atom:na - @angle:c2-cf-oh @atom:c2 @atom:cf @atom:oh - @angle:c3-cf-ch @atom:c3 @atom:cf @atom:ch - @angle:c3-cf-ne @atom:c3 @atom:cf @atom:ne - @angle:c3-cf-nh @atom:c3 @atom:cf @atom:nh - @angle:ca-cf-cf @atom:ca @atom:cf @atom:cf - @angle:ca-cf-cl @atom:ca @atom:cf @atom:cl - @angle:ca-cf-h4 @atom:ca @atom:cf @atom:h4 - @angle:ca-cf-nh @atom:ca @atom:cf @atom:nh - @angle:ca-cf-os @atom:ca @atom:cf @atom:os - @angle:ca-cf-ss @atom:ca @atom:cf @atom:ss - @angle:c-cf-ca @atom:c @atom:cf @atom:ca - @angle:cd-cf-cc @atom:cd @atom:cf @atom:cc - @angle:c-cf-cf @atom:c @atom:cf @atom:cf - @angle:c-cf-ch @atom:c @atom:cf @atom:ch - @angle:cd-cf-h4 @atom:cd @atom:cf @atom:h4 - @angle:c-cf-cl @atom:c @atom:cf @atom:cl - @angle:cd-cf-nh @atom:cd @atom:cf @atom:nh - @angle:c-cf-cy @atom:c @atom:cf @atom:cy - @angle:cf-cf-cl @atom:cf @atom:cf @atom:cl - @angle:cf-cf-oh @atom:cf @atom:cf @atom:oh - @angle:ce-cf-cy @atom:ce @atom:cf @atom:cy - @angle:ce-cf-h4 @atom:ce @atom:cf @atom:h4 - @angle:ce-cf-n1 @atom:ce @atom:cf @atom:n1 - @angle:ce-cf-nh @atom:ce @atom:cf @atom:nh - @angle:ch-cf-n2 @atom:ch @atom:cf @atom:n2 - @angle:c-cf-oh @atom:c @atom:cf @atom:oh - @angle:c-cf-os @atom:c @atom:cf @atom:os - @angle:h4-cf-n1 @atom:h4 @atom:cf @atom:n1 - @angle:h4-cf-nf @atom:h4 @atom:cf @atom:nf - @angle:n2-cf-os @atom:n2 @atom:cf @atom:os - @angle:n2-cf-ss @atom:n2 @atom:cf @atom:ss - @angle:nf-cf-nh @atom:nf @atom:cf @atom:nh - @angle:ne-cf-nh @atom:ne @atom:cf @atom:nh - @angle:ca-ce-cd @atom:ca @atom:ce @atom:cd - @angle:c-ce-cc @atom:c @atom:ce @atom:cc - @angle:c-ce-n2 @atom:c @atom:ce @atom:n2 - @angle:h4-ce-nf @atom:h4 @atom:ce @atom:nf - @angle:c1-ch-cd @atom:c1 @atom:ch @atom:cd - @angle:ch-cg-cg @atom:ch @atom:cg @atom:cg - @angle:n-c-nf @atom:n @atom:c @atom:nf - @angle:ca-cq-na @atom:ca @atom:cq @atom:na - @angle:nb-cq-nb @atom:nb @atom:cq @atom:nb - @angle:cd-cx-hc @atom:cd @atom:cx @atom:hc - @angle:cf-cy-h2 @atom:cf @atom:cy @atom:h2 - @angle:cf-cy-n @atom:cf @atom:cy @atom:n - @angle:cf-cy-ss @atom:cf @atom:cy @atom:ss - @angle:cd-n2-na @atom:cd @atom:n2 @atom:na - @angle:cd-n2-nh @atom:cd @atom:n2 @atom:nh - @angle:c3-n4-cd @atom:c3 @atom:n4 @atom:cd - @angle:c3-na-cq @atom:c3 @atom:na @atom:cq - @angle:ca-na-cq @atom:ca @atom:na @atom:cq - @angle:cd-na-cf @atom:cd @atom:na @atom:cf - @angle:cq-nb-nb @atom:cq @atom:nb @atom:nb - @angle:c-n-cf @atom:c @atom:n @atom:cf - @angle:ca-nc-nd @atom:ca @atom:nc @atom:nd - @angle:c2-nf-ch @atom:c2 @atom:nf @atom:ch - @angle:c-nf-sy @atom:c @atom:nf @atom:sy - @angle:c3-nh-ce @atom:c3 @atom:nh @atom:ce - @angle:cd-nh-n2 @atom:cd @atom:nh @atom:n2 - @angle:cd-nh-sy @atom:cd @atom:nh @atom:sy - @angle:cf-nh-sy @atom:cf @atom:nh @atom:sy - @angle:hn-n-nd @atom:hn @atom:n @atom:nd - @angle:cd-no-o @atom:cd @atom:no @atom:o - @angle:n3-py-nf @atom:n3 @atom:py @atom:nf - @angle:cd-s6-o @atom:cd @atom:s6 @atom:o - @angle:cd-sh-hs @atom:cd @atom:sh @atom:hs - @angle:c-ss-cd @atom:c @atom:ss @atom:cd - @angle:c3-sx-cd @atom:c3 @atom:sx @atom:cd - @angle:cd-sx-o @atom:cd @atom:sx @atom:o - @angle:c3-sy-cd @atom:c3 @atom:sy @atom:cd - @angle:ca-sy-cd @atom:ca @atom:sy @atom:cd - @angle:ca-sy-nf @atom:ca @atom:sy @atom:nf - @angle:cc-sy-nh @atom:cc @atom:sy @atom:nh - @angle:n3-sy-nf @atom:n3 @atom:sy @atom:nf - } # (end of Angles By Type) - - write_once("In Settings") { - dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 # - dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X - dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 - dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 - dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 - dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013 - dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value - dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value - dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh) - dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X - dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X - dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X - dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 # - dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 # - dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X - dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated - dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated - dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 # - dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 # - dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 # - dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 # - dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 # - dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 # - dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 # - dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 # - dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 # - dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 # - dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 # - dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 - dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 - dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 - dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94 - dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 - dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013 - dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 # - dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99 - dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99 - dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99 - dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond - dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond - dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94 - dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94 - dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol. - dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol. - dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 # - dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 # - dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 # - dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99 - dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99 - dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond - dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond - dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 # - dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! - dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! - dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! - dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 # - dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 # - dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 # - dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! - dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! - dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! - dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 # - dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 # - dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 # - dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 # - dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 # - dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! - dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! - dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! - dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 # - dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 # - dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 # - dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! - dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! - dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! - dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 # - dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 # - dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 # - dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X - dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X - dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X - dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X - dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 # - dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 # - dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 # - dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 # - dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 # - dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 # - dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 # - dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 # - dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 # - dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 # - dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 # - dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 # - dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X - dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X - dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 # - dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 # - dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 # - dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 # - dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 # - dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 # - dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X - dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X - dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X - dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 # - dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X - dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X - dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 # - dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99 - dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X - dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 # - dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X - dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X - dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 # - dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X - dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 # - dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X - dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 # - dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 # - dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X - dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 # - dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X - dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 # - dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 # - dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 # - dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 # - dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 # - dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 # - dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 # - dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 # - dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 # - dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 # - dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 # - dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 # - dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 # - dihedral_coeff @dihedral:X-n-pf-X fourier 1 1.0 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-pd-X fourier 1 4.8 2 180.0 # - dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 # - dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 # - dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 # - dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 # - dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 # - dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 # - dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 # - dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 # - dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 # - dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 # - dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 # - dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 # - dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol - dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol - dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X - dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X - dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 # - dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 # - dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 # - dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 # - dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 # - dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 # - dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 # - dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 # - dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 # - dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 # - dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 # - dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 # - dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 # - dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 # - dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 # - dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 # - dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 # - dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 # - dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 # - dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 # - dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 # - dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond - dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond - dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 # - dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 # - dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 # - dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 # - dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 # - dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 # - dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 # - dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 # - dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # - dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # - dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 # - dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 # - dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 # - dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 # - dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 # - dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 # - dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 # - dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 # - dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 # - dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 # - dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 # - dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 # - dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 # - dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 # - dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 # - dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 # - dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 # - dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 # - dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 # - dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 # - dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 # - dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 # - dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 # - dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 # - dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 # - dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 # - dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 # - dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 # - dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 # - dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 # - dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 # - dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 # - dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 # - dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 # - dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 # - dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 # - dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 # - dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 # - dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 # - dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 # - dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 # - dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 # - dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 # - dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 # - dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 # - dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 # - dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 # - dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 # - dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 # - dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 # - dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 # - dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 # - dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 # - dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 # - dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 # - dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 # - dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 # - dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 # - dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 # - dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 # - dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 # - dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 # - dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 # - dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 # - dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 # - dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 # - dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 # - dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 # - dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 # - dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 # - dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 # - dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 # - dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 # - dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 # - dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 # - dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 # - dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 # - dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 # - dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 # - dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 # - dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 # - dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 # - dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 # - dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 # - dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 # - dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 # - dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 # - dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 # - dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 # - dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 # - dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 # - dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 # - dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 # - dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 # - dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 # - dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 # - dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 # - dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 # - dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 # - dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 # - dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 # - dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 # - dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 # - dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 # - dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 # - dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 # - dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 # - dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 # - dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 # - dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 # - dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 # - dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 # - dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 # - dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 # - dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 # - dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 # - dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 # - dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 # - dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 # - dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 # - dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 # - dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 # - dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 # - dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 # - dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 # - dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 # - dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 # - dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 # - dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 # - dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 # - dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 # - dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 # - dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 # - dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 # - dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 # - dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 # - dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 # - dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 # - dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 # - dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 # - dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 # - dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 # - dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 # - dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 # - dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 # - dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 # - dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 # - dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 # - dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 # - dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 # - dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 # - dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 # - dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 # - dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 # - dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 # - dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 # - dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 # - dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 # - dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 # - dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 # - dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 # - dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 # - dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 # - dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 # - dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 # - dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 # - dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 # - dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 # - dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 # - dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 # - dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 # - dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 # - dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 # - dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 # - dihedral_coeff @dihedral:X-cf-pe-X fourier 1 6.65 2 180.0 # NEW - dihedral_coeff @dihedral:X-nd-os-X fourier 1 4.8 2 180.0 # NEW - dihedral_coeff @dihedral:X-nd-ss-X fourier 1 4.8 2 180.0 # NEW - dihedral_coeff @dihedral:X-nf-pe-X fourier 1 5.4 2 180.0 # NEW - dihedral_coeff @dihedral:c3-c-sh-hs fourier 2 2.25 2 180.0 1.3 1 180.0 # - dihedral_coeff @dihedral:c2-c2-ss-c3 fourier 2 1.1 2 180.0 0.7 3 180.0 # - dihedral_coeff @dihedral:c2-c2-n-c fourier 2 0.65 2 180.0 1.2 1 180.0 # - dihedral_coeff @dihedral:c-n-p2-c2 fourier 2 1.0 2 180.0 1.9 1 180.0 # - dihedral_coeff @dihedral:n-c3-c-n fourier 2 1.7 1 180.0 2.0 2 180.0 # - dihedral_coeff @dihedral:c-n-c3-c fourier 2 0.85 2 180.0 0.8 1 0.0 # - dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.5 4 180.0 0.15 3 180.0 0.53 1 0.0 # phi,psi,parm94 - dihedral_coeff @dihedral:c3-c3-c-n fourier 2 0.1 4 0.0 0.07 2 0.0 # phi,psi,parm94 - dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # - dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # - dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # - dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # - dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # - dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # - dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.5 2 0.0 0.6 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:c3-n3-nh-ca fourier 2 1.9 2 0.0 1.9 3 0.0 # - dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 # - dihedral_coeff @dihedral:ca-nh-oh-ho fourier 2 1.2 1 0.0 1.5 2 0.0 # - dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.15 3 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.16 3 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.38 3 180.0 1.15 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 2 0.16 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 6.65 2 180.0 1.9 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c3-c3-n3-c3 fourier 2 0.3 3 0.0 0.48 2 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c3-c3-os-c3 fourier 2 0.383 3 0.0 0.1 2 180.0 # - dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c3-os-c3-os fourier 3 0.1 3 0.0 0.85 2 180.0 1.35 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK - dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK - dihedral_coeff @dihedral:os-c3-c3-os fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK - dihedral_coeff @dihedral:os-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK - dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK - dihedral_coeff @dihedral:f-c3-c3-f fourier 2 0.0 3 0.0 1.2 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.0 3 0.0 0.45 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.0 3 0.0 0.0 1 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 - } # (end of dihedral_coeffs) - - write_once("Data Dihedrals By Type") { - @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:* - @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:* - @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:* - @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:* - @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:* - @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:* - @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:* - @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:* - @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:* - @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:* - @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:* - @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:* - @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:* - @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:* - @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:* - @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:* - @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:* - @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:* - @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:* - @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:* - @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:* - @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* - @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* - @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:* - @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:* - @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:* - @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:* - @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:* - @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:* - @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:* - @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:* - @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:* - @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:* - @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:* - @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:* - @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:* - @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:* - @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:* - @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:* - @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:* - @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:* - @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:* - @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:* - @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:* - @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:* - @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:* - @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:* - @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:* - @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:* - @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:* - @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:* - @dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:* - @dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:* - @dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:* - @dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:* - @dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:* - @dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:* - @dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:* - @dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:* - @dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:* - @dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:* - @dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:* - @dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:* - @dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:* - @dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:* - @dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:* - @dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:* - @dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:* - @dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:* - @dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:* - @dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:* - @dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:* - @dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:* - @dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:* - @dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:* - @dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:* - @dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:* - @dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:* - @dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:* - @dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:* - @dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:* - @dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:* - @dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:* - @dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:* - @dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:* - @dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:* - @dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:* - @dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:* - @dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:* - @dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:* - @dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:* - @dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:* - @dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:* - @dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:* - @dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:* - @dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:* - @dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:* - @dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:* - @dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:* - @dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:* - @dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:* - @dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:* - @dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:* - @dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:* - @dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:* - @dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:* - @dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:* - @dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:* - @dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:* - @dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:* - @dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:* - @dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:* - @dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:* - @dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:* - @dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:* - @dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:* - @dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:* - @dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:* - @dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:* - @dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:* - @dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:* - @dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:* - @dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:* - @dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:* - @dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:* - @dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:* - @dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:* - @dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:* - @dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:* - @dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:* - @dihedral:X-c2-pd-X @atom:* @atom:c2 @atom:pd @atom:* - @dihedral:X-cc-pc-X @atom:* @atom:cc @atom:pc @atom:* - @dihedral:X-cc-pd-X @atom:* @atom:cc @atom:pd @atom:* - @dihedral:X-cd-pc-X @atom:* @atom:cd @atom:pc @atom:* - @dihedral:X-cd-pd-X @atom:* @atom:cd @atom:pd @atom:* - @dihedral:X-c2-p3-X @atom:* @atom:c2 @atom:p3 @atom:* - @dihedral:X-c2-p4-X @atom:* @atom:c2 @atom:p4 @atom:* - @dihedral:X-ce-p4-X @atom:* @atom:ce @atom:p4 @atom:* - @dihedral:X-cf-p4-X @atom:* @atom:cf @atom:p4 @atom:* - @dihedral:X-c2-px-X @atom:* @atom:c2 @atom:px @atom:* - @dihedral:X-ce-px-X @atom:* @atom:ce @atom:px @atom:* - @dihedral:X-cf-px-X @atom:* @atom:cf @atom:px @atom:* - @dihedral:X-c2-p5-X @atom:* @atom:c2 @atom:p5 @atom:* - @dihedral:X-ce-p5-X @atom:* @atom:ce @atom:p5 @atom:* - @dihedral:X-cf-p5-X @atom:* @atom:cf @atom:p5 @atom:* - @dihedral:X-c2-py-X @atom:* @atom:c2 @atom:py @atom:* - @dihedral:X-ce-py-X @atom:* @atom:ce @atom:py @atom:* - @dihedral:X-cf-py-X @atom:* @atom:cf @atom:py @atom:* - @dihedral:X-c2-sh-X @atom:* @atom:c2 @atom:sh @atom:* - @dihedral:X-c2-ss-X @atom:* @atom:c2 @atom:ss @atom:* - @dihedral:X-c2-s4-X @atom:* @atom:c2 @atom:s4 @atom:* - @dihedral:X-ce-s4-X @atom:* @atom:ce @atom:s4 @atom:* - @dihedral:X-cf-s4-X @atom:* @atom:cf @atom:s4 @atom:* - @dihedral:X-c2-sx-X @atom:* @atom:c2 @atom:sx @atom:* - @dihedral:X-ce-sx-X @atom:* @atom:ce @atom:sx @atom:* - @dihedral:X-cf-sx-X @atom:* @atom:cf @atom:sx @atom:* - @dihedral:X-c2-s6-X @atom:* @atom:c2 @atom:s6 @atom:* - @dihedral:X-ce-s6-X @atom:* @atom:ce @atom:s6 @atom:* - @dihedral:X-cf-s6-X @atom:* @atom:cf @atom:s6 @atom:* - @dihedral:X-c2-sy-X @atom:* @atom:c2 @atom:sy @atom:* - @dihedral:X-ce-sy-X @atom:* @atom:ce @atom:sy @atom:* - @dihedral:X-cf-sy-X @atom:* @atom:cf @atom:sy @atom:* - @dihedral:X-c3-c3-X @atom:* @atom:c3 @atom:c3 @atom:* - @dihedral:X-cx-cx-X @atom:* @atom:cx @atom:cx @atom:* - @dihedral:X-cy-cy-X @atom:* @atom:cy @atom:cy @atom:* - @dihedral:X-c3-ca-X @atom:* @atom:c3 @atom:ca @atom:* - @dihedral:X-c3-n-X @atom:* @atom:c3 @atom:n @atom:* - @dihedral:X-cx-n-X @atom:* @atom:cx @atom:n @atom:* - @dihedral:X-cy-n-X @atom:* @atom:cy @atom:n @atom:* - @dihedral:X-c3-n2-X @atom:* @atom:c3 @atom:n2 @atom:* - @dihedral:X-c3-ne-X @atom:* @atom:c3 @atom:ne @atom:* - @dihedral:X-c3-nf-X @atom:* @atom:c3 @atom:nf @atom:* - @dihedral:X-c3-n3-X @atom:* @atom:c3 @atom:n3 @atom:* - @dihedral:X-c3-n4-X @atom:* @atom:c3 @atom:n4 @atom:* - @dihedral:X-c3-na-X @atom:* @atom:c3 @atom:na @atom:* - @dihedral:X-c3-nh-X @atom:* @atom:c3 @atom:nh @atom:* - @dihedral:X-c3-no-X @atom:* @atom:c3 @atom:no @atom:* - @dihedral:X-c3-oh-X @atom:* @atom:c3 @atom:oh @atom:* - @dihedral:X-c3-os-X @atom:* @atom:c3 @atom:os @atom:* - @dihedral:X-c3-p2-X @atom:* @atom:c3 @atom:p2 @atom:* - 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@dihedral:cf-ne-p5-o @atom:cf @atom:ne @atom:p5 @atom:o - @dihedral:cf-ne-p5-o @atom:cf @atom:ne @atom:p5 @atom:o - @dihedral:cf-nf-p5-o @atom:cf @atom:nf @atom:p5 @atom:o - @dihedral:cf-nf-p5-o @atom:cf @atom:nf @atom:p5 @atom:o - @dihedral:hn-n-c-o @atom:hn @atom:n @atom:c @atom:o - @dihedral:hn-n-c-o @atom:hn @atom:n @atom:c @atom:o - @dihedral:c3-ss-ss-c3 @atom:c3 @atom:ss @atom:ss @atom:c3 - @dihedral:c3-ss-ss-c3 @atom:c3 @atom:ss @atom:ss @atom:c3 - @dihedral:c3-n3-nh-ca @atom:c3 @atom:n3 @atom:nh @atom:ca - @dihedral:c3-n3-nh-ca @atom:c3 @atom:n3 @atom:nh @atom:ca - @dihedral:c3-n3-p5-o @atom:c3 @atom:n3 @atom:p5 @atom:o - @dihedral:c3-n3-p5-o @atom:c3 @atom:n3 @atom:p5 @atom:o - @dihedral:ca-nh-oh-ho @atom:ca @atom:nh @atom:oh @atom:ho - @dihedral:ca-nh-oh-ho @atom:ca @atom:nh @atom:oh @atom:ho - @dihedral:oh-p5-os-c3 @atom:oh @atom:p5 @atom:os @atom:c3 - @dihedral:oh-p5-os-c3 @atom:oh @atom:p5 @atom:os @atom:c3 - @dihedral:os-p5-os-c3 @atom:os @atom:p5 @atom:os @atom:c3 - @dihedral:os-p5-os-c3 @atom:os @atom:p5 @atom:os @atom:c3 - @dihedral:h1-c3-c-o @atom:h1 @atom:c3 @atom:c @atom:o - @dihedral:h1-c3-c-o @atom:h1 @atom:c3 @atom:c @atom:o - @dihedral:hc-c3-c-o @atom:hc @atom:c3 @atom:c @atom:o - @dihedral:hc-c3-c-o @atom:hc @atom:c3 @atom:c @atom:o - @dihedral:hc-c3-c3-hc @atom:hc @atom:c3 @atom:c3 @atom:hc - @dihedral:hc-c3-c3-c3 @atom:hc @atom:c3 @atom:c3 @atom:c3 - @dihedral:hc-c3-c2-c2 @atom:hc @atom:c3 @atom:c2 @atom:c2 - @dihedral:hc-c3-c2-c2 @atom:hc @atom:c3 @atom:c2 @atom:c2 - @dihedral:ho-oh-c3-c3 @atom:ho @atom:oh @atom:c3 @atom:c3 - @dihedral:ho-oh-c3-c3 @atom:ho @atom:oh @atom:c3 @atom:c3 - @dihedral:ho-oh-c-o @atom:ho @atom:oh @atom:c @atom:o - @dihedral:ho-oh-c-o @atom:ho @atom:oh @atom:c @atom:o - @dihedral:c2-c2-c-o @atom:c2 @atom:c2 @atom:c @atom:o - @dihedral:c2-c2-c-o @atom:c2 @atom:c2 @atom:c @atom:o - @dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3 - @dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3 - @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 - @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 - @dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3 - @dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3 - @dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3 - @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 - @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 - @dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c - @dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c - @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os - @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os - @dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os - @dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na - @dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na - @dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3 - @dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3 - @dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2 - @dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2 - @dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os - @dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os - @dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh - @dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh - @dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh - @dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh - @dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f - @dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f - @dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl - @dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl - @dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br - @dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br - @dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os - @dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os - @dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh - @dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh - @dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f - @dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f - @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl - @dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl - @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br - @dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br - @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os - @dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os - @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh - @dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh - @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f - @dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f - @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl - @dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl - @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br - @dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br - } # (end of Dihedrals By Type) - - write_once("In Settings") { - improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes - improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 # - improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 # - improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 # - improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 # - improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 # - improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 # - improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 # - improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 # - improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 # - improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!) - improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 # - improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 # - improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 - improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 # - improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 - } # (end of improper_coeffs) - - write_once("Data Impropers By Type (gaff_imp.py)") { - @improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o - @improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o - @improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha - @improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn - @improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn - @improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn - @improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3 - @improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2 - @improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3 - @improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3 - @improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn - @improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o - @improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3 - @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3 - @improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc - @improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc - @improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o - @improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh - @improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2 - @improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na - @improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2 - @improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na - @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2 - @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3 - @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f - @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl - @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br - @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i - @improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh - @improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3 - @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3 - @improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o - @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2 - @improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh - @improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os - @improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2 - @improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2 - @improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2 - } # (end of Impropers By Type) - - - write_once("In Init") { - # Default styles and settings for AMBER based force-fields: - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - improper_style hybrid cvff - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - kspace_style pppm 0.0001 - - # NOTE: If you do not want to use long-range coulombic forces, - # comment out the two lines above and uncomment this line: - # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 - - pair_modify mix arithmetic - special_bonds amber - } - -} - - diff --git a/tools/moltemplate/moltemplate/force_fields/gaff2.lt b/tools/moltemplate/moltemplate/force_fields/gaff2.lt deleted file mode 100644 index 9063b28cb9..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/gaff2.lt +++ /dev/null @@ -1,13357 +0,0 @@ -# This is the 2.1 version of GAFF (April 2016) -#################################################################### -# This moltemplate (LT) file was generated automatically using -# amberparm2lt.sh gaff2.dat GAFF2 > gaff2.lt -#################################################################### -# WARNING: As of 2017-10-03 this file has not yet been tested with -# moltemplate. Please report issues to jewett.aij -at- gmail.com -#################################################################### -# Background information and usage explanation: -# This file contanis a list of atom types and rules for generating bonded -# interactions between these atoms (hopefully) according to AMBER conventions. -# By using the atom types shown below in your own molecules, bonds and angular -# interactions will be automatically generated. -# AMBER (GAFF) force-field parameters will also be assigned to each angle -# interaction (according to these atom types). -# One way to apply the GAFF force field to a particular type of molecule, is -# to use the "inherits" keyword when you define that molecule. For example: -# import("gaff.lt") -# MoleculeType inherits GAFF { -# write_once("Data Atoms") { -# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285 -# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382 -# : : : -# } -# } -#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.) -#################################################################### -# Moltemplate can not assign atom charge. You must assign atomic -# charges yourself. (Moltemplate is only a simple text manipulation tool. -# You can do this afterwards using commands like "set atom 70 charge -0.212" -# For details, see http://lammps.sandia.gov/doc/set.html) -#################################################################### - - -GAFF2 { - - # ---------------------------------------------------------------------- - # The basic atom nomenclature and conventions are explained here: - # http://ambermd.org/antechamber/gaff.pdf - # For reference, the original gaff.dat file and format documentation are here: - # http://ambermd.org/AmberTools-get.html - # http://ambermd.org/formats.html#parm.dat - # ---------------------------------------------------------------------- - - write_once("Data Masses") { - @atom:c 12.01 # Sp2 C carbonyl group - @atom:cs 12.01 # Sp2 C in c=S - @atom:c1 12.01 # Sp C - @atom:c2 12.01 # Sp2 C - @atom:c3 12.01 # Sp3 C - @atom:ca 12.01 # Sp2 C in pure aromatic systems - @atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys. - @atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp - @atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems - @atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc - @atom:ce 12.01 # Inner Sp2 carbons in conjugated systems - @atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce - @atom:cg 12.01 # Inner Sp carbons in conjugated systems - @atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg - @atom:cx 12.01 # Sp3 carbons in triangle systems - @atom:cy 12.01 # Sp3 carbons in square systems - @atom:cu 12.01 # Sp2 carbons in triangle systems - @atom:cv 12.01 # Sp2 carbons in square systems - @atom:cz 12.01 # Sp2 carbon in guanidine group - @atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group - @atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group - @atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group - @atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group - @atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group - @atom:ha 1.008 # H bonded to aromatic carbon - @atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group - @atom:hn 1.008 # H bonded to nitrogen atoms - @atom:ho 1.008 # Hydroxyl group - @atom:hp 1.008 # H bonded to phosphate - @atom:hs 1.008 # Hydrogen bonded to sulphur - @atom:hw 1.008 # Hydrogen in water - @atom:hx 1.008 # H bonded to C next to positively charged group - @atom:f 19.00 # Fluorine - @atom:cl 35.45 # Chlorine - @atom:br 79.90 # Bromine - @atom:i 126.9 # Iodine - @atom:n 14.01 # Sp2 nitrogen in amide groups - @atom:n1 14.01 # Sp N - @atom:n2 14.01 # aliphatic Sp2 N with two connected atoms - @atom:n3 14.01 # Sp3 N with three connected atoms - @atom:n4 14.01 # Sp3 N with four connected atoms - @atom:na 14.01 # Sp2 N with three connected atoms - @atom:nb 14.01 # Sp2 N in pure aromatic systems - @atom:nc 14.01 # Sp2 N in non-pure aromatic systems - @atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc - @atom:ne 14.01 # Inner Sp2 N in conjugated systems - @atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne - @atom:nh 14.01 # Amine N connected one or more aromatic rings - @atom:no 14.01 # Nitro N - @atom:ns 14.01 # amind N, with 1 attached hydrogen atom - @atom:nt 14.01 # amide N, with 2 attached hydrogen atoms - @atom:nx 14.01 # like n4, but only has one hydrogen atom - @atom:ny 14.01 # like n4, but only has two hydrogen atoms - @atom:nz 14.01 # like n4, but only has three three hydrogen atoms - @atom:n+ 14.01 # NH4+ - @atom:nu 14.01 # like nh, but only has one attached hydrogen atom - @atom:nv 14.01 # like nh, but only has two attached hydrogen atoms - @atom:n7 14.01 # like n3, but only has one attached hydrogen atom - @atom:n8 14.01 # like n3, but only has two attached hydrogen atoms - @atom:n9 14.01 # NH3 - @atom:o 16.00 # Oxygen with one connected atom - @atom:oh 16.00 # Oxygen in hydroxyl group - @atom:os 16.00 # Ether and ester oxygen - @atom:ow 16.00 # Oxygen in water - @atom:p2 30.97 # Phosphate with two connected atoms - @atom:p3 30.97 # Phosphate with three connected atoms, such as PH3 - @atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2 - @atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3 - @atom:pb 30.97 # Sp2 P in pure aromatic systems - @atom:pc 30.97 # Sp2 P in non-pure aromatic systems - @atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc - @atom:pe 30.97 # Inner Sp2 P in conjugated systems - @atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe - @atom:px 30.97 # Special p4 in conjugated systems - @atom:py 30.97 # Special p5 in conjugated systems - @atom:s 32.06 # S with one connected atom - @atom:s2 32.06 # S with two connected atom, involved at least one double bond - @atom:s4 32.06 # S with three connected atoms - @atom:s6 32.06 # S with four connected atoms - @atom:sh 32.06 # Sp3 S connected with hydrogen - @atom:ss 32.06 # Sp3 S in thio-ester and thio-ether - @atom:sx 32.06 # Special s4 in conjugated systems - @atom:sy 32.06 # Special s6 in conjugated systems - } # (end of masses) - - write_once("In Settings") { - pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0208 2.60017699876 - pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0161 2.62547852236 - pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0100 1.10649620793 - pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0047 0.537924646013 - pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0124 1.08903459305 - pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0144 1.07460203382 - pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.1463 3.04812087425 - pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.0726 3.15609779888 - pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.0930 3.24287133403 - pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1078 3.39770953124 - pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.1596 3.47895949434 - pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1636 3.18086478325 - pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.0832 3.03422285424 - pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.2638 3.46595237305 - pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.3932 3.61259430206 - pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.4955 3.84119891313 - pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1098 3.27351824993 - pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.0941 3.38416787073 - pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.0858 3.36510263816 - pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.2042 3.20580994736 - pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.2150 3.18995195017 - pair_coeff @atom:n+ @atom:n+ lj/charmm/coul/long 0.7828 2.85586493087 - pair_coeff @atom:n9 @atom:n9 lj/charmm/coul/long 0.0095 4.04468018036 - pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0208 2.42199725514 - pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0208 2.24381751151 - pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0208 2.06563776788 - pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0208 1.88745802425 - pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0161 2.53638865055 - pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0161 2.44729877873 - pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.1078 3.39770953124 - pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.1078 3.39770953124 - pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cs @atom:cs lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.1596 3.47895949434 - pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.1596 3.47895949434 - pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0988 3.31521230994 - pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.0941 3.38416787073 - pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.0941 3.38416787073 - pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.0941 3.38416787073 - pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.0941 3.38416787073 - pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.0941 3.38416787073 - pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.0858 3.36510263816 - pair_coeff @atom:n7 @atom:n7 lj/charmm/coul/long 0.0522 3.50764643306 - pair_coeff @atom:n8 @atom:n8 lj/charmm/coul/long 0.0323 3.65019022796 - pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 3.8748 2.49950544361 - pair_coeff @atom:nx @atom:nx lj/charmm/coul/long 2.5453 2.58859531543 - pair_coeff @atom:ny @atom:ny lj/charmm/coul/long 1.6959 2.67768518724 - pair_coeff @atom:nz @atom:nz lj/charmm/coul/long 1.1450 2.76677505906 - pair_coeff @atom:ns @atom:ns lj/charmm/coul/long 0.1174 3.26995465506 - pair_coeff @atom:nt @atom:nt lj/charmm/coul/long 0.0851 3.35904452688 - pair_coeff @atom:nu @atom:nu lj/charmm/coul/long 0.1545 3.27904182199 - pair_coeff @atom:nv @atom:nv lj/charmm/coul/long 0.1120 3.3681316938 - pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2824 3.53241341743 - pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2295 3.6940224449 - pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2295 3.6940224449 - } # (end of pair_coeffs) - - write_once("In Settings") { - bond_coeff @bond:ow-hw harmonic 612.98 0.957 # TIP3P_Water 1 - bond_coeff @bond:hw-hw harmonic 15.17 1.514 # TIP3P_Water 1 - bond_coeff @bond:br-br harmonic 81.01 2.542 # SOURCE1 4 - bond_coeff @bond:br-c1 harmonic 227.01 1.787 # SOURCE2 4 0.0024 - bond_coeff @bond:br-c2 harmonic 168.91 1.893 # SOURCE1_SOURCE5 25 0.0078 - bond_coeff @bond:br-c harmonic 146.48 1.946 # SOURCE2 2 0.0285 - bond_coeff @bond:br-c3 harmonic 134.73 1.978 # SOURCE1_SOURCE5 146 0.0118 - bond_coeff @bond:br-ca harmonic 162.15 1.908 # SOURCE1_SOURCE5 462 0.0052 - bond_coeff @bond:br-cc harmonic 172.53 1.885 # SOURCE4_SOURCE5 128 0.0078 - bond_coeff @bond:br-cx harmonic 154.63 1.926 # SOURCE1_SOURCE5 11 0.0019 - bond_coeff @bond:br-n1 harmonic 141.51 1.860 # SOUECE3 1 - bond_coeff @bond:br-n2 harmonic 88.47 2.038 # SOURCE3 5 0.1082 - bond_coeff @bond:br-n harmonic 136.53 1.873 # SOURCE3 4 0.0046 - bond_coeff @bond:br-n3 harmonic 110.41 1.952 # SOURCE3 2 - bond_coeff @bond:br-n4 harmonic 118.29 1.926 # SOURCE3 3 0.0013 - bond_coeff @bond:br-na harmonic 96.95 2.002 # SOURCE3 7 0.2156 - bond_coeff @bond:br-nh harmonic 112.77 1.944 # SOURCE3 1 - bond_coeff @bond:br-no harmonic 75.65 2.101 # SOURCE3 1 - bond_coeff @bond:br-o harmonic 193.58 1.800 # SOUECE3 1 - bond_coeff @bond:br-oh harmonic 160.87 1.866 # SOURCE3 1 - bond_coeff @bond:br-os harmonic 151.88 1.887 # SOURCE3 2 - bond_coeff @bond:br-p2 harmonic 133.12 2.210 # SOURCE3 9 0.0510 - bond_coeff @bond:br-p3 harmonic 126.80 2.231 # SOURCE3 3 0.0101 - bond_coeff @bond:br-p4 harmonic 145.88 2.171 # SOUECE3 1 - bond_coeff @bond:br-p5 harmonic 137.54 2.196 # SOURCE3 3 0.0099 - bond_coeff @bond:br-s harmonic 169.20 2.220 # SOUECE3 1 - bond_coeff @bond:br-s4 harmonic 128.80 2.341 # SOURCE3 1 - bond_coeff @bond:br-s6 harmonic 171.57 2.214 # SOURCE3 3 0.0443 - bond_coeff @bond:br-sh harmonic 173.58 2.209 # SOURCE3 1 - bond_coeff @bond:br-ss harmonic 176.02 2.203 # SOURCE3 3 0.0035 - bond_coeff @bond:c1-c1 harmonic 837.28 1.198 # SOURCE1_SOURCE5 659 0.0039 - bond_coeff @bond:c1-c2 harmonic 535.85 1.307 # SOURCE1 18 - bond_coeff @bond:c1-c3 harmonic 295.86 1.467 # SOURCE1_SOURCE5 795 0.0034 - bond_coeff @bond:c1-ca harmonic 325.62 1.440 # SOUECE3 1 - bond_coeff @bond:c1-ce harmonic 518.69 1.315 # SOURCE4 6 0.0086 - bond_coeff @bond:c1-cg harmonic 776.82 1.216 # SOURCE3_SOURCE5 179 0.0036 - bond_coeff @bond:c1-ch harmonic 765.43 1.219 # SOURCE3_SOURCE5 13 0.0016 - bond_coeff @bond:c1-cl harmonic 261.49 1.631 # SOURCE2 6 0.0050 - bond_coeff @bond:c1-cx harmonic 320.55 1.444 # SOURCE1_SOURCE5 24 0.0043 - bond_coeff @bond:c1-f harmonic 482.19 1.270 # SOURCE2 2 0.0085 - bond_coeff @bond:c1-ha harmonic 433.72 1.067 # SOURCE3_SOURCE5 343 0.0013 - bond_coeff @bond:c1-hc harmonic 448.21 1.060 # SOUECE3 1 - bond_coeff @bond:c1-i harmonic 153.51 1.989 # SOURCE2 4 0.0032 - bond_coeff @bond:c1-n1 harmonic 891.54 1.153 # SOURCE1_SOURCE5 481 0.0035 - bond_coeff @bond:c1-n2 harmonic 736.75 1.197 # SOURCE3_SOURCE5 36 0.0076 - bond_coeff @bond:c1-n3 harmonic 400.99 1.347 # SOURCE2_SOURCE5 10 0.0093 - bond_coeff @bond:c1-n4 harmonic 309.65 1.417 # SOURCE3 3 0.0032 - bond_coeff @bond:c1-n harmonic 428.86 1.330 # SOUECE3 1 - bond_coeff @bond:c1-na harmonic 379.52 1.362 # SOURCE3 8 0.0034 - bond_coeff @bond:c1-ne harmonic 720.51 1.202 # SOURCE4_SOURCE5 31 0.0124 - bond_coeff @bond:c1-nf harmonic 720.51 1.202 # SOURCE4_SOURCE5 21 0.0141 - bond_coeff @bond:c1-nh harmonic 409.04 1.342 # SOURCE4_SOURCE5 33 0.0061 - bond_coeff @bond:c1-no harmonic 323.48 1.405 # SOURCE3 3 0.0005 - bond_coeff @bond:c1-o harmonic 794.98 1.172 # SOURCE2_SOURCE5 31 0.0068 - bond_coeff @bond:c1-oh harmonic 422.21 1.326 # SOURCE3 1 - bond_coeff @bond:c1-os harmonic 435.38 1.318 # SOURCE3_SOURCE5 8 0.0079 - bond_coeff @bond:c1-p2 harmonic 215.98 1.770 # SOUECE3 1 - bond_coeff @bond:c1-p3 harmonic 203.86 1.790 # SOUECE3 1 - bond_coeff @bond:c1-p4 harmonic 203.86 1.790 # SOUECE3 1 - bond_coeff @bond:c1-p5 harmonic 226.96 1.753 # SOURCE3 2 - bond_coeff @bond:c1-s2 harmonic 380.51 1.595 # SOURCE3 1 - bond_coeff @bond:c1-s harmonic 370.61 1.603 # SOURCE1_SOURCE5 37 0.0043 - bond_coeff @bond:c1-s4 harmonic 239.03 1.746 # SOURCE3 2 - bond_coeff @bond:c1-s6 harmonic 256.65 1.722 # SOURCE3 2 - bond_coeff @bond:c1-sh harmonic 291.39 1.680 # SOUECE3 1 - bond_coeff @bond:c1-ss harmonic 282.80 1.690 # SOURCE1_SOURCE5 49 0.0113 - bond_coeff @bond:c2-c2 harmonic 481.83 1.334 # SOURCE1_SOURCE5 3727 0.0053 - bond_coeff @bond:c2-c3 harmonic 255.56 1.510 # SOURCE1_SOURCE5 10204 0.0042 - bond_coeff @bond:c2-ca harmonic 398.37 1.385 # SOUECE3_SOURCE5 9 0.0149 - bond_coeff @bond:c2-cc harmonic 437.98 1.359 # SOURCE1_SOURCE5 882 0.0181 - bond_coeff @bond:c2-cd harmonic 437.98 1.359 # SOURCE1_SOURCE5 882 0.0181 - bond_coeff @bond:c2-ce harmonic 460.51 1.346 # SOURCE3_SOURCE5 3239 0.0058 - bond_coeff @bond:c2-cf harmonic 460.51 1.346 # SOURCE3_SOURCE5 3177 0.0057 - bond_coeff @bond:c2-cl harmonic 192.70 1.731 # SOURCE1_SOURCE5 290 0.0098 - bond_coeff @bond:c2-cu harmonic 500.05 1.325 # SOURCE2_SOURCE5 11 0.0010 - bond_coeff @bond:c2-cx harmonic 278.37 1.485 # SOURCE4_SOURCE5 102 0.0061 - bond_coeff @bond:c2-cy harmonic 255.91 1.509 # SOURCE4_SOURCE5 30 0.0063 - bond_coeff @bond:c2-f harmonic 368.08 1.339 # SOURCE1_SOURCE5 35 0.0085 - bond_coeff @bond:c2-h4 harmonic 394.23 1.087 # SOURCE3_SOURCE5 517 0.0028 - bond_coeff @bond:c2-h5 harmonic 386.13 1.091 # SOURCE4_SOURCE5 116 0.0021 - bond_coeff @bond:c2-ha harmonic 392.18 1.088 # SOURCE3_SOURCE5 5991 0.0019 - bond_coeff @bond:c2-hc harmonic 393.86 1.087 # SOURCE3 789 0.0046 - bond_coeff @bond:c2-hx harmonic 401.39 1.083 # SOURCE3 3 0.0008 - bond_coeff @bond:c2-i harmonic 98.09 2.170 # SOURCE3_SOURCE5 7 0.0194 - bond_coeff @bond:c2-n1 harmonic 470.94 1.306 # SOURCE3 4 0.0161 - bond_coeff @bond:c2-n2 harmonic 518.67 1.282 # SOURCE1_SOURCE5 1004 0.0051 - bond_coeff @bond:c2-n3 harmonic 412.66 1.340 # SOUECE3 1 - bond_coeff @bond:c2-n harmonic 330.19 1.399 # SOURCE3_SOURCE5 174 0.0100 - bond_coeff @bond:c2-n4 harmonic 221.45 1.512 # SOURCE3_SOURCE5 21 0.0133 - bond_coeff @bond:c2-na harmonic 327.66 1.401 # SOURCE3_SOURCE5 65 0.0179 - bond_coeff @bond:c2-nc harmonic 458.17 1.313 # SOURCE1 99 0.0095 - bond_coeff @bond:c2-nd harmonic 458.17 1.313 # SOURCE1 99 - bond_coeff @bond:c2-ne harmonic 498.75 1.292 # SOURCE3_SOURCE5 310 0.0099 - bond_coeff @bond:c2-nf harmonic 498.75 1.292 # SOURCE3_SOURCE5 273 0.0098 - bond_coeff @bond:c2-nh harmonic 345.39 1.387 # SOURCE3_SOURCE5 1559 0.0120 - bond_coeff @bond:c2-no harmonic 276.95 1.448 # SOURCE4_SOURCE5 27 0.0139 - bond_coeff @bond:c2-o harmonic 635.23 1.225 # SOURCE4_SOURCE5 35 0.0033 - bond_coeff @bond:c2-oh harmonic 402.33 1.339 # SOURCE1_SOURCE5 85 0.0126 - bond_coeff @bond:c2-os harmonic 371.26 1.360 # SOURCE1_SOURCE5 548 0.0107 - bond_coeff @bond:c2-p2 harmonic 292.48 1.669 # SOURCE3_SOURCE5 87 0.0126 - bond_coeff @bond:c2-p3 harmonic 179.93 1.834 # SOURCE3 5 0.0042 - bond_coeff @bond:c2-p4 harmonic 186.11 1.822 # SOUECE3 1 - bond_coeff @bond:c2-p5 harmonic 166.18 1.863 # SOURCE4_SOURCE5 15 0.0083 - bond_coeff @bond:c2-pe harmonic 275.11 1.689 # SOURCE3_SOURCE5 60 0.0472 - bond_coeff @bond:c2-pf harmonic 275.11 1.689 # SOURCE3_SOURCE5 8 0.0019 - bond_coeff @bond:c2-s2 harmonic 362.64 1.610 # SOURCE2 1 - bond_coeff @bond:c2-s harmonic 247.65 1.734 # SOURCE3 4 0.0034 - bond_coeff @bond:c2-s4 harmonic 229.42 1.760 # SOUECE3 1 - bond_coeff @bond:c2-s6 harmonic 229.42 1.760 # SOUECE3 1 - bond_coeff @bond:c2-sh harmonic 215.23 1.782 # SOURCE4_SOURCE5 13 0.0077 - bond_coeff @bond:c2-ss harmonic 246.19 1.736 # SOURCE1 209 0.0155 - bond_coeff @bond:c3-c3 harmonic 232.52 1.538 # SOURCE1_SOURCE5 88072 0.0058 - bond_coeff @bond:c3-ca harmonic 250.32 1.516 # SOURCE1_SOURCE5 10699 0.0054 - bond_coeff @bond:c3-cc harmonic 262.64 1.502 # SOURCE3_SOURCE5 3926 0.0049 - bond_coeff @bond:c3-cd harmonic 262.64 1.502 # SOURCE3_SOURCE5 3926 0.0049 - bond_coeff @bond:c3-ce harmonic 250.06 1.516 # SOURCE3_SOURCE5 1210 0.0060 - bond_coeff @bond:c3-cf harmonic 250.23 1.516 # SOURCE3_SOURCE5 345 0.0071 - bond_coeff @bond:c3-cl harmonic 155.52 1.804 # SOURCE1_SOURCE5 1173 0.0119 - bond_coeff @bond:c3-cu harmonic 284.82 1.478 # SOURCE1 7 - bond_coeff @bond:c3-cv harmonic 274.17 1.489 # SOURCE1 11 - bond_coeff @bond:c3-cx harmonic 247.95 1.518 # SOURCE1_SOURCE5 1561 0.0054 - bond_coeff @bond:c3-cy harmonic 236.93 1.532 # SOURCE1_SOURCE5 522 0.0055 - bond_coeff @bond:c3-f harmonic 352.65 1.350 # SOURCE1_SOURCE5 2188 0.0139 - bond_coeff @bond:c3-h1 harmonic 375.92 1.097 # SOURCE3_SOURCE5 112144 0.0055 - bond_coeff @bond:c3-h2 harmonic 377.33 1.096 # SOURCE3_SOURCE5 2681 0.0032 - bond_coeff @bond:c3-h3 harmonic 379.47 1.095 # SOURCE4_SOURCE5 64 0.0028 - bond_coeff @bond:c3-hc harmonic 375.92 1.097 # SOURCE3_SOURCE5 133628 0.0015 - bond_coeff @bond:c3-hx harmonic 386.49 1.091 # SOURCE3_SOURCE5 6495 0.0022 - bond_coeff @bond:c3-i harmonic 88.97 2.212 # SOURCE1_SOURCE5 35 0.0128 - bond_coeff @bond:c3-n1 harmonic 292.28 1.433 # SOURCE3_SOURCE5 7 0.0033 - bond_coeff @bond:c3-n2 harmonic 259.91 1.466 # SOURCE1_SOURCE5 816 0.0087 - bond_coeff @bond:c3-n harmonic 263.77 1.462 # SOURCE1_SOURCE5 4576 0.0061 - bond_coeff @bond:c3-n3 harmonic 261.19 1.465 # SOURCE1_SOURCE5 15206 0.0039 - bond_coeff @bond:c3-n4 harmonic 222.58 1.511 # SOURCE1_SOURCE5 2375 0.0125 - bond_coeff @bond:c3-na harmonic 262.85 1.463 # SOURCE3_SOURCE5 1732 0.0077 - bond_coeff @bond:c3-nc harmonic 269.31 1.456 # SOURCE3 9 0.0109 - bond_coeff @bond:c3-nd harmonic 269.31 1.456 # SOURCE3 9 - bond_coeff @bond:c3-nh harmonic 261.84 1.464 # SOURCE3_SOURCE5 3492 0.0064 - bond_coeff @bond:c3-no harmonic 206.37 1.533 # SOURCE1_SOURCE5 150 0.0187 - bond_coeff @bond:c3-o harmonic 438.11 1.317 # SOURCE4 8 0.0193 - bond_coeff @bond:c3-oh harmonic 293.40 1.423 # SOURCE1_SOURCE5 8884 0.0067 - bond_coeff @bond:c3-os harmonic 284.76 1.432 # SOURCE1_SOURCE5 17971 0.0103 - bond_coeff @bond:c3-p2 harmonic 169.71 1.855 # SOURCE3 9 0.0125 - bond_coeff @bond:c3-p3 harmonic 168.21 1.858 # SOURCE3_SOURCE5 221 0.0094 - bond_coeff @bond:c3-p4 harmonic 177.58 1.839 # SOURCE3_SOURCE5 45 0.0106 - bond_coeff @bond:c3-p5 harmonic 177.19 1.839 # SOURCE1_SOURCE5 408 0.0183 - bond_coeff @bond:c3-px harmonic 182.68 1.829 # SOURCE3_SOURCE5 35 0.0083 - bond_coeff @bond:c3-py harmonic 177.09 1.840 # SOURCE3_SOURCE5 39 0.0126 - bond_coeff @bond:c3-s harmonic 180.03 1.845 # SOURCE3 4 0.0185 - bond_coeff @bond:c3-s4 harmonic 187.48 1.831 # SOURCE1_SOURCE5 326 0.0096 - bond_coeff @bond:c3-s6 harmonic 200.07 1.808 # SOURCE1_SOURCE5 644 0.0143 - bond_coeff @bond:c3-sh harmonic 180.78 1.843 # SOURCE3_SOURCE5 189 0.0058 - bond_coeff @bond:c3-ss harmonic 182.96 1.839 # SOURCE1_SOURCE5 2732 0.0105 - bond_coeff @bond:c3-sx harmonic 181.64 1.842 # SOURCE3_SOURCE5 99 0.0121 - bond_coeff @bond:c3-sy harmonic 199.39 1.809 # SOURCE3_SOURCE5 162 0.0094 - bond_coeff @bond:ca-ca harmonic 378.57 1.398 # SOURCE1_SOURCE5 121206 0.0061 - bond_coeff @bond:ca-cc harmonic 308.19 1.456 # SOURCE1_SOURCE5 2424 0.0121 - bond_coeff @bond:ca-cd harmonic 308.19 1.456 # SOURCE1_SOURCE5 2424 0.0121 - bond_coeff @bond:ca-ce harmonic 286.51 1.476 # SOURCE1_SOURCE5 1750 0.0089 - bond_coeff @bond:ca-cf harmonic 286.51 1.476 # SOURCE1_SOURCE5 1750 0.0089 - bond_coeff @bond:ca-cg harmonic 334.12 1.433 # SOURCE1_SOURCE5 318 0.0029 - bond_coeff @bond:ca-ch harmonic 334.12 1.433 # SOURCE1_SOURCE5 318 0.0029 - bond_coeff @bond:ca-cl harmonic 181.97 1.750 # SOURCE1_SOURCE5 2919 0.0059 - bond_coeff @bond:ca-cp harmonic 368.44 1.406 # CORR_SOURCE5 2042 0.0049 - bond_coeff @bond:ca-cq harmonic 368.44 1.406 # CORR_SOURCE5 2042 0.0049 - bond_coeff @bond:ca-cx harmonic 273.13 1.490 # SOURCE1_SOURCE5 165 0.0091 - bond_coeff @bond:ca-cy harmonic 250.49 1.515 # SOURCE4_SOURCE5 35 0.0055 - bond_coeff @bond:ca-f harmonic 353.59 1.349 # SOURCE1_SOURCE5 1239 0.0057 - bond_coeff @bond:ca-h4 harmonic 390.15 1.089 # SOURCE3_SOURCE5 2643 0.0010 - bond_coeff @bond:ca-h5 harmonic 392.37 1.088 # SOURCE3_SOURCE5 299 0.0007 - bond_coeff @bond:ca-ha harmonic 395.72 1.086 # SOURCE3_SOURCE5 65456 0.0010 - bond_coeff @bond:ca-i harmonic 108.27 2.129 # SOURCE1_SOURCE5 61 0.0076 - bond_coeff @bond:ca-n1 harmonic 420.66 1.335 # SOURCE3_SOURCE5 6 0.0078 - bond_coeff @bond:ca-n2 harmonic 476.53 1.303 # SOURCE4 7 0.0058 - bond_coeff @bond:ca-n harmonic 315.21 1.412 # SOURCE3_SOURCE5 1254 0.0090 - bond_coeff @bond:ca-n4 harmonic 244.03 1.484 # SOURCE1_SOURCE5 28 0.0065 - bond_coeff @bond:ca-na harmonic 349.52 1.384 # SOURCE1_SOURCE5 2751 0.0095 - bond_coeff @bond:ca-nb harmonic 414.24 1.339 # SOURCE3_SOURCE5 6806 0.0055 - bond_coeff @bond:ca-nc harmonic 394.62 1.352 # SOURCE1_SOURCE5 2672 0.0030 - bond_coeff @bond:ca-nd harmonic 394.62 1.352 # SOURCE1_SOURCE5 2672 0.0030 - bond_coeff @bond:ca-ne harmonic 320.07 1.408 # SOURCE1_SOURCE5 276 0.0093 - bond_coeff @bond:ca-nf harmonic 320.07 1.408 # SOURCE1_SOURCE5 276 0.0093 - bond_coeff @bond:ca-nh harmonic 347.06 1.386 # SOURCE1_SOURCE5 2785 0.0134 - bond_coeff @bond:ca-no harmonic 257.38 1.469 # SOURCE1_SOURCE5 454 0.0049 - bond_coeff @bond:ca-o harmonic 606.45 1.236 # SOURCE4_SOURCE5 17 0.0088 - bond_coeff @bond:ca-oh harmonic 365.55 1.364 # SOURCE1_SOURCE5 3637 0.0062 - bond_coeff @bond:ca-os harmonic 357.53 1.370 # SOURCE1_SOURCE5 6900 0.0064 - bond_coeff @bond:ca-p2 harmonic 176.94 1.840 # SOUECE3 1 - bond_coeff @bond:ca-p3 harmonic 184.18 1.826 # SOURCE1_SOURCE5 156 0.0180 - bond_coeff @bond:ca-p4 harmonic 194.74 1.806 # SOUECE3 1 - bond_coeff @bond:ca-p5 harmonic 200.84 1.795 # SOURCE1_SOURCE5 577 0.0028 - bond_coeff @bond:ca-pe harmonic 182.48 1.829 # SOURCE3 10 0.0042 - bond_coeff @bond:ca-pf harmonic 182.48 1.829 # SOURCE3 10 0.0042 - bond_coeff @bond:ca-px harmonic 184.54 1.825 # SOURCE3 5 0.0168 - bond_coeff @bond:ca-py harmonic 189.18 1.816 # SOURCE4_SOURCE5 34 0.0098 - bond_coeff @bond:ca-s harmonic 244.02 1.739 # SOURCE3 2 - bond_coeff @bond:ca-s4 harmonic 211.54 1.788 # SOURCE1 51 0.0048 - bond_coeff @bond:ca-s6 harmonic 224.85 1.767 # SOURCE1_SOURCE5 258 0.0041 - bond_coeff @bond:ca-sh harmonic 215.91 1.781 # SOURCE4_SOURCE5 40 0.0053 - bond_coeff @bond:ca-ss harmonic 216.10 1.781 # SOURCE1_SOURCE5 1016 0.0068 - bond_coeff @bond:ca-sx harmonic 190.35 1.825 # SOURCE4_SOURCE5 90 0.0050 - bond_coeff @bond:ca-sy harmonic 209.78 1.791 # SOURCE3_SOURCE5 703 0.0076 - bond_coeff @bond:c-c1 harmonic 303.33 1.460 # SOUECE3 1 - bond_coeff @bond:c-c2 harmonic 368.17 1.406 # SOURCE3 2 0.0370 - bond_coeff @bond:c-c harmonic 224.38 1.548 # SOURCE1_SOURCE5 254 0.0090 - bond_coeff @bond:c-c3 harmonic 243.22 1.524 # SOURCE1_SOURCE5 12697 0.0077 - bond_coeff @bond:c-ca harmonic 272.66 1.491 # SOURCE1_SOURCE5 4357 0.0085 - bond_coeff @bond:c-cc harmonic 295.35 1.468 # SOURCE3_SOURCE5 1864 0.0130 - bond_coeff @bond:cc-cc harmonic 340.18 1.428 # SOURCE1_SOURCE5 4559 0.0096 - bond_coeff @bond:cc-cd harmonic 416.13 1.373 # SOURCE3_SOURCE5 8451 0.0091 - bond_coeff @bond:cc-ce harmonic 309.82 1.454 # CORR_SOURCE5 396 0.0089 - bond_coeff @bond:cc-cf harmonic 427.69 1.366 # CORR_SOURCE5 156 0.0107 - bond_coeff @bond:cc-cg harmonic 342.76 1.426 # SOURCE1_SOURCE5 109 0.0049 - bond_coeff @bond:cc-ch harmonic 341.16 1.427 # SOURCE1 560 - bond_coeff @bond:cc-cl harmonic 190.08 1.735 # CORR_SOURCE5 137 0.0076 - bond_coeff @bond:cc-cx harmonic 290.53 1.472 # CORR_SOURCE5 37 0.0035 - bond_coeff @bond:c-cd harmonic 295.35 1.468 # SOURCE3_SOURCE5 1864 0.0130 - bond_coeff @bond:c-ce harmonic 280.40 1.482 # SOURCE1_SOURCE5 3022 0.0115 - bond_coeff @bond:c-cf harmonic 280.40 1.482 # SOURCE1_SOURCE5 3022 0.0115 - bond_coeff @bond:cc-f harmonic 364.99 1.341 # SOURCE4_SOURCE5 70 0.0039 - bond_coeff @bond:c-cg harmonic 312.91 1.451 # SOURCE3_SOURCE5 11 0.0089 - bond_coeff @bond:c-ch harmonic 312.91 1.451 # SOURCE3_SOURCE5 11 0.0089 - bond_coeff @bond:cc-h4 harmonic 403.88 1.082 # SOURCE3_SOURCE5 4457 0.0016 - bond_coeff @bond:cc-h5 harmonic 403.49 1.082 # SOURCE3_SOURCE5 879 0.0012 - bond_coeff @bond:cc-ha harmonic 400.06 1.084 # SOURCE3_SOURCE5 4706 0.0018 - bond_coeff @bond:c-cl harmonic 156.23 1.803 # SOURCE3_SOURCE5 16 0.0187 - bond_coeff @bond:cc-n2 harmonic 500.74 1.290 # CORR_SOURCE5 156 0.0074 - bond_coeff @bond:cc-n harmonic 353.83 1.381 # SOURCE3_SOURCE5 1142 0.0085 - bond_coeff @bond:cc-n4 harmonic 236.72 1.493 # SOURCE4 7 0.0148 - bond_coeff @bond:cc-na harmonic 354.49 1.380 # SOURCE3_SOURCE5 6739 0.0088 - bond_coeff @bond:cc-nc harmonic 369.10 1.369 # SOURCE1_SOURCE5 2269 0.0086 - bond_coeff @bond:cc-nd harmonic 450.71 1.317 # SOURCE3_SOURCE5 4612 0.0083 - bond_coeff @bond:cc-ne harmonic 356.61 1.379 # SOURCE4_SOURCE5 82 0.0119 - bond_coeff @bond:cc-nf harmonic 485.08 1.298 # CORR_SOURCE5 41 0.0113 - bond_coeff @bond:cc-nh harmonic 363.47 1.373 # SOURCE3_SOURCE5 976 0.0106 - bond_coeff @bond:cc-no harmonic 296.62 1.429 # SOURCE4_SOURCE5 386 0.0074 - bond_coeff @bond:cc-oh harmonic 389.45 1.347 # CORR_SOURCE5 248 0.0073 - bond_coeff @bond:cc-os harmonic 367.90 1.362 # SOURCE3_SOURCE5 1859 0.0083 - bond_coeff @bond:cc-pd harmonic 240.75 1.733 # SOURCE3 84 0.0161 - bond_coeff @bond:cc-sh harmonic 223.28 1.769 # SOURCE4_SOURCE5 22 0.0030 - bond_coeff @bond:cc-ss harmonic 231.98 1.756 # SOURCE3_SOURCE5 2011 0.0134 - bond_coeff @bond:cc-sx harmonic 198.26 1.811 # SOURCE4_SOURCE5 44 0.0033 - bond_coeff @bond:cc-sy harmonic 214.05 1.784 # CORR_SOURCE5 73 0.0082 - bond_coeff @bond:c-cu harmonic 360.20 1.412 # SOURCE2 1 - bond_coeff @bond:c-cx harmonic 265.90 1.498 # SOURCE1_SOURCE5 246 0.0109 - bond_coeff @bond:c-cy harmonic 222.38 1.551 # SOURCE1_SOURCE5 374 0.0059 - bond_coeff @bond:cd-cd harmonic 340.18 1.428 # SOURCE1_SOURCE5 4559 0.0096 - bond_coeff @bond:cd-ce harmonic 427.69 1.366 # CORR_SOURCE5 156 0.0107 - bond_coeff @bond:cd-cf harmonic 309.82 1.454 # CORR_SOURCE5 396 0.0089 - bond_coeff @bond:cd-cg harmonic 341.16 1.427 # SOURCE1 560 - bond_coeff @bond:cd-ch harmonic 342.76 1.426 # SOURCE1_SOURCE5 109 0.0049 - bond_coeff @bond:cd-cl harmonic 190.08 1.735 # CORR_SOURCE5 137 0.0076 - bond_coeff @bond:cd-cx harmonic 290.53 1.472 # CORR_SOURCE5 37 0.0035 - bond_coeff @bond:cd-cy harmonic 259.34 1.505 # SOURCE4_SOURCE5 21 0.0007 - bond_coeff @bond:cd-h4 harmonic 403.88 1.082 # SOURCE3_SOURCE5 4457 0.0016 - bond_coeff @bond:cd-h5 harmonic 403.68 1.082 # SOURCE3_SOURCE5 578 0.0013 - bond_coeff @bond:cd-ha harmonic 400.06 1.084 # SOURCE3_SOURCE5 4706 0.0018 - bond_coeff @bond:cd-n2 harmonic 500.74 1.290 # CORR_SOURCE5 156 0.0074 - bond_coeff @bond:cd-n harmonic 353.83 1.381 # SOURCE3_SOURCE5 1142 0.0085 - bond_coeff @bond:cd-na harmonic 354.49 1.380 # SOURCE3_SOURCE5 6739 0.0088 - bond_coeff @bond:cd-nc harmonic 450.71 1.317 # SOURCE3_SOURCE5 4612 0.0083 - bond_coeff @bond:cd-nd harmonic 369.10 1.369 # SOURCE1_SOURCE5 2269 0.0086 - bond_coeff @bond:cd-ne harmonic 485.08 1.298 # CORR_SOURCE5 41 0.0113 - bond_coeff @bond:cd-nh harmonic 363.47 1.373 # SOURCE3_SOURCE5 976 0.0106 - bond_coeff @bond:cd-oh harmonic 389.45 1.347 # CORR_SOURCE5 248 0.0073 - bond_coeff @bond:cd-os harmonic 367.90 1.362 # SOURCE3_SOURCE5 1859 0.0083 - bond_coeff @bond:cd-pc harmonic 240.75 1.733 # SOURCE3 84 - bond_coeff @bond:cd-ss harmonic 231.98 1.756 # SOURCE3_SOURCE5 2011 0.0134 - bond_coeff @bond:cd-sy harmonic 214.05 1.784 # CORR_SOURCE5 73 0.0082 - bond_coeff @bond:ce-ce harmonic 306.13 1.457 # SOURCE1_SOURCE5 1000 0.0092 - bond_coeff @bond:ce-cf harmonic 452.16 1.351 # SOURCE1_SOURCE5 1908 0.0059 - bond_coeff @bond:ce-cg harmonic 341.16 1.427 # SOURCE1_SOURCE5 238 0.0053 - bond_coeff @bond:ce-ch harmonic 336.29 1.431 # SOURCE1 22 - bond_coeff @bond:ce-cl harmonic 174.72 1.764 # SOURCE4_SOURCE5 90 0.0111 - bond_coeff @bond:ce-cx harmonic 261.83 1.502 # SOURCE4_SOURCE5 31 0.0075 - bond_coeff @bond:ce-cy harmonic 250.06 1.516 # SOURCE4_SOURCE5 53 0.0043 - bond_coeff @bond:ce-h4 harmonic 385.40 1.092 # CORR_SOURCE5 315 0.0033 - bond_coeff @bond:ce-ha harmonic 391.44 1.088 # SOURCE3_SOURCE5 2751 0.0014 - bond_coeff @bond:ce-n1 harmonic 461.59 1.311 # CORR_SOURCE5 16 0.0049 - bond_coeff @bond:ce-n2 harmonic 506.97 1.287 # SOURCE1_SOURCE5 896 0.0038 - bond_coeff @bond:ce-n harmonic 301.69 1.424 # CORR_SOURCE5 209 0.0059 - bond_coeff @bond:ce-na harmonic 305.30 1.421 # SOURCE4_SOURCE5 11 0.0050 - bond_coeff @bond:ce-ne harmonic 336.57 1.394 # SOURCE3_SOURCE5 69 0.0151 - bond_coeff @bond:ce-nf harmonic 489.14 1.296 # CORR_SOURCE5 101 0.0097 - bond_coeff @bond:ce-nh harmonic 341.71 1.390 # CORR_SOURCE5 300 0.0133 - bond_coeff @bond:ce-oh harmonic 384.73 1.350 # CORR_SOURCE5 58 0.0102 - bond_coeff @bond:ce-os harmonic 355.66 1.371 # CORR_SOURCE5 96 0.0128 - bond_coeff @bond:ce-p2 harmonic 190.37 1.814 # SOUECE3 1 - bond_coeff @bond:ce-pe harmonic 188.22 1.818 # SOURCE3 8 0.0108 - bond_coeff @bond:ce-px harmonic 186.64 1.821 # SOURCE3 6 0.0046 - bond_coeff @bond:ce-py harmonic 194.96 1.806 # SOURCE3_SOURCE5 22 0.0142 - bond_coeff @bond:ce-s harmonic 291.39 1.680 # SOUECE3 1 - bond_coeff @bond:ce-ss harmonic 215.60 1.781 # SOURCE4_SOURCE5 56 0.0098 - bond_coeff @bond:ce-sx harmonic 193.92 1.819 # SOURCE3_SOURCE5 30 0.0101 - bond_coeff @bond:ce-sy harmonic 211.48 1.788 # SOURCE3_SOURCE5 41 0.0169 - bond_coeff @bond:c-f harmonic 387.77 1.325 # SOURCE2 6 0.0147 - bond_coeff @bond:cf-cf harmonic 306.13 1.457 # SOURCE1_SOURCE5 1000 0.0092 - bond_coeff @bond:cf-cg harmonic 336.29 1.431 # SOURCE1 22 - bond_coeff @bond:cf-ch harmonic 341.16 1.427 # SOURCE1_SOURCE5 238 0.0053 - bond_coeff @bond:cf-h4 harmonic 385.40 1.092 # CORR_SOURCE5 315 0.0033 - bond_coeff @bond:cf-ha harmonic 391.44 1.088 # SOURCE3_SOURCE5 2751 0.0014 - bond_coeff @bond:cf-n1 harmonic 461.59 1.311 # CORR_SOURCE5 16 0.0049 - bond_coeff @bond:cf-n2 harmonic 506.97 1.287 # SOURCE1_SOURCE5 896 0.0038 - bond_coeff @bond:cf-n harmonic 301.69 1.424 # CORR_SOURCE5 209 0.0059 - bond_coeff @bond:cf-ne harmonic 489.14 1.296 # CORR_SOURCE5 101 0.0097 - bond_coeff @bond:cf-nf harmonic 336.57 1.394 # SOURCE3_SOURCE5 62 0.0156 - bond_coeff @bond:cf-nh harmonic 341.71 1.390 # CORR_SOURCE5 300 0.0133 - bond_coeff @bond:cf-oh harmonic 384.73 1.350 # CORR_SOURCE5 58 0.0102 - bond_coeff @bond:cf-os harmonic 355.66 1.371 # CORR_SOURCE5 96 0.0128 - bond_coeff @bond:cf-p2 harmonic 190.37 1.814 # SOUECE3 1 - bond_coeff @bond:cf-pf harmonic 188.22 1.818 # SOURCE3 8 - bond_coeff @bond:cf-px harmonic 186.64 1.821 # SOURCE3 6 - bond_coeff @bond:cf-py harmonic 194.96 1.806 # SOURCE3_SOURCE5 17 0.0171 - bond_coeff @bond:cf-s harmonic 291.39 1.680 # SOUECE3 1 - bond_coeff @bond:cf-sx harmonic 193.92 1.819 # SOURCE3_SOURCE5 25 0.0105 - bond_coeff @bond:cf-sy harmonic 211.48 1.788 # SOURCE3_SOURCE5 36 0.0177 - bond_coeff @bond:cg-cg harmonic 421.79 1.369 # SOURCE1_SOURCE5 62 0.0025 - bond_coeff @bond:cg-ch harmonic 811.54 1.206 # SOURCE1_SOURCE5 156 0.0023 - bond_coeff @bond:cg-n1 harmonic 879.32 1.157 # SOURCE1_SOURCE5 879 0.0015 - bond_coeff @bond:cg-ne harmonic 435.38 1.326 # SOURCE4_SOURCE5 68 0.0013 - bond_coeff @bond:cg-pe harmonic 339.39 1.621 # SOURCE3 11 0.2008 - bond_coeff @bond:c-h4 harmonic 350.25 1.112 # SOURCE4_SOURCE5 506 0.0025 - bond_coeff @bond:c-h5 harmonic 361.80 1.105 # SOURCE4_SOURCE5 163 0.0038 - bond_coeff @bond:c-ha harmonic 368.78 1.101 # SOURCE3 53 0.0102 - bond_coeff @bond:ch-ch harmonic 421.79 1.369 # SOURCE1_SOURCE5 62 0.0025 - bond_coeff @bond:ch-n1 harmonic 879.32 1.157 # SOURCE1_SOURCE5 879 0.0015 - bond_coeff @bond:ch-nf harmonic 435.38 1.326 # SOURCE4_SOURCE5 51 0.0014 - bond_coeff @bond:ch-pf harmonic 339.39 1.621 # SOURCE3 11 - bond_coeff @bond:c-i harmonic 89.53 2.209 # SOURCE3 4 0.0365 - bond_coeff @bond:cl-cl harmonic 79.29 2.267 # SOURCE1 2 0.0395 - bond_coeff @bond:cl-cx harmonic 172.69 1.768 # SOURCE1_SOURCE5 42 0.0071 - bond_coeff @bond:cl-cy harmonic 161.13 1.792 # SOURCE2_SOURCE5 28 0.0103 - bond_coeff @bond:cl-n1 harmonic 217.59 1.630 # SOUECE3 1 - bond_coeff @bond:cl-n2 harmonic 123.81 1.819 # SOURCE3 6 0.1020 - bond_coeff @bond:cl-n3 harmonic 139.52 1.777 # SOURCE4_SOURCE5 16 0.0044 - bond_coeff @bond:cl-n harmonic 167.01 1.716 # SOURCE4_SOURCE5 17 0.0049 - bond_coeff @bond:cl-n4 harmonic 149.71 1.753 # SOURCE3 4 0.0098 - bond_coeff @bond:cl-na harmonic 118.36 1.835 # SOURCE3 7 0.2083 - bond_coeff @bond:cl-nh harmonic 145.39 1.763 # SOURCE3 1 - bond_coeff @bond:cl-no harmonic 116.71 1.840 # SOURCE2 1 - bond_coeff @bond:cl-o harmonic 331.00 1.483 # SOURCE3 4 - bond_coeff @bond:cl-oh harmonic 169.11 1.690 # SOURCE2 1 - bond_coeff @bond:cl-os harmonic 149.95 1.730 # SOURCE3 4 - bond_coeff @bond:cl-p2 harmonic 143.51 2.070 # SOURCE3 6 0.0108 - bond_coeff @bond:cl-p3 harmonic 167.79 2.008 # SOURCE1 111 - bond_coeff @bond:cl-p4 harmonic 167.79 2.008 # SOURCE1 111 - bond_coeff @bond:cl-p5 harmonic 167.79 2.008 # SOURCE1 111 - bond_coeff @bond:cl-pb harmonic 172.59 1.997 # SOURCE1 46 - bond_coeff @bond:cl-s harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:cl-s2 harmonic 185.62 2.161 # SOURCE2 1 - bond_coeff @bond:cl-s4 harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:cl-s6 harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:cl-sh harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:cl-ss harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:cl-sx harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:cl-sy harmonic 230.41 2.072 # SOURCE1 6 - bond_coeff @bond:c-n2 harmonic 306.30 1.420 # SOUECE3 1 - bond_coeff @bond:c-n4 harmonic 197.87 1.546 # SOURCE3 4 0.0388 - bond_coeff @bond:c-n harmonic 356.21 1.379 # SOURCE1_SOURCE5 9463 0.0137 - bond_coeff @bond:c-nc harmonic 346.03 1.387 # CORR_SOURCE5 179 0.0121 - bond_coeff @bond:c-nd harmonic 346.03 1.387 # CORR_SOURCE5 179 0.0121 - bond_coeff @bond:c-ne harmonic 340.70 1.391 # CORR_SOURCE5 87 0.0140 - bond_coeff @bond:c-nf harmonic 340.70 1.391 # CORR_SOURCE5 87 0.0140 - bond_coeff @bond:c-no harmonic 201.86 1.540 # SOUECE3 1 - bond_coeff @bond:c-o harmonic 652.57 1.218 # SOURCE1_SOURCE5 27083 0.0110 - bond_coeff @bond:c-oh harmonic 383.13 1.351 # SOURCE1_SOURCE5 3610 0.0055 - bond_coeff @bond:c-os harmonic 372.94 1.358 # SOURCE1_SOURCE5 5555 0.0163 - bond_coeff @bond:c-p2 harmonic 150.04 1.900 # SOUECE3 1 - bond_coeff @bond:c-p3 harmonic 157.13 1.883 # SOURCE3 6 0.0129 - bond_coeff @bond:c-p4 harmonic 158.42 1.880 # SOUECE3 1 - bond_coeff @bond:c-p5 harmonic 157.64 1.882 # SOURCE4_SOURCE5 25 0.0081 - bond_coeff @bond:cp-cp harmonic 277.60 1.485 # SOURCE1_SOURCE5 728 0.0059 - bond_coeff @bond:cp-cq harmonic 309.60 1.454 # SOURCE4_SOURCE5 34 0.0159 - bond_coeff @bond:c-pe harmonic 145.65 1.911 # SOURCE3 3 0.0025 - bond_coeff @bond:c-pf harmonic 145.65 1.911 # SOURCE3 3 - bond_coeff @bond:cp-na harmonic 349.52 1.384 # SOURCE4 7 0.0181 - bond_coeff @bond:cp-nb harmonic 414.72 1.339 # SOURCE4_SOURCE5 190 0.0068 - bond_coeff @bond:c-px harmonic 148.42 1.904 # SOURCE3 1 - bond_coeff @bond:c-py harmonic 164.17 1.867 # SOURCE3_SOURCE5 17 0.0103 - bond_coeff @bond:cq-cq harmonic 277.60 1.485 # SOURCE1_SOURCE5 728 0.0059 - bond_coeff @bond:c-s harmonic 298.35 1.672 # SOURCE1_SOURCE5 875 0.0114 - bond_coeff @bond:c-s4 harmonic 167.99 1.870 # SOUECE3 1 - bond_coeff @bond:c-s6 harmonic 167.99 1.870 # SOUECE3 1 - bond_coeff @bond:c-sh harmonic 206.09 1.797 # SOURCE3_SOURCE5 39 0.0097 - bond_coeff @bond:c-ss harmonic 204.39 1.800 # SOURCE1_SOURCE5 249 0.0157 - bond_coeff @bond:c-sx harmonic 161.23 1.885 # SOURCE3 5 0.0088 - bond_coeff @bond:c-sy harmonic 170.32 1.865 # SOURCE3 5 0.0085 - bond_coeff @bond:cu-cu harmonic 564.10 1.294 # SOURCE1 10 - bond_coeff @bond:cu-cx harmonic 277.70 1.485 # SOURCE1_SOURCE5 31 0.0066 - bond_coeff @bond:cu-ha harmonic 405.22 1.081 # SOURCE2 3 0.0111 - bond_coeff @bond:cv-cv harmonic 480.53 1.335 # SOURCE1 25 - bond_coeff @bond:cv-cy harmonic 250.66 1.515 # SOURCE1_SOURCE5 19 0.0057 - bond_coeff @bond:cv-ha harmonic 393.86 1.087 # SOURCE3 2 - bond_coeff @bond:cx-cv harmonic 256.87 1.508 # SOURCE1 2536 - bond_coeff @bond:cx-cx harmonic 260.31 1.504 # SOURCE1_SOURCE5 2781 0.0136 - bond_coeff @bond:cx-cy harmonic 250.83 1.515 # SOURCE3 2 - bond_coeff @bond:cx-f harmonic 339.01 1.360 # SOURCE2_SOURCE5 10 0.0045 - bond_coeff @bond:cx-h1 harmonic 390.15 1.089 # SOURCE3_SOURCE5 1142 0.0013 - bond_coeff @bond:cx-h2 harmonic 395.91 1.086 # SOURCE3_SOURCE5 5 0.0014 - bond_coeff @bond:cx-hc harmonic 393.86 1.087 # SOURCE3_SOURCE5 1702 0.0009 - bond_coeff @bond:cx-hx harmonic 397.60 1.085 # SOURCE4_SOURCE5 19 0.0002 - bond_coeff @bond:cx-n2 harmonic 245.89 1.482 # SOURCE3 2 - bond_coeff @bond:cx-n3 harmonic 256.30 1.470 # SOURCE1_SOURCE5 227 0.0050 - bond_coeff @bond:cx-n harmonic 283.33 1.442 # SOURCE4_SOURCE5 39 0.0103 - bond_coeff @bond:cx-na harmonic 264.52 1.461 # SOURCE4_SOURCE5 49 0.0026 - bond_coeff @bond:cx-nh harmonic 270.65 1.455 # SOURCE4_SOURCE5 192 0.0076 - bond_coeff @bond:cx-oh harmonic 369.30 1.361 # SOURCE3 3 0.0018 - bond_coeff @bond:cx-os harmonic 279.50 1.437 # SOURCE3_SOURCE5 703 0.0071 - bond_coeff @bond:cx-p3 harmonic 164.17 1.867 # SOURCE2 1 - bond_coeff @bond:cx-s4 harmonic 192.02 1.822 # SOURCE2 1 - bond_coeff @bond:cx-s6 harmonic 249.87 1.731 # SOURCE2 1 - bond_coeff @bond:cx-ss harmonic 186.43 1.833 # SOURCE2_SOURCE5 5 0.0011 - bond_coeff @bond:cy-cy harmonic 218.51 1.556 # SOURCE1_SOURCE5 1665 0.0053 - bond_coeff @bond:cy-f harmonic 344.83 1.356 # SOURCE4_SOURCE5 36 0.0095 - bond_coeff @bond:cy-h1 harmonic 379.11 1.095 # SOURCE3_SOURCE5 477 0.0019 - bond_coeff @bond:cy-h2 harmonic 382.87 1.093 # SOURCE4_SOURCE5 210 0.0017 - bond_coeff @bond:cy-hc harmonic 379.47 1.095 # SOURCE3_SOURCE5 840 0.0011 - bond_coeff @bond:cy-n harmonic 256.66 1.470 # SOURCE4_SOURCE5 618 0.0101 - bond_coeff @bond:cy-n3 harmonic 248.73 1.479 # SOURCE1_SOURCE5 67 0.0083 - bond_coeff @bond:cy-oh harmonic 305.23 1.412 # SOURCE3_SOURCE5 13 0.0082 - bond_coeff @bond:cy-os harmonic 277.32 1.439 # SOURCE4_SOURCE5 81 0.0141 - bond_coeff @bond:cy-s6 harmonic 177.00 1.851 # SOURCE4_SOURCE5 39 0.0142 - bond_coeff @bond:cy-ss harmonic 177.89 1.849 # SOURCE4_SOURCE5 201 0.0086 - bond_coeff @bond:cz-nh harmonic 414.24 1.339 # SOURCE4_SOURCE5 85 0.0046 - bond_coeff @bond:f-n1 harmonic 167.33 1.410 # SOUECE3 1 - bond_coeff @bond:f-n2 harmonic 148.04 1.444 # SOURCE3 5 0.0377 - bond_coeff @bond:f-n3 harmonic 169.79 1.406 # SOURCE1 9 - bond_coeff @bond:f-n harmonic 175.49 1.397 # SOURCE3 3 0.0112 - bond_coeff @bond:f-n4 harmonic 246.14 1.308 # SOURCE3 2 - bond_coeff @bond:f-na harmonic 166.72 1.411 # SOURCE3 7 0.0611 - bond_coeff @bond:f-nh harmonic 157.90 1.426 # SOURCE3 3 0.0085 - bond_coeff @bond:f-no harmonic 136.49 1.467 # SOURCE2 1 - bond_coeff @bond:f-o harmonic 198.07 1.330 # SOUECE3 1 - bond_coeff @bond:f-oh harmonic 129.79 1.444 # SOURCE3 1 - bond_coeff @bond:f-os harmonic 139.94 1.423 # SOURCE3 2 - bond_coeff @bond:f-p2 harmonic 522.31 1.536 # SOURCE3 7 0.2054 - bond_coeff @bond:f-p3 harmonic 454.68 1.578 # SOURCE2 8 0.0103 - bond_coeff @bond:f-p4 harmonic 437.32 1.590 # SOUECE3 1 - bond_coeff @bond:f-p5 harmonic 442.73 1.586 # SOURCE1_SOURCE5 18 0.0161 - bond_coeff @bond:f-s2 harmonic 363.47 1.643 # SOURCE2 1 - bond_coeff @bond:f-s harmonic 344.73 1.660 # SOUECE3 1 - bond_coeff @bond:f-s4 harmonic 428.80 1.591 # SOURCE2 4 0.0065 - bond_coeff @bond:f-s6 harmonic 400.85 1.612 # SOURCE2_SOURCE5 15 0.0133 - bond_coeff @bond:f-sh harmonic 356.72 1.649 # SOURCE3 1 - bond_coeff @bond:f-ss harmonic 373.87 1.634 # SOURCE3 3 0.0156 - bond_coeff @bond:hn-n1 harmonic 605.55 0.986 # SOURCE2 1 - bond_coeff @bond:hn-n2 harmonic 501.09 1.023 # SOURCE3_SOURCE5 732 0.0030 - bond_coeff @bond:hn-n3 harmonic 511.28 1.019 # SOURCE3_SOURCE5 5944 0.0012 - bond_coeff @bond:hn-n harmonic 527.31 1.013 # SOURCE3_SOURCE5 7593 0.0034 - bond_coeff @bond:hn-n4 harmonic 482.87 1.030 # SOURCE3_SOURCE5 756 0.0122 - bond_coeff @bond:hn-na harmonic 535.14 1.010 # SOURCE3_SOURCE5 1755 0.0019 - bond_coeff @bond:hn-nh harmonic 529.46 1.012 # SOURCE3_SOURCE5 7230 0.0022 - bond_coeff @bond:hn-no harmonic 501.09 1.023 # SOURCE3 1 - bond_coeff @bond:ho-o harmonic 540.28 0.981 # SOURCE3 1 - bond_coeff @bond:ho-oh harmonic 563.51 0.973 # SOURCE3_SOURCE5 21237 0.0034 - bond_coeff @bond:hp-p2 harmonic 266.54 1.336 # SOURCE3 87 0.1706 - bond_coeff @bond:hp-p3 harmonic 200.57 1.412 # SOURCE3_SOURCE5 123 0.0510 - bond_coeff @bond:hp-p4 harmonic 253.60 1.349 # SOURCE3 17 0.1577 - bond_coeff @bond:hp-p5 harmonic 196.39 1.418 # SOURCE3_SOURCE5 31 0.0077 - bond_coeff @bond:hs-s harmonic 288.27 1.353 # SOURCE3 1 - bond_coeff @bond:hs-s4 harmonic 265.33 1.375 # SOURCE3 5 0.0004 - bond_coeff @bond:hs-s6 harmonic 281.78 1.359 # SOURCE3 5 0.0015 - bond_coeff @bond:hs-sh harmonic 294.59 1.347 # SOURCE3_SOURCE5 477 0.0118 - bond_coeff @bond:i-i harmonic 50.27 2.917 # SOURCE1 1 - bond_coeff @bond:i-n1 harmonic 105.51 2.060 # SOUECE3 1 - bond_coeff @bond:i-n2 harmonic 59.35 2.304 # SOURCE3 6 0.1186 - bond_coeff @bond:i-n harmonic 96.05 2.098 # SOURCE3 5 0.0156 - bond_coeff @bond:i-n3 harmonic 77.95 2.185 # SOURCE3 3 0.0437 - bond_coeff @bond:i-n4 harmonic 83.69 2.155 # SOURCE3 3 0.0168 - bond_coeff @bond:i-na harmonic 89.07 2.129 # SOURCE3 8 0.1276 - bond_coeff @bond:i-nh harmonic 84.69 2.150 # SOURCE3 1 - bond_coeff @bond:i-no harmonic 70.03 2.231 # SOURCE3 1 - bond_coeff @bond:i-o harmonic 106.33 1.980 # SOUECE3 1 - bond_coeff @bond:i-oh harmonic 78.38 2.101 # SOURCE3 2 - bond_coeff @bond:i-os harmonic 73.23 2.129 # SOURCE3 3 0.0146 - bond_coeff @bond:i-p2 harmonic 66.30 2.643 # SOURCE3 6 0.0297 - bond_coeff @bond:i-p3 harmonic 77.18 2.566 # SOURCE3 3 0.0016 - bond_coeff @bond:i-p4 harmonic 120.75 2.352 # SOURCE3 4 0.2600 - bond_coeff @bond:i-p5 harmonic 72.70 2.596 # SOURCE3 3 0.0143 - bond_coeff @bond:i-s harmonic 115.77 2.430 # SOUECE3 1 - bond_coeff @bond:i-s4 harmonic 49.21 2.870 # SOUECE3 1 - bond_coeff @bond:i-s6 harmonic 49.21 2.870 # SOURCE3 1 - bond_coeff @bond:i-sh harmonic 88.56 2.560 # SOUECE3 1 - bond_coeff @bond:i-ss harmonic 86.63 2.571 # SOURCE3 3 0.0065 - bond_coeff @bond:n1-n1 harmonic 750.98 1.135 # SOURCE1_SOURCE5 78 0.0044 - bond_coeff @bond:n1-n2 harmonic 494.86 1.230 # SOURCE1_SOURCE5 36 0.0029 - bond_coeff @bond:n1-n3 harmonic 307.19 1.350 # SOUECE3 1 - bond_coeff @bond:n1-n4 harmonic 295.75 1.360 # SOUECE3 1 - bond_coeff @bond:n1-na harmonic 307.19 1.350 # SOUECE3 1 - bond_coeff @bond:n1-nc harmonic 525.73 1.216 # SOURCE1 38 - bond_coeff @bond:n1-nd harmonic 525.73 1.216 # SOURCE1 38 - bond_coeff @bond:n1-ne harmonic 452.52 1.252 # SOURCE2 1 - bond_coeff @bond:n1-nf harmonic 452.52 1.252 # SOURCE2 1 - bond_coeff @bond:n1-nh harmonic 319.16 1.340 # SOUECE3 1 - bond_coeff @bond:n1-no harmonic 254.81 1.400 # SOUECE3 1 - bond_coeff @bond:n1-o harmonic 298.40 1.277 # SOURCE3 5 0.0438 - bond_coeff @bond:n1-oh harmonic 272.24 1.300 # SOUECE3 1 - bond_coeff @bond:n1-os harmonic 261.73 1.310 # SOUECE3 1 - bond_coeff @bond:n1-p2 harmonic 268.95 1.678 # SOURCE3 2 0.0282 - bond_coeff @bond:n1-p3 harmonic 284.28 1.660 # SOUECE3 1 - bond_coeff @bond:n1-p4 harmonic 267.31 1.680 # SOURCE3 0 - bond_coeff @bond:n1-p5 harmonic 377.36 1.571 # SOURCE1 132 - bond_coeff @bond:n1-s2 harmonic 681.10 1.449 # SOURCE2 2 0.0010 - bond_coeff @bond:n1-s harmonic 339.70 1.659 # SOURCE3 6 0.0789 - bond_coeff @bond:n1-s4 harmonic 349.33 1.650 # SOUECE3 1 - bond_coeff @bond:n1-s6 harmonic 766.72 1.416 # SOURCE2 2 - bond_coeff @bond:n1-sh harmonic 396.29 1.610 # SOUECE3 1 - bond_coeff @bond:n1-ss harmonic 396.29 1.610 # SOUECE3 1 - bond_coeff @bond:n2-n2 harmonic 425.99 1.267 # SOURCE3_SOURCE5 40 0.0268 - bond_coeff @bond:n2-n3 harmonic 332.97 1.329 # SOURCE2 1 - bond_coeff @bond:n2-n4 harmonic 100.13 1.679 # SOURCE3 7 0.3138 - bond_coeff @bond:n2-na harmonic 287.40 1.368 # SOURCE4_SOURCE5 49 0.0087 - bond_coeff @bond:n2-nc harmonic 446.98 1.255 # SOURCE1 13 - bond_coeff @bond:n2-nd harmonic 446.98 1.255 # SOURCE1 13 - bond_coeff @bond:n2-ne harmonic 418.13 1.271 # SOURCE3_SOURCE5 57 0.0194 - bond_coeff @bond:n2-nf harmonic 418.13 1.271 # SOURCE3_SOURCE5 27 0.0074 - bond_coeff @bond:n2-nh harmonic 304.40 1.352 # SOURCE3_SOURCE5 210 0.0159 - bond_coeff @bond:n2-no harmonic 224.76 1.435 # SOURCE3_SOURCE5 15 0.0628 - bond_coeff @bond:n2-o harmonic 381.83 1.217 # SOURCE3_SOURCE5 112 0.0102 - bond_coeff @bond:n2-oh harmonic 192.13 1.391 # SOURCE1_SOURCE5 149 0.0171 - bond_coeff @bond:n2-os harmonic 184.98 1.401 # SOURCE3_SOURCE5 108 0.0101 - bond_coeff @bond:n2-p2 harmonic 338.04 1.605 # SOURCE3 35 0.0737 - bond_coeff @bond:n2-p3 harmonic 208.02 1.764 # SOURCE3 7 0.0374 - bond_coeff @bond:n2-p4 harmonic 234.05 1.724 # SOUECE3 1 - bond_coeff @bond:n2-p5 harmonic 344.61 1.599 # SOURCE1 7 - bond_coeff @bond:n2-pe harmonic 418.07 1.540 # SOURCE3 20 0.1392 - bond_coeff @bond:n2-pf harmonic 418.07 1.540 # SOURCE3 20 - bond_coeff @bond:n2-s2 harmonic 491.26 1.544 # SOURCE2_SOURCE5 11 0.0086 - bond_coeff @bond:n2-s4 harmonic 396.29 1.610 # SOUECE3 1 - bond_coeff @bond:n2-s harmonic 496.36 1.541 # SOURCE1 37 - bond_coeff @bond:n2-s6 harmonic 475.70 1.554 # SOURCE4_SOURCE5 16 0.0041 - bond_coeff @bond:n2-sh harmonic 267.45 1.738 # SOURCE3 5 0.0511 - bond_coeff @bond:n2-ss harmonic 342.87 1.656 # SOURCE1 36 - bond_coeff @bond:n3-n3 harmonic 219.29 1.442 # SOURCE1_SOURCE5 48 0.0063 - bond_coeff @bond:n3-n4 harmonic 228.50 1.430 # SOURCE1_SOURCE5 9 0.0040 - bond_coeff @bond:n3-na harmonic 236.90 1.420 # SOURCE1 68 - bond_coeff @bond:n3-nh harmonic 240.71 1.416 # SOURCE1_SOURCE5 66 0.0085 - bond_coeff @bond:n3-no harmonic 256.88 1.398 # SOURCE3_SOURCE5 19 0.0132 - bond_coeff @bond:n3-o harmonic 269.04 1.303 # SOURCE3 4 0.1217 - bond_coeff @bond:n3-oh harmonic 176.15 1.415 # SOURCE1_SOURCE5 17 0.0055 - bond_coeff @bond:n3-os harmonic 160.59 1.441 # SOURCE1_SOURCE5 84 0.0191 - bond_coeff @bond:n3-p2 harmonic 275.64 1.670 # SOUECE3 1 - bond_coeff @bond:n3-p3 harmonic 229.90 1.730 # SOURCE1 40 - bond_coeff @bond:n3-p4 harmonic 253.83 1.697 # SOURCE1 88 - bond_coeff @bond:n3-p5 harmonic 275.98 1.670 # SOURCE1_SOURCE5 680 0.0109 - bond_coeff @bond:n3-py harmonic 256.22 1.694 # SOURCE4_SOURCE5 16 0.0080 - bond_coeff @bond:n3-s harmonic 228.53 1.792 # SOURCE3 3 0.0178 - bond_coeff @bond:n3-s4 harmonic 254.85 1.754 # SOURCE3_SOURCE5 15 0.0416 - bond_coeff @bond:n3-s6 harmonic 326.04 1.672 # SOURCE1_SOURCE5 243 0.0144 - bond_coeff @bond:n3-sh harmonic 266.66 1.739 # SOURCE3 3 0.0154 - bond_coeff @bond:n3-ss harmonic 279.14 1.724 # SOURCE3_SOURCE5 25 0.0197 - bond_coeff @bond:n3-sy harmonic 303.10 1.696 # SOURCE4_SOURCE5 511 0.0083 - bond_coeff @bond:n4-n4 harmonic 188.86 1.484 # SOURCE3 4 0.0089 - bond_coeff @bond:n4-na harmonic 224.44 1.435 # SOURCE3 9 0.0390 - bond_coeff @bond:n4-nh harmonic 201.09 1.466 # SOURCE3 5 0.0108 - bond_coeff @bond:n4-no harmonic 191.50 1.480 # SOUECE3 1 - bond_coeff @bond:n4-o harmonic 215.08 1.361 # SOURCE3 3 0.0041 - bond_coeff @bond:n4-oh harmonic 186.01 1.400 # SOURCE3 3 0.0115 - bond_coeff @bond:n4-os harmonic 172.30 1.421 # SOURCE3 5 0.0249 - bond_coeff @bond:n4-p2 harmonic 126.91 1.942 # SOURCE3 10 0.0643 - bond_coeff @bond:n4-p3 harmonic 149.95 1.880 # SOURCE3 5 0.0146 - bond_coeff @bond:n4-p4 harmonic 128.26 1.938 # SOURCE3 1 - bond_coeff @bond:n4-p5 harmonic 172.23 1.830 # SOURCE3 5 0.0087 - bond_coeff @bond:n4-py harmonic 141.24 1.902 # SOURCE3 4 - bond_coeff @bond:n4-s harmonic 204.02 1.832 # SOURCE3 3 0.0004 - bond_coeff @bond:n4-s4 harmonic 139.73 1.972 # SOURCE3 3 0.0198 - bond_coeff @bond:n4-s6 harmonic 162.90 1.914 # SOURCE3 5 0.0432 - bond_coeff @bond:n4-sh harmonic 216.47 1.811 # SOURCE3 3 0.0027 - bond_coeff @bond:n4-ss harmonic 215.86 1.812 # SOURCE3 5 0.0064 - bond_coeff @bond:na-na harmonic 253.88 1.401 # SOURCE1 40 - bond_coeff @bond:na-nb harmonic 310.48 1.347 # SOURCE4_SOURCE5 26 0.0093 - bond_coeff @bond:na-nc harmonic 300.49 1.356 # SOURCE3_SOURCE5 899 0.0083 - bond_coeff @bond:na-nd harmonic 302.44 1.354 # SOURCE3_SOURCE5 362 0.0113 - bond_coeff @bond:na-nh harmonic 254.81 1.400 # SOURCE1_SOURCE5 20 0.0066 - bond_coeff @bond:na-no harmonic 224.76 1.435 # SOURCE3_SOURCE5 16 0.0192 - bond_coeff @bond:na-o harmonic 347.95 1.239 # SOURCE1_SOURCE5 93 0.0208 - bond_coeff @bond:na-oh harmonic 191.21 1.393 # SOURCE3_SOURCE5 18 0.0144 - bond_coeff @bond:na-os harmonic 158.65 1.444 # SOURCE3 45 0.0423 - bond_coeff @bond:na-p2 harmonic 217.35 1.749 # SOURCE3 11 0.0192 - bond_coeff @bond:na-p3 harmonic 209.23 1.762 # SOURCE3 8 0.0113 - bond_coeff @bond:na-p4 harmonic 386.12 1.564 # SOURCE3 5 0.2161 - bond_coeff @bond:na-p5 harmonic 240.43 1.715 # SOURCE3 11 0.0238 - bond_coeff @bond:na-pc harmonic 228.54 1.732 # SOURCE3 81 0.0207 - bond_coeff @bond:na-pd harmonic 228.54 1.732 # SOURCE3 81 - bond_coeff @bond:na-py harmonic 242.60 1.712 # SOURCE3 2 - bond_coeff @bond:na-s harmonic 247.08 1.765 # SOURCE3 8 0.0095 - bond_coeff @bond:na-s4 harmonic 227.88 1.793 # SOURCE3 10 0.0421 - bond_coeff @bond:na-s6 harmonic 279.89 1.723 # SOURCE3_SOURCE5 15 0.0153 - bond_coeff @bond:na-sh harmonic 281.31 1.721 # SOURCE3 9 0.0113 - bond_coeff @bond:na-ss harmonic 271.85 1.732 # SOURCE3_SOURCE5 50 0.0325 - bond_coeff @bond:na-sy harmonic 276.32 1.727 # SOURCE3 1 - bond_coeff @bond:nb-nb harmonic 327.23 1.333 # SOURCE1_SOURCE5 98 0.0106 - bond_coeff @bond:nb-pb harmonic 358.21 1.587 # SOURCE1 162 0.0091 - bond_coeff @bond:nc-nc harmonic 290.67 1.365 # SOURCE3_SOURCE5 271 0.0065 - bond_coeff @bond:nc-nd harmonic 374.73 1.299 # SOURCE3_SOURCE5 185 0.0074 - bond_coeff @bond:nc-os harmonic 185.12 1.401 # SOURCE1_SOURCE5 243 0.0096 - bond_coeff @bond:nc-ss harmonic 376.65 1.626 # SOURCE1_SOURCE5 114 0.0148 - bond_coeff @bond:nc-sy harmonic 473.81 1.555 # SOURCE3 2 - bond_coeff @bond:nd-nd harmonic 290.67 1.365 # SOURCE3_SOURCE5 271 0.0065 - bond_coeff @bond:nd-os harmonic 185.12 1.401 # SOURCE1_SOURCE5 243 0.0096 - bond_coeff @bond:nd-ss harmonic 376.65 1.626 # SOURCE1_SOURCE5 114 0.0148 - bond_coeff @bond:nd-sy harmonic 473.81 1.555 # SOURCE3 2 - bond_coeff @bond:ne-ne harmonic 235.02 1.422 # SOURCE3_SOURCE5 47 0.0776 - bond_coeff @bond:ne-nf harmonic 432.27 1.263 # SOURCE4_SOURCE5 78 0.0037 - bond_coeff @bond:ne-o harmonic 360.78 1.231 # SOURCE3_SOURCE5 55 0.0223 - bond_coeff @bond:ne-p2 harmonic 387.40 1.563 # SOURCE3 14 0.1325 - bond_coeff @bond:ne-pe harmonic 242.60 1.712 # SOURCE3 28 0.1076 - bond_coeff @bond:ne-px harmonic 250.02 1.702 # SOURCE3 11 0.0883 - bond_coeff @bond:ne-py harmonic 338.14 1.605 # SOURCE4_SOURCE5 94 0.0111 - bond_coeff @bond:ne-s harmonic 503.04 1.537 # SOURCE3 22 0.1708 - bond_coeff @bond:ne-sx harmonic 200.62 1.838 # SOURCE3 7 0.1060 - bond_coeff @bond:ne-sy harmonic 326.04 1.672 # SOURCE3_SOURCE5 49 0.0285 - bond_coeff @bond:nf-nf harmonic 235.02 1.422 # SOURCE3_SOURCE5 28 0.0146 - bond_coeff @bond:nf-o harmonic 360.78 1.231 # SOURCE3_SOURCE5 15 0.0138 - bond_coeff @bond:nf-p2 harmonic 387.40 1.563 # SOURCE3 14 - bond_coeff @bond:nf-pf harmonic 242.60 1.712 # SOURCE3 28 - bond_coeff @bond:nf-px harmonic 250.02 1.702 # SOURCE3 11 - bond_coeff @bond:nf-py harmonic 338.14 1.605 # SOURCE4_SOURCE5 84 0.0113 - bond_coeff @bond:nf-s harmonic 503.04 1.537 # SOURCE3 22 - bond_coeff @bond:nf-sx harmonic 200.62 1.838 # SOURCE3 7 - bond_coeff @bond:nf-sy harmonic 326.04 1.672 # SOURCE3_SOURCE5 42 0.0197 - bond_coeff @bond:nh-nh harmonic 252.77 1.402 # SOURCE1_SOURCE5 8 0.0109 - bond_coeff @bond:nh-no harmonic 267.93 1.386 # SOURCE4_SOURCE5 22 0.0046 - bond_coeff @bond:nh-o harmonic 316.06 1.263 # SOURCE3_SOURCE5 18 0.0143 - bond_coeff @bond:nh-oh harmonic 175.33 1.416 # SOURCE4_SOURCE5 63 0.0072 - bond_coeff @bond:nh-os harmonic 175.90 1.415 # SOURCE4_SOURCE5 26 0.0063 - bond_coeff @bond:nh-p2 harmonic 268.13 1.679 # SOURCE3 17 0.0872 - bond_coeff @bond:nh-p3 harmonic 229.90 1.730 # SOURCE3 3 0.0016 - bond_coeff @bond:nh-p4 harmonic 247.02 1.706 # SOURCE3 3 0.0008 - bond_coeff @bond:nh-p5 harmonic 274.79 1.671 # SOURCE3 3 0.0007 - bond_coeff @bond:nh-s harmonic 233.85 1.784 # SOURCE3 3 0.0076 - bond_coeff @bond:nh-s4 harmonic 258.92 1.749 # SOURCE3 3 0.0203 - bond_coeff @bond:nh-s6 harmonic 301.91 1.698 # SOURCE4_SOURCE5 93 0.0076 - bond_coeff @bond:nh-sh harmonic 292.49 1.708 # SOURCE3 1 - bond_coeff @bond:nh-ss harmonic 291.53 1.709 # SOURCE1_SOURCE5 58 0.0020 - bond_coeff @bond:nh-sy harmonic 287.18 1.714 # SOURCE4_SOURCE5 239 0.0099 - bond_coeff @bond:n-n1 harmonic 319.16 1.340 # SOUECE3 1 - bond_coeff @bond:n-n2 harmonic 295.31 1.360 # SOURCE3_SOURCE5 272 0.0114 - bond_coeff @bond:n-n3 harmonic 250.92 1.404 # SOURCE3_SOURCE5 87 0.0076 - bond_coeff @bond:n-n4 harmonic 226.87 1.432 # SOURCE3 5 0.0098 - bond_coeff @bond:n-n harmonic 250.83 1.404 # SOURCE3_SOURCE5 47 0.0125 - bond_coeff @bond:n-na harmonic 248.27 1.407 # SOURCE3_SOURCE5 56 0.0060 - bond_coeff @bond:n-nc harmonic 295.87 1.360 # CORR_SOURCE5 121 0.0130 - bond_coeff @bond:n-nd harmonic 295.87 1.360 # CORR_SOURCE5 121 0.0130 - bond_coeff @bond:n-nh harmonic 253.32 1.402 # SOURCE4_SOURCE5 51 0.0075 - bond_coeff @bond:n-no harmonic 208.29 1.456 # SOURCE3 4 0.0327 - bond_coeff @bond:n-o harmonic 342.80 1.243 # SOURCE3_SOURCE5 16 0.0255 - bond_coeff @bond:n-oh harmonic 181.83 1.406 # SOURCE3_SOURCE5 119 0.0062 - bond_coeff @bond:no-no harmonic 65.41 1.824 # SOURCE3 1 - bond_coeff @bond:no-o harmonic 367.95 1.226 # SOURCE1_SOURCE5 4403 0.0099 - bond_coeff @bond:no-oh harmonic 181.96 1.406 # SOURCE2 1 - bond_coeff @bond:no-os harmonic 172.24 1.421 # SOURCE4_SOURCE5 138 0.0070 - bond_coeff @bond:no-p2 harmonic 224.52 1.738 # SOURCE3 10 0.2231 - bond_coeff @bond:no-p3 harmonic 165.61 1.844 # SOURCE3 3 0.0005 - bond_coeff @bond:no-p4 harmonic 154.11 1.870 # SOURCE3 3 0.0006 - bond_coeff @bond:no-p5 harmonic 170.31 1.834 # SOURCE3 4 0.0020 - bond_coeff @bond:no-s harmonic 264.31 1.742 # SOURCE3 2 - bond_coeff @bond:n-os harmonic 180.04 1.409 # SOURCE4_SOURCE5 73 0.0121 - bond_coeff @bond:no-s4 harmonic 131.30 1.996 # SOURCE3 3 0.0313 - bond_coeff @bond:no-s6 harmonic 138.28 1.976 # SOURCE3 3 0.0520 - bond_coeff @bond:no-sh harmonic 220.82 1.804 # SOURCE3 1 - bond_coeff @bond:no-ss harmonic 206.32 1.828 # SOURCE3 3 0.0244 - bond_coeff @bond:n-p2 harmonic 227.87 1.733 # SOURCE3 8 0.0217 - bond_coeff @bond:n-p3 harmonic 204.42 1.770 # SOURCE3 9 0.0118 - bond_coeff @bond:n-p4 harmonic 227.19 1.734 # SOURCE3 1 - bond_coeff @bond:n-p5 harmonic 238.92 1.717 # SOURCE4_SOURCE5 25 0.0133 - bond_coeff @bond:n-pc harmonic 223.19 1.740 # SOURCE3 3 0.0010 - bond_coeff @bond:n-pd harmonic 223.19 1.740 # SOURCE3 3 - bond_coeff @bond:n-s harmonic 245.64 1.767 # SOURCE3 3 0.0011 - bond_coeff @bond:n-s4 harmonic 244.86 1.768 # SOURCE3_SOURCE5 9 0.0163 - bond_coeff @bond:n-s6 harmonic 283.34 1.719 # SOURCE4_SOURCE5 45 0.0154 - bond_coeff @bond:n-sh harmonic 275.50 1.728 # SOURCE3 4 0.0128 - bond_coeff @bond:n-ss harmonic 277.23 1.726 # SOURCE3_SOURCE5 22 0.0103 - bond_coeff @bond:n-sy harmonic 285.29 1.716 # SOURCE4_SOURCE5 126 0.0086 - bond_coeff @bond:oh-oh harmonic 123.13 1.469 # SOURCE3 1 - bond_coeff @bond:oh-os harmonic 129.12 1.456 # SOURCE4_SOURCE5 49 0.0046 - bond_coeff @bond:oh-p2 harmonic 329.87 1.630 # SOURCE3 8 0.0916 - bond_coeff @bond:oh-p3 harmonic 285.03 1.677 # SOURCE3 3 0.0148 - bond_coeff @bond:oh-p4 harmonic 318.66 1.641 # SOURCE3 4 0.0092 - bond_coeff @bond:oh-p5 harmonic 346.03 1.615 # SOURCE3_SOURCE5 1121 0.0129 - bond_coeff @bond:oh-py harmonic 344.61 1.616 # SOURCE3_SOURCE5 112 0.0110 - bond_coeff @bond:oh-s harmonic 219.79 1.812 # SOURCE3 2 - bond_coeff @bond:oh-s4 harmonic 309.00 1.696 # SOURCE4_SOURCE5 29 0.0100 - bond_coeff @bond:oh-s6 harmonic 373.26 1.635 # SOURCE3_SOURCE5 193 0.0162 - bond_coeff @bond:oh-sh harmonic 312.59 1.692 # SOURCE3 2 0.0003 - bond_coeff @bond:oh-ss harmonic 316.41 1.688 # SOURCE3_SOURCE5 12 0.0167 - bond_coeff @bond:oh-sy harmonic 356.03 1.650 # SOURCE4_SOURCE5 123 0.0037 - bond_coeff @bond:o-o harmonic 141.39 1.430 # SOURCE3 2 0.0500 - bond_coeff @bond:o-oh harmonic 104.37 1.517 # SOURCE3 2 - bond_coeff @bond:o-os harmonic 109.10 1.504 # SOURCE3 3 0.0117 - bond_coeff @bond:o-p2 harmonic 492.04 1.508 # SOURCE3 17 0.0306 - bond_coeff @bond:o-p3 harmonic 480.47 1.515 # SOURCE3 35 0.0297 - bond_coeff @bond:o-p4 harmonic 498.98 1.504 # SOURCE3_SOURCE5 60 0.0565 - bond_coeff @bond:o-p5 harmonic 529.55 1.487 # SOURCE1_SOURCE5 1318 0.0133 - bond_coeff @bond:o-pe harmonic 470.81 1.521 # SOURCE3 20 0.0171 - bond_coeff @bond:o-pf harmonic 470.81 1.521 # SOURCE3 20 - bond_coeff @bond:o-px harmonic 499.66 1.504 # SOURCE3_SOURCE5 45 0.0136 - bond_coeff @bond:o-py harmonic 527.91 1.488 # SOURCE3_SOURCE5 119 0.0072 - bond_coeff @bond:o-s harmonic 226.13 1.802 # SOURCE3 2 - bond_coeff @bond:o-s2 harmonic 417.99 1.599 # SOURCE3 3 0.0707 - bond_coeff @bond:o-s4 harmonic 572.26 1.504 # SOURCE1_SOURCE5 137 0.0127 - bond_coeff @bond:o-s6 harmonic 683.03 1.453 # SOURCE1_SOURCE5 2456 0.0105 - bond_coeff @bond:o-sh harmonic 410.02 1.605 # SOURCE3 2 - bond_coeff @bond:os-os harmonic 124.74 1.465 # SOURCE1_SOURCE5 69 0.0090 - bond_coeff @bond:os-p2 harmonic 396.10 1.573 # SOURCE1 16 - bond_coeff @bond:os-p3 harmonic 287.31 1.674 # SOURCE3_SOURCE5 22 0.0105 - bond_coeff @bond:os-p4 harmonic 323.70 1.636 # SOURCE3 4 0.0057 - bond_coeff @bond:os-p5 harmonic 346.25 1.615 # SOURCE1_SOURCE5 1200 0.0218 - bond_coeff @bond:os-py harmonic 342.10 1.619 # SOURCE3_SOURCE5 68 0.0106 - bond_coeff @bond:os-s harmonic 227.43 1.800 # SOURCE3 3 0.0052 - bond_coeff @bond:o-ss harmonic 567.21 1.507 # SOURCE3_SOURCE5 22 0.0235 - bond_coeff @bond:os-s4 harmonic 312.40 1.692 # SOURCE3_SOURCE5 25 0.0189 - bond_coeff @bond:os-s6 harmonic 387.79 1.623 # SOURCE1_SOURCE5 242 0.0147 - bond_coeff @bond:os-sh harmonic 333.31 1.671 # SOURCE3 3 0.0106 - bond_coeff @bond:os-ss harmonic 301.43 1.704 # SOURCE3 9 0.0277 - bond_coeff @bond:os-sy harmonic 306.02 1.699 # SOURCE3 1 - bond_coeff @bond:o-sx harmonic 555.55 1.513 # SOURCE3_SOURCE5 136 0.0072 - bond_coeff @bond:o-sy harmonic 653.16 1.466 # SOURCE3_SOURCE5 2007 0.0061 - bond_coeff @bond:p2-p2 harmonic 307.63 1.786 # SOURCE3 25 0.3488 - bond_coeff @bond:p2-p3 harmonic 118.00 2.152 # SOURCE3 9 0.1777 - bond_coeff @bond:p2-p4 harmonic 110.68 2.179 # SOUECE3 1 - bond_coeff @bond:p2-p5 harmonic 110.42 2.180 # SOUECE3 1 - bond_coeff @bond:p2-pe harmonic 244.92 1.867 # SOURCE3 16 0.3571 - bond_coeff @bond:p2-pf harmonic 244.92 1.867 # SOURCE3 16 - bond_coeff @bond:p2-s harmonic 375.05 1.772 # SOURCE3 26 0.3014 - bond_coeff @bond:p2-s4 harmonic 126.27 2.190 # SOUECE3 1 - bond_coeff @bond:p2-s6 harmonic 129.28 2.180 # SOUECE3 1 - bond_coeff @bond:p2-sh harmonic 217.02 1.971 # SOURCE3 10 0.2829 - bond_coeff @bond:p2-ss harmonic 219.87 1.966 # SOURCE3 10 0.2739 - bond_coeff @bond:p3-p3 harmonic 101.97 2.214 # SOURCE1 41 - bond_coeff @bond:p3-p4 harmonic 101.50 2.216 # SOURCE3 3 0.0011 - bond_coeff @bond:p3-p5 harmonic 102.21 2.213 # SOURCE3 9 0.0265 - bond_coeff @bond:p3-s harmonic 168.70 2.070 # SOUECE3 1 - bond_coeff @bond:p3-s4 harmonic 161.75 2.087 # SOURCE3 8 0.2235 - bond_coeff @bond:p3-s6 harmonic 165.79 2.077 # SOURCE3 11 0.1420 - bond_coeff @bond:p3-sh harmonic 144.95 2.132 # SOURCE3 3 0.0078 - bond_coeff @bond:p3-ss harmonic 148.86 2.121 # SOURCE3 3 0.0059 - bond_coeff @bond:p4-p4 harmonic 157.68 2.034 # SOURCE1 1 - bond_coeff @bond:p4-p5 harmonic 96.70 2.237 # SOUECE3 1 - bond_coeff @bond:p4-s harmonic 140.16 2.146 # SOURCE3 5 0.0601 - bond_coeff @bond:p4-s4 harmonic 109.64 2.251 # SOUECE3 1 - bond_coeff @bond:p4-s6 harmonic 105.24 2.269 # SOUECE3 1 - bond_coeff @bond:p4-sh harmonic 151.04 2.115 # SOURCE3 4 0.0008 - bond_coeff @bond:p4-ss harmonic 155.14 2.104 # SOURCE3 4 0.0044 - bond_coeff @bond:p5-p5 harmonic 149.95 2.054 # SOURCE1 1 - bond_coeff @bond:p5-s harmonic 239.16 1.934 # SOURCE1_SOURCE5 173 0.0138 - bond_coeff @bond:p5-s4 harmonic 181.84 2.040 # SOUECE3 1 - bond_coeff @bond:p5-s6 harmonic 181.84 2.040 # SOUECE3 1 - bond_coeff @bond:p5-sh harmonic 163.76 2.082 # SOURCE3 3 0.0035 - bond_coeff @bond:p5-ss harmonic 150.09 2.118 # SOURCE4_SOURCE5 70 0.0117 - bond_coeff @bond:pe-pe harmonic 136.46 2.092 # SOURCE3 7 0.1369 - bond_coeff @bond:pe-pf harmonic 149.57 2.055 # SOURCE3 1 - bond_coeff @bond:pe-px harmonic 169.76 2.005 # SOURCE3 12 0.2609 - bond_coeff @bond:pe-py harmonic 161.32 2.025 # SOURCE3 12 0.2617 - bond_coeff @bond:pe-s harmonic 390.65 1.758 # SOURCE3 31 0.3197 - bond_coeff @bond:pe-sx harmonic 133.00 2.168 # SOURCE3 9 0.1743 - bond_coeff @bond:pe-sy harmonic 119.67 2.213 # SOURCE3 6 0.0127 - bond_coeff @bond:pf-pf harmonic 136.46 2.092 # SOURCE3 7 - bond_coeff @bond:pf-px harmonic 169.76 2.005 # SOURCE3 12 - bond_coeff @bond:pf-py harmonic 161.32 2.025 # SOURCE3 12 - bond_coeff @bond:pf-s harmonic 390.65 1.758 # SOURCE3 31 - bond_coeff @bond:pf-sx harmonic 133.00 2.168 # SOURCE3 9 - bond_coeff @bond:pf-sy harmonic 119.67 2.213 # SOURCE3 6 - bond_coeff @bond:px-py harmonic 105.60 2.199 # SOURCE3 5 0.0238 - bond_coeff @bond:px-sx harmonic 111.92 2.242 # SOURCE3 3 0.0119 - bond_coeff @bond:px-sy harmonic 110.14 2.249 # SOURCE3 3 0.0272 - bond_coeff @bond:py-py harmonic 108.87 2.186 # SOURCE3 8 0.0132 - bond_coeff @bond:py-sx harmonic 107.66 2.259 # SOURCE3 7 0.0603 - bond_coeff @bond:py-sy harmonic 128.67 2.182 # SOURCE3 5 0.0047 - bond_coeff @bond:s4-s4 harmonic 243.62 2.080 # SOUECE3 1 - bond_coeff @bond:s4-s6 harmonic 243.62 2.080 # SOUECE3 1 - bond_coeff @bond:s4-sh harmonic 196.89 2.168 # SOURCE3 3 0.0227 - bond_coeff @bond:s4-ss harmonic 197.83 2.166 # SOURCE3 5 0.0247 - bond_coeff @bond:s6-s6 harmonic 243.62 2.080 # SOUECE3 1 - bond_coeff @bond:s6-sh harmonic 227.44 2.108 # SOURCE3 3 0.0144 - bond_coeff @bond:s6-ss harmonic 221.98 2.118 # SOURCE3 5 0.0209 - bond_coeff @bond:sh-sh harmonic 257.31 2.058 # SOURCE2 1 - bond_coeff @bond:sh-ss harmonic 251.60 2.067 # SOURCE3 3 0.0029 - bond_coeff @bond:s-s harmonic 276.08 2.030 # SOURCE3 1 - bond_coeff @bond:s-s2 harmonic 391.11 1.897 # SOURCE1 5 - bond_coeff @bond:s-s4 harmonic 246.05 2.076 # SOURCE3 4 0.0345 - bond_coeff @bond:s-s6 harmonic 270.56 2.038 # SOURCE3 3 0.0311 - bond_coeff @bond:s-sh harmonic 226.34 2.110 # SOURCE3 2 - bond_coeff @bond:s-ss harmonic 238.28 2.089 # SOURCE3 1 - bond_coeff @bond:ss-ss harmonic 248.01 2.073 # SOURCE1_SOURCE5 457 0.0074 - bond_coeff @bond:sx-sx harmonic 119.03 2.391 # SOURCE3 3 0.0185 - bond_coeff @bond:sx-sy harmonic 160.84 2.255 # SOURCE3 5 0.0737 - bond_coeff @bond:sy-sy harmonic 162.69 2.250 # SOURCE3 3 0.0289 - bond_coeff @bond:br-cd harmonic 172.53 1.885 # SOURCE4_SOURCE5 89 0.0082 - bond_coeff @bond:c1-cf harmonic 518.69 1.315 # SOURCE4 6 - bond_coeff @bond:cd-f harmonic 364.99 1.341 # SOURCE4_SOURCE5 46 0.0041 - bond_coeff @bond:cd-n4 harmonic 236.72 1.493 # SOURCE4 7 - bond_coeff @bond:cd-nf harmonic 356.61 1.379 # SOURCE4_SOURCE5 52 0.0115 - bond_coeff @bond:cd-no harmonic 296.62 1.429 # SOURCE4_SOURCE5 253 0.0081 - bond_coeff @bond:cd-sh harmonic 223.28 1.769 # SOURCE4_SOURCE5 14 0.0031 - bond_coeff @bond:cd-sx harmonic 198.26 1.811 # SOURCE4_SOURCE5 28 0.0024 - bond_coeff @bond:cc-cy harmonic 259.34 1.505 # SOURCE4_SOURCE5 11 0.0006 - bond_coeff @bond:cf-cl harmonic 174.72 1.764 # SOURCE4_SOURCE5 66 0.0129 - bond_coeff @bond:cf-cx harmonic 261.83 1.502 # SOURCE4_SOURCE5 26 0.0077 - bond_coeff @bond:cf-cy harmonic 250.06 1.516 # SOURCE4_SOURCE5 36 0.0052 - bond_coeff @bond:cf-na harmonic 305.30 1.421 # SOURCE4_SOURCE5 6 0.0049 - bond_coeff @bond:cf-ss harmonic 215.60 1.781 # SOURCE4_SOURCE5 46 0.0106 - bond_coeff @bond:cq-na harmonic 349.52 1.384 # SOURCE4 7 - bond_coeff @bond:cq-nb harmonic 414.72 1.339 # SOURCE4_SOURCE5 120 0.0071 - bond_coeff @bond:cl-py harmonic 152.76 2.045 # SOURCE5 45 0.0072 - bond_coeff @bond:f-py harmonic 456.16 1.577 # SOURCE5 25 0.0035 - bond_coeff @bond:py-s harmonic 215.89 1.973 # SOURCE5 17 0.0159 - bond_coeff @bond:cy-nh harmonic 251.08 1.476 # SOURCE5 16 0.0050 - bond_coeff @bond:cy-hx harmonic 386.49 1.091 # SOURCE5 13 0.0007 - bond_coeff @bond:br-ce harmonic 163.42 1.905 # SOURCE5 12 0.0099 - bond_coeff @bond:cc-i harmonic 110.60 2.120 # SOURCE5 11 0.0086 - bond_coeff @bond:cy-n4 harmonic 214.44 1.522 # SOURCE5 11 0.0076 - bond_coeff @bond:cy-p3 harmonic 146.83 1.908 # SOURCE5 10 0.0056 - bond_coeff @bond:cy-na harmonic 279.03 1.446 # SOURCE5 8 0.0049 - bond_coeff @bond:cx-n4 harmonic 234.29 1.496 # SOURCE5 9 0.0009 - bond_coeff @bond:ne-s4 harmonic 338.65 1.660 # SOURCE5 6 0.0027 - bond_coeff @bond:cv-ss harmonic 228.75 1.761 # SOURCE5 8 0.0086 - bond_coeff @bond:cy-no harmonic 216.62 1.519 # SOURCE5 7 0.0035 - bond_coeff @bond:ce-cv harmonic 436.82 1.360 # SOURCE5 6 0.0111 - bond_coeff @bond:cd-i harmonic 111.95 2.115 # SOURCE5 7 0.0138 - bond_coeff @bond:cy-s4 harmonic 149.47 1.913 # SOURCE5 5 0.0068 - bond_coeff @bond:n2-sy harmonic 491.42 1.544 # SOURCE5 7 0.0042 - bond_coeff @bond:cc-s6 harmonic 196.41 1.814 # SOURCE5 6 0.0108 - bond_coeff @bond:i-s2 harmonic 48.08 2.883 # SOURCE5 5 0.0165 - bond_coeff @bond:br-cy harmonic 144.56 1.951 # SOURCE5 5 0.0056 - bond_coeff @bond:br-cf harmonic 163.42 1.905 # SOURCE5 12 0.0099 - bond_coeff @bond:nf-s4 harmonic 338.65 1.660 # SOURCE5 6 0.0027 - bond_coeff @bond:cf-cv harmonic 436.82 1.360 # SOURCE5 6 0.0111 - bond_coeff @bond:cd-s6 harmonic 196.41 1.814 # SOURCE5 6 0.0108 - bond_coeff @bond:ss-sy harmonic 177.36 2.212 # SOURCE5 4 0.0105 - bond_coeff @bond:h5-ce harmonic 390.52 1.089 # SOURCE5 4 0.0006 - bond_coeff @bond:h5-cf harmonic 390.52 1.089 # SOURCE5 4 0.0006 - bond_coeff @bond:ce-s4 harmonic 226.75 1.764 # SOURCE5 4 0.0087 - bond_coeff @bond:cf-s4 harmonic 226.69 1.764 # SOURCE5 4 0.0087 - bond_coeff @bond:cy-py harmonic 136.02 1.937 # SOURCE5 4 0.0000 - bond_coeff @bond:cd-o harmonic 649.55 1.219 # SOURCE5 4 0.0015 - bond_coeff @bond:ne-s6 harmonic 412.23 1.598 # SOURCE5 3 0.0054 - bond_coeff @bond:nf-s6 harmonic 412.23 1.598 # SOURCE5 3 0.0054 - bond_coeff @bond:ce-no harmonic 262.66 1.463 # SOURCE5 3 0.0129 - bond_coeff @bond:cf-no harmonic 262.66 1.463 # SOURCE5 3 0.0129 - } # (end of bond_coeffs) - - write_once("Data Bonds By Type") { - @bond:ow-hw @atom:ow @atom:hw - @bond:hw-hw @atom:hw @atom:hw - @bond:br-br @atom:br @atom:br - @bond:br-c1 @atom:br @atom:c1 - @bond:br-c2 @atom:br @atom:c2 - @bond:br-c @atom:br @atom:c - @bond:br-c3 @atom:br @atom:c3 - @bond:br-ca @atom:br @atom:ca - @bond:br-cc @atom:br @atom:cc - @bond:br-cx @atom:br @atom:cx - @bond:br-n1 @atom:br @atom:n1 - @bond:br-n2 @atom:br @atom:n2 - @bond:br-n @atom:br @atom:n - @bond:br-n3 @atom:br @atom:n3 - @bond:br-n4 @atom:br @atom:n4 - @bond:br-na @atom:br @atom:na - @bond:br-nh @atom:br @atom:nh - @bond:br-no @atom:br @atom:no - @bond:br-o @atom:br @atom:o - @bond:br-oh @atom:br @atom:oh - @bond:br-os @atom:br @atom:os - @bond:br-p2 @atom:br @atom:p2 - @bond:br-p3 @atom:br @atom:p3 - @bond:br-p4 @atom:br @atom:p4 - @bond:br-p5 @atom:br @atom:p5 - @bond:br-s @atom:br @atom:s - @bond:br-s4 @atom:br @atom:s4 - @bond:br-s6 @atom:br @atom:s6 - @bond:br-sh @atom:br @atom:sh - @bond:br-ss @atom:br @atom:ss - @bond:c1-c1 @atom:c1 @atom:c1 - @bond:c1-c2 @atom:c1 @atom:c2 - @bond:c1-c3 @atom:c1 @atom:c3 - @bond:c1-ca @atom:c1 @atom:ca - @bond:c1-ce @atom:c1 @atom:ce - @bond:c1-cg @atom:c1 @atom:cg - @bond:c1-ch @atom:c1 @atom:ch - @bond:c1-cl @atom:c1 @atom:cl - @bond:c1-cx @atom:c1 @atom:cx - @bond:c1-f @atom:c1 @atom:f - @bond:c1-ha @atom:c1 @atom:ha - @bond:c1-hc @atom:c1 @atom:hc - @bond:c1-i @atom:c1 @atom:i - @bond:c1-n1 @atom:c1 @atom:n1 - @bond:c1-n2 @atom:c1 @atom:n2 - @bond:c1-n3 @atom:c1 @atom:n3 - @bond:c1-n4 @atom:c1 @atom:n4 - @bond:c1-n @atom:c1 @atom:n - @bond:c1-na @atom:c1 @atom:na - @bond:c1-ne @atom:c1 @atom:ne - @bond:c1-nf @atom:c1 @atom:nf - @bond:c1-nh @atom:c1 @atom:nh - @bond:c1-no @atom:c1 @atom:no - @bond:c1-o @atom:c1 @atom:o - @bond:c1-oh @atom:c1 @atom:oh - @bond:c1-os @atom:c1 @atom:os - @bond:c1-p2 @atom:c1 @atom:p2 - @bond:c1-p3 @atom:c1 @atom:p3 - @bond:c1-p4 @atom:c1 @atom:p4 - @bond:c1-p5 @atom:c1 @atom:p5 - @bond:c1-s2 @atom:c1 @atom:s2 - @bond:c1-s @atom:c1 @atom:s - @bond:c1-s4 @atom:c1 @atom:s4 - @bond:c1-s6 @atom:c1 @atom:s6 - @bond:c1-sh @atom:c1 @atom:sh - @bond:c1-ss @atom:c1 @atom:ss - @bond:c2-c2 @atom:c2 @atom:c2 - @bond:c2-c3 @atom:c2 @atom:c3 - @bond:c2-ca @atom:c2 @atom:ca - @bond:c2-cc @atom:c2 @atom:cc - @bond:c2-cd @atom:c2 @atom:cd - @bond:c2-ce @atom:c2 @atom:ce - @bond:c2-cf @atom:c2 @atom:cf - @bond:c2-cl @atom:c2 @atom:cl - @bond:c2-cu @atom:c2 @atom:cu - @bond:c2-cx @atom:c2 @atom:cx - @bond:c2-cy @atom:c2 @atom:cy - @bond:c2-f @atom:c2 @atom:f - @bond:c2-h4 @atom:c2 @atom:h4 - @bond:c2-h5 @atom:c2 @atom:h5 - @bond:c2-ha @atom:c2 @atom:ha - @bond:c2-hc @atom:c2 @atom:hc - @bond:c2-hx @atom:c2 @atom:hx - @bond:c2-i @atom:c2 @atom:i - @bond:c2-n1 @atom:c2 @atom:n1 - @bond:c2-n2 @atom:c2 @atom:n2 - @bond:c2-n3 @atom:c2 @atom:n3 - @bond:c2-n @atom:c2 @atom:n - @bond:c2-n4 @atom:c2 @atom:n4 - @bond:c2-na @atom:c2 @atom:na - @bond:c2-nc @atom:c2 @atom:nc - @bond:c2-nd @atom:c2 @atom:nd - @bond:c2-ne @atom:c2 @atom:ne - @bond:c2-nf @atom:c2 @atom:nf - @bond:c2-nh @atom:c2 @atom:nh - @bond:c2-no @atom:c2 @atom:no - @bond:c2-o @atom:c2 @atom:o - @bond:c2-oh @atom:c2 @atom:oh - @bond:c2-os @atom:c2 @atom:os - @bond:c2-p2 @atom:c2 @atom:p2 - @bond:c2-p3 @atom:c2 @atom:p3 - @bond:c2-p4 @atom:c2 @atom:p4 - @bond:c2-p5 @atom:c2 @atom:p5 - @bond:c2-pe @atom:c2 @atom:pe - @bond:c2-pf @atom:c2 @atom:pf - @bond:c2-s2 @atom:c2 @atom:s2 - @bond:c2-s @atom:c2 @atom:s - @bond:c2-s4 @atom:c2 @atom:s4 - @bond:c2-s6 @atom:c2 @atom:s6 - @bond:c2-sh @atom:c2 @atom:sh - @bond:c2-ss @atom:c2 @atom:ss - @bond:c3-c3 @atom:c3 @atom:c3 - @bond:c3-ca @atom:c3 @atom:ca - @bond:c3-cc @atom:c3 @atom:cc - @bond:c3-cd @atom:c3 @atom:cd - @bond:c3-ce @atom:c3 @atom:ce - @bond:c3-cf @atom:c3 @atom:cf - @bond:c3-cl @atom:c3 @atom:cl - @bond:c3-cu @atom:c3 @atom:cu - @bond:c3-cv @atom:c3 @atom:cv - @bond:c3-cx @atom:c3 @atom:cx - @bond:c3-cy @atom:c3 @atom:cy - @bond:c3-f @atom:c3 @atom:f - @bond:c3-h1 @atom:c3 @atom:h1 - @bond:c3-h2 @atom:c3 @atom:h2 - @bond:c3-h3 @atom:c3 @atom:h3 - @bond:c3-hc @atom:c3 @atom:hc - @bond:c3-hx @atom:c3 @atom:hx - @bond:c3-i @atom:c3 @atom:i - @bond:c3-n1 @atom:c3 @atom:n1 - @bond:c3-n2 @atom:c3 @atom:n2 - @bond:c3-n @atom:c3 @atom:n - @bond:c3-n3 @atom:c3 @atom:n3 - @bond:c3-n4 @atom:c3 @atom:n4 - @bond:c3-na @atom:c3 @atom:na - 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@bond:cc-ne @atom:cc @atom:ne - @bond:cc-nf @atom:cc @atom:nf - @bond:cc-nh @atom:cc @atom:nh - @bond:cc-no @atom:cc @atom:no - @bond:cc-oh @atom:cc @atom:oh - @bond:cc-os @atom:cc @atom:os - @bond:cc-pd @atom:cc @atom:pd - @bond:cc-sh @atom:cc @atom:sh - @bond:cc-ss @atom:cc @atom:ss - @bond:cc-sx @atom:cc @atom:sx - @bond:cc-sy @atom:cc @atom:sy - @bond:c-cu @atom:c @atom:cu - @bond:c-cx @atom:c @atom:cx - @bond:c-cy @atom:c @atom:cy - @bond:cd-cd @atom:cd @atom:cd - @bond:cd-ce @atom:cd @atom:ce - @bond:cd-cf @atom:cd @atom:cf - @bond:cd-cg @atom:cd @atom:cg - @bond:cd-ch @atom:cd @atom:ch - @bond:cd-cl @atom:cd @atom:cl - @bond:cd-cx @atom:cd @atom:cx - @bond:cd-cy @atom:cd @atom:cy - @bond:cd-h4 @atom:cd @atom:h4 - @bond:cd-h5 @atom:cd @atom:h5 - @bond:cd-ha @atom:cd @atom:ha - @bond:cd-n2 @atom:cd @atom:n2 - @bond:cd-n @atom:cd @atom:n - @bond:cd-na @atom:cd @atom:na - @bond:cd-nc @atom:cd @atom:nc - @bond:cd-nd @atom:cd @atom:nd - @bond:cd-ne @atom:cd @atom:ne - @bond:cd-nh @atom:cd @atom:nh - @bond:cd-oh @atom:cd @atom:oh - @bond:cd-os @atom:cd @atom:os - @bond:cd-pc @atom:cd @atom:pc - @bond:cd-ss @atom:cd @atom:ss - @bond:cd-sy @atom:cd @atom:sy - @bond:ce-ce @atom:ce @atom:ce - @bond:ce-cf @atom:ce @atom:cf - @bond:ce-cg @atom:ce @atom:cg - @bond:ce-ch @atom:ce @atom:ch - @bond:ce-cl @atom:ce @atom:cl - @bond:ce-cx @atom:ce @atom:cx - @bond:ce-cy @atom:ce @atom:cy - @bond:ce-h4 @atom:ce @atom:h4 - @bond:ce-ha @atom:ce @atom:ha - @bond:ce-n1 @atom:ce @atom:n1 - @bond:ce-n2 @atom:ce @atom:n2 - @bond:ce-n @atom:ce @atom:n - @bond:ce-na @atom:ce @atom:na - @bond:ce-ne @atom:ce @atom:ne - @bond:ce-nf @atom:ce @atom:nf - @bond:ce-nh @atom:ce @atom:nh - @bond:ce-oh @atom:ce @atom:oh - @bond:ce-os @atom:ce @atom:os - @bond:ce-p2 @atom:ce @atom:p2 - @bond:ce-pe @atom:ce @atom:pe - @bond:ce-px @atom:ce @atom:px - @bond:ce-py @atom:ce @atom:py - @bond:ce-s @atom:ce @atom:s - @bond:ce-ss @atom:ce @atom:ss - @bond:ce-sx @atom:ce @atom:sx - @bond:ce-sy @atom:ce @atom:sy - @bond:c-f @atom:c @atom:f - @bond:cf-cf @atom:cf @atom:cf - @bond:cf-cg @atom:cf @atom:cg - @bond:cf-ch @atom:cf @atom:ch - @bond:cf-h4 @atom:cf @atom:h4 - @bond:cf-ha @atom:cf @atom:ha - @bond:cf-n1 @atom:cf @atom:n1 - @bond:cf-n2 @atom:cf @atom:n2 - @bond:cf-n @atom:cf @atom:n - @bond:cf-ne @atom:cf @atom:ne - @bond:cf-nf @atom:cf @atom:nf - @bond:cf-nh @atom:cf @atom:nh - @bond:cf-oh @atom:cf @atom:oh - @bond:cf-os @atom:cf @atom:os - @bond:cf-p2 @atom:cf @atom:p2 - @bond:cf-pf @atom:cf @atom:pf - @bond:cf-px @atom:cf @atom:px - @bond:cf-py @atom:cf @atom:py - @bond:cf-s @atom:cf @atom:s - @bond:cf-sx @atom:cf @atom:sx - @bond:cf-sy @atom:cf @atom:sy - @bond:cg-cg @atom:cg @atom:cg - @bond:cg-ch @atom:cg @atom:ch - @bond:cg-n1 @atom:cg @atom:n1 - @bond:cg-ne @atom:cg @atom:ne - @bond:cg-pe @atom:cg @atom:pe - @bond:c-h4 @atom:c @atom:h4 - @bond:c-h5 @atom:c @atom:h5 - @bond:c-ha @atom:c @atom:ha - @bond:ch-ch @atom:ch @atom:ch - @bond:ch-n1 @atom:ch @atom:n1 - @bond:ch-nf @atom:ch @atom:nf - @bond:ch-pf @atom:ch @atom:pf - @bond:c-i @atom:c @atom:i - @bond:cl-cl @atom:cl @atom:cl - @bond:cl-cx @atom:cl @atom:cx - @bond:cl-cy @atom:cl @atom:cy - @bond:cl-n1 @atom:cl @atom:n1 - @bond:cl-n2 @atom:cl @atom:n2 - @bond:cl-n3 @atom:cl @atom:n3 - @bond:cl-n @atom:cl @atom:n - @bond:cl-n4 @atom:cl @atom:n4 - @bond:cl-na @atom:cl @atom:na - @bond:cl-nh @atom:cl @atom:nh - @bond:cl-no @atom:cl @atom:no - @bond:cl-o @atom:cl @atom:o - @bond:cl-oh @atom:cl @atom:oh - @bond:cl-os @atom:cl @atom:os - @bond:cl-p2 @atom:cl @atom:p2 - @bond:cl-p3 @atom:cl @atom:p3 - @bond:cl-p4 @atom:cl @atom:p4 - @bond:cl-p5 @atom:cl @atom:p5 - @bond:cl-pb @atom:cl @atom:pb - @bond:cl-s @atom:cl @atom:s - @bond:cl-s2 @atom:cl @atom:s2 - @bond:cl-s4 @atom:cl @atom:s4 - @bond:cl-s6 @atom:cl @atom:s6 - @bond:cl-sh @atom:cl @atom:sh - @bond:cl-ss @atom:cl @atom:ss - @bond:cl-sx @atom:cl @atom:sx - @bond:cl-sy @atom:cl @atom:sy - @bond:c-n2 @atom:c @atom:n2 - @bond:c-n4 @atom:c @atom:n4 - @bond:c-n @atom:c @atom:n - @bond:c-nc @atom:c @atom:nc - @bond:c-nd @atom:c @atom:nd - @bond:c-ne @atom:c @atom:ne - @bond:c-nf @atom:c @atom:nf - @bond:c-no @atom:c @atom:no - @bond:c-o @atom:c @atom:o - @bond:c-oh @atom:c @atom:oh - @bond:c-os @atom:c @atom:os - @bond:c-p2 @atom:c @atom:p2 - @bond:c-p3 @atom:c @atom:p3 - @bond:c-p4 @atom:c @atom:p4 - @bond:c-p5 @atom:c @atom:p5 - @bond:cp-cp @atom:cp @atom:cp - @bond:cp-cq @atom:cp @atom:cq - @bond:c-pe @atom:c @atom:pe - @bond:c-pf @atom:c @atom:pf - @bond:cp-na @atom:cp @atom:na - @bond:cp-nb @atom:cp @atom:nb - @bond:c-px @atom:c @atom:px - @bond:c-py @atom:c @atom:py - @bond:cq-cq @atom:cq @atom:cq - @bond:c-s @atom:c @atom:s - @bond:c-s4 @atom:c @atom:s4 - @bond:c-s6 @atom:c @atom:s6 - @bond:c-sh @atom:c @atom:sh - @bond:c-ss @atom:c @atom:ss - @bond:c-sx @atom:c @atom:sx - @bond:c-sy @atom:c @atom:sy - @bond:cu-cu @atom:cu @atom:cu - @bond:cu-cx @atom:cu @atom:cx - @bond:cu-ha @atom:cu @atom:ha - @bond:cv-cv @atom:cv @atom:cv - @bond:cv-cy @atom:cv @atom:cy - @bond:cv-ha @atom:cv @atom:ha - @bond:cx-cv @atom:cx @atom:cv - @bond:cx-cx @atom:cx @atom:cx - @bond:cx-cy @atom:cx @atom:cy - @bond:cx-f @atom:cx @atom:f - @bond:cx-h1 @atom:cx @atom:h1 - @bond:cx-h2 @atom:cx @atom:h2 - @bond:cx-hc @atom:cx @atom:hc - @bond:cx-hx @atom:cx @atom:hx - @bond:cx-n2 @atom:cx @atom:n2 - @bond:cx-n3 @atom:cx @atom:n3 - @bond:cx-n @atom:cx @atom:n - @bond:cx-na @atom:cx @atom:na - @bond:cx-nh @atom:cx @atom:nh - @bond:cx-oh @atom:cx @atom:oh - @bond:cx-os @atom:cx @atom:os - @bond:cx-p3 @atom:cx @atom:p3 - @bond:cx-s4 @atom:cx @atom:s4 - @bond:cx-s6 @atom:cx @atom:s6 - @bond:cx-ss @atom:cx @atom:ss - @bond:cy-cy @atom:cy @atom:cy - @bond:cy-f @atom:cy @atom:f - @bond:cy-h1 @atom:cy @atom:h1 - @bond:cy-h2 @atom:cy @atom:h2 - @bond:cy-hc @atom:cy @atom:hc - @bond:cy-n @atom:cy @atom:n - @bond:cy-n3 @atom:cy @atom:n3 - @bond:cy-oh @atom:cy @atom:oh - @bond:cy-os @atom:cy @atom:os - @bond:cy-s6 @atom:cy @atom:s6 - @bond:cy-ss @atom:cy @atom:ss - @bond:cz-nh @atom:cz @atom:nh - @bond:f-n1 @atom:f @atom:n1 - @bond:f-n2 @atom:f @atom:n2 - @bond:f-n3 @atom:f @atom:n3 - @bond:f-n @atom:f @atom:n - @bond:f-n4 @atom:f @atom:n4 - @bond:f-na @atom:f @atom:na - @bond:f-nh @atom:f @atom:nh - @bond:f-no @atom:f @atom:no - @bond:f-o @atom:f @atom:o - @bond:f-oh @atom:f @atom:oh - @bond:f-os @atom:f @atom:os - @bond:f-p2 @atom:f @atom:p2 - @bond:f-p3 @atom:f @atom:p3 - @bond:f-p4 @atom:f @atom:p4 - @bond:f-p5 @atom:f @atom:p5 - @bond:f-s2 @atom:f @atom:s2 - @bond:f-s @atom:f @atom:s - @bond:f-s4 @atom:f @atom:s4 - @bond:f-s6 @atom:f @atom:s6 - @bond:f-sh @atom:f @atom:sh - @bond:f-ss @atom:f @atom:ss - @bond:hn-n1 @atom:hn @atom:n1 - @bond:hn-n2 @atom:hn @atom:n2 - @bond:hn-n3 @atom:hn @atom:n3 - @bond:hn-n @atom:hn @atom:n - @bond:hn-n4 @atom:hn @atom:n4 - @bond:hn-na @atom:hn @atom:na - @bond:hn-nh @atom:hn @atom:nh - @bond:hn-no @atom:hn @atom:no - @bond:ho-o @atom:ho @atom:o - @bond:ho-oh @atom:ho @atom:oh - @bond:hp-p2 @atom:hp @atom:p2 - @bond:hp-p3 @atom:hp @atom:p3 - @bond:hp-p4 @atom:hp @atom:p4 - @bond:hp-p5 @atom:hp @atom:p5 - @bond:hs-s @atom:hs @atom:s - @bond:hs-s4 @atom:hs @atom:s4 - @bond:hs-s6 @atom:hs @atom:s6 - @bond:hs-sh @atom:hs @atom:sh - @bond:i-i @atom:i @atom:i - @bond:i-n1 @atom:i @atom:n1 - @bond:i-n2 @atom:i @atom:n2 - @bond:i-n @atom:i @atom:n - @bond:i-n3 @atom:i @atom:n3 - @bond:i-n4 @atom:i @atom:n4 - @bond:i-na @atom:i @atom:na - @bond:i-nh @atom:i @atom:nh - @bond:i-no @atom:i @atom:no - @bond:i-o @atom:i @atom:o - @bond:i-oh @atom:i @atom:oh - @bond:i-os @atom:i @atom:os - @bond:i-p2 @atom:i @atom:p2 - @bond:i-p3 @atom:i @atom:p3 - @bond:i-p4 @atom:i @atom:p4 - @bond:i-p5 @atom:i @atom:p5 - @bond:i-s @atom:i @atom:s - @bond:i-s4 @atom:i @atom:s4 - @bond:i-s6 @atom:i @atom:s6 - @bond:i-sh @atom:i @atom:sh - @bond:i-ss @atom:i @atom:ss - @bond:n1-n1 @atom:n1 @atom:n1 - @bond:n1-n2 @atom:n1 @atom:n2 - @bond:n1-n3 @atom:n1 @atom:n3 - @bond:n1-n4 @atom:n1 @atom:n4 - @bond:n1-na @atom:n1 @atom:na - @bond:n1-nc @atom:n1 @atom:nc - @bond:n1-nd @atom:n1 @atom:nd - @bond:n1-ne @atom:n1 @atom:ne - @bond:n1-nf @atom:n1 @atom:nf - @bond:n1-nh @atom:n1 @atom:nh - @bond:n1-no @atom:n1 @atom:no - @bond:n1-o @atom:n1 @atom:o - @bond:n1-oh @atom:n1 @atom:oh - @bond:n1-os @atom:n1 @atom:os - @bond:n1-p2 @atom:n1 @atom:p2 - @bond:n1-p3 @atom:n1 @atom:p3 - @bond:n1-p4 @atom:n1 @atom:p4 - @bond:n1-p5 @atom:n1 @atom:p5 - @bond:n1-s2 @atom:n1 @atom:s2 - @bond:n1-s @atom:n1 @atom:s - @bond:n1-s4 @atom:n1 @atom:s4 - @bond:n1-s6 @atom:n1 @atom:s6 - @bond:n1-sh @atom:n1 @atom:sh - @bond:n1-ss @atom:n1 @atom:ss - @bond:n2-n2 @atom:n2 @atom:n2 - @bond:n2-n3 @atom:n2 @atom:n3 - @bond:n2-n4 @atom:n2 @atom:n4 - @bond:n2-na @atom:n2 @atom:na - @bond:n2-nc @atom:n2 @atom:nc - @bond:n2-nd @atom:n2 @atom:nd - @bond:n2-ne @atom:n2 @atom:ne - @bond:n2-nf @atom:n2 @atom:nf - @bond:n2-nh @atom:n2 @atom:nh - @bond:n2-no @atom:n2 @atom:no - @bond:n2-o @atom:n2 @atom:o - @bond:n2-oh @atom:n2 @atom:oh - @bond:n2-os @atom:n2 @atom:os - @bond:n2-p2 @atom:n2 @atom:p2 - @bond:n2-p3 @atom:n2 @atom:p3 - @bond:n2-p4 @atom:n2 @atom:p4 - @bond:n2-p5 @atom:n2 @atom:p5 - @bond:n2-pe @atom:n2 @atom:pe - @bond:n2-pf @atom:n2 @atom:pf - @bond:n2-s2 @atom:n2 @atom:s2 - @bond:n2-s4 @atom:n2 @atom:s4 - @bond:n2-s @atom:n2 @atom:s - @bond:n2-s6 @atom:n2 @atom:s6 - @bond:n2-sh @atom:n2 @atom:sh - @bond:n2-ss @atom:n2 @atom:ss - @bond:n3-n3 @atom:n3 @atom:n3 - @bond:n3-n4 @atom:n3 @atom:n4 - @bond:n3-na @atom:n3 @atom:na - @bond:n3-nh @atom:n3 @atom:nh - @bond:n3-no @atom:n3 @atom:no - @bond:n3-o @atom:n3 @atom:o - @bond:n3-oh @atom:n3 @atom:oh - @bond:n3-os @atom:n3 @atom:os - @bond:n3-p2 @atom:n3 @atom:p2 - @bond:n3-p3 @atom:n3 @atom:p3 - @bond:n3-p4 @atom:n3 @atom:p4 - @bond:n3-p5 @atom:n3 @atom:p5 - @bond:n3-py @atom:n3 @atom:py - @bond:n3-s @atom:n3 @atom:s - @bond:n3-s4 @atom:n3 @atom:s4 - @bond:n3-s6 @atom:n3 @atom:s6 - @bond:n3-sh @atom:n3 @atom:sh - @bond:n3-ss @atom:n3 @atom:ss - @bond:n3-sy @atom:n3 @atom:sy - @bond:n4-n4 @atom:n4 @atom:n4 - @bond:n4-na @atom:n4 @atom:na - @bond:n4-nh @atom:n4 @atom:nh - @bond:n4-no @atom:n4 @atom:no - @bond:n4-o @atom:n4 @atom:o - @bond:n4-oh @atom:n4 @atom:oh - @bond:n4-os @atom:n4 @atom:os - @bond:n4-p2 @atom:n4 @atom:p2 - @bond:n4-p3 @atom:n4 @atom:p3 - @bond:n4-p4 @atom:n4 @atom:p4 - @bond:n4-p5 @atom:n4 @atom:p5 - @bond:n4-py @atom:n4 @atom:py - @bond:n4-s @atom:n4 @atom:s - @bond:n4-s4 @atom:n4 @atom:s4 - @bond:n4-s6 @atom:n4 @atom:s6 - @bond:n4-sh @atom:n4 @atom:sh - @bond:n4-ss @atom:n4 @atom:ss - @bond:na-na @atom:na @atom:na - @bond:na-nb @atom:na @atom:nb - @bond:na-nc @atom:na @atom:nc - @bond:na-nd @atom:na @atom:nd - @bond:na-nh @atom:na @atom:nh - @bond:na-no @atom:na @atom:no - @bond:na-o @atom:na @atom:o - @bond:na-oh @atom:na @atom:oh - @bond:na-os @atom:na @atom:os - @bond:na-p2 @atom:na @atom:p2 - @bond:na-p3 @atom:na @atom:p3 - @bond:na-p4 @atom:na @atom:p4 - @bond:na-p5 @atom:na @atom:p5 - @bond:na-pc @atom:na @atom:pc - @bond:na-pd @atom:na @atom:pd - @bond:na-py @atom:na @atom:py - @bond:na-s @atom:na @atom:s - @bond:na-s4 @atom:na @atom:s4 - @bond:na-s6 @atom:na @atom:s6 - @bond:na-sh @atom:na @atom:sh - @bond:na-ss @atom:na @atom:ss - @bond:na-sy @atom:na @atom:sy - @bond:nb-nb @atom:nb @atom:nb - @bond:nb-pb @atom:nb @atom:pb - @bond:nc-nc @atom:nc @atom:nc - @bond:nc-nd @atom:nc @atom:nd - @bond:nc-os @atom:nc @atom:os - @bond:nc-ss @atom:nc @atom:ss - @bond:nc-sy @atom:nc @atom:sy - @bond:nd-nd @atom:nd @atom:nd - @bond:nd-os @atom:nd @atom:os - @bond:nd-ss @atom:nd @atom:ss - @bond:nd-sy @atom:nd @atom:sy - @bond:ne-ne @atom:ne @atom:ne - @bond:ne-nf @atom:ne @atom:nf - @bond:ne-o @atom:ne @atom:o - @bond:ne-p2 @atom:ne @atom:p2 - @bond:ne-pe @atom:ne @atom:pe - @bond:ne-px @atom:ne @atom:px - @bond:ne-py @atom:ne @atom:py - @bond:ne-s @atom:ne @atom:s - @bond:ne-sx @atom:ne @atom:sx - @bond:ne-sy @atom:ne @atom:sy - @bond:nf-nf @atom:nf @atom:nf - @bond:nf-o @atom:nf @atom:o - @bond:nf-p2 @atom:nf @atom:p2 - @bond:nf-pf @atom:nf @atom:pf - @bond:nf-px @atom:nf @atom:px - @bond:nf-py @atom:nf @atom:py - @bond:nf-s @atom:nf @atom:s - @bond:nf-sx @atom:nf @atom:sx - @bond:nf-sy @atom:nf @atom:sy - @bond:nh-nh @atom:nh @atom:nh - @bond:nh-no @atom:nh @atom:no - @bond:nh-o @atom:nh @atom:o - @bond:nh-oh @atom:nh @atom:oh - @bond:nh-os @atom:nh @atom:os - @bond:nh-p2 @atom:nh @atom:p2 - @bond:nh-p3 @atom:nh @atom:p3 - @bond:nh-p4 @atom:nh @atom:p4 - @bond:nh-p5 @atom:nh @atom:p5 - @bond:nh-s @atom:nh @atom:s - @bond:nh-s4 @atom:nh @atom:s4 - @bond:nh-s6 @atom:nh @atom:s6 - @bond:nh-sh @atom:nh @atom:sh - @bond:nh-ss @atom:nh @atom:ss - @bond:nh-sy @atom:nh @atom:sy - @bond:n-n1 @atom:n @atom:n1 - @bond:n-n2 @atom:n @atom:n2 - @bond:n-n3 @atom:n @atom:n3 - @bond:n-n4 @atom:n @atom:n4 - @bond:n-n @atom:n @atom:n - @bond:n-na @atom:n @atom:na - @bond:n-nc @atom:n @atom:nc - @bond:n-nd @atom:n @atom:nd - @bond:n-nh @atom:n @atom:nh - @bond:n-no @atom:n @atom:no - @bond:n-o @atom:n @atom:o - @bond:n-oh @atom:n @atom:oh - @bond:no-no @atom:no @atom:no - @bond:no-o @atom:no @atom:o - @bond:no-oh @atom:no @atom:oh - @bond:no-os @atom:no @atom:os - @bond:no-p2 @atom:no @atom:p2 - @bond:no-p3 @atom:no @atom:p3 - @bond:no-p4 @atom:no @atom:p4 - @bond:no-p5 @atom:no @atom:p5 - @bond:no-s @atom:no @atom:s - @bond:n-os @atom:n @atom:os - @bond:no-s4 @atom:no @atom:s4 - @bond:no-s6 @atom:no @atom:s6 - @bond:no-sh @atom:no @atom:sh - @bond:no-ss @atom:no @atom:ss - @bond:n-p2 @atom:n @atom:p2 - @bond:n-p3 @atom:n @atom:p3 - @bond:n-p4 @atom:n @atom:p4 - @bond:n-p5 @atom:n @atom:p5 - @bond:n-pc @atom:n @atom:pc - @bond:n-pd @atom:n @atom:pd - @bond:n-s @atom:n @atom:s - @bond:n-s4 @atom:n @atom:s4 - @bond:n-s6 @atom:n @atom:s6 - @bond:n-sh @atom:n @atom:sh - @bond:n-ss @atom:n @atom:ss - @bond:n-sy @atom:n @atom:sy - @bond:oh-oh @atom:oh @atom:oh - @bond:oh-os @atom:oh @atom:os - @bond:oh-p2 @atom:oh @atom:p2 - @bond:oh-p3 @atom:oh @atom:p3 - @bond:oh-p4 @atom:oh @atom:p4 - @bond:oh-p5 @atom:oh @atom:p5 - @bond:oh-py @atom:oh @atom:py - @bond:oh-s @atom:oh @atom:s - @bond:oh-s4 @atom:oh @atom:s4 - @bond:oh-s6 @atom:oh @atom:s6 - @bond:oh-sh @atom:oh @atom:sh - @bond:oh-ss @atom:oh @atom:ss - @bond:oh-sy @atom:oh @atom:sy - @bond:o-o @atom:o @atom:o - @bond:o-oh @atom:o @atom:oh - @bond:o-os @atom:o @atom:os - @bond:o-p2 @atom:o @atom:p2 - @bond:o-p3 @atom:o @atom:p3 - @bond:o-p4 @atom:o @atom:p4 - @bond:o-p5 @atom:o @atom:p5 - @bond:o-pe @atom:o @atom:pe - @bond:o-pf @atom:o @atom:pf - @bond:o-px @atom:o @atom:px - @bond:o-py @atom:o @atom:py - @bond:o-s @atom:o @atom:s - @bond:o-s2 @atom:o @atom:s2 - @bond:o-s4 @atom:o @atom:s4 - @bond:o-s6 @atom:o @atom:s6 - @bond:o-sh @atom:o @atom:sh - @bond:os-os @atom:os @atom:os - @bond:os-p2 @atom:os @atom:p2 - @bond:os-p3 @atom:os @atom:p3 - @bond:os-p4 @atom:os @atom:p4 - @bond:os-p5 @atom:os @atom:p5 - @bond:os-py @atom:os @atom:py - @bond:os-s @atom:os @atom:s - @bond:o-ss @atom:o @atom:ss - @bond:os-s4 @atom:os @atom:s4 - @bond:os-s6 @atom:os @atom:s6 - @bond:os-sh @atom:os @atom:sh - @bond:os-ss @atom:os @atom:ss - @bond:os-sy @atom:os @atom:sy - @bond:o-sx @atom:o @atom:sx - @bond:o-sy @atom:o @atom:sy - @bond:p2-p2 @atom:p2 @atom:p2 - @bond:p2-p3 @atom:p2 @atom:p3 - @bond:p2-p4 @atom:p2 @atom:p4 - @bond:p2-p5 @atom:p2 @atom:p5 - @bond:p2-pe @atom:p2 @atom:pe - @bond:p2-pf @atom:p2 @atom:pf - @bond:p2-s @atom:p2 @atom:s - @bond:p2-s4 @atom:p2 @atom:s4 - @bond:p2-s6 @atom:p2 @atom:s6 - @bond:p2-sh @atom:p2 @atom:sh - @bond:p2-ss @atom:p2 @atom:ss - @bond:p3-p3 @atom:p3 @atom:p3 - @bond:p3-p4 @atom:p3 @atom:p4 - @bond:p3-p5 @atom:p3 @atom:p5 - @bond:p3-s @atom:p3 @atom:s - @bond:p3-s4 @atom:p3 @atom:s4 - @bond:p3-s6 @atom:p3 @atom:s6 - @bond:p3-sh @atom:p3 @atom:sh - @bond:p3-ss @atom:p3 @atom:ss - @bond:p4-p4 @atom:p4 @atom:p4 - @bond:p4-p5 @atom:p4 @atom:p5 - @bond:p4-s @atom:p4 @atom:s - @bond:p4-s4 @atom:p4 @atom:s4 - @bond:p4-s6 @atom:p4 @atom:s6 - @bond:p4-sh @atom:p4 @atom:sh - @bond:p4-ss @atom:p4 @atom:ss - @bond:p5-p5 @atom:p5 @atom:p5 - @bond:p5-s @atom:p5 @atom:s - @bond:p5-s4 @atom:p5 @atom:s4 - @bond:p5-s6 @atom:p5 @atom:s6 - @bond:p5-sh @atom:p5 @atom:sh - @bond:p5-ss @atom:p5 @atom:ss - @bond:pe-pe @atom:pe @atom:pe - @bond:pe-pf @atom:pe @atom:pf - @bond:pe-px @atom:pe @atom:px - @bond:pe-py @atom:pe @atom:py - @bond:pe-s @atom:pe @atom:s - @bond:pe-sx @atom:pe @atom:sx - @bond:pe-sy @atom:pe @atom:sy - @bond:pf-pf @atom:pf @atom:pf - @bond:pf-px @atom:pf @atom:px - @bond:pf-py @atom:pf @atom:py - @bond:pf-s @atom:pf @atom:s - @bond:pf-sx @atom:pf @atom:sx - @bond:pf-sy @atom:pf @atom:sy - @bond:px-py @atom:px @atom:py - @bond:px-sx @atom:px @atom:sx - @bond:px-sy @atom:px @atom:sy - @bond:py-py @atom:py @atom:py - @bond:py-sx @atom:py @atom:sx - @bond:py-sy @atom:py @atom:sy - @bond:s4-s4 @atom:s4 @atom:s4 - @bond:s4-s6 @atom:s4 @atom:s6 - @bond:s4-sh @atom:s4 @atom:sh - @bond:s4-ss @atom:s4 @atom:ss - @bond:s6-s6 @atom:s6 @atom:s6 - @bond:s6-sh @atom:s6 @atom:sh - @bond:s6-ss @atom:s6 @atom:ss - @bond:sh-sh @atom:sh @atom:sh - @bond:sh-ss @atom:sh @atom:ss - @bond:s-s @atom:s @atom:s - @bond:s-s2 @atom:s @atom:s2 - @bond:s-s4 @atom:s @atom:s4 - @bond:s-s6 @atom:s @atom:s6 - @bond:s-sh @atom:s @atom:sh - @bond:s-ss @atom:s @atom:ss - @bond:ss-ss @atom:ss @atom:ss - @bond:sx-sx @atom:sx @atom:sx - @bond:sx-sy @atom:sx @atom:sy - @bond:sy-sy @atom:sy @atom:sy - @bond:br-cd @atom:br @atom:cd - @bond:c1-cf @atom:c1 @atom:cf - @bond:cd-f @atom:cd @atom:f - @bond:cd-n4 @atom:cd @atom:n4 - @bond:cd-nf @atom:cd @atom:nf - @bond:cd-no @atom:cd @atom:no - @bond:cd-sh @atom:cd @atom:sh - @bond:cd-sx @atom:cd @atom:sx - @bond:cc-cy @atom:cc @atom:cy - @bond:cf-cl @atom:cf @atom:cl - @bond:cf-cx @atom:cf @atom:cx - @bond:cf-cy @atom:cf @atom:cy - @bond:cf-na @atom:cf @atom:na - @bond:cf-ss @atom:cf @atom:ss - @bond:cq-na @atom:cq @atom:na - @bond:cq-nb @atom:cq @atom:nb - @bond:cl-py @atom:cl @atom:py - @bond:f-py @atom:f @atom:py - @bond:py-s @atom:py @atom:s - @bond:cy-nh @atom:cy @atom:nh - @bond:cy-hx @atom:cy @atom:hx - @bond:br-ce @atom:br @atom:ce - @bond:cc-i @atom:cc @atom:i - @bond:cy-n4 @atom:cy @atom:n4 - @bond:cy-p3 @atom:cy @atom:p3 - @bond:cy-na @atom:cy @atom:na - @bond:cx-n4 @atom:cx @atom:n4 - @bond:ne-s4 @atom:ne @atom:s4 - @bond:cv-ss @atom:cv @atom:ss - @bond:cy-no @atom:cy @atom:no - @bond:ce-cv @atom:ce @atom:cv - @bond:cd-i @atom:cd @atom:i - @bond:cy-s4 @atom:cy @atom:s4 - @bond:n2-sy @atom:n2 @atom:sy - @bond:cc-s6 @atom:cc @atom:s6 - @bond:i-s2 @atom:i @atom:s2 - @bond:br-cy @atom:br @atom:cy - @bond:br-cf @atom:br @atom:cf - @bond:nf-s4 @atom:nf @atom:s4 - @bond:cf-cv @atom:cf @atom:cv - @bond:cd-s6 @atom:cd @atom:s6 - @bond:ss-sy @atom:ss @atom:sy - @bond:h5-ce @atom:h5 @atom:ce - @bond:h5-cf @atom:h5 @atom:cf - @bond:ce-s4 @atom:ce @atom:s4 - @bond:cf-s4 @atom:cf @atom:s4 - @bond:cy-py @atom:cy @atom:py - @bond:cd-o @atom:cd @atom:o - @bond:ne-s6 @atom:ne @atom:s6 - @bond:nf-s6 @atom:nf @atom:s6 - @bond:ce-no @atom:ce @atom:no - @bond:cf-no @atom:cf @atom:no - } # (end of Bonds By Type) - - write_once("In Settings") { - angle_coeff @angle:hw-ow-hw harmonic 43.276 104.520 # AMBER 1 TIP3P_water - angle_coeff @angle:hw-hw-ow harmonic 0.000 127.740 # AMBER 1 (found_in_crystallographic_water_with_3_bonds) - angle_coeff @angle:br-c1-br harmonic 58.432 180.000 # Guess 0 - angle_coeff @angle:br-c1-c1 harmonic 56.125 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-c1 harmonic 65.529 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-c2 harmonic 62.451 180.000 # SOURCE3 2 - angle_coeff @angle:c1-c1-c3 harmonic 57.975 178.510 # SOURCE4_SOURCE5 618 0.7369 - angle_coeff @angle:c1-c1-ca harmonic 58.535 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-cl harmonic 63.947 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-f harmonic 80.686 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-ha harmonic 44.782 179.110 # SOURCE3_SOURCE5 219 0.5885 - angle_coeff @angle:c1-c1-hc harmonic 44.772 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-i harmonic 52.986 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-n1 harmonic 83.562 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-n2 harmonic 82.100 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-n3 harmonic 76.721 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-n4 harmonic 74.244 179.560 # SOURCE3 3 0.3096 - angle_coeff @angle:c1-c1-n harmonic 77.977 177.180 # SOURCE3 1 - angle_coeff @angle:c1-c1-na harmonic 76.884 176.750 # SOURCE3 8 2.9328 - angle_coeff @angle:c1-c1-nh harmonic 77.069 179.270 # SOURCE3 3 0.2357 - angle_coeff @angle:c1-c1-no harmonic 74.597 180.000 # SOURCE3 3 - angle_coeff @angle:c1-c1-o harmonic 82.936 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-oh harmonic 78.242 176.650 # SOURCE3 1 - angle_coeff @angle:c1-c1-os harmonic 78.471 176.930 # SOURCE3_SOURCE5 5 1.1927 - angle_coeff @angle:c1-c1-p2 harmonic 68.155 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-p3 harmonic 69.444 169.630 # SOURCE3 2 - angle_coeff @angle:c1-c1-p4 harmonic 67.414 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-p5 harmonic 69.535 176.170 # SOURCE3 2 - angle_coeff @angle:c1-c1-s4 harmonic 55.785 167.470 # SOURCE3 2 - angle_coeff @angle:c1-c1-s6 harmonic 55.388 174.380 # SOURCE3 2 - angle_coeff @angle:c1-c1-s harmonic 58.129 179.970 # SOURCE3 1 - angle_coeff @angle:c1-c1-sh harmonic 55.773 180.000 # SOURCE3 1 - angle_coeff @angle:c1-c1-ss harmonic 56.169 175.600 # SOURCE3_SOURCE5 19 1.3679 - angle_coeff @angle:c2-c1-c2 harmonic 60.185 179.370 # SOURCE3_SOURCE5 14 0.3391 - angle_coeff @angle:c2-c1-ce harmonic 60.047 179.050 # SOURCE4_SOURCE5 15 0.4210 - angle_coeff @angle:c2-c1-n1 harmonic 79.308 180.000 # HF/6-31G* 1 - angle_coeff @angle:c2-c1-o harmonic 78.963 179.500 # SOURCE2 1 - angle_coeff @angle:c2-c1-s2 harmonic 58.516 172.980 # SOURCE3 1 - angle_coeff @angle:c3-c1-c3 harmonic 53.523 180.000 # Guess 0 - angle_coeff @angle:c3-c1-cg harmonic 57.770 178.430 # SOURCE4_SOURCE5 134 0.5502 - angle_coeff @angle:c3-c1-n1 harmonic 73.216 178.580 # SOURCE4_SOURCE5 245 0.5409 - angle_coeff @angle:ca-c1-ca harmonic 54.530 180.000 # Guess 0 - angle_coeff @angle:c-c1-c1 harmonic 57.944 180.000 # SOURCE3 1 - angle_coeff @angle:cg-c1-ha harmonic 44.392 178.830 # SOURCE3_SOURCE5 60 1.1251 - angle_coeff @angle:ch-c1-ha harmonic 44.307 178.830 # SOURCE3_SOURCE5 38 0.3321 - angle_coeff @angle:cl-c1-cl harmonic 70.163 180.000 # Guess 0 - angle_coeff @angle:f-c1-f harmonic 99.768 180.000 # Guess 0 - angle_coeff @angle:i-c1-i harmonic 58.397 180.000 # Guess 0 - angle_coeff @angle:n1-c1-n1 harmonic 141.802 102.010 # SOURCE3 1 - angle_coeff @angle:n1-c1-n3 harmonic 98.388 176.010 # SOURCE2_SOURCE5 5 0.1498 - angle_coeff @angle:n1-c1-nh harmonic 98.195 177.650 # SOURCE4_SOURCE5 18 0.7845 - angle_coeff @angle:n1-c1-os harmonic 99.150 178.590 # SOURCE3 1 - angle_coeff @angle:n1-c1-p3 harmonic 86.562 171.200 # SOURCE2 1 - angle_coeff @angle:n1-c1-ss harmonic 70.134 177.470 # SOURCE3_SOURCE5 15 0.7211 - angle_coeff @angle:n2-c1-n2 harmonic 102.862 180.000 # Guess 0 - angle_coeff @angle:n2-c1-o harmonic 106.076 172.730 # SOURCE3_SOURCE5 10 0.3647 - angle_coeff @angle:n2-c1-s harmonic 73.638 175.910 # SOURCE4_SOURCE5 29 0.2046 - angle_coeff @angle:n3-c1-n3 harmonic 91.381 180.000 # Guess 0 - angle_coeff @angle:n4-c1-n4 harmonic 86.899 180.000 # Guess 0 - angle_coeff @angle:na-c1-na harmonic 90.408 180.000 # Guess 0 - angle_coeff @angle:ne-c1-o harmonic 105.956 172.330 # SOURCE3 1 - angle_coeff @angle:ne-c1-s harmonic 73.610 175.820 # SOURCE4_SOURCE5 23 0.2168 - angle_coeff @angle:nf-c1-o harmonic 105.956 172.330 # SOURCE3 1 - angle_coeff @angle:nh-c1-nh harmonic 91.735 180.000 # Guess 0 - angle_coeff @angle:n-c1-n harmonic 92.583 180.000 # Guess 0 - angle_coeff @angle:no-c1-no harmonic 87.641 180.000 # Guess 0 - angle_coeff @angle:oh-c1-oh harmonic 92.863 180.000 # Guess 0 - angle_coeff @angle:o-c1-o harmonic 105.029 180.000 # Guess 0 - angle_coeff @angle:os-c1-os harmonic 93.419 180.000 # Guess 0 - angle_coeff @angle:p2-c1-p2 harmonic 85.393 180.000 # Guess 0 - angle_coeff @angle:p3-c1-p3 harmonic 84.439 180.000 # Guess 0 - angle_coeff @angle:p4-c1-p4 harmonic 84.439 180.000 # Guess 0 - angle_coeff @angle:p5-c1-p5 harmonic 86.221 180.000 # Guess 0 - angle_coeff @angle:s2-c1-s2 harmonic 57.538 180.000 # Guess 0 - angle_coeff @angle:s4-c1-s4 harmonic 52.562 180.000 # Guess 0 - angle_coeff @angle:s6-c1-s6 harmonic 53.295 180.000 # Guess 0 - angle_coeff @angle:sh-c1-sh harmonic 54.627 180.000 # Guess 0 - angle_coeff @angle:s-c1-s harmonic 57.244 180.000 # Guess 0 - angle_coeff @angle:ss-c1-ss harmonic 54.310 180.000 # Guess 0 - angle_coeff @angle:br-c2-br harmonic 68.999 115.060 # SOURCE3 1 - angle_coeff @angle:br-c2-c2 harmonic 64.458 121.030 # SOURCE4_SOURCE5 18 0.8426 - angle_coeff @angle:br-c2-c3 harmonic 64.834 115.320 # SOURCE4_SOURCE5 18 0.6855 - angle_coeff @angle:br-c2-ce harmonic 64.279 121.530 # SOURCE4_SOURCE5 18 0.7036 - angle_coeff @angle:br-c2-h4 harmonic 42.846 113.730 # SOURCE4_SOURCE5 17 0.5888 - angle_coeff @angle:br-c2-ha harmonic 42.937 113.280 # SOURCE3 1 - angle_coeff @angle:c1-c2-c1 harmonic 74.593 116.770 # SOURCE3 1 - angle_coeff @angle:c1-c2-c2 harmonic 72.319 121.620 # SOURCE3 1 - angle_coeff @angle:c1-c2-c3 harmonic 66.250 124.900 # SOURCE4_SOURCE5 44 0.7045 - angle_coeff @angle:c1-c2-f harmonic 90.501 124.900 # SOURCE2 1 - angle_coeff @angle:c1-c2-ha harmonic 51.141 120.420 # SOURCE3_SOURCE5 30 0.4602 - angle_coeff @angle:c2-c2-c2 harmonic 71.539 121.810 # SOURCE3 10 0.3843 - angle_coeff @angle:c2-c2-c3 harmonic 66.132 123.630 # SOURCE3_SOURCE5 4623 2.2803 - angle_coeff @angle:c2-c2-ca harmonic 71.595 117.000 # SOURCE3 1 - angle_coeff @angle:c2-c2-cc harmonic 72.240 117.210 # SOURCE3 2 0.3418 - angle_coeff @angle:c2-c2-cd harmonic 72.240 117.210 # SOURCE3 2 - angle_coeff @angle:c2-c2-cl harmonic 72.331 123.110 # SOURCE4_SOURCE5 103 1.0574 - angle_coeff @angle:c2-c2-cx harmonic 66.489 124.950 # SOURCE4_SOURCE5 51 1.8521 - angle_coeff @angle:c2-c2-cy harmonic 67.939 117.180 # SOURCE2_SOURCE5 11 1.7549 - angle_coeff @angle:c2-c2-f harmonic 90.338 122.870 # SOURCE4_SOURCE5 37 0.6494 - angle_coeff @angle:c2-c2-h4 harmonic 49.914 122.670 # SOURCE4_SOURCE5 266 1.3387 - angle_coeff @angle:c2-c2-ha harmonic 50.363 120.430 # SOURCE3_SOURCE5 3764 1.3300 - angle_coeff @angle:c2-c2-hc harmonic 50.527 119.700 # SOURCE3 1 - angle_coeff @angle:c2-c2-hx harmonic 49.204 126.450 # SOURCE3 3 0.0219 - angle_coeff @angle:c2-c2-i harmonic 59.321 121.030 # SOURCE3 2 - angle_coeff @angle:c2-c2-n1 harmonic 90.093 122.980 # HF/6-31G* 1 - angle_coeff @angle:c2-c2-n2 harmonic 89.778 126.010 # SOURCE3 1 - angle_coeff @angle:c2-c2-n3 harmonic 88.404 124.550 # SOURCE3 1 - angle_coeff @angle:c2-c2-n4 harmonic 83.421 121.520 # SOURCE3 5 1.2656 - angle_coeff @angle:c2-c2-n harmonic 86.693 123.670 # SOURCE4_SOURCE5 48 1.8326 - angle_coeff @angle:c2-c2-na harmonic 87.232 121.940 # SOURCE3_SOURCE5 35 5.4059 - angle_coeff @angle:c2-c2-nh harmonic 86.653 124.990 # SOURCE3 7 0.9929 - angle_coeff @angle:c2-c2-no harmonic 85.060 123.460 # SOURCE4_SOURCE5 26 1.6311 - angle_coeff @angle:c2-c2-o harmonic 89.793 130.890 # SOURCE3 2 0.0201 - angle_coeff @angle:c2-c2-oh harmonic 89.312 122.170 # SOURCE4_SOURCE5 18 1.1206 - angle_coeff @angle:c2-c2-os harmonic 88.706 121.870 # SOURCE4_SOURCE5 114 1.6810 - angle_coeff @angle:c2-c2-p2 harmonic 88.516 115.100 # SOURCE3 1 - angle_coeff @angle:c2-c2-p3 harmonic 78.573 124.830 # SOURCE3 5 2.1222 - angle_coeff @angle:c2-c2-p4 harmonic 80.685 119.760 # SOURCE3 1 - angle_coeff @angle:c2-c2-p5 harmonic 77.141 125.970 # SOURCE3 1 - angle_coeff @angle:c2-c2-s4 harmonic 64.747 119.840 # SOURCE3 1 - angle_coeff @angle:c2-c2-s6 harmonic 64.702 120.010 # SOURCE3 1 - angle_coeff @angle:c2-c2-s harmonic 63.092 129.370 # SOURCE3 2 - angle_coeff @angle:c2-c2-sh harmonic 62.559 125.700 # SOURCE3 3 1.3390 - angle_coeff @angle:c2-c2-ss harmonic 64.815 122.350 # SOURCE4_SOURCE5 54 2.2017 - angle_coeff @angle:c3-c2-c3 harmonic 64.898 115.650 # SOURCE3_SOURCE5 1743 1.5647 - angle_coeff @angle:c3-c2-cc harmonic 65.283 125.190 # CORR_SOURCE5 50 1.5929 - angle_coeff @angle:c3-c2-cd harmonic 65.283 125.190 # CORR_SOURCE5 50 1.5929 - angle_coeff @angle:c3-c2-ce harmonic 66.056 123.150 # CORR_SOURCE5 2644 2.0746 - angle_coeff @angle:c3-c2-cf harmonic 66.056 123.150 # CORR_SOURCE5 2644 2.0746 - angle_coeff @angle:c3-c2-h4 harmonic 45.760 119.020 # SOURCE4_SOURCE5 63 1.6077 - angle_coeff @angle:c3-c2-ha harmonic 46.411 115.680 # SOURCE3_SOURCE5 3991 1.1961 - angle_coeff @angle:c3-c2-hc harmonic 45.572 120.000 # SOURCE3 1 - angle_coeff @angle:c3-c2-n2 harmonic 83.960 123.430 # SOURCE4_SOURCE5 388 2.3609 - angle_coeff @angle:c3-c2-n harmonic 84.414 114.800 # SOURCE4 12 1.8112 - angle_coeff @angle:c3-c2-na harmonic 83.495 117.200 # SOURCE3_SOURCE5 5 0.8937 - angle_coeff @angle:c3-c2-ne harmonic 84.706 120.710 # SOURCE3_SOURCE5 11 0.9157 - angle_coeff @angle:c3-c2-nf harmonic 84.706 120.710 # SOURCE3_SOURCE5 7 1.3134 - angle_coeff @angle:c3-c2-nh harmonic 84.195 116.210 # SOURCE3_SOURCE5 339 2.4814 - angle_coeff @angle:c3-c2-o harmonic 85.206 122.820 # SOURCE4_SOURCE5 12 1.1220 - angle_coeff @angle:c3-c2-oh harmonic 85.711 115.160 # SOURCE4_SOURCE5 90 2.0675 - angle_coeff @angle:c3-c2-os harmonic 86.117 112.800 # SOURCE4_SOURCE5 148 2.4217 - angle_coeff @angle:c3-c2-p2 harmonic 82.609 122.740 # SOURCE3 2 - angle_coeff @angle:c3-c2-s harmonic 64.740 115.440 # SOURCE3 2 0.0115 - angle_coeff @angle:c3-c2-ss harmonic 63.539 119.660 # SOURCE4_SOURCE5 137 2.1299 - angle_coeff @angle:ca-c2-ca harmonic 70.080 117.880 # SOURCE3 1 - angle_coeff @angle:ca-c2-hc harmonic 48.375 123.300 # SOURCE3 1 - angle_coeff @angle:c-c2-c2 harmonic 69.891 120.700 # SOURCE3 1 - angle_coeff @angle:c-c2-c3 harmonic 65.889 119.700 # SOURCE3 1 - angle_coeff @angle:c-c2-c harmonic 68.722 118.880 # SOURCE3 1 - angle_coeff @angle:cc-c2-h4 harmonic 49.786 119.850 # SOURCE4_SOURCE5 23 0.5829 - angle_coeff @angle:cc-c2-ha harmonic 50.004 118.750 # SOURCE3_SOURCE5 72 1.1667 - angle_coeff @angle:cc-c2-nh harmonic 86.562 123.120 # SOURCE4_SOURCE5 27 1.0384 - angle_coeff @angle:cc-c2-o harmonic 91.352 123.590 # SOURCE4_SOURCE5 12 0.0560 - angle_coeff @angle:cd-c2-ha harmonic 50.004 118.750 # SOURCE3_SOURCE5 72 1.1667 - angle_coeff @angle:ce-c2-cl harmonic 72.107 123.470 # SOURCE4_SOURCE5 41 0.8440 - angle_coeff @angle:ce-c2-h4 harmonic 49.654 122.310 # SOURCE4_SOURCE5 220 1.5462 - angle_coeff @angle:ce-c2-ha harmonic 50.024 120.450 # SOURCE3_SOURCE5 2139 1.1520 - angle_coeff @angle:ce-c2-na harmonic 86.108 124.170 # SOURCE4_SOURCE5 12 1.9766 - angle_coeff @angle:ce-c2-nh harmonic 87.822 120.710 # SOURCE4_SOURCE5 243 2.3407 - angle_coeff @angle:ce-c2-no harmonic 86.097 119.650 # SOURCE4_SOURCE5 10 0.9817 - angle_coeff @angle:ce-c2-o harmonic 91.992 123.370 # SOURCE4_SOURCE5 14 0.7592 - angle_coeff @angle:ce-c2-oh harmonic 88.571 123.130 # SOURCE4_SOURCE5 104 1.7734 - angle_coeff @angle:ce-c2-os harmonic 87.995 122.800 # SOURCE4_SOURCE5 149 2.3406 - angle_coeff @angle:cf-c2-ha harmonic 50.024 120.450 # SOURCE3_SOURCE5 2017 1.1895 - angle_coeff @angle:c-c2-ha harmonic 48.160 121.330 # SOURCE3 4 0.2462 - angle_coeff @angle:c-c2-hc harmonic 48.494 119.700 # SOURCE3 1 - angle_coeff @angle:cl-c2-cl harmonic 82.957 114.340 # SOURCE4_SOURCE5 29 0.6417 - angle_coeff @angle:cl-c2-h4 harmonic 49.503 113.540 # SOURCE4_SOURCE5 33 0.7337 - angle_coeff @angle:cl-c2-ha harmonic 49.579 113.200 # SOURCE3 1 - angle_coeff @angle:cx-c2-ha harmonic 47.006 116.150 # SOURCE4_SOURCE5 64 0.8729 - angle_coeff @angle:f-c2-f harmonic 120.199 111.640 # SOURCE2_SOURCE5 12 0.8567 - angle_coeff @angle:f-c2-ha harmonic 66.780 110.000 # SOURCE2 1 - angle_coeff @angle:h4-c2-n2 harmonic 64.810 120.990 # SOURCE4_SOURCE5 77 1.9305 - angle_coeff @angle:h4-c2-n harmonic 62.621 113.440 # SOURCE4_SOURCE5 78 1.0580 - angle_coeff @angle:h4-c2-na harmonic 62.675 112.970 # SOURCE4_SOURCE5 27 0.6876 - angle_coeff @angle:h4-c2-ne harmonic 64.858 119.510 # SOURCE4_SOURCE5 52 1.6395 - angle_coeff @angle:h4-c2-nh harmonic 62.613 115.080 # SOURCE4_SOURCE5 109 1.1974 - angle_coeff @angle:h4-c2-no harmonic 60.883 113.380 # SOURCE4_SOURCE5 20 0.1373 - angle_coeff @angle:h4-c2-os harmonic 63.989 113.730 # SOURCE3_SOURCE5 89 1.3113 - angle_coeff @angle:h4-c2-ss harmonic 43.595 116.670 # SOURCE3_SOURCE5 49 1.4612 - angle_coeff @angle:h5-c2-n2 harmonic 64.543 121.700 # SOURCE4_SOURCE5 71 2.1538 - angle_coeff @angle:h5-c2-na harmonic 59.208 126.390 # SOURCE3 4 0.3299 - angle_coeff @angle:h5-c2-ne harmonic 64.691 119.850 # SOURCE4_SOURCE5 44 1.3576 - angle_coeff @angle:h5-c2-nh harmonic 62.882 113.910 # SOURCE4_SOURCE5 119 0.8516 - angle_coeff @angle:ha-c2-ha harmonic 37.684 116.900 # SOURCE3_SOURCE5 1456 0.6313 - angle_coeff @angle:ha-c2-n1 harmonic 63.987 120.760 # SOURCE3 8 0.6632 - angle_coeff @angle:ha-c2-n2 harmonic 64.911 120.540 # SOURCE3 92 1.4571 - angle_coeff @angle:ha-c2-n3 harmonic 64.744 113.540 # SOURCE3 1 - angle_coeff @angle:ha-c2-n harmonic 62.620 113.400 # SOURCE3 4 1.2182 - angle_coeff @angle:ha-c2-na harmonic 62.816 112.420 # SOURCE3 8 0.6507 - angle_coeff @angle:ha-c2-ne harmonic 64.391 121.180 # SOURCE3 68 0.6824 - angle_coeff @angle:ha-c2-nf harmonic 64.391 121.180 # SOURCE3 68 - angle_coeff @angle:ha-c2-nh harmonic 62.169 116.680 # SOURCE3 13 2.5734 - angle_coeff @angle:ha-c2-no harmonic 61.209 112.140 # SOURCE3 2 0.0264 - angle_coeff @angle:ha-c2-o harmonic 67.875 117.230 # SOURCE3 2 0.0201 - angle_coeff @angle:ha-c2-oh harmonic 64.058 116.180 # SOURCE3 2 - angle_coeff @angle:ha-c2-os harmonic 64.269 112.690 # SOURCE3 13 2.5851 - angle_coeff @angle:ha-c2-p2 harmonic 57.111 121.480 # SOURCE3 122 0.4329 - angle_coeff @angle:ha-c2-p3 harmonic 53.276 114.310 # SOURCE3 3 - angle_coeff @angle:ha-c2-p4 harmonic 52.849 117.860 # SOURCE3 1 - angle_coeff @angle:ha-c2-p5 harmonic 51.984 116.000 # SOURCE3_SOURCE5 6 0.1220 - angle_coeff @angle:ha-c2-pe harmonic 56.443 121.400 # SOURCE3_SOURCE5 119 0.8904 - angle_coeff @angle:ha-c2-pf harmonic 56.443 121.400 # SOURCE3_SOURCE5 15 1.6416 - angle_coeff @angle:ha-c2-s2 harmonic 46.632 118.740 # SOURCE3 2 - angle_coeff @angle:ha-c2-s4 harmonic 43.223 115.300 # SOURCE3 2 - angle_coeff @angle:ha-c2-s harmonic 43.832 115.700 # SOURCE3 2 - angle_coeff @angle:ha-c2-s6 harmonic 42.982 116.600 # SOURCE3 2 - angle_coeff @angle:ha-c2-sh harmonic 43.327 111.740 # SOURCE3 1 - angle_coeff @angle:ha-c2-ss harmonic 43.588 116.720 # SOURCE3 7 2.7543 - angle_coeff @angle:hc-c2-hc harmonic 37.394 118.920 # SOURCE3 1 - angle_coeff @angle:hc-c2-n2 harmonic 64.965 120.400 # SOURCE3 1 - angle_coeff @angle:hc-c2-n harmonic 62.454 114.040 # SOURCE3 1 - angle_coeff @angle:hc-c2-na harmonic 61.038 119.100 # SOURCE3 1 - angle_coeff @angle:hc-c2-nh harmonic 63.084 113.360 # SOURCE3 1 - angle_coeff @angle:hc-c2-no harmonic 61.222 112.120 # SOURCE3 1 - angle_coeff @angle:hc-c2-oh harmonic 64.060 116.220 # SOURCE3 1 - angle_coeff @angle:hc-c2-os harmonic 63.327 116.110 # SOURCE3 1 - angle_coeff @angle:hc-c2-p3 harmonic 52.613 117.190 # SOURCE3 1 - angle_coeff @angle:hc-c2-p5 harmonic 51.195 119.580 # SOURCE3 1 - angle_coeff @angle:hc-c2-s4 harmonic 43.068 116.120 # SOURCE3 1 - angle_coeff @angle:hc-c2-s6 harmonic 43.193 115.450 # SOURCE3 1 - angle_coeff @angle:hc-c2-sh harmonic 42.589 115.630 # SOURCE3 1 - angle_coeff @angle:hc-c2-ss harmonic 43.793 115.620 # SOURCE3 1 - angle_coeff @angle:hx-c2-n4 harmonic 58.717 113.030 # SOURCE3 3 0.3873 - angle_coeff @angle:i-c2-i harmonic 66.122 117.940 # SOURCE3 1 - angle_coeff @angle:n1-c2-n1 harmonic 113.528 124.150 # HF/6-31G* 1 - angle_coeff @angle:n2-c2-n2 harmonic 120.816 113.820 # SOURCE3 1 - angle_coeff @angle:n2-c2-n4 harmonic 109.745 112.970 # SOURCE4_SOURCE5 13 0.4034 - angle_coeff @angle:n2-c2-na harmonic 110.312 123.620 # SOURCE3 1 - angle_coeff @angle:n2-c2-nh harmonic 110.708 124.270 # SOURCE3 12 2.4114 - angle_coeff @angle:n2-c2-oh harmonic 114.021 122.080 # SOURCE3 1 - angle_coeff @angle:n2-c2-os harmonic 114.100 119.780 # SOURCE4_SOURCE5 55 1.3881 - angle_coeff @angle:n2-c2-ss harmonic 79.299 129.770 # SOURCE3 1 - angle_coeff @angle:n3-c2-n3 harmonic 113.269 118.470 # SOURCE3 1 - angle_coeff @angle:n4-c2-n4 harmonic 102.331 113.930 # SOURCE3 1 - angle_coeff @angle:n4-c2-ss harmonic 80.666 116.270 # SOURCE4_SOURCE5 14 2.4226 - angle_coeff @angle:na-c2-na harmonic 112.735 109.330 # SOURCE3 3 3.0187 - angle_coeff @angle:ne-c2-nh harmonic 110.728 123.460 # CORR_SOURCE5 241 2.3941 - angle_coeff @angle:ne-c2-os harmonic 114.213 118.760 # SOURCE4 5 0.3382 - angle_coeff @angle:ne-c2-ss harmonic 82.205 120.510 # SOURCE4_SOURCE5 32 2.1160 - angle_coeff @angle:nf-c2-nh harmonic 110.728 123.460 # CORR_SOURCE5 241 2.3941 - angle_coeff @angle:nh-c2-nh harmonic 112.122 112.820 # SOURCE4_SOURCE5 689 1.9577 - angle_coeff @angle:nh-c2-oh harmonic 111.944 117.110 # SOURCE4_SOURCE5 15 0.8639 - angle_coeff @angle:nh-c2-os harmonic 112.490 114.300 # SOURCE4_SOURCE5 50 1.3395 - angle_coeff @angle:nh-c2-ss harmonic 84.343 111.550 # SOURCE4 37 1.1778 - angle_coeff @angle:n-c2-n2 harmonic 110.772 122.820 # SOURCE3_SOURCE5 46 2.2661 - angle_coeff @angle:n-c2-n harmonic 110.943 113.230 # SOURCE3 1 - angle_coeff @angle:n-c2-na harmonic 114.893 105.420 # SOURCE3 1 - angle_coeff @angle:n-c2-ne harmonic 109.323 125.340 # SOURCE4_SOURCE5 25 1.6082 - angle_coeff @angle:n-c2-nh harmonic 113.384 109.350 # SOURCE4_SOURCE5 61 1.6924 - angle_coeff @angle:no-c2-no harmonic 106.896 113.900 # SOURCE3 1 - angle_coeff @angle:n-c2-ss harmonic 84.310 111.190 # SOURCE4_SOURCE5 24 0.6195 - angle_coeff @angle:oh-c2-oh harmonic 115.431 114.330 # SOURCE3 1 - angle_coeff @angle:o-c2-o harmonic 122.282 121.690 # SOURCE3 1 - angle_coeff @angle:o-c2-oh harmonic 116.614 121.230 # SOURCE4_SOURCE5 12 0.0958 - angle_coeff @angle:o-c2-s harmonic 80.412 127.680 # SOURCE3 2 0.0547 - angle_coeff @angle:os-c2-os harmonic 113.284 115.050 # SOURCE3_SOURCE5 6 1.2203 - angle_coeff @angle:p2-c2-p2 harmonic 106.670 129.800 # SOURCE3 1 - angle_coeff @angle:p3-c2-p3 harmonic 102.865 115.540 # SOURCE3 1 - angle_coeff @angle:p5-c2-p5 harmonic 98.628 121.850 # SOURCE3 1 - angle_coeff @angle:s4-c2-s4 harmonic 63.778 120.320 # SOURCE3 1 - angle_coeff @angle:s4-c2-s6 harmonic 63.877 119.950 # SOURCE3 1 - angle_coeff @angle:s6-c2-s6 harmonic 63.871 119.970 # SOURCE3 1 - angle_coeff @angle:sh-c2-sh harmonic 65.736 110.480 # SOURCE3 1 - angle_coeff @angle:sh-c2-ss harmonic 64.466 117.820 # SOURCE3 1 - angle_coeff @angle:s-c2-s harmonic 64.374 121.670 # SOURCE3 1 - angle_coeff @angle:ss-c2-ss harmonic 65.740 116.400 # SOURCE3_SOURCE5 22 2.3993 - angle_coeff @angle:br-c3-br harmonic 67.612 109.740 # SOURCE4_SOURCE5 24 0.9971 - angle_coeff @angle:br-c3-c1 harmonic 63.834 111.800 # SOURCE2 3 0.2160 - angle_coeff @angle:br-c3-c3 harmonic 63.860 110.010 # SOURCE3_SOURCE5 216 1.1568 - angle_coeff @angle:br-c3-c harmonic 64.284 108.920 # SOURCE4_SOURCE5 35 2.3703 - angle_coeff @angle:br-c3-h1 harmonic 42.433 105.070 # SOURCE3_SOURCE5 175 0.8275 - angle_coeff @angle:br-c3-h2 harmonic 42.082 106.800 # SOURCE4_SOURCE5 25 0.8044 - angle_coeff @angle:br-c3-hc harmonic 42.147 106.500 # SOURCE3 1 - angle_coeff @angle:c1-c3-c1 harmonic 68.433 110.110 # SOURCE2_SOURCE5 11 0.3454 - angle_coeff @angle:c1-c3-c2 harmonic 67.184 110.920 # SOURCE4_SOURCE5 35 0.5903 - angle_coeff @angle:c1-c3-c3 harmonic 66.276 111.710 # SOURCE4_SOURCE5 624 1.1320 - angle_coeff @angle:c1-c3-ca harmonic 67.047 110.890 # SOURCE4_SOURCE5 78 1.1306 - angle_coeff @angle:c1-c3-cc harmonic 66.403 114.190 # CORR_SOURCE5 15 0.1283 - angle_coeff @angle:c1-c3-cd harmonic 66.403 114.190 # CORR_SOURCE5 15 0.1283 - angle_coeff @angle:c1-c3-cl harmonic 72.363 110.630 # SOURCE2 3 1.2257 - angle_coeff @angle:c1-c3-h1 harmonic 48.917 109.240 # SOURCE4_SOURCE5 436 0.5758 - angle_coeff @angle:c1-c3-hc harmonic 48.879 109.410 # SOURCE3_SOURCE5 495 0.5104 - angle_coeff @angle:c1-c3-hx harmonic 48.339 112.040 # SOURCE4_SOURCE5 52 0.3815 - angle_coeff @angle:c1-c3-n3 harmonic 84.763 112.730 # SOURCE4_SOURCE5 99 0.7675 - angle_coeff @angle:c1-c3-n4 harmonic 83.658 112.060 # SOURCE4_SOURCE5 25 0.5395 - angle_coeff @angle:c1-c3-n harmonic 84.975 112.380 # SOURCE4_SOURCE5 55 0.9540 - angle_coeff @angle:c1-c3-nh harmonic 84.843 112.570 # SOURCE4_SOURCE5 21 0.9525 - angle_coeff @angle:c1-c3-oh harmonic 87.220 109.440 # SOURCE4_SOURCE5 127 0.9878 - angle_coeff @angle:c1-c3-os harmonic 87.159 109.000 # SOURCE4_SOURCE5 87 0.9531 - angle_coeff @angle:c2-c3-c2 harmonic 65.947 112.000 # SOURCE4_SOURCE5 453 0.8153 - angle_coeff @angle:c2-c3-c3 harmonic 65.459 111.560 # SOURCE4_SOURCE5 9345 1.7373 - angle_coeff @angle:c2-c3-ca harmonic 65.670 112.490 # SOURCE4_SOURCE5 475 1.6791 - angle_coeff @angle:c2-c3-cc harmonic 66.148 111.910 # CORR_SOURCE5 65 1.7402 - angle_coeff @angle:c2-c3-cd harmonic 66.148 111.910 # CORR_SOURCE5 65 1.7402 - angle_coeff @angle:c2-c3-ce harmonic 65.863 111.810 # CORR_SOURCE5 85 1.8411 - angle_coeff @angle:c2-c3-cf harmonic 65.867 111.810 # CORR_SOURCE5 85 1.8411 - angle_coeff @angle:c2-c3-cl harmonic 71.864 110.510 # SOURCE4_SOURCE5 60 1.4762 - angle_coeff @angle:c2-c3-cx harmonic 65.673 112.270 # SOURCE4_SOURCE5 76 1.2985 - angle_coeff @angle:c2-c3-cy harmonic 68.713 101.630 # SOURCE4_SOURCE5 164 1.0542 - angle_coeff @angle:c2-c3-f harmonic 88.392 110.760 # SOURCE4_SOURCE5 69 0.5776 - angle_coeff @angle:c2-c3-h1 harmonic 47.561 109.960 # SOURCE3_SOURCE5 2169 0.9645 - angle_coeff @angle:c2-c3-h2 harmonic 47.195 111.690 # SOURCE4_SOURCE5 49 0.9061 - angle_coeff @angle:c2-c3-hc harmonic 47.475 110.360 # SOURCE3_SOURCE5 11033 0.8531 - angle_coeff @angle:c2-c3-hx harmonic 47.293 111.340 # SOURCE4_SOURCE5 56 0.8089 - angle_coeff @angle:c2-c3-n2 harmonic 85.005 108.720 # SOURCE4_SOURCE5 36 1.3485 - angle_coeff @angle:c2-c3-n3 harmonic 84.006 111.420 # SOURCE4_SOURCE5 447 1.5436 - angle_coeff @angle:c2-c3-n harmonic 84.129 111.290 # SOURCE4_SOURCE5 180 1.8899 - angle_coeff @angle:c2-c3-na harmonic 83.365 113.270 # SOURCE4_SOURCE5 78 1.2929 - angle_coeff @angle:c2-c3-nh harmonic 84.408 110.410 # SOURCE4_SOURCE5 134 1.7670 - angle_coeff @angle:c2-c3-oh harmonic 85.495 110.350 # SOURCE4_SOURCE5 793 1.4429 - angle_coeff @angle:c2-c3-os harmonic 85.982 108.560 # SOURCE4_SOURCE5 763 1.7474 - angle_coeff @angle:c2-c3-s4 harmonic 63.867 109.890 # SOURCE4_SOURCE5 19 0.8365 - angle_coeff @angle:c2-c3-ss harmonic 65.117 104.970 # SOURCE3 2 2.2248 - angle_coeff @angle:c3-c3-c3 harmonic 64.888 111.510 # SOURCE3_SOURCE5 61999 1.8007 - angle_coeff @angle:c3-c3-ca harmonic 65.183 112.070 # SOURCE4_SOURCE5 11982 1.5875 - angle_coeff @angle:c3-c3-cc harmonic 65.515 111.930 # CORR_SOURCE5 2280 1.5614 - angle_coeff @angle:c3-c3-cd harmonic 65.515 111.930 # CORR_SOURCE5 2280 1.5614 - angle_coeff @angle:c3-c3-ce harmonic 65.514 110.920 # CORR_SOURCE5 1159 1.8552 - angle_coeff @angle:c3-c3-cf harmonic 65.518 110.920 # CORR_SOURCE5 1159 1.8552 - angle_coeff @angle:c3-c3-cl harmonic 71.515 110.410 # SOURCE3_SOURCE5 824 0.9824 - angle_coeff @angle:c3-c3-cx harmonic 65.198 111.820 # SOURCE4 179 2.4814 - angle_coeff @angle:c3-c3-cy harmonic 64.751 112.390 # SOURCE3_SOURCE5 322 1.3623 - angle_coeff @angle:c3-c3-f harmonic 87.947 109.240 # SOURCE3_SOURCE5 785 1.1106 - angle_coeff @angle:c3-c3-h1 harmonic 46.868 109.560 # SOURCE3_SOURCE5 55294 0.8125 - angle_coeff @angle:c3-c3-h2 harmonic 46.730 110.220 # SOURCE3_SOURCE5 1083 0.9457 - angle_coeff @angle:c3-c3-hc harmonic 46.816 109.800 # SOURCE3_SOURCE5 179054 0.7972 - angle_coeff @angle:c3-c3-hx harmonic 46.677 110.560 # SOURCE3_SOURCE5 1758 0.9658 - angle_coeff @angle:c3-c3-i harmonic 60.771 111.150 # SOURCE3_SOURCE5 48 1.3033 - angle_coeff @angle:c3-c3-n1 harmonic 84.875 108.980 # SOURCE4_SOURCE5 20 0.8416 - angle_coeff @angle:c3-c3-n2 harmonic 84.123 108.800 # SOURCE3_SOURCE5 665 2.1214 - angle_coeff @angle:c3-c3-n3 harmonic 83.305 111.040 # SOURCE3_SOURCE5 12086 1.5519 - angle_coeff @angle:c3-c3-n4 harmonic 80.976 114.210 # SOURCE4_SOURCE5 1537 2.4293 - angle_coeff @angle:c3-c3-n harmonic 83.161 111.610 # SOURCE3_SOURCE5 3543 1.6672 - angle_coeff @angle:c3-c3-na harmonic 82.668 112.880 # SOURCE4_SOURCE5 1677 1.4742 - angle_coeff @angle:c3-c3-nh harmonic 83.541 110.460 # SOURCE4_SOURCE5 3983 1.4189 - angle_coeff @angle:c3-c3-no harmonic 82.142 109.410 # SOURCE4_SOURCE5 111 1.3831 - angle_coeff @angle:c3-c3-o harmonic 85.929 113.010 # SOURCE4_SOURCE5 31 1.2728 - angle_coeff @angle:c3-c3-oh harmonic 84.642 110.190 # SOURCE3_SOURCE5 10188 1.4761 - angle_coeff @angle:c3-c3-os harmonic 85.306 107.970 # SOURCE3_SOURCE5 11384 1.3754 - angle_coeff @angle:c3-c3-p3 harmonic 79.425 113.360 # SOURCE4_SOURCE5 47 0.9033 - angle_coeff @angle:c3-c3-p5 harmonic 80.490 112.020 # SOURCE4_SOURCE5 346 1.5599 - angle_coeff @angle:c3-c3-s4 harmonic 63.481 110.120 # SOURCE4_SOURCE5 117 0.9869 - angle_coeff @angle:c3-c3-s6 harmonic 64.024 110.220 # SOURCE4_SOURCE5 420 1.6420 - angle_coeff @angle:c3-c3-sh harmonic 62.313 113.130 # SOURCE4_SOURCE5 226 1.3868 - angle_coeff @angle:c3-c3-ss harmonic 63.222 110.270 # SOURCE3_SOURCE5 1315 1.5441 - angle_coeff @angle:c3-c3-sy harmonic 64.081 109.920 # SOURCE4_SOURCE5 62 0.8825 - angle_coeff @angle:ca-c3-ca harmonic 65.611 112.240 # SOURCE4_SOURCE5 1062 1.7394 - angle_coeff @angle:ca-c3-cc harmonic 65.728 112.880 # CORR_SOURCE5 146 1.4369 - angle_coeff @angle:ca-c3-cd harmonic 65.728 112.880 # CORR_SOURCE5 146 1.4369 - angle_coeff @angle:ca-c3-ce harmonic 65.614 112.210 # SOURCE4_SOURCE5 144 1.2359 - angle_coeff @angle:ca-c3-cl harmonic 71.631 110.980 # SOURCE4_SOURCE5 62 0.7657 - angle_coeff @angle:ca-c3-cx harmonic 65.472 112.510 # SOURCE4_SOURCE5 24 2.0281 - angle_coeff @angle:ca-c3-f harmonic 87.765 111.770 # SOURCE4_SOURCE5 1080 0.3344 - angle_coeff @angle:ca-c3-h1 harmonic 47.477 109.560 # SOURCE3_SOURCE5 3349 0.8812 - angle_coeff @angle:ca-c3-h2 harmonic 47.451 109.700 # SOURCE4_SOURCE5 86 1.1507 - angle_coeff @angle:ca-c3-hc harmonic 47.281 110.470 # SOURCE3_SOURCE5 13973 0.8325 - angle_coeff @angle:ca-c3-hx harmonic 47.099 111.450 # SOURCE4_SOURCE5 113 0.5046 - angle_coeff @angle:ca-c3-n2 harmonic 83.424 112.390 # SOURCE4_SOURCE5 58 1.2061 - angle_coeff @angle:ca-c3-n3 harmonic 83.546 112.160 # SOURCE4_SOURCE5 1125 1.2435 - angle_coeff @angle:ca-c3-n4 harmonic 81.721 113.800 # SOURCE4_SOURCE5 79 2.4049 - angle_coeff @angle:ca-c3-n harmonic 83.537 112.380 # SOURCE4_SOURCE5 512 1.5411 - angle_coeff @angle:ca-c3-na harmonic 83.330 112.870 # SOURCE4_SOURCE5 240 1.5673 - angle_coeff @angle:ca-c3-nc harmonic 85.966 106.510 # SOURCE3 1 - angle_coeff @angle:ca-c3-nd harmonic 85.966 106.510 # SOURCE3 1 - angle_coeff @angle:ca-c3-nh harmonic 83.853 111.390 # SOURCE4_SOURCE5 349 0.9955 - angle_coeff @angle:ca-c3-oh harmonic 85.192 110.620 # SOURCE4_SOURCE5 1007 1.2078 - angle_coeff @angle:ca-c3-os harmonic 85.631 108.950 # SOURCE4_SOURCE5 1123 1.1238 - angle_coeff @angle:ca-c3-p5 harmonic 80.237 113.600 # SOURCE4_SOURCE5 41 1.4171 - angle_coeff @angle:ca-c3-s6 harmonic 63.909 111.540 # SOURCE4_SOURCE5 38 1.2112 - angle_coeff @angle:ca-c3-ss harmonic 63.252 111.020 # SOURCE4_SOURCE5 226 1.6105 - angle_coeff @angle:ca-c3-sx harmonic 63.255 110.780 # SOURCE4_SOURCE5 40 0.6145 - angle_coeff @angle:c-c3-c1 harmonic 66.399 112.380 # SOURCE4_SOURCE5 32 1.1114 - angle_coeff @angle:c-c3-c2 harmonic 65.824 111.330 # SOURCE4_SOURCE5 282 2.0882 - angle_coeff @angle:c-c3-c3 harmonic 65.307 111.040 # SOURCE3_SOURCE5 8161 1.7693 - angle_coeff @angle:c-c3-c harmonic 65.424 111.630 # SOURCE4_SOURCE5 409 2.2030 - angle_coeff @angle:c-c3-ca harmonic 65.788 111.010 # SOURCE4_SOURCE5 1282 1.7239 - angle_coeff @angle:c-c3-cc harmonic 65.455 113.170 # CORR_SOURCE5 164 1.3730 - angle_coeff @angle:cc-c3-cc harmonic 66.183 112.390 # CORR_SOURCE5 14 0.8688 - angle_coeff @angle:cc-c3-cd harmonic 66.037 112.890 # SOURCE3_SOURCE5 10 1.0674 - angle_coeff @angle:cc-c3-cx harmonic 65.894 112.100 # SOURCE4_SOURCE5 12 1.5999 - angle_coeff @angle:c-c3-cd harmonic 65.455 113.170 # CORR_SOURCE5 164 1.3730 - angle_coeff @angle:c-c3-ce harmonic 65.523 111.890 # SOURCE4_SOURCE5 75 1.6968 - angle_coeff @angle:cc-c3-f harmonic 88.472 111.310 # CORR_SOURCE5 105 0.4710 - angle_coeff @angle:cc-c3-h1 harmonic 47.855 109.640 # SOURCE3_SOURCE5 1145 0.8896 - angle_coeff @angle:cc-c3-hc harmonic 47.671 110.490 # SOURCE3_SOURCE5 6781 0.7714 - angle_coeff @angle:cc-c3-hx harmonic 47.588 111.010 # SOURCE4_SOURCE5 19 0.7303 - angle_coeff @angle:c-c3-cl harmonic 71.700 110.410 # SOURCE4_SOURCE5 146 1.5057 - angle_coeff @angle:cc-c3-n2 harmonic 84.630 110.310 # SOURCE4_SOURCE5 32 0.5465 - angle_coeff @angle:cc-c3-n3 harmonic 84.370 111.090 # CORR_SOURCE5 192 1.4026 - angle_coeff @angle:cc-c3-n4 harmonic 81.467 115.580 # SOURCE4_SOURCE5 12 1.1723 - angle_coeff @angle:cc-c3-n harmonic 84.192 111.760 # CORR_SOURCE5 51 1.5321 - angle_coeff @angle:cc-c3-na harmonic 83.647 113.150 # SOURCE4_SOURCE5 18 0.7152 - angle_coeff @angle:cc-c3-nc harmonic 86.190 107.040 # SOURCE3 2 - angle_coeff @angle:cc-c3-nh harmonic 83.918 112.340 # CORR_SOURCE5 25 1.8212 - angle_coeff @angle:cc-c3-oh harmonic 85.441 111.160 # CORR_SOURCE5 187 1.3741 - angle_coeff @angle:cc-c3-os harmonic 86.104 108.900 # CORR_SOURCE5 213 1.1488 - angle_coeff @angle:cc-c3-p5 harmonic 79.513 116.230 # SOURCE4_SOURCE5 12 0.7766 - angle_coeff @angle:cc-c3-sh harmonic 62.454 114.020 # SOURCE3 1 - angle_coeff @angle:cc-c3-ss harmonic 63.363 111.160 # CORR_SOURCE5 65 0.8483 - angle_coeff @angle:c-c3-cx harmonic 65.687 111.150 # SOURCE4_SOURCE5 48 1.8520 - angle_coeff @angle:cd-c3-cd harmonic 66.183 112.390 # CORR_SOURCE5 14 0.8688 - angle_coeff @angle:cd-c3-f harmonic 88.472 111.310 # CORR_SOURCE5 105 0.4710 - angle_coeff @angle:cd-c3-h1 harmonic 47.855 109.640 # SOURCE3_SOURCE5 1145 0.8896 - angle_coeff @angle:cd-c3-hc harmonic 47.671 110.490 # SOURCE3_SOURCE5 6781 0.7714 - angle_coeff @angle:cd-c3-n3 harmonic 84.370 111.090 # CORR_SOURCE5 192 1.4026 - angle_coeff @angle:cd-c3-n harmonic 84.192 111.760 # CORR_SOURCE5 51 1.5321 - angle_coeff @angle:cd-c3-nd harmonic 86.190 107.040 # SOURCE3 2 - angle_coeff @angle:cd-c3-nh harmonic 83.918 112.340 # CORR_SOURCE5 25 1.8212 - angle_coeff @angle:cd-c3-oh harmonic 85.441 111.160 # CORR_SOURCE5 187 1.3741 - angle_coeff @angle:cd-c3-os harmonic 86.104 108.900 # CORR_SOURCE5 213 1.1488 - angle_coeff @angle:cd-c3-sh harmonic 62.454 114.020 # SOURCE3 1 - angle_coeff @angle:cd-c3-ss harmonic 63.363 111.160 # CORR_SOURCE5 65 0.8483 - angle_coeff @angle:ce-c3-ce harmonic 65.825 111.470 # SOURCE4_SOURCE5 53 0.5207 - angle_coeff @angle:ce-c3-cy harmonic 68.161 102.860 # CORR_SOURCE5 72 0.2321 - angle_coeff @angle:ce-c3-h1 harmonic 47.473 109.540 # CORR_SOURCE5 252 0.8257 - angle_coeff @angle:ce-c3-hc harmonic 47.247 110.590 # SOURCE3_SOURCE5 2438 0.7216 - angle_coeff @angle:ce-c3-n3 harmonic 83.687 111.760 # CORR_SOURCE5 83 0.9878 - angle_coeff @angle:ce-c3-n harmonic 84.343 110.220 # SOURCE4_SOURCE5 16 1.1101 - angle_coeff @angle:ce-c3-oh harmonic 84.964 111.190 # SOURCE4_SOURCE5 74 1.5577 - angle_coeff @angle:ce-c3-os harmonic 85.406 109.500 # SOURCE4_SOURCE5 71 1.9041 - angle_coeff @angle:ce-c3-ss harmonic 63.335 110.720 # SOURCE4_SOURCE5 19 1.8179 - angle_coeff @angle:c-c3-f harmonic 88.148 110.000 # SOURCE4_SOURCE5 101 0.9951 - angle_coeff @angle:cf-c3-cy harmonic 68.165 102.860 # CORR_SOURCE5 72 0.2321 - angle_coeff @angle:cf-c3-h1 harmonic 47.479 109.540 # CORR_SOURCE5 252 0.8257 - angle_coeff @angle:cf-c3-hc harmonic 47.253 110.590 # SOURCE3_SOURCE5 2411 0.7279 - angle_coeff @angle:cf-c3-n3 harmonic 83.693 111.760 # CORR_SOURCE5 83 0.9878 - angle_coeff @angle:c-c3-h1 harmonic 47.531 108.220 # SOURCE3_SOURCE5 3484 0.9857 - angle_coeff @angle:c-c3-h2 harmonic 47.215 109.690 # SOURCE4_SOURCE5 100 1.0452 - angle_coeff @angle:c-c3-hc harmonic 47.411 108.770 # SOURCE3_SOURCE5 11750 0.9577 - angle_coeff @angle:c-c3-hx harmonic 47.419 108.850 # SOURCE4_SOURCE5 172 0.8753 - angle_coeff @angle:cl-c3-cl harmonic 81.372 109.330 # SOURCE2_SOURCE5 325 0.5772 - angle_coeff @angle:cl-c3-f harmonic 94.073 109.110 # SOURCE4_SOURCE5 57 0.3048 - angle_coeff @angle:cl-c3-h1 harmonic 48.859 106.780 # SOURCE3_SOURCE5 860 0.4999 - angle_coeff @angle:cl-c3-h2 harmonic 48.808 106.990 # SOURCE4_SOURCE5 147 0.6435 - angle_coeff @angle:cl-c3-hc harmonic 48.661 107.650 # SOURCE2 2 2.2500 - angle_coeff @angle:cl-c3-os harmonic 91.033 110.860 # SOURCE4_SOURCE5 26 1.1129 - angle_coeff @angle:cl-c3-ss harmonic 71.130 112.530 # SOURCE4_SOURCE5 39 1.6937 - angle_coeff @angle:c-c3-n2 harmonic 84.195 109.670 # SOURCE4_SOURCE5 157 1.3668 - angle_coeff @angle:c-c3-n3 harmonic 83.673 111.140 # SOURCE4_SOURCE5 1652 1.6694 - angle_coeff @angle:c-c3-n4 harmonic 82.611 110.730 # SOURCE4_SOURCE5 103 1.8311 - angle_coeff @angle:c-c3-n harmonic 84.540 109.060 # SOURCE3_SOURCE5 905 1.7615 - angle_coeff @angle:c-c3-na harmonic 83.584 111.500 # SOURCE4_SOURCE5 87 1.4027 - angle_coeff @angle:c-c3-nh harmonic 84.373 109.350 # SOURCE4_SOURCE5 106 1.8043 - angle_coeff @angle:c-c3-oh harmonic 85.627 108.790 # SOURCE4_SOURCE5 824 1.3178 - angle_coeff @angle:c-c3-os harmonic 85.254 109.210 # SOURCE3_SOURCE5 429 1.7229 - angle_coeff @angle:c-c3-p5 harmonic 81.107 110.850 # SOURCE4_SOURCE5 32 1.9944 - angle_coeff @angle:c-c3-s6 harmonic 64.058 110.670 # SOURCE4_SOURCE5 14 2.0336 - angle_coeff @angle:c-c3-sh harmonic 63.714 108.720 # SOURCE4_SOURCE5 31 0.7714 - angle_coeff @angle:c-c3-ss harmonic 63.788 108.840 # SOURCE3_SOURCE5 149 1.5563 - angle_coeff @angle:cx-c3-cx harmonic 65.100 113.590 # SOURCE4_SOURCE5 27 1.6971 - angle_coeff @angle:cx-c3-h1 harmonic 47.373 109.680 # SOURCE4_SOURCE5 611 0.9276 - angle_coeff @angle:cx-c3-hc harmonic 47.265 110.180 # SOURCE4_SOURCE5 1366 0.9055 - angle_coeff @angle:cx-c3-hx harmonic 46.751 112.740 # SOURCE4_SOURCE5 30 0.2036 - angle_coeff @angle:cx-c3-n3 harmonic 83.086 113.180 # SOURCE4_SOURCE5 97 1.4360 - angle_coeff @angle:cx-c3-n4 harmonic 86.467 101.460 # SOURCE4_SOURCE5 26 0.1569 - angle_coeff @angle:cx-c3-n harmonic 83.435 112.430 # SOURCE4_SOURCE5 68 0.9548 - angle_coeff @angle:cx-c3-oh harmonic 85.349 109.980 # SOURCE4_SOURCE5 145 1.5821 - angle_coeff @angle:cx-c3-os harmonic 85.968 107.870 # SOURCE4_SOURCE5 126 1.4698 - angle_coeff @angle:cy-c3-h1 harmonic 47.300 108.280 # SOURCE4_SOURCE5 415 1.0438 - angle_coeff @angle:cy-c3-hc harmonic 46.770 110.750 # SOURCE3_SOURCE5 539 0.9100 - angle_coeff @angle:cy-c3-n3 harmonic 82.598 113.410 # SOURCE4_SOURCE5 17 1.2266 - angle_coeff @angle:cy-c3-oh harmonic 84.330 111.490 # SOURCE4_SOURCE5 347 0.5753 - angle_coeff @angle:cy-c3-os harmonic 85.847 107.070 # SOURCE4_SOURCE5 16 1.1669 - angle_coeff @angle:f-c3-f harmonic 121.555 107.360 # SOURCE2_SOURCE5 1178 0.5429 - angle_coeff @angle:f-c3-h1 harmonic 66.869 107.900 # SOURCE3_SOURCE5 181 0.5803 - angle_coeff @angle:f-c3-h2 harmonic 66.607 108.790 # SOURCE3_SOURCE5 66 0.6474 - angle_coeff @angle:f-c3-h3 harmonic 66.233 110.080 # SOURCE4_SOURCE5 45 0.6178 - angle_coeff @angle:f-c3-hc harmonic 66.555 108.920 # SOURCE2 5 3.0534 - angle_coeff @angle:f-c3-n2 harmonic 112.898 110.400 # SOURCE2 3 2.6470 - angle_coeff @angle:f-c3-os harmonic 114.397 110.580 # SOURCE4_SOURCE5 114 1.2792 - angle_coeff @angle:f-c3-p5 harmonic 107.070 107.610 # SOURCE4_SOURCE5 35 1.1282 - angle_coeff @angle:f-c3-s6 harmonic 83.906 109.680 # SOURCE4_SOURCE5 57 0.4273 - angle_coeff @angle:f-c3-ss harmonic 81.883 111.750 # SOURCE4_SOURCE5 38 1.8571 - angle_coeff @angle:h1-c3-h1 harmonic 38.802 108.460 # SOURCE3_SOURCE5 50971 0.8222 - angle_coeff @angle:h1-c3-n1 harmonic 62.841 107.990 # HF/6-31G*_SOURCE5 7 0.3554 - angle_coeff @angle:h1-c3-n2 harmonic 61.133 109.810 # SOURCE3_SOURCE5 957 1.0346 - angle_coeff @angle:h1-c3-n3 harmonic 61.163 109.880 # SOURCE3_SOURCE5 20428 1.2681 - angle_coeff @angle:h1-c3-n harmonic 61.544 108.880 # SOURCE3_SOURCE5 6816 1.0842 - angle_coeff @angle:h1-c3-na harmonic 61.536 108.780 # SOURCE3_SOURCE5 2896 0.9339 - angle_coeff @angle:h1-c3-nc harmonic 61.844 108.570 # SOURCE3 6 0.0764 - angle_coeff @angle:h1-c3-nd harmonic 61.844 108.570 # SOURCE3 6 - angle_coeff @angle:h1-c3-nh harmonic 61.213 109.790 # SOURCE3_SOURCE5 6106 1.0471 - angle_coeff @angle:h1-c3-no harmonic 59.962 105.470 # SOURCE4_SOURCE5 73 0.6459 - angle_coeff @angle:h1-c3-o harmonic 64.637 116.450 # SOURCE3_SOURCE5 25 1.4798 - angle_coeff @angle:h1-c3-oh harmonic 62.540 110.260 # SOURCE3_SOURCE5 7971 1.1355 - angle_coeff @angle:h1-c3-os harmonic 62.377 109.780 # SOURCE3_SOURCE5 19982 1.1092 - angle_coeff @angle:h1-c3-p5 harmonic 54.608 108.270 # SOURCE4_SOURCE5 222 1.1376 - angle_coeff @angle:h1-c3-s4 harmonic 42.850 107.920 # SOURCE3_SOURCE5 496 0.6942 - angle_coeff @angle:h1-c3-s harmonic 41.631 112.370 # SOURCE3_SOURCE5 14 0.4580 - angle_coeff @angle:h1-c3-s6 harmonic 43.600 107.150 # SOURCE3_SOURCE5 1022 0.8992 - angle_coeff @angle:h1-c3-sh harmonic 42.420 108.420 # SOURCE3_SOURCE5 259 1.4350 - angle_coeff @angle:h1-c3-ss harmonic 42.463 108.760 # SOURCE3_SOURCE5 3369 1.0506 - angle_coeff @angle:h1-c3-sx harmonic 42.605 107.700 # SOURCE3_SOURCE5 201 0.7977 - angle_coeff @angle:h1-c3-sy harmonic 43.421 107.880 # SOURCE3_SOURCE5 377 1.1089 - angle_coeff @angle:h2-c3-h2 harmonic 38.523 110.200 # SOURCE3_SOURCE5 677 0.8586 - angle_coeff @angle:h2-c3-i harmonic 39.064 104.990 # SOURCE3 2 - angle_coeff @angle:h2-c3-n2 harmonic 61.031 110.200 # SOURCE3_SOURCE5 69 0.8494 - angle_coeff @angle:h2-c3-n3 harmonic 61.318 109.350 # SOURCE4_SOURCE5 660 0.9086 - angle_coeff @angle:h2-c3-n harmonic 62.008 107.280 # SOURCE4_SOURCE5 692 1.3634 - angle_coeff @angle:h2-c3-na harmonic 61.963 107.310 # SOURCE3_SOURCE5 428 0.9670 - angle_coeff @angle:h2-c3-nc harmonic 61.596 109.470 # SOURCE3 10 0.3133 - angle_coeff @angle:h2-c3-nd harmonic 61.596 109.470 # SOURCE3 10 - angle_coeff @angle:h2-c3-nh harmonic 61.159 110.010 # SOURCE4_SOURCE5 274 1.1061 - angle_coeff @angle:h2-c3-no harmonic 59.186 108.270 # SOURCE3_SOURCE5 13 0.4528 - angle_coeff @angle:h2-c3-o harmonic 66.832 108.970 # SOURCE3 4 - angle_coeff @angle:h2-c3-oh harmonic 62.785 109.430 # SOURCE3_SOURCE5 258 1.6998 - angle_coeff @angle:h2-c3-os harmonic 62.442 109.580 # SOURCE3_SOURCE5 2823 0.6377 - angle_coeff @angle:h2-c3-s4 harmonic 42.969 107.310 # SOURCE3_SOURCE5 29 0.3344 - angle_coeff @angle:h2-c3-s harmonic 42.709 106.750 # SOURCE3 4 - angle_coeff @angle:h2-c3-s6 harmonic 43.728 106.510 # SOURCE4_SOURCE5 67 1.0466 - angle_coeff @angle:h2-c3-sh harmonic 42.525 107.870 # SOURCE3 6 0.4376 - angle_coeff @angle:h2-c3-ss harmonic 42.544 108.330 # SOURCE3_SOURCE5 279 1.1804 - angle_coeff @angle:h3-c3-n3 harmonic 61.502 108.730 # SOURCE4_SOURCE5 32 1.8953 - angle_coeff @angle:h3-c3-nc harmonic 61.634 109.370 # SOURCE3 1 - angle_coeff @angle:h3-c3-nd harmonic 61.634 109.370 # SOURCE3 1 - angle_coeff @angle:h3-c3-nh harmonic 61.116 110.200 # SOURCE4_SOURCE5 11 1.4222 - angle_coeff @angle:h3-c3-os harmonic 61.911 111.510 # SOURCE4_SOURCE5 44 1.4444 - angle_coeff @angle:h3-c3-ss harmonic 42.391 109.090 # SOURCE4_SOURCE5 19 0.8547 - angle_coeff @angle:hc-c3-hc harmonic 38.960 107.580 # SOURCE3_SOURCE5 92717 0.5328 - angle_coeff @angle:hc-c3-i harmonic 39.071 104.990 # SOURCE3 1 - angle_coeff @angle:hc-c3-n2 harmonic 61.220 109.500 # SOURCE3 1 - angle_coeff @angle:hc-c3-n3 harmonic 61.186 109.800 # SOURCE2 5 2.0070 - angle_coeff @angle:hc-c3-n4 harmonic 60.071 107.900 # SOURCE3 1 - angle_coeff @angle:hc-c3-n harmonic 61.369 109.500 # SOURCE3 1 - angle_coeff @angle:hc-c3-na harmonic 61.334 109.500 # SOURCE3 1 - angle_coeff @angle:hc-c3-nh harmonic 60.731 111.540 # SOURCE3 1 - angle_coeff @angle:hc-c3-no harmonic 59.477 107.200 # SOURCE2 1 - angle_coeff @angle:hc-c3-oh harmonic 62.756 109.500 # SOURCE3 1 - angle_coeff @angle:hc-c3-os harmonic 62.686 108.700 # SOURCE2 13 2.3739 - angle_coeff @angle:hc-c3-p2 harmonic 53.633 110.180 # SOURCE3 25 0.4057 - angle_coeff @angle:hc-c3-p3 harmonic 53.601 109.890 # SOURCE3_SOURCE5 528 0.6740 - angle_coeff @angle:hc-c3-p4 harmonic 54.339 109.450 # SOURCE3_SOURCE5 128 0.4042 - angle_coeff @angle:hc-c3-p5 harmonic 54.567 108.430 # SOURCE3_SOURCE5 513 1.0539 - angle_coeff @angle:hc-c3-px harmonic 54.606 109.700 # SOURCE3_SOURCE5 103 0.3664 - angle_coeff @angle:hc-c3-py harmonic 54.373 109.180 # SOURCE3_SOURCE5 74 0.4506 - angle_coeff @angle:hc-c3-s4 harmonic 42.934 107.500 # SOURCE2 1 - angle_coeff @angle:hc-c3-s6 harmonic 43.388 108.200 # SOURCE3 1 - angle_coeff @angle:hc-c3-sh harmonic 42.529 107.870 # SOURCE2 3 2.0981 - angle_coeff @angle:hc-c3-ss harmonic 42.463 108.760 # SOURCE2 3 1.6891 - angle_coeff @angle:hx-c3-hx harmonic 38.782 109.750 # SOURCE3_SOURCE5 5075 0.8234 - angle_coeff @angle:hx-c3-n4 harmonic 60.076 108.010 # SOURCE3_SOURCE5 6129 1.3658 - angle_coeff @angle:i-c3-i harmonic 66.247 113.120 # SOURCE3 1 - angle_coeff @angle:n1-c3-n1 harmonic 112.470 105.070 # HF/6-31G* 1 - angle_coeff @angle:n2-c3-n2 harmonic 107.595 109.680 # SOURCE3_SOURCE5 6 0.6095 - angle_coeff @angle:n2-c3-nh harmonic 106.900 111.270 # SOURCE4_SOURCE5 19 0.9194 - angle_coeff @angle:n2-c3-oh harmonic 108.058 111.890 # SOURCE4_SOURCE5 31 0.2948 - angle_coeff @angle:n2-c3-os harmonic 108.177 111.040 # SOURCE4_SOURCE5 16 1.7109 - angle_coeff @angle:n3-c3-n3 harmonic 106.945 111.230 # SOURCE4_SOURCE5 123 1.3731 - angle_coeff @angle:n3-c3-nc harmonic 106.282 113.290 # SOURCE3 1 - angle_coeff @angle:n3-c3-nd harmonic 106.282 113.290 # SOURCE3 1 - angle_coeff @angle:n3-c3-nh harmonic 107.270 110.610 # SOURCE4_SOURCE5 58 1.2027 - angle_coeff @angle:n3-c3-oh harmonic 108.693 110.700 # SOURCE4_SOURCE5 52 0.9667 - angle_coeff @angle:n3-c3-os harmonic 109.486 108.510 # SOURCE4_SOURCE5 53 1.7879 - angle_coeff @angle:n3-c3-p5 harmonic 103.225 109.410 # SOURCE4_SOURCE5 26 1.5078 - angle_coeff @angle:n3-c3-ss harmonic 81.202 107.380 # SOURCE4_SOURCE5 50 1.6843 - angle_coeff @angle:n4-c3-n4 harmonic 102.708 113.320 # SOURCE3 1 - angle_coeff @angle:na-c3-na harmonic 106.005 113.490 # SOURCE3 1 - angle_coeff @angle:na-c3-os harmonic 109.296 109.030 # SOURCE4_SOURCE5 495 0.5894 - angle_coeff @angle:nc-c3-nc harmonic 107.885 110.610 # SOURCE3 1 - angle_coeff @angle:nc-c3-nh harmonic 106.714 112.430 # SOURCE3 1 - angle_coeff @angle:nc-c3-os harmonic 106.495 115.410 # SOURCE3 3 1.0288 - angle_coeff @angle:nd-c3-nd harmonic 107.885 110.610 # SOURCE3 1 - angle_coeff @angle:nd-c3-nh harmonic 106.714 112.430 # SOURCE3 1 - angle_coeff @angle:nd-c3-os harmonic 106.495 115.410 # SOURCE3 3 - angle_coeff @angle:nh-c3-nh harmonic 109.672 105.870 # SOURCE3 1 - angle_coeff @angle:nh-c3-oh harmonic 107.958 112.270 # SOURCE4_SOURCE5 43 0.9258 - angle_coeff @angle:nh-c3-os harmonic 109.202 109.130 # SOURCE4_SOURCE5 47 1.3529 - angle_coeff @angle:nh-c3-p5 harmonic 101.809 112.500 # SOURCE4 5 1.7371 - angle_coeff @angle:nh-c3-ss harmonic 80.602 109.010 # SOURCE4_SOURCE5 19 2.2237 - angle_coeff @angle:n-c3-n2 harmonic 106.958 111.310 # SOURCE4_SOURCE5 12 1.5991 - angle_coeff @angle:n-c3-n3 harmonic 107.105 111.110 # SOURCE4_SOURCE5 37 1.6907 - angle_coeff @angle:n-c3-n harmonic 106.473 112.650 # SOURCE3_SOURCE5 30 2.1166 - angle_coeff @angle:n-c3-nh harmonic 108.332 108.660 # SOURCE4_SOURCE5 26 1.9779 - angle_coeff @angle:n-c3-oh harmonic 107.902 112.560 # SOURCE4_SOURCE5 75 1.1310 - angle_coeff @angle:no-c3-no harmonic 105.051 105.180 # SOURCE4_SOURCE5 23 1.9192 - angle_coeff @angle:n-c3-os harmonic 109.285 109.130 # SOURCE4_SOURCE5 432 0.8256 - angle_coeff @angle:n-c3-p5 harmonic 102.749 110.520 # SOURCE4_SOURCE5 12 1.2739 - angle_coeff @angle:oh-c3-oh harmonic 110.720 109.900 # SOURCE4_SOURCE5 20 1.5118 - angle_coeff @angle:oh-c3-os harmonic 110.658 109.380 # SOURCE4_SOURCE5 280 1.2270 - angle_coeff @angle:oh-c3-p5 harmonic 104.174 108.680 # SOURCE4_SOURCE5 77 1.3087 - angle_coeff @angle:oh-c3-sh harmonic 78.616 115.460 # SOURCE3 1 - angle_coeff @angle:o-c3-o harmonic 113.472 122.300 # SOURCE3 1 - angle_coeff @angle:os-c3-os harmonic 110.893 108.290 # SOURCE3_SOURCE5 723 1.0283 - angle_coeff @angle:os-c3-p5 harmonic 104.392 107.990 # SOURCE4_SOURCE5 63 2.0205 - angle_coeff @angle:os-c3-ss harmonic 81.130 108.590 # SOURCE4_SOURCE5 54 1.6231 - angle_coeff @angle:p2-c3-p2 harmonic 104.003 110.480 # SOURCE3 1 - angle_coeff @angle:p3-c3-p3 harmonic 103.975 110.160 # SOURCE3 1 - angle_coeff @angle:p5-c3-p5 harmonic 105.046 110.130 # SOURCE4 33 2.4116 - angle_coeff @angle:p5-c3-ss harmonic 81.364 111.480 # SOURCE4_SOURCE5 12 1.9291 - angle_coeff @angle:s4-c3-s4 harmonic 63.477 112.290 # SOURCE3 2 1.2724 - angle_coeff @angle:s4-c3-s6 harmonic 63.526 113.520 # SOURCE3 1 - angle_coeff @angle:s6-c3-s6 harmonic 64.593 111.220 # SOURCE3_SOURCE5 6 1.7567 - angle_coeff @angle:sh-c3-sh harmonic 61.944 116.260 # SOURCE3 1 - angle_coeff @angle:sh-c3-ss harmonic 63.545 110.730 # SOURCE3 1 - angle_coeff @angle:s-c3-s harmonic 60.088 123.350 # SOURCE3 1 - angle_coeff @angle:ss-c3-ss harmonic 63.417 111.440 # SOURCE4_SOURCE5 66 1.6272 - angle_coeff @angle:br-ca-br harmonic 67.710 117.600 # SOURCE3 1 - angle_coeff @angle:br-ca-ca harmonic 64.160 119.300 # SOURCE3_SOURCE5 640 0.4898 - angle_coeff @angle:c1-ca-c1 harmonic 66.786 120.000 # SOURCE3 1 - angle_coeff @angle:c1-ca-ca harmonic 67.736 120.000 # SOURCE3 1 - angle_coeff @angle:c2-ca-c2 harmonic 69.458 120.000 # SOURCE3 1 - angle_coeff @angle:c2-ca-ca harmonic 68.938 120.600 # SOURCE3 1 - angle_coeff @angle:c3-ca-c2 harmonic 66.051 120.000 # SOURCE3 1 - angle_coeff @angle:c3-ca-c3 harmonic 64.318 116.800 # SOURCE3 1 - angle_coeff @angle:c3-ca-ca harmonic 65.583 120.770 # SOURCE3_SOURCE5 23865 1.2220 - angle_coeff @angle:c3-ca-cp harmonic 65.482 120.630 # CORR 120 - angle_coeff @angle:c3-ca-cq harmonic 65.482 120.630 # CORR 120 - angle_coeff @angle:c3-ca-na harmonic 83.171 118.720 # SOURCE4_SOURCE5 145 1.1124 - angle_coeff @angle:c3-ca-nb harmonic 84.916 116.680 # SOURCE4_SOURCE5 1062 0.9093 - angle_coeff @angle:ca-ca-ca harmonic 68.767 120.020 # SOURCE3_SOURCE5 108055 0.7701 - angle_coeff @angle:ca-ca-cc harmonic 67.122 120.790 # SOURCE3_SOURCE5 2048 2.0941 - angle_coeff @angle:ca-ca-cd harmonic 67.122 120.790 # SOURCE3_SOURCE5 2048 2.0941 - angle_coeff @angle:ca-ca-ce harmonic 66.584 120.820 # SOURCE3_SOURCE5 3962 1.5682 - angle_coeff @angle:ca-ca-cf harmonic 66.584 120.820 # SOURCE3_SOURCE5 3948 1.5732 - angle_coeff @angle:ca-ca-cg harmonic 67.841 120.270 # SOURCE3_SOURCE5 453 0.4194 - angle_coeff @angle:ca-ca-ch harmonic 67.841 120.270 # SOURCE3_SOURCE5 447 0.4218 - angle_coeff @angle:ca-ca-cl harmonic 72.112 119.390 # SOURCE4_SOURCE5 6669 0.5363 - angle_coeff @angle:ca-ca-cp harmonic 68.394 120.690 # CORR_SOURCE5 1915 0.8596 - angle_coeff @angle:ca-ca-cq harmonic 68.394 120.690 # CORR_SOURCE5 1915 0.8596 - angle_coeff @angle:ca-ca-cx harmonic 66.227 120.830 # SOURCE4 71 1.3062 - angle_coeff @angle:ca-ca-cy harmonic 65.564 120.860 # SOURCE4 17 2.0287 - angle_coeff @angle:ca-ca-f harmonic 89.261 118.960 # SOURCE4_SOURCE5 2636 0.3804 - angle_coeff @angle:ca-ca-h4 harmonic 48.561 120.340 # SOURCE3_SOURCE5 2590 0.5568 - angle_coeff @angle:ca-ca-ha harmonic 48.680 119.880 # SOURCE3_SOURCE5 126779 0.4424 - angle_coeff @angle:ca-ca-i harmonic 61.098 119.110 # SOURCE3_SOURCE5 123 0.9416 - angle_coeff @angle:ca-ca-n1 harmonic 88.104 119.780 # HF/6-31G*_SOURCE5 14 0.4655 - angle_coeff @angle:ca-ca-n2 harmonic 89.100 119.570 # SOURCE3 1 - angle_coeff @angle:ca-ca-n4 harmonic 83.650 119.310 # SOURCE3_SOURCE5 63 1.4960 - angle_coeff @angle:ca-ca-n harmonic 85.629 120.190 # SOURCE3_SOURCE5 3041 2.2480 - angle_coeff @angle:ca-ca-na harmonic 87.167 118.340 # SOURCE3 54 3.6168 - angle_coeff @angle:ca-ca-nb harmonic 86.849 122.940 # SOURCE3_SOURCE5 5507 1.1495 - angle_coeff @angle:ca-ca-nc harmonic 87.635 119.720 # SOURCE3 22 3.3994 - angle_coeff @angle:ca-ca-nd harmonic 87.635 119.720 # SOURCE3 22 3.3994 - angle_coeff @angle:ca-ca-ne harmonic 85.610 120.610 # SOURCE3_SOURCE5 349 2.0914 - angle_coeff @angle:ca-ca-nf harmonic 85.610 120.610 # SOURCE3_SOURCE5 349 2.0914 - angle_coeff @angle:ca-ca-nh harmonic 86.163 120.950 # SOURCE3_SOURCE5 4970 1.2168 - angle_coeff @angle:ca-ca-no harmonic 84.250 119.010 # SOURCE3_SOURCE5 854 0.7071 - angle_coeff @angle:ca-ca-o harmonic 89.534 123.260 # SOURCE4_SOURCE5 35 1.2620 - angle_coeff @angle:ca-ca-oh harmonic 87.211 119.900 # SOURCE3_SOURCE5 6384 1.7827 - angle_coeff @angle:ca-ca-os harmonic 87.289 119.200 # SOURCE3 52 0.5240 - angle_coeff @angle:ca-ca-p2 harmonic 81.329 114.360 # SOURCE3 1 - angle_coeff @angle:ca-ca-p3 harmonic 79.908 120.010 # SOURCE3_SOURCE5 24 1.1566 - angle_coeff @angle:ca-ca-p4 harmonic 80.525 120.300 # SOURCE3 1 - angle_coeff @angle:ca-ca-p5 harmonic 80.938 120.240 # SOURCE4_SOURCE5 15 0.0746 - angle_coeff @angle:ca-ca-pe harmonic 79.643 120.450 # SOURCE3 20 0.2719 - angle_coeff @angle:ca-ca-pf harmonic 79.643 120.450 # SOURCE3 20 0.2719 - angle_coeff @angle:ca-ca-px harmonic 79.761 120.530 # SOURCE3 10 0.4509 - angle_coeff @angle:ca-ca-py harmonic 80.172 120.250 # SOURCE3_SOURCE5 75 1.5353 - angle_coeff @angle:ca-ca-s4 harmonic 63.561 119.150 # SOURCE3 1 - angle_coeff @angle:ca-ca-s6 harmonic 63.822 120.430 # SOURCE4_SOURCE5 89 1.1843 - angle_coeff @angle:ca-ca-s harmonic 64.056 122.550 # SOURCE3 4 - angle_coeff @angle:ca-ca-sh harmonic 63.072 121.780 # SOURCE4_SOURCE5 54 1.3490 - angle_coeff @angle:ca-ca-ss harmonic 63.530 120.060 # SOURCE3_SOURCE5 1341 2.1632 - angle_coeff @angle:ca-ca-sx harmonic 62.473 119.280 # SOURCE3_SOURCE5 140 1.1919 - angle_coeff @angle:ca-ca-sy harmonic 63.407 119.420 # SOURCE3_SOURCE5 1489 0.7572 - angle_coeff @angle:c-ca-c3 harmonic 64.497 118.060 # SOURCE3 1 - angle_coeff @angle:c-ca-c harmonic 64.519 120.000 # SOURCE3 1 - angle_coeff @angle:c-ca-ca harmonic 66.351 120.330 # SOURCE3_SOURCE5 8320 1.9221 - angle_coeff @angle:cc-ca-cp harmonic 66.010 124.300 # SOURCE4_SOURCE5 20 0.6423 - angle_coeff @angle:cc-ca-nb harmonic 86.709 117.750 # CORR_SOURCE5 42 1.7067 - angle_coeff @angle:cd-ca-nb harmonic 86.709 117.750 # CORR_SOURCE5 42 1.7067 - angle_coeff @angle:ce-ca-na harmonic 84.062 119.920 # SOURCE4_SOURCE5 38 0.5659 - angle_coeff @angle:ce-ca-nb harmonic 86.028 117.560 # CORR_SOURCE5 91 0.8492 - angle_coeff @angle:cf-ca-nb harmonic 86.028 117.560 # CORR_SOURCE5 91 0.8492 - angle_coeff @angle:cg-ca-cp harmonic 67.320 121.530 # SOURCE4_SOURCE5 24 0.1831 - angle_coeff @angle:c-ca-ha harmonic 46.900 115.900 # SOURCE3 1 - angle_coeff @angle:cl-ca-cl harmonic 80.510 118.720 # SOURCE3 1 - angle_coeff @angle:cl-ca-cp harmonic 71.726 120.390 # SOURCE4_SOURCE5 52 0.5449 - angle_coeff @angle:cl-ca-nb harmonic 92.329 116.180 # SOURCE4_SOURCE5 152 0.5909 - angle_coeff @angle:c-ca-nb harmonic 85.429 117.780 # SOURCE4_SOURCE5 262 1.1507 - angle_coeff @angle:c-ca-nc harmonic 80.781 130.800 # SOURCE3 1 - angle_coeff @angle:c-ca-nd harmonic 80.781 130.800 # SOURCE3 1 - angle_coeff @angle:cp-ca-f harmonic 88.831 119.420 # SOURCE4_SOURCE5 46 0.2425 - angle_coeff @angle:cp-ca-h4 harmonic 48.404 120.090 # SOURCE4_SOURCE5 62 0.4243 - angle_coeff @angle:cp-ca-ha harmonic 48.475 119.860 # CORR_SOURCE5 1240 0.5472 - angle_coeff @angle:cp-ca-na harmonic 90.665 108.790 # SOURCE4_SOURCE5 514 0.5055 - angle_coeff @angle:cp-ca-nb harmonic 86.369 123.580 # SOURCE4_SOURCE5 129 0.8391 - angle_coeff @angle:cp-ca-nh harmonic 85.714 121.560 # SOURCE4_SOURCE5 30 0.5872 - angle_coeff @angle:cp-ca-oh harmonic 86.623 120.850 # SOURCE4_SOURCE5 41 1.3658 - angle_coeff @angle:cp-ca-ss harmonic 65.950 111.170 # SOURCE4_SOURCE5 24 1.8180 - angle_coeff @angle:cp-ca-sy harmonic 65.646 111.180 # CORR 4 - angle_coeff @angle:cq-ca-ha harmonic 48.475 119.860 # CORR_SOURCE5 1240 0.5472 - angle_coeff @angle:cq-ca-sy harmonic 65.646 111.180 # CORR 4 - angle_coeff @angle:f-ca-f harmonic 116.252 117.500 # SOURCE3 1 - angle_coeff @angle:f-ca-nb harmonic 116.437 114.670 # SOURCE4_SOURCE5 42 0.4295 - angle_coeff @angle:h4-ca-n harmonic 61.444 116.020 # SOURCE3 1 - angle_coeff @angle:h4-ca-na harmonic 62.367 116.320 # SOURCE3_SOURCE5 394 0.4031 - angle_coeff @angle:h4-ca-nb harmonic 64.066 116.030 # SOURCE3_SOURCE5 2217 0.2861 - angle_coeff @angle:h4-ca-nc harmonic 62.978 118.360 # SOURCE3 1 - angle_coeff @angle:h4-ca-nd harmonic 62.978 118.360 # SOURCE3 1 - angle_coeff @angle:h4-ca-os harmonic 64.330 111.150 # SOURCE3 1 - angle_coeff @angle:h4-ca-ss harmonic 42.528 116.190 # SOURCE3 1 - angle_coeff @angle:h5-ca-nb harmonic 64.141 115.820 # SOURCE3_SOURCE5 618 0.3893 - angle_coeff @angle:h5-ca-nc harmonic 62.019 122.110 # SOURCE3 1 - angle_coeff @angle:h5-ca-nd harmonic 62.019 122.110 # SOURCE3 1 - angle_coeff @angle:ha-ca-n2 harmonic 65.427 116.000 # SOURCE2 1 - angle_coeff @angle:ha-ca-p2 harmonic 51.256 122.560 # SOURCE3 1 - angle_coeff @angle:i-ca-i harmonic 67.026 119.280 # SOURCE3 1 - angle_coeff @angle:n1-ca-n1 harmonic 114.391 117.030 # HF/6-31G* 1 - angle_coeff @angle:n2-ca-n2 harmonic 115.741 120.000 # SOURCE3 1 - angle_coeff @angle:n2-ca-na harmonic 112.235 119.600 # SOURCE3 1 - angle_coeff @angle:n4-ca-n4 harmonic 102.984 116.820 # SOURCE3 1 - angle_coeff @angle:na-ca-na harmonic 115.064 107.620 # SOURCE4_SOURCE5 11 0.8382 - angle_coeff @angle:na-ca-nb harmonic 107.575 127.090 # SOURCE4_SOURCE5 708 1.9791 - angle_coeff @angle:na-ca-nh harmonic 109.505 118.660 # SOURCE4_SOURCE5 73 0.9977 - angle_coeff @angle:nb-ca-nb harmonic 109.369 127.260 # SOURCE4_SOURCE5 1586 1.1854 - angle_coeff @angle:nb-ca-nc harmonic 109.175 126.500 # CORR_SOURCE5 33 1.0453 - angle_coeff @angle:nb-ca-nd harmonic 109.175 126.500 # CORR_SOURCE5 33 1.0453 - angle_coeff @angle:nb-ca-nh harmonic 112.063 116.940 # SOURCE4_SOURCE5 2042 0.7868 - angle_coeff @angle:nb-ca-oh harmonic 112.676 117.680 # SOURCE4_SOURCE5 182 0.7979 - angle_coeff @angle:nb-ca-os harmonic 111.458 119.720 # SOURCE4_SOURCE5 194 0.7211 - angle_coeff @angle:nb-ca-sh harmonic 80.990 117.610 # SOURCE4_SOURCE5 35 1.3741 - angle_coeff @angle:nb-ca-ss harmonic 80.595 118.800 # SOURCE4_SOURCE5 111 1.8247 - angle_coeff @angle:nc-ca-nc harmonic 107.717 128.740 # SOURCE3 1 - angle_coeff @angle:nc-ca-nh harmonic 110.670 118.860 # SOURCE3 1 - angle_coeff @angle:nd-ca-nd harmonic 107.717 128.740 # SOURCE3 1 - angle_coeff @angle:nd-ca-nh harmonic 110.670 118.860 # SOURCE3 1 - angle_coeff @angle:nh-ca-nh harmonic 108.376 120.980 # SOURCE3 1 - angle_coeff @angle:n-ca-nc harmonic 107.316 123.860 # SOURCE3 1 - angle_coeff @angle:n-ca-nd harmonic 107.316 123.860 # SOURCE3 1 - angle_coeff @angle:n-ca-nh harmonic 109.547 116.160 # SOURCE3 1 - angle_coeff @angle:no-ca-no harmonic 103.915 117.140 # SOURCE3 1 - angle_coeff @angle:oh-ca-oh harmonic 110.589 120.000 # SOURCE3 1 - angle_coeff @angle:o-ca-o harmonic 118.708 126.820 # SOURCE3 1 - angle_coeff @angle:os-ca-os harmonic 113.107 113.730 # SOURCE3 1 - angle_coeff @angle:p2-ca-p2 harmonic 100.107 121.200 # SOURCE3 1 - angle_coeff @angle:p3-ca-p3 harmonic 100.783 121.460 # SOURCE3 1 - angle_coeff @angle:p5-ca-p5 harmonic 103.117 120.000 # SOURCE3 1 - angle_coeff @angle:s4-ca-s4 harmonic 66.946 105.810 # SOURCE3 1 - angle_coeff @angle:s6-ca-s6 harmonic 67.745 105.810 # SOURCE3 1 - angle_coeff @angle:sh-ca-sh harmonic 63.051 120.240 # SOURCE3 1 - angle_coeff @angle:s-ca-s harmonic 63.293 125.140 # SOURCE3 1 - angle_coeff @angle:ss-ca-ss harmonic 64.440 115.150 # SOURCE3 1 - angle_coeff @angle:br-c-br harmonic 67.692 113.100 # SOURCE3 1 - angle_coeff @angle:br-c-c3 harmonic 64.598 110.740 # SOURCE3 1 - angle_coeff @angle:br-c-o harmonic 78.490 121.460 # SOURCE3 5 1.6264 - angle_coeff @angle:c1-c-c1 harmonic 67.194 115.320 # SOURCE3 1 - angle_coeff @angle:c1-c-o harmonic 87.628 122.340 # SOURCE3 1 - angle_coeff @angle:c2-c-c2 harmonic 69.337 116.780 # SOURCE3 1 - angle_coeff @angle:c2-c-ha harmonic 49.151 115.950 # SOURCE3 1 - angle_coeff @angle:c2-c-o harmonic 91.182 119.120 # SOURCE3 2 - angle_coeff @angle:c2-c-s harmonic 66.780 119.160 # SOURCE3 2 - angle_coeff @angle:c3-c-c3 harmonic 64.041 116.500 # SOURCE3_SOURCE5 720 1.3034 - angle_coeff @angle:c3-c-ca harmonic 64.216 118.400 # SOURCE4_SOURCE5 749 1.4991 - angle_coeff @angle:c3-c-cc harmonic 64.984 117.290 # CORR_SOURCE5 118 1.7737 - angle_coeff @angle:c3-c-cd harmonic 64.984 117.290 # CORR_SOURCE5 118 1.7737 - angle_coeff @angle:c3-c-ce harmonic 64.919 116.440 # CORR_SOURCE5 543 1.3559 - angle_coeff @angle:c3-c-cf harmonic 64.919 116.440 # CORR_SOURCE5 543 1.3559 - angle_coeff @angle:c3-c-cg harmonic 65.958 115.000 # SOURCE2 1 - angle_coeff @angle:c3-c-ch harmonic 65.958 115.000 # SOURCE2 1 - angle_coeff @angle:c3-c-cl harmonic 71.237 111.990 # SOURCE3 2 0.0125 - angle_coeff @angle:c3-c-f harmonic 88.418 110.700 # SOURCE2 1 - angle_coeff @angle:c3-c-h4 harmonic 46.112 114.640 # SOURCE4_SOURCE5 193 0.4989 - angle_coeff @angle:c3-c-ha harmonic 46.047 115.220 # SOURCE3 15 0.3181 - angle_coeff @angle:c3-c-i harmonic 60.388 112.940 # SOURCE3 1 - angle_coeff @angle:c3-c-n2 harmonic 83.534 114.530 # SOURCE3 1 - angle_coeff @angle:c3-c-n4 harmonic 81.106 112.260 # SOURCE3 2 - angle_coeff @angle:c3-c-n harmonic 84.266 115.180 # SOURCE3_SOURCE5 2997 1.3885 - angle_coeff @angle:c3-c-ne harmonic 84.941 112.610 # CORR_SOURCE5 19 2.4426 - angle_coeff @angle:c3-c-nf harmonic 84.941 112.610 # CORR_SOURCE5 19 2.4426 - angle_coeff @angle:c3-c-o harmonic 84.552 123.200 # SOURCE3_SOURCE5 10083 1.8011 - angle_coeff @angle:c3-c-oh harmonic 85.803 112.730 # SOURCE3_SOURCE5 1989 1.3796 - angle_coeff @angle:c3-c-os harmonic 86.419 110.720 # SOURCE3_SOURCE5 1786 0.9391 - angle_coeff @angle:c3-c-p3 harmonic 77.773 116.420 # SOURCE3 3 0.1291 - angle_coeff @angle:c3-c-p5 harmonic 76.995 118.900 # SOURCE3 1 - angle_coeff @angle:c3-c-pe harmonic 77.418 114.850 # SOURCE3 1 - angle_coeff @angle:c3-c-pf harmonic 77.418 114.850 # SOURCE3 1 - angle_coeff @angle:c3-c-px harmonic 77.387 115.600 # SOURCE3 1 - angle_coeff @angle:c3-c-py harmonic 77.698 118.160 # SOURCE3 3 1.0735 - angle_coeff @angle:c3-c-s4 harmonic 61.352 114.790 # SOURCE3 1 - angle_coeff @angle:c3-c-s6 harmonic 61.371 114.720 # SOURCE3 1 - angle_coeff @angle:c3-c-s harmonic 63.941 123.150 # SOURCE3_SOURCE5 66 1.3121 - angle_coeff @angle:c3-c-sh harmonic 63.752 112.650 # SOURCE3_SOURCE5 9 1.5127 - angle_coeff @angle:c3-c-ss harmonic 63.438 113.510 # SOURCE3_SOURCE5 65 0.9334 - angle_coeff @angle:c3-c-sx harmonic 61.201 113.970 # SOURCE3 3 0.0610 - angle_coeff @angle:c3-c-sy harmonic 61.612 114.280 # SOURCE3 3 0.7341 - angle_coeff @angle:ca-c-ca harmonic 65.033 118.110 # SOURCE4_SOURCE5 506 1.8633 - angle_coeff @angle:ca-c-cc harmonic 66.124 116.000 # CORR_SOURCE5 670 1.7109 - angle_coeff @angle:ca-c-cd harmonic 66.124 116.000 # CORR_SOURCE5 670 1.7109 - angle_coeff @angle:ca-c-ce harmonic 64.959 119.020 # CORR_SOURCE5 83 1.3943 - angle_coeff @angle:ca-c-cf harmonic 64.959 119.020 # CORR_SOURCE5 83 1.3943 - angle_coeff @angle:ca-c-h4 harmonic 46.911 115.140 # SOURCE4_SOURCE5 122 0.7683 - angle_coeff @angle:ca-c-ha harmonic 47.184 114.120 # SOURCE3 1 - angle_coeff @angle:ca-c-n harmonic 85.392 115.250 # SOURCE4_SOURCE5 1494 1.4889 - angle_coeff @angle:ca-c-ne harmonic 85.290 114.710 # SOURCE4_SOURCE5 14 0.5855 - angle_coeff @angle:ca-c-o harmonic 86.207 122.600 # SOURCE3_SOURCE5 3960 1.5802 - angle_coeff @angle:ca-c-oh harmonic 86.748 113.450 # SOURCE4_SOURCE5 656 0.8414 - angle_coeff @angle:ca-c-os harmonic 86.963 112.440 # SOURCE3_SOURCE5 493 0.8365 - angle_coeff @angle:ca-c-s harmonic 64.593 122.680 # SOURCE4_SOURCE5 32 1.3788 - angle_coeff @angle:ca-c-sh harmonic 62.515 118.630 # SOURCE3 1 - angle_coeff @angle:ca-c-ss harmonic 63.406 115.050 # SOURCE4_SOURCE5 37 1.0695 - angle_coeff @angle:br-cc-c harmonic 65.156 116.280 # SOURCE4_SOURCE5 32 1.1116 - angle_coeff @angle:br-cc-cc harmonic 63.389 124.050 # SOURCE4_SOURCE5 31 1.9388 - angle_coeff @angle:br-cc-cd harmonic 63.686 124.230 # SOURCE4_SOURCE5 116 2.3356 - angle_coeff @angle:br-cc-na harmonic 80.565 121.580 # SOURCE4_SOURCE5 19 0.8500 - angle_coeff @angle:c2-cc-c3 harmonic 65.262 126.110 # SOURCE3 2 - angle_coeff @angle:c2-cc-ca harmonic 66.952 124.420 # CORR_SOURCE5 25 1.8245 - angle_coeff @angle:c2-cc-cc harmonic 68.308 122.190 # CORR_SOURCE5 46 2.3853 - angle_coeff @angle:c2-cc-cd harmonic 71.286 117.020 # SOURCE3 2 0.0703 - angle_coeff @angle:c2-cc-ha harmonic 49.231 122.720 # SOURCE3 2 0.0092 - angle_coeff @angle:c2-cc-n harmonic 86.150 124.910 # SOURCE3_SOURCE5 5 1.6803 - angle_coeff @angle:c2-cc-os harmonic 87.991 121.420 # CORR_SOURCE5 24 0.9570 - angle_coeff @angle:c-c-c3 harmonic 63.621 116.170 # SOURCE3_SOURCE5 58 1.1332 - angle_coeff @angle:c3-cc-ca harmonic 63.318 126.520 # CORR_SOURCE5 370 1.8946 - angle_coeff @angle:c3-cc-cc harmonic 66.709 115.970 # SOURCE3 4 3.0507 - angle_coeff @angle:c3-cc-cd harmonic 66.802 119.450 # SOURCE3 35 8.2040 - angle_coeff @angle:c3-cc-cf harmonic 67.395 117.840 # CORR 2 - angle_coeff @angle:c3-cc-ha harmonic 45.517 121.520 # SOURCE3 32 3.2091 - angle_coeff @angle:c3-cc-n2 harmonic 83.336 125.690 # CORR_SOURCE5 12 1.9935 - angle_coeff @angle:c3-cc-n harmonic 83.558 119.190 # CORR_SOURCE5 107 2.1078 - angle_coeff @angle:c3-cc-na harmonic 82.356 122.730 # CORR_SOURCE5 961 1.6482 - angle_coeff @angle:c3-cc-nc harmonic 83.215 120.950 # CORR_SOURCE5 456 0.8756 - angle_coeff @angle:c3-cc-nd harmonic 83.886 122.410 # CORR_SOURCE5 653 1.6992 - angle_coeff @angle:c3-cc-os harmonic 84.855 116.800 # CORR_SOURCE5 306 0.8990 - angle_coeff @angle:c3-cc-ss harmonic 62.656 121.530 # CORR_SOURCE5 270 1.0948 - angle_coeff @angle:c-c-c harmonic 64.391 111.680 # SOURCE3 2 6.1226 - angle_coeff @angle:c-c-ca harmonic 63.623 118.600 # SOURCE4_SOURCE5 90 1.0263 - angle_coeff @angle:ca-cc-cc harmonic 69.336 111.040 # SOURCE3 9 7.9455 - angle_coeff @angle:ca-cc-cd harmonic 69.802 113.510 # SOURCE3 26 7.4229 - angle_coeff @angle:ca-cc-ce harmonic 64.258 127.010 # SOURCE4_SOURCE5 38 1.6763 - angle_coeff @angle:ca-cc-h4 harmonic 45.368 129.250 # SOURCE3_SOURCE5 54 1.5632 - angle_coeff @angle:ca-cc-ha harmonic 46.300 124.040 # SOURCE3 34 3.6691 - angle_coeff @angle:ca-cc-n harmonic 85.642 117.670 # CORR 18 - angle_coeff @angle:ca-cc-nc harmonic 84.897 120.590 # CORR_SOURCE5 224 1.0853 - angle_coeff @angle:ca-cc-nd harmonic 85.294 123.240 # CORR_SOURCE5 246 2.3557 - angle_coeff @angle:ca-cc-nh harmonic 84.253 122.130 # SOURCE4_SOURCE5 20 1.7636 - angle_coeff @angle:ca-cc-oh harmonic 86.577 117.550 # CORR_SOURCE5 35 1.9318 - angle_coeff @angle:ca-cc-os harmonic 87.229 114.750 # CORR_SOURCE5 247 2.0579 - angle_coeff @angle:ca-cc-ss harmonic 63.408 120.800 # CORR_SOURCE5 80 2.1212 - angle_coeff @angle:c-cc-c2 harmonic 67.513 121.170 # CORR_SOURCE5 28 1.6484 - angle_coeff @angle:c-cc-c3 harmonic 65.378 117.760 # CORR_SOURCE5 566 1.9588 - angle_coeff @angle:c-cc-c harmonic 65.240 121.070 # CORR_SOURCE5 128 0.8902 - angle_coeff @angle:c-c-cc harmonic 66.020 111.670 # SOURCE3 4 5.5146 - angle_coeff @angle:c-cc-ca harmonic 65.005 122.950 # SOURCE3 1 - angle_coeff @angle:c-cc-cc harmonic 65.674 122.690 # SOURCE3 2 - angle_coeff @angle:cc-c-cc harmonic 66.696 115.840 # CORR_SOURCE5 115 1.4659 - angle_coeff @angle:cc-cc-cc harmonic 70.129 110.700 # SOURCE3 54 3.4091 - angle_coeff @angle:cc-cc-cd harmonic 70.348 114.190 # SOURCE3 517 6.5960 - angle_coeff @angle:cc-cc-ce harmonic 64.853 127.060 # CORR_SOURCE5 61 2.3233 - angle_coeff @angle:cc-cc-cf harmonic 68.022 122.720 # CORR_SOURCE5 66 1.9701 - angle_coeff @angle:cc-cc-cg harmonic 65.805 125.910 # CORR_SOURCE5 41 1.1646 - angle_coeff @angle:c-cc-cd harmonic 67.187 121.350 # CORR_SOURCE5 3554 2.2084 - angle_coeff @angle:cc-c-cd harmonic 67.592 112.790 # SOURCE3 1 - angle_coeff @angle:c-cc-ce harmonic 65.406 121.570 # CORR_SOURCE5 29 1.1305 - angle_coeff @angle:cc-c-ce harmonic 66.433 115.570 # SOURCE4_SOURCE5 14 1.2088 - angle_coeff @angle:cc-cc-f harmonic 88.377 119.190 # SOURCE4_SOURCE5 26 0.8983 - angle_coeff @angle:c-cc-cg harmonic 67.046 117.880 # SOURCE4_SOURCE5 26 0.6759 - angle_coeff @angle:cc-cc-h4 harmonic 46.348 127.960 # SOURCE3_SOURCE5 391 2.1732 - angle_coeff @angle:cc-cc-ha harmonic 47.634 121.070 # CORR_SOURCE5 2414 2.2010 - angle_coeff @angle:c-cc-cl harmonic 72.591 116.380 # CORR_SOURCE5 50 1.2099 - angle_coeff @angle:cc-cc-n2 harmonic 87.356 122.210 # CORR_SOURCE5 37 1.6493 - angle_coeff @angle:cc-cc-n harmonic 85.753 119.890 # SOURCE3 36 0.2095 - angle_coeff @angle:cc-cc-na harmonic 86.536 117.770 # SOURCE3_SOURCE5 865 1.5665 - angle_coeff @angle:cc-cc-nc harmonic 85.332 121.980 # CORR_SOURCE5 141 1.9633 - angle_coeff @angle:cc-cc-nd harmonic 90.306 112.560 # SOURCE3 141 4.2871 - angle_coeff @angle:cc-cc-nh harmonic 86.018 119.720 # CORR_SOURCE5 348 1.7785 - angle_coeff @angle:cc-cc-oh harmonic 86.201 121.270 # CORR_SOURCE5 11 2.2744 - angle_coeff @angle:cc-cc-os harmonic 87.213 117.340 # CORR_SOURCE5 217 1.9304 - angle_coeff @angle:cc-cc-pd harmonic 84.517 115.360 # SOURCE3 84 - angle_coeff @angle:cc-cc-ss harmonic 63.877 120.210 # CORR_SOURCE5 52 2.1160 - angle_coeff @angle:cc-cc-sy harmonic 61.106 128.250 # SOURCE4_SOURCE5 20 0.9014 - angle_coeff @angle:c-c-cd harmonic 66.020 111.670 # SOURCE3 4 5.5146 - angle_coeff @angle:cd-cc-cd harmonic 70.027 120.080 # CORR_SOURCE5 119 1.6139 - angle_coeff @angle:cd-cc-ce harmonic 65.759 128.050 # CORR_SOURCE5 350 2.4628 - angle_coeff @angle:cd-cc-cl harmonic 71.687 123.410 # CORR_SOURCE5 115 2.1217 - angle_coeff @angle:cd-cc-f harmonic 89.570 121.190 # SOURCE4_SOURCE5 82 0.7206 - angle_coeff @angle:cd-cc-h4 harmonic 47.759 128.480 # SOURCE3_SOURCE5 3291 2.3189 - angle_coeff @angle:cd-cc-ha harmonic 49.040 121.760 # SOURCE3_SOURCE5 4433 1.8701 - angle_coeff @angle:cd-cc-n harmonic 86.990 121.330 # SOURCE3_SOURCE5 821 1.9126 - angle_coeff @angle:cd-cc-na harmonic 92.653 106.990 # SOURCE3_SOURCE5 3003 2.3845 - angle_coeff @angle:cd-cc-nc harmonic 91.057 111.650 # CORR_SOURCE5 1656 1.8430 - angle_coeff @angle:cd-cc-nh harmonic 86.331 123.840 # CORR_SOURCE5 152 2.2360 - angle_coeff @angle:cd-cc-no harmonic 82.947 128.690 # SOURCE4_SOURCE5 314 1.4409 - angle_coeff @angle:cd-cc-oh harmonic 87.177 123.780 # CORR_SOURCE5 251 1.1988 - angle_coeff @angle:cd-cc-os harmonic 87.957 120.300 # SOURCE3 64 5.4354 - angle_coeff @angle:cd-cc-ss harmonic 66.887 111.550 # CORR_SOURCE5 1048 1.8648 - angle_coeff @angle:cd-cc-sy harmonic 62.501 124.550 # CORR_SOURCE5 56 1.7107 - angle_coeff @angle:ce-cc-na harmonic 83.371 124.350 # CORR_SOURCE5 87 1.3591 - angle_coeff @angle:ce-cc-nc harmonic 84.769 121.100 # CORR_SOURCE5 43 1.2959 - angle_coeff @angle:ce-cc-nd harmonic 85.887 121.700 # CORR_SOURCE5 58 1.4179 - angle_coeff @angle:ce-cc-os harmonic 85.796 118.760 # CORR_SOURCE5 92 1.3159 - angle_coeff @angle:ce-cc-ss harmonic 63.222 121.580 # CORR_SOURCE5 54 1.3126 - angle_coeff @angle:c-cc-f harmonic 87.759 116.980 # SOURCE4_SOURCE5 49 0.4690 - angle_coeff @angle:cg-cc-na harmonic 84.878 122.610 # SOURCE4_SOURCE5 12 0.9695 - angle_coeff @angle:cg-cc-ss harmonic 63.762 120.730 # SOURCE4_SOURCE5 27 0.9221 - angle_coeff @angle:cc-c-h4 harmonic 47.598 114.830 # SOURCE4_SOURCE5 25 0.5124 - angle_coeff @angle:c-cc-ha harmonic 47.405 116.640 # SOURCE3_SOURCE5 896 1.3075 - angle_coeff @angle:cl-cc-na harmonic 90.511 121.120 # SOURCE4_SOURCE5 37 0.7206 - angle_coeff @angle:cl-cc-nd harmonic 90.963 122.070 # CORR_SOURCE5 19 1.6973 - angle_coeff @angle:cl-cc-ss harmonic 71.934 119.850 # SOURCE4_SOURCE5 27 0.9529 - angle_coeff @angle:c-cc-n2 harmonic 85.228 123.930 # CORR_SOURCE5 6 0.0993 - angle_coeff @angle:c-cc-n harmonic 85.713 116.370 # CORR_SOURCE5 41 2.4875 - angle_coeff @angle:cc-c-n harmonic 87.145 112.700 # SOURCE3_SOURCE5 1124 1.8431 - angle_coeff @angle:c-cc-nc harmonic 83.549 123.320 # CORR_SOURCE5 27 2.2025 - angle_coeff @angle:cc-c-nd harmonic 85.602 116.240 # CORR_SOURCE5 38 1.0053 - angle_coeff @angle:c-cc-nd harmonic 85.323 121.880 # CORR_SOURCE5 54 2.0672 - angle_coeff @angle:c-cc-ne harmonic 84.503 119.880 # SOURCE4 6 0.3139 - angle_coeff @angle:cc-c-o harmonic 86.736 123.930 # SOURCE3_SOURCE5 3463 2.3073 - angle_coeff @angle:c-cc-oh harmonic 87.608 113.660 # CORR_SOURCE5 190 1.6462 - angle_coeff @angle:cc-c-oh harmonic 87.815 112.840 # CORR_SOURCE5 184 0.7264 - angle_coeff @angle:c-cc-os harmonic 85.149 119.260 # CORR_SOURCE5 104 2.4145 - angle_coeff @angle:cc-c-os harmonic 87.108 114.200 # SOURCE3_SOURCE5 427 2.2749 - angle_coeff @angle:cc-c-s harmonic 64.011 126.280 # SOURCE4_SOURCE5 69 1.9867 - angle_coeff @angle:cc-c-ss harmonic 64.406 112.400 # SOURCE4_SOURCE5 42 0.9902 - angle_coeff @angle:cx-cc-nd harmonic 83.147 127.820 # SOURCE4_SOURCE5 27 1.6288 - angle_coeff @angle:cx-cc-os harmonic 85.414 118.070 # SOURCE4_SOURCE5 23 0.0923 - angle_coeff @angle:cd-c-cd harmonic 66.696 115.840 # CORR_SOURCE5 115 1.4659 - angle_coeff @angle:cd-c-cx harmonic 65.553 117.430 # SOURCE4_SOURCE5 37 0.1506 - angle_coeff @angle:cd-c-n harmonic 87.145 112.700 # SOURCE3_SOURCE5 1124 1.8431 - angle_coeff @angle:cd-c-nc harmonic 85.602 116.240 # CORR_SOURCE5 38 1.0053 - angle_coeff @angle:cd-c-nd harmonic 86.534 113.750 # SOURCE4_SOURCE5 28 0.0860 - angle_coeff @angle:cd-c-o harmonic 86.736 123.930 # SOURCE3_SOURCE5 3463 2.3073 - angle_coeff @angle:cd-c-oh harmonic 87.815 112.840 # CORR_SOURCE5 184 0.7264 - angle_coeff @angle:cd-c-os harmonic 87.108 114.200 # SOURCE3_SOURCE5 427 2.2749 - angle_coeff @angle:ce-c-ce harmonic 66.032 115.820 # CORR_SOURCE5 103 0.7143 - angle_coeff @angle:ce-c-cf harmonic 65.875 116.370 # SOURCE4_SOURCE5 31 1.3157 - angle_coeff @angle:ce-c-cx harmonic 65.246 117.390 # SOURCE4_SOURCE5 19 0.7227 - angle_coeff @angle:ce-c-h4 harmonic 47.181 114.890 # SOURCE4_SOURCE5 113 0.4718 - angle_coeff @angle:ce-c-ha harmonic 47.181 115.220 # SOURCE3 7 2.4188 - angle_coeff @angle:ce-c-n harmonic 85.680 115.220 # CORR_SOURCE5 38 1.1173 - angle_coeff @angle:ce-c-o harmonic 86.348 123.200 # SOURCE3_SOURCE5 2306 2.0617 - angle_coeff @angle:ce-c-oh harmonic 86.976 113.620 # CORR_SOURCE5 273 1.4501 - angle_coeff @angle:ce-c-os harmonic 87.846 110.930 # CORR_SOURCE5 445 1.6899 - angle_coeff @angle:ce-c-s harmonic 64.731 122.630 # SOURCE3_SOURCE5 11 1.3034 - angle_coeff @angle:ce-c-ss harmonic 64.794 110.490 # SOURCE4_SOURCE5 13 0.5852 - angle_coeff @angle:cf-c-cf harmonic 66.032 115.820 # CORR_SOURCE5 103 0.7143 - angle_coeff @angle:cf-c-ha harmonic 47.181 115.220 # SOURCE3 7 - angle_coeff @angle:cf-c-n harmonic 85.680 115.220 # CORR_SOURCE5 38 1.1173 - angle_coeff @angle:cf-c-o harmonic 86.348 123.200 # SOURCE3_SOURCE5 2306 2.0617 - angle_coeff @angle:cf-c-oh harmonic 86.976 113.620 # CORR_SOURCE5 273 1.4501 - angle_coeff @angle:cf-c-os harmonic 87.846 110.930 # CORR_SOURCE5 445 1.6899 - angle_coeff @angle:cf-c-s harmonic 64.731 122.630 # SOURCE3_SOURCE5 11 1.3034 - angle_coeff @angle:cg-c-cg harmonic 67.584 115.380 # SOURCE3 1 - angle_coeff @angle:cg-c-ha harmonic 48.322 113.900 # SOURCE2 1 - angle_coeff @angle:cg-c-o harmonic 88.213 121.780 # SOURCE3_SOURCE5 13 0.8393 - angle_coeff @angle:c-c-h4 harmonic 45.243 115.800 # SOURCE4_SOURCE5 17 0.7492 - angle_coeff @angle:h4-cc-n harmonic 62.742 115.690 # SOURCE3_SOURCE5 425 0.9142 - angle_coeff @angle:h4-cc-na harmonic 61.487 120.530 # SOURCE3_SOURCE5 1801 1.3882 - angle_coeff @angle:h4-cc-nc harmonic 61.716 121.140 # SOURCE3_SOURCE5 574 0.5658 - angle_coeff @angle:h4-cc-nd harmonic 64.296 118.470 # SOURCE3_SOURCE5 435 1.3360 - angle_coeff @angle:h4-cc-os harmonic 63.640 114.900 # SOURCE3_SOURCE5 456 0.8638 - angle_coeff @angle:h4-cc-ss harmonic 42.456 119.970 # SOURCE3_SOURCE5 496 0.7119 - angle_coeff @angle:h5-cc-n harmonic 62.737 115.700 # CORR_SOURCE5 41 0.7665 - angle_coeff @angle:h5-cc-na harmonic 61.226 121.550 # SOURCE3_SOURCE5 1138 0.7136 - angle_coeff @angle:h5-cc-nc harmonic 61.265 122.920 # SOURCE3_SOURCE5 136 0.3532 - angle_coeff @angle:h5-cc-nd harmonic 62.461 125.520 # SOURCE3_SOURCE5 1309 0.7276 - angle_coeff @angle:h5-cc-os harmonic 63.110 116.830 # SOURCE3_SOURCE5 42 1.3051 - angle_coeff @angle:h5-cc-ss harmonic 42.272 121.020 # SOURCE3_SOURCE5 46 0.6462 - angle_coeff @angle:c-c-ha harmonic 45.358 115.430 # SOURCE2 3 0.6549 - angle_coeff @angle:ha-cc-na harmonic 61.218 121.500 # SOURCE2 1 - angle_coeff @angle:ha-cc-nc harmonic 62.898 116.540 # SOURCE3 5 1.4482 - angle_coeff @angle:ha-cc-nd harmonic 64.154 118.880 # SOURCE3 20 2.8923 - angle_coeff @angle:ha-cc-os harmonic 64.764 110.860 # SOURCE3 7 1.3846 - angle_coeff @angle:ha-cc-pd harmonic 54.856 121.760 # SOURCE3 84 - angle_coeff @angle:ha-cc-ss harmonic 42.168 121.640 # SOURCE2 5 1.3276 - angle_coeff @angle:ch-c-ch harmonic 67.584 115.380 # SOURCE3 1 - angle_coeff @angle:ch-c-ha harmonic 48.322 113.900 # SOURCE2 1 - angle_coeff @angle:ch-c-o harmonic 88.213 121.780 # SOURCE3_SOURCE5 13 0.8393 - angle_coeff @angle:cl-c-cl harmonic 80.720 111.300 # SOURCE2 1 - angle_coeff @angle:cl-c-f harmonic 93.155 112.000 # SOURCE2 1 - angle_coeff @angle:cl-c-ha harmonic 48.221 109.900 # SOURCE2 1 - angle_coeff @angle:cl-c-o harmonic 89.044 120.690 # SOURCE3_SOURCE5 14 1.1076 - angle_coeff @angle:cl-c-s harmonic 69.852 127.600 # SOURCE2 1 - angle_coeff @angle:c-c-n harmonic 84.329 112.740 # SOURCE4_SOURCE5 157 2.1770 - angle_coeff @angle:na-cc-nc harmonic 108.812 121.950 # CORR_SOURCE5 321 1.6221 - angle_coeff @angle:na-cc-nd harmonic 115.504 112.220 # SOURCE3_SOURCE5 2726 1.5103 - angle_coeff @angle:na-cc-no harmonic 105.313 124.590 # SOURCE4_SOURCE5 162 0.8093 - angle_coeff @angle:na-cc-oh harmonic 111.744 117.480 # SOURCE4_SOURCE5 39 0.9806 - angle_coeff @angle:na-cc-sx harmonic 79.683 117.020 # SOURCE4_SOURCE5 32 0.3937 - angle_coeff @angle:na-cc-sy harmonic 79.507 120.460 # SOURCE4_SOURCE5 15 1.7292 - angle_coeff @angle:nc-cc-nd harmonic 114.185 115.830 # CORR_SOURCE5 309 1.2424 - angle_coeff @angle:nc-cc-nh harmonic 111.255 117.230 # CORR_SOURCE5 51 1.7463 - angle_coeff @angle:nc-cc-no harmonic 106.922 121.730 # SOURCE4_SOURCE5 17 0.8729 - angle_coeff @angle:nc-cc-ss harmonic 79.922 122.640 # SOURCE3_SOURCE5 10 1.3100 - angle_coeff @angle:nd-cc-nd harmonic 110.827 128.070 # SOURCE4_SOURCE5 17 0.2580 - angle_coeff @angle:nd-cc-ne harmonic 107.796 129.010 # SOURCE4_SOURCE5 20 1.2478 - angle_coeff @angle:nd-cc-nh harmonic 111.697 120.650 # SOURCE3_SOURCE5 554 1.6769 - angle_coeff @angle:nd-cc-no harmonic 108.240 122.750 # SOURCE4_SOURCE5 80 0.3006 - angle_coeff @angle:nd-cc-oh harmonic 112.660 121.120 # CORR_SOURCE5 31 1.3923 - angle_coeff @angle:nd-cc-os harmonic 114.076 116.740 # CORR_SOURCE5 156 2.0183 - angle_coeff @angle:nd-cc-sh harmonic 79.198 124.970 # SOURCE4_SOURCE5 18 0.8493 - angle_coeff @angle:nd-cc-ss harmonic 83.264 114.510 # SOURCE3 8 0.3449 - angle_coeff @angle:nd-cc-sx harmonic 76.768 127.740 # SOURCE4_SOURCE5 33 0.6804 - angle_coeff @angle:nd-cc-sy harmonic 79.255 123.030 # SOURCE4_SOURCE5 33 1.1587 - angle_coeff @angle:ne-cc-ss harmonic 81.707 117.030 # SOURCE4_SOURCE5 17 0.2106 - angle_coeff @angle:nh-cc-nh harmonic 111.696 115.960 # SOURCE3 1 - angle_coeff @angle:nh-cc-os harmonic 111.815 116.680 # CORR_SOURCE5 36 0.7439 - angle_coeff @angle:nh-cc-ss harmonic 80.147 121.810 # CORR_SOURCE5 128 1.0728 - angle_coeff @angle:n-cc-n2 harmonic 112.932 119.420 # SOURCE4_SOURCE5 28 1.2985 - angle_coeff @angle:n-cc-na harmonic 108.295 122.120 # CORR_SOURCE5 15 1.1276 - angle_coeff @angle:n-cc-nc harmonic 106.932 126.230 # CORR_SOURCE5 118 0.4381 - angle_coeff @angle:n-cc-nd harmonic 110.304 123.000 # CORR_SOURCE5 354 1.4352 - angle_coeff @angle:n-cc-nh harmonic 110.935 116.940 # CORR_SOURCE5 126 0.5956 - angle_coeff @angle:no-cc-os harmonic 109.068 117.550 # SOURCE4_SOURCE5 144 0.2521 - angle_coeff @angle:no-cc-ss harmonic 79.693 121.060 # SOURCE4_SOURCE5 33 0.2051 - angle_coeff @angle:n-cc-ss harmonic 79.713 122.880 # CORR_SOURCE5 82 1.5666 - angle_coeff @angle:c-c-o harmonic 84.325 120.850 # SOURCE4_SOURCE5 712 2.3365 - angle_coeff @angle:c-c-oh harmonic 85.170 112.070 # SOURCE3_SOURCE5 45 0.4339 - angle_coeff @angle:c-c-os harmonic 85.272 111.410 # SOURCE4_SOURCE5 34 0.4577 - angle_coeff @angle:os-cc-ss harmonic 81.124 119.280 # SOURCE3_SOURCE5 10 1.6753 - angle_coeff @angle:ss-cc-ss harmonic 63.639 121.370 # CORR 22 - angle_coeff @angle:ss-cc-sy harmonic 63.048 121.700 # CORR_SOURCE5 43 0.4842 - angle_coeff @angle:cx-c-cx harmonic 87.506 64.600 # SOURCE2 1 - angle_coeff @angle:cx-c-n harmonic 85.409 114.530 # SOURCE4_SOURCE5 60 1.3306 - angle_coeff @angle:cx-c-o harmonic 85.839 122.750 # SOURCE4_SOURCE5 366 2.2300 - angle_coeff @angle:cx-c-oh harmonic 86.840 112.520 # SOURCE4_SOURCE5 43 1.3576 - angle_coeff @angle:cx-c-os harmonic 87.109 111.390 # SOURCE4_SOURCE5 64 2.0118 - angle_coeff @angle:cy-c-cy harmonic 70.855 91.910 # SOURCE2_SOURCE5 12 0.9858 - angle_coeff @angle:cy-c-n harmonic 93.471 91.560 # SOURCE4_SOURCE5 619 0.5374 - angle_coeff @angle:cy-c-o harmonic 79.625 135.160 # SOURCE4_SOURCE5 665 1.3860 - angle_coeff @angle:cy-c-oh harmonic 85.029 112.180 # SOURCE4_SOURCE5 17 0.7869 - angle_coeff @angle:cy-c-os harmonic 92.339 94.790 # SOURCE4_SOURCE5 25 0.5353 - angle_coeff @angle:c2-cd-c3 harmonic 65.262 126.110 # SOURCE3 2 - angle_coeff @angle:c2-cd-ca harmonic 66.952 124.420 # CORR_SOURCE5 25 1.8245 - angle_coeff @angle:c2-cd-cc harmonic 71.286 117.020 # SOURCE3 2 - angle_coeff @angle:c2-cd-cd harmonic 68.308 122.190 # CORR_SOURCE5 46 2.3853 - angle_coeff @angle:c2-cd-ha harmonic 49.231 122.720 # SOURCE3 2 - angle_coeff @angle:c2-cd-n harmonic 86.150 124.910 # SOURCE3_SOURCE5 5 1.6803 - angle_coeff @angle:c2-cd-os harmonic 87.991 121.420 # CORR_SOURCE5 24 0.9570 - angle_coeff @angle:c3-cd-ca harmonic 63.318 126.520 # CORR_SOURCE5 370 1.8946 - angle_coeff @angle:c3-cd-cc harmonic 66.802 119.450 # SOURCE3 35 8.2040 - angle_coeff @angle:c3-cd-cd harmonic 66.709 115.970 # SOURCE3 4 3.0507 - angle_coeff @angle:c3-cd-ce harmonic 67.395 117.840 # CORR 2 - angle_coeff @angle:c3-cd-ha harmonic 45.517 121.520 # SOURCE3 32 3.2091 - angle_coeff @angle:c3-cd-n2 harmonic 83.336 125.690 # CORR_SOURCE5 12 1.9935 - angle_coeff @angle:c3-cd-n harmonic 83.558 119.190 # CORR_SOURCE5 107 2.1078 - angle_coeff @angle:c3-cd-na harmonic 82.356 122.730 # CORR_SOURCE5 961 1.6482 - angle_coeff @angle:c3-cd-nc harmonic 83.886 122.410 # CORR_SOURCE5 653 1.6992 - angle_coeff @angle:c3-cd-nd harmonic 83.215 120.950 # CORR_SOURCE5 456 0.8756 - angle_coeff @angle:c3-cd-os harmonic 84.855 116.800 # CORR_SOURCE5 306 0.8990 - angle_coeff @angle:c3-cd-ss harmonic 62.656 121.530 # CORR_SOURCE5 270 1.0948 - angle_coeff @angle:ca-cd-cc harmonic 69.802 113.510 # SOURCE3 26 7.4229 - angle_coeff @angle:ca-cd-cd harmonic 69.336 111.040 # SOURCE3 9 7.9455 - angle_coeff @angle:ca-cd-ce harmonic 66.694 124.900 # SOURCE4_SOURCE5 41 1.7178 - angle_coeff @angle:ca-cd-h4 harmonic 45.368 129.250 # SOURCE3_SOURCE5 54 1.5632 - angle_coeff @angle:ca-cd-ha harmonic 46.300 124.040 # SOURCE3 34 3.6691 - angle_coeff @angle:ca-cd-n harmonic 85.642 117.670 # CORR 18 - angle_coeff @angle:ca-cd-na harmonic 83.626 123.450 # SOURCE4 39 1.9138 - angle_coeff @angle:ca-cd-nc harmonic 85.294 123.240 # CORR_SOURCE5 246 2.3557 - angle_coeff @angle:ca-cd-nd harmonic 84.897 120.590 # CORR_SOURCE5 224 1.0853 - angle_coeff @angle:ca-cd-oh harmonic 86.577 117.550 # CORR_SOURCE5 35 1.9318 - angle_coeff @angle:ca-cd-os harmonic 87.229 114.750 # CORR_SOURCE5 247 2.0579 - angle_coeff @angle:ca-cd-ss harmonic 63.408 120.800 # CORR_SOURCE5 80 2.1212 - angle_coeff @angle:c-cd-c2 harmonic 67.513 121.170 # CORR_SOURCE5 28 1.6484 - angle_coeff @angle:c-cd-c3 harmonic 65.378 117.760 # CORR_SOURCE5 566 1.9588 - angle_coeff @angle:c-cd-c harmonic 65.240 121.070 # CORR_SOURCE5 128 0.8902 - angle_coeff @angle:c-cd-ca harmonic 65.005 122.950 # SOURCE3 1 - angle_coeff @angle:c-cd-cc harmonic 67.187 121.350 # CORR_SOURCE5 3554 2.2084 - angle_coeff @angle:cc-cd-cc harmonic 70.027 120.080 # CORR_SOURCE5 119 1.6139 - angle_coeff @angle:cc-cd-cd harmonic 70.348 114.190 # SOURCE3 517 6.5960 - angle_coeff @angle:cc-cd-cf harmonic 65.759 128.050 # CORR_SOURCE5 350 2.4628 - angle_coeff @angle:cc-cd-ch harmonic 67.080 125.790 # SOURCE4_SOURCE5 84 1.6445 - angle_coeff @angle:cc-cd-cl harmonic 71.687 123.410 # CORR_SOURCE5 115 2.1217 - angle_coeff @angle:cc-cd-cy harmonic 65.987 122.050 # SOURCE4_SOURCE5 22 0.8483 - angle_coeff @angle:c-cd-cd harmonic 65.674 122.690 # SOURCE3 2 - angle_coeff @angle:c-cd-cf harmonic 65.406 121.570 # CORR_SOURCE5 29 1.1305 - angle_coeff @angle:cc-cd-h4 harmonic 47.759 128.480 # SOURCE3_SOURCE5 3291 2.3189 - angle_coeff @angle:cc-cd-ha harmonic 49.040 121.760 # SOURCE3_SOURCE5 4433 1.8701 - angle_coeff @angle:c-cd-cl harmonic 72.591 116.380 # CORR_SOURCE5 50 1.2099 - angle_coeff @angle:cc-cd-n harmonic 86.990 121.330 # SOURCE3_SOURCE5 821 1.9126 - angle_coeff @angle:cc-cd-na harmonic 92.653 106.990 # SOURCE3_SOURCE5 3003 2.3845 - angle_coeff @angle:cc-cd-nc harmonic 88.069 123.820 # SOURCE4_SOURCE5 28 0.3678 - angle_coeff @angle:cc-cd-nd harmonic 91.057 111.650 # CORR_SOURCE5 1656 1.8430 - angle_coeff @angle:cc-cd-nh harmonic 86.331 123.840 # CORR_SOURCE5 152 2.2360 - angle_coeff @angle:cc-cd-oh harmonic 87.177 123.780 # CORR_SOURCE5 251 1.1988 - angle_coeff @angle:cc-cd-os harmonic 87.957 120.300 # SOURCE3 64 5.4354 - angle_coeff @angle:cc-cd-ss harmonic 66.887 111.550 # CORR_SOURCE5 1048 1.8648 - angle_coeff @angle:cc-cd-sy harmonic 62.501 124.550 # CORR_SOURCE5 56 1.7107 - angle_coeff @angle:cd-cd-cd harmonic 70.129 110.700 # SOURCE3 54 3.4091 - angle_coeff @angle:cd-cd-ce harmonic 68.022 122.720 # CORR_SOURCE5 66 1.9701 - angle_coeff @angle:cd-cd-cf harmonic 64.853 127.060 # CORR_SOURCE5 61 2.3233 - angle_coeff @angle:cd-cd-ch harmonic 65.805 125.910 # CORR_SOURCE5 41 1.1646 - angle_coeff @angle:cd-cd-cy harmonic 64.938 122.040 # SOURCE4_SOURCE5 13 0.6868 - angle_coeff @angle:cd-cd-h4 harmonic 46.348 127.960 # SOURCE3_SOURCE5 391 2.1732 - angle_coeff @angle:cd-cd-ha harmonic 47.634 121.070 # CORR_SOURCE5 2414 2.2010 - angle_coeff @angle:cd-cd-n2 harmonic 87.356 122.210 # CORR_SOURCE5 37 1.6493 - angle_coeff @angle:cd-cd-n harmonic 85.753 119.890 # SOURCE3 36 0.2095 - angle_coeff @angle:cd-cd-na harmonic 86.536 117.770 # SOURCE3_SOURCE5 832 1.6037 - angle_coeff @angle:cd-cd-nc harmonic 90.306 112.560 # SOURCE3 141 4.2871 - angle_coeff @angle:cd-cd-nd harmonic 85.332 121.980 # CORR_SOURCE5 141 1.9633 - angle_coeff @angle:cd-cd-nh harmonic 86.018 119.720 # CORR_SOURCE5 348 1.7785 - angle_coeff @angle:cd-cd-oh harmonic 86.201 121.270 # CORR_SOURCE5 11 2.2744 - angle_coeff @angle:cd-cd-os harmonic 87.213 117.340 # CORR_SOURCE5 217 1.9304 - angle_coeff @angle:cd-cd-pc harmonic 84.517 115.360 # SOURCE3 84 3.2889 - angle_coeff @angle:cd-cd-ss harmonic 63.877 120.210 # CORR_SOURCE5 52 2.1160 - angle_coeff @angle:ce-cd-nd harmonic 86.641 123.980 # SOURCE4_SOURCE5 10 2.4097 - angle_coeff @angle:cf-cd-na harmonic 83.371 124.350 # CORR_SOURCE5 87 1.3591 - angle_coeff @angle:cf-cd-nc harmonic 85.887 121.700 # CORR_SOURCE5 58 1.4179 - angle_coeff @angle:cf-cd-nd harmonic 84.769 121.100 # CORR_SOURCE5 43 1.2959 - angle_coeff @angle:cf-cd-os harmonic 85.796 118.760 # CORR_SOURCE5 92 1.3159 - angle_coeff @angle:cf-cd-ss harmonic 63.222 121.580 # CORR_SOURCE5 54 1.3126 - angle_coeff @angle:c-cd-h4 harmonic 47.105 118.190 # SOURCE4_SOURCE5 16 0.2226 - angle_coeff @angle:c-cd-ha harmonic 47.405 116.640 # SOURCE3_SOURCE5 896 1.3075 - angle_coeff @angle:cl-cd-nc harmonic 90.963 122.070 # CORR_SOURCE5 19 1.6973 - angle_coeff @angle:c-cd-n2 harmonic 85.228 123.930 # CORR_SOURCE5 6 0.0993 - angle_coeff @angle:c-cd-n harmonic 85.713 116.370 # CORR_SOURCE5 41 2.4875 - angle_coeff @angle:c-cd-nc harmonic 85.323 121.880 # CORR_SOURCE5 54 2.0672 - angle_coeff @angle:c-cd-nd harmonic 83.549 123.320 # CORR_SOURCE5 27 2.2025 - angle_coeff @angle:c-cd-oh harmonic 87.608 113.660 # CORR_SOURCE5 190 1.6462 - angle_coeff @angle:c-cd-os harmonic 85.149 119.260 # CORR_SOURCE5 104 2.4145 - angle_coeff @angle:h4-cd-n harmonic 62.742 115.690 # SOURCE3_SOURCE5 425 0.9142 - angle_coeff @angle:h4-cd-na harmonic 61.487 120.530 # SOURCE3_SOURCE5 1801 1.3882 - angle_coeff @angle:h4-cd-nc harmonic 64.296 118.470 # SOURCE3_SOURCE5 435 1.3360 - angle_coeff @angle:h4-cd-nd harmonic 61.716 121.140 # SOURCE3_SOURCE5 574 0.5658 - angle_coeff @angle:h4-cd-os harmonic 63.640 114.900 # SOURCE3_SOURCE5 456 0.8638 - angle_coeff @angle:h4-cd-ss harmonic 42.456 119.970 # SOURCE3_SOURCE5 496 0.7119 - angle_coeff @angle:h5-cd-n harmonic 62.738 115.700 # CORR_SOURCE5 41 0.7665 - angle_coeff @angle:h5-cd-na harmonic 61.227 121.550 # SOURCE3_SOURCE5 1138 0.7136 - angle_coeff @angle:h5-cd-nc harmonic 62.462 125.520 # SOURCE3_SOURCE5 1309 0.7276 - angle_coeff @angle:h5-cd-nd harmonic 61.266 122.920 # SOURCE3_SOURCE5 136 0.3532 - angle_coeff @angle:h5-cd-os harmonic 63.111 116.830 # SOURCE3_SOURCE5 42 1.3051 - angle_coeff @angle:h5-cd-ss harmonic 42.271 121.020 # SOURCE3_SOURCE5 46 0.6462 - angle_coeff @angle:ha-cd-na harmonic 61.218 121.500 # SOURCE2 1 - angle_coeff @angle:ha-cd-nc harmonic 64.154 118.880 # SOURCE3 20 2.8923 - angle_coeff @angle:ha-cd-nd harmonic 62.898 116.540 # SOURCE3 5 1.4482 - angle_coeff @angle:ha-cd-os harmonic 64.764 110.860 # SOURCE3 7 1.3846 - angle_coeff @angle:ha-cd-pc harmonic 54.856 121.760 # SOURCE3 84 2.2216 - angle_coeff @angle:ha-cd-ss harmonic 42.168 121.640 # SOURCE2 5 - angle_coeff @angle:na-cd-nc harmonic 115.504 112.220 # SOURCE3_SOURCE5 2726 1.5103 - angle_coeff @angle:na-cd-nd harmonic 108.812 121.950 # CORR_SOURCE5 321 1.6221 - angle_coeff @angle:na-cd-nh harmonic 110.794 117.280 # SOURCE4_SOURCE5 100 1.6359 - angle_coeff @angle:na-cd-ss harmonic 83.703 111.460 # SOURCE4 20 0.8600 - angle_coeff @angle:nc-cd-nd harmonic 114.185 115.830 # CORR_SOURCE5 309 1.2424 - angle_coeff @angle:nc-cd-nh harmonic 111.697 120.650 # SOURCE3_SOURCE5 554 1.6769 - angle_coeff @angle:nc-cd-oh harmonic 112.660 121.120 # CORR_SOURCE5 31 1.3923 - angle_coeff @angle:nc-cd-os harmonic 114.076 116.740 # CORR_SOURCE5 156 2.0183 - angle_coeff @angle:nc-cd-ss harmonic 83.264 114.510 # SOURCE3 8 0.3449 - angle_coeff @angle:nd-cd-nd harmonic 107.603 125.700 # SOURCE4_SOURCE5 31 0.5900 - angle_coeff @angle:nd-cd-nh harmonic 111.255 117.230 # CORR_SOURCE5 51 1.7463 - angle_coeff @angle:nd-cd-ss harmonic 79.922 122.640 # SOURCE3_SOURCE5 10 1.3100 - angle_coeff @angle:nh-cd-nh harmonic 111.696 115.960 # SOURCE3 1 - angle_coeff @angle:nh-cd-os harmonic 111.815 116.680 # CORR_SOURCE5 36 0.7439 - angle_coeff @angle:nh-cd-ss harmonic 80.147 121.810 # CORR_SOURCE5 128 1.0728 - angle_coeff @angle:n-cd-na harmonic 108.295 122.120 # CORR_SOURCE5 15 1.1276 - angle_coeff @angle:n-cd-nc harmonic 110.304 123.000 # CORR_SOURCE5 354 1.4352 - angle_coeff @angle:n-cd-nd harmonic 106.932 126.230 # CORR_SOURCE5 118 0.4381 - angle_coeff @angle:n-cd-nh harmonic 110.935 116.940 # CORR_SOURCE5 126 0.5956 - angle_coeff @angle:n-cd-ss harmonic 79.713 122.880 # CORR_SOURCE5 82 1.5666 - angle_coeff @angle:oh-cd-os harmonic 115.442 111.610 # SOURCE4_SOURCE5 12 1.1909 - angle_coeff @angle:os-cd-ss harmonic 81.124 119.280 # SOURCE3_SOURCE5 10 1.6753 - angle_coeff @angle:ss-cd-ss harmonic 63.639 121.370 # CORR 22 - angle_coeff @angle:ss-cd-sy harmonic 63.048 121.700 # CORR_SOURCE5 43 0.4842 - angle_coeff @angle:c2-ce-c3 harmonic 66.042 122.530 # SOURCE3_SOURCE5 882 1.9288 - angle_coeff @angle:c2-ce-ca harmonic 67.362 121.780 # SOURCE3_SOURCE5 11 1.7099 - angle_coeff @angle:c2-ce-cc harmonic 67.560 123.320 # CORR_SOURCE5 132 1.9068 - angle_coeff @angle:c2-ce-ce harmonic 67.482 123.260 # SOURCE3_SOURCE5 791 1.8772 - angle_coeff @angle:c2-ce-cg harmonic 68.647 122.090 # CORR_SOURCE5 54 1.3612 - angle_coeff @angle:c2-ce-cl harmonic 72.080 119.760 # SOURCE4_SOURCE5 62 1.3986 - angle_coeff @angle:c2-ce-h4 harmonic 49.154 124.550 # SOURCE4_SOURCE5 43 1.6498 - angle_coeff @angle:c2-ce-ha harmonic 50.126 119.940 # SOURCE3_SOURCE5 1439 1.4338 - angle_coeff @angle:c2-ce-n1 harmonic 91.289 118.230 # SOURCE4_SOURCE5 18 0.9047 - angle_coeff @angle:c2-ce-n2 harmonic 88.228 128.700 # SOURCE3 1 - angle_coeff @angle:c2-ce-na harmonic 87.216 119.190 # SOURCE4_SOURCE5 10 0.8452 - angle_coeff @angle:c2-ce-ne harmonic 88.464 118.320 # SOURCE3 7 1.0468 - angle_coeff @angle:c2-ce-oh harmonic 87.984 123.700 # SOURCE4_SOURCE5 27 1.7525 - angle_coeff @angle:c2-ce-p2 harmonic 81.422 118.240 # SOURCE3 1 - angle_coeff @angle:c2-ce-pe harmonic 81.089 118.760 # SOURCE3 8 2.3984 - angle_coeff @angle:c2-ce-px harmonic 80.647 119.720 # SOURCE3 6 0.5213 - angle_coeff @angle:c2-ce-py harmonic 80.419 122.180 # SOURCE3_SOURCE5 12 1.9482 - angle_coeff @angle:c2-ce-sx harmonic 63.052 119.210 # SOURCE3_SOURCE5 14 0.9863 - angle_coeff @angle:c2-ce-sy harmonic 63.705 120.200 # SOURCE3_SOURCE5 17 1.3599 - angle_coeff @angle:c3-ce-ca harmonic 64.464 119.240 # CORR_SOURCE5 312 1.7689 - angle_coeff @angle:c3-ce-cc harmonic 65.246 118.030 # CORR_SOURCE5 77 1.5840 - angle_coeff @angle:c3-ce-ce harmonic 65.430 117.120 # CORR_SOURCE5 524 1.4790 - angle_coeff @angle:c3-ce-cf harmonic 65.999 122.380 # CORR_SOURCE5 490 2.0752 - angle_coeff @angle:c3-ce-cg harmonic 66.008 117.220 # SOURCE4_SOURCE5 34 1.7153 - angle_coeff @angle:c3-ce-n2 harmonic 83.839 122.730 # CORR_SOURCE5 149 1.8752 - angle_coeff @angle:c3-ce-nf harmonic 84.370 120.680 # SOURCE4_SOURCE5 13 2.1196 - angle_coeff @angle:c3-ce-nh harmonic 82.726 119.560 # SOURCE4_SOURCE5 10 1.0079 - angle_coeff @angle:ca-ce-ca harmonic 65.741 117.830 # CORR_SOURCE5 210 0.9675 - angle_coeff @angle:ca-ce-cc harmonic 66.149 118.130 # CORR_SOURCE5 30 0.7112 - angle_coeff @angle:ca-ce-ce harmonic 65.684 119.540 # SOURCE4_SOURCE5 32 1.9209 - angle_coeff @angle:ca-ce-cf harmonic 65.738 127.520 # CORR_SOURCE5 599 1.6916 - angle_coeff @angle:ca-ce-cl harmonic 72.181 114.590 # SOURCE4_SOURCE5 14 1.1195 - angle_coeff @angle:ca-ce-h4 harmonic 47.047 116.990 # SOURCE4_SOURCE5 255 1.0051 - angle_coeff @angle:ca-ce-ha harmonic 47.444 115.130 # CORR_SOURCE5 720 0.9389 - angle_coeff @angle:ca-ce-n2 harmonic 86.084 120.720 # SOURCE3 1 - angle_coeff @angle:ca-ce-nf harmonic 85.534 121.710 # CORR_SOURCE5 49 2.1313 - angle_coeff @angle:ca-ce-nh harmonic 85.466 115.580 # SOURCE4_SOURCE5 240 1.0372 - angle_coeff @angle:ca-ce-oh harmonic 86.291 116.100 # CORR_SOURCE5 15 0.6417 - angle_coeff @angle:ca-ce-os harmonic 85.838 115.910 # SOURCE4_SOURCE5 25 1.4247 - angle_coeff @angle:ca-ce-ss harmonic 63.378 117.520 # SOURCE4_SOURCE5 14 1.2435 - angle_coeff @angle:c-ce-c2 harmonic 67.566 120.420 # SOURCE3 13 1.8877 - angle_coeff @angle:c-ce-c3 harmonic 64.889 117.220 # CORR_SOURCE5 558 2.2754 - angle_coeff @angle:c-ce-c harmonic 64.277 122.230 # CORR_SOURCE5 52 2.1518 - angle_coeff @angle:c-ce-ca harmonic 65.478 118.280 # SOURCE4_SOURCE5 25 1.6999 - angle_coeff @angle:cc-ce-cd harmonic 65.259 130.610 # SOURCE4_SOURCE5 24 1.1422 - angle_coeff @angle:cc-ce-cf harmonic 66.704 126.140 # CORR_SOURCE5 122 1.8142 - angle_coeff @angle:c-ce-cd harmonic 67.092 120.770 # CORR_SOURCE5 15 1.8896 - angle_coeff @angle:c-ce-ce harmonic 65.150 120.980 # SOURCE4_SOURCE5 53 2.2319 - angle_coeff @angle:c-ce-cf harmonic 65.856 126.410 # SOURCE3 2 5.7847 - angle_coeff @angle:c-ce-cg harmonic 66.500 118.420 # SOURCE4_SOURCE5 49 1.0600 - angle_coeff @angle:cc-ce-h4 harmonic 47.935 115.680 # SOURCE4_SOURCE5 77 0.8454 - angle_coeff @angle:cc-ce-ha harmonic 48.006 115.440 # CORR_SOURCE5 179 0.9381 - angle_coeff @angle:c-ce-cl harmonic 71.821 115.470 # SOURCE4_SOURCE5 25 1.2041 - angle_coeff @angle:cc-ce-n2 harmonic 86.868 120.960 # CORR_SOURCE5 102 2.2421 - angle_coeff @angle:cc-ce-nh harmonic 85.299 118.050 # SOURCE4_SOURCE5 21 1.8052 - angle_coeff @angle:c-ce-cy harmonic 74.704 88.440 # SOURCE4_SOURCE5 53 0.9126 - angle_coeff @angle:cd-ce-ce harmonic 66.791 124.350 # CORR_SOURCE5 18 1.4583 - angle_coeff @angle:cd-ce-ha harmonic 50.638 114.950 # CORR_SOURCE5 95 1.4175 - angle_coeff @angle:ce-ce-ce harmonic 65.416 122.110 # SOURCE3_SOURCE5 9 2.4680 - angle_coeff @angle:ce-ce-cf harmonic 67.119 124.240 # CORR_SOURCE5 866 1.6941 - angle_coeff @angle:ce-ce-cl harmonic 71.617 117.220 # SOURCE4_SOURCE5 35 0.8344 - angle_coeff @angle:ce-ce-h4 harmonic 47.341 118.130 # CORR_SOURCE5 44 1.1161 - angle_coeff @angle:ce-ce-ha harmonic 47.662 116.650 # SOURCE3_SOURCE5 1159 0.9686 - angle_coeff @angle:ce-ce-n1 harmonic 84.049 127.150 # CORR 4 - angle_coeff @angle:ce-ce-n2 harmonic 87.472 118.930 # CORR_SOURCE5 13 1.3210 - angle_coeff @angle:ce-ce-oh harmonic 86.685 116.850 # SOURCE4_SOURCE5 30 1.7182 - angle_coeff @angle:cf-ce-cg harmonic 68.252 123.130 # CORR_SOURCE5 115 2.1292 - angle_coeff @angle:cf-ce-cy harmonic 62.247 137.580 # SOURCE4_SOURCE5 31 0.9919 - angle_coeff @angle:cf-ce-h4 harmonic 49.339 122.950 # SOURCE4_SOURCE5 23 1.1580 - angle_coeff @angle:cf-ce-ha harmonic 50.352 118.220 # CORR_SOURCE5 1522 1.3445 - angle_coeff @angle:cf-ce-n1 harmonic 90.464 119.940 # SOURCE4_SOURCE5 13 1.8896 - angle_coeff @angle:cf-ce-n harmonic 91.197 108.390 # CORR_SOURCE5 86 1.0066 - angle_coeff @angle:cf-ce-nh harmonic 87.337 121.380 # SOURCE4_SOURCE5 39 1.7667 - angle_coeff @angle:cf-ce-oh harmonic 88.551 121.690 # CORR_SOURCE5 37 1.2824 - angle_coeff @angle:cg-ce-cg harmonic 68.393 116.520 # CORR_SOURCE5 35 1.1031 - angle_coeff @angle:cg-ce-ha harmonic 48.557 116.460 # CORR_SOURCE5 58 0.6523 - angle_coeff @angle:cg-ce-n1 harmonic 87.835 119.500 # CORR 2 - angle_coeff @angle:cg-ce-n2 harmonic 87.851 121.140 # SOURCE4_SOURCE5 14 0.8974 - angle_coeff @angle:c-ce-ha harmonic 47.000 116.460 # SOURCE3_SOURCE5 1028 1.3091 - angle_coeff @angle:c-ce-n harmonic 83.338 118.450 # CORR_SOURCE5 213 1.4857 - angle_coeff @angle:c-ce-nh harmonic 85.341 115.360 # CORR_SOURCE5 28 2.1980 - angle_coeff @angle:c-ce-oh harmonic 86.196 115.760 # SOURCE4_SOURCE5 20 2.0254 - angle_coeff @angle:c-ce-os harmonic 86.086 114.670 # SOURCE4_SOURCE5 47 2.1291 - angle_coeff @angle:h4-ce-n1 harmonic 64.863 116.640 # SOURCE4_SOURCE5 19 0.4343 - angle_coeff @angle:h4-ce-n2 harmonic 64.393 121.480 # CORR_SOURCE5 257 1.1842 - angle_coeff @angle:h4-ce-ne harmonic 62.153 115.650 # SOURCE4_SOURCE5 19 1.8165 - angle_coeff @angle:ha-ce-n1 harmonic 65.106 115.960 # CORR 4 - angle_coeff @angle:ha-ce-n2 harmonic 64.979 119.510 # SOURCE3 2 0.4623 - angle_coeff @angle:ha-ce-ne harmonic 61.414 118.590 # SOURCE3 5 1.1113 - angle_coeff @angle:ha-ce-nh harmonic 62.516 114.990 # CORR 2 - angle_coeff @angle:ha-ce-p2 harmonic 52.606 120.110 # SOURCE3 1 - angle_coeff @angle:ha-ce-pe harmonic 52.651 119.330 # SOURCE3 6 0.8966 - angle_coeff @angle:ha-ce-px harmonic 52.873 117.900 # SOURCE3 6 0.1809 - angle_coeff @angle:ha-ce-py harmonic 53.346 117.990 # SOURCE3_SOURCE5 11 0.7169 - angle_coeff @angle:ha-ce-sx harmonic 41.698 115.450 # SOURCE3 3 0.6640 - angle_coeff @angle:ha-ce-sy harmonic 42.578 114.860 # SOURCE3 3 0.4717 - angle_coeff @angle:n2-ce-nh harmonic 110.010 125.090 # CORR_SOURCE5 163 1.6803 - angle_coeff @angle:n2-ce-os harmonic 114.215 117.950 # SOURCE4_SOURCE5 19 0.3524 - angle_coeff @angle:n2-ce-ss harmonic 81.512 117.230 # SOURCE4 6 2.0518 - angle_coeff @angle:ne-ce-ne harmonic 106.467 123.870 # SOURCE3 1 - angle_coeff @angle:ne-ce-nh harmonic 111.319 113.640 # SOURCE4_SOURCE5 41 1.4024 - angle_coeff @angle:nf-ce-nh harmonic 112.342 119.270 # SOURCE4_SOURCE5 23 1.5487 - angle_coeff @angle:pe-ce-pe harmonic 97.908 129.790 # SOURCE3 1 - angle_coeff @angle:py-ce-py harmonic 108.039 108.060 # SOURCE3 1 - angle_coeff @angle:sx-ce-sx harmonic 61.727 120.320 # SOURCE3 1 - angle_coeff @angle:sy-ce-sy harmonic 62.867 119.970 # SOURCE3 1 - angle_coeff @angle:c2-cf-c3 harmonic 66.048 122.530 # SOURCE3_SOURCE5 875 1.9359 - angle_coeff @angle:c2-cf-ca harmonic 67.362 121.780 # SOURCE3_SOURCE5 5 1.1712 - angle_coeff @angle:c2-cf-cd harmonic 67.560 123.320 # CORR_SOURCE5 132 1.9068 - angle_coeff @angle:c2-cf-cf harmonic 67.482 123.260 # SOURCE3_SOURCE5 779 1.8961 - angle_coeff @angle:c2-cf-ch harmonic 68.647 122.090 # CORR_SOURCE5 54 1.3612 - angle_coeff @angle:c2-cf-ha harmonic 50.126 119.940 # SOURCE3_SOURCE5 1393 1.4017 - angle_coeff @angle:c2-cf-n2 harmonic 88.228 128.700 # SOURCE3 1 - angle_coeff @angle:c2-cf-nf harmonic 88.464 118.320 # SOURCE3 7 - angle_coeff @angle:c2-cf-p2 harmonic 81.422 118.240 # SOURCE3 1 - angle_coeff @angle:c2-cf-pf harmonic 81.089 118.760 # SOURCE3 8 - angle_coeff @angle:c2-cf-px harmonic 80.647 119.720 # SOURCE3 6 - angle_coeff @angle:c2-cf-py harmonic 80.419 122.180 # SOURCE3_SOURCE5 7 1.0992 - angle_coeff @angle:c2-cf-sx harmonic 63.052 119.210 # SOURCE3_SOURCE5 9 1.0588 - angle_coeff @angle:c2-cf-sy harmonic 63.705 120.200 # SOURCE3_SOURCE5 12 1.7015 - angle_coeff @angle:c3-cf-ca harmonic 64.468 119.240 # CORR_SOURCE5 312 1.7689 - angle_coeff @angle:c3-cf-cd harmonic 65.251 118.030 # CORR_SOURCE5 77 1.5840 - angle_coeff @angle:c3-cf-ce harmonic 66.005 122.380 # CORR_SOURCE5 490 2.0752 - angle_coeff @angle:c3-cf-cf harmonic 65.435 117.120 # CORR_SOURCE5 524 1.4790 - angle_coeff @angle:c3-cf-n2 harmonic 83.846 122.730 # CORR_SOURCE5 149 1.8752 - angle_coeff @angle:ca-cf-ca harmonic 65.741 117.830 # CORR_SOURCE5 210 0.9675 - angle_coeff @angle:ca-cf-cc harmonic 64.611 130.880 # SOURCE4_SOURCE5 41 1.2386 - angle_coeff @angle:ca-cf-cd harmonic 66.149 118.130 # CORR_SOURCE5 30 0.7112 - angle_coeff @angle:ca-cf-ce harmonic 65.738 127.520 # CORR_SOURCE5 599 1.6916 - angle_coeff @angle:ca-cf-ha harmonic 47.444 115.130 # CORR_SOURCE5 720 0.9389 - angle_coeff @angle:ca-cf-n2 harmonic 86.084 120.720 # SOURCE3 1 - angle_coeff @angle:ca-cf-ne harmonic 85.534 121.710 # CORR_SOURCE5 49 2.1313 - angle_coeff @angle:ca-cf-oh harmonic 86.291 116.100 # CORR_SOURCE5 15 0.6417 - angle_coeff @angle:c-cf-c2 harmonic 67.566 120.420 # SOURCE3 13 - angle_coeff @angle:c-cf-c3 harmonic 64.893 117.220 # CORR_SOURCE5 558 2.2754 - angle_coeff @angle:c-cf-c harmonic 64.277 122.230 # CORR_SOURCE5 52 2.1518 - angle_coeff @angle:c-cf-cc harmonic 67.092 120.770 # CORR_SOURCE5 15 1.8896 - angle_coeff @angle:cc-cf-cf harmonic 66.791 124.350 # CORR_SOURCE5 18 1.4583 - angle_coeff @angle:c-cf-cd harmonic 66.092 117.820 # SOURCE4_SOURCE5 29 1.0204 - angle_coeff @angle:c-cf-ce harmonic 65.856 126.410 # SOURCE3 2 - angle_coeff @angle:cc-cf-ha harmonic 50.638 114.950 # CORR_SOURCE5 95 1.4175 - angle_coeff @angle:cd-cf-ce harmonic 66.704 126.140 # CORR_SOURCE5 122 1.8142 - angle_coeff @angle:cd-cf-ha harmonic 48.006 115.440 # CORR_SOURCE5 179 0.9381 - angle_coeff @angle:cd-cf-n2 harmonic 86.868 120.960 # CORR_SOURCE5 102 2.2421 - angle_coeff @angle:ce-cf-cf harmonic 67.119 124.240 # CORR_SOURCE5 866 1.6941 - angle_coeff @angle:ce-cf-ch harmonic 68.252 123.130 # CORR_SOURCE5 115 2.1292 - angle_coeff @angle:ce-cf-ha harmonic 50.352 118.220 # CORR_SOURCE5 1522 1.3445 - angle_coeff @angle:ce-cf-n harmonic 91.197 108.390 # CORR_SOURCE5 86 1.0066 - angle_coeff @angle:ce-cf-oh harmonic 88.551 121.690 # CORR_SOURCE5 37 1.2824 - angle_coeff @angle:cf-cf-cf harmonic 65.416 122.110 # SOURCE3_SOURCE5 9 2.4680 - angle_coeff @angle:cf-cf-h4 harmonic 47.341 118.130 # CORR_SOURCE5 44 1.1161 - angle_coeff @angle:cf-cf-ha harmonic 47.662 116.650 # SOURCE3_SOURCE5 1159 0.9686 - angle_coeff @angle:cf-cf-n1 harmonic 84.049 127.150 # CORR 4 - angle_coeff @angle:cf-cf-n2 harmonic 87.472 118.930 # CORR_SOURCE5 13 1.3210 - angle_coeff @angle:c-cf-ha harmonic 47.000 116.460 # SOURCE3_SOURCE5 1028 1.3091 - angle_coeff @angle:ch-cf-ch harmonic 68.393 116.520 # CORR_SOURCE5 35 1.1031 - angle_coeff @angle:ch-cf-ha harmonic 48.557 116.460 # CORR_SOURCE5 58 0.6523 - angle_coeff @angle:ch-cf-n1 harmonic 87.835 119.500 # CORR 2 - angle_coeff @angle:c-cf-n2 harmonic 88.177 114.410 # SOURCE4_SOURCE5 13 1.4243 - angle_coeff @angle:c-cf-n harmonic 83.338 118.450 # CORR_SOURCE5 213 1.4857 - angle_coeff @angle:c-cf-nh harmonic 85.341 115.360 # CORR_SOURCE5 28 2.1980 - angle_coeff @angle:f-c-f harmonic 123.826 107.350 # SOURCE2 2 0.2500 - angle_coeff @angle:h4-cf-n2 harmonic 64.393 121.480 # CORR_SOURCE5 257 1.1842 - angle_coeff @angle:h4-cf-ne harmonic 64.320 120.560 # SOURCE4_SOURCE5 39 0.8435 - angle_coeff @angle:ha-cf-n1 harmonic 65.106 115.960 # CORR 4 - angle_coeff @angle:ha-cf-n2 harmonic 64.979 119.510 # SOURCE3 2 - angle_coeff @angle:ha-cf-nf harmonic 61.414 118.590 # SOURCE3 5 - angle_coeff @angle:ha-cf-nh harmonic 62.516 114.990 # CORR 2 - angle_coeff @angle:ha-cf-p2 harmonic 52.606 120.110 # SOURCE3 1 - angle_coeff @angle:ha-cf-pf harmonic 52.651 119.330 # SOURCE3 6 - angle_coeff @angle:ha-cf-px harmonic 52.873 117.900 # SOURCE3 6 - angle_coeff @angle:ha-cf-py harmonic 53.346 117.990 # SOURCE3_SOURCE5 8 0.8708 - angle_coeff @angle:ha-cf-sx harmonic 41.698 115.450 # SOURCE3 3 - angle_coeff @angle:ha-cf-sy harmonic 42.578 114.860 # SOURCE3 3 - angle_coeff @angle:n2-cf-nh harmonic 110.010 125.090 # CORR_SOURCE5 163 1.6803 - angle_coeff @angle:nf-cf-nf harmonic 106.467 123.870 # SOURCE3 1 - angle_coeff @angle:f-c-o harmonic 118.196 123.440 # SOURCE3 1 - angle_coeff @angle:pf-cf-pf harmonic 97.908 129.790 # SOURCE3 1 - angle_coeff @angle:py-cf-py harmonic 108.039 108.060 # SOURCE3 1 - angle_coeff @angle:f-c-s harmonic 84.396 124.000 # SOURCE2 1 - angle_coeff @angle:sx-cf-sx harmonic 61.727 120.320 # SOURCE3 1 - angle_coeff @angle:sy-cf-sy harmonic 62.867 119.970 # SOURCE3 1 - angle_coeff @angle:c1-cg-ca harmonic 58.572 179.570 # CORR_SOURCE5 38 0.4711 - angle_coeff @angle:c1-cg-cc harmonic 58.934 178.610 # SOURCE4_SOURCE5 13 0.3677 - angle_coeff @angle:c1-cg-ce harmonic 58.989 178.050 # CORR_SOURCE5 15 0.1905 - angle_coeff @angle:c1-cg-cg harmonic 60.378 179.670 # CORR_SOURCE5 90 0.1487 - angle_coeff @angle:c1-cg-ne harmonic 79.305 170.020 # SOURCE3 4 1.1724 - angle_coeff @angle:c1-cg-pe harmonic 75.149 173.290 # SOURCE3 11 4.9305 - angle_coeff @angle:ca-cg-ch harmonic 58.741 179.430 # CORR_SOURCE5 40 0.6103 - angle_coeff @angle:ca-cg-n1 harmonic 74.346 179.490 # CORR_SOURCE5 186 0.6659 - angle_coeff @angle:c-cg-c1 harmonic 58.113 179.140 # SOURCE3 2 - angle_coeff @angle:cc-cg-n1 harmonic 74.809 178.620 # CORR_SOURCE5 43 0.6454 - angle_coeff @angle:ce-cg-ch harmonic 59.157 177.940 # CORR 17 - angle_coeff @angle:ce-cg-n1 harmonic 74.894 177.970 # CORR_SOURCE5 184 1.2220 - angle_coeff @angle:n1-cg-ne harmonic 99.946 174.030 # CORR_SOURCE5 30 0.6173 - angle_coeff @angle:h4-c-o harmonic 66.570 120.700 # SOURCE4_SOURCE5 491 0.4811 - angle_coeff @angle:h5-c-n harmonic 63.496 112.160 # SOURCE4_SOURCE5 98 0.3632 - angle_coeff @angle:h5-c-o harmonic 65.930 123.650 # SOURCE4_SOURCE5 150 0.7654 - angle_coeff @angle:ha-c-ha harmonic 37.443 115.610 # SOURCE3 4 0.0458 - angle_coeff @angle:ha-c-i harmonic 38.168 110.580 # SOURCE3 1 - angle_coeff @angle:ha-c-n harmonic 63.490 112.370 # SOURCE3 4 0.6424 - angle_coeff @angle:ha-c-o harmonic 66.484 121.940 # SOURCE3 51 2.3235 - angle_coeff @angle:ha-c-oh harmonic 64.638 111.820 # SOURCE3 4 1.9375 - angle_coeff @angle:ha-c-os harmonic 64.813 110.340 # SOURCE3 8 1.9344 - angle_coeff @angle:ha-c-s harmonic 44.760 119.560 # SOURCE3 3 0.7586 - angle_coeff @angle:c1-ch-ca harmonic 58.522 179.570 # CORR_SOURCE5 38 0.4711 - angle_coeff @angle:c1-ch-cf harmonic 58.938 178.050 # CORR_SOURCE5 15 0.1905 - angle_coeff @angle:c1-ch-ch harmonic 60.316 179.670 # CORR_SOURCE5 90 0.1487 - angle_coeff @angle:c1-ch-nf harmonic 79.216 170.020 # SOURCE3 4 - angle_coeff @angle:c1-ch-pf harmonic 75.117 173.290 # SOURCE3 11 - angle_coeff @angle:ca-ch-cg harmonic 58.741 179.430 # CORR_SOURCE5 40 0.6103 - angle_coeff @angle:ca-ch-n1 harmonic 74.346 179.490 # CORR_SOURCE5 186 0.6659 - angle_coeff @angle:c-ch-c1 harmonic 58.066 179.140 # SOURCE3 2 - angle_coeff @angle:cd-ch-n1 harmonic 74.807 178.630 # CORR_SOURCE5 49 0.3708 - angle_coeff @angle:cf-ch-cg harmonic 59.157 177.940 # CORR 17 - angle_coeff @angle:cf-ch-n1 harmonic 74.894 177.970 # CORR_SOURCE5 184 1.2220 - angle_coeff @angle:cg-ch-ch harmonic 60.571 179.580 # SOURCE4_SOURCE5 55 0.2973 - angle_coeff @angle:n1-ch-nf harmonic 99.946 174.030 # CORR_SOURCE5 30 0.6173 - angle_coeff @angle:i-c-i harmonic 65.372 116.450 # SOURCE3 1 - angle_coeff @angle:i-c-o harmonic 71.718 122.020 # SOURCE3 4 1.2961 - angle_coeff @angle:f-cl-f harmonic 0.000 87.500 # SOURCE2 1 - angle_coeff @angle:n2-c-n2 harmonic 110.771 110.310 # SOURCE3 1 - angle_coeff @angle:n2-c-o harmonic 111.836 122.500 # SOURCE3 1 - angle_coeff @angle:n4-c-n4 harmonic 99.803 114.640 # SOURCE3 1 - angle_coeff @angle:n4-c-o harmonic 106.610 118.830 # SOURCE3 4 3.8516 - angle_coeff @angle:nc-c-o harmonic 113.330 123.180 # CORR_SOURCE5 172 1.0508 - angle_coeff @angle:nd-c-o harmonic 113.330 123.180 # CORR_SOURCE5 172 1.0508 - angle_coeff @angle:ne-c-ne harmonic 113.088 110.310 # CORR 2 - angle_coeff @angle:ne-c-o harmonic 111.914 125.810 # CORR_SOURCE5 65 1.1135 - angle_coeff @angle:nf-c-nf harmonic 113.088 110.310 # CORR 2 - angle_coeff @angle:nf-c-o harmonic 111.914 125.810 # CORR_SOURCE5 65 1.1135 - angle_coeff @angle:n-c-n harmonic 112.428 113.560 # SOURCE4_SOURCE5 1747 1.4619 - angle_coeff @angle:n-c-nc harmonic 110.397 117.110 # CORR_SOURCE5 131 0.7717 - angle_coeff @angle:n-c-nd harmonic 110.397 117.110 # CORR_SOURCE5 131 0.7717 - angle_coeff @angle:n-c-ne harmonic 113.600 110.260 # SOURCE4_SOURCE5 25 1.7043 - angle_coeff @angle:n-c-o harmonic 113.811 123.050 # SOURCE3_SOURCE5 8454 1.5552 - angle_coeff @angle:n-c-oh harmonic 113.913 112.820 # SOURCE4_SOURCE5 14 1.4518 - angle_coeff @angle:no-c-no harmonic 102.620 109.280 # SOURCE3 1 - angle_coeff @angle:no-c-o harmonic 104.115 125.360 # SOURCE3 1 - angle_coeff @angle:n-c-os harmonic 115.486 109.220 # SOURCE4_SOURCE5 821 0.9352 - angle_coeff @angle:n-c-s harmonic 82.398 124.050 # SOURCE3_SOURCE5 514 1.4099 - angle_coeff @angle:n-c-sh harmonic 81.620 112.970 # SOURCE4_SOURCE5 26 1.1725 - angle_coeff @angle:n-c-ss harmonic 82.496 110.290 # SOURCE4_SOURCE5 160 1.6051 - angle_coeff @angle:oh-c-oh harmonic 116.271 110.560 # SOURCE3 2 0.5498 - angle_coeff @angle:oh-c-s harmonic 83.019 123.440 # SOURCE3 1 - angle_coeff @angle:o-c-o harmonic 118.817 130.250 # SOURCE4_SOURCE5 1037 1.2396 - angle_coeff @angle:o-c-oh harmonic 115.745 122.100 # SOURCE3_SOURCE5 2859 0.8497 - angle_coeff @angle:o-c-os harmonic 114.822 123.250 # SOURCE4_SOURCE5 5492 1.1411 - angle_coeff @angle:o-c-p2 harmonic 96.161 123.100 # SOURCE3 1 - angle_coeff @angle:o-c-p3 harmonic 97.971 120.790 # SOURCE3 1 - angle_coeff @angle:o-c-p5 harmonic 97.881 121.170 # SOURCE4_SOURCE5 18 1.1433 - angle_coeff @angle:o-c-pe harmonic 95.623 123.020 # SOURCE3 3 0.1404 - angle_coeff @angle:o-c-pf harmonic 95.623 123.020 # SOURCE3 3 - angle_coeff @angle:o-c-px harmonic 97.552 119.100 # SOURCE3 1 - angle_coeff @angle:o-c-py harmonic 98.325 122.010 # SOURCE4_SOURCE5 14 1.0132 - angle_coeff @angle:o-c-s4 harmonic 76.764 121.150 # SOURCE3 1 - angle_coeff @angle:o-c-s6 harmonic 77.308 119.450 # SOURCE3 1 - angle_coeff @angle:o-c-s harmonic 85.589 120.440 # SOURCE3 2 - angle_coeff @angle:o-c-sh harmonic 79.543 122.050 # SOURCE3_SOURCE5 10 1.1120 - angle_coeff @angle:os-c-os harmonic 115.283 111.290 # SOURCE4_SOURCE5 32 0.8183 - angle_coeff @angle:o-c-ss harmonic 79.009 123.320 # SOURCE3_SOURCE5 190 1.2053 - angle_coeff @angle:os-c-s harmonic 82.392 125.010 # SOURCE4_SOURCE5 62 1.0980 - angle_coeff @angle:os-c-ss harmonic 82.286 111.400 # SOURCE4_SOURCE5 23 1.7283 - angle_coeff @angle:o-c-sx harmonic 76.145 121.150 # SOURCE3 5 3.6452 - angle_coeff @angle:o-c-sy harmonic 77.559 119.320 # SOURCE3 5 2.4495 - angle_coeff @angle:p2-c-p2 harmonic 100.070 113.750 # SOURCE3 1 - angle_coeff @angle:p3-c-p3 harmonic 99.122 118.040 # SOURCE3 1 - angle_coeff @angle:p3-c-py harmonic 113.947 90.080 # SOURCE3 1 - angle_coeff @angle:p5-c-p5 harmonic 96.866 123.760 # SOURCE3 1 - angle_coeff @angle:ca-cp-ca harmonic 68.877 118.380 # CORR_SOURCE5 959 0.6763 - angle_coeff @angle:ca-cp-cp harmonic 66.121 121.110 # CORR_SOURCE5 1631 1.6425 - angle_coeff @angle:ca-cp-na harmonic 86.507 119.500 # SOURCE4_SOURCE5 59 0.7877 - angle_coeff @angle:ca-cp-nb harmonic 87.071 121.620 # SOURCE4_SOURCE5 174 0.6998 - angle_coeff @angle:cp-cp-cp harmonic 74.761 90.000 # SOURCE3 4 - angle_coeff @angle:cp-cp-cq harmonic 64.283 124.270 # CORR_SOURCE5 8 2.0477 - angle_coeff @angle:cp-cp-nb harmonic 86.053 116.610 # SOURCE4_SOURCE5 235 1.1595 - angle_coeff @angle:pe-c-pe harmonic 99.485 113.770 # SOURCE3 1 - angle_coeff @angle:pf-c-pf harmonic 99.485 113.770 # SOURCE3 1 - angle_coeff @angle:nb-cp-nb harmonic 110.031 125.790 # SOURCE4_SOURCE5 11 0.6658 - angle_coeff @angle:py-c-py harmonic 97.618 123.800 # SOURCE3 1 - angle_coeff @angle:ca-cq-ca harmonic 68.877 118.380 # CORR_SOURCE5 959 0.6763 - angle_coeff @angle:ca-cq-cq harmonic 66.121 121.110 # CORR_SOURCE5 1631 1.6425 - angle_coeff @angle:ca-cq-nb harmonic 87.071 121.620 # SOURCE4_SOURCE5 111 0.7244 - angle_coeff @angle:cp-cq-cq harmonic 64.278 124.290 # CORR_SOURCE5 8 1.4947 - angle_coeff @angle:cq-cq-cq harmonic 74.761 90.000 # SOURCE3 4 - angle_coeff @angle:cq-cq-nb harmonic 86.053 116.610 # SOURCE4_SOURCE5 147 1.1420 - angle_coeff @angle:s4-c-s4 harmonic 63.122 108.810 # SOURCE3 1 - angle_coeff @angle:s6-c-s6 harmonic 61.200 115.750 # SOURCE3 1 - angle_coeff @angle:sh-c-sh harmonic 63.799 115.330 # SOURCE3 1 - angle_coeff @angle:s-c-s harmonic 65.463 126.500 # SOURCE3_SOURCE5 14 1.3489 - angle_coeff @angle:s-c-sh harmonic 63.925 122.650 # SOURCE4_SOURCE5 37 1.5614 - angle_coeff @angle:s-c-ss harmonic 63.724 123.190 # SOURCE3_SOURCE5 85 1.7112 - angle_coeff @angle:ss-c-ss harmonic 64.515 112.420 # SOURCE3_SOURCE5 17 0.4533 - angle_coeff @angle:sx-c-sx harmonic 62.622 108.800 # SOURCE3 1 - angle_coeff @angle:sy-c-sy harmonic 61.356 115.780 # SOURCE3 1 - angle_coeff @angle:c2-cu-cx harmonic 61.131 148.500 # SOURCE4_SOURCE5 23 1.5654 - angle_coeff @angle:c-cu-cu harmonic 98.040 62.600 # SOURCE2 1 - angle_coeff @angle:cu-cu-cx harmonic 105.362 50.800 # SOURCE2 1 - angle_coeff @angle:cu-cu-ha harmonic 46.590 147.730 # SOURCE2 3 2.0950 - angle_coeff @angle:cv-cv-cy harmonic 75.476 94.410 # SOURCE3_SOURCE5 6 0.2122 - angle_coeff @angle:cv-cv-ha harmonic 47.789 133.700 # SOURCE3 2 - angle_coeff @angle:cx-cv-cx harmonic 87.395 63.900 # SOURCE2 1 - angle_coeff @angle:cy-cv-ha harmonic 43.281 132.140 # SOURCE3 2 - angle_coeff @angle:c1-cx-cx harmonic 65.298 119.570 # SOURCE4_SOURCE5 51 1.0503 - angle_coeff @angle:c2-cx-cx harmonic 64.271 120.300 # SOURCE4_SOURCE5 207 2.3490 - angle_coeff @angle:c2-cx-h1 harmonic 47.059 115.860 # SOURCE4_SOURCE5 34 0.6256 - angle_coeff @angle:c2-cx-hc harmonic 47.215 115.150 # SOURCE4_SOURCE5 45 0.9609 - angle_coeff @angle:c2-cx-os harmonic 83.614 116.550 # SOURCE4_SOURCE5 48 1.1122 - angle_coeff @angle:c3-cx-c3 harmonic 64.915 114.240 # SOURCE4_SOURCE5 207 2.2113 - angle_coeff @angle:c3-cx-cx harmonic 63.608 120.100 # SOURCE4_SOURCE5 1739 2.3197 - angle_coeff @angle:c3-cx-h1 harmonic 46.234 115.320 # SOURCE4_SOURCE5 326 1.1035 - angle_coeff @angle:c3-cx-hc harmonic 46.430 114.390 # SOURCE4_SOURCE5 291 1.4379 - angle_coeff @angle:c3-cx-n3 harmonic 81.063 118.500 # SOURCE4 17 2.4897 - angle_coeff @angle:c3-cx-os harmonic 82.886 115.680 # SOURCE4_SOURCE5 616 1.2862 - angle_coeff @angle:ca-cx-cx harmonic 63.720 121.950 # SOURCE4_SOURCE5 197 1.8192 - angle_coeff @angle:ca-cx-h1 harmonic 47.143 114.700 # SOURCE4_SOURCE5 19 0.6393 - angle_coeff @angle:ca-cx-hc harmonic 47.377 113.620 # SOURCE4_SOURCE5 57 0.9227 - angle_coeff @angle:ca-cx-oh harmonic 86.728 112.930 # SOURCE3 1 - angle_coeff @angle:ca-cx-os harmonic 82.823 118.310 # SOURCE4_SOURCE5 18 0.7292 - angle_coeff @angle:c-cx-c3 harmonic 64.445 117.470 # SOURCE4_SOURCE5 71 1.9181 - angle_coeff @angle:cc-cx-cx harmonic 64.711 119.620 # CORR_SOURCE5 73 1.1478 - angle_coeff @angle:cc-cx-hc harmonic 47.813 113.930 # SOURCE4_SOURCE5 44 0.6781 - angle_coeff @angle:c-cx-cx harmonic 64.620 117.970 # SOURCE4_SOURCE5 554 2.1023 - angle_coeff @angle:cd-cx-cx harmonic 64.711 119.620 # CORR_SOURCE5 73 1.1478 - angle_coeff @angle:c-cx-h1 harmonic 46.552 116.550 # SOURCE4_SOURCE5 86 1.1535 - angle_coeff @angle:c-cx-hc harmonic 46.546 116.630 # SOURCE4_SOURCE5 122 1.5743 - angle_coeff @angle:cl-cx-cl harmonic 82.588 110.550 # SOURCE2_SOURCE5 14 0.4864 - angle_coeff @angle:cl-cx-cx harmonic 70.087 119.850 # SOURCE4_SOURCE5 84 0.7070 - angle_coeff @angle:cl-cx-h1 harmonic 48.861 111.430 # SOURCE3 1 - angle_coeff @angle:cl-cx-hc harmonic 47.924 115.800 # SOURCE2 1 - angle_coeff @angle:c-cx-os harmonic 83.552 115.590 # SOURCE4 36 0.8227 - angle_coeff @angle:cu-cx-cu harmonic 95.990 54.600 # SOURCE2 1 - angle_coeff @angle:cu-cx-cx harmonic 92.184 58.450 # SOURCE4_SOURCE5 35 0.3844 - angle_coeff @angle:cu-cx-hc harmonic 46.510 118.570 # SOURCE4_SOURCE5 36 0.6733 - angle_coeff @angle:cx-cx-cx harmonic 90.424 60.000 # SOURCE4_SOURCE5 2370 0.7579 - angle_coeff @angle:cx-cx-cy harmonic 69.603 100.530 # SOURCE3 4 - angle_coeff @angle:cx-cx-f harmonic 85.391 118.550 # SOURCE4_SOURCE5 24 1.1971 - angle_coeff @angle:cx-cx-h1 harmonic 45.959 118.700 # SOURCE3_SOURCE5 1351 1.3656 - angle_coeff @angle:cx-cx-hc harmonic 46.163 117.700 # SOURCE3_SOURCE5 3574 0.9510 - angle_coeff @angle:cx-cx-hx harmonic 45.802 119.610 # SOURCE4_SOURCE5 29 0.1468 - angle_coeff @angle:cx-cx-n3 harmonic 114.892 59.590 # SOURCE4_SOURCE5 400 0.3281 - angle_coeff @angle:cx-cx-na harmonic 79.232 126.020 # SOURCE4_SOURCE5 69 1.6659 - angle_coeff @angle:cx-cx-nh harmonic 115.868 59.170 # SOURCE4_SOURCE5 276 0.6810 - angle_coeff @angle:cx-cx-os harmonic 116.592 59.090 # SOURCE4_SOURCE5 1094 0.5727 - angle_coeff @angle:cy-cx-hc harmonic 44.429 125.430 # SOURCE3 2 - angle_coeff @angle:f-cx-f harmonic 120.884 106.900 # SOURCE2 2 1.4000 - angle_coeff @angle:f-cx-h1 harmonic 65.454 111.680 # SOURCE3 1 - angle_coeff @angle:f-cx-hc harmonic 65.300 112.300 # SOURCE2 1 - angle_coeff @angle:h1-cx-h1 harmonic 37.880 115.460 # SOURCE4_SOURCE5 585 0.3332 - angle_coeff @angle:h1-cx-n3 harmonic 59.281 116.470 # SOURCE4_SOURCE5 463 1.4379 - angle_coeff @angle:h1-cx-n harmonic 60.648 115.050 # SOURCE4_SOURCE5 36 1.2404 - angle_coeff @angle:h1-cx-na harmonic 61.785 108.360 # SOURCE4_SOURCE5 35 1.1443 - angle_coeff @angle:h1-cx-nh harmonic 59.869 116.290 # SOURCE4_SOURCE5 349 1.0287 - angle_coeff @angle:h1-cx-os harmonic 60.853 114.930 # SOURCE3_SOURCE5 531 0.5509 - angle_coeff @angle:h2-cx-h2 harmonic 37.352 119.430 # SOURCE3 1 - angle_coeff @angle:h2-cx-n2 harmonic 58.708 117.180 # SOURCE3 4 - angle_coeff @angle:hc-cx-hc harmonic 38.120 114.430 # SOURCE3_SOURCE5 595 0.4830 - angle_coeff @angle:hc-cx-os harmonic 61.092 114.100 # SOURCE2 1 - angle_coeff @angle:hx-cx-n4 harmonic 58.913 114.470 # SOURCE4_SOURCE5 28 0.1963 - angle_coeff @angle:n2-cx-n2 harmonic 157.396 50.160 # SOURCE3 1 - angle_coeff @angle:n-cx-oh harmonic 107.552 119.750 # SOURCE3 2 - angle_coeff @angle:n-cx-os harmonic 141.311 65.980 # SOURCE3 1 - angle_coeff @angle:oh-cx-oh harmonic 116.883 107.850 # SOURCE3 1 - angle_coeff @angle:oh-cx-os harmonic 108.501 118.120 # SOURCE3 4 1.3581 - angle_coeff @angle:os-cx-os harmonic 106.734 116.050 # SOURCE4_SOURCE5 15 2.1532 - angle_coeff @angle:c2-cy-cy harmonic 68.568 100.400 # SOURCE2 1 - angle_coeff @angle:c3-cy-c3 harmonic 65.146 111.440 # SOURCE4_SOURCE5 53 1.0307 - angle_coeff @angle:c3-cy-cy harmonic 62.618 118.700 # SOURCE4 293 1.8510 - angle_coeff @angle:c3-cy-h1 harmonic 46.561 111.780 # SOURCE4_SOURCE5 309 0.4521 - angle_coeff @angle:c3-cy-hc harmonic 46.907 110.140 # SOURCE3_SOURCE5 291 0.5598 - angle_coeff @angle:c3-cy-n3 harmonic 82.158 113.650 # SOURCE3_SOURCE5 15 2.3547 - angle_coeff @angle:c3-cy-n harmonic 86.069 104.130 # SOURCE4_SOURCE5 306 0.5952 - angle_coeff @angle:c3-cy-os harmonic 83.640 112.310 # SOURCE4_SOURCE5 40 1.1099 - angle_coeff @angle:c-cy-c3 harmonic 63.261 116.710 # SOURCE4_SOURCE5 332 0.5683 - angle_coeff @angle:cc-cy-cy harmonic 62.477 121.220 # CORR_SOURCE5 27 0.4901 - angle_coeff @angle:c-cy-cy harmonic 73.514 85.090 # SOURCE4_SOURCE5 672 0.9017 - angle_coeff @angle:cd-cy-cy harmonic 62.477 121.220 # CORR_SOURCE5 27 0.4901 - angle_coeff @angle:ce-cy-h2 harmonic 45.874 117.400 # SOURCE4_SOURCE5 38 0.5598 - angle_coeff @angle:ce-cy-n harmonic 94.195 87.940 # SOURCE4_SOURCE5 38 0.1933 - angle_coeff @angle:ce-cy-ss harmonic 60.454 120.540 # SOURCE4_SOURCE5 34 1.4182 - angle_coeff @angle:c-cy-h1 harmonic 45.784 113.030 # SOURCE4_SOURCE5 167 0.8137 - angle_coeff @angle:c-cy-hc harmonic 46.135 111.320 # SOURCE3_SOURCE5 246 1.1605 - angle_coeff @angle:cl-cy-cy harmonic 69.535 117.010 # SOURCE3_SOURCE5 41 1.1740 - angle_coeff @angle:cl-cy-h1 harmonic 49.261 106.590 # SOURCE3 1 - angle_coeff @angle:cl-cy-hc harmonic 47.632 114.000 # SOURCE2 1 - angle_coeff @angle:c-cy-n harmonic 80.522 117.340 # SOURCE4_SOURCE5 164 1.1278 - angle_coeff @angle:c-cy-os harmonic 82.061 115.000 # SOURCE4_SOURCE5 17 1.7766 - angle_coeff @angle:cv-cy-cy harmonic 73.645 86.710 # SOURCE4_SOURCE5 30 1.1538 - angle_coeff @angle:cv-cy-hc harmonic 46.478 114.420 # SOURCE4_SOURCE5 25 1.1899 - angle_coeff @angle:cx-cy-cy harmonic 68.163 101.230 # SOURCE3 4 - angle_coeff @angle:cx-cy-hc harmonic 45.715 118.300 # SOURCE2 3 5.7799 - angle_coeff @angle:cy-cy-cy harmonic 72.002 88.400 # SOURCE3_SOURCE5 746 1.4921 - angle_coeff @angle:cy-cy-f harmonic 85.702 112.870 # SOURCE4 13 1.6772 - angle_coeff @angle:cy-cy-h1 harmonic 45.598 113.240 # SOURCE3_SOURCE5 501 1.2112 - angle_coeff @angle:cy-cy-h2 harmonic 44.908 116.780 # SOURCE4_SOURCE5 206 0.8496 - angle_coeff @angle:cy-cy-hc harmonic 45.290 114.790 # SOURCE3_SOURCE5 1632 2.3030 - angle_coeff @angle:cy-cy-n3 harmonic 92.778 87.580 # SOURCE3 4 0.6135 - angle_coeff @angle:cy-cy-n harmonic 91.445 90.630 # SOURCE3_SOURCE5 429 2.2980 - angle_coeff @angle:cy-cy-na harmonic 80.160 119.560 # SOURCE4_SOURCE5 26 0.4777 - angle_coeff @angle:cy-cy-oh harmonic 82.786 114.190 # SOURCE3 4 - angle_coeff @angle:cy-cy-os harmonic 83.069 111.770 # SOURCE4 18 2.1334 - angle_coeff @angle:cy-cy-s6 harmonic 60.829 117.220 # SOURCE4_SOURCE5 19 1.2938 - angle_coeff @angle:cy-cy-ss harmonic 60.567 118.400 # SOURCE4_SOURCE5 183 1.7650 - angle_coeff @angle:h1-cy-h1 harmonic 38.688 109.460 # SOURCE3_SOURCE5 73 0.6101 - angle_coeff @angle:h1-cy-n3 harmonic 59.591 113.930 # SOURCE3_SOURCE5 104 0.9602 - angle_coeff @angle:h1-cy-n harmonic 60.615 111.280 # SOURCE4_SOURCE5 377 0.6736 - angle_coeff @angle:h1-cy-oh harmonic 62.604 111.490 # SOURCE3 2 - angle_coeff @angle:h1-cy-os harmonic 62.029 110.130 # SOURCE3_SOURCE5 45 0.8913 - angle_coeff @angle:h1-cy-s6 harmonic 41.611 111.620 # SOURCE4_SOURCE5 16 1.2135 - angle_coeff @angle:h2-cy-n harmonic 59.772 114.500 # SOURCE4_SOURCE5 213 0.6904 - angle_coeff @angle:h2-cy-os harmonic 62.315 109.190 # SOURCE4_SOURCE5 19 0.6835 - angle_coeff @angle:h2-cy-s6 harmonic 41.906 110.010 # SOURCE4_SOURCE5 29 1.6175 - angle_coeff @angle:h2-cy-ss harmonic 41.997 109.770 # SOURCE4_SOURCE5 214 0.7540 - angle_coeff @angle:hc-cy-hc harmonic 38.780 108.980 # SOURCE3_SOURCE5 313 0.5379 - angle_coeff @angle:n-cy-os harmonic 109.575 107.420 # SOURCE4_SOURCE5 24 2.2897 - angle_coeff @angle:n-cy-s6 harmonic 82.361 103.180 # SOURCE4_SOURCE5 18 0.8204 - angle_coeff @angle:n-cy-ss harmonic 81.655 105.130 # SOURCE4_SOURCE5 165 0.4214 - angle_coeff @angle:nh-cz-nh harmonic 112.563 120.140 # SOURCE4_SOURCE5 67 0.3910 - angle_coeff @angle:br-n1-c1 harmonic 52.125 180.000 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-c1 harmonic 65.921 179.920 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-c2 harmonic 61.737 177.730 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-c3 harmonic 57.795 177.720 # HF/6-31G*_SOURCE5 6 0.4473 - angle_coeff @angle:c1-n1-ca harmonic 60.455 179.990 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-cl harmonic 62.197 179.950 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-f harmonic 73.857 179.960 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-hn harmonic 45.538 179.980 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-i harmonic 49.085 179.950 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n1 harmonic 83.205 180.000 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n2 harmonic 81.640 171.560 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n3 harmonic 76.060 175.590 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-n4 harmonic 74.800 179.690 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-na harmonic 75.122 180.000 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-nh harmonic 76.286 176.350 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-o harmonic 77.945 179.950 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-oh harmonic 78.300 174.310 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-os harmonic 77.399 176.610 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p2 harmonic 70.987 172.830 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p3 harmonic 71.573 173.510 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p4 harmonic 70.741 173.640 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-p5 harmonic 74.438 177.280 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s2 harmonic 61.878 178.110 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s4 harmonic 56.730 169.600 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s harmonic 54.789 179.990 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-s6 harmonic 63.372 175.920 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-sh harmonic 57.243 174.250 # HF/6-31G* 1 - angle_coeff @angle:c1-n1-ss harmonic 56.948 176.060 # HF/6-31G* 1 - angle_coeff @angle:c2-n1-n1 harmonic 77.250 180.000 # HF/6-31G* 1 - angle_coeff @angle:c2-n1-o harmonic 91.430 116.940 # SOURCE3 2 0.0060 - angle_coeff @angle:c2-n1-s harmonic 66.557 118.000 # SOURCE3 2 0.0121 - angle_coeff @angle:c3-n1-n1 harmonic 72.180 180.000 # HF/6-31G* 1 - angle_coeff @angle:ca-n1-n1 harmonic 76.091 180.000 # HF/6-31G* 1 - angle_coeff @angle:ce-n1-o harmonic 89.183 122.400 # CORR 2 - angle_coeff @angle:ce-n1-s harmonic 66.690 117.340 # CORR 2 - angle_coeff @angle:cf-n1-o harmonic 89.183 122.400 # CORR 2 - angle_coeff @angle:cf-n1-s harmonic 66.690 117.340 # CORR 2 - angle_coeff @angle:cl-n1-n1 harmonic 77.983 179.940 # HF/6-31G* 1 - angle_coeff @angle:f-n1-n1 harmonic 92.867 179.930 # HF/6-31G* 1 - angle_coeff @angle:hn-n1-n1 harmonic 57.688 179.910 # HF/6-31G* 1 - angle_coeff @angle:i-n1-n1 harmonic 61.297 179.940 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n1 harmonic 105.090 179.970 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n2 harmonic 102.546 172.850 # HF/6-31G*_SOURCE5 38 0.7957 - angle_coeff @angle:n1-n1-n3 harmonic 95.850 175.090 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-n4 harmonic 94.056 179.910 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-na harmonic 94.541 179.970 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-nh harmonic 96.108 176.000 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-o harmonic 98.200 179.940 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-oh harmonic 98.761 173.770 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-os harmonic 97.594 176.120 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-p2 harmonic 88.474 174.710 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-p3 harmonic 89.510 174.270 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-s harmonic 68.668 180.000 # SOURCE3 1 - angle_coeff @angle:n1-n1-sh harmonic 71.618 175.070 # HF/6-31G* 1 - angle_coeff @angle:n1-n1-ss harmonic 71.507 175.610 # HF/6-31G* 1 - angle_coeff @angle:o-n1-p2 harmonic 107.306 116.050 # SOURCE3 1 - angle_coeff @angle:p2-n1-s harmonic 83.718 119.930 # SOURCE3 1 - angle_coeff @angle:br-n2-br harmonic 64.457 106.600 # SOURCE3 1 - angle_coeff @angle:br-n2-c2 harmonic 60.247 112.400 # SOURCE3 1 - angle_coeff @angle:br-n2-n2 harmonic 76.071 110.420 # SOURCE3 1 - angle_coeff @angle:br-n2-o harmonic 74.480 114.470 # SOURCE3 1 - angle_coeff @angle:br-n2-p2 harmonic 82.651 111.030 # SOURCE3 1 - angle_coeff @angle:br-n2-s harmonic 63.537 115.780 # SOURCE3 1 - angle_coeff @angle:c1-n2-c1 harmonic 77.425 121.100 # SOURCE3 1 - angle_coeff @angle:c1-n2-c3 harmonic 60.897 151.880 # SOURCE3 4 15.8282 - angle_coeff @angle:c1-n2-cl harmonic 68.804 118.800 # SOURCE2 1 - angle_coeff @angle:c1-n2-hn harmonic 52.343 126.500 # SOURCE2 3 7.6267 - angle_coeff @angle:c1-n2-n2 harmonic 97.203 113.400 # SOURCE3 1 - angle_coeff @angle:c1-n2-o harmonic 99.262 113.590 # SOURCE3 1 - angle_coeff @angle:c1-n2-p2 harmonic 88.534 119.570 # SOURCE3 1 - angle_coeff @angle:c1-n2-s harmonic 71.943 117.670 # SOURCE3 1 - angle_coeff @angle:c2-n2-c2 harmonic 73.202 118.180 # SOURCE3 1 - angle_coeff @angle:c2-n2-c3 harmonic 68.517 115.300 # SOURCE3 8 4.2940 - angle_coeff @angle:c2-n2-ca harmonic 72.054 119.940 # SOURCE3 1 - angle_coeff @angle:c2-n2-cl harmonic 70.470 112.640 # SOURCE3 1 - angle_coeff @angle:c2-n2-f harmonic 90.773 108.140 # SOURCE3 1 - angle_coeff @angle:c2-n2-hn harmonic 53.185 110.800 # SOURCE3_SOURCE5 419 0.5563 - angle_coeff @angle:c2-n2-i harmonic 54.902 114.740 # SOURCE3 2 0.0139 - angle_coeff @angle:c2-n2-n1 harmonic 94.708 115.090 # HF/6-31G* 1 - angle_coeff @angle:c2-n2-n2 harmonic 98.476 103.590 # SOURCE3 2 - angle_coeff @angle:c2-n2-n3 harmonic 89.963 118.140 # SOURCE3 1 - angle_coeff @angle:c2-n2-n4 harmonic 78.566 112.220 # SOURCE3 3 0.0406 - angle_coeff @angle:c2-n2-n harmonic 88.873 117.930 # SOURCE4_SOURCE5 32 1.2067 - angle_coeff @angle:c2-n2-na harmonic 88.734 117.580 # SOURCE3 8 1.6671 - angle_coeff @angle:c2-n2-nh harmonic 89.294 117.610 # SOURCE3 6 3.2642 - angle_coeff @angle:c2-n2-no harmonic 86.019 118.020 # SOURCE3_SOURCE5 8 0.7772 - angle_coeff @angle:c2-n2-o harmonic 94.405 116.940 # SOURCE3 1 - angle_coeff @angle:c2-n2-oh harmonic 90.358 111.120 # SOURCE4_SOURCE5 59 1.2303 - angle_coeff @angle:c2-n2-os harmonic 90.019 110.960 # SOURCE4_SOURCE5 46 1.0478 - angle_coeff @angle:c2-n2-p2 harmonic 88.774 116.000 # SOURCE3 1 - angle_coeff @angle:c2-n2-p3 harmonic 80.914 119.300 # SOURCE3 3 2.8489 - angle_coeff @angle:c2-n2-p4 harmonic 82.737 118.770 # SOURCE3 1 - angle_coeff @angle:c2-n2-s4 harmonic 70.138 112.290 # SOURCE3 1 - angle_coeff @angle:c2-n2-s6 harmonic 70.821 116.240 # SOURCE3 1 - angle_coeff @angle:c2-n2-s harmonic 70.719 118.000 # SOURCE3 1 - angle_coeff @angle:c2-n2-sh harmonic 64.926 115.480 # SOURCE3 1 - angle_coeff @angle:c2-n2-ss harmonic 66.888 118.040 # SOURCE3 4 2.2804 - angle_coeff @angle:c3-n2-c3 harmonic 66.122 110.700 # SOURCE3 1 - angle_coeff @angle:c3-n2-ca harmonic 68.205 115.050 # SOURCE4_SOURCE5 12 1.0676 - angle_coeff @angle:c3-n2-ce harmonic 67.437 118.670 # CORR_SOURCE5 270 1.8559 - angle_coeff @angle:c3-n2-cf harmonic 67.437 118.670 # CORR_SOURCE5 270 1.8559 - angle_coeff @angle:c3-n2-hn harmonic 45.854 118.400 # SOURCE3 1 - angle_coeff @angle:c3-n2-n1 harmonic 86.587 116.100 # SOURCE4_SOURCE5 33 0.4557 - angle_coeff @angle:c3-n2-n2 harmonic 87.844 110.840 # SOURCE3_SOURCE5 20 1.2862 - angle_coeff @angle:c3-n2-nh harmonic 86.138 109.990 # SOURCE3 1 - angle_coeff @angle:c3-n2-o harmonic 88.263 112.400 # SOURCE2 1 - angle_coeff @angle:c3-n2-p2 harmonic 85.879 114.210 # SOURCE3 2 2.2772 - angle_coeff @angle:c3-n2-s6 harmonic 68.328 113.840 # SOURCE3 1 - angle_coeff @angle:c3-n2-s harmonic 67.797 116.720 # SOURCE3 1 - angle_coeff @angle:ca-n2-ca harmonic 73.899 112.200 # SOURCE3 1 - angle_coeff @angle:ca-n2-hn harmonic 50.447 120.000 # SOURCE3 1 - angle_coeff @angle:ca-n2-n2 harmonic 93.256 113.530 # SOURCE3 1 - angle_coeff @angle:ca-n2-o harmonic 93.893 116.000 # SOURCE2 1 - angle_coeff @angle:ca-n2-p2 harmonic 87.640 118.110 # SOURCE3 1 - angle_coeff @angle:ca-n2-s harmonic 69.770 120.110 # SOURCE3 1 - angle_coeff @angle:c-n2-c2 harmonic 68.290 120.970 # SOURCE3 1 - angle_coeff @angle:c-n2-c harmonic 64.555 123.800 # SOURCE3 1 - angle_coeff @angle:c-n2-ca harmonic 67.993 120.500 # SOURCE3 1 - angle_coeff @angle:cc-n2-cl harmonic 69.467 115.790 # CORR 2 - angle_coeff @angle:cc-n2-hn harmonic 52.795 111.250 # CORR_SOURCE5 44 0.9238 - angle_coeff @angle:cc-n2-na harmonic 91.793 109.240 # SOURCE4_SOURCE5 23 1.5921 - angle_coeff @angle:cc-n2-nh harmonic 88.704 118.470 # SOURCE4_SOURCE5 13 1.7276 - angle_coeff @angle:cd-n2-cl harmonic 69.467 115.790 # CORR 2 - angle_coeff @angle:cd-n2-hn harmonic 52.795 111.250 # CORR_SOURCE5 44 0.9238 - angle_coeff @angle:ce-n2-hn harmonic 52.954 111.000 # CORR_SOURCE5 129 0.3980 - angle_coeff @angle:ce-n2-n harmonic 88.686 117.980 # CORR_SOURCE5 153 0.9604 - angle_coeff @angle:ce-n2-nh harmonic 88.846 118.340 # CORR_SOURCE5 99 1.0308 - angle_coeff @angle:ce-n2-o harmonic 96.153 112.160 # SOURCE3 1 - angle_coeff @angle:ce-n2-oh harmonic 89.527 112.790 # CORR_SOURCE5 124 1.4261 - angle_coeff @angle:ce-n2-os harmonic 89.131 112.790 # CORR_SOURCE5 58 1.1282 - angle_coeff @angle:ce-n2-s harmonic 71.153 116.280 # SOURCE3 1 - angle_coeff @angle:cf-n2-hn harmonic 52.942 111.050 # CORR_SOURCE5 5 0.7460 - angle_coeff @angle:cf-n2-n harmonic 88.686 117.980 # CORR_SOURCE5 153 0.9604 - angle_coeff @angle:cf-n2-nh harmonic 88.846 118.340 # CORR_SOURCE5 99 1.0308 - angle_coeff @angle:cf-n2-o harmonic 96.153 112.160 # SOURCE3 1 - angle_coeff @angle:cf-n2-oh harmonic 89.527 112.790 # CORR_SOURCE5 124 1.4261 - angle_coeff @angle:cf-n2-os harmonic 89.131 112.790 # CORR_SOURCE5 58 1.1282 - angle_coeff @angle:cf-n2-s harmonic 71.153 116.280 # SOURCE3 1 - angle_coeff @angle:cl-n2-n1 harmonic 90.032 108.700 # SOURCE2 1 - angle_coeff @angle:cl-n2-n2 harmonic 89.183 110.470 # SOURCE3 1 - angle_coeff @angle:cl-n2-o harmonic 87.927 114.030 # SOURCE3 1 - angle_coeff @angle:cl-n2-p2 harmonic 93.146 112.980 # SOURCE3 1 - angle_coeff @angle:cl-n2-s harmonic 72.639 115.770 # SOURCE3 1 - angle_coeff @angle:cx-n2-n2 harmonic 113.932 64.920 # SOURCE3 2 - angle_coeff @angle:f-n2-n2 harmonic 110.866 114.600 # SOURCE2 1 - angle_coeff @angle:f-n2-o harmonic 114.530 110.100 # SOURCE2 1 - angle_coeff @angle:f-n2-p2 harmonic 113.300 107.100 # SOURCE3 1 - angle_coeff @angle:f-n2-s harmonic 88.996 110.730 # SOURCE3 1 - angle_coeff @angle:hn-n2-hn harmonic 38.294 120.000 # SOURCE3 1 - angle_coeff @angle:hn-n2-n1 harmonic 67.682 114.100 # SOURCE2 1 - angle_coeff @angle:hn-n2-n2 harmonic 69.032 105.010 # SOURCE3 19 1.5183 - angle_coeff @angle:hn-n2-ne harmonic 67.706 108.560 # SOURCE3 29 5.5708 - angle_coeff @angle:hn-n2-nf harmonic 67.706 108.560 # SOURCE3 29 - angle_coeff @angle:hn-n2-o harmonic 70.317 107.370 # SOURCE3 1 - angle_coeff @angle:hn-n2-p2 harmonic 59.815 112.090 # SOURCE3 18 4.0663 - angle_coeff @angle:hn-n2-p4 harmonic 55.602 111.330 # SOURCE3 1 - angle_coeff @angle:hn-n2-p5 harmonic 57.476 122.340 # SOURCE3 1 - angle_coeff @angle:hn-n2-pe harmonic 62.556 111.410 # SOURCE3 20 4.9895 - angle_coeff @angle:hn-n2-pf harmonic 62.556 111.410 # SOURCE3 20 - angle_coeff @angle:hn-n2-s2 harmonic 47.686 115.800 # SOURCE2 1 - angle_coeff @angle:hn-n2-s4 harmonic 46.643 111.210 # SOURCE3 1 - angle_coeff @angle:hn-n2-s harmonic 49.437 108.170 # SOURCE3 1 - angle_coeff @angle:hn-n2-s6 harmonic 48.367 111.170 # SOURCE3_SOURCE5 7 0.7012 - angle_coeff @angle:i-n2-n2 harmonic 69.513 111.790 # SOURCE3 1 - angle_coeff @angle:i-n2-o harmonic 67.472 116.820 # SOURCE3 1 - angle_coeff @angle:i-n2-p2 harmonic 77.614 113.260 # SOURCE3 1 - angle_coeff @angle:i-n2-s harmonic 59.644 116.850 # SOURCE3 1 - angle_coeff @angle:n1-n2-n1 harmonic 122.832 112.000 # HF/6-31G* 1 - angle_coeff @angle:n2-n2-n1 harmonic 95.438 180.000 # dac_for_azides 0 - angle_coeff @angle:n2-n2-n2 harmonic 120.662 109.490 # SOURCE3 2 - angle_coeff @angle:n2-n2-n3 harmonic 117.964 108.880 # SOURCE3 1 - angle_coeff @angle:n2-n2-n4 harmonic 101.207 106.450 # SOURCE3 1 - angle_coeff @angle:n2-n2-na harmonic 114.285 112.230 # SOURCE3 1 - angle_coeff @angle:n2-n2-nh harmonic 115.311 111.700 # SOURCE3 5 0.3475 - angle_coeff @angle:n2-n2-no harmonic 114.147 105.970 # SOURCE3 1 - angle_coeff @angle:n2-n2-o harmonic 122.449 110.430 # SOURCE3 1 - angle_coeff @angle:n2-n2-oh harmonic 113.470 111.510 # SOURCE3 1 - angle_coeff @angle:n2-n2-os harmonic 114.570 108.380 # SOURCE3 1 - angle_coeff @angle:n2-n2-p2 harmonic 114.892 109.150 # SOURCE3 1 - angle_coeff @angle:n2-n2-p3 harmonic 104.216 113.050 # SOURCE3 1 - angle_coeff @angle:n2-n2-p4 harmonic 103.768 118.770 # SOURCE3 1 - angle_coeff @angle:n2-n2-p5 harmonic 114.546 110.460 # SOURCE3 1 - angle_coeff @angle:n2-n2-s4 harmonic 90.072 107.300 # SOURCE3 1 - angle_coeff @angle:n2-n2-s6 harmonic 90.924 111.250 # SOURCE3 1 - angle_coeff @angle:n2-n2-s harmonic 89.630 115.910 # SOURCE3 1 - angle_coeff @angle:n2-n2-sh harmonic 83.010 111.100 # SOURCE3 1 - angle_coeff @angle:n2-n2-ss harmonic 86.115 112.140 # SOURCE3 1 - angle_coeff @angle:n3-n2-n3 harmonic 112.191 115.070 # SOURCE3 1 - angle_coeff @angle:n3-n2-o harmonic 117.213 114.000 # SOURCE2 1 - angle_coeff @angle:n3-n2-p2 harmonic 110.501 115.340 # SOURCE3 1 - angle_coeff @angle:n3-n2-s harmonic 87.944 117.130 # SOURCE3 1 - angle_coeff @angle:n4-n2-n4 harmonic 92.222 106.700 # SOURCE3 1 - angle_coeff @angle:n4-n2-o harmonic 99.103 112.200 # SOURCE3 1 - angle_coeff @angle:n4-n2-p2 harmonic 101.387 113.070 # SOURCE3 1 - angle_coeff @angle:n4-n2-s harmonic 78.497 118.500 # SOURCE3 1 - angle_coeff @angle:na-n2-na harmonic 113.061 107.000 # SOURCE3 1 - angle_coeff @angle:na-n2-o harmonic 115.589 113.090 # SOURCE3 1 - angle_coeff @angle:na-n2-p2 harmonic 107.835 119.160 # SOURCE3 1 - angle_coeff @angle:na-n2-s harmonic 86.691 118.260 # SOURCE3 1 - angle_coeff @angle:ne-n2-nh harmonic 114.300 113.340 # CORR_SOURCE5 18 1.2157 - angle_coeff @angle:ne-n2-o harmonic 122.270 110.310 # SOURCE3 1 - angle_coeff @angle:ne-n2-s harmonic 89.426 116.220 # SOURCE3 1 - angle_coeff @angle:nf-n2-nh harmonic 114.300 113.340 # CORR_SOURCE5 18 1.2157 - angle_coeff @angle:nf-n2-o harmonic 122.270 110.310 # SOURCE3 1 - angle_coeff @angle:nf-n2-s harmonic 89.426 116.220 # SOURCE3 1 - angle_coeff @angle:nh-n2-nh harmonic 107.426 121.200 # SOURCE3 1 - angle_coeff @angle:nh-n2-o harmonic 116.027 113.850 # SOURCE4_SOURCE5 33 1.0590 - angle_coeff @angle:nh-n2-p2 harmonic 108.341 118.830 # SOURCE3 2 0.1024 - angle_coeff @angle:nh-n2-s harmonic 87.530 116.900 # SOURCE3 2 0.2276 - angle_coeff @angle:n-n2-n2 harmonic 116.779 108.160 # SOURCE4_SOURCE5 18 0.3340 - angle_coeff @angle:n-n2-o harmonic 114.959 115.110 # SOURCE4_SOURCE5 85 0.2779 - angle_coeff @angle:no-n2-no harmonic 109.483 103.700 # SOURCE3 1 - angle_coeff @angle:no-n2-o harmonic 118.569 100.760 # SOURCE3 1 - angle_coeff @angle:no-n2-p2 harmonic 109.507 111.950 # SOURCE3 1 - angle_coeff @angle:n-n2-p2 harmonic 108.858 117.300 # SOURCE3 1 - angle_coeff @angle:n-n2-s harmonic 87.790 115.740 # SOURCE3 1 - angle_coeff @angle:oh-n2-oh harmonic 114.003 101.700 # SOURCE3 1 - angle_coeff @angle:oh-n2-p2 harmonic 109.132 115.110 # SOURCE3 1 - angle_coeff @angle:oh-n2-s harmonic 86.961 116.080 # SOURCE3 1 - angle_coeff @angle:o-n2-o harmonic 122.337 115.370 # SOURCE3 1 - angle_coeff @angle:o-n2-oh harmonic 114.777 112.150 # SOURCE2 2 1.4500 - angle_coeff @angle:o-n2-os harmonic 115.139 110.350 # SOURCE3 2 0.0042 - angle_coeff @angle:o-n2-p2 harmonic 112.237 116.080 # SOURCE3 1 - angle_coeff @angle:o-n2-p3 harmonic 104.358 113.430 # SOURCE3 1 - angle_coeff @angle:o-n2-p4 harmonic 107.967 110.610 # SOURCE3 1 - angle_coeff @angle:o-n2-p5 harmonic 116.129 109.110 # SOURCE3 1 - angle_coeff @angle:o-n2-pe harmonic 107.813 134.560 # SOURCE3 1 - angle_coeff @angle:o-n2-pf harmonic 107.813 134.560 # SOURCE3 1 - angle_coeff @angle:o-n2-s4 harmonic 90.054 108.910 # SOURCE3 1 - angle_coeff @angle:o-n2-s6 harmonic 91.703 111.340 # SOURCE3 1 - angle_coeff @angle:o-n2-s harmonic 89.978 117.180 # SOURCE3 1 - angle_coeff @angle:o-n2-sh harmonic 81.901 114.980 # SOURCE3 1 - angle_coeff @angle:os-n2-os harmonic 108.669 110.290 # SOURCE3 1 - angle_coeff @angle:os-n2-p2 harmonic 111.268 110.200 # SOURCE3 1 - angle_coeff @angle:o-n2-ss harmonic 85.259 115.770 # SOURCE3_SOURCE5 7 0.2342 - angle_coeff @angle:os-n2-s harmonic 88.194 112.230 # SOURCE3 1 - angle_coeff @angle:p2-n2-p2 harmonic 113.183 116.800 # SOURCE3 1 - angle_coeff @angle:p2-n2-p3 harmonic 103.997 124.480 # SOURCE3 1 - angle_coeff @angle:p2-n2-p4 harmonic 103.837 128.370 # SOURCE3 1 - angle_coeff @angle:p2-n2-p5 harmonic 110.289 123.470 # SOURCE3 1 - angle_coeff @angle:p2-n2-s4 harmonic 89.884 112.100 # SOURCE3 1 - angle_coeff @angle:p2-n2-s6 harmonic 90.002 115.700 # SOURCE3 1 - angle_coeff @angle:p2-n2-s harmonic 89.517 117.840 # SOURCE3 1 - angle_coeff @angle:p2-n2-sh harmonic 83.828 118.450 # SOURCE3 1 - angle_coeff @angle:p2-n2-ss harmonic 85.455 120.430 # SOURCE3 1 - angle_coeff @angle:p3-n2-p3 harmonic 101.430 120.400 # SOURCE3 1 - angle_coeff @angle:p3-n2-s harmonic 83.445 120.860 # SOURCE3 1 - angle_coeff @angle:p4-n2-s harmonic 81.102 131.840 # SOURCE3 1 - angle_coeff @angle:p5-n2-p5 harmonic 111.803 120.600 # SOURCE3 1 - angle_coeff @angle:p5-n2-s harmonic 88.930 119.890 # SOURCE3 1 - angle_coeff @angle:pe-n2-s harmonic 92.311 115.730 # SOURCE3 1 - angle_coeff @angle:pf-n2-s harmonic 92.311 115.730 # SOURCE3 1 - angle_coeff @angle:s4-n2-s4 harmonic 67.822 119.180 # SOURCE3 1 - angle_coeff @angle:s4-n2-s6 harmonic 68.983 119.180 # SOURCE3 1 - angle_coeff @angle:s6-n2-s6 harmonic 70.275 119.180 # SOURCE3 1 - angle_coeff @angle:sh-n2-sh harmonic 61.611 123.930 # SOURCE3 1 - angle_coeff @angle:sh-n2-ss harmonic 63.026 123.930 # SOURCE3 1 - angle_coeff @angle:s-n2-s harmonic 70.359 120.880 # SOURCE3 1 - angle_coeff @angle:s-n2-s4 harmonic 71.109 113.000 # SOURCE3 1 - angle_coeff @angle:s-n2-s6 harmonic 70.436 119.610 # SOURCE3 1 - angle_coeff @angle:s-n2-sh harmonic 65.341 122.050 # SOURCE3 1 - angle_coeff @angle:s-n2-ss harmonic 68.418 118.190 # SOURCE3 1 - angle_coeff @angle:ss-n2-ss harmonic 64.662 123.930 # SOURCE3 1 - angle_coeff @angle:br-n3-br harmonic 67.124 107.150 # SOURCE3 1 - angle_coeff @angle:br-n3-c3 harmonic 63.925 106.930 # SOURCE3 2 - angle_coeff @angle:c1-n3-c1 harmonic 68.156 123.340 # SOURCE3 1 - angle_coeff @angle:c1-n3-f harmonic 91.888 104.700 # SOURCE2 1 - angle_coeff @angle:c1-n3-hn harmonic 50.216 114.780 # SOURCE3_SOURCE5 7 0.4776 - angle_coeff @angle:c1-n3-o harmonic 89.192 116.630 # SOURCE3 1 - angle_coeff @angle:c2-n3-c2 harmonic 68.168 124.680 # SOURCE3 1 - angle_coeff @angle:c2-n3-hn harmonic 49.470 119.380 # SOURCE3 1 - angle_coeff @angle:c3-n3-c3 harmonic 65.697 112.350 # SOURCE3_SOURCE5 10425 1.3688 - angle_coeff @angle:c3-n3-cl harmonic 72.005 107.230 # SOURCE3 3 0.3673 - angle_coeff @angle:c3-n3-cx harmonic 64.536 116.000 # SOURCE4_SOURCE5 93 0.9654 - angle_coeff @angle:c3-n3-cy harmonic 63.919 117.550 # SOURCE4_SOURCE5 52 1.6649 - angle_coeff @angle:c3-n3-f harmonic 88.810 103.130 # SOURCE3 2 - angle_coeff @angle:c3-n3-hn harmonic 47.782 109.290 # SOURCE3_SOURCE5 6742 0.6614 - angle_coeff @angle:c3-n3-i harmonic 60.375 108.480 # SOURCE3 2 - angle_coeff @angle:c3-n3-n2 harmonic 83.514 118.750 # SOURCE2 2 2.6500 - angle_coeff @angle:c3-n3-n3 harmonic 83.494 110.800 # SOURCE3_SOURCE5 91 1.4698 - angle_coeff @angle:c3-n3-n4 harmonic 84.250 109.650 # SOURCE3 3 0.1146 - angle_coeff @angle:c3-n3-n harmonic 84.170 111.710 # SOURCE4_SOURCE5 108 1.7154 - angle_coeff @angle:c3-n3-nh harmonic 83.840 111.770 # SOURCE4_SOURCE5 54 1.2232 - angle_coeff @angle:c3-n3-no harmonic 82.437 116.930 # SOURCE3_SOURCE5 25 0.8475 - angle_coeff @angle:c3-n3-o harmonic 86.116 113.310 # SOURCE3 5 8.9081 - angle_coeff @angle:c3-n3-oh harmonic 85.913 106.490 # SOURCE4_SOURCE5 51 1.1723 - angle_coeff @angle:c3-n3-os harmonic 85.469 105.800 # SOURCE4_SOURCE5 28 1.5996 - angle_coeff @angle:c3-n3-p3 harmonic 79.872 119.670 # SOURCE3_SOURCE5 17 1.9089 - angle_coeff @angle:c3-n3-p5 harmonic 81.775 119.860 # SOURCE4_SOURCE5 188 2.0452 - angle_coeff @angle:c3-n3-s4 harmonic 62.997 114.490 # SOURCE3_SOURCE5 8 1.8120 - angle_coeff @angle:c3-n3-s6 harmonic 64.550 116.550 # SOURCE4_SOURCE5 179 1.8765 - angle_coeff @angle:c3-n3-s harmonic 63.268 110.020 # SOURCE3 1 - angle_coeff @angle:c3-n3-sh harmonic 63.898 112.700 # SOURCE3 1 - angle_coeff @angle:c3-n3-ss harmonic 63.312 116.250 # SOURCE3_SOURCE5 14 1.9512 - angle_coeff @angle:c3-n3-sy harmonic 64.295 115.250 # SOURCE4_SOURCE5 250 1.7586 - angle_coeff @angle:cl-n3-cl harmonic 80.378 108.280 # SOURCE3 1 - angle_coeff @angle:cl-n3-hn harmonic 48.266 104.390 # SOURCE3 2 - angle_coeff @angle:cl-n3-n3 harmonic 90.354 107.650 # SOURCE3 1 - angle_coeff @angle:cx-n3-cx harmonic 89.029 60.730 # SOURCE4_SOURCE5 147 0.2518 - angle_coeff @angle:cx-n3-hn harmonic 47.500 109.830 # SOURCE4_SOURCE5 76 0.6684 - angle_coeff @angle:cx-n3-p5 harmonic 81.827 119.410 # SOURCE4_SOURCE5 173 1.2386 - angle_coeff @angle:cx-n3-py harmonic 80.259 121.750 # SOURCE4_SOURCE5 20 1.0295 - angle_coeff @angle:cy-n3-cy harmonic 72.263 91.110 # SOURCE4_SOURCE5 36 0.9119 - angle_coeff @angle:cy-n3-hn harmonic 47.059 110.670 # SOURCE4_SOURCE5 48 0.9592 - angle_coeff @angle:f-n3-f harmonic 115.777 102.220 # SOURCE2 4 0.7562 - angle_coeff @angle:f-n3-hn harmonic 65.935 99.800 # SOURCE2 1 - angle_coeff @angle:hn-n3-hn harmonic 40.828 106.400 # SOURCE3_SOURCE5 2019 0.9777 - angle_coeff @angle:hn-n3-i harmonic 36.749 109.980 # SOURCE3 2 - angle_coeff @angle:hn-n3-n1 harmonic 64.085 110.170 # HF/6-31G* 1 - angle_coeff @angle:hn-n3-n2 harmonic 63.293 115.940 # SOURCE3 1 - angle_coeff @angle:hn-n3-n3 harmonic 61.180 107.680 # SOURCE3_SOURCE5 107 1.7630 - angle_coeff @angle:hn-n3-n4 harmonic 61.852 106.910 # SOURCE3_SOURCE5 18 0.7068 - angle_coeff @angle:hn-n3-n harmonic 62.520 108.120 # SOURCE3_SOURCE5 90 1.1435 - angle_coeff @angle:hn-n3-na harmonic 61.963 107.890 # SOURCE3 1 - angle_coeff @angle:hn-n3-nh harmonic 62.016 108.310 # SOURCE3_SOURCE5 85 1.2609 - angle_coeff @angle:hn-n3-no harmonic 63.767 104.780 # SOURCE3 3 1.1126 - angle_coeff @angle:hn-n3-o harmonic 65.058 113.320 # SOURCE3 3 4.3945 - angle_coeff @angle:hn-n3-oh harmonic 63.840 102.300 # SOURCE3_SOURCE5 14 0.6850 - angle_coeff @angle:hn-n3-os harmonic 62.667 102.750 # SOURCE3_SOURCE5 43 0.6086 - angle_coeff @angle:hn-n3-p2 harmonic 55.368 120.260 # SOURCE3 1 - angle_coeff @angle:hn-n3-p3 harmonic 54.032 116.890 # SOURCE3 9 3.8816 - angle_coeff @angle:hn-n3-p4 harmonic 56.121 113.050 # SOURCE3 2 - angle_coeff @angle:hn-n3-p5 harmonic 56.803 114.320 # SOURCE3_SOURCE5 63 1.6600 - angle_coeff @angle:hn-n3-s4 harmonic 42.895 109.140 # SOURCE3_SOURCE5 13 1.2903 - angle_coeff @angle:hn-n3-s harmonic 41.811 109.470 # SOURCE3 1 - angle_coeff @angle:hn-n3-s6 harmonic 45.126 109.600 # SOURCE4_SOURCE5 234 1.2605 - angle_coeff @angle:hn-n3-sh harmonic 43.414 108.670 # SOURCE3 3 2.5025 - angle_coeff @angle:hn-n3-ss harmonic 43.417 110.830 # SOURCE3_SOURCE5 14 1.1613 - angle_coeff @angle:hn-n3-sy harmonic 44.457 109.500 # SOURCE4_SOURCE5 617 0.8005 - angle_coeff @angle:i-n3-i harmonic 65.458 111.270 # SOURCE3 1 - angle_coeff @angle:n1-n3-n1 harmonic 111.350 113.210 # HF/6-31G* 1 - angle_coeff @angle:n2-n3-n2 harmonic 110.449 118.730 # SOURCE3 1 - angle_coeff @angle:n2-n3-o harmonic 113.356 114.910 # SOURCE3 1 - angle_coeff @angle:n3-n3-n3 harmonic 107.918 105.710 # SOURCE3 3 0.3561 - angle_coeff @angle:n4-n3-n4 harmonic 104.995 113.480 # SOURCE3 1 - angle_coeff @angle:n4-n3-nh harmonic 108.598 107.140 # SOURCE3 1 - angle_coeff @angle:na-n3-na harmonic 106.431 112.000 # SOURCE3 1 - angle_coeff @angle:nh-n3-nh harmonic 109.151 107.150 # SOURCE3 1 - angle_coeff @angle:n-n3-n harmonic 108.332 110.550 # SOURCE3 1 - angle_coeff @angle:no-n3-no harmonic 106.581 115.260 # SOURCE3 1 - angle_coeff @angle:oh-n3-oh harmonic 109.190 107.180 # SOURCE3 1 - angle_coeff @angle:o-n3-o harmonic 109.294 126.140 # SOURCE3 1 - angle_coeff @angle:o-n3-p2 harmonic 106.891 117.020 # SOURCE3 1 - angle_coeff @angle:o-n3-p4 harmonic 105.671 116.650 # SOURCE3 1 - angle_coeff @angle:o-n3-s4 harmonic 80.957 114.090 # SOURCE3 1 - angle_coeff @angle:o-n3-s6 harmonic 84.368 113.800 # SOURCE3 1 - angle_coeff @angle:o-n3-s harmonic 77.548 119.810 # SOURCE3 1 - angle_coeff @angle:os-n3-os harmonic 107.574 106.520 # SOURCE3 1 - angle_coeff @angle:p2-n3-p2 harmonic 103.056 130.130 # SOURCE3 1 - angle_coeff @angle:p3-n3-p3 harmonic 104.144 118.740 # SOURCE3 3 3.3755 - angle_coeff @angle:p4-n3-p4 harmonic 107.254 116.350 # SOURCE3 1 - angle_coeff @angle:p5-n3-p5 harmonic 107.603 119.420 # SOURCE3 1 - angle_coeff @angle:s4-n3-s4 harmonic 62.022 120.020 # SOURCE3 1 - angle_coeff @angle:s4-n3-s6 harmonic 63.190 120.950 # SOURCE3 1 - angle_coeff @angle:s6-n3-s6 harmonic 65.471 118.540 # SOURCE3_SOURCE5 18 1.1456 - angle_coeff @angle:sh-n3-sh harmonic 62.936 118.630 # SOURCE3 1 - angle_coeff @angle:sh-n3-ss harmonic 62.938 119.670 # SOURCE3 1 - angle_coeff @angle:s-n3-s harmonic 58.040 131.360 # SOURCE3 1 - angle_coeff @angle:ss-n3-ss harmonic 63.249 119.570 # SOURCE3 1 - angle_coeff @angle:br-n4-br harmonic 65.719 114.820 # SOURCE3 1 - angle_coeff @angle:br-n4-hn harmonic 41.251 108.440 # SOURCE3 7 0.5630 - angle_coeff @angle:c1-n4-c1 harmonic 67.454 113.870 # SOURCE3 1 - angle_coeff @angle:c1-n4-hn harmonic 48.997 110.190 # SOURCE3 7 1.0847 - angle_coeff @angle:c2-n4-c2 harmonic 63.556 112.580 # SOURCE3 1 - angle_coeff @angle:c2-n4-c3 harmonic 64.050 110.960 # SOURCE4 13 2.4632 - angle_coeff @angle:c2-n4-hn harmonic 46.094 110.370 # SOURCE3_SOURCE5 39 1.1227 - angle_coeff @angle:c3-n4-c3 harmonic 64.460 109.660 # SOURCE3_SOURCE5 2931 1.1695 - angle_coeff @angle:c3-n4-ca harmonic 64.770 110.530 # SOURCE4_SOURCE5 127 1.4968 - angle_coeff @angle:c3-n4-cc harmonic 64.438 111.040 # SOURCE4_SOURCE5 18 1.4876 - angle_coeff @angle:c3-n4-cl harmonic 71.792 108.040 # SOURCE3 3 - angle_coeff @angle:c3-n4-hn harmonic 46.193 110.110 # SOURCE3 100 1.3136 - angle_coeff @angle:c3-n4-n3 harmonic 83.568 107.700 # SOURCE3_SOURCE5 11 1.5498 - angle_coeff @angle:c3-n4-n4 harmonic 79.845 114.070 # SOURCE3 4 - angle_coeff @angle:c3-n4-n harmonic 82.738 109.740 # SOURCE4_SOURCE5 17 2.0520 - angle_coeff @angle:c3-n4-nh harmonic 81.141 111.730 # SOURCE3 1 - angle_coeff @angle:c3-n4-no harmonic 81.756 109.080 # SOURCE3 1 - angle_coeff @angle:c3-n4-o harmonic 84.145 110.520 # SOURCE3_SOURCE5 7 0.8910 - angle_coeff @angle:c3-n4-oh harmonic 82.047 113.730 # SOURCE3 1 - angle_coeff @angle:c3-n4-os harmonic 83.903 107.420 # SOURCE3 3 3.5920 - angle_coeff @angle:c3-n4-p2 harmonic 74.897 112.520 # SOURCE3 1 - angle_coeff @angle:c3-n4-p3 harmonic 77.458 110.730 # SOURCE3 3 2.1084 - angle_coeff @angle:c3-n4-p5 harmonic 78.172 113.220 # SOURCE3 3 0.4021 - angle_coeff @angle:c3-n4-s4 harmonic 58.766 108.230 # SOURCE3 3 0.4195 - angle_coeff @angle:c3-n4-s6 harmonic 59.297 111.560 # SOURCE3 3 1.8851 - angle_coeff @angle:c3-n4-s harmonic 60.776 113.550 # SOURCE3 1 - angle_coeff @angle:c3-n4-sh harmonic 60.690 115.810 # SOURCE3 1 - angle_coeff @angle:c3-n4-ss harmonic 61.231 113.680 # SOURCE3 3 1.1405 - angle_coeff @angle:ca-n4-ca harmonic 64.228 114.480 # SOURCE3 1 - angle_coeff @angle:ca-n4-hn harmonic 46.901 110.500 # SOURCE3_SOURCE5 23 1.4863 - angle_coeff @angle:c-n4-c harmonic 63.305 108.610 # SOURCE3 1 - angle_coeff @angle:c-n4-hn harmonic 44.970 111.120 # SOURCE3_SOURCE5 17 0.9627 - angle_coeff @angle:cl-n4-cl harmonic 79.101 114.910 # SOURCE3 1 - angle_coeff @angle:cl-n4-hn harmonic 48.065 108.870 # SOURCE3 7 0.7719 - angle_coeff @angle:f-n4-f harmonic 120.491 109.050 # SOURCE3 1 - angle_coeff @angle:f-n4-hn harmonic 67.122 108.390 # SOURCE3 4 - angle_coeff @angle:hn-n4-hn harmonic 40.020 108.300 # SOURCE3_SOURCE5 588 1.8224 - angle_coeff @angle:hn-n4-i harmonic 37.762 108.720 # SOURCE3 7 1.2717 - angle_coeff @angle:hn-n4-n1 harmonic 63.803 109.390 # HF/6-31G* 1 - angle_coeff @angle:hn-n4-n2 harmonic 52.071 109.680 # SOURCE3 19 0.6266 - angle_coeff @angle:hn-n4-n3 harmonic 60.801 110.400 # SOURCE3 11 0.7307 - angle_coeff @angle:hn-n4-n4 harmonic 59.235 108.660 # SOURCE3 18 1.2967 - angle_coeff @angle:hn-n4-n harmonic 61.091 109.080 # SOURCE3 13 1.6047 - angle_coeff @angle:hn-n4-na harmonic 60.973 109.090 # SOURCE3_SOURCE5 31 1.0459 - angle_coeff @angle:hn-n4-nh harmonic 59.568 109.920 # SOURCE3 12 0.7304 - angle_coeff @angle:hn-n4-no harmonic 60.590 104.380 # SOURCE3 2 - angle_coeff @angle:hn-n4-o harmonic 63.200 111.350 # SOURCE3_SOURCE5 11 1.4866 - angle_coeff @angle:hn-n4-oh harmonic 62.612 108.090 # SOURCE3 6 1.6728 - angle_coeff @angle:hn-n4-os harmonic 61.427 109.390 # SOURCE3 10 1.4403 - angle_coeff @angle:hn-n4-p2 harmonic 48.678 110.500 # SOURCE3 25 1.0664 - angle_coeff @angle:hn-n4-p3 harmonic 50.742 109.890 # SOURCE3 10 2.3870 - angle_coeff @angle:hn-n4-p4 harmonic 48.617 111.330 # SOURCE3 3 - angle_coeff @angle:hn-n4-p5 harmonic 52.339 110.000 # SOURCE3 10 1.0282 - angle_coeff @angle:hn-n4-py harmonic 48.319 117.890 # SOURCE3 8 - angle_coeff @angle:hn-n4-s4 harmonic 37.298 110.100 # SOURCE3 6 0.8471 - angle_coeff @angle:hn-n4-s harmonic 41.320 106.890 # SOURCE3 6 1.0775 - angle_coeff @angle:hn-n4-s6 harmonic 38.875 108.940 # SOURCE3 10 0.5715 - angle_coeff @angle:hn-n4-sh harmonic 41.549 108.560 # SOURCE3 6 0.8535 - angle_coeff @angle:hn-n4-ss harmonic 41.406 109.170 # SOURCE3 10 0.8455 - angle_coeff @angle:i-n4-i harmonic 64.315 118.490 # SOURCE3 1 - angle_coeff @angle:n1-n4-n1 harmonic 111.792 110.670 # HF/6-31G* 1 - angle_coeff @angle:n2-n4-n2 harmonic 91.394 108.640 # SOURCE3 1 - angle_coeff @angle:n3-n4-n3 harmonic 106.128 111.070 # SOURCE3 1 - angle_coeff @angle:n4-n4-n4 harmonic 100.290 115.490 # SOURCE3 1 - angle_coeff @angle:na-n4-na harmonic 101.917 119.600 # SOURCE3 1 - angle_coeff @angle:nh-n4-nh harmonic 104.319 109.380 # SOURCE3 1 - angle_coeff @angle:n-n4-n harmonic 102.552 118.620 # SOURCE3 1 - angle_coeff @angle:oh-n4-oh harmonic 109.836 108.190 # SOURCE3 1 - angle_coeff @angle:o-n4-o harmonic 106.848 120.970 # SOURCE3 1 - angle_coeff @angle:os-n4-os harmonic 110.159 104.400 # SOURCE3 1 - angle_coeff @angle:p2-n4-p2 harmonic 94.721 113.910 # SOURCE3 2 - angle_coeff @angle:p3-n4-p3 harmonic 94.786 121.380 # SOURCE3 1 - angle_coeff @angle:p5-n4-p5 harmonic 103.704 107.020 # SOURCE3 1 - angle_coeff @angle:py-n4-py harmonic 123.558 69.790 # SOURCE3 2 - angle_coeff @angle:s4-n4-s4 harmonic 56.264 115.430 # SOURCE3 1 - angle_coeff @angle:s6-n4-s6 harmonic 59.515 109.510 # SOURCE3 1 - angle_coeff @angle:sh-n4-sh harmonic 62.034 112.590 # SOURCE3 1 - angle_coeff @angle:s-n4-s harmonic 58.304 124.550 # SOURCE3 1 - angle_coeff @angle:ss-n4-ss harmonic 62.955 109.200 # SOURCE3 1 - angle_coeff @angle:br-na-br harmonic 61.086 123.000 # SOURCE3 1 - angle_coeff @angle:br-na-c2 harmonic 64.788 100.480 # SOURCE3 2 1.0536 - angle_coeff @angle:br-na-ca harmonic 58.177 124.810 # SOURCE3 1 - angle_coeff @angle:br-na-cc harmonic 58.230 124.620 # SOURCE3 3 0.5348 - angle_coeff @angle:br-na-cd harmonic 58.230 124.620 # SOURCE3 3 - angle_coeff @angle:br-na-nc harmonic 74.547 119.420 # SOURCE3 4 1.6703 - angle_coeff @angle:br-na-nd harmonic 74.550 119.420 # SOURCE3 4 - angle_coeff @angle:br-na-os harmonic 79.164 104.990 # SOURCE3 1 - angle_coeff @angle:br-na-p2 harmonic 78.377 121.010 # SOURCE3 1 - angle_coeff @angle:br-na-pc harmonic 78.871 120.260 # SOURCE3 3 2.1456 - angle_coeff @angle:br-na-pd harmonic 78.871 120.260 # SOURCE3 3 - angle_coeff @angle:br-na-ss harmonic 63.599 112.280 # SOURCE3 1 - angle_coeff @angle:c1-na-c1 harmonic 69.174 117.200 # SOURCE3 1 - angle_coeff @angle:c1-na-c2 harmonic 65.944 125.200 # SOURCE3 1 - angle_coeff @angle:c1-na-ca harmonic 67.645 120.570 # SOURCE3 1 - angle_coeff @angle:c1-na-cc harmonic 67.523 121.350 # SOURCE3 6 0.6517 - angle_coeff @angle:c1-na-cd harmonic 67.523 121.350 # SOURCE3 6 0.6517 - angle_coeff @angle:c1-na-nc harmonic 85.715 120.240 # SOURCE3 4 1.6849 - angle_coeff @angle:c1-na-nd harmonic 85.768 120.240 # SOURCE3 4 - angle_coeff @angle:c1-na-os harmonic 87.875 106.960 # SOURCE3 2 - angle_coeff @angle:c1-na-p2 harmonic 79.771 122.250 # SOURCE3 1 - angle_coeff @angle:c1-na-pc harmonic 80.652 121.480 # SOURCE3 3 2.1681 - angle_coeff @angle:c1-na-pd harmonic 80.652 121.480 # SOURCE3 3 - angle_coeff @angle:c1-na-ss harmonic 63.670 118.300 # SOURCE3 1 - angle_coeff @angle:c2-na-c2 harmonic 69.273 110.370 # SOURCE3 6 0.5121 - angle_coeff @angle:c2-na-c3 harmonic 65.723 117.200 # SOURCE3 2 - angle_coeff @angle:c2-na-ca harmonic 65.505 124.970 # SOURCE4_SOURCE5 19 0.9360 - angle_coeff @angle:c2-na-cc harmonic 65.181 126.550 # SOURCE3_SOURCE5 47 1.6996 - angle_coeff @angle:c2-na-cd harmonic 65.181 126.550 # SOURCE3_SOURCE5 47 1.6996 - angle_coeff @angle:c2-na-cl harmonic 73.039 101.010 # SOURCE3 2 1.5799 - angle_coeff @angle:c2-na-f harmonic 90.731 103.110 # SOURCE3 1 - angle_coeff @angle:c2-na-hn harmonic 47.660 119.280 # SOURCE3 14 6.6027 - angle_coeff @angle:c2-na-i harmonic 62.480 106.740 # SOURCE3 1 - angle_coeff @angle:c2-na-n1 harmonic 83.043 124.810 # HF/6-31G* 1 - angle_coeff @angle:c2-na-n2 harmonic 82.486 125.000 # SOURCE3 1 - angle_coeff @angle:c2-na-n3 harmonic 81.036 124.800 # SOURCE3 1 - angle_coeff @angle:c2-na-n4 harmonic 81.740 121.320 # SOURCE3 1 - angle_coeff @angle:c2-na-n harmonic 81.447 124.700 # SOURCE3 1 - angle_coeff @angle:c2-na-na harmonic 81.658 124.600 # SOURCE3 1 - angle_coeff @angle:c2-na-nc harmonic 84.246 120.800 # CORR_SOURCE5 5 1.0225 - angle_coeff @angle:c2-na-nd harmonic 84.294 120.800 # CORR_SOURCE5 5 1.0225 - angle_coeff @angle:c2-na-nh harmonic 81.563 124.980 # SOURCE3 1 - angle_coeff @angle:c2-na-no harmonic 80.798 124.200 # SOURCE3 1 - angle_coeff @angle:c2-na-o harmonic 85.559 125.900 # SOURCE3 1 - angle_coeff @angle:c2-na-oh harmonic 82.136 123.900 # SOURCE3 1 - angle_coeff @angle:c2-na-os harmonic 85.429 110.330 # SOURCE3 4 3.2172 - angle_coeff @angle:c2-na-p2 harmonic 79.329 122.140 # SOURCE3 1 - angle_coeff @angle:c2-na-p3 harmonic 77.626 126.100 # SOURCE3 1 - angle_coeff @angle:c2-na-p4 harmonic 84.849 125.000 # SOURCE3 1 - angle_coeff @angle:c2-na-p5 harmonic 79.565 125.100 # SOURCE3 1 - angle_coeff @angle:c2-na-pc harmonic 80.116 121.560 # SOURCE3 3 1.6252 - angle_coeff @angle:c2-na-pd harmonic 80.116 121.560 # SOURCE3 3 - angle_coeff @angle:c2-na-s4 harmonic 59.943 124.900 # SOURCE3 1 - angle_coeff @angle:c2-na-s6 harmonic 61.964 124.400 # SOURCE3 1 - angle_coeff @angle:c2-na-s harmonic 60.479 125.800 # SOURCE3 1 - angle_coeff @angle:c2-na-sh harmonic 61.837 125.100 # SOURCE3 1 - angle_coeff @angle:c2-na-ss harmonic 64.023 115.530 # SOURCE3 5 1.4036 - angle_coeff @angle:c3-na-c3 harmonic 62.214 125.590 # SOURCE3 1 - angle_coeff @angle:c3-na-ca harmonic 64.155 124.360 # SOURCE3 5 4.2557 - angle_coeff @angle:c3-na-cc harmonic 63.695 126.460 # SOURCE3_SOURCE5 2025 1.8293 - angle_coeff @angle:c3-na-cd harmonic 63.695 126.460 # SOURCE3_SOURCE5 2025 1.8293 - angle_coeff @angle:c3-na-cp harmonic 65.414 119.620 # SOURCE4_SOURCE5 17 0.4924 - angle_coeff @angle:c3-na-n2 harmonic 82.460 119.240 # SOURCE4_SOURCE5 15 0.8410 - angle_coeff @angle:c3-na-n harmonic 83.711 112.880 # SOURCE4_SOURCE5 34 0.6363 - angle_coeff @angle:c3-na-nc harmonic 82.430 120.180 # SOURCE3_SOURCE5 266 0.9487 - angle_coeff @angle:c3-na-nd harmonic 82.472 120.180 # SOURCE3_SOURCE5 266 0.9487 - angle_coeff @angle:c3-na-os harmonic 86.002 104.390 # SOURCE3 3 1.2017 - angle_coeff @angle:c3-na-p2 harmonic 78.161 123.120 # SOURCE3 1 - angle_coeff @angle:c3-na-pc harmonic 79.034 122.110 # SOURCE3 3 2.8504 - angle_coeff @angle:c3-na-pd harmonic 79.034 122.110 # SOURCE3 3 - angle_coeff @angle:c3-na-sh harmonic 65.096 110.280 # SOURCE3 1 - angle_coeff @angle:c3-na-ss harmonic 64.618 110.870 # SOURCE3 3 0.8260 - angle_coeff @angle:ca-na-ca harmonic 67.261 120.050 # SOURCE4_SOURCE5 899 1.7177 - angle_coeff @angle:ca-na-cc harmonic 69.377 113.150 # SOURCE3 18 9.8644 - angle_coeff @angle:ca-na-cd harmonic 69.377 113.150 # SOURCE3 18 9.8644 - angle_coeff @angle:ca-na-cl harmonic 65.846 124.790 # SOURCE3 1 - angle_coeff @angle:ca-na-cp harmonic 67.035 120.860 # SOURCE4_SOURCE5 58 1.3836 - angle_coeff @angle:ca-na-cx harmonic 64.141 124.590 # SOURCE4_SOURCE5 51 1.7589 - angle_coeff @angle:ca-na-f harmonic 85.915 116.400 # SOURCE3 1 - angle_coeff @angle:ca-na-hn harmonic 46.979 125.540 # SOURCE4_SOURCE5 1396 1.1217 - angle_coeff @angle:ca-na-i harmonic 58.530 121.620 # SOURCE3 1 - angle_coeff @angle:ca-na-n2 harmonic 85.072 119.070 # SOURCE4_SOURCE5 19 2.0667 - angle_coeff @angle:ca-na-n4 harmonic 82.602 120.190 # SOURCE3 1 - angle_coeff @angle:ca-na-n harmonic 82.849 122.000 # SOURCE3 1 - angle_coeff @angle:ca-na-na harmonic 82.443 123.760 # SOURCE3 1 - angle_coeff @angle:ca-na-nb harmonic 84.426 122.640 # SOURCE4_SOURCE5 30 1.1363 - angle_coeff @angle:ca-na-nc harmonic 85.867 117.850 # SOURCE3 6 3.6536 - angle_coeff @angle:ca-na-nd harmonic 85.918 117.850 # SOURCE3 6 - angle_coeff @angle:ca-na-nh harmonic 82.258 124.410 # SOURCE4_SOURCE5 15 1.3695 - angle_coeff @angle:ca-na-o harmonic 88.288 120.170 # SOURCE4_SOURCE5 161 1.3927 - angle_coeff @angle:ca-na-oh harmonic 83.969 120.050 # SOURCE3_SOURCE5 6 2.2969 - angle_coeff @angle:ca-na-os harmonic 86.259 109.460 # SOURCE3 1 - angle_coeff @angle:ca-na-p2 harmonic 78.367 125.850 # SOURCE3 1 - angle_coeff @angle:ca-na-p3 harmonic 78.367 124.380 # SOURCE3 1 - angle_coeff @angle:ca-na-p4 harmonic 85.239 124.970 # SOURCE3 1 - angle_coeff @angle:ca-na-p5 harmonic 80.389 123.300 # SOURCE3 1 - angle_coeff @angle:ca-na-pc harmonic 80.162 122.130 # SOURCE3 3 2.2393 - angle_coeff @angle:ca-na-pd harmonic 80.162 122.130 # SOURCE3 3 - angle_coeff @angle:ca-na-py harmonic 75.307 140.880 # SOURCE3 2 - angle_coeff @angle:ca-na-s4 harmonic 62.021 117.230 # SOURCE3 1 - angle_coeff @angle:ca-na-s6 harmonic 63.097 120.690 # SOURCE3 1 - angle_coeff @angle:ca-na-s harmonic 60.676 125.640 # SOURCE3 1 - angle_coeff @angle:ca-na-sh harmonic 61.938 125.440 # SOURCE3 1 - angle_coeff @angle:ca-na-ss harmonic 60.549 129.920 # SOURCE4_SOURCE5 17 0.1432 - angle_coeff @angle:cc-na-cc harmonic 70.492 109.900 # SOURCE3 109 1.5547 - angle_coeff @angle:cc-na-cd harmonic 65.316 128.010 # SOURCE3 1 - angle_coeff @angle:cc-na-ce harmonic 64.694 126.610 # SOURCE4_SOURCE5 16 0.5158 - angle_coeff @angle:cc-na-cl harmonic 65.922 124.610 # SOURCE3 3 0.5208 - angle_coeff @angle:cc-na-f harmonic 85.431 118.030 # SOURCE3 4 0.3081 - angle_coeff @angle:cc-na-hn harmonic 47.101 125.500 # CORR_SOURCE5 1758 1.2247 - angle_coeff @angle:cc-na-i harmonic 57.570 125.700 # SOURCE3 6 0.7821 - angle_coeff @angle:cc-na-n2 harmonic 84.478 121.090 # SOURCE3_SOURCE5 21 1.2340 - angle_coeff @angle:cc-na-n4 harmonic 82.458 120.910 # SOURCE3_SOURCE5 16 2.5151 - angle_coeff @angle:cc-na-n harmonic 87.346 110.050 # SOURCE3_SOURCE5 63 1.0193 - angle_coeff @angle:cc-na-na harmonic 84.774 117.360 # SOURCE3_SOURCE5 38 0.6452 - angle_coeff @angle:cc-na-nc harmonic 88.067 112.360 # SOURCE3_SOURCE5 209 2.0210 - angle_coeff @angle:cc-na-nd harmonic 83.137 126.230 # CORR_SOURCE5 157 1.3576 - angle_coeff @angle:cc-na-nh harmonic 82.640 123.590 # SOURCE3_SOURCE5 33 0.7437 - angle_coeff @angle:cc-na-no harmonic 81.621 123.440 # SOURCE3_SOURCE5 15 0.5273 - angle_coeff @angle:cc-na-o harmonic 86.644 125.210 # SOURCE3 10 0.0124 - angle_coeff @angle:cc-na-oh harmonic 83.278 122.380 # SOURCE3 10 0.1570 - angle_coeff @angle:cc-na-os harmonic 83.586 116.860 # CORR 48 - angle_coeff @angle:cc-na-p2 harmonic 78.409 125.860 # SOURCE3 14 2.2993 - angle_coeff @angle:cc-na-p3 harmonic 78.138 125.250 # SOURCE3 8 0.1998 - angle_coeff @angle:cc-na-p4 harmonic 84.394 127.730 # SOURCE3 7 3.6077 - angle_coeff @angle:cc-na-p5 harmonic 79.988 124.700 # SOURCE3 13 1.4225 - angle_coeff @angle:cc-na-s4 harmonic 61.070 121.030 # SOURCE3 10 0.5589 - angle_coeff @angle:cc-na-s6 harmonic 62.402 123.550 # SOURCE3_SOURCE5 18 0.8360 - angle_coeff @angle:cc-na-s harmonic 60.705 125.660 # SOURCE3 8 0.1880 - angle_coeff @angle:cc-na-sh harmonic 62.346 123.960 # SOURCE3 10 0.3424 - angle_coeff @angle:cc-na-ss harmonic 62.745 121.130 # CORR_SOURCE5 13 0.6360 - angle_coeff @angle:cd-na-cd harmonic 70.492 109.900 # SOURCE3 109 1.5547 - angle_coeff @angle:cd-na-cl harmonic 65.922 124.610 # SOURCE3 3 - angle_coeff @angle:cd-na-f harmonic 85.431 118.030 # SOURCE3 4 0.3081 - angle_coeff @angle:cd-na-hn harmonic 47.101 125.500 # CORR_SOURCE5 1758 1.2247 - angle_coeff @angle:cd-na-i harmonic 57.570 125.700 # SOURCE3 6 0.7821 - angle_coeff @angle:cd-na-n2 harmonic 84.478 121.090 # SOURCE3_SOURCE5 21 1.2340 - angle_coeff @angle:cd-na-n4 harmonic 82.458 120.910 # SOURCE3_SOURCE5 16 2.5151 - angle_coeff @angle:cd-na-n harmonic 87.346 110.050 # SOURCE3_SOURCE5 63 1.0193 - angle_coeff @angle:cd-na-na harmonic 84.774 117.360 # SOURCE3_SOURCE5 38 0.6452 - angle_coeff @angle:cd-na-nc harmonic 83.088 126.230 # CORR_SOURCE5 157 1.3576 - angle_coeff @angle:cd-na-nd harmonic 88.120 112.360 # SOURCE3_SOURCE5 209 2.0210 - angle_coeff @angle:cd-na-nh harmonic 82.624 123.640 # SOURCE3_SOURCE5 34 0.8283 - angle_coeff @angle:cd-na-no harmonic 81.621 123.440 # SOURCE3_SOURCE5 15 0.5273 - angle_coeff @angle:cd-na-o harmonic 86.644 125.210 # SOURCE3 10 0.0124 - angle_coeff @angle:cd-na-oh harmonic 83.278 122.380 # SOURCE3 10 0.1570 - angle_coeff @angle:cd-na-os harmonic 83.586 116.860 # CORR 48 - angle_coeff @angle:cd-na-p2 harmonic 78.409 125.860 # SOURCE3 14 2.2993 - angle_coeff @angle:cd-na-p3 harmonic 78.138 125.250 # SOURCE3 8 0.1998 - angle_coeff @angle:cd-na-p4 harmonic 84.394 127.730 # SOURCE3 7 - angle_coeff @angle:cd-na-p5 harmonic 79.988 124.700 # SOURCE3 13 1.4225 - angle_coeff @angle:cd-na-s4 harmonic 61.070 121.030 # SOURCE3 10 0.5589 - angle_coeff @angle:cd-na-s6 harmonic 62.402 123.550 # SOURCE3_SOURCE5 18 0.8360 - angle_coeff @angle:cd-na-s harmonic 60.705 125.660 # SOURCE3 8 0.1880 - angle_coeff @angle:cd-na-sh harmonic 62.346 123.960 # SOURCE3 10 0.3424 - angle_coeff @angle:cd-na-ss harmonic 62.745 121.130 # CORR_SOURCE5 13 0.6360 - angle_coeff @angle:cl-na-cl harmonic 73.099 122.800 # SOURCE3 1 - angle_coeff @angle:cl-na-nc harmonic 84.560 119.360 # SOURCE3 4 1.7128 - angle_coeff @angle:cl-na-nd harmonic 84.574 119.360 # SOURCE3 4 - angle_coeff @angle:cl-na-os harmonic 88.543 106.580 # SOURCE3 1 - angle_coeff @angle:cl-na-p2 harmonic 86.459 121.290 # SOURCE3 1 - angle_coeff @angle:cl-na-pc harmonic 87.107 120.510 # SOURCE3 3 2.1985 - angle_coeff @angle:cl-na-pd harmonic 87.107 120.510 # SOURCE3 3 - angle_coeff @angle:cl-na-ss harmonic 70.427 111.910 # SOURCE3 1 - angle_coeff @angle:f-na-f harmonic 106.388 120.200 # SOURCE3 1 - angle_coeff @angle:f-na-nc harmonic 107.856 118.050 # SOURCE3 4 1.7931 - angle_coeff @angle:f-na-nd harmonic 107.917 118.050 # SOURCE3 4 - angle_coeff @angle:f-na-os harmonic 111.494 103.860 # SOURCE3 1 - angle_coeff @angle:f-na-p2 harmonic 101.527 119.950 # SOURCE3 1 - angle_coeff @angle:f-na-pc harmonic 102.647 119.100 # SOURCE3 3 2.3967 - angle_coeff @angle:f-na-pd harmonic 102.647 119.100 # SOURCE3 3 - angle_coeff @angle:f-na-ss harmonic 83.972 108.010 # SOURCE3 1 - angle_coeff @angle:hn-na-hn harmonic 39.315 116.800 # SOURCE3 1 - angle_coeff @angle:hn-na-n harmonic 61.525 111.440 # SOURCE4_SOURCE5 14 1.2883 - angle_coeff @angle:hn-na-nc harmonic 61.377 119.550 # SOURCE3_SOURCE5 196 1.0024 - angle_coeff @angle:hn-na-nd harmonic 61.443 119.550 # SOURCE3_SOURCE5 196 1.0024 - angle_coeff @angle:hn-na-os harmonic 62.765 102.120 # SOURCE3_SOURCE5 20 2.5614 - angle_coeff @angle:hn-na-p2 harmonic 52.077 122.520 # SOURCE3 1 - angle_coeff @angle:hn-na-pc harmonic 52.878 121.480 # SOURCE3 3 2.9355 - angle_coeff @angle:hn-na-pd harmonic 52.878 121.480 # SOURCE3 3 - angle_coeff @angle:hn-na-ss harmonic 42.530 113.950 # SOURCE3 1 - angle_coeff @angle:i-na-i harmonic 63.587 124.200 # SOURCE3 1 - angle_coeff @angle:i-na-nc harmonic 73.745 120.030 # SOURCE3 4 2.0032 - angle_coeff @angle:i-na-nd harmonic 73.742 120.030 # SOURCE3 4 - angle_coeff @angle:i-na-os harmonic 77.062 109.910 # SOURCE3 1 - angle_coeff @angle:i-na-p2 harmonic 78.740 122.280 # SOURCE3 1 - angle_coeff @angle:i-na-pc harmonic 79.219 121.400 # SOURCE3 3 2.4763 - angle_coeff @angle:i-na-pd harmonic 79.219 121.400 # SOURCE3 3 - angle_coeff @angle:i-na-ss harmonic 62.502 118.400 # SOURCE3 1 - angle_coeff @angle:n2-na-n2 harmonic 108.256 116.710 # SOURCE3 1 - angle_coeff @angle:n2-na-nc harmonic 107.238 119.960 # SOURCE3 4 4.5041 - angle_coeff @angle:n2-na-nd harmonic 107.304 119.960 # SOURCE3 4 - angle_coeff @angle:n2-na-os harmonic 107.573 111.530 # SOURCE3 1 - angle_coeff @angle:n2-na-p2 harmonic 98.756 124.880 # SOURCE3 1 - angle_coeff @angle:n2-na-pc harmonic 100.212 123.180 # SOURCE3 3 4.7947 - angle_coeff @angle:n2-na-pd harmonic 100.212 123.180 # SOURCE3 3 - angle_coeff @angle:n2-na-ss harmonic 77.611 124.640 # SOURCE3 1 - angle_coeff @angle:n3-na-n3 harmonic 101.150 124.000 # SOURCE3 1 - angle_coeff @angle:n4-na-n4 harmonic 105.460 111.700 # SOURCE3 1 - angle_coeff @angle:n4-na-nc harmonic 106.051 116.440 # SOURCE3 4 3.6604 - angle_coeff @angle:n4-na-nd harmonic 106.108 116.440 # SOURCE3 4 - angle_coeff @angle:n4-na-os harmonic 109.494 102.970 # SOURCE3 1 - angle_coeff @angle:n4-na-p2 harmonic 98.207 123.560 # SOURCE3 1 - angle_coeff @angle:n4-na-pc harmonic 99.557 121.980 # SOURCE3 3 4.4884 - angle_coeff @angle:n4-na-pd harmonic 99.557 121.980 # SOURCE3 3 - angle_coeff @angle:na-na-na harmonic 102.688 123.600 # SOURCE3 1 - angle_coeff @angle:na-na-nc harmonic 106.027 119.640 # SOURCE3 4 1.6920 - angle_coeff @angle:na-na-nd harmonic 106.088 119.640 # SOURCE3 4 - angle_coeff @angle:na-na-os harmonic 107.416 109.470 # SOURCE3 1 - angle_coeff @angle:na-na-p2 harmonic 99.520 121.720 # SOURCE3 1 - angle_coeff @angle:na-na-pc harmonic 100.604 120.910 # SOURCE3 3 2.3033 - angle_coeff @angle:na-na-pd harmonic 100.604 120.910 # SOURCE3 3 - angle_coeff @angle:na-na-ss harmonic 79.845 116.500 # SOURCE3 1 - angle_coeff @angle:nc-na-nc harmonic 109.391 116.300 # SOURCE3_SOURCE5 57 1.3191 - angle_coeff @angle:nc-na-nd harmonic 106.540 122.760 # SOURCE4_SOURCE5 12 0.1496 - angle_coeff @angle:nc-na-nh harmonic 105.667 120.550 # SOURCE3 8 1.1436 - angle_coeff @angle:nc-na-no harmonic 104.829 119.210 # SOURCE3_SOURCE5 9 1.2751 - angle_coeff @angle:nc-na-o harmonic 110.789 122.790 # SOURCE3 6 1.3154 - angle_coeff @angle:nc-na-oh harmonic 106.562 119.220 # SOURCE3 4 1.7201 - angle_coeff @angle:nc-na-os harmonic 104.244 119.650 # SOURCE3 4 1.5019 - angle_coeff @angle:nc-na-p2 harmonic 100.917 119.990 # SOURCE3 4 3.6009 - angle_coeff @angle:nc-na-p3 harmonic 100.275 120.070 # SOURCE3 4 3.7188 - angle_coeff @angle:nc-na-p4 harmonic 109.789 119.770 # SOURCE3 3 0.3747 - angle_coeff @angle:nc-na-p5 harmonic 102.963 118.950 # SOURCE3 4 3.1194 - angle_coeff @angle:nc-na-pc harmonic 102.284 118.660 # SOURCE3 27 1.5082 - angle_coeff @angle:nc-na-s4 harmonic 77.292 119.200 # SOURCE3 4 2.3841 - angle_coeff @angle:nc-na-s6 harmonic 79.850 119.240 # SOURCE3 4 2.2262 - angle_coeff @angle:nc-na-s harmonic 77.325 122.260 # SOURCE3 4 0.9173 - angle_coeff @angle:nc-na-sh harmonic 79.494 120.500 # SOURCE3 4 1.5016 - angle_coeff @angle:nc-na-ss harmonic 79.073 120.500 # SOURCE3 4 1.5615 - angle_coeff @angle:nd-na-nd harmonic 109.528 116.300 # SOURCE3_SOURCE5 57 1.3191 - angle_coeff @angle:nd-na-nh harmonic 105.728 120.550 # SOURCE3 8 - angle_coeff @angle:nd-na-no harmonic 104.885 119.210 # SOURCE3_SOURCE5 5 1.0113 - angle_coeff @angle:nd-na-o harmonic 110.874 122.790 # SOURCE3 6 - angle_coeff @angle:nd-na-oh harmonic 106.624 119.220 # SOURCE3 4 - angle_coeff @angle:nd-na-os harmonic 104.299 119.650 # SOURCE3 4 - angle_coeff @angle:nd-na-p2 harmonic 100.941 119.990 # SOURCE3 4 - angle_coeff @angle:nd-na-p3 harmonic 100.297 120.070 # SOURCE3 4 - angle_coeff @angle:nd-na-p4 harmonic 109.833 119.770 # SOURCE3 3 - angle_coeff @angle:nd-na-p5 harmonic 102.991 118.950 # SOURCE3 4 - angle_coeff @angle:nd-na-pd harmonic 102.309 118.660 # SOURCE3 27 - angle_coeff @angle:nd-na-s4 harmonic 77.307 119.200 # SOURCE3 4 - angle_coeff @angle:nd-na-s6 harmonic 79.870 119.240 # SOURCE3 4 - angle_coeff @angle:nd-na-s harmonic 77.342 122.260 # SOURCE3 4 - angle_coeff @angle:nd-na-sh harmonic 79.514 120.500 # SOURCE3 4 - angle_coeff @angle:nd-na-ss harmonic 79.092 120.500 # SOURCE3 4 - angle_coeff @angle:nh-na-nh harmonic 102.761 123.600 # SOURCE3 1 - angle_coeff @angle:nh-na-os harmonic 106.530 111.370 # SOURCE3 1 - angle_coeff @angle:nh-na-p2 harmonic 99.889 120.860 # SOURCE3 1 - angle_coeff @angle:nh-na-pc harmonic 100.842 120.380 # SOURCE3 6 1.3513 - angle_coeff @angle:nh-na-pd harmonic 100.842 120.380 # SOURCE3 6 - angle_coeff @angle:nh-na-ss harmonic 81.320 112.350 # SOURCE3 2 5.2951 - angle_coeff @angle:n-na-n harmonic 102.160 123.800 # SOURCE3 1 - angle_coeff @angle:n-na-nc harmonic 105.685 119.850 # SOURCE3 4 1.6156 - angle_coeff @angle:n-na-nd harmonic 105.745 119.850 # SOURCE3 4 - angle_coeff @angle:no-na-no harmonic 100.609 122.800 # SOURCE3 1 - angle_coeff @angle:no-na-os harmonic 107.653 106.550 # SOURCE3 1 - angle_coeff @angle:no-na-pc harmonic 100.336 120.110 # SOURCE3 3 2.0821 - angle_coeff @angle:no-na-pd harmonic 100.336 120.110 # SOURCE3 3 - angle_coeff @angle:n-na-os harmonic 109.608 104.710 # SOURCE3 1 - angle_coeff @angle:no-na-ss harmonic 79.903 114.950 # SOURCE3 1 - angle_coeff @angle:n-na-p2 harmonic 99.572 121.350 # SOURCE3 1 - angle_coeff @angle:n-na-pc harmonic 100.611 120.640 # SOURCE3 3 2.0168 - angle_coeff @angle:n-na-pd harmonic 100.611 120.640 # SOURCE3 3 - angle_coeff @angle:n-na-ss harmonic 79.899 116.100 # SOURCE3 1 - angle_coeff @angle:oh-na-oh harmonic 103.905 122.200 # SOURCE3 1 - angle_coeff @angle:oh-na-p2 harmonic 100.050 120.760 # SOURCE3 1 - angle_coeff @angle:oh-na-pc harmonic 101.133 119.990 # SOURCE3 3 2.1734 - angle_coeff @angle:oh-na-pd harmonic 101.133 119.990 # SOURCE3 3 - angle_coeff @angle:oh-na-ss harmonic 81.173 113.040 # SOURCE3 1 - angle_coeff @angle:o-na-o harmonic 114.875 126.200 # SOURCE3 1 - angle_coeff @angle:o-na-os harmonic 108.116 118.780 # SOURCE3_SOURCE5 6 0.4047 - angle_coeff @angle:o-na-p2 harmonic 100.973 122.800 # SOURCE3 1 - angle_coeff @angle:o-na-pc harmonic 102.067 122.340 # SOURCE3 3 1.2908 - angle_coeff @angle:o-na-pd harmonic 102.067 122.340 # SOURCE3 3 - angle_coeff @angle:os-na-os harmonic 108.379 104.450 # SOURCE3 2 0.0983 - angle_coeff @angle:os-na-p2 harmonic 100.391 117.860 # SOURCE3 1 - angle_coeff @angle:os-na-p3 harmonic 105.930 104.700 # SOURCE3 1 - angle_coeff @angle:os-na-p5 harmonic 104.736 111.410 # SOURCE3 1 - angle_coeff @angle:os-na-pc harmonic 100.242 119.910 # SOURCE3 3 1.9002 - angle_coeff @angle:os-na-pd harmonic 100.242 119.910 # SOURCE3 3 - angle_coeff @angle:os-na-s4 harmonic 81.006 105.880 # SOURCE3 2 - angle_coeff @angle:os-na-s6 harmonic 81.137 112.000 # SOURCE3 2 - angle_coeff @angle:os-na-ss harmonic 81.670 109.640 # SOURCE3 3 4.1395 - angle_coeff @angle:p2-na-p2 harmonic 102.084 120.910 # SOURCE3 1 - angle_coeff @angle:p2-na-p3 harmonic 100.105 124.800 # SOURCE3 1 - angle_coeff @angle:p2-na-p5 harmonic 101.778 123.990 # SOURCE3 1 - angle_coeff @angle:p2-na-pc harmonic 102.658 120.720 # SOURCE3 3 0.2407 - angle_coeff @angle:p2-na-pd harmonic 102.658 120.720 # SOURCE3 3 - angle_coeff @angle:p2-na-s4 harmonic 78.032 122.470 # SOURCE3 1 - angle_coeff @angle:p2-na-s6 harmonic 79.617 122.500 # SOURCE3 1 - angle_coeff @angle:p2-na-s harmonic 78.874 121.850 # SOURCE3 1 - angle_coeff @angle:p2-na-sh harmonic 79.900 121.750 # SOURCE3 1 - angle_coeff @angle:p2-na-ss harmonic 79.600 121.880 # SOURCE3 1 - angle_coeff @angle:p3-na-p3 harmonic 99.027 126.600 # SOURCE3 1 - angle_coeff @angle:p3-na-pc harmonic 101.182 123.320 # SOURCE3 3 4.1781 - angle_coeff @angle:p3-na-pd harmonic 101.182 123.320 # SOURCE3 3 - angle_coeff @angle:p5-na-p5 harmonic 102.554 124.600 # SOURCE3 1 - angle_coeff @angle:p5-na-pc harmonic 102.835 122.690 # SOURCE3 3 3.6738 - angle_coeff @angle:p5-na-pd harmonic 102.835 122.690 # SOURCE3 3 - angle_coeff @angle:p5-na-ss harmonic 81.516 118.520 # SOURCE3 1 - angle_coeff @angle:pc-na-pc harmonic 103.141 120.780 # SOURCE3 27 1.6457 - angle_coeff @angle:pc-na-s4 harmonic 78.694 121.510 # SOURCE3 3 2.7242 - angle_coeff @angle:pc-na-s6 harmonic 80.329 121.550 # SOURCE3 3 2.7065 - angle_coeff @angle:pc-na-s harmonic 79.371 121.470 # SOURCE3 3 1.0668 - angle_coeff @angle:pc-na-sh harmonic 80.524 121.080 # SOURCE3 3 1.8942 - angle_coeff @angle:pc-na-ss harmonic 80.219 121.200 # SOURCE3 3 1.9295 - angle_coeff @angle:pd-na-pd harmonic 103.141 120.780 # SOURCE3 27 - angle_coeff @angle:pd-na-s4 harmonic 78.694 121.510 # SOURCE3 3 - angle_coeff @angle:pd-na-s6 harmonic 80.329 121.550 # SOURCE3 3 - angle_coeff @angle:pd-na-s harmonic 79.371 121.470 # SOURCE3 3 - angle_coeff @angle:pd-na-sh harmonic 80.524 121.080 # SOURCE3 3 - angle_coeff @angle:pd-na-ss harmonic 80.219 121.200 # SOURCE3 3 - angle_coeff @angle:py-na-py harmonic 129.638 78.250 # SOURCE3 1 - angle_coeff @angle:s4-na-s4 harmonic 59.656 124.200 # SOURCE3 1 - angle_coeff @angle:s4-na-s6 harmonic 63.782 112.860 # SOURCE3 1 - angle_coeff @angle:s4-na-ss harmonic 63.885 111.920 # SOURCE3 1 - angle_coeff @angle:s6-na-s6 harmonic 62.342 123.200 # SOURCE3 1 - angle_coeff @angle:s6-na-ss harmonic 63.225 119.100 # SOURCE3 1 - angle_coeff @angle:sh-na-sh harmonic 62.052 124.600 # SOURCE3 1 - angle_coeff @angle:sh-na-ss harmonic 63.339 118.790 # SOURCE3 1 - angle_coeff @angle:s-na-s harmonic 60.168 126.000 # SOURCE3 1 - angle_coeff @angle:s-na-ss harmonic 64.260 112.490 # SOURCE3 1 - angle_coeff @angle:ss-na-ss harmonic 64.658 113.240 # SOURCE3 2 6.6084 - angle_coeff @angle:sy-na-sy harmonic 62.187 123.200 # SOURCE3 1 - angle_coeff @angle:ca-nb-ca harmonic 70.356 117.220 # SOURCE3_SOURCE5 3343 1.0306 - angle_coeff @angle:ca-nb-cp harmonic 70.116 118.050 # SOURCE4_SOURCE5 160 0.7542 - angle_coeff @angle:ca-nb-cq harmonic 70.116 118.050 # SOURCE4_SOURCE5 102 0.7384 - angle_coeff @angle:ca-nb-nb harmonic 87.237 120.050 # SOURCE3_SOURCE5 159 0.6095 - angle_coeff @angle:cp-nb-nb harmonic 86.918 120.960 # SOURCE4_SOURCE5 32 0.5601 - angle_coeff @angle:nb-nb-nb harmonic 109.020 121.040 # SOURCE3 1 - angle_coeff @angle:br-n-br harmonic 67.176 116.200 # SOURCE3 1 - angle_coeff @angle:br-n-c harmonic 62.729 121.250 # SOURCE3_SOURCE5 10 1.6266 - angle_coeff @angle:br-n-ca harmonic 63.323 118.190 # SOURCE3 1 - angle_coeff @angle:br-n-cc harmonic 63.525 118.190 # SOURCE3 1 - angle_coeff @angle:br-n-cd harmonic 63.525 118.190 # SOURCE3 1 - angle_coeff @angle:c1-n-c1 harmonic 75.677 102.690 # SOURCE3 1 - angle_coeff @angle:c1-n-ca harmonic 68.108 118.880 # SOURCE3 1 - angle_coeff @angle:c1-n-cc harmonic 68.972 118.880 # SOURCE3 1 - angle_coeff @angle:c1-n-cd harmonic 68.972 118.880 # SOURCE3 1 - angle_coeff @angle:c2-n-c2 harmonic 67.455 116.750 # SOURCE3 1 - angle_coeff @angle:c2-n-c3 harmonic 64.992 120.100 # SOURCE4_SOURCE5 62 2.3796 - angle_coeff @angle:c2-n-ca harmonic 67.208 116.540 # SOURCE3 1 - angle_coeff @angle:c2-n-cc harmonic 67.963 116.540 # SOURCE3 1 - angle_coeff @angle:c2-n-cd harmonic 67.963 116.540 # SOURCE3 1 - angle_coeff @angle:c2-n-hn harmonic 47.988 117.900 # SOURCE4_SOURCE5 115 1.4688 - angle_coeff @angle:c3-n-c3 harmonic 64.880 115.640 # SOURCE4_SOURCE5 1017 2.0256 - angle_coeff @angle:c3-n-ca harmonic 64.801 119.830 # SOURCE4_SOURCE5 448 1.9961 - angle_coeff @angle:c3-n-cc harmonic 65.172 120.850 # CORR_SOURCE5 523 1.4176 - angle_coeff @angle:c3-n-cd harmonic 65.172 120.850 # CORR_SOURCE5 523 1.4176 - angle_coeff @angle:c3-n-cy harmonic 64.307 117.080 # SOURCE4_SOURCE5 120 1.3701 - angle_coeff @angle:c3-n-hn harmonic 46.147 117.680 # SOURCE3_SOURCE5 1934 1.5065 - angle_coeff @angle:c3-n-n2 harmonic 81.830 121.710 # SOURCE4_SOURCE5 131 1.2251 - angle_coeff @angle:c3-n-n harmonic 82.901 115.390 # SOURCE4_SOURCE5 28 1.0963 - angle_coeff @angle:c3-n-nc harmonic 84.094 115.280 # CORR_SOURCE5 61 0.8561 - angle_coeff @angle:c3-n-nd harmonic 84.094 115.280 # CORR_SOURCE5 61 0.8561 - angle_coeff @angle:c3-n-oh harmonic 83.734 112.970 # SOURCE4_SOURCE5 82 0.8203 - angle_coeff @angle:c3-n-os harmonic 83.821 112.540 # SOURCE4_SOURCE5 42 1.7642 - angle_coeff @angle:c3-n-sy harmonic 62.308 120.880 # SOURCE4_SOURCE5 13 1.1569 - angle_coeff @angle:ca-n-ca harmonic 66.671 117.370 # SOURCE4_SOURCE5 99 1.5139 - angle_coeff @angle:ca-n-cc harmonic 68.390 114.010 # CORR_SOURCE5 53 1.0051 - angle_coeff @angle:ca-n-cd harmonic 68.390 114.010 # CORR_SOURCE5 53 1.0051 - angle_coeff @angle:ca-n-cl harmonic 71.199 117.720 # SOURCE3 1 - angle_coeff @angle:ca-n-f harmonic 86.043 114.920 # SOURCE3 1 - angle_coeff @angle:ca-n-hn harmonic 47.989 116.000 # SOURCE4_SOURCE5 1451 1.8612 - angle_coeff @angle:ca-n-i harmonic 59.954 119.300 # SOURCE3 1 - angle_coeff @angle:ca-n-n2 harmonic 83.352 122.020 # SOURCE4_SOURCE5 12 0.9977 - angle_coeff @angle:ca-n-n4 harmonic 80.984 122.980 # SOURCE3 1 - angle_coeff @angle:ca-n-n harmonic 83.301 118.550 # SOURCE4_SOURCE5 46 0.3283 - angle_coeff @angle:ca-n-na harmonic 82.957 119.300 # SOURCE4_SOURCE5 47 0.3131 - angle_coeff @angle:ca-n-nc harmonic 85.318 116.500 # CORR_SOURCE5 14 1.6910 - angle_coeff @angle:ca-n-nd harmonic 85.318 116.500 # CORR_SOURCE5 14 1.6910 - angle_coeff @angle:ca-n-nh harmonic 84.129 116.450 # SOURCE3 1 - angle_coeff @angle:ca-n-p2 harmonic 83.158 112.320 # SOURCE3 1 - angle_coeff @angle:ca-n-p3 harmonic 77.529 125.110 # SOURCE3 1 - angle_coeff @angle:ca-n-s4 harmonic 62.152 118.400 # SOURCE3 1 - angle_coeff @angle:ca-n-s6 harmonic 63.800 117.320 # SOURCE3 1 - angle_coeff @angle:ca-n-ss harmonic 63.794 116.600 # SOURCE3 1 - angle_coeff @angle:c-n-c1 harmonic 69.561 117.040 # SOURCE3 1 - angle_coeff @angle:c-n-c2 harmonic 66.426 122.150 # SOURCE3 9 5.1016 - angle_coeff @angle:c-n-c3 harmonic 65.252 120.690 # SOURCE3_SOURCE5 4556 2.1510 - angle_coeff @angle:c3-nc-cd harmonic 69.940 109.510 # SOURCE3 9 5.4142 - angle_coeff @angle:c-n-c harmonic 65.616 127.080 # SOURCE4_SOURCE5 1415 2.1363 - angle_coeff @angle:c-n-ca harmonic 65.694 123.710 # SOURCE3 10 3.8159 - angle_coeff @angle:ca-nc-ca harmonic 71.962 109.950 # SOURCE3 1 - angle_coeff @angle:ca-nc-cd harmonic 74.608 104.880 # CORR_SOURCE5 766 1.8814 - angle_coeff @angle:ca-nc-n harmonic 92.070 104.690 # CORR 2 - angle_coeff @angle:ca-nc-na harmonic 93.072 102.760 # CORR_SOURCE5 25 0.7558 - angle_coeff @angle:ca-nc-os harmonic 90.719 104.480 # CORR_SOURCE5 16 0.1832 - angle_coeff @angle:ca-nc-ss harmonic 70.369 107.070 # SOURCE3_SOURCE5 17 0.3771 - angle_coeff @angle:c-n-cc harmonic 66.579 123.270 # SOURCE3_SOURCE5 805 2.2636 - angle_coeff @angle:c-nc-ca harmonic 67.794 120.660 # CORR 2 - angle_coeff @angle:cc-n-cc harmonic 70.783 108.920 # SOURCE3 11 0.3167 - angle_coeff @angle:cc-nc-cc harmonic 73.120 103.760 # CORR_SOURCE5 6 0.0439 - angle_coeff @angle:cc-nc-cd harmonic 73.871 105.490 # CORR_SOURCE5 1810 1.9032 - angle_coeff @angle:c-nc-cd harmonic 68.639 120.490 # CORR_SOURCE5 205 1.1318 - angle_coeff @angle:cc-n-cl harmonic 71.592 117.720 # SOURCE3 1 - angle_coeff @angle:cc-nc-na harmonic 92.369 102.970 # SOURCE3 1 - angle_coeff @angle:cc-nc-nd harmonic 91.732 108.620 # SOURCE3_SOURCE5 82 1.5614 - angle_coeff @angle:c-n-cd harmonic 66.579 123.270 # SOURCE3_SOURCE5 805 2.2636 - angle_coeff @angle:cd-nc-cd harmonic 71.496 117.300 # CORR_SOURCE5 18 0.3907 - angle_coeff @angle:cd-nc-n harmonic 88.099 117.190 # CORR 64 - angle_coeff @angle:cd-nc-na harmonic 93.753 103.820 # SOURCE3_SOURCE5 919 1.7445 - angle_coeff @angle:cd-nc-nc harmonic 91.676 107.820 # CORR_SOURCE5 457 1.5268 - angle_coeff @angle:cd-nc-os harmonic 91.671 104.670 # CORR_SOURCE5 184 0.8204 - angle_coeff @angle:cd-nc-ss harmonic 70.508 108.070 # CORR_SOURCE5 95 1.3804 - angle_coeff @angle:c-n-ce harmonic 63.457 131.380 # SOURCE4_SOURCE5 371 1.5975 - angle_coeff @angle:cc-n-f harmonic 87.015 114.920 # SOURCE3 1 - angle_coeff @angle:cc-n-hn harmonic 48.285 119.260 # CORR_SOURCE5 459 1.7223 - angle_coeff @angle:cc-n-i harmonic 59.973 119.300 # SOURCE3 1 - angle_coeff @angle:c-n-cl harmonic 72.034 116.350 # SOURCE4 11 0.6829 - angle_coeff @angle:cc-n-n2 harmonic 88.496 110.870 # SOURCE3 1 - angle_coeff @angle:cc-n-n harmonic 83.245 121.370 # SOURCE3 1 - angle_coeff @angle:cc-n-na harmonic 84.492 117.570 # SOURCE3 1 - angle_coeff @angle:cc-n-nc harmonic 88.107 111.890 # CORR_SOURCE5 20 0.7095 - angle_coeff @angle:cc-n-nh harmonic 84.683 117.520 # SOURCE3 1 - angle_coeff @angle:cc-n-no harmonic 83.522 115.920 # SOURCE3 1 - angle_coeff @angle:cc-n-o harmonic 88.192 120.540 # SOURCE3 1 - angle_coeff @angle:cc-n-oh harmonic 83.905 119.300 # SOURCE3_SOURCE5 7 0.3237 - angle_coeff @angle:cc-n-os harmonic 85.167 115.560 # SOURCE3 1 - angle_coeff @angle:cc-n-p2 harmonic 83.596 112.320 # SOURCE3 1 - angle_coeff @angle:cc-n-p3 harmonic 77.892 125.110 # SOURCE3 1 - angle_coeff @angle:cc-n-p5 harmonic 81.119 121.000 # SOURCE3 1 - angle_coeff @angle:cc-n-s4 harmonic 62.446 118.400 # SOURCE3 1 - angle_coeff @angle:cc-n-s6 harmonic 64.150 117.320 # SOURCE3 1 - angle_coeff @angle:cc-n-s harmonic 62.506 118.290 # SOURCE3 1 - angle_coeff @angle:cc-n-sh harmonic 63.393 119.130 # SOURCE3 1 - angle_coeff @angle:cc-n-ss harmonic 64.137 116.600 # SOURCE3 2 - angle_coeff @angle:c-n-cx harmonic 65.394 122.070 # SOURCE4 11 1.9478 - angle_coeff @angle:c-n-cy harmonic 73.625 94.220 # SOURCE4_SOURCE5 674 1.8186 - angle_coeff @angle:cd-n-cd harmonic 70.783 108.920 # SOURCE3 11 - angle_coeff @angle:cd-n-cl harmonic 71.592 117.720 # SOURCE3 1 - angle_coeff @angle:cd-n-f harmonic 87.015 114.920 # SOURCE3 1 - angle_coeff @angle:cd-n-hn harmonic 48.285 119.260 # CORR_SOURCE5 459 1.7223 - angle_coeff @angle:cd-n-i harmonic 59.973 119.300 # SOURCE3 1 - angle_coeff @angle:cd-n-n2 harmonic 88.496 110.870 # SOURCE3 1 - angle_coeff @angle:cd-n-n harmonic 83.245 121.370 # SOURCE3 1 - angle_coeff @angle:cd-n-na harmonic 84.492 117.570 # SOURCE3 1 - angle_coeff @angle:cd-n-nd harmonic 88.107 111.890 # CORR_SOURCE5 20 0.7095 - angle_coeff @angle:cd-n-nh harmonic 84.683 117.520 # SOURCE3 1 - angle_coeff @angle:cd-n-no harmonic 83.522 115.920 # SOURCE3 1 - angle_coeff @angle:cd-n-o harmonic 88.192 120.540 # SOURCE3 1 - angle_coeff @angle:cd-n-oh harmonic 83.905 119.300 # SOURCE3_SOURCE5 7 0.3237 - angle_coeff @angle:cd-n-os harmonic 85.167 115.560 # SOURCE3 1 - angle_coeff @angle:cd-n-p2 harmonic 83.596 112.320 # SOURCE3 1 - angle_coeff @angle:cd-n-p3 harmonic 77.892 125.110 # SOURCE3 1 - angle_coeff @angle:cd-n-p5 harmonic 81.119 121.000 # SOURCE3 1 - angle_coeff @angle:cd-n-s4 harmonic 62.446 118.400 # SOURCE3 1 - angle_coeff @angle:cd-n-s6 harmonic 64.150 117.320 # SOURCE3 1 - angle_coeff @angle:cd-n-s harmonic 62.506 118.290 # SOURCE3 1 - angle_coeff @angle:cd-n-sh harmonic 63.393 119.130 # SOURCE3 1 - angle_coeff @angle:cd-n-ss harmonic 64.137 116.600 # SOURCE3 2 1.8318 - angle_coeff @angle:ce-n-cy harmonic 66.660 111.710 # CORR_SOURCE5 226 2.0477 - angle_coeff @angle:c-n-f harmonic 89.555 108.630 # SOURCE3 3 4.6785 - angle_coeff @angle:cf-n-cy harmonic 66.660 111.710 # CORR_SOURCE5 226 2.0477 - angle_coeff @angle:c-n-hn harmonic 48.691 117.550 # SOURCE3_SOURCE5 5866 1.6058 - angle_coeff @angle:c-n-i harmonic 59.703 120.380 # SOURCE3 5 2.1600 - angle_coeff @angle:cl-n-cl harmonic 81.959 111.690 # SOURCE3 1 - angle_coeff @angle:c-n-n2 harmonic 85.152 119.910 # SOURCE3_SOURCE5 237 1.7782 - angle_coeff @angle:c-n-n3 harmonic 83.740 120.100 # SOURCE3_SOURCE5 90 1.4705 - angle_coeff @angle:c-n-n4 harmonic 85.688 112.320 # SOURCE3 5 1.2622 - angle_coeff @angle:c-n-n harmonic 84.328 118.420 # SOURCE3 10 2.8922 - angle_coeff @angle:c-n-na harmonic 86.815 111.500 # SOURCE3_SOURCE5 60 1.0005 - angle_coeff @angle:na-nc-nd harmonic 116.802 106.240 # SOURCE3_SOURCE5 145 0.6824 - angle_coeff @angle:c-n-nc harmonic 83.462 124.860 # CORR_SOURCE5 117 2.2930 - angle_coeff @angle:nc-nc-nd harmonic 113.624 111.460 # CORR_SOURCE5 97 0.5962 - angle_coeff @angle:c-n-nd harmonic 83.462 124.860 # CORR_SOURCE5 117 2.2930 - angle_coeff @angle:nd-nc-os harmonic 114.084 107.220 # SOURCE3 3 0.4707 - angle_coeff @angle:c-n-nh harmonic 84.310 118.710 # SOURCE4_SOURCE5 52 1.7764 - angle_coeff @angle:c-n-no harmonic 82.773 118.160 # SOURCE3 4 5.4870 - angle_coeff @angle:c-n-o harmonic 89.074 118.360 # SOURCE3_SOURCE5 14 3.9188 - angle_coeff @angle:c-n-oh harmonic 85.324 115.510 # SOURCE3_SOURCE5 128 0.8808 - angle_coeff @angle:c-n-os harmonic 86.126 113.140 # SOURCE3 7 3.0839 - angle_coeff @angle:c-n-p2 harmonic 79.405 124.560 # SOURCE3 8 3.6907 - angle_coeff @angle:c-n-p3 harmonic 78.725 122.540 # SOURCE3 9 4.4802 - angle_coeff @angle:c-n-p4 harmonic 79.728 123.440 # SOURCE3 1 - angle_coeff @angle:c-n-p5 harmonic 78.739 128.500 # SOURCE4 6 0.5353 - angle_coeff @angle:c-n-pc harmonic 79.905 122.230 # SOURCE3 3 2.8787 - angle_coeff @angle:c-n-pd harmonic 79.905 122.230 # SOURCE3 3 - angle_coeff @angle:c-n-s4 harmonic 61.938 120.410 # SOURCE3 4 3.1760 - angle_coeff @angle:c-n-s6 harmonic 62.226 124.760 # SOURCE4_SOURCE5 44 1.7490 - angle_coeff @angle:c-n-s harmonic 60.447 126.550 # SOURCE3 3 4.3365 - angle_coeff @angle:c-n-sh harmonic 63.302 119.540 # SOURCE3 4 1.7681 - angle_coeff @angle:c-n-ss harmonic 62.795 121.710 # SOURCE3_SOURCE5 23 1.8428 - angle_coeff @angle:c-n-sy harmonic 62.308 124.690 # SOURCE4_SOURCE5 124 1.1647 - angle_coeff @angle:cx-n-hn harmonic 46.588 118.500 # SOURCE4_SOURCE5 12 0.6959 - angle_coeff @angle:cx-n-os harmonic 121.869 54.040 # SOURCE3 1 - angle_coeff @angle:cy-n-hn harmonic 45.639 119.110 # SOURCE4_SOURCE5 156 1.4586 - angle_coeff @angle:c3-nd-cc harmonic 69.940 109.510 # SOURCE3 9 - angle_coeff @angle:ca-nd-ca harmonic 71.962 109.950 # SOURCE3 1 - angle_coeff @angle:ca-nd-cc harmonic 74.608 104.880 # CORR_SOURCE5 766 1.8814 - angle_coeff @angle:ca-nd-n harmonic 92.070 104.690 # CORR 2 - angle_coeff @angle:ca-nd-na harmonic 93.131 102.760 # CORR_SOURCE5 25 0.7558 - angle_coeff @angle:ca-nd-nc harmonic 92.520 108.340 # SOURCE4_SOURCE5 23 0.2293 - angle_coeff @angle:ca-nd-os harmonic 90.719 104.480 # CORR_SOURCE5 16 0.1832 - angle_coeff @angle:ca-nd-ss harmonic 70.369 107.070 # SOURCE3_SOURCE5 17 0.3771 - angle_coeff @angle:c-nd-ca harmonic 67.794 120.660 # CORR 2 - angle_coeff @angle:c-nd-cc harmonic 68.639 120.490 # CORR_SOURCE5 205 1.1318 - angle_coeff @angle:cc-nd-cc harmonic 71.496 117.300 # CORR_SOURCE5 18 0.3907 - angle_coeff @angle:cc-nd-cd harmonic 73.871 105.490 # CORR_SOURCE5 1810 1.9032 - angle_coeff @angle:cc-nd-n harmonic 88.099 117.190 # CORR 64 - angle_coeff @angle:cc-nd-na harmonic 93.815 103.820 # SOURCE3_SOURCE5 919 1.7445 - angle_coeff @angle:cc-nd-nd harmonic 91.676 107.820 # CORR_SOURCE5 457 1.5268 - angle_coeff @angle:cc-nd-os harmonic 91.671 104.670 # CORR_SOURCE5 184 0.8204 - angle_coeff @angle:cc-nd-ss harmonic 70.508 108.070 # CORR_SOURCE5 95 1.3804 - angle_coeff @angle:cd-nd-cd harmonic 73.120 103.760 # CORR_SOURCE5 6 0.0439 - angle_coeff @angle:cd-nd-na harmonic 92.426 102.970 # SOURCE3 1 - angle_coeff @angle:cd-nd-nc harmonic 91.732 108.620 # SOURCE3_SOURCE5 82 1.5614 - angle_coeff @angle:na-nd-nc harmonic 116.883 106.240 # SOURCE3_SOURCE5 145 0.6824 - angle_coeff @angle:nc-nd-nd harmonic 113.624 111.460 # CORR_SOURCE5 97 0.5962 - angle_coeff @angle:nc-nd-os harmonic 114.084 107.220 # SOURCE3 3 - angle_coeff @angle:c1-ne-ca harmonic 62.618 151.950 # CORR_SOURCE5 15 1.4352 - angle_coeff @angle:c1-ne-cg harmonic 67.861 140.000 # SOURCE2 1 - angle_coeff @angle:c2-ne-ca harmonic 68.492 120.830 # CORR_SOURCE5 103 1.9474 - angle_coeff @angle:c2-ne-ce harmonic 70.313 116.010 # SOURCE3_SOURCE5 34 2.0813 - angle_coeff @angle:c2-ne-cg harmonic 70.178 123.230 # SOURCE4_SOURCE5 39 1.0918 - angle_coeff @angle:c2-ne-n2 harmonic 93.623 113.310 # SOURCE3 1 - angle_coeff @angle:c2-ne-ne harmonic 88.990 110.860 # SOURCE3 7 4.5874 - angle_coeff @angle:c2-ne-p2 harmonic 84.105 134.030 # SOURCE3 1 - angle_coeff @angle:c2-ne-pe harmonic 82.533 120.520 # SOURCE3 8 8.1381 - angle_coeff @angle:c2-ne-px harmonic 83.910 117.750 # SOURCE3 5 0.8581 - angle_coeff @angle:c2-ne-py harmonic 88.230 117.040 # SOURCE3 3 1.4398 - angle_coeff @angle:c2-ne-sx harmonic 62.652 111.980 # SOURCE3 3 0.4090 - angle_coeff @angle:c2-ne-sy harmonic 65.555 120.600 # CORR_SOURCE5 19 1.1215 - angle_coeff @angle:ca-ne-cf harmonic 68.142 121.710 # CORR_SOURCE5 29 1.8572 - angle_coeff @angle:ca-ne-n2 harmonic 88.697 114.350 # CORR_SOURCE5 15 1.3133 - angle_coeff @angle:ca-ne-nf harmonic 88.592 115.170 # CORR_SOURCE5 98 0.8636 - angle_coeff @angle:ca-ne-o harmonic 89.200 115.690 # SOURCE3_SOURCE5 18 1.7090 - angle_coeff @angle:ca-ne-p2 harmonic 87.186 118.090 # SOURCE3 1 - angle_coeff @angle:ca-ne-s harmonic 68.068 120.110 # SOURCE3 1 - angle_coeff @angle:c-ne-c2 harmonic 69.660 118.530 # CORR 6 - angle_coeff @angle:ce-ne-n2 harmonic 90.497 111.190 # SOURCE3 1 - angle_coeff @angle:ce-ne-o harmonic 91.180 112.160 # SOURCE3 1 - angle_coeff @angle:ce-ne-p2 harmonic 87.896 117.020 # SOURCE3 1 - angle_coeff @angle:ce-ne-s harmonic 69.440 116.280 # SOURCE3 1 - angle_coeff @angle:cg-ne-n1 harmonic 90.226 120.200 # SOURCE2 1 - angle_coeff @angle:cg-ne-n2 harmonic 92.273 113.390 # SOURCE3 1 - angle_coeff @angle:cg-ne-o harmonic 93.028 114.700 # SOURCE2 1 - angle_coeff @angle:cg-ne-p2 harmonic 88.388 119.570 # SOURCE3 1 - angle_coeff @angle:cg-ne-s harmonic 70.232 117.700 # SOURCE3 1 - angle_coeff @angle:c-ne-sy harmonic 65.604 116.430 # SOURCE4_SOURCE5 16 1.7300 - angle_coeff @angle:n2-ne-n2 harmonic 121.491 107.220 # SOURCE3 1 - angle_coeff @angle:n2-ne-ne harmonic 112.157 110.720 # SOURCE3 9 6.1488 - angle_coeff @angle:n2-ne-o harmonic 119.624 114.100 # SOURCE3 1 - angle_coeff @angle:n2-ne-p2 harmonic 116.902 109.660 # SOURCE3 1 - angle_coeff @angle:n2-ne-pe harmonic 107.386 112.150 # SOURCE3 7 6.5273 - angle_coeff @angle:n2-ne-px harmonic 106.135 115.970 # SOURCE3 3 1.9854 - angle_coeff @angle:n2-ne-py harmonic 112.046 114.600 # SOURCE3 3 2.9261 - angle_coeff @angle:n2-ne-s harmonic 89.721 115.900 # SOURCE3 1 - angle_coeff @angle:n2-ne-sx harmonic 80.235 107.290 # SOURCE3 1 - angle_coeff @angle:n2-ne-sy harmonic 85.721 111.210 # SOURCE3 1 - angle_coeff @angle:ne-ne-o harmonic 113.544 110.450 # SOURCE3 10 1.8535 - angle_coeff @angle:ne-ne-p2 harmonic 110.510 114.390 # SOURCE3 6 4.0528 - angle_coeff @angle:ne-ne-s harmonic 86.406 115.950 # SOURCE3 6 3.4604 - angle_coeff @angle:o-ne-o harmonic 116.666 124.090 # SOURCE3 2 8.7534 - angle_coeff @angle:o-ne-pe harmonic 99.245 132.320 # SOURCE3 11 23.9559 - angle_coeff @angle:o-ne-px harmonic 109.115 110.620 # SOURCE3 1 - angle_coeff @angle:o-ne-py harmonic 114.678 110.790 # SOURCE3 4 1.6818 - angle_coeff @angle:o-ne-s harmonic 89.941 117.190 # SOURCE3 2 0.0225 - angle_coeff @angle:o-ne-sx harmonic 79.732 108.920 # SOURCE3 1 - angle_coeff @angle:o-ne-sy harmonic 86.078 111.340 # SOURCE3 1 - angle_coeff @angle:p2-ne-pe harmonic 110.473 116.810 # SOURCE3 1 - angle_coeff @angle:p2-ne-px harmonic 105.767 128.350 # SOURCE3 1 - angle_coeff @angle:p2-ne-py harmonic 111.507 123.470 # SOURCE3 1 - angle_coeff @angle:p2-ne-sx harmonic 83.857 112.120 # SOURCE3 1 - angle_coeff @angle:p2-ne-sy harmonic 87.708 115.730 # SOURCE3 1 - angle_coeff @angle:pe-ne-s harmonic 87.031 115.730 # SOURCE3 1 - angle_coeff @angle:px-ne-s harmonic 81.843 131.840 # SOURCE3 1 - angle_coeff @angle:py-ne-s harmonic 90.262 116.180 # SOURCE3 4 3.7135 - angle_coeff @angle:s-ne-s harmonic 70.545 120.870 # SOURCE3 1 - angle_coeff @angle:s-ne-sx harmonic 65.416 112.960 # SOURCE3 1 - angle_coeff @angle:s-ne-sy harmonic 67.679 119.630 # SOURCE3 1 - angle_coeff @angle:c1-nf-ca harmonic 62.618 151.950 # CORR_SOURCE5 15 1.4352 - angle_coeff @angle:c1-nf-ch harmonic 67.861 140.000 # SOURCE2 1 - angle_coeff @angle:c2-nf-ca harmonic 68.492 120.830 # CORR_SOURCE5 103 1.9474 - angle_coeff @angle:c2-nf-cf harmonic 70.313 116.010 # SOURCE3_SOURCE5 31 2.1630 - angle_coeff @angle:c2-nf-n2 harmonic 93.623 113.310 # SOURCE3 1 - angle_coeff @angle:c2-nf-nf harmonic 88.990 110.860 # SOURCE3 7 - angle_coeff @angle:c2-nf-p2 harmonic 84.105 134.030 # SOURCE3 1 - angle_coeff @angle:c2-nf-pf harmonic 82.533 120.520 # SOURCE3 8 - angle_coeff @angle:c2-nf-px harmonic 83.910 117.750 # SOURCE3 5 - angle_coeff @angle:c2-nf-py harmonic 88.230 117.040 # SOURCE3 3 - angle_coeff @angle:c2-nf-sx harmonic 62.652 111.980 # SOURCE3 3 - angle_coeff @angle:c2-nf-sy harmonic 65.555 120.600 # CORR_SOURCE5 19 1.1215 - angle_coeff @angle:ca-nf-ce harmonic 68.142 121.710 # CORR_SOURCE5 29 1.8572 - angle_coeff @angle:ca-nf-n2 harmonic 88.697 114.350 # CORR_SOURCE5 15 1.3133 - angle_coeff @angle:ca-nf-ne harmonic 88.592 115.170 # CORR_SOURCE5 98 0.8636 - angle_coeff @angle:ca-nf-o harmonic 89.200 115.690 # SOURCE3_SOURCE5 15 1.8257 - angle_coeff @angle:ca-nf-p2 harmonic 87.186 118.090 # SOURCE3 1 - angle_coeff @angle:ca-nf-s harmonic 68.068 120.110 # SOURCE3 1 - angle_coeff @angle:c-nf-c2 harmonic 69.660 118.530 # CORR 6 - angle_coeff @angle:cf-nf-n2 harmonic 90.497 111.190 # SOURCE3 1 - angle_coeff @angle:cf-nf-o harmonic 91.180 112.160 # SOURCE3 1 - angle_coeff @angle:cf-nf-p2 harmonic 87.896 117.020 # SOURCE3 1 - angle_coeff @angle:cf-nf-s harmonic 69.440 116.280 # SOURCE3 1 - angle_coeff @angle:ch-nf-n1 harmonic 90.226 120.200 # SOURCE2 1 - angle_coeff @angle:ch-nf-n2 harmonic 92.273 113.390 # SOURCE3 1 - angle_coeff @angle:ch-nf-o harmonic 93.028 114.700 # SOURCE2 1 - angle_coeff @angle:ch-nf-p2 harmonic 88.388 119.570 # SOURCE3 1 - angle_coeff @angle:ch-nf-s harmonic 70.232 117.700 # SOURCE3 1 - angle_coeff @angle:f-n-f harmonic 116.092 102.980 # SOURCE3 1 - angle_coeff @angle:n2-nf-n2 harmonic 121.491 107.220 # SOURCE3 1 - angle_coeff @angle:n2-nf-nf harmonic 112.157 110.720 # SOURCE3 9 - angle_coeff @angle:n2-nf-o harmonic 119.624 114.100 # SOURCE3 1 - angle_coeff @angle:n2-nf-p2 harmonic 116.902 109.660 # SOURCE3 1 - angle_coeff @angle:n2-nf-pf harmonic 107.386 112.150 # SOURCE3 7 - angle_coeff @angle:n2-nf-px harmonic 106.135 115.970 # SOURCE3 3 - angle_coeff @angle:n2-nf-py harmonic 112.046 114.600 # SOURCE3 3 - angle_coeff @angle:n2-nf-s harmonic 89.721 115.900 # SOURCE3 1 - angle_coeff @angle:n2-nf-sx harmonic 80.235 107.290 # SOURCE3 1 - angle_coeff @angle:n2-nf-sy harmonic 85.721 111.210 # SOURCE3 1 - angle_coeff @angle:nf-nf-o harmonic 113.544 110.450 # SOURCE3 10 - angle_coeff @angle:nf-nf-p2 harmonic 110.510 114.390 # SOURCE3 6 - angle_coeff @angle:nf-nf-s harmonic 86.406 115.950 # SOURCE3 6 - angle_coeff @angle:o-nf-o harmonic 116.666 124.090 # SOURCE3 2 - angle_coeff @angle:o-nf-pf harmonic 99.245 132.320 # SOURCE3 11 - angle_coeff @angle:o-nf-px harmonic 109.115 110.620 # SOURCE3 1 - angle_coeff @angle:o-nf-py harmonic 114.678 110.790 # SOURCE3 4 - angle_coeff @angle:o-nf-s harmonic 89.941 117.190 # SOURCE3 2 - angle_coeff @angle:o-nf-sx harmonic 79.732 108.920 # SOURCE3 1 - angle_coeff @angle:o-nf-sy harmonic 86.078 111.340 # SOURCE3 1 - angle_coeff @angle:p2-nf-pf harmonic 110.473 116.810 # SOURCE3 1 - angle_coeff @angle:p2-nf-px harmonic 105.767 128.350 # SOURCE3 1 - angle_coeff @angle:p2-nf-py harmonic 111.507 123.470 # SOURCE3 1 - angle_coeff @angle:p2-nf-sx harmonic 83.857 112.120 # SOURCE3 1 - angle_coeff @angle:p2-nf-sy harmonic 87.708 115.730 # SOURCE3 1 - angle_coeff @angle:pf-nf-s harmonic 87.031 115.730 # SOURCE3 1 - angle_coeff @angle:px-nf-s harmonic 81.843 131.840 # SOURCE3 1 - angle_coeff @angle:py-nf-s harmonic 90.262 116.180 # SOURCE3 4 - angle_coeff @angle:s-nf-s harmonic 70.545 120.870 # SOURCE3 1 - angle_coeff @angle:s-nf-sx harmonic 65.416 112.960 # SOURCE3 1 - angle_coeff @angle:s-nf-sy harmonic 67.679 119.630 # SOURCE3 1 - angle_coeff @angle:br-nh-br harmonic 67.679 106.270 # SOURCE3 1 - angle_coeff @angle:br-nh-ca harmonic 63.138 111.880 # SOURCE3 1 - angle_coeff @angle:br-nh-hn harmonic 41.986 101.560 # SOURCE3 1 - angle_coeff @angle:c1-nh-c1 harmonic 70.255 116.980 # SOURCE3 1 - angle_coeff @angle:c1-nh-c2 harmonic 67.255 123.350 # SOURCE4_SOURCE5 17 1.3108 - angle_coeff @angle:c1-nh-ca harmonic 67.561 122.360 # SOURCE3 3 1.2016 - angle_coeff @angle:c1-nh-hn harmonic 49.868 117.400 # SOURCE4_SOURCE5 22 0.6517 - angle_coeff @angle:c2-nh-c2 harmonic 65.835 124.730 # SOURCE4_SOURCE5 107 1.4158 - angle_coeff @angle:c2-nh-c3 harmonic 64.232 123.710 # SOURCE3 8 3.5348 - angle_coeff @angle:c2-nh-ca harmonic 65.131 127.560 # SOURCE4_SOURCE5 258 2.3985 - angle_coeff @angle:c2-nh-cc harmonic 65.733 126.350 # CORR_SOURCE5 14 0.8394 - angle_coeff @angle:c2-nh-cd harmonic 65.733 126.350 # CORR_SOURCE5 14 0.8394 - angle_coeff @angle:c2-nh-cx harmonic 64.299 124.350 # SOURCE4_SOURCE5 21 1.6877 - angle_coeff @angle:c2-nh-hn harmonic 48.954 115.090 # SOURCE4_SOURCE5 2743 1.5424 - angle_coeff @angle:c2-nh-n2 harmonic 85.013 120.220 # SOURCE4_SOURCE5 101 1.0922 - angle_coeff @angle:c2-nh-n3 harmonic 84.289 116.870 # SOURCE4_SOURCE5 35 1.4173 - angle_coeff @angle:c2-nh-no harmonic 82.173 125.620 # SOURCE4_SOURCE5 19 0.8850 - angle_coeff @angle:c2-nh-oh harmonic 86.014 112.180 # SOURCE4_SOURCE5 38 1.3409 - angle_coeff @angle:c2-nh-os harmonic 85.749 112.950 # SOURCE4_SOURCE5 14 0.4455 - angle_coeff @angle:c2-nh-sy harmonic 63.190 121.130 # SOURCE4_SOURCE5 20 0.5133 - angle_coeff @angle:c3-nh-c3 harmonic 65.106 114.510 # SOURCE4_SOURCE5 1386 2.1206 - angle_coeff @angle:c3-nh-ca harmonic 65.249 119.980 # SOURCE3_SOURCE5 1640 2.1716 - angle_coeff @angle:c3-nh-cc harmonic 65.571 119.720 # CORR_SOURCE5 638 2.4802 - angle_coeff @angle:c3-nh-cd harmonic 65.571 119.720 # CORR_SOURCE5 638 2.4802 - angle_coeff @angle:c3-nh-cf harmonic 65.126 120.120 # SOURCE4_SOURCE5 52 2.0459 - angle_coeff @angle:c3-nh-cz harmonic 64.716 125.460 # SOURCE4_SOURCE5 25 0.5651 - angle_coeff @angle:c3-nh-hn harmonic 46.421 115.990 # SOURCE3_SOURCE5 1206 1.7716 - angle_coeff @angle:c3-nh-n2 harmonic 85.302 112.350 # SOURCE3 9 4.0058 - angle_coeff @angle:c3-nh-n harmonic 84.428 111.270 # SOURCE4_SOURCE5 20 2.2657 - angle_coeff @angle:c3-nh-na harmonic 84.049 112.390 # SOURCE4_SOURCE5 18 1.3421 - angle_coeff @angle:c3-nh-p2 harmonic 80.321 123.350 # SOURCE3 1 - angle_coeff @angle:c3-nh-sy harmonic 63.547 116.320 # SOURCE4_SOURCE5 31 1.3018 - angle_coeff @angle:ca-nh-ca harmonic 65.187 127.460 # SOURCE3 2 0.0002 - angle_coeff @angle:ca-nh-cc harmonic 64.885 129.800 # CORR_SOURCE5 49 1.2126 - angle_coeff @angle:ca-nh-cd harmonic 64.885 129.800 # CORR_SOURCE5 49 1.2126 - angle_coeff @angle:ca-nh-cl harmonic 71.441 113.150 # SOURCE3 1 - angle_coeff @angle:ca-nh-cx harmonic 64.495 123.700 # SOURCE4_SOURCE5 80 0.6122 - angle_coeff @angle:ca-nh-f harmonic 89.432 106.090 # SOURCE3 3 1.0660 - angle_coeff @angle:ca-nh-hn harmonic 48.787 116.070 # SOURCE4_SOURCE5 5026 1.3182 - angle_coeff @angle:ca-nh-i harmonic 58.875 117.830 # SOURCE3 1 - angle_coeff @angle:ca-nh-n1 harmonic 86.539 117.130 # HF/6-31G* 1 - angle_coeff @angle:ca-nh-n2 harmonic 84.736 121.130 # SOURCE4_SOURCE5 61 1.2262 - angle_coeff @angle:ca-nh-n3 harmonic 83.982 117.830 # SOURCE3_SOURCE5 31 1.9504 - angle_coeff @angle:ca-nh-n4 harmonic 85.682 108.940 # SOURCE3 5 0.6562 - angle_coeff @angle:ca-nh-n harmonic 85.070 116.030 # SOURCE4_SOURCE5 31 1.0216 - angle_coeff @angle:ca-nh-na harmonic 85.145 115.960 # SOURCE3_SOURCE5 14 0.6985 - angle_coeff @angle:ca-nh-nh harmonic 85.491 114.840 # SOURCE3_SOURCE5 14 1.2270 - angle_coeff @angle:ca-nh-no harmonic 86.330 113.920 # SOURCE3 4 2.9561 - angle_coeff @angle:ca-nh-o harmonic 86.968 121.920 # SOURCE3 2 3.9630 - angle_coeff @angle:ca-nh-oh harmonic 85.751 112.970 # SOURCE3_SOURCE5 7 0.3980 - angle_coeff @angle:ca-nh-os harmonic 86.208 111.850 # SOURCE3_SOURCE5 8 0.6032 - angle_coeff @angle:ca-nh-p2 harmonic 81.008 125.270 # SOURCE3 8 5.1798 - angle_coeff @angle:ca-nh-p3 harmonic 79.062 125.700 # SOURCE3 3 5.7796 - angle_coeff @angle:ca-nh-p4 harmonic 80.454 124.010 # SOURCE3 3 2.5810 - angle_coeff @angle:ca-nh-p5 harmonic 80.367 128.170 # SOURCE3_SOURCE5 9 0.9847 - angle_coeff @angle:ca-nh-s4 harmonic 63.691 115.620 # SOURCE3 3 0.3434 - angle_coeff @angle:ca-nh-s6 harmonic 63.224 122.850 # SOURCE4_SOURCE5 92 2.1278 - angle_coeff @angle:ca-nh-s harmonic 60.896 122.540 # SOURCE3 3 2.7001 - angle_coeff @angle:ca-nh-sh harmonic 63.303 121.410 # SOURCE3 1 - angle_coeff @angle:ca-nh-ss harmonic 63.248 121.500 # SOURCE3 3 2.6255 - angle_coeff @angle:ca-nh-sy harmonic 62.161 125.230 # SOURCE4_SOURCE5 116 1.6241 - angle_coeff @angle:cc-nh-cx harmonic 64.747 123.700 # CORR_SOURCE5 82 1.6057 - angle_coeff @angle:cc-nh-hn harmonic 49.267 115.630 # SOURCE3_SOURCE5 1084 1.8598 - angle_coeff @angle:cc-nh-n2 harmonic 85.504 120.090 # SOURCE4_SOURCE5 21 1.0306 - angle_coeff @angle:cc-nh-sy harmonic 62.976 122.520 # SOURCE4_SOURCE5 60 1.2839 - angle_coeff @angle:cd-nh-cx harmonic 64.747 123.700 # CORR_SOURCE5 82 1.6057 - angle_coeff @angle:cd-nh-hn harmonic 49.267 115.630 # SOURCE3_SOURCE5 1084 1.8598 - angle_coeff @angle:ce-nh-hn harmonic 48.739 115.680 # CORR_SOURCE5 360 1.2286 - angle_coeff @angle:ce-nh-o harmonic 84.249 129.430 # CORR 2 - angle_coeff @angle:ce-nh-sy harmonic 65.279 113.390 # SOURCE4_SOURCE5 15 1.0862 - angle_coeff @angle:cf-nh-hn harmonic 48.739 115.680 # CORR_SOURCE5 360 1.2286 - angle_coeff @angle:cf-nh-o harmonic 84.249 129.430 # CORR 2 - angle_coeff @angle:cl-nh-cl harmonic 81.661 106.600 # SOURCE3 1 - angle_coeff @angle:cl-nh-hn harmonic 48.722 104.140 # SOURCE3 1 - angle_coeff @angle:cx-nh-cx harmonic 89.045 62.010 # SOURCE4_SOURCE5 98 0.5911 - angle_coeff @angle:cx-nh-hn harmonic 46.132 118.880 # SOURCE4_SOURCE5 23 0.1930 - angle_coeff @angle:cz-nh-hn harmonic 49.192 121.150 # SOURCE4_SOURCE5 116 0.7805 - angle_coeff @angle:f-nh-f harmonic 114.444 101.700 # SOURCE3 1 - angle_coeff @angle:f-nh-hn harmonic 64.681 101.230 # SOURCE3 1 - angle_coeff @angle:hn-nh-hn harmonic 39.519 115.120 # SOURCE4_SOURCE5 3024 2.1393 - angle_coeff @angle:hn-nh-i harmonic 37.873 107.570 # SOURCE3 1 - angle_coeff @angle:hn-nh-n1 harmonic 64.440 110.570 # HF/6-31G* 1 - angle_coeff @angle:hn-nh-n2 harmonic 61.856 118.140 # SOURCE4_SOURCE5 220 2.1956 - angle_coeff @angle:hn-nh-n3 harmonic 60.496 113.970 # SOURCE3_SOURCE5 53 1.8422 - angle_coeff @angle:hn-nh-n4 harmonic 61.193 104.400 # SOURCE3 3 0.5056 - angle_coeff @angle:hn-nh-n harmonic 62.655 108.170 # SOURCE4_SOURCE5 39 1.1076 - angle_coeff @angle:hn-nh-na harmonic 62.699 108.240 # SOURCE3_SOURCE5 48 1.3913 - angle_coeff @angle:hn-nh-nh harmonic 61.867 110.860 # SOURCE4_SOURCE5 20 1.2814 - angle_coeff @angle:hn-nh-no harmonic 62.754 109.940 # SOURCE4_SOURCE5 17 0.1843 - angle_coeff @angle:hn-nh-o harmonic 65.877 116.450 # SOURCE3 2 0.6063 - angle_coeff @angle:hn-nh-oh harmonic 62.561 106.490 # SOURCE4_SOURCE5 45 1.2492 - angle_coeff @angle:hn-nh-os harmonic 62.721 106.070 # SOURCE3_SOURCE5 11 1.1257 - angle_coeff @angle:hn-nh-p2 harmonic 55.498 118.180 # SOURCE3 21 3.6927 - angle_coeff @angle:hn-nh-p3 harmonic 54.152 116.190 # SOURCE3 3 3.0539 - angle_coeff @angle:hn-nh-p4 harmonic 55.870 112.600 # SOURCE3 3 0.8237 - angle_coeff @angle:hn-nh-p5 harmonic 56.530 115.090 # SOURCE3_SOURCE5 12 1.4234 - angle_coeff @angle:hn-nh-s4 harmonic 43.338 107.480 # SOURCE3 3 1.3960 - angle_coeff @angle:hn-nh-s harmonic 41.075 114.370 # SOURCE3 1 - angle_coeff @angle:hn-nh-s6 harmonic 44.306 109.920 # SOURCE4_SOURCE5 70 0.7219 - angle_coeff @angle:hn-nh-sh harmonic 43.546 112.250 # SOURCE3 1 - angle_coeff @angle:hn-nh-ss harmonic 43.161 114.100 # SOURCE3_SOURCE5 9 0.8638 - angle_coeff @angle:hn-nh-sy harmonic 43.636 110.910 # SOURCE4_SOURCE5 174 1.2855 - angle_coeff @angle:i-nh-i harmonic 65.204 115.820 # SOURCE3 1 - angle_coeff @angle:n1-nh-n1 harmonic 115.547 106.710 # HF/6-31G* 1 - angle_coeff @angle:n2-nh-n2 harmonic 109.104 117.500 # SOURCE3 2 1.1907 - angle_coeff @angle:n2-nh-n3 harmonic 105.802 119.060 # SOURCE3_SOURCE5 5 1.1057 - angle_coeff @angle:n2-nh-o harmonic 108.688 126.060 # SOURCE3 1 - angle_coeff @angle:n3-nh-n3 harmonic 107.251 110.980 # SOURCE3 1 - angle_coeff @angle:n4-nh-n4 harmonic 104.809 108.360 # SOURCE3 1 - angle_coeff @angle:na-nh-na harmonic 107.947 112.010 # SOURCE3 1 - angle_coeff @angle:hn-n-hn harmonic 39.011 117.950 # SOURCE3_SOURCE5 619 1.1004 - angle_coeff @angle:nh-nh-nh harmonic 107.672 112.230 # SOURCE3 1 - angle_coeff @angle:hn-n-i harmonic 37.457 117.240 # SOURCE3 2 0.4435 - angle_coeff @angle:hn-n-n2 harmonic 61.294 119.080 # SOURCE3_SOURCE5 133 1.1985 - angle_coeff @angle:hn-n-n3 harmonic 60.078 117.240 # SOURCE4_SOURCE5 85 1.3614 - angle_coeff @angle:hn-n-n4 harmonic 60.201 112.680 # SOURCE3 3 1.9746 - angle_coeff @angle:hn-n-n harmonic 61.137 113.200 # SOURCE3_SOURCE5 44 1.5099 - angle_coeff @angle:hn-n-na harmonic 60.720 114.350 # SOURCE3_SOURCE5 14 1.6595 - angle_coeff @angle:hn-n-nc harmonic 62.278 115.420 # SOURCE4_SOURCE5 34 0.6814 - angle_coeff @angle:hn-n-nh harmonic 61.240 113.210 # SOURCE4_SOURCE5 34 1.4195 - angle_coeff @angle:hn-n-no harmonic 59.968 110.110 # SOURCE3 1 - angle_coeff @angle:hn-n-o harmonic 66.701 116.320 # SOURCE3 2 0.0175 - angle_coeff @angle:n-nh-o harmonic 111.046 115.630 # SOURCE3 1 - angle_coeff @angle:hn-n-oh harmonic 61.737 110.740 # SOURCE4_SOURCE5 106 1.1526 - angle_coeff @angle:no-nh-no harmonic 110.729 108.550 # SOURCE3 1 - angle_coeff @angle:hn-n-os harmonic 61.835 110.010 # SOURCE4_SOURCE5 28 0.8603 - angle_coeff @angle:hn-n-p2 harmonic 53.625 118.050 # SOURCE3 7 3.0564 - angle_coeff @angle:hn-n-p3 harmonic 52.013 119.630 # SOURCE3 2 - angle_coeff @angle:hn-n-p4 harmonic 54.129 115.710 # SOURCE3 1 - angle_coeff @angle:hn-n-p5 harmonic 55.227 113.610 # SOURCE4_SOURCE5 12 0.8598 - angle_coeff @angle:hn-n-s4 harmonic 41.853 112.460 # SOURCE3 1 - angle_coeff @angle:hn-n-s harmonic 41.432 114.920 # SOURCE3 2 0.0260 - angle_coeff @angle:hn-n-s6 harmonic 43.193 112.560 # SOURCE4_SOURCE5 18 0.6934 - angle_coeff @angle:hn-n-sh harmonic 42.490 114.910 # SOURCE3 1 - angle_coeff @angle:hn-n-ss harmonic 42.420 115.600 # SOURCE3 3 0.6414 - angle_coeff @angle:hn-n-sy harmonic 43.301 112.330 # SOURCE4_SOURCE5 87 0.6324 - angle_coeff @angle:oh-nh-oh harmonic 109.556 106.270 # SOURCE3 1 - angle_coeff @angle:o-nh-o harmonic 111.924 128.060 # SOURCE3 1 - angle_coeff @angle:os-nh-os harmonic 110.145 105.270 # SOURCE3 1 - angle_coeff @angle:p2-nh-p2 harmonic 103.624 127.330 # SOURCE3 2 2.7857 - angle_coeff @angle:p3-nh-p3 harmonic 101.470 125.080 # SOURCE3 1 - angle_coeff @angle:p5-nh-p5 harmonic 110.643 112.760 # SOURCE3 1 - angle_coeff @angle:s4-nh-s4 harmonic 64.290 112.390 # SOURCE3 1 - angle_coeff @angle:s6-nh-s6 harmonic 64.034 120.270 # SOURCE3 1 - angle_coeff @angle:sh-nh-sh harmonic 63.979 119.000 # SOURCE3 1 - angle_coeff @angle:s-nh-s harmonic 61.323 118.730 # SOURCE3 1 - angle_coeff @angle:ss-nh-ss harmonic 63.871 119.250 # SOURCE3 1 - angle_coeff @angle:i-n-i harmonic 66.144 118.200 # SOURCE3 1 - angle_coeff @angle:n2-n-n2 harmonic 108.745 116.890 # SOURCE3 1 - angle_coeff @angle:n3-n-n3 harmonic 104.883 117.940 # SOURCE3 1 - angle_coeff @angle:n4-n-n4 harmonic 105.215 112.690 # SOURCE3 1 - angle_coeff @angle:na-n-na harmonic 104.916 117.380 # SOURCE3 1 - angle_coeff @angle:nc-n-nc harmonic 109.009 116.410 # CORR 2 - angle_coeff @angle:nc-n-p2 harmonic 102.805 117.210 # CORR 2 - angle_coeff @angle:nc-n-pc harmonic 102.474 117.210 # CORR 2 - angle_coeff @angle:nd-n-nd harmonic 109.009 116.410 # CORR 2 - angle_coeff @angle:nd-n-p2 harmonic 102.805 117.210 # CORR 2 - angle_coeff @angle:nd-n-pd harmonic 102.474 117.210 # CORR 2 - angle_coeff @angle:nh-n-nh harmonic 106.329 115.180 # SOURCE3 1 - angle_coeff @angle:n-n-n harmonic 106.384 114.620 # SOURCE3 1 - angle_coeff @angle:no-n-no harmonic 105.383 108.660 # SOURCE3 1 - angle_coeff @angle:br-no-o harmonic 72.469 113.190 # SOURCE3 2 - angle_coeff @angle:c1-no-o harmonic 89.075 116.630 # SOURCE3 6 - angle_coeff @angle:c2-no-o harmonic 86.856 117.670 # SOURCE3_SOURCE5 49 0.7530 - angle_coeff @angle:c3-no-o harmonic 83.512 116.930 # SOURCE3_SOURCE5 182 0.7108 - angle_coeff @angle:ca-no-o harmonic 85.942 117.760 # SOURCE3_SOURCE5 886 0.2929 - angle_coeff @angle:cc-no-o harmonic 87.737 117.490 # SOURCE4_SOURCE5 624 0.5662 - angle_coeff @angle:cl-no-o harmonic 86.532 115.080 # SOURCE3 2 - angle_coeff @angle:c-no-o harmonic 83.834 115.260 # SOURCE3 1 - angle_coeff @angle:hn-no-o harmonic 67.449 115.490 # SOURCE3 2 - angle_coeff @angle:oh-n-oh harmonic 109.825 107.260 # SOURCE3 1 - angle_coeff @angle:i-no-o harmonic 70.372 116.310 # SOURCE3 2 - angle_coeff @angle:n1-no-o harmonic 112.600 115.000 # HF/6-31G* 1 - angle_coeff @angle:n2-no-o harmonic 110.021 116.520 # SOURCE2_SOURCE5 17 2.4833 - angle_coeff @angle:n3-no-o harmonic 111.860 116.770 # SOURCE3_SOURCE5 35 0.4158 - angle_coeff @angle:n4-no-o harmonic 111.250 109.000 # SOURCE3 2 - angle_coeff @angle:na-no-o harmonic 110.472 115.570 # SOURCE3_SOURCE5 29 0.5293 - angle_coeff @angle:nh-no-o harmonic 112.798 116.080 # SOURCE3_SOURCE5 32 0.8573 - angle_coeff @angle:n-no-o harmonic 109.317 115.590 # SOURCE3_SOURCE5 14 0.7108 - angle_coeff @angle:no-no-o harmonic 91.614 112.380 # SOURCE3 4 - angle_coeff @angle:o-n-o harmonic 113.464 128.610 # SOURCE3 3 1.0626 - angle_coeff @angle:o-no-o harmonic 116.649 125.080 # SOURCE4_SOURCE5 1464 0.8585 - angle_coeff @angle:o-no-oh harmonic 112.426 114.700 # SOURCE3 2 - angle_coeff @angle:o-no-os harmonic 111.586 114.760 # SOURCE3_SOURCE5 147 2.2227 - angle_coeff @angle:o-no-p2 harmonic 103.970 117.380 # SOURCE3 20 0.8083 - angle_coeff @angle:o-no-p3 harmonic 98.510 116.780 # SOURCE3 6 0.4929 - angle_coeff @angle:o-no-p4 harmonic 97.206 116.640 # SOURCE3 6 0.0089 - angle_coeff @angle:o-no-p5 harmonic 99.077 116.690 # SOURCE3 8 0.4507 - angle_coeff @angle:o-no-s4 harmonic 71.457 114.490 # SOURCE3 6 0.5674 - angle_coeff @angle:o-no-s6 harmonic 72.259 114.390 # SOURCE3 6 0.8311 - angle_coeff @angle:o-no-s harmonic 80.020 119.810 # SOURCE3 4 0.0042 - angle_coeff @angle:o-no-sh harmonic 78.649 116.100 # SOURCE3 2 - angle_coeff @angle:o-no-ss harmonic 77.822 115.580 # SOURCE3 6 0.5860 - angle_coeff @angle:os-n-os harmonic 109.989 106.530 # SOURCE3 1 - angle_coeff @angle:p2-n-p2 harmonic 103.580 119.620 # SOURCE3 1 - angle_coeff @angle:p3-n-p3 harmonic 106.372 108.730 # SOURCE3 3 0.2591 - angle_coeff @angle:p4-n-p4 harmonic 108.671 108.550 # SOURCE3 1 - angle_coeff @angle:p5-n-p5 harmonic 114.341 99.990 # SOURCE3 1 - angle_coeff @angle:pc-n-pc harmonic 103.163 119.620 # SOURCE3 1 - angle_coeff @angle:pd-n-pd harmonic 103.163 119.620 # SOURCE3 1 - angle_coeff @angle:s4-n-s4 harmonic 63.214 113.750 # SOURCE3 1 - angle_coeff @angle:s6-n-s6 harmonic 63.403 119.680 # SOURCE3 1 - angle_coeff @angle:sh-n-sh harmonic 63.230 119.030 # SOURCE3 1 - angle_coeff @angle:s-n-s harmonic 60.100 126.000 # SOURCE3 1 - angle_coeff @angle:ss-n-ss harmonic 63.451 118.490 # SOURCE3 1 - angle_coeff @angle:br-oh-ho harmonic 43.172 101.600 # SOURCE3 1 - angle_coeff @angle:c1-oh-ho harmonic 51.954 108.760 # SOURCE3 1 - angle_coeff @angle:c2-oh-ho harmonic 51.795 107.630 # SOURCE3_SOURCE5 86 1.5038 - angle_coeff @angle:c3-oh-ho harmonic 49.027 107.260 # SOURCE3_SOURCE5 7781 0.7665 - angle_coeff @angle:ca-oh-ho harmonic 50.712 108.580 # SOURCE3_SOURCE5 3580 0.7052 - angle_coeff @angle:cc-oh-ho harmonic 51.627 107.120 # CORR_SOURCE5 226 1.6427 - angle_coeff @angle:cd-oh-ho harmonic 51.627 107.120 # CORR_SOURCE5 226 1.6427 - angle_coeff @angle:ce-oh-ho harmonic 51.587 106.830 # CORR_SOURCE5 48 1.2629 - angle_coeff @angle:cf-oh-ho harmonic 51.587 106.830 # CORR_SOURCE5 48 1.2629 - angle_coeff @angle:c-oh-ho harmonic 51.617 106.550 # SOURCE3_SOURCE5 2765 1.0627 - angle_coeff @angle:cl-oh-ho harmonic 50.601 102.400 # SOURCE2 1 - angle_coeff @angle:cx-oh-ho harmonic 51.376 106.170 # SOURCE3 3 0.0644 - angle_coeff @angle:cy-oh-ho harmonic 49.289 107.690 # SOURCE4_SOURCE5 21 0.5952 - angle_coeff @angle:f-oh-ho harmonic 64.650 96.800 # SOURCE2 1 - angle_coeff @angle:ho-oh-ho harmonic 42.178 106.490 # SOURCE2_SOURCE5 23 1.3050 - angle_coeff @angle:ho-oh-i harmonic 37.979 107.980 # SOURCE3 2 - angle_coeff @angle:ho-oh-n1 harmonic 66.474 107.810 # HF/6-31G* 1 - angle_coeff @angle:ho-oh-n2 harmonic 63.987 103.090 # SOURCE3_SOURCE5 185 1.2900 - angle_coeff @angle:ho-oh-n3 harmonic 63.233 102.260 # SOURCE3_SOURCE5 28 0.5790 - angle_coeff @angle:ho-oh-n4 harmonic 62.546 106.630 # SOURCE3 3 0.2770 - angle_coeff @angle:ho-oh-n harmonic 63.907 101.290 # SOURCE3_SOURCE5 114 1.0315 - angle_coeff @angle:ho-oh-na harmonic 63.538 104.370 # SOURCE3_SOURCE5 16 0.9188 - angle_coeff @angle:ho-oh-nh harmonic 63.021 102.770 # SOURCE4_SOURCE5 57 0.7554 - angle_coeff @angle:ho-oh-no harmonic 63.640 102.170 # SOURCE3 1 - angle_coeff @angle:ho-oh-o harmonic 59.432 100.870 # SOURCE3 1 - angle_coeff @angle:ho-oh-oh harmonic 62.055 98.720 # SOURCE3 2 - angle_coeff @angle:ho-oh-os harmonic 62.321 99.680 # SOURCE4_SOURCE5 45 0.3142 - angle_coeff @angle:ho-oh-p2 harmonic 58.567 109.450 # SOURCE3 8 3.3491 - angle_coeff @angle:ho-oh-p3 harmonic 56.437 110.640 # SOURCE3 3 0.5191 - angle_coeff @angle:ho-oh-p4 harmonic 57.939 110.190 # SOURCE3 4 0.2372 - angle_coeff @angle:ho-oh-p5 harmonic 58.997 110.080 # SOURCE3_SOURCE5 1074 1.1258 - angle_coeff @angle:ho-oh-py harmonic 58.835 110.490 # SOURCE3_SOURCE5 115 1.4927 - angle_coeff @angle:ho-oh-s4 harmonic 44.189 106.850 # SOURCE4_SOURCE5 28 0.5669 - angle_coeff @angle:ho-oh-s harmonic 42.242 100.150 # SOURCE3 2 - angle_coeff @angle:ho-oh-s6 harmonic 45.957 107.260 # SOURCE3_SOURCE5 180 0.7965 - angle_coeff @angle:ho-oh-sh harmonic 44.429 106.240 # SOURCE3 2 0.0661 - angle_coeff @angle:ho-oh-ss harmonic 44.367 107.110 # SOURCE3_SOURCE5 12 1.0472 - angle_coeff @angle:ho-oh-sy harmonic 45.671 106.420 # SOURCE4_SOURCE5 121 0.3216 - angle_coeff @angle:br-os-br harmonic 67.436 110.630 # SOURCE3 1 - angle_coeff @angle:c1-os-c1 harmonic 71.202 115.020 # SOURCE3 1 - angle_coeff @angle:c1-os-c3 harmonic 68.518 113.390 # SOURCE3 1 - angle_coeff @angle:c2-os-c2 harmonic 69.600 113.140 # SOURCE3 6 2.1932 - angle_coeff @angle:c2-os-c3 harmonic 66.993 115.590 # SOURCE3_SOURCE5 149 2.3501 - angle_coeff @angle:c2-os-ca harmonic 67.843 118.200 # SOURCE3_SOURCE5 13 0.6779 - angle_coeff @angle:c2-os-n2 harmonic 83.963 118.130 # SOURCE3 1 - angle_coeff @angle:c2-os-na harmonic 88.073 103.850 # SOURCE3 4 0.6297 - angle_coeff @angle:c2-os-os harmonic 87.781 102.770 # SOURCE3 1 - angle_coeff @angle:c2-os-p5 harmonic 82.312 126.370 # SOURCE4 7 1.7939 - angle_coeff @angle:c2-os-ss harmonic 66.609 108.130 # SOURCE3 1 - angle_coeff @angle:c3-os-c3 harmonic 66.293 112.480 # SOURCE4_SOURCE5 4012 1.7399 - angle_coeff @angle:c3-os-ca harmonic 66.103 117.960 # SOURCE4_SOURCE5 7354 1.4497 - angle_coeff @angle:c3-os-cc harmonic 66.432 117.370 # CORR_SOURCE5 411 1.1548 - angle_coeff @angle:c3-os-cd harmonic 66.432 117.370 # CORR_SOURCE5 411 1.1548 - angle_coeff @angle:c3-os-ce harmonic 66.603 116.090 # CORR_SOURCE5 59 1.9942 - angle_coeff @angle:c3-os-cf harmonic 66.603 116.090 # CORR_SOURCE5 59 1.9942 - angle_coeff @angle:c3-os-cl harmonic 71.832 110.500 # SOURCE2 1 - angle_coeff @angle:c3-os-cy harmonic 66.337 111.750 # SOURCE4_SOURCE5 19 0.7990 - angle_coeff @angle:c3-os-i harmonic 59.723 113.700 # SOURCE3 1 - angle_coeff @angle:c3-os-n1 harmonic 85.969 113.500 # HF/6-31G* 1 - angle_coeff @angle:c3-os-n2 harmonic 85.118 109.230 # SOURCE3_SOURCE5 93 0.8090 - angle_coeff @angle:c3-os-n3 harmonic 83.747 109.830 # SOURCE4_SOURCE5 46 1.7350 - angle_coeff @angle:c3-os-n4 harmonic 84.065 110.500 # SOURCE3 3 0.5426 - angle_coeff @angle:c3-os-n harmonic 84.730 109.680 # SOURCE4_SOURCE5 42 0.9897 - angle_coeff @angle:c3-os-na harmonic 83.212 110.980 # SOURCE3_SOURCE5 17 1.2781 - angle_coeff @angle:c3-os-nc harmonic 83.792 112.730 # SOURCE3 2 1.0358 - angle_coeff @angle:c3-os-nd harmonic 83.792 112.730 # SOURCE3 2 - angle_coeff @angle:c3-os-nh harmonic 84.502 109.790 # SOURCE4_SOURCE5 22 0.2157 - angle_coeff @angle:c3-os-no harmonic 82.802 113.890 # SOURCE4_SOURCE5 112 0.3140 - angle_coeff @angle:c3-os-o harmonic 84.510 103.000 # SOURCE3 1 - angle_coeff @angle:c3-os-oh harmonic 83.965 108.110 # SOURCE4_SOURCE5 34 0.5701 - angle_coeff @angle:c3-os-os harmonic 83.957 107.370 # SOURCE3_SOURCE5 55 0.9835 - angle_coeff @angle:c3-os-p2 harmonic 86.122 115.470 # SOURCE3 8 2.6374 - angle_coeff @angle:c3-os-p3 harmonic 81.943 117.510 # SOURCE3_SOURCE5 11 0.9552 - angle_coeff @angle:c3-os-p4 harmonic 83.257 117.480 # SOURCE3 4 0.3850 - angle_coeff @angle:c3-os-p5 harmonic 83.251 119.540 # SOURCE3_SOURCE5 665 1.1338 - angle_coeff @angle:c3-os-py harmonic 83.113 119.570 # SOURCE3_SOURCE5 59 1.1952 - angle_coeff @angle:c3-os-s4 harmonic 64.572 113.210 # SOURCE3_SOURCE5 18 1.1865 - angle_coeff @angle:c3-os-s6 harmonic 65.683 115.870 # SOURCE4_SOURCE5 144 1.2750 - angle_coeff @angle:c3-os-s harmonic 62.691 109.550 # SOURCE3 1 - angle_coeff @angle:c3-os-sh harmonic 65.257 112.820 # SOURCE3 1 - angle_coeff @angle:c3-os-ss harmonic 64.028 114.010 # SOURCE3_SOURCE5 8 0.2853 - angle_coeff @angle:ca-os-ca harmonic 67.119 119.890 # SOURCE4_SOURCE5 312 1.5712 - angle_coeff @angle:ca-os-cc harmonic 69.301 113.080 # CORR_SOURCE5 343 1.5098 - angle_coeff @angle:ca-os-cd harmonic 69.301 113.080 # CORR_SOURCE5 343 1.5098 - angle_coeff @angle:ca-os-n3 harmonic 84.583 112.190 # SOURCE3 1 - angle_coeff @angle:ca-os-na harmonic 85.998 108.240 # SOURCE3 1 - angle_coeff @angle:ca-os-nc harmonic 86.989 109.320 # SOURCE3_SOURCE5 7 0.0434 - angle_coeff @angle:ca-os-nd harmonic 86.989 109.320 # SOURCE3_SOURCE5 7 0.0434 - angle_coeff @angle:ca-os-p5 harmonic 83.193 123.180 # SOURCE4_SOURCE5 136 1.2191 - angle_coeff @angle:ca-os-s6 harmonic 66.238 117.180 # SOURCE4_SOURCE5 46 1.0420 - angle_coeff @angle:c-os-c2 harmonic 68.118 118.220 # SOURCE4_SOURCE5 22 0.6933 - angle_coeff @angle:c-os-c3 harmonic 66.906 115.980 # SOURCE3_SOURCE5 2731 1.0103 - angle_coeff @angle:c-os-c harmonic 67.462 120.640 # SOURCE4 7 1.5114 - angle_coeff @angle:c-os-ca harmonic 67.041 121.150 # SOURCE4_SOURCE5 731 1.7389 - angle_coeff @angle:c-os-cc harmonic 67.659 119.620 # SOURCE3 5 6.0675 - angle_coeff @angle:cc-os-cc harmonic 71.537 106.720 # CORR_SOURCE5 406 0.7345 - angle_coeff @angle:cc-os-cd harmonic 67.837 118.680 # SOURCE4_SOURCE5 49 2.2289 - angle_coeff @angle:c-os-cd harmonic 67.659 119.620 # SOURCE3 5 6.0675 - angle_coeff @angle:cc-os-na harmonic 84.874 111.660 # SOURCE3 28 4.1343 - angle_coeff @angle:cc-os-nc harmonic 87.598 108.370 # SOURCE3_SOURCE5 148 0.8594 - angle_coeff @angle:cc-os-os harmonic 85.382 108.470 # SOURCE3 2 - angle_coeff @angle:cc-os-ss harmonic 63.313 119.590 # SOURCE3 1 - angle_coeff @angle:c-os-cy harmonic 75.270 91.100 # SOURCE3 2 0.0155 - angle_coeff @angle:cd-os-cd harmonic 71.537 106.720 # CORR_SOURCE5 406 0.7345 - angle_coeff @angle:cd-os-na harmonic 84.874 111.660 # SOURCE3 28 4.1343 - angle_coeff @angle:cd-os-nd harmonic 87.598 108.370 # SOURCE3_SOURCE5 148 0.8594 - angle_coeff @angle:cd-os-os harmonic 85.382 108.470 # SOURCE3 2 - angle_coeff @angle:cd-os-ss harmonic 63.313 119.590 # SOURCE3 1 - angle_coeff @angle:cl-os-cl harmonic 80.567 110.760 # SOURCE3 2 - angle_coeff @angle:c-os-n2 harmonic 86.219 112.120 # SOURCE4_SOURCE5 16 0.1285 - angle_coeff @angle:c-os-n harmonic 85.927 112.240 # SOURCE4_SOURCE5 17 0.6206 - angle_coeff @angle:c-os-oh harmonic 85.021 110.500 # SOURCE3 1 - angle_coeff @angle:c-os-os harmonic 84.800 110.200 # SOURCE4_SOURCE5 22 1.3187 - angle_coeff @angle:c-os-p5 harmonic 83.749 122.130 # SOURCE4_SOURCE5 11 0.5685 - angle_coeff @angle:c-os-sy harmonic 65.179 113.490 # SOURCE3 1 - angle_coeff @angle:cx-os-cx harmonic 89.127 61.780 # SOURCE4_SOURCE5 379 0.2104 - angle_coeff @angle:cx-os-n harmonic 114.351 59.990 # SOURCE3 1 - angle_coeff @angle:cx-os-os harmonic 115.519 56.520 # SOURCE3 2 - angle_coeff @angle:cy-os-cy harmonic 72.980 91.860 # SOURCE2_SOURCE5 16 1.0042 - angle_coeff @angle:f-os-f harmonic 112.297 103.300 # SOURCE2 1 - angle_coeff @angle:f-os-os harmonic 105.904 109.500 # SOURCE2 1 - angle_coeff @angle:i-os-i harmonic 65.023 115.670 # SOURCE3 1 - angle_coeff @angle:n1-os-n1 harmonic 111.016 117.790 # HF/6-31G* 1 - angle_coeff @angle:n2-os-n2 harmonic 108.962 106.830 # SOURCE3 1 - angle_coeff @angle:n2-os-s6 harmonic 84.516 111.300 # SOURCE4_SOURCE5 14 0.5651 - angle_coeff @angle:n3-os-n3 harmonic 106.985 104.880 # SOURCE3 1 - angle_coeff @angle:n4-os-n4 harmonic 103.723 114.680 # SOURCE3 1 - angle_coeff @angle:na-os-na harmonic 104.414 109.590 # SOURCE3 1 - angle_coeff @angle:na-os-ss harmonic 83.603 104.340 # SOURCE3 1 - angle_coeff @angle:nc-os-nc harmonic 106.078 112.750 # SOURCE2_SOURCE5 12 0.7540 - angle_coeff @angle:nc-os-ss harmonic 81.743 110.970 # SOURCE3 1 - angle_coeff @angle:nd-os-nd harmonic 106.078 112.750 # SOURCE2_SOURCE5 12 0.7540 - angle_coeff @angle:nd-os-ss harmonic 81.743 110.970 # SOURCE3 1 - angle_coeff @angle:nh-os-nh harmonic 107.169 108.290 # SOURCE3 1 - angle_coeff @angle:n-os-n harmonic 107.646 108.310 # SOURCE3 1 - angle_coeff @angle:no-os-no harmonic 105.015 111.860 # SOURCE3 1 - angle_coeff @angle:n-os-s6 harmonic 83.504 113.630 # SOURCE4_SOURCE5 13 0.1799 - angle_coeff @angle:o-os-o harmonic 97.999 114.680 # SOURCE3 1 - angle_coeff @angle:p2-os-p2 harmonic 112.427 120.020 # SOURCE3 1 - angle_coeff @angle:p2-os-p5 harmonic 117.003 107.860 # SOURCE3 1 - angle_coeff @angle:p3-os-p3 harmonic 105.094 121.220 # SOURCE3 1 - angle_coeff @angle:p3-os-py harmonic 114.455 105.580 # SOURCE3 1 - angle_coeff @angle:p5-os-p5 harmonic 106.787 126.250 # SOURCE3 1 - angle_coeff @angle:s4-os-s4 harmonic 65.797 111.630 # SOURCE3 1 - angle_coeff @angle:s6-os-s6 harmonic 66.445 119.070 # SOURCE3 2 0.4318 - angle_coeff @angle:sh-os-sh harmonic 64.549 118.950 # SOURCE3 1 - angle_coeff @angle:s-os-s harmonic 60.143 118.080 # SOURCE3 1 - angle_coeff @angle:ss-os-ss harmonic 64.198 115.640 # SOURCE3 1 - angle_coeff @angle:br-p2-br harmonic 50.367 108.600 # SOURCE3 1 - angle_coeff @angle:br-p2-c2 harmonic 49.320 102.320 # SOURCE3 2 0.0146 - angle_coeff @angle:br-p2-n2 harmonic 61.779 103.330 # SOURCE3 1 - angle_coeff @angle:br-p2-o harmonic 59.925 110.870 # SOURCE3 1 - angle_coeff @angle:br-p2-p2 harmonic 63.559 115.460 # SOURCE3 4 7.8622 - angle_coeff @angle:br-p2-s harmonic 50.714 110.520 # SOURCE3 1 - angle_coeff @angle:c1-p2-c1 harmonic 49.523 99.040 # SOURCE3 1 - angle_coeff @angle:c1-p2-c2 harmonic 50.326 101.290 # SOURCE3 1 - angle_coeff @angle:c1-p2-n2 harmonic 63.856 101.790 # SOURCE3 1 - angle_coeff @angle:c1-p2-o harmonic 63.431 107.620 # SOURCE3 1 - angle_coeff @angle:c1-p2-p2 harmonic 68.223 99.540 # SOURCE3 1 - angle_coeff @angle:c1-p2-s harmonic 51.746 105.900 # SOURCE3 1 - angle_coeff @angle:c2-p2-c2 harmonic 51.141 104.500 # SOURCE3 1 - angle_coeff @angle:c2-p2-c3 harmonic 48.776 101.900 # SOURCE3 4 0.1132 - angle_coeff @angle:c2-p2-ca harmonic 49.013 101.950 # SOURCE3 1 - angle_coeff @angle:c2-p2-cl harmonic 54.318 102.720 # SOURCE3 2 - angle_coeff @angle:c2-p2-f harmonic 67.755 103.470 # SOURCE3 2 0.0136 - angle_coeff @angle:c2-p2-hp harmonic 37.280 97.190 # SOURCE3 3 0.0216 - angle_coeff @angle:c2-p2-i harmonic 44.010 101.940 # SOURCE3 2 0.0368 - angle_coeff @angle:c2-p2-n2 harmonic 66.728 99.880 # SOURCE3 1 - angle_coeff @angle:c2-p2-n3 harmonic 64.858 101.800 # SOURCE3 1 - angle_coeff @angle:c2-p2-n4 harmonic 60.347 98.260 # SOURCE3 6 0.1522 - angle_coeff @angle:c2-p2-n harmonic 63.154 103.280 # SOURCE3 4 3.3113 - angle_coeff @angle:c2-p2-na harmonic 62.619 103.990 # SOURCE3 8 1.6834 - angle_coeff @angle:c2-p2-nh harmonic 63.638 105.170 # SOURCE3 8 0.8263 - angle_coeff @angle:c2-p2-no harmonic 64.740 97.970 # SOURCE3 3 0.4175 - angle_coeff @angle:c2-p2-o harmonic 63.763 115.160 # SOURCE3 1 - angle_coeff @angle:c2-p2-oh harmonic 65.278 102.890 # SOURCE3 3 0.8191 - angle_coeff @angle:c2-p2-os harmonic 66.578 102.120 # SOURCE3 4 0.8783 - angle_coeff @angle:c2-p2-p2 harmonic 70.059 99.560 # SOURCE3 1 - angle_coeff @angle:c2-p2-p3 harmonic 61.583 99.270 # SOURCE3 4 1.1590 - angle_coeff @angle:c2-p2-p4 harmonic 61.685 96.940 # SOURCE3 1 - angle_coeff @angle:c2-p2-p5 harmonic 61.450 97.610 # SOURCE3 1 - angle_coeff @angle:c2-p2-s4 harmonic 48.314 95.150 # SOURCE3 1 - angle_coeff @angle:c2-p2-s6 harmonic 48.407 95.510 # SOURCE3 1 - angle_coeff @angle:c2-p2-s harmonic 53.268 105.530 # SOURCE3 1 - angle_coeff @angle:c2-p2-sh harmonic 50.735 101.490 # SOURCE3 3 0.0057 - angle_coeff @angle:c2-p2-ss harmonic 50.746 101.810 # SOURCE3 4 0.5883 - angle_coeff @angle:c3-p2-c3 harmonic 47.191 99.300 # SOURCE3 1 - angle_coeff @angle:c3-p2-n2 harmonic 62.233 100.820 # SOURCE3 1 - angle_coeff @angle:c3-p2-o harmonic 61.561 106.720 # SOURCE3 1 - angle_coeff @angle:c3-p2-os harmonic 62.459 101.340 # SOURCE3 1 - angle_coeff @angle:c3-p2-p2 harmonic 66.273 100.480 # SOURCE3 1 - angle_coeff @angle:c3-p2-s harmonic 50.533 105.680 # SOURCE3 1 - angle_coeff @angle:ca-p2-ca harmonic 47.481 99.700 # SOURCE3 1 - angle_coeff @angle:ca-p2-n2 harmonic 62.575 100.820 # SOURCE3 1 - angle_coeff @angle:ca-p2-n harmonic 64.349 89.970 # SOURCE3 1 - angle_coeff @angle:ca-p2-na harmonic 64.367 89.210 # SOURCE3 1 - angle_coeff @angle:ca-p2-o harmonic 61.891 106.880 # SOURCE3 1 - angle_coeff @angle:ca-p2-s harmonic 50.228 107.930 # SOURCE3 1 - angle_coeff @angle:c-p2-c2 harmonic 49.148 97.300 # SOURCE3 1 - angle_coeff @angle:c-p2-c harmonic 48.369 90.100 # SOURCE3 1 - angle_coeff @angle:ce-p2-o harmonic 62.381 107.440 # SOURCE3 1 - angle_coeff @angle:ce-p2-s harmonic 51.184 105.540 # SOURCE3 1 - angle_coeff @angle:cf-p2-o harmonic 62.381 107.440 # SOURCE3 1 - angle_coeff @angle:cf-p2-s harmonic 51.184 105.540 # SOURCE3 1 - angle_coeff @angle:cl-p2-cl harmonic 58.906 108.700 # SOURCE3 1 - angle_coeff @angle:cl-p2-n2 harmonic 68.360 103.380 # SOURCE3 1 - angle_coeff @angle:cl-p2-o harmonic 66.726 110.570 # SOURCE3 1 - angle_coeff @angle:cl-p2-p2 harmonic 73.823 103.110 # SOURCE3 1 - angle_coeff @angle:cl-p2-s harmonic 55.803 110.110 # SOURCE3 1 - angle_coeff @angle:f-p2-f harmonic 88.550 107.100 # SOURCE3 1 - angle_coeff @angle:f-p2-n2 harmonic 86.735 103.570 # SOURCE3 1 - angle_coeff @angle:f-p2-o harmonic 86.673 110.610 # SOURCE3 1 - angle_coeff @angle:f-p2-p2 harmonic 89.962 103.480 # SOURCE3 1 - angle_coeff @angle:f-p2-s harmonic 66.939 114.710 # SOURCE3 2 5.2794 - angle_coeff @angle:hp-p2-hp harmonic 27.644 98.760 # SOURCE3 1 - angle_coeff @angle:hp-p2-n1 harmonic 46.969 95.180 # SOURCE3 2 1.5708 - angle_coeff @angle:hp-p2-n2 harmonic 48.480 95.540 # SOURCE3 19 4.7352 - angle_coeff @angle:hp-p2-ne harmonic 48.264 100.100 # SOURCE3 14 6.1290 - angle_coeff @angle:hp-p2-nf harmonic 48.264 100.100 # SOURCE3 14 - angle_coeff @angle:hp-p2-o harmonic 48.141 105.580 # SOURCE3 1 - angle_coeff @angle:hp-p2-p2 harmonic 47.796 101.880 # SOURCE3 27 12.9535 - angle_coeff @angle:hp-p2-p4 harmonic 40.954 94.510 # SOURCE3 1 - angle_coeff @angle:hp-p2-p5 harmonic 42.165 89.070 # SOURCE3 1 - angle_coeff @angle:hp-p2-pe harmonic 47.048 97.250 # SOURCE3 16 8.8916 - angle_coeff @angle:hp-p2-pf harmonic 47.048 97.250 # SOURCE3 16 - angle_coeff @angle:hp-p2-s4 harmonic 32.527 89.990 # SOURCE3 1 - angle_coeff @angle:hp-p2-s harmonic 37.377 102.520 # SOURCE3 1 - angle_coeff @angle:hp-p2-s6 harmonic 33.031 88.130 # SOURCE3 1 - angle_coeff @angle:i-p2-i harmonic 47.836 104.160 # SOURCE3 1 - angle_coeff @angle:i-p2-n2 harmonic 55.025 101.770 # SOURCE3 1 - angle_coeff @angle:i-p2-o harmonic 52.674 109.510 # SOURCE3 1 - angle_coeff @angle:i-p2-p2 harmonic 60.877 102.630 # SOURCE3 1 - angle_coeff @angle:i-p2-s harmonic 45.705 110.600 # SOURCE3 1 - angle_coeff @angle:n1-p2-n1 harmonic 87.795 86.220 # HF/6-31G* 1 - angle_coeff @angle:n2-p2-n2 harmonic 86.095 98.000 # SOURCE3 1 - angle_coeff @angle:n2-p2-n3 harmonic 83.297 100.420 # SOURCE3 1 - angle_coeff @angle:n2-p2-n4 harmonic 78.374 93.420 # SOURCE3 1 - angle_coeff @angle:n2-p2-na harmonic 80.458 102.030 # SOURCE3 1 - angle_coeff @angle:n2-p2-nh harmonic 82.457 101.870 # SOURCE3 2 0.8491 - angle_coeff @angle:n2-p2-no harmonic 82.358 98.120 # SOURCE3 1 - angle_coeff @angle:n2-p2-o harmonic 81.674 115.340 # SOURCE3 1 - angle_coeff @angle:n2-p2-oh harmonic 80.728 109.720 # SOURCE3 1 - angle_coeff @angle:n2-p2-os harmonic 85.101 102.290 # SOURCE3 1 - angle_coeff @angle:n2-p2-p3 harmonic 77.520 99.510 # SOURCE3 1 - angle_coeff @angle:n2-p2-p4 harmonic 75.847 101.730 # SOURCE3 1 - angle_coeff @angle:n2-p2-p5 harmonic 79.007 93.680 # SOURCE3 1 - angle_coeff @angle:n2-p2-s4 harmonic 60.003 97.830 # SOURCE3 1 - angle_coeff @angle:n2-p2-s6 harmonic 60.149 98.140 # SOURCE3 1 - angle_coeff @angle:n2-p2-s harmonic 65.491 112.940 # SOURCE3 1 - angle_coeff @angle:n2-p2-sh harmonic 64.416 100.820 # SOURCE3 1 - angle_coeff @angle:n2-p2-ss harmonic 64.240 101.760 # SOURCE3 1 - angle_coeff @angle:n3-p2-n3 harmonic 79.448 106.300 # SOURCE3 1 - angle_coeff @angle:n3-p2-o harmonic 82.859 106.830 # SOURCE3 1 - angle_coeff @angle:n3-p2-p2 harmonic 87.256 100.580 # SOURCE3 1 - angle_coeff @angle:n3-p2-s harmonic 66.611 105.750 # SOURCE3 1 - angle_coeff @angle:n4-p2-n4 harmonic 74.750 88.800 # SOURCE3 1 - angle_coeff @angle:n4-p2-o harmonic 76.313 101.360 # SOURCE3 1 - angle_coeff @angle:n4-p2-p2 harmonic 82.466 96.530 # SOURCE3 1 - angle_coeff @angle:n4-p2-s harmonic 61.808 104.980 # SOURCE3 1 - angle_coeff @angle:na-p2-na harmonic 75.931 106.100 # SOURCE3 1 - angle_coeff @angle:na-p2-o harmonic 80.149 107.460 # SOURCE3 1 - angle_coeff @angle:na-p2-s harmonic 64.498 108.150 # SOURCE3 1 - angle_coeff @angle:ne-p2-o harmonic 85.784 107.710 # SOURCE3 1 - angle_coeff @angle:ne-p2-s harmonic 68.411 105.500 # SOURCE3 1 - angle_coeff @angle:nf-p2-o harmonic 85.784 107.710 # SOURCE3 1 - angle_coeff @angle:nf-p2-s harmonic 68.411 105.500 # SOURCE3 1 - angle_coeff @angle:nh-p2-nh harmonic 79.891 104.000 # SOURCE3 1 - angle_coeff @angle:nh-p2-o harmonic 82.088 108.110 # SOURCE3 2 0.6773 - angle_coeff @angle:nh-p2-p2 harmonic 84.120 107.730 # SOURCE3 3 3.1678 - angle_coeff @angle:nh-p2-s harmonic 65.274 109.620 # SOURCE3 2 1.7725 - angle_coeff @angle:n-p2-n2 harmonic 82.195 98.850 # SOURCE3 1 - angle_coeff @angle:n-p2-o harmonic 81.559 105.080 # SOURCE3 1 - angle_coeff @angle:no-p2-no harmonic 79.425 98.200 # SOURCE3 1 - angle_coeff @angle:no-p2-o harmonic 81.482 104.870 # SOURCE3 1 - angle_coeff @angle:no-p2-p2 harmonic 82.518 108.570 # SOURCE3 3 8.2121 - angle_coeff @angle:no-p2-s harmonic 64.423 109.060 # SOURCE3 2 5.4074 - angle_coeff @angle:n-p2-p2 harmonic 85.198 102.120 # SOURCE3 1 - angle_coeff @angle:n-p2-s harmonic 63.562 112.340 # SOURCE3 1 - angle_coeff @angle:oh-p2-oh harmonic 83.880 100.100 # SOURCE3 1 - angle_coeff @angle:oh-p2-p2 harmonic 85.099 107.820 # SOURCE3 2 2.6708 - angle_coeff @angle:oh-p2-s harmonic 66.041 109.750 # SOURCE3 1 - angle_coeff @angle:o-p2-o harmonic 82.822 119.960 # SOURCE3 1 - angle_coeff @angle:o-p2-oh harmonic 82.704 110.460 # SOURCE3 1 - angle_coeff @angle:o-p2-os harmonic 85.052 108.810 # SOURCE3 1 - angle_coeff @angle:o-p2-p2 harmonic 84.879 114.230 # SOURCE3 1 - angle_coeff @angle:o-p2-p3 harmonic 75.364 106.690 # SOURCE3 1 - angle_coeff @angle:o-p2-p4 harmonic 75.313 104.370 # SOURCE3 1 - angle_coeff @angle:o-p2-p5 harmonic 75.237 104.490 # SOURCE3 1 - angle_coeff @angle:o-p2-pe harmonic 72.675 145.960 # SOURCE3 1 - angle_coeff @angle:o-p2-pf harmonic 72.675 145.960 # SOURCE3 1 - angle_coeff @angle:o-p2-s4 harmonic 57.795 106.590 # SOURCE3 1 - angle_coeff @angle:o-p2-s6 harmonic 58.473 105.040 # SOURCE3 1 - angle_coeff @angle:o-p2-s harmonic 65.598 117.420 # SOURCE3 1 - angle_coeff @angle:o-p2-sh harmonic 62.592 109.600 # SOURCE3 1 - angle_coeff @angle:os-p2-os harmonic 87.712 98.300 # SOURCE3 1 - angle_coeff @angle:os-p2-p2 harmonic 88.869 101.460 # SOURCE3 1 - angle_coeff @angle:o-p2-ss harmonic 62.723 109.600 # SOURCE3 1 - angle_coeff @angle:os-p2-s harmonic 67.319 108.470 # SOURCE3 3 1.7065 - angle_coeff @angle:p2-p2-n2 harmonic 90.057 97.400 # SOURCE3 1 - angle_coeff @angle:p2-p2-p3 harmonic 83.101 101.730 # SOURCE3 1 - angle_coeff @angle:p2-p2-p4 harmonic 82.238 101.980 # SOURCE3 1 - angle_coeff @angle:p2-p2-p5 harmonic 83.299 99.330 # SOURCE3 1 - angle_coeff @angle:p2-p2-s4 harmonic 65.891 95.730 # SOURCE3 1 - angle_coeff @angle:p2-p2-s6 harmonic 66.042 95.950 # SOURCE3 1 - angle_coeff @angle:p2-p2-s harmonic 69.717 111.280 # SOURCE3 1 - angle_coeff @angle:p2-p2-sh harmonic 64.935 113.940 # SOURCE3 3 8.5009 - angle_coeff @angle:p3-p2-p3 harmonic 77.638 101.000 # SOURCE3 1 - angle_coeff @angle:p3-p2-s harmonic 61.492 113.280 # SOURCE3 2 6.7035 - angle_coeff @angle:p4-p2-s harmonic 63.615 103.890 # SOURCE3 1 - angle_coeff @angle:p5-p2-p5 harmonic 81.461 89.400 # SOURCE3 1 - angle_coeff @angle:p5-p2-s harmonic 64.429 101.210 # SOURCE3 1 - angle_coeff @angle:pe-p2-s harmonic 69.635 106.350 # SOURCE3 1 - angle_coeff @angle:pf-p2-s harmonic 69.635 106.350 # SOURCE3 1 - angle_coeff @angle:s4-p2-s4 harmonic 50.406 85.300 # SOURCE3 1 - angle_coeff @angle:s6-p2-s6 harmonic 47.194 98.200 # SOURCE3 1 - angle_coeff @angle:sh-p2-sh harmonic 52.119 98.500 # SOURCE3 1 - angle_coeff @angle:s-p2-s harmonic 55.726 106.600 # SOURCE3 1 - angle_coeff @angle:s-p2-s4 harmonic 49.051 105.290 # SOURCE3 1 - angle_coeff @angle:s-p2-s6 harmonic 48.843 106.930 # SOURCE3 1 - angle_coeff @angle:s-p2-sh harmonic 51.478 110.730 # SOURCE3 2 0.0232 - angle_coeff @angle:s-p2-ss harmonic 50.784 114.140 # SOURCE3 4 5.9223 - angle_coeff @angle:ss-p2-ss harmonic 52.411 97.900 # SOURCE3 1 - angle_coeff @angle:br-p3-br harmonic 51.098 103.540 # SOURCE3 1 - angle_coeff @angle:br-p3-hp harmonic 32.984 96.360 # SOURCE3 4 0.6701 - angle_coeff @angle:c1-p3-c1 harmonic 48.612 100.500 # SOURCE3 1 - angle_coeff @angle:c1-p3-f harmonic 66.318 96.900 # SOURCE2 1 - angle_coeff @angle:c1-p3-hp harmonic 34.779 97.670 # SOURCE3 2 - angle_coeff @angle:c2-p3-c2 harmonic 47.149 101.770 # SOURCE3 3 - angle_coeff @angle:c2-p3-hp harmonic 34.073 97.850 # SOURCE3 4 - angle_coeff @angle:c3-p3-c3 harmonic 47.098 99.350 # SOURCE3_SOURCE5 108 0.9814 - angle_coeff @angle:c3-p3-ca harmonic 46.899 101.940 # SOURCE3 2 - angle_coeff @angle:c3-p3-cl harmonic 54.343 99.890 # SOURCE3 1 - angle_coeff @angle:c3-p3-f harmonic 64.355 97.800 # SOURCE2 1 - angle_coeff @angle:c3-p3-hp harmonic 33.769 97.480 # SOURCE3_SOURCE5 20 0.3444 - angle_coeff @angle:c3-p3-n2 harmonic 61.301 96.550 # SOURCE3 2 - angle_coeff @angle:c3-p3-n3 harmonic 60.308 101.410 # SOURCE3_SOURCE5 22 1.5604 - angle_coeff @angle:c3-p3-n4 harmonic 59.355 96.940 # SOURCE3 6 0.4815 - angle_coeff @angle:c3-p3-n harmonic 59.620 101.770 # SOURCE3 12 2.4449 - angle_coeff @angle:c3-p3-na harmonic 60.213 100.170 # SOURCE3 4 0.0554 - angle_coeff @angle:c3-p3-nh harmonic 59.410 104.500 # SOURCE3 2 - angle_coeff @angle:c3-p3-no harmonic 59.922 96.980 # SOURCE3 2 - angle_coeff @angle:c3-p3-o harmonic 60.035 111.670 # SOURCE3 28 5.3387 - angle_coeff @angle:c3-p3-oh harmonic 62.034 98.210 # SOURCE3 2 - angle_coeff @angle:c3-p3-os harmonic 61.657 99.530 # SOURCE3 3 1.7678 - angle_coeff @angle:c3-p3-p3 harmonic 58.575 99.880 # SOURCE3_SOURCE5 26 1.6230 - angle_coeff @angle:c3-p3-p5 harmonic 58.297 100.900 # SOURCE3 10 2.7070 - angle_coeff @angle:c3-p3-s4 harmonic 47.756 98.880 # SOURCE3 8 6.2235 - angle_coeff @angle:c3-p3-s6 harmonic 47.355 101.180 # SOURCE3 12 6.4536 - angle_coeff @angle:c3-p3-sh harmonic 47.131 98.710 # SOURCE3 2 - angle_coeff @angle:c3-p3-ss harmonic 47.137 99.370 # SOURCE3 2 - angle_coeff @angle:ca-p3-ca harmonic 47.814 99.860 # SOURCE3 1 - angle_coeff @angle:ca-p3-hp harmonic 34.261 97.500 # SOURCE3 2 - angle_coeff @angle:c-p3-c3 harmonic 47.331 97.060 # SOURCE3 3 1.1490 - angle_coeff @angle:c-p3-c harmonic 46.120 100.900 # SOURCE3 1 - angle_coeff @angle:c-p3-hp harmonic 33.554 96.550 # SOURCE3 6 0.5223 - angle_coeff @angle:cl-p3-cl harmonic 62.437 102.820 # SOURCE3 1 - angle_coeff @angle:cl-p3-f harmonic 72.784 99.200 # SOURCE2 1 - angle_coeff @angle:cl-p3-hp harmonic 38.308 96.300 # SOURCE3 3 0.6203 - angle_coeff @angle:c-p3-os harmonic 67.637 81.320 # SOURCE3 1 - angle_coeff @angle:cx-p3-hp harmonic 34.036 95.200 # SOURCE2 1 - angle_coeff @angle:f-p3-f harmonic 90.383 97.400 # SOURCE2 8 1.6636 - angle_coeff @angle:f-p3-hp harmonic 48.664 96.410 # SOURCE3 2 - angle_coeff @angle:f-p3-n3 harmonic 83.292 100.600 # SOURCE2 1 - angle_coeff @angle:f-p3-os harmonic 85.509 99.230 # SOURCE2_SOURCE5 5 0.5316 - angle_coeff @angle:f-p3-p3 harmonic 77.745 97.200 # SOURCE2 1 - angle_coeff @angle:hp-p3-hp harmonic 26.638 95.220 # SOURCE3_SOURCE5 51 2.1059 - angle_coeff @angle:hp-p3-i harmonic 29.813 96.190 # SOURCE3 4 0.6454 - angle_coeff @angle:hp-p3-n1 harmonic 47.221 92.980 # HF/6-31G* 1 - angle_coeff @angle:hp-p3-n2 harmonic 43.917 98.280 # SOURCE3 10 1.8860 - angle_coeff @angle:hp-p3-n3 harmonic 45.466 94.460 # SOURCE3 2 - angle_coeff @angle:hp-p3-n4 harmonic 42.822 93.210 # SOURCE3 2 - angle_coeff @angle:hp-p3-n harmonic 44.516 95.150 # SOURCE3 2 - angle_coeff @angle:hp-p3-na harmonic 44.183 97.270 # SOURCE3 12 0.9318 - angle_coeff @angle:hp-p3-nh harmonic 45.553 94.100 # SOURCE3 2 - angle_coeff @angle:hp-p3-no harmonic 43.557 93.060 # SOURCE3 2 - angle_coeff @angle:hp-p3-o harmonic 48.052 101.020 # SOURCE3 2 - angle_coeff @angle:hp-p3-oh harmonic 46.151 95.950 # SOURCE3 2 - angle_coeff @angle:hp-p3-os harmonic 45.868 97.350 # SOURCE3 6 2.8326 - angle_coeff @angle:hp-p3-p2 harmonic 40.595 99.110 # SOURCE3 16 4.3022 - angle_coeff @angle:hp-p3-p3 harmonic 40.175 95.520 # SOURCE3 4 0.0844 - angle_coeff @angle:hp-p3-p4 harmonic 40.047 95.950 # SOURCE3 6 0.0489 - angle_coeff @angle:hp-p3-p5 harmonic 40.189 95.540 # SOURCE3 2 - angle_coeff @angle:hp-p3-s4 harmonic 33.215 95.490 # SOURCE3 2 - angle_coeff @angle:hp-p3-s6 harmonic 33.822 92.950 # SOURCE3 2 - angle_coeff @angle:hp-p3-sh harmonic 32.748 94.210 # SOURCE3 2 - angle_coeff @angle:hp-p3-ss harmonic 32.846 94.610 # SOURCE3 2 - angle_coeff @angle:i-p3-i harmonic 49.016 105.250 # SOURCE3 1 - angle_coeff @angle:n1-p3-n1 harmonic 86.652 90.440 # HF/6-31G* 1 - angle_coeff @angle:n2-p3-n2 harmonic 76.240 103.460 # SOURCE3 1 - angle_coeff @angle:n3-p3-n3 harmonic 74.122 113.800 # SOURCE3 1 - angle_coeff @angle:n3-p3-o harmonic 80.756 107.100 # SOURCE3 4 - angle_coeff @angle:n3-p3-oh harmonic 80.929 98.360 # SOURCE3 1 - angle_coeff @angle:n4-p3-n4 harmonic 72.570 100.530 # SOURCE3 1 - angle_coeff @angle:na-p3-na harmonic 75.328 106.220 # SOURCE3 1 - angle_coeff @angle:nh-p3-nh harmonic 75.698 109.110 # SOURCE3 1 - angle_coeff @angle:n-p3-n harmonic 75.573 104.580 # SOURCE3 1 - angle_coeff @angle:n-p3-o harmonic 80.307 104.990 # SOURCE3 4 - angle_coeff @angle:no-p3-no harmonic 74.810 98.330 # SOURCE3 1 - angle_coeff @angle:oh-p3-oh harmonic 79.802 104.480 # SOURCE3 1 - angle_coeff @angle:o-p3-o harmonic 81.687 122.180 # SOURCE3 2 7.8556 - angle_coeff @angle:o-p3-p3 harmonic 70.126 116.740 # SOURCE3 14 0.7525 - angle_coeff @angle:o-p3-p5 harmonic 73.068 107.620 # SOURCE3 4 - angle_coeff @angle:o-p3-s4 harmonic 59.257 110.700 # SOURCE3 4 0.7259 - angle_coeff @angle:o-p3-s6 harmonic 60.626 106.660 # SOURCE3 6 3.4017 - angle_coeff @angle:os-p3-os harmonic 81.795 99.760 # SOURCE3_SOURCE5 8 1.2613 - angle_coeff @angle:p2-p3-p2 harmonic 76.665 103.580 # SOURCE3 1 - angle_coeff @angle:p3-p3-p3 harmonic 73.903 105.310 # SOURCE3 4 3.5864 - angle_coeff @angle:p4-p3-p4 harmonic 76.119 99.090 # SOURCE3 1 - angle_coeff @angle:p5-p3-p5 harmonic 76.218 99.100 # SOURCE3 1 - angle_coeff @angle:s4-p3-s4 harmonic 49.282 98.260 # SOURCE3 1 - angle_coeff @angle:s6-p3-s6 harmonic 49.641 97.780 # SOURCE3 1 - angle_coeff @angle:sh-p3-sh harmonic 46.105 107.580 # SOURCE3 1 - angle_coeff @angle:s-p3-s harmonic 42.980 131.320 # SOURCE3 1 - angle_coeff @angle:ss-p3-ss harmonic 45.990 109.240 # SOURCE3 1 - angle_coeff @angle:br-p4-br harmonic 50.850 110.410 # SOURCE3 1 - angle_coeff @angle:br-p4-o harmonic 57.453 124.800 # SOURCE3 1 - angle_coeff @angle:c2-p4-c2 harmonic 46.901 104.210 # SOURCE3 1 - angle_coeff @angle:c2-p4-hp harmonic 34.221 99.500 # SOURCE3 2 - angle_coeff @angle:c2-p4-o harmonic 60.517 113.590 # SOURCE3 1 - angle_coeff @angle:c3-p4-c3 harmonic 46.849 102.550 # SOURCE3 4 0.0192 - angle_coeff @angle:c3-p4-n2 harmonic 60.249 103.170 # SOURCE3 1 - angle_coeff @angle:c3-p4-n3 harmonic 60.876 102.370 # SOURCE3 1 - angle_coeff @angle:c3-p4-n4 harmonic 57.893 99.570 # SOURCE3 1 - angle_coeff @angle:c3-p4-n harmonic 60.075 103.260 # SOURCE3 1 - angle_coeff @angle:c3-p4-na harmonic 58.423 117.670 # SOURCE3 5 19.0404 - angle_coeff @angle:c3-p4-nh harmonic 60.622 102.790 # SOURCE3 1 - angle_coeff @angle:c3-p4-no harmonic 58.960 99.800 # SOURCE3 3 0.2151 - angle_coeff @angle:c3-p4-o harmonic 59.565 115.670 # SOURCE3_SOURCE5 41 1.9882 - angle_coeff @angle:c3-p4-oh harmonic 62.836 98.560 # SOURCE3 2 0.4558 - angle_coeff @angle:c3-p4-os harmonic 63.080 98.010 # SOURCE3 2 0.0931 - angle_coeff @angle:c3-p4-p2 harmonic 56.813 109.270 # SOURCE3 1 - angle_coeff @angle:c3-p4-p3 harmonic 57.663 103.530 # SOURCE3 1 - angle_coeff @angle:c3-p4-p4 harmonic 61.536 102.120 # SOURCE3 1 - angle_coeff @angle:c3-p4-p5 harmonic 57.093 104.150 # SOURCE3 1 - angle_coeff @angle:c3-p4-sh harmonic 47.201 100.170 # SOURCE3 2 0.0815 - angle_coeff @angle:c3-p4-ss harmonic 47.127 101.190 # SOURCE3 1 - angle_coeff @angle:ca-p4-ca harmonic 46.528 107.770 # SOURCE3 1 - angle_coeff @angle:ca-p4-o harmonic 61.439 111.640 # SOURCE3 1 - angle_coeff @angle:cl-p4-cl harmonic 62.229 103.510 # SOURCE3 1 - angle_coeff @angle:cl-p4-o harmonic 66.762 116.530 # SOURCE3 2 - angle_coeff @angle:hp-p4-hp harmonic 27.316 99.210 # SOURCE3 4 6.4572 - angle_coeff @angle:hp-p4-n1 harmonic 45.702 99.910 # HF/6-31G* 1 - angle_coeff @angle:hp-p4-o harmonic 47.223 109.350 # SOURCE3 6 10.8284 - angle_coeff @angle:hp-p4-p3 harmonic 39.333 98.960 # SOURCE3 4 - angle_coeff @angle:hp-p4-s harmonic 30.046 110.240 # SOURCE3 4 4.1081 - angle_coeff @angle:i-p4-i harmonic 51.559 113.220 # SOURCE3 2 6.7916 - angle_coeff @angle:i-p4-o harmonic 59.585 110.220 # SOURCE3 4 9.7726 - angle_coeff @angle:n1-p4-n1 harmonic 81.177 100.610 # HF/6-31G* 1 - angle_coeff @angle:n1-p4-o harmonic 79.782 114.590 # HF/6-31G* 1 - angle_coeff @angle:n2-p4-n2 harmonic 78.358 102.540 # SOURCE3 1 - angle_coeff @angle:n2-p4-o harmonic 76.567 120.280 # SOURCE3 1 - angle_coeff @angle:n3-p4-o harmonic 79.727 113.270 # SOURCE3 1 - angle_coeff @angle:n4-p4-o harmonic 74.226 107.610 # SOURCE3 1 - angle_coeff @angle:na-p4-o harmonic 84.731 110.600 # SOURCE3 5 1.3133 - angle_coeff @angle:nh-p4-nh harmonic 82.137 95.300 # SOURCE3 1 - angle_coeff @angle:nh-p4-o harmonic 78.559 115.860 # SOURCE3 3 3.2712 - angle_coeff @angle:n-p4-o harmonic 77.006 117.990 # SOURCE3 1 - angle_coeff @angle:no-p4-o harmonic 73.956 114.690 # SOURCE3 3 0.1070 - angle_coeff @angle:oh-p4-oh harmonic 85.208 95.710 # SOURCE3 1 - angle_coeff @angle:o-p4-o harmonic 84.013 117.220 # SOURCE3 6 2.7792 - angle_coeff @angle:o-p4-oh harmonic 79.987 117.390 # SOURCE3 4 1.0083 - angle_coeff @angle:o-p4-os harmonic 80.383 116.670 # SOURCE3 4 0.6923 - angle_coeff @angle:o-p4-p2 harmonic 69.856 121.350 # SOURCE3 1 - angle_coeff @angle:o-p4-p3 harmonic 70.923 114.000 # SOURCE3 3 0.6663 - angle_coeff @angle:o-p4-p4 harmonic 75.914 116.430 # SOURCE3 1 - angle_coeff @angle:o-p4-p5 harmonic 71.622 109.760 # SOURCE3 1 - angle_coeff @angle:o-p4-s4 harmonic 54.866 112.190 # SOURCE3 1 - angle_coeff @angle:o-p4-s6 harmonic 54.029 113.890 # SOURCE3 1 - angle_coeff @angle:o-p4-s harmonic 57.277 112.780 # SOURCE3 2 - angle_coeff @angle:o-p4-sh harmonic 56.730 118.090 # SOURCE3 1 - angle_coeff @angle:os-p4-os harmonic 83.473 100.340 # SOURCE3 1 - angle_coeff @angle:o-p4-ss harmonic 57.476 116.140 # SOURCE3 4 1.0636 - angle_coeff @angle:p2-p4-p2 harmonic 73.236 110.710 # SOURCE3 1 - angle_coeff @angle:p3-p4-p3 harmonic 70.664 114.980 # SOURCE3 1 - angle_coeff @angle:p4-p4-p4 harmonic 79.664 107.380 # SOURCE3 1 - angle_coeff @angle:p5-p4-p5 harmonic 72.301 107.780 # SOURCE3 1 - angle_coeff @angle:s4-p4-s4 harmonic 46.168 96.240 # SOURCE3 1 - angle_coeff @angle:s6-p4-s6 harmonic 44.412 102.360 # SOURCE3 1 - angle_coeff @angle:sh-p4-sh harmonic 48.494 98.810 # SOURCE3 1 - angle_coeff @angle:s-p4-s harmonic 46.079 106.300 # SOURCE3 2 25.0119 - angle_coeff @angle:ss-p4-ss harmonic 47.422 104.410 # SOURCE3 1 - angle_coeff @angle:br-p5-br harmonic 51.952 103.380 # SOURCE3 1 - angle_coeff @angle:br-p5-o harmonic 59.322 114.650 # SOURCE3 3 1.0910 - angle_coeff @angle:br-p5-oh harmonic 62.204 102.920 # SOURCE3 4 0.5468 - angle_coeff @angle:c1-p5-c1 harmonic 49.058 102.890 # SOURCE3 1 - angle_coeff @angle:c1-p5-o harmonic 61.836 115.770 # SOURCE3 2 - angle_coeff @angle:c1-p5-oh harmonic 63.769 102.790 # SOURCE3 2 - angle_coeff @angle:c2-p5-c2 harmonic 45.370 106.560 # SOURCE3 1 - angle_coeff @angle:c2-p5-o harmonic 60.781 109.520 # SOURCE4_SOURCE5 15 2.0293 - angle_coeff @angle:c2-p5-oh harmonic 61.672 101.690 # SOURCE3 1 - angle_coeff @angle:c2-p5-os harmonic 63.109 97.120 # SOURCE3_SOURCE5 6 0.9178 - angle_coeff @angle:c3-p5-c3 harmonic 46.061 106.000 # SOURCE3_SOURCE5 107 1.6965 - angle_coeff @angle:c3-p5-hp harmonic 33.063 103.260 # SOURCE4_SOURCE5 20 1.3795 - angle_coeff @angle:c3-p5-n3 harmonic 60.649 104.400 # SOURCE3_SOURCE5 10 1.8148 - angle_coeff @angle:c3-p5-o harmonic 60.550 112.500 # SOURCE3 23 4.4203 - angle_coeff @angle:c3-p5-oh harmonic 61.886 102.690 # SOURCE3_SOURCE5 389 1.5370 - angle_coeff @angle:c3-p5-os harmonic 62.476 100.770 # SOURCE4 51 2.0928 - angle_coeff @angle:c3-p5-p4 harmonic 56.514 106.270 # SOURCE3 1 - angle_coeff @angle:c3-p5-s harmonic 46.672 114.400 # SOURCE3_SOURCE5 36 1.0844 - angle_coeff @angle:c3-p5-ss harmonic 45.854 105.940 # SOURCE3_SOURCE5 24 1.6358 - angle_coeff @angle:ca-p5-ca harmonic 46.780 107.900 # SOURCE3_SOURCE5 5 0.5519 - angle_coeff @angle:ca-p5-o harmonic 61.263 113.980 # SOURCE3 1 - angle_coeff @angle:ca-p5-oh harmonic 63.154 101.770 # SOURCE3 1 - angle_coeff @angle:ca-p5-os harmonic 62.551 103.750 # SOURCE3 1 - angle_coeff @angle:c-p5-c harmonic 45.421 104.160 # SOURCE3 1 - angle_coeff @angle:cl-p5-cl harmonic 62.172 103.700 # SOURCE2 1 - angle_coeff @angle:cl-p5-o harmonic 68.012 112.650 # SOURCE3_SOURCE5 7 1.0635 - angle_coeff @angle:cl-p5-oh harmonic 70.253 102.440 # SOURCE3 2 - angle_coeff @angle:c-p5-o harmonic 60.972 107.100 # SOURCE4_SOURCE5 37 0.4646 - angle_coeff @angle:c-p5-oh harmonic 61.112 102.120 # SOURCE3 1 - angle_coeff @angle:f-p5-f harmonic 92.407 92.220 # SOURCE2_SOURCE5 19 1.3661 - angle_coeff @angle:f-p5-o harmonic 85.135 112.070 # SOURCE4_SOURCE5 15 0.5195 - angle_coeff @angle:f-p5-oh harmonic 85.837 101.980 # SOURCE3 2 - angle_coeff @angle:f-p5-os harmonic 85.720 102.270 # SOURCE4_SOURCE5 16 1.0230 - angle_coeff @angle:f-p5-s harmonic 61.598 117.400 # SOURCE2 1 - angle_coeff @angle:hp-p5-hp harmonic 25.816 100.550 # SOURCE3_SOURCE5 11 0.5508 - angle_coeff @angle:hp-p5-n1 harmonic 46.858 101.320 # HF/6-31G* 1 - angle_coeff @angle:hp-p5-o harmonic 45.433 115.080 # SOURCE3_SOURCE5 27 1.7749 - angle_coeff @angle:hp-p5-oh harmonic 45.976 101.570 # SOURCE3_SOURCE5 16 1.3736 - angle_coeff @angle:hp-p5-s harmonic 31.882 119.200 # SOURCE2 1 - angle_coeff @angle:i-p5-i harmonic 48.013 107.170 # SOURCE3 1 - angle_coeff @angle:i-p5-o harmonic 52.148 115.930 # SOURCE3 3 0.0415 - angle_coeff @angle:i-p5-oh harmonic 55.980 102.260 # SOURCE3 4 1.9577 - angle_coeff @angle:n1-p5-n1 harmonic 86.407 101.550 # HF/6-31G* 1 - angle_coeff @angle:n1-p5-o harmonic 83.757 113.780 # HF/6-31G* 1 - angle_coeff @angle:n2-p5-n2 harmonic 82.960 106.340 # SOURCE3 1 - angle_coeff @angle:n2-p5-o harmonic 82.994 113.530 # SOURCE3 1 - angle_coeff @angle:n2-p5-oh harmonic 84.118 102.400 # SOURCE3 1 - angle_coeff @angle:n3-p5-n3 harmonic 80.585 103.370 # SOURCE4 47 2.1009 - angle_coeff @angle:n3-p5-nh harmonic 80.369 103.840 # SOURCE4_SOURCE5 11 1.8670 - angle_coeff @angle:n3-p5-o harmonic 80.416 114.640 # SOURCE4 76 2.2728 - angle_coeff @angle:n3-p5-oh harmonic 81.248 104.990 # SOURCE3_SOURCE5 18 0.6974 - angle_coeff @angle:n3-p5-os harmonic 82.342 102.230 # SOURCE4_SOURCE5 90 2.1717 - angle_coeff @angle:n3-p5-s harmonic 60.056 116.560 # SOURCE4_SOURCE5 28 0.9342 - angle_coeff @angle:n4-p5-n4 harmonic 73.942 102.200 # SOURCE3 1 - angle_coeff @angle:n4-p5-o harmonic 77.060 109.780 # SOURCE3 5 2.7519 - angle_coeff @angle:n4-p5-oh harmonic 79.407 98.480 # SOURCE3 6 0.4104 - angle_coeff @angle:n4-p5-os harmonic 81.044 94.550 # SOURCE3 2 - angle_coeff @angle:na-p5-na harmonic 76.550 108.570 # SOURCE3 1 - angle_coeff @angle:na-p5-o harmonic 79.422 113.430 # SOURCE3 11 0.8968 - angle_coeff @angle:na-p5-oh harmonic 81.176 102.070 # SOURCE3 16 1.4144 - angle_coeff @angle:na-p5-os harmonic 80.790 103.060 # SOURCE3 4 0.7463 - angle_coeff @angle:nh-p5-nh harmonic 82.064 99.510 # SOURCE3 1 - angle_coeff @angle:nh-p5-o harmonic 80.296 114.860 # SOURCE3_SOURCE5 11 1.6006 - angle_coeff @angle:nh-p5-oh harmonic 82.027 102.910 # SOURCE3_SOURCE5 6 0.9034 - angle_coeff @angle:nh-p5-os harmonic 81.134 105.200 # SOURCE3_SOURCE5 6 2.0688 - angle_coeff @angle:n-p5-n3 harmonic 79.065 104.310 # SOURCE4_SOURCE5 28 1.2397 - angle_coeff @angle:n-p5-n harmonic 78.462 103.090 # SOURCE3 1 - angle_coeff @angle:n-p5-o harmonic 79.797 112.180 # SOURCE4_SOURCE5 14 1.5068 - angle_coeff @angle:n-p5-oh harmonic 80.973 102.440 # SOURCE3 4 0.0999 - angle_coeff @angle:no-p5-no harmonic 76.253 95.680 # SOURCE3 1 - angle_coeff @angle:no-p5-o harmonic 75.912 112.750 # SOURCE3 4 3.3684 - angle_coeff @angle:no-p5-oh harmonic 78.162 101.350 # SOURCE3 2 - angle_coeff @angle:no-p5-os harmonic 78.031 101.700 # SOURCE3 4 0.0565 - angle_coeff @angle:n-p5-os harmonic 81.763 100.480 # SOURCE3 2 - angle_coeff @angle:oh-p5-oh harmonic 83.590 102.690 # SOURCE3_SOURCE5 359 1.1644 - angle_coeff @angle:oh-p5-os harmonic 83.902 101.940 # SOURCE3_SOURCE5 591 1.1251 - angle_coeff @angle:oh-p5-p2 harmonic 75.094 103.530 # SOURCE3 1 - angle_coeff @angle:oh-p5-p3 harmonic 74.007 103.830 # SOURCE3 13 0.4303 - angle_coeff @angle:oh-p5-p4 harmonic 74.032 101.790 # SOURCE3 1 - angle_coeff @angle:oh-p5-p5 harmonic 80.103 100.450 # SOURCE3 1 - angle_coeff @angle:oh-p5-s4 harmonic 61.903 103.240 # SOURCE3 1 - angle_coeff @angle:oh-p5-s6 harmonic 62.438 101.480 # SOURCE3 1 - angle_coeff @angle:oh-p5-s harmonic 62.070 111.300 # SOURCE3_SOURCE5 8 1.1112 - angle_coeff @angle:oh-p5-sh harmonic 61.449 101.410 # SOURCE3 2 - angle_coeff @angle:oh-p5-ss harmonic 59.814 104.090 # SOURCE3_SOURCE5 23 1.4682 - angle_coeff @angle:o-p5-o harmonic 85.510 115.800 # SOURCE3 17 5.7902 - angle_coeff @angle:o-p5-oh harmonic 81.901 115.210 # SOURCE4_SOURCE5 1716 1.3221 - angle_coeff @angle:o-p5-os harmonic 81.819 115.460 # SOURCE3_SOURCE5 843 2.3835 - angle_coeff @angle:o-p5-p2 harmonic 71.892 114.600 # SOURCE3 1 - angle_coeff @angle:o-p5-p3 harmonic 70.584 115.480 # SOURCE3 9 2.1084 - angle_coeff @angle:o-p5-p4 harmonic 70.090 114.660 # SOURCE3 1 - angle_coeff @angle:o-p5-p5 harmonic 76.354 113.440 # SOURCE3 1 - angle_coeff @angle:o-p5-s4 harmonic 60.725 110.230 # SOURCE3 1 - angle_coeff @angle:o-p5-s6 harmonic 60.311 111.750 # SOURCE3 1 - angle_coeff @angle:o-p5-s harmonic 61.702 116.940 # SOURCE3 3 2.9506 - angle_coeff @angle:o-p5-sh harmonic 58.488 114.560 # SOURCE3 3 1.7645 - angle_coeff @angle:os-p5-os harmonic 83.949 101.840 # SOURCE4_SOURCE5 608 1.9896 - angle_coeff @angle:os-p5-p3 harmonic 74.065 103.670 # SOURCE3 2 - angle_coeff @angle:os-p5-p5 harmonic 78.545 104.480 # SOURCE3 1 - angle_coeff @angle:os-p5-s4 harmonic 62.122 102.520 # SOURCE3 1 - angle_coeff @angle:os-p5-s6 harmonic 62.313 101.890 # SOURCE3 1 - angle_coeff @angle:o-p5-ss harmonic 57.641 114.340 # SOURCE3_SOURCE5 37 1.7416 - angle_coeff @angle:os-p5-s harmonic 60.508 117.130 # SOURCE4_SOURCE5 200 0.8203 - angle_coeff @angle:os-p5-sh harmonic 61.258 102.050 # SOURCE3_SOURCE5 7 0.5915 - angle_coeff @angle:os-p5-ss harmonic 60.283 102.480 # SOURCE4_SOURCE5 70 1.4633 - angle_coeff @angle:p2-p5-p2 harmonic 74.412 107.140 # SOURCE3 1 - angle_coeff @angle:p3-p5-p3 harmonic 73.965 105.230 # SOURCE3 3 5.1024 - angle_coeff @angle:p4-p5-p4 harmonic 74.460 101.620 # SOURCE3 1 - angle_coeff @angle:p5-p5-p5 harmonic 76.997 112.720 # SOURCE3 1 - angle_coeff @angle:s6-p5-s6 harmonic 48.731 105.180 # SOURCE3 1 - angle_coeff @angle:sh-p5-sh harmonic 47.889 104.560 # SOURCE3 1 - angle_coeff @angle:sh-p5-ss harmonic 46.903 107.130 # SOURCE3 1 - angle_coeff @angle:s-p5-s harmonic 49.342 114.130 # SOURCE3 1 - angle_coeff @angle:ss-p5-ss harmonic 45.986 109.610 # SOURCE3 1 - angle_coeff @angle:cd-pc-n harmonic 66.016 90.800 # SOURCE3 3 2.3423 - angle_coeff @angle:cd-pc-na harmonic 66.396 90.180 # SOURCE3 81 2.7619 - angle_coeff @angle:cc-pd-n harmonic 66.016 90.800 # SOURCE3 3 - angle_coeff @angle:cc-pd-na harmonic 66.396 90.180 # SOURCE3 81 - angle_coeff @angle:c2-pe-ca harmonic 49.088 101.440 # SOURCE3 3 0.7177 - angle_coeff @angle:c2-pe-ce harmonic 48.888 103.010 # SOURCE3 4 1.4470 - angle_coeff @angle:c2-pe-cg harmonic 51.641 104.030 # SOURCE3 3 3.8740 - angle_coeff @angle:c2-pe-n2 harmonic 69.448 94.140 # SOURCE3 1 - angle_coeff @angle:c2-pe-ne harmonic 64.662 98.700 # SOURCE3 12 5.3383 - angle_coeff @angle:c2-pe-o harmonic 63.086 115.160 # SOURCE3 2 0.0149 - angle_coeff @angle:c2-pe-p2 harmonic 65.232 107.820 # SOURCE3 1 - angle_coeff @angle:c2-pe-pe harmonic 61.668 102.990 # SOURCE3 9 8.2860 - angle_coeff @angle:c2-pe-px harmonic 65.444 97.370 # SOURCE3 4 0.6655 - angle_coeff @angle:c2-pe-py harmonic 65.200 96.710 # SOURCE3 4 1.2755 - angle_coeff @angle:c2-pe-s harmonic 51.862 111.160 # SOURCE3 2 - angle_coeff @angle:c2-pe-sx harmonic 48.622 95.110 # SOURCE3 4 0.2676 - angle_coeff @angle:c2-pe-sy harmonic 47.698 95.560 # SOURCE3 2 0.0462 - angle_coeff @angle:ca-pe-n2 harmonic 63.263 102.030 # SOURCE3 1 - angle_coeff @angle:ca-pe-o harmonic 62.025 106.880 # SOURCE3 2 0.0018 - angle_coeff @angle:ca-pe-p2 harmonic 65.219 100.790 # SOURCE3 1 - angle_coeff @angle:ca-pe-pf harmonic 61.993 99.700 # SOURCE3 2 - angle_coeff @angle:ca-pe-s harmonic 50.574 107.930 # SOURCE3 1 - angle_coeff @angle:c-pe-c2 harmonic 48.762 97.300 # SOURCE3 3 0.0335 - angle_coeff @angle:ce-pe-n2 harmonic 64.000 100.550 # SOURCE3 1 - angle_coeff @angle:ce-pe-o harmonic 62.134 107.440 # SOURCE3 1 - angle_coeff @angle:ce-pe-p2 harmonic 65.808 99.560 # SOURCE3 1 - angle_coeff @angle:ce-pe-s harmonic 51.312 105.540 # SOURCE3 1 - angle_coeff @angle:cg-pe-n2 harmonic 68.416 101.790 # SOURCE3 1 - angle_coeff @angle:cg-pe-o harmonic 66.891 107.620 # SOURCE3 1 - angle_coeff @angle:cg-pe-p2 harmonic 67.155 104.680 # SOURCE3 2 5.1435 - angle_coeff @angle:cg-pe-s harmonic 53.387 108.600 # SOURCE3 4 2.6981 - angle_coeff @angle:n2-pe-n2 harmonic 85.418 108.140 # SOURCE3 1 - angle_coeff @angle:n2-pe-ne harmonic 80.952 106.800 # SOURCE3 6 4.5981 - angle_coeff @angle:n2-pe-o harmonic 83.198 115.390 # SOURCE3 1 - angle_coeff @angle:n2-pe-p2 harmonic 82.679 111.600 # SOURCE3 1 - angle_coeff @angle:n2-pe-pe harmonic 76.187 109.400 # SOURCE3 1 - angle_coeff @angle:n2-pe-px harmonic 78.660 110.300 # SOURCE3 3 6.0548 - angle_coeff @angle:n2-pe-py harmonic 84.653 93.680 # SOURCE3 1 - angle_coeff @angle:n2-pe-s harmonic 66.247 114.840 # SOURCE3 3 3.6512 - angle_coeff @angle:n2-pe-sx harmonic 60.809 97.830 # SOURCE3 1 - angle_coeff @angle:n2-pe-sy harmonic 59.570 98.140 # SOURCE3 1 - angle_coeff @angle:ne-pe-o harmonic 80.037 110.240 # SOURCE3 3 3.8478 - angle_coeff @angle:ne-pe-p2 harmonic 82.546 104.480 # SOURCE3 2 7.1207 - angle_coeff @angle:ne-pe-s harmonic 65.116 109.190 # SOURCE3 5 3.6708 - angle_coeff @angle:o-pe-o harmonic 82.114 119.960 # SOURCE3 1 - angle_coeff @angle:o-pe-p2 harmonic 81.980 114.230 # SOURCE3 1 - angle_coeff @angle:o-pe-pe harmonic 66.057 145.960 # SOURCE3 1 - angle_coeff @angle:o-pe-px harmonic 81.034 104.370 # SOURCE3 1 - angle_coeff @angle:o-pe-py harmonic 80.312 104.490 # SOURCE3 1 - angle_coeff @angle:o-pe-s harmonic 65.783 117.420 # SOURCE3 2 0.0426 - angle_coeff @angle:o-pe-sx harmonic 58.314 106.590 # SOURCE3 1 - angle_coeff @angle:o-pe-sy harmonic 57.621 105.040 # SOURCE3 1 - angle_coeff @angle:p2-pe-pe harmonic 85.030 98.240 # SOURCE3 1 - angle_coeff @angle:p2-pe-px harmonic 83.137 108.280 # SOURCE3 2 6.2959 - angle_coeff @angle:p2-pe-py harmonic 81.676 110.870 # SOURCE3 3 8.1645 - angle_coeff @angle:p2-pe-s harmonic 68.307 111.280 # SOURCE3 1 - angle_coeff @angle:p2-pe-sx harmonic 65.549 95.730 # SOURCE3 1 - angle_coeff @angle:p2-pe-sy harmonic 64.541 95.950 # SOURCE3 1 - angle_coeff @angle:pe-pe-s harmonic 64.452 107.910 # SOURCE3 2 1.5577 - angle_coeff @angle:px-pe-s harmonic 66.458 107.620 # SOURCE3 2 3.7266 - angle_coeff @angle:py-pe-s harmonic 65.679 108.730 # SOURCE3 3 5.3201 - angle_coeff @angle:s-pe-s harmonic 43.414 178.440 # SOURCE3 1 - angle_coeff @angle:s-pe-sx harmonic 48.826 108.320 # SOURCE3 2 3.0318 - angle_coeff @angle:s-pe-sy harmonic 48.370 106.930 # SOURCE3 1 - angle_coeff @angle:c2-pf-ca harmonic 49.088 101.440 # SOURCE3 3 - angle_coeff @angle:c2-pf-cf harmonic 48.888 103.010 # SOURCE3 4 - angle_coeff @angle:c2-pf-ch harmonic 51.641 104.030 # SOURCE3 3 - angle_coeff @angle:c2-pf-n2 harmonic 69.448 94.140 # SOURCE3 1 - angle_coeff @angle:c2-pf-nf harmonic 64.662 98.700 # SOURCE3 12 - angle_coeff @angle:c2-pf-o harmonic 63.086 115.160 # SOURCE3 2 - angle_coeff @angle:c2-pf-p2 harmonic 65.232 107.820 # SOURCE3 1 - angle_coeff @angle:c2-pf-pf harmonic 61.668 102.990 # SOURCE3 9 - angle_coeff @angle:c2-pf-px harmonic 65.444 97.370 # SOURCE3 4 - angle_coeff @angle:c2-pf-py harmonic 65.200 96.710 # SOURCE3 4 - angle_coeff @angle:c2-pf-s harmonic 51.862 111.160 # SOURCE3 2 - angle_coeff @angle:c2-pf-sx harmonic 48.622 95.110 # SOURCE3 4 - angle_coeff @angle:c2-pf-sy harmonic 47.698 95.560 # SOURCE3 2 - angle_coeff @angle:ca-pf-n2 harmonic 63.263 102.030 # SOURCE3 1 - angle_coeff @angle:ca-pf-o harmonic 62.025 106.880 # SOURCE3 2 - angle_coeff @angle:ca-pf-p2 harmonic 65.219 100.790 # SOURCE3 1 - angle_coeff @angle:ca-pf-pe harmonic 61.993 99.700 # SOURCE3 2 - angle_coeff @angle:ca-pf-s harmonic 50.574 107.930 # SOURCE3 1 - angle_coeff @angle:c-pf-c2 harmonic 48.762 97.300 # SOURCE3 3 - angle_coeff @angle:cf-pf-n2 harmonic 64.000 100.550 # SOURCE3 1 - angle_coeff @angle:cf-pf-o harmonic 62.134 107.440 # SOURCE3 1 - angle_coeff @angle:cf-pf-p2 harmonic 65.808 99.560 # SOURCE3 1 - angle_coeff @angle:cf-pf-s harmonic 51.312 105.540 # SOURCE3 1 - angle_coeff @angle:ch-pf-n2 harmonic 68.416 101.790 # SOURCE3 1 - angle_coeff @angle:ch-pf-o harmonic 66.891 107.620 # SOURCE3 1 - angle_coeff @angle:ch-pf-p2 harmonic 67.155 104.680 # SOURCE3 2 - angle_coeff @angle:ch-pf-s harmonic 53.387 108.600 # SOURCE3 4 - angle_coeff @angle:n2-pf-n2 harmonic 85.418 108.140 # SOURCE3 1 - angle_coeff @angle:n2-pf-nf harmonic 80.952 106.800 # SOURCE3 6 - angle_coeff @angle:n2-pf-o harmonic 83.198 115.390 # SOURCE3 1 - angle_coeff @angle:n2-pf-p2 harmonic 82.679 111.600 # SOURCE3 1 - angle_coeff @angle:n2-pf-pf harmonic 76.187 109.400 # SOURCE3 1 - angle_coeff @angle:n2-pf-px harmonic 78.660 110.300 # SOURCE3 3 - angle_coeff @angle:n2-pf-py harmonic 84.653 93.680 # SOURCE3 1 - angle_coeff @angle:n2-pf-s harmonic 66.247 114.840 # SOURCE3 3 - angle_coeff @angle:n2-pf-sx harmonic 60.809 97.830 # SOURCE3 1 - angle_coeff @angle:n2-pf-sy harmonic 59.570 98.140 # SOURCE3 1 - angle_coeff @angle:nf-pf-o harmonic 80.037 110.240 # SOURCE3 3 - angle_coeff @angle:nf-pf-p2 harmonic 82.546 104.480 # SOURCE3 2 - angle_coeff @angle:nf-pf-s harmonic 65.116 109.190 # SOURCE3 5 - angle_coeff @angle:o-pf-o harmonic 82.114 119.960 # SOURCE3 1 - angle_coeff @angle:o-pf-p2 harmonic 81.980 114.230 # SOURCE3 1 - angle_coeff @angle:o-pf-pf harmonic 66.057 145.960 # SOURCE3 1 - angle_coeff @angle:o-pf-px harmonic 81.034 104.370 # SOURCE3 1 - angle_coeff @angle:o-pf-py harmonic 80.312 104.490 # SOURCE3 1 - angle_coeff @angle:o-pf-s harmonic 65.783 117.420 # SOURCE3 2 - angle_coeff @angle:o-pf-sx harmonic 58.314 106.590 # SOURCE3 1 - angle_coeff @angle:o-pf-sy harmonic 57.621 105.040 # SOURCE3 1 - angle_coeff @angle:p2-pf-pf harmonic 85.030 98.240 # SOURCE3 1 - angle_coeff @angle:p2-pf-px harmonic 83.137 108.280 # SOURCE3 2 - angle_coeff @angle:p2-pf-py harmonic 81.676 110.870 # SOURCE3 3 - angle_coeff @angle:p2-pf-s harmonic 68.307 111.280 # SOURCE3 1 - angle_coeff @angle:p2-pf-sx harmonic 65.549 95.730 # SOURCE3 1 - angle_coeff @angle:p2-pf-sy harmonic 64.541 95.950 # SOURCE3 1 - angle_coeff @angle:pf-pf-s harmonic 64.452 107.910 # SOURCE3 2 - angle_coeff @angle:px-pf-s harmonic 66.458 107.620 # SOURCE3 2 - angle_coeff @angle:py-pf-s harmonic 65.679 108.730 # SOURCE3 3 - angle_coeff @angle:s-pf-s harmonic 43.414 178.440 # SOURCE3 1 - angle_coeff @angle:s-pf-sx harmonic 48.826 108.320 # SOURCE3 2 - angle_coeff @angle:s-pf-sy harmonic 48.370 106.930 # SOURCE3 1 - angle_coeff @angle:c3-px-ca harmonic 46.648 104.790 # SOURCE3 1 - angle_coeff @angle:c3-px-ce harmonic 46.683 104.860 # SOURCE3 4 0.6354 - angle_coeff @angle:c3-px-cf harmonic 46.683 104.860 # SOURCE3 4 - angle_coeff @angle:c3-px-ne harmonic 60.976 102.460 # SOURCE3 7 1.8685 - angle_coeff @angle:c3-px-nf harmonic 60.976 102.460 # SOURCE3 7 - angle_coeff @angle:c3-px-o harmonic 60.307 113.790 # SOURCE3_SOURCE5 33 4.2352 - angle_coeff @angle:c3-px-pe harmonic 61.145 105.730 # SOURCE3 10 4.4059 - angle_coeff @angle:c3-px-pf harmonic 61.145 105.730 # SOURCE3 10 - angle_coeff @angle:c3-px-py harmonic 58.192 103.110 # SOURCE3 3 0.8680 - angle_coeff @angle:c3-px-sx harmonic 45.492 99.550 # SOURCE3 1 - angle_coeff @angle:c3-px-sy harmonic 44.530 103.410 # SOURCE3 1 - angle_coeff @angle:ca-px-ca harmonic 46.837 104.150 # SOURCE3 2 3.6168 - angle_coeff @angle:ca-px-o harmonic 62.137 107.500 # SOURCE3 5 5.7355 - angle_coeff @angle:c-px-c3 harmonic 46.307 101.720 # SOURCE3 1 - angle_coeff @angle:ce-px-ce harmonic 46.926 104.210 # SOURCE3 1 - angle_coeff @angle:ce-px-o harmonic 60.493 113.790 # SOURCE3 6 0.3877 - angle_coeff @angle:cf-px-cf harmonic 46.926 104.210 # SOURCE3 1 - angle_coeff @angle:cf-px-o harmonic 60.493 113.790 # SOURCE3 6 - angle_coeff @angle:c-px-o harmonic 58.294 114.470 # SOURCE3 1 - angle_coeff @angle:ne-px-ne harmonic 79.109 103.220 # SOURCE3 2 0.6807 - angle_coeff @angle:ne-px-o harmonic 79.281 114.130 # SOURCE3 11 8.9737 - angle_coeff @angle:nf-px-nf harmonic 79.109 103.220 # SOURCE3 2 - angle_coeff @angle:nf-px-o harmonic 79.281 114.130 # SOURCE3 11 - angle_coeff @angle:o-px-pe harmonic 76.837 116.500 # SOURCE3 12 8.2925 - angle_coeff @angle:o-px-pf harmonic 76.837 116.500 # SOURCE3 12 - angle_coeff @angle:o-px-py harmonic 71.388 114.200 # SOURCE3 5 1.7165 - angle_coeff @angle:o-px-sx harmonic 54.930 112.810 # SOURCE3 3 0.8799 - angle_coeff @angle:o-px-sy harmonic 54.586 113.540 # SOURCE3 3 0.5010 - angle_coeff @angle:pe-px-pe harmonic 79.592 110.710 # SOURCE3 1 - angle_coeff @angle:pf-px-pf harmonic 79.592 110.710 # SOURCE3 1 - angle_coeff @angle:py-px-py harmonic 73.550 107.780 # SOURCE3 1 - angle_coeff @angle:sx-px-sx harmonic 46.354 96.240 # SOURCE3 1 - angle_coeff @angle:sy-px-sy harmonic 44.807 102.360 # SOURCE3 1 - angle_coeff @angle:c3-py-n4 harmonic 57.271 103.830 # SOURCE3 4 - angle_coeff @angle:c3-py-na harmonic 59.344 106.890 # SOURCE3 2 - angle_coeff @angle:c3-py-o harmonic 59.442 116.680 # SOURCE3_SOURCE5 22 1.9051 - angle_coeff @angle:c3-py-oh harmonic 62.641 100.160 # SOURCE3 2 - angle_coeff @angle:c3-py-os harmonic 61.038 105.390 # SOURCE3 1 - angle_coeff @angle:c3-py-px harmonic 57.225 106.270 # SOURCE3 2 - angle_coeff @angle:c3-py-py harmonic 56.530 109.830 # SOURCE3_SOURCE5 16 1.4525 - angle_coeff @angle:c3-py-sx harmonic 43.696 106.360 # SOURCE3 4 - angle_coeff @angle:ca-py-ca harmonic 46.314 107.550 # SOURCE3 1 - angle_coeff @angle:ca-py-o harmonic 60.635 114.330 # SOURCE3_SOURCE5 20 1.3895 - angle_coeff @angle:ca-py-oh harmonic 62.332 102.870 # SOURCE4_SOURCE5 16 1.4519 - angle_coeff @angle:ca-py-os harmonic 62.763 101.360 # SOURCE3_SOURCE5 12 1.6676 - angle_coeff @angle:c-py-c3 harmonic 44.799 110.360 # SOURCE3 1 - angle_coeff @angle:c-py-c harmonic 45.772 104.200 # SOURCE3 1 - angle_coeff @angle:ce-py-ce harmonic 46.806 106.540 # SOURCE3 1 - angle_coeff @angle:ce-py-o harmonic 60.977 114.040 # SOURCE3_SOURCE5 17 2.0725 - angle_coeff @angle:ce-py-oh harmonic 61.997 104.770 # SOURCE3 6 2.1852 - angle_coeff @angle:ce-py-os harmonic 61.932 104.880 # SOURCE3_SOURCE5 7 1.2571 - angle_coeff @angle:cf-py-cf harmonic 46.806 106.540 # SOURCE3 1 - angle_coeff @angle:cf-py-o harmonic 60.977 114.040 # SOURCE3_SOURCE5 12 1.5779 - angle_coeff @angle:cf-py-oh harmonic 61.997 104.770 # SOURCE3 6 - angle_coeff @angle:cf-py-os harmonic 61.932 104.880 # SOURCE3_SOURCE5 7 1.2571 - angle_coeff @angle:c-py-o harmonic 59.457 114.000 # SOURCE3_SOURCE5 17 1.4765 - angle_coeff @angle:c-py-oh harmonic 61.100 103.220 # SOURCE3_SOURCE5 16 1.4543 - angle_coeff @angle:c-py-os harmonic 62.044 100.010 # SOURCE3_SOURCE5 14 3.2269 - angle_coeff @angle:n3-py-ne harmonic 79.409 108.760 # SOURCE4_SOURCE5 30 1.0660 - angle_coeff @angle:n4-py-o harmonic 72.867 115.580 # SOURCE3 4 - angle_coeff @angle:n4-py-py harmonic 98.929 55.100 # SOURCE3 4 - angle_coeff @angle:na-py-o harmonic 76.532 122.400 # SOURCE3 2 - angle_coeff @angle:na-py-py harmonic 105.838 50.880 # SOURCE3 2 - angle_coeff @angle:ne-py-ne harmonic 78.402 118.190 # SOURCE3_SOURCE5 35 1.2083 - angle_coeff @angle:ne-py-o harmonic 82.910 113.210 # SOURCE3 15 3.8894 - angle_coeff @angle:ne-py-oh harmonic 83.005 104.700 # SOURCE3 26 2.7513 - angle_coeff @angle:ne-py-os harmonic 81.559 108.290 # SOURCE3_SOURCE5 23 1.6881 - angle_coeff @angle:nf-py-nf harmonic 78.402 118.190 # SOURCE3_SOURCE5 35 1.2083 - angle_coeff @angle:nf-py-o harmonic 82.910 113.210 # SOURCE3 15 - angle_coeff @angle:nf-py-oh harmonic 83.005 104.700 # SOURCE3 26 - angle_coeff @angle:nf-py-os harmonic 81.559 108.290 # SOURCE3_SOURCE5 23 1.6881 - angle_coeff @angle:oh-py-oh harmonic 83.937 101.680 # SOURCE3_SOURCE5 49 1.9218 - angle_coeff @angle:oh-py-pe harmonic 79.277 104.840 # SOURCE3 22 2.0337 - angle_coeff @angle:oh-py-pf harmonic 79.277 104.840 # SOURCE3 22 - angle_coeff @angle:oh-py-px harmonic 74.246 104.300 # SOURCE3 8 1.2772 - angle_coeff @angle:oh-py-py harmonic 76.047 100.450 # SOURCE3 6 - angle_coeff @angle:oh-py-sx harmonic 57.417 100.940 # SOURCE3 4 - angle_coeff @angle:oh-py-sy harmonic 59.053 101.470 # SOURCE3 6 0.2490 - angle_coeff @angle:o-py-oh harmonic 81.623 115.830 # SOURCE3_SOURCE5 105 1.8918 - angle_coeff @angle:o-py-os harmonic 81.496 115.990 # SOURCE3_SOURCE5 47 1.2146 - angle_coeff @angle:o-py-pe harmonic 76.936 114.560 # SOURCE3 12 3.6114 - angle_coeff @angle:o-py-pf harmonic 76.936 114.560 # SOURCE3 12 - angle_coeff @angle:o-py-px harmonic 72.318 111.370 # SOURCE3 5 0.3803 - angle_coeff @angle:o-py-py harmonic 69.944 120.430 # SOURCE3 16 6.0629 - angle_coeff @angle:os-py-os harmonic 83.760 101.820 # SOURCE3_SOURCE5 27 1.5502 - angle_coeff @angle:os-py-py harmonic 74.513 104.590 # SOURCE3_SOURCE5 5 0.4023 - angle_coeff @angle:os-py-sx harmonic 56.596 103.860 # SOURCE3 2 - angle_coeff @angle:os-py-sy harmonic 58.853 102.120 # SOURCE3 2 - angle_coeff @angle:o-py-sx harmonic 53.190 118.560 # SOURCE3 7 6.2976 - angle_coeff @angle:o-py-sy harmonic 56.689 111.710 # SOURCE3 5 1.1937 - angle_coeff @angle:pe-py-pe harmonic 80.108 107.140 # SOURCE3 1 - angle_coeff @angle:pf-py-pf harmonic 80.108 107.140 # SOURCE3 1 - angle_coeff @angle:py-py-py harmonic 72.354 112.700 # SOURCE3 1 - angle_coeff @angle:py-py-sx harmonic 75.004 61.540 # SOURCE3 4 - angle_coeff @angle:sy-py-sy harmonic 45.561 105.170 # SOURCE3 1 - angle_coeff @angle:c1-s2-o harmonic 94.269 117.250 # SOURCE3 1 - angle_coeff @angle:c2-s2-n2 harmonic 98.098 110.840 # SOURCE3 1 - angle_coeff @angle:c2-s2-o harmonic 94.864 114.700 # SOURCE2 1 - angle_coeff @angle:cl-s2-n1 harmonic 92.974 117.700 # SOURCE2 1 - angle_coeff @angle:f-s2-n1 harmonic 122.911 116.900 # SOURCE2 1 - angle_coeff @angle:n1-s2-o harmonic 127.997 108.460 # HF/6-31G* 1 - angle_coeff @angle:n2-s2-o harmonic 117.918 121.200 # SOURCE2 2 0.8000 - angle_coeff @angle:o-s2-o harmonic 118.448 116.170 # SOURCE3 1 - angle_coeff @angle:o-s2-s harmonic 91.358 118.300 # SOURCE2 1 - angle_coeff @angle:s-s2-s harmonic 74.776 115.040 # SOURCE3 1 - angle_coeff @angle:br-s4-br harmonic 74.689 98.020 # SOURCE3 1 - angle_coeff @angle:br-s4-c3 harmonic 72.437 92.980 # SOURCE3 1 - angle_coeff @angle:br-s4-o harmonic 84.014 112.070 # SOURCE3 1 - angle_coeff @angle:c1-s4-c1 harmonic 77.086 93.550 # SOURCE3 1 - angle_coeff @angle:c1-s4-o harmonic 94.436 110.360 # SOURCE3 2 - angle_coeff @angle:c2-s4-c2 harmonic 73.133 102.290 # SOURCE3 1 - angle_coeff @angle:c2-s4-c3 harmonic 74.359 94.950 # SOURCE3 1 - angle_coeff @angle:c2-s4-o harmonic 95.340 107.090 # SOURCE3 1 - angle_coeff @angle:c3-s4-c3 harmonic 72.538 96.120 # SOURCE3_SOURCE5 72 1.2506 - angle_coeff @angle:c3-s4-ca harmonic 73.801 95.000 # SOURCE3 1 - angle_coeff @angle:c3-s4-f harmonic 99.956 91.700 # SOURCE3 1 - angle_coeff @angle:c3-s4-hs harmonic 53.159 90.600 # SOURCE3 1 - angle_coeff @angle:c3-s4-i harmonic 64.204 90.530 # SOURCE3 1 - angle_coeff @angle:c3-s4-n2 harmonic 98.749 90.590 # SOURCE3 1 - angle_coeff @angle:c3-s4-n3 harmonic 92.849 95.770 # SOURCE3_SOURCE5 10 1.8721 - angle_coeff @angle:c3-s4-n harmonic 92.379 96.070 # SOURCE3 4 1.0354 - angle_coeff @angle:c3-s4-n4 harmonic 88.918 92.470 # SOURCE3 1 - angle_coeff @angle:c3-s4-na harmonic 93.247 93.070 # SOURCE3 10 1.8813 - angle_coeff @angle:c3-s4-nh harmonic 92.347 97.080 # SOURCE3 1 - angle_coeff @angle:c3-s4-no harmonic 89.712 89.530 # SOURCE3 1 - angle_coeff @angle:c3-s4-o harmonic 92.851 106.710 # SOURCE3_SOURCE5 233 1.1391 - angle_coeff @angle:c3-s4-oh harmonic 97.024 90.280 # SOURCE4_SOURCE5 21 0.2709 - angle_coeff @angle:c3-s4-os harmonic 97.226 90.060 # SOURCE3 4 0.4484 - angle_coeff @angle:c3-s4-p2 harmonic 91.018 94.370 # SOURCE3 1 - angle_coeff @angle:c3-s4-p3 harmonic 93.042 96.540 # SOURCE3 4 1.3634 - angle_coeff @angle:c3-s4-p4 harmonic 87.791 97.400 # SOURCE3 1 - angle_coeff @angle:c3-s4-p5 harmonic 93.163 99.180 # SOURCE3 1 - angle_coeff @angle:c3-s4-s4 harmonic 75.465 89.500 # SOURCE3 1 - angle_coeff @angle:c3-s4-s harmonic 71.946 98.720 # SOURCE3 2 0.0185 - angle_coeff @angle:c3-s4-s6 harmonic 72.311 97.480 # SOURCE3 1 - angle_coeff @angle:c3-s4-sh harmonic 71.328 94.660 # SOURCE3 1 - angle_coeff @angle:c3-s4-ss harmonic 71.131 95.310 # SOURCE3 3 1.4101 - angle_coeff @angle:ca-s4-ca harmonic 74.616 95.210 # SOURCE3 1 - angle_coeff @angle:ca-s4-o harmonic 94.489 106.630 # SOURCE3 1 - angle_coeff @angle:c-s4-c3 harmonic 72.142 95.070 # SOURCE3 1 - angle_coeff @angle:c-s4-c harmonic 74.707 86.830 # SOURCE3 1 - angle_coeff @angle:cl-s4-cl harmonic 92.643 97.680 # SOURCE3 1 - angle_coeff @angle:cl-s4-o harmonic 100.538 108.340 # SOURCE3 2 - angle_coeff @angle:c-s4-o harmonic 91.597 106.170 # SOURCE3 1 - angle_coeff @angle:cx-s4-cx harmonic 102.278 48.800 # SOURCE2 1 - angle_coeff @angle:cx-s4-o harmonic 91.767 110.000 # SOURCE2 1 - angle_coeff @angle:f-s4-f harmonic 137.119 92.710 # SOURCE2 3 0.1490 - angle_coeff @angle:f-s4-o harmonic 129.265 106.810 # SOURCE2 2 0.0100 - angle_coeff @angle:f-s4-s harmonic 90.806 107.500 # SOURCE2 1 - angle_coeff @angle:hs-s4-hs harmonic 42.707 87.000 # SOURCE3 2 0.0202 - angle_coeff @angle:hs-s4-n1 harmonic 72.280 90.510 # HF/6-31G* 1 - angle_coeff @angle:hs-s4-o harmonic 69.666 110.270 # SOURCE3 5 0.1908 - angle_coeff @angle:i-s4-i harmonic 68.021 97.290 # SOURCE3 1 - angle_coeff @angle:i-s4-o harmonic 69.889 113.910 # SOURCE3 1 - angle_coeff @angle:n1-s4-n1 harmonic 127.594 94.020 # HF/6-31G* 1 - angle_coeff @angle:n1-s4-o harmonic 122.838 110.090 # HF/6-31G* 1 - angle_coeff @angle:n2-s4-n2 harmonic 133.526 90.170 # SOURCE3 1 - angle_coeff @angle:n2-s4-o harmonic 126.113 107.570 # SOURCE3 1 - angle_coeff @angle:n3-s4-n3 harmonic 121.849 91.190 # SOURCE3 1 - angle_coeff @angle:n3-s4-o harmonic 117.831 110.430 # SOURCE3_SOURCE5 13 1.9165 - angle_coeff @angle:n4-s4-n4 harmonic 106.426 94.610 # SOURCE3 1 - angle_coeff @angle:n4-s4-o harmonic 110.589 104.910 # SOURCE3 3 0.4370 - angle_coeff @angle:na-s4-na harmonic 112.128 103.100 # SOURCE3 1 - angle_coeff @angle:na-s4-o harmonic 116.397 109.750 # SOURCE3 10 2.6919 - angle_coeff @angle:nh-s4-nh harmonic 121.527 92.240 # SOURCE3 1 - angle_coeff @angle:nh-s4-o harmonic 119.657 107.540 # SOURCE3 3 0.0401 - angle_coeff @angle:n-s4-n harmonic 120.832 91.300 # SOURCE3 1 - angle_coeff @angle:n-s4-o harmonic 118.814 107.440 # SOURCE3_SOURCE5 9 1.2433 - angle_coeff @angle:no-s4-no harmonic 111.990 83.400 # SOURCE3 1 - angle_coeff @angle:no-s4-o harmonic 110.173 103.580 # SOURCE3 3 1.5109 - angle_coeff @angle:oh-s4-oh harmonic 120.174 100.340 # SOURCE3 1 - angle_coeff @angle:o-s4-o harmonic 127.045 114.110 # SOURCE3_SOURCE5 14 2.6371 - angle_coeff @angle:o-s4-oh harmonic 120.725 110.100 # SOURCE4_SOURCE5 30 0.8834 - angle_coeff @angle:o-s4-os harmonic 121.937 108.220 # SOURCE3_SOURCE5 19 1.5128 - angle_coeff @angle:o-s4-p2 harmonic 110.606 106.770 # SOURCE3 1 - angle_coeff @angle:o-s4-p3 harmonic 115.784 106.510 # SOURCE3 8 4.0943 - angle_coeff @angle:o-s4-p4 harmonic 109.471 103.360 # SOURCE3 1 - angle_coeff @angle:o-s4-p5 harmonic 123.827 96.950 # SOURCE3 1 - angle_coeff @angle:o-s4-s4 harmonic 91.337 104.550 # SOURCE3 1 - angle_coeff @angle:o-s4-s harmonic 88.312 112.220 # SOURCE3 4 2.8682 - angle_coeff @angle:o-s4-s6 harmonic 92.094 102.840 # SOURCE3 1 - angle_coeff @angle:o-s4-sh harmonic 86.714 107.510 # SOURCE3 3 0.7511 - angle_coeff @angle:os-s4-os harmonic 124.379 94.070 # SOURCE3_SOURCE5 7 2.3843 - angle_coeff @angle:o-s4-ss harmonic 86.001 109.490 # SOURCE3 5 1.8509 - angle_coeff @angle:p2-s4-p2 harmonic 118.888 92.620 # SOURCE3 1 - angle_coeff @angle:p3-s4-p3 harmonic 122.725 95.710 # SOURCE3 2 1.2239 - angle_coeff @angle:p5-s4-p5 harmonic 126.784 93.860 # SOURCE3 1 - angle_coeff @angle:s4-s4-s4 harmonic 77.030 90.170 # SOURCE3 1 - angle_coeff @angle:s4-s4-s6 harmonic 77.030 90.170 # SOURCE3 1 - angle_coeff @angle:s6-s4-s6 harmonic 75.638 93.520 # SOURCE3 1 - angle_coeff @angle:sh-s4-sh harmonic 69.229 102.760 # SOURCE3 1 - angle_coeff @angle:sh-s4-ss harmonic 69.301 102.640 # SOURCE3 1 - angle_coeff @angle:s-s4-s harmonic 70.495 108.080 # SOURCE3 1 - angle_coeff @angle:ss-s4-ss harmonic 71.889 95.470 # SOURCE3 1 - angle_coeff @angle:br-s6-br harmonic 77.581 101.570 # SOURCE3 1 - angle_coeff @angle:br-s6-c3 harmonic 73.519 98.990 # SOURCE3 1 - angle_coeff @angle:br-s6-f harmonic 94.581 100.600 # SOURCE2 1 - angle_coeff @angle:br-s6-o harmonic 90.691 107.580 # SOURCE3 6 0.3000 - angle_coeff @angle:c1-s6-c1 harmonic 75.601 99.990 # SOURCE3 1 - angle_coeff @angle:c1-s6-o harmonic 97.406 107.980 # SOURCE3_SOURCE5 7 0.4450 - angle_coeff @angle:c2-s6-c2 harmonic 72.969 102.750 # SOURCE3 1 - angle_coeff @angle:c2-s6-c3 harmonic 71.521 104.050 # SOURCE3 1 - angle_coeff @angle:c2-s6-o harmonic 96.507 106.580 # SOURCE3 1 - angle_coeff @angle:c3-s6-c3 harmonic 70.681 103.830 # SOURCE3_SOURCE5 74 2.0698 - angle_coeff @angle:c3-s6-ca harmonic 71.693 103.170 # SOURCE3 1 - angle_coeff @angle:c3-s6-cy harmonic 73.114 94.680 # SOURCE4_SOURCE5 19 0.4776 - angle_coeff @angle:c3-s6-f harmonic 98.119 95.900 # SOURCE3_SOURCE5 9 2.4171 - angle_coeff @angle:c3-s6-hs harmonic 51.078 100.620 # SOURCE3 1 - angle_coeff @angle:c3-s6-i harmonic 61.761 97.740 # SOURCE3 1 - angle_coeff @angle:c3-s6-n2 harmonic 90.421 112.480 # SOURCE4_SOURCE5 27 1.7086 - angle_coeff @angle:c3-s6-n3 harmonic 92.504 101.970 # SOURCE4_SOURCE5 162 1.1030 - angle_coeff @angle:c3-s6-n harmonic 90.797 103.440 # SOURCE3_SOURCE5 15 0.8616 - angle_coeff @angle:c3-s6-n4 harmonic 87.728 99.400 # SOURCE3 3 0.4695 - angle_coeff @angle:c3-s6-na harmonic 90.979 102.810 # SOURCE3 10 3.1256 - angle_coeff @angle:c3-s6-nh harmonic 90.894 104.320 # SOURCE4_SOURCE5 92 1.5234 - angle_coeff @angle:c3-s6-no harmonic 86.016 99.570 # SOURCE3 1 - angle_coeff @angle:c3-s6-o harmonic 93.703 108.610 # SOURCE3_SOURCE5 1062 1.0758 - angle_coeff @angle:c3-s6-oh harmonic 94.842 98.740 # SOURCE4_SOURCE5 121 0.7363 - angle_coeff @angle:c3-s6-os harmonic 96.240 96.420 # SOURCE4_SOURCE5 70 0.5868 - angle_coeff @angle:c3-s6-p2 harmonic 86.273 106.470 # SOURCE3 1 - angle_coeff @angle:c3-s6-p3 harmonic 90.571 103.400 # SOURCE3 3 0.8516 - angle_coeff @angle:c3-s6-p4 harmonic 84.641 104.120 # SOURCE3 1 - angle_coeff @angle:c3-s6-p5 harmonic 91.629 103.460 # SOURCE3 1 - angle_coeff @angle:c3-s6-s4 harmonic 72.386 98.100 # SOURCE3 1 - angle_coeff @angle:c3-s6-s harmonic 71.088 104.500 # SOURCE3 1 - angle_coeff @angle:c3-s6-s6 harmonic 71.006 101.950 # SOURCE3 1 - angle_coeff @angle:c3-s6-sh harmonic 70.399 101.840 # SOURCE3 1 - angle_coeff @angle:c3-s6-ss harmonic 69.952 102.470 # SOURCE3 3 1.7451 - angle_coeff @angle:ca-s6-ca harmonic 72.567 103.080 # SOURCE3 1 - angle_coeff @angle:ca-s6-o harmonic 97.373 104.090 # SOURCE4_SOURCE5 137 0.5743 - angle_coeff @angle:c-s6-c3 harmonic 70.322 101.240 # SOURCE3 1 - angle_coeff @angle:c-s6-c harmonic 69.677 99.820 # SOURCE3 1 - angle_coeff @angle:cc-s6-o harmonic 95.603 103.760 # SOURCE4_SOURCE5 24 0.8201 - angle_coeff @angle:cl-s6-cl harmonic 90.995 101.250 # SOURCE3 1 - angle_coeff @angle:cl-s6-f harmonic 105.577 99.000 # SOURCE2 1 - angle_coeff @angle:cl-s6-o harmonic 101.239 107.520 # SOURCE3_SOURCE5 6 0.2106 - angle_coeff @angle:c-s6-o harmonic 91.492 107.970 # SOURCE3 1 - angle_coeff @angle:c-s6-os harmonic 91.455 102.120 # SOURCE3 1 - angle_coeff @angle:cx-s6-cx harmonic 101.683 54.700 # SOURCE2 1 - angle_coeff @angle:cy-s6-o harmonic 91.172 110.520 # SOURCE4_SOURCE5 71 0.9427 - angle_coeff @angle:f-s6-f harmonic 137.577 89.710 # SOURCE2_SOURCE5 22 1.8574 - angle_coeff @angle:f-s6-o harmonic 130.197 106.540 # SOURCE3_SOURCE5 7 0.0793 - angle_coeff @angle:hs-s6-hs harmonic 40.502 99.020 # SOURCE3 2 0.0595 - angle_coeff @angle:hs-s6-n1 harmonic 77.206 97.270 # HF/6-31G* 1 - angle_coeff @angle:hs-s6-o harmonic 72.305 107.680 # SOURCE3_SOURCE5 17 0.0882 - angle_coeff @angle:i-s6-i harmonic 67.346 99.250 # SOURCE3 1 - angle_coeff @angle:i-s6-o harmonic 70.931 108.820 # SOURCE3_SOURCE5 6 0.6545 - angle_coeff @angle:n1-s6-n1 harmonic 147.507 95.520 # HF/6-31G* 1 - angle_coeff @angle:n1-s6-o harmonic 137.179 107.520 # HF/6-31G* 1 - angle_coeff @angle:n2-s6-n2 harmonic 132.302 98.610 # SOURCE3 1 - angle_coeff @angle:n2-s6-o harmonic 124.131 119.100 # SOURCE3_SOURCE5 11 3.0533 - angle_coeff @angle:n2-s6-oh harmonic 123.655 106.960 # SOURCE3 2 - angle_coeff @angle:n2-s6-os harmonic 126.381 103.250 # SOURCE3 1 - angle_coeff @angle:n3-s6-n3 harmonic 123.034 98.440 # SOURCE4_SOURCE5 16 0.3984 - angle_coeff @angle:n3-s6-o harmonic 124.794 107.430 # SOURCE3_SOURCE5 319 1.1452 - angle_coeff @angle:n3-s6-os harmonic 124.070 99.660 # SOURCE4_SOURCE5 27 0.8063 - angle_coeff @angle:n4-s6-n4 harmonic 105.682 101.850 # SOURCE3 1 - angle_coeff @angle:n4-s6-o harmonic 115.123 102.920 # SOURCE3 10 1.5434 - angle_coeff @angle:na-s6-na harmonic 119.677 98.040 # SOURCE3 1 - angle_coeff @angle:na-s6-o harmonic 123.180 105.820 # SOURCE3_SOURCE5 31 0.6987 - angle_coeff @angle:nh-s6-nh harmonic 123.669 94.560 # SOURCE3 1 - angle_coeff @angle:nh-s6-o harmonic 123.651 107.210 # SOURCE3_SOURCE5 106 1.3795 - angle_coeff @angle:n-s6-n harmonic 116.385 104.160 # SOURCE3 1 - angle_coeff @angle:n-s6-o harmonic 122.694 107.020 # SOURCE3_SOURCE5 63 1.7044 - angle_coeff @angle:no-s6-no harmonic 107.924 91.630 # SOURCE3 1 - angle_coeff @angle:no-s6-o harmonic 109.649 107.430 # SOURCE3 6 1.5494 - angle_coeff @angle:n-s6-os harmonic 122.468 99.230 # SOURCE4_SOURCE5 10 0.9794 - angle_coeff @angle:oh-s6-oh harmonic 124.674 100.340 # SOURCE3 6 0.0076 - angle_coeff @angle:oh-s6-os harmonic 127.394 96.810 # SOURCE4_SOURCE5 74 0.8201 - angle_coeff @angle:oh-s6-p2 harmonic 108.695 109.670 # SOURCE3 2 - angle_coeff @angle:o-s6-o harmonic 128.200 120.050 # SOURCE4_SOURCE5 971 1.8153 - angle_coeff @angle:o-s6-oh harmonic 126.323 108.050 # SOURCE3_SOURCE5 306 0.8954 - angle_coeff @angle:o-s6-os harmonic 126.629 108.560 # SOURCE3_SOURCE5 346 1.4469 - angle_coeff @angle:o-s6-p2 harmonic 111.304 106.610 # SOURCE3 1 - angle_coeff @angle:o-s6-p3 harmonic 116.333 107.070 # SOURCE3 22 1.0550 - angle_coeff @angle:o-s6-p4 harmonic 107.389 105.670 # SOURCE3 1 - angle_coeff @angle:o-s6-p5 harmonic 118.512 106.640 # SOURCE3 1 - angle_coeff @angle:o-s6-s4 harmonic 90.199 107.850 # SOURCE3 1 - angle_coeff @angle:o-s6-s harmonic 90.887 110.290 # SOURCE3 6 2.2405 - angle_coeff @angle:o-s6-s6 harmonic 90.953 106.070 # SOURCE3 1 - angle_coeff @angle:o-s6-sh harmonic 89.506 106.810 # SOURCE3 6 0.6292 - angle_coeff @angle:os-s6-os harmonic 126.643 98.700 # SOURCE3 1 - angle_coeff @angle:o-s6-ss harmonic 88.847 107.430 # SOURCE3 10 1.1423 - angle_coeff @angle:p3-s6-p3 harmonic 114.939 110.170 # SOURCE3 4 5.3678 - angle_coeff @angle:p5-s6-p5 harmonic 120.162 104.490 # SOURCE3 1 - angle_coeff @angle:s4-s6-s4 harmonic 72.429 101.990 # SOURCE3 1 - angle_coeff @angle:s4-s6-s6 harmonic 77.030 90.170 # SOURCE3 1 - angle_coeff @angle:s6-s6-s6 harmonic 71.972 103.290 # SOURCE3 1 - angle_coeff @angle:sh-s6-sh harmonic 69.961 106.430 # SOURCE3 1 - angle_coeff @angle:sh-s6-ss harmonic 71.071 102.640 # SOURCE3 1 - angle_coeff @angle:s-s6-s harmonic 71.394 109.340 # SOURCE3 1 - angle_coeff @angle:ss-s6-ss harmonic 71.189 101.820 # SOURCE3 1 - angle_coeff @angle:br-sh-hs harmonic 49.791 95.640 # SOURCE3 1 - angle_coeff @angle:c1-sh-hs harmonic 55.580 95.990 # calculated_based_on_C#C-SH 0 - angle_coeff @angle:c2-sh-hs harmonic 52.778 96.790 # SOURCE4_SOURCE5 12 0.5703 - angle_coeff @angle:c3-sh-hs harmonic 51.361 96.400 # SOURCE3_SOURCE5 191 0.6428 - angle_coeff @angle:ca-sh-hs harmonic 53.161 95.500 # SOURCE4_SOURCE5 44 0.8350 - angle_coeff @angle:cc-sh-hs harmonic 53.591 95.010 # SOURCE4_SOURCE5 23 1.3099 - angle_coeff @angle:c-sh-hs harmonic 53.042 94.470 # SOURCE3_SOURCE5 41 0.9733 - angle_coeff @angle:f-sh-hs harmonic 71.420 96.500 # SOURCE3 1 - angle_coeff @angle:hs-sh-hs harmonic 42.155 93.000 # SOURCE3_SOURCE5 3 0.4777 - angle_coeff @angle:hs-sh-i harmonic 44.148 96.440 # SOURCE3 1 - angle_coeff @angle:hs-sh-n1 harmonic 72.794 93.510 # HF/6-31G* 1 - angle_coeff @angle:hs-sh-n2 harmonic 67.814 95.820 # SOURCE3 5 3.1495 - angle_coeff @angle:hs-sh-n harmonic 68.213 95.590 # SOURCE3 4 3.9065 - angle_coeff @angle:hs-sh-n3 harmonic 67.725 95.980 # SOURCE3 3 1.1735 - angle_coeff @angle:hs-sh-n4 harmonic 66.458 93.130 # SOURCE3 3 0.1675 - angle_coeff @angle:hs-sh-na harmonic 67.804 97.380 # SOURCE3 9 1.0223 - angle_coeff @angle:hs-sh-nh harmonic 66.944 101.110 # SOURCE3 1 - angle_coeff @angle:hs-sh-no harmonic 66.751 92.930 # SOURCE3 1 - angle_coeff @angle:hs-sh-o harmonic 67.503 109.230 # SOURCE3 2 0.0068 - angle_coeff @angle:hs-sh-oh harmonic 68.281 98.640 # SOURCE3 2 0.0605 - angle_coeff @angle:hs-sh-os harmonic 69.115 98.150 # SOURCE3 3 0.1661 - angle_coeff @angle:hs-sh-p2 harmonic 66.084 99.120 # SOURCE3 10 5.4110 - angle_coeff @angle:hs-sh-p3 harmonic 62.144 95.810 # SOURCE3 3 0.4396 - angle_coeff @angle:hs-sh-p4 harmonic 63.188 94.220 # SOURCE3 4 0.7605 - angle_coeff @angle:hs-sh-p5 harmonic 64.112 94.520 # SOURCE3 3 0.5589 - angle_coeff @angle:hs-sh-s harmonic 47.237 102.870 # SOURCE3 2 - angle_coeff @angle:hs-sh-s4 harmonic 48.513 92.160 # SOURCE3 3 1.6519 - angle_coeff @angle:hs-sh-s6 harmonic 49.509 93.830 # SOURCE3 3 1.2561 - angle_coeff @angle:hs-sh-sh harmonic 49.372 99.070 # SOURCE3 2 - angle_coeff @angle:hs-sh-ss harmonic 49.131 99.170 # SOURCE3 3 0.2457 - angle_coeff @angle:br-ss-br harmonic 77.455 102.920 # SOURCE3 1 - angle_coeff @angle:br-ss-c3 harmonic 73.438 99.030 # SOURCE3 1 - angle_coeff @angle:c1-ss-c1 harmonic 77.701 98.300 # SOURCE2 1 - angle_coeff @angle:c1-ss-c3 harmonic 72.838 101.860 # SOURCE2_SOURCE5 24 1.0923 - angle_coeff @angle:c2-ss-c2 harmonic 75.153 99.560 # SOURCE3 1 - angle_coeff @angle:c2-ss-c3 harmonic 72.568 100.370 # SOURCE4 100 2.3280 - angle_coeff @angle:c2-ss-cy harmonic 76.860 88.910 # SOURCE4_SOURCE5 51 0.4794 - angle_coeff @angle:c2-ss-n2 harmonic 92.922 106.760 # SOURCE3 1 - angle_coeff @angle:c2-ss-na harmonic 93.759 100.510 # SOURCE3 6 6.9702 - angle_coeff @angle:c2-ss-os harmonic 100.020 89.760 # SOURCE3 1 - angle_coeff @angle:c2-ss-ss harmonic 75.743 92.260 # SOURCE3 1 - angle_coeff @angle:c3-ss-c3 harmonic 71.051 99.240 # SOURCE3_SOURCE5 443 1.3973 - angle_coeff @angle:c3-ss-ca harmonic 71.145 102.100 # SOURCE4_SOURCE5 393 1.3148 - angle_coeff @angle:c3-ss-cc harmonic 72.106 100.640 # CORR_SOURCE5 118 1.6668 - angle_coeff @angle:c3-ss-cd harmonic 72.106 100.640 # CORR_SOURCE5 118 1.6668 - angle_coeff @angle:c3-ss-cl harmonic 80.033 99.400 # SOURCE2 1 - angle_coeff @angle:c3-ss-cy harmonic 72.699 94.270 # SOURCE4_SOURCE5 150 0.4649 - angle_coeff @angle:c3-ss-f harmonic 95.769 97.490 # SOURCE3 1 - angle_coeff @angle:c3-ss-i harmonic 67.953 100.000 # SOURCE3 1 - angle_coeff @angle:c3-ss-n1 harmonic 94.433 98.440 # HF/6-31G* 1 - angle_coeff @angle:c3-ss-n2 harmonic 94.643 96.080 # SOURCE3_SOURCE5 11 1.2317 - angle_coeff @angle:c3-ss-n3 harmonic 91.857 98.830 # SOURCE3 3 0.2909 - angle_coeff @angle:c3-ss-n harmonic 91.130 100.300 # SOURCE3 4 0.6579 - angle_coeff @angle:c3-ss-n4 harmonic 90.288 97.790 # SOURCE3 3 0.2002 - angle_coeff @angle:c3-ss-na harmonic 92.714 96.590 # SOURCE3_SOURCE5 21 1.0132 - angle_coeff @angle:c3-ss-nh harmonic 91.350 100.630 # SOURCE3 1 - angle_coeff @angle:c3-ss-no harmonic 89.523 98.620 # SOURCE3 1 - angle_coeff @angle:c3-ss-o harmonic 92.362 106.990 # SOURCE3_SOURCE5 11 1.0097 - angle_coeff @angle:c3-ss-oh harmonic 92.897 98.280 # SOURCE3 2 1.4326 - angle_coeff @angle:c3-ss-os harmonic 92.581 98.210 # SOURCE3 4 1.7097 - angle_coeff @angle:c3-ss-p2 harmonic 95.479 98.410 # SOURCE3 8 0.9454 - angle_coeff @angle:c3-ss-p3 harmonic 90.885 98.700 # SOURCE3 3 0.0356 - angle_coeff @angle:c3-ss-p4 harmonic 91.629 98.160 # SOURCE3 4 0.1361 - angle_coeff @angle:c3-ss-p5 harmonic 90.364 100.060 # SOURCE4_SOURCE5 62 1.0141 - angle_coeff @angle:c3-ss-s4 harmonic 70.640 96.370 # SOURCE3 3 0.0202 - angle_coeff @angle:c3-ss-s harmonic 70.410 101.900 # SOURCE3 1 - angle_coeff @angle:c3-ss-s6 harmonic 71.595 96.760 # SOURCE3 3 1.5680 - angle_coeff @angle:c3-ss-sh harmonic 70.887 101.930 # SOURCE3 1 - angle_coeff @angle:c3-ss-ss harmonic 70.258 103.390 # SOURCE4_SOURCE5 237 1.0715 - angle_coeff @angle:ca-ss-ca harmonic 73.541 98.830 # SOURCE4_SOURCE5 225 1.3938 - angle_coeff @angle:ca-ss-cc harmonic 77.818 89.470 # CORR_SOURCE5 200 1.1779 - angle_coeff @angle:ca-ss-cd harmonic 77.818 89.470 # CORR_SOURCE5 200 1.1779 - angle_coeff @angle:ca-ss-cl harmonic 80.234 101.050 # SOURCE3 1 - angle_coeff @angle:ca-ss-n harmonic 97.427 90.990 # SOURCE3_SOURCE5 5 0.5202 - angle_coeff @angle:ca-ss-na harmonic 93.087 99.320 # SOURCE3 1 - angle_coeff @angle:ca-ss-nc harmonic 97.913 94.760 # SOURCE3 1 - angle_coeff @angle:ca-ss-nd harmonic 97.913 94.760 # SOURCE3 1 - angle_coeff @angle:ca-ss-ss harmonic 70.425 105.130 # SOURCE4_SOURCE5 69 1.0007 - angle_coeff @angle:c-ss-c2 harmonic 76.536 92.430 # SOURCE3 1 - angle_coeff @angle:c-ss-c3 harmonic 71.828 99.160 # SOURCE3_SOURCE5 108 1.2072 - angle_coeff @angle:c-ss-c harmonic 71.820 101.400 # SOURCE3 1 - angle_coeff @angle:c-ss-cc harmonic 75.135 94.890 # SOURCE4_SOURCE5 32 1.7205 - angle_coeff @angle:cc-ss-cc harmonic 78.031 90.240 # SOURCE3_SOURCE5 652 1.5043 - angle_coeff @angle:cc-ss-cd harmonic 77.807 90.760 # SOURCE4_SOURCE5 157 1.7485 - angle_coeff @angle:cc-ss-n harmonic 96.775 93.580 # SOURCE3_SOURCE5 6 2.0175 - angle_coeff @angle:cc-ss-na harmonic 93.760 99.330 # SOURCE3 18 - angle_coeff @angle:cc-ss-nc harmonic 99.545 93.220 # CORR_SOURCE5 25 1.5563 - angle_coeff @angle:cc-ss-os harmonic 94.746 98.810 # SOURCE3 2 2.1583 - angle_coeff @angle:cc-ss-ss harmonic 74.869 93.800 # CORR_SOURCE5 31 0.9858 - angle_coeff @angle:cd-ss-cd harmonic 78.031 90.240 # SOURCE3_SOURCE5 652 1.5043 - angle_coeff @angle:cd-ss-n harmonic 96.775 93.580 # SOURCE3_SOURCE5 6 2.0175 - angle_coeff @angle:cd-ss-na harmonic 93.760 99.330 # SOURCE3 18 2.5847 - angle_coeff @angle:cd-ss-nd harmonic 99.545 93.220 # CORR_SOURCE5 25 1.5563 - angle_coeff @angle:cd-ss-os harmonic 94.746 98.810 # SOURCE3 2 - angle_coeff @angle:cd-ss-ss harmonic 74.869 93.800 # CORR_SOURCE5 31 0.9858 - angle_coeff @angle:cl-ss-cl harmonic 90.057 103.370 # SOURCE3 1 - angle_coeff @angle:cx-ss-cx harmonic 102.217 48.300 # SOURCE2 1 - angle_coeff @angle:f-ss-f harmonic 129.659 98.300 # SOURCE2 1 - angle_coeff @angle:f-ss-ss harmonic 90.124 108.300 # SOURCE2 1 - angle_coeff @angle:i-ss-i harmonic 72.646 106.290 # SOURCE3 1 - angle_coeff @angle:n1-ss-n1 harmonic 128.766 96.960 # HF/6-31G* 1 - angle_coeff @angle:n2-ss-n2 harmonic 125.325 96.750 # SOURCE3 1 - angle_coeff @angle:n3-ss-n3 harmonic 117.075 102.340 # SOURCE3 1 - angle_coeff @angle:n4-ss-n4 harmonic 111.994 101.190 # SOURCE3 1 - angle_coeff @angle:na-ss-na harmonic 116.207 102.810 # SOURCE3 1 - angle_coeff @angle:nc-ss-nc harmonic 126.827 97.990 # CORR_SOURCE5 29 0.5000 - angle_coeff @angle:nd-ss-nd harmonic 126.827 97.990 # CORR_SOURCE5 29 0.5000 - angle_coeff @angle:nh-ss-nh harmonic 114.991 107.890 # SOURCE3 1 - angle_coeff @angle:n-ss-n harmonic 116.487 103.100 # SOURCE3 1 - angle_coeff @angle:no-ss-no harmonic 108.247 106.430 # SOURCE3 1 - angle_coeff @angle:oh-ss-oh harmonic 118.444 104.250 # SOURCE3 1 - angle_coeff @angle:o-ss-o harmonic 124.036 119.300 # SOURCE2 1 - angle_coeff @angle:o-ss-p5 harmonic 114.305 106.410 # SOURCE3 1 - angle_coeff @angle:o-ss-s6 harmonic 89.483 105.390 # SOURCE3 1 - angle_coeff @angle:os-ss-os harmonic 118.047 102.990 # SOURCE3 1 - angle_coeff @angle:o-ss-ss harmonic 88.228 112.700 # SOURCE2 1 - angle_coeff @angle:p2-ss-p2 harmonic 127.760 99.520 # SOURCE3 1 - angle_coeff @angle:p3-ss-p3 harmonic 117.165 101.670 # SOURCE3 1 - angle_coeff @angle:p5-ss-p5 harmonic 126.593 87.370 # SOURCE3_SOURCE5 11 1.2491 - angle_coeff @angle:s4-ss-s4 harmonic 71.661 96.080 # SOURCE3 1 - angle_coeff @angle:s4-ss-s6 harmonic 70.568 101.260 # SOURCE3 1 - angle_coeff @angle:s6-ss-s6 harmonic 71.193 101.810 # SOURCE3 1 - angle_coeff @angle:sh-ss-sh harmonic 70.979 107.540 # SOURCE3 1 - angle_coeff @angle:sh-ss-ss harmonic 71.215 106.530 # SOURCE3 1 - angle_coeff @angle:s-ss-s harmonic 67.904 115.040 # SOURCE3 1 - angle_coeff @angle:ss-ss-ss harmonic 70.653 107.930 # SOURCE4_SOURCE5 72 1.6368 - angle_coeff @angle:c3-sx-ca harmonic 72.223 96.640 # SOURCE4_SOURCE5 41 0.4942 - angle_coeff @angle:c3-sx-cc harmonic 73.054 95.180 # SOURCE4_SOURCE5 41 0.6549 - angle_coeff @angle:c3-sx-ce harmonic 72.861 95.290 # SOURCE3_SOURCE5 10 0.5723 - angle_coeff @angle:c3-sx-cf harmonic 72.861 95.290 # SOURCE3_SOURCE5 7 0.8172 - angle_coeff @angle:c3-sx-ne harmonic 93.362 90.060 # SOURCE3 5 1.9627 - angle_coeff @angle:c3-sx-nf harmonic 93.362 90.060 # SOURCE3 5 - angle_coeff @angle:c3-sx-o harmonic 91.942 107.520 # SOURCE3_SOURCE5 84 0.7996 - angle_coeff @angle:c3-sx-pe harmonic 91.537 94.320 # SOURCE3 7 0.5547 - angle_coeff @angle:c3-sx-pf harmonic 91.537 94.320 # SOURCE3 7 - angle_coeff @angle:c3-sx-px harmonic 88.346 96.460 # SOURCE3 3 1.3351 - angle_coeff @angle:c3-sx-py harmonic 88.211 95.670 # SOURCE3 1 - angle_coeff @angle:c3-sx-sx harmonic 67.226 91.470 # SOURCE3 4 1.9919 - angle_coeff @angle:c3-sx-sy harmonic 68.899 95.470 # SOURCE3 3 2.8422 - angle_coeff @angle:ca-sx-ca harmonic 72.893 95.750 # SOURCE3_SOURCE5 14 1.8607 - angle_coeff @angle:ca-sx-o harmonic 92.722 107.150 # SOURCE4_SOURCE5 86 0.9103 - angle_coeff @angle:c-sx-c3 harmonic 72.536 92.710 # SOURCE3 3 0.3095 - angle_coeff @angle:c-sx-c harmonic 74.104 86.850 # SOURCE3 1 - angle_coeff @angle:cc-sx-o harmonic 94.293 104.810 # SOURCE4_SOURCE5 45 1.5594 - angle_coeff @angle:ce-sx-ce harmonic 73.461 94.960 # SOURCE3 1 - angle_coeff @angle:ce-sx-o harmonic 92.502 108.230 # SOURCE3_SOURCE5 27 0.8358 - angle_coeff @angle:cf-sx-cf harmonic 73.461 94.960 # SOURCE3 1 - angle_coeff @angle:cf-sx-o harmonic 92.502 108.230 # SOURCE3_SOURCE5 22 0.9547 - angle_coeff @angle:c-sx-o harmonic 90.915 106.170 # SOURCE3 5 0.9477 - angle_coeff @angle:ne-sx-ne harmonic 107.648 106.450 # SOURCE3_SOURCE5 5 1.4815 - angle_coeff @angle:ne-sx-o harmonic 114.103 109.810 # SOURCE3_SOURCE5 13 1.0385 - angle_coeff @angle:nf-sx-nf harmonic 107.648 106.450 # SOURCE3_SOURCE5 5 1.4815 - angle_coeff @angle:nf-sx-o harmonic 114.103 109.810 # SOURCE3_SOURCE5 6 0.5536 - angle_coeff @angle:o-sx-pe harmonic 111.805 106.430 # SOURCE3 9 2.8345 - angle_coeff @angle:o-sx-pf harmonic 111.805 106.430 # SOURCE3 9 - angle_coeff @angle:o-sx-px harmonic 109.143 104.770 # SOURCE3 3 1.9810 - angle_coeff @angle:o-sx-py harmonic 106.155 109.130 # SOURCE3 7 5.6840 - angle_coeff @angle:o-sx-sx harmonic 79.764 104.650 # SOURCE3 6 3.0524 - angle_coeff @angle:o-sx-sy harmonic 85.123 103.410 # SOURCE3 5 0.9618 - angle_coeff @angle:pe-sx-pe harmonic 120.095 92.620 # SOURCE3 1 - angle_coeff @angle:pf-sx-pf harmonic 120.095 92.620 # SOURCE3 1 - angle_coeff @angle:py-sx-py harmonic 133.313 69.230 # SOURCE3 3 17.4143 - angle_coeff @angle:sx-sx-sx harmonic 69.059 84.900 # SOURCE3 1 - angle_coeff @angle:sy-sx-sy harmonic 69.768 93.520 # SOURCE3 1 - angle_coeff @angle:c3-sy-ca harmonic 70.945 103.930 # SOURCE4_SOURCE5 136 0.4172 - angle_coeff @angle:c3-sy-cc harmonic 71.767 101.950 # SOURCE4_SOURCE5 32 1.4362 - angle_coeff @angle:c3-sy-ce harmonic 71.136 103.530 # SOURCE3_SOURCE5 11 1.3594 - angle_coeff @angle:c3-sy-cf harmonic 71.136 103.530 # SOURCE3_SOURCE5 8 1.7429 - angle_coeff @angle:c3-sy-ne harmonic 92.368 102.190 # SOURCE3_SOURCE5 11 3.1966 - angle_coeff @angle:c3-sy-nf harmonic 92.368 102.190 # SOURCE3_SOURCE5 6 2.3703 - angle_coeff @angle:c3-sy-o harmonic 93.792 107.850 # SOURCE3_SOURCE5 283 0.5690 - angle_coeff @angle:c3-sy-pe harmonic 85.480 106.030 # SOURCE3 6 2.6117 - angle_coeff @angle:c3-sy-pf harmonic 85.480 106.030 # SOURCE3 6 - angle_coeff @angle:c3-sy-px harmonic 85.416 103.620 # SOURCE3 3 0.7078 - angle_coeff @angle:c3-sy-py harmonic 87.474 103.390 # SOURCE3 3 0.4563 - angle_coeff @angle:c3-sy-sx harmonic 66.097 104.640 # SOURCE3 3 4.6276 - angle_coeff @angle:c3-sy-sy harmonic 67.466 100.780 # SOURCE3 4 1.1633 - angle_coeff @angle:ca-sy-ca harmonic 71.127 104.440 # SOURCE4_SOURCE5 55 1.7845 - angle_coeff @angle:ca-sy-cc harmonic 71.045 105.090 # SOURCE4_SOURCE5 10 0.3628 - angle_coeff @angle:ca-sy-n3 harmonic 92.241 102.440 # SOURCE4_SOURCE5 407 1.1038 - angle_coeff @angle:ca-sy-n harmonic 90.479 105.370 # SOURCE4_SOURCE5 122 1.2203 - angle_coeff @angle:ca-sy-ne harmonic 92.539 103.010 # SOURCE4_SOURCE5 36 2.1672 - angle_coeff @angle:ca-sy-nh harmonic 90.475 105.500 # SOURCE4_SOURCE5 205 1.5936 - angle_coeff @angle:ca-sy-o harmonic 94.276 108.350 # SOURCE3_SOURCE5 1362 0.6985 - angle_coeff @angle:ca-sy-oh harmonic 93.834 101.300 # SOURCE4_SOURCE5 94 0.8210 - angle_coeff @angle:ca-sy-os harmonic 96.750 92.980 # SOURCE3 1 - angle_coeff @angle:c-sy-c3 harmonic 70.399 101.250 # SOURCE3 3 1.1850 - angle_coeff @angle:c-sy-c harmonic 69.867 99.810 # SOURCE3 1 - angle_coeff @angle:cc-sy-n3 harmonic 92.404 102.530 # CORR_SOURCE5 35 0.5689 - angle_coeff @angle:cc-sy-o harmonic 94.752 107.890 # CORR_SOURCE5 130 0.8911 - angle_coeff @angle:cd-sy-n3 harmonic 92.404 102.530 # CORR_SOURCE5 35 0.5689 - angle_coeff @angle:cd-sy-nh harmonic 94.463 97.200 # SOURCE4_SOURCE5 12 0.2429 - angle_coeff @angle:cd-sy-o harmonic 94.752 107.890 # CORR_SOURCE5 130 0.8911 - angle_coeff @angle:ce-sy-ce harmonic 71.811 102.780 # SOURCE3 1 - angle_coeff @angle:ce-sy-o harmonic 94.373 108.380 # SOURCE3_SOURCE5 66 0.9753 - angle_coeff @angle:cf-sy-cf harmonic 71.811 102.780 # SOURCE3 1 - angle_coeff @angle:cf-sy-o harmonic 94.373 108.380 # SOURCE3_SOURCE5 56 1.0516 - angle_coeff @angle:c-sy-o harmonic 91.740 107.480 # SOURCE3_SOURCE5 16 0.7996 - angle_coeff @angle:n2-sy-o harmonic 121.876 123.530 # SOURCE4 6 1.2388 - angle_coeff @angle:n3-sy-ne harmonic 120.039 101.930 # SOURCE4_SOURCE5 15 1.4395 - angle_coeff @angle:n3-sy-o harmonic 123.426 107.130 # SOURCE4_SOURCE5 863 1.1609 - angle_coeff @angle:na-sy-na harmonic 119.379 98.040 # SOURCE3 1 - angle_coeff @angle:nc-sy-nc harmonic 132.584 98.040 # SOURCE3 2 - angle_coeff @angle:nd-sy-nd harmonic 132.584 98.040 # SOURCE3 2 - angle_coeff @angle:ne-sy-ne harmonic 122.921 98.620 # SOURCE3 1 - angle_coeff @angle:ne-sy-o harmonic 123.169 109.650 # SOURCE3_SOURCE5 101 1.9902 - angle_coeff @angle:nf-sy-nf harmonic 122.921 98.620 # SOURCE3 1 - angle_coeff @angle:nf-sy-o harmonic 123.169 109.650 # SOURCE3_SOURCE5 87 1.9451 - angle_coeff @angle:nh-sy-o harmonic 123.056 106.230 # SOURCE4_SOURCE5 319 1.7353 - angle_coeff @angle:n-sy-o harmonic 122.195 107.540 # SOURCE4_SOURCE5 155 1.8699 - angle_coeff @angle:o-sy-o harmonic 126.375 121.410 # SOURCE3_SOURCE5 734 0.8526 - angle_coeff @angle:o-sy-oh harmonic 125.990 106.680 # SOURCE3_SOURCE5 166 0.5588 - angle_coeff @angle:o-sy-os harmonic 123.063 107.520 # SOURCE4_SOURCE5 38 1.6656 - angle_coeff @angle:o-sy-pe harmonic 109.504 106.900 # SOURCE3 12 1.4524 - angle_coeff @angle:o-sy-pf harmonic 109.504 106.900 # SOURCE3 12 - angle_coeff @angle:o-sy-px harmonic 108.122 106.170 # SOURCE3 6 0.7059 - angle_coeff @angle:o-sy-py harmonic 111.153 106.670 # SOURCE3 10 0.6478 - angle_coeff @angle:o-sy-sx harmonic 83.961 106.330 # SOURCE3 10 2.0456 - angle_coeff @angle:o-sy-sy harmonic 84.205 106.190 # SOURCE3 12 0.1754 - angle_coeff @angle:py-sy-py harmonic 112.342 104.490 # SOURCE3 1 - angle_coeff @angle:sx-sy-sx harmonic 66.808 101.990 # SOURCE3 1 - angle_coeff @angle:sy-sy-sy harmonic 66.534 103.290 # SOURCE3 1 - angle_coeff @angle:c2-c1-cf harmonic 60.047 179.050 # SOURCE4_SOURCE5 9 0.3913 - angle_coeff @angle:c3-c1-ch harmonic 57.725 178.430 # SOURCE4_SOURCE5 95 0.5682 - angle_coeff @angle:nf-c1-s harmonic 73.610 175.820 # SOURCE4_SOURCE5 15 0.2067 - angle_coeff @angle:br-c2-cf harmonic 64.279 121.530 # SOURCE4_SOURCE5 11 0.7009 - angle_coeff @angle:cd-c2-h4 harmonic 49.786 119.850 # SOURCE4_SOURCE5 16 0.8001 - angle_coeff @angle:cd-c2-nh harmonic 86.562 123.120 # SOURCE4_SOURCE5 17 1.2171 - angle_coeff @angle:cd-c2-o harmonic 91.352 123.590 # SOURCE4_SOURCE5 6 0.0560 - angle_coeff @angle:cf-c2-cl harmonic 72.107 123.470 # SOURCE4_SOURCE5 30 1.0225 - angle_coeff @angle:cf-c2-h4 harmonic 49.654 122.310 # SOURCE4_SOURCE5 145 1.6214 - angle_coeff @angle:cf-c2-na harmonic 86.108 124.170 # SOURCE4_SOURCE5 6 1.9423 - angle_coeff @angle:cf-c2-nh harmonic 87.822 120.710 # SOURCE4_SOURCE5 150 2.3947 - angle_coeff @angle:cf-c2-no harmonic 86.097 119.650 # SOURCE4_SOURCE5 5 0.9817 - angle_coeff @angle:cf-c2-o harmonic 91.992 123.370 # SOURCE4_SOURCE5 9 1.0481 - angle_coeff @angle:cf-c2-oh harmonic 88.571 123.130 # SOURCE4_SOURCE5 62 1.7479 - angle_coeff @angle:cf-c2-os harmonic 87.995 122.800 # SOURCE4_SOURCE5 98 2.2743 - angle_coeff @angle:h4-c2-nf harmonic 64.858 119.510 # SOURCE4_SOURCE5 42 1.6302 - angle_coeff @angle:h5-c2-nf harmonic 64.691 119.850 # SOURCE4_SOURCE5 27 1.3790 - angle_coeff @angle:nf-c2-os harmonic 114.213 118.760 # SOURCE4 5 - angle_coeff @angle:nf-c2-ss harmonic 82.205 120.510 # SOURCE4_SOURCE5 23 2.4188 - angle_coeff @angle:n-c2-nf harmonic 109.323 125.340 # SOURCE4_SOURCE5 15 1.5591 - angle_coeff @angle:ca-c3-cf harmonic 65.618 112.210 # SOURCE4_SOURCE5 93 1.2595 - angle_coeff @angle:cd-c3-cx harmonic 65.894 112.100 # SOURCE4_SOURCE5 7 1.7201 - angle_coeff @angle:c-c3-cf harmonic 65.527 111.890 # SOURCE4_SOURCE5 59 1.5769 - angle_coeff @angle:cd-c3-hx harmonic 47.588 111.010 # SOURCE4_SOURCE5 10 0.7123 - angle_coeff @angle:cd-c3-n2 harmonic 84.630 110.310 # SOURCE4_SOURCE5 21 0.5628 - angle_coeff @angle:cd-c3-n4 harmonic 81.467 115.580 # SOURCE4_SOURCE5 6 1.1723 - angle_coeff @angle:cd-c3-na harmonic 83.647 113.150 # SOURCE4_SOURCE5 10 0.6466 - angle_coeff @angle:cd-c3-p5 harmonic 79.513 116.230 # SOURCE4_SOURCE5 6 0.7766 - angle_coeff @angle:cf-c3-cf harmonic 65.833 111.470 # SOURCE4_SOURCE5 35 0.5985 - angle_coeff @angle:cf-c3-n harmonic 84.349 110.220 # SOURCE4_SOURCE5 10 1.0919 - angle_coeff @angle:cf-c3-oh harmonic 84.971 111.190 # SOURCE4_SOURCE5 57 1.5702 - angle_coeff @angle:cf-c3-os harmonic 85.412 109.500 # SOURCE4_SOURCE5 55 1.8883 - angle_coeff @angle:cf-c3-ss harmonic 63.337 110.720 # SOURCE4_SOURCE5 12 1.7025 - angle_coeff @angle:cd-ca-cq harmonic 66.010 124.300 # SOURCE4_SOURCE5 10 0.6423 - angle_coeff @angle:cf-ca-na harmonic 84.062 119.920 # SOURCE4_SOURCE5 29 0.5242 - angle_coeff @angle:ch-ca-cq harmonic 67.320 121.530 # SOURCE4_SOURCE5 12 0.1831 - angle_coeff @angle:cl-ca-cq harmonic 71.726 120.390 # SOURCE4_SOURCE5 34 0.5366 - angle_coeff @angle:cq-ca-f harmonic 88.831 119.420 # SOURCE4_SOURCE5 30 0.2799 - angle_coeff @angle:cq-ca-h4 harmonic 48.404 120.090 # SOURCE4_SOURCE5 35 0.4098 - angle_coeff @angle:cq-ca-na harmonic 90.665 108.790 # SOURCE4_SOURCE5 349 0.5003 - angle_coeff @angle:cq-ca-nb harmonic 86.369 123.580 # SOURCE4_SOURCE5 79 0.8527 - angle_coeff @angle:cq-ca-nh harmonic 85.714 121.560 # SOURCE4_SOURCE5 19 0.6123 - angle_coeff @angle:cq-ca-oh harmonic 86.623 120.850 # SOURCE4_SOURCE5 29 1.4592 - angle_coeff @angle:cq-ca-ss harmonic 65.950 111.170 # SOURCE4_SOURCE5 16 2.4162 - angle_coeff @angle:ca-c-nf harmonic 85.290 114.710 # SOURCE4_SOURCE5 9 0.7464 - angle_coeff @angle:br-cd-c harmonic 65.156 116.280 # SOURCE4_SOURCE5 24 1.3164 - angle_coeff @angle:br-cd-cd harmonic 63.389 124.050 # SOURCE4_SOURCE5 23 1.9356 - angle_coeff @angle:br-cd-cc harmonic 63.686 124.230 # SOURCE4_SOURCE5 84 2.2845 - angle_coeff @angle:br-cd-na harmonic 80.565 121.580 # SOURCE4_SOURCE5 13 0.9881 - angle_coeff @angle:ca-cd-cf harmonic 64.258 127.010 # SOURCE4_SOURCE5 27 1.6430 - angle_coeff @angle:ca-cd-nh harmonic 84.253 122.130 # SOURCE4_SOURCE5 11 2.0536 - angle_coeff @angle:cd-c-cf harmonic 66.433 115.570 # SOURCE4_SOURCE5 8 1.2130 - angle_coeff @angle:cd-cd-f harmonic 88.377 119.190 # SOURCE4_SOURCE5 19 1.0481 - angle_coeff @angle:c-cd-ch harmonic 67.046 117.880 # SOURCE4_SOURCE5 19 0.6396 - angle_coeff @angle:cd-cd-sy harmonic 61.106 128.250 # SOURCE4_SOURCE5 12 0.8482 - angle_coeff @angle:cc-cd-f harmonic 89.570 121.190 # SOURCE4_SOURCE5 54 0.6386 - angle_coeff @angle:cc-cd-no harmonic 82.947 128.690 # SOURCE4_SOURCE5 197 1.4212 - angle_coeff @angle:c-cd-f harmonic 87.759 116.980 # SOURCE4_SOURCE5 33 0.4384 - angle_coeff @angle:ch-cd-na harmonic 84.878 122.610 # SOURCE4_SOURCE5 7 1.0826 - angle_coeff @angle:ch-cd-ss harmonic 63.762 120.730 # SOURCE4_SOURCE5 15 0.9326 - angle_coeff @angle:cd-c-h4 harmonic 47.598 114.830 # SOURCE4_SOURCE5 20 0.4400 - angle_coeff @angle:cl-cd-na harmonic 90.511 121.120 # SOURCE4_SOURCE5 25 0.9015 - angle_coeff @angle:cl-cd-ss harmonic 71.934 119.850 # SOURCE4_SOURCE5 16 0.8775 - angle_coeff @angle:c-cd-nf harmonic 84.503 119.880 # SOURCE4 6 - angle_coeff @angle:cd-c-s harmonic 64.011 126.280 # SOURCE4_SOURCE5 57 2.2083 - angle_coeff @angle:cd-c-ss harmonic 64.406 112.400 # SOURCE4_SOURCE5 32 1.0830 - angle_coeff @angle:cx-cd-nc harmonic 83.147 127.820 # SOURCE4_SOURCE5 15 1.5594 - angle_coeff @angle:cx-cd-os harmonic 85.414 118.070 # SOURCE4_SOURCE5 13 0.0898 - angle_coeff @angle:cc-c-cx harmonic 65.553 117.430 # SOURCE4_SOURCE5 24 0.1441 - angle_coeff @angle:cc-c-nc harmonic 86.534 113.750 # SOURCE4_SOURCE5 14 0.0860 - angle_coeff @angle:cf-c-cx harmonic 65.246 117.390 # SOURCE4_SOURCE5 13 0.7631 - angle_coeff @angle:cf-c-h4 harmonic 47.181 114.890 # SOURCE4_SOURCE5 94 0.4993 - angle_coeff @angle:cf-c-ss harmonic 64.794 110.490 # SOURCE4_SOURCE5 8 0.5728 - angle_coeff @angle:na-cd-no harmonic 105.313 124.590 # SOURCE4_SOURCE5 114 0.8160 - angle_coeff @angle:na-cd-oh harmonic 111.744 117.480 # SOURCE4_SOURCE5 23 1.0304 - angle_coeff @angle:na-cd-sx harmonic 79.683 117.020 # SOURCE4_SOURCE5 19 0.3766 - angle_coeff @angle:na-cd-sy harmonic 79.507 120.460 # SOURCE4_SOURCE5 8 1.7069 - angle_coeff @angle:nd-cd-no harmonic 106.922 121.730 # SOURCE4_SOURCE5 10 0.8384 - angle_coeff @angle:nc-cd-nc harmonic 110.827 128.070 # SOURCE4_SOURCE5 10 0.4198 - angle_coeff @angle:nc-cd-nf harmonic 107.796 129.010 # SOURCE4_SOURCE5 13 1.6879 - angle_coeff @angle:nc-cd-no harmonic 108.240 122.750 # SOURCE4_SOURCE5 64 0.2909 - angle_coeff @angle:nc-cd-sh harmonic 79.198 124.970 # SOURCE4_SOURCE5 13 0.8081 - angle_coeff @angle:nc-cd-sx harmonic 76.768 127.740 # SOURCE4_SOURCE5 19 0.3234 - angle_coeff @angle:nc-cd-sy harmonic 79.255 123.030 # SOURCE4_SOURCE5 20 1.2273 - angle_coeff @angle:nf-cd-ss harmonic 81.707 117.030 # SOURCE4_SOURCE5 10 0.2421 - angle_coeff @angle:n-cd-n2 harmonic 112.932 119.420 # SOURCE4_SOURCE5 13 0.1189 - angle_coeff @angle:no-cd-os harmonic 109.068 117.550 # SOURCE4_SOURCE5 82 0.2764 - angle_coeff @angle:no-cd-ss harmonic 79.693 121.060 # SOURCE4_SOURCE5 23 0.2526 - angle_coeff @angle:ca-cc-cf harmonic 66.694 124.900 # SOURCE4_SOURCE5 32 1.6591 - angle_coeff @angle:ca-cc-na harmonic 83.626 123.450 # SOURCE4 39 - angle_coeff @angle:cd-cc-cg harmonic 67.080 125.790 # SOURCE4_SOURCE5 54 1.7418 - angle_coeff @angle:cd-cc-cy harmonic 65.987 122.050 # SOURCE4_SOURCE5 12 0.8462 - angle_coeff @angle:cd-cc-nd harmonic 88.069 123.820 # SOURCE4_SOURCE5 14 0.3678 - angle_coeff @angle:cc-cc-cy harmonic 64.938 122.040 # SOURCE4_SOURCE5 7 0.2293 - angle_coeff @angle:cf-cc-nc harmonic 86.641 123.980 # SOURCE4_SOURCE5 5 2.4219 - angle_coeff @angle:c-cc-h4 harmonic 47.105 118.190 # SOURCE4_SOURCE5 8 0.2226 - angle_coeff @angle:na-cc-nh harmonic 110.794 117.280 # SOURCE4_SOURCE5 54 1.7570 - angle_coeff @angle:na-cc-ss harmonic 83.703 111.460 # SOURCE4 20 - angle_coeff @angle:nc-cc-nc harmonic 107.603 125.700 # SOURCE4_SOURCE5 18 0.6787 - angle_coeff @angle:oh-cc-os harmonic 115.442 111.610 # SOURCE4_SOURCE5 6 1.1909 - angle_coeff @angle:c2-cf-cl harmonic 72.080 119.760 # SOURCE4_SOURCE5 38 1.3369 - angle_coeff @angle:c2-cf-h4 harmonic 49.154 124.550 # SOURCE4_SOURCE5 32 1.8945 - angle_coeff @angle:c2-cf-n1 harmonic 91.289 118.230 # SOURCE4_SOURCE5 11 1.2780 - angle_coeff @angle:c2-cf-na harmonic 87.216 119.190 # SOURCE4_SOURCE5 5 0.8452 - angle_coeff @angle:c2-cf-oh harmonic 87.984 123.700 # SOURCE4_SOURCE5 17 1.7138 - angle_coeff @angle:c3-cf-ch harmonic 66.013 117.220 # SOURCE4_SOURCE5 26 1.7890 - angle_coeff @angle:c3-cf-ne harmonic 84.378 120.680 # SOURCE4_SOURCE5 7 2.0560 - angle_coeff @angle:c3-cf-nh harmonic 82.733 119.560 # SOURCE4_SOURCE5 5 1.0524 - angle_coeff @angle:ca-cf-cf harmonic 65.684 119.540 # SOURCE4_SOURCE5 18 1.9239 - angle_coeff @angle:ca-cf-cl harmonic 72.181 114.590 # SOURCE4_SOURCE5 8 0.9719 - angle_coeff @angle:ca-cf-h4 harmonic 47.047 116.990 # SOURCE4_SOURCE5 181 1.0407 - angle_coeff @angle:ca-cf-nh harmonic 85.466 115.580 # SOURCE4_SOURCE5 147 1.1060 - angle_coeff @angle:ca-cf-os harmonic 85.838 115.910 # SOURCE4_SOURCE5 17 1.5899 - angle_coeff @angle:ca-cf-ss harmonic 63.378 117.520 # SOURCE4_SOURCE5 9 1.2901 - angle_coeff @angle:c-cf-ca harmonic 65.478 118.280 # SOURCE4_SOURCE5 17 1.7879 - angle_coeff @angle:cd-cf-cc harmonic 65.259 130.610 # SOURCE4_SOURCE5 19 0.8270 - angle_coeff @angle:c-cf-cf harmonic 65.150 120.980 # SOURCE4_SOURCE5 37 2.3876 - angle_coeff @angle:c-cf-ch harmonic 66.500 118.420 # SOURCE4_SOURCE5 34 1.0602 - angle_coeff @angle:cd-cf-h4 harmonic 47.935 115.680 # SOURCE4_SOURCE5 48 0.8279 - angle_coeff @angle:c-cf-cl harmonic 71.821 115.470 # SOURCE4_SOURCE5 19 1.2383 - angle_coeff @angle:cd-cf-nh harmonic 85.299 118.050 # SOURCE4_SOURCE5 13 1.6005 - angle_coeff @angle:c-cf-cy harmonic 74.704 88.440 # SOURCE4_SOURCE5 34 1.2419 - angle_coeff @angle:cf-cf-cl harmonic 71.617 117.220 # SOURCE4_SOURCE5 23 1.1321 - angle_coeff @angle:cf-cf-oh harmonic 86.685 116.850 # SOURCE4_SOURCE5 19 1.5331 - angle_coeff @angle:ce-cf-cy harmonic 62.247 137.580 # SOURCE4_SOURCE5 18 1.4229 - angle_coeff @angle:ce-cf-h4 harmonic 49.339 122.950 # SOURCE4_SOURCE5 18 1.1766 - angle_coeff @angle:ce-cf-n1 harmonic 90.464 119.940 # SOURCE4_SOURCE5 7 1.8420 - angle_coeff @angle:ce-cf-nh harmonic 87.337 121.380 # SOURCE4_SOURCE5 27 1.6583 - angle_coeff @angle:ch-cf-n2 harmonic 87.851 121.140 # SOURCE4_SOURCE5 8 0.9418 - angle_coeff @angle:c-cf-oh harmonic 86.196 115.760 # SOURCE4_SOURCE5 15 2.2145 - angle_coeff @angle:c-cf-os harmonic 86.086 114.670 # SOURCE4_SOURCE5 26 2.3740 - angle_coeff @angle:h4-cf-n1 harmonic 64.863 116.640 # SOURCE4_SOURCE5 12 0.5604 - angle_coeff @angle:h4-cf-nf harmonic 62.153 115.650 # SOURCE4_SOURCE5 12 1.7190 - angle_coeff @angle:n2-cf-os harmonic 114.215 117.950 # SOURCE4_SOURCE5 13 0.4519 - angle_coeff @angle:n2-cf-ss harmonic 81.512 117.230 # SOURCE4 6 - angle_coeff @angle:nf-cf-nh harmonic 111.319 113.640 # SOURCE4_SOURCE5 29 1.5167 - angle_coeff @angle:ne-cf-nh harmonic 112.342 119.270 # SOURCE4_SOURCE5 17 1.8891 - angle_coeff @angle:ca-ce-cd harmonic 64.611 130.880 # SOURCE4_SOURCE5 29 1.2258 - angle_coeff @angle:c-ce-cc harmonic 66.092 117.820 # SOURCE4_SOURCE5 19 0.9022 - angle_coeff @angle:c-ce-n2 harmonic 88.177 114.410 # SOURCE4_SOURCE5 8 1.4615 - angle_coeff @angle:h4-ce-nf harmonic 64.320 120.560 # SOURCE4_SOURCE5 33 0.8495 - angle_coeff @angle:c1-ch-cd harmonic 58.883 178.610 # SOURCE4_SOURCE5 7 0.3553 - angle_coeff @angle:ch-cg-cg harmonic 60.571 179.580 # SOURCE4_SOURCE5 48 0.3197 - angle_coeff @angle:n-c-nf harmonic 113.600 110.260 # SOURCE4_SOURCE5 15 1.6743 - angle_coeff @angle:ca-cq-na harmonic 86.507 119.500 # SOURCE4_SOURCE5 38 0.8587 - angle_coeff @angle:nb-cq-nb harmonic 110.031 125.790 # SOURCE4_SOURCE5 6 0.6645 - angle_coeff @angle:cd-cx-hc harmonic 47.813 113.930 # SOURCE4_SOURCE5 29 0.6832 - angle_coeff @angle:cf-cy-h2 harmonic 45.874 117.400 # SOURCE4_SOURCE5 21 0.5798 - angle_coeff @angle:cf-cy-n harmonic 94.195 87.940 # SOURCE4_SOURCE5 24 0.2234 - angle_coeff @angle:cf-cy-ss harmonic 60.454 120.540 # SOURCE4_SOURCE5 21 2.1971 - angle_coeff @angle:cd-n2-na harmonic 91.793 109.240 # SOURCE4_SOURCE5 14 1.5712 - angle_coeff @angle:cd-n2-nh harmonic 88.704 118.470 # SOURCE4_SOURCE5 7 1.6660 - angle_coeff @angle:c3-n4-cd harmonic 64.438 111.040 # SOURCE4_SOURCE5 11 1.9847 - angle_coeff @angle:c3-na-cq harmonic 65.414 119.620 # SOURCE4_SOURCE5 10 0.5495 - angle_coeff @angle:ca-na-cq harmonic 67.035 120.860 # SOURCE4_SOURCE5 38 1.4370 - angle_coeff @angle:cd-na-cf harmonic 64.694 126.610 # SOURCE4_SOURCE5 8 0.5158 - angle_coeff @angle:cq-nb-nb harmonic 86.918 120.960 # SOURCE4_SOURCE5 20 0.6372 - angle_coeff @angle:c-n-cf harmonic 63.457 131.380 # SOURCE4_SOURCE5 225 1.7874 - angle_coeff @angle:ca-nc-nd harmonic 92.520 108.340 # SOURCE4_SOURCE5 14 0.2755 - angle_coeff @angle:c2-nf-ch harmonic 70.178 123.230 # SOURCE4_SOURCE5 27 1.1966 - angle_coeff @angle:c-nf-sy harmonic 65.604 116.430 # SOURCE4_SOURCE5 10 2.0084 - angle_coeff @angle:c3-nh-ce harmonic 65.126 120.120 # SOURCE4_SOURCE5 32 2.1639 - angle_coeff @angle:cd-nh-n2 harmonic 85.504 120.090 # SOURCE4_SOURCE5 16 0.9182 - angle_coeff @angle:cd-nh-sy harmonic 62.976 122.520 # SOURCE4_SOURCE5 37 1.3342 - angle_coeff @angle:cf-nh-sy harmonic 65.279 113.390 # SOURCE4_SOURCE5 8 1.1060 - angle_coeff @angle:hn-n-nd harmonic 62.278 115.420 # SOURCE4_SOURCE5 24 0.7584 - angle_coeff @angle:cd-no-o harmonic 87.737 117.490 # SOURCE4_SOURCE5 426 0.5387 - angle_coeff @angle:n3-py-nf harmonic 79.409 108.760 # SOURCE4_SOURCE5 18 1.1434 - angle_coeff @angle:cd-s6-o harmonic 95.603 103.760 # SOURCE4_SOURCE5 15 0.9562 - angle_coeff @angle:cd-sh-hs harmonic 53.591 95.010 # SOURCE4_SOURCE5 15 1.4000 - angle_coeff @angle:c-ss-cd harmonic 75.135 94.890 # SOURCE4_SOURCE5 18 1.2231 - angle_coeff @angle:c3-sx-cd harmonic 73.054 95.180 # SOURCE4_SOURCE5 24 0.6543 - angle_coeff @angle:cd-sx-o harmonic 94.293 104.810 # SOURCE4_SOURCE5 28 1.4279 - angle_coeff @angle:c3-sy-cd harmonic 71.767 101.950 # SOURCE4_SOURCE5 20 1.3784 - angle_coeff @angle:ca-sy-cd harmonic 71.045 105.090 # SOURCE4_SOURCE5 5 0.3628 - angle_coeff @angle:ca-sy-nf harmonic 92.539 103.010 # SOURCE4_SOURCE5 25 2.4137 - angle_coeff @angle:cc-sy-nh harmonic 94.463 97.200 # SOURCE4_SOURCE5 6 0.2429 - angle_coeff @angle:n3-sy-nf harmonic 120.039 101.930 # SOURCE4_SOURCE5 10 1.4898 - angle_coeff @angle:cl-py-ne harmonic 67.181 109.160 # SOURCE5 79 0.9726 - angle_coeff @angle:ce-ce-nh harmonic 85.786 116.410 # SOURCE5 70 1.9262 - angle_coeff @angle:cp-ca-os harmonic 87.894 116.910 # SOURCE5 38 1.2997 - angle_coeff @angle:ca-cc-ca harmonic 65.280 122.940 # SOURCE5 37 2.3284 - angle_coeff @angle:h1-c3-i harmonic 39.280 103.880 # SOURCE5 43 0.8359 - angle_coeff @angle:h4-c2-h4 harmonic 37.559 117.920 # SOURCE5 46 1.0787 - angle_coeff @angle:c-ss-ss harmonic 72.810 97.680 # SOURCE5 29 1.7788 - angle_coeff @angle:f-py-ne harmonic 83.682 108.600 # SOURCE5 47 0.7739 - angle_coeff @angle:ca-nh-ce harmonic 65.017 127.740 # SOURCE5 32 0.9569 - angle_coeff @angle:ce-cx-cx harmonic 64.347 118.620 # SOURCE5 40 1.7472 - angle_coeff @angle:py-ne-py harmonic 111.020 121.410 # SOURCE5 34 1.5196 - angle_coeff @angle:c-cd-ss harmonic 62.961 121.970 # SOURCE5 29 2.1476 - angle_coeff @angle:s-p5-ss harmonic 46.401 116.670 # SOURCE5 27 1.1060 - angle_coeff @angle:cx-c3-nh harmonic 86.752 103.860 # SOURCE5 29 2.2522 - angle_coeff @angle:cc-cc-cl harmonic 72.034 119.990 # SOURCE5 43 1.9574 - angle_coeff @angle:cd-na-cx harmonic 66.440 116.390 # SOURCE5 14 0.5535 - angle_coeff @angle:h1-cy-nh harmonic 59.704 113.860 # SOURCE5 31 0.8499 - angle_coeff @angle:h5-c-os harmonic 63.962 113.090 # SOURCE5 20 0.1826 - angle_coeff @angle:c2-c3-n4 harmonic 81.944 113.640 # SOURCE5 18 2.3563 - angle_coeff @angle:c2-cx-c3 harmonic 65.275 115.480 # SOURCE5 22 1.1986 - angle_coeff @angle:c3-c2-cx harmonic 64.810 117.870 # SOURCE5 20 2.2886 - angle_coeff @angle:br-cx-cx harmonic 62.999 119.040 # SOURCE5 21 0.7114 - angle_coeff @angle:cc-cf-ch harmonic 68.168 122.270 # SOURCE5 30 0.9028 - angle_coeff @angle:c3-c3-sx harmonic 63.092 110.500 # SOURCE5 14 1.4461 - angle_coeff @angle:ca-cy-hc harmonic 46.450 114.530 # SOURCE5 17 1.6221 - angle_coeff @angle:cx-c1-n1 harmonic 74.188 178.250 # SOURCE5 17 0.8798 - angle_coeff @angle:cl-py-cl harmonic 61.568 101.950 # SOURCE5 12 0.7596 - angle_coeff @angle:c2-ce-cx harmonic 66.366 122.740 # SOURCE5 23 1.5745 - angle_coeff @angle:c3-c-cx harmonic 64.715 116.040 # SOURCE5 14 1.1793 - angle_coeff @angle:cf-cc-os harmonic 87.197 123.070 # SOURCE5 15 1.3662 - angle_coeff @angle:cd-cd-cl harmonic 72.034 119.990 # SOURCE5 43 1.9574 - angle_coeff @angle:c3-py-ca harmonic 46.073 107.270 # SOURCE5 20 1.8136 - angle_coeff @angle:c3-c3-py harmonic 80.645 111.570 # SOURCE5 14 1.9142 - angle_coeff @angle:c3-py-s harmonic 46.250 113.850 # SOURCE5 14 0.3847 - angle_coeff @angle:ca-c-cx harmonic 64.997 117.660 # SOURCE5 20 1.5268 - angle_coeff @angle:ce-ce-os harmonic 86.756 115.190 # SOURCE5 15 2.1777 - angle_coeff @angle:c3-n4-cx harmonic 62.636 117.290 # SOURCE5 15 0.3164 - angle_coeff @angle:h4-ce-sy harmonic 42.563 115.000 # SOURCE5 20 1.1588 - angle_coeff @angle:hx-cy-n4 harmonic 58.977 110.620 # SOURCE5 14 1.8211 - angle_coeff @angle:cy-no-o harmonic 84.157 116.830 # SOURCE5 17 1.1181 - angle_coeff @angle:cc-cd-cx harmonic 66.301 124.150 # SOURCE5 10 1.8770 - angle_coeff @angle:ca-nb-na harmonic 87.254 118.780 # SOURCE5 10 0.6408 - angle_coeff @angle:cl-c3-cy harmonic 71.118 111.890 # SOURCE5 12 0.7377 - angle_coeff @angle:f-c2-h4 harmonic 66.183 112.050 # SOURCE5 13 0.7763 - angle_coeff @angle:ca-py-s harmonic 45.997 116.310 # SOURCE5 11 1.2602 - angle_coeff @angle:cl-c3-cx harmonic 71.664 110.760 # SOURCE5 9 1.3315 - angle_coeff @angle:ca-nh-cy harmonic 63.219 126.620 # SOURCE5 12 1.1353 - angle_coeff @angle:cy-cy-no harmonic 79.836 115.430 # SOURCE5 15 1.0848 - angle_coeff @angle:ce-n1-n1 harmonic 77.561 177.620 # SOURCE5 10 0.5740 - angle_coeff @angle:cy-cy-hx harmonic 45.080 115.920 # SOURCE5 9 1.5918 - angle_coeff @angle:ce-n-hn harmonic 48.071 113.830 # SOURCE5 11 1.3642 - angle_coeff @angle:c3-cx-cu harmonic 63.779 120.910 # SOURCE5 11 0.4272 - angle_coeff @angle:cf-cf-ne harmonic 86.585 120.790 # SOURCE5 9 1.8014 - angle_coeff @angle:f-p5-na harmonic 88.711 89.260 # SOURCE5 12 1.2991 - angle_coeff @angle:h4-ce-nh harmonic 62.318 115.580 # SOURCE5 10 0.8050 - angle_coeff @angle:ne-c-s harmonic 82.148 124.230 # SOURCE5 9 1.7990 - angle_coeff @angle:ca-os-py harmonic 83.011 123.310 # SOURCE5 12 0.8994 - angle_coeff @angle:cf-ce-cl harmonic 71.390 121.940 # SOURCE5 20 1.2372 - angle_coeff @angle:cy-cy-n4 harmonic 90.361 89.940 # SOURCE5 10 0.7009 - angle_coeff @angle:na-cc-sh harmonic 79.224 122.950 # SOURCE5 9 1.1542 - angle_coeff @angle:nb-na-o harmonic 113.391 118.130 # SOURCE5 11 0.6838 - angle_coeff @angle:c-cx-n3 harmonic 82.187 116.960 # SOURCE5 11 1.3298 - angle_coeff @angle:cd-cy-hc harmonic 48.302 107.200 # SOURCE5 8 0.5300 - angle_coeff @angle:f-c3-no harmonic 111.081 107.760 # SOURCE5 11 0.3179 - angle_coeff @angle:ce-cd-na harmonic 85.967 124.930 # SOURCE5 9 0.9918 - angle_coeff @angle:cq-cp-cq harmonic 69.705 108.020 # SOURCE5 24 0.5633 - angle_coeff @angle:os-py-s harmonic 59.825 116.220 # SOURCE5 11 0.4580 - angle_coeff @angle:c-c3-cy harmonic 65.476 110.880 # SOURCE5 9 1.4172 - angle_coeff @angle:cy-c2-ha harmonic 45.849 118.590 # SOURCE5 5 1.8406 - angle_coeff @angle:cp-cq-cp harmonic 69.705 108.020 # SOURCE5 24 0.5633 - angle_coeff @angle:cx-cu-cx harmonic 89.228 63.190 # SOURCE5 12 0.2140 - angle_coeff @angle:cu-c2-ha harmonic 50.414 121.490 # SOURCE5 12 0.1524 - angle_coeff @angle:cd-ce-cg harmonic 68.168 122.270 # SOURCE5 30 0.9028 - angle_coeff @angle:cf-ne-ne harmonic 87.949 113.170 # SOURCE5 15 1.6715 - angle_coeff @angle:c3-c2-no harmonic 82.781 115.940 # SOURCE5 9 0.9963 - angle_coeff @angle:f-cy-f harmonic 120.355 108.560 # SOURCE5 9 1.2393 - angle_coeff @angle:c2-cy-hc harmonic 46.979 112.800 # SOURCE5 10 0.5936 - angle_coeff @angle:c3-c2-cy harmonic 64.260 117.990 # SOURCE5 10 1.8958 - angle_coeff @angle:c-ce-h4 harmonic 46.659 118.080 # SOURCE5 8 2.4522 - angle_coeff @angle:cf-cc-n harmonic 86.203 124.200 # SOURCE5 10 0.8706 - angle_coeff @angle:cd-cc-i harmonic 60.056 124.280 # SOURCE5 14 1.7120 - angle_coeff @angle:ce-cf-cl harmonic 71.390 121.940 # SOURCE5 20 1.2372 - angle_coeff @angle:cl-c3-p5 harmonic 92.521 109.520 # SOURCE5 9 0.8307 - angle_coeff @angle:c2-c3-no harmonic 83.742 107.190 # SOURCE5 9 0.5470 - angle_coeff @angle:ce-nf-nf harmonic 87.949 113.170 # SOURCE5 15 1.6715 - angle_coeff @angle:c1-c3-cx harmonic 66.544 112.350 # SOURCE5 11 0.3186 - angle_coeff @angle:ce-c3-h2 harmonic 46.896 112.270 # SOURCE5 9 0.2011 - angle_coeff @angle:na-cd-na harmonic 115.931 106.600 # SOURCE5 10 1.3968 - angle_coeff @angle:cx-cx-n4 harmonic 113.255 60.300 # SOURCE5 10 0.1253 - angle_coeff @angle:c1-cx-hc harmonic 48.408 114.860 # SOURCE5 6 0.1269 - angle_coeff @angle:cg-ca-nb harmonic 87.852 116.870 # SOURCE5 10 0.6088 - angle_coeff @angle:ce-c2-f harmonic 90.032 122.620 # SOURCE5 11 1.4117 - angle_coeff @angle:cp-ca-cq harmonic 70.964 111.520 # SOURCE5 8 0.0849 - angle_coeff @angle:cl-py-nf harmonic 67.181 109.160 # SOURCE5 79 0.9726 - angle_coeff @angle:ca-c3-cy harmonic 65.233 112.320 # SOURCE5 7 0.8064 - angle_coeff @angle:ch-cd-nd harmonic 85.036 123.030 # SOURCE5 7 0.2371 - angle_coeff @angle:h1-cy-ss harmonic 41.667 111.560 # SOURCE5 6 1.1376 - angle_coeff @angle:h5-cc-n2 harmonic 63.976 123.280 # SOURCE5 5 1.2554 - angle_coeff @angle:cc-na-cy harmonic 64.047 126.730 # SOURCE5 13 0.8228 - angle_coeff @angle:c-c3-no harmonic 83.428 106.990 # SOURCE5 8 1.0618 - angle_coeff @angle:c3-py-c3 harmonic 46.116 105.720 # SOURCE5 10 2.4094 - angle_coeff @angle:hx-c3-n3 harmonic 60.702 111.730 # SOURCE5 10 0.1463 - angle_coeff @angle:cf-cf-nh harmonic 85.786 116.410 # SOURCE5 70 1.9262 - angle_coeff @angle:c3-n3-py harmonic 81.527 118.270 # SOURCE5 8 1.5513 - angle_coeff @angle:h5-c2-os harmonic 64.726 110.950 # SOURCE5 9 1.4177 - angle_coeff @angle:cc-c3-ce harmonic 66.308 110.890 # SOURCE5 7 2.0183 - angle_coeff @angle:n4-c3-p5 harmonic 104.054 106.090 # SOURCE5 10 1.7975 - angle_coeff @angle:ne-cd-ss harmonic 79.536 126.000 # SOURCE5 6 1.6775 - angle_coeff @angle:na-cd-ne harmonic 111.251 122.470 # SOURCE5 7 2.4448 - angle_coeff @angle:cl-c3-h3 harmonic 48.652 107.660 # SOURCE5 10 0.1942 - angle_coeff @angle:h5-c-s harmonic 44.037 123.510 # SOURCE5 6 0.5125 - angle_coeff @angle:cf-ce-ss harmonic 63.673 120.950 # SOURCE5 15 1.8784 - angle_coeff @angle:c3-c2-f harmonic 87.663 113.280 # SOURCE5 8 1.0861 - angle_coeff @angle:h4-c2-oh harmonic 64.512 114.610 # SOURCE5 8 1.2250 - angle_coeff @angle:ne-ce-nf harmonic 108.272 127.960 # SOURCE5 10 1.2321 - angle_coeff @angle:cc-n-cd harmonic 67.143 121.050 # SOURCE5 7 0.3580 - angle_coeff @angle:f-py-f harmonic 90.389 97.510 # SOURCE5 5 0.2281 - angle_coeff @angle:n-cc-os harmonic 110.414 119.020 # SOURCE5 8 1.4066 - angle_coeff @angle:cq-cp-nb harmonic 85.943 120.010 # SOURCE5 14 1.1266 - angle_coeff @angle:c-c-s harmonic 64.027 121.310 # SOURCE5 8 0.9033 - angle_coeff @angle:cf-ce-os harmonic 88.396 120.230 # SOURCE5 8 2.3122 - angle_coeff @angle:br-ce-c2 harmonic 64.169 120.520 # SOURCE5 8 0.4148 - angle_coeff @angle:cp-nb-na harmonic 87.511 118.110 # SOURCE5 5 0.5760 - angle_coeff @angle:n-s6-oh harmonic 123.280 97.300 # SOURCE5 8 0.9381 - angle_coeff @angle:cd-c3-h2 harmonic 47.679 110.470 # SOURCE5 12 1.1111 - angle_coeff @angle:nb-ca-sy harmonic 81.256 115.730 # SOURCE5 6 0.4033 - angle_coeff @angle:na-sy-o harmonic 122.952 105.300 # SOURCE5 5 1.0811 - angle_coeff @angle:hx-cx-hx harmonic 37.969 115.770 # SOURCE5 9 0.0901 - angle_coeff @angle:cd-cf-ne harmonic 86.147 122.390 # SOURCE5 7 1.4919 - angle_coeff @angle:h5-c-oh harmonic 65.262 109.490 # SOURCE5 7 0.3600 - angle_coeff @angle:cy-n-cy harmonic 71.371 94.550 # SOURCE5 5 0.6286 - angle_coeff @angle:br-c3-no harmonic 81.143 106.960 # SOURCE5 6 2.2092 - angle_coeff @angle:c2-ss-s4 harmonic 73.233 92.420 # SOURCE5 8 0.4009 - angle_coeff @angle:c3-nh-o harmonic 85.477 117.530 # SOURCE5 7 1.0041 - angle_coeff @angle:br-cc-ss harmonic 65.672 120.060 # SOURCE5 6 0.2609 - angle_coeff @angle:c-ce-ss harmonic 64.495 113.230 # SOURCE5 6 1.9344 - angle_coeff @angle:c3-n-n3 harmonic 82.135 117.560 # SOURCE5 6 2.4546 - angle_coeff @angle:h5-ca-na harmonic 62.521 115.800 # SOURCE5 8 0.4738 - angle_coeff @angle:n2-nh-oh harmonic 106.301 117.890 # SOURCE5 6 0.2008 - angle_coeff @angle:c2-c3-p5 harmonic 80.813 112.220 # SOURCE5 6 0.6523 - angle_coeff @angle:c3-cx-nh harmonic 82.121 116.580 # SOURCE5 7 1.1795 - angle_coeff @angle:c2-cc-ss harmonic 62.687 127.480 # SOURCE5 6 0.3389 - angle_coeff @angle:c-ca-na harmonic 84.333 117.810 # SOURCE5 7 2.2477 - angle_coeff @angle:cl-c2-n2 harmonic 91.772 121.450 # SOURCE5 8 0.8251 - angle_coeff @angle:n2-s4-ne harmonic 122.203 104.290 # SOURCE5 8 0.9503 - angle_coeff @angle:nc-c-s harmonic 82.136 124.470 # SOURCE5 7 1.3793 - angle_coeff @angle:o-sy-ss harmonic 85.092 107.590 # SOURCE5 7 2.0694 - angle_coeff @angle:c2-ce-ss harmonic 62.956 123.860 # SOURCE5 5 1.0553 - angle_coeff @angle:c3-cx-ca harmonic 64.734 117.010 # SOURCE5 6 1.1320 - angle_coeff @angle:cc-cc-nf harmonic 87.342 121.680 # SOURCE5 7 1.9093 - angle_coeff @angle:ca-nd-cd harmonic 73.420 104.240 # SOURCE5 8 0.2625 - angle_coeff @angle:cc-n2-oh harmonic 89.258 113.250 # SOURCE5 7 1.6484 - angle_coeff @angle:ca-os-sy harmonic 63.798 118.010 # SOURCE5 8 2.0392 - angle_coeff @angle:hx-c3-p5 harmonic 54.750 107.590 # SOURCE5 7 1.8329 - angle_coeff @angle:ca-ce-n harmonic 83.340 118.990 # SOURCE5 8 0.3821 - angle_coeff @angle:h4-ce-sx harmonic 41.742 115.270 # SOURCE5 5 0.1053 - angle_coeff @angle:c3-ce-ne harmonic 83.806 116.230 # SOURCE5 5 1.2988 - angle_coeff @angle:c1-n1-ce harmonic 61.729 176.870 # SOURCE5 7 0.6686 - angle_coeff @angle:c3-n2-cd harmonic 67.858 117.010 # SOURCE5 6 1.8279 - angle_coeff @angle:cc-c3-h2 harmonic 47.679 110.470 # SOURCE5 12 1.1111 - angle_coeff @angle:ca-ce-cg harmonic 67.208 116.470 # SOURCE5 5 1.0847 - angle_coeff @angle:c2-cc-na harmonic 86.738 123.270 # SOURCE5 6 1.9888 - angle_coeff @angle:ca-c3-s4 harmonic 63.907 109.520 # SOURCE5 7 1.3239 - angle_coeff @angle:n2-cf-nf harmonic 111.801 120.690 # SOURCE5 6 1.4522 - angle_coeff @angle:ce-cf-ss harmonic 63.673 120.950 # SOURCE5 15 1.8784 - angle_coeff @angle:c3-cx-ss harmonic 62.514 114.160 # SOURCE5 7 0.1562 - angle_coeff @angle:nh-ce-nh harmonic 108.620 119.710 # SOURCE5 6 0.4946 - angle_coeff @angle:cd-c-ne harmonic 87.008 112.220 # SOURCE5 6 0.1806 - angle_coeff @angle:na-c3-ss harmonic 82.873 103.150 # SOURCE5 8 0.3361 - angle_coeff @angle:cf-cf-os harmonic 86.756 115.190 # SOURCE5 15 2.1777 - angle_coeff @angle:cx-c3-h2 harmonic 46.468 114.010 # SOURCE5 8 0.8649 - angle_coeff @angle:cv-ss-cy harmonic 79.244 82.620 # SOURCE5 8 0.2654 - angle_coeff @angle:ss-cy-ss harmonic 68.296 95.040 # SOURCE5 6 0.9436 - angle_coeff @angle:ce-cx-os harmonic 82.835 117.210 # SOURCE5 6 1.3466 - angle_coeff @angle:nb-ca-ne harmonic 109.027 121.410 # SOURCE5 6 1.6965 - angle_coeff @angle:br-ca-nb harmonic 81.701 116.350 # SOURCE5 5 0.4508 - angle_coeff @angle:c3-nh-os harmonic 84.400 110.370 # SOURCE5 6 2.4123 - angle_coeff @angle:c2-nh-p5 harmonic 81.068 125.900 # SOURCE5 6 1.8594 - angle_coeff @angle:br-ca-cp harmonic 63.564 121.390 # SOURCE5 7 0.3403 - angle_coeff @angle:cc-ce-cc harmonic 67.224 116.170 # SOURCE5 6 0.4089 - angle_coeff @angle:c3-nh-s6 harmonic 63.928 116.490 # SOURCE5 6 0.5375 - angle_coeff @angle:cx-c3-na harmonic 82.551 114.780 # SOURCE5 7 1.7481 - angle_coeff @angle:ca-os-p3 harmonic 85.566 110.460 # SOURCE5 5 0.0025 - angle_coeff @angle:ce-cf-sy harmonic 62.892 123.190 # SOURCE5 5 0.3760 - angle_coeff @angle:ca-n2-n1 harmonic 92.483 118.480 # SOURCE5 5 0.1464 - angle_coeff @angle:cd-cd-no harmonic 82.299 125.950 # SOURCE5 5 2.2787 - angle_coeff @angle:na-n2-os harmonic 113.058 104.340 # SOURCE5 6 0.3185 - angle_coeff @angle:ce-c3-f harmonic 88.332 110.310 # SOURCE5 6 0.9204 - angle_coeff @angle:cx-cc-na harmonic 81.840 127.210 # SOURCE5 7 2.0873 - angle_coeff @angle:n-n2-na harmonic 113.870 106.040 # SOURCE5 6 0.3975 - angle_coeff @angle:c3-cf-cc harmonic 67.117 117.430 # SOURCE5 5 2.0116 - angle_coeff @angle:ca-na-cy harmonic 63.636 128.060 # SOURCE5 7 0.2603 - angle_coeff @angle:h1-c3-py harmonic 54.323 109.380 # SOURCE5 7 0.4767 - angle_coeff @angle:cy-s6-cy harmonic 75.496 86.770 # SOURCE5 5 1.5405 - angle_coeff @angle:ce-ce-s4 harmonic 63.624 119.120 # SOURCE5 6 0.0093 - angle_coeff @angle:c3-p3-cy harmonic 45.442 103.850 # SOURCE5 6 0.6245 - angle_coeff @angle:h2-cx-os harmonic 60.942 114.700 # SOURCE5 7 1.4166 - angle_coeff @angle:c-c-ce harmonic 64.646 115.440 # SOURCE5 5 1.0373 - angle_coeff @angle:ce-cy-h1 harmonic 46.242 115.490 # SOURCE5 5 0.2559 - angle_coeff @angle:cx-c3-ss harmonic 64.879 105.420 # SOURCE5 7 0.4078 - angle_coeff @angle:cg-ce-ss harmonic 63.731 118.190 # SOURCE5 5 1.0760 - angle_coeff @angle:br-cy-cy harmonic 61.847 119.270 # SOURCE5 6 1.4624 - angle_coeff @angle:c-cy-cl harmonic 71.094 112.180 # SOURCE5 5 2.4165 - angle_coeff @angle:c-cx-n harmonic 81.704 120.510 # SOURCE5 7 1.7811 - angle_coeff @angle:br-c3-f harmonic 82.493 109.620 # SOURCE5 7 0.6251 - angle_coeff @angle:c3-n4-cy harmonic 63.514 112.130 # SOURCE5 5 0.7180 - angle_coeff @angle:ce-cv-ss harmonic 61.912 130.090 # SOURCE5 7 2.1973 - angle_coeff @angle:cc-cd-i harmonic 60.200 124.280 # SOURCE5 14 1.7120 - angle_coeff @angle:c2-ss-ca harmonic 73.005 102.780 # SOURCE5 5 0.7426 - angle_coeff @angle:c-cx-ce harmonic 64.969 116.840 # SOURCE5 7 1.2393 - angle_coeff @angle:cy-nh-cy harmonic 71.537 93.310 # SOURCE5 6 0.3047 - angle_coeff @angle:cx-c-h4 harmonic 46.665 115.380 # SOURCE5 7 0.1819 - angle_coeff @angle:c-n4-c3 harmonic 63.969 108.760 # SOURCE5 7 1.5097 - angle_coeff @angle:f-cy-py harmonic 99.595 113.190 # SOURCE5 8 0.9744 - angle_coeff @angle:n2-c3-ss harmonic 80.436 109.390 # SOURCE5 5 1.4343 - angle_coeff @angle:c3-ss-cf harmonic 71.418 101.280 # SOURCE5 6 2.4411 - angle_coeff @angle:ce-cy-hc harmonic 46.374 114.840 # SOURCE5 5 0.4991 - angle_coeff @angle:br-cc-nc harmonic 82.466 116.250 # SOURCE5 5 0.0824 - angle_coeff @angle:h3-c3-n harmonic 61.280 109.880 # SOURCE5 6 0.7497 - angle_coeff @angle:ca-ne-cd harmonic 67.557 123.670 # SOURCE5 5 2.0742 - angle_coeff @angle:cx-n-cy harmonic 64.984 116.210 # SOURCE5 6 0.4758 - angle_coeff @angle:cl-c3-s4 harmonic 71.477 111.990 # SOURCE5 6 1.5116 - angle_coeff @angle:cp-cq-nb harmonic 85.943 120.010 # SOURCE5 14 1.1266 - angle_coeff @angle:cc-cd-o harmonic 86.659 136.060 # SOURCE5 5 0.5251 - angle_coeff @angle:hx-cy-hx harmonic 38.598 110.800 # SOURCE5 5 0.4155 - angle_coeff @angle:cc-na-sy harmonic 61.877 125.170 # SOURCE5 5 1.1548 - angle_coeff @angle:h1-cy-na harmonic 62.857 106.380 # SOURCE5 5 0.0918 - angle_coeff @angle:h4-cf-sy harmonic 42.563 115.000 # SOURCE5 20 1.1588 - angle_coeff @angle:c-p5-c3 harmonic 44.432 111.280 # SOURCE5 6 2.1227 - angle_coeff @angle:ca-c-nc harmonic 84.546 117.030 # SOURCE5 5 0.2959 - angle_coeff @angle:c3-os-sy harmonic 63.872 115.050 # SOURCE5 5 0.9975 - angle_coeff @angle:cd-ne-sy harmonic 65.441 120.780 # SOURCE5 5 1.2762 - angle_coeff @angle:cx-ca-nb harmonic 85.768 116.900 # SOURCE5 5 0.8439 - angle_coeff @angle:nc-ss-ss harmonic 93.760 97.440 # SOURCE5 6 0.0880 - angle_coeff @angle:hp-p5-os harmonic 45.642 103.080 # SOURCE5 5 0.8064 - angle_coeff @angle:ca-n-oh harmonic 84.294 115.620 # SOURCE5 5 1.0474 - angle_coeff @angle:c3-s6-ne harmonic 91.348 108.190 # SOURCE5 5 0.2914 - angle_coeff @angle:c1-cx-h1 harmonic 48.407 114.800 # SOURCE5 5 0.4789 - angle_coeff @angle:na-c3-oh harmonic 109.816 108.590 # SOURCE5 6 1.4542 - angle_coeff @angle:n-nc-nd harmonic 109.773 119.880 # SOURCE5 5 0.1982 - angle_coeff @angle:c3-na-nb harmonic 85.173 113.140 # SOURCE5 5 0.4557 - angle_coeff @angle:ne-c-os harmonic 113.522 112.010 # SOURCE5 5 1.9012 - angle_coeff @angle:br-ce-ce harmonic 64.975 115.220 # SOURCE5 6 0.2328 - angle_coeff @angle:cc-c2-oh harmonic 91.119 115.180 # SOURCE5 6 0.1517 - angle_coeff @angle:c1-cx-os harmonic 84.507 117.430 # SOURCE5 5 0.5408 - angle_coeff @angle:nc-cc-os harmonic 109.642 121.720 # SOURCE5 5 2.3919 - angle_coeff @angle:br-ce-cf harmonic 63.865 121.600 # SOURCE5 5 1.8246 - angle_coeff @angle:cy-c3-f harmonic 87.269 111.480 # SOURCE5 5 0.6981 - angle_coeff @angle:h5-ce-ne harmonic 62.727 113.650 # SOURCE5 5 0.5892 - angle_coeff @angle:n3-py-n3 harmonic 78.976 104.560 # SOURCE5 5 0.5659 - angle_coeff @angle:br-cc-ca harmonic 62.532 126.640 # SOURCE5 5 0.3204 - angle_coeff @angle:f-c3-na harmonic 113.041 110.410 # SOURCE5 5 0.7067 - angle_coeff @angle:cc-c3-s4 harmonic 63.350 112.000 # SOURCE5 5 0.1216 - angle_coeff @angle:ce-cf-sx harmonic 64.738 112.970 # SOURCE5 5 1.7021 - angle_coeff @angle:cc-cc-i harmonic 59.680 125.790 # SOURCE5 5 1.4784 - angle_coeff @angle:c-cg-ch harmonic 58.652 176.690 # SOURCE5 5 0.2913 - angle_coeff @angle:ce-c3-hx harmonic 47.212 110.880 # SOURCE5 5 0.3335 - angle_coeff @angle:cd-na-cy harmonic 64.047 126.730 # SOURCE5 13 0.8228 - angle_coeff @angle:br-c3-c2 harmonic 63.737 111.170 # SOURCE5 5 1.2445 - angle_coeff @angle:ce-ce-cg harmonic 68.210 114.640 # SOURCE5 5 0.4759 - angle_coeff @angle:cl-cd-nd harmonic 90.599 121.290 # SOURCE5 5 0.8123 - angle_coeff @angle:n-ca-na harmonic 109.145 117.170 # SOURCE5 5 0.3934 - angle_coeff @angle:cx-cd-nd harmonic 83.980 121.600 # SOURCE5 5 0.1341 - angle_coeff @angle:cl-p5-os harmonic 69.550 104.530 # SOURCE5 5 0.1303 - angle_coeff @angle:cx-ss-cy harmonic 73.867 91.640 # SOURCE5 5 0.0761 - angle_coeff @angle:cc-cg-ch harmonic 59.342 177.060 # SOURCE5 5 0.7516 - angle_coeff @angle:cc-sy-oh harmonic 92.772 104.120 # SOURCE5 5 0.3761 - angle_coeff @angle:cq-ca-os harmonic 87.894 116.910 # SOURCE5 38 1.2997 - angle_coeff @angle:ca-cd-ca harmonic 65.280 122.940 # SOURCE5 37 2.3284 - angle_coeff @angle:f-py-nf harmonic 83.682 108.600 # SOURCE5 47 0.7739 - angle_coeff @angle:ca-nh-cf harmonic 65.017 127.740 # SOURCE5 32 0.9569 - angle_coeff @angle:cf-cx-cx harmonic 64.347 118.620 # SOURCE5 40 1.7472 - angle_coeff @angle:py-nf-py harmonic 111.020 121.410 # SOURCE5 34 1.5196 - angle_coeff @angle:c-cc-ss harmonic 62.961 121.970 # SOURCE5 29 2.1476 - angle_coeff @angle:cc-na-cx harmonic 66.440 116.390 # SOURCE5 14 0.5535 - angle_coeff @angle:c2-cf-cx harmonic 66.366 122.740 # SOURCE5 23 1.5745 - angle_coeff @angle:ce-cd-os harmonic 87.197 123.070 # SOURCE5 15 1.3662 - angle_coeff @angle:cd-cc-cx harmonic 66.301 124.150 # SOURCE5 10 1.8770 - angle_coeff @angle:cf-n1-n1 harmonic 77.561 177.620 # SOURCE5 10 0.5740 - angle_coeff @angle:cf-n-hn harmonic 48.071 113.830 # SOURCE5 11 1.3642 - angle_coeff @angle:ce-ce-nf harmonic 86.585 120.790 # SOURCE5 9 1.8014 - angle_coeff @angle:cf-no-o harmonic 86.024 118.220 # SOURCE5 11 0.7792 - angle_coeff @angle:h4-cf-nh harmonic 62.318 115.580 # SOURCE5 10 0.8050 - angle_coeff @angle:nf-c-s harmonic 82.148 124.230 # SOURCE5 9 1.7990 - angle_coeff @angle:na-cd-sh harmonic 79.224 122.950 # SOURCE5 9 1.1542 - angle_coeff @angle:cc-cy-hc harmonic 48.302 107.200 # SOURCE5 8 0.5300 - angle_coeff @angle:cf-cc-na harmonic 85.967 124.930 # SOURCE5 9 0.9918 - angle_coeff @angle:c-cf-h4 harmonic 46.659 118.080 # SOURCE5 8 2.4522 - angle_coeff @angle:ce-cd-n harmonic 86.203 124.200 # SOURCE5 10 0.8706 - angle_coeff @angle:cf-c3-h2 harmonic 46.902 112.270 # SOURCE5 9 0.2011 - angle_coeff @angle:na-cc-na harmonic 115.931 106.600 # SOURCE5 10 1.3968 - angle_coeff @angle:ch-ca-nb harmonic 87.852 116.870 # SOURCE5 10 0.6088 - angle_coeff @angle:cf-c2-f harmonic 90.032 122.620 # SOURCE5 11 1.4117 - angle_coeff @angle:cg-cc-nc harmonic 85.036 123.030 # SOURCE5 7 0.2371 - angle_coeff @angle:h5-cd-n2 harmonic 63.978 123.280 # SOURCE5 5 1.2554 - angle_coeff @angle:cd-c3-cf harmonic 66.313 110.890 # SOURCE5 7 2.0183 - angle_coeff @angle:nf-cc-ss harmonic 79.536 126.000 # SOURCE5 6 1.6775 - angle_coeff @angle:na-cc-nf harmonic 111.251 122.470 # SOURCE5 7 2.4448 - angle_coeff @angle:nf-cf-ne harmonic 108.272 127.960 # SOURCE5 10 1.2321 - angle_coeff @angle:n-cd-os harmonic 110.414 119.020 # SOURCE5 8 1.4066 - angle_coeff @angle:ce-cf-os harmonic 88.396 120.230 # SOURCE5 8 2.3122 - angle_coeff @angle:br-cf-c2 harmonic 64.169 120.520 # SOURCE5 8 0.4148 - angle_coeff @angle:cq-nb-na harmonic 87.511 118.110 # SOURCE5 5 0.5760 - angle_coeff @angle:cc-ce-nf harmonic 86.147 122.390 # SOURCE5 7 1.4919 - angle_coeff @angle:cf-s4-ss harmonic 74.492 88.650 # SOURCE5 8 0.4156 - angle_coeff @angle:br-cd-ss harmonic 65.672 120.060 # SOURCE5 6 0.2609 - angle_coeff @angle:c-cf-ss harmonic 64.495 113.230 # SOURCE5 6 1.9344 - angle_coeff @angle:c2-cd-ss harmonic 62.687 127.480 # SOURCE5 6 0.3389 - angle_coeff @angle:n2-s4-nf harmonic 122.203 104.290 # SOURCE5 8 0.9503 - angle_coeff @angle:nd-c-s harmonic 82.136 124.470 # SOURCE5 7 1.3793 - angle_coeff @angle:c2-cf-ss harmonic 62.956 123.860 # SOURCE5 5 1.0553 - angle_coeff @angle:cd-cd-ne harmonic 87.342 121.680 # SOURCE5 7 1.9093 - angle_coeff @angle:ca-nc-cc harmonic 73.420 104.240 # SOURCE5 8 0.2625 - angle_coeff @angle:cd-n2-oh harmonic 89.258 113.250 # SOURCE5 7 1.6484 - angle_coeff @angle:ca-cf-n harmonic 83.340 118.990 # SOURCE5 8 0.3821 - angle_coeff @angle:h4-cf-sx harmonic 41.742 115.270 # SOURCE5 5 0.1053 - angle_coeff @angle:c3-cf-nf harmonic 83.812 116.230 # SOURCE5 5 1.2988 - angle_coeff @angle:c1-n1-cf harmonic 61.729 176.870 # SOURCE5 7 0.6686 - angle_coeff @angle:c3-n2-cc harmonic 67.858 117.010 # SOURCE5 6 1.8279 - angle_coeff @angle:ca-cf-ch harmonic 67.208 116.470 # SOURCE5 5 1.0847 - angle_coeff @angle:c2-cd-na harmonic 86.738 123.270 # SOURCE5 6 1.9888 - angle_coeff @angle:n2-ce-ne harmonic 111.801 120.690 # SOURCE5 6 1.4522 - angle_coeff @angle:nh-cf-nh harmonic 108.620 119.710 # SOURCE5 6 0.4946 - angle_coeff @angle:cc-c-nf harmonic 87.008 112.220 # SOURCE5 6 0.1806 - angle_coeff @angle:cf-cx-os harmonic 82.835 117.210 # SOURCE5 6 1.3466 - angle_coeff @angle:nb-ca-nf harmonic 109.027 121.410 # SOURCE5 6 1.6965 - angle_coeff @angle:br-ca-cq harmonic 63.564 121.390 # SOURCE5 7 0.3403 - angle_coeff @angle:cd-cf-cd harmonic 67.224 116.170 # SOURCE5 6 0.4089 - angle_coeff @angle:cf-ce-sy harmonic 62.892 123.190 # SOURCE5 5 0.3760 - angle_coeff @angle:cc-cc-no harmonic 82.299 125.950 # SOURCE5 5 2.2787 - angle_coeff @angle:cf-c3-f harmonic 88.340 110.310 # SOURCE5 6 0.9204 - angle_coeff @angle:cx-cd-na harmonic 81.840 127.210 # SOURCE5 7 2.0873 - angle_coeff @angle:c3-ce-cd harmonic 67.111 117.430 # SOURCE5 5 2.0116 - angle_coeff @angle:cf-cf-s4 harmonic 63.624 119.120 # SOURCE5 6 0.0093 - angle_coeff @angle:c-c-cf harmonic 64.646 115.440 # SOURCE5 5 1.0373 - angle_coeff @angle:cf-cy-h1 harmonic 46.242 115.490 # SOURCE5 5 0.2559 - angle_coeff @angle:ch-cf-ss harmonic 63.731 118.190 # SOURCE5 5 1.0760 - angle_coeff @angle:cf-cv-ss harmonic 61.912 130.090 # SOURCE5 7 2.1973 - angle_coeff @angle:c-cx-cf harmonic 64.969 116.840 # SOURCE5 7 1.2393 - angle_coeff @angle:c3-ss-ce harmonic 71.418 101.280 # SOURCE5 6 2.4411 - angle_coeff @angle:cf-cy-hc harmonic 46.374 114.840 # SOURCE5 5 0.4991 - angle_coeff @angle:br-cd-nd harmonic 82.466 116.250 # SOURCE5 5 0.0824 - angle_coeff @angle:ca-nf-cc harmonic 67.557 123.670 # SOURCE5 5 2.0742 - angle_coeff @angle:cd-cc-o harmonic 86.659 136.060 # SOURCE5 5 0.5251 - angle_coeff @angle:cd-na-sy harmonic 61.877 125.170 # SOURCE5 5 1.1548 - angle_coeff @angle:ca-c-nd harmonic 84.546 117.030 # SOURCE5 5 0.2959 - angle_coeff @angle:cc-nf-sy harmonic 65.441 120.780 # SOURCE5 5 1.2762 - angle_coeff @angle:nd-ss-ss harmonic 93.760 97.440 # SOURCE5 6 0.0880 - angle_coeff @angle:c3-s6-nf harmonic 91.348 108.190 # SOURCE5 5 0.2914 - angle_coeff @angle:n-nd-nc harmonic 109.773 119.880 # SOURCE5 5 0.1982 - angle_coeff @angle:nf-c-os harmonic 113.522 112.010 # SOURCE5 5 1.9012 - angle_coeff @angle:br-cf-cf harmonic 64.975 115.220 # SOURCE5 6 0.2328 - angle_coeff @angle:cd-c2-oh harmonic 91.119 115.180 # SOURCE5 6 0.1517 - angle_coeff @angle:nd-cd-os harmonic 109.642 121.720 # SOURCE5 5 2.3919 - angle_coeff @angle:br-cf-ce harmonic 63.865 121.600 # SOURCE5 5 1.8246 - angle_coeff @angle:h5-cf-nf harmonic 62.727 113.650 # SOURCE5 5 0.5892 - angle_coeff @angle:br-cd-ca harmonic 62.532 126.640 # SOURCE5 5 0.3204 - angle_coeff @angle:cd-c3-s4 harmonic 63.350 112.000 # SOURCE5 5 0.1216 - angle_coeff @angle:cf-ce-sx harmonic 64.738 112.970 # SOURCE5 5 1.7021 - angle_coeff @angle:cd-cd-i harmonic 59.818 125.790 # SOURCE5 5 1.4784 - angle_coeff @angle:c-ch-cg harmonic 58.652 176.690 # SOURCE5 5 0.2913 - angle_coeff @angle:cf-c3-hx harmonic 47.217 110.880 # SOURCE5 5 0.3335 - angle_coeff @angle:cf-cf-ch harmonic 68.210 114.640 # SOURCE5 5 0.4759 - angle_coeff @angle:cl-cc-nc harmonic 90.599 121.290 # SOURCE5 5 0.8123 - angle_coeff @angle:cx-cc-nc harmonic 83.980 121.600 # SOURCE5 5 0.1341 - angle_coeff @angle:cd-ch-cg harmonic 59.342 177.060 # SOURCE5 5 0.7516 - angle_coeff @angle:cd-sy-oh harmonic 92.772 104.120 # SOURCE5 5 0.3761 - } # (end of angle_coeffs) - - write_once("Data Angles By Type") { - @angle:hw-ow-hw @atom:hw @atom:ow @atom:hw - @angle:hw-hw-ow @atom:hw @atom:hw @atom:ow - @angle:br-c1-br @atom:br @atom:c1 @atom:br - @angle:br-c1-c1 @atom:br @atom:c1 @atom:c1 - @angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1 - @angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2 - @angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3 - @angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca - @angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl - @angle:c1-c1-f @atom:c1 @atom:c1 @atom:f - @angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha - @angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc - @angle:c1-c1-i @atom:c1 @atom:c1 @atom:i - @angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1 - @angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2 - @angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3 - @angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4 - @angle:c1-c1-n @atom:c1 @atom:c1 @atom:n - @angle:c1-c1-na @atom:c1 @atom:c1 @atom:na - @angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh - @angle:c1-c1-no @atom:c1 @atom:c1 @atom:no - @angle:c1-c1-o @atom:c1 @atom:c1 @atom:o - @angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh - @angle:c1-c1-os @atom:c1 @atom:c1 @atom:os - @angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2 - @angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3 - @angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4 - @angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5 - @angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4 - @angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6 - @angle:c1-c1-s @atom:c1 @atom:c1 @atom:s - @angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh - @angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss - @angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2 - @angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce - @angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1 - @angle:c2-c1-o @atom:c2 @atom:c1 @atom:o - @angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2 - @angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3 - @angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg - @angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1 - @angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca - @angle:c-c1-c1 @atom:c @atom:c1 @atom:c1 - @angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha - @angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha - @angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl - @angle:f-c1-f @atom:f @atom:c1 @atom:f - @angle:i-c1-i @atom:i @atom:c1 @atom:i - @angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1 - @angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3 - @angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh - @angle:n1-c1-os @atom:n1 @atom:c1 @atom:os - @angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3 - @angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss - @angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2 - @angle:n2-c1-o @atom:n2 @atom:c1 @atom:o - @angle:n2-c1-s @atom:n2 @atom:c1 @atom:s - @angle:n3-c1-n3 @atom:n3 @atom:c1 @atom:n3 - @angle:n4-c1-n4 @atom:n4 @atom:c1 @atom:n4 - @angle:na-c1-na @atom:na @atom:c1 @atom:na - @angle:ne-c1-o @atom:ne @atom:c1 @atom:o - @angle:ne-c1-s @atom:ne @atom:c1 @atom:s - @angle:nf-c1-o @atom:nf @atom:c1 @atom:o - @angle:nh-c1-nh @atom:nh @atom:c1 @atom:nh - @angle:n-c1-n @atom:n @atom:c1 @atom:n - @angle:no-c1-no @atom:no @atom:c1 @atom:no - @angle:oh-c1-oh @atom:oh @atom:c1 @atom:oh - @angle:o-c1-o @atom:o @atom:c1 @atom:o - @angle:os-c1-os @atom:os @atom:c1 @atom:os - @angle:p2-c1-p2 @atom:p2 @atom:c1 @atom:p2 - @angle:p3-c1-p3 @atom:p3 @atom:c1 @atom:p3 - @angle:p4-c1-p4 @atom:p4 @atom:c1 @atom:p4 - @angle:p5-c1-p5 @atom:p5 @atom:c1 @atom:p5 - @angle:s2-c1-s2 @atom:s2 @atom:c1 @atom:s2 - @angle:s4-c1-s4 @atom:s4 @atom:c1 @atom:s4 - @angle:s6-c1-s6 @atom:s6 @atom:c1 @atom:s6 - @angle:sh-c1-sh @atom:sh @atom:c1 @atom:sh - @angle:s-c1-s @atom:s @atom:c1 @atom:s - @angle:ss-c1-ss @atom:ss @atom:c1 @atom:ss - @angle:br-c2-br @atom:br @atom:c2 @atom:br - @angle:br-c2-c2 @atom:br @atom:c2 @atom:c2 - @angle:br-c2-c3 @atom:br @atom:c2 @atom:c3 - @angle:br-c2-ce @atom:br @atom:c2 @atom:ce - @angle:br-c2-h4 @atom:br @atom:c2 @atom:h4 - @angle:br-c2-ha @atom:br @atom:c2 @atom:ha - @angle:c1-c2-c1 @atom:c1 @atom:c2 @atom:c1 - @angle:c1-c2-c2 @atom:c1 @atom:c2 @atom:c2 - @angle:c1-c2-c3 @atom:c1 @atom:c2 @atom:c3 - @angle:c1-c2-f @atom:c1 @atom:c2 @atom:f - @angle:c1-c2-ha @atom:c1 @atom:c2 @atom:ha - @angle:c2-c2-c2 @atom:c2 @atom:c2 @atom:c2 - @angle:c2-c2-c3 @atom:c2 @atom:c2 @atom:c3 - @angle:c2-c2-ca @atom:c2 @atom:c2 @atom:ca - @angle:c2-c2-cc @atom:c2 @atom:c2 @atom:cc - @angle:c2-c2-cd @atom:c2 @atom:c2 @atom:cd - @angle:c2-c2-cl @atom:c2 @atom:c2 @atom:cl - @angle:c2-c2-cx @atom:c2 @atom:c2 @atom:cx - @angle:c2-c2-cy @atom:c2 @atom:c2 @atom:cy - @angle:c2-c2-f @atom:c2 @atom:c2 @atom:f - @angle:c2-c2-h4 @atom:c2 @atom:c2 @atom:h4 - @angle:c2-c2-ha @atom:c2 @atom:c2 @atom:ha - @angle:c2-c2-hc @atom:c2 @atom:c2 @atom:hc - @angle:c2-c2-hx @atom:c2 @atom:c2 @atom:hx - @angle:c2-c2-i @atom:c2 @atom:c2 @atom:i - @angle:c2-c2-n1 @atom:c2 @atom:c2 @atom:n1 - @angle:c2-c2-n2 @atom:c2 @atom:c2 @atom:n2 - @angle:c2-c2-n3 @atom:c2 @atom:c2 @atom:n3 - @angle:c2-c2-n4 @atom:c2 @atom:c2 @atom:n4 - @angle:c2-c2-n @atom:c2 @atom:c2 @atom:n - @angle:c2-c2-na @atom:c2 @atom:c2 @atom:na - @angle:c2-c2-nh @atom:c2 @atom:c2 @atom:nh - @angle:c2-c2-no @atom:c2 @atom:c2 @atom:no - @angle:c2-c2-o @atom:c2 @atom:c2 @atom:o - @angle:c2-c2-oh @atom:c2 @atom:c2 @atom:oh - @angle:c2-c2-os @atom:c2 @atom:c2 @atom:os - @angle:c2-c2-p2 @atom:c2 @atom:c2 @atom:p2 - @angle:c2-c2-p3 @atom:c2 @atom:c2 @atom:p3 - @angle:c2-c2-p4 @atom:c2 @atom:c2 @atom:p4 - @angle:c2-c2-p5 @atom:c2 @atom:c2 @atom:p5 - @angle:c2-c2-s4 @atom:c2 @atom:c2 @atom:s4 - @angle:c2-c2-s6 @atom:c2 @atom:c2 @atom:s6 - @angle:c2-c2-s @atom:c2 @atom:c2 @atom:s - @angle:c2-c2-sh @atom:c2 @atom:c2 @atom:sh - @angle:c2-c2-ss @atom:c2 @atom:c2 @atom:ss - @angle:c3-c2-c3 @atom:c3 @atom:c2 @atom:c3 - @angle:c3-c2-cc @atom:c3 @atom:c2 @atom:cc - @angle:c3-c2-cd @atom:c3 @atom:c2 @atom:cd - @angle:c3-c2-ce @atom:c3 @atom:c2 @atom:ce - @angle:c3-c2-cf @atom:c3 @atom:c2 @atom:cf - @angle:c3-c2-h4 @atom:c3 @atom:c2 @atom:h4 - @angle:c3-c2-ha @atom:c3 @atom:c2 @atom:ha - @angle:c3-c2-hc @atom:c3 @atom:c2 @atom:hc - @angle:c3-c2-n2 @atom:c3 @atom:c2 @atom:n2 - @angle:c3-c2-n @atom:c3 @atom:c2 @atom:n - @angle:c3-c2-na @atom:c3 @atom:c2 @atom:na - @angle:c3-c2-ne @atom:c3 @atom:c2 @atom:ne - @angle:c3-c2-nf @atom:c3 @atom:c2 @atom:nf - @angle:c3-c2-nh @atom:c3 @atom:c2 @atom:nh - @angle:c3-c2-o @atom:c3 @atom:c2 @atom:o - @angle:c3-c2-oh @atom:c3 @atom:c2 @atom:oh - @angle:c3-c2-os @atom:c3 @atom:c2 @atom:os - @angle:c3-c2-p2 @atom:c3 @atom:c2 @atom:p2 - @angle:c3-c2-s @atom:c3 @atom:c2 @atom:s - @angle:c3-c2-ss @atom:c3 @atom:c2 @atom:ss - @angle:ca-c2-ca @atom:ca @atom:c2 @atom:ca - @angle:ca-c2-hc @atom:ca @atom:c2 @atom:hc - @angle:c-c2-c2 @atom:c @atom:c2 @atom:c2 - @angle:c-c2-c3 @atom:c @atom:c2 @atom:c3 - @angle:c-c2-c @atom:c @atom:c2 @atom:c - @angle:cc-c2-h4 @atom:cc @atom:c2 @atom:h4 - @angle:cc-c2-ha @atom:cc @atom:c2 @atom:ha - @angle:cc-c2-nh @atom:cc @atom:c2 @atom:nh - @angle:cc-c2-o @atom:cc @atom:c2 @atom:o - @angle:cd-c2-ha @atom:cd @atom:c2 @atom:ha - @angle:ce-c2-cl @atom:ce @atom:c2 @atom:cl - @angle:ce-c2-h4 @atom:ce @atom:c2 @atom:h4 - @angle:ce-c2-ha @atom:ce @atom:c2 @atom:ha - @angle:ce-c2-na @atom:ce @atom:c2 @atom:na - @angle:ce-c2-nh @atom:ce @atom:c2 @atom:nh - @angle:ce-c2-no @atom:ce @atom:c2 @atom:no - @angle:ce-c2-o @atom:ce @atom:c2 @atom:o - @angle:ce-c2-oh @atom:ce @atom:c2 @atom:oh - @angle:ce-c2-os @atom:ce @atom:c2 @atom:os - @angle:cf-c2-ha @atom:cf @atom:c2 @atom:ha - @angle:c-c2-ha @atom:c @atom:c2 @atom:ha - @angle:c-c2-hc @atom:c @atom:c2 @atom:hc - @angle:cl-c2-cl @atom:cl @atom:c2 @atom:cl - @angle:cl-c2-h4 @atom:cl @atom:c2 @atom:h4 - @angle:cl-c2-ha @atom:cl @atom:c2 @atom:ha - @angle:cx-c2-ha @atom:cx @atom:c2 @atom:ha - @angle:f-c2-f @atom:f @atom:c2 @atom:f - @angle:f-c2-ha @atom:f @atom:c2 @atom:ha - @angle:h4-c2-n2 @atom:h4 @atom:c2 @atom:n2 - @angle:h4-c2-n @atom:h4 @atom:c2 @atom:n - @angle:h4-c2-na @atom:h4 @atom:c2 @atom:na - @angle:h4-c2-ne @atom:h4 @atom:c2 @atom:ne - @angle:h4-c2-nh @atom:h4 @atom:c2 @atom:nh - @angle:h4-c2-no @atom:h4 @atom:c2 @atom:no - @angle:h4-c2-os @atom:h4 @atom:c2 @atom:os - @angle:h4-c2-ss @atom:h4 @atom:c2 @atom:ss - @angle:h5-c2-n2 @atom:h5 @atom:c2 @atom:n2 - @angle:h5-c2-na @atom:h5 @atom:c2 @atom:na - @angle:h5-c2-ne @atom:h5 @atom:c2 @atom:ne - @angle:h5-c2-nh @atom:h5 @atom:c2 @atom:nh - @angle:ha-c2-ha @atom:ha @atom:c2 @atom:ha - @angle:ha-c2-n1 @atom:ha @atom:c2 @atom:n1 - @angle:ha-c2-n2 @atom:ha @atom:c2 @atom:n2 - @angle:ha-c2-n3 @atom:ha @atom:c2 @atom:n3 - @angle:ha-c2-n @atom:ha @atom:c2 @atom:n - @angle:ha-c2-na @atom:ha @atom:c2 @atom:na - @angle:ha-c2-ne @atom:ha @atom:c2 @atom:ne - @angle:ha-c2-nf @atom:ha @atom:c2 @atom:nf - @angle:ha-c2-nh @atom:ha @atom:c2 @atom:nh - @angle:ha-c2-no @atom:ha @atom:c2 @atom:no - @angle:ha-c2-o @atom:ha @atom:c2 @atom:o - @angle:ha-c2-oh @atom:ha @atom:c2 @atom:oh - @angle:ha-c2-os @atom:ha @atom:c2 @atom:os - @angle:ha-c2-p2 @atom:ha @atom:c2 @atom:p2 - @angle:ha-c2-p3 @atom:ha @atom:c2 @atom:p3 - @angle:ha-c2-p4 @atom:ha @atom:c2 @atom:p4 - @angle:ha-c2-p5 @atom:ha @atom:c2 @atom:p5 - @angle:ha-c2-pe @atom:ha @atom:c2 @atom:pe - @angle:ha-c2-pf @atom:ha @atom:c2 @atom:pf - @angle:ha-c2-s2 @atom:ha @atom:c2 @atom:s2 - @angle:ha-c2-s4 @atom:ha @atom:c2 @atom:s4 - @angle:ha-c2-s @atom:ha @atom:c2 @atom:s - @angle:ha-c2-s6 @atom:ha @atom:c2 @atom:s6 - @angle:ha-c2-sh @atom:ha @atom:c2 @atom:sh - @angle:ha-c2-ss @atom:ha @atom:c2 @atom:ss - @angle:hc-c2-hc @atom:hc @atom:c2 @atom:hc - @angle:hc-c2-n2 @atom:hc @atom:c2 @atom:n2 - @angle:hc-c2-n @atom:hc @atom:c2 @atom:n - @angle:hc-c2-na @atom:hc @atom:c2 @atom:na - @angle:hc-c2-nh @atom:hc @atom:c2 @atom:nh - @angle:hc-c2-no @atom:hc @atom:c2 @atom:no - @angle:hc-c2-oh @atom:hc @atom:c2 @atom:oh - @angle:hc-c2-os @atom:hc @atom:c2 @atom:os - @angle:hc-c2-p3 @atom:hc @atom:c2 @atom:p3 - @angle:hc-c2-p5 @atom:hc @atom:c2 @atom:p5 - @angle:hc-c2-s4 @atom:hc @atom:c2 @atom:s4 - @angle:hc-c2-s6 @atom:hc @atom:c2 @atom:s6 - @angle:hc-c2-sh @atom:hc @atom:c2 @atom:sh - @angle:hc-c2-ss @atom:hc @atom:c2 @atom:ss - 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@angle:n2-s4-ne @atom:n2 @atom:s4 @atom:ne - @angle:nc-c-s @atom:nc @atom:c @atom:s - @angle:o-sy-ss @atom:o @atom:sy @atom:ss - @angle:c2-ce-ss @atom:c2 @atom:ce @atom:ss - @angle:c3-cx-ca @atom:c3 @atom:cx @atom:ca - @angle:cc-cc-nf @atom:cc @atom:cc @atom:nf - @angle:ca-nd-cd @atom:ca @atom:nd @atom:cd - @angle:cc-n2-oh @atom:cc @atom:n2 @atom:oh - @angle:ca-os-sy @atom:ca @atom:os @atom:sy - @angle:hx-c3-p5 @atom:hx @atom:c3 @atom:p5 - @angle:ca-ce-n @atom:ca @atom:ce @atom:n - @angle:h4-ce-sx @atom:h4 @atom:ce @atom:sx - @angle:c3-ce-ne @atom:c3 @atom:ce @atom:ne - @angle:c1-n1-ce @atom:c1 @atom:n1 @atom:ce - @angle:c3-n2-cd @atom:c3 @atom:n2 @atom:cd - @angle:cc-c3-h2 @atom:cc @atom:c3 @atom:h2 - @angle:ca-ce-cg @atom:ca @atom:ce @atom:cg - @angle:c2-cc-na @atom:c2 @atom:cc @atom:na - @angle:ca-c3-s4 @atom:ca @atom:c3 @atom:s4 - @angle:n2-cf-nf @atom:n2 @atom:cf @atom:nf - @angle:ce-cf-ss @atom:ce @atom:cf @atom:ss - @angle:c3-cx-ss @atom:c3 @atom:cx @atom:ss - @angle:nh-ce-nh @atom:nh @atom:ce @atom:nh - @angle:cd-c-ne @atom:cd @atom:c @atom:ne - @angle:na-c3-ss @atom:na @atom:c3 @atom:ss - @angle:cf-cf-os @atom:cf @atom:cf @atom:os - @angle:cx-c3-h2 @atom:cx @atom:c3 @atom:h2 - @angle:cv-ss-cy @atom:cv @atom:ss @atom:cy - @angle:ss-cy-ss @atom:ss @atom:cy @atom:ss - @angle:ce-cx-os @atom:ce @atom:cx @atom:os - @angle:nb-ca-ne @atom:nb @atom:ca @atom:ne - @angle:br-ca-nb @atom:br @atom:ca @atom:nb - @angle:c3-nh-os @atom:c3 @atom:nh @atom:os - @angle:c2-nh-p5 @atom:c2 @atom:nh @atom:p5 - @angle:br-ca-cp @atom:br @atom:ca @atom:cp - @angle:cc-ce-cc @atom:cc @atom:ce @atom:cc - @angle:c3-nh-s6 @atom:c3 @atom:nh @atom:s6 - @angle:cx-c3-na @atom:cx @atom:c3 @atom:na - @angle:ca-os-p3 @atom:ca @atom:os @atom:p3 - @angle:ce-cf-sy @atom:ce @atom:cf @atom:sy - @angle:ca-n2-n1 @atom:ca @atom:n2 @atom:n1 - @angle:cd-cd-no @atom:cd @atom:cd @atom:no - @angle:na-n2-os @atom:na @atom:n2 @atom:os - @angle:ce-c3-f @atom:ce @atom:c3 @atom:f - @angle:cx-cc-na @atom:cx @atom:cc @atom:na - @angle:n-n2-na @atom:n @atom:n2 @atom:na - @angle:c3-cf-cc @atom:c3 @atom:cf @atom:cc - @angle:ca-na-cy @atom:ca @atom:na @atom:cy - @angle:h1-c3-py @atom:h1 @atom:c3 @atom:py - @angle:cy-s6-cy @atom:cy @atom:s6 @atom:cy - @angle:ce-ce-s4 @atom:ce @atom:ce @atom:s4 - @angle:c3-p3-cy @atom:c3 @atom:p3 @atom:cy - @angle:h2-cx-os @atom:h2 @atom:cx @atom:os - @angle:c-c-ce @atom:c @atom:c @atom:ce - @angle:ce-cy-h1 @atom:ce @atom:cy @atom:h1 - @angle:cx-c3-ss @atom:cx @atom:c3 @atom:ss - @angle:cg-ce-ss @atom:cg @atom:ce @atom:ss - @angle:br-cy-cy @atom:br @atom:cy @atom:cy - @angle:c-cy-cl @atom:c @atom:cy @atom:cl - @angle:c-cx-n @atom:c @atom:cx @atom:n - @angle:br-c3-f @atom:br @atom:c3 @atom:f - @angle:c3-n4-cy @atom:c3 @atom:n4 @atom:cy - @angle:ce-cv-ss @atom:ce @atom:cv @atom:ss - @angle:cc-cd-i @atom:cc @atom:cd @atom:i - @angle:c2-ss-ca @atom:c2 @atom:ss @atom:ca - @angle:c-cx-ce @atom:c @atom:cx @atom:ce - @angle:cy-nh-cy @atom:cy @atom:nh @atom:cy - @angle:cx-c-h4 @atom:cx @atom:c @atom:h4 - @angle:c-n4-c3 @atom:c @atom:n4 @atom:c3 - @angle:f-cy-py @atom:f @atom:cy @atom:py - @angle:n2-c3-ss @atom:n2 @atom:c3 @atom:ss - @angle:c3-ss-cf @atom:c3 @atom:ss @atom:cf - @angle:ce-cy-hc @atom:ce @atom:cy @atom:hc - @angle:br-cc-nc @atom:br @atom:cc @atom:nc - @angle:h3-c3-n @atom:h3 @atom:c3 @atom:n - @angle:ca-ne-cd @atom:ca @atom:ne @atom:cd - @angle:cx-n-cy @atom:cx @atom:n @atom:cy - @angle:cl-c3-s4 @atom:cl @atom:c3 @atom:s4 - @angle:cp-cq-nb @atom:cp @atom:cq @atom:nb - @angle:cc-cd-o @atom:cc @atom:cd @atom:o - @angle:hx-cy-hx @atom:hx @atom:cy @atom:hx - @angle:cc-na-sy @atom:cc @atom:na @atom:sy - @angle:h1-cy-na @atom:h1 @atom:cy @atom:na - @angle:h4-cf-sy @atom:h4 @atom:cf @atom:sy - @angle:c-p5-c3 @atom:c @atom:p5 @atom:c3 - @angle:ca-c-nc @atom:ca @atom:c @atom:nc - @angle:c3-os-sy @atom:c3 @atom:os @atom:sy - @angle:cd-ne-sy @atom:cd @atom:ne @atom:sy - @angle:cx-ca-nb @atom:cx @atom:ca @atom:nb - @angle:nc-ss-ss @atom:nc @atom:ss @atom:ss - @angle:hp-p5-os @atom:hp @atom:p5 @atom:os - @angle:ca-n-oh @atom:ca @atom:n @atom:oh - @angle:c3-s6-ne @atom:c3 @atom:s6 @atom:ne - @angle:c1-cx-h1 @atom:c1 @atom:cx @atom:h1 - @angle:na-c3-oh @atom:na @atom:c3 @atom:oh - @angle:n-nc-nd @atom:n @atom:nc @atom:nd - @angle:c3-na-nb @atom:c3 @atom:na @atom:nb - @angle:ne-c-os @atom:ne @atom:c @atom:os - @angle:br-ce-ce @atom:br @atom:ce @atom:ce - @angle:cc-c2-oh @atom:cc @atom:c2 @atom:oh - @angle:c1-cx-os @atom:c1 @atom:cx @atom:os - @angle:nc-cc-os @atom:nc @atom:cc @atom:os - @angle:br-ce-cf @atom:br @atom:ce @atom:cf - @angle:cy-c3-f @atom:cy @atom:c3 @atom:f - @angle:h5-ce-ne @atom:h5 @atom:ce @atom:ne - @angle:n3-py-n3 @atom:n3 @atom:py @atom:n3 - @angle:br-cc-ca @atom:br @atom:cc @atom:ca - @angle:f-c3-na @atom:f @atom:c3 @atom:na - @angle:cc-c3-s4 @atom:cc @atom:c3 @atom:s4 - @angle:ce-cf-sx @atom:ce @atom:cf @atom:sx - @angle:cc-cc-i @atom:cc @atom:cc @atom:i - @angle:c-cg-ch @atom:c @atom:cg @atom:ch - @angle:ce-c3-hx @atom:ce @atom:c3 @atom:hx - @angle:cd-na-cy @atom:cd @atom:na @atom:cy - @angle:br-c3-c2 @atom:br @atom:c3 @atom:c2 - @angle:ce-ce-cg @atom:ce @atom:ce @atom:cg - @angle:cl-cd-nd @atom:cl @atom:cd @atom:nd - @angle:n-ca-na @atom:n @atom:ca @atom:na - @angle:cx-cd-nd @atom:cx @atom:cd @atom:nd - @angle:cl-p5-os @atom:cl @atom:p5 @atom:os - @angle:cx-ss-cy @atom:cx @atom:ss @atom:cy - @angle:cc-cg-ch @atom:cc @atom:cg @atom:ch - @angle:cc-sy-oh @atom:cc @atom:sy @atom:oh - @angle:cq-ca-os @atom:cq @atom:ca @atom:os - @angle:ca-cd-ca @atom:ca @atom:cd @atom:ca - @angle:f-py-nf @atom:f @atom:py @atom:nf - @angle:ca-nh-cf @atom:ca @atom:nh @atom:cf - @angle:cf-cx-cx @atom:cf @atom:cx @atom:cx - @angle:py-nf-py @atom:py @atom:nf @atom:py - @angle:c-cc-ss @atom:c @atom:cc @atom:ss - @angle:cc-na-cx @atom:cc @atom:na @atom:cx - @angle:c2-cf-cx @atom:c2 @atom:cf @atom:cx - @angle:ce-cd-os @atom:ce @atom:cd @atom:os - @angle:cd-cc-cx @atom:cd @atom:cc @atom:cx - @angle:cf-n1-n1 @atom:cf @atom:n1 @atom:n1 - @angle:cf-n-hn @atom:cf @atom:n @atom:hn - @angle:ce-ce-nf @atom:ce @atom:ce @atom:nf - @angle:cf-no-o @atom:cf @atom:no @atom:o - @angle:h4-cf-nh @atom:h4 @atom:cf @atom:nh - @angle:nf-c-s @atom:nf @atom:c @atom:s - @angle:na-cd-sh @atom:na @atom:cd @atom:sh - @angle:cc-cy-hc @atom:cc @atom:cy @atom:hc - @angle:cf-cc-na @atom:cf @atom:cc @atom:na - @angle:c-cf-h4 @atom:c @atom:cf @atom:h4 - @angle:ce-cd-n @atom:ce @atom:cd @atom:n - @angle:cf-c3-h2 @atom:cf @atom:c3 @atom:h2 - @angle:na-cc-na @atom:na @atom:cc @atom:na - @angle:ch-ca-nb @atom:ch @atom:ca @atom:nb - @angle:cf-c2-f @atom:cf @atom:c2 @atom:f - @angle:cg-cc-nc @atom:cg @atom:cc @atom:nc - @angle:h5-cd-n2 @atom:h5 @atom:cd @atom:n2 - @angle:cd-c3-cf @atom:cd @atom:c3 @atom:cf - @angle:nf-cc-ss @atom:nf @atom:cc @atom:ss - @angle:na-cc-nf @atom:na @atom:cc @atom:nf - @angle:nf-cf-ne @atom:nf @atom:cf @atom:ne - @angle:n-cd-os @atom:n @atom:cd @atom:os - @angle:ce-cf-os @atom:ce @atom:cf @atom:os - @angle:br-cf-c2 @atom:br @atom:cf @atom:c2 - @angle:cq-nb-na @atom:cq @atom:nb @atom:na - @angle:cc-ce-nf @atom:cc @atom:ce @atom:nf - @angle:cf-s4-ss @atom:cf @atom:s4 @atom:ss - @angle:br-cd-ss @atom:br @atom:cd @atom:ss - @angle:c-cf-ss @atom:c @atom:cf @atom:ss - @angle:c2-cd-ss @atom:c2 @atom:cd @atom:ss - @angle:n2-s4-nf @atom:n2 @atom:s4 @atom:nf - @angle:nd-c-s @atom:nd @atom:c @atom:s - @angle:c2-cf-ss @atom:c2 @atom:cf @atom:ss - @angle:cd-cd-ne @atom:cd @atom:cd @atom:ne - @angle:ca-nc-cc @atom:ca @atom:nc @atom:cc - @angle:cd-n2-oh @atom:cd @atom:n2 @atom:oh - @angle:ca-cf-n @atom:ca @atom:cf @atom:n - @angle:h4-cf-sx @atom:h4 @atom:cf @atom:sx - @angle:c3-cf-nf @atom:c3 @atom:cf @atom:nf - @angle:c1-n1-cf @atom:c1 @atom:n1 @atom:cf - @angle:c3-n2-cc @atom:c3 @atom:n2 @atom:cc - @angle:ca-cf-ch @atom:ca @atom:cf @atom:ch - @angle:c2-cd-na @atom:c2 @atom:cd @atom:na - @angle:n2-ce-ne @atom:n2 @atom:ce @atom:ne - @angle:nh-cf-nh @atom:nh @atom:cf @atom:nh - @angle:cc-c-nf @atom:cc @atom:c @atom:nf - @angle:cf-cx-os @atom:cf @atom:cx @atom:os - @angle:nb-ca-nf @atom:nb @atom:ca @atom:nf - @angle:br-ca-cq @atom:br @atom:ca @atom:cq - @angle:cd-cf-cd @atom:cd @atom:cf @atom:cd - @angle:cf-ce-sy @atom:cf @atom:ce @atom:sy - @angle:cc-cc-no @atom:cc @atom:cc @atom:no - @angle:cf-c3-f @atom:cf @atom:c3 @atom:f - @angle:cx-cd-na @atom:cx @atom:cd @atom:na - @angle:c3-ce-cd @atom:c3 @atom:ce @atom:cd - @angle:cf-cf-s4 @atom:cf @atom:cf @atom:s4 - @angle:c-c-cf @atom:c @atom:c @atom:cf - @angle:cf-cy-h1 @atom:cf @atom:cy @atom:h1 - @angle:ch-cf-ss @atom:ch @atom:cf @atom:ss - @angle:cf-cv-ss @atom:cf @atom:cv @atom:ss - @angle:c-cx-cf @atom:c @atom:cx @atom:cf - @angle:c3-ss-ce @atom:c3 @atom:ss @atom:ce - @angle:cf-cy-hc @atom:cf @atom:cy @atom:hc - @angle:br-cd-nd @atom:br @atom:cd @atom:nd - @angle:ca-nf-cc @atom:ca @atom:nf @atom:cc - @angle:cd-cc-o @atom:cd @atom:cc @atom:o - @angle:cd-na-sy @atom:cd @atom:na @atom:sy - @angle:ca-c-nd @atom:ca @atom:c @atom:nd - @angle:cc-nf-sy @atom:cc @atom:nf @atom:sy - @angle:nd-ss-ss @atom:nd @atom:ss @atom:ss - @angle:c3-s6-nf @atom:c3 @atom:s6 @atom:nf - @angle:n-nd-nc @atom:n @atom:nd @atom:nc - @angle:nf-c-os @atom:nf @atom:c @atom:os - @angle:br-cf-cf @atom:br @atom:cf @atom:cf - @angle:cd-c2-oh @atom:cd @atom:c2 @atom:oh - @angle:nd-cd-os @atom:nd @atom:cd @atom:os - @angle:br-cf-ce @atom:br @atom:cf @atom:ce - @angle:h5-cf-nf @atom:h5 @atom:cf @atom:nf - @angle:br-cd-ca @atom:br @atom:cd @atom:ca - @angle:cd-c3-s4 @atom:cd @atom:c3 @atom:s4 - @angle:cf-ce-sx @atom:cf @atom:ce @atom:sx - @angle:cd-cd-i @atom:cd @atom:cd @atom:i - @angle:c-ch-cg @atom:c @atom:ch @atom:cg - @angle:cf-c3-hx @atom:cf @atom:c3 @atom:hx - @angle:cf-cf-ch @atom:cf @atom:cf @atom:ch - @angle:cl-cc-nc @atom:cl @atom:cc @atom:nc - @angle:cx-cc-nc @atom:cx @atom:cc @atom:nc - @angle:cd-ch-cg @atom:cd @atom:ch @atom:cg - @angle:cd-sy-oh @atom:cd @atom:sy @atom:oh - } # (end of Angles By Type) - - write_once("In Settings") { - dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 - dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X - dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 - dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 - dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230 - dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013 - dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value - dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value - dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh) - dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X - dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X - dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X - dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 - dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 - dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X - dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated - dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated - dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond - dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 - dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 - dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 - dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 - dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 - dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 - dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 - dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 - dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 - dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 - dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 - dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds - dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 - dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99 - dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 - dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94 - dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94 - dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013 - dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 - dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99 - dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99 - dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99 - dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond - dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond - dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94 - dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94 - dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol. - dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol. - dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 - dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 - dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 - dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99 - dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99 - dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond - dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond - dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond - dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated - dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 - dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! - dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! - dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!! - dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 - dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 - dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 - dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! - dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! - dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!! - dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 - dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 - dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 - dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 - dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 - dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! - dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! - dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!! - dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 - dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 - dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 - dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! - dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! - dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!! - dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 - dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 - dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 - dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X - dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X - dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X - dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X - dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999 - dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 - dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 - dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 - dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 - dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 - dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 - dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 - dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 - dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230 - dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 - dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 - dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 - dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 - dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X - dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X - dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6 - dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 - dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 - dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 - dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 - dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 - dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 - dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X - dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X - dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X - dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 - dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X - dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X - dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 - dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99 - dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X - dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 - dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X - dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X - dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 - dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X - dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 - dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X - dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 - dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 - dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X - dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 - dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X - dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94 - dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 - dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 - dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 - dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 - dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 - dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 - dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 - dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 - dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 - dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 - dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 - dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 - dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 - dihedral_coeff @dihedral:X-n-pf-X fourier 1 1.0 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n-pd-X fourier 1 4.8 2 180.0 - dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 - dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 - dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 - dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 - dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 - dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 - dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 - dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 - dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 - dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 - dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 - dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 - dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond - dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol - dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol - dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol - dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X - dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X - dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 - dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 - dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 - dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 - dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 - dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 - dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 - dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 - dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 - dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 - dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 - dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 - dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 - dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 - dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 - dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 - dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 - dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 - dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 - dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 - dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 - dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond - dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond - dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 - dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 - dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 - dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 - dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 - dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 - dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 - dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 - dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 - dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 - dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 - dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 - dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 - dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 - dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 - dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 - dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 - dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 - dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 - dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 - dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 - dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 - dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 - dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 - dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 - dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 - dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 - dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 - dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 - dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 - dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 - dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 - dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 - dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 - dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 - dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 - dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 - dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 - dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 - dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 - dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 - dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 - dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 - dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 - dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 - dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 - dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 - dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 - dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 - dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 - dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 - dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 - dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 - dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 - dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 - dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 - dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 - dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 - dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 - dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 - dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 - dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 - dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 - dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 - dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 - dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 - dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 - dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 - dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 - dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 - dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 - dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 - dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 - dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 - dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 - dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 - dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 - dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 - dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 - dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 - dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 - dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 - dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 - dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 - dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 - dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 - dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 - dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 - dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 - dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 - dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 - dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 - dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 - dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 - dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 - dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 - dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 - dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 - dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 - dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 - dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 - dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 - dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 - dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 - dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 - dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 - dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 - dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 - dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 - dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 - dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 - dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 - dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 - dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 - dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 - dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 - dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 - dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 - dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 - dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 - dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 - dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 - dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 - dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 - dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 - dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 - dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 - dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 - dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 - dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 - dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 - dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 - dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond - dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol. - dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 - dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 - dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 - dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 - dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 - dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 - dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 - dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 - dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 - dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 - dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 - dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 - dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 - dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 - dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 - dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 - dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 - dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 - dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 - dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 - dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 - dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 - dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 - dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 - dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 - dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 - dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 - dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 - dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 - dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 - dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 - dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 - dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 - dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 - dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 - dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 - dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 - dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 - dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 - dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 - dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 - dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 - dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 - dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 - dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 - dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 - dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 - dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 - dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 - dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 - dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 - dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!! - dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 - dihedral_coeff @dihedral:X-cf-pe-X fourier 1 6.65 2 180.0 # NEW - dihedral_coeff @dihedral:X-nd-os-X fourier 1 4.8 2 180.0 # NEW - dihedral_coeff @dihedral:X-nd-ss-X fourier 1 4.8 2 180.0 # NEW - dihedral_coeff @dihedral:X-nf-pe-X fourier 1 5.4 2 180.0 # NEW - dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 - dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 - dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 - dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 - dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 - dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 # TorType=1 - dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230 TorType=1 - dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 # TorType=1 - dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230 TorType=1 - dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK TorType=1 - dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK TorType=1 - dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999 TorType=1 - dihedral_coeff @dihedral:c3-n4-c3-ca fourier 2 0.156 3 0.0 0.7 2 0.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:oh-c3-c3-n4 fourier 2 0.144 3 0.0 1.3 2 0.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:c3-c3-n4-c3 fourier 1 0.156 3 0.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:c3-c-os-p5 fourier 2 2.7 2 180.0 2.0 1 180.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:c-os-p5-o fourier 3 0.8 2 0.0 1.1 1 0.0 0.5 3 180.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:c3-c3-os-p5 fourier 2 0.383 3 0.0 3.95 1 180.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:c3-os-p5-o fourier 2 0.8 2 0.0 0.55 3 0.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:ca-ca-os-p5 fourier 1 1.75 2 180.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:ca-os-p5-o fourier 2 0.8 2 180.0 0.1 3 0.0 # Junmei, 2015 TorType=1 - dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.5 3 0.0 1.82 1 0.0 # m9 GA AUE=0.9626 RMSE=1.1958 TorType=2 - dihedral_coeff @dihedral:c-n-c2-c2 fourier 2 1.57 2 180.0 1.53 1 180.0 # c25 GA AUE=0.3367 RMSE=0.3900 TorType=2 - dihedral_coeff @dihedral:c3-ss-c2-c2 fourier 2 1.28 2 180.0 1.2 3 180.0 # c39 GA AUE=0.3908 RMSE=0.4760 TorType=2 - dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 5.29 2 180.0 0.4 1 180.0 # c22 GA AUE=2.0091 RMSE=3.0745 TorType=2 - dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.13 3 0.0 0.29 2 180.0 0.11 1 0.0 # c42 GA AUE=0.2975 RMSE=0.3306 TorType=2 - dihedral_coeff @dihedral:n-c-c3-c3 fourier 2 0.0 4 180.0 0.71 2 180.0 # p20 GA AUE=0.5445 RMSE=0.7015 TorType=2 - dihedral_coeff @dihedral:c3-os-c3-c3 fourier 2 0.24 3 0.0 0.16 2 0.0 # p29 GA AUE=0.4256 RMSE=0.5201 TorType=2 - dihedral_coeff @dihedral:ca-nh-n3-c3 fourier 1 1.12 2 0.0 # c115 SS AUE=2.2848 RMSE=2.9445 TorType=2 - dihedral_coeff @dihedral:hs-sh-ss-c3 fourier 2 1.6 3 0.0 2.81 2 0.0 # c223 GA AUE=0.7163 RMSE=0.8348 TorType=2 - dihedral_coeff @dihedral:ho-oh-nh-ca fourier 2 1.43 1 0.0 0.5 2 0.0 # c156 GA AUE=0.4441 RMSE=0.5406 TorType=2 - dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.5 3 0.0 0.93 1 0.0 # m8 GA AUE=0.9322 RMSE=1.0556 TorType=2 - dihedral_coeff @dihedral:c-n-c3-c3 fourier 3 0.1 4 180.0 0.17 3 0.0 1.02 1 180.0 # p19 GA AUE=0.2882 RMSE=0.4031 TorType=2 - dihedral_coeff @dihedral:c2-p2-n-c fourier 2 1.48 2 180.0 2.15 1 180.0 # c88 GA AUE=0.5049 RMSE=0.6214 TorType=2 - dihedral_coeff @dihedral:f-c3-c3-f fourier 2 1.0 3 0.0 0.64 1 180.0 # m7 GA AUE=1.3130 RMSE=1.6963 TorType=2 - dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.36 3 180.0 1.47 1 0.0 # c23 GA AUE=0.0738 RMSE=0.0893 TorType=2 - dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.21 3 0.0 0.08 1 0.0 # m5 GA AUE=0.2036 RMSE=0.2389 TorType=2 - dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.08 3 0.0 # m2 SS AUE=0.2468 RMSE=0.2989 TorType=2 - dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.22 3 0.0 0.25 1 180.0 # m4 GA AUE=0.1732 RMSE=0.2055 TorType=2 - dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.22 3 0.0 1.97 1 180.0 # m3 GA AUE=0.0868 RMSE=0.1021 TorType=2 - dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.12 3 0.0 # m1 SS AUE=0.2420 RMSE=0.2944 TorType=2 - dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.18 3 0.0 0.51 1 0.0 # m11 GA AUE=0.1021 RMSE=0.1307 TorType=2 - dihedral_coeff @dihedral:n-c-c3-n fourier 2 0.1 1 180.0 2.12 2 180.0 # p17 GA AUE=0.9129 RMSE=1.0401 TorType=2 - dihedral_coeff @dihedral:oh-c3-c3-os fourier 3 1.01 3 0.0 0.0 2 0.0 0.02 1 180.0 # suger5ring,suger6ring GA AUE=0.6597 RMSE=0.8978 TorType=2 - dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.0 3 0.0 2.61 2 0.0 # c191 GA AUE=0.2324 RMSE=0.3542 TorType=2 - dihedral_coeff @dihedral:c3-n-c-c3 fourier 2 0.26 2 180.0 0.5 1 0.0 # c5 GA AUE=0.9706 RMSE=1.2796 TorType=2 - dihedral_coeff @dihedral:c3-os-c-c3 fourier 3 1.58 1 180.0 3.18 2 180.0 0.73 3 0.0 # c13 GA AUE=0.2469 RMSE=0.2990 TorType=2 - dihedral_coeff @dihedral:hs-sh-c-c3 fourier 2 1.08 2 180.0 1.92 1 180.0 # c18 GA AUE=0.2126 RMSE=0.3029 TorType=2 - dihedral_coeff @dihedral:os-c3-os-c3 fourier 3 0.0 3 180.0 1.24 2 0.0 0.97 1 180.0 # cococ,lactose2,t12 GA AUE=0.8913 RMSE=1.4261 TorType=2 - dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.15 2 0.0 0.89 3 0.0 # c226,p2 GA AUE=0.4785 RMSE=0.5249 TorType=2 - dihedral_coeff @dihedral:o-c-c3-hc fourier 2 0.83 1 0.0 0.04 3 180.0 # CH3COO,CH3COOH GA AUE=0.0144 RMSE=0.0193 TorType=2 - dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 1 0.0 3 0.0 # m19 SS AUE=0.1539 RMSE=0.2110 TorType=2 - dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.9 3 0.0 1.13 2 0.0 # p5,ch2oh2 GA AUE=0.9894 RMSE=1.1930 TorType=2 - dihedral_coeff @dihedral:os-c3-c3-os fourier 3 0.0 3 0.0 0.0 2 180.0 0.17 1 180.0 # p28,suger5ring,suger6ring,coccoc GA AUE=1.1750 RMSE=1.6708 TorType=2 - dihedral_coeff @dihedral:c1-c1-c3-c1 fourier 1 0.0 2 0.0 # t5 SS AUE=0.0048 RMSE=0.0058 TorType=3 - dihedral_coeff @dihedral:c2-c2-c3-c2 fourier 1 0.112 2 0.0 # t4 SS AUE=0.5917 RMSE=0.7276 TorType=3 - dihedral_coeff @dihedral:c2-ce-ca-ca fourier 1 0.505 2 180.0 # add6f SS AUE=0.2273 RMSE=0.3302 TorType=3 - dihedral_coeff @dihedral:c2-ce-ce-c3 fourier 1 0.5 2 180.0 # set1_2 SS AUE=0.6541 RMSE=0.8643 TorType=3 - dihedral_coeff @dihedral:c2-cf-cd-cc fourier 1 0.5 2 180.0 # add6d SS AUE=0.3708 RMSE=0.4956 TorType=3 - dihedral_coeff @dihedral:c2-n2-c3-n2 fourier 2 1.57 2 180.0 2.73 1 180.0 # t14 GA AUE=1.3428 RMSE=1.6221 TorType=3 - dihedral_coeff @dihedral:c2-n2-na-cd fourier 1 1.575 2 180.0 # c99 SS AUE=0.2455 RMSE=0.3271 TorType=3 - dihedral_coeff @dihedral:c2-n2-n-c fourier 1 2.79 1 180.0 # c80 SS AUE=2.1704 RMSE=2.7351 TorType=3 - dihedral_coeff @dihedral:c2-n2-nh-c2 fourier 1 1.2 2 0.0 # set3_6 SS AUE=1.7161 RMSE=2.4147 TorType=3 - dihedral_coeff @dihedral:c2-ne-ca-ca fourier 1 0.495 3 0.0 # c63 SS AUE=1.1301 RMSE=1.4142 TorType=3 - dihedral_coeff @dihedral:c2-ne-ce-c2 fourier 1 0.17 2 180.0 # c26 SS AUE=0.7462 RMSE=0.9083 TorType=3 - dihedral_coeff @dihedral:c2-ne-ce-c3 fourier 1 0.82 2 0.0 # set1_6 SS AUE=0.2966 RMSE=0.4200 TorType=3 - dihedral_coeff @dihedral:c2-nh-c2-c2 fourier 1 0.98 2 180.0 # set3_2 SS AUE=0.5762 RMSE=0.7682 TorType=3 - dihedral_coeff @dihedral:c2-nh-c2-c3 fourier 1 3.14 2 180.0 # set3_26 SS AUE=0.5612 RMSE=0.7360 TorType=3 - dihedral_coeff @dihedral:c2-nh-c3-h1 fourier 1 0.4 3 0.0 # set3_3 SS AUE=0.2455 RMSE=0.3092 TorType=3 - dihedral_coeff @dihedral:c2-nh-ca-ca fourier 1 0.55 2 180.0 # set3_4 SS AUE=0.8992 RMSE=1.3720 TorType=3 - dihedral_coeff @dihedral:c2-nh-nh-c2 fourier 1 2.93 3 0.0 # set3_24 SS AUE=2.3906 RMSE=3.0117 TorType=3 - dihedral_coeff @dihedral:c2-p2-c3-p2 fourier 1 2.07 1 180.0 # t18 SS AUE=0.4761 RMSE=0.6635 TorType=3 - dihedral_coeff @dihedral:c2-p2-n4-hn fourier 1 0.0 3 180.0 # c133 SS AUE=0.2623 RMSE=0.3265 TorType=3 - dihedral_coeff @dihedral:c2-p2-na-cc fourier 1 1.83 2 180.0 # c146 SS AUE=0.3236 RMSE=0.3673 TorType=3 - dihedral_coeff @dihedral:c2-p2-nh-c2 fourier 1 1.33 2 180.0 # set3_14 SS AUE=0.4660 RMSE=0.7730 TorType=3 - dihedral_coeff @dihedral:c2-p2-nh-c3 fourier 1 2.4 2 180.0 # c119 SS AUE=1.0662 RMSE=1.4725 TorType=3 - dihedral_coeff @dihedral:c2-p2-nh-ca fourier 1 1.88 1 180.0 # c158 SS AUE=1.5854 RMSE=1.8810 TorType=3 - dihedral_coeff @dihedral:c2-pe-ca-ca fourier 1 1.065 2 180.0 # c71 SS AUE=0.2838 RMSE=0.3291 TorType=3 - dihedral_coeff @dihedral:c2-pe-ce-c2 fourier 1 0.825 2 180.0 # c34 SS AUE=0.3082 RMSE=0.3467 TorType=3 - dihedral_coeff @dihedral:c2-pe-ce-c3 fourier 1 3.64 1 180.0 # set1_14 SS AUE=0.2869 RMSE=0.3329 TorType=3 - dihedral_coeff @dihedral:c2-pe-ne-c2 fourier 1 0.29 1 0.0 # c104 SS AUE=0.4118 RMSE=0.5379 TorType=3 - dihedral_coeff @dihedral:c2-pe-pe-c2 fourier 1 0.68 2 180.0 # c196 SS AUE=0.2486 RMSE=0.3241 TorType=3 - dihedral_coeff @dihedral:c3-c2-nh-ca fourier 2 1.16 2 180.0 1.88 1 0.0 # set1_10 GA AUE=0.3625 RMSE=0.5970 TorType=3 - dihedral_coeff @dihedral:c3-c3-c3-hc fourier 1 0.08 3 0.0 # t2 SS AUE=0.2507 RMSE=0.3027 TorType=3 - dihedral_coeff @dihedral:c3-c3-cc-ca fourier 1 0.082 3 0.0 # p3 SS AUE=0.4586 RMSE=0.5633 TorType=3 - dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.65 4 180.0 0.03 3 180.0 2.26 1 0.0 # sialic2 GA AUE=1.1541 RMSE=1.2847 TorType=3 - dihedral_coeff @dihedral:c3-c-c3-c3 fourier 1 0.332 2 180.0 # p10 SS AUE=0.3226 RMSE=0.4401 TorType=3 - dihedral_coeff @dihedral:c3-c-ce-c3 fourier 1 4.11 2 0.0 # set3_25 SS AUE=0.6933 RMSE=1.1187 TorType=3 - dihedral_coeff @dihedral:c3-ce-ce-c3 fourier 1 0.5 2 180.0 # set3_22 SS AUE=1.0809 RMSE=1.3455 TorType=3 - dihedral_coeff @dihedral:c3-n2-c2-c3 fourier 1 10.37 2 180.0 # c7 SS AUE=1.1629 RMSE=1.3902 TorType=3 - dihedral_coeff @dihedral:c3-n3-n3-c3 fourier 1 2.31 2 0.0 # c112 SS AUE=0.8815 RMSE=1.0390 TorType=3 - dihedral_coeff @dihedral:c3-n3-nh-c2 fourier 1 1.355 2 0.0 # set3_7 SS AUE=1.4104 RMSE=1.6750 TorType=3 - dihedral_coeff @dihedral:c3-n4-ca-ca fourier 1 1.495 2 0.0 # c65 SS AUE=0.2872 RMSE=0.3575 TorType=3 - dihedral_coeff @dihedral:c3-n4-n4-c3 fourier 1 0.244 3 0.0 # c127 SS AUE=0.6207 RMSE=0.7993 TorType=3 - dihedral_coeff @dihedral:c3-nh-c2-c2 fourier 2 0.95 2 180.0 1.12 3 180.0 # c27 GA AUE=0.7690 RMSE=1.0440 TorType=3 - dihedral_coeff @dihedral:c3-nh-c2-c3 fourier 1 2.495 2 180.0 # set1_7 SS AUE=0.8853 RMSE=1.2321 TorType=3 - dihedral_coeff @dihedral:c3-os-c2-c2 fourier 2 2.52 2 180.0 2.0 1 180.0 # c33 GA AUE=0.9155 RMSE=1.0796 TorType=3 - dihedral_coeff @dihedral:c3-os-c2-c3 fourier 1 4.79 2 180.0 # set1_13 SS AUE=0.9973 RMSE=1.5097 TorType=3 - dihedral_coeff @dihedral:c3-os-c3-h1 fourier 1 0.337 3 0.0 # c52 SS AUE=0.2706 RMSE=0.3300 TorType=3 - dihedral_coeff @dihedral:c3-os-ca-ca fourier 1 1.61 2 180.0 # c70 SS AUE=0.3151 RMSE=0.3580 TorType=3 - dihedral_coeff @dihedral:c3-os-n2-c2 fourier 2 2.2 2 180.0 0.9 3 180.0 # c103 SS AUE=1.2430 RMSE=1.4817 TorType=3 - dihedral_coeff @dihedral:c3-os-n3-c3 fourier 1 0.84 2 0.0 # c118 SS AUE=0.7374 RMSE=0.9683 TorType=3 - dihedral_coeff @dihedral:c3-os-n4-c3 fourier 1 0.62 3 180.0 # c132 SS AUE=0.8090 RMSE=0.9444 TorType=3 - dihedral_coeff @dihedral:c3-os-na-cc fourier 1 0.19 2 0.0 # c145 SS AUE=0.2720 RMSE=0.3305 TorType=3 - dihedral_coeff @dihedral:c3-os-n-c fourier 1 0.42 2 0.0 # c87 SS AUE=0.3019 RMSE=0.3567 TorType=3 - dihedral_coeff @dihedral:c3-os-nh-c2 fourier 1 1.15 1 0.0 # set3_13 SS AUE=0.9655 RMSE=1.1845 TorType=3 - dihedral_coeff @dihedral:c3-os-nh-ca fourier 1 0.5 1 0.0 # c157 SS AUE=0.8647 RMSE=1.0585 TorType=3 - dihedral_coeff @dihedral:c3-os-no-o fourier 1 2.515 2 180.0 # c168 SS AUE=0.3706 RMSE=0.4248 TorType=3 - dihedral_coeff @dihedral:c3-os-oh-ho fourier 1 1.01 2 0.0 # c178 SS AUE=0.2810 RMSE=0.3796 TorType=3 - dihedral_coeff @dihedral:c3-os-os-c3 fourier 1 0.38 1 0.0 # c187 SS AUE=0.4838 RMSE=0.6593 TorType=3 - dihedral_coeff @dihedral:c3-os-p2-c2 fourier 2 2.94 2 180.0 1.85 1 180.0 # c188 GA AUE=0.3661 RMSE=0.4565 TorType=3 - dihedral_coeff @dihedral:c3-p3-c2-c2 fourier 1 0.297 2 0.0 # c35 SS AUE=1.0902 RMSE=1.4763 TorType=3 - dihedral_coeff @dihedral:c3-p3-c2-c3 fourier 1 0.95 2 180.0 # set1_15 SS AUE=0.4182 RMSE=0.4905 TorType=3 - dihedral_coeff @dihedral:c3-p3-ca-ca fourier 1 0.177 2 180.0 # c72 SS AUE=0.2797 RMSE=0.3319 TorType=3 - dihedral_coeff @dihedral:c3-p3-n2-c2 fourier 1 5.0 2 180.0 # c105 SS AUE=0.8649 RMSE=1.0889 TorType=3 - dihedral_coeff @dihedral:c3-p3-n3-c3 fourier 1 2.85 2 0.0 # c120 SS AUE=0.8776 RMSE=1.2067 TorType=3 - dihedral_coeff @dihedral:c3-p3-n4-c3 fourier 1 0.067 3 0.0 # c134 SS AUE=0.1760 RMSE=0.2433 TorType=3 - dihedral_coeff @dihedral:c3-p3-na-cc fourier 1 1.025 2 0.0 # c147 SS AUE=0.2741 RMSE=0.3331 TorType=3 - dihedral_coeff @dihedral:c3-p3-n-c fourier 1 1.83 2 0.0 # c89 SS AUE=0.9690 RMSE=1.3708 TorType=3 - dihedral_coeff @dihedral:c3-p3-nh-c2 fourier 1 1.85 2 0.0 # set3_15 SS AUE=0.8611 RMSE=0.9832 TorType=3 - dihedral_coeff @dihedral:c3-p3-no-o fourier 1 1.4 2 180.0 # c170 SS AUE=0.5082 RMSE=0.5728 TorType=3 - dihedral_coeff @dihedral:c3-p3-oh-ho fourier 1 0.24 3 180.0 # c180 SS AUE=0.9983 RMSE=1.2838 TorType=3 - dihedral_coeff @dihedral:c3-p3-p2-c2 fourier 1 0.2 1 0.0 # c197 SS AUE=0.5014 RMSE=0.7016 TorType=3 - dihedral_coeff @dihedral:c3-p3-p3-c3 fourier 1 0.375 3 0.0 # c204 SS AUE=0.8032 RMSE=0.9405 TorType=3 - dihedral_coeff @dihedral:c3-p4-n3-c3 fourier 1 1.778 2 180.0 # c121 SS AUE=1.1246 RMSE=1.4091 TorType=3 - dihedral_coeff @dihedral:c3-p4-n4-hn fourier 1 0.005 3 0.0 # c135 SS AUE=0.2627 RMSE=0.3254 TorType=3 - dihedral_coeff @dihedral:c3-p4-na-cc fourier 2 1.0 3 0.0 0.64 2 180.0 # c148 GA AUE=0.9954 RMSE=1.1119 TorType=3 - dihedral_coeff @dihedral:c3-p4-nh-c2 fourier 1 0.9 1 0.0 # set3_16 SS AUE=1.0315 RMSE=1.1976 TorType=3 - dihedral_coeff @dihedral:c3-p4-nh-ca fourier 2 0.0 3 180.0 0.84 2 180.0 # c160 GA AUE=1.0676 RMSE=1.4622 TorType=3 - dihedral_coeff @dihedral:c3-p4-os-c3 fourier 1 0.6 2 180.0 # c190 SS AUE=0.5663 RMSE=0.6640 TorType=3 - dihedral_coeff @dihedral:c3-p4-p3-c3 fourier 1 1.4 1 0.0 # c205 SS AUE=0.7593 RMSE=0.9141 TorType=3 - dihedral_coeff @dihedral:c3-px-ca-ca fourier 1 0.432 2 180.0 # c73 SS AUE=0.4755 RMSE=0.6108 TorType=3 - dihedral_coeff @dihedral:c3-px-c-c3 fourier 2 0.0 2 0.0 0.58 1 180.0 # c16 GA AUE=1.0361 RMSE=1.3175 TorType=3 - dihedral_coeff @dihedral:c3-px-ce-c2 fourier 1 1.13 2 0.0 # c36 SS AUE=1.2444 RMSE=1.6024 TorType=3 - dihedral_coeff @dihedral:c3-px-ce-c3 fourier 1 0.81 2 180.0 # set1_16 SS AUE=0.9969 RMSE=1.2788 TorType=3 - dihedral_coeff @dihedral:c3-px-ne-c2 fourier 2 0.61 3 0.0 1.44 1 0.0 # c106 GA AUE=1.6606 RMSE=2.1207 TorType=3 - dihedral_coeff @dihedral:c3-px-pe-c2 fourier 1 1.565 2 0.0 # c198 SS AUE=1.0967 RMSE=1.2917 TorType=3 - dihedral_coeff @dihedral:c3-s4-c3-h1 fourier 1 0.117 3 0.0 # c59 SS AUE=0.2210 RMSE=0.2792 TorType=3 - dihedral_coeff @dihedral:c3-s4-n3-c3 fourier 1 3.1 2 0.0 # c125 SS AUE=1.3654 RMSE=1.8896 TorType=3 - dihedral_coeff @dihedral:c3-s4-n4-c3 fourier 1 0.2 3 0.0 # c139 SS AUE=0.7713 RMSE=0.9400 TorType=3 - dihedral_coeff @dihedral:c3-s4-na-cc fourier 1 0.55 2 0.0 # c152 SS AUE=0.5159 RMSE=0.7408 TorType=3 - dihedral_coeff @dihedral:c3-s4-nh-c2 fourier 3 0.235 2 180.0 0.5 3 0.0 1.302 1 0.0 # set3_20 GA AUE=1.5742 RMSE=1.9736 TorType=3 - dihedral_coeff @dihedral:c3-s4-no-o fourier 1 1.13 2 180.0 # c175 SS AUE=0.7753 RMSE=0.8760 TorType=3 - dihedral_coeff @dihedral:c3-s4-oh-ho fourier 1 0.0 1 180.0 # c185 SS AUE=1.7272 RMSE=2.1061 TorType=3 - dihedral_coeff @dihedral:c3-s4-os-c3 fourier 1 1.31 1 180.0 # c194 SS AUE=0.9618 RMSE=1.1506 TorType=3 - dihedral_coeff @dihedral:c3-s4-p3-c3 fourier 1 2.22 2 0.0 # c209 SS AUE=1.9189 RMSE=2.5861 TorType=3 - dihedral_coeff @dihedral:c3-s4-sh-hs fourier 2 0.0 3 0.0 0.56 2 180.0 # c224 GA AUE=1.1511 RMSE=1.3863 TorType=3 - dihedral_coeff @dihedral:c3-s4-ss-c3 fourier 1 0.05 3 0.0 # c227 SS AUE=0.7707 RMSE=0.9378 TorType=3 - dihedral_coeff @dihedral:c3-s6-c3-h1 fourier 1 0.089 3 0.0 # c60 SS AUE=0.0648 RMSE=0.0808 TorType=3 - dihedral_coeff @dihedral:c3-s6-n3-c3 fourier 1 3.61 2 0.0 # c126 SS AUE=1.8933 RMSE=2.6424 TorType=3 - dihedral_coeff @dihedral:c3-s6-n4-c3 fourier 1 1.47 1 0.0 # c140 SS AUE=0.2994 RMSE=0.3260 TorType=3 - dihedral_coeff @dihedral:c3-s6-na-cc fourier 1 3.938 2 180.0 # c153 SS AUE=0.8118 RMSE=1.0393 TorType=3 - dihedral_coeff @dihedral:c3-s6-n-c fourier 1 0.768 2 180.0 # c95 SS AUE=0.4645 RMSE=0.6488 TorType=3 - dihedral_coeff @dihedral:c3-s6-nh-c2 fourier 1 0.667 2 0.0 # set3_21 SS AUE=1.6191 RMSE=2.2150 TorType=3 - dihedral_coeff @dihedral:c3-s6-no-o fourier 1 0.348 2 0.0 # c176 SS AUE=0.2701 RMSE=0.3306 TorType=3 - dihedral_coeff @dihedral:c3-s6-oh-ho fourier 1 11.69 1 180.0 # c186 SS AUE=0.6401 RMSE=0.8081 TorType=3 - dihedral_coeff @dihedral:c3-s6-os-c3 fourier 1 0.533 2 180.0 # c195 SS AUE=0.9691 RMSE=1.1571 TorType=3 - dihedral_coeff @dihedral:c3-s6-p3-c3 fourier 1 0.183 3 0.0 # c210 SS AUE=0.5556 RMSE=0.6476 TorType=3 - dihedral_coeff @dihedral:c3-s6-sh-hs fourier 1 4.317 2 180.0 # c225 SS AUE=1.0170 RMSE=1.0970 TorType=3 - dihedral_coeff @dihedral:c3-s6-ss-c3 fourier 1 2.4 2 180.0 # c228 SS AUE=0.8201 RMSE=1.0146 TorType=3 - dihedral_coeff @dihedral:c3-ss-c2-c3 fourier 1 2.025 2 180.0 # set1_19 SS AUE=0.5269 RMSE=0.6098 TorType=3 - dihedral_coeff @dihedral:c3-ss-c3-c3 fourier 1 0.167 3 0.0 # p9 SS AUE=0.4614 RMSE=0.5750 TorType=3 - dihedral_coeff @dihedral:c3-ss-c3-h1 fourier 1 0.22 3 0.0 # c58 SS AUE=0.2551 RMSE=0.3303 TorType=3 - dihedral_coeff @dihedral:c3-ss-ca-ca fourier 1 0.75 2 180.0 # c76 SS AUE=0.2509 RMSE=0.3297 TorType=3 - dihedral_coeff @dihedral:c3-ss-n2-c2 fourier 2 1.35 2 180.0 1.38 1 180.0 # c109 GA AUE=0.6324 RMSE=0.7825 TorType=3 - dihedral_coeff @dihedral:c3-ss-n3-c3 fourier 1 2.68 2 0.0 # c124 SS AUE=1.0072 RMSE=1.2488 TorType=3 - dihedral_coeff @dihedral:c3-ss-n4-c3 fourier 1 0.39 3 0.0 # c138 SS AUE=0.3868 RMSE=0.4909 TorType=3 - dihedral_coeff @dihedral:c3-ss-n-c fourier 1 0.5 2 0.0 # c93 SS AUE=0.5560 RMSE=0.7560 TorType=3 - dihedral_coeff @dihedral:c3-ss-nh-c2 fourier 1 1.1 2 0.0 # set3_19 SS AUE=0.9372 RMSE=1.1240 TorType=3 - dihedral_coeff @dihedral:c3-ss-no-o fourier 1 2.295 2 180.0 # c174 SS AUE=0.3406 RMSE=0.3839 TorType=3 - dihedral_coeff @dihedral:c3-ss-oh-ho fourier 1 2.13 2 0.0 # c184 SS AUE=0.2806 RMSE=0.3277 TorType=3 - dihedral_coeff @dihedral:c3-ss-os-c3 fourier 1 1.74 2 0.0 # c193 SS AUE=0.5504 RMSE=0.6616 TorType=3 - dihedral_coeff @dihedral:c3-ss-p2-c2 fourier 1 2.97 2 180.0 # c201 SS AUE=0.8463 RMSE=1.2678 TorType=3 - dihedral_coeff @dihedral:c3-ss-p3-c3 fourier 1 3.75 2 0.0 # c208 SS AUE=0.5096 RMSE=0.5972 TorType=3 - dihedral_coeff @dihedral:c3-ss-p4-c3 fourier 1 0.57 2 180.0 # c214 SS AUE=0.7214 RMSE=0.9325 TorType=3 - dihedral_coeff @dihedral:c3-sx-ca-ca fourier 1 0.64 2 0.0 # c77 SS AUE=0.6566 RMSE=0.8245 TorType=3 - dihedral_coeff @dihedral:c3-sx-ce-c2 fourier 2 1.46 2 0.0 1.5 3 180.0 # c40 GA AUE=1.8189 RMSE=2.2140 TorType=3 - dihedral_coeff @dihedral:c3-sx-ce-c3 fourier 3 1.5 3 0.0 4.16 2 0.0 3.1 1 180.0 # set1_20 GA AUE=2.1436 RMSE=3.2053 TorType=3 - dihedral_coeff @dihedral:c3-sx-ne-c2 fourier 2 1.0 3 180.0 1.9 1 180.0 # c110 GA AUE=1.5150 RMSE=1.7663 TorType=3 - dihedral_coeff @dihedral:c3-sx-pe-c2 fourier 1 4.19 2 0.0 # c202 SS AUE=2.6033 RMSE=3.2866 TorType=3 - dihedral_coeff @dihedral:c3-sx-px-c3 fourier 1 2.67 1 0.0 # c215 SS AUE=0.8306 RMSE=1.0179 TorType=3 - dihedral_coeff @dihedral:c3-sx-sx-c3 fourier 1 2.92 1 0.0 # c229 SS AUE=2.7179 RMSE=3.6787 TorType=3 - dihedral_coeff @dihedral:c3-sx-sy-c3 fourier 1 4.94 2 180.0 # c230 SS AUE=1.7022 RMSE=1.9951 TorType=3 - dihedral_coeff @dihedral:c3-sy-ca-ca fourier 1 1.22 2 180.0 # c78 SS AUE=0.2941 RMSE=0.3313 TorType=3 - dihedral_coeff @dihedral:c3-sy-ce-c2 fourier 1 0.935 2 180.0 # c41 SS AUE=0.9708 RMSE=1.2822 TorType=3 - dihedral_coeff @dihedral:c3-sy-ce-c3 fourier 3 0.64 3 0.0 0.333 2 180.0 1.04 1 180.0 # set1_21 GA AUE=0.6383 RMSE=0.7388 TorType=3 - dihedral_coeff @dihedral:c3-sy-ne-c2 fourier 2 0.34 3 180.0 7.467 1 180.0 # c111 GA AUE=0.2248 RMSE=0.3231 TorType=3 - dihedral_coeff @dihedral:c3-sy-pe-c2 fourier 1 0.237 3 180.0 # c203 SS AUE=0.3743 RMSE=0.4294 TorType=3 - dihedral_coeff @dihedral:c3-sy-px-c3 fourier 1 0.062 3 0.0 # c216 SS AUE=0.6353 RMSE=0.7537 TorType=3 - dihedral_coeff @dihedral:c3-sy-sy-c3 fourier 1 0.378 2 0.0 # c231 SS AUE=1.1799 RMSE=1.3634 TorType=3 - dihedral_coeff @dihedral:ca-c3-c3-c fourier 1 0.1 3 0.0 # p22 SS AUE=0.8008 RMSE=1.0051 TorType=3 - dihedral_coeff @dihedral:ca-c3-c3-n fourier 1 0.21 3 0.0 # p16 SS AUE=0.6330 RMSE=0.8053 TorType=3 - dihedral_coeff @dihedral:ca-ca-c3-ca fourier 1 0.0 2 180.0 # t1 SS AUE=0.1988 RMSE=0.2606 TorType=3 - dihedral_coeff @dihedral:ca-ca-ce-c2 fourier 1 0.618 2 180.0 # c24 SS AUE=0.2364 RMSE=0.3330 TorType=3 - dihedral_coeff @dihedral:ca-ca-ce-c3 fourier 1 0.54 2 180.0 # set1_4 SS AUE=0.2602 RMSE=0.3333 TorType=3 - dihedral_coeff @dihedral:ca-ca-os-c fourier 1 0.65 2 180.0 # t35b SS AUE=0.2491 RMSE=0.3333 TorType=3 - dihedral_coeff @dihedral:ca-cf-ce-ca fourier 1 8.51 2 180.0 # add6b SS AUE=4.0000 RMSE=5.4296 TorType=3 - dihedral_coeff @dihedral:ca-c-os-c3 fourier 1 2.685 2 180.0 # t36b SS AUE=1.2217 RMSE=1.4489 TorType=3 - dihedral_coeff @dihedral:ca-cp-cp-ca fourier 1 0.795 2 180.0 # c61 SS AUE=0.2914 RMSE=0.3303 TorType=3 - dihedral_coeff @dihedral:ca-nh-c2-c2 fourier 1 1.92 1 180.0 # c30 SS AUE=0.8599 RMSE=1.1406 TorType=3 - dihedral_coeff @dihedral:ca-nh-n2-c2 fourier 3 1.37 3 180.0 2.0 2 0.0 0.0 1 180.0 # c100 GA AUE=2.0208 RMSE=2.4869 TorType=3 - dihedral_coeff @dihedral:ca-nh-n4-c3 fourier 1 0.1 3 0.0 # c129 SS AUE=1.1901 RMSE=1.4071 TorType=3 - dihedral_coeff @dihedral:ca-nh-na-cd fourier 1 0.7 2 0.0 # c142 SS AUE=0.5118 RMSE=0.8838 TorType=3 - dihedral_coeff @dihedral:ca-nh-n-c fourier 1 0.605 2 0.0 # c84 SS AUE=1.2184 RMSE=1.3197 TorType=3 - dihedral_coeff @dihedral:ca-nh-nh-c2 fourier 1 1.49 3 0.0 # set3_10 SS AUE=2.7548 RMSE=3.5233 TorType=3 - dihedral_coeff @dihedral:ca-nh-nh-ca fourier 1 4.59 1 0.0 # c154 SS AUE=3.6427 RMSE=5.6136 TorType=3 - dihedral_coeff @dihedral:ca-nh-no-o fourier 1 0.62 2 180.0 # c155 SS AUE=1.3263 RMSE=1.9039 TorType=3 - dihedral_coeff @dihedral:ca-nh-p3-c3 fourier 2 1.94 2 180.0 0.54 3 0.0 # c159 GA AUE=0.8724 RMSE=1.1678 TorType=3 - dihedral_coeff @dihedral:ca-nh-p5-os fourier 1 0.467 2 0.0 # c161 SS AUE=0.8323 RMSE=0.9798 TorType=3 - dihedral_coeff @dihedral:ca-nh-s4-c3 fourier 2 1.245 2 0.0 0.225 3 0.0 # c164 GA AUE=1.5450 RMSE=1.8592 TorType=3 - dihedral_coeff @dihedral:ca-nh-s6-c3 fourier 1 1.93 3 0.0 # c165 SS AUE=0.7711 RMSE=0.9257 TorType=3 - dihedral_coeff @dihedral:ca-nh-ss-c3 fourier 2 1.29 2 180.0 1.19 1 180.0 # c163 GA AUE=0.9564 RMSE=1.5597 TorType=3 - dihedral_coeff @dihedral:ca-nh-sy-ca fourier 2 0.1 2 180.0 0.99 3 0.0 # add6a SS AUE=0.6854 RMSE=0.9512 TorType=3 - dihedral_coeff @dihedral:ca-os-c-o fourier 1 1.275 2 180.0 # t35a SS AUE=1.2481 RMSE=1.5211 TorType=3 - dihedral_coeff @dihedral:c-c3-c3-n fourier 1 0.21 3 0.0 # p26 SS AUE=1.0437 RMSE=1.3000 TorType=3 - dihedral_coeff @dihedral:c-c3-n-c fourier 2 0.39 2 180.0 0.64 1 0.0 # p18 GA AUE=0.4030 RMSE=0.5768 TorType=3 - dihedral_coeff @dihedral:cc-na-c2-c2 fourier 1 0.728 2 180.0 # c29 SS AUE=0.2592 RMSE=0.3329 TorType=3 - dihedral_coeff @dihedral:cc-na-c2-c3 fourier 1 1.125 2 180.0 # set1_9 SS AUE=0.3784 RMSE=0.4839 TorType=3 - dihedral_coeff @dihedral:cc-na-ca-ca fourier 1 0.603 2 180.0 # c66 SS AUE=0.2705 RMSE=0.3328 TorType=3 - dihedral_coeff @dihedral:cc-na-na-cd fourier 1 0.4 2 0.0 # c141 SS AUE=0.5320 RMSE=0.6402 TorType=3 - dihedral_coeff @dihedral:cc-na-nh-c2 fourier 1 0.7 2 0.0 # set3_9 SS AUE=0.7727 RMSE=0.9375 TorType=3 - dihedral_coeff @dihedral:cc-n-c-c3 fourier 1 0.5 2 180.0 # set2_9 SS AUE=0.2224 RMSE=0.3240 TorType=3 - dihedral_coeff @dihedral:cd-cc-c3-c3 fourier 1 0.157 3 180.0 # p1 SS AUE=0.2727 RMSE=0.3320 TorType=3 - dihedral_coeff @dihedral:cd-na-c3-na fourier 1 0.023 2 0.0 # t16 SS AUE=0.2606 RMSE=0.3332 TorType=3 - dihedral_coeff @dihedral:c-n-c2-c3 fourier 1 1.51 1 180.0 # set1_5 SS AUE=0.6699 RMSE=0.8754 TorType=3 - dihedral_coeff @dihedral:c-n-c3-n fourier 1 2.08 2 0.0 # t17 SS AUE=0.8425 RMSE=1.0798 TorType=3 - dihedral_coeff @dihedral:c-n-ca-ca fourier 1 0.95 2 180.0 # c62 SS AUE=0.8788 RMSE=0.9694 TorType=3 - dihedral_coeff @dihedral:c-n-n-c fourier 2 3.0 2 180.0 2.49 1 0.0 # c79 GA AUE=1.1290 RMSE=1.3734 TorType=3 - dihedral_coeff @dihedral:c-n-nh-c2 fourier 1 0.6 2 0.0 # set3_5 SS AUE=0.7968 RMSE=0.8909 TorType=3 - dihedral_coeff @dihedral:c-os-c-c3 fourier 1 1.98 1 180.0 # set3_29 SS AUE=0.2568 RMSE=0.3303 TorType=3 - dihedral_coeff @dihedral:cz-nh-c3-c3 fourier 1 0.248 2 180.0 # p11 SS AUE=0.2819 RMSE=0.3532 TorType=3 - dihedral_coeff @dihedral:h1-c3-n2-c2 fourier 1 0.165 3 180.0 # c45 SS AUE=0.6984 RMSE=0.9045 TorType=3 - dihedral_coeff @dihedral:h1-c3-n3-c3 fourier 1 0.225 3 0.0 # c46 SS AUE=0.2936 RMSE=0.3481 TorType=3 - dihedral_coeff @dihedral:h1-c3-na-cc fourier 1 0.0 2 180.0 # c48 SS AUE=0.0685 RMSE=0.0813 TorType=3 - dihedral_coeff @dihedral:h1-c3-n-c fourier 1 0.0 2 180.0 # c44 SS AUE=0.1670 RMSE=0.1874 TorType=3 - dihedral_coeff @dihedral:h1-c3-nh-ca fourier 1 0.332 2 0.0 # c49 SS AUE=1.0901 RMSE=1.3252 TorType=3 - dihedral_coeff @dihedral:h1-c3-no-o fourier 1 0.0 2 180.0 # c50 SS AUE=0.0210 RMSE=0.0225 TorType=3 - dihedral_coeff @dihedral:h1-c3-os-p5 fourier 1 0.217 3 0.0 # c56 SS AUE=0.3987 RMSE=0.4985 TorType=3 - dihedral_coeff @dihedral:hc-c3-c2-c3 fourier 1 0.31 2 0.0 # set1_3 SS AUE=0.6796 RMSE=0.8466 TorType=3 - dihedral_coeff @dihedral:hc-c3-c3-i fourier 1 0.21 3 0.0 # m6 SS AUE=0.3234 RMSE=0.3857 TorType=3 - dihedral_coeff @dihedral:hc-c3-c3-n3 fourier 1 0.1 3 0.0 # m12 SS AUE=0.1396 RMSE=0.1646 TorType=3 - dihedral_coeff @dihedral:hc-c3-ca-ca fourier 1 0.0 2 180.0 # c43 SS AUE=0.0203 RMSE=0.0347 TorType=3 - dihedral_coeff @dihedral:hc-c3-p2-c2 fourier 1 0.933 2 180.0 # c53 SS AUE=0.3657 RMSE=0.4529 TorType=3 - dihedral_coeff @dihedral:hc-c3-p3-c3 fourier 1 0.145 3 0.0 # c54 SS AUE=0.2605 RMSE=0.3289 TorType=3 - dihedral_coeff @dihedral:hc-c3-p4-c3 fourier 1 0.05 3 0.0 # c55 SS AUE=0.1589 RMSE=0.2005 TorType=3 - dihedral_coeff @dihedral:hn-n3-c3-c3 fourier 1 0.217 3 0.0 # m20 SS AUE=0.7039 RMSE=0.8271 TorType=3 - dihedral_coeff @dihedral:hn-n4-c2-c2 fourier 1 0.082 3 180.0 # c28 SS AUE=0.6341 RMSE=0.7948 TorType=3 - dihedral_coeff @dihedral:hn-n4-c2-c3 fourier 1 0.087 3 0.0 # set1_8 SS AUE=0.2828 RMSE=0.3296 TorType=3 - dihedral_coeff @dihedral:hn-n4-c3-hx fourier 1 0.109 3 0.0 # c47 SS AUE=0.2716 RMSE=0.3296 TorType=3 - dihedral_coeff @dihedral:hn-n4-n2-c2 fourier 1 8.663 2 180.0 # c98 SS AUE=0.3876 RMSE=0.4783 TorType=3 - dihedral_coeff @dihedral:hn-n4-n3-c3 fourier 1 0.188 3 0.0 # c113 SS AUE=0.3464 RMSE=0.4155 TorType=3 - dihedral_coeff @dihedral:hn-n4-na-cd fourier 1 0.15 3 0.0 # c128 SS AUE=0.1276 RMSE=0.1509 TorType=3 - dihedral_coeff @dihedral:hn-n4-n-c fourier 1 1.445 2 0.0 # c82 SS AUE=0.4066 RMSE=0.5885 TorType=3 - dihedral_coeff @dihedral:hn-n4-nh-c2 fourier 1 0.213 3 0.0 # set3_8 SS AUE=0.2620 RMSE=0.3316 TorType=3 - dihedral_coeff @dihedral:hn-nh-na-cd fourier 1 0.802 2 0.0 # c114 SS AUE=0.2869 RMSE=0.3676 TorType=3 - dihedral_coeff @dihedral:ho-oh-c2-c2 fourier 1 1.12 2 180.0 # c32 SS AUE=0.2661 RMSE=0.3303 TorType=3 - dihedral_coeff @dihedral:ho-oh-c2-c3 fourier 1 1.51 1 180.0 # set1_12 SS AUE=1.5331 RMSE=1.7625 TorType=3 - dihedral_coeff @dihedral:ho-oh-c3-h1 fourier 1 0.113 3 0.0 # c51 SS AUE=0.2631 RMSE=0.3230 TorType=3 - dihedral_coeff @dihedral:ho-oh-ca-ca fourier 1 0.835 2 180.0 # c69 SS AUE=0.2718 RMSE=0.3256 TorType=3 - dihedral_coeff @dihedral:ho-oh-n2-c2 fourier 1 2.37 2 180.0 # c102 SS AUE=0.3163 RMSE=0.3944 TorType=3 - dihedral_coeff @dihedral:ho-oh-n3-c3 fourier 1 1.23 2 0.0 # c117 SS AUE=0.7804 RMSE=0.9479 TorType=3 - dihedral_coeff @dihedral:ho-oh-n4-c3 fourier 1 0.34 3 0.0 # c131 SS AUE=0.4375 RMSE=0.5350 TorType=3 - dihedral_coeff @dihedral:ho-oh-na-cc fourier 1 0.44 2 0.0 # c144 SS AUE=0.2865 RMSE=0.3255 TorType=3 - dihedral_coeff @dihedral:ho-oh-nh-c2 fourier 1 0.85 2 0.0 # set3_12 SS AUE=0.6311 RMSE=0.7217 TorType=3 - dihedral_coeff @dihedral:ho-oh-no-o fourier 1 1.36 2 180.0 # c167 SS AUE=0.2872 RMSE=0.3226 TorType=3 - dihedral_coeff @dihedral:ho-oh-oh-ho fourier 1 1.21 2 0.0 # c177 SS AUE=0.6716 RMSE=0.7402 TorType=3 - dihedral_coeff @dihedral:ho-oh-p2-c2 fourier 1 1.41 2 180.0 # c179 SS AUE=0.6083 RMSE=0.8611 TorType=3 - dihedral_coeff @dihedral:ho-oh-p4-c3 fourier 1 0.83 1 180.0 # c181 SS AUE=0.8966 RMSE=1.0772 TorType=3 - dihedral_coeff @dihedral:ho-oh-p5-o fourier 1 0.367 3 0.0 # c182 SS AUE=0.8891 RMSE=1.0397 TorType=3 - dihedral_coeff @dihedral:hs-sh-c2-c2 fourier 1 0.64 2 180.0 # c38 SS AUE=0.5356 RMSE=0.6146 TorType=3 - dihedral_coeff @dihedral:hs-sh-c2-c3 fourier 1 1.46 1 180.0 # set1_18 SS AUE=1.6292 RMSE=1.8635 TorType=3 - dihedral_coeff @dihedral:hs-sh-c3-h1 fourier 1 0.143 3 0.0 # c57 SS AUE=0.2676 RMSE=0.3251 TorType=3 - dihedral_coeff @dihedral:hs-sh-ca-ca fourier 1 0.105 2 180.0 # c75 SS AUE=0.2588 RMSE=0.3299 TorType=3 - dihedral_coeff @dihedral:hs-sh-n2-c2 fourier 1 1.91 2 180.0 # c108 SS AUE=0.5066 RMSE=0.9568 TorType=3 - dihedral_coeff @dihedral:hs-sh-n3-c3 fourier 1 3.34 2 0.0 # c123 SS AUE=1.0521 RMSE=1.3809 TorType=3 - dihedral_coeff @dihedral:hs-sh-n4-c3 fourier 1 0.5 3 0.0 # c137 SS AUE=1.0514 RMSE=1.3202 TorType=3 - dihedral_coeff @dihedral:hs-sh-na-cc fourier 1 1.255 2 0.0 # c150 SS AUE=0.2920 RMSE=0.3622 TorType=3 - dihedral_coeff @dihedral:hs-sh-nh-c2 fourier 1 0.795 2 0.0 # set3_18 SS AUE=1.0130 RMSE=1.2554 TorType=3 - dihedral_coeff @dihedral:hs-sh-no-o fourier 1 1.3 2 180.0 # c173 SS AUE=0.2229 RMSE=0.2551 TorType=3 - dihedral_coeff @dihedral:hs-sh-oh-ho fourier 1 2.01 2 0.0 # c183 SS AUE=0.2853 RMSE=0.3308 TorType=3 - dihedral_coeff @dihedral:hs-sh-os-c3 fourier 1 1.85 2 0.0 # c192 SS AUE=0.4441 RMSE=0.5536 TorType=3 - dihedral_coeff @dihedral:hs-sh-p2-c2 fourier 1 0.89 2 180.0 # c200 SS AUE=0.2562 RMSE=0.3521 TorType=3 - dihedral_coeff @dihedral:hs-sh-p3-c3 fourier 1 3.6 2 0.0 # c207 SS AUE=0.5012 RMSE=0.6062 TorType=3 - dihedral_coeff @dihedral:hs-sh-p4-c3 fourier 1 0.585 1 180.0 # c213 SS AUE=1.2130 RMSE=1.4705 TorType=3 - dihedral_coeff @dihedral:hs-sh-p5-os fourier 2 2.89 2 0.0 1.29 1 0.0 # c218 GA AUE=0.8635 RMSE=1.2959 TorType=3 - dihedral_coeff @dihedral:hs-sh-sh-hs fourier 1 2.64 2 0.0 # c222 SS AUE=0.2962 RMSE=0.3759 TorType=3 - dihedral_coeff @dihedral:n2-c2-c3-c2 fourier 1 0.558 2 180.0 # t9 SS AUE=0.7685 RMSE=0.9760 TorType=3 - dihedral_coeff @dihedral:n3-c3-c3-c3 fourier 1 0.21 3 0.0 # p8 SS AUE=0.4096 RMSE=0.5005 TorType=3 - dihedral_coeff @dihedral:n3-c3-c3-ca fourier 1 0.1 3 0.0 # m16 SS AUE=0.8325 RMSE=1.0411 TorType=3 - dihedral_coeff @dihedral:n3-c3-n3-hn fourier 1 1.75 2 0.0 # t13 SS AUE=0.6939 RMSE=0.8306 TorType=3 - dihedral_coeff @dihedral:n4-c3-c3-c3 fourier 1 0.21 3 0.0 # p12 SS AUE=0.5399 RMSE=0.6216 TorType=3 - dihedral_coeff @dihedral:n4-c3-n4-hn fourier 1 0.1 3 0.0 # t26 SS AUE=0.0245 RMSE=0.0373 TorType=3 - dihedral_coeff @dihedral:n-c3-c3-c3 fourier 1 0.1 3 0.0 # p23 SS AUE=0.2641 RMSE=0.3317 TorType=3 - dihedral_coeff @dihedral:nh-c3-c3-c3 fourier 1 0.21 3 0.0 # p13 SS AUE=0.8361 RMSE=0.9491 TorType=3 - dihedral_coeff @dihedral:o-c-c3-c3 fourier 1 0.27 2 180.0 # p14 SS AUE=0.2361 RMSE=0.3321 TorType=3 - dihedral_coeff @dihedral:oh-c3-c3-c3 fourier 1 0.21 3 0.0 # p7 SS AUE=0.6517 RMSE=0.7713 TorType=3 - dihedral_coeff @dihedral:oh-c3-c3-c fourier 1 0.21 3 0.0 # p25 SS AUE=0.3653 RMSE=0.6406 TorType=3 - dihedral_coeff @dihedral:oh-c3-c3-n fourier 1 0.101 3 0.0 # p24 SS AUE=0.9998 RMSE=1.2475 TorType=3 - dihedral_coeff @dihedral:oh-c3-oh-ho fourier 1 1.57 2 0.0 # t11 SS AUE=0.6180 RMSE=0.8544 TorType=3 - dihedral_coeff @dihedral:o-no-c2-c2 fourier 1 0.398 2 180.0 # c31 SS AUE=0.2143 RMSE=0.3292 TorType=3 - dihedral_coeff @dihedral:o-no-c2-c3 fourier 1 0.66 2 180.0 # set1_11 SS AUE=0.2915 RMSE=0.3323 TorType=3 - dihedral_coeff @dihedral:o-no-c3-no fourier 1 5.02 2 180.0 # t15 SS AUE=0.7609 RMSE=0.9238 TorType=3 - dihedral_coeff @dihedral:o-no-ca-ca fourier 1 0.7 2 180.0 # c68 SS AUE=0.2638 RMSE=0.3293 TorType=3 - dihedral_coeff @dihedral:o-no-cd-cc fourier 1 1.075 2 180.0 # add6e SS AUE=0.2138 RMSE=0.3290 TorType=3 - dihedral_coeff @dihedral:o-no-n2-c2 fourier 1 1.03 2 180.0 # c101 SS AUE=0.3306 RMSE=0.4189 TorType=3 - dihedral_coeff @dihedral:o-no-n3-c3 fourier 1 2.17 2 180.0 # c116 SS AUE=2.5004 RMSE=3.2115 TorType=3 - dihedral_coeff @dihedral:o-no-n4-c3 fourier 1 1.25 2 180.0 # c130 SS AUE=0.1901 RMSE=0.4144 TorType=3 - dihedral_coeff @dihedral:o-no-na-cc fourier 1 1.09 2 180.0 # c143 SS AUE=0.5033 RMSE=0.6912 TorType=3 - dihedral_coeff @dihedral:o-no-nh-c2 fourier 1 0.0 2 180.0 # set3_11 SS AUE=2.0620 RMSE=2.8356 TorType=3 - dihedral_coeff @dihedral:o-no-no-o fourier 2 0.15 4 180.0 1.45 2 180.0 # c166 GA AUE=0.3903 RMSE=0.4419 TorType=3 - dihedral_coeff @dihedral:o-no-p2-c2 fourier 1 0.99 2 180.0 # c169 SS AUE=0.2765 RMSE=0.3321 TorType=3 - dihedral_coeff @dihedral:o-no-p4-c3 fourier 1 0.502 2 180.0 # c171 SS AUE=0.3449 RMSE=0.3960 TorType=3 - dihedral_coeff @dihedral:o-py-ne-c2 fourier 2 0.9 3 180.0 2.46 1 0.0 # c107 GA AUE=0.4990 RMSE=0.6000 TorType=3 - dihedral_coeff @dihedral:o-s4-c3-s4 fourier 1 1.34 1 180.0 # t25 SS AUE=1.1411 RMSE=1.4982 TorType=3 - dihedral_coeff @dihedral:o-s6-c3-s6 fourier 1 0.092 3 0.0 # t24 SS AUE=0.4257 RMSE=0.4949 TorType=3 - dihedral_coeff @dihedral:os-c-c3-c fourier 2 2.0 2 180.0 1.85 1 180.0 # t42 GA AUE=0.4321 RMSE=0.5299 TorType=3 - dihedral_coeff @dihedral:os-p3-os-c3 fourier 1 2.04 2 0.0 # c189 SS AUE=1.0926 RMSE=1.3514 TorType=3 - dihedral_coeff @dihedral:os-p5-n3-c3 fourier 1 5.0 2 180.0 # c122 SS AUE=2.8241 RMSE=3.6042 TorType=3 - dihedral_coeff @dihedral:os-p5-n4-c3 fourier 1 0.143 3 0.0 # c136 SS AUE=0.4630 RMSE=0.6433 TorType=3 - dihedral_coeff @dihedral:os-p5-na-cc fourier 1 2.18 2 180.0 # c149 SS AUE=0.6556 RMSE=0.9113 TorType=3 - dihedral_coeff @dihedral:os-p5-nh-c2 fourier 1 0.5 2 0.0 # set3_17 SS AUE=0.9578 RMSE=1.1771 TorType=3 - dihedral_coeff @dihedral:os-p5-no-o fourier 2 2.733 2 0.0 0.317 3 0.0 # c172 GA AUE=0.6484 RMSE=0.8206 TorType=3 - dihedral_coeff @dihedral:os-p5-p3-c3 fourier 1 2.005 2 180.0 # c206 SS AUE=1.1482 RMSE=1.4324 TorType=3 - dihedral_coeff @dihedral:os-p5-ss-c3 fourier 1 4.467 2 180.0 # c219 SS AUE=0.9050 RMSE=1.1227 TorType=3 - dihedral_coeff @dihedral:os-py-ca-ca fourier 1 1.8 2 180.0 # c74 SS AUE=0.8528 RMSE=1.0796 TorType=3 - dihedral_coeff @dihedral:os-py-ce-c2 fourier 1 1.767 2 180.0 # c37 SS AUE=0.8275 RMSE=1.0644 TorType=3 - dihedral_coeff @dihedral:os-py-ce-c3 fourier 1 4.2 2 180.0 # set1_17 SS AUE=0.9222 RMSE=1.1571 TorType=3 - dihedral_coeff @dihedral:os-py-pe-c2 fourier 1 2.567 1 0.0 # c199 SS AUE=0.6931 RMSE=0.8807 TorType=3 - dihedral_coeff @dihedral:os-py-py-c3 fourier 1 0.386 2 0.0 # c212 SS AUE=0.6618 RMSE=0.8385 TorType=3 - dihedral_coeff @dihedral:os-py-py-os fourier 1 0.387 2 0.0 # c217 SS AUE=0.6636 RMSE=1.0913 TorType=3 - dihedral_coeff @dihedral:os-py-sx-c3 fourier 1 0.348 3 0.0 # c220 SS AUE=0.6436 RMSE=0.8137 TorType=3 - dihedral_coeff @dihedral:os-py-sy-c3 fourier 2 2.86 2 0.0 0.38 1 0.0 # c221 GA AUE=1.1694 RMSE=1.4143 TorType=3 - dihedral_coeff @dihedral:p3-c3-p3-hp fourier 1 0.215 3 0.0 # t19 SS AUE=1.0811 RMSE=1.2418 TorType=3 - dihedral_coeff @dihedral:s-c-c3-c fourier 1 0.332 2 180.0 # t10 SS AUE=0.9021 RMSE=1.2368 TorType=3 - dihedral_coeff @dihedral:sh-c3-c3-n fourier 1 0.21 3 0.0 # p4 SS AUE=1.1296 RMSE=1.3941 TorType=3 - dihedral_coeff @dihedral:sh-c3-sh-hs fourier 1 0.083 3 0.0 # t22 SS AUE=0.4554 RMSE=0.5406 TorType=3 - dihedral_coeff @dihedral:ss-c3-ss-c3 fourier 1 0.497 3 0.0 # t23 SS AUE=0.5714 RMSE=0.8553 TorType=3 - dihedral_coeff @dihedral:c3-c3-ca-ca fourier 1 0.245 2 180.0 # m15,m17 SS AUE=0.2499 RMSE=0.3414 TorType=3 - dihedral_coeff @dihedral:c3-c3-c-o fourier 3 0.03 2 180.0 0.55 3 180.0 0.74 1 0.0 # sialic1,t37,t41 GA AUE=0.7374 RMSE=0.9897 TorType=3 - dihedral_coeff @dihedral:c3-c3-os-c3 fourier 3 0.91 3 0.0 1.0 2 0.0 0.0 1 0.0 # lactose1,ccoc GA AUE=1.5236 RMSE=2.4206 TorType=3 - dihedral_coeff @dihedral:ca-ca-c-o fourier 1 0.5225 2 180.0 # phcooh,t36a SS AUE=0.2702 RMSE=0.3317 TorType=3 - dihedral_coeff @dihedral:o-c-c3-c fourier 2 1.36 1 0.0 0.18 3 180.0 # t6,t7,t8 GA AUE=0.3790 RMSE=0.4991 TorType=3 - dihedral_coeff @dihedral:os-c3-c-o fourier 3 0.63 2 180.0 1.0 3 180.0 0.08 1 0.0 # iduronic2,t39,t40 GA AUE=1.0545 RMSE=1.4852 TorType=3 - dihedral_coeff @dihedral:c2-ce-cs-c3 fourier 1 2.18 2 0.0 # set2_2 SS AUE=0.8412 RMSE=1.0280 TorType=3 - dihedral_coeff @dihedral:c2-ce-c-c3 fourier 1 2.97 2 0.0 # c2 SS AUE=0.5377 RMSE=0.6518 TorType=3 - dihedral_coeff @dihedral:c2-ce-ce-c2 fourier 1 0.5 2 180.0 # c232,t3 SS AUE=0.7154 RMSE=0.9564 TorType=3 - dihedral_coeff @dihedral:c2-n-c-c3 fourier 1 0.77 1 180.0 # set3_1 SS AUE=1.1124 RMSE=1.4578 TorType=3 - dihedral_coeff @dihedral:c2-n-cs-c3 fourier 1 2.833 2 180.0 # set3_27 SS AUE=0.3805 RMSE=0.4661 TorType=3 - dihedral_coeff @dihedral:c2-ne-c-c3 fourier 1 2.08 1 180.0 # c6 SS AUE=0.4876 RMSE=0.8222 TorType=3 - dihedral_coeff @dihedral:c2-ne-cs-c3 fourier 1 4.67 1 180.0 # set2_6 SS AUE=1.2531 RMSE=1.5945 TorType=3 - dihedral_coeff @dihedral:c2-pe-c-c3 fourier 1 1.75 1 180.0 # c14 SS AUE=1.0447 RMSE=1.2490 TorType=3 - dihedral_coeff @dihedral:c2-pe-cs-c3 fourier 1 2.96 1 180.0 # set2_14 SS AUE=0.8598 RMSE=1.0604 TorType=3 - dihedral_coeff @dihedral:c3-cs-cs-c3 fourier 1 0.455 2 180.0 # set3_23 SS AUE=0.7278 RMSE=1.0389 TorType=3 - dihedral_coeff @dihedral:c3-c-c-c3 fourier 1 0.512 2 180.0 # c1 SS AUE=0.2443 RMSE=0.3313 TorType=3 - dihedral_coeff @dihedral:c3-c-cs-c3 fourier 1 0.8 2 180.0 # set2_1 SS AUE=1.0068 RMSE=1.3922 TorType=3 - dihedral_coeff @dihedral:c3-c-n-ca fourier 2 0.75 2 180.0 0.5 3 0.0 # c10 GA AUE=1.0418 RMSE=1.1578 TorType=3 - dihedral_coeff @dihedral:c3-cs-n-ca fourier 1 3.913 2 180.0 # set2_10 SS AUE=1.3234 RMSE=1.7703 TorType=3 - dihedral_coeff @dihedral:c3-n7-c3-c3 fourier 2 0.02 3 180.0 0.05 2 0.0 # m13 GA AUE=0.3404 RMSE=0.4405 TorType=3 - dihedral_coeff @dihedral:c3-n3-c3-c3 fourier 2 0.58 3 0.0 0.28 2 180.0 # m14 GA AUE=0.4298 RMSE=0.5205 TorType=3 - dihedral_coeff @dihedral:c3-n-cs-c3 fourier 2 2.0 2 180.0 2.31 1 0.0 # set2_7 GA AUE=0.7571 RMSE=0.9582 TorType=3 - dihedral_coeff @dihedral:c3-nu-ca-ca fourier 1 0.55 2 180.0 # c67 SS AUE=0.5825 RMSE=0.8345 TorType=3 - dihedral_coeff @dihedral:c3-nh-ca-ca fourier 1 0.733 2 180.0 # c64 SS AUE=0.6264 RMSE=0.7797 TorType=3 - dihedral_coeff @dihedral:c3-os-cs-c3 fourier 3 0.12 1 0.0 3.47 2 180.0 0.73 3 0.0 # set2_13 GA AUE=0.2180 RMSE=0.2948 TorType=3 - dihedral_coeff @dihedral:c3-p3-c-c3 fourier 1 1.538 2 180.0 # c15 SS AUE=0.3737 RMSE=0.4391 TorType=3 - dihedral_coeff @dihedral:c3-p3-cs-c3 fourier 1 2.05 2 180.0 # set2_15 SS AUE=0.4669 RMSE=0.6407 TorType=3 - dihedral_coeff @dihedral:c3-ss-c-c3 fourier 1 2.1 2 180.0 # c19 SS AUE=0.9147 RMSE=1.1012 TorType=3 - dihedral_coeff @dihedral:c3-ss-cs-c3 fourier 1 3.585 2 180.0 # set2_19 SS AUE=0.3546 RMSE=0.4561 TorType=3 - dihedral_coeff @dihedral:c3-sx-c-c3 fourier 2 0.95 2 0.0 1.46 1 180.0 # c20 GA AUE=1.4077 RMSE=1.8160 TorType=3 - dihedral_coeff @dihedral:c3-sx-cs-c3 fourier 2 0.0 2 180.0 0.82 1 180.0 # set2_20 GA AUE=1.3014 RMSE=1.5331 TorType=3 - dihedral_coeff @dihedral:c3-sy-cs-c3 fourier 1 0.167 2 0.0 # set2_21 SS AUE=0.4320 RMSE=0.5527 TorType=3 - dihedral_coeff @dihedral:c3-sy-c-c3 fourier 1 0.833 2 0.0 # c21 SS AUE=1.1437 RMSE=1.4496 TorType=3 - dihedral_coeff @dihedral:ca-ca-c-c3 fourier 1 0.552 2 180.0 # c4 SS AUE=0.2254 RMSE=0.3313 TorType=3 - dihedral_coeff @dihedral:ca-ca-cs-c3 fourier 1 0.63 2 180.0 # set2_4 SS AUE=0.2690 RMSE=0.3277 TorType=3 - dihedral_coeff @dihedral:c-c3-c3-c3 fourier 1 0.1 3 0.0 # p15,p21 SS AUE=0.6594 RMSE=0.8092 TorType=3 - dihedral_coeff @dihedral:c-n-cs-c3 fourier 1 0.57 2 0.0 # set2_5 SS AUE=1.0844 RMSE=1.5574 TorType=3 - dihedral_coeff @dihedral:c-n-c-c3 fourier 2 0.0 2 180.0 1.72 1 180.0 # set3_28 GA AUE=1.6503 RMSE=2.2241 TorType=3 - dihedral_coeff @dihedral:hc-c3-c-c3 fourier 1 0.0 2 0.0 # c3 SS AUE=0.0845 RMSE=0.1001 TorType=3 - dihedral_coeff @dihedral:hc-c3-cs-c3 fourier 1 0.665 2 0.0 # set2_3 SS AUE=0.5619 RMSE=0.7242 TorType=3 - dihedral_coeff @dihedral:hn-n4-c-c3 fourier 2 1.025 2 180.0 0.365 4 180.0 # c8 GA AUE=0.2852 RMSE=0.3192 TorType=3 - dihedral_coeff @dihedral:hn-n4-cs-c3 fourier 2 0.95 2 180.0 0.745 4 0.0 # set2_8 GA AUE=0.7027 RMSE=0.8556 TorType=3 - dihedral_coeff @dihedral:ho-oh-c-c3 fourier 1 1.78 2 180.0 # c12 SS AUE=0.3293 RMSE=0.3814 TorType=3 - dihedral_coeff @dihedral:ho-oh-cs-c3 fourier 1 2.92 2 180.0 # set2_12 SS AUE=0.3286 RMSE=0.4081 TorType=3 - dihedral_coeff @dihedral:hs-sh-cs-c3 fourier 2 2.69 2 180.0 1.39 1 180.0 # set2_18 GA AUE=0.2516 RMSE=0.2978 TorType=3 - dihedral_coeff @dihedral:o-n-c-c3 fourier 1 0.37 2 180.0 # c11 SS AUE=0.3392 RMSE=0.4173 TorType=3 - dihedral_coeff @dihedral:o-n-cs-c3 fourier 1 0.52 2 0.0 # set2_11 SS AUE=0.2859 RMSE=0.3263 TorType=3 - dihedral_coeff @dihedral:o-p5-c3-p5 fourier 2 2.59 2 180.0 3.17 1 0.0 # t20 GA AUE=1.4330 RMSE=1.6847 TorType=3 - dihedral_coeff @dihedral:os-py-c-c3 fourier 1 2.37 2 0.0 # c17 SS AUE=1.1966 RMSE=1.4736 TorType=3 - dihedral_coeff @dihedral:os-py-cs-c3 fourier 1 0.5 2 0.0 # set2_17 SS AUE=0.8458 RMSE=1.0943 TorType=3 - } # (end of dihedral_coeffs) - - write_once("Data Dihedrals By Type") { - @dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:* - @dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:* - @dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:* - @dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:* - @dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:* - @dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:* - @dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:* - @dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:* - @dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:* - @dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:* - @dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:* - @dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:* - @dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:* - @dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:* - @dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:* - @dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:* - @dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:* - @dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:* - @dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:* - @dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:* - @dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:* - @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* - @dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:* - @dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:* - @dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:* - @dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:* - @dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:* - @dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:* - @dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:* - @dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:* - @dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:* - @dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:* - @dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:* - @dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:* - @dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:* - @dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:* - @dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:* - @dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:* - @dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:* - @dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:* - @dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:* - @dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:* - @dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:* - @dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:* - @dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:* - @dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:* - @dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:* - @dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:* - @dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:* - @dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:* - @dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:* - @dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:* - @dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:* - @dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:* - @dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:* - @dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:* - @dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:* - @dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:* - @dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:* - @dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:* - @dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:* - @dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:* - @dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:* - @dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:* - @dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:* - @dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:* - @dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:* - @dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:* - @dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:* - @dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:* - @dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:* - @dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:* - @dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:* - @dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:* - @dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:* - @dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:* - @dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:* - @dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:* - @dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:* - @dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:* - @dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:* - @dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:* - @dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:* - @dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:* - @dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:* - @dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:* - @dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:* - @dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:* - @dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:* - @dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:* - @dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:* - @dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:* - @dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:* - @dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:* - @dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:* - @dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:* - @dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:* - @dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:* - @dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:* - @dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:* - @dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:* - @dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:* - @dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:* - @dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:* - @dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:* - @dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:* - @dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:* - @dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:* - @dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:* - @dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:* - @dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:* - @dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:* - @dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:* - @dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:* - @dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:* - @dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:* - @dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:* - @dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:* - @dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:* - @dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:* - @dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:* - @dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:* - @dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:* - @dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:* - @dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:* - @dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:* - @dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:* - @dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:* - @dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:* - @dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:* - 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@dihedral:p3-c3-p3-hp @atom:p3 @atom:c3 @atom:p3 @atom:hp - @dihedral:s-c-c3-c @atom:s @atom:c @atom:c3 @atom:c - @dihedral:sh-c3-c3-n @atom:sh @atom:c3 @atom:c3 @atom:n - @dihedral:sh-c3-sh-hs @atom:sh @atom:c3 @atom:sh @atom:hs - @dihedral:ss-c3-ss-c3 @atom:ss @atom:c3 @atom:ss @atom:c3 - @dihedral:c3-c3-ca-ca @atom:c3 @atom:c3 @atom:ca @atom:ca - @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o - @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o - @dihedral:c3-c3-c-o @atom:c3 @atom:c3 @atom:c @atom:o - @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 - @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 - @dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3 - @dihedral:ca-ca-c-o @atom:ca @atom:ca @atom:c @atom:o - @dihedral:o-c-c3-c @atom:o @atom:c @atom:c3 @atom:c - @dihedral:o-c-c3-c @atom:o @atom:c @atom:c3 @atom:c - @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o - @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o - @dihedral:os-c3-c-o @atom:os @atom:c3 @atom:c @atom:o - @dihedral:c2-ce-cs-c3 @atom:c2 @atom:ce @atom:cs @atom:c3 - @dihedral:c2-ce-c-c3 @atom:c2 @atom:ce @atom:c @atom:c3 - @dihedral:c2-ce-ce-c2 @atom:c2 @atom:ce @atom:ce @atom:c2 - @dihedral:c2-n-c-c3 @atom:c2 @atom:n @atom:c @atom:c3 - @dihedral:c2-n-cs-c3 @atom:c2 @atom:n @atom:cs @atom:c3 - @dihedral:c2-ne-c-c3 @atom:c2 @atom:ne @atom:c @atom:c3 - @dihedral:c2-ne-cs-c3 @atom:c2 @atom:ne @atom:cs @atom:c3 - @dihedral:c2-pe-c-c3 @atom:c2 @atom:pe @atom:c @atom:c3 - @dihedral:c2-pe-cs-c3 @atom:c2 @atom:pe @atom:cs @atom:c3 - @dihedral:c3-cs-cs-c3 @atom:c3 @atom:cs @atom:cs @atom:c3 - @dihedral:c3-c-c-c3 @atom:c3 @atom:c @atom:c @atom:c3 - @dihedral:c3-c-cs-c3 @atom:c3 @atom:c @atom:cs @atom:c3 - @dihedral:c3-c-n-ca @atom:c3 @atom:c @atom:n @atom:ca - @dihedral:c3-c-n-ca @atom:c3 @atom:c @atom:n @atom:ca - @dihedral:c3-cs-n-ca @atom:c3 @atom:cs @atom:n @atom:ca - @dihedral:c3-n7-c3-c3 @atom:c3 @atom:n7 @atom:c3 @atom:c3 - @dihedral:c3-n7-c3-c3 @atom:c3 @atom:n7 @atom:c3 @atom:c3 - @dihedral:c3-n3-c3-c3 @atom:c3 @atom:n3 @atom:c3 @atom:c3 - @dihedral:c3-n3-c3-c3 @atom:c3 @atom:n3 @atom:c3 @atom:c3 - @dihedral:c3-n-cs-c3 @atom:c3 @atom:n @atom:cs @atom:c3 - @dihedral:c3-n-cs-c3 @atom:c3 @atom:n @atom:cs @atom:c3 - @dihedral:c3-nu-ca-ca @atom:c3 @atom:nu @atom:ca @atom:ca - @dihedral:c3-nh-ca-ca @atom:c3 @atom:nh @atom:ca @atom:ca - @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 - @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 - @dihedral:c3-os-cs-c3 @atom:c3 @atom:os @atom:cs @atom:c3 - @dihedral:c3-p3-c-c3 @atom:c3 @atom:p3 @atom:c @atom:c3 - @dihedral:c3-p3-cs-c3 @atom:c3 @atom:p3 @atom:cs @atom:c3 - @dihedral:c3-ss-c-c3 @atom:c3 @atom:ss @atom:c @atom:c3 - @dihedral:c3-ss-cs-c3 @atom:c3 @atom:ss @atom:cs @atom:c3 - @dihedral:c3-sx-c-c3 @atom:c3 @atom:sx @atom:c @atom:c3 - @dihedral:c3-sx-c-c3 @atom:c3 @atom:sx @atom:c @atom:c3 - @dihedral:c3-sx-cs-c3 @atom:c3 @atom:sx @atom:cs @atom:c3 - @dihedral:c3-sx-cs-c3 @atom:c3 @atom:sx @atom:cs @atom:c3 - @dihedral:c3-sy-cs-c3 @atom:c3 @atom:sy @atom:cs @atom:c3 - @dihedral:c3-sy-c-c3 @atom:c3 @atom:sy @atom:c @atom:c3 - @dihedral:ca-ca-c-c3 @atom:ca @atom:ca @atom:c @atom:c3 - @dihedral:ca-ca-cs-c3 @atom:ca @atom:ca @atom:cs @atom:c3 - @dihedral:c-c3-c3-c3 @atom:c @atom:c3 @atom:c3 @atom:c3 - @dihedral:c-n-cs-c3 @atom:c @atom:n @atom:cs @atom:c3 - @dihedral:c-n-c-c3 @atom:c @atom:n @atom:c @atom:c3 - @dihedral:c-n-c-c3 @atom:c @atom:n @atom:c @atom:c3 - @dihedral:hc-c3-c-c3 @atom:hc @atom:c3 @atom:c @atom:c3 - @dihedral:hc-c3-cs-c3 @atom:hc @atom:c3 @atom:cs @atom:c3 - @dihedral:hn-n4-c-c3 @atom:hn @atom:n4 @atom:c @atom:c3 - @dihedral:hn-n4-c-c3 @atom:hn @atom:n4 @atom:c @atom:c3 - @dihedral:hn-n4-cs-c3 @atom:hn @atom:n4 @atom:cs @atom:c3 - @dihedral:hn-n4-cs-c3 @atom:hn @atom:n4 @atom:cs @atom:c3 - @dihedral:ho-oh-c-c3 @atom:ho @atom:oh @atom:c @atom:c3 - @dihedral:ho-oh-cs-c3 @atom:ho @atom:oh @atom:cs @atom:c3 - @dihedral:hs-sh-cs-c3 @atom:hs @atom:sh @atom:cs @atom:c3 - @dihedral:hs-sh-cs-c3 @atom:hs @atom:sh @atom:cs @atom:c3 - @dihedral:o-n-c-c3 @atom:o @atom:n @atom:c @atom:c3 - @dihedral:o-n-cs-c3 @atom:o @atom:n @atom:cs @atom:c3 - @dihedral:o-p5-c3-p5 @atom:o @atom:p5 @atom:c3 @atom:p5 - @dihedral:o-p5-c3-p5 @atom:o @atom:p5 @atom:c3 @atom:p5 - @dihedral:os-py-c-c3 @atom:os @atom:py @atom:c @atom:c3 - @dihedral:os-py-cs-c3 @atom:os @atom:py @atom:cs @atom:c3 - } # (end of Dihedrals By Type) - - write_once("In Settings") { - improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes - improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230 - improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 - improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 - improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 - improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 - improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 - improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 - improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 - improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 - improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 - improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!) - improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 - improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 - improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 - improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999 - improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 - improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94 - improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94 - } # (end of improper_coeffs) - - write_once("Data Impropers By Type (gaff_imp.py)") { - @improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o - @improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o - @improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha - @improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn - @improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn - @improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn - @improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3 - @improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2 - @improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3 - @improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3 - @improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn - @improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o - @improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3 - @improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3 - @improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc - @improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc - @improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o - @improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh - @improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2 - @improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na - @improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2 - @improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na - @improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2 - @improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3 - @improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f - @improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl - @improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br - @improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i - @improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh - @improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3 - @improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3 - @improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o - @improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2 - @improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh - @improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os - @improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2 - @improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2 - @improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2 - } # (end of Impropers By Type) - - - write_once("In Init") { - # Default styles and settings for AMBER based force-fields: - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - improper_style hybrid cvff - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - kspace_style pppm 0.0001 - - # NOTE: If you do not want to use long-range coulombic forces, - # comment out the two lines above and uncomment this line: - # pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 - - pair_modify mix arithmetic - special_bonds amber - } - -} - - diff --git a/tools/moltemplate/moltemplate/force_fields/graphene.lt b/tools/moltemplate/moltemplate/force_fields/graphene.lt deleted file mode 100644 index 3bc476c3ab..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/graphene.lt +++ /dev/null @@ -1,61 +0,0 @@ -# The minimal unit cell for graphine contains only 2 atoms: -# (which I arbitrarily named "C1" and "C2") - -Graphene { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0000 - $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0000 - } - - # Now define the "C" atom type - write_once("Data Masses") { - @atom:C 12.0 - } - write_once("In Settings") { - # i j epsilon sigma - pair_coeff @atom:C @atom:C lj/cut/coul/long 0.068443 3.407 - - # The Lennard-Jones parameters above were chosen to realistically model - # the interaction between graphene and water - # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, - # Chem Phys Lett, 348:187 (2001) - # NOTE: If you want to simulate movement of the carbon atoms, then you must - # choose a more appropriate force field for the carbon atoms, such as - # AIREBO or Tersoff. You can do this by editing the "pair_coeff" above. - # (The paper by C.F. Cornwell, C.R. Welch, J. Chem. Phys. (2011), Vol 134, - # demonstrates how to use the AIREBO potential in LAMMPS.) - - # Define a group consisting of only carbon atoms in graphene molecules - group Cgraphene type @atom:C - } - write_once("In Init") { - # -- Default styles (used in this file for graphene carbon) -- - units real - atom_style full #(full enables you to to add other molecules later) - pair_style hybrid lj/cut/coul/long 10.0 - } -} # Graphene - - - - -# This is a 2-dimensional hexagonal unit cell. The unit vectors are: -# -# (2.4595121467478, 0, 0) -# (1.2297560733739, 2.13, 0) -# -# You can create a sheet of single-layer graphene this way: -# -# small_crystal = new Graphene [3].move(2.45951214, 0, 0) -# [3].move(1.229756, 2.13, 0) -# -# For thicker sheets, follow the instructions in the "graphite.lt" file. -# -# Note: The length of each carbon-carbon bond is currently 1.42 Angstroms. -# To increase it to 1.422 Angstroms, uncomment the following line: -# -# Graphene.scale(1.0014084507042254) # 1.0014084507042254 = 1.422 / 1.42 -# -# You will have to change the unit cell lattice vectors (see above) accordingly diff --git a/tools/moltemplate/moltemplate/force_fields/graphite.lt b/tools/moltemplate/moltemplate/force_fields/graphite.lt deleted file mode 100644 index 49fb49fb08..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/graphite.lt +++ /dev/null @@ -1,61 +0,0 @@ -import "graphene.lt" # defines "Graphene" - - -# ------------ Graphite ----------- -# -# Note: For graphite: sheets stacked in the Z direction are separated by a -# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction -# by a distance of d (1.42 Angstroms). To add additional graphene layers -# you could use: -# sheet2 = new Graphene [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet2[*][*].move(0, 1.42, 3.35) -# sheet3 = new Graphene [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet3[*][*].move(0, -1.42, 6.70) -# etc... -# -# This should work fine. -# However, to build a thick sheet of graphite, it may be less trouble -# to use a 4-atom unit cell which includes two graphene layers. -# Here is one way to do that: - -Graphite inherits Graphene { - - # This allows us to access access the "@atom:C" carbon atom type - # whose properties are defined in the "Graphene" object (see "graphene.lt"). - # That atom is NOT globally defined. It belongs to the "Graphene" object. - # This is one way to access it. Alternately, you could redefine it here - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C1 $mol:... @atom:C 0.0 -0.61487803668695 -0.355 0.0 - $atom:C2 $mol:... @atom:C 0.0 0.61487803668695 0.355 0.0 - $atom:C3 $mol:... @atom:C 0.0 -0.61487803668695 1.065 3.35 - $atom:C4 $mol:... @atom:C 0.0 0.61487803668695 1.775 3.35 - } - - # Note: The first two lines in the "Data Atoms" section override the positions - # of the $atom:C1 and $atom:C2 atoms previously defined in "Graphene" - # (which this object inherits). This is okay. - -} # Graphite - - - - - - -# This is a 3-dimensional hexagonal unit cell. The unit vectors are: -# -# (2.4595121467478, 0, 0 ) -# (1.2297560733739, 2.13, 0 ) -# ( 0, 0, 6.70) - -# Then you could create a thick sheet of graphite this way: -# -# graphite = new Graphite [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# [5].move(0,0,6.70) -# -# (Your graphite slab will contain an even number of graphene sheets.) diff --git a/tools/moltemplate/moltemplate/force_fields/images/graphene_unit_cell.jpg b/tools/moltemplate/moltemplate/force_fields/images/graphene_unit_cell.jpg deleted file mode 100644 index 12dbf8fca2..0000000000 Binary files a/tools/moltemplate/moltemplate/force_fields/images/graphene_unit_cell.jpg and /dev/null differ diff --git a/tools/moltemplate/moltemplate/force_fields/images/ice_rect8_unitcell.png b/tools/moltemplate/moltemplate/force_fields/images/ice_rect8_unitcell.png deleted file mode 100644 index 5bd6057e1e..0000000000 Binary files a/tools/moltemplate/moltemplate/force_fields/images/ice_rect8_unitcell.png and /dev/null differ diff --git a/tools/moltemplate/moltemplate/force_fields/images/spce_ball_and_stick.jpg b/tools/moltemplate/moltemplate/force_fields/images/spce_ball_and_stick.jpg deleted file mode 100644 index 60aaf90b95..0000000000 Binary files a/tools/moltemplate/moltemplate/force_fields/images/spce_ball_and_stick.jpg and /dev/null differ diff --git a/tools/moltemplate/moltemplate/force_fields/loplsaa.lt b/tools/moltemplate/moltemplate/force_fields/loplsaa.lt deleted file mode 100644 index 017411a75f..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/loplsaa.lt +++ /dev/null @@ -1,271 +0,0 @@ -############################################################################ -## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## -## SOURCES: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8(4), 1459 -## Pluhackova,...,Böckmann, J.Phys.Chem.B (2015), 119(49), 15287 ## -## CREDIT: Sebastian Echeverri (file format conversion) ## -############################################################################ -# This file was generated using: -# tinkerparm2lt.py -name OPLSAA -file loplsaa_ext.prm -dihedral-style opls -zeropad 3 -# (...and then EDITED manually to make sure the default bond, angle, -# and improper interactions for these atoms remain unchanged) - - -import "oplsaa.lt" # <-- Load the ordinary OPLS parameters first - # We will augment and override them below - - - -OPLSAA { - - # Additional atom types and parameters appended to the OPLSAA force-field: - - write_once("In Charges") { - set type @atom:80L charge -0.222 # "Alkane CH3- (LOPLS CT_CH3)" - set type @atom:81L charge -0.148 # "Alkane -CH2- (LOPLS CT_CH2)" - set type @atom:81LL charge 0.19 # "Alkane -CH2- (LOPLS ALT)" - set type @atom:85LCH3 charge 0.074 # "Alkane H-C CH3 (LOPLS HC_CH3)" - set type @atom:85LCH2 charge 0.074 # "Alkane H-C CH2 (LOPLS HC_CH2)" - set type @atom:87L charge -0.16 # "Alkene RH-C= (LOPLS CM_CH)" - set type @atom:89L charge 0.16 # "Alkene H-C= (LOPLS HC_CH)" - set type @atom:86L charge 0.0 # "Alkene R2-C= (LOPLS)" - set type @atom:88L charge -0.23 # "Alkene H2-C= (LOPLS)" - set type @atom:96L charge -0.683 # "Alcohol -OH (LOPLS)" - set type @atom:97L charge 0.418 # "Alcohol -OH (LOPLS)" - set type @atom:111L charge -0.7 # "Diol -OH (LOPLS)" - set type @atom:112L charge 0.435 # "Diol -OH (LOPLS)" - set type @atom:113L charge -0.73 # "Triol -OH (LOPLS)" - set type @atom:114L charge 0.465 # "Triol -OH (LOPLS)" - set type @atom:118L charge 0.06 # "Diol & Triol H-COH (LOPLS)" - set type @atom:169L charge 0.005 # "Chloroalkene Cl-CH= (LOPLS)" - set type @atom:266L charge -0.07 # "Uracil & Thymine C5 (LOPLS)" - set type @atom:267L charge 0.08 # "Uracil & Thymine C6 (LOPLS)" - set type @atom:280L charge -0.06 # "Cytosine C5 (LOPLS)" - set type @atom:281L charge 0.1 # "Cytosine C6 (LOPLS)" - set type @atom:324L charge -0.06 # "CytosineH+ C5 (LOPLS)" - set type @atom:325L charge 0.1 # "CytosineH+ C6 (LOPLS)" - set type @atom:340L charge 0.18 # "Trifluorothymine CF3- (LOPLS)" - set type @atom:342L charge 0.12 # "Chloroalkene Cl2-C= (LOPLS)" - set type @atom:406L charge 0.75 # "Ester -COOR (LOPLS)" - set type @atom:407L charge -0.55 # "Ester C=O (LOPLS)" - set type @atom:408L charge -0.45 # "Ester CO-O-R (LOPLS)" - set type @atom:458L charge -0.03 # "Vinyl Ether =CH-OR (LOPLS)" - set type @atom:459L charge 0.085 # "Vinyl Ether =CR-OR (LOPLS)" - set type @atom:649L charge -0.344 # "Cl..CH3..Cl- Sn2 TS (LOPLS)" - set type @atom:718L charge 0.06 # "Propylene Carbonate CH2 (LOPLS)" - set type @atom:718LL charge 0.03 # "Propylene Carbonate CH2 (LOPLS ALT)" - set type @atom:900L charge -0.25 # "Allene/Ketene H2C=C=X (LOPLS)" - set type @atom:901L charge -0.1 # "Allene/Ketene HRC=C=X (LOPLS)" - set type @atom:902L charge 0.05 # "Allene/Ketene R2C=C=X (LOPLS)" - } #(end of atom partial charges) - - - write_once("Data Masses") { - @atom:80L 12.011 - @atom:81L 12.011 - @atom:81LL 12.011 - @atom:85LCH3 1.008 - @atom:85LCH2 1.008 - @atom:87L 12.011 - @atom:89L 1.008 - @atom:86L 12.011 - @atom:88L 12.011 - @atom:96L 15.999 - @atom:97L 1.008 - @atom:111L 15.999 - @atom:112L 1.008 - @atom:113L 15.999 - @atom:114L 1.008 - @atom:118L 1.008 - @atom:169L 12.011 - @atom:266L 12.011 - @atom:267L 12.011 - @atom:280L 12.011 - @atom:281L 12.011 - @atom:324L 12.011 - @atom:325L 12.011 - @atom:340L 12.011 - @atom:342L 12.011 - @atom:406L 12.011 - @atom:407L 15.999 - @atom:408L 15.999 - @atom:458L 12.011 - @atom:459L 12.011 - @atom:649L 12.011 - @atom:718L 1.008 - @atom:718LL 1.008 - @atom:900L 12.011 - @atom:901L 12.011 - @atom:902L 12.011 - } #(end of atom masses) - - - # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- - # Each type of atom has a separate ID used for looking up bond parameters - # and a separate ID for looking up 3-body angle interaction parameters - # and a separate ID for looking up 4-body dihedral interaction parameters - # and a separate ID for looking up 4-body improper interaction parameters - # The complete @atom type name includes ALL of these ID numbers. There's - # no need to force the end-user to type the complete name of each atom. - # The "replace" command used below informs moltemplate that the short - # @atom names we have been using abovee are equivalent to the complete - # @atom names used below: - - replace{ @atom:80L @atom:80L_b013_a013_d013L_i013 } - replace{ @atom:81L @atom:81L_b013_a013_d013L_i013 } - replace{ @atom:81LL @atom:81LL_b013_a013_d013LL_i013 } - replace{ @atom:85LCH3 @atom:85LCH3_b046_a046_d046_i046 } - replace{ @atom:85LCH2 @atom:85LCH2_b046_a046_d046_i046 } - replace{ @atom:87L @atom:87L_b047_a047_d047L_i047 } - replace{ @atom:89L @atom:89L_b046_a046_d046_i046 } - replace{ @atom:86L @atom:86L_b047_a047_d047L_i047 } - replace{ @atom:88L @atom:88L_b047_a047_d047L_i047 } - replace{ @atom:96L @atom:96L_b005_a005_d005L_i005 } - replace{ @atom:97L @atom:97L_b007_a007_d007L_i007 } - replace{ @atom:111L @atom:111L_b005_a005_d005L_i005 } - replace{ @atom:112L @atom:112L_b007_a007_d007L_i007 } - replace{ @atom:113L @atom:113L_b005_a005_d005L_i005 } - replace{ @atom:114L @atom:114L_b007_a007_d007L_i007 } - replace{ @atom:118L @atom:118L_b046_a046_d046L_i046 } - replace{ @atom:169L @atom:169L_b047_a047_d047L_i047 } - replace{ @atom:266L @atom:266L_b047_a047_d047L_i047 } - replace{ @atom:267L @atom:267L_b047_a047_d047L_i047 } - replace{ @atom:280L @atom:280L_b047_a047_d047L_i047 } - replace{ @atom:281L @atom:281L_b047_a047_d047L_i047 } - replace{ @atom:324L @atom:324L_b047_a047_d047L_i047 } - replace{ @atom:325L @atom:325L_b047_a047_d047L_i047 } - replace{ @atom:340L @atom:340L_b047_a047_d047L_i047 } - replace{ @atom:342L @atom:342L_b047_a047_d047L_i047 } - replace{ @atom:406L @atom:406L_b003_a003_d003L_i003 } - replace{ @atom:407L @atom:407L_b004_a004_d004L_i004 } - replace{ @atom:408L @atom:408L_b020_a020_d020L_i020 } - replace{ @atom:458L @atom:458L_b047_a047_d047L_i047 } - replace{ @atom:459L @atom:459L_b047_a047_d047L_i047 } - replace{ @atom:649L @atom:649L_b047_a047_d047L_i047 } - replace{ @atom:718L @atom:718L_b046_a046_d046L_i046 } - replace{ @atom:718LL @atom:718LL_b046_a046_d046L_i046 } - replace{ @atom:900L @atom:900L_b047_a047_d047L_i047 } - replace{ @atom:901L @atom:901L_b047_a047_d047L_i047 } - replace{ @atom:902L @atom:902L_b047_a047_d047L_i047 } - - - - - # --------------- Non-Bonded interactions: --------------------- - # http://lammps.sandia.gov/doc/pair_lj.html - # Syntax: - # pair_coeff AtomType1 AtomType2 parameters... - - write_once("In Settings") { - pair_coeff @atom:80L_b013_a013_d013L_i013 @atom:80L_b013_a013_d013L_i013 0.066 3.5 - pair_coeff @atom:81L_b013_a013_d013L_i013 @atom:81L_b013_a013_d013L_i013 0.066 3.5 - pair_coeff @atom:81LL_b013_a013_d013LL_i013 @atom:81LL_b013_a013_d013LL_i013 0.066 0.35 - pair_coeff @atom:85LCH3_b046_a046_d046_i046 @atom:85LCH3_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:85LCH2_b046_a046_d046_i046 @atom:85LCH2_b046_a046_d046_i046 0.026290630975 2.5 - pair_coeff @atom:87L_b047_a047_d047L_i047 @atom:87L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:89L_b046_a046_d046_i046 @atom:89L_b046_a046_d046_i046 0.03 2.42 - pair_coeff @atom:86L_b047_a047_d047L_i047 @atom:86L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:88L_b047_a047_d047L_i047 @atom:88L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:96L_b005_a005_d005L_i005 @atom:96L_b005_a005_d005L_i005 0.17 0.312 - pair_coeff @atom:97L_b007_a007_d007L_i007 @atom:97L_b007_a007_d007L_i007 0.0 0.0 - pair_coeff @atom:111L_b005_a005_d005L_i005 @atom:111L_b005_a005_d005L_i005 0.17 0.307 - pair_coeff @atom:112L_b007_a007_d007L_i007 @atom:112L_b007_a007_d007L_i007 0.0 0.0 - pair_coeff @atom:113L_b005_a005_d005L_i005 @atom:113L_b005_a005_d005L_i005 0.17 0.307 - pair_coeff @atom:114L_b007_a007_d007L_i007 @atom:114L_b007_a007_d007L_i007 0.0 0.0 - pair_coeff @atom:118L_b046_a046_d046L_i046 @atom:118L_b046_a046_d046L_i046 0.03 0.25 - pair_coeff @atom:169L_b047_a047_d047L_i047 @atom:169L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:266L_b047_a047_d047L_i047 @atom:266L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:267L_b047_a047_d047L_i047 @atom:267L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:280L_b047_a047_d047L_i047 @atom:280L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:281L_b047_a047_d047L_i047 @atom:281L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:324L_b047_a047_d047L_i047 @atom:324L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:325L_b047_a047_d047L_i047 @atom:325L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:340L_b047_a047_d047L_i047 @atom:340L_b047_a047_d047L_i047 0.08 3.5 - pair_coeff @atom:342L_b047_a047_d047L_i047 @atom:342L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:406L_b003_a003_d003L_i003 @atom:406L_b003_a003_d003L_i003 0.105 0.31875 - pair_coeff @atom:407L_b004_a004_d004L_i004 @atom:407L_b004_a004_d004L_i004 0.168 0.3108 - pair_coeff @atom:408L_b020_a020_d020L_i020 @atom:408L_b020_a020_d020L_i020 0.17 0.255 - pair_coeff @atom:458L_b047_a047_d047L_i047 @atom:458L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:459L_b047_a047_d047L_i047 @atom:459L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:649L_b047_a047_d047L_i047 @atom:649L_b047_a047_d047L_i047 0.076 3.55 - pair_coeff @atom:718L_b046_a046_d046L_i046 @atom:718L_b046_a046_d046L_i046 0.15 0.242 - pair_coeff @atom:718LL_b046_a046_d046L_i046 @atom:718LL_b046_a046_d046L_i046 0.15 0.242 - pair_coeff @atom:900L_b047_a047_d047L_i047 @atom:900L_b047_a047_d047L_i047 0.086 3.3 - pair_coeff @atom:901L_b047_a047_d047L_i047 @atom:901L_b047_a047_d047L_i047 0.086 3.3 - pair_coeff @atom:902L_b047_a047_d047L_i047 @atom:902L_b047_a047_d047L_i047 0.086 3.3 - } #(end of pair_coeffs) - - - # Bond parameters for these atoms are not modified - - # Angle parameters for these atoms are not modified - - # Improper parameters for these atoms are not modified - - # Dihedral parameters for some of these atoms are modified: - - # ----------- Dihedral Interactions: ------------ - # http://lammps.sandia.gov/doc/dihedral_opls.html - # Syntax: - # dihedral_coeff DihedralTypeName parameters... - - write_once("In Settings") { - dihedral_coeff @dihedral:013L_013L_013L_013L 0.6446926386 -0.2143420172 0.1782194073 0.0 - dihedral_coeff @dihedral:X_047L_047L_X 0.0 12.2502629063 0.0 0.0 - dihedral_coeff @dihedral:047L_047L_013L_013L -0.8050121893 0.3218905354 -0.1032768881 0.0 - dihedral_coeff @dihedral:013L_013L_013L_047L 0.4821902486 0.1343683078 0.1777461759 0.0 - dihedral_coeff @dihedral:046L_013LL_005L_007L 0.00962596 -0.0145554 0.381091 0.0 - dihedral_coeff @dihedral:046L_013LL_013LL_005L 0.0143774 0.033021 0.26687 0.0 - dihedral_coeff @dihedral:013LL_013LL_005L_007L -0.675785 -0.0160421 0.373199 0.0 - dihedral_coeff @dihedral:013LL_013LL_013LL_005L 1.31261 -0.266307 0.637867 0.0 - dihedral_coeff @dihedral:005L_013LL_013LL_005L 2.69106 -0.849706 0.725731 0.0 - dihedral_coeff @dihedral:013LL_003L_020L_013LL 3.11923 5.73771 0.0 0.0 - dihedral_coeff @dihedral:013LL_020L_003L_004L 0.0 5.73772 0.0 0.0 - dihedral_coeff @dihedral:046L_013LL_003L_020L -0.00742471 0.00217734 0.111803 0.0 - dihedral_coeff @dihedral:003L_020L_013LL_013LL -1.7354 -1.24844 0.623897 0.0 - dihedral_coeff @dihedral:046L_013LL_013LL_020L 0.0113337 0.0236209 0.429747 0.0 - dihedral_coeff @dihedral:013LL_013LL_003L_020L 0.884988 -0.626905 -0.493344 0.0 - dihedral_coeff @dihedral:013LL_013LL_003L_004L -0.276019 1.23685 -0.670745 0.0 - dihedral_coeff @dihedral:003L_013LL_013LL_046L -0.0021152 0.0173542 -0.295208 0.0 - dihedral_coeff @dihedral:003L_013LL_013LL_013LL -2.30738 -0.627326 0.621951 0.0 - dihedral_coeff @dihedral:013LL_013LL_013LL_020L 2.25871 -1.02408 1.0071 0.0 - dihedral_coeff @dihedral:020L_013LL_013LL_020L 4.66787 -2.62698 1.3248 0.0 - dihedral_coeff @dihedral:005L_013LL_013LL_020L 5.03208 -2.37742 1.23809 0.0 - } #(end of dihedral_coeffs) - - # Rules for creating dihedral interactions according to atom type: - # DihedralTypeName AtomType1 AtomType2 AtomType3 AtomType4 - # (* = wildcard) - - write_once("Data Dihedrals By Type") { - @dihedral:013L_013L_013L_013L @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* - @dihedral:X_047L_047L_X @atom:* @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d047L_i* @atom:* - @dihedral:047L_047L_013L_013L @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d047L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* - @dihedral:013L_013L_013L_047L @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d013L_i* @atom:*_b*_a*_d047L_i* - @dihedral:046L_013LL_005L_007L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d007L_i* - @dihedral:046L_013LL_013LL_005L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* - @dihedral:013LL_013LL_005L_007L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d007L_i* - @dihedral:013LL_013LL_013LL_005L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* - @dihedral:005L_013LL_013LL_005L @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d005L_i* - @dihedral:013LL_003L_020L_013LL @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* - @dihedral:013LL_020L_003L_004L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d004L_i* - @dihedral:046L_013LL_003L_020L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* - @dihedral:003L_020L_013LL_013LL @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* - @dihedral:046L_013LL_013LL_020L @atom:*_b*_a*_d046L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* - @dihedral:013LL_013LL_003L_020L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d020L_i* - @dihedral:013LL_013LL_003L_004L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d004L_i* - @dihedral:003L_013LL_013LL_046L @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d046L_i* - @dihedral:003L_013LL_013LL_013LL @atom:*_b*_a*_d003L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* - @dihedral:013LL_013LL_013LL_020L @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* - @dihedral:020L_013LL_013LL_020L @atom:*_b*_a*_d020L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* - @dihedral:005L_013LL_013LL_020L @atom:*_b*_a*_d005L_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d013LL_i* @atom:*_b*_a*_d020L_i* - } #(end of dihedrals by type) - - - # ----------- New Dihedral Interactions: ------------ - # http://lammps.sandia.gov/doc/dihedral_opls.html - # Syntax: - # dihedral_coeff DihedralTypeName parameters... - - -} # OPLSAA - diff --git a/tools/moltemplate/moltemplate/force_fields/martini.lt b/tools/moltemplate/moltemplate/force_fields/martini.lt deleted file mode 100644 index 9304de004a..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini.lt +++ /dev/null @@ -1,2227 +0,0 @@ -# Autogenerated by EMC 2 LT tool v0.1 on 2017-06-28 -# -# cd martini/ -# emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini -# mv -f martini.lt ../ -# -# For details see the "README.txt" file (located in "force_fields/martini/") -# -# (Note: The rigid bond constraints used original MARTINI model for -# cholesterol have been replaced by stiff but flexible bonds. -# There is a trade-off between increasing the stiffness of the bonds, and -# using larger time steps. To alter the stiffness of the bonds, and edit -# the "ITEM BOND" section of the "cholesterol.prm", edit the "k" parameters -# (3rd column, for the "S..." entries), and run "emcprm2lt.py" again.) -# -# Adapted from EMC by Pieter J. in 't Veld -# Originally written as, FFNAME:MARTINI STYLE:COARSE VERSION:V2.0 on Feb 2014 -# "emcprm2lt.py" was written by David Stelter. - - -MARTINI { - - write_once("Data Masses") { - @atom:BP4 72.000000 # BP4 - @atom:C1 72.000000 # C1 - @atom:C2 72.000000 # C2 - @atom:C3 72.000000 # C3 - @atom:C4 72.000000 # C4 - @atom:C5 72.000000 # C5 - @atom:N0 72.000000 # N0 - @atom:Na 72.000000 # Na - @atom:Nd 72.000000 # Nd - @atom:Nda 72.000000 # Nda - @atom:P1 72.000000 # P1 - @atom:P2 72.000000 # P2 - @atom:P3 72.000000 # P3 - @atom:P4 72.000000 # P4 - @atom:P5 72.000000 # P5 - @atom:Q0 72.000000 # Q0 - @atom:Qa 72.000000 # Qa - @atom:Qd 72.000000 # Qd - @atom:Qda 72.000000 # Qda - @atom:SC1 54.000000 # SC1 - @atom:SC2 54.000000 # SC2 - @atom:SC3 54.000000 # SC3 - @atom:SC4 54.000000 # SC4 - @atom:SC5 54.000000 # SC5 - @atom:SN0 54.000000 # SN0 - @atom:SNa 54.000000 # SNa - @atom:SNd 54.000000 # SNd - @atom:SNda 54.000000 # SNda - @atom:SP1 54.000000 # SP1 - @atom:SP2 54.000000 # SP2 - @atom:SP3 54.000000 # SP3 - @atom:SP4 54.000000 # SP4 - @atom:SP5 54.000000 # SP5 - @atom:SQ0 54.000000 # SQ0 - @atom:SQa 54.000000 # SQa - @atom:SQd 54.000000 # SQd - @atom:SQda 54.000000 # SQda - @atom:C41 72.000000 # C41 - @atom:C42 72.000000 # C42 - @atom:Na1 72.000000 # Na1 - @atom:Na2 72.000000 # Na2 - @atom:Qa1 72.000000 # Qa1 - @atom:Qa2 72.000000 # Qa2 - @atom:SC11 54.000000 # SC11 - @atom:SC110 54.000000 # SC110 - @atom:SC111 54.000000 # SC111 - @atom:SC112 54.000000 # SC112 - @atom:SC12 54.000000 # SC12 - @atom:SC13 54.000000 # SC13 - @atom:SC14 54.000000 # SC14 - @atom:SC15 54.000000 # SC15 - @atom:SC16 54.000000 # SC16 - @atom:SC17 54.000000 # SC17 - @atom:SC18 54.000000 # SC18 - @atom:SC19 54.000000 # SC19 - @atom:SC31 54.000000 # SC31 - @atom:SC32 54.000000 # SC32 - @atom:SC33 54.000000 # SC33 - @atom:SP11 54.000000 # SP11 - @atom:SP12 54.000000 # SP12 - } # end of atom masses - - # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup ----- - replace{ @atom:BP4 @atom:BP4_bBP4_aBP4_dBP4_iBP4} - replace{ @atom:C1 @atom:C1_bC1_aC1_dC1_iC1} - replace{ @atom:C2 @atom:C2_bC2_aC2_dC2_iC2} - replace{ @atom:C3 @atom:C3_bC3_aC3_dC3_iC3} - replace{ @atom:C4 @atom:C4_bC4_aC4_dC4_iC4} - replace{ @atom:C5 @atom:C5_bC5_aC5_dC5_iC5} - replace{ @atom:N0 @atom:N0_bN0_aN0_dN0_iN0} - replace{ @atom:Na @atom:Na_bNa_aNa_dNa_iNa} - replace{ @atom:Nd @atom:Nd_bNd_aNd_dNd_iNd} - replace{ @atom:Nda @atom:Nda_bNda_aNda_dNda_iNda} - replace{ @atom:P1 @atom:P1_bP1_aP1_dP1_iP1} - replace{ @atom:P2 @atom:P2_bP2_aP2_dP2_iP2} - replace{ @atom:P3 @atom:P3_bP3_aP3_dP3_iP3} - replace{ @atom:P4 @atom:P4_bP4_aP4_dP4_iP4} - replace{ @atom:P5 @atom:P5_bP5_aP5_dP5_iP5} - replace{ @atom:Q0 @atom:Q0_bQ0_aQ0_dQ0_iQ0} - replace{ @atom:Qa @atom:Qa_bQa_aQa_dQa_iQa} - replace{ @atom:Qd @atom:Qd_bQd_aQd_dQd_iQd} - replace{ @atom:Qda @atom:Qda_bQda_aQda_dQda_iQda} - replace{ @atom:SC1 @atom:SC1_bSC1_aSC1_dSC1_iSC1} - replace{ @atom:SC2 @atom:SC2_bSC2_aSC2_dSC2_iSC2} - replace{ @atom:SC3 @atom:SC3_bSC3_aSC3_dSC3_iSC3} - replace{ @atom:SC4 @atom:SC4_bSC4_aSC4_dSC4_iSC4} - replace{ @atom:SC5 @atom:SC5_bSC5_aSC5_dSC5_iSC5} - replace{ @atom:SN0 @atom:SN0_bSN0_aSN0_dSN0_iSN0} - replace{ @atom:SNa @atom:SNa_bSNa_aSNa_dSNa_iSNa} - replace{ @atom:SNd @atom:SNd_bSNd_aSNd_dSNd_iSNd} - replace{ @atom:SNda @atom:SNda_bSNda_aSNda_dSNda_iSNda} - replace{ @atom:SP1 @atom:SP1_bSP1_aSP1_dSP1_iSP1} - replace{ @atom:SP2 @atom:SP2_bSP2_aSP2_dSP2_iSP2} - replace{ @atom:SP3 @atom:SP3_bSP3_aSP3_dSP3_iSP3} - replace{ @atom:SP4 @atom:SP4_bSP4_aSP4_dSP4_iSP4} - replace{ @atom:SP5 @atom:SP5_bSP5_aSP5_dSP5_iSP5} - replace{ @atom:SQ0 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0} - replace{ @atom:SQa @atom:SQa_bSQa_aSQa_dSQa_iSQa} - replace{ @atom:SQd @atom:SQd_bSQd_aSQd_dSQd_iSQd} - replace{ @atom:SQda @atom:SQda_bSQda_aSQda_dSQda_iSQda} - replace{ @atom:C41 @atom:C41_bC4_aC41_dC41_iC41} - replace{ @atom:C42 @atom:C42_bC4_aC42_dC42_iC42} - replace{ @atom:Na1 @atom:Na1_bNa1_aNa1_dNa1_iNa1} - replace{ @atom:Na2 @atom:Na2_bNa2_aNa2_dNa2_iNa2} - replace{ @atom:Qa1 @atom:Qa1_bQa1_aQa1_dQa1_iQa1} - replace{ @atom:Qa2 @atom:Qa2_bQa2_aQa2_dQa2_iQa2} - replace{ @atom:SC11 @atom:SC11_bSC11_aSC11_dSC11_iSC11} - replace{ @atom:SC110 @atom:SC110_bSC110_aSC110_dSC110_iSC110} - replace{ @atom:SC111 @atom:SC111_bSC111_aSC111_dSC111_iSC111} - replace{ @atom:SC112 @atom:SC112_bSC112_aSC112_dSC112_iSC112} - replace{ @atom:SC12 @atom:SC12_bSC12_aSC12_dSC12_iSC12} - replace{ @atom:SC13 @atom:SC13_bSC13_aSC13_dSC13_iSC13} - replace{ @atom:SC14 @atom:SC14_bSC14_aSC14_dSC14_iSC14} - replace{ @atom:SC15 @atom:SC15_bSC15_aSC15_dSC15_iSC15} - replace{ @atom:SC16 @atom:SC16_bSC16_aSC16_dSC16_iSC16} - replace{ @atom:SC17 @atom:SC17_bSC17_aSC17_dSC17_iSC17} - replace{ @atom:SC18 @atom:SC18_bSC18_aSC18_dSC18_iSC18} - replace{ @atom:SC19 @atom:SC19_bSC19_aSC19_dSC19_iSC19} - replace{ @atom:SC31 @atom:SC31_bSC31_aSC31_dSC31_iSC31} - replace{ @atom:SC32 @atom:SC32_bSC32_aSC32_dSC32_iSC32} - replace{ @atom:SC33 @atom:SC33_bSC33_aSC33_dSC33_iSC33} - replace{ @atom:SP11 @atom:SP11_bSP11_aSP11_dSP11_iSP11} - replace{ @atom:SP12 @atom:SP12_bSP12_aSP12_dSP12_iSP12} - # END EQUIVALENCE - - write_once("In Settings") { - # ----- Non-Bonded interactions ----- - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 1.195030 4.700000 # BP4-BP4 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.478012 4.700000 # BP4-C1 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.549714 4.700000 # BP4-C2 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # BP4-C3 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # BP4-C4 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # BP4-C5 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # BP4-N0 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.956024 4.700000 # BP4-Na - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.956024 4.700000 # BP4-Nd - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.956024 4.700000 # BP4-Nda - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # BP4-P1 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # BP4-P2 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.195030 4.700000 # BP4-P3 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.338434 5.700000 # BP4-P4 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-P5 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-Q0 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-Qa - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-Qd - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-Qda - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 4.700000 # BP4-SC1 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.549714 4.700000 # BP4-SC2 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # BP4-SC3 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # BP4-SC4 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # BP4-SC5 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # BP4-SN0 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # BP4-SNa - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.956024 4.700000 # BP4-SNd - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.956024 4.700000 # BP4-SNda - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # BP4-SP1 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # BP4-SP2 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.195030 4.700000 # BP4-SP3 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.195030 4.700000 # BP4-SP4 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-SP5 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-SQ0 - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-SQa - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-SQd - pair_coeff @atom:BP4_bBP4_aBP4_dBP4_iBP4 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # BP4-SQda - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C1-C1 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C1-C2 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C1-C3 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # C1-C4 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # C1-C5 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-N0 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-Na - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-Nd - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-Nda - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-P1 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # C1-P2 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # C1-P3 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # C1-P4 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # C1-P5 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-Q0 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-Qa - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-Qd - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-Qda - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C1-SC1 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C1-SC2 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C1-SC3 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # C1-SC4 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # C1-SC5 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-SN0 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-SNa - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-SNd - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-SNda - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # C1-SP1 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # C1-SP2 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # C1-SP3 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # C1-SP4 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # C1-SP5 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-SQ0 - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-SQa - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-SQd - pair_coeff @atom:C1_bC1_aC1_dC1_iC1 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # C1-SQda - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C2-C2 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C2-C3 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-C4 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-C5 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-N0 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-Na - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-Nd - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-Nda - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-P1 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-P2 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-P3 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.549714 4.700000 # C2-P4 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.549714 4.700000 # C2-P5 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-Q0 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-Qa - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-Qd - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-Qda - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C2-SC1 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C2-SC2 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C2-SC3 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-SC4 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-SC5 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-SN0 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-SNa - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-SNd - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-SNda - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C2-SP1 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-SP2 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.645316 4.700000 # C2-SP3 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.549714 4.700000 # C2-SP4 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.549714 4.700000 # C2-SP5 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-SQ0 - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-SQa - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-SQd - pair_coeff @atom:C2_bC2_aC2_dC2_iC2 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # C2-SQda - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-C3 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-C4 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-C5 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-N0 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-Na - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-Nd - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-Nda - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-P1 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C3-P2 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C3-P3 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-P4 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-P5 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-Q0 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-Qa - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-Qd - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-Qda - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SC1 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SC2 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SC3 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SC4 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SC5 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SN0 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-SNa - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-SNd - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-SNda - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C3-SP1 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C3-SP2 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C3-SP3 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-SP4 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C3-SP5 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-SQ0 - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-SQa - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-SQd - pair_coeff @atom:C3_bC3_aC3_dC3_iC3 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.549714 4.700000 # C3-SQda - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-C4 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-C5 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-N0 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-Na - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-Nd - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-Nda - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-P1 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-P2 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-P3 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-P4 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-P5 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-Q0 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-Qa - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-Qd - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-Qda - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-SC1 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-SC2 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-SC3 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-SC4 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-SC5 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-SN0 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-SNa - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-SNd - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-SNda - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-SP1 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C4-SP2 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C4-SP3 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-SP4 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-SP5 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-SQ0 - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-SQa - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-SQd - pair_coeff @atom:C4_bC4_aC4_dC4_iC4 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.645316 4.700000 # C4-SQda - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-C5 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-N0 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-Na - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-Nd - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-Nda - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-P1 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-P2 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-P3 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-P4 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-P5 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-Q0 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-Qa - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-Qd - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-Qda - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SC1 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SC2 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SC3 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SC4 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SC5 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SN0 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SNa - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SNd - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SNda - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SP1 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SP2 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C5-SP3 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SP4 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SP5 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SQ0 - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SQa - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SQd - pair_coeff @atom:C5_bC5_aC5_dC5_iC5 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.740919 4.700000 # C5-SQda - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-N0 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Na - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Nd - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Nda - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.956024 4.700000 # N0-P1 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.956024 4.700000 # N0-P2 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-P3 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-P4 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-P5 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Q0 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Qa - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Qd - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-Qda - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # N0-SC1 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # N0-SC2 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SC3 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SC4 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SC5 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SN0 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SNa - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SNd - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SNda - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.956024 4.700000 # N0-SP1 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.956024 4.700000 # N0-SP2 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SP3 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SP4 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SP5 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SQ0 - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SQa - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SQd - pair_coeff @atom:N0_bN0_aN0_dN0_iN0 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.836521 4.700000 # N0-SQda - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-Na - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-Nd - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-Nda - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-P1 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-P2 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-P3 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-P4 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Na-P5 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-Q0 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-Qa - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Na-Qd - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Na-Qda - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na-SC1 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na-SC2 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na-SC3 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na-SC4 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na-SC5 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na-SN0 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-SNa - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-SNd - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-SNda - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-SP1 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-SP2 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na-SP3 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-SP4 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Na-SP5 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-SQ0 - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na-SQa - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Na-SQd - pair_coeff @atom:Na_bNa_aNa_dNa_iNa @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Na-SQda - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-Nd - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-Nda - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-P1 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-P2 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-P3 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-P4 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Nd-P5 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-Q0 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Nd-Qa - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-Qd - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Nd-Qda - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Nd-SC1 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Nd-SC2 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Nd-SC3 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Nd-SC4 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Nd-SC5 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Nd-SN0 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-SNa - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-SNd - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-SNda - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-SP1 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-SP2 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nd-SP3 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-SP4 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Nd-SP5 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-SQ0 - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Nd-SQa - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.956024 4.700000 # Nd-SQd - pair_coeff @atom:Nd_bNd_aNd_dNd_iNd @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Nd-SQda - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-Nda - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-P1 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-P2 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-P3 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nda-P4 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-P5 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nda-Q0 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-Qa - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-Qd - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-Qda - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Nda-SC1 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Nda-SC2 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Nda-SC3 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Nda-SC4 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Nda-SC5 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Nda-SN0 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-SNa - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-SNd - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-SNda - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-SP1 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-SP2 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Nda-SP3 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nda-SP4 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-SP5 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Nda-SQ0 - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-SQa - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-SQd - pair_coeff @atom:Nda_bNda_aNda_dNda_iNda @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Nda-SQda - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-P1 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-P2 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-P3 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-P4 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P1-P5 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # P1-Q0 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # P1-Qa - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # P1-Qd - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # P1-Qda - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # P1-SC1 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # P1-SC2 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # P1-SC3 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # P1-SC4 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # P1-SC5 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.956024 4.700000 # P1-SN0 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SNa - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SNd - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SNda - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SP1 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SP2 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SP3 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # P1-SP4 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P1-SP5 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # P1-SQ0 - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # P1-SQa - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # P1-SQd - pair_coeff @atom:P1_bP1_aP1_dP1_iP1 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # P1-SQda - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-P2 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-P3 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-P4 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P2-P5 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-Q0 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # P2-Qa - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # P2-Qd - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # P2-Qda - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.549714 4.700000 # P2-SC1 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # P2-SC2 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.740919 4.700000 # P2-SC3 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # P2-SC4 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # P2-SC5 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.956024 4.700000 # P2-SN0 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SNa - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SNd - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SNda - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SP1 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SP2 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SP3 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SP4 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P2-SP5 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # P2-SQ0 - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # P2-SQa - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # P2-SQd - pair_coeff @atom:P2_bP2_aP2_dP2_iP2 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # P2-SQda - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.195030 4.700000 # P3-P3 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.195030 4.700000 # P3-P4 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-P5 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.195030 4.700000 # P3-Q0 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-Qa - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-Qd - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-Qda - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.549714 4.700000 # P3-SC1 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # P3-SC2 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.740919 4.700000 # P3-SC3 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # P3-SC4 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # P3-SC5 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # P3-SN0 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.075527 4.700000 # P3-SNa - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # P3-SNd - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # P3-SNda - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # P3-SP1 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # P3-SP2 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.195030 4.700000 # P3-SP3 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.195030 4.700000 # P3-SP4 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-SP5 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.195030 4.700000 # P3-SQ0 - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-SQa - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-SQd - pair_coeff @atom:P3_bP3_aP3_dP3_iP3 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # P3-SQda - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.195030 4.700000 # P4-P4 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-P5 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-Q0 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-Qa - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-Qd - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-Qda - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 4.700000 # P4-SC1 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.549714 4.700000 # P4-SC2 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # P4-SC3 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # P4-SC4 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # P4-SC5 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # P4-SN0 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # P4-SNa - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.956024 4.700000 # P4-SNd - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.956024 4.700000 # P4-SNda - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # P4-SP1 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # P4-SP2 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.195030 4.700000 # P4-SP3 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.195030 4.700000 # P4-SP4 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-SP5 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-SQ0 - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-SQa - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-SQd - pair_coeff @atom:P4_bP4_aP4_dP4_iP4 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # P4-SQda - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-P5 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.195030 4.700000 # P5-Q0 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-Qa - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-Qd - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-Qda - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 4.700000 # P5-SC1 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.549714 4.700000 # P5-SC2 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # P5-SC3 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # P5-SC4 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # P5-SC5 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # P5-SN0 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.195030 4.700000 # P5-SNa - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.195030 4.700000 # P5-SNd - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.195030 4.700000 # P5-SNda - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SP1 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SP2 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SP3 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SP4 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SP5 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.195030 4.700000 # P5-SQ0 - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SQa - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SQd - pair_coeff @atom:P5_bP5_aP5_dP5_iP5 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # P5-SQda - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Q0-Q0 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-Qa - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-Qd - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-Qda - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Q0-SC1 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Q0-SC2 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Q0-SC3 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Q0-SC4 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Q0-SC5 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Q0-SN0 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Q0-SNa - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.956024 4.700000 # Q0-SNd - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.956024 4.700000 # Q0-SNda - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.956024 4.700000 # Q0-SP1 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-SP2 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.195030 4.700000 # Q0-SP3 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Q0-SP4 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Q0-SP5 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Q0-SQ0 - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-SQa - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-SQd - pair_coeff @atom:Q0_bQ0_aQ0_dQ0_iQ0 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.075527 4.700000 # Q0-SQda - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa-Qa - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-Qd - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-Qda - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa-SC1 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa-SC2 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qa-SC3 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa-SC4 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qa-SC5 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qa-SN0 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa-SNa - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa-SNd - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa-SNda - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa-SP1 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa-SP2 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-SP3 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-SP4 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-SP5 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qa-SQ0 - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa-SQa - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-SQd - pair_coeff @atom:Qa_bQa_aQa_dQa_iQa @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa-SQda - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qd-Qd - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qd-Qda - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qd-SC1 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qd-SC2 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qd-SC3 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qd-SC4 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qd-SC5 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qd-SN0 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qd-SNa - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.956024 4.700000 # Qd-SNd - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qd-SNda - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qd-SP1 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qd-SP2 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qd-SP3 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qd-SP4 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qd-SP5 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qd-SQ0 - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.338434 4.700000 # Qd-SQa - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qd-SQd - pair_coeff @atom:Qd_bQd_aQd_dQd_iQd @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qd-SQda - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-Qda - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qda-SC1 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qda-SC2 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qda-SC3 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qda-SC4 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qda-SC5 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qda-SN0 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qda-SNa - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qda-SNd - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qda-SNda - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qda-SP1 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qda-SP2 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-SP3 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-SP4 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-SP5 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qda-SQ0 - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-SQa - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-SQd - pair_coeff @atom:Qda_bQda_aQda_dQda_iQda @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qda-SQda - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC1-SC1 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC1-SC2 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC1-SC3 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC1-SC4 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC1-SC5 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC1-SN0 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC1-SNa - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC1-SNd - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC1-SNda - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC1-SP1 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC1-SP2 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC1-SP3 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC1-SP4 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC1-SP5 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC1-SQ0 - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC1-SQa - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC1-SQd - pair_coeff @atom:SC1_bSC1_aSC1_dSC1_iSC1 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC1-SQda - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC2-SC2 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC2-SC3 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC2-SC4 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC2-SC5 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC2-SN0 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC2-SNa - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC2-SNd - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC2-SNda - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC2-SP1 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC2-SP2 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC2-SP3 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC2-SP4 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC2-SP5 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC2-SQ0 - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC2-SQa - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC2-SQd - pair_coeff @atom:SC2_bSC2_aSC2_dSC2_iSC2 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC2-SQda - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC3-SC3 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC3-SC4 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC3-SC5 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC3-SN0 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC3-SNa - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC3-SNd - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC3-SNda - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC3-SP1 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC3-SP2 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC3-SP3 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC3-SP4 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC3-SP5 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC3-SQ0 - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.412285 4.300000 # SC3-SQa - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.412285 4.300000 # SC3-SQd - pair_coeff @atom:SC3_bSC3_aSC3_dSC3_iSC3 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.412285 4.300000 # SC3-SQda - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC4-SC4 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC4-SC5 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC4-SN0 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.555689 4.300000 # SC4-SNa - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.555689 4.300000 # SC4-SNd - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.555689 4.300000 # SC4-SNda - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC4-SP1 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC4-SP2 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC4-SP3 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC4-SP4 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC4-SP5 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC4-SQ0 - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC4-SQa - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC4-SQd - pair_coeff @atom:SC4_bSC4_aSC4_dSC4_iSC4 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC4-SQda - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SC5 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SN0 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SNa - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SNd - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SNda - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SP1 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SP2 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC5-SP3 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC5-SP4 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC5-SP5 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC5-SQ0 - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.555689 4.300000 # SC5-SQa - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.555689 4.300000 # SC5-SQd - pair_coeff @atom:SC5_bSC5_aSC5_dSC5_iSC5 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.555689 4.300000 # SC5-SQda - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SN0 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SNa - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SNd - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SNda - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.717018 4.300000 # SN0-SP1 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.717018 4.300000 # SN0-SP2 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SP3 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SP4 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SP5 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SQ0 - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SQa - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SQd - pair_coeff @atom:SN0_bSN0_aSN0_dSN0_iSN0 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.627391 4.300000 # SN0-SQda - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.717018 4.300000 # SNa-SNa - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.806645 4.300000 # SNa-SNd - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.806645 4.300000 # SNa-SNda - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNa-SP1 - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNa-SP2 - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNa-SP3 - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.717018 4.300000 # SNa-SP4 - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.896273 4.300000 # SNa-SP5 - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SNa-SQ0 - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.717018 4.300000 # SNa-SQa - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SNa-SQd - pair_coeff @atom:SNa_bSNa_aSNa_dSNa_iSNa @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SNa-SQda - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.717018 4.300000 # SNd-SNd - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.806645 4.300000 # SNd-SNda - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNd-SP1 - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNd-SP2 - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNd-SP3 - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.717018 4.300000 # SNd-SP4 - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.896273 4.300000 # SNd-SP5 - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SNd-SQ0 - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SNd-SQa - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.717018 4.300000 # SNd-SQd - pair_coeff @atom:SNd_bSNd_aSNd_dSNd_iSNd @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SNd-SQda - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.806645 4.300000 # SNda-SNda - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNda-SP1 - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNda-SP2 - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SNda-SP3 - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.717018 4.300000 # SNda-SP4 - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.896273 4.300000 # SNda-SP5 - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SNda-SQ0 - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SNda-SQa - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SNda-SQd - pair_coeff @atom:SNda_bSNda_aSNda_dSNda_iSNda @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SNda-SQda - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP1-SP1 - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP1-SP2 - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP1-SP3 - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP1-SP4 - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP1-SP5 - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SP1-SQ0 - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SP1-SQa - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SP1-SQd - pair_coeff @atom:SP1_bSP1_aSP1_dSP1_iSP1 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SP1-SQda - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP2-SP2 - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP2-SP3 - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP2-SP4 - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP2-SP5 - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP2-SQ0 - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SP2-SQa - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SP2-SQd - pair_coeff @atom:SP2_bSP2_aSP2_dSP2_iSP2 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SP2-SQda - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.896273 4.300000 # SP3-SP3 - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.896273 4.300000 # SP3-SP4 - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP3-SP5 - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.896273 4.300000 # SP3-SQ0 - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.003825 4.300000 # SP3-SQa - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.003825 4.300000 # SP3-SQd - pair_coeff @atom:SP3_bSP3_aSP3_dSP3_iSP3 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.003825 4.300000 # SP3-SQda - pair_coeff @atom:SP4_bSP4_aSP4_dSP4_iSP4 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.896273 4.300000 # SP4-SP4 - pair_coeff @atom:SP4_bSP4_aSP4_dSP4_iSP4 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP4-SP5 - pair_coeff @atom:SP4_bSP4_aSP4_dSP4_iSP4 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP4-SQ0 - pair_coeff @atom:SP4_bSP4_aSP4_dSP4_iSP4 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.003825 4.300000 # SP4-SQa - pair_coeff @atom:SP4_bSP4_aSP4_dSP4_iSP4 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.003825 4.300000 # SP4-SQd - pair_coeff @atom:SP4_bSP4_aSP4_dSP4_iSP4 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.003825 4.300000 # SP4-SQda - pair_coeff @atom:SP5_bSP5_aSP5_dSP5_iSP5 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP5-SP5 - pair_coeff @atom:SP5_bSP5_aSP5_dSP5_iSP5 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.896273 4.300000 # SP5-SQ0 - pair_coeff @atom:SP5_bSP5_aSP5_dSP5_iSP5 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.003825 4.300000 # SP5-SQa - pair_coeff @atom:SP5_bSP5_aSP5_dSP5_iSP5 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.003825 4.300000 # SP5-SQd - pair_coeff @atom:SP5_bSP5_aSP5_dSP5_iSP5 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.003825 4.300000 # SP5-SQda - pair_coeff @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SQ0-SQ0 - pair_coeff @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.806645 4.300000 # SQ0-SQa - pair_coeff @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.806645 4.300000 # SQ0-SQd - pair_coeff @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.806645 4.300000 # SQ0-SQda - pair_coeff @atom:SQa_bSQa_aSQa_dSQa_iSQa @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SQa-SQa - pair_coeff @atom:SQa_bSQa_aSQa_dSQa_iSQa @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.003825 4.300000 # SQa-SQd - pair_coeff @atom:SQa_bSQa_aSQa_dSQa_iSQa @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.003825 4.300000 # SQa-SQda - pair_coeff @atom:SQd_bSQd_aSQd_dSQd_iSQd @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SQd-SQd - pair_coeff @atom:SQd_bSQd_aSQd_dSQd_iSQd @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.003825 4.300000 # SQd-SQda - pair_coeff @atom:SQda_bSQda_aSQda_dSQda_iSQda @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.003825 4.300000 # SQda-SQda - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-BP4 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-C1 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-C2 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-C3 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-C41 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-C4 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-C5 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-N0 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-Na - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-Nd - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-Nda - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-P1 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-P2 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-P3 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-P4 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-P5 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-Q0 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-Qa - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-Qd - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-Qda - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-SC1 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-SC2 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-SC3 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-SC4 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-SC5 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-SN0 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-SNa - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-SNd - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-SNda - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-SP1 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C41-SP2 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C41-SP3 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-SP4 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-SP5 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-SQ0 - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-SQa - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-SQd - pair_coeff @atom:C41_bC4_aC41_dC41_iC41 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.645316 4.700000 # C41-SQda - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-BP4 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-C1 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-C2 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-C3 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-C42 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-C4 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-C5 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-N0 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-Na - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-Nd - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-Nda - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-P1 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-P2 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-P3 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-P4 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-P5 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-Q0 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-Qa - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-Qd - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-Qda - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-SC1 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-SC2 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-SC3 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-SC4 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-SC5 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-SN0 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-SNa - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-SNd - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-SNda - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-SP1 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-SP2 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # C42-SP3 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-SP4 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-SP5 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-SQ0 - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-SQa - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-SQd - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.645316 4.700000 # C42-SQda - pair_coeff @atom:C42_bC4_aC42_dC42_iC42 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # C42-C41 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-BP4 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na1-C1 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na1-C2 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na1-C3 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na1-C4 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na1-C5 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na1-N0 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-Na1 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-Na - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-Nd - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-Nda - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-P1 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-P2 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-P3 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-P4 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Na1-P5 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-Q0 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-Qa - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Na1-Qd - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Na1-Qda - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na1-SC1 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na1-SC2 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na1-SC3 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na1-SC4 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na1-SC5 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na1-SN0 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-SNa - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-SNd - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-SNda - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-SP1 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-SP2 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na1-SP3 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-SP4 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Na1-SP5 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-SQ0 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na1-SQa - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Na1-SQd - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Na1-SQda - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na1-C41 - pair_coeff @atom:Na1_bNa1_aNa1_dNa1_iNa1 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na1-C42 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-BP4 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na2-C1 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na2-C2 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na2-C3 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na2-C4 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na2-C5 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na2-N0 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-Na2 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-Na - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-Nd - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-Nda - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-P1 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-P2 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-P3 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-P4 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Na2-P5 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-Q0 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-Qa - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Na2-Qd - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Na2-Qda - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na2-SC1 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na2-SC2 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.645316 4.700000 # Na2-SC3 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na2-SC4 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na2-SC5 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Na2-SN0 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-SNa - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-SNd - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-SNda - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-SP1 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-SP2 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # Na2-SP3 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-SP4 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.195030 4.700000 # Na2-SP5 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-SQ0 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-SQa - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.195030 4.700000 # Na2-SQd - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.195030 4.700000 # Na2-SQda - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na2-C41 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # Na2-C42 - pair_coeff @atom:Na2_bNa2_aNa2_dNa2_iNa2 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.956024 4.700000 # Na2-Na1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-BP4 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa1-C1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa1-C2 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qa1-C3 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa1-C4 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qa1-C5 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qa1-N0 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa1-Na - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-Nd - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-Nda - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-P1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-P2 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-P3 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-P4 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-P5 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qa1-Q0 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-Qa1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-Qa - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-Qd - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-Qda - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa1-SC1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa1-SC2 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qa1-SC3 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa1-SC4 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qa1-SC5 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qa1-SN0 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa1-SNa - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-SNd - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-SNda - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-SP1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-SP2 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-SP3 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-SP4 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-SP5 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qa1-SQ0 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa1-SQa - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-SQd - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa1-SQda - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa1-C41 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa1-C42 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa1-Na1 - pair_coeff @atom:Qa1_bQa1_aQa1_dQa1_iQa1 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa1-Na2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-BP4 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa2-C1 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa2-C2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qa2-C3 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa2-C4 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qa2-C5 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qa2-N0 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa2-Na - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-Nd - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-Nda - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-P1 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-P2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-P3 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-P4 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-P5 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qa2-Q0 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-Qa2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-Qa - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-Qd - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-Qda - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa2-SC1 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.478012 6.200000 # Qa2-SC2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.549714 4.700000 # Qa2-SC3 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa2-SC4 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # Qa2-SC5 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # Qa2-SN0 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa2-SNa - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-SNd - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-SNda - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-SP1 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-SP2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-SP3 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-SP4 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-SP5 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 1.075527 4.700000 # Qa2-SQ0 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-SQa - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-SQd - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 1.338434 4.700000 # Qa2-SQda - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa2-C41 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.645316 4.700000 # Qa2-C42 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa2-Na1 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.956024 4.700000 # Qa2-Na2 - pair_coeff @atom:Qa2_bQa2_aQa2_dQa2_iQa2 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 1.195030 4.700000 # Qa2-Qa1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC11-BP4 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC11-C1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC11-C2 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC11-C3 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC11-C4 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC11-C5 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-N0 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-Na - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-Nd - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-Nda - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-P1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC11-P2 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC11-P3 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC11-P4 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC11-P5 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-Q0 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-Qa - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-Qd - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-Qda - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC11-SC11 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC11-SC1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC11-SC2 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC11-SC3 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC11-SC4 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC11-SC5 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC11-SN0 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC11-SNa - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC11-SNd - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC11-SNda - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC11-SP1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC11-SP2 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC11-SP3 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC11-SP4 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC11-SP5 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-SQ0 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-SQa - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-SQd - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-SQda - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC11-C41 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC11-C42 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-Na1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC11-Na2 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-Qa1 - pair_coeff @atom:SC11_bSC11_aSC11_dSC11_iSC11 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC11-Qa2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC110-BP4 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC110-C1 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC110-C2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC110-C3 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC110-C4 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC110-C5 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-N0 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-Na - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-Nd - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-Nda - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-P1 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC110-P2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC110-P3 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC110-P4 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC110-P5 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-Q0 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-Qa - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-Qd - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-Qda - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC110-SC110 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC110-SC1 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC110-SC2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC110-SC3 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC110-SC4 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC110-SC5 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC110-SN0 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC110-SNa - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC110-SNd - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC110-SNda - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC110-SP1 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC110-SP2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC110-SP3 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC110-SP4 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC110-SP5 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-SQ0 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-SQa - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-SQd - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-SQda - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC110-C41 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC110-C42 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-Na1 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC110-Na2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-Qa1 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC110-Qa2 - pair_coeff @atom:SC110_bSC110_aSC110_dSC110_iSC110 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC110-SC11 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC111-BP4 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC111-C1 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC111-C2 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC111-C3 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC111-C4 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC111-C5 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-N0 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-Na - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-Nd - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-Nda - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-P1 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC111-P2 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC111-P3 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC111-P4 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC111-P5 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-Q0 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-Qa - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-Qd - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-Qda - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC111-SC111 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC111-SC1 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC111-SC2 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC111-SC3 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC111-SC4 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC111-SC5 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC111-SN0 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC111-SNa - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC111-SNd - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC111-SNda - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC111-SP1 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC111-SP2 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC111-SP3 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC111-SP4 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC111-SP5 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-SQ0 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-SQa - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-SQd - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-SQda - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC111-C41 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC111-C42 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-Na1 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC111-Na2 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-Qa1 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC111-Qa2 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC111-SC11 - pair_coeff @atom:SC111_bSC111_aSC111_dSC111_iSC111 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC111-SC110 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC112-BP4 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC112-C1 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC112-C2 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC112-C3 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC112-C4 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC112-C5 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-N0 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-Na - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-Nd - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-Nda - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-P1 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC112-P2 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC112-P3 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC112-P4 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC112-P5 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-Q0 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-Qa - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-Qd - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-Qda - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC112 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC1 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC2 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC3 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC112-SC4 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC112-SC5 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC112-SN0 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC112-SNa - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC112-SNd - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC112-SNda - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC112-SP1 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC112-SP2 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC112-SP3 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC112-SP4 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC112-SP5 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-SQ0 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-SQa - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-SQd - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-SQda - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC112-C41 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC112-C42 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-Na1 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC112-Na2 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-Qa1 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC112-Qa2 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC11 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC110 - pair_coeff @atom:SC112_bSC112_aSC112_dSC112_iSC112 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC112-SC111 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC12-BP4 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC12-C1 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC12-C2 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC12-C3 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC12-C4 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC12-C5 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-N0 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-Na - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-Nd - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-Nda - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-P1 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC12-P2 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC12-P3 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC12-P4 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC12-P5 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-Q0 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-Qa - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-Qd - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-Qda - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC12 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC1 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC2 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC3 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC12-SC4 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC12-SC5 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC12-SN0 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC12-SNa - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC12-SNd - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC12-SNda - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC12-SP1 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC12-SP2 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC12-SP3 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC12-SP4 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC12-SP5 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-SQ0 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-SQa - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-SQd - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-SQda - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC12-C41 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC12-C42 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-Na1 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC12-Na2 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-Qa1 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC12-Qa2 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC11 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC110 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC111 - pair_coeff @atom:SC12_bSC12_aSC12_dSC12_iSC12 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC12-SC112 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC13-BP4 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC13-C1 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC13-C2 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC13-C3 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC13-C4 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC13-C5 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-N0 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-Na - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-Nd - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-Nda - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-P1 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC13-P2 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC13-P3 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC13-P4 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC13-P5 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-Q0 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-Qa - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-Qd - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-Qda - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC13 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC1 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC2 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC3 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC13-SC4 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC13-SC5 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC13-SN0 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC13-SNa - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC13-SNd - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC13-SNda - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC13-SP1 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC13-SP2 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC13-SP3 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC13-SP4 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC13-SP5 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-SQ0 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-SQa - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-SQd - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-SQda - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC13-C41 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC13-C42 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-Na1 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC13-Na2 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-Qa1 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC13-Qa2 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC11 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC110 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC111 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC112 - pair_coeff @atom:SC13_bSC13_aSC13_dSC13_iSC13 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC13-SC12 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC14-BP4 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC14-C1 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC14-C2 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC14-C3 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC14-C4 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC14-C5 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-N0 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-Na - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-Nd - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-Nda - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-P1 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC14-P2 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC14-P3 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC14-P4 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC14-P5 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-Q0 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-Qa - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-Qd - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-Qda - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC14 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC1 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC2 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC3 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC14-SC4 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC14-SC5 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC14-SN0 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC14-SNa - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC14-SNd - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC14-SNda - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC14-SP1 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC14-SP2 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC14-SP3 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC14-SP4 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC14-SP5 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-SQ0 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-SQa - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-SQd - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-SQda - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC14-C41 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC14-C42 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-Na1 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC14-Na2 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-Qa1 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC14-Qa2 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC11 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC110 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC111 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC112 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC12 - pair_coeff @atom:SC14_bSC14_aSC14_dSC14_iSC14 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC14-SC13 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC15-BP4 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC15-C1 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC15-C2 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC15-C3 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC15-C4 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC15-C5 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-N0 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-Na - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-Nd - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-Nda - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-P1 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC15-P2 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC15-P3 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC15-P4 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC15-P5 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-Q0 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-Qa - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-Qd - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-Qda - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC15 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC1 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC2 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC3 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC15-SC4 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC15-SC5 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC15-SN0 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC15-SNa - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC15-SNd - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC15-SNda - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC15-SP1 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC15-SP2 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC15-SP3 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC15-SP4 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC15-SP5 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-SQ0 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-SQa - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-SQd - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-SQda - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC15-C41 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC15-C42 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-Na1 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC15-Na2 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-Qa1 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC15-Qa2 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC11 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC110 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC111 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC112 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC12 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC13 - pair_coeff @atom:SC15_bSC15_aSC15_dSC15_iSC15 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC15-SC14 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC16-BP4 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC16-C1 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC16-C2 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC16-C3 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC16-C4 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC16-C5 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-N0 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-Na - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-Nd - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-Nda - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-P1 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC16-P2 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC16-P3 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC16-P4 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC16-P5 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-Q0 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-Qa - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-Qd - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-Qda - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC16 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC1 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC2 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC3 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC16-SC4 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC16-SC5 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC16-SN0 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC16-SNa - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC16-SNd - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC16-SNda - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC16-SP1 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC16-SP2 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC16-SP3 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC16-SP4 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC16-SP5 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-SQ0 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-SQa - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-SQd - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-SQda - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC16-C41 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC16-C42 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-Na1 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC16-Na2 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-Qa1 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC16-Qa2 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC11 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC110 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC111 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC112 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC12 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC13 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC14 - pair_coeff @atom:SC16_bSC16_aSC16_dSC16_iSC16 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC16-SC15 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC17-BP4 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC17-C1 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC17-C2 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC17-C3 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC17-C4 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC17-C5 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-N0 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-Na - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-Nd - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-Nda - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-P1 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC17-P2 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC17-P3 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC17-P4 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC17-P5 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-Q0 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-Qa - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-Qd - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-Qda - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC17 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC1 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC2 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC3 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC17-SC4 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC17-SC5 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC17-SN0 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC17-SNa - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC17-SNd - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC17-SNda - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC17-SP1 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC17-SP2 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC17-SP3 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC17-SP4 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC17-SP5 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-SQ0 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-SQa - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-SQd - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-SQda - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC17-C41 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC17-C42 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-Na1 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC17-Na2 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-Qa1 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC17-Qa2 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC11 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC110 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC111 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC112 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC12 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC13 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC14 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC15 - pair_coeff @atom:SC17_bSC17_aSC17_dSC17_iSC17 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC17-SC16 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC18-BP4 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC18-C1 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC18-C2 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC18-C3 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC18-C4 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC18-C5 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-N0 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-Na - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-Nd - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-Nda - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-P1 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC18-P2 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC18-P3 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC18-P4 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC18-P5 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-Q0 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-Qa - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-Qd - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-Qda - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC18 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC1 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC2 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC3 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC18-SC4 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC18-SC5 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC18-SN0 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC18-SNa - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC18-SNd - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC18-SNda - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC18-SP1 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC18-SP2 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC18-SP3 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC18-SP4 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC18-SP5 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-SQ0 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-SQa - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-SQd - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-SQda - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC18-C41 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC18-C42 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-Na1 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC18-Na2 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-Qa1 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC18-Qa2 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC11 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC110 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC111 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC112 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC12 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC13 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC14 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC15 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC16 - pair_coeff @atom:SC18_bSC18_aSC18_dSC18_iSC18 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC18-SC17 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC19-BP4 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC19-C1 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC19-C2 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC19-C3 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC19-C4 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC19-C5 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-N0 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-Na - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-Nd - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-Nda - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-P1 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC19-P2 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC19-P3 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC19-P4 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.478012 4.700000 # SC19-P5 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-Q0 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-Qa - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-Qd - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-Qda - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC19_bSC19_aSC19_dSC19_iSC19 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC19 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC1 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC2 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC3 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC19-SC4 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC19-SC5 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC19-SN0 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC19-SNa - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC19-SNd - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC19-SNda - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC19-SP1 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC19-SP2 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC19-SP3 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC19-SP4 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.358509 4.300000 # SC19-SP5 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-SQ0 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-SQa - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-SQd - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-SQda - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC19-C41 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC19-C42 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-Na1 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC19-Na2 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-Qa1 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.478012 6.200000 # SC19-Qa2 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC11 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC110 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC111 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC112 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC12 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC13 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC14 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC15 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC16 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC17 - pair_coeff @atom:SC19_bSC19_aSC19_dSC19_iSC19 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC19-SC18 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-BP4 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C1 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C2 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C3 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C4 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C5 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-N0 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-Na - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-Nd - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-Nda - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-P1 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC31-P2 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC31-P3 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-P4 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-P5 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC31-Q0 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.549714 4.700000 # SC31-Qa - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.549714 4.700000 # SC31-Qd - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.549714 4.700000 # SC31-Qda - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC1 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC2 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC31_bSC31_aSC31_dSC31_iSC31 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC31 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC3 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC4 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC5 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SN0 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC31-SNa - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC31-SNd - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC31-SNda - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SP1 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC31-SP2 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC31-SP3 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC31-SP4 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC31-SP5 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC31-SQ0 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.412285 4.300000 # SC31-SQa - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.412285 4.300000 # SC31-SQd - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.412285 4.300000 # SC31-SQda - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C41 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC31-C42 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-Na1 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC31-Na2 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC31-Qa1 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC31-Qa2 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC11 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC110 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC111 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC112 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC12 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC13 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC14 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC15 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC16 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC17 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC18 - pair_coeff @atom:SC31_bSC31_aSC31_dSC31_iSC31 @atom:SC19_bSC19_aSC19_dSC19_iSC19 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC31-SC19 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-BP4 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C1 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C2 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C3 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C4 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C5 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-N0 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-Na - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-Nd - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-Nda - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-P1 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC32-P2 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC32-P3 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-P4 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-P5 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC32-Q0 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.549714 4.700000 # SC32-Qa - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.549714 4.700000 # SC32-Qd - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.549714 4.700000 # SC32-Qda - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC1 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC2 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC32_bSC32_aSC32_dSC32_iSC32 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC32 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC3 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC4 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC5 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SN0 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC32-SNa - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC32-SNd - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC32-SNda - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SP1 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC32-SP2 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC32-SP3 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC32-SP4 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC32-SP5 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC32-SQ0 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.412285 4.300000 # SC32-SQa - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.412285 4.300000 # SC32-SQd - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.412285 4.300000 # SC32-SQda - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C41 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC32-C42 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-Na1 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC32-Na2 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC32-Qa1 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC32-Qa2 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC11 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC110 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC111 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC112 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC12 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC13 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC14 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC15 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC16 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC17 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC18 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC19_bSC19_aSC19_dSC19_iSC19 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC19 - pair_coeff @atom:SC32_bSC32_aSC32_dSC32_iSC32 @atom:SC31_bSC31_aSC31_dSC31_iSC31 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC32-SC31 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-BP4 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C1 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C2 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C3 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C4 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C5 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-N0 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-Na - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-Nd - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-Nda - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-P1 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC33-P2 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 0.740919 4.700000 # SC33-P3 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-P4 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-P5 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC33-Q0 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 0.549714 4.700000 # SC33-Qa - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 0.549714 4.700000 # SC33-Qd - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 0.549714 4.700000 # SC33-Qda - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC1 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC2 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC33_bSC33_aSC33_dSC33_iSC33 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC33 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC3 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC4 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC5 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SN0 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.483987 4.300000 # SC33-SNa - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.483987 4.300000 # SC33-SNd - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.483987 4.300000 # SC33-SNda - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SP1 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC33-SP2 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.555689 4.300000 # SC33-SP3 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC33-SP4 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 0.483987 4.300000 # SC33-SP5 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.412285 4.300000 # SC33-SQ0 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.412285 4.300000 # SC33-SQa - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.412285 4.300000 # SC33-SQd - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.412285 4.300000 # SC33-SQda - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C41 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.836521 4.700000 # SC33-C42 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-Na1 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 0.645316 4.700000 # SC33-Na2 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC33-Qa1 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 0.549714 4.700000 # SC33-Qa2 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC11 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC110 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC111 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC112 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC12 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC13 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC14 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC15 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC16 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC17 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC18 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC19_bSC19_aSC19_dSC19_iSC19 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC19 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC31_bSC31_aSC31_dSC31_iSC31 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC31 - pair_coeff @atom:SC33_bSC33_aSC33_dSC33_iSC33 @atom:SC32_bSC32_aSC32_dSC32_iSC32 lj/gromacs/coul/gromacs 0.627391 4.300000 # SC33-SC32 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-BP4 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SP11-C1 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # SP11-C2 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP11-C3 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP11-C4 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP11-C5 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.956024 4.700000 # SP11-N0 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-Na - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-Nd - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-Nda - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-P1 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-P2 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-P3 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-P4 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # SP11-P5 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # SP11-Q0 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # SP11-Qa - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # SP11-Qd - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # SP11-Qda - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC1 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.555689 4.300000 # SP11-SC2 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP11-SC3 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP11-SC4 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP11-SC5 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SP11-SN0 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SNa - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SNd - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SNda - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SP11_bSP11_aSP11_dSP11_iSP11 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SP11 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SP1 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SP2 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SP3 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP11-SP4 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP11-SP5 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SP11-SQ0 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SP11-SQa - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SP11-SQd - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SP11-SQda - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP11-C41 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP11-C42 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-Na1 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP11-Na2 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 1.195030 4.700000 # SP11-Qa1 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 1.195030 4.700000 # SP11-Qa2 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC11 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC110 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC111 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC112 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC12 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC13 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC14 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC15 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC16 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC17 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC18 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC19_bSC19_aSC19_dSC19_iSC19 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP11-SC19 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC31_bSC31_aSC31_dSC31_iSC31 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP11-SC31 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC32_bSC32_aSC32_dSC32_iSC32 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP11-SC32 - pair_coeff @atom:SP11_bSP11_aSP11_dSP11_iSP11 @atom:SC33_bSC33_aSC33_dSC33_iSC33 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP11-SC33 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:BP4_bBP4_aBP4_dBP4_iBP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-BP4 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C1_bC1_aC1_dC1_iC1 lj/gromacs/coul/gromacs 0.645316 4.700000 # SP12-C1 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C2_bC2_aC2_dC2_iC2 lj/gromacs/coul/gromacs 0.740919 4.700000 # SP12-C2 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C3_bC3_aC3_dC3_iC3 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP12-C3 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C4_bC4_aC4_dC4_iC4 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP12-C4 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C5_bC5_aC5_dC5_iC5 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP12-C5 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:N0_bN0_aN0_dN0_iN0 lj/gromacs/coul/gromacs 0.956024 4.700000 # SP12-N0 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Na_bNa_aNa_dNa_iNa lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-Na - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Nd_bNd_aNd_dNd_iNd lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-Nd - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Nda_bNda_aNda_dNda_iNda lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-Nda - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:P1_bP1_aP1_dP1_iP1 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-P1 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:P2_bP2_aP2_dP2_iP2 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-P2 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:P3_bP3_aP3_dP3_iP3 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-P3 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:P4_bP4_aP4_dP4_iP4 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-P4 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:P5_bP5_aP5_dP5_iP5 lj/gromacs/coul/gromacs 1.338434 4.700000 # SP12-P5 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Q0_bQ0_aQ0_dQ0_iQ0 lj/gromacs/coul/gromacs 0.956024 4.700000 # SP12-Q0 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Qa_bQa_aQa_dQa_iQa lj/gromacs/coul/gromacs 1.195030 4.700000 # SP12-Qa - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Qd_bQd_aQd_dQd_iQd lj/gromacs/coul/gromacs 1.195030 4.700000 # SP12-Qd - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Qda_bQda_aQda_dQda_iQda lj/gromacs/coul/gromacs 1.195030 4.700000 # SP12-Qda - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC1_bSC1_aSC1_dSC1_iSC1 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC1 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC2_bSC2_aSC2_dSC2_iSC2 lj/gromacs/coul/gromacs 0.555689 4.300000 # SP12-SC2 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC3_bSC3_aSC3_dSC3_iSC3 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP12-SC3 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC4_bSC4_aSC4_dSC4_iSC4 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP12-SC4 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC5_bSC5_aSC5_dSC5_iSC5 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP12-SC5 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SN0_bSN0_aSN0_dSN0_iSN0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SP12-SN0 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SNa_bSNa_aSNa_dSNa_iSNa lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SNa - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SNd_bSNd_aSNd_dSNd_iSNd lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SNd - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SNda_bSNda_aSNda_dSNda_iSNda lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SNda - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP12_bSP12_aSP12_dSP12_iSP12 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SP12 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP1_bSP1_aSP1_dSP1_iSP1 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SP1 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP2_bSP2_aSP2_dSP2_iSP2 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SP2 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP3_bSP3_aSP3_dSP3_iSP3 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SP3 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP4_bSP4_aSP4_dSP4_iSP4 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SP4 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP5_bSP5_aSP5_dSP5_iSP5 lj/gromacs/coul/gromacs 1.003825 4.300000 # SP12-SP5 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SQ0_bSQ0_aSQ0_dSQ0_iSQ0 lj/gromacs/coul/gromacs 0.717018 4.300000 # SP12-SQ0 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SQa_bSQa_aSQa_dSQa_iSQa lj/gromacs/coul/gromacs 0.896273 4.300000 # SP12-SQa - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SQd_bSQd_aSQd_dSQd_iSQd lj/gromacs/coul/gromacs 0.896273 4.300000 # SP12-SQd - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SQda_bSQda_aSQda_dSQda_iSQda lj/gromacs/coul/gromacs 0.896273 4.300000 # SP12-SQda - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C41_bC4_aC41_dC41_iC41 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP12-C41 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:C42_bC4_aC42_dC42_iC42 lj/gromacs/coul/gromacs 0.836521 4.700000 # SP12-C42 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Na1_bNa1_aNa1_dNa1_iNa1 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-Na1 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Na2_bNa2_aNa2_dNa2_iNa2 lj/gromacs/coul/gromacs 1.075527 4.700000 # SP12-Na2 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Qa1_bQa1_aQa1_dQa1_iQa1 lj/gromacs/coul/gromacs 1.195030 4.700000 # SP12-Qa1 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:Qa2_bQa2_aQa2_dQa2_iQa2 lj/gromacs/coul/gromacs 1.195030 4.700000 # SP12-Qa2 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC11_bSC11_aSC11_dSC11_iSC11 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC11 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC110_bSC110_aSC110_dSC110_iSC110 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC110 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC111_bSC111_aSC111_dSC111_iSC111 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC111 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC112_bSC112_aSC112_dSC112_iSC112 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC112 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC12_bSC12_aSC12_dSC12_iSC12 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC12 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC13_bSC13_aSC13_dSC13_iSC13 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC13 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC14_bSC14_aSC14_dSC14_iSC14 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC14 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC15_bSC15_aSC15_dSC15_iSC15 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC15 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC16_bSC16_aSC16_dSC16_iSC16 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC16 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC17_bSC17_aSC17_dSC17_iSC17 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC17 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC18_bSC18_aSC18_dSC18_iSC18 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC18 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC19_bSC19_aSC19_dSC19_iSC19 lj/gromacs/coul/gromacs 0.483987 4.300000 # SP12-SC19 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC31_bSC31_aSC31_dSC31_iSC31 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP12-SC31 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC32_bSC32_aSC32_dSC32_iSC32 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP12-SC32 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SC33_bSC33_aSC33_dSC33_iSC33 lj/gromacs/coul/gromacs 0.627391 4.300000 # SP12-SC33 - pair_coeff @atom:SP12_bSP12_aSP12_dSP12_iSP12 @atom:SP11_bSP11_aSP11_dSP11_iSP11 lj/gromacs/coul/gromacs 0.806645 4.300000 # SP12-SP11 - } # end of nonbonded parameters - - write_once("In Settings") { - # ----- Bonds ----- - bond_coeff @bond:C1-C1 harmonic 1.493787 4.700000 # C1-C1 - bond_coeff @bond:C1-C3 harmonic 1.493787 4.700000 # C1-C3 - bond_coeff @bond:C1-C4 harmonic 1.493787 4.700000 # C1-C4 - bond_coeff @bond:C1-Na harmonic 1.493787 4.700000 # C1-Na - bond_coeff @bond:C1-Na1 harmonic 1.493787 4.700000 # C1-Na1 - bond_coeff @bond:C1-Na2 harmonic 1.493787 4.700000 # C1-Na2 - bond_coeff @bond:C1-P5 harmonic 1.493787 4.700000 # C1-P5 - bond_coeff @bond:C2-C4 harmonic 1.493787 4.700000 # C2-C4 - bond_coeff @bond:C3-P1 harmonic 1.493787 4.700000 # C3-P1 - bond_coeff @bond:C4-C4 harmonic 1.493787 4.700000 # C4-C4 - bond_coeff @bond:C4-Na harmonic 1.493787 4.700000 # C4-Na - bond_coeff @bond:Na-Na harmonic 1.493787 3.700000 # Na-Na - bond_coeff @bond:Na-Na1 harmonic 1.493787 3.700000 # Na-Na1 - bond_coeff @bond:Na-Na2 harmonic 1.493787 3.700000 # Na-Na2 - bond_coeff @bond:Na-Qa harmonic 1.493787 4.700000 # Na-Qa - bond_coeff @bond:Na-Qa1 harmonic 1.493787 3.700000 # Na-Qa1 - bond_coeff @bond:Na-Qa2 harmonic 1.493787 3.700000 # Na-Qa2 - bond_coeff @bond:Na1-Qa harmonic 1.493787 3.700000 # Na1-Qa - bond_coeff @bond:Na2-Qa harmonic 1.493787 3.700000 # Na2-Qa - bond_coeff @bond:P1-P5 harmonic 1.493787 3.700000 # P1-P5 - bond_coeff @bond:P4-Qa harmonic 1.493787 3.700000 # P4-Qa - bond_coeff @bond:P5-Qa harmonic 1.493787 4.700000 # P5-Qa - bond_coeff @bond:P5-Qa1 harmonic 1.493787 3.700000 # P5-Qa1 - bond_coeff @bond:P5-Qa2 harmonic 1.493787 3.700000 # P5-Qa2 - bond_coeff @bond:Q0-Qa harmonic 1.493787 4.700000 # Q0-Qa - bond_coeff @bond:Qa-Qd harmonic 1.493787 4.700000 # Qa-Qd - bond_coeff @bond:C1-C1 harmonic 1.493787 4.700000 # C1-C1 - bond_coeff @bond:C1-C3 harmonic 1.493787 4.700000 # C1-C3 - bond_coeff @bond:C1-Na harmonic 1.493787 4.700000 # C1-Na - bond_coeff @bond:C1-SC12 harmonic 1.493787 4.250000 # C1-SC12 - bond_coeff @bond:C1-SC17 harmonic 1.493787 4.250000 # C1-SC17 - bond_coeff @bond:Na-SC1 harmonic 1.493787 4.700000 # Na-SC1 - bond_coeff @bond:Qa-SC111 harmonic 1.493787 4.250000 # Qa-SC111 - bond_coeff @bond:SC1-SC11 harmonic 23.900600 3.410000 # SC1-SC11 - bond_coeff @bond:SC1-SC13 harmonic 23.900600 2.030000 # SC1-SC13 - bond_coeff @bond:SC1-SC15 harmonic 23.900600 2.420000 # SC1-SC15 - bond_coeff @bond:SC1-SC16 harmonic 23.900600 2.940000 # SC1-SC16 - bond_coeff @bond:SC1-SC17 harmonic 23.900600 4.060000 # SC1-SC17 - bond_coeff @bond:SC1-SC18 harmonic 23.900600 2.030000 # SC1-SC18 - bond_coeff @bond:SC1-SC3 harmonic 23.900600 2.600000 # SC1-SC3 - bond_coeff @bond:SC1-SC32 harmonic 23.900600 3.460000 # SC1-SC32 - bond_coeff @bond:SC1-SP1 harmonic 23.900600 2.420000 # SC1-SP1 - bond_coeff @bond:SC11-SC12 harmonic 23.900600 5.440000 # SC11-SC12 - bond_coeff @bond:SC11-SC13 harmonic 23.900600 2.130000 # SC11-SC13 - bond_coeff @bond:SC11-SC14 harmonic 23.900600 2.940000 # SC11-SC14 - bond_coeff @bond:SC11-SC31 harmonic 23.900600 2.720000 # SC11-SC31 - bond_coeff @bond:SC11-SP1 harmonic 23.900600 6.040000 # SC11-SP1 - bond_coeff @bond:SC110-SC3 harmonic 23.900600 2.600000 # SC110-SC3 - bond_coeff @bond:SC110-SP1 harmonic 23.900600 2.420000 # SC110-SP1 - bond_coeff @bond:SC110-SP11 harmonic 23.900600 3.410000 # SC110-SP11 - bond_coeff @bond:SC111-SC112 harmonic 23.900600 3.680000 # SC111-SC112 - bond_coeff @bond:SC111-SP11 harmonic 23.900600 5.440000 # SC111-SP11 - bond_coeff @bond:SC111-SP12 harmonic 23.900600 4.060000 # SC111-SP12 - bond_coeff @bond:SC112-SP1 harmonic 23.900600 2.030000 # SC112-SP1 - bond_coeff @bond:SC112-SP11 harmonic 23.900600 2.130000 # SC112-SP11 - bond_coeff @bond:SC12-SC13 harmonic 23.900600 3.680000 # SC12-SC13 - bond_coeff @bond:SC12-SC14 harmonic 23.900600 4.060000 # SC12-SC14 - bond_coeff @bond:SC14-SC31 harmonic 23.900600 3.460000 # SC14-SC31 - bond_coeff @bond:SC15-SC16 harmonic 23.900600 3.410000 # SC15-SC16 - bond_coeff @bond:SC15-SC3 harmonic 23.900600 2.600000 # SC15-SC3 - bond_coeff @bond:SC16-SC17 harmonic 23.900600 5.440000 # SC16-SC17 - bond_coeff @bond:SC16-SC18 harmonic 23.900600 2.130000 # SC16-SC18 - bond_coeff @bond:SC16-SC19 harmonic 23.900600 6.040000 # SC16-SC19 - bond_coeff @bond:SC16-SC32 harmonic 23.900600 2.720000 # SC16-SC32 - bond_coeff @bond:SC17-SC18 harmonic 23.900600 3.680000 # SC17-SC18 - bond_coeff @bond:SC19-SC32 harmonic 23.900600 4.930000 # SC19-SC32 - bond_coeff @bond:SC31-SP1 harmonic 23.900600 4.930000 # SC31-SP1 - bond_coeff @bond:SC33-SP1 harmonic 23.900600 4.930000 # SC33-SP1 - bond_coeff @bond:SC33-SP11 harmonic 23.900600 2.720000 # SC33-SP11 - bond_coeff @bond:SC33-SP12 harmonic 23.900600 3.460000 # SC33-SP12 - bond_coeff @bond:SP1-SP11 harmonic 23.900600 6.040000 # SP1-SP11 - bond_coeff @bond:SP11-SP12 harmonic 23.900600 2.940000 # SP11-SP12 - } - - write_once("Data Bonds By Type") { - @bond:C1-C1 @atom:*_bC1_a*_d*_i* @atom:*_bC1_a*_d*_i* - @bond:C1-C3 @atom:*_bC1_a*_d*_i* @atom:*_bC3_a*_d*_i* - @bond:C1-C4 @atom:*_bC1_a*_d*_i* @atom:*_bC4_a*_d*_i* - @bond:C1-Na @atom:*_bC1_a*_d*_i* @atom:*_bNa_a*_d*_i* - @bond:C1-Na1 @atom:*_bC1_a*_d*_i* @atom:*_bNa1_a*_d*_i* - @bond:C1-Na2 @atom:*_bC1_a*_d*_i* @atom:*_bNa2_a*_d*_i* - @bond:C1-P5 @atom:*_bC1_a*_d*_i* @atom:*_bP5_a*_d*_i* - @bond:C2-C4 @atom:*_bC2_a*_d*_i* @atom:*_bC4_a*_d*_i* - @bond:C3-P1 @atom:*_bC3_a*_d*_i* @atom:*_bP1_a*_d*_i* - @bond:C4-C4 @atom:*_bC4_a*_d*_i* @atom:*_bC4_a*_d*_i* - @bond:C4-Na @atom:*_bC4_a*_d*_i* @atom:*_bNa_a*_d*_i* - @bond:Na-Na @atom:*_bNa_a*_d*_i* @atom:*_bNa_a*_d*_i* - @bond:Na-Na1 @atom:*_bNa_a*_d*_i* @atom:*_bNa1_a*_d*_i* - @bond:Na-Na2 @atom:*_bNa_a*_d*_i* @atom:*_bNa2_a*_d*_i* - @bond:Na-Qa @atom:*_bNa_a*_d*_i* @atom:*_bQa_a*_d*_i* - @bond:Na-Qa1 @atom:*_bNa_a*_d*_i* @atom:*_bQa1_a*_d*_i* - @bond:Na-Qa2 @atom:*_bNa_a*_d*_i* @atom:*_bQa2_a*_d*_i* - @bond:Na1-Qa @atom:*_bNa1_a*_d*_i* @atom:*_bQa_a*_d*_i* - @bond:Na2-Qa @atom:*_bNa2_a*_d*_i* @atom:*_bQa_a*_d*_i* - @bond:P1-P5 @atom:*_bP1_a*_d*_i* @atom:*_bP5_a*_d*_i* - @bond:P4-Qa @atom:*_bP4_a*_d*_i* @atom:*_bQa_a*_d*_i* - @bond:P5-Qa @atom:*_bP5_a*_d*_i* @atom:*_bQa_a*_d*_i* - @bond:P5-Qa1 @atom:*_bP5_a*_d*_i* @atom:*_bQa1_a*_d*_i* - @bond:P5-Qa2 @atom:*_bP5_a*_d*_i* @atom:*_bQa2_a*_d*_i* - @bond:Q0-Qa @atom:*_bQ0_a*_d*_i* @atom:*_bQa_a*_d*_i* - @bond:Qa-Qd @atom:*_bQa_a*_d*_i* @atom:*_bQd_a*_d*_i* - @bond:C1-C1 @atom:*_bC1_a*_d*_i* @atom:*_bC1_a*_d*_i* - @bond:C1-C3 @atom:*_bC1_a*_d*_i* @atom:*_bC3_a*_d*_i* - @bond:C1-Na @atom:*_bC1_a*_d*_i* @atom:*_bNa_a*_d*_i* - @bond:C1-SC12 @atom:*_bC1_a*_d*_i* @atom:*_bSC12_a*_d*_i* - @bond:C1-SC17 @atom:*_bC1_a*_d*_i* @atom:*_bSC17_a*_d*_i* - @bond:Na-SC1 @atom:*_bNa_a*_d*_i* @atom:*_bSC1_a*_d*_i* - @bond:Qa-SC111 @atom:*_bQa_a*_d*_i* @atom:*_bSC111_a*_d*_i* - @bond:SC1-SC11 @atom:*_bSC1_a*_d*_i* @atom:*_bSC11_a*_d*_i* - @bond:SC1-SC13 @atom:*_bSC1_a*_d*_i* @atom:*_bSC13_a*_d*_i* - @bond:SC1-SC15 @atom:*_bSC1_a*_d*_i* @atom:*_bSC15_a*_d*_i* - @bond:SC1-SC16 @atom:*_bSC1_a*_d*_i* @atom:*_bSC16_a*_d*_i* - @bond:SC1-SC17 @atom:*_bSC1_a*_d*_i* @atom:*_bSC17_a*_d*_i* - @bond:SC1-SC18 @atom:*_bSC1_a*_d*_i* @atom:*_bSC18_a*_d*_i* - @bond:SC1-SC3 @atom:*_bSC1_a*_d*_i* @atom:*_bSC3_a*_d*_i* - @bond:SC1-SC32 @atom:*_bSC1_a*_d*_i* @atom:*_bSC32_a*_d*_i* - @bond:SC1-SP1 @atom:*_bSC1_a*_d*_i* @atom:*_bSP1_a*_d*_i* - @bond:SC11-SC12 @atom:*_bSC11_a*_d*_i* @atom:*_bSC12_a*_d*_i* - @bond:SC11-SC13 @atom:*_bSC11_a*_d*_i* @atom:*_bSC13_a*_d*_i* - @bond:SC11-SC14 @atom:*_bSC11_a*_d*_i* @atom:*_bSC14_a*_d*_i* - @bond:SC11-SC31 @atom:*_bSC11_a*_d*_i* @atom:*_bSC31_a*_d*_i* - @bond:SC11-SP1 @atom:*_bSC11_a*_d*_i* @atom:*_bSP1_a*_d*_i* - @bond:SC110-SC3 @atom:*_bSC110_a*_d*_i* @atom:*_bSC3_a*_d*_i* - @bond:SC110-SP1 @atom:*_bSC110_a*_d*_i* @atom:*_bSP1_a*_d*_i* - @bond:SC110-SP11 @atom:*_bSC110_a*_d*_i* @atom:*_bSP11_a*_d*_i* - @bond:SC111-SC112 @atom:*_bSC111_a*_d*_i* @atom:*_bSC112_a*_d*_i* - @bond:SC111-SP11 @atom:*_bSC111_a*_d*_i* @atom:*_bSP11_a*_d*_i* - @bond:SC111-SP12 @atom:*_bSC111_a*_d*_i* @atom:*_bSP12_a*_d*_i* - @bond:SC112-SP1 @atom:*_bSC112_a*_d*_i* @atom:*_bSP1_a*_d*_i* - @bond:SC112-SP11 @atom:*_bSC112_a*_d*_i* @atom:*_bSP11_a*_d*_i* - @bond:SC12-SC13 @atom:*_bSC12_a*_d*_i* @atom:*_bSC13_a*_d*_i* - @bond:SC12-SC14 @atom:*_bSC12_a*_d*_i* @atom:*_bSC14_a*_d*_i* - @bond:SC14-SC31 @atom:*_bSC14_a*_d*_i* @atom:*_bSC31_a*_d*_i* - @bond:SC15-SC16 @atom:*_bSC15_a*_d*_i* @atom:*_bSC16_a*_d*_i* - @bond:SC15-SC3 @atom:*_bSC15_a*_d*_i* @atom:*_bSC3_a*_d*_i* - @bond:SC16-SC17 @atom:*_bSC16_a*_d*_i* @atom:*_bSC17_a*_d*_i* - @bond:SC16-SC18 @atom:*_bSC16_a*_d*_i* @atom:*_bSC18_a*_d*_i* - @bond:SC16-SC19 @atom:*_bSC16_a*_d*_i* @atom:*_bSC19_a*_d*_i* - @bond:SC16-SC32 @atom:*_bSC16_a*_d*_i* @atom:*_bSC32_a*_d*_i* - @bond:SC17-SC18 @atom:*_bSC17_a*_d*_i* @atom:*_bSC18_a*_d*_i* - @bond:SC19-SC32 @atom:*_bSC19_a*_d*_i* @atom:*_bSC32_a*_d*_i* - @bond:SC31-SP1 @atom:*_bSC31_a*_d*_i* @atom:*_bSP1_a*_d*_i* - @bond:SC33-SP1 @atom:*_bSC33_a*_d*_i* @atom:*_bSP1_a*_d*_i* - @bond:SC33-SP11 @atom:*_bSC33_a*_d*_i* @atom:*_bSP11_a*_d*_i* - @bond:SC33-SP12 @atom:*_bSC33_a*_d*_i* @atom:*_bSP12_a*_d*_i* - @bond:SP1-SP11 @atom:*_bSP1_a*_d*_i* @atom:*_bSP11_a*_d*_i* - @bond:SP11-SP12 @atom:*_bSP11_a*_d*_i* @atom:*_bSP12_a*_d*_i* - } # end of bonds - - write_once("In Settings") { - # ----- Angles ----- - angle_coeff @angle:C1-C1-C1 cosine/squared 2.987575 180.000000 # C1-C1-C1 - angle_coeff @angle:C1-C1-C3 cosine/squared 2.987575 180.000000 # C1-C1-C3 - angle_coeff @angle:C1-C1-Na cosine/squared 2.987575 180.000000 # C1-C1-Na - angle_coeff @angle:C1-C1-Na1 cosine/squared 2.987575 180.000000 # C1-C1-Na1 - angle_coeff @angle:C1-C1-Na2 cosine/squared 2.987575 180.000000 # C1-C1-Na2 - angle_coeff @angle:C1-C1-P5 cosine/squared 2.987575 180.000000 # C1-C1-P5 - angle_coeff @angle:C1-C3-C1 cosine/squared 5.377635 120.000000 # C1-C3-C1 - angle_coeff @angle:C1-C3-P1 cosine/squared 5.377635 180.000000 # C1-C3-P1 - angle_coeff @angle:C1-C4-C41 cosine/squared 5.377635 120.000000 # C1-C4-C41 - angle_coeff @angle:C1-C4-C42 cosine/squared 5.377635 120.000000 # C1-C4-C42 - angle_coeff @angle:C1-C41-C4 cosine/squared 1.195030 100.000000 # C1-C41-C4 - angle_coeff @angle:C1-C42-C4 cosine/squared 1.195030 100.000000 # C1-C42-C4 - angle_coeff @angle:C1-Na-Qa cosine/squared 2.987575 180.000000 # C1-Na-Qa - angle_coeff @angle:C1-Na-Qa1 cosine/squared 2.987575 180.000000 # C1-Na-Qa1 - angle_coeff @angle:C1-Na-Qa2 cosine/squared 2.987575 180.000000 # C1-Na-Qa2 - angle_coeff @angle:C1-Na1-Qa cosine/squared 2.987575 180.000000 # C1-Na1-Qa - angle_coeff @angle:C1-Na2-Qa cosine/squared 2.987575 180.000000 # C1-Na2-Qa - angle_coeff @angle:C1-P5-Qa cosine/squared 2.987575 180.000000 # C1-P5-Qa - angle_coeff @angle:C2-C4-C4 cosine/squared 5.377635 120.000000 # C2-C4-C4 - angle_coeff @angle:C4-C4-C4 cosine/squared 1.195030 100.000000 # C4-C4-C4 - angle_coeff @angle:C4-C4-Na cosine/squared 1.195030 100.000000 # C4-C4-Na - angle_coeff @angle:C4-Na-Qa cosine/squared 2.987575 180.000000 # C4-Na-Qa - angle_coeff @angle:C41-C1-Na cosine/squared 2.987575 180.000000 # C41-C1-Na - angle_coeff @angle:C42-C1-Na cosine/squared 2.987575 180.000000 # C42-C1-Na - angle_coeff @angle:Na-Na-Qa cosine/squared 2.987575 120.000000 # Na-Na-Qa - angle_coeff @angle:Na-Na-Qa1 cosine/squared 2.987575 120.000000 # Na-Na-Qa1 - angle_coeff @angle:Na-Na-Qa2 cosine/squared 2.987575 120.000000 # Na-Na-Qa2 - angle_coeff @angle:Na-Na1-Qa cosine/squared 2.987575 120.000000 # Na-Na1-Qa - angle_coeff @angle:Na-Na2-Qa cosine/squared 2.987575 120.000000 # Na-Na2-Qa - angle_coeff @angle:P1-P5-Qa cosine/squared 2.987575 120.000000 # P1-P5-Qa - angle_coeff @angle:C1-C1-C3 cosine/squared 2.987575 180.000000 # C1-C1-C3 - angle_coeff @angle:C1-C3-C1 cosine/squared 5.377635 120.000000 # C1-C3-C1 - angle_coeff @angle:C1-Na-SC19 cosine/squared 2.987575 180.000000 # C1-Na-SC19 - angle_coeff @angle:C1-SC12-SC11 cosine/squared 2.987575 180.000000 # C1-SC12-SC11 - angle_coeff @angle:C1-SC17-SC16 cosine/squared 2.987575 180.000000 # C1-SC17-SC16 - angle_coeff @angle:C3-C1-Na cosine/squared 2.987575 180.000000 # C3-C1-Na - angle_coeff @angle:Qa-SC111-SP11 cosine/squared 2.987575 180.000000 # Qa-SC111-SP11 - } - - write_once("Data Angles By Type") { - @angle:C1-C1-C1 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* - @angle:C1-C1-C3 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aC3_d*_i* - @angle:C1-C1-Na @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* - @angle:C1-C1-Na1 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa1_d*_i* - @angle:C1-C1-Na2 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa2_d*_i* - @angle:C1-C1-P5 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aP5_d*_i* - @angle:C1-C3-C1 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC3_d*_i* @atom:*_b*_aC1_d*_i* - @angle:C1-C3-P1 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC3_d*_i* @atom:*_b*_aP1_d*_i* - @angle:C1-C4-C41 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC4_d*_i* @atom:*_b*_aC41_d*_i* - @angle:C1-C4-C42 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC4_d*_i* @atom:*_b*_aC42_d*_i* - @angle:C1-C41-C4 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC41_d*_i* @atom:*_b*_aC4_d*_i* - @angle:C1-C42-C4 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC42_d*_i* @atom:*_b*_aC4_d*_i* - @angle:C1-Na-Qa @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa_d*_i* - @angle:C1-Na-Qa1 @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa1_d*_i* - @angle:C1-Na-Qa2 @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa2_d*_i* - @angle:C1-Na1-Qa @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa1_d*_i* @atom:*_b*_aQa_d*_i* - @angle:C1-Na2-Qa @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa2_d*_i* @atom:*_b*_aQa_d*_i* - @angle:C1-P5-Qa @atom:*_b*_aC1_d*_i* @atom:*_b*_aP5_d*_i* @atom:*_b*_aQa_d*_i* - @angle:C2-C4-C4 @atom:*_b*_aC2_d*_i* @atom:*_b*_aC4_d*_i* @atom:*_b*_aC4_d*_i* - @angle:C4-C4-C4 @atom:*_b*_aC4_d*_i* @atom:*_b*_aC4_d*_i* @atom:*_b*_aC4_d*_i* - @angle:C4-C4-Na @atom:*_b*_aC4_d*_i* @atom:*_b*_aC4_d*_i* @atom:*_b*_aNa_d*_i* - @angle:C4-Na-Qa @atom:*_b*_aC4_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa_d*_i* - @angle:C41-C1-Na @atom:*_b*_aC41_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* - @angle:C42-C1-Na @atom:*_b*_aC42_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* - @angle:Na-Na-Qa @atom:*_b*_aNa_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa_d*_i* - @angle:Na-Na-Qa1 @atom:*_b*_aNa_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa1_d*_i* - @angle:Na-Na-Qa2 @atom:*_b*_aNa_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aQa2_d*_i* - @angle:Na-Na1-Qa @atom:*_b*_aNa_d*_i* @atom:*_b*_aNa1_d*_i* @atom:*_b*_aQa_d*_i* - @angle:Na-Na2-Qa @atom:*_b*_aNa_d*_i* @atom:*_b*_aNa2_d*_i* @atom:*_b*_aQa_d*_i* - @angle:P1-P5-Qa @atom:*_b*_aP1_d*_i* @atom:*_b*_aP5_d*_i* @atom:*_b*_aQa_d*_i* - @angle:C1-C1-C3 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aC3_d*_i* - @angle:C1-C3-C1 @atom:*_b*_aC1_d*_i* @atom:*_b*_aC3_d*_i* @atom:*_b*_aC1_d*_i* - @angle:C1-Na-SC19 @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* @atom:*_b*_aSC19_d*_i* - @angle:C1-SC12-SC11 @atom:*_b*_aC1_d*_i* @atom:*_b*_aSC12_d*_i* @atom:*_b*_aSC11_d*_i* - @angle:C1-SC17-SC16 @atom:*_b*_aC1_d*_i* @atom:*_b*_aSC17_d*_i* @atom:*_b*_aSC16_d*_i* - @angle:C3-C1-Na @atom:*_b*_aC3_d*_i* @atom:*_b*_aC1_d*_i* @atom:*_b*_aNa_d*_i* - @angle:Qa-SC111-SP11 @atom:*_b*_aQa_d*_i* @atom:*_b*_aSC111_d*_i* @atom:*_b*_aSP11_d*_i* - } # end of angles - - write_once("In Init") { - # Warning: This is a very generic "In Init" section, further - # modification prior to any simulation is extremely likely - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid cosine/squared - pair_style hybrid lj/gromacs/coul/gromacs 9.000000 12.000000 - special_bonds lj/coul 0.0 0.0 0.0 - } # end init - -} # MARTINI - diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt deleted file mode 100644 index 2e20697a43..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/README.txt +++ /dev/null @@ -1,42 +0,0 @@ -The files in this directory are used to create the "martini.lt" file -(containing MARTINI force field parameters for moltemplate). -These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld. -The original MARTINI files are distributed at http://cgmartini.nl - -Conversion from EMC (.PRM) format to moltemplate (.LT) format was -done using the "emcprm2lt.py" script written by David Stelter. -Here is an example how to use the emcprm2lt.py script: - -emcprm2lt.py martini.prm lipids.prm cholesterol.prm --bond-style=harmonic --angle-style=cosine/squared --pair-style=lj/gromacs/coul/gromacs --name=martini - -This will generate a file named "martini.lt" which (in this example) -only includes the force field parameters for lipids and cholestrol. -Later you can define new molecules in moltemplate using: - -import "martini.lt" -NewMolecule inherits MARTINI { - write("Data Atoms") {...atom coordinates and types go here...} - write("Data Bond List") {...list of bonds goes here...} -} - -See "DOPC.lt" in /examples/coarse_grained/MARTINI_examples/ for more details. - -(Note: The rigid bond constraints used for cholesterol in the original MARTINI - model for cholesterol have been replaced by stiff but flexible bonds. - There is a trade-off between increasing the stiffness of the bonds - and using larger time steps. To alter the stiffness of the bonds - edit the "ITEM BOND" section of the "cholesterol.prm", edit the "k" - parameters (3rd column, for the "S..." entries, and run "emcprm2lt.py" again.) - ----- Credits: ---- -emcprm2lt.py was written by David Stelter -EMC was written by Pieter J. in 't Veld -MARTINI was created by S.J. Marrink and coworkers (http://cgmartini.nl) - ----- additional citation request ---- - -Since we borrowed force field parameters from files distributed with EMC, -if you use files generated by "emcprm2lt.py", please also cite the EMC paper: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 - - diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm deleted file mode 100644 index 844fafe100..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/aminoacids.prm +++ /dev/null @@ -1,164 +0,0 @@ -# -# Martini interaction parameters using martini.30634.tmp -# converted by martini.pl v1.2, February 10, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME MARTINI -FFTYPE COARSE -VERSION 2011 -CREATED Feb 2014 -LENGTH NANOMETER -ENERGY KJ/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 0.9 -CUTOFF 1.2 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Masses - -ITEM MASS - -# type mass element ncons charge comment - -P51 72 P5 2 0 polar -P52 72 P5 2 0 polar -P53 72 P5 2 0 polar -P54 72 P5 2 0 polar -P55 72 P5 2 0 polar -P56 72 P5 2 0 polar -P57 72 P5 2 0 polar -P58 72 P5 2 0 polar -P59 72 P5 2 0 polar - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -P51 P5 P51 P51 P51 P51 -P52 P5 P52 P52 P52 P52 -P53 P5 P53 P53 P53 P53 -P54 P5 P54 P54 P54 P54 -P55 P5 P55 P55 P55 P55 -P56 P5 P56 P56 P56 P56 -P57 P5 P57 P57 P57 P57 -P58 P5 P58 P58 P58 P58 -P59 P5 P59 P59 P59 P59 - -ITEM END - -# Bond parameters - -ITEM BOND - -# type1 type2 k l0 - -AC1 P5 7500 0.33 -AC1 P51 20000 0.31 -AC2 P5 20000 0.265 -AC2 P53 7500 0.3 -C3 P1 5000 0.28 -C3 P5 5000 0.33 -C3 Qd 5000 0.28 -C5 P5 7500 0.31 -C5 P52 2500 0.4 -N0 P4 5000 0.34 -N0 P5 5000 0.33 -N0 Qd 5000 0.34 -P1 P5 5000 0.4 -P1 P55 20000 0.26 -P1 P56 7500 0.25 -P3 P5 7500 0.32 -P4 P5 5000 0.4 -P5 P5 5000 0.32 -P5 Qa 7500 0.32 -P5 SC4 7500 0.32 -P54 Qa 5000 0.4 -P57 SC4 7500 0.31 -P58 SC4 5000 0.32 -P59 SC4 5000 0.3 -SC4 SC4 20000 0.27 -SC4 SP1 20000 0.27 -SP1 SP1 20000 0.27 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 - -P1 C3 P5 25 180 -P4 N0 P5 25 180 -P5 C3 Qd 25 180 -P5 N0 Qd 25 180 -P5 SC4 SP1 50 150 -P57 SC4 SC4 50 150 -P58 SC4 SC4 50 150 -P58 SC4 SP1 50 150 -P59 SC4 SC4 50 90 -P59 SC4 SP1 50 210 - -ITEM END - -# Improper parameters - -ITEM IMPROPER - -# type1 type2 type3 type4 k psi0 - -P5 SC4 SP1 SP1 50 0 -P57 SC4 SC4 SC4 50 0 -P58 SC4 SC4 SP1 50 0 -P59 SC4 SC4 SP1 50 0 -SC4 SC4 SC4 SP1 200 0 - -ITEM END - -# Templates - -ITEM TEMPLATES - -# name smiles - -ALA [P4] -ARG [P5][N0][Qd+1] -ARG0 [P5][N0][P4] -ASN [P5][P5] -ASP [P5][Qa-1] -ASP0 [P5][P3] -CYS [P5][C5] -GLN [P5][P4] -GLU [P54][Qa-1] -GLU0 [P5][P1] -GLY [P5] -HIS [P5][SC4]1[SP1][SP1]1 -ILE [P51][AC1] -LEU [P5][AC1] -LYS [P5][C3][Qd+1] -LYS0 [P5][C3][P1] -MET [P52][C5] -PHE [P57][SC4]1[SC4][SC4]1 -PRO [P53][AC2] -SER [P56][P1] -THR [P55][P1] -TRP [P59][SC4]1[SP1]2[SC4]1[SC4]2 -TYR [P58][SC4]1[SC4][SP1]1 -VAL [P5][AC2] - -ITEM END diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm deleted file mode 100644 index f9b4f7b8d0..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/cholesterol.prm +++ /dev/null @@ -1,198 +0,0 @@ -# -# Martini interaction parameters using martini.30636.tmp -# converted by martini.pl v1.2, February 10, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME MARTINI -FFTYPE COARSE -VERSION 2011 -CREATED Feb 2014 -LENGTH NANOMETER -ENERGY KJ/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 0.9 -CUTOFF 1.2 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Masses - -ITEM MASS - -# type mass element ncons charge comment - -SC11 54 SC1 2 0 ring apolar -SC110 54 SC1 2 0 ring apolar -SC111 54 SC1 2 0 ring apolar -SC112 54 SC1 2 0 ring apolar -SC12 54 SC1 2 0 ring apolar -SC13 54 SC1 2 0 ring apolar -SC14 54 SC1 2 0 ring apolar -SC15 54 SC1 2 0 ring apolar -SC16 54 SC1 2 0 ring apolar -SC17 54 SC1 2 0 ring apolar -SC18 54 SC1 2 0 ring apolar -SC19 54 SC1 2 0 ring apolar -SC31 54 SC3 2 0 ring apolar -SC32 54 SC3 2 0 ring apolar -SC33 54 SC3 2 0 ring apolar -SP11 54 SP1 2 0 ring polar -SP12 54 SP1 2 0 ring polar - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -SC11 SC1 SC11 SC11 SC11 SC11 -SC110 SC1 SC110 SC110 SC110 SC110 -SC111 SC1 SC111 SC111 SC111 SC111 -SC112 SC1 SC112 SC112 SC112 SC112 -SC12 SC1 SC12 SC12 SC12 SC12 -SC13 SC1 SC13 SC13 SC13 SC13 -SC14 SC1 SC14 SC14 SC14 SC14 -SC15 SC1 SC15 SC15 SC15 SC15 -SC16 SC1 SC16 SC16 SC16 SC16 -SC17 SC1 SC17 SC17 SC17 SC17 -SC18 SC1 SC18 SC18 SC18 SC18 -SC19 SC1 SC19 SC19 SC19 SC19 -SC31 SC3 SC31 SC31 SC31 SC31 -SC32 SC3 SC32 SC32 SC32 SC32 -SC33 SC3 SC33 SC33 SC33 SC33 -SP11 SP1 SP11 SP11 SP11 SP11 -SP12 SP1 SP12 SP12 SP12 SP12 - -ITEM END - -# Bond parameters -# To change the bond stiffness, edit the "k" parameter - -ITEM BOND - -# type1 type2 k l0 - -C1 C1 1250 0.47 -C1 C3 1250 0.47 -C1 Na 1250 0.47 -C1 SC12 1250 0.425 -C1 SC17 1250 0.425 -Na SC1 1250 0.47 -Qa SC111 1250 0.425 -SC1 SC11 20000 0.341 -SC1 SC13 20000 0.203 -SC1 SC15 20000 0.242 -SC1 SC16 20000 0.294 -SC1 SC17 20000 0.406 -SC1 SC18 20000 0.203 -SC1 SC3 20000 0.26 -SC1 SC32 20000 0.346 -SC1 SP1 20000 0.242 -SC11 SC12 20000 0.544 -SC11 SC13 20000 0.213 -SC11 SC14 20000 0.294 -SC11 SC31 20000 0.272 -SC11 SP1 20000 0.604 -SC110 SC3 20000 0.26 -SC110 SP1 20000 0.242 -SC110 SP11 20000 0.341 -SC111 SC112 20000 0.368 -SC111 SP11 20000 0.544 -SC111 SP12 20000 0.406 -SC112 SP1 20000 0.203 -SC112 SP11 20000 0.213 -SC12 SC13 20000 0.368 -SC12 SC14 20000 0.406 -SC14 SC31 20000 0.346 -SC15 SC16 20000 0.341 -SC15 SC3 20000 0.26 -SC16 SC17 20000 0.544 -SC16 SC18 20000 0.213 -SC16 SC19 20000 0.604 -SC16 SC32 20000 0.272 -SC17 SC18 20000 0.368 -SC19 SC32 20000 0.493 -SC31 SP1 20000 0.493 -SC33 SP1 20000 0.493 -SC33 SP11 20000 0.272 -SC33 SP12 20000 0.346 -SP1 SP11 20000 0.604 -SP11 SP12 20000 0.294 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 - -C1 C1 C3 25 180 -C1 C3 C1 45 120 -C1 Na SC19 25 180 -C1 SC12 SC11 25 180 -C1 SC17 SC16 25 180 -C3 C1 Na 25 180 -Qa SC111 SP11 25 180 - -ITEM END - -# Improper parameters - -ITEM IMPROPER - -# type1 type2 type3 type4 k psi0 - -SC1 SC11 SC31 SP1 300 45 -SC1 SC11 SP1 SC31 300 -45 -SC11 SC12 SC14 SC31 100 0 -SC110 SC33 SP1 SP11 300 45 -SC110 SC33 SP11 SP1 300 -45 -SC112 SC111 SP11 SP12 300 -45 -SC112 SC111 SP12 SP11 300 45 -SC13 SC11 SC12 SC14 300 45 -SC13 SC11 SC14 SC12 300 -45 -SC15 SC16 SC19 SC32 300 -45 -SC15 SC16 SC32 SC19 300 45 -SC16 SC1 SC32 SC17 100 0 -SC18 SC1 SC16 SC17 300 45 -SC18 SC1 SC17 SC16 300 -45 -SC19 SC1 SC16 SC32 100 0 -SC19 SC1 SC17 SC32 100 0 -SC19 SC1 SC32 SC16 100 0 -SC31 SC11 SC14 SC12 100 0 -SC32 SC1 SC17 SC16 100 0 -SC33 SC111 SP11 SP12 100 0 -SP1 SC11 SC14 SC31 100 0 -SP1 SC11 SC31 SC14 100 0 -SP1 SC111 SC33 SP12 100 0 -SP1 SC12 SC31 SC14 100 0 -SP1 SC33 SP11 SP12 100 0 -SP1 SC33 SP12 SP11 100 0 -SP11 SC111 SP12 SC33 100 0 - -ITEM END - -# Templates - -ITEM TEMPLATES - -# name smiles - -CHOA [SP1]1[SC110]3[SC33]2[SP11]1[SC112]6[SP12]4[SC111]5[Qa-1] -CHOL [SP1]1[SC1]3[SC31]2[SC11]1[SC13]6[SC14]4[SC12]5[C1] -CO [SC19]1([SC15]3[SC32]2[SC16]1[SC18]6[SC1]4[SC17]5[C1])[Na][C1][C3][C1][C1] - -ITEM END diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm deleted file mode 100644 index 1139c421da..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/lipids.prm +++ /dev/null @@ -1,160 +0,0 @@ -# -# Martini interaction parameters using martini.30640.tmp -# converted by martini.pl v1.2, February 10, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME MARTINI -FFTYPE COARSE -VERSION 2011 -CREATED Feb 2014 -LENGTH NANOMETER -ENERGY KJ/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 0.9 -CUTOFF 1.2 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Masses - -ITEM MASS - -# type mass element ncons charge comment - -C41 72 C4 2 0 apolar -C42 72 C4 2 0 apolar -Na1 72 Na 2 0 intermediate -Na2 72 Na 2 0 intermediate -Qa1 72 Qa 2 0 charged -Qa2 72 Qa 2 0 charged - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -C41 C4 C4 C41 C41 C41 -C42 C4 C4 C42 C42 C42 -Na1 Na Na1 Na1 Na1 Na1 -Na2 Na Na2 Na2 Na2 Na2 -Qa1 Qa Qa1 Qa1 Qa1 Qa1 -Qa2 Qa Qa2 Qa2 Qa2 Qa2 - -ITEM END - -# Bond parameters - -ITEM BOND - -# type1 type2 k l0 - -C1 C1 1250 0.47 -C1 C3 1250 0.47 -C1 C4 1250 0.47 -C1 Na 1250 0.47 -C1 Na1 1250 0.47 -C1 Na2 1250 0.47 -C1 P5 1250 0.47 -C2 C4 1250 0.47 -C3 P1 1250 0.47 -C4 C4 1250 0.47 -C4 Na 1250 0.47 -Na Na 1250 0.37 -Na Na1 1250 0.37 -Na Na2 1250 0.37 -Na Qa 1250 0.47 -Na Qa1 1250 0.37 -Na Qa2 1250 0.37 -Na1 Qa 1250 0.37 -Na2 Qa 1250 0.37 -P1 P5 1250 0.37 -P4 Qa 1250 0.37 -P5 Qa 1250 0.47 -P5 Qa1 1250 0.37 -P5 Qa2 1250 0.37 -Q0 Qa 1250 0.47 -Qa Qd 1250 0.47 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 - -C1 C1 C1 25 180 -C1 C1 C3 25 180 -C1 C1 Na 25 180 -C1 C1 Na1 25 180 -C1 C1 Na2 25 180 -C1 C1 P5 25 180 -C1 C3 C1 45 120 -C1 C3 P1 45 180 -C1 C4 C41 45 120 -C1 C4 C42 45 120 -C1 C41 C4 10 100 -C1 C42 C4 10 100 -C1 Na Qa 25 180 -C1 Na Qa1 25 180 -C1 Na Qa2 25 180 -C1 Na1 Qa 25 180 -C1 Na2 Qa 25 180 -C1 P5 Qa 25 180 -C2 C4 C4 45 120 -C4 C4 C4 10 100 -C4 C4 Na 10 100 -C4 Na Qa 25 180 -C41 C1 Na 25 180 -C42 C1 Na 25 180 -Na Na Qa 25 120 -Na Na Qa1 25 120 -Na Na Qa2 25 120 -Na Na1 Qa 25 120 -Na Na2 Qa 25 120 -P1 P5 Qa 25 120 - -ITEM END - -# Templates - -ITEM TEMPLATES - -# name smiles - -BOLA [Q0+1][Qa-1][Na][Na][C1][C1][C1][C1][C1][C1][C1][C1][Na][Na]([Qa-1][Q0+1])[C1][C1][C1][C1][C1][C1][C1][C1] -BOLB [Q0+1][Qa-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C1][C1][C1][C1][C1][C1][Na]([Qa-1][Q0+1])[Na][C1][C1][C1][C1] -DAPC [Q0+1][Qa-1][Na]([Na][C4][C4][C4][C4][C2])[C4][C4][C4][C4][C2] -DHPC [Q0+1][Qa-1][Na]([Na][C1][C1])[C1][C1] -DHPE [Qd+1][Qa-1][Na]([Na][C1][C1])[C1][C1] -DLPC [Q0+1][Qa-1][Na]([Na][C1][C1][C1])[C1][C1][C1] -DLPE [Qd+1][Qa-1][Na]([Na][C1][C1][C1])[C1][C1][C1] -DOPC [Q0+1][Qa-1][Na]([Na][C1][C1][C3][C1][C1])[C1][C1][C3][C1][C1] -DOPE [Qd+1][Qa-1][Na]([Na][C1][C1][C3][C1][C1])[C1][C1][C3][C1][C1] -DOPG [P4][Qa-1][Na1]([Na][C1][C1][C3][C1][C1])[C1][C1][C3][C1][C1] -DOPS [P5][Qa1-1][Na]([Na][C1][C1][C3][C1][C1])[C1][C1][C3][C1][C1] -DPPC [Q0+1][Qa-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C1][C1] -DPPE [Qd+1][Qa-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C1][C1] -DSPC [Q0+1][Qa-1][Na]([Na][C1][C1][C1][C1][C1])[C1][C1][C1][C1][C1] -DSPE [Qd+1][Qa-1][Na]([Na][C1][C1][C1][C1][C1])[C1][C1][C1][C1][C1] -DUPC [Q0+1][Qa-1][Na]([Na][C1][C42][C4][C1])[C1][C41][C4][C1] -POPC [Q0+1][Qa-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C3][C1][C1] -POPE [Qd+1][Qa-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C3][C1][C1] -POPG [P4][Qa-1][Na2]([Na][C1][C1][C1][C1])[C1][C1][C3][C1][C1] -POPS [P5][Qa2-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C3][C1][C1] -PPCS [Q0+1][Qa-1][P5]([P1][C3][C1][C1][C1])[C1][C1][C1][C1] - -ITEM END diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm deleted file mode 100644 index dc2c186764..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/martini.prm +++ /dev/null @@ -1,852 +0,0 @@ -# -# Martini interaction parameters using martini.30642.tmp -# converted by martini.pl v1.2, February 10, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME MARTINI -FFTYPE COARSE -VERSION V2.0 -CREATED Feb 2014 -LENGTH NANOMETER -ENERGY KJ/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 0.9 -CUTOFF 1.2 -PAIR14 OFF -ANGLE IGNORE -TORSION IGNORE -IMPROP IGNORE - -ITEM END - -# Masses - -ITEM MASS - -# type mass element ncons charge comment - -BP4 72.0 BP4 2 0.000 big particle -C1 72.0 C1 2 0.000 apolar -C2 72.0 C2 2 0.000 apolar -C3 72.0 C3 2 0.000 apolar -C4 72.0 C4 2 0.000 apolar -C5 72.0 C5 2 0.000 apolar -N0 72.0 N0 2 0.000 intermediate -Na 72.0 Na 2 0.000 intermediate -Nd 72.0 Nd 2 0.000 intermediate -Nda 72.0 Nda 2 0.000 intermediate -P1 72.0 P1 2 0.000 polar -P2 72.0 P2 2 0.000 polar -P3 72.0 P3 2 0.000 polar -P4 72.0 P4 2 0.000 polar -P5 72.0 P5 2 0.000 polar -Q0 72.0 Q0 2 0.000 charged -Qa 72.0 Qa 2 0.000 charged -Qd 72.0 Qd 2 0.000 charged -Qda 72.0 Qda 2 0.000 charged -SC1 54.0 SC1 2 0.000 ring apolar -SC2 54.0 SC2 2 0.000 ring apolar -SC3 54.0 SC3 2 0.000 ring apolar -SC4 54.0 SC4 2 0.000 ring apolar -SC5 54.0 SC5 2 0.000 ring apolar -SN0 54.0 SN0 2 0.000 ring intermediate -SNa 54.0 SNa 2 0.000 ring intermediate -SNd 54.0 SNd 2 0.000 ring intermediate -SNda 54.0 SNda 2 0.000 ring intermediate -SP1 54.0 SP1 2 0.000 ring polar -SP2 54.0 SP2 2 0.000 ring polar -SP3 54.0 SP3 2 0.000 ring polar -SP4 54.0 SP4 2 0.000 ring polar -SP5 54.0 SP5 2 0.000 ring polar -SQ0 54.0 SQ0 2 0.000 ring charged -SQa 54.0 SQa 2 0.000 ring charged -SQd 54.0 SQd 2 0.000 ring charged -SQda 54.0 SQda 2 0.000 ring charged - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -BP4 BP4 BP4 BP4 BP4 BP4 -C1 C1 C1 C1 C1 C1 -C2 C2 C2 C2 C2 C2 -C3 C3 C3 C3 C3 C3 -C4 C4 C4 C4 C4 C4 -C5 C5 C5 C5 C5 C5 -N0 N0 N0 N0 N0 N0 -Na Na Na Na Na Na -Nd Nd Nd Nd Nd Nd -Nda Nda Nda Nda Nda Nda -P1 P1 P1 P1 P1 P1 -P2 P2 P2 P2 P2 P2 -P3 P3 P3 P3 P3 P3 -P4 P4 P4 P4 P4 P4 -P5 P5 P5 P5 P5 P5 -Q0 Q0 Q0 Q0 Q0 Q0 -Qa Qa Qa Qa Qa Qa -Qd Qd Qd Qd Qd Qd -Qda Qda Qda Qda Qda Qda -SC1 SC1 SC1 SC1 SC1 SC1 -SC2 SC2 SC2 SC2 SC2 SC2 -SC3 SC3 SC3 SC3 SC3 SC3 -SC4 SC4 SC4 SC4 SC4 SC4 -SC5 SC5 SC5 SC5 SC5 SC5 -SN0 SN0 SN0 SN0 SN0 SN0 -SNa SNa SNa SNa SNa SNa -SNd SNd SNd SNd SNd SNd -SNda SNda SNda SNda SNda SNda -SP1 SP1 SP1 SP1 SP1 SP1 -SP2 SP2 SP2 SP2 SP2 SP2 -SP3 SP3 SP3 SP3 SP3 SP3 -SP4 SP4 SP4 SP4 SP4 SP4 -SP5 SP5 SP5 SP5 SP5 SP5 -SQ0 SQ0 SQ0 SQ0 SQ0 SQ0 -SQa SQa SQa SQa SQa SQa -SQd SQd SQd SQd SQd SQd -SQda SQda SQda SQda SQda SQda - -ITEM END - -# Nonbonded parameters - -ITEM NONBOND - -# type1 type2 sigma epsilon - -BP4 BP4 0.47 5 -BP4 C1 0.47 2 -BP4 C2 0.47 2.3 -BP4 C3 0.47 2.7 -BP4 C4 0.47 2.7 -BP4 C5 0.47 3.1 -BP4 N0 0.47 3.5 -BP4 Na 0.47 4 -BP4 Nd 0.47 4 -BP4 Nda 0.47 4 -BP4 P1 0.47 4.5 -BP4 P2 0.47 4.5 -BP4 P3 0.47 5 -BP4 P4 0.57 5.6 -BP4 P5 0.47 5.6 -BP4 Q0 0.47 5.6 -BP4 Qa 0.47 5.6 -BP4 Qd 0.47 5.6 -BP4 Qda 0.47 5.6 -BP4 SC1 0.47 2 -BP4 SC2 0.47 2.3 -BP4 SC3 0.47 2.7 -BP4 SC4 0.47 2.7 -BP4 SC5 0.47 3.1 -BP4 SN0 0.47 3.5 -BP4 SNa 0.47 4 -BP4 SNd 0.47 4 -BP4 SNda 0.47 4 -BP4 SP1 0.47 4.5 -BP4 SP2 0.47 4.5 -BP4 SP3 0.47 5 -BP4 SP4 0.47 5 -BP4 SP5 0.47 5.6 -BP4 SQ0 0.47 5.6 -BP4 SQa 0.47 5.6 -BP4 SQd 0.47 5.6 -BP4 SQda 0.47 5.6 -C1 C1 0.47 3.5 -C1 C2 0.47 3.5 -C1 C3 0.47 3.5 -C1 C4 0.47 3.1 -C1 C5 0.47 3.1 -C1 N0 0.47 2.7 -C1 Na 0.47 2.7 -C1 Nd 0.47 2.7 -C1 Nda 0.47 2.7 -C1 P1 0.47 2.7 -C1 P2 0.47 2.3 -C1 P3 0.47 2.3 -C1 P4 0.47 2 -C1 P5 0.47 2 -C1 Q0 0.62 2 -C1 Qa 0.62 2 -C1 Qd 0.62 2 -C1 Qda 0.62 2 -C1 SC1 0.47 3.5 -C1 SC2 0.47 3.5 -C1 SC3 0.47 3.5 -C1 SC4 0.47 3.1 -C1 SC5 0.47 3.1 -C1 SN0 0.47 2.7 -C1 SNa 0.47 2.7 -C1 SNd 0.47 2.7 -C1 SNda 0.47 2.7 -C1 SP1 0.47 2.7 -C1 SP2 0.47 2.3 -C1 SP3 0.47 2.3 -C1 SP4 0.47 2 -C1 SP5 0.47 2 -C1 SQ0 0.62 2 -C1 SQa 0.62 2 -C1 SQd 0.62 2 -C1 SQda 0.62 2 -C2 C2 0.47 3.5 -C2 C3 0.47 3.5 -C2 C4 0.47 3.1 -C2 C5 0.47 3.1 -C2 N0 0.47 3.1 -C2 Na 0.47 2.7 -C2 Nd 0.47 2.7 -C2 Nda 0.47 2.7 -C2 P1 0.47 3.1 -C2 P2 0.47 2.7 -C2 P3 0.47 2.7 -C2 P4 0.47 2.3 -C2 P5 0.47 2.3 -C2 Q0 0.62 2 -C2 Qa 0.62 2 -C2 Qd 0.62 2 -C2 Qda 0.62 2 -C2 SC1 0.47 3.5 -C2 SC2 0.47 3.5 -C2 SC3 0.47 3.5 -C2 SC4 0.47 3.1 -C2 SC5 0.47 3.1 -C2 SN0 0.47 3.1 -C2 SNa 0.47 2.7 -C2 SNd 0.47 2.7 -C2 SNda 0.47 2.7 -C2 SP1 0.47 3.1 -C2 SP2 0.47 2.7 -C2 SP3 0.47 2.7 -C2 SP4 0.47 2.3 -C2 SP5 0.47 2.3 -C2 SQ0 0.62 2 -C2 SQa 0.62 2 -C2 SQd 0.62 2 -C2 SQda 0.62 2 -C3 C3 0.47 3.5 -C3 C4 0.47 3.5 -C3 C5 0.47 3.5 -C3 N0 0.47 3.5 -C3 Na 0.47 2.7 -C3 Nd 0.47 2.7 -C3 Nda 0.47 2.7 -C3 P1 0.47 3.5 -C3 P2 0.47 3.1 -C3 P3 0.47 3.1 -C3 P4 0.47 2.7 -C3 P5 0.47 2.7 -C3 Q0 0.47 2.3 -C3 Qa 0.47 2.3 -C3 Qd 0.47 2.3 -C3 Qda 0.47 2.3 -C3 SC1 0.47 3.5 -C3 SC2 0.47 3.5 -C3 SC3 0.47 3.5 -C3 SC4 0.47 3.5 -C3 SC5 0.47 3.5 -C3 SN0 0.47 3.5 -C3 SNa 0.47 2.7 -C3 SNd 0.47 2.7 -C3 SNda 0.47 2.7 -C3 SP1 0.47 3.5 -C3 SP2 0.47 3.1 -C3 SP3 0.47 3.1 -C3 SP4 0.47 2.7 -C3 SP5 0.47 2.7 -C3 SQ0 0.47 2.3 -C3 SQa 0.47 2.3 -C3 SQd 0.47 2.3 -C3 SQda 0.47 2.3 -C4 C4 0.47 3.5 -C4 C5 0.47 3.5 -C4 N0 0.47 3.5 -C4 Na 0.47 3.1 -C4 Nd 0.47 3.1 -C4 Nda 0.47 3.1 -C4 P1 0.47 3.5 -C4 P2 0.47 3.5 -C4 P3 0.47 3.1 -C4 P4 0.47 2.7 -C4 P5 0.47 2.7 -C4 Q0 0.47 2.7 -C4 Qa 0.47 2.7 -C4 Qd 0.47 2.7 -C4 Qda 0.47 2.7 -C4 SC1 0.47 3.1 -C4 SC2 0.47 3.1 -C4 SC3 0.47 3.5 -C4 SC4 0.47 3.5 -C4 SC5 0.47 3.5 -C4 SN0 0.47 3.5 -C4 SNa 0.47 3.1 -C4 SNd 0.47 3.1 -C4 SNda 0.47 3.1 -C4 SP1 0.47 3.5 -C4 SP2 0.47 3.5 -C4 SP3 0.47 3.1 -C4 SP4 0.47 2.7 -C4 SP5 0.47 2.7 -C4 SQ0 0.47 2.7 -C4 SQa 0.47 2.7 -C4 SQd 0.47 2.7 -C4 SQda 0.47 2.7 -C5 C5 0.47 3.5 -C5 N0 0.47 3.5 -C5 Na 0.47 3.5 -C5 Nd 0.47 3.5 -C5 Nda 0.47 3.5 -C5 P1 0.47 3.5 -C5 P2 0.47 3.5 -C5 P3 0.47 3.5 -C5 P4 0.47 3.1 -C5 P5 0.47 3.1 -C5 Q0 0.47 3.1 -C5 Qa 0.47 3.1 -C5 Qd 0.47 3.1 -C5 Qda 0.47 3.1 -C5 SC1 0.47 3.1 -C5 SC2 0.47 3.1 -C5 SC3 0.47 3.5 -C5 SC4 0.47 3.5 -C5 SC5 0.47 3.5 -C5 SN0 0.47 3.5 -C5 SNa 0.47 3.5 -C5 SNd 0.47 3.5 -C5 SNda 0.47 3.5 -C5 SP1 0.47 3.5 -C5 SP2 0.47 3.5 -C5 SP3 0.47 3.5 -C5 SP4 0.47 3.1 -C5 SP5 0.47 3.1 -C5 SQ0 0.47 3.1 -C5 SQa 0.47 3.1 -C5 SQd 0.47 3.1 -C5 SQda 0.47 3.1 -N0 N0 0.47 3.5 -N0 Na 0.47 3.5 -N0 Nd 0.47 3.5 -N0 Nda 0.47 3.5 -N0 P1 0.47 4 -N0 P2 0.47 4 -N0 P3 0.47 3.5 -N0 P4 0.47 3.5 -N0 P5 0.47 3.5 -N0 Q0 0.47 3.5 -N0 Qa 0.47 3.5 -N0 Qd 0.47 3.5 -N0 Qda 0.47 3.5 -N0 SC1 0.47 2.7 -N0 SC2 0.47 3.1 -N0 SC3 0.47 3.5 -N0 SC4 0.47 3.5 -N0 SC5 0.47 3.5 -N0 SN0 0.47 3.5 -N0 SNa 0.47 3.5 -N0 SNd 0.47 3.5 -N0 SNda 0.47 3.5 -N0 SP1 0.47 4 -N0 SP2 0.47 4 -N0 SP3 0.47 3.5 -N0 SP4 0.47 3.5 -N0 SP5 0.47 3.5 -N0 SQ0 0.47 3.5 -N0 SQa 0.47 3.5 -N0 SQd 0.47 3.5 -N0 SQda 0.47 3.5 -Na Na 0.47 4 -Na Nd 0.47 4.5 -Na Nda 0.47 4.5 -Na P1 0.47 4.5 -Na P2 0.47 4.5 -Na P3 0.47 4.5 -Na P4 0.47 4 -Na P5 0.47 5 -Na Q0 0.47 4 -Na Qa 0.47 4 -Na Qd 0.47 5 -Na Qda 0.47 5 -Na SC1 0.47 2.7 -Na SC2 0.47 2.7 -Na SC3 0.47 2.7 -Na SC4 0.47 3.1 -Na SC5 0.47 3.5 -Na SN0 0.47 3.5 -Na SNa 0.47 4 -Na SNd 0.47 4.5 -Na SNda 0.47 4.5 -Na SP1 0.47 4.5 -Na SP2 0.47 4.5 -Na SP3 0.47 4.5 -Na SP4 0.47 4 -Na SP5 0.47 5 -Na SQ0 0.47 4 -Na SQa 0.47 4 -Na SQd 0.47 5 -Na SQda 0.47 5 -Nd Nd 0.47 4 -Nd Nda 0.47 4.5 -Nd P1 0.47 4.5 -Nd P2 0.47 4.5 -Nd P3 0.47 4.5 -Nd P4 0.47 4 -Nd P5 0.47 5 -Nd Q0 0.47 4 -Nd Qa 0.47 5 -Nd Qd 0.47 4 -Nd Qda 0.47 5 -Nd SC1 0.47 2.7 -Nd SC2 0.47 2.7 -Nd SC3 0.47 2.7 -Nd SC4 0.47 3.1 -Nd SC5 0.47 3.5 -Nd SN0 0.47 3.5 -Nd SNa 0.47 4.5 -Nd SNd 0.47 4 -Nd SNda 0.47 4.5 -Nd SP1 0.47 4.5 -Nd SP2 0.47 4.5 -Nd SP3 0.47 4.5 -Nd SP4 0.47 4 -Nd SP5 0.47 5 -Nd SQ0 0.47 4 -Nd SQa 0.47 5 -Nd SQd 0.47 4 -Nd SQda 0.47 5 -Nda Nda 0.47 4.5 -Nda P1 0.47 4.5 -Nda P2 0.47 4.5 -Nda P3 0.47 4.5 -Nda P4 0.47 4 -Nda P5 0.47 5 -Nda Q0 0.47 4 -Nda Qa 0.47 5 -Nda Qd 0.47 5 -Nda Qda 0.47 5 -Nda SC1 0.47 2.7 -Nda SC2 0.47 2.7 -Nda SC3 0.47 2.7 -Nda SC4 0.47 3.1 -Nda SC5 0.47 3.5 -Nda SN0 0.47 3.5 -Nda SNa 0.47 4.5 -Nda SNd 0.47 4.5 -Nda SNda 0.47 4.5 -Nda SP1 0.47 4.5 -Nda SP2 0.47 4.5 -Nda SP3 0.47 4.5 -Nda SP4 0.47 4 -Nda SP5 0.47 5 -Nda SQ0 0.47 4 -Nda SQa 0.47 5 -Nda SQd 0.47 5 -Nda SQda 0.47 5 -P1 P1 0.47 4.5 -P1 P2 0.47 4.5 -P1 P3 0.47 4.5 -P1 P4 0.47 4.5 -P1 P5 0.47 5.6 -P1 Q0 0.47 4 -P1 Qa 0.47 5 -P1 Qd 0.47 5 -P1 Qda 0.47 5 -P1 SC1 0.47 2.7 -P1 SC2 0.47 3.1 -P1 SC3 0.47 3.5 -P1 SC4 0.47 3.5 -P1 SC5 0.47 3.5 -P1 SN0 0.47 4 -P1 SNa 0.47 4.5 -P1 SNd 0.47 4.5 -P1 SNda 0.47 4.5 -P1 SP1 0.47 4.5 -P1 SP2 0.47 4.5 -P1 SP3 0.47 4.5 -P1 SP4 0.47 4.5 -P1 SP5 0.47 5.6 -P1 SQ0 0.47 4 -P1 SQa 0.47 5 -P1 SQd 0.47 5 -P1 SQda 0.47 5 -P2 P2 0.47 4.5 -P2 P3 0.47 4.5 -P2 P4 0.47 4.5 -P2 P5 0.47 5.6 -P2 Q0 0.47 4.5 -P2 Qa 0.47 5 -P2 Qd 0.47 5 -P2 Qda 0.47 5 -P2 SC1 0.47 2.3 -P2 SC2 0.47 2.7 -P2 SC3 0.47 3.1 -P2 SC4 0.47 3.5 -P2 SC5 0.47 3.5 -P2 SN0 0.47 4 -P2 SNa 0.47 4.5 -P2 SNd 0.47 4.5 -P2 SNda 0.47 4.5 -P2 SP1 0.47 4.5 -P2 SP2 0.47 4.5 -P2 SP3 0.47 4.5 -P2 SP4 0.47 4.5 -P2 SP5 0.47 5.6 -P2 SQ0 0.47 4.5 -P2 SQa 0.47 5 -P2 SQd 0.47 5 -P2 SQda 0.47 5 -P3 P3 0.47 5 -P3 P4 0.47 5 -P3 P5 0.47 5.6 -P3 Q0 0.47 5 -P3 Qa 0.47 5.6 -P3 Qd 0.47 5.6 -P3 Qda 0.47 5.6 -P3 SC1 0.47 2.3 -P3 SC2 0.47 2.7 -P3 SC3 0.47 3.1 -P3 SC4 0.47 3.1 -P3 SC5 0.47 3.5 -P3 SN0 0.47 3.5 -P3 SNa 0.47 4.5 -P3 SNd 0.47 4.5 -P3 SNda 0.47 4.5 -P3 SP1 0.47 4.5 -P3 SP2 0.47 4.5 -P3 SP3 0.47 5 -P3 SP4 0.47 5 -P3 SP5 0.47 5.6 -P3 SQ0 0.47 5 -P3 SQa 0.47 5.6 -P3 SQd 0.47 5.6 -P3 SQda 0.47 5.6 -P4 P4 0.47 5 -P4 P5 0.47 5.6 -P4 Q0 0.47 5.6 -P4 Qa 0.47 5.6 -P4 Qd 0.47 5.6 -P4 Qda 0.47 5.6 -P4 SC1 0.47 2 -P4 SC2 0.47 2.3 -P4 SC3 0.47 2.7 -P4 SC4 0.47 2.7 -P4 SC5 0.47 3.1 -P4 SN0 0.47 3.5 -P4 SNa 0.47 4 -P4 SNd 0.47 4 -P4 SNda 0.47 4 -P4 SP1 0.47 4.5 -P4 SP2 0.47 4.5 -P4 SP3 0.47 5 -P4 SP4 0.47 5 -P4 SP5 0.47 5.6 -P4 SQ0 0.47 5.6 -P4 SQa 0.47 5.6 -P4 SQd 0.47 5.6 -P4 SQda 0.47 5.6 -P5 P5 0.47 5.6 -P5 Q0 0.47 5 -P5 Qa 0.47 5.6 -P5 Qd 0.47 5.6 -P5 Qda 0.47 5.6 -P5 SC1 0.47 2 -P5 SC2 0.47 2.3 -P5 SC3 0.47 2.7 -P5 SC4 0.47 2.7 -P5 SC5 0.47 3.1 -P5 SN0 0.47 3.5 -P5 SNa 0.47 5 -P5 SNd 0.47 5 -P5 SNda 0.47 5 -P5 SP1 0.47 5.6 -P5 SP2 0.47 5.6 -P5 SP3 0.47 5.6 -P5 SP4 0.47 5.6 -P5 SP5 0.47 5.6 -P5 SQ0 0.47 5 -P5 SQa 0.47 5.6 -P5 SQd 0.47 5.6 -P5 SQda 0.47 5.6 -Q0 Q0 0.47 3.5 -Q0 Qa 0.47 4.5 -Q0 Qd 0.47 4.5 -Q0 Qda 0.47 4.5 -Q0 SC1 0.62 2 -Q0 SC2 0.62 2 -Q0 SC3 0.47 2.3 -Q0 SC4 0.47 2.7 -Q0 SC5 0.47 3.1 -Q0 SN0 0.47 3.5 -Q0 SNa 0.47 4 -Q0 SNd 0.47 4 -Q0 SNda 0.47 4 -Q0 SP1 0.47 4 -Q0 SP2 0.47 4.5 -Q0 SP3 0.47 5 -Q0 SP4 0.47 5.6 -Q0 SP5 0.47 5 -Q0 SQ0 0.47 3.5 -Q0 SQa 0.47 4.5 -Q0 SQd 0.47 4.5 -Q0 SQda 0.47 4.5 -Qa Qa 0.47 5 -Qa Qd 0.47 5.6 -Qa Qda 0.47 5.6 -Qa SC1 0.62 2 -Qa SC2 0.62 2 -Qa SC3 0.47 2.3 -Qa SC4 0.47 2.7 -Qa SC5 0.47 3.1 -Qa SN0 0.47 3.5 -Qa SNa 0.47 4 -Qa SNd 0.47 5 -Qa SNda 0.47 5 -Qa SP1 0.47 5 -Qa SP2 0.47 5 -Qa SP3 0.47 5.6 -Qa SP4 0.47 5.6 -Qa SP5 0.47 5.6 -Qa SQ0 0.47 4.5 -Qa SQa 0.47 5 -Qa SQd 0.47 5.6 -Qa SQda 0.47 5.6 -Qd Qd 0.47 5 -Qd Qda 0.47 5.6 -Qd SC1 0.62 2 -Qd SC2 0.62 2 -Qd SC3 0.47 2.3 -Qd SC4 0.47 2.7 -Qd SC5 0.47 3.1 -Qd SN0 0.47 3.5 -Qd SNa 0.47 5 -Qd SNd 0.47 4 -Qd SNda 0.47 5 -Qd SP1 0.47 5 -Qd SP2 0.47 5 -Qd SP3 0.47 5.6 -Qd SP4 0.47 5.6 -Qd SP5 0.47 5.6 -Qd SQ0 0.47 4.5 -Qd SQa 0.47 5.6 -Qd SQd 0.47 5 -Qd SQda 0.47 5.6 -Qda Qda 0.47 5.6 -Qda SC1 0.62 2 -Qda SC2 0.62 2 -Qda SC3 0.47 2.3 -Qda SC4 0.47 2.7 -Qda SC5 0.47 3.1 -Qda SN0 0.47 3.5 -Qda SNa 0.47 5 -Qda SNd 0.47 5 -Qda SNda 0.47 5 -Qda SP1 0.47 5 -Qda SP2 0.47 5 -Qda SP3 0.47 5.6 -Qda SP4 0.47 5.6 -Qda SP5 0.47 5.6 -Qda SQ0 0.47 4.5 -Qda SQa 0.47 5.6 -Qda SQd 0.47 5.6 -Qda SQda 0.47 5.6 -SC1 SC1 0.43 2.625 -SC1 SC2 0.43 2.625 -SC1 SC3 0.43 2.625 -SC1 SC4 0.43 2.325 -SC1 SC5 0.43 2.325 -SC1 SN0 0.43 2.025 -SC1 SNa 0.43 2.025 -SC1 SNd 0.43 2.025 -SC1 SNda 0.43 2.025 -SC1 SP1 0.43 2.025 -SC1 SP2 0.43 1.725 -SC1 SP3 0.43 1.725 -SC1 SP4 0.43 1.5 -SC1 SP5 0.43 1.5 -SC1 SQ0 0.62 2 -SC1 SQa 0.62 2 -SC1 SQd 0.62 2 -SC1 SQda 0.62 2 -SC2 SC2 0.43 2.625 -SC2 SC3 0.43 2.625 -SC2 SC4 0.43 2.325 -SC2 SC5 0.43 2.325 -SC2 SN0 0.43 2.325 -SC2 SNa 0.43 2.025 -SC2 SNd 0.43 2.025 -SC2 SNda 0.43 2.025 -SC2 SP1 0.43 2.325 -SC2 SP2 0.43 2.025 -SC2 SP3 0.43 2.025 -SC2 SP4 0.43 1.725 -SC2 SP5 0.43 1.725 -SC2 SQ0 0.62 2 -SC2 SQa 0.62 2 -SC2 SQd 0.62 2 -SC2 SQda 0.62 2 -SC3 SC3 0.43 2.625 -SC3 SC4 0.43 2.625 -SC3 SC5 0.43 2.625 -SC3 SN0 0.43 2.625 -SC3 SNa 0.43 2.025 -SC3 SNd 0.43 2.025 -SC3 SNda 0.43 2.025 -SC3 SP1 0.43 2.625 -SC3 SP2 0.43 2.325 -SC3 SP3 0.43 2.325 -SC3 SP4 0.43 2.025 -SC3 SP5 0.43 2.025 -SC3 SQ0 0.43 1.725 -SC3 SQa 0.43 1.725 -SC3 SQd 0.43 1.725 -SC3 SQda 0.43 1.725 -SC4 SC4 0.43 2.625 -SC4 SC5 0.43 2.625 -SC4 SN0 0.43 2.625 -SC4 SNa 0.43 2.325 -SC4 SNd 0.43 2.325 -SC4 SNda 0.43 2.325 -SC4 SP1 0.43 2.625 -SC4 SP2 0.43 2.625 -SC4 SP3 0.43 2.325 -SC4 SP4 0.43 2.025 -SC4 SP5 0.43 2.025 -SC4 SQ0 0.43 2.025 -SC4 SQa 0.43 2.025 -SC4 SQd 0.43 2.025 -SC4 SQda 0.43 2.025 -SC5 SC5 0.43 2.625 -SC5 SN0 0.43 2.625 -SC5 SNa 0.43 2.625 -SC5 SNd 0.43 2.625 -SC5 SNda 0.43 2.625 -SC5 SP1 0.43 2.625 -SC5 SP2 0.43 2.625 -SC5 SP3 0.43 2.625 -SC5 SP4 0.43 2.325 -SC5 SP5 0.43 2.325 -SC5 SQ0 0.43 2.325 -SC5 SQa 0.43 2.325 -SC5 SQd 0.43 2.325 -SC5 SQda 0.43 2.325 -SN0 SN0 0.43 2.625 -SN0 SNa 0.43 2.625 -SN0 SNd 0.43 2.625 -SN0 SNda 0.43 2.625 -SN0 SP1 0.43 3 -SN0 SP2 0.43 3 -SN0 SP3 0.43 2.625 -SN0 SP4 0.43 2.625 -SN0 SP5 0.43 2.625 -SN0 SQ0 0.43 2.625 -SN0 SQa 0.43 2.625 -SN0 SQd 0.43 2.625 -SN0 SQda 0.43 2.625 -SNa SNa 0.43 3 -SNa SNd 0.43 3.375 -SNa SNda 0.43 3.375 -SNa SP1 0.43 3.375 -SNa SP2 0.43 3.375 -SNa SP3 0.43 3.375 -SNa SP4 0.43 3 -SNa SP5 0.43 3.75 -SNa SQ0 0.43 3 -SNa SQa 0.43 3 -SNa SQd 0.43 3.75 -SNa SQda 0.43 3.75 -SNd SNd 0.43 3 -SNd SNda 0.43 3.375 -SNd SP1 0.43 3.375 -SNd SP2 0.43 3.375 -SNd SP3 0.43 3.375 -SNd SP4 0.43 3 -SNd SP5 0.43 3.75 -SNd SQ0 0.43 3 -SNd SQa 0.43 3.75 -SNd SQd 0.43 3 -SNd SQda 0.43 3.75 -SNda SNda 0.43 3.375 -SNda SP1 0.43 3.375 -SNda SP2 0.43 3.375 -SNda SP3 0.43 3.375 -SNda SP4 0.43 3 -SNda SP5 0.43 3.75 -SNda SQ0 0.43 3 -SNda SQa 0.43 3.75 -SNda SQd 0.43 3.75 -SNda SQda 0.43 3.75 -SP1 SP1 0.43 3.375 -SP1 SP2 0.43 3.375 -SP1 SP3 0.43 3.375 -SP1 SP4 0.43 3.375 -SP1 SP5 0.43 4.2 -SP1 SQ0 0.43 3 -SP1 SQa 0.43 3.75 -SP1 SQd 0.43 3.75 -SP1 SQda 0.43 3.75 -SP2 SP2 0.43 3.375 -SP2 SP3 0.43 3.375 -SP2 SP4 0.43 3.375 -SP2 SP5 0.43 4.2 -SP2 SQ0 0.43 3.375 -SP2 SQa 0.43 3.75 -SP2 SQd 0.43 3.75 -SP2 SQda 0.43 3.75 -SP3 SP3 0.43 3.75 -SP3 SP4 0.43 3.75 -SP3 SP5 0.43 4.2 -SP3 SQ0 0.43 3.75 -SP3 SQa 0.43 4.2 -SP3 SQd 0.43 4.2 -SP3 SQda 0.43 4.2 -SP4 SP4 0.43 3.75 -SP4 SP5 0.43 4.2 -SP4 SQ0 0.43 4.2 -SP4 SQa 0.43 4.2 -SP4 SQd 0.43 4.2 -SP4 SQda 0.43 4.2 -SP5 SP5 0.43 4.2 -SP5 SQ0 0.43 3.75 -SP5 SQa 0.43 4.2 -SP5 SQd 0.43 4.2 -SP5 SQda 0.43 4.2 -SQ0 SQ0 0.43 2.625 -SQ0 SQa 0.43 3.375 -SQ0 SQd 0.43 3.375 -SQ0 SQda 0.43 3.375 -SQa SQa 0.43 3.75 -SQa SQd 0.43 4.2 -SQa SQda 0.43 4.2 -SQd SQd 0.43 3.75 -SQd SQda 0.43 4.2 -SQda SQda 0.43 4.2 - -ITEM END - -# Bond wildcard parameters - -ITEM BOND_AUTO - -# type1 type2 k l0 - -* * 1250 0.47 - -ITEM END - -# Templates - -ITEM TEMPLATES - -# name smiles - -W [P4] -WF [BP4] - -ITEM END diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm deleted file mode 100644 index eb039bde53..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/polymers.prm +++ /dev/null @@ -1,376 +0,0 @@ -# -# Martini interaction parameters using martini.30646.tmp -# converted by martini.pl v1.2, February 10, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME MARTINI -FFTYPE COARSE -VERSION 2011 -CREATED Feb 2014 -LENGTH NANOMETER -ENERGY KJ/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 0.9 -CUTOFF 1.2 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Masses - -ITEM MASS - -# type mass element ncons charge comment - -SN01 54 SN0 2 0 ring intermediate -SN010 54 SN0 2 0 ring intermediate -SN011 54 SN0 2 0 ring intermediate -SN012 54 SN0 2 0 ring intermediate -SN013 54 SN0 2 0 ring intermediate -SN014 54 SN0 2 0 ring intermediate -SN015 54 SN0 2 0 ring intermediate -SN016 54 SN0 2 0 ring intermediate -SN017 54 SN0 2 0 ring intermediate -SN018 54 SN0 2 0 ring intermediate -SN019 54 SN0 2 0 ring intermediate -SN02 54 SN0 2 0 ring intermediate -SN020 54 SN0 2 0 ring intermediate -SN021 54 SN0 2 0 ring intermediate -SN022 54 SN0 2 0 ring intermediate -SN023 54 SN0 2 0 ring intermediate -SN024 54 SN0 2 0 ring intermediate -SN025 54 SN0 2 0 ring intermediate -SN026 54 SN0 2 0 ring intermediate -SN027 54 SN0 2 0 ring intermediate -SN028 54 SN0 2 0 ring intermediate -SN029 54 SN0 2 0 ring intermediate -SN03 54 SN0 2 0 ring intermediate -SN030 54 SN0 2 0 ring intermediate -SN031 54 SN0 2 0 ring intermediate -SN032 54 SN0 2 0 ring intermediate -SN033 54 SN0 2 0 ring intermediate -SN034 54 SN0 2 0 ring intermediate -SN035 54 SN0 2 0 ring intermediate -SN036 54 SN0 2 0 ring intermediate -SN037 54 SN0 2 0 ring intermediate -SN038 54 SN0 2 0 ring intermediate -SN039 54 SN0 2 0 ring intermediate -SN04 54 SN0 2 0 ring intermediate -SN040 54 SN0 2 0 ring intermediate -SN041 54 SN0 2 0 ring intermediate -SN042 54 SN0 2 0 ring intermediate -SN043 54 SN0 2 0 ring intermediate -SN044 54 SN0 2 0 ring intermediate -SN045 54 SN0 2 0 ring intermediate -SN046 54 SN0 2 0 ring intermediate -SN047 54 SN0 2 0 ring intermediate -SN048 54 SN0 2 0 ring intermediate -SN049 54 SN0 2 0 ring intermediate -SN05 54 SN0 2 0 ring intermediate -SN050 54 SN0 2 0 ring intermediate -SN051 54 SN0 2 0 ring intermediate -SN052 54 SN0 2 0 ring intermediate -SN053 54 SN0 2 0 ring intermediate -SN054 54 SN0 2 0 ring intermediate -SN055 54 SN0 2 0 ring intermediate -SN056 54 SN0 2 0 ring intermediate -SN057 54 SN0 2 0 ring intermediate -SN058 54 SN0 2 0 ring intermediate -SN059 54 SN0 2 0 ring intermediate -SN06 54 SN0 2 0 ring intermediate -SN060 54 SN0 2 0 ring intermediate -SN061 54 SN0 2 0 ring intermediate -SN062 54 SN0 2 0 ring intermediate -SN063 54 SN0 2 0 ring intermediate -SN064 54 SN0 2 0 ring intermediate -SN065 54 SN0 2 0 ring intermediate -SN066 54 SN0 2 0 ring intermediate -SN067 54 SN0 2 0 ring intermediate -SN068 54 SN0 2 0 ring intermediate -SN069 54 SN0 2 0 ring intermediate -SN07 54 SN0 2 0 ring intermediate -SN070 54 SN0 2 0 ring intermediate -SN071 54 SN0 2 0 ring intermediate -SN072 54 SN0 2 0 ring intermediate -SN073 54 SN0 2 0 ring intermediate -SN074 54 SN0 2 0 ring intermediate -SN08 54 SN0 2 0 ring intermediate -SN09 54 SN0 2 0 ring intermediate - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -SN01 SN0 SN0 SN0 SN01 SN01 -SN010 SN0 SN0 SN0 SN010 SN010 -SN011 SN0 SN0 SN0 SN011 SN011 -SN012 SN0 SN0 SN0 SN012 SN012 -SN013 SN0 SN0 SN0 SN013 SN013 -SN014 SN0 SN0 SN0 SN014 SN014 -SN015 SN0 SN0 SN0 SN015 SN015 -SN016 SN0 SN0 SN0 SN016 SN016 -SN017 SN0 SN0 SN0 SN017 SN017 -SN018 SN0 SN0 SN0 SN018 SN018 -SN019 SN0 SN0 SN0 SN019 SN019 -SN02 SN0 SN0 SN0 SN02 SN02 -SN020 SN0 SN0 SN0 SN020 SN020 -SN021 SN0 SN0 SN0 SN021 SN021 -SN022 SN0 SN0 SN0 SN022 SN022 -SN023 SN0 SN0 SN0 SN023 SN023 -SN024 SN0 SN0 SN0 SN024 SN024 -SN025 SN0 SN0 SN0 SN025 SN025 -SN026 SN0 SN0 SN0 SN026 SN026 -SN027 SN0 SN0 SN0 SN027 SN027 -SN028 SN0 SN0 SN0 SN028 SN028 -SN029 SN0 SN0 SN0 SN029 SN029 -SN03 SN0 SN0 SN0 SN03 SN03 -SN030 SN0 SN0 SN0 SN030 SN030 -SN031 SN0 SN0 SN0 SN031 SN031 -SN032 SN0 SN0 SN032 SN032 SN032 -SN033 SN0 SN0 SN033 SN033 SN033 -SN034 SN0 SN0 SN034 SN034 SN034 -SN035 SN0 SN0 SN035 SN035 SN035 -SN036 SN0 SN0 SN036 SN036 SN036 -SN037 SN0 SN0 SN037 SN037 SN037 -SN038 SN0 SN0 SN038 SN038 SN038 -SN039 SN0 SN0 SN039 SN039 SN039 -SN04 SN0 SN0 SN0 SN04 SN04 -SN040 SN0 SN0 SN040 SN040 SN040 -SN041 SN0 SN0 SN041 SN041 SN041 -SN042 SN0 SN0 SN042 SN042 SN042 -SN043 SN0 SN0 SN043 SN043 SN043 -SN044 SN0 SN0 SN044 SN044 SN044 -SN045 SN0 SN0 SN045 SN045 SN045 -SN046 SN0 SN0 SN046 SN046 SN046 -SN047 SN0 SN0 SN047 SN047 SN047 -SN048 SN0 SN0 SN048 SN048 SN048 -SN049 SN0 SN0 SN049 SN049 SN049 -SN05 SN0 SN0 SN0 SN05 SN05 -SN050 SN0 SN0 SN050 SN050 SN050 -SN051 SN0 SN0 SN051 SN051 SN051 -SN052 SN0 SN0 SN052 SN052 SN052 -SN053 SN0 SN0 SN053 SN053 SN053 -SN054 SN0 SN0 SN054 SN054 SN054 -SN055 SN0 SN0 SN055 SN055 SN055 -SN056 SN0 SN0 SN056 SN056 SN056 -SN057 SN0 SN0 SN057 SN057 SN057 -SN058 SN0 SN0 SN058 SN058 SN058 -SN059 SN0 SN0 SN059 SN059 SN059 -SN06 SN0 SN0 SN0 SN06 SN06 -SN060 SN0 SN0 SN060 SN060 SN060 -SN061 SN0 SN0 SN061 SN061 SN061 -SN062 SN0 SN0 SN062 SN062 SN062 -SN063 SN0 SN0 SN063 SN063 SN063 -SN064 SN0 SN0 SN064 SN064 SN064 -SN065 SN0 SN0 SN065 SN065 SN065 -SN066 SN0 SN0 SN066 SN066 SN066 -SN067 SN0 SN0 SN067 SN067 SN067 -SN068 SN0 SN0 SN068 SN068 SN068 -SN069 SN0 SN0 SN069 SN069 SN069 -SN07 SN0 SN0 SN0 SN07 SN07 -SN070 SN0 SN0 SN070 SN070 SN070 -SN071 SN0 SN0 SN071 SN071 SN071 -SN072 SN0 SN0 SN072 SN072 SN072 -SN073 SN0 SN0 SN073 SN073 SN073 -SN074 SN0 SN0 SN074 SN074 SN074 -SN08 SN0 SN0 SN0 SN08 SN08 -SN09 SN0 SN0 SN0 SN09 SN09 - -ITEM END - -# Bond parameters - -ITEM BOND - -# type1 type2 k l0 - -C1 C1 1250 0.47 -C1 Na 1250 0.47 -N0 N0 1250 0.38 -N0 Nda 1250 0.5 -Na Na 1250 0.37 -Na Qa 1250 0.47 -Nda Qd 1250 0.5 -P5 Qa 1250 0.47 -P5 SN0 17000 0.33 -SCY STY 8000 0.27 -SN0 SN0 17000 0.33 -STY STY 20000 0.27 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 - -C1 C1 C1 25 180 -C1 C1 Na 25 180 -C1 Na Qa 25 180 -N0 N0 Nda 150 120 -N0 Nda N0 150 180 -N0 Nda Qd 150 180 -Na Na Qa 25 120 -Nda N0 Nda 150 120 -P5 SN032 SN033 85 130 -SCY STY SCY 550 52 -SCY STY STY 100 136 -SN0 SN0 SN0 50 130 -SN0 SN0 SN074 85 130 -SN0 SN074 SN073 85 130 -SN032 SN033 SN034 85 130 -SN033 SN034 SN035 85 130 -SN034 SN035 SN036 85 130 -SN035 SN036 SN037 85 130 -SN036 SN037 SN038 85 130 -SN037 SN038 SN039 85 130 -SN038 SN039 SN040 85 130 -SN039 SN040 SN041 85 130 -SN040 SN041 SN042 85 130 -SN041 SN042 SN043 85 130 -SN042 SN043 SN044 85 130 -SN043 SN044 SN045 85 130 -SN044 SN045 SN046 85 130 -SN045 SN046 SN047 85 130 -SN046 SN047 SN048 85 130 -SN047 SN048 SN049 85 130 -SN048 SN049 SN050 85 130 -SN049 SN050 SN051 85 130 -SN050 SN051 SN052 85 130 -SN051 SN052 SN053 85 130 -SN052 SN053 SN054 85 130 -SN053 SN054 SN055 85 130 -SN054 SN055 SN056 85 130 -SN055 SN056 SN057 85 130 -SN056 SN057 SN058 85 130 -SN057 SN058 SN059 85 130 -SN058 SN059 SN060 85 130 -SN059 SN060 SN061 85 130 -SN060 SN061 SN062 85 130 -SN061 SN062 SN063 85 130 -SN062 SN063 SN064 85 130 -SN063 SN064 SN065 85 130 -SN064 SN065 SN066 85 130 -SN065 SN066 SN067 85 130 -SN066 SN067 SN068 85 130 -SN067 SN068 SN069 85 130 -SN068 SN069 SN070 85 130 -SN069 SN070 SN071 85 130 -SN070 SN071 SN072 85 130 -SN071 SN072 SN073 85 130 -SN072 SN073 SN074 85 130 -STY SCY STY 25 120 - -ITEM END - -# Torsion parameters - -ITEM TORSION - -# type1 type2 type3 type4 k n delta ... - -SN0 SN0 SN0 SN0 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN0 SN0 SN031 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN0 SN01 SN02 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN0 SN031 SN030 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN0 SN074 SN073 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN01 SN02 SN03 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN031 SN030 SN029 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN0 SN074 SN073 SN072 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN01 SN02 SN03 SN04 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN010 SN011 SN012 SN013 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN010 SN09 SN08 SN07 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN011 SN010 SN09 SN08 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN011 SN012 SN013 SN014 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN012 SN011 SN010 SN09 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN012 SN013 SN014 SN015 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN013 SN014 SN015 SN016 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN014 SN015 SN016 SN017 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN015 SN016 SN017 SN018 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN016 SN017 SN018 SN019 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN017 SN018 SN019 SN020 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN018 SN019 SN020 SN021 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN019 SN020 SN021 SN022 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN02 SN03 SN04 SN05 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN020 SN021 SN022 SN023 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN021 SN022 SN023 SN024 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN022 SN023 SN024 SN025 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN023 SN024 SN025 SN026 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN024 SN025 SN026 SN027 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN025 SN026 SN027 SN028 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN026 SN027 SN028 SN029 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN027 SN028 SN029 SN030 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN028 SN029 SN030 SN031 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN03 SN04 SN05 SN06 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN032 SN033 SN034 SN035 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN033 SN034 SN035 SN036 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN034 SN035 SN036 SN037 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN035 SN036 SN037 SN038 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN036 SN037 SN038 SN039 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN037 SN038 SN039 SN040 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN038 SN039 SN040 SN041 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN039 SN040 SN041 SN042 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN04 SN05 SN06 SN07 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN040 SN041 SN042 SN043 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN041 SN042 SN043 SN044 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN042 SN043 SN044 SN045 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN043 SN044 SN045 SN046 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN044 SN045 SN046 SN047 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN045 SN046 SN047 SN048 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN046 SN047 SN048 SN049 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN047 SN048 SN049 SN050 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN048 SN049 SN050 SN051 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN049 SN050 SN051 SN052 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN05 SN06 SN07 SN08 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN050 SN051 SN052 SN053 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN051 SN052 SN053 SN054 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN052 SN053 SN054 SN055 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN053 SN054 SN055 SN056 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN054 SN055 SN056 SN057 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN055 SN056 SN057 SN058 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN056 SN057 SN058 SN059 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN057 SN058 SN059 SN060 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN058 SN059 SN060 SN061 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN059 SN060 SN061 SN062 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN06 SN07 SN08 SN09 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN060 SN061 SN062 SN063 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN061 SN062 SN063 SN064 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN062 SN063 SN064 SN065 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN063 SN064 SN065 SN066 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN064 SN065 SN066 SN067 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN065 SN066 SN067 SN068 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN066 SN067 SN068 SN069 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN067 SN068 SN069 SN070 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN068 SN069 SN070 SN071 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN069 SN070 SN071 SN072 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN070 SN071 SN072 SN073 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 -SN071 SN072 SN073 SN074 1.96 1 180 0.18 2 0 0.33 3 0 0.12 4 0 - -ITEM END - -# Templates - -ITEM TEMPLATES - -# name smiles - -DEN [N0]([N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])([Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][N0]([Nda][Qd+1])[Nda][Qd+1])[Nda][N0]([Nda][Qd+1])[Nda][Qd+1] -PEL [P5]([Qa-1][Na]([Na][C1][C1][C1][C1])[C1][C1][C1][C1])[SN032][SN033][SN034][SN035][SN036][SN037][SN038][SN039][SN040][SN041][SN042][SN043][SN044][SN045][SN046][SN047][SN048][SN049][SN050][SN051][SN052][SN053][SN054][SN055][SN056][SN057][SN058][SN059][SN060][SN061][SN062][SN063][SN064][SN065][SN066][SN067][SN068][SN069][SN070][SN071][SN072][SN073][SN074][SN0][SN0] -PEO [SN0][SN0][SN01][SN02][SN03][SN04][SN05][SN06][SN07][SN08][SN09][SN010][SN011][SN012][SN013][SN014][SN015][SN016][SN017][SN018][SN019][SN020][SN021][SN022][SN023][SN024][SN025][SN026][SN027][SN028][SN029][SN030][SN031][SN0][SN0][SN0][SN0] -PS100 [SCY]([STY]2[STY][STY]2)[STY]1([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY][STY]([SCY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY])[STY][STY]1 - -ITEM END diff --git a/tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm b/tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm deleted file mode 100644 index a58b9ccd61..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/martini_original_format/sugars.prm +++ /dev/null @@ -1,394 +0,0 @@ -# -# Martini interaction parameters using martini.30651.tmp -# converted by martini.pl v1.2, February 10, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME MARTINI -FFTYPE COARSE -VERSION 2011 -CREATED Feb 2014 -LENGTH NANOMETER -ENERGY KJ/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 0.9 -CUTOFF 1.2 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Masses - -ITEM MASS - -# type mass element ncons charge comment - -P11 60.0528 P1 2 0 polar -P12 60.0528 P1 2 0 polar -P13 60.0528 P1 2 0 polar -P14 59.0448 P1 2 0 polar -P15 44.0534 P1 2 0 polar -P16 43.0454 P1 2 0 polar -P21 60.0528 P2 2 0 polar -P210 75.0442 P2 2 0 polar -P211 60.0528 P2 2 0 polar -P212 59.0448 P2 2 0 polar -P213 43.0454 P2 2 0 polar -P214 75.0442 P2 2 0 polar -P215 44.0534 P2 2 0 polar -P216 75.0442 P2 2 0 polar -P217 58.0368 P2 2 0 polar -P218 58.0368 P2 2 0 polar -P219 58.0368 P2 2 0 polar -P22 59.0448 P2 2 0 polar -P220 58.0368 P2 2 0 polar -P221 58.0368 P2 2 0 polar -P222 59.0448 P2 2 0 polar -P223 60.0528 P2 2 0 polar -P224 43.0454 P2 2 0 polar -P225 60.0528 P2 2 0 polar -P226 43.0454 P2 2 0 polar -P227 60.0528 P2 2 0 polar -P228 43.0454 P2 2 0 polar -P23 43.0454 P2 2 0 polar -P24 75.0442 P2 2 0 polar -P25 58.0368 P2 2 0 polar -P26 59.1168 P2 2 0 polar -P27 75.0442 P2 2 0 polar -P28 75.0442 P2 2 0 polar -P29 59.1168 P2 2 0 polar -P31 60.0528 P3 2 0 polar -P41 60.0528 P4 2 0 polar -P42 60.0528 P4 2 0 polar -P43 43.0454 P4 2 0 polar - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -P11 P1 P11 P11 P11 P11 -P12 P1 P12 P12 P12 P12 -P13 P1 P13 P13 P13 P13 -P14 P1 P14 P14 P14 P14 -P15 P1 P15 P15 P15 P15 -P16 P1 P16 P16 P16 P16 -P21 P2 P21 P21 P21 P21 -P210 P2 P210 P210 P210 P210 -P211 P2 P211 P211 P211 P211 -P212 P2 P212 P212 P212 P212 -P213 P2 P213 P213 P213 P213 -P214 P2 P214 P214 P214 P214 -P215 P2 P215 P215 P215 P215 -P216 P2 P216 P216 P216 P216 -P217 P2 P217 P217 P217 P217 -P218 P2 P218 P218 P218 P218 -P219 P2 P219 P219 P219 P219 -P22 P2 P22 P22 P22 P22 -P220 P2 P220 P220 P220 P220 -P221 P2 P221 P221 P221 P221 -P222 P2 P222 P222 P222 P222 -P223 P2 P223 P223 P223 P223 -P224 P2 P224 P224 P224 P224 -P225 P2 P225 P225 P225 P225 -P226 P2 P226 P226 P226 P226 -P227 P2 P227 P227 P227 P227 -P228 P2 P228 P228 P228 P228 -P23 P2 P23 P23 P23 P23 -P24 P2 P24 P24 P24 P24 -P25 P2 P25 P25 P25 P25 -P26 P2 P26 P26 P26 P26 -P27 P2 P27 P27 P27 P27 -P28 P2 P28 P28 P28 P28 -P29 P2 P29 P29 P29 P29 -P31 P3 P31 P31 P31 P31 -P41 P4 P41 P41 P41 P41 -P42 P4 P42 P42 P42 P42 -P43 P4 P43 P43 P43 P43 - -ITEM END - -# Bond parameters - -ITEM BOND - -# type1 type2 k l0 - -P12 P31 10000 0.309 -P12 P41 35000 0.375 -P12 P42 35000 0.331 -P13 P13 30000 0.293 -P13 P21 30000 0.429 -P13 P212 30000 0.329 -P13 P213 30000 0.372 -P13 P22 30000 0.222 -P13 P222 30000 0.376 -P13 P223 30000 0.22 -P13 P224 30000 0.376 -P13 P225 30000 0.22 -P13 P226 30000 0.376 -P13 P227 30000 0.22 -P13 P228 30000 0.376 -P13 P23 30000 0.239 -P13 P42 35000 0.303 -P13 P43 30000 0.372 -P14 P21 30000 0.222 -P15 P210 30000 0.222 -P15 P214 30000 0.222 -P15 P215 30000 0.231 -P15 P216 30000 0.246 -P15 P217 30000 0.281 -P15 P218 30000 0.246 -P15 P219 30000 0.281 -P15 P220 30000 0.246 -P15 P221 30000 0.281 -P15 P222 30000 0.246 -P15 P24 30000 0.242 -P15 P25 30000 0.234 -P15 P26 30000 0.394 -P15 P27 30000 0.222 -P15 P28 30000 0.222 -P15 P29 30000 0.399 -P16 P211 30000 0.424 -P21 P42 30000 0.247 -P210 P211 30000 0.413 -P210 P42 30000 0.247 -P211 P42 30000 0.294 -P212 P213 30000 0.356 -P212 P42 30000 0.376 -P213 P42 30000 0.276 -P214 P215 30000 0.512 -P214 P42 30000 0.246 -P215 P42 30000 0.22 -P216 P217 30000 0.561 -P216 P42 30000 0.222 -P217 P218 30000 0.561 -P217 P42 30000 0.239 -P218 P219 30000 0.561 -P218 P42 30000 0.222 -P219 P220 30000 0.561 -P219 P42 30000 0.239 -P22 P23 30000 0.561 -P22 P42 30000 0.246 -P220 P221 30000 0.561 -P220 P42 30000 0.222 -P221 P222 30000 0.561 -P221 P42 30000 0.239 -P222 P223 30000 0.356 -P222 P41 30000 0.329 -P222 P42 30000 0.222 -P223 P224 30000 0.356 -P223 P41 30000 0.276 -P224 P225 30000 0.356 -P224 P41 30000 0.329 -P225 P226 30000 0.356 -P225 P41 30000 0.276 -P226 P227 30000 0.356 -P226 P41 30000 0.329 -P227 P228 30000 0.356 -P227 P41 30000 0.276 -P228 P41 30000 0.329 -P23 P42 30000 0.281 -P24 P25 30000 0.518 -P24 P42 30000 0.284 -P25 P42 30000 0.278 -P26 P27 30000 0.47 -P26 P42 30000 0.358 -P27 P42 30000 0.247 -P28 P29 30000 0.432 -P28 P42 30000 0.247 -P29 P42 30000 0.384 -P31 P42 50000 0.42 -P41 P42 50000 0.322 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 - -P13 P13 P21 50 20 -P13 P21 P14 10 130 -P13 P21 P42 150 110 -P13 P212 P213 80 54 -P13 P213 P212 800 67 -P13 P22 P23 50 150 -P13 P222 P223 200 124 -P13 P223 P222 800 67 -P13 P223 P224 200 124 -P13 P224 P223 800 67 -P13 P224 P225 200 124 -P13 P225 P224 800 67 -P13 P225 P226 200 124 -P13 P226 P225 800 67 -P13 P226 P227 200 124 -P13 P227 P226 800 67 -P13 P227 P228 200 124 -P13 P228 P227 800 67 -P13 P23 P22 100 70 -P15 P210 P211 5 87 -P15 P214 P215 100 150 -P15 P215 P214 80 120 -P15 P216 P217 50 140 -P15 P217 P216 25 50 -P15 P217 P218 50 140 -P15 P218 P217 25 50 -P15 P218 P219 50 140 -P15 P219 P218 25 50 -P15 P219 P220 50 140 -P15 P220 P219 25 50 -P15 P220 P221 50 140 -P15 P221 P220 25 50 -P15 P221 P222 50 140 -P15 P222 P221 25 50 -P15 P24 P25 50 126 -P15 P25 P24 100 60 -P15 P26 P27 200 120 -P15 P27 P26 50 127 -P15 P28 P29 20 90 -P15 P29 P28 300 125 -P16 P211 P210 250 96 -P21 P13 P43 150 85 -P210 P211 P42 250 50 -P211 P210 P42 125 130 -P212 P213 P42 500 44 -P213 P212 P42 200 124 -P214 P215 P42 180 65 -P215 P214 P42 250 95 -P216 P217 P218 100 154 -P216 P217 P42 100 70 -P217 P216 P42 50 150 -P217 P218 P219 100 154 -P217 P218 P42 100 70 -P218 P217 P42 50 150 -P218 P219 P220 100 154 -P218 P219 P42 100 70 -P219 P218 P42 50 150 -P219 P220 P221 100 154 -P219 P220 P42 100 70 -P22 P23 P42 25 50 -P220 P219 P42 50 150 -P220 P221 P222 100 154 -P220 P221 P42 100 70 -P221 P220 P42 50 150 -P221 P222 P42 100 70 -P222 P221 P42 50 150 -P222 P223 P224 500 136 -P222 P223 P41 500 44 -P223 P222 P41 80 54 -P223 P224 P225 500 136 -P223 P224 P41 500 44 -P224 P223 P41 80 54 -P224 P225 P226 500 136 -P224 P225 P41 500 44 -P225 P224 P41 80 54 -P225 P226 P227 500 136 -P225 P226 P41 500 44 -P226 P225 P41 80 54 -P226 P227 P228 500 136 -P226 P227 P41 500 44 -P227 P226 P41 80 54 -P227 P228 P41 500 44 -P228 P227 P41 80 54 -P23 P22 P42 50 140 -P24 P25 P42 25 65 -P25 P24 P42 50 120 -P26 P27 P42 200 81 -P27 P26 P42 400 75 -P28 P29 P42 350 90 -P29 P28 P42 200 125 - -ITEM END - -# Torsion parameters - -ITEM TORSION - -# type1 type2 type3 type4 k n delta ... - -P13 P13 P21 P14 25 1 130 -P13 P13 P21 P42 20 1 290 -P13 P212 P213 P13 5 1 55 -P13 P212 P213 P42 15 1 20 -P13 P22 P23 P13 8 1 110 -P13 P22 P23 P42 5 1 340 -P13 P223 P224 P41 5 1 42 -P13 P224 P223 P41 5 1 55 -P13 P225 P226 P41 5 1 42 -P13 P226 P225 P41 5 1 55 -P13 P227 P228 P41 5 1 42 -P13 P228 P227 P41 5 1 55 -P13 P23 P22 P42 5 1 280 -P14 P21 P13 P43 2 1 80 -P15 P210 P211 P16 15 1 338 -P15 P210 P211 P42 15 1 345 -P15 P214 P215 P15 8 1 280 -P15 P214 P215 P42 5 1 123 -P15 P215 P214 P42 20 1 320 -P15 P216 P217 P42 5 1 280 -P15 P217 P216 P42 5 1 340 -P15 P217 P218 P42 5 1 280 -P15 P218 P217 P42 5 1 340 -P15 P218 P219 P42 5 1 280 -P15 P219 P218 P42 5 1 340 -P15 P219 P220 P42 5 1 280 -P15 P220 P219 P42 5 1 340 -P15 P220 P221 P42 5 1 280 -P15 P221 P220 P42 5 1 340 -P15 P222 P221 P42 5 1 340 -P15 P24 P25 P15 8 1 30 -P15 P24 P25 P42 5 1 210 -P15 P25 P24 P42 5 1 210 -P15 P26 P27 P15 10 1 110 -P15 P27 P26 P42 8 1 165 -P15 P28 P29 P15 10 1 55 -P15 P28 P29 P42 8 1 40 -P41 P223 P224 P41 15 1 20 -P41 P225 P226 P41 15 1 20 -P41 P227 P228 P41 15 1 20 -P42 P210 P211 P42 1 1 160 -P42 P212 P213 P42 5 1 42 -P42 P216 P217 P42 8 1 110 -P42 P217 P218 P42 8 1 110 -P42 P218 P219 P42 8 1 110 -P42 P219 P220 P42 8 1 110 -P42 P220 P221 P42 8 1 110 -P42 P221 P222 P42 8 1 110 -P42 P26 P27 P42 30 1 5 -P42 P28 P29 P42 5 1 225 - -ITEM END - -# Templates - -ITEM TEMPLATES - -# name smiles - -CELL [P15][P24]([P42])[P25]([P15])[P42] -FRUC [P13]1[P31][P42]1 -GLUC [P12]1[P41][P42]1 -KOJI [P15][P27]([P42])[P26]([P42])[P15] -LAMI [P13][P212]([P42])[P213]([P42])[P13] -Laminaraheptabiose [P222]([P41])([P13])[P223]([P41])([P13])[P224]([P41])([P13])[P225]([P41])([P13])[P226]([P41])([P13])[P227]([P41])([P13])[P228]([P41])[P13] -MALT [P13][P22]([P42])[P23]([P13])[P42] -Maltoheptaose [P216]([P42])([P15])[P217]([P42])([P15])[P218]([P42])([P15])[P219]([P42])([P15])[P220]([P42])([P15])[P221]([P42])([P15])[P222]([P42])[P15] -NIGE [P15][P210]([P42])[P211]([P42])[P16] -SOPH [P15][P28]([P42])[P29]([P42])[P15] -SUCR [P14][P21]([P42])[P13]([P13])[P43] -TREH [P15][P214]([P42])[P215]([P15])[P42] - -ITEM END diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa.lt b/tools/moltemplate/moltemplate/force_fields/oplsaa.lt deleted file mode 100644 index 7bb69a7445..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa.lt +++ /dev/null @@ -1,9036 +0,0 @@ -# This file contains OPLSAA parameters and rules for creating angle, dihedral, -# and improper interactions according to OPLSAA conventions, taken from -# "OPLS All-Atom Parameters for Organic Molecules, Ions, -# Peptides & Nucleic Acids, July 2008" and distributed with BOSS Version 4.8. -# This file was generated automatically using this script: -# -# tinkerparm2lt.py -name OPLSAA -file oplsaa.prm -dihedral-style opls -zeropad 3 -# -# The "oplsaa.prm" file was downloaded on 2018-6-15 from the TINKER website -# https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm -# (Corrections to imrpopers were added by David Huang (adelaide.edu.au)) -# (Additional conversion details are explained at the end of this file.) -# Urey-Bradley parameters are not included, and a quadratic energy function -# is used (rather than a cosine) for the improper interactions (in order -# to take advantage of available GPU acceleration in LAMMPS at this time). -# -# USAGE: You can create molecules using this force-field this way: -# -# MyMolecule inherits OPLSAA { -# # atom-id mol-id atom-type charge X Y Z -# write('Data Atoms') { -# $atom:C1 $mol @atom:88 0.00 -0.6695 0.000000 0.000000 -# $atom:H11 $mol @atom:89 0.00 -1.234217 -0.854458 0.000000 -# : : : : : : -# } -# } -# -# You can omit the atom charge in your molecule definition. -# (Partial charges will be assigned later according to the force field rules.) -# Responsibility for choosing the atom types (eg "@atom:88", "@atom:89") falls -# on the user. You must select the type of each atom in the molecule carefully -# by looking at the description in the "In Charges" section of this file -# (see below), and looking for a reasonable match. If your simulation is -# non-neutral, or moltemplate complains that you have missing bond, angle, or -# dihedral types, this means at least one of your atom types is incorrect. - - - - -OPLSAA { - - # Below we will use lammps "set" command to assign atom charges - # by atom type. http://lammps.sandia.gov/doc/set.html - - write_once("In Charges") { - set type @atom:1 charge -0.22 # "Fluoride -CH2-F (UA)" - set type @atom:2 charge 0.22 # "Fluoride -CH2-F (UA)" - set type @atom:3 charge 0.55 # "Acetic Acid -COOH (UA)" - set type @atom:4 charge -0.5 # "Acetic Acid >C=O (UA)" - set type @atom:5 charge -0.58 # "Acetic Acid -OH (UA)" - set type @atom:6 charge 0.08 # "Acetic Acid CH3- (UA)" - set type @atom:7 charge 0.45 # "Acetic Acid -OH (UA)" - set type @atom:8 charge 0.0 # "Methane CH4 (UA)" - set type @atom:9 charge 0.0 # "Ethane CH3- (UA)" - set type @atom:10 charge 0.0 # "N-Alkane CH3- (UA)" - set type @atom:11 charge 0.0 # "Isobutane CH3- (UA)" - set type @atom:12 charge 0.0 # "Neopentane CH3- (UA)" - set type @atom:13 charge 0.0 # "Alkanes -CH2- (UA)" - set type @atom:14 charge 0.0 # "1-Alkene CH2= (UA)" - set type @atom:15 charge 0.0 # "Isobutane CH (UA)" - set type @atom:16 charge 0.0 # "2-Alkene -CH= (UA)" - set type @atom:17 charge 0.0 # "Aromatic CH (UA)" - set type @atom:18 charge 0.0 # "Neopentane C (UA)" - set type @atom:19 charge 0.0 # "Isobutene >C= (UA)" - set type @atom:20 charge -0.7 # "Alcohol OH (UA)" - set type @atom:21 charge 0.435 # "Alcohol OH (UA)" - set type @atom:22 charge 0.265 # "Methanol CH3- (UA)" - set type @atom:23 charge 0.265 # "Ethanol -CH2OH (UA)" - set type @atom:24 charge -0.47 # "Hydrogen Sulfide H2S" - set type @atom:25 charge -0.45 # "Alkyl Sulfide RSH (UA)" - set type @atom:26 charge -0.47 # "Thioether RSR (UA)" - set type @atom:27 charge -0.3 # "Disulfide RSSR (UA)" - set type @atom:28 charge 0.235 # "Hydrogen Sulfide H2S" - set type @atom:29 charge 0.27 # "Alkyl Sulfide RSH (UA)" - set type @atom:30 charge 0.18 # "Methyl Sulfide CH3 (UA)" - set type @atom:31 charge 0.18 # "Alkyl Sulfide CH2 (UA)" - set type @atom:32 charge 0.235 # "Thioether CH3 (UA)" - set type @atom:33 charge 0.235 # "Thioether CH2 (UA)" - set type @atom:34 charge 0.3 # "Disulfide CH3 (UA)" - set type @atom:35 charge 0.3 # "Disulfide CH2 (UA)" - set type @atom:36 charge -0.43 # "Acetonitrile -CN (UA)" - set type @atom:37 charge 0.28 # "Acetonitrile -CN (UA)" - set type @atom:38 charge 0.15 # "Acetonitrile CH3 (UA)" - set type @atom:39 charge 0.265 # "Isopropanol >CHOH (UA)" - set type @atom:40 charge 0.265 # "t-Butanol COH (UA)" - set type @atom:41 charge -0.5 # "Ether ROR (UA)" - set type @atom:42 charge 0.25 # "Ether CH3-OR (UA)" - set type @atom:43 charge 0.25 # "Ether -CH2-OR (UA)" - set type @atom:44 charge 0.5 # "Methylene Chloride (UA)" - set type @atom:45 charge -0.25 # "Methylene Chloride (UA)" - set type @atom:46 charge 0.42 # "Chloroform CHCl3 (UA)" - set type @atom:47 charge -0.14 # "Chloroform CHCl3 (UA)" - set type @atom:48 charge 0.248 # "Carbon Tetrachloride" - set type @atom:49 charge -0.062 # "Carbon Tetrachloride" - set type @atom:50 charge 0.139 # "DMSO >S=O (UA)" - set type @atom:51 charge -0.459 # "DMSO >S=O (UA)" - set type @atom:52 charge 0.16 # "DMSO CH3- (UA)" - set type @atom:53 charge -0.5 # "DMF C=O (UA)" - set type @atom:54 charge -0.57 # "DMF CON< (UA)" - set type @atom:55 charge 0.5 # "DMF C=O (UA)" - set type @atom:56 charge 0.285 # "DMF CH3- (UA)" - set type @atom:57 charge 0.0 # "Dummy Atom" - set type @atom:58 charge 0.0 # "Helium Atom" - set type @atom:59 charge 0.0 # "Neon Atom" - set type @atom:60 charge 0.0 # "Argon Atom" - set type @atom:61 charge 0.0 # "Krypton Atom" - set type @atom:62 charge 0.0 # "Xenon Atom" - set type @atom:63 charge -0.834 # "TIP3P Water O" - set type @atom:64 charge 0.417 # "TIP3P Water H" - set type @atom:65 charge 0.0 # "TIP4P Water O" - set type @atom:66 charge 0.52 # "TIP4P Water H" - set type @atom:67 charge -1.04 # "TIP4P Water M" - set type @atom:68 charge -0.822 # "TIP3F Water O" - set type @atom:69 charge 0.411 # "TIP3F Water H" - set type @atom:70 charge 0.0 # "TIP4F Water O" - set type @atom:71 charge 0.511 # "TIP4F Water H" - set type @atom:72 charge -1.022 # "TIP4F Water M" - set type @atom:73 charge 0.0 # "TIP5P Water O" - set type @atom:74 charge 0.241 # "TIP5P Water H" - set type @atom:75 charge -0.241 # "TIP5P Water LP" - set type @atom:76 charge -0.82 # "SPC Water O" - set type @atom:77 charge 0.41 # "SPC Water H" - set type @atom:78 charge -1.02 # "Ammonia NH3" - set type @atom:79 charge 0.34 # "Ammonia NH3" - set type @atom:80 charge -0.18 # "Alkane CH3-" - set type @atom:81 charge -0.12 # "Alkane -CH2-" - set type @atom:82 charge -0.06 # "Alkane >CH-" - set type @atom:83 charge -0.24 # "Methane CH4" - set type @atom:84 charge 0.0 # "Alkane >C<" - set type @atom:85 charge 0.06 # "Alkane H-C" - set type @atom:86 charge 0.0 # "Alkene R2-C=" - set type @atom:87 charge -0.115 # "Alkene RH-C=" - set type @atom:88 charge -0.23 # "Alkene H2-C=" - set type @atom:89 charge 0.115 # "Alkene H-C=" - set type @atom:90 charge -0.115 # "Aromatic C" - set type @atom:91 charge 0.115 # "Aromatic H-C" - set type @atom:92 charge 0.0 # "Naphthalene Fusion C" - set type @atom:93 charge -0.065 # "Ethyl Benzene CH3-" - set type @atom:94 charge -0.005 # "Ethyl Benzene -CH2-" - set type @atom:95 charge -0.115 # "Diene =CH-CH=" - set type @atom:96 charge -0.683 # "Alcohol -OH" - set type @atom:97 charge 0.418 # "Alcohol -OH" - set type @atom:98 charge 0.04 # "Methanol CH3-" - set type @atom:99 charge 0.145 # "Alcohol CH3OH & RCH2OH" - set type @atom:100 charge 0.205 # "Alcohol R2CHOH" - set type @atom:101 charge 0.265 # "Alcohol R3COH" - set type @atom:102 charge 0.1263 # "Trifluoroethanol -CH2-" - set type @atom:103 charge 0.5323 # "Trifluoroethanol CF3-" - set type @atom:104 charge -0.6351 # "Trifluoroethanol -OH" - set type @atom:105 charge 0.4286 # "Trifluoroethanol -OH" - set type @atom:106 charge -0.2057 # "Trifluoroethanol F" - set type @atom:107 charge 0.0825 # "Trifluoroethanol -CH2-" - set type @atom:108 charge 0.15 # "Phenol C-OH" - set type @atom:109 charge -0.585 # "Phenol -OH" - set type @atom:110 charge 0.435 # "Phenol -OH" - set type @atom:111 charge -0.7 # "Diol -OH" - set type @atom:112 charge 0.435 # "Diol -OH" - set type @atom:113 charge -0.73 # "Triol -OH" - set type @atom:114 charge 0.465 # "Triol -OH" - set type @atom:115 charge 0.145 # "Diol & Triol -CH2OH" - set type @atom:116 charge 0.205 # "Diol & Triol -CHROH" - set type @atom:117 charge 0.265 # "Diol & Triol -CR2OH" - set type @atom:118 charge 0.06 # "Diol & Triol H-COH" - set type @atom:119 charge -0.17 # "Diphenyl Ether" - set type @atom:120 charge 0.0 # "Diene =CR-CR=" - set type @atom:121 charge -0.285 # "Anisole -OCH3" - set type @atom:122 charge -0.4 # "Dialkyl Ether -O-" - set type @atom:123 charge 0.11 # "Methyl Ether CH3OR" - set type @atom:124 charge 0.14 # "Ethyl Ether -CH2OR" - set type @atom:125 charge 0.17 # "Isopropyl Ether >CHOR" - set type @atom:126 charge 0.2 # "t-Butyl Ether COR" - set type @atom:127 charge 0.03 # "Alkyl Ether H-COR" - set type @atom:128 charge -0.4 # "Acetal RO-CR2OX" - set type @atom:129 charge -0.7 # "Hemiacetal -OH" - set type @atom:130 charge 0.435 # "Hemiacetal -OH" - set type @atom:131 charge 0.2 # "Acetal RO-CH2-OR" - set type @atom:132 charge 0.1 # "Acetal RO-CH2-OR" - set type @atom:133 charge 0.265 # "Hemiacetal RO-CH2-OH" - set type @atom:134 charge 0.1 # "Hemiacetal RO-CH2-OH" - set type @atom:135 charge 0.3 # "Acetal RO-CHR-OR" - set type @atom:136 charge 0.1 # "Acetal RO-CHR-OR" - set type @atom:137 charge 0.365 # "Hemiacetal RO-CHR-OH" - set type @atom:138 charge 0.1 # "Hemiacetal RO-CHR-OH" - set type @atom:139 charge 0.4 # "Acetal RO-CR2-OR" - set type @atom:140 charge 0.465 # "Hemiacetal RO-CR2-OH" - set type @atom:141 charge 0.085 # "Anisole C-OCH3" - set type @atom:142 charge -0.335 # "Thiol -SH" - set type @atom:143 charge -0.47 # "Hydrogen Sulfide H2S" - set type @atom:144 charge -0.435 # "Sulfide -S-" - set type @atom:145 charge -0.2175 # "Disulfide -S-S-" - set type @atom:146 charge 0.155 # "Thiol -SH" - set type @atom:147 charge 0.235 # "Hydrogen Sulfide H2S" - set type @atom:148 charge 0.06 # "Thiol -CH2-SH" - set type @atom:149 charge 0.12 # "Thiol >CH-SH" - set type @atom:150 charge 0.18 # "Thiol C-SH" - set type @atom:151 charge 0.0375 # "Methyl Sulfide CH3-SR" - set type @atom:152 charge 0.0975 # "Sulfide RCH2-SR" - set type @atom:153 charge 0.1575 # "Sulfide R2CH-SR" - set type @atom:154 charge 0.2175 # "Sulfide R3C-SR" - set type @atom:155 charge 0.0375 # "Disulfide CH3-S-SR" - set type @atom:156 charge 0.0975 # "Disulfide RCH2-S-SR" - set type @atom:157 charge 0.1575 # "Disulfide R2CH-S-SR" - set type @atom:158 charge 0.2175 # "Disulfide R3C-S-SR" - set type @atom:159 charge 0.0 # "Methanethiol CH3-SH" - set type @atom:160 charge 0.2 # "Benzyl Alcohol -CH2OH" - set type @atom:161 charge 0.26 # "Benzyl Alcohol -CHROH" - set type @atom:162 charge 0.32 # "Benzyl Alcohol -CR2OH" - set type @atom:163 charge -0.055 # "Benzyl Alcohol/Nitrile" - set type @atom:164 charge -0.32 # "Thioanisole -SCH3" - set type @atom:165 charge 0.08 # "RCH2-NH2 & GLY CA" - set type @atom:166 charge 0.14 # "RCHR-NH2 & ALA CA" - set type @atom:167 charge 0.2 # "R3C-NH2 & AIB CA" - set type @atom:168 charge -0.12 # "Chloroalkene Cl-CH=" - set type @atom:169 charge 0.005 # "Chloroalkene Cl-CH=" - set type @atom:170 charge 0.1025 # "Thioanisole C-SCH3" - set type @atom:171 charge 0.14 # "Amide -NH-CHR2" - set type @atom:172 charge 0.2 # "Amide -NH-CR3" - set type @atom:173 charge 0.7 # "Benzophenone C=O" - set type @atom:174 charge 0.565 # "Benzaldehyde C=O" - set type @atom:175 charge 0.585 # "Acetophenone C=O" - set type @atom:176 charge 0.615 # "Benzamide C=O" - set type @atom:177 charge 0.5 # "Amide C=O" - set type @atom:178 charge -0.5 # "Amide C=O" - set type @atom:179 charge -0.76 # "Amide -CO-NH2" - set type @atom:180 charge -0.5 # "Amide -CO-NHR" - set type @atom:181 charge -0.14 # "Amide -CO-NR2" - set type @atom:182 charge 0.38 # "Amide -CO-NH2" - set type @atom:183 charge 0.3 # "Amide -CO-NHR" - set type @atom:184 charge 0.02 # "Amide -NH-CH3" - set type @atom:185 charge -0.11 # "Amide -NR-CH3" - set type @atom:186 charge 0.08 # "Amide -NH-CH2R" - set type @atom:187 charge -0.05 # "Amide -NR-CH2R & PRO CD" - set type @atom:188 charge 0.01 # "Amide -NR-CHR2 & PRO CA" - set type @atom:189 charge 0.142 # "Urea C=O" - set type @atom:190 charge -0.39 # "Urea C=O" - set type @atom:191 charge -0.542 # "Urea -NH2" - set type @atom:192 charge 0.333 # "Urea -NH2" - set type @atom:193 charge -0.49 # "Imide -NH-" - set type @atom:194 charge 0.42 # "Imide C=O" - set type @atom:195 charge -0.42 # "Imide C=O" - set type @atom:196 charge 0.37 # "Imide -NH-" - set type @atom:197 charge 0.06 # "Formimide H-C=O" - set type @atom:198 charge -0.12 # "Imide CH3-CONHCO-" - set type @atom:199 charge -0.06 # "Imide -CH2-CONHCO-" - set type @atom:200 charge 0.0 # "Imide >CH-CONHCO-" - set type @atom:201 charge 0.06 # "Imide C-CONHCO-" - set type @atom:202 charge 0.035 # "Benzonitrile C-CN" - set type @atom:203 charge 0.395 # "Benzonitrile -CN" - set type @atom:204 charge -0.43 # "Benzonitrile -CN" - set type @atom:205 charge 0.18 # "Chlorobenzene C-Cl" - set type @atom:206 charge -0.18 # "Chlorobenzene C-Cl" - set type @atom:207 charge -0.385 # "N-Phenylacetamide N" - set type @atom:208 charge 0.085 # "N-Phenylacetamide N-CA" - set type @atom:209 charge 0.52 # "Carboxylic Acid -COOH" - set type @atom:210 charge -0.44 # "Carboxylic Acid C=O" - set type @atom:211 charge -0.53 # "Carboxylic Acid -OH" - set type @atom:212 charge 0.45 # "Carboxylic Acid -COOH" - set type @atom:213 charge 0.7 # "Carboxylate COO-" - set type @atom:214 charge -0.8 # "Carboxylate COO-" - set type @atom:215 charge -0.28 # "Carboxylate CH3-COO-" - set type @atom:216 charge -0.22 # "Carboxylate RCH2-COO-" - set type @atom:217 charge -0.16 # "Carboxylate R2CH-COO-" - set type @atom:218 charge -0.1 # "Carboxylate R3C-COO-" - set type @atom:219 charge 0.45 # "Aldehyde/Acyl Halide C=O" - set type @atom:220 charge -0.45 # "Aldehyde/Acyl Halide C=O" - set type @atom:221 charge 0.0 # "Aldehyde/Formamide H-C=O" - set type @atom:222 charge 0.47 # "Ketone C=O" - set type @atom:223 charge -0.47 # "Ketone C=O" - set type @atom:224 charge 0.06 # "Acyl H-C-COX" - set type @atom:225 charge 0.04 # "C-Terminal ALA CA" - set type @atom:226 charge -0.02 # "C-Terminal GLY CA" - set type @atom:227 charge 0.1 # "C-Terminal AIB CA" - set type @atom:228 charge -0.09 # "C-Terminal PRO CA" - set type @atom:229 charge -0.4 # "Ammonium NH4+" - set type @atom:230 charge -0.3 # "Ammonium RNH3+" - set type @atom:231 charge 0.0 # "Ammonium R4N+" - set type @atom:232 charge 0.35 # "Ammonium NH4+" - set type @atom:233 charge 0.33 # "Ammonium RNH3+" - set type @atom:234 charge 0.13 # "Ammonium CH3-NH3+" - set type @atom:235 charge 0.19 # "CH3NH3+/N-Term GLY CA" - set type @atom:236 charge 0.25 # "RCH2NH3+/N-Term ALA CA" - set type @atom:237 charge 0.31 # "R3C-NH3+/N-Term AIB CA" - set type @atom:238 charge 0.23 # "N-Terminal PRO CA" - set type @atom:239 charge 0.17 # "N-Terminal PRO CD" - set type @atom:240 charge 0.11 # "Ammonium CH3-NH2R+" - set type @atom:241 charge 0.09 # "GLY Zwitterion CA" - set type @atom:242 charge 0.15 # "ALA Zwitterion CA" - set type @atom:243 charge -0.8 # "Guanidinium -NH2" - set type @atom:244 charge 0.46 # "Guanidinium -NH2" - set type @atom:245 charge 0.64 # "Guanidinium C+" - set type @atom:246 charge -0.7 # "Guanidinium -NHR" - set type @atom:247 charge 0.44 # "Guanidinium -NHR" - set type @atom:248 charge 0.2 # "Me Guanidinium CH3-" - set type @atom:249 charge -0.11 # "Et Guanidinium CH3-" - set type @atom:250 charge 0.19 # "Et Guan -CH2- & ARG CD" - set type @atom:251 charge -0.05 # "Pr Guan -CH2- & ARG CG" - set type @atom:252 charge -0.2 # "Ammonium R2NH2+" - set type @atom:253 charge 0.31 # "Ammonium R2NH2+" - set type @atom:254 charge -0.46 # "Diaminopyridine N1" - set type @atom:255 charge 0.36 # "Diaminopyridine C2" - set type @atom:256 charge -0.85 # "Diaminopyridine -NH2" - set type @atom:257 charge 0.37 # "Diaminopyridine -NH2" - set type @atom:258 charge -0.15 # "Diaminopyridine C3" - set type @atom:259 charge 0.1 # "Diaminopyridine H3" - set type @atom:260 charge -0.04 # "Diaminopyridine C4" - set type @atom:261 charge 0.1 # "Diaminopyridine H4" - set type @atom:262 charge -0.6 # "Uracil & Thymine N1" - set type @atom:263 charge 0.5 # "Uracil & Thymine C2" - set type @atom:264 charge -0.51 # "Uracil & Thymine N3" - set type @atom:265 charge 0.45 # "Uracil & Thymine C4" - set type @atom:266 charge -0.07 # "Uracil & Thymine C5" - set type @atom:267 charge 0.08 # "Uracil & Thymine C6" - set type @atom:268 charge 0.41 # "Uracil & Thymine HN1" - set type @atom:269 charge -0.4 # "Uracil & Thymine O2" - set type @atom:270 charge 0.36 # "Uracil & Thymine HN3" - set type @atom:271 charge -0.42 # "Uracil & Thymine O4" - set type @atom:272 charge 0.1 # "Uracil & Thymine HC5" - set type @atom:273 charge 0.1 # "Uracil & Thymine HC6" - set type @atom:274 charge -0.14 # "Thymine CH3-" - set type @atom:275 charge 0.08 # "Thymine CH3-" - set type @atom:276 charge -0.56 # "Cytosine N1" - set type @atom:277 charge 0.55 # "Cytosine C2" - set type @atom:278 charge -0.54 # "Cytosine N3" - set type @atom:279 charge 0.46 # "Cytosine C4" - set type @atom:280 charge -0.06 # "Cytosine C5" - set type @atom:281 charge 0.1 # "Cytosine C6" - set type @atom:282 charge 0.38 # "Cytosine HN1" - set type @atom:283 charge -0.48 # "Cytosine O2" - set type @atom:284 charge -0.79 # "Cytosine NH2-" - set type @atom:285 charge 0.385 # "Cytosine NH2- (N3)" - set type @atom:286 charge 0.355 # "Cytosine NH2- (C5)" - set type @atom:287 charge 0.1 # "Cytosine HC5" - set type @atom:288 charge 0.1 # "Cytosine HC6" - set type @atom:289 charge -0.53 # "Adenine N1" - set type @atom:290 charge 0.22 # "Adenine C2" - set type @atom:291 charge -0.55 # "Adenine N3" - set type @atom:292 charge 0.38 # "Adenine C4" - set type @atom:293 charge 0.15 # "Adenine C5" - set type @atom:294 charge 0.44 # "Adenine C6" - set type @atom:295 charge -0.49 # "Adenine & Guanine N7" - set type @atom:296 charge 0.2 # "Adenine & Guanine C8" - set type @atom:297 charge -0.5 # "Adenine & Guanine N9" - set type @atom:298 charge 0.2 # "Adenine HC2" - set type @atom:299 charge -0.81 # "Adenine NH2-" - set type @atom:300 charge 0.385 # "Adenine NH2- (N1)" - set type @atom:301 charge 0.355 # "Adenine NH2- (C5)" - set type @atom:302 charge 0.2 # "Adenine & Guanine HC8" - set type @atom:303 charge 0.35 # "Adenine & Guanine HN9" - set type @atom:304 charge -0.56 # "Guanine N1" - set type @atom:305 charge 0.46 # "Guanine C2" - set type @atom:306 charge -0.51 # "Guanine N3" - set type @atom:307 charge 0.34 # "Guanine C4" - set type @atom:308 charge 0.12 # "Guanine C5" - set type @atom:309 charge 0.52 # "Guanine C6" - set type @atom:310 charge 0.38 # "Guanine HN1" - set type @atom:311 charge -0.8 # "Guanine NH2-" - set type @atom:312 charge 0.4 # "Guanine NH2-" - set type @atom:313 charge -0.51 # "Guanine O6" - set type @atom:314 charge -0.01 # "9-Me A & 9-Me-G CH3-" - set type @atom:315 charge 0.12 # "9-Me-A & 9-Me-G CH3-" - set type @atom:316 charge -0.01 # "1-Me-U & 1-Me-T CH3-" - set type @atom:317 charge 0.14 # "1-Me-U & 1-Me-T CH3-" - set type @atom:318 charge -0.01 # "1-Me-Cytosine CH3-" - set type @atom:319 charge 0.13 # "1-Me-Cytosine CH3-" - set type @atom:320 charge -0.64 # "CytosineH+ N1" - set type @atom:321 charge 0.65 # "CytosineH+ C2" - set type @atom:322 charge -0.74 # "CytosineH+ N3" - set type @atom:323 charge 0.66 # "CytosineH+ C4" - set type @atom:324 charge -0.06 # "CytosineH+ C5" - set type @atom:325 charge 0.1 # "CytosineH+ C6" - set type @atom:326 charge 0.49 # "CytosineH+ HN1" - set type @atom:327 charge -0.3 # "CytosineH+ O2" - set type @atom:328 charge 0.48 # "CytosineH+ HN3" - set type @atom:329 charge -0.81 # "CytosineH+ NH2-" - set type @atom:330 charge 0.46 # "CytosineH+ NH2- (N3)" - set type @atom:331 charge 0.43 # "CytosineH+ NH2- (C5)" - set type @atom:332 charge 0.14 # "CytosineH+ HC5" - set type @atom:333 charge 0.14 # "CytosineH+ HC6" - set type @atom:334 charge 0.01 # "1-Me-CytosineH+ CH3-" - set type @atom:335 charge 0.16 # "1-Me-CytosineH+ CH3-" - set type @atom:336 charge 0.78 # "DiMePhosphate P (UA)" - set type @atom:337 charge -0.66 # "DiMePhosphate O=P-O (UA)" - set type @atom:338 charge -0.43 # "DiMePhosphate CH3-O (UA)" - set type @atom:339 charge 0.2 # "DiMePhosphate CH3-O (UA)" - set type @atom:340 charge 0.18 # "Trifluorothymine CF3-" - set type @atom:341 charge -0.06 # "Chloroalkene Cl2-C=" - set type @atom:342 charge 0.12 # "Chloroalkene Cl2-C=" - set type @atom:343 charge -1.0 # "Fluoride Ion F-" - set type @atom:344 charge -1.0 # "Chloride Ion Cl-" - set type @atom:345 charge -1.0 # "Bromide Ion Br-" - set type @atom:346 charge -1.0 # "Iodide Ion I-" - set type @atom:347 charge 1.0 # "Ammonium Ion NH4+ (UA)" - set type @atom:348 charge 1.0 # "Lithium Ion Li+" - set type @atom:349 charge 1.0 # "Sodium Ion Na+" - set type @atom:350 charge 1.0 # "Potassium Ion K+" - set type @atom:351 charge 1.0 # "Rubidium Ion Rb+" - set type @atom:352 charge 1.0 # "Cesium Ion Cs+" - set type @atom:353 charge 2.0 # "Magnesium Ion Mg+2" - set type @atom:354 charge 2.0 # "Calcium Ion Ca+2" - set type @atom:355 charge 2.0 # "Strontium Ion Sr+2" - set type @atom:356 charge 2.0 # "Barium Ion Ba+2" - set type @atom:357 charge -0.4 # "Methyl Thiolate CH3S-" - set type @atom:358 charge 0.1 # "Methyl Thiolate CH3S-" - set type @atom:359 charge -0.9 # "Methyl Thiolate CH3S-" - set type @atom:360 charge -0.2 # "Methoxide CH3O-" - set type @atom:361 charge 0.06 # "Methoxide CH3O-" - set type @atom:362 charge -0.98 # "Methoxide CH3O-" - set type @atom:363 charge -1.07 # "Nitrile Anion CNCH2-" - set type @atom:364 charge 0.19 # "Nitrile Anion CNCH2-" - set type @atom:365 charge 0.51 # "Nitrile Anion CNCH2-" - set type @atom:366 charge -0.82 # "Nitrile Anion CNCH2-" - set type @atom:367 charge -0.3 # "Me Amine Anion CH3NH-" - set type @atom:368 charge 0.07 # "Me Amine Anion CH3NH-" - set type @atom:369 charge -1.31 # "Me Amine Anion CH3NH-" - set type @atom:370 charge 0.4 # "Methyl Amine Anion" - set type @atom:371 charge -0.4 # "Ethyl Anion CH3-CH2-" - set type @atom:372 charge 0.08 # "Ethyl Anion CH3-CH2-" - set type @atom:373 charge 0.0 # "Ethyl Anion CH3-CH2-" - set type @atom:374 charge 0.07 # "Ethyl Anion CH3-CH2-" - set type @atom:375 charge -0.98 # "Ethyl Anion CH3-CH2-" - set type @atom:376 charge -1.3 # "Hydroxide Ion OH-" - set type @atom:377 charge 0.3 # "Hydroxide Ion OH-" - set type @atom:378 charge 2.5 # "Uranyl Ion UO2+" - set type @atom:379 charge -0.25 # "Uranyl Ion UO2+" - set type @atom:380 charge -0.865 # "GTP O-(POn)2" - set type @atom:381 charge 1.62 # "DiMe Phosphate P" - set type @atom:382 charge -0.92 # "DiMe Phosphate O=P-O" - set type @atom:383 charge -0.6 # "DiMe Phosphate CH3-O" - set type @atom:384 charge 0.3 # "DiMe Phosphate CH3-O" - set type @atom:385 charge -0.03 # "DiMe Phosphate CH3-O" - set type @atom:386 charge 1.92 # "Me Phosphate P" - set type @atom:387 charge -1.12 # "Me Phosphate O=PO2" - set type @atom:388 charge -0.7 # "Me Phosphate CH3-O" - set type @atom:389 charge 0.44 # "Me Phosphate CH3-O" - set type @atom:390 charge -0.1 # "Me Phosphate CH3-O" - set type @atom:391 charge 1.62 # "Me MePhosphonate P" - set type @atom:392 charge -0.97 # "Me MePhosphonate O=P-O" - set type @atom:393 charge -0.63 # "Me MePhosphonate CH3-O" - set type @atom:394 charge 0.28 # "Me MePhosphonate CH3-O" - set type @atom:395 charge -0.02 # "Me MePhosphonate CH3-O" - set type @atom:396 charge -0.51 # "Me MePhosphonate CH3-P" - set type @atom:397 charge 0.08 # "Me MePhosphonate CH3-P" - set type @atom:398 charge -0.14 # "Bz MePhosphonate Cipso" - set type @atom:399 charge 0.32 # "Bz MePhosphonate CH3-O" - set type @atom:400 charge 0.02 # "Bz MePhosphonate CH3-O" - set type @atom:401 charge -0.04 # "Me BzPhosphonate Cipso" - set type @atom:402 charge -0.47 # "Me BzPhosphonate CH3-P" - set type @atom:403 charge 0.12 # "Me BzPhosphonate CH3-P" - set type @atom:404 charge 0.14 # "Ph Phosphate Cipso" - set type @atom:405 charge 0.24 # "Barbiturate C6(R2)" - set type @atom:406 charge 0.51 # "Ester -COOR" - set type @atom:407 charge -0.43 # "Ester C=O" - set type @atom:408 charge -0.33 # "Ester CO-O-R" - set type @atom:409 charge 0.16 # "Methyl Ester -OCH3" - set type @atom:410 charge 0.03 # "Ester -OCH<" - set type @atom:411 charge 0.635 # "Benzoic Acid -COOH" - set type @atom:412 charge 0.625 # "Aryl Ester -COOR" - set type @atom:413 charge 0.135 # "Phenyl Ester Cipso" - set type @atom:414 charge -0.215 # "Phenyl Ester -OPh" - set type @atom:415 charge 1.48 # "Sulfonamide -SO2N<" - set type @atom:416 charge -0.68 # "Sulfonamide -SO2N<" - set type @atom:417 charge -0.54 # "Sulfonamide CH3-S" - set type @atom:418 charge 0.18 # "Sulfonamide CH3-S" - set type @atom:419 charge -1.0 # "Sulfonamide -SO2NH2" - set type @atom:420 charge 0.44 # "Sulfonamide -SO2NH2" - set type @atom:421 charge -0.8 # "Sulfonamide -SO2NHR" - set type @atom:422 charge 0.41 # "Sulfonamide -SO2NHR" - set type @atom:423 charge 0.18 # "N-Me Sulfonamide CH3-" - set type @atom:424 charge 0.03 # "N-Me Sulfonamide CH3-" - set type @atom:425 charge 0.39 # "Sulfonamide N-CH2-R" - set type @atom:426 charge -0.06 # "Sulfonamide N-CH2-R" - set type @atom:427 charge -0.18 # "N-Et Sulfonamide CH3-" - set type @atom:428 charge 0.06 # "N-Et Sulfonamide CH3-" - set type @atom:429 charge 0.0 # "Aryl Sulfonamide C-SO2N" - set type @atom:430 charge 0.03 # "Aryl Sulfoxide C-S=O" - set type @atom:431 charge 0.19 # "Et Ester -OCH2R" - set type @atom:432 charge 0.22 # "i-Pr Ester -OCHR2" - set type @atom:433 charge 0.25 # "t-Bu Ester -OCR3" - set type @atom:434 charge 1.374 # "Sulfone R-SO2-R" - set type @atom:435 charge -0.687 # "Sulfone R-SO2-R" - set type @atom:436 charge 0.245 # "Alkyl Aryl Sulfoxide" - set type @atom:437 charge 0.13 # "Dialkyl Sulfoxide" - set type @atom:438 charge -0.42 # "Sulfoxide R-SO-R" - set type @atom:439 charge -0.035 # "Sulfoxide CH3-SO-R" - set type @atom:440 charge 0.025 # "Sulfoxide -CH2-SO-R" - set type @atom:441 charge 0.075 # "TRP CG" - set type @atom:442 charge -0.055 # "TRP CD" - set type @atom:443 charge 0.13 # "TRP CE" - set type @atom:444 charge -0.57 # "TRP NE, HID ND & HIE NE" - set type @atom:445 charge 0.42 # "TRP HNE & HID/HIE HN" - set type @atom:446 charge -0.005 # "HIS CB" - set type @atom:447 charge 0.295 # "HID & HIE CE1" - set type @atom:448 charge -0.015 # "HID CD2 & HIE CG" - set type @atom:449 charge 0.015 # "HID CG & HIE CD2" - set type @atom:450 charge 0.385 # "HIP CE1" - set type @atom:451 charge 0.215 # "HIP CG & CD2" - set type @atom:452 charge -0.49 # "HID NE & HIE ND" - set type @atom:453 charge -0.54 # "HIP ND & NE" - set type @atom:454 charge 0.46 # "HIP HND & HNE" - set type @atom:455 charge -0.115 # "TRP CD1" - set type @atom:456 charge 0.055 # "i-Pr Benzene -CHMe2" - set type @atom:457 charge 0.115 # "t-Bu Benzene -CMe3" - set type @atom:458 charge -0.03 # "Vinyl Ether =CH-OR" - set type @atom:459 charge 0.085 # "Vinyl Ether =CR-OR" - set type @atom:460 charge 0.0 # "Biphenyl C1" - set type @atom:461 charge -0.678 # "Pyridine N" - set type @atom:462 charge 0.473 # "Pyridine C1" - set type @atom:463 charge -0.447 # "Pyridine C2" - set type @atom:464 charge 0.227 # "Pyridine C3" - set type @atom:465 charge 0.012 # "Pyridine H1" - set type @atom:466 charge 0.155 # "Pyridine H2" - set type @atom:467 charge 0.065 # "Pyridine H3" - set type @atom:468 charge -0.468 # "Pyrazine N" - set type @atom:469 charge 0.192 # "Pyrazine CH" - set type @atom:470 charge 0.042 # "Pyrazine CH" - set type @atom:471 charge -0.839 # "Pyrimidine N" - set type @atom:472 charge 0.874 # "Pyrimidine C2" - set type @atom:473 charge 0.653 # "Pyrimidine C4" - set type @atom:474 charge -0.689 # "Pyrimidine C5" - set type @atom:475 charge -0.032 # "Pyrimidine HC2" - set type @atom:476 charge 0.011 # "Pyrimidine HC4" - set type @atom:477 charge 0.197 # "Pyrimidine HC5" - set type @atom:478 charge -0.331 # "Pyridazine N" - set type @atom:479 charge 0.378 # "Pyridazine C3" - set type @atom:480 charge -0.16 # "Pyridazine C4" - set type @atom:481 charge -0.009 # "Pyridazine HC3" - set type @atom:482 charge 0.122 # "Pyridazine HC4" - set type @atom:483 charge -0.239 # "Pyrrole N" - set type @atom:484 charge -0.163 # "Pyrrole C2" - set type @atom:485 charge -0.149 # "Pyrrole C3" - set type @atom:486 charge 0.317 # "Pyrrole HN" - set type @atom:487 charge 0.155 # "Pyrrole HC2" - set type @atom:488 charge 0.118 # "Pyrrole HC3" - set type @atom:489 charge -0.059 # "Pyrazole N1" - set type @atom:490 charge -0.491 # "Pyrazole N2" - set type @atom:491 charge 0.246 # "Pyrazole C3" - set type @atom:492 charge -0.32 # "Pyrazole C4" - set type @atom:493 charge -0.034 # "Pyrazole C5" - set type @atom:494 charge 0.301 # "Pyrazole HN1" - set type @atom:495 charge 0.072 # "Pyrazole HC3" - set type @atom:496 charge 0.15 # "Pyrazole HC4" - set type @atom:497 charge 0.135 # "Pyrazole HC5" - set type @atom:498 charge -0.257 # "Imidazole N1" - set type @atom:499 charge 0.275 # "Imidazole C2" - set type @atom:500 charge -0.563 # "Imidazole N3" - set type @atom:501 charge 0.185 # "Imidazole C4" - set type @atom:502 charge -0.286 # "Imidazole C5" - set type @atom:503 charge 0.306 # "Imidazole HN1" - set type @atom:504 charge 0.078 # "Imidazole HC2" - set type @atom:505 charge 0.075 # "Imidazole HC4" - set type @atom:506 charge 0.187 # "Imidazole HC5" - set type @atom:507 charge -0.19 # "Furan O" - set type @atom:508 charge -0.019 # "Furan C2" - set type @atom:509 charge -0.154 # "Furan C3" - set type @atom:510 charge 0.142 # "Furan HC2" - set type @atom:511 charge 0.126 # "Furan HC3" - set type @atom:512 charge -0.257 # "Oxazole O" - set type @atom:513 charge 0.511 # "Oxazole C2" - set type @atom:514 charge -0.59 # "Oxazole N" - set type @atom:515 charge 0.169 # "Oxazole C4" - set type @atom:516 charge -0.148 # "Oxazole C5" - set type @atom:517 charge 0.043 # "Oxazole HC2" - set type @atom:518 charge 0.091 # "Oxazole HC4" - set type @atom:519 charge 0.181 # "Oxazole HC5" - set type @atom:520 charge -0.122 # "Isoxazole O" - set type @atom:521 charge -0.413 # "Isoxazole N" - set type @atom:522 charge 0.405 # "Isoxazole C3" - set type @atom:523 charge -0.455 # "Isoxazole C4" - set type @atom:524 charge 0.25 # "Isoxazole C5" - set type @atom:525 charge 0.053 # "Isoxazole HC3" - set type @atom:526 charge 0.184 # "Isoxazole HC4" - set type @atom:527 charge 0.098 # "Isoxazole HC5" - set type @atom:528 charge -0.5 # "Indole N1" - set type @atom:529 charge 0.001 # "Indole C2" - set type @atom:530 charge -0.39 # "Indole C3" - set type @atom:531 charge -0.27 # "Indole C4" - set type @atom:532 charge -0.127 # "Indole C5" - set type @atom:533 charge -0.108 # "Indole C6" - set type @atom:534 charge -0.258 # "Indole C7" - set type @atom:535 charge 0.22 # "Indole C8" - set type @atom:536 charge 0.225 # "Indole C9" - set type @atom:537 charge 0.376 # "Indole HN1" - set type @atom:538 charge 0.147 # "Indole HC2" - set type @atom:539 charge 0.172 # "Indole HC3" - set type @atom:540 charge 0.155 # "Indole HC4" - set type @atom:541 charge 0.107 # "Indole HC5" - set type @atom:542 charge 0.11 # "Indole HC6" - set type @atom:543 charge 0.14 # "Indole HC7" - set type @atom:544 charge -0.694 # "Quinoline N1" - set type @atom:545 charge 0.425 # "Quinoline C2" - set type @atom:546 charge -0.359 # "Quinoline C3" - set type @atom:547 charge -0.008 # "Quinoline C4" - set type @atom:548 charge -0.197 # "Quinoline C5" - set type @atom:549 charge -0.112 # "Quinoline C6" - set type @atom:550 charge -0.07 # "Quinoline C7" - set type @atom:551 charge -0.307 # "Quinoline C8" - set type @atom:552 charge 0.563 # "Quinoline C9" - set type @atom:553 charge -0.051 # "Quinoline C10" - set type @atom:554 charge 0.028 # "Quinoline HC2" - set type @atom:555 charge 0.146 # "Quinoline HC3" - set type @atom:556 charge 0.119 # "Quinoline HC4" - set type @atom:557 charge 0.133 # "Quinoline HC5" - set type @atom:558 charge 0.113 # "Quinoline HC6" - set type @atom:559 charge 0.114 # "Quinoline HC7" - set type @atom:560 charge 0.157 # "Quinoline HC8" - set type @atom:561 charge -0.76 # "Purine N1" - set type @atom:562 charge 0.679 # "Purine C2" - set type @atom:563 charge -0.788 # "Purine N3" - set type @atom:564 charge 0.736 # "Purine C4" - set type @atom:565 charge 0.038 # "Purine C5" - set type @atom:566 charge 0.343 # "Purine C6" - set type @atom:567 charge -0.642 # "Purine N7" - set type @atom:568 charge 0.452 # "Purine C8" - set type @atom:569 charge -0.682 # "Purine N9" - set type @atom:570 charge 0.024 # "Purine HC2" - set type @atom:571 charge 0.101 # "Purine HC6" - set type @atom:572 charge 0.086 # "Purine HC8" - set type @atom:573 charge 0.413 # "Purine HN9" - set type @atom:574 charge -0.03 # "Thiazole S" - set type @atom:575 charge 0.242 # "Thiazole C2" - set type @atom:576 charge -0.515 # "Thiazole N" - set type @atom:577 charge 0.228 # "Thiazole C4" - set type @atom:578 charge -0.299 # "Thiazole C5" - set type @atom:579 charge 0.101 # "Thiazole HC2" - set type @atom:580 charge 0.068 # "Thiazole HC4" - set type @atom:581 charge 0.205 # "Thiazole HC5" - set type @atom:582 charge -0.951 # "1,3,5-Triazine N" - set type @atom:583 charge 0.965 # "1,3,5-Triazine CH" - set type @atom:584 charge -0.014 # "1,3,5-Triazine CH" - set type @atom:585 charge 0.13 # "Serotonin C5-OH" - set type @atom:586 charge 0.052 # "Serotonin CH2 on C3" - set type @atom:587 charge -0.599 # "1,10-Phenanthroline N" - set type @atom:588 charge 0.392 # "1,10-Phenanthroline C2" - set type @atom:589 charge -0.348 # "1,10-Phenanthroline C3" - set type @atom:590 charge 0.02 # "1,10-Phenanthroline C4" - set type @atom:591 charge -0.042 # "1,10-Phenanthroline C12" - set type @atom:592 charge 0.347 # "1,10-Phenanthroline C11" - set type @atom:593 charge -0.196 # "1,10-Phenanthroline C5" - set type @atom:594 charge 0.032 # "1,10-Phenanthroline HC2" - set type @atom:595 charge 0.146 # "1,10-Phenanthroline HC3" - set type @atom:596 charge 0.108 # "1,10-Phenanthroline HC4" - set type @atom:597 charge 0.14 # "1,10-Phenanthroline HC5" - set type @atom:598 charge 0.122 # "1-Methylimidazole N1" - set type @atom:599 charge 0.166 # "1-Methylimidazole C2" - set type @atom:600 charge -0.58 # "1-Methylimidazole N3" - set type @atom:601 charge 0.173 # "1-Methylimidazole C4" - set type @atom:602 charge -0.395 # "1-Methylimidazole C5" - set type @atom:603 charge -0.199 # "1-Methylimidazole CH3-" - set type @atom:604 charge 0.118 # "1-Methylimidazole HC2" - set type @atom:605 charge 0.093 # "1-Methylimidazole HC4" - set type @atom:606 charge 0.208 # "1-Methylimidazole HC5" - set type @atom:607 charge 0.098 # "1-Methylimidazole CH3-" - set type @atom:608 charge -0.139 # "1-Et Imidazole RCH2-" - set type @atom:609 charge -0.079 # "1-iPr Imidazole R2CH-" - set type @atom:610 charge 0.099 # "1-MeO-Me-Imidazole CH2" - set type @atom:611 charge -0.168 # "2-Me Pyridine CH3" - set type @atom:612 charge -0.108 # "2-Et Pyridine CH2" - set type @atom:613 charge -0.189 # "3-Me Pyridazine CH3" - set type @atom:614 charge -0.129 # "3-Et Pyridazine CH2" - set type @atom:615 charge -0.169 # "4-Me Pyrimidine CH3" - set type @atom:616 charge -0.109 # "4-Et Pyrimidine CH2" - set type @atom:617 charge -0.138 # "2-Me Pyrazine CH3" - set type @atom:618 charge -0.078 # "2-Et Pyrazine CH2" - set type @atom:619 charge -0.025 # "2-Me Pyrrole CH3" - set type @atom:620 charge 0.035 # "2-Et Pyrrole CH2" - set type @atom:621 charge -0.038 # "2-Me Furan CH3" - set type @atom:622 charge 0.022 # "2-Et Furan CH2" - set type @atom:623 charge -0.334 # "6-Mercaptopurine SH" - set type @atom:624 charge 0.255 # "6-Mercaptopurine SH" - set type @atom:625 charge 0.523 # "6-Mercaptopurine C6" - set type @atom:626 charge 0.5 # "Beta-Lactam N-C=O" - set type @atom:627 charge -0.14 # "Beta-Lactam N-C=O" - set type @atom:628 charge 0.2275 # "Penicillin CH-N" - set type @atom:629 charge 0.14 # "Penicillin CH-CO" - set type @atom:630 charge -0.008 # "3-Me Indole CH3" - set type @atom:631 charge 0.588 # "2-Phenyl Pyridine C2" - set type @atom:632 charge -0.103 # "2-Phenyl Pyridine C2'" - set type @atom:633 charge -0.332 # "2-Phenyl Pyridine C3" - set type @atom:634 charge 0.04 # "2-Phenyl Pyridine C3'" - set type @atom:635 charge 0.342 # "2-Phenyl Pyridine C4" - set type @atom:636 charge -0.05 # "2-Phenyl Pyridine C4'" - set type @atom:637 charge -0.205 # "Diphenyl Thioether S" - set type @atom:638 charge 3.0 # "Actinium Ion Ac+3" - set type @atom:639 charge 4.0 # "Thorium Ion Th+4" - set type @atom:640 charge 3.0 # "Americium Ion Am+3" - set type @atom:641 charge 0.619 # "t-Butyl Cation C+" - set type @atom:642 charge -0.395 # "t-Butyl Cation CH3-" - set type @atom:643 charge 0.174 # "t-Butyl Cation CH3-" - set type @atom:644 charge 3.0 # "Lanthanum Ion La+3" - set type @atom:645 charge 3.0 # "Neodymium Ion Nd+3" - set type @atom:646 charge 3.0 # "Europium Ion Eu+3" - set type @atom:647 charge 3.0 # "Gadolinium Ion Gd+3" - set type @atom:648 charge 3.0 # "Ytterbium Ion Yb+3" - set type @atom:649 charge -0.344 # "Cl..CH3..Cl- Sn2 TS" - set type @atom:650 charge -0.628 # "Cl..CH3..Cl- Sn2 TS" - set type @atom:651 charge 0.2 # "Cl..CH3..Cl- Sn2 TS" - set type @atom:652 charge -0.12 # "Cyclopropane -CH2-" - set type @atom:653 charge -0.06 # "Cyclopropane -CHR-" - set type @atom:654 charge 0.0 # "Cyclopropane -CR2-" - set type @atom:655 charge -0.23 # "Cyclopentadienyl Anion" - set type @atom:656 charge 0.03 # "Cyclopentadienyl Anion" - set type @atom:657 charge -0.099 # "Cyclopentadienyl Radical" - set type @atom:658 charge 0.099 # "Cyclopentadienyl Radical" - set type @atom:659 charge 0.22 # "Fluorobenzene CF" - set type @atom:660 charge -0.22 # "Fluorobenzene CF" - set type @atom:661 charge 0.13 # "Hexafluorobenzene CF" - set type @atom:662 charge -0.13 # "Hexafluorobenzene CF" - set type @atom:663 charge -0.22 # "Bromide -CH2-Br (UA)" - set type @atom:664 charge 0.22 # "Bromide -CH2-Br (UA)" - set type @atom:665 charge 0.15 # "TrifluoroMeBenzene C-CF3" - set type @atom:666 charge 0.45 # "TrifluoroMeBenzene CF3-" - set type @atom:667 charge -0.2 # "TrifluoroMeBenzene CF3-" - set type @atom:668 charge 0.2 # "Difluorobenzene CF" - set type @atom:669 charge -0.2 # "Difluorobenzene CF" - set type @atom:670 charge 0.2 # "Bromobenzene CBr" - set type @atom:671 charge -0.2 # "Bromobenzene CBr" - set type @atom:672 charge 0.1 # "Iodobenzene CI" - set type @atom:673 charge -0.1 # "Iodobenzene CI" - set type @atom:674 charge 0.055 # "cProp/cBut Benzene C-Ar" - set type @atom:675 charge -0.22 # "Thiophenol SH" - set type @atom:676 charge 0.065 # "Thiophenol C-SH" - set type @atom:677 charge 0.013 # "Benzamidine CG" - set type @atom:678 charge -0.106 # "Benzamidine CD" - set type @atom:679 charge -0.09 # "Benzamidine CE" - set type @atom:680 charge -0.119 # "Benzamidine CZ" - set type @atom:681 charge 0.141 # "Benzamidine HCD" - set type @atom:682 charge 0.129 # "Benzamidine HCE" - set type @atom:683 charge 0.827 # "Benzamidine C+" - set type @atom:684 charge -0.885 # "Benzamidine -NH2" - set type @atom:685 charge 0.426 # "Benzamidine H1-N" - set type @atom:686 charge 0.465 # "Benzamidine H2-N" - set type @atom:687 charge 0.119 # "Benzamidine HCG" - set type @atom:688 charge -0.02 # "Neutral MeGdn CH3-" - set type @atom:689 charge 0.04 # "Neutral ARG CD" - set type @atom:690 charge -0.62 # "Neutral ARG NE" - set type @atom:691 charge -0.785 # "Neutral ARG N1 (HN=C)" - set type @atom:692 charge -0.785 # "Neutral ARG N2 (H2N-C)" - set type @atom:693 charge 0.55 # "Neutral ARG CZ (>C=)" - set type @atom:694 charge -0.56 # "Alkyl Nitrile -CN" - set type @atom:695 charge 0.46 # "Alkyl Nitrile -CN" - set type @atom:696 charge -0.08 # "Acetonitrile CH3-CN" - set type @atom:697 charge -0.02 # "Alkyl Nitrile RCH2-CN" - set type @atom:698 charge 0.04 # "Alkyl Nitrile R2CH-CN" - set type @atom:699 charge 0.1 # "Alkyl Nitrile R3C-CN" - set type @atom:700 charge 0.06 # "Alkyl Nitrile H-C-CN" - set type @atom:701 charge 0.54 # "Nitroalkane -NO2" - set type @atom:702 charge -0.37 # "Nitroalkane -NO2" - set type @atom:703 charge 0.02 # "Nitromethane CH3-NO2" - set type @atom:704 charge 0.06 # "Nitroalkane H-C-NO2" - set type @atom:705 charge 0.08 # "Nitroalkane RCH2-NO2" - set type @atom:706 charge 0.14 # "Nitroalkane R2CH-NO2" - set type @atom:707 charge 0.2 # "Nitroalkane R3C-NO2" - set type @atom:708 charge 0.65 # "Nitrobenzene -NO2" - set type @atom:709 charge 0.09 # "Nitrobenzene C-NO2" - set type @atom:710 charge 0.035 # "Benzonitrile -CH2-" - set type @atom:711 charge -0.9 # "Neutral Benzamidine N" - set type @atom:712 charge -0.5 # "Propylene Carbonate C=O" - set type @atom:713 charge 0.86 # "Propylene Carbonate C=O" - set type @atom:714 charge -0.45 # "Propylene Carbonate C-O" - set type @atom:715 charge 0.21 # "Propylene Carbonate CH2" - set type @atom:716 charge 0.16 # "Propylene Carbonate CH" - set type @atom:717 charge -0.1 # "Propylene Carbonate CH3" - set type @atom:718 charge 0.03 # "Propylene Carbonate CH2" - set type @atom:719 charge 0.03 # "Propylene Carbonate CH" - set type @atom:720 charge 0.06 # "Propylene Carbonate CH3" - set type @atom:721 charge -0.78 # "GTP O-(POn)2" - set type @atom:722 charge 0.9684 # "Phosphonium R4P+" - set type @atom:723 charge -0.5081 # "Phosphonium CH3-PR3+" - set type @atom:724 charge -0.008 # "Phosphonium RCH2-PR3+" - set type @atom:725 charge 0.172 # "Phosphonium CH3-PR3+" - set type @atom:726 charge 1.34 # "Hexafluorophosphate Ion" - set type @atom:727 charge -0.39 # "Hexafluorophosphate Ion" - set type @atom:728 charge 0.794 # "Nitrate Ion NO3-" - set type @atom:729 charge -0.598 # "Nitrate Ion NO3-" - set type @atom:730 charge -0.9 # "Amine RNH2" - set type @atom:731 charge -0.78 # "Amine R2NH" - set type @atom:732 charge -0.63 # "Amine R3N" - set type @atom:733 charge 0.0 # "Amine CH3-NH2" - set type @atom:734 charge 0.02 # "Amine CH3-NHR" - set type @atom:735 charge 0.03 # "Amine CH3-NR2" - set type @atom:736 charge 0.06 # "Amine RCH2-NH2" - set type @atom:737 charge 0.08 # "Amine RCH2-NHR" - set type @atom:738 charge 0.09 # "Amine RCH2-NR2" - set type @atom:739 charge 0.36 # "Amine RNH2" - set type @atom:740 charge 0.38 # "Amine R2NH" - set type @atom:741 charge 0.06 # "Amine H-C-N" - set type @atom:742 charge 0.12 # "Amine R2CH-NH2" - set type @atom:743 charge 0.18 # "Amine R3C-NH2" - set type @atom:744 charge 0.14 # "Amine R2CH-NHR" - set type @atom:745 charge 0.15 # "Amine R2CH-NR2" - set type @atom:746 charge 0.18 # "Aniline C-NH2" - set type @atom:747 charge 0.2 # "N-Me Aniline C-NHR" - set type @atom:748 charge 0.21 # "N-DiMe Aniline C-NR2" - set type @atom:749 charge 0.115 # "Benzyl Amine -CH2NH2" - set type @atom:750 charge 0.175 # "Benzyl Amine -CHRNH2" - set type @atom:751 charge 0.235 # "Benzyl Amine -CR2NH2" - set type @atom:752 charge 0.195 # "Benzyl Ether -CH2OR" - set type @atom:753 charge 0.1525 # "Benzyl Sulfide -CH2SH" - set type @atom:754 charge 0.135 # "Benzyl Amine -CH2NHR" - set type @atom:755 charge -0.21 # "Alkyne HCC-" - set type @atom:756 charge 0.2 # "Alkyne HCC-" - set type @atom:757 charge 0.01 # "Alkyne RCCH R w/ 2/3 H" - set type @atom:758 charge 0.01 # "Alkyne RCCH R w/ 1 H" - set type @atom:759 charge 0.01 # "Alkyne RCCH R w/ O H/Ph" - set type @atom:760 charge 0.06 # "Alkyne H-C-CC-" - set type @atom:761 charge 0.45 # "A & G Sugar C1'" - set type @atom:762 charge 0.48 # "C Sugar C1'" - set type @atom:763 charge 0.51 # "U & T Sugar C1'" - set type @atom:764 charge -0.655 # "Sugar O5'" - set type @atom:765 charge 0.39 # "Sugar H3' (-OH)" - set type @atom:766 charge -0.5 # "A & G Nucleoside N9" - set type @atom:767 charge -0.56 # "C Nucleoside N1" - set type @atom:768 charge -0.6 # "U & T Nucleoside N1" - set type @atom:769 charge 0.0 # "Alkyne RCCR" - set type @atom:770 charge -0.1 # "Ammonium R3NH+" - set type @atom:771 charge 0.29 # "Ammonium R3NH+" - set type @atom:772 charge 0.09 # "Ammonium CH3-NHR2+" - set type @atom:773 charge 0.15 # "Ammonium RCH2-NHR2+" - set type @atom:774 charge 0.21 # "Ammonium R2CH-NHR2+" - set type @atom:775 charge 0.27 # "Ammonium R3C-NHR2+" - set type @atom:776 charge 0.096 # "2-Phenyl Furan C2" - set type @atom:777 charge -0.039 # "2-Phenyl Furan C3" - set type @atom:778 charge 0.027 # "2-Phenyl Furan C2'" - set type @atom:779 charge 0.011 # "2-Phenyl Furan C3'" - set type @atom:780 charge 0.074 # "GLY Zwitterion HA" - set type @atom:781 charge -0.029 # "GLY Zwitterion CA" - set type @atom:782 charge 0.7 # "GLY Zwitterion C" - set type @atom:783 charge -0.352 # "GLY Zwitterion N" - set type @atom:784 charge -0.709 # "GLY Zwitterion O" - set type @atom:785 charge 0.317 # "GLY Zwitterion HN" - set type @atom:786 charge -0.22 # "Alkyl Fluoride C-F" - set type @atom:787 charge 0.02 # "Alkyl Fluoride RCH2-F" - set type @atom:788 charge 0.1 # "Alkyl Fluoride H-C-F" - set type @atom:789 charge 0.12 # "Alkyl Fluoride R2CH-F" - set type @atom:790 charge 0.22 # "Alkyl Fluoride R3C-F" - set type @atom:791 charge 0.36 # "Perfluoroalkane CF3-" - set type @atom:792 charge 0.24 # "Perfluoroalkane -CF2-" - set type @atom:793 charge 0.12 # "Perfluoroalkane >CF-" - set type @atom:794 charge 0.48 # "Tetrafluoromethane CF4" - set type @atom:795 charge -0.12 # "Perfluoroalkane C-F" - set type @atom:796 charge 0.25 # "DifluoroMeBenzene -CHF2" - set type @atom:797 charge 0.15 # "DifluoroMeBenzene -CHF2" - set type @atom:798 charge -0.08 # "Fluoroacetate FCH2-COO-" - set type @atom:799 charge -0.106 # "Chloroacetate ClCH2-COO-" - set type @atom:800 charge -0.2 # "Alkyl Chloride C-Cl" - set type @atom:801 charge -0.006 # "Alkyl Chloride RCH2-Cl" - set type @atom:802 charge 0.103 # "Alkyl Chloride H-C-Cl" - set type @atom:803 charge 0.097 # "Alkyl Chloride R2CH-Cl" - set type @atom:804 charge 0.2 # "Alkyl Chloride R3C-Cl" - set type @atom:805 charge -0.2 # "Alkyl Bromide C-Br" - set type @atom:806 charge -0.006 # "Alkyl Bromide RCH2-Br" - set type @atom:807 charge 0.103 # "Alkyl Bromide H-C-Br" - set type @atom:808 charge 0.097 # "Alkyl Bromide R2CH-Br" - set type @atom:809 charge 0.2 # "Alkyl Bromide R3C-Br" - set type @atom:810 charge -0.08 # "Acyl Fluoride F-C=O" - set type @atom:811 charge -0.08 # "Acyl Chloride Cl-C=O" - set type @atom:812 charge -0.08 # "Acyl Bromide Br-C=O" - set type @atom:813 charge 0.1 # "Trifluoroanisole C-OCF3" - set type @atom:814 charge -0.25 # "Trifluoroanisole -OCF3" - set type @atom:815 charge 0.6 # "Trifluoroanisole -OCF3" - set type @atom:816 charge -0.15 # "Trifluoroanisole -OCF3" - set type @atom:817 charge -0.025 # "N-Me,N-PhAcetamide N" - set type @atom:818 charge -0.045 # "N-Me,N-PhAcetamide Cipso" - set type @atom:819 charge 0.145 # "Benzyl Amine -CH2NR2" - set type @atom:820 charge 0.888 # "Alkyl Hydroxamic Acid C" - set type @atom:821 charge 1.003 # "Aryl Hydroxamic Acid C" - set type @atom:822 charge -0.658 # "Hydroxamic Acid C=O" - set type @atom:823 charge -0.634 # "Hydroxamic Acid N" - set type @atom:824 charge 0.411 # "Hydroxamic Acid HN" - set type @atom:825 charge -0.442 # "Hydroxamic Acid OH" - set type @atom:826 charge 0.435 # "Hydroxamic Acid OH" - set type @atom:827 charge 0.225 # "Benzyl Ether -CHROR" - set type @atom:828 charge 0.255 # "Benzyl Ether -CR2OR" - set type @atom:829 charge -0.034 # "3-Phenyl Pyrrole C3" - set type @atom:830 charge 0.003 # "3-Phenyl Pyrrole C3'" - set type @atom:831 charge 0.3 # "4-Phenyl Imidazole C4" - set type @atom:832 charge -0.04 # "4-Phenyl Imidazole C4'" - set type @atom:833 charge -0.0575 # "Diphenylmethane Cipso" - set type @atom:834 charge 2.0 # "Zinc Ion Zn+2" - set type @atom:835 charge -0.07 # "Alkyl Iodide RCH2-I" - set type @atom:836 charge 0.03 # "Alkyl Iodide R2CH-I" - set type @atom:837 charge 0.13 # "Alkyl Iodide R3C-I" - set type @atom:838 charge -0.13 # "Alkyl Iodide C-I" - set type @atom:839 charge 0.1 # "Alkyl Iodide H-C-I" - set type @atom:840 charge -0.685 # "N-Ph Sulfonamide -NHPh" - set type @atom:841 charge 0.155 # "N-Ph Sulfonamide Cipso" - set type @atom:842 charge -0.1 # "Benzoate C-COO-" - set type @atom:843 charge -0.427 # "N-Phenyl Urea N" - set type @atom:844 charge 0.218 # "N-Phenyl Urea Cipso" - set type @atom:845 charge 0.6 # "Tertiary Amide -CO-NR2" - set type @atom:846 charge -0.6 # "Tertiary Amide -CO-NR2" - set type @atom:847 charge -0.36 # "Tertiary Amide -CO-NR2" - set type @atom:848 charge 0.0 # "Tertiary Amide -NRCH3" - set type @atom:849 charge 0.06 # "Tertiary Amide -NRCH2R" - set type @atom:850 charge 0.12 # "Tertiary Amide -NRCHR2" - set type @atom:851 charge 0.18 # "Tertiary Amide -NRCR3" - set type @atom:852 charge 0.06 # "Tertiary Amide H-C-N" - set type @atom:853 charge 0.57 # "Tertiary Formamide C=O" - set type @atom:854 charge -0.57 # "Tertiary Formamide C=O" - set type @atom:855 charge 0.0 # "Tertiary Formamide H-C=O" - set type @atom:856 charge 0.02 # "B2-Peptide CA" - set type @atom:857 charge -0.04 # "B3-Peptide CA Main/N-Ter" - set type @atom:858 charge 0.0 # "B3-Pep CB GLY Main/C-Ter" - set type @atom:859 charge 0.06 # "B3-Pep CB ALA Main/C-Ter" - set type @atom:860 charge -0.07 # "B3-Pep CB PRO Main/C-Ter" - set type @atom:861 charge -0.14 # "B3-Peptide CA C-Ter" - set type @atom:862 charge 0.17 # "B3-Peptide CB ALA N-Ter" - set type @atom:863 charge 0.11 # "B3-Peptide CB GLY N-Ter" - set type @atom:864 charge 0.15 # "B3-Peptide CB PRO N-Ter" - set type @atom:865 charge 0.17 # "B3-Peptide CE PRO N-Ter" - set type @atom:866 charge 1.0 # "Alkyl Silane R4Si" - set type @atom:867 charge 0.85 # "Alkyl Silane R3SiH" - set type @atom:868 charge 0.7 # "Alkyl Silane R2SiH2" - set type @atom:869 charge 0.55 # "Alkyl Silane RSiH3" - set type @atom:870 charge -0.1 # "Alkyl Silane H-C-Si" - set type @atom:871 charge -0.43 # "Methyl Silane CH3-Si" - set type @atom:872 charge -0.37 # "Alkyl Silane RCH2-Si" - set type @atom:873 charge -0.31 # "Alkyl Silane R2CH-Si" - set type @atom:874 charge -0.25 # "Alkyl Silane R3C-Si" - set type @atom:875 charge -1.0 # "Fluoride Ion (GBSA)" - set type @atom:876 charge -1.0 # "Chloride Ion (GBSA)" - set type @atom:877 charge -1.0 # "Bromide Ion (GBSA)" - set type @atom:878 charge -1.0 # "Iodide Ion (GBSA)" - set type @atom:879 charge 1.0 # "Lithium Ion (GBSA)" - set type @atom:880 charge 1.0 # "Sodium Ion (GBSA)" - set type @atom:881 charge 1.0 # "Potassium Ion (GBSA)" - set type @atom:882 charge 1.0 # "Rubidium Ion (GBSA)" - set type @atom:883 charge 1.0 # "Cesium Ion (GBSA)" - set type @atom:884 charge 2.0 # "Magnesium Ion (GBSA)" - set type @atom:885 charge 2.0 # "Calcium Ion (GBSA)" - set type @atom:886 charge 2.0 # "Strontium Ion (GBSA)" - set type @atom:887 charge 2.0 # "Barium Ion (GBSA)" - set type @atom:888 charge -0.05 # "Ammonium CH3-NR3+" - set type @atom:889 charge 0.05 # "Ammonium RCH2-NR3+" - set type @atom:890 charge 0.15 # "Ammonium R2CH-NR3+" - set type @atom:891 charge 0.25 # "Ammonium R3C-NR3+" - set type @atom:892 charge 0.1 # "Ammonium CH3-NR3+" - set type @atom:893 charge 0.115 # "Anilinium Ar-NR3+" - set type @atom:894 charge 0.135 # "Anilinium C-NR3+" - set type @atom:895 charge 0.015 # "Anilinium Ar-NHR2+" - set type @atom:896 charge 0.155 # "Anilinium C-NHR2+" - set type @atom:897 charge 0.0 # "Triene R2-C= (mid C=C)" - set type @atom:898 charge -0.115 # "Triene RH-C= (mid C=C)" - set type @atom:899 charge 0.15 # "Allene/Ketene H-C=C=X" - set type @atom:900 charge -0.25 # "Allene/Ketene H2C=C=X" - set type @atom:901 charge -0.1 # "Allene/Ketene HRC=C=X" - set type @atom:902 charge 0.05 # "Allene/Ketene R2C=C=X" - set type @atom:903 charge -0.1 # "Allene =C=" - set type @atom:904 charge 0.2 # "Ketene =C=" - set type @atom:905 charge -0.25 # "Ketene C=O" - set type @atom:906 charge 0.088 # "N-Me-HIS CB" - } #(end of atom partial charges) - - - write_once("Data Masses") { - @atom:1 18.998 - @atom:2 14.027 - @atom:3 12.011 - @atom:4 15.999 - @atom:5 15.999 - @atom:6 15.035 - @atom:7 1.008 - @atom:8 16.043 - @atom:9 15.035 - @atom:10 15.035 - @atom:11 15.035 - @atom:12 15.035 - @atom:13 14.027 - @atom:14 14.027 - @atom:15 13.019 - @atom:16 13.019 - @atom:17 13.019 - @atom:18 12.011 - @atom:19 12.011 - 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@atom:725 1.008 - @atom:726 30.974 - @atom:727 18.998 - @atom:728 14.007 - @atom:729 15.999 - @atom:730 14.007 - @atom:731 14.007 - @atom:732 14.007 - @atom:733 12.011 - @atom:734 12.011 - @atom:735 12.011 - @atom:736 12.011 - @atom:737 12.011 - @atom:738 12.011 - @atom:739 1.008 - @atom:740 1.008 - @atom:741 1.008 - @atom:742 12.011 - @atom:743 12.011 - @atom:744 12.011 - @atom:745 12.011 - @atom:746 12.011 - @atom:747 12.011 - @atom:748 12.011 - @atom:749 12.011 - @atom:750 12.011 - @atom:751 12.011 - @atom:752 12.011 - @atom:753 12.011 - @atom:754 12.011 - @atom:755 12.011 - @atom:756 1.008 - @atom:757 12.011 - @atom:758 12.011 - @atom:759 12.011 - @atom:760 1.008 - @atom:761 12.011 - @atom:762 12.011 - @atom:763 12.011 - @atom:764 15.999 - @atom:765 1.008 - @atom:766 14.007 - @atom:767 14.007 - @atom:768 14.007 - @atom:769 12.011 - @atom:770 14.007 - @atom:771 1.008 - @atom:772 12.011 - @atom:773 12.011 - @atom:774 12.011 - @atom:775 12.011 - @atom:776 12.011 - @atom:777 12.011 - @atom:778 12.011 - @atom:779 12.011 - @atom:780 1.008 - @atom:781 12.011 - @atom:782 12.011 - @atom:783 14.007 - @atom:784 15.999 - @atom:785 1.008 - @atom:786 18.998 - @atom:787 12.011 - @atom:788 1.008 - @atom:789 12.011 - @atom:790 12.011 - @atom:791 12.011 - @atom:792 12.011 - @atom:793 12.011 - @atom:794 12.011 - @atom:795 18.998 - @atom:796 12.011 - @atom:797 1.008 - @atom:798 12.011 - @atom:799 12.011 - @atom:800 35.453 - @atom:801 12.011 - @atom:802 1.008 - @atom:803 12.011 - @atom:804 12.011 - @atom:805 79.904 - @atom:806 12.011 - @atom:807 1.008 - @atom:808 12.011 - @atom:809 12.011 - @atom:810 18.998 - @atom:811 35.453 - @atom:812 79.904 - @atom:813 12.011 - @atom:814 15.999 - @atom:815 12.011 - @atom:816 18.998 - @atom:817 14.007 - @atom:818 12.011 - @atom:819 12.011 - @atom:820 12.011 - @atom:821 12.011 - @atom:822 15.999 - @atom:823 14.007 - @atom:824 1.008 - @atom:825 15.999 - @atom:826 1.008 - @atom:827 12.011 - @atom:828 12.011 - @atom:829 12.011 - @atom:830 12.011 - @atom:831 12.011 - @atom:832 12.011 - @atom:833 12.011 - @atom:834 1e-30 - @atom:835 12.011 - @atom:836 12.011 - @atom:837 12.011 - @atom:838 126.905 - @atom:839 1.008 - @atom:840 14.007 - @atom:841 12.011 - @atom:842 12.011 - @atom:843 14.007 - @atom:844 12.011 - @atom:845 12.011 - @atom:846 15.999 - @atom:847 14.007 - @atom:848 12.011 - @atom:849 12.011 - @atom:850 12.011 - @atom:851 12.011 - @atom:852 1.008 - @atom:853 12.011 - @atom:854 15.999 - @atom:855 1.008 - @atom:856 12.011 - @atom:857 12.011 - @atom:858 12.011 - @atom:859 12.011 - @atom:860 12.011 - @atom:861 12.011 - @atom:862 12.011 - @atom:863 12.011 - @atom:864 12.011 - @atom:865 12.011 - @atom:866 28.086 - @atom:867 28.086 - @atom:868 28.086 - @atom:869 28.086 - @atom:870 1.008 - @atom:871 12.011 - @atom:872 12.011 - @atom:873 12.011 - @atom:874 12.011 - @atom:875 18.998 - @atom:876 35.453 - @atom:877 79.904 - @atom:878 126.905 - @atom:879 6.941 - @atom:880 22.99 - @atom:881 39.098 - @atom:882 85.468 - @atom:883 132.905 - @atom:884 24.305 - @atom:885 40.08 - @atom:886 87.62 - @atom:887 137.33 - @atom:888 12.011 - @atom:889 12.011 - @atom:890 12.011 - @atom:891 12.011 - @atom:892 1.008 - @atom:893 14.007 - @atom:894 12.011 - @atom:895 14.007 - @atom:896 12.011 - @atom:897 12.011 - @atom:898 12.011 - @atom:899 1.008 - @atom:900 12.011 - @atom:901 12.011 - @atom:902 12.011 - @atom:903 12.011 - @atom:904 12.011 - @atom:905 15.999 - @atom:906 12.011 - } #(end of atom masses) - - - # ---------- EQUIVALENCE CATEGORIES for bonded interaction lookup ---------- - # Each type of atom has a separate ID used for looking up bond parameters - # and a separate ID for looking up 3-body angle interaction parameters - # and a separate ID for looking up 4-body dihedral interaction parameters - # and a separate ID for looking up 4-body improper interaction parameters - # The complete @atom type name includes ALL of these ID numbers. There's - # no need to force the end-user to type the complete name of each atom. - # The "replace" command used below informs moltemplate that the short - # @atom names we have been using abovee are equivalent to the complete - # @atom names used below: - - replace{ @atom:1 @atom:1_b001_a001_d001_i001 } - replace{ @atom:2 @atom:2_b002_a002_d002_i002 } - replace{ @atom:3 @atom:3_b003_a003_d003_i003 } - replace{ @atom:4 @atom:4_b004_a004_d004_i004 } - replace{ @atom:5 @atom:5_b005_a005_d005_i005 } - replace{ @atom:6 @atom:6_b006_a006_d006_i006 } - replace{ @atom:7 @atom:7_b007_a007_d007_i007 } - replace{ @atom:8 @atom:8_b008_a008_d008_i008 } - replace{ @atom:9 @atom:9_b006_a006_d006_i006 } - replace{ @atom:10 @atom:10_b006_a006_d006_i006 } - replace{ @atom:11 @atom:11_b006_a006_d006_i006 } - replace{ @atom:12 @atom:12_b006_a006_d006_i006 } - replace{ @atom:13 @atom:13_b002_a002_d002_i002 } - replace{ @atom:14 @atom:14_b009_a009_d009_i009 } - replace{ @atom:15 @atom:15_b010_a010_d010_i010 } - replace{ @atom:16 @atom:16_b011_a011_d011_i011 } - replace{ @atom:17 @atom:17_b012_a012_d012_i012 } - replace{ @atom:18 @atom:18_b013_a013_d013_i013 } - replace{ @atom:19 @atom:19_b014_a014_d014_i014 } - replace{ @atom:20 @atom:20_b005_a005_d005_i005 } - replace{ @atom:21 @atom:21_b007_a007_d007_i007 } - replace{ @atom:22 @atom:22_b006_a006_d006_i006 } - replace{ @atom:23 @atom:23_b002_a002_d002_i002 } - replace{ @atom:24 @atom:24_b015_a015_d015_i015 } - replace{ @atom:25 @atom:25_b015_a015_d015_i015 } - replace{ @atom:26 @atom:26_b016_a016_d016_i016 } - replace{ @atom:27 @atom:27_b016_a016_d016_i016 } - replace{ @atom:28 @atom:28_b017_a017_d017_i017 } - replace{ @atom:29 @atom:29_b017_a017_d017_i017 } - replace{ @atom:30 @atom:30_b006_a006_d006_i006 } - replace{ @atom:31 @atom:31_b002_a002_d002_i002 } - replace{ @atom:32 @atom:32_b006_a006_d006_i006 } - replace{ @atom:33 @atom:33_b002_a002_d002_i002 } - replace{ @atom:34 @atom:34_b006_a006_d006_i006 } - replace{ @atom:35 @atom:35_b002_a002_d002_i002 } - replace{ @atom:36 @atom:36_b018_a018_d018_i018 } - replace{ @atom:37 @atom:37_b019_a019_d019_i019 } - replace{ @atom:38 @atom:38_b006_a006_d006_i006 } - replace{ @atom:39 @atom:39_b010_a010_d010_i010 } - replace{ @atom:40 @atom:40_b013_a013_d013_i013 } - replace{ @atom:41 @atom:41_b020_a020_d020_i020 } - replace{ @atom:42 @atom:42_b006_a006_d006_i006 } - replace{ @atom:43 @atom:43_b002_a002_d002_i002 } - replace{ @atom:44 @atom:44_b002_a002_d002_i002 } - replace{ @atom:45 @atom:45_b021_a021_d021_i021 } - replace{ @atom:46 @atom:46_b010_a010_d010_i010 } - replace{ @atom:47 @atom:47_b021_a021_d021_i021 } - replace{ @atom:48 @atom:48_b013_a013_d013_i013 } - replace{ @atom:49 @atom:49_b021_a021_d021_i021 } - replace{ @atom:50 @atom:50_b022_a022_d022_i022 } - replace{ @atom:51 @atom:51_b023_a023_d023_i023 } - replace{ @atom:52 @atom:52_b006_a006_d006_i006 } - replace{ @atom:53 @atom:53_b004_a004_d004_i004 } - replace{ @atom:54 @atom:54_b024_a024_d024_i024 } - replace{ @atom:55 @atom:55_b003_a003_d003_i003 } - replace{ @atom:56 @atom:56_b006_a006_d006_i006 } - replace{ @atom:57 @atom:57_b025_a025_d025_i025 } - replace{ @atom:58 @atom:58_b026_a026_d026_i026 } - replace{ @atom:59 @atom:59_b027_a027_d027_i027 } - replace{ @atom:60 @atom:60_b028_a028_d028_i028 } - replace{ @atom:61 @atom:61_b029_a029_d029_i029 } - replace{ @atom:62 @atom:62_b030_a030_d030_i030 } - replace{ @atom:63 @atom:63_b031_a031_d031_i031 } - replace{ @atom:64 @atom:64_b032_a032_d032_i032 } - replace{ @atom:65 @atom:65_b031_a031_d031_i031 } - replace{ @atom:66 @atom:66_b032_a032_d032_i032 } - replace{ @atom:67 @atom:67_b033_a033_d033_i033 } - replace{ @atom:68 @atom:68_b034_a034_d034_i034 } - replace{ @atom:69 @atom:69_b035_a035_d035_i035 } - replace{ @atom:70 @atom:70_b036_a036_d036_i036 } - replace{ @atom:71 @atom:71_b037_a037_d037_i037 } - replace{ @atom:72 @atom:72_b038_a038_d038_i038 } - replace{ @atom:73 @atom:73_b039_a039_d039_i039 } - replace{ @atom:74 @atom:74_b040_a040_d040_i040 } - replace{ @atom:75 @atom:75_b041_a041_d041_i041 } - replace{ @atom:76 @atom:76_b042_a042_d042_i042 } - replace{ @atom:77 @atom:77_b043_a043_d043_i043 } - replace{ @atom:78 @atom:78_b044_a044_d044_i044 } - replace{ @atom:79 @atom:79_b045_a045_d045_i045 } - replace{ @atom:80 @atom:80_b013_a013_d013_i013 } - replace{ @atom:81 @atom:81_b013_a013_d013_i013 } - replace{ @atom:82 @atom:82_b013_a013_d013_i013 } - replace{ @atom:83 @atom:83_b013_a013_d013_i013 } - replace{ @atom:84 @atom:84_b013_a013_d013_i013 } - replace{ @atom:85 @atom:85_b046_a046_d046_i046 } - replace{ @atom:86 @atom:86_b047_a047_d047_i047 } - replace{ @atom:87 @atom:87_b047_a047_d047_i047 } - replace{ @atom:88 @atom:88_b047_a047_d047_i047 } - replace{ @atom:89 @atom:89_b046_a046_d046_i046 } - replace{ @atom:90 @atom:90_b048_a048_d048_i048 } - replace{ @atom:91 @atom:91_b049_a049_d049_i049 } - replace{ @atom:92 @atom:92_b048_a048_d048_i048 } - replace{ @atom:93 @atom:93_b013_a013_d013_i013 } - replace{ @atom:94 @atom:94_b013_a013_d013_i013 } - replace{ @atom:95 @atom:95_b050_a050_d050_i050 } - replace{ @atom:96 @atom:96_b005_a005_d005_i005 } - replace{ @atom:97 @atom:97_b007_a007_d007_i007 } - replace{ @atom:98 @atom:98_b046_a046_d046_i046 } - replace{ @atom:99 @atom:99_b013_a013_d013_i013 } - replace{ @atom:100 @atom:100_b013_a013_d013_i013 } - replace{ @atom:101 @atom:101_b013_a013_d013_i013 } - replace{ @atom:102 @atom:102_b013_a013_d013_i013 } - replace{ @atom:103 @atom:103_b013_a013_d013_i013 } - replace{ @atom:104 @atom:104_b005_a005_d005_i005 } - replace{ @atom:105 @atom:105_b007_a007_d007_i007 } - replace{ @atom:106 @atom:106_b001_a001_d001_i001 } - replace{ @atom:107 @atom:107_b046_a046_d046_i046 } - replace{ @atom:108 @atom:108_b048_a048_d048_i048 } - replace{ @atom:109 @atom:109_b005_a005_d005_i005 } - replace{ @atom:110 @atom:110_b007_a007_d007_i007 } - replace{ @atom:111 @atom:111_b005_a005_d005_i005 } - replace{ @atom:112 @atom:112_b007_a007_d007_i007 } - replace{ @atom:113 @atom:113_b005_a005_d005_i005 } - replace{ @atom:114 @atom:114_b007_a007_d007_i007 } - replace{ @atom:115 @atom:115_b013_a013_d013_i013 } - replace{ @atom:116 @atom:116_b013_a013_d013_i013 } - replace{ @atom:117 @atom:117_b013_a013_d013_i013 } - replace{ @atom:118 @atom:118_b046_a046_d046_i046 } - replace{ @atom:119 @atom:119_b020_a020_d020_i020 } - replace{ @atom:120 @atom:120_b050_a050_d050_i050 } - replace{ @atom:121 @atom:121_b020_a020_d020_i020 } - replace{ @atom:122 @atom:122_b020_a020_d020_i020 } - replace{ @atom:123 @atom:123_b013_a013_d013_i013 } - replace{ @atom:124 @atom:124_b013_a013_d013_i013 } - replace{ @atom:125 @atom:125_b013_a013_d013_i013 } - replace{ @atom:126 @atom:126_b013_a013_d013_i013 } - replace{ @atom:127 @atom:127_b046_a046_d046_i046 } - replace{ @atom:128 @atom:128_b020_a020_d020_i020 } - replace{ @atom:129 @atom:129_b005_a005_d005_i005 } - replace{ @atom:130 @atom:130_b007_a007_d007_i007 } - replace{ @atom:131 @atom:131_b051_a051_d051_i051 } - replace{ @atom:132 @atom:132_b046_a046_d046_i046 } - replace{ @atom:133 @atom:133_b051_a051_d051_i051 } - replace{ @atom:134 @atom:134_b046_a046_d046_i046 } - replace{ @atom:135 @atom:135_b051_a051_d051_i051 } - replace{ @atom:136 @atom:136_b046_a046_d046_i046 } - replace{ @atom:137 @atom:137_b051_a051_d051_i051 } - replace{ @atom:138 @atom:138_b046_a046_d046_i046 } - replace{ @atom:139 @atom:139_b051_a051_d051_i051 } - replace{ @atom:140 @atom:140_b051_a051_d051_i051 } - replace{ @atom:141 @atom:141_b048_a048_d048_i048 } - replace{ @atom:142 @atom:142_b015_a015_d015_i015 } - replace{ @atom:143 @atom:143_b015_a015_d015_i015 } - replace{ @atom:144 @atom:144_b016_a016_d016_i016 } - replace{ @atom:145 @atom:145_b016_a016_d016_i016 } - replace{ @atom:146 @atom:146_b017_a017_d017_i017 } - replace{ @atom:147 @atom:147_b017_a017_d017_i017 } - replace{ @atom:148 @atom:148_b013_a013_d013_i013 } - replace{ @atom:149 @atom:149_b013_a013_d013_i013 } - replace{ @atom:150 @atom:150_b013_a013_d013_i013 } - replace{ @atom:151 @atom:151_b013_a013_d013_i013 } - replace{ @atom:152 @atom:152_b013_a013_d013_i013 } - replace{ @atom:153 @atom:153_b013_a013_d013_i013 } - replace{ @atom:154 @atom:154_b013_a013_d013_i013 } - replace{ @atom:155 @atom:155_b013_a013_d013_i013 } - replace{ @atom:156 @atom:156_b013_a013_d013_i013 } - replace{ @atom:157 @atom:157_b013_a013_d013_i013 } - replace{ @atom:158 @atom:158_b013_a013_d013_i013 } - replace{ @atom:159 @atom:159_b013_a013_d013_i013 } - replace{ @atom:160 @atom:160_b013_a013_d013_i013 } - replace{ @atom:161 @atom:161_b013_a013_d013_i013 } - replace{ @atom:162 @atom:162_b013_a013_d013_i013 } - replace{ @atom:163 @atom:163_b048_a048_d048_i048 } - replace{ @atom:164 @atom:164_b016_a016_d016_i016 } - replace{ @atom:165 @atom:165_b013_a013_d013_i013 } - replace{ @atom:166 @atom:166_b013_a013_d013_i013 } - replace{ @atom:167 @atom:167_b013_a013_d013_i013 } - replace{ @atom:168 @atom:168_b021_a021_d021_i021 } - replace{ @atom:169 @atom:169_b047_a047_d047_i047 } - replace{ @atom:170 @atom:170_b048_a048_d048_i048 } - replace{ @atom:171 @atom:171_b013_a013_d013_i013 } - replace{ @atom:172 @atom:172_b013_a013_d013_i013 } - replace{ @atom:173 @atom:173_b003_a003_d003_i003 } - replace{ @atom:174 @atom:174_b003_a003_d003_i003 } - replace{ @atom:175 @atom:175_b003_a003_d003_i003 } - replace{ @atom:176 @atom:176_b003_a003_d003_i003 } - replace{ @atom:177 @atom:177_b003_a003_d003_i003 } - replace{ @atom:178 @atom:178_b004_a004_d004_i004 } - replace{ @atom:179 @atom:179_b024_a024_d024_i024 } - replace{ @atom:180 @atom:180_b024_a024_d024_i024 } - replace{ @atom:181 @atom:181_b024_a024_d024_i024 } - replace{ @atom:182 @atom:182_b045_a045_d045_i045 } - replace{ @atom:183 @atom:183_b045_a045_d045_i045 } - replace{ @atom:184 @atom:184_b013_a013_d013_i013 } - replace{ @atom:185 @atom:185_b013_a013_d013_i013 } - replace{ @atom:186 @atom:186_b013_a013_d013_i013 } - replace{ @atom:187 @atom:187_b013_a013_d013_i013 } - replace{ @atom:188 @atom:188_b013_a013_d013_i013 } - replace{ @atom:189 @atom:189_b003_a003_d003_i003 } - replace{ @atom:190 @atom:190_b004_a004_d004_i004 } - replace{ @atom:191 @atom:191_b024_a024_d024_i024 } - replace{ @atom:192 @atom:192_b045_a045_d045_i045 } - replace{ @atom:193 @atom:193_b024_a024_d024_i024 } - replace{ @atom:194 @atom:194_b003_a003_d003_i003 } - replace{ @atom:195 @atom:195_b004_a004_d004_i004 } - replace{ @atom:196 @atom:196_b045_a045_d045_i045 } - replace{ @atom:197 @atom:197_b046_a046_d046_i046 } - replace{ @atom:198 @atom:198_b013_a013_d013_i013 } - replace{ @atom:199 @atom:199_b013_a013_d013_i013 } - replace{ @atom:200 @atom:200_b013_a013_d013_i013 } - replace{ @atom:201 @atom:201_b013_a013_d013_i013 } - replace{ @atom:202 @atom:202_b048_a048_d048_i048 } - replace{ @atom:203 @atom:203_b019_a019_d019_i019 } - replace{ @atom:204 @atom:204_b018_a018_d018_i018 } - replace{ @atom:205 @atom:205_b048_a048_d048_i048 } - replace{ @atom:206 @atom:206_b021_a021_d021_i021 } - replace{ @atom:207 @atom:207_b024_a024_d024_i024 } - replace{ @atom:208 @atom:208_b048_a048_d048_i048 } - replace{ @atom:209 @atom:209_b003_a003_d003_i003 } - replace{ @atom:210 @atom:210_b004_a004_d004_i004 } - replace{ @atom:211 @atom:211_b005_a005_d005_i005 } - replace{ @atom:212 @atom:212_b007_a007_d007_i007 } - replace{ @atom:213 @atom:213_b003_a003_d003_i003 } - replace{ @atom:214 @atom:214_b052_a052_d052_i052 } - replace{ @atom:215 @atom:215_b013_a013_d013_i013 } - replace{ @atom:216 @atom:216_b013_a013_d013_i013 } - replace{ @atom:217 @atom:217_b013_a013_d013_i013 } - replace{ @atom:218 @atom:218_b013_a013_d013_i013 } - replace{ @atom:219 @atom:219_b003_a003_d003_i003 } - replace{ @atom:220 @atom:220_b004_a004_d004_i004 } - replace{ @atom:221 @atom:221_b046_a046_d046_i046 } - replace{ @atom:222 @atom:222_b003_a003_d003_i003 } - replace{ @atom:223 @atom:223_b004_a004_d004_i004 } - replace{ @atom:224 @atom:224_b046_a046_d046_i046 } - replace{ @atom:225 @atom:225_b013_a013_d013_i013 } - replace{ @atom:226 @atom:226_b013_a013_d013_i013 } - replace{ @atom:227 @atom:227_b013_a013_d013_i013 } - replace{ @atom:228 @atom:228_b013_a013_d013_i013 } - replace{ @atom:229 @atom:229_b053_a053_d053_i053 } - replace{ @atom:230 @atom:230_b053_a053_d053_i053 } - replace{ @atom:231 @atom:231_b053_a053_d053_i053 } - replace{ @atom:232 @atom:232_b054_a054_d054_i054 } - replace{ @atom:233 @atom:233_b054_a054_d054_i054 } - replace{ @atom:234 @atom:234_b013_a013_d013_i013 } - replace{ @atom:235 @atom:235_b013_a013_d013_i013 } - replace{ @atom:236 @atom:236_b013_a013_d013_i013 } - replace{ @atom:237 @atom:237_b013_a013_d013_i013 } - replace{ @atom:238 @atom:238_b013_a013_d013_i013 } - replace{ @atom:239 @atom:239_b013_a013_d013_i013 } - replace{ @atom:240 @atom:240_b013_a013_d013_i013 } - replace{ @atom:241 @atom:241_b013_a013_d013_i013 } - replace{ @atom:242 @atom:242_b013_a013_d013_i013 } - replace{ @atom:243 @atom:243_b055_a055_d055_i055 } - replace{ @atom:244 @atom:244_b054_a054_d054_i054 } - replace{ @atom:245 @atom:245_b048_a048_d048_i048 } - replace{ @atom:246 @atom:246_b055_a055_d055_i055 } - replace{ @atom:247 @atom:247_b054_a054_d054_i054 } - replace{ @atom:248 @atom:248_b013_a013_d013_i013 } - replace{ @atom:249 @atom:249_b013_a013_d013_i013 } - replace{ @atom:250 @atom:250_b013_a013_d013_i013 } - replace{ @atom:251 @atom:251_b013_a013_d013_i013 } - replace{ @atom:252 @atom:252_b053_a053_d053_i053 } - replace{ @atom:253 @atom:253_b054_a054_d054_i054 } - replace{ @atom:254 @atom:254_b056_a056_d056_i056 } - replace{ @atom:255 @atom:255_b048_a048_d048_i048 } - replace{ @atom:256 @atom:256_b055_a055_d055_i055 } - replace{ @atom:257 @atom:257_b045_a045_d045_i045 } - replace{ @atom:258 @atom:258_b048_a048_d048_i048 } - replace{ @atom:259 @atom:259_b049_a049_d049_i049 } - replace{ @atom:260 @atom:260_b048_a048_d048_i048 } - replace{ @atom:261 @atom:261_b049_a049_d049_i049 } - replace{ @atom:262 @atom:262_b057_a057_d057_i057 } - replace{ @atom:263 @atom:263_b003_a003_d003_i003 } - replace{ @atom:264 @atom:264_b057_a057_d057_i057 } - replace{ @atom:265 @atom:265_b003_a003_d003_i003 } - replace{ @atom:266 @atom:266_b047_a047_d047_i047 } - replace{ @atom:267 @atom:267_b047_a047_d047_i047 } - replace{ @atom:268 @atom:268_b045_a045_d045_i045 } - replace{ @atom:269 @atom:269_b004_a004_d004_i004 } - replace{ @atom:270 @atom:270_b045_a045_d045_i045 } - replace{ @atom:271 @atom:271_b004_a004_d004_i004 } - replace{ @atom:272 @atom:272_b046_a046_d046_i046 } - replace{ @atom:273 @atom:273_b046_a046_d046_i046 } - replace{ @atom:274 @atom:274_b013_a013_d013_i013 } - replace{ @atom:275 @atom:275_b046_a046_d046_i046 } - replace{ @atom:276 @atom:276_b057_a057_d057_i057 } - replace{ @atom:277 @atom:277_b003_a003_d003_i003 } - replace{ @atom:278 @atom:278_b056_a056_d056_i056 } - replace{ @atom:279 @atom:279_b048_a048_d048_i048 } - replace{ @atom:280 @atom:280_b047_a047_d047_i047 } - replace{ @atom:281 @atom:281_b047_a047_d047_i047 } - replace{ @atom:282 @atom:282_b045_a045_d045_i045 } - replace{ @atom:283 @atom:283_b004_a004_d004_i004 } - replace{ @atom:284 @atom:284_b055_a055_d055_i055 } - replace{ @atom:285 @atom:285_b045_a045_d045_i045 } - replace{ @atom:286 @atom:286_b045_a045_d045_i045 } - replace{ @atom:287 @atom:287_b046_a046_d046_i046 } - replace{ @atom:288 @atom:288_b058_a058_d058_i058 } - replace{ @atom:289 @atom:289_b056_a056_d056_i056 } - replace{ @atom:290 @atom:290_b059_a059_d059_i059 } - replace{ @atom:291 @atom:291_b056_a056_d056_i056 } - replace{ @atom:292 @atom:292_b060_a060_d060_i060 } - replace{ @atom:293 @atom:293_b060_a060_d060_i060 } - replace{ @atom:294 @atom:294_b048_a048_d048_i048 } - replace{ @atom:295 @atom:295_b061_a061_d061_i061 } - replace{ @atom:296 @atom:296_b062_a062_d062_i062 } - replace{ @atom:297 @atom:297_b057_a057_d057_i057 } - replace{ @atom:298 @atom:298_b063_a063_d063_i063 } - replace{ @atom:299 @atom:299_b055_a055_d055_i055 } - replace{ @atom:300 @atom:300_b045_a045_d045_i045 } - replace{ @atom:301 @atom:301_b045_a045_d045_i045 } - replace{ @atom:302 @atom:302_b063_a063_d063_i063 } - replace{ @atom:303 @atom:303_b045_a045_d045_i045 } - replace{ @atom:304 @atom:304_b057_a057_d057_i057 } - replace{ @atom:305 @atom:305_b048_a048_d048_i048 } - replace{ @atom:306 @atom:306_b056_a056_d056_i056 } - replace{ @atom:307 @atom:307_b060_a060_d060_i060 } - replace{ @atom:308 @atom:308_b060_a060_d060_i060 } - replace{ @atom:309 @atom:309_b003_a003_d003_i003 } - replace{ @atom:310 @atom:310_b045_a045_d045_i045 } - replace{ @atom:311 @atom:311_b055_a055_d055_i055 } - replace{ @atom:312 @atom:312_b045_a045_d045_i045 } - replace{ @atom:313 @atom:313_b004_a004_d004_i004 } - replace{ @atom:314 @atom:314_b013_a013_d013_i013 } - replace{ @atom:315 @atom:315_b046_a046_d046_i046 } - replace{ @atom:316 @atom:316_b013_a013_d013_i013 } - replace{ @atom:317 @atom:317_b046_a046_d046_i046 } - replace{ @atom:318 @atom:318_b013_a013_d013_i013 } - replace{ @atom:319 @atom:319_b046_a046_d046_i046 } - replace{ @atom:320 @atom:320_b057_a057_d057_i057 } - replace{ @atom:321 @atom:321_b003_a003_d003_i003 } - replace{ @atom:322 @atom:322_b057_a057_d057_i057 } - replace{ @atom:323 @atom:323_b048_a048_d048_i048 } - replace{ @atom:324 @atom:324_b047_a047_d047_i047 } - replace{ @atom:325 @atom:325_b047_a047_d047_i047 } - replace{ @atom:326 @atom:326_b045_a045_d045_i045 } - replace{ @atom:327 @atom:327_b004_a004_d004_i004 } - replace{ @atom:328 @atom:328_b045_a045_d045_i045 } - replace{ @atom:329 @atom:329_b055_a055_d055_i055 } - replace{ @atom:330 @atom:330_b045_a045_d045_i045 } - replace{ @atom:331 @atom:331_b045_a045_d045_i045 } - replace{ @atom:332 @atom:332_b049_a049_d049_i049 } - replace{ @atom:333 @atom:333_b058_a058_d058_i058 } - replace{ @atom:334 @atom:334_b013_a013_d013_i013 } - replace{ @atom:335 @atom:335_b046_a046_d046_i046 } - replace{ @atom:336 @atom:336_b064_a064_d064_i064 } - replace{ @atom:337 @atom:337_b052_a052_d052_i052 } - replace{ @atom:338 @atom:338_b020_a020_d020_i020 } - replace{ @atom:339 @atom:339_b013_a013_d013_i013 } - replace{ @atom:340 @atom:340_b047_a047_d047_i047 } - replace{ @atom:341 @atom:341_b021_a021_d021_i021 } - replace{ @atom:342 @atom:342_b047_a047_d047_i047 } - replace{ @atom:343 @atom:343_b001_a001_d001_i001 } - replace{ @atom:344 @atom:344_b021_a021_d021_i021 } - replace{ @atom:345 @atom:345_b065_a065_d065_i065 } - replace{ @atom:346 @atom:346_b066_a066_d066_i066 } - replace{ @atom:347 @atom:347_b067_a067_d067_i067 } - replace{ @atom:348 @atom:348_b068_a068_d068_i068 } - replace{ @atom:349 @atom:349_b069_a069_d069_i069 } - replace{ @atom:350 @atom:350_b070_a070_d070_i070 } - replace{ @atom:351 @atom:351_b071_a071_d071_i071 } - replace{ @atom:352 @atom:352_b072_a072_d072_i072 } - replace{ @atom:353 @atom:353_b073_a073_d073_i073 } - replace{ @atom:354 @atom:354_b074_a074_d074_i074 } - replace{ @atom:355 @atom:355_b075_a075_d075_i075 } - replace{ @atom:356 @atom:356_b076_a076_d076_i076 } - replace{ @atom:357 @atom:357_b006_a006_d006_i006 } - replace{ @atom:358 @atom:358_b046_a046_d046_i046 } - replace{ @atom:359 @atom:359_b015_a015_d015_i015 } - replace{ @atom:360 @atom:360_b006_a006_d006_i006 } - replace{ @atom:361 @atom:361_b046_a046_d046_i046 } - replace{ @atom:362 @atom:362_b005_a005_d005_i005 } - replace{ @atom:363 @atom:363_b013_a013_d013_i013 } - replace{ @atom:364 @atom:364_b046_a046_d046_i046 } - replace{ @atom:365 @atom:365_b019_a019_d019_i019 } - replace{ @atom:366 @atom:366_b018_a018_d018_i018 } - replace{ @atom:367 @atom:367_b006_a006_d006_i006 } - replace{ @atom:368 @atom:368_b046_a046_d046_i046 } - replace{ @atom:369 @atom:369_b053_a053_d053_i053 } - replace{ @atom:370 @atom:370_b045_a045_d045_i045 } - replace{ @atom:371 @atom:371_b006_a006_d006_i006 } - replace{ @atom:372 @atom:372_b046_a046_d046_i046 } - replace{ @atom:373 @atom:373_b013_a013_d013_i013 } - replace{ @atom:374 @atom:374_b046_a046_d046_i046 } - replace{ @atom:375 @atom:375_b033_a033_d033_i033 } - replace{ @atom:376 @atom:376_b005_a005_d005_i005 } - replace{ @atom:377 @atom:377_b007_a007_d007_i007 } - replace{ @atom:378 @atom:378_b077_a077_d077_i077 } - replace{ @atom:379 @atom:379_b078_a078_d078_i078 } - replace{ @atom:380 @atom:380_b020_a020_d020_i020 } - replace{ @atom:381 @atom:381_b064_a064_d064_i064 } - replace{ @atom:382 @atom:382_b052_a052_d052_i052 } - replace{ @atom:383 @atom:383_b020_a020_d020_i020 } - replace{ @atom:384 @atom:384_b013_a013_d013_i013 } - replace{ @atom:385 @atom:385_b046_a046_d046_i046 } - replace{ @atom:386 @atom:386_b064_a064_d064_i064 } - replace{ @atom:387 @atom:387_b052_a052_d052_i052 } - replace{ @atom:388 @atom:388_b020_a020_d020_i020 } - replace{ @atom:389 @atom:389_b013_a013_d013_i013 } - replace{ @atom:390 @atom:390_b046_a046_d046_i046 } - replace{ @atom:391 @atom:391_b064_a064_d064_i064 } - replace{ @atom:392 @atom:392_b052_a052_d052_i052 } - replace{ @atom:393 @atom:393_b020_a020_d020_i020 } - replace{ @atom:394 @atom:394_b013_a013_d013_i013 } - replace{ @atom:395 @atom:395_b046_a046_d046_i046 } - replace{ @atom:396 @atom:396_b013_a013_d013_i013 } - replace{ @atom:397 @atom:397_b046_a046_d046_i046 } - replace{ @atom:398 @atom:398_b048_a048_d048_i048 } - replace{ @atom:399 @atom:399_b013_a013_d013_i013 } - replace{ @atom:400 @atom:400_b046_a046_d046_i046 } - replace{ @atom:401 @atom:401_b048_a048_d048_i048 } - replace{ @atom:402 @atom:402_b013_a013_d013_i013 } - replace{ @atom:403 @atom:403_b046_a046_d046_i046 } - replace{ @atom:404 @atom:404_b048_a048_d048_i048 } - replace{ @atom:405 @atom:405_b013_a013_d013_i013 } - replace{ @atom:406 @atom:406_b003_a003_d003_i003 } - replace{ @atom:407 @atom:407_b004_a004_d004_i004 } - replace{ @atom:408 @atom:408_b020_a020_d020_i020 } - replace{ @atom:409 @atom:409_b013_a013_d013_i013 } - replace{ @atom:410 @atom:410_b046_a046_d046_i046 } - replace{ @atom:411 @atom:411_b003_a003_d003_i003 } - replace{ @atom:412 @atom:412_b003_a003_d003_i003 } - replace{ @atom:413 @atom:413_b048_a048_d048_i048 } - replace{ @atom:414 @atom:414_b020_a020_d020_i020 } - replace{ @atom:415 @atom:415_b079_a079_d079_i079 } - replace{ @atom:416 @atom:416_b023_a023_d023_i023 } - replace{ @atom:417 @atom:417_b013_a013_d013_i013 } - replace{ @atom:418 @atom:418_b046_a046_d046_i046 } - replace{ @atom:419 @atom:419_b024_a024_d024_i024 } - replace{ @atom:420 @atom:420_b045_a045_d045_i045 } - replace{ @atom:421 @atom:421_b024_a024_d024_i024 } - replace{ @atom:422 @atom:422_b045_a045_d045_i045 } - replace{ @atom:423 @atom:423_b013_a013_d013_i013 } - replace{ @atom:424 @atom:424_b046_a046_d046_i046 } - replace{ @atom:425 @atom:425_b013_a013_d013_i013 } - replace{ @atom:426 @atom:426_b046_a046_d046_i046 } - replace{ @atom:427 @atom:427_b013_a013_d013_i013 } - replace{ @atom:428 @atom:428_b046_a046_d046_i046 } - replace{ @atom:429 @atom:429_b048_a048_d048_i048 } - replace{ @atom:430 @atom:430_b048_a048_d048_i048 } - replace{ @atom:431 @atom:431_b013_a013_d013_i013 } - replace{ @atom:432 @atom:432_b013_a013_d013_i013 } - replace{ @atom:433 @atom:433_b013_a013_d013_i013 } - replace{ @atom:434 @atom:434_b079_a079_d079_i079 } - replace{ @atom:435 @atom:435_b023_a023_d023_i023 } - replace{ @atom:436 @atom:436_b022_a022_d022_i022 } - replace{ @atom:437 @atom:437_b022_a022_d022_i022 } - replace{ @atom:438 @atom:438_b023_a023_d023_i023 } - replace{ @atom:439 @atom:439_b013_a013_d013_i013 } - replace{ @atom:440 @atom:440_b013_a013_d013_i013 } - replace{ @atom:441 @atom:441_b080_a080_d080_i080 } - replace{ @atom:442 @atom:442_b060_a060_d060_i060 } - replace{ @atom:443 @atom:443_b081_a081_d081_i081 } - replace{ @atom:444 @atom:444_b057_a057_d057_i057 } - replace{ @atom:445 @atom:445_b045_a045_d045_i045 } - replace{ @atom:446 @atom:446_b013_a013_d013_i013 } - replace{ @atom:447 @atom:447_b082_a082_d082_i082 } - replace{ @atom:448 @atom:448_b083_a083_d083_i083 } - replace{ @atom:449 @atom:449_b084_a084_d084_i084 } - replace{ @atom:450 @atom:450_b082_a082_d082_i082 } - replace{ @atom:451 @atom:451_b085_a085_d085_i085 } - replace{ @atom:452 @atom:452_b061_a061_d061_i061 } - replace{ @atom:453 @atom:453_b057_a057_d057_i057 } - replace{ @atom:454 @atom:454_b045_a045_d045_i045 } - replace{ @atom:455 @atom:455_b084_a084_d084_i084 } - replace{ @atom:456 @atom:456_b013_a013_d013_i013 } - replace{ @atom:457 @atom:457_b013_a013_d013_i013 } - replace{ @atom:458 @atom:458_b047_a047_d047_i047 } - replace{ @atom:459 @atom:459_b047_a047_d047_i047 } - replace{ @atom:460 @atom:460_b086_a086_d086_i086 } - replace{ @atom:461 @atom:461_b056_a056_d056_i056 } - replace{ @atom:462 @atom:462_b048_a048_d048_i048 } - replace{ @atom:463 @atom:463_b048_a048_d048_i048 } - replace{ @atom:464 @atom:464_b048_a048_d048_i048 } - replace{ @atom:465 @atom:465_b049_a049_d049_i049 } - replace{ @atom:466 @atom:466_b049_a049_d049_i049 } - replace{ @atom:467 @atom:467_b049_a049_d049_i049 } - replace{ @atom:468 @atom:468_b056_a056_d056_i056 } - replace{ @atom:469 @atom:469_b048_a048_d048_i048 } - replace{ @atom:470 @atom:470_b049_a049_d049_i049 } - replace{ @atom:471 @atom:471_b056_a056_d056_i056 } - replace{ @atom:472 @atom:472_b059_a059_d059_i059 } - replace{ @atom:473 @atom:473_b048_a048_d048_i048 } - replace{ @atom:474 @atom:474_b048_a048_d048_i048 } - replace{ @atom:475 @atom:475_b049_a049_d049_i049 } - replace{ @atom:476 @atom:476_b049_a049_d049_i049 } - replace{ @atom:477 @atom:477_b049_a049_d049_i049 } - replace{ @atom:478 @atom:478_b056_a056_d056_i056 } - replace{ @atom:479 @atom:479_b048_a048_d048_i048 } - replace{ @atom:480 @atom:480_b048_a048_d048_i048 } - replace{ @atom:481 @atom:481_b049_a049_d049_i049 } - replace{ @atom:482 @atom:482_b049_a049_d049_i049 } - replace{ @atom:483 @atom:483_b057_a057_d057_i057 } - replace{ @atom:484 @atom:484_b084_a084_d084_i084 } - replace{ @atom:485 @atom:485_b087_a087_d087_i087 } - replace{ @atom:486 @atom:486_b045_a045_d045_i045 } - replace{ @atom:487 @atom:487_b049_a049_d049_i049 } - replace{ @atom:488 @atom:488_b049_a049_d049_i049 } - replace{ @atom:489 @atom:489_b057_a057_d057_i057 } - replace{ @atom:490 @atom:490_b061_a061_d061_i061 } - replace{ @atom:491 @atom:491_b088_a088_d088_i088 } - replace{ @atom:492 @atom:492_b087_a087_d087_i087 } - replace{ @atom:493 @atom:493_b084_a084_d084_i084 } - replace{ @atom:494 @atom:494_b045_a045_d045_i045 } - replace{ @atom:495 @atom:495_b049_a049_d049_i049 } - replace{ @atom:496 @atom:496_b049_a049_d049_i049 } - replace{ @atom:497 @atom:497_b049_a049_d049_i049 } - replace{ @atom:498 @atom:498_b057_a057_d057_i057 } - replace{ @atom:499 @atom:499_b082_a082_d082_i082 } - replace{ @atom:500 @atom:500_b061_a061_d061_i061 } - replace{ @atom:501 @atom:501_b083_a083_d083_i083 } - replace{ @atom:502 @atom:502_b084_a084_d084_i084 } - replace{ @atom:503 @atom:503_b045_a045_d045_i045 } - replace{ @atom:504 @atom:504_b049_a049_d049_i049 } - replace{ @atom:505 @atom:505_b049_a049_d049_i049 } - replace{ @atom:506 @atom:506_b049_a049_d049_i049 } - replace{ @atom:507 @atom:507_b020_a020_d020_i020 } - replace{ @atom:508 @atom:508_b084_a084_d084_i084 } - replace{ @atom:509 @atom:509_b087_a087_d087_i087 } - replace{ @atom:510 @atom:510_b049_a049_d049_i049 } - replace{ @atom:511 @atom:511_b049_a049_d049_i049 } - replace{ @atom:512 @atom:512_b020_a020_d020_i020 } - replace{ @atom:513 @atom:513_b082_a082_d082_i082 } - replace{ @atom:514 @atom:514_b061_a061_d061_i061 } - replace{ @atom:515 @atom:515_b083_a083_d083_i083 } - replace{ @atom:516 @atom:516_b084_a084_d084_i084 } - replace{ @atom:517 @atom:517_b049_a049_d049_i049 } - replace{ @atom:518 @atom:518_b049_a049_d049_i049 } - replace{ @atom:519 @atom:519_b049_a049_d049_i049 } - replace{ @atom:520 @atom:520_b020_a020_d020_i020 } - replace{ @atom:521 @atom:521_b061_a061_d061_i061 } - replace{ @atom:522 @atom:522_b088_a088_d088_i088 } - replace{ @atom:523 @atom:523_b087_a087_d087_i087 } - replace{ @atom:524 @atom:524_b084_a084_d084_i084 } - replace{ @atom:525 @atom:525_b049_a049_d049_i049 } - replace{ @atom:526 @atom:526_b049_a049_d049_i049 } - replace{ @atom:527 @atom:527_b049_a049_d049_i049 } - replace{ @atom:528 @atom:528_b057_a057_d057_i057 } - replace{ @atom:529 @atom:529_b084_a084_d084_i084 } - replace{ @atom:530 @atom:530_b087_a087_d087_i087 } - replace{ @atom:531 @atom:531_b048_a048_d048_i048 } - replace{ @atom:532 @atom:532_b048_a048_d048_i048 } - replace{ @atom:533 @atom:533_b048_a048_d048_i048 } - replace{ @atom:534 @atom:534_b048_a048_d048_i048 } - replace{ @atom:535 @atom:535_b081_a081_d081_i081 } - replace{ @atom:536 @atom:536_b060_a060_d060_i060 } - replace{ @atom:537 @atom:537_b045_a045_d045_i045 } - replace{ @atom:538 @atom:538_b049_a049_d049_i049 } - replace{ @atom:539 @atom:539_b049_a049_d049_i049 } - replace{ @atom:540 @atom:540_b049_a049_d049_i049 } - replace{ @atom:541 @atom:541_b049_a049_d049_i049 } - replace{ @atom:542 @atom:542_b049_a049_d049_i049 } - replace{ @atom:543 @atom:543_b049_a049_d049_i049 } - replace{ @atom:544 @atom:544_b056_a056_d056_i056 } - replace{ @atom:545 @atom:545_b048_a048_d048_i048 } - replace{ @atom:546 @atom:546_b048_a048_d048_i048 } - replace{ @atom:547 @atom:547_b048_a048_d048_i048 } - replace{ @atom:548 @atom:548_b048_a048_d048_i048 } - replace{ @atom:549 @atom:549_b048_a048_d048_i048 } - replace{ @atom:550 @atom:550_b048_a048_d048_i048 } - replace{ @atom:551 @atom:551_b048_a048_d048_i048 } - replace{ @atom:552 @atom:552_b048_a048_d048_i048 } - replace{ @atom:553 @atom:553_b048_a048_d048_i048 } - replace{ @atom:554 @atom:554_b049_a049_d049_i049 } - replace{ @atom:555 @atom:555_b049_a049_d049_i049 } - replace{ @atom:556 @atom:556_b049_a049_d049_i049 } - replace{ @atom:557 @atom:557_b049_a049_d049_i049 } - replace{ @atom:558 @atom:558_b049_a049_d049_i049 } - replace{ @atom:559 @atom:559_b049_a049_d049_i049 } - replace{ @atom:560 @atom:560_b049_a049_d049_i049 } - replace{ @atom:561 @atom:561_b056_a056_d056_i056 } - replace{ @atom:562 @atom:562_b059_a059_d059_i059 } - replace{ @atom:563 @atom:563_b056_a056_d056_i056 } - replace{ @atom:564 @atom:564_b060_a060_d060_i060 } - replace{ @atom:565 @atom:565_b060_a060_d060_i060 } - replace{ @atom:566 @atom:566_b048_a048_d048_i048 } - replace{ @atom:567 @atom:567_b061_a061_d061_i061 } - replace{ @atom:568 @atom:568_b062_a062_d062_i062 } - replace{ @atom:569 @atom:569_b057_a057_d057_i057 } - replace{ @atom:570 @atom:570_b049_a049_d049_i049 } - replace{ @atom:571 @atom:571_b049_a049_d049_i049 } - replace{ @atom:572 @atom:572_b049_a049_d049_i049 } - replace{ @atom:573 @atom:573_b045_a045_d045_i045 } - replace{ @atom:574 @atom:574_b016_a016_d016_i016 } - replace{ @atom:575 @atom:575_b082_a082_d082_i082 } - replace{ @atom:576 @atom:576_b061_a061_d061_i061 } - replace{ @atom:577 @atom:577_b083_a083_d083_i083 } - replace{ @atom:578 @atom:578_b084_a084_d084_i084 } - replace{ @atom:579 @atom:579_b049_a049_d049_i049 } - replace{ @atom:580 @atom:580_b049_a049_d049_i049 } - replace{ @atom:581 @atom:581_b049_a049_d049_i049 } - replace{ @atom:582 @atom:582_b056_a056_d056_i056 } - replace{ @atom:583 @atom:583_b059_a059_d059_i059 } - replace{ @atom:584 @atom:584_b049_a049_d049_i049 } - replace{ @atom:585 @atom:585_b048_a048_d048_i048 } - replace{ @atom:586 @atom:586_b013_a013_d013_i013 } - replace{ @atom:587 @atom:587_b056_a056_d056_i056 } - replace{ @atom:588 @atom:588_b048_a048_d048_i048 } - replace{ @atom:589 @atom:589_b048_a048_d048_i048 } - replace{ @atom:590 @atom:590_b048_a048_d048_i048 } - replace{ @atom:591 @atom:591_b048_a048_d048_i048 } - replace{ @atom:592 @atom:592_b048_a048_d048_i048 } - replace{ @atom:593 @atom:593_b048_a048_d048_i048 } - replace{ @atom:594 @atom:594_b049_a049_d049_i049 } - replace{ @atom:595 @atom:595_b049_a049_d049_i049 } - replace{ @atom:596 @atom:596_b049_a049_d049_i049 } - replace{ @atom:597 @atom:597_b049_a049_d049_i049 } - replace{ @atom:598 @atom:598_b057_a057_d057_i057 } - replace{ @atom:599 @atom:599_b082_a082_d082_i082 } - replace{ @atom:600 @atom:600_b061_a061_d061_i061 } - replace{ @atom:601 @atom:601_b083_a083_d083_i083 } - replace{ @atom:602 @atom:602_b084_a084_d084_i084 } - replace{ @atom:603 @atom:603_b013_a013_d013_i013 } - replace{ @atom:604 @atom:604_b049_a049_d049_i049 } - replace{ @atom:605 @atom:605_b049_a049_d049_i049 } - replace{ @atom:606 @atom:606_b049_a049_d049_i049 } - replace{ @atom:607 @atom:607_b046_a046_d046_i046 } - replace{ @atom:608 @atom:608_b013_a013_d013_i013 } - replace{ @atom:609 @atom:609_b013_a013_d013_i013 } - replace{ @atom:610 @atom:610_b013_a013_d013_i013 } - replace{ @atom:611 @atom:611_b013_a013_d013_i013 } - replace{ @atom:612 @atom:612_b013_a013_d013_i013 } - replace{ @atom:613 @atom:613_b013_a013_d013_i013 } - replace{ @atom:614 @atom:614_b013_a013_d013_i013 } - replace{ @atom:615 @atom:615_b013_a013_d013_i013 } - replace{ @atom:616 @atom:616_b013_a013_d013_i013 } - replace{ @atom:617 @atom:617_b013_a013_d013_i013 } - replace{ @atom:618 @atom:618_b013_a013_d013_i013 } - replace{ @atom:619 @atom:619_b013_a013_d013_i013 } - replace{ @atom:620 @atom:620_b013_a013_d013_i013 } - replace{ @atom:621 @atom:621_b013_a013_d013_i013 } - replace{ @atom:622 @atom:622_b013_a013_d013_i013 } - replace{ @atom:623 @atom:623_b015_a015_d015_i015 } - replace{ @atom:624 @atom:624_b017_a017_d017_i017 } - replace{ @atom:625 @atom:625_b048_a048_d048_i048 } - replace{ @atom:626 @atom:626_b089_a089_d089_i089 } - replace{ @atom:627 @atom:627_b090_a090_d090_i090 } - replace{ @atom:628 @atom:628_b091_a091_d091_i091 } - replace{ @atom:629 @atom:629_b091_a091_d091_i091 } - replace{ @atom:630 @atom:630_b013_a013_d013_i013 } - replace{ @atom:631 @atom:631_b086_a086_d086_i086 } - replace{ @atom:632 @atom:632_b086_a086_d086_i086 } - replace{ @atom:633 @atom:633_b086_a086_d086_i086 } - replace{ @atom:634 @atom:634_b086_a086_d086_i086 } - replace{ @atom:635 @atom:635_b086_a086_d086_i086 } - replace{ @atom:636 @atom:636_b086_a086_d086_i086 } - replace{ @atom:637 @atom:637_b016_a016_d016_i016 } - replace{ @atom:638 @atom:638_b092_a092_d092_i092 } - replace{ @atom:639 @atom:639_b093_a093_d093_i093 } - replace{ @atom:640 @atom:640_b094_a094_d094_i094 } - replace{ @atom:641 @atom:641_b095_a095_d095_i095 } - replace{ @atom:642 @atom:642_b013_a013_d013_i013 } - replace{ @atom:643 @atom:643_b046_a046_d046_i046 } - replace{ @atom:644 @atom:644_b096_a096_d096_i096 } - replace{ @atom:645 @atom:645_b097_a097_d097_i097 } - replace{ @atom:646 @atom:646_b098_a098_d098_i098 } - replace{ @atom:647 @atom:647_b099_a099_d099_i099 } - replace{ @atom:648 @atom:648_b100_a100_d100_i100 } - replace{ @atom:649 @atom:649_b047_a047_d047_i047 } - replace{ @atom:650 @atom:650_b021_a021_d021_i021 } - replace{ @atom:651 @atom:651_b046_a046_d046_i046 } - replace{ @atom:652 @atom:652_b091_a091_d091_i091 } - replace{ @atom:653 @atom:653_b091_a091_d091_i091 } - replace{ @atom:654 @atom:654_b091_a091_d091_i091 } - replace{ @atom:655 @atom:655_b048_a048_d048_i048 } - replace{ @atom:656 @atom:656_b049_a049_d049_i049 } - replace{ @atom:657 @atom:657_b048_a048_d048_i048 } - replace{ @atom:658 @atom:658_b049_a049_d049_i049 } - replace{ @atom:659 @atom:659_b048_a048_d048_i048 } - replace{ @atom:660 @atom:660_b001_a001_d001_i001 } - replace{ @atom:661 @atom:661_b048_a048_d048_i048 } - replace{ @atom:662 @atom:662_b001_a001_d001_i001 } - replace{ @atom:663 @atom:663_b065_a065_d065_i065 } - replace{ @atom:664 @atom:664_b002_a002_d002_i002 } - replace{ @atom:665 @atom:665_b048_a048_d048_i048 } - replace{ @atom:666 @atom:666_b013_a013_d013_i013 } - replace{ @atom:667 @atom:667_b001_a001_d001_i001 } - replace{ @atom:668 @atom:668_b048_a048_d048_i048 } - replace{ @atom:669 @atom:669_b001_a001_d001_i001 } - replace{ @atom:670 @atom:670_b048_a048_d048_i048 } - replace{ @atom:671 @atom:671_b065_a065_d065_i065 } - replace{ @atom:672 @atom:672_b048_a048_d048_i048 } - replace{ @atom:673 @atom:673_b066_a066_d066_i066 } - replace{ @atom:674 @atom:674_b091_a091_d091_i091 } - replace{ @atom:675 @atom:675_b015_a015_d015_i015 } - replace{ @atom:676 @atom:676_b048_a048_d048_i048 } - replace{ @atom:677 @atom:677_b048_a048_d048_i048 } - replace{ @atom:678 @atom:678_b048_a048_d048_i048 } - replace{ @atom:679 @atom:679_b048_a048_d048_i048 } - replace{ @atom:680 @atom:680_b048_a048_d048_i048 } - replace{ @atom:681 @atom:681_b049_a049_d049_i049 } - replace{ @atom:682 @atom:682_b049_a049_d049_i049 } - replace{ @atom:683 @atom:683_b048_a048_d048_i048 } - replace{ @atom:684 @atom:684_b055_a055_d055_i055 } - replace{ @atom:685 @atom:685_b045_a045_d045_i045 } - replace{ @atom:686 @atom:686_b045_a045_d045_i045 } - replace{ @atom:687 @atom:687_b049_a049_d049_i049 } - replace{ @atom:688 @atom:688_b013_a013_d013_i013 } - replace{ @atom:689 @atom:689_b013_a013_d013_i013 } - replace{ @atom:690 @atom:690_b101_a101_d101_i101 } - replace{ @atom:691 @atom:691_b056_a056_d056_i056 } - replace{ @atom:692 @atom:692_b101_a101_d101_i101 } - replace{ @atom:693 @atom:693_b048_a048_d048_i048 } - replace{ @atom:694 @atom:694_b018_a018_d018_i018 } - replace{ @atom:695 @atom:695_b019_a019_d019_i019 } - replace{ @atom:696 @atom:696_b013_a013_d013_i013 } - replace{ @atom:697 @atom:697_b013_a013_d013_i013 } - replace{ @atom:698 @atom:698_b013_a013_d013_i013 } - replace{ @atom:699 @atom:699_b013_a013_d013_i013 } - replace{ @atom:700 @atom:700_b046_a046_d046_i046 } - replace{ @atom:701 @atom:701_b102_a102_d102_i102 } - replace{ @atom:702 @atom:702_b103_a103_d103_i103 } - replace{ @atom:703 @atom:703_b013_a013_d013_i013 } - replace{ @atom:704 @atom:704_b046_a046_d046_i046 } - replace{ @atom:705 @atom:705_b013_a013_d013_i013 } - replace{ @atom:706 @atom:706_b013_a013_d013_i013 } - replace{ @atom:707 @atom:707_b013_a013_d013_i013 } - replace{ @atom:708 @atom:708_b102_a102_d102_i102 } - replace{ @atom:709 @atom:709_b048_a048_d048_i048 } - replace{ @atom:710 @atom:710_b013_a013_d013_i013 } - replace{ @atom:711 @atom:711_b056_a056_d056_i056 } - replace{ @atom:712 @atom:712_b004_a004_d004_i004 } - replace{ @atom:713 @atom:713_b003_a003_d003_i003 } - replace{ @atom:714 @atom:714_b020_a020_d020_i020 } - replace{ @atom:715 @atom:715_b013_a013_d013_i013 } - replace{ @atom:716 @atom:716_b013_a013_d013_i013 } - replace{ @atom:717 @atom:717_b013_a013_d013_i013 } - replace{ @atom:718 @atom:718_b046_a046_d046_i046 } - replace{ @atom:719 @atom:719_b046_a046_d046_i046 } - replace{ @atom:720 @atom:720_b046_a046_d046_i046 } - replace{ @atom:721 @atom:721_b020_a020_d020_i020 } - replace{ @atom:722 @atom:722_b104_a104_d104_i104 } - replace{ @atom:723 @atom:723_b013_a013_d013_i013 } - replace{ @atom:724 @atom:724_b013_a013_d013_i013 } - replace{ @atom:725 @atom:725_b046_a046_d046_i046 } - replace{ @atom:726 @atom:726_b064_a064_d064_i064 } - replace{ @atom:727 @atom:727_b001_a001_d001_i001 } - replace{ @atom:728 @atom:728_b024_a024_d024_i024 } - replace{ @atom:729 @atom:729_b004_a004_d004_i004 } - replace{ @atom:730 @atom:730_b044_a044_d044_i044 } - replace{ @atom:731 @atom:731_b044_a044_d044_i044 } - replace{ @atom:732 @atom:732_b044_a044_d044_i044 } - replace{ @atom:733 @atom:733_b013_a013_d013_i013 } - replace{ @atom:734 @atom:734_b013_a013_d013_i013 } - replace{ @atom:735 @atom:735_b013_a013_d013_i013 } - replace{ @atom:736 @atom:736_b013_a013_d013_i013 } - replace{ @atom:737 @atom:737_b013_a013_d013_i013 } - replace{ @atom:738 @atom:738_b013_a013_d013_i013 } - replace{ @atom:739 @atom:739_b045_a045_d045_i045 } - replace{ @atom:740 @atom:740_b045_a045_d045_i045 } - replace{ @atom:741 @atom:741_b046_a046_d046_i046 } - replace{ @atom:742 @atom:742_b013_a013_d013_i013 } - replace{ @atom:743 @atom:743_b013_a013_d013_i013 } - replace{ @atom:744 @atom:744_b013_a013_d013_i013 } - replace{ @atom:745 @atom:745_b013_a013_d013_i013 } - replace{ @atom:746 @atom:746_b048_a048_d048_i048 } - replace{ @atom:747 @atom:747_b048_a048_d048_i048 } - replace{ @atom:748 @atom:748_b048_a048_d048_i048 } - replace{ @atom:749 @atom:749_b013_a013_d013_i013 } - replace{ @atom:750 @atom:750_b013_a013_d013_i013 } - replace{ @atom:751 @atom:751_b013_a013_d013_i013 } - replace{ @atom:752 @atom:752_b013_a013_d013_i013 } - replace{ @atom:753 @atom:753_b013_a013_d013_i013 } - replace{ @atom:754 @atom:754_b013_a013_d013_i013 } - replace{ @atom:755 @atom:755_b019_a019_d019_i019 } - replace{ @atom:756 @atom:756_b046_a046_d046_i046 } - replace{ @atom:757 @atom:757_b019_a019_d019_i019 } - replace{ @atom:758 @atom:758_b019_a019_d019_i019 } - replace{ @atom:759 @atom:759_b019_a019_d019_i019 } - replace{ @atom:760 @atom:760_b046_a046_d046_i046 } - replace{ @atom:761 @atom:761_b051_a051_d051_i051 } - replace{ @atom:762 @atom:762_b051_a051_d051_i051 } - replace{ @atom:763 @atom:763_b051_a051_d051_i051 } - replace{ @atom:764 @atom:764_b005_a005_d005_i005 } - replace{ @atom:765 @atom:765_b007_a007_d007_i007 } - replace{ @atom:766 @atom:766_b105_a105_d105_i105 } - replace{ @atom:767 @atom:767_b105_a105_d105_i105 } - replace{ @atom:768 @atom:768_b105_a105_d105_i105 } - replace{ @atom:769 @atom:769_b019_a019_d019_i019 } - replace{ @atom:770 @atom:770_b053_a053_d053_i053 } - replace{ @atom:771 @atom:771_b054_a054_d054_i054 } - replace{ @atom:772 @atom:772_b013_a013_d013_i013 } - replace{ @atom:773 @atom:773_b013_a013_d013_i013 } - replace{ @atom:774 @atom:774_b013_a013_d013_i013 } - replace{ @atom:775 @atom:775_b013_a013_d013_i013 } - replace{ @atom:776 @atom:776_b084_a084_d084_i084 } - replace{ @atom:777 @atom:777_b087_a087_d087_i087 } - replace{ @atom:778 @atom:778_b086_a086_d086_i086 } - replace{ @atom:779 @atom:779_b086_a086_d086_i086 } - replace{ @atom:780 @atom:780_b046_a046_d046_i046 } - replace{ @atom:781 @atom:781_b013_a013_d013_i013 } - replace{ @atom:782 @atom:782_b003_a003_d003_i003 } - replace{ @atom:783 @atom:783_b053_a053_d053_i053 } - replace{ @atom:784 @atom:784_b052_a052_d052_i052 } - replace{ @atom:785 @atom:785_b054_a054_d054_i054 } - replace{ @atom:786 @atom:786_b001_a001_d001_i001 } - replace{ @atom:787 @atom:787_b013_a013_d013_i013 } - replace{ @atom:788 @atom:788_b046_a046_d046_i046 } - replace{ @atom:789 @atom:789_b013_a013_d013_i013 } - replace{ @atom:790 @atom:790_b013_a013_d013_i013 } - replace{ @atom:791 @atom:791_b013_a013_d013_i013 } - replace{ @atom:792 @atom:792_b013_a013_d013_i013 } - replace{ @atom:793 @atom:793_b013_a013_d013_i013 } - replace{ @atom:794 @atom:794_b013_a013_d013_i013 } - replace{ @atom:795 @atom:795_b001_a001_d001_i001 } - replace{ @atom:796 @atom:796_b013_a013_d013_i013 } - replace{ @atom:797 @atom:797_b046_a046_d046_i046 } - replace{ @atom:798 @atom:798_b013_a013_d013_i013 } - replace{ @atom:799 @atom:799_b013_a013_d013_i013 } - replace{ @atom:800 @atom:800_b021_a021_d021_i021 } - replace{ @atom:801 @atom:801_b013_a013_d013_i013 } - replace{ @atom:802 @atom:802_b046_a046_d046_i046 } - replace{ @atom:803 @atom:803_b013_a013_d013_i013 } - replace{ @atom:804 @atom:804_b013_a013_d013_i013 } - replace{ @atom:805 @atom:805_b065_a065_d065_i065 } - replace{ @atom:806 @atom:806_b013_a013_d013_i013 } - replace{ @atom:807 @atom:807_b046_a046_d046_i046 } - replace{ @atom:808 @atom:808_b013_a013_d013_i013 } - replace{ @atom:809 @atom:809_b013_a013_d013_i013 } - replace{ @atom:810 @atom:810_b001_a001_d001_i001 } - replace{ @atom:811 @atom:811_b021_a021_d021_i021 } - replace{ @atom:812 @atom:812_b065_a065_d065_i065 } - replace{ @atom:813 @atom:813_b048_a048_d048_i048 } - replace{ @atom:814 @atom:814_b020_a020_d020_i020 } - replace{ @atom:815 @atom:815_b013_a013_d013_i013 } - replace{ @atom:816 @atom:816_b001_a001_d001_i001 } - replace{ @atom:817 @atom:817_b024_a024_d024_i024 } - replace{ @atom:818 @atom:818_b048_a048_d048_i048 } - replace{ @atom:819 @atom:819_b013_a013_d013_i013 } - replace{ @atom:820 @atom:820_b003_a003_d003_i003 } - replace{ @atom:821 @atom:821_b003_a003_d003_i003 } - replace{ @atom:822 @atom:822_b004_a004_d004_i004 } - replace{ @atom:823 @atom:823_b024_a024_d024_i024 } - replace{ @atom:824 @atom:824_b045_a045_d045_i045 } - replace{ @atom:825 @atom:825_b005_a005_d005_i005 } - replace{ @atom:826 @atom:826_b007_a007_d007_i007 } - replace{ @atom:827 @atom:827_b013_a013_d013_i013 } - replace{ @atom:828 @atom:828_b013_a013_d013_i013 } - replace{ @atom:829 @atom:829_b086_a086_d086_i086 } - replace{ @atom:830 @atom:830_b086_a086_d086_i086 } - replace{ @atom:831 @atom:831_b086_a086_d086_i086 } - replace{ @atom:832 @atom:832_b086_a086_d086_i086 } - replace{ @atom:833 @atom:833_b048_a048_d048_i048 } - replace{ @atom:834 @atom:834_b106_a106_d106_i106 } - replace{ @atom:835 @atom:835_b013_a013_d013_i013 } - replace{ @atom:836 @atom:836_b013_a013_d013_i013 } - replace{ @atom:837 @atom:837_b013_a013_d013_i013 } - replace{ @atom:838 @atom:838_b066_a066_d066_i066 } - replace{ @atom:839 @atom:839_b046_a046_d046_i046 } - replace{ @atom:840 @atom:840_b024_a024_d024_i024 } - replace{ @atom:841 @atom:841_b048_a048_d048_i048 } - replace{ @atom:842 @atom:842_b048_a048_d048_i048 } - replace{ @atom:843 @atom:843_b024_a024_d024_i024 } - replace{ @atom:844 @atom:844_b048_a048_d048_i048 } - replace{ @atom:845 @atom:845_b003_a003_d003_i003 } - replace{ @atom:846 @atom:846_b004_a004_d004_i004 } - replace{ @atom:847 @atom:847_b107_a107_d107_i107 } - replace{ @atom:848 @atom:848_b013_a013_d013_i013 } - replace{ @atom:849 @atom:849_b013_a013_d013_i013 } - replace{ @atom:850 @atom:850_b013_a013_d013_i013 } - replace{ @atom:851 @atom:851_b013_a013_d013_i013 } - replace{ @atom:852 @atom:852_b046_a046_d046_i046 } - replace{ @atom:853 @atom:853_b003_a003_d003_i003 } - replace{ @atom:854 @atom:854_b004_a004_d004_i004 } - replace{ @atom:855 @atom:855_b046_a046_d046_i046 } - replace{ @atom:856 @atom:856_b013_a013_d013_i013 } - replace{ @atom:857 @atom:857_b013_a013_d013_i013 } - replace{ @atom:858 @atom:858_b013_a013_d013_i013 } - replace{ @atom:859 @atom:859_b013_a013_d013_i013 } - replace{ @atom:860 @atom:860_b013_a013_d013_i013 } - replace{ @atom:861 @atom:861_b013_a013_d013_i013 } - replace{ @atom:862 @atom:862_b013_a013_d013_i013 } - replace{ @atom:863 @atom:863_b013_a013_d013_i013 } - replace{ @atom:864 @atom:864_b013_a013_d013_i013 } - replace{ @atom:865 @atom:865_b013_a013_d013_i013 } - replace{ @atom:866 @atom:866_b108_a108_d108_i108 } - replace{ @atom:867 @atom:867_b108_a108_d108_i108 } - replace{ @atom:868 @atom:868_b108_a108_d108_i108 } - replace{ @atom:869 @atom:869_b108_a108_d108_i108 } - replace{ @atom:870 @atom:870_b045_a045_d045_i045 } - replace{ @atom:871 @atom:871_b013_a013_d013_i013 } - replace{ @atom:872 @atom:872_b013_a013_d013_i013 } - replace{ @atom:873 @atom:873_b013_a013_d013_i013 } - replace{ @atom:874 @atom:874_b013_a013_d013_i013 } - replace{ @atom:875 @atom:875_b001_a001_d001_i001 } - replace{ @atom:876 @atom:876_b021_a021_d021_i021 } - replace{ @atom:877 @atom:877_b065_a065_d065_i065 } - replace{ @atom:878 @atom:878_b066_a066_d066_i066 } - replace{ @atom:879 @atom:879_b068_a068_d068_i068 } - replace{ @atom:880 @atom:880_b069_a069_d069_i069 } - replace{ @atom:881 @atom:881_b070_a070_d070_i070 } - replace{ @atom:882 @atom:882_b071_a071_d071_i071 } - replace{ @atom:883 @atom:883_b072_a072_d072_i072 } - replace{ @atom:884 @atom:884_b073_a073_d073_i073 } - replace{ @atom:885 @atom:885_b074_a074_d074_i074 } - replace{ @atom:886 @atom:886_b075_a075_d075_i075 } - replace{ @atom:887 @atom:887_b076_a076_d076_i076 } - replace{ @atom:888 @atom:888_b013_a013_d013_i013 } - replace{ @atom:889 @atom:889_b013_a013_d013_i013 } - replace{ @atom:890 @atom:890_b013_a013_d013_i013 } - replace{ @atom:891 @atom:891_b013_a013_d013_i013 } - replace{ @atom:892 @atom:892_b046_a046_d046_i046 } - replace{ @atom:893 @atom:893_b053_a053_d053_i053 } - replace{ @atom:894 @atom:894_b048_a048_d048_i048 } - replace{ @atom:895 @atom:895_b053_a053_d053_i053 } - replace{ @atom:896 @atom:896_b048_a048_d048_i048 } - replace{ @atom:897 @atom:897_b109_a109_d109_i109 } - replace{ @atom:898 @atom:898_b109_a109_d109_i109 } - replace{ @atom:899 @atom:899_b046_a046_d046_i046 } - replace{ @atom:900 @atom:900_b047_a047_d047_i047 } - replace{ @atom:901 @atom:901_b047_a047_d047_i047 } - replace{ @atom:902 @atom:902_b047_a047_d047_i047 } - replace{ @atom:903 @atom:903_b110_a110_d110_i110 } - replace{ @atom:904 @atom:904_b110_a110_d110_i110 } - replace{ @atom:905 @atom:905_b004_a004_d004_i004 } - replace{ @atom:906 @atom:906_b013_a013_d013_i013 } - - - - - # --------------- Non-Bonded interactions: --------------------- - # http://lammps.sandia.gov/doc/pair_lj.html - # Syntax: - # pair_coeff AtomType1 AtomType2 parameters... - - write_once("In Settings") { - pair_coeff @atom:1_b001_a001_d001_i001 @atom:1_b001_a001_d001_i001 0.061 2.94 - pair_coeff @atom:2_b002_a002_d002_i002 @atom:2_b002_a002_d002_i002 0.118 3.905 - pair_coeff @atom:3_b003_a003_d003_i003 @atom:3_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:4_b004_a004_d004_i004 @atom:4_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:5_b005_a005_d005_i005 @atom:5_b005_a005_d005_i005 0.17 3.0 - pair_coeff @atom:6_b006_a006_d006_i006 @atom:6_b006_a006_d006_i006 0.16 3.91 - pair_coeff @atom:7_b007_a007_d007_i007 @atom:7_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:8_b008_a008_d008_i008 @atom:8_b008_a008_d008_i008 0.294 3.73 - pair_coeff @atom:9_b006_a006_d006_i006 @atom:9_b006_a006_d006_i006 0.207 3.775 - pair_coeff @atom:10_b006_a006_d006_i006 @atom:10_b006_a006_d006_i006 0.175 3.905 - pair_coeff @atom:11_b006_a006_d006_i006 @atom:11_b006_a006_d006_i006 0.16 3.91 - pair_coeff @atom:12_b006_a006_d006_i006 @atom:12_b006_a006_d006_i006 0.145 3.96 - pair_coeff @atom:13_b002_a002_d002_i002 @atom:13_b002_a002_d002_i002 0.118 3.905 - pair_coeff @atom:14_b009_a009_d009_i009 @atom:14_b009_a009_d009_i009 0.14 3.85 - pair_coeff @atom:15_b010_a010_d010_i010 @atom:15_b010_a010_d010_i010 0.08 3.85 - pair_coeff @atom:16_b011_a011_d011_i011 @atom:16_b011_a011_d011_i011 0.115 3.8 - pair_coeff @atom:17_b012_a012_d012_i012 @atom:17_b012_a012_d012_i012 0.11 3.75 - pair_coeff @atom:18_b013_a013_d013_i013 @atom:18_b013_a013_d013_i013 0.05 3.8 - pair_coeff @atom:19_b014_a014_d014_i014 @atom:19_b014_a014_d014_i014 0.105 3.75 - pair_coeff @atom:20_b005_a005_d005_i005 @atom:20_b005_a005_d005_i005 0.17 3.07 - pair_coeff @atom:21_b007_a007_d007_i007 @atom:21_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:22_b006_a006_d006_i006 @atom:22_b006_a006_d006_i006 0.207 3.775 - pair_coeff @atom:23_b002_a002_d002_i002 @atom:23_b002_a002_d002_i002 0.118 3.905 - pair_coeff @atom:24_b015_a015_d015_i015 @atom:24_b015_a015_d015_i015 0.25 3.7 - pair_coeff @atom:25_b015_a015_d015_i015 @atom:25_b015_a015_d015_i015 0.25 3.55 - pair_coeff @atom:26_b016_a016_d016_i016 @atom:26_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:27_b016_a016_d016_i016 @atom:27_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:28_b017_a017_d017_i017 @atom:28_b017_a017_d017_i017 0.0 0.0 - pair_coeff @atom:29_b017_a017_d017_i017 @atom:29_b017_a017_d017_i017 0.0 0.0 - pair_coeff @atom:30_b006_a006_d006_i006 @atom:30_b006_a006_d006_i006 0.207 3.775 - pair_coeff @atom:31_b002_a002_d002_i002 @atom:31_b002_a002_d002_i002 0.118 3.905 - pair_coeff @atom:32_b006_a006_d006_i006 @atom:32_b006_a006_d006_i006 0.17 3.8 - pair_coeff @atom:33_b002_a002_d002_i002 @atom:33_b002_a002_d002_i002 0.118 3.8 - pair_coeff @atom:34_b006_a006_d006_i006 @atom:34_b006_a006_d006_i006 0.17 3.8 - pair_coeff @atom:35_b002_a002_d002_i002 @atom:35_b002_a002_d002_i002 0.118 3.8 - pair_coeff @atom:36_b018_a018_d018_i018 @atom:36_b018_a018_d018_i018 0.17 3.2 - pair_coeff @atom:37_b019_a019_d019_i019 @atom:37_b019_a019_d019_i019 0.15 3.65 - pair_coeff @atom:38_b006_a006_d006_i006 @atom:38_b006_a006_d006_i006 0.207 3.775 - pair_coeff @atom:39_b010_a010_d010_i010 @atom:39_b010_a010_d010_i010 0.08 3.85 - pair_coeff @atom:40_b013_a013_d013_i013 @atom:40_b013_a013_d013_i013 0.05 3.8 - pair_coeff @atom:41_b020_a020_d020_i020 @atom:41_b020_a020_d020_i020 0.17 3.0 - pair_coeff @atom:42_b006_a006_d006_i006 @atom:42_b006_a006_d006_i006 0.17 3.8 - pair_coeff @atom:43_b002_a002_d002_i002 @atom:43_b002_a002_d002_i002 0.118 3.8 - pair_coeff @atom:44_b002_a002_d002_i002 @atom:44_b002_a002_d002_i002 0.118 3.8 - pair_coeff @atom:45_b021_a021_d021_i021 @atom:45_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:46_b010_a010_d010_i010 @atom:46_b010_a010_d010_i010 0.08 3.8 - pair_coeff @atom:47_b021_a021_d021_i021 @atom:47_b021_a021_d021_i021 0.3 3.47 - pair_coeff @atom:48_b013_a013_d013_i013 @atom:48_b013_a013_d013_i013 0.05 3.8 - pair_coeff @atom:49_b021_a021_d021_i021 @atom:49_b021_a021_d021_i021 0.266 3.47 - pair_coeff @atom:50_b022_a022_d022_i022 @atom:50_b022_a022_d022_i022 0.395 3.56 - pair_coeff @atom:51_b023_a023_d023_i023 @atom:51_b023_a023_d023_i023 0.28 2.93 - pair_coeff @atom:52_b006_a006_d006_i006 @atom:52_b006_a006_d006_i006 0.16 3.81 - pair_coeff @atom:53_b004_a004_d004_i004 @atom:53_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:54_b024_a024_d024_i024 @atom:54_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:55_b003_a003_d003_i003 @atom:55_b003_a003_d003_i003 0.115 3.8 - pair_coeff @atom:56_b006_a006_d006_i006 @atom:56_b006_a006_d006_i006 0.17 3.8 - pair_coeff @atom:57_b025_a025_d025_i025 @atom:57_b025_a025_d025_i025 0.0 0.0 - pair_coeff @atom:58_b026_a026_d026_i026 @atom:58_b026_a026_d026_i026 0.02 2.556 - pair_coeff @atom:59_b027_a027_d027_i027 @atom:59_b027_a027_d027_i027 0.069 2.78 - pair_coeff @atom:60_b028_a028_d028_i028 @atom:60_b028_a028_d028_i028 0.2339 3.401 - pair_coeff @atom:61_b029_a029_d029_i029 @atom:61_b029_a029_d029_i029 0.317 3.624 - pair_coeff @atom:62_b030_a030_d030_i030 @atom:62_b030_a030_d030_i030 0.433 3.935 - pair_coeff @atom:63_b031_a031_d031_i031 @atom:63_b031_a031_d031_i031 0.1521 3.15061 - pair_coeff @atom:64_b032_a032_d032_i032 @atom:64_b032_a032_d032_i032 0.0 0.0 - pair_coeff @atom:65_b031_a031_d031_i031 @atom:65_b031_a031_d031_i031 0.155 3.15365 - pair_coeff @atom:66_b032_a032_d032_i032 @atom:66_b032_a032_d032_i032 0.0 0.0 - pair_coeff @atom:67_b033_a033_d033_i033 @atom:67_b033_a033_d033_i033 0.0 0.0 - pair_coeff @atom:68_b034_a034_d034_i034 @atom:68_b034_a034_d034_i034 0.15 3.176 - pair_coeff @atom:69_b035_a035_d035_i035 @atom:69_b035_a035_d035_i035 0.0 0.0 - pair_coeff @atom:70_b036_a036_d036_i036 @atom:70_b036_a036_d036_i036 0.1 3.27 - pair_coeff @atom:71_b037_a037_d037_i037 @atom:71_b037_a037_d037_i037 0.0 0.0 - pair_coeff @atom:72_b038_a038_d038_i038 @atom:72_b038_a038_d038_i038 0.0 0.0 - pair_coeff @atom:73_b039_a039_d039_i039 @atom:73_b039_a039_d039_i039 0.16 3.12 - pair_coeff @atom:74_b040_a040_d040_i040 @atom:74_b040_a040_d040_i040 0.0 0.0 - pair_coeff @atom:75_b041_a041_d041_i041 @atom:75_b041_a041_d041_i041 0.0 0.0 - pair_coeff @atom:76_b042_a042_d042_i042 @atom:76_b042_a042_d042_i042 0.1554 3.16557 - pair_coeff @atom:77_b043_a043_d043_i043 @atom:77_b043_a043_d043_i043 0.0 0.0 - pair_coeff @atom:78_b044_a044_d044_i044 @atom:78_b044_a044_d044_i044 0.17 3.42 - pair_coeff @atom:79_b045_a045_d045_i045 @atom:79_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:80_b013_a013_d013_i013 @atom:80_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:81_b013_a013_d013_i013 @atom:81_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:82_b013_a013_d013_i013 @atom:82_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:83_b013_a013_d013_i013 @atom:83_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:84_b013_a013_d013_i013 @atom:84_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:85_b046_a046_d046_i046 @atom:85_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:86_b047_a047_d047_i047 @atom:86_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:87_b047_a047_d047_i047 @atom:87_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:88_b047_a047_d047_i047 @atom:88_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:89_b046_a046_d046_i046 @atom:89_b046_a046_d046_i046 0.03 2.42 - pair_coeff @atom:90_b048_a048_d048_i048 @atom:90_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:91_b049_a049_d049_i049 @atom:91_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:92_b048_a048_d048_i048 @atom:92_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:93_b013_a013_d013_i013 @atom:93_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:94_b013_a013_d013_i013 @atom:94_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:95_b050_a050_d050_i050 @atom:95_b050_a050_d050_i050 0.076 3.55 - pair_coeff @atom:96_b005_a005_d005_i005 @atom:96_b005_a005_d005_i005 0.17 3.12 - pair_coeff @atom:97_b007_a007_d007_i007 @atom:97_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:98_b046_a046_d046_i046 @atom:98_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:99_b013_a013_d013_i013 @atom:99_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:100_b013_a013_d013_i013 @atom:100_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:101_b013_a013_d013_i013 @atom:101_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:102_b013_a013_d013_i013 @atom:102_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:103_b013_a013_d013_i013 @atom:103_b013_a013_d013_i013 0.062 3.25 - pair_coeff @atom:104_b005_a005_d005_i005 @atom:104_b005_a005_d005_i005 0.17 3.07 - pair_coeff @atom:105_b007_a007_d007_i007 @atom:105_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:106_b001_a001_d001_i001 @atom:106_b001_a001_d001_i001 0.061 2.94 - pair_coeff @atom:107_b046_a046_d046_i046 @atom:107_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:108_b048_a048_d048_i048 @atom:108_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:109_b005_a005_d005_i005 @atom:109_b005_a005_d005_i005 0.17 3.07 - pair_coeff @atom:110_b007_a007_d007_i007 @atom:110_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:111_b005_a005_d005_i005 @atom:111_b005_a005_d005_i005 0.17 3.07 - pair_coeff @atom:112_b007_a007_d007_i007 @atom:112_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:113_b005_a005_d005_i005 @atom:113_b005_a005_d005_i005 0.17 3.07 - pair_coeff @atom:114_b007_a007_d007_i007 @atom:114_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:115_b013_a013_d013_i013 @atom:115_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:116_b013_a013_d013_i013 @atom:116_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:117_b013_a013_d013_i013 @atom:117_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:118_b046_a046_d046_i046 @atom:118_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:119_b020_a020_d020_i020 @atom:119_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:120_b050_a050_d050_i050 @atom:120_b050_a050_d050_i050 0.076 3.55 - pair_coeff @atom:121_b020_a020_d020_i020 @atom:121_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:122_b020_a020_d020_i020 @atom:122_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:123_b013_a013_d013_i013 @atom:123_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:124_b013_a013_d013_i013 @atom:124_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:125_b013_a013_d013_i013 @atom:125_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:126_b013_a013_d013_i013 @atom:126_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:127_b046_a046_d046_i046 @atom:127_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:128_b020_a020_d020_i020 @atom:128_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:129_b005_a005_d005_i005 @atom:129_b005_a005_d005_i005 0.17 3.07 - pair_coeff @atom:130_b007_a007_d007_i007 @atom:130_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:131_b051_a051_d051_i051 @atom:131_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:132_b046_a046_d046_i046 @atom:132_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:133_b051_a051_d051_i051 @atom:133_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:134_b046_a046_d046_i046 @atom:134_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:135_b051_a051_d051_i051 @atom:135_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:136_b046_a046_d046_i046 @atom:136_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:137_b051_a051_d051_i051 @atom:137_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:138_b046_a046_d046_i046 @atom:138_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:139_b051_a051_d051_i051 @atom:139_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:140_b051_a051_d051_i051 @atom:140_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:141_b048_a048_d048_i048 @atom:141_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:142_b015_a015_d015_i015 @atom:142_b015_a015_d015_i015 0.25 3.55 - pair_coeff @atom:143_b015_a015_d015_i015 @atom:143_b015_a015_d015_i015 0.25 3.7 - pair_coeff @atom:144_b016_a016_d016_i016 @atom:144_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:145_b016_a016_d016_i016 @atom:145_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:146_b017_a017_d017_i017 @atom:146_b017_a017_d017_i017 0.0 0.0 - pair_coeff @atom:147_b017_a017_d017_i017 @atom:147_b017_a017_d017_i017 0.0 0.0 - pair_coeff @atom:148_b013_a013_d013_i013 @atom:148_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:149_b013_a013_d013_i013 @atom:149_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:150_b013_a013_d013_i013 @atom:150_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:151_b013_a013_d013_i013 @atom:151_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:152_b013_a013_d013_i013 @atom:152_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:153_b013_a013_d013_i013 @atom:153_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:154_b013_a013_d013_i013 @atom:154_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:155_b013_a013_d013_i013 @atom:155_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:156_b013_a013_d013_i013 @atom:156_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:157_b013_a013_d013_i013 @atom:157_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:158_b013_a013_d013_i013 @atom:158_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:159_b013_a013_d013_i013 @atom:159_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:160_b013_a013_d013_i013 @atom:160_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:161_b013_a013_d013_i013 @atom:161_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:162_b013_a013_d013_i013 @atom:162_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:163_b048_a048_d048_i048 @atom:163_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:164_b016_a016_d016_i016 @atom:164_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:165_b013_a013_d013_i013 @atom:165_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:166_b013_a013_d013_i013 @atom:166_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:167_b013_a013_d013_i013 @atom:167_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:168_b021_a021_d021_i021 @atom:168_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:169_b047_a047_d047_i047 @atom:169_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:170_b048_a048_d048_i048 @atom:170_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:171_b013_a013_d013_i013 @atom:171_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:172_b013_a013_d013_i013 @atom:172_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:173_b003_a003_d003_i003 @atom:173_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:174_b003_a003_d003_i003 @atom:174_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:175_b003_a003_d003_i003 @atom:175_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:176_b003_a003_d003_i003 @atom:176_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:177_b003_a003_d003_i003 @atom:177_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:178_b004_a004_d004_i004 @atom:178_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:179_b024_a024_d024_i024 @atom:179_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:180_b024_a024_d024_i024 @atom:180_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:181_b024_a024_d024_i024 @atom:181_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:182_b045_a045_d045_i045 @atom:182_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:183_b045_a045_d045_i045 @atom:183_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:184_b013_a013_d013_i013 @atom:184_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:185_b013_a013_d013_i013 @atom:185_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:186_b013_a013_d013_i013 @atom:186_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:187_b013_a013_d013_i013 @atom:187_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:188_b013_a013_d013_i013 @atom:188_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:189_b003_a003_d003_i003 @atom:189_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:190_b004_a004_d004_i004 @atom:190_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:191_b024_a024_d024_i024 @atom:191_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:192_b045_a045_d045_i045 @atom:192_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:193_b024_a024_d024_i024 @atom:193_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:194_b003_a003_d003_i003 @atom:194_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:195_b004_a004_d004_i004 @atom:195_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:196_b045_a045_d045_i045 @atom:196_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:197_b046_a046_d046_i046 @atom:197_b046_a046_d046_i046 0.02 2.5 - pair_coeff @atom:198_b013_a013_d013_i013 @atom:198_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:199_b013_a013_d013_i013 @atom:199_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:200_b013_a013_d013_i013 @atom:200_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:201_b013_a013_d013_i013 @atom:201_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:202_b048_a048_d048_i048 @atom:202_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:203_b019_a019_d019_i019 @atom:203_b019_a019_d019_i019 0.15 3.65 - pair_coeff @atom:204_b018_a018_d018_i018 @atom:204_b018_a018_d018_i018 0.17 3.2 - pair_coeff @atom:205_b048_a048_d048_i048 @atom:205_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:206_b021_a021_d021_i021 @atom:206_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:207_b024_a024_d024_i024 @atom:207_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:208_b048_a048_d048_i048 @atom:208_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:209_b003_a003_d003_i003 @atom:209_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:210_b004_a004_d004_i004 @atom:210_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:211_b005_a005_d005_i005 @atom:211_b005_a005_d005_i005 0.17 3.0 - pair_coeff @atom:212_b007_a007_d007_i007 @atom:212_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:213_b003_a003_d003_i003 @atom:213_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:214_b052_a052_d052_i052 @atom:214_b052_a052_d052_i052 0.21 2.96 - pair_coeff @atom:215_b013_a013_d013_i013 @atom:215_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:216_b013_a013_d013_i013 @atom:216_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:217_b013_a013_d013_i013 @atom:217_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:218_b013_a013_d013_i013 @atom:218_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:219_b003_a003_d003_i003 @atom:219_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:220_b004_a004_d004_i004 @atom:220_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:221_b046_a046_d046_i046 @atom:221_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:222_b003_a003_d003_i003 @atom:222_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:223_b004_a004_d004_i004 @atom:223_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:224_b046_a046_d046_i046 @atom:224_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:225_b013_a013_d013_i013 @atom:225_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:226_b013_a013_d013_i013 @atom:226_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:227_b013_a013_d013_i013 @atom:227_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:228_b013_a013_d013_i013 @atom:228_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:229_b053_a053_d053_i053 @atom:229_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:230_b053_a053_d053_i053 @atom:230_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:231_b053_a053_d053_i053 @atom:231_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:232_b054_a054_d054_i054 @atom:232_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:233_b054_a054_d054_i054 @atom:233_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:234_b013_a013_d013_i013 @atom:234_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:235_b013_a013_d013_i013 @atom:235_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:236_b013_a013_d013_i013 @atom:236_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:237_b013_a013_d013_i013 @atom:237_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:238_b013_a013_d013_i013 @atom:238_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:239_b013_a013_d013_i013 @atom:239_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:240_b013_a013_d013_i013 @atom:240_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:241_b013_a013_d013_i013 @atom:241_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:242_b013_a013_d013_i013 @atom:242_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:243_b055_a055_d055_i055 @atom:243_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:244_b054_a054_d054_i054 @atom:244_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:245_b048_a048_d048_i048 @atom:245_b048_a048_d048_i048 0.05 3.55 - pair_coeff @atom:246_b055_a055_d055_i055 @atom:246_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:247_b054_a054_d054_i054 @atom:247_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:248_b013_a013_d013_i013 @atom:248_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:249_b013_a013_d013_i013 @atom:249_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:250_b013_a013_d013_i013 @atom:250_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:251_b013_a013_d013_i013 @atom:251_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:252_b053_a053_d053_i053 @atom:252_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:253_b054_a054_d054_i054 @atom:253_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:254_b056_a056_d056_i056 @atom:254_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:255_b048_a048_d048_i048 @atom:255_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:256_b055_a055_d055_i055 @atom:256_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:257_b045_a045_d045_i045 @atom:257_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:258_b048_a048_d048_i048 @atom:258_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:259_b049_a049_d049_i049 @atom:259_b049_a049_d049_i049 0.05 2.5 - pair_coeff @atom:260_b048_a048_d048_i048 @atom:260_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:261_b049_a049_d049_i049 @atom:261_b049_a049_d049_i049 0.05 2.5 - pair_coeff @atom:262_b057_a057_d057_i057 @atom:262_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:263_b003_a003_d003_i003 @atom:263_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:264_b057_a057_d057_i057 @atom:264_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:265_b003_a003_d003_i003 @atom:265_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:266_b047_a047_d047_i047 @atom:266_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:267_b047_a047_d047_i047 @atom:267_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:268_b045_a045_d045_i045 @atom:268_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:269_b004_a004_d004_i004 @atom:269_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:270_b045_a045_d045_i045 @atom:270_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:271_b004_a004_d004_i004 @atom:271_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:272_b046_a046_d046_i046 @atom:272_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:273_b046_a046_d046_i046 @atom:273_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:274_b013_a013_d013_i013 @atom:274_b013_a013_d013_i013 0.08 3.5 - pair_coeff @atom:275_b046_a046_d046_i046 @atom:275_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:276_b057_a057_d057_i057 @atom:276_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:277_b003_a003_d003_i003 @atom:277_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:278_b056_a056_d056_i056 @atom:278_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:279_b048_a048_d048_i048 @atom:279_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:280_b047_a047_d047_i047 @atom:280_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:281_b047_a047_d047_i047 @atom:281_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:282_b045_a045_d045_i045 @atom:282_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:283_b004_a004_d004_i004 @atom:283_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:284_b055_a055_d055_i055 @atom:284_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:285_b045_a045_d045_i045 @atom:285_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:286_b045_a045_d045_i045 @atom:286_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:287_b046_a046_d046_i046 @atom:287_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:288_b058_a058_d058_i058 @atom:288_b058_a058_d058_i058 0.05 2.5 - pair_coeff @atom:289_b056_a056_d056_i056 @atom:289_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:290_b059_a059_d059_i059 @atom:290_b059_a059_d059_i059 0.08 3.5 - pair_coeff @atom:291_b056_a056_d056_i056 @atom:291_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:292_b060_a060_d060_i060 @atom:292_b060_a060_d060_i060 0.08 3.5 - pair_coeff @atom:293_b060_a060_d060_i060 @atom:293_b060_a060_d060_i060 0.08 3.5 - pair_coeff @atom:294_b048_a048_d048_i048 @atom:294_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:295_b061_a061_d061_i061 @atom:295_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:296_b062_a062_d062_i062 @atom:296_b062_a062_d062_i062 0.08 3.5 - pair_coeff @atom:297_b057_a057_d057_i057 @atom:297_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:298_b063_a063_d063_i063 @atom:298_b063_a063_d063_i063 0.05 2.5 - pair_coeff @atom:299_b055_a055_d055_i055 @atom:299_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:300_b045_a045_d045_i045 @atom:300_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:301_b045_a045_d045_i045 @atom:301_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:302_b063_a063_d063_i063 @atom:302_b063_a063_d063_i063 0.05 2.5 - pair_coeff @atom:303_b045_a045_d045_i045 @atom:303_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:304_b057_a057_d057_i057 @atom:304_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:305_b048_a048_d048_i048 @atom:305_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:306_b056_a056_d056_i056 @atom:306_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:307_b060_a060_d060_i060 @atom:307_b060_a060_d060_i060 0.08 3.5 - pair_coeff @atom:308_b060_a060_d060_i060 @atom:308_b060_a060_d060_i060 0.08 3.5 - pair_coeff @atom:309_b003_a003_d003_i003 @atom:309_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:310_b045_a045_d045_i045 @atom:310_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:311_b055_a055_d055_i055 @atom:311_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:312_b045_a045_d045_i045 @atom:312_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:313_b004_a004_d004_i004 @atom:313_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:314_b013_a013_d013_i013 @atom:314_b013_a013_d013_i013 0.08 3.5 - pair_coeff @atom:315_b046_a046_d046_i046 @atom:315_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:316_b013_a013_d013_i013 @atom:316_b013_a013_d013_i013 0.08 3.5 - pair_coeff @atom:317_b046_a046_d046_i046 @atom:317_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:318_b013_a013_d013_i013 @atom:318_b013_a013_d013_i013 0.08 3.5 - pair_coeff @atom:319_b046_a046_d046_i046 @atom:319_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:320_b057_a057_d057_i057 @atom:320_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:321_b003_a003_d003_i003 @atom:321_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:322_b057_a057_d057_i057 @atom:322_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:323_b048_a048_d048_i048 @atom:323_b048_a048_d048_i048 0.08 3.5 - pair_coeff @atom:324_b047_a047_d047_i047 @atom:324_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:325_b047_a047_d047_i047 @atom:325_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:326_b045_a045_d045_i045 @atom:326_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:327_b004_a004_d004_i004 @atom:327_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:328_b045_a045_d045_i045 @atom:328_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:329_b055_a055_d055_i055 @atom:329_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:330_b045_a045_d045_i045 @atom:330_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:331_b045_a045_d045_i045 @atom:331_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:332_b049_a049_d049_i049 @atom:332_b049_a049_d049_i049 0.05 2.5 - pair_coeff @atom:333_b058_a058_d058_i058 @atom:333_b058_a058_d058_i058 0.05 2.5 - pair_coeff @atom:334_b013_a013_d013_i013 @atom:334_b013_a013_d013_i013 0.08 3.5 - pair_coeff @atom:335_b046_a046_d046_i046 @atom:335_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:336_b064_a064_d064_i064 @atom:336_b064_a064_d064_i064 0.2 3.74 - pair_coeff @atom:337_b052_a052_d052_i052 @atom:337_b052_a052_d052_i052 0.21 2.96 - pair_coeff @atom:338_b020_a020_d020_i020 @atom:338_b020_a020_d020_i020 0.17 3.0 - pair_coeff @atom:339_b013_a013_d013_i013 @atom:339_b013_a013_d013_i013 0.066 3.55 - pair_coeff @atom:340_b047_a047_d047_i047 @atom:340_b047_a047_d047_i047 0.08 3.5 - pair_coeff @atom:341_b021_a021_d021_i021 @atom:341_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:342_b047_a047_d047_i047 @atom:342_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:343_b001_a001_d001_i001 @atom:343_b001_a001_d001_i001 0.71 3.05 - pair_coeff @atom:344_b021_a021_d021_i021 @atom:344_b021_a021_d021_i021 0.71 4.02 - pair_coeff @atom:345_b065_a065_d065_i065 @atom:345_b065_a065_d065_i065 0.71 4.28 - pair_coeff @atom:346_b066_a066_d066_i066 @atom:346_b066_a066_d066_i066 0.71 4.81 - pair_coeff @atom:347_b067_a067_d067_i067 @atom:347_b067_a067_d067_i067 0.0005 5.34 - pair_coeff @atom:348_b068_a068_d068_i068 @atom:348_b068_a068_d068_i068 0.0005 2.87 - pair_coeff @atom:349_b069_a069_d069_i069 @atom:349_b069_a069_d069_i069 0.0005 4.07 - pair_coeff @atom:350_b070_a070_d070_i070 @atom:350_b070_a070_d070_i070 0.0005 5.17 - pair_coeff @atom:351_b071_a071_d071_i071 @atom:351_b071_a071_d071_i071 0.0005 5.6 - pair_coeff @atom:352_b072_a072_d072_i072 @atom:352_b072_a072_d072_i072 0.0005 6.2 - pair_coeff @atom:353_b073_a073_d073_i073 @atom:353_b073_a073_d073_i073 0.875044 1.644471 - pair_coeff @atom:354_b074_a074_d074_i074 @atom:354_b074_a074_d074_i074 0.449657 2.412031 - pair_coeff @atom:355_b075_a075_d075_i075 @atom:355_b075_a075_d075_i075 0.118226 3.102688 - pair_coeff @atom:356_b076_a076_d076_i076 @atom:356_b076_a076_d076_i076 0.047096 3.81661 - pair_coeff @atom:357_b006_a006_d006_i006 @atom:357_b006_a006_d006_i006 0.3 4.2 - pair_coeff @atom:358_b046_a046_d046_i046 @atom:358_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:359_b015_a015_d015_i015 @atom:359_b015_a015_d015_i015 0.5 4.25 - pair_coeff @atom:360_b006_a006_d006_i006 @atom:360_b006_a006_d006_i006 0.3 4.2 - pair_coeff @atom:361_b046_a046_d046_i046 @atom:361_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:362_b005_a005_d005_i005 @atom:362_b005_a005_d005_i005 0.25 3.15 - pair_coeff @atom:363_b013_a013_d013_i013 @atom:363_b013_a013_d013_i013 0.3 4.2 - pair_coeff @atom:364_b046_a046_d046_i046 @atom:364_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:365_b019_a019_d019_i019 @atom:365_b019_a019_d019_i019 0.15 3.65 - pair_coeff @atom:366_b018_a018_d018_i018 @atom:366_b018_a018_d018_i018 0.25 3.4 - pair_coeff @atom:367_b006_a006_d006_i006 @atom:367_b006_a006_d006_i006 0.3 4.2 - pair_coeff @atom:368_b046_a046_d046_i046 @atom:368_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:369_b053_a053_d053_i053 @atom:369_b053_a053_d053_i053 0.25 3.4 - pair_coeff @atom:370_b045_a045_d045_i045 @atom:370_b045_a045_d045_i045 0.05 2.5 - pair_coeff @atom:371_b006_a006_d006_i006 @atom:371_b006_a006_d006_i006 0.3 4.2 - pair_coeff @atom:372_b046_a046_d046_i046 @atom:372_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:373_b013_a013_d013_i013 @atom:373_b013_a013_d013_i013 0.3 4.2 - pair_coeff @atom:374_b046_a046_d046_i046 @atom:374_b046_a046_d046_i046 0.05 2.5 - pair_coeff @atom:375_b033_a033_d033_i033 @atom:375_b033_a033_d033_i033 0.0 0.0 - pair_coeff @atom:376_b005_a005_d005_i005 @atom:376_b005_a005_d005_i005 0.25 3.2 - pair_coeff @atom:377_b007_a007_d007_i007 @atom:377_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:378_b077_a077_d077_i077 @atom:378_b077_a077_d077_i077 0.4 2.81524 - pair_coeff @atom:379_b078_a078_d078_i078 @atom:379_b078_a078_d078_i078 0.2 3.11815 - pair_coeff @atom:380_b020_a020_d020_i020 @atom:380_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:381_b064_a064_d064_i064 @atom:381_b064_a064_d064_i064 0.2 3.74 - pair_coeff @atom:382_b052_a052_d052_i052 @atom:382_b052_a052_d052_i052 0.2 3.15 - pair_coeff @atom:383_b020_a020_d020_i020 @atom:383_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:384_b013_a013_d013_i013 @atom:384_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:385_b046_a046_d046_i046 @atom:385_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:386_b064_a064_d064_i064 @atom:386_b064_a064_d064_i064 0.2 3.74 - pair_coeff @atom:387_b052_a052_d052_i052 @atom:387_b052_a052_d052_i052 0.2 3.15 - pair_coeff @atom:388_b020_a020_d020_i020 @atom:388_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:389_b013_a013_d013_i013 @atom:389_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:390_b046_a046_d046_i046 @atom:390_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:391_b064_a064_d064_i064 @atom:391_b064_a064_d064_i064 0.2 3.74 - pair_coeff @atom:392_b052_a052_d052_i052 @atom:392_b052_a052_d052_i052 0.2 3.15 - pair_coeff @atom:393_b020_a020_d020_i020 @atom:393_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:394_b013_a013_d013_i013 @atom:394_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:395_b046_a046_d046_i046 @atom:395_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:396_b013_a013_d013_i013 @atom:396_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:397_b046_a046_d046_i046 @atom:397_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:398_b048_a048_d048_i048 @atom:398_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:399_b013_a013_d013_i013 @atom:399_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:400_b046_a046_d046_i046 @atom:400_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:401_b048_a048_d048_i048 @atom:401_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:402_b013_a013_d013_i013 @atom:402_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:403_b046_a046_d046_i046 @atom:403_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:404_b048_a048_d048_i048 @atom:404_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:405_b013_a013_d013_i013 @atom:405_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:406_b003_a003_d003_i003 @atom:406_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:407_b004_a004_d004_i004 @atom:407_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:408_b020_a020_d020_i020 @atom:408_b020_a020_d020_i020 0.17 3.0 - pair_coeff @atom:409_b013_a013_d013_i013 @atom:409_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:410_b046_a046_d046_i046 @atom:410_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:411_b003_a003_d003_i003 @atom:411_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:412_b003_a003_d003_i003 @atom:412_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:413_b048_a048_d048_i048 @atom:413_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:414_b020_a020_d020_i020 @atom:414_b020_a020_d020_i020 0.17 3.0 - pair_coeff @atom:415_b079_a079_d079_i079 @atom:415_b079_a079_d079_i079 0.25 3.55 - pair_coeff @atom:416_b023_a023_d023_i023 @atom:416_b023_a023_d023_i023 0.17 2.96 - pair_coeff @atom:417_b013_a013_d013_i013 @atom:417_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:418_b046_a046_d046_i046 @atom:418_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:419_b024_a024_d024_i024 @atom:419_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:420_b045_a045_d045_i045 @atom:420_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:421_b024_a024_d024_i024 @atom:421_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:422_b045_a045_d045_i045 @atom:422_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:423_b013_a013_d013_i013 @atom:423_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:424_b046_a046_d046_i046 @atom:424_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:425_b013_a013_d013_i013 @atom:425_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:426_b046_a046_d046_i046 @atom:426_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:427_b013_a013_d013_i013 @atom:427_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:428_b046_a046_d046_i046 @atom:428_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:429_b048_a048_d048_i048 @atom:429_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:430_b048_a048_d048_i048 @atom:430_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:431_b013_a013_d013_i013 @atom:431_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:432_b013_a013_d013_i013 @atom:432_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:433_b013_a013_d013_i013 @atom:433_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:434_b079_a079_d079_i079 @atom:434_b079_a079_d079_i079 0.25 3.55 - pair_coeff @atom:435_b023_a023_d023_i023 @atom:435_b023_a023_d023_i023 0.17 2.96 - pair_coeff @atom:436_b022_a022_d022_i022 @atom:436_b022_a022_d022_i022 0.395 3.56 - pair_coeff @atom:437_b022_a022_d022_i022 @atom:437_b022_a022_d022_i022 0.395 3.56 - pair_coeff @atom:438_b023_a023_d023_i023 @atom:438_b023_a023_d023_i023 0.28 2.93 - pair_coeff @atom:439_b013_a013_d013_i013 @atom:439_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:440_b013_a013_d013_i013 @atom:440_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:441_b080_a080_d080_i080 @atom:441_b080_a080_d080_i080 0.07 3.55 - pair_coeff @atom:442_b060_a060_d060_i060 @atom:442_b060_a060_d060_i060 0.07 3.55 - pair_coeff @atom:443_b081_a081_d081_i081 @atom:443_b081_a081_d081_i081 0.07 3.55 - pair_coeff @atom:444_b057_a057_d057_i057 @atom:444_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:445_b045_a045_d045_i045 @atom:445_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:446_b013_a013_d013_i013 @atom:446_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:447_b082_a082_d082_i082 @atom:447_b082_a082_d082_i082 0.07 3.55 - pair_coeff @atom:448_b083_a083_d083_i083 @atom:448_b083_a083_d083_i083 0.07 3.55 - pair_coeff @atom:449_b084_a084_d084_i084 @atom:449_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:450_b082_a082_d082_i082 @atom:450_b082_a082_d082_i082 0.07 3.55 - pair_coeff @atom:451_b085_a085_d085_i085 @atom:451_b085_a085_d085_i085 0.07 3.55 - pair_coeff @atom:452_b061_a061_d061_i061 @atom:452_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:453_b057_a057_d057_i057 @atom:453_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:454_b045_a045_d045_i045 @atom:454_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:455_b084_a084_d084_i084 @atom:455_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:456_b013_a013_d013_i013 @atom:456_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:457_b013_a013_d013_i013 @atom:457_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:458_b047_a047_d047_i047 @atom:458_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:459_b047_a047_d047_i047 @atom:459_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:460_b086_a086_d086_i086 @atom:460_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:461_b056_a056_d056_i056 @atom:461_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:462_b048_a048_d048_i048 @atom:462_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:463_b048_a048_d048_i048 @atom:463_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:464_b048_a048_d048_i048 @atom:464_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:465_b049_a049_d049_i049 @atom:465_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:466_b049_a049_d049_i049 @atom:466_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:467_b049_a049_d049_i049 @atom:467_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:468_b056_a056_d056_i056 @atom:468_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:469_b048_a048_d048_i048 @atom:469_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:470_b049_a049_d049_i049 @atom:470_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:471_b056_a056_d056_i056 @atom:471_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:472_b059_a059_d059_i059 @atom:472_b059_a059_d059_i059 0.07 3.55 - pair_coeff @atom:473_b048_a048_d048_i048 @atom:473_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:474_b048_a048_d048_i048 @atom:474_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:475_b049_a049_d049_i049 @atom:475_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:476_b049_a049_d049_i049 @atom:476_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:477_b049_a049_d049_i049 @atom:477_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:478_b056_a056_d056_i056 @atom:478_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:479_b048_a048_d048_i048 @atom:479_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:480_b048_a048_d048_i048 @atom:480_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:481_b049_a049_d049_i049 @atom:481_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:482_b049_a049_d049_i049 @atom:482_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:483_b057_a057_d057_i057 @atom:483_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:484_b084_a084_d084_i084 @atom:484_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:485_b087_a087_d087_i087 @atom:485_b087_a087_d087_i087 0.07 3.55 - pair_coeff @atom:486_b045_a045_d045_i045 @atom:486_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:487_b049_a049_d049_i049 @atom:487_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:488_b049_a049_d049_i049 @atom:488_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:489_b057_a057_d057_i057 @atom:489_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:490_b061_a061_d061_i061 @atom:490_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:491_b088_a088_d088_i088 @atom:491_b088_a088_d088_i088 0.07 3.55 - pair_coeff @atom:492_b087_a087_d087_i087 @atom:492_b087_a087_d087_i087 0.07 3.55 - pair_coeff @atom:493_b084_a084_d084_i084 @atom:493_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:494_b045_a045_d045_i045 @atom:494_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:495_b049_a049_d049_i049 @atom:495_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:496_b049_a049_d049_i049 @atom:496_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:497_b049_a049_d049_i049 @atom:497_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:498_b057_a057_d057_i057 @atom:498_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:499_b082_a082_d082_i082 @atom:499_b082_a082_d082_i082 0.07 3.55 - pair_coeff @atom:500_b061_a061_d061_i061 @atom:500_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:501_b083_a083_d083_i083 @atom:501_b083_a083_d083_i083 0.07 3.55 - pair_coeff @atom:502_b084_a084_d084_i084 @atom:502_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:503_b045_a045_d045_i045 @atom:503_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:504_b049_a049_d049_i049 @atom:504_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:505_b049_a049_d049_i049 @atom:505_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:506_b049_a049_d049_i049 @atom:506_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:507_b020_a020_d020_i020 @atom:507_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:508_b084_a084_d084_i084 @atom:508_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:509_b087_a087_d087_i087 @atom:509_b087_a087_d087_i087 0.076 3.55 - pair_coeff @atom:510_b049_a049_d049_i049 @atom:510_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:511_b049_a049_d049_i049 @atom:511_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:512_b020_a020_d020_i020 @atom:512_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:513_b082_a082_d082_i082 @atom:513_b082_a082_d082_i082 0.07 3.55 - pair_coeff @atom:514_b061_a061_d061_i061 @atom:514_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:515_b083_a083_d083_i083 @atom:515_b083_a083_d083_i083 0.07 3.55 - pair_coeff @atom:516_b084_a084_d084_i084 @atom:516_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:517_b049_a049_d049_i049 @atom:517_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:518_b049_a049_d049_i049 @atom:518_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:519_b049_a049_d049_i049 @atom:519_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:520_b020_a020_d020_i020 @atom:520_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:521_b061_a061_d061_i061 @atom:521_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:522_b088_a088_d088_i088 @atom:522_b088_a088_d088_i088 0.07 3.55 - pair_coeff @atom:523_b087_a087_d087_i087 @atom:523_b087_a087_d087_i087 0.07 3.55 - pair_coeff @atom:524_b084_a084_d084_i084 @atom:524_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:525_b049_a049_d049_i049 @atom:525_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:526_b049_a049_d049_i049 @atom:526_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:527_b049_a049_d049_i049 @atom:527_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:528_b057_a057_d057_i057 @atom:528_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:529_b084_a084_d084_i084 @atom:529_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:530_b087_a087_d087_i087 @atom:530_b087_a087_d087_i087 0.07 3.55 - pair_coeff @atom:531_b048_a048_d048_i048 @atom:531_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:532_b048_a048_d048_i048 @atom:532_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:533_b048_a048_d048_i048 @atom:533_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:534_b048_a048_d048_i048 @atom:534_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:535_b081_a081_d081_i081 @atom:535_b081_a081_d081_i081 0.07 3.55 - pair_coeff @atom:536_b060_a060_d060_i060 @atom:536_b060_a060_d060_i060 0.07 3.55 - pair_coeff @atom:537_b045_a045_d045_i045 @atom:537_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:538_b049_a049_d049_i049 @atom:538_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:539_b049_a049_d049_i049 @atom:539_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:540_b049_a049_d049_i049 @atom:540_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:541_b049_a049_d049_i049 @atom:541_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:542_b049_a049_d049_i049 @atom:542_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:543_b049_a049_d049_i049 @atom:543_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:544_b056_a056_d056_i056 @atom:544_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:545_b048_a048_d048_i048 @atom:545_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:546_b048_a048_d048_i048 @atom:546_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:547_b048_a048_d048_i048 @atom:547_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:548_b048_a048_d048_i048 @atom:548_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:549_b048_a048_d048_i048 @atom:549_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:550_b048_a048_d048_i048 @atom:550_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:551_b048_a048_d048_i048 @atom:551_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:552_b048_a048_d048_i048 @atom:552_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:553_b048_a048_d048_i048 @atom:553_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:554_b049_a049_d049_i049 @atom:554_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:555_b049_a049_d049_i049 @atom:555_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:556_b049_a049_d049_i049 @atom:556_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:557_b049_a049_d049_i049 @atom:557_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:558_b049_a049_d049_i049 @atom:558_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:559_b049_a049_d049_i049 @atom:559_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:560_b049_a049_d049_i049 @atom:560_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:561_b056_a056_d056_i056 @atom:561_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:562_b059_a059_d059_i059 @atom:562_b059_a059_d059_i059 0.07 3.55 - pair_coeff @atom:563_b056_a056_d056_i056 @atom:563_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:564_b060_a060_d060_i060 @atom:564_b060_a060_d060_i060 0.07 3.55 - pair_coeff @atom:565_b060_a060_d060_i060 @atom:565_b060_a060_d060_i060 0.07 3.55 - pair_coeff @atom:566_b048_a048_d048_i048 @atom:566_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:567_b061_a061_d061_i061 @atom:567_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:568_b062_a062_d062_i062 @atom:568_b062_a062_d062_i062 0.07 3.55 - pair_coeff @atom:569_b057_a057_d057_i057 @atom:569_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:570_b049_a049_d049_i049 @atom:570_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:571_b049_a049_d049_i049 @atom:571_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:572_b049_a049_d049_i049 @atom:572_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:573_b045_a045_d045_i045 @atom:573_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:574_b016_a016_d016_i016 @atom:574_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:575_b082_a082_d082_i082 @atom:575_b082_a082_d082_i082 0.07 3.55 - pair_coeff @atom:576_b061_a061_d061_i061 @atom:576_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:577_b083_a083_d083_i083 @atom:577_b083_a083_d083_i083 0.07 3.55 - pair_coeff @atom:578_b084_a084_d084_i084 @atom:578_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:579_b049_a049_d049_i049 @atom:579_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:580_b049_a049_d049_i049 @atom:580_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:581_b049_a049_d049_i049 @atom:581_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:582_b056_a056_d056_i056 @atom:582_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:583_b059_a059_d059_i059 @atom:583_b059_a059_d059_i059 0.07 3.55 - pair_coeff @atom:584_b049_a049_d049_i049 @atom:584_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:585_b048_a048_d048_i048 @atom:585_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:586_b013_a013_d013_i013 @atom:586_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:587_b056_a056_d056_i056 @atom:587_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:588_b048_a048_d048_i048 @atom:588_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:589_b048_a048_d048_i048 @atom:589_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:590_b048_a048_d048_i048 @atom:590_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:591_b048_a048_d048_i048 @atom:591_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:592_b048_a048_d048_i048 @atom:592_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:593_b048_a048_d048_i048 @atom:593_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:594_b049_a049_d049_i049 @atom:594_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:595_b049_a049_d049_i049 @atom:595_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:596_b049_a049_d049_i049 @atom:596_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:597_b049_a049_d049_i049 @atom:597_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:598_b057_a057_d057_i057 @atom:598_b057_a057_d057_i057 0.17 3.25 - pair_coeff @atom:599_b082_a082_d082_i082 @atom:599_b082_a082_d082_i082 0.07 3.55 - pair_coeff @atom:600_b061_a061_d061_i061 @atom:600_b061_a061_d061_i061 0.17 3.25 - pair_coeff @atom:601_b083_a083_d083_i083 @atom:601_b083_a083_d083_i083 0.07 3.55 - pair_coeff @atom:602_b084_a084_d084_i084 @atom:602_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:603_b013_a013_d013_i013 @atom:603_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:604_b049_a049_d049_i049 @atom:604_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:605_b049_a049_d049_i049 @atom:605_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:606_b049_a049_d049_i049 @atom:606_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:607_b046_a046_d046_i046 @atom:607_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:608_b013_a013_d013_i013 @atom:608_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:609_b013_a013_d013_i013 @atom:609_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:610_b013_a013_d013_i013 @atom:610_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:611_b013_a013_d013_i013 @atom:611_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:612_b013_a013_d013_i013 @atom:612_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:613_b013_a013_d013_i013 @atom:613_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:614_b013_a013_d013_i013 @atom:614_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:615_b013_a013_d013_i013 @atom:615_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:616_b013_a013_d013_i013 @atom:616_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:617_b013_a013_d013_i013 @atom:617_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:618_b013_a013_d013_i013 @atom:618_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:619_b013_a013_d013_i013 @atom:619_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:620_b013_a013_d013_i013 @atom:620_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:621_b013_a013_d013_i013 @atom:621_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:622_b013_a013_d013_i013 @atom:622_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:623_b015_a015_d015_i015 @atom:623_b015_a015_d015_i015 0.25 3.55 - pair_coeff @atom:624_b017_a017_d017_i017 @atom:624_b017_a017_d017_i017 0.0 0.0 - pair_coeff @atom:625_b048_a048_d048_i048 @atom:625_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:626_b089_a089_d089_i089 @atom:626_b089_a089_d089_i089 0.105 3.75 - pair_coeff @atom:627_b090_a090_d090_i090 @atom:627_b090_a090_d090_i090 0.17 3.25 - pair_coeff @atom:628_b091_a091_d091_i091 @atom:628_b091_a091_d091_i091 0.066 3.5 - pair_coeff @atom:629_b091_a091_d091_i091 @atom:629_b091_a091_d091_i091 0.066 3.5 - pair_coeff @atom:630_b013_a013_d013_i013 @atom:630_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:631_b086_a086_d086_i086 @atom:631_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:632_b086_a086_d086_i086 @atom:632_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:633_b086_a086_d086_i086 @atom:633_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:634_b086_a086_d086_i086 @atom:634_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:635_b086_a086_d086_i086 @atom:635_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:636_b086_a086_d086_i086 @atom:636_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:637_b016_a016_d016_i016 @atom:637_b016_a016_d016_i016 0.25 3.55 - pair_coeff @atom:638_b092_a092_d092_i092 @atom:638_b092_a092_d092_i092 0.054 3.473 - pair_coeff @atom:639_b093_a093_d093_i093 @atom:639_b093_a093_d093_i093 0.05 3.3 - pair_coeff @atom:640_b094_a094_d094_i094 @atom:640_b094_a094_d094_i094 0.05 3.3 - pair_coeff @atom:641_b095_a095_d095_i095 @atom:641_b095_a095_d095_i095 0.076 3.55 - pair_coeff @atom:642_b013_a013_d013_i013 @atom:642_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:643_b046_a046_d046_i046 @atom:643_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:644_b096_a096_d096_i096 @atom:644_b096_a096_d096_i096 0.06 3.75 - pair_coeff @atom:645_b097_a097_d097_i097 @atom:645_b097_a097_d097_i097 0.054 3.473 - pair_coeff @atom:646_b098_a098_d098_i098 @atom:646_b098_a098_d098_i098 0.05 3.3 - pair_coeff @atom:647_b099_a099_d099_i099 @atom:647_b099_a099_d099_i099 0.05 3.3 - pair_coeff @atom:648_b100_a100_d100_i100 @atom:648_b100_a100_d100_i100 0.04 2.95 - pair_coeff @atom:649_b047_a047_d047_i047 @atom:649_b047_a047_d047_i047 0.076 3.55 - pair_coeff @atom:650_b021_a021_d021_i021 @atom:650_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:651_b046_a046_d046_i046 @atom:651_b046_a046_d046_i046 0.03 2.42 - pair_coeff @atom:652_b091_a091_d091_i091 @atom:652_b091_a091_d091_i091 0.066 3.5 - pair_coeff @atom:653_b091_a091_d091_i091 @atom:653_b091_a091_d091_i091 0.066 3.5 - pair_coeff @atom:654_b091_a091_d091_i091 @atom:654_b091_a091_d091_i091 0.066 3.5 - pair_coeff @atom:655_b048_a048_d048_i048 @atom:655_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:656_b049_a049_d049_i049 @atom:656_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:657_b048_a048_d048_i048 @atom:657_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:658_b049_a049_d049_i049 @atom:658_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:659_b048_a048_d048_i048 @atom:659_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:660_b001_a001_d001_i001 @atom:660_b001_a001_d001_i001 0.061 2.85 - pair_coeff @atom:661_b048_a048_d048_i048 @atom:661_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:662_b001_a001_d001_i001 @atom:662_b001_a001_d001_i001 0.061 2.85 - pair_coeff @atom:663_b065_a065_d065_i065 @atom:663_b065_a065_d065_i065 0.47 3.47 - pair_coeff @atom:664_b002_a002_d002_i002 @atom:664_b002_a002_d002_i002 0.118 3.905 - pair_coeff @atom:665_b048_a048_d048_i048 @atom:665_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:666_b013_a013_d013_i013 @atom:666_b013_a013_d013_i013 0.062 3.25 - pair_coeff @atom:667_b001_a001_d001_i001 @atom:667_b001_a001_d001_i001 0.061 2.94 - pair_coeff @atom:668_b048_a048_d048_i048 @atom:668_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:669_b001_a001_d001_i001 @atom:669_b001_a001_d001_i001 0.061 2.85 - pair_coeff @atom:670_b048_a048_d048_i048 @atom:670_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:671_b065_a065_d065_i065 @atom:671_b065_a065_d065_i065 0.47 3.47 - pair_coeff @atom:672_b048_a048_d048_i048 @atom:672_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:673_b066_a066_d066_i066 @atom:673_b066_a066_d066_i066 0.6 3.75 - pair_coeff @atom:674_b091_a091_d091_i091 @atom:674_b091_a091_d091_i091 0.066 3.5 - pair_coeff @atom:675_b015_a015_d015_i015 @atom:675_b015_a015_d015_i015 0.25 3.55 - pair_coeff @atom:676_b048_a048_d048_i048 @atom:676_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:677_b048_a048_d048_i048 @atom:677_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:678_b048_a048_d048_i048 @atom:678_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:679_b048_a048_d048_i048 @atom:679_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:680_b048_a048_d048_i048 @atom:680_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:681_b049_a049_d049_i049 @atom:681_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:682_b049_a049_d049_i049 @atom:682_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:683_b048_a048_d048_i048 @atom:683_b048_a048_d048_i048 0.05 3.55 - pair_coeff @atom:684_b055_a055_d055_i055 @atom:684_b055_a055_d055_i055 0.17 3.25 - pair_coeff @atom:685_b045_a045_d045_i045 @atom:685_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:686_b045_a045_d045_i045 @atom:686_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:687_b049_a049_d049_i049 @atom:687_b049_a049_d049_i049 0.03 2.42 - pair_coeff @atom:688_b013_a013_d013_i013 @atom:688_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:689_b013_a013_d013_i013 @atom:689_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:690_b101_a101_d101_i101 @atom:690_b101_a101_d101_i101 0.17 3.25 - pair_coeff @atom:691_b056_a056_d056_i056 @atom:691_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:692_b101_a101_d101_i101 @atom:692_b101_a101_d101_i101 0.17 3.25 - pair_coeff @atom:693_b048_a048_d048_i048 @atom:693_b048_a048_d048_i048 0.05 3.55 - pair_coeff @atom:694_b018_a018_d018_i018 @atom:694_b018_a018_d018_i018 0.17 3.2 - pair_coeff @atom:695_b019_a019_d019_i019 @atom:695_b019_a019_d019_i019 0.066 3.3 - pair_coeff @atom:696_b013_a013_d013_i013 @atom:696_b013_a013_d013_i013 0.066 3.3 - pair_coeff @atom:697_b013_a013_d013_i013 @atom:697_b013_a013_d013_i013 0.066 3.3 - pair_coeff @atom:698_b013_a013_d013_i013 @atom:698_b013_a013_d013_i013 0.066 3.3 - pair_coeff @atom:699_b013_a013_d013_i013 @atom:699_b013_a013_d013_i013 0.066 3.3 - pair_coeff @atom:700_b046_a046_d046_i046 @atom:700_b046_a046_d046_i046 0.015 2.5 - pair_coeff @atom:701_b102_a102_d102_i102 @atom:701_b102_a102_d102_i102 0.12 3.25 - pair_coeff @atom:702_b103_a103_d103_i103 @atom:702_b103_a103_d103_i103 0.17 2.96 - pair_coeff @atom:703_b013_a013_d013_i013 @atom:703_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:704_b046_a046_d046_i046 @atom:704_b046_a046_d046_i046 0.015 2.5 - pair_coeff @atom:705_b013_a013_d013_i013 @atom:705_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:706_b013_a013_d013_i013 @atom:706_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:707_b013_a013_d013_i013 @atom:707_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:708_b102_a102_d102_i102 @atom:708_b102_a102_d102_i102 0.12 3.25 - pair_coeff @atom:709_b048_a048_d048_i048 @atom:709_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:710_b013_a013_d013_i013 @atom:710_b013_a013_d013_i013 0.066 3.3 - pair_coeff @atom:711_b056_a056_d056_i056 @atom:711_b056_a056_d056_i056 0.17 3.25 - pair_coeff @atom:712_b004_a004_d004_i004 @atom:712_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:713_b003_a003_d003_i003 @atom:713_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:714_b020_a020_d020_i020 @atom:714_b020_a020_d020_i020 0.17 3.0 - pair_coeff @atom:715_b013_a013_d013_i013 @atom:715_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:716_b013_a013_d013_i013 @atom:716_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:717_b013_a013_d013_i013 @atom:717_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:718_b046_a046_d046_i046 @atom:718_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:719_b046_a046_d046_i046 @atom:719_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:720_b046_a046_d046_i046 @atom:720_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:721_b020_a020_d020_i020 @atom:721_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:722_b104_a104_d104_i104 @atom:722_b104_a104_d104_i104 0.2 3.74 - pair_coeff @atom:723_b013_a013_d013_i013 @atom:723_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:724_b013_a013_d013_i013 @atom:724_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:725_b046_a046_d046_i046 @atom:725_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:726_b064_a064_d064_i064 @atom:726_b064_a064_d064_i064 0.2 3.74 - pair_coeff @atom:727_b001_a001_d001_i001 @atom:727_b001_a001_d001_i001 0.061 3.1181 - pair_coeff @atom:728_b024_a024_d024_i024 @atom:728_b024_a024_d024_i024 0.17 3.15 - pair_coeff @atom:729_b004_a004_d004_i004 @atom:729_b004_a004_d004_i004 0.21 2.86 - pair_coeff @atom:730_b044_a044_d044_i044 @atom:730_b044_a044_d044_i044 0.17 3.3 - pair_coeff @atom:731_b044_a044_d044_i044 @atom:731_b044_a044_d044_i044 0.17 3.3 - pair_coeff @atom:732_b044_a044_d044_i044 @atom:732_b044_a044_d044_i044 0.17 3.3 - pair_coeff @atom:733_b013_a013_d013_i013 @atom:733_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:734_b013_a013_d013_i013 @atom:734_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:735_b013_a013_d013_i013 @atom:735_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:736_b013_a013_d013_i013 @atom:736_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:737_b013_a013_d013_i013 @atom:737_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:738_b013_a013_d013_i013 @atom:738_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:739_b045_a045_d045_i045 @atom:739_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:740_b045_a045_d045_i045 @atom:740_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:741_b046_a046_d046_i046 @atom:741_b046_a046_d046_i046 0.015 2.5 - pair_coeff @atom:742_b013_a013_d013_i013 @atom:742_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:743_b013_a013_d013_i013 @atom:743_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:744_b013_a013_d013_i013 @atom:744_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:745_b013_a013_d013_i013 @atom:745_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:746_b048_a048_d048_i048 @atom:746_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:747_b048_a048_d048_i048 @atom:747_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:748_b048_a048_d048_i048 @atom:748_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:749_b013_a013_d013_i013 @atom:749_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:750_b013_a013_d013_i013 @atom:750_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:751_b013_a013_d013_i013 @atom:751_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:752_b013_a013_d013_i013 @atom:752_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:753_b013_a013_d013_i013 @atom:753_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:754_b013_a013_d013_i013 @atom:754_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:755_b019_a019_d019_i019 @atom:755_b019_a019_d019_i019 0.086 3.3 - pair_coeff @atom:756_b046_a046_d046_i046 @atom:756_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:757_b019_a019_d019_i019 @atom:757_b019_a019_d019_i019 0.21 3.3 - pair_coeff @atom:758_b019_a019_d019_i019 @atom:758_b019_a019_d019_i019 0.135 3.3 - pair_coeff @atom:759_b019_a019_d019_i019 @atom:759_b019_a019_d019_i019 0.1 3.3 - pair_coeff @atom:760_b046_a046_d046_i046 @atom:760_b046_a046_d046_i046 0.015 2.5 - pair_coeff @atom:761_b051_a051_d051_i051 @atom:761_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:762_b051_a051_d051_i051 @atom:762_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:763_b051_a051_d051_i051 @atom:763_b051_a051_d051_i051 0.066 3.5 - pair_coeff @atom:764_b005_a005_d005_i005 @atom:764_b005_a005_d005_i005 0.17 3.12 - pair_coeff @atom:765_b007_a007_d007_i007 @atom:765_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:766_b105_a105_d105_i105 @atom:766_b105_a105_d105_i105 0.17 3.25 - pair_coeff @atom:767_b105_a105_d105_i105 @atom:767_b105_a105_d105_i105 0.17 3.25 - pair_coeff @atom:768_b105_a105_d105_i105 @atom:768_b105_a105_d105_i105 0.17 3.25 - pair_coeff @atom:769_b019_a019_d019_i019 @atom:769_b019_a019_d019_i019 0.21 3.3 - pair_coeff @atom:770_b053_a053_d053_i053 @atom:770_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:771_b054_a054_d054_i054 @atom:771_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:772_b013_a013_d013_i013 @atom:772_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:773_b013_a013_d013_i013 @atom:773_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:774_b013_a013_d013_i013 @atom:774_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:775_b013_a013_d013_i013 @atom:775_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:776_b084_a084_d084_i084 @atom:776_b084_a084_d084_i084 0.07 3.55 - pair_coeff @atom:777_b087_a087_d087_i087 @atom:777_b087_a087_d087_i087 0.076 3.55 - pair_coeff @atom:778_b086_a086_d086_i086 @atom:778_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:779_b086_a086_d086_i086 @atom:779_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:780_b046_a046_d046_i046 @atom:780_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:781_b013_a013_d013_i013 @atom:781_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:782_b003_a003_d003_i003 @atom:782_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:783_b053_a053_d053_i053 @atom:783_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:784_b052_a052_d052_i052 @atom:784_b052_a052_d052_i052 0.21 2.96 - pair_coeff @atom:785_b054_a054_d054_i054 @atom:785_b054_a054_d054_i054 0.0 0.0 - pair_coeff @atom:786_b001_a001_d001_i001 @atom:786_b001_a001_d001_i001 0.061 2.94 - pair_coeff @atom:787_b013_a013_d013_i013 @atom:787_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:788_b046_a046_d046_i046 @atom:788_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:789_b013_a013_d013_i013 @atom:789_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:790_b013_a013_d013_i013 @atom:790_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:791_b013_a013_d013_i013 @atom:791_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:792_b013_a013_d013_i013 @atom:792_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:793_b013_a013_d013_i013 @atom:793_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:794_b013_a013_d013_i013 @atom:794_b013_a013_d013_i013 0.097 3.5 - pair_coeff @atom:795_b001_a001_d001_i001 @atom:795_b001_a001_d001_i001 0.053 2.95 - pair_coeff @atom:796_b013_a013_d013_i013 @atom:796_b013_a013_d013_i013 0.062 3.25 - pair_coeff @atom:797_b046_a046_d046_i046 @atom:797_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:798_b013_a013_d013_i013 @atom:798_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:799_b013_a013_d013_i013 @atom:799_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:800_b021_a021_d021_i021 @atom:800_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:801_b013_a013_d013_i013 @atom:801_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:802_b046_a046_d046_i046 @atom:802_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:803_b013_a013_d013_i013 @atom:803_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:804_b013_a013_d013_i013 @atom:804_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:805_b065_a065_d065_i065 @atom:805_b065_a065_d065_i065 0.47 3.47 - pair_coeff @atom:806_b013_a013_d013_i013 @atom:806_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:807_b046_a046_d046_i046 @atom:807_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:808_b013_a013_d013_i013 @atom:808_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:809_b013_a013_d013_i013 @atom:809_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:810_b001_a001_d001_i001 @atom:810_b001_a001_d001_i001 0.061 2.94 - pair_coeff @atom:811_b021_a021_d021_i021 @atom:811_b021_a021_d021_i021 0.3 3.4 - pair_coeff @atom:812_b065_a065_d065_i065 @atom:812_b065_a065_d065_i065 0.47 3.47 - pair_coeff @atom:813_b048_a048_d048_i048 @atom:813_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:814_b020_a020_d020_i020 @atom:814_b020_a020_d020_i020 0.14 2.9 - pair_coeff @atom:815_b013_a013_d013_i013 @atom:815_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:816_b001_a001_d001_i001 @atom:816_b001_a001_d001_i001 0.06 2.9 - pair_coeff @atom:817_b024_a024_d024_i024 @atom:817_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:818_b048_a048_d048_i048 @atom:818_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:819_b013_a013_d013_i013 @atom:819_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:820_b003_a003_d003_i003 @atom:820_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:821_b003_a003_d003_i003 @atom:821_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:822_b004_a004_d004_i004 @atom:822_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:823_b024_a024_d024_i024 @atom:823_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:824_b045_a045_d045_i045 @atom:824_b045_a045_d045_i045 0.0 0.0 - pair_coeff @atom:825_b005_a005_d005_i005 @atom:825_b005_a005_d005_i005 0.17 3.12 - pair_coeff @atom:826_b007_a007_d007_i007 @atom:826_b007_a007_d007_i007 0.0 0.0 - pair_coeff @atom:827_b013_a013_d013_i013 @atom:827_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:828_b013_a013_d013_i013 @atom:828_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:829_b086_a086_d086_i086 @atom:829_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:830_b086_a086_d086_i086 @atom:830_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:831_b086_a086_d086_i086 @atom:831_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:832_b086_a086_d086_i086 @atom:832_b086_a086_d086_i086 0.07 3.55 - pair_coeff @atom:833_b048_a048_d048_i048 @atom:833_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:834_b106_a106_d106_i106 @atom:834_b106_a106_d106_i106 0.0125 1.96 - pair_coeff @atom:835_b013_a013_d013_i013 @atom:835_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:836_b013_a013_d013_i013 @atom:836_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:837_b013_a013_d013_i013 @atom:837_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:838_b066_a066_d066_i066 @atom:838_b066_a066_d066_i066 0.6 3.75 - pair_coeff @atom:839_b046_a046_d046_i046 @atom:839_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:840_b024_a024_d024_i024 @atom:840_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:841_b048_a048_d048_i048 @atom:841_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:842_b048_a048_d048_i048 @atom:842_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:843_b024_a024_d024_i024 @atom:843_b024_a024_d024_i024 0.17 3.25 - pair_coeff @atom:844_b048_a048_d048_i048 @atom:844_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:845_b003_a003_d003_i003 @atom:845_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:846_b004_a004_d004_i004 @atom:846_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:847_b107_a107_d107_i107 @atom:847_b107_a107_d107_i107 0.17 3.25 - pair_coeff @atom:848_b013_a013_d013_i013 @atom:848_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:849_b013_a013_d013_i013 @atom:849_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:850_b013_a013_d013_i013 @atom:850_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:851_b013_a013_d013_i013 @atom:851_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:852_b046_a046_d046_i046 @atom:852_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:853_b003_a003_d003_i003 @atom:853_b003_a003_d003_i003 0.105 3.75 - pair_coeff @atom:854_b004_a004_d004_i004 @atom:854_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:855_b046_a046_d046_i046 @atom:855_b046_a046_d046_i046 0.015 2.42 - pair_coeff @atom:856_b013_a013_d013_i013 @atom:856_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:857_b013_a013_d013_i013 @atom:857_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:858_b013_a013_d013_i013 @atom:858_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:859_b013_a013_d013_i013 @atom:859_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:860_b013_a013_d013_i013 @atom:860_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:861_b013_a013_d013_i013 @atom:861_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:862_b013_a013_d013_i013 @atom:862_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:863_b013_a013_d013_i013 @atom:863_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:864_b013_a013_d013_i013 @atom:864_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:865_b013_a013_d013_i013 @atom:865_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:866_b108_a108_d108_i108 @atom:866_b108_a108_d108_i108 0.1 4.0 - pair_coeff @atom:867_b108_a108_d108_i108 @atom:867_b108_a108_d108_i108 0.1 4.0 - pair_coeff @atom:868_b108_a108_d108_i108 @atom:868_b108_a108_d108_i108 0.1 4.0 - pair_coeff @atom:869_b108_a108_d108_i108 @atom:869_b108_a108_d108_i108 0.1 4.0 - pair_coeff @atom:870_b045_a045_d045_i045 @atom:870_b045_a045_d045_i045 0.03 2.5 - pair_coeff @atom:871_b013_a013_d013_i013 @atom:871_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:872_b013_a013_d013_i013 @atom:872_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:873_b013_a013_d013_i013 @atom:873_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:874_b013_a013_d013_i013 @atom:874_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:875_b001_a001_d001_i001 @atom:875_b001_a001_d001_i001 0.72 3.08 - pair_coeff @atom:876_b021_a021_d021_i021 @atom:876_b021_a021_d021_i021 0.11779 4.18 - pair_coeff @atom:877_b065_a065_d065_i065 @atom:877_b065_a065_d065_i065 0.09 4.51 - pair_coeff @atom:878_b066_a066_d066_i066 @atom:878_b066_a066_d066_i066 0.07 5.15 - pair_coeff @atom:879_b068_a068_d068_i068 @atom:879_b068_a068_d068_i068 0.018279 2.7 - pair_coeff @atom:880_b069_a069_d069_i069 @atom:880_b069_a069_d069_i069 0.002772 3.35 - pair_coeff @atom:881_b070_a070_d070_i070 @atom:881_b070_a070_d070_i070 0.000328 4.06 - pair_coeff @atom:882_b071_a071_d071_i071 @atom:882_b071_a071_d071_i071 0.000171 4.32 - pair_coeff @atom:883_b072_a072_d072_i072 @atom:883_b072_a072_d072_i072 8.1e-05 4.82 - pair_coeff @atom:884_b073_a073_d073_i073 @atom:884_b073_a073_d073_i073 0.875044 2.91 - pair_coeff @atom:885_b074_a074_d074_i074 @atom:885_b074_a074_d074_i074 0.449657 3.47 - pair_coeff @atom:886_b075_a075_d075_i075 @atom:886_b075_a075_d075_i075 0.118226 3.82 - pair_coeff @atom:887_b076_a076_d076_i076 @atom:887_b076_a076_d076_i076 0.047096 4.18 - pair_coeff @atom:888_b013_a013_d013_i013 @atom:888_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:889_b013_a013_d013_i013 @atom:889_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:890_b013_a013_d013_i013 @atom:890_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:891_b013_a013_d013_i013 @atom:891_b013_a013_d013_i013 0.066 3.5 - pair_coeff @atom:892_b046_a046_d046_i046 @atom:892_b046_a046_d046_i046 0.03 2.5 - pair_coeff @atom:893_b053_a053_d053_i053 @atom:893_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:894_b048_a048_d048_i048 @atom:894_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:895_b053_a053_d053_i053 @atom:895_b053_a053_d053_i053 0.17 3.25 - pair_coeff @atom:896_b048_a048_d048_i048 @atom:896_b048_a048_d048_i048 0.07 3.55 - pair_coeff @atom:897_b109_a109_d109_i109 @atom:897_b109_a109_d109_i109 0.076 3.55 - pair_coeff @atom:898_b109_a109_d109_i109 @atom:898_b109_a109_d109_i109 0.076 3.55 - pair_coeff @atom:899_b046_a046_d046_i046 @atom:899_b046_a046_d046_i046 0.03 2.42 - pair_coeff @atom:900_b047_a047_d047_i047 @atom:900_b047_a047_d047_i047 0.086 3.3 - pair_coeff @atom:901_b047_a047_d047_i047 @atom:901_b047_a047_d047_i047 0.086 3.3 - pair_coeff @atom:902_b047_a047_d047_i047 @atom:902_b047_a047_d047_i047 0.086 3.3 - pair_coeff @atom:903_b110_a110_d110_i110 @atom:903_b110_a110_d110_i110 0.086 3.3 - pair_coeff @atom:904_b110_a110_d110_i110 @atom:904_b110_a110_d110_i110 0.086 3.3 - pair_coeff @atom:905_b004_a004_d004_i004 @atom:905_b004_a004_d004_i004 0.21 2.96 - pair_coeff @atom:906_b013_a013_d013_i013 @atom:906_b013_a013_d013_i013 0.066 3.5 - } #(end of pair_coeffs) - - - - # ------- Bonded Interactions: ------- - # http://lammps.sandia.gov/doc/bond_harmonic.html - # Syntax: - # bond_coeff BondTypeName parameters... - - write_once("In Settings") { - bond_coeff @bond:001_002 367.0 1.38 - bond_coeff @bond:001_003 420.0 1.357 - bond_coeff @bond:001_013 367.0 1.36 - bond_coeff @bond:001_019 450.0 1.279 - bond_coeff @bond:001_025 300.0 0.3 - bond_coeff @bond:001_047 420.0 1.34 - bond_coeff @bond:001_048 420.0 1.354 - bond_coeff @bond:001_082 420.0 1.354 - bond_coeff @bond:001_083 420.0 1.354 - bond_coeff @bond:001_084 420.0 1.354 - bond_coeff @bond:001_087 420.0 1.354 - bond_coeff @bond:001_088 420.0 1.354 - bond_coeff @bond:001_108 461.0 1.57 - bond_coeff @bond:002_002 260.0 1.526 - bond_coeff @bond:002_003 317.0 1.522 - bond_coeff @bond:002_005 386.0 1.425 - bond_coeff @bond:002_006 260.0 1.526 - bond_coeff @bond:002_010 260.0 1.526 - bond_coeff @bond:002_011 317.0 1.5 - bond_coeff @bond:002_012 317.0 1.51 - bond_coeff @bond:002_013 260.0 1.526 - bond_coeff @bond:002_014 317.0 1.5 - bond_coeff @bond:002_015 222.0 1.81 - bond_coeff @bond:002_016 222.0 1.81 - bond_coeff @bond:002_020 320.0 1.425 - bond_coeff @bond:002_024 337.0 1.449 - bond_coeff @bond:002_044 382.0 1.448 - bond_coeff @bond:002_048 317.0 1.51 - bond_coeff @bond:002_051 260.0 1.526 - bond_coeff @bond:002_053 367.0 1.471 - bond_coeff @bond:002_055 337.0 1.463 - bond_coeff @bond:002_080 317.0 1.495 - bond_coeff @bond:003_003 350.0 1.51 - bond_coeff @bond:003_004 570.0 1.229 - bond_coeff @bond:003_005 450.0 1.364 - bond_coeff @bond:003_006 317.0 1.522 - bond_coeff @bond:003_010 317.0 1.522 - bond_coeff @bond:003_012 469.0 1.4 - bond_coeff @bond:003_013 317.0 1.522 - bond_coeff @bond:003_019 400.0 1.444 - bond_coeff @bond:003_020 214.0 1.327 - bond_coeff @bond:003_021 300.0 1.79 - bond_coeff @bond:003_024 490.0 1.335 - bond_coeff @bond:003_044 317.0 1.522 - bond_coeff @bond:003_046 340.0 1.09 - bond_coeff @bond:003_047 410.0 1.444 - bond_coeff @bond:003_048 400.0 1.49 - bond_coeff @bond:003_050 385.0 1.46 - bond_coeff @bond:003_052 656.0 1.25 - bond_coeff @bond:003_056 457.0 1.358 - bond_coeff @bond:003_057 418.0 1.388 - bond_coeff @bond:003_060 447.0 1.419 - bond_coeff @bond:003_065 300.0 1.98 - bond_coeff @bond:003_084 400.0 1.49 - bond_coeff @bond:003_086 385.0 1.46 - bond_coeff @bond:003_105 424.0 1.383 - bond_coeff @bond:003_107 490.0 1.335 - bond_coeff @bond:004_025 553.0 0.3 - bond_coeff @bond:004_064 525.0 1.48 - bond_coeff @bond:004_089 570.0 1.229 - bond_coeff @bond:004_110 700.0 1.171 - bond_coeff @bond:005_006 386.0 1.425 - bond_coeff @bond:005_007 553.0 0.945 - bond_coeff @bond:005_010 386.0 1.425 - bond_coeff @bond:005_013 320.0 1.41 - bond_coeff @bond:005_020 250.0 1.47 - bond_coeff @bond:005_024 400.0 1.38 - bond_coeff @bond:005_025 340.0 0.3 - bond_coeff @bond:005_044 320.0 1.45 - bond_coeff @bond:005_047 450.0 1.37 - bond_coeff @bond:005_048 450.0 1.364 - bond_coeff @bond:005_051 320.0 1.38 - bond_coeff @bond:005_064 230.0 1.61 - bond_coeff @bond:005_079 450.0 1.67 - bond_coeff @bond:005_106 94.0 1.8 - bond_coeff @bond:005_108 374.0 1.64 - bond_coeff @bond:006_006 260.0 1.526 - bond_coeff @bond:006_010 260.0 1.526 - bond_coeff @bond:006_011 317.0 1.5 - bond_coeff @bond:006_013 260.0 1.526 - bond_coeff @bond:006_014 317.0 1.5 - bond_coeff @bond:006_015 222.0 1.81 - bond_coeff @bond:006_016 222.0 1.81 - bond_coeff @bond:006_020 320.0 1.425 - bond_coeff @bond:006_024 337.0 1.449 - bond_coeff @bond:006_044 382.0 1.448 - bond_coeff @bond:006_047 317.0 1.51 - bond_coeff @bond:006_051 260.0 1.526 - bond_coeff @bond:006_053 367.0 1.471 - bond_coeff @bond:006_055 337.0 1.463 - bond_coeff @bond:006_079 222.0 1.81 - bond_coeff @bond:006_105 337.0 1.475 - bond_coeff @bond:007_020 553.0 0.945 - bond_coeff @bond:007_025 340.0 0.1 - bond_coeff @bond:009_009 530.0 1.34 - bond_coeff @bond:009_011 530.0 1.34 - bond_coeff @bond:009_014 530.0 1.34 - bond_coeff @bond:010_010 260.0 1.526 - bond_coeff @bond:010_011 317.0 1.5 - bond_coeff @bond:010_014 317.0 1.5 - bond_coeff @bond:010_020 320.0 1.425 - bond_coeff @bond:010_024 337.0 1.449 - bond_coeff @bond:010_044 382.0 1.448 - bond_coeff @bond:010_105 337.0 1.475 - bond_coeff @bond:011_011 530.0 1.34 - bond_coeff @bond:011_013 317.0 1.5 - bond_coeff @bond:011_014 530.0 1.34 - bond_coeff @bond:011_079 222.0 1.76 - bond_coeff @bond:012_012 469.0 1.4 - bond_coeff @bond:012_048 469.0 1.4 - bond_coeff @bond:012_060 469.0 1.4 - bond_coeff @bond:012_081 469.0 1.4 - bond_coeff @bond:013_013 268.0 1.529 - bond_coeff @bond:013_014 317.0 1.5 - bond_coeff @bond:013_015 222.0 1.81 - bond_coeff @bond:013_016 222.0 1.81 - bond_coeff @bond:013_018 390.0 1.43 - bond_coeff @bond:013_019 390.0 1.47 - bond_coeff @bond:013_020 320.0 1.41 - bond_coeff @bond:013_021 245.0 1.781 - bond_coeff @bond:013_022 340.0 1.79 - bond_coeff @bond:013_024 337.0 1.449 - bond_coeff @bond:013_025 340.0 0.3 - bond_coeff @bond:013_044 382.0 1.448 - bond_coeff @bond:013_046 340.0 1.09 - bond_coeff @bond:013_047 317.0 1.51 - bond_coeff @bond:013_048 317.0 1.51 - bond_coeff @bond:013_050 317.0 1.51 - bond_coeff @bond:013_051 268.0 1.529 - bond_coeff @bond:013_053 367.0 1.471 - bond_coeff @bond:013_055 337.0 1.463 - bond_coeff @bond:013_056 337.0 1.449 - bond_coeff @bond:013_057 337.0 1.475 - bond_coeff @bond:013_060 317.0 1.51 - bond_coeff @bond:013_064 212.0 1.843 - bond_coeff @bond:013_065 245.0 1.945 - bond_coeff @bond:013_066 200.0 2.19 - bond_coeff @bond:013_079 340.0 1.77 - bond_coeff @bond:013_080 317.0 1.495 - bond_coeff @bond:013_083 317.0 1.504 - bond_coeff @bond:013_084 317.0 1.504 - bond_coeff @bond:013_085 317.0 1.504 - bond_coeff @bond:013_087 317.0 1.495 - bond_coeff @bond:013_090 337.0 1.449 - bond_coeff @bond:013_091 280.0 1.51 - bond_coeff @bond:013_095 532.8 1.46 - bond_coeff @bond:013_101 382.0 1.448 - bond_coeff @bond:013_102 375.0 1.49 - bond_coeff @bond:013_104 212.0 1.82 - bond_coeff @bond:013_105 337.0 1.475 - bond_coeff @bond:013_107 337.0 1.449 - bond_coeff @bond:013_108 187.0 1.86 - bond_coeff @bond:013_109 317.0 1.51 - bond_coeff @bond:014_014 530.0 1.34 - bond_coeff @bond:015_017 274.0 1.336 - bond_coeff @bond:015_048 250.0 1.74 - bond_coeff @bond:016_016 166.0 2.038 - bond_coeff @bond:016_019 300.0 1.685 - bond_coeff @bond:016_024 250.0 1.73 - bond_coeff @bond:016_025 340.0 0.5 - bond_coeff @bond:016_047 250.0 1.76 - bond_coeff @bond:016_048 250.0 1.76 - bond_coeff @bond:016_061 250.0 1.73 - bond_coeff @bond:016_082 250.0 1.76 - bond_coeff @bond:016_084 250.0 1.74 - bond_coeff @bond:016_091 222.0 1.81 - bond_coeff @bond:016_108 144.0 2.15 - bond_coeff @bond:017_025 340.0 0.1 - bond_coeff @bond:018_018 550.0 1.12 - bond_coeff @bond:018_019 650.0 1.157 - bond_coeff @bond:018_048 400.0 1.41 - bond_coeff @bond:018_056 550.0 1.24 - bond_coeff @bond:019_019 1150.0 1.21 - bond_coeff @bond:019_021 330.0 1.637 - bond_coeff @bond:019_046 420.0 1.08 - bond_coeff @bond:019_047 400.0 1.426 - bond_coeff @bond:019_048 400.0 1.451 - bond_coeff @bond:019_050 400.0 1.426 - bond_coeff @bond:019_065 330.0 1.784 - bond_coeff @bond:019_088 400.0 1.451 - bond_coeff @bond:019_091 400.0 1.451 - bond_coeff @bond:020_020 250.0 1.47 - bond_coeff @bond:020_021 200.0 1.69 - bond_coeff @bond:020_024 320.0 1.45 - bond_coeff @bond:020_025 340.0 0.3 - bond_coeff @bond:020_044 320.0 1.45 - bond_coeff @bond:020_047 450.0 1.37 - bond_coeff @bond:020_048 450.0 1.364 - bond_coeff @bond:020_051 320.0 1.38 - bond_coeff @bond:020_060 340.0 1.36 - bond_coeff @bond:020_061 462.0 1.399 - bond_coeff @bond:020_064 230.0 1.61 - bond_coeff @bond:020_082 462.0 1.357 - bond_coeff @bond:020_084 340.0 1.36 - bond_coeff @bond:020_108 374.0 1.64 - bond_coeff @bond:021_025 300.0 0.3 - bond_coeff @bond:021_047 300.0 1.725 - bond_coeff @bond:021_048 300.0 1.725 - bond_coeff @bond:021_082 300.0 1.725 - bond_coeff @bond:021_083 300.0 1.725 - bond_coeff @bond:021_084 300.0 1.725 - bond_coeff @bond:021_087 300.0 1.725 - bond_coeff @bond:021_088 300.0 1.725 - bond_coeff @bond:021_108 223.0 2.02 - bond_coeff @bond:022_023 700.0 1.53 - bond_coeff @bond:022_025 340.0 0.5 - bond_coeff @bond:023_025 340.0 0.3 - bond_coeff @bond:023_079 700.0 1.44 - bond_coeff @bond:024_025 367.0 0.3 - bond_coeff @bond:024_045 434.0 1.01 - bond_coeff @bond:024_048 427.0 1.381 - bond_coeff @bond:024_059 427.0 1.381 - bond_coeff @bond:024_079 434.0 1.67 - bond_coeff @bond:024_084 427.0 1.381 - bond_coeff @bond:024_088 427.0 1.381 - bond_coeff @bond:024_091 337.0 1.449 - bond_coeff @bond:024_103 500.0 1.27 - bond_coeff @bond:024_106 40.0 2.05 - bond_coeff @bond:025_025 340.0 0.3 - bond_coeff @bond:025_044 340.0 0.3 - bond_coeff @bond:025_045 340.0 0.1 - bond_coeff @bond:025_046 340.0 0.3 - bond_coeff @bond:025_047 340.0 0.3 - bond_coeff @bond:025_048 367.0 0.3 - bond_coeff @bond:025_049 340.0 0.3 - bond_coeff @bond:025_053 340.0 0.3 - bond_coeff @bond:025_056 367.0 0.3 - bond_coeff @bond:025_061 367.0 0.3 - bond_coeff @bond:025_065 300.0 0.3 - bond_coeff @bond:025_103 340.0 0.1 - bond_coeff @bond:031_032 600.0 0.9572 - bond_coeff @bond:031_033 900.0 0.15 - bond_coeff @bond:031_106 40.0 2.05 - bond_coeff @bond:034_035 529.6 0.9572 - bond_coeff @bond:036_037 600.0 0.9572 - bond_coeff @bond:036_038 900.0 0.175 - bond_coeff @bond:039_040 600.0 0.9572 - bond_coeff @bond:039_041 900.0 0.7 - bond_coeff @bond:042_043 600.0 1.0 - bond_coeff @bond:044_044 350.0 1.445 - bond_coeff @bond:044_045 434.0 1.01 - bond_coeff @bond:044_048 481.0 1.34 - bond_coeff @bond:044_079 340.0 1.77 - bond_coeff @bond:044_091 382.0 1.448 - bond_coeff @bond:044_108 266.0 1.74 - bond_coeff @bond:045_053 434.0 1.01 - bond_coeff @bond:045_055 434.0 1.01 - bond_coeff @bond:045_056 434.0 1.01 - bond_coeff @bond:045_057 434.0 1.01 - bond_coeff @bond:045_101 434.0 1.01 - bond_coeff @bond:045_105 434.0 1.01 - bond_coeff @bond:045_108 166.0 1.48 - bond_coeff @bond:046_047 340.0 1.08 - bond_coeff @bond:046_050 340.0 1.08 - bond_coeff @bond:046_051 340.0 1.09 - bond_coeff @bond:046_080 340.0 1.08 - bond_coeff @bond:046_091 340.0 1.088 - bond_coeff @bond:046_095 532.8 1.084 - bond_coeff @bond:046_108 166.0 1.48 - bond_coeff @bond:046_109 340.0 1.08 - bond_coeff @bond:047_047 549.0 1.34 - bond_coeff @bond:047_048 427.0 1.433 - bond_coeff @bond:047_050 549.0 1.34 - bond_coeff @bond:047_057 448.0 1.365 - bond_coeff @bond:047_058 367.0 1.08 - bond_coeff @bond:047_065 300.0 1.9 - bond_coeff @bond:047_066 250.0 2.08 - bond_coeff @bond:047_086 385.0 1.46 - bond_coeff @bond:047_091 317.0 1.51 - bond_coeff @bond:047_105 448.0 1.365 - bond_coeff @bond:047_110 700.0 1.305 - bond_coeff @bond:048_048 469.0 1.4 - bond_coeff @bond:048_049 367.0 1.08 - bond_coeff @bond:048_050 427.0 1.433 - bond_coeff @bond:048_053 400.0 1.45 - bond_coeff @bond:048_055 481.0 1.34 - bond_coeff @bond:048_056 483.0 1.339 - bond_coeff @bond:048_057 427.0 1.381 - bond_coeff @bond:048_060 469.0 1.404 - bond_coeff @bond:048_061 414.0 1.391 - bond_coeff @bond:048_064 220.0 1.78 - bond_coeff @bond:048_065 300.0 1.87 - bond_coeff @bond:048_066 250.0 2.08 - bond_coeff @bond:048_079 340.0 1.77 - bond_coeff @bond:048_081 469.0 1.4 - bond_coeff @bond:048_084 546.0 1.367 - bond_coeff @bond:048_086 469.0 1.4 - bond_coeff @bond:048_088 469.0 1.421 - bond_coeff @bond:048_091 317.0 1.49 - bond_coeff @bond:048_101 382.0 1.385 - bond_coeff @bond:048_102 400.0 1.46 - bond_coeff @bond:048_109 427.0 1.433 - bond_coeff @bond:049_059 367.0 1.08 - bond_coeff @bond:049_062 340.0 1.08 - bond_coeff @bond:049_082 367.0 1.08 - bond_coeff @bond:049_083 367.0 1.08 - bond_coeff @bond:049_084 367.0 1.08 - bond_coeff @bond:049_085 367.0 1.08 - bond_coeff @bond:049_087 367.0 1.08 - bond_coeff @bond:049_088 367.0 1.08 - bond_coeff @bond:050_050 385.0 1.46 - bond_coeff @bond:050_056 457.0 1.29 - bond_coeff @bond:050_084 549.0 1.365 - bond_coeff @bond:050_109 385.0 1.46 - bond_coeff @bond:051_105 337.0 1.475 - bond_coeff @bond:052_064 525.0 1.48 - bond_coeff @bond:053_054 434.0 1.01 - bond_coeff @bond:054_055 434.0 1.01 - bond_coeff @bond:055_059 481.0 1.34 - bond_coeff @bond:055_082 481.0 1.34 - bond_coeff @bond:056_056 500.0 1.32 - bond_coeff @bond:056_059 502.0 1.324 - bond_coeff @bond:056_060 461.0 1.354 - bond_coeff @bond:056_082 461.0 1.354 - bond_coeff @bond:056_086 483.0 1.339 - bond_coeff @bond:056_103 550.0 1.21 - bond_coeff @bond:056_109 457.0 1.29 - bond_coeff @bond:057_060 436.0 1.374 - bond_coeff @bond:057_061 400.0 1.349 - bond_coeff @bond:057_062 440.0 1.371 - bond_coeff @bond:057_081 428.0 1.38 - bond_coeff @bond:057_082 477.0 1.343 - bond_coeff @bond:057_084 427.0 1.381 - bond_coeff @bond:057_085 427.0 1.381 - bond_coeff @bond:057_086 385.0 1.44 - bond_coeff @bond:058_083 367.0 1.08 - bond_coeff @bond:058_084 367.0 1.08 - bond_coeff @bond:059_063 367.0 1.08 - bond_coeff @bond:060_060 520.0 1.37 - bond_coeff @bond:060_061 414.0 1.391 - bond_coeff @bond:060_080 388.0 1.459 - bond_coeff @bond:060_081 447.0 1.419 - bond_coeff @bond:060_087 469.0 1.424 - bond_coeff @bond:060_105 436.0 1.374 - bond_coeff @bond:061_061 400.0 1.28 - bond_coeff @bond:061_062 529.0 1.304 - bond_coeff @bond:061_082 488.0 1.335 - bond_coeff @bond:061_083 410.0 1.394 - bond_coeff @bond:061_084 410.0 1.394 - bond_coeff @bond:061_088 410.0 1.32 - bond_coeff @bond:062_063 367.0 1.08 - bond_coeff @bond:062_105 440.0 1.371 - bond_coeff @bond:063_082 367.0 1.08 - bond_coeff @bond:064_108 108.0 2.25 - bond_coeff @bond:065_082 300.0 1.87 - bond_coeff @bond:065_083 300.0 1.87 - bond_coeff @bond:065_084 300.0 1.87 - bond_coeff @bond:065_087 300.0 1.87 - bond_coeff @bond:065_088 300.0 1.87 - bond_coeff @bond:065_108 151.0 2.19 - bond_coeff @bond:066_082 250.0 2.08 - bond_coeff @bond:066_083 250.0 2.08 - bond_coeff @bond:066_084 250.0 2.08 - bond_coeff @bond:066_087 250.0 2.08 - bond_coeff @bond:066_088 250.0 2.08 - bond_coeff @bond:066_108 108.0 2.44 - bond_coeff @bond:077_078 500.0 1.8 - bond_coeff @bond:080_084 546.0 1.352 - bond_coeff @bond:082_086 385.0 1.46 - bond_coeff @bond:082_087 520.0 1.37 - bond_coeff @bond:083_084 520.0 1.37 - bond_coeff @bond:083_086 385.0 1.46 - bond_coeff @bond:084_084 512.0 1.375 - bond_coeff @bond:084_086 385.0 1.46 - bond_coeff @bond:084_087 546.0 1.367 - bond_coeff @bond:084_088 520.0 1.37 - bond_coeff @bond:085_085 520.0 1.37 - bond_coeff @bond:086_086 385.0 1.46 - bond_coeff @bond:086_087 385.0 1.46 - bond_coeff @bond:086_088 385.0 1.46 - bond_coeff @bond:087_087 469.0 1.424 - bond_coeff @bond:087_088 469.0 1.424 - bond_coeff @bond:089_090 490.0 1.335 - bond_coeff @bond:089_091 317.0 1.522 - bond_coeff @bond:090_091 337.0 1.449 - bond_coeff @bond:091_091 260.0 1.52 - bond_coeff @bond:102_103 550.0 1.225 - bond_coeff @bond:108_108 94.0 2.32 - bond_coeff @bond:109_109 549.0 1.345 - } #(end of bond_coeffs) - - # Rules for assigning bond types by atom type: - # BondTypeName AtomType1 AtomType2 - # (* = wildcard) - - write_once("Data Bonds By Type") { - @bond:001_002 @atom:*_b001*_a*_d*_i* @atom:*_b002*_a*_d*_i* - @bond:001_003 @atom:*_b001*_a*_d*_i* @atom:*_b003*_a*_d*_i* - @bond:001_013 @atom:*_b001*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:001_019 @atom:*_b001*_a*_d*_i* @atom:*_b019*_a*_d*_i* - @bond:001_025 @atom:*_b001*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:001_047 @atom:*_b001*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:001_048 @atom:*_b001*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:001_082 @atom:*_b001*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:001_083 @atom:*_b001*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:001_084 @atom:*_b001*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:001_087 @atom:*_b001*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:001_088 @atom:*_b001*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:001_108 @atom:*_b001*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:002_002 @atom:*_b002*_a*_d*_i* @atom:*_b002*_a*_d*_i* - @bond:002_003 @atom:*_b002*_a*_d*_i* @atom:*_b003*_a*_d*_i* - @bond:002_005 @atom:*_b002*_a*_d*_i* @atom:*_b005*_a*_d*_i* - @bond:002_006 @atom:*_b002*_a*_d*_i* @atom:*_b006*_a*_d*_i* - @bond:002_010 @atom:*_b002*_a*_d*_i* @atom:*_b010*_a*_d*_i* - @bond:002_011 @atom:*_b002*_a*_d*_i* @atom:*_b011*_a*_d*_i* - @bond:002_012 @atom:*_b002*_a*_d*_i* @atom:*_b012*_a*_d*_i* - @bond:002_013 @atom:*_b002*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:002_014 @atom:*_b002*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:002_015 @atom:*_b002*_a*_d*_i* @atom:*_b015*_a*_d*_i* - @bond:002_016 @atom:*_b002*_a*_d*_i* @atom:*_b016*_a*_d*_i* - @bond:002_020 @atom:*_b002*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:002_024 @atom:*_b002*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:002_044 @atom:*_b002*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:002_048 @atom:*_b002*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:002_051 @atom:*_b002*_a*_d*_i* @atom:*_b051*_a*_d*_i* - @bond:002_053 @atom:*_b002*_a*_d*_i* @atom:*_b053*_a*_d*_i* - @bond:002_055 @atom:*_b002*_a*_d*_i* @atom:*_b055*_a*_d*_i* - @bond:002_080 @atom:*_b002*_a*_d*_i* @atom:*_b080*_a*_d*_i* - @bond:003_003 @atom:*_b003*_a*_d*_i* @atom:*_b003*_a*_d*_i* - @bond:003_004 @atom:*_b003*_a*_d*_i* @atom:*_b004*_a*_d*_i* - @bond:003_005 @atom:*_b003*_a*_d*_i* @atom:*_b005*_a*_d*_i* - @bond:003_006 @atom:*_b003*_a*_d*_i* @atom:*_b006*_a*_d*_i* - @bond:003_010 @atom:*_b003*_a*_d*_i* @atom:*_b010*_a*_d*_i* - @bond:003_012 @atom:*_b003*_a*_d*_i* @atom:*_b012*_a*_d*_i* - @bond:003_013 @atom:*_b003*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:003_019 @atom:*_b003*_a*_d*_i* @atom:*_b019*_a*_d*_i* - @bond:003_020 @atom:*_b003*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:003_021 @atom:*_b003*_a*_d*_i* @atom:*_b021*_a*_d*_i* - @bond:003_024 @atom:*_b003*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:003_044 @atom:*_b003*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:003_046 @atom:*_b003*_a*_d*_i* @atom:*_b046*_a*_d*_i* - @bond:003_047 @atom:*_b003*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:003_048 @atom:*_b003*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:003_050 @atom:*_b003*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:003_052 @atom:*_b003*_a*_d*_i* @atom:*_b052*_a*_d*_i* - @bond:003_056 @atom:*_b003*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:003_057 @atom:*_b003*_a*_d*_i* @atom:*_b057*_a*_d*_i* - @bond:003_060 @atom:*_b003*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:003_065 @atom:*_b003*_a*_d*_i* @atom:*_b065*_a*_d*_i* - @bond:003_084 @atom:*_b003*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:003_086 @atom:*_b003*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:003_105 @atom:*_b003*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:003_107 @atom:*_b003*_a*_d*_i* @atom:*_b107*_a*_d*_i* - @bond:004_025 @atom:*_b004*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:004_064 @atom:*_b004*_a*_d*_i* @atom:*_b064*_a*_d*_i* - @bond:004_089 @atom:*_b004*_a*_d*_i* @atom:*_b089*_a*_d*_i* - @bond:004_110 @atom:*_b004*_a*_d*_i* @atom:*_b110*_a*_d*_i* - @bond:005_006 @atom:*_b005*_a*_d*_i* @atom:*_b006*_a*_d*_i* - @bond:005_007 @atom:*_b005*_a*_d*_i* @atom:*_b007*_a*_d*_i* - @bond:005_010 @atom:*_b005*_a*_d*_i* @atom:*_b010*_a*_d*_i* - @bond:005_013 @atom:*_b005*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:005_020 @atom:*_b005*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:005_024 @atom:*_b005*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:005_025 @atom:*_b005*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:005_044 @atom:*_b005*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:005_047 @atom:*_b005*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:005_048 @atom:*_b005*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:005_051 @atom:*_b005*_a*_d*_i* @atom:*_b051*_a*_d*_i* - @bond:005_064 @atom:*_b005*_a*_d*_i* @atom:*_b064*_a*_d*_i* - @bond:005_079 @atom:*_b005*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:005_106 @atom:*_b005*_a*_d*_i* @atom:*_b106*_a*_d*_i* - @bond:005_108 @atom:*_b005*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:006_006 @atom:*_b006*_a*_d*_i* @atom:*_b006*_a*_d*_i* - @bond:006_010 @atom:*_b006*_a*_d*_i* @atom:*_b010*_a*_d*_i* - @bond:006_011 @atom:*_b006*_a*_d*_i* @atom:*_b011*_a*_d*_i* - @bond:006_013 @atom:*_b006*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:006_014 @atom:*_b006*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:006_015 @atom:*_b006*_a*_d*_i* @atom:*_b015*_a*_d*_i* - @bond:006_016 @atom:*_b006*_a*_d*_i* @atom:*_b016*_a*_d*_i* - @bond:006_020 @atom:*_b006*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:006_024 @atom:*_b006*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:006_044 @atom:*_b006*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:006_047 @atom:*_b006*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:006_051 @atom:*_b006*_a*_d*_i* @atom:*_b051*_a*_d*_i* - @bond:006_053 @atom:*_b006*_a*_d*_i* @atom:*_b053*_a*_d*_i* - @bond:006_055 @atom:*_b006*_a*_d*_i* @atom:*_b055*_a*_d*_i* - @bond:006_079 @atom:*_b006*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:006_105 @atom:*_b006*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:007_020 @atom:*_b007*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:007_025 @atom:*_b007*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:009_009 @atom:*_b009*_a*_d*_i* @atom:*_b009*_a*_d*_i* - @bond:009_011 @atom:*_b009*_a*_d*_i* @atom:*_b011*_a*_d*_i* - @bond:009_014 @atom:*_b009*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:010_010 @atom:*_b010*_a*_d*_i* @atom:*_b010*_a*_d*_i* - @bond:010_011 @atom:*_b010*_a*_d*_i* @atom:*_b011*_a*_d*_i* - @bond:010_014 @atom:*_b010*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:010_020 @atom:*_b010*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:010_024 @atom:*_b010*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:010_044 @atom:*_b010*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:010_105 @atom:*_b010*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:011_011 @atom:*_b011*_a*_d*_i* @atom:*_b011*_a*_d*_i* - @bond:011_013 @atom:*_b011*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:011_014 @atom:*_b011*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:011_079 @atom:*_b011*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:012_012 @atom:*_b012*_a*_d*_i* @atom:*_b012*_a*_d*_i* - @bond:012_048 @atom:*_b012*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:012_060 @atom:*_b012*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:012_081 @atom:*_b012*_a*_d*_i* @atom:*_b081*_a*_d*_i* - @bond:013_013 @atom:*_b013*_a*_d*_i* @atom:*_b013*_a*_d*_i* - @bond:013_014 @atom:*_b013*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:013_015 @atom:*_b013*_a*_d*_i* @atom:*_b015*_a*_d*_i* - @bond:013_016 @atom:*_b013*_a*_d*_i* @atom:*_b016*_a*_d*_i* - @bond:013_018 @atom:*_b013*_a*_d*_i* @atom:*_b018*_a*_d*_i* - @bond:013_019 @atom:*_b013*_a*_d*_i* @atom:*_b019*_a*_d*_i* - @bond:013_020 @atom:*_b013*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:013_021 @atom:*_b013*_a*_d*_i* @atom:*_b021*_a*_d*_i* - @bond:013_022 @atom:*_b013*_a*_d*_i* @atom:*_b022*_a*_d*_i* - @bond:013_024 @atom:*_b013*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:013_025 @atom:*_b013*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:013_044 @atom:*_b013*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:013_046 @atom:*_b013*_a*_d*_i* @atom:*_b046*_a*_d*_i* - @bond:013_047 @atom:*_b013*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:013_048 @atom:*_b013*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:013_050 @atom:*_b013*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:013_051 @atom:*_b013*_a*_d*_i* @atom:*_b051*_a*_d*_i* - @bond:013_053 @atom:*_b013*_a*_d*_i* @atom:*_b053*_a*_d*_i* - @bond:013_055 @atom:*_b013*_a*_d*_i* @atom:*_b055*_a*_d*_i* - @bond:013_056 @atom:*_b013*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:013_057 @atom:*_b013*_a*_d*_i* @atom:*_b057*_a*_d*_i* - @bond:013_060 @atom:*_b013*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:013_064 @atom:*_b013*_a*_d*_i* @atom:*_b064*_a*_d*_i* - @bond:013_065 @atom:*_b013*_a*_d*_i* @atom:*_b065*_a*_d*_i* - @bond:013_066 @atom:*_b013*_a*_d*_i* @atom:*_b066*_a*_d*_i* - @bond:013_079 @atom:*_b013*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:013_080 @atom:*_b013*_a*_d*_i* @atom:*_b080*_a*_d*_i* - @bond:013_083 @atom:*_b013*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:013_084 @atom:*_b013*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:013_085 @atom:*_b013*_a*_d*_i* @atom:*_b085*_a*_d*_i* - @bond:013_087 @atom:*_b013*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:013_090 @atom:*_b013*_a*_d*_i* @atom:*_b090*_a*_d*_i* - @bond:013_091 @atom:*_b013*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:013_095 @atom:*_b013*_a*_d*_i* @atom:*_b095*_a*_d*_i* - @bond:013_101 @atom:*_b013*_a*_d*_i* @atom:*_b101*_a*_d*_i* - @bond:013_102 @atom:*_b013*_a*_d*_i* @atom:*_b102*_a*_d*_i* - @bond:013_104 @atom:*_b013*_a*_d*_i* @atom:*_b104*_a*_d*_i* - @bond:013_105 @atom:*_b013*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:013_107 @atom:*_b013*_a*_d*_i* @atom:*_b107*_a*_d*_i* - @bond:013_108 @atom:*_b013*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:013_109 @atom:*_b013*_a*_d*_i* @atom:*_b109*_a*_d*_i* - @bond:014_014 @atom:*_b014*_a*_d*_i* @atom:*_b014*_a*_d*_i* - @bond:015_017 @atom:*_b015*_a*_d*_i* @atom:*_b017*_a*_d*_i* - @bond:015_048 @atom:*_b015*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:016_016 @atom:*_b016*_a*_d*_i* @atom:*_b016*_a*_d*_i* - @bond:016_019 @atom:*_b016*_a*_d*_i* @atom:*_b019*_a*_d*_i* - @bond:016_024 @atom:*_b016*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:016_025 @atom:*_b016*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:016_047 @atom:*_b016*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:016_048 @atom:*_b016*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:016_061 @atom:*_b016*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:016_082 @atom:*_b016*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:016_084 @atom:*_b016*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:016_091 @atom:*_b016*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:016_108 @atom:*_b016*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:017_025 @atom:*_b017*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:018_018 @atom:*_b018*_a*_d*_i* @atom:*_b018*_a*_d*_i* - @bond:018_019 @atom:*_b018*_a*_d*_i* @atom:*_b019*_a*_d*_i* - @bond:018_048 @atom:*_b018*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:018_056 @atom:*_b018*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:019_019 @atom:*_b019*_a*_d*_i* @atom:*_b019*_a*_d*_i* - @bond:019_021 @atom:*_b019*_a*_d*_i* @atom:*_b021*_a*_d*_i* - @bond:019_046 @atom:*_b019*_a*_d*_i* @atom:*_b046*_a*_d*_i* - @bond:019_047 @atom:*_b019*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:019_048 @atom:*_b019*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:019_050 @atom:*_b019*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:019_065 @atom:*_b019*_a*_d*_i* @atom:*_b065*_a*_d*_i* - @bond:019_088 @atom:*_b019*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:019_091 @atom:*_b019*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:020_020 @atom:*_b020*_a*_d*_i* @atom:*_b020*_a*_d*_i* - @bond:020_021 @atom:*_b020*_a*_d*_i* @atom:*_b021*_a*_d*_i* - @bond:020_024 @atom:*_b020*_a*_d*_i* @atom:*_b024*_a*_d*_i* - @bond:020_025 @atom:*_b020*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:020_044 @atom:*_b020*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:020_047 @atom:*_b020*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:020_048 @atom:*_b020*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:020_051 @atom:*_b020*_a*_d*_i* @atom:*_b051*_a*_d*_i* - @bond:020_060 @atom:*_b020*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:020_061 @atom:*_b020*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:020_064 @atom:*_b020*_a*_d*_i* @atom:*_b064*_a*_d*_i* - @bond:020_082 @atom:*_b020*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:020_084 @atom:*_b020*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:020_108 @atom:*_b020*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:021_025 @atom:*_b021*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:021_047 @atom:*_b021*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:021_048 @atom:*_b021*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:021_082 @atom:*_b021*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:021_083 @atom:*_b021*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:021_084 @atom:*_b021*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:021_087 @atom:*_b021*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:021_088 @atom:*_b021*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:021_108 @atom:*_b021*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:022_023 @atom:*_b022*_a*_d*_i* @atom:*_b023*_a*_d*_i* - @bond:022_025 @atom:*_b022*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:023_025 @atom:*_b023*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:023_079 @atom:*_b023*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:024_025 @atom:*_b024*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:024_045 @atom:*_b024*_a*_d*_i* @atom:*_b045*_a*_d*_i* - @bond:024_048 @atom:*_b024*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:024_059 @atom:*_b024*_a*_d*_i* @atom:*_b059*_a*_d*_i* - @bond:024_079 @atom:*_b024*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:024_084 @atom:*_b024*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:024_088 @atom:*_b024*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:024_091 @atom:*_b024*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:024_103 @atom:*_b024*_a*_d*_i* @atom:*_b103*_a*_d*_i* - @bond:024_106 @atom:*_b024*_a*_d*_i* @atom:*_b106*_a*_d*_i* - @bond:025_025 @atom:*_b025*_a*_d*_i* @atom:*_b025*_a*_d*_i* - @bond:025_044 @atom:*_b025*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:025_045 @atom:*_b025*_a*_d*_i* @atom:*_b045*_a*_d*_i* - @bond:025_046 @atom:*_b025*_a*_d*_i* @atom:*_b046*_a*_d*_i* - @bond:025_047 @atom:*_b025*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:025_048 @atom:*_b025*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:025_049 @atom:*_b025*_a*_d*_i* @atom:*_b049*_a*_d*_i* - @bond:025_053 @atom:*_b025*_a*_d*_i* @atom:*_b053*_a*_d*_i* - @bond:025_056 @atom:*_b025*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:025_061 @atom:*_b025*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:025_065 @atom:*_b025*_a*_d*_i* @atom:*_b065*_a*_d*_i* - @bond:025_103 @atom:*_b025*_a*_d*_i* @atom:*_b103*_a*_d*_i* - @bond:031_032 @atom:*_b031*_a*_d*_i* @atom:*_b032*_a*_d*_i* - @bond:031_033 @atom:*_b031*_a*_d*_i* @atom:*_b033*_a*_d*_i* - @bond:031_106 @atom:*_b031*_a*_d*_i* @atom:*_b106*_a*_d*_i* - @bond:034_035 @atom:*_b034*_a*_d*_i* @atom:*_b035*_a*_d*_i* - @bond:036_037 @atom:*_b036*_a*_d*_i* @atom:*_b037*_a*_d*_i* - @bond:036_038 @atom:*_b036*_a*_d*_i* @atom:*_b038*_a*_d*_i* - @bond:039_040 @atom:*_b039*_a*_d*_i* @atom:*_b040*_a*_d*_i* - @bond:039_041 @atom:*_b039*_a*_d*_i* @atom:*_b041*_a*_d*_i* - @bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i* - @bond:044_044 @atom:*_b044*_a*_d*_i* @atom:*_b044*_a*_d*_i* - @bond:044_045 @atom:*_b044*_a*_d*_i* @atom:*_b045*_a*_d*_i* - @bond:044_048 @atom:*_b044*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:044_079 @atom:*_b044*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:044_091 @atom:*_b044*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:044_108 @atom:*_b044*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:045_053 @atom:*_b045*_a*_d*_i* @atom:*_b053*_a*_d*_i* - @bond:045_055 @atom:*_b045*_a*_d*_i* @atom:*_b055*_a*_d*_i* - @bond:045_056 @atom:*_b045*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:045_057 @atom:*_b045*_a*_d*_i* @atom:*_b057*_a*_d*_i* - @bond:045_101 @atom:*_b045*_a*_d*_i* @atom:*_b101*_a*_d*_i* - @bond:045_105 @atom:*_b045*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:045_108 @atom:*_b045*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:046_047 @atom:*_b046*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:046_050 @atom:*_b046*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:046_051 @atom:*_b046*_a*_d*_i* @atom:*_b051*_a*_d*_i* - @bond:046_080 @atom:*_b046*_a*_d*_i* @atom:*_b080*_a*_d*_i* - @bond:046_091 @atom:*_b046*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:046_095 @atom:*_b046*_a*_d*_i* @atom:*_b095*_a*_d*_i* - @bond:046_108 @atom:*_b046*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:046_109 @atom:*_b046*_a*_d*_i* @atom:*_b109*_a*_d*_i* - @bond:047_047 @atom:*_b047*_a*_d*_i* @atom:*_b047*_a*_d*_i* - @bond:047_048 @atom:*_b047*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:047_050 @atom:*_b047*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:047_057 @atom:*_b047*_a*_d*_i* @atom:*_b057*_a*_d*_i* - @bond:047_058 @atom:*_b047*_a*_d*_i* @atom:*_b058*_a*_d*_i* - @bond:047_065 @atom:*_b047*_a*_d*_i* @atom:*_b065*_a*_d*_i* - @bond:047_066 @atom:*_b047*_a*_d*_i* @atom:*_b066*_a*_d*_i* - @bond:047_086 @atom:*_b047*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:047_091 @atom:*_b047*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:047_105 @atom:*_b047*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:047_110 @atom:*_b047*_a*_d*_i* @atom:*_b110*_a*_d*_i* - @bond:048_048 @atom:*_b048*_a*_d*_i* @atom:*_b048*_a*_d*_i* - @bond:048_049 @atom:*_b048*_a*_d*_i* @atom:*_b049*_a*_d*_i* - @bond:048_050 @atom:*_b048*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:048_053 @atom:*_b048*_a*_d*_i* @atom:*_b053*_a*_d*_i* - @bond:048_055 @atom:*_b048*_a*_d*_i* @atom:*_b055*_a*_d*_i* - @bond:048_056 @atom:*_b048*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:048_057 @atom:*_b048*_a*_d*_i* @atom:*_b057*_a*_d*_i* - @bond:048_060 @atom:*_b048*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:048_061 @atom:*_b048*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:048_064 @atom:*_b048*_a*_d*_i* @atom:*_b064*_a*_d*_i* - @bond:048_065 @atom:*_b048*_a*_d*_i* @atom:*_b065*_a*_d*_i* - @bond:048_066 @atom:*_b048*_a*_d*_i* @atom:*_b066*_a*_d*_i* - @bond:048_079 @atom:*_b048*_a*_d*_i* @atom:*_b079*_a*_d*_i* - @bond:048_081 @atom:*_b048*_a*_d*_i* @atom:*_b081*_a*_d*_i* - @bond:048_084 @atom:*_b048*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:048_086 @atom:*_b048*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:048_088 @atom:*_b048*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:048_091 @atom:*_b048*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:048_101 @atom:*_b048*_a*_d*_i* @atom:*_b101*_a*_d*_i* - @bond:048_102 @atom:*_b048*_a*_d*_i* @atom:*_b102*_a*_d*_i* - @bond:048_109 @atom:*_b048*_a*_d*_i* @atom:*_b109*_a*_d*_i* - @bond:049_059 @atom:*_b049*_a*_d*_i* @atom:*_b059*_a*_d*_i* - @bond:049_062 @atom:*_b049*_a*_d*_i* @atom:*_b062*_a*_d*_i* - @bond:049_082 @atom:*_b049*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:049_083 @atom:*_b049*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:049_084 @atom:*_b049*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:049_085 @atom:*_b049*_a*_d*_i* @atom:*_b085*_a*_d*_i* - @bond:049_087 @atom:*_b049*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:049_088 @atom:*_b049*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:050_050 @atom:*_b050*_a*_d*_i* @atom:*_b050*_a*_d*_i* - @bond:050_056 @atom:*_b050*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:050_084 @atom:*_b050*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:050_109 @atom:*_b050*_a*_d*_i* @atom:*_b109*_a*_d*_i* - @bond:051_105 @atom:*_b051*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:052_064 @atom:*_b052*_a*_d*_i* @atom:*_b064*_a*_d*_i* - @bond:053_054 @atom:*_b053*_a*_d*_i* @atom:*_b054*_a*_d*_i* - @bond:054_055 @atom:*_b054*_a*_d*_i* @atom:*_b055*_a*_d*_i* - @bond:055_059 @atom:*_b055*_a*_d*_i* @atom:*_b059*_a*_d*_i* - @bond:055_082 @atom:*_b055*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:056_056 @atom:*_b056*_a*_d*_i* @atom:*_b056*_a*_d*_i* - @bond:056_059 @atom:*_b056*_a*_d*_i* @atom:*_b059*_a*_d*_i* - @bond:056_060 @atom:*_b056*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:056_082 @atom:*_b056*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:056_086 @atom:*_b056*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:056_103 @atom:*_b056*_a*_d*_i* @atom:*_b103*_a*_d*_i* - @bond:056_109 @atom:*_b056*_a*_d*_i* @atom:*_b109*_a*_d*_i* - @bond:057_060 @atom:*_b057*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:057_061 @atom:*_b057*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:057_062 @atom:*_b057*_a*_d*_i* @atom:*_b062*_a*_d*_i* - @bond:057_081 @atom:*_b057*_a*_d*_i* @atom:*_b081*_a*_d*_i* - @bond:057_082 @atom:*_b057*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:057_084 @atom:*_b057*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:057_085 @atom:*_b057*_a*_d*_i* @atom:*_b085*_a*_d*_i* - @bond:057_086 @atom:*_b057*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:058_083 @atom:*_b058*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:058_084 @atom:*_b058*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:059_063 @atom:*_b059*_a*_d*_i* @atom:*_b063*_a*_d*_i* - @bond:060_060 @atom:*_b060*_a*_d*_i* @atom:*_b060*_a*_d*_i* - @bond:060_061 @atom:*_b060*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:060_080 @atom:*_b060*_a*_d*_i* @atom:*_b080*_a*_d*_i* - @bond:060_081 @atom:*_b060*_a*_d*_i* @atom:*_b081*_a*_d*_i* - @bond:060_087 @atom:*_b060*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:060_105 @atom:*_b060*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:061_061 @atom:*_b061*_a*_d*_i* @atom:*_b061*_a*_d*_i* - @bond:061_062 @atom:*_b061*_a*_d*_i* @atom:*_b062*_a*_d*_i* - @bond:061_082 @atom:*_b061*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:061_083 @atom:*_b061*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:061_084 @atom:*_b061*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:061_088 @atom:*_b061*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:062_063 @atom:*_b062*_a*_d*_i* @atom:*_b063*_a*_d*_i* - @bond:062_105 @atom:*_b062*_a*_d*_i* @atom:*_b105*_a*_d*_i* - @bond:063_082 @atom:*_b063*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:064_108 @atom:*_b064*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:065_082 @atom:*_b065*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:065_083 @atom:*_b065*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:065_084 @atom:*_b065*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:065_087 @atom:*_b065*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:065_088 @atom:*_b065*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:065_108 @atom:*_b065*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:066_082 @atom:*_b066*_a*_d*_i* @atom:*_b082*_a*_d*_i* - @bond:066_083 @atom:*_b066*_a*_d*_i* @atom:*_b083*_a*_d*_i* - @bond:066_084 @atom:*_b066*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:066_087 @atom:*_b066*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:066_088 @atom:*_b066*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:066_108 @atom:*_b066*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:077_078 @atom:*_b077*_a*_d*_i* @atom:*_b078*_a*_d*_i* - @bond:080_084 @atom:*_b080*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:082_086 @atom:*_b082*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:082_087 @atom:*_b082*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:083_084 @atom:*_b083*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:083_086 @atom:*_b083*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:084_084 @atom:*_b084*_a*_d*_i* @atom:*_b084*_a*_d*_i* - @bond:084_086 @atom:*_b084*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:084_087 @atom:*_b084*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:084_088 @atom:*_b084*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:085_085 @atom:*_b085*_a*_d*_i* @atom:*_b085*_a*_d*_i* - @bond:086_086 @atom:*_b086*_a*_d*_i* @atom:*_b086*_a*_d*_i* - @bond:086_087 @atom:*_b086*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:086_088 @atom:*_b086*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:087_087 @atom:*_b087*_a*_d*_i* @atom:*_b087*_a*_d*_i* - @bond:087_088 @atom:*_b087*_a*_d*_i* @atom:*_b088*_a*_d*_i* - @bond:089_090 @atom:*_b089*_a*_d*_i* @atom:*_b090*_a*_d*_i* - @bond:089_091 @atom:*_b089*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:090_091 @atom:*_b090*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:091_091 @atom:*_b091*_a*_d*_i* @atom:*_b091*_a*_d*_i* - @bond:102_103 @atom:*_b102*_a*_d*_i* @atom:*_b103*_a*_d*_i* - @bond:108_108 @atom:*_b108*_a*_d*_i* @atom:*_b108*_a*_d*_i* - @bond:109_109 @atom:*_b109*_a*_d*_i* @atom:*_b109*_a*_d*_i* - } #(end of bonds by type) - - - - - # ------- Angle Interactions: ------- - # http://lammps.sandia.gov/doc/angle_harmonic.html - # Syntax: - # angle_coeff AngleTypeName parameters... - - write_once("In Settings") { - angle_coeff @angle:025_001_025 33.0 109.47 - angle_coeff @angle:001_002_002 50.0 109.5 - angle_coeff @angle:002_002_002 63.0 112.4 - angle_coeff @angle:002_002_003 63.0 112.4 - angle_coeff @angle:002_002_005 80.0 109.5 - angle_coeff @angle:002_002_006 63.0 112.4 - angle_coeff @angle:006_002_006 63.0 112.4 - angle_coeff @angle:005_002_006 80.0 109.5 - angle_coeff @angle:002_002_010 63.0 112.4 - angle_coeff @angle:003_002_010 63.0 112.4 - angle_coeff @angle:006_002_010 63.0 112.4 - angle_coeff @angle:010_002_010 63.0 112.4 - angle_coeff @angle:005_002_010 80.0 109.5 - angle_coeff @angle:010_002_012 63.0 114.0 - angle_coeff @angle:006_002_013 63.0 112.4 - angle_coeff @angle:010_002_015 50.0 108.6 - angle_coeff @angle:002_002_016 50.0 114.7 - angle_coeff @angle:010_002_016 50.0 114.7 - angle_coeff @angle:002_002_020 80.0 109.5 - angle_coeff @angle:006_002_020 80.0 109.5 - angle_coeff @angle:010_002_020 80.0 109.5 - angle_coeff @angle:003_002_024 80.0 110.3 - angle_coeff @angle:002_002_024 80.0 111.2 - angle_coeff @angle:002_002_044 56.2 109.47 - angle_coeff @angle:006_002_044 56.2 109.47 - angle_coeff @angle:010_002_044 56.2 109.47 - angle_coeff @angle:013_002_044 56.2 109.47 - angle_coeff @angle:003_002_044 80.0 111.2 - angle_coeff @angle:002_002_048 63.0 112.4 - angle_coeff @angle:010_002_048 63.0 114.0 - angle_coeff @angle:002_002_051 63.0 112.4 - angle_coeff @angle:006_002_051 63.0 112.4 - angle_coeff @angle:002_002_053 80.0 111.2 - angle_coeff @angle:002_002_055 80.0 111.2 - angle_coeff @angle:010_002_080 63.0 115.6 - angle_coeff @angle:002_003_004 80.0 120.4 - angle_coeff @angle:001_003_004 80.0 121.0 - angle_coeff @angle:003_003_004 80.0 121.4 - angle_coeff @angle:004_003_004 80.0 126.0 - angle_coeff @angle:004_003_005 80.0 121.0 - angle_coeff @angle:004_003_006 80.0 120.4 - angle_coeff @angle:005_003_010 70.0 115.0 - angle_coeff @angle:004_003_010 80.0 120.4 - angle_coeff @angle:005_003_012 70.0 120.0 - angle_coeff @angle:012_003_012 85.0 120.0 - angle_coeff @angle:005_003_013 70.0 108.0 - angle_coeff @angle:013_003_013 70.0 116.0 - angle_coeff @angle:001_003_013 80.0 111.0 - angle_coeff @angle:003_003_013 80.0 117.2 - angle_coeff @angle:004_003_013 80.0 120.4 - angle_coeff @angle:010_003_020 81.0 111.4 - angle_coeff @angle:013_003_020 81.0 111.4 - angle_coeff @angle:004_003_020 83.0 123.4 - angle_coeff @angle:013_003_021 75.0 109.0 - angle_coeff @angle:004_003_021 75.0 119.0 - angle_coeff @angle:024_003_024 70.0 114.2 - angle_coeff @angle:002_003_024 70.0 116.6 - angle_coeff @angle:003_003_024 70.0 116.6 - angle_coeff @angle:006_003_024 70.0 116.6 - angle_coeff @angle:010_003_024 70.0 116.6 - angle_coeff @angle:013_003_024 70.0 116.6 - angle_coeff @angle:004_003_024 80.0 122.9 - angle_coeff @angle:020_003_024 81.0 111.4 - angle_coeff @angle:013_003_044 70.0 116.0 - angle_coeff @angle:004_003_044 80.0 120.4 - angle_coeff @angle:013_003_046 35.0 115.0 - angle_coeff @angle:046_003_046 35.0 115.0 - angle_coeff @angle:004_003_046 35.0 123.0 - angle_coeff @angle:024_003_046 40.0 114.0 - angle_coeff @angle:005_003_046 40.0 115.0 - angle_coeff @angle:020_003_046 40.0 115.0 - angle_coeff @angle:024_003_047 70.0 115.5 - angle_coeff @angle:004_003_047 80.0 125.3 - angle_coeff @angle:046_003_048 35.0 115.0 - angle_coeff @angle:024_003_048 70.0 115.5 - angle_coeff @angle:013_003_048 70.0 116.0 - angle_coeff @angle:005_003_048 70.0 120.0 - angle_coeff @angle:004_003_048 80.0 120.4 - angle_coeff @angle:020_003_048 81.0 111.4 - angle_coeff @angle:048_003_048 85.0 120.0 - angle_coeff @angle:013_003_050 70.0 116.0 - angle_coeff @angle:046_003_050 80.0 116.0 - angle_coeff @angle:004_003_050 80.0 124.0 - angle_coeff @angle:010_003_052 65.0 117.0 - angle_coeff @angle:002_003_052 70.0 117.0 - angle_coeff @angle:006_003_052 70.0 117.0 - angle_coeff @angle:013_003_052 70.0 117.0 - angle_coeff @angle:048_003_052 70.0 117.0 - angle_coeff @angle:004_003_052 80.0 126.0 - angle_coeff @angle:052_003_052 80.0 126.0 - angle_coeff @angle:046_003_056 35.0 122.0 - angle_coeff @angle:004_003_056 80.0 122.5 - angle_coeff @angle:047_003_057 70.0 114.1 - angle_coeff @angle:056_003_057 70.0 118.6 - angle_coeff @angle:057_003_057 70.0 118.6 - angle_coeff @angle:004_003_057 80.0 120.6 - angle_coeff @angle:024_003_060 70.0 111.3 - angle_coeff @angle:057_003_060 70.0 111.3 - angle_coeff @angle:004_003_060 80.0 128.8 - angle_coeff @angle:013_003_065 75.0 109.0 - angle_coeff @angle:004_003_065 75.0 119.0 - angle_coeff @angle:044_003_084 70.0 116.0 - angle_coeff @angle:004_003_084 80.0 120.4 - angle_coeff @angle:004_003_087 80.0 128.2 - angle_coeff @angle:057_003_105 70.0 115.4 - angle_coeff @angle:056_003_105 70.0 118.6 - angle_coeff @angle:004_003_105 80.0 120.9 - angle_coeff @angle:013_003_107 70.0 116.6 - angle_coeff @angle:004_003_107 80.0 122.9 - angle_coeff @angle:025_004_025 10.0 117.0 - angle_coeff @angle:003_004_025 35.0 113.0 - angle_coeff @angle:003_005_007 35.0 113.0 - angle_coeff @angle:002_005_007 55.0 108.5 - angle_coeff @angle:006_005_007 55.0 108.5 - angle_coeff @angle:007_005_010 55.0 108.5 - angle_coeff @angle:007_005_013 55.0 108.5 - angle_coeff @angle:007_005_024 49.0 105.4 - angle_coeff @angle:025_005_025 5.0 109.47 - angle_coeff @angle:007_005_025 10.0 109.47 - angle_coeff @angle:013_005_025 10.0 109.47 - angle_coeff @angle:007_005_047 35.0 109.0 - angle_coeff @angle:025_005_048 10.0 109.47 - angle_coeff @angle:007_005_048 35.0 113.0 - angle_coeff @angle:007_005_051 55.0 108.5 - angle_coeff @angle:007_005_064 55.0 108.5 - angle_coeff @angle:013_005_064 100.0 120.5 - angle_coeff @angle:007_005_079 74.0 110.0 - angle_coeff @angle:007_005_106 100.0 126.0 - angle_coeff @angle:005_007_025 10.0 109.47 - angle_coeff @angle:025_007_025 33.0 109.47 - angle_coeff @angle:002_010_002 63.0 112.4 - angle_coeff @angle:002_010_003 63.0 111.1 - angle_coeff @angle:002_010_005 80.0 109.5 - angle_coeff @angle:003_010_006 63.0 111.1 - angle_coeff @angle:006_010_006 63.0 111.5 - angle_coeff @angle:002_010_006 63.0 112.4 - angle_coeff @angle:005_010_006 80.0 109.5 - angle_coeff @angle:003_010_010 63.0 111.1 - angle_coeff @angle:002_010_010 63.0 111.5 - angle_coeff @angle:006_010_010 63.0 111.5 - angle_coeff @angle:010_010_010 63.0 111.5 - angle_coeff @angle:005_010_010 80.0 109.5 - angle_coeff @angle:002_010_020 80.0 109.5 - angle_coeff @angle:006_010_020 80.0 109.5 - angle_coeff @angle:010_010_020 80.0 109.5 - angle_coeff @angle:003_010_024 63.0 110.1 - angle_coeff @angle:006_010_024 80.0 109.5 - angle_coeff @angle:002_010_024 80.0 109.7 - angle_coeff @angle:010_010_024 80.0 109.7 - angle_coeff @angle:002_010_044 56.2 109.47 - angle_coeff @angle:006_010_044 56.2 109.47 - angle_coeff @angle:010_010_044 56.2 109.47 - angle_coeff @angle:013_010_044 56.2 109.47 - angle_coeff @angle:003_010_044 80.0 109.7 - angle_coeff @angle:002_010_048 63.0 112.4 - angle_coeff @angle:020_010_048 80.0 109.5 - angle_coeff @angle:002_010_105 80.0 109.5 - angle_coeff @angle:010_010_105 80.0 109.5 - angle_coeff @angle:020_010_105 80.0 109.5 - 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angle_coeff @angle:046_087_084 35.0 126.8 - angle_coeff @angle:084_087_084 70.0 103.8 - angle_coeff @angle:082_087_084 70.0 110.4 - angle_coeff @angle:002_087_084 70.0 125.0 - angle_coeff @angle:013_087_084 70.0 125.0 - angle_coeff @angle:003_087_084 70.0 130.0 - angle_coeff @angle:060_087_084 85.0 106.4 - angle_coeff @angle:084_087_086 70.0 125.7 - angle_coeff @angle:049_087_087 35.0 127.5 - angle_coeff @angle:060_087_087 70.0 107.3 - angle_coeff @angle:084_087_087 70.0 107.3 - angle_coeff @angle:086_087_087 70.0 127.5 - angle_coeff @angle:084_087_088 70.0 103.8 - angle_coeff @angle:048_088_049 35.0 128.6 - angle_coeff @angle:049_088_061 35.0 118.9 - angle_coeff @angle:013_088_061 70.0 118.9 - angle_coeff @angle:019_088_061 70.0 118.9 - angle_coeff @angle:061_088_087 70.0 111.9 - angle_coeff @angle:004_089_090 80.0 134.0 - angle_coeff @angle:090_089_091 70.0 91.0 - angle_coeff @angle:004_089_091 80.0 134.0 - angle_coeff @angle:013_090_089 55.0 127.0 - angle_coeff @angle:089_090_091 50.0 94.0 - angle_coeff @angle:013_090_091 50.0 126.0 - angle_coeff @angle:024_091_046 35.0 108.0 - angle_coeff @angle:013_091_046 35.0 114.3 - angle_coeff @angle:044_091_046 35.0 114.3 - angle_coeff @angle:046_091_046 35.0 114.3 - angle_coeff @angle:016_091_046 37.5 108.0 - angle_coeff @angle:046_091_047 35.0 109.5 - angle_coeff @angle:046_091_089 37.5 110.0 - angle_coeff @angle:024_091_089 70.0 117.0 - angle_coeff @angle:046_091_090 35.0 111.0 - angle_coeff @angle:016_091_090 55.0 109.0 - angle_coeff @angle:091_091_091 30.0 79.2 - angle_coeff @angle:013_091_091 37.5 117.2 - angle_coeff @angle:044_091_091 37.5 117.2 - angle_coeff @angle:046_091_091 37.5 117.2 - angle_coeff @angle:024_091_091 37.5 126.0 - angle_coeff @angle:016_091_091 55.0 128.0 - angle_coeff @angle:089_091_091 63.0 85.0 - angle_coeff @angle:047_091_091 63.0 114.0 - angle_coeff @angle:090_091_091 80.0 89.0 - angle_coeff @angle:013_095_013 172.8 120.0 - angle_coeff @angle:013_095_046 144.0 120.0 - angle_coeff @angle:013_101_045 35.0 109.5 - angle_coeff @angle:045_101_045 43.6 106.4 - angle_coeff @angle:045_101_048 50.0 112.5 - angle_coeff @angle:013_101_048 50.0 120.5 - angle_coeff @angle:013_102_103 80.0 117.5 - angle_coeff @angle:048_102_103 80.0 117.5 - angle_coeff @angle:103_102_103 80.0 125.0 - angle_coeff @angle:025_103_025 10.0 109.5 - angle_coeff @angle:025_103_102 10.0 109.5 - angle_coeff @angle:013_104_013 45.0 109.5 - angle_coeff @angle:003_105_010 70.0 117.6 - angle_coeff @angle:003_105_013 70.0 117.6 - angle_coeff @angle:003_105_045 35.0 119.2 - angle_coeff @angle:045_105_047 35.0 119.2 - angle_coeff @angle:013_105_047 70.0 121.2 - angle_coeff @angle:003_105_047 70.0 121.6 - angle_coeff @angle:003_105_051 70.0 117.6 - angle_coeff @angle:047_105_051 70.0 121.2 - angle_coeff @angle:045_105_060 30.0 125.8 - angle_coeff @angle:006_105_060 70.0 125.8 - angle_coeff @angle:010_105_060 70.0 125.8 - angle_coeff @angle:013_105_060 70.0 125.8 - angle_coeff @angle:051_105_060 70.0 125.8 - angle_coeff @angle:045_105_062 30.0 128.8 - angle_coeff @angle:060_105_062 70.0 105.4 - angle_coeff @angle:006_105_062 70.0 128.8 - angle_coeff @angle:010_105_062 70.0 128.8 - angle_coeff @angle:013_105_062 70.0 128.8 - angle_coeff @angle:051_105_062 70.0 128.8 - angle_coeff @angle:004_106_024 20.0 109.5 - angle_coeff @angle:024_106_024 20.0 109.5 - angle_coeff @angle:013_107_013 50.0 118.0 - angle_coeff @angle:003_107_013 50.0 121.9 - angle_coeff @angle:001_108_013 35.0 110.5 - angle_coeff @angle:013_108_013 60.0 110.0 - angle_coeff @angle:013_108_020 60.0 100.0 - angle_coeff @angle:020_108_020 60.0 110.0 - angle_coeff @angle:013_108_021 35.0 110.5 - angle_coeff @angle:045_108_045 35.0 109.5 - angle_coeff @angle:013_108_045 35.0 110.5 - angle_coeff @angle:046_108_046 35.0 109.5 - angle_coeff @angle:013_108_046 35.0 110.5 - angle_coeff @angle:013_108_065 35.0 110.5 - angle_coeff @angle:013_108_066 35.0 110.5 - angle_coeff @angle:013_108_108 50.0 112.0 - angle_coeff @angle:046_109_048 35.0 123.3 - angle_coeff @angle:046_109_050 35.0 120.0 - angle_coeff @angle:013_109_050 70.0 124.0 - angle_coeff @angle:046_109_109 35.0 120.0 - angle_coeff @angle:013_109_109 70.0 124.0 - angle_coeff @angle:050_109_109 70.0 124.0 - angle_coeff @angle:048_109_109 85.0 117.0 - angle_coeff @angle:004_110_047 160.0 180.0 - angle_coeff @angle:047_110_047 160.0 180.0 - } #(end of angle_coeffs) - - # Rules for creating angle interactions according to atom type: - # AngleTypeName AtomType1 AtomType2 AtomType3 - # (* = wildcard) - - write_once("Data Angles By Type") { - @angle:025_001_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a001*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:001_002_002 @atom:*_b*_a001*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_002_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_002_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:002_002_005 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a005*_d*_i* - @angle:002_002_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:006_002_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:005_002_006 @atom:*_b*_a005*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_002_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:003_002_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:006_002_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_002_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:005_002_010 @atom:*_b*_a005*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_002_012 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:006_002_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:010_002_015 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a015*_d*_i* - @angle:002_002_016 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:010_002_016 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:002_002_020 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:006_002_020 @atom:*_b*_a006*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:010_002_020 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:003_002_024 @atom:*_b*_a003*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:002_002_024 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:002_002_044 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:006_002_044 @atom:*_b*_a006*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:010_002_044 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:013_002_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:003_002_044 @atom:*_b*_a003*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:002_002_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:010_002_048 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_002_051 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:006_002_051 @atom:*_b*_a006*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:002_002_053 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a053*_d*_i* - @angle:002_002_055 @atom:*_b*_a002*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:010_002_080 @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:002_003_004 @atom:*_b*_a002*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* - @angle:001_003_004 @atom:*_b*_a001*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* - @angle:003_003_004 @atom:*_b*_a003*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* - @angle:004_003_004 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* - @angle:004_003_005 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a005*_d*_i* - @angle:004_003_006 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:005_003_010 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:004_003_010 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:005_003_012 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:012_003_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:005_003_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_003_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:001_003_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_003_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:004_003_013 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:010_003_020 @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:013_003_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:004_003_020 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:013_003_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a021*_d*_i* - @angle:004_003_021 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a021*_d*_i* - @angle:024_003_024 @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:002_003_024 @atom:*_b*_a002*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:003_003_024 @atom:*_b*_a003*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:006_003_024 @atom:*_b*_a006*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:010_003_024 @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:013_003_024 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:004_003_024 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:020_003_024 @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:013_003_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:004_003_044 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:013_003_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:046_003_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:004_003_046 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:024_003_046 @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:005_003_046 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:020_003_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:024_003_047 @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:004_003_047 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_003_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:024_003_048 @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_003_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:005_003_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:004_003_048 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:020_003_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_003_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_003_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:046_003_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:004_003_050 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:010_003_052 @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:002_003_052 @atom:*_b*_a002*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:006_003_052 @atom:*_b*_a006*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:013_003_052 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:048_003_052 @atom:*_b*_a048*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:004_003_052 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:052_003_052 @atom:*_b*_a052*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:046_003_056 @atom:*_b*_a046*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:004_003_056 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:047_003_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:056_003_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:057_003_057 @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:004_003_057 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:024_003_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:057_003_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:004_003_060 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_003_065 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:004_003_065 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:044_003_084 @atom:*_b*_a044*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:004_003_084 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:004_003_087 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:057_003_105 @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:056_003_105 @atom:*_b*_a056*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:004_003_105 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:013_003_107 @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* - @angle:004_003_107 @atom:*_b*_a004*_d*_i* @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* - @angle:025_004_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a004*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:003_004_025 @atom:*_b*_a003*_d*_i* @atom:*_b*_a004*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:003_005_007 @atom:*_b*_a003*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* - @angle:002_005_007 @atom:*_b*_a002*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* - @angle:006_005_007 @atom:*_b*_a006*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* - @angle:007_005_010 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:007_005_013 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:007_005_024 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:025_005_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:007_005_025 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_005_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:007_005_047 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:025_005_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:007_005_048 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:007_005_051 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:007_005_064 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:013_005_064 @atom:*_b*_a013*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:007_005_079 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:007_005_106 @atom:*_b*_a007*_d*_i* @atom:*_b*_a005*_d*_i* @atom:*_b*_a106*_d*_i* - @angle:005_007_025 @atom:*_b*_a005*_d*_i* @atom:*_b*_a007*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:025_007_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a007*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:002_010_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_010_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:002_010_005 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a005*_d*_i* - @angle:003_010_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:006_010_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_010_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:005_010_006 @atom:*_b*_a005*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:003_010_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_010_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:006_010_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_010_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:005_010_010 @atom:*_b*_a005*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_010_020 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:006_010_020 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:010_010_020 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:003_010_024 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:006_010_024 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:002_010_024 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:010_010_024 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:002_010_044 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:006_010_044 @atom:*_b*_a006*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:010_010_044 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:013_010_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:003_010_044 @atom:*_b*_a003*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:002_010_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:020_010_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_010_105 @atom:*_b*_a002*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:010_010_105 @atom:*_b*_a010*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:020_010_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:002_011_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_011_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:006_011_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_011_009 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a009*_d*_i* - @angle:006_011_009 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a009*_d*_i* - @angle:009_011_010 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_011_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:006_011_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_011_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_011_011 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:006_011_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:009_011_011 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:010_011_011 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:011_011_011 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:009_011_013 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:011_011_013 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:002_011_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:006_011_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:010_011_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_011_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:009_011_014 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:011_011_014 @atom:*_b*_a011*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:009_011_079 @atom:*_b*_a009*_d*_i* @atom:*_b*_a011*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:002_012_012 @atom:*_b*_a002*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:003_012_012 @atom:*_b*_a003*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:012_012_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:012_012_048 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:012_012_060 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:012_012_081 @atom:*_b*_a012*_d*_i* @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:001_013_001 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a001*_d*_i* - @angle:002_013_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:001_013_003 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:002_013_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:003_013_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:002_013_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:006_013_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:003_013_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:001_013_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:005_013_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_013_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_013_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_013_015 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* - @angle:013_013_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:013_013_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* - @angle:003_013_020 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:013_013_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:003_013_021 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a021*_d*_i* - @angle:013_013_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a021*_d*_i* - @angle:021_013_021 @atom:*_b*_a021*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a021*_d*_i* - @angle:013_013_022 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a022*_d*_i* - @angle:020_013_024 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:003_013_024 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:002_013_024 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:013_013_024 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:016_013_044 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:002_013_044 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:006_013_044 @atom:*_b*_a006*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:010_013_044 @atom:*_b*_a010*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:013_013_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:003_013_044 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:046_013_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:018_013_046 @atom:*_b*_a018*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:019_013_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:002_013_046 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:003_013_046 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:005_013_046 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:015_013_046 @atom:*_b*_a015*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:016_013_046 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:020_013_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:022_013_046 @atom:*_b*_a022*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:024_013_046 @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:044_013_046 @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_013_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:001_013_046 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:021_013_046 @atom:*_b*_a021*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:046_013_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:001_013_047 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:013_013_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:047_013_047 @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_013_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:047_013_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_013_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:001_013_048 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:005_013_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:020_013_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:016_013_048 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_013_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_013_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_013_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:044_013_048 @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:046_013_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:046_013_051 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:005_013_051 @atom:*_b*_a005*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:013_013_051 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:046_013_053 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* - @angle:003_013_053 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* - @angle:013_013_053 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* - @angle:046_013_055 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:013_013_055 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:046_013_056 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:003_013_056 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:013_013_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:046_013_057 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:048_013_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:046_013_060 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_013_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:046_013_064 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:013_013_064 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:048_013_064 @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:046_013_065 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:003_013_065 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:013_013_065 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:048_013_065 @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:065_013_065 @atom:*_b*_a065*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:046_013_066 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a066*_d*_i* - @angle:013_013_066 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a066*_d*_i* - @angle:046_013_079 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:013_013_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:001_013_079 @atom:*_b*_a001*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:046_013_080 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:013_013_080 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:046_013_083 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:013_013_083 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:046_013_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:016_013_084 @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:013_013_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:046_013_085 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:013_013_085 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:046_013_087 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:013_013_087 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:046_013_090 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* - @angle:013_013_090 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* - @angle:003_013_090 @atom:*_b*_a003*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* - @angle:046_013_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:046_013_095 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* - @angle:013_013_095 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* - @angle:046_013_101 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* - @angle:013_013_101 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* - @angle:046_013_102 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* - @angle:013_013_102 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* - @angle:046_013_104 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* - @angle:013_013_104 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* - @angle:046_013_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:013_013_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:020_013_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:046_013_107 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* - @angle:013_013_107 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* - @angle:046_013_108 @atom:*_b*_a046*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* - @angle:013_013_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* - @angle:002_014_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_014_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:006_014_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_014_009 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a009*_d*_i* - @angle:006_014_009 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a009*_d*_i* - @angle:009_014_010 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_014_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:006_014_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_014_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_014_011 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:006_014_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:009_014_011 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:010_014_011 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:011_014_011 @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:009_014_013 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:011_014_013 @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:002_014_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:006_014_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:010_014_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_014_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:002_014_014 @atom:*_b*_a002*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:006_014_014 @atom:*_b*_a006*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:009_014_014 @atom:*_b*_a009*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:010_014_014 @atom:*_b*_a010*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:011_014_014 @atom:*_b*_a011*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:013_014_014 @atom:*_b*_a013*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:014_014_014 @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* @atom:*_b*_a014*_d*_i* - @angle:017_015_017 @atom:*_b*_a017*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* - @angle:002_015_017 @atom:*_b*_a002*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* - @angle:006_015_017 @atom:*_b*_a006*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* - @angle:013_015_017 @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* - @angle:025_015_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_015_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:033_015_033 @atom:*_b*_a033*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:002_015_033 @atom:*_b*_a002*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:006_015_033 @atom:*_b*_a006*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:013_015_033 @atom:*_b*_a013*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:017_015_033 @atom:*_b*_a017*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:017_015_048 @atom:*_b*_a017*_d*_i* @atom:*_b*_a015*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_016_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:013_016_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:002_016_016 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:006_016_016 @atom:*_b*_a006*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:013_016_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:013_016_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a019*_d*_i* - @angle:025_016_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_016_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:033_016_033 @atom:*_b*_a033*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:002_016_033 @atom:*_b*_a002*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:006_016_033 @atom:*_b*_a006*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:013_016_033 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:016_016_033 @atom:*_b*_a016*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:013_016_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:047_016_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:024_016_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:025_016_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:025_016_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:060_016_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:025_016_084 @atom:*_b*_a025*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:082_016_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_016_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:084_016_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:013_016_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:015_017_025 @atom:*_b*_a015*_d*_i* @atom:*_b*_a017*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:025_017_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a017*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_018_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* - @angle:019_018_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:018_018_056 @atom:*_b*_a018*_d*_i* @atom:*_b*_a018*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:013_019_018 @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a018*_d*_i* - @angle:016_019_019 @atom:*_b*_a016*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* - @angle:013_019_019 @atom:*_b*_a013*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* - @angle:018_019_025 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:019_019_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:018_019_047 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:019_019_047 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:018_019_048 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:019_019_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:019_019_050 @atom:*_b*_a019*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:018_019_055 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:018_019_088 @atom:*_b*_a018*_d*_i* @atom:*_b*_a019*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:002_020_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_020_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:003_020_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_020_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_020_007 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a007*_d*_i* - @angle:007_020_010 @atom:*_b*_a007*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:003_020_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_020_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:013_020_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_020_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:025_020_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_020_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_020_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:025_020_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_020_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:047_020_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_020_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_020_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_020_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_020_051 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:002_020_051 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:006_020_051 @atom:*_b*_a006*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:010_020_051 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:024_020_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:025_020_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:002_020_064 @atom:*_b*_a002*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:006_020_064 @atom:*_b*_a006*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:010_020_064 @atom:*_b*_a010*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:013_020_064 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:048_020_064 @atom:*_b*_a048*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:064_020_064 @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:025_020_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:060_020_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:082_020_082 @atom:*_b*_a082*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:025_020_084 @atom:*_b*_a025*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:082_020_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_020_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:084_020_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:061_020_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:108_020_108 @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* - @angle:013_020_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* - @angle:025_021_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a021*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_022_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a022*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_022_023 @atom:*_b*_a013*_d*_i* @atom:*_b*_a022*_d*_i* @atom:*_b*_a023*_d*_i* - @angle:023_022_025 @atom:*_b*_a023*_d*_i* @atom:*_b*_a022*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:002_024_003 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:003_024_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:003_024_005 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a005*_d*_i* - @angle:002_024_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:003_024_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_024_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:003_024_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:013_024_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_024_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_024_016 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:003_024_020 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:003_024_025 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:025_024_045 @atom:*_b*_a025*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:005_024_045 @atom:*_b*_a005*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:003_024_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_024_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:002_024_045 @atom:*_b*_a002*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:006_024_045 @atom:*_b*_a006*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:010_024_045 @atom:*_b*_a010*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:013_024_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_024_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_024_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_024_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_024_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:054_024_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:045_024_059 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* - @angle:003_024_059 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* - @angle:013_024_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:045_024_079 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:045_024_084 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:048_024_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:016_024_086 @atom:*_b*_a016*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:045_024_087 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:048_024_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:045_024_088 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:048_024_088 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:045_024_091 @atom:*_b*_a045*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:003_024_091 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:048_024_103 @atom:*_b*_a048*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a103*_d*_i* - @angle:003_024_106 @atom:*_b*_a003*_d*_i* @atom:*_b*_a024*_d*_i* @atom:*_b*_a106*_d*_i* - @angle:025_025_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a025*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:032_031_032 @atom:*_b*_a032*_d*_i* @atom:*_b*_a031*_d*_i* @atom:*_b*_a032*_d*_i* - @angle:032_031_033 @atom:*_b*_a032*_d*_i* @atom:*_b*_a031*_d*_i* @atom:*_b*_a033*_d*_i* - @angle:035_034_035 @atom:*_b*_a035*_d*_i* @atom:*_b*_a034*_d*_i* @atom:*_b*_a035*_d*_i* - @angle:037_036_037 @atom:*_b*_a037*_d*_i* @atom:*_b*_a036*_d*_i* @atom:*_b*_a037*_d*_i* - @angle:037_036_038 @atom:*_b*_a037*_d*_i* @atom:*_b*_a036*_d*_i* @atom:*_b*_a038*_d*_i* - @angle:040_039_040 @atom:*_b*_a040*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a040*_d*_i* - @angle:041_039_041 @atom:*_b*_a041*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a041*_d*_i* - @angle:040_039_041 @atom:*_b*_a040*_d*_i* @atom:*_b*_a039*_d*_i* @atom:*_b*_a041*_d*_i* - @angle:043_042_043 @atom:*_b*_a043*_d*_i* @atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i* - @angle:002_044_002 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a002*_d*_i* - @angle:002_044_006 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:006_044_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:002_044_010 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:006_044_010 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:010_044_010 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:002_044_013 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:006_044_013 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:010_044_013 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_044_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_044_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:025_044_045 @atom:*_b*_a025*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:013_044_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:002_044_045 @atom:*_b*_a002*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:006_044_045 @atom:*_b*_a006*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:010_044_045 @atom:*_b*_a010*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_044_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:025_044_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:045_044_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_044_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_044_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_044_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:045_044_079 @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:013_044_079 @atom:*_b*_a013*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:048_044_079 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:048_044_091 @atom:*_b*_a048*_d*_i* @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:025_045_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a045*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:025_045_044 @atom:*_b*_a025*_d*_i* @atom:*_b*_a045*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:025_046_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a046*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:013_046_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a046*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:001_047_001 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a001*_d*_i* - @angle:001_047_003 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:003_047_006 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:003_047_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_047_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:025_047_046 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:020_047_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_047_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:046_047_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:003_047_046 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:019_047_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:001_047_046 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:021_047_046 @atom:*_b*_a021*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:025_047_047 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_047_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:005_047_047 @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:020_047_047 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:013_047_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:019_047_047 @atom:*_b*_a019*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:021_047_047 @atom:*_b*_a021*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:001_047_047 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:016_047_047 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:003_047_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_047_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:047_047_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_047_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:025_047_050 @atom:*_b*_a025*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:046_047_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:005_047_050 @atom:*_b*_a005*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:020_047_050 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:013_047_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:046_047_057 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:013_047_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:020_047_057 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:047_047_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:016_047_057 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:057_047_058 @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a058*_d*_i* - @angle:047_047_058 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a058*_d*_i* - @angle:046_047_065 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:047_047_065 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:046_047_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:003_047_091 @atom:*_b*_a003*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:047_047_091 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:046_047_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:058_047_105 @atom:*_b*_a058*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:013_047_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:020_047_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:047_047_105 @atom:*_b*_a047*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:016_047_105 @atom:*_b*_a016*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:046_047_110 @atom:*_b*_a046*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* - @angle:013_047_110 @atom:*_b*_a013*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* - @angle:048_047_110 @atom:*_b*_a048*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* - @angle:001_047_110 @atom:*_b*_a001*_d*_i* @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* - @angle:002_048_012 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:012_048_012 @atom:*_b*_a012*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a012*_d*_i* - @angle:003_048_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:025_048_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_048_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_048_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:005_048_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:010_048_048 @atom:*_b*_a010*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_048_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:015_048_048 @atom:*_b*_a015*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:019_048_048 @atom:*_b*_a019*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:020_048_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:024_048_048 @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:044_048_048 @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:047_048_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:021_048_048 @atom:*_b*_a021*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:001_048_048 @atom:*_b*_a001*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:018_048_048 @atom:*_b*_a018*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:016_048_048 @atom:*_b*_a016*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_048_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:025_048_049 @atom:*_b*_a025*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:024_048_049 @atom:*_b*_a024*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:003_048_049 @atom:*_b*_a003*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:048_048_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:048_048_050 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:048_048_053 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a053*_d*_i* - @angle:055_048_055 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:047_048_055 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:048_048_055 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:049_048_056 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:013_048_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:044_048_056 @atom:*_b*_a044*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:055_048_056 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:005_048_056 @atom:*_b*_a005*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:047_048_056 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:050_048_056 @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:048_048_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:021_048_056 @atom:*_b*_a021*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:049_048_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:048_048_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:055_048_057 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:013_048_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:047_048_057 @atom:*_b*_a047*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:056_048_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:049_048_060 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:048_048_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:057_048_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:056_048_060 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:055_048_060 @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:002_048_060 @atom:*_b*_a002*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_048_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:049_048_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:048_048_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:057_048_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:048_048_064 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a064*_d*_i* - @angle:048_048_065 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:048_048_066 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a066*_d*_i* - @angle:048_048_079 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:049_048_081 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:048_048_081 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:049_048_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_048_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:048_048_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:049_048_086 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:048_048_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:056_048_086 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:049_048_088 @atom:*_b*_a049*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:101_048_101 @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a101*_d*_i* - @angle:056_048_101 @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a101*_d*_i* - @angle:048_048_102 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a102*_d*_i* - @angle:048_048_109 @atom:*_b*_a048*_d*_i* @atom:*_b*_a048*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:025_050_046 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:019_050_046 @atom:*_b*_a019*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:025_050_047 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_050_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:003_050_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:013_050_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_050_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:047_050_048 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:025_050_050 @atom:*_b*_a025*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:046_050_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:013_050_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:047_050_050 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:050_050_084 @atom:*_b*_a050*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:046_050_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:046_050_109 @atom:*_b*_a046*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:013_050_109 @atom:*_b*_a013*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:047_050_109 @atom:*_b*_a047*_d*_i* @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:006_051_006 @atom:*_b*_a006*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a006*_d*_i* - @angle:005_051_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_051_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:002_051_020 @atom:*_b*_a002*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:006_051_020 @atom:*_b*_a006*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:005_051_020 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:020_051_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:046_051_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:005_051_046 @atom:*_b*_a005*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:020_051_046 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_051_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:046_051_105 @atom:*_b*_a046*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:013_051_105 @atom:*_b*_a013*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:020_051_105 @atom:*_b*_a020*_d*_i* @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:013_053_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_053_025 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:045_053_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:025_053_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_053_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_053_054 @atom:*_b*_a002*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:006_053_054 @atom:*_b*_a006*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:013_053_054 @atom:*_b*_a013*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:048_053_054 @atom:*_b*_a048*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:054_053_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:025_053_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a053*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:013_055_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:045_055_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:013_055_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_055_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_055_048 @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:006_055_048 @atom:*_b*_a006*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_055_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:002_055_054 @atom:*_b*_a002*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:013_055_054 @atom:*_b*_a013*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:048_055_054 @atom:*_b*_a048*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:054_055_054 @atom:*_b*_a054*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a054*_d*_i* - @angle:045_055_059 @atom:*_b*_a045*_d*_i* @atom:*_b*_a055*_d*_i* @atom:*_b*_a059*_d*_i* - @angle:003_056_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_056_018 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a018*_d*_i* - @angle:025_056_048 @atom:*_b*_a025*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:045_056_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_056_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_056_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_056_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_056_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:048_056_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:025_056_059 @atom:*_b*_a025*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* - @angle:048_056_059 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* - @angle:059_056_059 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* - @angle:059_056_060 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:048_056_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:059_056_082 @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:048_056_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:013_056_103 @atom:*_b*_a013*_d*_i* @atom:*_b*_a056*_d*_i* @atom:*_b*_a103*_d*_i* - @angle:003_057_003 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a003*_d*_i* - @angle:003_057_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_057_047 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:003_057_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:045_057_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:003_057_048 @atom:*_b*_a003*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_057_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:045_057_060 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_057_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:060_057_061 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:045_057_061 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:013_057_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:048_057_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:045_057_062 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:060_057_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:048_057_062 @atom:*_b*_a048*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:013_057_062 @atom:*_b*_a013*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:045_057_081 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:045_057_082 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:061_057_082 @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:060_057_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:045_057_084 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:061_057_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_057_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:082_057_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:084_057_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:081_057_084 @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:045_057_085 @atom:*_b*_a045*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:082_057_085 @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:024_059_055 @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a055*_d*_i* - @angle:049_059_056 @atom:*_b*_a049*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:013_059_056 @atom:*_b*_a013*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:055_059_056 @atom:*_b*_a055*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:024_059_056 @atom:*_b*_a024*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:056_059_056 @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:056_059_063 @atom:*_b*_a056*_d*_i* @atom:*_b*_a059*_d*_i* @atom:*_b*_a063*_d*_i* - @angle:013_060_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_060_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:056_060_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:057_060_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:020_060_060 @atom:*_b*_a020*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:016_060_060 @atom:*_b*_a016*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_060_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:024_060_060 @atom:*_b*_a024*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:056_060_060 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:048_060_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:003_060_060 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:060_060_061 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:024_060_061 @atom:*_b*_a024*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:003_060_061 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:048_060_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:012_060_080 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:048_060_080 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:080_060_081 @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:012_060_081 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:048_060_081 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a081*_d*_i* - @angle:003_060_084 @atom:*_b*_a003*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_060_087 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:057_060_087 @atom:*_b*_a057*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:081_060_087 @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:012_060_087 @atom:*_b*_a012*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:048_060_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:060_060_105 @atom:*_b*_a060*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:056_060_105 @atom:*_b*_a056*_d*_i* @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:048_061_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:025_061_057 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:025_061_061 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:060_061_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:025_061_082 @atom:*_b*_a025*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:061_061_082 @atom:*_b*_a061*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:060_061_082 @atom:*_b*_a060*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:082_061_083 @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:057_061_084 @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:082_061_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:057_061_088 @atom:*_b*_a057*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:020_061_088 @atom:*_b*_a020*_d*_i* @atom:*_b*_a061*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:049_062_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:049_062_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:057_062_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:057_062_063 @atom:*_b*_a057*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a063*_d*_i* - @angle:061_062_063 @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a063*_d*_i* - @angle:049_062_105 @atom:*_b*_a049*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:063_062_105 @atom:*_b*_a063*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:061_062_105 @atom:*_b*_a061*_d*_i* @atom:*_b*_a062*_d*_i* @atom:*_b*_a105*_d*_i* - @angle:005_064_005 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a005*_d*_i* - @angle:004_064_005 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a005*_d*_i* - @angle:004_064_013 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:005_064_020 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:020_064_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:013_064_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:004_064_020 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:004_064_048 @atom:*_b*_a004*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:005_064_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:020_064_048 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:005_064_052 @atom:*_b*_a005*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:013_064_052 @atom:*_b*_a013*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:020_064_052 @atom:*_b*_a020*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:052_064_052 @atom:*_b*_a052*_d*_i* @atom:*_b*_a064*_d*_i* @atom:*_b*_a052*_d*_i* - @angle:025_065_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a065*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:025_066_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a066*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:078_077_078 @atom:*_b*_a078*_d*_i* @atom:*_b*_a077*_d*_i* @atom:*_b*_a078*_d*_i* - @angle:006_079_011 @atom:*_b*_a006*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a011*_d*_i* - @angle:013_079_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:005_079_013 @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:005_079_023 @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a023*_d*_i* - @angle:013_079_023 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a023*_d*_i* - @angle:023_079_023 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a023*_d*_i* - @angle:013_079_024 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:023_079_024 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:013_079_044 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:023_079_044 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:013_079_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:023_079_048 @atom:*_b*_a023*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:005_079_048 @atom:*_b*_a005*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:024_079_048 @atom:*_b*_a024*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_079_082 @atom:*_b*_a013*_d*_i* @atom:*_b*_a079*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:046_080_060 @atom:*_b*_a046*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:002_080_060 @atom:*_b*_a002*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_080_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:046_080_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:002_080_084 @atom:*_b*_a002*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:013_080_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_080_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a080*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:012_081_057 @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:048_081_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:057_081_060 @atom:*_b*_a057*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:012_081_060 @atom:*_b*_a012*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:048_081_060 @atom:*_b*_a048*_d*_i* @atom:*_b*_a081*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_082_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:016_082_024 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:016_082_044 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a044*_d*_i* - @angle:020_082_049 @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:016_082_049 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:049_082_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:057_082_057 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:013_082_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:048_082_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:056_082_057 @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:049_082_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:016_082_061 @atom:*_b*_a016*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:020_082_061 @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:057_082_061 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:013_082_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:044_082_061 @atom:*_b*_a044*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:024_082_061 @atom:*_b*_a024*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:057_082_079 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:061_082_079 @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a079*_d*_i* - @angle:020_082_086 @atom:*_b*_a020*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:061_082_086 @atom:*_b*_a061*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:057_082_087 @atom:*_b*_a057*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:056_082_087 @atom:*_b*_a056*_d*_i* @atom:*_b*_a082*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:049_083_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:048_083_061 @atom:*_b*_a048*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:013_083_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:049_083_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:061_083_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:013_083_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a083*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:013_084_016 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a016*_d*_i* - @angle:013_084_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:016_084_024 @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:020_084_049 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:016_084_049 @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:048_084_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:049_084_050 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:020_084_050 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:049_084_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:013_084_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:048_084_057 @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:003_084_057 @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:057_084_058 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a058*_d*_i* - @angle:013_084_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:049_084_080 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:057_084_080 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a080*_d*_i* - @angle:049_084_083 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:057_084_083 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:020_084_083 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:016_084_083 @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:013_084_083 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:013_084_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:057_084_084 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:061_084_084 @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:020_084_086 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:057_084_086 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:049_084_087 @atom:*_b*_a049*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:057_084_087 @atom:*_b*_a057*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:020_084_087 @atom:*_b*_a020*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:016_084_087 @atom:*_b*_a016*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:061_084_087 @atom:*_b*_a061*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:013_084_087 @atom:*_b*_a013*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:048_084_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:086_084_087 @atom:*_b*_a086*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:003_084_087 @atom:*_b*_a003*_d*_i* @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:049_085_057 @atom:*_b*_a049*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:013_085_057 @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a057*_d*_i* - @angle:049_085_085 @atom:*_b*_a049*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:057_085_085 @atom:*_b*_a057*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:013_085_085 @atom:*_b*_a013*_d*_i* @atom:*_b*_a085*_d*_i* @atom:*_b*_a085*_d*_i* - @angle:048_086_048 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:048_086_056 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a056*_d*_i* - @angle:048_086_082 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a082*_d*_i* - @angle:048_086_083 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a083*_d*_i* - @angle:048_086_084 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:048_086_086 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:056_086_086 @atom:*_b*_a056*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:048_086_087 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:048_086_088 @atom:*_b*_a048*_d*_i* @atom:*_b*_a086*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:049_087_060 @atom:*_b*_a049*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:046_087_060 @atom:*_b*_a046*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_087_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:049_087_084 @atom:*_b*_a049*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:046_087_084 @atom:*_b*_a046*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:084_087_084 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:082_087_084 @atom:*_b*_a082*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:002_087_084 @atom:*_b*_a002*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:013_087_084 @atom:*_b*_a013*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:003_087_084 @atom:*_b*_a003*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:060_087_084 @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a084*_d*_i* - @angle:084_087_086 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a086*_d*_i* - @angle:049_087_087 @atom:*_b*_a049*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:060_087_087 @atom:*_b*_a060*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:084_087_087 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:086_087_087 @atom:*_b*_a086*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:084_087_088 @atom:*_b*_a084*_d*_i* @atom:*_b*_a087*_d*_i* @atom:*_b*_a088*_d*_i* - @angle:048_088_049 @atom:*_b*_a048*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a049*_d*_i* - @angle:049_088_061 @atom:*_b*_a049*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:013_088_061 @atom:*_b*_a013*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:019_088_061 @atom:*_b*_a019*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a061*_d*_i* - @angle:061_088_087 @atom:*_b*_a061*_d*_i* @atom:*_b*_a088*_d*_i* @atom:*_b*_a087*_d*_i* - @angle:004_089_090 @atom:*_b*_a004*_d*_i* @atom:*_b*_a089*_d*_i* @atom:*_b*_a090*_d*_i* - @angle:090_089_091 @atom:*_b*_a090*_d*_i* @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:004_089_091 @atom:*_b*_a004*_d*_i* @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:013_090_089 @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* @atom:*_b*_a089*_d*_i* - @angle:089_090_091 @atom:*_b*_a089*_d*_i* @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:013_090_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:024_091_046 @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_091_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:044_091_046 @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:046_091_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:016_091_046 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:046_091_047 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:046_091_089 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a089*_d*_i* - @angle:024_091_089 @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a089*_d*_i* - @angle:046_091_090 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a090*_d*_i* - @angle:016_091_090 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a090*_d*_i* - @angle:091_091_091 @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:013_091_091 @atom:*_b*_a013*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:044_091_091 @atom:*_b*_a044*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:046_091_091 @atom:*_b*_a046*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:024_091_091 @atom:*_b*_a024*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:016_091_091 @atom:*_b*_a016*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:089_091_091 @atom:*_b*_a089*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:047_091_091 @atom:*_b*_a047*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:090_091_091 @atom:*_b*_a090*_d*_i* @atom:*_b*_a091*_d*_i* @atom:*_b*_a091*_d*_i* - @angle:013_095_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_095_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a095*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_101_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_101_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_101_048 @atom:*_b*_a045*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_101_048 @atom:*_b*_a013*_d*_i* @atom:*_b*_a101*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:013_102_103 @atom:*_b*_a013*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* - @angle:048_102_103 @atom:*_b*_a048*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* - @angle:103_102_103 @atom:*_b*_a103*_d*_i* @atom:*_b*_a102*_d*_i* @atom:*_b*_a103*_d*_i* - @angle:025_103_025 @atom:*_b*_a025*_d*_i* @atom:*_b*_a103*_d*_i* @atom:*_b*_a025*_d*_i* - @angle:025_103_102 @atom:*_b*_a025*_d*_i* @atom:*_b*_a103*_d*_i* @atom:*_b*_a102*_d*_i* - @angle:013_104_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a104*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_105_010 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a010*_d*_i* - @angle:003_105_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_105_045 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:045_105_047 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:013_105_047 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:003_105_047 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:003_105_051 @atom:*_b*_a003*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:047_105_051 @atom:*_b*_a047*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a051*_d*_i* - @angle:045_105_060 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:006_105_060 @atom:*_b*_a006*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:010_105_060 @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:013_105_060 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:051_105_060 @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a060*_d*_i* - @angle:045_105_062 @atom:*_b*_a045*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:060_105_062 @atom:*_b*_a060*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:006_105_062 @atom:*_b*_a006*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:010_105_062 @atom:*_b*_a010*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:013_105_062 @atom:*_b*_a013*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:051_105_062 @atom:*_b*_a051*_d*_i* @atom:*_b*_a105*_d*_i* @atom:*_b*_a062*_d*_i* - @angle:004_106_024 @atom:*_b*_a004*_d*_i* @atom:*_b*_a106*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:024_106_024 @atom:*_b*_a024*_d*_i* @atom:*_b*_a106*_d*_i* @atom:*_b*_a024*_d*_i* - @angle:013_107_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a107*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:003_107_013 @atom:*_b*_a003*_d*_i* @atom:*_b*_a107*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:001_108_013 @atom:*_b*_a001*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_108_013 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a013*_d*_i* - @angle:013_108_020 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:020_108_020 @atom:*_b*_a020*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a020*_d*_i* - @angle:013_108_021 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a021*_d*_i* - @angle:045_108_045 @atom:*_b*_a045*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:013_108_045 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a045*_d*_i* - @angle:046_108_046 @atom:*_b*_a046*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_108_046 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a046*_d*_i* - @angle:013_108_065 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a065*_d*_i* - @angle:013_108_066 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a066*_d*_i* - @angle:013_108_108 @atom:*_b*_a013*_d*_i* @atom:*_b*_a108*_d*_i* @atom:*_b*_a108*_d*_i* - @angle:046_109_048 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a048*_d*_i* - @angle:046_109_050 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:013_109_050 @atom:*_b*_a013*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a050*_d*_i* - @angle:046_109_109 @atom:*_b*_a046*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:013_109_109 @atom:*_b*_a013*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:050_109_109 @atom:*_b*_a050*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:048_109_109 @atom:*_b*_a048*_d*_i* @atom:*_b*_a109*_d*_i* @atom:*_b*_a109*_d*_i* - @angle:004_110_047 @atom:*_b*_a004*_d*_i* @atom:*_b*_a110*_d*_i* @atom:*_b*_a047*_d*_i* - @angle:047_110_047 @atom:*_b*_a047*_d*_i* @atom:*_b*_a110*_d*_i* @atom:*_b*_a047*_d*_i* - } #(end of angles by type) - - - - - # ----------- Dihedral Interactions: ------------ - # http://lammps.sandia.gov/doc/dihedral_opls.html - # Syntax: - # dihedral_coeff DihedralTypeName parameters... - - write_once("In Settings") { - dihedral_coeff @dihedral:X_002_002_002 -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:X_002_002_006 -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:001_002_002_002 -2.0 0.7 3.0 0.0 - dihedral_coeff @dihedral:001_002_002_006 -2.0 0.7 3.0 0.0 - dihedral_coeff @dihedral:002_002_002_002 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_002_006 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_002_010 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_002_013 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_002_065 -2.0 0.5 3.25 0.0 - dihedral_coeff @dihedral:006_002_002_006 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:006_002_002_065 -2.0 0.5 3.25 0.0 - dihedral_coeff @dihedral:010_002_002_010 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_005_007 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:006_002_005_007 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:010_002_005_007 0.3 0.0 1.3 0.0 - dihedral_coeff @dihedral:X_002_010_002 -2.5 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_010_002 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:002_002_013_002 -3.4 1.25 3.1 0.0 - dihedral_coeff @dihedral:006_002_020_002 -7.4 3.0 1.8 0.0 - dihedral_coeff @dihedral:006_002_020_006 -8.4 3.0 1.8 0.0 - dihedral_coeff @dihedral:004_003_003_004 1.6 3.2 0.0 0.0 - dihedral_coeff @dihedral:004_003_003_013 0.0 0.5 0.0 0.0 - dihedral_coeff @dihedral:004_003_003_024 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_003_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:013_003_003_013 0.7 -1.5 0.0 0.0 - dihedral_coeff @dihedral:013_003_003_024 -0.5 0.2 0.0 0.0 - dihedral_coeff @dihedral:013_003_003_046 0.8 -0.76 0.0 0.0 - dihedral_coeff @dihedral:024_003_003_046 -0.9 0.3 0.0 0.0 - dihedral_coeff @dihedral:046_003_003_046 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:003_003_005_007 3.0 5.5 0.0 0.0 - dihedral_coeff @dihedral:004_003_005_007 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:013_003_005_007 1.5 5.5 0.0 0.0 - dihedral_coeff @dihedral:024_003_005_007 -2.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:046_003_005_007 1.5 5.5 0.0 0.0 - dihedral_coeff @dihedral:048_003_005_007 4.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:001_003_013_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:001_003_013_046 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:003_003_013_046 0.0 0.0 0.085 0.0 - dihedral_coeff @dihedral:004_003_013_X 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_013_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_013_021 -0.65 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_013_044 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:004_003_013_024 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_013_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_013_048 0.0 0.546 0.0 0.0 - dihedral_coeff @dihedral:005_003_013_013 0.0 1.412 0.0 0.0 - dihedral_coeff @dihedral:005_003_013_044 5.26 0.82 0.0 0.0 - dihedral_coeff @dihedral:005_003_013_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:013_003_013_013 1.454 -0.144 -0.775 0.0 - dihedral_coeff @dihedral:013_003_013_046 0.0 0.0 0.275 0.0 - dihedral_coeff @dihedral:020_003_013_013 0.0 0.0 -0.553 0.0 - dihedral_coeff @dihedral:020_003_013_046 0.0 0.0 0.132 0.0 - dihedral_coeff @dihedral:021_003_013_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:021_003_013_046 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:024_003_013_013 1.173 0.189 -1.2 0.0 - dihedral_coeff @dihedral:024_003_013_021 0.65 0.0 0.0 0.0 - dihedral_coeff @dihedral:024_003_013_024 1.816 1.222 1.581 0.0 - dihedral_coeff @dihedral:024_003_013_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:046_003_013_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:046_003_013_046 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:048_003_013_046 0.0 0.0 0.275 0.0 - dihedral_coeff @dihedral:052_003_013_013 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:052_003_013_044 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:052_003_013_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:065_003_013_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:065_003_013_046 0.0 0.0 0.36 0.0 - dihedral_coeff @dihedral:107_003_013_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_003_020_013 0.0 5.124 0.0 0.0 - dihedral_coeff @dihedral:004_003_020_048 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:013_003_020_013 4.669 5.124 0.0 0.0 - dihedral_coeff @dihedral:013_003_020_048 1.5 5.0 0.0 0.0 - dihedral_coeff @dihedral:024_003_020_013 -2.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:046_003_020_013 4.669 5.124 0.0 0.0 - dihedral_coeff @dihedral:048_003_020_013 4.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:003_003_024_013 0.4 4.9 0.0 0.0 - dihedral_coeff @dihedral:003_003_024_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:004_003_024_005 0.0 6.603 0.0 0.0 - dihedral_coeff @dihedral:004_003_024_013 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:004_003_024_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:004_003_024_047 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:004_003_024_048 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:004_003_024_091 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:005_003_024_013 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:005_003_024_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:013_003_024_005 4.542 6.603 1.045 0.0 - dihedral_coeff @dihedral:013_003_024_013 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:013_003_024_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:013_003_024_048 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:020_003_024_013 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:020_003_024_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:024_003_024_003 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:024_003_024_013 4.6 0.0 0.0 0.0 - dihedral_coeff @dihedral:024_003_024_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:046_003_024_013 2.3 6.089 0.0 0.0 - 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dihedral_coeff @dihedral:046_047_048_048 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:046_047_048_056 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:047_047_048_048 1.241 3.353 -0.286 0.0 - dihedral_coeff @dihedral:013_047_050_013 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_047_050_046 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_047_050_048 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_047_050_050 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_047_050_109 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:024_047_050_003 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_047_050_013 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_047_050_046 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_047_050_048 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_047_050_050 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_047_050_109 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:X_047_084_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_047_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:003_047_086_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_047_086_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_047_086_024 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_047_087_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_047_088_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:013_047_110_047 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:046_047_110_047 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_048_048_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_048_048_013 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_048_048_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:001_048_048_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:001_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:013_048_048_013 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:013_048_048_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:013_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:013_048_048_050 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:021_048_048_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:021_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:044_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:047_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_050 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_055 0.0 1.62 0.0 -0.44 - dihedral_coeff @dihedral:048_048_048_060 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_065 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_066 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_048_109 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_050 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_060 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_065 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_066 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_048_109 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:056_048_048_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_050_046 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:048_048_050_047 1.241 3.353 -0.286 0.0 - dihedral_coeff @dihedral:056_048_050_046 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:056_048_050_047 1.241 3.353 -0.286 0.0 - dihedral_coeff @dihedral:048_048_053_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:048_048_053_054 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_048_055_045 0.0 2.03 0.0 0.0 - dihedral_coeff @dihedral:048_048_055_045 0.0 3.9 0.0 0.0 - dihedral_coeff @dihedral:055_048_055_013 0.0 7.936 0.0 0.0 - dihedral_coeff @dihedral:055_048_055_045 0.0 3.9 0.0 0.0 - dihedral_coeff @dihedral:060_048_055_045 0.0 2.03 0.0 0.0 - dihedral_coeff @dihedral:X_048_056_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_056_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_056_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_048_060_X 0.0 7.0 0.0 0.0 - dihedral_coeff @dihedral:X_048_079_023 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:048_048_079_013 0.0 -0.9 0.0 0.0 - dihedral_coeff @dihedral:048_048_079_024 1.656 -0.768 -0.117 0.0 - dihedral_coeff @dihedral:048_048_086_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_086_056 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_048_086_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_086_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_086_056 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_086_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:056_048_086_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:056_048_086_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_048_088_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:056_048_101_013 0.0 3.651 0.0 0.0 - dihedral_coeff @dihedral:048_048_102_103 0.0 1.15 0.0 0.0 - dihedral_coeff @dihedral:048_048_109_013 0.205 -0.531 0.0 0.0 - dihedral_coeff @dihedral:048_048_109_046 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:048_048_109_109 1.241 3.353 -0.286 0.0 - dihedral_coeff @dihedral:X_050_050_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:003_050_050_003 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:013_050_050_013 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:013_050_050_046 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:013_050_050_047 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:046_050_050_046 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:046_050_050_047 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:047_050_050_047 1.423 4.055 0.858 0.0 - dihedral_coeff @dihedral:013_050_109_013 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:013_050_109_109 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:046_050_109_013 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:046_050_109_046 0.0 0.0 0.3 0.0 - dihedral_coeff @dihedral:046_050_109_109 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:047_050_109_013 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:047_050_109_046 0.0 0.0 -0.372 0.0 - dihedral_coeff @dihedral:047_050_109_109 1.423 4.055 0.858 0.0 - dihedral_coeff @dihedral:013_053_082_061 0.0 2.1 0.0 0.0 - dihedral_coeff @dihedral:048_053_082_061 0.0 2.1 0.0 0.0 - dihedral_coeff @dihedral:045_055_059_X 0.0 2.03 0.0 0.0 - dihedral_coeff @dihedral:013_056_056_013 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:013_056_056_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_056_056_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_056_059_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_056_059_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_056_060_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_056_062_X 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:X_056_082_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_056_086_048 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_056_086_086 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_057_060_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:045_057_060_X 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:X_057_061_X 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:X_057_062_X 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:X_057_081_X 0.0 3.05 0.0 0.0 - dihedral_coeff @dihedral:X_057_082_X 0.0 4.65 0.0 0.0 - dihedral_coeff @dihedral:X_057_082_049 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:045_057_082_X 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:X_057_084_X 0.0 2.8 0.0 0.0 - dihedral_coeff @dihedral:045_057_084_X 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:061_057_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:084_057_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_060_060_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_060_061_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_060_080_X 0.0 3.35 0.0 0.0 - dihedral_coeff @dihedral:X_060_081_X 0.0 6.0 0.0 0.0 - dihedral_coeff @dihedral:X_060_087_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_060_087_084 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:060_060_087_084 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_061_061_X 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:X_061_062_X 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:X_061_082_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_061_082_049 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:083_061_082_016 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:088_061_082_016 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:088_061_082_020 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_061_083_X 0.0 4.8 0.0 0.0 - dihedral_coeff @dihedral:082_061_083_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:082_061_083_084 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_061_084_X 0.0 10.0 0.0 0.0 - dihedral_coeff @dihedral:X_061_088_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:082_061_088_084 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_080_084_X 0.0 13.05 0.0 0.0 - dihedral_coeff @dihedral:X_082_084_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:016_082_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:020_082_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:057_082_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:061_082_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_082_087_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_083_084_X 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:X_083_084_049 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:049_083_084_X 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:049_083_084_016 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:049_083_084_049 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:061_083_084_016 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:061_083_084_020 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:061_083_084_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_083_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:061_083_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:061_083_087_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:084_083_087_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_084_084_X 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:X_084_084_049 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:016_084_084_049 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:049_084_084_049 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:X_084_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:016_084_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:020_084_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:057_084_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_084_087_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_084_087_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_084_087_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_084_088_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:016_084_088_049 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:016_084_088_061 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:020_084_088_061 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_084_088_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:049_084_088_061 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:048_086_086_048 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:048_086_086_056 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:048_086_087_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:048_086_088_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:048_086_088_061 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:056_086_088_X 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_087_087_020 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_087_087_057 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:X_087_087_087 0.0 2.17 0.0 0.0 - dihedral_coeff @dihedral:049_087_087_049 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:004_089_090_013 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:004_089_090_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:004_089_090_048 0.0 6.089 0.0 0.0 - dihedral_coeff @dihedral:004_089_090_091 0.0 20.0 0.0 0.0 - dihedral_coeff @dihedral:091_089_090_013 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:091_089_090_045 0.0 4.9 0.0 0.0 - dihedral_coeff @dihedral:091_089_090_048 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:091_089_090_091 2.3 6.089 0.0 0.0 - dihedral_coeff @dihedral:X_089_091_X 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_089_091_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:004_089_091_091 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:090_089_091_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:090_089_091_091 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_090_091_X 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_090_091_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_090_091_091 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_091_091_X 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_091_091_024 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:013_091_091_013 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:013_091_091_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:046_091_091_046 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:046_091_091_091 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:091_091_091_091 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:X_109_109_X 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_109_109_013 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_109_109_046 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_109_109_048 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_109_109_050 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:013_109_109_109 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_109_109_046 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_109_109_048 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_109_109_050 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:046_109_109_109 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:048_109_109_048 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:048_109_109_050 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:048_109_109_109 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:050_109_109_050 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:050_109_109_109 0.0 14.0 0.0 0.0 - dihedral_coeff @dihedral:109_109_109_109 1.423 4.055 0.858 0.0 - dihedral_coeff @dihedral:024_003_013_053 1.816 1.222 1.581 0.0 - dihedral_coeff @dihedral:052_003_013_024 0.0 0.82 0.0 0.0 - dihedral_coeff @dihedral:003_013_013_053 1.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:003_013_013_083 -1.697 -0.456 0.585 0.0 - dihedral_coeff @dihedral:003_013_013_084 -1.697 -0.456 0.585 0.0 - dihedral_coeff @dihedral:003_013_013_085 -1.697 -0.456 0.585 0.0 - dihedral_coeff @dihedral:005_013_013_053 6.28 -1.467 2.03 0.0 - dihedral_coeff @dihedral:015_013_013_053 1.428 0.086 0.029 0.0 - dihedral_coeff @dihedral:016_013_013_053 1.428 0.086 0.029 0.0 - dihedral_coeff @dihedral:013_013_013_055 2.732 -0.229 0.485 0.0 - dihedral_coeff @dihedral:024_013_013_083 0.845 -0.962 0.713 0.0 - dihedral_coeff @dihedral:053_013_013_083 1.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:024_013_013_084 0.845 -0.962 0.713 0.0 - dihedral_coeff @dihedral:053_013_013_084 1.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:024_013_013_085 0.845 -0.962 0.713 0.0 - dihedral_coeff @dihedral:046_013_013_085 0.0 0.0 0.462 0.0 - dihedral_coeff @dihedral:053_013_013_085 1.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:003_013_053_013 1.438 -0.124 0.264 0.0 - dihedral_coeff @dihedral:003_013_053_054 0.0 0.0 0.347 0.0 - dihedral_coeff @dihedral:013_013_053_054 0.0 0.0 0.347 0.0 - dihedral_coeff @dihedral:046_013_055_054 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:013_013_085_X 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:013_013_085_057 1.7 -0.6 0.0 0.0 - dihedral_coeff @dihedral:046_013_085_X 0.0 0.0 0.0 0.0 - dihedral_coeff @dihedral:055_048_055_054 0.0 3.9 0.0 0.0 - dihedral_coeff @dihedral:X_048_081_X 0.0 7.25 0.0 0.0 - dihedral_coeff @dihedral:X_057_085_X 0.0 5.0 0.0 0.0 - dihedral_coeff @dihedral:X_085_085_X 0.0 10.75 0.0 0.0 - dihedral_coeff @dihedral:013_013_013_020 1.3 -0.05 0.2 0.0 - dihedral_coeff @dihedral:013_013_013_047 1.3 -0.05 0.2 0.0 - } #(end of dihedral_coeffs) - - # Rules for creating dihedral interactions according to atom type: - # DihedralTypeName AtomType1 AtomType2 AtomType3 AtomType4 - # (* = wildcard) - - write_once("Data Dihedrals By Type") { - @dihedral:X_002_002_002 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* - @dihedral:X_002_002_006 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* - @dihedral:001_002_002_002 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* - @dihedral:001_002_002_006 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* - @dihedral:002_002_002_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* - @dihedral:002_002_002_006 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* - @dihedral:002_002_002_010 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* - @dihedral:002_002_002_013 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d013*_i* - @dihedral:002_002_002_065 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d065*_i* - @dihedral:006_002_002_006 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d006*_i* - @dihedral:006_002_002_065 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d065*_i* - @dihedral:010_002_002_010 @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* - @dihedral:002_002_005_007 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:006_002_005_007 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:010_002_005_007 @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:X_002_010_002 @atom:* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* - @dihedral:002_002_010_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* - @dihedral:002_002_013_002 @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d002*_i* - @dihedral:006_002_020_002 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d002*_i* - @dihedral:006_002_020_006 @atom:*_b*_a*_d006*_i* @atom:*_b*_a*_d002*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d006*_i* - @dihedral:004_003_003_004 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d004*_i* - @dihedral:004_003_003_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_003_024 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* - @dihedral:004_003_003_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_003_003_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_003_003_024 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* - @dihedral:013_003_003_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* - @dihedral:024_003_003_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_003_003_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d046*_i* - @dihedral:003_003_005_007 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:004_003_005_007 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:013_003_005_007 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:024_003_005_007 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:046_003_005_007 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:048_003_005_007 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d007*_i* - @dihedral:001_003_013_013 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:001_003_013_046 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:003_003_013_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:004_003_013_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:* - @dihedral:004_003_013_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_013_021 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* - @dihedral:004_003_013_044 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:004_003_013_024 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:004_003_013_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:004_003_013_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* - @dihedral:005_003_013_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:005_003_013_044 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:005_003_013_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_003_013_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_003_013_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:020_003_013_013 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:020_003_013_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:021_003_013_013 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:021_003_013_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:024_003_013_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:024_003_013_021 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* - @dihedral:024_003_013_024 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:024_003_013_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_003_013_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_003_013_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:048_003_013_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:052_003_013_013 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:052_003_013_044 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:052_003_013_046 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:065_003_013_013 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:065_003_013_046 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:107_003_013_046 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:004_003_020_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_020_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_003_020_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_003_020_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* - @dihedral:024_003_020_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_003_020_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:048_003_020_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:003_003_024_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:003_003_024_045 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:004_003_024_005 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d005*_i* - @dihedral:004_003_024_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_024_045 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:004_003_024_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d047*_i* - @dihedral:004_003_024_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* - @dihedral:004_003_024_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* - @dihedral:005_003_024_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:005_003_024_045 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_003_024_005 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d005*_i* - @dihedral:013_003_024_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_003_024_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_003_024_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* - @dihedral:020_003_024_013 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:020_003_024_045 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:024_003_024_003 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* - @dihedral:024_003_024_013 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:024_003_024_045 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_003_024_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_003_024_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:047_003_024_045 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:048_003_024_045 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:048_003_024_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_003_024_084 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* - @dihedral:048_003_024_087 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* - @dihedral:084_003_024_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* - @dihedral:084_003_024_084 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* - @dihedral:084_003_024_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* - @dihedral:087_003_024_045 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:087_003_024_048 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* - @dihedral:087_003_024_084 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* - @dihedral:087_003_024_087 @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* - @dihedral:X_003_047_013 @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_047_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:004_003_047_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:005_003_047_047 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:024_003_047_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:024_003_047_047 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:107_003_047_046 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:107_003_047_047 @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:004_003_048_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:005_003_048_048 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_003_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:020_003_048_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:024_003_048_048 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_003_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_003_050_013 @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_050_047 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:005_003_050_047 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_003_050_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_003_056_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:* - @dihedral:013_003_056_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_003_056_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:* - @dihedral:046_003_056_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d045*_i* - @dihedral:X_003_060_X @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:004_003_060_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:004_003_082_X @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:004_003_082_057 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d057*_i* - @dihedral:004_003_082_061 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:082_003_082_057 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d057*_i* - @dihedral:082_003_082_061 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:004_003_084_020 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* - @dihedral:004_003_084_087 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* - @dihedral:084_003_084_020 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* - @dihedral:084_003_084_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* - @dihedral:048_003_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_003_087_X @atom:* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:004_003_087_084 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* - @dihedral:004_003_087_087 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* - @dihedral:024_003_087_084 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* - @dihedral:024_003_087_087 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* - @dihedral:004_003_107_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_003_107_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_003_109_109 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:005_003_109_109 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:X_004_106_X @atom:* @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d106*_i* @atom:* - @dihedral:007_005_010_002 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d002*_i* - @dihedral:007_005_010_006 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d010*_i* @atom:*_b*_a*_d006*_i* - @dihedral:007_005_013_002 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d002*_i* - @dihedral:007_005_013_006 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d006*_i* - @dihedral:007_005_013_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:007_005_013_046 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:007_005_013_047 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* - @dihedral:007_005_013_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* - @dihedral:007_005_013_050 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* - @dihedral:007_005_044_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* - @dihedral:007_005_044_045 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* - @dihedral:007_005_024_003 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* - @dihedral:007_005_024_045 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:007_005_047_047 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:007_005_048_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:007_005_051_020 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* - @dihedral:007_005_056_003 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d003*_i* - @dihedral:007_005_064_004 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d004*_i* - @dihedral:007_005_064_005 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d005*_i* - @dihedral:007_005_079_013 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* - @dihedral:007_005_079_023 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* - @dihedral:007_005_079_048 @atom:*_b*_a*_d007*_i* @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_013_013_003 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* - @dihedral:X_013_013_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:X_013_013_024 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:001_013_013_001 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d001*_i* - @dihedral:001_013_013_005 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* - @dihedral:001_013_013_013 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:001_013_013_046 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:003_013_013_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d003*_i* - @dihedral:003_013_013_005 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* - @dihedral:003_013_013_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:003_013_013_015 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* - @dihedral:003_013_013_016 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* - @dihedral:003_013_013_024 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:003_013_013_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:003_013_013_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* - @dihedral:003_013_013_080 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* - @dihedral:005_013_013_005 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d005*_i* - @dihedral:005_013_013_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:005_013_013_020 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* - @dihedral:005_013_013_044 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:005_013_013_024 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:005_013_013_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_013_013_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_013_015 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* - @dihedral:013_013_013_016 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* - @dihedral:013_013_013_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* - @dihedral:013_013_013_021 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* - @dihedral:013_013_013_044 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:013_013_013_024 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:013_013_013_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_013_013_051 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* - @dihedral:013_013_013_053 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:013_013_013_065 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d065*_i* - @dihedral:013_013_013_066 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d066*_i* - @dihedral:013_013_013_079 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* - @dihedral:013_013_013_107 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* - @dihedral:013_013_013_108 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* - @dihedral:015_013_013_046 @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:016_013_013_046 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:019_013_013_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:020_013_013_020 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* - @dihedral:020_013_013_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:021_013_013_021 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d021*_i* - @dihedral:021_013_013_044 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:021_013_013_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:044_013_013_044 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* - @dihedral:044_013_013_046 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:044_013_013_048 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* - @dihedral:024_013_013_046 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:024_013_013_048 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* - @dihedral:024_013_013_080 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* - @dihedral:046_013_013_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_013_013_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_013_013_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_013_013_051 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* - @dihedral:046_013_013_053 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:046_013_013_055 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* - @dihedral:046_013_013_059 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* - @dihedral:046_013_013_062 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* - @dihedral:046_013_013_065 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d065*_i* - @dihedral:046_013_013_066 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d066*_i* - @dihedral:046_013_013_079 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* - @dihedral:046_013_013_080 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* - @dihedral:046_013_013_082 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* - @dihedral:046_013_013_083 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* - @dihedral:046_013_013_084 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* - @dihedral:046_013_013_087 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* - @dihedral:046_013_013_088 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* - @dihedral:046_013_013_102 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* - @dihedral:046_013_013_104 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* - @dihedral:046_013_013_107 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* - @dihedral:046_013_013_108 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* - @dihedral:046_013_013_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* - @dihedral:048_013_013_053 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:108_013_013_108 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* - @dihedral:013_013_015_017 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d017*_i* - @dihedral:046_013_015_017 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d017*_i* - @dihedral:013_013_016_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_016_016 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* - @dihedral:046_013_016_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_016_016 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* - @dihedral:046_013_016_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_013_018_019 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d019*_i* - @dihedral:046_013_018_019 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d019*_i* - @dihedral:X_013_019_018 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* - @dihedral:X_013_019_019 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* - @dihedral:013_013_019_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* - @dihedral:046_013_019_019 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* - @dihedral:X_013_020_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:056_013_020_013 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:057_013_020_013 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_020_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* - @dihedral:013_013_020_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_020_064 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* - @dihedral:046_013_020_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:* - @dihedral:046_013_020_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d003*_i* - @dihedral:046_013_020_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_013_020_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_013_020_051 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* - @dihedral:046_013_020_064 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* - @dihedral:X_013_024_045 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:003_013_024_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* - @dihedral:003_013_024_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:003_013_024_045 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_013_024_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* - @dihedral:013_013_024_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_024_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_013_024_059 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* - @dihedral:013_013_024_079 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* - @dihedral:013_013_024_091 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* - @dihedral:046_013_024_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* - @dihedral:046_013_024_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_024_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_024_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_013_024_079 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* - @dihedral:048_013_024_059 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* - @dihedral:013_013_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_044_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_044_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_044_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_013_047_013 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:X_013_047_046 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:X_013_047_047 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:X_013_047_050 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* - @dihedral:001_013_047_047 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_013_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_047_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_013_047_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* - @dihedral:046_013_047_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_047_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_013_047_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_013_047_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* - @dihedral:046_013_047_110 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* - @dihedral:047_013_047_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:047_013_047_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:X_013_048_048 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:001_013_048_048 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_013_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_013_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* - @dihedral:021_013_048_048 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_013_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:064_013_048_048 @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:065_013_048_048 @atom:*_b*_a*_d065*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_013_050_047 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_013_050_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* - @dihedral:046_013_050_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_013_050_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* - @dihedral:046_013_050_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* - @dihedral:013_013_051_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:* - @dihedral:013_013_051_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_013_051_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* - @dihedral:013_013_053_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_053_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_053_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_053_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_053_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_013_053_054 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* - @dihedral:013_013_055_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_013_055_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_013_055_054 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* - @dihedral:046_013_055_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_055_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_055_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_013_056_018 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d018*_i* - @dihedral:X_013_057_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* - @dihedral:013_013_057_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* - @dihedral:013_013_057_062 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* - @dihedral:013_013_057_082 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* - @dihedral:020_013_057_X @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:* - @dihedral:020_013_057_062 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* - @dihedral:020_013_057_082 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* - @dihedral:013_013_059_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:* - @dihedral:013_013_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* - @dihedral:046_013_059_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d059*_i* @atom:* - @dihedral:013_013_062_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* @atom:* - @dihedral:046_013_062_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d062*_i* @atom:* - @dihedral:046_013_064_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* - @dihedral:046_013_064_052 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* - @dihedral:048_013_064_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* - @dihedral:048_013_064_052 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* - @dihedral:X_013_079_023 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* - @dihedral:X_013_079_024 @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d024*_i* - @dihedral:013_013_079_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_079_023 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* - @dihedral:046_013_079_005 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d005*_i* - @dihedral:046_013_079_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_079_023 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* - @dihedral:046_013_079_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_013_080_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:* - @dihedral:013_013_080_060 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d060*_i* - @dihedral:013_013_080_084 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* - @dihedral:046_013_080_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:* - @dihedral:046_013_080_060 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d060*_i* - @dihedral:046_013_080_084 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* - @dihedral:013_013_082_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:046_013_082_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:013_013_083_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* @atom:* - @dihedral:046_013_083_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* @atom:* - @dihedral:001_013_084_X @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:013_013_084_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:013_013_084_057 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d057*_i* - @dihedral:021_013_084_X @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:046_013_084_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:001_013_087_X @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:013_013_087_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:021_013_087_X @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:046_013_087_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:013_013_088_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:046_013_088_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:X_013_090_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d090*_i* @atom:* - @dihedral:046_013_090_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d090*_i* @atom:* - @dihedral:046_013_091_091 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:013_013_095_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d095*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_095_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d095*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_013_102_103 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* - @dihedral:046_013_102_103 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* - @dihedral:013_013_104_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_104_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d104*_i* @atom:*_b*_a*_d013*_i* - @dihedral:X_013_105_X @atom:* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* - @dihedral:013_013_105_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* - @dihedral:013_013_105_062 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d062*_i* - @dihedral:013_013_105_082 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d082*_i* - @dihedral:020_013_105_X @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:* - @dihedral:020_013_105_062 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d062*_i* - @dihedral:020_013_105_082 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d105*_i* @atom:*_b*_a*_d082*_i* - @dihedral:003_013_107_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_107_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* - @dihedral:013_013_107_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_107_003 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d003*_i* - @dihedral:046_013_107_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_107_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d107*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_013_108_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_013_108_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d045*_i* - @dihedral:046_013_108_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_108_020 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* - @dihedral:046_013_108_045 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_013_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:046_013_109_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_013_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_013_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:017_015_048_X @atom:*_b*_a*_d017*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d048*_i* @atom:* - @dihedral:017_015_048_048 @atom:*_b*_a*_d017*_i* @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_016_016_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_016_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_016_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* - @dihedral:013_016_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* - @dihedral:084_016_082_X @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:084_016_082_061 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:082_016_084_049 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:082_016_084_083 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d083*_i* - @dihedral:082_016_084_088 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* - @dihedral:X_016_091_X @atom:* @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d091*_i* @atom:* - @dihedral:019_018_048_X @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d048*_i* @atom:* - @dihedral:019_018_048_048 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:018_018_056_013 @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* - @dihedral:018_018_056_046 @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d018*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d046*_i* - @dihedral:X_019_019_X @atom:* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:* - @dihedral:013_019_019_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_019_019_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_019_019_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_019_019_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d109*_i* - @dihedral:046_019_019_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_019_019_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d109*_i* - @dihedral:019_019_047_013 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:019_019_047_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:019_019_047_047 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_020_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_020_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_020_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_020_047_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_020_047_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_020_047_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* - @dihedral:003_020_048_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_020_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_020_048_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* - @dihedral:064_020_048_048 @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_020_051_005 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d005*_i* - @dihedral:013_020_051_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_020_051_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d020*_i* - @dihedral:013_020_051_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d051*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_020_056_003 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d003*_i* - @dihedral:013_020_059_056 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d056*_i* - @dihedral:X_020_064_052 @atom:* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* - @dihedral:013_020_064_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_020_064_052 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d052*_i* - @dihedral:048_020_064_004 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d064*_i* @atom:*_b*_a*_d004*_i* - @dihedral:084_020_082_061 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:082_020_084_088 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* - @dihedral:084_020_084_049 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:084_020_084_087 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* - @dihedral:108_020_108_013 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d013*_i* - @dihedral:108_020_108_020 @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d108*_i* @atom:*_b*_a*_d020*_i* - @dihedral:X_024_048_048 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:003_024_048_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_024_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:045_024_048_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:059_024_048_048 @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:082_024_048_048 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:084_024_048_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_024_059_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:* - @dihedral:X_024_059_049 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d049*_i* - @dihedral:045_024_059_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d059*_i* @atom:* - @dihedral:X_024_060_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:X_024_079_023 @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* - @dihedral:013_024_079_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* - @dihedral:045_024_079_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_024_082_061 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:045_024_082_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* - @dihedral:045_024_082_020 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* - @dihedral:045_024_082_061 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:048_024_082_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* - @dihedral:048_024_082_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* - @dihedral:048_024_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:X_024_084_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:003_024_084_084 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* - @dihedral:045_024_084_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* - @dihedral:045_024_084_020 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* - @dihedral:048_024_084_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* - @dihedral:048_024_084_020 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* - @dihedral:003_024_086_048 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:003_024_086_056 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* - @dihedral:003_024_086_086 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* - @dihedral:047_024_086_048 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:047_024_086_056 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* - @dihedral:X_024_087_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:X_024_088_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:003_024_091_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:003_024_091_089 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* - @dihedral:003_024_091_091 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:045_024_091_046 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:045_024_091_089 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* - @dihedral:045_024_091_091 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:X_024_106_X @atom:* @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d106*_i* @atom:* - @dihedral:013_044_044_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_044_044_045 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* - @dihedral:045_044_044_045 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d045*_i* - @dihedral:013_044_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:045_044_048_048 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:059_044_048_048 @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:082_044_048_048 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:084_044_048_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:045_044_082_016 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* - @dihedral:045_044_082_061 @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:048_044_082_016 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* - @dihedral:048_044_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:047_046_047_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:047_046_047_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:X_047_047_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:* - @dihedral:X_047_047_019 @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d019*_i* - @dihedral:003_047_047_024 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d024*_i* - @dihedral:003_047_047_046 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:005_047_047_013 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:005_047_047_046 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_047_047_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_047_047_019 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d019*_i* - @dihedral:013_047_047_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d020*_i* - @dihedral:013_047_047_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:019_047_047_046 @atom:*_b*_a*_d019*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:020_047_047_046 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:021_047_047_021 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d021*_i* - @dihedral:021_047_047_046 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_047_047_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_047_047_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_047_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_047_048_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_047_048_056 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* - @dihedral:047_047_048_048 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_047_050_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_047_050_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_047_050_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_047_050_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* - @dihedral:013_047_050_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* - @dihedral:024_047_050_003 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d003*_i* - @dihedral:046_047_050_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_047_050_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_047_050_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_047_050_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* - @dihedral:046_047_050_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* - @dihedral:X_047_084_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:X_047_086_048 @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:003_047_086_086 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* - @dihedral:049_047_086_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:* - @dihedral:049_047_086_024 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d024*_i* - @dihedral:X_047_087_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:X_047_088_X @atom:* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:013_047_110_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_047_110_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d110*_i* @atom:*_b*_a*_d047*_i* - @dihedral:X_048_048_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:* - @dihedral:X_048_048_013 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* - @dihedral:X_048_048_048 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_048_048_049 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:001_048_048_048 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:001_048_048_049 @atom:*_b*_a*_d001*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:013_048_048_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_048_048_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_048_048_049 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:013_048_048_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* - @dihedral:021_048_048_048 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:021_048_048_049 @atom:*_b*_a*_d021*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:044_048_048_049 @atom:*_b*_a*_d044*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:047_048_048_049 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:048_048_048_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_048_048_049 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:048_048_048_050 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* - @dihedral:048_048_048_055 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* - @dihedral:048_048_048_060 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* - @dihedral:048_048_048_065 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d065*_i* - @dihedral:048_048_048_066 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d066*_i* - @dihedral:048_048_048_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* - @dihedral:048_048_048_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* - @dihedral:049_048_048_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d049*_i* - @dihedral:049_048_048_050 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* - @dihedral:049_048_048_060 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* - @dihedral:049_048_048_065 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d065*_i* - @dihedral:049_048_048_066 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d066*_i* - @dihedral:049_048_048_086 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* - @dihedral:049_048_048_109 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* - @dihedral:056_048_048_086 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* - @dihedral:048_048_050_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* - @dihedral:048_048_050_047 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:056_048_050_046 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* - @dihedral:056_048_050_047 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:048_048_053_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* - @dihedral:048_048_053_054 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* - @dihedral:X_048_055_045 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* - @dihedral:048_048_055_045 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* - @dihedral:055_048_055_013 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d013*_i* - @dihedral:055_048_055_045 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* - @dihedral:060_048_055_045 @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d045*_i* - @dihedral:X_048_056_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:* - @dihedral:048_048_056_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* - @dihedral:049_048_056_048 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_048_060_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:X_048_079_023 @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d023*_i* - @dihedral:048_048_079_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d013*_i* - @dihedral:048_048_079_024 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d079*_i* @atom:*_b*_a*_d024*_i* - @dihedral:048_048_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_048_086_056 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* - @dihedral:048_048_086_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* - @dihedral:049_048_086_048 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:049_048_086_056 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* - @dihedral:049_048_086_086 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* - @dihedral:056_048_086_048 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:056_048_086_086 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* - @dihedral:049_048_088_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* - @dihedral:056_048_101_013 @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d101*_i* @atom:*_b*_a*_d013*_i* - @dihedral:048_048_102_103 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d102*_i* @atom:*_b*_a*_d103*_i* - @dihedral:048_048_109_013 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* - @dihedral:048_048_109_046 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* - @dihedral:048_048_109_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:X_050_050_049 @atom:* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d049*_i* - @dihedral:003_050_050_003 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d003*_i* - @dihedral:013_050_050_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_050_050_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_050_050_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:046_050_050_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_050_050_047 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:047_050_050_047 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d047*_i* - @dihedral:013_050_109_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_050_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:046_050_109_013 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* - @dihedral:046_050_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_050_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:047_050_109_013 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* - @dihedral:047_050_109_046 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* - @dihedral:047_050_109_109 @atom:*_b*_a*_d047*_i* @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:013_053_082_061 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:048_053_082_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* - @dihedral:045_055_059_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d059*_i* @atom:* - @dihedral:013_056_056_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_056_056_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_056_056_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_056_059_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d059*_i* @atom:* - @dihedral:X_056_059_049 @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d059*_i* @atom:*_b*_a*_d049*_i* - @dihedral:X_056_060_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:X_056_062_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d062*_i* @atom:* - @dihedral:X_056_082_X @atom:* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:048_056_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_056_086_086 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* - @dihedral:X_057_060_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:045_057_060_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:X_057_061_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d061*_i* @atom:* - @dihedral:X_057_062_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d062*_i* @atom:* - @dihedral:X_057_081_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d081*_i* @atom:* - @dihedral:X_057_082_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:X_057_082_049 @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d049*_i* - @dihedral:045_057_082_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:X_057_084_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:045_057_084_X @atom:*_b*_a*_d045*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:061_057_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:084_057_086_048 @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_060_060_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d060*_i* @atom:* - @dihedral:X_060_061_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d061*_i* @atom:* - @dihedral:X_060_080_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d080*_i* @atom:* - @dihedral:X_060_081_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d081*_i* @atom:* - @dihedral:X_060_087_X @atom:* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:048_060_087_084 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* - @dihedral:060_060_087_084 @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d060*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d084*_i* - @dihedral:X_061_061_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d061*_i* @atom:* - @dihedral:X_061_062_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d062*_i* @atom:* - @dihedral:X_061_082_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:* - @dihedral:X_061_082_049 @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d049*_i* - @dihedral:083_061_082_016 @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* - @dihedral:088_061_082_016 @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d016*_i* - @dihedral:088_061_082_020 @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d020*_i* - @dihedral:X_061_083_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:* - @dihedral:082_061_083_049 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d049*_i* - @dihedral:082_061_083_084 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* - @dihedral:X_061_084_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:X_061_088_X @atom:* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:082_061_088_084 @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d084*_i* - @dihedral:X_080_084_X @atom:* @atom:*_b*_a*_d080*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:X_082_084_X @atom:* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:016_082_086_048 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:020_082_086_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:057_082_086_048 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:061_082_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_082_087_X @atom:* @atom:*_b*_a*_d082*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:X_083_084_X @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:X_083_084_049 @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:049_083_084_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:049_083_084_016 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* - @dihedral:049_083_084_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:061_083_084_016 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d016*_i* - @dihedral:061_083_084_020 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d020*_i* - @dihedral:061_083_084_049 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:X_083_086_048 @atom:* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:061_083_086_048 @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:061_083_087_X @atom:*_b*_a*_d061*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:084_083_087_X @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d083*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:X_084_084_X @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:* - @dihedral:X_084_084_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:016_084_084_049 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:049_084_084_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d049*_i* - @dihedral:X_084_086_048 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:016_084_086_048 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:020_084_086_048 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:057_084_086_048 @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:X_084_087_X @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:X_084_087_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* - @dihedral:049_084_087_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* - @dihedral:X_084_088_049 @atom:* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* - @dihedral:016_084_088_049 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d049*_i* - @dihedral:016_084_088_061 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* - @dihedral:020_084_088_061 @atom:*_b*_a*_d020*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* - @dihedral:049_084_088_X @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:049_084_088_061 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d084*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* - @dihedral:048_086_086_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_086_086_056 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d056*_i* - @dihedral:048_086_087_X @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d087*_i* @atom:* - @dihedral:048_086_088_X @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:048_086_088_061 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:*_b*_a*_d061*_i* - @dihedral:056_086_088_X @atom:*_b*_a*_d056*_i* @atom:*_b*_a*_d086*_i* @atom:*_b*_a*_d088*_i* @atom:* - @dihedral:X_087_087_020 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d020*_i* - @dihedral:X_087_087_057 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d057*_i* - @dihedral:X_087_087_087 @atom:* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* - @dihedral:049_087_087_049 @atom:*_b*_a*_d049*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d087*_i* @atom:*_b*_a*_d049*_i* - @dihedral:004_089_090_013 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d013*_i* - @dihedral:004_089_090_045 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d045*_i* - @dihedral:004_089_090_048 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d048*_i* - @dihedral:004_089_090_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* - @dihedral:091_089_090_013 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d013*_i* - @dihedral:091_089_090_045 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d045*_i* - @dihedral:091_089_090_048 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d048*_i* - @dihedral:091_089_090_091 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* - @dihedral:X_089_091_X @atom:* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:* - @dihedral:004_089_091_046 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:004_089_091_091 @atom:*_b*_a*_d004*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:090_089_091_046 @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:090_089_091_091 @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d089*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:X_090_091_X @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:* - @dihedral:X_090_091_046 @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:X_090_091_091 @atom:* @atom:*_b*_a*_d090*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:X_091_091_X @atom:* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:* - @dihedral:X_091_091_024 @atom:* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d024*_i* - @dihedral:013_091_091_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_091_091_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_091_091_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_091_091_091 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:091_091_091_091 @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* @atom:*_b*_a*_d091*_i* - @dihedral:X_109_109_X @atom:* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:* - @dihedral:013_109_109_013 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d013*_i* - @dihedral:013_109_109_046 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* - @dihedral:013_109_109_048 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* - @dihedral:013_109_109_050 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* - @dihedral:013_109_109_109 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:046_109_109_046 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d046*_i* - @dihedral:046_109_109_048 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* - @dihedral:046_109_109_050 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* - @dihedral:046_109_109_109 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:048_109_109_048 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d048*_i* - @dihedral:048_109_109_050 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* - @dihedral:048_109_109_109 @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:050_109_109_050 @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d050*_i* - @dihedral:050_109_109_109 @atom:*_b*_a*_d050*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:109_109_109_109 @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* @atom:*_b*_a*_d109*_i* - @dihedral:024_003_013_053 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:052_003_013_024 @atom:*_b*_a*_d052*_i* @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d024*_i* - @dihedral:003_013_013_053 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:003_013_013_083 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* - @dihedral:003_013_013_084 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* - @dihedral:003_013_013_085 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* - @dihedral:005_013_013_053 @atom:*_b*_a*_d005*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:015_013_013_053 @atom:*_b*_a*_d015*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:016_013_013_053 @atom:*_b*_a*_d016*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* - @dihedral:013_013_013_055 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* - @dihedral:024_013_013_083 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* - @dihedral:053_013_013_083 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d083*_i* - @dihedral:024_013_013_084 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* - @dihedral:053_013_013_084 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d084*_i* - @dihedral:024_013_013_085 @atom:*_b*_a*_d024*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* - @dihedral:046_013_013_085 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* - @dihedral:053_013_013_085 @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* - @dihedral:003_013_053_013 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d013*_i* - @dihedral:003_013_053_054 @atom:*_b*_a*_d003*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* - @dihedral:013_013_053_054 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d053*_i* @atom:*_b*_a*_d054*_i* - @dihedral:046_013_055_054 @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* - @dihedral:013_013_085_X @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:* - @dihedral:013_013_085_057 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:*_b*_a*_d057*_i* - @dihedral:046_013_085_X @atom:*_b*_a*_d046*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d085*_i* @atom:* - @dihedral:055_048_055_054 @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d055*_i* @atom:*_b*_a*_d054*_i* - @dihedral:X_048_081_X @atom:* @atom:*_b*_a*_d048*_i* @atom:*_b*_a*_d081*_i* @atom:* - @dihedral:X_057_085_X @atom:* @atom:*_b*_a*_d057*_i* @atom:*_b*_a*_d085*_i* @atom:* - @dihedral:X_085_085_X @atom:* @atom:*_b*_a*_d085*_i* @atom:*_b*_a*_d085*_i* @atom:* - @dihedral:013_013_013_020 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d020*_i* - @dihedral:013_013_013_047 @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d013*_i* @atom:*_b*_a*_d047*_i* - } #(end of dihedrals by type) - - - - - # ---------- Improper Interactions: ---------- - # http://lammps.sandia.gov/doc/improper_harmonic.html - # Syntax: - # improper_coeff ImproperTypeName parameters - - write_once("In Settings") { - # The following force field parameters were converted from - # the tinker parameter file (oplsaa.prm) and then edited by hand: - # Thanks to David Huang (adelaide.edu.au) for the corrections: - - improper_coeff @improper:X_X_003_004 10.5 180.0 # (moltemplate) - # <==> "imptors 0 0 3 4 21.000 180.0 2" in oplsaa.prm (tinker) - # <==> "define improper_O_C_X_Y 180.0 43.93200 2" in oplsaa.ff (gromacs) - - improper_coeff @improper:X_X_003_052 10.5 180.0 # (moltemplate) - # <==> "imptors 0 0 3 52 21.000 180.0 2" in oplsaa.prm (tinker) - # <==> "define improper_O_C_X_Y 180.0 43.93200 2" in oplsaa.ff (gromacs) - - improper_coeff @improper:X_X_024_X 1.0 180.0 # (moltemplate) - # <==> "imptors 0 0 24 0 5.000 180.0 2" in oplsaa.prm (tinker) - INCORRECT? - # <==> "define improper_Z_N_X_Y 180.0 4.18400 2" in oplsaa.ff (gromacs) - - improper_coeff @improper:X_X_047_X 15.0 180.0 # (moltemplate) - # <==> "imptors 0 0 47 0 30.000 180.0 2" in oplsaa.prm (tinker) - # <==> "define improper_Z_CM_X_Y 180.0 62.76000 2" in oplsaa.ff (gromacs) - - improper_coeff @improper:X_X_048_X 1.1 180.0 # (moltemplate) - # <==> "imptors 0 0 48 0 5.000 180.0 2" in oplsaa.prm (tinker) - INCORRECT? - # <==> "define improper_Z_CA_X_Y 180.0 4.60240 2" in oplsaa.ff (gromacs) - - improper_coeff @improper:055_055_X_055 10.5 180.0 - # <==> "define improper_N2_X_N2_N2 180.0 43.93200" in oplsaa.ff (gromacs) - # <==> no corresponding line found in oplsaa.prm (tinker) - - # --- As of 2017-9-13, I am unsure if I should add this rule: ---- - # The gromacs file for oplsaa include the following line: - # "define improper_X_NO_ON_NO 180.0 43.93200" in oplsaa.ff (gromacs) - # but there is no corresponding line found in oplsaa.prm (tinker) - # and there is no corresponding line from opls-a.prm (emc (BASF)) - # I'm not sure what the "NO" and "ON" correspond to. If I had to guess, - # the corresponding moltemplate line might be one of these two choices: - # improper_coeff @improper:X_103_102_102 10.5 180.0 ? - # improper_coeff @improper:X_102_103_103 10.5 180.0 ? - # but I'd prefer to leave this out. - - } #(end of improper_coeffs) - - - # Rules for creating improper interactions according to atom type: - # ImproperTypeName AtomType1 AtomType2 AtomType3 AtomType4 - # (* = wildcard) - write_once("Data Impropers By Type (opls_imp.py)") { - @improper:X_X_003_004 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i004* - @improper:X_X_003_052 @atom:* @atom:* @atom:*_b*_a*_d*_i003* @atom:*_b*_a*_d*_i052* - @improper:X_X_024_X @atom:* @atom:* @atom:*_b*_a*_d*_i024* @atom:* - @improper:X_X_047_X @atom:* @atom:* @atom:*_b*_a*_d*_i047* @atom:* - @improper:X_X_048_X @atom:* @atom:* @atom:*_b*_a*_d*_i048* @atom:* - @improper:055_055_X_055 @atom:*_b*_a*_d*_i55 @atom:*_b*_a*_d*_i55 @atom:* @atom:*_b*_a*_d*_i55 - } #(end of impropers by type) - - - - - # -------- (descriptive comment) -------- - # ---- biologically relevant atom types: ---- - # biotype 1 N "Glycine" 180 - # biotype 2 CA "Glycine" 165 - # biotype 3 C "Glycine" 177 - # biotype 4 HN "Glycine" 183 - # biotype 5 O "Glycine" 178 - # biotype 6 HA "Glycine" 85 - # biotype 7 N "Alanine" 180 - # biotype 8 CA "Alanine" 166 - # biotype 9 C "Alanine" 177 - # biotype 10 HN "Alanine" 183 - # biotype 11 O "Alanine" 178 - # biotype 12 HA "Alanine" 85 - # biotype 13 CB "Alanine" 80 - # biotype 14 HB "Alanine" 85 - # biotype 15 N "Valine" 180 - # biotype 16 CA "Valine" 166 - # biotype 17 C "Valine" 177 - # biotype 18 HN "Valine" 183 - # biotype 19 O "Valine" 178 - # biotype 20 HA "Valine" 85 - # biotype 21 CB "Valine" 82 - # biotype 22 HB "Valine" 85 - # biotype 23 CG1 "Valine" 80 - # biotype 24 HG1 "Valine" 85 - # biotype 25 CG2 "Valine" 80 - # biotype 26 HG2 "Valine" 85 - # biotype 27 N "Leucine" 180 - # biotype 28 CA "Leucine" 166 - # biotype 29 C "Leucine" 177 - # biotype 30 HN "Leucine" 183 - # biotype 31 O "Leucine" 178 - # biotype 32 HA "Leucine" 85 - # biotype 33 CB "Leucine" 81 - # biotype 34 HB "Leucine" 85 - # biotype 35 CG "Leucine" 82 - # biotype 36 HG "Leucine" 85 - # biotype 37 CD1 "Leucine" 80 - # biotype 38 HD1 "Leucine" 85 - # biotype 39 CD2 "Leucine" 80 - # biotype 40 HD2 "Leucine" 85 - # biotype 41 N "Isoleucine" 180 - # biotype 42 CA "Isoleucine" 166 - # biotype 43 C "Isoleucine" 177 - # biotype 44 HN "Isoleucine" 183 - # biotype 45 O "Isoleucine" 178 - # biotype 46 HA "Isoleucine" 85 - # biotype 47 CB "Isoleucine" 82 - # biotype 48 HB "Isoleucine" 85 - # biotype 49 CG1 "Isoleucine" 80 - # biotype 50 HG1 "Isoleucine" 85 - # biotype 51 CG2 "Isoleucine" 81 - # biotype 52 HG2 "Isoleucine" 85 - # biotype 53 CD "Isoleucine" 80 - # biotype 54 HD "Isoleucine" 85 - # biotype 55 N "Serine" 180 - # biotype 56 CA "Serine" 166 - # biotype 57 C "Serine" 177 - # biotype 58 HN "Serine" 183 - # biotype 59 O "Serine" 178 - # biotype 60 HA "Serine" 85 - # biotype 61 CB "Serine" 99 - # biotype 62 HB "Serine" 85 - # biotype 63 OG "Serine" 96 - # biotype 64 HG "Serine" 97 - # biotype 65 N "Threonine" 180 - # biotype 66 CA "Threonine" 166 - # biotype 67 C "Threonine" 177 - # biotype 68 HN "Threonine" 183 - # biotype 69 O "Threonine" 178 - # biotype 70 HA "Threonine" 85 - # biotype 71 CB "Threonine" 100 - # biotype 72 HB "Threonine" 85 - # biotype 73 OG1 "Threonine" 96 - # biotype 74 HG1 "Threonine" 97 - # biotype 75 CG2 "Threonine" 80 - # biotype 76 HG2 "Threonine" 85 - # biotype 77 N "Cysteine (SH)" 180 - # biotype 78 CA "Cysteine (SH)" 166 - # biotype 79 C "Cysteine (SH)" 177 - # biotype 80 HN "Cysteine (SH)" 183 - # biotype 81 O "Cysteine (SH)" 178 - # biotype 82 HA "Cysteine (SH)" 85 - # biotype 83 CB "Cysteine (SH)" 148 - # biotype 84 HB "Cysteine (SH)" 85 - # biotype 85 SG "Cysteine (SH)" 142 - # biotype 86 HG "Cysteine (SH)" 146 - # biotype 87 N "Cystine (SS)" 180 - # biotype 88 CA "Cystine (SS)" 166 - # biotype 89 C "Cystine (SS)" 177 - # biotype 90 HN "Cystine (SS)" 183 - # biotype 91 O "Cystine (SS)" 178 - # biotype 92 HA "Cystine (SS)" 85 - # biotype 93 CB "Cystine (SS)" 156 - # biotype 94 HB "Cystine (SS)" 85 - # biotype 95 SG "Cystine (SS)" 145 - # biotype 96 N "Cysteine (S-)" -1 - # biotype 97 CA "Cysteine (S-)" -1 - # biotype 98 C "Cysteine (S-)" -1 - # biotype 99 HN "Cysteine (S-)" -1 - # biotype 100 O "Cysteine (S-)" -1 - # biotype 101 HA "Cysteine (S-)" -1 - # biotype 102 CB "Cysteine (S-)" -1 - # biotype 103 HB "Cysteine (S-)" -1 - # biotype 104 SG "Cysteine (S-)" -1 - # biotype 105 N "Proline" 181 - # biotype 106 CA "Proline" 188 - # biotype 107 C "Proline" 177 - # biotype 108 O "Proline" 178 - # biotype 109 HA "Proline" 85 - # biotype 110 CB "Proline" 81 - # biotype 111 HB "Proline" 85 - # biotype 112 CG "Proline" 81 - # biotype 113 HG "Proline" 85 - # biotype 114 CD "Proline" 187 - # biotype 115 HD "Proline" 85 - # biotype 116 N "Phenylalanine" 180 - # biotype 117 CA "Phenylalanine" 166 - # biotype 118 C "Phenylalanine" 177 - # biotype 119 HN "Phenylalanine" 183 - # biotype 120 O "Phenylalanine" 178 - # biotype 121 HA "Phenylalanine" 85 - # biotype 122 CB "Phenylalanine" 94 - # biotype 123 HB "Phenylalanine" 85 - # biotype 124 CG "Phenylalanine" 90 - # biotype 125 CD "Phenylalanine" 90 - # biotype 126 HD "Phenylalanine" 91 - # biotype 127 CE "Phenylalanine" 90 - # biotype 128 HE "Phenylalanine" 91 - # biotype 129 CZ "Phenylalanine" 90 - # biotype 130 HZ "Phenylalanine" 91 - # biotype 131 N "Tyrosine" 180 - # biotype 132 CA "Tyrosine" 166 - # biotype 133 C "Tyrosine" 177 - # biotype 134 HN "Tyrosine" 183 - # biotype 135 O "Tyrosine" 178 - # biotype 136 HA "Tyrosine" 85 - # biotype 137 CB "Tyrosine" 94 - # biotype 138 HB "Tyrosine" 85 - # biotype 139 CG "Tyrosine" 90 - # biotype 140 CD "Tyrosine" 90 - # biotype 141 HD "Tyrosine" 91 - # biotype 142 CE "Tyrosine" 90 - # biotype 143 HE "Tyrosine" 91 - # biotype 144 CZ "Tyrosine" 108 - # biotype 145 OH "Tyrosine" 109 - # biotype 146 HH "Tyrosine" 110 - # biotype 147 N "Tyrosine (O-)" -1 - # biotype 148 CA "Tyrosine (O-)" -1 - # biotype 149 C "Tyrosine (O-)" -1 - # biotype 150 HN "Tyrosine (O-)" -1 - # biotype 151 O "Tyrosine (O-)" -1 - # biotype 152 HA "Tyrosine (O-)" -1 - # biotype 153 CB "Tyrosine (O-)" -1 - # biotype 154 HB "Tyrosine (O-)" -1 - # biotype 155 CG "Tyrosine (O-)" -1 - # biotype 156 CD "Tyrosine (O-)" -1 - # biotype 157 HD "Tyrosine (O-)" -1 - # biotype 158 CE "Tyrosine (O-)" -1 - # biotype 159 HE "Tyrosine (O-)" -1 - # biotype 160 CZ "Tyrosine (O-)" -1 - # biotype 161 OH "Tyrosine (O-)" -1 - # biotype 162 N "Tryptophan" 180 - # biotype 163 CA "Tryptophan" 166 - # biotype 164 C "Tryptophan" 177 - # biotype 165 HN "Tryptophan" 183 - # biotype 166 O "Tryptophan" 178 - # biotype 167 HA "Tryptophan" 85 - # biotype 168 CB "Tryptophan" 81 - # biotype 169 HB "Tryptophan" 85 - # biotype 170 CG "Tryptophan" 441 - # biotype 171 CD1 "Tryptophan" 455 - # biotype 172 HD1 "Tryptophan" 91 - # biotype 173 CD2 "Tryptophan" 442 - # biotype 174 NE1 "Tryptophan" 444 - # biotype 175 HE1 "Tryptophan" 445 - # biotype 176 CE2 "Tryptophan" 443 - # biotype 177 CE3 "Tryptophan" 90 - # biotype 178 HE3 "Tryptophan" 91 - # biotype 179 CZ2 "Tryptophan" 90 - # biotype 180 HZ2 "Tryptophan" 91 - # biotype 181 CZ3 "Tryptophan" 90 - # biotype 182 HZ3 "Tryptophan" 91 - # biotype 183 CH2 "Tryptophan" 90 - # biotype 184 HH2 "Tryptophan" 91 - # biotype 185 N "Histidine (+)" 180 - # biotype 186 CA "Histidine (+)" 166 - # biotype 187 C "Histidine (+)" 177 - # biotype 188 HN "Histidine (+)" 183 - # biotype 189 O "Histidine (+)" 178 - # biotype 190 HA "Histidine (+)" 85 - # biotype 191 CB "Histidine (+)" 446 - # biotype 192 HB "Histidine (+)" 85 - # biotype 193 CG "Histidine (+)" 451 - # biotype 194 ND1 "Histidine (+)" 453 - # biotype 195 HD1 "Histidine (+)" 454 - # biotype 196 CD2 "Histidine (+)" 451 - # biotype 197 HD2 "Histidine (+)" 91 - # biotype 198 CE1 "Histidine (+)" 450 - # biotype 199 HE1 "Histidine (+)" 91 - # biotype 200 NE2 "Histidine (+)" 453 - # biotype 201 HE2 "Histidine (+)" 454 - # biotype 202 N "Histidine (HD)" 180 - # biotype 203 CA "Histidine (HD)" 166 - # biotype 204 C "Histidine (HD)" 177 - # biotype 205 HN "Histidine (HD)" 183 - # biotype 206 O "Histidine (HD)" 178 - # biotype 207 HA "Histidine (HD)" 85 - # biotype 208 CB "Histidine (HD)" 446 - # biotype 209 HB "Histidine (HD)" 85 - # biotype 210 CG "Histidine (HD)" 449 - # biotype 211 ND1 "Histidine (HD)" 444 - # biotype 212 HD1 "Histidine (HD)" 445 - # biotype 213 CD2 "Histidine (HD)" 448 - # biotype 214 HD2 "Histidine (HD)" 91 - # biotype 215 CE1 "Histidine (HD)" 447 - # biotype 216 HE1 "Histidine (HD)" 91 - # biotype 217 NE2 "Histidine (HD)" 452 - # biotype 218 N "Histidine (HE)" 180 - # biotype 219 CA "Histidine (HE)" 166 - # biotype 220 C "Histidine (HE)" 177 - # biotype 221 HN "Histidine (HE)" 183 - # biotype 222 O "Histidine (HE)" 178 - # biotype 223 HA "Histidine (HE)" 85 - # biotype 224 CB "Histidine (HE)" 446 - # biotype 225 HB "Histidine (HE)" 85 - # biotype 226 CG "Histidine (HE)" 448 - # biotype 227 ND1 "Histidine (HE)" 452 - # biotype 228 CD2 "Histidine (HE)" 449 - # biotype 229 HD2 "Histidine (HE)" 91 - # biotype 230 CE1 "Histidine (HE)" 447 - # biotype 231 HE1 "Histidine (HE)" 91 - # biotype 232 NE2 "Histidine (HE)" 444 - # biotype 233 HE2 "Histidine (HE)" 445 - # biotype 234 N "Aspartic Acid" 180 - # biotype 235 CA "Aspartic Acid" 166 - # biotype 236 C "Aspartic Acid" 177 - # biotype 237 HN "Aspartic Acid" 183 - # biotype 238 O "Aspartic Acid" 178 - # biotype 239 HA "Aspartic Acid" 85 - # biotype 240 CB "Aspartic Acid" 216 - # biotype 241 HB "Aspartic Acid" 85 - # biotype 242 CG "Aspartic Acid" 213 - # biotype 243 OD "Aspartic Acid" 214 - # biotype 244 N "Aspartic Acid (COOH)" -1 - # biotype 245 CA "Aspartic Acid (COOH)" -1 - # biotype 246 C "Aspartic Acid (COOH)" -1 - # biotype 247 HN "Aspartic Acid (COOH)" -1 - # biotype 248 O "Aspartic Acid (COOH)" -1 - # biotype 249 HA "Aspartic Acid (COOH)" -1 - # biotype 250 CB "Aspartic Acid (COOH)" -1 - # biotype 251 HB "Aspartic Acid (COOH)" -1 - # biotype 252 CG "Aspartic Acid (COOH)" -1 - # biotype 253 OD1 "Aspartic Acid (COOH)" -1 - # biotype 254 OD2 "Aspartic Acid (COOH)" -1 - # biotype 255 HD2 "Aspartic Acid (COOH)" -1 - # biotype 256 N "Asparagine" 180 - # biotype 257 CA "Asparagine" 166 - # biotype 258 C "Asparagine" 177 - # biotype 259 HN "Asparagine" 183 - # biotype 260 O "Asparagine" 178 - # biotype 261 HA "Asparagine" 85 - # biotype 262 CB "Asparagine" 81 - # biotype 263 HB "Asparagine" 85 - # biotype 264 CG "Asparagine" 177 - # biotype 265 OD1 "Asparagine" 178 - # biotype 266 ND2 "Asparagine" 179 - # biotype 267 HD2 "Asparagine" 182 - # biotype 268 N "Glutamic Acid" 180 - # biotype 269 CA "Glutamic Acid" 166 - # biotype 270 C "Glutamic Acid" 177 - # biotype 271 HN "Glutamic Acid" 183 - # biotype 272 O "Glutamic Acid" 178 - # biotype 273 HA "Glutamic Acid" 85 - # biotype 274 CB "Glutamic Acid" 81 - # biotype 275 HB "Glutamic Acid" 85 - # biotype 276 CG "Glutamic Acid" 216 - # biotype 277 HG "Glutamic Acid" 85 - # biotype 278 CD "Glutamic Acid" 213 - # biotype 279 OE "Glutamic Acid" 214 - # biotype 280 N "Glutamic Acid (COOH)" -1 - # biotype 281 CA "Glutamic Acid (COOH)" -1 - # biotype 282 C "Glutamic Acid (COOH)" -1 - # biotype 283 HN "Glutamic Acid (COOH)" -1 - # biotype 284 O "Glutamic Acid (COOH)" -1 - # biotype 285 HA "Glutamic Acid (COOH)" -1 - # biotype 286 CB "Glutamic Acid (COOH)" -1 - # biotype 287 HB "Glutamic Acid (COOH)" -1 - # biotype 288 CG "Glutamic Acid (COOH)" -1 - # biotype 289 HG "Glutamic Acid (COOH)" -1 - # biotype 290 CD "Glutamic Acid (COOH)" -1 - # biotype 291 OE1 "Glutamic Acid (COOH)" -1 - # biotype 292 OE2 "Glutamic Acid (COOH)" -1 - # biotype 293 HE2 "Glutamic Acid (COOH)" -1 - # biotype 294 N "Glutamine" 180 - # biotype 295 CA "Glutamine" 166 - # biotype 296 C "Glutamine" 177 - # biotype 297 HN "Glutamine" 183 - # biotype 298 O "Glutamine" 178 - # biotype 299 HA "Glutamine" 85 - # biotype 300 CB "Glutamine" 81 - # biotype 301 HB "Glutamine" 85 - # biotype 302 CG "Glutamine" 81 - # biotype 303 HG "Glutamine" 85 - # biotype 304 CD "Glutamine" 177 - # biotype 305 OE1 "Glutamine" 178 - # biotype 306 NE2 "Glutamine" 179 - # biotype 307 HE2 "Glutamine" 182 - # biotype 308 N "Methionine" 180 - # biotype 309 CA "Methionine" 166 - # biotype 310 C "Methionine" 177 - # biotype 311 HN "Methionine" 183 - # biotype 312 O "Methionine" 178 - # biotype 313 HA "Methionine" 85 - # biotype 314 CB "Methionine" 81 - # biotype 315 HB "Methionine" 85 - # biotype 316 CG "Methionine" 152 - # biotype 317 HG "Methionine" 85 - # biotype 318 SD "Methionine" 144 - # biotype 319 CE "Methionine" 151 - # biotype 320 HE "Methionine" 85 - # biotype 321 N "Lysine" 180 - # biotype 322 CA "Lysine" 166 - # biotype 323 C "Lysine" 177 - # biotype 324 HN "Lysine" 183 - # biotype 325 O "Lysine" 178 - # biotype 326 HA "Lysine" 85 - # biotype 327 CB "Lysine" 81 - # biotype 328 HB "Lysine" 85 - # biotype 329 CG "Lysine" 81 - # biotype 330 HG "Lysine" 85 - # biotype 331 CD "Lysine" 81 - # biotype 332 HD "Lysine" 85 - # biotype 333 CE "Lysine" 235 - # biotype 334 HE "Lysine" 85 - # biotype 335 NZ "Lysine" 230 - # biotype 336 HZ "Lysine" 233 - # biotype 337 N "Lysine (NH2)" -1 - # biotype 338 CA "Lysine (NH2)" -1 - # biotype 339 C "Lysine (NH2)" -1 - # biotype 340 HN "Lysine (NH2)" -1 - # biotype 341 O "Lysine (NH2)" -1 - # biotype 342 HA "Lysine (NH2)" -1 - # biotype 343 CB "Lysine (NH2)" -1 - # biotype 344 HB "Lysine (NH2)" -1 - # biotype 345 CG "Lysine (NH2)" -1 - # biotype 346 HG "Lysine (NH2)" -1 - # biotype 347 CD "Lysine (NH2)" -1 - # biotype 348 HD "Lysine (NH2)" -1 - # biotype 349 CE "Lysine (NH2)" -1 - # biotype 350 HE "Lysine (NH2)" -1 - # biotype 351 NZ "Lysine (NH2)" -1 - # biotype 352 HZ "Lysine (NH2)" -1 - # biotype 353 N "Arginine" 180 - # biotype 354 CA "Arginine" 166 - # biotype 355 C "Arginine" 177 - # biotype 356 HN "Arginine" 183 - # biotype 357 O "Arginine" 178 - # biotype 358 HA "Arginine" 85 - # biotype 359 CB "Arginine" 81 - # biotype 360 HB "Arginine" 85 - # biotype 361 CG "Arginine" 251 - # biotype 362 HG "Arginine" 85 - # biotype 363 CD "Arginine" 250 - # biotype 364 HD "Arginine" 85 - # biotype 365 NE "Arginine" 246 - # biotype 366 HE "Arginine" 247 - # biotype 367 CZ "Arginine" 245 - # biotype 368 NH "Arginine" 243 - # biotype 369 HH "Arginine" 244 - # biotype 370 N "Ornithine" 180 - # biotype 371 CA "Ornithine" 166 - # biotype 372 C "Ornithine" 177 - # biotype 373 HN "Ornithine" 183 - # biotype 374 O "Ornithine" 178 - # biotype 375 HA "Ornithine" 85 - # biotype 376 CB "Ornithine" 81 - # biotype 377 HB "Ornithine" 85 - # biotype 378 CG "Ornithine" 81 - # biotype 379 HG "Ornithine" 85 - # biotype 380 CD "Ornithine" 235 - # biotype 381 HD "Ornithine" 85 - # biotype 382 NE "Ornithine" 230 - # biotype 383 HE "Ornithine" 233 - # biotype 384 N "MethylAlanine (AIB)" 180 - # biotype 385 CA "MethylAlanine (AIB)" 167 - # biotype 386 C "MethylAlanine (AIB)" 177 - # biotype 387 HN "MethylAlanine (AIB)" 183 - # biotype 388 O "MethylAlanine (AIB)" 178 - # biotype 389 CB "MethylAlanine (AIB)" 80 - # biotype 390 HB "MethylAlanine (AIB)" 85 - # biotype 391 N "Pyroglutamic Acid" 180 - # biotype 392 CA "Pyroglutamic Acid" 166 - # biotype 393 C "Pyroglutamic Acid" 177 - # biotype 394 HN "Pyroglutamic Acid" 183 - # biotype 395 O "Pyroglutamic Acid" 178 - # biotype 396 HA "Pyroglutamic Acid" 85 - # biotype 397 CB "Pyroglutamic Acid" 81 - # biotype 398 HB "Pyroglutamic Acid" 85 - # biotype 399 CG "Pyroglutamic Acid" 216 - # biotype 400 HG "Pyroglutamic Acid" 85 - # biotype 401 CD "Pyroglutamic Acid" 177 - # biotype 402 OE "Pyroglutamic Acid" 178 - # biotype 403 N "N-Terminal GLY" 230 - # biotype 404 CA "N-Terminal GLY" 235 - # biotype 405 C "N-Terminal GLY" 177 - # biotype 406 HN "N-Terminal GLY" 233 - # biotype 407 O "N-Terminal GLY" 178 - # biotype 408 HA "N-Terminal GLY" 85 - # biotype 409 N "N-Terminal ALA" 230 - # biotype 410 CA "N-Terminal ALA" 236 - # biotype 411 C "N-Terminal ALA" 177 - # biotype 412 HN "N-Terminal ALA" 233 - # biotype 413 O "N-Terminal ALA" 178 - # biotype 414 HA "N-Terminal ALA" 85 - # biotype 415 N "N-Terminal VAL" 230 - # biotype 416 CA "N-Terminal VAL" 236 - # biotype 417 C "N-Terminal VAL" 177 - # biotype 418 HN "N-Terminal VAL" 233 - # biotype 419 O "N-Terminal VAL" 178 - # biotype 420 HA "N-Terminal VAL" 85 - # biotype 421 N "N-Terminal LEU" 230 - # biotype 422 CA "N-Terminal LEU" 236 - # biotype 423 C "N-Terminal LEU" 177 - # biotype 424 HN "N-Terminal LEU" 233 - # biotype 425 O "N-Terminal LEU" 178 - # biotype 426 HA "N-Terminal LEU" 85 - # biotype 427 N "N-Terminal ILE" 230 - # biotype 428 CA "N-Terminal ILE" 236 - # biotype 429 C "N-Terminal ILE" 177 - # biotype 430 HN "N-Terminal ILE" 233 - # biotype 431 O "N-Terminal ILE" 178 - # biotype 432 HA "N-Terminal ILE" 85 - # biotype 433 N "N-Terminal SER" 230 - # biotype 434 CA "N-Terminal SER" 236 - # biotype 435 C "N-Terminal SER" 177 - # biotype 436 HN "N-Terminal SER" 233 - # biotype 437 O "N-Terminal SER" 178 - # biotype 438 HA "N-Terminal SER" 85 - # biotype 439 N "N-Terminal THR" 230 - # biotype 440 CA "N-Terminal THR" 236 - # biotype 441 C "N-Terminal THR" 177 - # biotype 442 HN "N-Terminal THR" 233 - # biotype 443 O "N-Terminal THR" 178 - # biotype 444 HA "N-Terminal THR" 85 - # biotype 445 N "N-Terminal CYS (SH)" 230 - # biotype 446 CA "N-Terminal CYS (SH)" 236 - # biotype 447 C "N-Terminal CYS (SH)" 177 - # biotype 448 HN "N-Terminal CYS (SH)" 233 - # biotype 449 O "N-Terminal CYS (SH)" 178 - # biotype 450 HA "N-Terminal CYS (SH)" 85 - # biotype 451 N "N-Terminal CYX (SS)" 230 - # biotype 452 CA "N-Terminal CYX (SS)" 236 - # biotype 453 C "N-Terminal CYX (SS)" 177 - # biotype 454 HN "N-Terminal CYX (SS)" 233 - # biotype 455 O "N-Terminal CYX (SS)" 178 - # biotype 456 HA "N-Terminal CYX (SS)" 85 - # biotype 457 N "N-Terminal CYD (S-)" -1 - # biotype 458 CA "N-Terminal CYD (S-)" -1 - # biotype 459 C "N-Terminal CYD (S-)" -1 - # biotype 460 HN "N-Terminal CYD (S-)" -1 - # biotype 461 O "N-Terminal CYD (S-)" -1 - # biotype 462 HA "N-Terminal CYD (S-)" -1 - # biotype 463 N "N-Terminal PRO" 252 - # biotype 464 CA "N-Terminal PRO" 238 - # biotype 465 C "N-Terminal PRO" 177 - # biotype 466 HN "N-Terminal PRO" 253 - # biotype 467 O "N-Terminal PRO" 178 - # biotype 468 HA "N-Terminal PRO" 85 - # biotype 469 CD "N-Terminal PRO" 239 - # biotype 470 HD "N-Terminal PRO" 85 - # biotype 471 N "N-Terminal PHE" 230 - # biotype 472 CA "N-Terminal PHE" 236 - # biotype 473 C "N-Terminal PHE" 177 - # biotype 474 HN "N-Terminal PHE" 233 - # biotype 475 O "N-Terminal PHE" 178 - # biotype 476 HA "N-Terminal PHE" 85 - # biotype 477 N "N-Terminal TYR" 230 - # biotype 478 CA "N-Terminal TYR" 236 - # biotype 479 C "N-Terminal TYR" 177 - # biotype 480 HN "N-Terminal TYR" 233 - # biotype 481 O "N-Terminal TYR" 178 - # biotype 482 HA "N-Terminal TYR" 85 - # biotype 483 N "N-Terminal TYD (O-)" -1 - # biotype 484 CA "N-Terminal TYD (O-)" -1 - # biotype 485 C "N-Terminal TYD (O-)" -1 - # biotype 486 HN "N-Terminal TYD (O-)" -1 - # biotype 487 O "N-Terminal TYD (O-)" -1 - # biotype 488 HA "N-Terminal TYD (O-)" -1 - # biotype 489 N "N-Terminal TRP" 230 - # biotype 490 CA "N-Terminal TRP" 236 - # biotype 491 C "N-Terminal TRP" 177 - # biotype 492 HN "N-Terminal TRP" 233 - # biotype 493 O "N-Terminal TRP" 178 - # biotype 494 HA "N-Terminal TRP" 85 - # biotype 495 N "N-Terminal HIS (+)" 230 - # biotype 496 CA "N-Terminal HIS (+)" 236 - # biotype 497 C "N-Terminal HIS (+)" 177 - # biotype 498 HN "N-Terminal HIS (+)" 233 - # biotype 499 O "N-Terminal HIS (+)" 178 - # biotype 500 HA "N-Terminal HIS (+)" 85 - # biotype 501 N "N-Terminal HIS (HD)" 230 - # biotype 502 CA "N-Terminal HIS (HD)" 236 - # biotype 503 C "N-Terminal HIS (HD)" 177 - # biotype 504 HN "N-Terminal HIS (HD)" 233 - # biotype 505 O "N-Terminal HIS (HD)" 178 - # biotype 506 HA "N-Terminal HIS (HD)" 85 - # biotype 507 N "N-Terminal HIS (HE)" 230 - # biotype 508 CA "N-Terminal HIS (HE)" 236 - # biotype 509 C "N-Terminal HIS (HE)" 177 - # biotype 510 HN "N-Terminal HIS (HE)" 233 - # biotype 511 O "N-Terminal HIS (HE)" 178 - # biotype 512 HA "N-Terminal HIS (HE)" 85 - # biotype 513 N "N-Terminal ASP" 230 - # biotype 514 CA "N-Terminal ASP" 236 - # biotype 515 C "N-Terminal ASP" 177 - # biotype 516 HN "N-Terminal ASP" 233 - # biotype 517 O "N-Terminal ASP" 178 - # biotype 518 HA "N-Terminal ASP" 85 - # biotype 519 N "N-Terminal ASH (COOH)" -1 - # biotype 520 CA "N-Terminal ASH (COOH)" -1 - # biotype 521 C "N-Terminal ASH (COOH)" -1 - # biotype 522 HN "N-Terminal ASH (COOH)" -1 - # biotype 523 O "N-Terminal ASH (COOH)" -1 - # biotype 524 HA "N-Terminal ASH (COOH)" -1 - # biotype 525 N "N-Terminal ASN" 230 - # biotype 526 CA "N-Terminal ASN" 236 - # biotype 527 C "N-Terminal ASN" 177 - # biotype 528 HN "N-Terminal ASN" 233 - # biotype 529 O "N-Terminal ASN" 178 - # biotype 530 HA "N-Terminal ASN" 85 - # biotype 531 N "N-Terminal GLU" 230 - # biotype 532 CA "N-Terminal GLU" 236 - # biotype 533 C "N-Terminal GLU" 177 - # biotype 534 HN "N-Terminal GLU" 233 - # biotype 535 O "N-Terminal GLU" 178 - # biotype 536 HA "N-Terminal GLU" 85 - # biotype 537 N "N-Terminal GLH (COOH)" -1 - # biotype 538 CA "N-Terminal GLH (COOH)" -1 - # biotype 539 C "N-Terminal GLH (COOH)" -1 - # biotype 540 HN "N-Terminal GLH (COOH)" -1 - # biotype 541 O "N-Terminal GLH (COOH)" -1 - # biotype 542 HA "N-Terminal GLH (COOH)" -1 - # biotype 543 N "N-Terminal GLN" 230 - # biotype 544 CA "N-Terminal GLN" 236 - # biotype 545 C "N-Terminal GLN" 177 - # biotype 546 HN "N-Terminal GLN" 233 - # biotype 547 O "N-Terminal GLN" 178 - # biotype 548 HA "N-Terminal GLN" 85 - # biotype 549 N "N-Terminal MET" 230 - # biotype 550 CA "N-Terminal MET" 236 - # biotype 551 C "N-Terminal MET" 177 - # biotype 552 HN "N-Terminal MET" 233 - # biotype 553 O "N-Terminal MET" 178 - # biotype 554 HA "N-Terminal MET" 85 - # biotype 555 N "N-Terminal LYS" 230 - # biotype 556 CA "N-Terminal LYS" 236 - # biotype 557 C "N-Terminal LYS" 177 - # biotype 558 HN "N-Terminal LYS" 233 - # biotype 559 O "N-Terminal LYS" 178 - # biotype 560 HA "N-Terminal LYS" 85 - # biotype 561 N "N-Terminal LYD (NH2)" -1 - # biotype 562 CA "N-Terminal LYD (NH2)" -1 - # biotype 563 C "N-Terminal LYD (NH2)" -1 - # biotype 564 HN "N-Terminal LYD (NH2)" -1 - # biotype 565 O "N-Terminal LYD (NH2)" -1 - # biotype 566 HA "N-Terminal LYD (NH2)" -1 - # biotype 567 N "N-Terminal ARG" 230 - # biotype 568 CA "N-Terminal ARG" 236 - # biotype 569 C "N-Terminal ARG" 177 - # biotype 570 HN "N-Terminal ARG" 233 - # biotype 571 O "N-Terminal ARG" 178 - # biotype 572 HA "N-Terminal ARG" 85 - # biotype 573 N "N-Terminal ORN" 230 - # biotype 574 CA "N-Terminal ORN" 236 - # biotype 575 C "N-Terminal ORN" 177 - # biotype 576 HN "N-Terminal ORN" 233 - # biotype 577 O "N-Terminal ORN" 178 - # biotype 578 HA "N-Terminal ORN" 85 - # biotype 579 N "N-Terminal AIB" 230 - # biotype 580 CA "N-Terminal AIB" 237 - # biotype 581 C "N-Terminal AIB" 177 - # biotype 582 HN "N-Terminal AIB" 233 - # biotype 583 O "N-Terminal AIB" 178 - # biotype 584 N "C-Terminal GLY" 180 - # biotype 585 CA "C-Terminal GLY" 226 - # biotype 586 C "C-Terminal GLY" 213 - # biotype 587 HN "C-Terminal GLY" 183 - # biotype 588 OXT "C-Terminal GLY" 214 - # biotype 589 HA "C-Terminal GLY" 85 - # biotype 590 N "C-Terminal ALA" 180 - # biotype 591 CA "C-Terminal ALA" 225 - # biotype 592 C "C-Terminal ALA" 213 - # biotype 593 HN "C-Terminal ALA" 183 - # biotype 594 OXT "C-Terminal ALA" 214 - # biotype 595 HA "C-Terminal ALA" 85 - # biotype 596 N "C-Terminal VAL" 180 - # biotype 597 CA "C-Terminal VAL" 225 - # biotype 598 C "C-Terminal VAL" 213 - # biotype 599 HN "C-Terminal VAL" 183 - # biotype 600 OXT "C-Terminal VAL" 214 - # biotype 601 HA "C-Terminal VAL" 85 - # biotype 602 N "C-Terminal LEU" 180 - # biotype 603 CA "C-Terminal LEU" 225 - # biotype 604 C "C-Terminal LEU" 213 - # biotype 605 HN "C-Terminal LEU" 183 - # biotype 606 OXT "C-Terminal LEU" 214 - # biotype 607 HA "C-Terminal LEU" 85 - # biotype 608 N "C-Terminal ILE" 180 - # biotype 609 CA "C-Terminal ILE" 225 - # biotype 610 C "C-Terminal ILE" 213 - # biotype 611 HN "C-Terminal ILE" 183 - # biotype 612 OXT "C-Terminal ILE" 214 - # biotype 613 HA "C-Terminal ILE" 85 - # biotype 614 N "C-Terminal SER" 180 - # biotype 615 CA "C-Terminal SER" 225 - # biotype 616 C "C-Terminal SER" 213 - # biotype 617 HN "C-Terminal SER" 183 - # biotype 618 OXT "C-Terminal SER" 214 - # biotype 619 HA "C-Terminal SER" 85 - # biotype 620 N "C-Terminal THR" 180 - # biotype 621 CA "C-Terminal THR" 225 - # biotype 622 C "C-Terminal THR" 213 - # biotype 623 HN "C-Terminal THR" 183 - # biotype 624 OXT "C-Terminal THR" 214 - # biotype 625 HA "C-Terminal THR" 85 - # biotype 626 N "C-Terminal CYS (SH)" 180 - # biotype 627 CA "C-Terminal CYS (SH)" 225 - # biotype 628 C "C-Terminal CYS (SH)" 213 - # biotype 629 HN "C-Terminal CYS (SH)" 183 - # biotype 630 OXT "C-Terminal CYS (SH)" 214 - # biotype 631 HA "C-Terminal CYS (SH)" 85 - # biotype 632 N "C-Terminal CYX (SS)" 180 - # biotype 633 CA "C-Terminal CYX (SS)" 225 - # biotype 634 C "C-Terminal CYX (SS)" 213 - # biotype 635 HN "C-Terminal CYX (SS)" 183 - # biotype 636 OXT "C-Terminal CYX (SS)" 214 - # biotype 637 HA "C-Terminal CYX (SS)" 85 - # biotype 638 N "C-Terminal CYD (S-)" -1 - # biotype 639 CA "C-Terminal CYD (S-)" -1 - # biotype 640 C "C-Terminal CYD (S-)" -1 - # biotype 641 HN "C-Terminal CYD (S-)" -1 - # biotype 642 OXT "C-Terminal CYD (S-)" -1 - # biotype 643 HA "C-Terminal CYD (S-)" -1 - # biotype 644 N "C-Terminal PRO" 181 - # biotype 645 CA "C-Terminal PRO" 228 - # biotype 646 C "C-Terminal PRO" 213 - # biotype 647 OXT "C-Terminal PRO" 214 - # biotype 648 HA "C-Terminal PRO" 85 - # biotype 649 N "C-Terminal PHE" 180 - # biotype 650 CA "C-Terminal PHE" 225 - # biotype 651 C "C-Terminal PHE" 213 - # biotype 652 HN "C-Terminal PHE" 183 - # biotype 653 OXT "C-Terminal PHE" 214 - # biotype 654 HA "C-Terminal PHE" 85 - # biotype 655 N "C-Terminal TYR" 180 - # biotype 656 CA "C-Terminal TYR" 225 - # biotype 657 C "C-Terminal TYR" 213 - # biotype 658 HN "C-Terminal TYR" 183 - # biotype 659 OXT "C-Terminal TYR" 214 - # biotype 660 HA "C-Terminal TYR" 85 - # biotype 661 N "C-Terminal TYD (O-)" -1 - # biotype 662 CA "C-Terminal TYD (O-)" -1 - # biotype 663 C "C-Terminal TYD (O-)" -1 - # biotype 664 HN "C-Terminal TYD (O-)" -1 - # biotype 665 OXT "C-Terminal TYD (O-)" -1 - # biotype 666 HA "C-Terminal TYD (O-)" -1 - # biotype 667 N "C-Terminal TRP" 180 - # biotype 668 CA "C-Terminal TRP" 225 - # biotype 669 C "C-Terminal TRP" 213 - # biotype 670 HN "C-Terminal TRP" 183 - # biotype 671 OXT "C-Terminal TRP" 214 - # biotype 672 HA "C-Terminal TRP" 85 - # biotype 673 N "C-Terminal HIS (+)" 180 - # biotype 674 CA "C-Terminal HIS (+)" 225 - # biotype 675 C "C-Terminal HIS (+)" 213 - # biotype 676 HN "C-Terminal HIS (+)" 183 - # biotype 677 OXT "C-Terminal HIS (+)" 214 - # biotype 678 HA "C-Terminal HIS (+)" 85 - # biotype 679 N "C-Terminal HIS (HD)" 180 - # biotype 680 CA "C-Terminal HIS (HD)" 225 - # biotype 681 C "C-Terminal HIS (HD)" 213 - # biotype 682 HN "C-Terminal HIS (HD)" 183 - # biotype 683 OXT "C-Terminal HIS (HD)" 214 - # biotype 684 HA "C-Terminal HIS (HD)" 85 - # biotype 685 N "C-Terminal HIS (HE)" 180 - # biotype 686 CA "C-Terminal HIS (HE)" 225 - # biotype 687 C "C-Terminal HIS (HE)" 213 - # biotype 688 HN "C-Terminal HIS (HE)" 183 - # biotype 689 OXT "C-Terminal HIS (HE)" 214 - # biotype 690 HA "C-Terminal HIS (HE)" 85 - # biotype 691 N "C-Terminal ASP" 180 - # biotype 692 CA "C-Terminal ASP" 225 - # biotype 693 C "C-Terminal ASP" 213 - # biotype 694 HN "C-Terminal ASP" 183 - # biotype 695 OXT "C-Terminal ASP" 214 - # biotype 696 HA "C-Terminal ASP" 85 - # biotype 697 N "C-Terminal ASH (COOH)" -1 - # biotype 698 CA "C-Terminal ASH (COOH)" -1 - # biotype 699 C "C-Terminal ASH (COOH)" -1 - # biotype 700 HN "C-Terminal ASH (COOH)" -1 - # biotype 701 OXT "C-Terminal ASH (COOH)" -1 - # biotype 702 HA "C-Terminal ASH (COOH)" -1 - # biotype 703 N "C-Terminal ASN" 180 - # biotype 704 CA "C-Terminal ASN" 225 - # biotype 705 C "C-Terminal ASN" 213 - # biotype 706 HN "C-Terminal ASN" 183 - # biotype 707 OXT "C-Terminal ASN" 214 - # biotype 708 HA "C-Terminal ASN" 85 - # biotype 709 N "C-Terminal GLU" 180 - # biotype 710 CA "C-Terminal GLU" 225 - # biotype 711 C "C-Terminal GLU" 213 - # biotype 712 HN "C-Terminal GLU" 183 - # biotype 713 OXT "C-Terminal GLU" 214 - # biotype 714 HA "C-Terminal GLU" 85 - # biotype 715 N "C-Terminal GLH (COOH)" -1 - # biotype 716 CA "C-Terminal GLH (COOH)" -1 - # biotype 717 C "C-Terminal GLH (COOH)" -1 - # biotype 718 HN "C-Terminal GLH (COOH)" -1 - # biotype 719 OXT "C-Terminal GLH (COOH)" -1 - # biotype 720 HA "C-Terminal GLH (COOH)" -1 - # biotype 721 N "C-Terminal GLN" 180 - # biotype 722 CA "C-Terminal GLN" 225 - # biotype 723 C "C-Terminal GLN" 213 - # biotype 724 HN "C-Terminal GLN" 183 - # biotype 725 OXT "C-Terminal GLN" 214 - # biotype 726 HA "C-Terminal GLN" 85 - # biotype 727 N "C-Terminal MET" 180 - # biotype 728 CA "C-Terminal MET" 225 - # biotype 729 C "C-Terminal MET" 213 - # biotype 730 HN "C-Terminal MET" 183 - # biotype 731 OXT "C-Terminal MET" 214 - # biotype 732 HA "C-Terminal MET" 85 - # biotype 733 N "C-Terminal LYS" 180 - # biotype 734 CA "C-Terminal LYS" 225 - # biotype 735 C "C-Terminal LYS" 213 - # biotype 736 HN "C-Terminal LYS" 183 - # biotype 737 OXT "C-Terminal LYS" 214 - # biotype 738 HA "C-Terminal LYS" 85 - # biotype 739 N "C-Terminal LYD (NH2)" -1 - # biotype 740 CA "C-Terminal LYD (NH2)" -1 - # biotype 741 C "C-Terminal LYD (NH2)" -1 - # biotype 742 HN "C-Terminal LYD (NH2)" -1 - # biotype 743 OXT "C-Terminal LYD (NH2)" -1 - # biotype 744 HA "C-Terminal LYD (NH2)" -1 - # biotype 745 N "C-Terminal ARG" 180 - # biotype 746 CA "C-Terminal ARG" 225 - # biotype 747 C "C-Terminal ARG" 213 - # biotype 748 HN "C-Terminal ARG" 183 - # biotype 749 OXT "C-Terminal ARG" 214 - # biotype 750 HA "C-Terminal ARG" 85 - # biotype 751 N "C-Terminal ORN" 180 - # biotype 752 CA "C-Terminal ORN" 225 - # biotype 753 C "C-Terminal ORN" 213 - # biotype 754 HN "C-Terminal ORN" 183 - # biotype 755 OXT "C-Terminal ORN" 214 - # biotype 756 HA "C-Terminal ORN" 85 - # biotype 757 N "C-Terminal AIB" 180 - # biotype 758 CA "C-Terminal AIB" 227 - # biotype 759 C "C-Terminal AIB" 213 - # biotype 760 HN "C-Terminal AIB" 183 - # biotype 761 OXT "C-Terminal AIB" 214 - # biotype 762 N "Deprotonated N-Terminus" -1 - # biotype 763 H "Deprotonated N-Terminus" -1 - # biotype 764 C "Formyl N-Terminus" 177 - # biotype 765 H "Formyl N-Terminus" 221 - # biotype 766 O "Formyl N-Terminus" 178 - # biotype 767 CH3 "Acetyl N-Terminus" 80 - # biotype 768 H "Acetyl N-Terminus" 85 - # biotype 769 C "Acetyl N-Terminus" 177 - # biotype 770 O "Acetyl N-Terminus" 178 - # biotype 771 C "Protonated C-Terminus" -1 - # biotype 772 O "Protonated C-Terminus" -1 - # biotype 773 OH "Protonated C-Terminus" -1 - # biotype 774 HO "Protonated C-Terminus" -1 - # biotype 775 N "Amide C-Terminus" 179 - # biotype 776 HN "Amide C-Terminus" 182 - # biotype 777 N "N-MeAmide C-Terminus" 180 - # biotype 778 HN "N-MeAmide C-Terminus" 183 - # biotype 779 CH3 "N-MeAmide C-Terminus" 184 - # biotype 780 H "N-MeAmide C-Terminus" 85 - # biotype 2001 O "Water" 63 - # biotype 2002 H "Water" 64 - # biotype 2003 NA "Sodium Ion" -1 - # biotype 2004 K "Potassium Ion" -1 - # biotype 2005 MG "Magnesium Ion" -1 - # biotype 2006 CA "Calcium Ion" -1 - # biotype 2007 CL "Chloride Ion" -1 - # ---------- (end of comment) ---------- - - - - - # LAMMPS supports many different kinds of bonded and non-bonded - # interactions which can be selected at run time. Eventually - # we must inform LAMMPS which of them we will need. We specify - # this in the "In Init" section: - - write_once("In Init") { - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style opls - improper_style harmonic - pair_style lj/cut/coul/long 10.0 10.0 - pair_modify mix geometric - special_bonds lj/coul 0.0 0.0 0.5 - kspace_style pppm 0.0001 - } #end of init parameters - - # Note: We use "hybrid" styles in case the user later wishes to - # combine the molecules built using this force-field with other - # molecules that use other styles. (This is not necessarily - # a good idea, but LAMMPS and moltemplate both allow it.) - # For more information: - # http://lammps.sandia.gov/doc/pair_hybrid.html - # http://lammps.sandia.gov/doc/bond_hybrid.html - # http://lammps.sandia.gov/doc/angle_hybrid.html - # http://lammps.sandia.gov/doc/dihedral_hybrid.html - # http://lammps.sandia.gov/doc/improper_hybrid.html - - -} # OPLSAA - diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt deleted file mode 100644 index 5874b5926b..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/AUTHOR.txt +++ /dev/null @@ -1,7 +0,0 @@ - -OPLSAA force-field conversion tools provided by -Jason Lambert and Andrew Jewett. - -LOPLSAA force-field conversion provided by Sebastian Echeverri. - - diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt deleted file mode 100644 index 2412c4aa7d..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/README.txt +++ /dev/null @@ -1,10 +0,0 @@ -The "oplsaa.lt" file contains force field parameters which we found in the -"oplsaa.prm" file which is distributed with TINKER. -Jay Ponder, (the author of TINKER) preferred that we do not distribute -that file with moltemplate. However you can download that file here: - -https://dasher.wustl.edu/tinker/distribution/params/oplsaa.prm - -This directory does contain other files ("loplsaa.prm") containing additional -force field parameters that modify the original OPLSAA force field. - diff --git a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm b/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm deleted file mode 100644 index bf89d9a341..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/oplsaa_original_format/loplsaa_ext.prm +++ /dev/null @@ -1,153 +0,0 @@ - ############################################################################ - ## Extra OPLSAA parameters and atom types for long hydrocarbon chains ## - ## SOURCES: Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8(4), 1459 - ## Pluhackova,...,Böckmann, J.Phys.Chem.B (2015), 119(49), 15287 ## - ## CREDIT: Sebastian Echeverri (file format conversion) ## - ############################################################################ - ## This file was used with "tinkerparm2lt.py" to create "loplsaa.lt" ## - ############################################################################ - -atom 80L 13L CT "Alkane CH3- (LOPLS CT_CH3)" 6 12.011 4 -atom 81L 13L CT "Alkane -CH2- (LOPLS CT_CH2)" 6 12.011 4 -atom 81LL 13LL CT "Alkane -CH2- (LOPLS ALT)" 6 12.011 4 -atom 85LCH3 46 HC "Alkane H-C CH3 (LOPLS HC_CH3)" 1 1.008 1 -atom 85LCH2 46 HC "Alkane H-C CH2 (LOPLS HC_CH2)" 1 1.008 1 -atom 87L 47L CM "Alkene RH-C= (LOPLS CM_CH)" 6 12.011 3 -atom 89L 46 HC "Alkene H-C= (LOPLS HC_CH)" 1 1.008 1 -atom 86L 47L CM "Alkene R2-C= (LOPLS)" 6 12.011 3 -atom 88L 47L CM "Alkene H2-C= (LOPLS)" 6 12.011 3 -atom 96L 5L OH "Alcohol -OH (LOPLS)" 8 15.999 2 -atom 97L 7L HO "Alcohol -OH (LOPLS)" 1 1.008 1 -atom 111L 5L OH "Diol -OH (LOPLS)" 8 15.999 2 -atom 112L 7L HO "Diol -OH (LOPLS)" 1 1.008 1 -atom 113L 5L OH "Triol -OH (LOPLS)" 8 15.999 2 -atom 114L 7L HO "Triol -OH (LOPLS)" 1 1.008 1 -atom 118L 46L HC "Diol & Triol H-COH (LOPLS)" 1 1.008 1 -atom 169L 47L CM "Chloroalkene Cl-CH= (LOPLS)" 6 12.011 3 -atom 266L 47L CM "Uracil & Thymine C5 (LOPLS)" 6 12.011 3 -atom 267L 47L CM "Uracil & Thymine C6 (LOPLS)" 6 12.011 3 -atom 280L 47L CM "Cytosine C5 (LOPLS)" 6 12.011 3 -atom 281L 47L CM "Cytosine C6 (LOPLS)" 6 12.011 3 -atom 324L 47L CM "CytosineH+ C5 (LOPLS)" 6 12.011 3 -atom 325L 47L CM "CytosineH+ C6 (LOPLS)" 6 12.011 3 -atom 340L 47L CM "Trifluorothymine CF3- (LOPLS)" 6 12.011 4 -atom 342L 47L CM "Chloroalkene Cl2-C= (LOPLS)" 6 12.011 3 -atom 406L 3L C_2 "Ester -COOR (LOPLS)" 6 12.011 3 -atom 407L 4L O_2 "Ester C=O (LOPLS)" 8 15.999 1 -atom 408L 20L OS "Ester CO-O-R (LOPLS)" 8 15.999 2 -atom 458L 47L CM "Vinyl Ether =CH-OR (LOPLS)" 6 12.011 3 -atom 459L 47L CM "Vinyl Ether =CR-OR (LOPLS)" 6 12.011 3 -atom 649L 47L CM "Cl..CH3..Cl- Sn2 TS (LOPLS)" 6 12.011 5 -atom 718L 46L HC "Propylene Carbonate CH2 (LOPLS)" 1 1.008 1 -atom 718LL 46L HC "Propylene Carbonate CH2 (LOPLS ALT)" 1 1.008 1 -atom 900L 47L CM "Allene/Ketene H2C=C=X (LOPLS)" 6 12.011 3 -atom 901L 47L CM "Allene/Ketene HRC=C=X (LOPLS)" 6 12.011 3 -atom 902L 47L CM "Allene/Ketene R2C=C=X (LOPLS)" 6 12.011 3 - -###################### - -vdw 80L 3.5000 0.0660 -vdw 81L 3.5000 0.0660 -vdw 81LL 0.3500 0.0660 -vdw 85LCH3 2.5000 0.0300 -vdw 85LCH2 2.5000 0.026290630975 -vdw 87L 3.5500 0.0760 -vdw 89L 2.4200 0.0300 -vdw 86L 3.5500 0.0760 -vdw 88L 3.5500 0.0760 -vdw 96L 0.3120 0.1700 -vdw 97L 0.0000 0.0000 -vdw 111L 0.3070 0.1700 -vdw 112L 0.0000 0.0000 -vdw 113L 0.3070 0.1700 -vdw 114L 0.0000 0.0000 -vdw 118L 0.2500 0.0300 -vdw 169L 3.5500 0.0760 -vdw 266L 3.5000 0.0800 -vdw 267L 3.5000 0.0800 -vdw 280L 3.5000 0.0800 -vdw 281L 3.5000 0.0800 -vdw 324L 3.5000 0.0800 -vdw 325L 3.5000 0.0800 -vdw 340L 3.5000 0.0800 -vdw 342L 3.5500 0.0760 -vdw 406L 0.31875 0.1050 -vdw 407L 0.3108 0.1680 -vdw 408L 0.2550 0.1700 -vdw 458L 3.5500 0.0760 -vdw 459L 3.5500 0.0760 -vdw 649L 3.5500 0.0760 -vdw 718L 0.2420 0.1500 -vdw 718LL 0.2420 0.1500 -vdw 900L 3.3000 0.0860 -vdw 901L 3.3000 0.0860 -vdw 902L 3.3000 0.0860 - -###################### - - -# New torsion angle parameters -# Taken from table 2 of -# Sui, Pluhackova, Böckmann, J.Chem.Theory.Comp (2012), 8, 1459 -torsion 13L 13L 13L 13L 0.6446926386 0 1 -0.2143420172 180 2 0.1782194073 0 3 0 180 4 # offset V0=-0.0731209369 -torsion 0 47L 47L 0 0.0 0 1 12.2502629063 180 2 0.0 0 3 0 180 4 # offset V0=0.0 -torsion 47L 47L 13L 13L -0.8050121893 0 1 0.3218905354 180 2 -0.1032768881 0 3 0 180 4 # offset V0=-0.3574832696 -torsion 13L 13L 13L 47L 0.4821902486 0 1 0.1343683078 180 2 0.1777461759 0 3 0 180 4 # offset V0=0.4405726577 - -###################### -torsion 46L 13LL 5L 7L 0.00962596 0 1 -0.0145554 180 2 0.381091 0 3 0 180 4 # offset V0=0.00133126 -torsion 46L 13LL 13LL 5L 0.0143774 0 1 0.033021 180 2 0.26687 0 3 0 180 4 # offset V0=-0.0291993 -torsion 13LL 13LL 5L 7L -0.675785 0 1 -0.0160421 180 2 0.373199 0 3 0 180 4 # offset V0=-0.0225884 -torsion 13LL 13LL 13LL 5L 1.31261 0 1 -0.266307 180 2 0.637867 0 3 0 180 4 # offset V0=0.00224187 -torsion 5L 13LL 13LL 5L 2.69106 0 1 -0.849706 180 2 0.725731 0 3 0 180 4 # offset V0=-0.3326 -torsion 13LL 3L 20L 13LL 3.11923 0 1 5.73771 180 2 0.0 0 3 0 180 4 # offset V0=0.493475 -torsion 13LL 20L 3L 4L 0.0 0 1 5.73772 180 2 0.0 0 3 0 180 4 # offset V0=-0.28142 -torsion 46L 13LL 3L 20L -0.00742471 0 1 0.00217734 180 2 0.111803 0 3 0 180 4 # offset V0=-0.012512 -torsion 3L 20L 13LL 13LL -1.7354 0 1 -1.24844 180 2 0.623897 0 3 0 180 4 # offset V0=0.11706 -torsion 46L 13LL 13LL 20L 0.0113337 0 1 0.0236209 180 2 0.429747 0 3 0 180 4 # offset V0=-0.0255306 -torsion 13LL 13LL 3L 20L 0.884988 0 1 -0.626905 180 2 -0.493344 0 3 0 180 4 # offset V0=-0.0195172 -torsion 13LL 13LL 3L 4L -0.276019 0 1 1.23685 180 2 -0.670745 0 3 0 180 4 # offset V0=-0.0322467 -torsion 3L 13LL 13LL 46L -0.0021152 0 1 0.0173542 180 2 -0.295208 0 3 0 180 4 # offset V0=-0.0433963 -torsion 3L 13LL 13LL 13LL -2.30738 0 1 -0.627326 180 2 0.621951 0 3 0 180 4 # offset V0=0.0323566 -torsion 13LL 13LL 13LL 20L 2.25871 0 1 -1.02408 180 2 1.0071 0 3 0 180 4 # offset V0=0.0297084 -torsion 20L 13LL 13LL 20L 4.66787 0 1 -2.62698 180 2 1.3248 0 3 0 180 4 # offset V0=-1.48385 -torsion 5L 13LL 13LL 20L 5.03208 0 1 -2.37742 180 2 1.23809 0 3 0 180 4 # offset V0=0.223141 -###################### - -charge 80L -0.222 #"Alkane CH3- (LOPLS)" "CT_CH3" 3.50 0.0660 -charge 81L -0.148 #"Alkane -CH2- (LOPLS)" "CT_CH2" 3.50 0.0660 -charge 81LL 0.19 -charge 85LCH3 0.074 #"Alkane H-C CH3 (LOPLS)" "HC_CH3" 2.50 0.0300 -charge 85LCH2 0.074 #"Alkane H-C CH2 (LOPLS)" "HC_CH2" 2.50 0.0263 -charge 87L -0.160 #"Alkene RH-C= (LOPLS)" "CM_CH" 3.55 0.0760 -charge 89L 0.160 #"Alkene H-C= (LOPLS)" "HC_CH" 2.42 0.0300 -charge 86L 0.0000 -charge 88L -0.2300 -charge 96L -0.683 -charge 97L 0.418 -charge 111L -0.7 -charge 112L 0.435 -charge 113L -0.73 -charge 114L 0.465 -charge 118L 0.06 -charge 169L 0.0050 -charge 266L -0.0700 -charge 267L 0.0800 -charge 280L -0.0600 -charge 281L 0.1000 -charge 324L -0.0600 -charge 325L 0.1000 -charge 340L 0.1800 -charge 342L 0.1200 -charge 406L 0.75 -charge 407L -0.55 -charge 408L -0.45 -charge 458L -0.0300 -charge 459L 0.0850 -charge 649L -0.3440 -charge 718L 0.06 -charge 718LL 0.03 -charge 900L -0.2500 -charge 901L -0.1000 -charge 902L 0.0500 - diff --git a/tools/moltemplate/moltemplate/force_fields/sdk.lt b/tools/moltemplate/moltemplate/force_fields/sdk.lt deleted file mode 100644 index 8207614282..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk.lt +++ /dev/null @@ -1,435 +0,0 @@ -# Autogenerated by EMC 2 LT tool v0.2 on 2017-06-29 -# -# cd sdk/ -# emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=sdk --units -# mv -f sdk.lt ../ -# -# This file contains force field parameters for lipids and cholesterol from: -# Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 -# MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 -# For details see the "README.txt" file (located in "force_fields/sdk/") -# -# Adapted from EMC by Pieter J. in 't Veld -# Originally written as, FFNAME:SDK STYLE:COARSE VERSION:1.0 on Oct 2014 -# "emcprm2lt.py" was written by David Stelter. - - -SDK { - - write_once("Data Masses") { - @atom:CM 42.080400 # CM - @atom:CMD2 26.037800 # CMD2 - @atom:CT 43.088300 # CT - @atom:CT2 29.061500 # CT2 - @atom:EST1 58.036600 # EST1 - @atom:EST2 58.036600 # EST2 - @atom:GL 41.072500 # GL - @atom:NC 87.164400 # NC - @atom:NH 44.076100 # NH - @atom:PH 94.971600 # PH - @atom:PHE 94.971600 # PHE - @atom:W 54.045600 # W - @atom:C2T 43.090000 # C2T - @atom:CM2 28.050000 # CM2 - @atom:CM2R 28.050000 # CM2R - @atom:CMDB 39.060000 # CMDB - @atom:CMB 40.060000 # CMB - @atom:CMR 41.070000 # CMR - @atom:CMR5 41.070000 # CMR5 - @atom:CTB 42.080000 # CTB - @atom:CTBA 27.050000 # CTBA - @atom:CTBB 27.050000 # CTBB - @atom:OAB 30.030000 # OAB - } # end of atom masses - - # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup ----- - replace{ @atom:CM @atom:CM_bCM_aCM_dCM_iCM} - replace{ @atom:CMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2} - replace{ @atom:CT @atom:CT_bCT_aCT_dCT_iCT} - replace{ @atom:CT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2} - replace{ @atom:EST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1} - replace{ @atom:EST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2} - replace{ @atom:GL @atom:GL_bGL_aGL_dGL_iGL} - replace{ @atom:NC @atom:NC_bNC_aNC_dNC_iNC} - replace{ @atom:NH @atom:NH_bNH_aNH_dNH_iNH} - replace{ @atom:PH @atom:PH_bPH_aPH_dPH_iPH} - replace{ @atom:PHE @atom:PHE_bPHE_aPHE_dPHE_iPHE} - replace{ @atom:W @atom:W_bW_aW_dW_iW} - replace{ @atom:C2T @atom:C2T_bC2T_aC2T_dC2T_iC2T} - replace{ @atom:CM2 @atom:CM2_bCM2_aCM2_dCM2_iCM2} - replace{ @atom:CM2R @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R} - replace{ @atom:CMDB @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB} - replace{ @atom:CMB @atom:CMB_bCMB_aCMB_dCMB_iCMB} - replace{ @atom:CMR @atom:CMR_bCMR_aCMR_dCMR_iCMR} - replace{ @atom:CMR5 @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5} - replace{ @atom:CTB @atom:CTB_bCTB_aCTB_dCTB_iCTB} - replace{ @atom:CTBA @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA} - replace{ @atom:CTBB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB} - replace{ @atom:OAB @atom:OAB_bOAB_aOAB_dOAB_iOAB} - # END EQUIVALENCE - - write_once("In Settings") { - # ----- Non-Bonded interactions ----- - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.420000 4.506000 # CM-CM - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.312000 4.255500 # CM-CMD2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CM-CT - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.362000 4.363500 # CM-CT2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.403000 # CM-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.403000 # CM-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # CM-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.400000 5.128000 # CM-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.330000 4.553000 # CM-NH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.953000 # CM-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.953000 # CM-PHE - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:W_bW_aW_dW_iW lj12_4 0.340000 4.438500 # CM-W - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.232000 4.005000 # CMD2-CMD2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.330000 4.295000 # CMD2-CT - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.269000 4.113000 # CMD2-CT2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.440000 4.005000 # CMD2-EST1 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.440000 4.005000 # CMD2-EST2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.312000 4.255500 # CMD2-GL - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.350000 4.877500 # CMD2-NC - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.300000 4.302500 # CMD2-NH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.702500 # CMD2-PH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.702500 # CMD2-PHE - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:W_bW_aW_dW_iW lj12_4 0.270000 4.188000 # CMD2-W - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.469000 4.585000 # CT-CT - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.383000 4.403000 # CT-CT2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CT-EST1 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CT-EST2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CT-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CT-NC - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.340000 4.925000 # CT-NH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CT-PH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.320000 4.992500 # CT-PHE - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CT-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.312000 4.221000 # CT2-CT2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CT2-EST1 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CT2-EST2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.365000 # CT2-GL - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CT2-NC - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.320000 4.410500 # CT2-NH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CT2-PH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.280000 4.810500 # CT2-PHE - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CT2-W - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.495000 4.300000 # EST1-EST1 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST1-EST2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST1-GL - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST1-NC - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST1-NH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST1-PH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST1-PHE - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST1-W - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST2-EST2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST2-GL - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST2-NC - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST2-NH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST2-PH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST2-PHE - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST2-W - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # GL-GL - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.650000 4.620000 # GL-NC - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.750000 4.190000 # GL-NH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.750000 # GL-PH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.750000 # GL-PHE - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:W_bW_aW_dW_iW lj12_4 0.640000 4.438500 # GL-W - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.700000 5.750000 # NC-NC - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.880000 5.175000 # NC-NH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.150000 4.200000 # NC-PH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.150000 4.200000 # NC-PHE - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:W_bW_aW_dW_iW lj12_4 0.900000 4.610000 # NC-W - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:NH_bNH_aNH_dNH_iNH lj9_6 1.100000 4.600000 # NH-NH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.200000 3.800000 # NH-PH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.200000 3.800000 # NH-PHE - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:W_bW_aW_dW_iW lj12_4 0.800000 3.950000 # NH-W - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.400000 5.400000 # PH-PH - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 5.000000 # PH-PHE - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PH-W - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 4.600000 # PHE-PHE - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PHE-W - pair_coeff @atom:W_bW_aW_dW_iW @atom:W_bW_aW_dW_iW lj12_4 0.895000 4.371000 # W-W - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # C2T-NC - pair_coeff @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CMR5-CT - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.252000 4.767700 # C2T-CTBA - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.469000 4.585000 # CT-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMR_bCMR_aCMR_dCMR_iCMR lj9_6 0.331000 4.771400 # C2T-CMR - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.383000 4.403000 # CT-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.252000 4.767700 # C2T-CTBB - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.383000 4.403000 # CT-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # C2T-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # CT-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.254000 4.610100 # C2T-CM2R - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.383000 4.403000 # CT2-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.330000 4.295000 # C2T-CMD2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.312000 4.221000 # CT2-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.331000 4.771400 # C2T-CMR5 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.312000 4.221000 # CT2-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # C2T-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.415000 3.950500 # CT2-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:C2T_bC2T_aC2T_dC2T_iC2T lj9_6 0.400000 4.811500 # C2T-C2T - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.269000 5.015500 # CTB-CTB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # C2T-OAB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CTB-EST1 - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # C2T-PH - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CTB-EST2 - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.354000 4.894100 # C2T-CMDB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CTB-NC - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.297000 4.527200 # C2T-CT2 - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.265000 4.464800 # CTB-CTBA - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.291000 4.588000 # C2T-CM2 - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.464800 # CTB-CTBB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.391000 4.545500 # C2T-CM - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CTB-GL - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.409000 4.860100 # C2T-CT - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CTB-W - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.283000 4.910900 # C2T-CTB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.437000 4.033000 # CTB-OAB - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.310000 4.656400 # C2T-CMB - pair_coeff @atom:CTB_bCTB_aCTB_dCTB_iCTB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CTB-PH - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # C2T-EST1 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CTBA-NC - pair_coeff @atom:C2T_bC2T_aC2T_dC2T_iC2T @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # C2T-EST2 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CTBA-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMR_bCMR_aCMR_dCMR_iCMR lj9_6 0.420000 4.506000 # CM-CMR - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CTBA-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.390000 4.434200 # CM-CM2R - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CTBA-W - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.420000 4.506000 # CM-CMR5 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.363500 # CTBA-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.561000 4.093000 # CM-OAB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.265000 4.461000 # CTBA-CTBA - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.362000 4.379000 # CM-CMDB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.461000 # CTBA-CTBB - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.336000 4.461900 # CM-CM2 - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CTBA-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.444000 4.545500 # CM-CTB - pair_coeff @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.380000 3.840000 # CTBA-OAB - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.420000 4.506000 # CM-CMB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CTBB-W - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTBA_bCTBA_aCTBA_dCTBA_iCTBA lj9_6 0.362000 4.363500 # CM-CTBA - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CTBB-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.362000 4.363500 # CM-CTBB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.363500 # CTBB-GL - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.248000 4.936800 # CM2-PH - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CTBB-EST1 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.413000 4.066900 # CM2-OAB - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CTBB-EST2 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CM2R_bCM2R_aCM2R_dCM2R_iCM2R lj9_6 0.237000 4.440300 # CM2-CM2R - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CTBB-PH - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.248000 4.231300 # CM2-CMD2 - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.380000 3.840000 # CTBB-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMR5_bCMR5_aCMR5_dCMR5_iCMR5 lj9_6 0.333000 4.484600 # CM2-CMR5 - pair_coeff @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB @atom:CTBB_bCTBB_aCTBB_dCTBB_iCTBB lj9_6 0.265000 4.461000 # CTBB-CTBB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.228000 4.319900 # CM2-CT2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 1.100000 3.990000 # EST1-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CM2_bCM2_aCM2_dCM2_iCM2 lj9_6 0.265000 4.461000 # CM2-CM2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 1.100000 3.990000 # EST2-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMDB_bCMDB_aCMDB_dCMDB_iCMDB lj9_6 0.267000 4.369700 # CM2-CMDB - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.669000 4.093000 # GL-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.301000 4.454600 # CM2-CT - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.637000 3.931900 # NC-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CTB_bCTB_aCTB_dCTB_iCTB lj9_6 0.353000 4.524600 # CM2-CTB - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:W_bW_aW_dW_iW lj9_6 1.026000 4.025500 # OAB-W - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:CMB_bCMB_aCMB_dCMB_iCMB lj9_6 0.333000 4.484600 # CM2-CMB - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.928000 3.616600 # OAB-PH - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.306000 5.113800 # CM2-NC - pair_coeff @atom:OAB_bOAB_aOAB_dOAB_iOAB @atom:OAB_bOAB_aOAB_dOAB_iOAB lj9_6 0.580000 3.680000 # OAB-OAB - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.366000 4.380500 # CM2-EST1 - pair_coeff @atom:CM2_bCM2_aCM2_dCM2_iCM2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.366000 4.380500 # CM2-EST2 - } # end of nonbonded parameters - - write_once("In Settings") { - # ----- Bonds ----- - bond_coeff @bond:CM-CM harmonic 6.160000 3.640000 # CM-CM - bond_coeff @bond:CM-CMD2 harmonic 8.000000 3.030000 # CM-CMD2 - bond_coeff @bond:CM-CT harmonic 6.160000 3.650000 # CM-CT - bond_coeff @bond:CM-CT2 harmonic 9.000000 3.130000 # CM-CT2 - bond_coeff @bond:CM-EST1 harmonic 4.700000 3.550000 # CM-EST1 - bond_coeff @bond:CM-EST2 harmonic 5.100000 3.610000 # CM-EST2 - bond_coeff @bond:CM-PHE harmonic 12.000000 3.690000 # CM-PHE - bond_coeff @bond:CM-SO4 harmonic 11.000000 3.630000 # CM-SO4 - bond_coeff @bond:CMD2-CT harmonic 8.000000 3.090000 # CMD2-CT - bond_coeff @bond:CMD2-CT2 harmonic 60.000000 2.540000 # CMD2-CT2 - bond_coeff @bond:CT-CT harmonic 6.955000 3.710000 # CT-CT - bond_coeff @bond:EST1-GL harmonic 30.000000 2.880000 # EST1-GL - bond_coeff @bond:EST2-GL harmonic 8.400000 3.480000 # EST2-GL - bond_coeff @bond:GL-PHE harmonic 8.900000 3.520000 # GL-PHE - bond_coeff @bond:NC-PHE harmonic 4.800000 4.250000 # NC-PHE - bond_coeff @bond:NH-PHE harmonic 9.400000 3.600000 # NH-PHE - bond_coeff @bond:PHE1-PHE2 harmonic 2.500000 150.000000 # PHE1-PHE2 - bond_coeff @bond:C2T-CM2 harmonic 55.000000 2.500000 # C2T-CM2 - bond_coeff @bond:CM2-CTB harmonic 42.500000 2.900000 # CM2-CTB - bond_coeff @bond:CM2R-CTBA harmonic 45.000000 2.400000 # CM2R-CTBA - bond_coeff @bond:CM2R-OAB harmonic 50.000000 2.600000 # CM2R-OAB - bond_coeff @bond:CMB-CMDB harmonic 75.000000 3.500000 # CMB-CMDB - bond_coeff @bond:CMB-CMR5 harmonic 50.000000 3.000000 # CMB-CMR5 - bond_coeff @bond:CMB-CTBA harmonic 35.000000 3.400000 # CMB-CTBA - bond_coeff @bond:CMB-CTBB harmonic 50.000000 3.000000 # CMB-CTBB - bond_coeff @bond:CMDB-CTBA harmonic 40.000000 2.500000 # CMDB-CTBA - bond_coeff @bond:CMDB-OAB harmonic 55.000000 3.100000 # CMDB-OAB - bond_coeff @bond:CMR5-CTBB harmonic 60.000000 2.300000 # CMR5-CTBB - bond_coeff @bond:CMR-CTBA harmonic 50.000000 3.000000 # CMR-CTBA - bond_coeff @bond:CMR-CTBB harmonic 55.000000 2.500000 # CMR-CTBB - bond_coeff @bond:CTB-CTBB harmonic 22.500000 3.400000 # CTB-CTBB - bond_coeff @bond:CMR5-CTB harmonic 35.000000 3.100000 # CMR5-CTB - } - - write_once("Data Bonds By Type") { - @bond:CM-CM @atom:*_bCM_a*_d*_i* @atom:*_bCM_a*_d*_i* - @bond:CM-CMD2 @atom:*_bCM_a*_d*_i* @atom:*_bCMD2_a*_d*_i* - @bond:CM-CT @atom:*_bCM_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CM-CT2 @atom:*_bCM_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CM-EST1 @atom:*_bCM_a*_d*_i* @atom:*_bEST1_a*_d*_i* - @bond:CM-EST2 @atom:*_bCM_a*_d*_i* @atom:*_bEST2_a*_d*_i* - @bond:CM-PHE @atom:*_bCM_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:CM-SO4 @atom:*_bCM_a*_d*_i* @atom:*_bSO4_a*_d*_i* - @bond:CMD2-CT @atom:*_bCMD2_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CMD2-CT2 @atom:*_bCMD2_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CT-CT @atom:*_bCT_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:EST1-GL @atom:*_bEST1_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:EST2-GL @atom:*_bEST2_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:GL-PHE @atom:*_bGL_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NC-PHE @atom:*_bNC_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NH-PHE @atom:*_bNH_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:PHE1-PHE2 @atom:*_bPHE1_a*_d*_i* @atom:*_bPHE2_a*_d*_i* - @bond:C2T-CM2 @atom:*_bC2T_a*_d*_i* @atom:*_bCM2_a*_d*_i* - @bond:CM2-CTB @atom:*_bCM2_a*_d*_i* @atom:*_bCTB_a*_d*_i* - @bond:CM2R-CTBA @atom:*_bCM2R_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CM2R-OAB @atom:*_bCM2R_a*_d*_i* @atom:*_bOAB_a*_d*_i* - @bond:CMB-CMDB @atom:*_bCMB_a*_d*_i* @atom:*_bCMDB_a*_d*_i* - @bond:CMB-CMR5 @atom:*_bCMB_a*_d*_i* @atom:*_bCMR5_a*_d*_i* - @bond:CMB-CTBA @atom:*_bCMB_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMB-CTBB @atom:*_bCMB_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMDB-CTBA @atom:*_bCMDB_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMDB-OAB @atom:*_bCMDB_a*_d*_i* @atom:*_bOAB_a*_d*_i* - @bond:CMR5-CTBB @atom:*_bCMR5_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMR-CTBA @atom:*_bCMR_a*_d*_i* @atom:*_bCTBA_a*_d*_i* - @bond:CMR-CTBB @atom:*_bCMR_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CTB-CTBB @atom:*_bCTB_a*_d*_i* @atom:*_bCTBB_a*_d*_i* - @bond:CMR5-CTB @atom:*_bCMR5_a*_d*_i* @atom:*_bCTB_a*_d*_i* - } # end of bonds - - write_once("In Settings") { - # ----- Angles ----- - angle_coeff @angle:CM-CM-CM sdk 1.190000 173.000000 # CM-CM-CM - angle_coeff @angle:CM-CM-CMD2 sdk 1.900000 161.000000 # CM-CM-CMD2 - angle_coeff @angle:CM-CM-CT sdk 1.190000 175.000000 # CM-CM-CT - angle_coeff @angle:CM-CM-CT2 sdk 1.600000 172.000000 # CM-CM-CT2 - angle_coeff @angle:CM-CM-EST1 sdk 1.000000 178.000000 # CM-CM-EST1 - angle_coeff @angle:CM-CM-EST2 sdk 1.000000 178.000000 # CM-CM-EST2 - angle_coeff @angle:CM-CM-PHE sdk 1.100000 178.000000 # CM-CM-PHE - angle_coeff @angle:CM-CMD2-CM sdk 6.000000 110.000000 # CM-CMD2-CM - angle_coeff @angle:CM-EST1-GL sdk 0.800000 168.000000 # CM-EST1-GL - angle_coeff @angle:CM-EST2-GL sdk 0.800000 172.000000 # CM-EST2-GL - angle_coeff @angle:CM-PHE-NC sdk 3.300000 112.000000 # CM-PHE-NC - angle_coeff @angle:CT-CM-CT sdk 1.093000 175.500000 # CT-CM-CT - angle_coeff @angle:CT-CM-CT2 sdk 1.600000 172.000000 # CT-CM-CT2 - angle_coeff @angle:CT-CMD2-CT sdk 7.700000 116.000000 # CT-CMD2-CT - angle_coeff @angle:CT2-CM-CT2 sdk 1.700000 173.000000 # CT2-CM-CT2 - angle_coeff @angle:CT2-CMD2-CT2 sdk 12.000000 110.000000 # CT2-CMD2-CT2 - angle_coeff @angle:EST1-GL-EST2 sdk 1.000000 95.000000 # EST1-GL-EST2 - angle_coeff @angle:EST1-GL-PHE sdk 1.400000 124.000000 # EST1-GL-PHE - angle_coeff @angle:EST2-GL-PHE sdk 2.000000 138.000000 # EST2-GL-PHE - angle_coeff @angle:GL-PHE-NC sdk 3.100000 112.000000 # GL-PHE-NC - angle_coeff @angle:GL-PHE-NH sdk 4.000000 102.000000 # GL-PHE-NH - angle_coeff @angle:C2T-CM2-CTB sdk 8.000000 160.000000 # C2T-CM2-CTB - angle_coeff @angle:CM2-CTB-CTBB sdk 4.000000 130.000000 # CM2-CTB-CTBB - angle_coeff @angle:CM2R-CTBA-CMB harmonic 40.000000 112.500000 # CM2R-CTBA-CMB - angle_coeff @angle:CM2R-CTBA-CMDB harmonic 22.500000 75.900000 # CM2R-CTBA-CMDB - angle_coeff @angle:CM2R-CTBA-CMR harmonic 35.000000 98.700000 # CM2R-CTBA-CMR - angle_coeff @angle:CM2R-OAB-CMDB harmonic 40.000000 63.900000 # CM2R-OAB-CMDB - angle_coeff @angle:CMB-CMDB-CTBA harmonic 45.000000 68.600000 # CMB-CMDB-CTBA - angle_coeff @angle:CMB-CMDB-OAB harmonic 65.000000 146.600000 # CMB-CMDB-OAB - angle_coeff @angle:CMB-CMR5-CTBB harmonic 35.000000 67.800000 # CMB-CMR5-CTBB - angle_coeff @angle:CMB-CTBA-CMDB harmonic 25.000000 68.900000 # CMB-CTBA-CMDB - angle_coeff @angle:CMB-CTBA-CMR harmonic 75.000000 47.800000 # CMB-CTBA-CMR - angle_coeff @angle:CMB-CTBB-CMR5 harmonic 25.000000 68.200000 # CMB-CTBB-CMR5 - angle_coeff @angle:CMB-CTBB-CMR harmonic 50.000000 56.300000 # CMB-CTBB-CMR - angle_coeff @angle:CMB-CTBB-CTB sdk 35.000000 120.700000 # CMB-CTBB-CTB - angle_coeff @angle:CMDB-CMB-CMR5 harmonic 150.000000 175.600000 # CMDB-CMB-CMR5 - angle_coeff @angle:CMDB-CMB-CTBA harmonic 62.500000 42.500000 # CMDB-CMB-CTBA - angle_coeff @angle:CMDB-CMB-CTBB harmonic 25.000000 134.200000 # CMDB-CMB-CTBB - angle_coeff @angle:CMDB-CTBA-CMR harmonic 50.000000 108.600000 # CMDB-CTBA-CMR - angle_coeff @angle:CMR5-CNB-CTBA harmonic 15.000000 135.800000 # CMR5-CNB-CTBA - angle_coeff @angle:CMR5-CMB-CTBB harmonic 45.000000 44.000000 # CMR5-CMB-CTBB - angle_coeff @angle:CMR5-CTBB-CTB harmonic 20.000000 62.700000 # CMR5-CTBB-CTB - angle_coeff @angle:CMR-CTBB-CMR5 harmonic 75.000000 107.000000 # CMR-CTBB-CMR5 - angle_coeff @angle:CMR-CTBB-CTB sdk 37.500000 110.100000 # CMR-CTBB-CTB - angle_coeff @angle:CTBA-CM2R-OAB harmonic 25.000000 107.400000 # CTBA-CM2R-OAB - angle_coeff @angle:CTBA-CMB-CTBB harmonic 20.000000 92.200000 # CTBA-CMB-CTBB - angle_coeff @angle:CTBA-CMDB-OAB harmonic 20.000000 91.800000 # CTBA-CMDB-OAB - angle_coeff @angle:CTBA-CMR-CTBB harmonic 15.000000 115.000000 # CTBA-CMR-CTBB - angle_coeff @angle:CMB-CMR5-CTB harmonic 88.000000 131.700000 # CMB-CMR5-CTB - angle_coeff @angle:CTBB-CMR5-CTB harmonic 20.000000 77.400000 # CTBB-CMR5-CTB - angle_coeff @angle:CM2-CTB-CMR5 sdk 20.000000 118.000000 # CM2-CTB-CMR5 - angle_coeff @angle:CMR5-CTB-CTBB harmonic 62.500000 39.700000 # CMR5-CTB-CTBB - } - - write_once("Data Angles By Type") { - @angle:CM-CM-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-CM-CMD2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* - @angle:CM-CM-CT @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CM-CM-CT2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CM-CM-EST1 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* - @angle:CM-CM-EST2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:CM-CM-PHE @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:CM-CMD2-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-EST1-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-EST2-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-PHE-NC @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:CT-CM-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT-CM-CT2 @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT-CMD2-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT2-CM-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT2-CMD2-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:EST1-GL-EST2 @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:EST1-GL-PHE @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:EST2-GL-PHE @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:GL-PHE-NC @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:GL-PHE-NH @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNH_d*_i* - @angle:C2T-CM2-CTB @atom:*_b*_aC2T_d*_i* @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CM2-CTB-CTBB @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CM2R-CTBA-CMB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMB_d*_i* - @angle:CM2R-CTBA-CMDB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CM2R-CTBA-CMR @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CM2R-OAB-CMDB @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aOAB_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CMB-CMDB-CTBA @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMB-CMDB-OAB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CMB-CMR5-CTBB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMB-CTBA-CMDB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* - @angle:CMB-CTBA-CMR @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMB-CTBB-CMR5 @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMB-CTBB-CMR @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMB-CTBB-CTB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CMDB-CMB-CMR5 @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMDB-CMB-CTBA @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMDB-CMB-CTBB @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMDB-CTBA-CMR @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* - @angle:CMR5-CNB-CTBA @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCNB_d*_i* @atom:*_b*_aCTBA_d*_i* - @angle:CMR5-CMB-CTBB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMR5-CTBB-CTB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CMR-CTBB-CMR5 @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMR-CTBB-CTB @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CTBA-CM2R-OAB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCM2R_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CTBA-CMB-CTBB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CTBA-CMDB-OAB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMDB_d*_i* @atom:*_b*_aOAB_d*_i* - @angle:CTBA-CMR-CTBB @atom:*_b*_aCTBA_d*_i* @atom:*_b*_aCMR_d*_i* @atom:*_b*_aCTBB_d*_i* - @angle:CMB-CMR5-CTB @atom:*_b*_aCMB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CTBB-CMR5-CTB @atom:*_b*_aCTBB_d*_i* @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* - @angle:CM2-CTB-CMR5 @atom:*_b*_aCM2_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCMR5_d*_i* - @angle:CMR5-CTB-CTBB @atom:*_b*_aCMR5_d*_i* @atom:*_b*_aCTB_d*_i* @atom:*_b*_aCTBB_d*_i* - } # end of angles - - write_once("In Init") { - # Warning: This is a very generic "In Init" section, further - # modification prior to any simulation is extremely likely - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid sdk - pair_style hybrid lj/sdk/coul/long 9.000000 12.000000 - special_bonds lj/coul 0.0 0.0 0.0 - } # end init - -} # SDK - diff --git a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt deleted file mode 100644 index eb2eed836d..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/README.txt +++ /dev/null @@ -1,84 +0,0 @@ -The files in this directory are used to create the "sdk.lt" file -(containing SDK force field parameters for moltemplate). -These .PRM files are distributed with "EMC" written by Pieter J. in 't Veld. - -Conversion from EMC (.PRM) format to moltemplate (.LT) format was -done using the "emcprm2lt.py" script written by David Stelter. -Here is an example how to use the emcprm2lt.py script: - -emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=sdk sdk_lipids.prm sdk_cholesterol.prm --name=SDK_lipid+chol --units - -This will generate a file named "sdk.lt" which (in this example) -only includes the force field parameters for lipids and cholestrol. -Later you can define new molecules in moltemplate using: - -import "sdk.lt" -NewMolecule inherits SDK { - write("Data Atoms") {...atom coordinates and types go here...} - write("Data Bond List") {...list of bonds goes here...} -} - -This is only part of the SDK force field and is to be used for lipids -and cholesterol only. Lipid parameters were taken from: - -Shinoda et al. J. Phys. Chem. B, Vol. 114, No. 20, 2010 -http://dx.doi.org/10.1021/jp9107206 - -Cholesterol parameters were taken from: -MacDermaid et al. J. Chem. Phys, 143(24), 243144, 2015 -http://dx.doi.org/10.1063/1.4937153 - -You can define lipids with any topology built using the following types: - -Name Structure Charge -NC -CH2CH2-N-(CH3)3 +1 -NH -CH2CH2-NH3 +1 -PH -PO4- -1 -PHE -PO4- (PE lipid) -1 -GL -CH2CH-CH2- -EST1 -CH2CO2- -EST2 -H2CO2- -CMD2 -HC=CH- (cis) -CM -CH2CH2CH2- -CT CH3CH2CH2- -CT2 CH3CH2- -W (H2O)3 - -This coarse-grainng allows for design of a wide variety of lipids. - -The following types are defined specifically for cholesterol: - -Name Structure Location -C2T -CH-(CH3)2 Tail -CM2 -CH2-CH2- Tail -CM2R -CH2-CH2- Ring A -CMDB -CH2-C=CH- Ring A/B -CMB -CH2-CH-CH- Ring B/C -CMR -CH-CH2-CH2- Ring B/C -CMR5 -CH2-CH2-CH- Ring D -CTB -CH2-CH-CH3- Tail -CTBA -C-CH3 Ring A/B -CTBB -C-CH3 Ring C/D -OAB -CH-OH Ring A - -See the provided reference for details on the CG cholesterol topology. -A 5.0-10.0 timestep is used when using cholesterol. - -Several limiations, due to missing parameters: --use of cholesterol with type "NH" is not possible. --use of cholesterol with type "PHE" is not possible. - ----- Credits: ---- - -emcprm2lt.py was written by David Stelter -EMC was written by Pieter J. in 't Veld -SDK was created by Shinoda, DeVane, Klein, J.Phys.Chem.B, Vol. 114, No. 20, 2010 - ----- additional citation request ---- - -Since we borrowed force field parameters from files distributed with EMC, -if you use files generated by "emcprm2lt.py", please also cite the EMC paper: -P. J. in ‘t Veld and G. C. Rutledge, Macromolecules 2003, 36, 7358 - - - diff --git a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt deleted file mode 100644 index de10509439..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/SDK_lipidONLY.lt +++ /dev/null @@ -1,221 +0,0 @@ -# Autogenerated by EMC 2 LT tool v0.2 on 2017-02-27 -# -# ./emcprm2lt.py --pair-style=lj/sdk/coul/long --bond-style=harmonic --angle-style=harmonic sdk_lipids.prm --name=SDK_lipidONLY -# -# Adapted from EMC by Pieter J. in 't Veld -# Originally written as, FFNAME:SDK STYLE:COARSE VERSION:1.0 on Oct 2014 - -SDK { - write_once("Data Masses") { - @atom:CM 42.080400 # CM - @atom:CMD2 26.037800 # CMD2 - @atom:CT 43.088300 # CT - @atom:CT2 29.061500 # CT2 - @atom:EST1 58.036600 # EST1 - @atom:EST2 58.036600 # EST2 - @atom:GL 41.072500 # GL - @atom:NC 87.164400 # NC - @atom:NH 44.076100 # NH - @atom:PH 94.971600 # PH - @atom:PHE 94.971600 # PHE - @atom:W 54.045600 # W - } # end of atom masses - - # ----- EQUIVALENCE CATEGORIES for bonded interaction lookup ----- - replace{ @atom:CM @atom:CM_bCM_aCM_dCM_iCM} - replace{ @atom:CMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2} - replace{ @atom:CT @atom:CT_bCT_aCT_dCT_iCT} - replace{ @atom:CT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2} - replace{ @atom:EST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1} - replace{ @atom:EST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2} - replace{ @atom:GL @atom:GL_bGL_aGL_dGL_iGL} - replace{ @atom:NC @atom:NC_bNC_aNC_dNC_iNC} - replace{ @atom:NH @atom:NH_bNH_aNH_dNH_iNH} - replace{ @atom:PH @atom:PH_bPH_aPH_dPH_iPH} - replace{ @atom:PHE @atom:PHE_bPHE_aPHE_dPHE_iPHE} - replace{ @atom:W @atom:W_bW_aW_dW_iW} - # END EQUIVALENCE - - write_once("In Settings") { - # ----- Non-Bonded interactions ----- - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CM_bCM_aCM_dCM_iCM lj9_6 0.420000 4.506000 # CM-CM - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.312000 4.255500 # CM-CMD2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.444000 4.545500 # CM-CT - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.362000 4.363500 # CM-CT2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.403000 # CM-EST1 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.403000 # CM-EST2 - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # CM-GL - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.400000 5.128000 # CM-NC - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.330000 4.553000 # CM-NH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.953000 # CM-PH - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.953000 # CM-PHE - pair_coeff @atom:CM_bCM_aCM_dCM_iCM @atom:W_bW_aW_dW_iW lj12_4 0.340000 4.438500 # CM-W - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 lj9_6 0.232000 4.005000 # CMD2-CMD2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.330000 4.295000 # CMD2-CT - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.269000 4.113000 # CMD2-CT2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.440000 4.005000 # CMD2-EST1 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.440000 4.005000 # CMD2-EST2 - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.312000 4.255500 # CMD2-GL - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.350000 4.877500 # CMD2-NC - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.300000 4.302500 # CMD2-NH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.702500 # CMD2-PH - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.702500 # CMD2-PHE - pair_coeff @atom:CMD2_bCMD2_aCMD2_dCMD2_iCMD2 @atom:W_bW_aW_dW_iW lj12_4 0.270000 4.188000 # CMD2-W - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT_bCT_aCT_dCT_iCT lj9_6 0.469000 4.585000 # CT-CT - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.383000 4.403000 # CT-CT2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.470000 4.442500 # CT-EST1 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.470000 4.442500 # CT-EST2 - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.444000 4.545500 # CT-GL - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.420000 5.167500 # CT-NC - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.340000 4.925000 # CT-NH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.320000 4.992500 # CT-PH - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.320000 4.992500 # CT-PHE - pair_coeff @atom:CT_bCT_aCT_dCT_iCT @atom:W_bW_aW_dW_iW lj12_4 0.360000 4.478000 # CT-W - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:CT2_bCT2_aCT2_dCT2_iCT2 lj9_6 0.312000 4.221000 # CT2-CT2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.390000 4.260500 # CT2-EST1 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.390000 4.260500 # CT2-EST2 - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.362000 4.365000 # CT2-GL - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.320000 4.985500 # CT2-NC - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.320000 4.410500 # CT2-NH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.280000 4.810500 # CT2-PH - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.280000 4.810500 # CT2-PHE - pair_coeff @atom:CT2_bCT2_aCT2_dCT2_iCT2 @atom:W_bW_aW_dW_iW lj12_4 0.290000 4.296000 # CT2-W - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST1_bEST1_aEST1_dEST1_iEST1 lj9_6 0.495000 4.300000 # EST1-EST1 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST1-EST2 - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST1-GL - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST1-NC - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST1-NH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST1-PH - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST1-PHE - pair_coeff @atom:EST1_bEST1_aEST1_dEST1_iEST1 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST1-W - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:EST2_bEST2_aEST2_dEST2_iEST2 lj9_6 0.495000 4.300000 # EST2-EST2 - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.470000 4.403000 # EST2-GL - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.750000 4.475000 # EST2-NC - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.850000 4.110000 # EST2-NH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.500000 4.550000 # EST2-PH - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.500000 4.550000 # EST2-PHE - pair_coeff @atom:EST2_bEST2_aEST2_dEST2_iEST2 @atom:W_bW_aW_dW_iW lj12_4 0.820000 4.290000 # EST2-W - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:GL_bGL_aGL_dGL_iGL lj9_6 0.420000 4.506000 # GL-GL - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.650000 4.620000 # GL-NC - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.750000 4.190000 # GL-NH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PH_bPH_aPH_dPH_iPH lj9_6 0.300000 4.750000 # GL-PH - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 0.300000 4.750000 # GL-PHE - pair_coeff @atom:GL_bGL_aGL_dGL_iGL @atom:W_bW_aW_dW_iW lj12_4 0.640000 4.438500 # GL-W - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NC_bNC_aNC_dNC_iNC lj9_6 0.700000 5.750000 # NC-NC - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:NH_bNH_aNH_dNH_iNH lj9_6 0.880000 5.175000 # NC-NH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.150000 4.200000 # NC-PH - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.150000 4.200000 # NC-PHE - pair_coeff @atom:NC_bNC_aNC_dNC_iNC @atom:W_bW_aW_dW_iW lj12_4 0.900000 4.610000 # NC-W - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:NH_bNH_aNH_dNH_iNH lj9_6 1.100000 4.600000 # NH-NH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.200000 3.800000 # NH-PH - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.200000 3.800000 # NH-PHE - pair_coeff @atom:NH_bNH_aNH_dNH_iNH @atom:W_bW_aW_dW_iW lj12_4 0.800000 3.950000 # NH-W - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PH_bPH_aPH_dPH_iPH lj9_6 1.400000 5.400000 # PH-PH - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 5.000000 # PH-PHE - pair_coeff @atom:PH_bPH_aPH_dPH_iPH @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PH-W - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:PHE_bPHE_aPHE_dPHE_iPHE lj9_6 1.400000 4.600000 # PHE-PHE - pair_coeff @atom:PHE_bPHE_aPHE_dPHE_iPHE @atom:W_bW_aW_dW_iW lj12_4 1.000000 4.030000 # PHE-W - pair_coeff @atom:W_bW_aW_dW_iW @atom:W_bW_aW_dW_iW lj12_4 0.895000 4.371000 # W-W - } # end of nonbonded parameters - - write_once("In Settings") { - # ----- Bonds ----- - bond_coeff @bond:CM-CM harmonic 3.080000 3.640000 - bond_coeff @bond:CM-CMD2 harmonic 4.000000 3.030000 - bond_coeff @bond:CM-CT harmonic 3.080000 3.650000 - bond_coeff @bond:CM-CT2 harmonic 4.500000 3.130000 - bond_coeff @bond:CM-EST1 harmonic 2.350000 3.550000 - bond_coeff @bond:CM-EST2 harmonic 2.550000 3.610000 - bond_coeff @bond:CM-PHE harmonic 6.000000 3.690000 - bond_coeff @bond:CM-SO4 harmonic 5.500000 3.630000 - bond_coeff @bond:CMD2-CT harmonic 4.000000 3.090000 - bond_coeff @bond:CMD2-CT2 harmonic 30.000000 2.540000 - bond_coeff @bond:CT-CT harmonic 3.477500 3.710000 - bond_coeff @bond:EST1-GL harmonic 15.000000 2.880000 - bond_coeff @bond:EST2-GL harmonic 4.200000 3.480000 - bond_coeff @bond:GL-PHE harmonic 4.450000 3.520000 - bond_coeff @bond:NC-PHE harmonic 2.400000 4.250000 - bond_coeff @bond:NH-PHE harmonic 4.700000 3.600000 - bond_coeff @bond:PHE1-PHE2 harmonic 1.250000 150.000000 - } - - write_once("Data Bonds By Type") { - @bond:CM-CM @atom:*_bCM_a*_d*_i* @atom:*_bCM_a*_d*_i* - @bond:CM-CMD2 @atom:*_bCM_a*_d*_i* @atom:*_bCMD2_a*_d*_i* - @bond:CM-CT @atom:*_bCM_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CM-CT2 @atom:*_bCM_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CM-EST1 @atom:*_bCM_a*_d*_i* @atom:*_bEST1_a*_d*_i* - @bond:CM-EST2 @atom:*_bCM_a*_d*_i* @atom:*_bEST2_a*_d*_i* - @bond:CM-PHE @atom:*_bCM_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:CM-SO4 @atom:*_bCM_a*_d*_i* @atom:*_bSO4_a*_d*_i* - @bond:CMD2-CT @atom:*_bCMD2_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:CMD2-CT2 @atom:*_bCMD2_a*_d*_i* @atom:*_bCT2_a*_d*_i* - @bond:CT-CT @atom:*_bCT_a*_d*_i* @atom:*_bCT_a*_d*_i* - @bond:EST1-GL @atom:*_bEST1_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:EST2-GL @atom:*_bEST2_a*_d*_i* @atom:*_bGL_a*_d*_i* - @bond:GL-PHE @atom:*_bGL_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NC-PHE @atom:*_bNC_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:NH-PHE @atom:*_bNH_a*_d*_i* @atom:*_bPHE_a*_d*_i* - @bond:PHE1-PHE2 @atom:*_bPHE1_a*_d*_i* @atom:*_bPHE2_a*_d*_i* - } # end of bonds - - write_once("In Settings") { - # ----- Angles ----- - angle_coeff @angle:CM-CM-CM harmonic 1.190000 173.000000 - angle_coeff @angle:CM-CM-CMD2 harmonic 1.900000 161.000000 - angle_coeff @angle:CM-CM-CT harmonic 1.190000 175.000000 - angle_coeff @angle:CM-CM-CT2 harmonic 1.600000 172.000000 - angle_coeff @angle:CM-CM-EST1 harmonic 1.000000 178.000000 - angle_coeff @angle:CM-CM-EST2 harmonic 1.000000 178.000000 - angle_coeff @angle:CM-CM-PHE harmonic 1.100000 178.000000 - angle_coeff @angle:CM-CMD2-CM harmonic 6.000000 110.000000 - angle_coeff @angle:CM-EST1-GL harmonic 0.800000 168.000000 - angle_coeff @angle:CM-EST2-GL harmonic 0.800000 172.000000 - angle_coeff @angle:CM-PHE-NC harmonic 3.300000 112.000000 - angle_coeff @angle:CT-CM-CT harmonic 1.093000 175.500000 - angle_coeff @angle:CT-CM-CT2 harmonic 1.600000 172.000000 - angle_coeff @angle:CT-CMD2-CT harmonic 7.700000 116.000000 - angle_coeff @angle:CT2-CM-CT2 harmonic 1.700000 173.000000 - angle_coeff @angle:CT2-CMD2-CT2 harmonic 12.000000 110.000000 - angle_coeff @angle:EST1-GL-EST2 harmonic 1.000000 95.000000 - angle_coeff @angle:EST1-GL-PHE harmonic 1.400000 124.000000 - angle_coeff @angle:EST2-GL-PHE harmonic 2.000000 138.000000 - angle_coeff @angle:GL-PHE-NC harmonic 3.100000 112.000000 - angle_coeff @angle:GL-PHE-NH harmonic 4.000000 102.000000 - } - - write_once("Data Angles By Type") { - @angle:CM-CM-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-CM-CMD2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* - @angle:CM-CM-CT @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CM-CM-CT2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CM-CM-EST1 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* - @angle:CM-CM-EST2 @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:CM-CM-PHE @atom:*_b*_aCM_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:CM-CMD2-CM @atom:*_b*_aCM_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCM_d*_i* - @angle:CM-EST1-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-EST2-GL @atom:*_b*_aCM_d*_i* @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* - @angle:CM-PHE-NC @atom:*_b*_aCM_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:CT-CM-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT-CM-CT2 @atom:*_b*_aCT_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT-CMD2-CT @atom:*_b*_aCT_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT_d*_i* - @angle:CT2-CM-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCM_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:CT2-CMD2-CT2 @atom:*_b*_aCT2_d*_i* @atom:*_b*_aCMD2_d*_i* @atom:*_b*_aCT2_d*_i* - @angle:EST1-GL-EST2 @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aEST2_d*_i* - @angle:EST1-GL-PHE @atom:*_b*_aEST1_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:EST2-GL-PHE @atom:*_b*_aEST2_d*_i* @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* - @angle:GL-PHE-NC @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNC_d*_i* - @angle:GL-PHE-NH @atom:*_b*_aGL_d*_i* @atom:*_b*_aPHE_d*_i* @atom:*_b*_aNH_d*_i* - } # end of angles - - write_once("In Init") { - # Warning: This is a very generic "In Init" section, further - # modification prior to any simulation is extremely likely - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - pair_style hybrid lj/sdk/coul/long 9.000000 12.000000 - special_bonds lj/coul 0.0 0.0 0.0 - } # end init -} # SDK diff --git a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm deleted file mode 100644 index 8bf9cf5caa..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_cholesterol.prm +++ /dev/null @@ -1,233 +0,0 @@ -# -# SDK interaction parameters using sdk.92172.tmp -# converted on Feb 28, 2017 by David Stelter -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME SDK -FFTYPE COARSE -VERSION 1.0 -CREATED Feb 2017 -LENGTH ANGSTROM -ENERGY KCAL/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 9 -CUTOFF 12 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Literature references - -ITEM REFERENCES - -# year volume page journal - -2015 143 243144 J. Phys. Chem. B - -ITEM END - -# Masses - -ITEM MASS - -# type mass ncons charge -C2T 43.09 0 0 -CM2 28.05 0 0 -CM2R 28.05 0 0 -CMDB 39.06 0 0 -CMB 40.06 0 0 -CMR 41.07 0 0 -CMR5 41.07 0 0 -CTB 42.08 0 0 -CTBA 27.05 0 0 -CTBB 27.05 0 0 -OAB 30.03 0 0 - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper -C2T C2T C2T C2T C2T C2T -CM2 CM2 CM2 CM2 CM2 CM2 -CM2R CM2R CM2R CM2R CM2R CM2R -CMDB CMDB CMDB CMDB CMDB CMDB -CMB CMB CMB CMB CMB CMB -CMR CMR CMR CMR CMR CMR -CMR5 CMR5 CMR5 CMR5 CMR5 CMR5 -CTB CTB CTB CTB CTB CTB -CTBA CTBA CTBA CTBA CTBA CTBA -CTBB CTBB CTBB CTBB CTBB CTBB -OAB OAB OAB OAB OAB OAB - -ITEM END - -# Nonbonded parameters - -ITEM NONBOND - -# type1 type2 sigma epsilon m n -C2T NC 5.1675 0.42 9 6 -CMR5 CT 4.5455 0.444 9 6 -C2T CTBA 4.7677 0.252 9 6 -CT CTB 4.585 0.469 9 6 -C2T CMR 4.7714 0.331 9 6 -CT CTBA 4.403 0.383 9 6 -C2T CTBB 4.7677 0.252 9 6 -CT CTBB 4.403 0.383 9 6 -C2T GL 4.5455 0.444 9 6 -CT OAB 4.033 0.437 9 6 -C2T CM2R 4.6101 0.254 9 6 -CT2 CTB 4.403 0.383 9 6 -C2T CMD2 4.295 0.33 9 6 -CT2 CTBA 4.221 0.312 9 6 -C2T CMR5 4.7714 0.331 9 6 -CT2 CTBB 4.221 0.312 9 6 -C2T W 4.478 0.36 12 4 -CT2 OAB 3.9505 0.415 9 6 -C2T C2T 4.8115 0.4 9 6 -CTB CTB 5.0155 0.269 9 6 -C2T OAB 4.033 0.437 9 6 -CTB EST1 4.4425 0.47 9 6 -C2T PH 4.9925 0.32 9 6 -CTB EST2 4.4425 0.47 9 6 -C2T CMDB 4.8941 0.354 9 6 -CTB NC 5.1675 0.42 9 6 -C2T CT2 4.5272 0.297 9 6 -CTB CTBA 4.4648 0.265 9 6 -C2T CM2 4.588 0.291 9 6 -CTB CTBB 4.4648 0.265 9 6 -C2T CM 4.5455 0.391 9 6 -CTB GL 4.5455 0.444 9 6 -C2T CT 4.8601 0.409 9 6 -CTB W 4.478 0.36 12 4 -C2T CTB 4.9109 0.283 9 6 -CTB OAB 4.033 0.437 9 6 -C2T CMB 4.6564 0.31 9 6 -CTB PH 4.9925 0.32 9 6 -C2T EST1 4.4425 0.47 9 6 -CTBA NC 4.9855 0.32 9 6 -C2T EST2 4.4425 0.47 9 6 -CTBA EST1 4.2605 0.39 9 6 -CM CMR 4.506 0.42 9 6 -CTBA EST2 4.2605 0.39 9 6 -CM CM2R 4.4342 0.39 9 6 -CTBA W 4.296 0.29 12 4 -CM CMR5 4.506 0.42 9 6 -CTBA GL 4.3635 0.362 9 6 -CM OAB 4.093 0.561 9 6 -CTBA CTBA 4.461 0.265 9 6 -CM CMDB 4.379 0.362 9 6 -CTBA CTBB 4.461 0.265 9 6 -CM CM2 4.4619 0.336 9 6 -CTBA PH 4.8105 0.28 9 6 -CM CTB 4.5455 0.444 9 6 -CTBA OAB 3.84 0.38 9 6 -CM CMB 4.506 0.42 9 6 -CTBB W 4.296 0.29 12 4 -CM CTBA 4.3635 0.362 9 6 -CTBB NC 4.9855 0.32 9 6 -CM CTBB 4.3635 0.362 9 6 -CTBB GL 4.3635 0.362 9 6 -CM2 PH 4.9368 0.248 9 6 -CTBB EST1 4.2605 0.39 9 6 -CM2 OAB 4.0669 0.413 9 6 -CTBB EST2 4.2605 0.39 9 6 -CM2 CM2R 4.4403 0.237 9 6 -CTBB PH 4.8105 0.28 9 6 -CM2 CMD2 4.2313 0.248 9 6 -CTBB OAB 3.84 0.38 9 6 -CM2 CMR5 4.4846 0.333 9 6 -CTBB CTBB 4.461 0.265 9 6 -CM2 CT2 4.3199 0.228 9 6 -EST1 OAB 3.99 1.1 9 6 -CM2 CM2 4.461 0.265 9 6 -EST2 OAB 3.99 1.1 9 6 -CM2 CMDB 4.3697 0.267 9 6 -GL OAB 4.093 0.669 9 6 -CM2 CT 4.4546 0.301 9 6 -NC OAB 3.9319 0.637 9 6 -CM2 CTB 4.5246 0.353 9 6 -OAB W 4.0255 1.026 9 6 -CM2 CMB 4.4846 0.333 9 6 -OAB PH 3.6166 0.928 9 6 -CM2 NC 5.1138 0.306 9 6 -OAB OAB 3.68 0.58 9 6 -CM2 EST1 4.3805 0.366 9 6 -CM2 EST2 4.3805 0.366 9 6 - -ITEM END - -# Bond parameters - -ITEM BOND - -# type1 type2 k l0 -C2T CM2 55 2.5 -CM2 CTB 42.5 2.9 -CM2R CTBA 45 2.4 -CM2R OAB 50 2.6 -CMB CMDB 75 3.5 -CMB CMR5 50 3.0 -CMB CTBA 35 3.4 -CMB CTBB 50 3.0 -CMDB CTBA 40 2.5 -CMDB OAB 55 3.1 -CMR5 CTBB 60 2.3 -CMR CTBA 50 3.0 -CMR CTBB 55 2.5 -CTB CTBB 22.5 3.4 -CMR5 CTB 35 3.1 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 type -C2T CM2 CTB 8 160.0 sdk -CM2 CTB CTBB 4 130.0 sdk -CM2R CTBA CMB 40 112.5 harmonic -CM2R CTBA CMDB 22.5 75.9 harmonic -CM2R CTBA CMR 35 98.7 harmonic -CM2R OAB CMDB 40 63.9 harmonic -CMB CMDB CTBA 45 68.6 harmonic -CMB CMDB OAB 65 146.6 harmonic -CMB CMR5 CTBB 35 67.8 harmonic -CMB CTBA CMDB 25 68.9 harmonic -CMB CTBA CMR 75 47.8 harmonic -CMB CTBB CMR5 25 68.2 harmonic -CMB CTBB CMR 50 56.3 harmonic -CMB CTBB CTB 35 120.7 sdk -CMDB CMB CMR5 150 175.6 harmonic -CMDB CMB CTBA 62.5 42.5 harmonic -CMDB CMB CTBB 25 134.2 harmonic -CMDB CTBA CMR 50 108.6 harmonic -CMR5 CNB CTBA 15 135.8 harmonic -CMR5 CMB CTBB 45 44.0 harmonic -CMR5 CTBB CTB 20 62.7 harmonic -CMR CTBB CMR5 75 107.0 harmonic -CMR CTBB CTB 37.5 110.1 sdk -CTBA CM2R OAB 25 107.4 harmonic -CTBA CMB CTBB 20 92.2 harmonic -CTBA CMDB OAB 20 91.8 harmonic -CTBA CMR CTBB 15 115.0 harmonic -CMB CMR5 CTB 88 131.7 harmonic -CTBB CMR5 CTB 20 77.4 harmonic -CM2 CTB CMR5 20 118.0 sdk -CMR5 CTB CTBB 62.5 39.7 harmonic - -ITEM END - diff --git a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm b/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm deleted file mode 100644 index 2bf0769c6d..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/sdk_original_format/sdk_lipids.prm +++ /dev/null @@ -1,222 +0,0 @@ -# -# SDK interaction parameters using sdk.92172.tmp -# converted by sdk.pl v1.0, August 31, 2014 by Pieter J. in 't Veld -# to be used in conjuction with EMC v9.3.7 or higher -# - -# Force field definition - -ITEM DEFINE - -FFNAME SDK -FFTYPE COARSE -VERSION 1.0 -CREATED Oct 2014 -LENGTH ANGSTROM -ENERGY KCAL/MOL -DENSITY G/CC -MIX NONE -NBONDED 1 -INNER 9 -CUTOFF 12 -PAIR14 OFF -ANGLE WARN -TORSION IGNORE - -ITEM END - -# Literature references - -ITEM REFERENCES - -# year volume page journal - -2010 114 6836 [4] J. Phys. Chem. B - -ITEM END - -# Masses - -ITEM MASS - -# type mass ncons charge cite comment - -CM 42.0804 2 0 1 >CCC< -CMD2 26.0378 2 0 4 >\C=C/< -CT 43.0883 1 0 1 CCC< -CT2 29.0615 1 0 1 CC< -EST1 58.0366 2 0 4 >CC(=O)O< -EST2 58.0366 2 0 4 >CC(=O)O< -GL 41.0725 3 0 4 >CCCCN(C)(C)C -NH 44.0761 1 1 4 >CCN -PH 94.9716 2 -1 4 >OP(O)(O)O< -PHE 94.9716 2 -1 4 >OP(O)(O)O< -W 54.0456 0 0 1 O.O.O - -ITEM END - -# Typing equivalences - -ITEM EQUIVALENCE - -# type pair bond angle torsion improper - -CM CM CM CM CM CM -CMD2 CMD2 CMD2 CMD2 CMD2 CMD2 -CT CT CT CT CT CT -CT2 CT2 CT2 CT2 CT2 CT2 -EST1 EST1 EST1 EST1 EST1 EST1 -EST2 EST2 EST2 EST2 EST2 EST2 -GL GL GL GL GL GL -NC NC NC NC NC NC -NH NH NH NH NH NH -PH PH PH PH PH PH -PHE PHE PHE PHE PHE PHE -W W W W W W - -ITEM END - -# Nonbonded parameters - -ITEM NONBOND - -# type1 type2 sigma epsilon m n - -CM CM 4.506 0.42 9 6 -CM CMD2 4.2555 0.312 9 6 -CM CT 4.5455 0.444 9 6 -CM CT2 4.3635 0.362 9 6 -CM EST1 4.403 0.47 9 6 -CM EST2 4.403 0.47 9 6 -CM GL 4.506 0.42 9 6 -CM NC 5.128 0.4 9 6 -CM NH 4.553 0.33 9 6 -CM PH 4.953 0.3 9 6 -CM PHE 4.953 0.3 9 6 -CM W 4.4385 0.34 12 4 -CMD2 CMD2 4.005 0.232 9 6 -CMD2 CT 4.295 0.33 9 6 -CMD2 CT2 4.113 0.269 9 6 -CMD2 EST1 4.005 0.44 9 6 -CMD2 EST2 4.005 0.44 9 6 -CMD2 GL 4.2555 0.312 9 6 -CMD2 NC 4.8775 0.35 9 6 -CMD2 NH 4.3025 0.3 9 6 -CMD2 PH 4.7025 0.3 9 6 -CMD2 PHE 4.7025 0.3 9 6 -CMD2 W 4.188 0.27 12 4 -CT CT 4.585 0.469 9 6 -CT CT2 4.403 0.383 9 6 -CT EST1 4.4425 0.47 9 6 -CT EST2 4.4425 0.47 9 6 -CT GL 4.5455 0.444 9 6 -CT NC 5.1675 0.42 9 6 -CT NH 4.925 0.34 9 6 -CT PH 4.9925 0.32 9 6 -CT PHE 4.9925 0.32 9 6 -CT W 4.478 0.36 12 4 -CT2 CT2 4.221 0.312 9 6 -CT2 EST1 4.2605 0.39 9 6 -CT2 EST2 4.2605 0.39 9 6 -CT2 GL 4.365 0.362 9 6 -CT2 NC 4.9855 0.32 9 6 -CT2 NH 4.4105 0.32 9 6 -CT2 PH 4.8105 0.28 9 6 -CT2 PHE 4.8105 0.28 9 6 -CT2 W 4.296 0.29 12 4 -EST1 EST1 4.3 0.495 9 6 -EST1 EST2 4.3 0.495 9 6 -EST1 GL 4.403 0.47 9 6 -EST1 NC 4.475 0.75 9 6 -EST1 NH 4.11 0.85 9 6 -EST1 PH 4.55 0.5 9 6 -EST1 PHE 4.55 0.5 9 6 -EST1 W 4.29 0.82 12 4 -EST2 EST2 4.3 0.495 9 6 -EST2 GL 4.403 0.47 9 6 -EST2 NC 4.475 0.75 9 6 -EST2 NH 4.11 0.85 9 6 -EST2 PH 4.55 0.5 9 6 -EST2 PHE 4.55 0.5 9 6 -EST2 W 4.29 0.82 12 4 -GL GL 4.506 0.42 9 6 -GL NC 4.62 0.65 9 6 -GL NH 4.19 0.75 9 6 -GL PH 4.75 0.3 9 6 -GL PHE 4.75 0.3 9 6 -GL W 4.4385 0.64 12 4 -NC NC 5.75 0.7 9 6 -NC NH 5.175 0.88 9 6 -NC PH 4.2 1.15 9 6 -NC PHE 4.2 1.15 9 6 -NC W 4.61 0.9 12 4 -NH NH 4.6 1.1 9 6 -NH PH 3.8 1.2 9 6 -NH PHE 3.8 1.2 9 6 -NH W 3.95 0.8 12 4 -PH PH 5.4 1.4 9 6 -PH PHE 5 1.4 9 6 -PH W 4.03 1 12 4 -PHE PHE 4.6 1.4 9 6 -PHE W 4.03 1 12 4 -W W 4.371 0.895 12 4 - -ITEM END - -# Bond parameters - -ITEM BOND - -# type1 type2 k l0 - -CM CM 6.16 3.64 -CM CMD2 8 3.03 -CM CT 6.16 3.65 -CM CT2 9 3.13 -CM EST1 4.7 3.55 -CM EST2 5.1 3.61 -CM PHE 12 3.69 -CM SO4 11 3.63 -CMD2 CT 8 3.09 -CMD2 CT2 60 2.54 -CT CT 6.955 3.71 -EST1 GL 30 2.88 -EST2 GL 8.4 3.48 -GL PHE 8.9 3.52 -NC PHE 4.8 4.25 -NH PHE 9.4 3.6 -PHE1 PHE2 2.5 150 - -ITEM END - -# Angle parameters - -ITEM ANGLE - -# type1 type2 type3 k theta0 - -CM CM CM 1.19 173 -CM CM CMD2 1.9 161 -CM CM CT 1.19 175 -CM CM CT2 1.6 172 -CM CM EST1 1 178 -CM CM EST2 1 178 -CM CM PHE 1.1 178 -CM CMD2 CM 6 110 -CM EST1 GL 0.8 168 -CM EST2 GL 0.8 172 -CM PHE NC 3.3 112 -CT CM CT 1.093 175.5 -CT CM CT2 1.6 172 -CT CMD2 CT 7.7 116 -CT2 CM CT2 1.7 173 -CT2 CMD2 CT2 12 110 -EST1 GL EST2 1 95 -EST1 GL PHE 1.4 124 -EST2 GL PHE 2 138 -GL PHE NC 3.1 112 -GL PHE NH 4 102 - -ITEM END - diff --git a/tools/moltemplate/moltemplate/force_fields/spce.lt b/tools/moltemplate/moltemplate/force_fields/spce.lt deleted file mode 100644 index 1f0f0f61b5..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 600.0 1.0 - angle_coeff @angle:HOH harmonic 75.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 0.0 - group spce type @atom:O @atom:H - fix fShakeSPCE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeSPCE during minimization.) - } - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/moltemplate/force_fields/spce_ice_rect16.lt b/tools/moltemplate/moltemplate/force_fields/spce_ice_rect16.lt deleted file mode 100644 index e67b228e9e..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/spce_ice_rect16.lt +++ /dev/null @@ -1,81 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 16 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 9.043 7.832 7.361 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect16 { - - # Create a 3-dimensional array of 16 water molecules - - wat = new SPCE[4][2][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 3.545 1.970 - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.371 1.711 - $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300 - $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970 - $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 2.611 3.291 - $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381 - $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711 - $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 1.305 0.390 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 5.221 0.390 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291 - $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381 - $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711 - $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 4.287 1.711 - $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300 - $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970 - $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 2.611 4.070 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.972 - $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061 - $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391 - $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 3.545 5.391 - $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981 - $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651 - $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 0.371 5.651 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 4.287 5.651 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391 - $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981 - $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651 - $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 5.221 6.972 - $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061 - $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391 - $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070 - } -} # SpceIceRect16 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/moltemplate/force_fields/spce_ice_rect32.lt b/tools/moltemplate/moltemplate/force_fields/spce_ice_rect32.lt deleted file mode 100644 index 0a52d82981..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/spce_ice_rect32.lt +++ /dev/null @@ -1,129 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 32 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 9.043 15.663 7.361 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect32 { - - # Create a 3-dimensional array of 32 water molecules - - wat = new SPCE[4][4][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.322 2.144 1.970 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.291 - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.711 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 1.305 0.390 - $atom:wat[2][0][0]/O $mol:wat[2][0][0] @atom:SPCE/O -0.8476 5.652 2.611 2.300 - $atom:wat[2][0][0]/H1 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 4.843 2.144 1.970 - $atom:wat[2][0][0]/H2 $mol:wat[2][0][0] @atom:SPCE/H 0.4238 5.652 3.545 1.970 - $atom:wat[3][0][0]/O $mol:wat[3][0][0] @atom:SPCE/O -0.8476 7.912 1.305 1.381 - $atom:wat[3][0][0]/H1 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.103 1.772 1.711 - $atom:wat[3][0][0]/H2 $mol:wat[3][0][0] @atom:SPCE/H 0.4238 7.912 0.371 1.711 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.940 5.688 1.711 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.287 1.711 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 4.200 6.059 1.970 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.291 - $atom:wat[2][1][0]/O $mol:wat[2][1][0] @atom:SPCE/O -0.8476 5.652 5.221 1.381 - $atom:wat[2][1][0]/H1 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 6.461 5.688 1.711 - $atom:wat[2][1][0]/H2 $mol:wat[2][1][0] @atom:SPCE/H 0.4238 5.652 5.221 0.390 - $atom:wat[3][1][0]/O $mol:wat[3][1][0] @atom:SPCE/O -0.8476 7.912 6.526 2.300 - $atom:wat[3][1][0]/H1 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 8.721 6.059 1.970 - $atom:wat[3][1][0]/H2 $mol:wat[3][1][0] @atom:SPCE/H 0.4238 7.912 7.460 1.970 - $atom:wat[0][2][0]/O $mol:wat[0][2][0] @atom:SPCE/O -0.8476 1.131 10.443 2.300 - $atom:wat[0][2][0]/H1 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 0.322 9.976 1.970 - $atom:wat[0][2][0]/H2 $mol:wat[0][2][0] @atom:SPCE/H 0.4238 1.131 11.377 1.970 - $atom:wat[1][2][0]/O $mol:wat[1][2][0] @atom:SPCE/O -0.8476 3.391 9.137 1.381 - $atom:wat[1][2][0]/H1 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 2.582 9.604 1.711 - $atom:wat[1][2][0]/H2 $mol:wat[1][2][0] @atom:SPCE/H 0.4238 3.391 8.203 1.711 - $atom:wat[2][2][0]/O $mol:wat[2][2][0] @atom:SPCE/O -0.8476 5.652 10.443 2.300 - $atom:wat[2][2][0]/H1 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 4.843 9.976 1.970 - $atom:wat[2][2][0]/H2 $mol:wat[2][2][0] @atom:SPCE/H 0.4238 5.652 10.443 3.291 - $atom:wat[3][2][0]/O $mol:wat[3][2][0] @atom:SPCE/O -0.8476 7.912 9.137 1.381 - $atom:wat[3][2][0]/H1 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.103 9.604 1.711 - $atom:wat[3][2][0]/H2 $mol:wat[3][2][0] @atom:SPCE/H 0.4238 7.912 9.137 0.390 - $atom:wat[0][3][0]/O $mol:wat[0][3][0] @atom:SPCE/O -0.8476 1.131 13.053 1.381 - $atom:wat[0][3][0]/H1 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.940 13.520 1.711 - $atom:wat[0][3][0]/H2 $mol:wat[0][3][0] @atom:SPCE/H 0.4238 1.131 13.053 0.390 - $atom:wat[1][3][0]/O $mol:wat[1][3][0] @atom:SPCE/O -0.8476 3.391 14.358 2.300 - $atom:wat[1][3][0]/H1 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 4.200 13.891 1.970 - $atom:wat[1][3][0]/H2 $mol:wat[1][3][0] @atom:SPCE/H 0.4238 3.391 15.292 1.970 - $atom:wat[2][3][0]/O $mol:wat[2][3][0] @atom:SPCE/O -0.8476 5.652 13.053 1.381 - $atom:wat[2][3][0]/H1 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 6.461 13.520 1.711 - $atom:wat[2][3][0]/H2 $mol:wat[2][3][0] @atom:SPCE/H 0.4238 5.652 12.119 1.711 - $atom:wat[3][3][0]/O $mol:wat[3][3][0] @atom:SPCE/O -0.8476 7.912 14.358 2.300 - $atom:wat[3][3][0]/H1 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 8.721 13.891 1.970 - $atom:wat[3][3][0]/H2 $mol:wat[3][3][0] @atom:SPCE/H 0.4238 7.912 14.358 3.291 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.144 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.545 5.391 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.651 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 0.371 5.651 - $atom:wat[2][0][1]/O $mol:wat[2][0][1] @atom:SPCE/O -0.8476 5.652 2.611 5.061 - $atom:wat[2][0][1]/H1 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 6.461 2.144 5.391 - $atom:wat[2][0][1]/H2 $mol:wat[2][0][1] @atom:SPCE/H 0.4238 5.652 2.611 4.070 - $atom:wat[3][0][1]/O $mol:wat[3][0][1] @atom:SPCE/O -0.8476 7.912 1.305 5.981 - $atom:wat[3][0][1]/H1 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 8.721 1.772 5.651 - $atom:wat[3][0][1]/H2 $mol:wat[3][0][1] @atom:SPCE/H 0.4238 7.912 1.305 6.972 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 0.322 5.688 5.651 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.972 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 2.582 6.059 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.460 5.391 - $atom:wat[2][1][1]/O $mol:wat[2][1][1] @atom:SPCE/O -0.8476 5.652 5.221 5.981 - $atom:wat[2][1][1]/H1 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 4.843 5.688 5.651 - $atom:wat[2][1][1]/H2 $mol:wat[2][1][1] @atom:SPCE/H 0.4238 5.652 4.287 5.651 - $atom:wat[3][1][1]/O $mol:wat[3][1][1] @atom:SPCE/O -0.8476 7.912 6.526 5.061 - $atom:wat[3][1][1]/H1 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.103 6.059 5.391 - $atom:wat[3][1][1]/H2 $mol:wat[3][1][1] @atom:SPCE/H 0.4238 7.912 6.526 4.070 - $atom:wat[0][2][1]/O $mol:wat[0][2][1] @atom:SPCE/O -0.8476 1.131 10.443 5.061 - $atom:wat[0][2][1]/H1 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.940 9.976 5.391 - $atom:wat[0][2][1]/H2 $mol:wat[0][2][1] @atom:SPCE/H 0.4238 1.131 10.443 4.070 - $atom:wat[1][2][1]/O $mol:wat[1][2][1] @atom:SPCE/O -0.8476 3.391 9.137 5.981 - $atom:wat[1][2][1]/H1 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 4.200 9.604 5.651 - $atom:wat[1][2][1]/H2 $mol:wat[1][2][1] @atom:SPCE/H 0.4238 3.391 9.137 6.972 - $atom:wat[2][2][1]/O $mol:wat[2][2][1] @atom:SPCE/O -0.8476 5.652 10.443 5.061 - $atom:wat[2][2][1]/H1 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 6.461 9.976 5.391 - $atom:wat[2][2][1]/H2 $mol:wat[2][2][1] @atom:SPCE/H 0.4238 5.652 11.377 5.391 - $atom:wat[3][2][1]/O $mol:wat[3][2][1] @atom:SPCE/O -0.8476 7.912 9.137 5.981 - $atom:wat[3][2][1]/H1 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 8.721 9.604 5.651 - $atom:wat[3][2][1]/H2 $mol:wat[3][2][1] @atom:SPCE/H 0.4238 7.912 8.203 5.651 - $atom:wat[0][3][1]/O $mol:wat[0][3][1] @atom:SPCE/O -0.8476 1.131 13.053 5.981 - $atom:wat[0][3][1]/H1 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 0.322 13.520 5.651 - $atom:wat[0][3][1]/H2 $mol:wat[0][3][1] @atom:SPCE/H 0.4238 1.131 12.119 5.651 - $atom:wat[1][3][1]/O $mol:wat[1][3][1] @atom:SPCE/O -0.8476 3.391 14.358 5.061 - $atom:wat[1][3][1]/H1 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 2.582 13.891 5.391 - $atom:wat[1][3][1]/H2 $mol:wat[1][3][1] @atom:SPCE/H 0.4238 3.391 14.358 4.070 - $atom:wat[2][3][1]/O $mol:wat[2][3][1] @atom:SPCE/O -0.8476 5.652 13.053 5.981 - $atom:wat[2][3][1]/H1 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 4.843 13.520 5.651 - $atom:wat[2][3][1]/H2 $mol:wat[2][3][1] @atom:SPCE/H 0.4238 5.652 13.053 6.972 - $atom:wat[3][3][1]/O $mol:wat[3][3][1] @atom:SPCE/O -0.8476 7.912 14.358 5.061 - $atom:wat[3][3][1]/H1 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.103 13.891 5.391 - $atom:wat[3][3][1]/H2 $mol:wat[3][3][1] @atom:SPCE/H 0.4238 7.912 15.292 5.391 - } -} # SpceIceRect32 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/moltemplate/force_fields/spce_ice_rect8.lt b/tools/moltemplate/moltemplate/force_fields/spce_ice_rect8.lt deleted file mode 100644 index ae5d22a77e..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/spce_ice_rect8.lt +++ /dev/null @@ -1,57 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 8 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect8 { - - # Create a 3-dimensional array of 8 water molecules - - wat = new SPCE[2][2][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 - } -} # IceRect8 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/moltemplate/force_fields/tip3p_1983.lt b/tools/moltemplate/moltemplate/force_fields/tip3p_1983.lt deleted file mode 100644 index 4a792691e2..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/tip3p_1983.lt +++ /dev/null @@ -1,119 +0,0 @@ -############################################################# -# WARNING: THIS FILE HAS NOT BEEN TESTED! -# (If you use this file in a simulation, please email me to let me know -# if it worked. -Andrew 2014-5, (jewett dot aij at gmail dot com)) -######################################################### -# There are two different versions of TIP3P: -# -# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). -# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model -# # which uses long-range coulombics -######################################################### - -# file "tip3p_1983.lt" -# -# H1 H2 -# \ / -# O -# -# I think this is the TIP3P water model used by CHARMM (and AMBER?). See: -# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983) - - -TIP3P_1983 { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766 - $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 450.0 0.9572 - angle_coeff @angle:HOH harmonic 55.0 104.52 - - ######################################################################### - #### There are two choices for for the O-O interactions - ######################################################################### - #### O-O nonbonded interactions - - # For the 1983 Jorgensen version of TIP3P use: - pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 - - # For the 2004 Price & Brooks version of TIP3P use: - #pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188 - - ######################################################################### - #### There are three choices for for the O-H and H-H interactions - ######################################################################### - #### 1) The original Jorgensen 1983 and 2004 Price & Brooks models have no - # mixed OH or HH interactions. For this behavior, uncomment these lines: - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 - pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 - ######################################################################### - #### 2) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter - #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753#arithmetic - ######################################################################### - #### 3) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, - #### If you want to use this, uncomment the following two lines: - #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric - ######################################################################### - - # Define a group for the tip3p water molecules: - group tip3p type @atom:O @atom:H - - # Optional: Constrain the angles and distances. - # (Most implementations use this, but it is optional.) - fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeTIP3P during minimization.) - } - - - write_once("In Init") { - # -- Default styles (for solo "TIP3P_1983" water) -- - units real - atom_style full - - # I'm not sure exactly which cutoffs distances are traditionally used in - # in the 1983 "TIP3P" model by Jorgensen model, (used by CHARMM). - # (See the Price JCP 2004 paper for a review.) - # My first guess was this: - pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5 - - # However, in the LAMMPS "peptide" example, they use these parameters: - # pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0 - - bond_style hybrid harmonic - angle_style hybrid harmonic - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # "TIP3P_1983" water molecule type - - - - -# (note to self:) -# In the LAMMPS "peptide" example, these (nearly identical) parameters were used -# and they left the O-H parameters to be determined by the default mixing rules -#pair_style lj/charmm/coul/long 8.0 10.0 10.0 -#pair_coeff @atom:H @atom:H 0.046 0.400014 0.046 0.400014 -#pair_coeff @atom:O @atom:O 0.1521 3.15057 0.1521 3.15057 -#angle_style charmm -#angle_coeff @angle:HOH 55.0 104.52 0.0 0.0 diff --git a/tools/moltemplate/moltemplate/force_fields/tip3p_1983_charmm.lt b/tools/moltemplate/moltemplate/force_fields/tip3p_1983_charmm.lt deleted file mode 100644 index 1b89435be4..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/tip3p_1983_charmm.lt +++ /dev/null @@ -1,119 +0,0 @@ -############################################################# -# WARNING: THIS FILE HAS NOT BEEN TESTED! -# (If you use this file in a simulation, please email me to let me know -# if it worked. -Andrew 2014-5, (jewett dot aij at gmail dot com)) -######################################################### -# There are two different versions of TIP3P: -# -# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). -# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model -# # which uses long-range coulombics -######################################################### - -# file "tip3p_1983_charmm.lt" -# -# H1 H2 -# \ / -# O -# -# I think this is the TIP3P water model used by CHARMM (and AMBER?). See: -# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983) - - -TIP3P_1983_CHARMM { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766 - $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 450.0 0.9572 - angle_coeff @angle:HOH harmonic 55.0 104.52 - - ######################################################################### - #### There are two choices for for the O-O interactions - ######################################################################### - #### O-O nonbonded interactions - - # For the 1983 Jorgensen version of TIP3P use: - pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 - - # For the 2004 Price & Brooks version of TIP3P use: - #pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188 - - ######################################################################### - #### There are three choices for for the O-H and H-H interactions - ######################################################################### - #### 1) The original Jorgensen 1983 and 2004 Price & Brooks models have no - # mixed OH or HH interactions. For this behavior, uncomment these lines: - #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 - #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 - ######################################################################### - #### 2) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic - ######################################################################### - #### 3) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, - #### If you want to use this, uncomment the following two lines: - #pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - #pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric - ######################################################################### - - # Define a group for the tip3p water molecules: - group tip3p type @atom:O @atom:H - - # Optional: Constrain the angles and distances. - # (Most implementations use this, but it is optional.) - fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeTIP3P during minimization.) - } - - - write_once("In Init") { - # -- Default styles (for solo "TIP3P_1983_CHARMM" water) -- - units real - atom_style full - - # I'm not sure exactly which cutoffs distances are traditionally used in - # in the 1983 "TIP3P" model by Jorgensen model, (used by CHARMM). - # (See the Price JCP 2004 paper for a review.) - # My first guess was this: - pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5 - - # However, in the LAMMPS "peptide" example, they use these parameters: - # pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0 - - bond_style hybrid harmonic - angle_style hybrid harmonic - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # "TIP3P_1983_CHARMM" water molecule type - - - - -# (note to self:) -# In the LAMMPS "peptide" example, these (nearly identical) parameters were used -# and they left the O-H parameters to be determined by the default mixing rules -#pair_style lj/charmm/coul/long 8.0 10.0 10.0 -#pair_coeff @atom:H @atom:H 0.046 0.400014 0.046 0.400014 -#pair_coeff @atom:O @atom:O 0.1521 3.15057 0.1521 3.15057 -#angle_style charmm -#angle_coeff @angle:HOH 55.0 104.52 0.0 0.0 diff --git a/tools/moltemplate/moltemplate/force_fields/tip3p_2004.lt b/tools/moltemplate/moltemplate/force_fields/tip3p_2004.lt deleted file mode 100644 index 0c8da1bc5b..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/tip3p_2004.lt +++ /dev/null @@ -1,107 +0,0 @@ -######################################################### -# WARNING: THIS FILE HAS NOT BEEN TESTED! -# (If you use this file in a simulation, please email me to let me know -# if it worked. -Andrew 2014-5, (jewett dot aij at gmail dot com)) -######################################################### -# There are two different versions of TIP3P: -# -# tip3p_1983.lt # The implementation of TIP3P used by CHARMM (I think). -# tip3p_2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model -# # which uses long-range coulombics -######################################################### - -# file "tip3p_2004.lt" -# -# H1 H2 -# \ / -# O -# -# I think this is the TIP3P water described in the paper by -# Daniel J. Price and Charles L. Brooks III -# J. Chem. Phys., 121(20): 10096 (2004) -# Specifically I think it refers to the "Model B" version of long-range TIP3P -# described in the 3rd-to-last column of "Table I", on p.10099. - -TIP3P_2004 { - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.830 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.415 0.756950327 0.00000 0.5858822766 - $atom:H2 $mol:. @atom:H 0.415 -0.756950327 0.00000 0.5858822766 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 450.0 0.9572 - angle_coeff @angle:HOH harmonic 55.0 104.52 - - ######################################################################### - #### There are two choices for for the O-O interactions - ######################################################################### - #### O-O nonbonded interactions - - # For the 1983 Jorgensen version of TIP3P use: - #pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 - - # For the 2004 Price & Brooks version of TIP3P use: - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.102 3.188 - - ######################################################################### - #### There are three choices for for the O-H and H-H interactions - ######################################################################### - #### 1) The original Jorgensen 1983 and 2004 Price & Brooks models have no - # mixed OH or HH interactions. For this behavior, uncomment these lines: - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.00 0.4000 - pair_coeff @atom:O @atom:H lj/charmm/coul/long 0.00 1.7753 - ######################################################################### - #### 2) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter - #pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0460 0.4000 - #pair_coeff @atom:O @atom:H lj/charmm/coul/long 0.0836 1.7753 #arithmetic - ######################################################################### - #### 3) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, - #### If you want to use this, uncomment the following two lines: - #pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0460 0.4000 - #pair_coeff @atom:O @atom:H lj/charmm/coul/long 0.0836 1.1226 #geometric - ######################################################################### - - # Define a group for the tip3p water molecules: - group tip3p type @atom:O @atom:H - - # Optional: Constrain the angles and distances. - # (Most implementations use this, but it is optional.) - fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fShakeTIP3P during minimization.) - } - - - write_once("In Init") { - # -- Default styles (for solo "TIP3P_2004" water) -- - units real - atom_style full - - pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 - - # Note: in the LAMMPS "peptide" example, they use these parameters: - # pair_style hybrid lj/charmm/coul/long 8.0 10.0 10.0 - - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - #pair_modify mix arithmetic # LEAVE THIS UNSPECIFIED! - } - -} # "TIP3P_2004" water molecule type - diff --git a/tools/moltemplate/moltemplate/force_fields/trappe1998.lt b/tools/moltemplate/moltemplate/force_fields/trappe1998.lt deleted file mode 100644 index 1227b2aeba..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/trappe1998.lt +++ /dev/null @@ -1,53 +0,0 @@ -# This file stores complete LAMMPS data for the TraPPE model of saturated -# hydrocarbon chains. In this "united-atom" model, each methyl group is -# represented by a single atom. Forces between "atoms" are taken from the -# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) - -TraPPE { - - write_once("Data Masses") { - @atom:CH2 14.1707 - @atom:CH3 15.2507 - @atom:CH4 16.3307 - } - - write_once("Data Angles By Type") { - @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated - } - - write_once("Data Dihedrals By Type") { - @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated - } - - write_once("In Settings") { - pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 - pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 - pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 - bond_coeff @bond:saturated harmonic 120.0 1.54 - angle_coeff @angle:backbone harmonic 62.0022 114 - dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 - } - - # Optional: Create a group corresponding to atoms used by the TraPPE force- - # field. (This is useful if you mix force-fields together.) - - write_once("In Settings") { - group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 - } - - write_once("In Init") { - # -- Default styles for "TraPPE" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style none - pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - -} # class TraPPE - diff --git a/tools/moltemplate/moltemplate/force_fields/watmw.lt b/tools/moltemplate/moltemplate/force_fields/watmw.lt deleted file mode 100644 index f4eedc4049..0000000000 --- a/tools/moltemplate/moltemplate/force_fields/watmw.lt +++ /dev/null @@ -1,77 +0,0 @@ -# This file stores LAMMPS data for the "mW" water model. -# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) -# -# In this model, each water molecule is represented by a single "mW" particle. -# These particles interact with their neighbors via 3-body Stillinger-Weber -# forces whose parameters are tuned to mimic directional hydrogen-bonding -# in liquid water (as well as hexagonal ice, type II ice, and -# low-density super-cooled liquid/amorphous water phases). - -#### -# -# NOTE: THIS FILE IS INTENDED FOR SIMULATIONS OF PURE WATER ONLY. -# IF YOU HAVE OTHER ATOMS IN YOUR SYSTEM (BESIDES WATER), -# YOU MUST REPLACE THIS LINE: -# -# pair_coeff * * sw system.in.sw mW -# -# WITH THIS LINE: -# -# pair_coeff * * sw system.in.sw mW NULL NULL NULL -# -# ...IN THE FILE BELOW. -# -# (Note:The number of "NULL" entries in the list should match the -# number of other atom types defined somewhere in your simulation. -# In the "3bodyWater+hydrocarbons_MW+TraPPE" example, there are 3 -# types of carbon defined in "trappe1998.lt", so "NULL" appears 3 times. -#### - - - - -WatMW { - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 - } - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # --Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW # SEE COMMENT ABOVE - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) - } - - # -- optional -- - - write_once("In Settings") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/moltemplate/genpoly_lt.py b/tools/moltemplate/moltemplate/genpoly_lt.py deleted file mode 100755 index 9d8ec84608..0000000000 --- a/tools/moltemplate/moltemplate/genpoly_lt.py +++ /dev/null @@ -1,746 +0,0 @@ -#!/usr/bin/env python - -""" - Generate a moltemplate (.lt) file containing a definition of a polymer - molecule whose monomers are located at the positions specified in - "coords.raw" (a 3-column text file). Monomers will be rotated so - that they point in the direction connecting neighbors (r[i+1]-r[i]) - The user can specify the subunits to use when building the polymer, - the atoms to to build bonds (and angles, and dihedrals) between monomers - and the helical pitch of the polymer. The output of this program is - a text file in moltemplate (.lt) format containing the sequence of - moltemplate commands needed to build this polymer molecule(s). (One must - then run moltemplate on this file to build the LAMMPS simulation files.) - Multiple Polymers: - To make it easier to create polymer melts, multiple polymers can be created - from coordinates in the same file by using the "-cuts" command line argument. - Encapsulation: - If the "-polymer-name PolyName" command line option is given, then these - moltemplate commands will be nested within the definition of a moltemplate - object (named "PolyName", in this example. Later in your moltemplate files, - you must remember to instantiate a copy of this moltemplate object using - a command like "polymer = new PolyName" Atoms within this object will - share the same molecule-ID number.) If multiple polymers are requested, then - each of them will have their own polymer object. - -""" - - -g_usage_msg = """ -Usage: - - genpoly_lt.py \\ - [-bond btype a1 a2] \\ - [-helix deltaphi] \\ - [-axis x,y,z] \\ - [-circular yes/no/connected] \\ - [-dir-indices ia ib] \\ - [-angle atype a1 a2 a3 i1 i2 i3] \\ - [-dihedral dtype a1 a2 a3 a4 i1 i2 i3 i4] \\ - [-improper itype a1 a2 a3 a4 i1 i2 i3 i4] \\ - [-monomer-name mname] \\ - [-sequence sequence.txt] \\ - [-polymer-name pname] \\ - [-inherits ForceFieldObject] \\ - [-header "import \"monomer.lt\""] \\ - [-cuts cuts.txt] \\ - [-box paddingX,paddingY,paddingZ] \\ - < coords.raw > polymer.lt - -""" - - -import sys -import random -from math import * - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - (Raising this exception implies that the caller has provided - a faulty input file or argument.) - - """ - - def __init__(self, err_msg): - self.err_msg = err_msg - - def __str__(self): - return self.err_msg - - def __repr__(self): - return str(self) - - -class GPSettings(object): - - def __init__(self): - self.direction_orig = [1.0, 0.0, 0.0] - self.is_circular = False - self.connect_ends = False - self.delta_phi = 0.0 - self.header = 'import \"forcefield.lt\"' - self.name_monomer = 'Monomer' - self.name_polymer = '' - self.inherits = '' - self.name_sequence = [] - self.dir_index_offsets = (-1,1) - self.cuts = [] - self.box_padding = None - self.bonds_name = [] - self.bonds_type = [] - self.bonds_atoms = [] - self.bonds_index_offsets = [] - self.angles_name = [] - self.angles_type = [] - self.angles_atoms = [] - self.angles_index_offsets = [] - self.dihedrals_name = [] - self.dihedrals_type = [] - self.dihedrals_atoms = [] - self.dihedrals_index_offsets = [] - self.impropers_name = [] - self.impropers_type = [] - self.impropers_atoms = [] - self.impropers_index_offsets = [] - - def ParseArgs(self, argv): - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if argv[i].lower() == '-bond': - if i + 3 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by 4 strings.\n') - # self.bonds_name.append(argv[i+1]) - self.bonds_type.append(argv[i + 1]) - self.bonds_atoms.append((argv[i + 2], - argv[i + 3])) - self.bonds_index_offsets.append((0, 1)) - del(argv[i:i + 4]) - elif argv[i].lower() == '-angle': - if i + 7 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by 5 strings and 3 integers.\n') - # self.angles_name.append(argv[i+1]) - self.angles_type.append(argv[i + 1]) - self.angles_atoms.append((argv[i + 2], - argv[i + 3], - argv[i + 4])) - self.angles_index_offsets.append((int(argv[i + 5]), - int(argv[i + 6]), - int(argv[i + 7]))) - if ((self.angles_index_offsets[-1][0] < 0) or - (self.angles_index_offsets[-1][1] < 0) or - (self.angles_index_offsets[-1][2] < 0)): - raise InputError( - 'Error: ' + argv[i] + ' indices (i1 i2 i3) must be >= 0\n') - del(argv[i:i + 8]) - elif argv[i].lower() == '-dihedral': - if i + 9 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by 6 strings and 4 integers.\n') - # self.dihedrals_name.append(argv[i+1]) - self.dihedrals_type.append(argv[i + 1]) - self.dihedrals_atoms.append((argv[i + 2], - argv[i + 3], - argv[i + 4], - argv[i + 5])) - self.dihedrals_index_offsets.append((int(argv[i + 6]), - int(argv[i + 7]), - int(argv[i + 8]), - int(argv[i + 9]))) - if ((self.dihedrals_index_offsets[-1][0] < 0) or - (self.dihedrals_index_offsets[-1][1] < 0) or - (self.dihedrals_index_offsets[-1][2] < 0) or - (self.dihedrals_index_offsets[-1][3] < 0)): - raise InputError( - 'Error: ' + argv[i] + ' indices (i1 i2 i3 i4) must be >= 0\n') - del(argv[i:i + 10]) - elif argv[i].lower() == '-improper': - if i + 9 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by 6 strings and 4 integers.\n') - # self.impropers_name.append(argv[i+1]) - self.impropers_type.append(argv[i + 1]) - self.impropers_atoms.append((argv[i + 2], - argv[i + 3], - argv[i + 4], - argv[i + 5])) - self.impropers_index_offsets.append((int(argv[i + 6]), - int(argv[i + 7]), - int(argv[i + 8]), - int(argv[i + 9]))) - if ((self.impropers_index_offsets[-1][0] < 0) or - (self.impropers_index_offsets[-1][1] < 0) or - (self.impropers_index_offsets[-1][2] < 0) or - (self.impropers_index_offsets[-1][3] < 0)): - raise InputError( - 'Error: ' + argv[i] + ' indices (i1 i2 i3 i4) must be >= 0\n') - del(argv[i:i + 10]) - elif (argv[i].lower() == '-monomer-name'): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a string\n') - self.name_monomer = argv[i + 1] - del(argv[i:i + 2]) - elif (argv[i].lower() == '-sequence'): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a file name\n') - try: - f = open(argv[i + 1], "r") - except IOError: - raise InputError( - 'Error: file ' + argv[i + 1] + ' could not be opened for reading\n') - self.name_sequence = [] - for line_orig in f: - line = line_orig.strip() - ic = line.find('#') - if ic != -1: - line = line[:ic] - else: - line = line.strip() - if len(line) > 0: - self.name_sequence.append(line) - del(argv[i:i + 2]) - elif (argv[i].lower() == '-cuts'): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a file name\n') - try: - f = open(argv[i + 1], "r") - except IOError: - raise InputError( - 'Error: file ' + argv[i + 1] + ' could not be opened for reading\n') - self.name_sequence = [] - for line_orig in f: - line = line_orig.strip() - ic = line.find('#') - if ic != -1: - line = line[:ic] - else: - line = line.strip() - if len(line) > 0: - try: - self.cuts.append(int(line)) - except ValueError: - raise InputError( - 'Error: file ' + argv[i + 1] + ' should contain only nonnegative integers.\n') - del(argv[i:i + 2]) - elif (argv[i].lower() == '-polymer-name'): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a string\n') - self.name_polymer = argv[i + 1] - del(argv[i:i + 2]) - elif (argv[i].lower() == '-inherits'): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a string\n') - self.inherits = argv[i + 1] - if self.inherits.find('inherits ') == 0: - self.inherits = ' ' + self.inherits - else: - self.inherits = ' inherits ' + self.inherits - if self.name_polymer == '': - self.name_polymer = 'Polymer' # supply a default name - del(argv[i:i + 2]) - elif (argv[i].lower() == '-header'): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a string (usually in quotes)\n') - self.header = argv[i + 1] - del(argv[i:i + 2]) - elif argv[i].lower() == '-axis': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed ' + - 'by 3 numbers separated by commas (no spaces)\n') - self.direction_orig = list(map(float, argv[i + 1].split(','))) - del(argv[i:i + 2]) - elif argv[i].lower() == '-circular': - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by an argument\n' + - ' ("yes", "no", or "connected")\n') - if argv[i + 1].lower() == 'yes': - self.connect_ends = True - self.is_circular = True - elif argv[i + 1].lower() == 'connected': - self.connect_ends = True - self.is_circular = False - elif argv[i + 1].lower() == 'no': - self.connect_ends = False - self.is_circular = False - else: - raise InputError('Error: ' + argv[i] + ' flag should be followed by an argument\n' + - ' ("yes", "no", or "connected")\n') - del(argv[i:i + 2]) - elif argv[i].lower() == '-helix': - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a number (angle in degrees)\n') - self.delta_phi = float(argv[i + 1]) - del(argv[i:i + 2]) - elif (argv[i].lower() == '-dir-indices'): - if i + 2 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by two integers\n') - self.dir_index_offsets = (int(argv[i + 1]), int(argv[i + 2])) - if self.dir_index_offsets[0] == self.dir_index_offsets[1]: - raise InputError( - 'Error: The two numbers following ' + argv[i] + ' must not be equal.\n') - del(argv[i:i + 3]) - elif (argv[i].lower() == '-box'): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed ' + - 'by 3 numbers separated by commas (no spaces)\n') - self.box_padding = list(map(float, argv[i + 1].split(','))) - if len(self.box_padding) == 1: - self.box_padding = self.box_padding * 3 - del(argv[i:i + 2]) - - # elif ((argv[i][0] == '-') and (__name__ == '__main__')): - # - # raise InputError('Error('+g_program_name+'):\n'+\ - # 'Unrecogized command line argument \"'+argv[i]+\ - # '\"\n\n'+\ - # __doc__) - else: - i += 1 - - for b in range(0, len(self.bonds_type)): - if len(self.bonds_type) > 1: - self.bonds_name.append('genpoly' + str(b + 1) + '_') - else: - self.bonds_name.append('genpoly') - for b in range(0, len(self.angles_type)): - if len(self.angles_type) > 1: - self.angles_name.append('genpoly' + str(b + 1) + '_') - else: - self.angles_name.append('genpoly') - for b in range(0, len(self.dihedrals_type)): - if len(self.dihedrals_type) > 1: - self.dihedrals_name.append('genpoly' + str(b + 1) + '_') - else: - self.dihedrals_name.append('genpoly') - for b in range(0, len(self.impropers_type)): - if len(self.impropers_type) > 1: - self.impropers_name.append('genpoly' + str(b + 1) + '_') - else: - self.impropers_name.append('genpoly') - - -class WrapPeriodic(object): - """ Wrap() calculates the remainder of i % N. - It turns out to be convenient to do this multiple times and later - query whether i/N != 0 in any of them once (by checking bounds_err). - - """ - bounds_err = False - - @classmethod - def Wrap(obj, i, N): - if i // N != 0: - obj.bounds_err = True - return i % N - - def WrapF(obj, x, L): - i = floor(x / L) - if i != 0: - obj.bounds_err = True - return x - i * L - - -class GenPoly(object): - """ - Read coordinates from a file, and generate a list of \"new\" commands - in moltemplate format with the position of each monomer located - at these positions, oriented appropriately, with bonds (and angles, - dihedrals, etc...) connecting successive monomers together. - By default (if settings.cuts==False) only a single polymer is created. - However this class can create multiple polymers of different lengths. - The list of coordinates for each polymer are saved separately within - the "self.coords_multi" member. - - """ - - def __init__(self): - self.settings = GPSettings() - self.coords_multi = [] # a list-of-list-of-lists of numbers Nxnx3 - self.direction_vects = [] - self.box_bounds_min = [0.0, 0.0, 0.0] - self.box_bounds_max = [0.0, 0.0, 0.0] - self.N = 0 - - def ParseArgs(self, argv): - # The command above will remove arguments from argv which are - # understood by GPSettings.ParseArgs(argv). - # The remaining arguments will be handled below. - self.settings.ParseArgs(argv) - - def ReadCoords(self, infile): - coords = [] - lines = infile.readlines() - for i in range(0, len(lines)): - tokens = lines[i].strip().split() - if (len(tokens) == 3): - coords.append(list(map(float, tokens))) - - self.N = len(coords) - if self.N < 2: - raise InputError( - "Error: Coordinate file must have at least 2 positions.\n") - # Now generate self.settings.name_sequence: - if len(self.settings.name_sequence) != self.N: - self.settings.name_sequence = [self.settings.name_monomer] * self.N - - self.settings.cuts.append(self.N + 1) - self.settings.cuts.sort() - i = 0 - for j in self.settings.cuts: - self.coords_multi.append(coords[i:j]) - i = j - - def ChooseDirections(self, coords): - """ - Calculate the direction each monomer subunit should be pointing at: - - """ - - self.N = len(coords) - self.direction_vects = [[0.0, 0.0, 0.0] for i in range(0, self.N + 1)] - - if self.settings.is_circular: - for i in range(0, self.N): - # By default, the direction that monomer "i" is pointing is - # determined by the position of the monomers before and after it - # (at index i-1, and i+1). More generally, we allow the user - # to choose what these offsets are ("dir_index_offsets[") - ia = WrapPeriodic.Wrap(i + self.settings.dir_index_offsets[0], - self.N) - ib = WrapPeriodic.Wrap(i + self.settings.dir_index_offsets[1], - self.N) - for d in range(0, 3): - self.direction_vects[i][d] = coords[ - ib][d] - coords[ia][d] - else: - for i in range(1, self.N - 1): - for d in range(0, 3): - self.direction_vects[i][d] = coords[ - i + self.settings.dir_index_offsets[1]][d] - coords[ - i + self.settings.dir_index_offsets[0]][d] - - for d in range(0, 3): - self.direction_vects[0][d] = coords[1][d] - coords[0][d] - self.direction_vects[ - self.N - 1][d] = coords[self.N - 1][d] - coords[self.N - 2][d] - - # Optional: normalize the direction vectors - - for i in range(0, self.N): - direction_len = 0.0 - for d in range(0, 3): - direction_len += (self.direction_vects[i][d])**2 - direction_len = sqrt(direction_len) - for d in range(0, 3): - self.direction_vects[i][d] /= direction_len - - # Special case: self.direction_vects[-1] is the direction that the original monomer - # in "monomer.lt" was pointing. (By default, 1,0,0 <--> the "x" - # direction) - - self.direction_vects[-1] = self.settings.direction_orig - - def WriteLTFile(self, outfile): - """ Write an moltemplate (.lt) file containing the definition of - this polymer object. (If multiple polymer objects were requested by - the user (using the -cuts argument), then their definitions will - appear nested within this object, and each of them will be - instantiated once when the parent object is instantiated.) - - """ - - outfile.write(self.settings.header + "\n\n\n") - if len(self.coords_multi) == 1: - self.WritePolymer(outfile, - self.settings.name_polymer + - self.settings.inherits, - self.coords_multi[0]) - else: - if self.settings.name_polymer != '': - outfile.write(self.settings.name_polymer + " {\n\n") - outfile.write('# Definitions of individual polymers to follow\n\n') - for i in range(0, len(self.coords_multi)): - self.WritePolymer(outfile, - self.settings.name_polymer + '_sub' + str(i + 1) + - self.settings.inherits, - self.coords_multi[i]) - outfile.write('\n\n' - '# Now instantiate all the polymers (once each)\n\n') - - for i in range(0, len(self.coords_multi)): - outfile.write('polymers[' + str(i) + '] = new ' + - self.settings.name_polymer + '_sub' + str(i + 1) + '\n') - - if self.settings.name_polymer != '': - outfile.write('\n\n' - '} # ' + self.settings.name_polymer + '\n\n') - - if self.settings.box_padding != None: - for i in range(0, len(self.coords_multi)): - # calculate the box big enough to collectively enclose - # all of the coordinates (even multiple coordinate sets) - self.CalcBoxBoundaries(self.coords_multi[i]) - self.WriteBoxBoundaries(outfile) - - def WritePolymer(self, - outfile, - name_polymer, - coords): - """ Write a single polymer object to a file. - This function is invoked by WriteLTFile() - - """ - self.ChooseDirections(coords) - - if name_polymer != '': - outfile.write(name_polymer + ' {\n' - '\n\n\n' - 'create_var {$mol}\n' - '# The line above forces all monomer subunits to share the same molecule-ID\n' - '# (Note: Setting the molecule-ID number is optional and is usually ignored.)\n\n\n\n') - - outfile.write(""" -# ------------ List of Monomers: ------------ -# -# (Note: move(), rot(), and rotvv() commands control the position -# of each monomer. (See the moltemplate manual for an explanation -# of what they do.) Commands enclosed in push() are cumulative -# and remain in effect until removed by pop().) - - - -""" - ) - - outfile.write("push(move(0,0,0))\n") - - for i in range(0, self.N): - #im1 = i-1 - # if im1 < 0 or self.settings.connect_ends: - # if im1 < 0: - # im1 += self.N - outfile.write("pop()\n") - outfile.write("push(rotvv(" + - str(self.direction_vects[i - 1][0]) + "," + - str(self.direction_vects[i - 1][1]) + "," + - str(self.direction_vects[i - 1][2]) + "," + - str(self.direction_vects[i][0]) + "," + - str(self.direction_vects[i][1]) + "," + - str(self.direction_vects[i][2]) + "))\n") - # Recall that self.direction_vects[-1] = - # self.settings.direction_orig (usually 1,0,0) - outfile.write("push(move(" + - str(coords[i][0]) + "," + - str(coords[i][1]) + "," + - str(coords[i][2]) + "))\n") - - outfile.write("mon[" + str(i) + "] = new " + - self.settings.name_sequence[i] + - ".rot(" + str(self.settings.delta_phi * i) + ",1,0,0)\n") - - assert(len(self.settings.bonds_name) == - len(self.settings.bonds_type) == - len(self.settings.bonds_atoms) == - len(self.settings.bonds_index_offsets)) - if len(self.settings.bonds_type) > 0: - outfile.write("\n" - "\n" - "write(\"Data Bonds\") {\n") - WrapPeriodic.bounds_err = False - for i in range(0, self.N): - test = False - for b in range(0, len(self.settings.bonds_type)): - I = i + self.settings.bonds_index_offsets[b][0] - J = i + self.settings.bonds_index_offsets[b][1] - I = WrapPeriodic.Wrap(I, self.N) - J = WrapPeriodic.Wrap(J, self.N) - if WrapPeriodic.bounds_err: - WrapPeriodic.bounds_err = False - if not self.settings.connect_ends: - continue - outfile.write( - " $bond:" + self.settings.bonds_name[b] + str(i + 1)) - if len(self.settings.bonds_type) > 1: - outfile.write("_" + str(b + 1)) - outfile.write(" @bond:" + self.settings.bonds_type[b] + " $atom:mon[" + str(I) + "]/" + self.settings.bonds_atoms[ - b][0] + " $atom:mon[" + str(J) + "]/" + self.settings.bonds_atoms[b][1] + "\n") - if len(self.settings.bonds_type) > 0: - outfile.write("} # write(\"Data Bonds\") {...\n\n\n") - - assert(len(self.settings.angles_name) == - len(self.settings.angles_type) == - len(self.settings.angles_atoms) == - len(self.settings.angles_index_offsets)) - if len(self.settings.angles_type) > 0: - outfile.write("\n" - "\n" - "write(\"Data Angles\") {\n") - for i in range(0, self.N): - for b in range(0, len(self.settings.angles_type)): - I = i + self.settings.angles_index_offsets[b][0] - J = i + self.settings.angles_index_offsets[b][1] - K = i + self.settings.angles_index_offsets[b][2] - I = WrapPeriodic.Wrap(I, self.N) - J = WrapPeriodic.Wrap(J, self.N) - K = WrapPeriodic.Wrap(K, self.N) - if WrapPeriodic.bounds_err: - WrapPeriodic.bounds_err = False - if not self.settings.connect_ends: - continue - outfile.write( - " $angle:" + self.settings.angles_name[b] + str(i + 1)) - if len(self.settings.angles_type) > 1: - outfile.write("_" + str(b + 1)) - outfile.write(" @angle:" + self.settings.angles_type[b] + - " $atom:mon[" + str(I) + "]/" + self.settings.angles_atoms[b][0] + - " $atom:mon[" + str(J) + "]/" + self.settings.angles_atoms[b][1] + - " $atom:mon[" + str(K) + "]/" + self.settings.angles_atoms[b][2] + - "\n") - if len(self.settings.angles_type) > 0: - outfile.write("} # write(\"Data Angles\") {...\n\n\n") - - assert(len(self.settings.dihedrals_name) == - len(self.settings.dihedrals_type) == - len(self.settings.dihedrals_atoms) == - len(self.settings.dihedrals_index_offsets)) - if len(self.settings.dihedrals_type) > 0: - outfile.write("\n" - "\n" - "write(\"Data Dihedrals\") {\n") - for i in range(0, self.N): - for b in range(0, len(self.settings.dihedrals_type)): - I = i + self.settings.dihedrals_index_offsets[b][0] - J = i + self.settings.dihedrals_index_offsets[b][1] - K = i + self.settings.dihedrals_index_offsets[b][2] - L = i + self.settings.dihedrals_index_offsets[b][3] - I = WrapPeriodic.Wrap(I, self.N) - J = WrapPeriodic.Wrap(J, self.N) - K = WrapPeriodic.Wrap(K, self.N) - L = WrapPeriodic.Wrap(L, self.N) - if WrapPeriodic.bounds_err: - WrapPeriodic.bounds_err = False - if not self.settings.connect_ends: - continue - outfile.write(" $dihedral:" + - self.settings.dihedrals_name[b] + str(i + 1)) - if len(self.settings.dihedrals_type) > 1: - outfile.write("_" + str(b + 1)) - outfile.write(" @dihedral:" + self.settings.dihedrals_type[b] + - " $atom:mon[" + str(I) + "]/" + self.settings.dihedrals_atoms[b][0] + - " $atom:mon[" + str(J) + "]/" + self.settings.dihedrals_atoms[b][1] + - " $atom:mon[" + str(K) + "]/" + self.settings.dihedrals_atoms[b][2] + - " $atom:mon[" + str(L) + "]/" + self.settings.dihedrals_atoms[b][3] + - "\n") - if len(self.settings.dihedrals_type) > 0: - outfile.write("} # write(\"Data Dihedrals\") {...\n\n\n") - - assert(len(self.settings.impropers_name) == - len(self.settings.impropers_type) == - len(self.settings.impropers_atoms) == - len(self.settings.impropers_index_offsets)) - if len(self.settings.impropers_type) > 0: - outfile.write("\n" - "\n" - "write(\"Data Impropers\") {\n") - for i in range(0, self.N): - for b in range(0, len(self.settings.impropers_type)): - I = i + self.settings.impropers_index_offsets[b][0] - J = i + self.settings.impropers_index_offsets[b][1] - K = i + self.settings.impropers_index_offsets[b][2] - L = i + self.settings.impropers_index_offsets[b][3] - I = WrapPeriodic.Wrap(I, self.N) - J = WrapPeriodic.Wrap(J, self.N) - K = WrapPeriodic.Wrap(K, self.N) - L = WrapPeriodic.Wrap(L, self.N) - if WrapPeriodic.bounds_err: - WrapPeriodic.bounds_err = False - if not self.settings.connect_ends: - continue - outfile.write(" $improper:" + - self.settings.impropers_name[b] + str(i + 1)) - if len(self.settings.impropers_type) > 1: - outfile.write("_" + str(b + 1)) - outfile.write(" @improper:" + self.settings.impropers_type[b] + - " $atom:mon[" + str(I) + "]/" + self.settings.impropers_atoms[b][0] + - " $atom:mon[" + str(J) + "]/" + self.settings.impropers_atoms[b][1] + - " $atom:mon[" + str(K) + "]/" + self.settings.impropers_atoms[b][2] + - " $atom:mon[" + str(L) + "]/" + self.settings.impropers_atoms[b][3] + - "\n") - if len(self.settings.impropers_type) > 0: - outfile.write("} # write(\"Data Impropers\") {...\n\n\n") - - if name_polymer != '': - outfile.write("} # " + name_polymer + "\n\n\n\n") - - def CalcBoxBoundaries(self, coords): - N = len(coords) - for i in range(0, N): - for d in range(0, 3): - if not self.box_bounds_min: - assert(not self.box_bounds_max) - self.box_bounds_min = [xd for xd in coords[i]] - self.box_bounds_max = [xd for xd in coords[i]] - else: - if coords[i][d] > self.box_bounds_max[d]: - self.box_bounds_max[d] = coords[i][d] - if coords[i][d] < self.box_bounds_min[d]: - self.box_bounds_min[d] = coords[i][d] - - def WriteBoxBoundaries(self, outfile): - for d in range(0, 3): - self.box_bounds_min[d] -= self.settings.box_padding[d] - self.box_bounds_max[d] += self.settings.box_padding[d] - outfile.write("\n# ---------------- simulation box -----------------\n" - - "# Now define a box big enough to hold a polymer with this (initial) shape\n" - "\n\n" - "write_once(\"Data Boundary\") {\n" - + str(self.box_bounds_min[0]) + " " + - str(self.box_bounds_max[0]) + " xlo xhi\n" - + str(self.box_bounds_min[1]) + " " + - str(self.box_bounds_max[1]) + " ylo yhi\n" - + str(self.box_bounds_min[2]) + " " + - str(self.box_bounds_max[2]) + " zlo zhi\n" - "}\n\n\n") - - -def main(): - try: - g_program_name = __file__.split('/')[-1] - g_version_str = '0.0.5' - g_date_str = '2017-4-14' - sys.stderr.write(g_program_name + ' v' + - g_version_str + ' ' + g_date_str + '\n') - argv = [arg for arg in sys.argv] - infile = sys.stdin - outfile = sys.stdout - genpoly = GenPoly() - genpoly.ParseArgs(argv) - # Any remain arguments? - if len(argv) > 1: - raise InputError('Error(' + g_program_name + '):\n' + - 'Unrecogized command line argument \"' + argv[1] + - '\"\n\n' + - g_usage_msg) - genpoly.ReadCoords(infile) - genpoly.WriteLTFile(outfile) - - except (ValueError, InputError) as err: - sys.stderr.write('\n' + str(err) + '\n') - sys.exit(-1) - - return - -if __name__ == '__main__': - main() diff --git a/tools/moltemplate/moltemplate/ltemplify.py b/tools/moltemplate/moltemplate/ltemplify.py deleted file mode 100755 index 2fa20b0d05..0000000000 --- a/tools/moltemplate/moltemplate/ltemplify.py +++ /dev/null @@ -1,3590 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -# Author: Andrew Jewett (jewett.aij at g mail) -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2012, Regents of the University of California -# All rights reserved. - -""" -ltemplify.py - -The "ltemplify.py" script can be used to convert existing LAMMPS -input script and data files into a single .lt file -(which includes both topology and force-field information - for a single molecule in your system). - -Example: - - ltemplify.py -name Mol file.in file.data > mol.lt - -This creates a template for a new type of molecule (named "Mol"), -consisting of all the atoms in the lammps files you included, -and saves this data in a single ttree file ("mol.lt"). -This file can be used with moltemplate (ttree) to -define large systems containing this molecule. - -""" - -import sys -try: - from .ttree_lex import * - from .lttree_styles import * -except (ImportError, SystemError, ValueError): - # not installed as a package - from ttree_lex import * - from lttree_styles import * - -g_program_name = __file__.split('/')[-1] # = 'ltemplify.py' -g_version_str = '0.54.0' -g_date_str = '2017-10-03' - -def Intify(s): - if s.isdigit(): - return int(s) - elif s[0:2] == 'id': - return int(s[2:]) - elif s[0:4] == 'type': - return int(s[4:]) - else: - return s - - -def IsNumber(s): - try: - float(s) - return True - except (ValueError, TypeError): - return False - - -def StringToInterval(sel_str, slice_delim='*'): - # Split a string into 1-3 tokens using the slice_delim and convert to int. - # What a mess. I should rewrite this function - - i_slice = sel_str.find(slice_delim) - - if i_slice == -1: - a = sel_str - b = sel_str - c = '' - else: - a = sel_str[:i_slice] - bc = sel_str[i_slice + len(slice_delim):] - b = '' - c = '' - i_slice = bc.find(slice_delim) - if i_slice == -1: - b = bc - c = '' - else: - b = bc[:i_slice] - c = bc[i_slice + len(slice_delim):] - - if a == '': - a = None - elif a.isdigit(): - a = int(a) - else: - raise InputError('Error: invalid selection string \"' + - sel_str + '\"\n') - - if b == '': - b = None - elif b.isdigit(): - b = int(b) - else: - raise InputError('Error: invalid selection string \"' + - sel_str + '\"\n') - - if c == '': - c = None - elif c.isdigit(): - c = int(c) - else: - raise InputError('Error: invalid selection string \"' + - sel_str + '\"\n') - - if c == None: - return (a, b) - else: - return (a, b, c) - - -# Selections are simply lists of 2-tuples (pairs) - -def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '): - """ - This function converts a string such as "1*4 6 9*12 50*70*10" into - a list of tuples, for example: [(1,4), (6,6), (9,12), (50,50), (60,60), (70,70)] - In general, the of intervals has the form: - [(a1,b1), (a2,b2), (a3,b3), ... ] - - An atom is considered to belong to this selection - if it happens to lie within the closed interval [a,b] - for any pair of a,b values in the list of intervals. - If for a given pair a,b, either a or b is "None", then that a or b - value is not used to disqualify membership in the interval. - (Similar to -infinity or +infinity. In other words if a is set to None, - then to belong to the interval it is enough to be less than b.) - - """ - selection_list = [] - # tokens = sel_str.split(or_delim) <-- Not what we want when - # len(or_delim)>1 - tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False) - for token in tokens: - token = token.strip() - interval = StringToInterval(token, slice_delim) - - if len(interval) == 2: - # Normally, "interval" should be a tuple containing 2 entries - selection_list.append(interval) - else: - assert(len(interval) == 3) - # Handle 1000:2000:10 notation - # (corresponding to 1000, 1010, 1020, 1030, ..., 1990, 2000) - a = interval[0] - b = interval[1] - incr = interval[2] - i = a - while i <= b: - selection_list.append((i, i)) - i += incr - - return selection_list - - -def IntervalListToMinMax(interval_list): - min_a = None - max_b = None - for (a, b) in interval_list: - if ((not (type(a) is int)) or (not (type(b) is int))): - return None, None # only integer min/max makes sense. otherwise skip - - if (min_a == None) or (a < min_a): - min_a = a - if (max_b == None) or (b > max_b): - max_b = b - return min_a, max_b - - -def MergeIntervals(interval_list): - """ - A crude simple function that merges consecutive intervals in the list - whenever they overlap. (This function does not bother to compare - non-consecutive entries in the interval_list.) - - """ - i = 1 - while i < len(interval_list): - if ((interval_list[i - 1][1] == None) or - (interval_list[i - 1][1] + 1 >= interval_list[i][0])): - interval_list[i - 1] = (interval_list[i - 1] - [0], interval_list[i][1]) - del interval_list[i] - else: - i += 1 - - -def BelongsToSel(i, sel): - if (i == None) or (sel == None) or (len(sel) == 0): - # If the user has not specified a selection for this category, - # then by default all objects are accepted - return True - - elif (type(i) is str): - if i.isdigit(): - i = int(i) - else: - return True - - belongs = False - for interval in sel: - assert(len(interval) == 2) - if interval[0]: - if i >= interval[0]: - if (interval[1] == None) or (i <= interval[1]): - belongs = True - break - elif interval[1]: - if i <= interval[1]: - belongs = True - break - else: - # In that case, the user entered something like "*" - # which covers all possible numbers - belongs = True - break - - return belongs - - -def main(): - try: - sys.stderr.write(g_program_name + ' v' + - g_version_str + ' ' + g_date_str + '\n') - - non_empty_output = False - no_warnings = True - indent = 2 - cindent = 0 - atomid_selection = [] - atomtype_selection = [] - molid_selection = [] - mol_name = '' - - min_sel_atomid = None - min_sel_atomtype = None - min_sel_bondid = None - min_sel_bondtype = None - min_sel_angleid = None - min_sel_angletype = None - min_sel_dihedralid = None - min_sel_dihedraltype = None - min_sel_improperid = None - min_sel_impropertype = None - - max_sel_atomid = None - max_sel_atomtype = None - max_sel_bondid = None - max_sel_bondtype = None - max_sel_angleid = None - max_sel_angletype = None - max_sel_dihedralid = None - max_sel_dihedraltype = None - max_sel_improperid = None - max_sel_impropertype = None - - needed_atomids = set([]) - needed_atomtypes = set([]) - needed_molids = set([]) - needed_bondids = set([]) - needed_bondtypes = set([]) - needed_angleids = set([]) - needed_angletypes = set([]) - needed_dihedralids = set([]) - needed_dihedraltypes = set([]) - needed_improperids = set([]) - needed_impropertypes = set([]) - - min_needed_atomtype = None - max_needed_atomtype = None - min_needed_bondtype = None - max_needed_bondtype = None - min_needed_angletype = None - max_needed_angletype = None - min_needed_dihedraltype = None - max_needed_dihedraltype = None - min_needed_impropertype = None - max_needed_impropertype = None - - min_needed_atomid = None - max_needed_atomid = None - min_needed_molid = None - max_needed_molid = None - min_needed_bondid = None - max_needed_bondid = None - min_needed_angleid = None - max_needed_angleid = None - min_needed_dihedralid = None - max_needed_dihedralid = None - min_needed_improperid = None - max_needed_improperid = None - - # To process the selections, we need to know the atom style: - atom_style_undefined = True - - i_atomid = None - i_atomtype = None - i_molid = None - i_x = None - i_y = None - i_z = None - - l_in_init = [] - l_in_settings = [] - l_in_masses = [] - l_in_pair_coeffs = [] - l_in_bond_coeffs = [] - l_in_angle_coeffs = [] - l_in_dihedral_coeffs = [] - l_in_improper_coeffs = [] - l_in_group = [] - l_in_set = [] - l_in_set_static = [] - l_in_fix_shake = [] - l_in_fix_rigid = [] - l_in_fix_poems = [] - l_in_fix_qeq = [] - l_in_fix_qmmm = [] - l_data_masses = [] - l_data_bond_coeffs = [] - l_data_angle_coeffs = [] - l_data_dihedral_coeffs = [] - l_data_improper_coeffs = [] - l_data_pair_coeffs = [] - l_data_pairij_coeffs = [] - l_data_atoms = [] - l_data_velocities = [] - l_data_bonds = [] - l_data_angles = [] - l_data_dihedrals = [] - l_data_impropers = [] - - # class2 force fields - # l_in_bondbond_coeffs = [] <--not needed, included in l_in_angle_coeff - # l_in_bondangle_coeffs = [] <--not needed, included in l_in_angle_coeff - # l_in_middlebondtorsion_coeffs = [] not needed, included in l_in_dihedral_coeff - # l_in_endbondtorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff - # l_in_angletorsion_coeffs = [] <--not needed, included in l_in_dihedral_coeff - # l_in_angleangletorsion_coeffs = [] not needed, included in l_in_dihedral_coeff - # l_in_bondbond13_coeffs = [] <--not needed, included in l_in_dihedral_coeff - # l_in_angleangle_coeffs = [] <--not needed, included in - # l_in_improper_coeff - l_data_bondbond_coeffs = [] - l_data_bondangle_coeffs = [] - l_data_middlebondtorsion_coeffs = [] - l_data_endbondtorsion_coeffs = [] - l_data_angletorsion_coeffs = [] - l_data_angleangletorsion_coeffs = [] - l_data_bondbond13_coeffs = [] - l_data_angleangle_coeffs = [] - - # non-point-like particles: - l_data_ellipsoids = [] - l_data_lines = [] - l_data_triangles = [] - - # automatic generation of bonded interactions by type: - l_data_angles_by_type = [] - l_data_dihedrals_by_type = [] - l_data_impropers_by_type = [] - - atoms_already_read = False - some_pair_coeffs_read = False - complained_atom_style_mismatch = False - infer_types_from_comments = False - remove_coeffs_from_data_file = True - - argv = [arg for arg in sys.argv] - - i = 1 - - while i < len(argv): - - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - - if argv[i] == '-columns': - if i + 1 >= len(argv): - raise InputError('Error: the \"' + argv[i] + '\" argument should be followed by a quoted\n' - ' string which contains a space-delimited list of the names of\n' - ' of columns in the \"Atoms\" section of the LAMMPS data file.\n' - ' If the list contains the symbols:\n' - ' \"atom-ID\" or \"atomid\", they are interpreted\n' - ' as unique atom ID numbers, and columns named\n' - ' \"atom-type\" or \"atomtype\" are interpreted\n' - ' as atom types. Finally, columns named\n' - ' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n' - ' are interpreted as unique molecule id numbers.\n' - 'Example:\n' - ' ' + - argv[ - i] + ' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n' - ' defines a custom atom_style containing the properties\n' - ' atom-ID atom-type q polarizability molecule-ID x y z\n' - ' Make sure you enclose the entire list in quotes.\n') - column_names = argv[i + 1].strip('\"\'').strip().split() - del argv[i:i + 2] - - elif (argv[i] == '-ignore-comments'): - infer_types_from_comments = False - del argv[i:i + 1] - - elif (argv[i] == '-infer-comments'): - infer_types_from_comments = True - del argv[i:i + 1] - - elif ((argv[i] == '-name') or - (argv[i] == '-molname') or - (argv[i] == '-molecule-name') or - (argv[i] == '-molecule_name')): - if i + 1 >= len(argv): - raise InputError( - 'Error: ' + argv[i] + ' flag should be followed by a a molecule type name.\n') - cindent = 2 - indent += cindent - mol_name = argv[i + 1] - del argv[i:i + 2] - - elif ((argv[i].lower() == '-atomstyle') or - (argv[i].lower() == '-atom_style') or - (argv[i].lower() == '-atom-style')): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by a an atom_style name.\n' - ' (or single quoted string which includes a space-separated\n' - ' list of column names).\n') - atom_style_undefined = False - column_names = AtomStyle2ColNames(argv[i + 1]) - if (argv[i + 1].strip().split()[0] in g_style_map): - l_in_init.append((' ' * indent) + - 'atom_style ' + argv[i + 1] + '\n') - sys.stderr.write('\n \"Atoms\" column format:\n') - sys.stderr.write(' ' + (' '.join(column_names)) + '\n') - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid( - column_names) - # Which columns contain the coordinates? - ii_coords = ColNames2Coords(column_names) - assert(len(ii_coords) == 1) - i_x = ii_coords[0][0] - i_y = ii_coords[0][1] - i_z = ii_coords[0][2] - - if i_molid: - sys.stderr.write(' (i_atomid=' + str(i_atomid + 1) + ', i_atomtype=' + str( - i_atomtype + 1) + ', i_molid=' + str(i_molid + 1) + ')\n\n') - else: - sys.stderr.write(' (i_atomid=' + str(i_atomid + 1) + - ', i_atomtype=' + str(i_atomtype + 1) + ')\n') - del argv[i:i + 2] - - elif ((argv[i].lower() == '-id') or - #(argv[i].lower() == '-a') or - #(argv[i].lower() == '-atoms') or - (argv[i].lower() == '-atomid') or - #(argv[i].lower() == '-atomids') or - (argv[i].lower() == '-atom-id') - #(argv[i].lower() == '-atom-ids') or - #(argv[i].lower() == '-$atom') or - #(argv[i].lower() == '-$atoms') - ): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by a list of integers\n' - ' (or strings). These identify the group of atoms you want to\n' - ' to include in the template you are creating.\n') - atomid_selection += LammpsSelectToIntervals(argv[i + 1]) - min_sel_atomid, max_sel_atomid = IntervalListToMinMax( - atomid_selection) - del argv[i:i + 2] - elif ((argv[i].lower() == '-datacoeffs') or - (argv[i].lower() == '-datacoeff') or - (argv[i].lower() == '-Coeff') or - (argv[i].lower() == '-Coeffs')): - remove_coeffs_from_data_file = False - del argv[i:i + 1] - elif ((argv[i].lower() == '-type') or - #(argv[i].lower() == '-t') or - (argv[i].lower() == '-atomtype') or - (argv[i].lower() == '-atom-type') - #(argv[i].lower() == '-atomtypes') or - #(argv[i].lower() == '-atom-types') or - #(argv[i].lower() == '-@atom') or - #(argv[i].lower() == '-@atoms') or - #(argv[i].lower() == '-@atomtype') or - #(argv[i].lower() == '-@atomtypes') - ): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by a list of integers.\n' - ' (or strings). These identify the group of atom types you want to\n' - ' to include in the template you are creating.\n') - atomtype_selection += LammpsSelectToIntervals(argv[i + 1]) - min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax( - atomtype_selection) - del argv[i:i + 2] - elif ((argv[i].lower() == '-mol') or - #(argv[i].lower() == '-m') or - (argv[i].lower() == '-molid') or - #(argv[i].lower() == '-molids') or - (argv[i].lower() == '-mol-id') or - #(argv[i].lower() == '-mol-ids') or - #(argv[i].lower() == '-molecule') or - (argv[i].lower() == '-moleculeid') or - (argv[i].lower() == '-molecule-id') - #(argv[i].lower() == '-molecules') or - #(argv[i].lower() == '-molecule-ids') or - #(argv[i].lower() == '-$mol') or - #(argv[i].lower() == '-$molecule') - ): - if i + 1 >= len(argv): - sys.stderr.write('Error: ' + argv[i] + ' flag should be followed by a list of integers.\n' - ' (or strings). These identify the group of molecules you want to\n' - ' include in the template you are creating.\n') - molid_selection += LammpsSelectToIntervals(argv[i + 1]) - del argv[i:i + 2] - else: - i += 1 - - # We might need to parse the simulation boundary-box. - # If so, use these variables. (None means uninitialized.) - boundary_xlo = None - boundary_xhi = None - boundary_ylo = None - boundary_yhi = None - boundary_zlo = None - boundary_zhi = None - boundary_xy = None - boundary_yz = None - boundary_xz = None - - # atom type names - atomtypes_name2int = {} - atomtypes_int2name = {} - # atomids_name2int = {} not needed - atomids_int2name = {} - atomids_by_type = {} - - if atom_style_undefined: - # The default atom_style is "full" - column_names = AtomStyle2ColNames('full') - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) - # Which columns contain the coordinates? - ii_coords = ColNames2Coords(column_names) - assert(len(ii_coords) == 1) - i_x = ii_coords[0][0] - i_y = ii_coords[0][1] - i_z = ii_coords[0][2] - - #--------------------------------------------------------- - #-- The remaining arguments are files that the user wants - #-- us to read and convert. It is typical to have - #-- multiple input files, because LAMMPS users often - #-- store their force field parameters in either the LAMMPS - #-- data files and input script files, or both. - #-- We want to search all of the LAMMPS input files in - #-- order to make sure we extracted all the force field - #-- parameters (coeff commands). - #--------------------------------------------------------- - - for i_arg in range(1, len(argv)): - fname = argv[i_arg] - try: - lammps_file = open(fname, 'r') - except IOError: - raise InputError('Error: unrecognized argument (\"' + fname + '\"),\n' - ' OR unable to open file:\n' - '\n' - ' \"' + fname + '\"\n' - ' for reading.\n' - '\n' - ' (If you were not trying to open a file with this name,\n' - ' then there is a problem in your argument list.)\n') - - sys.stderr.write('reading file \"' + fname + '\"\n') - - atomid2type = {} - atomid2mol = {} - data_file_header_names = set(['LAMMPS Description', - 'Atoms', 'Masses', 'Velocities', 'Bonds', - 'Angles', 'Dihedrals', 'Impropers', - 'Pair Coeffs', - 'Bond Coeffs', 'Angle Coeffs', - 'Dihedral Coeffs', 'Improper Coeffs', - # class2 force fields: - 'BondBond Coeffs', 'BondAngle Coeffs', - 'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs', - 'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs', - 'BondBond13 Coeffs', - 'AngleAngle Coeffs', - # non-point-like particles: - 'Ellipsoids', 'Triangles', 'Lines', - # specifying bonded interactions by type: - 'Angles By Type', 'Dihedrals By Type', 'Impropers By Type' - ]) - - lex = LineLex(lammps_file, fname) - lex.source_triggers = set(['include', 'import']) - # set up lex to accept most characters in file names: - lex.wordterminators = '(){}' + lex.whitespace - # set up lex to understand the "include" statement: - lex.source = 'include' - lex.escape = '\\' - - while lex: - infile = lex.infile - lineno = lex.lineno - line = lex.ReadLine() - if (lex.infile != infile): - infile = lex.infile - lineno = lex.lineno - - #sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n') - - if line == '': - break - - tokens = line.strip().split() - if (len(tokens) > 0): - if ((tokens[0] == 'atom_style') and - atom_style_undefined): - - sys.stderr.write( - ' Atom Style found. Processing: \"' + line.strip() + '\"\n') - if atoms_already_read: - raise InputError('Error: The file containing the \"atom_style\" command must\n' - ' come before the data file in the argument list.\n' - ' (The templify program needs to know the atom style before reading\n' - ' the data file. Either change the order of arguments so that the\n' - ' LAMMPS input script file is processed before the data file, or use\n' - ' the \"-atom_style\" command line argument to specify the atom_style.)\n') - - column_names = AtomStyle2ColNames(line.split()[1]) - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid( - column_names) - # Which columns contain the coordinates? - ii_coords = ColNames2Coords(column_names) - assert(len(ii_coords) == 1) - i_x = ii_coords[0][0] - i_y = ii_coords[0][1] - i_z = ii_coords[0][2] - - sys.stderr.write('\n \"Atoms\" column format:\n') - sys.stderr.write(' ' + (' '.join(column_names)) + '\n') - if i_molid: - sys.stderr.write(' (i_atomid=' + str(i_atomid + 1) + ', i_atomtype=' + str( - i_atomtype + 1) + ', i_molid=' + str(i_molid + 1) + ')\n\n') - else: - sys.stderr.write( - ' (i_atomid=' + str(i_atomid + 1) + ', i_atomtype=' + str(i_atomtype + 1) + ')\n\n') - l_in_init.append((' ' * indent) + line.lstrip()) - - elif (tokens[0] in set(['units', - 'angle_style', - 'bond_style', - 'dihedral_style', - 'improper_style', - 'min_style', - 'pair_style', - 'pair_modify', - 'special_bonds', - 'kspace_style', - 'kspace_modify'])): - l_in_init.append((' ' * indent) + line.lstrip()) - - # if (line.strip() == 'LAMMPS Description'): - # sys.stderr.write(' reading \"'+line.strip()+'\"\n') - # # skip over this section - # while lex: - # line = lex.ReadLine() - # if line.strip() in data_file_header_names: - # lex.push_raw_text(line) # <- Save line for later - # break - - elif (line.strip() == 'Atoms'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - atoms_already_read = True - - # Before attempting to read atomic coordinates, first find - # the lattice vectors of the simulation's boundary box: - # Why do we care about the Simulation Boundary? - # Some LAMMPS data files store atomic coordinates in a - # complex format with 6 numbers, 3 floats, and 3 integers. - # The 3 floats are x,y,z coordinates. Any additional numbers - # following these are integers which tell LAMMPS which cell - # the particle belongs to, (in case it has wandered out of - # the original periodic boundary box). In order to find - # the true location of the particle, we need to offset that - # particle's position with the unit-cell lattice vectors: - # avec, bvec, cvec (or multiples thereof) - # avec, bvec, cvec are the axis of the parallelepiped which - # define the simulation's boundary. They are described here: - # http://lammps.sandia.gov/doc/Section_howto.html#howto-12 - if ((boundary_xlo == None) or (boundary_xhi == None) or - (boundary_ylo == None) or (boundary_yhi == None) or - (boundary_zlo == None) or (boundary_zhi == None)): - - raise InputError('Error: Either DATA file lacks a boundary-box header, or it is in the wrong\n' - ' place. At the beginning of the file, you need to specify the box size:\n' - ' xlo xhi ylo yhi zlo zhi (and xy xz yz if triclinic)\n' - ' These numbers should appear BEFORE the other sections in the data file\n' - ' (such as the \"Atoms\", \"Masses\", \"Bonds\", \"Pair Coeffs\" sections)\n' - '\n' - ' Use this format (example):\n' - ' -100.0 100.0 xhi xlo\n' - ' 0.0 200.0 yhi ylo\n' - ' -25.0 50.0 zhi zlo\n' - '\n' - 'For details, see http://lammps.sandia.gov/doc/read_data.html\n' - '\n' - ' (NOTE: If the atom coordinates are NOT followed by integers, then\n' - ' these numbers are all ignored, however you must still specify\n' - ' xlo, xhi, ylo, yhi, zlo, zhi. You can set them all to 0.0.)\n') - - if not (boundary_xy and boundary_yz and boundary_xz): - # Then use a simple rectangular boundary box: - avec = (boundary_xhi - boundary_xlo, 0.0, 0.0) - bvec = (0.0, boundary_yhi - boundary_ylo, 0.0) - cvec = (0.0, 0.0, boundary_zhi - boundary_zlo) - else: - # Triclinic geometry in LAMMPS is explained here: - # http://lammps.sandia.gov/doc/Section_howto.html#howto-12 - # http://lammps.sandia.gov/doc/read_data.html - avec = (boundary_xhi - boundary_xlo, 0.0, 0.0) - bvec = (boundary_xy, boundary_yhi - boundary_ylo, 0.0) - cvec = (boundary_xz, boundary_yz, - boundary_zhi - boundary_zlo) - - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if ((len(tokens) <= i_atomid) or - (len(tokens) <= i_atomtype) or - ((i_molid != None) and - (len(tokens) <= i_molid))): - raise InputError('Error: The number of columns in the \"Atoms\" section does\n' - ' not match the atom_style (see column name list above).\n') - elif ((len(tokens) != len(column_names)) and - (len(tokens) != len(column_names) + 3) and - (not complained_atom_style_mismatch)): - complained_atom_style_mismatch = True - sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n' - ' not match the atom_style (see column name list above).\n') - # this is not a very serious warning. - # no_warnings = False <--no need. commenting - # out - - atomid = Intify(tokens[i_atomid]) - atomtype = Intify(tokens[i_atomtype]) - - molid = None - if i_molid: - molid = Intify(tokens[i_molid]) - - atomid2type[atomid] = atomtype - if i_molid: - atomid2mol[atomid] = molid - - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - - tokens[i_atomid] = '$atom:id' + \ - tokens[i_atomid] - #tokens[i_atomid] = '$atom:'+atomids_int2name[atomid] - # fill atomtype_int2str[] with a default name (change later): - #tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype] - atomtype_name = 'type' + tokens[i_atomtype] - atomtypes_int2name[atomtype] = atomtype_name - tokens[i_atomtype] = '@atom:' + atomtype_name - - # Interpreting unit-cell counters - # If present, then unit-cell "flags" must be - # added to the x,y,z coordinates. - # - # For more details on unit-cell "flags", see: - # http://lammps.sandia.gov/doc/read_data.html - # "In the data file, atom lines (all lines or - # none of them) can optionally list 3 trailing - # integer values (nx,ny,nz), which are used to - # initialize the atom’s image flags. - # If nx,ny,nz values are not listed in the - # data file, LAMMPS initializes them to 0. - # Note that the image flags are immediately - # updated if an atom’s coordinates need to - # wrapped back into the simulation box." - - if (len(tokens) == len(column_names) + 3): - nx = int(tokens[-3]) - ny = int(tokens[-2]) - nz = int(tokens[-1]) - x = float( - tokens[i_x]) + nx * avec[0] + ny * bvec[0] + nz * cvec[0] - y = float( - tokens[i_y]) + nx * avec[1] + ny * bvec[1] + nz * cvec[1] - z = float( - tokens[i_z]) + nx * avec[2] + ny * bvec[2] + nz * cvec[2] - tokens[i_x] = str(x) - tokens[i_y] = str(y) - tokens[i_z] = str(z) - # Now get rid of them: - del tokens[-3:] - - # I can't use atomids_int2name or atomtypes_int2name yet - # because they probably have not been defined yet. - # (Instead assign these names in a later pass.) - - if i_molid: - tokens[i_molid] = '$mol:id' + \ - tokens[i_molid] - l_data_atoms.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - needed_atomids.add(atomid) - - needed_atomtypes.add(atomtype) - # Not all atom_styles have molids. - # Check for this before adding. - if molid != None: - needed_molids.add(molid) - - for atomtype in needed_atomtypes: - assert(type(atomtype) is int) - if ((min_needed_atomtype == None) or - (min_needed_atomtype > atomtype)): - min_needed_atomtype = atomtype - if ((max_needed_atomtype == None) or - (max_needed_atomtype < atomtype)): - max_needed_atomtype = atomtype - - for atomid in needed_atomids: - assert(type(atomid) is int) - if ((min_needed_atomid == None) or - (min_needed_atomid > atomid)): - min_needed_atomid = atomid - if ((max_needed_atomid == None) or - (max_needed_atomid < atomid)): - max_needed_atomid = atomid - for molid in needed_molids: - assert(type(molid) is int) - if ((min_needed_molid == None) or - (min_needed_molid > molid)): - min_needed_molid = molid - if ((max_needed_molid == None) or - (max_needed_molid < molid)): - max_needed_molid = molid - - elif (line.strip() == 'Masses'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - # Read the next line of text but don't skip comments - comment_char_backup = lex.commenters - lex.commenters = '' - line = lex.ReadLine() - lex.commenters = comment_char_backup - - comment_text = '' - ic = line.find('#') - if ic != -1: - line = line[:ic] - comment_text = line[ic + 1:].strip() - line = line.rstrip() - - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - - tokens = line.strip().split() - if len(tokens) > 0: - atomtype = Intify(tokens[0]) - atomtype_name = str(atomtype) - - if comment_text != '': - comment_tokens = comment_text.split() - # Assume the first word after the # is the atom - # type name - atomtype_name = comment_tokens[0] - - if BelongsToSel(atomtype, atomtype_selection): - #tokens[0] = '@atom:type'+tokens[0] - l_data_masses.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - # infer atom type names from comment strings? - if infer_types_from_comments: - if atomtype_name in atomtypes_name2int: - raise InputError('Error: duplicate atom type names in mass section: \"' + atomtype_name + '\"\n' - ' (By default ' + g_program_name + - ' attempts to infer atom type names from\n' - ' comments which appear in the \"Masses\" section of your data file.)\n' - ' You can avoid this error by adding the \"-ignore-comments\" argument.\n') - atomtypes_name2int[ - atomtype_name] = atomtype - atomtypes_int2name[ - atomtype] = atomtype_name - else: - atomtypes_int2name[ - atomtype] = 'type' + str(atomtype) - - elif (line.strip() == 'Velocities'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id' + tokens[0] - #tokens[0] = '$atom:'+atomids_int2name[atomid] - # NOTE:I can't use "atomids_int2name" yet because - # they probably have not been defined yet. - # (Instead assign these names in a later pass.) - l_data_velocities.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - # non-point-like-particles: - elif (line.strip() == 'Ellipsoids'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id' + tokens[0] - #tokens[0] = '$atom:'+atomids_int2name[atomid] - # NOTE:I can't use "atomids_int2name" yet because - # they probably have not been defined yet. - # (Instead assign these names in a later pass.) - l_data_ellipsoids.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (line.strip() == 'Lines'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id' + tokens[0] - #tokens[0] = '$atom:'+atomids_int2name[atomid] - # NOTE:I can't use "atomids_int2name" yet because - # they probably have not been defined yet. - # (Instead assign these names in a later pass.) - l_data_lines.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (line.strip() == 'Triangles'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id' + tokens[0] - #tokens[0] = '$atom:'+atomids_int2name[atomid] - # NOTE:I can't use "atomids_int2name" yet because - # they probably have not been defined yet. - # (Instead assign these names in a later pass.) - l_data_triangles.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Bonds'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 4): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical line in Bonds section:\n' - ' \"' + line.strip() + '\"\n') - #tokens[0] = '$bond:id'+tokens[0] - #tokens[1] = '@bond:type'+tokens[1] - atomids = [None, None] - atomtypes = [None, None] - molids = [None, None] - in_selections = True - some_in_selection = False - for n in range(0, 2): - atomids[n] = Intify(tokens[2 + n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_bonds.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif some_in_selection: - sys.stderr.write( - 'WARNING: SELECTION BREAKS BONDS\n') - sys.stderr.write( - ' (between atom ids: ') - - for n in range(0, 2): - sys.stderr.write(str(atomids[n]) + ' ') - sys.stderr.write(')\n' - ' The atoms you selected are bonded\n' - ' to other atoms you didn\'t select.\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - elif (line.strip() == 'Angles'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line == '': - break - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 5): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical line in Angles section:\n' - ' \"' + line.strip() + '\"\n') - #tokens[0] = '$angle:id'+tokens[0] - #tokens[1] = '@angle:type'+tokens[1] - atomids = [None, None, None] - atomtypes = [None, None, None] - molids = [None, None, None] - in_selections = True - some_in_selection = False - for n in range(0, 3): - atomids[n] = Intify(tokens[2 + n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_angles.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif some_in_selection: - sys.stderr.write( - 'WARNING: SELECTION BREAKS ANGLES\n') - sys.stderr.write( - ' (between atom ids: ') - for n in range(0, 3): - sys.stderr.write(str(atomids[n]) + ' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 3-body \"Angle\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - elif (line.strip() == 'Dihedrals'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 6): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical line in Dihedrals section:\n' - ' \"' + line.strip() + '\"\n') - #tokens[0] = '$dihedral:id'+tokens[0] - #tokens[1] = '@dihedral:type'+tokens[1] - atomids = [None, None, None, None] - atomtypes = [None, None, None, None] - molids = [None, None, None, None] - in_selections = True - some_in_selection = False - for n in range(0, 4): - atomids[n] = Intify(tokens[2 + n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_dihedrals.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif some_in_selection: - sys.stderr.write( - 'WARNING: SELECTION BREAKS DIHEDRALS\n') - sys.stderr.write( - ' (between atom ids: ') - for n in range(0, 4): - sys.stderr.write(str(atomids[n]) + ' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 4-body \"Dihedral\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - elif (line.strip() == 'Impropers'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 6): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical line in Impropers section:\n' - ' \"' + line.strip() + '\"\n') - #tokens[0] = '$improper:id'+tokens[0] - #tokens[1] = '@improper:type'+tokens[1] - atomids = [None, None, None, None] - atomtypes = [None, None, None, None] - molids = [None, None, None, None] - in_selections = True - some_in_selection = False - for n in range(0, 4): - atomids[n] = Intify(tokens[2 + n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - #tokens[2+n] = '$atom:'+atomids_int2name[atomids[n]] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_impropers.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif some_in_selection: - sys.stderr.write( - 'WARNING: SELECTION BREAKS IMPROPERS\n') - sys.stderr.write( - ' (between atom ids: ') - for n in range(0, 4): - sys.stderr.write(str(atomids[n]) + ' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 4-body \"Improper\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - elif (line.strip() == 'Bond Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@bond:type'+tokens[0] - l_data_bond_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Angle Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@angle:type'+tokens[0] - l_data_angle_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Dihedral Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_dihedral_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Improper Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@improper:type'+tokens[0] - l_data_improper_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Pair Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - some_pair_coeffs_read = True - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 2): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical line in Pair Coeffs section:\n' - ' \"' + line.strip() + '\"\n') - atomtype_i_str = tokens[0] - if '*' in atomtype_i_str: - raise InputError('PROBLEM near or before ' + ErrorLeader(infile, lineno) + '\n' - ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' - ' character in the \"Pair Coeffs\" section.\n') - else: - i = int(atomtype_i_str) - if ((not i) or - BelongsToSel(i, atomtype_selection)): - i_str = '@atom:type' + str(i) - tokens[0] = i_str - l_data_pair_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'PairIJ Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - some_pair_coeffs_read = True - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 2): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical line in Pair Coeffs section:\n' - ' \"' + line.strip() + '\"\n') - atomtype_i_str = tokens[0] - atomtype_j_str = tokens[1] - if (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): - raise InputError('PROBLEM near or before ' + ErrorLeader(infile, lineno) + '\n' - ' As of 2017-10, moltemplate forbids use of the "\*\" wildcard\n' - ' character in the \"PairIJ Coeffs\" section.\n') - else: - i = int(atomtype_i_str) - j = int(atomtype_j_str) - if (((not i) or BelongsToSel(i, atomtype_selection)) and - ((not j) or BelongsToSel(j, atomtype_selection))): - i_str = '@atom:type' + str(i) - j_str = '@atom:type' + str(j) - tokens[0] = i_str - tokens[1] = j_str - l_data_pair_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (tokens[0] == 'pair_coeff'): - some_pair_coeffs_read = True - if (len(tokens) < 3): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical pair_coeff command:\n' - ' \"' + line.strip() + '\"\n') - l_in_pair_coeffs.append(' ' * indent + line.strip()) - - elif (tokens[0] == 'mass'): - some_pair_coeffs_read = True - if (len(tokens) < 3): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical \"mass\" command:\n' - ' \"' + line.strip() + '\"\n') - l_in_masses.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (tokens[0] == 'bond_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical bond_coeff command:\n' - ' \"' + line.strip() + '\"\n') - #tokens[1] = '@bond:type'+tokens[1] - l_in_bond_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (tokens[0] == 'angle_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical angle_coeff command:\n' - ' \"' + line.strip() + '\"\n') - #tokens[1] = '@angle:type'+tokens[1] - l_in_angle_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (tokens[0] == 'dihedral_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical dihedral_coeff command:\n' - ' \"' + line.strip() + '\"\n') - #tokens[1] = '@dihedral:type'+tokens[1] - l_in_dihedral_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (tokens[0] == 'improper_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical improper_coeff command:\n' - ' \"' + line.strip() + '\"\n') - #tokens[1] = '@improper:type'+tokens[1] - l_in_improper_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - # -- class2 force fields -- - elif (line.strip() == 'BondBond Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@angle:type'+tokens[0] - l_data_bondbond_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'BondAngle Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@angle:type'+tokens[0] - l_data_bondangle_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'MiddleBondTorsion Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_middlebondtorsion_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'EndBondTorsion Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_endbondtorsion_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'AngleTorsion Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_angletorsion_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'AngleAngleTorsion Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_angleangletorsion_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'BondBond13 Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_bondbond13_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'AngleAngle Coeffs'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@improper:type'+tokens[0] - l_data_angleangle_coeffs.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Angles By Type'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@angle:type' + tokens[0] - l_data_angles_by_type.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Dihedrals By Type'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type' + tokens[0] - l_data_dihedrals_by_type.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (line.strip() == 'Impropers By Type'): - sys.stderr.write(' reading \"' + line.strip() + '\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@improper:type' + tokens[0] - l_data_impropers_by_type.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - # Figure out the size of the simulation box boundary: - elif ((len(tokens) == 4) and - (tokens[2] == 'xlo') and - (tokens[3] == 'xhi') and - IsNumber(tokens[0]) and - IsNumber(tokens[1])): - boundary_xlo = float(tokens[0]) - boundary_xhi = float(tokens[1]) - - elif ((len(tokens) == 4) and - (tokens[2] == 'ylo') and - (tokens[3] == 'yhi') and - IsNumber(tokens[0]) and - IsNumber(tokens[1])): - boundary_ylo = float(tokens[0]) - boundary_yhi = float(tokens[1]) - - elif ((len(tokens) == 4) and - (tokens[2] == 'zlo') and - (tokens[3] == 'zhi') and - IsNumber(tokens[0]) and - IsNumber(tokens[1])): - boundary_zlo = float(tokens[0]) - boundary_zhi = float(tokens[1]) - - elif ((len(tokens) == 6) and - (tokens[3] == 'xy') and - (tokens[4] == 'xz') and - (tokens[5] == 'yz') and - IsNumber(tokens[0]) and - IsNumber(tokens[1]) and - IsNumber(tokens[2])): - boundary_xy = float(tokens[0]) - boundary_xz = float(tokens[1]) - boundary_yz = float(tokens[2]) - - elif (tokens[0] == 'group'): - if (len(tokens) < 3): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical group command:\n' - ' \"' + line.strip() + '\"\n') - l_in_group.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif (tokens[0] == 'set'): - if (len(tokens) < 3): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical set command:\n' - ' \"' + line.strip() + '\"\n') - l_in_set.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - - elif ((tokens[0] == 'fix') and (len(tokens) >= 4)): - if (tokens[3].find('rigid') == 0): - if (len(tokens) < 6): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical ' + - tokens[0] + ' ' + - tokens[3] + ' command:\n' - ' \"' + line.strip() + '\"\n') - l_in_fix_rigid.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (tokens[3].find('shake') == 0): - if (len(tokens) < 7): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical ' + - tokens[0] + ' ' + - tokens[3] + ' command:\n' - ' \"' + line.strip() + '\"\n') - l_in_fix_shake.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (tokens[3].find('poems') == 0): - if (len(tokens) < 4): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical ' + - tokens[0] + ' ' + - tokens[3] + ' command:\n' - ' \"' + line.strip() + '\"\n') - l_in_fix_poems.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (tokens[3].find('qeq') == 0): - if (len(tokens) < 8): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical ' + - tokens[0] + ' ' + - tokens[3] + ' command:\n' - ' \"' + line.strip() + '\"\n') - l_in_fix_qeq.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (tokens[3].find('qmmm') == 0): - if (len(tokens) < 8): - raise InputError('Error: near or before ' + ErrorLeader(infile, lineno) + '\n' - ' Nonsensical ' + - tokens[0] + ' ' + - tokens[3] + ' command:\n' - ' \"' + line.strip() + '\"\n') - l_in_fix_qmmm.append( - (' ' * indent) + (' '.join(tokens) + '\n')) - elif (tokens[3].find('restrain') == 0): - sys.stderr('WARNING: fix \"' + tokens[3] + '\" commands are NOT understood by ' + g_program_name + '.\n' - ' If you need restraints, add them to your final .LT file (eg. \"system.lt\"),\n' - ' (And be sure to use unique (full, long) moltemplate names for each $atom:.)\n' - ' Ignoring line \"' + line.strip() + '\"\n') - - else: - sys.stderr.write(' Ignoring line \"' + - line.strip() + '\"\n') - - sys.stderr.write('\n\n') - - sys.stderr.write(' processing \"Atoms\" section (') - - # post-processing: - - if len(l_data_masses) == 0: - infer_types_from_comments = False - - # Pass 1 through l_data_atoms: - # Now do a second-pass throught the "l_data_atoms" section, and - # finish dealing with "infer_types_from_comments". - # During this pass, peplace the atomtype names and atomid names with - # atom type names which were inferred from comments read earlier. - - sys.stderr.write('pass1') - for i in range(0, len(l_data_atoms)): - tokens = l_data_atoms[i].split() - atomid = tokens[i_atomid] - if atomid.find('$atom:') == 0: - atomid = atomid[6:] - # convert to an integer - atomid = Intify(atomid) - - if infer_types_from_comments: - atomtype = tokens[i_atomtype] - # remove the "@atom:" prefix (we will put it back later) - if atomtype.find('@atom:') == 0: - atomtype = atomtype[6:] - # convert to an integer - atomtype = Intify(atomtype) - atomtype_name = atomtypes_int2name[atomtype] - if atomtype in atomids_by_type: - l_atomids = atomids_by_type[atomtype] - prev_count = len(l_atomids) - # lookup the most recently added atom of this type: - #prev_atomid_name = l_atomids[-1] - #ic = prev_atomid_name.rfind('_') - #prev_count = int(prev_atomid_name[ic+1:]) - atomid_name = atomtype_name + '_' + str(prev_count + 1) - atomids_by_type[atomtype].append(atomid) - else: - atomids_by_type[atomtype] = [atomid] - atomid_name = atomtype_name + '_1' - atomids_int2name[atomid] = atomid_name - #atomids_name2str[atomid_name] = atomid - else: - atomids_int2name[atomid] = 'id' + str(atomid) - - sys.stderr.write(', pass2') - # Pass 2: If any atom types only appear once, simplify their atomid names. - for i in range(0, len(l_data_atoms)): - tokens = l_data_atoms[i].split() - - # remove the "@atom:" prefix (we will put it back later) - atomtype = tokens[i_atomtype] - if atomtype.find('@atom:') == 0: - atomtype = atomtype[6:] - atomtype = Intify(atomtype) - if infer_types_from_comments: - if len(atomids_by_type[atomtype]) == 1: - atomid = tokens[i_atomid] - if atomid.find('$atom:') == 0: - atomid = atomid[6:] - atomid = Intify(atomid) - atomtype_name = atomtypes_int2name[atomtype] - atomids_int2name[atomid] = atomtype_name - - sys.stderr.write(', pass3') - # Pass 3: substitute the atomid names and atom type names into l_data_atoms - for i in range(0, len(l_data_atoms)): - tokens = l_data_atoms[i].split() - atomid = tokens[i_atomid] - if atomid.find('$atom:') == 0: - atomid = atomid[6:] - # convert to an integer - atomid = Intify(atomid) - atomtype = tokens[i_atomtype] - if atomtype.find('@atom:') == 0: - atomtype = atomtype[6:] - atomtype = Intify(atomtype) - tokens = l_data_atoms[i].split() - tokens[i_atomid] = '$atom:' + atomids_int2name[atomid] - tokens[i_atomtype] = '@atom:' + atomtypes_int2name[atomtype] - l_data_atoms[i] = (' ' * indent) + (' '.join(tokens) + '\n') - sys.stderr.write(')\n') - - if len(l_data_atoms) == 0: - raise InputError('Error(' + g_program_name + '): You have no atoms in you selection!\n' - '\n' - ' Either you have chosen a set of atoms, molecules, or atom types which\n' - ' does not exist, or there is a problem with (the format of) your\n' - ' arguments. Check the documentation and examples.\n') - - # --- Now delete items that were not selected from the other lists --- - - # --- MASSES --- - - # delete masses for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_data_masses): - line = l_data_masses[i_line] - tokens = line.strip().split() - atomtype = Intify(tokens[0]) - if ((not (atomtype in needed_atomtypes)) and - (not ((len(atomtype_selection) > 0) and - BelongsToSel(atomtype, atomtype_selection)))): - del l_data_masses[i_line] - else: - atomtype_name = atomtypes_int2name[atomtype] - tokens[0] = '@atom:' + atomtype_name - l_data_masses[i_line] = (' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # --- PAIR COEFFS --- - - # delete data_pair_coeffs for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_data_pair_coeffs): - line = l_data_pair_coeffs[i_line] - tokens = line.strip().split() - assert(len(tokens) > 0) - split_colon = tokens[0].split(':') - assert(len(split_colon) == 2) - atomtype = Intify(split_colon[1]) - if ((not (atomtype in needed_atomtypes)) and - (not ((len(atomtype_selection) > 0) and - BelongsToSel(atomtype, atomtype_selection)))): - del l_data_pair_coeffs[i_line] - else: - i_line += 1 - - # delete data_pairij_coeffs for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_data_pairij_coeffs): - line = l_data_pairij_coeffs[i_line] - tokens = line.strip().split() - assert(len(tokens) > 0) - split_colon_I = tokens[0].split(':') - assert(len(split_colon_I) == 2) - atomtype_I = Intify(split_colon_I[1]) - split_colon_J = tokens[1].split(':') - assert(len(split_colon_J) == 2) - atomtype_J = Intify(split_colon_J[1]) - if (((not (atomtype_I in needed_atomtypes)) and - (not ((len(atomtype_selection) > 0) and - BelongsToSel(atomtype_I, atomtype_selection)))) - or - ((not (atomtype_J in needed_atomtypes)) and - (not ((len(atomtype_selection) > 0) and - BelongsToSel(atomtype_J, atomtype_selection))))): - del l_data_pairij_coeffs[i_line] - else: - i_line += 1 - - # delete in_pair_coeffs for atom we don't care about anymore: - i_line = 0 - while i_line < len(l_in_pair_coeffs): - line = l_in_pair_coeffs[i_line] - tokens = line.strip().split() - atomtype_i_str = tokens[1] - atomtype_j_str = tokens[2] - # if (('*' in atomtype_i_str) or - # ('*' in atomtype_j_str)): - # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' - # ' pair_coeff command contains a \"*\" character.\n' - # ' Keep in mind that using moltemplate.sh you can manually change the\n' - # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' - # ' nor to accidentally change the order of atom types in one of these\n' - # ' pair_coeff commands. For example, commands like\n' - # ' pair_coeff 10*4 20*10 0.15 3.6\n' - # ' can be generated by moltemplate.sh, however\n' - # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' - # ' pair_coeff 4*10 10*20 0.15 3.6)\n' - # ' Later on, you may want to check to make sure moltemplate.sh\n' - # ' is not doing this. (Fortunately you never have to worry unless\n' - # ' you are using the -a or -b arguments with moltemplate.sh)\n') - - if ('*' in atomtype_i_str): - atomtype_i_tokens = atomtype_i_str.split('*') - - if atomtype_i_tokens[0] == '': - if (min_sel_atomtype and - (min_sel_atomtype < min_needed_atomtype)): - i_a = min_sel_atomtype - else: - i_a = min_needed_atomtype - else: - i_a = Intify(atomtype_i_tokens[0]) - - if atomtype_i_tokens[1] == '': - if (max_sel_atomtype and - (max_sel_atomtype > max_needed_atomtype)): - i_b = max_sel_atomtype - else: - i_b = max_needed_atomtype - else: - i_b = Intify(atomtype_i_tokens[1]) - - else: - i_a = i_b = Intify(atomtype_i_str) - - assert((type(i_a) is int) and (type(i_b) is int)) - - i_a_final = None - i_b_final = None - - for i in range(i_a, i_b + 1): - if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): - i_a_final = i - break - for i in reversed(range(i_a, i_b + 1)): - if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): - i_b_final = i - break - - # if i_a_final and i_b_final: - # if i_a_final == i_b_final: - # i_str = '@atom:type'+str(i_a_final) - # tokens[1] = i_str - # else: - # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' - - if ('*' in atomtype_j_str): - atomtype_j_tokens = atomtype_j_str.split('*') - - if atomtype_j_tokens[0] == '': - if (min_sel_atomtype and - (min_sel_atomtype < min_needed_atomtype)): - j_a = min_sel_atomtype - else: - j_a = min_needed_atomtype - else: - j_a = Intify(atomtype_j_tokens[0]) - - if atomtype_j_tokens[1] == '': - if (max_sel_atomtype and - (max_sel_atomtype > max_needed_atomtype)): - j_b = max_sel_atomtype - else: - j_b = max_needed_atomtype - else: - j_b = Intify(atomtype_j_tokens[1]) - - else: - j_a = j_b = Intify(atomtype_j_str) - - j_a_final = None - j_b_final = None - for j in range(j_a, j_b + 1): - if ((j in needed_atomtypes) or (min_sel_atomtype <= j)): - j_a_final = j - break - for j in reversed(range(j_a, j_b + 1)): - if ((j in needed_atomtypes) or (max_sel_atomtype >= j)): - j_b_final = j - break - - # if j_a_final and j_b_final: - # if j_a_final == j_b_final: - # j_str = '@atom:type'+str(j_a_final) - # tokens[1] = j_str - # else: - # j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}' - - if not (i_a_final and i_b_final and j_a_final and j_b_final): - del l_in_pair_coeffs[i_line] - elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): - del l_in_pair_coeffs[i_line] - for i in range(i_a_final, i_b_final + 1): - for j in range(j_a_final, j_b_final + 1): - if j >= i: - #tokens[1] = '@atom:type'+str(i) - #tokens[2] = '@atom:type'+str(j) - tokens[1] = '@atom:' + atomtypes_int2name[i] - tokens[2] = '@atom:' + atomtypes_int2name[j] - l_in_pair_coeffs.insert(i_line, - (' ' * indent) + (' '.join(tokens) + '\n')) - i_line += 1 - else: - #tokens[1] = '@atom:type'+tokens[1] - #tokens[2] = '@atom:type'+tokens[2] - tokens[1] = '@atom:' + atomtypes_int2name[int(tokens[1])] - tokens[2] = '@atom:' + atomtypes_int2name[int(tokens[2])] - l_in_pair_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # delete mass commands for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_in_masses): - line = l_in_masses[i_line] - tokens = line.strip().split() - atomtype_i_str = tokens[1] - # if (('*' in atomtype_i_str) or - # ('*' in atomtype_j_str)): - # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' - # ' pair_coeff command contains a \"*\" character.\n' - # ' Keep in mind that using moltemplate.sh you can manually change the\n' - # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' - # ' nor to accidentally change the order of atom types in one of these\n' - # ' pair_coeff commands. For example, commands like\n' - # ' pair_coeff 10*4 20*10 0.15 3.6\n' - # ' can be generated by moltemplate.sh, however\n' - # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' - # ' pair_coeff 4*10 10*20 0.15 3.6)\n' - # ' Later on, you may want to check to make sure moltemplate.sh\n' - # ' is not doing this. (Fortunately you never have to worry unless\n' - # ' you are using the -a or -b arguments with moltemplate.sh)\n') - - if ('*' in atomtype_i_str): - atomtype_i_tokens = atomtype_i_str.split('*') - - if atomtype_i_tokens[0] == '': - if (min_sel_atomtype and - (min_sel_atomtype < min_needed_atomtype)): - i_a = min_sel_atomtype - else: - i_a = min_needed_atomtype - else: - i_a = Intify(atomtype_i_tokens[0]) - - if atomtype_i_tokens[1] == '': - if (max_sel_atomtype and - (max_sel_atomtype > max_needed_atomtype)): - i_b = max_sel_atomtype - else: - i_b = max_needed_atomtype - else: - i_b = Intify(atomtype_i_tokens[1]) - - else: - i_a = i_b = Intify(atomtype_i_str) - - i_a_final = None - i_b_final = None - for i in range(i_a, i_b + 1): - if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): - i_a_final = i - break - for i in reversed(range(i_a, i_b + 1)): - if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): - i_b_final = i - break - # if i_a_final and i_b_final: - # if i_a_final == i_b_final: - # i_str = '@atom:type'+str(i_a_final) - # tokens[1] = i_str - # else: - # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' - - if not (i_a_final and i_b_final and j_a_final and j_b_final): - del l_in_masses[i_line] - elif ('*' in atomtype_i_str): - del l_in_masses[i_line] - for i in range(i_a_final, i_b_final + 1): - #tokens[1] = '@atom:type'+str(i) - tokens[1] = '@atom:' + atomtypes_int2name[i] - # CONTINUEHERE: CHECK THAT THIS IS WORKING - l_in_masses.insert(i_line, (' ' * indent) + - (' '.join(tokens) + '\n')) - i_line += 1 - else: - assert(i_a == i_b) - #tokens[1] = '@atom:type'+str(i_a) - tokens[1] = '@atom:' + atomtypes_int2name[i_a] - # CONTINUEHERE: CHECK THAT THIS IS WORKING - l_in_masses[i_line] = (' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # --- BONDS AND BOND COEFFS --- - - # delete lines from data_bonds if they involve atoms we don't care about - i_line = 0 - while i_line < len(l_data_bonds): - line = l_data_bonds[i_line] - tokens = line.strip().split() - assert(len(tokens) == 4) - - bondid = Intify(tokens[0]) - bondtype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - # if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$bond:id' + str(bondid) - tokens[1] = '@bond:type' + str(bondtype) - #tokens[2] = '$atom:id'+str(atomid1) - #tokens[3] = '$atom:id'+str(atomid2) - tokens[2] = '$atom:' + atomids_int2name[atomid1] - tokens[3] = '$atom:' + atomids_int2name[atomid2] - needed_bondids.add(bondid) - needed_bondtypes.add(bondtype) - l_data_bonds[i_line] = (' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # else: - # del l_data_bonds[i_line] - - # delete data_bond_coeffs for bondtypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_bond_coeffs): - line = l_data_bond_coeffs[i_line] - tokens = line.strip().split() - bondtype = Intify(tokens[0]) - if (not (bondtype in needed_bondtypes)): - del l_data_bond_coeffs[i_line] - else: - tokens[0] = '@bond:type' + str(bondtype) - l_data_bond_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # delete in_bond_coeffs for bondtypes we don't care about anymore: - for bondtype in needed_bondtypes: - assert(type(bondtype) is int) - if ((min_needed_bondtype == None) or - (min_needed_bondtype > bondtype)): - min_needed_bondtype = bondtype - if ((max_needed_bondtype == None) or - (max_needed_bondtype < bondtype)): - max_needed_bondtype = bondtype - for bondid in needed_bondids: - assert(type(bondid) is int) - if ((min_needed_bondid == None) or - (min_needed_bondid > bondid)): - min_needed_bondid = bondid - if ((max_needed_bondid == None) or - (max_needed_bondid < bondid)): - max_needed_bondid = bondid - - i_line = 0 - while i_line < len(l_in_bond_coeffs): - line = l_in_bond_coeffs[i_line] - tokens = line.strip().split() - bondtype_str = tokens[1] - - if ('*' in bondtype_str): - bondtype_tokens = bondtype_str.split('*') - - if bondtype_tokens[0] == '': - i_a = min_needed_bondtype - else: - i_a = Intify(bondtype_tokens[0]) - - if bondtype_tokens[1] == '': - i_b = max_needed_bondtype - else: - i_b = Intify(bondtype_tokens[1]) - - else: - i_a = Intify(bondtype_str) - i_b = i_a - - if i_a < min_needed_bondtype: - i_a = min_needed_bondtype - if i_b > max_needed_bondtype: - i_b = max_needed_bondtype - - # if i_a == i_b: - # i_str = '@bond:type'+str(i_a) - # tokens[1] = i_str - # else: - # i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}' - - if ('*' in bondtype_str): - del l_in_bond_coeffs[i_line] - for i in range(i_a, i_b + 1): - if (i in needed_bondtypes): - tokens[1] = '@bond:type' + str(i) - l_in_bond_coeffs.insert(i_line, - (' ' * indent) + (' '.join(tokens) + '\n')) - i_line += 1 - else: - if i_a < i_b: - raise InputError('Error: number of bond types in data file is not consistent with the\n' - ' number of bond types you have define bond_coeffs for.\n') - if (i_a == i_b) and (i_a in needed_bondtypes): - tokens[1] = '@bond:type' + str(i_a) - l_in_bond_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - else: - del l_in_bond_coeffs[i_line] - - # --- ANGLES AND ANGLE COEFFS --- - - # delete lines from data_angles if they involve atoms we don't care about - i_line = 0 - while i_line < len(l_data_angles): - line = l_data_angles[i_line] - tokens = line.strip().split() - assert(len(tokens) == 5) - - angleid = Intify(tokens[0]) - angletype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - atomid3 = Intify(tokens[4]) - # if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$angle:id' + str(angleid) - tokens[1] = '@angle:type' + str(angletype) - #tokens[2] = '$atom:id'+str(atomid1) - #tokens[3] = '$atom:id'+str(atomid2) - #tokens[4] = '$atom:id'+str(atomid3) - tokens[2] = '$atom:' + atomids_int2name[atomid1] - tokens[3] = '$atom:' + atomids_int2name[atomid2] - tokens[4] = '$atom:' + atomids_int2name[atomid3] - needed_angleids.add(angleid) - needed_angletypes.add(angletype) - l_data_angles[i_line] = (' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # else: - # del l_data_angles[i_line] - - # delete data_angle_coeffs for angletypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_angle_coeffs): - line = l_data_angle_coeffs[i_line] - tokens = line.strip().split() - angletype = Intify(tokens[0]) - if (not (angletype in needed_angletypes)): - del l_data_angle_coeffs[i_line] - else: - tokens[0] = '@angle:type' + str(angletype) - l_data_angle_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # --- class2specific ---- - # Do the same for BondBond and BondAngle Coeffs: - # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by: - # angle_coeff, dihedral_coeff, and improper_coeff commands. - # THERE ARE NO bondbond_coeff commands, or bondangle_coeff commands, - # etc..., so we dont have to worry about l_in_bondbond_coeffs,... - # delete data_bondbond_coeffs for angletypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_bondbond_coeffs): - line = l_data_bondbond_coeffs[i_line] - tokens = line.strip().split() - angletype = Intify(tokens[0]) - if (not (angletype in needed_angletypes)): - del l_data_bondbond_coeffs[i_line] - else: - tokens[0] = '@angle:type' + str(angletype) - l_data_bondbond_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # delete data_bondangle_coeffs for angletypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_bondangle_coeffs): - line = l_data_bondangle_coeffs[i_line] - tokens = line.strip().split() - angletype = Intify(tokens[0]) - if (not (angletype in needed_angletypes)): - del l_data_bondangle_coeffs[i_line] - else: - tokens[0] = '@angle:type' + str(angletype) - l_data_bondangle_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # --- end of class2specific ---- - - # delete in_angle_coeffs for angletypes we don't care about anymore: - for angletype in needed_angletypes: - assert(type(angletype) is int) - if ((min_needed_angletype == None) or - (min_needed_angletype > angletype)): - min_needed_angletype = angletype - if ((max_needed_angletype == None) or - (max_needed_angletype < angletype)): - max_needed_angletype = angletype - for angleid in needed_angleids: - assert(type(angleid) is int) - if ((min_needed_angleid == None) or - (min_needed_angleid > angleid)): - min_needed_angleid = angleid - if ((max_needed_angleid == None) or - (max_needed_angleid < angleid)): - max_needed_angleid = angleid - - i_line = 0 - while i_line < len(l_in_angle_coeffs): - line = l_in_angle_coeffs[i_line] - tokens = line.strip().split() - angletype_str = tokens[1] - - if ('*' in angletype_str): - angletype_tokens = angletype_str.split('*') - - if angletype_tokens[0] == '': - i_a = min_needed_angletype - else: - i_a = Intify(angletype_tokens[0]) - - if angletype_tokens[1] == '': - i_b = max_needed_angletype - else: - i_b = Intify(angletype_tokens[1]) - - else: - i_a = i_b = Intify(angletype_str) - - if i_a < min_needed_angletype: - i_a = min_needed_angletype - if i_b > max_needed_angletype: - i_b = max_needed_angletype - - # if i_a == i_b: - # i_str = '@angle:type'+str(i_a) - # tokens[1] = i_str - # else: - # i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}' - - if ('*' in angletype_str): - del l_in_angle_coeffs[i_line] - for i in range(i_a, i_b + 1): - if (i in needed_angletypes): - tokens[1] = '@angle:type' + str(i) - l_in_angle_coeffs.insert(i_line, - (' ' * indent) + (' '.join(tokens) + '\n')) - i_line += 1 - else: - if i_a < i_b: - raise InputError('Error: number of angle types in data file is not consistent with the\n' - ' number of angle types you have define angle_coeffs for.\n') - if (i_a == i_b) and (i_a in needed_angletypes): - tokens[1] = '@angle:type' + str(i_a) - l_in_angle_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - else: - del l_in_angle_coeffs[i_line] - - # --- DIHEDRALS AND DIHEDRAL COEFFS --- - - # delete lines from data_dihedrals if they involve atoms we don't care - # about - i_line = 0 - while i_line < len(l_data_dihedrals): - line = l_data_dihedrals[i_line] - tokens = line.strip().split() - assert(len(tokens) == 6) - - dihedralid = Intify(tokens[0]) - dihedraltype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - atomid3 = Intify(tokens[4]) - atomid4 = Intify(tokens[5]) - # if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$dihedral:id' + str(dihedralid) - tokens[1] = '@dihedral:type' + str(dihedraltype) - #tokens[2] = '$atom:id'+str(atomid1) - #tokens[3] = '$atom:id'+str(atomid2) - #tokens[4] = '$atom:id'+str(atomid3) - #tokens[5] = '$atom:id'+str(atomid4) - tokens[2] = '$atom:' + atomids_int2name[atomid1] - tokens[3] = '$atom:' + atomids_int2name[atomid2] - tokens[4] = '$atom:' + atomids_int2name[atomid3] - tokens[5] = '$atom:' + atomids_int2name[atomid4] - - needed_dihedralids.add(dihedralid) - needed_dihedraltypes.add(dihedraltype) - l_data_dihedrals[i_line] = (' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # else: - # del l_data_dihedrals[i_line] - - # delete data_dihedral_coeffs for dihedraltypes we don't care about - # anymore: - i_line = 0 - while i_line < len(l_data_dihedral_coeffs): - line = l_data_dihedral_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del l_data_dihedral_coeffs[i_line] - else: - tokens[0] = '@dihedral:type' + str(dihedraltype) - l_data_dihedral_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # --- class2specific ---- - # Do the same for MiddleBondTorsion, EndBondTorsion, AngleTorsion, - # AngleAngleTorsion, and BondBond13 Coeffs - # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by: - # angle_coeff, dihedral_coeff, and improper_coeff commands. - # THERE ARE NO "middlebondtorsion_coeff" commands, etc...so we don't - # have to worry about dealing with "l_in_middlebondtorsion_coeffs",... - # delete data_middlebondtorsion_coeffs for dihedraltypes we don't care - # about anymore: - i_line = 0 - while i_line < len(l_data_middlebondtorsion_coeffs): - line = l_data_middlebondtorsion_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del l_data_middlebondtorsion_coeffs[i_line] - else: - tokens[0] = '@dihedral:type' + str(dihedraltype) - l_data_middlebondtorsion_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # delete data_endbondtorsion_coeffs for dihedraltypes we don't care about - # anymore: - i_line = 0 - while i_line < len(l_data_endbondtorsion_coeffs): - line = l_data_endbondtorsion_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del l_data_endbondtorsion_coeffs[i_line] - else: - tokens[0] = '@dihedral:type' + str(dihedraltype) - l_data_endbondtorsion_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # delete data_angletorsion_coeffs for dihedraltypes we don't care about - # anymore: - i_line = 0 - while i_line < len(l_data_angletorsion_coeffs): - line = l_data_angletorsion_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del l_data_angletorsion_coeffs[i_line] - else: - tokens[0] = '@dihedral:type' + str(dihedraltype) - l_data_angletorsion_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # delete data_angleangletorsion_coeffs for dihedraltypes we don't care - # about anymore: - i_line = 0 - while i_line < len(l_data_angleangletorsion_coeffs): - line = l_data_angleangletorsion_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del l_data_angleangletorsion_coeffs[i_line] - else: - tokens[0] = '@dihedral:type' + str(dihedraltype) - l_data_angleangletorsion_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # delete data_bondbond13_coeffs for dihedraltypes we don't care about - # anymore: - i_line = 0 - while i_line < len(l_data_bondbond13_coeffs): - line = l_data_bondbond13_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del l_data_bondbond13_coeffs[i_line] - else: - tokens[0] = '@dihedral:type' + str(dihedraltype) - l_data_bondbond13_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # --- end of class2specific ---- - - # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore: - for dihedraltype in needed_dihedraltypes: - assert(type(dihedraltype) is int) - if ((min_needed_dihedraltype == None) or - (min_needed_dihedraltype > dihedraltype)): - min_needed_dihedraltype = dihedraltype - if ((max_needed_dihedraltype == None) or - (max_needed_dihedraltype < dihedraltype)): - max_needed_dihedraltype = dihedraltype - for dihedralid in needed_dihedralids: - assert(type(dihedralid) is int) - if ((min_needed_dihedralid == None) or - (min_needed_dihedralid > dihedralid)): - min_needed_dihedralid = dihedralid - if ((max_needed_dihedralid == None) or - (max_needed_dihedralid < dihedralid)): - max_needed_dihedralid = dihedralid - - i_line = 0 - while i_line < len(l_in_dihedral_coeffs): - line = l_in_dihedral_coeffs[i_line] - tokens = line.strip().split() - dihedraltype_str = tokens[1] - - if ('*' in dihedraltype_str): - dihedraltype_tokens = dihedraltype_str.split('*') - - if dihedraltype_tokens[0] == '': - i_a = min_needed_dihedraltype - else: - i_a = Intify(dihedraltype_tokens[0]) - - if dihedraltype_tokens[1] == '': - i_b = max_needed_dihedraltype - else: - i_b = Intify(dihedraltype_tokens[1]) - - else: - i_a = i_b = Intify(dihedraltype_str) - - if i_a < min_needed_dihedraltype: - i_a = min_needed_dihedraltype - if i_b > max_needed_dihedraltype: - i_b = max_needed_dihedraltype - - # if i_a == i_b: - # i_str = '@dihedral:type'+str(i_a) - # tokens[1] = i_str - # else: - # i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}' - - if ('*' in dihedraltype_str): - del l_in_dihedral_coeffs[i_line] - for i in range(i_a, i_b + 1): - if (i in needed_dihedraltypes): - tokens[1] = '@dihedral:type' + str(i) - l_in_dihedral_coeffs.insert(i_line, - (' ' * indent) + (' '.join(tokens) + '\n')) - i_line += 1 - else: - if i_a < i_b: - raise InputError('Error: number of dihedral types in data file is not consistent with the\n' - ' number of dihedral types you have define dihedral_coeffs for.\n') - if (i_a == i_b) and (i_a in needed_dihedraltypes): - tokens[1] = '@dihedral:type' + str(i_a) - l_in_dihedral_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - else: - del l_in_dihedral_coeffs[i_line] - - # --- IMPROPERS AND IMPROPER COEFFS --- - - # delete lines from data_impropers if they involve atoms we don't care - # about - i_line = 0 - while i_line < len(l_data_impropers): - line = l_data_impropers[i_line] - tokens = line.strip().split() - assert(len(tokens) == 6) - - improperid = Intify(tokens[0]) - impropertype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - atomid3 = Intify(tokens[4]) - atomid4 = Intify(tokens[5]) - # if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$improper:id' + str(improperid) - tokens[1] = '@improper:type' + str(impropertype) - #tokens[2] = '$atom:id'+str(atomid1) - #tokens[3] = '$atom:id'+str(atomid2) - #tokens[4] = '$atom:id'+str(atomid3) - #tokens[5] = '$atom:id'+str(atomid4) - tokens[2] = '$atom:' + atomids_int2name[atomid1] - tokens[3] = '$atom:' + atomids_int2name[atomid2] - tokens[4] = '$atom:' + atomids_int2name[atomid3] - tokens[5] = '$atom:' + atomids_int2name[atomid4] - - needed_improperids.add(improperid) - needed_impropertypes.add(impropertype) - l_data_impropers[i_line] = (' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # else: - # del l_data_impropers[i_line] - - # delete data_improper_coeffs for impropertypes we don't care about - # anymore: - i_line = 0 - while i_line < len(l_data_improper_coeffs): - line = l_data_improper_coeffs[i_line] - tokens = line.strip().split() - impropertype = Intify(tokens[0]) - if (not (impropertype in needed_impropertypes)): - del l_data_improper_coeffs[i_line] - else: - tokens[0] = '@improper:type' + str(impropertype) - l_data_improper_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - - # --- class2specific ---- - # Do the same for AngleAngle Coeffs - # NOTE: LAMMPS INPUT SCRIPTS, ALL CLASS2 COEFFS are represented by: - # angle_coeff, dihedral_coeff, and improper_coeff commands. - # THERE ARE NO "angleangle_coeff" commands, etc...so we don't - # have to worry about dealing with "l_in_angleangle_coeffs",... - # delete data_middlebondtorsion_coeffs for dihedraltypes we don't care about anymore: - # delete data_angleangle_coeffs for impropertypes we don't care about - # anymore: - i_line = 0 - while i_line < len(l_data_angleangle_coeffs): - line = l_data_angleangle_coeffs[i_line] - tokens = line.strip().split() - impropertype = Intify(tokens[0]) - if (not (impropertype in needed_impropertypes)): - del l_data_angleangle_coeffs[i_line] - else: - tokens[0] = '@improper:type' + str(impropertype) - l_data_angleangle_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - # --- end of class2specific ---- - - # delete in_improper_coeffs for impropertypes we don't care about anymore: - for impropertype in needed_impropertypes: - assert(type(impropertype) is int) - if ((min_needed_impropertype == None) or - (min_needed_impropertype > impropertype)): - min_needed_impropertype = impropertype - if ((max_needed_impropertype == None) or - (max_needed_impropertype < impropertype)): - max_needed_impropertype = impropertype - for improperid in needed_improperids: - assert(type(improperid) is int) - if ((min_needed_improperid == None) or - (min_needed_improperid > improperid)): - min_needed_improperid = improperid - if ((max_needed_improperid == None) or - (max_needed_improperid < improperid)): - max_needed_improperid = improperid - - i_line = 0 - while i_line < len(l_in_improper_coeffs): - line = l_in_improper_coeffs[i_line] - tokens = line.strip().split() - impropertype_str = tokens[1] - - if ('*' in impropertype_str): - impropertype_tokens = impropertype_str.split('*') - - if impropertype_tokens[0] == '': - i_a = min_needed_impropertype - else: - i_a = Intify(impropertype_tokens[0]) - - if impropertype_tokens[1] == '': - i_b = max_needed_impropertype - else: - i_b = Intify(impropertype_tokens[1]) - - else: - i_a = i_b = Intify(impropertype_str) - - if i_a < min_needed_impropertype: - i_a = min_needed_impropertype - if i_b > max_needed_impropertype: - i_b = max_needed_impropertype - - # if i_a == i_b: - # i_str = '@improper:type'+str(i_a) - # tokens[1] = i_str - # else: - # i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}' - - if ('*' in impropertype_str): - del l_in_improper_coeffs[i_line] - for i in range(i_a, i_b + 1): - if (i in needed_impropertypes): - tokens[1] = '@improper:type' + str(i) - l_in_improper_coeffs.insert(i_line, - (' ' * indent) + (' '.join(tokens) + '\n')) - i_line += 1 - else: - if i_a < i_b: - raise InputError('Error: number of improper types in data file is not consistent with the\n' - ' number of improper types you have define improper_coeffs for.\n') - if (i_a == i_b) and (i_a in needed_impropertypes): - tokens[1] = '@improper:type' + str(i_a) - l_in_improper_coeffs[i_line] = ( - ' ' * indent) + (' '.join(tokens) + '\n') - i_line += 1 - else: - del l_in_improper_coeffs[i_line] - - # --- GROUPS --- - - # Now parse through all of the "group" commands and try and figure - # out if any of these groups contain any of the atoms we are keeping. - # If so, then save the group and write it out. - # (I hate trying to parse this kind of text.) - - # if len(l_in_group) > 0: - # sys.stderr.write('\n' - # ' --groups-- Attempting to parse \"group\" commands.\n' - # ' This may cause '+g_program_name+' to crash.\n' - # ' If so, comment out all group commands in your input script(s), and\n' - # ' try again. (And please report the error. -Andrew 2017-10)\n') - - i_line = 0 - groups_needed = set(['all']) - while i_line < len(l_in_group): - line = l_in_group[i_line] - tokens = line.strip().split() - delete_this_command = False - explicit_definition = False - if len(tokens) < 3: - delete_this_command = True - group_name = tokens[1] - specifier_style = tokens[2] - str_logical = '' - str_selection = '' - if specifier_style[0:4] == 'type': - str_logical += specifier_style[4:] - explicit_definition = True - specifier_style = 'type' - elif specifier_style == 'id': - str_logical += specifier_style[2:] - explicit_definition = True - specifier_style = 'id' - elif specifier_style == 'molecule': - str_logical += specifier_style[8:] - specifier_style = 'molecule' - explicit_definition = True - - if explicit_definition: - i_token_sel_min = 3 - if len(tokens) <= i_token_sel_min: - sys.stderr.write('WARNING: possible syntax error on this line:\n' - + ' ' + l_in_group[i_line] + '\n') - delete_this_command = True - if str_logical == '': - str_logical = tokens[i_token_sel_min] - if not str_logical[0].isdigit(): - i_token_sel_min += 1 - if len(tokens) <= i_token_sel_min: - tokens.append('') - else: - tokens.insert(i_token_sel_min, str_logical) - - i_token_sel_max = len(tokens) - 1 - - for i in range(i_token_sel_min, len(tokens)): - if tokens[i].isdigit(): - break - else: - i_token_sel_max = i - - assert(len(tokens) > i_token_sel_min) - - if str_logical[0:2] in ('<=', '>=', '==', '!=', '<>'): - tokens[i_token_sel_min] = str_logical[ - 2:] + tokens[i_token_sel_min] - str_logical = str_logical[0:2] - if str_logical == '<=': - l_group_selection = [(None, int(tokens[i_token_sel_min]))] - elif str_logical == '>=': - l_group_selection = [(int(tokens[i_token_sel_min]), None)] - elif str_logical == '==': - l_group_selection = [(int(tokens[i_token_sel_min]), - int(tokens[i_token_sel_min]))] - elif str_logical == '!=': - l_group_selection = [(None, int(tokens[i_token_sel_min]) - 1), - (int(tokens[i_token_sel_min]) + 1, None)] - elif str_logical == '<>': - l_group_selection = [(int(tokens[i_token_sel_min]), - int(tokens[i_token_sel_max]))] - - elif str_logical[0:1] in ('<', '>'): - tokens[i_token_sel_min] = str_logical[ - 1:] + tokens[i_token_sel_min] - str_logical = str_logical[0:1] - if str_logical == '<': - l_group_selection = [ - (None, int(tokens[i_token_sel_min]) - 1)] - elif str_logical == '>': - l_group_selection = [ - (int(tokens[i_token_sel_min]) + 1, None)] - else: - str_selection = ' '.join( - tokens[i_token_sel_min:i_token_sel_max + 1]) - l_group_selection = LammpsSelectToIntervals(str_selection, - slice_delim=':', - or_delim=' ') - - mn, mx = IntervalListToMinMax(l_group_selection) - if mn == None: - mn = 1 - filtered_selection = [] - if specifier_style == 'type': - if mx == None: - mx = max_needed_atomtype - for i in range(mn, mx + 1): - if (BelongsToSel(i, l_group_selection) - and (i in needed_atomtypes)): - filtered_selection.append((i, i)) - elif specifier_style == 'id': - if mx == None: - mx = max_needed_atomid - for i in range(mn, mx + 1): - if (BelongsToSel(i, l_group_selection) - and (i in needed_atomids)): - filtered_selection.append((i, i)) - elif specifier_style == 'molecule': - if mx == None: - mx = max_needed_molid - for i in range(mn, mx + 1): - if (BelongsToSel(i, l_group_selection) - and (i in needed_molids)): - filtered_selection.append((i, i)) - - MergeIntervals(filtered_selection) - - if len(filtered_selection) > 0: - - tokens = ['group', group_name, specifier_style] - for interval in filtered_selection: - a = interval[0] - b = interval[1] - - if specifier_style == 'type': - if a == b: - tokens.append('@atom:type' + str(a)) - else: - tokens.append('@{atom:type' + str(a) + - '}:@{atom:type' + str(b) + '}') - - if specifier_style == 'id': - if a == b: - tokens.append('$atom:id' + str(a)) - else: - tokens.append('${atom:id' + str(a) - + '}:${atom:id' + str(b) + '}') - - if specifier_style == 'molecule': - if a == b: - tokens.append('$mol:id' + str(a)) - else: - tokens.append('${mol:id' + str(a) + - '}:${mol:id' + str(b) + '}') - - # Commenting out next two lines. (This is handled later.) - #l_in_group[i_line] = ' '.join(tokens) - # groups_needed.add(group_name) - - else: - delete_this_command = True - - else: - if len(tokens) > 3: - if tokens[2] == 'union': - i_token = 3 - while i_token < len(tokens): - if not (tokens[i_token] in groups_needed): - del tokens[i_token] - else: - i_token += 1 - # if none of the groups contain atoms we need, - # then delete the entire command - if len(tokens) <= 3: - delete_this_command = True - elif tokens[2] == 'intersect': - i_token = 3 - while i_token < len(tokens): - if not (tokens[i_token] in groups_needed): - # if any of the groups we need are empty - # then delete the command - delete_this_command = True - break - i_token += 1 - elif (tokens[2] == 'subtract') and (len(tokens) >= 5): - if not (tokens[3] in groups_needed): - delete_this_command = True - i_token = 4 - while i_token < len(tokens): - if not (tokens[i_token] in groups_needed): - del tokens[i_token] - else: - i_token += 1 - else: - # Otherwise I don't recongize the syntax of this - # group command. In that case, I just delete it. - delete_this_command = True - - elif tokens[2] == 'clear': - pass - elif tokens[2] == 'delete': - pass - else: - delete_this_command = True - if delete_this_command: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_group[i_line].rstrip() + '\"\n') - del l_in_group[i_line] - else: - groups_needed.add(group_name) - l_in_group[i_line] = (' ' * indent) + ' '.join(tokens) + '\n' - i_line += 1 - - # --- fix rigid --- - - i_line = 0 - while i_line < len(l_in_fix_rigid): - line = l_in_fix_rigid[i_line] - tokens = line.strip().split() - if len(tokens) < 4: - break - fixid = tokens[1] - group_name = tokens[2] - delete_this_command = True - assert(tokens[3].find('rigid') == 0) - if group_name in groups_needed: - delete_this_command = False - - if delete_this_command: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_fix_rigid[i_line].rstrip() + '\"\n') - del l_in_fix_rigid[i_line] - else: - l_in_fix_rigid[i_line] = (' ' * indent) + ' '.join(tokens) + '\n' - i_line += 1 - - # --- set --- - - i_line = 0 - while i_line < len(l_in_set): - line = l_in_set[i_line] - tokens = line.strip().split() - l_new_set_commands = [] - l_new_set_static_commands = [] - if len(tokens) < 4: - break - if tokens[1] == 'type': - pattern = tokens[2].split('*') - if pattern[0] == '': - types_lo = min_needed_atomtype - else: - types_lo = types_hi = int(pattern[0]) - if types_lo < min_needed_atomtype: - types_lo = min_needed_atomtype - if len(pattern) == 2: - if pattern[1] == '': - types_hi = max_needed_atomtype - else: - types_hi = min(int(pattern[1]), max_needed_atomtype) - for i in range(types_lo, types_hi+1): - if i in needed_atomtypes: - l_new_set_static_commands.append((' ' * indent) + - ' '.join(tokens[0:2])+' '+ - '@atom:type'+str(i) + ' ' + - ' '.join(tokens[3:])) - elif tokens[1] == 'atom': - pattern = tokens[2].split('*') - if pattern[0] == '': - atomids_lo = min_needed_atomid - else: - atomids_lo = atomids_hi = int(pattern[0]) - if atomids_lo < min_needed_atomid: - atomids_lo = min_needed_atomid - if len(pattern) == 2: - if pattern[1] == '': - atomids_hi = max_needed_atomid - else: - atomids_hi = min(int(pattern[1]), max_needed_atomid) - for i in range(atomids_lo, atomids_hi+1): - if i in needed_atomids: - l_new_set_commands.append((' ' * indent) + - ' '.join(tokens[0:2])+' '+ - str(i) + ' ' + - ' '.join(tokens[3:])) - elif tokens[1] == 'mol': - pattern = tokens[2].split('*') - if pattern[0] == '': - molids_lo = min_needed_molid - else: - molids_lo = molids_hi = int(pattern[0]) - if molids_lo < min_needed_molid: - molids_lo = min_needed_molid - if len(pattern) == 2: - if pattern[1] == '': - molids_hi = max_needed_molid - else: - molids_hi = min(int(pattern[1]), max_needed_molid) - for i in range(molids_lo, molids_hi+1): - if i in needed_molids: - l_new_set_commands.append(' '.join(tokens[0:2])+' '+ - str(i) + ' ' + - ' '.join(tokens[3:])) - elif tokens[0] == 'group': - group_name = tokens[2] - if group_name in groups_needed: - l_new_set_static_commands = [l_in_set[i_line]] - - if len(l_new_set_commands) > 0: - l_in_set[i_line:i_line+1] = l_new_set_commands - i_line += len(l_new_set_commands) - elif len(l_new_set_static_commands) > 0: - l_in_set_static += l_new_set_static_commands - del l_in_set[i_line] - else: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_set[i_line].rstrip() + '\"\n') - del l_in_set[i_line] - - - # --- fix shake --- - - i_line = 0 - while i_line < len(l_in_fix_shake): - line = l_in_fix_shake[i_line] - tokens = line.strip().split() - if len(tokens) < 4: - break - fixid = tokens[1] - group_name = tokens[2] - delete_this_command = True - assert(tokens[3].find('shake') == 0) - - # parse the list of angle types - #i_token = tokens.index('a') - for i_token in range(0, len(tokens)): - if tokens[i_token] == 'a': - break - if i_token != len(tokens): - i_token += 1 - while (i_token < len(tokens)) and tokens[i_token].isdigit(): - # delete angle types from the list which - # do not belong to the selection - btype = int(tokens[i_token]) - if int(tokens[i_token]) in needed_angletypes: - tokens[i_token] = '@angle:type' + tokens[i_token] - i_token += 1 - delete_this_command = False - else: - del tokens[i_token] - - # parse the list of bond types - #i_token = tokens.index('b') - for i_token in range(0, len(tokens)): - if tokens[i_token] == 'b': - break - if i_token != len(tokens): - i_token += 1 - while (i_token < len(tokens)) and tokens[i_token].isdigit(): - # delete bond types from the list which - # do not belong to the selection - btype = int(tokens[i_token]) - if int(tokens[i_token]) in needed_bondtypes: - tokens[i_token] = '@bond:type' + tokens[i_token] - i_token += 1 - delete_this_command = False - else: - del tokens[i_token] - - # parse the list of atom types - # i_token = tokens.index('t') - for i_token in range(0, len(tokens)): - if tokens[i_token] == 't': - break - if i_token != len(tokens): - i_token += 1 - while (i_token < len(tokens)) and tokens[i_token].isdigit(): - # delete atom types from the list which - # do not belong to the selection - btype = int(tokens[i_token]) - if int(tokens[i_token]) in needed_atomtypes: - tokens[i_token] = '@atom:type' + tokens[i_token] - i_token += 1 - delete_this_command = False - else: - del tokens[i_token] - - # Selecting atoms by mass feature should still work, so we - # don't need to delete or ignore these kinds of commands. - # for i_token in range(0, len(tokens)): - # if tokens[i_token] == 'm': - # break - # if i_token != len(tokens): - # delete_this_command = True - - if 'mol' in tokens: - delete_this_command = True - - if not (group_name in groups_needed): - delete_this_command = True - - if delete_this_command: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_fix_shake[i_line].rstrip() + '\"\n') - del l_in_fix_shake[i_line] - else: - l_in_fix_shake[i_line] = (' ' * indent) + ' '.join(tokens) + '\n' - i_line += 1 - - # --- fix poems --- - - i_line = 0 - while i_line < len(l_in_fix_poems): - line = l_in_fix_poems[i_line] - tokens = line.strip().split() - if len(tokens) < 4: - break - fixid = tokens[1] - group_name = tokens[2] - delete_this_command = True - assert(tokens[3].find('poems') == 0) - if group_name in groups_needed: - delete_this_command = False - if tokens[4] != 'molecule': - delete_this_command = True - sys.stderr.write('WARNING: ' + g_program_name + ' ONLY supports \"fix poems\" commands\n' - ' which use the \"molecule\" keyword.\n') - if tokens[4] == 'file': - sys.stderr.write(' If you want use external files with fix poems, then you will have to\n' - ' generate the file yourself. You ask use moltemplate to generate\n' - ' this file for you, by manually adding a section at the end of your\n' - ' final .LT file (eg. \"system.lt\") which resembles the following:\n\n' - 'write(\"poems_file.txt\") {\n' - ' 1 1 $atom:idname1a $atom:idname2a $atom:idname3a ...\n' - ' 2 1 $atom:idname1b $atom:idname2b $atom:idname3b ...\n' - ' 3 1 $atom:idname1c $atom:idname2c $atom:idname3c ...\n' - ' : : etc...\n' - '}\n\n' - ' ...where $atom:idname1a, $atom:idname2a, ... are moltemplate-compatible\n' - ' unique (full,long) id-names for the atoms in each rigid body.\n' - ' This will insure the atom-id numbers in this file are correct.\n' - - ' See the documentation for fix poems for details.\n') - - if delete_this_command: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_fix_poems[i_line].rstrip() + '\"\n') - del l_in_fix_poems[i_line] - else: - l_in_fix_poems[i_line] = (' ' * indent) + ' '.join(tokens) + '\n' - i_line += 1 - - # --- fix qeq --- - - i_line = 0 - while i_line < len(l_in_fix_qeq): - line = l_in_fix_qeq[i_line] - tokens = line.strip().split() - if len(tokens) < 4: - break - fixid = tokens[1] - group_name = tokens[2] - delete_this_command = True - assert(tokens[3].find('qeq') == 0) - if group_name in groups_needed: - delete_this_command = False - - if delete_this_command: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_fix_qeq[i_line].rstrip() + '\"\n') - del l_in_fix_qeq[i_line] - else: - l_in_fix_qeq[i_line] = (' ' * indent) + ' '.join(tokens) + '\n' - i_line += 1 - - # --- fix qmmm --- - - i_line = 0 - while i_line < len(l_in_fix_qmmm): - line = l_in_fix_qmmm[i_line] - tokens = line.strip().split() - if len(tokens) < 4: - break - fixid = tokens[1] - group_name = tokens[2] - delete_this_command = True - assert(tokens[3].find('qmmm') == 0) - if group_name in groups_needed: - delete_this_command = False - - if delete_this_command: - sys.stderr.write('WARNING: Ignoring line \n\"' + - l_in_fix_qmmm[i_line].rstrip() + '\"\n') - del l_in_fix_qmmm[i_line] - else: - l_in_fix_qmmm[i_line] = (' ' * indent) + ' '.join(tokens) + '\n' - i_line += 1 - - ######################################## - ### Now begin writing the template. ### - ######################################## - - if not some_pair_coeffs_read: - sys.stderr.write('Warning: No \"pair coeffs\" set.\n' - ' (No interactions between non-bonded atoms defined.)\n') - no_warnings = False - - # sys.stderr.write('Writing ttree data to standard out.\n' - # ' You can redirect this to a file using:\n'+ - # ' '+' '.join(sys.argv)+' > filename.ttree\n' - # ' ----------------------\n') - - if mol_name != '': - sys.stdout.write(mol_name + ' {\n') - - if len(l_in_init) > 0: - sys.stdout.write('\n ### LAMMPS commands for initialization\n' - ' ### (These can be overridden later.)\n\n') - l_in_init.insert(0, (' ' * cindent) + - 'write_once(\"' + in_init + '\") {\n') - l_in_init.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_init)) - if len(l_in_settings) > 0: - sys.stdout.write('\n ### LAMMPS commands for settings\n' - ' ### (These can be overridden later.)\n\n') - l_in_settings.insert(0, (' ' * cindent) + - 'write_once(\"' + in_settings + '\") {\n') - l_in_settings.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_settings)) - non_empty_output = True - if len(l_in_masses) > 0: - l_in_masses.insert(0, (' ' * cindent) + - 'write_once(\"' + in_settings + '\") {\n') - l_in_masses.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_masses)) - non_empty_output = True - - if remove_coeffs_from_data_file: - if len(l_data_pair_coeffs) > 0: - for line in l_data_pair_coeffs: - tokens = line.strip().split() - atomtype_str = tokens[0] - l_in_pair_coeffs.append((' ' * cindent) + ' pair_coeff ' + atomtype_str + - ' ' + atomtype_str + ' ' + ' '.join(tokens[1:]) + '\n') - l_data_pair_coeffs = [] - if len(l_data_pairij_coeffs) > 0: - for line in l_data_pairij_coeffs: - l_in_pair_coeffs.append( - (' ' * cindent) + ' pair_coeff ' + line.strip() + '\n') - l_data_pairij_coeffs = [] - if len(l_in_pair_coeffs) > 0: - l_in_pair_coeffs.insert(0, (' ' * cindent) + - 'write_once(\"' + in_settings + '\") {\n') - l_in_pair_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_pair_coeffs)) - non_empty_output = True - - if (remove_coeffs_from_data_file and (len(l_data_bond_coeffs) > 0)): - for line in l_data_bond_coeffs: - l_in_bond_coeffs.append( - (' ' * cindent) + ' bond_coeff ' + line.strip() + '\n') - l_data_bond_coeffs = [] - if len(l_in_bond_coeffs) > 0: - l_in_bond_coeffs.insert(0, (' ' * cindent) + - 'write_once(\"' + in_settings + '\") {\n') - l_in_bond_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_bond_coeffs)) - non_empty_output = True - - if (remove_coeffs_from_data_file and (len(l_data_angle_coeffs) > 0)): - for line in l_data_angle_coeffs: - l_in_angle_coeffs.append( - (' ' * cindent) + ' angle_coeff ' + line.strip() + '\n') - l_data_angle_coeffs = [] - for line in l_data_bondbond_coeffs: - tokens = line.strip().split() - l_in_angle_coeffs.append( - (' ' * cindent) + ' angle_coeff ' + tokens[0] + ' bb ' + ' '.join(tokens[1:]) + '\n') - l_data_bondbond_coeffs = [] - for line in l_data_bondangle_coeffs: - tokens = line.strip().split() - l_in_angle_coeffs.append( - (' ' * cindent) + ' angle_coeff ' + tokens[0] + ' ba ' + ' '.join(tokens[1:]) + '\n') - l_data_bondangle_coeffs = [] - if len(l_in_angle_coeffs) > 0: - l_in_angle_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + in_settings + '\") {\n') - l_in_angle_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_angle_coeffs)) - non_empty_output = True - - if (remove_coeffs_from_data_file and (len(l_data_dihedral_coeffs) > 0)): - for line in l_data_dihedral_coeffs: - l_in_dihedral_coeffs.append( - (' ' * cindent) + ' dihedral_coeff ' + line.strip() + '\n') - l_data_dihedral_coeffs = [] - - for line in l_data_middlebondtorsion_coeffs: - tokens = line.strip().split() - l_in_dihedral_coeffs.append( - (' ' * cindent) + ' dihedral_coeff ' + tokens[0] + ' mbt ' + ' '.join(tokens[1:]) + '\n') - l_data_middlebondtorsion_coeffs = [] - - for line in l_data_endbondtorsion_coeffs: - tokens = line.strip().split() - l_in_dihedral_coeffs.append( - (' ' * cindent) + ' dihedral_coeff ' + tokens[0] + ' ebt ' + ' '.join(tokens[1:]) + '\n') - l_data_endbondtorsion_coeffs = [] - - for line in l_data_angletorsion_coeffs: - tokens = line.strip().split() - l_in_dihedral_coeffs.append( - (' ' * cindent) + ' dihedral_coeff ' + tokens[0] + ' at ' + ' '.join(tokens[1:]) + '\n') - l_data_angletorsion_coeffs = [] - - for line in l_data_angleangletorsion_coeffs: - tokens = line.strip().split() - l_in_dihedral_coeffs.append( - (' ' * cindent) + ' dihedral_coeff ' + tokens[0] + ' aat ' + ' '.join(tokens[1:]) + '\n') - l_data_angleangletorsion_coeffs = [] - - for line in l_data_bondbond13_coeffs: - tokens = line.strip().split() - l_in_dihedral_coeffs.append( - (' ' * cindent) + ' dihedral_coeff ' + tokens[0] + ' bb13 ' + ' '.join(tokens[1:]) + '\n') - l_data_bondbond13_coeffs = [] - - if len(l_in_dihedral_coeffs) > 0: - l_in_dihedral_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + in_settings + '\") {\n') - l_in_dihedral_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_dihedral_coeffs)) - non_empty_output = True - - if (remove_coeffs_from_data_file and (len(l_data_improper_coeffs) > 0)): - for line in l_data_improper_coeffs: - l_in_improper_coeffs.append( - (' ' * cindent) + ' improper_coeff ' + line.strip() + '\n') - l_data_improper_coeffs = [] - - for line in l_data_angleangle_coeffs: - tokens = line.strip().split() - l_in_improper_coeffs.append( - (' ' * cindent) + ' improper_coeff ' + tokens[0] + ' aa ' + ' '.join(tokens[1:]) + '\n') - l_data_angleangle_coeffs = [] - - if len(l_in_improper_coeffs) > 0: - l_in_improper_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + in_settings + '\") {\n') - l_in_improper_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_improper_coeffs)) - non_empty_output = True - - if non_empty_output: - sys.stdout.write('\n\n ### DATA sections\n\n') - - if len(l_data_masses) > 0: - l_data_masses.insert(0, (' ' * cindent) + - 'write_once(\"' + data_masses + '\") {\n') - l_data_masses.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_masses)) - non_empty_output = True - if len(l_data_bond_coeffs) > 0: - l_data_bond_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_bond_coeffs + '\") {\n') - l_data_bond_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bond_coeffs)) - non_empty_output = True - if len(l_data_angle_coeffs) > 0: - l_data_angle_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_angle_coeffs + '\") {\n') - l_data_angle_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angle_coeffs)) - non_empty_output = True - if len(l_data_dihedral_coeffs) > 0: - l_data_dihedral_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_dihedral_coeffs + '\") {\n') - l_data_dihedral_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_dihedral_coeffs)) - non_empty_output = True - if len(l_data_improper_coeffs) > 0: - l_data_improper_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_improper_coeffs + '\") {\n') - l_data_improper_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_improper_coeffs)) - non_empty_output = True - if len(l_data_pair_coeffs) > 0: - l_data_pair_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_pair_coeffs + '\") {\n') - l_data_pair_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_pair_coeffs)) - non_empty_output = True - if len(l_data_pairij_coeffs) > 0: - l_data_pairij_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_pairij_coeffs + '\") {\n') - l_data_pairij_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_pairij_coeffs)) - non_empty_output = True - - # class2 force fields: - if len(l_data_bondbond_coeffs) > 0: - l_data_bondbond_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_bondbond_coeffs + '\") {\n') - l_data_bondbond_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bondbond_coeffs)) - non_empty_output = True - if len(l_data_bondangle_coeffs) > 0: - l_data_bondangle_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_bondangle_coeffs + '\") {\n') - l_data_bondangle_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bondangle_coeffs)) - non_empty_output = True - if len(l_data_middlebondtorsion_coeffs) > 0: - l_data_middlebondtorsion_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_middlebondtorsion_coeffs + '\") {\n') - l_data_middlebondtorsion_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs)) - non_empty_output = True - if len(l_data_endbondtorsion_coeffs) > 0: - l_data_endbondtorsion_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_endbondtorsion_coeffs + '\") {\n') - l_data_endbondtorsion_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_endbondtorsion_coeffs)) - non_empty_output = True - if len(l_data_angletorsion_coeffs) > 0: - l_data_angletorsion_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_angletorsion_coeffs + '\") {\n') - l_data_angletorsion_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angletorsion_coeffs)) - non_empty_output = True - if len(l_data_angleangletorsion_coeffs) > 0: - l_data_angleangletorsion_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_angleangletorsion_coeffs + '\") {\n') - l_data_angleangletorsion_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angleangletorsion_coeffs)) - non_empty_output = True - if len(l_data_bondbond13_coeffs) > 0: - l_data_bondbond13_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_bondbond13_coeffs + '\") {\n') - l_data_bondbond13_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bondbond13_coeffs)) - non_empty_output = True - if len(l_data_angleangle_coeffs) > 0: - l_data_angleangle_coeffs.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_angleangle_coeffs + '\") {\n') - l_data_angleangle_coeffs.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angleangle_coeffs)) - non_empty_output = True - - # automatic generation of bonded interactions by type: - if len(l_data_angles_by_type) > 0: - l_data_angles_by_type.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_angles_by_type + '\") {\n') - l_data_angles_by_type.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angles_by_type)) - non_empty_output = True - if len(l_data_dihedrals_by_type) > 0: - l_data_dihedrals_by_type.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_dihedrals_by_type + '\") {\n') - l_data_dihedrals_by_type.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_dihedrals_by_type)) - non_empty_output = True - if len(l_data_impropers_by_type) > 0: - l_data_impropers_by_type.insert( - 0, (' ' * cindent) + 'write_once(\"' + data_impropers_by_type + '\") {\n') - l_data_impropers_by_type.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_impropers_by_type)) - non_empty_output = True - - if len(l_data_atoms) > 0: - l_data_atoms.insert(0, (' ' * cindent) + - 'write(\"' + data_atoms + '\") {\n') - l_data_atoms.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_atoms)) - non_empty_output = True - else: - sys.stderr.write('Warning: missing \"Atoms\" section.\n' - ' (Did you include a LAMMPS data file in your argument list?)\n') - no_warnings = False - - # non-point-like particles - if len(l_data_ellipsoids) > 0: - l_data_ellipsoids.insert( - 0, (' ' * cindent) + 'write(\"' + data_ellipsoids + '\") {\n') - l_data_ellipsoids.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_ellipsoids)) - if len(l_data_lines) > 0: - l_data_lines.insert(0, (' ' * cindent) + - 'write(\"' + data_lines + '\") {\n') - l_data_lines.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_lines)) - if len(l_data_triangles) > 0: - l_data_triangles.insert(0, (' ' * cindent) + - 'write(\"' + data_triangles + '\") {\n') - l_data_triangles.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_triangles)) - - # DO NOT WRITE OUT VELOCITY DATA - # (Why: because it makes it difficult to combine this molecular template - # with molecule templates from other sources which lack velocity data. - # LAMMPS (and topotools) will crash if the number of entries in the - # Velocities section of a data file does not match the number of atoms.) - # COMMENTING OUT: - # if len(l_data_velocities) > 0: - # l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') - # l_data_velocities.append((' '*cindent)+'}\n') - # sys.stdout.write('\n') - # sys.stdout.write(''.join(l_data_velocities)) - if len(l_data_bonds) > 0: - l_data_bonds.insert(0, (' ' * cindent) + - 'write(\"' + data_bonds + '\") {\n') - l_data_bonds.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bonds)) - non_empty_output = True - if len(l_data_angles) > 0: - l_data_angles.insert(0, (' ' * cindent) + - 'write(\"' + data_angles + '\") {\n') - l_data_angles.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angles)) - non_empty_output = True - if len(l_data_dihedrals) > 0: - l_data_dihedrals.insert(0, (' ' * cindent) + - 'write(\"' + data_dihedrals + '\") {\n') - l_data_dihedrals.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_dihedrals)) - non_empty_output = True - if len(l_data_impropers) > 0: - l_data_impropers.insert(0, (' ' * cindent) + - 'write(\"' + data_impropers + '\") {\n') - l_data_impropers.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_impropers)) - non_empty_output = True - - if len(l_in_group) > 0: - no_warnings = False - l_in_group.insert(0, (' ' * cindent) + - 'write(\"' + in_settings + '\") {\n') - l_in_group.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_group)) - # sys.stderr.write('######################################################\n' - # 'WARNING: One or more \"group\" commands appear to refer to relevant atoms.\n' - # ' Please check to make sure that the group(s) generated by\n' - # ' '+g_program_name+' contain the correct atoms. (-Andrew 2017-10)\n' - # '######################################################\n') - assert(non_empty_output) - - if len(l_in_set) > 0: - l_in_set.insert(0, ((' ' * cindent) + - 'write(\"' + in_settings + '\") {')) - l_in_set.append((' ' * cindent) + '} # end of list of \"set\" commands\n') - sys.stdout.write('\n') - sys.stdout.write((' ' * cindent) + '# list of \"set\" commands:\n') - sys.stdout.write('\n'.join(l_in_set)) - - if len(l_in_set_static) > 0: - l_in_set_static.insert(0, ((' ' * cindent) + - 'write_once(\"' + in_settings + '\") {')) - l_in_set_static.append((' ' * cindent) + '} # end of list of (static) \"set\" commands\n') - sys.stdout.write('\n') - sys.stdout.write((' ' * cindent) + '# list of (static) \"set\" commands:\n') - sys.stdout.write('\n'.join(l_in_set_static)) - - if len(l_in_fix_rigid) > 0: - no_warnings = False - l_in_fix_rigid.insert(0, (' ' * cindent) + - 'write(\"' + in_settings + '\") {\n') - l_in_fix_rigid.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_fix_rigid)) - sys.stderr.write('WARNING: \"fix rigid\" style command(s) applied to selected atoms.\n' - ' Please make sure that the fix group(s) are defined correctly.\n' - '######################################################\n') - assert(non_empty_output) - - if len(l_in_fix_shake) > 0: - no_warnings = False - l_in_fix_shake.insert(0, (' ' * cindent) + - 'write(\"' + in_settings + '\") {\n') - l_in_fix_shake.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_fix_shake)) - sys.stderr.write('WARNING: \"fix shake\" style command(s) applied to selected atoms.\n' - ' Please check to make sure that the fix group(s) are defined correctly,\n' - - ' and also check that the atom, bond, and angle types are correct.\n' - '######################################################\n') - assert(non_empty_output) - - if len(l_in_fix_poems) > 0: - no_warnings = False - l_in_fix_poems.insert(0, (' ' * cindent) + - 'write(\"' + in_settings + '\") {\n') - l_in_fix_poems.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_fix_poems)) - sys.stderr.write('WARNING: \"fix poems\" style command(s) applied to selected atoms.\n' - ' Please make sure that the fix group(s) are defined correctly.\n' - '######################################################\n') - assert(non_empty_output) - - if len(l_in_fix_qeq) > 0: - no_warnings = False - l_in_fix_qeq.insert(0, (' ' * cindent) + - 'write(\"' + in_settings + '\") {\n') - l_in_fix_qeq.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_fix_qeq)) - sys.stderr.write('WARNING: \"fix qeq\" style command(s) applied to selected atoms.\n' - ' Please make sure that the fix group(s) are defined correctly.\n' - '######################################################\n') - assert(non_empty_output) - - if len(l_in_fix_qmmm) > 0: - no_warnings = False - l_in_fix_qmmm.insert(0, (' ' * cindent) + - 'write(\"' + in_settings + '\") {\n') - l_in_fix_qmmm.append((' ' * cindent) + '}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_fix_qmmm)) - sys.stderr.write('WARNING: \"fix qmmm\" style command(s) applied to selected atoms.\n' - ' Please make sure that the fix group(s) are defined correctly.\n' - '######################################################\n') - assert(non_empty_output) - - if mol_name != '': - sys.stdout.write('\n} # end of \"' + mol_name + '\" type definition\n') - - # if non_empty_output and no_warnings: - if non_empty_output: - sys.stderr.write('WARNING: The ' + g_program_name + ' script has not been rigorously tested.\n' - ' Exotic (many-body) pair-styles and pair-styles with\n' - ' unusual syntax (such hbond/dreiding) are not understood\n' - ' by ' + g_program_name + - ' (...although they are supported by moltemplate).\n' - ' Please look over the resulting LT file and check for errors.\n' - ' Convert any remaining atom, bond, angle, dihedral, or improper id\n' - ' or type numbers to the corresponding $ or @-style counter variables.\n' - ' Feel free to report any bugs you find. (-Andrew Jewett 2017-10)\n') - - - except (ValueError, InputError) as err: - sys.stderr.write('\n' + str(err) + '\n') - sys.exit(-1) - - return - -if __name__ == '__main__': - main() diff --git a/tools/moltemplate/moltemplate/lttree.py b/tools/moltemplate/moltemplate/lttree.py deleted file mode 100755 index 9d5ee07ac2..0000000000 --- a/tools/moltemplate/moltemplate/lttree.py +++ /dev/null @@ -1,834 +0,0 @@ -#!/usr/bin/env python - -# Author: Andrew Jewett (jewett.aij at g mail) -# http://www.moltemplate.org -# http://www.chem.ucsb.edu/~sheagroup -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2011, Regents of the University of California -# All rights reserved. - -""" -lttree.py - -lttree.py is an extension of the generic ttree.py program. -This version can understand and manipulate ttree-style templates which -are specialized for storing molecule-specific data for use in LAMMPS. - -The main difference between lttree.py and ttree.py is: -Unlike ttree.py, lttree.py understands rigid-body movement commands like -"rot()" and "move()" which allows it to reorient and move each copy -of a molecule to a new location. (ttree.py just ignores these commands. -Consequently LAMMPS input file (fragments) created with ttree.py have -invalid (overlapping) atomic coordinates and must be modified or aguemted -later (by loading atomic coordinates from a PDB file or an XYZ file). -lttree.py understands the "Data Atoms" section of a LAMMPS -data file (in addition to the various "atom_styles" which effect it). - -Additional LAMMPS-specific features may be added in the future. - -""" - -g_program_name = __file__.split('/')[-1] # ='lttree.py' -g_date_str = '2018-3-15' -g_version_str = '0.77.0' - - -import sys -from collections import defaultdict -import pkg_resources - -try: - from .ttree import BasicUISettings, BasicUIParseArgs, EraseTemplateFiles, \ - StackableCommand, PopCommand, PopRightCommand, PopLeftCommand, \ - PushCommand, PushLeftCommand, PushRightCommand, ScopeCommand, \ - WriteVarBindingsFile, StaticObj, InstanceObj, \ - BasicUI, ScopeBegin, ScopeEnd, WriteFileCommand, Render - from .ttree_lex import InputError, TextBlock, DeleteLinesWithBadVars, \ - TemplateLexer - from .lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid, \ - ColNames2Coords, ColNames2Vects, \ - data_atoms, data_prefix, data_masses, \ - data_velocities, data_ellipsoids, data_triangles, data_lines, \ - data_pair_coeffs, data_bond_coeffs, data_angle_coeffs, \ - data_dihedral_coeffs, data_improper_coeffs, data_bondbond_coeffs, \ - data_bondangle_coeffs, data_middlebondtorsion_coeffs, \ - data_endbondtorsion_coeffs, data_angletorsion_coeffs, \ - data_angleangletorsion_coeffs, data_bondbond13_coeffs, \ - data_angleangle_coeffs, data_bonds_by_type, data_angles_by_type, \ - data_dihedrals_by_type, data_impropers_by_type, \ - data_bonds, data_bond_list, data_angles, data_dihedrals, data_impropers, \ - data_boundary, data_pbc, data_prefix_no_space, in_init, in_settings, \ - in_prefix - from .ttree_matrix_stack import AffineTransform, MultiAffineStack, \ - LinTransform -except (ImportError, SystemError, ValueError): - # not installed as a package - from ttree import * - from ttree_lex import * - from lttree_styles import * - from ttree_matrix_stack import * - - - -try: - unicode -except NameError: - # Python 3 - basestring = unicode = str - - -class LttreeSettings(BasicUISettings): - - def __init__(self, - user_bindings_x=None, - user_bindings=None, - order_method='by_command'): - - BasicUISettings.__init__(self, - user_bindings_x, - user_bindings, - order_method) - - # The following new member data indicate which columns store - # LAMMPS-specific information. - # The next 6 members store keep track of the different columns - # of the "Data Atoms" section of a LAMMPS data file: - self.column_names = [] # <--A list of column names (optional) - self.ii_coords = [] # <--A list of triplets of column indexes storing coordinate data - self.ii_vects = [] # <--A list of triplets of column indexes storing directional data - # (such as dipole or ellipsoid orientations) - self.i_atomid = None # <--An integer indicating which column has the atomid - self.i_atomtype = None # <--An integer indicating which column has the atomtype - self.i_molid = None # <--An integer indicating which column has the molid, if applicable - - -def LttreeParseArgs(argv, settings, main=False, show_warnings=True): - # By default, include force_fields provided with the package - argv.extend(["-import-path", - pkg_resources.resource_filename(__name__, 'force_fields/')]) - - BasicUIParseArgs(argv, settings) - - # Loop over the remaining arguments not processed yet. - # These arguments are specific to the lttree.py program - # and are not understood by ttree.py: - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if ((argv[i].lower() == '-atomstyle') or - (argv[i].lower() == '-atom-style') or - (argv[i].lower() == '-atom_style')): - if i + 1 >= len(argv): - raise InputError('Error(' + g_program_name + '): The ' + argv[i] + ' flag should be followed by a LAMMPS\n' - ' atom_style name (or single quoted string containing a space-separated\n' - ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n') - settings.column_names = AtomStyle2ColNames(argv[i + 1]) - sys.stderr.write('\n \"' + data_atoms + '\" column format:\n') - sys.stderr.write( - ' ' + (' '.join(settings.column_names)) + '\n\n') - settings.ii_coords = ColNames2Coords(settings.column_names) - settings.ii_vects = ColNames2Vects(settings.column_names) - settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid( - settings.column_names) - del(argv[i:i + 2]) - elif (argv[i].lower() == '-icoord'): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers\n' - ' corresponding to column numbers for coordinates in\n' - ' the \"' + data_atoms + '\" section of a LAMMPS data file.\n') - ilist = argv[i + 1].split() - if (len(ilist) % 3) != 0: - raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers.\n' - ' This is usually a list of 3 integers, but it can contain more.\n' - ' The number of cooridnate columns must be divisible by 3,\n' - ' (even if the simulation is in 2 dimensions)\n') - settings.iaffinevects = [] - for i in range(0, len(ilist) / 3): - cols = [int(ilist[3 * i]) + 1, - int(ilist[3 * i + 1]) + 1, - int(ilist[3 * i + 2]) + 1] - settings.iaffinevects.append(cols) - del(argv[i:i + 2]) - elif (argv[i].lower() == '-ivect'): - if i + 1 >= len(argv): - raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers\n' - ' corresponding to column numbers for direction vectors in\n' - ' the \"' + data_atoms + '\" section of a LAMMPS data file.\n') - ilist = argv[i + 1].split() - if (len(ilist) % 3) != 0: - raise InputError('Error: ' + argv[i] + ' flag should be followed by list of integers.\n' - ' This is usually a list of 3 integers, but it can contain more.\n' - ' The number of cooridnate columns must be divisible by 3,\n' - ' (even if the simulation is in 2 dimensions)\n') - settings.ivects = [] - for i in range(0, len(ilist) / 3): - cols = [int(ilist[3 * i]) + 1, - int(ilist[3 * i + 1]) + 1, - int(ilist[3 * i + 2]) + 1] - settings.ivects.append(cols) - del(argv[i:i + 2]) - elif ((argv[i].lower() == '-iatomid') or - (argv[i].lower() == '-iid') or - (argv[i].lower() == '-iatom-id')): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error: ' + argv[i] + ' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"' + - data_atoms + '\" section of a\n' - ' LAMMPS data file contains the atom id number (typically 1).\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_atomid = int(argv[i + 1]) - 1 - del(argv[i:i + 2]) - elif ((argv[i].lower() == '-iatomtype') or - (argv[i].lower() == '-itype') or - (argv[i].lower() == '-iatom-type')): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error: ' + argv[i] + ' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"' + - data_atoms + '\" section of a\n' - ' LAMMPS data file contains the atom type.\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_atomtype = int(argv[i + 1]) - 1 - del(argv[i:i + 2]) - elif ((argv[i].lower() == '-imolid') or - (argv[i].lower() == '-imol') or - (argv[i].lower() == '-imol-id') or - (argv[i].lower() == '-imoleculeid') or - (argv[i].lower() == '-imolecule-id')): - if ((i + 1 >= len(argv)) or (not str.isdigit(argv[i + 1]))): - raise InputError('Error: ' + argv[i] + ' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"' + - data_atoms + '\" section of a\n' - ' LAMMPS data file contains the molecule id number.\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_molid = int(argv[i + 1]) - 1 - del(argv[i:i + 2]) - - elif (argv[i].find('-') == 0) and main: - # elif (__name__ == "__main__"): - raise InputError('Error(' + g_program_name + '):\n' - 'Unrecogized command line argument \"' + argv[i] + '\"\n') - else: - i += 1 - - - if main: - - # Instantiate the lexer we will be using. - # (The lexer's __init__() function requires an openned file. - # Assuming __name__ == "__main__", then the name of that file should - # be the last remaining (unprocessed) argument in the argument list. - # Otherwise, then name of that file will be determined later by the - # python script which imports this module, so we let them handle it.) - - if len(argv) == 1: - raise InputError('Error: This program requires at least one argument\n' - ' the name of a file containing ttree template commands\n') - elif len(argv) == 2: - try: - # Parse text from the file named argv[1] - settings.lex.infile = argv[1] - settings.lex.instream = open(argv[1], 'r') - except IOError: - sys.stderr.write('Error: unable to open file\n' - ' \"' + argv[1] + '\"\n' - ' for reading.\n') - sys.exit(1) - del(argv[1:2]) - - else: - # if there are more than 2 remaining arguments, - problem_args = ['\"' + arg + '\"' for arg in argv[1:]] - raise InputError('Syntax Error(' + g_program_name + '):\n\n' - ' Problem with argument list.\n' - ' The remaining arguments are:\n\n' - ' ' + (' '.join(problem_args)) + '\n\n' - ' (The actual problem may be earlier in the argument list.\n' - ' If these arguments are source files, then keep in mind\n' - ' that this program can not parse multiple source files.)\n' - ' Check the syntax of the entire argument list.\n') - - if len(settings.ii_coords) == 0 and show_warnings: - sys.stderr.write('########################################################\n' - '## WARNING: atom_style unspecified ##\n' - '## --> \"' + data_atoms + '\" column data has an unknown format ##\n' - '## Assuming atom_style = \"full\" ##\n' - # '########################################################\n' - # '## To specify the \"'+data_atoms+'\" column format you can: ##\n' - # '## 1) Use the -atomstyle \"STYLE\" argument ##\n' - # '## where \"STYLE\" is a string indicating a LAMMPS ##\n' - # '## atom_style, including hybrid styles.(Standard ##\n' - # '## atom styles defined in 2011 are supported.) ##\n' - # '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n' - # '## where \"COL_LIST" is a quoted list of strings ##\n' - # '## indicating the name of each column. ##\n' - # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' - # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' - # '## are interpreted as direction vectors. ##\n' - # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' - # '## where \"cx cy cz\" is a list of integers ##\n' - # '## indicating the column numbers for the x,y,z ##\n' - # '## coordinates of each atom. ##\n' - # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' - # '## where \"cmux cmuy cmuz...\" is a list of ##\n' - # '## integers indicating the column numbers for ##\n' - # '## the vector that determines the direction of a ##\n' - # '## dipole or ellipsoid (ie. a rotateable vector).##\n' - # '## (More than one triplet can be specified. The ##\n' - # '## number of entries must be divisible by 3.) ##\n' - '########################################################\n') - - # The default atom_style is "full" - settings.column_names = AtomStyle2ColNames('full') - settings.ii_coords = ColNames2Coords(settings.column_names) - settings.ii_vects = ColNames2Vects(settings.column_names) - settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid( - settings.column_names) - - return - - -def TransformAtomText(text, matrix, settings): - """ Apply transformations to the coordinates and other vector degrees - of freedom stored in the \"Data Atoms\" section of a LAMMPS data file. - This is the \"text\" argument. - The \"matrix\" stores the aggregate sum of combined transformations - to be applied. - - """ - - #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') - - lines = text.split('\n') - - for i in range(0, len(lines)): - line_orig = lines[i] - ic = line_orig.find('#') - if ic != -1: - line = line_orig[:ic] - comment = ' ' + line_orig[ic:].rstrip('\n') - else: - line = line_orig.rstrip('\n') - comment = '' - - columns = line.split() - if len(columns) > 0: - if len(columns) == len(settings.column_names) + 3: - raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n' - ' within the \"' + data_atoms + '\" section of a LAMMPS data file.\n' - ' Instead please add the appropriate offsets (these offsets\n' - ' should be multiples of the cell size) to the atom coordinates\n' - ' in the data file, and eliminate the extra columns. Then try again.\n' - ' (If you get this message often, email me and I\'ll fix this limitation.)') - if len(columns) < len(settings.column_names): - raise InputError('Error: The number of columns in your data file does not\n' - ' match the LAMMPS atom_style you selected.\n' - ' Use the -atomstyle